Pathway_GSEA_mRNA
Uveal Melanoma (Primary solid tumor)
13 July 2018  |  None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
Overview
Introduction

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:

  1. 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.

  2. Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).

  3. Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).

  4. Checks if the top core genes are up-regulated or down-regulated.

  5. Checks if the top core genes are high expressed or low expressed.

  6. Checks if the top core genes are significantly differently expressed genes.

Summary

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

Results
Subtype clus1 enriched pathways

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
genes ES table in pathway: KEGG ABC TRANSPORTERS

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

genes ES table in pathway: KEGG HOMOLOGOUS RECOMBINATION

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

genes ES table in pathway: WANG LMO4 TARGETS DN

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

genes ES table in pathway: KIM WT1 TARGETS DN

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

genes ES table in pathway: BIDUS METASTASIS UP

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

genes ES table in pathway: MAYBURD RESPONSE TO L663536 DN

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

genes ES table in pathway: ENK UV RESPONSE KERATINOCYTE DN

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

genes ES table in pathway: SEIDEN ONCOGENESIS BY MET

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

genes ES table in pathway: DACOSTA UV RESPONSE VIA ERCC3 COMMON DN

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

genes ES table in pathway: NIKOLSKY BREAST CANCER 8Q12 Q22 AMPLICON

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

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus2 enriched pathways

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
genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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

genes ES table in pathway: KEGG GALACTOSE METABOLISM

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

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

genes ES table in pathway: KEGG PURINE METABOLISM

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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

genes ES table in pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

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

genes ES table in pathway: KEGG ARGININE AND PROLINE METABOLISM

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

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus3 enriched pathways

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
genes ES table in pathway: KEGG RIBOSOME

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

genes ES table in pathway: PID P53 REGULATION PATHWAY

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

genes ES table in pathway: REACTOME TRANSLATION

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

genes ES table in pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE

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

genes ES table in pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

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

genes ES table in pathway: REACTOME GENERIC TRANSCRIPTION PATHWAY

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

genes ES table in pathway: REACTOME PEPTIDE CHAIN ELONGATION

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

genes ES table in pathway: REACTOME MRNA PROCESSING

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

genes ES table in pathway: REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION

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

genes ES table in pathway: REACTOME INFLUENZA LIFE CYCLE

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

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus4 enriched pathways

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
genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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

genes ES table in pathway: SCHLOSSER MYC AND SERUM RESPONSE SYNERGY

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

genes ES table in pathway: DACOSTA UV RESPONSE VIA ERCC3 UP

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

genes ES table in pathway: DAIRKEE TERT TARGETS UP

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

genes ES table in pathway: SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP

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

genes ES table in pathway: LOCKWOOD AMPLIFIED IN LUNG CANCER

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

genes ES table in pathway: PENG LEUCINE DEPRIVATION DN

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

genes ES table in pathway: MOOTHA VOXPHOS

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

genes ES table in pathway: PENG GLUTAMINE DEPRIVATION DN

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

genes ES table in pathway: FAELT B CLL WITH VH3 21 UP

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

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus5 enriched pathways

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
genes ES table in pathway: KEGG PROTEASOME

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

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

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

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

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

genes ES table in pathway: KEGG APOPTOSIS

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

genes ES table in pathway: KEGG CELL ADHESION MOLECULES CAMS

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

genes ES table in pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY

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

genes ES table in pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY

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

genes ES table in pathway: KEGG JAK STAT SIGNALING PATHWAY

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

genes ES table in pathway: KEGG HEMATOPOIETIC CELL LINEAGE

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

genes ES table in pathway: KEGG B CELL RECEPTOR SIGNALING PATHWAY

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

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Methods & Data
Input
  • 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

GSEA analysis

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

References
[1] Subramanian, A. et al, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles., Proc. Natl. Acad. Sci. USA 102(43) (2005)