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 mRNAseq_cNMF subtypes having more than three samples and the input expression file "ESCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:
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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.
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Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).
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Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).
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Checks if the top core genes are up-regulated or down-regulated.
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Checks if the top core genes are high expressed or low expressed.
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Checks if the top core genes are significantly differently expressed genes.
Table 1. Get Full Table basic data info
basic data info |
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Number of Gene Sets: 724 |
Number of samples: 184 |
Original number of Gene Sets: 1320 |
Maximum gene set size: 933 |
Table 2. Get Full Table pheno data info
phenotype info |
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pheno.type: 1 - 6 :[ clus1 ] 74 |
pheno.type: 2 - 6 :[ clus2 ] 14 |
pheno.type: 3 - 6 :[ clus3 ] 42 |
pheno.type: 4 - 6 :[ clus4 ] 29 |
pheno.type: 5 - 6 :[ clus5 ] 9 |
pheno.type: 6 - 6 :[ clus6 ] 16 |
For the expression subtypes of 18768 genes in 185 samples, GSEA found enriched gene sets in each cluster using 184 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.
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clus1
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Top enriched gene sets are KEGG HISTIDINE METABOLISM, KEGG SPHINGOLIPID METABOLISM, KEGG PROPANOATE METABOLISM, KEGG PEROXISOME, KEGG VASOPRESSIN REGULATED WATER REABSORPTION, KEGG VIBRIO CHOLERAE INFECTION, BIOCARTA DEATH PATHWAY, BIOCARTA PPARA PATHWAY, BIOCARTA RHO PATHWAY, ST INTERLEUKIN 4 PATHWAY
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And common core enriched genes are MUC2, ABCD1, ABCD3, ABCD4, ACAA1, ACOT8, ACOX1, ACOX2, ACSL5, AGXT
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clus2
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Top enriched gene sets are KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG RNA DEGRADATION, KEGG BASAL TRANSCRIPTION FACTORS, KEGG SPLICEOSOME, PID FANCONI PATHWAY, PID AURORA B PATHWAY, PID ATR PATHWAY, PID ATM PATHWAY, PID PLK1 PATHWAY, PID FOXM1PATHWAY
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And common core enriched genes are E2F5, RBL1, BRCA1, CDC25A, CDC25C, CHEK2, H2AFX, NUP107, NUP133, NUP43
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clus3
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Top enriched gene sets are KEGG BLADDER CANCER, BIOCARTA ERK PATHWAY, PID P73PATHWAY, PID AVB3 OPN PATHWAY, PID MTOR 4PATHWAY, PID ERBB1 RECEPTOR PROXIMAL PATHWAY, PID MYC PATHWAY, PID ECADHERIN NASCENTAJ PATHWAY, PID DELTANP63PATHWAY, PID A6B1 A6B4 INTEGRIN PATHWAY
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And common core enriched genes are ADA, SFN, TP63, CDKN1A, MYC, CCT2, CCT4, CCT5, CCT6A, CCT7
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clus4
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Top enriched gene sets are KEGG GLUTATHIONE METABOLISM, KEGG NEUROTROPHIN SIGNALING PATHWAY, KEGG BASAL CELL CARCINOMA, BIOCARTA CHREBP2 PATHWAY, ST P38 MAPK PATHWAY, WNT SIGNALING, SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES, PID P75NTRPATHWAY, PID TRKRPATHWAY, PID HEDGEHOG GLIPATHWAY
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And common core enriched genes are GPC1, BDNF, NGF, NGFR, NTF3, NTF4, NTRK2, PIK3CA, GPC2, GPC3
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clus5
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Top enriched gene sets are KEGG PURINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG ABC TRANSPORTERS, KEGG MAPK SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION, KEGG LYSOSOME
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And common core enriched genes are AKT3, PIK3CD, PIK3R1, PIK3CG, PIK3R5, BTK, INPP5D, NFATC2, VAV1, CAB39L
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clus6
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Top enriched gene sets are KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG NOTCH SIGNALING PATHWAY, KEGG THYROID CANCER, PID FOXOPATHWAY, PID ECADHERIN NASCENTAJ PATHWAY, PID RETINOIC ACID PATHWAY, PID TAP63PATHWAY, PID MAPKTRKPATHWAY, REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS, REACTOME TRIF MEDIATED TLR3 SIGNALING
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And common core enriched genes are MAP2K1, MAPK3, CDH1, AGER, DUSP4, DUSP7, FOS, IKBKB, IRAK2, MAP2K3
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 |
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KEGG HISTIDINE METABOLISM | 29 | genes.ES.table | 0.61 | 1.6 | 0.01 | 0.65 | 0.95 | 0.21 | 0.035 | 0.2 | 0.32 | 0.18 |
KEGG SPHINGOLIPID METABOLISM | 39 | genes.ES.table | 0.55 | 1.6 | 0.0062 | 0.69 | 0.92 | 0.41 | 0.17 | 0.34 | 0.32 | 0.18 |
KEGG PROPANOATE METABOLISM | 32 | genes.ES.table | 0.51 | 1.7 | 0.03 | 0.74 | 0.9 | 0.53 | 0.26 | 0.39 | 0.32 | 0.19 |
KEGG PEROXISOME | 75 | genes.ES.table | 0.54 | 1.9 | 0.0062 | 1 | 0.44 | 0.48 | 0.24 | 0.37 | 0 | 0.33 |
KEGG VASOPRESSIN REGULATED WATER REABSORPTION | 43 | genes.ES.table | 0.42 | 1.7 | 0.018 | 0.81 | 0.87 | 0.12 | 0.057 | 0.11 | 0.34 | 0.21 |
KEGG VIBRIO CHOLERAE INFECTION | 53 | genes.ES.table | 0.48 | 1.9 | 0.0039 | 1 | 0.51 | 0.15 | 0.071 | 0.14 | 0.32 | 0.25 |
BIOCARTA DEATH PATHWAY | 33 | genes.ES.table | 0.49 | 1.7 | 0.032 | 0.69 | 0.9 | 0.52 | 0.26 | 0.38 | 0.29 | 0.18 |
BIOCARTA PPARA PATHWAY | 56 | genes.ES.table | 0.46 | 1.6 | 0.028 | 0.71 | 0.95 | 0.29 | 0.2 | 0.23 | 0.34 | 0.19 |
BIOCARTA RHO PATHWAY | 32 | genes.ES.table | 0.44 | 1.8 | 0.01 | 1 | 0.67 | 0.062 | 0.03 | 0.061 | 0.4 | 0.27 |
ST INTERLEUKIN 4 PATHWAY | 25 | genes.ES.table | 0.55 | 1.7 | 0.016 | 0.96 | 0.83 | 0.16 | 0.073 | 0.15 | 0.36 | 0.22 |
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 | ACSL5 | ACSL5 | ACSL5 | 244 | 0.86 | 0.06 | YES |
2 | FAR2 | FAR2 | FAR2 | 354 | 0.75 | 0.12 | YES |
3 | NOS2 | NOS2 | NOS2 | 414 | 0.7 | 0.18 | YES |
4 | SLC27A2 | SLC27A2 | SLC27A2 | 532 | 0.63 | 0.22 | YES |
5 | AGXT | AGXT | AGXT | 636 | 0.57 | 0.27 | YES |
6 | BAAT | BAAT | BAAT | 698 | 0.55 | 0.31 | YES |
7 | PHYH | PHYH | PHYH | 1516 | 0.32 | 0.29 | YES |
8 | HAO2 | HAO2 | HAO2 | 1693 | 0.3 | 0.31 | YES |
9 | PECR | PECR | PECR | 1786 | 0.28 | 0.33 | YES |
10 | PEX11A | PEX11A | PEX11A | 1920 | 0.26 | 0.34 | YES |
11 | EPHX2 | EPHX2 | EPHX2 | 2240 | 0.23 | 0.35 | YES |
12 | PEX11G | PEX11G | PEX11G | 2310 | 0.22 | 0.36 | YES |
13 | DECR2 | DECR2 | DECR2 | 2496 | 0.21 | 0.37 | YES |
14 | DDO | DDO | DDO | 2532 | 0.21 | 0.39 | YES |
15 | ABCD1 | ABCD1 | ABCD1 | 2811 | 0.18 | 0.39 | YES |
16 | ABCD3 | ABCD3 | ABCD3 | 2862 | 0.18 | 0.4 | YES |
17 | PEX7 | PEX7 | PEX7 | 2938 | 0.18 | 0.41 | YES |
18 | CAT | CAT | CAT | 3005 | 0.17 | 0.42 | YES |
19 | PIPOX | PIPOX | PIPOX | 3202 | 0.16 | 0.42 | YES |
20 | AMACR | AMACR | AMACR | 3203 | 0.16 | 0.44 | YES |
21 | HACL1 | HACL1 | HACL1 | 3278 | 0.15 | 0.45 | YES |
22 | CRAT | CRAT | CRAT | 3358 | 0.15 | 0.46 | YES |
23 | ACOX1 | ACOX1 | ACOX1 | 3419 | 0.14 | 0.46 | YES |
24 | MLYCD | MLYCD | MLYCD | 3453 | 0.14 | 0.47 | YES |
25 | HMGCL | HMGCL | HMGCL | 3502 | 0.14 | 0.48 | YES |
26 | ACAA1 | ACAA1 | ACAA1 | 3521 | 0.14 | 0.49 | YES |
27 | NUDT12 | NUDT12 | NUDT12 | 3611 | 0.13 | 0.5 | YES |
28 | IDH1 | IDH1 | IDH1 | 3708 | 0.13 | 0.51 | YES |
29 | PXMP2 | PXMP2 | PXMP2 | 3793 | 0.12 | 0.51 | YES |
30 | PEX1 | PEX1 | PEX1 | 3912 | 0.12 | 0.52 | YES |
31 | GSTK1 | GSTK1 | GSTK1 | 3954 | 0.12 | 0.52 | YES |
32 | SCP2 | SCP2 | SCP2 | 4107 | 0.11 | 0.53 | YES |
33 | ACOT8 | ACOT8 | ACOT8 | 4126 | 0.11 | 0.53 | YES |
34 | PXMP4 | PXMP4 | PXMP4 | 4269 | 0.1 | 0.54 | YES |
35 | ABCD4 | ABCD4 | ABCD4 | 4370 | 0.1 | 0.54 | YES |
36 | ACOX2 | ACOX2 | ACOX2 | 4464 | 0.097 | 0.54 | YES |
37 | IDH2 | IDH2 | IDH2 | 4732 | 0.088 | 0.54 | NO |
38 | PEX6 | PEX6 | PEX6 | 5313 | 0.07 | 0.51 | NO |
39 | GNPAT | GNPAT | GNPAT | 5705 | 0.06 | 0.49 | NO |
40 | ECH1 | ECH1 | ECH1 | 5804 | 0.057 | 0.49 | NO |
41 | PEX2 | PEX2 | PEX2 | 6241 | 0.047 | 0.48 | NO |
42 | HSD17B4 | HSD17B4 | HSD17B4 | 6282 | 0.046 | 0.48 | NO |
43 | ACSL4 | ACSL4 | ACSL4 | 6343 | 0.044 | 0.48 | NO |
44 | PEX16 | PEX16 | PEX16 | 6423 | 0.043 | 0.48 | NO |
45 | ABCD2 | ABCD2 | ABCD2 | 6490 | 0.041 | 0.48 | NO |
46 | ACSL3 | ACSL3 | ACSL3 | 6551 | 0.04 | 0.48 | NO |
47 | PEX11B | PEX11B | PEX11B | 6991 | 0.031 | 0.46 | NO |
48 | AGPS | AGPS | AGPS | 7660 | 0.017 | 0.42 | NO |
49 | FAR1 | FAR1 | FAR1 | 8127 | 0.0081 | 0.4 | NO |
50 | PEX26 | PEX26 | PEX26 | 8278 | 0.0055 | 0.39 | NO |
51 | ACOX3 | ACOX3 | ACOX3 | 8779 | -0.0031 | 0.36 | NO |
52 | XDH | XDH | XDH | 8849 | -0.0043 | 0.36 | NO |
53 | SOD1 | SOD1 | SOD1 | 9585 | -0.017 | 0.32 | NO |
54 | PEX19 | PEX19 | PEX19 | 10076 | -0.025 | 0.3 | NO |
55 | ACSL6 | ACSL6 | ACSL6 | 10080 | -0.025 | 0.3 | NO |
56 | PMVK | PMVK | PMVK | 10281 | -0.029 | 0.29 | NO |
57 | EHHADH | EHHADH | EHHADH | 10318 | -0.03 | 0.29 | NO |
58 | PEX14 | PEX14 | PEX14 | 10900 | -0.04 | 0.26 | NO |
59 | PEX13 | PEX13 | PEX13 | 10959 | -0.041 | 0.26 | NO |
60 | PRDX5 | PRDX5 | PRDX5 | 11154 | -0.045 | 0.26 | NO |
61 | PEX3 | PEX3 | PEX3 | 11169 | -0.046 | 0.26 | NO |
62 | SOD2 | SOD2 | SOD2 | 11739 | -0.058 | 0.24 | NO |
63 | PEX12 | PEX12 | PEX12 | 11743 | -0.058 | 0.24 | NO |
64 | PEX5 | PEX5 | PEX5 | 11799 | -0.059 | 0.24 | NO |
65 | PEX10 | PEX10 | PEX10 | 12210 | -0.068 | 0.23 | NO |
66 | NUDT19 | NUDT19 | NUDT19 | 12999 | -0.089 | 0.19 | NO |
67 | PRDX1 | PRDX1 | PRDX1 | 13119 | -0.093 | 0.19 | NO |
68 | MPV17 | MPV17 | MPV17 | 13581 | -0.11 | 0.18 | NO |
69 | SLC25A17 | SLC25A17 | SLC25A17 | 14089 | -0.12 | 0.16 | NO |
70 | DHRS4 | DHRS4 | DHRS4 | 14586 | -0.14 | 0.15 | NO |
71 | PAOX | PAOX | PAOX | 14841 | -0.16 | 0.15 | NO |
72 | ACSL1 | ACSL1 | ACSL1 | 14894 | -0.16 | 0.16 | NO |
73 | MPV17L | MPV17L | MPV17L | 14937 | -0.16 | 0.17 | NO |
74 | MVK | MVK | MVK | 15154 | -0.17 | 0.17 | NO |
75 | CROT | CROT | CROT | 15994 | -0.23 | 0.15 | NO |
Figure S1. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HISTIDINE METABOLISM.

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

Table S2. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CFTR | CFTR | CFTR | 97 | 1.1 | 0.11 | YES |
2 | KCNQ1 | KCNQ1 | KCNQ1 | 284 | 0.81 | 0.19 | YES |
3 | PRKACG | PRKACG | PRKACG | 330 | 0.77 | 0.27 | YES |
4 | MUC2 | MUC2 | MUC2 | 421 | 0.7 | 0.34 | YES |
5 | PRKCG | PRKCG | PRKCG | 617 | 0.58 | 0.39 | YES |
6 | SLC12A2 | SLC12A2 | SLC12A2 | 842 | 0.5 | 0.43 | YES |
7 | KDELR3 | KDELR3 | KDELR3 | 1259 | 0.37 | 0.44 | YES |
8 | PRKCA | PRKCA | PRKCA | 1339 | 0.35 | 0.48 | YES |
9 | TJP2 | TJP2 | TJP2 | 2460 | 0.21 | 0.44 | NO |
10 | ATP6V1C2 | ATP6V1C2 | ATP6V1C2 | 2772 | 0.19 | 0.44 | NO |
11 | TCIRG1 | TCIRG1 | TCIRG1 | 3399 | 0.14 | 0.42 | NO |
12 | KDELR2 | KDELR2 | KDELR2 | 3490 | 0.14 | 0.44 | NO |
13 | KDELR1 | KDELR1 | KDELR1 | 4615 | 0.092 | 0.38 | NO |
14 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 4637 | 0.091 | 0.39 | NO |
15 | PDIA4 | PDIA4 | PDIA4 | 5193 | 0.074 | 0.37 | NO |
16 | ATP6V0B | ATP6V0B | ATP6V0B | 5589 | 0.063 | 0.36 | NO |
17 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 5749 | 0.058 | 0.36 | NO |
18 | PRKCB | PRKCB | PRKCB | 5846 | 0.056 | 0.36 | NO |
19 | SEC61A2 | SEC61A2 | SEC61A2 | 6436 | 0.042 | 0.33 | NO |
20 | ATP6V0E2 | ATP6V0E2 | ATP6V0E2 | 6619 | 0.038 | 0.32 | NO |
21 | ARF1 | ARF1 | ARF1 | 6635 | 0.038 | 0.33 | NO |
22 | TJP1 | TJP1 | TJP1 | 7082 | 0.029 | 0.3 | NO |
23 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 7622 | 0.017 | 0.28 | NO |
24 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 7813 | 0.014 | 0.27 | NO |
25 | SEC61A1 | SEC61A1 | SEC61A1 | 8614 | -0.00027 | 0.23 | NO |
26 | SEC61B | SEC61B | SEC61B | 8791 | -0.0032 | 0.22 | NO |
27 | SEC61G | SEC61G | SEC61G | 9424 | -0.014 | 0.18 | NO |
28 | ACTG1 | ACTG1 | ACTG1 | 9649 | -0.018 | 0.18 | NO |
29 | ACTB | ACTB | ACTB | 9675 | -0.019 | 0.18 | NO |
30 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 10567 | -0.034 | 0.13 | NO |
31 | ATP6V0E1 | ATP6V0E1 | ATP6V0E1 | 10583 | -0.034 | 0.14 | NO |
32 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 10867 | -0.04 | 0.12 | NO |
33 | GNAS | GNAS | GNAS | 11553 | -0.054 | 0.093 | NO |
34 | ERO1L | ERO1L | ERO1L | 11692 | -0.057 | 0.091 | NO |
35 | ADCY9 | ADCY9 | ADCY9 | 11954 | -0.062 | 0.084 | NO |
36 | ATP6V0C | ATP6V0C | ATP6V0C | 12065 | -0.064 | 0.085 | NO |
37 | ATP6V1G1 | ATP6V1G1 | ATP6V1G1 | 12167 | -0.067 | 0.087 | NO |
38 | ATP6V1A | ATP6V1A | ATP6V1A | 12390 | -0.072 | 0.082 | NO |
39 | ATP6V1H | ATP6V1H | ATP6V1H | 12408 | -0.073 | 0.089 | NO |
40 | ATP6V1D | ATP6V1D | ATP6V1D | 12600 | -0.078 | 0.087 | NO |
41 | PRKACB | PRKACB | PRKACB | 12868 | -0.085 | 0.082 | NO |
42 | PRKACA | PRKACA | PRKACA | 13025 | -0.09 | 0.083 | NO |
43 | PLCG1 | PLCG1 | PLCG1 | 13245 | -0.096 | 0.082 | NO |
44 | ATP6V1F | ATP6V1F | ATP6V1F | 13361 | -0.099 | 0.086 | NO |
45 | ATP6V1G2 | ATP6V1G2 | ATP6V1G2 | 13652 | -0.11 | 0.082 | NO |
46 | PLCG2 | PLCG2 | PLCG2 | 13748 | -0.11 | 0.088 | NO |
47 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 13946 | -0.12 | 0.09 | NO |
48 | ADCY3 | ADCY3 | ADCY3 | 14503 | -0.14 | 0.076 | NO |
49 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 14622 | -0.15 | 0.085 | NO |
50 | PRKX | PRKX | PRKX | 15967 | -0.23 | 0.037 | NO |
51 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 16910 | -0.33 | 0.022 | NO |
52 | ATP6V1E2 | ATP6V1E2 | ATP6V1E2 | 16995 | -0.35 | 0.054 | NO |
53 | ATP6V1B1 | ATP6V1B1 | ATP6V1B1 | 17180 | -0.37 | 0.084 | NO |
Figure S3. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SPHINGOLIPID METABOLISM.

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

Table S3. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PIP5K1B | PIP5K1B | PIP5K1B | 67 | 1.2 | 0.31 | YES |
2 | ARHGAP6 | ARHGAP6 | ARHGAP6 | 554 | 0.62 | 0.44 | YES |
3 | ARHGAP4 | ARHGAP4 | ARHGAP4 | 2875 | 0.18 | 0.36 | NO |
4 | SRC | SRC | SRC | 3144 | 0.16 | 0.39 | NO |
5 | ARPC1B | ARPC1B | ARPC1B | 5049 | 0.078 | 0.31 | NO |
6 | ARPC4 | ARPC4 | ARPC4 | 5758 | 0.058 | 0.28 | NO |
7 | RHOA | RHOA | RHOA | 5932 | 0.054 | 0.29 | NO |
8 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 6035 | 0.051 | 0.3 | NO |
9 | PPP1R12B | PPP1R12B | PPP1R12B | 6312 | 0.045 | 0.29 | NO |
10 | ARHGEF1 | ARHGEF1 | ARHGEF1 | 6919 | 0.032 | 0.27 | NO |
11 | DIAPH1 | DIAPH1 | DIAPH1 | 7025 | 0.03 | 0.27 | NO |
12 | OPHN1 | OPHN1 | OPHN1 | 7434 | 0.021 | 0.26 | NO |
13 | ROCK1 | ROCK1 | ROCK1 | 7484 | 0.02 | 0.26 | NO |
14 | CFL1 | CFL1 | CFL1 | 7883 | 0.013 | 0.24 | NO |
15 | ARHGAP5 | ARHGAP5 | ARHGAP5 | 8425 | 0.0028 | 0.21 | NO |
16 | ACTR2 | ACTR2 | ACTR2 | 8596 | 0.000041 | 0.2 | NO |
17 | ARPC5 | ARPC5 | ARPC5 | 8676 | -0.0014 | 0.2 | NO |
18 | ARPC1A | ARPC1A | ARPC1A | 8786 | -0.0032 | 0.19 | NO |
19 | TLN1 | TLN1 | TLN1 | 8913 | -0.0055 | 0.19 | NO |
20 | PFN1 | PFN1 | PFN1 | 10062 | -0.025 | 0.13 | NO |
21 | PIP5K1A | PIP5K1A | PIP5K1A | 10540 | -0.033 | 0.12 | NO |
22 | ARPC3 | ARPC3 | ARPC3 | 10658 | -0.035 | 0.12 | NO |
23 | VCL | VCL | VCL | 10883 | -0.04 | 0.12 | NO |
24 | GSN | GSN | GSN | 11855 | -0.06 | 0.081 | NO |
25 | ARHGAP1 | ARHGAP1 | ARHGAP1 | 11926 | -0.062 | 0.093 | NO |
26 | MYL2 | MYL2 | MYL2 | 12129 | -0.066 | 0.099 | NO |
27 | ACTR3 | ACTR3 | ACTR3 | 12166 | -0.067 | 0.11 | NO |
28 | ARPC2 | ARPC2 | ARPC2 | 12473 | -0.074 | 0.12 | NO |
29 | LIMK1 | LIMK1 | LIMK1 | 14829 | -0.16 | 0.032 | NO |
30 | ARHGEF5 | ARHGEF5 | ARHGEF5 | 14905 | -0.16 | 0.069 | NO |
31 | MYLK | MYLK | MYLK | 16127 | -0.24 | 0.067 | NO |
32 | BAIAP2 | BAIAP2 | BAIAP2 | 16503 | -0.28 | 0.12 | NO |
Figure S5. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PROPANOATE METABOLISM.
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Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PROPANOATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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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 | MUC13 | MUC13 | MUC13 | 17 | 1.4 | 0.034 | YES |
2 | MUC17 | MUC17 | MUC17 | 53 | 1.3 | 0.064 | YES |
3 | ARSE | ARSE | ARSE | 108 | 1.1 | 0.087 | YES |
4 | GCNT3 | GCNT3 | GCNT3 | 109 | 1.1 | 0.11 | YES |
5 | MUC6 | MUC6 | MUC6 | 255 | 0.84 | 0.13 | YES |
6 | B3GNT3 | B3GNT3 | B3GNT3 | 263 | 0.83 | 0.15 | YES |
7 | MUC5B | MUC5B | MUC5B | 280 | 0.81 | 0.16 | YES |
8 | B3GNT7 | B3GNT7 | B3GNT7 | 285 | 0.8 | 0.18 | YES |
9 | MGAT3 | MGAT3 | MGAT3 | 316 | 0.78 | 0.2 | YES |
10 | GCNT1 | GCNT1 | GCNT1 | 327 | 0.78 | 0.22 | YES |
11 | MUC12 | MUC12 | MUC12 | 332 | 0.77 | 0.24 | YES |
12 | MUC2 | MUC2 | MUC2 | 421 | 0.7 | 0.25 | YES |
13 | GALNT5 | GALNT5 | GALNT5 | 535 | 0.63 | 0.26 | YES |
14 | MGAT4A | MGAT4A | MGAT4A | 589 | 0.6 | 0.27 | YES |
15 | MUC4 | MUC4 | MUC4 | 826 | 0.5 | 0.27 | YES |
16 | GALNT12 | GALNT12 | GALNT12 | 898 | 0.47 | 0.28 | YES |
17 | GALNT8 | GALNT8 | GALNT8 | 905 | 0.47 | 0.29 | YES |
18 | ALG11 | ALG11 | ALG11 | 928 | 0.46 | 0.3 | YES |
19 | F10 | F10 | F10 | 982 | 0.45 | 0.31 | YES |
20 | STS | STS | STS | 1074 | 0.41 | 0.31 | YES |
21 | ST6GALNAC3 | ST6GALNAC3 | ST6GALNAC3 | 1075 | 0.41 | 0.32 | YES |
22 | GALNTL6 | GALNTL6 | GALNTL6 | 1098 | 0.41 | 0.33 | YES |
23 | ST6GAL1 | ST6GAL1 | ST6GAL1 | 1183 | 0.39 | 0.34 | YES |
24 | ST8SIA3 | ST8SIA3 | ST8SIA3 | 1227 | 0.38 | 0.34 | YES |
25 | F7 | F7 | F7 | 1254 | 0.37 | 0.35 | YES |
26 | C1GALT1 | C1GALT1 | C1GALT1 | 1295 | 0.36 | 0.36 | YES |
27 | PROZ | PROZ | PROZ | 1344 | 0.35 | 0.36 | YES |
28 | FUT8 | FUT8 | FUT8 | 1351 | 0.35 | 0.37 | YES |
29 | PROC | PROC | PROC | 1490 | 0.32 | 0.37 | YES |
30 | B3GNT6 | B3GNT6 | B3GNT6 | 1569 | 0.31 | 0.38 | YES |
31 | ARSH | ARSH | ARSH | 1762 | 0.29 | 0.37 | YES |
32 | MGAT5 | MGAT5 | MGAT5 | 1811 | 0.28 | 0.38 | YES |
33 | GALNT9 | GALNT9 | GALNT9 | 1915 | 0.27 | 0.38 | YES |
34 | GALNT7 | GALNT7 | GALNT7 | 1951 | 0.26 | 0.38 | YES |
35 | GALNT3 | GALNT3 | GALNT3 | 2013 | 0.26 | 0.39 | YES |
36 | MAN1A1 | MAN1A1 | MAN1A1 | 2070 | 0.25 | 0.39 | YES |
37 | MGAT4B | MGAT4B | MGAT4B | 2132 | 0.24 | 0.39 | YES |
38 | GALNT6 | GALNT6 | GALNT6 | 2150 | 0.24 | 0.4 | YES |
39 | ALG5 | ALG5 | ALG5 | 2280 | 0.23 | 0.4 | YES |
40 | F2 | F2 | F2 | 2306 | 0.23 | 0.4 | YES |
41 | B3GNTL1 | B3GNTL1 | B3GNTL1 | 2375 | 0.22 | 0.4 | YES |
42 | MLEC | MLEC | MLEC | 2383 | 0.22 | 0.41 | YES |
43 | PLAUR | PLAUR | PLAUR | 2415 | 0.22 | 0.41 | YES |
44 | GMPPB | GMPPB | GMPPB | 2500 | 0.21 | 0.41 | YES |
45 | UGGT2 | UGGT2 | UGGT2 | 2661 | 0.2 | 0.41 | YES |
46 | EDEM3 | EDEM3 | EDEM3 | 2663 | 0.2 | 0.41 | YES |
47 | ALG14 | ALG14 | ALG14 | 2713 | 0.19 | 0.41 | YES |
48 | ST6GALNAC4 | ST6GALNAC4 | ST6GALNAC4 | 2731 | 0.19 | 0.42 | YES |
49 | GALNT10 | GALNT10 | GALNT10 | 2737 | 0.19 | 0.42 | YES |
50 | C1GALT1C1 | C1GALT1C1 | C1GALT1C1 | 2925 | 0.18 | 0.42 | NO |
51 | DPAGT1 | DPAGT1 | DPAGT1 | 2948 | 0.18 | 0.42 | NO |
52 | PGM3 | PGM3 | PGM3 | 3096 | 0.16 | 0.42 | NO |
53 | GMPPA | GMPPA | GMPPA | 3125 | 0.16 | 0.42 | NO |
54 | SEC24D | SEC24D | SEC24D | 3169 | 0.16 | 0.42 | NO |
55 | ALG1 | ALG1 | ALG1 | 3229 | 0.16 | 0.42 | NO |
56 | PIGG | PIGG | PIGG | 3306 | 0.15 | 0.42 | NO |
57 | ST3GAL2 | ST3GAL2 | ST3GAL2 | 3346 | 0.15 | 0.42 | NO |
58 | GNPNAT1 | GNPNAT1 | GNPNAT1 | 3431 | 0.14 | 0.42 | NO |
59 | PIGT | PIGT | PIGT | 3663 | 0.13 | 0.41 | NO |
60 | MAN1C1 | MAN1C1 | MAN1C1 | 3673 | 0.13 | 0.41 | NO |
61 | PIGM | PIGM | PIGM | 3776 | 0.12 | 0.41 | NO |
62 | B4GALT6 | B4GALT6 | B4GALT6 | 3799 | 0.12 | 0.41 | NO |
63 | B4GALT5 | B4GALT5 | B4GALT5 | 4048 | 0.11 | 0.4 | NO |
64 | STT3A | STT3A | STT3A | 4158 | 0.11 | 0.4 | NO |
65 | SUMF2 | SUMF2 | SUMF2 | 4459 | 0.097 | 0.38 | NO |
66 | SEC13 | SEC13 | SEC13 | 4475 | 0.097 | 0.39 | NO |
67 | MAN2A1 | MAN2A1 | MAN2A1 | 4480 | 0.097 | 0.39 | NO |
68 | PMM2 | PMM2 | PMM2 | 4504 | 0.096 | 0.39 | NO |
69 | EDEM2 | EDEM2 | EDEM2 | 4538 | 0.095 | 0.39 | NO |
70 | PIGO | PIGO | PIGO | 4573 | 0.094 | 0.39 | NO |
71 | ALG8 | ALG8 | ALG8 | 4950 | 0.082 | 0.37 | NO |
72 | RPN2 | RPN2 | RPN2 | 5032 | 0.079 | 0.37 | NO |
73 | SUMF1 | SUMF1 | SUMF1 | 5070 | 0.078 | 0.37 | NO |
74 | PDIA3 | PDIA3 | PDIA3 | 5114 | 0.076 | 0.37 | NO |
75 | B3GNT2 | B3GNT2 | B3GNT2 | 5180 | 0.074 | 0.37 | NO |
76 | ALG2 | ALG2 | ALG2 | 5231 | 0.072 | 0.37 | NO |
77 | PROS1 | PROS1 | PROS1 | 5253 | 0.072 | 0.37 | NO |
78 | RFT1 | RFT1 | RFT1 | 5308 | 0.07 | 0.37 | NO |
79 | ALG13 | ALG13 | ALG13 | 5505 | 0.065 | 0.36 | NO |
80 | CANX | CANX | CANX | 5701 | 0.06 | 0.35 | NO |
81 | DPM3 | DPM3 | DPM3 | 5730 | 0.059 | 0.35 | NO |
82 | PIGB | PIGB | PIGB | 5773 | 0.058 | 0.35 | NO |
83 | SAR1B | SAR1B | SAR1B | 5856 | 0.056 | 0.34 | NO |
84 | DDOST | DDOST | DDOST | 5938 | 0.054 | 0.34 | NO |
85 | PIGK | PIGK | PIGK | 5990 | 0.052 | 0.34 | NO |
86 | UGGT1 | UGGT1 | UGGT1 | 6208 | 0.047 | 0.33 | NO |
87 | PIGH | PIGH | PIGH | 6285 | 0.046 | 0.33 | NO |
88 | PIGU | PIGU | PIGU | 6289 | 0.046 | 0.33 | NO |
89 | B4GALT3 | B4GALT3 | B4GALT3 | 6421 | 0.043 | 0.32 | NO |
90 | ALG9 | ALG9 | ALG9 | 6443 | 0.042 | 0.32 | NO |
91 | PIGF | PIGF | PIGF | 6485 | 0.042 | 0.32 | NO |
92 | PREB | PREB | PREB | 6660 | 0.037 | 0.31 | NO |
93 | DOLPP1 | DOLPP1 | DOLPP1 | 6821 | 0.034 | 0.3 | NO |
94 | PIGS | PIGS | PIGS | 7201 | 0.026 | 0.28 | NO |
95 | B4GALT4 | B4GALT4 | B4GALT4 | 7222 | 0.025 | 0.28 | NO |
96 | PIGL | PIGL | PIGL | 7247 | 0.025 | 0.28 | NO |
97 | MCFD2 | MCFD2 | MCFD2 | 7432 | 0.021 | 0.27 | NO |
98 | CALR | CALR | CALR | 7663 | 0.017 | 0.26 | NO |
99 | EDEM1 | EDEM1 | EDEM1 | 7671 | 0.016 | 0.26 | NO |
100 | GPAA1 | GPAA1 | GPAA1 | 7710 | 0.016 | 0.26 | NO |
101 | FURIN | FURIN | FURIN | 7740 | 0.015 | 0.26 | NO |
102 | RPN1 | RPN1 | RPN1 | 7892 | 0.012 | 0.25 | NO |
103 | PIGC | PIGC | PIGC | 7913 | 0.012 | 0.25 | NO |
104 | GALNTL2 | GALNTL2 | GALNTL2 | 7917 | 0.012 | 0.25 | NO |
105 | MAN1A2 | MAN1A2 | MAN1A2 | 7987 | 0.011 | 0.25 | NO |
106 | DAD1 | DAD1 | DAD1 | 8078 | 0.0093 | 0.24 | NO |
107 | DPM2 | DPM2 | DPM2 | 8128 | 0.0081 | 0.24 | NO |
108 | SEC24C | SEC24C | SEC24C | 8175 | 0.0073 | 0.24 | NO |
109 | MOGS | MOGS | MOGS | 8197 | 0.007 | 0.24 | NO |
110 | DOLK | DOLK | DOLK | 8303 | 0.0051 | 0.23 | NO |
111 | B4GALT1 | B4GALT1 | B4GALT1 | 8311 | 0.005 | 0.23 | NO |
112 | MPI | MPI | MPI | 8349 | 0.0044 | 0.23 | NO |
113 | ALG6 | ALG6 | ALG6 | 8563 | 0.00061 | 0.22 | NO |
114 | MGAT2 | MGAT2 | MGAT2 | 8672 | -0.0013 | 0.21 | NO |
115 | PIGQ | PIGQ | PIGQ | 9004 | -0.007 | 0.19 | NO |
116 | GANAB | GANAB | GANAB | 9048 | -0.0078 | 0.19 | NO |
117 | PRKCSH | PRKCSH | PRKCSH | 9369 | -0.013 | 0.17 | NO |
118 | PIGP | PIGP | PIGP | 9571 | -0.017 | 0.16 | NO |
119 | SEC31A | SEC31A | SEC31A | 9722 | -0.019 | 0.16 | NO |
120 | PIGA | PIGA | PIGA | 9824 | -0.021 | 0.15 | NO |
121 | MAN1B1 | MAN1B1 | MAN1B1 | 9942 | -0.023 | 0.15 | NO |
122 | DPM1 | DPM1 | DPM1 | 10037 | -0.025 | 0.14 | NO |
123 | SEC23A | SEC23A | SEC23A | 10077 | -0.025 | 0.14 | NO |
124 | MANEA | MANEA | MANEA | 10282 | -0.029 | 0.13 | NO |
125 | ALG12 | ALG12 | ALG12 | 10408 | -0.031 | 0.12 | NO |
126 | GALNTL1 | GALNTL1 | GALNTL1 | 10501 | -0.033 | 0.12 | NO |
127 | DOHH | DOHH | DOHH | 10535 | -0.033 | 0.12 | NO |
128 | SEC24B | SEC24B | SEC24B | 10580 | -0.034 | 0.12 | NO |
129 | MGAT1 | MGAT1 | MGAT1 | 10700 | -0.036 | 0.11 | NO |
130 | ARSA | ARSA | ARSA | 11234 | -0.047 | 0.084 | NO |
131 | ALG3 | ALG3 | ALG3 | 11328 | -0.049 | 0.08 | NO |
132 | GALNT2 | GALNT2 | GALNT2 | 11342 | -0.049 | 0.08 | NO |
133 | GGCX | GGCX | GGCX | 11418 | -0.051 | 0.078 | NO |
134 | LMAN1 | LMAN1 | LMAN1 | 11500 | -0.053 | 0.074 | NO |
135 | ARSG | ARSG | ARSG | 11707 | -0.057 | 0.065 | NO |
136 | DHPS | DHPS | DHPS | 11726 | -0.058 | 0.065 | NO |
137 | ALG10 | ALG10 | ALG10 | 11924 | -0.062 | 0.056 | NO |
138 | ST3GAL1 | ST3GAL1 | ST3GAL1 | 11952 | -0.062 | 0.056 | NO |
139 | PIGW | PIGW | PIGW | 12169 | -0.067 | 0.046 | NO |
140 | WBSCR17 | WBSCR17 | WBSCR17 | 12747 | -0.082 | 0.017 | NO |
141 | PIGV | PIGV | PIGV | 12848 | -0.084 | 0.014 | NO |
142 | PIGN | PIGN | PIGN | 12864 | -0.085 | 0.015 | NO |
143 | VKORC1 | VKORC1 | VKORC1 | 12884 | -0.085 | 0.016 | NO |
144 | EIF5A | EIF5A | EIF5A | 12934 | -0.087 | 0.016 | NO |
145 | MUC21 | MUC21 | MUC21 | 12972 | -0.088 | 0.016 | NO |
146 | EIF5A2 | EIF5A2 | EIF5A2 | 13105 | -0.092 | 0.011 | NO |
147 | ALG10B | ALG10B | ALG10B | 13406 | -0.1 | -0.0029 | NO |
148 | GCNT4 | GCNT4 | GCNT4 | 13460 | -0.1 | -0.0032 | NO |
149 | ARSB | ARSB | ARSB | 13674 | -0.11 | -0.012 | NO |
150 | GALNT1 | GALNT1 | GALNT1 | 14031 | -0.12 | -0.028 | NO |
151 | GALNT11 | GALNT11 | GALNT11 | 14056 | -0.12 | -0.027 | NO |
152 | B3GNT8 | B3GNT8 | B3GNT8 | 14435 | -0.14 | -0.044 | NO |
153 | ARSK | ARSK | ARSK | 14789 | -0.15 | -0.059 | NO |
154 | B4GALT2 | B4GALT2 | B4GALT2 | 14863 | -0.16 | -0.059 | NO |
155 | PMM1 | PMM1 | PMM1 | 15171 | -0.18 | -0.071 | NO |
156 | MUC16 | MUC16 | MUC16 | 15183 | -0.18 | -0.068 | NO |
157 | ARSF | ARSF | ARSF | 15230 | -0.18 | -0.066 | NO |
158 | PGAP1 | PGAP1 | PGAP1 | 15690 | -0.21 | -0.085 | NO |
159 | B3GNT9 | B3GNT9 | B3GNT9 | 15926 | -0.23 | -0.092 | NO |
160 | B3GNT5 | B3GNT5 | B3GNT5 | 15978 | -0.23 | -0.09 | NO |
161 | SEMA6D | SEMA6D | SEMA6D | 16198 | -0.25 | -0.095 | NO |
162 | PIGX | PIGX | PIGX | 16306 | -0.26 | -0.094 | NO |
163 | ARSJ | ARSJ | ARSJ | 16375 | -0.27 | -0.092 | NO |
164 | MGAT4C | MGAT4C | MGAT4C | 17225 | -0.38 | -0.13 | NO |
165 | ST8SIA6 | ST8SIA6 | ST8SIA6 | 17274 | -0.39 | -0.12 | NO |
166 | ST3GAL3 | ST3GAL3 | ST3GAL3 | 17775 | -0.49 | -0.14 | NO |
167 | MUCL1 | MUCL1 | MUCL1 | 17797 | -0.5 | -0.12 | NO |
168 | GFPT2 | GFPT2 | GFPT2 | 17931 | -0.54 | -0.12 | NO |
169 | ST8SIA2 | ST8SIA2 | ST8SIA2 | 17971 | -0.55 | -0.11 | NO |
170 | GALNTL4 | GALNTL4 | GALNTL4 | 17980 | -0.55 | -0.095 | NO |
171 | MUC15 | MUC15 | MUC15 | 18100 | -0.59 | -0.087 | NO |
172 | GALNT13 | GALNT13 | GALNT13 | 18116 | -0.6 | -0.073 | NO |
173 | ST6GALNAC2 | ST6GALNAC2 | ST6GALNAC2 | 18457 | -0.76 | -0.073 | NO |
174 | B3GNT4 | B3GNT4 | B3GNT4 | 18479 | -0.78 | -0.055 | NO |
175 | ARSI | ARSI | ARSI | 18577 | -0.85 | -0.04 | NO |
176 | TUSC3 | TUSC3 | TUSC3 | 18643 | -0.93 | -0.021 | NO |
177 | GALNT14 | GALNT14 | GALNT14 | 18702 | -1.1 | 0.0025 | NO |
Figure S7. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PEROXISOME.

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

Table S5. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | TPK1 | TPK1 | TPK1 | 454 | 0.67 | 0.07 | YES |
2 | SLC19A3 | SLC19A3 | SLC19A3 | 572 | 0.61 | 0.15 | YES |
3 | ENPP1 | ENPP1 | ENPP1 | 831 | 0.5 | 0.2 | YES |
4 | GSTO2 | GSTO2 | GSTO2 | 1125 | 0.4 | 0.24 | YES |
5 | QPRT | QPRT | QPRT | 1292 | 0.36 | 0.29 | YES |
6 | RFK | RFK | RFK | 1296 | 0.36 | 0.34 | YES |
7 | PANK1 | PANK1 | PANK1 | 1500 | 0.32 | 0.37 | YES |
8 | NMNAT2 | NMNAT2 | NMNAT2 | 1716 | 0.29 | 0.4 | YES |
9 | SLC23A1 | SLC23A1 | SLC23A1 | 2444 | 0.21 | 0.39 | YES |
10 | NMNAT1 | NMNAT1 | NMNAT1 | 2664 | 0.2 | 0.41 | YES |
11 | MTHFR | MTHFR | MTHFR | 2714 | 0.19 | 0.43 | YES |
12 | CYB5A | CYB5A | CYB5A | 3257 | 0.15 | 0.42 | YES |
13 | SLC19A2 | SLC19A2 | SLC19A2 | 3390 | 0.14 | 0.44 | YES |
14 | SLC46A1 | SLC46A1 | SLC46A1 | 3412 | 0.14 | 0.46 | YES |
15 | NADK | NADK | NADK | 3878 | 0.12 | 0.45 | YES |
16 | SLC19A1 | SLC19A1 | SLC19A1 | 3929 | 0.12 | 0.46 | YES |
17 | MOCOS | MOCOS | MOCOS | 4356 | 0.1 | 0.45 | YES |
18 | PDXK | PDXK | PDXK | 4372 | 0.1 | 0.47 | YES |
19 | SLC5A6 | SLC5A6 | SLC5A6 | 4651 | 0.091 | 0.46 | YES |
20 | PPCDC | PPCDC | PPCDC | 4828 | 0.085 | 0.47 | YES |
21 | PANK3 | PANK3 | PANK3 | 5037 | 0.079 | 0.47 | YES |
22 | GPHN | GPHN | GPHN | 5051 | 0.078 | 0.48 | YES |
23 | PPCS | PPCS | PPCS | 5542 | 0.064 | 0.46 | NO |
24 | SLC25A16 | SLC25A16 | SLC25A16 | 5703 | 0.06 | 0.46 | NO |
25 | FPGS | FPGS | FPGS | 5803 | 0.057 | 0.46 | NO |
26 | DHFR | DHFR | DHFR | 6301 | 0.045 | 0.44 | NO |
27 | SLC25A32 | SLC25A32 | SLC25A32 | 6557 | 0.04 | 0.43 | NO |
28 | SLC2A3 | SLC2A3 | SLC2A3 | 6672 | 0.037 | 0.43 | NO |
29 | MOCS3 | MOCS3 | MOCS3 | 7036 | 0.029 | 0.42 | NO |
30 | PNPO | PNPO | PNPO | 7064 | 0.029 | 0.42 | NO |
31 | NFS1 | NFS1 | NFS1 | 8137 | 0.008 | 0.36 | NO |
32 | COASY | COASY | COASY | 8474 | 0.002 | 0.35 | NO |
33 | THTPA | THTPA | THTPA | 8883 | -0.0049 | 0.32 | NO |
34 | SHMT1 | SHMT1 | SHMT1 | 9502 | -0.016 | 0.3 | NO |
35 | PANK4 | PANK4 | PANK4 | 9781 | -0.02 | 0.28 | NO |
36 | FASN | FASN | FASN | 9936 | -0.023 | 0.28 | NO |
37 | MTHFD1 | MTHFD1 | MTHFD1 | 10362 | -0.03 | 0.26 | NO |
38 | MOCS2 | MOCS2 | MOCS2 | 10912 | -0.04 | 0.24 | NO |
39 | PANK2 | PANK2 | PANK2 | 11190 | -0.046 | 0.23 | NO |
40 | FLAD1 | FLAD1 | FLAD1 | 11586 | -0.054 | 0.21 | NO |
41 | GSTO1 | GSTO1 | GSTO1 | 11988 | -0.063 | 0.2 | NO |
42 | AASDHPPT | AASDHPPT | AASDHPPT | 12386 | -0.072 | 0.19 | NO |
43 | NADSYN1 | NADSYN1 | NADSYN1 | 12392 | -0.072 | 0.2 | NO |
44 | CYB5R3 | CYB5R3 | CYB5R3 | 12584 | -0.077 | 0.2 | NO |
45 | SLC23A2 | SLC23A2 | SLC23A2 | 12610 | -0.078 | 0.21 | NO |
46 | MOCS1 | MOCS1 | MOCS1 | 13437 | -0.1 | 0.18 | NO |
47 | NMNAT3 | NMNAT3 | NMNAT3 | 13801 | -0.11 | 0.18 | NO |
48 | NAMPT | NAMPT | NAMPT | 14039 | -0.12 | 0.18 | NO |
49 | ACP5 | ACP5 | ACP5 | 14955 | -0.16 | 0.15 | NO |
50 | SLC2A1 | SLC2A1 | SLC2A1 | 17006 | -0.35 | 0.093 | NO |
Figure S9. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VASOPRESSIN REGULATED WATER REABSORPTION.

