This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets.
For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNA_cNMF subtypes having more than three samples and the input expression file "TCGA-UVM-TP.mRNA_FPKM_log2_protein.coding.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run.
This pipeline has the following features:
-
For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.
-
Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).
-
Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).
-
Checks if the top core genes are up-regulated or down-regulated.
-
Checks if the top core genes are high expressed or low expressed.
-
Checks if the top core genes are significantly differently expressed genes.
Table 1. Get Full Table basic data info
basic data info |
---|
Number of Gene Sets: 2888 |
Number of samples: 80 |
Original number of Gene Sets: 4738 |
Maximum gene set size: 1972 |
Table 2. Get Full Table pheno data info
phenotype info |
---|
pheno.type: 1 - 5 :[ clus1 ] 11 |
pheno.type: 2 - 5 :[ clus2 ] 11 |
pheno.type: 3 - 5 :[ clus3 ] 29 |
pheno.type: 4 - 5 :[ clus4 ] 21 |
pheno.type: 5 - 5 :[ clus5 ] 8 |
For the expression subtypes of 18131 genes in 81 samples, GSEA found enriched gene sets in each cluster using 80 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.
-
clus1
-
Top enriched gene sets are KEGG ABC TRANSPORTERS, KEGG HOMOLOGOUS RECOMBINATION, WANG LMO4 TARGETS DN, KIM WT1 TARGETS DN, BIDUS METASTASIS UP, MAYBURD RESPONSE TO L663536 DN, ENK UV RESPONSE KERATINOCYTE DN, SEIDEN ONCOGENESIS BY MET, DACOSTA UV RESPONSE VIA ERCC3 COMMON DN, NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON
-
And common core enriched genes are CDK1, EPS8, RRM1, UBA2, AURKA, BUB1, CCNA2, RRM2, TOP2A, CERS6
-
clus2
-
Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG GALACTOSE METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG PURINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG LYSINE DEGRADATION, KEGG ARGININE AND PROLINE METABOLISM
-
And common core enriched genes are SYT1, DUSP1, MAPK10, ACTC1, AK4, AKAP12, ALDOC, ALPL, AMH, ANGPTL4
-
clus3
-
Top enriched gene sets are KEGG RIBOSOME, PID P53 REGULATION PATHWAY, REACTOME TRANSLATION, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, REACTOME GENERIC TRANSCRIPTION PATHWAY, REACTOME PEPTIDE CHAIN ELONGATION, REACTOME MRNA PROCESSING, REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION, REACTOME INFLUENZA LIFE CYCLE
-
And common core enriched genes are ATR, KAT2B, UBE2D1, ZFP2, CCNG1, CDK2, CSNK1G3, DAXX, FBXO11, GSK3B
-
clus4
-
Top enriched gene sets are KEGG OXIDATIVE PHOSPHORYLATION, SCHLOSSER MYC AND SERUM RESPONSE SYNERGY, DACOSTA UV RESPONSE VIA ERCC3 UP, DAIRKEE TERT TARGETS UP, SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP, LOCKWOOD AMPLIFIED IN LUNG CANCER, PENG LEUCINE DEPRIVATION DN, MOOTHA VOXPHOS, PENG GLUTAMINE DEPRIVATION DN, FAELT B CLL WITH VH3 21 UP
-
And common core enriched genes are CDK4, DDT, MRPS12, ANXA11, ATIC, CAD, CHAF1A, CLTA, CYC1, EIF4G1
-
clus5
-
Top enriched gene sets are KEGG PROTEASOME, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG APOPTOSIS, KEGG CELL ADHESION MOLECULES CAMS, KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY, KEGG JAK STAT SIGNALING PATHWAY, KEGG HEMATOPOIETIC CELL LINEAGE, KEGG B CELL RECEPTOR SIGNALING PATHWAY
-
And common core enriched genes are PSMA1, PSMA2, PSMB8, PSMB9, BCL10, BLNK, CARD11, CDKN1A, CHUK, CREB1
Table 3. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG ABC TRANSPORTERS | 44 | genes.ES.table | 0.61 | 1.5 | 0.018 | 1 | 1 | 0.3 | 0.094 | 0.27 | 1 | 0.86 |
KEGG HOMOLOGOUS RECOMBINATION | 28 | genes.ES.table | 0.52 | 1.5 | 0.063 | 1 | 1 | 0.32 | 0.25 | 0.24 | 1 | 0.89 |
WANG LMO4 TARGETS DN | 329 | genes.ES.table | 0.32 | 1.5 | 0.031 | 1 | 1 | 0.44 | 0.37 | 0.28 | 1 | 0.87 |
KIM WT1 TARGETS DN | 434 | genes.ES.table | 0.38 | 1.5 | 0.025 | 1 | 1 | 0.44 | 0.32 | 0.31 | 1 | 0.89 |
BIDUS METASTASIS UP | 210 | genes.ES.table | 0.44 | 1.6 | 0.046 | 1 | 0.98 | 0.52 | 0.39 | 0.32 | 1 | 0.96 |
MAYBURD RESPONSE TO L663536 DN | 53 | genes.ES.table | 0.44 | 1.5 | 0.053 | 1 | 1 | 0.6 | 0.4 | 0.36 | 1 | 0.89 |
ENK UV RESPONSE KERATINOCYTE DN | 482 | genes.ES.table | 0.33 | 1.6 | 0.036 | 1 | 1 | 0.58 | 0.43 | 0.34 | 1 | 0.91 |
SEIDEN ONCOGENESIS BY MET | 86 | genes.ES.table | 0.53 | 1.6 | 0.0066 | 1 | 0.96 | 0.77 | 0.4 | 0.46 | 1 | 0.96 |
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN | 474 | genes.ES.table | 0.45 | 1.6 | 0.033 | 1 | 1 | 0.56 | 0.36 | 0.36 | 1 | 0.87 |
NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON | 120 | genes.ES.table | 0.64 | 1.6 | 0.012 | 1 | 1 | 0.7 | 0.25 | 0.53 | 1 | 0.9 |
Table S1. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | EREG | EREG | EREG | 390 | 0.42 | 0.033 | YES |
2 | EEF1A2 | EEF1A2 | EEF1A2 | 1381 | 0.25 | 0.011 | YES |
3 | LYPLA1 | LYPLA1 | LYPLA1 | 1655 | 0.22 | 0.026 | YES |
4 | COMMD8 | COMMD8 | COMMD8 | 1860 | 0.21 | 0.042 | YES |
5 | CXCL5 | CXCL5 | CXCL5 | 1939 | 0.2 | 0.064 | YES |
6 | ADAM9 | ADAM9 | ADAM9 | 2307 | 0.18 | 0.067 | YES |
7 | ITGA6 | ITGA6 | ITGA6 | 2390 | 0.18 | 0.085 | YES |
8 | CDK1 | CDK1 | CDK1 | 2611 | 0.16 | 0.095 | YES |
9 | SLC38A2 | SLC38A2 | SLC38A2 | 2899 | 0.15 | 0.099 | YES |
10 | IFNGR1 | IFNGR1 | IFNGR1 | 2904 | 0.15 | 0.12 | YES |
11 | CERS6 | CERS6 | CERS6 | 3079 | 0.14 | 0.13 | YES |
12 | TRAM1 | TRAM1 | TRAM1 | 3096 | 0.14 | 0.15 | YES |
13 | TCERG1 | TCERG1 | TCERG1 | 3192 | 0.14 | 0.16 | YES |
14 | F2RL1 | F2RL1 | F2RL1 | 3218 | 0.14 | 0.18 | YES |
15 | ANXA3 | ANXA3 | ANXA3 | 3254 | 0.14 | 0.19 | YES |
16 | FAM208B | FAM208B | FAM208B | 3418 | 0.13 | 0.2 | YES |
17 | EPS8 | EPS8 | EPS8 | 3449 | 0.13 | 0.22 | YES |
18 | TCEA1 | TCEA1 | TCEA1 | 3520 | 0.13 | 0.23 | YES |
19 | CD46 | CD46 | CD46 | 3613 | 0.13 | 0.24 | YES |
20 | CAPZA1 | CAPZA1 | CAPZA1 | 3661 | 0.12 | 0.25 | YES |
21 | P4HA1 | P4HA1 | P4HA1 | 3843 | 0.12 | 0.26 | YES |
22 | ACTR3 | ACTR3 | ACTR3 | 3865 | 0.12 | 0.27 | YES |
23 | CLIC4 | CLIC4 | CLIC4 | 3868 | 0.12 | 0.29 | YES |
24 | GBAS | GBAS | GBAS | 3871 | 0.12 | 0.3 | YES |
25 | ANXA4 | ANXA4 | ANXA4 | 3970 | 0.12 | 0.32 | YES |
26 | UGDH | UGDH | UGDH | 4116 | 0.11 | 0.32 | YES |
27 | SEC23A | SEC23A | SEC23A | 4272 | 0.11 | 0.33 | YES |
28 | GLS | GLS | GLS | 4309 | 0.11 | 0.34 | YES |
29 | ATP2A1 | ATP2A1 | ATP2A1 | 4363 | 0.1 | 0.35 | YES |
30 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 4487 | 0.1 | 0.36 | YES |
31 | NCKAP1 | NCKAP1 | NCKAP1 | 4624 | 0.098 | 0.36 | YES |
32 | UBA2 | UBA2 | UBA2 | 4641 | 0.098 | 0.37 | YES |
33 | TMEM123 | TMEM123 | TMEM123 | 4768 | 0.095 | 0.38 | YES |
34 | HAT1 | HAT1 | HAT1 | 4786 | 0.095 | 0.39 | YES |
35 | LAMB1 | LAMB1 | LAMB1 | 4924 | 0.091 | 0.4 | YES |
36 | TMX1 | TMX1 | TMX1 | 5009 | 0.089 | 0.4 | YES |
37 | SEP15 | SEP15 | SEP15 | 5013 | 0.089 | 0.41 | YES |
38 | ZBED5 | ZBED5 | ZBED5 | 5435 | 0.079 | 0.4 | YES |
39 | RIOK3 | RIOK3 | RIOK3 | 5453 | 0.079 | 0.41 | YES |
40 | RRM1 | RRM1 | RRM1 | 5468 | 0.078 | 0.42 | YES |
41 | PAPOLA | PAPOLA | PAPOLA | 5503 | 0.078 | 0.43 | YES |
42 | IPO7 | IPO7 | IPO7 | 5540 | 0.077 | 0.44 | YES |
43 | PDE8A | PDE8A | PDE8A | 5583 | 0.076 | 0.44 | YES |
44 | PPP1CB | PPP1CB | PPP1CB | 5734 | 0.072 | 0.44 | YES |
45 | PCMT1 | PCMT1 | PCMT1 | 5736 | 0.072 | 0.46 | YES |
46 | AASDHPPT | AASDHPPT | AASDHPPT | 5777 | 0.072 | 0.46 | YES |
47 | EIF5 | EIF5 | EIF5 | 5791 | 0.071 | 0.47 | YES |
48 | MSMO1 | MSMO1 | MSMO1 | 5847 | 0.07 | 0.48 | YES |
49 | SLC25A24 | SLC25A24 | SLC25A24 | 5864 | 0.07 | 0.48 | YES |
50 | TAF1D | TAF1D | TAF1D | 5911 | 0.069 | 0.49 | YES |
51 | YME1L1 | YME1L1 | YME1L1 | 5942 | 0.068 | 0.5 | YES |
52 | ARHGEF12 | ARHGEF12 | ARHGEF12 | 6018 | 0.066 | 0.5 | YES |
53 | SPTLC1 | SPTLC1 | SPTLC1 | 6114 | 0.064 | 0.51 | YES |
54 | SERINC1 | SERINC1 | SERINC1 | 6136 | 0.064 | 0.51 | YES |
55 | SRP72 | SRP72 | SRP72 | 6140 | 0.064 | 0.52 | YES |
56 | MBNL1 | MBNL1 | MBNL1 | 6259 | 0.061 | 0.52 | YES |
57 | SUB1 | SUB1 | SUB1 | 6535 | 0.056 | 0.52 | YES |
58 | C6orf62 | C6orf62 | C6orf62 | 6708 | 0.053 | 0.51 | YES |
59 | HSPA4 | HSPA4 | HSPA4 | 6792 | 0.051 | 0.52 | YES |
60 | PLS3 | PLS3 | PLS3 | 6856 | 0.05 | 0.52 | YES |
61 | AIDA | AIDA | AIDA | 6901 | 0.049 | 0.52 | YES |
62 | MBIP | MBIP | MBIP | 6916 | 0.049 | 0.53 | YES |
63 | DPM1 | DPM1 | DPM1 | 7212 | 0.043 | 0.52 | YES |
64 | RSL24D1 | RSL24D1 | RSL24D1 | 7224 | 0.043 | 0.52 | YES |
65 | SH3BGRL | SH3BGRL | SH3BGRL | 7233 | 0.043 | 0.53 | YES |
66 | SLC39A6 | SLC39A6 | SLC39A6 | 7293 | 0.042 | 0.53 | YES |
67 | CCT6A | CCT6A | CCT6A | 8213 | 0.024 | 0.48 | NO |
68 | SCP2 | SCP2 | SCP2 | 8527 | 0.018 | 0.47 | NO |
69 | NPM1 | NPM1 | NPM1 | 8726 | 0.015 | 0.46 | NO |
70 | GRSF1 | GRSF1 | GRSF1 | 8750 | 0.014 | 0.46 | NO |
71 | COMMD3 | COMMD3 | COMMD3 | 8835 | 0.013 | 0.46 | NO |
72 | PNRC2 | PNRC2 | PNRC2 | 8969 | 0.01 | 0.45 | NO |
73 | HNRNPA3 | HNRNPA3 | HNRNPA3 | 9057 | 0.009 | 0.45 | NO |
74 | HIGD1A | HIGD1A | HIGD1A | 9189 | 0.0065 | 0.44 | NO |
75 | PTEN | PTEN | PTEN | 9208 | 0.0062 | 0.44 | NO |
76 | MMADHC | MMADHC | MMADHC | 9240 | 0.0055 | 0.44 | NO |
77 | NSA2 | NSA2 | NSA2 | 9769 | -0.0035 | 0.41 | NO |
78 | HNRNPH2 | HNRNPH2 | HNRNPH2 | 9923 | -0.0057 | 0.4 | NO |
79 | STAT1 | STAT1 | STAT1 | 10081 | -0.0088 | 0.39 | NO |
80 | SERBP1 | SERBP1 | SERBP1 | 10107 | -0.0091 | 0.39 | NO |
81 | PLOD2 | PLOD2 | PLOD2 | 11051 | -0.024 | 0.34 | NO |
82 | GNAI3 | GNAI3 | GNAI3 | 11059 | -0.024 | 0.35 | NO |
83 | CSDE1 | CSDE1 | CSDE1 | 11648 | -0.032 | 0.32 | NO |
84 | IFITM1 | IFITM1 | IFITM1 | 14451 | -0.076 | 0.17 | NO |
85 | SERP1 | SERP1 | SERP1 | 14548 | -0.078 | 0.18 | NO |
86 | TSPAN8 | TSPAN8 | TSPAN8 | 16618 | -0.14 | 0.082 | NO |
Figure S1. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG ABC TRANSPORTERS.

Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ABC TRANSPORTERS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S2. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ARX | ARX | ARX | 46 | 0.66 | 0.038 | YES |
2 | PPP1R14C | PPP1R14C | PPP1R14C | 55 | 0.63 | 0.075 | YES |
3 | SUMO4 | SUMO4 | SUMO4 | 430 | 0.41 | 0.079 | YES |
4 | DEPDC1 | DEPDC1 | DEPDC1 | 847 | 0.32 | 0.075 | YES |
5 | MPHOSPH9 | MPHOSPH9 | MPHOSPH9 | 1153 | 0.28 | 0.075 | YES |
6 | CREB5 | CREB5 | CREB5 | 1246 | 0.26 | 0.086 | YES |
7 | CASC5 | CASC5 | CASC5 | 1370 | 0.25 | 0.094 | YES |
8 | DLGAP5 | DLGAP5 | DLGAP5 | 1617 | 0.23 | 0.094 | YES |
9 | SMC4 | SMC4 | SMC4 | 1650 | 0.22 | 0.11 | YES |
10 | MCM10 | MCM10 | MCM10 | 1723 | 0.22 | 0.12 | YES |
11 | DBF4 | DBF4 | DBF4 | 1799 | 0.21 | 0.12 | YES |
12 | SQLE | SQLE | SQLE | 1902 | 0.2 | 0.13 | YES |
13 | CENPF | CENPF | CENPF | 2060 | 0.19 | 0.13 | YES |
14 | MTDH | MTDH | MTDH | 2079 | 0.19 | 0.14 | YES |
15 | ERCC6L | ERCC6L | ERCC6L | 2249 | 0.18 | 0.15 | YES |
16 | KLHL23 | KLHL23 | KLHL23 | 2317 | 0.18 | 0.15 | YES |
17 | STRN3 | STRN3 | STRN3 | 2365 | 0.18 | 0.16 | YES |
18 | UBXN2B | UBXN2B | UBXN2B | 2368 | 0.18 | 0.17 | YES |
19 | PLK4 | PLK4 | PLK4 | 2370 | 0.18 | 0.18 | YES |
20 | CDK1 | CDK1 | CDK1 | 2611 | 0.16 | 0.18 | YES |
21 | GAS2L3 | GAS2L3 | GAS2L3 | 2637 | 0.16 | 0.19 | YES |
22 | IFT81 | IFT81 | IFT81 | 2706 | 0.16 | 0.19 | YES |
23 | PAGE2B | PAGE2B | PAGE2B | 2739 | 0.16 | 0.2 | YES |
24 | DNAAF2 | DNAAF2 | DNAAF2 | 2793 | 0.16 | 0.21 | YES |
25 | PBK | PBK | PBK | 2810 | 0.15 | 0.22 | YES |
26 | KIF11 | KIF11 | KIF11 | 2819 | 0.15 | 0.23 | YES |
27 | PRKDC | PRKDC | PRKDC | 2824 | 0.15 | 0.24 | YES |
28 | BUB1 | BUB1 | BUB1 | 2923 | 0.15 | 0.24 | YES |
29 | CCNA2 | CCNA2 | CCNA2 | 2981 | 0.15 | 0.24 | YES |
30 | LARP4 | LARP4 | LARP4 | 3033 | 0.15 | 0.25 | YES |
31 | AZIN1 | AZIN1 | AZIN1 | 3165 | 0.14 | 0.25 | YES |
32 | RRM2 | RRM2 | RRM2 | 3209 | 0.14 | 0.26 | YES |
33 | MAD2L1 | MAD2L1 | MAD2L1 | 3286 | 0.14 | 0.26 | YES |
34 | ATF2 | ATF2 | ATF2 | 3390 | 0.13 | 0.26 | YES |
35 | SGMS2 | SGMS2 | SGMS2 | 3603 | 0.13 | 0.26 | YES |
36 | FSD1L | FSD1L | FSD1L | 3642 | 0.12 | 0.27 | YES |
37 | WDHD1 | WDHD1 | WDHD1 | 3770 | 0.12 | 0.27 | YES |
38 | CDC6 | CDC6 | CDC6 | 3820 | 0.12 | 0.27 | YES |
39 | CENPA | CENPA | CENPA | 3835 | 0.12 | 0.28 | YES |
40 | NCAPH | NCAPH | NCAPH | 3837 | 0.12 | 0.28 | YES |
41 | P4HA1 | P4HA1 | P4HA1 | 3843 | 0.12 | 0.29 | YES |
42 | ECT2 | ECT2 | ECT2 | 3859 | 0.12 | 0.3 | YES |
43 | CEBPG | CEBPG | CEBPG | 3965 | 0.12 | 0.3 | YES |
44 | CBFB | CBFB | CBFB | 3969 | 0.12 | 0.31 | YES |
45 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 3977 | 0.12 | 0.31 | YES |
46 | DDX21 | DDX21 | DDX21 | 3988 | 0.12 | 0.32 | YES |
47 | EIF4E | EIF4E | EIF4E | 4001 | 0.12 | 0.32 | YES |
48 | CCNB2 | CCNB2 | CCNB2 | 4060 | 0.11 | 0.33 | YES |
49 | DHFR | DHFR | DHFR | 4075 | 0.11 | 0.34 | YES |
50 | MRPL42 | MRPL42 | MRPL42 | 4199 | 0.11 | 0.34 | YES |
51 | ZIC2 | ZIC2 | ZIC2 | 4210 | 0.11 | 0.34 | YES |
52 | SEC23A | SEC23A | SEC23A | 4272 | 0.11 | 0.34 | YES |
53 | MLLT10 | MLLT10 | MLLT10 | 4278 | 0.11 | 0.35 | YES |
54 | HMGXB4 | HMGXB4 | HMGXB4 | 4333 | 0.1 | 0.35 | YES |
55 | CAND1 | CAND1 | CAND1 | 4340 | 0.1 | 0.36 | YES |
56 | NUSAP1 | NUSAP1 | NUSAP1 | 4380 | 0.1 | 0.36 | YES |
57 | TMEM33 | TMEM33 | TMEM33 | 4446 | 0.1 | 0.37 | YES |
58 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 4487 | 0.1 | 0.37 | YES |
59 | LCA5L | LCA5L | LCA5L | 4562 | 0.1 | 0.37 | YES |
60 | FANCI | FANCI | FANCI | 4598 | 0.099 | 0.38 | YES |
61 | RNF138 | RNF138 | RNF138 | 4625 | 0.098 | 0.38 | YES |
62 | SLMO2 | SLMO2 | SLMO2 | 4630 | 0.098 | 0.39 | YES |
63 | SEC24B | SEC24B | SEC24B | 4693 | 0.096 | 0.39 | YES |
64 | PAIP1 | PAIP1 | PAIP1 | 4723 | 0.096 | 0.39 | YES |
65 | NF1 | NF1 | NF1 | 4923 | 0.091 | 0.39 | YES |
66 | CENPN | CENPN | CENPN | 4925 | 0.091 | 0.39 | YES |
67 | HBS1L | HBS1L | HBS1L | 4962 | 0.09 | 0.4 | YES |
68 | TYMS | TYMS | TYMS | 5025 | 0.088 | 0.4 | YES |
69 | WHSC1 | WHSC1 | WHSC1 | 5181 | 0.085 | 0.4 | YES |
70 | RHBDL3 | RHBDL3 | RHBDL3 | 5219 | 0.084 | 0.4 | YES |
71 | TMEM194A | TMEM194A | TMEM194A | 5270 | 0.083 | 0.4 | YES |
72 | GMNN | GMNN | GMNN | 5332 | 0.082 | 0.4 | YES |
73 | KDM6A | KDM6A | KDM6A | 5374 | 0.08 | 0.4 | YES |
74 | RRM1 | RRM1 | RRM1 | 5468 | 0.078 | 0.4 | YES |
75 | AURKA | AURKA | AURKA | 5686 | 0.074 | 0.4 | YES |
76 | ARPP19 | ARPP19 | ARPP19 | 5747 | 0.072 | 0.4 | YES |
77 | TFRC | TFRC | TFRC | 5756 | 0.072 | 0.4 | YES |
78 | PCNX | PCNX | PCNX | 5815 | 0.071 | 0.4 | YES |
79 | RACGAP1 | RACGAP1 | RACGAP1 | 5817 | 0.071 | 0.41 | YES |
80 | DCTN4 | DCTN4 | DCTN4 | 5823 | 0.07 | 0.41 | YES |
81 | VBP1 | VBP1 | VBP1 | 5833 | 0.07 | 0.42 | YES |
82 | FBXO3 | FBXO3 | FBXO3 | 5842 | 0.07 | 0.42 | YES |
83 | CCDC47 | CCDC47 | CCDC47 | 5846 | 0.07 | 0.42 | YES |
84 | PHF10 | PHF10 | PHF10 | 5936 | 0.068 | 0.42 | YES |
85 | RLIM | RLIM | RLIM | 5955 | 0.068 | 0.42 | YES |
86 | RCOR1 | RCOR1 | RCOR1 | 6173 | 0.063 | 0.42 | YES |
87 | CEP57 | CEP57 | CEP57 | 6281 | 0.061 | 0.42 | YES |
88 | RRN3 | RRN3 | RRN3 | 6304 | 0.06 | 0.42 | YES |
89 | USP9X | USP9X | USP9X | 6382 | 0.059 | 0.42 | YES |
90 | RAB22A | RAB22A | RAB22A | 6402 | 0.059 | 0.42 | YES |
91 | BPTF | BPTF | BPTF | 6414 | 0.058 | 0.42 | YES |
92 | RAB28 | RAB28 | RAB28 | 6482 | 0.057 | 0.42 | YES |
93 | WAC | WAC | WAC | 6483 | 0.057 | 0.42 | YES |
94 | CCDC15 | CCDC15 | CCDC15 | 6563 | 0.055 | 0.42 | YES |
95 | SRSF2 | SRSF2 | SRSF2 | 6603 | 0.054 | 0.42 | YES |
96 | ZNF550 | ZNF550 | ZNF550 | 6764 | 0.052 | 0.42 | YES |
97 | MAPKAPK5 | MAPKAPK5 | MAPKAPK5 | 6800 | 0.051 | 0.42 | YES |
98 | KLC1 | KLC1 | KLC1 | 6811 | 0.051 | 0.42 | YES |
99 | BIRC5 | BIRC5 | BIRC5 | 6826 | 0.051 | 0.42 | YES |
100 | SRSF1 | SRSF1 | SRSF1 | 6830 | 0.051 | 0.43 | YES |
101 | EFHC1 | EFHC1 | EFHC1 | 6859 | 0.05 | 0.43 | YES |
102 | C5orf22 | C5orf22 | C5orf22 | 6885 | 0.05 | 0.43 | YES |
103 | MED14 | MED14 | MED14 | 6887 | 0.05 | 0.43 | YES |
104 | MNS1 | MNS1 | MNS1 | 6933 | 0.049 | 0.44 | YES |
105 | TLK2 | TLK2 | TLK2 | 6958 | 0.048 | 0.44 | YES |
106 | PREPL | PREPL | PREPL | 7017 | 0.047 | 0.44 | YES |
107 | MAPK1 | MAPK1 | MAPK1 | 7042 | 0.046 | 0.44 | YES |
108 | CDC23 | CDC23 | CDC23 | 7097 | 0.045 | 0.44 | YES |
109 | CRY1 | CRY1 | CRY1 | 7106 | 0.045 | 0.44 | YES |
110 | CDK2AP1 | CDK2AP1 | CDK2AP1 | 7118 | 0.045 | 0.44 | YES |
111 | CCNB1 | CCNB1 | CCNB1 | 7222 | 0.043 | 0.44 | NO |
112 | CSE1L | CSE1L | CSE1L | 7287 | 0.042 | 0.44 | NO |
113 | LMNB1 | LMNB1 | LMNB1 | 7315 | 0.041 | 0.44 | NO |
114 | SFPQ | SFPQ | SFPQ | 7372 | 0.04 | 0.44 | NO |
115 | PSMD10 | PSMD10 | PSMD10 | 7471 | 0.038 | 0.44 | NO |
116 | NRAS | NRAS | NRAS | 7519 | 0.037 | 0.43 | NO |
117 | COPS8 | COPS8 | COPS8 | 7581 | 0.036 | 0.43 | NO |
118 | PPP2CA | PPP2CA | PPP2CA | 7614 | 0.036 | 0.43 | NO |
119 | HNRNPA2B1 | HNRNPA2B1 | HNRNPA2B1 | 7650 | 0.035 | 0.43 | NO |
120 | TPX2 | TPX2 | TPX2 | 7743 | 0.033 | 0.43 | NO |
121 | PTP4A1 | PTP4A1 | PTP4A1 | 7747 | 0.033 | 0.43 | NO |
122 | SNRPD1 | SNRPD1 | SNRPD1 | 7828 | 0.031 | 0.43 | NO |
123 | RFC5 | RFC5 | RFC5 | 7947 | 0.029 | 0.42 | NO |
124 | KIF1B | KIF1B | KIF1B | 8036 | 0.027 | 0.42 | NO |
125 | ADNP | ADNP | ADNP | 8098 | 0.026 | 0.42 | NO |
126 | H2AFY | H2AFY | H2AFY | 8166 | 0.025 | 0.42 | NO |
127 | SRSF9 | SRSF9 | SRSF9 | 8184 | 0.025 | 0.42 | NO |
128 | HNRNPR | HNRNPR | HNRNPR | 8227 | 0.024 | 0.42 | NO |
129 | TSR1 | TSR1 | TSR1 | 8259 | 0.023 | 0.42 | NO |
130 | HNRNPH3 | HNRNPH3 | HNRNPH3 | 8302 | 0.022 | 0.42 | NO |
131 | RABGAP1L | RABGAP1L | RABGAP1L | 8303 | 0.022 | 0.42 | NO |
132 | HSF2 | HSF2 | HSF2 | 8306 | 0.022 | 0.42 | NO |
133 | RABGGTB | RABGGTB | RABGGTB | 8315 | 0.022 | 0.42 | NO |
134 | HMGB3 | HMGB3 | HMGB3 | 8321 | 0.022 | 0.42 | NO |
135 | SLC35B4 | SLC35B4 | SLC35B4 | 8356 | 0.021 | 0.42 | NO |
136 | BCL7A | BCL7A | BCL7A | 8458 | 0.019 | 0.42 | NO |
137 | G3BP1 | G3BP1 | G3BP1 | 8462 | 0.019 | 0.42 | NO |
138 | CBLL1 | CBLL1 | CBLL1 | 8491 | 0.019 | 0.42 | NO |
139 | SMS | SMS | SMS | 8562 | 0.018 | 0.41 | NO |
140 | CKAP5 | CKAP5 | CKAP5 | 8609 | 0.017 | 0.41 | NO |
141 | AMD1 | AMD1 | AMD1 | 8613 | 0.017 | 0.41 | NO |
142 | VDAC1 | VDAC1 | VDAC1 | 8640 | 0.016 | 0.41 | NO |
143 | KIF4A | KIF4A | KIF4A | 8766 | 0.014 | 0.41 | NO |
144 | TTF2 | TTF2 | TTF2 | 8875 | 0.012 | 0.4 | NO |
145 | WRB | WRB | WRB | 8959 | 0.011 | 0.4 | NO |
146 | SNRNP27 | SNRNP27 | SNRNP27 | 8974 | 0.01 | 0.4 | NO |
147 | NUP153 | NUP153 | NUP153 | 8989 | 0.01 | 0.4 | NO |
148 | PTGES3 | PTGES3 | PTGES3 | 9026 | 0.0095 | 0.4 | NO |
149 | AZI2 | AZI2 | AZI2 | 9130 | 0.0076 | 0.39 | NO |
150 | DKC1 | DKC1 | DKC1 | 9175 | 0.0067 | 0.39 | NO |
151 | PNMA1 | PNMA1 | PNMA1 | 9180 | 0.0067 | 0.39 | NO |
152 | AGAP1 | AGAP1 | AGAP1 | 9211 | 0.0061 | 0.39 | NO |
153 | SRSF12 | SRSF12 | SRSF12 | 9277 | 0.0049 | 0.38 | NO |
154 | TFDP1 | TFDP1 | TFDP1 | 9281 | 0.0048 | 0.38 | NO |
155 | USP13 | USP13 | USP13 | 9348 | 0.0036 | 0.38 | NO |
156 | ASF1B | ASF1B | ASF1B | 9378 | 0.0031 | 0.38 | NO |
157 | HNRNPK | HNRNPK | HNRNPK | 9392 | 0.0028 | 0.38 | NO |
158 | TUBGCP4 | TUBGCP4 | TUBGCP4 | 9446 | 0.002 | 0.38 | NO |
159 | RBBP4 | RBBP4 | RBBP4 | 9476 | 0.0015 | 0.37 | NO |
160 | YWHAE | YWHAE | YWHAE | 9538 | 0.00025 | 0.37 | NO |
161 | SMC1A | SMC1A | SMC1A | 9540 | 0.00022 | 0.37 | NO |
162 | CHEK1 | CHEK1 | CHEK1 | 9545 | 0.00017 | 0.37 | NO |
163 | TRA2B | TRA2B | TRA2B | 9572 | -0.00021 | 0.37 | NO |
164 | ZNF318 | ZNF318 | ZNF318 | 9606 | -0.00072 | 0.37 | NO |
165 | YTHDF1 | YTHDF1 | YTHDF1 | 9624 | -0.0011 | 0.37 | NO |
166 | RMND5A | RMND5A | RMND5A | 9962 | -0.0062 | 0.35 | NO |
167 | KHDRBS1 | KHDRBS1 | KHDRBS1 | 9985 | -0.0067 | 0.35 | NO |
168 | NAP1L1 | NAP1L1 | NAP1L1 | 10032 | -0.0079 | 0.34 | NO |
169 | FEN1 | FEN1 | FEN1 | 10067 | -0.0085 | 0.34 | NO |
170 | EIF4A3 | EIF4A3 | EIF4A3 | 10077 | -0.0086 | 0.34 | NO |
171 | PLD6 | PLD6 | PLD6 | 10102 | -0.0091 | 0.34 | NO |
172 | CDYL | CDYL | CDYL | 10110 | -0.0092 | 0.34 | NO |
173 | HNRNPU | HNRNPU | HNRNPU | 10232 | -0.011 | 0.34 | NO |
174 | NDRG3 | NDRG3 | NDRG3 | 10250 | -0.011 | 0.34 | NO |
175 | RFC4 | RFC4 | RFC4 | 10318 | -0.012 | 0.33 | NO |
176 | WBP11 | WBP11 | WBP11 | 10322 | -0.012 | 0.33 | NO |
177 | UBQLN2 | UBQLN2 | UBQLN2 | 10409 | -0.014 | 0.33 | NO |
178 | UBE2C | UBE2C | UBE2C | 10745 | -0.019 | 0.31 | NO |
179 | PNMAL1 | PNMAL1 | PNMAL1 | 10756 | -0.019 | 0.31 | NO |
180 | ODC1 | ODC1 | ODC1 | 10780 | -0.019 | 0.31 | NO |
181 | SRD5A1 | SRD5A1 | SRD5A1 | 10893 | -0.021 | 0.31 | NO |
182 | UNK | UNK | UNK | 10925 | -0.022 | 0.31 | NO |
183 | PLOD2 | PLOD2 | PLOD2 | 11051 | -0.024 | 0.3 | NO |
184 | H2AFZ | H2AFZ | H2AFZ | 11115 | -0.024 | 0.3 | NO |
185 | PCBP1 | PCBP1 | PCBP1 | 11226 | -0.026 | 0.3 | NO |
186 | YBX1 | YBX1 | YBX1 | 11430 | -0.029 | 0.28 | NO |
187 | PAK2 | PAK2 | PAK2 | 11496 | -0.03 | 0.28 | NO |
188 | PATL1 | PATL1 | PATL1 | 11613 | -0.032 | 0.28 | NO |
189 | TARDBP | TARDBP | TARDBP | 11658 | -0.032 | 0.28 | NO |
190 | ELAVL1 | ELAVL1 | ELAVL1 | 11673 | -0.033 | 0.28 | NO |
191 | NCBP2 | NCBP2 | NCBP2 | 11736 | -0.034 | 0.28 | NO |
192 | CCNY | CCNY | CCNY | 12058 | -0.038 | 0.26 | NO |
193 | CRKL | CRKL | CRKL | 12085 | -0.039 | 0.26 | NO |
194 | MEAF6 | MEAF6 | MEAF6 | 12122 | -0.039 | 0.26 | NO |
195 | SSRP1 | SSRP1 | SSRP1 | 12127 | -0.039 | 0.27 | NO |
196 | HNRNPD | HNRNPD | HNRNPD | 12193 | -0.04 | 0.26 | NO |
197 | NONO | NONO | NONO | 12252 | -0.041 | 0.26 | NO |
198 | RAE1 | RAE1 | RAE1 | 12272 | -0.041 | 0.27 | NO |
199 | CCDC57 | CCDC57 | CCDC57 | 12308 | -0.042 | 0.27 | NO |
200 | HUWE1 | HUWE1 | HUWE1 | 13002 | -0.052 | 0.23 | NO |
201 | EIF1 | EIF1 | EIF1 | 13023 | -0.052 | 0.23 | NO |
202 | FEM1A | FEM1A | FEM1A | 13671 | -0.063 | 0.2 | NO |
203 | ANKRD54 | ANKRD54 | ANKRD54 | 13809 | -0.065 | 0.2 | NO |
204 | KCTD6 | KCTD6 | KCTD6 | 14181 | -0.071 | 0.18 | NO |
205 | RAB7A | RAB7A | RAB7A | 14855 | -0.084 | 0.15 | NO |
206 | MARCKS | MARCKS | MARCKS | 14916 | -0.085 | 0.15 | NO |
207 | DSP | DSP | DSP | 15514 | -0.098 | 0.12 | NO |
208 | NFIB | NFIB | NFIB | 15945 | -0.11 | 0.1 | NO |
209 | STK24 | STK24 | STK24 | 15994 | -0.11 | 0.11 | NO |
210 | FNDC5 | FNDC5 | FNDC5 | 16465 | -0.13 | 0.091 | NO |
Figure S3. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG HOMOLOGOUS RECOMBINATION.

Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HOMOLOGOUS RECOMBINATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S3. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | RAD54B | RAD54B | RAD54B | 982 | 0.3 | -0.04 | YES |
2 | BAG2 | BAG2 | BAG2 | 1065 | 0.29 | -0.03 | YES |
3 | GTF2H2 | GTF2H2 | GTF2H2 | 1099 | 0.28 | -0.017 | YES |
4 | SACS | SACS | SACS | 1378 | 0.25 | -0.02 | YES |
5 | HS3ST3B1 | HS3ST3B1 | HS3ST3B1 | 1578 | 0.23 | -0.02 | YES |
6 | FBXL7 | FBXL7 | FBXL7 | 1583 | 0.23 | -0.008 | YES |
7 | JMJD1C | JMJD1C | JMJD1C | 1730 | 0.22 | -0.0051 | YES |
8 | TOP2A | TOP2A | TOP2A | 1842 | 0.21 | -0.00069 | YES |
9 | SMARCA5 | SMARCA5 | SMARCA5 | 2126 | 0.19 | -0.0069 | YES |
10 | NLRC4 | NLRC4 | NLRC4 | 2194 | 0.19 | -0.0012 | YES |
11 | ANLN | ANLN | ANLN | 2262 | 0.18 | 0.0044 | YES |
12 | TBK1 | TBK1 | TBK1 | 2326 | 0.18 | 0.0099 | YES |
13 | WEE1 | WEE1 | WEE1 | 2345 | 0.18 | 0.018 | YES |
14 | VCAN | VCAN | VCAN | 2527 | 0.17 | 0.016 | YES |
15 | STK17B | STK17B | STK17B | 2572 | 0.17 | 0.022 | YES |
16 | CDK1 | CDK1 | CDK1 | 2611 | 0.16 | 0.028 | YES |
17 | C8orf76 | C8orf76 | C8orf76 | 2680 | 0.16 | 0.033 | YES |
18 | FNDC3A | FNDC3A | FNDC3A | 2774 | 0.16 | 0.036 | YES |
19 | NET1 | NET1 | NET1 | 2776 | 0.16 | 0.044 | YES |
20 | DNAAF2 | DNAAF2 | DNAAF2 | 2793 | 0.16 | 0.05 | YES |
21 | KIF11 | KIF11 | KIF11 | 2819 | 0.15 | 0.057 | YES |
22 | PKN2 | PKN2 | PKN2 | 2850 | 0.15 | 0.063 | YES |
23 | BUB1 | BUB1 | BUB1 | 2923 | 0.15 | 0.067 | YES |
24 | JAG1 | JAG1 | JAG1 | 2927 | 0.15 | 0.074 | YES |
25 | CCNA2 | CCNA2 | CCNA2 | 2981 | 0.15 | 0.079 | YES |
26 | TDG | TDG | TDG | 3011 | 0.15 | 0.085 | YES |
27 | RBM25 | RBM25 | RBM25 | 3037 | 0.15 | 0.091 | YES |
28 | TCERG1 | TCERG1 | TCERG1 | 3192 | 0.14 | 0.089 | YES |
29 | BTAF1 | BTAF1 | BTAF1 | 3223 | 0.14 | 0.095 | YES |
30 | MAP3K7 | MAP3K7 | MAP3K7 | 3283 | 0.14 | 0.098 | YES |
31 | PSMD14 | PSMD14 | PSMD14 | 3295 | 0.14 | 0.1 | YES |
32 | CEP55 | CEP55 | CEP55 | 3299 | 0.14 | 0.11 | YES |
33 | RAP1B | RAP1B | RAP1B | 3326 | 0.14 | 0.12 | YES |
34 | DCK | DCK | DCK | 3327 | 0.14 | 0.12 | YES |
35 | OGT | OGT | OGT | 3373 | 0.13 | 0.13 | YES |
36 | ARFGEF2 | ARFGEF2 | ARFGEF2 | 3409 | 0.13 | 0.13 | YES |
37 | EPS8 | EPS8 | EPS8 | 3449 | 0.13 | 0.14 | YES |
38 | FRYL | FRYL | FRYL | 3457 | 0.13 | 0.14 | YES |
39 | RBM27 | RBM27 | RBM27 | 3459 | 0.13 | 0.15 | YES |
40 | ZMYM2 | ZMYM2 | ZMYM2 | 3468 | 0.13 | 0.16 | YES |
41 | TIAM2 | TIAM2 | TIAM2 | 3508 | 0.13 | 0.16 | YES |
42 | MRPL1 | MRPL1 | MRPL1 | 3572 | 0.13 | 0.16 | YES |
43 | BIRC2 | BIRC2 | BIRC2 | 3676 | 0.12 | 0.16 | YES |
44 | RAB2A | RAB2A | RAB2A | 3691 | 0.12 | 0.17 | YES |
45 | PSMC6 | PSMC6 | PSMC6 | 3695 | 0.12 | 0.18 | YES |
46 | TMPO | TMPO | TMPO | 3737 | 0.12 | 0.18 | YES |
47 | HERC4 | HERC4 | HERC4 | 3790 | 0.12 | 0.18 | YES |
48 | TP53INP1 | TP53INP1 | TP53INP1 | 3823 | 0.12 | 0.19 | YES |
49 | USP8 | USP8 | USP8 | 3891 | 0.12 | 0.19 | YES |
50 | FBXL3 | FBXL3 | FBXL3 | 3936 | 0.12 | 0.19 | YES |
51 | GOPC | GOPC | GOPC | 3946 | 0.12 | 0.2 | YES |
52 | ACSL3 | ACSL3 | ACSL3 | 3971 | 0.12 | 0.2 | YES |
53 | DDX21 | DDX21 | DDX21 | 3988 | 0.12 | 0.21 | YES |
54 | NOC3L | NOC3L | NOC3L | 4050 | 0.11 | 0.21 | YES |
55 | CDC27 | CDC27 | CDC27 | 4104 | 0.11 | 0.21 | YES |
56 | CRLF3 | CRLF3 | CRLF3 | 4120 | 0.11 | 0.22 | YES |
57 | PHF6 | PHF6 | PHF6 | 4122 | 0.11 | 0.22 | YES |
58 | RSRC2 | RSRC2 | RSRC2 | 4204 | 0.11 | 0.22 | YES |
59 | BLZF1 | BLZF1 | BLZF1 | 4225 | 0.11 | 0.23 | YES |
60 | CXXC5 | CXXC5 | CXXC5 | 4228 | 0.11 | 0.24 | YES |
61 | ELOVL6 | ELOVL6 | ELOVL6 | 4247 | 0.11 | 0.24 | YES |
62 | CCNH | CCNH | CCNH | 4288 | 0.11 | 0.24 | YES |
63 | ATG5 | ATG5 | ATG5 | 4292 | 0.11 | 0.25 | YES |
64 | STK17A | STK17A | STK17A | 4295 | 0.11 | 0.25 | YES |
65 | TARBP1 | TARBP1 | TARBP1 | 4349 | 0.1 | 0.26 | YES |
66 | BIRC6 | BIRC6 | BIRC6 | 4383 | 0.1 | 0.26 | YES |
67 | FOSL1 | FOSL1 | FOSL1 | 4412 | 0.1 | 0.26 | YES |
68 | GCC2 | GCC2 | GCC2 | 4445 | 0.1 | 0.27 | YES |
69 | PSMA4 | PSMA4 | PSMA4 | 4526 | 0.1 | 0.27 | YES |
70 | SRPK2 | SRPK2 | SRPK2 | 4530 | 0.1 | 0.27 | YES |
71 | CORO1C | CORO1C | CORO1C | 4589 | 0.099 | 0.27 | YES |
72 | PEX1 | PEX1 | PEX1 | 4612 | 0.098 | 0.28 | YES |
73 | UBA2 | UBA2 | UBA2 | 4641 | 0.098 | 0.28 | YES |
74 | CDC42BPA | CDC42BPA | CDC42BPA | 4828 | 0.094 | 0.28 | YES |
75 | HIST1H4B | HIST1H4B | HIST1H4B | 4845 | 0.093 | 0.28 | YES |
76 | SIRT1 | SIRT1 | SIRT1 | 4910 | 0.092 | 0.28 | YES |
77 | PJA2 | PJA2 | PJA2 | 4927 | 0.091 | 0.28 | YES |
78 | MRPL15 | MRPL15 | MRPL15 | 4955 | 0.09 | 0.29 | YES |
79 | LBR | LBR | LBR | 4974 | 0.09 | 0.29 | YES |
80 | CDC25C | CDC25C | CDC25C | 5056 | 0.088 | 0.29 | YES |
81 | LHFPL2 | LHFPL2 | LHFPL2 | 5064 | 0.088 | 0.29 | YES |
82 | TRIM24 | TRIM24 | TRIM24 | 5142 | 0.086 | 0.29 | YES |
83 | GAPVD1 | GAPVD1 | GAPVD1 | 5189 | 0.085 | 0.3 | YES |
84 | ATF1 | ATF1 | ATF1 | 5197 | 0.085 | 0.3 | YES |
85 | SYNE1 | SYNE1 | SYNE1 | 5198 | 0.085 | 0.3 | YES |
86 | DIS3 | DIS3 | DIS3 | 5237 | 0.084 | 0.31 | YES |
87 | PTPRK | PTPRK | PTPRK | 5247 | 0.084 | 0.31 | YES |
88 | ZNF281 | ZNF281 | ZNF281 | 5295 | 0.083 | 0.31 | YES |
89 | TXNRD1 | TXNRD1 | TXNRD1 | 5360 | 0.081 | 0.31 | YES |
90 | GABPB2 | GABPB2 | GABPB2 | 5390 | 0.08 | 0.32 | YES |
91 | CFLAR | CFLAR | CFLAR | 5405 | 0.08 | 0.32 | YES |
92 | HSPH1 | HSPH1 | HSPH1 | 5416 | 0.08 | 0.32 | YES |
93 | MED17 | MED17 | MED17 | 5423 | 0.08 | 0.32 | YES |
94 | UBE2T | UBE2T | UBE2T | 5430 | 0.079 | 0.33 | YES |
95 | ZMYND8 | ZMYND8 | ZMYND8 | 5528 | 0.077 | 0.33 | YES |
96 | IPO7 | IPO7 | IPO7 | 5540 | 0.077 | 0.33 | YES |
97 | SAMD4A | SAMD4A | SAMD4A | 5570 | 0.076 | 0.33 | YES |
98 | PPP2R5E | PPP2R5E | PPP2R5E | 5597 | 0.076 | 0.34 | YES |
99 | CDK7 | CDK7 | CDK7 | 5642 | 0.074 | 0.34 | YES |
100 | AURKA | AURKA | AURKA | 5686 | 0.074 | 0.34 | YES |
101 | MRPS35 | MRPS35 | MRPS35 | 5746 | 0.072 | 0.34 | YES |
102 | RSPRY1 | RSPRY1 | RSPRY1 | 5834 | 0.07 | 0.34 | YES |
103 | RAB6A | RAB6A | RAB6A | 5908 | 0.069 | 0.34 | YES |
104 | FAM175B | FAM175B | FAM175B | 5921 | 0.069 | 0.34 | YES |
105 | DNAJA2 | DNAJA2 | DNAJA2 | 5945 | 0.068 | 0.34 | YES |
106 | SSFA2 | SSFA2 | SSFA2 | 5961 | 0.068 | 0.34 | YES |
107 | USP12 | USP12 | USP12 | 6014 | 0.066 | 0.34 | YES |
108 | SLC4A1AP | SLC4A1AP | SLC4A1AP | 6042 | 0.066 | 0.35 | YES |
109 | C11orf30 | C11orf30 | C11orf30 | 6083 | 0.065 | 0.35 | YES |
110 | MTIF2 | MTIF2 | MTIF2 | 6166 | 0.063 | 0.35 | YES |
111 | RCOR1 | RCOR1 | RCOR1 | 6173 | 0.063 | 0.35 | YES |
112 | CDC5L | CDC5L | CDC5L | 6233 | 0.062 | 0.35 | YES |
113 | GTF2H1 | GTF2H1 | GTF2H1 | 6283 | 0.061 | 0.35 | YES |
114 | TOP1 | TOP1 | TOP1 | 6332 | 0.06 | 0.35 | YES |
115 | MAP3K4 | MAP3K4 | MAP3K4 | 6353 | 0.059 | 0.35 | YES |
116 | EPS15 | EPS15 | EPS15 | 6509 | 0.056 | 0.35 | YES |
117 | HDAC2 | HDAC2 | HDAC2 | 6513 | 0.056 | 0.35 | YES |
118 | PLAG1 | PLAG1 | PLAG1 | 6539 | 0.056 | 0.35 | YES |
119 | DTL | DTL | DTL | 6550 | 0.055 | 0.35 | YES |
120 | EIF3A | EIF3A | EIF3A | 6561 | 0.055 | 0.36 | YES |
121 | HIST1H4C | HIST1H4C | HIST1H4C | 6567 | 0.055 | 0.36 | YES |
122 | PRKD3 | PRKD3 | PRKD3 | 6609 | 0.054 | 0.36 | YES |
123 | RNF14 | RNF14 | RNF14 | 6724 | 0.052 | 0.35 | YES |
124 | RAB1A | RAB1A | RAB1A | 6732 | 0.052 | 0.36 | YES |
125 | RAD23B | RAD23B | RAD23B | 6741 | 0.052 | 0.36 | YES |
126 | MAP7D3 | MAP7D3 | MAP7D3 | 6751 | 0.052 | 0.36 | YES |
127 | GLRX | GLRX | GLRX | 6761 | 0.052 | 0.36 | YES |
128 | RABGAP1 | RABGAP1 | RABGAP1 | 6781 | 0.052 | 0.36 | YES |
129 | MAPKAPK5 | MAPKAPK5 | MAPKAPK5 | 6800 | 0.051 | 0.37 | YES |
130 | FZD1 | FZD1 | FZD1 | 6820 | 0.051 | 0.37 | YES |
131 | PCNA | PCNA | PCNA | 6844 | 0.05 | 0.37 | YES |
132 | PANX1 | PANX1 | PANX1 | 6862 | 0.05 | 0.37 | YES |
133 | UBR7 | UBR7 | UBR7 | 6875 | 0.05 | 0.37 | YES |
134 | VEGFC | VEGFC | VEGFC | 6920 | 0.049 | 0.37 | YES |
135 | PSMC2 | PSMC2 | PSMC2 | 6935 | 0.049 | 0.37 | YES |
136 | LRRC8C | LRRC8C | LRRC8C | 6993 | 0.047 | 0.37 | YES |
137 | SUPV3L1 | SUPV3L1 | SUPV3L1 | 6994 | 0.047 | 0.38 | YES |
138 | EML4 | EML4 | EML4 | 7087 | 0.046 | 0.37 | YES |
139 | CDC23 | CDC23 | CDC23 | 7097 | 0.045 | 0.37 | YES |
140 | IMMP2L | IMMP2L | IMMP2L | 7173 | 0.044 | 0.37 | YES |
141 | CDK5R1 | CDK5R1 | CDK5R1 | 7187 | 0.044 | 0.37 | YES |
142 | PRIM2 | PRIM2 | PRIM2 | 7322 | 0.041 | 0.37 | YES |
143 | PRKACB | PRKACB | PRKACB | 7350 | 0.04 | 0.37 | YES |
144 | NPAS2 | NPAS2 | NPAS2 | 7361 | 0.04 | 0.37 | YES |
145 | GGPS1 | GGPS1 | GGPS1 | 7399 | 0.04 | 0.37 | YES |
146 | KIAA1279 | KIAA1279 | KIAA1279 | 7416 | 0.039 | 0.37 | YES |
147 | CRK | CRK | CRK | 7439 | 0.039 | 0.37 | YES |
148 | HSPA8 | HSPA8 | HSPA8 | 7505 | 0.038 | 0.37 | YES |
149 | MYCBP2 | MYCBP2 | MYCBP2 | 7599 | 0.036 | 0.37 | YES |
150 | DDX20 | DDX20 | DDX20 | 7601 | 0.036 | 0.37 | YES |
151 | CMPK1 | CMPK1 | CMPK1 | 7676 | 0.034 | 0.37 | YES |
152 | MTMR4 | MTMR4 | MTMR4 | 7683 | 0.034 | 0.37 | YES |
153 | ZNF345 | ZNF345 | ZNF345 | 7686 | 0.034 | 0.37 | YES |
154 | POLD3 | POLD3 | POLD3 | 7723 | 0.033 | 0.37 | YES |
155 | HSPE1 | HSPE1 | HSPE1 | 7726 | 0.033 | 0.37 | YES |
156 | SRSF3 | SRSF3 | SRSF3 | 7753 | 0.033 | 0.37 | YES |
157 | UCK2 | UCK2 | UCK2 | 7758 | 0.033 | 0.37 | YES |
158 | C15orf41 | C15orf41 | C15orf41 | 7759 | 0.033 | 0.37 | YES |
159 | SON | SON | SON | 7775 | 0.032 | 0.38 | YES |
160 | FNTA | FNTA | FNTA | 7777 | 0.032 | 0.38 | YES |
161 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 7819 | 0.032 | 0.38 | YES |
162 | FKBP15 | FKBP15 | FKBP15 | 7845 | 0.031 | 0.38 | YES |
163 | B4GALT5 | B4GALT5 | B4GALT5 | 7856 | 0.031 | 0.38 | YES |
164 | BUB3 | BUB3 | BUB3 | 7867 | 0.031 | 0.38 | YES |
165 | PDGFB | PDGFB | PDGFB | 7894 | 0.03 | 0.38 | YES |
166 | GTF2B | GTF2B | GTF2B | 7895 | 0.03 | 0.38 | YES |
167 | GDI2 | GDI2 | GDI2 | 7898 | 0.03 | 0.38 | YES |
168 | LSM14A | LSM14A | LSM14A | 7907 | 0.03 | 0.38 | YES |
169 | UBE2D3 | UBE2D3 | UBE2D3 | 7972 | 0.029 | 0.38 | NO |
170 | RBM17 | RBM17 | RBM17 | 8029 | 0.028 | 0.38 | NO |
171 | EGFR | EGFR | EGFR | 8067 | 0.027 | 0.38 | NO |
172 | SRSF9 | SRSF9 | SRSF9 | 8184 | 0.025 | 0.37 | NO |
173 | ERCC3 | ERCC3 | ERCC3 | 8188 | 0.025 | 0.37 | NO |
174 | SPIN1 | SPIN1 | SPIN1 | 8223 | 0.024 | 0.37 | NO |
175 | RABGGTB | RABGGTB | RABGGTB | 8315 | 0.022 | 0.37 | NO |
176 | MAT2A | MAT2A | MAT2A | 8350 | 0.022 | 0.37 | NO |
177 | XRCC5 | XRCC5 | XRCC5 | 8430 | 0.02 | 0.36 | NO |
178 | SLC25A17 | SLC25A17 | SLC25A17 | 8444 | 0.02 | 0.36 | NO |
179 | DLG5 | DLG5 | DLG5 | 8449 | 0.02 | 0.37 | NO |
180 | TSFM | TSFM | TSFM | 8475 | 0.019 | 0.36 | NO |
181 | USP3 | USP3 | USP3 | 8496 | 0.019 | 0.36 | NO |
182 | PLK1 | PLK1 | PLK1 | 8673 | 0.016 | 0.36 | NO |
183 | OSBP | OSBP | OSBP | 8749 | 0.014 | 0.35 | NO |
184 | MFAP1 | MFAP1 | MFAP1 | 8815 | 0.013 | 0.35 | NO |
185 | MAPK14 | MAPK14 | MAPK14 | 8951 | 0.011 | 0.34 | NO |
186 | TRIP4 | TRIP4 | TRIP4 | 8979 | 0.01 | 0.34 | NO |
187 | PTGES3 | PTGES3 | PTGES3 | 9026 | 0.0095 | 0.34 | NO |
188 | CCT4 | CCT4 | CCT4 | 9031 | 0.0094 | 0.34 | NO |
189 | PSMB1 | PSMB1 | PSMB1 | 9115 | 0.0079 | 0.34 | NO |
190 | DKC1 | DKC1 | DKC1 | 9175 | 0.0067 | 0.33 | NO |
191 | UBE2D2 | UBE2D2 | UBE2D2 | 9210 | 0.0061 | 0.33 | NO |
192 | OSBPL9 | OSBPL9 | OSBPL9 | 9220 | 0.0059 | 0.33 | NO |
193 | PPP2R1B | PPP2R1B | PPP2R1B | 9336 | 0.0037 | 0.32 | NO |
194 | MID1IP1 | MID1IP1 | MID1IP1 | 9478 | 0.0014 | 0.32 | NO |
195 | MYC | MYC | MYC | 9503 | 0.00089 | 0.32 | NO |
196 | MICAL2 | MICAL2 | MICAL2 | 9509 | 0.00078 | 0.32 | NO |
197 | YWHAE | YWHAE | YWHAE | 9538 | 0.00025 | 0.31 | NO |
198 | ZDHHC5 | ZDHHC5 | ZDHHC5 | 9553 | 0.000053 | 0.31 | NO |
199 | C5orf30 | C5orf30 | C5orf30 | 9558 | -8.9e-06 | 0.31 | NO |
200 | PPP1CC | PPP1CC | PPP1CC | 9637 | -0.0012 | 0.31 | NO |
201 | PSMA5 | PSMA5 | PSMA5 | 9715 | -0.0026 | 0.3 | NO |
202 | NUFIP1 | NUFIP1 | NUFIP1 | 9752 | -0.0031 | 0.3 | NO |
203 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 9774 | -0.0036 | 0.3 | NO |
204 | RIPK1 | RIPK1 | RIPK1 | 9787 | -0.0038 | 0.3 | NO |
205 | PAFAH2 | PAFAH2 | PAFAH2 | 9977 | -0.0065 | 0.29 | NO |
206 | SERBP1 | SERBP1 | SERBP1 | 10107 | -0.0091 | 0.28 | NO |
207 | MCTS1 | MCTS1 | MCTS1 | 10227 | -0.011 | 0.28 | NO |
208 | PSME3 | PSME3 | PSME3 | 10248 | -0.011 | 0.28 | NO |
209 | CYHR1 | CYHR1 | CYHR1 | 10280 | -0.012 | 0.28 | NO |
210 | ADSL | ADSL | ADSL | 10284 | -0.012 | 0.28 | NO |
211 | CPSF7 | CPSF7 | CPSF7 | 10288 | -0.012 | 0.28 | NO |
212 | MCM3 | MCM3 | MCM3 | 10332 | -0.012 | 0.28 | NO |
213 | FOXK2 | FOXK2 | FOXK2 | 10374 | -0.013 | 0.27 | NO |
214 | FADD | FADD | FADD | 10398 | -0.014 | 0.27 | NO |
215 | ARFGAP1 | ARFGAP1 | ARFGAP1 | 10539 | -0.016 | 0.27 | NO |
216 | EP400 | EP400 | EP400 | 10593 | -0.017 | 0.26 | NO |
217 | CDH11 | CDH11 | CDH11 | 10655 | -0.018 | 0.26 | NO |
218 | UBE2C | UBE2C | UBE2C | 10745 | -0.019 | 0.26 | NO |
219 | RCC1 | RCC1 | RCC1 | 10758 | -0.019 | 0.26 | NO |
220 | ARPC5L | ARPC5L | ARPC5L | 10791 | -0.02 | 0.26 | NO |
221 | PSMG2 | PSMG2 | PSMG2 | 10835 | -0.02 | 0.26 | NO |
222 | SRRM2 | SRRM2 | SRRM2 | 10889 | -0.021 | 0.25 | NO |
223 | ZNHIT3 | ZNHIT3 | ZNHIT3 | 10982 | -0.022 | 0.25 | NO |
224 | C16orf62 | C16orf62 | C16orf62 | 11057 | -0.024 | 0.25 | NO |
225 | EIF2A | EIF2A | EIF2A | 11120 | -0.025 | 0.24 | NO |
226 | EPB41 | EPB41 | EPB41 | 11122 | -0.025 | 0.24 | NO |
227 | NMI | NMI | NMI | 11212 | -0.026 | 0.24 | NO |
228 | USP22 | USP22 | USP22 | 11263 | -0.027 | 0.24 | NO |
229 | SPRY2 | SPRY2 | SPRY2 | 11345 | -0.028 | 0.24 | NO |
230 | CTGF | CTGF | CTGF | 11360 | -0.028 | 0.24 | NO |
231 | FAF1 | FAF1 | FAF1 | 11539 | -0.03 | 0.23 | NO |
232 | TARDBP | TARDBP | TARDBP | 11658 | -0.032 | 0.22 | NO |
233 | UBN1 | UBN1 | UBN1 | 11691 | -0.033 | 0.22 | NO |
234 | KDM1A | KDM1A | KDM1A | 11800 | -0.035 | 0.22 | NO |
235 | RAB5A | RAB5A | RAB5A | 11894 | -0.036 | 0.22 | NO |
236 | SRSF4 | SRSF4 | SRSF4 | 11951 | -0.037 | 0.22 | NO |
237 | LUZP1 | LUZP1 | LUZP1 | 12018 | -0.038 | 0.21 | NO |
238 | EIF4B | EIF4B | EIF4B | 12036 | -0.038 | 0.21 | NO |
239 | RPP14 | RPP14 | RPP14 | 12065 | -0.038 | 0.22 | NO |
240 | THRAP3 | THRAP3 | THRAP3 | 12073 | -0.039 | 0.22 | NO |
241 | MEAF6 | MEAF6 | MEAF6 | 12122 | -0.039 | 0.22 | NO |
242 | ZDHHC16 | ZDHHC16 | ZDHHC16 | 12260 | -0.041 | 0.21 | NO |
243 | TGIF1 | TGIF1 | TGIF1 | 12262 | -0.041 | 0.21 | NO |
244 | STAU1 | STAU1 | STAU1 | 12343 | -0.042 | 0.21 | NO |
245 | NCOA6 | NCOA6 | NCOA6 | 12461 | -0.044 | 0.2 | NO |
246 | SNIP1 | SNIP1 | SNIP1 | 13009 | -0.052 | 0.18 | NO |
247 | BCL2L1 | BCL2L1 | BCL2L1 | 13085 | -0.053 | 0.18 | NO |
248 | TSPAN14 | TSPAN14 | TSPAN14 | 13091 | -0.053 | 0.18 | NO |
249 | IGF2BP2 | IGF2BP2 | IGF2BP2 | 13287 | -0.056 | 0.17 | NO |
250 | RBM14 | RBM14 | RBM14 | 13372 | -0.058 | 0.17 | NO |
251 | LRRC42 | LRRC42 | LRRC42 | 13561 | -0.061 | 0.16 | NO |
252 | SLC2A1 | SLC2A1 | SLC2A1 | 13669 | -0.063 | 0.16 | NO |
253 | METTL13 | METTL13 | METTL13 | 13755 | -0.064 | 0.16 | NO |
254 | ARHGEF2 | ARHGEF2 | ARHGEF2 | 14249 | -0.073 | 0.13 | NO |
255 | CLCN7 | CLCN7 | CLCN7 | 14280 | -0.073 | 0.14 | NO |
256 | SEC16A | SEC16A | SEC16A | 14441 | -0.076 | 0.13 | NO |
257 | MAGEF1 | MAGEF1 | MAGEF1 | 15128 | -0.09 | 0.096 | NO |
258 | RNF220 | RNF220 | RNF220 | 15143 | -0.09 | 0.1 | NO |
259 | SIRPA | SIRPA | SIRPA | 15276 | -0.092 | 0.097 | NO |
260 | KDM4B | KDM4B | KDM4B | 15361 | -0.094 | 0.097 | NO |
261 | BTG1 | BTG1 | BTG1 | 15926 | -0.11 | 0.071 | NO |
262 | FYN | FYN | FYN | 16207 | -0.12 | 0.061 | NO |
263 | TMEM53 | TMEM53 | TMEM53 | 16629 | -0.14 | 0.045 | NO |
264 | HSPA1L | HSPA1L | HSPA1L | 16822 | -0.15 | 0.042 | NO |
265 | WNT5B | WNT5B | WNT5B | 17002 | -0.16 | 0.04 | NO |
266 | NLRP2 | NLRP2 | NLRP2 | 17205 | -0.18 | 0.038 | NO |
267 | PAMR1 | PAMR1 | PAMR1 | 17458 | -0.22 | 0.035 | NO |
Figure S5. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: WANG LMO4 TARGETS DN.