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

Table S6. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ARRB1 | ARRB1 | ARRB1 | 544 | 0.62 | 0.072 | YES |
2 | DNAJC6 | DNAJC6 | DNAJC6 | 1735 | 0.29 | 0.056 | YES |
3 | TBC1D8B | TBC1D8B | TBC1D8B | 1752 | 0.29 | 0.1 | YES |
4 | AP1M2 | AP1M2 | AP1M2 | 2257 | 0.23 | 0.11 | YES |
5 | AP4B1 | AP4B1 | AP4B1 | 2399 | 0.22 | 0.14 | YES |
6 | TPD52 | TPD52 | TPD52 | 2587 | 0.2 | 0.16 | YES |
7 | TGOLN2 | TGOLN2 | TGOLN2 | 2779 | 0.19 | 0.18 | YES |
8 | GAK | GAK | GAK | 2956 | 0.18 | 0.2 | YES |
9 | SORT1 | SORT1 | SORT1 | 3213 | 0.16 | 0.22 | YES |
10 | CPD | CPD | CPD | 3223 | 0.16 | 0.24 | YES |
11 | HIP1R | HIP1R | HIP1R | 3547 | 0.14 | 0.24 | YES |
12 | SNX9 | SNX9 | SNX9 | 3584 | 0.14 | 0.26 | YES |
13 | DTNBP1 | DTNBP1 | DTNBP1 | 3792 | 0.12 | 0.27 | YES |
14 | CTSZ | CTSZ | CTSZ | 3883 | 0.12 | 0.29 | YES |
15 | DNM2 | DNM2 | DNM2 | 4041 | 0.11 | 0.3 | YES |
16 | YIPF6 | YIPF6 | YIPF6 | 4357 | 0.1 | 0.3 | YES |
17 | PIK3C2A | PIK3C2A | PIK3C2A | 4398 | 0.1 | 0.31 | YES |
18 | GNS | GNS | GNS | 4654 | 0.091 | 0.31 | YES |
19 | SNAP23 | SNAP23 | SNAP23 | 4703 | 0.089 | 0.33 | YES |
20 | AP1S1 | AP1S1 | AP1S1 | 4928 | 0.082 | 0.33 | YES |
21 | TXNDC5 | TXNDC5 | TXNDC5 | 4962 | 0.081 | 0.34 | YES |
22 | SH3D19 | SH3D19 | SH3D19 | 5031 | 0.079 | 0.35 | YES |
23 | CNO | CNO | CNO | 5507 | 0.065 | 0.33 | NO |
24 | BLOC1S1 | BLOC1S1 | BLOC1S1 | 6094 | 0.05 | 0.31 | NO |
25 | NECAP1 | NECAP1 | NECAP1 | 6297 | 0.045 | 0.31 | NO |
26 | SNX5 | SNX5 | SNX5 | 6310 | 0.045 | 0.31 | NO |
27 | RAB5C | RAB5C | RAB5C | 6353 | 0.044 | 0.32 | NO |
28 | CLTC | CLTC | CLTC | 6607 | 0.039 | 0.31 | NO |
29 | ARF1 | ARF1 | ARF1 | 6635 | 0.038 | 0.32 | NO |
30 | OCRL | OCRL | OCRL | 6763 | 0.035 | 0.32 | NO |
31 | HSPA8 | HSPA8 | HSPA8 | 6855 | 0.034 | 0.32 | NO |
32 | GBF1 | GBF1 | GBF1 | 7375 | 0.022 | 0.29 | NO |
33 | FTL | FTL | FTL | 7541 | 0.019 | 0.29 | NO |
34 | CLTA | CLTA | CLTA | 7588 | 0.018 | 0.29 | NO |
35 | PICALM | PICALM | PICALM | 7720 | 0.016 | 0.28 | NO |
36 | VAMP8 | VAMP8 | VAMP8 | 8233 | 0.0064 | 0.26 | NO |
37 | AP1G1 | AP1G1 | AP1G1 | 8235 | 0.0063 | 0.26 | NO |
38 | VAMP7 | VAMP7 | VAMP7 | 8488 | 0.0018 | 0.24 | NO |
39 | SNX2 | SNX2 | SNX2 | 8580 | 0.00037 | 0.24 | NO |
40 | STX4 | STX4 | STX4 | 8695 | -0.0016 | 0.23 | NO |
41 | PUM1 | PUM1 | PUM1 | 8727 | -0.0023 | 0.23 | NO |
42 | FTH1 | FTH1 | FTH1 | 8731 | -0.0024 | 0.23 | NO |
43 | AP3B1 | AP3B1 | AP3B1 | 9016 | -0.0072 | 0.22 | NO |
44 | IGF2R | IGF2R | IGF2R | 9176 | -0.01 | 0.21 | NO |
45 | NAPA | NAPA | NAPA | 9773 | -0.02 | 0.18 | NO |
46 | DNASE2 | DNASE2 | DNASE2 | 9995 | -0.024 | 0.17 | NO |
47 | PLDN | PLDN | PLDN | 10222 | -0.028 | 0.17 | NO |
48 | BLOC1S3 | BLOC1S3 | BLOC1S3 | 10258 | -0.029 | 0.17 | NO |
49 | M6PR | M6PR | M6PR | 11830 | -0.06 | 0.095 | NO |
50 | TFRC | TFRC | TFRC | 12023 | -0.064 | 0.095 | NO |
51 | AP1B1 | AP1B1 | AP1B1 | 12156 | -0.067 | 0.099 | NO |
52 | VAMP2 | VAMP2 | VAMP2 | 12979 | -0.088 | 0.069 | NO |
53 | AP3S1 | AP3S1 | AP3S1 | 13353 | -0.099 | 0.066 | NO |
54 | AP4E1 | AP4E1 | AP4E1 | 13744 | -0.11 | 0.063 | NO |
55 | SNAPIN | SNAPIN | SNAPIN | 13909 | -0.12 | 0.073 | NO |
56 | AP1M1 | AP1M1 | AP1M1 | 14183 | -0.13 | 0.08 | NO |
57 | SH3GL2 | SH3GL2 | SH3GL2 | 15397 | -0.19 | 0.045 | NO |
58 | AP1S2 | AP1S2 | AP1S2 | 15505 | -0.2 | 0.071 | NO |
59 | TPD52L1 | TPD52L1 | TPD52L1 | 18193 | -0.62 | 0.03 | NO |
Figure S11. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VIBRIO CHOLERAE INFECTION.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VIBRIO CHOLERAE INFECTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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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 | HNF1B | HNF1B | HNF1B | 8 | 1.5 | 0.1 | YES |
2 | HNF4A | HNF4A | HNF4A | 15 | 1.5 | 0.2 | YES |
3 | PDX1 | PDX1 | PDX1 | 33 | 1.4 | 0.3 | YES |
4 | FOXA3 | FOXA3 | FOXA3 | 38 | 1.4 | 0.39 | YES |
5 | HNF1A | HNF1A | HNF1A | 60 | 1.2 | 0.47 | YES |
6 | FOXA2 | FOXA2 | FOXA2 | 82 | 1.2 | 0.55 | YES |
7 | HNF4G | HNF4G | HNF4G | 92 | 1.1 | 0.63 | YES |
8 | NR5A2 | NR5A2 | NR5A2 | 249 | 0.85 | 0.68 | YES |
9 | NEUROG3 | NEUROG3 | NEUROG3 | 386 | 0.72 | 0.72 | YES |
10 | ONECUT3 | ONECUT3 | ONECUT3 | 420 | 0.7 | 0.76 | YES |
11 | INSM1 | INSM1 | INSM1 | 1683 | 0.3 | 0.72 | NO |
12 | SLC2A2 | SLC2A2 | SLC2A2 | 1943 | 0.26 | 0.72 | NO |
13 | NEUROD1 | NEUROD1 | NEUROD1 | 2429 | 0.22 | 0.71 | NO |
14 | FGF10 | FGF10 | FGF10 | 2513 | 0.21 | 0.72 | NO |
15 | ONECUT1 | ONECUT1 | ONECUT1 | 6484 | 0.042 | 0.51 | NO |
16 | AKT1 | AKT1 | AKT1 | 8693 | -0.0016 | 0.39 | NO |
17 | RBPJ | RBPJ | RBPJ | 9731 | -0.02 | 0.34 | NO |
18 | PAX6 | PAX6 | PAX6 | 10416 | -0.031 | 0.3 | NO |
19 | HES1 | HES1 | HES1 | 10807 | -0.038 | 0.29 | NO |
20 | NKX2-2 | NKX2-2 | NKX2-2 | 11751 | -0.058 | 0.24 | NO |
21 | FOXO1 | FOXO1 | FOXO1 | 12118 | -0.066 | 0.22 | NO |
22 | AKT2 | AKT2 | AKT2 | 12528 | -0.076 | 0.21 | NO |
23 | PKLR | PKLR | PKLR | 13172 | -0.094 | 0.18 | NO |
24 | GCK | GCK | GCK | 13345 | -0.099 | 0.18 | NO |
25 | AKT3 | AKT3 | AKT3 | 16341 | -0.26 | 0.036 | NO |
26 | MAFA | MAFA | MAFA | 17415 | -0.42 | 0.0066 | NO |
27 | NKX6-1 | NKX6-1 | NKX6-1 | 17455 | -0.43 | 0.034 | NO |
28 | IAPP | IAPP | IAPP | 17884 | -0.52 | 0.046 | NO |
Figure S13. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA DEATH PATHWAY.

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

Table S8. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NR0B2 | NR0B2 | NR0B2 | 75 | 1.2 | 0.24 | YES |
2 | SERPINA4 | SERPINA4 | SERPINA4 | 141 | 1 | 0.44 | YES |
3 | IL2RG | IL2RG | IL2RG | 790 | 0.51 | 0.51 | YES |
4 | INPP5D | INPP5D | INPP5D | 1370 | 0.35 | 0.55 | YES |
5 | JAK2 | JAK2 | JAK2 | 2402 | 0.22 | 0.54 | NO |
6 | SRC | SRC | SRC | 3144 | 0.16 | 0.54 | NO |
7 | JAK3 | JAK3 | JAK3 | 4094 | 0.11 | 0.51 | NO |
8 | IL13RA1 | IL13RA1 | IL13RA1 | 4281 | 0.1 | 0.52 | NO |
9 | JAK1 | JAK1 | JAK1 | 4973 | 0.081 | 0.5 | NO |
10 | CISH | CISH | CISH | 4981 | 0.08 | 0.52 | NO |
11 | STAT6 | STAT6 | STAT6 | 6002 | 0.052 | 0.47 | NO |
12 | IARS | IARS | IARS | 7223 | 0.025 | 0.41 | NO |
13 | TYK2 | TYK2 | TYK2 | 7257 | 0.024 | 0.42 | NO |
14 | GRB2 | GRB2 | GRB2 | 7394 | 0.021 | 0.41 | NO |
15 | IL4R | IL4R | IL4R | 8495 | 0.0017 | 0.35 | NO |
16 | AKT1 | AKT1 | AKT1 | 8693 | -0.0016 | 0.34 | NO |
17 | PPP1R13B | PPP1R13B | PPP1R13B | 10459 | -0.032 | 0.26 | NO |
18 | SOS1 | SOS1 | SOS1 | 10685 | -0.036 | 0.25 | NO |
19 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 10896 | -0.04 | 0.25 | NO |
20 | SOS2 | SOS2 | SOS2 | 11949 | -0.062 | 0.2 | NO |
21 | AKT2 | AKT2 | AKT2 | 12528 | -0.076 | 0.19 | NO |
22 | SHC1 | SHC1 | SHC1 | 13302 | -0.098 | 0.17 | NO |
23 | PI3 | PI3 | PI3 | 14458 | -0.14 | 0.14 | NO |
24 | PIK3CA | PIK3CA | PIK3CA | 15423 | -0.19 | 0.12 | NO |
25 | AKT3 | AKT3 | AKT3 | 16341 | -0.26 | 0.13 | NO |
Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PPARA PATHWAY.

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

Table S9. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SLC44A4 | SLC44A4 | SLC44A4 | 46 | 1.3 | 0.031 | YES |
2 | GAL3ST1 | GAL3ST1 | GAL3ST1 | 61 | 1.2 | 0.062 | YES |
3 | PIP5K1B | PIP5K1B | PIP5K1B | 67 | 1.2 | 0.092 | YES |
4 | PLA2G10 | PLA2G10 | PLA2G10 | 96 | 1.1 | 0.12 | YES |
5 | ARSE | ARSE | ARSE | 108 | 1.1 | 0.15 | YES |
6 | GPD1 | GPD1 | GPD1 | 142 | 1 | 0.17 | YES |
7 | SMPD3 | SMPD3 | SMPD3 | 145 | 0.99 | 0.2 | YES |
8 | SLC44A3 | SLC44A3 | SLC44A3 | 310 | 0.79 | 0.21 | YES |
9 | ACHE | ACHE | ACHE | 337 | 0.77 | 0.22 | YES |
10 | PLA2G16 | PLA2G16 | PLA2G16 | 344 | 0.76 | 0.24 | YES |
11 | NEU4 | NEU4 | NEU4 | 398 | 0.72 | 0.26 | YES |
12 | DEGS2 | DEGS2 | DEGS2 | 490 | 0.66 | 0.27 | YES |
13 | PLA2G2A | PLA2G2A | PLA2G2A | 704 | 0.55 | 0.27 | YES |
14 | LPIN2 | LPIN2 | LPIN2 | 788 | 0.52 | 0.28 | YES |
15 | CHKA | CHKA | CHKA | 876 | 0.48 | 0.29 | YES |
16 | GBA3 | GBA3 | GBA3 | 945 | 0.46 | 0.3 | YES |
17 | INPP5J | INPP5J | INPP5J | 980 | 0.45 | 0.31 | YES |
18 | ACER2 | ACER2 | ACER2 | 1055 | 0.42 | 0.31 | YES |
19 | STS | STS | STS | 1074 | 0.41 | 0.32 | YES |
20 | DGAT2 | DGAT2 | DGAT2 | 1077 | 0.41 | 0.33 | YES |
21 | GALC | GALC | GALC | 1182 | 0.39 | 0.34 | YES |
22 | CHPT1 | CHPT1 | CHPT1 | 1382 | 0.35 | 0.34 | YES |
23 | PLBD1 | PLBD1 | PLBD1 | 1537 | 0.32 | 0.34 | YES |
24 | MGLL | MGLL | MGLL | 1582 | 0.31 | 0.34 | YES |
25 | PIK3C2B | PIK3C2B | PIK3C2B | 1654 | 0.3 | 0.35 | YES |
26 | AGPAT2 | AGPAT2 | AGPAT2 | 1744 | 0.29 | 0.35 | YES |
27 | ENPP7 | ENPP7 | ENPP7 | 1750 | 0.29 | 0.36 | YES |
28 | ARSH | ARSH | ARSH | 1762 | 0.29 | 0.36 | YES |
29 | DGAT1 | DGAT1 | DGAT1 | 1837 | 0.28 | 0.36 | YES |
30 | GPD1L | GPD1L | GPD1L | 2037 | 0.25 | 0.36 | YES |
31 | MBOAT1 | MBOAT1 | MBOAT1 | 2136 | 0.24 | 0.36 | YES |
32 | ETNK1 | ETNK1 | ETNK1 | 2172 | 0.24 | 0.37 | YES |
33 | INPP4B | INPP4B | INPP4B | 2174 | 0.24 | 0.37 | YES |
34 | GBA2 | GBA2 | GBA2 | 2191 | 0.24 | 0.38 | YES |
35 | PIK3CG | PIK3CG | PIK3CG | 2208 | 0.24 | 0.38 | YES |
36 | AGPAT9 | AGPAT9 | AGPAT9 | 2293 | 0.23 | 0.38 | YES |
37 | LPCAT4 | LPCAT4 | LPCAT4 | 2328 | 0.22 | 0.39 | YES |
38 | GLB1 | GLB1 | GLB1 | 2331 | 0.22 | 0.39 | YES |
39 | SMPD2 | SMPD2 | SMPD2 | 2391 | 0.22 | 0.4 | YES |
40 | SYNJ2 | SYNJ2 | SYNJ2 | 2394 | 0.22 | 0.4 | YES |
41 | PNPLA2 | PNPLA2 | PNPLA2 | 2405 | 0.22 | 0.41 | YES |
42 | NEU3 | NEU3 | NEU3 | 2409 | 0.22 | 0.41 | YES |
43 | SGPP2 | SGPP2 | SGPP2 | 2503 | 0.21 | 0.41 | YES |
44 | SGMS2 | SGMS2 | SGMS2 | 2540 | 0.21 | 0.42 | YES |
45 | PCYT2 | PCYT2 | PCYT2 | 2560 | 0.2 | 0.42 | YES |
46 | PLA2G4F | PLA2G4F | PLA2G4F | 2937 | 0.18 | 0.4 | NO |
47 | CRLS1 | CRLS1 | CRLS1 | 3000 | 0.17 | 0.4 | NO |
48 | PLA2G4A | PLA2G4A | PLA2G4A | 3029 | 0.17 | 0.41 | NO |
49 | SPHK2 | SPHK2 | SPHK2 | 3059 | 0.17 | 0.41 | NO |
50 | ASAH2 | ASAH2 | ASAH2 | 3100 | 0.16 | 0.41 | NO |
51 | PPAP2C | PPAP2C | PPAP2C | 3182 | 0.16 | 0.41 | NO |
52 | PIK3R3 | PIK3R3 | PIK3R3 | 3297 | 0.15 | 0.41 | NO |
53 | LPIN1 | LPIN1 | LPIN1 | 3382 | 0.14 | 0.41 | NO |
54 | AGPAT5 | AGPAT5 | AGPAT5 | 3458 | 0.14 | 0.41 | NO |
55 | CDS1 | CDS1 | CDS1 | 3542 | 0.14 | 0.41 | NO |
56 | CTSA | CTSA | CTSA | 3787 | 0.12 | 0.4 | NO |
57 | MTMR14 | MTMR14 | MTMR14 | 3812 | 0.12 | 0.4 | NO |
58 | HEXB | HEXB | HEXB | 3849 | 0.12 | 0.4 | NO |
59 | SPTLC2 | SPTLC2 | SPTLC2 | 3910 | 0.12 | 0.4 | NO |
60 | ASAH1 | ASAH1 | ASAH1 | 3928 | 0.12 | 0.4 | NO |
61 | PIK3C2G | PIK3C2G | PIK3C2G | 3956 | 0.12 | 0.4 | NO |
62 | GPAM | GPAM | GPAM | 4127 | 0.11 | 0.4 | NO |
63 | MTMR6 | MTMR6 | MTMR6 | 4172 | 0.11 | 0.4 | NO |
64 | AGPAT6 | AGPAT6 | AGPAT6 | 4222 | 0.11 | 0.4 | NO |
65 | GPAT2 | GPAT2 | GPAT2 | 4312 | 0.1 | 0.4 | NO |
66 | PIK3C2A | PIK3C2A | PIK3C2A | 4398 | 0.1 | 0.39 | NO |
67 | PLA2G1B | PLA2G1B | PLA2G1B | 4430 | 0.099 | 0.39 | NO |
68 | AGPAT1 | AGPAT1 | AGPAT1 | 4453 | 0.098 | 0.4 | NO |
69 | SUMF2 | SUMF2 | SUMF2 | 4459 | 0.097 | 0.4 | NO |
70 | PIP4K2A | PIP4K2A | PIP4K2A | 4562 | 0.094 | 0.4 | NO |
71 | FIG4 | FIG4 | FIG4 | 4665 | 0.09 | 0.39 | NO |
72 | PIK3CB | PIK3CB | PIK3CB | 4789 | 0.087 | 0.39 | NO |
73 | NEU1 | NEU1 | NEU1 | 4819 | 0.086 | 0.39 | NO |
74 | PIK3R5 | PIK3R5 | PIK3R5 | 4885 | 0.084 | 0.39 | NO |
75 | SACM1L | SACM1L | SACM1L | 4917 | 0.083 | 0.39 | NO |
76 | PLA2G2F | PLA2G2F | PLA2G2F | 4957 | 0.081 | 0.39 | NO |
77 | OSBP | OSBP | OSBP | 4968 | 0.081 | 0.39 | NO |
78 | SUMF1 | SUMF1 | SUMF1 | 5070 | 0.078 | 0.38 | NO |
79 | CERK | CERK | CERK | 5199 | 0.073 | 0.38 | NO |
80 | PHOSPHO1 | PHOSPHO1 | PHOSPHO1 | 5227 | 0.072 | 0.38 | NO |
81 | PLA2G12A | PLA2G12A | PLA2G12A | 5449 | 0.066 | 0.37 | NO |
82 | PTDSS2 | PTDSS2 | PTDSS2 | 5487 | 0.066 | 0.37 | NO |
83 | GBA | GBA | GBA | 5525 | 0.064 | 0.37 | NO |
84 | LPGAT1 | LPGAT1 | LPGAT1 | 5545 | 0.064 | 0.37 | NO |
85 | TPTE2 | TPTE2 | TPTE2 | 5602 | 0.062 | 0.37 | NO |
86 | GNPAT | GNPAT | GNPAT | 5705 | 0.06 | 0.36 | NO |
87 | INPPL1 | INPPL1 | INPPL1 | 5839 | 0.056 | 0.36 | NO |
88 | LPIN3 | LPIN3 | LPIN3 | 5858 | 0.056 | 0.36 | NO |
89 | PPAP2A | PPAP2A | PPAP2A | 6019 | 0.052 | 0.35 | NO |
90 | VAPB | VAPB | VAPB | 6044 | 0.051 | 0.35 | NO |
91 | LPCAT1 | LPCAT1 | LPCAT1 | 6104 | 0.05 | 0.35 | NO |
92 | MBOAT7 | MBOAT7 | MBOAT7 | 6160 | 0.048 | 0.35 | NO |
93 | SLC44A2 | SLC44A2 | SLC44A2 | 6242 | 0.047 | 0.34 | NO |
94 | HEXA | HEXA | HEXA | 6349 | 0.044 | 0.34 | NO |
95 | MTM1 | MTM1 | MTM1 | 6497 | 0.041 | 0.33 | NO |
96 | SYNJ1 | SYNJ1 | SYNJ1 | 6552 | 0.04 | 0.33 | NO |
97 | ARF1 | ARF1 | ARF1 | 6635 | 0.038 | 0.33 | NO |
98 | LPCAT3 | LPCAT3 | LPCAT3 | 6711 | 0.036 | 0.32 | NO |
99 | PLA2G2D | PLA2G2D | PLA2G2D | 6726 | 0.036 | 0.33 | NO |
100 | OCRL | OCRL | OCRL | 6763 | 0.035 | 0.32 | NO |
101 | MTMR7 | MTMR7 | MTMR7 | 7059 | 0.029 | 0.31 | NO |
102 | PPM1L | PPM1L | PPM1L | 7060 | 0.029 | 0.31 | NO |
103 | CEPT1 | CEPT1 | CEPT1 | 7063 | 0.029 | 0.31 | NO |
104 | PPAP2B | PPAP2B | PPAP2B | 7186 | 0.026 | 0.3 | NO |
105 | PIKFYVE | PIKFYVE | PIKFYVE | 7195 | 0.026 | 0.3 | NO |
106 | HADHA | HADHA | HADHA | 7895 | 0.012 | 0.27 | NO |
107 | MTMR4 | MTMR4 | MTMR4 | 7944 | 0.012 | 0.26 | NO |
108 | SGMS1 | SGMS1 | SGMS1 | 7963 | 0.011 | 0.26 | NO |
109 | LCLAT1 | LCLAT1 | LCLAT1 | 8336 | 0.0046 | 0.24 | NO |
110 | PI4K2B | PI4K2B | PI4K2B | 8343 | 0.0045 | 0.24 | NO |
111 | CDS2 | CDS2 | CDS2 | 8354 | 0.0042 | 0.24 | NO |
112 | ACER3 | ACER3 | ACER3 | 8477 | 0.002 | 0.24 | NO |
113 | TAZ | TAZ | TAZ | 8507 | 0.0016 | 0.24 | NO |
114 | PSAP | PSAP | PSAP | 8523 | 0.0013 | 0.24 | NO |
115 | COL4A3BP | COL4A3BP | COL4A3BP | 8583 | 0.0003 | 0.23 | NO |
116 | AGPAT3 | AGPAT3 | AGPAT3 | 8628 | -0.00053 | 0.23 | NO |
117 | PIK3R1 | PIK3R1 | PIK3R1 | 9030 | -0.0074 | 0.21 | NO |
118 | PI4KB | PI4KB | PI4KB | 9249 | -0.011 | 0.2 | NO |
119 | SMPD4 | SMPD4 | SMPD4 | 9266 | -0.012 | 0.2 | NO |
120 | SLC44A1 | SLC44A1 | SLC44A1 | 9591 | -0.017 | 0.18 | NO |
121 | PTEN | PTEN | PTEN | 9633 | -0.018 | 0.18 | NO |
122 | SMPD1 | SMPD1 | SMPD1 | 9648 | -0.018 | 0.18 | NO |
123 | GPCPD1 | GPCPD1 | GPCPD1 | 9721 | -0.019 | 0.17 | NO |
124 | PI4KA | PI4KA | PI4KA | 9726 | -0.019 | 0.17 | NO |
125 | SPTLC1 | SPTLC1 | SPTLC1 | 10073 | -0.025 | 0.16 | NO |
126 | UGCG | UGCG | UGCG | 10219 | -0.028 | 0.15 | NO |
127 | VAPA | VAPA | VAPA | 10339 | -0.03 | 0.14 | NO |
128 | SGPL1 | SGPL1 | SGPL1 | 10364 | -0.03 | 0.14 | NO |
129 | MTMR2 | MTMR2 | MTMR2 | 10385 | -0.031 | 0.14 | NO |
130 | CDIPT | CDIPT | CDIPT | 10589 | -0.034 | 0.13 | NO |
131 | GLA | GLA | GLA | 10591 | -0.034 | 0.13 | NO |
132 | PGS1 | PGS1 | PGS1 | 10645 | -0.035 | 0.13 | NO |
133 | PIP4K2B | PIP4K2B | PIP4K2B | 10698 | -0.036 | 0.13 | NO |
134 | ARF3 | ARF3 | ARF3 | 10745 | -0.037 | 0.13 | NO |
135 | ARSA | ARSA | ARSA | 11234 | -0.047 | 0.1 | NO |
136 | PIP5K1C | PIP5K1C | PIP5K1C | 11441 | -0.051 | 0.093 | NO |
137 | PLA2G6 | PLA2G6 | PLA2G6 | 11451 | -0.052 | 0.094 | NO |
138 | CHKB | CHKB | CHKB | 11495 | -0.053 | 0.093 | NO |
139 | PNPLA8 | PNPLA8 | PNPLA8 | 11499 | -0.053 | 0.094 | NO |
140 | EPT1 | EPT1 | EPT1 | 11620 | -0.055 | 0.089 | NO |
141 | ARSG | ARSG | ARSG | 11707 | -0.057 | 0.086 | NO |
142 | SGPP1 | SGPP1 | SGPP1 | 11810 | -0.059 | 0.082 | NO |
143 | VAC14 | VAC14 | VAC14 | 12121 | -0.066 | 0.067 | NO |
144 | HADHB | HADHB | HADHB | 12125 | -0.066 | 0.069 | NO |
145 | CSNK1G2 | CSNK1G2 | CSNK1G2 | 12273 | -0.069 | 0.062 | NO |
146 | MTMR3 | MTMR3 | MTMR3 | 12801 | -0.083 | 0.036 | NO |
147 | INPP5K | INPP5K | INPP5K | 12863 | -0.085 | 0.035 | NO |
148 | PIK3R2 | PIK3R2 | PIK3R2 | 12960 | -0.088 | 0.032 | NO |
149 | PTDSS1 | PTDSS1 | PTDSS1 | 13018 | -0.09 | 0.031 | NO |
150 | PLD3 | PLD3 | PLD3 | 13129 | -0.093 | 0.028 | NO |
151 | PLD6 | PLD6 | PLD6 | 13354 | -0.099 | 0.018 | NO |
152 | INPP5E | INPP5E | INPP5E | 13428 | -0.1 | 0.017 | NO |
153 | ARSB | ARSB | ARSB | 13674 | -0.11 | 0.0064 | NO |
154 | PIK3R4 | PIK3R4 | PIK3R4 | 13727 | -0.11 | 0.0065 | NO |
155 | PIK3C3 | PIK3C3 | PIK3C3 | 13832 | -0.11 | 0.0038 | NO |
156 | KDSR | KDSR | KDSR | 13891 | -0.12 | 0.0036 | NO |
157 | PEMT | PEMT | PEMT | 13952 | -0.12 | 0.0034 | NO |
158 | PITPNB | PITPNB | PITPNB | 14108 | -0.12 | -0.0017 | NO |
159 | PIK3R6 | PIK3R6 | PIK3R6 | 14478 | -0.14 | -0.018 | NO |
160 | PI4K2A | PI4K2A | PI4K2A | 14779 | -0.15 | -0.03 | NO |
161 | ARSK | ARSK | ARSK | 14789 | -0.15 | -0.027 | NO |
162 | PLA2G4C | PLA2G4C | PLA2G4C | 14847 | -0.16 | -0.026 | NO |
163 | PLD4 | PLD4 | PLD4 | 14992 | -0.17 | -0.029 | NO |
164 | MTMR1 | MTMR1 | MTMR1 | 15022 | -0.17 | -0.027 | NO |
165 | LPCAT2 | LPCAT2 | LPCAT2 | 15087 | -0.17 | -0.026 | NO |
166 | MBOAT2 | MBOAT2 | MBOAT2 | 15155 | -0.17 | -0.025 | NO |
167 | ARSF | ARSF | ARSF | 15230 | -0.18 | -0.024 | NO |
168 | PLD1 | PLD1 | PLD1 | 15375 | -0.19 | -0.027 | NO |
169 | PIK3CA | PIK3CA | PIK3CA | 15423 | -0.19 | -0.025 | NO |
170 | DEGS1 | DEGS1 | DEGS1 | 15474 | -0.19 | -0.023 | NO |
171 | AGPAT4 | AGPAT4 | AGPAT4 | 15711 | -0.21 | -0.03 | NO |
172 | PLD2 | PLD2 | PLD2 | 15758 | -0.21 | -0.027 | NO |
173 | PCYT1A | PCYT1A | PCYT1A | 15789 | -0.22 | -0.023 | NO |
174 | PLA2G4D | PLA2G4D | PLA2G4D | 16148 | -0.25 | -0.036 | NO |
175 | ARSJ | ARSJ | ARSJ | 16375 | -0.27 | -0.042 | NO |
176 | SLC44A5 | SLC44A5 | SLC44A5 | 16972 | -0.34 | -0.065 | NO |
177 | PNPLA3 | PNPLA3 | PNPLA3 | 16978 | -0.34 | -0.056 | NO |
178 | PIK3CD | PIK3CD | PIK3CD | 17055 | -0.35 | -0.052 | NO |
179 | PLA2G5 | PLA2G5 | PLA2G5 | 17194 | -0.37 | -0.049 | NO |
180 | PLA2G3 | PLA2G3 | PLA2G3 | 17258 | -0.39 | -0.043 | NO |
181 | GM2A | GM2A | GM2A | 17286 | -0.39 | -0.034 | NO |
182 | ACER1 | ACER1 | ACER1 | 17517 | -0.44 | -0.036 | NO |
183 | PRKD1 | PRKD1 | PRKD1 | 17522 | -0.44 | -0.024 | NO |
184 | NEU2 | NEU2 | NEU2 | 17607 | -0.46 | -0.017 | NO |
185 | SPHK1 | SPHK1 | SPHK1 | 17947 | -0.54 | -0.022 | NO |
186 | PCYT1B | PCYT1B | PCYT1B | 18547 | -0.83 | -0.033 | NO |
187 | ETNK2 | ETNK2 | ETNK2 | 18576 | -0.85 | -0.013 | NO |
188 | ARSI | ARSI | ARSI | 18577 | -0.85 | 0.0092 | NO |
Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA RHO PATHWAY.

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

Table S10. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | C4BPB | C4BPB | C4BPB | 31 | 1.4 | 0.11 | YES |
2 | FOXA3 | FOXA3 | FOXA3 | 38 | 1.4 | 0.21 | YES |
3 | TFF1 | TFF1 | TFF1 | 68 | 1.2 | 0.3 | YES |
4 | FOXA2 | FOXA2 | FOXA2 | 82 | 1.2 | 0.39 | YES |
5 | SHH | SHH | SHH | 180 | 0.93 | 0.46 | YES |
6 | SERPINA1 | SERPINA1 | SERPINA1 | 349 | 0.75 | 0.51 | YES |
7 | SFTPA2 | SFTPA2 | SFTPA2 | 760 | 0.53 | 0.52 | YES |
8 | FOXA1 | FOXA1 | FOXA1 | 1063 | 0.42 | 0.54 | YES |
9 | VTN | VTN | VTN | 1447 | 0.33 | 0.55 | YES |
10 | CYP2C18 | CYP2C18 | CYP2C18 | 1622 | 0.3 | 0.56 | YES |
11 | KLK3 | KLK3 | KLK3 | 1796 | 0.28 | 0.57 | YES |
12 | NR2F2 | NR2F2 | NR2F2 | 2164 | 0.24 | 0.57 | NO |
13 | XBP1 | XBP1 | XBP1 | 2674 | 0.2 | 0.56 | NO |
14 | APOB | APOB | APOB | 3028 | 0.17 | 0.56 | NO |
15 | NFIB | NFIB | NFIB | 4918 | 0.083 | 0.46 | NO |
16 | POU2F1 | POU2F1 | POU2F1 | 6400 | 0.043 | 0.38 | NO |
17 | PISD | PISD | PISD | 8160 | 0.0076 | 0.29 | NO |
18 | FOS | FOS | FOS | 8164 | 0.0075 | 0.29 | NO |
19 | SP1 | SP1 | SP1 | 8353 | 0.0042 | 0.28 | NO |
20 | CDKN1B | CDKN1B | CDKN1B | 9503 | -0.016 | 0.22 | NO |
21 | NFIA | NFIA | NFIA | 9534 | -0.016 | 0.22 | NO |
22 | SOD1 | SOD1 | SOD1 | 9585 | -0.017 | 0.22 | NO |
23 | BRCA1 | BRCA1 | BRCA1 | 9960 | -0.023 | 0.2 | NO |
24 | EP300 | EP300 | EP300 | 10581 | -0.034 | 0.17 | NO |
25 | COL18A1 | COL18A1 | COL18A1 | 10879 | -0.04 | 0.16 | NO |
26 | CREBBP | CREBBP | CREBBP | 11638 | -0.056 | 0.12 | NO |
27 | NDUFV3 | NDUFV3 | NDUFV3 | 11887 | -0.061 | 0.11 | NO |
28 | ATP5J | ATP5J | ATP5J | 12106 | -0.065 | 0.11 | NO |
29 | AP1B1 | AP1B1 | AP1B1 | 12156 | -0.067 | 0.11 | NO |
30 | PRDM15 | PRDM15 | PRDM15 | 12503 | -0.075 | 0.097 | NO |
31 | JUN | JUN | JUN | 13371 | -0.1 | 0.058 | NO |
32 | NFIC | NFIC | NFIC | 13890 | -0.12 | 0.039 | NO |
33 | NRIP1 | NRIP1 | NRIP1 | 13955 | -0.12 | 0.045 | NO |
34 | NCOA3 | NCOA3 | NCOA3 | 13997 | -0.12 | 0.052 | NO |
35 | AR | AR | AR | 14291 | -0.13 | 0.047 | NO |
36 | SCGB1A1 | SCGB1A1 | SCGB1A1 | 14511 | -0.14 | 0.046 | NO |
37 | CEBPB | CEBPB | CEBPB | 15126 | -0.17 | 0.026 | NO |
38 | SFTPA1 | SFTPA1 | SFTPA1 | 15868 | -0.22 | 0.0041 | NO |
39 | NKX3-1 | NKX3-1 | NKX3-1 | 17450 | -0.43 | -0.047 | NO |
40 | DSCAM | DSCAM | DSCAM | 17547 | -0.45 | -0.018 | NO |
41 | ESR1 | ESR1 | ESR1 | 17810 | -0.5 | 0.0068 | NO |
42 | SFTPD | SFTPD | SFTPD | 18014 | -0.56 | 0.039 | NO |
Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST INTERLEUKIN 4 PATHWAY.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: ST INTERLEUKIN 4 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
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 CYSTEINE AND METHIONINE METABOLISM | 34 | genes.ES.table | 0.52 | 1.6 | 0.028 | 1 | 0.96 | 0.35 | 0.18 | 0.29 | 0.7 | 0.37 |
KEGG RNA DEGRADATION | 57 | genes.ES.table | 0.4 | 1.8 | 0.024 | 1 | 0.67 | 0.72 | 0.54 | 0.34 | 1 | 0.59 |
KEGG BASAL TRANSCRIPTION FACTORS | 34 | genes.ES.table | 0.41 | 1.6 | 0.069 | 1 | 0.96 | 0.5 | 0.46 | 0.27 | 0.78 | 0.41 |
KEGG SPLICEOSOME | 114 | genes.ES.table | 0.4 | 1.6 | 0.097 | 1 | 0.95 | 0.74 | 0.52 | 0.35 | 0.8 | 0.43 |
PID FANCONI PATHWAY | 46 | genes.ES.table | 0.52 | 1.6 | 0.093 | 1 | 0.93 | 0.85 | 0.44 | 0.48 | 0.93 | 0.48 |
PID AURORA B PATHWAY | 39 | genes.ES.table | 0.51 | 1.6 | 0.043 | 1 | 0.92 | 0.51 | 0.32 | 0.35 | 0.92 | 0.48 |
PID ATR PATHWAY | 39 | genes.ES.table | 0.51 | 1.6 | 0.11 | 1 | 0.97 | 0.59 | 0.33 | 0.4 | 0.7 | 0.38 |
PID ATM PATHWAY | 34 | genes.ES.table | 0.48 | 1.6 | 0.059 | 1 | 0.91 | 0.71 | 0.48 | 0.37 | 1 | 0.53 |
PID PLK1 PATHWAY | 45 | genes.ES.table | 0.49 | 1.5 | 0.12 | 1 | 0.99 | 0.44 | 0.29 | 0.32 | 0.78 | 0.42 |
PID FOXM1PATHWAY | 39 | genes.ES.table | 0.51 | 1.6 | 0.053 | 1 | 0.94 | 0.54 | 0.29 | 0.38 | 0.95 | 0.48 |
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 | ENO3 | ENO3 | ENO3 | 201 | 0.6 | 0.12 | YES |
2 | PAPOLB | PAPOLB | PAPOLB | 539 | 0.49 | 0.2 | YES |
3 | DCP2 | DCP2 | DCP2 | 3641 | 0.2 | 0.075 | YES |
4 | LSM6 | LSM6 | LSM6 | 3827 | 0.2 | 0.11 | YES |
5 | DCP1B | DCP1B | DCP1B | 4253 | 0.18 | 0.12 | YES |
6 | EXOSC9 | EXOSC9 | EXOSC9 | 4868 | 0.16 | 0.12 | YES |
7 | PAPOLG | PAPOLG | PAPOLG | 5292 | 0.14 | 0.13 | YES |
8 | LSM2 | LSM2 | LSM2 | 5661 | 0.13 | 0.14 | YES |
9 | PNPT1 | PNPT1 | PNPT1 | 5838 | 0.12 | 0.15 | YES |
10 | CNOT3 | CNOT3 | CNOT3 | 6272 | 0.11 | 0.15 | YES |
11 | CNOT10 | CNOT10 | CNOT10 | 6322 | 0.11 | 0.17 | YES |
12 | EDC3 | EDC3 | EDC3 | 6441 | 0.11 | 0.19 | YES |
13 | CNOT7 | CNOT7 | CNOT7 | 6673 | 0.1 | 0.2 | YES |
14 | EXOSC5 | EXOSC5 | EXOSC5 | 6755 | 0.1 | 0.22 | YES |
15 | EXOSC3 | EXOSC3 | EXOSC3 | 7533 | 0.086 | 0.19 | YES |
16 | EXOSC8 | EXOSC8 | EXOSC8 | 7550 | 0.086 | 0.21 | YES |
17 | HSPD1 | HSPD1 | HSPD1 | 7575 | 0.085 | 0.23 | YES |
18 | C1D | C1D | C1D | 7649 | 0.084 | 0.24 | YES |
19 | CNOT6 | CNOT6 | CNOT6 | 7774 | 0.082 | 0.25 | YES |
20 | PARN | PARN | PARN | 7786 | 0.081 | 0.27 | YES |
21 | ZCCHC7 | ZCCHC7 | ZCCHC7 | 8014 | 0.077 | 0.27 | YES |
22 | RQCD1 | RQCD1 | RQCD1 | 8185 | 0.074 | 0.28 | YES |
23 | XRN2 | XRN2 | XRN2 | 8193 | 0.074 | 0.29 | YES |
24 | DCPS | DCPS | DCPS | 8227 | 0.073 | 0.3 | YES |
25 | EXOSC10 | EXOSC10 | EXOSC10 | 8307 | 0.072 | 0.32 | YES |
26 | LSM1 | LSM1 | LSM1 | 8415 | 0.07 | 0.32 | YES |
27 | DCP1A | DCP1A | DCP1A | 8441 | 0.07 | 0.34 | YES |
28 | LSM4 | LSM4 | LSM4 | 8581 | 0.067 | 0.34 | YES |
29 | EDC4 | EDC4 | EDC4 | 8967 | 0.06 | 0.34 | YES |
30 | CNOT6L | CNOT6L | CNOT6L | 9078 | 0.058 | 0.34 | YES |
31 | SKIV2L2 | SKIV2L2 | SKIV2L2 | 9082 | 0.058 | 0.36 | YES |
32 | CNOT2 | CNOT2 | CNOT2 | 9146 | 0.057 | 0.36 | YES |
33 | LSM5 | LSM5 | LSM5 | 9434 | 0.052 | 0.36 | YES |
34 | EXOSC2 | EXOSC2 | EXOSC2 | 9522 | 0.05 | 0.36 | YES |
35 | NAA38 | NAA38 | NAA38 | 9576 | 0.049 | 0.37 | YES |
36 | PAPOLA | PAPOLA | PAPOLA | 9792 | 0.045 | 0.37 | YES |
37 | LSM3 | LSM3 | LSM3 | 9802 | 0.045 | 0.38 | YES |
38 | PATL1 | PATL1 | PATL1 | 9830 | 0.044 | 0.39 | YES |
39 | EXOSC4 | EXOSC4 | EXOSC4 | 9879 | 0.043 | 0.39 | YES |
40 | SKIV2L | SKIV2L | SKIV2L | 10017 | 0.041 | 0.39 | YES |
41 | EXOSC6 | EXOSC6 | EXOSC6 | 10045 | 0.041 | 0.4 | YES |
42 | WDR61 | WDR61 | WDR61 | 10223 | 0.038 | 0.4 | NO |
43 | PAPD7 | PAPD7 | PAPD7 | 10713 | 0.029 | 0.38 | NO |
44 | CNOT4 | CNOT4 | CNOT4 | 11075 | 0.022 | 0.36 | NO |
45 | DDX6 | DDX6 | DDX6 | 11189 | 0.021 | 0.36 | NO |
46 | CNOT8 | CNOT8 | CNOT8 | 11650 | 0.013 | 0.34 | NO |
47 | HSPA9 | HSPA9 | HSPA9 | 11651 | 0.013 | 0.34 | NO |
48 | MPHOSPH6 | MPHOSPH6 | MPHOSPH6 | 12006 | 0.0066 | 0.33 | NO |
49 | EXOSC1 | EXOSC1 | EXOSC1 | 12075 | 0.0054 | 0.32 | NO |
50 | TTC37 | TTC37 | TTC37 | 12185 | 0.0032 | 0.32 | NO |
51 | ENO2 | ENO2 | ENO2 | 12280 | 0.0014 | 0.31 | NO |
52 | ENO1 | ENO1 | ENO1 | 12965 | -0.012 | 0.28 | NO |
53 | LSM7 | LSM7 | LSM7 | 13155 | -0.015 | 0.27 | NO |
54 | EXOSC7 | EXOSC7 | EXOSC7 | 13169 | -0.016 | 0.28 | NO |
55 | XRN1 | XRN1 | XRN1 | 13287 | -0.018 | 0.27 | NO |
56 | CNOT1 | CNOT1 | CNOT1 | 13778 | -0.028 | 0.25 | NO |
57 | DIS3 | DIS3 | DIS3 | 15159 | -0.063 | 0.19 | NO |
Figure S21. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CYSTEINE AND METHIONINE METABOLISM.

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

Table S12. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ZNF569 | ZNF569 | ZNF569 | 110 | 0.65 | 0.005 | YES |
2 | ZNF418 | ZNF418 | ZNF418 | 144 | 0.62 | 0.014 | YES |
3 | ZNF331 | ZNF331 | ZNF331 | 173 | 0.61 | 0.022 | YES |
4 | ZNF221 | ZNF221 | ZNF221 | 195 | 0.6 | 0.031 | YES |
5 | ZNF157 | ZNF157 | ZNF157 | 207 | 0.6 | 0.041 | YES |
6 | ZNF606 | ZNF606 | ZNF606 | 212 | 0.6 | 0.05 | YES |
7 | ZNF256 | ZNF256 | ZNF256 | 247 | 0.58 | 0.058 | YES |
8 | ZNF420 | ZNF420 | ZNF420 | 258 | 0.57 | 0.067 | YES |
9 | ZNF98 | ZNF98 | ZNF98 | 281 | 0.56 | 0.076 | YES |
10 | ZNF570 | ZNF570 | ZNF570 | 308 | 0.55 | 0.083 | YES |
11 | ZNF571 | ZNF571 | ZNF571 | 350 | 0.54 | 0.09 | YES |
12 | ZNF607 | ZNF607 | ZNF607 | 386 | 0.53 | 0.097 | YES |
13 | ZNF492 | ZNF492 | ZNF492 | 409 | 0.52 | 0.1 | YES |
14 | ZNF334 | ZNF334 | ZNF334 | 424 | 0.51 | 0.11 | YES |
15 | ZNF439 | ZNF439 | ZNF439 | 443 | 0.51 | 0.12 | YES |
16 | ZNF285 | ZNF285 | ZNF285 | 455 | 0.51 | 0.13 | YES |
17 | ZNF433 | ZNF433 | ZNF433 | 589 | 0.48 | 0.13 | YES |
18 | ZIK1 | ZIK1 | ZIK1 | 624 | 0.47 | 0.14 | YES |
19 | ZNF347 | ZNF347 | ZNF347 | 633 | 0.47 | 0.14 | YES |
20 | ZNF442 | ZNF442 | ZNF442 | 703 | 0.46 | 0.15 | YES |
21 | ZNF43 | ZNF43 | ZNF43 | 735 | 0.45 | 0.15 | YES |
22 | ZNF599 | ZNF599 | ZNF599 | 738 | 0.45 | 0.16 | YES |
23 | ZNF620 | ZNF620 | ZNF620 | 747 | 0.45 | 0.17 | YES |
24 | TBX5 | TBX5 | TBX5 | 755 | 0.45 | 0.17 | YES |
25 | ZIM2 | ZIM2 | ZIM2 | 762 | 0.45 | 0.18 | YES |
26 | ZNF519 | ZNF519 | ZNF519 | 778 | 0.44 | 0.19 | YES |
27 | ZNF311 | ZNF311 | ZNF311 | 806 | 0.44 | 0.19 | YES |
28 | ZNF540 | ZNF540 | ZNF540 | 813 | 0.44 | 0.2 | YES |
29 | ZNF454 | ZNF454 | ZNF454 | 887 | 0.43 | 0.2 | YES |
30 | ZNF354C | ZNF354C | ZNF354C | 922 | 0.42 | 0.21 | YES |
31 | ZNF577 | ZNF577 | ZNF577 | 945 | 0.42 | 0.21 | YES |
32 | ZNF613 | ZNF613 | ZNF613 | 962 | 0.42 | 0.22 | YES |
33 | ZNF773 | ZNF773 | ZNF773 | 990 | 0.41 | 0.22 | YES |
34 | ZNF605 | ZNF605 | ZNF605 | 1062 | 0.4 | 0.23 | YES |
35 | ZNF254 | ZNF254 | ZNF254 | 1086 | 0.4 | 0.23 | YES |
36 | ZNF10 | ZNF10 | ZNF10 | 1134 | 0.39 | 0.24 | YES |
37 | ZNF595 | ZNF595 | ZNF595 | 1141 | 0.39 | 0.24 | YES |
38 | ZNF649 | ZNF649 | ZNF649 | 1145 | 0.39 | 0.25 | YES |
39 | TEAD2 | TEAD2 | TEAD2 | 1193 | 0.39 | 0.25 | YES |
40 | ZNF547 | ZNF547 | ZNF547 | 1241 | 0.38 | 0.26 | YES |
41 | ZNF566 | ZNF566 | ZNF566 | 1249 | 0.38 | 0.26 | YES |
42 | ZNF167 | ZNF167 | ZNF167 | 1295 | 0.37 | 0.27 | YES |
43 | E2F5 | E2F5 | E2F5 | 1297 | 0.37 | 0.27 | YES |
44 | ZNF596 | ZNF596 | ZNF596 | 1327 | 0.37 | 0.28 | YES |
45 | ZNF563 | ZNF563 | ZNF563 | 1385 | 0.36 | 0.28 | YES |
46 | ZNF567 | ZNF567 | ZNF567 | 1397 | 0.36 | 0.29 | YES |
47 | NR1I3 | NR1I3 | NR1I3 | 1407 | 0.36 | 0.29 | YES |
48 | ZNF214 | ZNF214 | ZNF214 | 1473 | 0.35 | 0.3 | YES |
49 | ZNF30 | ZNF30 | ZNF30 | 1524 | 0.35 | 0.3 | YES |
50 | ZNF614 | ZNF614 | ZNF614 | 1528 | 0.35 | 0.3 | YES |
51 | ZNF583 | ZNF583 | ZNF583 | 1554 | 0.35 | 0.31 | YES |
52 | TGIF2 | TGIF2 | TGIF2 | 1562 | 0.34 | 0.31 | YES |
53 | ZNF529 | ZNF529 | ZNF529 | 1597 | 0.34 | 0.32 | YES |
54 | ESRRG | ESRRG | ESRRG | 1604 | 0.34 | 0.32 | YES |
55 | ZNF615 | ZNF615 | ZNF615 | 1618 | 0.34 | 0.33 | YES |
56 | ZNF643 | ZNF643 | ZNF643 | 1702 | 0.33 | 0.33 | YES |
57 | ZNF415 | ZNF415 | ZNF415 | 1706 | 0.33 | 0.33 | YES |
58 | ZNF559 | ZNF559 | ZNF559 | 1724 | 0.33 | 0.34 | YES |
59 | ZNF546 | ZNF546 | ZNF546 | 1750 | 0.33 | 0.34 | YES |
60 | ZNF350 | ZNF350 | ZNF350 | 1799 | 0.32 | 0.35 | YES |
61 | ZNF560 | ZNF560 | ZNF560 | 1812 | 0.32 | 0.35 | YES |
62 | ZFP28 | ZFP28 | ZFP28 | 1834 | 0.32 | 0.36 | YES |
63 | ZNF530 | ZNF530 | ZNF530 | 1835 | 0.32 | 0.36 | YES |
64 | ZNF483 | ZNF483 | ZNF483 | 1837 | 0.32 | 0.36 | YES |
65 | ZNF585A | ZNF585A | ZNF585A | 1934 | 0.31 | 0.36 | YES |
66 | ZNF155 | ZNF155 | ZNF155 | 2025 | 0.3 | 0.36 | YES |
67 | SMARCD3 | SMARCD3 | SMARCD3 | 2076 | 0.3 | 0.37 | YES |
68 | ZFP37 | ZFP37 | ZFP37 | 2127 | 0.29 | 0.37 | YES |
69 | NR2E3 | NR2E3 | NR2E3 | 2132 | 0.29 | 0.37 | YES |
70 | ZNF382 | ZNF382 | ZNF382 | 2174 | 0.29 | 0.38 | YES |
71 | ZNF658 | ZNF658 | ZNF658 | 2203 | 0.29 | 0.38 | YES |
72 | ZNF443 | ZNF443 | ZNF443 | 2223 | 0.29 | 0.38 | YES |
73 | ZNF419 | ZNF419 | ZNF419 | 2230 | 0.29 | 0.39 | YES |
74 | ZNF286A | ZNF286A | ZNF286A | 2271 | 0.28 | 0.39 | YES |
75 | ESRRB | ESRRB | ESRRB | 2278 | 0.28 | 0.4 | YES |
76 | ZNF26 | ZNF26 | ZNF26 | 2358 | 0.28 | 0.4 | YES |
77 | ZNF273 | ZNF273 | ZNF273 | 2365 | 0.28 | 0.4 | YES |
78 | ZNF140 | ZNF140 | ZNF140 | 2378 | 0.28 | 0.4 | YES |
79 | ZNF528 | ZNF528 | ZNF528 | 2401 | 0.28 | 0.41 | YES |
80 | ZFP2 | ZFP2 | ZFP2 | 2437 | 0.27 | 0.41 | YES |
81 | NR2E1 | NR2E1 | NR2E1 | 2439 | 0.27 | 0.42 | YES |
82 | ZNF14 | ZNF14 | ZNF14 | 2440 | 0.27 | 0.42 | YES |
83 | ZNF235 | ZNF235 | ZNF235 | 2453 | 0.27 | 0.42 | YES |
84 | ZNF92 | ZNF92 | ZNF92 | 2567 | 0.26 | 0.42 | YES |
85 | ZNF222 | ZNF222 | ZNF222 | 2608 | 0.26 | 0.42 | YES |
86 | ZNF230 | ZNF230 | ZNF230 | 2644 | 0.26 | 0.43 | YES |
87 | ZNF287 | ZNF287 | ZNF287 | 2695 | 0.26 | 0.43 | YES |
88 | ZNF184 | ZNF184 | ZNF184 | 2752 | 0.25 | 0.43 | YES |
89 | ZFP112 | ZFP112 | ZFP112 | 2756 | 0.25 | 0.43 | YES |
90 | ZNF610 | ZNF610 | ZNF610 | 2766 | 0.25 | 0.44 | YES |
91 | ZNF300 | ZNF300 | ZNF300 | 2788 | 0.25 | 0.44 | YES |
92 | ZNF642 | ZNF642 | ZNF642 | 2798 | 0.25 | 0.44 | YES |
93 | ZNF100 | ZNF100 | ZNF100 | 2863 | 0.24 | 0.44 | YES |
94 | ZNF585B | ZNF585B | ZNF585B | 2874 | 0.24 | 0.45 | YES |
95 | ZNF225 | ZNF225 | ZNF225 | 2961 | 0.24 | 0.45 | YES |
96 | ZNF354A | ZNF354A | ZNF354A | 2970 | 0.24 | 0.45 | YES |
97 | ZNF227 | ZNF227 | ZNF227 | 3037 | 0.23 | 0.45 | YES |
98 | ZNF208 | ZNF208 | ZNF208 | 3071 | 0.23 | 0.45 | YES |
99 | ZNF160 | ZNF160 | ZNF160 | 3195 | 0.23 | 0.45 | YES |
100 | ZNF154 | ZNF154 | ZNF154 | 3216 | 0.22 | 0.45 | YES |
101 | ZKSCAN4 | ZKSCAN4 | ZKSCAN4 | 3237 | 0.22 | 0.46 | YES |
102 | ZNF558 | ZNF558 | ZNF558 | 3241 | 0.22 | 0.46 | YES |
103 | ESR2 | ESR2 | ESR2 | 3246 | 0.22 | 0.46 | YES |
104 | ZNF551 | ZNF551 | ZNF551 | 3265 | 0.22 | 0.46 | YES |
105 | ZNF138 | ZNF138 | ZNF138 | 3279 | 0.22 | 0.47 | YES |
106 | ZNF320 | ZNF320 | ZNF320 | 3482 | 0.21 | 0.46 | YES |
107 | ESR1 | ESR1 | ESR1 | 3484 | 0.21 | 0.46 | YES |
108 | ZNF2 | ZNF2 | ZNF2 | 3522 | 0.21 | 0.47 | YES |
109 | NR5A1 | NR5A1 | NR5A1 | 3586 | 0.21 | 0.47 | YES |
110 | ZNF493 | ZNF493 | ZNF493 | 3613 | 0.2 | 0.47 | YES |
111 | ZNF136 | ZNF136 | ZNF136 | 3635 | 0.2 | 0.47 | YES |
112 | ZNF114 | ZNF114 | ZNF114 | 3646 | 0.2 | 0.47 | YES |
113 | ZNF471 | ZNF471 | ZNF471 | 3698 | 0.2 | 0.47 | YES |
114 | ZNF383 | ZNF383 | ZNF383 | 3711 | 0.2 | 0.48 | YES |
115 | ZNF548 | ZNF548 | ZNF548 | 3736 | 0.2 | 0.48 | YES |
116 | ZNF544 | ZNF544 | ZNF544 | 3785 | 0.2 | 0.48 | YES |
117 | ZNF223 | ZNF223 | ZNF223 | 3800 | 0.2 | 0.48 | YES |
118 | ZNF234 | ZNF234 | ZNF234 | 3805 | 0.2 | 0.48 | YES |
119 | ZNF417 | ZNF417 | ZNF417 | 3833 | 0.2 | 0.49 | YES |
120 | ZNF496 | ZNF496 | ZNF496 | 3918 | 0.19 | 0.48 | YES |
121 | ZNF180 | ZNF180 | ZNF180 | 3922 | 0.19 | 0.49 | YES |
122 | ZNF517 | ZNF517 | ZNF517 | 3923 | 0.19 | 0.49 | YES |
123 | ZNF304 | ZNF304 | ZNF304 | 3954 | 0.19 | 0.49 | YES |
124 | ZNF192 | ZNF192 | ZNF192 | 3988 | 0.19 | 0.49 | YES |
125 | ZNF485 | ZNF485 | ZNF485 | 3999 | 0.19 | 0.5 | YES |
126 | ZNF354B | ZNF354B | ZNF354B | 4036 | 0.19 | 0.5 | YES |
127 | ZNF45 | ZNF45 | ZNF45 | 4055 | 0.19 | 0.5 | YES |
128 | RBL1 | RBL1 | RBL1 | 4106 | 0.18 | 0.5 | YES |
129 | ZNF248 | ZNF248 | ZNF248 | 4107 | 0.18 | 0.5 | YES |
130 | ZKSCAN5 | ZKSCAN5 | ZKSCAN5 | 4127 | 0.18 | 0.51 | YES |
131 | ZNF582 | ZNF582 | ZNF582 | 4351 | 0.17 | 0.5 | YES |
132 | ZNF625 | ZNF625 | ZNF625 | 4364 | 0.17 | 0.5 | YES |
133 | ZNF215 | ZNF215 | ZNF215 | 4455 | 0.17 | 0.5 | YES |
134 | ZNF212 | ZNF212 | ZNF212 | 4544 | 0.17 | 0.5 | YES |
135 | ZNF473 | ZNF473 | ZNF473 | 4585 | 0.16 | 0.5 | YES |
136 | ZFP1 | ZFP1 | ZFP1 | 4595 | 0.16 | 0.5 | YES |
137 | ZNF627 | ZNF627 | ZNF627 | 4605 | 0.16 | 0.5 | YES |
138 | ZNF23 | ZNF23 | ZNF23 | 4643 | 0.16 | 0.5 | YES |
139 | ZNF498 | ZNF498 | ZNF498 | 4645 | 0.16 | 0.5 | YES |
140 | ZNF17 | ZNF17 | ZNF17 | 4724 | 0.16 | 0.5 | YES |
141 | AR | AR | AR | 4765 | 0.16 | 0.5 | YES |
142 | ZNF624 | ZNF624 | ZNF624 | 4842 | 0.16 | 0.5 | YES |
143 | ZNF274 | ZNF274 | ZNF274 | 4897 | 0.15 | 0.5 | YES |
144 | ZNF555 | ZNF555 | ZNF555 | 4912 | 0.15 | 0.5 | YES |
145 | ZKSCAN3 | ZKSCAN3 | ZKSCAN3 | 4922 | 0.15 | 0.5 | YES |
146 | RORB | RORB | RORB | 4924 | 0.15 | 0.51 | YES |
147 | ZNF226 | ZNF226 | ZNF226 | 4990 | 0.15 | 0.51 | YES |
148 | ZNF416 | ZNF416 | ZNF416 | 5074 | 0.15 | 0.5 | YES |
149 | ZNF446 | ZNF446 | ZNF446 | 5080 | 0.15 | 0.51 | YES |
150 | SMAD4 | SMAD4 | SMAD4 | 5142 | 0.15 | 0.5 | YES |
151 | ZNF200 | ZNF200 | ZNF200 | 5293 | 0.14 | 0.5 | YES |
152 | ZNF655 | ZNF655 | ZNF655 | 5297 | 0.14 | 0.5 | YES |
153 | ZNF436 | ZNF436 | ZNF436 | 5311 | 0.14 | 0.5 | YES |
154 | ZNF141 | ZNF141 | ZNF141 | 5360 | 0.14 | 0.5 | YES |
155 | ZNF616 | ZNF616 | ZNF616 | 5418 | 0.14 | 0.5 | YES |
156 | PGR | PGR | PGR | 5433 | 0.14 | 0.5 | YES |
157 | ZNF708 | ZNF708 | ZNF708 | 5451 | 0.14 | 0.5 | YES |
158 | ZNF641 | ZNF641 | ZNF641 | 5485 | 0.14 | 0.5 | YES |
159 | ZNF33B | ZNF33B | ZNF33B | 5499 | 0.13 | 0.51 | YES |
160 | ZNF333 | ZNF333 | ZNF333 | 5626 | 0.13 | 0.5 | NO |
161 | ZNF175 | ZNF175 | ZNF175 | 5644 | 0.13 | 0.5 | NO |
162 | ZNF202 | ZNF202 | ZNF202 | 5697 | 0.13 | 0.5 | NO |
163 | ZNF3 | ZNF3 | ZNF3 | 5815 | 0.12 | 0.5 | NO |
164 | MED12 | MED12 | MED12 | 5831 | 0.12 | 0.5 | NO |
165 | ZNF543 | ZNF543 | ZNF543 | 5847 | 0.12 | 0.5 | NO |
166 | ZNF445 | ZNF445 | ZNF445 | 5935 | 0.12 | 0.5 | NO |
167 | ZNF33A | ZNF33A | ZNF33A | 5948 | 0.12 | 0.5 | NO |
168 | SMAD2 | SMAD2 | SMAD2 | 5952 | 0.12 | 0.5 | NO |
169 | TGS1 | TGS1 | TGS1 | 6013 | 0.12 | 0.5 | NO |
170 | NR2F1 | NR2F1 | NR2F1 | 6058 | 0.12 | 0.5 | NO |
171 | KAT2A | KAT2A | KAT2A | 6061 | 0.12 | 0.5 | NO |
172 | ZNF584 | ZNF584 | ZNF584 | 6266 | 0.11 | 0.49 | NO |
173 | TRIM33 | TRIM33 | TRIM33 | 6277 | 0.11 | 0.49 | NO |
174 | ZNF28 | ZNF28 | ZNF28 | 6370 | 0.11 | 0.49 | NO |
175 | TRIM28 | TRIM28 | TRIM28 | 6380 | 0.11 | 0.49 | NO |
176 | ZNF514 | ZNF514 | ZNF514 | 6392 | 0.11 | 0.49 | NO |
177 | PARP1 | PARP1 | PARP1 | 6537 | 0.11 | 0.49 | NO |
178 | ZNF432 | ZNF432 | ZNF432 | 6590 | 0.11 | 0.49 | NO |
179 | ZNF441 | ZNF441 | ZNF441 | 6653 | 0.1 | 0.48 | NO |
180 | ZNF611 | ZNF611 | ZNF611 | 6837 | 0.1 | 0.48 | NO |
181 | TEAD4 | TEAD4 | TEAD4 | 6886 | 0.1 | 0.48 | NO |
182 | ZFP90 | ZFP90 | ZFP90 | 6967 | 0.098 | 0.47 | NO |
183 | MEN1 | MEN1 | MEN1 | 7096 | 0.095 | 0.47 | NO |
184 | NR5A2 | NR5A2 | NR5A2 | 7116 | 0.095 | 0.47 | NO |
185 | ZNF510 | ZNF510 | ZNF510 | 7117 | 0.095 | 0.47 | NO |
186 | RBPJ | RBPJ | RBPJ | 7152 | 0.094 | 0.47 | NO |
187 | NR1H3 | NR1H3 | NR1H3 | 7238 | 0.092 | 0.47 | NO |
188 | SMURF2 | SMURF2 | SMURF2 | 7240 | 0.092 | 0.47 | NO |
189 | NR2C2AP | NR2C2AP | NR2C2AP | 7316 | 0.091 | 0.46 | NO |
190 | ZNF490 | ZNF490 | ZNF490 | 7358 | 0.09 | 0.46 | NO |
191 | MED17 | MED17 | MED17 | 7374 | 0.089 | 0.46 | NO |
192 | ZNF250 | ZNF250 | ZNF250 | 7433 | 0.088 | 0.46 | NO |
193 | ZNF552 | ZNF552 | ZNF552 | 7448 | 0.088 | 0.46 | NO |
194 | ZNF565 | ZNF565 | ZNF565 | 7528 | 0.086 | 0.46 | NO |
195 | SMAD7 | SMAD7 | SMAD7 | 7535 | 0.086 | 0.46 | NO |
196 | ZNF468 | ZNF468 | ZNF468 | 7623 | 0.085 | 0.46 | NO |
197 | ZNF25 | ZNF25 | ZNF25 | 7670 | 0.084 | 0.46 | NO |
198 | MED30 | MED30 | MED30 | 7700 | 0.083 | 0.46 | NO |
199 | NOTCH2 | NOTCH2 | NOTCH2 | 7756 | 0.082 | 0.46 | NO |
200 | SKI | SKI | SKI | 7796 | 0.081 | 0.46 | NO |
201 | ZNF266 | ZNF266 | ZNF266 | 7827 | 0.081 | 0.46 | NO |
202 | ZNF224 | ZNF224 | ZNF224 | 7852 | 0.08 | 0.46 | NO |
203 | ZNF394 | ZNF394 | ZNF394 | 7963 | 0.078 | 0.45 | NO |
204 | ZNF12 | ZNF12 | ZNF12 | 8088 | 0.076 | 0.44 | NO |
205 | ZNF169 | ZNF169 | ZNF169 | 8156 | 0.075 | 0.44 | NO |
206 | TEAD3 | TEAD3 | TEAD3 | 8173 | 0.074 | 0.44 | NO |
207 | MAMLD1 | MAMLD1 | MAMLD1 | 8211 | 0.074 | 0.44 | NO |
208 | CCNT2 | CCNT2 | CCNT2 | 8336 | 0.071 | 0.44 | NO |
209 | RXRB | RXRB | RXRB | 8360 | 0.071 | 0.44 | NO |
210 | NR6A1 | NR6A1 | NR6A1 | 8473 | 0.069 | 0.43 | NO |
211 | NCOR2 | NCOR2 | NCOR2 | 8530 | 0.068 | 0.43 | NO |
212 | ZNF589 | ZNF589 | ZNF589 | 8535 | 0.068 | 0.43 | NO |
213 | NPPA | NPPA | NPPA | 8683 | 0.065 | 0.42 | NO |
214 | ZNF500 | ZNF500 | ZNF500 | 8685 | 0.065 | 0.42 | NO |
215 | CCNC | CCNC | CCNC | 8715 | 0.065 | 0.42 | NO |
216 | ZNF189 | ZNF189 | ZNF189 | 8726 | 0.064 | 0.42 | NO |
217 | RARA | RARA | RARA | 8737 | 0.064 | 0.42 | NO |
218 | ZNF587 | ZNF587 | ZNF587 | 8757 | 0.064 | 0.42 | NO |
219 | MED31 | MED31 | MED31 | 8764 | 0.064 | 0.43 | NO |
220 | ZNF621 | ZNF621 | ZNF621 | 8831 | 0.062 | 0.42 | NO |
221 | MED1 | MED1 | MED1 | 8840 | 0.062 | 0.42 | NO |
222 | MED7 | MED7 | MED7 | 8897 | 0.061 | 0.42 | NO |
223 | ZNF480 | ZNF480 | ZNF480 | 9056 | 0.058 | 0.42 | NO |
224 | ZNF20 | ZNF20 | ZNF20 | 9061 | 0.058 | 0.42 | NO |
225 | MED20 | MED20 | MED20 | 9073 | 0.058 | 0.42 | NO |
226 | ZNF101 | ZNF101 | ZNF101 | 9136 | 0.057 | 0.41 | NO |
227 | ZNF434 | ZNF434 | ZNF434 | 9173 | 0.056 | 0.41 | NO |
228 | ZNF37A | ZNF37A | ZNF37A | 9372 | 0.052 | 0.4 | NO |
229 | MED26 | MED26 | MED26 | 9390 | 0.052 | 0.4 | NO |
230 | TEAD1 | TEAD1 | TEAD1 | 9485 | 0.05 | 0.4 | NO |
231 | UBE2D1 | UBE2D1 | UBE2D1 | 9550 | 0.049 | 0.4 | NO |
232 | MED24 | MED24 | MED24 | 9679 | 0.047 | 0.39 | NO |
233 | WWTR1 | WWTR1 | WWTR1 | 9694 | 0.047 | 0.39 | NO |
234 | SP1 | SP1 | SP1 | 9723 | 0.046 | 0.39 | NO |
235 | NR3C1 | NR3C1 | NR3C1 | 9803 | 0.045 | 0.38 | NO |
236 | ZNF506 | ZNF506 | ZNF506 | 9826 | 0.044 | 0.38 | NO |
237 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 9870 | 0.044 | 0.38 | NO |
238 | NCOA6 | NCOA6 | NCOA6 | 9929 | 0.042 | 0.38 | NO |
239 | MAML1 | MAML1 | MAML1 | 9940 | 0.042 | 0.38 | NO |
240 | NR4A3 | NR4A3 | NR4A3 | 10000 | 0.041 | 0.38 | NO |
241 | MED6 | MED6 | MED6 | 10093 | 0.04 | 0.37 | NO |
242 | ZNF564 | ZNF564 | ZNF564 | 10159 | 0.039 | 0.37 | NO |
243 | TGIF1 | TGIF1 | TGIF1 | 10260 | 0.037 | 0.37 | NO |
244 | CCNT1 | CCNT1 | CCNT1 | 10306 | 0.036 | 0.36 | NO |
245 | ZNF425 | ZNF425 | ZNF425 | 10308 | 0.036 | 0.36 | NO |
246 | ZNF557 | ZNF557 | ZNF557 | 10356 | 0.035 | 0.36 | NO |
247 | ZNF282 | ZNF282 | ZNF282 | 10382 | 0.035 | 0.36 | NO |
248 | ZNF211 | ZNF211 | ZNF211 | 10456 | 0.033 | 0.36 | NO |
249 | SNW1 | SNW1 | SNW1 | 10516 | 0.032 | 0.36 | NO |
250 | ZNF267 | ZNF267 | ZNF267 | 10676 | 0.03 | 0.35 | NO |
251 | MED23 | MED23 | MED23 | 10678 | 0.03 | 0.35 | NO |
252 | ZNF263 | ZNF263 | ZNF263 | 10747 | 0.028 | 0.34 | NO |
253 | RPS27A | RPS27A | RPS27A | 10751 | 0.028 | 0.34 | NO |
254 | MED25 | MED25 | MED25 | 10971 | 0.024 | 0.33 | NO |
255 | YAP1 | YAP1 | YAP1 | 11077 | 0.022 | 0.33 | NO |
256 | E2F4 | E2F4 | E2F4 | 11146 | 0.021 | 0.32 | NO |
257 | NRBP1 | NRBP1 | NRBP1 | 11204 | 0.02 | 0.32 | NO |
258 | TBL1X | TBL1X | TBL1X | 11366 | 0.018 | 0.31 | NO |
259 | NR2F6 | NR2F6 | NR2F6 | 11403 | 0.017 | 0.31 | NO |
260 | RXRG | RXRG | RXRG | 11443 | 0.016 | 0.31 | NO |
261 | TFDP1 | TFDP1 | TFDP1 | 11496 | 0.015 | 0.31 | NO |
262 | MAML3 | MAML3 | MAML3 | 11512 | 0.015 | 0.31 | NO |
263 | ZNF398 | ZNF398 | ZNF398 | 11541 | 0.015 | 0.31 | NO |
264 | NR4A1 | NR4A1 | NR4A1 | 11599 | 0.014 | 0.3 | NO |
265 | NOTCH3 | NOTCH3 | NOTCH3 | 11600 | 0.014 | 0.3 | NO |
266 | MED4 | MED4 | MED4 | 11676 | 0.013 | 0.3 | NO |
267 | NCOR1 | NCOR1 | NCOR1 | 11678 | 0.013 | 0.3 | NO |
268 | USP9X | USP9X | USP9X | 11705 | 0.012 | 0.3 | NO |
269 | CREBBP | CREBBP | CREBBP | 11727 | 0.012 | 0.3 | NO |
270 | UBE2D3 | UBE2D3 | UBE2D3 | 11817 | 0.01 | 0.29 | NO |
271 | ZNF205 | ZNF205 | ZNF205 | 11830 | 0.01 | 0.29 | NO |
272 | NCOA2 | NCOA2 | NCOA2 | 11834 | 0.01 | 0.29 | NO |
273 | ZNF343 | ZNF343 | ZNF343 | 11847 | 0.0098 | 0.29 | NO |
274 | PPM1A | PPM1A | PPM1A | 11886 | 0.009 | 0.29 | NO |
275 | ZNF317 | ZNF317 | ZNF317 | 12104 | 0.0048 | 0.28 | NO |
276 | ZNF460 | ZNF460 | ZNF460 | 12115 | 0.0046 | 0.28 | NO |
277 | ZNF18 | ZNF18 | ZNF18 | 12138 | 0.0041 | 0.28 | NO |
278 | NCOA1 | NCOA1 | NCOA1 | 12307 | 0.00092 | 0.27 | NO |
279 | ZNF324 | ZNF324 | ZNF324 | 12341 | 0.00035 | 0.27 | NO |
280 | ZNF19 | ZNF19 | ZNF19 | 12390 | -0.00073 | 0.26 | NO |
281 | ZNF597 | ZNF597 | ZNF597 | 12409 | -0.0011 | 0.26 | NO |
282 | HDAC1 | HDAC1 | HDAC1 | 12427 | -0.0015 | 0.26 | NO |
283 | MAML2 | MAML2 | MAML2 | 12497 | -0.0026 | 0.26 | NO |
284 | NR1D2 | NR1D2 | NR1D2 | 12584 | -0.0042 | 0.25 | NO |
285 | MED14 | MED14 | MED14 | 12613 | -0.0046 | 0.25 | NO |
286 | NCOA3 | NCOA3 | NCOA3 | 12623 | -0.0048 | 0.25 | NO |
287 | UBA52 | UBA52 | UBA52 | 12729 | -0.0067 | 0.25 | NO |
288 | CTGF | CTGF | CTGF | 12791 | -0.0079 | 0.24 | NO |
289 | SKIL | SKIL | SKIL | 12861 | -0.0092 | 0.24 | NO |
290 | ZKSCAN1 | ZKSCAN1 | ZKSCAN1 | 12863 | -0.0092 | 0.24 | NO |
291 | RARG | RARG | RARG | 13044 | -0.013 | 0.23 | NO |
292 | ZNF440 | ZNF440 | ZNF440 | 13156 | -0.015 | 0.22 | NO |
293 | ZNF556 | ZNF556 | ZNF556 | 13197 | -0.016 | 0.22 | NO |
294 | CDK9 | CDK9 | CDK9 | 13288 | -0.018 | 0.22 | NO |
295 | ZNF431 | ZNF431 | ZNF431 | 13307 | -0.018 | 0.22 | NO |
296 | NOTCH4 | NOTCH4 | NOTCH4 | 13330 | -0.019 | 0.22 | NO |
297 | ZNF264 | ZNF264 | ZNF264 | 13350 | -0.02 | 0.22 | NO |
298 | ZNF619 | ZNF619 | ZNF619 | 13535 | -0.023 | 0.2 | NO |
299 | NRBF2 | NRBF2 | NRBF2 | 13782 | -0.029 | 0.19 | NO |
300 | CDK8 | CDK8 | CDK8 | 13801 | -0.029 | 0.19 | NO |
301 | MED8 | MED8 | MED8 | 13829 | -0.03 | 0.19 | NO |
302 | ZNF561 | ZNF561 | ZNF561 | 13931 | -0.032 | 0.19 | NO |
303 | MED27 | MED27 | MED27 | 14067 | -0.035 | 0.18 | NO |
304 | MED15 | MED15 | MED15 | 14209 | -0.038 | 0.17 | NO |
305 | MED16 | MED16 | MED16 | 14501 | -0.045 | 0.16 | NO |
306 | ZNF197 | ZNF197 | ZNF197 | 14616 | -0.048 | 0.15 | NO |
307 | MED10 | MED10 | MED10 | 14642 | -0.049 | 0.15 | NO |
308 | ZNF426 | ZNF426 | ZNF426 | 14658 | -0.049 | 0.15 | NO |
309 | ZNF337 | ZNF337 | ZNF337 | 15046 | -0.059 | 0.13 | NO |
310 | ZNF600 | ZNF600 | ZNF600 | 15080 | -0.06 | 0.13 | NO |
311 | ZNF213 | ZNF213 | ZNF213 | 15135 | -0.062 | 0.13 | NO |
312 | ZNF484 | ZNF484 | ZNF484 | 15219 | -0.065 | 0.12 | NO |
313 | KAT2B | KAT2B | KAT2B | 15245 | -0.066 | 0.12 | NO |
314 | NR1H2 | NR1H2 | NR1H2 | 15700 | -0.08 | 0.1 | NO |
315 | RUNX2 | RUNX2 | RUNX2 | 15749 | -0.082 | 0.1 | NO |
316 | THRA | THRA | THRA | 15905 | -0.088 | 0.093 | NO |
317 | NR4A2 | NR4A2 | NR4A2 | 15933 | -0.089 | 0.094 | NO |
318 | PRIC285 | PRIC285 | PRIC285 | 16130 | -0.096 | 0.084 | NO |
319 | NR3C2 | NR3C2 | NR3C2 | 16234 | -0.1 | 0.08 | NO |
320 | PPARD | PPARD | PPARD | 16440 | -0.11 | 0.071 | NO |
321 | JUNB | JUNB | JUNB | 16578 | -0.12 | 0.066 | NO |
322 | PPARA | PPARA | PPARA | 16608 | -0.12 | 0.066 | NO |
323 | RXRA | RXRA | RXRA | 16647 | -0.12 | 0.066 | NO |
324 | RORA | RORA | RORA | 16652 | -0.12 | 0.068 | NO |
325 | RORC | RORC | RORC | 16738 | -0.13 | 0.066 | NO |
326 | THRB | THRB | THRB | 16811 | -0.13 | 0.064 | NO |
327 | NR0B2 | NR0B2 | NR0B2 | 16819 | -0.13 | 0.066 | NO |
328 | MYC | MYC | MYC | 16826 | -0.13 | 0.068 | NO |
329 | SMAD3 | SMAD3 | SMAD3 | 16883 | -0.14 | 0.067 | NO |
330 | HNF4G | HNF4G | HNF4G | 16914 | -0.14 | 0.067 | NO |
331 | ZNF430 | ZNF430 | ZNF430 | 17032 | -0.14 | 0.064 | NO |
332 | PPARG | PPARG | PPARG | 17062 | -0.15 | 0.064 | NO |
333 | NR1I2 | NR1I2 | NR1I2 | 17105 | -0.15 | 0.065 | NO |
334 | ESRRA | ESRRA | ESRRA | 17305 | -0.17 | 0.057 | NO |
335 | HNF4A | HNF4A | HNF4A | 17427 | -0.18 | 0.053 | NO |
336 | CDKN2B | CDKN2B | CDKN2B | 17527 | -0.19 | 0.051 | NO |
337 | VDR | VDR | VDR | 17774 | -0.22 | 0.041 | NO |
338 | SERPINE1 | SERPINE1 | SERPINE1 | 17827 | -0.22 | 0.042 | NO |
339 | NR1D1 | NR1D1 | NR1D1 | 17898 | -0.24 | 0.042 | NO |
340 | NR0B1 | NR0B1 | NR0B1 | 17926 | -0.24 | 0.045 | NO |
Figure S23. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RNA DEGRADATION.

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

Table S13. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SMC1B | SMC1B | SMC1B | 11 | 0.85 | 0.016 | YES |
2 | HIST1H2BN | HIST1H2BN | HIST1H2BN | 353 | 0.54 | 0.0079 | YES |
3 | HIST3H2BB | HIST3H2BB | HIST3H2BB | 507 | 0.5 | 0.0093 | YES |
4 | HIST1H4I | HIST1H4I | HIST1H4I | 550 | 0.49 | 0.016 | YES |
5 | HIST1H4E | HIST1H4E | HIST1H4E | 608 | 0.47 | 0.023 | YES |
6 | PSMA8 | PSMA8 | PSMA8 | 619 | 0.47 | 0.031 | YES |
7 | SYCP2 | SYCP2 | SYCP2 | 664 | 0.46 | 0.038 | YES |
8 | HIST1H2BF | HIST1H2BF | HIST1H2BF | 685 | 0.46 | 0.046 | YES |
9 | HIST1H4D | HIST1H4D | HIST1H4D | 772 | 0.44 | 0.05 | YES |
10 | HIST1H2BJ | HIST1H2BJ | HIST1H2BJ | 856 | 0.43 | 0.054 | YES |
11 | HIST1H2BO | HIST1H2BO | HIST1H2BO | 961 | 0.42 | 0.056 | YES |
12 | TERT | TERT | TERT | 1147 | 0.39 | 0.054 | YES |
13 | HIST2H4A | HIST2H4A | HIST2H4A | 1189 | 0.39 | 0.059 | YES |
14 | HIST1H2BE | HIST1H2BE | HIST1H2BE | 1201 | 0.38 | 0.066 | YES |
15 | E2F5 | E2F5 | E2F5 | 1297 | 0.37 | 0.068 | YES |
16 | CDC7 | CDC7 | CDC7 | 1300 | 0.37 | 0.075 | YES |
17 | SKA1 | SKA1 | SKA1 | 1475 | 0.35 | 0.073 | YES |
18 | GINS4 | GINS4 | GINS4 | 1632 | 0.34 | 0.071 | YES |
19 | DNA2 | DNA2 | DNA2 | 1771 | 0.32 | 0.07 | YES |
20 | HIST1H2AE | HIST1H2AE | HIST1H2AE | 1849 | 0.32 | 0.072 | YES |
21 | STAG3 | STAG3 | STAG3 | 1905 | 0.31 | 0.075 | YES |
22 | HIST1H2BB | HIST1H2BB | HIST1H2BB | 1926 | 0.31 | 0.08 | YES |
23 | PRIM1 | PRIM1 | PRIM1 | 1946 | 0.31 | 0.085 | YES |
24 | SGOL1 | SGOL1 | SGOL1 | 2018 | 0.3 | 0.087 | YES |
25 | NUF2 | NUF2 | NUF2 | 2020 | 0.3 | 0.092 | YES |
26 | TYMS | TYMS | TYMS | 2072 | 0.3 | 0.096 | YES |
27 | HIST1H2BL | HIST1H2BL | HIST1H2BL | 2118 | 0.3 | 0.099 | YES |
28 | HIST1H4K | HIST1H4K | HIST1H4K | 2125 | 0.29 | 0.1 | YES |
29 | FBXO5 | FBXO5 | FBXO5 | 2129 | 0.29 | 0.11 | YES |
30 | HIST1H4C | HIST1H4C | HIST1H4C | 2144 | 0.29 | 0.12 | YES |
31 | NDC80 | NDC80 | NDC80 | 2159 | 0.29 | 0.12 | YES |
32 | HIST1H2AD | HIST1H2AD | HIST1H2AD | 2214 | 0.29 | 0.12 | YES |
33 | MLF1IP | MLF1IP | MLF1IP | 2249 | 0.29 | 0.13 | YES |
34 | PLK4 | PLK4 | PLK4 | 2297 | 0.28 | 0.13 | YES |
35 | OIP5 | OIP5 | OIP5 | 2299 | 0.28 | 0.14 | YES |
36 | HIST1H4L | HIST1H4L | HIST1H4L | 2318 | 0.28 | 0.14 | YES |
37 | HIST1H4B | HIST1H4B | HIST1H4B | 2349 | 0.28 | 0.14 | YES |
38 | CDC25A | CDC25A | CDC25A | 2369 | 0.28 | 0.15 | YES |
39 | E2F3 | E2F3 | E2F3 | 2420 | 0.27 | 0.15 | YES |
40 | HIST1H2BG | HIST1H2BG | HIST1H2BG | 2460 | 0.27 | 0.15 | YES |
41 | MCM10 | MCM10 | MCM10 | 2535 | 0.27 | 0.15 | YES |
42 | GMNN | GMNN | GMNN | 2609 | 0.26 | 0.16 | YES |
43 | HIST1H2BI | HIST1H2BI | HIST1H2BI | 2713 | 0.25 | 0.16 | YES |
44 | POLE2 | POLE2 | POLE2 | 2715 | 0.25 | 0.16 | YES |
45 | NEK2 | NEK2 | NEK2 | 2725 | 0.25 | 0.16 | YES |
46 | BIRC5 | BIRC5 | BIRC5 | 2742 | 0.25 | 0.17 | YES |
47 | HIST1H4H | HIST1H4H | HIST1H4H | 2753 | 0.25 | 0.17 | YES |
48 | HIST1H2BH | HIST1H2BH | HIST1H2BH | 2758 | 0.25 | 0.18 | YES |
49 | SPC24 | SPC24 | SPC24 | 2787 | 0.25 | 0.18 | YES |
50 | HIST1H4A | HIST1H4A | HIST1H4A | 2801 | 0.25 | 0.18 | YES |
51 | CENPA | CENPA | CENPA | 2883 | 0.24 | 0.18 | YES |
52 | PRKAR2B | PRKAR2B | PRKAR2B | 2891 | 0.24 | 0.19 | YES |
53 | LIN9 | LIN9 | LIN9 | 2915 | 0.24 | 0.19 | YES |
54 | CENPH | CENPH | CENPH | 2953 | 0.24 | 0.2 | YES |
55 | CHEK2 | CHEK2 | CHEK2 | 2965 | 0.24 | 0.2 | YES |
56 | CDK2 | CDK2 | CDK2 | 2966 | 0.24 | 0.2 | YES |
57 | CEP135 | CEP135 | CEP135 | 2981 | 0.24 | 0.21 | YES |
58 | CEP290 | CEP290 | CEP290 | 2984 | 0.24 | 0.21 | YES |
59 | CCNE2 | CCNE2 | CCNE2 | 2994 | 0.24 | 0.22 | YES |
60 | KIF20A | KIF20A | KIF20A | 3020 | 0.24 | 0.22 | YES |
61 | MAD2L1 | MAD2L1 | MAD2L1 | 3033 | 0.24 | 0.22 | YES |
62 | HIST1H2AB | HIST1H2AB | HIST1H2AB | 3038 | 0.23 | 0.23 | YES |
63 | KNTC1 | KNTC1 | KNTC1 | 3076 | 0.23 | 0.23 | YES |
64 | CDC25C | CDC25C | CDC25C | 3137 | 0.23 | 0.23 | YES |
65 | HIST1H2BM | HIST1H2BM | HIST1H2BM | 3161 | 0.23 | 0.24 | YES |
66 | AURKB | AURKB | AURKB | 3165 | 0.23 | 0.24 | YES |
67 | CHEK1 | CHEK1 | CHEK1 | 3175 | 0.23 | 0.24 | YES |
68 | HIST1H2BD | HIST1H2BD | HIST1H2BD | 3211 | 0.22 | 0.25 | YES |
69 | CDC14A | CDC14A | CDC14A | 3224 | 0.22 | 0.25 | YES |
70 | ERCC6L | ERCC6L | ERCC6L | 3300 | 0.22 | 0.25 | YES |
71 | KIF2C | KIF2C | KIF2C | 3305 | 0.22 | 0.25 | YES |
72 | UBE2C | UBE2C | UBE2C | 3372 | 0.22 | 0.26 | YES |
73 | ZWINT | ZWINT | ZWINT | 3380 | 0.22 | 0.26 | YES |
74 | E2F1 | E2F1 | E2F1 | 3390 | 0.22 | 0.26 | YES |
75 | CENPQ | CENPQ | CENPQ | 3437 | 0.21 | 0.26 | YES |
76 | HIST1H4J | HIST1H4J | HIST1H4J | 3439 | 0.21 | 0.27 | YES |
77 | SGOL2 | SGOL2 | SGOL2 | 3444 | 0.21 | 0.27 | YES |
78 | KIF18A | KIF18A | KIF18A | 3476 | 0.21 | 0.27 | YES |
79 | KIF23 | KIF23 | KIF23 | 3496 | 0.21 | 0.28 | YES |
80 | ITGB3BP | ITGB3BP | ITGB3BP | 3556 | 0.21 | 0.28 | YES |
81 | ALMS1 | ALMS1 | ALMS1 | 3567 | 0.21 | 0.28 | YES |
82 | NUP107 | NUP107 | NUP107 | 3597 | 0.21 | 0.28 | YES |
83 | CENPL | CENPL | CENPL | 3611 | 0.2 | 0.29 | YES |
84 | NSL1 | NSL1 | NSL1 | 3648 | 0.2 | 0.29 | YES |
85 | CENPO | CENPO | CENPO | 3654 | 0.2 | 0.29 | YES |
86 | BUB1B | BUB1B | BUB1B | 3694 | 0.2 | 0.3 | YES |
87 | LMNB1 | LMNB1 | LMNB1 | 3704 | 0.2 | 0.3 | YES |
88 | HJURP | HJURP | HJURP | 3722 | 0.2 | 0.3 | YES |
89 | DBF4 | DBF4 | DBF4 | 3729 | 0.2 | 0.3 | YES |
90 | HIST1H2BC | HIST1H2BC | HIST1H2BC | 3741 | 0.2 | 0.31 | YES |
91 | RFC4 | RFC4 | RFC4 | 3743 | 0.2 | 0.31 | YES |
92 | CDC6 | CDC6 | CDC6 | 3821 | 0.2 | 0.31 | YES |
93 | CDKN1B | CDKN1B | CDKN1B | 3846 | 0.2 | 0.31 | YES |
94 | HIST1H2BK | HIST1H2BK | HIST1H2BK | 3849 | 0.2 | 0.32 | YES |
95 | HIST1H4F | HIST1H4F | HIST1H4F | 3856 | 0.2 | 0.32 | YES |
96 | CCNE1 | CCNE1 | CCNE1 | 3871 | 0.19 | 0.32 | YES |
97 | CENPI | CENPI | CENPI | 3940 | 0.19 | 0.32 | YES |
98 | TEX12 | TEX12 | TEX12 | 3942 | 0.19 | 0.33 | YES |
99 | PRIM2 | PRIM2 | PRIM2 | 3943 | 0.19 | 0.33 | YES |
100 | CCDC99 | CCDC99 | CCDC99 | 3986 | 0.19 | 0.33 | YES |
101 | RFC5 | RFC5 | RFC5 | 4058 | 0.19 | 0.33 | YES |
102 | SPC25 | SPC25 | SPC25 | 4102 | 0.18 | 0.34 | YES |
103 | FKBP6 | FKBP6 | FKBP6 | 4105 | 0.18 | 0.34 | YES |
104 | RBL1 | RBL1 | RBL1 | 4106 | 0.18 | 0.34 | YES |
105 | POLE | POLE | POLE | 4145 | 0.18 | 0.34 | YES |
106 | CDC45 | CDC45 | CDC45 | 4182 | 0.18 | 0.34 | YES |
107 | CENPK | CENPK | CENPK | 4193 | 0.18 | 0.35 | YES |
108 | GINS1 | GINS1 | GINS1 | 4198 | 0.18 | 0.35 | YES |
109 | CKS1B | CKS1B | CKS1B | 4201 | 0.18 | 0.35 | YES |
110 | APITD1 | APITD1 | APITD1 | 4251 | 0.18 | 0.36 | YES |
111 | CEP70 | CEP70 | CEP70 | 4266 | 0.18 | 0.36 | YES |
112 | SKP2 | SKP2 | SKP2 | 4280 | 0.18 | 0.36 | YES |
113 | CEP250 | CEP250 | CEP250 | 4286 | 0.18 | 0.36 | YES |
114 | HIST4H4 | HIST4H4 | HIST4H4 | 4288 | 0.18 | 0.37 | YES |
115 | CDK4 | CDK4 | CDK4 | 4328 | 0.18 | 0.37 | YES |
116 | RFC3 | RFC3 | RFC3 | 4422 | 0.17 | 0.37 | YES |
117 | MYBL2 | MYBL2 | MYBL2 | 4434 | 0.17 | 0.37 | YES |
118 | RBBP4 | RBBP4 | RBBP4 | 4461 | 0.17 | 0.37 | YES |
119 | MCM6 | MCM6 | MCM6 | 4464 | 0.17 | 0.38 | YES |
120 | HIST2H2AC | HIST2H2AC | HIST2H2AC | 4484 | 0.17 | 0.38 | YES |
121 | HIST2H2BE | HIST2H2BE | HIST2H2BE | 4543 | 0.17 | 0.38 | YES |
122 | POLD1 | POLD1 | POLD1 | 4561 | 0.17 | 0.38 | YES |
123 | RFC2 | RFC2 | RFC2 | 4613 | 0.16 | 0.38 | YES |
124 | CCNA2 | CCNA2 | CCNA2 | 4616 | 0.16 | 0.38 | YES |
125 | DHFR | DHFR | DHFR | 4626 | 0.16 | 0.38 | YES |
126 | CCNB2 | CCNB2 | CCNB2 | 4658 | 0.16 | 0.39 | YES |
127 | RPA2 | RPA2 | RPA2 | 4846 | 0.16 | 0.38 | YES |
128 | POT1 | POT1 | POT1 | 4850 | 0.16 | 0.38 | YES |
129 | CENPM | CENPM | CENPM | 4902 | 0.15 | 0.38 | YES |
130 | DSN1 | DSN1 | DSN1 | 4936 | 0.15 | 0.38 | YES |
131 | CDKN2C | CDKN2C | CDKN2C | 4974 | 0.15 | 0.38 | YES |
132 | LIN52 | LIN52 | LIN52 | 5021 | 0.15 | 0.38 | YES |
133 | MIS12 | MIS12 | MIS12 | 5024 | 0.15 | 0.39 | YES |
134 | PPP2R3B | PPP2R3B | PPP2R3B | 5090 | 0.15 | 0.39 | YES |
135 | CDK1 | CDK1 | CDK1 | 5112 | 0.15 | 0.39 | YES |
136 | AKAP9 | AKAP9 | AKAP9 | 5147 | 0.15 | 0.39 | YES |
137 | MCM2 | MCM2 | MCM2 | 5157 | 0.15 | 0.39 | YES |
138 | FGFR1OP | FGFR1OP | FGFR1OP | 5160 | 0.15 | 0.4 | YES |
139 | AURKA | AURKA | AURKA | 5164 | 0.14 | 0.4 | YES |
140 | CDCA8 | CDCA8 | CDCA8 | 5191 | 0.14 | 0.4 | YES |
141 | LIG1 | LIG1 | LIG1 | 5289 | 0.14 | 0.4 | YES |
142 | CEP76 | CEP76 | CEP76 | 5290 | 0.14 | 0.4 | YES |
143 | ZWILCH | ZWILCH | ZWILCH | 5302 | 0.14 | 0.4 | YES |
144 | BRCA1 | BRCA1 | BRCA1 | 5328 | 0.14 | 0.4 | YES |
145 | NEDD1 | NEDD1 | NEDD1 | 5336 | 0.14 | 0.41 | YES |
146 | AZI1 | AZI1 | AZI1 | 5369 | 0.14 | 0.41 | YES |
147 | CCNB1 | CCNB1 | CCNB1 | 5404 | 0.14 | 0.41 | YES |
148 | HIST1H2AJ | HIST1H2AJ | HIST1H2AJ | 5413 | 0.14 | 0.41 | YES |
149 | CDC20 | CDC20 | CDC20 | 5428 | 0.14 | 0.41 | YES |
150 | NINL | NINL | NINL | 5429 | 0.14 | 0.41 | YES |
151 | CDT1 | CDT1 | CDT1 | 5458 | 0.14 | 0.42 | YES |
152 | MCM8 | MCM8 | MCM8 | 5468 | 0.14 | 0.42 | YES |
153 | WEE1 | WEE1 | WEE1 | 5489 | 0.14 | 0.42 | YES |
154 | GINS2 | GINS2 | GINS2 | 5494 | 0.14 | 0.42 | YES |
155 | BUB1 | BUB1 | BUB1 | 5498 | 0.13 | 0.42 | YES |
156 | ANAPC10 | ANAPC10 | ANAPC10 | 5528 | 0.13 | 0.42 | YES |
157 | TUBG2 | TUBG2 | TUBG2 | 5583 | 0.13 | 0.42 | YES |
158 | MCM4 | MCM4 | MCM4 | 5587 | 0.13 | 0.43 | YES |
159 | HIST2H2AA3 | HIST2H2AA3 | HIST2H2AA3 | 5588 | 0.13 | 0.43 | YES |
160 | H2AFX | H2AFX | H2AFX | 5591 | 0.13 | 0.43 | YES |
161 | ANAPC4 | ANAPC4 | ANAPC4 | 5606 | 0.13 | 0.43 | YES |
162 | POLA1 | POLA1 | POLA1 | 5620 | 0.13 | 0.44 | YES |
163 | SMC3 | SMC3 | SMC3 | 5757 | 0.13 | 0.43 | YES |
164 | XPO1 | XPO1 | XPO1 | 5786 | 0.13 | 0.43 | YES |
165 | CENPJ | CENPJ | CENPJ | 5798 | 0.13 | 0.43 | YES |
166 | TUBA1A | TUBA1A | TUBA1A | 5863 | 0.12 | 0.43 | YES |
167 | RCC2 | RCC2 | RCC2 | 5915 | 0.12 | 0.43 | YES |
168 | CASC5 | CASC5 | CASC5 | 5969 | 0.12 | 0.43 | YES |
169 | RPA1 | RPA1 | RPA1 | 5974 | 0.12 | 0.43 | YES |
170 | NUP43 | NUP43 | NUP43 | 6040 | 0.12 | 0.43 | YES |
171 | AHCTF1 | AHCTF1 | AHCTF1 | 6050 | 0.12 | 0.43 | YES |
172 | NUP133 | NUP133 | NUP133 | 6083 | 0.12 | 0.44 | YES |
173 | RAD9A | RAD9A | RAD9A | 6109 | 0.12 | 0.44 | YES |
174 | MCM7 | MCM7 | MCM7 | 6121 | 0.12 | 0.44 | YES |
175 | WRAP53 | WRAP53 | WRAP53 | 6246 | 0.11 | 0.43 | YES |
176 | E2F2 | E2F2 | E2F2 | 6261 | 0.11 | 0.44 | YES |
177 | CDC23 | CDC23 | CDC23 | 6263 | 0.11 | 0.44 | YES |
178 | PCNT | PCNT | PCNT | 6312 | 0.11 | 0.44 | YES |
179 | MCM3 | MCM3 | MCM3 | 6318 | 0.11 | 0.44 | YES |
180 | DYRK1A | DYRK1A | DYRK1A | 6427 | 0.11 | 0.44 | NO |
181 | PSMB4 | PSMB4 | PSMB4 | 6469 | 0.11 | 0.43 | NO |
182 | TUBB | TUBB | TUBB | 6557 | 0.11 | 0.43 | NO |
183 | SKA2 | SKA2 | SKA2 | 6572 | 0.11 | 0.43 | NO |
184 | PTTG1 | PTTG1 | PTTG1 | 6650 | 0.1 | 0.43 | NO |
185 | NUP37 | NUP37 | NUP37 | 6701 | 0.1 | 0.43 | NO |
186 | MDM2 | MDM2 | MDM2 | 6712 | 0.1 | 0.43 | NO |
187 | POLA2 | POLA2 | POLA2 | 6754 | 0.1 | 0.43 | NO |
188 | PCM1 | PCM1 | PCM1 | 6762 | 0.1 | 0.43 | NO |
189 | MCM5 | MCM5 | MCM5 | 6776 | 0.1 | 0.43 | NO |
190 | FEN1 | FEN1 | FEN1 | 6801 | 0.1 | 0.44 | NO |
191 | RAD21 | RAD21 | RAD21 | 6846 | 0.1 | 0.44 | NO |
192 | SEH1L | SEH1L | SEH1L | 6870 | 0.1 | 0.44 | NO |
193 | HIST1H2AC | HIST1H2AC | HIST1H2AC | 6949 | 0.098 | 0.43 | NO |
194 | H2AFZ | H2AFZ | H2AFZ | 6960 | 0.098 | 0.43 | NO |
195 | HSPA2 | HSPA2 | HSPA2 | 6992 | 0.097 | 0.44 | NO |
196 | CEP57 | CEP57 | CEP57 | 7069 | 0.096 | 0.43 | NO |
197 | ANAPC5 | ANAPC5 | ANAPC5 | 7211 | 0.093 | 0.43 | NO |
198 | ANAPC7 | ANAPC7 | ANAPC7 | 7234 | 0.092 | 0.43 | NO |
199 | RAD1 | RAD1 | RAD1 | 7246 | 0.092 | 0.43 | NO |
200 | PMF1 | PMF1 | PMF1 | 7251 | 0.092 | 0.43 | NO |
201 | ATM | ATM | ATM | 7338 | 0.09 | 0.43 | NO |
202 | STAG2 | STAG2 | STAG2 | 7416 | 0.088 | 0.42 | NO |
203 | CENPC1 | CENPC1 | CENPC1 | 7472 | 0.087 | 0.42 | NO |
204 | RRM2 | RRM2 | RRM2 | 7557 | 0.086 | 0.42 | NO |
205 | CEP192 | CEP192 | CEP192 | 7561 | 0.086 | 0.42 | NO |
206 | PSMD4 | PSMD4 | PSMD4 | 7581 | 0.085 | 0.42 | NO |
207 | CUL1 | CUL1 | CUL1 | 7594 | 0.085 | 0.42 | NO |
208 | YWHAE | YWHAE | YWHAE | 7630 | 0.084 | 0.42 | NO |
209 | UBE2E1 | UBE2E1 | UBE2E1 | 7638 | 0.084 | 0.42 | NO |
210 | LIN37 | LIN37 | LIN37 | 7683 | 0.083 | 0.42 | NO |
211 | SMARCA5 | SMARCA5 | SMARCA5 | 7695 | 0.083 | 0.42 | NO |
212 | CKAP5 | CKAP5 | CKAP5 | 7765 | 0.082 | 0.42 | NO |
213 | DKC1 | DKC1 | DKC1 | 7771 | 0.082 | 0.42 | NO |
214 | RUVBL1 | RUVBL1 | RUVBL1 | 7877 | 0.08 | 0.42 | NO |
215 | BUB3 | BUB3 | BUB3 | 7927 | 0.079 | 0.42 | NO |
216 | OFD1 | OFD1 | OFD1 | 7965 | 0.078 | 0.42 | NO |
217 | RAD17 | RAD17 | RAD17 | 8001 | 0.077 | 0.42 | NO |
218 | PPP1CC | PPP1CC | PPP1CC | 8049 | 0.076 | 0.42 | NO |
219 | TERF1 | TERF1 | TERF1 | 8062 | 0.076 | 0.42 | NO |
220 | SYNE1 | SYNE1 | SYNE1 | 8078 | 0.076 | 0.42 | NO |
221 | SYCP3 | SYCP3 | SYCP3 | 8118 | 0.075 | 0.42 | NO |
222 | LIN54 | LIN54 | LIN54 | 8129 | 0.075 | 0.42 | NO |
223 | PSMD10 | PSMD10 | PSMD10 | 8313 | 0.072 | 0.41 | NO |
224 | TP53 | TP53 | TP53 | 8356 | 0.071 | 0.41 | NO |
225 | NUP85 | NUP85 | NUP85 | 8454 | 0.07 | 0.4 | NO |
226 | TUBG1 | TUBG1 | TUBG1 | 8478 | 0.069 | 0.4 | NO |
227 | SMC1A | SMC1A | SMC1A | 8495 | 0.069 | 0.41 | NO |
228 | CEP63 | CEP63 | CEP63 | 8533 | 0.068 | 0.4 | NO |
229 | CENPT | CENPT | CENPT | 8534 | 0.068 | 0.41 | NO |
230 | MAPRE1 | MAPRE1 | MAPRE1 | 8607 | 0.067 | 0.4 | NO |
231 | CENPN | CENPN | CENPN | 8711 | 0.065 | 0.4 | NO |
232 | NPM1 | NPM1 | NPM1 | 8743 | 0.064 | 0.4 | NO |
233 | PSMC4 | PSMC4 | PSMC4 | 8744 | 0.064 | 0.4 | NO |
234 | SDCCAG8 | SDCCAG8 | SDCCAG8 | 8907 | 0.061 | 0.39 | NO |
235 | ATRIP | ATRIP | ATRIP | 8916 | 0.061 | 0.39 | NO |
236 | ACD | ACD | ACD | 8922 | 0.061 | 0.39 | NO |
237 | RUVBL2 | RUVBL2 | RUVBL2 | 8923 | 0.061 | 0.4 | NO |
238 | PSMA4 | PSMA4 | PSMA4 | 8951 | 0.06 | 0.4 | NO |
239 | RFWD2 | RFWD2 | RFWD2 | 8971 | 0.06 | 0.4 | NO |
240 | PKMYT1 | PKMYT1 | PKMYT1 | 8979 | 0.06 | 0.4 | NO |
241 | PSMD9 | PSMD9 | PSMD9 | 9150 | 0.057 | 0.39 | NO |
242 | RPA3 | RPA3 | RPA3 | 9154 | 0.057 | 0.39 | NO |
243 | PSMD12 | PSMD12 | PSMD12 | 9224 | 0.055 | 0.39 | NO |
244 | PLK1 | PLK1 | PLK1 | 9263 | 0.055 | 0.38 | NO |
245 | RPA4 | RPA4 | RPA4 | 9300 | 0.054 | 0.38 | NO |
246 | MNAT1 | MNAT1 | MNAT1 | 9314 | 0.054 | 0.38 | NO |
247 | PSMC6 | PSMC6 | PSMC6 | 9339 | 0.053 | 0.38 | NO |
248 | PSMB6 | PSMB6 | PSMB6 | 9365 | 0.053 | 0.38 | NO |
249 | ZW10 | ZW10 | ZW10 | 9543 | 0.049 | 0.38 | NO |
250 | UBE2D1 | UBE2D1 | UBE2D1 | 9550 | 0.049 | 0.38 | NO |
251 | PCNA | PCNA | PCNA | 9562 | 0.049 | 0.38 | NO |
252 | STAG1 | STAG1 | STAG1 | 9606 | 0.048 | 0.38 | NO |
253 | DIDO1 | DIDO1 | DIDO1 | 9644 | 0.047 | 0.37 | NO |
254 | CEP164 | CEP164 | CEP164 | 9831 | 0.044 | 0.36 | NO |
255 | PRKACA | PRKACA | PRKACA | 9845 | 0.044 | 0.36 | NO |
256 | ANAPC1 | ANAPC1 | ANAPC1 | 9976 | 0.042 | 0.36 | NO |
257 | PSMB2 | PSMB2 | PSMB2 | 10086 | 0.04 | 0.35 | NO |
258 | CETN2 | CETN2 | CETN2 | 10189 | 0.038 | 0.35 | NO |
259 | PSME4 | PSME4 | PSME4 | 10274 | 0.037 | 0.34 | NO |
260 | PSMC2 | PSMC2 | PSMC2 | 10331 | 0.036 | 0.34 | NO |
261 | RBBP7 | RBBP7 | RBBP7 | 10358 | 0.035 | 0.34 | NO |
262 | ATR | ATR | ATR | 10374 | 0.035 | 0.34 | NO |
263 | PSMA5 | PSMA5 | PSMA5 | 10483 | 0.033 | 0.34 | NO |
264 | HIST3H3 | HIST3H3 | HIST3H3 | 10519 | 0.032 | 0.34 | NO |
265 | TUBGCP5 | TUBGCP5 | TUBGCP5 | 10584 | 0.031 | 0.33 | NO |
266 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 10596 | 0.031 | 0.33 | NO |
267 | PSMC3 | PSMC3 | PSMC3 | 10608 | 0.031 | 0.33 | NO |
268 | PSMD13 | PSMD13 | PSMD13 | 10627 | 0.03 | 0.33 | NO |
269 | NUMA1 | NUMA1 | NUMA1 | 10715 | 0.029 | 0.33 | NO |
270 | NUDC | NUDC | NUDC | 10726 | 0.029 | 0.33 | NO |
271 | RPS27A | RPS27A | RPS27A | 10751 | 0.028 | 0.33 | NO |
272 | PSMD3 | PSMD3 | PSMD3 | 10753 | 0.028 | 0.33 | NO |
273 | PSMD2 | PSMD2 | PSMD2 | 10772 | 0.028 | 0.33 | NO |
274 | TERF2IP | TERF2IP | TERF2IP | 10788 | 0.028 | 0.33 | NO |
275 | POLD2 | POLD2 | POLD2 | 10805 | 0.027 | 0.33 | NO |
276 | CSNK1E | CSNK1E | CSNK1E | 10881 | 0.026 | 0.32 | NO |
277 | PSMA7 | PSMA7 | PSMA7 | 10927 | 0.025 | 0.32 | NO |
278 | CDC27 | CDC27 | CDC27 | 10956 | 0.025 | 0.32 | NO |
279 | PSMD11 | PSMD11 | PSMD11 | 10968 | 0.024 | 0.32 | NO |
280 | HAUS2 | HAUS2 | HAUS2 | 10976 | 0.024 | 0.32 | NO |
281 | TUBGCP2 | TUBGCP2 | TUBGCP2 | 10983 | 0.024 | 0.32 | NO |
282 | PSMA3 | PSMA3 | PSMA3 | 11053 | 0.023 | 0.32 | NO |
283 | CDK5RAP2 | CDK5RAP2 | CDK5RAP2 | 11057 | 0.023 | 0.32 | NO |
284 | PSMD14 | PSMD14 | PSMD14 | 11094 | 0.022 | 0.32 | NO |
285 | E2F4 | E2F4 | E2F4 | 11146 | 0.021 | 0.31 | NO |
286 | DCTN1 | DCTN1 | DCTN1 | 11149 | 0.021 | 0.31 | NO |
287 | DYNLL1 | DYNLL1 | DYNLL1 | 11220 | 0.02 | 0.31 | NO |
288 | PSMA1 | PSMA1 | PSMA1 | 11259 | 0.019 | 0.31 | NO |
289 | NHP2 | NHP2 | NHP2 | 11262 | 0.019 | 0.31 | NO |
290 | CCND1 | CCND1 | CCND1 | 11265 | 0.019 | 0.31 | NO |
291 | PPP2R1B | PPP2R1B | PPP2R1B | 11326 | 0.018 | 0.3 | NO |
292 | PSMD5 | PSMD5 | PSMD5 | 11365 | 0.018 | 0.3 | NO |
293 | RANGAP1 | RANGAP1 | RANGAP1 | 11372 | 0.017 | 0.3 | NO |
294 | KIF2A | KIF2A | KIF2A | 11373 | 0.017 | 0.3 | NO |
295 | TFDP1 | TFDP1 | TFDP1 | 11496 | 0.015 | 0.3 | NO |
296 | MAD1L1 | MAD1L1 | MAD1L1 | 11597 | 0.014 | 0.29 | NO |
297 | PSMB1 | PSMB1 | PSMB1 | 11681 | 0.013 | 0.29 | NO |
298 | TUBGCP6 | TUBGCP6 | TUBGCP6 | 11683 | 0.012 | 0.29 | NO |
299 | PSMB3 | PSMB3 | PSMB3 | 11685 | 0.012 | 0.29 | NO |
300 | TUBGCP3 | TUBGCP3 | TUBGCP3 | 11695 | 0.012 | 0.29 | NO |
301 | TERF2 | TERF2 | TERF2 | 11772 | 0.011 | 0.28 | NO |
302 | CLASP1 | CLASP1 | CLASP1 | 11785 | 0.011 | 0.28 | NO |
303 | PSMA6 | PSMA6 | PSMA6 | 11858 | 0.0097 | 0.28 | NO |
304 | RSF1 | RSF1 | RSF1 | 11991 | 0.0069 | 0.27 | NO |
305 | CEP72 | CEP72 | CEP72 | 12002 | 0.0066 | 0.27 | NO |
306 | PPP2R1A | PPP2R1A | PPP2R1A | 12010 | 0.0065 | 0.27 | NO |
307 | CDK6 | CDK6 | CDK6 | 12048 | 0.0058 | 0.27 | NO |
308 | PSMB5 | PSMB5 | PSMB5 | 12081 | 0.0053 | 0.27 | NO |
309 | PSMC1 | PSMC1 | PSMC1 | 12239 | 0.002 | 0.26 | NO |
310 | INCENP | INCENP | INCENP | 12252 | 0.0018 | 0.26 | NO |
311 | UBE2I | UBE2I | UBE2I | 12306 | 0.00092 | 0.26 | NO |
312 | CDC16 | CDC16 | CDC16 | 12335 | 0.0005 | 0.26 | NO |
313 | CDC26 | CDC26 | CDC26 | 12339 | 0.0004 | 0.26 | NO |
314 | PPP2CB | PPP2CB | PPP2CB | 12401 | -0.00094 | 0.25 | NO |
315 | RANBP2 | RANBP2 | RANBP2 | 12406 | -0.001 | 0.25 | NO |
316 | HDAC1 | HDAC1 | HDAC1 | 12427 | -0.0015 | 0.25 | NO |
317 | DCTN2 | DCTN2 | DCTN2 | 12450 | -0.002 | 0.25 | NO |
318 | YWHAG | YWHAG | YWHAG | 12610 | -0.0045 | 0.24 | NO |
319 | PSMD1 | PSMD1 | PSMD1 | 12616 | -0.0047 | 0.24 | NO |
320 | RPS27 | RPS27 | RPS27 | 12635 | -0.0049 | 0.24 | NO |
321 | SKP1 | SKP1 | SKP1 | 12674 | -0.0056 | 0.24 | NO |
322 | UBA52 | UBA52 | UBA52 | 12729 | -0.0067 | 0.24 | NO |
323 | PSMD6 | PSMD6 | PSMD6 | 12782 | -0.0077 | 0.23 | NO |
324 | CCNH | CCNH | CCNH | 12810 | -0.0082 | 0.23 | NO |
325 | PSMC5 | PSMC5 | PSMC5 | 12833 | -0.0086 | 0.23 | NO |
326 | PSMA2 | PSMA2 | PSMA2 | 12903 | -0.01 | 0.23 | NO |
327 | PSMD7 | PSMD7 | PSMD7 | 12970 | -0.012 | 0.22 | NO |
328 | PPP2R5D | PPP2R5D | PPP2R5D | 12977 | -0.012 | 0.22 | NO |
329 | PSME2 | PSME2 | PSME2 | 12986 | -0.012 | 0.22 | NO |
330 | PSMD8 | PSMD8 | PSMD8 | 12993 | -0.012 | 0.22 | NO |
331 | PSMB7 | PSMB7 | PSMB7 | 13001 | -0.012 | 0.22 | NO |
332 | PAFAH1B1 | PAFAH1B1 | PAFAH1B1 | 13122 | -0.015 | 0.22 | NO |
333 | PPP2R5E | PPP2R5E | PPP2R5E | 13265 | -0.018 | 0.21 | NO |
334 | PPP2CA | PPP2CA | PPP2CA | 13332 | -0.019 | 0.21 | NO |
335 | TAOK1 | TAOK1 | TAOK1 | 13423 | -0.021 | 0.2 | NO |
336 | MAX | MAX | MAX | 13436 | -0.021 | 0.2 | NO |
337 | ANAPC11 | ANAPC11 | ANAPC11 | 13464 | -0.022 | 0.2 | NO |
338 | CSNK1D | CSNK1D | CSNK1D | 13556 | -0.024 | 0.2 | NO |
339 | RBL2 | RBL2 | RBL2 | 13757 | -0.028 | 0.18 | NO |
340 | TK2 | TK2 | TK2 | 13772 | -0.028 | 0.18 | NO |
341 | CDKN2A | CDKN2A | CDKN2A | 13834 | -0.03 | 0.18 | NO |
342 | B9D2 | B9D2 | B9D2 | 13858 | -0.03 | 0.18 | NO |
343 | BTRC | BTRC | BTRC | 13865 | -0.03 | 0.18 | NO |
344 | SSNA1 | SSNA1 | SSNA1 | 13924 | -0.032 | 0.18 | NO |
345 | POLD3 | POLD3 | POLD3 | 14001 | -0.033 | 0.18 | NO |
346 | CLIP1 | CLIP1 | CLIP1 | 14227 | -0.039 | 0.16 | NO |
347 | ANAPC2 | ANAPC2 | ANAPC2 | 14242 | -0.039 | 0.16 | NO |
348 | PSME1 | PSME1 | PSME1 | 14245 | -0.039 | 0.16 | NO |
349 | PPP2R2A | PPP2R2A | PPP2R2A | 14249 | -0.039 | 0.17 | NO |
350 | SYNE2 | SYNE2 | SYNE2 | 14371 | -0.042 | 0.16 | NO |
351 | CDK7 | CDK7 | CDK7 | 14513 | -0.045 | 0.15 | NO |
352 | DYNC1I2 | DYNC1I2 | DYNC1I2 | 14558 | -0.046 | 0.15 | NO |
353 | SUN2 | SUN2 | SUN2 | 14578 | -0.047 | 0.15 | NO |
354 | SEC13 | SEC13 | SEC13 | 14619 | -0.048 | 0.15 | NO |
355 | DYNC1H1 | DYNC1H1 | DYNC1H1 | 14622 | -0.048 | 0.15 | NO |
356 | GORASP1 | GORASP1 | GORASP1 | 15022 | -0.058 | 0.13 | NO |
357 | HUS1 | HUS1 | HUS1 | 15052 | -0.059 | 0.13 | NO |
358 | ACTR1A | ACTR1A | ACTR1A | 15096 | -0.061 | 0.13 | NO |
359 | CDC25B | CDC25B | CDC25B | 15113 | -0.061 | 0.13 | NO |
360 | DCTN3 | DCTN3 | DCTN3 | 15224 | -0.065 | 0.12 | NO |
361 | TINF2 | TINF2 | TINF2 | 15334 | -0.068 | 0.12 | NO |
362 | PSMF1 | PSMF1 | PSMF1 | 15381 | -0.07 | 0.12 | NO |
363 | PSMB9 | PSMB9 | PSMB9 | 15382 | -0.07 | 0.12 | NO |
364 | PPP2R5C | PPP2R5C | PPP2R5C | 15662 | -0.079 | 0.11 | NO |
365 | PSMB8 | PSMB8 | PSMB8 | 15680 | -0.079 | 0.11 | NO |
366 | CENPP | CENPP | CENPP | 16191 | -0.098 | 0.081 | NO |
367 | CCND3 | CCND3 | CCND3 | 16425 | -0.11 | 0.071 | NO |
368 | CDKN2D | CDKN2D | CDKN2D | 16455 | -0.11 | 0.071 | NO |
369 | NDEL1 | NDEL1 | NDEL1 | 16510 | -0.12 | 0.071 | NO |
370 | RB1 | RB1 | RB1 | 16623 | -0.12 | 0.067 | NO |
371 | REC8 | REC8 | REC8 | 16722 | -0.13 | 0.064 | NO |
372 | LMNA | LMNA | LMNA | 16755 | -0.13 | 0.065 | NO |
373 | MYC | MYC | MYC | 16826 | -0.13 | 0.064 | NO |
374 | PSMB10 | PSMB10 | PSMB10 | 16983 | -0.14 | 0.058 | NO |
375 | CCND2 | CCND2 | CCND2 | 17107 | -0.15 | 0.054 | NO |
376 | PPP2R5A | PPP2R5A | PPP2R5A | 17206 | -0.16 | 0.052 | NO |
377 | CDKN2B | CDKN2B | CDKN2B | 17527 | -0.19 | 0.038 | NO |
378 | CCNA1 | CCNA1 | CCNA1 | 17549 | -0.19 | 0.041 | NO |
379 | PPP2R5B | PPP2R5B | PPP2R5B | 17974 | -0.24 | 0.022 | NO |
380 | POLD4 | POLD4 | POLD4 | 18162 | -0.28 | 0.018 | NO |
381 | CDKN1A | CDKN1A | CDKN1A | 18175 | -0.28 | 0.023 | NO |
382 | TUBA4A | TUBA4A | TUBA4A | 18575 | -0.43 | 0.0094 | NO |
Figure S25. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BASAL TRANSCRIPTION FACTORS.