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: WANG LMO4 TARGETS DN, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S4. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ZNF878 | ZNF878 | ZNF878 | 167 | 0.51 | 0.0041 | YES |
2 | GLRB | GLRB | GLRB | 242 | 0.47 | 0.012 | YES |
3 | EDAR | EDAR | EDAR | 462 | 0.4 | 0.011 | YES |
4 | NCAPG | NCAPG | NCAPG | 813 | 0.32 | -0.0005 | YES |
5 | AP1S3 | AP1S3 | AP1S3 | 834 | 0.32 | 0.0068 | YES |
6 | DEPDC1 | DEPDC1 | DEPDC1 | 847 | 0.32 | 0.014 | YES |
7 | MATR3 | MATR3 | MATR3 | 858 | 0.31 | 0.022 | YES |
8 | CDCA7 | CDCA7 | CDCA7 | 923 | 0.31 | 0.027 | YES |
9 | RNF128 | RNF128 | RNF128 | 1050 | 0.29 | 0.027 | YES |
10 | GTF2H2 | GTF2H2 | GTF2H2 | 1099 | 0.28 | 0.032 | YES |
11 | KITLG | KITLG | KITLG | 1188 | 0.27 | 0.034 | YES |
12 | LCORL | LCORL | LCORL | 1198 | 0.27 | 0.041 | YES |
13 | TRIM59 | TRIM59 | TRIM59 | 1243 | 0.26 | 0.046 | YES |
14 | TSPAN2 | TSPAN2 | TSPAN2 | 1255 | 0.26 | 0.052 | YES |
15 | PLCB1 | PLCB1 | PLCB1 | 1256 | 0.26 | 0.059 | YES |
16 | N4BP2 | N4BP2 | N4BP2 | 1266 | 0.26 | 0.066 | YES |
17 | COL25A1 | COL25A1 | COL25A1 | 1287 | 0.26 | 0.072 | YES |
18 | RPS6KA6 | RPS6KA6 | RPS6KA6 | 1379 | 0.25 | 0.073 | YES |
19 | SGOL2 | SGOL2 | SGOL2 | 1385 | 0.25 | 0.079 | YES |
20 | ESCO2 | ESCO2 | ESCO2 | 1534 | 0.24 | 0.077 | YES |
21 | ATAD2 | ATAD2 | ATAD2 | 1576 | 0.23 | 0.081 | YES |
22 | MYB | MYB | MYB | 1585 | 0.23 | 0.087 | YES |
23 | AKAP9 | AKAP9 | AKAP9 | 1629 | 0.23 | 0.09 | YES |
24 | SMC4 | SMC4 | SMC4 | 1650 | 0.22 | 0.095 | YES |
25 | CASP8AP2 | CASP8AP2 | CASP8AP2 | 1673 | 0.22 | 0.1 | YES |
26 | TAF2 | TAF2 | TAF2 | 1745 | 0.22 | 0.1 | YES |
27 | PUS7L | PUS7L | PUS7L | 1789 | 0.21 | 0.1 | YES |
28 | DBF4 | DBF4 | DBF4 | 1799 | 0.21 | 0.11 | YES |
29 | PABPC4L | PABPC4L | PABPC4L | 1837 | 0.21 | 0.11 | YES |
30 | TOP2A | TOP2A | TOP2A | 1842 | 0.21 | 0.12 | YES |
31 | RELL1 | RELL1 | RELL1 | 1854 | 0.21 | 0.12 | YES |
32 | ZNF799 | ZNF799 | ZNF799 | 1906 | 0.2 | 0.13 | YES |
33 | PDK1 | PDK1 | PDK1 | 1920 | 0.2 | 0.13 | YES |
34 | PPIP5K2 | PPIP5K2 | PPIP5K2 | 1928 | 0.2 | 0.14 | YES |
35 | LRRC40 | LRRC40 | LRRC40 | 2005 | 0.2 | 0.14 | YES |
36 | CENPF | CENPF | CENPF | 2060 | 0.19 | 0.14 | YES |
37 | MTDH | MTDH | MTDH | 2079 | 0.19 | 0.14 | YES |
38 | CEP192 | CEP192 | CEP192 | 2118 | 0.19 | 0.15 | YES |
39 | SMARCA5 | SMARCA5 | SMARCA5 | 2126 | 0.19 | 0.15 | YES |
40 | ANLN | ANLN | ANLN | 2262 | 0.18 | 0.15 | YES |
41 | SERTAD4 | SERTAD4 | SERTAD4 | 2273 | 0.18 | 0.15 | YES |
42 | WEE1 | WEE1 | WEE1 | 2345 | 0.18 | 0.15 | YES |
43 | NUDCD1 | NUDCD1 | NUDCD1 | 2346 | 0.18 | 0.16 | YES |
44 | RBBP8 | RBBP8 | RBBP8 | 2361 | 0.18 | 0.16 | YES |
45 | RBAK | RBAK | RBAK | 2369 | 0.18 | 0.17 | YES |
46 | EZH2 | EZH2 | EZH2 | 2371 | 0.18 | 0.17 | YES |
47 | ANKRD26 | ANKRD26 | ANKRD26 | 2373 | 0.18 | 0.18 | YES |
48 | MIS18BP1 | MIS18BP1 | MIS18BP1 | 2381 | 0.18 | 0.18 | YES |
49 | ITGA6 | ITGA6 | ITGA6 | 2390 | 0.18 | 0.18 | YES |
50 | ERI2 | ERI2 | ERI2 | 2514 | 0.17 | 0.18 | YES |
51 | AHR | AHR | AHR | 2537 | 0.17 | 0.18 | YES |
52 | FAM76B | FAM76B | FAM76B | 2542 | 0.17 | 0.19 | YES |
53 | SMCHD1 | SMCHD1 | SMCHD1 | 2594 | 0.16 | 0.19 | YES |
54 | SHCBP1 | SHCBP1 | SHCBP1 | 2618 | 0.16 | 0.19 | YES |
55 | BCAP29 | BCAP29 | BCAP29 | 2621 | 0.16 | 0.2 | YES |
56 | SAP30 | SAP30 | SAP30 | 2670 | 0.16 | 0.2 | YES |
57 | IFT81 | IFT81 | IFT81 | 2706 | 0.16 | 0.2 | YES |
58 | PROM1 | PROM1 | PROM1 | 2719 | 0.16 | 0.2 | YES |
59 | GPSM2 | GPSM2 | GPSM2 | 2731 | 0.16 | 0.21 | YES |
60 | PBK | PBK | PBK | 2810 | 0.15 | 0.21 | YES |
61 | HRSP12 | HRSP12 | HRSP12 | 2830 | 0.15 | 0.21 | YES |
62 | POLA1 | POLA1 | POLA1 | 2861 | 0.15 | 0.21 | YES |
63 | SMEK2 | SMEK2 | SMEK2 | 2913 | 0.15 | 0.21 | YES |
64 | BUB1 | BUB1 | BUB1 | 2923 | 0.15 | 0.22 | YES |
65 | CXorf23 | CXorf23 | CXorf23 | 2946 | 0.15 | 0.22 | YES |
66 | CA12 | CA12 | CA12 | 2962 | 0.15 | 0.22 | YES |
67 | CCNA2 | CCNA2 | CCNA2 | 2981 | 0.15 | 0.23 | YES |
68 | TMEM209 | TMEM209 | TMEM209 | 2990 | 0.15 | 0.23 | YES |
69 | ARL6IP6 | ARL6IP6 | ARL6IP6 | 2993 | 0.15 | 0.23 | YES |
70 | UCHL5 | UCHL5 | UCHL5 | 2994 | 0.15 | 0.24 | YES |
71 | FGFR1OP2 | FGFR1OP2 | FGFR1OP2 | 2995 | 0.15 | 0.24 | YES |
72 | NEK1 | NEK1 | NEK1 | 3004 | 0.15 | 0.24 | YES |
73 | XPO1 | XPO1 | XPO1 | 3018 | 0.15 | 0.25 | YES |
74 | CDC40 | CDC40 | CDC40 | 3026 | 0.15 | 0.25 | YES |
75 | GTPBP10 | GTPBP10 | GTPBP10 | 3056 | 0.14 | 0.25 | YES |
76 | FGFR1OP | FGFR1OP | FGFR1OP | 3067 | 0.14 | 0.26 | YES |
77 | MOXD1 | MOXD1 | MOXD1 | 3113 | 0.14 | 0.26 | YES |
78 | CD2AP | CD2AP | CD2AP | 3138 | 0.14 | 0.26 | YES |
79 | RAD21 | RAD21 | RAD21 | 3147 | 0.14 | 0.26 | YES |
80 | AZIN1 | AZIN1 | AZIN1 | 3165 | 0.14 | 0.27 | YES |
81 | RRM2 | RRM2 | RRM2 | 3209 | 0.14 | 0.27 | YES |
82 | TRPS1 | TRPS1 | TRPS1 | 3221 | 0.14 | 0.27 | YES |
83 | CEP55 | CEP55 | CEP55 | 3299 | 0.14 | 0.27 | YES |
84 | RIF1 | RIF1 | RIF1 | 3303 | 0.14 | 0.27 | YES |
85 | DCK | DCK | DCK | 3327 | 0.14 | 0.28 | YES |
86 | AEBP2 | AEBP2 | AEBP2 | 3342 | 0.14 | 0.28 | YES |
87 | SEMA5A | SEMA5A | SEMA5A | 3354 | 0.13 | 0.28 | YES |
88 | PDS5B | PDS5B | PDS5B | 3377 | 0.13 | 0.28 | YES |
89 | ZNF770 | ZNF770 | ZNF770 | 3378 | 0.13 | 0.29 | YES |
90 | RNF6 | RNF6 | RNF6 | 3402 | 0.13 | 0.29 | YES |
91 | EPS8 | EPS8 | EPS8 | 3449 | 0.13 | 0.29 | YES |
92 | CTDSPL2 | CTDSPL2 | CTDSPL2 | 3453 | 0.13 | 0.3 | YES |
93 | TCEA1 | TCEA1 | TCEA1 | 3520 | 0.13 | 0.3 | YES |
94 | SMC2 | SMC2 | SMC2 | 3605 | 0.13 | 0.29 | YES |
95 | ANKRD32 | ANKRD32 | ANKRD32 | 3614 | 0.13 | 0.3 | YES |
96 | CDC73 | CDC73 | CDC73 | 3619 | 0.13 | 0.3 | YES |
97 | OXCT1 | OXCT1 | OXCT1 | 3621 | 0.13 | 0.3 | YES |
98 | ZRANB2 | ZRANB2 | ZRANB2 | 3624 | 0.13 | 0.31 | YES |
99 | BUB1B | BUB1B | BUB1B | 3683 | 0.12 | 0.31 | YES |
100 | CAPZA2 | CAPZA2 | CAPZA2 | 3685 | 0.12 | 0.31 | YES |
101 | CLDN12 | CLDN12 | CLDN12 | 3700 | 0.12 | 0.31 | YES |
102 | SSB | SSB | SSB | 3711 | 0.12 | 0.31 | YES |
103 | EFCAB7 | EFCAB7 | EFCAB7 | 3736 | 0.12 | 0.32 | YES |
104 | TMPO | TMPO | TMPO | 3737 | 0.12 | 0.32 | YES |
105 | DSG2 | DSG2 | DSG2 | 3774 | 0.12 | 0.32 | YES |
106 | USP34 | USP34 | USP34 | 3817 | 0.12 | 0.32 | YES |
107 | CDC6 | CDC6 | CDC6 | 3820 | 0.12 | 0.32 | YES |
108 | WDR11 | WDR11 | WDR11 | 3826 | 0.12 | 0.33 | YES |
109 | CTTNBP2 | CTTNBP2 | CTTNBP2 | 3851 | 0.12 | 0.33 | YES |
110 | ECT2 | ECT2 | ECT2 | 3859 | 0.12 | 0.33 | YES |
111 | TRMT11 | TRMT11 | TRMT11 | 3884 | 0.12 | 0.33 | YES |
112 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 3904 | 0.12 | 0.34 | YES |
113 | ZC3HAV1L | ZC3HAV1L | ZC3HAV1L | 3931 | 0.12 | 0.34 | YES |
114 | PPAT | PPAT | PPAT | 3952 | 0.12 | 0.34 | YES |
115 | ACSL3 | ACSL3 | ACSL3 | 3971 | 0.12 | 0.34 | YES |
116 | MELK | MELK | MELK | 4012 | 0.12 | 0.34 | YES |
117 | PSAT1 | PSAT1 | PSAT1 | 4031 | 0.11 | 0.34 | YES |
118 | C11orf54 | C11orf54 | C11orf54 | 4036 | 0.11 | 0.35 | YES |
119 | FIGNL1 | FIGNL1 | FIGNL1 | 4061 | 0.11 | 0.35 | YES |
120 | ALG13 | ALG13 | ALG13 | 4076 | 0.11 | 0.35 | YES |
121 | SYDE2 | SYDE2 | SYDE2 | 4099 | 0.11 | 0.35 | YES |
122 | UGDH | UGDH | UGDH | 4116 | 0.11 | 0.36 | YES |
123 | PHF6 | PHF6 | PHF6 | 4122 | 0.11 | 0.36 | YES |
124 | MET | MET | MET | 4123 | 0.11 | 0.36 | YES |
125 | SLC39A10 | SLC39A10 | SLC39A10 | 4133 | 0.11 | 0.36 | YES |
126 | SBNO1 | SBNO1 | SBNO1 | 4147 | 0.11 | 0.36 | YES |
127 | WDR75 | WDR75 | WDR75 | 4148 | 0.11 | 0.37 | YES |
128 | RBL1 | RBL1 | RBL1 | 4150 | 0.11 | 0.37 | YES |
129 | EID1 | EID1 | EID1 | 4163 | 0.11 | 0.37 | YES |
130 | MBNL3 | MBNL3 | MBNL3 | 4216 | 0.11 | 0.37 | YES |
131 | C1orf131 | C1orf131 | C1orf131 | 4220 | 0.11 | 0.38 | YES |
132 | UBLCP1 | UBLCP1 | UBLCP1 | 4229 | 0.11 | 0.38 | YES |
133 | NUP107 | NUP107 | NUP107 | 4270 | 0.11 | 0.38 | YES |
134 | NANP | NANP | NANP | 4275 | 0.11 | 0.38 | YES |
135 | C21orf91 | C21orf91 | C21orf91 | 4334 | 0.1 | 0.38 | YES |
136 | GPM6B | GPM6B | GPM6B | 4348 | 0.1 | 0.38 | YES |
137 | PHF14 | PHF14 | PHF14 | 4438 | 0.1 | 0.38 | YES |
138 | TMEM33 | TMEM33 | TMEM33 | 4446 | 0.1 | 0.38 | YES |
139 | ACAT2 | ACAT2 | ACAT2 | 4466 | 0.1 | 0.38 | YES |
140 | COL4A5 | COL4A5 | COL4A5 | 4488 | 0.1 | 0.39 | YES |
141 | ZNF367 | ZNF367 | ZNF367 | 4490 | 0.1 | 0.39 | YES |
142 | UHRF1 | UHRF1 | UHRF1 | 4499 | 0.1 | 0.39 | YES |
143 | NCAPD3 | NCAPD3 | NCAPD3 | 4542 | 0.1 | 0.39 | YES |
144 | DLAT | DLAT | DLAT | 4570 | 0.1 | 0.39 | YES |
145 | SGOL1 | SGOL1 | SGOL1 | 4583 | 0.099 | 0.4 | YES |
146 | FAM13B | FAM13B | FAM13B | 4590 | 0.099 | 0.4 | YES |
147 | SLMO2 | SLMO2 | SLMO2 | 4630 | 0.098 | 0.4 | YES |
148 | USP1 | USP1 | USP1 | 4637 | 0.098 | 0.4 | YES |
149 | UBA2 | UBA2 | UBA2 | 4641 | 0.098 | 0.4 | YES |
150 | ACTR6 | ACTR6 | ACTR6 | 4669 | 0.097 | 0.4 | YES |
151 | POT1 | POT1 | POT1 | 4673 | 0.097 | 0.4 | YES |
152 | SRSF10 | SRSF10 | SRSF10 | 4676 | 0.097 | 0.41 | YES |
153 | APPBP2 | APPBP2 | APPBP2 | 4727 | 0.096 | 0.41 | YES |
154 | HAT1 | HAT1 | HAT1 | 4786 | 0.095 | 0.41 | YES |
155 | DNAJC9 | DNAJC9 | DNAJC9 | 4823 | 0.094 | 0.41 | YES |
156 | MOB4 | MOB4 | MOB4 | 4904 | 0.092 | 0.4 | YES |
157 | ADK | ADK | ADK | 4920 | 0.091 | 0.41 | YES |
158 | HACE1 | HACE1 | HACE1 | 4937 | 0.091 | 0.41 | YES |
159 | TRDMT1 | TRDMT1 | TRDMT1 | 4946 | 0.091 | 0.41 | YES |
160 | CETN3 | CETN3 | CETN3 | 4966 | 0.09 | 0.41 | YES |
161 | STRBP | STRBP | STRBP | 4968 | 0.09 | 0.41 | YES |
162 | IDH3A | IDH3A | IDH3A | 4971 | 0.09 | 0.42 | YES |
163 | HMGB2 | HMGB2 | HMGB2 | 4995 | 0.089 | 0.42 | YES |
164 | TSPAN13 | TSPAN13 | TSPAN13 | 5033 | 0.088 | 0.42 | YES |
165 | PDZD8 | PDZD8 | PDZD8 | 5037 | 0.088 | 0.42 | YES |
166 | TTC3 | TTC3 | TTC3 | 5050 | 0.088 | 0.42 | YES |
167 | ZNF148 | ZNF148 | ZNF148 | 5073 | 0.088 | 0.42 | YES |
168 | ANP32E | ANP32E | ANP32E | 5093 | 0.087 | 0.42 | YES |
169 | VPS54 | VPS54 | VPS54 | 5105 | 0.087 | 0.43 | YES |
170 | CALM2 | CALM2 | CALM2 | 5193 | 0.085 | 0.42 | YES |
171 | PAIP2 | PAIP2 | PAIP2 | 5214 | 0.084 | 0.42 | YES |
172 | NFYB | NFYB | NFYB | 5239 | 0.084 | 0.42 | YES |
173 | RFX3 | RFX3 | RFX3 | 5255 | 0.084 | 0.43 | YES |
174 | ARNT2 | ARNT2 | ARNT2 | 5258 | 0.084 | 0.43 | YES |
175 | SEPHS2 | SEPHS2 | SEPHS2 | 5261 | 0.084 | 0.43 | YES |
176 | GRHL2 | GRHL2 | GRHL2 | 5272 | 0.083 | 0.43 | YES |
177 | GMNN | GMNN | GMNN | 5332 | 0.082 | 0.43 | YES |
178 | IPO8 | IPO8 | IPO8 | 5345 | 0.081 | 0.43 | YES |
179 | G3BP2 | G3BP2 | G3BP2 | 5388 | 0.08 | 0.43 | YES |
180 | SUCLA2 | SUCLA2 | SUCLA2 | 5419 | 0.08 | 0.43 | YES |
181 | TIMM17A | TIMM17A | TIMM17A | 5427 | 0.079 | 0.43 | YES |
182 | RNMT | RNMT | RNMT | 5460 | 0.079 | 0.44 | YES |
183 | ORC5 | ORC5 | ORC5 | 5482 | 0.078 | 0.44 | YES |
184 | ZFAND6 | ZFAND6 | ZFAND6 | 5492 | 0.078 | 0.44 | YES |
185 | TGFA | TGFA | TGFA | 5529 | 0.077 | 0.44 | YES |
186 | RFC1 | RFC1 | RFC1 | 5532 | 0.077 | 0.44 | YES |
187 | SKP2 | SKP2 | SKP2 | 5614 | 0.075 | 0.44 | YES |
188 | SETX | SETX | SETX | 5636 | 0.075 | 0.44 | YES |
189 | ENPP3 | ENPP3 | ENPP3 | 5658 | 0.074 | 0.44 | YES |
190 | AURKA | AURKA | AURKA | 5686 | 0.074 | 0.44 | YES |
191 | ZBTB44 | ZBTB44 | ZBTB44 | 5690 | 0.073 | 0.44 | YES |
192 | NCBP1 | NCBP1 | NCBP1 | 5725 | 0.073 | 0.44 | YES |
193 | AUTS2 | AUTS2 | AUTS2 | 5739 | 0.072 | 0.44 | YES |
194 | CTNND2 | CTNND2 | CTNND2 | 5742 | 0.072 | 0.44 | YES |
195 | ARPP19 | ARPP19 | ARPP19 | 5747 | 0.072 | 0.44 | YES |
196 | CCDC90B | CCDC90B | CCDC90B | 5748 | 0.072 | 0.45 | YES |
197 | TFRC | TFRC | TFRC | 5756 | 0.072 | 0.45 | YES |
198 | HELLS | HELLS | HELLS | 5799 | 0.071 | 0.45 | YES |
199 | VBP1 | VBP1 | VBP1 | 5833 | 0.07 | 0.45 | YES |
200 | E2F7 | E2F7 | E2F7 | 5888 | 0.069 | 0.45 | YES |
201 | TAF1D | TAF1D | TAF1D | 5911 | 0.069 | 0.45 | YES |
202 | CNOT6 | CNOT6 | CNOT6 | 5962 | 0.068 | 0.45 | YES |
203 | MDH1 | MDH1 | MDH1 | 5970 | 0.067 | 0.45 | YES |
204 | ZNF841 | ZNF841 | ZNF841 | 5971 | 0.067 | 0.45 | YES |
205 | TRIM37 | TRIM37 | TRIM37 | 5975 | 0.067 | 0.45 | YES |
206 | PRIM1 | PRIM1 | PRIM1 | 6038 | 0.066 | 0.45 | YES |
207 | NAE1 | NAE1 | NAE1 | 6040 | 0.066 | 0.45 | YES |
208 | FAM199X | FAM199X | FAM199X | 6076 | 0.065 | 0.45 | YES |
209 | ZNF229 | ZNF229 | ZNF229 | 6107 | 0.064 | 0.45 | YES |
210 | NFU1 | NFU1 | NFU1 | 6127 | 0.064 | 0.45 | YES |
211 | TCEANC | TCEANC | TCEANC | 6144 | 0.064 | 0.45 | YES |
212 | NUP155 | NUP155 | NUP155 | 6171 | 0.063 | 0.45 | YES |
213 | RBM45 | RBM45 | RBM45 | 6205 | 0.062 | 0.45 | YES |
214 | ZNF24 | ZNF24 | ZNF24 | 6242 | 0.062 | 0.45 | YES |
215 | NVL | NVL | NVL | 6256 | 0.062 | 0.45 | YES |
216 | PCM1 | PCM1 | PCM1 | 6285 | 0.061 | 0.45 | YES |
217 | DPY30 | DPY30 | DPY30 | 6287 | 0.061 | 0.45 | YES |
218 | ATXN1 | ATXN1 | ATXN1 | 6294 | 0.061 | 0.46 | YES |
219 | MPHOSPH8 | MPHOSPH8 | MPHOSPH8 | 6315 | 0.06 | 0.46 | YES |
220 | SYNCRIP | SYNCRIP | SYNCRIP | 6330 | 0.06 | 0.46 | YES |
221 | ACYP1 | ACYP1 | ACYP1 | 6357 | 0.059 | 0.46 | YES |
222 | POLR2B | POLR2B | POLR2B | 6426 | 0.058 | 0.46 | YES |
223 | ATR | ATR | ATR | 6441 | 0.058 | 0.46 | YES |
224 | C1orf112 | C1orf112 | C1orf112 | 6449 | 0.058 | 0.46 | YES |
225 | PAICS | PAICS | PAICS | 6456 | 0.058 | 0.46 | YES |
226 | TRIP13 | TRIP13 | TRIP13 | 6476 | 0.057 | 0.46 | YES |
227 | MARCH6 | MARCH6 | MARCH6 | 6542 | 0.056 | 0.46 | NO |
228 | ZNF239 | ZNF239 | ZNF239 | 6591 | 0.055 | 0.46 | NO |
229 | C1D | C1D | C1D | 6612 | 0.054 | 0.46 | NO |
230 | ATAD1 | ATAD1 | ATAD1 | 6651 | 0.054 | 0.45 | NO |
231 | LRBA | LRBA | LRBA | 6652 | 0.054 | 0.46 | NO |
232 | PRR14L | PRR14L | PRR14L | 6681 | 0.053 | 0.46 | NO |
233 | CRLS1 | CRLS1 | CRLS1 | 6703 | 0.053 | 0.46 | NO |
234 | ZCCHC8 | ZCCHC8 | ZCCHC8 | 6744 | 0.052 | 0.46 | NO |
235 | PCMTD2 | PCMTD2 | PCMTD2 | 6777 | 0.052 | 0.46 | NO |
236 | PIGF | PIGF | PIGF | 6794 | 0.051 | 0.46 | NO |
237 | TRMT6 | TRMT6 | TRMT6 | 6833 | 0.051 | 0.45 | NO |
238 | TOPBP1 | TOPBP1 | TOPBP1 | 6890 | 0.049 | 0.45 | NO |
239 | KIF16B | KIF16B | KIF16B | 6905 | 0.049 | 0.45 | NO |
240 | ZNF846 | ZNF846 | ZNF846 | 6931 | 0.049 | 0.45 | NO |
241 | PSPC1 | PSPC1 | PSPC1 | 6946 | 0.048 | 0.45 | NO |
242 | BET1 | BET1 | BET1 | 7003 | 0.047 | 0.45 | NO |
243 | UBE2B | UBE2B | UBE2B | 7016 | 0.047 | 0.45 | NO |
244 | ING3 | ING3 | ING3 | 7179 | 0.044 | 0.44 | NO |
245 | SESN3 | SESN3 | SESN3 | 7197 | 0.044 | 0.44 | NO |
246 | MLLT3 | MLLT3 | MLLT3 | 7228 | 0.043 | 0.44 | NO |
247 | UTP15 | UTP15 | UTP15 | 7232 | 0.043 | 0.44 | NO |
248 | NDUFS4 | NDUFS4 | NDUFS4 | 7251 | 0.043 | 0.44 | NO |
249 | SHMT1 | SHMT1 | SHMT1 | 7321 | 0.041 | 0.44 | NO |
250 | SFPQ | SFPQ | SFPQ | 7372 | 0.04 | 0.44 | NO |
251 | HUS1 | HUS1 | HUS1 | 7376 | 0.04 | 0.44 | NO |
252 | ABHD13 | ABHD13 | ABHD13 | 7407 | 0.039 | 0.44 | NO |
253 | BMI1 | BMI1 | BMI1 | 7463 | 0.038 | 0.44 | NO |
254 | WIF1 | WIF1 | WIF1 | 7478 | 0.038 | 0.44 | NO |
255 | SMNDC1 | SMNDC1 | SMNDC1 | 7493 | 0.038 | 0.44 | NO |
256 | TRAPPC10 | TRAPPC10 | TRAPPC10 | 7517 | 0.037 | 0.44 | NO |
257 | NRAS | NRAS | NRAS | 7519 | 0.037 | 0.44 | NO |
258 | UBA3 | UBA3 | UBA3 | 7585 | 0.036 | 0.44 | NO |
259 | LYRM5 | LYRM5 | LYRM5 | 7612 | 0.036 | 0.44 | NO |
260 | BRCA1 | BRCA1 | BRCA1 | 7649 | 0.035 | 0.44 | NO |
261 | HNRNPA2B1 | HNRNPA2B1 | HNRNPA2B1 | 7650 | 0.035 | 0.44 | NO |
262 | ANAPC1 | ANAPC1 | ANAPC1 | 7654 | 0.035 | 0.44 | NO |
263 | PCYOX1 | PCYOX1 | PCYOX1 | 7701 | 0.034 | 0.44 | NO |
264 | NUP85 | NUP85 | NUP85 | 7704 | 0.034 | 0.44 | NO |
265 | CPSF6 | CPSF6 | CPSF6 | 7707 | 0.034 | 0.44 | NO |
266 | POLD3 | POLD3 | POLD3 | 7723 | 0.033 | 0.44 | NO |
267 | STARD7 | STARD7 | STARD7 | 7748 | 0.033 | 0.44 | NO |
268 | SRSF3 | SRSF3 | SRSF3 | 7753 | 0.033 | 0.44 | NO |
269 | MRPS31 | MRPS31 | MRPS31 | 7754 | 0.033 | 0.44 | NO |
270 | BRD7 | BRD7 | BRD7 | 7768 | 0.033 | 0.44 | NO |
271 | ACTR3B | ACTR3B | ACTR3B | 7791 | 0.032 | 0.44 | NO |
272 | SKA2 | SKA2 | SKA2 | 7793 | 0.032 | 0.44 | NO |
273 | PPM1B | PPM1B | PPM1B | 7915 | 0.03 | 0.43 | NO |
274 | NDUFA4 | NDUFA4 | NDUFA4 | 8003 | 0.028 | 0.43 | NO |
275 | STRAP | STRAP | STRAP | 8051 | 0.027 | 0.43 | NO |
276 | TMEM117 | TMEM117 | TMEM117 | 8078 | 0.027 | 0.42 | NO |
277 | TP53BP1 | TP53BP1 | TP53BP1 | 8089 | 0.027 | 0.42 | NO |
278 | DNAJA1 | DNAJA1 | DNAJA1 | 8115 | 0.026 | 0.42 | NO |
279 | BCL2 | BCL2 | BCL2 | 8141 | 0.026 | 0.42 | NO |
280 | SPIN1 | SPIN1 | SPIN1 | 8223 | 0.024 | 0.42 | NO |
281 | SNRPB2 | SNRPB2 | SNRPB2 | 8367 | 0.021 | 0.41 | NO |
282 | SLC38A1 | SLC38A1 | SLC38A1 | 8369 | 0.021 | 0.41 | NO |
283 | MED6 | MED6 | MED6 | 8395 | 0.021 | 0.41 | NO |
284 | XRCC5 | XRCC5 | XRCC5 | 8430 | 0.02 | 0.41 | NO |
285 | IMMP1L | IMMP1L | IMMP1L | 8602 | 0.017 | 0.4 | NO |
286 | RBBP5 | RBBP5 | RBBP5 | 8621 | 0.017 | 0.4 | NO |
287 | VDAC1 | VDAC1 | VDAC1 | 8640 | 0.016 | 0.4 | NO |
288 | ANKLE2 | ANKLE2 | ANKLE2 | 8656 | 0.016 | 0.4 | NO |
289 | RAD51 | RAD51 | RAD51 | 8668 | 0.016 | 0.4 | NO |
290 | SNX5 | SNX5 | SNX5 | 8693 | 0.015 | 0.4 | NO |
291 | WDR3 | WDR3 | WDR3 | 8717 | 0.015 | 0.4 | NO |
292 | CAV2 | CAV2 | CAV2 | 8792 | 0.014 | 0.39 | NO |
293 | NME7 | NME7 | NME7 | 8796 | 0.014 | 0.39 | NO |
294 | GEMIN6 | GEMIN6 | GEMIN6 | 8830 | 0.013 | 0.39 | NO |
295 | TTF2 | TTF2 | TTF2 | 8875 | 0.012 | 0.39 | NO |
296 | TNIK | TNIK | TNIK | 8881 | 0.012 | 0.39 | NO |
297 | MTHFD1 | MTHFD1 | MTHFD1 | 8901 | 0.012 | 0.39 | NO |
298 | ZNF22 | ZNF22 | ZNF22 | 8922 | 0.012 | 0.39 | NO |
299 | YWHAB | YWHAB | YWHAB | 8939 | 0.011 | 0.39 | NO |
300 | PFN2 | PFN2 | PFN2 | 8949 | 0.011 | 0.39 | NO |
301 | TASP1 | TASP1 | TASP1 | 8961 | 0.011 | 0.39 | NO |
302 | PWP1 | PWP1 | PWP1 | 8970 | 0.01 | 0.39 | NO |
303 | ADH5 | ADH5 | ADH5 | 8987 | 0.01 | 0.39 | NO |
304 | DUSP11 | DUSP11 | DUSP11 | 9022 | 0.0095 | 0.38 | NO |
305 | MRPS18C | MRPS18C | MRPS18C | 9038 | 0.0093 | 0.38 | NO |
306 | PRPS2 | PRPS2 | PRPS2 | 9049 | 0.0091 | 0.38 | NO |
307 | HNRNPA3 | HNRNPA3 | HNRNPA3 | 9057 | 0.009 | 0.38 | NO |
308 | FH | FH | FH | 9140 | 0.0074 | 0.38 | NO |
309 | UBE2D2 | UBE2D2 | UBE2D2 | 9210 | 0.0061 | 0.38 | NO |
310 | ARMC10 | ARMC10 | ARMC10 | 9321 | 0.004 | 0.37 | NO |
311 | SNAPIN | SNAPIN | SNAPIN | 9340 | 0.0036 | 0.37 | NO |
312 | VDAC3 | VDAC3 | VDAC3 | 9353 | 0.0035 | 0.37 | NO |
313 | C1orf74 | C1orf74 | C1orf74 | 9375 | 0.0031 | 0.37 | NO |
314 | FARSB | FARSB | FARSB | 9397 | 0.0028 | 0.37 | NO |
315 | CSTF2 | CSTF2 | CSTF2 | 9405 | 0.0027 | 0.37 | NO |
316 | NAF1 | NAF1 | NAF1 | 9423 | 0.0024 | 0.36 | NO |
317 | MPZL1 | MPZL1 | MPZL1 | 9504 | 0.00085 | 0.36 | NO |
318 | IDUA | IDUA | IDUA | 9506 | 0.00083 | 0.36 | NO |
319 | IK | IK | IK | 9533 | 0.00038 | 0.36 | NO |
320 | CHEK1 | CHEK1 | CHEK1 | 9545 | 0.00017 | 0.36 | NO |
321 | PTPN14 | PTPN14 | PTPN14 | 9607 | -0.00072 | 0.36 | NO |
322 | SSBP1 | SSBP1 | SSBP1 | 9631 | -0.0011 | 0.35 | NO |
323 | LPHN3 | LPHN3 | LPHN3 | 9680 | -0.002 | 0.35 | NO |
324 | CRYZ | CRYZ | CRYZ | 9728 | -0.0028 | 0.35 | NO |
325 | PARP1 | PARP1 | PARP1 | 9795 | -0.004 | 0.34 | NO |
326 | CDCA8 | CDCA8 | CDCA8 | 9862 | -0.0048 | 0.34 | NO |
327 | KIF2C | KIF2C | KIF2C | 9917 | -0.0056 | 0.34 | NO |
328 | EWSR1 | EWSR1 | EWSR1 | 9920 | -0.0056 | 0.34 | NO |
329 | EIF4H | EIF4H | EIF4H | 10016 | -0.0074 | 0.33 | NO |
330 | RPRD2 | RPRD2 | RPRD2 | 10057 | -0.0084 | 0.33 | NO |
331 | SERBP1 | SERBP1 | SERBP1 | 10107 | -0.0091 | 0.33 | NO |
332 | DFNA5 | DFNA5 | DFNA5 | 10123 | -0.0094 | 0.33 | NO |
333 | PEX7 | PEX7 | PEX7 | 10138 | -0.0096 | 0.33 | NO |
334 | HNRNPU | HNRNPU | HNRNPU | 10232 | -0.011 | 0.32 | NO |
335 | POLR3K | POLR3K | POLR3K | 10285 | -0.012 | 0.32 | NO |
336 | TMTC4 | TMTC4 | TMTC4 | 10309 | -0.012 | 0.32 | NO |
337 | SLC7A1 | SLC7A1 | SLC7A1 | 10321 | -0.012 | 0.32 | NO |
338 | CAPRIN1 | CAPRIN1 | CAPRIN1 | 10390 | -0.013 | 0.32 | NO |
339 | LSM5 | LSM5 | LSM5 | 10472 | -0.015 | 0.31 | NO |
340 | ASXL1 | ASXL1 | ASXL1 | 10553 | -0.016 | 0.31 | NO |
341 | TRRAP | TRRAP | TRRAP | 10609 | -0.017 | 0.3 | NO |
342 | METTL9 | METTL9 | METTL9 | 10643 | -0.017 | 0.3 | NO |
343 | RRAGD | RRAGD | RRAGD | 10723 | -0.018 | 0.3 | NO |
344 | PARK7 | PARK7 | PARK7 | 10796 | -0.02 | 0.3 | NO |
345 | LSM7 | LSM7 | LSM7 | 11026 | -0.023 | 0.28 | NO |
346 | KBTBD8 | KBTBD8 | KBTBD8 | 11038 | -0.023 | 0.28 | NO |
347 | KCTD15 | KCTD15 | KCTD15 | 11091 | -0.024 | 0.28 | NO |
348 | H2AFZ | H2AFZ | H2AFZ | 11115 | -0.024 | 0.28 | NO |
349 | STXBP6 | STXBP6 | STXBP6 | 11129 | -0.025 | 0.28 | NO |
350 | POLR1C | POLR1C | POLR1C | 11204 | -0.026 | 0.28 | NO |
351 | PLEKHB1 | PLEKHB1 | PLEKHB1 | 11309 | -0.027 | 0.27 | NO |
352 | ACTL6A | ACTL6A | ACTL6A | 11413 | -0.029 | 0.27 | NO |
353 | PKP4 | PKP4 | PKP4 | 11490 | -0.03 | 0.26 | NO |
354 | SLC20A2 | SLC20A2 | SLC20A2 | 11517 | -0.03 | 0.26 | NO |
355 | ILF3 | ILF3 | ILF3 | 11602 | -0.032 | 0.26 | NO |
356 | EFTUD2 | EFTUD2 | EFTUD2 | 11655 | -0.032 | 0.26 | NO |
357 | TOMM70A | TOMM70A | TOMM70A | 11694 | -0.033 | 0.26 | NO |
358 | PANK1 | PANK1 | PANK1 | 11750 | -0.034 | 0.25 | NO |
359 | TP63 | TP63 | TP63 | 11752 | -0.034 | 0.25 | NO |
360 | MRPS33 | MRPS33 | MRPS33 | 11788 | -0.034 | 0.25 | NO |
361 | AHCY | AHCY | AHCY | 11834 | -0.035 | 0.25 | NO |
362 | RPA3 | RPA3 | RPA3 | 11838 | -0.035 | 0.25 | NO |
363 | C11orf74 | C11orf74 | C11orf74 | 11925 | -0.037 | 0.25 | NO |
364 | EIF4B | EIF4B | EIF4B | 12036 | -0.038 | 0.24 | NO |
365 | STMN1 | STMN1 | STMN1 | 12046 | -0.038 | 0.24 | NO |
366 | ZIK1 | ZIK1 | ZIK1 | 12134 | -0.039 | 0.24 | NO |
367 | CD24 | CD24 | CD24 | 12138 | -0.039 | 0.24 | NO |
368 | CTCF | CTCF | CTCF | 12199 | -0.04 | 0.24 | NO |
369 | TULP3 | TULP3 | TULP3 | 12251 | -0.041 | 0.24 | NO |
370 | HARS | HARS | HARS | 12255 | -0.041 | 0.24 | NO |
371 | NDUFC2 | NDUFC2 | NDUFC2 | 12280 | -0.041 | 0.24 | NO |
372 | NDUFC1 | NDUFC1 | NDUFC1 | 12294 | -0.042 | 0.24 | NO |
373 | ZNF317 | ZNF317 | ZNF317 | 12381 | -0.043 | 0.23 | NO |
374 | HNRNPA1 | HNRNPA1 | HNRNPA1 | 12476 | -0.044 | 0.23 | NO |
375 | EMID1 | EMID1 | EMID1 | 12651 | -0.047 | 0.22 | NO |
376 | RPA1 | RPA1 | RPA1 | 12707 | -0.048 | 0.22 | NO |
377 | SNRNP200 | SNRNP200 | SNRNP200 | 12755 | -0.048 | 0.22 | NO |
378 | RNF44 | RNF44 | RNF44 | 12844 | -0.05 | 0.21 | NO |
379 | NCAPD2 | NCAPD2 | NCAPD2 | 12920 | -0.051 | 0.21 | NO |
380 | UNG | UNG | UNG | 12939 | -0.051 | 0.21 | NO |
381 | TRPM3 | TRPM3 | TRPM3 | 13017 | -0.052 | 0.21 | NO |
382 | CEP164 | CEP164 | CEP164 | 13141 | -0.054 | 0.2 | NO |
383 | TTC9C | TTC9C | TTC9C | 13173 | -0.055 | 0.2 | NO |
384 | SEC22C | SEC22C | SEC22C | 13306 | -0.057 | 0.2 | NO |
385 | PPP2R1A | PPP2R1A | PPP2R1A | 13405 | -0.058 | 0.19 | NO |
386 | PIN1 | PIN1 | PIN1 | 13758 | -0.064 | 0.17 | NO |
387 | VPS26B | VPS26B | VPS26B | 13786 | -0.064 | 0.17 | NO |
388 | PHB2 | PHB2 | PHB2 | 13956 | -0.067 | 0.17 | NO |
389 | RNF7 | RNF7 | RNF7 | 14030 | -0.069 | 0.16 | NO |
390 | DDR1 | DDR1 | DDR1 | 14207 | -0.072 | 0.16 | NO |
391 | CHCHD4 | CHCHD4 | CHCHD4 | 14392 | -0.075 | 0.15 | NO |
392 | MAP7D2 | MAP7D2 | MAP7D2 | 14476 | -0.077 | 0.14 | NO |
393 | POLR3H | POLR3H | POLR3H | 14495 | -0.077 | 0.15 | NO |
394 | PCDH18 | PCDH18 | PCDH18 | 14828 | -0.083 | 0.13 | NO |
395 | ST6GAL1 | ST6GAL1 | ST6GAL1 | 15003 | -0.087 | 0.12 | NO |
396 | PATZ1 | PATZ1 | PATZ1 | 15179 | -0.09 | 0.12 | NO |
397 | RPS3 | RPS3 | RPS3 | 15277 | -0.092 | 0.11 | NO |
398 | ARAP2 | ARAP2 | ARAP2 | 15746 | -0.1 | 0.088 | NO |
399 | RPL15 | RPL15 | RPL15 | 16129 | -0.12 | 0.069 | NO |
400 | HOOK1 | HOOK1 | HOOK1 | 16233 | -0.12 | 0.067 | NO |
401 | ZNF532 | ZNF532 | ZNF532 | 16347 | -0.13 | 0.064 | NO |
402 | CDC25A | CDC25A | CDC25A | 16387 | -0.13 | 0.065 | NO |
403 | NEO1 | NEO1 | NEO1 | 16454 | -0.13 | 0.065 | NO |
404 | ZNF362 | ZNF362 | ZNF362 | 16496 | -0.13 | 0.066 | NO |
405 | CTH | CTH | CTH | 16903 | -0.16 | 0.047 | NO |
406 | MCM2 | MCM2 | MCM2 | 16950 | -0.16 | 0.049 | NO |
407 | NFIA | NFIA | NFIA | 17546 | -0.24 | 0.021 | NO |
408 | BCL11A | BCL11A | BCL11A | 17865 | -0.34 | 0.012 | NO |
Figure S7. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KIM WT1 TARGETS DN.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: KIM WT1 TARGETS DN, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S5. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ABCC2 | ABCC2 | ABCC2 | 427 | 0.41 | 0.0014 | YES |
2 | ASIP | ASIP | ASIP | 530 | 0.38 | 0.019 | YES |
3 | ANKRD18A | ANKRD18A | ANKRD18A | 711 | 0.34 | 0.03 | YES |
4 | TRIM73 | TRIM73 | TRIM73 | 768 | 0.33 | 0.047 | YES |
5 | E2F8 | E2F8 | E2F8 | 885 | 0.31 | 0.06 | YES |
6 | REEP1 | REEP1 | REEP1 | 887 | 0.31 | 0.079 | YES |
7 | ANKRD36 | ANKRD36 | ANKRD36 | 1067 | 0.29 | 0.087 | YES |
8 | ADAM22 | ADAM22 | ADAM22 | 1098 | 0.28 | 0.1 | YES |
9 | DNA2 | DNA2 | DNA2 | 1218 | 0.27 | 0.11 | YES |
10 | GOLGA8B | GOLGA8B | GOLGA8B | 1352 | 0.25 | 0.12 | YES |
11 | CCDC150 | CCDC150 | CCDC150 | 1354 | 0.25 | 0.14 | YES |
12 | GOLGA8A | GOLGA8A | GOLGA8A | 1366 | 0.25 | 0.15 | YES |
13 | ESCO2 | ESCO2 | ESCO2 | 1534 | 0.24 | 0.16 | YES |
14 | ATAD2 | ATAD2 | ATAD2 | 1576 | 0.23 | 0.17 | YES |
15 | DEPDC7 | DEPDC7 | DEPDC7 | 1594 | 0.23 | 0.18 | YES |
16 | RAD51AP1 | RAD51AP1 | RAD51AP1 | 1626 | 0.23 | 0.19 | YES |
17 | PILRB | PILRB | PILRB | 1667 | 0.22 | 0.2 | YES |
18 | PHTF2 | PHTF2 | PHTF2 | 1788 | 0.21 | 0.21 | YES |
19 | TTLL7 | TTLL7 | TTLL7 | 1822 | 0.21 | 0.22 | YES |
20 | GPR126 | GPR126 | GPR126 | 1828 | 0.21 | 0.24 | YES |
21 | TOP2A | TOP2A | TOP2A | 1842 | 0.21 | 0.25 | YES |
22 | SH3GL2 | SH3GL2 | SH3GL2 | 1970 | 0.2 | 0.25 | YES |
23 | BRIP1 | BRIP1 | BRIP1 | 2070 | 0.19 | 0.26 | YES |
24 | SLC22A3 | SLC22A3 | SLC22A3 | 2133 | 0.19 | 0.27 | YES |
25 | C5orf42 | C5orf42 | C5orf42 | 2159 | 0.19 | 0.28 | YES |
26 | CREBZF | CREBZF | CREBZF | 2274 | 0.18 | 0.28 | YES |
27 | LYRM7 | LYRM7 | LYRM7 | 2313 | 0.18 | 0.29 | YES |
28 | CDH24 | CDH24 | CDH24 | 2319 | 0.18 | 0.3 | YES |
29 | PHIP | PHIP | PHIP | 2359 | 0.18 | 0.31 | YES |
30 | RBBP8 | RBBP8 | RBBP8 | 2361 | 0.18 | 0.32 | YES |
31 | EZH2 | EZH2 | EZH2 | 2371 | 0.18 | 0.33 | YES |
32 | KIAA1598 | KIAA1598 | KIAA1598 | 2468 | 0.17 | 0.34 | YES |
33 | MASTL | MASTL | MASTL | 2478 | 0.17 | 0.35 | YES |
34 | DMXL2 | DMXL2 | DMXL2 | 2549 | 0.17 | 0.35 | YES |
35 | CPNE8 | CPNE8 | CPNE8 | 2651 | 0.16 | 0.36 | YES |
36 | CENPQ | CENPQ | CENPQ | 2664 | 0.16 | 0.37 | YES |
37 | MAP3K2 | MAP3K2 | MAP3K2 | 2701 | 0.16 | 0.38 | YES |
38 | POLA1 | POLA1 | POLA1 | 2861 | 0.15 | 0.38 | YES |
39 | SLC38A2 | SLC38A2 | SLC38A2 | 2899 | 0.15 | 0.38 | YES |
40 | PHTF1 | PHTF1 | PHTF1 | 2935 | 0.15 | 0.39 | YES |
41 | RMI1 | RMI1 | RMI1 | 2971 | 0.15 | 0.4 | YES |
42 | CDKN2AIP | CDKN2AIP | CDKN2AIP | 3077 | 0.14 | 0.4 | YES |
43 | CERS6 | CERS6 | CERS6 | 3079 | 0.14 | 0.41 | YES |
44 | DNAJC6 | DNAJC6 | DNAJC6 | 3135 | 0.14 | 0.41 | YES |
45 | RRM2 | RRM2 | RRM2 | 3209 | 0.14 | 0.42 | YES |
46 | DSCC1 | DSCC1 | DSCC1 | 3329 | 0.14 | 0.42 | YES |
47 | OGT | OGT | OGT | 3373 | 0.13 | 0.43 | YES |
48 | OSGIN2 | OSGIN2 | OSGIN2 | 3417 | 0.13 | 0.43 | YES |
49 | CDC7 | CDC7 | CDC7 | 3471 | 0.13 | 0.44 | YES |
50 | ENOSF1 | ENOSF1 | ENOSF1 | 3708 | 0.12 | 0.43 | YES |
51 | IFIT1 | IFIT1 | IFIT1 | 3751 | 0.12 | 0.44 | YES |
52 | DONSON | DONSON | DONSON | 3831 | 0.12 | 0.44 | YES |
53 | KIFC2 | KIFC2 | KIFC2 | 3928 | 0.12 | 0.44 | YES |
54 | DHFR | DHFR | DHFR | 4075 | 0.11 | 0.44 | YES |
55 | NAB1 | NAB1 | NAB1 | 4086 | 0.11 | 0.45 | YES |
56 | DNAJB4 | DNAJB4 | DNAJB4 | 4170 | 0.11 | 0.45 | YES |
57 | RSRC2 | RSRC2 | RSRC2 | 4204 | 0.11 | 0.45 | YES |
58 | ARHGAP42 | ARHGAP42 | ARHGAP42 | 4208 | 0.11 | 0.46 | YES |
59 | MCM8 | MCM8 | MCM8 | 4214 | 0.11 | 0.47 | YES |
60 | CCDC84 | CCDC84 | CCDC84 | 4239 | 0.11 | 0.47 | YES |
61 | GCLM | GCLM | GCLM | 4307 | 0.11 | 0.48 | YES |
62 | PTAR1 | PTAR1 | PTAR1 | 4425 | 0.1 | 0.48 | YES |
63 | DYNC1LI2 | DYNC1LI2 | DYNC1LI2 | 4573 | 0.1 | 0.47 | YES |
64 | FANCI | FANCI | FANCI | 4598 | 0.099 | 0.48 | YES |
65 | USP1 | USP1 | USP1 | 4637 | 0.098 | 0.48 | YES |
66 | SRSF10 | SRSF10 | SRSF10 | 4676 | 0.097 | 0.48 | YES |
67 | FAM178A | FAM178A | FAM178A | 4696 | 0.096 | 0.49 | YES |
68 | RHOBTB3 | RHOBTB3 | RHOBTB3 | 4728 | 0.096 | 0.49 | YES |
69 | HIST1H4B | HIST1H4B | HIST1H4B | 4845 | 0.093 | 0.49 | YES |
70 | TYMS | TYMS | TYMS | 5025 | 0.088 | 0.49 | YES |
71 | CALM2 | CALM2 | CALM2 | 5193 | 0.085 | 0.48 | YES |
72 | ORC3 | ORC3 | ORC3 | 5196 | 0.085 | 0.49 | YES |
73 | SLC25A27 | SLC25A27 | SLC25A27 | 5238 | 0.084 | 0.49 | YES |
74 | HSPB8 | HSPB8 | HSPB8 | 5267 | 0.083 | 0.5 | YES |
75 | NUP160 | NUP160 | NUP160 | 5300 | 0.082 | 0.5 | YES |
76 | UBE2T | UBE2T | UBE2T | 5430 | 0.079 | 0.5 | YES |
77 | ZBED5 | ZBED5 | ZBED5 | 5435 | 0.079 | 0.5 | YES |
78 | ACPP | ACPP | ACPP | 5440 | 0.079 | 0.51 | YES |
79 | RRM1 | RRM1 | RRM1 | 5468 | 0.078 | 0.51 | YES |
80 | KAT2A | KAT2A | KAT2A | 5516 | 0.078 | 0.51 | YES |
81 | CHML | CHML | CHML | 5577 | 0.076 | 0.51 | YES |
82 | NFE2L2 | NFE2L2 | NFE2L2 | 5631 | 0.075 | 0.52 | YES |
83 | CCDC14 | CCDC14 | CCDC14 | 5664 | 0.074 | 0.52 | YES |
84 | DCAF16 | DCAF16 | DCAF16 | 5703 | 0.073 | 0.52 | YES |
85 | HELLS | HELLS | HELLS | 5799 | 0.071 | 0.52 | YES |
86 | CALD1 | CALD1 | CALD1 | 5901 | 0.069 | 0.52 | YES |
87 | MAN1A2 | MAN1A2 | MAN1A2 | 5964 | 0.068 | 0.52 | YES |
88 | INTS7 | INTS7 | INTS7 | 5979 | 0.067 | 0.52 | YES |
89 | PRIM1 | PRIM1 | PRIM1 | 6038 | 0.066 | 0.52 | YES |
90 | BLM | BLM | BLM | 6072 | 0.065 | 0.52 | YES |
91 | PHOSPHO2 | PHOSPHO2 | PHOSPHO2 | 6446 | 0.058 | 0.51 | NO |
92 | CDC45 | CDC45 | CDC45 | 6457 | 0.058 | 0.51 | NO |
93 | BIVM | BIVM | BIVM | 6518 | 0.056 | 0.51 | NO |
94 | HIST1H4C | HIST1H4C | HIST1H4C | 6567 | 0.055 | 0.51 | NO |
95 | SRSF5 | SRSF5 | SRSF5 | 6649 | 0.054 | 0.51 | NO |
96 | CRLS1 | CRLS1 | CRLS1 | 6703 | 0.053 | 0.51 | NO |
97 | EFHC1 | EFHC1 | EFHC1 | 6859 | 0.05 | 0.51 | NO |
98 | SVIP | SVIP | SVIP | 6883 | 0.05 | 0.51 | NO |
99 | NT5DC1 | NT5DC1 | NT5DC1 | 6962 | 0.048 | 0.51 | NO |
100 | INSIG2 | INSIG2 | INSIG2 | 7049 | 0.046 | 0.5 | NO |
101 | DCUN1D3 | DCUN1D3 | DCUN1D3 | 7071 | 0.046 | 0.51 | NO |
102 | BBS2 | BBS2 | BBS2 | 7083 | 0.046 | 0.51 | NO |
103 | PRIM2 | PRIM2 | PRIM2 | 7322 | 0.041 | 0.5 | NO |
104 | COL7A1 | COL7A1 | COL7A1 | 7412 | 0.039 | 0.5 | NO |
105 | BMI1 | BMI1 | BMI1 | 7463 | 0.038 | 0.49 | NO |
106 | MYCBP2 | MYCBP2 | MYCBP2 | 7599 | 0.036 | 0.49 | NO |
107 | HIST1H2AM | HIST1H2AM | HIST1H2AM | 7636 | 0.035 | 0.49 | NO |
108 | BRCA1 | BRCA1 | BRCA1 | 7649 | 0.035 | 0.49 | NO |
109 | MZF1 | MZF1 | MZF1 | 7681 | 0.034 | 0.49 | NO |
110 | ZWINT | ZWINT | ZWINT | 7724 | 0.033 | 0.49 | NO |
111 | NRD1 | NRD1 | NRD1 | 7760 | 0.033 | 0.49 | NO |
112 | UBL3 | UBL3 | UBL3 | 7825 | 0.032 | 0.49 | NO |
113 | NSUN3 | NSUN3 | NSUN3 | 8313 | 0.022 | 0.46 | NO |
114 | RAD18 | RAD18 | RAD18 | 8355 | 0.021 | 0.46 | NO |
115 | EXO1 | EXO1 | EXO1 | 8368 | 0.021 | 0.46 | NO |
116 | CAPS | CAPS | CAPS | 8373 | 0.021 | 0.46 | NO |
117 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 8415 | 0.02 | 0.46 | NO |
118 | SHC1 | SHC1 | SHC1 | 8498 | 0.019 | 0.46 | NO |
119 | RAD51 | RAD51 | RAD51 | 8668 | 0.016 | 0.45 | NO |
120 | KAT2B | KAT2B | KAT2B | 8684 | 0.016 | 0.45 | NO |
121 | C4BPB | C4BPB | C4BPB | 8742 | 0.015 | 0.45 | NO |
122 | COQ9 | COQ9 | COQ9 | 8980 | 0.01 | 0.44 | NO |
123 | ASF1B | ASF1B | ASF1B | 9378 | 0.0031 | 0.41 | NO |
124 | MITF | MITF | MITF | 9398 | 0.0027 | 0.41 | NO |
125 | RAD54L | RAD54L | RAD54L | 9494 | 0.0011 | 0.41 | NO |
126 | FANCA | FANCA | FANCA | 9625 | -0.0011 | 0.4 | NO |
127 | RHPN1 | RHPN1 | RHPN1 | 9626 | -0.0011 | 0.4 | NO |
128 | RFC2 | RFC2 | RFC2 | 9853 | -0.0047 | 0.39 | NO |
129 | FEN1 | FEN1 | FEN1 | 10067 | -0.0085 | 0.38 | NO |
130 | TRIM45 | TRIM45 | TRIM45 | 10186 | -0.01 | 0.37 | NO |
131 | CENPM | CENPM | CENPM | 10478 | -0.015 | 0.36 | NO |
132 | CDCA5 | CDCA5 | CDCA5 | 10540 | -0.016 | 0.35 | NO |
133 | PKMYT1 | PKMYT1 | PKMYT1 | 10763 | -0.019 | 0.34 | NO |
134 | SP1 | SP1 | SP1 | 10801 | -0.02 | 0.34 | NO |
135 | ABCC5 | ABCC5 | ABCC5 | 10860 | -0.02 | 0.34 | NO |
136 | MBD4 | MBD4 | MBD4 | 11028 | -0.023 | 0.33 | NO |
137 | TTC31 | TTC31 | TTC31 | 11311 | -0.027 | 0.32 | NO |
138 | TMCC1 | TMCC1 | TMCC1 | 11506 | -0.03 | 0.31 | NO |
139 | RPA2 | RPA2 | RPA2 | 11739 | -0.034 | 0.3 | NO |
140 | ABHD10 | ABHD10 | ABHD10 | 11873 | -0.036 | 0.29 | NO |
141 | EIF4EBP2 | EIF4EBP2 | EIF4EBP2 | 12131 | -0.039 | 0.28 | NO |
142 | SAP30BP | SAP30BP | SAP30BP | 12310 | -0.042 | 0.27 | NO |
143 | LIPH | LIPH | LIPH | 13011 | -0.052 | 0.24 | NO |
144 | ZNF217 | ZNF217 | ZNF217 | 13403 | -0.058 | 0.22 | NO |
145 | LMO4 | LMO4 | LMO4 | 13801 | -0.065 | 0.2 | NO |
146 | HIST1H4H | HIST1H4H | HIST1H4H | 14083 | -0.07 | 0.19 | NO |
147 | CASP2 | CASP2 | CASP2 | 14307 | -0.074 | 0.18 | NO |
148 | H1F0 | H1F0 | H1F0 | 14887 | -0.085 | 0.16 | NO |
149 | HIST3H2A | HIST3H2A | HIST3H2A | 15225 | -0.092 | 0.14 | NO |
150 | KDELC1 | KDELC1 | KDELC1 | 16446 | -0.13 | 0.082 | NO |
151 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 16852 | -0.15 | 0.069 | NO |
Figure S9. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: BIDUS METASTASIS UP.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: BIDUS METASTASIS UP, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S6. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MATR3 | MATR3 | MATR3 | 858 | 0.31 | -0.024 | YES |
2 | MPHOSPH9 | MPHOSPH9 | MPHOSPH9 | 1153 | 0.28 | -0.019 | YES |
3 | OTUD6B | OTUD6B | OTUD6B | 1200 | 0.27 | -0.00039 | YES |
4 | SGOL2 | SGOL2 | SGOL2 | 1385 | 0.25 | 0.0086 | YES |
5 | ABHD3 | ABHD3 | ABHD3 | 1489 | 0.24 | 0.021 | YES |
6 | TAF2 | TAF2 | TAF2 | 1745 | 0.22 | 0.024 | YES |
7 | DBF4 | DBF4 | DBF4 | 1799 | 0.21 | 0.037 | YES |
8 | PPP1R12A | PPP1R12A | PPP1R12A | 1836 | 0.21 | 0.051 | YES |
9 | DNAJB14 | DNAJB14 | DNAJB14 | 1881 | 0.2 | 0.065 | YES |
10 | PPIP5K2 | PPIP5K2 | PPIP5K2 | 1928 | 0.2 | 0.078 | YES |
11 | CEP152 | CEP152 | CEP152 | 1982 | 0.2 | 0.09 | YES |
12 | LRRC40 | LRRC40 | LRRC40 | 2005 | 0.2 | 0.1 | YES |
13 | TERF1 | TERF1 | TERF1 | 2124 | 0.19 | 0.11 | YES |
14 | C5orf28 | C5orf28 | C5orf28 | 2281 | 0.18 | 0.12 | YES |
15 | EZH2 | EZH2 | EZH2 | 2371 | 0.18 | 0.13 | YES |
16 | ZNF567 | ZNF567 | ZNF567 | 2401 | 0.17 | 0.14 | YES |
17 | ASF1A | ASF1A | ASF1A | 2440 | 0.17 | 0.15 | YES |
18 | TMEM165 | TMEM165 | TMEM165 | 2577 | 0.16 | 0.15 | YES |
19 | CDK1 | CDK1 | CDK1 | 2611 | 0.16 | 0.16 | YES |
20 | ANKRD49 | ANKRD49 | ANKRD49 | 2661 | 0.16 | 0.18 | YES |
21 | SPAST | SPAST | SPAST | 2773 | 0.16 | 0.18 | YES |
22 | PRKDC | PRKDC | PRKDC | 2824 | 0.15 | 0.19 | YES |
23 | KRIT1 | KRIT1 | KRIT1 | 3013 | 0.15 | 0.19 | YES |
24 | STAM2 | STAM2 | STAM2 | 3088 | 0.14 | 0.2 | YES |
25 | NOL8 | NOL8 | NOL8 | 3101 | 0.14 | 0.21 | YES |
26 | TRIB1 | TRIB1 | TRIB1 | 3388 | 0.13 | 0.2 | YES |
27 | BARD1 | BARD1 | BARD1 | 3488 | 0.13 | 0.21 | YES |
28 | NNT | NNT | NNT | 3699 | 0.12 | 0.2 | YES |
29 | IFT74 | IFT74 | IFT74 | 3743 | 0.12 | 0.21 | YES |
30 | DENND4A | DENND4A | DENND4A | 3910 | 0.12 | 0.21 | YES |
31 | DHX29 | DHX29 | DHX29 | 4015 | 0.11 | 0.22 | YES |
32 | C11orf54 | C11orf54 | C11orf54 | 4036 | 0.11 | 0.22 | YES |
33 | IREB2 | IREB2 | IREB2 | 4085 | 0.11 | 0.23 | YES |
34 | PAPD4 | PAPD4 | PAPD4 | 4095 | 0.11 | 0.24 | YES |
35 | MET | MET | MET | 4123 | 0.11 | 0.24 | YES |
36 | HAUS1 | HAUS1 | HAUS1 | 4157 | 0.11 | 0.25 | YES |
37 | ZCCHC10 | ZCCHC10 | ZCCHC10 | 4161 | 0.11 | 0.26 | YES |
38 | ZNF131 | ZNF131 | ZNF131 | 4171 | 0.11 | 0.27 | YES |
39 | RFX7 | RFX7 | RFX7 | 4212 | 0.11 | 0.27 | YES |
40 | C1orf131 | C1orf131 | C1orf131 | 4220 | 0.11 | 0.28 | YES |
41 | BTBD1 | BTBD1 | BTBD1 | 4238 | 0.11 | 0.29 | YES |
42 | LEMD3 | LEMD3 | LEMD3 | 4243 | 0.11 | 0.3 | YES |
43 | IARS | IARS | IARS | 4369 | 0.1 | 0.3 | YES |
44 | FAM188A | FAM188A | FAM188A | 4389 | 0.1 | 0.3 | YES |
45 | FANCL | FANCL | FANCL | 4461 | 0.1 | 0.31 | YES |
46 | TATDN1 | TATDN1 | TATDN1 | 4489 | 0.1 | 0.32 | YES |
47 | ZNF367 | ZNF367 | ZNF367 | 4490 | 0.1 | 0.32 | YES |
48 | LAP3 | LAP3 | LAP3 | 4527 | 0.1 | 0.33 | YES |
49 | NCAPD3 | NCAPD3 | NCAPD3 | 4542 | 0.1 | 0.34 | YES |
50 | RSF1 | RSF1 | RSF1 | 4565 | 0.1 | 0.34 | YES |
51 | PEX1 | PEX1 | PEX1 | 4612 | 0.098 | 0.35 | YES |
52 | DDX1 | DDX1 | DDX1 | 4653 | 0.097 | 0.35 | YES |
53 | ACTR6 | ACTR6 | ACTR6 | 4669 | 0.097 | 0.36 | YES |
54 | PAIP1 | PAIP1 | PAIP1 | 4723 | 0.096 | 0.36 | YES |
55 | MRPL19 | MRPL19 | MRPL19 | 4809 | 0.094 | 0.37 | YES |
56 | PSMA3 | PSMA3 | PSMA3 | 4824 | 0.094 | 0.37 | YES |
57 | MINPP1 | MINPP1 | MINPP1 | 4853 | 0.093 | 0.38 | YES |
58 | TYMS | TYMS | TYMS | 5025 | 0.088 | 0.38 | YES |
59 | PAK1IP1 | PAK1IP1 | PAK1IP1 | 5174 | 0.085 | 0.37 | YES |
60 | ANAPC10 | ANAPC10 | ANAPC10 | 5254 | 0.084 | 0.38 | YES |
61 | SPATA5L1 | SPATA5L1 | SPATA5L1 | 5290 | 0.083 | 0.38 | YES |
62 | TMEM135 | TMEM135 | TMEM135 | 5327 | 0.082 | 0.38 | YES |
63 | FEM1B | FEM1B | FEM1B | 5361 | 0.081 | 0.39 | YES |
64 | ZNF277 | ZNF277 | ZNF277 | 5415 | 0.08 | 0.39 | YES |
65 | ORC5 | ORC5 | ORC5 | 5482 | 0.078 | 0.39 | YES |
66 | SLC25A36 | SLC25A36 | SLC25A36 | 5486 | 0.078 | 0.4 | YES |
67 | PAPOLA | PAPOLA | PAPOLA | 5503 | 0.078 | 0.4 | YES |
68 | NUDCD2 | NUDCD2 | NUDCD2 | 5572 | 0.076 | 0.41 | YES |
69 | UPF3A | UPF3A | UPF3A | 5762 | 0.072 | 0.4 | YES |
70 | AASDHPPT | AASDHPPT | AASDHPPT | 5777 | 0.072 | 0.41 | YES |
71 | RACGAP1 | RACGAP1 | RACGAP1 | 5817 | 0.071 | 0.41 | YES |
72 | MRPL50 | MRPL50 | MRPL50 | 5891 | 0.069 | 0.41 | YES |
73 | CYP2R1 | CYP2R1 | CYP2R1 | 5893 | 0.069 | 0.42 | YES |
74 | PFDN4 | PFDN4 | PFDN4 | 6054 | 0.066 | 0.41 | YES |
75 | NASP | NASP | NASP | 6106 | 0.064 | 0.42 | YES |
76 | DDX18 | DDX18 | DDX18 | 6213 | 0.062 | 0.41 | YES |
77 | CCT2 | CCT2 | CCT2 | 6247 | 0.062 | 0.42 | YES |
78 | CEP57 | CEP57 | CEP57 | 6281 | 0.061 | 0.42 | YES |
79 | RPL26L1 | RPL26L1 | RPL26L1 | 6314 | 0.06 | 0.42 | YES |
80 | AVL9 | AVL9 | AVL9 | 6397 | 0.059 | 0.42 | NO |
81 | DARS | DARS | DARS | 6739 | 0.052 | 0.41 | NO |
82 | RNF111 | RNF111 | RNF111 | 7064 | 0.046 | 0.39 | NO |
83 | SLC33A1 | SLC33A1 | SLC33A1 | 7088 | 0.046 | 0.4 | NO |
84 | CDC23 | CDC23 | CDC23 | 7097 | 0.045 | 0.4 | NO |
85 | WDR61 | WDR61 | WDR61 | 7203 | 0.043 | 0.4 | NO |
86 | FAM98B | FAM98B | FAM98B | 7364 | 0.04 | 0.39 | NO |
87 | ELAC1 | ELAC1 | ELAC1 | 7377 | 0.04 | 0.39 | NO |
88 | CHMP4A | CHMP4A | CHMP4A | 7507 | 0.038 | 0.39 | NO |
89 | CCT5 | CCT5 | CCT5 | 7554 | 0.037 | 0.39 | NO |
90 | TLE4 | TLE4 | TLE4 | 7557 | 0.036 | 0.39 | NO |
91 | PPP2R5C | PPP2R5C | PPP2R5C | 7597 | 0.036 | 0.39 | NO |
92 | PDCD6 | PDCD6 | PDCD6 | 7671 | 0.034 | 0.39 | NO |
93 | SNX19 | SNX19 | SNX19 | 7695 | 0.034 | 0.39 | NO |
94 | C15orf41 | C15orf41 | C15orf41 | 7759 | 0.033 | 0.39 | NO |
95 | SNRPD1 | SNRPD1 | SNRPD1 | 7828 | 0.031 | 0.39 | NO |
96 | BUB3 | BUB3 | BUB3 | 7867 | 0.031 | 0.39 | NO |
97 | TMEM126A | TMEM126A | TMEM126A | 8013 | 0.028 | 0.38 | NO |
98 | GCSH | GCSH | GCSH | 8142 | 0.026 | 0.38 | NO |
99 | TDP2 | TDP2 | TDP2 | 8347 | 0.022 | 0.37 | NO |
100 | SLC38A1 | SLC38A1 | SLC38A1 | 8369 | 0.021 | 0.37 | NO |
101 | G3BP1 | G3BP1 | G3BP1 | 8462 | 0.019 | 0.37 | NO |
102 | C1QBP | C1QBP | C1QBP | 8648 | 0.016 | 0.36 | NO |
103 | NUDT5 | NUDT5 | NUDT5 | 9016 | 0.0096 | 0.34 | NO |
104 | KLF13 | KLF13 | KLF13 | 9154 | 0.0072 | 0.33 | NO |
105 | DKC1 | DKC1 | DKC1 | 9175 | 0.0067 | 0.33 | NO |
106 | RAN | RAN | RAN | 9179 | 0.0067 | 0.33 | NO |
107 | NAA50 | NAA50 | NAA50 | 9206 | 0.0063 | 0.33 | NO |
108 | GEMIN5 | GEMIN5 | GEMIN5 | 9346 | 0.0036 | 0.32 | NO |
109 | DDX31 | DDX31 | DDX31 | 9355 | 0.0034 | 0.32 | NO |
110 | CMC1 | CMC1 | CMC1 | 9515 | 0.00071 | 0.31 | NO |
111 | IK | IK | IK | 9533 | 0.00038 | 0.31 | NO |
112 | CHEK1 | CHEK1 | CHEK1 | 9545 | 0.00017 | 0.31 | NO |
113 | C11orf73 | C11orf73 | C11orf73 | 9615 | -0.00084 | 0.31 | NO |
114 | SSBP1 | SSBP1 | SSBP1 | 9631 | -0.0011 | 0.31 | NO |
115 | PAAF1 | PAAF1 | PAAF1 | 9686 | -0.0022 | 0.3 | NO |
116 | THYN1 | THYN1 | THYN1 | 9738 | -0.0029 | 0.3 | NO |
117 | TSHZ1 | TSHZ1 | TSHZ1 | 9784 | -0.0038 | 0.3 | NO |
118 | MCM3AP | MCM3AP | MCM3AP | 9876 | -0.005 | 0.29 | NO |
119 | CHCHD1 | CHCHD1 | CHCHD1 | 9904 | -0.0054 | 0.29 | NO |
120 | C19orf52 | C19orf52 | C19orf52 | 10205 | -0.01 | 0.28 | NO |
121 | SLC16A1 | SLC16A1 | SLC16A1 | 10319 | -0.012 | 0.27 | NO |
122 | PTPMT1 | PTPMT1 | PTPMT1 | 10338 | -0.013 | 0.27 | NO |
123 | NMT1 | NMT1 | NMT1 | 10416 | -0.014 | 0.27 | NO |
124 | SHFM1 | SHFM1 | SHFM1 | 10442 | -0.014 | 0.27 | NO |
125 | LSM5 | LSM5 | LSM5 | 10472 | -0.015 | 0.27 | NO |
126 | EBNA1BP2 | EBNA1BP2 | EBNA1BP2 | 10589 | -0.017 | 0.26 | NO |
127 | PSMC4 | PSMC4 | PSMC4 | 10914 | -0.021 | 0.25 | NO |
128 | GLT8D1 | GLT8D1 | GLT8D1 | 10936 | -0.022 | 0.25 | NO |
129 | FANCF | FANCF | FANCF | 10950 | -0.022 | 0.25 | NO |
130 | EIF3M | EIF3M | EIF3M | 10969 | -0.022 | 0.25 | NO |
131 | MBD4 | MBD4 | MBD4 | 11028 | -0.023 | 0.25 | NO |
132 | AIMP2 | AIMP2 | AIMP2 | 11137 | -0.025 | 0.24 | NO |
133 | MYLIP | MYLIP | MYLIP | 11314 | -0.027 | 0.24 | NO |
134 | TBCB | TBCB | TBCB | 11379 | -0.028 | 0.23 | NO |
135 | ACTL6A | ACTL6A | ACTL6A | 11413 | -0.029 | 0.23 | NO |
136 | NCLN | NCLN | NCLN | 11505 | -0.03 | 0.23 | NO |
137 | MINA | MINA | MINA | 11525 | -0.03 | 0.23 | NO |
138 | IFT57 | IFT57 | IFT57 | 11597 | -0.031 | 0.23 | NO |
139 | ILF3 | ILF3 | ILF3 | 11602 | -0.032 | 0.23 | NO |
140 | EFTUD2 | EFTUD2 | EFTUD2 | 11655 | -0.032 | 0.23 | NO |
141 | KEAP1 | KEAP1 | KEAP1 | 11742 | -0.034 | 0.23 | NO |
142 | PSMD8 | PSMD8 | PSMD8 | 11815 | -0.035 | 0.23 | NO |
143 | LSM4 | LSM4 | LSM4 | 11851 | -0.036 | 0.23 | NO |
144 | ATP5L | ATP5L | ATP5L | 11960 | -0.037 | 0.23 | NO |
145 | CIRH1A | CIRH1A | CIRH1A | 12353 | -0.042 | 0.21 | NO |
146 | MRPS12 | MRPS12 | MRPS12 | 12405 | -0.043 | 0.21 | NO |
147 | SMARCA4 | SMARCA4 | SMARCA4 | 12770 | -0.048 | 0.19 | NO |
148 | SF3B2 | SF3B2 | SF3B2 | 12875 | -0.05 | 0.19 | NO |
149 | TIMM50 | TIMM50 | TIMM50 | 13554 | -0.061 | 0.16 | NO |
150 | RUVBL2 | RUVBL2 | RUVBL2 | 13791 | -0.065 | 0.15 | NO |
151 | RNF7 | RNF7 | RNF7 | 14030 | -0.069 | 0.14 | NO |
152 | MRPL43 | MRPL43 | MRPL43 | 14086 | -0.07 | 0.14 | NO |
153 | NDUFA13 | NDUFA13 | NDUFA13 | 14190 | -0.072 | 0.14 | NO |
154 | FIBP | FIBP | FIBP | 14250 | -0.073 | 0.14 | NO |
155 | COMMD4 | COMMD4 | COMMD4 | 14851 | -0.084 | 0.12 | NO |
156 | CCDC94 | CCDC94 | CCDC94 | 15192 | -0.091 | 0.11 | NO |
157 | NADSYN1 | NADSYN1 | NADSYN1 | 15319 | -0.094 | 0.11 | NO |
158 | ERCC1 | ERCC1 | ERCC1 | 15474 | -0.097 | 0.1 | NO |
159 | IP6K2 | IP6K2 | IP6K2 | 15684 | -0.1 | 0.1 | NO |
160 | EIF3G | EIF3G | EIF3G | 16066 | -0.12 | 0.089 | NO |
161 | ACD | ACD | ACD | 16728 | -0.14 | 0.063 | NO |
162 | MCM2 | MCM2 | MCM2 | 16950 | -0.16 | 0.063 | NO |
Figure S11. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: MAYBURD RESPONSE TO L663536 DN.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: MAYBURD RESPONSE TO L663536 DN, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S7. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SOCS2 | SOCS2 | SOCS2 | 1148 | 0.28 | -0.045 | YES |
2 | GAS2 | GAS2 | GAS2 | 1473 | 0.24 | -0.047 | YES |
3 | PHTF2 | PHTF2 | PHTF2 | 1788 | 0.21 | -0.049 | YES |
4 | MAP4K3 | MAP4K3 | MAP4K3 | 1803 | 0.21 | -0.036 | YES |
5 | ADAM9 | ADAM9 | ADAM9 | 2307 | 0.18 | -0.051 | YES |
6 | STRN3 | STRN3 | STRN3 | 2365 | 0.18 | -0.042 | YES |
7 | F2R | F2R | F2R | 2387 | 0.18 | -0.031 | YES |
8 | ITGA6 | ITGA6 | ITGA6 | 2390 | 0.18 | -0.02 | YES |
9 | TGS1 | TGS1 | TGS1 | 2501 | 0.17 | -0.014 | YES |
10 | MPHOSPH10 | MPHOSPH10 | MPHOSPH10 | 2544 | 0.17 | -0.0047 | YES |
11 | ESF1 | ESF1 | ESF1 | 2709 | 0.16 | -0.0028 | YES |
12 | NOP58 | NOP58 | NOP58 | 2728 | 0.16 | 0.0071 | YES |
13 | HRSP12 | HRSP12 | HRSP12 | 2830 | 0.15 | 0.012 | YES |
14 | CHD1 | CHD1 | CHD1 | 2834 | 0.15 | 0.022 | YES |
15 | SLC38A2 | SLC38A2 | SLC38A2 | 2899 | 0.15 | 0.029 | YES |
16 | SMARCAD1 | SMARCAD1 | SMARCAD1 | 2977 | 0.15 | 0.035 | YES |
17 | XPO1 | XPO1 | XPO1 | 3018 | 0.15 | 0.043 | YES |
18 | SLC4A7 | SLC4A7 | SLC4A7 | 3110 | 0.14 | 0.048 | YES |
19 | XPOT | XPOT | XPOT | 3117 | 0.14 | 0.058 | YES |
20 | BACH1 | BACH1 | BACH1 | 3234 | 0.14 | 0.061 | YES |
21 | TBC1D15 | TBC1D15 | TBC1D15 | 3321 | 0.14 | 0.065 | YES |
22 | STXBP3 | STXBP3 | STXBP3 | 3404 | 0.13 | 0.07 | YES |
23 | WDR43 | WDR43 | WDR43 | 3421 | 0.13 | 0.078 | YES |
24 | MARCH7 | MARCH7 | MARCH7 | 3445 | 0.13 | 0.086 | YES |
25 | PACRGL | PACRGL | PACRGL | 3597 | 0.13 | 0.086 | YES |
26 | PTPN2 | PTPN2 | PTPN2 | 3620 | 0.13 | 0.094 | YES |
27 | RNFT1 | RNFT1 | RNFT1 | 3637 | 0.12 | 0.1 | YES |
28 | TXNDC9 | TXNDC9 | TXNDC9 | 3641 | 0.12 | 0.11 | YES |
29 | DICER1 | DICER1 | DICER1 | 3656 | 0.12 | 0.12 | YES |
30 | CWC22 | CWC22 | CWC22 | 3670 | 0.12 | 0.13 | YES |
31 | KRAS | KRAS | KRAS | 3701 | 0.12 | 0.13 | YES |
32 | MTMR10 | MTMR10 | MTMR10 | 3734 | 0.12 | 0.14 | YES |
33 | IMPAD1 | IMPAD1 | IMPAD1 | 3747 | 0.12 | 0.15 | YES |
34 | PSMD12 | PSMD12 | PSMD12 | 4072 | 0.11 | 0.14 | YES |
35 | ZCCHC10 | ZCCHC10 | ZCCHC10 | 4161 | 0.11 | 0.14 | YES |
36 | RSRC2 | RSRC2 | RSRC2 | 4204 | 0.11 | 0.14 | YES |
37 | TNPO1 | TNPO1 | TNPO1 | 4219 | 0.11 | 0.15 | YES |
38 | ZFX | ZFX | ZFX | 4222 | 0.11 | 0.16 | YES |
39 | BLZF1 | BLZF1 | BLZF1 | 4225 | 0.11 | 0.17 | YES |
40 | MDFIC | MDFIC | MDFIC | 4237 | 0.11 | 0.17 | YES |
41 | ELOVL6 | ELOVL6 | ELOVL6 | 4247 | 0.11 | 0.18 | YES |
42 | SEC23A | SEC23A | SEC23A | 4272 | 0.11 | 0.19 | YES |
43 | GCLM | GCLM | GCLM | 4307 | 0.11 | 0.19 | YES |
44 | IARS | IARS | IARS | 4369 | 0.1 | 0.2 | YES |
45 | GAB1 | GAB1 | GAB1 | 4415 | 0.1 | 0.2 | YES |
46 | PCF11 | PCF11 | PCF11 | 4426 | 0.1 | 0.21 | YES |
47 | EIF3J | EIF3J | EIF3J | 4447 | 0.1 | 0.21 | YES |
48 | SRSF6 | SRSF6 | SRSF6 | 4458 | 0.1 | 0.22 | YES |
49 | ACAT2 | ACAT2 | ACAT2 | 4466 | 0.1 | 0.23 | YES |
50 | KIF2A | KIF2A | KIF2A | 4610 | 0.098 | 0.22 | YES |
51 | RNF138 | RNF138 | RNF138 | 4625 | 0.098 | 0.23 | YES |
52 | DDX1 | DDX1 | DDX1 | 4653 | 0.097 | 0.24 | YES |
53 | RAB18 | RAB18 | RAB18 | 4683 | 0.097 | 0.24 | YES |
54 | PKD2 | PKD2 | PKD2 | 4757 | 0.095 | 0.24 | YES |
55 | MED23 | MED23 | MED23 | 4787 | 0.095 | 0.25 | YES |
56 | PLA2G6 | PLA2G6 | PLA2G6 | 4807 | 0.094 | 0.25 | YES |
57 | FBXO38 | FBXO38 | FBXO38 | 4822 | 0.094 | 0.26 | YES |
58 | RASA1 | RASA1 | RASA1 | 4867 | 0.093 | 0.26 | YES |
59 | SEC23IP | SEC23IP | SEC23IP | 4881 | 0.092 | 0.27 | YES |
60 | ROCK2 | ROCK2 | ROCK2 | 4936 | 0.091 | 0.27 | YES |
61 | ACADM | ACADM | ACADM | 4985 | 0.09 | 0.28 | YES |
62 | PPIC | PPIC | PPIC | 4989 | 0.09 | 0.28 | YES |
63 | ZNF644 | ZNF644 | ZNF644 | 4993 | 0.09 | 0.29 | YES |
64 | EPRS | EPRS | EPRS | 5020 | 0.089 | 0.29 | YES |
65 | LIMA1 | LIMA1 | LIMA1 | 5032 | 0.088 | 0.3 | YES |
66 | KLHL7 | KLHL7 | KLHL7 | 5202 | 0.085 | 0.29 | YES |
67 | TBRG1 | TBRG1 | TBRG1 | 5218 | 0.084 | 0.3 | YES |
68 | ZNF281 | ZNF281 | ZNF281 | 5295 | 0.083 | 0.3 | YES |
69 | TXNRD1 | TXNRD1 | TXNRD1 | 5360 | 0.081 | 0.3 | YES |
70 | UBE2T | UBE2T | UBE2T | 5430 | 0.079 | 0.3 | YES |
71 | MSH2 | MSH2 | MSH2 | 5497 | 0.078 | 0.31 | YES |
72 | STAM | STAM | STAM | 5508 | 0.078 | 0.31 | YES |
73 | ZC3H14 | ZC3H14 | ZC3H14 | 5629 | 0.075 | 0.31 | YES |
74 | RNF145 | RNF145 | RNF145 | 5693 | 0.073 | 0.31 | YES |
75 | RARS2 | RARS2 | RARS2 | 5699 | 0.073 | 0.32 | YES |
76 | UTP20 | UTP20 | UTP20 | 5713 | 0.073 | 0.32 | YES |
77 | FHL1 | FHL1 | FHL1 | 5784 | 0.072 | 0.32 | YES |
78 | YAP1 | YAP1 | YAP1 | 5824 | 0.07 | 0.32 | YES |
79 | TOM1L1 | TOM1L1 | TOM1L1 | 5994 | 0.067 | 0.32 | YES |
80 | YES1 | YES1 | YES1 | 6105 | 0.064 | 0.32 | YES |
81 | ITGB1 | ITGB1 | ITGB1 | 6191 | 0.063 | 0.32 | YES |
82 | SLC7A6 | SLC7A6 | SLC7A6 | 6240 | 0.062 | 0.32 | YES |
83 | IARS2 | IARS2 | IARS2 | 6241 | 0.062 | 0.32 | YES |
84 | ANKRD17 | ANKRD17 | ANKRD17 | 6297 | 0.061 | 0.32 | YES |
85 | RRN3 | RRN3 | RRN3 | 6304 | 0.06 | 0.33 | YES |
86 | USP9X | USP9X | USP9X | 6382 | 0.059 | 0.33 | YES |
87 | ARIH1 | ARIH1 | ARIH1 | 6458 | 0.058 | 0.33 | YES |
88 | COPS4 | COPS4 | COPS4 | 6554 | 0.055 | 0.33 | YES |
89 | CTBP2 | CTBP2 | CTBP2 | 6589 | 0.055 | 0.33 | YES |
90 | GNL2 | GNL2 | GNL2 | 6633 | 0.054 | 0.33 | YES |
91 | ELP2 | ELP2 | ELP2 | 6689 | 0.053 | 0.33 | YES |
92 | NUP35 | NUP35 | NUP35 | 6695 | 0.053 | 0.33 | YES |
93 | C5orf51 | C5orf51 | C5orf51 | 6711 | 0.053 | 0.34 | YES |
94 | RAD23B | RAD23B | RAD23B | 6741 | 0.052 | 0.34 | YES |
95 | LAPTM4B | LAPTM4B | LAPTM4B | 6778 | 0.052 | 0.34 | YES |
96 | HSPA4 | HSPA4 | HSPA4 | 6792 | 0.051 | 0.34 | YES |
97 | ZMYM4 | ZMYM4 | ZMYM4 | 6809 | 0.051 | 0.34 | YES |
98 | TPP2 | TPP2 | TPP2 | 6843 | 0.05 | 0.35 | YES |
99 | NDUFAF1 | NDUFAF1 | NDUFAF1 | 6852 | 0.05 | 0.35 | YES |
100 | PLS3 | PLS3 | PLS3 | 6856 | 0.05 | 0.35 | YES |
101 | FKBP11 | FKBP11 | FKBP11 | 6922 | 0.049 | 0.35 | NO |
102 | PPA1 | PPA1 | PPA1 | 7020 | 0.047 | 0.35 | NO |
103 | FCF1 | FCF1 | FCF1 | 7096 | 0.045 | 0.35 | NO |
104 | CDK2AP1 | CDK2AP1 | CDK2AP1 | 7118 | 0.045 | 0.35 | NO |
105 | FBXO8 | FBXO8 | FBXO8 | 7166 | 0.044 | 0.35 | NO |
106 | WBP5 | WBP5 | WBP5 | 7379 | 0.04 | 0.34 | NO |
107 | EIF4G2 | EIF4G2 | EIF4G2 | 7430 | 0.039 | 0.34 | NO |
108 | WDR55 | WDR55 | WDR55 | 7535 | 0.037 | 0.34 | NO |
109 | RNF4 | RNF4 | RNF4 | 7587 | 0.036 | 0.34 | NO |
110 | PPP1R2 | PPP1R2 | PPP1R2 | 7595 | 0.036 | 0.34 | NO |
111 | SRSF3 | SRSF3 | SRSF3 | 7753 | 0.033 | 0.33 | NO |
112 | MRPS31 | MRPS31 | MRPS31 | 7754 | 0.033 | 0.34 | NO |
113 | SMAD1 | SMAD1 | SMAD1 | 8121 | 0.026 | 0.32 | NO |
114 | ZZZ3 | ZZZ3 | ZZZ3 | 8127 | 0.026 | 0.32 | NO |
115 | ARCN1 | ARCN1 | ARCN1 | 8130 | 0.026 | 0.32 | NO |
116 | GCSH | GCSH | GCSH | 8142 | 0.026 | 0.32 | NO |
117 | RYK | RYK | RYK | 8224 | 0.024 | 0.32 | NO |
118 | SH3D19 | SH3D19 | SH3D19 | 8287 | 0.023 | 0.32 | NO |
119 | RABGGTB | RABGGTB | RABGGTB | 8315 | 0.022 | 0.32 | NO |
120 | CTTN | CTTN | CTTN | 8324 | 0.022 | 0.32 | NO |
121 | UPP1 | UPP1 | UPP1 | 8361 | 0.021 | 0.32 | NO |
122 | NDUFAF4 | NDUFAF4 | NDUFAF4 | 8374 | 0.021 | 0.32 | NO |
123 | PSMD11 | PSMD11 | PSMD11 | 8423 | 0.02 | 0.32 | NO |
124 | XRCC5 | XRCC5 | XRCC5 | 8430 | 0.02 | 0.32 | NO |
125 | LAPTM4A | LAPTM4A | LAPTM4A | 8523 | 0.018 | 0.32 | NO |
126 | RSL1D1 | RSL1D1 | RSL1D1 | 8525 | 0.018 | 0.32 | NO |
127 | SUCLG2 | SUCLG2 | SUCLG2 | 8689 | 0.015 | 0.31 | NO |
128 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 8743 | 0.014 | 0.31 | NO |
129 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 8760 | 0.014 | 0.31 | NO |
130 | LRRC58 | LRRC58 | LRRC58 | 8850 | 0.013 | 0.3 | NO |
131 | CDKN1A | CDKN1A | CDKN1A | 8903 | 0.012 | 0.3 | NO |
132 | YWHAB | YWHAB | YWHAB | 8939 | 0.011 | 0.3 | NO |
133 | TJP1 | TJP1 | TJP1 | 9093 | 0.0082 | 0.29 | NO |
134 | UBE2D2 | UBE2D2 | UBE2D2 | 9210 | 0.0061 | 0.28 | NO |
135 | ZNF639 | ZNF639 | ZNF639 | 9225 | 0.0058 | 0.28 | NO |
136 | NOP56 | NOP56 | NOP56 | 9268 | 0.005 | 0.28 | NO |
137 | GARS | GARS | GARS | 9290 | 0.0046 | 0.28 | NO |
138 | PPP2R1B | PPP2R1B | PPP2R1B | 9336 | 0.0037 | 0.28 | NO |
139 | YWHAH | YWHAH | YWHAH | 9427 | 0.0023 | 0.27 | NO |
140 | MRPL34 | MRPL34 | MRPL34 | 9483 | 0.0013 | 0.27 | NO |
141 | CCND1 | CCND1 | CCND1 | 9518 | 0.00061 | 0.27 | NO |
142 | PDCD2 | PDCD2 | PDCD2 | 9551 | 0.000087 | 0.27 | NO |
143 | DTYMK | DTYMK | DTYMK | 9611 | -0.00078 | 0.26 | NO |
144 | ERCC5 | ERCC5 | ERCC5 | 9651 | -0.0014 | 0.26 | NO |
145 | GHR | GHR | GHR | 9660 | -0.0016 | 0.26 | NO |
146 | TARS2 | TARS2 | TARS2 | 9695 | -0.0023 | 0.26 | NO |
147 | DNAJB6 | DNAJB6 | DNAJB6 | 9796 | -0.004 | 0.26 | NO |
148 | MRPS10 | MRPS10 | MRPS10 | 9837 | -0.0045 | 0.25 | NO |
149 | GLO1 | GLO1 | GLO1 | 9864 | -0.0048 | 0.25 | NO |
150 | PAFAH2 | PAFAH2 | PAFAH2 | 9977 | -0.0065 | 0.25 | NO |
151 | PEX7 | PEX7 | PEX7 | 10138 | -0.0096 | 0.24 | NO |
152 | USP10 | USP10 | USP10 | 10202 | -0.01 | 0.24 | NO |
153 | SMAD2 | SMAD2 | SMAD2 | 10230 | -0.011 | 0.23 | NO |
154 | GSTA4 | GSTA4 | GSTA4 | 10561 | -0.016 | 0.22 | NO |
155 | CBR3 | CBR3 | CBR3 | 10692 | -0.018 | 0.21 | NO |
156 | COPS7A | COPS7A | COPS7A | 10718 | -0.018 | 0.21 | NO |
157 | MRPL17 | MRPL17 | MRPL17 | 10767 | -0.019 | 0.21 | NO |
158 | RCN1 | RCN1 | RCN1 | 10927 | -0.022 | 0.2 | NO |
159 | LAS1L | LAS1L | LAS1L | 10990 | -0.023 | 0.2 | NO |
160 | KCNAB3 | KCNAB3 | KCNAB3 | 11054 | -0.024 | 0.2 | NO |
161 | MRPL3 | MRPL3 | MRPL3 | 11312 | -0.027 | 0.19 | NO |
162 | MRPL45 | MRPL45 | MRPL45 | 11707 | -0.033 | 0.17 | NO |
163 | TMEM183A | TMEM183A | TMEM183A | 11809 | -0.035 | 0.16 | NO |
164 | PIGX | PIGX | PIGX | 11880 | -0.036 | 0.16 | NO |
165 | RPP14 | RPP14 | RPP14 | 12065 | -0.038 | 0.15 | NO |
166 | CAD | CAD | CAD | 12082 | -0.039 | 0.16 | NO |
167 | MPDU1 | MPDU1 | MPDU1 | 12194 | -0.04 | 0.15 | NO |
168 | GNB1 | GNB1 | GNB1 | 12218 | -0.04 | 0.15 | NO |
169 | DCTPP1 | DCTPP1 | DCTPP1 | 12234 | -0.041 | 0.16 | NO |
170 | CIRH1A | CIRH1A | CIRH1A | 12353 | -0.042 | 0.15 | NO |
171 | PRPSAP1 | PRPSAP1 | PRPSAP1 | 12483 | -0.044 | 0.15 | NO |
172 | DPH5 | DPH5 | DPH5 | 12740 | -0.048 | 0.14 | NO |
173 | TGIF2 | TGIF2 | TGIF2 | 13071 | -0.053 | 0.12 | NO |
174 | SNX12 | SNX12 | SNX12 | 13144 | -0.054 | 0.12 | NO |
175 | FKBP9 | FKBP9 | FKBP9 | 13242 | -0.056 | 0.12 | NO |
176 | INTS5 | INTS5 | INTS5 | 13267 | -0.056 | 0.12 | NO |
177 | MRPS2 | MRPS2 | MRPS2 | 13360 | -0.058 | 0.12 | NO |
178 | RCL1 | RCL1 | RCL1 | 13457 | -0.059 | 0.12 | NO |
179 | SNRPC | SNRPC | SNRPC | 13468 | -0.059 | 0.12 | NO |
180 | MDFI | MDFI | MDFI | 13566 | -0.061 | 0.12 | NO |
181 | C12orf45 | C12orf45 | C12orf45 | 13581 | -0.061 | 0.13 | NO |
182 | LSG1 | LSG1 | LSG1 | 13627 | -0.062 | 0.13 | NO |
183 | GCAT | GCAT | GCAT | 14321 | -0.074 | 0.094 | NO |
184 | TRIP6 | TRIP6 | TRIP6 | 14349 | -0.075 | 0.098 | NO |
185 | CRTAP | CRTAP | CRTAP | 14359 | -0.075 | 0.1 | NO |
186 | BYSL | BYSL | BYSL | 14363 | -0.075 | 0.11 | NO |
187 | RPUSD4 | RPUSD4 | RPUSD4 | 14537 | -0.078 | 0.1 | NO |
188 | GRWD1 | GRWD1 | GRWD1 | 14625 | -0.079 | 0.1 | NO |
189 | UMPS | UMPS | UMPS | 14668 | -0.08 | 0.11 | NO |
190 | GFER | GFER | GFER | 14749 | -0.082 | 0.11 | NO |
191 | PRPF6 | PRPF6 | PRPF6 | 15181 | -0.09 | 0.09 | NO |
192 | RPL22 | RPL22 | RPL22 | 15418 | -0.096 | 0.084 | NO |
193 | ZMAT3 | ZMAT3 | ZMAT3 | 15575 | -0.1 | 0.082 | NO |
194 | CPXM1 | CPXM1 | CPXM1 | 15589 | -0.1 | 0.088 | NO |
195 | TEAD2 | TEAD2 | TEAD2 | 16013 | -0.11 | 0.072 | NO |
196 | ZNF213 | ZNF213 | ZNF213 | 16034 | -0.11 | 0.079 | NO |
197 | LSM2 | LSM2 | LSM2 | 16053 | -0.11 | 0.086 | NO |
198 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 16220 | -0.12 | 0.085 | NO |
199 | JAGN1 | JAGN1 | JAGN1 | 16573 | -0.14 | 0.075 | NO |
200 | KANK3 | KANK3 | KANK3 | 16623 | -0.14 | 0.082 | NO |
Figure S13. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: ENK UV RESPONSE KERATINOCYTE DN.

Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: ENK UV RESPONSE KERATINOCYTE DN, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S8. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SLCO5A1 | SLCO5A1 | SLCO5A1 | 102 | 0.56 | 0.021 | YES |
2 | CDH17 | CDH17 | CDH17 | 160 | 0.51 | 0.042 | YES |
3 | PI15 | PI15 | PI15 | 210 | 0.49 | 0.062 | YES |
4 | SLC26A7 | SLC26A7 | SLC26A7 | 254 | 0.47 | 0.082 | YES |
5 | MMP16 | MMP16 | MMP16 | 274 | 0.45 | 0.1 | YES |
6 | PMP2 | PMP2 | PMP2 | 282 | 0.45 | 0.12 | YES |
7 | CCNE2 | CCNE2 | CCNE2 | 303 | 0.44 | 0.14 | YES |
8 | TTPA | TTPA | TTPA | 413 | 0.41 | 0.16 | YES |
9 | OSR2 | OSR2 | OSR2 | 455 | 0.4 | 0.17 | YES |
10 | CLVS1 | CLVS1 | CLVS1 | 521 | 0.38 | 0.19 | YES |
11 | CALB1 | CALB1 | CALB1 | 541 | 0.38 | 0.2 | YES |
12 | JPH1 | JPH1 | JPH1 | 579 | 0.37 | 0.22 | YES |
13 | RIMS2 | RIMS2 | RIMS2 | 600 | 0.36 | 0.24 | YES |
14 | FBXO43 | FBXO43 | FBXO43 | 614 | 0.36 | 0.25 | YES |
15 | IL7 | IL7 | IL7 | 654 | 0.35 | 0.27 | YES |
16 | SDC2 | SDC2 | SDC2 | 715 | 0.34 | 0.28 | YES |
17 | KCNB2 | KCNB2 | KCNB2 | 731 | 0.34 | 0.29 | YES |
18 | XKR9 | XKR9 | XKR9 | 824 | 0.32 | 0.3 | YES |
19 | C8orf37 | C8orf37 | C8orf37 | 863 | 0.31 | 0.32 | YES |
20 | TPD52 | TPD52 | TPD52 | 889 | 0.31 | 0.33 | YES |
21 | RGS22 | RGS22 | RGS22 | 957 | 0.3 | 0.34 | YES |
22 | GEM | GEM | GEM | 972 | 0.3 | 0.35 | YES |
23 | RAD54B | RAD54B | RAD54B | 982 | 0.3 | 0.37 | YES |
24 | OTUD6B | OTUD6B | OTUD6B | 1200 | 0.27 | 0.37 | YES |
25 | PRDM14 | PRDM14 | PRDM14 | 1212 | 0.27 | 0.38 | YES |
26 | SLC10A5 | SLC10A5 | SLC10A5 | 1358 | 0.25 | 0.38 | YES |
27 | SPAG1 | SPAG1 | SPAG1 | 1427 | 0.24 | 0.39 | YES |
28 | IMPA1 | IMPA1 | IMPA1 | 1502 | 0.24 | 0.4 | YES |
29 | PKIA | PKIA | PKIA | 1547 | 0.23 | 0.41 | YES |
30 | SNX31 | SNX31 | SNX31 | 1570 | 0.23 | 0.42 | YES |
31 | TMEM67 | TMEM67 | TMEM67 | 1698 | 0.22 | 0.42 | YES |
32 | DPY19L4 | DPY19L4 | DPY19L4 | 1808 | 0.21 | 0.42 | YES |
33 | CYP7A1 | CYP7A1 | CYP7A1 | 1812 | 0.21 | 0.43 | YES |
34 | ZFHX4 | ZFHX4 | ZFHX4 | 1988 | 0.2 | 0.43 | YES |
35 | UBE2W | UBE2W | UBE2W | 2037 | 0.2 | 0.44 | YES |
36 | MTDH | MTDH | MTDH | 2079 | 0.19 | 0.45 | YES |
37 | SNX16 | SNX16 | SNX16 | 2109 | 0.19 | 0.46 | YES |
38 | TERF1 | TERF1 | TERF1 | 2124 | 0.19 | 0.46 | YES |
39 | LACTB2 | LACTB2 | LACTB2 | 2156 | 0.19 | 0.47 | YES |
40 | TMEM64 | TMEM64 | TMEM64 | 2162 | 0.19 | 0.48 | YES |
41 | YTHDF3 | YTHDF3 | YTHDF3 | 2193 | 0.19 | 0.49 | YES |
42 | PLEKHF2 | PLEKHF2 | PLEKHF2 | 2258 | 0.18 | 0.49 | YES |
43 | LY96 | LY96 | LY96 | 2350 | 0.18 | 0.49 | YES |
44 | NBN | NBN | NBN | 2352 | 0.18 | 0.5 | YES |
45 | UBXN2B | UBXN2B | UBXN2B | 2368 | 0.18 | 0.51 | YES |
46 | RNF19A | RNF19A | RNF19A | 2505 | 0.17 | 0.51 | YES |
47 | NIPAL2 | NIPAL2 | NIPAL2 | 2593 | 0.16 | 0.51 | YES |
48 | ASPH | ASPH | ASPH | 2672 | 0.16 | 0.52 | YES |
49 | FABP5 | FABP5 | FABP5 | 2692 | 0.16 | 0.52 | YES |
50 | VPS13B | VPS13B | VPS13B | 2699 | 0.16 | 0.53 | YES |
51 | TMEM70 | TMEM70 | TMEM70 | 2708 | 0.16 | 0.54 | YES |
52 | STAU2 | STAU2 | STAU2 | 2741 | 0.16 | 0.54 | YES |
53 | INTS8 | INTS8 | INTS8 | 2750 | 0.16 | 0.55 | YES |
54 | HRSP12 | HRSP12 | HRSP12 | 2830 | 0.15 | 0.55 | YES |
55 | FAM92A1 | FAM92A1 | FAM92A1 | 2878 | 0.15 | 0.56 | YES |
56 | STK3 | STK3 | STK3 | 2928 | 0.15 | 0.56 | YES |
57 | MRPS28 | MRPS28 | MRPS28 | 3047 | 0.15 | 0.56 | YES |
58 | TRAM1 | TRAM1 | TRAM1 | 3096 | 0.14 | 0.57 | YES |
59 | TMEM55A | TMEM55A | TMEM55A | 3150 | 0.14 | 0.57 | YES |
60 | AZIN1 | AZIN1 | AZIN1 | 3165 | 0.14 | 0.57 | YES |
61 | PDP1 | PDP1 | PDP1 | 3174 | 0.14 | 0.58 | YES |
62 | RUNX1T1 | RUNX1T1 | RUNX1T1 | 3248 | 0.14 | 0.58 | YES |
63 | SLC25A32 | SLC25A32 | SLC25A32 | 3335 | 0.14 | 0.59 | YES |
64 | DCAF13 | DCAF13 | DCAF13 | 3338 | 0.14 | 0.59 | YES |
65 | CHD7 | CHD7 | CHD7 | 3344 | 0.14 | 0.6 | YES |
66 | NCOA2 | NCOA2 | NCOA2 | 3370 | 0.13 | 0.6 | YES |
67 | BAALC | BAALC | BAALC | 3383 | 0.13 | 0.61 | YES |
68 | OSGIN2 | OSGIN2 | OSGIN2 | 3417 | 0.13 | 0.61 | YES |
69 | NSMAF | NSMAF | NSMAF | 3524 | 0.13 | 0.61 | YES |
70 | ZNF704 | ZNF704 | ZNF704 | 3586 | 0.13 | 0.62 | YES |
71 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 3627 | 0.13 | 0.62 | YES |
72 | TSPYL5 | TSPYL5 | TSPYL5 | 3662 | 0.12 | 0.62 | YES |
73 | RAB2A | RAB2A | RAB2A | 3691 | 0.12 | 0.63 | YES |
74 | KIAA1429 | KIAA1429 | KIAA1429 | 3755 | 0.12 | 0.63 | YES |
75 | TP53INP1 | TP53INP1 | TP53INP1 | 3823 | 0.12 | 0.63 | YES |
76 | PAG1 | PAG1 | PAG1 | 3895 | 0.12 | 0.63 | YES |
77 | TCEB1 | TCEB1 | TCEB1 | 4142 | 0.11 | 0.62 | YES |
78 | KCNS2 | KCNS2 | KCNS2 | 4165 | 0.11 | 0.63 | YES |
79 | ZBTB10 | ZBTB10 | ZBTB10 | 4233 | 0.11 | 0.63 | YES |
80 | RDH10 | RDH10 | RDH10 | 4339 | 0.1 | 0.63 | YES |
81 | RBM12B | RBM12B | RBM12B | 4347 | 0.1 | 0.63 | YES |
82 | GDF6 | GDF6 | GDF6 | 4359 | 0.1 | 0.64 | YES |
83 | GGH | GGH | GGH | 4402 | 0.1 | 0.64 | YES |
84 | GDAP1 | GDAP1 | GDAP1 | 4486 | 0.1 | 0.64 | YES |
85 | PEX2 | PEX2 | PEX2 | 4857 | 0.093 | 0.62 | NO |
86 | POLR2K | POLR2K | POLR2K | 4970 | 0.09 | 0.62 | NO |
87 | HEY1 | HEY1 | HEY1 | 4987 | 0.09 | 0.63 | NO |
88 | ZFAND1 | ZFAND1 | ZFAND1 | 5040 | 0.088 | 0.63 | NO |
89 | GRHL2 | GRHL2 | GRHL2 | 5272 | 0.083 | 0.62 | NO |
90 | YWHAZ | YWHAZ | YWHAZ | 5526 | 0.077 | 0.61 | NO |
91 | ANKRD46 | ANKRD46 | ANKRD46 | 5648 | 0.074 | 0.6 | NO |
92 | POP1 | POP1 | POP1 | 5675 | 0.074 | 0.61 | NO |
93 | DECR1 | DECR1 | DECR1 | 5741 | 0.072 | 0.61 | NO |
94 | SDCBP | SDCBP | SDCBP | 5940 | 0.068 | 0.6 | NO |
95 | COX6C | COX6C | COX6C | 6523 | 0.056 | 0.57 | NO |
96 | FABP4 | FABP4 | FABP4 | 6707 | 0.053 | 0.56 | NO |
97 | RALYL | RALYL | RALYL | 6727 | 0.052 | 0.56 | NO |
98 | LAPTM4B | LAPTM4B | LAPTM4B | 6778 | 0.052 | 0.56 | NO |
99 | NECAB1 | NECAB1 | NECAB1 | 6951 | 0.048 | 0.56 | NO |
100 | FZD6 | FZD6 | FZD6 | 7155 | 0.044 | 0.55 | NO |
101 | PABPC1 | PABPC1 | PABPC1 | 7365 | 0.04 | 0.54 | NO |
102 | ZNF706 | ZNF706 | ZNF706 | 7467 | 0.038 | 0.53 | NO |
103 | UQCRB | UQCRB | UQCRB | 8105 | 0.026 | 0.5 | NO |
104 | ESRP1 | ESRP1 | ESRP1 | 8185 | 0.025 | 0.5 | NO |
105 | RIPK2 | RIPK2 | RIPK2 | 8210 | 0.024 | 0.5 | NO |
106 | NKAIN3 | NKAIN3 | NKAIN3 | 8243 | 0.024 | 0.49 | NO |
107 | RPL7 | RPL7 | RPL7 | 8666 | 0.016 | 0.47 | NO |
108 | KLF10 | KLF10 | KLF10 | 8955 | 0.011 | 0.46 | NO |
109 | PTDSS1 | PTDSS1 | PTDSS1 | 9099 | 0.0081 | 0.45 | NO |
110 | CRISPLD1 | CRISPLD1 | CRISPLD1 | 9102 | 0.008 | 0.45 | NO |
111 | STMN2 | STMN2 | STMN2 | 9121 | 0.0078 | 0.45 | NO |
112 | MATN2 | MATN2 | MATN2 | 10978 | -0.022 | 0.35 | NO |
113 | RPL30 | RPL30 | RPL30 | 11102 | -0.024 | 0.34 | NO |
114 | HNF4G | HNF4G | HNF4G | 11135 | -0.025 | 0.34 | NO |
115 | CTHRC1 | CTHRC1 | CTHRC1 | 12525 | -0.045 | 0.26 | NO |
116 | SULF1 | SULF1 | SULF1 | 14074 | -0.07 | 0.18 | NO |
117 | EYA1 | EYA1 | EYA1 | 15373 | -0.095 | 0.11 | NO |
118 | TRPA1 | TRPA1 | TRPA1 | 15519 | -0.098 | 0.11 | NO |
119 | CHMP4C | CHMP4C | CHMP4C | 17036 | -0.17 | 0.034 | NO |
120 | MSC | MSC | MSC | 18065 | -0.52 | 0.0011 | NO |
Figure S15. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: SEIDEN ONCOGENESIS BY MET.

Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: SEIDEN ONCOGENESIS BY MET, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S9. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | IGF2BP3 | IGF2BP3 | IGF2BP3 | 109 | 0.56 | 0.0092 | YES |
2 | DKK1 | DKK1 | DKK1 | 474 | 0.4 | -0.00056 | YES |
3 | PTHLH | PTHLH | PTHLH | 505 | 0.39 | 0.0084 | YES |
4 | BIRC3 | BIRC3 | BIRC3 | 956 | 0.3 | -0.0088 | YES |
5 | HSPA4L | HSPA4L | HSPA4L | 1167 | 0.27 | -0.013 | YES |
6 | GOLGA8A | GOLGA8A | GOLGA8A | 1366 | 0.25 | -0.018 | YES |
7 | NRG1 | NRG1 | NRG1 | 1417 | 0.25 | -0.014 | YES |
8 | PAWR | PAWR | PAWR | 1464 | 0.24 | -0.0094 | YES |
9 | IMPA1 | IMPA1 | IMPA1 | 1502 | 0.24 | -0.0049 | YES |
10 | USP6 | USP6 | USP6 | 1503 | 0.24 | 0.0016 | YES |
11 | FLRT2 | FLRT2 | FLRT2 | 1522 | 0.24 | 0.0071 | YES |
12 | PYROXD1 | PYROXD1 | PYROXD1 | 1706 | 0.22 | 0.0028 | YES |
13 | CD58 | CD58 | CD58 | 1809 | 0.21 | 0.0028 | YES |
14 | ARFGEF1 | ARFGEF1 | ARFGEF1 | 1816 | 0.21 | 0.0083 | YES |
15 | TOP2A | TOP2A | TOP2A | 1842 | 0.21 | 0.013 | YES |
16 | FKBP5 | FKBP5 | FKBP5 | 1849 | 0.21 | 0.018 | YES |
17 | PTPRZ1 | PTPRZ1 | PTPRZ1 | 1885 | 0.2 | 0.022 | YES |
18 | SQLE | SQLE | SQLE | 1902 | 0.2 | 0.026 | YES |
19 | VSNL1 | VSNL1 | VSNL1 | 1933 | 0.2 | 0.03 | YES |
20 | KTN1 | KTN1 | KTN1 | 1957 | 0.2 | 0.034 | YES |
21 | CYP51A1 | CYP51A1 | CYP51A1 | 2035 | 0.2 | 0.036 | YES |
22 | FOS | FOS | FOS | 2050 | 0.19 | 0.04 | YES |
23 | SRSF11 | SRSF11 | SRSF11 | 2099 | 0.19 | 0.043 | YES |
24 | TERF1 | TERF1 | TERF1 | 2124 | 0.19 | 0.046 | YES |
25 | FEZ1 | FEZ1 | FEZ1 | 2235 | 0.18 | 0.045 | YES |
26 | RDX | RDX | RDX | 2306 | 0.18 | 0.046 | YES |
27 | CTAGE5 | CTAGE5 | CTAGE5 | 2347 | 0.18 | 0.049 | YES |
28 | NBN | NBN | NBN | 2352 | 0.18 | 0.054 | YES |
29 | RBBP8 | RBBP8 | RBBP8 | 2361 | 0.18 | 0.058 | YES |
30 | STRN3 | STRN3 | STRN3 | 2365 | 0.18 | 0.063 | YES |
31 | HOXA9 | HOXA9 | HOXA9 | 2379 | 0.18 | 0.067 | YES |
32 | ACADSB | ACADSB | ACADSB | 2402 | 0.17 | 0.07 | YES |
33 | MAP3K5 | MAP3K5 | MAP3K5 | 2429 | 0.17 | 0.074 | YES |
34 | RGS2 | RGS2 | RGS2 | 2470 | 0.17 | 0.076 | YES |
35 | MAN2A1 | MAN2A1 | MAN2A1 | 2524 | 0.17 | 0.078 | YES |
36 | TSNAX | TSNAX | TSNAX | 2609 | 0.16 | 0.078 | YES |
37 | LUC7L3 | LUC7L3 | LUC7L3 | 2662 | 0.16 | 0.079 | YES |
38 | UBR5 | UBR5 | UBR5 | 2770 | 0.16 | 0.077 | YES |
39 | FPGT | FPGT | FPGT | 2784 | 0.16 | 0.081 | YES |
40 | PRKDC | PRKDC | PRKDC | 2824 | 0.15 | 0.083 | YES |
41 | SCAF11 | SCAF11 | SCAF11 | 2839 | 0.15 | 0.086 | YES |
42 | TROVE2 | TROVE2 | TROVE2 | 2882 | 0.15 | 0.088 | YES |
43 | STK3 | STK3 | STK3 | 2928 | 0.15 | 0.09 | YES |
44 | AUH | AUH | AUH | 2941 | 0.15 | 0.093 | YES |
45 | IFI44L | IFI44L | IFI44L | 2969 | 0.15 | 0.096 | YES |
46 | XPO1 | XPO1 | XPO1 | 3018 | 0.15 | 0.097 | YES |
47 | CLIP1 | CLIP1 | CLIP1 | 3039 | 0.15 | 0.1 | YES |
48 | CD2AP | CD2AP | CD2AP | 3138 | 0.14 | 0.098 | YES |
49 | AZIN1 | AZIN1 | AZIN1 | 3165 | 0.14 | 0.1 | YES |
50 | TCERG1 | TCERG1 | TCERG1 | 3192 | 0.14 | 0.1 | YES |
51 | ZNF638 | ZNF638 | ZNF638 | 3201 | 0.14 | 0.11 | YES |
52 | TPR | TPR | TPR | 3257 | 0.14 | 0.11 | YES |
53 | MAD2L1 | MAD2L1 | MAD2L1 | 3286 | 0.14 | 0.11 | YES |
54 | PPIG | PPIG | PPIG | 3313 | 0.14 | 0.11 | YES |
55 | ME2 | ME2 | ME2 | 3341 | 0.14 | 0.11 | YES |
56 | OGT | OGT | OGT | 3373 | 0.13 | 0.12 | YES |
57 | STXBP3 | STXBP3 | STXBP3 | 3404 | 0.13 | 0.12 | YES |
58 | TRIM23 | TRIM23 | TRIM23 | 3408 | 0.13 | 0.12 | YES |
59 | MARCH7 | MARCH7 | MARCH7 | 3445 | 0.13 | 0.12 | YES |
60 | ZMYM2 | ZMYM2 | ZMYM2 | 3468 | 0.13 | 0.12 | YES |
61 | CDC7 | CDC7 | CDC7 | 3471 | 0.13 | 0.13 | YES |
62 | RP2 | RP2 | RP2 | 3491 | 0.13 | 0.13 | YES |
63 | KLF9 | KLF9 | KLF9 | 3545 | 0.13 | 0.13 | YES |
64 | CD46 | CD46 | CD46 | 3613 | 0.13 | 0.13 | YES |
65 | ZFR | ZFR | ZFR | 3615 | 0.13 | 0.14 | YES |
66 | AKAP10 | AKAP10 | AKAP10 | 3647 | 0.12 | 0.14 | YES |
67 | PRPF4B | PRPF4B | PRPF4B | 3658 | 0.12 | 0.14 | YES |
68 | CEBPD | CEBPD | CEBPD | 3659 | 0.12 | 0.14 | YES |
69 | BIRC2 | BIRC2 | BIRC2 | 3676 | 0.12 | 0.14 | YES |
70 | KRAS | KRAS | KRAS | 3701 | 0.12 | 0.15 | YES |
71 | CPNE3 | CPNE3 | CPNE3 | 3702 | 0.12 | 0.15 | YES |
72 | ATRX | ATRX | ATRX | 3705 | 0.12 | 0.15 | YES |
73 | ENOSF1 | ENOSF1 | ENOSF1 | 3708 | 0.12 | 0.16 | YES |
74 | SSB | SSB | SSB | 3711 | 0.12 | 0.16 | YES |
75 | IFIT1 | IFIT1 | IFIT1 | 3751 | 0.12 | 0.16 | YES |
76 | IFI44 | IFI44 | IFI44 | 3825 | 0.12 | 0.16 | YES |
77 | VAMP4 | VAMP4 | VAMP4 | 3844 | 0.12 | 0.16 | YES |
78 | ACTR3 | ACTR3 | ACTR3 | 3865 | 0.12 | 0.16 | YES |
79 | GBAS | GBAS | GBAS | 3871 | 0.12 | 0.17 | YES |
80 | ITSN2 | ITSN2 | ITSN2 | 3893 | 0.12 | 0.17 | YES |
81 | EBAG9 | EBAG9 | EBAG9 | 3896 | 0.12 | 0.17 | YES |
82 | TOPORS | TOPORS | TOPORS | 3922 | 0.12 | 0.18 | YES |
83 | SCFD1 | SCFD1 | SCFD1 | 3966 | 0.12 | 0.18 | YES |
84 | ACSL3 | ACSL3 | ACSL3 | 3971 | 0.12 | 0.18 | YES |
85 | DYRK2 | DYRK2 | DYRK2 | 3990 | 0.12 | 0.18 | YES |
86 | CREB1 | CREB1 | CREB1 | 3994 | 0.12 | 0.18 | YES |
87 | UGDH | UGDH | UGDH | 4116 | 0.11 | 0.18 | YES |
88 | CTNNAL1 | CTNNAL1 | CTNNAL1 | 4119 | 0.11 | 0.18 | YES |
89 | FAT2 | FAT2 | FAT2 | 4128 | 0.11 | 0.19 | YES |
90 | EID1 | EID1 | EID1 | 4163 | 0.11 | 0.19 | YES |
91 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 4188 | 0.11 | 0.19 | YES |
92 | SEC23A | SEC23A | SEC23A | 4272 | 0.11 | 0.19 | YES |
93 | PCGF3 | PCGF3 | PCGF3 | 4284 | 0.11 | 0.19 | YES |
94 | NDUFS1 | NDUFS1 | NDUFS1 | 4286 | 0.11 | 0.19 | YES |
95 | ABCE1 | ABCE1 | ABCE1 | 4293 | 0.11 | 0.2 | YES |
96 | SLC11A2 | SLC11A2 | SLC11A2 | 4306 | 0.11 | 0.2 | YES |
97 | AKAP11 | AKAP11 | AKAP11 | 4322 | 0.11 | 0.2 | YES |
98 | TARBP1 | TARBP1 | TARBP1 | 4349 | 0.1 | 0.2 | YES |
99 | RPGR | RPGR | RPGR | 4408 | 0.1 | 0.2 | YES |
100 | YAF2 | YAF2 | YAF2 | 4421 | 0.1 | 0.2 | YES |
101 | PCF11 | PCF11 | PCF11 | 4426 | 0.1 | 0.2 | YES |
102 | WWTR1 | WWTR1 | WWTR1 | 4434 | 0.1 | 0.21 | YES |
103 | EIF3J | EIF3J | EIF3J | 4447 | 0.1 | 0.21 | YES |
104 | TGDS | TGDS | TGDS | 4465 | 0.1 | 0.21 | YES |
105 | COPB1 | COPB1 | COPB1 | 4520 | 0.1 | 0.21 | YES |
106 | MARK3 | MARK3 | MARK3 | 4539 | 0.1 | 0.21 | YES |
107 | VRK1 | VRK1 | VRK1 | 4593 | 0.099 | 0.21 | YES |
108 | KIF2A | KIF2A | KIF2A | 4610 | 0.098 | 0.21 | YES |
109 | AGL | AGL | AGL | 4622 | 0.098 | 0.22 | YES |
110 | MED7 | MED7 | MED7 | 4626 | 0.098 | 0.22 | YES |
111 | MALT1 | MALT1 | MALT1 | 4634 | 0.098 | 0.22 | YES |
112 | MYO5A | MYO5A | MYO5A | 4635 | 0.098 | 0.22 | YES |
113 | USP1 | USP1 | USP1 | 4637 | 0.098 | 0.23 | YES |
114 | UBA2 | UBA2 | UBA2 | 4641 | 0.098 | 0.23 | YES |
115 | DEK | DEK | DEK | 4666 | 0.097 | 0.23 | YES |
116 | MTF2 | MTF2 | MTF2 | 4682 | 0.097 | 0.23 | YES |
117 | SEC24B | SEC24B | SEC24B | 4693 | 0.096 | 0.23 | YES |
118 | PURA | PURA | PURA | 4712 | 0.096 | 0.24 | YES |
119 | PKD2 | PKD2 | PKD2 | 4757 | 0.095 | 0.24 | YES |
120 | COPS2 | COPS2 | COPS2 | 4783 | 0.095 | 0.24 | YES |
121 | CAP2 | CAP2 | CAP2 | 4785 | 0.095 | 0.24 | YES |
122 | RASA1 | RASA1 | RASA1 | 4867 | 0.093 | 0.24 | YES |
123 | USP14 | USP14 | USP14 | 4892 | 0.092 | 0.24 | YES |
124 | CBX3 | CBX3 | CBX3 | 4915 | 0.091 | 0.24 | YES |
125 | ROCK2 | ROCK2 | ROCK2 | 4936 | 0.091 | 0.24 | YES |
126 | PEX3 | PEX3 | PEX3 | 4964 | 0.09 | 0.24 | YES |
127 | CETN3 | CETN3 | CETN3 | 4966 | 0.09 | 0.24 | YES |
128 | LBR | LBR | LBR | 4974 | 0.09 | 0.25 | YES |
129 | SNTB2 | SNTB2 | SNTB2 | 4976 | 0.09 | 0.25 | YES |
130 | ACADM | ACADM | ACADM | 4985 | 0.09 | 0.25 | YES |
131 | ADCY7 | ADCY7 | ADCY7 | 4994 | 0.09 | 0.25 | YES |
132 | TMX1 | TMX1 | TMX1 | 5009 | 0.089 | 0.26 | YES |
133 | GMFB | GMFB | GMFB | 5010 | 0.089 | 0.26 | YES |
134 | EPRS | EPRS | EPRS | 5020 | 0.089 | 0.26 | YES |
135 | TYMS | TYMS | TYMS | 5025 | 0.088 | 0.26 | YES |
136 | SLC35A1 | SLC35A1 | SLC35A1 | 5063 | 0.088 | 0.26 | YES |
137 | ZNF148 | ZNF148 | ZNF148 | 5073 | 0.088 | 0.26 | YES |
138 | CDK14 | CDK14 | CDK14 | 5119 | 0.087 | 0.26 | YES |
139 | HES1 | HES1 | HES1 | 5172 | 0.085 | 0.26 | YES |
140 | DHX15 | DHX15 | DHX15 | 5216 | 0.084 | 0.26 | YES |
141 | DLD | DLD | DLD | 5266 | 0.084 | 0.26 | YES |
142 | FAT1 | FAT1 | FAT1 | 5310 | 0.082 | 0.26 | YES |
143 | RANBP2 | RANBP2 | RANBP2 | 5359 | 0.081 | 0.26 | YES |
144 | ACBD3 | ACBD3 | ACBD3 | 5370 | 0.081 | 0.26 | YES |
145 | G3BP2 | G3BP2 | G3BP2 | 5388 | 0.08 | 0.26 | YES |
146 | RRM1 | RRM1 | RRM1 | 5468 | 0.078 | 0.26 | YES |
147 | ZNF146 | ZNF146 | ZNF146 | 5470 | 0.078 | 0.26 | YES |
148 | TCEAL1 | TCEAL1 | TCEAL1 | 5500 | 0.078 | 0.26 | YES |
149 | ZMYND8 | ZMYND8 | ZMYND8 | 5528 | 0.077 | 0.27 | YES |
150 | IPO7 | IPO7 | IPO7 | 5540 | 0.077 | 0.27 | YES |
151 | AGPS | AGPS | AGPS | 5559 | 0.076 | 0.27 | YES |
152 | PPP2R5E | PPP2R5E | PPP2R5E | 5597 | 0.076 | 0.27 | YES |
153 | CUL1 | CUL1 | CUL1 | 5621 | 0.075 | 0.27 | YES |
154 | PAFAH1B1 | PAFAH1B1 | PAFAH1B1 | 5627 | 0.075 | 0.27 | YES |
155 | SMAD4 | SMAD4 | SMAD4 | 5645 | 0.074 | 0.27 | YES |
156 | SCML2 | SCML2 | SCML2 | 5691 | 0.073 | 0.27 | YES |
157 | CDKN1B | CDKN1B | CDKN1B | 5692 | 0.073 | 0.27 | YES |
158 | SERPINE2 | SERPINE2 | SERPINE2 | 5698 | 0.073 | 0.28 | YES |
159 | ACTR2 | ACTR2 | ACTR2 | 5712 | 0.073 | 0.28 | YES |
160 | PCMT1 | PCMT1 | PCMT1 | 5736 | 0.072 | 0.28 | YES |
161 | UPF3A | UPF3A | UPF3A | 5762 | 0.072 | 0.28 | YES |
162 | AASDHPPT | AASDHPPT | AASDHPPT | 5777 | 0.072 | 0.28 | YES |
163 | SORL1 | SORL1 | SORL1 | 5785 | 0.071 | 0.28 | YES |
164 | ZMYND11 | ZMYND11 | ZMYND11 | 5789 | 0.071 | 0.28 | YES |
165 | FMR1 | FMR1 | FMR1 | 5809 | 0.071 | 0.28 | YES |
166 | DDX17 | DDX17 | DDX17 | 5827 | 0.07 | 0.28 | YES |
167 | MSMO1 | MSMO1 | MSMO1 | 5847 | 0.07 | 0.28 | YES |
168 | JAG2 | JAG2 | JAG2 | 5879 | 0.069 | 0.28 | YES |
169 | SLC2A3 | SLC2A3 | SLC2A3 | 5920 | 0.069 | 0.28 | YES |
170 | YME1L1 | YME1L1 | YME1L1 | 5942 | 0.068 | 0.29 | YES |
171 | COG5 | COG5 | COG5 | 5943 | 0.068 | 0.29 | YES |
172 | MDH1 | MDH1 | MDH1 | 5970 | 0.067 | 0.29 | YES |
173 | MCM6 | MCM6 | MCM6 | 6013 | 0.066 | 0.29 | YES |
174 | NPEPPS | NPEPPS | NPEPPS | 6022 | 0.066 | 0.29 | YES |
175 | PSMD5 | PSMD5 | PSMD5 | 6037 | 0.066 | 0.29 | YES |
176 | NAE1 | NAE1 | NAE1 | 6040 | 0.066 | 0.29 | YES |
177 | PFDN4 | PFDN4 | PFDN4 | 6054 | 0.066 | 0.29 | YES |
178 | XPA | XPA | XPA | 6071 | 0.065 | 0.29 | YES |
179 | DUSP5 | DUSP5 | DUSP5 | 6089 | 0.065 | 0.29 | YES |
180 | YES1 | YES1 | YES1 | 6105 | 0.064 | 0.3 | YES |
181 | UBE4A | UBE4A | UBE4A | 6141 | 0.064 | 0.3 | YES |
182 | PAPD7 | PAPD7 | PAPD7 | 6192 | 0.062 | 0.29 | YES |
183 | RB1 | RB1 | RB1 | 6195 | 0.062 | 0.3 | YES |
184 | GNAQ | GNAQ | GNAQ | 6209 | 0.062 | 0.3 | YES |
185 | STX7 | STX7 | STX7 | 6218 | 0.062 | 0.3 | YES |
186 | DLEU1 | DLEU1 | DLEU1 | 6228 | 0.062 | 0.3 | YES |
187 | MCL1 | MCL1 | MCL1 | 6243 | 0.062 | 0.3 | YES |
188 | MBNL1 | MBNL1 | MBNL1 | 6259 | 0.061 | 0.3 | YES |
189 | PCDH7 | PCDH7 | PCDH7 | 6262 | 0.061 | 0.3 | YES |
190 | COL16A1 | COL16A1 | COL16A1 | 6263 | 0.061 | 0.3 | YES |
191 | SLBP | SLBP | SLBP | 6275 | 0.061 | 0.3 | YES |
192 | H2AFV | H2AFV | H2AFV | 6303 | 0.06 | 0.3 | YES |
193 | GOLGA4 | GOLGA4 | GOLGA4 | 6349 | 0.06 | 0.3 | YES |
194 | ACYP1 | ACYP1 | ACYP1 | 6357 | 0.059 | 0.3 | YES |
195 | RGS20 | RGS20 | RGS20 | 6363 | 0.059 | 0.31 | YES |
196 | SP100 | SP100 | SP100 | 6371 | 0.059 | 0.31 | YES |
197 | RBFOX2 | RBFOX2 | RBFOX2 | 6393 | 0.059 | 0.31 | YES |
198 | SDHD | SDHD | SDHD | 6395 | 0.059 | 0.31 | YES |
199 | BPTF | BPTF | BPTF | 6414 | 0.058 | 0.31 | YES |
200 | PUM2 | PUM2 | PUM2 | 6415 | 0.058 | 0.31 | YES |
201 | POLR2B | POLR2B | POLR2B | 6426 | 0.058 | 0.31 | YES |
202 | ATR | ATR | ATR | 6441 | 0.058 | 0.31 | YES |
203 | CLTC | CLTC | CLTC | 6444 | 0.058 | 0.32 | YES |
204 | PAICS | PAICS | PAICS | 6456 | 0.058 | 0.32 | YES |
205 | TRIP13 | TRIP13 | TRIP13 | 6476 | 0.057 | 0.32 | YES |
206 | LYST | LYST | LYST | 6488 | 0.057 | 0.32 | YES |
207 | NCOA3 | NCOA3 | NCOA3 | 6492 | 0.057 | 0.32 | YES |
208 | ARHGEF4 | ARHGEF4 | ARHGEF4 | 6503 | 0.056 | 0.32 | YES |
209 | EPS15 | EPS15 | EPS15 | 6509 | 0.056 | 0.32 | YES |
210 | CPOX | CPOX | CPOX | 6540 | 0.056 | 0.32 | YES |
211 | GNE | GNE | GNE | 6549 | 0.055 | 0.32 | YES |
212 | HIST1H4C | HIST1H4C | HIST1H4C | 6567 | 0.055 | 0.32 | YES |
213 | CDC123 | CDC123 | CDC123 | 6569 | 0.055 | 0.32 | YES |
214 | CRIM1 | CRIM1 | CRIM1 | 6579 | 0.055 | 0.33 | YES |
215 | C1D | C1D | C1D | 6612 | 0.054 | 0.32 | YES |
216 | CDH13 | CDH13 | CDH13 | 6706 | 0.053 | 0.32 | YES |
217 | AFF1 | AFF1 | AFF1 | 6725 | 0.052 | 0.32 | YES |
218 | BRD8 | BRD8 | BRD8 | 6737 | 0.052 | 0.32 | YES |
219 | RABGAP1 | RABGAP1 | RABGAP1 | 6781 | 0.052 | 0.32 | YES |
220 | RAPGEF5 | RAPGEF5 | RAPGEF5 | 6788 | 0.051 | 0.32 | YES |
221 | MAPKAPK5 | MAPKAPK5 | MAPKAPK5 | 6800 | 0.051 | 0.32 | YES |
222 | SIAH1 | SIAH1 | SIAH1 | 6818 | 0.051 | 0.32 | YES |
223 | DUT | DUT | DUT | 6824 | 0.051 | 0.32 | YES |
224 | SRSF1 | SRSF1 | SRSF1 | 6830 | 0.051 | 0.33 | YES |
225 | HSPD1 | HSPD1 | HSPD1 | 6929 | 0.049 | 0.32 | YES |
226 | TLK2 | TLK2 | TLK2 | 6958 | 0.048 | 0.32 | YES |
227 | TACC1 | TACC1 | TACC1 | 6963 | 0.048 | 0.32 | YES |
228 | SFRP1 | SFRP1 | SFRP1 | 7001 | 0.047 | 0.32 | YES |
229 | BET1 | BET1 | BET1 | 7003 | 0.047 | 0.32 | YES |
230 | SUGP2 | SUGP2 | SUGP2 | 7030 | 0.047 | 0.32 | YES |
231 | WNK1 | WNK1 | WNK1 | 7040 | 0.046 | 0.32 | YES |
232 | ATP2A2 | ATP2A2 | ATP2A2 | 7055 | 0.046 | 0.32 | YES |
233 | ANXA7 | ANXA7 | ANXA7 | 7084 | 0.046 | 0.32 | YES |
234 | CDC23 | CDC23 | CDC23 | 7097 | 0.045 | 0.32 | YES |
235 | HPS5 | HPS5 | HPS5 | 7108 | 0.045 | 0.32 | YES |
236 | MACF1 | MACF1 | MACF1 | 7109 | 0.045 | 0.33 | YES |
237 | PICALM | PICALM | PICALM | 7150 | 0.044 | 0.32 | YES |
238 | FZD6 | FZD6 | FZD6 | 7155 | 0.044 | 0.33 | YES |
239 | ATXN2 | ATXN2 | ATXN2 | 7181 | 0.044 | 0.33 | YES |
240 | MBD2 | MBD2 | MBD2 | 7194 | 0.044 | 0.33 | YES |
241 | DNMT1 | DNMT1 | DNMT1 | 7218 | 0.043 | 0.33 | YES |
242 | SYPL1 | SYPL1 | SYPL1 | 7238 | 0.043 | 0.33 | YES |
243 | LAMP3 | LAMP3 | LAMP3 | 7248 | 0.043 | 0.33 | YES |
244 | SNX7 | SNX7 | SNX7 | 7270 | 0.042 | 0.33 | YES |
245 | CSE1L | CSE1L | CSE1L | 7287 | 0.042 | 0.33 | YES |
246 | CNOT4 | CNOT4 | CNOT4 | 7303 | 0.041 | 0.33 | YES |
247 | CNOT2 | CNOT2 | CNOT2 | 7335 | 0.041 | 0.33 | YES |
248 | ARL6IP5 | ARL6IP5 | ARL6IP5 | 7367 | 0.04 | 0.33 | YES |
249 | RPP38 | RPP38 | RPP38 | 7417 | 0.039 | 0.32 | YES |
250 | KLF7 | KLF7 | KLF7 | 7445 | 0.039 | 0.32 | YES |
251 | SLC31A1 | SLC31A1 | SLC31A1 | 7456 | 0.039 | 0.32 | YES |
252 | RARS | RARS | RARS | 7459 | 0.039 | 0.33 | YES |
253 | BMI1 | BMI1 | BMI1 | 7463 | 0.038 | 0.33 | YES |
254 | ELOVL5 | ELOVL5 | ELOVL5 | 7489 | 0.038 | 0.33 | YES |
255 | SNX4 | SNX4 | SNX4 | 7539 | 0.037 | 0.32 | YES |
256 | TMEM5 | TMEM5 | TMEM5 | 7540 | 0.037 | 0.33 | YES |
257 | NPTN | NPTN | NPTN | 7549 | 0.037 | 0.33 | YES |
258 | CRADD | CRADD | CRADD | 7550 | 0.037 | 0.33 | YES |
259 | UTP3 | UTP3 | UTP3 | 7551 | 0.037 | 0.33 | YES |
260 | KDM5A | KDM5A | KDM5A | 7560 | 0.036 | 0.33 | YES |
261 | TRIP12 | TRIP12 | TRIP12 | 7568 | 0.036 | 0.33 | YES |
262 | KIFAP3 | KIFAP3 | KIFAP3 | 7584 | 0.036 | 0.33 | YES |
263 | GNPAT | GNPAT | GNPAT | 7624 | 0.035 | 0.33 | YES |
264 | CCDC6 | CCDC6 | CCDC6 | 7633 | 0.035 | 0.33 | YES |
265 | CXADR | CXADR | CXADR | 7635 | 0.035 | 0.33 | YES |
266 | ADCY3 | ADCY3 | ADCY3 | 7643 | 0.035 | 0.33 | YES |
267 | SNRPG | SNRPG | SNRPG | 7664 | 0.034 | 0.33 | YES |
268 | MTMR4 | MTMR4 | MTMR4 | 7683 | 0.034 | 0.33 | YES |
269 | PRRG1 | PRRG1 | PRRG1 | 7715 | 0.034 | 0.33 | YES |
270 | ZWINT | ZWINT | ZWINT | 7724 | 0.033 | 0.33 | YES |
271 | AFAP1 | AFAP1 | AFAP1 | 7725 | 0.033 | 0.33 | YES |
272 | HSPE1 | HSPE1 | HSPE1 | 7726 | 0.033 | 0.33 | YES |
273 | PSPH | PSPH | PSPH | 7739 | 0.033 | 0.33 | YES |
274 | TPX2 | TPX2 | TPX2 | 7743 | 0.033 | 0.33 | YES |
275 | STARD7 | STARD7 | STARD7 | 7748 | 0.033 | 0.33 | YES |
276 | TCFL5 | TCFL5 | TCFL5 | 7762 | 0.033 | 0.33 | YES |
277 | SUMO1 | SUMO1 | SUMO1 | 7778 | 0.032 | 0.33 | YES |
278 | NOLC1 | NOLC1 | NOLC1 | 7790 | 0.032 | 0.33 | YES |
279 | YTHDC1 | YTHDC1 | YTHDC1 | 7794 | 0.032 | 0.33 | YES |
280 | ERAP1 | ERAP1 | ERAP1 | 7836 | 0.031 | 0.33 | NO |
281 | BUB3 | BUB3 | BUB3 | 7867 | 0.031 | 0.33 | NO |
282 | RAB14 | RAB14 | RAB14 | 7945 | 0.029 | 0.33 | NO |
283 | RBM6 | RBM6 | RBM6 | 7963 | 0.029 | 0.33 | NO |
284 | UBE2D3 | UBE2D3 | UBE2D3 | 7972 | 0.029 | 0.33 | NO |
285 | MPHOSPH6 | MPHOSPH6 | MPHOSPH6 | 7998 | 0.028 | 0.33 | NO |
286 | AFG3L2 | AFG3L2 | AFG3L2 | 8066 | 0.027 | 0.32 | NO |
287 | RNF13 | RNF13 | RNF13 | 8076 | 0.027 | 0.32 | NO |
288 | IKBKAP | IKBKAP | IKBKAP | 8081 | 0.027 | 0.33 | NO |
289 | TP53BP1 | TP53BP1 | TP53BP1 | 8089 | 0.027 | 0.33 | NO |
290 | DNAJA1 | DNAJA1 | DNAJA1 | 8115 | 0.026 | 0.32 | NO |
291 | SLC9A6 | SLC9A6 | SLC9A6 | 8123 | 0.026 | 0.33 | NO |
292 | GCSH | GCSH | GCSH | 8142 | 0.026 | 0.32 | NO |
293 | PSMG1 | PSMG1 | PSMG1 | 8164 | 0.025 | 0.32 | NO |
294 | TRIM13 | TRIM13 | TRIM13 | 8204 | 0.024 | 0.32 | NO |
295 | LAMP2 | LAMP2 | LAMP2 | 8221 | 0.024 | 0.32 | NO |
296 | HNRNPR | HNRNPR | HNRNPR | 8227 | 0.024 | 0.32 | NO |
297 | DHX9 | DHX9 | DHX9 | 8248 | 0.023 | 0.32 | NO |
298 | UBE2N | UBE2N | UBE2N | 8299 | 0.022 | 0.32 | NO |
299 | DLG5 | DLG5 | DLG5 | 8449 | 0.02 | 0.31 | NO |
300 | G3BP1 | G3BP1 | G3BP1 | 8462 | 0.019 | 0.31 | NO |
301 | ATP1B3 | ATP1B3 | ATP1B3 | 8596 | 0.017 | 0.31 | NO |
302 | CAMKK2 | CAMKK2 | CAMKK2 | 8607 | 0.017 | 0.3 | NO |
303 | TM9SF2 | TM9SF2 | TM9SF2 | 8636 | 0.016 | 0.3 | NO |
304 | PRKAR1A | PRKAR1A | PRKAR1A | 8663 | 0.016 | 0.3 | NO |
305 | GOSR1 | GOSR1 | GOSR1 | 8725 | 0.015 | 0.3 | NO |
306 | GRSF1 | GRSF1 | GRSF1 | 8750 | 0.014 | 0.3 | NO |
307 | BCAR3 | BCAR3 | BCAR3 | 8767 | 0.014 | 0.3 | NO |
308 | PIK3R3 | PIK3R3 | PIK3R3 | 8768 | 0.014 | 0.3 | NO |
309 | BNIP3L | BNIP3L | BNIP3L | 8824 | 0.013 | 0.3 | NO |
310 | TRIM38 | TRIM38 | TRIM38 | 8836 | 0.013 | 0.3 | NO |
311 | PTP4A2 | PTP4A2 | PTP4A2 | 8839 | 0.013 | 0.3 | NO |
312 | MTHFD1 | MTHFD1 | MTHFD1 | 8901 | 0.012 | 0.29 | NO |
313 | DDX42 | DDX42 | DDX42 | 8940 | 0.011 | 0.29 | NO |
314 | ADH5 | ADH5 | ADH5 | 8987 | 0.01 | 0.29 | NO |
315 | PGRMC2 | PGRMC2 | PGRMC2 | 8992 | 0.01 | 0.29 | NO |
316 | MT1H | MT1H | MT1H | 8993 | 0.01 | 0.29 | NO |
317 | DCAF8 | DCAF8 | DCAF8 | 8994 | 0.0099 | 0.29 | NO |
318 | FH | FH | FH | 9140 | 0.0074 | 0.28 | NO |
319 | DKC1 | DKC1 | DKC1 | 9175 | 0.0067 | 0.28 | NO |
320 | SRI | SRI | SRI | 9209 | 0.0062 | 0.28 | NO |
321 | TOMM20 | TOMM20 | TOMM20 | 9222 | 0.0058 | 0.28 | NO |
322 | DOPEY2 | DOPEY2 | DOPEY2 | 9235 | 0.0056 | 0.28 | NO |
323 | GTF2F2 | GTF2F2 | GTF2F2 | 9269 | 0.005 | 0.28 | NO |
324 | PRKCI | PRKCI | PRKCI | 9280 | 0.0048 | 0.28 | NO |
325 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 9329 | 0.0038 | 0.27 | NO |
326 | ENTPD4 | ENTPD4 | ENTPD4 | 9337 | 0.0037 | 0.27 | NO |
327 | CCNG2 | CCNG2 | CCNG2 | 9377 | 0.0031 | 0.27 | NO |
328 | ZFAND5 | ZFAND5 | ZFAND5 | 9424 | 0.0023 | 0.27 | NO |
329 | PRPF4 | PRPF4 | PRPF4 | 9439 | 0.0022 | 0.27 | NO |
330 | CPD | CPD | CPD | 9440 | 0.0021 | 0.27 | NO |
331 | STT3A | STT3A | STT3A | 9451 | 0.0019 | 0.27 | NO |
332 | GOT1 | GOT1 | GOT1 | 9458 | 0.0019 | 0.27 | NO |
333 | NOL7 | NOL7 | NOL7 | 9459 | 0.0018 | 0.27 | NO |
334 | EEF1E1 | EEF1E1 | EEF1E1 | 9468 | 0.0016 | 0.26 | NO |
335 | ERH | ERH | ERH | 9472 | 0.0016 | 0.26 | NO |
336 | STX6 | STX6 | STX6 | 9507 | 0.00081 | 0.26 | NO |
337 | SMC1A | SMC1A | SMC1A | 9540 | 0.00022 | 0.26 | NO |
338 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 9557 | -2.6e-06 | 0.26 | NO |
339 | TRA2B | TRA2B | TRA2B | 9572 | -0.00021 | 0.26 | NO |
340 | ITSN1 | ITSN1 | ITSN1 | 9612 | -0.0008 | 0.26 | NO |
341 | ATP6V1A | ATP6V1A | ATP6V1A | 9629 | -0.0011 | 0.26 | NO |
342 | ATP5B | ATP5B | ATP5B | 9636 | -0.0012 | 0.26 | NO |
343 | ERCC5 | ERCC5 | ERCC5 | 9651 | -0.0014 | 0.26 | NO |
344 | RPP30 | RPP30 | RPP30 | 9678 | -0.002 | 0.25 | NO |
345 | RBM8A | RBM8A | RBM8A | 9693 | -0.0023 | 0.25 | NO |
346 | RNF2 | RNF2 | RNF2 | 9705 | -0.0025 | 0.25 | NO |
347 | CTNNA1 | CTNNA1 | CTNNA1 | 9772 | -0.0035 | 0.25 | NO |
348 | PARP1 | PARP1 | PARP1 | 9795 | -0.004 | 0.25 | NO |
349 | RABIF | RABIF | RABIF | 9800 | -0.0041 | 0.25 | NO |
350 | TBL2 | TBL2 | TBL2 | 9842 | -0.0046 | 0.25 | NO |
351 | IPO5 | IPO5 | IPO5 | 9845 | -0.0046 | 0.25 | NO |
352 | TOR1A | TOR1A | TOR1A | 9857 | -0.0047 | 0.24 | NO |
353 | MCM3AP | MCM3AP | MCM3AP | 9876 | -0.005 | 0.24 | NO |
354 | RBMX | RBMX | RBMX | 9893 | -0.0052 | 0.24 | NO |
355 | CNN3 | CNN3 | CNN3 | 9912 | -0.0055 | 0.24 | NO |
356 | PFKM | PFKM | PFKM | 9927 | -0.0057 | 0.24 | NO |
357 | CBX1 | CBX1 | CBX1 | 9934 | -0.0058 | 0.24 | NO |
358 | ZNF133 | ZNF133 | ZNF133 | 9938 | -0.0059 | 0.24 | NO |
359 | CTBP1 | CTBP1 | CTBP1 | 9947 | -0.006 | 0.24 | NO |
360 | TRIM44 | TRIM44 | TRIM44 | 9950 | -0.0061 | 0.24 | NO |
361 | EIF4H | EIF4H | EIF4H | 10016 | -0.0074 | 0.24 | NO |
362 | BCAT2 | BCAT2 | BCAT2 | 10062 | -0.0084 | 0.24 | NO |
363 | FEN1 | FEN1 | FEN1 | 10067 | -0.0085 | 0.24 | NO |
364 | TOP2B | TOP2B | TOP2B | 10094 | -0.009 | 0.24 | NO |
365 | ANP32A | ANP32A | ANP32A | 10097 | -0.009 | 0.24 | NO |
366 | HSPB11 | HSPB11 | HSPB11 | 10116 | -0.0093 | 0.23 | NO |
367 | DFNA5 | DFNA5 | DFNA5 | 10123 | -0.0094 | 0.23 | NO |
368 | DSCR3 | DSCR3 | DSCR3 | 10132 | -0.0095 | 0.23 | NO |
369 | KAT6A | KAT6A | KAT6A | 10157 | -0.0098 | 0.23 | NO |
370 | CYB5B | CYB5B | CYB5B | 10176 | -0.01 | 0.23 | NO |
371 | USP7 | USP7 | USP7 | 10178 | -0.01 | 0.23 | NO |
372 | RABEPK | RABEPK | RABEPK | 10211 | -0.011 | 0.23 | NO |
373 | IRS1 | IRS1 | IRS1 | 10291 | -0.012 | 0.23 | NO |
374 | ADCY9 | ADCY9 | ADCY9 | 10316 | -0.012 | 0.23 | NO |
375 | SLC16A1 | SLC16A1 | SLC16A1 | 10319 | -0.012 | 0.23 | NO |
376 | CCND2 | CCND2 | CCND2 | 10405 | -0.014 | 0.22 | NO |
377 | SMARCA1 | SMARCA1 | SMARCA1 | 10495 | -0.015 | 0.22 | NO |
378 | CUX1 | CUX1 | CUX1 | 10503 | -0.015 | 0.22 | NO |
379 | GSK3B | GSK3B | GSK3B | 10551 | -0.016 | 0.22 | NO |
380 | MYO10 | MYO10 | MYO10 | 10620 | -0.017 | 0.21 | NO |
381 | PHB | PHB | PHB | 10724 | -0.018 | 0.21 | NO |
382 | UBE2C | UBE2C | UBE2C | 10745 | -0.019 | 0.2 | NO |
383 | NMT2 | NMT2 | NMT2 | 10810 | -0.02 | 0.2 | NO |
384 | PTPN1 | PTPN1 | PTPN1 | 10825 | -0.02 | 0.2 | NO |
385 | MMS19 | MMS19 | MMS19 | 10834 | -0.02 | 0.2 | NO |
386 | ABCC5 | ABCC5 | ABCC5 | 10860 | -0.02 | 0.2 | NO |
387 | MECP2 | MECP2 | MECP2 | 10967 | -0.022 | 0.2 | NO |
388 | GTF3C2 | GTF3C2 | GTF3C2 | 10968 | -0.022 | 0.2 | NO |
389 | MBD4 | MBD4 | MBD4 | 11028 | -0.023 | 0.19 | NO |
390 | PLSCR1 | PLSCR1 | PLSCR1 | 11053 | -0.024 | 0.19 | NO |
391 | PTMA | PTMA | PTMA | 11126 | -0.025 | 0.19 | NO |
392 | GAPDH | GAPDH | GAPDH | 11170 | -0.025 | 0.19 | NO |
393 | NMI | NMI | NMI | 11212 | -0.026 | 0.19 | NO |
394 | ELAC2 | ELAC2 | ELAC2 | 11229 | -0.026 | 0.19 | NO |
395 | IL10RB | IL10RB | IL10RB | 11305 | -0.027 | 0.18 | NO |
396 | MRPL3 | MRPL3 | MRPL3 | 11312 | -0.027 | 0.18 | NO |
397 | GBE1 | GBE1 | GBE1 | 11324 | -0.027 | 0.18 | NO |
398 | ACTL6A | ACTL6A | ACTL6A | 11413 | -0.029 | 0.18 | NO |
399 | CD44 | CD44 | CD44 | 11448 | -0.029 | 0.18 | NO |
400 | SLC25A5 | SLC25A5 | SLC25A5 | 11456 | -0.029 | 0.18 | NO |
401 | SMARCA2 | SMARCA2 | SMARCA2 | 11472 | -0.029 | 0.18 | NO |
402 | TPST2 | TPST2 | TPST2 | 11551 | -0.031 | 0.17 | NO |
403 | RND3 | RND3 | RND3 | 11588 | -0.031 | 0.17 | NO |
404 | ITGB5 | ITGB5 | ITGB5 | 11615 | -0.032 | 0.17 | NO |
405 | BCL6 | BCL6 | BCL6 | 11639 | -0.032 | 0.17 | NO |
406 | TP63 | TP63 | TP63 | 11752 | -0.034 | 0.17 | NO |
407 | RPA3 | RPA3 | RPA3 | 11838 | -0.035 | 0.16 | NO |
408 | TMEM187 | TMEM187 | TMEM187 | 11876 | -0.036 | 0.16 | NO |
409 | HNRNPA0 | HNRNPA0 | HNRNPA0 | 11883 | -0.036 | 0.16 | NO |
410 | DUSP4 | DUSP4 | DUSP4 | 12120 | -0.039 | 0.15 | NO |
411 | FOXO3 | FOXO3 | FOXO3 | 12182 | -0.04 | 0.15 | NO |
412 | HNRNPD | HNRNPD | HNRNPD | 12193 | -0.04 | 0.15 | NO |
413 | CTCF | CTCF | CTCF | 12199 | -0.04 | 0.15 | NO |
414 | MKRN1 | MKRN1 | MKRN1 | 12249 | -0.041 | 0.15 | NO |
415 | BLMH | BLMH | BLMH | 12296 | -0.042 | 0.15 | NO |
416 | WASF1 | WASF1 | WASF1 | 12322 | -0.042 | 0.15 | NO |
417 | STAU1 | STAU1 | STAU1 | 12343 | -0.042 | 0.15 | NO |
418 | FASN | FASN | FASN | 12457 | -0.044 | 0.14 | NO |
419 | TBXA2R | TBXA2R | TBXA2R | 12472 | -0.044 | 0.14 | NO |
420 | PIP4K2B | PIP4K2B | PIP4K2B | 12473 | -0.044 | 0.14 | NO |
421 | LPCAT3 | LPCAT3 | LPCAT3 | 12662 | -0.047 | 0.13 | NO |
422 | RCBTB2 | RCBTB2 | RCBTB2 | 12665 | -0.047 | 0.13 | NO |
423 | ASH2L | ASH2L | ASH2L | 12708 | -0.048 | 0.13 | NO |
424 | SNRNP200 | SNRNP200 | SNRNP200 | 12755 | -0.048 | 0.13 | NO |
425 | SNRPF | SNRPF | SNRPF | 12792 | -0.049 | 0.13 | NO |
426 | IFNGR2 | IFNGR2 | IFNGR2 | 12822 | -0.049 | 0.13 | NO |
427 | PEX11B | PEX11B | PEX11B | 12919 | -0.051 | 0.13 | NO |
428 | RGS19 | RGS19 | RGS19 | 12944 | -0.051 | 0.13 | NO |
429 | KHSRP | KHSRP | KHSRP | 13093 | -0.053 | 0.12 | NO |
430 | TGFBR2 | TGFBR2 | TGFBR2 | 13161 | -0.054 | 0.12 | NO |
431 | FNTB | FNTB | FNTB | 13570 | -0.061 | 0.096 | NO |
432 | NME6 | NME6 | NME6 | 13656 | -0.062 | 0.093 | NO |
433 | SLC2A1 | SLC2A1 | SLC2A1 | 13669 | -0.063 | 0.094 | NO |
434 | RRBP1 | RRBP1 | RRBP1 | 13724 | -0.064 | 0.093 | NO |
435 | MTMR3 | MTMR3 | MTMR3 | 13783 | -0.064 | 0.091 | NO |
436 | GAS2L1 | GAS2L1 | GAS2L1 | 13806 | -0.065 | 0.092 | NO |
437 | TFAP4 | TFAP4 | TFAP4 | 13954 | -0.067 | 0.085 | NO |
438 | MICB | MICB | MICB | 13955 | -0.067 | 0.087 | NO |
439 | ATP2C1 | ATP2C1 | ATP2C1 | 14055 | -0.069 | 0.083 | NO |
440 | SEMA3F | SEMA3F | SEMA3F | 14288 | -0.074 | 0.072 | NO |
441 | BAIAP2 | BAIAP2 | BAIAP2 | 14317 | -0.074 | 0.073 | NO |
442 | GCAT | GCAT | GCAT | 14321 | -0.074 | 0.074 | NO |
443 | CPSF4 | CPSF4 | CPSF4 | 14335 | -0.074 | 0.076 | NO |
444 | PTOV1 | PTOV1 | PTOV1 | 14394 | -0.075 | 0.075 | NO |
445 | GSK3A | GSK3A | GSK3A | 14449 | -0.076 | 0.074 | NO |
446 | MT1G | MT1G | MT1G | 14468 | -0.077 | 0.075 | NO |
447 | TUBGCP2 | TUBGCP2 | TUBGCP2 | 14471 | -0.077 | 0.077 | NO |
448 | UMPS | UMPS | UMPS | 14668 | -0.08 | 0.068 | NO |
449 | GNB2L1 | GNB2L1 | GNB2L1 | 14680 | -0.081 | 0.07 | NO |
450 | BHLHE40 | BHLHE40 | BHLHE40 | 14748 | -0.082 | 0.068 | NO |
451 | SRF | SRF | SRF | 14862 | -0.084 | 0.064 | NO |
452 | SVIL | SVIL | SVIL | 14874 | -0.084 | 0.066 | NO |
453 | H1F0 | H1F0 | H1F0 | 14887 | -0.085 | 0.067 | NO |
454 | KATNB1 | KATNB1 | KATNB1 | 15075 | -0.088 | 0.059 | NO |
455 | ENTPD6 | ENTPD6 | ENTPD6 | 15233 | -0.092 | 0.053 | NO |
456 | PAK1 | PAK1 | PAK1 | 15235 | -0.092 | 0.055 | NO |
457 | MAP4 | MAP4 | MAP4 | 15422 | -0.096 | 0.047 | NO |
458 | WNT5A | WNT5A | WNT5A | 15562 | -0.099 | 0.042 | NO |
459 | CDK2 | CDK2 | CDK2 | 15604 | -0.1 | 0.042 | NO |
460 | ZDHHC3 | ZDHHC3 | ZDHHC3 | 15606 | -0.1 | 0.045 | NO |
461 | TNC | TNC | TNC | 15797 | -0.11 | 0.037 | NO |
462 | CELSR2 | CELSR2 | CELSR2 | 15813 | -0.11 | 0.039 | NO |
463 | EFEMP1 | EFEMP1 | EFEMP1 | 15840 | -0.11 | 0.041 | NO |
464 | WWOX | WWOX | WWOX | 15948 | -0.11 | 0.038 | NO |
465 | EXTL3 | EXTL3 | EXTL3 | 16006 | -0.11 | 0.038 | NO |
466 | STEAP1 | STEAP1 | STEAP1 | 16169 | -0.12 | 0.032 | NO |
467 | B4GALT2 | B4GALT2 | B4GALT2 | 16181 | -0.12 | 0.034 | NO |
468 | RUVBL1 | RUVBL1 | RUVBL1 | 16256 | -0.12 | 0.034 | NO |
469 | IGSF3 | IGSF3 | IGSF3 | 16382 | -0.13 | 0.03 | NO |
470 | TJP2 | TJP2 | TJP2 | 16413 | -0.13 | 0.032 | NO |
471 | PEX6 | PEX6 | PEX6 | 16445 | -0.13 | 0.034 | NO |
472 | ID1 | ID1 | ID1 | 16455 | -0.13 | 0.037 | NO |
473 | TUSC2 | TUSC2 | TUSC2 | 16611 | -0.14 | 0.032 | NO |
474 | DHRS3 | DHRS3 | DHRS3 | 16617 | -0.14 | 0.036 | NO |
475 | SEMA3C | SEMA3C | SEMA3C | 16626 | -0.14 | 0.039 | NO |
476 | FDFT1 | FDFT1 | FDFT1 | 16657 | -0.14 | 0.041 | NO |
477 | MT3 | MT3 | MT3 | 16883 | -0.16 | 0.033 | NO |
478 | MAOA | MAOA | MAOA | 17440 | -0.22 | 0.007 | NO |
479 | PPP1R3C | PPP1R3C | PPP1R3C | 17447 | -0.22 | 0.013 | NO |
480 | ADRB2 | ADRB2 | ADRB2 | 17502 | -0.23 | 0.016 | NO |
481 | DDX3Y | DDX3Y | DDX3Y | 17712 | -0.27 | 0.012 | NO |
482 | CNTN1 | CNTN1 | CNTN1 | 17880 | -0.35 | 0.012 | NO |
Figure S17. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: DACOSTA UV RESPONSE VIA ERCC3 COMMON DN.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: DACOSTA UV RESPONSE VIA ERCC3 COMMON DN, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S10. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | DLX2 | DLX2 | DLX2 | 113 | 0.55 | 0.018 | YES |
2 | KIF18A | KIF18A | KIF18A | 450 | 0.4 | 0.018 | YES |
3 | TMEFF1 | TMEFF1 | TMEFF1 | 557 | 0.37 | 0.028 | YES |
4 | PTGS2 | PTGS2 | PTGS2 | 781 | 0.33 | 0.03 | YES |
5 | BIRC3 | BIRC3 | BIRC3 | 956 | 0.3 | 0.034 | YES |
6 | GEM | GEM | GEM | 972 | 0.3 | 0.047 | YES |
7 | SCG5 | SCG5 | SCG5 | 1091 | 0.28 | 0.053 | YES |
8 | CREB5 | CREB5 | CREB5 | 1246 | 0.26 | 0.056 | YES |
9 | GAD1 | GAD1 | GAD1 | 1264 | 0.26 | 0.067 | YES |
10 | ZNF107 | ZNF107 | ZNF107 | 1293 | 0.26 | 0.077 | YES |
11 | TRPC1 | TRPC1 | TRPC1 | 1332 | 0.26 | 0.086 | YES |
12 | CHAC1 | CHAC1 | CHAC1 | 1527 | 0.24 | 0.086 | YES |
13 | CLK4 | CLK4 | CLK4 | 1588 | 0.23 | 0.093 | YES |
14 | ZNF23 | ZNF23 | ZNF23 | 1614 | 0.23 | 0.1 | YES |
15 | PYROXD1 | PYROXD1 | PYROXD1 | 1706 | 0.22 | 0.11 | YES |
16 | SREK1 | SREK1 | SREK1 | 1725 | 0.22 | 0.12 | YES |
17 | JMJD1C | JMJD1C | JMJD1C | 1730 | 0.22 | 0.12 | YES |
18 | TAF2 | TAF2 | TAF2 | 1745 | 0.22 | 0.13 | YES |
19 | PPP1R12A | PPP1R12A | PPP1R12A | 1836 | 0.21 | 0.14 | YES |
20 | LIG4 | LIG4 | LIG4 | 1841 | 0.21 | 0.15 | YES |
21 | DMTF1 | DMTF1 | DMTF1 | 1922 | 0.2 | 0.15 | YES |
22 | LIF | LIF | LIF | 1965 | 0.2 | 0.16 | YES |
23 | FOS | FOS | FOS | 2050 | 0.19 | 0.16 | YES |
24 | BDKRB1 | BDKRB1 | BDKRB1 | 2072 | 0.19 | 0.17 | YES |
25 | C1orf27 | C1orf27 | C1orf27 | 2102 | 0.19 | 0.18 | YES |
26 | SNX16 | SNX16 | SNX16 | 2109 | 0.19 | 0.18 | YES |
27 | CHD9 | CHD9 | CHD9 | 2143 | 0.19 | 0.19 | YES |
28 | ZNF267 | ZNF267 | ZNF267 | 2205 | 0.18 | 0.2 | YES |
29 | PIBF1 | PIBF1 | PIBF1 | 2291 | 0.18 | 0.2 | YES |
30 | ATAD2B | ATAD2B | ATAD2B | 2312 | 0.18 | 0.21 | YES |
31 | TBK1 | TBK1 | TBK1 | 2326 | 0.18 | 0.21 | YES |
32 | CCNT2 | CCNT2 | CCNT2 | 2335 | 0.18 | 0.22 | YES |
33 | STRN3 | STRN3 | STRN3 | 2365 | 0.18 | 0.23 | YES |
34 | DAAM1 | DAAM1 | DAAM1 | 2398 | 0.17 | 0.23 | YES |
35 | THUMPD2 | THUMPD2 | THUMPD2 | 2473 | 0.17 | 0.24 | YES |
36 | DCLRE1C | DCLRE1C | DCLRE1C | 2559 | 0.17 | 0.24 | YES |
37 | ARID4B | ARID4B | ARID4B | 2591 | 0.16 | 0.25 | YES |
38 | SMCHD1 | SMCHD1 | SMCHD1 | 2594 | 0.16 | 0.25 | YES |
39 | CLK1 | CLK1 | CLK1 | 2619 | 0.16 | 0.26 | YES |
40 | NEMF | NEMF | NEMF | 2625 | 0.16 | 0.27 | YES |
41 | TBX3 | TBX3 | TBX3 | 2803 | 0.16 | 0.26 | YES |
42 | IFRD1 | IFRD1 | IFRD1 | 2908 | 0.15 | 0.26 | YES |
43 | ZNF451 | ZNF451 | ZNF451 | 2936 | 0.15 | 0.27 | YES |
44 | VEGFA | VEGFA | VEGFA | 2975 | 0.15 | 0.27 | YES |
45 | ZNF468 | ZNF468 | ZNF468 | 3000 | 0.15 | 0.28 | YES |
46 | NEK1 | NEK1 | NEK1 | 3004 | 0.15 | 0.29 | YES |
47 | ZNF195 | ZNF195 | ZNF195 | 3010 | 0.15 | 0.29 | YES |
48 | TDG | TDG | TDG | 3011 | 0.15 | 0.3 | YES |
49 | CLEC4A | CLEC4A | CLEC4A | 3044 | 0.15 | 0.3 | YES |
50 | CDKN2AIP | CDKN2AIP | CDKN2AIP | 3077 | 0.14 | 0.31 | YES |
51 | KRCC1 | KRCC1 | KRCC1 | 3152 | 0.14 | 0.31 | YES |
52 | ZNF432 | ZNF432 | ZNF432 | 3166 | 0.14 | 0.32 | YES |
53 | SEC24A | SEC24A | SEC24A | 3182 | 0.14 | 0.32 | YES |
54 | PPWD1 | PPWD1 | PPWD1 | 3189 | 0.14 | 0.33 | YES |
55 | PELI1 | PELI1 | PELI1 | 3208 | 0.14 | 0.33 | YES |
56 | SOX30 | SOX30 | SOX30 | 3227 | 0.14 | 0.34 | YES |
57 | BACH1 | BACH1 | BACH1 | 3234 | 0.14 | 0.34 | YES |
58 | MTHFD2L | MTHFD2L | MTHFD2L | 3294 | 0.14 | 0.35 | YES |
59 | PPIG | PPIG | PPIG | 3313 | 0.14 | 0.35 | YES |
60 | DNAJC2 | DNAJC2 | DNAJC2 | 3356 | 0.13 | 0.36 | YES |
61 | MORC3 | MORC3 | MORC3 | 3420 | 0.13 | 0.36 | YES |
62 | PTBP2 | PTBP2 | PTBP2 | 3422 | 0.13 | 0.36 | YES |
63 | MARCH7 | MARCH7 | MARCH7 | 3445 | 0.13 | 0.37 | YES |
64 | FNBP4 | FNBP4 | FNBP4 | 3478 | 0.13 | 0.37 | YES |
65 | ZNF136 | ZNF136 | ZNF136 | 3496 | 0.13 | 0.38 | YES |
66 | ZNF180 | ZNF180 | ZNF180 | 3575 | 0.13 | 0.38 | YES |
67 | PTPN2 | PTPN2 | PTPN2 | 3620 | 0.13 | 0.38 | YES |
68 | AKAP10 | AKAP10 | AKAP10 | 3647 | 0.12 | 0.39 | YES |
69 | ATF3 | ATF3 | ATF3 | 3665 | 0.12 | 0.39 | YES |
70 | BIRC2 | BIRC2 | BIRC2 | 3676 | 0.12 | 0.4 | YES |
71 | NSUN6 | NSUN6 | NSUN6 | 3693 | 0.12 | 0.4 | YES |
72 | CREM | CREM | CREM | 3745 | 0.12 | 0.4 | YES |
73 | TANK | TANK | TANK | 3802 | 0.12 | 0.4 | YES |
74 | ZNF14 | ZNF14 | ZNF14 | 3849 | 0.12 | 0.41 | YES |
75 | CEBPG | CEBPG | CEBPG | 3965 | 0.12 | 0.41 | YES |
76 | EGR1 | EGR1 | EGR1 | 4000 | 0.12 | 0.41 | YES |
77 | INTS6 | INTS6 | INTS6 | 4040 | 0.11 | 0.41 | YES |
78 | NOC3L | NOC3L | NOC3L | 4050 | 0.11 | 0.42 | YES |
79 | ALG13 | ALG13 | ALG13 | 4076 | 0.11 | 0.42 | YES |
80 | ZCCHC10 | ZCCHC10 | ZCCHC10 | 4161 | 0.11 | 0.42 | YES |
81 | ZNF131 | ZNF131 | ZNF131 | 4171 | 0.11 | 0.42 | YES |
82 | RSRC2 | RSRC2 | RSRC2 | 4204 | 0.11 | 0.43 | YES |
83 | KLF5 | KLF5 | KLF5 | 4332 | 0.1 | 0.43 | YES |
84 | C21orf91 | C21orf91 | C21orf91 | 4334 | 0.1 | 0.43 | YES |
85 | GPATCH2 | GPATCH2 | GPATCH2 | 4367 | 0.1 | 0.43 | YES |
86 | ASNS | ASNS | ASNS | 4496 | 0.1 | 0.43 | YES |
87 | TNFRSF9 | TNFRSF9 | TNFRSF9 | 4519 | 0.1 | 0.43 | YES |
88 | TSC22D1 | TSC22D1 | TSC22D1 | 4536 | 0.1 | 0.44 | YES |
89 | MARK3 | MARK3 | MARK3 | 4539 | 0.1 | 0.44 | YES |
90 | RLF | RLF | RLF | 4576 | 0.1 | 0.44 | YES |
91 | FAM13B | FAM13B | FAM13B | 4590 | 0.099 | 0.45 | YES |
92 | FEM1C | FEM1C | FEM1C | 4600 | 0.099 | 0.45 | YES |
93 | RBM39 | RBM39 | RBM39 | 4616 | 0.098 | 0.46 | YES |
94 | SRSF10 | SRSF10 | SRSF10 | 4676 | 0.097 | 0.46 | YES |
95 | CASP3 | CASP3 | CASP3 | 4689 | 0.096 | 0.46 | YES |
96 | CDK17 | CDK17 | CDK17 | 4743 | 0.096 | 0.46 | YES |
97 | ZNF280D | ZNF280D | ZNF280D | 4755 | 0.095 | 0.47 | YES |
98 | ZNF44 | ZNF44 | ZNF44 | 4780 | 0.095 | 0.47 | YES |
99 | FBXO38 | FBXO38 | FBXO38 | 4822 | 0.094 | 0.47 | YES |
100 | PRPF38B | PRPF38B | PRPF38B | 4980 | 0.09 | 0.47 | YES |
101 | CEP76 | CEP76 | CEP76 | 5035 | 0.088 | 0.47 | YES |
102 | ZNF557 | ZNF557 | ZNF557 | 5061 | 0.088 | 0.47 | YES |
103 | CCNL1 | CCNL1 | CCNL1 | 5205 | 0.085 | 0.46 | YES |
104 | SPATA5L1 | SPATA5L1 | SPATA5L1 | 5290 | 0.083 | 0.46 | YES |
105 | ZNF222 | ZNF222 | ZNF222 | 5294 | 0.083 | 0.47 | YES |
106 | DPP8 | DPP8 | DPP8 | 5316 | 0.082 | 0.47 | YES |
107 | TAF1A | TAF1A | TAF1A | 5321 | 0.082 | 0.47 | YES |
108 | RBBP6 | RBBP6 | RBBP6 | 5434 | 0.079 | 0.47 | YES |
109 | PMAIP1 | PMAIP1 | PMAIP1 | 5491 | 0.078 | 0.47 | YES |
110 | KIAA0907 | KIAA0907 | KIAA0907 | 5551 | 0.077 | 0.47 | YES |
111 | IFI16 | IFI16 | IFI16 | 5589 | 0.076 | 0.47 | YES |
112 | CDK7 | CDK7 | CDK7 | 5642 | 0.074 | 0.47 | YES |
113 | RIC8B | RIC8B | RIC8B | 5652 | 0.074 | 0.48 | YES |
114 | CAB39 | CAB39 | CAB39 | 5671 | 0.074 | 0.48 | YES |
115 | NUPL1 | NUPL1 | NUPL1 | 5718 | 0.073 | 0.48 | YES |
116 | ZNF45 | ZNF45 | ZNF45 | 5722 | 0.073 | 0.48 | YES |
117 | ARNTL | ARNTL | ARNTL | 5743 | 0.072 | 0.48 | YES |
118 | ZNF331 | ZNF331 | ZNF331 | 5773 | 0.072 | 0.49 | YES |
119 | ZNF184 | ZNF184 | ZNF184 | 5778 | 0.072 | 0.49 | YES |
120 | EIF5 | EIF5 | EIF5 | 5791 | 0.071 | 0.49 | YES |
121 | AGTPBP1 | AGTPBP1 | AGTPBP1 | 5863 | 0.07 | 0.49 | YES |
122 | TAF1D | TAF1D | TAF1D | 5911 | 0.069 | 0.49 | YES |
123 | ZNF274 | ZNF274 | ZNF274 | 5989 | 0.067 | 0.49 | YES |
124 | DUSP5 | DUSP5 | DUSP5 | 6089 | 0.065 | 0.49 | YES |
125 | KIN | KIN | KIN | 6143 | 0.064 | 0.49 | YES |
126 | RCHY1 | RCHY1 | RCHY1 | 6210 | 0.062 | 0.49 | YES |
127 | MCL1 | MCL1 | MCL1 | 6243 | 0.062 | 0.49 | YES |
128 | BCL10 | BCL10 | BCL10 | 6254 | 0.062 | 0.49 | YES |
129 | LRIF1 | LRIF1 | LRIF1 | 6279 | 0.061 | 0.49 | YES |
130 | ZNF227 | ZNF227 | ZNF227 | 6309 | 0.06 | 0.49 | YES |
131 | POLR3F | POLR3F | POLR3F | 6329 | 0.06 | 0.49 | YES |
132 | AVL9 | AVL9 | AVL9 | 6397 | 0.059 | 0.49 | YES |
133 | NFIL3 | NFIL3 | NFIL3 | 6418 | 0.058 | 0.49 | YES |
134 | ARIH1 | ARIH1 | ARIH1 | 6458 | 0.058 | 0.49 | YES |
135 | AKIRIN1 | AKIRIN1 | AKIRIN1 | 6474 | 0.057 | 0.5 | YES |
136 | WAC | WAC | WAC | 6483 | 0.057 | 0.5 | YES |
137 | NCOA3 | NCOA3 | NCOA3 | 6492 | 0.057 | 0.5 | YES |
138 | NRBF2 | NRBF2 | NRBF2 | 6494 | 0.057 | 0.5 | YES |
139 | BTN2A1 | BTN2A1 | BTN2A1 | 6669 | 0.053 | 0.5 | NO |
140 | KDM3A | KDM3A | KDM3A | 6678 | 0.053 | 0.5 | NO |
141 | C6orf62 | C6orf62 | C6orf62 | 6708 | 0.053 | 0.5 | NO |
142 | ZCCHC8 | ZCCHC8 | ZCCHC8 | 6744 | 0.052 | 0.5 | NO |
143 | STC2 | STC2 | STC2 | 6823 | 0.051 | 0.5 | NO |
144 | SUV420H1 | SUV420H1 | SUV420H1 | 6894 | 0.049 | 0.49 | NO |
145 | PSPC1 | PSPC1 | PSPC1 | 6946 | 0.048 | 0.49 | NO |
146 | TLK2 | TLK2 | TLK2 | 6958 | 0.048 | 0.5 | NO |
147 | ZCCHC6 | ZCCHC6 | ZCCHC6 | 7022 | 0.047 | 0.49 | NO |
148 | RNF111 | RNF111 | RNF111 | 7064 | 0.046 | 0.49 | NO |
149 | CRY1 | CRY1 | CRY1 | 7106 | 0.045 | 0.49 | NO |
150 | ING3 | ING3 | ING3 | 7179 | 0.044 | 0.49 | NO |
151 | LINS | LINS | LINS | 7196 | 0.044 | 0.49 | NO |
152 | SLTM | SLTM | SLTM | 7250 | 0.043 | 0.49 | NO |
153 | RBM15 | RBM15 | RBM15 | 7299 | 0.042 | 0.49 | NO |
154 | CNOT4 | CNOT4 | CNOT4 | 7303 | 0.041 | 0.49 | NO |
155 | CNOT2 | CNOT2 | CNOT2 | 7335 | 0.041 | 0.49 | NO |
156 | SFPQ | SFPQ | SFPQ | 7372 | 0.04 | 0.49 | NO |
157 | SCYL3 | SCYL3 | SCYL3 | 7441 | 0.039 | 0.49 | NO |
158 | KLF6 | KLF6 | KLF6 | 7722 | 0.033 | 0.48 | NO |
159 | JUNB | JUNB | JUNB | 7974 | 0.029 | 0.46 | NO |
160 | UIMC1 | UIMC1 | UIMC1 | 8090 | 0.027 | 0.46 | NO |
161 | ADNP | ADNP | ADNP | 8098 | 0.026 | 0.46 | NO |
162 | ZZZ3 | ZZZ3 | ZZZ3 | 8127 | 0.026 | 0.46 | NO |
163 | RCAN1 | RCAN1 | RCAN1 | 8167 | 0.025 | 0.46 | NO |
164 | ZSCAN16 | ZSCAN16 | ZSCAN16 | 8197 | 0.024 | 0.46 | NO |
165 | RIPK2 | RIPK2 | RIPK2 | 8210 | 0.024 | 0.46 | NO |
166 | RABGGTB | RABGGTB | RABGGTB | 8315 | 0.022 | 0.45 | NO |
167 | PRPF3 | PRPF3 | PRPF3 | 8581 | 0.017 | 0.44 | NO |
168 | RBM5 | RBM5 | RBM5 | 8680 | 0.016 | 0.43 | NO |
169 | SNX5 | SNX5 | SNX5 | 8693 | 0.015 | 0.43 | NO |
170 | ZNF426 | ZNF426 | ZNF426 | 8924 | 0.011 | 0.42 | NO |
171 | KLF10 | KLF10 | KLF10 | 8955 | 0.011 | 0.42 | NO |
172 | PNRC2 | PNRC2 | PNRC2 | 8969 | 0.01 | 0.42 | NO |
173 | ZNF155 | ZNF155 | ZNF155 | 9092 | 0.0082 | 0.41 | NO |
174 | HLX | HLX | HLX | 9502 | 0.00089 | 0.39 | NO |
175 | IER2 | IER2 | IER2 | 9527 | 0.00049 | 0.39 | NO |
176 | TSC22D2 | TSC22D2 | TSC22D2 | 9699 | -0.0024 | 0.38 | NO |
177 | ZNF3 | ZNF3 | ZNF3 | 9822 | -0.0044 | 0.37 | NO |
178 | PRKRIP1 | PRKRIP1 | PRKRIP1 | 10129 | -0.0095 | 0.36 | NO |
179 | TNFRSF10B | TNFRSF10B | TNFRSF10B | 10470 | -0.015 | 0.34 | NO |
180 | C2orf42 | C2orf42 | C2orf42 | 10510 | -0.015 | 0.34 | NO |
181 | PTN | PTN | PTN | 10703 | -0.018 | 0.33 | NO |
182 | HRH1 | HRH1 | HRH1 | 10732 | -0.019 | 0.32 | NO |
183 | CEBPB | CEBPB | CEBPB | 10733 | -0.019 | 0.33 | NO |
184 | GADD45B | GADD45B | GADD45B | 10802 | -0.02 | 0.32 | NO |
185 | ETS2 | ETS2 | ETS2 | 10838 | -0.02 | 0.32 | NO |
186 | FAM53C | FAM53C | FAM53C | 11152 | -0.025 | 0.31 | NO |
187 | FOSL2 | FOSL2 | FOSL2 | 11183 | -0.025 | 0.3 | NO |
188 | CARS | CARS | CARS | 11274 | -0.027 | 0.3 | NO |
189 | RELB | RELB | RELB | 11407 | -0.029 | 0.3 | NO |
190 | NFKBIA | NFKBIA | NFKBIA | 11409 | -0.029 | 0.3 | NO |
191 | ZNF165 | ZNF165 | ZNF165 | 11420 | -0.029 | 0.3 | NO |
192 | IRF7 | IRF7 | IRF7 | 11460 | -0.029 | 0.3 | NO |
193 | JUN | JUN | JUN | 11660 | -0.032 | 0.29 | NO |
194 | DUSP6 | DUSP6 | DUSP6 | 11821 | -0.035 | 0.28 | NO |
195 | FOXO3 | FOXO3 | FOXO3 | 12182 | -0.04 | 0.26 | NO |
196 | PGS1 | PGS1 | PGS1 | 12269 | -0.041 | 0.26 | NO |
197 | SAT1 | SAT1 | SAT1 | 12297 | -0.042 | 0.26 | NO |
198 | RYBP | RYBP | RYBP | 12635 | -0.047 | 0.24 | NO |
199 | SETDB1 | SETDB1 | SETDB1 | 13054 | -0.053 | 0.22 | NO |
200 | TUFT1 | TUFT1 | TUFT1 | 13379 | -0.058 | 0.2 | NO |
201 | MAFF | MAFF | MAFF | 13493 | -0.06 | 0.2 | NO |
202 | NFKBIE | NFKBIE | NFKBIE | 14005 | -0.068 | 0.18 | NO |
203 | F3 | F3 | F3 | 14339 | -0.074 | 0.16 | NO |
204 | SNAI2 | SNAI2 | SNAI2 | 14723 | -0.082 | 0.14 | NO |
205 | YY1AP1 | YY1AP1 | YY1AP1 | 14814 | -0.083 | 0.14 | NO |
206 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 15159 | -0.09 | 0.13 | NO |
207 | IP6K2 | IP6K2 | IP6K2 | 15684 | -0.1 | 0.1 | NO |
208 | TIPARP | TIPARP | TIPARP | 16166 | -0.12 | 0.08 | NO |
209 | FOSB | FOSB | FOSB | 16409 | -0.13 | 0.072 | NO |
210 | DUSP8 | DUSP8 | DUSP8 | 16531 | -0.14 | 0.072 | NO |
211 | CTH | CTH | CTH | 16903 | -0.16 | 0.058 | NO |
212 | NEDD9 | NEDD9 | NEDD9 | 17196 | -0.18 | 0.05 | NO |
Figure S19. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 4. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus2. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG GLYCOLYSIS GLUCONEOGENESIS | 57 | genes.ES.table | 0.42 | 1.2 | 0.13 | 0.23 | 1 | 0.26 | 0.25 | 0.2 | 0.19 | 0 |
KEGG PENTOSE PHOSPHATE PATHWAY | 25 | genes.ES.table | 0.47 | 1.4 | 0.09 | 0.12 | 1 | 0.36 | 0.32 | 0.25 | 0.084 | 0 |
KEGG FRUCTOSE AND MANNOSE METABOLISM | 34 | genes.ES.table | 0.44 | 1.5 | 0.059 | 0.085 | 1 | 0.24 | 0.25 | 0.18 | 0.058 | 0 |
KEGG GALACTOSE METABOLISM | 25 | genes.ES.table | 0.57 | 1.5 | 0.042 | 0.077 | 1 | 0.12 | 0.055 | 0.11 | 0.051 | 0 |
KEGG STEROID HORMONE BIOSYNTHESIS | 36 | genes.ES.table | 0.61 | 1.4 | 0.042 | 0.12 | 1 | 0.28 | 0.12 | 0.24 | 0.085 | 0 |
KEGG PURINE METABOLISM | 154 | genes.ES.table | 0.49 | 1.8 | 0.0057 | 0.047 | 0.75 | 0.23 | 0.24 | 0.18 | 0.017 | 0 |
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM | 31 | genes.ES.table | 0.52 | 1.5 | 0.047 | 0.091 | 1 | 0.36 | 0.26 | 0.26 | 0.063 | 0 |
KEGG GLYCINE SERINE AND THREONINE METABOLISM | 30 | genes.ES.table | 0.69 | 1.7 | 0.0041 | 0.053 | 0.95 | 0.37 | 0.15 | 0.31 | 0.027 | 0 |
KEGG LYSINE DEGRADATION | 44 | genes.ES.table | 0.43 | 1.9 | 0.023 | 0.052 | 0.61 | 0.046 | 0.073 | 0.042 | 0.015 | 0.003 |
KEGG ARGININE AND PROLINE METABOLISM | 52 | genes.ES.table | 0.49 | 1.5 | 0.049 | 0.091 | 1 | 0.36 | 0.3 | 0.26 | 0.064 | 0 |
Table S11. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SYT1 | SYT1 | SYT1 | 37 | 0.97 | 0.41 | YES |
2 | MAPK10 | MAPK10 | MAPK10 | 551 | 0.54 | 0.62 | YES |
3 | MAPK8IP3 | MAPK8IP3 | MAPK8IP3 | 4457 | 0.09 | 0.44 | NO |
4 | MAPK8IP1 | MAPK8IP1 | MAPK8IP1 | 4508 | 0.088 | 0.47 | NO |
5 | DUSP1 | DUSP1 | DUSP1 | 4548 | 0.087 | 0.51 | NO |
6 | CD40 | CD40 | CD40 | 5523 | 0.052 | 0.48 | NO |
7 | MAPK3 | MAPK3 | MAPK3 | 5934 | 0.042 | 0.47 | NO |
8 | MAPK11 | MAPK11 | MAPK11 | 6173 | 0.037 | 0.47 | NO |
9 | NFKBIA | NFKBIA | NFKBIA | 6978 | 0.025 | 0.44 | NO |
10 | MAPK13 | MAPK13 | MAPK13 | 7751 | 0.018 | 0.4 | NO |
11 | NFKBIB | NFKBIB | NFKBIB | 7899 | 0.016 | 0.4 | NO |
12 | TRAF3 | TRAF3 | TRAF3 | 8040 | 0.015 | 0.4 | NO |
13 | IKBKG | IKBKG | IKBKG | 8100 | 0.014 | 0.4 | NO |
14 | NFKB2 | NFKB2 | NFKB2 | 8297 | 0.013 | 0.4 | NO |
15 | GORASP1 | GORASP1 | GORASP1 | 8820 | 0.0088 | 0.37 | NO |
16 | NFKBIE | NFKBIE | NFKBIE | 9057 | 0.0072 | 0.36 | NO |
17 | PIK3R1 | PIK3R1 | PIK3R1 | 9201 | 0.0061 | 0.36 | NO |
18 | TRAF2 | TRAF2 | TRAF2 | 9205 | 0.0061 | 0.36 | NO |
19 | MAP2K4 | MAP2K4 | MAP2K4 | 9245 | 0.0058 | 0.36 | NO |
20 | MAPK12 | MAPK12 | MAPK12 | 9570 | 0.0035 | 0.34 | NO |
21 | MAP2K7 | MAP2K7 | MAP2K7 | 10392 | -0.0021 | 0.3 | NO |
22 | MAPK8 | MAPK8 | MAPK8 | 11038 | -0.0064 | 0.27 | NO |
23 | NFKBIL1 | NFKBIL1 | NFKBIL1 | 11078 | -0.0067 | 0.27 | NO |
24 | MAPK1 | MAPK1 | MAPK1 | 11428 | -0.0091 | 0.25 | NO |
25 | MAPKAPK5 | MAPKAPK5 | MAPKAPK5 | 11694 | -0.011 | 0.24 | NO |
26 | NFKB1 | NFKB1 | NFKB1 | 12083 | -0.013 | 0.23 | NO |
27 | TRAF5 | TRAF5 | TRAF5 | 12282 | -0.015 | 0.22 | NO |
28 | MAPK9 | MAPK9 | MAPK9 | 12340 | -0.015 | 0.22 | NO |
29 | TONSL | TONSL | TONSL | 13320 | -0.022 | 0.18 | NO |
30 | PIK3CD | PIK3CD | PIK3CD | 14377 | -0.031 | 0.14 | NO |
31 | MAPK14 | MAPK14 | MAPK14 | 14720 | -0.034 | 0.13 | NO |
32 | TRAF6 | TRAF6 | TRAF6 | 14823 | -0.035 | 0.14 | NO |
33 | MAPK8IP2 | MAPK8IP2 | MAPK8IP2 | 15166 | -0.039 | 0.14 | NO |
34 | PIK3CA | PIK3CA | PIK3CA | 16220 | -0.057 | 0.1 | NO |
Figure S21. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS.

Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S12. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ACTC1 | ACTC1 | ACTC1 | 57 | 0.92 | 0.052 | YES |
2 | CDCP1 | CDCP1 | CDCP1 | 847 | 0.44 | 0.034 | YES |
3 | NEFL | NEFL | NEFL | 860 | 0.44 | 0.059 | YES |
4 | CLDN3 | CLDN3 | CLDN3 | 954 | 0.41 | 0.078 | YES |
5 | KCNMA1 | KCNMA1 | KCNMA1 | 1044 | 0.39 | 0.097 | YES |
6 | MYOD1 | MYOD1 | MYOD1 | 1066 | 0.39 | 0.12 | YES |
7 | STC2 | STC2 | STC2 | 1251 | 0.36 | 0.13 | YES |
8 | GPR39 | GPR39 | GPR39 | 1275 | 0.35 | 0.15 | YES |
9 | CA12 | CA12 | CA12 | 1448 | 0.32 | 0.16 | YES |
10 | CCNJL | CCNJL | CCNJL | 1450 | 0.32 | 0.18 | YES |
11 | ANGPTL4 | ANGPTL4 | ANGPTL4 | 1552 | 0.31 | 0.19 | YES |
12 | MAOA | MAOA | MAOA | 1644 | 0.3 | 0.2 | YES |
13 | HEMGN | HEMGN | HEMGN | 1727 | 0.29 | 0.22 | YES |
14 | SYT13 | SYT13 | SYT13 | 1728 | 0.29 | 0.23 | YES |
15 | ENO2 | ENO2 | ENO2 | 1838 | 0.27 | 0.24 | YES |
16 | DPP4 | DPP4 | DPP4 | 1912 | 0.26 | 0.25 | YES |
17 | HLF | HLF | HLF | 1955 | 0.26 | 0.27 | YES |
18 | FEZ1 | FEZ1 | FEZ1 | 2460 | 0.21 | 0.25 | YES |
19 | SERPINE1 | SERPINE1 | SERPINE1 | 2529 | 0.2 | 0.26 | YES |
20 | ITGB4 | ITGB4 | ITGB4 | 2617 | 0.2 | 0.27 | YES |
21 | CAPG | CAPG | CAPG | 2677 | 0.19 | 0.28 | YES |
22 | PDGFC | PDGFC | PDGFC | 2837 | 0.18 | 0.28 | YES |
23 | ARHGAP8 | ARHGAP8 | ARHGAP8 | 2947 | 0.17 | 0.28 | YES |
24 | SLC2A3 | SLC2A3 | SLC2A3 | 2950 | 0.17 | 0.29 | YES |
25 | ALDOC | ALDOC | ALDOC | 3020 | 0.17 | 0.3 | YES |
26 | GPRC5A | GPRC5A | GPRC5A | 3046 | 0.17 | 0.31 | YES |
27 | MDK | MDK | MDK | 3185 | 0.16 | 0.31 | YES |
28 | CORO1A | CORO1A | CORO1A | 3253 | 0.15 | 0.31 | YES |
29 | SLC2A1 | SLC2A1 | SLC2A1 | 3306 | 0.15 | 0.32 | YES |
30 | CFD | CFD | CFD | 3330 | 0.15 | 0.33 | YES |
31 | IL9R | IL9R | IL9R | 3455 | 0.14 | 0.33 | YES |
32 | ASB15 | ASB15 | ASB15 | 3645 | 0.13 | 0.32 | YES |
33 | CKB | CKB | CKB | 3708 | 0.13 | 0.33 | YES |
34 | AK4 | AK4 | AK4 | 3756 | 0.12 | 0.33 | YES |
35 | NT5E | NT5E | NT5E | 3783 | 0.12 | 0.34 | YES |
36 | HMOX1 | HMOX1 | HMOX1 | 3807 | 0.12 | 0.35 | YES |
37 | AMH | AMH | AMH | 3814 | 0.12 | 0.35 | YES |
38 | TIMP1 | TIMP1 | TIMP1 | 4056 | 0.11 | 0.34 | YES |
39 | TGM2 | TGM2 | TGM2 | 4180 | 0.1 | 0.34 | YES |
40 | CITED2 | CITED2 | CITED2 | 4346 | 0.095 | 0.34 | YES |
41 | ALPL | ALPL | ALPL | 4347 | 0.095 | 0.35 | YES |
42 | PLOD2 | PLOD2 | PLOD2 | 4392 | 0.093 | 0.35 | YES |
43 | AKAP12 | AKAP12 | AKAP12 | 4401 | 0.093 | 0.36 | YES |
44 | LGALSL | LGALSL | LGALSL | 4416 | 0.093 | 0.36 | YES |
45 | JUN | JUN | JUN | 4433 | 0.092 | 0.36 | YES |
46 | CCND2 | CCND2 | CCND2 | 4479 | 0.09 | 0.37 | YES |
47 | TSC22D3 | TSC22D3 | TSC22D3 | 4492 | 0.089 | 0.37 | YES |
48 | GAL3ST1 | GAL3ST1 | GAL3ST1 | 4519 | 0.088 | 0.38 | YES |
49 | DUSP1 | DUSP1 | DUSP1 | 4548 | 0.087 | 0.38 | YES |
50 | PTPRU | PTPRU | PTPRU | 4560 | 0.086 | 0.38 | YES |
51 | PFKFB4 | PFKFB4 | PFKFB4 | 4581 | 0.085 | 0.39 | YES |
52 | LGALS1 | LGALS1 | LGALS1 | 4582 | 0.085 | 0.39 | YES |
53 | IGFBP3 | IGFBP3 | IGFBP3 | 4597 | 0.084 | 0.4 | YES |
54 | NDRG2 | NDRG2 | NDRG2 | 4600 | 0.084 | 0.4 | YES |
55 | MAP2K6 | MAP2K6 | MAP2K6 | 4684 | 0.08 | 0.4 | YES |
56 | LARP6 | LARP6 | LARP6 | 4740 | 0.078 | 0.4 | YES |
57 | FAM84A | FAM84A | FAM84A | 4755 | 0.078 | 0.41 | YES |
58 | SESN2 | SESN2 | SESN2 | 4771 | 0.077 | 0.41 | YES |
59 | PEA15 | PEA15 | PEA15 | 4783 | 0.076 | 0.42 | YES |
60 | EHD2 | EHD2 | EHD2 | 4800 | 0.076 | 0.42 | YES |
61 | LRP1 | LRP1 | LRP1 | 4971 | 0.069 | 0.41 | NO |
62 | SGCE | SGCE | SGCE | 5147 | 0.063 | 0.41 | NO |
63 | UPP1 | UPP1 | UPP1 | 5223 | 0.061 | 0.41 | NO |
64 | IFI30 | IFI30 | IFI30 | 5433 | 0.054 | 0.4 | NO |
65 | ZFP36 | ZFP36 | ZFP36 | 5469 | 0.053 | 0.4 | NO |
66 | TMEM38A | TMEM38A | TMEM38A | 5519 | 0.052 | 0.4 | NO |
67 | MESDC1 | MESDC1 | MESDC1 | 5534 | 0.051 | 0.4 | NO |
68 | GADD45B | GADD45B | GADD45B | 5661 | 0.048 | 0.4 | NO |
69 | PRODH | PRODH | PRODH | 5687 | 0.047 | 0.4 | NO |
70 | PIGU | PIGU | PIGU | 5857 | 0.043 | 0.39 | NO |
71 | PI4K2A | PI4K2A | PI4K2A | 5861 | 0.043 | 0.39 | NO |
72 | PLIN2 | PLIN2 | PLIN2 | 5869 | 0.043 | 0.4 | NO |
73 | CD9 | CD9 | CD9 | 5911 | 0.042 | 0.4 | NO |
74 | SNX10 | SNX10 | SNX10 | 5967 | 0.041 | 0.4 | NO |
75 | GSTA1 | GSTA1 | GSTA1 | 5968 | 0.041 | 0.4 | NO |
76 | SEPT2 | SEPT2 | SEPT2 | 5977 | 0.041 | 0.4 | NO |
77 | CPNE1 | CPNE1 | CPNE1 | 5990 | 0.04 | 0.4 | NO |
78 | SOD2 | SOD2 | SOD2 | 5995 | 0.04 | 0.4 | NO |
79 | SPRYD3 | SPRYD3 | SPRYD3 | 6049 | 0.039 | 0.4 | NO |
80 | SNTA1 | SNTA1 | SNTA1 | 6067 | 0.039 | 0.4 | NO |
81 | CC2D1A | CC2D1A | CC2D1A | 6080 | 0.039 | 0.41 | NO |
82 | PIN4 | PIN4 | PIN4 | 6180 | 0.037 | 0.4 | NO |
83 | SYNC | SYNC | SYNC | 6205 | 0.036 | 0.4 | NO |
84 | H3F3B | H3F3B | H3F3B | 6352 | 0.034 | 0.4 | NO |
85 | ARHGAP19 | ARHGAP19 | ARHGAP19 | 6379 | 0.033 | 0.4 | NO |
86 | CD2BP2 | CD2BP2 | CD2BP2 | 6451 | 0.032 | 0.4 | NO |
87 | RAB20 | RAB20 | RAB20 | 6487 | 0.032 | 0.4 | NO |
88 | MSMO1 | MSMO1 | MSMO1 | 6517 | 0.031 | 0.4 | NO |
89 | PSMB10 | PSMB10 | PSMB10 | 6540 | 0.031 | 0.4 | NO |
90 | SPATA20 | SPATA20 | SPATA20 | 6722 | 0.029 | 0.39 | NO |
91 | MAP1LC3B | MAP1LC3B | MAP1LC3B | 6836 | 0.027 | 0.38 | NO |
92 | SERGEF | SERGEF | SERGEF | 6855 | 0.027 | 0.38 | NO |
93 | BNIP3L | BNIP3L | BNIP3L | 6971 | 0.025 | 0.38 | NO |
94 | ALKBH5 | ALKBH5 | ALKBH5 | 6977 | 0.025 | 0.38 | NO |
95 | NFKBIA | NFKBIA | NFKBIA | 6978 | 0.025 | 0.38 | NO |
96 | TSKU | TSKU | TSKU | 6981 | 0.025 | 0.38 | NO |
97 | HOXA4 | HOXA4 | HOXA4 | 6989 | 0.025 | 0.38 | NO |
98 | SDC4 | SDC4 | SDC4 | 7000 | 0.025 | 0.38 | NO |
99 | TRNAU1AP | TRNAU1AP | TRNAU1AP | 7137 | 0.024 | 0.38 | NO |
100 | SAP30BP | SAP30BP | SAP30BP | 7154 | 0.023 | 0.38 | NO |
101 | C1orf35 | C1orf35 | C1orf35 | 7175 | 0.023 | 0.38 | NO |
102 | RHBDD3 | RHBDD3 | RHBDD3 | 7178 | 0.023 | 0.38 | NO |
103 | FAM162A | FAM162A | FAM162A | 7222 | 0.023 | 0.38 | NO |
104 | PEX26 | PEX26 | PEX26 | 7231 | 0.023 | 0.38 | NO |
105 | NUCKS1 | NUCKS1 | NUCKS1 | 7254 | 0.022 | 0.38 | NO |
106 | NUPR1 | NUPR1 | NUPR1 | 7282 | 0.022 | 0.38 | NO |
107 | ASPH | ASPH | ASPH | 7286 | 0.022 | 0.38 | NO |
108 | PPP1R15A | PPP1R15A | PPP1R15A | 7342 | 0.022 | 0.38 | NO |
109 | SPAG7 | SPAG7 | SPAG7 | 7347 | 0.022 | 0.38 | NO |
110 | DTX3L | DTX3L | DTX3L | 7429 | 0.021 | 0.38 | NO |
111 | DHCR7 | DHCR7 | DHCR7 | 7561 | 0.019 | 0.37 | NO |
112 | TCEA3 | TCEA3 | TCEA3 | 7670 | 0.018 | 0.37 | NO |
113 | FOSL2 | FOSL2 | FOSL2 | 7675 | 0.018 | 0.37 | NO |
114 | SLC3A2 | SLC3A2 | SLC3A2 | 7681 | 0.018 | 0.37 | NO |
115 | GM2A | GM2A | GM2A | 7695 | 0.018 | 0.37 | NO |
116 | ZNF395 | ZNF395 | ZNF395 | 7739 | 0.018 | 0.37 | NO |
117 | C19orf53 | C19orf53 | C19orf53 | 7773 | 0.017 | 0.37 | NO |
118 | STOM | STOM | STOM | 7800 | 0.017 | 0.37 | NO |
119 | OBSL1 | OBSL1 | OBSL1 | 7811 | 0.017 | 0.37 | NO |
120 | HSP90B1 | HSP90B1 | HSP90B1 | 7830 | 0.017 | 0.37 | NO |
121 | SQLE | SQLE | SQLE | 7839 | 0.017 | 0.37 | NO |
122 | FTH1 | FTH1 | FTH1 | 7884 | 0.016 | 0.36 | NO |
123 | RFX3 | RFX3 | RFX3 | 7943 | 0.016 | 0.36 | NO |
124 | IMP3 | IMP3 | IMP3 | 7973 | 0.016 | 0.36 | NO |
125 | HSPA5 | HSPA5 | HSPA5 | 8020 | 0.015 | 0.36 | NO |
126 | CDK8 | CDK8 | CDK8 | 8027 | 0.015 | 0.36 | NO |
127 | DDX19B | DDX19B | DDX19B | 8106 | 0.014 | 0.36 | NO |
128 | AGPAT2 | AGPAT2 | AGPAT2 | 8183 | 0.014 | 0.35 | NO |
129 | CDC34 | CDC34 | CDC34 | 8209 | 0.014 | 0.35 | NO |
130 | DDX41 | DDX41 | DDX41 | 8258 | 0.013 | 0.35 | NO |
131 | CNNM4 | CNNM4 | CNNM4 | 8264 | 0.013 | 0.35 | NO |
132 | C14orf2 | C14orf2 | C14orf2 | 8312 | 0.013 | 0.35 | NO |
133 | MVK | MVK | MVK | 8325 | 0.013 | 0.35 | NO |
134 | RER1 | RER1 | RER1 | 8363 | 0.012 | 0.35 | NO |
135 | PLCD1 | PLCD1 | PLCD1 | 8493 | 0.012 | 0.34 | NO |
136 | FASN | FASN | FASN | 8547 | 0.011 | 0.34 | NO |
137 | LAMC1 | LAMC1 | LAMC1 | 8560 | 0.011 | 0.34 | NO |
138 | PIM2 | PIM2 | PIM2 | 8563 | 0.011 | 0.34 | NO |
139 | LSR | LSR | LSR | 8564 | 0.011 | 0.34 | NO |
140 | PIP4K2B | PIP4K2B | PIP4K2B | 8570 | 0.011 | 0.34 | NO |
141 | P4HB | P4HB | P4HB | 8639 | 0.01 | 0.34 | NO |
142 | AP3M2 | AP3M2 | AP3M2 | 8642 | 0.01 | 0.34 | NO |
143 | BLVRB | BLVRB | BLVRB | 8664 | 0.01 | 0.34 | NO |
144 | CTSO | CTSO | CTSO | 8746 | 0.0095 | 0.34 | NO |
145 | NIT1 | NIT1 | NIT1 | 8785 | 0.0091 | 0.33 | NO |
146 | PLAGL2 | PLAGL2 | PLAGL2 | 8801 | 0.0089 | 0.33 | NO |
147 | ARHGEF2 | ARHGEF2 | ARHGEF2 | 8802 | 0.0089 | 0.33 | NO |
148 | SLC30A1 | SLC30A1 | SLC30A1 | 8942 | 0.008 | 0.33 | NO |
149 | MAPK7 | MAPK7 | MAPK7 | 8953 | 0.0078 | 0.33 | NO |
150 | MCL1 | MCL1 | MCL1 | 8970 | 0.0077 | 0.32 | NO |
151 | ARPC1A | ARPC1A | ARPC1A | 9111 | 0.0068 | 0.32 | NO |
152 | RBKS | RBKS | RBKS | 9128 | 0.0066 | 0.32 | NO |
153 | GNPDA1 | GNPDA1 | GNPDA1 | 9157 | 0.0064 | 0.32 | NO |
154 | ZFP36L1 | ZFP36L1 | ZFP36L1 | 9196 | 0.0061 | 0.31 | NO |
155 | MYH9 | MYH9 | MYH9 | 9219 | 0.006 | 0.31 | NO |
156 | VAPB | VAPB | VAPB | 9228 | 0.0059 | 0.31 | NO |
157 | MLF1 | MLF1 | MLF1 | 9286 | 0.0055 | 0.31 | NO |
158 | GXYLT1 | GXYLT1 | GXYLT1 | 9320 | 0.0052 | 0.31 | NO |
159 | MOAP1 | MOAP1 | MOAP1 | 9390 | 0.0048 | 0.3 | NO |
160 | ADAR | ADAR | ADAR | 9463 | 0.0042 | 0.3 | NO |
161 | TUBA1B | TUBA1B | TUBA1B | 9466 | 0.0042 | 0.3 | NO |
162 | SNX9 | SNX9 | SNX9 | 9545 | 0.0036 | 0.3 | NO |
163 | AP2B1 | AP2B1 | AP2B1 | 9599 | 0.0033 | 0.3 | NO |
164 | RALGDS | RALGDS | RALGDS | 9623 | 0.0031 | 0.29 | NO |
165 | UBE2O | UBE2O | UBE2O | 9678 | 0.0028 | 0.29 | NO |
166 | MUT | MUT | MUT | 9808 | 0.0018 | 0.28 | NO |
167 | ADAM10 | ADAM10 | ADAM10 | 9935 | 0.00098 | 0.28 | NO |
168 | SERTAD2 | SERTAD2 | SERTAD2 | 10070 | -0.000052 | 0.27 | NO |
169 | NCL | NCL | NCL | 10179 | -0.00073 | 0.26 | NO |
170 | STAU1 | STAU1 | STAU1 | 10191 | -0.00078 | 0.26 | NO |
171 | PFDN1 | PFDN1 | PFDN1 | 10197 | -0.00081 | 0.26 | NO |
172 | HIF1A | HIF1A | HIF1A | 10285 | -0.0014 | 0.26 | NO |
173 | YWHAZ | YWHAZ | YWHAZ | 10331 | -0.0017 | 0.26 | NO |
174 | RNF114 | RNF114 | RNF114 | 10333 | -0.0018 | 0.26 | NO |
175 | PTP4A2 | PTP4A2 | PTP4A2 | 10337 | -0.0018 | 0.26 | NO |
176 | SDCBP | SDCBP | SDCBP | 10353 | -0.0019 | 0.25 | NO |
177 | BSG | BSG | BSG | 10367 | -0.0019 | 0.25 | NO |
178 | GRB10 | GRB10 | GRB10 | 10440 | -0.0025 | 0.25 | NO |
179 | ADD3 | ADD3 | ADD3 | 10450 | -0.0026 | 0.25 | NO |
180 | SYF2 | SYF2 | SYF2 | 10470 | -0.0027 | 0.25 | NO |
181 | ATF7IP | ATF7IP | ATF7IP | 10481 | -0.0027 | 0.25 | NO |
182 | RPL29 | RPL29 | RPL29 | 10492 | -0.0029 | 0.25 | NO |
183 | UBE2H | UBE2H | UBE2H | 10606 | -0.0036 | 0.24 | NO |
184 | XPNPEP1 | XPNPEP1 | XPNPEP1 | 10628 | -0.0037 | 0.24 | NO |
185 | NARS | NARS | NARS | 10672 | -0.004 | 0.24 | NO |
186 | KDM2B | KDM2B | KDM2B | 10705 | -0.0042 | 0.24 | NO |
187 | SGPL1 | SGPL1 | SGPL1 | 10728 | -0.0044 | 0.24 | NO |
188 | PKD1 | PKD1 | PKD1 | 10778 | -0.0046 | 0.23 | NO |
189 | RPS27L | RPS27L | RPS27L | 10782 | -0.0046 | 0.23 | NO |
190 | CDC42 | CDC42 | CDC42 | 10785 | -0.0047 | 0.23 | NO |
191 | PPP1R11 | PPP1R11 | PPP1R11 | 10792 | -0.0047 | 0.23 | NO |
192 | RYBP | RYBP | RYBP | 10901 | -0.0055 | 0.23 | NO |
193 | ZCCHC3 | ZCCHC3 | ZCCHC3 | 11146 | -0.0072 | 0.22 | NO |
194 | YPEL5 | YPEL5 | YPEL5 | 11214 | -0.0078 | 0.21 | NO |
195 | SLC35E1 | SLC35E1 | SLC35E1 | 11247 | -0.008 | 0.21 | NO |
196 | CECR5 | CECR5 | CECR5 | 11295 | -0.0082 | 0.21 | NO |
197 | TMEM30A | TMEM30A | TMEM30A | 11304 | -0.0083 | 0.21 | NO |
198 | AFF4 | AFF4 | AFF4 | 11353 | -0.0086 | 0.21 | NO |
199 | CANX | CANX | CANX | 11362 | -0.0087 | 0.21 | NO |
200 | NMT1 | NMT1 | NMT1 | 11389 | -0.0088 | 0.2 | NO |
201 | MED10 | MED10 | MED10 | 11392 | -0.0089 | 0.2 | NO |
202 | KLHL36 | KLHL36 | KLHL36 | 11413 | -0.009 | 0.2 | NO |
203 | USP9X | USP9X | USP9X | 11462 | -0.0093 | 0.2 | NO |
204 | IFNGR1 | IFNGR1 | IFNGR1 | 11520 | -0.0097 | 0.2 | NO |
205 | HNRNPU | HNRNPU | HNRNPU | 11559 | -0.01 | 0.2 | NO |
206 | WIPF2 | WIPF2 | WIPF2 | 11591 | -0.01 | 0.2 | NO |
207 | NOL3 | NOL3 | NOL3 | 11642 | -0.011 | 0.2 | NO |
208 | SIRPA | SIRPA | SIRPA | 11703 | -0.011 | 0.19 | NO |
209 | KCMF1 | KCMF1 | KCMF1 | 11722 | -0.011 | 0.19 | NO |
210 | ORMDL1 | ORMDL1 | ORMDL1 | 11724 | -0.011 | 0.19 | NO |
211 | SCD | SCD | SCD | 11873 | -0.012 | 0.18 | NO |
212 | RPL12 | RPL12 | RPL12 | 11897 | -0.012 | 0.18 | NO |
213 | EIF2S2 | EIF2S2 | EIF2S2 | 11903 | -0.012 | 0.18 | NO |
214 | IMMP2L | IMMP2L | IMMP2L | 11958 | -0.012 | 0.18 | NO |
215 | ARL1 | ARL1 | ARL1 | 11971 | -0.013 | 0.18 | NO |
216 | MFGE8 | MFGE8 | MFGE8 | 11980 | -0.013 | 0.18 | NO |
217 | ANKRD17 | ANKRD17 | ANKRD17 | 11990 | -0.013 | 0.18 | NO |
218 | STAMBP | STAMBP | STAMBP | 12001 | -0.013 | 0.18 | NO |
219 | KPNB1 | KPNB1 | KPNB1 | 12170 | -0.014 | 0.18 | NO |
220 | SERBP1 | SERBP1 | SERBP1 | 12249 | -0.014 | 0.17 | NO |
221 | A2M | A2M | A2M | 12276 | -0.015 | 0.17 | NO |
222 | RNF146 | RNF146 | RNF146 | 12421 | -0.016 | 0.16 | NO |
223 | NAP1L1 | NAP1L1 | NAP1L1 | 12560 | -0.016 | 0.16 | NO |
224 | RPL10 | RPL10 | RPL10 | 12575 | -0.017 | 0.16 | NO |
225 | ATP1B3 | ATP1B3 | ATP1B3 | 12603 | -0.017 | 0.16 | NO |
226 | KHDRBS3 | KHDRBS3 | KHDRBS3 | 12655 | -0.017 | 0.15 | NO |
227 | FBXO8 | FBXO8 | FBXO8 | 12691 | -0.017 | 0.15 | NO |
228 | AK2 | AK2 | AK2 | 12694 | -0.017 | 0.15 | NO |
229 | ANXA4 | ANXA4 | ANXA4 | 12716 | -0.018 | 0.15 | NO |
230 | RDH14 | RDH14 | RDH14 | 12732 | -0.018 | 0.16 | NO |
231 | ZFP91 | ZFP91 | ZFP91 | 12736 | -0.018 | 0.16 | NO |
232 | CSDE1 | CSDE1 | CSDE1 | 12824 | -0.018 | 0.15 | NO |
233 | PSMD6 | PSMD6 | PSMD6 | 12931 | -0.019 | 0.15 | NO |
234 | PJA2 | PJA2 | PJA2 | 12938 | -0.019 | 0.15 | NO |
235 | FAM189A2 | FAM189A2 | FAM189A2 | 12970 | -0.02 | 0.15 | NO |
236 | ARHGEF1 | ARHGEF1 | ARHGEF1 | 12993 | -0.02 | 0.15 | NO |
237 | CPD | CPD | CPD | 13256 | -0.022 | 0.13 | NO |
238 | MARCKS | MARCKS | MARCKS | 13306 | -0.022 | 0.13 | NO |
239 | KLF6 | KLF6 | KLF6 | 13323 | -0.022 | 0.13 | NO |
240 | UGP2 | UGP2 | UGP2 | 13380 | -0.023 | 0.13 | NO |
241 | EIF4B | EIF4B | EIF4B | 13459 | -0.023 | 0.13 | NO |
242 | CHPT1 | CHPT1 | CHPT1 | 13467 | -0.023 | 0.13 | NO |
243 | SRRM2 | SRRM2 | SRRM2 | 13476 | -0.023 | 0.13 | NO |
244 | RPL30 | RPL30 | RPL30 | 13495 | -0.023 | 0.13 | NO |
245 | ANAPC10 | ANAPC10 | ANAPC10 | 13551 | -0.024 | 0.13 | NO |
246 | ZBTB47 | ZBTB47 | ZBTB47 | 13568 | -0.024 | 0.13 | NO |
247 | KPNA4 | KPNA4 | KPNA4 | 13570 | -0.024 | 0.13 | NO |
248 | HNRNPC | HNRNPC | HNRNPC | 13617 | -0.024 | 0.13 | NO |
249 | LOX | LOX | LOX | 13665 | -0.025 | 0.13 | NO |
250 | TOMM20 | TOMM20 | TOMM20 | 13668 | -0.025 | 0.13 | NO |
251 | IGF2BP2 | IGF2BP2 | IGF2BP2 | 13682 | -0.025 | 0.13 | NO |
252 | G3BP2 | G3BP2 | G3BP2 | 13696 | -0.025 | 0.13 | NO |
253 | GRSF1 | GRSF1 | GRSF1 | 13719 | -0.025 | 0.13 | NO |
254 | GNA13 | GNA13 | GNA13 | 13741 | -0.025 | 0.13 | NO |
255 | DCAF6 | DCAF6 | DCAF6 | 13747 | -0.025 | 0.13 | NO |
256 | TFG | TFG | TFG | 13809 | -0.026 | 0.13 | NO |
257 | RPS3 | RPS3 | RPS3 | 13881 | -0.027 | 0.13 | NO |
258 | RBM12 | RBM12 | RBM12 | 13912 | -0.027 | 0.13 | NO |
259 | ARIH2 | ARIH2 | ARIH2 | 13924 | -0.027 | 0.13 | NO |
260 | CD164 | CD164 | CD164 | 14002 | -0.028 | 0.13 | NO |
261 | BNIP3 | BNIP3 | BNIP3 | 14037 | -0.028 | 0.13 | NO |
262 | MXI1 | MXI1 | MXI1 | 14075 | -0.028 | 0.13 | NO |
263 | UGCG | UGCG | UGCG | 14139 | -0.029 | 0.12 | NO |
264 | CAV1 | CAV1 | CAV1 | 14193 | -0.029 | 0.12 | NO |
265 | C2orf49 | C2orf49 | C2orf49 | 14194 | -0.029 | 0.12 | NO |
266 | EEF1A1 | EEF1A1 | EEF1A1 | 14297 | -0.03 | 0.12 | NO |
267 | SIKE1 | SIKE1 | SIKE1 | 14399 | -0.031 | 0.12 | NO |
268 | PTER | PTER | PTER | 14411 | -0.031 | 0.12 | NO |
269 | GTPBP2 | GTPBP2 | GTPBP2 | 14444 | -0.031 | 0.12 | NO |
270 | PGRMC2 | PGRMC2 | PGRMC2 | 14532 | -0.032 | 0.12 | NO |
271 | P4HA1 | P4HA1 | P4HA1 | 14554 | -0.033 | 0.12 | NO |
272 | UBE2E1 | UBE2E1 | UBE2E1 | 14629 | -0.033 | 0.11 | NO |
273 | WAPAL | WAPAL | WAPAL | 14650 | -0.034 | 0.12 | NO |
274 | YAP1 | YAP1 | YAP1 | 14828 | -0.035 | 0.11 | NO |
275 | SMG1 | SMG1 | SMG1 | 14882 | -0.036 | 0.11 | NO |
276 | TXNIP | TXNIP | TXNIP | 14894 | -0.036 | 0.11 | NO |
277 | SNX4 | SNX4 | SNX4 | 15152 | -0.039 | 0.095 | NO |
278 | BTG1 | BTG1 | BTG1 | 15198 | -0.04 | 0.095 | NO |
279 | PTPN12 | PTPN12 | PTPN12 | 15218 | -0.04 | 0.096 | NO |
280 | SAT1 | SAT1 | SAT1 | 15268 | -0.04 | 0.096 | NO |
281 | HOOK2 | HOOK2 | HOOK2 | 15292 | -0.041 | 0.097 | NO |
282 | SLC30A9 | SLC30A9 | SLC30A9 | 15380 | -0.042 | 0.095 | NO |
283 | GPATCH8 | GPATCH8 | GPATCH8 | 15413 | -0.042 | 0.095 | NO |
284 | NEK6 | NEK6 | NEK6 | 15607 | -0.045 | 0.087 | NO |
285 | STXBP2 | STXBP2 | STXBP2 | 15622 | -0.045 | 0.089 | NO |
286 | EIF1AX | EIF1AX | EIF1AX | 15733 | -0.047 | 0.086 | NO |
287 | TSNAX | TSNAX | TSNAX | 15773 | -0.048 | 0.086 | NO |
288 | RHOF | RHOF | RHOF | 15914 | -0.05 | 0.082 | NO |
289 | RIPK4 | RIPK4 | RIPK4 | 16052 | -0.053 | 0.077 | NO |
290 | RSL24D1 | RSL24D1 | RSL24D1 | 16137 | -0.055 | 0.076 | NO |
291 | MAGT1 | MAGT1 | MAGT1 | 16265 | -0.058 | 0.072 | NO |
292 | NDRG1 | NDRG1 | NDRG1 | 16271 | -0.058 | 0.075 | NO |
293 | CIDEB | CIDEB | CIDEB | 16281 | -0.058 | 0.078 | NO |
294 | RPL9 | RPL9 | RPL9 | 16331 | -0.059 | 0.079 | NO |
295 | IKBIP | IKBIP | IKBIP | 16459 | -0.063 | 0.075 | NO |
296 | PPP1R3C | PPP1R3C | PPP1R3C | 16734 | -0.073 | 0.064 | NO |
297 | ENOSF1 | ENOSF1 | ENOSF1 | 17035 | -0.087 | 0.053 | NO |
298 | ELL2 | ELL2 | ELL2 | 17265 | -0.11 | 0.046 | NO |
Figure S23. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG PENTOSE PHOSPHATE PATHWAY.

Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE PHOSPHATE PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S13. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ADCY8 | ADCY8 | ADCY8 | 322 | 0.66 | 0.061 | YES |
2 | ADCYAP1R1 | ADCYAP1R1 | ADCYAP1R1 | 379 | 0.62 | 0.13 | YES |
3 | PRKCG | PRKCG | PRKCG | 765 | 0.47 | 0.17 | YES |
4 | NTRK1 | NTRK1 | NTRK1 | 934 | 0.42 | 0.21 | YES |
5 | NGF | NGF | NGF | 1095 | 0.38 | 0.25 | YES |
6 | NTRK2 | NTRK2 | NTRK2 | 1244 | 0.36 | 0.28 | YES |
7 | SH3GL2 | SH3GL2 | SH3GL2 | 1246 | 0.36 | 0.32 | YES |
8 | SHC3 | SHC3 | SHC3 | 1314 | 0.35 | 0.36 | YES |
9 | PDE1A | PDE1A | PDE1A | 1404 | 0.33 | 0.4 | YES |
10 | ADCY1 | ADCY1 | ADCY1 | 1439 | 0.32 | 0.44 | YES |
11 | ADCYAP1 | ADCYAP1 | ADCYAP1 | 1742 | 0.29 | 0.45 | YES |
12 | RIT2 | RIT2 | RIT2 | 1872 | 0.27 | 0.48 | YES |
13 | ADCY5 | ADCY5 | ADCY5 | 2073 | 0.25 | 0.5 | YES |
14 | ADCY2 | ADCY2 | ADCY2 | 2124 | 0.24 | 0.52 | YES |
15 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 2919 | 0.18 | 0.5 | NO |
16 | CDKN1A | CDKN1A | CDKN1A | 3643 | 0.13 | 0.48 | NO |
17 | PRKAR2B | PRKAR2B | PRKAR2B | 3999 | 0.11 | 0.47 | NO |
18 | ADCY4 | ADCY4 | ADCY4 | 4291 | 0.098 | 0.46 | NO |
19 | ITPR2 | ITPR2 | ITPR2 | 5111 | 0.064 | 0.43 | NO |
20 | PIK3R2 | PIK3R2 | PIK3R2 | 5353 | 0.056 | 0.42 | NO |
21 | BAD | BAD | BAD | 5511 | 0.052 | 0.42 | NO |
22 | PDE1B | PDE1B | PDE1B | 5526 | 0.052 | 0.42 | NO |
23 | MAPK3 | MAPK3 | MAPK3 | 5934 | 0.042 | 0.41 | NO |
24 | MAPK11 | MAPK11 | MAPK11 | 6173 | 0.037 | 0.4 | NO |
25 | CAMK4 | CAMK4 | CAMK4 | 6187 | 0.036 | 0.4 | NO |
26 | CALM1 | CALM1 | CALM1 | 6339 | 0.034 | 0.4 | NO |
27 | SHC1 | SHC1 | SHC1 | 6374 | 0.033 | 0.4 | NO |
28 | PRKACA | PRKACA | PRKACA | 6545 | 0.031 | 0.39 | NO |
29 | MLST8 | MLST8 | MLST8 | 6607 | 0.03 | 0.39 | NO |
30 | ADCY3 | ADCY3 | ADCY3 | 6689 | 0.029 | 0.39 | NO |
31 | AP2S1 | AP2S1 | AP2S1 | 6885 | 0.026 | 0.38 | NO |
32 | DNM1 | DNM1 | DNM1 | 6911 | 0.026 | 0.39 | NO |
33 | PPP2R1A | PPP2R1A | PPP2R1A | 6924 | 0.026 | 0.39 | NO |
34 | CALM3 | CALM3 | CALM3 | 7065 | 0.024 | 0.38 | NO |
35 | DUSP4 | DUSP4 | DUSP4 | 7079 | 0.024 | 0.39 | NO |
36 | YWHAB | YWHAB | YWHAB | 7174 | 0.023 | 0.38 | NO |
37 | AKT1S1 | AKT1S1 | AKT1S1 | 7177 | 0.023 | 0.39 | NO |
38 | AKT3 | AKT3 | AKT3 | 7192 | 0.023 | 0.39 | NO |
39 | HRAS | HRAS | HRAS | 7301 | 0.022 | 0.38 | NO |
40 | GSK3A | GSK3A | GSK3A | 7625 | 0.019 | 0.37 | NO |
41 | SRC | SRC | SRC | 7673 | 0.018 | 0.37 | NO |
42 | ADCY7 | ADCY7 | ADCY7 | 7742 | 0.018 | 0.37 | NO |
43 | MAPK13 | MAPK13 | MAPK13 | 7751 | 0.018 | 0.37 | NO |
44 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 7872 | 0.016 | 0.36 | NO |
45 | AP2A1 | AP2A1 | AP2A1 | 7968 | 0.016 | 0.36 | NO |
46 | PLCG1 | PLCG1 | PLCG1 | 8052 | 0.015 | 0.36 | NO |
47 | DNAL4 | DNAL4 | DNAL4 | 8107 | 0.014 | 0.36 | NO |
48 | AP2M1 | AP2M1 | AP2M1 | 8324 | 0.013 | 0.35 | NO |
49 | PRKAR1B | PRKAR1B | PRKAR1B | 8425 | 0.012 | 0.34 | NO |
50 | ADRBK1 | ADRBK1 | ADRBK1 | 8446 | 0.012 | 0.34 | NO |
51 | MDM2 | MDM2 | MDM2 | 8545 | 0.011 | 0.34 | NO |
52 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 8574 | 0.011 | 0.34 | NO |
53 | STAT3 | STAT3 | STAT3 | 8832 | 0.0088 | 0.32 | NO |
54 | MAPK7 | MAPK7 | MAPK7 | 8953 | 0.0078 | 0.32 | NO |
55 | RALB | RALB | RALB | 9065 | 0.0071 | 0.31 | NO |
56 | AKT1 | AKT1 | AKT1 | 9099 | 0.0069 | 0.31 | NO |
57 | PIK3R1 | PIK3R1 | PIK3R1 | 9201 | 0.0061 | 0.31 | NO |
58 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 9226 | 0.0059 | 0.31 | NO |
59 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 9336 | 0.0052 | 0.3 | NO |
60 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 9479 | 0.0041 | 0.29 | NO |
61 | MAPK12 | MAPK12 | MAPK12 | 9570 | 0.0035 | 0.29 | NO |
62 | AP2A2 | AP2A2 | AP2A2 | 9578 | 0.0034 | 0.29 | NO |
63 | AP2B1 | AP2B1 | AP2B1 | 9599 | 0.0033 | 0.29 | NO |
64 | CASP9 | CASP9 | CASP9 | 9617 | 0.0032 | 0.29 | NO |
65 | RALGDS | RALGDS | RALGDS | 9623 | 0.0031 | 0.29 | NO |
66 | GRB2 | GRB2 | GRB2 | 9778 | 0.0021 | 0.28 | NO |
67 | FOXO3 | FOXO3 | FOXO3 | 9791 | 0.002 | 0.28 | NO |
68 | RIT1 | RIT1 | RIT1 | 9820 | 0.0018 | 0.28 | NO |
69 | IRS2 | IRS2 | IRS2 | 9829 | 0.0017 | 0.28 | NO |
70 | FOXO1 | FOXO1 | FOXO1 | 10081 | -0.00012 | 0.26 | NO |
71 | PTEN | PTEN | PTEN | 10413 | -0.0023 | 0.25 | NO |
72 | MAP2K5 | MAP2K5 | MAP2K5 | 10431 | -0.0024 | 0.24 | NO |
73 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 10436 | -0.0024 | 0.24 | NO |
74 | MAP2K2 | MAP2K2 | MAP2K2 | 10520 | -0.003 | 0.24 | NO |
75 | SHC2 | SHC2 | SHC2 | 10760 | -0.0045 | 0.23 | NO |
76 | MEF2C | MEF2C | MEF2C | 10835 | -0.0051 | 0.22 | NO |
77 | TRIB3 | TRIB3 | TRIB3 | 10853 | -0.0052 | 0.22 | NO |
78 | KIDINS220 | KIDINS220 | KIDINS220 | 10898 | -0.0055 | 0.22 | NO |
79 | AKT2 | AKT2 | AKT2 | 10968 | -0.0059 | 0.22 | NO |
80 | MEF2A | MEF2A | MEF2A | 11071 | -0.0067 | 0.22 | NO |
81 | DUSP7 | DUSP7 | DUSP7 | 11086 | -0.0068 | 0.22 | NO |
82 | CLTA | CLTA | CLTA | 11199 | -0.0077 | 0.21 | NO |
83 | MAPK1 | MAPK1 | MAPK1 | 11428 | -0.0091 | 0.2 | NO |
84 | PPP2CB | PPP2CB | PPP2CB | 11605 | -0.01 | 0.19 | NO |
85 | MAP2K1 | MAP2K1 | MAP2K1 | 11622 | -0.01 | 0.19 | NO |
86 | PPP2CA | PPP2CA | PPP2CA | 11696 | -0.011 | 0.19 | NO |
87 | RHOA | RHOA | RHOA | 11701 | -0.011 | 0.19 | NO |
88 | CLTC | CLTC | CLTC | 11702 | -0.011 | 0.19 | NO |
89 | SOS1 | SOS1 | SOS1 | 11772 | -0.011 | 0.19 | NO |
90 | FOXO4 | FOXO4 | FOXO4 | 11934 | -0.012 | 0.18 | NO |
91 | CALM2 | CALM2 | CALM2 | 11981 | -0.013 | 0.18 | NO |
92 | DNM2 | DNM2 | DNM2 | 12212 | -0.014 | 0.17 | NO |
93 | ADCY9 | ADCY9 | ADCY9 | 12328 | -0.015 | 0.16 | NO |
94 | DUSP6 | DUSP6 | DUSP6 | 12357 | -0.015 | 0.16 | NO |
95 | PPP2R5D | PPP2R5D | PPP2R5D | 12361 | -0.015 | 0.16 | NO |
96 | RAF1 | RAF1 | RAF1 | 12375 | -0.015 | 0.17 | NO |
97 | ELK1 | ELK1 | ELK1 | 12450 | -0.016 | 0.16 | NO |
98 | PPP2R1B | PPP2R1B | PPP2R1B | 12533 | -0.016 | 0.16 | NO |
99 | KRAS | KRAS | KRAS | 12551 | -0.016 | 0.16 | NO |
100 | RALA | RALA | RALA | 12606 | -0.017 | 0.16 | NO |
101 | PRKCA | PRKCA | PRKCA | 12632 | -0.017 | 0.16 | NO |
102 | PRKAR2A | PRKAR2A | PRKAR2A | 12708 | -0.018 | 0.16 | NO |
103 | PDPK1 | PDPK1 | PDPK1 | 12850 | -0.019 | 0.15 | NO |
104 | THEM4 | THEM4 | THEM4 | 12873 | -0.019 | 0.16 | NO |
105 | BRAF | BRAF | BRAF | 13058 | -0.02 | 0.15 | NO |
106 | CRK | CRK | CRK | 13231 | -0.022 | 0.14 | NO |
107 | CDKN1B | CDKN1B | CDKN1B | 13470 | -0.023 | 0.13 | NO |
108 | RAP1A | RAP1A | RAP1A | 13477 | -0.023 | 0.13 | NO |
109 | MTOR | MTOR | MTOR | 13656 | -0.025 | 0.12 | NO |
110 | NRAS | NRAS | NRAS | 13674 | -0.025 | 0.13 | NO |
111 | RICTOR | RICTOR | RICTOR | 13808 | -0.026 | 0.12 | NO |
112 | PRKACB | PRKACB | PRKACB | 13822 | -0.026 | 0.12 | NO |
113 | IRS1 | IRS1 | IRS1 | 13944 | -0.027 | 0.12 | NO |
114 | TSC2 | TSC2 | TSC2 | 14010 | -0.028 | 0.12 | NO |
115 | CHUK | CHUK | CHUK | 14156 | -0.029 | 0.12 | NO |
116 | PRKCD | PRKCD | PRKCD | 14188 | -0.029 | 0.12 | NO |
117 | PHLPP1 | PHLPP1 | PHLPP1 | 14209 | -0.029 | 0.12 | NO |
118 | CDK1 | CDK1 | CDK1 | 14228 | -0.029 | 0.12 | NO |
119 | MAPK14 | MAPK14 | MAPK14 | 14720 | -0.034 | 0.1 | NO |
120 | FRS2 | FRS2 | FRS2 | 14956 | -0.037 | 0.092 | NO |
121 | ATF1 | ATF1 | ATF1 | 15099 | -0.038 | 0.088 | NO |
122 | PRKCE | PRKCE | PRKCE | 15102 | -0.038 | 0.093 | NO |
123 | DUSP3 | DUSP3 | DUSP3 | 15202 | -0.04 | 0.092 | NO |
124 | NR4A1 | NR4A1 | NR4A1 | 15312 | -0.041 | 0.091 | NO |
125 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 15319 | -0.041 | 0.096 | NO |
126 | CREB1 | CREB1 | CREB1 | 15370 | -0.042 | 0.098 | NO |
127 | PRKAR1A | PRKAR1A | PRKAR1A | 15550 | -0.044 | 0.093 | NO |
128 | ITPR3 | ITPR3 | ITPR3 | 15575 | -0.045 | 0.097 | NO |
129 | ADCY6 | ADCY6 | ADCY6 | 16150 | -0.055 | 0.072 | NO |
130 | PIK3CB | PIK3CB | PIK3CB | 16165 | -0.056 | 0.078 | NO |
131 | PIK3CA | PIK3CA | PIK3CA | 16220 | -0.057 | 0.082 | NO |
132 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 16829 | -0.077 | 0.057 | NO |
133 | ADORA2A | ADORA2A | ADORA2A | 17244 | -0.1 | 0.047 | NO |
Figure S25. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM.