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

Table S14. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NUP210 | NUP210 | NUP210 | 2650 | 0.26 | -0.044 | YES |
2 | NUP107 | NUP107 | NUP107 | 3597 | 0.21 | -0.018 | YES |
3 | GCK | GCK | GCK | 3804 | 0.2 | 0.045 | YES |
4 | NUP153 | NUP153 | NUP153 | 4692 | 0.16 | 0.058 | YES |
5 | AAAS | AAAS | AAAS | 4885 | 0.16 | 0.1 | YES |
6 | NUP35 | NUP35 | NUP35 | 5118 | 0.15 | 0.15 | YES |
7 | RAE1 | RAE1 | RAE1 | 5265 | 0.14 | 0.19 | YES |
8 | NUP43 | NUP43 | NUP43 | 6040 | 0.12 | 0.2 | YES |
9 | NUP133 | NUP133 | NUP133 | 6083 | 0.12 | 0.24 | YES |
10 | TPR | TPR | TPR | 6157 | 0.12 | 0.28 | YES |
11 | NUP54 | NUP54 | NUP54 | 6363 | 0.11 | 0.31 | YES |
12 | NUP93 | NUP93 | NUP93 | 6478 | 0.11 | 0.34 | YES |
13 | NUP37 | NUP37 | NUP37 | 6701 | 0.1 | 0.37 | YES |
14 | NUP155 | NUP155 | NUP155 | 6807 | 0.1 | 0.4 | YES |
15 | SEH1L | SEH1L | SEH1L | 6870 | 0.1 | 0.44 | YES |
16 | NUP205 | NUP205 | NUP205 | 7362 | 0.09 | 0.44 | YES |
17 | NUP88 | NUP88 | NUP88 | 7828 | 0.081 | 0.45 | YES |
18 | NUP85 | NUP85 | NUP85 | 8454 | 0.07 | 0.44 | YES |
19 | NUP62 | NUP62 | NUP62 | 8562 | 0.067 | 0.46 | YES |
20 | NUPL2 | NUPL2 | NUPL2 | 9205 | 0.056 | 0.45 | NO |
21 | NUPL1 | NUPL1 | NUPL1 | 9641 | 0.047 | 0.44 | NO |
22 | POM121 | POM121 | POM121 | 10514 | 0.032 | 0.41 | NO |
23 | NUP188 | NUP188 | NUP188 | 11115 | 0.022 | 0.38 | NO |
24 | NUP214 | NUP214 | NUP214 | 11663 | 0.013 | 0.36 | NO |
25 | NUP50 | NUP50 | NUP50 | 12151 | 0.0038 | 0.34 | NO |
26 | RANBP2 | RANBP2 | RANBP2 | 12406 | -0.001 | 0.32 | NO |
27 | GCKR | GCKR | GCKR | 14377 | -0.042 | 0.23 | NO |
Figure S27. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SPLICEOSOME.

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

Table S15. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CDC25A | CDC25A | CDC25A | 2369 | 0.28 | -0.04 | YES |
2 | CHEK2 | CHEK2 | CHEK2 | 2965 | 0.24 | 0.0032 | YES |
3 | CDC25C | CDC25C | CDC25C | 3137 | 0.23 | 0.066 | YES |
4 | BLM | BLM | BLM | 4447 | 0.17 | 0.049 | YES |
5 | FANCD2 | FANCD2 | FANCD2 | 5135 | 0.15 | 0.058 | YES |
6 | FAM175A | FAM175A | FAM175A | 5205 | 0.14 | 0.1 | YES |
7 | BRCA1 | BRCA1 | BRCA1 | 5328 | 0.14 | 0.14 | YES |
8 | H2AFX | H2AFX | H2AFX | 5591 | 0.13 | 0.16 | YES |
9 | MDC1 | MDC1 | MDC1 | 5652 | 0.13 | 0.2 | YES |
10 | SMC3 | SMC3 | SMC3 | 5757 | 0.13 | 0.24 | YES |
11 | RBBP8 | RBBP8 | RBBP8 | 5841 | 0.12 | 0.27 | YES |
12 | RAD9A | RAD9A | RAD9A | 6109 | 0.12 | 0.29 | YES |
13 | NBN | NBN | NBN | 6130 | 0.12 | 0.33 | YES |
14 | TP53BP1 | TP53BP1 | TP53BP1 | 6282 | 0.11 | 0.36 | YES |
15 | TRIM28 | TRIM28 | TRIM28 | 6380 | 0.11 | 0.39 | YES |
16 | MDM2 | MDM2 | MDM2 | 6712 | 0.1 | 0.4 | YES |
17 | TOP3A | TOP3A | TOP3A | 7108 | 0.095 | 0.41 | YES |
18 | MRE11A | MRE11A | MRE11A | 7248 | 0.092 | 0.43 | YES |
19 | ATM | ATM | ATM | 7338 | 0.09 | 0.46 | YES |
20 | UBE2N | UBE2N | UBE2N | 7967 | 0.078 | 0.45 | YES |
21 | RAD17 | RAD17 | RAD17 | 8001 | 0.077 | 0.47 | YES |
22 | SMC1A | SMC1A | SMC1A | 8495 | 0.069 | 0.46 | YES |
23 | RFWD2 | RFWD2 | RFWD2 | 8971 | 0.06 | 0.46 | YES |
24 | DCLRE1C | DCLRE1C | DCLRE1C | 8978 | 0.06 | 0.48 | YES |
25 | RAD50 | RAD50 | RAD50 | 11221 | 0.02 | 0.36 | NO |
26 | CTBP1 | CTBP1 | CTBP1 | 11760 | 0.011 | 0.34 | NO |
27 | TERF2 | TERF2 | TERF2 | 11772 | 0.011 | 0.34 | NO |
28 | XRCC4 | XRCC4 | XRCC4 | 11949 | 0.0075 | 0.33 | NO |
29 | KAT5 | KAT5 | KAT5 | 12272 | 0.0015 | 0.32 | NO |
30 | YWHAB | YWHAB | YWHAB | 13079 | -0.014 | 0.28 | NO |
31 | RNF8 | RNF8 | RNF8 | 13238 | -0.017 | 0.27 | NO |
32 | ABL1 | ABL1 | ABL1 | 13329 | -0.019 | 0.28 | NO |
33 | BID | BID | BID | 13440 | -0.021 | 0.28 | NO |
34 | UIMC1 | UIMC1 | UIMC1 | 13650 | -0.026 | 0.27 | NO |
Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FANCONI PATHWAY.

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

Table S16. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SGOL1 | SGOL1 | SGOL1 | 2018 | 0.3 | -0.044 | YES |
2 | NDC80 | NDC80 | NDC80 | 2159 | 0.29 | 0.011 | YES |
3 | STMN1 | STMN1 | STMN1 | 2444 | 0.27 | 0.054 | YES |
4 | BIRC5 | BIRC5 | BIRC5 | 2742 | 0.25 | 0.092 | YES |
5 | CENPA | CENPA | CENPA | 2883 | 0.24 | 0.14 | YES |
6 | KIF20A | KIF20A | KIF20A | 3020 | 0.24 | 0.18 | YES |
7 | AURKB | AURKB | AURKB | 3165 | 0.23 | 0.22 | YES |
8 | KIF2C | KIF2C | KIF2C | 3305 | 0.22 | 0.26 | YES |
9 | KIF23 | KIF23 | KIF23 | 3496 | 0.21 | 0.29 | YES |
10 | NCAPG | NCAPG | NCAPG | 3633 | 0.2 | 0.33 | YES |
11 | NCAPH | NCAPH | NCAPH | 3916 | 0.19 | 0.36 | YES |
12 | NCAPD2 | NCAPD2 | NCAPD2 | 5029 | 0.15 | 0.33 | YES |
13 | KLHL13 | KLHL13 | KLHL13 | 5107 | 0.15 | 0.35 | YES |
14 | AURKA | AURKA | AURKA | 5164 | 0.14 | 0.38 | YES |
15 | CDCA8 | CDCA8 | CDCA8 | 5191 | 0.14 | 0.41 | YES |
16 | SMC4 | SMC4 | SMC4 | 5246 | 0.14 | 0.44 | YES |
17 | CBX5 | CBX5 | CBX5 | 5325 | 0.14 | 0.46 | YES |
18 | BUB1 | BUB1 | BUB1 | 5498 | 0.13 | 0.48 | YES |
19 | PEBP1 | PEBP1 | PEBP1 | 5564 | 0.13 | 0.51 | YES |
20 | RACGAP1 | RACGAP1 | RACGAP1 | 5973 | 0.12 | 0.51 | YES |
21 | SMC2 | SMC2 | SMC2 | 6892 | 0.1 | 0.48 | NO |
22 | AURKC | AURKC | AURKC | 7650 | 0.084 | 0.46 | NO |
23 | PPP1CC | PPP1CC | PPP1CC | 8049 | 0.076 | 0.46 | NO |
24 | NCL | NCL | NCL | 8221 | 0.073 | 0.46 | NO |
25 | KLHL9 | KLHL9 | KLHL9 | 8482 | 0.069 | 0.46 | NO |
26 | NPM1 | NPM1 | NPM1 | 8743 | 0.064 | 0.46 | NO |
27 | SEPT1 | SEPT1 | SEPT1 | 9523 | 0.05 | 0.43 | NO |
28 | VIM | VIM | VIM | 10517 | 0.032 | 0.39 | NO |
29 | CUL3 | CUL3 | CUL3 | 10827 | 0.027 | 0.38 | NO |
30 | PSMA3 | PSMA3 | PSMA3 | 11053 | 0.023 | 0.37 | NO |
31 | NSUN2 | NSUN2 | NSUN2 | 12187 | 0.0032 | 0.31 | NO |
32 | INCENP | INCENP | INCENP | 12252 | 0.0018 | 0.3 | NO |
33 | TACC1 | TACC1 | TACC1 | 12353 | 0.00017 | 0.3 | NO |
34 | RASA1 | RASA1 | RASA1 | 12480 | -0.0024 | 0.29 | NO |
35 | PPP2R5D | PPP2R5D | PPP2R5D | 12977 | -0.012 | 0.27 | NO |
36 | MYLK | MYLK | MYLK | 12991 | -0.012 | 0.27 | NO |
37 | EVI5 | EVI5 | EVI5 | 13027 | -0.013 | 0.27 | NO |
38 | RHOA | RHOA | RHOA | 13606 | -0.025 | 0.25 | NO |
39 | DES | DES | DES | 16817 | -0.13 | 0.1 | NO |
Figure S31. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID AURORA B PATHWAY.

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

Table S17. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SSPO | SSPO | SSPO | 1016 | 0.41 | 0.011 | YES |
2 | C19orf40 | C19orf40 | C19orf40 | 1088 | 0.4 | 0.072 | YES |
3 | FANCL | FANCL | FANCL | 2569 | 0.26 | 0.035 | YES |
4 | BRIP1 | BRIP1 | BRIP1 | 2867 | 0.24 | 0.059 | YES |
5 | CHEK1 | CHEK1 | CHEK1 | 3175 | 0.23 | 0.079 | YES |
6 | RFC4 | RFC4 | RFC4 | 3743 | 0.2 | 0.081 | YES |
7 | FANCB | FANCB | FANCB | 3811 | 0.2 | 0.11 | YES |
8 | RFC5 | RFC5 | RFC5 | 4058 | 0.19 | 0.13 | YES |
9 | USP1 | USP1 | USP1 | 4089 | 0.18 | 0.15 | YES |
10 | APITD1 | APITD1 | APITD1 | 4251 | 0.18 | 0.17 | YES |
11 | RFC3 | RFC3 | RFC3 | 4422 | 0.17 | 0.19 | YES |
12 | BLM | BLM | BLM | 4447 | 0.17 | 0.22 | YES |
13 | RFC2 | RFC2 | RFC2 | 4613 | 0.16 | 0.24 | YES |
14 | FANCC | FANCC | FANCC | 4639 | 0.16 | 0.26 | YES |
15 | UBE2T | UBE2T | UBE2T | 4644 | 0.16 | 0.29 | YES |
16 | RPA2 | RPA2 | RPA2 | 4846 | 0.16 | 0.3 | YES |
17 | FANCD2 | FANCD2 | FANCD2 | 5135 | 0.15 | 0.31 | YES |
18 | BRCA1 | BRCA1 | BRCA1 | 5328 | 0.14 | 0.32 | YES |
19 | FANCI | FANCI | FANCI | 5406 | 0.14 | 0.34 | YES |
20 | BRCA2 | BRCA2 | BRCA2 | 5474 | 0.14 | 0.36 | YES |
21 | FANCG | FANCG | FANCG | 5572 | 0.13 | 0.37 | YES |
22 | H2AFX | H2AFX | H2AFX | 5591 | 0.13 | 0.4 | YES |
23 | RPA1 | RPA1 | RPA1 | 5974 | 0.12 | 0.39 | YES |
24 | FANCA | FANCA | FANCA | 6065 | 0.12 | 0.41 | YES |
25 | RAD9A | RAD9A | RAD9A | 6109 | 0.12 | 0.42 | YES |
26 | NBN | NBN | NBN | 6130 | 0.12 | 0.44 | YES |
27 | RMI1 | RMI1 | RMI1 | 6497 | 0.11 | 0.44 | YES |
28 | FANCM | FANCM | FANCM | 6779 | 0.1 | 0.44 | YES |
29 | TOP3A | TOP3A | TOP3A | 7108 | 0.095 | 0.44 | YES |
30 | RAD1 | RAD1 | RAD1 | 7246 | 0.092 | 0.45 | YES |
31 | MRE11A | MRE11A | MRE11A | 7248 | 0.092 | 0.46 | YES |
32 | ATM | ATM | ATM | 7338 | 0.09 | 0.47 | YES |
33 | TOPBP1 | TOPBP1 | TOPBP1 | 7354 | 0.09 | 0.48 | YES |
34 | PALB2 | PALB2 | PALB2 | 7495 | 0.087 | 0.49 | YES |
35 | FANCE | FANCE | FANCE | 7519 | 0.086 | 0.5 | YES |
36 | WDR48 | WDR48 | WDR48 | 7673 | 0.083 | 0.51 | YES |
37 | FANCF | FANCF | FANCF | 7939 | 0.078 | 0.51 | YES |
38 | RAD17 | RAD17 | RAD17 | 8001 | 0.077 | 0.52 | YES |
39 | XRCC3 | XRCC3 | XRCC3 | 8164 | 0.074 | 0.52 | YES |
40 | ATRIP | ATRIP | ATRIP | 8916 | 0.061 | 0.49 | NO |
41 | HES1 | HES1 | HES1 | 9298 | 0.054 | 0.48 | NO |
42 | ATR | ATR | ATR | 10374 | 0.035 | 0.43 | NO |
43 | RAD50 | RAD50 | RAD50 | 11221 | 0.02 | 0.38 | NO |
44 | C17orf70 | C17orf70 | C17orf70 | 11316 | 0.018 | 0.38 | NO |
45 | FBXW11 | FBXW11 | FBXW11 | 13833 | -0.03 | 0.25 | NO |
46 | HUS1 | HUS1 | HUS1 | 15052 | -0.059 | 0.2 | NO |
Figure S33. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ATR PATHWAY.

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

Table S18. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NEK2 | NEK2 | NEK2 | 2725 | 0.25 | -0.096 | YES |
2 | BIRC5 | BIRC5 | BIRC5 | 2742 | 0.25 | -0.048 | YES |
3 | CENPA | CENPA | CENPA | 2883 | 0.24 | -0.008 | YES |
4 | CHEK2 | CHEK2 | CHEK2 | 2965 | 0.24 | 0.034 | YES |
5 | CDK2 | CDK2 | CDK2 | 2966 | 0.24 | 0.081 | YES |
6 | GAS1 | GAS1 | GAS1 | 3009 | 0.24 | 0.12 | YES |
7 | ONECUT1 | ONECUT1 | ONECUT1 | 3026 | 0.24 | 0.17 | YES |
8 | AURKB | AURKB | AURKB | 3165 | 0.23 | 0.21 | YES |
9 | ESR1 | ESR1 | ESR1 | 3484 | 0.21 | 0.23 | YES |
10 | CCNE1 | CCNE1 | CCNE1 | 3871 | 0.19 | 0.25 | YES |
11 | CKS1B | CKS1B | CKS1B | 4201 | 0.18 | 0.26 | YES |
12 | CENPF | CENPF | CENPF | 4227 | 0.18 | 0.3 | YES |
13 | SKP2 | SKP2 | SKP2 | 4280 | 0.18 | 0.33 | YES |
14 | CDK4 | CDK4 | CDK4 | 4328 | 0.18 | 0.36 | YES |
15 | FOXM1 | FOXM1 | FOXM1 | 4379 | 0.17 | 0.39 | YES |
16 | CCNA2 | CCNA2 | CCNA2 | 4616 | 0.16 | 0.41 | YES |
17 | CCNB2 | CCNB2 | CCNB2 | 4658 | 0.16 | 0.44 | YES |
18 | CDK1 | CDK1 | CDK1 | 5112 | 0.15 | 0.45 | YES |
19 | ETV5 | ETV5 | ETV5 | 5357 | 0.14 | 0.46 | YES |
20 | CCNB1 | CCNB1 | CCNB1 | 5404 | 0.14 | 0.48 | YES |
21 | BRCA2 | BRCA2 | BRCA2 | 5474 | 0.14 | 0.51 | YES |
22 | NFATC3 | NFATC3 | NFATC3 | 6419 | 0.11 | 0.48 | NO |
23 | XRCC1 | XRCC1 | XRCC1 | 9261 | 0.055 | 0.34 | NO |
24 | PLK1 | PLK1 | PLK1 | 9263 | 0.055 | 0.35 | NO |
25 | MMP2 | MMP2 | MMP2 | 9718 | 0.046 | 0.33 | NO |
26 | SP1 | SP1 | SP1 | 9723 | 0.046 | 0.34 | NO |
27 | EP300 | EP300 | EP300 | 11000 | 0.024 | 0.28 | NO |
28 | CCND1 | CCND1 | CCND1 | 11265 | 0.019 | 0.27 | NO |
29 | GSK3A | GSK3A | GSK3A | 11338 | 0.018 | 0.27 | NO |
30 | CREBBP | CREBBP | CREBBP | 11727 | 0.012 | 0.25 | NO |
31 | LAMA4 | LAMA4 | LAMA4 | 11902 | 0.0084 | 0.24 | NO |
32 | CENPB | CENPB | CENPB | 13783 | -0.029 | 0.15 | NO |
33 | CDKN2A | CDKN2A | CDKN2A | 13834 | -0.03 | 0.15 | NO |
34 | CDC25B | CDC25B | CDC25B | 15113 | -0.061 | 0.092 | NO |
35 | MAP2K1 | MAP2K1 | MAP2K1 | 15166 | -0.063 | 0.1 | NO |
36 | TGFA | TGFA | TGFA | 15367 | -0.069 | 0.1 | NO |
37 | RB1 | RB1 | RB1 | 16623 | -0.12 | 0.061 | NO |
38 | MYC | MYC | MYC | 16826 | -0.13 | 0.076 | NO |
39 | FOS | FOS | FOS | 16903 | -0.14 | 0.099 | NO |
Figure S35. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ATM PATHWAY.

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

Table S19. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NUP210 | NUP210 | NUP210 | 2650 | 0.26 | -0.085 | YES |
2 | DDX20 | DDX20 | DDX20 | 3282 | 0.22 | -0.07 | YES |
3 | NUP107 | NUP107 | NUP107 | 3597 | 0.21 | -0.041 | YES |
4 | GEMIN6 | GEMIN6 | GEMIN6 | 3854 | 0.2 | -0.012 | YES |
5 | NUP153 | NUP153 | NUP153 | 4692 | 0.16 | -0.021 | YES |
6 | SMN2 | SMN2 | SMN2 | 4694 | 0.16 | 0.014 | YES |
7 | AAAS | AAAS | AAAS | 4885 | 0.16 | 0.038 | YES |
8 | NUP35 | NUP35 | NUP35 | 5118 | 0.15 | 0.058 | YES |
9 | SNRPG | SNRPG | SNRPG | 5236 | 0.14 | 0.083 | YES |
10 | RAE1 | RAE1 | RAE1 | 5265 | 0.14 | 0.11 | YES |
11 | SNRPE | SNRPE | SNRPE | 5630 | 0.13 | 0.12 | YES |
12 | SNRPF | SNRPF | SNRPF | 5855 | 0.12 | 0.14 | YES |
13 | TGS1 | TGS1 | TGS1 | 6013 | 0.12 | 0.16 | YES |
14 | NUP43 | NUP43 | NUP43 | 6040 | 0.12 | 0.18 | YES |
15 | NUP133 | NUP133 | NUP133 | 6083 | 0.12 | 0.2 | YES |
16 | TPR | TPR | TPR | 6157 | 0.12 | 0.23 | YES |
17 | NUP54 | NUP54 | NUP54 | 6363 | 0.11 | 0.24 | YES |
18 | NUP93 | NUP93 | NUP93 | 6478 | 0.11 | 0.26 | YES |
19 | WDR77 | WDR77 | WDR77 | 6576 | 0.11 | 0.28 | YES |
20 | SNUPN | SNUPN | SNUPN | 6578 | 0.11 | 0.3 | YES |
21 | NUP37 | NUP37 | NUP37 | 6701 | 0.1 | 0.32 | YES |
22 | NUP155 | NUP155 | NUP155 | 6807 | 0.1 | 0.33 | YES |
23 | SEH1L | SEH1L | SEH1L | 6870 | 0.1 | 0.35 | YES |
24 | GEMIN5 | GEMIN5 | GEMIN5 | 6882 | 0.1 | 0.37 | YES |
25 | SNRPD1 | SNRPD1 | SNRPD1 | 7101 | 0.095 | 0.38 | YES |
26 | SNRPD3 | SNRPD3 | SNRPD3 | 7126 | 0.095 | 0.4 | YES |
27 | PHAX | PHAX | PHAX | 7309 | 0.091 | 0.41 | YES |
28 | NUP205 | NUP205 | NUP205 | 7362 | 0.09 | 0.43 | YES |
29 | NCBP2 | NCBP2 | NCBP2 | 7458 | 0.088 | 0.44 | YES |
30 | SMN1 | SMN1 | SMN1 | 7749 | 0.082 | 0.44 | YES |
31 | NUP88 | NUP88 | NUP88 | 7828 | 0.081 | 0.46 | YES |
32 | NUP85 | NUP85 | NUP85 | 8454 | 0.07 | 0.44 | NO |
33 | NUP62 | NUP62 | NUP62 | 8562 | 0.067 | 0.45 | NO |
34 | GEMIN4 | GEMIN4 | GEMIN4 | 9134 | 0.057 | 0.43 | NO |
35 | NUPL2 | NUPL2 | NUPL2 | 9205 | 0.056 | 0.44 | NO |
36 | PRMT5 | PRMT5 | PRMT5 | 9360 | 0.053 | 0.44 | NO |
37 | NUPL1 | NUPL1 | NUPL1 | 9641 | 0.047 | 0.44 | NO |
38 | SNRPD2 | SNRPD2 | SNRPD2 | 9745 | 0.046 | 0.44 | NO |
39 | CLNS1A | CLNS1A | CLNS1A | 10257 | 0.037 | 0.42 | NO |
40 | POM121 | POM121 | POM121 | 10514 | 0.032 | 0.42 | NO |
41 | GEMIN7 | GEMIN7 | GEMIN7 | 10937 | 0.025 | 0.4 | NO |
42 | NUP188 | NUP188 | NUP188 | 11115 | 0.022 | 0.4 | NO |
43 | NCBP1 | NCBP1 | NCBP1 | 11289 | 0.019 | 0.39 | NO |
44 | SNRPB | SNRPB | SNRPB | 11404 | 0.017 | 0.39 | NO |
45 | NUP214 | NUP214 | NUP214 | 11663 | 0.013 | 0.38 | NO |
46 | NUP50 | NUP50 | NUP50 | 12151 | 0.0038 | 0.35 | NO |
47 | RANBP2 | RANBP2 | RANBP2 | 12406 | -0.001 | 0.34 | NO |
Figure S37. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID PLK1 PATHWAY.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: PID PLK1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S20. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | LZTS1 | LZTS1 | LZTS1 | 2229 | 0.29 | -0.0034 | YES |
2 | POLR3B | POLR3B | POLR3B | 3772 | 0.2 | -0.006 | YES |
3 | NFIB | NFIB | NFIB | 4754 | 0.16 | 0.0059 | YES |
4 | SSB | SSB | SSB | 5784 | 0.13 | 0.0017 | YES |
5 | TBP | TBP | TBP | 6317 | 0.11 | 0.019 | YES |
6 | BRF2 | BRF2 | BRF2 | 6644 | 0.1 | 0.044 | YES |
7 | SNAPC4 | SNAPC4 | SNAPC4 | 6940 | 0.098 | 0.067 | YES |
8 | SNAPC5 | SNAPC5 | SNAPC5 | 7020 | 0.097 | 0.1 | YES |
9 | POLR3F | POLR3F | POLR3F | 7059 | 0.096 | 0.14 | YES |
10 | POLR2K | POLR2K | POLR2K | 7073 | 0.096 | 0.18 | YES |
11 | GTF3C2 | GTF3C2 | GTF3C2 | 7600 | 0.085 | 0.18 | YES |
12 | POLR3C | POLR3C | POLR3C | 7784 | 0.081 | 0.21 | YES |
13 | ZNF143 | ZNF143 | ZNF143 | 7791 | 0.081 | 0.24 | YES |
14 | POLR2F | POLR2F | POLR2F | 7874 | 0.08 | 0.27 | YES |
15 | POU2F1 | POU2F1 | POU2F1 | 8309 | 0.072 | 0.27 | YES |
16 | GTF3C3 | GTF3C3 | GTF3C3 | 8429 | 0.07 | 0.29 | YES |
17 | POLR3A | POLR3A | POLR3A | 8459 | 0.069 | 0.32 | YES |
18 | POLR2H | POLR2H | POLR2H | 8522 | 0.068 | 0.34 | YES |
19 | POLR3E | POLR3E | POLR3E | 8945 | 0.06 | 0.35 | YES |
20 | POLR1C | POLR1C | POLR1C | 9447 | 0.051 | 0.34 | YES |
21 | POLR3D | POLR3D | POLR3D | 9742 | 0.046 | 0.34 | YES |
22 | SNAPC1 | SNAPC1 | SNAPC1 | 9896 | 0.043 | 0.35 | YES |
23 | BRF1 | BRF1 | BRF1 | 9927 | 0.042 | 0.37 | YES |
24 | POLR3H | POLR3H | POLR3H | 9985 | 0.042 | 0.38 | YES |
25 | GTF3C4 | GTF3C4 | GTF3C4 | 10158 | 0.039 | 0.39 | YES |
26 | POLR2L | POLR2L | POLR2L | 10169 | 0.039 | 0.4 | YES |
27 | POLR3K | POLR3K | POLR3K | 11504 | 0.015 | 0.34 | NO |
28 | POLR3GL | POLR3GL | POLR3GL | 11752 | 0.011 | 0.33 | NO |
29 | POLR2E | POLR2E | POLR2E | 12793 | -0.0079 | 0.28 | NO |
30 | SNAPC2 | SNAPC2 | SNAPC2 | 12959 | -0.011 | 0.27 | NO |
31 | POLR1D | POLR1D | POLR1D | 13689 | -0.026 | 0.24 | NO |
32 | SNAPC3 | SNAPC3 | SNAPC3 | 13897 | -0.031 | 0.24 | NO |
33 | GTF3C5 | GTF3C5 | GTF3C5 | 14087 | -0.035 | 0.25 | NO |
Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FOXM1PATHWAY.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: PID FOXM1PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 5. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus3. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG BLADDER CANCER | 42 | genes.ES.table | 0.48 | 1.6 | 0.014 | 0.67 | 0.92 | 0.43 | 0.18 | 0.35 | 0.33 | 0.18 |
BIOCARTA ERK PATHWAY | 28 | genes.ES.table | 0.5 | 1.7 | 0.022 | 0.66 | 0.91 | 0.29 | 0.13 | 0.25 | 0.32 | 0.17 |
PID P73PATHWAY | 79 | genes.ES.table | 0.48 | 1.8 | 0 | 0.67 | 0.56 | 0.28 | 0.14 | 0.24 | 0.16 | 0.14 |
PID AVB3 OPN PATHWAY | 31 | genes.ES.table | 0.51 | 1.6 | 0.033 | 0.64 | 0.93 | 0.36 | 0.22 | 0.28 | 0.32 | 0.16 |
PID MTOR 4PATHWAY | 67 | genes.ES.table | 0.39 | 1.8 | 0.023 | 0.57 | 0.62 | 0.43 | 0.28 | 0.32 | 0.14 | 0.13 |
PID ERBB1 RECEPTOR PROXIMAL PATHWAY | 35 | genes.ES.table | 0.48 | 1.8 | 0.014 | 0.81 | 0.54 | 0.4 | 0.22 | 0.31 | 0.19 | 0.16 |
PID MYC PATHWAY | 25 | genes.ES.table | 0.47 | 1.7 | 0.023 | 0.68 | 0.79 | 0.52 | 0.24 | 0.4 | 0.25 | 0.17 |
PID ECADHERIN NASCENTAJ PATHWAY | 39 | genes.ES.table | 0.37 | 1.6 | 0.072 | 0.62 | 0.94 | 0.64 | 0.35 | 0.42 | 0.32 | 0.16 |
PID DELTANP63PATHWAY | 47 | genes.ES.table | 0.69 | 1.9 | 0 | 0.87 | 0.33 | 0.32 | 0.084 | 0.29 | 0 | 0.15 |
PID A6B1 A6B4 INTEGRIN PATHWAY | 46 | genes.ES.table | 0.52 | 1.7 | 0.027 | 0.6 | 0.81 | 0.35 | 0.16 | 0.29 | 0.23 | 0.15 |
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 | SPHK1 | SPHK1 | SPHK1 | 494 | 0.43 | 0.2 | YES |
2 | KIFC3 | KIFC3 | KIFC3 | 1359 | 0.24 | 0.28 | YES |
3 | KIF13A | KIF13A | KIF13A | 2250 | 0.16 | 0.31 | YES |
4 | FBXO6 | FBXO6 | FBXO6 | 2294 | 0.16 | 0.39 | YES |
5 | FKBP9 | FKBP9 | FKBP9 | 2768 | 0.12 | 0.43 | YES |
6 | CCT5 | CCT5 | CCT5 | 2871 | 0.12 | 0.48 | YES |
7 | FBXO4 | FBXO4 | FBXO4 | 4617 | 0.062 | 0.42 | YES |
8 | CCT4 | CCT4 | CCT4 | 4638 | 0.061 | 0.45 | YES |
9 | CCT8 | CCT8 | CCT8 | 4730 | 0.059 | 0.48 | YES |
10 | CCT6A | CCT6A | CCT6A | 4779 | 0.057 | 0.5 | YES |
11 | CCT7 | CCT7 | CCT7 | 5308 | 0.046 | 0.5 | YES |
12 | TCP1 | TCP1 | TCP1 | 5549 | 0.041 | 0.51 | YES |
13 | CCT2 | CCT2 | CCT2 | 5781 | 0.036 | 0.52 | YES |
14 | FBXW4 | FBXW4 | FBXW4 | 5922 | 0.033 | 0.52 | YES |
15 | CCT3 | CCT3 | CCT3 | 6214 | 0.028 | 0.52 | NO |
16 | XRN2 | XRN2 | XRN2 | 6633 | 0.021 | 0.51 | NO |
17 | NOP56 | NOP56 | NOP56 | 6711 | 0.02 | 0.52 | NO |
18 | LONP2 | LONP2 | LONP2 | 6832 | 0.018 | 0.52 | NO |
19 | FBXW7 | FBXW7 | FBXW7 | 7151 | 0.012 | 0.51 | NO |
20 | FBXW2 | FBXW2 | FBXW2 | 7245 | 0.011 | 0.51 | NO |
21 | FBXL5 | FBXL5 | FBXL5 | 7736 | 0.0023 | 0.49 | NO |
22 | FBXL3 | FBXL3 | FBXL3 | 7820 | 0.0012 | 0.48 | NO |
23 | USP11 | USP11 | USP11 | 8760 | -0.014 | 0.44 | NO |
24 | FBXW5 | FBXW5 | FBXW5 | 9651 | -0.029 | 0.41 | NO |
25 | AP3M1 | AP3M1 | AP3M1 | 11080 | -0.057 | 0.36 | NO |
26 | ARFGEF2 | ARFGEF2 | ARFGEF2 | 12581 | -0.095 | 0.33 | NO |
Figure S41. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BLADDER CANCER.

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

Table S22. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | KRT14 | KRT14 | KRT14 | 14 | 0.9 | 0.091 | YES |
2 | IL1A | IL1A | IL1A | 17 | 0.88 | 0.18 | YES |
3 | RAB38 | RAB38 | RAB38 | 77 | 0.71 | 0.25 | YES |
4 | TP63 | TP63 | TP63 | 80 | 0.7 | 0.32 | YES |
5 | KRT5 | KRT5 | KRT5 | 85 | 0.7 | 0.39 | YES |
6 | NRG1 | NRG1 | NRG1 | 86 | 0.7 | 0.46 | YES |
7 | DLX5 | DLX5 | DLX5 | 275 | 0.52 | 0.5 | YES |
8 | SFN | SFN | SFN | 341 | 0.49 | 0.55 | YES |
9 | ADA | ADA | ADA | 752 | 0.35 | 0.57 | YES |
10 | TCF7L1 | TCF7L1 | TCF7L1 | 949 | 0.31 | 0.59 | YES |
11 | PERP | PERP | PERP | 1025 | 0.3 | 0.61 | YES |
12 | ITGA3 | ITGA3 | ITGA3 | 1060 | 0.29 | 0.64 | YES |
13 | SEC14L2 | SEC14L2 | SEC14L2 | 1170 | 0.27 | 0.66 | YES |
14 | COL5A1 | COL5A1 | COL5A1 | 1364 | 0.24 | 0.68 | YES |
15 | DLX6 | DLX6 | DLX6 | 1576 | 0.22 | 0.69 | YES |
16 | BDKRB2 | BDKRB2 | BDKRB2 | 2102 | 0.17 | 0.68 | NO |
17 | VDR | VDR | VDR | 2601 | 0.13 | 0.66 | NO |
18 | T | T | T | 3537 | 0.091 | 0.62 | NO |
19 | CEBPD | CEBPD | CEBPD | 3554 | 0.091 | 0.63 | NO |
20 | NOTCH1 | NOTCH1 | NOTCH1 | 3791 | 0.083 | 0.63 | NO |
21 | GSK3B | GSK3B | GSK3B | 4023 | 0.077 | 0.62 | NO |
22 | RUNX1 | RUNX1 | RUNX1 | 4260 | 0.07 | 0.62 | NO |
23 | AXL | AXL | AXL | 5035 | 0.052 | 0.58 | NO |
24 | CCNB2 | CCNB2 | CCNB2 | 5487 | 0.042 | 0.56 | NO |
25 | RRAD | RRAD | RRAD | 5507 | 0.042 | 0.56 | NO |
26 | FOSL2 | FOSL2 | FOSL2 | 5533 | 0.041 | 0.57 | NO |
27 | ADRM1 | ADRM1 | ADRM1 | 5856 | 0.035 | 0.55 | NO |
28 | YAP1 | YAP1 | YAP1 | 6461 | 0.024 | 0.52 | NO |
29 | GNB2L1 | GNB2L1 | GNB2L1 | 6547 | 0.022 | 0.52 | NO |
30 | FASN | FASN | FASN | 6927 | 0.016 | 0.5 | NO |
31 | FBXW7 | FBXW7 | FBXW7 | 7151 | 0.012 | 0.49 | NO |
32 | HBP1 | HBP1 | HBP1 | 8259 | -0.006 | 0.43 | NO |
33 | ITCH | ITCH | ITCH | 8266 | -0.0061 | 0.43 | NO |
34 | POU2F2 | POU2F2 | POU2F2 | 8385 | -0.0083 | 0.43 | NO |
35 | STXBP4 | STXBP4 | STXBP4 | 8788 | -0.014 | 0.41 | NO |
36 | HELLS | HELLS | HELLS | 8999 | -0.018 | 0.4 | NO |
37 | WWP1 | WWP1 | WWP1 | 9684 | -0.03 | 0.36 | NO |
38 | HES1 | HES1 | HES1 | 10219 | -0.039 | 0.34 | NO |
39 | MDM2 | MDM2 | MDM2 | 10508 | -0.045 | 0.33 | NO |
40 | IGFBP3 | IGFBP3 | IGFBP3 | 10797 | -0.051 | 0.32 | NO |
41 | PPP2R5A | PPP2R5A | PPP2R5A | 11360 | -0.063 | 0.3 | NO |
42 | TOP2A | TOP2A | TOP2A | 11742 | -0.072 | 0.28 | NO |
43 | BRCA2 | BRCA2 | BRCA2 | 11805 | -0.074 | 0.29 | NO |
44 | MRE11A | MRE11A | MRE11A | 11855 | -0.075 | 0.29 | NO |
45 | ATM | ATM | ATM | 12577 | -0.095 | 0.26 | NO |
46 | CDKN2A | CDKN2A | CDKN2A | 15767 | -0.24 | 0.12 | NO |
47 | GPX2 | GPX2 | GPX2 | 17435 | -0.42 | 0.07 | NO |
Figure S43. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA ERK PATHWAY.

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

Table S23. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CCNA1 | CCNA1 | CCNA1 | 92 | 0.69 | 0.16 | YES |
2 | PKMYT1 | PKMYT1 | PKMYT1 | 1509 | 0.22 | 0.14 | YES |
3 | CDKN1A | CDKN1A | CDKN1A | 1685 | 0.21 | 0.18 | YES |
4 | MNAT1 | MNAT1 | MNAT1 | 2070 | 0.17 | 0.2 | YES |
5 | MYC | MYC | MYC | 2458 | 0.14 | 0.21 | YES |
6 | PSMD9 | PSMD9 | PSMD9 | 2880 | 0.12 | 0.22 | YES |
7 | CDK7 | CDK7 | CDK7 | 3002 | 0.11 | 0.24 | YES |
8 | PSMC1 | PSMC1 | PSMC1 | 3013 | 0.11 | 0.26 | YES |
9 | PSMD2 | PSMD2 | PSMD2 | 3071 | 0.11 | 0.28 | YES |
10 | PSMB7 | PSMB7 | PSMB7 | 3404 | 0.096 | 0.29 | YES |
11 | PSMB6 | PSMB6 | PSMB6 | 3480 | 0.093 | 0.31 | YES |
12 | PSMA6 | PSMA6 | PSMA6 | 3633 | 0.088 | 0.32 | YES |
13 | CCNE2 | CCNE2 | CCNE2 | 3871 | 0.081 | 0.33 | YES |
14 | PSMC2 | PSMC2 | PSMC2 | 3970 | 0.078 | 0.34 | YES |
15 | SKP2 | SKP2 | SKP2 | 3971 | 0.078 | 0.36 | YES |
16 | PSMB2 | PSMB2 | PSMB2 | 4134 | 0.074 | 0.37 | YES |
17 | CKS1B | CKS1B | CKS1B | 4232 | 0.071 | 0.38 | YES |
18 | PSMC3 | PSMC3 | PSMC3 | 4274 | 0.07 | 0.39 | YES |
19 | PSMD12 | PSMD12 | PSMD12 | 4475 | 0.064 | 0.4 | YES |
20 | CCNA2 | CCNA2 | CCNA2 | 4498 | 0.064 | 0.41 | YES |
21 | PSMD10 | PSMD10 | PSMD10 | 4572 | 0.062 | 0.42 | YES |
22 | PSMC6 | PSMC6 | PSMC6 | 4636 | 0.061 | 0.43 | YES |
23 | PSMD7 | PSMD7 | PSMD7 | 4828 | 0.056 | 0.44 | YES |
24 | PSMD5 | PSMD5 | PSMD5 | 4859 | 0.055 | 0.45 | YES |
25 | PSMB5 | PSMB5 | PSMB5 | 4911 | 0.054 | 0.46 | YES |
26 | PSMD14 | PSMD14 | PSMD14 | 4922 | 0.054 | 0.47 | YES |
27 | PSMA3 | PSMA3 | PSMA3 | 5221 | 0.048 | 0.47 | YES |
28 | PSMC5 | PSMC5 | PSMC5 | 5421 | 0.043 | 0.47 | YES |
29 | PSMB1 | PSMB1 | PSMB1 | 5541 | 0.041 | 0.47 | YES |
30 | RB1 | RB1 | RB1 | 5545 | 0.041 | 0.48 | YES |
31 | PSMA1 | PSMA1 | PSMA1 | 5623 | 0.039 | 0.48 | YES |
32 | SKP1 | SKP1 | SKP1 | 5666 | 0.038 | 0.49 | YES |
33 | PSMD11 | PSMD11 | PSMD11 | 5753 | 0.037 | 0.5 | YES |
34 | PSMA7 | PSMA7 | PSMA7 | 5805 | 0.036 | 0.5 | YES |
35 | PSMD6 | PSMD6 | PSMD6 | 5806 | 0.036 | 0.51 | YES |
36 | PSMA4 | PSMA4 | PSMA4 | 5914 | 0.033 | 0.51 | YES |
37 | PSMA2 | PSMA2 | PSMA2 | 5923 | 0.033 | 0.52 | YES |
38 | CDK2 | CDK2 | CDK2 | 5986 | 0.032 | 0.52 | YES |
39 | PSMD8 | PSMD8 | PSMD8 | 6131 | 0.03 | 0.52 | YES |
40 | PSMA5 | PSMA5 | PSMA5 | 6198 | 0.028 | 0.53 | YES |
41 | PSMF1 | PSMF1 | PSMF1 | 6337 | 0.026 | 0.52 | YES |
42 | PSMD13 | PSMD13 | PSMD13 | 6378 | 0.025 | 0.53 | YES |
43 | WEE1 | WEE1 | WEE1 | 6658 | 0.021 | 0.52 | NO |
44 | PSMD4 | PSMD4 | PSMD4 | 6735 | 0.02 | 0.52 | NO |
45 | CUL1 | CUL1 | CUL1 | 7044 | 0.014 | 0.51 | NO |
46 | PSMD1 | PSMD1 | PSMD1 | 7082 | 0.014 | 0.51 | NO |
47 | UBA52 | UBA52 | UBA52 | 7138 | 0.013 | 0.51 | NO |
48 | PSMB9 | PSMB9 | PSMB9 | 7334 | 0.0092 | 0.5 | NO |
49 | MAX | MAX | MAX | 8106 | -0.0033 | 0.46 | NO |
50 | PSME2 | PSME2 | PSME2 | 8120 | -0.0035 | 0.46 | NO |
51 | PSMB3 | PSMB3 | PSMB3 | 8191 | -0.0048 | 0.46 | NO |
52 | CCNE1 | CCNE1 | CCNE1 | 8196 | -0.0048 | 0.46 | NO |
53 | PSMD3 | PSMD3 | PSMD3 | 8356 | -0.0077 | 0.45 | NO |
54 | PSMB4 | PSMB4 | PSMB4 | 8445 | -0.0093 | 0.45 | NO |
55 | PSME1 | PSME1 | PSME1 | 8636 | -0.012 | 0.44 | NO |
56 | CCNH | CCNH | CCNH | 9016 | -0.018 | 0.42 | NO |
57 | RPS27A | RPS27A | RPS27A | 9423 | -0.025 | 0.41 | NO |
58 | PSMC4 | PSMC4 | PSMC4 | 9597 | -0.028 | 0.41 | NO |
59 | PSMB8 | PSMB8 | PSMB8 | 11168 | -0.059 | 0.34 | NO |
60 | PSMB10 | PSMB10 | PSMB10 | 12074 | -0.081 | 0.31 | NO |
61 | CDKN1B | CDKN1B | CDKN1B | 12766 | -0.1 | 0.29 | NO |
62 | CDC25A | CDC25A | CDC25A | 13086 | -0.11 | 0.3 | NO |
Figure S45. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID P73PATHWAY.

Figure S46. Get High-res Image For the top 5 core enriched genes in the pathway: PID P73PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S24. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | GNAI1 | GNAI1 | GNAI1 | 352 | 0.48 | 0.12 | YES |
2 | EGFR | EGFR | EGFR | 718 | 0.36 | 0.21 | YES |
3 | PIK3CD | PIK3CD | PIK3CD | 961 | 0.3 | 0.28 | YES |
4 | HRAS | HRAS | HRAS | 1167 | 0.27 | 0.35 | YES |
5 | SHC1 | SHC1 | SHC1 | 2384 | 0.15 | 0.33 | YES |
6 | EGF | EGF | EGF | 2792 | 0.12 | 0.34 | YES |
7 | GNAI3 | GNAI3 | GNAI3 | 2964 | 0.11 | 0.37 | YES |
8 | PTPN1 | PTPN1 | PTPN1 | 3096 | 0.11 | 0.39 | YES |
9 | PLCG1 | PLCG1 | PLCG1 | 3677 | 0.086 | 0.39 | YES |
10 | PIK3CA | PIK3CA | PIK3CA | 3684 | 0.086 | 0.41 | YES |
11 | NCK1 | NCK1 | NCK1 | 3749 | 0.085 | 0.43 | YES |
12 | STAT1 | STAT1 | STAT1 | 3899 | 0.08 | 0.45 | YES |
13 | NRAS | NRAS | NRAS | 4053 | 0.076 | 0.46 | YES |
14 | RASA1 | RASA1 | RASA1 | 4086 | 0.075 | 0.48 | YES |
15 | MAPK1 | MAPK1 | MAPK1 | 4698 | 0.06 | 0.47 | NO |
16 | PIP5K1C | PIP5K1C | PIP5K1C | 5146 | 0.049 | 0.46 | NO |
17 | PTK2 | PTK2 | PTK2 | 5685 | 0.038 | 0.44 | NO |
18 | NCK2 | NCK2 | NCK2 | 7154 | 0.012 | 0.36 | NO |
19 | STAT3 | STAT3 | STAT3 | 7542 | 0.0057 | 0.34 | NO |
20 | PIK3R2 | PIK3R2 | PIK3R2 | 7590 | 0.0048 | 0.34 | NO |
21 | PTPN11 | PTPN11 | PTPN11 | 7961 | -0.00098 | 0.32 | NO |
22 | SOS1 | SOS1 | SOS1 | 8043 | -0.0023 | 0.32 | NO |
23 | GSN | GSN | GSN | 8616 | -0.012 | 0.29 | NO |
24 | TLN1 | TLN1 | TLN1 | 8932 | -0.017 | 0.28 | NO |
25 | GRB2 | GRB2 | GRB2 | 8985 | -0.018 | 0.28 | NO |
26 | PAK1 | PAK1 | PAK1 | 9180 | -0.021 | 0.28 | NO |
27 | WASL | WASL | WASL | 10038 | -0.036 | 0.24 | NO |
28 | PIK3R1 | PIK3R1 | PIK3R1 | 10668 | -0.048 | 0.22 | NO |
29 | PTPN6 | PTPN6 | PTPN6 | 10781 | -0.05 | 0.23 | NO |
30 | GAB1 | GAB1 | GAB1 | 10935 | -0.054 | 0.24 | NO |
31 | MAPK3 | MAPK3 | MAPK3 | 11470 | -0.066 | 0.23 | NO |
32 | SRC | SRC | SRC | 12821 | -0.1 | 0.19 | NO |
33 | KRAS | KRAS | KRAS | 12846 | -0.1 | 0.22 | NO |
34 | PIK3CB | PIK3CB | PIK3CB | 13249 | -0.12 | 0.23 | NO |
35 | PIK3R3 | PIK3R3 | PIK3R3 | 15426 | -0.22 | 0.18 | NO |
Figure S47. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID AVB3 OPN PATHWAY.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: PID AVB3 OPN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S25. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CLCA2 | CLCA2 | CLCA2 | 42 | 0.77 | 0.058 | YES |
2 | S100A2 | S100A2 | S100A2 | 59 | 0.73 | 0.11 | YES |
3 | TP63 | TP63 | TP63 | 80 | 0.7 | 0.17 | YES |
4 | TP53AIP1 | TP53AIP1 | TP53AIP1 | 93 | 0.69 | 0.22 | YES |
5 | SERPINE1 | SERPINE1 | SERPINE1 | 325 | 0.5 | 0.25 | YES |
6 | SFN | SFN | SFN | 341 | 0.49 | 0.28 | YES |
7 | IL1RAP | IL1RAP | IL1RAP | 402 | 0.46 | 0.32 | YES |
8 | TP73 | TP73 | TP73 | 407 | 0.46 | 0.35 | YES |
9 | MAPK11 | MAPK11 | MAPK11 | 484 | 0.43 | 0.38 | YES |
10 | D4S234E | D4S234E | D4S234E | 702 | 0.37 | 0.4 | YES |
11 | ADA | ADA | ADA | 752 | 0.35 | 0.42 | YES |
12 | JAG2 | JAG2 | JAG2 | 932 | 0.31 | 0.44 | YES |
13 | CDK6 | CDK6 | CDK6 | 1662 | 0.21 | 0.42 | YES |
14 | CDKN1A | CDKN1A | CDKN1A | 1685 | 0.21 | 0.43 | YES |
15 | WT1 | WT1 | WT1 | 1735 | 0.2 | 0.44 | YES |
16 | FBXO45 | FBXO45 | FBXO45 | 1938 | 0.18 | 0.45 | YES |
17 | HEY2 | HEY2 | HEY2 | 2115 | 0.17 | 0.45 | YES |
18 | PML | PML | PML | 2189 | 0.16 | 0.46 | YES |
19 | MYC | MYC | MYC | 2458 | 0.14 | 0.46 | YES |
20 | IL4R | IL4R | IL4R | 2550 | 0.14 | 0.46 | YES |
21 | CCNB1 | CCNB1 | CCNB1 | 2567 | 0.14 | 0.47 | YES |
22 | HSF1 | HSF1 | HSF1 | 2585 | 0.14 | 0.48 | YES |
23 | TUBA1A | TUBA1A | TUBA1A | 3259 | 0.1 | 0.46 | NO |
24 | PLK1 | PLK1 | PLK1 | 3487 | 0.093 | 0.45 | NO |
25 | BAK1 | BAK1 | BAK1 | 3803 | 0.083 | 0.44 | NO |
26 | PLK3 | PLK3 | PLK3 | 3827 | 0.082 | 0.44 | NO |
27 | CCNE2 | CCNE2 | CCNE2 | 3871 | 0.081 | 0.45 | NO |
28 | PIN1 | PIN1 | PIN1 | 3993 | 0.078 | 0.45 | NO |
29 | FAS | FAS | FAS | 4163 | 0.073 | 0.44 | NO |
30 | CCNA2 | CCNA2 | CCNA2 | 4498 | 0.064 | 0.43 | NO |
31 | CHEK1 | CHEK1 | CHEK1 | 4594 | 0.062 | 0.43 | NO |
32 | RAD51 | RAD51 | RAD51 | 4627 | 0.061 | 0.43 | NO |
33 | NTRK1 | NTRK1 | NTRK1 | 4693 | 0.06 | 0.44 | NO |
34 | RELA | RELA | RELA | 5179 | 0.049 | 0.41 | NO |
35 | RB1 | RB1 | RB1 | 5545 | 0.041 | 0.4 | NO |
36 | PEA15 | PEA15 | PEA15 | 5622 | 0.039 | 0.4 | NO |
37 | KAT5 | KAT5 | KAT5 | 5885 | 0.034 | 0.38 | NO |
38 | CDK2 | CDK2 | CDK2 | 5986 | 0.032 | 0.38 | NO |
39 | FLOT2 | FLOT2 | FLOT2 | 6455 | 0.024 | 0.36 | NO |
40 | YAP1 | YAP1 | YAP1 | 6461 | 0.024 | 0.36 | NO |
41 | GNB2L1 | GNB2L1 | GNB2L1 | 6547 | 0.022 | 0.36 | NO |
42 | CDK1 | CDK1 | CDK1 | 6578 | 0.022 | 0.36 | NO |
43 | MAPK14 | MAPK14 | MAPK14 | 6675 | 0.02 | 0.35 | NO |
44 | FASN | FASN | FASN | 6927 | 0.016 | 0.34 | NO |
45 | ABL1 | ABL1 | ABL1 | 6983 | 0.015 | 0.34 | NO |
46 | UBE4B | UBE4B | UBE4B | 7161 | 0.012 | 0.33 | NO |
47 | EP300 | EP300 | EP300 | 7243 | 0.011 | 0.33 | NO |
48 | BUB1 | BUB1 | BUB1 | 7490 | 0.0066 | 0.32 | NO |
49 | GRAMD4 | GRAMD4 | GRAMD4 | 7959 | -0.00097 | 0.29 | NO |
50 | DEDD | DEDD | DEDD | 8039 | -0.0022 | 0.29 | NO |
51 | CASP2 | CASP2 | CASP2 | 8230 | -0.0056 | 0.28 | NO |
52 | ITCH | ITCH | ITCH | 8266 | -0.0061 | 0.28 | NO |
53 | BUB3 | BUB3 | BUB3 | 8282 | -0.0064 | 0.28 | NO |
54 | PFDN5 | PFDN5 | PFDN5 | 8611 | -0.012 | 0.26 | NO |
55 | HAGH | HAGH | HAGH | 8984 | -0.018 | 0.24 | NO |
56 | AEN | AEN | AEN | 9319 | -0.024 | 0.22 | NO |
57 | PRKACB | PRKACB | PRKACB | 9570 | -0.028 | 0.21 | NO |
58 | JAK1 | JAK1 | JAK1 | 9733 | -0.03 | 0.21 | NO |
59 | MDM2 | MDM2 | MDM2 | 10508 | -0.045 | 0.17 | NO |
60 | SP1 | SP1 | SP1 | 10608 | -0.047 | 0.17 | NO |
61 | BCL2L11 | BCL2L11 | BCL2L11 | 10624 | -0.047 | 0.17 | NO |
62 | FOXO3 | FOXO3 | FOXO3 | 11766 | -0.073 | 0.11 | NO |
63 | BRCA2 | BRCA2 | BRCA2 | 11805 | -0.074 | 0.12 | NO |
64 | BAX | BAX | BAX | 11911 | -0.077 | 0.12 | NO |
65 | NDUFS2 | NDUFS2 | NDUFS2 | 11989 | -0.079 | 0.12 | NO |
66 | PPAP2A | PPAP2A | PPAP2A | 12724 | -0.1 | 0.089 | NO |
67 | WWOX | WWOX | WWOX | 12881 | -0.1 | 0.088 | NO |
68 | NEDD4L | NEDD4L | NEDD4L | 13369 | -0.12 | 0.072 | NO |
69 | SIRT1 | SIRT1 | SIRT1 | 13511 | -0.12 | 0.074 | NO |
70 | AFP | AFP | AFP | 13533 | -0.13 | 0.082 | NO |
71 | BIN1 | BIN1 | BIN1 | 13575 | -0.13 | 0.09 | NO |
72 | RCHY1 | RCHY1 | RCHY1 | 13604 | -0.13 | 0.099 | NO |
73 | TP53I3 | TP53I3 | TP53I3 | 14009 | -0.14 | 0.088 | NO |
74 | RNF43 | RNF43 | RNF43 | 14112 | -0.15 | 0.095 | NO |
75 | DCP1B | DCP1B | DCP1B | 15005 | -0.19 | 0.062 | NO |
76 | BBC3 | BBC3 | BBC3 | 16230 | -0.28 | 0.018 | NO |
77 | GATA1 | GATA1 | GATA1 | 16576 | -0.31 | 0.023 | NO |
78 | SERPINA1 | SERPINA1 | SERPINA1 | 17804 | -0.49 | -0.0044 | NO |
79 | GDF15 | GDF15 | GDF15 | 18425 | -0.7 | 0.017 | NO |
Figure S49. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MTOR 4PATHWAY.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: PID MTOR 4PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S26. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | CCNA1 | CCNA1 | CCNA1 | 92 | 0.69 | 0.2 | YES |
2 | CDKN1A | CDKN1A | CDKN1A | 1685 | 0.21 | 0.18 | YES |
3 | PSMD9 | PSMD9 | PSMD9 | 2880 | 0.12 | 0.15 | YES |
4 | PSMC1 | PSMC1 | PSMC1 | 3013 | 0.11 | 0.17 | YES |
5 | PSMD2 | PSMD2 | PSMD2 | 3071 | 0.11 | 0.2 | YES |
6 | PSMB7 | PSMB7 | PSMB7 | 3404 | 0.096 | 0.21 | YES |
7 | PSMB6 | PSMB6 | PSMB6 | 3480 | 0.093 | 0.24 | YES |
8 | PSMA6 | PSMA6 | PSMA6 | 3633 | 0.088 | 0.26 | YES |
9 | CCNE2 | CCNE2 | CCNE2 | 3871 | 0.081 | 0.27 | YES |
10 | PSMC2 | PSMC2 | PSMC2 | 3970 | 0.078 | 0.28 | YES |
11 | SKP2 | SKP2 | SKP2 | 3971 | 0.078 | 0.31 | YES |
12 | PSMB2 | PSMB2 | PSMB2 | 4134 | 0.074 | 0.32 | YES |
13 | CKS1B | CKS1B | CKS1B | 4232 | 0.071 | 0.34 | YES |
14 | PSMC3 | PSMC3 | PSMC3 | 4274 | 0.07 | 0.36 | YES |
15 | PSMD12 | PSMD12 | PSMD12 | 4475 | 0.064 | 0.36 | YES |
16 | CCNA2 | CCNA2 | CCNA2 | 4498 | 0.064 | 0.38 | YES |
17 | PSMD10 | PSMD10 | PSMD10 | 4572 | 0.062 | 0.4 | YES |
18 | PSMC6 | PSMC6 | PSMC6 | 4636 | 0.061 | 0.41 | YES |
19 | PSMD7 | PSMD7 | PSMD7 | 4828 | 0.056 | 0.42 | YES |
20 | PSMD5 | PSMD5 | PSMD5 | 4859 | 0.055 | 0.43 | YES |
21 | PSMB5 | PSMB5 | PSMB5 | 4911 | 0.054 | 0.45 | YES |
22 | PSMD14 | PSMD14 | PSMD14 | 4922 | 0.054 | 0.46 | YES |
23 | PSMA3 | PSMA3 | PSMA3 | 5221 | 0.048 | 0.46 | YES |
24 | PSMC5 | PSMC5 | PSMC5 | 5421 | 0.043 | 0.46 | YES |
25 | PSMB1 | PSMB1 | PSMB1 | 5541 | 0.041 | 0.47 | YES |
26 | PSMA1 | PSMA1 | PSMA1 | 5623 | 0.039 | 0.48 | YES |
27 | SKP1 | SKP1 | SKP1 | 5666 | 0.038 | 0.48 | YES |
28 | PSMD11 | PSMD11 | PSMD11 | 5753 | 0.037 | 0.49 | YES |
29 | PSMA7 | PSMA7 | PSMA7 | 5805 | 0.036 | 0.5 | YES |
30 | PSMD6 | PSMD6 | PSMD6 | 5806 | 0.036 | 0.51 | YES |
31 | PSMA4 | PSMA4 | PSMA4 | 5914 | 0.033 | 0.51 | YES |
32 | PSMA2 | PSMA2 | PSMA2 | 5923 | 0.033 | 0.52 | YES |
33 | CDK2 | CDK2 | CDK2 | 5986 | 0.032 | 0.53 | YES |
34 | PSMD8 | PSMD8 | PSMD8 | 6131 | 0.03 | 0.53 | YES |
35 | PSMA5 | PSMA5 | PSMA5 | 6198 | 0.028 | 0.54 | YES |
36 | PSMF1 | PSMF1 | PSMF1 | 6337 | 0.026 | 0.54 | YES |
37 | PSMD13 | PSMD13 | PSMD13 | 6378 | 0.025 | 0.54 | YES |
38 | PSMD4 | PSMD4 | PSMD4 | 6735 | 0.02 | 0.53 | NO |
39 | CUL1 | CUL1 | CUL1 | 7044 | 0.014 | 0.52 | NO |
40 | PSMD1 | PSMD1 | PSMD1 | 7082 | 0.014 | 0.52 | NO |
41 | UBA52 | UBA52 | UBA52 | 7138 | 0.013 | 0.52 | NO |
42 | PSMB9 | PSMB9 | PSMB9 | 7334 | 0.0092 | 0.51 | NO |
43 | PSME2 | PSME2 | PSME2 | 8120 | -0.0035 | 0.47 | NO |
44 | PSMB3 | PSMB3 | PSMB3 | 8191 | -0.0048 | 0.47 | NO |
45 | CCNE1 | CCNE1 | CCNE1 | 8196 | -0.0048 | 0.47 | NO |
46 | PSMD3 | PSMD3 | PSMD3 | 8356 | -0.0077 | 0.46 | NO |
47 | PSMB4 | PSMB4 | PSMB4 | 8445 | -0.0093 | 0.46 | NO |
48 | PSME1 | PSME1 | PSME1 | 8636 | -0.012 | 0.45 | NO |
49 | RPS27A | RPS27A | RPS27A | 9423 | -0.025 | 0.42 | NO |
50 | PSMC4 | PSMC4 | PSMC4 | 9597 | -0.028 | 0.42 | NO |
51 | PSMB8 | PSMB8 | PSMB8 | 11168 | -0.059 | 0.35 | NO |
52 | PSMB10 | PSMB10 | PSMB10 | 12074 | -0.081 | 0.33 | NO |
53 | CDKN1B | CDKN1B | CDKN1B | 12766 | -0.1 | 0.32 | NO |
Figure S51. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ERBB1 RECEPTOR PROXIMAL PATHWAY.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: PID ERBB1 RECEPTOR PROXIMAL PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S27. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | BNIP3 | BNIP3 | BNIP3 | 152 | 0.62 | 0.086 | YES |
2 | SFN | SFN | SFN | 341 | 0.49 | 0.15 | YES |
3 | HRAS | HRAS | HRAS | 1167 | 0.27 | 0.15 | YES |
4 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 1711 | 0.2 | 0.15 | YES |
5 | DDIT4 | DDIT4 | DDIT4 | 1870 | 0.19 | 0.17 | YES |
6 | IRS1 | IRS1 | IRS1 | 1884 | 0.19 | 0.2 | YES |
7 | ULK2 | ULK2 | ULK2 | 2059 | 0.17 | 0.21 | YES |
8 | PLD2 | PLD2 | PLD2 | 2072 | 0.17 | 0.24 | YES |
9 | RRAGC | RRAGC | RRAGC | 2082 | 0.17 | 0.26 | YES |
10 | SGK1 | SGK1 | SGK1 | 2109 | 0.17 | 0.29 | YES |
11 | PML | PML | PML | 2189 | 0.16 | 0.31 | YES |
12 | CLIP1 | CLIP1 | CLIP1 | 2248 | 0.16 | 0.33 | YES |
13 | ULK1 | ULK1 | ULK1 | 2325 | 0.15 | 0.35 | YES |
14 | PXN | PXN | PXN | 2575 | 0.14 | 0.36 | YES |
15 | YWHAQ | YWHAQ | YWHAQ | 2588 | 0.14 | 0.38 | YES |
16 | YWHAG | YWHAG | YWHAG | 2940 | 0.12 | 0.37 | YES |
17 | PLD1 | PLD1 | PLD1 | 3114 | 0.11 | 0.38 | YES |
18 | MAP2K1 | MAP2K1 | MAP2K1 | 3329 | 0.099 | 0.38 | YES |
19 | YWHAZ | YWHAZ | YWHAZ | 3654 | 0.087 | 0.38 | YES |
20 | NRAS | NRAS | NRAS | 4053 | 0.076 | 0.37 | YES |
21 | EIF4A1 | EIF4A1 | EIF4A1 | 4138 | 0.073 | 0.38 | YES |
22 | RICTOR | RICTOR | RICTOR | 4381 | 0.067 | 0.37 | YES |
23 | MAPK1 | MAPK1 | MAPK1 | 4698 | 0.06 | 0.37 | YES |
24 | RPTOR | RPTOR | RPTOR | 4742 | 0.059 | 0.37 | YES |
25 | YWHAE | YWHAE | YWHAE | 4879 | 0.055 | 0.37 | YES |
26 | YY1 | YY1 | YY1 | 4971 | 0.053 | 0.38 | YES |
27 | SREBF1 | SREBF1 | SREBF1 | 5081 | 0.051 | 0.38 | YES |
28 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 5147 | 0.049 | 0.38 | YES |
29 | YWHAH | YWHAH | YWHAH | 5166 | 0.049 | 0.39 | YES |
30 | TSC2 | TSC2 | TSC2 | 5512 | 0.042 | 0.38 | NO |
31 | MLST8 | MLST8 | MLST8 | 5556 | 0.041 | 0.38 | NO |
32 | RRAGA | RRAGA | RRAGA | 5671 | 0.038 | 0.38 | NO |
33 | AKT1 | AKT1 | AKT1 | 5951 | 0.033 | 0.37 | NO |
34 | CDK2 | CDK2 | CDK2 | 5986 | 0.032 | 0.37 | NO |
35 | MAP2K2 | MAP2K2 | MAP2K2 | 6205 | 0.028 | 0.37 | NO |
36 | RAC1 | RAC1 | RAC1 | 6388 | 0.025 | 0.36 | NO |
37 | POLDIP3 | POLDIP3 | POLDIP3 | 6496 | 0.023 | 0.36 | NO |
38 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 6527 | 0.023 | 0.36 | NO |
39 | EEF2K | EEF2K | EEF2K | 6642 | 0.021 | 0.36 | NO |
40 | RRN3 | RRN3 | RRN3 | 6659 | 0.021 | 0.36 | NO |
41 | EEF2 | EEF2 | EEF2 | 6841 | 0.018 | 0.35 | NO |
42 | EIF4E | EIF4E | EIF4E | 7041 | 0.014 | 0.34 | NO |
43 | AKT1S1 | AKT1S1 | AKT1S1 | 7271 | 0.01 | 0.33 | NO |
44 | RHEB | RHEB | RHEB | 7445 | 0.0074 | 0.32 | NO |
45 | FBXW11 | FBXW11 | FBXW11 | 7645 | 0.0039 | 0.32 | NO |
46 | RB1CC1 | RB1CC1 | RB1CC1 | 7666 | 0.0035 | 0.32 | NO |
47 | MTOR | MTOR | MTOR | 7694 | 0.0032 | 0.31 | NO |
48 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 8136 | -0.0038 | 0.29 | NO |
49 | CCNE1 | CCNE1 | CCNE1 | 8196 | -0.0048 | 0.29 | NO |
50 | PDPK1 | PDPK1 | PDPK1 | 8229 | -0.0055 | 0.29 | NO |
51 | YWHAB | YWHAB | YWHAB | 9276 | -0.023 | 0.24 | NO |
52 | TSC1 | TSC1 | TSC1 | 9393 | -0.025 | 0.23 | NO |
53 | BRAF | BRAF | BRAF | 9500 | -0.027 | 0.23 | NO |
54 | EIF4B | EIF4B | EIF4B | 9548 | -0.027 | 0.23 | NO |
55 | PRR5 | PRR5 | PRR5 | 9568 | -0.028 | 0.24 | NO |
56 | CYCS | CYCS | CYCS | 9916 | -0.034 | 0.22 | NO |
57 | RHOA | RHOA | RHOA | 10119 | -0.037 | 0.22 | NO |
58 | RAF1 | RAF1 | RAF1 | 10294 | -0.041 | 0.21 | NO |
59 | PDCD4 | PDCD4 | PDCD4 | 11433 | -0.065 | 0.16 | NO |
60 | MAPK3 | MAPK3 | MAPK3 | 11470 | -0.066 | 0.17 | NO |
61 | RRAGD | RRAGD | RRAGD | 11747 | -0.073 | 0.17 | NO |
62 | RRAGB | RRAGB | RRAGB | 12732 | -0.1 | 0.13 | NO |
63 | KRAS | KRAS | KRAS | 12846 | -0.1 | 0.14 | NO |
64 | PRKCA | PRKCA | PRKCA | 13401 | -0.12 | 0.13 | NO |
65 | IKBKB | IKBKB | IKBKB | 13422 | -0.12 | 0.15 | NO |
66 | SSPO | SSPO | SSPO | 17576 | -0.44 | -0.0097 | NO |
67 | PPARGC1A | PPARGC1A | PPARGC1A | 17734 | -0.48 | 0.054 | NO |
Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MYC PATHWAY.

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

Table S28. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | JUB | JUB | JUB | 1282 | 0.25 | 0.043 | YES |
2 | GADD45A | GADD45A | GADD45A | 1828 | 0.19 | 0.098 | YES |
3 | NDEL1 | NDEL1 | NDEL1 | 2181 | 0.16 | 0.15 | YES |
4 | BIRC5 | BIRC5 | BIRC5 | 2432 | 0.14 | 0.2 | YES |
5 | DLGAP5 | DLGAP5 | DLGAP5 | 2703 | 0.13 | 0.24 | YES |
6 | CENPA | CENPA | CENPA | 2749 | 0.13 | 0.29 | YES |
7 | AURKB | AURKB | AURKB | 3363 | 0.098 | 0.3 | YES |
8 | FZR1 | FZR1 | FZR1 | 3493 | 0.093 | 0.34 | YES |
9 | RAN | RAN | RAN | 3645 | 0.087 | 0.37 | YES |
10 | CDC25B | CDC25B | CDC25B | 3836 | 0.082 | 0.39 | YES |
11 | NFKBIA | NFKBIA | NFKBIA | 3923 | 0.08 | 0.42 | YES |
12 | GSK3B | GSK3B | GSK3B | 4023 | 0.077 | 0.45 | YES |
13 | CPEB1 | CPEB1 | CPEB1 | 4055 | 0.076 | 0.48 | YES |
14 | RASA1 | RASA1 | RASA1 | 4086 | 0.075 | 0.52 | YES |
15 | CKAP5 | CKAP5 | CKAP5 | 5348 | 0.045 | 0.47 | NO |
16 | TPX2 | TPX2 | TPX2 | 5406 | 0.044 | 0.48 | NO |
17 | PRKACA | PRKACA | PRKACA | 5698 | 0.038 | 0.49 | NO |
18 | OAZ1 | OAZ1 | OAZ1 | 5903 | 0.033 | 0.49 | NO |
19 | AKT1 | AKT1 | AKT1 | 5951 | 0.033 | 0.5 | NO |
20 | AURKAIP1 | AURKAIP1 | AURKAIP1 | 6953 | 0.016 | 0.46 | NO |
21 | TP53 | TP53 | TP53 | 7029 | 0.014 | 0.46 | NO |
22 | PPP2R5D | PPP2R5D | PPP2R5D | 7839 | 0.0009 | 0.41 | NO |
23 | TACC3 | TACC3 | TACC3 | 7884 | 0.00021 | 0.41 | NO |
24 | TDRD7 | TDRD7 | TDRD7 | 8257 | -0.006 | 0.4 | NO |
25 | GIT1 | GIT1 | GIT1 | 8355 | -0.0077 | 0.39 | NO |
26 | BRCA1 | BRCA1 | BRCA1 | 9017 | -0.018 | 0.36 | NO |
27 | PAK1 | PAK1 | PAK1 | 9180 | -0.021 | 0.37 | NO |
28 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 9895 | -0.033 | 0.34 | NO |
29 | AURKA | AURKA | AURKA | 9900 | -0.033 | 0.36 | NO |
30 | MDM2 | MDM2 | MDM2 | 10508 | -0.045 | 0.34 | NO |
31 | TACC1 | TACC1 | TACC1 | 15443 | -0.22 | 0.18 | NO |
Figure S55. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ECADHERIN NASCENTAJ PATHWAY.

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

Table S29. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | MRC2 | MRC2 | MRC2 | 1228 | 0.26 | 0.017 | YES |
2 | MRC1 | MRC1 | MRC1 | 1309 | 0.25 | 0.093 | YES |
3 | FCGR1A | FCGR1A | FCGR1A | 1889 | 0.18 | 0.12 | YES |
4 | CD207 | CD207 | CD207 | 2530 | 0.14 | 0.13 | YES |
5 | FCGR1B | FCGR1B | FCGR1B | 2836 | 0.12 | 0.15 | YES |
6 | PSMD9 | PSMD9 | PSMD9 | 2880 | 0.12 | 0.19 | YES |
7 | PSMC1 | PSMC1 | PSMC1 | 3013 | 0.11 | 0.22 | YES |
8 | PSMD2 | PSMD2 | PSMD2 | 3071 | 0.11 | 0.25 | YES |
9 | PSMB7 | PSMB7 | PSMB7 | 3404 | 0.096 | 0.26 | YES |
10 | PSMB6 | PSMB6 | PSMB6 | 3480 | 0.093 | 0.29 | YES |
11 | PSMA6 | PSMA6 | PSMA6 | 3633 | 0.088 | 0.31 | YES |
12 | PSMC2 | PSMC2 | PSMC2 | 3970 | 0.078 | 0.31 | YES |
13 | PSMB2 | PSMB2 | PSMB2 | 4134 | 0.074 | 0.33 | YES |
14 | PSMC3 | PSMC3 | PSMC3 | 4274 | 0.07 | 0.34 | YES |
15 | PSMD12 | PSMD12 | PSMD12 | 4475 | 0.064 | 0.35 | YES |
16 | PSMD10 | PSMD10 | PSMD10 | 4572 | 0.062 | 0.37 | YES |
17 | PSMC6 | PSMC6 | PSMC6 | 4636 | 0.061 | 0.38 | YES |
18 | PSMD7 | PSMD7 | PSMD7 | 4828 | 0.056 | 0.39 | YES |
19 | PSMD5 | PSMD5 | PSMD5 | 4859 | 0.055 | 0.41 | YES |
20 | PSMB5 | PSMB5 | PSMB5 | 4911 | 0.054 | 0.42 | YES |
21 | PSMD14 | PSMD14 | PSMD14 | 4922 | 0.054 | 0.44 | YES |
22 | PSMA3 | PSMA3 | PSMA3 | 5221 | 0.048 | 0.44 | YES |
23 | PSME4 | PSME4 | PSME4 | 5363 | 0.044 | 0.44 | YES |
24 | PSMC5 | PSMC5 | PSMC5 | 5421 | 0.043 | 0.46 | YES |
25 | PSMB1 | PSMB1 | PSMB1 | 5541 | 0.041 | 0.46 | YES |
26 | PSMA1 | PSMA1 | PSMA1 | 5623 | 0.039 | 0.47 | YES |
27 | PSMD11 | PSMD11 | PSMD11 | 5753 | 0.037 | 0.47 | YES |
28 | PSMA7 | PSMA7 | PSMA7 | 5805 | 0.036 | 0.48 | YES |
29 | PSMD6 | PSMD6 | PSMD6 | 5806 | 0.036 | 0.49 | YES |
30 | PSMA4 | PSMA4 | PSMA4 | 5914 | 0.033 | 0.5 | YES |
31 | PSMA2 | PSMA2 | PSMA2 | 5923 | 0.033 | 0.51 | YES |
32 | PSMD8 | PSMD8 | PSMD8 | 6131 | 0.03 | 0.51 | YES |
33 | PSMA5 | PSMA5 | PSMA5 | 6198 | 0.028 | 0.51 | YES |
34 | PSMF1 | PSMF1 | PSMF1 | 6337 | 0.026 | 0.51 | YES |
35 | PSMD13 | PSMD13 | PSMD13 | 6378 | 0.025 | 0.52 | YES |
36 | PSMD4 | PSMD4 | PSMD4 | 6735 | 0.02 | 0.51 | NO |
37 | PSMD1 | PSMD1 | PSMD1 | 7082 | 0.014 | 0.49 | NO |
38 | PSMB9 | PSMB9 | PSMB9 | 7334 | 0.0092 | 0.48 | NO |
39 | PSME2 | PSME2 | PSME2 | 8120 | -0.0035 | 0.44 | NO |
40 | PSMB3 | PSMB3 | PSMB3 | 8191 | -0.0048 | 0.44 | NO |
41 | PSMD3 | PSMD3 | PSMD3 | 8356 | -0.0077 | 0.43 | NO |
42 | PSMB4 | PSMB4 | PSMB4 | 8445 | -0.0093 | 0.43 | NO |
43 | PSME1 | PSME1 | PSME1 | 8636 | -0.012 | 0.42 | NO |
44 | PSMC4 | PSMC4 | PSMC4 | 9597 | -0.028 | 0.38 | NO |
45 | PSMB8 | PSMB8 | PSMB8 | 11168 | -0.059 | 0.32 | NO |
46 | PSMB10 | PSMB10 | PSMB10 | 12074 | -0.081 | 0.3 | NO |
47 | PSMA8 | PSMA8 | PSMA8 | 15037 | -0.2 | 0.2 | NO |
Figure S57. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID DELTANP63PATHWAY.

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: PID DELTANP63PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S30. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PML | PML | PML | 2189 | 0.16 | -0.025 | YES |
2 | MYC | MYC | MYC | 2458 | 0.14 | 0.043 | YES |
3 | TAF12 | TAF12 | TAF12 | 2706 | 0.13 | 0.1 | YES |
4 | ZBTB17 | ZBTB17 | ZBTB17 | 2972 | 0.11 | 0.15 | YES |
5 | RUVBL1 | RUVBL1 | RUVBL1 | 3620 | 0.088 | 0.17 | YES |
6 | PAK2 | PAK2 | PAK2 | 3777 | 0.084 | 0.21 | YES |
7 | SUPT3H | SUPT3H | SUPT3H | 3885 | 0.08 | 0.25 | YES |
8 | SKP2 | SKP2 | SKP2 | 3971 | 0.078 | 0.29 | YES |
9 | PIN1 | PIN1 | PIN1 | 3993 | 0.078 | 0.33 | YES |
10 | GSK3B | GSK3B | GSK3B | 4023 | 0.077 | 0.38 | YES |
11 | PPP2CA | PPP2CA | PPP2CA | 4083 | 0.075 | 0.42 | YES |
12 | ACTL6A | ACTL6A | ACTL6A | 4171 | 0.073 | 0.45 | YES |
13 | AXIN1 | AXIN1 | AXIN1 | 4479 | 0.064 | 0.47 | YES |
14 | TAF9 | TAF9 | TAF9 | 5181 | 0.048 | 0.46 | NO |
15 | KAT5 | KAT5 | KAT5 | 5885 | 0.034 | 0.44 | NO |
16 | FBXW7 | FBXW7 | FBXW7 | 7151 | 0.012 | 0.38 | NO |
17 | RUVBL2 | RUVBL2 | RUVBL2 | 7396 | 0.0083 | 0.38 | NO |
18 | SUPT7L | SUPT7L | SUPT7L | 7711 | 0.0028 | 0.36 | NO |
19 | MAX | MAX | MAX | 8106 | -0.0033 | 0.34 | NO |
20 | HBP1 | HBP1 | HBP1 | 8259 | -0.006 | 0.34 | NO |
21 | TAF10 | TAF10 | TAF10 | 8766 | -0.014 | 0.32 | NO |
22 | KAT2A | KAT2A | KAT2A | 8839 | -0.015 | 0.32 | NO |
23 | TRRAP | TRRAP | TRRAP | 11144 | -0.058 | 0.23 | NO |
24 | PPP2R5A | PPP2R5A | PPP2R5A | 11360 | -0.063 | 0.26 | NO |
25 | CDKN2A | CDKN2A | CDKN2A | 15767 | -0.24 | 0.16 | NO |
Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID A6B1 A6B4 INTEGRIN PATHWAY.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: PID A6B1 A6B4 INTEGRIN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
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 GLUTATHIONE METABOLISM | 46 | genes.ES.table | 0.54 | 1.6 | 0.042 | 1 | 0.97 | 0.28 | 0.071 | 0.26 | 0.59 | 0.31 |
KEGG NEUROTROPHIN SIGNALING PATHWAY | 126 | genes.ES.table | 0.44 | 1.7 | 0.0062 | 1 | 0.79 | 0.18 | 0.15 | 0.16 | 0.86 | 0.46 |
KEGG BASAL CELL CARCINOMA | 54 | genes.ES.table | 0.61 | 1.6 | 0.014 | 1 | 0.97 | 0.54 | 0.16 | 0.45 | 0.62 | 0.33 |
BIOCARTA CHREBP2 PATHWAY | 42 | genes.ES.table | 0.42 | 1.6 | 0.032 | 1 | 0.94 | 0.12 | 0.089 | 0.11 | 0.68 | 0.36 |
ST P38 MAPK PATHWAY | 37 | genes.ES.table | 0.41 | 1.6 | 0.045 | 1 | 0.97 | 0.14 | 0.12 | 0.12 | 0.61 | 0.32 |
WNT SIGNALING | 87 | genes.ES.table | 0.51 | 1.6 | 0.014 | 1 | 0.96 | 0.34 | 0.16 | 0.29 | 0.6 | 0.32 |
SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES | 34 | genes.ES.table | 0.48 | 1.6 | 0.044 | 0.98 | 0.98 | 0.26 | 0.17 | 0.22 | 0.61 | 0.32 |
PID P75NTRPATHWAY | 68 | genes.ES.table | 0.39 | 1.6 | 0.029 | 0.95 | 0.97 | 0.19 | 0.15 | 0.16 | 0.56 | 0.3 |
PID TRKRPATHWAY | 61 | genes.ES.table | 0.46 | 1.7 | 0.01 | 1 | 0.82 | 0.23 | 0.19 | 0.19 | 0.62 | 0.35 |
PID HEDGEHOG GLIPATHWAY | 48 | genes.ES.table | 0.47 | 1.8 | 0.0063 | 1 | 0.73 | 0.17 | 0.1 | 0.15 | 0.99 | 0.5 |
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 | HS6ST2 | HS6ST2 | HS6ST2 | 99 | 0.77 | 0.11 | YES |
2 | HS3ST6 | HS3ST6 | HS3ST6 | 243 | 0.63 | 0.2 | YES |
3 | GPC3 | GPC3 | GPC3 | 337 | 0.57 | 0.28 | YES |
4 | HS3ST3A1 | HS3ST3A1 | HS3ST3A1 | 479 | 0.5 | 0.35 | YES |
5 | GPC1 | GPC1 | GPC1 | 704 | 0.43 | 0.41 | YES |
6 | HS3ST4 | HS3ST4 | HS3ST4 | 846 | 0.39 | 0.46 | YES |
7 | HS3ST5 | HS3ST5 | HS3ST5 | 938 | 0.38 | 0.51 | YES |
8 | GPC2 | GPC2 | GPC2 | 1046 | 0.35 | 0.56 | YES |
9 | GPC5 | GPC5 | GPC5 | 1050 | 0.35 | 0.61 | YES |
10 | HS6ST3 | HS6ST3 | HS6ST3 | 1420 | 0.29 | 0.64 | YES |
11 | HS3ST3B1 | HS3ST3B1 | HS3ST3B1 | 1592 | 0.27 | 0.67 | YES |
12 | HS6ST1 | HS6ST1 | HS6ST1 | 1713 | 0.26 | 0.7 | YES |
13 | SDC1 | SDC1 | SDC1 | 2356 | 0.2 | 0.7 | NO |
14 | SDC2 | SDC2 | SDC2 | 5423 | 0.07 | 0.55 | NO |
15 | EXT1 | EXT1 | EXT1 | 5814 | 0.061 | 0.54 | NO |
16 | NDST3 | NDST3 | NDST3 | 7649 | 0.028 | 0.44 | NO |
17 | EXT2 | EXT2 | EXT2 | 9178 | 0.0035 | 0.36 | NO |
18 | AGRN | AGRN | AGRN | 9400 | 0.000091 | 0.35 | NO |
19 | NDST2 | NDST2 | NDST2 | 10237 | -0.014 | 0.31 | NO |
20 | GPC6 | GPC6 | GPC6 | 10619 | -0.021 | 0.29 | NO |
21 | GPC4 | GPC4 | GPC4 | 10790 | -0.024 | 0.28 | NO |
22 | NDST1 | NDST1 | NDST1 | 11215 | -0.032 | 0.27 | NO |
23 | GLCE | GLCE | GLCE | 12489 | -0.059 | 0.21 | NO |
24 | HS3ST2 | HS3ST2 | HS3ST2 | 12538 | -0.06 | 0.21 | NO |
25 | SDC3 | SDC3 | SDC3 | 13083 | -0.073 | 0.2 | NO |
26 | HSPG2 | HSPG2 | HSPG2 | 13787 | -0.093 | 0.17 | NO |
27 | NDST4 | NDST4 | NDST4 | 13966 | -0.099 | 0.18 | NO |
28 | HS2ST1 | HS2ST1 | HS2ST1 | 14166 | -0.11 | 0.18 | NO |
29 | SDC4 | SDC4 | SDC4 | 15521 | -0.16 | 0.14 | NO |
30 | HS3ST1 | HS3ST1 | HS3ST1 | 16640 | -0.24 | 0.11 | NO |
Figure S61. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLUTATHIONE METABOLISM.

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

Table S32. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | GLI2 | GLI2 | GLI2 | 75 | 0.81 | 0.13 | YES |
2 | GLI1 | GLI1 | GLI1 | 180 | 0.68 | 0.24 | YES |
3 | SMO | SMO | SMO | 281 | 0.6 | 0.34 | YES |
4 | MTSS1 | MTSS1 | MTSS1 | 1348 | 0.3 | 0.33 | YES |
5 | GNAI1 | GNAI1 | GNAI1 | 1483 | 0.29 | 0.37 | YES |
6 | GLI3 | GLI3 | GLI3 | 1567 | 0.28 | 0.41 | YES |
7 | PTCH1 | PTCH1 | PTCH1 | 1869 | 0.24 | 0.44 | YES |
8 | GNAZ | GNAZ | GNAZ | 1958 | 0.23 | 0.47 | YES |
9 | GNAO1 | GNAO1 | GNAO1 | 4947 | 0.081 | 0.32 | NO |
10 | SIN3A | SIN3A | SIN3A | 5809 | 0.062 | 0.29 | NO |
11 | GSK3B | GSK3B | GSK3B | 6462 | 0.049 | 0.26 | NO |
12 | CSNK1G2 | CSNK1G2 | CSNK1G2 | 6537 | 0.047 | 0.26 | NO |
13 | SAP18 | SAP18 | SAP18 | 6686 | 0.044 | 0.26 | NO |
14 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 7124 | 0.036 | 0.25 | NO |
15 | PRKACA | PRKACA | PRKACA | 7334 | 0.033 | 0.24 | NO |
16 | AKT1 | AKT1 | AKT1 | 7784 | 0.025 | 0.22 | NO |
17 | XPO1 | XPO1 | XPO1 | 7840 | 0.024 | 0.22 | NO |
18 | RBBP4 | RBBP4 | RBBP4 | 7992 | 0.022 | 0.22 | NO |
19 | SPOP | SPOP | SPOP | 8084 | 0.02 | 0.22 | NO |
20 | CREBBP | CREBBP | CREBBP | 8234 | 0.018 | 0.21 | NO |
21 | SIN3B | SIN3B | SIN3B | 8259 | 0.018 | 0.21 | NO |
22 | CSNK1G1 | CSNK1G1 | CSNK1G1 | 8477 | 0.015 | 0.2 | NO |
23 | CSNK1E | CSNK1E | CSNK1E | 8782 | 0.01 | 0.19 | NO |
24 | SUFU | SUFU | SUFU | 9069 | 0.0056 | 0.18 | NO |
25 | HDAC2 | HDAC2 | HDAC2 | 9285 | 0.0018 | 0.16 | NO |
26 | IFT172 | IFT172 | IFT172 | 9388 | 0.00026 | 0.16 | NO |
27 | RAB23 | RAB23 | RAB23 | 9488 | -0.0012 | 0.15 | NO |
28 | HDAC1 | HDAC1 | HDAC1 | 9910 | -0.0086 | 0.13 | NO |
29 | MAP2K1 | MAP2K1 | MAP2K1 | 9916 | -0.0086 | 0.14 | NO |
30 | CSNK1D | CSNK1D | CSNK1D | 10911 | -0.026 | 0.086 | NO |
31 | SSPO | SSPO | SSPO | 11291 | -0.034 | 0.071 | NO |
32 | GNB1 | GNB1 | GNB1 | 11297 | -0.034 | 0.076 | NO |
33 | GNAI2 | GNAI2 | GNAI2 | 11312 | -0.034 | 0.082 | NO |
34 | RBBP7 | RBBP7 | RBBP7 | 11367 | -0.035 | 0.084 | NO |
35 | IFT88 | IFT88 | IFT88 | 11368 | -0.035 | 0.09 | NO |
36 | GNAI3 | GNAI3 | GNAI3 | 11477 | -0.038 | 0.091 | NO |
37 | FBXW11 | FBXW11 | FBXW11 | 11991 | -0.048 | 0.071 | NO |
38 | CSNK1G3 | CSNK1G3 | CSNK1G3 | 12462 | -0.058 | 0.056 | NO |
39 | KIF3A | KIF3A | KIF3A | 12650 | -0.062 | 0.056 | NO |
40 | SAP30 | SAP30 | SAP30 | 12855 | -0.067 | 0.057 | NO |
41 | PIAS1 | PIAS1 | PIAS1 | 13133 | -0.074 | 0.054 | NO |
42 | PRKCD | PRKCD | PRKCD | 13355 | -0.08 | 0.056 | NO |
43 | STK36 | STK36 | STK36 | 13525 | -0.085 | 0.061 | NO |
44 | SHH | SHH | SHH | 13830 | -0.095 | 0.061 | NO |
45 | ARRB2 | ARRB2 | ARRB2 | 14235 | -0.11 | 0.057 | NO |
46 | GNG2 | GNG2 | GNG2 | 16378 | -0.22 | -0.021 | NO |
47 | LGALS3 | LGALS3 | LGALS3 | 16506 | -0.22 | 0.0094 | NO |
48 | FOXA2 | FOXA2 | FOXA2 | 18579 | -0.66 | 0.009 | NO |
Figure S63. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NEUROTROPHIN SIGNALING PATHWAY.