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S14. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MYOC | MYOC | MYOC | 177 | 0.77 | 0.25 | YES |
2 | KCNJ9 | KCNJ9 | KCNJ9 | 507 | 0.56 | 0.42 | YES |
3 | SCG5 | SCG5 | SCG5 | 543 | 0.54 | 0.6 | YES |
4 | MAP1B | MAP1B | MAP1B | 1000 | 0.41 | 0.71 | YES |
5 | FOLH1 | FOLH1 | FOLH1 | 4029 | 0.11 | 0.58 | NO |
6 | PAM | PAM | PAM | 4892 | 0.072 | 0.56 | NO |
7 | COL4A1 | COL4A1 | COL4A1 | 5494 | 0.052 | 0.54 | NO |
8 | GNB1 | GNB1 | GNB1 | 5809 | 0.044 | 0.54 | NO |
9 | PRDX2 | PRDX2 | PRDX2 | 6576 | 0.03 | 0.5 | NO |
10 | RGS19 | RGS19 | RGS19 | 7296 | 0.022 | 0.47 | NO |
11 | PTTG1 | PTTG1 | PTTG1 | 8160 | 0.014 | 0.43 | NO |
12 | OCEL1 | OCEL1 | OCEL1 | 8196 | 0.014 | 0.43 | NO |
13 | ALAD | ALAD | ALAD | 10178 | -0.00072 | 0.32 | NO |
14 | CAP1 | CAP1 | CAP1 | 10199 | -0.00083 | 0.32 | NO |
15 | MEF2C | MEF2C | MEF2C | 10835 | -0.0051 | 0.29 | NO |
16 | C4orf3 | C4orf3 | C4orf3 | 10945 | -0.0058 | 0.28 | NO |
17 | TOX4 | TOX4 | TOX4 | 11147 | -0.0072 | 0.28 | NO |
18 | PSTK | PSTK | PSTK | 11344 | -0.0085 | 0.27 | NO |
19 | MTIF2 | MTIF2 | MTIF2 | 11382 | -0.0088 | 0.27 | NO |
20 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 12333 | -0.015 | 0.22 | NO |
21 | ACAA1 | ACAA1 | ACAA1 | 12501 | -0.016 | 0.22 | NO |
22 | BCAT2 | BCAT2 | BCAT2 | 12986 | -0.02 | 0.2 | NO |
23 | TULP3 | TULP3 | TULP3 | 13199 | -0.021 | 0.19 | NO |
24 | THUMPD1 | THUMPD1 | THUMPD1 | 13518 | -0.024 | 0.18 | NO |
25 | CPSF2 | CPSF2 | CPSF2 | 13931 | -0.027 | 0.17 | NO |
26 | VPS52 | VPS52 | VPS52 | 14018 | -0.028 | 0.17 | NO |
27 | RPP14 | RPP14 | RPP14 | 14638 | -0.034 | 0.15 | NO |
28 | PDXDC1 | PDXDC1 | PDXDC1 | 15008 | -0.037 | 0.14 | NO |
29 | C5orf34 | C5orf34 | C5orf34 | 15029 | -0.038 | 0.15 | NO |
30 | PHLDA1 | PHLDA1 | PHLDA1 | 15599 | -0.045 | 0.14 | NO |
Figure S27. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG GALACTOSE METABOLISM.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GALACTOSE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S15. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | GRIA1 | GRIA1 | GRIA1 | 27 | 1 | 0.23 | YES |
2 | SYT1 | SYT1 | SYT1 | 37 | 0.97 | 0.46 | YES |
3 | VSNL1 | VSNL1 | VSNL1 | 915 | 0.42 | 0.51 | YES |
4 | PTGDS | PTGDS | PTGDS | 1241 | 0.36 | 0.58 | YES |
5 | ACHE | ACHE | ACHE | 1972 | 0.26 | 0.6 | YES |
6 | CPE | CPE | CPE | 2174 | 0.24 | 0.64 | YES |
7 | ATP1B2 | ATP1B2 | ATP1B2 | 2338 | 0.22 | 0.69 | YES |
8 | DLG4 | DLG4 | DLG4 | 3673 | 0.13 | 0.64 | NO |
9 | EPAS1 | EPAS1 | EPAS1 | 5998 | 0.04 | 0.52 | NO |
10 | ATP9A | ATP9A | ATP9A | 6162 | 0.037 | 0.52 | NO |
11 | GDI1 | GDI1 | GDI1 | 6168 | 0.037 | 0.53 | NO |
12 | GNAI2 | GNAI2 | GNAI2 | 6228 | 0.036 | 0.54 | NO |
13 | APOE | APOE | APOE | 6386 | 0.033 | 0.54 | NO |
14 | DNM1 | DNM1 | DNM1 | 6911 | 0.026 | 0.51 | NO |
15 | PPP2R1A | PPP2R1A | PPP2R1A | 6924 | 0.026 | 0.52 | NO |
16 | UBC | UBC | UBC | 7091 | 0.024 | 0.52 | NO |
17 | MAGED1 | MAGED1 | MAGED1 | 7207 | 0.023 | 0.51 | NO |
18 | PLD3 | PLD3 | PLD3 | 7302 | 0.022 | 0.51 | NO |
19 | GPX4 | GPX4 | GPX4 | 7325 | 0.022 | 0.52 | NO |
20 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 7494 | 0.02 | 0.51 | NO |
21 | STIP1 | STIP1 | STIP1 | 7892 | 0.016 | 0.5 | NO |
22 | ATP6V0C | ATP6V0C | ATP6V0C | 7909 | 0.016 | 0.5 | NO |
23 | CAMK2G | CAMK2G | CAMK2G | 7933 | 0.016 | 0.5 | NO |
24 | AP2M1 | AP2M1 | AP2M1 | 8324 | 0.013 | 0.48 | NO |
25 | SARS | SARS | SARS | 8652 | 0.01 | 0.47 | NO |
26 | DNAJA2 | DNAJA2 | DNAJA2 | 8744 | 0.0095 | 0.46 | NO |
27 | EPRS | EPRS | EPRS | 8849 | 0.0086 | 0.46 | NO |
28 | DHX30 | DHX30 | DHX30 | 8999 | 0.0075 | 0.45 | NO |
29 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 9021 | 0.0073 | 0.45 | NO |
30 | DDB1 | DDB1 | DDB1 | 10035 | 0.0002 | 0.4 | NO |
31 | CS | CS | CS | 10631 | -0.0037 | 0.37 | NO |
32 | ATP2A2 | ATP2A2 | ATP2A2 | 10997 | -0.0061 | 0.35 | NO |
33 | CANX | CANX | CANX | 11362 | -0.0087 | 0.33 | NO |
34 | VTI1B | VTI1B | VTI1B | 11948 | -0.012 | 0.3 | NO |
35 | ACO2 | ACO2 | ACO2 | 12625 | -0.017 | 0.27 | NO |
36 | PRKACB | PRKACB | PRKACB | 13822 | -0.026 | 0.21 | NO |
37 | MGAT2 | MGAT2 | MGAT2 | 14229 | -0.029 | 0.19 | NO |
38 | EEF1A1 | EEF1A1 | EEF1A1 | 14297 | -0.03 | 0.19 | NO |
39 | RAB18 | RAB18 | RAB18 | 14590 | -0.033 | 0.18 | NO |
40 | KIF5B | KIF5B | KIF5B | 14948 | -0.037 | 0.17 | NO |
Figure S29. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S16. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | GFAP | GFAP | GFAP | 113 | 0.84 | 0.043 | YES |
2 | PCP4 | PCP4 | PCP4 | 209 | 0.74 | 0.082 | YES |
3 | RGN | RGN | RGN | 279 | 0.69 | 0.12 | YES |
4 | CHI3L1 | CHI3L1 | CHI3L1 | 365 | 0.63 | 0.15 | YES |
5 | WFDC2 | WFDC2 | WFDC2 | 369 | 0.63 | 0.19 | YES |
6 | PVALB | PVALB | PVALB | 458 | 0.58 | 0.22 | YES |
7 | DKK3 | DKK3 | DKK3 | 533 | 0.55 | 0.25 | YES |
8 | TRDN | TRDN | TRDN | 553 | 0.54 | 0.28 | YES |
9 | PSG1 | PSG1 | PSG1 | 778 | 0.46 | 0.29 | YES |
10 | CLDN10 | CLDN10 | CLDN10 | 806 | 0.45 | 0.32 | YES |
11 | BDNF | BDNF | BDNF | 862 | 0.44 | 0.34 | YES |
12 | BCL2A1 | BCL2A1 | BCL2A1 | 890 | 0.43 | 0.36 | YES |
13 | DDAH1 | DDAH1 | DDAH1 | 1261 | 0.35 | 0.36 | YES |
14 | ALAS2 | ALAS2 | ALAS2 | 1519 | 0.31 | 0.37 | YES |
15 | CYP3A7 | CYP3A7 | CYP3A7 | 1910 | 0.26 | 0.36 | YES |
16 | ROPN1L | ROPN1L | ROPN1L | 1932 | 0.26 | 0.38 | YES |
17 | MNDA | MNDA | MNDA | 1968 | 0.26 | 0.39 | YES |
18 | FGR | FGR | FGR | 1987 | 0.26 | 0.4 | YES |
19 | CD8A | CD8A | CD8A | 2074 | 0.25 | 0.41 | YES |
20 | CACNA1D | CACNA1D | CACNA1D | 2104 | 0.24 | 0.42 | YES |
21 | SLAMF8 | SLAMF8 | SLAMF8 | 2265 | 0.23 | 0.43 | YES |
22 | IGFBP6 | IGFBP6 | IGFBP6 | 2298 | 0.22 | 0.44 | YES |
23 | ROBO2 | ROBO2 | ROBO2 | 2303 | 0.22 | 0.45 | YES |
24 | CSF3R | CSF3R | CSF3R | 2423 | 0.21 | 0.46 | YES |
25 | TUBA4A | TUBA4A | TUBA4A | 2457 | 0.21 | 0.47 | YES |
26 | IL2RB | IL2RB | IL2RB | 2511 | 0.2 | 0.48 | YES |
27 | SLC6A12 | SLC6A12 | SLC6A12 | 2553 | 0.2 | 0.49 | YES |
28 | PBX1 | PBX1 | PBX1 | 2705 | 0.19 | 0.49 | YES |
29 | SPINT2 | SPINT2 | SPINT2 | 2891 | 0.18 | 0.49 | YES |
30 | IGF2 | IGF2 | IGF2 | 2937 | 0.17 | 0.5 | YES |
31 | EPB42 | EPB42 | EPB42 | 3084 | 0.16 | 0.5 | YES |
32 | GGT5 | GGT5 | GGT5 | 3469 | 0.14 | 0.49 | NO |
33 | SLC16A2 | SLC16A2 | SLC16A2 | 3569 | 0.14 | 0.49 | NO |
34 | PDE6G | PDE6G | PDE6G | 3651 | 0.13 | 0.49 | NO |
35 | TM4SF1 | TM4SF1 | TM4SF1 | 3891 | 0.12 | 0.49 | NO |
36 | ECE1 | ECE1 | ECE1 | 3949 | 0.12 | 0.49 | NO |
37 | CCL14 | CCL14 | CCL14 | 4148 | 0.1 | 0.49 | NO |
38 | SGK1 | SGK1 | SGK1 | 4150 | 0.1 | 0.49 | NO |
39 | PLEKHG5 | PLEKHG5 | PLEKHG5 | 4982 | 0.069 | 0.45 | NO |
40 | HS6ST1 | HS6ST1 | HS6ST1 | 5079 | 0.065 | 0.45 | NO |
41 | LRRC17 | LRRC17 | LRRC17 | 5177 | 0.062 | 0.45 | NO |
42 | ARHGDIB | ARHGDIB | ARHGDIB | 5390 | 0.056 | 0.44 | NO |
43 | DGKA | DGKA | DGKA | 5399 | 0.055 | 0.44 | NO |
44 | ST14 | ST14 | ST14 | 5498 | 0.052 | 0.44 | NO |
45 | DHCR24 | DHCR24 | DHCR24 | 5598 | 0.049 | 0.44 | NO |
46 | TIAF1 | TIAF1 | TIAF1 | 5666 | 0.048 | 0.44 | NO |
47 | AMMECR1 | AMMECR1 | AMMECR1 | 5672 | 0.048 | 0.44 | NO |
48 | ITSN1 | ITSN1 | ITSN1 | 5835 | 0.044 | 0.43 | NO |
49 | APOL6 | APOL6 | APOL6 | 5932 | 0.042 | 0.43 | NO |
50 | RND3 | RND3 | RND3 | 6076 | 0.039 | 0.42 | NO |
51 | TMSB10 | TMSB10 | TMSB10 | 6109 | 0.038 | 0.42 | NO |
52 | H3F3B | H3F3B | H3F3B | 6352 | 0.034 | 0.41 | NO |
53 | RALY | RALY | RALY | 6357 | 0.034 | 0.41 | NO |
54 | IL13RA1 | IL13RA1 | IL13RA1 | 6389 | 0.033 | 0.41 | NO |
55 | PTOV1 | PTOV1 | PTOV1 | 6457 | 0.032 | 0.41 | NO |
56 | DRAP1 | DRAP1 | DRAP1 | 6470 | 0.032 | 0.41 | NO |
57 | WWTR1 | WWTR1 | WWTR1 | 6528 | 0.031 | 0.41 | NO |
58 | CDC20 | CDC20 | CDC20 | 6580 | 0.03 | 0.41 | NO |
59 | AIP | AIP | AIP | 6590 | 0.03 | 0.41 | NO |
60 | GABBR1 | GABBR1 | GABBR1 | 6690 | 0.029 | 0.41 | NO |
61 | SMARCB1 | SMARCB1 | SMARCB1 | 6696 | 0.029 | 0.41 | NO |
62 | POLR2J | POLR2J | POLR2J | 6732 | 0.028 | 0.41 | NO |
63 | USP6NL | USP6NL | USP6NL | 6788 | 0.028 | 0.41 | NO |
64 | TNRC6B | TNRC6B | TNRC6B | 6867 | 0.027 | 0.4 | NO |
65 | PDAP1 | PDAP1 | PDAP1 | 6980 | 0.025 | 0.4 | NO |
66 | RALGAPA2 | RALGAPA2 | RALGAPA2 | 6996 | 0.025 | 0.4 | NO |
67 | SDC4 | SDC4 | SDC4 | 7000 | 0.025 | 0.4 | NO |
68 | NHSL1 | NHSL1 | NHSL1 | 7006 | 0.025 | 0.4 | NO |
69 | BEX2 | BEX2 | BEX2 | 7109 | 0.024 | 0.4 | NO |
70 | IRF9 | IRF9 | IRF9 | 7147 | 0.023 | 0.4 | NO |
71 | MADD | MADD | MADD | 7255 | 0.022 | 0.39 | NO |
72 | C17orf99 | C17orf99 | C17orf99 | 7318 | 0.022 | 0.39 | NO |
73 | SNRNP27 | SNRNP27 | SNRNP27 | 7367 | 0.021 | 0.39 | NO |
74 | CYTH1 | CYTH1 | CYTH1 | 7487 | 0.02 | 0.38 | NO |
75 | ZNF629 | ZNF629 | ZNF629 | 7566 | 0.019 | 0.38 | NO |
76 | GM2A | GM2A | GM2A | 7695 | 0.018 | 0.38 | NO |
77 | ADCY7 | ADCY7 | ADCY7 | 7742 | 0.018 | 0.37 | NO |
78 | MYL6 | MYL6 | MYL6 | 7770 | 0.017 | 0.37 | NO |
79 | ZBTB4 | ZBTB4 | ZBTB4 | 7813 | 0.017 | 0.37 | NO |
80 | PRCC | PRCC | PRCC | 7901 | 0.016 | 0.37 | NO |
81 | INPPL1 | INPPL1 | INPPL1 | 7922 | 0.016 | 0.37 | NO |
82 | CDC27 | CDC27 | CDC27 | 8188 | 0.014 | 0.35 | NO |
83 | DAD1 | DAD1 | DAD1 | 8356 | 0.012 | 0.34 | NO |
84 | POLR2A | POLR2A | POLR2A | 8365 | 0.012 | 0.34 | NO |
85 | MIA3 | MIA3 | MIA3 | 8386 | 0.012 | 0.34 | NO |
86 | MEF2BNB | MEF2BNB | MEF2BNB | 8418 | 0.012 | 0.34 | NO |
87 | RPL28 | RPL28 | RPL28 | 8489 | 0.012 | 0.34 | NO |
88 | DDT | DDT | DDT | 8578 | 0.011 | 0.34 | NO |
89 | LGMN | LGMN | LGMN | 8775 | 0.0091 | 0.33 | NO |
90 | FGFR2 | FGFR2 | FGFR2 | 8778 | 0.0091 | 0.33 | NO |
91 | GSTO1 | GSTO1 | GSTO1 | 8783 | 0.0091 | 0.33 | NO |
92 | NUCB1 | NUCB1 | NUCB1 | 8904 | 0.0083 | 0.32 | NO |
93 | SMARCA1 | SMARCA1 | SMARCA1 | 9037 | 0.0072 | 0.31 | NO |
94 | DPF2 | DPF2 | DPF2 | 9063 | 0.0071 | 0.31 | NO |
95 | ARPC1A | ARPC1A | ARPC1A | 9111 | 0.0068 | 0.31 | NO |
96 | AAMP | AAMP | AAMP | 9154 | 0.0065 | 0.31 | NO |
97 | MAP2K4 | MAP2K4 | MAP2K4 | 9245 | 0.0058 | 0.3 | NO |
98 | DYRK4 | DYRK4 | DYRK4 | 9326 | 0.0052 | 0.3 | NO |
99 | BRE | BRE | BRE | 9360 | 0.005 | 0.3 | NO |
100 | VEZF1 | VEZF1 | VEZF1 | 9383 | 0.0049 | 0.3 | NO |
101 | ADAR | ADAR | ADAR | 9463 | 0.0042 | 0.29 | NO |
102 | RNPS1 | RNPS1 | RNPS1 | 9529 | 0.0037 | 0.29 | NO |
103 | GSTM4 | GSTM4 | GSTM4 | 9547 | 0.0036 | 0.29 | NO |
104 | MED22 | MED22 | MED22 | 9550 | 0.0036 | 0.29 | NO |
105 | KARS | KARS | KARS | 9703 | 0.0026 | 0.28 | NO |
106 | ARPC2 | ARPC2 | ARPC2 | 9777 | 0.0021 | 0.28 | NO |
107 | GRB2 | GRB2 | GRB2 | 9778 | 0.0021 | 0.28 | NO |
108 | TGFBR2 | TGFBR2 | TGFBR2 | 9798 | 0.0019 | 0.28 | NO |
109 | RIT1 | RIT1 | RIT1 | 9820 | 0.0018 | 0.27 | NO |
110 | SNRPD2 | SNRPD2 | SNRPD2 | 9832 | 0.0017 | 0.27 | NO |
111 | CLK2 | CLK2 | CLK2 | 9873 | 0.0014 | 0.27 | NO |
112 | NPAS2 | NPAS2 | NPAS2 | 9878 | 0.0014 | 0.27 | NO |
113 | AMFR | AMFR | AMFR | 9903 | 0.0012 | 0.27 | NO |
114 | MCFD2 | MCFD2 | MCFD2 | 9963 | 0.00072 | 0.27 | NO |
115 | UFD1L | UFD1L | UFD1L | 9973 | 0.00064 | 0.27 | NO |
116 | PSEN1 | PSEN1 | PSEN1 | 10027 | 0.00025 | 0.26 | NO |
117 | LRBA | LRBA | LRBA | 10030 | 0.00023 | 0.26 | NO |
118 | CKAP5 | CKAP5 | CKAP5 | 10043 | 0.00014 | 0.26 | NO |
119 | TMEM187 | TMEM187 | TMEM187 | 10045 | 0.00011 | 0.26 | NO |
120 | AKAP17A | AKAP17A | AKAP17A | 10099 | -0.00025 | 0.26 | NO |
121 | WDR48 | WDR48 | WDR48 | 10406 | -0.0022 | 0.24 | NO |
122 | CDC123 | CDC123 | CDC123 | 10442 | -0.0025 | 0.24 | NO |
123 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 10549 | -0.0032 | 0.24 | NO |
124 | PPP6C | PPP6C | PPP6C | 10577 | -0.0034 | 0.23 | NO |
125 | METTL2A | METTL2A | METTL2A | 10587 | -0.0034 | 0.23 | NO |
126 | STX5 | STX5 | STX5 | 10661 | -0.004 | 0.23 | NO |
127 | MTCH2 | MTCH2 | MTCH2 | 10690 | -0.0041 | 0.23 | NO |
128 | SUMO1 | SUMO1 | SUMO1 | 10692 | -0.0041 | 0.23 | NO |
129 | SLC22A9 | SLC22A9 | SLC22A9 | 10704 | -0.0042 | 0.23 | NO |
130 | HDHD1 | HDHD1 | HDHD1 | 10744 | -0.0045 | 0.23 | NO |
131 | COG2 | COG2 | COG2 | 10753 | -0.0045 | 0.23 | NO |
132 | INSR | INSR | INSR | 10951 | -0.0058 | 0.22 | NO |
133 | STK38 | STK38 | STK38 | 11056 | -0.0066 | 0.21 | NO |
134 | MPI | MPI | MPI | 11192 | -0.0076 | 0.2 | NO |
135 | COASY | COASY | COASY | 11503 | -0.0096 | 0.19 | NO |
136 | POLRMT | POLRMT | POLRMT | 11512 | -0.0097 | 0.19 | NO |
137 | TJP2 | TJP2 | TJP2 | 11532 | -0.0098 | 0.19 | NO |
138 | TXNRD1 | TXNRD1 | TXNRD1 | 11679 | -0.011 | 0.18 | NO |
139 | HCCS | HCCS | HCCS | 11709 | -0.011 | 0.18 | NO |
140 | PSMD14 | PSMD14 | PSMD14 | 11719 | -0.011 | 0.18 | NO |
141 | NEDD4 | NEDD4 | NEDD4 | 11924 | -0.012 | 0.17 | NO |
142 | METTL1 | METTL1 | METTL1 | 11957 | -0.012 | 0.17 | NO |
143 | ABR | ABR | ABR | 12019 | -0.013 | 0.16 | NO |
144 | CNN2 | CNN2 | CNN2 | 12118 | -0.014 | 0.16 | NO |
145 | ZFP36L2 | ZFP36L2 | ZFP36L2 | 12120 | -0.014 | 0.16 | NO |
146 | CDK2AP1 | CDK2AP1 | CDK2AP1 | 12122 | -0.014 | 0.16 | NO |
147 | BAZ2A | BAZ2A | BAZ2A | 12422 | -0.016 | 0.14 | NO |
148 | ZNF32 | ZNF32 | ZNF32 | 12481 | -0.016 | 0.14 | NO |
149 | ATP1B3 | ATP1B3 | ATP1B3 | 12603 | -0.017 | 0.14 | NO |
150 | SLC30A7 | SLC30A7 | SLC30A7 | 12676 | -0.017 | 0.13 | NO |
151 | PSMA5 | PSMA5 | PSMA5 | 12803 | -0.018 | 0.13 | NO |
152 | UBE2N | UBE2N | UBE2N | 12818 | -0.018 | 0.13 | NO |
153 | MRPL4 | MRPL4 | MRPL4 | 12825 | -0.018 | 0.13 | NO |
154 | CYFIP1 | CYFIP1 | CYFIP1 | 12842 | -0.018 | 0.13 | NO |
155 | SRSF1 | SRSF1 | SRSF1 | 12904 | -0.019 | 0.13 | NO |
156 | DPM1 | DPM1 | DPM1 | 12912 | -0.019 | 0.13 | NO |
157 | BZW1 | BZW1 | BZW1 | 12921 | -0.019 | 0.13 | NO |
158 | IGF2R | IGF2R | IGF2R | 12978 | -0.02 | 0.12 | NO |
159 | VKORC1L1 | VKORC1L1 | VKORC1L1 | 13095 | -0.02 | 0.12 | NO |
160 | ZNF449 | ZNF449 | ZNF449 | 13129 | -0.021 | 0.12 | NO |
161 | FAM120A | FAM120A | FAM120A | 13439 | -0.023 | 0.1 | NO |
162 | BAP1 | BAP1 | BAP1 | 13623 | -0.024 | 0.095 | NO |
163 | ZNF440 | ZNF440 | ZNF440 | 13828 | -0.026 | 0.085 | NO |
164 | TFDP2 | TFDP2 | TFDP2 | 13971 | -0.027 | 0.079 | NO |
165 | THOC1 | THOC1 | THOC1 | 13987 | -0.028 | 0.079 | NO |
166 | COPS5 | COPS5 | COPS5 | 14091 | -0.028 | 0.075 | NO |
167 | TMED1 | TMED1 | TMED1 | 14106 | -0.028 | 0.076 | NO |
168 | PWP1 | PWP1 | PWP1 | 14195 | -0.029 | 0.073 | NO |
169 | MGAT2 | MGAT2 | MGAT2 | 14229 | -0.029 | 0.073 | NO |
170 | KCTD4 | KCTD4 | KCTD4 | 14291 | -0.03 | 0.071 | NO |
171 | MTMR3 | MTMR3 | MTMR3 | 14381 | -0.031 | 0.068 | NO |
172 | MED13L | MED13L | MED13L | 14382 | -0.031 | 0.07 | NO |
173 | LPIN1 | LPIN1 | LPIN1 | 14409 | -0.031 | 0.07 | NO |
174 | FXN | FXN | FXN | 14485 | -0.032 | 0.068 | NO |
175 | GALC | GALC | GALC | 14513 | -0.032 | 0.068 | NO |
176 | CBX3 | CBX3 | CBX3 | 14584 | -0.033 | 0.066 | NO |
177 | MCM2 | MCM2 | MCM2 | 14613 | -0.033 | 0.067 | NO |
178 | STAM | STAM | STAM | 14770 | -0.035 | 0.06 | NO |
179 | HNRNPF | HNRNPF | HNRNPF | 14773 | -0.035 | 0.062 | NO |
180 | CAPZA1 | CAPZA1 | CAPZA1 | 14911 | -0.036 | 0.056 | NO |
181 | USP34 | USP34 | USP34 | 14925 | -0.036 | 0.058 | NO |
182 | USP4 | USP4 | USP4 | 14932 | -0.037 | 0.06 | NO |
183 | KIF5B | KIF5B | KIF5B | 14948 | -0.037 | 0.061 | NO |
184 | CABLES1 | CABLES1 | CABLES1 | 14983 | -0.037 | 0.061 | NO |
185 | GPATCH2 | GPATCH2 | GPATCH2 | 15004 | -0.037 | 0.062 | NO |
186 | PDXDC1 | PDXDC1 | PDXDC1 | 15008 | -0.037 | 0.064 | NO |
187 | HINT1 | HINT1 | HINT1 | 15162 | -0.039 | 0.058 | NO |
188 | FOXM1 | FOXM1 | FOXM1 | 15233 | -0.04 | 0.057 | NO |
189 | SAV1 | SAV1 | SAV1 | 15306 | -0.041 | 0.055 | NO |
190 | HNRNPH1 | HNRNPH1 | HNRNPH1 | 15377 | -0.042 | 0.054 | NO |
191 | GPATCH8 | GPATCH8 | GPATCH8 | 15413 | -0.042 | 0.054 | NO |
192 | ALG13 | ALG13 | ALG13 | 15455 | -0.043 | 0.054 | NO |
193 | MCM9 | MCM9 | MCM9 | 15541 | -0.044 | 0.052 | NO |
194 | DDX17 | DDX17 | DDX17 | 15593 | -0.045 | 0.052 | NO |
195 | BECN1 | BECN1 | BECN1 | 15606 | -0.045 | 0.054 | NO |
196 | ATP7A | ATP7A | ATP7A | 15616 | -0.045 | 0.056 | NO |
197 | CTDSPL | CTDSPL | CTDSPL | 15623 | -0.045 | 0.058 | NO |
198 | PFDN4 | PFDN4 | PFDN4 | 15669 | -0.046 | 0.059 | NO |
199 | PAN3 | PAN3 | PAN3 | 15718 | -0.047 | 0.059 | NO |
200 | LPP | LPP | LPP | 15737 | -0.047 | 0.061 | NO |
201 | CUL2 | CUL2 | CUL2 | 15741 | -0.047 | 0.063 | NO |
202 | CCT2 | CCT2 | CCT2 | 15784 | -0.048 | 0.064 | NO |
203 | SLC35A1 | SLC35A1 | SLC35A1 | 15792 | -0.048 | 0.066 | NO |
204 | EIF2AK1 | EIF2AK1 | EIF2AK1 | 15798 | -0.048 | 0.069 | NO |
205 | C11orf58 | C11orf58 | C11orf58 | 15838 | -0.049 | 0.07 | NO |
206 | PHKB | PHKB | PHKB | 15842 | -0.049 | 0.072 | NO |
207 | SLC25A16 | SLC25A16 | SLC25A16 | 15883 | -0.05 | 0.073 | NO |
208 | USO1 | USO1 | USO1 | 15904 | -0.05 | 0.075 | NO |
209 | FAIM3 | FAIM3 | FAIM3 | 15942 | -0.051 | 0.076 | NO |
210 | MORC3 | MORC3 | MORC3 | 16182 | -0.056 | 0.066 | NO |
211 | AADAC | AADAC | AADAC | 16260 | -0.058 | 0.065 | NO |
212 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 16264 | -0.058 | 0.068 | NO |
213 | SFTPA2 | SFTPA2 | SFTPA2 | 16270 | -0.058 | 0.071 | NO |
214 | LTBP1 | LTBP1 | LTBP1 | 17063 | -0.089 | 0.032 | NO |
215 | ZC3HAV1L | ZC3HAV1L | ZC3HAV1L | 17101 | -0.092 | 0.035 | NO |
216 | LRRIQ3 | LRRIQ3 | LRRIQ3 | 17961 | -0.33 | 0.0069 | NO |
Figure S31. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG PURINE METABOLISM.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PURINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S17. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | HP | HP | HP | 345 | 0.64 | 0.036 | YES |
2 | CAMP | CAMP | CAMP | 530 | 0.55 | 0.073 | YES |
3 | GDF5 | GDF5 | GDF5 | 594 | 0.52 | 0.12 | YES |
4 | CA2 | CA2 | CA2 | 724 | 0.48 | 0.15 | YES |
5 | RETN | RETN | RETN | 879 | 0.43 | 0.18 | YES |
6 | THRSP | THRSP | THRSP | 888 | 0.43 | 0.22 | YES |
7 | LUM | LUM | LUM | 921 | 0.42 | 0.25 | YES |
8 | ABCD2 | ABCD2 | ABCD2 | 1049 | 0.39 | 0.28 | YES |
9 | G0S2 | G0S2 | G0S2 | 1303 | 0.35 | 0.29 | YES |
10 | HSD11B1 | HSD11B1 | HSD11B1 | 1328 | 0.34 | 0.32 | YES |
11 | GPD1 | GPD1 | GPD1 | 1344 | 0.34 | 0.35 | YES |
12 | LCN2 | LCN2 | LCN2 | 1512 | 0.31 | 0.37 | YES |
13 | AOC3 | AOC3 | AOC3 | 1879 | 0.27 | 0.37 | YES |
14 | PARM1 | PARM1 | PARM1 | 1922 | 0.26 | 0.39 | YES |
15 | NNMT | NNMT | NNMT | 1994 | 0.26 | 0.41 | YES |
16 | CA3 | CA3 | CA3 | 2111 | 0.24 | 0.42 | YES |
17 | ME1 | ME1 | ME1 | 2220 | 0.23 | 0.44 | YES |
18 | S100A8 | S100A8 | S100A8 | 2346 | 0.22 | 0.45 | YES |
19 | RARRES2 | RARRES2 | RARRES2 | 2401 | 0.22 | 0.46 | YES |
20 | LTC4S | LTC4S | LTC4S | 2486 | 0.21 | 0.48 | YES |
21 | CD1D | CD1D | CD1D | 3006 | 0.17 | 0.46 | NO |
22 | CFD | CFD | CFD | 3330 | 0.15 | 0.46 | NO |
23 | COL15A1 | COL15A1 | COL15A1 | 4025 | 0.11 | 0.43 | NO |
24 | UNC119 | UNC119 | UNC119 | 4042 | 0.11 | 0.44 | NO |
25 | APOC1 | APOC1 | APOC1 | 4520 | 0.088 | 0.42 | NO |
26 | ORM2 | ORM2 | ORM2 | 4596 | 0.084 | 0.42 | NO |
27 | CDKN2C | CDKN2C | CDKN2C | 4765 | 0.077 | 0.42 | NO |
28 | ACADL | ACADL | ACADL | 4844 | 0.074 | 0.42 | NO |
29 | MGST1 | MGST1 | MGST1 | 4935 | 0.071 | 0.42 | NO |
30 | MGLL | MGLL | MGLL | 5152 | 0.063 | 0.42 | NO |
31 | NDUFB8 | NDUFB8 | NDUFB8 | 5380 | 0.056 | 0.41 | NO |
32 | C9orf16 | C9orf16 | C9orf16 | 5576 | 0.05 | 0.4 | NO |
33 | AGPAT3 | AGPAT3 | AGPAT3 | 5704 | 0.046 | 0.4 | NO |
34 | PGM1 | PGM1 | PGM1 | 5716 | 0.046 | 0.4 | NO |
35 | ITGA6 | ITGA6 | ITGA6 | 5757 | 0.045 | 0.4 | NO |
36 | TP53INP2 | TP53INP2 | TP53INP2 | 5782 | 0.045 | 0.41 | NO |
37 | SFXN1 | SFXN1 | SFXN1 | 5831 | 0.044 | 0.41 | NO |
38 | ADIPOQ | ADIPOQ | ADIPOQ | 5836 | 0.044 | 0.41 | NO |
39 | FAH | FAH | FAH | 5904 | 0.042 | 0.41 | NO |
40 | PSAT1 | PSAT1 | PSAT1 | 6315 | 0.034 | 0.39 | NO |
41 | IMPDH1 | IMPDH1 | IMPDH1 | 6342 | 0.034 | 0.39 | NO |
42 | UQCR10 | UQCR10 | UQCR10 | 6370 | 0.033 | 0.39 | NO |
43 | APOE | APOE | APOE | 6386 | 0.033 | 0.4 | NO |
44 | RBPMS | RBPMS | RBPMS | 6561 | 0.031 | 0.39 | NO |
45 | REEP6 | REEP6 | REEP6 | 6632 | 0.03 | 0.39 | NO |
46 | MRAP | MRAP | MRAP | 6655 | 0.029 | 0.39 | NO |
47 | PPP2R5A | PPP2R5A | PPP2R5A | 6886 | 0.026 | 0.38 | NO |
48 | PLIN4 | PLIN4 | PLIN4 | 6901 | 0.026 | 0.38 | NO |
49 | PDAP1 | PDAP1 | PDAP1 | 6980 | 0.025 | 0.38 | NO |
50 | CIB2 | CIB2 | CIB2 | 7070 | 0.024 | 0.37 | NO |
51 | QDPR | QDPR | QDPR | 7103 | 0.024 | 0.38 | NO |
52 | C20orf27 | C20orf27 | C20orf27 | 7194 | 0.023 | 0.37 | NO |
53 | NDUFC1 | NDUFC1 | NDUFC1 | 7305 | 0.022 | 0.37 | NO |
54 | CD151 | CD151 | CD151 | 7427 | 0.021 | 0.36 | NO |
55 | CCRN4L | CCRN4L | CCRN4L | 7436 | 0.02 | 0.36 | NO |
56 | MCAM | MCAM | MCAM | 7442 | 0.02 | 0.36 | NO |
57 | PEMT | PEMT | PEMT | 7543 | 0.02 | 0.36 | NO |
58 | DHCR7 | DHCR7 | DHCR7 | 7561 | 0.019 | 0.36 | NO |
59 | MPDU1 | MPDU1 | MPDU1 | 7651 | 0.018 | 0.36 | NO |
60 | NDUFB7 | NDUFB7 | NDUFB7 | 7672 | 0.018 | 0.36 | NO |
61 | COX5B | COX5B | COX5B | 7743 | 0.018 | 0.36 | NO |
62 | SLC25A1 | SLC25A1 | SLC25A1 | 7825 | 0.017 | 0.35 | NO |
63 | ACAA2 | ACAA2 | ACAA2 | 7844 | 0.017 | 0.35 | NO |
64 | PSEN2 | PSEN2 | PSEN2 | 7868 | 0.016 | 0.35 | NO |
65 | EHD1 | EHD1 | EHD1 | 7944 | 0.016 | 0.35 | NO |
66 | UCK1 | UCK1 | UCK1 | 8131 | 0.014 | 0.34 | NO |
67 | NDUFS3 | NDUFS3 | NDUFS3 | 8137 | 0.014 | 0.34 | NO |
68 | DLST | DLST | DLST | 8156 | 0.014 | 0.34 | NO |
69 | DGAT1 | DGAT1 | DGAT1 | 8169 | 0.014 | 0.34 | NO |
70 | GSR | GSR | GSR | 8354 | 0.012 | 0.34 | NO |
71 | UQCRC1 | UQCRC1 | UQCRC1 | 8532 | 0.011 | 0.33 | NO |
72 | FASN | FASN | FASN | 8547 | 0.011 | 0.33 | NO |
73 | DDT | DDT | DDT | 8578 | 0.011 | 0.32 | NO |
74 | RTN3 | RTN3 | RTN3 | 8646 | 0.01 | 0.32 | NO |
75 | UQCRQ | UQCRQ | UQCRQ | 8711 | 0.0097 | 0.32 | NO |
76 | SCARB1 | SCARB1 | SCARB1 | 8731 | 0.0095 | 0.32 | NO |
77 | NDUFB9 | NDUFB9 | NDUFB9 | 8770 | 0.0092 | 0.32 | NO |
78 | ALAS1 | ALAS1 | ALAS1 | 8842 | 0.0087 | 0.32 | NO |
79 | PNPLA2 | PNPLA2 | PNPLA2 | 9023 | 0.0073 | 0.3 | NO |
80 | TSPAN12 | TSPAN12 | TSPAN12 | 9088 | 0.0069 | 0.3 | NO |
81 | ATP5O | ATP5O | ATP5O | 9233 | 0.0058 | 0.3 | NO |
82 | C9orf72 | C9orf72 | C9orf72 | 9274 | 0.0056 | 0.29 | NO |
83 | CIDEC | CIDEC | CIDEC | 9292 | 0.0054 | 0.29 | NO |
84 | CYB5B | CYB5B | CYB5B | 9356 | 0.005 | 0.29 | NO |
85 | COX7A2 | COX7A2 | COX7A2 | 9501 | 0.0039 | 0.28 | NO |
86 | MRPL51 | MRPL51 | MRPL51 | 9533 | 0.0037 | 0.28 | NO |
87 | CBR1 | CBR1 | CBR1 | 9594 | 0.0034 | 0.28 | NO |
88 | CYB5A | CYB5A | CYB5A | 9669 | 0.0028 | 0.27 | NO |
89 | ACYP2 | ACYP2 | ACYP2 | 9713 | 0.0025 | 0.27 | NO |
90 | C6orf136 | C6orf136 | C6orf136 | 9745 | 0.0022 | 0.27 | NO |
91 | REEP5 | REEP5 | REEP5 | 9810 | 0.0018 | 0.27 | NO |
92 | S100A1 | S100A1 | S100A1 | 9833 | 0.0017 | 0.26 | NO |
93 | PEX19 | PEX19 | PEX19 | 9856 | 0.0015 | 0.26 | NO |
94 | NDUFA9 | NDUFA9 | NDUFA9 | 9962 | 0.00072 | 0.26 | NO |
95 | MAP4K4 | MAP4K4 | MAP4K4 | 9986 | 0.00058 | 0.26 | NO |
96 | PXMP2 | PXMP2 | PXMP2 | 10025 | 0.00026 | 0.26 | NO |
97 | DNAJC15 | DNAJC15 | DNAJC15 | 10066 | -0.000031 | 0.25 | NO |
98 | ALAD | ALAD | ALAD | 10178 | -0.00072 | 0.25 | NO |
99 | ATP5D | ATP5D | ATP5D | 10218 | -0.00097 | 0.24 | NO |
100 | SDHA | SDHA | SDHA | 10293 | -0.0015 | 0.24 | NO |
101 | PCYOX1 | PCYOX1 | PCYOX1 | 10310 | -0.0016 | 0.24 | NO |
102 | ETFDH | ETFDH | ETFDH | 10360 | -0.0019 | 0.24 | NO |
103 | CS | CS | CS | 10631 | -0.0037 | 0.22 | NO |
104 | SLC19A1 | SLC19A1 | SLC19A1 | 10682 | -0.0041 | 0.22 | NO |
105 | OGDH | OGDH | OGDH | 10863 | -0.0052 | 0.21 | NO |
106 | LONP2 | LONP2 | LONP2 | 10872 | -0.0053 | 0.21 | NO |
107 | DECR1 | DECR1 | DECR1 | 10925 | -0.0056 | 0.21 | NO |
108 | QKI | QKI | QKI | 11203 | -0.0077 | 0.19 | NO |
109 | TUFM | TUFM | TUFM | 11230 | -0.0079 | 0.19 | NO |
110 | GSTZ1 | GSTZ1 | GSTZ1 | 11340 | -0.0085 | 0.19 | NO |
111 | NDUFB3 | NDUFB3 | NDUFB3 | 11358 | -0.0086 | 0.19 | NO |
112 | TAB3 | TAB3 | TAB3 | 11367 | -0.0087 | 0.19 | NO |
113 | ACADS | ACADS | ACADS | 11442 | -0.0092 | 0.18 | NO |
114 | PDHB | PDHB | PDHB | 11562 | -0.01 | 0.18 | NO |
115 | NDUFB6 | NDUFB6 | NDUFB6 | 11595 | -0.01 | 0.18 | NO |
116 | SDHB | SDHB | SDHB | 11685 | -0.011 | 0.17 | NO |
117 | ISCA1 | ISCA1 | ISCA1 | 11765 | -0.011 | 0.17 | NO |
118 | ACAD9 | ACAD9 | ACAD9 | 11859 | -0.012 | 0.16 | NO |
119 | UQCRB | UQCRB | UQCRB | 11871 | -0.012 | 0.17 | NO |
120 | SCD | SCD | SCD | 11873 | -0.012 | 0.17 | NO |
121 | HIPK2 | HIPK2 | HIPK2 | 11953 | -0.012 | 0.16 | NO |
122 | DHRS7B | DHRS7B | DHRS7B | 11962 | -0.013 | 0.16 | NO |
123 | RAB3D | RAB3D | RAB3D | 11965 | -0.013 | 0.16 | NO |
124 | RETSAT | RETSAT | RETSAT | 12040 | -0.013 | 0.16 | NO |
125 | LDHB | LDHB | LDHB | 12057 | -0.013 | 0.16 | NO |
126 | SETD8 | SETD8 | SETD8 | 12088 | -0.013 | 0.16 | NO |
127 | SDHC | SDHC | SDHC | 12146 | -0.014 | 0.16 | NO |
128 | SAMM50 | SAMM50 | SAMM50 | 12671 | -0.017 | 0.13 | NO |
129 | RNF11 | RNF11 | RNF11 | 12765 | -0.018 | 0.13 | NO |
130 | HSD17B4 | HSD17B4 | HSD17B4 | 12783 | -0.018 | 0.13 | NO |
131 | CMBL | CMBL | CMBL | 12964 | -0.02 | 0.12 | NO |
132 | BCAT2 | BCAT2 | BCAT2 | 12986 | -0.02 | 0.12 | NO |
133 | LPL | LPL | LPL | 13077 | -0.02 | 0.12 | NO |
134 | COX7B | COX7B | COX7B | 13078 | -0.02 | 0.12 | NO |
135 | HIBCH | HIBCH | HIBCH | 13205 | -0.021 | 0.12 | NO |
136 | SGCD | SGCD | SGCD | 13228 | -0.021 | 0.12 | NO |
137 | CCNG2 | CCNG2 | CCNG2 | 13266 | -0.022 | 0.12 | NO |
138 | CHPT1 | CHPT1 | CHPT1 | 13467 | -0.023 | 0.11 | NO |
139 | SUCLG1 | SUCLG1 | SUCLG1 | 13484 | -0.023 | 0.11 | NO |
140 | NDUFA5 | NDUFA5 | NDUFA5 | 13584 | -0.024 | 0.1 | NO |
141 | SLC2A4 | SLC2A4 | SLC2A4 | 13598 | -0.024 | 0.1 | NO |
142 | NR1H3 | NR1H3 | NR1H3 | 13640 | -0.024 | 0.1 | NO |
143 | TKT | TKT | TKT | 13642 | -0.024 | 0.11 | NO |
144 | SDPR | SDPR | SDPR | 13677 | -0.025 | 0.11 | NO |
145 | TANK | TANK | TANK | 13695 | -0.025 | 0.11 | NO |
146 | NDUFS1 | NDUFS1 | NDUFS1 | 13758 | -0.026 | 0.11 | NO |
147 | FAM49B | FAM49B | FAM49B | 13904 | -0.027 | 0.1 | NO |
148 | KAT2B | KAT2B | KAT2B | 13946 | -0.027 | 0.1 | NO |
149 | DLD | DLD | DLD | 13960 | -0.027 | 0.1 | NO |
150 | BNIP3 | BNIP3 | BNIP3 | 14037 | -0.028 | 0.1 | NO |
151 | UQCRC2 | UQCRC2 | UQCRC2 | 14082 | -0.028 | 0.1 | NO |
152 | COQ5 | COQ5 | COQ5 | 14123 | -0.028 | 0.1 | NO |
153 | HSD17B12 | HSD17B12 | HSD17B12 | 14303 | -0.03 | 0.094 | NO |
154 | FXN | FXN | FXN | 14485 | -0.032 | 0.086 | NO |
155 | CHCHD3 | CHCHD3 | CHCHD3 | 14492 | -0.032 | 0.089 | NO |
156 | SLC25A5 | SLC25A5 | SLC25A5 | 14599 | -0.033 | 0.086 | NO |
157 | DLAT | DLAT | DLAT | 14707 | -0.034 | 0.083 | NO |
158 | SCP2 | SCP2 | SCP2 | 14723 | -0.034 | 0.085 | NO |
159 | TST | TST | TST | 14747 | -0.034 | 0.087 | NO |
160 | NDUFB5 | NDUFB5 | NDUFB5 | 14832 | -0.036 | 0.085 | NO |
161 | HIBADH | HIBADH | HIBADH | 15027 | -0.037 | 0.077 | NO |
162 | PLA2G6 | PLA2G6 | PLA2G6 | 15059 | -0.038 | 0.079 | NO |
163 | HADHB | HADHB | HADHB | 15085 | -0.038 | 0.081 | NO |
164 | ISOC1 | ISOC1 | ISOC1 | 15156 | -0.039 | 0.08 | NO |
165 | HADH | HADH | HADH | 15291 | -0.041 | 0.076 | NO |
166 | MCCC1 | MCCC1 | MCCC1 | 15313 | -0.041 | 0.079 | NO |
167 | ARL4A | ARL4A | ARL4A | 15415 | -0.042 | 0.077 | NO |
168 | PON2 | PON2 | PON2 | 15421 | -0.042 | 0.08 | NO |
169 | PHTF2 | PHTF2 | PHTF2 | 15545 | -0.044 | 0.077 | NO |
170 | GBE1 | GBE1 | GBE1 | 15549 | -0.044 | 0.081 | NO |
171 | ABCA1 | ABCA1 | ABCA1 | 15573 | -0.045 | 0.083 | NO |
172 | FAM132A | FAM132A | FAM132A | 15688 | -0.047 | 0.081 | NO |
173 | DBT | DBT | DBT | 16016 | -0.052 | 0.067 | NO |
174 | LIAS | LIAS | LIAS | 16131 | -0.055 | 0.065 | NO |
175 | ADCY6 | ADCY6 | ADCY6 | 16150 | -0.055 | 0.069 | NO |
176 | AQP7 | AQP7 | AQP7 | 16565 | -0.066 | 0.052 | NO |
177 | BCKDHB | BCKDHB | BCKDHB | 16566 | -0.066 | 0.058 | NO |
178 | GCSH | GCSH | GCSH | 16587 | -0.067 | 0.062 | NO |
179 | CAT | CAT | CAT | 16998 | -0.085 | 0.047 | NO |
180 | SLC25A10 | SLC25A10 | SLC25A10 | 17621 | -0.16 | 0.026 | NO |
Figure S33. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S18. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NTRK1 | NTRK1 | NTRK1 | 934 | 0.42 | 0.16 | YES |
2 | NGF | NGF | NGF | 1095 | 0.38 | 0.35 | YES |
3 | SHC3 | SHC3 | SHC3 | 1314 | 0.35 | 0.52 | YES |
4 | RIT2 | RIT2 | RIT2 | 1872 | 0.27 | 0.62 | YES |
5 | MAPK3 | MAPK3 | MAPK3 | 5934 | 0.042 | 0.42 | NO |
6 | MAPK11 | MAPK11 | MAPK11 | 6173 | 0.037 | 0.43 | NO |
7 | SHC1 | SHC1 | SHC1 | 6374 | 0.033 | 0.43 | NO |
8 | YWHAB | YWHAB | YWHAB | 7174 | 0.023 | 0.4 | NO |
9 | HRAS | HRAS | HRAS | 7301 | 0.022 | 0.4 | NO |
10 | SRC | SRC | SRC | 7673 | 0.018 | 0.39 | NO |
11 | MAPK13 | MAPK13 | MAPK13 | 7751 | 0.018 | 0.4 | NO |
12 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 7872 | 0.016 | 0.4 | NO |
13 | PLCG1 | PLCG1 | PLCG1 | 8052 | 0.015 | 0.4 | NO |
14 | RALB | RALB | RALB | 9065 | 0.0071 | 0.34 | NO |
15 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 9336 | 0.0052 | 0.33 | NO |
16 | MAPK12 | MAPK12 | MAPK12 | 9570 | 0.0035 | 0.32 | NO |
17 | RALGDS | RALGDS | RALGDS | 9623 | 0.0031 | 0.32 | NO |
18 | GRB2 | GRB2 | GRB2 | 9778 | 0.0021 | 0.31 | NO |
19 | RIT1 | RIT1 | RIT1 | 9820 | 0.0018 | 0.31 | NO |
20 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 10436 | -0.0024 | 0.28 | NO |
21 | MAP2K2 | MAP2K2 | MAP2K2 | 10520 | -0.003 | 0.28 | NO |
22 | SHC2 | SHC2 | SHC2 | 10760 | -0.0045 | 0.26 | NO |
23 | KIDINS220 | KIDINS220 | KIDINS220 | 10898 | -0.0055 | 0.26 | NO |
24 | MAPK1 | MAPK1 | MAPK1 | 11428 | -0.0091 | 0.24 | NO |
25 | MAP2K1 | MAP2K1 | MAP2K1 | 11622 | -0.01 | 0.23 | NO |
26 | SOS1 | SOS1 | SOS1 | 11772 | -0.011 | 0.23 | NO |
27 | RAF1 | RAF1 | RAF1 | 12375 | -0.015 | 0.2 | NO |
28 | KRAS | KRAS | KRAS | 12551 | -0.016 | 0.2 | NO |
29 | RALA | RALA | RALA | 12606 | -0.017 | 0.21 | NO |
30 | BRAF | BRAF | BRAF | 13058 | -0.02 | 0.19 | NO |
31 | CRK | CRK | CRK | 13231 | -0.022 | 0.19 | NO |
32 | RAP1A | RAP1A | RAP1A | 13477 | -0.023 | 0.19 | NO |
33 | NRAS | NRAS | NRAS | 13674 | -0.025 | 0.19 | NO |
34 | CDK1 | CDK1 | CDK1 | 14228 | -0.029 | 0.18 | NO |
35 | MAPK14 | MAPK14 | MAPK14 | 14720 | -0.034 | 0.17 | NO |
36 | FRS2 | FRS2 | FRS2 | 14956 | -0.037 | 0.17 | NO |
Figure S35. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S19. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | WIF1 | WIF1 | WIF1 | 34 | 0.98 | 0.54 | YES |
2 | WNT1 | WNT1 | WNT1 | 1379 | 0.33 | 0.65 | YES |
3 | LEF1 | LEF1 | LEF1 | 3798 | 0.12 | 0.59 | NO |
4 | TLE1 | TLE1 | TLE1 | 7270 | 0.022 | 0.41 | NO |
5 | MAP3K7 | MAP3K7 | MAP3K7 | 7632 | 0.019 | 0.4 | NO |
6 | DVL1 | DVL1 | DVL1 | 8023 | 0.015 | 0.38 | NO |
7 | TAB1 | TAB1 | TAB1 | 8469 | 0.012 | 0.36 | NO |
8 | PPARD | PPARD | PPARD | 8658 | 0.01 | 0.36 | NO |
9 | CTBP1 | CTBP1 | CTBP1 | 9069 | 0.0071 | 0.34 | NO |
10 | NLK | NLK | NLK | 9288 | 0.0055 | 0.33 | NO |
11 | BTRC | BTRC | BTRC | 9400 | 0.0047 | 0.33 | NO |
12 | CCND1 | CCND1 | CCND1 | 9425 | 0.0045 | 0.33 | NO |
13 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 9554 | 0.0036 | 0.32 | NO |
14 | FRAT1 | FRAT1 | FRAT1 | 10584 | -0.0034 | 0.27 | NO |
15 | HDAC1 | HDAC1 | HDAC1 | 10590 | -0.0035 | 0.27 | NO |
16 | CREBBP | CREBBP | CREBBP | 10865 | -0.0052 | 0.26 | NO |
17 | FZD1 | FZD1 | FZD1 | 11028 | -0.0064 | 0.25 | NO |
18 | AXIN1 | AXIN1 | AXIN1 | 11339 | -0.0085 | 0.24 | NO |
19 | PPP2CA | PPP2CA | PPP2CA | 11696 | -0.011 | 0.23 | NO |
20 | GSK3B | GSK3B | GSK3B | 11809 | -0.012 | 0.23 | NO |
21 | CSNK1D | CSNK1D | CSNK1D | 12564 | -0.016 | 0.2 | NO |
22 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 13349 | -0.022 | 0.16 | NO |
23 | APC | APC | APC | 13691 | -0.025 | 0.16 | NO |
24 | SMAD4 | SMAD4 | SMAD4 | 14573 | -0.033 | 0.13 | NO |
25 | MYC | MYC | MYC | 16184 | -0.056 | 0.07 | NO |
26 | CTNNB1 | CTNNB1 | CTNNB1 | 16446 | -0.063 | 0.091 | NO |
Figure S37. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG LYSINE DEGRADATION.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S20. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SYT1 | SYT1 | SYT1 | 37 | 0.97 | 0.21 | YES |
2 | CCK | CCK | CCK | 75 | 0.88 | 0.39 | YES |
3 | GABRA1 | GABRA1 | GABRA1 | 752 | 0.47 | 0.46 | YES |
4 | KCNMA1 | KCNMA1 | KCNMA1 | 1044 | 0.39 | 0.53 | YES |
5 | PTGDS | PTGDS | PTGDS | 1241 | 0.36 | 0.59 | YES |
6 | NPTX1 | NPTX1 | NPTX1 | 2208 | 0.23 | 0.59 | YES |
7 | ATP1B2 | ATP1B2 | ATP1B2 | 2338 | 0.22 | 0.63 | YES |
8 | TUBB3 | TUBB3 | TUBB3 | 3917 | 0.12 | 0.57 | NO |
9 | MAG | MAG | MAG | 4857 | 0.073 | 0.53 | NO |
10 | MGLL | MGLL | MGLL | 5152 | 0.063 | 0.53 | NO |
11 | CPLX1 | CPLX1 | CPLX1 | 5490 | 0.052 | 0.52 | NO |
12 | EEF1G | EEF1G | EEF1G | 6023 | 0.04 | 0.5 | NO |
13 | NME1 | NME1 | NME1 | 6332 | 0.034 | 0.49 | NO |
14 | TUBB4B | TUBB4B | TUBB4B | 6344 | 0.034 | 0.5 | NO |
15 | APOE | APOE | APOE | 6386 | 0.033 | 0.5 | NO |
16 | CDK16 | CDK16 | CDK16 | 6846 | 0.027 | 0.48 | NO |
17 | DNM1 | DNM1 | DNM1 | 6911 | 0.026 | 0.48 | NO |
18 | NSF | NSF | NSF | 7027 | 0.025 | 0.48 | NO |
19 | OAZ2 | OAZ2 | OAZ2 | 7221 | 0.023 | 0.48 | NO |
20 | PLD3 | PLD3 | PLD3 | 7302 | 0.022 | 0.48 | NO |
21 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 7494 | 0.02 | 0.47 | NO |
22 | PFN1 | PFN1 | PFN1 | 7674 | 0.018 | 0.46 | NO |
23 | DYNC1H1 | DYNC1H1 | DYNC1H1 | 7801 | 0.017 | 0.46 | NO |
24 | DCTN1 | DCTN1 | DCTN1 | 8136 | 0.014 | 0.45 | NO |
25 | AP2M1 | AP2M1 | AP2M1 | 8324 | 0.013 | 0.44 | NO |
26 | DAD1 | DAD1 | DAD1 | 8356 | 0.012 | 0.44 | NO |
27 | EIF4G3 | EIF4G3 | EIF4G3 | 8482 | 0.012 | 0.44 | NO |
28 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 9021 | 0.0073 | 0.41 | NO |
29 | RAB2A | RAB2A | RAB2A | 9720 | 0.0024 | 0.37 | NO |
30 | NCL | NCL | NCL | 10179 | -0.00073 | 0.34 | NO |
31 | DNAJB11 | DNAJB11 | DNAJB11 | 10454 | -0.0026 | 0.33 | NO |
32 | CS | CS | CS | 10631 | -0.0037 | 0.32 | NO |
33 | GORASP2 | GORASP2 | GORASP2 | 10638 | -0.0038 | 0.32 | NO |
34 | SEPT7 | SEPT7 | SEPT7 | 10908 | -0.0055 | 0.31 | NO |
35 | ATP2A2 | ATP2A2 | ATP2A2 | 10997 | -0.0061 | 0.3 | NO |
36 | PPP2CA | PPP2CA | PPP2CA | 11696 | -0.011 | 0.27 | NO |
37 | SKP1 | SKP1 | SKP1 | 11824 | -0.012 | 0.26 | NO |
38 | CALM2 | CALM2 | CALM2 | 11981 | -0.013 | 0.26 | NO |
39 | RAB14 | RAB14 | RAB14 | 11987 | -0.013 | 0.26 | NO |
40 | PGK1 | PGK1 | PGK1 | 12049 | -0.013 | 0.26 | NO |
41 | ATP1A1 | ATP1A1 | ATP1A1 | 12341 | -0.015 | 0.24 | NO |
42 | ACO2 | ACO2 | ACO2 | 12625 | -0.017 | 0.23 | NO |
43 | ARPP19 | ARPP19 | ARPP19 | 12718 | -0.018 | 0.23 | NO |
44 | CSDE1 | CSDE1 | CSDE1 | 12824 | -0.018 | 0.23 | NO |
45 | HSP90AB1 | HSP90AB1 | HSP90AB1 | 12929 | -0.019 | 0.23 | NO |
46 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 13349 | -0.022 | 0.21 | NO |
47 | PPP1CB | PPP1CB | PPP1CB | 13418 | -0.023 | 0.21 | NO |
48 | EEF2 | EEF2 | EEF2 | 13778 | -0.026 | 0.2 | NO |
49 | PRKACB | PRKACB | PRKACB | 13822 | -0.026 | 0.2 | NO |
50 | PPM1A | PPM1A | PPM1A | 14100 | -0.028 | 0.19 | NO |
51 | ACTR3 | ACTR3 | ACTR3 | 14248 | -0.03 | 0.19 | NO |
52 | DDX3X | DDX3X | DDX3X | 14859 | -0.036 | 0.16 | NO |
53 | SRSF5 | SRSF5 | SRSF5 | 14942 | -0.037 | 0.17 | NO |
54 | TIA1 | TIA1 | TIA1 | 15300 | -0.041 | 0.15 | NO |
Figure S39. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG ARGININE AND PROLINE METABOLISM.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ARGININE AND PROLINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 5. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus3. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG RIBOSOME | 87 | genes.ES.table | 0.59 | 1.4 | 0.22 | 1 | 1 | 0.78 | 0.34 | 0.52 | 1 | 0.78 |
PID P53 REGULATION PATHWAY | 59 | genes.ES.table | 0.41 | 1.9 | 0.027 | 1 | 0.57 | 0.34 | 0.27 | 0.25 | 0.25 | 0.23 |
REACTOME TRANSLATION | 145 | genes.ES.table | 0.49 | 1.4 | 0.18 | 1 | 1 | 0.58 | 0.34 | 0.39 | 1 | 0.82 |
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE | 108 | genes.ES.table | 0.54 | 1.4 | 0.17 | 1 | 1 | 0.67 | 0.34 | 0.44 | 1 | 0.78 |
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S | 56 | genes.ES.table | 0.53 | 1.4 | 0.19 | 1 | 1 | 0.8 | 0.39 | 0.49 | 1 | 0.78 |
REACTOME GENERIC TRANSCRIPTION PATHWAY | 333 | genes.ES.table | 0.53 | 1.8 | 0.0083 | 1 | 0.84 | 0.5 | 0.23 | 0.39 | 0.62 | 0.37 |
REACTOME PEPTIDE CHAIN ELONGATION | 85 | genes.ES.table | 0.61 | 1.4 | 0.19 | 1 | 1 | 0.8 | 0.34 | 0.53 | 1 | 0.79 |
REACTOME MRNA PROCESSING | 152 | genes.ES.table | 0.25 | 1.4 | 0.14 | 1 | 1 | 1 | 0.75 | 0.25 | 1 | 0.8 |
REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION | 105 | genes.ES.table | 0.57 | 1.4 | 0.17 | 1 | 1 | 0.71 | 0.34 | 0.48 | 1 | 0.79 |
REACTOME INFLUENZA LIFE CYCLE | 135 | genes.ES.table | 0.44 | 1.4 | 0.22 | 1 | 1 | 0.56 | 0.34 | 0.38 | 1 | 0.78 |
Table S21. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | TP53AIP1 | TP53AIP1 | TP53AIP1 | 134 | 0.45 | 0.14 | YES |
2 | KAT2B | KAT2B | KAT2B | 1154 | 0.19 | 0.14 | YES |
3 | ATR | ATR | ATR | 1468 | 0.16 | 0.18 | YES |
4 | PPP1R13L | PPP1R13L | PPP1R13L | 1916 | 0.14 | 0.2 | YES |
5 | PRKCD | PRKCD | PRKCD | 1961 | 0.13 | 0.24 | YES |
6 | CDK2 | CDK2 | CDK2 | 2672 | 0.1 | 0.23 | YES |
7 | RPL5 | RPL5 | RPL5 | 2860 | 0.096 | 0.25 | YES |
8 | UBE2D1 | UBE2D1 | UBE2D1 | 2904 | 0.094 | 0.28 | YES |
9 | CCNG1 | CCNG1 | CCNG1 | 3305 | 0.082 | 0.28 | YES |
10 | RCHY1 | RCHY1 | RCHY1 | 3585 | 0.074 | 0.29 | YES |
11 | SKP2 | SKP2 | SKP2 | 3873 | 0.068 | 0.3 | YES |
12 | MAPK8 | MAPK8 | MAPK8 | 4064 | 0.064 | 0.31 | YES |
13 | DAXX | DAXX | DAXX | 4197 | 0.061 | 0.32 | YES |
14 | RPL11 | RPL11 | RPL11 | 4262 | 0.06 | 0.34 | YES |
15 | SMYD2 | SMYD2 | SMYD2 | 4416 | 0.056 | 0.35 | YES |
16 | RPL23 | RPL23 | RPL23 | 4461 | 0.056 | 0.36 | YES |
17 | GSK3B | GSK3B | GSK3B | 4494 | 0.055 | 0.38 | YES |
18 | CSNK1G3 | CSNK1G3 | CSNK1G3 | 4572 | 0.054 | 0.39 | YES |
19 | HIPK2 | HIPK2 | HIPK2 | 4666 | 0.052 | 0.4 | YES |
20 | RASSF1 | RASSF1 | RASSF1 | 4834 | 0.049 | 0.41 | YES |
21 | MDM4 | MDM4 | MDM4 | 5386 | 0.041 | 0.39 | NO |
22 | RFWD2 | RFWD2 | RFWD2 | 5418 | 0.04 | 0.4 | NO |
23 | FBXO11 | FBXO11 | FBXO11 | 6017 | 0.032 | 0.38 | NO |
24 | MAPK9 | MAPK9 | MAPK9 | 6260 | 0.029 | 0.38 | NO |
25 | MAPK14 | MAPK14 | MAPK14 | 6291 | 0.028 | 0.38 | NO |
26 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 7058 | 0.019 | 0.35 | NO |
27 | YY1 | YY1 | YY1 | 7166 | 0.018 | 0.35 | NO |
28 | CSNK1D | CSNK1D | CSNK1D | 7282 | 0.016 | 0.34 | NO |
29 | TTC5 | TTC5 | TTC5 | 7807 | 0.01 | 0.32 | NO |
30 | KAT8 | KAT8 | KAT8 | 8008 | 0.0078 | 0.31 | NO |
31 | PPP2CA | PPP2CA | PPP2CA | 8062 | 0.0073 | 0.31 | NO |
32 | PPM1D | PPM1D | PPM1D | 8196 | 0.0059 | 0.3 | NO |
33 | TRIM28 | TRIM28 | TRIM28 | 8720 | -0.00025 | 0.28 | NO |
34 | CSNK1G2 | CSNK1G2 | CSNK1G2 | 9131 | -0.0051 | 0.26 | NO |
35 | PIN1 | PIN1 | PIN1 | 9138 | -0.0051 | 0.26 | NO |
36 | HUWE1 | HUWE1 | HUWE1 | 9278 | -0.0069 | 0.25 | NO |
37 | CSE1L | CSE1L | CSE1L | 9507 | -0.0096 | 0.24 | NO |
38 | CSNK1G1 | CSNK1G1 | CSNK1G1 | 9526 | -0.0097 | 0.24 | NO |
39 | SETD8 | SETD8 | SETD8 | 9611 | -0.011 | 0.24 | NO |
40 | EP300 | EP300 | EP300 | 9615 | -0.011 | 0.24 | NO |
41 | PRMT5 | PRMT5 | PRMT5 | 9665 | -0.012 | 0.25 | NO |
42 | CREBBP | CREBBP | CREBBP | 9738 | -0.012 | 0.25 | NO |
43 | ATM | ATM | ATM | 10055 | -0.016 | 0.23 | NO |
44 | USP7 | USP7 | USP7 | 10260 | -0.018 | 0.23 | NO |
45 | CHEK1 | CHEK1 | CHEK1 | 10375 | -0.02 | 0.23 | NO |
46 | E4F1 | E4F1 | E4F1 | 10460 | -0.021 | 0.23 | NO |
47 | KAT5 | KAT5 | KAT5 | 10525 | -0.022 | 0.23 | NO |
48 | AKT1 | AKT1 | AKT1 | 10567 | -0.022 | 0.24 | NO |
49 | CCNA2 | CCNA2 | CCNA2 | 10990 | -0.028 | 0.22 | NO |
50 | ABL1 | ABL1 | ABL1 | 11633 | -0.036 | 0.2 | NO |
51 | NEDD8 | NEDD8 | NEDD8 | 11708 | -0.037 | 0.21 | NO |
52 | CSNK1E | CSNK1E | CSNK1E | 11789 | -0.039 | 0.22 | NO |
53 | DYRK2 | DYRK2 | DYRK2 | 12261 | -0.045 | 0.2 | NO |
54 | TP53 | TP53 | TP53 | 12471 | -0.049 | 0.21 | NO |
55 | SETD7 | SETD7 | SETD7 | 12621 | -0.052 | 0.22 | NO |
56 | CDKN2A | CDKN2A | CDKN2A | 12842 | -0.055 | 0.22 | NO |
57 | MDM2 | MDM2 | MDM2 | 13289 | -0.064 | 0.22 | NO |
58 | CHEK2 | CHEK2 | CHEK2 | 13622 | -0.072 | 0.22 | NO |
59 | PPP2R4 | PPP2R4 | PPP2R4 | 13796 | -0.076 | 0.24 | NO |
Figure S41. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG RIBOSOME.

Figure S42. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIBOSOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S22. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ZNF492 | ZNF492 | ZNF492 | 6 | 0.78 | 0.022 | YES |
2 | ZNF415 | ZNF415 | ZNF415 | 39 | 0.61 | 0.038 | YES |
3 | ZNF454 | ZNF454 | ZNF454 | 48 | 0.58 | 0.055 | YES |
4 | ZNF382 | ZNF382 | ZNF382 | 59 | 0.55 | 0.07 | YES |
5 | ZNF98 | ZNF98 | ZNF98 | 80 | 0.52 | 0.084 | YES |
6 | RORC | RORC | RORC | 95 | 0.49 | 0.097 | YES |
7 | NR6A1 | NR6A1 | NR6A1 | 112 | 0.48 | 0.11 | YES |
8 | ZIM2 | ZIM2 | ZIM2 | 120 | 0.46 | 0.12 | YES |
9 | ZNF208 | ZNF208 | ZNF208 | 149 | 0.44 | 0.13 | YES |
10 | ESRRG | ESRRG | ESRRG | 183 | 0.42 | 0.14 | YES |
11 | ZNF560 | ZNF560 | ZNF560 | 209 | 0.4 | 0.16 | YES |
12 | ZNF154 | ZNF154 | ZNF154 | 336 | 0.35 | 0.16 | YES |
13 | ZNF285 | ZNF285 | ZNF285 | 360 | 0.34 | 0.17 | YES |
14 | ZNF215 | ZNF215 | ZNF215 | 393 | 0.34 | 0.17 | YES |
15 | ZNF471 | ZNF471 | ZNF471 | 401 | 0.33 | 0.18 | YES |
16 | PPARG | PPARG | PPARG | 423 | 0.32 | 0.19 | YES |
17 | ZFP2 | ZFP2 | ZFP2 | 461 | 0.32 | 0.2 | YES |
18 | ZNF433 | ZNF433 | ZNF433 | 463 | 0.32 | 0.21 | YES |
19 | ZNF157 | ZNF157 | ZNF157 | 475 | 0.31 | 0.22 | YES |
20 | NR5A1 | NR5A1 | NR5A1 | 513 | 0.3 | 0.22 | YES |
21 | NPPA | NPPA | NPPA | 518 | 0.3 | 0.23 | YES |
22 | ZNF214 | ZNF214 | ZNF214 | 547 | 0.29 | 0.24 | YES |
23 | ZFP37 | ZFP37 | ZFP37 | 558 | 0.29 | 0.25 | YES |
24 | ZNF610 | ZNF610 | ZNF610 | 661 | 0.27 | 0.25 | YES |
25 | ZNF439 | ZNF439 | ZNF439 | 773 | 0.24 | 0.25 | YES |
26 | ZNF114 | ZNF114 | ZNF114 | 812 | 0.24 | 0.25 | YES |
27 | ZNF334 | ZNF334 | ZNF334 | 855 | 0.23 | 0.26 | YES |
28 | ZNF354C | ZNF354C | ZNF354C | 873 | 0.23 | 0.26 | YES |
29 | ZIM3 | ZIM3 | ZIM3 | 895 | 0.22 | 0.27 | YES |
30 | ZNF311 | ZNF311 | ZNF311 | 922 | 0.22 | 0.27 | YES |
31 | ZNF544 | ZNF544 | ZNF544 | 931 | 0.22 | 0.28 | YES |
32 | ZNF577 | ZNF577 | ZNF577 | 964 | 0.21 | 0.28 | YES |
33 | ZIK1 | ZIK1 | ZIK1 | 982 | 0.21 | 0.29 | YES |
34 | ZNF197 | ZNF197 | ZNF197 | 983 | 0.21 | 0.3 | YES |
35 | ZNF287 | ZNF287 | ZNF287 | 1101 | 0.2 | 0.29 | YES |
36 | KAT2B | KAT2B | KAT2B | 1154 | 0.19 | 0.3 | YES |
37 | ZNF620 | ZNF620 | ZNF620 | 1162 | 0.19 | 0.3 | YES |
38 | ZNF23 | ZNF23 | ZNF23 | 1168 | 0.19 | 0.31 | YES |
39 | ZNF300 | ZNF300 | ZNF300 | 1169 | 0.19 | 0.31 | YES |
40 | ZNF619 | ZNF619 | ZNF619 | 1187 | 0.19 | 0.32 | YES |
41 | ZNF221 | ZNF221 | ZNF221 | 1277 | 0.18 | 0.32 | YES |
42 | ZNF621 | ZNF621 | ZNF621 | 1312 | 0.18 | 0.32 | YES |
43 | ZNF599 | ZNF599 | ZNF599 | 1335 | 0.18 | 0.32 | YES |
44 | ZNF773 | ZNF773 | ZNF773 | 1369 | 0.17 | 0.33 | YES |
45 | ZNF33B | ZNF33B | ZNF33B | 1505 | 0.16 | 0.32 | YES |
46 | ZNF649 | ZNF649 | ZNF649 | 1506 | 0.16 | 0.33 | YES |
47 | ZNF540 | ZNF540 | ZNF540 | 1518 | 0.16 | 0.33 | YES |
48 | ZNF418 | ZNF418 | ZNF418 | 1527 | 0.16 | 0.34 | YES |
49 | ZNF442 | ZNF442 | ZNF442 | 1533 | 0.16 | 0.34 | YES |
50 | ZNF493 | ZNF493 | ZNF493 | 1544 | 0.16 | 0.35 | YES |
51 | ZNF354B | ZNF354B | ZNF354B | 1548 | 0.16 | 0.35 | YES |
52 | ZNF607 | ZNF607 | ZNF607 | 1551 | 0.16 | 0.36 | YES |
53 | NR1D2 | NR1D2 | NR1D2 | 1553 | 0.16 | 0.36 | YES |
54 | ZNF519 | ZNF519 | ZNF519 | 1621 | 0.15 | 0.36 | YES |
55 | ZNF419 | ZNF419 | ZNF419 | 1626 | 0.15 | 0.36 | YES |
56 | ZNF347 | ZNF347 | ZNF347 | 1689 | 0.15 | 0.37 | YES |
57 | ZNF551 | ZNF551 | ZNF551 | 1780 | 0.14 | 0.36 | YES |
58 | ZNF320 | ZNF320 | ZNF320 | 1870 | 0.14 | 0.36 | YES |
59 | NR0B2 | NR0B2 | NR0B2 | 1872 | 0.14 | 0.37 | YES |
60 | ZNF184 | ZNF184 | ZNF184 | 1900 | 0.14 | 0.37 | YES |
61 | ZNF614 | ZNF614 | ZNF614 | 1910 | 0.14 | 0.37 | YES |
62 | ZNF528 | ZNF528 | ZNF528 | 1917 | 0.14 | 0.38 | YES |
63 | ZNF570 | ZNF570 | ZNF570 | 1970 | 0.13 | 0.38 | YES |
64 | ZNF286A | ZNF286A | ZNF286A | 1975 | 0.13 | 0.38 | YES |
65 | ZKSCAN3 | ZKSCAN3 | ZKSCAN3 | 1992 | 0.13 | 0.38 | YES |
66 | ZNF354A | ZNF354A | ZNF354A | 2070 | 0.13 | 0.38 | YES |
67 | ZNF559 | ZNF559 | ZNF559 | 2081 | 0.13 | 0.39 | YES |
68 | ZNF615 | ZNF615 | ZNF615 | 2096 | 0.13 | 0.39 | YES |
69 | ZNF627 | ZNF627 | ZNF627 | 2126 | 0.12 | 0.39 | YES |
70 | ZNF564 | ZNF564 | ZNF564 | 2155 | 0.12 | 0.39 | YES |
71 | ZKSCAN4 | ZKSCAN4 | ZKSCAN4 | 2180 | 0.12 | 0.4 | YES |
72 | ZNF569 | ZNF569 | ZNF569 | 2208 | 0.12 | 0.4 | YES |
73 | ZNF445 | ZNF445 | ZNF445 | 2214 | 0.12 | 0.4 | YES |
74 | ZNF211 | ZNF211 | ZNF211 | 2221 | 0.12 | 0.4 | YES |
75 | ZNF529 | ZNF529 | ZNF529 | 2235 | 0.12 | 0.41 | YES |
76 | ZNF443 | ZNF443 | ZNF443 | 2248 | 0.12 | 0.41 | YES |
77 | ZNF441 | ZNF441 | ZNF441 | 2262 | 0.12 | 0.41 | YES |
78 | ZNF10 | ZNF10 | ZNF10 | 2269 | 0.12 | 0.42 | YES |
79 | ZNF235 | ZNF235 | ZNF235 | 2296 | 0.12 | 0.42 | YES |
80 | ZNF440 | ZNF440 | ZNF440 | 2298 | 0.12 | 0.42 | YES |
81 | ZFP28 | ZFP28 | ZFP28 | 2321 | 0.12 | 0.42 | YES |
82 | ZNF30 | ZNF30 | ZNF30 | 2350 | 0.12 | 0.42 | YES |
83 | ZNF616 | ZNF616 | ZNF616 | 2359 | 0.11 | 0.43 | YES |
84 | ZNF583 | ZNF583 | ZNF583 | 2401 | 0.11 | 0.43 | YES |
85 | ZNF558 | ZNF558 | ZNF558 | 2421 | 0.11 | 0.43 | YES |
86 | ZNF223 | ZNF223 | ZNF223 | 2458 | 0.11 | 0.43 | YES |
87 | ZNF555 | ZNF555 | ZNF555 | 2463 | 0.11 | 0.44 | YES |
88 | ZNF160 | ZNF160 | ZNF160 | 2470 | 0.11 | 0.44 | YES |
89 | ZNF514 | ZNF514 | ZNF514 | 2486 | 0.11 | 0.44 | YES |
90 | ZNF613 | ZNF613 | ZNF613 | 2512 | 0.11 | 0.44 | YES |
91 | ZNF530 | ZNF530 | ZNF530 | 2513 | 0.11 | 0.44 | YES |
92 | ZNF14 | ZNF14 | ZNF14 | 2533 | 0.11 | 0.45 | YES |
93 | ZNF606 | ZNF606 | ZNF606 | 2563 | 0.11 | 0.45 | YES |
94 | ZNF548 | ZNF548 | ZNF548 | 2564 | 0.11 | 0.45 | YES |
95 | ZNF155 | ZNF155 | ZNF155 | 2577 | 0.11 | 0.45 | YES |
96 | ZNF600 | ZNF600 | ZNF600 | 2620 | 0.1 | 0.46 | YES |
97 | RORA | RORA | RORA | 2651 | 0.1 | 0.46 | YES |
98 | ZNF563 | ZNF563 | ZNF563 | 2657 | 0.1 | 0.46 | YES |
99 | MED20 | MED20 | MED20 | 2689 | 0.1 | 0.46 | YES |
100 | ZNF20 | ZNF20 | ZNF20 | 2712 | 0.1 | 0.46 | YES |
101 | ZNF552 | ZNF552 | ZNF552 | 2718 | 0.1 | 0.46 | YES |
102 | SKIL | SKIL | SKIL | 2789 | 0.098 | 0.46 | YES |
103 | ZNF658 | ZNF658 | ZNF658 | 2805 | 0.098 | 0.46 | YES |
104 | ZNF304 | ZNF304 | ZNF304 | 2850 | 0.096 | 0.46 | YES |
105 | ZNF605 | ZNF605 | ZNF605 | 2865 | 0.096 | 0.47 | YES |
106 | ZNF587 | ZNF587 | ZNF587 | 2878 | 0.095 | 0.47 | YES |
107 | ZNF426 | ZNF426 | ZNF426 | 2889 | 0.095 | 0.47 | YES |
108 | UBE2D1 | UBE2D1 | UBE2D1 | 2904 | 0.094 | 0.47 | YES |
109 | NR3C2 | NR3C2 | NR3C2 | 2914 | 0.094 | 0.48 | YES |
110 | ZNF169 | ZNF169 | ZNF169 | 2930 | 0.093 | 0.48 | YES |
111 | ZNF567 | ZNF567 | ZNF567 | 2934 | 0.093 | 0.48 | YES |
112 | ZNF611 | ZNF611 | ZNF611 | 2939 | 0.093 | 0.48 | YES |
113 | ZNF625 | ZNF625 | ZNF625 | 2954 | 0.093 | 0.48 | YES |
114 | ZNF19 | ZNF19 | ZNF19 | 2980 | 0.092 | 0.49 | YES |
115 | ZNF350 | ZNF350 | ZNF350 | 2988 | 0.092 | 0.49 | YES |
116 | ZNF431 | ZNF431 | ZNF431 | 3001 | 0.091 | 0.49 | YES |
117 | ZNF141 | ZNF141 | ZNF141 | 3054 | 0.09 | 0.49 | YES |
118 | ZNF582 | ZNF582 | ZNF582 | 3057 | 0.09 | 0.49 | YES |
119 | NR4A3 | NR4A3 | NR4A3 | 3108 | 0.088 | 0.49 | YES |
120 | ZNF230 | ZNF230 | ZNF230 | 3114 | 0.088 | 0.49 | YES |
121 | ZNF571 | ZNF571 | ZNF571 | 3116 | 0.088 | 0.5 | YES |
122 | ZNF585A | ZNF585A | ZNF585A | 3171 | 0.086 | 0.5 | YES |
123 | ZNF543 | ZNF543 | ZNF543 | 3176 | 0.086 | 0.5 | YES |
124 | ZNF506 | ZNF506 | ZNF506 | 3206 | 0.085 | 0.5 | YES |
125 | ZNF561 | ZNF561 | ZNF561 | 3257 | 0.084 | 0.5 | YES |
126 | RXRB | RXRB | RXRB | 3306 | 0.082 | 0.5 | YES |
127 | ZNF589 | ZNF589 | ZNF589 | 3318 | 0.082 | 0.5 | YES |
128 | ZNF425 | ZNF425 | ZNF425 | 3339 | 0.081 | 0.5 | YES |
129 | NR3C1 | NR3C1 | NR3C1 | 3340 | 0.081 | 0.5 | YES |
130 | ZNF274 | ZNF274 | ZNF274 | 3366 | 0.08 | 0.5 | YES |
131 | ZNF254 | ZNF254 | ZNF254 | 3442 | 0.078 | 0.5 | YES |
132 | ZNF224 | ZNF224 | ZNF224 | 3465 | 0.078 | 0.5 | YES |
133 | ZFP90 | ZFP90 | ZFP90 | 3503 | 0.077 | 0.5 | YES |
134 | ZNF28 | ZNF28 | ZNF28 | 3527 | 0.076 | 0.5 | YES |
135 | ZNF26 | ZNF26 | ZNF26 | 3539 | 0.076 | 0.51 | YES |
136 | ZNF383 | ZNF383 | ZNF383 | 3553 | 0.075 | 0.51 | YES |
137 | ZNF547 | ZNF547 | ZNF547 | 3579 | 0.075 | 0.51 | YES |
138 | NR1I2 | NR1I2 | NR1I2 | 3597 | 0.074 | 0.51 | YES |
139 | SMURF2 | SMURF2 | SMURF2 | 3614 | 0.074 | 0.51 | YES |
140 | ZNF175 | ZNF175 | ZNF175 | 3668 | 0.072 | 0.51 | YES |
141 | ZNF490 | ZNF490 | ZNF490 | 3683 | 0.072 | 0.51 | YES |
142 | ZNF432 | ZNF432 | ZNF432 | 3697 | 0.072 | 0.51 | YES |
143 | ZNF416 | ZNF416 | ZNF416 | 3706 | 0.072 | 0.51 | YES |
144 | ZNF655 | ZNF655 | ZNF655 | 3752 | 0.071 | 0.51 | YES |
145 | ZNF331 | ZNF331 | ZNF331 | 3778 | 0.07 | 0.51 | YES |
146 | ZNF202 | ZNF202 | ZNF202 | 3784 | 0.07 | 0.52 | YES |
147 | ZNF337 | ZNF337 | ZNF337 | 3802 | 0.07 | 0.52 | YES |
148 | ZNF266 | ZNF266 | ZNF266 | 3838 | 0.069 | 0.52 | YES |
149 | ZNF485 | ZNF485 | ZNF485 | 3855 | 0.068 | 0.52 | YES |
150 | NR1I3 | NR1I3 | NR1I3 | 3863 | 0.068 | 0.52 | YES |
151 | ZNF624 | ZNF624 | ZNF624 | 3879 | 0.068 | 0.52 | YES |
152 | ZNF180 | ZNF180 | ZNF180 | 3907 | 0.067 | 0.52 | YES |
153 | RPS27A | RPS27A | RPS27A | 3935 | 0.067 | 0.52 | YES |
154 | ZNF566 | ZNF566 | ZNF566 | 3942 | 0.066 | 0.52 | YES |
155 | ZNF227 | ZNF227 | ZNF227 | 3967 | 0.066 | 0.52 | YES |
156 | ZNF45 | ZNF45 | ZNF45 | 3978 | 0.066 | 0.52 | YES |
157 | TEAD1 | TEAD1 | TEAD1 | 4027 | 0.065 | 0.52 | YES |
158 | ZNF484 | ZNF484 | ZNF484 | 4081 | 0.064 | 0.52 | YES |
159 | ZNF417 | ZNF417 | ZNF417 | 4094 | 0.063 | 0.52 | YES |
160 | ZNF17 | ZNF17 | ZNF17 | 4126 | 0.062 | 0.52 | YES |
161 | ZNF394 | ZNF394 | ZNF394 | 4181 | 0.062 | 0.52 | YES |
162 | MYC | MYC | MYC | 4190 | 0.061 | 0.52 | YES |
163 | ZNF420 | ZNF420 | ZNF420 | 4193 | 0.061 | 0.53 | YES |
164 | ZNF333 | ZNF333 | ZNF333 | 4198 | 0.061 | 0.53 | YES |
165 | ZNF430 | ZNF430 | ZNF430 | 4203 | 0.061 | 0.53 | YES |
166 | ZNF136 | ZNF136 | ZNF136 | 4238 | 0.06 | 0.53 | NO |
167 | TGIF1 | TGIF1 | TGIF1 | 4327 | 0.058 | 0.53 | NO |
168 | ZNF234 | ZNF234 | ZNF234 | 4361 | 0.058 | 0.52 | NO |
169 | CCNC | CCNC | CCNC | 4518 | 0.055 | 0.52 | NO |
170 | NOTCH2 | NOTCH2 | NOTCH2 | 4565 | 0.054 | 0.52 | NO |
171 | ZNF468 | ZNF468 | ZNF468 | 4584 | 0.054 | 0.52 | NO |
172 | ZNF264 | ZNF264 | ZNF264 | 4592 | 0.053 | 0.52 | NO |
173 | ZNF225 | ZNF225 | ZNF225 | 4625 | 0.053 | 0.52 | NO |
174 | TEAD3 | TEAD3 | TEAD3 | 4632 | 0.052 | 0.52 | NO |
175 | ZNF256 | ZNF256 | ZNF256 | 4656 | 0.052 | 0.52 | NO |
176 | ZNF460 | ZNF460 | ZNF460 | 4657 | 0.052 | 0.52 | NO |
177 | ZNF595 | ZNF595 | ZNF595 | 4660 | 0.052 | 0.52 | NO |
178 | ZNF222 | ZNF222 | ZNF222 | 4726 | 0.051 | 0.52 | NO |
179 | ZNF473 | ZNF473 | ZNF473 | 4737 | 0.05 | 0.52 | NO |
180 | ZKSCAN1 | ZKSCAN1 | ZKSCAN1 | 4778 | 0.05 | 0.52 | NO |
181 | CCNT2 | CCNT2 | CCNT2 | 4800 | 0.05 | 0.52 | NO |
182 | ZFP1 | ZFP1 | ZFP1 | 4874 | 0.048 | 0.52 | NO |
183 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 4945 | 0.047 | 0.52 | NO |
184 | TEAD2 | TEAD2 | TEAD2 | 5005 | 0.046 | 0.51 | NO |
185 | ZNF343 | ZNF343 | ZNF343 | 5028 | 0.046 | 0.51 | NO |
186 | ZNF37A | ZNF37A | ZNF37A | 5051 | 0.046 | 0.51 | NO |
187 | ZNF248 | ZNF248 | ZNF248 | 5065 | 0.045 | 0.51 | NO |
188 | TGIF2 | TGIF2 | TGIF2 | 5084 | 0.045 | 0.52 | NO |
189 | TRIM33 | TRIM33 | TRIM33 | 5168 | 0.044 | 0.51 | NO |
190 | ZNF3 | ZNF3 | ZNF3 | 5175 | 0.044 | 0.51 | NO |
191 | ZNF189 | ZNF189 | ZNF189 | 5235 | 0.043 | 0.51 | NO |
192 | ZNF708 | ZNF708 | ZNF708 | 5255 | 0.042 | 0.51 | NO |
193 | MED23 | MED23 | MED23 | 5281 | 0.042 | 0.51 | NO |
194 | SMAD4 | SMAD4 | SMAD4 | 5310 | 0.042 | 0.51 | NO |
195 | ZNF140 | ZNF140 | ZNF140 | 5313 | 0.042 | 0.51 | NO |
196 | PPM1A | PPM1A | PPM1A | 5446 | 0.04 | 0.5 | NO |
197 | NCOA1 | NCOA1 | NCOA1 | 5497 | 0.039 | 0.5 | NO |
198 | ZNF556 | ZNF556 | ZNF556 | 5498 | 0.039 | 0.5 | NO |
199 | RXRG | RXRG | RXRG | 5521 | 0.038 | 0.5 | NO |
200 | ZNF500 | ZNF500 | ZNF500 | 5612 | 0.037 | 0.5 | NO |
201 | ZNF101 | ZNF101 | ZNF101 | 5618 | 0.037 | 0.5 | NO |
202 | SMAD7 | SMAD7 | SMAD7 | 5682 | 0.036 | 0.5 | NO |
203 | ZNF33A | ZNF33A | ZNF33A | 5701 | 0.036 | 0.5 | NO |
204 | ZNF12 | ZNF12 | ZNF12 | 5711 | 0.036 | 0.5 | NO |
205 | ZNF597 | ZNF597 | ZNF597 | 5733 | 0.036 | 0.5 | NO |
206 | MED17 | MED17 | MED17 | 5774 | 0.035 | 0.5 | NO |
207 | ZNF510 | ZNF510 | ZNF510 | 5860 | 0.034 | 0.49 | NO |
208 | ZNF324 | ZNF324 | ZNF324 | 5954 | 0.032 | 0.49 | NO |
209 | ZNF585B | ZNF585B | ZNF585B | 6096 | 0.031 | 0.48 | NO |
210 | TBL1X | TBL1X | TBL1X | 6103 | 0.03 | 0.48 | NO |
211 | ZNF496 | ZNF496 | ZNF496 | 6117 | 0.03 | 0.48 | NO |
212 | CDKN2B | CDKN2B | CDKN2B | 6221 | 0.029 | 0.48 | NO |
213 | ZNF138 | ZNF138 | ZNF138 | 6258 | 0.029 | 0.48 | NO |
214 | ZNF273 | ZNF273 | ZNF273 | 6546 | 0.025 | 0.46 | NO |
215 | ESRRA | ESRRA | ESRRA | 6549 | 0.025 | 0.46 | NO |
216 | MED10 | MED10 | MED10 | 6565 | 0.025 | 0.46 | NO |
217 | ZNF596 | ZNF596 | ZNF596 | 6625 | 0.024 | 0.46 | NO |
218 | ZNF226 | ZNF226 | ZNF226 | 6626 | 0.024 | 0.46 | NO |
219 | SKI | SKI | SKI | 6677 | 0.024 | 0.46 | NO |
220 | THRB | THRB | THRB | 6703 | 0.023 | 0.46 | NO |
221 | ZNF200 | ZNF200 | ZNF200 | 6729 | 0.023 | 0.46 | NO |
222 | SP1 | SP1 | SP1 | 6764 | 0.023 | 0.46 | NO |
223 | ZNF557 | ZNF557 | ZNF557 | 6871 | 0.021 | 0.45 | NO |
224 | NR4A2 | NR4A2 | NR4A2 | 7016 | 0.019 | 0.44 | NO |
225 | RBL1 | RBL1 | RBL1 | 7150 | 0.018 | 0.44 | NO |
226 | MED14 | MED14 | MED14 | 7155 | 0.018 | 0.44 | NO |
227 | ZNF2 | ZNF2 | ZNF2 | 7172 | 0.017 | 0.44 | NO |
228 | ZNF480 | ZNF480 | ZNF480 | 7221 | 0.017 | 0.43 | NO |
229 | ZNF25 | ZNF25 | ZNF25 | 7233 | 0.017 | 0.43 | NO |
230 | SMAD2 | SMAD2 | SMAD2 | 7267 | 0.016 | 0.43 | NO |
231 | ZNF250 | ZNF250 | ZNF250 | 7304 | 0.016 | 0.43 | NO |
232 | PPARD | PPARD | PPARD | 7333 | 0.016 | 0.43 | NO |
233 | E2F4 | E2F4 | E2F4 | 7375 | 0.015 | 0.43 | NO |
234 | ZNF43 | ZNF43 | ZNF43 | 7391 | 0.015 | 0.43 | NO |
235 | ZNF641 | ZNF641 | ZNF641 | 7443 | 0.014 | 0.42 | NO |
236 | ZNF565 | ZNF565 | ZNF565 | 7485 | 0.014 | 0.42 | NO |
237 | ZNF317 | ZNF317 | ZNF317 | 7501 | 0.014 | 0.42 | NO |
238 | ZKSCAN5 | ZKSCAN5 | ZKSCAN5 | 7620 | 0.012 | 0.42 | NO |
239 | ZNF398 | ZNF398 | ZNF398 | 7665 | 0.012 | 0.41 | NO |
240 | NRBF2 | NRBF2 | NRBF2 | 7700 | 0.011 | 0.41 | NO |
241 | MED4 | MED4 | MED4 | 7728 | 0.011 | 0.41 | NO |
242 | CCNT1 | CCNT1 | CCNT1 | 7736 | 0.011 | 0.41 | NO |
243 | NR2C2AP | NR2C2AP | NR2C2AP | 7750 | 0.011 | 0.41 | NO |
244 | ZNF212 | ZNF212 | ZNF212 | 7760 | 0.01 | 0.41 | NO |
245 | PPARA | PPARA | PPARA | 7817 | 0.01 | 0.41 | NO |
246 | ZNF436 | ZNF436 | ZNF436 | 7835 | 0.0099 | 0.41 | NO |
247 | ZNF205 | ZNF205 | ZNF205 | 7850 | 0.0097 | 0.4 | NO |
248 | MAML1 | MAML1 | MAML1 | 7886 | 0.0093 | 0.4 | NO |
249 | MED7 | MED7 | MED7 | 7996 | 0.008 | 0.4 | NO |
250 | ZNF546 | ZNF546 | ZNF546 | 8003 | 0.0079 | 0.4 | NO |
251 | UBE2D3 | UBE2D3 | UBE2D3 | 8050 | 0.0074 | 0.4 | NO |
252 | UBA52 | UBA52 | UBA52 | 8081 | 0.0071 | 0.39 | NO |
253 | ZNF92 | ZNF92 | ZNF92 | 8082 | 0.0071 | 0.39 | NO |
254 | ZNF584 | ZNF584 | ZNF584 | 8123 | 0.0067 | 0.39 | NO |
255 | MED1 | MED1 | MED1 | 8178 | 0.0061 | 0.39 | NO |
256 | NR2E1 | NR2E1 | NR2E1 | 8186 | 0.006 | 0.39 | NO |
257 | NR1H2 | NR1H2 | NR1H2 | 8287 | 0.0047 | 0.38 | NO |
258 | USP9X | USP9X | USP9X | 8405 | 0.0034 | 0.38 | NO |
259 | YAP1 | YAP1 | YAP1 | 8438 | 0.0031 | 0.38 | NO |
260 | ZNF263 | ZNF263 | ZNF263 | 8446 | 0.003 | 0.38 | NO |
261 | CDK8 | CDK8 | CDK8 | 8450 | 0.0029 | 0.38 | NO |
262 | MAMLD1 | MAMLD1 | MAMLD1 | 8483 | 0.0025 | 0.37 | NO |
263 | TRIM28 | TRIM28 | TRIM28 | 8720 | -0.00025 | 0.36 | NO |
264 | NCOA6 | NCOA6 | NCOA6 | 9030 | -0.0039 | 0.34 | NO |
265 | NCOA3 | NCOA3 | NCOA3 | 9096 | -0.0046 | 0.34 | NO |
266 | TFDP1 | TFDP1 | TFDP1 | 9101 | -0.0047 | 0.34 | NO |
267 | ZNF100 | ZNF100 | ZNF100 | 9558 | -0.01 | 0.31 | NO |
268 | CREBBP | CREBBP | CREBBP | 9738 | -0.012 | 0.3 | NO |
269 | ZNF267 | ZNF267 | ZNF267 | 9750 | -0.012 | 0.3 | NO |
270 | ZNF446 | ZNF446 | ZNF446 | 9788 | -0.013 | 0.3 | NO |
271 | RXRA | RXRA | RXRA | 9793 | -0.013 | 0.3 | NO |
272 | MED27 | MED27 | MED27 | 9848 | -0.014 | 0.3 | NO |
273 | NRBP1 | NRBP1 | NRBP1 | 9970 | -0.015 | 0.29 | NO |
274 | MED8 | MED8 | MED8 | 10262 | -0.018 | 0.28 | NO |
275 | MED26 | MED26 | MED26 | 10275 | -0.019 | 0.28 | NO |
276 | MED12 | MED12 | MED12 | 10293 | -0.019 | 0.28 | NO |
277 | MED31 | MED31 | MED31 | 10352 | -0.02 | 0.27 | NO |
278 | MED30 | MED30 | MED30 | 10517 | -0.022 | 0.26 | NO |
279 | NR4A1 | NR4A1 | NR4A1 | 10536 | -0.022 | 0.26 | NO |
280 | ZNF282 | ZNF282 | ZNF282 | 10687 | -0.024 | 0.26 | NO |
281 | ZNF18 | ZNF18 | ZNF18 | 10751 | -0.025 | 0.25 | NO |
282 | MAML2 | MAML2 | MAML2 | 10781 | -0.025 | 0.25 | NO |
283 | SNW1 | SNW1 | SNW1 | 10793 | -0.025 | 0.25 | NO |
284 | MED6 | MED6 | MED6 | 10800 | -0.026 | 0.25 | NO |
285 | RARA | RARA | RARA | 10819 | -0.026 | 0.25 | NO |
286 | THRA | THRA | THRA | 10832 | -0.026 | 0.25 | NO |
287 | HDAC1 | HDAC1 | HDAC1 | 10867 | -0.026 | 0.25 | NO |
288 | NOTCH4 | NOTCH4 | NOTCH4 | 10925 | -0.027 | 0.25 | NO |
289 | NCOR1 | NCOR1 | NCOR1 | 10931 | -0.027 | 0.25 | NO |
290 | KAT2A | KAT2A | KAT2A | 11035 | -0.028 | 0.24 | NO |
291 | CTGF | CTGF | CTGF | 11122 | -0.03 | 0.24 | NO |
292 | PARP1 | PARP1 | PARP1 | 11372 | -0.033 | 0.23 | NO |
293 | NR2F6 | NR2F6 | NR2F6 | 11409 | -0.033 | 0.23 | NO |
294 | ZNF213 | ZNF213 | ZNF213 | 11475 | -0.034 | 0.22 | NO |
295 | CDK9 | CDK9 | CDK9 | 11741 | -0.038 | 0.21 | NO |
296 | RARG | RARG | RARG | 11852 | -0.039 | 0.21 | NO |
297 | MED24 | MED24 | MED24 | 12069 | -0.042 | 0.2 | NO |
298 | NCOR2 | NCOR2 | NCOR2 | 12133 | -0.044 | 0.19 | NO |
299 | MAML3 | MAML3 | MAML3 | 12197 | -0.044 | 0.19 | NO |
300 | NCOA2 | NCOA2 | NCOA2 | 12211 | -0.044 | 0.19 | NO |
301 | E2F5 | E2F5 | E2F5 | 12234 | -0.045 | 0.19 | NO |
302 | SMAD3 | SMAD3 | SMAD3 | 12254 | -0.045 | 0.19 | NO |
303 | RBPJ | RBPJ | RBPJ | 12759 | -0.054 | 0.16 | NO |
304 | NR1D1 | NR1D1 | NR1D1 | 12821 | -0.055 | 0.16 | NO |
305 | MED16 | MED16 | MED16 | 12913 | -0.057 | 0.16 | NO |
306 | ZNF517 | ZNF517 | ZNF517 | 12926 | -0.057 | 0.16 | NO |
307 | MEN1 | MEN1 | MEN1 | 13104 | -0.061 | 0.15 | NO |
308 | MED25 | MED25 | MED25 | 13438 | -0.068 | 0.14 | NO |
309 | NR1H3 | NR1H3 | NR1H3 | 13495 | -0.069 | 0.13 | NO |
310 | TGS1 | TGS1 | TGS1 | 13526 | -0.07 | 0.13 | NO |
311 | JUNB | JUNB | JUNB | 13584 | -0.071 | 0.13 | NO |
312 | ESRRB | ESRRB | ESRRB | 13643 | -0.072 | 0.13 | NO |
313 | MED15 | MED15 | MED15 | 14537 | -0.097 | 0.084 | NO |
314 | TEAD4 | TEAD4 | TEAD4 | 14896 | -0.11 | 0.067 | NO |
315 | SMARCD3 | SMARCD3 | SMARCD3 | 14974 | -0.12 | 0.066 | NO |
316 | ZNF483 | ZNF483 | ZNF483 | 15145 | -0.12 | 0.06 | NO |
317 | RORB | RORB | RORB | 15269 | -0.13 | 0.057 | NO |
318 | TBX5 | TBX5 | TBX5 | 15465 | -0.14 | 0.05 | NO |
319 | WWTR1 | WWTR1 | WWTR1 | 15472 | -0.14 | 0.054 | NO |
320 | ESR1 | ESR1 | ESR1 | 15495 | -0.14 | 0.056 | NO |
321 | AR | AR | AR | 15633 | -0.15 | 0.053 | NO |
322 | VDR | VDR | VDR | 15913 | -0.16 | 0.042 | NO |
323 | NOTCH3 | NOTCH3 | NOTCH3 | 15918 | -0.16 | 0.047 | NO |
324 | ESR2 | ESR2 | ESR2 | 16320 | -0.19 | 0.03 | NO |
325 | NR2F1 | NR2F1 | NR2F1 | 16439 | -0.2 | 0.029 | NO |
326 | RUNX2 | RUNX2 | RUNX2 | 16701 | -0.22 | 0.02 | NO |
327 | PGR | PGR | PGR | 16865 | -0.24 | 0.018 | NO |
328 | HNF4A | HNF4A | HNF4A | 16901 | -0.24 | 0.023 | NO |
329 | NR2E3 | NR2E3 | NR2E3 | 16963 | -0.24 | 0.027 | NO |
330 | HNF4G | HNF4G | HNF4G | 17271 | -0.28 | 0.018 | NO |
331 | SERPINE1 | SERPINE1 | SERPINE1 | 17292 | -0.28 | 0.025 | NO |
332 | NR5A2 | NR5A2 | NR5A2 | 17487 | -0.32 | 0.023 | NO |
333 | NR0B1 | NR0B1 | NR0B1 | 17745 | -0.38 | 0.019 | NO |
Figure S43. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: PID P53 REGULATION PATHWAY.

Figure S44. Get High-res Image For the top 5 core enriched genes in the pathway: PID P53 REGULATION PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S23. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | EFS | EFS | EFS | 299 | 0.36 | 0.095 | YES |
2 | SLC25A38 | SLC25A38 | SLC25A38 | 973 | 0.21 | 0.12 | YES |
3 | PSD3 | PSD3 | PSD3 | 1289 | 0.18 | 0.16 | YES |
4 | TSC22D2 | TSC22D2 | TSC22D2 | 1304 | 0.18 | 0.22 | YES |
5 | PRUNE2 | PRUNE2 | PRUNE2 | 1866 | 0.14 | 0.23 | YES |
6 | PTP4A1 | PTP4A1 | PTP4A1 | 2917 | 0.094 | 0.2 | YES |
7 | TBPL1 | TBPL1 | TBPL1 | 3329 | 0.082 | 0.2 | YES |
8 | ERCC6 | ERCC6 | ERCC6 | 3477 | 0.078 | 0.22 | YES |
9 | CCHCR1 | CCHCR1 | CCHCR1 | 3536 | 0.076 | 0.24 | YES |
10 | TMEM231 | TMEM231 | TMEM231 | 3786 | 0.07 | 0.24 | YES |
11 | TRMT61B | TRMT61B | TRMT61B | 3841 | 0.069 | 0.26 | YES |
12 | NPRL2 | NPRL2 | NPRL2 | 4093 | 0.063 | 0.27 | YES |
13 | U2AF1 | U2AF1 | U2AF1 | 4140 | 0.062 | 0.28 | YES |
14 | TIMM9 | TIMM9 | TIMM9 | 4300 | 0.059 | 0.29 | YES |
15 | RNF138 | RNF138 | RNF138 | 4408 | 0.057 | 0.3 | YES |
16 | FBXO21 | FBXO21 | FBXO21 | 4428 | 0.056 | 0.32 | YES |
17 | VEZT | VEZT | VEZT | 4739 | 0.05 | 0.32 | YES |
18 | PCF11 | PCF11 | PCF11 | 4856 | 0.049 | 0.33 | YES |
19 | EIF1AX | EIF1AX | EIF1AX | 4918 | 0.048 | 0.34 | YES |
20 | NAP1L3 | NAP1L3 | NAP1L3 | 5004 | 0.046 | 0.35 | YES |
21 | DDX10 | DDX10 | DDX10 | 5530 | 0.038 | 0.33 | YES |
22 | NAA16 | NAA16 | NAA16 | 5730 | 0.036 | 0.33 | YES |
23 | TRAPPC2 | TRAPPC2 | TRAPPC2 | 5878 | 0.034 | 0.33 | YES |
24 | TMPO | TMPO | TMPO | 5973 | 0.032 | 0.34 | YES |
25 | FBXO11 | FBXO11 | FBXO11 | 6017 | 0.032 | 0.34 | YES |
26 | VEZF1 | VEZF1 | VEZF1 | 6225 | 0.029 | 0.34 | YES |
27 | SRSF3 | SRSF3 | SRSF3 | 6278 | 0.028 | 0.35 | YES |
28 | CARS2 | CARS2 | CARS2 | 6301 | 0.028 | 0.36 | YES |
29 | ZFP64 | ZFP64 | ZFP64 | 6387 | 0.027 | 0.36 | YES |
30 | RBBP6 | RBBP6 | RBBP6 | 6421 | 0.027 | 0.36 | YES |
31 | PAPOLA | PAPOLA | PAPOLA | 6470 | 0.026 | 0.37 | YES |
32 | UBQLN4 | UBQLN4 | UBQLN4 | 6997 | 0.02 | 0.35 | NO |
33 | RBBP7 | RBBP7 | RBBP7 | 7352 | 0.015 | 0.33 | NO |
34 | HIC2 | HIC2 | HIC2 | 7742 | 0.011 | 0.31 | NO |
35 | PTPN2 | PTPN2 | PTPN2 | 8137 | 0.0066 | 0.29 | NO |
36 | TTC27 | TTC27 | TTC27 | 8284 | 0.0048 | 0.29 | NO |
37 | FARP1 | FARP1 | FARP1 | 8288 | 0.0047 | 0.29 | NO |
38 | MIA3 | MIA3 | MIA3 | 8328 | 0.0042 | 0.29 | NO |
39 | CNOT2 | CNOT2 | CNOT2 | 8354 | 0.004 | 0.29 | NO |
40 | EIF5B | EIF5B | EIF5B | 8485 | 0.0024 | 0.28 | NO |
41 | ZDHHC6 | ZDHHC6 | ZDHHC6 | 8661 | 0.00052 | 0.27 | NO |
42 | STX18 | STX18 | STX18 | 8835 | -0.0017 | 0.26 | NO |
43 | RAD51C | RAD51C | RAD51C | 8929 | -0.0028 | 0.26 | NO |
44 | GON4L | GON4L | GON4L | 9051 | -0.0041 | 0.25 | NO |
45 | UBR7 | UBR7 | UBR7 | 9152 | -0.0053 | 0.25 | NO |
46 | YTHDF1 | YTHDF1 | YTHDF1 | 9320 | -0.0074 | 0.24 | NO |
47 | CSE1L | CSE1L | CSE1L | 9507 | -0.0096 | 0.24 | NO |
48 | RAD23B | RAD23B | RAD23B | 9627 | -0.011 | 0.23 | NO |
49 | EMG1 | EMG1 | EMG1 | 9952 | -0.015 | 0.22 | NO |
50 | MAX | MAX | MAX | 10485 | -0.021 | 0.2 | NO |
51 | HCFC1 | HCFC1 | HCFC1 | 10594 | -0.023 | 0.2 | NO |
52 | NXT1 | NXT1 | NXT1 | 10669 | -0.024 | 0.2 | NO |
53 | PCMT1 | PCMT1 | PCMT1 | 10775 | -0.025 | 0.2 | NO |
54 | ISG20L2 | ISG20L2 | ISG20L2 | 11144 | -0.03 | 0.19 | NO |
55 | GOSR2 | GOSR2 | GOSR2 | 11437 | -0.034 | 0.18 | NO |
56 | ANP32E | ANP32E | ANP32E | 11652 | -0.037 | 0.18 | NO |
57 | SMARCA4 | SMARCA4 | SMARCA4 | 12259 | -0.045 | 0.16 | NO |
58 | BCS1L | BCS1L | BCS1L | 12420 | -0.048 | 0.17 | NO |
59 | SLC35A2 | SLC35A2 | SLC35A2 | 12447 | -0.049 | 0.18 | NO |
60 | RUVBL2 | RUVBL2 | RUVBL2 | 12841 | -0.055 | 0.18 | NO |
61 | TCEA1 | TCEA1 | TCEA1 | 13207 | -0.063 | 0.18 | NO |
62 | IGFBP5 | IGFBP5 | IGFBP5 | 13730 | -0.074 | 0.17 | NO |
63 | PHGDH | PHGDH | PHGDH | 14902 | -0.11 | 0.14 | NO |
64 | TNFAIP8 | TNFAIP8 | TNFAIP8 | 15021 | -0.12 | 0.17 | NO |
Figure S45. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME TRANSLATION.