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

Table S33. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NTRK2 | NTRK2 | NTRK2 | 30 | 0.95 | 0.055 | YES |
2 | MAPK10 | MAPK10 | MAPK10 | 67 | 0.83 | 0.1 | YES |
3 | BDNF | BDNF | BDNF | 69 | 0.82 | 0.15 | YES |
4 | NTF4 | NTF4 | NTF4 | 94 | 0.77 | 0.19 | YES |
5 | IRS4 | IRS4 | IRS4 | 106 | 0.76 | 0.24 | YES |
6 | CALML3 | CALML3 | CALML3 | 150 | 0.71 | 0.28 | YES |
7 | NGFR | NGFR | NGFR | 498 | 0.5 | 0.29 | YES |
8 | NGFRAP1 | NGFRAP1 | NGFRAP1 | 547 | 0.48 | 0.32 | YES |
9 | MAPK12 | MAPK12 | MAPK12 | 607 | 0.46 | 0.34 | YES |
10 | TP73 | TP73 | TP73 | 735 | 0.43 | 0.36 | YES |
11 | RPS6KA6 | RPS6KA6 | RPS6KA6 | 879 | 0.39 | 0.37 | YES |
12 | CALML5 | CALML5 | CALML5 | 1078 | 0.35 | 0.38 | YES |
13 | CAMK2B | CAMK2B | CAMK2B | 1268 | 0.32 | 0.39 | YES |
14 | IRS2 | IRS2 | IRS2 | 1620 | 0.27 | 0.39 | YES |
15 | BCL2 | BCL2 | BCL2 | 1698 | 0.26 | 0.4 | YES |
16 | NGF | NGF | NGF | 1783 | 0.25 | 0.41 | YES |
17 | AKT3 | AKT3 | AKT3 | 1898 | 0.24 | 0.42 | YES |
18 | NTF3 | NTF3 | NTF3 | 2287 | 0.2 | 0.41 | YES |
19 | MAPK11 | MAPK11 | MAPK11 | 2323 | 0.2 | 0.42 | YES |
20 | CALML6 | CALML6 | CALML6 | 2363 | 0.2 | 0.43 | YES |
21 | PIK3CA | PIK3CA | PIK3CA | 2620 | 0.18 | 0.43 | YES |
22 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 2720 | 0.17 | 0.43 | YES |
23 | CAMK4 | CAMK4 | CAMK4 | 2733 | 0.17 | 0.44 | YES |
24 | NFKBIA | NFKBIA | NFKBIA | 3378 | 0.14 | 0.41 | NO |
25 | HRAS | HRAS | HRAS | 3585 | 0.13 | 0.41 | NO |
26 | PIK3R2 | PIK3R2 | PIK3R2 | 3630 | 0.12 | 0.42 | NO |
27 | CRKL | CRKL | CRKL | 3954 | 0.11 | 0.4 | NO |
28 | PDK1 | PDK1 | PDK1 | 4115 | 0.11 | 0.4 | NO |
29 | BRAF | BRAF | BRAF | 4432 | 0.096 | 0.39 | NO |
30 | IKBKB | IKBKB | IKBKB | 4558 | 0.093 | 0.39 | NO |
31 | YWHAG | YWHAG | YWHAG | 4750 | 0.087 | 0.38 | NO |
32 | YWHAQ | YWHAQ | YWHAQ | 4932 | 0.082 | 0.38 | NO |
33 | KIDINS220 | KIDINS220 | KIDINS220 | 5095 | 0.077 | 0.38 | NO |
34 | SHC4 | SHC4 | SHC4 | 5204 | 0.075 | 0.37 | NO |
35 | BAD | BAD | BAD | 5369 | 0.071 | 0.37 | NO |
36 | YWHAE | YWHAE | YWHAE | 5431 | 0.069 | 0.37 | NO |
37 | BAX | BAX | BAX | 6179 | 0.054 | 0.33 | NO |
38 | AKT2 | AKT2 | AKT2 | 6189 | 0.053 | 0.34 | NO |
39 | PIK3CD | PIK3CD | PIK3CD | 6219 | 0.053 | 0.34 | NO |
40 | ATF4 | ATF4 | ATF4 | 6318 | 0.051 | 0.34 | NO |
41 | GSK3B | GSK3B | GSK3B | 6462 | 0.049 | 0.33 | NO |
42 | MAPK7 | MAPK7 | MAPK7 | 6692 | 0.044 | 0.32 | NO |
43 | MAP2K5 | MAP2K5 | MAP2K5 | 6804 | 0.042 | 0.32 | NO |
44 | MAP2K7 | MAP2K7 | MAP2K7 | 6808 | 0.042 | 0.32 | NO |
45 | MAP2K2 | MAP2K2 | MAP2K2 | 7036 | 0.038 | 0.31 | NO |
46 | SHC1 | SHC1 | SHC1 | 7367 | 0.033 | 0.29 | NO |
47 | YWHAZ | YWHAZ | YWHAZ | 7375 | 0.032 | 0.3 | NO |
48 | GAB1 | GAB1 | GAB1 | 7534 | 0.03 | 0.29 | NO |
49 | CALM1 | CALM1 | CALM1 | 7552 | 0.03 | 0.29 | NO |
50 | CAMK2A | CAMK2A | CAMK2A | 7668 | 0.027 | 0.28 | NO |
51 | AKT1 | AKT1 | AKT1 | 7784 | 0.025 | 0.28 | NO |
52 | SHC3 | SHC3 | SHC3 | 7817 | 0.024 | 0.28 | NO |
53 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 7863 | 0.024 | 0.28 | NO |
54 | IRAK4 | IRAK4 | IRAK4 | 7933 | 0.022 | 0.28 | NO |
55 | SH2B2 | SH2B2 | SH2B2 | 7949 | 0.022 | 0.28 | NO |
56 | TRAF6 | TRAF6 | TRAF6 | 8093 | 0.02 | 0.27 | NO |
57 | ABL1 | ABL1 | ABL1 | 8133 | 0.02 | 0.27 | NO |
58 | CRK | CRK | CRK | 8239 | 0.018 | 0.26 | NO |
59 | PLCG2 | PLCG2 | PLCG2 | 8254 | 0.018 | 0.26 | NO |
60 | MAPK1 | MAPK1 | MAPK1 | 8337 | 0.017 | 0.26 | NO |
61 | NTRK3 | NTRK3 | NTRK3 | 8345 | 0.016 | 0.26 | NO |
62 | SH2B1 | SH2B1 | SH2B1 | 8479 | 0.014 | 0.26 | NO |
63 | MAPK13 | MAPK13 | MAPK13 | 8700 | 0.012 | 0.24 | NO |
64 | IRAK1 | IRAK1 | IRAK1 | 8788 | 0.01 | 0.24 | NO |
65 | TP53 | TP53 | TP53 | 9175 | 0.0035 | 0.22 | NO |
66 | ZNF274 | ZNF274 | ZNF274 | 9210 | 0.003 | 0.22 | NO |
67 | RAC1 | RAC1 | RAC1 | 9414 | -0.0002 | 0.21 | NO |
68 | MAP3K1 | MAP3K1 | MAP3K1 | 9498 | -0.0015 | 0.2 | NO |
69 | FRS2 | FRS2 | FRS2 | 9515 | -0.0018 | 0.2 | NO |
70 | CAMK2G | CAMK2G | CAMK2G | 9530 | -0.002 | 0.2 | NO |
71 | SOS1 | SOS1 | SOS1 | 9615 | -0.0034 | 0.2 | NO |
72 | GRB2 | GRB2 | GRB2 | 9721 | -0.005 | 0.19 | NO |
73 | ARHGDIA | ARHGDIA | ARHGDIA | 9883 | -0.0082 | 0.18 | NO |
74 | MAGED1 | MAGED1 | MAGED1 | 9912 | -0.0086 | 0.18 | NO |
75 | MAP2K1 | MAP2K1 | MAP2K1 | 9916 | -0.0086 | 0.18 | NO |
76 | PIK3R1 | PIK3R1 | PIK3R1 | 10011 | -0.01 | 0.18 | NO |
77 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 10016 | -0.01 | 0.18 | NO |
78 | CSK | CSK | CSK | 10179 | -0.013 | 0.17 | NO |
79 | JUN | JUN | JUN | 10308 | -0.015 | 0.17 | NO |
80 | PTPN11 | PTPN11 | PTPN11 | 10355 | -0.016 | 0.16 | NO |
81 | RELA | RELA | RELA | 10408 | -0.017 | 0.16 | NO |
82 | RAF1 | RAF1 | RAF1 | 10491 | -0.018 | 0.16 | NO |
83 | PIK3CB | PIK3CB | PIK3CB | 10498 | -0.018 | 0.16 | NO |
84 | KRAS | KRAS | KRAS | 10549 | -0.019 | 0.16 | NO |
85 | MAP3K3 | MAP3K3 | MAP3K3 | 10589 | -0.02 | 0.16 | NO |
86 | CALM2 | CALM2 | CALM2 | 10641 | -0.021 | 0.16 | NO |
87 | RAP1B | RAP1B | RAP1B | 10691 | -0.022 | 0.16 | NO |
88 | YWHAH | YWHAH | YWHAH | 10769 | -0.024 | 0.15 | NO |
89 | PLCG1 | PLCG1 | PLCG1 | 10903 | -0.026 | 0.15 | NO |
90 | NFKBIB | NFKBIB | NFKBIB | 11058 | -0.029 | 0.14 | NO |
91 | NFKB1 | NFKB1 | NFKB1 | 11303 | -0.034 | 0.13 | NO |
92 | SHC2 | SHC2 | SHC2 | 11604 | -0.04 | 0.12 | NO |
93 | PRDM4 | PRDM4 | PRDM4 | 11855 | -0.045 | 0.1 | NO |
94 | YWHAB | YWHAB | YWHAB | 12111 | -0.05 | 0.093 | NO |
95 | SOS2 | SOS2 | SOS2 | 12220 | -0.052 | 0.091 | NO |
96 | CDC42 | CDC42 | CDC42 | 12250 | -0.053 | 0.092 | NO |
97 | CAMK2D | CAMK2D | CAMK2D | 12306 | -0.054 | 0.092 | NO |
98 | MAPK9 | MAPK9 | MAPK9 | 12344 | -0.055 | 0.094 | NO |
99 | FOXO3 | FOXO3 | FOXO3 | 12524 | -0.06 | 0.088 | NO |
100 | MAPK14 | MAPK14 | MAPK14 | 12584 | -0.061 | 0.088 | NO |
101 | RPS6KA4 | RPS6KA4 | RPS6KA4 | 12601 | -0.061 | 0.091 | NO |
102 | PSEN1 | PSEN1 | PSEN1 | 12648 | -0.062 | 0.092 | NO |
103 | MAP3K5 | MAP3K5 | MAP3K5 | 12686 | -0.063 | 0.094 | NO |
104 | RHOA | RHOA | RHOA | 13111 | -0.074 | 0.075 | NO |
105 | IRS1 | IRS1 | IRS1 | 13332 | -0.079 | 0.068 | NO |
106 | PRKCD | PRKCD | PRKCD | 13355 | -0.08 | 0.072 | NO |
107 | ARHGDIB | ARHGDIB | ARHGDIB | 13732 | -0.091 | 0.057 | NO |
108 | NRAS | NRAS | NRAS | 13763 | -0.092 | 0.061 | NO |
109 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 13768 | -0.092 | 0.066 | NO |
110 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 13816 | -0.094 | 0.069 | NO |
111 | NTRK1 | NTRK1 | NTRK1 | 14230 | -0.11 | 0.053 | NO |
112 | CALM3 | CALM3 | CALM3 | 14277 | -0.11 | 0.057 | NO |
113 | RAP1A | RAP1A | RAP1A | 14410 | -0.11 | 0.057 | NO |
114 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 14697 | -0.12 | 0.049 | NO |
115 | MAPK3 | MAPK3 | MAPK3 | 14864 | -0.13 | 0.048 | NO |
116 | MAPK8 | MAPK8 | MAPK8 | 14983 | -0.14 | 0.05 | NO |
117 | PIK3R3 | PIK3R3 | PIK3R3 | 15679 | -0.17 | 0.022 | NO |
118 | RIPK2 | RIPK2 | RIPK2 | 15752 | -0.18 | 0.029 | NO |
119 | SORT1 | SORT1 | SORT1 | 16020 | -0.19 | 0.026 | NO |
120 | FASLG | FASLG | FASLG | 16140 | -0.2 | 0.032 | NO |
121 | NFKBIE | NFKBIE | NFKBIE | 16368 | -0.21 | 0.032 | NO |
122 | SH2B3 | SH2B3 | SH2B3 | 16655 | -0.24 | 0.03 | NO |
123 | IRAK3 | IRAK3 | IRAK3 | 17232 | -0.29 | 0.017 | NO |
124 | PIK3R5 | PIK3R5 | PIK3R5 | 17337 | -0.3 | 0.029 | NO |
125 | IRAK2 | IRAK2 | IRAK2 | 17649 | -0.35 | 0.033 | NO |
126 | PIK3CG | PIK3CG | PIK3CG | 18123 | -0.45 | 0.034 | NO |
Figure S65. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BASAL CELL CARCINOMA.

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

Table S34. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PAK7 | PAK7 | PAK7 | 49 | 0.88 | 0.19 | YES |
2 | SRGAP3 | SRGAP3 | SRGAP3 | 604 | 0.46 | 0.27 | YES |
3 | PFN2 | PFN2 | PFN2 | 622 | 0.46 | 0.37 | YES |
4 | GPC1 | GPC1 | GPC1 | 704 | 0.43 | 0.46 | YES |
5 | ROBO2 | ROBO2 | ROBO2 | 1687 | 0.26 | 0.46 | YES |
6 | PAK6 | PAK6 | PAK6 | 1776 | 0.25 | 0.52 | YES |
7 | SLIT2 | SLIT2 | SLIT2 | 1825 | 0.25 | 0.57 | YES |
8 | NCK1 | NCK1 | NCK1 | 2543 | 0.18 | 0.57 | YES |
9 | EVL | EVL | EVL | 2687 | 0.17 | 0.6 | YES |
10 | CLASP1 | CLASP1 | CLASP1 | 4199 | 0.1 | 0.55 | NO |
11 | PAK1 | PAK1 | PAK1 | 4224 | 0.1 | 0.57 | NO |
12 | PAK2 | PAK2 | PAK2 | 4698 | 0.089 | 0.56 | NO |
13 | ENAH | ENAH | ENAH | 4836 | 0.084 | 0.57 | NO |
14 | SRGAP2 | SRGAP2 | SRGAP2 | 6031 | 0.057 | 0.52 | NO |
15 | ABL2 | ABL2 | ABL2 | 7172 | 0.036 | 0.47 | NO |
16 | PAK4 | PAK4 | PAK4 | 7442 | 0.031 | 0.46 | NO |
17 | ABL1 | ABL1 | ABL1 | 8133 | 0.02 | 0.43 | NO |
18 | ROBO1 | ROBO1 | ROBO1 | 8936 | 0.0077 | 0.39 | NO |
19 | RAC1 | RAC1 | RAC1 | 9414 | -0.0002 | 0.36 | NO |
20 | CAP2 | CAP2 | CAP2 | 9532 | -0.002 | 0.36 | NO |
21 | SOS1 | SOS1 | SOS1 | 9615 | -0.0034 | 0.35 | NO |
22 | PFN1 | PFN1 | PFN1 | 10228 | -0.014 | 0.32 | NO |
23 | NCK2 | NCK2 | NCK2 | 12216 | -0.052 | 0.23 | NO |
24 | SOS2 | SOS2 | SOS2 | 12220 | -0.052 | 0.24 | NO |
25 | CDC42 | CDC42 | CDC42 | 12250 | -0.053 | 0.25 | NO |
26 | CAP1 | CAP1 | CAP1 | 12293 | -0.054 | 0.26 | NO |
27 | ROBO3 | ROBO3 | ROBO3 | 13659 | -0.089 | 0.21 | NO |
28 | VASP | VASP | VASP | 14121 | -0.1 | 0.2 | NO |
29 | SRGAP1 | SRGAP1 | SRGAP1 | 15962 | -0.19 | 0.15 | NO |
Figure S67. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CHREBP2 PATHWAY.

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S35. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NTRK2 | NTRK2 | NTRK2 | 30 | 0.95 | 0.12 | YES |
2 | BDNF | BDNF | BDNF | 69 | 0.82 | 0.22 | YES |
3 | NTF4 | NTF4 | NTF4 | 94 | 0.77 | 0.31 | YES |
4 | NGFR | NGFR | NGFR | 498 | 0.5 | 0.35 | YES |
5 | RIT1 | RIT1 | RIT1 | 965 | 0.37 | 0.37 | YES |
6 | DNM1 | DNM1 | DNM1 | 1663 | 0.26 | 0.37 | YES |
7 | ELMO1 | ELMO1 | ELMO1 | 1773 | 0.25 | 0.39 | YES |
8 | NGF | NGF | NGF | 1783 | 0.25 | 0.42 | YES |
9 | TIAM1 | TIAM1 | TIAM1 | 1794 | 0.25 | 0.46 | YES |
10 | NTF3 | NTF3 | NTF3 | 2287 | 0.2 | 0.45 | YES |
11 | PIK3CA | PIK3CA | PIK3CA | 2620 | 0.18 | 0.46 | YES |
12 | FAIM | FAIM | FAIM | 3062 | 0.15 | 0.45 | YES |
13 | MATK | MATK | MATK | 3375 | 0.14 | 0.45 | YES |
14 | HRAS | HRAS | HRAS | 3585 | 0.13 | 0.46 | YES |
15 | CRKL | CRKL | CRKL | 3954 | 0.11 | 0.45 | NO |
16 | NEDD4L | NEDD4L | NEDD4L | 4414 | 0.097 | 0.44 | NO |
17 | CCND1 | CCND1 | CCND1 | 5267 | 0.073 | 0.4 | NO |
18 | SQSTM1 | SQSTM1 | SQSTM1 | 5645 | 0.065 | 0.39 | NO |
19 | MCF2L | MCF2L | MCF2L | 5783 | 0.062 | 0.39 | NO |
20 | PRKCI | PRKCI | PRKCI | 5833 | 0.061 | 0.4 | NO |
21 | DNAJA3 | DNAJA3 | DNAJA3 | 6101 | 0.055 | 0.39 | NO |
22 | RGS19 | RGS19 | RGS19 | 7086 | 0.037 | 0.34 | NO |
23 | SHC1 | SHC1 | SHC1 | 7367 | 0.033 | 0.33 | NO |
24 | GAB1 | GAB1 | GAB1 | 7534 | 0.03 | 0.32 | NO |
25 | GIPC1 | GIPC1 | GIPC1 | 7694 | 0.027 | 0.32 | NO |
26 | SHC3 | SHC3 | SHC3 | 7817 | 0.024 | 0.32 | NO |
27 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 7863 | 0.024 | 0.32 | NO |
28 | ABL1 | ABL1 | ABL1 | 8133 | 0.02 | 0.3 | NO |
29 | CRK | CRK | CRK | 8239 | 0.018 | 0.3 | NO |
30 | MAPK1 | MAPK1 | MAPK1 | 8337 | 0.017 | 0.3 | NO |
31 | NTRK3 | NTRK3 | NTRK3 | 8345 | 0.016 | 0.3 | NO |
32 | SH2B1 | SH2B1 | SH2B1 | 8479 | 0.014 | 0.3 | NO |
33 | RAC1 | RAC1 | RAC1 | 9414 | -0.0002 | 0.24 | NO |
34 | FRS2 | FRS2 | FRS2 | 9515 | -0.0018 | 0.24 | NO |
35 | SOS1 | SOS1 | SOS1 | 9615 | -0.0034 | 0.24 | NO |
36 | GRB2 | GRB2 | GRB2 | 9721 | -0.005 | 0.23 | NO |
37 | MAGED1 | MAGED1 | MAGED1 | 9912 | -0.0086 | 0.22 | NO |
38 | MAP2K1 | MAP2K1 | MAP2K1 | 9916 | -0.0086 | 0.22 | NO |
39 | PIK3R1 | PIK3R1 | PIK3R1 | 10011 | -0.01 | 0.22 | NO |
40 | DOCK1 | DOCK1 | DOCK1 | 10157 | -0.013 | 0.21 | NO |
41 | PTPN11 | PTPN11 | PTPN11 | 10355 | -0.016 | 0.2 | NO |
42 | KRAS | KRAS | KRAS | 10549 | -0.019 | 0.2 | NO |
43 | RAP1B | RAP1B | RAP1B | 10691 | -0.022 | 0.19 | NO |
44 | PLCG1 | PLCG1 | PLCG1 | 10903 | -0.026 | 0.18 | NO |
45 | DYNLT1 | DYNLT1 | DYNLT1 | 11013 | -0.028 | 0.18 | NO |
46 | STAT3 | STAT3 | STAT3 | 11258 | -0.033 | 0.17 | NO |
47 | SHC2 | SHC2 | SHC2 | 11604 | -0.04 | 0.16 | NO |
48 | CDC42 | CDC42 | CDC42 | 12250 | -0.053 | 0.13 | NO |
49 | RHOG | RHOG | RHOG | 12523 | -0.06 | 0.12 | NO |
50 | FRS3 | FRS3 | FRS3 | 12633 | -0.062 | 0.12 | NO |
51 | RHOA | RHOA | RHOA | 13111 | -0.074 | 0.11 | NO |
52 | ARHGAP32 | ARHGAP32 | ARHGAP32 | 13240 | -0.077 | 0.11 | NO |
53 | RASA1 | RASA1 | RASA1 | 13242 | -0.077 | 0.12 | NO |
54 | EHD4 | EHD4 | EHD4 | 13556 | -0.086 | 0.11 | NO |
55 | NRAS | NRAS | NRAS | 13763 | -0.092 | 0.12 | NO |
56 | PRKCZ | PRKCZ | PRKCZ | 13955 | -0.098 | 0.12 | NO |
57 | NTRK1 | NTRK1 | NTRK1 | 14230 | -0.11 | 0.12 | NO |
58 | RAP1A | RAP1A | RAP1A | 14410 | -0.11 | 0.12 | NO |
59 | MAPK3 | MAPK3 | MAPK3 | 14864 | -0.13 | 0.11 | NO |
60 | GAB2 | GAB2 | GAB2 | 16980 | -0.26 | 0.031 | NO |
61 | RASGRF1 | RASGRF1 | RASGRF1 | 18334 | -0.51 | 0.022 | NO |
Figure S69. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST P38 MAPK PATHWAY.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: ST P38 MAPK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S36. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SNAPC1 | SNAPC1 | SNAPC1 | 1659 | 0.26 | 0.074 | YES |
2 | SNAPC5 | SNAPC5 | SNAPC5 | 3871 | 0.12 | 0.026 | YES |
3 | POLR2H | POLR2H | POLR2H | 3962 | 0.11 | 0.09 | YES |
4 | GTF3C5 | GTF3C5 | GTF3C5 | 4227 | 0.1 | 0.14 | YES |
5 | BRF2 | BRF2 | BRF2 | 4460 | 0.096 | 0.18 | YES |
6 | SNAPC2 | SNAPC2 | SNAPC2 | 4495 | 0.095 | 0.24 | YES |
7 | POLR1D | POLR1D | POLR1D | 4838 | 0.084 | 0.28 | YES |
8 | POLR2F | POLR2F | POLR2F | 4843 | 0.084 | 0.33 | YES |
9 | POLR2E | POLR2E | POLR2E | 4957 | 0.081 | 0.37 | YES |
10 | GTF3C2 | GTF3C2 | GTF3C2 | 5671 | 0.064 | 0.37 | YES |
11 | POLR3H | POLR3H | POLR3H | 5815 | 0.061 | 0.4 | YES |
12 | GTF3C3 | GTF3C3 | GTF3C3 | 5983 | 0.058 | 0.43 | YES |
13 | POLR3D | POLR3D | POLR3D | 7189 | 0.036 | 0.38 | NO |
14 | SSB | SSB | SSB | 7666 | 0.027 | 0.38 | NO |
15 | LZTS1 | LZTS1 | LZTS1 | 7739 | 0.026 | 0.39 | NO |
16 | POLR3K | POLR3K | POLR3K | 7833 | 0.024 | 0.4 | NO |
17 | GTF3C4 | GTF3C4 | GTF3C4 | 7887 | 0.023 | 0.41 | NO |
18 | POLR3C | POLR3C | POLR3C | 8336 | 0.017 | 0.4 | NO |
19 | BRF1 | BRF1 | BRF1 | 8361 | 0.016 | 0.4 | NO |
20 | SNAPC4 | SNAPC4 | SNAPC4 | 9131 | 0.0043 | 0.37 | NO |
21 | POLR2K | POLR2K | POLR2K | 9300 | 0.0016 | 0.36 | NO |
22 | POU2F1 | POU2F1 | POU2F1 | 9333 | 0.0011 | 0.36 | NO |
23 | POLR3E | POLR3E | POLR3E | 9526 | -0.002 | 0.35 | NO |
24 | POLR3F | POLR3F | POLR3F | 9634 | -0.0036 | 0.34 | NO |
25 | POLR3B | POLR3B | POLR3B | 9646 | -0.0038 | 0.35 | NO |
26 | SNAPC3 | SNAPC3 | SNAPC3 | 9650 | -0.0038 | 0.35 | NO |
27 | POLR1C | POLR1C | POLR1C | 10010 | -0.01 | 0.34 | NO |
28 | POLR2L | POLR2L | POLR2L | 10611 | -0.02 | 0.32 | NO |
29 | ZNF143 | ZNF143 | ZNF143 | 10650 | -0.021 | 0.33 | NO |
30 | NFIB | NFIB | NFIB | 10704 | -0.022 | 0.34 | NO |
31 | POLR3GL | POLR3GL | POLR3GL | 10729 | -0.023 | 0.35 | NO |
32 | TBP | TBP | TBP | 11878 | -0.045 | 0.32 | NO |
33 | POLR3A | POLR3A | POLR3A | 13398 | -0.082 | 0.29 | NO |
Figure S71. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: WNT SIGNALING.

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

Table S37. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | NUP210 | NUP210 | NUP210 | 1769 | 0.25 | 0.053 | YES |
2 | SLC25A4 | SLC25A4 | SLC25A4 | 3294 | 0.14 | 0.053 | YES |
3 | NUP205 | NUP205 | NUP205 | 4504 | 0.095 | 0.044 | YES |
4 | NUP93 | NUP93 | NUP93 | 4507 | 0.095 | 0.099 | YES |
5 | NUP37 | NUP37 | NUP37 | 4582 | 0.092 | 0.15 | YES |
6 | KPNA1 | KPNA1 | KPNA1 | 4768 | 0.086 | 0.19 | YES |
7 | SLC25A5 | SLC25A5 | SLC25A5 | 5456 | 0.069 | 0.19 | YES |
8 | NUP35 | NUP35 | NUP35 | 5943 | 0.059 | 0.2 | YES |
9 | NUP155 | NUP155 | NUP155 | 5967 | 0.058 | 0.23 | YES |
10 | PSIP1 | PSIP1 | PSIP1 | 6057 | 0.056 | 0.26 | YES |
11 | BANF1 | BANF1 | BANF1 | 6073 | 0.056 | 0.29 | YES |
12 | NUP133 | NUP133 | NUP133 | 6185 | 0.054 | 0.32 | YES |
13 | AAAS | AAAS | AAAS | 6252 | 0.052 | 0.34 | YES |
14 | NUPL2 | NUPL2 | NUPL2 | 6275 | 0.052 | 0.37 | YES |
15 | NUP188 | NUP188 | NUP188 | 6310 | 0.051 | 0.4 | YES |
16 | NUP88 | NUP88 | NUP88 | 6716 | 0.044 | 0.4 | YES |
17 | NUP62 | NUP62 | NUP62 | 7161 | 0.036 | 0.4 | YES |
18 | NUP214 | NUP214 | NUP214 | 7292 | 0.034 | 0.42 | YES |
19 | NUP153 | NUP153 | NUP153 | 7446 | 0.031 | 0.42 | YES |
20 | NUP50 | NUP50 | NUP50 | 7608 | 0.028 | 0.43 | YES |
21 | RAE1 | RAE1 | RAE1 | 7702 | 0.026 | 0.44 | YES |
22 | POM121 | POM121 | POM121 | 7880 | 0.023 | 0.45 | YES |
23 | NUP107 | NUP107 | NUP107 | 8000 | 0.022 | 0.45 | YES |
24 | NUP54 | NUP54 | NUP54 | 8046 | 0.021 | 0.46 | YES |
25 | SEH1L | SEH1L | SEH1L | 8476 | 0.015 | 0.45 | NO |
26 | HMGA1 | HMGA1 | HMGA1 | 9267 | 0.0021 | 0.41 | NO |
27 | NUP85 | NUP85 | NUP85 | 10072 | -0.011 | 0.37 | NO |
28 | TPR | TPR | TPR | 10224 | -0.014 | 0.37 | NO |
29 | SLC25A6 | SLC25A6 | SLC25A6 | 10521 | -0.019 | 0.37 | NO |
30 | NUPL1 | NUPL1 | NUPL1 | 10660 | -0.022 | 0.37 | NO |
31 | RANBP2 | RANBP2 | RANBP2 | 12092 | -0.05 | 0.32 | NO |
32 | NUP43 | NUP43 | NUP43 | 12285 | -0.054 | 0.34 | NO |
Figure S73. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S38. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | SNAPC1 | SNAPC1 | SNAPC1 | 1659 | 0.26 | 0.11 | YES |
2 | SNAPC5 | SNAPC5 | SNAPC5 | 3871 | 0.12 | 0.082 | YES |
3 | POLR2H | POLR2H | POLR2H | 3962 | 0.11 | 0.16 | YES |
4 | BRF2 | BRF2 | BRF2 | 4460 | 0.096 | 0.21 | YES |
5 | SNAPC2 | SNAPC2 | SNAPC2 | 4495 | 0.095 | 0.28 | YES |
6 | POLR1D | POLR1D | POLR1D | 4838 | 0.084 | 0.32 | YES |
7 | POLR2F | POLR2F | POLR2F | 4843 | 0.084 | 0.39 | YES |
8 | POLR2E | POLR2E | POLR2E | 4957 | 0.081 | 0.44 | YES |
9 | POLR3H | POLR3H | POLR3H | 5815 | 0.061 | 0.44 | YES |
10 | POLR3D | POLR3D | POLR3D | 7189 | 0.036 | 0.4 | NO |
11 | LZTS1 | LZTS1 | LZTS1 | 7739 | 0.026 | 0.39 | NO |
12 | POLR3K | POLR3K | POLR3K | 7833 | 0.024 | 0.4 | NO |
13 | POLR3C | POLR3C | POLR3C | 8336 | 0.017 | 0.39 | NO |
14 | SNAPC4 | SNAPC4 | SNAPC4 | 9131 | 0.0043 | 0.35 | NO |
15 | POLR2K | POLR2K | POLR2K | 9300 | 0.0016 | 0.34 | NO |
16 | POU2F1 | POU2F1 | POU2F1 | 9333 | 0.0011 | 0.34 | NO |
17 | POLR3E | POLR3E | POLR3E | 9526 | -0.002 | 0.33 | NO |
18 | POLR3F | POLR3F | POLR3F | 9634 | -0.0036 | 0.33 | NO |
19 | POLR3B | POLR3B | POLR3B | 9646 | -0.0038 | 0.33 | NO |
20 | SNAPC3 | SNAPC3 | SNAPC3 | 9650 | -0.0038 | 0.33 | NO |
21 | POLR1C | POLR1C | POLR1C | 10010 | -0.01 | 0.32 | NO |
22 | POLR2L | POLR2L | POLR2L | 10611 | -0.02 | 0.3 | NO |
23 | ZNF143 | ZNF143 | ZNF143 | 10650 | -0.021 | 0.32 | NO |
24 | POLR3GL | POLR3GL | POLR3GL | 10729 | -0.023 | 0.33 | NO |
25 | TBP | TBP | TBP | 11878 | -0.045 | 0.3 | NO |
26 | POLR3A | POLR3A | POLR3A | 13398 | -0.082 | 0.29 | NO |
Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID P75NTRPATHWAY.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: PID P75NTRPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S39. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | TP63 | TP63 | TP63 | 136 | 0.73 | 0.079 | YES |
2 | CLCA2 | CLCA2 | CLCA2 | 287 | 0.6 | 0.14 | YES |
3 | SMARCD3 | SMARCD3 | SMARCD3 | 562 | 0.48 | 0.18 | YES |
4 | TFAP2C | TFAP2C | TFAP2C | 570 | 0.47 | 0.24 | YES |
5 | S100A2 | S100A2 | S100A2 | 638 | 0.45 | 0.29 | YES |
6 | GPX2 | GPX2 | GPX2 | 821 | 0.4 | 0.33 | YES |
7 | IGFBP3 | IGFBP3 | IGFBP3 | 1208 | 0.33 | 0.35 | YES |
8 | NQO1 | NQO1 | NQO1 | 1500 | 0.28 | 0.36 | YES |
9 | EGR2 | EGR2 | EGR2 | 1517 | 0.28 | 0.4 | YES |
10 | SERPINB5 | SERPINB5 | SERPINB5 | 1708 | 0.26 | 0.42 | YES |
11 | PERP | PERP | PERP | 1957 | 0.23 | 0.43 | YES |
12 | PMAIP1 | PMAIP1 | PMAIP1 | 2085 | 0.22 | 0.45 | YES |
13 | FDXR | FDXR | FDXR | 2177 | 0.21 | 0.47 | YES |
14 | DST | DST | DST | 3652 | 0.12 | 0.41 | NO |
15 | FLOT2 | FLOT2 | FLOT2 | 3866 | 0.12 | 0.41 | NO |
16 | EVPL | EVPL | EVPL | 3875 | 0.12 | 0.42 | NO |
17 | DHRS3 | DHRS3 | DHRS3 | 4290 | 0.1 | 0.41 | NO |
18 | IKBKB | IKBKB | IKBKB | 4558 | 0.093 | 0.41 | NO |
19 | YWHAQ | YWHAQ | YWHAQ | 4932 | 0.082 | 0.4 | NO |
20 | HBP1 | HBP1 | HBP1 | 5710 | 0.063 | 0.36 | NO |
21 | JAG1 | JAG1 | JAG1 | 6127 | 0.055 | 0.35 | NO |
22 | BAX | BAX | BAX | 6179 | 0.054 | 0.35 | NO |
23 | ADA | ADA | ADA | 6778 | 0.043 | 0.33 | NO |
24 | MDM2 | MDM2 | MDM2 | 7197 | 0.036 | 0.31 | NO |
25 | SSRP1 | SSRP1 | SSRP1 | 7900 | 0.023 | 0.27 | NO |
26 | ABL1 | ABL1 | ABL1 | 8133 | 0.02 | 0.26 | NO |
27 | GADD45A | GADD45A | GADD45A | 8776 | 0.01 | 0.23 | NO |
28 | EP300 | EP300 | EP300 | 9002 | 0.0066 | 0.22 | NO |
29 | MFGE8 | MFGE8 | MFGE8 | 9185 | 0.0034 | 0.21 | NO |
30 | CDKN1A | CDKN1A | CDKN1A | 9289 | 0.0018 | 0.2 | NO |
31 | BBC3 | BBC3 | BBC3 | 9291 | 0.0018 | 0.2 | NO |
32 | DICER1 | DICER1 | DICER1 | 9545 | -0.0023 | 0.19 | NO |
33 | WWP1 | WWP1 | WWP1 | 9632 | -0.0036 | 0.19 | NO |
34 | PLK1 | PLK1 | PLK1 | 9686 | -0.0044 | 0.18 | NO |
35 | SP1 | SP1 | SP1 | 9939 | -0.0091 | 0.17 | NO |
36 | PML | PML | PML | 10235 | -0.014 | 0.16 | NO |
37 | ITGB4 | ITGB4 | ITGB4 | 10376 | -0.016 | 0.15 | NO |
38 | FAS | FAS | FAS | 11276 | -0.033 | 0.11 | NO |
39 | SSPO | SSPO | SSPO | 11291 | -0.034 | 0.11 | NO |
40 | TRAF4 | TRAF4 | TRAF4 | 11799 | -0.043 | 0.089 | NO |
41 | ITCH | ITCH | ITCH | 12701 | -0.064 | 0.049 | NO |
42 | OGG1 | OGG1 | OGG1 | 12998 | -0.071 | 0.041 | NO |
43 | NOC2L | NOC2L | NOC2L | 13068 | -0.073 | 0.046 | NO |
44 | PRKCD | PRKCD | PRKCD | 13355 | -0.08 | 0.04 | NO |
45 | CHUK | CHUK | CHUK | 13605 | -0.088 | 0.037 | NO |
46 | AEN | AEN | AEN | 13779 | -0.093 | 0.039 | NO |
47 | SHH | SHH | SHH | 13830 | -0.095 | 0.048 | NO |
48 | ITGA3 | ITGA3 | ITGA3 | 15114 | -0.14 | -0.0039 | NO |
49 | SPATA18 | SPATA18 | SPATA18 | 15204 | -0.15 | 0.0088 | NO |
50 | TP53I3 | TP53I3 | TP53I3 | 15285 | -0.15 | 0.023 | NO |
51 | VDR | VDR | VDR | 15709 | -0.18 | 0.021 | NO |
52 | GDF15 | GDF15 | GDF15 | 17590 | -0.34 | -0.04 | NO |
53 | CDKN2A | CDKN2A | CDKN2A | 17826 | -0.38 | -0.0072 | NO |
54 | CABLES1 | CABLES1 | CABLES1 | 18224 | -0.48 | 0.028 | NO |
Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TRKRPATHWAY.

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

Table S40. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PPP2R2B | PPP2R2B | PPP2R2B | 128 | 0.74 | 0.15 | YES |
2 | PPP2R2C | PPP2R2C | PPP2R2C | 377 | 0.55 | 0.26 | YES |
3 | PRKAA2 | PRKAA2 | PRKAA2 | 580 | 0.47 | 0.35 | YES |
4 | PPP2R3A | PPP2R3A | PPP2R3A | 1058 | 0.35 | 0.4 | YES |
5 | PRKAR2B | PRKAR2B | PRKAR2B | 1667 | 0.26 | 0.42 | YES |
6 | PPP2R3B | PPP2R3B | PPP2R3B | 2634 | 0.18 | 0.41 | NO |
7 | PRKAG3 | PRKAG3 | PRKAG3 | 3530 | 0.13 | 0.39 | NO |
8 | PPP2R5A | PPP2R5A | PPP2R5A | 3861 | 0.12 | 0.4 | NO |
9 | YWHAG | YWHAG | YWHAG | 4750 | 0.087 | 0.37 | NO |
10 | YWHAQ | YWHAQ | YWHAQ | 4932 | 0.082 | 0.38 | NO |
11 | YWHAE | YWHAE | YWHAE | 5431 | 0.069 | 0.36 | NO |
12 | PPP2R4 | PPP2R4 | PPP2R4 | 5547 | 0.067 | 0.37 | NO |
13 | ACACA | ACACA | ACACA | 5682 | 0.064 | 0.38 | NO |
14 | PPP2R2D | PPP2R2D | PPP2R2D | 6725 | 0.044 | 0.33 | NO |
15 | FASN | FASN | FASN | 7238 | 0.035 | 0.31 | NO |
16 | PRKAG1 | PRKAG1 | PRKAG1 | 7241 | 0.035 | 0.32 | NO |
17 | PRKACA | PRKACA | PRKACA | 7334 | 0.033 | 0.32 | NO |
18 | YWHAZ | YWHAZ | YWHAZ | 7375 | 0.032 | 0.33 | NO |
19 | PPP2CA | PPP2CA | PPP2CA | 8471 | 0.015 | 0.27 | NO |
20 | PRKACB | PRKACB | PRKACB | 8801 | 0.01 | 0.26 | NO |
21 | PPP2R5C | PPP2R5C | PPP2R5C | 8856 | 0.0091 | 0.26 | NO |
22 | PPP2R5D | PPP2R5D | PPP2R5D | 9108 | 0.0048 | 0.24 | NO |
23 | PPP2CB | PPP2CB | PPP2CB | 9233 | 0.0026 | 0.24 | NO |
24 | PPP2R5B | PPP2R5B | PPP2R5B | 9483 | -0.0012 | 0.22 | NO |
25 | PPP2R2A | PPP2R2A | PPP2R2A | 9628 | -0.0036 | 0.22 | NO |
26 | PRKAR1B | PRKAR1B | PRKAR1B | 9887 | -0.0082 | 0.2 | NO |
27 | MLX | MLX | MLX | 10092 | -0.012 | 0.2 | NO |
28 | PRKAR1A | PRKAR1A | PRKAR1A | 10118 | -0.012 | 0.2 | NO |
29 | PRKAB2 | PRKAB2 | PRKAB2 | 10231 | -0.014 | 0.19 | NO |
30 | PRKAA1 | PRKAA1 | PRKAA1 | 10306 | -0.015 | 0.19 | NO |
31 | PPP2R1A | PPP2R1A | PPP2R1A | 10448 | -0.018 | 0.19 | NO |
32 | PPP2R5E | PPP2R5E | PPP2R5E | 10558 | -0.02 | 0.19 | NO |
33 | YWHAH | YWHAH | YWHAH | 10769 | -0.024 | 0.18 | NO |
34 | PRKAB1 | PRKAB1 | PRKAB1 | 11409 | -0.036 | 0.16 | NO |
35 | PRKAG2 | PRKAG2 | PRKAG2 | 11440 | -0.037 | 0.16 | NO |
36 | GCK | GCK | GCK | 11448 | -0.037 | 0.17 | NO |
37 | YWHAB | YWHAB | YWHAB | 12111 | -0.05 | 0.14 | NO |
38 | PPP2R1B | PPP2R1B | PPP2R1B | 13397 | -0.082 | 0.094 | NO |
39 | MLXIPL | MLXIPL | MLXIPL | 13560 | -0.086 | 0.1 | NO |
40 | PKLR | PKLR | PKLR | 14695 | -0.12 | 0.07 | NO |
41 | PRKAR2A | PRKAR2A | PRKAR2A | 15619 | -0.17 | 0.057 | NO |
42 | PRKACG | PRKACG | PRKACG | 18339 | -0.51 | 0.022 | NO |
Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID HEDGEHOG GLIPATHWAY.

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

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 7. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.
GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val |
---|---|---|---|---|---|---|---|---|---|---|---|---|
KEGG PURINE METABOLISM | 154 | genes.ES.table | 0.4 | 1.7 | 0.0063 | 0.19 | 0.91 | 0.21 | 0.16 | 0.18 | 0.094 | 0.024 |
KEGG TRYPTOPHAN METABOLISM | 39 | genes.ES.table | 0.52 | 1.5 | 0.044 | 0.19 | 1 | 0.28 | 0.15 | 0.24 | 0.14 | 0.003 |
KEGG ABC TRANSPORTERS | 43 | genes.ES.table | 0.55 | 1.5 | 0.035 | 0.18 | 1 | 0.21 | 0.083 | 0.19 | 0.13 | 0.004 |
KEGG MAPK SIGNALING PATHWAY | 256 | genes.ES.table | 0.4 | 1.5 | 0.0096 | 0.18 | 0.99 | 0.32 | 0.26 | 0.24 | 0.12 | 0.004 |
KEGG CALCIUM SIGNALING PATHWAY | 175 | genes.ES.table | 0.56 | 1.6 | 0.0023 | 0.19 | 0.93 | 0.46 | 0.22 | 0.36 | 0.094 | 0.023 |
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION | 244 | genes.ES.table | 0.58 | 1.5 | 0.032 | 0.19 | 1 | 0.42 | 0.16 | 0.36 | 0.13 | 0.005 |
KEGG CHEMOKINE SIGNALING PATHWAY | 186 | genes.ES.table | 0.61 | 1.7 | 0.0081 | 0.24 | 0.78 | 0.38 | 0.18 | 0.31 | 0.086 | 0.06 |
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM | 76 | genes.ES.table | 0.4 | 1.5 | 0.051 | 0.18 | 1 | 0.33 | 0.25 | 0.25 | 0.13 | 0.004 |
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION | 242 | genes.ES.table | 0.55 | 1.5 | 0.0074 | 0.18 | 0.99 | 0.43 | 0.18 | 0.35 | 0.12 | 0.004 |
KEGG LYSOSOME | 121 | genes.ES.table | 0.34 | 1.6 | 0.052 | 0.17 | 0.96 | 0.5 | 0.4 | 0.3 | 0.099 | 0.011 |
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 | IGF1 | IGF1 | IGF1 | 151 | 0.94 | 0.1 | YES |
2 | PIK3CG | PIK3CG | PIK3CG | 466 | 0.77 | 0.18 | YES |
3 | PIK3R5 | PIK3R5 | PIK3R5 | 589 | 0.72 | 0.26 | YES |
4 | FIGF | FIGF | FIGF | 784 | 0.67 | 0.32 | YES |
5 | RPS6KA6 | RPS6KA6 | RPS6KA6 | 1637 | 0.49 | 0.34 | YES |
6 | AKT3 | AKT3 | AKT3 | 1994 | 0.43 | 0.37 | YES |
7 | PRKAA2 | PRKAA2 | PRKAA2 | 2160 | 0.41 | 0.41 | YES |
8 | VEGFC | VEGFC | VEGFC | 2187 | 0.4 | 0.46 | YES |
9 | CAB39L | CAB39L | CAB39L | 2477 | 0.36 | 0.48 | YES |
10 | PIK3CD | PIK3CD | PIK3CD | 2845 | 0.32 | 0.5 | YES |
11 | PIK3R1 | PIK3R1 | PIK3R1 | 3194 | 0.28 | 0.52 | YES |
12 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 3868 | 0.22 | 0.51 | NO |
13 | PIK3R3 | PIK3R3 | PIK3R3 | 4641 | 0.17 | 0.48 | NO |
14 | VEGFB | VEGFB | VEGFB | 4843 | 0.16 | 0.49 | NO |
15 | ULK2 | ULK2 | ULK2 | 4881 | 0.15 | 0.51 | NO |
16 | PIK3CA | PIK3CA | PIK3CA | 6306 | 0.09 | 0.44 | NO |
17 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 6506 | 0.083 | 0.44 | NO |
18 | RICTOR | RICTOR | RICTOR | 6724 | 0.076 | 0.44 | NO |
19 | STRADA | STRADA | STRADA | 7121 | 0.064 | 0.43 | NO |
20 | ULK1 | ULK1 | ULK1 | 7455 | 0.054 | 0.41 | NO |
21 | BRAF | BRAF | BRAF | 7839 | 0.044 | 0.4 | NO |
22 | EIF4B | EIF4B | EIF4B | 7910 | 0.042 | 0.4 | NO |
23 | MTOR | MTOR | MTOR | 8400 | 0.03 | 0.38 | NO |
24 | RPS6 | RPS6 | RPS6 | 8645 | 0.024 | 0.37 | NO |
25 | RPTOR | RPTOR | RPTOR | 8668 | 0.023 | 0.37 | NO |
26 | AKT2 | AKT2 | AKT2 | 8672 | 0.023 | 0.37 | NO |
27 | TSC2 | TSC2 | TSC2 | 8705 | 0.022 | 0.37 | NO |
28 | TSC1 | TSC1 | TSC1 | 8783 | 0.02 | 0.37 | NO |
29 | HIF1A | HIF1A | HIF1A | 8959 | 0.016 | 0.36 | NO |
30 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 9041 | 0.014 | 0.36 | NO |
31 | PIK3CB | PIK3CB | PIK3CB | 9191 | 0.011 | 0.35 | NO |
32 | PRKAA1 | PRKAA1 | PRKAA1 | 9320 | 0.0086 | 0.35 | NO |
33 | PGF | PGF | PGF | 9343 | 0.0082 | 0.35 | NO |
34 | STK11 | STK11 | STK11 | 9962 | -0.0042 | 0.32 | NO |
35 | MAPK1 | MAPK1 | MAPK1 | 10237 | -0.01 | 0.3 | NO |
36 | PDPK1 | PDPK1 | PDPK1 | 10781 | -0.021 | 0.28 | NO |
37 | AKT1 | AKT1 | AKT1 | 10842 | -0.022 | 0.27 | NO |
38 | MAPK3 | MAPK3 | MAPK3 | 11157 | -0.028 | 0.26 | NO |
39 | CAB39 | CAB39 | CAB39 | 11217 | -0.029 | 0.26 | NO |
40 | RHEB | RHEB | RHEB | 11505 | -0.035 | 0.25 | NO |
41 | EIF4E | EIF4E | EIF4E | 11636 | -0.038 | 0.25 | NO |
42 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 12422 | -0.054 | 0.21 | NO |
43 | PIK3R2 | PIK3R2 | PIK3R2 | 13461 | -0.078 | 0.17 | NO |
44 | DDIT4 | DDIT4 | DDIT4 | 14043 | -0.092 | 0.14 | NO |
45 | ULK3 | ULK3 | ULK3 | 14177 | -0.096 | 0.15 | NO |
46 | EIF4E2 | EIF4E2 | EIF4E2 | 14300 | -0.099 | 0.16 | NO |
47 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 14652 | -0.11 | 0.15 | NO |
48 | MLST8 | MLST8 | MLST8 | 15033 | -0.12 | 0.14 | NO |
49 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 17055 | -0.23 | 0.062 | NO |
50 | VEGFA | VEGFA | VEGFA | 17128 | -0.24 | 0.087 | NO |
Figure S81. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PURINE METABOLISM.
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Figure S82. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PURINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table 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 | ITGA8 | ITGA8 | ITGA8 | 135 | 0.95 | 0.069 | YES |
2 | SLC2A4 | SLC2A4 | SLC2A4 | 276 | 0.86 | 0.13 | YES |
3 | AVPR2 | AVPR2 | AVPR2 | 277 | 0.86 | 0.2 | YES |
4 | AGTR1 | AGTR1 | AGTR1 | 291 | 0.85 | 0.27 | YES |
5 | ITGA9 | ITGA9 | ITGA9 | 425 | 0.78 | 0.32 | YES |
6 | ITGA7 | ITGA7 | ITGA7 | 628 | 0.71 | 0.37 | YES |
7 | ITGA10 | ITGA10 | ITGA10 | 798 | 0.66 | 0.41 | YES |
8 | ACAP1 | ACAP1 | ACAP1 | 854 | 0.65 | 0.46 | YES |
9 | IL2RA | IL2RA | IL2RA | 1095 | 0.6 | 0.5 | YES |
10 | EDNRB | EDNRB | EDNRB | 1130 | 0.59 | 0.54 | YES |
11 | ITGA4 | ITGA4 | ITGA4 | 1354 | 0.55 | 0.57 | YES |
12 | TSHR | TSHR | TSHR | 1428 | 0.54 | 0.61 | YES |
13 | CPE | CPE | CPE | 1566 | 0.5 | 0.64 | YES |
14 | ITGA11 | ITGA11 | ITGA11 | 2127 | 0.41 | 0.65 | YES |
15 | ITGA1 | ITGA1 | ITGA1 | 2517 | 0.36 | 0.66 | YES |
16 | PIP5K1C | PIP5K1C | PIP5K1C | 4243 | 0.19 | 0.58 | NO |
17 | ITGAV | ITGAV | ITGAV | 5316 | 0.13 | 0.53 | NO |
18 | ADRB2 | ADRB2 | ADRB2 | 5625 | 0.12 | 0.52 | NO |
19 | ITGA5 | ITGA5 | ITGA5 | 6119 | 0.096 | 0.51 | NO |
20 | MAPK8IP3 | MAPK8IP3 | MAPK8IP3 | 6228 | 0.092 | 0.51 | NO |
21 | ITGB1 | ITGB1 | ITGB1 | 6891 | 0.07 | 0.48 | NO |
22 | EXOC2 | EXOC2 | EXOC2 | 7343 | 0.058 | 0.46 | NO |
23 | KLC1 | KLC1 | KLC1 | 7388 | 0.057 | 0.46 | NO |
24 | EXOC6 | EXOC6 | EXOC6 | 7532 | 0.052 | 0.46 | NO |
25 | EXOC5 | EXOC5 | EXOC5 | 8236 | 0.034 | 0.42 | NO |
26 | EXOC4 | EXOC4 | EXOC4 | 8273 | 0.033 | 0.42 | NO |
27 | EXOC7 | EXOC7 | EXOC7 | 8455 | 0.029 | 0.42 | NO |
28 | VAMP3 | VAMP3 | VAMP3 | 8918 | 0.016 | 0.39 | NO |
29 | SPAG9 | SPAG9 | SPAG9 | 8961 | 0.016 | 0.39 | NO |
30 | EXOC1 | EXOC1 | EXOC1 | 10325 | -0.012 | 0.32 | NO |
31 | CTNNB1 | CTNNB1 | CTNNB1 | 10472 | -0.015 | 0.31 | NO |
32 | EXOC3 | EXOC3 | EXOC3 | 10676 | -0.019 | 0.3 | NO |
33 | DNM2 | DNM2 | DNM2 | 11520 | -0.036 | 0.26 | NO |
34 | ARF6 | ARF6 | ARF6 | 11790 | -0.041 | 0.25 | NO |
35 | BIN1 | BIN1 | BIN1 | 11889 | -0.043 | 0.25 | NO |
36 | PLD2 | PLD2 | PLD2 | 12358 | -0.053 | 0.23 | NO |
37 | CLTC | CLTC | CLTC | 12426 | -0.054 | 0.23 | NO |
38 | PLD1 | PLD1 | PLD1 | 12660 | -0.06 | 0.22 | NO |
39 | ITGA2 | ITGA2 | ITGA2 | 13103 | -0.07 | 0.2 | NO |
40 | CTNNA1 | CTNNA1 | CTNNA1 | 13342 | -0.075 | 0.2 | NO |
41 | SCAMP2 | SCAMP2 | SCAMP2 | 13978 | -0.09 | 0.17 | NO |
42 | CTNND1 | CTNND1 | CTNND1 | 14297 | -0.099 | 0.16 | NO |
43 | RALA | RALA | RALA | 15018 | -0.12 | 0.13 | NO |
44 | ASAP2 | ASAP2 | ASAP2 | 15063 | -0.12 | 0.14 | NO |
45 | ITGA3 | ITGA3 | ITGA3 | 15736 | -0.15 | 0.12 | NO |
46 | NME1 | NME1 | NME1 | 16288 | -0.18 | 0.1 | NO |
47 | ITGA6 | ITGA6 | ITGA6 | 16344 | -0.18 | 0.11 | NO |
48 | CDH1 | CDH1 | CDH1 | 16729 | -0.21 | 0.11 | NO |
Figure S83. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TRYPTOPHAN METABOLISM.

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

Table S43. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FLT3 | FLT3 | FLT3 | 60 | 1.1 | 0.092 | YES |
2 | ZBTB16 | ZBTB16 | ZBTB16 | 77 | 1 | 0.18 | YES |
3 | RUNX1T1 | RUNX1T1 | RUNX1T1 | 136 | 0.95 | 0.26 | YES |
4 | PIK3CG | PIK3CG | PIK3CG | 466 | 0.77 | 0.31 | YES |
5 | PIK3R5 | PIK3R5 | PIK3R5 | 589 | 0.72 | 0.37 | YES |
6 | KIT | KIT | KIT | 630 | 0.71 | 0.43 | YES |
7 | SPI1 | SPI1 | SPI1 | 1466 | 0.53 | 0.43 | YES |
8 | AKT3 | AKT3 | AKT3 | 1994 | 0.43 | 0.44 | YES |
9 | LEF1 | LEF1 | LEF1 | 2441 | 0.37 | 0.45 | YES |
10 | PIM2 | PIM2 | PIM2 | 2475 | 0.36 | 0.48 | YES |
11 | PIK3CD | PIK3CD | PIK3CD | 2845 | 0.32 | 0.49 | YES |
12 | PIK3R1 | PIK3R1 | PIK3R1 | 3194 | 0.28 | 0.5 | YES |
13 | STAT5A | STAT5A | STAT5A | 3423 | 0.26 | 0.51 | YES |
14 | TCF7L1 | TCF7L1 | TCF7L1 | 3629 | 0.24 | 0.52 | YES |
15 | TCF7 | TCF7 | TCF7 | 3882 | 0.22 | 0.52 | YES |
16 | STAT5B | STAT5B | STAT5B | 4489 | 0.18 | 0.51 | NO |
17 | PIK3R3 | PIK3R3 | PIK3R3 | 4641 | 0.17 | 0.51 | NO |
18 | SOS2 | SOS2 | SOS2 | 5457 | 0.12 | 0.48 | NO |
19 | RUNX1 | RUNX1 | RUNX1 | 5644 | 0.12 | 0.48 | NO |
20 | RARA | RARA | RARA | 5928 | 0.1 | 0.47 | NO |
21 | PIK3CA | PIK3CA | PIK3CA | 6306 | 0.09 | 0.46 | NO |
22 | NFKB1 | NFKB1 | NFKB1 | 6664 | 0.078 | 0.45 | NO |
23 | IKBKB | IKBKB | IKBKB | 6765 | 0.074 | 0.45 | NO |
24 | PIM1 | PIM1 | PIM1 | 7160 | 0.063 | 0.44 | NO |
25 | BRAF | BRAF | BRAF | 7839 | 0.044 | 0.4 | NO |
26 | PML | PML | PML | 7973 | 0.041 | 0.4 | NO |
27 | MTOR | MTOR | MTOR | 8400 | 0.03 | 0.38 | NO |
28 | SOS1 | SOS1 | SOS1 | 8517 | 0.027 | 0.38 | NO |
29 | STAT3 | STAT3 | STAT3 | 8641 | 0.024 | 0.37 | NO |
30 | AKT2 | AKT2 | AKT2 | 8672 | 0.023 | 0.37 | NO |
31 | RAF1 | RAF1 | RAF1 | 8957 | 0.016 | 0.36 | NO |
32 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 9041 | 0.014 | 0.35 | NO |
33 | ARAF | ARAF | ARAF | 9066 | 0.013 | 0.35 | NO |
34 | GRB2 | GRB2 | GRB2 | 9071 | 0.013 | 0.36 | NO |
35 | PIK3CB | PIK3CB | PIK3CB | 9191 | 0.011 | 0.35 | NO |
36 | BAD | BAD | BAD | 9780 | -0.00056 | 0.32 | NO |
37 | RELA | RELA | RELA | 9850 | -0.0018 | 0.32 | NO |
38 | MAP2K2 | MAP2K2 | MAP2K2 | 10161 | -0.0085 | 0.3 | NO |
39 | MAPK1 | MAPK1 | MAPK1 | 10237 | -0.01 | 0.3 | NO |
40 | AKT1 | AKT1 | AKT1 | 10842 | -0.022 | 0.26 | NO |
41 | KRAS | KRAS | KRAS | 10908 | -0.023 | 0.26 | NO |
42 | TCF7L2 | TCF7L2 | TCF7L2 | 11051 | -0.026 | 0.26 | NO |
43 | MAPK3 | MAPK3 | MAPK3 | 11157 | -0.028 | 0.26 | NO |
44 | IKBKG | IKBKG | IKBKG | 11455 | -0.034 | 0.24 | NO |
45 | CHUK | CHUK | CHUK | 11542 | -0.036 | 0.24 | NO |
46 | PPARD | PPARD | PPARD | 12456 | -0.055 | 0.2 | NO |
47 | CCND1 | CCND1 | CCND1 | 12647 | -0.059 | 0.19 | NO |
48 | PIK3R2 | PIK3R2 | PIK3R2 | 13461 | -0.078 | 0.16 | NO |
49 | MYC | MYC | MYC | 13915 | -0.089 | 0.14 | NO |
50 | MAP2K1 | MAP2K1 | MAP2K1 | 13954 | -0.09 | 0.14 | NO |
51 | NRAS | NRAS | NRAS | 14139 | -0.095 | 0.14 | NO |
52 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 14652 | -0.11 | 0.12 | NO |
53 | CEBPA | CEBPA | CEBPA | 15385 | -0.14 | 0.098 | NO |
54 | CCNA1 | CCNA1 | CCNA1 | 16147 | -0.17 | 0.073 | NO |
55 | HRAS | HRAS | HRAS | 17024 | -0.23 | 0.046 | NO |
56 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 17055 | -0.23 | 0.065 | NO |
57 | JUP | JUP | JUP | 17683 | -0.29 | 0.057 | NO |
Figure S85. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ABC TRANSPORTERS.

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

Table 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 | BTK | BTK | BTK | 280 | 0.86 | 0.069 | YES |
2 | CD22 | CD22 | CD22 | 541 | 0.74 | 0.13 | YES |
3 | VAV1 | VAV1 | VAV1 | 625 | 0.71 | 0.19 | YES |
4 | MAP4K1 | MAP4K1 | MAP4K1 | 633 | 0.71 | 0.26 | YES |
5 | ITPR1 | ITPR1 | ITPR1 | 905 | 0.64 | 0.31 | YES |
6 | PTPRC | PTPRC | PTPRC | 1016 | 0.62 | 0.36 | YES |
7 | BCL2 | BCL2 | BCL2 | 1151 | 0.59 | 0.41 | YES |
8 | CD19 | CD19 | CD19 | 1393 | 0.54 | 0.45 | YES |
9 | PLCG2 | PLCG2 | PLCG2 | 1818 | 0.46 | 0.48 | YES |
10 | NFATC2 | NFATC2 | NFATC2 | 1823 | 0.46 | 0.52 | YES |
11 | INPP5D | INPP5D | INPP5D | 1889 | 0.45 | 0.56 | YES |
12 | AKT3 | AKT3 | AKT3 | 1994 | 0.43 | 0.6 | YES |
13 | CR2 | CR2 | CR2 | 2066 | 0.42 | 0.64 | YES |
14 | PIK3CD | PIK3CD | PIK3CD | 2845 | 0.32 | 0.62 | YES |
15 | PIK3R1 | PIK3R1 | PIK3R1 | 3194 | 0.28 | 0.63 | YES |
16 | NFATC1 | NFATC1 | NFATC1 | 3954 | 0.21 | 0.62 | YES |
17 | ITPR2 | ITPR2 | ITPR2 | 4094 | 0.2 | 0.63 | YES |
18 | PPP3CC | PPP3CC | PPP3CC | 4150 | 0.2 | 0.64 | YES |
19 | CD81 | CD81 | CD81 | 4806 | 0.16 | 0.62 | NO |
20 | SOS2 | SOS2 | SOS2 | 5457 | 0.12 | 0.6 | NO |
21 | BLNK | BLNK | BLNK | 5711 | 0.11 | 0.6 | NO |
22 | PPP3CB | PPP3CB | PPP3CB | 5754 | 0.11 | 0.61 | NO |
23 | PIK3CA | PIK3CA | PIK3CA | 6306 | 0.09 | 0.59 | NO |
24 | LYN | LYN | LYN | 7450 | 0.055 | 0.53 | NO |
25 | PDK1 | PDK1 | PDK1 | 7930 | 0.042 | 0.51 | NO |
26 | SYK | SYK | SYK | 7935 | 0.042 | 0.51 | NO |
27 | FLOT1 | FLOT1 | FLOT1 | 8001 | 0.04 | 0.51 | NO |
28 | SOS1 | SOS1 | SOS1 | 8517 | 0.027 | 0.49 | NO |
29 | AKT2 | AKT2 | AKT2 | 8672 | 0.023 | 0.48 | NO |
30 | PPP3CA | PPP3CA | PPP3CA | 8872 | 0.018 | 0.47 | NO |
31 | DAG1 | DAG1 | DAG1 | 8885 | 0.018 | 0.48 | NO |
32 | RAF1 | RAF1 | RAF1 | 8957 | 0.016 | 0.47 | NO |
33 | GRB2 | GRB2 | GRB2 | 9071 | 0.013 | 0.47 | NO |
34 | FLOT2 | FLOT2 | FLOT2 | 9335 | 0.0083 | 0.45 | NO |
35 | BAD | BAD | BAD | 9780 | -0.00056 | 0.43 | NO |
36 | MAPK1 | MAPK1 | MAPK1 | 10237 | -0.01 | 0.41 | NO |
37 | CSK | CSK | CSK | 10735 | -0.02 | 0.38 | NO |
38 | AKT1 | AKT1 | AKT1 | 10842 | -0.022 | 0.38 | NO |
39 | SHC1 | SHC1 | SHC1 | 11142 | -0.028 | 0.37 | NO |
40 | MAPK3 | MAPK3 | MAPK3 | 11157 | -0.028 | 0.37 | NO |
41 | GSK3B | GSK3B | GSK3B | 11562 | -0.036 | 0.35 | NO |
42 | GSK3A | GSK3A | GSK3A | 11893 | -0.043 | 0.34 | NO |
43 | PPP1R13B | PPP1R13B | PPP1R13B | 12120 | -0.047 | 0.33 | NO |
44 | BCR | BCR | BCR | 12502 | -0.056 | 0.31 | NO |
45 | NR0B2 | NR0B2 | NR0B2 | 13976 | -0.09 | 0.24 | NO |
46 | ITPR3 | ITPR3 | ITPR3 | 14717 | -0.11 | 0.22 | NO |
Figure S87. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG MAPK SIGNALING PATHWAY.

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

Table S45. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | FCER1A | FCER1A | FCER1A | 260 | 0.86 | 0.044 | YES |
2 | ITK | ITK | ITK | 278 | 0.86 | 0.1 | YES |
3 | BTK | BTK | BTK | 280 | 0.86 | 0.16 | YES |
4 | KLRG1 | KLRG1 | KLRG1 | 302 | 0.84 | 0.22 | YES |
5 | PRKCB | PRKCB | PRKCB | 319 | 0.83 | 0.27 | YES |
6 | FCGR2B | FCGR2B | FCGR2B | 342 | 0.82 | 0.32 | YES |
7 | VAV1 | VAV1 | VAV1 | 625 | 0.71 | 0.36 | YES |
8 | MS4A2 | MS4A2 | MS4A2 | 914 | 0.64 | 0.38 | YES |
9 | S1PR1 | S1PR1 | S1PR1 | 975 | 0.63 | 0.42 | YES |
10 | LAT | LAT | LAT | 1224 | 0.57 | 0.45 | YES |
11 | LAT2 | LAT2 | LAT2 | 1418 | 0.54 | 0.48 | YES |
12 | HCLS1 | HCLS1 | HCLS1 | 1471 | 0.52 | 0.51 | YES |
13 | LCP2 | LCP2 | LCP2 | 1731 | 0.48 | 0.53 | YES |
14 | NFATC2 | NFATC2 | NFATC2 | 1823 | 0.46 | 0.55 | YES |
15 | INPP5D | INPP5D | INPP5D | 1889 | 0.45 | 0.58 | YES |
16 | WIPF1 | WIPF1 | WIPF1 | 1931 | 0.44 | 0.61 | YES |
17 | FCER1G | FCER1G | FCER1G | 2602 | 0.35 | 0.6 | YES |
18 | PPAP2A | PPAP2A | PPAP2A | 2686 | 0.34 | 0.61 | YES |
19 | FYN | FYN | FYN | 2797 | 0.33 | 0.63 | YES |
20 | PIK3R1 | PIK3R1 | PIK3R1 | 3194 | 0.28 | 0.63 | NO |
21 | GAB2 | GAB2 | GAB2 | 3939 | 0.22 | 0.6 | NO |
22 | DUSP1 | DUSP1 | DUSP1 | 3977 | 0.21 | 0.62 | NO |
23 | DOK1 | DOK1 | DOK1 | 4131 | 0.2 | 0.62 | NO |
24 | PLA2G1B | PLA2G1B | PLA2G1B | 4456 | 0.18 | 0.62 | NO |
25 | PLCG1 | PLCG1 | PLCG1 | 5718 | 0.11 | 0.56 | NO |
26 | MAP3K1 | MAP3K1 | MAP3K1 | 5776 | 0.11 | 0.56 | NO |
27 | CBLB | CBLB | CBLB | 5823 | 0.11 | 0.56 | NO |
28 | FOS | FOS | FOS | 6241 | 0.092 | 0.55 | NO |
29 | PIK3CA | PIK3CA | PIK3CA | 6306 | 0.09 | 0.55 | NO |
30 | NFKB1 | NFKB1 | NFKB1 | 6664 | 0.078 | 0.54 | NO |
31 | IKBKB | IKBKB | IKBKB | 6765 | 0.074 | 0.54 | NO |
32 | CBL | CBL | CBL | 6956 | 0.068 | 0.53 | NO |
33 | LYN | LYN | LYN | 7450 | 0.055 | 0.51 | NO |
34 | MAP2K7 | MAP2K7 | MAP2K7 | 7493 | 0.053 | 0.51 | NO |
35 | RASA1 | RASA1 | RASA1 | 7517 | 0.053 | 0.51 | NO |
36 | FER | FER | FER | 7770 | 0.045 | 0.5 | NO |
37 | SYK | SYK | SYK | 7935 | 0.042 | 0.5 | NO |
38 | PTPN13 | PTPN13 | PTPN13 | 8049 | 0.039 | 0.49 | NO |
39 | SPHK1 | SPHK1 | SPHK1 | 8215 | 0.034 | 0.48 | NO |
40 | JUN | JUN | JUN | 8357 | 0.031 | 0.48 | NO |
41 | SOS1 | SOS1 | SOS1 | 8517 | 0.027 | 0.47 | NO |
42 | RAF1 | RAF1 | RAF1 | 8957 | 0.016 | 0.45 | NO |
43 | GRB2 | GRB2 | GRB2 | 9071 | 0.013 | 0.45 | NO |
44 | PTPN11 | PTPN11 | PTPN11 | 9307 | 0.0089 | 0.43 | NO |
45 | RELA | RELA | RELA | 9850 | -0.0018 | 0.4 | NO |
46 | MAP2K2 | MAP2K2 | MAP2K2 | 10161 | -0.0085 | 0.39 | NO |
47 | PAK2 | PAK2 | PAK2 | 10232 | -0.01 | 0.39 | NO |
48 | MAPK1 | MAPK1 | MAPK1 | 10237 | -0.01 | 0.39 | NO |
49 | AKT1 | AKT1 | AKT1 | 10842 | -0.022 | 0.36 | NO |
50 | SHC1 | SHC1 | SHC1 | 11142 | -0.028 | 0.34 | NO |
51 | MAPK3 | MAPK3 | MAPK3 | 11157 | -0.028 | 0.34 | NO |
52 | IKBKG | IKBKG | IKBKG | 11455 | -0.034 | 0.33 | NO |
53 | MAP2K4 | MAP2K4 | MAP2K4 | 11499 | -0.035 | 0.33 | NO |
54 | CHUK | CHUK | CHUK | 11542 | -0.036 | 0.33 | NO |
55 | PXN | PXN | PXN | 11794 | -0.041 | 0.32 | NO |
56 | PLD2 | PLD2 | PLD2 | 12358 | -0.053 | 0.29 | NO |
57 | PTK2 | PTK2 | PTK2 | 12846 | -0.064 | 0.27 | NO |
58 | MAP2K1 | MAP2K1 | MAP2K1 | 13954 | -0.09 | 0.22 | NO |
59 | MAPK8 | MAPK8 | MAPK8 | 14059 | -0.093 | 0.22 | NO |
60 | HRAS | HRAS | HRAS | 17024 | -0.23 | 0.075 | NO |
61 | PLA2G4A | PLA2G4A | PLA2G4A | 17372 | -0.26 | 0.074 | NO |
Figure S89. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CALCIUM SIGNALING PATHWAY.

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

Table S46. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | VAV1 | VAV1 | VAV1 | 625 | 0.71 | 0.04 | YES |
2 | KIT | KIT | KIT | 630 | 0.71 | 0.11 | YES |
3 | MAP4K1 | MAP4K1 | MAP4K1 | 633 | 0.71 | 0.18 | YES |
4 | STAP1 | STAP1 | STAP1 | 659 | 0.7 | 0.26 | YES |
5 | GRAP2 | GRAP2 | GRAP2 | 746 | 0.68 | 0.32 | YES |
6 | BCL2 | BCL2 | BCL2 | 1151 | 0.59 | 0.36 | YES |
7 | MITF | MITF | MITF | 1182 | 0.58 | 0.42 | YES |
8 | MATK | MATK | MATK | 1664 | 0.49 | 0.44 | YES |
9 | PTPRO | PTPRO | PTPRO | 2244 | 0.4 | 0.45 | YES |
10 | PIK3R1 | PIK3R1 | PIK3R1 | 3194 | 0.28 | 0.43 | YES |
11 | SH2B2 | SH2B2 | SH2B2 | 3286 | 0.27 | 0.45 | YES |
12 | STAT5A | STAT5A | STAT5A | 3423 | 0.26 | 0.47 | YES |
13 | JAK2 | JAK2 | JAK2 | 3425 | 0.26 | 0.5 | YES |
14 | SH2B3 | SH2B3 | SH2B3 | 3668 | 0.24 | 0.51 | YES |
15 | GAB1 | GAB1 | GAB1 | 3792 | 0.23 | 0.53 | YES |
16 | EPOR | EPOR | EPOR | 4130 | 0.2 | 0.53 | YES |
17 | DOK1 | DOK1 | DOK1 | 4131 | 0.2 | 0.55 | YES |
18 | SOCS1 | SOCS1 | SOCS1 | 4271 | 0.19 | 0.56 | YES |
19 | TEC | TEC | TEC | 4579 | 0.17 | 0.56 | YES |
20 | PTPN6 | PTPN6 | PTPN6 | 4889 | 0.15 | 0.56 | NO |
21 | KITLG | KITLG | KITLG | 6150 | 0.095 | 0.5 | NO |
22 | PIK3CA | PIK3CA | PIK3CA | 6306 | 0.09 | 0.51 | NO |
23 | PIK3C2B | PIK3C2B | PIK3C2B | 6778 | 0.074 | 0.49 | NO |
24 | CBL | CBL | CBL | 6956 | 0.068 | 0.49 | NO |
25 | PTEN | PTEN | PTEN | 6974 | 0.068 | 0.49 | NO |
26 | STAT1 | STAT1 | STAT1 | 7136 | 0.063 | 0.49 | NO |
27 | FOXO3 | FOXO3 | FOXO3 | 7341 | 0.058 | 0.48 | NO |
28 | LYN | LYN | LYN | 7450 | 0.055 | 0.48 | NO |
29 | FER | FER | FER | 7770 | 0.045 | 0.47 | NO |
30 | CREBBP | CREBBP | CREBBP | 7811 | 0.044 | 0.48 | NO |
31 | SPRED1 | SPRED1 | SPRED1 | 8374 | 0.031 | 0.45 | NO |
32 | SOS1 | SOS1 | SOS1 | 8517 | 0.027 | 0.44 | NO |
33 | STAT3 | STAT3 | STAT3 | 8641 | 0.024 | 0.44 | NO |
34 | RAF1 | RAF1 | RAF1 | 8957 | 0.016 | 0.42 | NO |
35 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 9041 | 0.014 | 0.42 | NO |
36 | GRB2 | GRB2 | GRB2 | 9071 | 0.013 | 0.42 | NO |
37 | PTPN11 | PTPN11 | PTPN11 | 9307 | 0.0089 | 0.41 | NO |
38 | SNAI2 | SNAI2 | SNAI2 | 9627 | 0.0026 | 0.39 | NO |
39 | BAD | BAD | BAD | 9780 | -0.00056 | 0.38 | NO |
40 | MAP2K2 | MAP2K2 | MAP2K2 | 10161 | -0.0085 | 0.36 | NO |
41 | PDPK1 | PDPK1 | PDPK1 | 10781 | -0.021 | 0.33 | NO |
42 | AKT1 | AKT1 | AKT1 | 10842 | -0.022 | 0.33 | NO |
43 | SHC1 | SHC1 | SHC1 | 11142 | -0.028 | 0.32 | NO |
44 | MAPK3 | MAPK3 | MAPK3 | 11157 | -0.028 | 0.32 | NO |
45 | SPRED2 | SPRED2 | SPRED2 | 11268 | -0.03 | 0.32 | NO |
46 | GSK3B | GSK3B | GSK3B | 11562 | -0.036 | 0.31 | NO |
47 | CRKL | CRKL | CRKL | 12903 | -0.065 | 0.24 | NO |
48 | GRB10 | GRB10 | GRB10 | 12933 | -0.066 | 0.25 | NO |
49 | MAP2K1 | MAP2K1 | MAP2K1 | 13954 | -0.09 | 0.2 | NO |
50 | MAPK8 | MAPK8 | MAPK8 | 14059 | -0.093 | 0.21 | NO |
51 | EPO | EPO | EPO | 16688 | -0.2 | 0.086 | NO |
52 | HRAS | HRAS | HRAS | 17024 | -0.23 | 0.092 | NO |
Figure S91. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION.

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

Table 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 | BTK | BTK | BTK | 280 | 0.86 | 0.091 | YES |
2 | PIK3R5 | PIK3R5 | PIK3R5 | 589 | 0.72 | 0.16 | YES |
3 | VAV1 | VAV1 | VAV1 | 625 | 0.71 | 0.25 | YES |
4 | ITPR1 | ITPR1 | ITPR1 | 905 | 0.64 | 0.32 | YES |
5 | PTPRC | PTPRC | PTPRC | 1016 | 0.62 | 0.39 | YES |
6 | CD19 | CD19 | CD19 | 1393 | 0.54 | 0.43 | YES |
7 | NR4A3 | NR4A3 | NR4A3 | 1530 | 0.51 | 0.49 | YES |
8 | PLCG2 | PLCG2 | PLCG2 | 1818 | 0.46 | 0.53 | YES |
9 | PREX1 | PREX1 | PREX1 | 1883 | 0.45 | 0.58 | YES |
10 | AKT3 | AKT3 | AKT3 | 1994 | 0.43 | 0.63 | YES |
11 | GAB1 | GAB1 | GAB1 | 3792 | 0.23 | 0.56 | NO |
12 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 3868 | 0.22 | 0.59 | NO |
13 | ITPR2 | ITPR2 | ITPR2 | 4094 | 0.2 | 0.6 | NO |
14 | DAPP1 | DAPP1 | DAPP1 | 4273 | 0.19 | 0.61 | NO |
15 | CYTH3 | CYTH3 | CYTH3 | 5922 | 0.1 | 0.54 | NO |
16 | PIK3CA | PIK3CA | PIK3CA | 6306 | 0.09 | 0.53 | NO |
17 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 6506 | 0.083 | 0.53 | NO |
18 | PHF11 | PHF11 | PHF11 | 6524 | 0.082 | 0.54 | NO |
19 | PTEN | PTEN | PTEN | 6974 | 0.068 | 0.52 | NO |
20 | FOXO3 | FOXO3 | FOXO3 | 7341 | 0.058 | 0.51 | NO |
21 | LYN | LYN | LYN | 7450 | 0.055 | 0.51 | NO |
22 | PDK1 | PDK1 | PDK1 | 7930 | 0.042 | 0.49 | NO |
23 | SYK | SYK | SYK | 7935 | 0.042 | 0.5 | NO |
24 | FLOT1 | FLOT1 | FLOT1 | 8001 | 0.04 | 0.5 | NO |
25 | AKT2 | AKT2 | AKT2 | 8672 | 0.023 | 0.46 | NO |
26 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 9041 | 0.014 | 0.45 | NO |
27 | PITX2 | PITX2 | PITX2 | 9210 | 0.011 | 0.44 | NO |
28 | FLOT2 | FLOT2 | FLOT2 | 9335 | 0.0083 | 0.43 | NO |
29 | AKT1 | AKT1 | AKT1 | 10842 | -0.022 | 0.36 | NO |
30 | PPP1R13B | PPP1R13B | PPP1R13B | 12120 | -0.047 | 0.29 | NO |
31 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 12422 | -0.054 | 0.28 | NO |
32 | BCR | BCR | BCR | 12502 | -0.056 | 0.29 | NO |
33 | NR0B2 | NR0B2 | NR0B2 | 13976 | -0.09 | 0.22 | NO |
34 | ITPR3 | ITPR3 | ITPR3 | 14717 | -0.11 | 0.19 | NO |
35 | CDKN2A | CDKN2A | CDKN2A | 16228 | -0.18 | 0.14 | NO |
Figure S93. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY.

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

Table 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 | TLR10 | TLR10 | TLR10 | 54 | 1.1 | 0.16 | YES |
2 | TLR7 | TLR7 | TLR7 | 186 | 0.91 | 0.29 | YES |
3 | TLR9 | TLR9 | TLR9 | 889 | 0.64 | 0.34 | YES |
4 | TLR4 | TLR4 | TLR4 | 939 | 0.63 | 0.44 | YES |
5 | LY96 | LY96 | LY96 | 1135 | 0.59 | 0.51 | YES |
6 | TLR6 | TLR6 | TLR6 | 1630 | 0.49 | 0.56 | YES |
7 | MAP3K14 | MAP3K14 | MAP3K14 | 2960 | 0.31 | 0.53 | YES |
8 | CD14 | CD14 | CD14 | 2986 | 0.3 | 0.58 | YES |
9 | TLR3 | TLR3 | TLR3 | 4061 | 0.2 | 0.55 | NO |
10 | PGLYRP1 | PGLYRP1 | PGLYRP1 | 4415 | 0.18 | 0.56 | NO |
11 | TIRAP | TIRAP | TIRAP | 5643 | 0.12 | 0.51 | NO |
12 | MAP3K1 | MAP3K1 | MAP3K1 | 5776 | 0.11 | 0.52 | NO |
13 | FOS | FOS | FOS | 6241 | 0.092 | 0.51 | NO |
14 | NFKB1 | NFKB1 | NFKB1 | 6664 | 0.078 | 0.5 | NO |
15 | IKBKB | IKBKB | IKBKB | 6765 | 0.074 | 0.5 | NO |
16 | TAB1 | TAB1 | TAB1 | 7231 | 0.061 | 0.49 | NO |
17 | TLR2 | TLR2 | TLR2 | 7321 | 0.059 | 0.49 | NO |
18 | TAB2 | TAB2 | TAB2 | 7522 | 0.052 | 0.49 | NO |
19 | NFKBIA | NFKBIA | NFKBIA | 8099 | 0.038 | 0.46 | NO |
20 | JUN | JUN | JUN | 8357 | 0.031 | 0.45 | NO |
21 | TRAF6 | TRAF6 | TRAF6 | 8677 | 0.023 | 0.44 | NO |
22 | PPARA | PPARA | PPARA | 9726 | 0.00057 | 0.38 | NO |
23 | MAPK14 | MAPK14 | MAPK14 | 9842 | -0.0016 | 0.38 | NO |
24 | RELA | RELA | RELA | 9850 | -0.0018 | 0.38 | NO |
25 | ELK1 | ELK1 | ELK1 | 10073 | -0.0066 | 0.37 | NO |
26 | MYD88 | MYD88 | MYD88 | 10242 | -0.01 | 0.36 | NO |
27 | ECSIT | ECSIT | ECSIT | 10451 | -0.015 | 0.35 | NO |
28 | MAP3K7 | MAP3K7 | MAP3K7 | 10559 | -0.017 | 0.35 | NO |
29 | IKBKG | IKBKG | IKBKG | 11455 | -0.034 | 0.3 | NO |
30 | MAP2K4 | MAP2K4 | MAP2K4 | 11499 | -0.035 | 0.31 | NO |
31 | CHUK | CHUK | CHUK | 11542 | -0.036 | 0.31 | NO |
32 | TOLLIP | TOLLIP | TOLLIP | 12184 | -0.049 | 0.28 | NO |
33 | MAP2K6 | MAP2K6 | MAP2K6 | 12394 | -0.054 | 0.28 | NO |
34 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 13957 | -0.09 | 0.21 | NO |
35 | MAPK8 | MAPK8 | MAPK8 | 14059 | -0.093 | 0.22 | NO |
36 | MAP2K3 | MAP2K3 | MAP2K3 | 14140 | -0.095 | 0.23 | NO |
37 | IRAK1 | IRAK1 | IRAK1 | 15253 | -0.13 | 0.19 | NO |
Figure S95. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM.

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

Table S49. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | ITGA8 | ITGA8 | ITGA8 | 135 | 0.95 | 0.03 | YES |
2 | PIK3R6 | PIK3R6 | PIK3R6 | 287 | 0.85 | 0.056 | YES |
3 | CXCL12 | CXCL12 | CXCL12 | 358 | 0.82 | 0.084 | YES |
4 | ITGA9 | ITGA9 | ITGA9 | 425 | 0.78 | 0.11 | YES |
5 | PIK3CG | PIK3CG | PIK3CG | 466 | 0.77 | 0.14 | YES |
6 | PIK3R5 | PIK3R5 | PIK3R5 | 589 | 0.72 | 0.16 | YES |
7 | VAV1 | VAV1 | VAV1 | 625 | 0.71 | 0.19 | YES |
8 | ITGA7 | ITGA7 | ITGA7 | 628 | 0.71 | 0.22 | YES |
9 | GNAO1 | GNAO1 | GNAO1 | 646 | 0.7 | 0.24 | YES |
10 | ITGA10 | ITGA10 | ITGA10 | 798 | 0.66 | 0.26 | YES |
11 | CD3G | CD3G | CD3G | 849 | 0.65 | 0.28 | YES |
12 | FGR | FGR | FGR | 902 | 0.64 | 0.3 | YES |
13 | CD3E | CD3E | CD3E | 990 | 0.62 | 0.32 | YES |
14 | PTPRC | PTPRC | PTPRC | 1016 | 0.62 | 0.35 | YES |
15 | PLCB2 | PLCB2 | PLCB2 | 1048 | 0.61 | 0.37 | YES |
16 | CD247 | CD247 | CD247 | 1126 | 0.59 | 0.39 | YES |
17 | BLK | BLK | BLK | 1195 | 0.58 | 0.41 | YES |
18 | CD3D | CD3D | CD3D | 1245 | 0.57 | 0.43 | YES |
19 | ITGA4 | ITGA4 | ITGA4 | 1354 | 0.55 | 0.44 | YES |
20 | CD4 | CD4 | CD4 | 1455 | 0.53 | 0.46 | YES |
21 | LCK | LCK | LCK | 1469 | 0.53 | 0.48 | YES |
22 | GNG2 | GNG2 | GNG2 | 1498 | 0.52 | 0.5 | YES |
23 | CXCR4 | CXCR4 | CXCR4 | 1555 | 0.51 | 0.52 | YES |
24 | RGS1 | RGS1 | RGS1 | 1675 | 0.49 | 0.53 | YES |
25 | INPP5D | INPP5D | INPP5D | 1889 | 0.45 | 0.53 | YES |
26 | HCK | HCK | HCK | 1937 | 0.44 | 0.55 | YES |
27 | GNAZ | GNAZ | GNAZ | 2055 | 0.42 | 0.56 | YES |
28 | ITGA11 | ITGA11 | ITGA11 | 2127 | 0.41 | 0.57 | YES |
29 | ITGA1 | ITGA1 | ITGA1 | 2517 | 0.36 | 0.56 | YES |
30 | HLA-DRB1 | HLA-DRB1 | HLA-DRB1 | 2649 | 0.34 | 0.57 | YES |
31 | HLA-DRA | HLA-DRA | HLA-DRA | 2698 | 0.34 | 0.58 | YES |
32 | FYN | FYN | FYN | 2797 | 0.33 | 0.59 | YES |
33 | PIK3CD | PIK3CD | PIK3CD | 2845 | 0.32 | 0.6 | YES |
34 | PIK3R1 | PIK3R1 | PIK3R1 | 3194 | 0.28 | 0.59 | YES |
35 | STAT5A | STAT5A | STAT5A | 3423 | 0.26 | 0.59 | YES |
36 | JAK2 | JAK2 | JAK2 | 3425 | 0.26 | 0.6 | YES |
37 | MMP9 | MMP9 | MMP9 | 3622 | 0.24 | 0.6 | NO |
38 | PAG1 | PAG1 | PAG1 | 4411 | 0.18 | 0.56 | NO |
39 | STAT5B | STAT5B | STAT5B | 4489 | 0.18 | 0.57 | NO |
40 | FOXO1 | FOXO1 | FOXO1 | 4544 | 0.17 | 0.57 | NO |
41 | PLCB1 | PLCB1 | PLCB1 | 4587 | 0.17 | 0.58 | NO |
42 | ARRB2 | ARRB2 | ARRB2 | 4623 | 0.17 | 0.58 | NO |
43 | PIK3R3 | PIK3R3 | PIK3R3 | 4641 | 0.17 | 0.59 | NO |
44 | PTPN6 | PTPN6 | PTPN6 | 4889 | 0.15 | 0.58 | NO |
45 | GNAI2 | GNAI2 | GNAI2 | 5053 | 0.14 | 0.58 | NO |
46 | ITGAV | ITGAV | ITGAV | 5316 | 0.13 | 0.57 | NO |
47 | RHOB | RHOB | RHOB | 5366 | 0.13 | 0.57 | NO |
48 | STAT2 | STAT2 | STAT2 | 5379 | 0.13 | 0.57 | NO |
49 | DNM1 | DNM1 | DNM1 | 6000 | 0.1 | 0.55 | NO |
50 | SSH1 | SSH1 | SSH1 | 6023 | 0.1 | 0.55 | NO |
51 | ITGA5 | ITGA5 | ITGA5 | 6119 | 0.096 | 0.55 | NO |
52 | PIK3CA | PIK3CA | PIK3CA | 6306 | 0.09 | 0.54 | NO |
53 | RICTOR | RICTOR | RICTOR | 6724 | 0.076 | 0.52 | NO |
54 | ITGB1 | ITGB1 | ITGB1 | 6891 | 0.07 | 0.51 | NO |
55 | PTK2B | PTK2B | PTK2B | 6900 | 0.07 | 0.52 | NO |
56 | PTEN | PTEN | PTEN | 6974 | 0.068 | 0.52 | NO |
57 | STAT1 | STAT1 | STAT1 | 7136 | 0.063 | 0.51 | NO |
58 | GNA13 | GNA13 | GNA13 | 7330 | 0.058 | 0.5 | NO |
59 | LYN | LYN | LYN | 7450 | 0.055 | 0.5 | NO |
60 | RAP1B | RAP1B | RAP1B | 8087 | 0.038 | 0.46 | NO |
61 | RHOA | RHOA | RHOA | 8254 | 0.033 | 0.46 | NO |
62 | MTOR | MTOR | MTOR | 8400 | 0.03 | 0.45 | NO |
63 | STAT3 | STAT3 | STAT3 | 8641 | 0.024 | 0.44 | NO |
64 | GNB1 | GNB1 | GNB1 | 8671 | 0.023 | 0.44 | NO |
65 | LIMK1 | LIMK1 | LIMK1 | 8732 | 0.021 | 0.44 | NO |
66 | ADRBK1 | ADRBK1 | ADRBK1 | 8747 | 0.021 | 0.44 | NO |
67 | PIK3CB | PIK3CB | PIK3CB | 9191 | 0.011 | 0.41 | NO |
68 | GRK6 | GRK6 | GRK6 | 9223 | 0.01 | 0.41 | NO |
69 | PTPN11 | PTPN11 | PTPN11 | 9307 | 0.0089 | 0.41 | NO |
70 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 9570 | 0.0035 | 0.39 | NO |
71 | BAD | BAD | BAD | 9780 | -0.00056 | 0.38 | NO |
72 | GNAI1 | GNAI1 | GNAI1 | 10047 | -0.0059 | 0.37 | NO |
73 | CDC42 | CDC42 | CDC42 | 10168 | -0.0086 | 0.36 | NO |
74 | ITCH | ITCH | ITCH | 10194 | -0.0091 | 0.36 | NO |
75 | GNB2L1 | GNB2L1 | GNB2L1 | 10375 | -0.013 | 0.35 | NO |
76 | CSK | CSK | CSK | 10735 | -0.02 | 0.33 | NO |
77 | PDPK1 | PDPK1 | PDPK1 | 10781 | -0.021 | 0.33 | NO |
78 | CRK | CRK | CRK | 10836 | -0.022 | 0.33 | NO |
79 | AKT1 | AKT1 | AKT1 | 10842 | -0.022 | 0.33 | NO |
80 | RHOC | RHOC | RHOC | 11354 | -0.032 | 0.3 | NO |
81 | VPS4A | VPS4A | VPS4A | 11366 | -0.032 | 0.3 | NO |
82 | PXN | PXN | PXN | 11794 | -0.041 | 0.28 | NO |
83 | PAK1 | PAK1 | PAK1 | 12097 | -0.047 | 0.27 | NO |
84 | ARR3 | ARR3 | ARR3 | 12509 | -0.056 | 0.25 | NO |
85 | PTK2 | PTK2 | PTK2 | 12846 | -0.064 | 0.23 | NO |
86 | UBQLN1 | UBQLN1 | UBQLN1 | 13065 | -0.069 | 0.22 | NO |
87 | ITGA2 | ITGA2 | ITGA2 | 13103 | -0.07 | 0.22 | NO |
88 | CFL1 | CFL1 | CFL1 | 13239 | -0.073 | 0.22 | NO |
89 | GNAI3 | GNAI3 | GNAI3 | 13389 | -0.076 | 0.22 | NO |
90 | PIK3R2 | PIK3R2 | PIK3R2 | 13461 | -0.078 | 0.22 | NO |
91 | RALB | RALB | RALB | 14415 | -0.1 | 0.17 | NO |
92 | HGS | HGS | HGS | 14469 | -0.1 | 0.17 | NO |
93 | RAC1 | RAC1 | RAC1 | 14861 | -0.12 | 0.15 | NO |
94 | BCAR1 | BCAR1 | BCAR1 | 15014 | -0.12 | 0.15 | NO |
95 | VPS4B | VPS4B | VPS4B | 15015 | -0.12 | 0.15 | NO |
96 | MLST8 | MLST8 | MLST8 | 15033 | -0.12 | 0.16 | NO |
97 | SRC | SRC | SRC | 15611 | -0.15 | 0.13 | NO |
98 | ITGA3 | ITGA3 | ITGA3 | 15736 | -0.15 | 0.13 | NO |
99 | PRKCZ | PRKCZ | PRKCZ | 16193 | -0.17 | 0.11 | NO |
100 | YES1 | YES1 | YES1 | 16269 | -0.18 | 0.12 | NO |
101 | ITGA6 | ITGA6 | ITGA6 | 16344 | -0.18 | 0.12 | NO |
102 | PLCB3 | PLCB3 | PLCB3 | 16755 | -0.21 | 0.11 | NO |
Figure S97. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION.