Figure S46. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S24. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PDGFD | PDGFD | PDGFD | 357 | 0.34 | 0.082 | YES |
2 | COX6A2 | COX6A2 | COX6A2 | 382 | 0.34 | 0.18 | YES |
3 | FAM129A | FAM129A | FAM129A | 808 | 0.24 | 0.23 | YES |
4 | ID2 | ID2 | ID2 | 946 | 0.22 | 0.28 | YES |
5 | H2AFY2 | H2AFY2 | H2AFY2 | 999 | 0.21 | 0.34 | YES |
6 | PTPRN2 | PTPRN2 | PTPRN2 | 1405 | 0.17 | 0.37 | YES |
7 | ATR | ATR | ATR | 1468 | 0.16 | 0.42 | YES |
8 | MBNL1 | MBNL1 | MBNL1 | 1965 | 0.13 | 0.43 | YES |
9 | CCP110 | CCP110 | CCP110 | 2287 | 0.12 | 0.44 | YES |
10 | EEF1A1 | EEF1A1 | EEF1A1 | 2749 | 0.1 | 0.45 | YES |
11 | CLK4 | CLK4 | CLK4 | 2949 | 0.093 | 0.46 | YES |
12 | RPL9 | RPL9 | RPL9 | 3179 | 0.086 | 0.48 | YES |
13 | MRPS25 | MRPS25 | MRPS25 | 3266 | 0.083 | 0.5 | YES |
14 | HAUS4 | HAUS4 | HAUS4 | 3627 | 0.073 | 0.5 | YES |
15 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 3898 | 0.068 | 0.5 | YES |
16 | GLTSCR2 | GLTSCR2 | GLTSCR2 | 4130 | 0.062 | 0.51 | YES |
17 | ALOX5AP | ALOX5AP | ALOX5AP | 4460 | 0.056 | 0.51 | YES |
18 | RABGGTB | RABGGTB | RABGGTB | 4568 | 0.054 | 0.52 | YES |
19 | TMEM47 | TMEM47 | TMEM47 | 4769 | 0.05 | 0.52 | YES |
20 | EXTL2 | EXTL2 | EXTL2 | 4860 | 0.049 | 0.53 | YES |
21 | BCL2L2 | BCL2L2 | BCL2L2 | 4868 | 0.048 | 0.54 | YES |
22 | PHTF2 | PHTF2 | PHTF2 | 4990 | 0.047 | 0.55 | YES |
23 | RWDD2B | RWDD2B | RWDD2B | 5075 | 0.045 | 0.56 | YES |
24 | CGRRF1 | CGRRF1 | CGRRF1 | 5370 | 0.041 | 0.55 | YES |
25 | ERMAP | ERMAP | ERMAP | 5649 | 0.037 | 0.55 | YES |
26 | RASIP1 | RASIP1 | RASIP1 | 5679 | 0.036 | 0.56 | YES |
27 | HDGFRP3 | HDGFRP3 | HDGFRP3 | 5714 | 0.036 | 0.57 | YES |
28 | FERMT2 | FERMT2 | FERMT2 | 5961 | 0.032 | 0.56 | YES |
29 | PTEN | PTEN | PTEN | 6037 | 0.031 | 0.57 | YES |
30 | CWC27 | CWC27 | CWC27 | 6460 | 0.026 | 0.55 | YES |
31 | RPF2 | RPF2 | RPF2 | 6485 | 0.026 | 0.56 | YES |
32 | NEK1 | NEK1 | NEK1 | 6537 | 0.025 | 0.56 | YES |
33 | SCAF11 | SCAF11 | SCAF11 | 6617 | 0.024 | 0.57 | YES |
34 | SPG20 | SPG20 | SPG20 | 6639 | 0.024 | 0.57 | YES |
35 | FBXO33 | FBXO33 | FBXO33 | 7111 | 0.018 | 0.55 | NO |
36 | FNDC3A | FNDC3A | FNDC3A | 7378 | 0.015 | 0.54 | NO |
37 | TUBGCP3 | TUBGCP3 | TUBGCP3 | 7435 | 0.014 | 0.54 | NO |
38 | PNMA1 | PNMA1 | PNMA1 | 9517 | -0.0096 | 0.43 | NO |
39 | CAST | CAST | CAST | 11514 | -0.035 | 0.33 | NO |
40 | FKBP3 | FKBP3 | FKBP3 | 11539 | -0.035 | 0.34 | NO |
41 | RHOC | RHOC | RHOC | 14004 | -0.081 | 0.23 | NO |
Figure S47. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S25. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | RNASE4 | RNASE4 | RNASE4 | 243 | 0.39 | 0.098 | YES |
2 | ZFP2 | ZFP2 | ZFP2 | 461 | 0.32 | 0.18 | YES |
3 | C11orf63 | C11orf63 | C11orf63 | 1064 | 0.2 | 0.2 | YES |
4 | DYNC2H1 | DYNC2H1 | DYNC2H1 | 1359 | 0.18 | 0.24 | YES |
5 | DIXDC1 | DIXDC1 | DIXDC1 | 1384 | 0.17 | 0.28 | YES |
6 | WDR19 | WDR19 | WDR19 | 1796 | 0.14 | 0.3 | YES |
7 | NYNRIN | NYNRIN | NYNRIN | 2246 | 0.12 | 0.31 | YES |
8 | SYNC | SYNC | SYNC | 2294 | 0.12 | 0.34 | YES |
9 | DZANK1 | DZANK1 | DZANK1 | 2485 | 0.11 | 0.36 | YES |
10 | SESN1 | SESN1 | SESN1 | 2808 | 0.098 | 0.37 | YES |
11 | ZNF395 | ZNF395 | ZNF395 | 2995 | 0.091 | 0.39 | YES |
12 | ECHDC2 | ECHDC2 | ECHDC2 | 3581 | 0.074 | 0.38 | YES |
13 | NME5 | NME5 | NME5 | 3670 | 0.072 | 0.39 | YES |
14 | MARCH8 | MARCH8 | MARCH8 | 3704 | 0.072 | 0.41 | YES |
15 | ZNF862 | ZNF862 | ZNF862 | 3924 | 0.067 | 0.42 | YES |
16 | KIF13B | KIF13B | KIF13B | 3989 | 0.066 | 0.43 | YES |
17 | LAMB2 | LAMB2 | LAMB2 | 4049 | 0.064 | 0.45 | YES |
18 | BBS1 | BBS1 | BBS1 | 4305 | 0.059 | 0.45 | YES |
19 | TPT1 | TPT1 | TPT1 | 4675 | 0.052 | 0.45 | YES |
20 | CRY2 | CRY2 | CRY2 | 4746 | 0.05 | 0.46 | YES |
21 | CYBRD1 | CYBRD1 | CYBRD1 | 5232 | 0.043 | 0.44 | NO |
22 | CX3CR1 | CX3CR1 | CX3CR1 | 5292 | 0.042 | 0.45 | NO |
23 | CASP9 | CASP9 | CASP9 | 5693 | 0.036 | 0.44 | NO |
24 | IFT88 | IFT88 | IFT88 | 6018 | 0.032 | 0.43 | NO |
25 | MPHOSPH8 | MPHOSPH8 | MPHOSPH8 | 6145 | 0.03 | 0.43 | NO |
26 | SIRT3 | SIRT3 | SIRT3 | 6314 | 0.028 | 0.43 | NO |
27 | CIRBP | CIRBP | CIRBP | 6584 | 0.025 | 0.42 | NO |
28 | CRTC3 | CRTC3 | CRTC3 | 6591 | 0.025 | 0.43 | NO |
29 | AKAP11 | AKAP11 | AKAP11 | 6860 | 0.021 | 0.42 | NO |
30 | AASS | AASS | AASS | 7335 | 0.016 | 0.4 | NO |
31 | SLC24A1 | SLC24A1 | SLC24A1 | 7572 | 0.013 | 0.39 | NO |
32 | SMARCA2 | SMARCA2 | SMARCA2 | 7841 | 0.0098 | 0.38 | NO |
33 | NBR1 | NBR1 | NBR1 | 8104 | 0.0068 | 0.36 | NO |
34 | IFT46 | IFT46 | IFT46 | 8237 | 0.0054 | 0.36 | NO |
35 | ARHGEF12 | ARHGEF12 | ARHGEF12 | 8522 | 0.0018 | 0.34 | NO |
36 | STAT5B | STAT5B | STAT5B | 8559 | 0.0015 | 0.34 | NO |
37 | TUBGCP4 | TUBGCP4 | TUBGCP4 | 9209 | -0.006 | 0.31 | NO |
38 | TBC1D17 | TBC1D17 | TBC1D17 | 9362 | -0.008 | 0.3 | NO |
39 | ARHGEF40 | ARHGEF40 | ARHGEF40 | 9776 | -0.013 | 0.28 | NO |
40 | NF1 | NF1 | NF1 | 9972 | -0.015 | 0.28 | NO |
41 | PIGV | PIGV | PIGV | 10506 | -0.022 | 0.25 | NO |
42 | CTDSP1 | CTDSP1 | CTDSP1 | 10682 | -0.024 | 0.25 | NO |
43 | SNX1 | SNX1 | SNX1 | 11049 | -0.029 | 0.24 | NO |
44 | LTBP3 | LTBP3 | LTBP3 | 11564 | -0.035 | 0.22 | NO |
45 | DEAF1 | DEAF1 | DEAF1 | 12286 | -0.046 | 0.19 | NO |
46 | STARD13 | STARD13 | STARD13 | 12807 | -0.055 | 0.18 | NO |
47 | FOS | FOS | FOS | 13404 | -0.067 | 0.17 | NO |
48 | FRY | FRY | FRY | 15100 | -0.12 | 0.11 | NO |
49 | RUNX1 | RUNX1 | RUNX1 | 16511 | -0.2 | 0.087 | NO |
Figure S49. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S26. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | EHHADH | EHHADH | EHHADH | 749 | 0.25 | -0.006 | YES |
2 | CELSR3 | CELSR3 | CELSR3 | 917 | 0.22 | 0.016 | YES |
3 | TFDP2 | TFDP2 | TFDP2 | 1068 | 0.2 | 0.037 | YES |
4 | SPICE1 | SPICE1 | SPICE1 | 1094 | 0.2 | 0.064 | YES |
5 | GTPBP8 | GTPBP8 | GTPBP8 | 1115 | 0.2 | 0.091 | YES |
6 | RNF32 | RNF32 | RNF32 | 1120 | 0.2 | 0.12 | YES |
7 | WNK3 | WNK3 | WNK3 | 1306 | 0.18 | 0.13 | YES |
8 | ZFR2 | ZFR2 | ZFR2 | 1374 | 0.17 | 0.16 | YES |
9 | HLTF | HLTF | HLTF | 1549 | 0.16 | 0.17 | YES |
10 | NR1D2 | NR1D2 | NR1D2 | 1553 | 0.16 | 0.19 | YES |
11 | RAD18 | RAD18 | RAD18 | 1627 | 0.15 | 0.21 | YES |
12 | MEIS1 | MEIS1 | MEIS1 | 1808 | 0.14 | 0.22 | YES |
13 | PDCD10 | PDCD10 | PDCD10 | 1836 | 0.14 | 0.24 | YES |
14 | TMEM41A | TMEM41A | TMEM41A | 1868 | 0.14 | 0.26 | YES |
15 | KIAA2022 | KIAA2022 | KIAA2022 | 1960 | 0.13 | 0.27 | YES |
16 | MYNN | MYNN | MYNN | 2003 | 0.13 | 0.29 | YES |
17 | TBCCD1 | TBCCD1 | TBCCD1 | 2026 | 0.13 | 0.3 | YES |
18 | GK5 | GK5 | GK5 | 2188 | 0.12 | 0.31 | YES |
19 | ACTL6A | ACTL6A | ACTL6A | 2284 | 0.12 | 0.32 | YES |
20 | SENP5 | SENP5 | SENP5 | 2334 | 0.12 | 0.34 | YES |
21 | MSL2 | MSL2 | MSL2 | 2361 | 0.11 | 0.35 | YES |
22 | SYCP2 | SYCP2 | SYCP2 | 2402 | 0.11 | 0.36 | YES |
23 | TOPBP1 | TOPBP1 | TOPBP1 | 2582 | 0.11 | 0.37 | YES |
24 | RFC4 | RFC4 | RFC4 | 2607 | 0.1 | 0.38 | YES |
25 | RNF168 | RNF168 | RNF168 | 2633 | 0.1 | 0.4 | YES |
26 | WDR53 | WDR53 | WDR53 | 2679 | 0.1 | 0.41 | YES |
27 | NDUFB5 | NDUFB5 | NDUFB5 | 2757 | 0.1 | 0.42 | YES |
28 | RMI1 | RMI1 | RMI1 | 2872 | 0.095 | 0.43 | YES |
29 | OPA1 | OPA1 | OPA1 | 3241 | 0.084 | 0.42 | YES |
30 | MCM2 | MCM2 | MCM2 | 3284 | 0.083 | 0.43 | YES |
31 | STMN1 | STMN1 | STMN1 | 3451 | 0.078 | 0.43 | YES |
32 | ANKRD32 | ANKRD32 | ANKRD32 | 3497 | 0.077 | 0.44 | YES |
33 | EIF2B5 | EIF2B5 | EIF2B5 | 3518 | 0.076 | 0.45 | YES |
34 | SYCE2 | SYCE2 | SYCE2 | 3586 | 0.074 | 0.46 | YES |
35 | RAP2B | RAP2B | RAP2B | 3621 | 0.073 | 0.46 | YES |
36 | KCNS1 | KCNS1 | KCNS1 | 3701 | 0.072 | 0.47 | YES |
37 | MLH1 | MLH1 | MLH1 | 3813 | 0.069 | 0.47 | YES |
38 | FMR1 | FMR1 | FMR1 | 3891 | 0.068 | 0.48 | YES |
39 | CENPK | CENPK | CENPK | 4256 | 0.06 | 0.47 | NO |
40 | PRPF38A | PRPF38A | PRPF38A | 4662 | 0.052 | 0.45 | NO |
41 | POLR2H | POLR2H | POLR2H | 4929 | 0.048 | 0.44 | NO |
42 | RMI2 | RMI2 | RMI2 | 5262 | 0.042 | 0.43 | NO |
43 | MRPL47 | MRPL47 | MRPL47 | 5286 | 0.042 | 0.44 | NO |
44 | CXCL17 | CXCL17 | CXCL17 | 6326 | 0.028 | 0.38 | NO |
45 | RPA2 | RPA2 | RPA2 | 6433 | 0.027 | 0.38 | NO |
46 | ING2 | ING2 | ING2 | 6571 | 0.025 | 0.38 | NO |
47 | USP1 | USP1 | USP1 | 6732 | 0.023 | 0.37 | NO |
48 | INPP5B | INPP5B | INPP5B | 6929 | 0.02 | 0.36 | NO |
49 | TAF7L | TAF7L | TAF7L | 6995 | 0.02 | 0.36 | NO |
50 | MORN2 | MORN2 | MORN2 | 7187 | 0.017 | 0.35 | NO |
51 | CDC7 | CDC7 | CDC7 | 7292 | 0.016 | 0.35 | NO |
52 | HAUS5 | HAUS5 | HAUS5 | 7537 | 0.013 | 0.34 | NO |
53 | NR2C2AP | NR2C2AP | NR2C2AP | 7750 | 0.011 | 0.33 | NO |
54 | KIF15 | KIF15 | KIF15 | 7788 | 0.01 | 0.33 | NO |
55 | NUP210 | NUP210 | NUP210 | 8086 | 0.007 | 0.31 | NO |
56 | DHFR | DHFR | DHFR | 8263 | 0.0051 | 0.3 | NO |
57 | SLFN13 | SLFN13 | SLFN13 | 8330 | 0.0042 | 0.3 | NO |
58 | C9orf40 | C9orf40 | C9orf40 | 9625 | -0.011 | 0.23 | NO |
59 | ALG6 | ALG6 | ALG6 | 9775 | -0.013 | 0.22 | NO |
60 | NMU | NMU | NMU | 10152 | -0.017 | 0.2 | NO |
61 | CENPW | CENPW | CENPW | 10721 | -0.024 | 0.18 | NO |
62 | C5orf34 | C5orf34 | C5orf34 | 11066 | -0.029 | 0.16 | NO |
63 | EZH2 | EZH2 | EZH2 | 11842 | -0.039 | 0.12 | NO |
64 | LIG1 | LIG1 | LIG1 | 12068 | -0.042 | 0.12 | NO |
65 | MCM6 | MCM6 | MCM6 | 12811 | -0.055 | 0.084 | NO |
66 | CDKN2A | CDKN2A | CDKN2A | 12842 | -0.055 | 0.09 | NO |
67 | HES1 | HES1 | HES1 | 12960 | -0.058 | 0.092 | NO |
68 | HS6ST2 | HS6ST2 | HS6ST2 | 13011 | -0.059 | 0.098 | NO |
69 | YBX2 | YBX2 | YBX2 | 13628 | -0.072 | 0.074 | NO |
70 | WEE1 | WEE1 | WEE1 | 13961 | -0.08 | 0.067 | NO |
71 | CDKN2C | CDKN2C | CDKN2C | 13976 | -0.08 | 0.078 | NO |
72 | DNAJC13 | DNAJC13 | DNAJC13 | 14190 | -0.087 | 0.078 | NO |
73 | RIBC2 | RIBC2 | RIBC2 | 14723 | -0.1 | 0.064 | NO |
74 | FAM111B | FAM111B | FAM111B | 15007 | -0.12 | 0.064 | NO |
75 | C11orf85 | C11orf85 | C11orf85 | 15466 | -0.14 | 0.059 | NO |
76 | ASS1 | ASS1 | ASS1 | 15557 | -0.14 | 0.074 | NO |
77 | SYNGR3 | SYNGR3 | SYNGR3 | 15621 | -0.15 | 0.092 | NO |
78 | MEI1 | MEI1 | MEI1 | 15771 | -0.16 | 0.11 | NO |
79 | NEFH | NEFH | NEFH | 15805 | -0.16 | 0.13 | NO |
Figure S51. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME GENERIC TRANSCRIPTION PATHWAY.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME GENERIC TRANSCRIPTION PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S27. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | BEX1 | BEX1 | BEX1 | 181 | 0.42 | 0.011 | YES |
2 | RNASE4 | RNASE4 | RNASE4 | 243 | 0.39 | 0.028 | YES |
3 | BEX5 | BEX5 | BEX5 | 310 | 0.36 | 0.042 | YES |
4 | SHE | SHE | SHE | 404 | 0.33 | 0.054 | YES |
5 | LNP1 | LNP1 | LNP1 | 498 | 0.31 | 0.064 | YES |
6 | ANG | ANG | ANG | 512 | 0.3 | 0.079 | YES |
7 | GXYLT2 | GXYLT2 | GXYLT2 | 557 | 0.29 | 0.092 | YES |
8 | SLC16A10 | SLC16A10 | SLC16A10 | 686 | 0.26 | 0.098 | YES |
9 | PAIP2B | PAIP2B | PAIP2B | 829 | 0.23 | 0.1 | YES |
10 | TFDP2 | TFDP2 | TFDP2 | 1068 | 0.2 | 0.099 | YES |
11 | LMLN | LMLN | LMLN | 1106 | 0.2 | 0.11 | YES |
12 | MARVELD2 | MARVELD2 | MARVELD2 | 1163 | 0.19 | 0.11 | YES |
13 | ZNF711 | ZNF711 | ZNF711 | 1248 | 0.18 | 0.12 | YES |
14 | ZNF621 | ZNF621 | ZNF621 | 1312 | 0.18 | 0.12 | YES |
15 | MEST | MEST | MEST | 1525 | 0.16 | 0.12 | YES |
16 | MFAP3L | MFAP3L | MFAP3L | 1582 | 0.16 | 0.12 | YES |
17 | SFMBT1 | SFMBT1 | SFMBT1 | 1662 | 0.15 | 0.13 | YES |
18 | ZNF789 | ZNF789 | ZNF789 | 1671 | 0.15 | 0.14 | YES |
19 | JAM3 | JAM3 | JAM3 | 1743 | 0.15 | 0.14 | YES |
20 | C3orf17 | C3orf17 | C3orf17 | 1758 | 0.15 | 0.15 | YES |
21 | TIGD7 | TIGD7 | TIGD7 | 1776 | 0.14 | 0.15 | YES |
22 | BOC | BOC | BOC | 1786 | 0.14 | 0.16 | YES |
23 | FAM161A | FAM161A | FAM161A | 1793 | 0.14 | 0.17 | YES |
24 | SENP2 | SENP2 | SENP2 | 1825 | 0.14 | 0.17 | YES |
25 | CAND2 | CAND2 | CAND2 | 1831 | 0.14 | 0.18 | YES |
26 | DCUN1D1 | DCUN1D1 | DCUN1D1 | 1946 | 0.13 | 0.18 | YES |
27 | MDM1 | MDM1 | MDM1 | 1962 | 0.13 | 0.18 | YES |
28 | BEX4 | BEX4 | BEX4 | 2044 | 0.13 | 0.19 | YES |
29 | TSPAN6 | TSPAN6 | TSPAN6 | 2142 | 0.12 | 0.19 | YES |
30 | ARL17A | ARL17A | ARL17A | 2177 | 0.12 | 0.19 | YES |
31 | BHLHB9 | BHLHB9 | BHLHB9 | 2189 | 0.12 | 0.2 | YES |
32 | BEX2 | BEX2 | BEX2 | 2226 | 0.12 | 0.2 | YES |
33 | CCP110 | CCP110 | CCP110 | 2287 | 0.12 | 0.2 | YES |
34 | VHL | VHL | VHL | 2315 | 0.12 | 0.21 | YES |
35 | MSL2 | MSL2 | MSL2 | 2361 | 0.11 | 0.21 | YES |
36 | ITGA9 | ITGA9 | ITGA9 | 2442 | 0.11 | 0.21 | YES |
37 | SPATA7 | SPATA7 | SPATA7 | 2474 | 0.11 | 0.22 | YES |
38 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 2487 | 0.11 | 0.22 | YES |
39 | GPRASP2 | GPRASP2 | GPRASP2 | 2500 | 0.11 | 0.23 | YES |
40 | ZNF606 | ZNF606 | ZNF606 | 2563 | 0.11 | 0.23 | YES |
41 | USP13 | USP13 | USP13 | 2666 | 0.1 | 0.23 | YES |
42 | SEC62 | SEC62 | SEC62 | 2674 | 0.1 | 0.23 | YES |
43 | TMEM97 | TMEM97 | TMEM97 | 2776 | 0.099 | 0.23 | YES |
44 | SNED1 | SNED1 | SNED1 | 2922 | 0.094 | 0.23 | YES |
45 | MAGEH1 | MAGEH1 | MAGEH1 | 2926 | 0.093 | 0.23 | YES |
46 | MAGEF1 | MAGEF1 | MAGEF1 | 3109 | 0.088 | 0.23 | YES |
47 | ACVR2A | ACVR2A | ACVR2A | 3132 | 0.087 | 0.23 | YES |
48 | ARMCX1 | ARMCX1 | ARMCX1 | 3235 | 0.084 | 0.23 | YES |
49 | PASK | PASK | PASK | 3248 | 0.084 | 0.23 | YES |
50 | PNN | PNN | PNN | 3258 | 0.084 | 0.24 | YES |
51 | TFAM | TFAM | TFAM | 3268 | 0.083 | 0.24 | YES |
52 | RASSF8 | RASSF8 | RASSF8 | 3293 | 0.082 | 0.24 | YES |
53 | ARMCX6 | ARMCX6 | ARMCX6 | 3313 | 0.082 | 0.25 | YES |
54 | NKAP | NKAP | NKAP | 3365 | 0.08 | 0.25 | YES |
55 | NUP54 | NUP54 | NUP54 | 3439 | 0.078 | 0.25 | YES |
56 | CCNB1IP1 | CCNB1IP1 | CCNB1IP1 | 3448 | 0.078 | 0.25 | YES |
57 | ZFP90 | ZFP90 | ZFP90 | 3503 | 0.077 | 0.25 | YES |
58 | LRP6 | LRP6 | LRP6 | 3506 | 0.077 | 0.26 | YES |
59 | EPM2AIP1 | EPM2AIP1 | EPM2AIP1 | 3540 | 0.076 | 0.26 | YES |
60 | TMEM5 | TMEM5 | TMEM5 | 3566 | 0.075 | 0.26 | YES |
61 | LRP4 | LRP4 | LRP4 | 3598 | 0.074 | 0.26 | YES |
62 | ETV5 | ETV5 | ETV5 | 3700 | 0.072 | 0.26 | YES |
63 | RPL22 | RPL22 | RPL22 | 3771 | 0.07 | 0.26 | YES |
64 | SLC25A14 | SLC25A14 | SLC25A14 | 3791 | 0.07 | 0.26 | YES |
65 | SMARCA1 | SMARCA1 | SMARCA1 | 3816 | 0.069 | 0.26 | YES |
66 | ST13 | ST13 | ST13 | 3820 | 0.069 | 0.27 | YES |
67 | ALS2 | ALS2 | ALS2 | 3866 | 0.068 | 0.27 | YES |
68 | JAGN1 | JAGN1 | JAGN1 | 3878 | 0.068 | 0.27 | YES |
69 | TIGD1 | TIGD1 | TIGD1 | 3903 | 0.067 | 0.28 | YES |
70 | PLEKHA5 | PLEKHA5 | PLEKHA5 | 3910 | 0.067 | 0.28 | YES |
71 | PKP4 | PKP4 | PKP4 | 3993 | 0.065 | 0.28 | YES |
72 | PRCP | PRCP | PRCP | 4004 | 0.065 | 0.28 | YES |
73 | NUDT7 | NUDT7 | NUDT7 | 4020 | 0.065 | 0.28 | YES |
74 | TAF9B | TAF9B | TAF9B | 4053 | 0.064 | 0.28 | YES |
75 | EPC2 | EPC2 | EPC2 | 4246 | 0.06 | 0.28 | YES |
76 | SVIP | SVIP | SVIP | 4272 | 0.059 | 0.28 | YES |
77 | MAGEE1 | MAGEE1 | MAGEE1 | 4284 | 0.059 | 0.28 | YES |
78 | CETN2 | CETN2 | CETN2 | 4329 | 0.058 | 0.28 | YES |
79 | CCDC43 | CCDC43 | CCDC43 | 4333 | 0.058 | 0.28 | YES |
80 | EEF1B2 | EEF1B2 | EEF1B2 | 4375 | 0.057 | 0.28 | YES |
81 | SLC25A33 | SLC25A33 | SLC25A33 | 4420 | 0.056 | 0.28 | YES |
82 | PILRB | PILRB | PILRB | 4552 | 0.054 | 0.28 | YES |
83 | MMGT1 | MMGT1 | MMGT1 | 4563 | 0.054 | 0.28 | YES |
84 | MOB1B | MOB1B | MOB1B | 4628 | 0.053 | 0.28 | YES |
85 | APOOL | APOOL | APOOL | 4692 | 0.052 | 0.28 | YES |
86 | PPIG | PPIG | PPIG | 4696 | 0.052 | 0.28 | YES |
87 | FAM13B | FAM13B | FAM13B | 4782 | 0.05 | 0.28 | YES |
88 | PARL | PARL | PARL | 4803 | 0.05 | 0.28 | YES |
89 | ZNF449 | ZNF449 | ZNF449 | 4826 | 0.049 | 0.28 | YES |
90 | TCEAL8 | TCEAL8 | TCEAL8 | 4827 | 0.049 | 0.28 | YES |
91 | ETV4 | ETV4 | ETV4 | 4886 | 0.048 | 0.28 | YES |
92 | HNRNPH1 | HNRNPH1 | HNRNPH1 | 4979 | 0.047 | 0.28 | YES |
93 | C2orf44 | C2orf44 | C2orf44 | 5034 | 0.046 | 0.28 | YES |
94 | IFT52 | IFT52 | IFT52 | 5039 | 0.046 | 0.28 | YES |
95 | SNRPN | SNRPN | SNRPN | 5056 | 0.046 | 0.28 | YES |
96 | TMED8 | TMED8 | TMED8 | 5121 | 0.045 | 0.28 | YES |
97 | C18orf21 | C18orf21 | C18orf21 | 5138 | 0.044 | 0.28 | YES |
98 | ZNF75A | ZNF75A | ZNF75A | 5173 | 0.044 | 0.28 | YES |
99 | PPWD1 | PPWD1 | PPWD1 | 5186 | 0.044 | 0.29 | YES |
100 | NGFRAP1 | NGFRAP1 | NGFRAP1 | 5231 | 0.043 | 0.29 | YES |
101 | ANKRD40 | ANKRD40 | ANKRD40 | 5243 | 0.043 | 0.29 | YES |
102 | ZNF133 | ZNF133 | ZNF133 | 5270 | 0.042 | 0.29 | YES |
103 | FAM133B | FAM133B | FAM133B | 5280 | 0.042 | 0.29 | YES |
104 | NAT9 | NAT9 | NAT9 | 5291 | 0.042 | 0.29 | YES |
105 | ZMYND11 | ZMYND11 | ZMYND11 | 5340 | 0.041 | 0.29 | YES |
106 | IDH1 | IDH1 | IDH1 | 5417 | 0.04 | 0.29 | YES |
107 | CREB1 | CREB1 | CREB1 | 5519 | 0.038 | 0.28 | YES |
108 | NAP1L5 | NAP1L5 | NAP1L5 | 5528 | 0.038 | 0.29 | YES |
109 | KIAA1467 | KIAA1467 | KIAA1467 | 5560 | 0.038 | 0.29 | YES |
110 | CTCF | CTCF | CTCF | 5593 | 0.038 | 0.29 | YES |
111 | LRRC23 | LRRC23 | LRRC23 | 5750 | 0.035 | 0.28 | YES |
112 | GGT7 | GGT7 | GGT7 | 5776 | 0.035 | 0.28 | YES |
113 | ITGBL1 | ITGBL1 | ITGBL1 | 5832 | 0.034 | 0.28 | YES |
114 | STAG2 | STAG2 | STAG2 | 5846 | 0.034 | 0.28 | YES |
115 | PSMD10 | PSMD10 | PSMD10 | 5877 | 0.034 | 0.28 | YES |
116 | ZNF24 | ZNF24 | ZNF24 | 5919 | 0.033 | 0.28 | YES |
117 | BBS9 | BBS9 | BBS9 | 5933 | 0.033 | 0.28 | YES |
118 | DNAJB11 | DNAJB11 | DNAJB11 | 5955 | 0.032 | 0.28 | YES |
119 | TXNDC15 | TXNDC15 | TXNDC15 | 5956 | 0.032 | 0.28 | YES |
120 | HSD17B11 | HSD17B11 | HSD17B11 | 5963 | 0.032 | 0.28 | YES |
121 | DHX35 | DHX35 | DHX35 | 5980 | 0.032 | 0.28 | YES |
122 | E2F6 | E2F6 | E2F6 | 5991 | 0.032 | 0.28 | YES |
123 | TCEAL4 | TCEAL4 | TCEAL4 | 5995 | 0.032 | 0.29 | YES |
124 | PLCB4 | PLCB4 | PLCB4 | 6024 | 0.032 | 0.29 | YES |
125 | SH3BGRL2 | SH3BGRL2 | SH3BGRL2 | 6098 | 0.031 | 0.28 | YES |
126 | YTHDC1 | YTHDC1 | YTHDC1 | 6134 | 0.03 | 0.28 | YES |
127 | BEND7 | BEND7 | BEND7 | 6152 | 0.03 | 0.28 | YES |
128 | COX11 | COX11 | COX11 | 6157 | 0.03 | 0.29 | YES |
129 | MAGI2 | MAGI2 | MAGI2 | 6192 | 0.03 | 0.28 | YES |
130 | METTL9 | METTL9 | METTL9 | 6204 | 0.029 | 0.29 | YES |
131 | SALL4 | SALL4 | SALL4 | 6220 | 0.029 | 0.29 | YES |
132 | ZNF397 | ZNF397 | ZNF397 | 6222 | 0.029 | 0.29 | YES |
133 | INO80D | INO80D | INO80D | 6250 | 0.029 | 0.29 | YES |
134 | LAMA2 | LAMA2 | LAMA2 | 6275 | 0.029 | 0.29 | YES |
135 | RLIM | RLIM | RLIM | 6288 | 0.028 | 0.29 | YES |
136 | PRR3 | PRR3 | PRR3 | 6294 | 0.028 | 0.29 | YES |
137 | TAF1C | TAF1C | TAF1C | 6356 | 0.028 | 0.29 | YES |
138 | SRSF6 | SRSF6 | SRSF6 | 6386 | 0.027 | 0.29 | YES |
139 | RBMX2 | RBMX2 | RBMX2 | 6396 | 0.027 | 0.29 | YES |
140 | TP53BP1 | TP53BP1 | TP53BP1 | 6407 | 0.027 | 0.29 | YES |
141 | RBBP6 | RBBP6 | RBBP6 | 6421 | 0.027 | 0.29 | YES |
142 | MUTYH | MUTYH | MUTYH | 6436 | 0.027 | 0.29 | YES |
143 | C17orf80 | C17orf80 | C17orf80 | 6458 | 0.026 | 0.29 | YES |
144 | PAPOLA | PAPOLA | PAPOLA | 6470 | 0.026 | 0.29 | YES |
145 | UPF3B | UPF3B | UPF3B | 6530 | 0.025 | 0.29 | NO |
146 | AHI1 | AHI1 | AHI1 | 6561 | 0.025 | 0.29 | NO |
147 | TMLHE | TMLHE | TMLHE | 6570 | 0.025 | 0.29 | NO |
148 | TMEM18 | TMEM18 | TMEM18 | 6628 | 0.024 | 0.29 | NO |
149 | ACP1 | ACP1 | ACP1 | 6667 | 0.024 | 0.29 | NO |
150 | EFHD1 | EFHD1 | EFHD1 | 6692 | 0.023 | 0.29 | NO |
151 | ARMCX3 | ARMCX3 | ARMCX3 | 6722 | 0.023 | 0.29 | NO |
152 | VPS45 | VPS45 | VPS45 | 6741 | 0.023 | 0.29 | NO |
153 | RAD17 | RAD17 | RAD17 | 6775 | 0.022 | 0.29 | NO |
154 | SDAD1 | SDAD1 | SDAD1 | 6782 | 0.022 | 0.29 | NO |
155 | NUDT4 | NUDT4 | NUDT4 | 6787 | 0.022 | 0.29 | NO |
156 | MPDZ | MPDZ | MPDZ | 6793 | 0.022 | 0.29 | NO |
157 | MGA | MGA | MGA | 6813 | 0.022 | 0.29 | NO |
158 | LOH12CR1 | LOH12CR1 | LOH12CR1 | 6869 | 0.021 | 0.29 | NO |
159 | MRPS35 | MRPS35 | MRPS35 | 6908 | 0.02 | 0.29 | NO |
160 | MTA3 | MTA3 | MTA3 | 6949 | 0.02 | 0.28 | NO |
161 | LMAN2L | LMAN2L | LMAN2L | 6991 | 0.02 | 0.28 | NO |
162 | NUP107 | NUP107 | NUP107 | 6994 | 0.02 | 0.28 | NO |
163 | YY1AP1 | YY1AP1 | YY1AP1 | 7009 | 0.019 | 0.28 | NO |
164 | LMTK2 | LMTK2 | LMTK2 | 7036 | 0.019 | 0.28 | NO |
165 | ARL16 | ARL16 | ARL16 | 7044 | 0.019 | 0.28 | NO |
166 | ZBTB33 | ZBTB33 | ZBTB33 | 7046 | 0.019 | 0.28 | NO |
167 | CENPBD1 | CENPBD1 | CENPBD1 | 7095 | 0.018 | 0.28 | NO |
168 | EFCAB11 | EFCAB11 | EFCAB11 | 7175 | 0.017 | 0.28 | NO |
169 | MORN2 | MORN2 | MORN2 | 7187 | 0.017 | 0.28 | NO |
170 | WDR12 | WDR12 | WDR12 | 7192 | 0.017 | 0.28 | NO |
171 | METTL21A | METTL21A | METTL21A | 7234 | 0.017 | 0.28 | NO |
172 | FARP2 | FARP2 | FARP2 | 7244 | 0.016 | 0.28 | NO |
173 | RBM15 | RBM15 | RBM15 | 7245 | 0.016 | 0.28 | NO |
174 | TTC17 | TTC17 | TTC17 | 7250 | 0.016 | 0.28 | NO |
175 | SALL2 | SALL2 | SALL2 | 7359 | 0.015 | 0.28 | NO |
176 | THOC2 | THOC2 | THOC2 | 7370 | 0.015 | 0.28 | NO |
177 | ATAD2B | ATAD2B | ATAD2B | 7388 | 0.015 | 0.28 | NO |
178 | PDRG1 | PDRG1 | PDRG1 | 7397 | 0.015 | 0.28 | NO |
179 | CAND1 | CAND1 | CAND1 | 7431 | 0.014 | 0.28 | NO |
180 | ATXN3 | ATXN3 | ATXN3 | 7471 | 0.014 | 0.27 | NO |
181 | OSCP1 | OSCP1 | OSCP1 | 7482 | 0.014 | 0.27 | NO |
182 | PABPN1 | PABPN1 | PABPN1 | 7562 | 0.013 | 0.27 | NO |
183 | PHC1 | PHC1 | PHC1 | 7657 | 0.012 | 0.26 | NO |
184 | ERCC8 | ERCC8 | ERCC8 | 7731 | 0.011 | 0.26 | NO |
185 | TTC5 | TTC5 | TTC5 | 7807 | 0.01 | 0.26 | NO |
186 | PRKD1 | PRKD1 | PRKD1 | 7825 | 0.01 | 0.26 | NO |
187 | TTLL5 | TTLL5 | TTLL5 | 7853 | 0.0097 | 0.26 | NO |
188 | CHST10 | CHST10 | CHST10 | 7895 | 0.0093 | 0.26 | NO |
189 | FIP1L1 | FIP1L1 | FIP1L1 | 7962 | 0.0084 | 0.25 | NO |
190 | KAT8 | KAT8 | KAT8 | 8008 | 0.0078 | 0.25 | NO |
191 | ABCD4 | ABCD4 | ABCD4 | 8009 | 0.0078 | 0.25 | NO |
192 | VBP1 | VBP1 | VBP1 | 8057 | 0.0074 | 0.25 | NO |
193 | ZNF92 | ZNF92 | ZNF92 | 8082 | 0.0071 | 0.25 | NO |
194 | NBR1 | NBR1 | NBR1 | 8104 | 0.0068 | 0.24 | NO |
195 | MPHOSPH10 | MPHOSPH10 | MPHOSPH10 | 8151 | 0.0064 | 0.24 | NO |
196 | PPM1D | PPM1D | PPM1D | 8196 | 0.0059 | 0.24 | NO |
197 | ATRX | ATRX | ATRX | 8283 | 0.0048 | 0.24 | NO |
198 | IFT43 | IFT43 | IFT43 | 8389 | 0.0036 | 0.23 | NO |
199 | RBM25 | RBM25 | RBM25 | 8420 | 0.0033 | 0.23 | NO |
200 | LCLAT1 | LCLAT1 | LCLAT1 | 8422 | 0.0032 | 0.23 | NO |
201 | SUPT7L | SUPT7L | SUPT7L | 8445 | 0.003 | 0.23 | NO |
202 | ZNF263 | ZNF263 | ZNF263 | 8446 | 0.003 | 0.23 | NO |
203 | NDUFS1 | NDUFS1 | NDUFS1 | 8494 | 0.0022 | 0.23 | NO |
204 | MTHFSD | MTHFSD | MTHFSD | 8495 | 0.0022 | 0.23 | NO |
205 | ISCA2 | ISCA2 | ISCA2 | 8499 | 0.0022 | 0.23 | NO |
206 | PGRMC1 | PGRMC1 | PGRMC1 | 8503 | 0.0021 | 0.23 | NO |
207 | GLRX5 | GLRX5 | GLRX5 | 8543 | 0.0016 | 0.22 | NO |
208 | BOLA1 | BOLA1 | BOLA1 | 8551 | 0.0015 | 0.22 | NO |
209 | ZMYM3 | ZMYM3 | ZMYM3 | 8585 | 0.0012 | 0.22 | NO |
210 | SUMO1 | SUMO1 | SUMO1 | 8619 | 0.00088 | 0.22 | NO |
211 | APBA2 | APBA2 | APBA2 | 8685 | 0.00021 | 0.22 | NO |
212 | GATC | GATC | GATC | 8715 | -0.00018 | 0.21 | NO |
213 | HSD17B12 | HSD17B12 | HSD17B12 | 8732 | -0.00037 | 0.21 | NO |
214 | APPBP2 | APPBP2 | APPBP2 | 8765 | -0.00067 | 0.21 | NO |
215 | TRIP12 | TRIP12 | TRIP12 | 8783 | -0.00094 | 0.21 | NO |
216 | ADAM17 | ADAM17 | ADAM17 | 8807 | -0.0013 | 0.21 | NO |
217 | AKAP1 | AKAP1 | AKAP1 | 8809 | -0.0013 | 0.21 | NO |
218 | MRPL1 | MRPL1 | MRPL1 | 8823 | -0.0015 | 0.21 | NO |
219 | TMEM128 | TMEM128 | TMEM128 | 8887 | -0.0023 | 0.21 | NO |
220 | YIPF6 | YIPF6 | YIPF6 | 8921 | -0.0027 | 0.2 | NO |
221 | B4GALT5 | B4GALT5 | B4GALT5 | 8946 | -0.003 | 0.2 | NO |
222 | DTX3 | DTX3 | DTX3 | 8950 | -0.0031 | 0.2 | NO |
223 | SLC37A3 | SLC37A3 | SLC37A3 | 8953 | -0.0031 | 0.2 | NO |
224 | DYRK4 | DYRK4 | DYRK4 | 8982 | -0.0034 | 0.2 | NO |
225 | IPO8 | IPO8 | IPO8 | 8991 | -0.0035 | 0.2 | NO |
226 | USP51 | USP51 | USP51 | 9006 | -0.0037 | 0.2 | NO |
227 | UBFD1 | UBFD1 | UBFD1 | 9009 | -0.0037 | 0.2 | NO |
228 | RPE | RPE | RPE | 9022 | -0.0038 | 0.2 | NO |
229 | NOL9 | NOL9 | NOL9 | 9045 | -0.0041 | 0.2 | NO |
230 | TCTN3 | TCTN3 | TCTN3 | 9180 | -0.0056 | 0.19 | NO |
231 | TUBGCP4 | TUBGCP4 | TUBGCP4 | 9209 | -0.006 | 0.19 | NO |
232 | PSMD1 | PSMD1 | PSMD1 | 9483 | -0.0093 | 0.18 | NO |
233 | HEBP1 | HEBP1 | HEBP1 | 9497 | -0.0094 | 0.18 | NO |
234 | ABI2 | ABI2 | ABI2 | 9510 | -0.0096 | 0.18 | NO |
235 | APOLD1 | APOLD1 | APOLD1 | 9544 | -0.01 | 0.17 | NO |
236 | NCL | NCL | NCL | 9582 | -0.01 | 0.17 | NO |
237 | ITGB5 | ITGB5 | ITGB5 | 9587 | -0.01 | 0.17 | NO |
238 | ABCB7 | ABCB7 | ABCB7 | 9606 | -0.011 | 0.17 | NO |
239 | ELP2 | ELP2 | ELP2 | 9628 | -0.011 | 0.17 | NO |
240 | QPCT | QPCT | QPCT | 9708 | -0.012 | 0.17 | NO |
241 | DPY30 | DPY30 | DPY30 | 9725 | -0.012 | 0.17 | NO |
242 | DDR2 | DDR2 | DDR2 | 9753 | -0.012 | 0.17 | NO |
243 | ACVR1B | ACVR1B | ACVR1B | 9864 | -0.014 | 0.16 | NO |
244 | CKAP5 | CKAP5 | CKAP5 | 9941 | -0.015 | 0.16 | NO |
245 | PDXDC1 | PDXDC1 | PDXDC1 | 9982 | -0.015 | 0.16 | NO |
246 | DNAJC18 | DNAJC18 | DNAJC18 | 10187 | -0.017 | 0.14 | NO |
247 | PFKM | PFKM | PFKM | 10272 | -0.018 | 0.14 | NO |
248 | MECP2 | MECP2 | MECP2 | 10349 | -0.02 | 0.14 | NO |
249 | GNAS | GNAS | GNAS | 10434 | -0.02 | 0.14 | NO |
250 | GIGYF2 | GIGYF2 | GIGYF2 | 10514 | -0.022 | 0.13 | NO |
251 | BDH2 | BDH2 | BDH2 | 10540 | -0.022 | 0.13 | NO |
252 | EP400 | EP400 | EP400 | 10544 | -0.022 | 0.13 | NO |
253 | CDK5RAP3 | CDK5RAP3 | CDK5RAP3 | 10642 | -0.023 | 0.13 | NO |
254 | AGFG1 | AGFG1 | AGFG1 | 10668 | -0.024 | 0.13 | NO |
255 | MGP | MGP | MGP | 10677 | -0.024 | 0.13 | NO |
256 | YARS2 | YARS2 | YARS2 | 10752 | -0.025 | 0.12 | NO |
257 | VKORC1L1 | VKORC1L1 | VKORC1L1 | 10830 | -0.026 | 0.12 | NO |
258 | NOP58 | NOP58 | NOP58 | 10896 | -0.027 | 0.12 | NO |
259 | ZNF764 | ZNF764 | ZNF764 | 10917 | -0.027 | 0.12 | NO |
260 | NEK9 | NEK9 | NEK9 | 10922 | -0.027 | 0.12 | NO |
261 | MRPL44 | MRPL44 | MRPL44 | 11091 | -0.029 | 0.11 | NO |
262 | PDZD11 | PDZD11 | PDZD11 | 11117 | -0.03 | 0.11 | NO |
263 | C11orf49 | C11orf49 | C11orf49 | 11118 | -0.03 | 0.12 | NO |
264 | PDIA4 | PDIA4 | PDIA4 | 11130 | -0.03 | 0.12 | NO |
265 | FASTKD2 | FASTKD2 | FASTKD2 | 11244 | -0.031 | 0.11 | NO |
266 | EDAR | EDAR | EDAR | 11450 | -0.034 | 0.1 | NO |
267 | AMZ2 | AMZ2 | AMZ2 | 11713 | -0.037 | 0.089 | NO |
268 | SCFD2 | SCFD2 | SCFD2 | 11721 | -0.038 | 0.09 | NO |
269 | PHB | PHB | PHB | 11750 | -0.038 | 0.091 | NO |
270 | FAM134A | FAM134A | FAM134A | 11800 | -0.039 | 0.09 | NO |
271 | NMT1 | NMT1 | NMT1 | 11841 | -0.039 | 0.09 | NO |
272 | TMX4 | TMX4 | TMX4 | 11866 | -0.04 | 0.09 | NO |
273 | CNPY2 | CNPY2 | CNPY2 | 11889 | -0.04 | 0.091 | NO |
274 | SEC14L4 | SEC14L4 | SEC14L4 | 12033 | -0.042 | 0.085 | NO |
275 | NAT10 | NAT10 | NAT10 | 12037 | -0.042 | 0.087 | NO |
276 | GPRC5B | GPRC5B | GPRC5B | 12089 | -0.043 | 0.086 | NO |
277 | TPST1 | TPST1 | TPST1 | 12177 | -0.044 | 0.084 | NO |
278 | TMEM201 | TMEM201 | TMEM201 | 12225 | -0.045 | 0.083 | NO |
279 | DYRK2 | DYRK2 | DYRK2 | 12261 | -0.045 | 0.084 | NO |
280 | RNF25 | RNF25 | RNF25 | 12313 | -0.046 | 0.083 | NO |
281 | DHX8 | DHX8 | DHX8 | 12360 | -0.047 | 0.083 | NO |
282 | COPS8 | COPS8 | COPS8 | 12376 | -0.047 | 0.085 | NO |
283 | DDIT3 | DDIT3 | DDIT3 | 12478 | -0.049 | 0.082 | NO |
284 | NUDT9 | NUDT9 | NUDT9 | 12491 | -0.049 | 0.083 | NO |
285 | WBSCR22 | WBSCR22 | WBSCR22 | 12496 | -0.049 | 0.086 | NO |
286 | DIS3L2 | DIS3L2 | DIS3L2 | 12509 | -0.05 | 0.088 | NO |
287 | MFF | MFF | MFF | 12575 | -0.051 | 0.086 | NO |
288 | C1orf56 | C1orf56 | C1orf56 | 13008 | -0.059 | 0.065 | NO |
289 | DNAL1 | DNAL1 | DNAL1 | 13111 | -0.061 | 0.062 | NO |
290 | SH3RF3 | SH3RF3 | SH3RF3 | 13174 | -0.062 | 0.062 | NO |
291 | SNF8 | SNF8 | SNF8 | 13198 | -0.063 | 0.064 | NO |
292 | FGF19 | FGF19 | FGF19 | 13402 | -0.067 | 0.056 | NO |
293 | HIRIP3 | HIRIP3 | HIRIP3 | 13692 | -0.073 | 0.044 | NO |
294 | ATP9A | ATP9A | ATP9A | 13733 | -0.074 | 0.045 | NO |
295 | SEPHS2 | SEPHS2 | SEPHS2 | 13882 | -0.078 | 0.041 | NO |
296 | DTX4 | DTX4 | DTX4 | 13948 | -0.08 | 0.041 | NO |
297 | ZNF704 | ZNF704 | ZNF704 | 14025 | -0.082 | 0.041 | NO |
298 | GCAT | GCAT | GCAT | 14026 | -0.082 | 0.045 | NO |
299 | ILKAP | ILKAP | ILKAP | 14031 | -0.082 | 0.049 | NO |
300 | SLC11A2 | SLC11A2 | SLC11A2 | 14092 | -0.084 | 0.05 | NO |
301 | FAM19A5 | FAM19A5 | FAM19A5 | 14319 | -0.09 | 0.042 | NO |
302 | ACACB | ACACB | ACACB | 14627 | -0.1 | 0.03 | NO |
303 | HJURP | HJURP | HJURP | 14648 | -0.1 | 0.034 | NO |
304 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 14825 | -0.11 | 0.03 | NO |
305 | GAS7 | GAS7 | GAS7 | 14827 | -0.11 | 0.035 | NO |
306 | CDCA3 | CDCA3 | CDCA3 | 14915 | -0.11 | 0.036 | NO |
307 | APITD1 | APITD1 | APITD1 | 15014 | -0.12 | 0.036 | NO |
308 | RASL12 | RASL12 | RASL12 | 15724 | -0.15 | 0.0043 | NO |
309 | VSTM4 | VSTM4 | VSTM4 | 15744 | -0.16 | 0.011 | NO |
310 | METTL7B | METTL7B | METTL7B | 16062 | -0.17 | 0.0021 | NO |
311 | GPR19 | GPR19 | GPR19 | 16195 | -0.18 | 0.004 | NO |
312 | FRZB | FRZB | FRZB | 16250 | -0.19 | 0.01 | NO |
313 | SLC22A17 | SLC22A17 | SLC22A17 | 16614 | -0.21 | 0.00091 | NO |
314 | ADAMTS9 | ADAMTS9 | ADAMTS9 | 16669 | -0.22 | 0.009 | NO |
315 | PXDN | PXDN | PXDN | 17443 | -0.31 | -0.019 | NO |
316 | LGR6 | LGR6 | LGR6 | 17503 | -0.32 | -0.0057 | NO |
317 | GEM | GEM | GEM | 17699 | -0.36 | 0.0016 | NO |
318 | CADM1 | CADM1 | CADM1 | 17789 | -0.39 | 0.017 | NO |
Figure S53. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME PEPTIDE CHAIN ELONGATION.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PEPTIDE CHAIN ELONGATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S28. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FAM153A | FAM153A | FAM153A | 171 | 0.42 | 0.064 | YES |
2 | RPL3L | RPL3L | RPL3L | 1067 | 0.2 | 0.049 | YES |
3 | RPL35A | RPL35A | RPL35A | 1790 | 0.14 | 0.034 | YES |
4 | RPL15 | RPL15 | RPL15 | 1873 | 0.14 | 0.054 | YES |
5 | RPL24 | RPL24 | RPL24 | 2091 | 0.13 | 0.063 | YES |
6 | RPSA | RPSA | RPSA | 2101 | 0.13 | 0.084 | YES |
7 | RPL32 | RPL32 | RPL32 | 2306 | 0.12 | 0.093 | YES |
8 | RPL14 | RPL14 | RPL14 | 2343 | 0.12 | 0.11 | YES |
9 | RPS3A | RPS3A | RPS3A | 2351 | 0.12 | 0.13 | YES |
10 | RPS10 | RPS10 | RPS10 | 2727 | 0.1 | 0.13 | YES |
11 | RPS18 | RPS18 | RPS18 | 2815 | 0.097 | 0.14 | YES |
12 | RPL5 | RPL5 | RPL5 | 2860 | 0.096 | 0.15 | YES |
13 | RPS7 | RPS7 | RPS7 | 2933 | 0.093 | 0.17 | YES |
14 | RPS12 | RPS12 | RPS12 | 2965 | 0.092 | 0.18 | YES |
15 | RPL10A | RPL10A | RPL10A | 2969 | 0.092 | 0.2 | YES |
16 | NCBP2 | NCBP2 | NCBP2 | 3097 | 0.088 | 0.2 | YES |
17 | RPL9 | RPL9 | RPL9 | 3179 | 0.086 | 0.21 | YES |
18 | RPS6 | RPS6 | RPS6 | 3252 | 0.084 | 0.22 | YES |
19 | RPL17 | RPL17 | RPL17 | 3264 | 0.083 | 0.24 | YES |
20 | RPL29 | RPL29 | RPL29 | 3363 | 0.08 | 0.25 | YES |
21 | RPL26 | RPL26 | RPL26 | 3475 | 0.078 | 0.25 | YES |
22 | RPS15A | RPS15A | RPS15A | 3592 | 0.074 | 0.26 | YES |
23 | RPL31 | RPL31 | RPL31 | 3742 | 0.071 | 0.26 | YES |
24 | RPL21 | RPL21 | RPL21 | 3755 | 0.07 | 0.28 | YES |
25 | RPL22 | RPL22 | RPL22 | 3771 | 0.07 | 0.29 | YES |
26 | RPS8 | RPS8 | RPS8 | 3840 | 0.069 | 0.3 | YES |
27 | RPL34 | RPL34 | RPL34 | 3875 | 0.068 | 0.3 | YES |
28 | RPS23 | RPS23 | RPS23 | 3933 | 0.067 | 0.31 | YES |
29 | RPS27A | RPS27A | RPS27A | 3935 | 0.067 | 0.32 | YES |
30 | RPS17 | RPS17 | RPS17 | 4062 | 0.064 | 0.33 | YES |
31 | RPL36A | RPL36A | RPL36A | 4091 | 0.063 | 0.34 | YES |
32 | RPS24 | RPS24 | RPS24 | 4096 | 0.063 | 0.35 | YES |
33 | RPL3 | RPL3 | RPL3 | 4125 | 0.062 | 0.36 | YES |
34 | RPL39 | RPL39 | RPL39 | 4188 | 0.061 | 0.37 | YES |
35 | PPP2R2A | PPP2R2A | PPP2R2A | 4245 | 0.06 | 0.37 | YES |
36 | RPL11 | RPL11 | RPL11 | 4262 | 0.06 | 0.38 | YES |
37 | RPS29 | RPS29 | RPS29 | 4266 | 0.06 | 0.39 | YES |
38 | RPL12 | RPL12 | RPL12 | 4386 | 0.057 | 0.4 | YES |
39 | RPL13A | RPL13A | RPL13A | 4390 | 0.057 | 0.41 | YES |
40 | RPS3 | RPS3 | RPS3 | 4443 | 0.056 | 0.41 | YES |
41 | RPL23 | RPL23 | RPL23 | 4461 | 0.056 | 0.42 | YES |
42 | RPS27 | RPS27 | RPS27 | 4594 | 0.053 | 0.42 | YES |
43 | RPS25 | RPS25 | RPS25 | 4613 | 0.053 | 0.43 | YES |
44 | RPS19 | RPS19 | RPS19 | 4712 | 0.051 | 0.44 | YES |
45 | RPLP1 | RPLP1 | RPLP1 | 4714 | 0.051 | 0.44 | YES |
46 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 4718 | 0.051 | 0.45 | YES |
47 | RPL38 | RPL38 | RPL38 | 4734 | 0.051 | 0.46 | YES |
48 | SMG1 | SMG1 | SMG1 | 4753 | 0.05 | 0.47 | YES |
49 | RPLP0 | RPLP0 | RPLP0 | 4777 | 0.05 | 0.48 | YES |
50 | RPL4 | RPL4 | RPL4 | 4798 | 0.05 | 0.48 | YES |
51 | RPL6 | RPL6 | RPL6 | 4932 | 0.048 | 0.48 | YES |
52 | SMG8 | SMG8 | SMG8 | 4993 | 0.046 | 0.49 | YES |
53 | RPS9 | RPS9 | RPS9 | 5177 | 0.044 | 0.48 | YES |
54 | RPL7A | RPL7A | RPL7A | 5194 | 0.044 | 0.49 | YES |
55 | EIF4G1 | EIF4G1 | EIF4G1 | 5311 | 0.042 | 0.49 | YES |
56 | RPS14 | RPS14 | RPS14 | 5427 | 0.04 | 0.49 | YES |
57 | RPS5 | RPS5 | RPS5 | 5485 | 0.039 | 0.5 | YES |
58 | RPS4X | RPS4X | RPS4X | 5510 | 0.039 | 0.5 | YES |
59 | RPL18 | RPL18 | RPL18 | 5615 | 0.037 | 0.5 | YES |
60 | RPS13 | RPS13 | RPS13 | 5631 | 0.037 | 0.51 | YES |
61 | RPL27 | RPL27 | RPL27 | 5643 | 0.037 | 0.51 | YES |
62 | RPL13 | RPL13 | RPL13 | 5684 | 0.036 | 0.52 | YES |
63 | RPL10 | RPL10 | RPL10 | 5695 | 0.036 | 0.52 | YES |
64 | RPS21 | RPS21 | RPS21 | 5728 | 0.036 | 0.53 | YES |
65 | RPL27A | RPL27A | RPL27A | 5751 | 0.035 | 0.53 | YES |
66 | RPL41 | RPL41 | RPL41 | 5839 | 0.034 | 0.53 | YES |
67 | RPS28 | RPS28 | RPS28 | 5856 | 0.034 | 0.54 | YES |
68 | RPL37 | RPL37 | RPL37 | 5859 | 0.034 | 0.55 | YES |
69 | RPS2 | RPS2 | RPS2 | 5894 | 0.033 | 0.55 | YES |
70 | RPL37A | RPL37A | RPL37A | 5936 | 0.033 | 0.55 | YES |
71 | RPL35 | RPL35 | RPL35 | 6061 | 0.031 | 0.55 | YES |
72 | RPL18A | RPL18A | RPL18A | 6112 | 0.03 | 0.55 | YES |
73 | RPLP2 | RPLP2 | RPLP2 | 6479 | 0.026 | 0.54 | NO |
74 | UPF3B | UPF3B | UPF3B | 6530 | 0.025 | 0.54 | NO |
75 | RPS16 | RPS16 | RPS16 | 6545 | 0.025 | 0.54 | NO |
76 | RPS11 | RPS11 | RPS11 | 6717 | 0.023 | 0.54 | NO |
77 | PABPC1 | PABPC1 | PABPC1 | 6719 | 0.023 | 0.54 | NO |
78 | UPF3A | UPF3A | UPF3A | 6844 | 0.021 | 0.54 | NO |
79 | FAU | FAU | FAU | 6968 | 0.02 | 0.53 | NO |
80 | RPL19 | RPL19 | RPL19 | 7035 | 0.019 | 0.53 | NO |
81 | RPS15 | RPS15 | RPS15 | 7048 | 0.019 | 0.54 | NO |
82 | RPL7 | RPL7 | RPL7 | 7334 | 0.016 | 0.52 | NO |
83 | RPL36 | RPL36 | RPL36 | 7419 | 0.015 | 0.52 | NO |
84 | RPL23A | RPL23A | RPL23A | 7663 | 0.012 | 0.51 | NO |
85 | RPL30 | RPL30 | RPL30 | 7712 | 0.011 | 0.51 | NO |
86 | PPP2CA | PPP2CA | PPP2CA | 8062 | 0.0073 | 0.49 | NO |
87 | ETF1 | ETF1 | ETF1 | 8068 | 0.0073 | 0.49 | NO |
88 | RBM8A | RBM8A | RBM8A | 8070 | 0.0072 | 0.49 | NO |
89 | UBA52 | UBA52 | UBA52 | 8081 | 0.0071 | 0.49 | NO |
90 | UPF2 | UPF2 | UPF2 | 8255 | 0.0051 | 0.48 | NO |
91 | RPL28 | RPL28 | RPL28 | 8581 | 0.0013 | 0.47 | NO |
92 | RPL8 | RPL8 | RPL8 | 8857 | -0.002 | 0.45 | NO |
93 | GSPT2 | GSPT2 | GSPT2 | 9288 | -0.007 | 0.43 | NO |
94 | RNPS1 | RNPS1 | RNPS1 | 9398 | -0.0085 | 0.42 | NO |
95 | SMG7 | SMG7 | SMG7 | 9456 | -0.009 | 0.42 | NO |
96 | SMG6 | SMG6 | SMG6 | 9458 | -0.009 | 0.42 | NO |
97 | RPS20 | RPS20 | RPS20 | 9586 | -0.01 | 0.42 | NO |
98 | MAGOH | MAGOH | MAGOH | 9922 | -0.015 | 0.4 | NO |
99 | NCBP1 | NCBP1 | NCBP1 | 10026 | -0.016 | 0.4 | NO |
100 | RPS26 | RPS26 | RPS26 | 10232 | -0.018 | 0.39 | NO |
101 | CASC3 | CASC3 | CASC3 | 11286 | -0.032 | 0.34 | NO |
102 | PPP2R1A | PPP2R1A | PPP2R1A | 11859 | -0.04 | 0.31 | NO |
103 | EIF4A3 | EIF4A3 | EIF4A3 | 11886 | -0.04 | 0.32 | NO |
104 | RPL26L1 | RPL26L1 | RPL26L1 | 11970 | -0.041 | 0.32 | NO |
105 | SMG5 | SMG5 | SMG5 | 12622 | -0.052 | 0.3 | NO |
106 | SMG9 | SMG9 | SMG9 | 12646 | -0.052 | 0.3 | NO |
Figure S55. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME MRNA PROCESSING.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MRNA PROCESSING, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S29. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FAM153A | FAM153A | FAM153A | 171 | 0.42 | 0.05 | YES |
2 | RPL3L | RPL3L | RPL3L | 1067 | 0.2 | 0.029 | YES |
3 | EIF4A2 | EIF4A2 | EIF4A2 | 1268 | 0.18 | 0.044 | YES |
4 | RPL35A | RPL35A | RPL35A | 1790 | 0.14 | 0.035 | YES |
5 | RPL15 | RPL15 | RPL15 | 1873 | 0.14 | 0.05 | YES |
6 | RPL24 | RPL24 | RPL24 | 2091 | 0.13 | 0.056 | YES |
7 | RPSA | RPSA | RPSA | 2101 | 0.13 | 0.073 | YES |
8 | RPL32 | RPL32 | RPL32 | 2306 | 0.12 | 0.078 | YES |
9 | RPL14 | RPL14 | RPL14 | 2343 | 0.12 | 0.092 | YES |
10 | RPS3A | RPS3A | RPS3A | 2351 | 0.12 | 0.11 | YES |
11 | RPS10 | RPS10 | RPS10 | 2727 | 0.1 | 0.1 | YES |
12 | EEF1A1 | EEF1A1 | EEF1A1 | 2749 | 0.1 | 0.11 | YES |
13 | RPS18 | RPS18 | RPS18 | 2815 | 0.097 | 0.12 | YES |
14 | RPL5 | RPL5 | RPL5 | 2860 | 0.096 | 0.14 | YES |
15 | RPS7 | RPS7 | RPS7 | 2933 | 0.093 | 0.14 | YES |
16 | RPS12 | RPS12 | RPS12 | 2965 | 0.092 | 0.16 | YES |
17 | RPL10A | RPL10A | RPL10A | 2969 | 0.092 | 0.17 | YES |
18 | RPL9 | RPL9 | RPL9 | 3179 | 0.086 | 0.17 | YES |
19 | RPS6 | RPS6 | RPS6 | 3252 | 0.084 | 0.18 | YES |
20 | RPL17 | RPL17 | RPL17 | 3264 | 0.083 | 0.19 | YES |
21 | RPL29 | RPL29 | RPL29 | 3363 | 0.08 | 0.19 | YES |
22 | RPL26 | RPL26 | RPL26 | 3475 | 0.078 | 0.2 | YES |
23 | EIF2B5 | EIF2B5 | EIF2B5 | 3518 | 0.076 | 0.21 | YES |
24 | SSR3 | SSR3 | SSR3 | 3557 | 0.075 | 0.22 | YES |
25 | RPS15A | RPS15A | RPS15A | 3592 | 0.074 | 0.22 | YES |
26 | EIF2S3 | EIF2S3 | EIF2S3 | 3732 | 0.071 | 0.23 | YES |
27 | RPL31 | RPL31 | RPL31 | 3742 | 0.071 | 0.24 | YES |
28 | RPL21 | RPL21 | RPL21 | 3755 | 0.07 | 0.25 | YES |
29 | RPL22 | RPL22 | RPL22 | 3771 | 0.07 | 0.26 | YES |
30 | RPS8 | RPS8 | RPS8 | 3840 | 0.069 | 0.26 | YES |
31 | RPL34 | RPL34 | RPL34 | 3875 | 0.068 | 0.27 | YES |
32 | RPS23 | RPS23 | RPS23 | 3933 | 0.067 | 0.27 | YES |
33 | RPS27A | RPS27A | RPS27A | 3935 | 0.067 | 0.28 | YES |
34 | RPS17 | RPS17 | RPS17 | 4062 | 0.064 | 0.29 | YES |
35 | RPL36A | RPL36A | RPL36A | 4091 | 0.063 | 0.29 | YES |
36 | RPS24 | RPS24 | RPS24 | 4096 | 0.063 | 0.3 | YES |
37 | RPL3 | RPL3 | RPL3 | 4125 | 0.062 | 0.31 | YES |
38 | RPL39 | RPL39 | RPL39 | 4188 | 0.061 | 0.31 | YES |
39 | RPL11 | RPL11 | RPL11 | 4262 | 0.06 | 0.32 | YES |
40 | RPS29 | RPS29 | RPS29 | 4266 | 0.06 | 0.33 | YES |
41 | EEF1B2 | EEF1B2 | EEF1B2 | 4375 | 0.057 | 0.33 | YES |
42 | RPL12 | RPL12 | RPL12 | 4386 | 0.057 | 0.34 | YES |
43 | RPL13A | RPL13A | RPL13A | 4390 | 0.057 | 0.34 | YES |
44 | RPS3 | RPS3 | RPS3 | 4443 | 0.056 | 0.35 | YES |
45 | RPL23 | RPL23 | RPL23 | 4461 | 0.056 | 0.36 | YES |
46 | RPS27 | RPS27 | RPS27 | 4594 | 0.053 | 0.36 | YES |
47 | RPS25 | RPS25 | RPS25 | 4613 | 0.053 | 0.36 | YES |
48 | RPS19 | RPS19 | RPS19 | 4712 | 0.051 | 0.36 | YES |
49 | RPLP1 | RPLP1 | RPLP1 | 4714 | 0.051 | 0.37 | YES |
50 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 4718 | 0.051 | 0.38 | YES |
51 | EIF4B | EIF4B | EIF4B | 4730 | 0.051 | 0.38 | YES |
52 | RPL38 | RPL38 | RPL38 | 4734 | 0.051 | 0.39 | YES |
53 | RPLP0 | RPLP0 | RPLP0 | 4777 | 0.05 | 0.4 | YES |
54 | RPL4 | RPL4 | RPL4 | 4798 | 0.05 | 0.4 | YES |
55 | SRPRB | SRPRB | SRPRB | 4871 | 0.048 | 0.41 | YES |
56 | EIF1AX | EIF1AX | EIF1AX | 4918 | 0.048 | 0.41 | YES |
57 | RPL6 | RPL6 | RPL6 | 4932 | 0.048 | 0.42 | YES |
58 | RPS9 | RPS9 | RPS9 | 5177 | 0.044 | 0.41 | YES |
59 | SPCS1 | SPCS1 | SPCS1 | 5181 | 0.044 | 0.42 | YES |
60 | RPL7A | RPL7A | RPL7A | 5194 | 0.044 | 0.42 | YES |
61 | EIF5 | EIF5 | EIF5 | 5297 | 0.042 | 0.42 | YES |
62 | EIF4G1 | EIF4G1 | EIF4G1 | 5311 | 0.042 | 0.42 | YES |
63 | RPS14 | RPS14 | RPS14 | 5427 | 0.04 | 0.42 | YES |
64 | RPS5 | RPS5 | RPS5 | 5485 | 0.039 | 0.43 | YES |
65 | RPS4X | RPS4X | RPS4X | 5510 | 0.039 | 0.43 | YES |
66 | SEC11A | SEC11A | SEC11A | 5548 | 0.038 | 0.43 | YES |
67 | RPL18 | RPL18 | RPL18 | 5615 | 0.037 | 0.44 | YES |
68 | RPS13 | RPS13 | RPS13 | 5631 | 0.037 | 0.44 | YES |
69 | RPL27 | RPL27 | RPL27 | 5643 | 0.037 | 0.44 | YES |
70 | RPL13 | RPL13 | RPL13 | 5684 | 0.036 | 0.45 | YES |
71 | RPL10 | RPL10 | RPL10 | 5695 | 0.036 | 0.45 | YES |
72 | RPS21 | RPS21 | RPS21 | 5728 | 0.036 | 0.46 | YES |
73 | RPL27A | RPL27A | RPL27A | 5751 | 0.035 | 0.46 | YES |
74 | SSR1 | SSR1 | SSR1 | 5790 | 0.035 | 0.46 | YES |
75 | RPL41 | RPL41 | RPL41 | 5839 | 0.034 | 0.46 | YES |
76 | RPS28 | RPS28 | RPS28 | 5856 | 0.034 | 0.47 | YES |
77 | RPL37 | RPL37 | RPL37 | 5859 | 0.034 | 0.47 | YES |
78 | RPS2 | RPS2 | RPS2 | 5894 | 0.033 | 0.48 | YES |
79 | RPL37A | RPL37A | RPL37A | 5936 | 0.033 | 0.48 | YES |
80 | EIF3D | EIF3D | EIF3D | 5964 | 0.032 | 0.48 | YES |
81 | EIF3A | EIF3A | EIF3A | 6012 | 0.032 | 0.48 | YES |
82 | RPL35 | RPL35 | RPL35 | 6061 | 0.031 | 0.48 | YES |
83 | RPL18A | RPL18A | RPL18A | 6112 | 0.03 | 0.49 | YES |
84 | EIF3C | EIF3C | EIF3C | 6119 | 0.03 | 0.49 | YES |
85 | EIF3H | EIF3H | EIF3H | 6304 | 0.028 | 0.48 | NO |
86 | EEF2 | EEF2 | EEF2 | 6332 | 0.028 | 0.49 | NO |
87 | RPLP2 | RPLP2 | RPLP2 | 6479 | 0.026 | 0.48 | NO |
88 | EIF3F | EIF3F | EIF3F | 6492 | 0.026 | 0.48 | NO |
89 | EIF3E | EIF3E | EIF3E | 6509 | 0.026 | 0.49 | NO |
90 | RPS16 | RPS16 | RPS16 | 6545 | 0.025 | 0.49 | NO |
91 | RPS11 | RPS11 | RPS11 | 6717 | 0.023 | 0.48 | NO |
92 | PABPC1 | PABPC1 | PABPC1 | 6719 | 0.023 | 0.49 | NO |
93 | EIF4A1 | EIF4A1 | EIF4A1 | 6809 | 0.022 | 0.48 | NO |
94 | FAU | FAU | FAU | 6968 | 0.02 | 0.48 | NO |
95 | RPL19 | RPL19 | RPL19 | 7035 | 0.019 | 0.48 | NO |
96 | RPS15 | RPS15 | RPS15 | 7048 | 0.019 | 0.48 | NO |
97 | EIF3G | EIF3G | EIF3G | 7054 | 0.019 | 0.48 | NO |
98 | SRP19 | SRP19 | SRP19 | 7123 | 0.018 | 0.48 | NO |
99 | EIF3K | EIF3K | EIF3K | 7252 | 0.016 | 0.48 | NO |
100 | RPL7 | RPL7 | RPL7 | 7334 | 0.016 | 0.47 | NO |
101 | RPL36 | RPL36 | RPL36 | 7419 | 0.015 | 0.47 | NO |
102 | RPL23A | RPL23A | RPL23A | 7663 | 0.012 | 0.46 | NO |
103 | RPL30 | RPL30 | RPL30 | 7712 | 0.011 | 0.46 | NO |
104 | EEF1G | EEF1G | EEF1G | 7729 | 0.011 | 0.46 | NO |
105 | SSR2 | SSR2 | SSR2 | 7803 | 0.01 | 0.46 | NO |
106 | RPN1 | RPN1 | RPN1 | 7861 | 0.0096 | 0.45 | NO |
107 | SRP9 | SRP9 | SRP9 | 7980 | 0.0082 | 0.45 | NO |
108 | EIF2B1 | EIF2B1 | EIF2B1 | 8044 | 0.0074 | 0.45 | NO |
109 | ETF1 | ETF1 | ETF1 | 8068 | 0.0073 | 0.45 | NO |
110 | UBA52 | UBA52 | UBA52 | 8081 | 0.0071 | 0.45 | NO |
111 | EIF4E | EIF4E | EIF4E | 8171 | 0.0062 | 0.44 | NO |
112 | EIF2S2 | EIF2S2 | EIF2S2 | 8212 | 0.0057 | 0.44 | NO |
113 | EIF5B | EIF5B | EIF5B | 8485 | 0.0024 | 0.43 | NO |
114 | RPL28 | RPL28 | RPL28 | 8581 | 0.0013 | 0.42 | NO |
115 | SRP72 | SRP72 | SRP72 | 8590 | 0.0012 | 0.42 | NO |
116 | EIF4H | EIF4H | EIF4H | 8770 | -0.00075 | 0.41 | NO |
117 | DDOST | DDOST | DDOST | 8771 | -0.00076 | 0.41 | NO |
118 | EIF3J | EIF3J | EIF3J | 8772 | -0.00076 | 0.41 | NO |
119 | RPL8 | RPL8 | RPL8 | 8857 | -0.002 | 0.41 | NO |
120 | SEC61A1 | SEC61A1 | SEC61A1 | 8877 | -0.0022 | 0.4 | NO |
121 | EIF2B3 | EIF2B3 | EIF2B3 | 9041 | -0.004 | 0.4 | NO |
122 | EIF3I | EIF3I | EIF3I | 9272 | -0.0068 | 0.38 | NO |
123 | GSPT2 | GSPT2 | GSPT2 | 9288 | -0.007 | 0.38 | NO |
124 | RPS20 | RPS20 | RPS20 | 9586 | -0.01 | 0.37 | NO |
125 | SRP54 | SRP54 | SRP54 | 9592 | -0.01 | 0.37 | NO |
126 | SEC61B | SEC61B | SEC61B | 9910 | -0.014 | 0.36 | NO |
127 | SRP14 | SRP14 | SRP14 | 10142 | -0.017 | 0.34 | NO |
128 | SSR4 | SSR4 | SSR4 | 10147 | -0.017 | 0.35 | NO |
129 | SRP68 | SRP68 | SRP68 | 10211 | -0.018 | 0.35 | NO |
130 | RPS26 | RPS26 | RPS26 | 10232 | -0.018 | 0.35 | NO |
131 | SPCS3 | SPCS3 | SPCS3 | 10284 | -0.019 | 0.35 | NO |
132 | EEF1D | EEF1D | EEF1D | 10294 | -0.019 | 0.35 | NO |
133 | EIF2B2 | EIF2B2 | EIF2B2 | 10398 | -0.02 | 0.35 | NO |
134 | SEC61A2 | SEC61A2 | SEC61A2 | 11053 | -0.029 | 0.31 | NO |
135 | RPN2 | RPN2 | RPN2 | 11397 | -0.033 | 0.3 | NO |
136 | EIF2S1 | EIF2S1 | EIF2S1 | 11538 | -0.035 | 0.3 | NO |
137 | SRPR | SRPR | SRPR | 11648 | -0.036 | 0.3 | NO |
138 | RPL26L1 | RPL26L1 | RPL26L1 | 11970 | -0.041 | 0.28 | NO |
139 | SEC11C | SEC11C | SEC11C | 12222 | -0.045 | 0.28 | NO |
140 | SEC61G | SEC61G | SEC61G | 12440 | -0.048 | 0.27 | NO |
141 | EIF2B4 | EIF2B4 | EIF2B4 | 12676 | -0.052 | 0.26 | NO |
142 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 12818 | -0.055 | 0.26 | NO |
143 | EIF3B | EIF3B | EIF3B | 13153 | -0.062 | 0.26 | NO |
144 | TRAM1 | TRAM1 | TRAM1 | 13252 | -0.064 | 0.26 | NO |
145 | SPCS2 | SPCS2 | SPCS2 | 13699 | -0.074 | 0.24 | NO |
Figure S57. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION.

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S30. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | TARDBP | TARDBP | TARDBP | 301 | 0.36 | 0.12 | YES |
2 | ZNF544 | ZNF544 | ZNF544 | 931 | 0.22 | 0.17 | YES |
3 | FAM60A | FAM60A | FAM60A | 1920 | 0.14 | 0.17 | YES |
4 | TOMM70A | TOMM70A | TOMM70A | 2342 | 0.12 | 0.19 | YES |
5 | CMTM6 | CMTM6 | CMTM6 | 2432 | 0.11 | 0.22 | YES |
6 | UBE2E1 | UBE2E1 | UBE2E1 | 2704 | 0.1 | 0.25 | YES |
7 | NAP1L1 | NAP1L1 | NAP1L1 | 3121 | 0.088 | 0.26 | YES |
8 | ST13 | ST13 | ST13 | 3820 | 0.069 | 0.24 | YES |
9 | CCDC90B | CCDC90B | CCDC90B | 3865 | 0.068 | 0.27 | YES |
10 | PLEKHA5 | PLEKHA5 | PLEKHA5 | 3910 | 0.067 | 0.29 | YES |
11 | PUM2 | PUM2 | PUM2 | 4220 | 0.061 | 0.3 | YES |
12 | PPP2R2A | PPP2R2A | PPP2R2A | 4245 | 0.06 | 0.32 | YES |
13 | COMMD3 | COMMD3 | COMMD3 | 4288 | 0.059 | 0.34 | YES |
14 | PRPF4B | PRPF4B | PRPF4B | 4334 | 0.058 | 0.36 | YES |
15 | RAPGEF2 | RAPGEF2 | RAPGEF2 | 4456 | 0.056 | 0.37 | YES |
16 | RRAGC | RRAGC | RRAGC | 4680 | 0.052 | 0.38 | YES |
17 | SRPRB | SRPRB | SRPRB | 4871 | 0.048 | 0.39 | YES |
18 | RBBP4 | RBBP4 | RBBP4 | 4981 | 0.047 | 0.4 | YES |
19 | SEC11A | SEC11A | SEC11A | 5548 | 0.038 | 0.38 | YES |
20 | DUT | DUT | DUT | 5576 | 0.038 | 0.4 | YES |
21 | SLC25A46 | SLC25A46 | SLC25A46 | 5678 | 0.036 | 0.4 | YES |
22 | MRFAP1L1 | MRFAP1L1 | MRFAP1L1 | 5873 | 0.034 | 0.41 | YES |
23 | RALA | RALA | RALA | 6292 | 0.028 | 0.39 | NO |
24 | TSPO | TSPO | TSPO | 7541 | 0.013 | 0.33 | NO |
25 | GMFB | GMFB | GMFB | 7566 | 0.013 | 0.33 | NO |
26 | SEC23B | SEC23B | SEC23B | 7831 | 0.0099 | 0.32 | NO |
27 | MTRF1L | MTRF1L | MTRF1L | 7944 | 0.0086 | 0.32 | NO |
28 | GORASP2 | GORASP2 | GORASP2 | 8824 | -0.0015 | 0.27 | NO |
29 | ATP5A1 | ATP5A1 | ATP5A1 | 9157 | -0.0054 | 0.26 | NO |
30 | HSPA4 | HSPA4 | HSPA4 | 9429 | -0.0088 | 0.24 | NO |
31 | PLEKHJ1 | PLEKHJ1 | PLEKHJ1 | 9487 | -0.0094 | 0.24 | NO |
32 | CCT3 | CCT3 | CCT3 | 9816 | -0.013 | 0.23 | NO |
33 | R3HDM1 | R3HDM1 | R3HDM1 | 10634 | -0.023 | 0.19 | NO |
34 | TTYH2 | TTYH2 | TTYH2 | 10951 | -0.027 | 0.19 | NO |
35 | IL17RA | IL17RA | IL17RA | 12212 | -0.044 | 0.13 | NO |
36 | C20orf24 | C20orf24 | C20orf24 | 12417 | -0.048 | 0.14 | NO |
37 | FTL | FTL | FTL | 13066 | -0.06 | 0.13 | NO |
38 | C11orf21 | C11orf21 | C11orf21 | 15645 | -0.15 | 0.041 | NO |
39 | CD52 | CD52 | CD52 | 16994 | -0.25 | 0.06 | NO |
Figure S59. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: REACTOME INFLUENZA LIFE CYCLE.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME INFLUENZA LIFE CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 6. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus4. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG OXIDATIVE PHOSPHORYLATION | 114 | genes.ES.table | 0.46 | 1.7 | 0.033 | 0.44 | 0.9 | 0.67 | 0.32 | 0.46 | 0.19 | 0.11 |
SCHLOSSER MYC AND SERUM RESPONSE SYNERGY | 32 | genes.ES.table | 0.62 | 1.7 | 0.0039 | 0.41 | 0.9 | 0.66 | 0.2 | 0.53 | 0.18 | 0.1 |
DACOSTA UV RESPONSE VIA ERCC3 UP | 300 | genes.ES.table | 0.44 | 1.8 | 0.002 | 0.53 | 0.7 | 0.56 | 0.26 | 0.42 | 0.18 | 0.11 |
DAIRKEE TERT TARGETS UP | 349 | genes.ES.table | 0.38 | 1.7 | 0.002 | 0.44 | 0.88 | 0.59 | 0.25 | 0.45 | 0.19 | 0.1 |
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP | 469 | genes.ES.table | 0.36 | 1.8 | 0.012 | 0.44 | 0.83 | 0.5 | 0.25 | 0.38 | 0.17 | 0.1 |
LOCKWOOD AMPLIFIED IN LUNG CANCER | 207 | genes.ES.table | 0.26 | 1.7 | 0.0061 | 0.4 | 0.9 | 0.45 | 0.25 | 0.34 | 0.17 | 0.096 |
PENG LEUCINE DEPRIVATION DN | 183 | genes.ES.table | 0.35 | 1.7 | 0.032 | 0.4 | 0.91 | 0.51 | 0.31 | 0.36 | 0.18 | 0.095 |
MOOTHA VOXPHOS | 86 | genes.ES.table | 0.57 | 1.7 | 0.018 | 0.47 | 0.86 | 0.74 | 0.32 | 0.51 | 0.2 | 0.11 |
PENG GLUTAMINE DEPRIVATION DN | 327 | genes.ES.table | 0.3 | 1.8 | 0.036 | 0.43 | 0.8 | 0.49 | 0.31 | 0.34 | 0.16 | 0.093 |
FAELT B CLL WITH VH3 21 UP | 42 | genes.ES.table | 0.59 | 1.7 | 0.018 | 0.44 | 0.89 | 0.76 | 0.27 | 0.56 | 0.19 | 0.1 |
Table S31. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SLC19A1 | SLC19A1 | SLC19A1 | 452 | 0.16 | -0.0098 | YES |
2 | FASN | FASN | FASN | 504 | 0.16 | 0.0022 | YES |
3 | BOP1 | BOP1 | BOP1 | 517 | 0.16 | 0.016 | YES |
4 | GAL | GAL | GAL | 567 | 0.15 | 0.028 | YES |
5 | PKN1 | PKN1 | PKN1 | 659 | 0.15 | 0.036 | YES |
6 | GALK1 | GALK1 | GALK1 | 694 | 0.14 | 0.048 | YES |
7 | CDC25B | CDC25B | CDC25B | 711 | 0.14 | 0.06 | YES |
8 | FARSA | FARSA | FARSA | 759 | 0.14 | 0.071 | YES |
9 | CCDC85B | CCDC85B | CCDC85B | 762 | 0.14 | 0.084 | YES |
10 | SLC1A5 | SLC1A5 | SLC1A5 | 768 | 0.14 | 0.097 | YES |
11 | SRM | SRM | SRM | 805 | 0.14 | 0.11 | YES |
12 | CAD | CAD | CAD | 858 | 0.14 | 0.12 | YES |
13 | TRAP1 | TRAP1 | TRAP1 | 913 | 0.13 | 0.13 | YES |
14 | RELA | RELA | RELA | 972 | 0.13 | 0.14 | YES |
15 | NOS2 | NOS2 | NOS2 | 1030 | 0.13 | 0.14 | YES |
16 | ALG3 | ALG3 | ALG3 | 1248 | 0.12 | 0.14 | YES |
17 | CYC1 | CYC1 | CYC1 | 1282 | 0.12 | 0.15 | YES |
18 | HRAS | HRAS | HRAS | 1298 | 0.12 | 0.16 | YES |
19 | POLRMT | POLRMT | POLRMT | 1315 | 0.12 | 0.17 | YES |
20 | MRPS12 | MRPS12 | MRPS12 | 1319 | 0.12 | 0.19 | YES |
21 | HSF1 | HSF1 | HSF1 | 1345 | 0.12 | 0.2 | YES |
22 | EIF3B | EIF3B | EIF3B | 1392 | 0.12 | 0.2 | YES |
23 | ANXA11 | ANXA11 | ANXA11 | 1464 | 0.12 | 0.21 | YES |
24 | CHAF1A | CHAF1A | CHAF1A | 1536 | 0.11 | 0.22 | YES |
25 | SMARCA4 | SMARCA4 | SMARCA4 | 1566 | 0.11 | 0.23 | YES |
26 | AIMP2 | AIMP2 | AIMP2 | 1568 | 0.11 | 0.24 | YES |
27 | PRKACA | PRKACA | PRKACA | 1672 | 0.11 | 0.24 | YES |
28 | PWP2 | PWP2 | PWP2 | 1709 | 0.11 | 0.25 | YES |
29 | FKBP4 | FKBP4 | FKBP4 | 1763 | 0.11 | 0.26 | YES |
30 | USP5 | USP5 | USP5 | 1986 | 0.1 | 0.25 | YES |
31 | NAT6 | NAT6 | NAT6 | 1992 | 0.1 | 0.26 | YES |
32 | HDLBP | HDLBP | HDLBP | 2016 | 0.1 | 0.27 | YES |
33 | PHKG2 | PHKG2 | PHKG2 | 2065 | 0.1 | 0.28 | YES |
34 | NME3 | NME3 | NME3 | 2127 | 0.1 | 0.28 | YES |
35 | NUP214 | NUP214 | NUP214 | 2249 | 0.098 | 0.29 | YES |
36 | HCFC1 | HCFC1 | HCFC1 | 2253 | 0.098 | 0.3 | YES |
37 | ATIC | ATIC | ATIC | 2297 | 0.097 | 0.3 | YES |
38 | PPM1F | PPM1F | PPM1F | 2311 | 0.097 | 0.31 | YES |
39 | PRRC2A | PRRC2A | PRRC2A | 2316 | 0.097 | 0.32 | YES |
40 | DHCR24 | DHCR24 | DHCR24 | 2394 | 0.095 | 0.32 | YES |
41 | PIEZO1 | PIEZO1 | PIEZO1 | 2609 | 0.091 | 0.32 | YES |
42 | SCAP | SCAP | SCAP | 2641 | 0.09 | 0.33 | YES |
43 | BYSL | BYSL | BYSL | 2695 | 0.089 | 0.33 | YES |
44 | P2RX4 | P2RX4 | P2RX4 | 2739 | 0.088 | 0.34 | YES |
45 | LMNB2 | LMNB2 | LMNB2 | 2906 | 0.085 | 0.34 | YES |
46 | NSDHL | NSDHL | NSDHL | 2934 | 0.085 | 0.34 | YES |
47 | MOGS | MOGS | MOGS | 2974 | 0.084 | 0.35 | YES |
48 | PDCD11 | PDCD11 | PDCD11 | 3063 | 0.082 | 0.35 | YES |
49 | SF3B2 | SF3B2 | SF3B2 | 3091 | 0.081 | 0.36 | YES |
50 | CDK4 | CDK4 | CDK4 | 3156 | 0.08 | 0.36 | YES |
51 | POLD1 | POLD1 | POLD1 | 3291 | 0.077 | 0.36 | YES |
52 | EIF4G1 | EIF4G1 | EIF4G1 | 3321 | 0.076 | 0.37 | YES |
53 | UBL4A | UBL4A | UBL4A | 3330 | 0.076 | 0.38 | YES |
54 | RXRA | RXRA | RXRA | 3340 | 0.076 | 0.38 | YES |
55 | PMPCA | PMPCA | PMPCA | 3359 | 0.076 | 0.39 | YES |
56 | SCRIB | SCRIB | SCRIB | 3360 | 0.076 | 0.4 | YES |
57 | SSRP1 | SSRP1 | SSRP1 | 3378 | 0.075 | 0.4 | YES |
58 | CDC37 | CDC37 | CDC37 | 3477 | 0.074 | 0.4 | YES |
59 | KDM5C | KDM5C | KDM5C | 3491 | 0.073 | 0.41 | YES |
60 | FGFR3 | FGFR3 | FGFR3 | 3509 | 0.073 | 0.41 | YES |
61 | PABPC4 | PABPC4 | PABPC4 | 3527 | 0.072 | 0.42 | YES |
62 | NUP188 | NUP188 | NUP188 | 3625 | 0.07 | 0.42 | YES |
63 | AP3D1 | AP3D1 | AP3D1 | 3684 | 0.069 | 0.42 | YES |
64 | GTF3C2 | GTF3C2 | GTF3C2 | 3829 | 0.067 | 0.42 | YES |
65 | SKIV2L | SKIV2L | SKIV2L | 3848 | 0.066 | 0.43 | YES |
66 | DDT | DDT | DDT | 3853 | 0.066 | 0.43 | YES |
67 | AGPAT2 | AGPAT2 | AGPAT2 | 3917 | 0.065 | 0.44 | YES |
68 | NDRG1 | NDRG1 | NDRG1 | 3923 | 0.065 | 0.44 | YES |
69 | SEC24C | SEC24C | SEC24C | 3947 | 0.065 | 0.45 | YES |
70 | H1FX | H1FX | H1FX | 3950 | 0.064 | 0.45 | YES |
71 | HK1 | HK1 | HK1 | 3960 | 0.064 | 0.46 | YES |
72 | TCOF1 | TCOF1 | TCOF1 | 3995 | 0.064 | 0.46 | YES |
73 | EIF2B2 | EIF2B2 | EIF2B2 | 4006 | 0.064 | 0.47 | YES |
74 | VDAC1 | VDAC1 | VDAC1 | 4080 | 0.062 | 0.47 | YES |
75 | FDFT1 | FDFT1 | FDFT1 | 4100 | 0.062 | 0.47 | YES |
76 | SMAD6 | SMAD6 | SMAD6 | 4214 | 0.06 | 0.47 | YES |
77 | SLC6A8 | SLC6A8 | SLC6A8 | 4242 | 0.059 | 0.48 | YES |
78 | POLG | POLG | POLG | 4359 | 0.057 | 0.48 | YES |
79 | NMT1 | NMT1 | NMT1 | 4417 | 0.056 | 0.48 | YES |
80 | MCM2 | MCM2 | MCM2 | 4501 | 0.054 | 0.48 | YES |
81 | RAE1 | RAE1 | RAE1 | 4536 | 0.053 | 0.48 | YES |
82 | EMG1 | EMG1 | EMG1 | 4684 | 0.05 | 0.48 | YES |
83 | CLTA | CLTA | CLTA | 4689 | 0.05 | 0.48 | YES |
84 | MANF | MANF | MANF | 4697 | 0.05 | 0.49 | YES |
85 | UBAP2L | UBAP2L | UBAP2L | 4810 | 0.048 | 0.49 | YES |
86 | MAP2K5 | MAP2K5 | MAP2K5 | 4838 | 0.048 | 0.49 | YES |
87 | SSBP1 | SSBP1 | SSBP1 | 5147 | 0.042 | 0.48 | YES |
88 | SLC7A5 | SLC7A5 | SLC7A5 | 5149 | 0.042 | 0.48 | YES |
89 | CKAP4 | CKAP4 | CKAP4 | 5152 | 0.042 | 0.48 | YES |
90 | SAFB | SAFB | SAFB | 5234 | 0.041 | 0.48 | YES |
91 | SLC39A7 | SLC39A7 | SLC39A7 | 5241 | 0.04 | 0.49 | YES |
92 | MTHFD1 | MTHFD1 | MTHFD1 | 5294 | 0.04 | 0.49 | YES |
93 | CHD4 | CHD4 | CHD4 | 5326 | 0.039 | 0.49 | YES |
94 | RRP1B | RRP1B | RRP1B | 5373 | 0.038 | 0.49 | YES |
95 | RCC1 | RCC1 | RCC1 | 5476 | 0.036 | 0.49 | NO |
96 | EDC4 | EDC4 | EDC4 | 5530 | 0.035 | 0.49 | NO |
97 | RABEPK | RABEPK | RABEPK | 5589 | 0.034 | 0.49 | NO |
98 | NOLC1 | NOLC1 | NOLC1 | 5794 | 0.03 | 0.48 | NO |
99 | APEX1 | APEX1 | APEX1 | 5807 | 0.03 | 0.48 | NO |
100 | SLC29A1 | SLC29A1 | SLC29A1 | 6063 | 0.024 | 0.47 | NO |
101 | CCND1 | CCND1 | CCND1 | 6088 | 0.024 | 0.47 | NO |
102 | EIF4H | EIF4H | EIF4H | 6109 | 0.024 | 0.47 | NO |
103 | CCNE1 | CCNE1 | CCNE1 | 6128 | 0.023 | 0.47 | NO |
104 | SNRNP70 | SNRNP70 | SNRNP70 | 6188 | 0.022 | 0.47 | NO |
105 | RASSF7 | RASSF7 | RASSF7 | 6341 | 0.019 | 0.46 | NO |
106 | SF3A3 | SF3A3 | SF3A3 | 6400 | 0.018 | 0.46 | NO |
107 | MLEC | MLEC | MLEC | 6696 | 0.012 | 0.45 | NO |
108 | XRCC5 | XRCC5 | XRCC5 | 6748 | 0.011 | 0.45 | NO |
109 | RPIA | RPIA | RPIA | 6792 | 0.01 | 0.44 | NO |
110 | KAT2A | KAT2A | KAT2A | 6808 | 0.01 | 0.44 | NO |
111 | BRD2 | BRD2 | BRD2 | 7124 | 0.003 | 0.43 | NO |
112 | TAF1C | TAF1C | TAF1C | 7217 | 0.001 | 0.42 | NO |
113 | CDC123 | CDC123 | CDC123 | 7257 | -0.000062 | 0.42 | NO |
114 | PSMD1 | PSMD1 | PSMD1 | 7280 | -0.00037 | 0.42 | NO |
115 | MYC | MYC | MYC | 7768 | -0.011 | 0.39 | NO |
116 | RARS | RARS | RARS | 7958 | -0.015 | 0.38 | NO |
117 | DNAJC7 | DNAJC7 | DNAJC7 | 7996 | -0.016 | 0.38 | NO |
118 | NARS | NARS | NARS | 8061 | -0.017 | 0.38 | NO |
119 | BMS1 | BMS1 | BMS1 | 8243 | -0.021 | 0.37 | NO |
120 | EZR | EZR | EZR | 8286 | -0.022 | 0.37 | NO |
121 | MCL1 | MCL1 | MCL1 | 8897 | -0.034 | 0.34 | NO |
122 | HSP90B1 | HSP90B1 | HSP90B1 | 8957 | -0.036 | 0.34 | NO |
123 | SON | SON | SON | 9097 | -0.039 | 0.34 | NO |
124 | GCSH | GCSH | GCSH | 9215 | -0.042 | 0.34 | NO |
125 | STC1 | STC1 | STC1 | 9355 | -0.044 | 0.33 | NO |
126 | EIF3E | EIF3E | EIF3E | 9474 | -0.047 | 0.33 | NO |
127 | KRT6B | KRT6B | KRT6B | 9966 | -0.058 | 0.31 | NO |
128 | SNRPA1 | SNRPA1 | SNRPA1 | 10110 | -0.061 | 0.3 | NO |
129 | MGST1 | MGST1 | MGST1 | 10215 | -0.064 | 0.31 | NO |
130 | U2AF1 | U2AF1 | U2AF1 | 10361 | -0.067 | 0.3 | NO |
131 | SRPK1 | SRPK1 | SRPK1 | 10729 | -0.075 | 0.29 | NO |
132 | DUSP1 | DUSP1 | DUSP1 | 11194 | -0.086 | 0.27 | NO |
133 | SOX4 | SOX4 | SOX4 | 11239 | -0.087 | 0.28 | NO |
134 | PPAT | PPAT | PPAT | 11891 | -0.1 | 0.25 | NO |
135 | DDX10 | DDX10 | DDX10 | 12747 | -0.12 | 0.22 | NO |
136 | DNTTIP2 | DNTTIP2 | DNTTIP2 | 14485 | -0.18 | 0.14 | NO |
137 | HIST1H4C | HIST1H4C | HIST1H4C | 15244 | -0.21 | 0.11 | NO |
138 | SRSF11 | SRSF11 | SRSF11 | 15476 | -0.23 | 0.12 | NO |
139 | SLC1A3 | SLC1A3 | SLC1A3 | 15876 | -0.25 | 0.12 | NO |
Figure S61. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION.

Figure S62. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S32. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MRPL23 | MRPL23 | MRPL23 | 416 | 0.17 | -0.0031 | YES |
2 | NDUFS8 | NDUFS8 | NDUFS8 | 480 | 0.16 | 0.012 | YES |
3 | PHGDH | PHGDH | PHGDH | 524 | 0.16 | 0.029 | YES |
4 | NT5DC2 | NT5DC2 | NT5DC2 | 525 | 0.16 | 0.047 | YES |
5 | DCXR | DCXR | DCXR | 542 | 0.16 | 0.065 | YES |
6 | SCO2 | SCO2 | SCO2 | 597 | 0.15 | 0.08 | YES |
7 | DGCR6 | DGCR6 | DGCR6 | 719 | 0.14 | 0.09 | YES |
8 | EXOSC4 | EXOSC4 | EXOSC4 | 724 | 0.14 | 0.11 | YES |
9 | TST | TST | TST | 738 | 0.14 | 0.12 | YES |
10 | RUVBL2 | RUVBL2 | RUVBL2 | 900 | 0.13 | 0.13 | YES |
11 | C12orf10 | C12orf10 | C12orf10 | 903 | 0.13 | 0.14 | YES |
12 | DEAF1 | DEAF1 | DEAF1 | 919 | 0.13 | 0.16 | YES |
13 | ETFB | ETFB | ETFB | 950 | 0.13 | 0.17 | YES |
14 | NDUFS7 | NDUFS7 | NDUFS7 | 951 | 0.13 | 0.19 | YES |
15 | AP2S1 | AP2S1 | AP2S1 | 1013 | 0.13 | 0.2 | YES |
16 | NDUFB7 | NDUFB7 | NDUFB7 | 1015 | 0.13 | 0.22 | YES |
17 | MAP2K2 | MAP2K2 | MAP2K2 | 1016 | 0.13 | 0.23 | YES |
18 | MTX1 | MTX1 | MTX1 | 1128 | 0.13 | 0.24 | YES |
19 | CYC1 | CYC1 | CYC1 | 1282 | 0.12 | 0.25 | YES |
20 | MRPS12 | MRPS12 | MRPS12 | 1319 | 0.12 | 0.26 | YES |
21 | EIF3G | EIF3G | EIF3G | 1342 | 0.12 | 0.27 | YES |
22 | ENO1 | ENO1 | ENO1 | 1424 | 0.12 | 0.28 | YES |
23 | APRT | APRT | APRT | 1517 | 0.11 | 0.29 | YES |
24 | DGCR14 | DGCR14 | DGCR14 | 1532 | 0.11 | 0.3 | YES |
25 | CHAF1A | CHAF1A | CHAF1A | 1536 | 0.11 | 0.32 | YES |
26 | CUEDC2 | CUEDC2 | CUEDC2 | 1567 | 0.11 | 0.33 | YES |
27 | IDH3G | IDH3G | IDH3G | 1603 | 0.11 | 0.34 | YES |
28 | TRIB3 | TRIB3 | TRIB3 | 1636 | 0.11 | 0.35 | YES |
29 | WDR74 | WDR74 | WDR74 | 1652 | 0.11 | 0.36 | YES |
30 | CHMP2A | CHMP2A | CHMP2A | 1688 | 0.11 | 0.37 | YES |
31 | UQCRC1 | UQCRC1 | UQCRC1 | 1749 | 0.11 | 0.38 | YES |
32 | TCEB2 | TCEB2 | TCEB2 | 1811 | 0.11 | 0.39 | YES |
33 | MRPL12 | MRPL12 | MRPL12 | 1879 | 0.11 | 0.4 | YES |
34 | UBXN6 | UBXN6 | UBXN6 | 1889 | 0.1 | 0.41 | YES |
35 | DUS1L | DUS1L | DUS1L | 1900 | 0.1 | 0.43 | YES |
36 | ZNF593 | ZNF593 | ZNF593 | 1928 | 0.1 | 0.44 | YES |
37 | FLII | FLII | FLII | 1939 | 0.1 | 0.45 | YES |
38 | HSD17B10 | HSD17B10 | HSD17B10 | 2175 | 0.1 | 0.45 | YES |
39 | WDR45 | WDR45 | WDR45 | 2229 | 0.098 | 0.46 | YES |
40 | NDUFA13 | NDUFA13 | NDUFA13 | 2301 | 0.097 | 0.46 | YES |
41 | POLR2L | POLR2L | POLR2L | 2409 | 0.095 | 0.47 | YES |
42 | PPIB | PPIB | PPIB | 2430 | 0.094 | 0.48 | YES |
43 | RPS5 | RPS5 | RPS5 | 2458 | 0.094 | 0.49 | YES |
44 | HMOX2 | HMOX2 | HMOX2 | 2459 | 0.094 | 0.5 | YES |
45 | EEF1D | EEF1D | EEF1D | 2495 | 0.093 | 0.51 | YES |
46 | PDXK | PDXK | PDXK | 2830 | 0.087 | 0.5 | YES |
47 | APEH | APEH | APEH | 2994 | 0.084 | 0.5 | YES |
48 | PPP1R7 | PPP1R7 | PPP1R7 | 3012 | 0.083 | 0.51 | YES |
49 | PSMC3 | PSMC3 | PSMC3 | 3029 | 0.083 | 0.52 | YES |
50 | TRAPPC2L | TRAPPC2L | TRAPPC2L | 3052 | 0.082 | 0.53 | YES |
51 | PSMC5 | PSMC5 | PSMC5 | 3070 | 0.082 | 0.54 | YES |
52 | EDF1 | EDF1 | EDF1 | 3105 | 0.081 | 0.54 | YES |
53 | TACO1 | TACO1 | TACO1 | 3162 | 0.08 | 0.55 | YES |
54 | GLTSCR2 | GLTSCR2 | GLTSCR2 | 3217 | 0.079 | 0.56 | YES |
55 | RFC2 | RFC2 | RFC2 | 3309 | 0.077 | 0.56 | YES |
56 | STRA13 | STRA13 | STRA13 | 3320 | 0.076 | 0.57 | YES |
57 | FAM50A | FAM50A | FAM50A | 3747 | 0.068 | 0.55 | NO |
58 | ADA | ADA | ADA | 3858 | 0.066 | 0.56 | NO |
59 | MRPS11 | MRPS11 | MRPS11 | 3865 | 0.066 | 0.56 | NO |
60 | UFC1 | UFC1 | UFC1 | 4087 | 0.062 | 0.56 | NO |
61 | NARF | NARF | NARF | 4234 | 0.059 | 0.56 | NO |
62 | FAHD2A | FAHD2A | FAHD2A | 4313 | 0.057 | 0.56 | NO |
63 | MRTO4 | MRTO4 | MRTO4 | 4742 | 0.05 | 0.54 | NO |
64 | NOP56 | NOP56 | NOP56 | 4755 | 0.049 | 0.55 | NO |
65 | SAP30BP | SAP30BP | SAP30BP | 4885 | 0.047 | 0.55 | NO |
66 | LSM3 | LSM3 | LSM3 | 5521 | 0.035 | 0.51 | NO |
67 | SRRM2 | SRRM2 | SRRM2 | 5907 | 0.028 | 0.5 | NO |
68 | RPSA | RPSA | RPSA | 5944 | 0.027 | 0.5 | NO |
69 | PITRM1 | PITRM1 | PITRM1 | 6206 | 0.022 | 0.48 | NO |
70 | SPEN | SPEN | SPEN | 6659 | 0.013 | 0.46 | NO |
71 | NQO2 | NQO2 | NQO2 | 6694 | 0.012 | 0.46 | NO |
72 | BID | BID | BID | 6883 | 0.0078 | 0.45 | NO |
73 | JMJD6 | JMJD6 | JMJD6 | 7735 | -0.0099 | 0.41 | NO |
74 | MAT1A | MAT1A | MAT1A | 8460 | -0.025 | 0.37 | NO |
75 | NOL7 | NOL7 | NOL7 | 8461 | -0.025 | 0.37 | NO |
76 | NME6 | NME6 | NME6 | 8470 | -0.025 | 0.37 | NO |
77 | HSP90B1 | HSP90B1 | HSP90B1 | 8957 | -0.036 | 0.35 | NO |
78 | GATAD1 | GATAD1 | GATAD1 | 9492 | -0.048 | 0.33 | NO |
79 | ACBD3 | ACBD3 | ACBD3 | 10651 | -0.073 | 0.27 | NO |
80 | TPR | TPR | TPR | 11689 | -0.097 | 0.23 | NO |
81 | TTC3 | TTC3 | TTC3 | 11849 | -0.1 | 0.23 | NO |
82 | NAA15 | NAA15 | NAA15 | 12337 | -0.11 | 0.22 | NO |
83 | SMC3 | SMC3 | SMC3 | 12434 | -0.12 | 0.22 | NO |
84 | PRPF40A | PRPF40A | PRPF40A | 12962 | -0.13 | 0.21 | NO |
85 | BAZ1A | BAZ1A | BAZ1A | 14160 | -0.17 | 0.16 | NO |
86 | DNTTIP2 | DNTTIP2 | DNTTIP2 | 14485 | -0.18 | 0.17 | NO |
87 | DLEC1 | DLEC1 | DLEC1 | 16262 | -0.28 | 0.1 | NO |
Figure S63. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: SCHLOSSER MYC AND SERUM RESPONSE SYNERGY.

Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: SCHLOSSER MYC AND SERUM RESPONSE SYNERGY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S33. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | TMEM160 | TMEM160 | TMEM160 | 598 | 0.15 | -0.021 | YES |
2 | KRTCAP2 | KRTCAP2 | KRTCAP2 | 800 | 0.14 | -0.021 | YES |
3 | C8orf82 | C8orf82 | C8orf82 | 828 | 0.14 | -0.011 | YES |
4 | TAF10 | TAF10 | TAF10 | 850 | 0.14 | -0.001 | YES |
5 | CLPB | CLPB | CLPB | 914 | 0.13 | 0.0064 | YES |
6 | NDUFB7 | NDUFB7 | NDUFB7 | 1015 | 0.13 | 0.012 | YES |
7 | UBE2S | UBE2S | UBE2S | 1096 | 0.13 | 0.018 | YES |
8 | IMPDH2 | IMPDH2 | IMPDH2 | 1237 | 0.12 | 0.02 | YES |
9 | MRPL2 | MRPL2 | MRPL2 | 1257 | 0.12 | 0.029 | YES |
10 | MRPS12 | MRPS12 | MRPS12 | 1319 | 0.12 | 0.035 | YES |
11 | DDX54 | DDX54 | DDX54 | 1361 | 0.12 | 0.043 | YES |
12 | CENPB | CENPB | CENPB | 1391 | 0.12 | 0.051 | YES |
13 | TIMM13 | TIMM13 | TIMM13 | 1453 | 0.12 | 0.057 | YES |
14 | SLC25A39 | SLC25A39 | SLC25A39 | 1560 | 0.11 | 0.06 | YES |
15 | SLC39A4 | SLC39A4 | SLC39A4 | 1575 | 0.11 | 0.069 | YES |
16 | PRELID1 | PRELID1 | PRELID1 | 1584 | 0.11 | 0.078 | YES |
17 | NDUFA11 | NDUFA11 | NDUFA11 | 1614 | 0.11 | 0.085 | YES |
18 | RPS6KA4 | RPS6KA4 | RPS6KA4 | 1658 | 0.11 | 0.092 | YES |
19 | AURKAIP1 | AURKAIP1 | AURKAIP1 | 1693 | 0.11 | 0.099 | YES |
20 | NDUFS6 | NDUFS6 | NDUFS6 | 1752 | 0.11 | 0.1 | YES |
21 | UBA1 | UBA1 | UBA1 | 1806 | 0.11 | 0.11 | YES |
22 | MRPL21 | MRPL21 | MRPL21 | 1842 | 0.11 | 0.12 | YES |
23 | MRPS34 | MRPS34 | MRPS34 | 1848 | 0.11 | 0.13 | YES |
24 | MDH2 | MDH2 | MDH2 | 1852 | 0.11 | 0.14 | YES |
25 | LMNA | LMNA | LMNA | 1862 | 0.11 | 0.14 | YES |
26 | COPS6 | COPS6 | COPS6 | 1965 | 0.1 | 0.15 | YES |
27 | FKBP1A | FKBP1A | FKBP1A | 2094 | 0.1 | 0.15 | YES |
28 | COPE | COPE | COPE | 2178 | 0.099 | 0.15 | YES |
29 | LRPAP1 | LRPAP1 | LRPAP1 | 2187 | 0.099 | 0.16 | YES |
30 | AKT1 | AKT1 | AKT1 | 2208 | 0.099 | 0.16 | YES |
31 | PUF60 | PUF60 | PUF60 | 2279 | 0.097 | 0.17 | YES |
32 | PSMD8 | PSMD8 | PSMD8 | 2381 | 0.095 | 0.17 | YES |
33 | NR2F6 | NR2F6 | NR2F6 | 2386 | 0.095 | 0.18 | YES |
34 | N6AMT2 | N6AMT2 | N6AMT2 | 2393 | 0.095 | 0.19 | YES |
35 | VPS25 | VPS25 | VPS25 | 2442 | 0.094 | 0.19 | YES |
36 | TUBB | TUBB | TUBB | 2444 | 0.094 | 0.2 | YES |
37 | PC | PC | PC | 2494 | 0.093 | 0.2 | YES |
38 | LSM4 | LSM4 | LSM4 | 2543 | 0.092 | 0.21 | YES |
39 | NDUFS3 | NDUFS3 | NDUFS3 | 2580 | 0.091 | 0.22 | YES |
40 | DLGAP4 | DLGAP4 | DLGAP4 | 2598 | 0.091 | 0.22 | YES |
41 | TALDO1 | TALDO1 | TALDO1 | 2599 | 0.091 | 0.23 | YES |
42 | NAA10 | NAA10 | NAA10 | 2610 | 0.091 | 0.24 | YES |
43 | EXOC7 | EXOC7 | EXOC7 | 2637 | 0.09 | 0.24 | YES |
44 | RAMP2 | RAMP2 | RAMP2 | 2645 | 0.09 | 0.25 | YES |
45 | TGFB1I1 | TGFB1I1 | TGFB1I1 | 2703 | 0.089 | 0.25 | YES |
46 | STUB1 | STUB1 | STUB1 | 2751 | 0.088 | 0.26 | YES |
47 | CSNK2B | CSNK2B | CSNK2B | 2798 | 0.087 | 0.26 | YES |
48 | IFI35 | IFI35 | IFI35 | 2852 | 0.086 | 0.27 | YES |
49 | TMEM109 | TMEM109 | TMEM109 | 2942 | 0.085 | 0.27 | YES |
50 | DPP3 | DPP3 | DPP3 | 2944 | 0.085 | 0.28 | YES |
51 | HMBS | HMBS | HMBS | 2971 | 0.084 | 0.28 | YES |
52 | ACTB | ACTB | ACTB | 2987 | 0.084 | 0.29 | YES |
53 | RUVBL1 | RUVBL1 | RUVBL1 | 3039 | 0.082 | 0.29 | YES |
54 | PSMB6 | PSMB6 | PSMB6 | 3048 | 0.082 | 0.3 | YES |
55 | NDUFB9 | NDUFB9 | NDUFB9 | 3064 | 0.082 | 0.3 | YES |
56 | MRPL51 | MRPL51 | MRPL51 | 3074 | 0.082 | 0.31 | YES |
57 | ERP29 | ERP29 | ERP29 | 3108 | 0.081 | 0.31 | YES |
58 | TOR2A | TOR2A | TOR2A | 3114 | 0.081 | 0.32 | YES |
59 | CDK4 | CDK4 | CDK4 | 3156 | 0.08 | 0.32 | YES |
60 | ROMO1 | ROMO1 | ROMO1 | 3181 | 0.08 | 0.33 | YES |
61 | TWF2 | TWF2 | TWF2 | 3244 | 0.078 | 0.33 | YES |
62 | SAMM50 | SAMM50 | SAMM50 | 3272 | 0.078 | 0.34 | YES |
63 | MRPL36 | MRPL36 | MRPL36 | 3327 | 0.076 | 0.34 | YES |
64 | UBL4A | UBL4A | UBL4A | 3330 | 0.076 | 0.35 | YES |
65 | PTDSS1 | PTDSS1 | PTDSS1 | 3444 | 0.074 | 0.35 | YES |
66 | LAMTOR1 | LAMTOR1 | LAMTOR1 | 3462 | 0.074 | 0.35 | YES |
67 | POLR3K | POLR3K | POLR3K | 3612 | 0.071 | 0.35 | YES |
68 | PHB2 | PHB2 | PHB2 | 3641 | 0.07 | 0.35 | YES |
69 | MARCKSL1 | MARCKSL1 | MARCKSL1 | 3660 | 0.07 | 0.36 | YES |
70 | DRAP1 | DRAP1 | DRAP1 | 3667 | 0.07 | 0.36 | YES |
71 | SLIRP | SLIRP | SLIRP | 3680 | 0.07 | 0.37 | YES |
72 | GRPEL1 | GRPEL1 | GRPEL1 | 3707 | 0.069 | 0.37 | YES |
73 | EI24 | EI24 | EI24 | 3762 | 0.068 | 0.38 | YES |
74 | DDT | DDT | DDT | 3853 | 0.066 | 0.38 | YES |
75 | MRPS11 | MRPS11 | MRPS11 | 3865 | 0.066 | 0.38 | YES |
76 | PDAP1 | PDAP1 | PDAP1 | 3911 | 0.065 | 0.38 | YES |
77 | ADSL | ADSL | ADSL | 4070 | 0.062 | 0.38 | YES |
78 | LSM7 | LSM7 | LSM7 | 4073 | 0.062 | 0.39 | YES |
79 | PSMD13 | PSMD13 | PSMD13 | 4076 | 0.062 | 0.39 | YES |
80 | UFC1 | UFC1 | UFC1 | 4087 | 0.062 | 0.4 | YES |
81 | GSTP1 | GSTP1 | GSTP1 | 4093 | 0.062 | 0.4 | YES |
82 | HNRNPD | HNRNPD | HNRNPD | 4142 | 0.06 | 0.4 | YES |
83 | DDOST | DDOST | DDOST | 4231 | 0.059 | 0.4 | YES |
84 | EIF4A3 | EIF4A3 | EIF4A3 | 4288 | 0.058 | 0.4 | YES |
85 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 4326 | 0.057 | 0.41 | YES |
86 | CYB5R1 | CYB5R1 | CYB5R1 | 4402 | 0.056 | 0.41 | YES |
87 | EVL | EVL | EVL | 4459 | 0.055 | 0.41 | YES |
88 | SAE1 | SAE1 | SAE1 | 4468 | 0.055 | 0.41 | YES |
89 | EIF4E2 | EIF4E2 | EIF4E2 | 4499 | 0.054 | 0.42 | YES |
90 | DCTN2 | DCTN2 | DCTN2 | 4530 | 0.053 | 0.42 | YES |
91 | BAG1 | BAG1 | BAG1 | 4666 | 0.051 | 0.42 | YES |
92 | CKB | CKB | CKB | 4702 | 0.05 | 0.42 | YES |
93 | CRYGD | CRYGD | CRYGD | 4758 | 0.049 | 0.42 | YES |
94 | MRPS7 | MRPS7 | MRPS7 | 4967 | 0.046 | 0.41 | YES |
95 | UQCRQ | UQCRQ | UQCRQ | 4999 | 0.045 | 0.41 | YES |
96 | FAM96B | FAM96B | FAM96B | 5048 | 0.044 | 0.41 | YES |
97 | SRSF9 | SRSF9 | SRSF9 | 5052 | 0.044 | 0.42 | YES |
98 | VDAC3 | VDAC3 | VDAC3 | 5093 | 0.043 | 0.42 | YES |
99 | PARL | PARL | PARL | 5104 | 0.043 | 0.42 | YES |
100 | GOSR2 | GOSR2 | GOSR2 | 5274 | 0.04 | 0.41 | NO |
101 | TRAPPC4 | TRAPPC4 | TRAPPC4 | 5553 | 0.035 | 0.4 | NO |
102 | TNFAIP1 | TNFAIP1 | TNFAIP1 | 5556 | 0.035 | 0.4 | NO |
103 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 5762 | 0.031 | 0.4 | NO |
104 | ALG5 | ALG5 | ALG5 | 5912 | 0.027 | 0.39 | NO |
105 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 5917 | 0.027 | 0.39 | NO |
106 | ICT1 | ICT1 | ICT1 | 5928 | 0.027 | 0.39 | NO |
107 | SLC39A9 | SLC39A9 | SLC39A9 | 6169 | 0.022 | 0.38 | NO |
108 | CCDC12 | CCDC12 | CCDC12 | 6226 | 0.021 | 0.38 | NO |
109 | INPP5A | INPP5A | INPP5A | 6378 | 0.018 | 0.37 | NO |
110 | PIAS3 | PIAS3 | PIAS3 | 6402 | 0.018 | 0.37 | NO |
111 | NDUFV2 | NDUFV2 | NDUFV2 | 6409 | 0.018 | 0.38 | NO |
112 | RPN2 | RPN2 | RPN2 | 6471 | 0.017 | 0.37 | NO |
113 | FAM162A | FAM162A | FAM162A | 6553 | 0.015 | 0.37 | NO |
114 | MRPS15 | MRPS15 | MRPS15 | 6625 | 0.014 | 0.37 | NO |
115 | PSMG1 | PSMG1 | PSMG1 | 6653 | 0.013 | 0.37 | NO |
116 | PSMB7 | PSMB7 | PSMB7 | 6681 | 0.012 | 0.37 | NO |
117 | CKS1B | CKS1B | CKS1B | 6699 | 0.012 | 0.37 | NO |
118 | XRCC5 | XRCC5 | XRCC5 | 6748 | 0.011 | 0.36 | NO |
119 | STARD7 | STARD7 | STARD7 | 6894 | 0.0075 | 0.36 | NO |
120 | CALM1 | CALM1 | CALM1 | 7018 | 0.005 | 0.35 | NO |
121 | ARL2BP | ARL2BP | ARL2BP | 7063 | 0.0039 | 0.35 | NO |
122 | KRT10 | KRT10 | KRT10 | 7105 | 0.0032 | 0.35 | NO |
123 | FAF1 | FAF1 | FAF1 | 7193 | 0.0016 | 0.34 | NO |
124 | TMED10 | TMED10 | TMED10 | 7208 | 0.0013 | 0.34 | NO |
125 | MRPS14 | MRPS14 | MRPS14 | 7279 | -0.00037 | 0.34 | NO |
126 | NDUFB6 | NDUFB6 | NDUFB6 | 7284 | -0.00047 | 0.34 | NO |
127 | MRPL18 | MRPL18 | MRPL18 | 7344 | -0.0019 | 0.33 | NO |
128 | MRPL16 | MRPL16 | MRPL16 | 7347 | -0.0019 | 0.33 | NO |
129 | RNF7 | RNF7 | RNF7 | 7516 | -0.0055 | 0.32 | NO |
130 | SDHB | SDHB | SDHB | 7520 | -0.0055 | 0.32 | NO |
131 | TPM4 | TPM4 | TPM4 | 7605 | -0.007 | 0.32 | NO |
132 | MRPL34 | MRPL34 | MRPL34 | 7608 | -0.007 | 0.32 | NO |
133 | TCP1 | TCP1 | TCP1 | 7766 | -0.01 | 0.31 | NO |
134 | ARF4 | ARF4 | ARF4 | 7773 | -0.011 | 0.31 | NO |
135 | CAPN2 | CAPN2 | CAPN2 | 7803 | -0.011 | 0.31 | NO |
136 | PPAP2A | PPAP2A | PPAP2A | 8055 | -0.017 | 0.3 | NO |
137 | CMBL | CMBL | CMBL | 8157 | -0.019 | 0.3 | NO |
138 | BPGM | BPGM | BPGM | 8213 | -0.02 | 0.3 | NO |
139 | PSMA7 | PSMA7 | PSMA7 | 8289 | -0.022 | 0.29 | NO |
140 | CORO1C | CORO1C | CORO1C | 8355 | -0.023 | 0.29 | NO |
141 | SET | SET | SET | 8459 | -0.025 | 0.29 | NO |
142 | ERCC3 | ERCC3 | ERCC3 | 8584 | -0.028 | 0.28 | NO |
143 | COQ7 | COQ7 | COQ7 | 8641 | -0.029 | 0.28 | NO |
144 | FUCA1 | FUCA1 | FUCA1 | 8840 | -0.033 | 0.27 | NO |
145 | MRPS22 | MRPS22 | MRPS22 | 9075 | -0.038 | 0.26 | NO |
146 | HSD17B4 | HSD17B4 | HSD17B4 | 9096 | -0.039 | 0.27 | NO |
147 | TCEA1 | TCEA1 | TCEA1 | 9337 | -0.044 | 0.26 | NO |
148 | LIAS | LIAS | LIAS | 9357 | -0.045 | 0.26 | NO |
149 | ARL3 | ARL3 | ARL3 | 9378 | -0.045 | 0.26 | NO |
150 | NAP1L1 | NAP1L1 | NAP1L1 | 9467 | -0.047 | 0.26 | NO |
151 | PDCD2 | PDCD2 | PDCD2 | 9851 | -0.056 | 0.24 | NO |
152 | ARPC5 | ARPC5 | ARPC5 | 9912 | -0.057 | 0.24 | NO |
153 | TOMM70A | TOMM70A | TOMM70A | 10089 | -0.061 | 0.24 | NO |
154 | TRAM1 | TRAM1 | TRAM1 | 10136 | -0.062 | 0.24 | NO |
155 | GNG10 | GNG10 | GNG10 | 10156 | -0.062 | 0.25 | NO |
156 | DDX1 | DDX1 | DDX1 | 10164 | -0.063 | 0.25 | NO |
157 | DNAJC19 | DNAJC19 | DNAJC19 | 10321 | -0.066 | 0.25 | NO |
158 | TMEM5 | TMEM5 | TMEM5 | 10338 | -0.066 | 0.25 | NO |
159 | MTIF2 | MTIF2 | MTIF2 | 10402 | -0.068 | 0.25 | NO |
160 | PTPLAD1 | PTPLAD1 | PTPLAD1 | 10526 | -0.07 | 0.25 | NO |
161 | COPS5 | COPS5 | COPS5 | 10560 | -0.071 | 0.26 | NO |
162 | TXNRD1 | TXNRD1 | TXNRD1 | 10703 | -0.074 | 0.26 | NO |
163 | YIPF5 | YIPF5 | YIPF5 | 10788 | -0.076 | 0.26 | NO |
164 | HSD17B12 | HSD17B12 | HSD17B12 | 11091 | -0.084 | 0.25 | NO |
165 | CMPK1 | CMPK1 | CMPK1 | 11593 | -0.095 | 0.23 | NO |
166 | SMAP1 | SMAP1 | SMAP1 | 11631 | -0.096 | 0.23 | NO |
167 | PSMD14 | PSMD14 | PSMD14 | 12024 | -0.1 | 0.22 | NO |
168 | WTAP | WTAP | WTAP | 12122 | -0.11 | 0.22 | NO |
169 | BCAP29 | BCAP29 | BCAP29 | 12128 | -0.11 | 0.23 | NO |
170 | HMGCS1 | HMGCS1 | HMGCS1 | 12718 | -0.12 | 0.21 | NO |
171 | C11orf54 | C11orf54 | C11orf54 | 12765 | -0.12 | 0.22 | NO |
172 | USP1 | USP1 | USP1 | 13154 | -0.14 | 0.21 | NO |
173 | LYPLA1 | LYPLA1 | LYPLA1 | 13368 | -0.14 | 0.21 | NO |
174 | GCLM | GCLM | GCLM | 13928 | -0.16 | 0.19 | NO |
175 | MAP3K7 | MAP3K7 | MAP3K7 | 14948 | -0.2 | 0.15 | NO |
176 | AQP4 | AQP4 | AQP4 | 16812 | -0.34 | 0.071 | NO |
Figure S65. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: DACOSTA UV RESPONSE VIA ERCC3 UP.

Figure S66. Get High-res Image For the top 5 core enriched genes in the pathway: DACOSTA UV RESPONSE VIA ERCC3 UP, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S34. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MTRNR2L8 | MTRNR2L8 | MTRNR2L8 | 53 | 0.29 | 0.0088 | YES |
2 | CCND2 | CCND2 | CCND2 | 257 | 0.2 | 0.0055 | YES |
3 | UBE2C | UBE2C | UBE2C | 271 | 0.2 | 0.013 | YES |
4 | EEF1G | EEF1G | EEF1G | 395 | 0.17 | 0.013 | YES |
5 | FMOD | FMOD | FMOD | 468 | 0.16 | 0.015 | YES |
6 | PDLIM1 | PDLIM1 | PDLIM1 | 484 | 0.16 | 0.021 | YES |
7 | MGST2 | MGST2 | MGST2 | 787 | 0.14 | 0.0097 | YES |
8 | ARHGAP1 | ARHGAP1 | ARHGAP1 | 892 | 0.13 | 0.0093 | YES |
9 | GAPDH | GAPDH | GAPDH | 937 | 0.13 | 0.012 | YES |
10 | ALDOA | ALDOA | ALDOA | 981 | 0.13 | 0.015 | YES |
11 | CST3 | CST3 | CST3 | 994 | 0.13 | 0.02 | YES |
12 | CAPNS1 | CAPNS1 | CAPNS1 | 1014 | 0.13 | 0.024 | YES |
13 | GPS1 | GPS1 | GPS1 | 1036 | 0.13 | 0.028 | YES |
14 | CD81 | CD81 | CD81 | 1047 | 0.13 | 0.033 | YES |
15 | RPL28 | RPL28 | RPL28 | 1053 | 0.13 | 0.038 | YES |
16 | USP11 | USP11 | USP11 | 1105 | 0.13 | 0.04 | YES |
17 | NCOR2 | NCOR2 | NCOR2 | 1162 | 0.12 | 0.042 | YES |
18 | RPL18A | RPL18A | RPL18A | 1193 | 0.12 | 0.046 | YES |
19 | LGALS1 | LGALS1 | LGALS1 | 1239 | 0.12 | 0.048 | YES |
20 | COMT | COMT | COMT | 1338 | 0.12 | 0.047 | YES |
21 | TRIM28 | TRIM28 | TRIM28 | 1360 | 0.12 | 0.051 | YES |
22 | MAZ | MAZ | MAZ | 1387 | 0.12 | 0.054 | YES |
23 | ENO1 | ENO1 | ENO1 | 1424 | 0.12 | 0.057 | YES |
24 | ANXA11 | ANXA11 | ANXA11 | 1464 | 0.12 | 0.06 | YES |
25 | UBA52 | UBA52 | UBA52 | 1515 | 0.11 | 0.062 | YES |
26 | ARAF | ARAF | ARAF | 1516 | 0.11 | 0.066 | YES |
27 | RPS15 | RPS15 | RPS15 | 1550 | 0.11 | 0.069 | YES |
28 | CFL1 | CFL1 | CFL1 | 1556 | 0.11 | 0.073 | YES |
29 | ILK | ILK | ILK | 1595 | 0.11 | 0.076 | YES |
30 | ATP5G2 | ATP5G2 | ATP5G2 | 1635 | 0.11 | 0.078 | YES |
31 | GPX4 | GPX4 | GPX4 | 1644 | 0.11 | 0.082 | YES |
32 | ATP5G1 | ATP5G1 | ATP5G1 | 1647 | 0.11 | 0.087 | YES |
33 | IFITM1 | IFITM1 | IFITM1 | 1734 | 0.11 | 0.086 | YES |
34 | FKBP4 | FKBP4 | FKBP4 | 1763 | 0.11 | 0.089 | YES |
35 | UBA1 | UBA1 | UBA1 | 1806 | 0.11 | 0.091 | YES |
36 | RBPMS | RBPMS | RBPMS | 1810 | 0.11 | 0.095 | YES |
37 | LASP1 | LASP1 | LASP1 | 1877 | 0.11 | 0.096 | YES |
38 | RPS28 | RPS28 | RPS28 | 1886 | 0.11 | 0.1 | YES |
39 | CD34 | CD34 | CD34 | 1911 | 0.1 | 0.1 | YES |
40 | COPS6 | COPS6 | COPS6 | 1965 | 0.1 | 0.1 | YES |
41 | MLF2 | MLF2 | MLF2 | 2001 | 0.1 | 0.11 | YES |
42 | GUSB | GUSB | GUSB | 2051 | 0.1 | 0.11 | YES |
43 | ARF3 | ARF3 | ARF3 | 2054 | 0.1 | 0.11 | YES |
44 | FKBP1A | FKBP1A | FKBP1A | 2094 | 0.1 | 0.11 | YES |
45 | ITPK1 | ITPK1 | ITPK1 | 2104 | 0.1 | 0.12 | YES |
46 | AARS | AARS | AARS | 2123 | 0.1 | 0.12 | YES |
47 | CD151 | CD151 | CD151 | 2135 | 0.1 | 0.12 | YES |
48 | RPLP2 | RPLP2 | RPLP2 | 2212 | 0.099 | 0.12 | YES |
49 | JUND | JUND | JUND | 2220 | 0.099 | 0.13 | YES |
50 | TAGLN2 | TAGLN2 | TAGLN2 | 2235 | 0.098 | 0.13 | YES |
51 | SLC25A6 | SLC25A6 | SLC25A6 | 2267 | 0.098 | 0.13 | YES |
52 | MSN | MSN | MSN | 2278 | 0.097 | 0.14 | YES |
53 | ATIC | ATIC | ATIC | 2297 | 0.097 | 0.14 | YES |
54 | RPL18 | RPL18 | RPL18 | 2304 | 0.097 | 0.14 | YES |
55 | ATP6V1F | ATP6V1F | ATP6V1F | 2354 | 0.096 | 0.14 | YES |
56 | SF1 | SF1 | SF1 | 2362 | 0.096 | 0.15 | YES |
57 | HSPB1 | HSPB1 | HSPB1 | 2366 | 0.096 | 0.15 | YES |
58 | PFN1 | PFN1 | PFN1 | 2372 | 0.096 | 0.16 | YES |
59 | DHPS | DHPS | DHPS | 2378 | 0.095 | 0.16 | YES |
60 | PSMD8 | PSMD8 | PSMD8 | 2381 | 0.095 | 0.16 | YES |
61 | CASC3 | CASC3 | CASC3 | 2407 | 0.095 | 0.16 | YES |
62 | POLR2L | POLR2L | POLR2L | 2409 | 0.095 | 0.17 | YES |
63 | CSTB | CSTB | CSTB | 2410 | 0.095 | 0.17 | YES |
64 | TUBB | TUBB | TUBB | 2444 | 0.094 | 0.17 | YES |
65 | RPS5 | RPS5 | RPS5 | 2458 | 0.094 | 0.18 | YES |
66 | RPL13 | RPL13 | RPL13 | 2489 | 0.093 | 0.18 | YES |
67 | EEF1D | EEF1D | EEF1D | 2495 | 0.093 | 0.18 | YES |
68 | COX8A | COX8A | COX8A | 2502 | 0.093 | 0.19 | YES |
69 | RPS26 | RPS26 | RPS26 | 2544 | 0.092 | 0.19 | YES |
70 | COX6B1 | COX6B1 | COX6B1 | 2555 | 0.092 | 0.19 | YES |
71 | EIF3F | EIF3F | EIF3F | 2617 | 0.091 | 0.19 | YES |
72 | BCAP31 | BCAP31 | BCAP31 | 2636 | 0.09 | 0.19 | YES |
73 | LAMP1 | LAMP1 | LAMP1 | 2717 | 0.089 | 0.19 | YES |
74 | FBL | FBL | FBL | 2725 | 0.089 | 0.2 | YES |
75 | OS9 | OS9 | OS9 | 2779 | 0.088 | 0.2 | YES |
76 | MYH9 | MYH9 | MYH9 | 2781 | 0.088 | 0.2 | YES |
77 | DDB1 | DDB1 | DDB1 | 2783 | 0.088 | 0.2 | YES |
78 | RPS9 | RPS9 | RPS9 | 2797 | 0.087 | 0.21 | YES |
79 | CSNK2B | CSNK2B | CSNK2B | 2798 | 0.087 | 0.21 | YES |
80 | RPS2 | RPS2 | RPS2 | 2804 | 0.087 | 0.21 | YES |
81 | RPL37A | RPL37A | RPL37A | 2817 | 0.087 | 0.22 | YES |
82 | RPS19 | RPS19 | RPS19 | 2834 | 0.086 | 0.22 | YES |
83 | EEF2 | EEF2 | EEF2 | 2874 | 0.086 | 0.22 | YES |
84 | NEDD8 | NEDD8 | NEDD8 | 2895 | 0.085 | 0.22 | YES |
85 | VPS72 | VPS72 | VPS72 | 2948 | 0.084 | 0.22 | YES |
86 | ACTB | ACTB | ACTB | 2987 | 0.084 | 0.22 | YES |
87 | NCSTN | NCSTN | NCSTN | 3001 | 0.083 | 0.23 | YES |
88 | DYNLL1 | DYNLL1 | DYNLL1 | 3002 | 0.083 | 0.23 | YES |
89 | SSR2 | SSR2 | SSR2 | 3009 | 0.083 | 0.23 | YES |
90 | RPL8 | RPL8 | RPL8 | 3015 | 0.083 | 0.24 | YES |
91 | DVL3 | DVL3 | DVL3 | 3030 | 0.083 | 0.24 | YES |
92 | PSMB6 | PSMB6 | PSMB6 | 3048 | 0.082 | 0.24 | YES |
93 | SURF1 | SURF1 | SURF1 | 3065 | 0.082 | 0.24 | YES |
94 | FCGRT | FCGRT | FCGRT | 3079 | 0.082 | 0.25 | YES |
95 | CYB5R3 | CYB5R3 | CYB5R3 | 3082 | 0.082 | 0.25 | YES |
96 | ACTG1 | ACTG1 | ACTG1 | 3087 | 0.082 | 0.25 | YES |
97 | AAMP | AAMP | AAMP | 3088 | 0.082 | 0.26 | YES |
98 | SF3B2 | SF3B2 | SF3B2 | 3091 | 0.081 | 0.26 | YES |
99 | WARS | WARS | WARS | 3123 | 0.08 | 0.26 | YES |
100 | GPX1 | GPX1 | GPX1 | 3127 | 0.08 | 0.26 | YES |
101 | AGPAT1 | AGPAT1 | AGPAT1 | 3138 | 0.08 | 0.27 | YES |
102 | GNB2L1 | GNB2L1 | GNB2L1 | 3148 | 0.08 | 0.27 | YES |
103 | ATOX1 | ATOX1 | ATOX1 | 3155 | 0.08 | 0.27 | YES |
104 | PSMB3 | PSMB3 | PSMB3 | 3222 | 0.079 | 0.27 | YES |
105 | SQSTM1 | SQSTM1 | SQSTM1 | 3233 | 0.078 | 0.28 | YES |
106 | ISG20 | ISG20 | ISG20 | 3252 | 0.078 | 0.28 | YES |
107 | RPS16 | RPS16 | RPS16 | 3281 | 0.077 | 0.28 | YES |
108 | PSMB5 | PSMB5 | PSMB5 | 3305 | 0.077 | 0.28 | YES |
109 | PI4KA | PI4KA | PI4KA | 3338 | 0.076 | 0.28 | YES |
110 | SCN1B | SCN1B | SCN1B | 3341 | 0.076 | 0.28 | YES |
111 | ATP5B | ATP5B | ATP5B | 3349 | 0.076 | 0.29 | YES |
112 | COX6A1 | COX6A1 | COX6A1 | 3351 | 0.076 | 0.29 | YES |
113 | UBB | UBB | UBB | 3383 | 0.075 | 0.29 | YES |
114 | FTL | FTL | FTL | 3436 | 0.074 | 0.29 | YES |
115 | PGAM1 | PGAM1 | PGAM1 | 3443 | 0.074 | 0.3 | YES |
116 | PTDSS1 | PTDSS1 | PTDSS1 | 3444 | 0.074 | 0.3 | YES |
117 | FLNA | FLNA | FLNA | 3502 | 0.073 | 0.3 | YES |
118 | IRAK1 | IRAK1 | IRAK1 | 3525 | 0.072 | 0.3 | YES |
119 | RPL29 | RPL29 | RPL29 | 3542 | 0.072 | 0.3 | YES |
120 | TRAF4 | TRAF4 | TRAF4 | 3546 | 0.072 | 0.3 | YES |
121 | CD63 | CD63 | CD63 | 3582 | 0.071 | 0.31 | YES |
122 | FTH1 | FTH1 | FTH1 | 3606 | 0.071 | 0.31 | YES |
123 | PHB2 | PHB2 | PHB2 | 3641 | 0.07 | 0.31 | YES |
124 | CIRBP | CIRBP | CIRBP | 3659 | 0.07 | 0.31 | YES |
125 | YWHAH | YWHAH | YWHAH | 3666 | 0.07 | 0.31 | YES |
126 | AES | AES | AES | 3690 | 0.069 | 0.31 | YES |
127 | RPS11 | RPS11 | RPS11 | 3718 | 0.069 | 0.32 | YES |
128 | ECHS1 | ECHS1 | ECHS1 | 3724 | 0.069 | 0.32 | YES |
129 | PCBP2 | PCBP2 | PCBP2 | 3739 | 0.068 | 0.32 | YES |
130 | PLP2 | PLP2 | PLP2 | 3755 | 0.068 | 0.32 | YES |
131 | HTRA1 | HTRA1 | HTRA1 | 3763 | 0.068 | 0.32 | YES |
132 | PRDX6 | PRDX6 | PRDX6 | 3828 | 0.067 | 0.32 | YES |
133 | DDT | DDT | DDT | 3853 | 0.066 | 0.32 | YES |
134 | RPL27A | RPL27A | RPL27A | 3855 | 0.066 | 0.33 | YES |
135 | FUS | FUS | FUS | 3900 | 0.065 | 0.33 | YES |
136 | RPS29 | RPS29 | RPS29 | 3909 | 0.065 | 0.33 | YES |
137 | NDRG1 | NDRG1 | NDRG1 | 3923 | 0.065 | 0.33 | YES |
138 | RPL35 | RPL35 | RPL35 | 3964 | 0.064 | 0.33 | YES |
139 | SNRPD2 | SNRPD2 | SNRPD2 | 3968 | 0.064 | 0.33 | YES |
140 | QARS | QARS | QARS | 4010 | 0.063 | 0.34 | YES |
141 | GSTP1 | GSTP1 | GSTP1 | 4093 | 0.062 | 0.33 | YES |
142 | RPS3 | RPS3 | RPS3 | 4135 | 0.061 | 0.33 | YES |
143 | RAC1 | RAC1 | RAC1 | 4180 | 0.06 | 0.33 | YES |
144 | SPTBN1 | SPTBN1 | SPTBN1 | 4197 | 0.06 | 0.33 | YES |
145 | CD3E | CD3E | CD3E | 4208 | 0.06 | 0.34 | YES |
146 | RPL41 | RPL41 | RPL41 | 4209 | 0.06 | 0.34 | YES |
147 | ARF1 | ARF1 | ARF1 | 4227 | 0.059 | 0.34 | YES |
148 | OAZ1 | OAZ1 | OAZ1 | 4238 | 0.059 | 0.34 | YES |
149 | SLC6A8 | SLC6A8 | SLC6A8 | 4242 | 0.059 | 0.34 | YES |
150 | RPLP1 | RPLP1 | RPLP1 | 4263 | 0.059 | 0.34 | YES |
151 | PPIA | PPIA | PPIA | 4283 | 0.058 | 0.35 | YES |
152 | EIF4A3 | EIF4A3 | EIF4A3 | 4288 | 0.058 | 0.35 | YES |
153 | COX4I1 | COX4I1 | COX4I1 | 4312 | 0.058 | 0.35 | YES |
154 | CLIC1 | CLIC1 | CLIC1 | 4330 | 0.057 | 0.35 | YES |
155 | RPS14 | RPS14 | RPS14 | 4331 | 0.057 | 0.35 | YES |
156 | PSMD2 | PSMD2 | PSMD2 | 4340 | 0.057 | 0.36 | YES |
157 | VIM | VIM | VIM | 4385 | 0.056 | 0.36 | YES |
158 | RPL19 | RPL19 | RPL19 | 4392 | 0.056 | 0.36 | YES |
159 | MT2A | MT2A | MT2A | 4473 | 0.054 | 0.36 | YES |
160 | NDUFA12 | NDUFA12 | NDUFA12 | 4508 | 0.054 | 0.36 | YES |
161 | PSMB4 | PSMB4 | PSMB4 | 4512 | 0.054 | 0.36 | YES |
162 | RPL23 | RPL23 | RPL23 | 4524 | 0.054 | 0.36 | YES |
163 | DCTN2 | DCTN2 | DCTN2 | 4530 | 0.053 | 0.36 | YES |
164 | RPL12 | RPL12 | RPL12 | 4547 | 0.053 | 0.36 | YES |
165 | RER1 | RER1 | RER1 | 4564 | 0.053 | 0.36 | YES |
166 | NPC2 | NPC2 | NPC2 | 4593 | 0.052 | 0.36 | YES |
167 | RPL38 | RPL38 | RPL38 | 4640 | 0.051 | 0.36 | YES |
168 | CTDSP2 | CTDSP2 | CTDSP2 | 4649 | 0.051 | 0.36 | YES |
169 | ATP5G3 | ATP5G3 | ATP5G3 | 4685 | 0.05 | 0.36 | YES |
170 | CLTA | CLTA | CLTA | 4689 | 0.05 | 0.37 | YES |
171 | SARS | SARS | SARS | 4710 | 0.05 | 0.37 | YES |
172 | SEC61B | SEC61B | SEC61B | 4729 | 0.05 | 0.37 | YES |
173 | RPL36AL | RPL36AL | RPL36AL | 4731 | 0.05 | 0.37 | YES |
174 | HLA-A | HLA-A | HLA-A | 4766 | 0.049 | 0.37 | YES |
175 | RPL7A | RPL7A | RPL7A | 4792 | 0.049 | 0.37 | YES |
176 | COPA | COPA | COPA | 4799 | 0.049 | 0.37 | YES |
177 | PARP1 | PARP1 | PARP1 | 4816 | 0.048 | 0.37 | YES |
178 | ANXA2 | ANXA2 | ANXA2 | 4823 | 0.048 | 0.38 | YES |
179 | C1QBP | C1QBP | C1QBP | 4847 | 0.048 | 0.38 | YES |
180 | MPRIP | MPRIP | MPRIP | 4852 | 0.048 | 0.38 | YES |
181 | SLC25A3 | SLC25A3 | SLC25A3 | 4856 | 0.048 | 0.38 | YES |
182 | UBC | UBC | UBC | 4865 | 0.047 | 0.38 | YES |
183 | RHOA | RHOA | RHOA | 4874 | 0.047 | 0.38 | YES |
184 | EIF1 | EIF1 | EIF1 | 4884 | 0.047 | 0.38 | YES |
185 | RPS21 | RPS21 | RPS21 | 4887 | 0.047 | 0.39 | YES |
186 | ARPC2 | ARPC2 | ARPC2 | 4892 | 0.047 | 0.39 | YES |
187 | UQCRH | UQCRH | UQCRH | 4920 | 0.046 | 0.39 | YES |
188 | COX7A2 | COX7A2 | COX7A2 | 4956 | 0.046 | 0.39 | YES |
189 | FAM193A | FAM193A | FAM193A | 4959 | 0.046 | 0.39 | YES |
190 | S100A10 | S100A10 | S100A10 | 4985 | 0.045 | 0.39 | YES |
191 | RPL32 | RPL32 | RPL32 | 4994 | 0.045 | 0.39 | YES |
192 | APLP2 | APLP2 | APLP2 | 5023 | 0.044 | 0.39 | YES |
193 | COX6C | COX6C | COX6C | 5067 | 0.044 | 0.39 | YES |
194 | H2AFZ | H2AFZ | H2AFZ | 5099 | 0.043 | 0.39 | YES |
195 | VDAC2 | VDAC2 | VDAC2 | 5105 | 0.043 | 0.39 | YES |
196 | ERH | ERH | ERH | 5115 | 0.043 | 0.39 | YES |
197 | SOD1 | SOD1 | SOD1 | 5151 | 0.042 | 0.39 | YES |
198 | COX7C | COX7C | COX7C | 5204 | 0.041 | 0.39 | YES |
199 | RPL27 | RPL27 | RPL27 | 5248 | 0.04 | 0.39 | YES |
200 | PSAP | PSAP | PSAP | 5273 | 0.04 | 0.39 | YES |
201 | CES2 | CES2 | CES2 | 5276 | 0.04 | 0.39 | YES |
202 | GNAS | GNAS | GNAS | 5390 | 0.038 | 0.39 | YES |
203 | LDHA | LDHA | LDHA | 5407 | 0.038 | 0.39 | YES |
204 | RPS17 | RPS17 | RPS17 | 5417 | 0.037 | 0.39 | YES |
205 | PSME1 | PSME1 | PSME1 | 5418 | 0.037 | 0.39 | YES |
206 | TMSB10 | TMSB10 | TMSB10 | 5431 | 0.037 | 0.39 | YES |
207 | RPL3 | RPL3 | RPL3 | 5482 | 0.036 | 0.39 | YES |
208 | CHKB | CHKB | CHKB | 5483 | 0.036 | 0.39 | YES |
209 | RPL13A | RPL13A | RPL13A | 5496 | 0.036 | 0.39 | YES |
210 | RPL39 | RPL39 | RPL39 | 5503 | 0.036 | 0.4 | YES |
211 | PSMB2 | PSMB2 | PSMB2 | 5570 | 0.034 | 0.39 | YES |
212 | ATP5O | ATP5O | ATP5O | 5579 | 0.034 | 0.39 | YES |
213 | NACA | NACA | NACA | 5591 | 0.034 | 0.39 | YES |
214 | TXN | TXN | TXN | 5594 | 0.034 | 0.4 | YES |
215 | SLC25A5 | SLC25A5 | SLC25A5 | 5614 | 0.034 | 0.4 | YES |
216 | ATF4 | ATF4 | ATF4 | 5615 | 0.034 | 0.4 | YES |
217 | LDHB | LDHB | LDHB | 5639 | 0.033 | 0.4 | YES |
218 | HNRNPL | HNRNPL | HNRNPL | 5645 | 0.033 | 0.4 | YES |
219 | SEPW1 | SEPW1 | SEPW1 | 5654 | 0.033 | 0.4 | YES |
220 | RPS25 | RPS25 | RPS25 | 5723 | 0.032 | 0.4 | NO |
221 | COX10 | COX10 | COX10 | 5755 | 0.031 | 0.4 | NO |
222 | KARS | KARS | KARS | 5756 | 0.031 | 0.4 | NO |
223 | APEX1 | APEX1 | APEX1 | 5807 | 0.03 | 0.4 | NO |
224 | RPS10 | RPS10 | RPS10 | 5821 | 0.029 | 0.4 | NO |
225 | RPL36A | RPL36A | RPL36A | 5824 | 0.029 | 0.4 | NO |
226 | RPL14 | RPL14 | RPL14 | 5827 | 0.029 | 0.4 | NO |
227 | GSTO1 | GSTO1 | GSTO1 | 5869 | 0.028 | 0.4 | NO |
228 | CD74 | CD74 | CD74 | 5871 | 0.028 | 0.4 | NO |
229 | PRDX1 | PRDX1 | PRDX1 | 5920 | 0.027 | 0.4 | NO |
230 | RPLP0 | RPLP0 | RPLP0 | 5940 | 0.027 | 0.4 | NO |
231 | RPSA | RPSA | RPSA | 5944 | 0.027 | 0.4 | NO |
232 | PEBP1 | PEBP1 | PEBP1 | 5973 | 0.026 | 0.4 | NO |
233 | RPL11 | RPL11 | RPL11 | 5977 | 0.026 | 0.4 | NO |
234 | ANP32B | ANP32B | ANP32B | 6003 | 0.026 | 0.4 | NO |
235 | RPS18 | RPS18 | RPS18 | 6015 | 0.025 | 0.4 | NO |
236 | RPL10A | RPL10A | RPL10A | 6034 | 0.025 | 0.4 | NO |
237 | PSEN1 | PSEN1 | PSEN1 | 6055 | 0.025 | 0.4 | NO |
238 | JOSD1 | JOSD1 | JOSD1 | 6096 | 0.024 | 0.4 | NO |
239 | CETN2 | CETN2 | CETN2 | 6105 | 0.024 | 0.4 | NO |
240 | EIF4H | EIF4H | EIF4H | 6109 | 0.024 | 0.4 | NO |
241 | YBX1 | YBX1 | YBX1 | 6133 | 0.023 | 0.4 | NO |
242 | SNRNP70 | SNRNP70 | SNRNP70 | 6188 | 0.022 | 0.4 | NO |
243 | HDAC1 | HDAC1 | HDAC1 | 6200 | 0.022 | 0.4 | NO |
244 | SERPINB6 | SERPINB6 | SERPINB6 | 6237 | 0.021 | 0.4 | NO |
245 | NONO | NONO | NONO | 6276 | 0.02 | 0.39 | NO |
246 | RPS23 | RPS23 | RPS23 | 6288 | 0.02 | 0.39 | NO |
247 | CCNI | CCNI | CCNI | 6336 | 0.019 | 0.39 | NO |
248 | TMBIM6 | TMBIM6 | TMBIM6 | 6369 | 0.019 | 0.39 | NO |
249 | HLA-E | HLA-E | HLA-E | 6372 | 0.019 | 0.39 | NO |
250 | NDUFV2 | NDUFV2 | NDUFV2 | 6409 | 0.018 | 0.39 | NO |
251 | STAT3 | STAT3 | STAT3 | 6425 | 0.017 | 0.39 | NO |
252 | PFDN5 | PFDN5 | PFDN5 | 6426 | 0.017 | 0.39 | NO |
253 | PTPN6 | PTPN6 | PTPN6 | 6446 | 0.017 | 0.39 | NO |
254 | RPS27A | RPS27A | RPS27A | 6462 | 0.017 | 0.39 | NO |
255 | RPN2 | RPN2 | RPN2 | 6471 | 0.017 | 0.39 | NO |
256 | DAZAP2 | DAZAP2 | DAZAP2 | 6526 | 0.016 | 0.39 | NO |
257 | RPL21 | RPL21 | RPL21 | 6533 | 0.015 | 0.39 | NO |
258 | HNRNPC | HNRNPC | HNRNPC | 6582 | 0.014 | 0.39 | NO |
259 | HYAL2 | HYAL2 | HYAL2 | 6597 | 0.014 | 0.39 | NO |
260 | NFKBIA | NFKBIA | NFKBIA | 6648 | 0.013 | 0.38 | NO |
261 | CLU | CLU | CLU | 6658 | 0.013 | 0.38 | NO |
262 | HSP90AB1 | HSP90AB1 | HSP90AB1 | 6677 | 0.012 | 0.38 | NO |
263 | UQCRB | UQCRB | UQCRB | 6692 | 0.012 | 0.38 | NO |
264 | RPS15A | RPS15A | RPS15A | 6702 | 0.012 | 0.38 | NO |
265 | RPL4 | RPL4 | RPL4 | 6756 | 0.011 | 0.38 | NO |
266 | GNB1 | GNB1 | GNB1 | 6770 | 0.011 | 0.38 | NO |
267 | H3F3B | H3F3B | H3F3B | 6809 | 0.01 | 0.38 | NO |
268 | RFTN1 | RFTN1 | RFTN1 | 6876 | 0.008 | 0.38 | NO |
269 | HLA-DQB1 | HLA-DQB1 | HLA-DQB1 | 6919 | 0.007 | 0.37 | NO |
270 | NCL | NCL | NCL | 6926 | 0.0068 | 0.37 | NO |
271 | PTMA | PTMA | PTMA | 6936 | 0.0066 | 0.37 | NO |
272 | RPS8 | RPS8 | RPS8 | 6971 | 0.0059 | 0.37 | NO |
273 | RPL34 | RPL34 | RPL34 | 6990 | 0.0055 | 0.37 | NO |
274 | RPL31 | RPL31 | RPL31 | 7032 | 0.0046 | 0.37 | NO |
275 | ATP5A1 | ATP5A1 | ATP5A1 | 7069 | 0.0038 | 0.37 | NO |
276 | HINT1 | HINT1 | HINT1 | 7070 | 0.0037 | 0.37 | NO |
277 | BUD31 | BUD31 | BUD31 | 7074 | 0.0037 | 0.37 | NO |
278 | ATP5C1 | ATP5C1 | ATP5C1 | 7078 | 0.0036 | 0.37 | NO |
279 | ESD | ESD | ESD | 7094 | 0.0034 | 0.36 | NO |
280 | HNRNPA1 | HNRNPA1 | HNRNPA1 | 7120 | 0.003 | 0.36 | NO |
281 | BRD2 | BRD2 | BRD2 | 7124 | 0.003 | 0.36 | NO |
282 | GLUL | GLUL | GLUL | 7132 | 0.0028 | 0.36 | NO |
283 | NDUFA4 | NDUFA4 | NDUFA4 | 7152 | 0.0025 | 0.36 | NO |
284 | HNRNPK | HNRNPK | HNRNPK | 7160 | 0.0024 | 0.36 | NO |
285 | BECN1 | BECN1 | BECN1 | 7173 | 0.0021 | 0.36 | NO |
286 | HMGN2 | HMGN2 | HMGN2 | 7194 | 0.0016 | 0.36 | NO |
287 | AP3S1 | AP3S1 | AP3S1 | 7195 | 0.0016 | 0.36 | NO |
288 | TMED10 | TMED10 | TMED10 | 7208 | 0.0013 | 0.36 | NO |
289 | RPL24 | RPL24 | RPL24 | 7293 | -0.00072 | 0.36 | NO |
290 | B2M | B2M | B2M | 7392 | -0.0028 | 0.35 | NO |
291 | ARL6IP1 | ARL6IP1 | ARL6IP1 | 7407 | -0.0031 | 0.35 | NO |
292 | TPT1 | TPT1 | TPT1 | 7414 | -0.0031 | 0.35 | NO |
293 | PSMC1 | PSMC1 | PSMC1 | 7429 | -0.0034 | 0.35 | NO |
294 | CCT4 | CCT4 | CCT4 | 7449 | -0.0038 | 0.35 | NO |
295 | RPL35A | RPL35A | RPL35A | 7467 | -0.0042 | 0.35 | NO |
296 | RPL7 | RPL7 | RPL7 | 7501 | -0.0051 | 0.34 | NO |
297 | HNRNPF | HNRNPF | HNRNPF | 7517 | -0.0055 | 0.34 | NO |
298 | CAP1 | CAP1 | CAP1 | 7527 | -0.0057 | 0.34 | NO |
299 | SRP14 | SRP14 | SRP14 | 7659 | -0.0083 | 0.34 | NO |
300 | RPL6 | RPL6 | RPL6 | 7663 | -0.0083 | 0.34 | NO |
301 | YWHAB | YWHAB | YWHAB | 7693 | -0.0091 | 0.34 | NO |
302 | PSD | PSD | PSD | 7749 | -0.01 | 0.33 | NO |
303 | ARF4 | ARF4 | ARF4 | 7773 | -0.011 | 0.33 | NO |
304 | MGP | MGP | MGP | 7799 | -0.011 | 0.33 | NO |
305 | CAPN2 | CAPN2 | CAPN2 | 7803 | -0.011 | 0.33 | NO |
306 | HLA-DPA1 | HLA-DPA1 | HLA-DPA1 | 7827 | -0.012 | 0.33 | NO |
307 | YWHAQ | YWHAQ | YWHAQ | 7900 | -0.013 | 0.33 | NO |
308 | JUNB | JUNB | JUNB | 7904 | -0.013 | 0.33 | NO |
309 | MDH1 | MDH1 | MDH1 | 7918 | -0.014 | 0.33 | NO |
310 | TXNIP | TXNIP | TXNIP | 7964 | -0.015 | 0.33 | NO |
311 | ARHGDIB | ARHGDIB | ARHGDIB | 7998 | -0.016 | 0.32 | NO |
312 | MORF4L2 | MORF4L2 | MORF4L2 | 8060 | -0.017 | 0.32 | NO |
313 | ZFP36 | ZFP36 | ZFP36 | 8100 | -0.018 | 0.32 | NO |
314 | RPA2 | RPA2 | RPA2 | 8101 | -0.018 | 0.32 | NO |
315 | LTA4H | LTA4H | LTA4H | 8125 | -0.018 | 0.32 | NO |
316 | FHL1 | FHL1 | FHL1 | 8149 | -0.019 | 0.32 | NO |
317 | YWHAZ | YWHAZ | YWHAZ | 8246 | -0.021 | 0.32 | NO |
318 | EZR | EZR | EZR | 8286 | -0.022 | 0.31 | NO |
319 | PGK1 | PGK1 | PGK1 | 8354 | -0.023 | 0.31 | NO |
320 | SET | SET | SET | 8459 | -0.025 | 0.31 | NO |
321 | UBE2D3 | UBE2D3 | UBE2D3 | 8468 | -0.025 | 0.31 | NO |
322 | MLH1 | MLH1 | MLH1 | 8518 | -0.026 | 0.3 | NO |
323 | GDI2 | GDI2 | GDI2 | 8531 | -0.026 | 0.31 | NO |
324 | CANX | CANX | CANX | 8625 | -0.028 | 0.3 | NO |
325 | CALM2 | CALM2 | CALM2 | 8667 | -0.03 | 0.3 | NO |
326 | DSTN | DSTN | DSTN | 8668 | -0.03 | 0.3 | NO |
327 | CLTC | CLTC | CLTC | 8705 | -0.03 | 0.3 | NO |
328 | EEF1B2 | EEF1B2 | EEF1B2 | 8728 | -0.031 | 0.3 | NO |
329 | RPS6 | RPS6 | RPS6 | 8735 | -0.031 | 0.3 | NO |
330 | FUCA1 | FUCA1 | FUCA1 | 8840 | -0.033 | 0.3 | NO |
331 | GPS2 | GPS2 | GPS2 | 8858 | -0.034 | 0.3 | NO |
332 | BTG2 | BTG2 | BTG2 | 9044 | -0.038 | 0.29 | NO |
333 | STMN1 | STMN1 | STMN1 | 9085 | -0.039 | 0.29 | NO |
334 | SON | SON | SON | 9097 | -0.039 | 0.29 | NO |
335 | PABPC1 | PABPC1 | PABPC1 | 9114 | -0.04 | 0.29 | NO |
336 | RPL17 | RPL17 | RPL17 | 9131 | -0.04 | 0.29 | NO |
337 | FYN | FYN | FYN | 9207 | -0.041 | 0.29 | NO |
338 | RPL9 | RPL9 | RPL9 | 9234 | -0.042 | 0.29 | NO |
339 | TMSB4X | TMSB4X | TMSB4X | 9307 | -0.044 | 0.29 | NO |
340 | TCEA1 | TCEA1 | TCEA1 | 9337 | -0.044 | 0.29 | NO |
341 | NPM1 | NPM1 | NPM1 | 9421 | -0.046 | 0.28 | NO |
342 | HSPD1 | HSPD1 | HSPD1 | 9426 | -0.046 | 0.28 | NO |
343 | LGALS3 | LGALS3 | LGALS3 | 9445 | -0.047 | 0.29 | NO |
344 | NAP1L1 | NAP1L1 | NAP1L1 | 9467 | -0.047 | 0.29 | NO |
345 | EIF3E | EIF3E | EIF3E | 9474 | -0.047 | 0.29 | NO |
346 | KAT6A | KAT6A | KAT6A | 9478 | -0.047 | 0.29 | NO |
347 | PSMD7 | PSMD7 | PSMD7 | 9546 | -0.049 | 0.29 | NO |
348 | PTP4A2 | PTP4A2 | PTP4A2 | 9554 | -0.049 | 0.29 | NO |
349 | RPS7 | RPS7 | RPS7 | 9590 | -0.05 | 0.29 | NO |
350 | ATP5F1 | ATP5F1 | ATP5F1 | 9623 | -0.051 | 0.29 | NO |
351 | STOM | STOM | STOM | 9791 | -0.055 | 0.28 | NO |
352 | EEF1A1 | EEF1A1 | EEF1A1 | 9792 | -0.055 | 0.28 | NO |
353 | SEPT2 | SEPT2 | SEPT2 | 9986 | -0.058 | 0.28 | NO |
354 | HLA-DRA | HLA-DRA | HLA-DRA | 10015 | -0.059 | 0.28 | NO |
355 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 10314 | -0.066 | 0.26 | NO |
356 | ITGB1 | ITGB1 | ITGB1 | 10550 | -0.071 | 0.25 | NO |
357 | IQGAP1 | IQGAP1 | IQGAP1 | 10579 | -0.072 | 0.26 | NO |
358 | NFIB | NFIB | NFIB | 10645 | -0.073 | 0.25 | NO |
359 | HMGB1 | HMGB1 | HMGB1 | 10662 | -0.074 | 0.26 | NO |
360 | HLA-DOA | HLA-DOA | HLA-DOA | 10691 | -0.074 | 0.26 | NO |
361 | EIF4G2 | EIF4G2 | EIF4G2 | 10974 | -0.082 | 0.24 | NO |
362 | CAST | CAST | CAST | 11151 | -0.085 | 0.24 | NO |
363 | DUSP1 | DUSP1 | DUSP1 | 11194 | -0.086 | 0.24 | NO |
364 | FNTA | FNTA | FNTA | 11206 | -0.086 | 0.24 | NO |
365 | CTNNB1 | CTNNB1 | CTNNB1 | 11215 | -0.086 | 0.25 | NO |
366 | EIF4A1 | EIF4A1 | EIF4A1 | 11354 | -0.09 | 0.24 | NO |
367 | DDX5 | DDX5 | DDX5 | 11393 | -0.09 | 0.24 | NO |
368 | CAPZA1 | CAPZA1 | CAPZA1 | 11398 | -0.091 | 0.25 | NO |
369 | TPR | TPR | TPR | 11689 | -0.097 | 0.23 | NO |
370 | BCLAF1 | BCLAF1 | BCLAF1 | 11738 | -0.098 | 0.24 | NO |
371 | MARCKS | MARCKS | MARCKS | 11744 | -0.098 | 0.24 | NO |
372 | RPS3A | RPS3A | RPS3A | 11771 | -0.099 | 0.24 | NO |
373 | EIF4A2 | EIF4A2 | EIF4A2 | 12099 | -0.11 | 0.23 | NO |
374 | PIM1 | PIM1 | PIM1 | 12177 | -0.11 | 0.23 | NO |
375 | SSB | SSB | SSB | 12265 | -0.11 | 0.23 | NO |
376 | CD164 | CD164 | CD164 | 12653 | -0.12 | 0.21 | NO |
377 | ABLIM1 | ABLIM1 | ABLIM1 | 12946 | -0.13 | 0.2 | NO |
378 | XPO1 | XPO1 | XPO1 | 13006 | -0.13 | 0.2 | NO |
379 | PAX6 | PAX6 | PAX6 | 13307 | -0.14 | 0.19 | NO |
380 | DDX39B | DDX39B | DDX39B | 13465 | -0.14 | 0.19 | NO |
381 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 13831 | -0.16 | 0.17 | NO |
382 | ZNF91 | ZNF91 | ZNF91 | 14640 | -0.19 | 0.14 | NO |
383 | CHI3L2 | CHI3L2 | CHI3L2 | 14709 | -0.19 | 0.14 | NO |
384 | FAS | FAS | FAS | 15115 | -0.21 | 0.12 | NO |
385 | NEFL | NEFL | NEFL | 15864 | -0.25 | 0.092 | NO |
386 | SERPINA3 | SERPINA3 | SERPINA3 | 16996 | -0.36 | 0.043 | NO |
387 | CCR9 | CCR9 | CCR9 | 17509 | -0.45 | 0.032 | NO |
Figure S67. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: DAIRKEE TERT TARGETS UP.

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: DAIRKEE TERT TARGETS UP, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S35. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NKAIN1 | NKAIN1 | NKAIN1 | 322 | 0.18 | -0.00076 | YES |
2 | GALK1 | GALK1 | GALK1 | 694 | 0.14 | -0.008 | YES |
3 | C9orf16 | C9orf16 | C9orf16 | 794 | 0.14 | -0.00064 | YES |
4 | ARHGDIA | ARHGDIA | ARHGDIA | 830 | 0.14 | 0.01 | YES |
5 | CAD | CAD | CAD | 858 | 0.14 | 0.021 | YES |
6 | GAPDH | GAPDH | GAPDH | 937 | 0.13 | 0.029 | YES |
7 | ACTA1 | ACTA1 | ACTA1 | 954 | 0.13 | 0.041 | YES |
8 | PPP1R14B | PPP1R14B | PPP1R14B | 978 | 0.13 | 0.052 | YES |
9 | GPS1 | GPS1 | GPS1 | 1036 | 0.13 | 0.06 | YES |
10 | IPO4 | IPO4 | IPO4 | 1092 | 0.13 | 0.069 | YES |
11 | BAX | BAX | BAX | 1114 | 0.13 | 0.08 | YES |
12 | ASL | ASL | ASL | 1117 | 0.13 | 0.092 | YES |
13 | DDX41 | DDX41 | DDX41 | 1157 | 0.12 | 0.1 | YES |
14 | MYBBP1A | MYBBP1A | MYBBP1A | 1161 | 0.12 | 0.11 | YES |
15 | CARM1 | CARM1 | CARM1 | 1292 | 0.12 | 0.12 | YES |
16 | PTOV1 | PTOV1 | PTOV1 | 1304 | 0.12 | 0.13 | YES |
17 | UBE2M | UBE2M | UBE2M | 1308 | 0.12 | 0.14 | YES |
18 | JAG2 | JAG2 | JAG2 | 1312 | 0.12 | 0.15 | YES |
19 | PTP4A3 | PTP4A3 | PTP4A3 | 1435 | 0.12 | 0.15 | YES |
20 | CTSD | CTSD | CTSD | 1498 | 0.12 | 0.16 | YES |
21 | PES1 | PES1 | PES1 | 1505 | 0.12 | 0.17 | YES |
22 | ERGIC1 | ERGIC1 | ERGIC1 | 1519 | 0.11 | 0.18 | YES |
23 | PIGQ | PIGQ | PIGQ | 1555 | 0.11 | 0.19 | YES |
24 | SMARCA4 | SMARCA4 | SMARCA4 | 1566 | 0.11 | 0.2 | YES |
25 | WDR74 | WDR74 | WDR74 | 1652 | 0.11 | 0.2 | YES |
26 | NME1 | NME1 | NME1 | 1790 | 0.11 | 0.21 | YES |
27 | VARS | VARS | VARS | 1827 | 0.11 | 0.22 | YES |
28 | PTH1R | PTH1R | PTH1R | 1859 | 0.11 | 0.22 | YES |
29 | MRPL12 | MRPL12 | MRPL12 | 1879 | 0.11 | 0.23 | YES |
30 | RAB34 | RAB34 | RAB34 | 1926 | 0.1 | 0.24 | YES |
31 | COL18A1 | COL18A1 | COL18A1 | 1934 | 0.1 | 0.25 | YES |
32 | TMEM147 | TMEM147 | TMEM147 | 1971 | 0.1 | 0.26 | YES |
33 | HDLBP | HDLBP | HDLBP | 2016 | 0.1 | 0.26 | YES |
34 | NDE1 | NDE1 | NDE1 | 2082 | 0.1 | 0.27 | YES |
35 | SND1 | SND1 | SND1 | 2103 | 0.1 | 0.28 | YES |
36 | HTRA2 | HTRA2 | HTRA2 | 2259 | 0.098 | 0.28 | YES |
37 | GGA1 | GGA1 | GGA1 | 2320 | 0.097 | 0.28 | YES |
38 | FKBP11 | FKBP11 | FKBP11 | 2404 | 0.095 | 0.29 | YES |
39 | PRMT1 | PRMT1 | PRMT1 | 2467 | 0.094 | 0.29 | YES |
40 | EFTUD2 | EFTUD2 | EFTUD2 | 2548 | 0.092 | 0.3 | YES |
41 | BANF1 | BANF1 | BANF1 | 2553 | 0.092 | 0.31 | YES |
42 | GATAD2A | GATAD2A | GATAD2A | 2570 | 0.091 | 0.31 | YES |
43 | FBL | FBL | FBL | 2725 | 0.089 | 0.31 | YES |
44 | PADI2 | PADI2 | PADI2 | 2752 | 0.088 | 0.32 | YES |
45 | CS | CS | CS | 2864 | 0.086 | 0.32 | YES |
46 | CLPTM1L | CLPTM1L | CLPTM1L | 2926 | 0.085 | 0.33 | YES |
47 | SSR2 | SSR2 | SSR2 | 3009 | 0.083 | 0.33 | YES |
48 | NHP2 | NHP2 | NHP2 | 3034 | 0.083 | 0.34 | YES |
49 | LMAN2 | LMAN2 | LMAN2 | 3057 | 0.082 | 0.34 | YES |
50 | CDK4 | CDK4 | CDK4 | 3156 | 0.08 | 0.34 | YES |
51 | TUBB3 | TUBB3 | TUBB3 | 3209 | 0.079 | 0.35 | YES |
52 | PSMB3 | PSMB3 | PSMB3 | 3222 | 0.079 | 0.36 | YES |
53 | PSMB5 | PSMB5 | PSMB5 | 3305 | 0.077 | 0.36 | YES |
54 | RGS19 | RGS19 | RGS19 | 3317 | 0.077 | 0.36 | YES |
55 | EIF4G1 | EIF4G1 | EIF4G1 | 3321 | 0.076 | 0.37 | YES |
56 | SERPINH1 | SERPINH1 | SERPINH1 | 3409 | 0.075 | 0.37 | YES |
57 | IRAK1 | IRAK1 | IRAK1 | 3525 | 0.072 | 0.37 | YES |
58 | YKT6 | YKT6 | YKT6 | 3539 | 0.072 | 0.38 | YES |
59 | TBCB | TBCB | TBCB | 3550 | 0.072 | 0.39 | YES |
60 | MRPL20 | MRPL20 | MRPL20 | 3717 | 0.069 | 0.38 | YES |
61 | DCTPP1 | DCTPP1 | DCTPP1 | 3873 | 0.066 | 0.38 | YES |
62 | MRPS18B | MRPS18B | MRPS18B | 3914 | 0.065 | 0.38 | YES |
63 | SEC61A1 | SEC61A1 | SEC61A1 | 3951 | 0.064 | 0.39 | YES |
64 | DTYMK | DTYMK | DTYMK | 4027 | 0.063 | 0.39 | YES |
65 | CCT3 | CCT3 | CCT3 | 4319 | 0.057 | 0.38 | YES |
66 | RPN1 | RPN1 | RPN1 | 4337 | 0.057 | 0.38 | YES |
67 | ATF6B | ATF6B | ATF6B | 4369 | 0.056 | 0.39 | YES |
68 | THOP1 | THOP1 | THOP1 | 4483 | 0.054 | 0.39 | YES |
69 | PDIA3 | PDIA3 | PDIA3 | 4538 | 0.053 | 0.39 | YES |
70 | TMEM97 | TMEM97 | TMEM97 | 4555 | 0.053 | 0.39 | YES |
71 | SEC61B | SEC61B | SEC61B | 4729 | 0.05 | 0.39 | NO |
72 | PKDCC | PKDCC | PKDCC | 5031 | 0.044 | 0.38 | NO |
73 | NUBP1 | NUBP1 | NUBP1 | 5129 | 0.043 | 0.37 | NO |
74 | SNRPD3 | SNRPD3 | SNRPD3 | 5180 | 0.042 | 0.37 | NO |
75 | SLC39A7 | SLC39A7 | SLC39A7 | 5241 | 0.04 | 0.38 | NO |
76 | CALCA | CALCA | CALCA | 5242 | 0.04 | 0.38 | NO |
77 | C6orf136 | C6orf136 | C6orf136 | 5401 | 0.038 | 0.37 | NO |
78 | PDIA4 | PDIA4 | PDIA4 | 5488 | 0.036 | 0.37 | NO |
79 | SEC13 | SEC13 | SEC13 | 5559 | 0.035 | 0.37 | NO |
80 | RAN | RAN | RAN | 5564 | 0.034 | 0.37 | NO |
81 | SLC25A5 | SLC25A5 | SLC25A5 | 5614 | 0.034 | 0.38 | NO |
82 | GORASP2 | GORASP2 | GORASP2 | 5725 | 0.032 | 0.37 | NO |
83 | CCT8 | CCT8 | CCT8 | 5736 | 0.031 | 0.37 | NO |
84 | RANBP1 | RANBP1 | RANBP1 | 5738 | 0.031 | 0.38 | NO |
85 | UBFD1 | UBFD1 | UBFD1 | 5740 | 0.031 | 0.38 | NO |
86 | APEX1 | APEX1 | APEX1 | 5807 | 0.03 | 0.38 | NO |
87 | TUBB6 | TUBB6 | TUBB6 | 5926 | 0.027 | 0.38 | NO |
88 | SERPINE2 | SERPINE2 | SERPINE2 | 6020 | 0.025 | 0.37 | NO |
89 | CDK2AP1 | CDK2AP1 | CDK2AP1 | 6142 | 0.023 | 0.37 | NO |
90 | EIF2B5 | EIF2B5 | EIF2B5 | 6254 | 0.021 | 0.36 | NO |
91 | ODC1 | ODC1 | ODC1 | 6294 | 0.02 | 0.36 | NO |
92 | TUBA1A | TUBA1A | TUBA1A | 6403 | 0.018 | 0.36 | NO |
93 | RCN1 | RCN1 | RCN1 | 6459 | 0.017 | 0.36 | NO |
94 | NSUN2 | NSUN2 | NSUN2 | 6498 | 0.016 | 0.36 | NO |
95 | PREP | PREP | PREP | 6641 | 0.013 | 0.35 | NO |
96 | UBE2N | UBE2N | UBE2N | 7012 | 0.0051 | 0.33 | NO |
97 | VCL | VCL | VCL | 7051 | 0.0042 | 0.33 | NO |
98 | CCT6A | CCT6A | CCT6A | 7275 | -0.00027 | 0.32 | NO |
99 | PSMD1 | PSMD1 | PSMD1 | 7280 | -0.00037 | 0.32 | NO |
100 | METAP1 | METAP1 | METAP1 | 7658 | -0.0083 | 0.3 | NO |
101 | RARS | RARS | RARS | 7958 | -0.015 | 0.28 | NO |
102 | MORF4L2 | MORF4L2 | MORF4L2 | 8060 | -0.017 | 0.28 | NO |
103 | NARS | NARS | NARS | 8061 | -0.017 | 0.28 | NO |
104 | SRSF1 | SRSF1 | SRSF1 | 8234 | -0.021 | 0.27 | NO |
105 | TMEM14C | TMEM14C | TMEM14C | 8647 | -0.029 | 0.25 | NO |
106 | CISD1 | CISD1 | CISD1 | 8716 | -0.031 | 0.25 | NO |
107 | PSMD6 | PSMD6 | PSMD6 | 8772 | -0.032 | 0.25 | NO |
108 | GALM | GALM | GALM | 8806 | -0.033 | 0.25 | NO |
109 | SSR1 | SSR1 | SSR1 | 8915 | -0.035 | 0.25 | NO |
110 | EBNA1BP2 | EBNA1BP2 | EBNA1BP2 | 8925 | -0.035 | 0.25 | NO |
111 | MRPS10 | MRPS10 | MRPS10 | 9042 | -0.038 | 0.25 | NO |
112 | IPO5 | IPO5 | IPO5 | 9233 | -0.042 | 0.24 | NO |
113 | MRPS28 | MRPS28 | MRPS28 | 9258 | -0.042 | 0.24 | NO |
114 | TCEA1 | TCEA1 | TCEA1 | 9337 | -0.044 | 0.24 | NO |
115 | SYNCRIP | SYNCRIP | SYNCRIP | 9385 | -0.045 | 0.24 | NO |
116 | PPA1 | PPA1 | PPA1 | 9799 | -0.055 | 0.23 | NO |
117 | PRRC1 | PRRC1 | PRRC1 | 9883 | -0.057 | 0.23 | NO |
118 | TOMM70A | TOMM70A | TOMM70A | 10089 | -0.061 | 0.22 | NO |
119 | SNRPA1 | SNRPA1 | SNRPA1 | 10110 | -0.061 | 0.22 | NO |
120 | SMYD2 | SMYD2 | SMYD2 | 10225 | -0.064 | 0.22 | NO |
121 | SSR3 | SSR3 | SSR3 | 10242 | -0.064 | 0.23 | NO |
122 | GSTM2 | GSTM2 | GSTM2 | 10362 | -0.067 | 0.23 | NO |
123 | PDLIM3 | PDLIM3 | PDLIM3 | 10710 | -0.074 | 0.22 | NO |
124 | MME | MME | MME | 10805 | -0.077 | 0.22 | NO |
125 | PSME4 | PSME4 | PSME4 | 11114 | -0.084 | 0.21 | NO |
126 | GOLGA5 | GOLGA5 | GOLGA5 | 11189 | -0.086 | 0.21 | NO |
127 | GNPNAT1 | GNPNAT1 | GNPNAT1 | 12066 | -0.11 | 0.18 | NO |
128 | RB1 | RB1 | RB1 | 12157 | -0.11 | 0.18 | NO |
129 | TMEM167A | TMEM167A | TMEM167A | 12368 | -0.11 | 0.18 | NO |
130 | SLMO2 | SLMO2 | SLMO2 | 12441 | -0.12 | 0.18 | NO |
131 | DNAJC2 | DNAJC2 | DNAJC2 | 13095 | -0.13 | 0.16 | NO |
132 | SLAIN1 | SLAIN1 | SLAIN1 | 13432 | -0.14 | 0.16 | NO |
133 | TCERG1 | TCERG1 | TCERG1 | 13769 | -0.15 | 0.15 | NO |
134 | TANK | TANK | TANK | 15366 | -0.22 | 0.083 | NO |
135 | HMGN5 | HMGN5 | HMGN5 | 15509 | -0.23 | 0.097 | NO |
136 | FGF1 | FGF1 | FGF1 | 15739 | -0.24 | 0.11 | NO |
137 | IRG1 | IRG1 | IRG1 | 15914 | -0.26 | 0.12 | NO |
Figure S69. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S36. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | C21orf33 | C21orf33 | C21orf33 | 83 | 0.26 | 0.0058 | YES |
2 | MYBL2 | MYBL2 | MYBL2 | 112 | 0.24 | 0.014 | YES |
3 | KCNJ4 | KCNJ4 | KCNJ4 | 158 | 0.23 | 0.02 | YES |
4 | CDT1 | CDT1 | CDT1 | 179 | 0.22 | 0.028 | YES |
5 | PKMYT1 | PKMYT1 | PKMYT1 | 208 | 0.21 | 0.035 | YES |
6 | TK1 | TK1 | TK1 | 218 | 0.21 | 0.043 | YES |
7 | SULT1A1 | SULT1A1 | SULT1A1 | 301 | 0.19 | 0.046 | YES |
8 | MRPL23 | MRPL23 | MRPL23 | 416 | 0.17 | 0.046 | YES |
9 | PLTP | PLTP | PLTP | 458 | 0.16 | 0.05 | YES |
10 | MPDU1 | MPDU1 | MPDU1 | 568 | 0.15 | 0.05 | YES |
11 | PGF | PGF | PGF | 590 | 0.15 | 0.055 | YES |
12 | SCO2 | SCO2 | SCO2 | 597 | 0.15 | 0.061 | YES |
13 | BTBD2 | BTBD2 | BTBD2 | 603 | 0.15 | 0.066 | YES |
14 | E2F1 | E2F1 | E2F1 | 613 | 0.15 | 0.072 | YES |
15 | GCAT | GCAT | GCAT | 617 | 0.15 | 0.078 | YES |
16 | PAFAH1B3 | PAFAH1B3 | PAFAH1B3 | 621 | 0.15 | 0.083 | YES |
17 | TNFSF9 | TNFSF9 | TNFSF9 | 633 | 0.15 | 0.089 | YES |
18 | LY6E | LY6E | LY6E | 700 | 0.14 | 0.091 | YES |
19 | LMF2 | LMF2 | LMF2 | 722 | 0.14 | 0.095 | YES |
20 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 726 | 0.14 | 0.1 | YES |
21 | TST | TST | TST | 738 | 0.14 | 0.11 | YES |
22 | CCDC85B | CCDC85B | CCDC85B | 762 | 0.14 | 0.11 | YES |
23 | SLC1A5 | SLC1A5 | SLC1A5 | 768 | 0.14 | 0.12 | YES |
24 | IFITM2 | IFITM2 | IFITM2 | 785 | 0.14 | 0.12 | YES |
25 | ERBB2 | ERBB2 | ERBB2 | 815 | 0.14 | 0.12 | YES |
26 | SHMT2 | SHMT2 | SHMT2 | 895 | 0.13 | 0.12 | YES |
27 | ERCC2 | ERCC2 | ERCC2 | 920 | 0.13 | 0.13 | YES |
28 | NDUFS7 | NDUFS7 | NDUFS7 | 951 | 0.13 | 0.13 | YES |
29 | RELA | RELA | RELA | 972 | 0.13 | 0.14 | YES |
30 | TCIRG1 | TCIRG1 | TCIRG1 | 974 | 0.13 | 0.14 | YES |
31 | ALDOA | ALDOA | ALDOA | 981 | 0.13 | 0.15 | YES |
32 | ABHD14A | ABHD14A | ABHD14A | 990 | 0.13 | 0.15 | YES |
33 | RNF40 | RNF40 | RNF40 | 1002 | 0.13 | 0.16 | YES |
34 | AP2S1 | AP2S1 | AP2S1 | 1013 | 0.13 | 0.16 | YES |
35 | NDUFB7 | NDUFB7 | NDUFB7 | 1015 | 0.13 | 0.17 | YES |
36 | SAC3D1 | SAC3D1 | SAC3D1 | 1018 | 0.13 | 0.17 | YES |
37 | NDUFV1 | NDUFV1 | NDUFV1 | 1066 | 0.13 | 0.17 | YES |
38 | ASL | ASL | ASL | 1117 | 0.13 | 0.18 | YES |
39 | MCM5 | MCM5 | MCM5 | 1154 | 0.12 | 0.18 | YES |
40 | ERCC1 | ERCC1 | ERCC1 | 1165 | 0.12 | 0.18 | YES |
41 | ZFPL1 | ZFPL1 | ZFPL1 | 1172 | 0.12 | 0.19 | YES |
42 | FDXR | FDXR | FDXR | 1176 | 0.12 | 0.19 | YES |
43 | SLC30A3 | SLC30A3 | SLC30A3 | 1197 | 0.12 | 0.2 | YES |
44 | ECI1 | ECI1 | ECI1 | 1202 | 0.12 | 0.2 | YES |
45 | CBX2 | CBX2 | CBX2 | 1210 | 0.12 | 0.21 | YES |
46 | GRINA | GRINA | GRINA | 1215 | 0.12 | 0.21 | YES |
47 | BSG | BSG | BSG | 1223 | 0.12 | 0.22 | YES |
48 | DGAT1 | DGAT1 | DGAT1 | 1235 | 0.12 | 0.22 | YES |
49 | BRMS1 | BRMS1 | BRMS1 | 1268 | 0.12 | 0.22 | YES |
50 | MRPL28 | MRPL28 | MRPL28 | 1280 | 0.12 | 0.23 | YES |
51 | BAD | BAD | BAD | 1299 | 0.12 | 0.23 | YES |
52 | MRPS12 | MRPS12 | MRPS12 | 1319 | 0.12 | 0.23 | YES |
53 | LIN37 | LIN37 | LIN37 | 1325 | 0.12 | 0.24 | YES |
54 | EPHX1 | EPHX1 | EPHX1 | 1351 | 0.12 | 0.24 | YES |
55 | MAZ | MAZ | MAZ | 1387 | 0.12 | 0.24 | YES |
56 | PHLDA2 | PHLDA2 | PHLDA2 | 1420 | 0.12 | 0.25 | YES |
57 | NCLN | NCLN | NCLN | 1452 | 0.12 | 0.25 | YES |
58 | PPP1CA | PPP1CA | PPP1CA | 1460 | 0.12 | 0.26 | YES |
59 | SNRPA | SNRPA | SNRPA | 1481 | 0.12 | 0.26 | YES |
60 | SMARCD3 | SMARCD3 | SMARCD3 | 1530 | 0.11 | 0.26 | YES |
61 | DGCR14 | DGCR14 | DGCR14 | 1532 | 0.11 | 0.26 | YES |
62 | PLD3 | PLD3 | PLD3 | 1582 | 0.11 | 0.27 | YES |
63 | TP53 | TP53 | TP53 | 1585 | 0.11 | 0.27 | YES |
64 | ABCB6 | ABCB6 | ABCB6 | 1631 | 0.11 | 0.27 | YES |
65 | ERGIC3 | ERGIC3 | ERGIC3 | 1671 | 0.11 | 0.28 | YES |
66 | NOP2 | NOP2 | NOP2 | 1691 | 0.11 | 0.28 | YES |
67 | PDLIM7 | PDLIM7 | PDLIM7 | 1731 | 0.11 | 0.28 | YES |
68 | UQCRC1 | UQCRC1 | UQCRC1 | 1749 | 0.11 | 0.28 | YES |
69 | MBOAT7 | MBOAT7 | MBOAT7 | 1799 | 0.11 | 0.28 | YES |
70 | UBA1 | UBA1 | UBA1 | 1806 | 0.11 | 0.29 | YES |
71 | POLR2A | POLR2A | POLR2A | 1868 | 0.11 | 0.29 | YES |
72 | ZNHIT1 | ZNHIT1 | ZNHIT1 | 1947 | 0.1 | 0.29 | YES |
73 | CNP | CNP | CNP | 1973 | 0.1 | 0.29 | YES |
74 | ISG15 | ISG15 | ISG15 | 1983 | 0.1 | 0.3 | YES |
75 | CDK16 | CDK16 | CDK16 | 2017 | 0.1 | 0.3 | YES |
76 | IDH2 | IDH2 | IDH2 | 2028 | 0.1 | 0.3 | YES |
77 | CLTB | CLTB | CLTB | 2036 | 0.1 | 0.31 | YES |
78 | SMPD1 | SMPD1 | SMPD1 | 2039 | 0.1 | 0.31 | YES |
79 | LHX2 | LHX2 | LHX2 | 2047 | 0.1 | 0.31 | YES |
80 | PQBP1 | PQBP1 | PQBP1 | 2059 | 0.1 | 0.32 | YES |
81 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 2084 | 0.1 | 0.32 | YES |
82 | FKBP1A | FKBP1A | FKBP1A | 2094 | 0.1 | 0.32 | YES |
83 | NME3 | NME3 | NME3 | 2127 | 0.1 | 0.32 | YES |
84 | IGFBP6 | IGFBP6 | IGFBP6 | 2164 | 0.1 | 0.33 | YES |
85 | TMED1 | TMED1 | TMED1 | 2174 | 0.1 | 0.33 | YES |
86 | SPR | SPR | SPR | 2188 | 0.099 | 0.33 | YES |
87 | S100A13 | S100A13 | S100A13 | 2210 | 0.099 | 0.34 | YES |
88 | SIGMAR1 | SIGMAR1 | SIGMAR1 | 2329 | 0.096 | 0.33 | YES |
89 | ATP6V1F | ATP6V1F | ATP6V1F | 2354 | 0.096 | 0.34 | YES |
90 | PSMD8 | PSMD8 | PSMD8 | 2381 | 0.095 | 0.34 | YES |
91 | EEF1D | EEF1D | EEF1D | 2495 | 0.093 | 0.34 | YES |
92 | OGFR | OGFR | OGFR | 2573 | 0.091 | 0.34 | YES |
93 | NCDN | NCDN | NCDN | 2667 | 0.09 | 0.33 | YES |
94 | CCND3 | CCND3 | CCND3 | 2715 | 0.089 | 0.34 | YES |
95 | OSR2 | OSR2 | OSR2 | 2718 | 0.089 | 0.34 | YES |
96 | GRHPR | GRHPR | GRHPR | 2753 | 0.088 | 0.34 | YES |
97 | STK25 | STK25 | STK25 | 2777 | 0.088 | 0.34 | YES |
98 | ABCF3 | ABCF3 | ABCF3 | 2807 | 0.087 | 0.34 | YES |
99 | ASNA1 | ASNA1 | ASNA1 | 2826 | 0.087 | 0.35 | YES |
100 | GNL1 | GNL1 | GNL1 | 2838 | 0.086 | 0.35 | YES |
101 | PPP2R5D | PPP2R5D | PPP2R5D | 2925 | 0.085 | 0.35 | YES |
102 | CDC34 | CDC34 | CDC34 | 2927 | 0.085 | 0.35 | YES |
103 | TMEM109 | TMEM109 | TMEM109 | 2942 | 0.085 | 0.35 | YES |
104 | FRAT2 | FRAT2 | FRAT2 | 2990 | 0.084 | 0.36 | YES |
105 | NR4A1 | NR4A1 | NR4A1 | 3016 | 0.083 | 0.36 | YES |
106 | PSMC3 | PSMC3 | PSMC3 | 3029 | 0.083 | 0.36 | YES |
107 | AAMP | AAMP | AAMP | 3088 | 0.082 | 0.36 | YES |
108 | PLXNA3 | PLXNA3 | PLXNA3 | 3093 | 0.081 | 0.36 | YES |
109 | PPIF | PPIF | PPIF | 3094 | 0.081 | 0.36 | YES |
110 | MVD | MVD | MVD | 3095 | 0.081 | 0.37 | YES |
111 | TYK2 | TYK2 | TYK2 | 3110 | 0.081 | 0.37 | YES |
112 | MEA1 | MEA1 | MEA1 | 3177 | 0.08 | 0.37 | YES |
113 | RBM38 | RBM38 | RBM38 | 3202 | 0.079 | 0.37 | YES |
114 | TUBB3 | TUBB3 | TUBB3 | 3209 | 0.079 | 0.38 | YES |
115 | THAP3 | THAP3 | THAP3 | 3226 | 0.078 | 0.38 | YES |
116 | SQSTM1 | SQSTM1 | SQSTM1 | 3233 | 0.078 | 0.38 | YES |
117 | RPUSD2 | RPUSD2 | RPUSD2 | 3257 | 0.078 | 0.38 | YES |
118 | BAK1 | BAK1 | BAK1 | 3295 | 0.077 | 0.38 | YES |
119 | RFC2 | RFC2 | RFC2 | 3309 | 0.077 | 0.39 | YES |
120 | GPRC5B | GPRC5B | GPRC5B | 3316 | 0.077 | 0.39 | YES |
121 | RBM4 | RBM4 | RBM4 | 3401 | 0.075 | 0.39 | YES |
122 | PAQR4 | PAQR4 | PAQR4 | 3405 | 0.075 | 0.39 | YES |
123 | SERPINH1 | SERPINH1 | SERPINH1 | 3409 | 0.075 | 0.39 | YES |
124 | MDK | MDK | MDK | 3416 | 0.075 | 0.4 | YES |
125 | CBR3 | CBR3 | CBR3 | 3496 | 0.073 | 0.39 | YES |
126 | FLNA | FLNA | FLNA | 3502 | 0.073 | 0.4 | YES |
127 | FGFR3 | FGFR3 | FGFR3 | 3509 | 0.073 | 0.4 | YES |
128 | CDKN1C | CDKN1C | CDKN1C | 3512 | 0.073 | 0.4 | YES |
129 | CBX4 | CBX4 | CBX4 | 3526 | 0.072 | 0.4 | YES |
130 | YKT6 | YKT6 | YKT6 | 3539 | 0.072 | 0.41 | YES |
131 | IL11RA | IL11RA | IL11RA | 3554 | 0.072 | 0.41 | YES |
132 | ARPC4 | ARPC4 | ARPC4 | 3688 | 0.069 | 0.4 | YES |
133 | U2AF2 | U2AF2 | U2AF2 | 3770 | 0.068 | 0.4 | YES |
134 | UROS | UROS | UROS | 3795 | 0.067 | 0.4 | YES |
135 | RABAC1 | RABAC1 | RABAC1 | 3827 | 0.067 | 0.4 | YES |
136 | KLHDC3 | KLHDC3 | KLHDC3 | 3850 | 0.066 | 0.4 | YES |
137 | ADA | ADA | ADA | 3858 | 0.066 | 0.41 | YES |
138 | PDAP1 | PDAP1 | PDAP1 | 3911 | 0.065 | 0.41 | YES |
139 | AGPAT2 | AGPAT2 | AGPAT2 | 3917 | 0.065 | 0.41 | YES |
140 | PLEKHO2 | PLEKHO2 | PLEKHO2 | 3963 | 0.064 | 0.41 | YES |
141 | FEN1 | FEN1 | FEN1 | 3985 | 0.064 | 0.41 | YES |
142 | SDF2 | SDF2 | SDF2 | 4004 | 0.064 | 0.41 | YES |
143 | TP53I3 | TP53I3 | TP53I3 | 4009 | 0.063 | 0.42 | YES |
144 | C2CD2L | C2CD2L | C2CD2L | 4062 | 0.062 | 0.41 | YES |
145 | PLCB3 | PLCB3 | PLCB3 | 4063 | 0.062 | 0.42 | YES |
146 | OAZ2 | OAZ2 | OAZ2 | 4090 | 0.062 | 0.42 | YES |
147 | GSTP1 | GSTP1 | GSTP1 | 4093 | 0.062 | 0.42 | YES |
148 | SHMT1 | SHMT1 | SHMT1 | 4106 | 0.061 | 0.42 | YES |
149 | TERF2 | TERF2 | TERF2 | 4144 | 0.06 | 0.42 | YES |
150 | RNF113A | RNF113A | RNF113A | 4230 | 0.059 | 0.42 | YES |
151 | WBSCR22 | WBSCR22 | WBSCR22 | 4236 | 0.059 | 0.42 | YES |
152 | SLC6A8 | SLC6A8 | SLC6A8 | 4242 | 0.059 | 0.42 | YES |
153 | TNFRSF10D | TNFRSF10D | TNFRSF10D | 4271 | 0.058 | 0.42 | YES |
154 | RPN1 | RPN1 | RPN1 | 4337 | 0.057 | 0.42 | YES |
155 | UROD | UROD | UROD | 4372 | 0.056 | 0.42 | YES |
156 | RAB8A | RAB8A | RAB8A | 4387 | 0.056 | 0.42 | YES |
157 | CYB5R1 | CYB5R1 | CYB5R1 | 4402 | 0.056 | 0.43 | YES |
158 | GALNT2 | GALNT2 | GALNT2 | 4408 | 0.056 | 0.43 | YES |
159 | HSPA1A | HSPA1A | HSPA1A | 4434 | 0.055 | 0.43 | YES |
160 | ARRB2 | ARRB2 | ARRB2 | 4437 | 0.055 | 0.43 | YES |
161 | PSMB10 | PSMB10 | PSMB10 | 4495 | 0.054 | 0.43 | YES |
162 | PPIE | PPIE | PPIE | 4580 | 0.052 | 0.43 | YES |
163 | SAP18 | SAP18 | SAP18 | 4626 | 0.052 | 0.43 | YES |
164 | NEU1 | NEU1 | NEU1 | 4653 | 0.051 | 0.43 | YES |
165 | DNASE2 | DNASE2 | DNASE2 | 4661 | 0.051 | 0.43 | YES |
166 | BAG1 | BAG1 | BAG1 | 4666 | 0.051 | 0.43 | YES |
167 | PVR | PVR | PVR | 4681 | 0.051 | 0.43 | YES |
168 | CDC6 | CDC6 | CDC6 | 4696 | 0.05 | 0.43 | YES |
169 | TRIM25 | TRIM25 | TRIM25 | 4700 | 0.05 | 0.44 | YES |
170 | HLA-A | HLA-A | HLA-A | 4766 | 0.049 | 0.43 | NO |
171 | MGAT1 | MGAT1 | MGAT1 | 4772 | 0.049 | 0.44 | NO |
172 | TYMS | TYMS | TYMS | 4831 | 0.048 | 0.43 | NO |
173 | RAD9A | RAD9A | RAD9A | 4891 | 0.047 | 0.43 | NO |
174 | CYB5B | CYB5B | CYB5B | 5025 | 0.044 | 0.43 | NO |
175 | ALAS1 | ALAS1 | ALAS1 | 5054 | 0.044 | 0.43 | NO |
176 | C1orf123 | C1orf123 | C1orf123 | 5059 | 0.044 | 0.43 | NO |
177 | CEBPD | CEBPD | CEBPD | 5266 | 0.04 | 0.42 | NO |
178 | TRIM21 | TRIM21 | TRIM21 | 5452 | 0.037 | 0.41 | NO |
179 | RHOB | RHOB | RHOB | 5464 | 0.036 | 0.41 | NO |
180 | NFE2L1 | NFE2L1 | NFE2L1 | 5501 | 0.036 | 0.41 | NO |
181 | DMPK | DMPK | DMPK | 5560 | 0.035 | 0.41 | NO |
182 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 5583 | 0.034 | 0.41 | NO |
183 | EIF3I | EIF3I | EIF3I | 5587 | 0.034 | 0.41 | NO |
184 | NFKBIE | NFKBIE | NFKBIE | 5644 | 0.033 | 0.41 | NO |
185 | SEPW1 | SEPW1 | SEPW1 | 5654 | 0.033 | 0.41 | NO |
186 | TM7SF2 | TM7SF2 | TM7SF2 | 5679 | 0.032 | 0.41 | NO |
187 | NPRL2 | NPRL2 | NPRL2 | 5747 | 0.031 | 0.41 | NO |
188 | PRPF4 | PRPF4 | PRPF4 | 5764 | 0.031 | 0.41 | NO |
189 | CDKN2C | CDKN2C | CDKN2C | 5867 | 0.028 | 0.4 | NO |
190 | DUSP3 | DUSP3 | DUSP3 | 5992 | 0.026 | 0.4 | NO |
191 | HEXIM1 | HEXIM1 | HEXIM1 | 6021 | 0.025 | 0.4 | NO |
192 | ZNF263 | ZNF263 | ZNF263 | 6032 | 0.025 | 0.4 | NO |
193 | PIM2 | PIM2 | PIM2 | 6035 | 0.025 | 0.4 | NO |
194 | HNRNPU | HNRNPU | HNRNPU | 6100 | 0.024 | 0.39 | NO |
195 | CCNE1 | CCNE1 | CCNE1 | 6128 | 0.023 | 0.39 | NO |
196 | FADS1 | FADS1 | FADS1 | 6218 | 0.021 | 0.39 | NO |
197 | TBCC | TBCC | TBCC | 6295 | 0.02 | 0.39 | NO |
198 | PROSC | PROSC | PROSC | 6322 | 0.02 | 0.38 | NO |
199 | TMBIM6 | TMBIM6 | TMBIM6 | 6369 | 0.019 | 0.38 | NO |
200 | HLA-E | HLA-E | HLA-E | 6372 | 0.019 | 0.38 | NO |
201 | PSMC3IP | PSMC3IP | PSMC3IP | 6444 | 0.017 | 0.38 | NO |
202 | DAXX | DAXX | DAXX | 6473 | 0.017 | 0.38 | NO |
203 | CLK3 | CLK3 | CLK3 | 6475 | 0.016 | 0.38 | NO |
204 | EWSR1 | EWSR1 | EWSR1 | 6507 | 0.016 | 0.38 | NO |
205 | ACAA1 | ACAA1 | ACAA1 | 6542 | 0.015 | 0.38 | NO |
206 | EPOR | EPOR | EPOR | 6561 | 0.015 | 0.38 | NO |
207 | PER2 | PER2 | PER2 | 6567 | 0.015 | 0.38 | NO |
208 | HYAL2 | HYAL2 | HYAL2 | 6597 | 0.014 | 0.38 | NO |
209 | TUBA4A | TUBA4A | TUBA4A | 6598 | 0.014 | 0.38 | NO |
210 | RPS15A | RPS15A | RPS15A | 6702 | 0.012 | 0.37 | NO |
211 | THBS1 | THBS1 | THBS1 | 6752 | 0.011 | 0.37 | NO |
212 | PITX2 | PITX2 | PITX2 | 6761 | 0.011 | 0.37 | NO |
213 | CEP68 | CEP68 | CEP68 | 6906 | 0.0072 | 0.36 | NO |
214 | RFC5 | RFC5 | RFC5 | 6967 | 0.006 | 0.36 | NO |
215 | BRD2 | BRD2 | BRD2 | 7124 | 0.003 | 0.35 | NO |
216 | GLUL | GLUL | GLUL | 7132 | 0.0028 | 0.35 | NO |
217 | TRIM13 | TRIM13 | TRIM13 | 7175 | 0.0021 | 0.35 | NO |
218 | TPM2 | TPM2 | TPM2 | 7219 | 0.00097 | 0.34 | NO |
219 | NAT1 | NAT1 | NAT1 | 7227 | 0.00069 | 0.34 | NO |
220 | MCM4 | MCM4 | MCM4 | 7253 | 0.000045 | 0.34 | NO |
221 | MED6 | MED6 | MED6 | 7398 | -0.003 | 0.34 | NO |
222 | CDK2 | CDK2 | CDK2 | 7423 | -0.0033 | 0.33 | NO |
223 | PNRC1 | PNRC1 | PNRC1 | 7462 | -0.0041 | 0.33 | NO |
224 | TRIAP1 | TRIAP1 | TRIAP1 | 7522 | -0.0056 | 0.33 | NO |
225 | OGG1 | OGG1 | OGG1 | 7523 | -0.0056 | 0.33 | NO |
226 | IRF1 | IRF1 | IRF1 | 7580 | -0.0066 | 0.33 | NO |
227 | NXF1 | NXF1 | NXF1 | 7638 | -0.0079 | 0.32 | NO |
228 | FBXL14 | FBXL14 | FBXL14 | 7669 | -0.0085 | 0.32 | NO |
229 | TSPYL2 | TSPYL2 | TSPYL2 | 7724 | -0.0097 | 0.32 | NO |
230 | JUNB | JUNB | JUNB | 7904 | -0.013 | 0.31 | NO |
231 | BTG1 | BTG1 | BTG1 | 7915 | -0.014 | 0.31 | NO |
232 | NPTXR | NPTXR | NPTXR | 7978 | -0.015 | 0.31 | NO |
233 | CLCN2 | CLCN2 | CLCN2 | 7981 | -0.015 | 0.31 | NO |
234 | SAT1 | SAT1 | SAT1 | 8081 | -0.018 | 0.3 | NO |
235 | MAT2A | MAT2A | MAT2A | 8097 | -0.018 | 0.3 | NO |
236 | ZNF330 | ZNF330 | ZNF330 | 8207 | -0.02 | 0.3 | NO |
237 | AP3M2 | AP3M2 | AP3M2 | 8251 | -0.021 | 0.3 | NO |
238 | HLA-G | HLA-G | HLA-G | 8282 | -0.022 | 0.3 | NO |
239 | PCNA | PCNA | PCNA | 8296 | -0.022 | 0.3 | NO |
240 | ADO | ADO | ADO | 8305 | -0.022 | 0.3 | NO |
241 | ATF3 | ATF3 | ATF3 | 8527 | -0.026 | 0.28 | NO |
242 | GDI2 | GDI2 | GDI2 | 8531 | -0.026 | 0.28 | NO |
243 | HLA-F | HLA-F | HLA-F | 8634 | -0.029 | 0.28 | NO |
244 | EIF2S3 | EIF2S3 | EIF2S3 | 8707 | -0.031 | 0.28 | NO |
245 | EFNA1 | EFNA1 | EFNA1 | 8711 | -0.031 | 0.28 | NO |
246 | CTH | CTH | CTH | 8904 | -0.034 | 0.27 | NO |
247 | BTG2 | BTG2 | BTG2 | 9044 | -0.038 | 0.26 | NO |
248 | PNP | PNP | PNP | 9116 | -0.04 | 0.26 | NO |
249 | SLC25A4 | SLC25A4 | SLC25A4 | 9163 | -0.04 | 0.26 | NO |
250 | GABARAPL1 | GABARAPL1 | GABARAPL1 | 9203 | -0.041 | 0.26 | NO |
251 | TOB1 | TOB1 | TOB1 | 9235 | -0.042 | 0.26 | NO |
252 | ITM2B | ITM2B | ITM2B | 9240 | -0.042 | 0.26 | NO |
253 | RNF103 | RNF103 | RNF103 | 9242 | -0.042 | 0.26 | NO |
254 | RSL1D1 | RSL1D1 | RSL1D1 | 9383 | -0.045 | 0.26 | NO |
255 | IFI30 | IFI30 | IFI30 | 9514 | -0.048 | 0.25 | NO |
256 | HSPA2 | HSPA2 | HSPA2 | 9722 | -0.053 | 0.24 | NO |
257 | MOAP1 | MOAP1 | MOAP1 | 9751 | -0.054 | 0.24 | NO |
258 | TMX4 | TMX4 | TMX4 | 9806 | -0.055 | 0.24 | NO |
259 | CSRNP2 | CSRNP2 | CSRNP2 | 9815 | -0.055 | 0.24 | NO |
260 | GLUD1 | GLUD1 | GLUD1 | 9903 | -0.057 | 0.24 | NO |
261 | MICB | MICB | MICB | 10018 | -0.059 | 0.24 | NO |
262 | NCBP2 | NCBP2 | NCBP2 | 10261 | -0.065 | 0.22 | NO |
263 | PDCL | PDCL | PDCL | 10387 | -0.068 | 0.22 | NO |
264 | HOXD9 | HOXD9 | HOXD9 | 10422 | -0.068 | 0.22 | NO |
265 | ZKSCAN1 | ZKSCAN1 | ZKSCAN1 | 10440 | -0.069 | 0.22 | NO |
266 | GAS1 | GAS1 | GAS1 | 10522 | -0.07 | 0.22 | NO |
267 | TREX1 | TREX1 | TREX1 | 10553 | -0.071 | 0.22 | NO |
268 | CREM | CREM | CREM | 10594 | -0.072 | 0.22 | NO |
269 | PTPN11 | PTPN11 | PTPN11 | 10615 | -0.072 | 0.22 | NO |
270 | CREG1 | CREG1 | CREG1 | 10755 | -0.076 | 0.22 | NO |
271 | CCNG2 | CCNG2 | CCNG2 | 11168 | -0.086 | 0.2 | NO |
272 | CASP3 | CASP3 | CASP3 | 11281 | -0.088 | 0.2 | NO |
273 | STX16 | STX16 | STX16 | 11387 | -0.09 | 0.2 | NO |
274 | ACYP1 | ACYP1 | ACYP1 | 11454 | -0.092 | 0.2 | NO |
275 | MFAP3 | MFAP3 | MFAP3 | 11736 | -0.098 | 0.18 | NO |
276 | RGS2 | RGS2 | RGS2 | 11755 | -0.098 | 0.19 | NO |
277 | HHEX | HHEX | HHEX | 11909 | -0.1 | 0.18 | NO |
278 | MLLT11 | MLLT11 | MLLT11 | 11940 | -0.1 | 0.18 | NO |
279 | SIX1 | SIX1 | SIX1 | 12078 | -0.11 | 0.18 | NO |
280 | SYNM | SYNM | SYNM | 12242 | -0.11 | 0.18 | NO |
281 | CDKN2B | CDKN2B | CDKN2B | 12484 | -0.12 | 0.17 | NO |
282 | SHOX2 | SHOX2 | SHOX2 | 12618 | -0.12 | 0.16 | NO |
283 | FAM8A1 | FAM8A1 | FAM8A1 | 12804 | -0.12 | 0.16 | NO |
284 | MBD4 | MBD4 | MBD4 | 12831 | -0.13 | 0.16 | NO |
285 | GCH1 | GCH1 | GCH1 | 12837 | -0.13 | 0.17 | NO |
286 | GLS | GLS | GLS | 12956 | -0.13 | 0.17 | NO |
287 | TPBG | TPBG | TPBG | 13131 | -0.13 | 0.16 | NO |
288 | TFAM | TFAM | TFAM | 13701 | -0.15 | 0.14 | NO |
289 | SMPDL3A | SMPDL3A | SMPDL3A | 14096 | -0.16 | 0.12 | NO |
290 | IFIT1 | IFIT1 | IFIT1 | 14134 | -0.17 | 0.12 | NO |
291 | ZNF510 | ZNF510 | ZNF510 | 14427 | -0.18 | 0.12 | NO |
292 | CREBZF | CREBZF | CREBZF | 14463 | -0.18 | 0.12 | NO |
293 | HAUS3 | HAUS3 | HAUS3 | 14624 | -0.19 | 0.12 | NO |
294 | CYP1B1 | CYP1B1 | CYP1B1 | 14765 | -0.19 | 0.12 | NO |
295 | ICAM3 | ICAM3 | ICAM3 | 14808 | -0.19 | 0.12 | NO |
296 | CDO1 | CDO1 | CDO1 | 14911 | -0.2 | 0.13 | NO |
297 | CLK1 | CLK1 | CLK1 | 15630 | -0.24 | 0.096 | NO |
298 | PMAIP1 | PMAIP1 | PMAIP1 | 16604 | -0.32 | 0.053 | NO |
299 | CCNE2 | CCNE2 | CCNE2 | 16620 | -0.32 | 0.065 | NO |
300 | PCDH9 | PCDH9 | PCDH9 | 17415 | -0.43 | 0.038 | NO |
Figure S71. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: LOCKWOOD AMPLIFIED IN LUNG CANCER.

Figure S72. Get High-res Image For the top 5 core enriched genes in the pathway: LOCKWOOD AMPLIFIED IN LUNG CANCER, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S37. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | POLD2 | POLD2 | POLD2 | 557 | 0.15 | 0.0036 | YES |
2 | FARSA | FARSA | FARSA | 759 | 0.14 | 0.024 | YES |
3 | RUVBL2 | RUVBL2 | RUVBL2 | 900 | 0.13 | 0.046 | YES |
4 | TRAP1 | TRAP1 | TRAP1 | 913 | 0.13 | 0.076 | YES |
5 | ERCC2 | ERCC2 | ERCC2 | 920 | 0.13 | 0.1 | YES |
6 | SSSCA1 | SSSCA1 | SSSCA1 | 924 | 0.13 | 0.14 | YES |
7 | PFKL | PFKL | PFKL | 1371 | 0.12 | 0.14 | YES |
8 | EIF3B | EIF3B | EIF3B | 1392 | 0.12 | 0.16 | YES |
9 | SNRPA | SNRPA | SNRPA | 1481 | 0.12 | 0.18 | YES |
10 | ATP5G2 | ATP5G2 | ATP5G2 | 1635 | 0.11 | 0.2 | YES |
11 | TIMM17B | TIMM17B | TIMM17B | 1690 | 0.11 | 0.22 | YES |
12 | TUBG1 | TUBG1 | TUBG1 | 1795 | 0.11 | 0.24 | YES |
13 | FANCG | FANCG | FANCG | 2035 | 0.1 | 0.25 | YES |
14 | RHOC | RHOC | RHOC | 2181 | 0.099 | 0.26 | YES |
15 | SLC25A6 | SLC25A6 | SLC25A6 | 2267 | 0.098 | 0.28 | YES |
16 | EEF1D | EEF1D | EEF1D | 2495 | 0.093 | 0.29 | YES |
17 | NDUFS3 | NDUFS3 | NDUFS3 | 2580 | 0.091 | 0.3 | YES |
18 | TKT | TKT | TKT | 2714 | 0.089 | 0.32 | YES |
19 | EML2 | EML2 | EML2 | 2980 | 0.084 | 0.32 | YES |
20 | CDK4 | CDK4 | CDK4 | 3156 | 0.08 | 0.33 | YES |
21 | MCM7 | MCM7 | MCM7 | 3167 | 0.08 | 0.35 | YES |
22 | QDPR | QDPR | QDPR | 3390 | 0.075 | 0.35 | YES |
23 | PGAM1 | PGAM1 | PGAM1 | 3443 | 0.074 | 0.36 | YES |
24 | RPL29 | RPL29 | RPL29 | 3542 | 0.072 | 0.38 | YES |
25 | RRM2 | RRM2 | RRM2 | 3738 | 0.068 | 0.38 | YES |
26 | PA2G4 | PA2G4 | PA2G4 | 4017 | 0.063 | 0.38 | YES |
27 | COX4I1 | COX4I1 | COX4I1 | 4312 | 0.058 | 0.38 | YES |
28 | RPS14 | RPS14 | RPS14 | 4331 | 0.057 | 0.39 | YES |
29 | NOP16 | NOP16 | NOP16 | 4605 | 0.052 | 0.38 | YES |
30 | ATP5G3 | ATP5G3 | ATP5G3 | 4685 | 0.05 | 0.39 | YES |
31 | HADHA | HADHA | HADHA | 4730 | 0.05 | 0.4 | YES |
32 | POLR2H | POLR2H | POLR2H | 4749 | 0.049 | 0.41 | YES |
33 | NOP56 | NOP56 | NOP56 | 4755 | 0.049 | 0.42 | YES |
34 | FARSB | FARSB | FARSB | 4790 | 0.049 | 0.43 | YES |
35 | SNRPC | SNRPC | SNRPC | 4807 | 0.048 | 0.44 | YES |
36 | UQCRH | UQCRH | UQCRH | 4920 | 0.046 | 0.44 | YES |
37 | TIMM23 | TIMM23 | TIMM23 | 5181 | 0.042 | 0.44 | YES |
38 | NDUFB2 | NDUFB2 | NDUFB2 | 5194 | 0.042 | 0.45 | YES |
39 | MTHFD1 | MTHFD1 | MTHFD1 | 5294 | 0.04 | 0.45 | YES |
40 | RPSA | RPSA | RPSA | 5944 | 0.027 | 0.42 | NO |
41 | FABP5 | FABP5 | FABP5 | 5960 | 0.026 | 0.43 | NO |
42 | SNRPD1 | SNRPD1 | SNRPD1 | 6487 | 0.016 | 0.4 | NO |
43 | HNRNPC | HNRNPC | HNRNPC | 6582 | 0.014 | 0.4 | NO |
44 | HARS2 | HARS2 | HARS2 | 6603 | 0.014 | 0.4 | NO |
45 | ABCA3 | ABCA3 | ABCA3 | 6665 | 0.013 | 0.4 | NO |
46 | ZFYVE26 | ZFYVE26 | ZFYVE26 | 6738 | 0.011 | 0.4 | NO |
47 | RPL4 | RPL4 | RPL4 | 6756 | 0.011 | 0.4 | NO |
48 | AKAP13 | AKAP13 | AKAP13 | 6829 | 0.0095 | 0.4 | NO |
49 | RFC5 | RFC5 | RFC5 | 6967 | 0.006 | 0.39 | NO |
50 | NDUFB6 | NDUFB6 | NDUFB6 | 7284 | -0.00047 | 0.38 | NO |
51 | GTF3A | GTF3A | GTF3A | 7410 | -0.0031 | 0.37 | NO |
52 | RPL15 | RPL15 | RPL15 | 7491 | -0.0049 | 0.36 | NO |
53 | SUPT16H | SUPT16H | SUPT16H | 7662 | -0.0083 | 0.36 | NO |
54 | MYC | MYC | MYC | 7768 | -0.011 | 0.35 | NO |
55 | RRM1 | RRM1 | RRM1 | 7860 | -0.013 | 0.35 | NO |
56 | ABCC4 | ABCC4 | ABCC4 | 8009 | -0.016 | 0.35 | NO |
57 | MRPL3 | MRPL3 | MRPL3 | 8087 | -0.018 | 0.35 | NO |
58 | MSH6 | MSH6 | MSH6 | 8554 | -0.027 | 0.33 | NO |
59 | GTF2H4 | GTF2H4 | GTF2H4 | 9086 | -0.039 | 0.31 | NO |
60 | SNRPA1 | SNRPA1 | SNRPA1 | 10110 | -0.061 | 0.26 | NO |
61 | SLC27A2 | SLC27A2 | SLC27A2 | 10165 | -0.063 | 0.28 | NO |
62 | ZNF200 | ZNF200 | ZNF200 | 10843 | -0.078 | 0.25 | NO |
63 | MYB | MYB | MYB | 11806 | -0.1 | 0.22 | NO |
64 | IDH3A | IDH3A | IDH3A | 11980 | -0.1 | 0.24 | NO |
65 | PRIM1 | PRIM1 | PRIM1 | 12457 | -0.12 | 0.24 | NO |
66 | SLK | SLK | SLK | 12593 | -0.12 | 0.26 | NO |
67 | PIK3CA | PIK3CA | PIK3CA | 15296 | -0.22 | 0.16 | NO |
Figure S73. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: PENG LEUCINE DEPRIVATION DN.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: PENG LEUCINE DEPRIVATION DN, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S38. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NRGN | NRGN | NRGN | 176 | 0.22 | 0.0073 | YES |
2 | COX7A1 | COX7A1 | COX7A1 | 310 | 0.19 | 0.014 | YES |
3 | MRPL23 | MRPL23 | MRPL23 | 416 | 0.17 | 0.022 | YES |
4 | COL9A3 | COL9A3 | COL9A3 | 477 | 0.16 | 0.031 | YES |
5 | NDUFS8 | NDUFS8 | NDUFS8 | 480 | 0.16 | 0.044 | YES |
6 | SEC14L5 | SEC14L5 | SEC14L5 | 515 | 0.16 | 0.054 | YES |
7 | DCXR | DCXR | DCXR | 542 | 0.16 | 0.065 | YES |
8 | PAFAH1B3 | PAFAH1B3 | PAFAH1B3 | 621 | 0.15 | 0.072 | YES |
9 | ENDOG | ENDOG | ENDOG | 702 | 0.14 | 0.079 | YES |
10 | C9orf16 | C9orf16 | C9orf16 | 794 | 0.14 | 0.085 | YES |
11 | ACTL6B | ACTL6B | ACTL6B | 804 | 0.14 | 0.095 | YES |
12 | ECSIT | ECSIT | ECSIT | 810 | 0.14 | 0.1 | YES |
13 | NTHL1 | NTHL1 | NTHL1 | 874 | 0.14 | 0.11 | YES |
14 | RUVBL2 | RUVBL2 | RUVBL2 | 900 | 0.13 | 0.12 | YES |
15 | TRAP1 | TRAP1 | TRAP1 | 913 | 0.13 | 0.13 | YES |
16 | ETFB | ETFB | ETFB | 950 | 0.13 | 0.14 | YES |
17 | NDUFS7 | NDUFS7 | NDUFS7 | 951 | 0.13 | 0.15 | YES |
18 | NBL1 | NBL1 | NBL1 | 960 | 0.13 | 0.16 | YES |
19 | MAL | MAL | MAL | 967 | 0.13 | 0.17 | YES |
20 | HCFC1R1 | HCFC1R1 | HCFC1R1 | 1017 | 0.13 | 0.18 | YES |
21 | SAC3D1 | SAC3D1 | SAC3D1 | 1018 | 0.13 | 0.19 | YES |
22 | TPI1 | TPI1 | TPI1 | 1028 | 0.13 | 0.2 | YES |
23 | MAPK3 | MAPK3 | MAPK3 | 1041 | 0.13 | 0.21 | YES |
24 | CX3CL1 | CX3CL1 | CX3CL1 | 1058 | 0.13 | 0.22 | YES |
25 | EXOC3 | EXOC3 | EXOC3 | 1109 | 0.13 | 0.22 | YES |
26 | VPS28 | VPS28 | VPS28 | 1140 | 0.13 | 0.23 | YES |
27 | ECI1 | ECI1 | ECI1 | 1202 | 0.12 | 0.24 | YES |
28 | IMPDH2 | IMPDH2 | IMPDH2 | 1237 | 0.12 | 0.24 | YES |
29 | EIF6 | EIF6 | EIF6 | 1285 | 0.12 | 0.25 | YES |
30 | HRAS | HRAS | HRAS | 1298 | 0.12 | 0.26 | YES |
31 | EIF3G | EIF3G | EIF3G | 1342 | 0.12 | 0.27 | YES |
32 | SLC25A11 | SLC25A11 | SLC25A11 | 1366 | 0.12 | 0.28 | YES |
33 | CTDNEP1 | CTDNEP1 | CTDNEP1 | 1402 | 0.12 | 0.28 | YES |
34 | SNRPA | SNRPA | SNRPA | 1481 | 0.12 | 0.29 | YES |
35 | RNH1 | RNH1 | RNH1 | 1503 | 0.12 | 0.3 | YES |
36 | PES1 | PES1 | PES1 | 1505 | 0.12 | 0.3 | YES |
37 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 1605 | 0.11 | 0.31 | YES |
38 | NDUFAF3 | NDUFAF3 | NDUFAF3 | 1634 | 0.11 | 0.32 | YES |
39 | ATP5G1 | ATP5G1 | ATP5G1 | 1647 | 0.11 | 0.32 | YES |
40 | CHMP2A | CHMP2A | CHMP2A | 1688 | 0.11 | 0.33 | YES |
41 | TUFM | TUFM | TUFM | 1872 | 0.11 | 0.33 | YES |
42 | DTX4 | DTX4 | DTX4 | 1881 | 0.11 | 0.34 | YES |
43 | TMEM147 | TMEM147 | TMEM147 | 1971 | 0.1 | 0.34 | YES |
44 | PUF60 | PUF60 | PUF60 | 2279 | 0.097 | 0.33 | YES |
45 | RBM10 | RBM10 | RBM10 | 2284 | 0.097 | 0.34 | YES |
46 | DHPS | DHPS | DHPS | 2378 | 0.095 | 0.34 | YES |
47 | CRYAB | CRYAB | CRYAB | 2391 | 0.095 | 0.34 | YES |
48 | HAX1 | HAX1 | HAX1 | 2418 | 0.095 | 0.35 | YES |
49 | ESYT1 | ESYT1 | ESYT1 | 2428 | 0.094 | 0.36 | YES |
50 | RPL13 | RPL13 | RPL13 | 2489 | 0.093 | 0.36 | YES |
51 | PIN1 | PIN1 | PIN1 | 2493 | 0.093 | 0.37 | YES |
52 | COX8A | COX8A | COX8A | 2502 | 0.093 | 0.38 | YES |
53 | HDGF | HDGF | HDGF | 2575 | 0.091 | 0.38 | YES |
54 | SFXN3 | SFXN3 | SFXN3 | 2582 | 0.091 | 0.39 | YES |
55 | NUDC | NUDC | NUDC | 2583 | 0.091 | 0.39 | YES |
56 | TALDO1 | TALDO1 | TALDO1 | 2599 | 0.091 | 0.4 | YES |
57 | CCT7 | CCT7 | CCT7 | 2627 | 0.091 | 0.4 | YES |
58 | BCAP31 | BCAP31 | BCAP31 | 2636 | 0.09 | 0.41 | YES |
59 | ACOT7 | ACOT7 | ACOT7 | 2748 | 0.088 | 0.41 | YES |
60 | GRHPR | GRHPR | GRHPR | 2753 | 0.088 | 0.42 | YES |
61 | OS9 | OS9 | OS9 | 2779 | 0.088 | 0.42 | YES |
62 | CREB3 | CREB3 | CREB3 | 2829 | 0.087 | 0.43 | YES |
63 | GDI1 | GDI1 | GDI1 | 2869 | 0.086 | 0.43 | YES |
64 | NDUFA7 | NDUFA7 | NDUFA7 | 2898 | 0.085 | 0.44 | YES |
65 | GTF3C1 | GTF3C1 | GTF3C1 | 3071 | 0.082 | 0.44 | YES |
66 | SF3B2 | SF3B2 | SF3B2 | 3091 | 0.081 | 0.44 | YES |
67 | GPX1 | GPX1 | GPX1 | 3127 | 0.08 | 0.44 | YES |
68 | ATOX1 | ATOX1 | ATOX1 | 3155 | 0.08 | 0.45 | YES |
69 | SPAG7 | SPAG7 | SPAG7 | 3218 | 0.079 | 0.45 | YES |
70 | AMPD2 | AMPD2 | AMPD2 | 3229 | 0.078 | 0.46 | YES |
71 | CDIPT | CDIPT | CDIPT | 3234 | 0.078 | 0.46 | YES |
72 | ATP6V0B | ATP6V0B | ATP6V0B | 3283 | 0.077 | 0.47 | YES |
73 | PSMB5 | PSMB5 | PSMB5 | 3305 | 0.077 | 0.47 | YES |
74 | AKR1A1 | AKR1A1 | AKR1A1 | 3449 | 0.074 | 0.47 | YES |
75 | ACTR1A | ACTR1A | ACTR1A | 3547 | 0.072 | 0.47 | YES |
76 | STOML1 | STOML1 | STOML1 | 3557 | 0.072 | 0.48 | YES |
77 | DHX30 | DHX30 | DHX30 | 3558 | 0.072 | 0.48 | YES |
78 | MARCKSL1 | MARCKSL1 | MARCKSL1 | 3660 | 0.07 | 0.48 | YES |
79 | ACD | ACD | ACD | 3692 | 0.069 | 0.48 | YES |
80 | PMM1 | PMM1 | PMM1 | 3700 | 0.069 | 0.49 | YES |
81 | AKR1B1 | AKR1B1 | AKR1B1 | 3767 | 0.068 | 0.49 | YES |
82 | RABAC1 | RABAC1 | RABAC1 | 3827 | 0.067 | 0.49 | YES |
83 | DPF2 | DPF2 | DPF2 | 3847 | 0.066 | 0.5 | YES |
84 | PEF1 | PEF1 | PEF1 | 3849 | 0.066 | 0.5 | YES |
85 | RPS29 | RPS29 | RPS29 | 3909 | 0.065 | 0.5 | YES |
86 | DNAJB2 | DNAJB2 | DNAJB2 | 4033 | 0.063 | 0.5 | YES |
87 | ATP6V0E2 | ATP6V0E2 | ATP6V0E2 | 4039 | 0.063 | 0.51 | YES |
88 | MADD | MADD | MADD | 4215 | 0.06 | 0.5 | YES |
89 | NUP93 | NUP93 | NUP93 | 4222 | 0.059 | 0.51 | YES |
90 | PPIA | PPIA | PPIA | 4283 | 0.058 | 0.51 | YES |
91 | COX4I1 | COX4I1 | COX4I1 | 4312 | 0.058 | 0.51 | YES |
92 | SUMO3 | SUMO3 | SUMO3 | 4429 | 0.055 | 0.51 | YES |
93 | ARRB2 | ARRB2 | ARRB2 | 4437 | 0.055 | 0.51 | YES |
94 | GNPDA1 | GNPDA1 | GNPDA1 | 4470 | 0.054 | 0.51 | YES |
95 | DCTN2 | DCTN2 | DCTN2 | 4530 | 0.053 | 0.52 | YES |
96 | NDUFA1 | NDUFA1 | NDUFA1 | 4535 | 0.053 | 0.52 | YES |
97 | CLTA | CLTA | CLTA | 4689 | 0.05 | 0.52 | YES |
98 | CKB | CKB | CKB | 4702 | 0.05 | 0.52 | YES |
99 | PARP1 | PARP1 | PARP1 | 4816 | 0.048 | 0.52 | YES |
100 | ARPC2 | ARPC2 | ARPC2 | 4892 | 0.047 | 0.52 | YES |
101 | NCALD | NCALD | NCALD | 4978 | 0.045 | 0.51 | YES |
102 | UQCRQ | UQCRQ | UQCRQ | 4999 | 0.045 | 0.52 | YES |
103 | AHSA1 | AHSA1 | AHSA1 | 5038 | 0.044 | 0.52 | YES |
104 | NDUFC1 | NDUFC1 | NDUFC1 | 5060 | 0.044 | 0.52 | YES |
105 | COX7C | COX7C | COX7C | 5204 | 0.041 | 0.52 | NO |
106 | LMAN2L | LMAN2L | LMAN2L | 5214 | 0.041 | 0.52 | NO |
107 | RAP1GAP2 | RAP1GAP2 | RAP1GAP2 | 5318 | 0.039 | 0.52 | NO |
108 | RNPS1 | RNPS1 | RNPS1 | 5413 | 0.037 | 0.51 | NO |
109 | KLHL21 | KLHL21 | KLHL21 | 5489 | 0.036 | 0.51 | NO |
110 | FNDC4 | FNDC4 | FNDC4 | 5769 | 0.031 | 0.5 | NO |
111 | MAST3 | MAST3 | MAST3 | 5779 | 0.03 | 0.5 | NO |
112 | NDUFB1 | NDUFB1 | NDUFB1 | 5805 | 0.03 | 0.5 | NO |
113 | NIPSNAP1 | NIPSNAP1 | NIPSNAP1 | 5846 | 0.029 | 0.5 | NO |
114 | FTO | FTO | FTO | 6104 | 0.024 | 0.49 | NO |
115 | PLA2G16 | PLA2G16 | PLA2G16 | 6315 | 0.02 | 0.48 | NO |
116 | GNAZ | GNAZ | GNAZ | 6421 | 0.018 | 0.47 | NO |
117 | TUBA4A | TUBA4A | TUBA4A | 6598 | 0.014 | 0.46 | NO |
118 | UQCRB | UQCRB | UQCRB | 6692 | 0.012 | 0.46 | NO |
119 | GPR37 | GPR37 | GPR37 | 6815 | 0.0098 | 0.46 | NO |
120 | STARD7 | STARD7 | STARD7 | 6894 | 0.0075 | 0.45 | NO |
121 | RPS8 | RPS8 | RPS8 | 6971 | 0.0059 | 0.45 | NO |
122 | SUCLG1 | SUCLG1 | SUCLG1 | 7490 | -0.0049 | 0.42 | NO |
123 | DEGS1 | DEGS1 | DEGS1 | 7627 | -0.0075 | 0.41 | NO |
124 | PFDN1 | PFDN1 | PFDN1 | 7804 | -0.011 | 0.4 | NO |
125 | ZMAT4 | ZMAT4 | ZMAT4 | 8214 | -0.02 | 0.38 | NO |
126 | PTGDS | PTGDS | PTGDS | 8274 | -0.022 | 0.38 | NO |
127 | FXYD7 | FXYD7 | FXYD7 | 8498 | -0.026 | 0.37 | NO |
128 | PMP22 | PMP22 | PMP22 | 8947 | -0.036 | 0.35 | NO |
129 | ARL4A | ARL4A | ARL4A | 9128 | -0.04 | 0.34 | NO |
130 | B3GAT1 | B3GAT1 | B3GAT1 | 9650 | -0.052 | 0.32 | NO |
131 | FBXO9 | FBXO9 | FBXO9 | 10580 | -0.072 | 0.27 | NO |
132 | C16orf45 | C16orf45 | C16orf45 | 11379 | -0.09 | 0.23 | NO |
133 | STX7 | STX7 | STX7 | 11801 | -0.099 | 0.22 | NO |
134 | CLASP2 | CLASP2 | CLASP2 | 12486 | -0.12 | 0.19 | NO |
135 | SNX6 | SNX6 | SNX6 | 12701 | -0.12 | 0.18 | NO |
136 | CACNG3 | CACNG3 | CACNG3 | 13449 | -0.14 | 0.16 | NO |
137 | GABBR1 | GABBR1 | GABBR1 | 13543 | -0.15 | 0.16 | NO |
138 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 13831 | -0.16 | 0.16 | NO |
139 | CX3CR1 | CX3CR1 | CX3CR1 | 14328 | -0.17 | 0.14 | NO |
140 | PAK6 | PAK6 | PAK6 | 15282 | -0.22 | 0.11 | NO |
141 | KLK6 | KLK6 | KLK6 | 16367 | -0.29 | 0.07 | NO |
142 | HMP19 | HMP19 | HMP19 | 16751 | -0.33 | 0.074 | NO |
Figure S75. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: MOOTHA VOXPHOS.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: MOOTHA VOXPHOS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S39. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SYT5 | SYT5 | SYT5 | 113 | 0.24 | 0.0043 | YES |
2 | MAD1L1 | MAD1L1 | MAD1L1 | 226 | 0.21 | 0.007 | YES |
3 | LHB | LHB | LHB | 292 | 0.19 | 0.012 | YES |
4 | EHD2 | EHD2 | EHD2 | 434 | 0.17 | 0.011 | YES |
5 | G6PC3 | G6PC3 | G6PC3 | 451 | 0.16 | 0.017 | YES |
6 | SPATA20 | SPATA20 | SPATA20 | 642 | 0.15 | 0.013 | YES |
7 | PLOD3 | PLOD3 | PLOD3 | 667 | 0.14 | 0.018 | YES |
8 | EXOSC4 | EXOSC4 | EXOSC4 | 724 | 0.14 | 0.021 | YES |
9 | GYS1 | GYS1 | GYS1 | 744 | 0.14 | 0.026 | YES |
10 | SLC1A5 | SLC1A5 | SLC1A5 | 768 | 0.14 | 0.031 | YES |
11 | NOSIP | NOSIP | NOSIP | 786 | 0.14 | 0.036 | YES |
12 | EPN1 | EPN1 | EPN1 | 806 | 0.14 | 0.041 | YES |
13 | OPLAH | OPLAH | OPLAH | 846 | 0.14 | 0.045 | YES |
14 | SHARPIN | SHARPIN | SHARPIN | 877 | 0.14 | 0.049 | YES |
15 | RUVBL2 | RUVBL2 | RUVBL2 | 900 | 0.13 | 0.054 | YES |
16 | GPR124 | GPR124 | GPR124 | 959 | 0.13 | 0.056 | YES |
17 | ZNF787 | ZNF787 | ZNF787 | 977 | 0.13 | 0.061 | YES |
18 | TSTA3 | TSTA3 | TSTA3 | 999 | 0.13 | 0.066 | YES |
19 | GRWD1 | GRWD1 | GRWD1 | 1009 | 0.13 | 0.071 | YES |
20 | AP2S1 | AP2S1 | AP2S1 | 1013 | 0.13 | 0.076 | YES |
21 | ZC3H3 | ZC3H3 | ZC3H3 | 1027 | 0.13 | 0.081 | YES |
22 | DBP | DBP | DBP | 1048 | 0.13 | 0.086 | YES |
23 | GPAA1 | GPAA1 | GPAA1 | 1084 | 0.13 | 0.089 | YES |
24 | GRN | GRN | GRN | 1094 | 0.13 | 0.094 | YES |
25 | EXOC3 | EXOC3 | EXOC3 | 1109 | 0.13 | 0.099 | YES |
26 | BAX | BAX | BAX | 1114 | 0.13 | 0.1 | YES |
27 | ASL | ASL | ASL | 1117 | 0.13 | 0.11 | YES |
28 | FIS1 | FIS1 | FIS1 | 1137 | 0.13 | 0.11 | YES |
29 | VPS28 | VPS28 | VPS28 | 1140 | 0.13 | 0.12 | YES |
30 | ZNF444 | ZNF444 | ZNF444 | 1152 | 0.12 | 0.12 | YES |
31 | PAK4 | PAK4 | PAK4 | 1204 | 0.12 | 0.13 | YES |
32 | KAT7 | KAT7 | KAT7 | 1206 | 0.12 | 0.13 | YES |
33 | DGAT1 | DGAT1 | DGAT1 | 1235 | 0.12 | 0.14 | YES |
34 | INTS1 | INTS1 | INTS1 | 1278 | 0.12 | 0.14 | YES |
35 | CYC1 | CYC1 | CYC1 | 1282 | 0.12 | 0.14 | YES |
36 | MRPS12 | MRPS12 | MRPS12 | 1319 | 0.12 | 0.15 | YES |
37 | CASKIN2 | CASKIN2 | CASKIN2 | 1333 | 0.12 | 0.15 | YES |
38 | NUCB1 | NUCB1 | NUCB1 | 1383 | 0.12 | 0.15 | YES |
39 | SARS2 | SARS2 | SARS2 | 1407 | 0.12 | 0.16 | YES |
40 | SLC12A9 | SLC12A9 | SLC12A9 | 1497 | 0.12 | 0.16 | YES |
41 | PRKD2 | PRKD2 | PRKD2 | 1544 | 0.11 | 0.16 | YES |
42 | SLC39A4 | SLC39A4 | SLC39A4 | 1575 | 0.11 | 0.16 | YES |
43 | TLN1 | TLN1 | TLN1 | 1583 | 0.11 | 0.17 | YES |
44 | GNB2 | GNB2 | GNB2 | 1642 | 0.11 | 0.17 | YES |
45 | ATP5G1 | ATP5G1 | ATP5G1 | 1647 | 0.11 | 0.18 | YES |
46 | CNOT3 | CNOT3 | CNOT3 | 1675 | 0.11 | 0.18 | YES |
47 | ZDHHC24 | ZDHHC24 | ZDHHC24 | 1727 | 0.11 | 0.18 | YES |
48 | NDUFS6 | NDUFS6 | NDUFS6 | 1752 | 0.11 | 0.18 | YES |
49 | STRN4 | STRN4 | STRN4 | 1753 | 0.11 | 0.19 | YES |
50 | NME1 | NME1 | NME1 | 1790 | 0.11 | 0.19 | YES |
51 | MBOAT7 | MBOAT7 | MBOAT7 | 1799 | 0.11 | 0.2 | YES |
52 | NAPA | NAPA | NAPA | 1836 | 0.11 | 0.2 | YES |
53 | LIG1 | LIG1 | LIG1 | 1923 | 0.1 | 0.2 | YES |
54 | SIX5 | SIX5 | SIX5 | 1929 | 0.1 | 0.2 | YES |
55 | KDELR1 | KDELR1 | KDELR1 | 1933 | 0.1 | 0.21 | YES |
56 | ZNHIT1 | ZNHIT1 | ZNHIT1 | 1947 | 0.1 | 0.21 | YES |
57 | SNF8 | SNF8 | SNF8 | 2041 | 0.1 | 0.21 | YES |
58 | MPP2 | MPP2 | MPP2 | 2072 | 0.1 | 0.21 | YES |
59 | KIAA0195 | KIAA0195 | KIAA0195 | 2172 | 0.1 | 0.21 | YES |
60 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 2193 | 0.099 | 0.21 | YES |
61 | TSEN34 | TSEN34 | TSEN34 | 2228 | 0.098 | 0.22 | YES |
62 | ARFRP1 | ARFRP1 | ARFRP1 | 2268 | 0.098 | 0.22 | YES |
63 | GSDMD | GSDMD | GSDMD | 2274 | 0.098 | 0.22 | YES |
64 | ZNF580 | ZNF580 | ZNF580 | 2283 | 0.097 | 0.23 | YES |
65 | RPL18 | RPL18 | RPL18 | 2304 | 0.097 | 0.23 | YES |
66 | PDK2 | PDK2 | PDK2 | 2306 | 0.097 | 0.23 | YES |
67 | PSME3 | PSME3 | PSME3 | 2313 | 0.097 | 0.24 | YES |
68 | PSMD8 | PSMD8 | PSMD8 | 2381 | 0.095 | 0.24 | YES |
69 | ORAI2 | ORAI2 | ORAI2 | 2431 | 0.094 | 0.24 | YES |
70 | PRPF6 | PRPF6 | PRPF6 | 2440 | 0.094 | 0.24 | YES |
71 | PRMT1 | PRMT1 | PRMT1 | 2467 | 0.094 | 0.25 | YES |
72 | EEF1D | EEF1D | EEF1D | 2495 | 0.093 | 0.25 | YES |
73 | SIRT2 | SIRT2 | SIRT2 | 2551 | 0.092 | 0.25 | YES |
74 | NUDC | NUDC | NUDC | 2583 | 0.091 | 0.25 | YES |
75 | LRRC59 | LRRC59 | LRRC59 | 2612 | 0.091 | 0.25 | YES |
76 | PHB | PHB | PHB | 2699 | 0.089 | 0.25 | YES |
77 | RPS9 | RPS9 | RPS9 | 2797 | 0.087 | 0.25 | YES |
78 | CREB3 | CREB3 | CREB3 | 2829 | 0.087 | 0.25 | YES |
79 | PPP2R5D | PPP2R5D | PPP2R5D | 2925 | 0.085 | 0.25 | YES |
80 | EML2 | EML2 | EML2 | 2980 | 0.084 | 0.25 | YES |
81 | PAF1 | PAF1 | PAF1 | 3006 | 0.083 | 0.25 | YES |
82 | CNPY3 | CNPY3 | CNPY3 | 3019 | 0.083 | 0.26 | YES |
83 | RCN3 | RCN3 | RCN3 | 3022 | 0.083 | 0.26 | YES |
84 | NKIRAS2 | NKIRAS2 | NKIRAS2 | 3027 | 0.083 | 0.26 | YES |
85 | NR1H2 | NR1H2 | NR1H2 | 3081 | 0.082 | 0.26 | YES |
86 | SDHA | SDHA | SDHA | 3106 | 0.081 | 0.27 | YES |
87 | IRF3 | IRF3 | IRF3 | 3150 | 0.08 | 0.27 | YES |
88 | CYHR1 | CYHR1 | CYHR1 | 3207 | 0.079 | 0.27 | YES |
89 | TMUB2 | TMUB2 | TMUB2 | 3225 | 0.078 | 0.27 | YES |
90 | MICALL2 | MICALL2 | MICALL2 | 3285 | 0.077 | 0.27 | YES |
91 | SCRIB | SCRIB | SCRIB | 3360 | 0.076 | 0.27 | YES |
92 | XYLT2 | XYLT2 | XYLT2 | 3607 | 0.071 | 0.26 | YES |
93 | RAB5C | RAB5C | RAB5C | 3621 | 0.071 | 0.26 | YES |
94 | TRRAP | TRRAP | TRRAP | 3664 | 0.07 | 0.26 | YES |
95 | TAF6 | TAF6 | TAF6 | 3675 | 0.07 | 0.26 | YES |
96 | EIF3K | EIF3K | EIF3K | 3713 | 0.069 | 0.27 | YES |
97 | PLEKHG3 | PLEKHG3 | PLEKHG3 | 3732 | 0.069 | 0.27 | YES |
98 | LAMA5 | LAMA5 | LAMA5 | 3754 | 0.068 | 0.27 | YES |
99 | U2AF2 | U2AF2 | U2AF2 | 3770 | 0.068 | 0.27 | YES |
100 | MYL6 | MYL6 | MYL6 | 3786 | 0.067 | 0.27 | YES |
101 | SPAG8 | SPAG8 | SPAG8 | 3801 | 0.067 | 0.28 | YES |
102 | OPA3 | OPA3 | OPA3 | 3805 | 0.067 | 0.28 | YES |
103 | FUT1 | FUT1 | FUT1 | 3834 | 0.067 | 0.28 | YES |
104 | DDT | DDT | DDT | 3853 | 0.066 | 0.28 | YES |
105 | MYL10 | MYL10 | MYL10 | 3868 | 0.066 | 0.28 | YES |
106 | ITGA3 | ITGA3 | ITGA3 | 3884 | 0.066 | 0.29 | YES |
107 | NDRG1 | NDRG1 | NDRG1 | 3923 | 0.065 | 0.29 | YES |
108 | SNRPD2 | SNRPD2 | SNRPD2 | 3968 | 0.064 | 0.29 | YES |
109 | PLEKHA4 | PLEKHA4 | PLEKHA4 | 4013 | 0.063 | 0.29 | YES |
110 | CD3EAP | CD3EAP | CD3EAP | 4015 | 0.063 | 0.29 | YES |
111 | AARSD1 | AARSD1 | AARSD1 | 4095 | 0.062 | 0.29 | YES |
112 | MLX | MLX | MLX | 4165 | 0.06 | 0.29 | YES |
113 | FAM117A | FAM117A | FAM117A | 4194 | 0.06 | 0.29 | YES |
114 | ZGPAT | ZGPAT | ZGPAT | 4211 | 0.06 | 0.29 | YES |
115 | SHFM1 | SHFM1 | SHFM1 | 4219 | 0.059 | 0.29 | YES |
116 | SLC35B1 | SLC35B1 | SLC35B1 | 4239 | 0.059 | 0.29 | YES |
117 | SNX11 | SNX11 | SNX11 | 4248 | 0.059 | 0.3 | YES |
118 | CPSF1 | CPSF1 | CPSF1 | 4270 | 0.058 | 0.3 | YES |
119 | TMEM8B | TMEM8B | TMEM8B | 4300 | 0.058 | 0.3 | YES |
120 | FAM134C | FAM134C | FAM134C | 4350 | 0.057 | 0.3 | YES |
121 | RGP1 | RGP1 | RGP1 | 4368 | 0.057 | 0.3 | YES |
122 | NUP62 | NUP62 | NUP62 | 4374 | 0.056 | 0.3 | YES |
123 | NPR2 | NPR2 | NPR2 | 4377 | 0.056 | 0.3 | YES |
124 | NMT1 | NMT1 | NMT1 | 4417 | 0.056 | 0.3 | YES |
125 | DPF1 | DPF1 | DPF1 | 4566 | 0.053 | 0.3 | NO |
126 | CLTA | CLTA | CLTA | 4689 | 0.05 | 0.29 | NO |
127 | RPS21 | RPS21 | RPS21 | 4887 | 0.047 | 0.28 | NO |
128 | SMURF1 | SMURF1 | SMURF1 | 4889 | 0.047 | 0.29 | NO |
129 | PNPO | PNPO | PNPO | 4952 | 0.046 | 0.28 | NO |
130 | MAP4K1 | MAP4K1 | MAP4K1 | 4977 | 0.045 | 0.29 | NO |
131 | ARPC1B | ARPC1B | ARPC1B | 5029 | 0.044 | 0.28 | NO |
132 | ID1 | ID1 | ID1 | 5070 | 0.044 | 0.28 | NO |
133 | MAFK | MAFK | MAFK | 5092 | 0.043 | 0.28 | NO |
134 | ACLY | ACLY | ACLY | 5207 | 0.041 | 0.28 | NO |
135 | UBE2Z | UBE2Z | UBE2Z | 5213 | 0.041 | 0.28 | NO |
136 | RPL27 | RPL27 | RPL27 | 5248 | 0.04 | 0.28 | NO |
137 | BRD9 | BRD9 | BRD9 | 5256 | 0.04 | 0.28 | NO |
138 | CEP72 | CEP72 | CEP72 | 5352 | 0.039 | 0.28 | NO |
139 | SLC25A13 | SLC25A13 | SLC25A13 | 5389 | 0.038 | 0.28 | NO |
140 | ARPC1A | ARPC1A | ARPC1A | 5400 | 0.038 | 0.28 | NO |
141 | GARS | GARS | GARS | 5469 | 0.036 | 0.28 | NO |
142 | RPL13A | RPL13A | RPL13A | 5496 | 0.036 | 0.28 | NO |
143 | BRF2 | BRF2 | BRF2 | 5545 | 0.035 | 0.28 | NO |
144 | DMPK | DMPK | DMPK | 5560 | 0.035 | 0.28 | NO |
145 | HNRNPL | HNRNPL | HNRNPL | 5645 | 0.033 | 0.27 | NO |
146 | LPCAT1 | LPCAT1 | LPCAT1 | 5675 | 0.032 | 0.27 | NO |
147 | STAT5B | STAT5B | STAT5B | 5742 | 0.031 | 0.27 | NO |
148 | CDKN2A | CDKN2A | CDKN2A | 5774 | 0.031 | 0.27 | NO |
149 | RABGEF1 | RABGEF1 | RABGEF1 | 5870 | 0.028 | 0.27 | NO |
150 | PCTP | PCTP | PCTP | 5898 | 0.028 | 0.27 | NO |
151 | TPD52L2 | TPD52L2 | TPD52L2 | 5952 | 0.027 | 0.26 | NO |
152 | DUSP3 | DUSP3 | DUSP3 | 5992 | 0.026 | 0.26 | NO |
153 | HEXIM1 | HEXIM1 | HEXIM1 | 6021 | 0.025 | 0.26 | NO |
154 | AP4M1 | AP4M1 | AP4M1 | 6040 | 0.025 | 0.26 | NO |
155 | PDCD6 | PDCD6 | PDCD6 | 6069 | 0.024 | 0.26 | NO |
156 | NFKBIB | NFKBIB | NFKBIB | 6168 | 0.022 | 0.26 | NO |
157 | SNRNP70 | SNRNP70 | SNRNP70 | 6188 | 0.022 | 0.26 | NO |
158 | PQLC3 | PQLC3 | PQLC3 | 6314 | 0.02 | 0.25 | NO |
159 | MAPK1IP1L | MAPK1IP1L | MAPK1IP1L | 6358 | 0.019 | 0.25 | NO |
160 | SAMD4A | SAMD4A | SAMD4A | 6364 | 0.019 | 0.25 | NO |
161 | RSAD1 | RSAD1 | RSAD1 | 6435 | 0.017 | 0.25 | NO |
162 | PSMC3IP | PSMC3IP | PSMC3IP | 6444 | 0.017 | 0.25 | NO |
163 | DERL1 | DERL1 | DERL1 | 6457 | 0.017 | 0.25 | NO |
164 | ARHGAP35 | ARHGAP35 | ARHGAP35 | 6647 | 0.013 | 0.24 | NO |
165 | KPNB1 | KPNB1 | KPNB1 | 6690 | 0.012 | 0.24 | NO |
166 | EZH1 | EZH1 | EZH1 | 6812 | 0.01 | 0.23 | NO |
167 | EPN3 | EPN3 | EPN3 | 6859 | 0.0085 | 0.23 | NO |
168 | WDYHV1 | WDYHV1 | WDYHV1 | 6899 | 0.0075 | 0.23 | NO |
169 | YTHDF1 | YTHDF1 | YTHDF1 | 7044 | 0.0044 | 0.22 | NO |
170 | CABYR | CABYR | CABYR | 7101 | 0.0033 | 0.22 | NO |
171 | KRT10 | KRT10 | KRT10 | 7105 | 0.0032 | 0.22 | NO |
172 | ATP5E | ATP5E | ATP5E | 7144 | 0.0026 | 0.21 | NO |
173 | BECN1 | BECN1 | BECN1 | 7173 | 0.0021 | 0.21 | NO |
174 | BMP4 | BMP4 | BMP4 | 7199 | 0.0015 | 0.21 | NO |
175 | TCFL5 | TCFL5 | TCFL5 | 7205 | 0.0014 | 0.21 | NO |
176 | TPM2 | TPM2 | TPM2 | 7219 | 0.00097 | 0.21 | NO |
177 | UCKL1 | UCKL1 | UCKL1 | 7325 | -0.0014 | 0.2 | NO |
178 | CBLL1 | CBLL1 | CBLL1 | 7330 | -0.0015 | 0.2 | NO |
179 | NSF | NSF | NSF | 7352 | -0.002 | 0.2 | NO |
180 | TAF4 | TAF4 | TAF4 | 7365 | -0.0022 | 0.2 | NO |
181 | ASH2L | ASH2L | ASH2L | 7395 | -0.003 | 0.2 | NO |
182 | NPC1 | NPC1 | NPC1 | 7483 | -0.0047 | 0.2 | NO |
183 | PPP1R3D | PPP1R3D | PPP1R3D | 7549 | -0.006 | 0.19 | NO |
184 | MYC | MYC | MYC | 7768 | -0.011 | 0.18 | NO |
185 | C18orf8 | C18orf8 | C18orf8 | 7805 | -0.011 | 0.18 | NO |
186 | SYPL1 | SYPL1 | SYPL1 | 7875 | -0.013 | 0.18 | NO |
187 | PPP1R13L | PPP1R13L | PPP1R13L | 7893 | -0.013 | 0.18 | NO |
188 | NBR1 | NBR1 | NBR1 | 7916 | -0.014 | 0.18 | NO |
189 | ANKRD40 | ANKRD40 | ANKRD40 | 7966 | -0.015 | 0.17 | NO |
190 | UTP18 | UTP18 | UTP18 | 8014 | -0.016 | 0.17 | NO |
191 | ATXN7L1 | ATXN7L1 | ATXN7L1 | 8059 | -0.017 | 0.17 | NO |
192 | DKKL1 | DKKL1 | DKKL1 | 8092 | -0.018 | 0.17 | NO |
193 | LSM1 | LSM1 | LSM1 | 8184 | -0.02 | 0.16 | NO |
194 | PSMA7 | PSMA7 | PSMA7 | 8289 | -0.022 | 0.16 | NO |
195 | DLD | DLD | DLD | 8443 | -0.025 | 0.15 | NO |
196 | WDR3 | WDR3 | WDR3 | 8464 | -0.025 | 0.15 | NO |
197 | ZNF623 | ZNF623 | ZNF623 | 8491 | -0.026 | 0.15 | NO |
198 | PTK2 | PTK2 | PTK2 | 8513 | -0.026 | 0.15 | NO |
199 | ACTR10 | ACTR10 | ACTR10 | 8585 | -0.028 | 0.15 | NO |
200 | LMTK2 | LMTK2 | LMTK2 | 8774 | -0.032 | 0.14 | NO |
201 | CMAS | CMAS | CMAS | 8860 | -0.034 | 0.14 | NO |
202 | OSBPL2 | OSBPL2 | OSBPL2 | 8893 | -0.034 | 0.14 | NO |
203 | WHSC1L1 | WHSC1L1 | WHSC1L1 | 8969 | -0.036 | 0.13 | NO |
204 | CRCP | CRCP | CRCP | 8996 | -0.036 | 0.13 | NO |
205 | ZNF460 | ZNF460 | ZNF460 | 9023 | -0.037 | 0.13 | NO |
206 | SMARCE1 | SMARCE1 | SMARCE1 | 9174 | -0.041 | 0.13 | NO |
207 | KIAA0196 | KIAA0196 | KIAA0196 | 9179 | -0.041 | 0.13 | NO |
208 | ZNF134 | ZNF134 | ZNF134 | 9182 | -0.041 | 0.13 | NO |
209 | BET1 | BET1 | BET1 | 9219 | -0.042 | 0.13 | NO |
210 | ACSF2 | ACSF2 | ACSF2 | 9266 | -0.042 | 0.13 | NO |
211 | CBX1 | CBX1 | CBX1 | 9332 | -0.044 | 0.13 | NO |
212 | ZNF264 | ZNF264 | ZNF264 | 9363 | -0.045 | 0.13 | NO |
213 | ZKSCAN5 | ZKSCAN5 | ZKSCAN5 | 9416 | -0.046 | 0.13 | NO |
214 | RNF139 | RNF139 | RNF139 | 9441 | -0.047 | 0.13 | NO |
215 | DLGAP5 | DLGAP5 | DLGAP5 | 9486 | -0.048 | 0.13 | NO |
216 | NPEPPS | NPEPPS | NPEPPS | 9530 | -0.049 | 0.13 | NO |
217 | EAPP | EAPP | EAPP | 9582 | -0.05 | 0.13 | NO |
218 | OSBPL1A | OSBPL1A | OSBPL1A | 9626 | -0.051 | 0.12 | NO |
219 | MTAP | MTAP | MTAP | 9667 | -0.052 | 0.12 | NO |
220 | COX11 | COX11 | COX11 | 9779 | -0.054 | 0.12 | NO |
221 | CDC27 | CDC27 | CDC27 | 9811 | -0.055 | 0.12 | NO |
222 | GPATCH8 | GPATCH8 | GPATCH8 | 9834 | -0.056 | 0.12 | NO |
223 | RNF38 | RNF38 | RNF38 | 9949 | -0.058 | 0.12 | NO |
224 | ZNF652 | ZNF652 | ZNF652 | 10025 | -0.059 | 0.12 | NO |
225 | KCTD7 | KCTD7 | KCTD7 | 10053 | -0.06 | 0.12 | NO |
226 | PRKCH | PRKCH | PRKCH | 10190 | -0.063 | 0.11 | NO |
227 | NUBPL | NUBPL | NUBPL | 10340 | -0.066 | 0.11 | NO |
228 | MRPL13 | MRPL13 | MRPL13 | 10412 | -0.068 | 0.11 | NO |
229 | NPAS3 | NPAS3 | NPAS3 | 10414 | -0.068 | 0.11 | NO |
230 | C5AR1 | C5AR1 | C5AR1 | 10565 | -0.072 | 0.1 | NO |
231 | SPOP | SPOP | SPOP | 10570 | -0.072 | 0.11 | NO |
232 | PARP4 | PARP4 | PARP4 | 10589 | -0.072 | 0.11 | NO |
233 | ASNS | ASNS | ASNS | 10685 | -0.074 | 0.11 | NO |
234 | SPAG9 | SPAG9 | SPAG9 | 10708 | -0.074 | 0.11 | NO |
235 | MPP3 | MPP3 | MPP3 | 10715 | -0.075 | 0.11 | NO |
236 | FAM49B | FAM49B | FAM49B | 10725 | -0.075 | 0.12 | NO |
237 | AP4S1 | AP4S1 | AP4S1 | 10825 | -0.077 | 0.11 | NO |
238 | DDHD2 | DDHD2 | DDHD2 | 10891 | -0.079 | 0.11 | NO |
239 | ACN9 | ACN9 | ACN9 | 10893 | -0.079 | 0.12 | NO |
240 | UPF3A | UPF3A | UPF3A | 10941 | -0.08 | 0.12 | NO |
241 | PON2 | PON2 | PON2 | 10962 | -0.081 | 0.12 | NO |
242 | FBXO34 | FBXO34 | FBXO34 | 11286 | -0.088 | 0.11 | NO |
243 | ZNF146 | ZNF146 | ZNF146 | 11374 | -0.09 | 0.1 | NO |
244 | ZNF304 | ZNF304 | ZNF304 | 11482 | -0.092 | 0.1 | NO |
245 | SCFD1 | SCFD1 | SCFD1 | 11943 | -0.1 | 0.082 | NO |
246 | ARHGAP5 | ARHGAP5 | ARHGAP5 | 12042 | -0.11 | 0.081 | NO |
247 | CASD1 | CASD1 | CASD1 | 12054 | -0.11 | 0.085 | NO |
248 | RIOK3 | RIOK3 | RIOK3 | 12224 | -0.11 | 0.08 | NO |
249 | HIF1A | HIF1A | HIF1A | 12267 | -0.11 | 0.083 | NO |
250 | WDHD1 | WDHD1 | WDHD1 | 12341 | -0.11 | 0.084 | NO |
251 | ZNF211 | ZNF211 | ZNF211 | 12349 | -0.11 | 0.088 | NO |
252 | SLMO2 | SLMO2 | SLMO2 | 12441 | -0.12 | 0.088 | NO |
253 | BAG4 | BAG4 | BAG4 | 12503 | -0.12 | 0.09 | NO |
254 | ZNF573 | ZNF573 | ZNF573 | 12681 | -0.12 | 0.085 | NO |
255 | SNX6 | SNX6 | SNX6 | 12701 | -0.12 | 0.09 | NO |
256 | TAF2 | TAF2 | TAF2 | 13139 | -0.13 | 0.071 | NO |
257 | RASA4 | RASA4 | RASA4 | 13187 | -0.14 | 0.074 | NO |
258 | SS18L1 | SS18L1 | SS18L1 | 13273 | -0.14 | 0.075 | NO |
259 | PDK4 | PDK4 | PDK4 | 13448 | -0.14 | 0.072 | NO |
260 | TTF2 | TTF2 | TTF2 | 13519 | -0.15 | 0.074 | NO |
261 | MTMR6 | MTMR6 | MTMR6 | 13524 | -0.15 | 0.08 | NO |
262 | DOCK4 | DOCK4 | DOCK4 | 13644 | -0.15 | 0.08 | NO |
263 | SNAPC1 | SNAPC1 | SNAPC1 | 13797 | -0.16 | 0.079 | NO |
264 | PON3 | PON3 | PON3 | 13855 | -0.16 | 0.082 | NO |
265 | PHF20L1 | PHF20L1 | PHF20L1 | 13885 | -0.16 | 0.088 | NO |
266 | ZNF419 | ZNF419 | ZNF419 | 13912 | -0.16 | 0.093 | NO |
267 | EXOC5 | EXOC5 | EXOC5 | 13959 | -0.16 | 0.098 | NO |
268 | HAS2 | HAS2 | HAS2 | 14039 | -0.16 | 0.1 | NO |
269 | RNF6 | RNF6 | RNF6 | 14131 | -0.17 | 0.1 | NO |
270 | ZNF331 | ZNF331 | ZNF331 | 14155 | -0.17 | 0.11 | NO |
271 | LUC7L3 | LUC7L3 | LUC7L3 | 14534 | -0.18 | 0.095 | NO |
272 | HLF | HLF | HLF | 14792 | -0.19 | 0.089 | NO |
273 | AOC2 | AOC2 | AOC2 | 14877 | -0.2 | 0.093 | NO |
274 | KTN1 | KTN1 | KTN1 | 15048 | -0.2 | 0.092 | NO |
275 | ZBTB1 | ZBTB1 | ZBTB1 | 15100 | -0.21 | 0.099 | NO |
276 | CYP3A5 | CYP3A5 | CYP3A5 | 15847 | -0.25 | 0.068 | NO |
277 | SLC26A4 | SLC26A4 | SLC26A4 | 15955 | -0.26 | 0.073 | NO |
278 | KLK13 | KLK13 | KLK13 | 16688 | -0.32 | 0.046 | NO |
279 | GIPR | GIPR | GIPR | 16970 | -0.36 | 0.046 | NO |
280 | ANXA13 | ANXA13 | ANXA13 | 17101 | -0.38 | 0.055 | NO |
Figure S77. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: PENG GLUTAMINE DEPRIVATION DN.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: PENG GLUTAMINE DEPRIVATION DN, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S40. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | EHD2 | EHD2 | EHD2 | 434 | 0.17 | 0.032 | YES |
2 | G6PC3 | G6PC3 | G6PC3 | 451 | 0.16 | 0.086 | YES |
3 | PCDHGC3 | PCDHGC3 | PCDHGC3 | 527 | 0.16 | 0.13 | YES |
4 | ANPEP | ANPEP | ANPEP | 831 | 0.14 | 0.16 | YES |
5 | PPAP2C | PPAP2C | PPAP2C | 1005 | 0.13 | 0.2 | YES |
6 | INO80B | INO80B | INO80B | 1141 | 0.13 | 0.23 | YES |
7 | H2AFX | H2AFX | H2AFX | 1449 | 0.12 | 0.25 | YES |
8 | MYL9 | MYL9 | MYL9 | 1637 | 0.11 | 0.28 | YES |
9 | FJX1 | FJX1 | FJX1 | 1905 | 0.1 | 0.3 | YES |
10 | KDELR1 | KDELR1 | KDELR1 | 1933 | 0.1 | 0.34 | YES |
11 | ST6GALNAC4 | ST6GALNAC4 | ST6GALNAC4 | 2061 | 0.1 | 0.36 | YES |
12 | WNT5B | WNT5B | WNT5B | 2153 | 0.1 | 0.39 | YES |
13 | GEMIN4 | GEMIN4 | GEMIN4 | 2385 | 0.095 | 0.41 | YES |
14 | FAM127A | FAM127A | FAM127A | 2767 | 0.088 | 0.42 | YES |
15 | UBTF | UBTF | UBTF | 3297 | 0.077 | 0.41 | YES |
16 | TOMM22 | TOMM22 | TOMM22 | 3373 | 0.075 | 0.44 | YES |
17 | SERPINH1 | SERPINH1 | SERPINH1 | 3409 | 0.075 | 0.46 | YES |
18 | SYNGR2 | SYNGR2 | SYNGR2 | 3428 | 0.074 | 0.48 | YES |
19 | DDT | DDT | DDT | 3853 | 0.066 | 0.48 | YES |
20 | HMGB3 | HMGB3 | HMGB3 | 3921 | 0.065 | 0.5 | YES |
21 | FEN1 | FEN1 | FEN1 | 3985 | 0.064 | 0.52 | YES |
22 | AP1S1 | AP1S1 | AP1S1 | 3987 | 0.064 | 0.54 | YES |
23 | LOXL1 | LOXL1 | LOXL1 | 4002 | 0.064 | 0.56 | YES |
24 | PRR16 | PRR16 | PRR16 | 4475 | 0.054 | 0.55 | YES |
25 | TMEM97 | TMEM97 | TMEM97 | 4555 | 0.053 | 0.56 | YES |
26 | GM2A | GM2A | GM2A | 4927 | 0.046 | 0.56 | YES |
27 | CBX6 | CBX6 | CBX6 | 5014 | 0.045 | 0.57 | YES |
28 | SV2A | SV2A | SV2A | 5061 | 0.044 | 0.58 | YES |
29 | ANP32A | ANP32A | ANP32A | 5126 | 0.043 | 0.59 | YES |
30 | CKAP4 | CKAP4 | CKAP4 | 5152 | 0.042 | 0.6 | YES |
31 | GLG1 | GLG1 | GLG1 | 5198 | 0.041 | 0.62 | YES |
32 | LPCAT1 | LPCAT1 | LPCAT1 | 5675 | 0.032 | 0.6 | NO |
33 | SLC29A1 | SLC29A1 | SLC29A1 | 6063 | 0.024 | 0.59 | NO |
34 | FZD2 | FZD2 | FZD2 | 6344 | 0.019 | 0.58 | NO |
35 | AKAP1 | AKAP1 | AKAP1 | 7377 | -0.0024 | 0.52 | NO |
36 | MAT2A | MAT2A | MAT2A | 8097 | -0.018 | 0.49 | NO |
37 | SKP2 | SKP2 | SKP2 | 11626 | -0.096 | 0.32 | NO |
38 | MARCKS | MARCKS | MARCKS | 11744 | -0.098 | 0.35 | NO |
Figure S79. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: FAELT B CLL WITH VH3 21 UP.

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: FAELT B CLL WITH VH3 21 UP, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 7. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG PROTEASOME | 44 | genes.ES.table | 0.54 | 1.6 | 0.028 | 0.19 | 0.97 | 0.34 | 0.27 | 0.25 | 0.1 | 0.021 |
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION | 236 | genes.ES.table | 0.74 | 1.7 | 0 | 0.23 | 0.93 | 0.51 | 0.12 | 0.46 | 0.1 | 0.037 |
KEGG CHEMOKINE SIGNALING PATHWAY | 184 | genes.ES.table | 0.65 | 1.6 | 0.0041 | 0.19 | 0.98 | 0.32 | 0.11 | 0.28 | 0.1 | 0.02 |
KEGG APOPTOSIS | 84 | genes.ES.table | 0.54 | 1.7 | 0.0039 | 0.25 | 0.9 | 0.27 | 0.18 | 0.22 | 0.11 | 0.041 |
KEGG CELL ADHESION MOLECULES CAMS | 128 | genes.ES.table | 0.65 | 1.5 | 0.0038 | 0.2 | 1 | 0.49 | 0.18 | 0.41 | 0.13 | 0.014 |
KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY | 60 | genes.ES.table | 0.63 | 1.6 | 0.027 | 0.19 | 1 | 0.28 | 0.066 | 0.26 | 0.11 | 0.014 |
KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY | 58 | genes.ES.table | 0.55 | 1.7 | 0.018 | 0.21 | 0.96 | 0.34 | 0.24 | 0.26 | 0.11 | 0.028 |
KEGG JAK STAT SIGNALING PATHWAY | 131 | genes.ES.table | 0.63 | 1.7 | 0 | 0.22 | 0.96 | 0.37 | 0.13 | 0.33 | 0.11 | 0.034 |
KEGG HEMATOPOIETIC CELL LINEAGE | 83 | genes.ES.table | 0.78 | 1.6 | 0 | 0.19 | 0.98 | 0.66 | 0.14 | 0.57 | 0.1 | 0.02 |
KEGG B CELL RECEPTOR SIGNALING PATHWAY | 74 | genes.ES.table | 0.55 | 1.7 | 0.02 | 0.23 | 0.9 | 0.32 | 0.18 | 0.27 | 0.098 | 0.036 |
Table S41. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PSMA1 | PSMA1 | PSMA1 | 48 | 1 | 0.077 | YES |
2 | RASGRP1 | RASGRP1 | RASGRP1 | 202 | 0.75 | 0.13 | YES |
3 | PSMB9 | PSMB9 | PSMB9 | 463 | 0.57 | 0.16 | YES |
4 | CD79A | CD79A | CD79A | 827 | 0.45 | 0.17 | YES |
5 | VAV1 | VAV1 | VAV1 | 843 | 0.44 | 0.21 | YES |
6 | BLNK | BLNK | BLNK | 907 | 0.43 | 0.24 | YES |
7 | PSMA2 | PSMA2 | PSMA2 | 1121 | 0.39 | 0.26 | YES |
8 | PIK3AP1 | PIK3AP1 | PIK3AP1 | 1402 | 0.34 | 0.27 | YES |
9 | ITPR2 | ITPR2 | ITPR2 | 1523 | 0.33 | 0.29 | YES |
10 | CARD11 | CARD11 | CARD11 | 1571 | 0.32 | 0.31 | YES |
11 | BLK | BLK | BLK | 1774 | 0.3 | 0.32 | YES |
12 | PSMB8 | PSMB8 | PSMB8 | 1900 | 0.28 | 0.34 | YES |
13 | BTK | BTK | BTK | 1985 | 0.27 | 0.35 | YES |
14 | PRKCB | PRKCB | PRKCB | 2506 | 0.22 | 0.34 | YES |
15 | CD19 | CD19 | CD19 | 2561 | 0.21 | 0.36 | YES |
16 | PSMB10 | PSMB10 | PSMB10 | 2806 | 0.19 | 0.36 | YES |
17 | SYK | SYK | SYK | 2950 | 0.18 | 0.36 | YES |
18 | MDM2 | MDM2 | MDM2 | 3085 | 0.18 | 0.37 | YES |
19 | PSME2 | PSME2 | PSME2 | 3309 | 0.16 | 0.37 | YES |
20 | LYN | LYN | LYN | 3311 | 0.16 | 0.38 | YES |
21 | CD79B | CD79B | CD79B | 3740 | 0.14 | 0.37 | YES |
22 | PSMA3 | PSMA3 | PSMA3 | 3757 | 0.14 | 0.38 | YES |
23 | PSMA4 | PSMA4 | PSMA4 | 3809 | 0.14 | 0.39 | YES |
24 | RICTOR | RICTOR | RICTOR | 3827 | 0.14 | 0.4 | YES |
25 | PSME4 | PSME4 | PSME4 | 3830 | 0.14 | 0.41 | YES |
26 | BCL10 | BCL10 | BCL10 | 3960 | 0.13 | 0.41 | YES |
27 | PLCG2 | PLCG2 | PLCG2 | 4066 | 0.13 | 0.42 | YES |
28 | PSMD14 | PSMD14 | PSMD14 | 4117 | 0.12 | 0.42 | YES |
29 | CDKN1A | CDKN1A | CDKN1A | 4411 | 0.11 | 0.42 | YES |
30 | PSMA5 | PSMA5 | PSMA5 | 4534 | 0.11 | 0.42 | YES |
31 | PSMA6 | PSMA6 | PSMA6 | 4713 | 0.1 | 0.42 | YES |
32 | PSME1 | PSME1 | PSME1 | 4764 | 0.1 | 0.42 | YES |
33 | PSMC6 | PSMC6 | PSMC6 | 4926 | 0.096 | 0.42 | YES |
34 | CREB1 | CREB1 | CREB1 | 4987 | 0.095 | 0.42 | YES |
35 | MALT1 | MALT1 | MALT1 | 5195 | 0.089 | 0.42 | YES |
36 | KRAS | KRAS | KRAS | 5250 | 0.087 | 0.42 | YES |
37 | SH3KBP1 | SH3KBP1 | SH3KBP1 | 5254 | 0.087 | 0.43 | YES |
38 | NFKBIA | NFKBIA | NFKBIA | 5278 | 0.086 | 0.44 | YES |
39 | MAP3K7 | MAP3K7 | MAP3K7 | 5345 | 0.085 | 0.44 | YES |
40 | SOS1 | SOS1 | SOS1 | 5572 | 0.079 | 0.43 | YES |
41 | PIK3R1 | PIK3R1 | PIK3R1 | 5635 | 0.078 | 0.44 | YES |
42 | PSMD12 | PSMD12 | PSMD12 | 5705 | 0.076 | 0.44 | YES |
43 | CHUK | CHUK | CHUK | 5716 | 0.076 | 0.44 | YES |
44 | NRAS | NRAS | NRAS | 5741 | 0.075 | 0.45 | YES |
45 | CDKN1B | CDKN1B | CDKN1B | 6180 | 0.066 | 0.43 | NO |
46 | CUL1 | CUL1 | CUL1 | 6182 | 0.066 | 0.44 | NO |
47 | PSMA7 | PSMA7 | PSMA7 | 6580 | 0.057 | 0.42 | NO |
48 | NCK1 | NCK1 | NCK1 | 6636 | 0.056 | 0.42 | NO |
49 | PSMD7 | PSMD7 | PSMD7 | 6717 | 0.054 | 0.42 | NO |
50 | PSMB2 | PSMB2 | PSMB2 | 6742 | 0.054 | 0.42 | NO |
51 | CALM1 | CALM1 | CALM1 | 6897 | 0.051 | 0.42 | NO |
52 | PSMC2 | PSMC2 | PSMC2 | 6949 | 0.05 | 0.42 | NO |
53 | ITPR3 | ITPR3 | ITPR3 | 6950 | 0.05 | 0.42 | NO |
54 | CALM2 | CALM2 | CALM2 | 6990 | 0.049 | 0.42 | NO |
55 | PTEN | PTEN | PTEN | 7167 | 0.046 | 0.42 | NO |
56 | PSMC1 | PSMC1 | PSMC1 | 7331 | 0.043 | 0.41 | NO |
57 | ORAI1 | ORAI1 | ORAI1 | 7476 | 0.04 | 0.41 | NO |
58 | REL | REL | REL | 7712 | 0.036 | 0.4 | NO |
59 | MTOR | MTOR | MTOR | 7906 | 0.032 | 0.39 | NO |
60 | PSMD5 | PSMD5 | PSMD5 | 7928 | 0.032 | 0.39 | NO |
61 | SHC1 | SHC1 | SHC1 | 8213 | 0.027 | 0.38 | NO |
62 | PSMB3 | PSMB3 | PSMB3 | 8251 | 0.026 | 0.38 | NO |
63 | PSMB1 | PSMB1 | PSMB1 | 8257 | 0.026 | 0.38 | NO |
64 | CBLB | CBLB | CBLB | 8315 | 0.026 | 0.38 | NO |
65 | NFKBIE | NFKBIE | NFKBIE | 8333 | 0.025 | 0.38 | NO |
66 | PSMD11 | PSMD11 | PSMD11 | 8401 | 0.024 | 0.38 | NO |
67 | PSMD10 | PSMD10 | PSMD10 | 8914 | 0.016 | 0.35 | NO |
68 | GRB2 | GRB2 | GRB2 | 9080 | 0.013 | 0.34 | NO |
69 | PSMA8 | PSMA8 | PSMA8 | 9540 | 0.007 | 0.32 | NO |
70 | STIM1 | STIM1 | STIM1 | 9622 | 0.0057 | 0.31 | NO |
71 | PDPK1 | PDPK1 | PDPK1 | 9634 | 0.0054 | 0.31 | NO |
72 | SKP1 | SKP1 | SKP1 | 9662 | 0.005 | 0.31 | NO |
73 | PSMC4 | PSMC4 | PSMC4 | 9796 | 0.0029 | 0.3 | NO |
74 | PSMD1 | PSMD1 | PSMD1 | 9820 | 0.0026 | 0.3 | NO |
75 | NFKBIB | NFKBIB | NFKBIB | 9852 | 0.0021 | 0.3 | NO |
76 | PSMC3 | PSMC3 | PSMC3 | 9891 | 0.0015 | 0.3 | NO |
77 | PIK3CD | PIK3CD | PIK3CD | 10253 | -0.0038 | 0.28 | NO |
78 | PSMD13 | PSMD13 | PSMD13 | 10277 | -0.0043 | 0.28 | NO |
79 | PSMC5 | PSMC5 | PSMC5 | 10429 | -0.0064 | 0.27 | NO |
80 | PSMB6 | PSMB6 | PSMB6 | 10559 | -0.0085 | 0.26 | NO |
81 | PSMD3 | PSMD3 | PSMD3 | 10590 | -0.0091 | 0.26 | NO |
82 | AKT3 | AKT3 | AKT3 | 10665 | -0.01 | 0.26 | NO |
83 | PSMB7 | PSMB7 | PSMB7 | 10709 | -0.011 | 0.26 | NO |
84 | CBL | CBL | CBL | 10752 | -0.012 | 0.26 | NO |
85 | RASGRP3 | RASGRP3 | RASGRP3 | 10912 | -0.013 | 0.25 | NO |
86 | PSMD8 | PSMD8 | PSMD8 | 11103 | -0.016 | 0.24 | NO |
87 | PSMB4 | PSMB4 | PSMB4 | 11164 | -0.017 | 0.24 | NO |
88 | FBXW11 | FBXW11 | FBXW11 | 11172 | -0.017 | 0.24 | NO |
89 | IKBKB | IKBKB | IKBKB | 11311 | -0.019 | 0.23 | NO |
90 | PSMB5 | PSMB5 | PSMB5 | 11414 | -0.02 | 0.23 | NO |
91 | CASP9 | CASP9 | CASP9 | 11514 | -0.021 | 0.22 | NO |
92 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 11527 | -0.022 | 0.22 | NO |
93 | THEM4 | THEM4 | THEM4 | 11813 | -0.026 | 0.21 | NO |
94 | PSMD4 | PSMD4 | PSMD4 | 12032 | -0.029 | 0.2 | NO |
95 | PSMD9 | PSMD9 | PSMD9 | 12076 | -0.03 | 0.2 | NO |
96 | BTRC | BTRC | BTRC | 12089 | -0.03 | 0.2 | NO |
97 | PLCG1 | PLCG1 | PLCG1 | 12268 | -0.032 | 0.2 | NO |
98 | PSMD6 | PSMD6 | PSMD6 | 12416 | -0.035 | 0.19 | NO |
99 | IKBKG | IKBKG | IKBKG | 12564 | -0.037 | 0.18 | NO |
100 | FOXO4 | FOXO4 | FOXO4 | 12784 | -0.041 | 0.18 | NO |
101 | BAD | BAD | BAD | 12966 | -0.044 | 0.17 | NO |
102 | PHLPP1 | PHLPP1 | PHLPP1 | 13022 | -0.044 | 0.17 | NO |
103 | HRAS | HRAS | HRAS | 13052 | -0.045 | 0.17 | NO |
104 | CALM3 | CALM3 | CALM3 | 13185 | -0.047 | 0.17 | NO |
105 | MLST8 | MLST8 | MLST8 | 13868 | -0.058 | 0.14 | NO |
106 | GSK3A | GSK3A | GSK3A | 13892 | -0.059 | 0.14 | NO |
107 | AKT1S1 | AKT1S1 | AKT1S1 | 14088 | -0.062 | 0.13 | NO |
108 | FYN | FYN | FYN | 14091 | -0.062 | 0.14 | NO |
109 | FOXO1 | FOXO1 | FOXO1 | 14202 | -0.064 | 0.14 | NO |
110 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 14302 | -0.066 | 0.14 | NO |
111 | AKT2 | AKT2 | AKT2 | 14395 | -0.067 | 0.14 | NO |
112 | AKT1 | AKT1 | AKT1 | 14488 | -0.069 | 0.14 | NO |
113 | PSMD2 | PSMD2 | PSMD2 | 14824 | -0.076 | 0.12 | NO |
114 | TSC2 | TSC2 | TSC2 | 14943 | -0.079 | 0.12 | NO |
115 | PSMF1 | PSMF1 | PSMF1 | 15085 | -0.082 | 0.12 | NO |
116 | NR4A1 | NR4A1 | NR4A1 | 15125 | -0.084 | 0.13 | NO |
117 | TRIB3 | TRIB3 | TRIB3 | 15304 | -0.088 | 0.12 | NO |
118 | RELA | RELA | RELA | 15341 | -0.09 | 0.13 | NO |
119 | RPS27A | RPS27A | RPS27A | 15344 | -0.09 | 0.14 | NO |
120 | FOXO3 | FOXO3 | FOXO3 | 15765 | -0.1 | 0.12 | NO |
121 | UBA52 | UBA52 | UBA52 | 16002 | -0.11 | 0.12 | NO |
Figure S81. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG PROTEASOME.

Figure S82. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PROTEASOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S42. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | RHOH | RHOH | RHOH | 97 | 0.88 | 0.037 | YES |
2 | PTPN22 | PTPN22 | PTPN22 | 126 | 0.84 | 0.077 | YES |
3 | PTPN7 | PTPN7 | PTPN7 | 181 | 0.78 | 0.11 | YES |
4 | PTPRC | PTPRC | PTPRC | 204 | 0.75 | 0.15 | YES |
5 | SAMSN1 | SAMSN1 | SAMSN1 | 226 | 0.73 | 0.18 | YES |
6 | PIK3CG | PIK3CG | PIK3CG | 323 | 0.65 | 0.21 | YES |
7 | LRMP | LRMP | LRMP | 339 | 0.64 | 0.24 | YES |
8 | NKG7 | NKG7 | NKG7 | 386 | 0.61 | 0.26 | YES |
9 | BIN2 | BIN2 | BIN2 | 507 | 0.55 | 0.29 | YES |
10 | IKZF1 | IKZF1 | IKZF1 | 508 | 0.55 | 0.31 | YES |
11 | MYB | MYB | MYB | 588 | 0.52 | 0.33 | YES |
12 | SLA | SLA | SLA | 592 | 0.52 | 0.36 | YES |
13 | NCKAP1L | NCKAP1L | NCKAP1L | 819 | 0.45 | 0.37 | YES |
14 | CORO1A | CORO1A | CORO1A | 846 | 0.44 | 0.39 | YES |
15 | CD53 | CD53 | CD53 | 975 | 0.42 | 0.4 | YES |
16 | INPP5D | INPP5D | INPP5D | 1187 | 0.38 | 0.41 | YES |
17 | ARHGAP15 | ARHGAP15 | ARHGAP15 | 1200 | 0.38 | 0.42 | YES |
18 | HCLS1 | HCLS1 | HCLS1 | 1211 | 0.37 | 0.44 | YES |
19 | RAC2 | RAC2 | RAC2 | 1427 | 0.34 | 0.45 | YES |
20 | GMFG | GMFG | GMFG | 1456 | 0.33 | 0.46 | YES |
21 | SELPLG | SELPLG | SELPLG | 1480 | 0.33 | 0.48 | YES |
22 | ATP2A3 | ATP2A3 | ATP2A3 | 2512 | 0.22 | 0.43 | NO |
23 | ARHGAP29 | ARHGAP29 | ARHGAP29 | 2518 | 0.22 | 0.44 | NO |
24 | KIF21B | KIF21B | KIF21B | 2654 | 0.21 | 0.44 | NO |
25 | ARHGAP4 | ARHGAP4 | ARHGAP4 | 3213 | 0.17 | 0.42 | NO |
26 | WWTR1 | WWTR1 | WWTR1 | 3253 | 0.17 | 0.43 | NO |
27 | STIL | STIL | STIL | 3505 | 0.15 | 0.42 | NO |
28 | MYOF | MYOF | MYOF | 3818 | 0.14 | 0.41 | NO |
29 | NASP | NASP | NASP | 3912 | 0.13 | 0.41 | NO |
30 | CD93 | CD93 | CD93 | 4082 | 0.12 | 0.41 | NO |
31 | FZD7 | FZD7 | FZD7 | 4092 | 0.12 | 0.41 | NO |
32 | HMHA1 | HMHA1 | HMHA1 | 4236 | 0.12 | 0.41 | NO |
33 | DEF6 | DEF6 | DEF6 | 4293 | 0.12 | 0.41 | NO |
34 | TNFRSF12A | TNFRSF12A | TNFRSF12A | 4336 | 0.12 | 0.42 | NO |
35 | SCAF11 | SCAF11 | SCAF11 | 4564 | 0.11 | 0.41 | NO |
36 | CAPRIN2 | CAPRIN2 | CAPRIN2 | 4579 | 0.11 | 0.41 | NO |
37 | PLCD4 | PLCD4 | PLCD4 | 4830 | 0.099 | 0.4 | NO |
38 | CNTRL | CNTRL | CNTRL | 4886 | 0.097 | 0.4 | NO |
39 | ELF1 | ELF1 | ELF1 | 4908 | 0.097 | 0.41 | NO |
40 | FAM114A1 | FAM114A1 | FAM114A1 | 4978 | 0.095 | 0.41 | NO |
41 | TMPO | TMPO | TMPO | 5002 | 0.094 | 0.41 | NO |
42 | ITGAV | ITGAV | ITGAV | 5025 | 0.094 | 0.42 | NO |
43 | TPP2 | TPP2 | TPP2 | 5294 | 0.086 | 0.4 | NO |
44 | TRIM14 | TRIM14 | TRIM14 | 5481 | 0.081 | 0.4 | NO |
45 | CALD1 | CALD1 | CALD1 | 5521 | 0.08 | 0.4 | NO |
46 | YIPF6 | YIPF6 | YIPF6 | 6013 | 0.069 | 0.38 | NO |
47 | USP14 | USP14 | USP14 | 6146 | 0.066 | 0.37 | NO |
48 | TAF4B | TAF4B | TAF4B | 6191 | 0.065 | 0.37 | NO |
49 | LAMB1 | LAMB1 | LAMB1 | 6224 | 0.065 | 0.37 | NO |
50 | PDSS1 | PDSS1 | PDSS1 | 6238 | 0.064 | 0.38 | NO |
51 | INTS7 | INTS7 | INTS7 | 6413 | 0.06 | 0.37 | NO |
52 | CAMSAP2 | CAMSAP2 | CAMSAP2 | 6561 | 0.058 | 0.36 | NO |
53 | LINS | LINS | LINS | 6566 | 0.058 | 0.37 | NO |
54 | OTUD4 | OTUD4 | OTUD4 | 6644 | 0.056 | 0.37 | NO |
55 | RBFOX2 | RBFOX2 | RBFOX2 | 6699 | 0.055 | 0.36 | NO |
56 | DOCK1 | DOCK1 | DOCK1 | 6842 | 0.052 | 0.36 | NO |
57 | ZNF200 | ZNF200 | ZNF200 | 6963 | 0.05 | 0.36 | NO |
58 | ZFHX3 | ZFHX3 | ZFHX3 | 7293 | 0.044 | 0.34 | NO |
59 | S100A13 | S100A13 | S100A13 | 7463 | 0.041 | 0.33 | NO |
60 | ZBTB33 | ZBTB33 | ZBTB33 | 7582 | 0.039 | 0.33 | NO |
61 | LAPTM4B | LAPTM4B | LAPTM4B | 7669 | 0.037 | 0.32 | NO |
62 | RNASEH2B | RNASEH2B | RNASEH2B | 7742 | 0.035 | 0.32 | NO |
63 | PTK2B | PTK2B | PTK2B | 7798 | 0.034 | 0.32 | NO |
64 | SNRPG | SNRPG | SNRPG | 7843 | 0.033 | 0.32 | NO |
65 | SRSF1 | SRSF1 | SRSF1 | 7892 | 0.032 | 0.32 | NO |
66 | ORC1 | ORC1 | ORC1 | 8006 | 0.03 | 0.31 | NO |
67 | S100A10 | S100A10 | S100A10 | 8067 | 0.029 | 0.31 | NO |
68 | PFN2 | PFN2 | PFN2 | 8441 | 0.024 | 0.29 | NO |
69 | RBBP4 | RBBP4 | RBBP4 | 8525 | 0.022 | 0.29 | NO |
70 | ULK2 | ULK2 | ULK2 | 8839 | 0.018 | 0.27 | NO |
71 | PLS3 | PLS3 | PLS3 | 8964 | 0.015 | 0.27 | NO |
72 | DIP2C | DIP2C | DIP2C | 8982 | 0.015 | 0.27 | NO |
73 | LAPTM4A | LAPTM4A | LAPTM4A | 9002 | 0.014 | 0.26 | NO |
74 | TMEM184B | TMEM184B | TMEM184B | 9198 | 0.012 | 0.26 | NO |
75 | C2orf43 | C2orf43 | C2orf43 | 9280 | 0.011 | 0.25 | NO |
76 | RHBDF1 | RHBDF1 | RHBDF1 | 9294 | 0.01 | 0.25 | NO |
77 | HIP1 | HIP1 | HIP1 | 9315 | 0.01 | 0.25 | NO |
78 | ANXA2 | ANXA2 | ANXA2 | 9385 | 0.0091 | 0.25 | NO |
79 | ADCY9 | ADCY9 | ADCY9 | 9509 | 0.0074 | 0.24 | NO |
80 | ZNF22 | ZNF22 | ZNF22 | 9569 | 0.0065 | 0.24 | NO |
81 | ZNF207 | ZNF207 | ZNF207 | 9628 | 0.0056 | 0.23 | NO |
82 | ENAH | ENAH | ENAH | 9800 | 0.0028 | 0.22 | NO |
83 | CTTN | CTTN | CTTN | 9893 | 0.0015 | 0.22 | NO |
84 | LAMC1 | LAMC1 | LAMC1 | 9921 | 0.001 | 0.22 | NO |
85 | CNN3 | CNN3 | CNN3 | 9970 | 0.00034 | 0.22 | NO |
86 | C9orf78 | C9orf78 | C9orf78 | 10106 | -0.0018 | 0.21 | NO |
87 | SMARCA1 | SMARCA1 | SMARCA1 | 10126 | -0.0021 | 0.21 | NO |
88 | DUT | DUT | DUT | 10146 | -0.0024 | 0.21 | NO |
89 | CCND1 | CCND1 | CCND1 | 10254 | -0.0038 | 0.2 | NO |
90 | POLR3E | POLR3E | POLR3E | 10348 | -0.0053 | 0.2 | NO |
91 | ELL | ELL | ELL | 10432 | -0.0065 | 0.19 | NO |
92 | PLK2 | PLK2 | PLK2 | 10492 | -0.0074 | 0.19 | NO |
93 | NFYA | NFYA | NFYA | 10513 | -0.0078 | 0.19 | NO |
94 | ITGB1BP1 | ITGB1BP1 | ITGB1BP1 | 10581 | -0.0089 | 0.18 | NO |
95 | PTMS | PTMS | PTMS | 10734 | -0.011 | 0.18 | NO |
96 | USP7 | USP7 | USP7 | 10966 | -0.014 | 0.16 | NO |
97 | MFSD11 | MFSD11 | MFSD11 | 11007 | -0.014 | 0.16 | NO |
98 | VAMP3 | VAMP3 | VAMP3 | 11078 | -0.015 | 0.16 | NO |
99 | LPPR2 | LPPR2 | LPPR2 | 11228 | -0.018 | 0.15 | NO |
100 | ANXA5 | ANXA5 | ANXA5 | 11233 | -0.018 | 0.15 | NO |
101 | LPP | LPP | LPP | 11345 | -0.019 | 0.15 | NO |
102 | GPC1 | GPC1 | GPC1 | 11468 | -0.021 | 0.14 | NO |
103 | ANP32A | ANP32A | ANP32A | 11480 | -0.021 | 0.14 | NO |
104 | AMD1 | AMD1 | AMD1 | 11482 | -0.021 | 0.14 | NO |
105 | MXD1 | MXD1 | MXD1 | 11675 | -0.024 | 0.13 | NO |
106 | RAB13 | RAB13 | RAB13 | 11752 | -0.025 | 0.13 | NO |
107 | RAD51 | RAD51 | RAD51 | 11783 | -0.025 | 0.13 | NO |
108 | CDC42BPB | CDC42BPB | CDC42BPB | 11948 | -0.028 | 0.12 | NO |
109 | TCEAL4 | TCEAL4 | TCEAL4 | 12094 | -0.03 | 0.12 | NO |
110 | LMNA | LMNA | LMNA | 12172 | -0.031 | 0.11 | NO |
111 | ITGB1 | ITGB1 | ITGB1 | 12218 | -0.032 | 0.11 | NO |
112 | SLC25A12 | SLC25A12 | SLC25A12 | 12222 | -0.032 | 0.11 | NO |
113 | OCRL | OCRL | OCRL | 12326 | -0.033 | 0.11 | NO |
114 | HNRNPD | HNRNPD | HNRNPD | 12474 | -0.036 | 0.1 | NO |
115 | HDLBP | HDLBP | HDLBP | 12587 | -0.038 | 0.098 | NO |
116 | DLG5 | DLG5 | DLG5 | 12589 | -0.038 | 0.1 | NO |
117 | DAZAP1 | DAZAP1 | DAZAP1 | 12671 | -0.039 | 0.097 | NO |
118 | RPIA | RPIA | RPIA | 12749 | -0.04 | 0.095 | NO |
119 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 12872 | -0.042 | 0.09 | NO |
120 | ANP32B | ANP32B | ANP32B | 12891 | -0.043 | 0.091 | NO |
121 | CDK16 | CDK16 | CDK16 | 13002 | -0.044 | 0.087 | NO |
122 | CD63 | CD63 | CD63 | 13005 | -0.044 | 0.089 | NO |
123 | TJP1 | TJP1 | TJP1 | 13054 | -0.045 | 0.089 | NO |
124 | MAPRE2 | MAPRE2 | MAPRE2 | 13055 | -0.045 | 0.091 | NO |
125 | TSPAN4 | TSPAN4 | TSPAN4 | 13069 | -0.045 | 0.092 | NO |
126 | AGRN | AGRN | AGRN | 13149 | -0.046 | 0.09 | NO |
127 | ABT1 | ABT1 | ABT1 | 13198 | -0.047 | 0.09 | NO |
128 | SSBP3 | SSBP3 | SSBP3 | 13381 | -0.05 | 0.082 | NO |
129 | PPP6R1 | PPP6R1 | PPP6R1 | 13403 | -0.05 | 0.084 | NO |
130 | PCGF2 | PCGF2 | PCGF2 | 13443 | -0.051 | 0.084 | NO |
131 | VRK3 | VRK3 | VRK3 | 13510 | -0.052 | 0.083 | NO |
132 | RPS8 | RPS8 | RPS8 | 13883 | -0.058 | 0.065 | NO |
133 | NOC4L | NOC4L | NOC4L | 13891 | -0.059 | 0.067 | NO |
134 | SIK2 | SIK2 | SIK2 | 13924 | -0.059 | 0.068 | NO |
135 | TRIM27 | TRIM27 | TRIM27 | 14066 | -0.062 | 0.063 | NO |
136 | FKBP9 | FKBP9 | FKBP9 | 14100 | -0.062 | 0.065 | NO |
137 | MYC | MYC | MYC | 14208 | -0.064 | 0.062 | NO |
138 | SH3BP4 | SH3BP4 | SH3BP4 | 14229 | -0.064 | 0.064 | NO |
139 | SLC19A1 | SLC19A1 | SLC19A1 | 14277 | -0.065 | 0.064 | NO |
140 | CSK | CSK | CSK | 14511 | -0.069 | 0.055 | NO |
141 | PML | PML | PML | 14527 | -0.07 | 0.057 | NO |
142 | DDX51 | DDX51 | DDX51 | 14837 | -0.076 | 0.044 | NO |
143 | TXNRD3 | TXNRD3 | TXNRD3 | 14946 | -0.079 | 0.042 | NO |
144 | DAG1 | DAG1 | DAG1 | 15097 | -0.083 | 0.037 | NO |
145 | DST | DST | DST | 15122 | -0.084 | 0.04 | NO |
146 | NXN | NXN | NXN | 15408 | -0.092 | 0.028 | NO |
147 | NFIB | NFIB | NFIB | 15435 | -0.093 | 0.032 | NO |
148 | SYDE1 | SYDE1 | SYDE1 | 15470 | -0.094 | 0.034 | NO |
149 | ATN1 | ATN1 | ATN1 | 15581 | -0.097 | 0.033 | NO |
150 | CRTAP | CRTAP | CRTAP | 15636 | -0.099 | 0.035 | NO |
151 | POLD1 | POLD1 | POLD1 | 15675 | -0.1 | 0.037 | NO |
152 | KIF1C | KIF1C | KIF1C | 15689 | -0.1 | 0.042 | NO |
153 | ZNF532 | ZNF532 | ZNF532 | 15718 | -0.1 | 0.045 | NO |
154 | KANK2 | KANK2 | KANK2 | 15746 | -0.1 | 0.048 | NO |
155 | KATNB1 | KATNB1 | KATNB1 | 15855 | -0.11 | 0.048 | NO |
156 | REXO4 | REXO4 | REXO4 | 16077 | -0.12 | 0.041 | NO |
157 | APBB1 | APBB1 | APBB1 | 16087 | -0.12 | 0.046 | NO |
158 | PRMT7 | PRMT7 | PRMT7 | 16238 | -0.12 | 0.044 | NO |
159 | CCNJL | CCNJL | CCNJL | 16280 | -0.13 | 0.048 | NO |
160 | GNG11 | GNG11 | GNG11 | 16556 | -0.14 | 0.039 | NO |
161 | LAMB2 | LAMB2 | LAMB2 | 16677 | -0.15 | 0.04 | NO |
162 | AMOTL2 | AMOTL2 | AMOTL2 | 16706 | -0.16 | 0.046 | NO |
163 | ADCY6 | ADCY6 | ADCY6 | 16778 | -0.16 | 0.05 | NO |
164 | PCBP4 | PCBP4 | PCBP4 | 16780 | -0.16 | 0.058 | NO |
165 | MID1 | MID1 | MID1 | 17583 | -0.3 | 0.028 | NO |
Figure S83. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION.

Figure S84. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S43. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PSMA1 | PSMA1 | PSMA1 | 48 | 1 | 0.12 | YES |
2 | RASGRP1 | RASGRP1 | RASGRP1 | 202 | 0.75 | 0.19 | YES |
3 | PSMB9 | PSMB9 | PSMB9 | 463 | 0.57 | 0.25 | YES |
4 | PSMA2 | PSMA2 | PSMA2 | 1121 | 0.39 | 0.26 | YES |
5 | CARD11 | CARD11 | CARD11 | 1571 | 0.32 | 0.27 | YES |
6 | PSMB8 | PSMB8 | PSMB8 | 1900 | 0.28 | 0.28 | YES |
7 | PRKCB | PRKCB | PRKCB | 2506 | 0.22 | 0.27 | YES |
8 | PSMB10 | PSMB10 | PSMB10 | 2806 | 0.19 | 0.28 | YES |
9 | MDM2 | MDM2 | MDM2 | 3085 | 0.18 | 0.29 | YES |
10 | PSME2 | PSME2 | PSME2 | 3309 | 0.16 | 0.29 | YES |
11 | PSMA3 | PSMA3 | PSMA3 | 3757 | 0.14 | 0.28 | YES |
12 | PSMA4 | PSMA4 | PSMA4 | 3809 | 0.14 | 0.3 | YES |
13 | RICTOR | RICTOR | RICTOR | 3827 | 0.14 | 0.31 | YES |
14 | PSME4 | PSME4 | PSME4 | 3830 | 0.14 | 0.33 | YES |
15 | BCL10 | BCL10 | BCL10 | 3960 | 0.13 | 0.34 | YES |
16 | PSMD14 | PSMD14 | PSMD14 | 4117 | 0.12 | 0.34 | YES |
17 | CDKN1A | CDKN1A | CDKN1A | 4411 | 0.11 | 0.34 | YES |
18 | PSMA5 | PSMA5 | PSMA5 | 4534 | 0.11 | 0.34 | YES |
19 | PSMA6 | PSMA6 | PSMA6 | 4713 | 0.1 | 0.35 | YES |
20 | PSME1 | PSME1 | PSME1 | 4764 | 0.1 | 0.36 | YES |
21 | PSMC6 | PSMC6 | PSMC6 | 4926 | 0.096 | 0.36 | YES |
22 | CREB1 | CREB1 | CREB1 | 4987 | 0.095 | 0.37 | YES |
23 | MALT1 | MALT1 | MALT1 | 5195 | 0.089 | 0.36 | YES |
24 | KRAS | KRAS | KRAS | 5250 | 0.087 | 0.37 | YES |
25 | NFKBIA | NFKBIA | NFKBIA | 5278 | 0.086 | 0.38 | YES |
26 | MAP3K7 | MAP3K7 | MAP3K7 | 5345 | 0.085 | 0.39 | YES |
27 | PSMD12 | PSMD12 | PSMD12 | 5705 | 0.076 | 0.38 | YES |
28 | CHUK | CHUK | CHUK | 5716 | 0.076 | 0.38 | YES |
29 | NRAS | NRAS | NRAS | 5741 | 0.075 | 0.39 | YES |
30 | CDKN1B | CDKN1B | CDKN1B | 6180 | 0.066 | 0.38 | NO |
31 | CUL1 | CUL1 | CUL1 | 6182 | 0.066 | 0.38 | NO |
32 | PSMA7 | PSMA7 | PSMA7 | 6580 | 0.057 | 0.37 | NO |
33 | PSMD7 | PSMD7 | PSMD7 | 6717 | 0.054 | 0.37 | NO |
34 | PSMB2 | PSMB2 | PSMB2 | 6742 | 0.054 | 0.37 | NO |
35 | PSMC2 | PSMC2 | PSMC2 | 6949 | 0.05 | 0.36 | NO |
36 | PTEN | PTEN | PTEN | 7167 | 0.046 | 0.36 | NO |
37 | PSMC1 | PSMC1 | PSMC1 | 7331 | 0.043 | 0.36 | NO |
38 | REL | REL | REL | 7712 | 0.036 | 0.34 | NO |
39 | MTOR | MTOR | MTOR | 7906 | 0.032 | 0.33 | NO |
40 | PSMD5 | PSMD5 | PSMD5 | 7928 | 0.032 | 0.33 | NO |
41 | PSMB3 | PSMB3 | PSMB3 | 8251 | 0.026 | 0.32 | NO |
42 | PSMB1 | PSMB1 | PSMB1 | 8257 | 0.026 | 0.32 | NO |
43 | NFKBIE | NFKBIE | NFKBIE | 8333 | 0.025 | 0.32 | NO |
44 | PSMD11 | PSMD11 | PSMD11 | 8401 | 0.024 | 0.32 | NO |
45 | PSMD10 | PSMD10 | PSMD10 | 8914 | 0.016 | 0.29 | NO |
46 | PSMA8 | PSMA8 | PSMA8 | 9540 | 0.007 | 0.26 | NO |
47 | PDPK1 | PDPK1 | PDPK1 | 9634 | 0.0054 | 0.25 | NO |
48 | SKP1 | SKP1 | SKP1 | 9662 | 0.005 | 0.25 | NO |
49 | PSMC4 | PSMC4 | PSMC4 | 9796 | 0.0029 | 0.25 | NO |
50 | PSMD1 | PSMD1 | PSMD1 | 9820 | 0.0026 | 0.24 | NO |
51 | NFKBIB | NFKBIB | NFKBIB | 9852 | 0.0021 | 0.24 | NO |
52 | PSMC3 | PSMC3 | PSMC3 | 9891 | 0.0015 | 0.24 | NO |
53 | PSMD13 | PSMD13 | PSMD13 | 10277 | -0.0043 | 0.22 | NO |
54 | PSMC5 | PSMC5 | PSMC5 | 10429 | -0.0064 | 0.21 | NO |
55 | PSMB6 | PSMB6 | PSMB6 | 10559 | -0.0085 | 0.21 | NO |
56 | PSMD3 | PSMD3 | PSMD3 | 10590 | -0.0091 | 0.21 | NO |
57 | AKT3 | AKT3 | AKT3 | 10665 | -0.01 | 0.2 | NO |
58 | PSMB7 | PSMB7 | PSMB7 | 10709 | -0.011 | 0.2 | NO |
59 | RASGRP3 | RASGRP3 | RASGRP3 | 10912 | -0.013 | 0.19 | NO |
60 | PSMD8 | PSMD8 | PSMD8 | 11103 | -0.016 | 0.18 | NO |
61 | PSMB4 | PSMB4 | PSMB4 | 11164 | -0.017 | 0.18 | NO |
62 | FBXW11 | FBXW11 | FBXW11 | 11172 | -0.017 | 0.18 | NO |
63 | IKBKB | IKBKB | IKBKB | 11311 | -0.019 | 0.18 | NO |
64 | PSMB5 | PSMB5 | PSMB5 | 11414 | -0.02 | 0.18 | NO |
65 | CASP9 | CASP9 | CASP9 | 11514 | -0.021 | 0.17 | NO |
66 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 11527 | -0.022 | 0.17 | NO |
67 | THEM4 | THEM4 | THEM4 | 11813 | -0.026 | 0.16 | NO |
68 | PSMD4 | PSMD4 | PSMD4 | 12032 | -0.029 | 0.15 | NO |
69 | PSMD9 | PSMD9 | PSMD9 | 12076 | -0.03 | 0.15 | NO |
70 | BTRC | BTRC | BTRC | 12089 | -0.03 | 0.16 | NO |
71 | PSMD6 | PSMD6 | PSMD6 | 12416 | -0.035 | 0.14 | NO |
72 | IKBKG | IKBKG | IKBKG | 12564 | -0.037 | 0.14 | NO |
73 | FOXO4 | FOXO4 | FOXO4 | 12784 | -0.041 | 0.13 | NO |
74 | BAD | BAD | BAD | 12966 | -0.044 | 0.13 | NO |
75 | PHLPP1 | PHLPP1 | PHLPP1 | 13022 | -0.044 | 0.13 | NO |
76 | HRAS | HRAS | HRAS | 13052 | -0.045 | 0.13 | NO |
77 | MLST8 | MLST8 | MLST8 | 13868 | -0.058 | 0.094 | NO |
78 | GSK3A | GSK3A | GSK3A | 13892 | -0.059 | 0.099 | NO |
79 | AKT1S1 | AKT1S1 | AKT1S1 | 14088 | -0.062 | 0.096 | NO |
80 | FOXO1 | FOXO1 | FOXO1 | 14202 | -0.064 | 0.097 | NO |
81 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 14302 | -0.066 | 0.099 | NO |
82 | AKT2 | AKT2 | AKT2 | 14395 | -0.067 | 0.1 | NO |
83 | AKT1 | AKT1 | AKT1 | 14488 | -0.069 | 0.1 | NO |
84 | PSMD2 | PSMD2 | PSMD2 | 14824 | -0.076 | 0.095 | NO |
85 | TSC2 | TSC2 | TSC2 | 14943 | -0.079 | 0.098 | NO |
86 | PSMF1 | PSMF1 | PSMF1 | 15085 | -0.082 | 0.1 | NO |
87 | NR4A1 | NR4A1 | NR4A1 | 15125 | -0.084 | 0.11 | NO |
88 | TRIB3 | TRIB3 | TRIB3 | 15304 | -0.088 | 0.11 | NO |
89 | RELA | RELA | RELA | 15341 | -0.09 | 0.12 | NO |
90 | RPS27A | RPS27A | RPS27A | 15344 | -0.09 | 0.13 | NO |
91 | FOXO3 | FOXO3 | FOXO3 | 15765 | -0.1 | 0.12 | NO |
92 | UBA52 | UBA52 | UBA52 | 16002 | -0.11 | 0.12 | NO |
Figure S85. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY.

Figure S86. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S44. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PSMA1 | PSMA1 | PSMA1 | 48 | 1 | 0.077 | YES |
2 | CD8B | CD8B | CD8B | 104 | 0.87 | 0.14 | YES |
3 | LCK | LCK | LCK | 149 | 0.81 | 0.2 | YES |
4 | CD247 | CD247 | CD247 | 228 | 0.73 | 0.26 | YES |
5 | PSMB9 | PSMB9 | PSMB9 | 463 | 0.57 | 0.29 | YES |
6 | DOCK2 | DOCK2 | DOCK2 | 659 | 0.5 | 0.32 | YES |
7 | CD28 | CD28 | CD28 | 979 | 0.42 | 0.33 | YES |
8 | PSMA2 | PSMA2 | PSMA2 | 1121 | 0.39 | 0.36 | YES |
9 | HCK | HCK | HCK | 1463 | 0.33 | 0.36 | YES |
10 | AP1M2 | AP1M2 | AP1M2 | 1499 | 0.33 | 0.39 | YES |
11 | B2M | B2M | B2M | 1883 | 0.28 | 0.39 | YES |
12 | PSMB8 | PSMB8 | PSMB8 | 1900 | 0.28 | 0.41 | YES |
13 | ELMO1 | ELMO1 | ELMO1 | 1935 | 0.27 | 0.43 | YES |
14 | APOBEC3G | APOBEC3G | APOBEC3G | 2013 | 0.27 | 0.45 | YES |
15 | CD4 | CD4 | CD4 | 2531 | 0.22 | 0.43 | NO |
16 | PSMB10 | PSMB10 | PSMB10 | 2806 | 0.19 | 0.43 | NO |
17 | HLA-A | HLA-A | HLA-A | 3039 | 0.18 | 0.44 | NO |
18 | PSME2 | PSME2 | PSME2 | 3309 | 0.16 | 0.43 | NO |
19 | PSMA3 | PSMA3 | PSMA3 | 3757 | 0.14 | 0.42 | NO |
20 | PSMA4 | PSMA4 | PSMA4 | 3809 | 0.14 | 0.43 | NO |
21 | PSME4 | PSME4 | PSME4 | 3830 | 0.14 | 0.44 | NO |
22 | PSMD14 | PSMD14 | PSMD14 | 4117 | 0.12 | 0.43 | NO |
23 | TPR | TPR | TPR | 4140 | 0.12 | 0.44 | NO |
24 | TCEB1 | TCEB1 | TCEB1 | 4471 | 0.11 | 0.43 | NO |
25 | PSMA5 | PSMA5 | PSMA5 | 4534 | 0.11 | 0.44 | NO |
26 | PSMA6 | PSMA6 | PSMA6 | 4713 | 0.1 | 0.43 | NO |
27 | PSME1 | PSME1 | PSME1 | 4764 | 0.1 | 0.44 | NO |
28 | XPO1 | XPO1 | XPO1 | 4911 | 0.097 | 0.44 | NO |
29 | PSMC6 | PSMC6 | PSMC6 | 4926 | 0.096 | 0.44 | NO |
30 | ATP6V1H | ATP6V1H | ATP6V1H | 5322 | 0.085 | 0.43 | NO |
31 | CUL5 | CUL5 | CUL5 | 5421 | 0.083 | 0.43 | NO |
32 | NUPL2 | NUPL2 | NUPL2 | 5528 | 0.08 | 0.43 | NO |
33 | PSMD12 | PSMD12 | PSMD12 | 5705 | 0.076 | 0.43 | NO |
34 | NUP88 | NUP88 | NUP88 | 6290 | 0.063 | 0.4 | NO |
35 | NUP50 | NUP50 | NUP50 | 6291 | 0.063 | 0.4 | NO |
36 | NUP107 | NUP107 | NUP107 | 6464 | 0.06 | 0.4 | NO |
37 | PSMA7 | PSMA7 | PSMA7 | 6580 | 0.057 | 0.4 | NO |
38 | PSMD7 | PSMD7 | PSMD7 | 6717 | 0.054 | 0.4 | NO |
39 | PSMB2 | PSMB2 | PSMB2 | 6742 | 0.054 | 0.4 | NO |
40 | PSMC2 | PSMC2 | PSMC2 | 6949 | 0.05 | 0.39 | NO |
41 | RANBP2 | RANBP2 | RANBP2 | 7028 | 0.049 | 0.39 | NO |
42 | NUP54 | NUP54 | NUP54 | 7046 | 0.048 | 0.39 | NO |
43 | PSIP1 | PSIP1 | PSIP1 | 7319 | 0.043 | 0.38 | NO |
44 | PSMC1 | PSMC1 | PSMC1 | 7331 | 0.043 | 0.38 | NO |
45 | CCNT1 | CCNT1 | CCNT1 | 7489 | 0.04 | 0.38 | NO |
46 | NUP43 | NUP43 | NUP43 | 7512 | 0.04 | 0.38 | NO |
47 | NUPL1 | NUPL1 | NUPL1 | 7523 | 0.04 | 0.38 | NO |
48 | AP1G1 | AP1G1 | AP1G1 | 7783 | 0.034 | 0.37 | NO |
49 | PSMD5 | PSMD5 | PSMD5 | 7928 | 0.032 | 0.37 | NO |
50 | NUP85 | NUP85 | NUP85 | 8043 | 0.03 | 0.36 | NO |
51 | RBX1 | RBX1 | RBX1 | 8095 | 0.029 | 0.36 | NO |
52 | SEH1L | SEH1L | SEH1L | 8173 | 0.028 | 0.36 | NO |
53 | PSMB3 | PSMB3 | PSMB3 | 8251 | 0.026 | 0.36 | NO |
54 | PSMB1 | PSMB1 | PSMB1 | 8257 | 0.026 | 0.36 | NO |
55 | PSMD11 | PSMD11 | PSMD11 | 8401 | 0.024 | 0.35 | NO |
56 | KPNB1 | KPNB1 | KPNB1 | 8422 | 0.024 | 0.35 | NO |
57 | NUP155 | NUP155 | NUP155 | 8910 | 0.016 | 0.33 | NO |
58 | PSMD10 | PSMD10 | PSMD10 | 8914 | 0.016 | 0.33 | NO |
59 | NUP205 | NUP205 | NUP205 | 9376 | 0.0091 | 0.3 | NO |
60 | PSMA8 | PSMA8 | PSMA8 | 9540 | 0.007 | 0.3 | NO |
61 | SKP1 | SKP1 | SKP1 | 9662 | 0.005 | 0.29 | NO |
62 | PSMC4 | PSMC4 | PSMC4 | 9796 | 0.0029 | 0.28 | NO |
63 | NUP37 | NUP37 | NUP37 | 9807 | 0.0027 | 0.28 | NO |
64 | PSMD1 | PSMD1 | PSMD1 | 9820 | 0.0026 | 0.28 | NO |
65 | SLC25A4 | SLC25A4 | SLC25A4 | 9868 | 0.0019 | 0.28 | NO |
66 | PSMC3 | PSMC3 | PSMC3 | 9891 | 0.0015 | 0.28 | NO |
67 | CDK9 | CDK9 | CDK9 | 10119 | -0.002 | 0.26 | NO |
68 | AP2A2 | AP2A2 | AP2A2 | 10203 | -0.003 | 0.26 | NO |
69 | PSMD13 | PSMD13 | PSMD13 | 10277 | -0.0043 | 0.26 | NO |
70 | NUP35 | NUP35 | NUP35 | 10404 | -0.0062 | 0.25 | NO |
71 | PSMC5 | PSMC5 | PSMC5 | 10429 | -0.0064 | 0.25 | NO |
72 | AP1S2 | AP1S2 | AP1S2 | 10471 | -0.0071 | 0.25 | NO |
73 | PSMB6 | PSMB6 | PSMB6 | 10559 | -0.0085 | 0.24 | NO |
74 | PSMD3 | PSMD3 | PSMD3 | 10590 | -0.0091 | 0.24 | NO |
75 | NUP210 | NUP210 | NUP210 | 10642 | -0.0099 | 0.24 | NO |
76 | ARF1 | ARF1 | ARF1 | 10666 | -0.01 | 0.24 | NO |
77 | PSMB7 | PSMB7 | PSMB7 | 10709 | -0.011 | 0.24 | NO |
78 | RAN | RAN | RAN | 10991 | -0.014 | 0.22 | NO |
79 | NUP133 | NUP133 | NUP133 | 11041 | -0.015 | 0.22 | NO |
80 | PSMD8 | PSMD8 | PSMD8 | 11103 | -0.016 | 0.22 | NO |
81 | NUP188 | NUP188 | NUP188 | 11140 | -0.016 | 0.22 | NO |
82 | PSMB4 | PSMB4 | PSMB4 | 11164 | -0.017 | 0.22 | NO |
83 | PSMB5 | PSMB5 | PSMB5 | 11414 | -0.02 | 0.21 | NO |
84 | NUP62 | NUP62 | NUP62 | 11433 | -0.02 | 0.21 | NO |
85 | AP2B1 | AP2B1 | AP2B1 | 11562 | -0.022 | 0.2 | NO |
86 | KPNA1 | KPNA1 | KPNA1 | 11635 | -0.023 | 0.2 | NO |
87 | PAK2 | PAK2 | PAK2 | 11766 | -0.025 | 0.2 | NO |
88 | AP1S1 | AP1S1 | AP1S1 | 11858 | -0.026 | 0.19 | NO |
89 | PPIA | PPIA | PPIA | 11867 | -0.027 | 0.19 | NO |
90 | RCC1 | RCC1 | RCC1 | 11876 | -0.027 | 0.2 | NO |
91 | PSMD4 | PSMD4 | PSMD4 | 12032 | -0.029 | 0.19 | NO |
92 | NUP153 | NUP153 | NUP153 | 12054 | -0.029 | 0.19 | NO |
93 | PSMD9 | PSMD9 | PSMD9 | 12076 | -0.03 | 0.19 | NO |
94 | BTRC | BTRC | BTRC | 12089 | -0.03 | 0.19 | NO |
95 | AP1M1 | AP1M1 | AP1M1 | 12354 | -0.034 | 0.18 | NO |
96 | PSMD6 | PSMD6 | PSMD6 | 12416 | -0.035 | 0.18 | NO |
97 | SLC25A5 | SLC25A5 | SLC25A5 | 12434 | -0.036 | 0.18 | NO |
98 | RAC1 | RAC1 | RAC1 | 12511 | -0.036 | 0.18 | NO |
99 | NPM1 | NPM1 | NPM1 | 12549 | -0.037 | 0.18 | NO |
100 | RANBP1 | RANBP1 | RANBP1 | 12640 | -0.038 | 0.18 | NO |
101 | AP1B1 | AP1B1 | AP1B1 | 12772 | -0.04 | 0.18 | NO |
102 | TCEB2 | TCEB2 | TCEB2 | 13312 | -0.049 | 0.15 | NO |
103 | AAAS | AAAS | AAAS | 13390 | -0.05 | 0.15 | NO |
104 | AP2A1 | AP2A1 | AP2A1 | 13477 | -0.052 | 0.15 | NO |
105 | RAE1 | RAE1 | RAE1 | 13491 | -0.052 | 0.15 | NO |
106 | AP2S1 | AP2S1 | AP2S1 | 13652 | -0.054 | 0.15 | NO |
107 | FYN | FYN | FYN | 14091 | -0.062 | 0.13 | NO |
108 | NUP93 | NUP93 | NUP93 | 14315 | -0.066 | 0.12 | NO |
109 | NUP214 | NUP214 | NUP214 | 14487 | -0.069 | 0.12 | NO |
110 | BANF1 | BANF1 | BANF1 | 14660 | -0.072 | 0.11 | NO |
111 | RANGAP1 | RANGAP1 | RANGAP1 | 14734 | -0.074 | 0.12 | NO |
112 | PSMD2 | PSMD2 | PSMD2 | 14824 | -0.076 | 0.12 | NO |
113 | PSMF1 | PSMF1 | PSMF1 | 15085 | -0.082 | 0.11 | NO |
114 | POM121 | POM121 | POM121 | 15123 | -0.084 | 0.11 | NO |
115 | RPS27A | RPS27A | RPS27A | 15344 | -0.09 | 0.11 | NO |
116 | AP2M1 | AP2M1 | AP2M1 | 15657 | -0.1 | 0.098 | NO |
117 | PACS1 | PACS1 | PACS1 | 15739 | -0.1 | 0.1 | NO |
118 | HMGA1 | HMGA1 | HMGA1 | 15943 | -0.11 | 0.099 | NO |
119 | UBA52 | UBA52 | UBA52 | 16002 | -0.11 | 0.1 | NO |
120 | SLC25A6 | SLC25A6 | SLC25A6 | 16532 | -0.14 | 0.086 | NO |
Figure S87. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG APOPTOSIS.

Figure S88. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG APOPTOSIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S45. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | LCK | LCK | LCK | 149 | 0.81 | 0.038 | YES |
2 | IL7R | IL7R | IL7R | 217 | 0.74 | 0.077 | YES |
3 | IL2RB | IL2RB | IL2RB | 380 | 0.62 | 0.1 | YES |
4 | IL2RA | IL2RA | IL2RA | 385 | 0.62 | 0.14 | YES |
5 | NOD2 | NOD2 | NOD2 | 404 | 0.6 | 0.17 | YES |
6 | CSF2 | CSF2 | CSF2 | 406 | 0.6 | 0.21 | YES |
7 | IL2RG | IL2RG | IL2RG | 438 | 0.58 | 0.24 | YES |
8 | IL1B | IL1B | IL1B | 454 | 0.57 | 0.27 | YES |
9 | IL1R2 | IL1R2 | IL1R2 | 462 | 0.57 | 0.3 | YES |
10 | IL7 | IL7 | IL7 | 476 | 0.56 | 0.33 | YES |
11 | IL18 | IL18 | IL18 | 558 | 0.53 | 0.36 | YES |
12 | CSF2RB | CSF2RB | CSF2RB | 579 | 0.52 | 0.39 | YES |
13 | VAV1 | VAV1 | VAV1 | 843 | 0.44 | 0.4 | YES |
14 | IL6 | IL6 | IL6 | 878 | 0.44 | 0.42 | YES |
15 | BLNK | BLNK | BLNK | 907 | 0.43 | 0.44 | YES |
16 | CASP1 | CASP1 | CASP1 | 961 | 0.42 | 0.46 | YES |
17 | PTPN6 | PTPN6 | PTPN6 | 1036 | 0.4 | 0.48 | YES |
18 | STAT1 | STAT1 | STAT1 | 1132 | 0.39 | 0.5 | YES |
19 | IRAK3 | IRAK3 | IRAK3 | 1190 | 0.38 | 0.52 | YES |
20 | IL5RA | IL5RA | IL5RA | 1379 | 0.35 | 0.53 | YES |
21 | IL1RN | IL1RN | IL1RN | 1389 | 0.34 | 0.55 | YES |
22 | IL1A | IL1A | IL1A | 1457 | 0.33 | 0.56 | YES |
23 | HCK | HCK | HCK | 1463 | 0.33 | 0.58 | YES |
24 | JAK3 | JAK3 | JAK3 | 1618 | 0.31 | 0.59 | YES |
25 | IL1R1 | IL1R1 | IL1R1 | 1945 | 0.27 | 0.59 | YES |
26 | HGF | HGF | HGF | 2068 | 0.26 | 0.6 | YES |
27 | PELI1 | PELI1 | PELI1 | 2138 | 0.26 | 0.61 | YES |
28 | JAK2 | JAK2 | JAK2 | 2164 | 0.25 | 0.62 | YES |
29 | MAP3K8 | MAP3K8 | MAP3K8 | 2331 | 0.23 | 0.62 | YES |
30 | IL5 | IL5 | IL5 | 2355 | 0.23 | 0.64 | YES |
31 | CSF2RA | CSF2RA | CSF2RA | 2504 | 0.22 | 0.64 | YES |
32 | SYK | SYK | SYK | 2950 | 0.18 | 0.63 | NO |
33 | PIK3R3 | PIK3R3 | PIK3R3 | 3232 | 0.17 | 0.62 | NO |
34 | SOCS3 | SOCS3 | SOCS3 | 3284 | 0.16 | 0.63 | NO |
35 | LYN | LYN | LYN | 3311 | 0.16 | 0.64 | NO |
36 | IRAK2 | IRAK2 | IRAK2 | 3825 | 0.14 | 0.62 | NO |
37 | IRAK4 | IRAK4 | IRAK4 | 4325 | 0.12 | 0.59 | NO |
38 | IL6R | IL6R | IL6R | 4663 | 0.1 | 0.58 | NO |
39 | STAT3 | STAT3 | STAT3 | 5153 | 0.09 | 0.56 | NO |
40 | KRAS | KRAS | KRAS | 5250 | 0.087 | 0.56 | NO |
41 | MAP3K7 | MAP3K7 | MAP3K7 | 5345 | 0.085 | 0.56 | NO |
42 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 5548 | 0.08 | 0.55 | NO |
43 | SOS1 | SOS1 | SOS1 | 5572 | 0.079 | 0.56 | NO |
44 | PIK3CA | PIK3CA | PIK3CA | 5611 | 0.078 | 0.56 | NO |
45 | PIK3R1 | PIK3R1 | PIK3R1 | 5635 | 0.078 | 0.56 | NO |
46 | IL6ST | IL6ST | IL6ST | 5661 | 0.077 | 0.56 | NO |
47 | YWHAZ | YWHAZ | YWHAZ | 5664 | 0.077 | 0.57 | NO |
48 | CHUK | CHUK | CHUK | 5716 | 0.076 | 0.57 | NO |
49 | NRAS | NRAS | NRAS | 5741 | 0.075 | 0.57 | NO |
50 | CUL1 | CUL1 | CUL1 | 6182 | 0.066 | 0.55 | NO |
51 | PRKACB | PRKACB | PRKACB | 6385 | 0.061 | 0.54 | NO |
52 | RIPK2 | RIPK2 | RIPK2 | 6847 | 0.052 | 0.52 | NO |
53 | TEC | TEC | TEC | 7422 | 0.041 | 0.49 | NO |
54 | MAPK1 | MAPK1 | MAPK1 | 7460 | 0.041 | 0.49 | NO |
55 | MAP2K4 | MAP2K4 | MAP2K4 | 7722 | 0.036 | 0.48 | NO |
56 | PTK2B | PTK2B | PTK2B | 7798 | 0.034 | 0.48 | NO |
57 | RBX1 | RBX1 | RBX1 | 8095 | 0.029 | 0.46 | NO |
58 | MAP2K1 | MAP2K1 | MAP2K1 | 8121 | 0.028 | 0.46 | NO |
59 | SHC1 | SHC1 | SHC1 | 8213 | 0.027 | 0.46 | NO |
60 | CRK | CRK | CRK | 8287 | 0.026 | 0.46 | NO |
61 | IRAK1 | IRAK1 | IRAK1 | 8416 | 0.024 | 0.45 | NO |
62 | TAB2 | TAB2 | TAB2 | 8419 | 0.024 | 0.45 | NO |
63 | CDK1 | CDK1 | CDK1 | 8444 | 0.024 | 0.45 | NO |
64 | MAP2K6 | MAP2K6 | MAP2K6 | 8478 | 0.023 | 0.45 | NO |
65 | MYD88 | MYD88 | MYD88 | 8783 | 0.018 | 0.44 | NO |
66 | JAK1 | JAK1 | JAK1 | 8835 | 0.018 | 0.43 | NO |
67 | TRAF6 | TRAF6 | TRAF6 | 8887 | 0.017 | 0.43 | NO |
68 | TAB3 | TAB3 | TAB3 | 8936 | 0.016 | 0.43 | NO |
69 | NFKB2 | NFKB2 | NFKB2 | 8994 | 0.015 | 0.43 | NO |
70 | GRB2 | GRB2 | GRB2 | 9080 | 0.013 | 0.42 | NO |
71 | YWHAB | YWHAB | YWHAB | 9223 | 0.012 | 0.42 | NO |
72 | UBE2N | UBE2N | UBE2N | 9344 | 0.0096 | 0.41 | NO |
73 | IL3RA | IL3RA | IL3RA | 9586 | 0.0062 | 0.4 | NO |
74 | SKP1 | SKP1 | SKP1 | 9662 | 0.005 | 0.39 | NO |
75 | YES1 | YES1 | YES1 | 9663 | 0.005 | 0.39 | NO |
76 | NOD1 | NOD1 | NOD1 | 9856 | 0.0021 | 0.38 | NO |
77 | SQSTM1 | SQSTM1 | SQSTM1 | 10048 | -0.00088 | 0.37 | NO |
78 | STAT5B | STAT5B | STAT5B | 10100 | -0.0016 | 0.37 | NO |
79 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 10221 | -0.0034 | 0.36 | NO |
80 | PIK3CD | PIK3CD | PIK3CD | 10253 | -0.0038 | 0.36 | NO |
81 | PIK3CB | PIK3CB | PIK3CB | 10313 | -0.0048 | 0.36 | NO |
82 | CBL | CBL | CBL | 10752 | -0.012 | 0.34 | NO |
83 | TNIP2 | TNIP2 | TNIP2 | 10961 | -0.014 | 0.32 | NO |
84 | TYK2 | TYK2 | TYK2 | 11019 | -0.015 | 0.32 | NO |
85 | IKBKB | IKBKB | IKBKB | 11311 | -0.019 | 0.31 | NO |
86 | INPPL1 | INPPL1 | INPPL1 | 11316 | -0.019 | 0.31 | NO |
87 | BTRC | BTRC | BTRC | 12089 | -0.03 | 0.27 | NO |
88 | IKBKG | IKBKG | IKBKG | 12564 | -0.037 | 0.24 | NO |
89 | MAP3K3 | MAP3K3 | MAP3K3 | 12809 | -0.041 | 0.23 | NO |
90 | CRKL | CRKL | CRKL | 12892 | -0.043 | 0.23 | NO |
91 | STAT5A | STAT5A | STAT5A | 12930 | -0.043 | 0.23 | NO |
92 | GAB2 | GAB2 | GAB2 | 13006 | -0.044 | 0.23 | NO |
93 | HRAS | HRAS | HRAS | 13052 | -0.045 | 0.23 | NO |
94 | TAB1 | TAB1 | TAB1 | 13130 | -0.046 | 0.23 | NO |
95 | TOLLIP | TOLLIP | TOLLIP | 13406 | -0.05 | 0.21 | NO |
96 | FYN | FYN | FYN | 14091 | -0.062 | 0.18 | NO |
97 | MAPK3 | MAPK3 | MAPK3 | 14380 | -0.067 | 0.17 | NO |
98 | MAP2K2 | MAP2K2 | MAP2K2 | 14942 | -0.079 | 0.14 | NO |
99 | PELI2 | PELI2 | PELI2 | 14965 | -0.079 | 0.14 | NO |
100 | RAF1 | RAF1 | RAF1 | 15263 | -0.087 | 0.13 | NO |
101 | RELA | RELA | RELA | 15341 | -0.09 | 0.13 | NO |
102 | PIK3R2 | PIK3R2 | PIK3R2 | 15774 | -0.1 | 0.12 | NO |
103 | IL1RAP | IL1RAP | IL1RAP | 15978 | -0.11 | 0.11 | NO |
104 | PELI3 | PELI3 | PELI3 | 16265 | -0.12 | 0.1 | NO |
Figure S89. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG CELL ADHESION MOLECULES CAMS.

Figure S90. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CELL ADHESION MOLECULES CAMS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S46. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | STAP1 | STAP1 | STAP1 | 79 | 0.91 | 0.031 | YES |
2 | TNFRSF17 | TNFRSF17 | TNFRSF17 | 89 | 0.89 | 0.066 | YES |
3 | IGJ | IGJ | IGJ | 95 | 0.88 | 0.1 | YES |
4 | PTPN22 | PTPN22 | PTPN22 | 126 | 0.84 | 0.13 | YES |
5 | LCK | LCK | LCK | 149 | 0.81 | 0.16 | YES |
6 | TOX | TOX | TOX | 160 | 0.81 | 0.19 | YES |
7 | PTPRC | PTPRC | PTPRC | 204 | 0.75 | 0.22 | YES |
8 | CD38 | CD38 | CD38 | 225 | 0.73 | 0.25 | YES |
9 | LY9 | LY9 | LY9 | 240 | 0.72 | 0.28 | YES |
10 | RGS13 | RGS13 | RGS13 | 295 | 0.68 | 0.3 | YES |
11 | LRMP | LRMP | LRMP | 339 | 0.64 | 0.32 | YES |
12 | IRF8 | IRF8 | IRF8 | 518 | 0.55 | 0.33 | YES |
13 | ADAM19 | ADAM19 | ADAM19 | 684 | 0.49 | 0.34 | YES |
14 | VAV1 | VAV1 | VAV1 | 843 | 0.44 | 0.35 | YES |
15 | CD86 | CD86 | CD86 | 883 | 0.43 | 0.37 | YES |
16 | TUBB3 | TUBB3 | TUBB3 | 1027 | 0.41 | 0.38 | YES |
17 | IFI30 | IFI30 | IFI30 | 1167 | 0.38 | 0.38 | YES |
18 | LEF1 | LEF1 | LEF1 | 1293 | 0.36 | 0.39 | YES |
19 | EAF2 | EAF2 | EAF2 | 1383 | 0.35 | 0.4 | YES |
20 | RAC2 | RAC2 | RAC2 | 1427 | 0.34 | 0.41 | YES |
21 | RUNX3 | RUNX3 | RUNX3 | 1590 | 0.32 | 0.41 | YES |
22 | MAP4K1 | MAP4K1 | MAP4K1 | 1612 | 0.32 | 0.42 | YES |
23 | BLK | BLK | BLK | 1774 | 0.3 | 0.43 | YES |
24 | MEIS2 | MEIS2 | MEIS2 | 1788 | 0.29 | 0.44 | YES |
25 | SNX10 | SNX10 | SNX10 | 1910 | 0.28 | 0.44 | YES |
26 | BTK | BTK | BTK | 1985 | 0.27 | 0.45 | YES |
27 | LAP3 | LAP3 | LAP3 | 2101 | 0.26 | 0.45 | YES |
28 | CCDC109B | CCDC109B | CCDC109B | 2281 | 0.24 | 0.45 | YES |
29 | KCNN3 | KCNN3 | KCNN3 | 2328 | 0.24 | 0.46 | YES |
30 | PLEKHF2 | PLEKHF2 | PLEKHF2 | 2970 | 0.18 | 0.43 | NO |
31 | ITGB7 | ITGB7 | ITGB7 | 3103 | 0.18 | 0.43 | NO |
32 | RFTN1 | RFTN1 | RFTN1 | 3123 | 0.18 | 0.44 | NO |
33 | CAB39L | CAB39L | CAB39L | 3705 | 0.14 | 0.41 | NO |
34 | PRKCA | PRKCA | PRKCA | 4001 | 0.13 | 0.4 | NO |
35 | MAPK6 | MAPK6 | MAPK6 | 4028 | 0.13 | 0.4 | NO |
36 | RNF19B | RNF19B | RNF19B | 4037 | 0.13 | 0.4 | NO |
37 | CDK14 | CDK14 | CDK14 | 4046 | 0.13 | 0.41 | NO |
38 | MYBL1 | MYBL1 | MYBL1 | 4151 | 0.12 | 0.41 | NO |
39 | COTL1 | COTL1 | COTL1 | 4195 | 0.12 | 0.41 | NO |
40 | SMC4 | SMC4 | SMC4 | 4308 | 0.12 | 0.41 | NO |
41 | SERINC5 | SERINC5 | SERINC5 | 4377 | 0.12 | 0.41 | NO |
42 | RAP1B | RAP1B | RAP1B | 4386 | 0.11 | 0.41 | NO |
43 | SGCB | SGCB | SGCB | 4392 | 0.11 | 0.42 | NO |
44 | CREM | CREM | CREM | 4545 | 0.11 | 0.41 | NO |
45 | TMEM194A | TMEM194A | TMEM194A | 4782 | 0.1 | 0.4 | NO |
46 | PITX1 | PITX1 | PITX1 | 5045 | 0.093 | 0.39 | NO |
47 | TCEA1 | TCEA1 | TCEA1 | 5080 | 0.092 | 0.4 | NO |
48 | PEX3 | PEX3 | PEX3 | 5121 | 0.09 | 0.4 | NO |
49 | HSPH1 | HSPH1 | HSPH1 | 5135 | 0.09 | 0.4 | NO |
50 | DEPTOR | DEPTOR | DEPTOR | 5144 | 0.09 | 0.4 | NO |
51 | ZNF93 | ZNF93 | ZNF93 | 5344 | 0.085 | 0.4 | NO |
52 | NR3C1 | NR3C1 | NR3C1 | 5454 | 0.082 | 0.39 | NO |
53 | CPNE3 | CPNE3 | CPNE3 | 5501 | 0.081 | 0.39 | NO |
54 | SYNE1 | SYNE1 | SYNE1 | 5720 | 0.076 | 0.38 | NO |
55 | PPP3CC | PPP3CC | PPP3CC | 5824 | 0.073 | 0.38 | NO |
56 | MBD2 | MBD2 | MBD2 | 5851 | 0.073 | 0.38 | NO |
57 | ENDOD1 | ENDOD1 | ENDOD1 | 5980 | 0.07 | 0.38 | NO |
58 | SHMT1 | SHMT1 | SHMT1 | 6034 | 0.069 | 0.38 | NO |
59 | BASP1 | BASP1 | BASP1 | 6074 | 0.068 | 0.38 | NO |
60 | SRP54 | SRP54 | SRP54 | 6133 | 0.066 | 0.38 | NO |
61 | EMP3 | EMP3 | EMP3 | 6296 | 0.063 | 0.37 | NO |
62 | HMGB1 | HMGB1 | HMGB1 | 6355 | 0.062 | 0.37 | NO |
63 | HBS1L | HBS1L | HBS1L | 6405 | 0.061 | 0.37 | NO |
64 | USP34 | USP34 | USP34 | 6435 | 0.06 | 0.37 | NO |
65 | MAST2 | MAST2 | MAST2 | 6452 | 0.06 | 0.37 | NO |
66 | SS18 | SS18 | SS18 | 6582 | 0.057 | 0.37 | NO |
67 | SDHB | SDHB | SDHB | 6741 | 0.054 | 0.36 | NO |
68 | LSR | LSR | LSR | 6776 | 0.053 | 0.36 | NO |
69 | TIMELESS | TIMELESS | TIMELESS | 6983 | 0.049 | 0.35 | NO |
70 | ARPP19 | ARPP19 | ARPP19 | 6991 | 0.049 | 0.35 | NO |
71 | HDAC1 | HDAC1 | HDAC1 | 6995 | 0.049 | 0.35 | NO |
72 | COPS2 | COPS2 | COPS2 | 7036 | 0.048 | 0.35 | NO |
73 | CAP1 | CAP1 | CAP1 | 7194 | 0.046 | 0.35 | NO |
74 | TBC1D1 | TBC1D1 | TBC1D1 | 7294 | 0.043 | 0.34 | NO |
75 | ALDH4A1 | ALDH4A1 | ALDH4A1 | 7543 | 0.039 | 0.33 | NO |
76 | ARPC1B | ARPC1B | ARPC1B | 7630 | 0.038 | 0.33 | NO |
77 | AGPAT5 | AGPAT5 | AGPAT5 | 7710 | 0.036 | 0.32 | NO |
78 | PCMT1 | PCMT1 | PCMT1 | 7716 | 0.036 | 0.32 | NO |
79 | PCM1 | PCM1 | PCM1 | 7953 | 0.031 | 0.31 | NO |
80 | GCHFR | GCHFR | GCHFR | 8292 | 0.026 | 0.3 | NO |
81 | GM2A | GM2A | GM2A | 8332 | 0.025 | 0.29 | NO |
82 | RHEB | RHEB | RHEB | 8406 | 0.024 | 0.29 | NO |
83 | SYPL1 | SYPL1 | SYPL1 | 8428 | 0.024 | 0.29 | NO |
84 | NUSAP1 | NUSAP1 | NUSAP1 | 8437 | 0.024 | 0.29 | NO |
85 | NQO2 | NQO2 | NQO2 | 8448 | 0.023 | 0.29 | NO |
86 | COPS3 | COPS3 | COPS3 | 8466 | 0.023 | 0.29 | NO |
87 | XRCC5 | XRCC5 | XRCC5 | 8498 | 0.023 | 0.29 | NO |
88 | PEX1 | PEX1 | PEX1 | 8676 | 0.02 | 0.28 | NO |
89 | ARPC2 | ARPC2 | ARPC2 | 8691 | 0.02 | 0.28 | NO |
90 | G3BP1 | G3BP1 | G3BP1 | 8815 | 0.018 | 0.28 | NO |
91 | FOXN3 | FOXN3 | FOXN3 | 8841 | 0.018 | 0.27 | NO |
92 | PRPSAP2 | PRPSAP2 | PRPSAP2 | 8918 | 0.016 | 0.27 | NO |
93 | DDX39A | DDX39A | DDX39A | 8922 | 0.016 | 0.27 | NO |
94 | CD22 | CD22 | CD22 | 8973 | 0.015 | 0.27 | NO |
95 | ALDH2 | ALDH2 | ALDH2 | 9254 | 0.011 | 0.25 | NO |
96 | TSFM | TSFM | TSFM | 9317 | 0.01 | 0.25 | NO |
97 | MAK16 | MAK16 | MAK16 | 9396 | 0.0089 | 0.25 | NO |
98 | SNX19 | SNX19 | SNX19 | 9522 | 0.0073 | 0.24 | NO |
99 | ISCU | ISCU | ISCU | 9549 | 0.0069 | 0.24 | NO |
100 | EPB41L2 | EPB41L2 | EPB41L2 | 9601 | 0.006 | 0.24 | NO |
101 | PARN | PARN | PARN | 9866 | 0.0019 | 0.22 | NO |
102 | TRMT12 | TRMT12 | TRMT12 | 10008 | -0.0003 | 0.21 | NO |
103 | PFDN2 | PFDN2 | PFDN2 | 10063 | -0.0011 | 0.21 | NO |
104 | GSR | GSR | GSR | 10098 | -0.0015 | 0.21 | NO |
105 | ATP8A1 | ATP8A1 | ATP8A1 | 10139 | -0.0022 | 0.21 | NO |
106 | DUT | DUT | DUT | 10146 | -0.0024 | 0.21 | NO |
107 | TACC1 | TACC1 | TACC1 | 10209 | -0.0031 | 0.2 | NO |
108 | CLSTN1 | CLSTN1 | CLSTN1 | 10258 | -0.0039 | 0.2 | NO |
109 | BIN3 | BIN3 | BIN3 | 10270 | -0.0041 | 0.2 | NO |
110 | SNRPD1 | SNRPD1 | SNRPD1 | 10274 | -0.0042 | 0.2 | NO |
111 | ETS2 | ETS2 | ETS2 | 10298 | -0.0046 | 0.2 | NO |
112 | FNTA | FNTA | FNTA | 10366 | -0.0056 | 0.2 | NO |
113 | CHMP7 | CHMP7 | CHMP7 | 10859 | -0.013 | 0.17 | NO |
114 | NBEAL2 | NBEAL2 | NBEAL2 | 10942 | -0.014 | 0.16 | NO |
115 | PARP1 | PARP1 | PARP1 | 10947 | -0.014 | 0.16 | NO |
116 | NRGN | NRGN | NRGN | 10979 | -0.014 | 0.16 | NO |
117 | MRPS22 | MRPS22 | MRPS22 | 11225 | -0.018 | 0.15 | NO |
118 | CKAP4 | CKAP4 | CKAP4 | 11254 | -0.018 | 0.15 | NO |
119 | ENSA | ENSA | ENSA | 11287 | -0.018 | 0.15 | NO |
120 | SH2B2 | SH2B2 | SH2B2 | 11365 | -0.02 | 0.14 | NO |
121 | LGALSL | LGALSL | LGALSL | 11529 | -0.022 | 0.14 | NO |
122 | GNAS | GNAS | GNAS | 11678 | -0.024 | 0.13 | NO |
123 | MEF2C | MEF2C | MEF2C | 11759 | -0.025 | 0.13 | NO |
124 | PAK2 | PAK2 | PAK2 | 11766 | -0.025 | 0.13 | NO |
125 | DENND1C | DENND1C | DENND1C | 11829 | -0.026 | 0.12 | NO |
126 | MRPL34 | MRPL34 | MRPL34 | 11838 | -0.026 | 0.12 | NO |
127 | DEDD | DEDD | DEDD | 11951 | -0.028 | 0.12 | NO |
128 | NUDT11 | NUDT11 | NUDT11 | 12004 | -0.029 | 0.12 | NO |
129 | HMGB3 | HMGB3 | HMGB3 | 12042 | -0.029 | 0.12 | NO |
130 | FANCA | FANCA | FANCA | 12096 | -0.03 | 0.12 | NO |
131 | ITGB1 | ITGB1 | ITGB1 | 12218 | -0.032 | 0.11 | NO |
132 | ARF3 | ARF3 | ARF3 | 12360 | -0.034 | 0.1 | NO |
133 | CYB5R1 | CYB5R1 | CYB5R1 | 12389 | -0.035 | 0.1 | NO |
134 | ADCK2 | ADCK2 | ADCK2 | 12394 | -0.035 | 0.1 | NO |
135 | KIAA0226 | KIAA0226 | KIAA0226 | 12465 | -0.036 | 0.1 | NO |
136 | CNOT7 | CNOT7 | CNOT7 | 12477 | -0.036 | 0.1 | NO |
137 | PPP2R2A | PPP2R2A | PPP2R2A | 12676 | -0.039 | 0.093 | NO |
138 | GRK6 | GRK6 | GRK6 | 12726 | -0.04 | 0.092 | NO |
139 | LSM4 | LSM4 | LSM4 | 12748 | -0.04 | 0.092 | NO |
140 | TMEM147 | TMEM147 | TMEM147 | 12925 | -0.043 | 0.084 | NO |
141 | LSM1 | LSM1 | LSM1 | 13159 | -0.046 | 0.073 | NO |
142 | CDKN3 | CDKN3 | CDKN3 | 13176 | -0.046 | 0.074 | NO |
143 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 13178 | -0.046 | 0.076 | NO |
144 | C6orf106 | C6orf106 | C6orf106 | 13253 | -0.048 | 0.073 | NO |
145 | MAGEH1 | MAGEH1 | MAGEH1 | 13259 | -0.048 | 0.075 | NO |
146 | HGSNAT | HGSNAT | HGSNAT | 13324 | -0.049 | 0.073 | NO |
147 | TUBB2A | TUBB2A | TUBB2A | 13325 | -0.049 | 0.075 | NO |
148 | MAP4K4 | MAP4K4 | MAP4K4 | 13331 | -0.049 | 0.077 | NO |
149 | TUBA1B | TUBA1B | TUBA1B | 13384 | -0.05 | 0.076 | NO |
150 | PPP6R1 | PPP6R1 | PPP6R1 | 13403 | -0.05 | 0.077 | NO |
151 | TUBA1C | TUBA1C | TUBA1C | 13404 | -0.05 | 0.079 | NO |
152 | CLTB | CLTB | CLTB | 13459 | -0.051 | 0.078 | NO |
153 | FLII | FLII | FLII | 13515 | -0.052 | 0.077 | NO |
154 | RNF126 | RNF126 | RNF126 | 13545 | -0.053 | 0.077 | NO |
155 | SBF1 | SBF1 | SBF1 | 13573 | -0.053 | 0.078 | NO |
156 | XPO7 | XPO7 | XPO7 | 13720 | -0.056 | 0.072 | NO |
157 | ACAT1 | ACAT1 | ACAT1 | 13747 | -0.056 | 0.073 | NO |
158 | NCOR2 | NCOR2 | NCOR2 | 13897 | -0.059 | 0.067 | NO |
159 | NHP2L1 | NHP2L1 | NHP2L1 | 13962 | -0.06 | 0.065 | NO |
160 | KIAA0930 | KIAA0930 | KIAA0930 | 14160 | -0.063 | 0.057 | NO |
161 | COPS6 | COPS6 | COPS6 | 14276 | -0.065 | 0.053 | NO |
162 | DDX3Y | DDX3Y | DDX3Y | 14292 | -0.066 | 0.055 | NO |
163 | CUX1 | CUX1 | CUX1 | 14328 | -0.066 | 0.055 | NO |
164 | MFHAS1 | MFHAS1 | MFHAS1 | 14416 | -0.068 | 0.053 | NO |
165 | MYH10 | MYH10 | MYH10 | 14614 | -0.071 | 0.045 | NO |
166 | PARD6A | PARD6A | PARD6A | 14649 | -0.072 | 0.046 | NO |
167 | MRPS33 | MRPS33 | MRPS33 | 14703 | -0.073 | 0.046 | NO |
168 | PXMP4 | PXMP4 | PXMP4 | 14745 | -0.074 | 0.046 | NO |
169 | ASH2L | ASH2L | ASH2L | 14810 | -0.076 | 0.046 | NO |
170 | PPP2CB | PPP2CB | PPP2CB | 14874 | -0.077 | 0.045 | NO |
171 | DST | DST | DST | 15122 | -0.084 | 0.035 | NO |
172 | HSPBP1 | HSPBP1 | HSPBP1 | 15161 | -0.084 | 0.036 | NO |
173 | TMEM106C | TMEM106C | TMEM106C | 15387 | -0.091 | 0.027 | NO |
174 | NFIB | NFIB | NFIB | 15435 | -0.093 | 0.028 | NO |
175 | INTS9 | INTS9 | INTS9 | 15454 | -0.093 | 0.031 | NO |
176 | MYO1E | MYO1E | MYO1E | 15510 | -0.095 | 0.031 | NO |
177 | PDLIM2 | PDLIM2 | PDLIM2 | 15580 | -0.097 | 0.031 | NO |
178 | PEMT | PEMT | PEMT | 15596 | -0.098 | 0.034 | NO |
179 | USP13 | USP13 | USP13 | 15623 | -0.098 | 0.037 | NO |
180 | E2F1 | E2F1 | E2F1 | 15643 | -0.099 | 0.04 | NO |
181 | GTF2F1 | GTF2F1 | GTF2F1 | 15660 | -0.1 | 0.043 | NO |
182 | GTF2IRD1 | GTF2IRD1 | GTF2IRD1 | 16004 | -0.11 | 0.028 | NO |
183 | GTPBP6 | GTPBP6 | GTPBP6 | 16056 | -0.12 | 0.03 | NO |
184 | CD99 | CD99 | CD99 | 16057 | -0.12 | 0.034 | NO |
185 | KDM5D | KDM5D | KDM5D | 16150 | -0.12 | 0.034 | NO |
186 | DPYSL2 | DPYSL2 | DPYSL2 | 16197 | -0.12 | 0.036 | NO |
187 | D4S234E | D4S234E | D4S234E | 16377 | -0.13 | 0.031 | NO |
188 | SLCO4A1 | SLCO4A1 | SLCO4A1 | 16490 | -0.14 | 0.03 | NO |
189 | CYP39A1 | CYP39A1 | CYP39A1 | 16502 | -0.14 | 0.035 | NO |
190 | SLC25A6 | SLC25A6 | SLC25A6 | 16532 | -0.14 | 0.039 | NO |
191 | LTBP1 | LTBP1 | LTBP1 | 17151 | -0.2 | 0.013 | NO |
192 | PEG10 | PEG10 | PEG10 | 17269 | -0.23 | 0.015 | NO |
193 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 17318 | -0.24 | 0.022 | NO |
194 | MEST | MEST | MEST | 17404 | -0.26 | 0.027 | NO |
195 | PDGFD | PDGFD | PDGFD | 17500 | -0.28 | 0.033 | NO |
Figure S91. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY.

Figure S92. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S47. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PSMA1 | PSMA1 | PSMA1 | 48 | 1 | 0.14 | YES |
2 | PSMB9 | PSMB9 | PSMB9 | 463 | 0.57 | 0.21 | YES |
3 | TAP1 | TAP1 | TAP1 | 1000 | 0.41 | 0.24 | YES |
4 | PSMA2 | PSMA2 | PSMA2 | 1121 | 0.39 | 0.29 | YES |
5 | HLA-B | HLA-B | HLA-B | 1484 | 0.33 | 0.32 | YES |
6 | ERAP2 | ERAP2 | ERAP2 | 1578 | 0.32 | 0.36 | YES |
7 | TAP2 | TAP2 | TAP2 | 1751 | 0.3 | 0.39 | YES |
8 | PSMB8 | PSMB8 | PSMB8 | 1900 | 0.28 | 0.43 | YES |
9 | HLA-C | HLA-C | HLA-C | 2116 | 0.26 | 0.45 | YES |
10 | TAPBPL | TAPBPL | TAPBPL | 2419 | 0.23 | 0.47 | YES |
11 | PSMB10 | PSMB10 | PSMB10 | 2806 | 0.19 | 0.48 | YES |
12 | HLA-A | HLA-A | HLA-A | 3039 | 0.18 | 0.49 | YES |
13 | ERAP1 | ERAP1 | ERAP1 | 3175 | 0.17 | 0.51 | YES |
14 | PSME2 | PSME2 | PSME2 | 3309 | 0.16 | 0.52 | YES |
15 | PSMA3 | PSMA3 | PSMA3 | 3757 | 0.14 | 0.52 | YES |
16 | PSMA4 | PSMA4 | PSMA4 | 3809 | 0.14 | 0.54 | YES |
17 | PSME4 | PSME4 | PSME4 | 3830 | 0.14 | 0.56 | YES |
18 | DERL1 | DERL1 | DERL1 | 3899 | 0.13 | 0.57 | YES |
19 | PSMD14 | PSMD14 | PSMD14 | 4117 | 0.12 | 0.58 | YES |
20 | TAPBP | TAPBP | TAPBP | 4292 | 0.12 | 0.58 | YES |
21 | PSMA6 | PSMA6 | PSMA6 | 4713 | 0.1 | 0.58 | YES |
22 | PSME1 | PSME1 | PSME1 | 4764 | 0.1 | 0.59 | YES |
23 | PSMC6 | PSMC6 | PSMC6 | 4926 | 0.096 | 0.59 | YES |
24 | PSMA7 | PSMA7 | PSMA7 | 6580 | 0.057 | 0.51 | NO |
25 | PSMD7 | PSMD7 | PSMD7 | 6717 | 0.054 | 0.51 | NO |
26 | PSMB2 | PSMB2 | PSMB2 | 6742 | 0.054 | 0.52 | NO |
27 | PSMC2 | PSMC2 | PSMC2 | 6949 | 0.05 | 0.51 | NO |
28 | PSMC1 | PSMC1 | PSMC1 | 7331 | 0.043 | 0.5 | NO |
29 | PDIA3 | PDIA3 | PDIA3 | 7718 | 0.036 | 0.48 | NO |
30 | PSMD5 | PSMD5 | PSMD5 | 7928 | 0.032 | 0.48 | NO |
31 | CANX | CANX | CANX | 7996 | 0.03 | 0.48 | NO |
32 | PSMD11 | PSMD11 | PSMD11 | 8401 | 0.024 | 0.46 | NO |
33 | HMGCS1 | HMGCS1 | HMGCS1 | 9099 | 0.013 | 0.42 | NO |
34 | PDIA6 | PDIA6 | PDIA6 | 9636 | 0.0054 | 0.39 | NO |
35 | PSMC3 | PSMC3 | PSMC3 | 9891 | 0.0015 | 0.38 | NO |
36 | PSMC5 | PSMC5 | PSMC5 | 10429 | -0.0064 | 0.35 | NO |
37 | PSMB6 | PSMB6 | PSMB6 | 10559 | -0.0085 | 0.34 | NO |
38 | PSMD8 | PSMD8 | PSMD8 | 11103 | -0.016 | 0.32 | NO |
39 | NGLY1 | NGLY1 | NGLY1 | 11290 | -0.018 | 0.31 | NO |
40 | PSME3 | PSME3 | PSME3 | 11322 | -0.019 | 0.31 | NO |
41 | PSMB5 | PSMB5 | PSMB5 | 11414 | -0.02 | 0.31 | NO |
42 | TMED4 | TMED4 | TMED4 | 12203 | -0.032 | 0.27 | NO |
43 | KDELR1 | KDELR1 | KDELR1 | 12224 | -0.032 | 0.27 | NO |
44 | PDIA5 | PDIA5 | PDIA5 | 12601 | -0.038 | 0.26 | NO |
45 | GGA3 | GGA3 | GGA3 | 13186 | -0.047 | 0.23 | NO |
46 | ATF4 | ATF4 | ATF4 | 13656 | -0.055 | 0.21 | NO |
47 | SERP1 | SERP1 | SERP1 | 13665 | -0.055 | 0.22 | NO |
48 | SEC22C | SEC22C | SEC22C | 14992 | -0.08 | 0.16 | NO |
49 | PSMF1 | PSMF1 | PSMF1 | 15085 | -0.082 | 0.17 | NO |
Figure S93. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY.

Figure S94. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S48. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PSMA1 | PSMA1 | PSMA1 | 48 | 1 | 0.056 | YES |
2 | CD8B | CD8B | CD8B | 104 | 0.87 | 0.1 | YES |
3 | LCK | LCK | LCK | 149 | 0.81 | 0.15 | YES |
4 | CCR5 | CCR5 | CCR5 | 185 | 0.77 | 0.19 | YES |
5 | CD247 | CD247 | CD247 | 228 | 0.73 | 0.23 | YES |
6 | PSMB9 | PSMB9 | PSMB9 | 463 | 0.57 | 0.25 | YES |
7 | DOCK2 | DOCK2 | DOCK2 | 659 | 0.5 | 0.27 | YES |
8 | CD28 | CD28 | CD28 | 979 | 0.42 | 0.28 | YES |
9 | PSMA2 | PSMA2 | PSMA2 | 1121 | 0.39 | 0.29 | YES |
10 | HCK | HCK | HCK | 1463 | 0.33 | 0.29 | YES |
11 | AP1M2 | AP1M2 | AP1M2 | 1499 | 0.33 | 0.31 | YES |
12 | B2M | B2M | B2M | 1883 | 0.28 | 0.3 | YES |
13 | PSMB8 | PSMB8 | PSMB8 | 1900 | 0.28 | 0.32 | YES |
14 | ELMO1 | ELMO1 | ELMO1 | 1935 | 0.27 | 0.33 | YES |
15 | APOBEC3G | APOBEC3G | APOBEC3G | 2013 | 0.27 | 0.34 | YES |
16 | CD4 | CD4 | CD4 | 2531 | 0.22 | 0.33 | YES |
17 | PSMB10 | PSMB10 | PSMB10 | 2806 | 0.19 | 0.32 | YES |
18 | HLA-A | HLA-A | HLA-A | 3039 | 0.18 | 0.32 | YES |
19 | LIG4 | LIG4 | LIG4 | 3181 | 0.17 | 0.32 | YES |
20 | PSME2 | PSME2 | PSME2 | 3309 | 0.16 | 0.32 | YES |
21 | CXCR4 | CXCR4 | CXCR4 | 3512 | 0.15 | 0.32 | YES |
22 | PSMA3 | PSMA3 | PSMA3 | 3757 | 0.14 | 0.32 | YES |
23 | PSMA4 | PSMA4 | PSMA4 | 3809 | 0.14 | 0.32 | YES |
24 | PSME4 | PSME4 | PSME4 | 3830 | 0.14 | 0.33 | YES |
25 | CCNT2 | CCNT2 | CCNT2 | 4109 | 0.12 | 0.32 | YES |
26 | PSMD14 | PSMD14 | PSMD14 | 4117 | 0.12 | 0.33 | YES |
27 | TPR | TPR | TPR | 4140 | 0.12 | 0.33 | YES |
28 | TAF13 | TAF13 | TAF13 | 4289 | 0.12 | 0.33 | YES |
29 | TAF5 | TAF5 | TAF5 | 4368 | 0.12 | 0.33 | YES |
30 | TCEB1 | TCEB1 | TCEB1 | 4471 | 0.11 | 0.34 | YES |
31 | POLR2F | POLR2F | POLR2F | 4514 | 0.11 | 0.34 | YES |
32 | PSMA5 | PSMA5 | PSMA5 | 4534 | 0.11 | 0.34 | YES |
33 | XRCC4 | XRCC4 | XRCC4 | 4686 | 0.1 | 0.34 | YES |
34 | PSMA6 | PSMA6 | PSMA6 | 4713 | 0.1 | 0.35 | YES |
35 | PSME1 | PSME1 | PSME1 | 4764 | 0.1 | 0.35 | YES |
36 | XPO1 | XPO1 | XPO1 | 4911 | 0.097 | 0.35 | YES |
37 | PSMC6 | PSMC6 | PSMC6 | 4926 | 0.096 | 0.35 | YES |
38 | POLR2K | POLR2K | POLR2K | 4998 | 0.094 | 0.35 | YES |
39 | TCEA1 | TCEA1 | TCEA1 | 5080 | 0.092 | 0.35 | YES |
40 | CCNH | CCNH | CCNH | 5165 | 0.089 | 0.36 | YES |
41 | GTF2A1 | GTF2A1 | GTF2A1 | 5212 | 0.088 | 0.36 | YES |
42 | ATP6V1H | ATP6V1H | ATP6V1H | 5322 | 0.085 | 0.36 | YES |
43 | CUL5 | CUL5 | CUL5 | 5421 | 0.083 | 0.36 | YES |
44 | NUPL2 | NUPL2 | NUPL2 | 5528 | 0.08 | 0.35 | YES |
45 | GTF2B | GTF2B | GTF2B | 5626 | 0.078 | 0.35 | YES |
46 | GTF2F2 | GTF2F2 | GTF2F2 | 5690 | 0.076 | 0.35 | YES |
47 | PSMD12 | PSMD12 | PSMD12 | 5705 | 0.076 | 0.36 | YES |
48 | GTF2H3 | GTF2H3 | GTF2H3 | 5906 | 0.071 | 0.35 | NO |
49 | RNGTT | RNGTT | RNGTT | 6051 | 0.068 | 0.35 | NO |
50 | TAF4B | TAF4B | TAF4B | 6191 | 0.065 | 0.34 | NO |
51 | NUP88 | NUP88 | NUP88 | 6290 | 0.063 | 0.34 | NO |
52 | NUP50 | NUP50 | NUP50 | 6291 | 0.063 | 0.34 | NO |
53 | NCBP1 | NCBP1 | NCBP1 | 6369 | 0.062 | 0.34 | NO |
54 | NUP107 | NUP107 | NUP107 | 6464 | 0.06 | 0.34 | NO |
55 | PSMA7 | PSMA7 | PSMA7 | 6580 | 0.057 | 0.34 | NO |
56 | PSMD7 | PSMD7 | PSMD7 | 6717 | 0.054 | 0.34 | NO |
57 | PSMB2 | PSMB2 | PSMB2 | 6742 | 0.054 | 0.34 | NO |
58 | PSMC2 | PSMC2 | PSMC2 | 6949 | 0.05 | 0.33 | NO |
59 | TCEB3 | TCEB3 | TCEB3 | 7007 | 0.049 | 0.33 | NO |
60 | RANBP2 | RANBP2 | RANBP2 | 7028 | 0.049 | 0.33 | NO |
61 | POLR2B | POLR2B | POLR2B | 7038 | 0.048 | 0.33 | NO |
62 | NUP54 | NUP54 | NUP54 | 7046 | 0.048 | 0.33 | NO |
63 | TAF9 | TAF9 | TAF9 | 7130 | 0.047 | 0.33 | NO |
64 | PSIP1 | PSIP1 | PSIP1 | 7319 | 0.043 | 0.32 | NO |
65 | PSMC1 | PSMC1 | PSMC1 | 7331 | 0.043 | 0.33 | NO |
66 | RNMT | RNMT | RNMT | 7344 | 0.042 | 0.33 | NO |
67 | CCNT1 | CCNT1 | CCNT1 | 7489 | 0.04 | 0.32 | NO |
68 | NUP43 | NUP43 | NUP43 | 7512 | 0.04 | 0.32 | NO |
69 | NUPL1 | NUPL1 | NUPL1 | 7523 | 0.04 | 0.32 | NO |
70 | GTF2H1 | GTF2H1 | GTF2H1 | 7706 | 0.036 | 0.32 | NO |
71 | AP1G1 | AP1G1 | AP1G1 | 7783 | 0.034 | 0.32 | NO |
72 | PSMD5 | PSMD5 | PSMD5 | 7928 | 0.032 | 0.31 | NO |
73 | TAF12 | TAF12 | TAF12 | 8037 | 0.03 | 0.3 | NO |
74 | NUP85 | NUP85 | NUP85 | 8043 | 0.03 | 0.31 | NO |
75 | SUPT16H | SUPT16H | SUPT16H | 8081 | 0.029 | 0.3 | NO |
76 | GTF2H2 | GTF2H2 | GTF2H2 | 8094 | 0.029 | 0.31 | NO |
77 | RBX1 | RBX1 | RBX1 | 8095 | 0.029 | 0.31 | NO |
78 | SEH1L | SEH1L | SEH1L | 8173 | 0.028 | 0.3 | NO |
79 | PSMB3 | PSMB3 | PSMB3 | 8251 | 0.026 | 0.3 | NO |
80 | PSMB1 | PSMB1 | PSMB1 | 8257 | 0.026 | 0.3 | NO |
81 | PSMD11 | PSMD11 | PSMD11 | 8401 | 0.024 | 0.3 | NO |
82 | KPNB1 | KPNB1 | KPNB1 | 8422 | 0.024 | 0.3 | NO |
83 | CDK7 | CDK7 | CDK7 | 8481 | 0.023 | 0.3 | NO |
84 | XRCC5 | XRCC5 | XRCC5 | 8498 | 0.023 | 0.3 | NO |
85 | GTF2A2 | GTF2A2 | GTF2A2 | 8508 | 0.023 | 0.3 | NO |
86 | TAF1 | TAF1 | TAF1 | 8574 | 0.021 | 0.29 | NO |
87 | NUP155 | NUP155 | NUP155 | 8910 | 0.016 | 0.28 | NO |
88 | PSMD10 | PSMD10 | PSMD10 | 8914 | 0.016 | 0.28 | NO |
89 | POLR2D | POLR2D | POLR2D | 9151 | 0.012 | 0.26 | NO |
90 | VPS37A | VPS37A | VPS37A | 9259 | 0.011 | 0.26 | NO |
91 | NMT1 | NMT1 | NMT1 | 9300 | 0.01 | 0.26 | NO |
92 | NUP205 | NUP205 | NUP205 | 9376 | 0.0091 | 0.25 | NO |
93 | VPS28 | VPS28 | VPS28 | 9423 | 0.0086 | 0.25 | NO |
94 | PSMA8 | PSMA8 | PSMA8 | 9540 | 0.007 | 0.25 | NO |
95 | GTF2E2 | GTF2E2 | GTF2E2 | 9607 | 0.0059 | 0.24 | NO |
96 | SKP1 | SKP1 | SKP1 | 9662 | 0.005 | 0.24 | NO |
97 | PSMC4 | PSMC4 | PSMC4 | 9796 | 0.0029 | 0.23 | NO |
98 | NUP37 | NUP37 | NUP37 | 9807 | 0.0027 | 0.23 | NO |
99 | PSMD1 | PSMD1 | PSMD1 | 9820 | 0.0026 | 0.23 | NO |
100 | SLC25A4 | SLC25A4 | SLC25A4 | 9868 | 0.0019 | 0.23 | NO |
101 | PSMC3 | PSMC3 | PSMC3 | 9891 | 0.0015 | 0.23 | NO |
102 | CDK9 | CDK9 | CDK9 | 10119 | -0.002 | 0.22 | NO |
103 | AP2A2 | AP2A2 | AP2A2 | 10203 | -0.003 | 0.21 | NO |
104 | PSMD13 | PSMD13 | PSMD13 | 10277 | -0.0043 | 0.21 | NO |
105 | ERCC3 | ERCC3 | ERCC3 | 10316 | -0.0048 | 0.21 | NO |
106 | POLR2A | POLR2A | POLR2A | 10350 | -0.0053 | 0.2 | NO |
107 | NUP35 | NUP35 | NUP35 | 10404 | -0.0062 | 0.2 | NO |
108 | PSMC5 | PSMC5 | PSMC5 | 10429 | -0.0064 | 0.2 | NO |
109 | ELL | ELL | ELL | 10432 | -0.0065 | 0.2 | NO |
110 | AP1S2 | AP1S2 | AP1S2 | 10471 | -0.0071 | 0.2 | NO |
111 | FEN1 | FEN1 | FEN1 | 10547 | -0.0084 | 0.2 | NO |
112 | PSMB6 | PSMB6 | PSMB6 | 10559 | -0.0085 | 0.2 | NO |
113 | PSMD3 | PSMD3 | PSMD3 | 10590 | -0.0091 | 0.19 | NO |
114 | NUP210 | NUP210 | NUP210 | 10642 | -0.0099 | 0.19 | NO |
115 | ARF1 | ARF1 | ARF1 | 10666 | -0.01 | 0.19 | NO |
116 | MNAT1 | MNAT1 | MNAT1 | 10679 | -0.01 | 0.19 | NO |
117 | PSMB7 | PSMB7 | PSMB7 | 10709 | -0.011 | 0.19 | NO |
118 | TSG101 | TSG101 | TSG101 | 10898 | -0.013 | 0.18 | NO |
119 | RAN | RAN | RAN | 10991 | -0.014 | 0.18 | NO |
120 | NUP133 | NUP133 | NUP133 | 11041 | -0.015 | 0.17 | NO |
121 | PSMD8 | PSMD8 | PSMD8 | 11103 | -0.016 | 0.17 | NO |
122 | NUP188 | NUP188 | NUP188 | 11140 | -0.016 | 0.17 | NO |
123 | PSMB4 | PSMB4 | PSMB4 | 11164 | -0.017 | 0.17 | NO |
124 | TBP | TBP | TBP | 11293 | -0.018 | 0.16 | NO |
125 | POLR2C | POLR2C | POLR2C | 11372 | -0.02 | 0.16 | NO |
126 | PSMB5 | PSMB5 | PSMB5 | 11414 | -0.02 | 0.16 | NO |
127 | POLR2G | POLR2G | POLR2G | 11425 | -0.02 | 0.16 | NO |
128 | NUP62 | NUP62 | NUP62 | 11433 | -0.02 | 0.16 | NO |
129 | AP2B1 | AP2B1 | AP2B1 | 11562 | -0.022 | 0.16 | NO |
130 | KPNA1 | KPNA1 | KPNA1 | 11635 | -0.023 | 0.15 | NO |
131 | PAK2 | PAK2 | PAK2 | 11766 | -0.025 | 0.15 | NO |
132 | AP1S1 | AP1S1 | AP1S1 | 11858 | -0.026 | 0.14 | NO |
133 | PPIA | PPIA | PPIA | 11867 | -0.027 | 0.14 | NO |
134 | RCC1 | RCC1 | RCC1 | 11876 | -0.027 | 0.14 | NO |
135 | PSMD4 | PSMD4 | PSMD4 | 12032 | -0.029 | 0.14 | NO |
136 | CTDP1 | CTDP1 | CTDP1 | 12044 | -0.029 | 0.14 | NO |
137 | NUP153 | NUP153 | NUP153 | 12054 | -0.029 | 0.14 | NO |
138 | PSMD9 | PSMD9 | PSMD9 | 12076 | -0.03 | 0.14 | NO |
139 | BTRC | BTRC | BTRC | 12089 | -0.03 | 0.14 | NO |
140 | TAF4 | TAF4 | TAF4 | 12159 | -0.031 | 0.14 | NO |
141 | NCBP2 | NCBP2 | NCBP2 | 12230 | -0.032 | 0.14 | NO |
142 | GTF2E1 | GTF2E1 | GTF2E1 | 12246 | -0.032 | 0.14 | NO |
143 | AP1M1 | AP1M1 | AP1M1 | 12354 | -0.034 | 0.14 | NO |
144 | PSMD6 | PSMD6 | PSMD6 | 12416 | -0.035 | 0.13 | NO |
145 | SLC25A5 | SLC25A5 | SLC25A5 | 12434 | -0.036 | 0.14 | NO |
146 | TAF11 | TAF11 | TAF11 | 12436 | -0.036 | 0.14 | NO |
147 | POLR2E | POLR2E | POLR2E | 12438 | -0.036 | 0.14 | NO |
148 | RAC1 | RAC1 | RAC1 | 12511 | -0.036 | 0.14 | NO |
149 | NPM1 | NPM1 | NPM1 | 12549 | -0.037 | 0.14 | NO |
150 | XRCC6 | XRCC6 | XRCC6 | 12605 | -0.038 | 0.14 | NO |
151 | POLR2J | POLR2J | POLR2J | 12607 | -0.038 | 0.14 | NO |
152 | RANBP1 | RANBP1 | RANBP1 | 12640 | -0.038 | 0.14 | NO |
153 | AP1B1 | AP1B1 | AP1B1 | 12772 | -0.04 | 0.13 | NO |
154 | GTF2H4 | GTF2H4 | GTF2H4 | 12881 | -0.042 | 0.13 | NO |
155 | LIG1 | LIG1 | LIG1 | 13150 | -0.046 | 0.12 | NO |
156 | TCEB2 | TCEB2 | TCEB2 | 13312 | -0.049 | 0.11 | NO |
157 | AAAS | AAAS | AAAS | 13390 | -0.05 | 0.11 | NO |
158 | AP2A1 | AP2A1 | AP2A1 | 13477 | -0.052 | 0.11 | NO |
159 | RAE1 | RAE1 | RAE1 | 13491 | -0.052 | 0.11 | NO |
160 | NMT2 | NMT2 | NMT2 | 13509 | -0.052 | 0.11 | NO |
161 | POLR2L | POLR2L | POLR2L | 13561 | -0.053 | 0.11 | NO |
162 | AP2S1 | AP2S1 | AP2S1 | 13652 | -0.054 | 0.11 | NO |
163 | SSRP1 | SSRP1 | SSRP1 | 13834 | -0.058 | 0.1 | NO |
164 | VPS37B | VPS37B | VPS37B | 14036 | -0.061 | 0.097 | NO |
165 | FYN | FYN | FYN | 14091 | -0.062 | 0.098 | NO |
166 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 14125 | -0.062 | 0.1 | NO |
167 | TAF10 | TAF10 | TAF10 | 14260 | -0.065 | 0.096 | NO |
168 | NUP93 | NUP93 | NUP93 | 14315 | -0.066 | 0.097 | NO |
169 | NUP214 | NUP214 | NUP214 | 14487 | -0.069 | 0.091 | NO |
170 | BANF1 | BANF1 | BANF1 | 14660 | -0.072 | 0.086 | NO |
171 | POLR2I | POLR2I | POLR2I | 14685 | -0.073 | 0.089 | NO |
172 | RANGAP1 | RANGAP1 | RANGAP1 | 14734 | -0.074 | 0.09 | NO |
173 | PSMD2 | PSMD2 | PSMD2 | 14824 | -0.076 | 0.09 | NO |
174 | VPS37C | VPS37C | VPS37C | 14957 | -0.079 | 0.087 | NO |
175 | SUPT5H | SUPT5H | SUPT5H | 14989 | -0.08 | 0.09 | NO |
176 | PSMF1 | PSMF1 | PSMF1 | 15085 | -0.082 | 0.09 | NO |
177 | POM121 | POM121 | POM121 | 15123 | -0.084 | 0.092 | NO |
178 | TAF6 | TAF6 | TAF6 | 15218 | -0.086 | 0.092 | NO |
179 | RPS27A | RPS27A | RPS27A | 15344 | -0.09 | 0.09 | NO |
180 | POLR2H | POLR2H | POLR2H | 15373 | -0.091 | 0.094 | NO |
181 | AP2M1 | AP2M1 | AP2M1 | 15657 | -0.1 | 0.084 | NO |
182 | GTF2F1 | GTF2F1 | GTF2F1 | 15660 | -0.1 | 0.09 | NO |
183 | PACS1 | PACS1 | PACS1 | 15739 | -0.1 | 0.091 | NO |
184 | HMGA1 | HMGA1 | HMGA1 | 15943 | -0.11 | 0.086 | NO |
185 | UBA52 | UBA52 | UBA52 | 16002 | -0.11 | 0.09 | NO |
186 | SLC25A6 | SLC25A6 | SLC25A6 | 16532 | -0.14 | 0.068 | NO |
187 | VPS37D | VPS37D | VPS37D | 16698 | -0.16 | 0.068 | NO |
188 | ERCC2 | ERCC2 | ERCC2 | 16737 | -0.16 | 0.075 | NO |
Figure S95. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG JAK STAT SIGNALING PATHWAY.

Figure S96. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG JAK STAT SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S49. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PSMA1 | PSMA1 | PSMA1 | 48 | 1 | 0.042 | YES |
2 | FCGR1B | FCGR1B | FCGR1B | 211 | 0.75 | 0.066 | YES |
3 | FCGR1A | FCGR1A | FCGR1A | 443 | 0.58 | 0.078 | YES |
4 | PSMB9 | PSMB9 | PSMB9 | 463 | 0.57 | 0.1 | YES |
5 | HLA-F | HLA-F | HLA-F | 940 | 0.42 | 0.095 | YES |
6 | TAP1 | TAP1 | TAP1 | 1000 | 0.41 | 0.11 | YES |
7 | TRIM36 | TRIM36 | TRIM36 | 1065 | 0.4 | 0.12 | YES |
8 | PSMA2 | PSMA2 | PSMA2 | 1121 | 0.39 | 0.14 | YES |
9 | CTSS | CTSS | CTSS | 1161 | 0.38 | 0.15 | YES |
10 | CYBB | CYBB | CYBB | 1171 | 0.38 | 0.17 | YES |
11 | ASB2 | ASB2 | ASB2 | 1410 | 0.34 | 0.17 | YES |
12 | UBE2L6 | UBE2L6 | UBE2L6 | 1436 | 0.34 | 0.18 | YES |
13 | ASB15 | ASB15 | ASB15 | 1481 | 0.33 | 0.2 | YES |
14 | HLA-B | HLA-B | HLA-B | 1484 | 0.33 | 0.21 | YES |
15 | NCF4 | NCF4 | NCF4 | 1706 | 0.3 | 0.21 | YES |
16 | MRC1 | MRC1 | MRC1 | 1714 | 0.3 | 0.22 | YES |
17 | TAP2 | TAP2 | TAP2 | 1751 | 0.3 | 0.24 | YES |
18 | B2M | B2M | B2M | 1883 | 0.28 | 0.24 | YES |
19 | PSMB8 | PSMB8 | PSMB8 | 1900 | 0.28 | 0.25 | YES |
20 | HLA-C | HLA-C | HLA-C | 2116 | 0.26 | 0.25 | YES |
21 | DTX3L | DTX3L | DTX3L | 2117 | 0.26 | 0.26 | YES |
22 | MRC2 | MRC2 | MRC2 | 2134 | 0.26 | 0.27 | YES |
23 | SEC24D | SEC24D | SEC24D | 2179 | 0.25 | 0.28 | YES |
24 | NCF2 | NCF2 | NCF2 | 2291 | 0.24 | 0.29 | YES |
25 | UBA7 | UBA7 | UBA7 | 2458 | 0.22 | 0.29 | YES |
26 | TRIM9 | TRIM9 | TRIM9 | 2486 | 0.22 | 0.3 | YES |
27 | CD207 | CD207 | CD207 | 2751 | 0.2 | 0.29 | YES |
28 | PSMB10 | PSMB10 | PSMB10 | 2806 | 0.19 | 0.3 | YES |
29 | UBE2W | UBE2W | UBE2W | 2959 | 0.18 | 0.3 | YES |
30 | HLA-A | HLA-A | HLA-A | 3039 | 0.18 | 0.3 | YES |
31 | RNF182 | RNF182 | RNF182 | 3151 | 0.17 | 0.3 | YES |
32 | ERAP1 | ERAP1 | ERAP1 | 3175 | 0.17 | 0.31 | YES |
33 | WSB1 | WSB1 | WSB1 | 3244 | 0.17 | 0.31 | YES |
34 | SOCS3 | SOCS3 | SOCS3 | 3284 | 0.16 | 0.32 | YES |
35 | PSME2 | PSME2 | PSME2 | 3309 | 0.16 | 0.32 | YES |
36 | UBR1 | UBR1 | UBR1 | 3527 | 0.15 | 0.32 | YES |
37 | UBE2V2 | UBE2V2 | UBE2V2 | 3554 | 0.15 | 0.32 | YES |
38 | HLA-G | HLA-G | HLA-G | 3610 | 0.15 | 0.32 | YES |
39 | FBXO6 | FBXO6 | FBXO6 | 3613 | 0.15 | 0.33 | YES |
40 | PSMA3 | PSMA3 | PSMA3 | 3757 | 0.14 | 0.33 | YES |
41 | SAR1B | SAR1B | SAR1B | 3787 | 0.14 | 0.33 | YES |
42 | PSMA4 | PSMA4 | PSMA4 | 3809 | 0.14 | 0.34 | YES |
43 | PSME4 | PSME4 | PSME4 | 3830 | 0.14 | 0.34 | YES |
44 | TRIM21 | TRIM21 | TRIM21 | 3875 | 0.13 | 0.35 | YES |
45 | ASB5 | ASB5 | ASB5 | 3893 | 0.13 | 0.35 | YES |
46 | SOCS1 | SOCS1 | SOCS1 | 3905 | 0.13 | 0.36 | YES |
47 | UBA6 | UBA6 | UBA6 | 4088 | 0.12 | 0.35 | YES |
48 | PSMD14 | PSMD14 | PSMD14 | 4117 | 0.12 | 0.36 | YES |
49 | WWP1 | WWP1 | WWP1 | 4395 | 0.11 | 0.34 | YES |
50 | TCEB1 | TCEB1 | TCEB1 | 4471 | 0.11 | 0.35 | YES |
51 | CDC27 | CDC27 | CDC27 | 4505 | 0.11 | 0.35 | YES |
52 | RNF6 | RNF6 | RNF6 | 4511 | 0.11 | 0.35 | YES |
53 | PSMA5 | PSMA5 | PSMA5 | 4534 | 0.11 | 0.36 | YES |
54 | CUL2 | CUL2 | CUL2 | 4585 | 0.11 | 0.36 | YES |
55 | PSMA6 | PSMA6 | PSMA6 | 4713 | 0.1 | 0.36 | YES |
56 | NEDD4 | NEDD4 | NEDD4 | 4715 | 0.1 | 0.36 | YES |
57 | PSME1 | PSME1 | PSME1 | 4764 | 0.1 | 0.36 | YES |
58 | SEC61A2 | SEC61A2 | SEC61A2 | 4922 | 0.096 | 0.36 | NO |
59 | PSMC6 | PSMC6 | PSMC6 | 4926 | 0.096 | 0.36 | NO |
60 | ITGAV | ITGAV | ITGAV | 5025 | 0.094 | 0.36 | NO |
61 | UBE2A | UBE2A | UBE2A | 5131 | 0.09 | 0.36 | NO |
62 | ANAPC4 | ANAPC4 | ANAPC4 | 5155 | 0.09 | 0.36 | NO |
63 | TPP2 | TPP2 | TPP2 | 5294 | 0.086 | 0.36 | NO |
64 | ASB11 | ASB11 | ASB11 | 5407 | 0.083 | 0.36 | NO |
65 | CUL5 | CUL5 | CUL5 | 5421 | 0.083 | 0.36 | NO |
66 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 5548 | 0.08 | 0.35 | NO |
67 | FBXW7 | FBXW7 | FBXW7 | 5579 | 0.079 | 0.36 | NO |
68 | UBE2J1 | UBE2J1 | UBE2J1 | 5630 | 0.078 | 0.36 | NO |
69 | PSMD12 | PSMD12 | PSMD12 | 5705 | 0.076 | 0.36 | NO |
70 | SEC23A | SEC23A | SEC23A | 5717 | 0.076 | 0.36 | NO |
71 | LNPEP | LNPEP | LNPEP | 5739 | 0.075 | 0.36 | NO |
72 | UBE2Q2 | UBE2Q2 | UBE2Q2 | 5904 | 0.071 | 0.36 | NO |
73 | UBE3A | UBE3A | UBE3A | 5994 | 0.07 | 0.35 | NO |
74 | UBA2 | UBA2 | UBA2 | 5996 | 0.069 | 0.36 | NO |
75 | HERC2 | HERC2 | HERC2 | 6099 | 0.067 | 0.35 | NO |
76 | CUL1 | CUL1 | CUL1 | 6182 | 0.066 | 0.35 | NO |
77 | LRR1 | LRR1 | LRR1 | 6190 | 0.065 | 0.35 | NO |
78 | ASB9 | ASB9 | ASB9 | 6235 | 0.064 | 0.35 | NO |
79 | UBR2 | UBR2 | UBR2 | 6244 | 0.064 | 0.36 | NO |
80 | UBE2K | UBE2K | UBE2K | 6273 | 0.064 | 0.36 | NO |
81 | CD36 | CD36 | CD36 | 6303 | 0.063 | 0.36 | NO |
82 | HSPA5 | HSPA5 | HSPA5 | 6445 | 0.06 | 0.35 | NO |
83 | PSMA7 | PSMA7 | PSMA7 | 6580 | 0.057 | 0.35 | NO |
84 | CUL3 | CUL3 | CUL3 | 6660 | 0.056 | 0.35 | NO |
85 | FBXO3 | FBXO3 | FBXO3 | 6703 | 0.055 | 0.35 | NO |
86 | PJA2 | PJA2 | PJA2 | 6716 | 0.054 | 0.35 | NO |
87 | PSMD7 | PSMD7 | PSMD7 | 6717 | 0.054 | 0.35 | NO |
88 | PSMB2 | PSMB2 | PSMB2 | 6742 | 0.054 | 0.35 | NO |
89 | ASB7 | ASB7 | ASB7 | 6791 | 0.053 | 0.35 | NO |
90 | UBE2D1 | UBE2D1 | UBE2D1 | 6889 | 0.051 | 0.35 | NO |
91 | FBXO4 | FBXO4 | FBXO4 | 6898 | 0.051 | 0.35 | NO |
92 | ANAPC10 | ANAPC10 | ANAPC10 | 6907 | 0.051 | 0.35 | NO |
93 | PSMC2 | PSMC2 | PSMC2 | 6949 | 0.05 | 0.35 | NO |
94 | FBXO2 | FBXO2 | FBXO2 | 7055 | 0.048 | 0.35 | NO |
95 | ASB8 | ASB8 | ASB8 | 7084 | 0.048 | 0.35 | NO |
96 | PSMC1 | PSMC1 | PSMC1 | 7331 | 0.043 | 0.34 | NO |
97 | UBE2F | UBE2F | UBE2F | 7352 | 0.042 | 0.34 | NO |
98 | KLHL20 | KLHL20 | KLHL20 | 7547 | 0.039 | 0.33 | NO |
99 | SEC24B | SEC24B | SEC24B | 7597 | 0.038 | 0.33 | NO |
100 | RNF138 | RNF138 | RNF138 | 7607 | 0.038 | 0.33 | NO |
101 | PDIA3 | PDIA3 | PDIA3 | 7718 | 0.036 | 0.32 | NO |
102 | UBE2B | UBE2B | UBE2B | 7850 | 0.033 | 0.32 | NO |
103 | UBA3 | UBA3 | UBA3 | 7851 | 0.033 | 0.32 | NO |
104 | NPEPPS | NPEPPS | NPEPPS | 7882 | 0.033 | 0.32 | NO |
105 | PSMD5 | PSMD5 | PSMD5 | 7928 | 0.032 | 0.32 | NO |
106 | SPSB1 | SPSB1 | SPSB1 | 7955 | 0.031 | 0.32 | NO |
107 | CANX | CANX | CANX | 7996 | 0.03 | 0.32 | NO |
108 | CDC26 | CDC26 | CDC26 | 8025 | 0.03 | 0.32 | NO |
109 | RBX1 | RBX1 | RBX1 | 8095 | 0.029 | 0.32 | NO |
110 | PSMB3 | PSMB3 | PSMB3 | 8251 | 0.026 | 0.31 | NO |
111 | UBE4A | UBE4A | UBE4A | 8255 | 0.026 | 0.31 | NO |
112 | PSMB1 | PSMB1 | PSMB1 | 8257 | 0.026 | 0.31 | NO |
113 | CBLB | CBLB | CBLB | 8315 | 0.026 | 0.31 | NO |
114 | UBE2Z | UBE2Z | UBE2Z | 8323 | 0.025 | 0.31 | NO |
115 | RCHY1 | RCHY1 | RCHY1 | 8328 | 0.025 | 0.31 | NO |
116 | UBE2D3 | UBE2D3 | UBE2D3 | 8370 | 0.025 | 0.31 | NO |
117 | PSMD11 | PSMD11 | PSMD11 | 8401 | 0.024 | 0.31 | NO |
118 | KEAP1 | KEAP1 | KEAP1 | 8430 | 0.024 | 0.31 | NO |
119 | TRIP12 | TRIP12 | TRIP12 | 8473 | 0.023 | 0.3 | NO |
120 | SMURF2 | SMURF2 | SMURF2 | 8520 | 0.022 | 0.3 | NO |
121 | RNF34 | RNF34 | RNF34 | 8545 | 0.022 | 0.3 | NO |
122 | UBE2G1 | UBE2G1 | UBE2G1 | 8549 | 0.022 | 0.3 | NO |
123 | TRIM37 | TRIM37 | TRIM37 | 8702 | 0.02 | 0.3 | NO |
124 | UBA5 | UBA5 | UBA5 | 8831 | 0.018 | 0.29 | NO |
125 | UBE3C | UBE3C | UBE3C | 8882 | 0.017 | 0.29 | NO |
126 | PSMD10 | PSMD10 | PSMD10 | 8914 | 0.016 | 0.29 | NO |
127 | UBE2J2 | UBE2J2 | UBE2J2 | 9133 | 0.013 | 0.28 | NO |
128 | KLHL9 | KLHL9 | KLHL9 | 9178 | 0.012 | 0.27 | NO |
129 | ANAPC7 | ANAPC7 | ANAPC7 | 9265 | 0.011 | 0.27 | NO |
130 | UBE2N | UBE2N | UBE2N | 9344 | 0.0096 | 0.26 | NO |
131 | SEC31A | SEC31A | SEC31A | 9410 | 0.0088 | 0.26 | NO |
132 | RNF4 | RNF4 | RNF4 | 9465 | 0.0081 | 0.26 | NO |
133 | SKP2 | SKP2 | SKP2 | 9528 | 0.0072 | 0.26 | NO |
134 | PSMA8 | PSMA8 | PSMA8 | 9540 | 0.007 | 0.26 | NO |
135 | SKP1 | SKP1 | SKP1 | 9662 | 0.005 | 0.25 | NO |
136 | CALR | CALR | CALR | 9694 | 0.0046 | 0.25 | NO |
137 | CDC16 | CDC16 | CDC16 | 9710 | 0.0043 | 0.25 | NO |
138 | CYBA | CYBA | CYBA | 9754 | 0.0037 | 0.24 | NO |
139 | PSMC4 | PSMC4 | PSMC4 | 9796 | 0.0029 | 0.24 | NO |
140 | PSMD1 | PSMD1 | PSMD1 | 9820 | 0.0026 | 0.24 | NO |
141 | CDC23 | CDC23 | CDC23 | 9821 | 0.0026 | 0.24 | NO |
142 | PSMC3 | PSMC3 | PSMC3 | 9891 | 0.0015 | 0.24 | NO |
143 | UBE2H | UBE2H | UBE2H | 9910 | 0.0013 | 0.24 | NO |
144 | HECTD3 | HECTD3 | HECTD3 | 9916 | 0.0011 | 0.24 | NO |
145 | ANAPC5 | ANAPC5 | ANAPC5 | 10170 | -0.0027 | 0.22 | NO |
146 | UBR4 | UBR4 | UBR4 | 10196 | -0.0029 | 0.22 | NO |
147 | UBE2D2 | UBE2D2 | UBE2D2 | 10247 | -0.0038 | 0.22 | NO |
148 | PSMD13 | PSMD13 | PSMD13 | 10277 | -0.0043 | 0.22 | NO |
149 | RNF220 | RNF220 | RNF220 | 10414 | -0.0063 | 0.21 | NO |
150 | PSMC5 | PSMC5 | PSMC5 | 10429 | -0.0064 | 0.21 | NO |
151 | TRIM32 | TRIM32 | TRIM32 | 10457 | -0.0069 | 0.21 | NO |
152 | VHL | VHL | VHL | 10534 | -0.0082 | 0.2 | NO |
153 | PSMB6 | PSMB6 | PSMB6 | 10559 | -0.0085 | 0.2 | NO |
154 | PSMD3 | PSMD3 | PSMD3 | 10590 | -0.0091 | 0.2 | NO |
155 | PSMB7 | PSMB7 | PSMB7 | 10709 | -0.011 | 0.2 | NO |
156 | ITGB5 | ITGB5 | ITGB5 | 10785 | -0.012 | 0.19 | NO |
157 | DZIP3 | DZIP3 | DZIP3 | 10789 | -0.012 | 0.19 | NO |
158 | SAE1 | SAE1 | SAE1 | 10870 | -0.013 | 0.19 | NO |
159 | FBXO44 | FBXO44 | FBXO44 | 10998 | -0.014 | 0.18 | NO |
160 | GAN | GAN | GAN | 11086 | -0.016 | 0.18 | NO |
161 | PSMD8 | PSMD8 | PSMD8 | 11103 | -0.016 | 0.18 | NO |
162 | PSMB4 | PSMB4 | PSMB4 | 11164 | -0.017 | 0.18 | NO |
163 | FBXW11 | FBXW11 | FBXW11 | 11172 | -0.017 | 0.18 | NO |
164 | MKRN1 | MKRN1 | MKRN1 | 11189 | -0.017 | 0.18 | NO |
165 | SEC61B | SEC61B | SEC61B | 11318 | -0.019 | 0.17 | NO |
166 | SEC61G | SEC61G | SEC61G | 11351 | -0.019 | 0.17 | NO |
167 | PSMB5 | PSMB5 | PSMB5 | 11414 | -0.02 | 0.16 | NO |
168 | ASB16 | ASB16 | ASB16 | 11457 | -0.021 | 0.16 | NO |
169 | UBE2G2 | UBE2G2 | UBE2G2 | 11553 | -0.022 | 0.16 | NO |
170 | PARK2 | PARK2 | PARK2 | 11591 | -0.022 | 0.16 | NO |
171 | UBE3B | UBE3B | UBE3B | 11663 | -0.024 | 0.16 | NO |
172 | RNF41 | RNF41 | RNF41 | 11937 | -0.028 | 0.14 | NO |
173 | RNF25 | RNF25 | RNF25 | 11976 | -0.028 | 0.14 | NO |
174 | PJA1 | PJA1 | PJA1 | 11995 | -0.029 | 0.14 | NO |
175 | PSMD4 | PSMD4 | PSMD4 | 12032 | -0.029 | 0.14 | NO |
176 | UBA1 | UBA1 | UBA1 | 12047 | -0.029 | 0.14 | NO |
177 | UBE2L3 | UBE2L3 | UBE2L3 | 12056 | -0.029 | 0.14 | NO |
178 | PSMD9 | PSMD9 | PSMD9 | 12076 | -0.03 | 0.14 | NO |
179 | BTRC | BTRC | BTRC | 12089 | -0.03 | 0.14 | NO |
180 | SEC24C | SEC24C | SEC24C | 12158 | -0.031 | 0.14 | NO |
181 | UBE2M | UBE2M | UBE2M | 12188 | -0.031 | 0.14 | NO |
182 | ARIH2 | ARIH2 | ARIH2 | 12195 | -0.031 | 0.14 | NO |
183 | UBE2Q1 | UBE2Q1 | UBE2Q1 | 12197 | -0.031 | 0.14 | NO |
184 | LRRC41 | LRRC41 | LRRC41 | 12274 | -0.032 | 0.14 | NO |
185 | LRSAM1 | LRSAM1 | LRSAM1 | 12368 | -0.034 | 0.14 | NO |
186 | CDC20 | CDC20 | CDC20 | 12386 | -0.035 | 0.14 | NO |
187 | PSMD6 | PSMD6 | PSMD6 | 12416 | -0.035 | 0.14 | NO |
188 | ANAPC11 | ANAPC11 | ANAPC11 | 12523 | -0.037 | 0.13 | NO |
189 | TRIM63 | TRIM63 | TRIM63 | 12814 | -0.041 | 0.12 | NO |
190 | ANAPC1 | ANAPC1 | ANAPC1 | 12841 | -0.042 | 0.12 | NO |
191 | HUWE1 | HUWE1 | HUWE1 | 12899 | -0.043 | 0.12 | NO |
192 | UBE2E3 | UBE2E3 | UBE2E3 | 12951 | -0.043 | 0.12 | NO |
193 | SEC61A1 | SEC61A1 | SEC61A1 | 13152 | -0.046 | 0.11 | NO |
194 | TRIM11 | TRIM11 | TRIM11 | 13219 | -0.047 | 0.1 | NO |
195 | TCEB2 | TCEB2 | TCEB2 | 13312 | -0.049 | 0.1 | NO |
196 | RBCK1 | RBCK1 | RBCK1 | 13358 | -0.049 | 0.1 | NO |
197 | ASB1 | ASB1 | ASB1 | 13412 | -0.05 | 0.1 | NO |
198 | ATG7 | ATG7 | ATG7 | 13444 | -0.051 | 0.1 | NO |
199 | UBE2E1 | UBE2E1 | UBE2E1 | 13445 | -0.051 | 0.1 | NO |
200 | ASB6 | ASB6 | ASB6 | 13484 | -0.052 | 0.1 | NO |
201 | UBE2S | UBE2S | UBE2S | 13546 | -0.053 | 0.1 | NO |
202 | UBE2E2 | UBE2E2 | UBE2E2 | 13557 | -0.053 | 0.1 | NO |
203 | UBOX5 | UBOX5 | UBOX5 | 13627 | -0.054 | 0.1 | NO |
204 | SEC13 | SEC13 | SEC13 | 13697 | -0.055 | 0.1 | NO |
205 | BLMH | BLMH | BLMH | 13798 | -0.057 | 0.099 | NO |
206 | ASB13 | ASB13 | ASB13 | 13859 | -0.058 | 0.098 | NO |
207 | UBE2C | UBE2C | UBE2C | 13986 | -0.06 | 0.093 | NO |
208 | UBE2D4 | UBE2D4 | UBE2D4 | 14012 | -0.06 | 0.095 | NO |
209 | ANAPC2 | ANAPC2 | ANAPC2 | 14085 | -0.062 | 0.093 | NO |
210 | CDC34 | CDC34 | CDC34 | 14123 | -0.062 | 0.094 | NO |
211 | SPSB2 | SPSB2 | SPSB2 | 14154 | -0.063 | 0.095 | NO |
212 | SMURF1 | SMURF1 | SMURF1 | 14368 | -0.067 | 0.086 | NO |
213 | FBXW8 | FBXW8 | FBXW8 | 14674 | -0.073 | 0.072 | NO |
214 | UBE2O | UBE2O | UBE2O | 14747 | -0.074 | 0.072 | NO |
215 | ANAPC13 | ANAPC13 | ANAPC13 | 14765 | -0.075 | 0.074 | NO |
216 | SPSB4 | SPSB4 | SPSB4 | 14768 | -0.075 | 0.077 | NO |
217 | PSMD2 | PSMD2 | PSMD2 | 14824 | -0.076 | 0.078 | NO |
218 | UBE2R2 | UBE2R2 | UBE2R2 | 14928 | -0.079 | 0.075 | NO |
219 | PSMF1 | PSMF1 | PSMF1 | 15085 | -0.082 | 0.07 | NO |
220 | STUB1 | STUB1 | STUB1 | 15099 | -0.083 | 0.073 | NO |
221 | VPRBP | VPRBP | VPRBP | 15108 | -0.083 | 0.076 | NO |
222 | RPS27A | RPS27A | RPS27A | 15344 | -0.09 | 0.067 | NO |
223 | CUL7 | CUL7 | CUL7 | 15431 | -0.092 | 0.066 | NO |
224 | RNF144B | RNF144B | RNF144B | 15441 | -0.093 | 0.07 | NO |
225 | FBXO27 | FBXO27 | FBXO27 | 15696 | -0.1 | 0.06 | NO |
226 | UBE2U | UBE2U | UBE2U | 15759 | -0.1 | 0.061 | NO |
227 | DET1 | DET1 | DET1 | 15784 | -0.1 | 0.065 | NO |
228 | UBA52 | UBA52 | UBA52 | 16002 | -0.11 | 0.058 | NO |
229 | ASB12 | ASB12 | ASB12 | 16263 | -0.12 | 0.048 | NO |
230 | RNF123 | RNF123 | RNF123 | 16505 | -0.14 | 0.041 | NO |
231 | ZBTB16 | ZBTB16 | ZBTB16 | 16739 | -0.16 | 0.035 | NO |
232 | KLHL13 | KLHL13 | KLHL13 | 16838 | -0.17 | 0.037 | NO |
233 | ASB4 | ASB4 | ASB4 | 17730 | -0.35 | 0.0027 | NO |
234 | FBXO17 | FBXO17 | FBXO17 | 17813 | -0.39 | 0.015 | NO |
Figure S97. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG HEMATOPOIETIC CELL LINEAGE.

Figure S98. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HEMATOPOIETIC CELL LINEAGE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S50. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PSMA1 | PSMA1 | PSMA1 | 48 | 1 | 0.091 | YES |
2 | FCGR1B | FCGR1B | FCGR1B | 211 | 0.75 | 0.15 | YES |
3 | FCGR1A | FCGR1A | FCGR1A | 443 | 0.58 | 0.19 | YES |
4 | PSMB9 | PSMB9 | PSMB9 | 463 | 0.57 | 0.24 | YES |
5 | HLA-F | HLA-F | HLA-F | 940 | 0.42 | 0.26 | YES |
6 | TAP1 | TAP1 | TAP1 | 1000 | 0.41 | 0.29 | YES |
7 | PSMA2 | PSMA2 | PSMA2 | 1121 | 0.39 | 0.32 | YES |
8 | CTSS | CTSS | CTSS | 1161 | 0.38 | 0.36 | YES |
9 | CYBB | CYBB | CYBB | 1171 | 0.38 | 0.39 | YES |
10 | HLA-B | HLA-B | HLA-B | 1484 | 0.33 | 0.4 | YES |
11 | NCF4 | NCF4 | NCF4 | 1706 | 0.3 | 0.42 | YES |
12 | MRC1 | MRC1 | MRC1 | 1714 | 0.3 | 0.45 | YES |
13 | TAP2 | TAP2 | TAP2 | 1751 | 0.3 | 0.47 | YES |
14 | B2M | B2M | B2M | 1883 | 0.28 | 0.49 | YES |
15 | PSMB8 | PSMB8 | PSMB8 | 1900 | 0.28 | 0.52 | YES |
16 | HLA-C | HLA-C | HLA-C | 2116 | 0.26 | 0.53 | YES |
17 | MRC2 | MRC2 | MRC2 | 2134 | 0.26 | 0.55 | YES |
18 | NCF2 | NCF2 | NCF2 | 2291 | 0.24 | 0.56 | YES |
19 | CD207 | CD207 | CD207 | 2751 | 0.2 | 0.56 | YES |
20 | PSMB10 | PSMB10 | PSMB10 | 2806 | 0.19 | 0.57 | YES |
21 | HLA-A | HLA-A | HLA-A | 3039 | 0.18 | 0.58 | YES |
22 | PSME2 | PSME2 | PSME2 | 3309 | 0.16 | 0.58 | YES |
23 | HLA-G | HLA-G | HLA-G | 3610 | 0.15 | 0.57 | YES |
24 | PSMA3 | PSMA3 | PSMA3 | 3757 | 0.14 | 0.58 | YES |
25 | PSMA4 | PSMA4 | PSMA4 | 3809 | 0.14 | 0.59 | YES |
26 | PSME4 | PSME4 | PSME4 | 3830 | 0.14 | 0.6 | YES |
27 | PSMD14 | PSMD14 | PSMD14 | 4117 | 0.12 | 0.6 | YES |
28 | PSMA5 | PSMA5 | PSMA5 | 4534 | 0.11 | 0.58 | YES |
29 | PSMA6 | PSMA6 | PSMA6 | 4713 | 0.1 | 0.58 | YES |
30 | PSME1 | PSME1 | PSME1 | 4764 | 0.1 | 0.59 | YES |
31 | SEC61A2 | SEC61A2 | SEC61A2 | 4922 | 0.096 | 0.59 | YES |
32 | PSMC6 | PSMC6 | PSMC6 | 4926 | 0.096 | 0.6 | YES |
33 | ITGAV | ITGAV | ITGAV | 5025 | 0.094 | 0.6 | YES |
34 | PSMD12 | PSMD12 | PSMD12 | 5705 | 0.076 | 0.57 | NO |
35 | LNPEP | LNPEP | LNPEP | 5739 | 0.075 | 0.58 | NO |
36 | CD36 | CD36 | CD36 | 6303 | 0.063 | 0.55 | NO |
37 | PSMA7 | PSMA7 | PSMA7 | 6580 | 0.057 | 0.54 | NO |
38 | PSMD7 | PSMD7 | PSMD7 | 6717 | 0.054 | 0.54 | NO |
39 | PSMB2 | PSMB2 | PSMB2 | 6742 | 0.054 | 0.54 | NO |
40 | PSMC2 | PSMC2 | PSMC2 | 6949 | 0.05 | 0.54 | NO |
41 | PSMC1 | PSMC1 | PSMC1 | 7331 | 0.043 | 0.52 | NO |
42 | PDIA3 | PDIA3 | PDIA3 | 7718 | 0.036 | 0.5 | NO |
43 | PSMD5 | PSMD5 | PSMD5 | 7928 | 0.032 | 0.49 | NO |
44 | PSMB3 | PSMB3 | PSMB3 | 8251 | 0.026 | 0.48 | NO |
45 | PSMB1 | PSMB1 | PSMB1 | 8257 | 0.026 | 0.48 | NO |
46 | PSMD11 | PSMD11 | PSMD11 | 8401 | 0.024 | 0.47 | NO |
47 | PSMD10 | PSMD10 | PSMD10 | 8914 | 0.016 | 0.45 | NO |
48 | PSMA8 | PSMA8 | PSMA8 | 9540 | 0.007 | 0.41 | NO |
49 | CALR | CALR | CALR | 9694 | 0.0046 | 0.4 | NO |
50 | CYBA | CYBA | CYBA | 9754 | 0.0037 | 0.4 | NO |
51 | PSMC4 | PSMC4 | PSMC4 | 9796 | 0.0029 | 0.4 | NO |
52 | PSMD1 | PSMD1 | PSMD1 | 9820 | 0.0026 | 0.4 | NO |
53 | PSMC3 | PSMC3 | PSMC3 | 9891 | 0.0015 | 0.39 | NO |
54 | PSMD13 | PSMD13 | PSMD13 | 10277 | -0.0043 | 0.37 | NO |
55 | PSMC5 | PSMC5 | PSMC5 | 10429 | -0.0064 | 0.36 | NO |
56 | PSMB6 | PSMB6 | PSMB6 | 10559 | -0.0085 | 0.36 | NO |
57 | PSMD3 | PSMD3 | PSMD3 | 10590 | -0.0091 | 0.36 | NO |
58 | PSMB7 | PSMB7 | PSMB7 | 10709 | -0.011 | 0.35 | NO |
59 | ITGB5 | ITGB5 | ITGB5 | 10785 | -0.012 | 0.35 | NO |
60 | PSMD8 | PSMD8 | PSMD8 | 11103 | -0.016 | 0.33 | NO |
61 | PSMB4 | PSMB4 | PSMB4 | 11164 | -0.017 | 0.33 | NO |
62 | SEC61B | SEC61B | SEC61B | 11318 | -0.019 | 0.32 | NO |
63 | SEC61G | SEC61G | SEC61G | 11351 | -0.019 | 0.32 | NO |
64 | PSMB5 | PSMB5 | PSMB5 | 11414 | -0.02 | 0.32 | NO |
65 | PSMD4 | PSMD4 | PSMD4 | 12032 | -0.029 | 0.29 | NO |
66 | PSMD9 | PSMD9 | PSMD9 | 12076 | -0.03 | 0.29 | NO |
67 | PSMD6 | PSMD6 | PSMD6 | 12416 | -0.035 | 0.28 | NO |
68 | SEC61A1 | SEC61A1 | SEC61A1 | 13152 | -0.046 | 0.24 | NO |
69 | PSMD2 | PSMD2 | PSMD2 | 14824 | -0.076 | 0.15 | NO |
70 | PSMF1 | PSMF1 | PSMF1 | 15085 | -0.082 | 0.15 | NO |
71 | RPS27A | RPS27A | RPS27A | 15344 | -0.09 | 0.14 | NO |
72 | UBA52 | UBA52 | UBA52 | 16002 | -0.11 | 0.12 | NO |
Figure S99. Get High-res Image This plot shows mRNA_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) ofgenes in the pathway: KEGG B CELL RECEPTOR SIGNALING PATHWAY.

Figure S100. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG B CELL RECEPTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
-
Gene set database = c2.all.v6.1.symbols.gmt
-
Expression data file = TCGA-UVM-TP.mRNA_FPKM_log2_protein.coding.txt
-
Phenotype data file = TCGA-UVM-TP.mergedcluster.txt
For the Gene Set Enrichment Analysis (GSEA),Broad GSEA-P-R.1.0 version is used with class2: canonical pathways genes from MSigDB v6.1.Further details about statistics are available inThe Broad GSEA website.
MSigDB releases (v6.0 and above) are available under a Creative Commons style license, plus additional terms for some gene sets. The full license terms are available