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

Table S50. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.
Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT |
---|---|---|---|---|---|---|---|
1 | PIK3R6 | PIK3R6 | PIK3R6 | 287 | 0.85 | 0.027 | YES |
2 | MYOCD | MYOCD | MYOCD | 298 | 0.84 | 0.068 | YES |
3 | PIK3CG | PIK3CG | PIK3CG | 466 | 0.77 | 0.097 | YES |
4 | PIK3R5 | PIK3R5 | PIK3R5 | 589 | 0.72 | 0.13 | YES |
5 | FGR | FGR | FGR | 902 | 0.64 | 0.14 | YES |
6 | S1PR1 | S1PR1 | S1PR1 | 975 | 0.63 | 0.17 | YES |
7 | SLA | SLA | SLA | 1027 | 0.62 | 0.2 | YES |
8 | ITGB3 | ITGB3 | ITGB3 | 1140 | 0.59 | 0.22 | YES |
9 | BLK | BLK | BLK | 1195 | 0.58 | 0.25 | YES |
10 | TAGLN | TAGLN | TAGLN | 1325 | 0.55 | 0.27 | YES |
11 | LCK | LCK | LCK | 1469 | 0.53 | 0.28 | YES |
12 | ACTA2 | ACTA2 | ACTA2 | 1543 | 0.51 | 0.31 | YES |
13 | MAPK10 | MAPK10 | MAPK10 | 1557 | 0.51 | 0.33 | YES |
14 | CYFIP2 | CYFIP2 | CYFIP2 | 1680 | 0.48 | 0.35 | YES |
15 | HCK | HCK | HCK | 1937 | 0.44 | 0.36 | YES |
16 | PPP2R2B | PPP2R2B | PPP2R2B | 2121 | 0.41 | 0.37 | YES |
17 | FYN | FYN | FYN | 2797 | 0.33 | 0.35 | YES |
18 | PIK3CD | PIK3CD | PIK3CD | 2845 | 0.32 | 0.36 | YES |
19 | PDGFRB | PDGFRB | PDGFRB | 3000 | 0.3 | 0.37 | YES |
20 | PIK3R1 | PIK3R1 | PIK3R1 | 3194 | 0.28 | 0.37 | YES |
21 | STAT5A | STAT5A | STAT5A | 3423 | 0.26 | 0.37 | YES |
22 | JAK2 | JAK2 | JAK2 | 3425 | 0.26 | 0.38 | YES |
23 | DOCK4 | DOCK4 | DOCK4 | 3529 | 0.25 | 0.39 | YES |
24 | GAB1 | GAB1 | GAB1 | 3792 | 0.23 | 0.39 | YES |
25 | SIPA1 | SIPA1 | SIPA1 | 3829 | 0.22 | 0.4 | YES |
26 | DOK1 | DOK1 | DOK1 | 4131 | 0.2 | 0.39 | YES |
27 | RAP1A | RAP1A | RAP1A | 4284 | 0.19 | 0.39 | YES |
28 | PAG1 | PAG1 | PAG1 | 4411 | 0.18 | 0.4 | YES |
29 | STAT5B | STAT5B | STAT5B | 4489 | 0.18 | 0.4 | YES |
30 | PIK3R3 | PIK3R3 | PIK3R3 | 4641 | 0.17 | 0.4 | YES |
31 | PDGFB | PDGFB | PDGFB | 4682 | 0.16 | 0.41 | YES |
32 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 4855 | 0.16 | 0.4 | NO |
33 | PTPRJ | PTPRJ | PTPRJ | 5024 | 0.15 | 0.4 | NO |
34 | ITGAV | ITGAV | ITGAV | 5316 | 0.13 | 0.39 | NO |
35 | PRKCE | PRKCE | PRKCE | 5438 | 0.12 | 0.39 | NO |
36 | PLCG1 | PLCG1 | PLCG1 | 5718 | 0.11 | 0.38 | NO |
37 | ABL1 | ABL1 | ABL1 | 5725 | 0.11 | 0.39 | NO |
38 | LRP1 | LRP1 | LRP1 | 5833 | 0.11 | 0.39 | NO |
39 | PRKCA | PRKCA | PRKCA | 5896 | 0.1 | 0.39 | NO |
40 | SLC9A3R2 | SLC9A3R2 | SLC9A3R2 | 6087 | 0.098 | 0.38 | NO |
41 | FOS | FOS | FOS | 6241 | 0.092 | 0.38 | NO |
42 | PIK3CA | PIK3CA | PIK3CA | 6306 | 0.09 | 0.38 | NO |
43 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 6506 | 0.083 | 0.38 | NO |
44 | EPS8 | EPS8 | EPS8 | 6816 | 0.073 | 0.36 | NO |
45 | ARAP1 | ARAP1 | ARAP1 | 6904 | 0.07 | 0.36 | NO |
46 | CBL | CBL | CBL | 6956 | 0.068 | 0.36 | NO |
47 | PTEN | PTEN | PTEN | 6974 | 0.068 | 0.36 | NO |
48 | STAT1 | STAT1 | STAT1 | 7136 | 0.063 | 0.36 | NO |
49 | YWHAH | YWHAH | YWHAH | 7168 | 0.062 | 0.36 | NO |
50 | LYN | LYN | LYN | 7450 | 0.055 | 0.35 | NO |
51 | MAP2K7 | MAP2K7 | MAP2K7 | 7493 | 0.053 | 0.35 | NO |
52 | RASA1 | RASA1 | RASA1 | 7517 | 0.053 | 0.35 | NO |
53 | BRAF | BRAF | BRAF | 7839 | 0.044 | 0.34 | NO |
54 | SRF | SRF | SRF | 8083 | 0.038 | 0.32 | NO |
55 | RAP1B | RAP1B | RAP1B | 8087 | 0.038 | 0.32 | NO |
56 | SPHK1 | SPHK1 | SPHK1 | 8215 | 0.034 | 0.32 | NO |
57 | RHOA | RHOA | RHOA | 8254 | 0.033 | 0.32 | NO |
58 | NCK1 | NCK1 | NCK1 | 8310 | 0.032 | 0.32 | NO |
59 | JUN | JUN | JUN | 8357 | 0.031 | 0.32 | NO |
60 | SOS1 | SOS1 | SOS1 | 8517 | 0.027 | 0.31 | NO |
61 | JUND | JUND | JUND | 8583 | 0.026 | 0.31 | NO |
62 | STAT3 | STAT3 | STAT3 | 8641 | 0.024 | 0.31 | NO |
63 | KSR1 | KSR1 | KSR1 | 8881 | 0.018 | 0.29 | NO |
64 | RAF1 | RAF1 | RAF1 | 8957 | 0.016 | 0.29 | NO |
65 | PTPN1 | PTPN1 | PTPN1 | 9051 | 0.014 | 0.29 | NO |
66 | GRB2 | GRB2 | GRB2 | 9071 | 0.013 | 0.29 | NO |
67 | PIN1 | PIN1 | PIN1 | 9116 | 0.012 | 0.28 | NO |
68 | PIK3CB | PIK3CB | PIK3CB | 9191 | 0.011 | 0.28 | NO |
69 | PTPN11 | PTPN11 | PTPN11 | 9307 | 0.0089 | 0.28 | NO |
70 | MAPK9 | MAPK9 | MAPK9 | 9618 | 0.0027 | 0.26 | NO |
71 | ELK1 | ELK1 | ELK1 | 10073 | -0.0066 | 0.24 | NO |
72 | MAP2K2 | MAP2K2 | MAP2K2 | 10161 | -0.0085 | 0.23 | NO |
73 | WASF2 | WASF2 | WASF2 | 10211 | -0.0095 | 0.23 | NO |
74 | MAPK1 | MAPK1 | MAPK1 | 10237 | -0.01 | 0.23 | NO |
75 | IQGAP1 | IQGAP1 | IQGAP1 | 10404 | -0.014 | 0.22 | NO |
76 | ARPC1B | ARPC1B | ARPC1B | 10434 | -0.014 | 0.22 | NO |
77 | RAB4A | RAB4A | RAB4A | 10459 | -0.015 | 0.22 | NO |
78 | PTPN2 | PTPN2 | PTPN2 | 10513 | -0.016 | 0.22 | NO |
79 | RAB5A | RAB5A | RAB5A | 10558 | -0.017 | 0.21 | NO |
80 | ARPC4 | ARPC4 | ARPC4 | 10587 | -0.018 | 0.21 | NO |
81 | CSK | CSK | CSK | 10735 | -0.02 | 0.21 | NO |
82 | ACTR2 | ACTR2 | ACTR2 | 10791 | -0.021 | 0.2 | NO |
83 | CRK | CRK | CRK | 10836 | -0.022 | 0.2 | NO |
84 | KRAS | KRAS | KRAS | 10908 | -0.023 | 0.2 | NO |
85 | SHC1 | SHC1 | SHC1 | 11142 | -0.028 | 0.19 | NO |
86 | MAPK3 | MAPK3 | MAPK3 | 11157 | -0.028 | 0.19 | NO |
87 | ARPC5 | ARPC5 | ARPC5 | 11171 | -0.028 | 0.19 | NO |
88 | ARPC2 | ARPC2 | ARPC2 | 11249 | -0.03 | 0.19 | NO |
89 | ACTR3 | ACTR3 | ACTR3 | 11291 | -0.031 | 0.19 | NO |
90 | YWHAB | YWHAB | YWHAB | 11329 | -0.032 | 0.19 | NO |
91 | ABI1 | ABI1 | ABI1 | 11461 | -0.034 | 0.18 | NO |
92 | MAP2K4 | MAP2K4 | MAP2K4 | 11499 | -0.035 | 0.18 | NO |
93 | DNM2 | DNM2 | DNM2 | 11520 | -0.036 | 0.18 | NO |
94 | WASL | WASL | WASL | 11589 | -0.037 | 0.18 | NO |
95 | USP6NL | USP6NL | USP6NL | 11605 | -0.037 | 0.18 | NO |
96 | PRKCD | PRKCD | PRKCD | 11618 | -0.038 | 0.18 | NO |
97 | NCK2 | NCK2 | NCK2 | 11807 | -0.041 | 0.18 | NO |
98 | PPP2R1A | PPP2R1A | PPP2R1A | 11863 | -0.042 | 0.17 | NO |
99 | PAK1 | PAK1 | PAK1 | 12097 | -0.047 | 0.16 | NO |
100 | ARHGDIA | ARHGDIA | ARHGDIA | 12119 | -0.047 | 0.16 | NO |
101 | NCKAP1 | NCKAP1 | NCKAP1 | 12232 | -0.05 | 0.16 | NO |
102 | ARPC3 | ARPC3 | ARPC3 | 12258 | -0.05 | 0.16 | NO |
103 | ACTN4 | ACTN4 | ACTN4 | 12566 | -0.057 | 0.15 | NO |
104 | GRB10 | GRB10 | GRB10 | 12933 | -0.066 | 0.13 | NO |
105 | PPP2CA | PPP2CA | PPP2CA | 13138 | -0.07 | 0.12 | NO |
106 | PIK3R2 | PIK3R2 | PIK3R2 | 13461 | -0.078 | 0.11 | NO |
107 | MLLT4 | MLLT4 | MLLT4 | 13793 | -0.086 | 0.098 | NO |
108 | MYC | MYC | MYC | 13915 | -0.089 | 0.096 | NO |
109 | MAP2K1 | MAP2K1 | MAP2K1 | 13954 | -0.09 | 0.099 | NO |
110 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 13957 | -0.09 | 0.1 | NO |
111 | MAPK8 | MAPK8 | MAPK8 | 14059 | -0.093 | 0.1 | NO |
112 | NRAS | NRAS | NRAS | 14139 | -0.095 | 0.1 | NO |
113 | YWHAQ | YWHAQ | YWHAQ | 14250 | -0.098 | 0.1 | NO |
114 | YWHAE | YWHAE | YWHAE | 14808 | -0.11 | 0.077 | NO |
115 | RAC1 | RAC1 | RAC1 | 14861 | -0.12 | 0.08 | NO |
116 | BCAR1 | BCAR1 | BCAR1 | 15014 | -0.12 | 0.078 | NO |
117 | YWHAG | YWHAG | YWHAG | 15414 | -0.14 | 0.064 | NO |
118 | SRC | SRC | SRC | 15611 | -0.15 | 0.06 | NO |
119 | YWHAZ | YWHAZ | YWHAZ | 15694 | -0.15 | 0.063 | NO |
120 | VAV2 | VAV2 | VAV2 | 15928 | -0.16 | 0.059 | NO |
121 | YES1 | YES1 | YES1 | 16269 | -0.18 | 0.049 | NO |
122 | SLC9A3R1 | SLC9A3R1 | SLC9A3R1 | 16558 | -0.2 | 0.044 | NO |
123 | HRAS | HRAS | HRAS | 17024 | -0.23 | 0.03 | NO |
124 | CTTN | CTTN | CTTN | 17050 | -0.23 | 0.04 | NO |
125 | PLA2G4A | PLA2G4A | PLA2G4A | 17372 | -0.26 | 0.036 | NO |
126 | BAIAP2 | BAIAP2 | BAIAP2 | 17518 | -0.28 | 0.042 | NO |
127 | SFN | SFN | SFN | 18560 | -0.49 | 0.01 | NO |
Figure S99. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG LYSOSOME.

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

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
Table 8. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus6. 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES | 26 | genes.ES.table | 0.65 | 1.7 | 0.0041 | 0.86 | 0.83 | 0.54 | 0.17 | 0.45 | 0.37 | 0.23 |
KEGG NOTCH SIGNALING PATHWAY | 47 | genes.ES.table | 0.43 | 1.7 | 0.011 | 0.94 | 0.78 | 0.17 | 0.17 | 0.14 | 0.38 | 0.23 |
KEGG THYROID CANCER | 29 | genes.ES.table | 0.51 | 1.8 | 0.0021 | 0.75 | 0.55 | 0.59 | 0.32 | 0.4 | 0.18 | 0.16 |
PID FOXOPATHWAY | 49 | genes.ES.table | 0.37 | 1.7 | 0.024 | 0.93 | 0.83 | 0.39 | 0.32 | 0.27 | 0.39 | 0.24 |
PID ECADHERIN NASCENTAJ PATHWAY | 39 | genes.ES.table | 0.46 | 1.9 | 0.0081 | 0.99 | 0.35 | 0.54 | 0.31 | 0.37 | 0 | 0.17 |
PID RETINOIC ACID PATHWAY | 30 | genes.ES.table | 0.42 | 1.7 | 0.027 | 0.74 | 0.9 | 0.33 | 0.22 | 0.26 | 0.37 | 0.21 |
PID TAP63PATHWAY | 54 | genes.ES.table | 0.48 | 1.7 | 0.014 | 0.72 | 0.84 | 0.24 | 0.14 | 0.21 | 0.32 | 0.2 |
PID MAPKTRKPATHWAY | 33 | genes.ES.table | 0.41 | 1.7 | 0.027 | 0.77 | 0.84 | 0.58 | 0.32 | 0.39 | 0.34 | 0.21 |
REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS | 38 | genes.ES.table | 0.51 | 1.8 | 0.012 | 0.91 | 0.54 | 0.34 | 0.2 | 0.27 | 0.22 | 0.18 |
REACTOME TRIF MEDIATED TLR3 SIGNALING | 72 | genes.ES.table | 0.46 | 2 | 0.004 | 1 | 0.23 | 0.44 | 0.28 | 0.32 | 0 | 0.18 |
Table S51. 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 | S100A12 | S100A12 | S100A12 | 122 | 0.87 | 0.13 | YES |
2 | NOD2 | NOD2 | NOD2 | 471 | 0.51 | 0.19 | YES |
3 | DUSP7 | DUSP7 | DUSP7 | 1431 | 0.26 | 0.17 | YES |
4 | TLR3 | TLR3 | TLR3 | 1496 | 0.25 | 0.21 | YES |
5 | TAB3 | TAB3 | TAB3 | 1716 | 0.22 | 0.23 | YES |
6 | TICAM1 | TICAM1 | TICAM1 | 2166 | 0.18 | 0.23 | YES |
7 | MAP2K4 | MAP2K4 | MAP2K4 | 2331 | 0.17 | 0.25 | YES |
8 | RIPK3 | RIPK3 | RIPK3 | 2338 | 0.17 | 0.28 | YES |
9 | SAA1 | SAA1 | SAA1 | 2445 | 0.16 | 0.3 | YES |
10 | MAPK10 | MAPK10 | MAPK10 | 2583 | 0.15 | 0.31 | YES |
11 | MAPK7 | MAPK7 | MAPK7 | 2596 | 0.15 | 0.33 | YES |
12 | S100B | S100B | S100B | 2766 | 0.14 | 0.35 | YES |
13 | IKBKE | IKBKE | IKBKE | 3032 | 0.13 | 0.35 | YES |
14 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 3107 | 0.12 | 0.37 | YES |
15 | AGER | AGER | AGER | 3342 | 0.11 | 0.37 | YES |
16 | IRF7 | IRF7 | IRF7 | 3551 | 0.1 | 0.38 | YES |
17 | FOS | FOS | FOS | 3710 | 0.099 | 0.38 | YES |
18 | MAPK3 | MAPK3 | MAPK3 | 3788 | 0.096 | 0.39 | YES |
19 | MAP2K6 | MAP2K6 | MAP2K6 | 3853 | 0.094 | 0.4 | YES |
20 | IRAK2 | IRAK2 | IRAK2 | 3953 | 0.091 | 0.41 | YES |
21 | TRAF6 | TRAF6 | TRAF6 | 4107 | 0.086 | 0.42 | YES |
22 | MAP2K3 | MAP2K3 | MAP2K3 | 4681 | 0.068 | 0.4 | YES |
23 | MAP2K1 | MAP2K1 | MAP2K1 | 4731 | 0.066 | 0.4 | YES |
24 | IKBKB | IKBKB | IKBKB | 4796 | 0.064 | 0.41 | YES |
25 | TAB2 | TAB2 | TAB2 | 4850 | 0.063 | 0.42 | YES |
26 | RIPK1 | RIPK1 | RIPK1 | 5003 | 0.06 | 0.42 | YES |
27 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 5029 | 0.059 | 0.43 | YES |
28 | NFKBIA | NFKBIA | NFKBIA | 5030 | 0.059 | 0.44 | YES |
29 | DUSP4 | DUSP4 | DUSP4 | 5090 | 0.057 | 0.44 | YES |
30 | PPP2CA | PPP2CA | PPP2CA | 5103 | 0.057 | 0.45 | YES |
31 | ZBP1 | ZBP1 | ZBP1 | 5109 | 0.056 | 0.46 | YES |
32 | PPP2CB | PPP2CB | PPP2CB | 5154 | 0.055 | 0.46 | YES |
33 | PPP2R1A | PPP2R1A | PPP2R1A | 5429 | 0.049 | 0.46 | NO |
34 | MAPK14 | MAPK14 | MAPK14 | 5651 | 0.045 | 0.45 | NO |
35 | MAPK1 | MAPK1 | MAPK1 | 5750 | 0.043 | 0.45 | NO |
36 | MAP2K2 | MAP2K2 | MAP2K2 | 6043 | 0.037 | 0.44 | NO |
37 | UBA52 | UBA52 | UBA52 | 6322 | 0.032 | 0.43 | NO |
38 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 6596 | 0.027 | 0.42 | NO |
39 | CREB1 | CREB1 | CREB1 | 6747 | 0.025 | 0.42 | NO |
40 | RELA | RELA | RELA | 7206 | 0.018 | 0.4 | NO |
41 | PPP2R1B | PPP2R1B | PPP2R1B | 7217 | 0.018 | 0.4 | NO |
42 | NFKBIB | NFKBIB | NFKBIB | 7341 | 0.016 | 0.4 | NO |
43 | IKBKG | IKBKG | IKBKG | 7381 | 0.015 | 0.4 | NO |
44 | MAPK8 | MAPK8 | MAPK8 | 7737 | 0.01 | 0.38 | NO |
45 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 7750 | 0.01 | 0.38 | NO |
46 | RPS27A | RPS27A | RPS27A | 7799 | 0.0093 | 0.38 | NO |
47 | MEF2A | MEF2A | MEF2A | 7918 | 0.0077 | 0.37 | NO |
48 | MAPK11 | MAPK11 | MAPK11 | 8375 | 0.00081 | 0.35 | NO |
49 | MAP2K7 | MAP2K7 | MAP2K7 | 8710 | -0.0035 | 0.33 | NO |
50 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 9158 | -0.0093 | 0.31 | NO |
51 | JUN | JUN | JUN | 9203 | -0.0098 | 0.31 | NO |
52 | ATF1 | ATF1 | ATF1 | 9903 | -0.019 | 0.27 | NO |
53 | TAB1 | TAB1 | TAB1 | 10109 | -0.022 | 0.26 | NO |
54 | IRAK1 | IRAK1 | IRAK1 | 10151 | -0.022 | 0.27 | NO |
55 | TBK1 | TBK1 | TBK1 | 10974 | -0.033 | 0.23 | NO |
56 | DUSP3 | DUSP3 | DUSP3 | 11169 | -0.036 | 0.22 | NO |
57 | MAP3K7 | MAP3K7 | MAP3K7 | 11201 | -0.036 | 0.23 | NO |
58 | CHUK | CHUK | CHUK | 11405 | -0.039 | 0.22 | NO |
59 | IRF3 | IRF3 | IRF3 | 11761 | -0.044 | 0.21 | NO |
60 | ELK1 | ELK1 | ELK1 | 11866 | -0.046 | 0.21 | NO |
61 | HMGB1 | HMGB1 | HMGB1 | 12445 | -0.054 | 0.19 | NO |
62 | NFKB2 | NFKB2 | NFKB2 | 12736 | -0.058 | 0.18 | NO |
63 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 12831 | -0.059 | 0.18 | NO |
64 | NOD1 | NOD1 | NOD1 | 13148 | -0.064 | 0.18 | NO |
65 | PPP2R5D | PPP2R5D | PPP2R5D | 13190 | -0.065 | 0.19 | NO |
66 | DUSP6 | DUSP6 | DUSP6 | 13946 | -0.078 | 0.16 | NO |
67 | APP | APP | APP | 13997 | -0.079 | 0.17 | NO |
68 | MAPK9 | MAPK9 | MAPK9 | 14790 | -0.096 | 0.14 | NO |
69 | CDK1 | CDK1 | CDK1 | 15015 | -0.1 | 0.14 | NO |
70 | ATF2 | ATF2 | ATF2 | 15165 | -0.1 | 0.15 | NO |
71 | RIPK2 | RIPK2 | RIPK2 | 15633 | -0.12 | 0.14 | NO |
72 | MEF2C | MEF2C | MEF2C | 16416 | -0.15 | 0.12 | NO |
Figure S101. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

Figure S102. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S52. 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 | TIAM1 | TIAM1 | TIAM1 | 266 | 0.64 | 0.16 | YES |
2 | ITGB7 | ITGB7 | ITGB7 | 1400 | 0.26 | 0.18 | YES |
3 | MLLT4 | MLLT4 | MLLT4 | 1828 | 0.21 | 0.21 | YES |
4 | TJP1 | TJP1 | TJP1 | 2421 | 0.16 | 0.22 | YES |
5 | JUP | JUP | JUP | 2623 | 0.15 | 0.25 | YES |
6 | ARF6 | ARF6 | ARF6 | 2844 | 0.14 | 0.28 | YES |
7 | WASF2 | WASF2 | WASF2 | 3101 | 0.12 | 0.3 | YES |
8 | CTNND1 | CTNND1 | CTNND1 | 3145 | 0.12 | 0.33 | YES |
9 | CCND1 | CCND1 | CCND1 | 3243 | 0.12 | 0.36 | YES |
10 | DLG1 | DLG1 | DLG1 | 3463 | 0.11 | 0.38 | YES |
11 | ABI1 | ABI1 | ABI1 | 3485 | 0.11 | 0.4 | YES |
12 | CTTN | CTTN | CTTN | 3748 | 0.098 | 0.42 | YES |
13 | CDH1 | CDH1 | CDH1 | 3805 | 0.096 | 0.44 | YES |
14 | CTNNA1 | CTNNA1 | CTNNA1 | 4258 | 0.081 | 0.44 | YES |
15 | RAC1 | RAC1 | RAC1 | 4795 | 0.064 | 0.43 | YES |
16 | IQGAP1 | IQGAP1 | IQGAP1 | 4915 | 0.062 | 0.44 | YES |
17 | CYFIP2 | CYFIP2 | CYFIP2 | 4972 | 0.06 | 0.45 | YES |
18 | ITGAE | ITGAE | ITGAE | 5191 | 0.054 | 0.46 | YES |
19 | NCKAP1 | NCKAP1 | NCKAP1 | 5542 | 0.047 | 0.45 | YES |
20 | RHOA | RHOA | RHOA | 5703 | 0.044 | 0.46 | YES |
21 | RAP1A | RAP1A | RAP1A | 5747 | 0.043 | 0.46 | YES |
22 | CDC42 | CDC42 | CDC42 | 7315 | 0.016 | 0.38 | NO |
23 | PIP5K1C | PIP5K1C | PIP5K1C | 7382 | 0.015 | 0.39 | NO |
24 | CSNK2B | CSNK2B | CSNK2B | 8033 | 0.0058 | 0.35 | NO |
25 | PIK3CA | PIK3CA | PIK3CA | 8331 | 0.0014 | 0.34 | NO |
26 | KLHL20 | KLHL20 | KLHL20 | 8585 | -0.0019 | 0.32 | NO |
27 | CRK | CRK | CRK | 8953 | -0.0066 | 0.31 | NO |
28 | CTNNB1 | CTNNB1 | CTNNB1 | 9385 | -0.012 | 0.29 | NO |
29 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 10129 | -0.022 | 0.25 | NO |
30 | CSNK2A2 | CSNK2A2 | CSNK2A2 | 11236 | -0.037 | 0.2 | NO |
31 | SRC | SRC | SRC | 11251 | -0.037 | 0.21 | NO |
32 | PIK3R1 | PIK3R1 | PIK3R1 | 11570 | -0.041 | 0.21 | NO |
33 | AKT1 | AKT1 | AKT1 | 12218 | -0.05 | 0.19 | NO |
34 | AP1M1 | AP1M1 | AP1M1 | 12532 | -0.055 | 0.19 | NO |
35 | RAP1B | RAP1B | RAP1B | 12889 | -0.06 | 0.18 | NO |
36 | ENAH | ENAH | ENAH | 12996 | -0.062 | 0.2 | NO |
37 | NME1 | NME1 | NME1 | 14536 | -0.09 | 0.14 | NO |
38 | RAPGEF1 | RAPGEF1 | RAPGEF1 | 15076 | -0.1 | 0.14 | NO |
39 | VAV2 | VAV2 | VAV2 | 17595 | -0.21 | 0.062 | NO |
Figure S103. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NOTCH SIGNALING PATHWAY.

Figure S104. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOTCH SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S53. 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 | S100A12 | S100A12 | S100A12 | 122 | 0.87 | 0.12 | YES |
2 | NOD2 | NOD2 | NOD2 | 471 | 0.51 | 0.18 | YES |
3 | DUSP7 | DUSP7 | DUSP7 | 1431 | 0.26 | 0.17 | YES |
4 | TAB3 | TAB3 | TAB3 | 1716 | 0.22 | 0.19 | YES |
5 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 1821 | 0.21 | 0.22 | YES |
6 | MAP2K4 | MAP2K4 | MAP2K4 | 2331 | 0.17 | 0.21 | YES |
7 | PELI1 | PELI1 | PELI1 | 2369 | 0.16 | 0.24 | YES |
8 | SAA1 | SAA1 | SAA1 | 2445 | 0.16 | 0.26 | YES |
9 | MAPK10 | MAPK10 | MAPK10 | 2583 | 0.15 | 0.27 | YES |
10 | MAPK7 | MAPK7 | MAPK7 | 2596 | 0.15 | 0.3 | YES |
11 | S100B | S100B | S100B | 2766 | 0.14 | 0.31 | YES |
12 | MYD88 | MYD88 | MYD88 | 2979 | 0.13 | 0.32 | YES |
13 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 3107 | 0.12 | 0.33 | YES |
14 | MAP3K1 | MAP3K1 | MAP3K1 | 3209 | 0.12 | 0.34 | YES |
15 | AGER | AGER | AGER | 3342 | 0.11 | 0.35 | YES |
16 | IRAK4 | IRAK4 | IRAK4 | 3425 | 0.11 | 0.36 | YES |
17 | FOS | FOS | FOS | 3710 | 0.099 | 0.36 | YES |
18 | MAPK3 | MAPK3 | MAPK3 | 3788 | 0.096 | 0.37 | YES |
19 | MAP2K6 | MAP2K6 | MAP2K6 | 3853 | 0.094 | 0.38 | YES |
20 | IRAK2 | IRAK2 | IRAK2 | 3953 | 0.091 | 0.39 | YES |
21 | TRAF6 | TRAF6 | TRAF6 | 4107 | 0.086 | 0.4 | YES |
22 | TLR9 | TLR9 | TLR9 | 4392 | 0.077 | 0.39 | YES |
23 | MAP2K3 | MAP2K3 | MAP2K3 | 4681 | 0.068 | 0.39 | YES |
24 | MAP2K1 | MAP2K1 | MAP2K1 | 4731 | 0.066 | 0.4 | YES |
25 | IKBKB | IKBKB | IKBKB | 4796 | 0.064 | 0.4 | YES |
26 | TAB2 | TAB2 | TAB2 | 4850 | 0.063 | 0.41 | YES |
27 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 5029 | 0.059 | 0.41 | YES |
28 | NFKBIA | NFKBIA | NFKBIA | 5030 | 0.059 | 0.42 | YES |
29 | DUSP4 | DUSP4 | DUSP4 | 5090 | 0.057 | 0.42 | YES |
30 | PPP2CA | PPP2CA | PPP2CA | 5103 | 0.057 | 0.43 | YES |
31 | PPP2CB | PPP2CB | PPP2CB | 5154 | 0.055 | 0.44 | YES |
32 | PPP2R1A | PPP2R1A | PPP2R1A | 5429 | 0.049 | 0.43 | NO |
33 | MAPK14 | MAPK14 | MAPK14 | 5651 | 0.045 | 0.42 | NO |
34 | MAPK1 | MAPK1 | MAPK1 | 5750 | 0.043 | 0.43 | NO |
35 | MAP2K2 | MAP2K2 | MAP2K2 | 6043 | 0.037 | 0.42 | NO |
36 | UBA52 | UBA52 | UBA52 | 6322 | 0.032 | 0.41 | NO |
37 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 6596 | 0.027 | 0.4 | NO |
38 | CREB1 | CREB1 | CREB1 | 6747 | 0.025 | 0.39 | NO |
39 | RELA | RELA | RELA | 7206 | 0.018 | 0.37 | NO |
40 | PPP2R1B | PPP2R1B | PPP2R1B | 7217 | 0.018 | 0.37 | NO |
41 | PELI3 | PELI3 | PELI3 | 7251 | 0.017 | 0.37 | NO |
42 | NFKBIB | NFKBIB | NFKBIB | 7341 | 0.016 | 0.37 | NO |
43 | IKBKG | IKBKG | IKBKG | 7381 | 0.015 | 0.37 | NO |
44 | UBE2N | UBE2N | UBE2N | 7653 | 0.011 | 0.36 | NO |
45 | MAPK8 | MAPK8 | MAPK8 | 7737 | 0.01 | 0.35 | NO |
46 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 7750 | 0.01 | 0.36 | NO |
47 | RPS27A | RPS27A | RPS27A | 7799 | 0.0093 | 0.35 | NO |
48 | MEF2A | MEF2A | MEF2A | 7918 | 0.0077 | 0.35 | NO |
49 | MAPK11 | MAPK11 | MAPK11 | 8375 | 0.00081 | 0.32 | NO |
50 | MAP2K7 | MAP2K7 | MAP2K7 | 8710 | -0.0035 | 0.31 | NO |
51 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 9158 | -0.0093 | 0.28 | NO |
52 | JUN | JUN | JUN | 9203 | -0.0098 | 0.28 | NO |
53 | ATF1 | ATF1 | ATF1 | 9903 | -0.019 | 0.25 | NO |
54 | TAB1 | TAB1 | TAB1 | 10109 | -0.022 | 0.24 | NO |
55 | IRAK1 | IRAK1 | IRAK1 | 10151 | -0.022 | 0.24 | NO |
56 | TLR7 | TLR7 | TLR7 | 10325 | -0.024 | 0.24 | NO |
57 | DUSP3 | DUSP3 | DUSP3 | 11169 | -0.036 | 0.2 | NO |
58 | MAP3K7 | MAP3K7 | MAP3K7 | 11201 | -0.036 | 0.2 | NO |
59 | CHUK | CHUK | CHUK | 11405 | -0.039 | 0.2 | NO |
60 | ELK1 | ELK1 | ELK1 | 11866 | -0.046 | 0.18 | NO |
61 | ECSIT | ECSIT | ECSIT | 12031 | -0.048 | 0.18 | NO |
62 | HMGB1 | HMGB1 | HMGB1 | 12445 | -0.054 | 0.16 | NO |
63 | TLR8 | TLR8 | TLR8 | 12515 | -0.055 | 0.17 | NO |
64 | NFKB2 | NFKB2 | NFKB2 | 12736 | -0.058 | 0.16 | NO |
65 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 12831 | -0.059 | 0.17 | NO |
66 | NOD1 | NOD1 | NOD1 | 13148 | -0.064 | 0.16 | NO |
67 | PPP2R5D | PPP2R5D | PPP2R5D | 13190 | -0.065 | 0.17 | NO |
68 | DUSP6 | DUSP6 | DUSP6 | 13946 | -0.078 | 0.14 | NO |
69 | APP | APP | APP | 13997 | -0.079 | 0.15 | NO |
70 | MAPK9 | MAPK9 | MAPK9 | 14790 | -0.096 | 0.12 | NO |
71 | CDK1 | CDK1 | CDK1 | 15015 | -0.1 | 0.13 | NO |
72 | ATF2 | ATF2 | ATF2 | 15165 | -0.1 | 0.13 | NO |
73 | PELI2 | PELI2 | PELI2 | 15506 | -0.12 | 0.13 | NO |
74 | RIPK2 | RIPK2 | RIPK2 | 15633 | -0.12 | 0.14 | NO |
75 | MEF2C | MEF2C | MEF2C | 16416 | -0.15 | 0.12 | NO |
Figure S105. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG THYROID CANCER.

Figure S106. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG THYROID CANCER, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S54. 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 | DSG1 | DSG1 | DSG1 | 226 | 0.69 | 0.12 | YES |
2 | DSG3 | DSG3 | DSG3 | 278 | 0.64 | 0.25 | YES |
3 | PKP1 | PKP1 | PKP1 | 394 | 0.56 | 0.35 | YES |
4 | MAPT | MAPT | MAPT | 748 | 0.39 | 0.41 | YES |
5 | DSP | DSP | DSP | 1039 | 0.32 | 0.46 | YES |
6 | GAS2 | GAS2 | GAS2 | 1980 | 0.19 | 0.44 | YES |
7 | TJP1 | TJP1 | TJP1 | 2421 | 0.16 | 0.45 | YES |
8 | OCLN | OCLN | OCLN | 2706 | 0.14 | 0.46 | YES |
9 | DBNL | DBNL | DBNL | 2715 | 0.14 | 0.49 | YES |
10 | GSN | GSN | GSN | 3404 | 0.11 | 0.48 | YES |
11 | STK24 | STK24 | STK24 | 3691 | 0.1 | 0.48 | YES |
12 | APC | APC | APC | 3782 | 0.096 | 0.5 | YES |
13 | CDH1 | CDH1 | CDH1 | 3805 | 0.096 | 0.51 | YES |
14 | SATB1 | SATB1 | SATB1 | 4122 | 0.085 | 0.51 | NO |
15 | TJP2 | TJP2 | TJP2 | 4537 | 0.072 | 0.5 | NO |
16 | BMX | BMX | BMX | 5422 | 0.049 | 0.47 | NO |
17 | PRKCD | PRKCD | PRKCD | 6000 | 0.038 | 0.44 | NO |
18 | PRKCQ | PRKCQ | PRKCQ | 6479 | 0.029 | 0.42 | NO |
19 | LMNA | LMNA | LMNA | 6654 | 0.026 | 0.42 | NO |
20 | MST4 | MST4 | MST4 | 6951 | 0.022 | 0.41 | NO |
21 | ADD1 | ADD1 | ADD1 | 7332 | 0.016 | 0.39 | NO |
22 | SPTAN1 | SPTAN1 | SPTAN1 | 8881 | -0.0056 | 0.31 | NO |
23 | BCAP31 | BCAP31 | BCAP31 | 9268 | -0.011 | 0.29 | NO |
24 | CTNNB1 | CTNNB1 | CTNNB1 | 9385 | -0.012 | 0.29 | NO |
25 | FNTA | FNTA | FNTA | 9576 | -0.015 | 0.28 | NO |
26 | CASP3 | CASP3 | CASP3 | 9621 | -0.015 | 0.28 | NO |
27 | CASP7 | CASP7 | CASP7 | 9798 | -0.018 | 0.28 | NO |
28 | PLEC | PLEC | PLEC | 10637 | -0.028 | 0.24 | NO |
29 | ACIN1 | ACIN1 | ACIN1 | 10831 | -0.031 | 0.23 | NO |
30 | BIRC2 | BIRC2 | BIRC2 | 12570 | -0.056 | 0.15 | NO |
31 | CASP8 | CASP8 | CASP8 | 13284 | -0.066 | 0.12 | NO |
32 | ROCK1 | ROCK1 | ROCK1 | 13398 | -0.068 | 0.13 | NO |
33 | LMNB1 | LMNB1 | LMNB1 | 14726 | -0.095 | 0.08 | NO |
34 | PTK2 | PTK2 | PTK2 | 15230 | -0.11 | 0.074 | NO |
35 | DSG2 | DSG2 | DSG2 | 15681 | -0.12 | 0.073 | NO |
36 | VIM | VIM | VIM | 15896 | -0.13 | 0.087 | NO |
37 | LOC647859 | LOC647859 | LOC647859 | 16783 | -0.16 | 0.072 | NO |
38 | CASP6 | CASP6 | CASP6 | 16839 | -0.17 | 0.1 | NO |
Figure S107. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FOXOPATHWAY.

Figure S108. Get High-res Image For the top 5 core enriched genes in the pathway: PID FOXOPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S55. 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 | RXRG | RXRG | RXRG | 1421 | 0.26 | 0.07 | YES |
2 | CCND1 | CCND1 | CCND1 | 3243 | 0.12 | 0.038 | YES |
3 | LEF1 | LEF1 | LEF1 | 3510 | 0.11 | 0.084 | YES |
4 | HRAS | HRAS | HRAS | 3658 | 0.1 | 0.13 | YES |
5 | TCF7L1 | TCF7L1 | TCF7L1 | 3771 | 0.097 | 0.18 | YES |
6 | MAPK3 | MAPK3 | MAPK3 | 3788 | 0.096 | 0.24 | YES |
7 | CDH1 | CDH1 | CDH1 | 3805 | 0.096 | 0.29 | YES |
8 | CCDC6 | CCDC6 | CCDC6 | 3833 | 0.095 | 0.34 | YES |
9 | RET | RET | RET | 3981 | 0.09 | 0.38 | YES |
10 | RXRA | RXRA | RXRA | 4050 | 0.088 | 0.43 | YES |
11 | MAP2K1 | MAP2K1 | MAP2K1 | 4731 | 0.066 | 0.43 | YES |
12 | BRAF | BRAF | BRAF | 5091 | 0.057 | 0.44 | YES |
13 | NCOA4 | NCOA4 | NCOA4 | 5500 | 0.047 | 0.45 | YES |
14 | MAPK1 | MAPK1 | MAPK1 | 5750 | 0.043 | 0.46 | YES |
15 | PPARG | PPARG | PPARG | 5879 | 0.04 | 0.48 | YES |
16 | TFG | TFG | TFG | 5941 | 0.039 | 0.49 | YES |
17 | MAP2K2 | MAP2K2 | MAP2K2 | 6043 | 0.037 | 0.51 | YES |
18 | NRAS | NRAS | NRAS | 7695 | 0.011 | 0.43 | NO |
19 | PAX8 | PAX8 | PAX8 | 8116 | 0.0044 | 0.41 | NO |
20 | RXRB | RXRB | RXRB | 8335 | 0.0014 | 0.4 | NO |
21 | TP53 | TP53 | TP53 | 8497 | -0.00087 | 0.39 | NO |
22 | CTNNB1 | CTNNB1 | CTNNB1 | 9385 | -0.012 | 0.35 | NO |
23 | MYC | MYC | MYC | 9670 | -0.016 | 0.34 | NO |
24 | KRAS | KRAS | KRAS | 9959 | -0.02 | 0.34 | NO |
25 | NTRK1 | NTRK1 | NTRK1 | 10450 | -0.026 | 0.32 | NO |
26 | TPR | TPR | TPR | 10623 | -0.028 | 0.33 | NO |
27 | TCF7 | TCF7 | TCF7 | 11719 | -0.043 | 0.3 | NO |
28 | TPM3 | TPM3 | TPM3 | 12017 | -0.048 | 0.31 | NO |
29 | TCF7L2 | TCF7L2 | TCF7L2 | 14525 | -0.09 | 0.23 | NO |
Figure S109. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ECADHERIN NASCENTAJ PATHWAY.

Figure S110. Get High-res Image For the top 5 core enriched genes in the pathway: PID ECADHERIN NASCENTAJ PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S56. 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 | IL1RN | IL1RN | IL1RN | 147 | 0.82 | 0.15 | YES |
2 | IL1A | IL1A | IL1A | 363 | 0.57 | 0.24 | YES |
3 | NOD2 | NOD2 | NOD2 | 471 | 0.51 | 0.34 | YES |
4 | TAB3 | TAB3 | TAB3 | 1716 | 0.22 | 0.31 | YES |
5 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 1821 | 0.21 | 0.34 | YES |
6 | MAP3K8 | MAP3K8 | MAP3K8 | 1898 | 0.2 | 0.38 | YES |
7 | IL1R2 | IL1R2 | IL1R2 | 1924 | 0.2 | 0.41 | YES |
8 | TOLLIP | TOLLIP | TOLLIP | 1988 | 0.19 | 0.45 | YES |
9 | IL1RAP | IL1RAP | IL1RAP | 2151 | 0.18 | 0.47 | YES |
10 | MAP2K4 | MAP2K4 | MAP2K4 | 2331 | 0.17 | 0.49 | YES |
11 | PELI1 | PELI1 | PELI1 | 2369 | 0.16 | 0.52 | YES |
12 | BTRC | BTRC | BTRC | 2900 | 0.13 | 0.52 | YES |
13 | MYD88 | MYD88 | MYD88 | 2979 | 0.13 | 0.54 | YES |
14 | IRAK4 | IRAK4 | IRAK4 | 3425 | 0.11 | 0.54 | YES |
15 | MAP2K6 | MAP2K6 | MAP2K6 | 3853 | 0.094 | 0.53 | YES |
16 | IRAK2 | IRAK2 | IRAK2 | 3953 | 0.091 | 0.54 | YES |
17 | TRAF6 | TRAF6 | TRAF6 | 4107 | 0.086 | 0.55 | YES |
18 | MAP2K1 | MAP2K1 | MAP2K1 | 4731 | 0.066 | 0.53 | NO |
19 | IKBKB | IKBKB | IKBKB | 4796 | 0.064 | 0.54 | NO |
20 | TAB2 | TAB2 | TAB2 | 4850 | 0.063 | 0.55 | NO |
21 | RBX1 | RBX1 | RBX1 | 5588 | 0.046 | 0.52 | NO |
22 | SKP1 | SKP1 | SKP1 | 6990 | 0.021 | 0.45 | NO |
23 | MAP3K3 | MAP3K3 | MAP3K3 | 7013 | 0.021 | 0.45 | NO |
24 | PELI3 | PELI3 | PELI3 | 7251 | 0.017 | 0.44 | NO |
25 | IKBKG | IKBKG | IKBKG | 7381 | 0.015 | 0.44 | NO |
26 | UBE2N | UBE2N | UBE2N | 7653 | 0.011 | 0.42 | NO |
27 | CUL1 | CUL1 | CUL1 | 9974 | -0.02 | 0.3 | NO |
28 | TAB1 | TAB1 | TAB1 | 10109 | -0.022 | 0.3 | NO |
29 | IRAK1 | IRAK1 | IRAK1 | 10151 | -0.022 | 0.3 | NO |
30 | MAP3K7 | MAP3K7 | MAP3K7 | 11201 | -0.036 | 0.25 | NO |
31 | CHUK | CHUK | CHUK | 11405 | -0.039 | 0.25 | NO |
32 | TNIP2 | TNIP2 | TNIP2 | 11638 | -0.042 | 0.25 | NO |
33 | NOD1 | NOD1 | NOD1 | 13148 | -0.064 | 0.18 | NO |
34 | IL1R1 | IL1R1 | IL1R1 | 13976 | -0.078 | 0.15 | NO |
35 | SQSTM1 | SQSTM1 | SQSTM1 | 15160 | -0.1 | 0.1 | NO |
36 | IL1B | IL1B | IL1B | 15359 | -0.11 | 0.12 | NO |
37 | IRAK3 | IRAK3 | IRAK3 | 15458 | -0.11 | 0.13 | NO |
38 | PELI2 | PELI2 | PELI2 | 15506 | -0.12 | 0.15 | NO |
39 | RIPK2 | RIPK2 | RIPK2 | 15633 | -0.12 | 0.17 | NO |
Figure S111. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID RETINOIC ACID PATHWAY.

Figure S112. Get High-res Image For the top 5 core enriched genes in the pathway: PID RETINOIC ACID PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S57. 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 | HES5 | HES5 | HES5 | 152 | 0.8 | 0.11 | YES |
2 | KAT2B | KAT2B | KAT2B | 733 | 0.4 | 0.14 | YES |
3 | DLK1 | DLK1 | DLK1 | 847 | 0.37 | 0.19 | YES |
4 | DTX1 | DTX1 | DTX1 | 1055 | 0.31 | 0.22 | YES |
5 | NEURL | NEURL | NEURL | 1139 | 0.3 | 0.26 | YES |
6 | MAML3 | MAML3 | MAML3 | 1152 | 0.3 | 0.31 | YES |
7 | TLE2 | TLE2 | TLE2 | 1236 | 0.28 | 0.35 | YES |
8 | CNTN1 | CNTN1 | CNTN1 | 1758 | 0.22 | 0.35 | YES |
9 | DTX2 | DTX2 | DTX2 | 1902 | 0.2 | 0.37 | YES |
10 | TLE4 | TLE4 | TLE4 | 2271 | 0.17 | 0.38 | YES |
11 | TLE3 | TLE3 | TLE3 | 2776 | 0.14 | 0.37 | YES |
12 | TBL1X | TBL1X | TBL1X | 2811 | 0.14 | 0.39 | YES |
13 | FBXW7 | FBXW7 | FBXW7 | 2830 | 0.14 | 0.41 | YES |
14 | HDAC11 | HDAC11 | HDAC11 | 3308 | 0.12 | 0.4 | NO |
15 | DLL1 | DLL1 | DLL1 | 3768 | 0.097 | 0.39 | NO |
16 | HDAC5 | HDAC5 | HDAC5 | 4118 | 0.085 | 0.39 | NO |
17 | HDAC4 | HDAC4 | HDAC4 | 4376 | 0.077 | 0.38 | NO |
18 | HES1 | HES1 | HES1 | 4519 | 0.072 | 0.39 | NO |
19 | MAML2 | MAML2 | MAML2 | 4605 | 0.07 | 0.4 | NO |
20 | CCNC | CCNC | CCNC | 5341 | 0.051 | 0.36 | NO |
21 | HDAC6 | HDAC6 | HDAC6 | 5540 | 0.047 | 0.36 | NO |
22 | RBX1 | RBX1 | RBX1 | 5588 | 0.046 | 0.36 | NO |
23 | MIB2 | MIB2 | MIB2 | 5720 | 0.043 | 0.36 | NO |
24 | JAG1 | JAG1 | JAG1 | 5730 | 0.043 | 0.37 | NO |
25 | PSEN2 | PSEN2 | PSEN2 | 5809 | 0.041 | 0.37 | NO |
26 | EP300 | EP300 | EP300 | 5848 | 0.04 | 0.38 | NO |
27 | PSENEN | PSENEN | PSENEN | 6020 | 0.037 | 0.37 | NO |
28 | ADAM17 | ADAM17 | ADAM17 | 6181 | 0.034 | 0.37 | NO |
29 | DNER | DNER | DNER | 6263 | 0.033 | 0.37 | NO |
30 | UBA52 | UBA52 | UBA52 | 6322 | 0.032 | 0.37 | NO |
31 | JAG2 | JAG2 | JAG2 | 6719 | 0.025 | 0.35 | NO |
32 | HEY1 | HEY1 | HEY1 | 6937 | 0.022 | 0.34 | NO |
33 | SKP1 | SKP1 | SKP1 | 6990 | 0.021 | 0.34 | NO |
34 | HDAC3 | HDAC3 | HDAC3 | 7731 | 0.01 | 0.31 | NO |
35 | RPS27A | RPS27A | RPS27A | 7799 | 0.0093 | 0.3 | NO |
36 | HEY2 | HEY2 | HEY2 | 7801 | 0.0093 | 0.31 | NO |
37 | HDAC2 | HDAC2 | HDAC2 | 8187 | 0.0036 | 0.29 | NO |
38 | HDAC1 | HDAC1 | HDAC1 | 8194 | 0.0035 | 0.29 | NO |
39 | NUMB | NUMB | NUMB | 8284 | 0.002 | 0.28 | NO |
40 | CREBBP | CREBBP | CREBBP | 8347 | 0.0012 | 0.28 | NO |
41 | HDAC7 | HDAC7 | HDAC7 | 9305 | -0.011 | 0.23 | NO |
42 | CDK8 | CDK8 | CDK8 | 9407 | -0.013 | 0.23 | NO |
43 | MYC | MYC | MYC | 9670 | -0.016 | 0.21 | NO |
44 | APH1A | APH1A | APH1A | 9794 | -0.018 | 0.21 | NO |
45 | CUL1 | CUL1 | CUL1 | 9974 | -0.02 | 0.2 | NO |
46 | PSEN1 | PSEN1 | PSEN1 | 10029 | -0.02 | 0.2 | NO |
47 | NCOR1 | NCOR1 | NCOR1 | 10065 | -0.021 | 0.2 | NO |
48 | HIF1A | HIF1A | HIF1A | 10251 | -0.023 | 0.2 | NO |
49 | ADAM10 | ADAM10 | ADAM10 | 10264 | -0.023 | 0.2 | NO |
50 | NCSTN | NCSTN | NCSTN | 10476 | -0.026 | 0.19 | NO |
51 | ARRB1 | ARRB1 | ARRB1 | 10487 | -0.026 | 0.2 | NO |
52 | NCOR2 | NCOR2 | NCOR2 | 10542 | -0.027 | 0.2 | NO |
53 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 11543 | -0.041 | 0.15 | NO |
54 | MAML1 | MAML1 | MAML1 | 11705 | -0.043 | 0.15 | NO |
55 | RBPJ | RBPJ | RBPJ | 12048 | -0.048 | 0.14 | NO |
56 | SNW1 | SNW1 | SNW1 | 12348 | -0.052 | 0.13 | NO |
57 | HDAC9 | HDAC9 | HDAC9 | 12378 | -0.053 | 0.14 | NO |
58 | HDAC10 | HDAC10 | HDAC10 | 12536 | -0.055 | 0.14 | NO |
59 | HDAC8 | HDAC8 | HDAC8 | 12737 | -0.058 | 0.13 | NO |
60 | MIB1 | MIB1 | MIB1 | 13233 | -0.065 | 0.12 | NO |
61 | APH1B | APH1B | APH1B | 13701 | -0.073 | 0.1 | NO |
62 | KAT2A | KAT2A | KAT2A | 15016 | -0.1 | 0.048 | NO |
63 | ARRB2 | ARRB2 | ARRB2 | 15174 | -0.1 | 0.055 | NO |
64 | TLE1 | TLE1 | TLE1 | 15201 | -0.11 | 0.07 | NO |
65 | DTX4 | DTX4 | DTX4 | 15330 | -0.11 | 0.079 | NO |
66 | DLL4 | DLL4 | DLL4 | 16297 | -0.14 | 0.049 | NO |
67 | MAMLD1 | MAMLD1 | MAMLD1 | 17060 | -0.18 | 0.035 | NO |
68 | HEYL | HEYL | HEYL | 18558 | -0.37 | 0.01 | NO |
Figure S113. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TAP63PATHWAY.

Figure S114. Get High-res Image For the top 5 core enriched genes in the pathway: PID TAP63PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S58. 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 | HES5 | HES5 | HES5 | 152 | 0.8 | 0.19 | YES |
2 | KAT2B | KAT2B | KAT2B | 733 | 0.4 | 0.26 | YES |
3 | DTX1 | DTX1 | DTX1 | 1055 | 0.31 | 0.32 | YES |
4 | MAML3 | MAML3 | MAML3 | 1152 | 0.3 | 0.39 | YES |
5 | DTX2 | DTX2 | DTX2 | 1902 | 0.2 | 0.4 | YES |
6 | NOTCH2 | NOTCH2 | NOTCH2 | 2351 | 0.16 | 0.41 | YES |
7 | DLL3 | DLL3 | DLL3 | 3129 | 0.12 | 0.4 | YES |
8 | NOTCH3 | NOTCH3 | NOTCH3 | 3197 | 0.12 | 0.43 | YES |
9 | DLL1 | DLL1 | DLL1 | 3768 | 0.097 | 0.42 | NO |
10 | HES1 | HES1 | HES1 | 4519 | 0.072 | 0.4 | NO |
11 | MAML2 | MAML2 | MAML2 | 4605 | 0.07 | 0.41 | NO |
12 | JAG1 | JAG1 | JAG1 | 5730 | 0.043 | 0.36 | NO |
13 | PSEN2 | PSEN2 | PSEN2 | 5809 | 0.041 | 0.37 | NO |
14 | EP300 | EP300 | EP300 | 5848 | 0.04 | 0.38 | NO |
15 | PSENEN | PSENEN | PSENEN | 6020 | 0.037 | 0.38 | NO |
16 | DVL1 | DVL1 | DVL1 | 6109 | 0.036 | 0.38 | NO |
17 | ADAM17 | ADAM17 | ADAM17 | 6181 | 0.034 | 0.39 | NO |
18 | JAG2 | JAG2 | JAG2 | 6719 | 0.025 | 0.36 | NO |
19 | PTCRA | PTCRA | PTCRA | 6945 | 0.022 | 0.36 | NO |
20 | MFNG | MFNG | MFNG | 7438 | 0.014 | 0.34 | NO |
21 | HDAC2 | HDAC2 | HDAC2 | 8187 | 0.0036 | 0.3 | NO |
22 | HDAC1 | HDAC1 | HDAC1 | 8194 | 0.0035 | 0.3 | NO |
23 | NUMB | NUMB | NUMB | 8284 | 0.002 | 0.29 | NO |
24 | CREBBP | CREBBP | CREBBP | 8347 | 0.0012 | 0.29 | NO |
25 | NOTCH1 | NOTCH1 | NOTCH1 | 9060 | -0.0081 | 0.25 | NO |
26 | RFNG | RFNG | RFNG | 9302 | -0.011 | 0.24 | NO |
27 | DVL3 | DVL3 | DVL3 | 9468 | -0.013 | 0.24 | NO |
28 | APH1A | APH1A | APH1A | 9794 | -0.018 | 0.22 | NO |
29 | DVL2 | DVL2 | DVL2 | 9839 | -0.018 | 0.23 | NO |
30 | DTX3 | DTX3 | DTX3 | 9893 | -0.019 | 0.23 | NO |
31 | PSEN1 | PSEN1 | PSEN1 | 10029 | -0.02 | 0.23 | NO |
32 | DTX3L | DTX3L | DTX3L | 10352 | -0.025 | 0.22 | NO |
33 | NCSTN | NCSTN | NCSTN | 10476 | -0.026 | 0.22 | NO |
34 | CTBP2 | CTBP2 | CTBP2 | 10520 | -0.027 | 0.22 | NO |
35 | NCOR2 | NCOR2 | NCOR2 | 10542 | -0.027 | 0.22 | NO |
36 | CTBP1 | CTBP1 | CTBP1 | 11578 | -0.041 | 0.18 | NO |
37 | MAML1 | MAML1 | MAML1 | 11705 | -0.043 | 0.18 | NO |
38 | NUMBL | NUMBL | NUMBL | 11731 | -0.044 | 0.19 | NO |
39 | CIR1 | CIR1 | CIR1 | 11897 | -0.046 | 0.2 | NO |
40 | RBPJ | RBPJ | RBPJ | 12048 | -0.048 | 0.2 | NO |
41 | SNW1 | SNW1 | SNW1 | 12348 | -0.052 | 0.2 | NO |
42 | LFNG | LFNG | LFNG | 13183 | -0.064 | 0.17 | NO |
43 | NOTCH4 | NOTCH4 | NOTCH4 | 13320 | -0.067 | 0.18 | NO |
44 | RBPJL | RBPJL | RBPJL | 14998 | -0.1 | 0.11 | NO |
45 | KAT2A | KAT2A | KAT2A | 15016 | -0.1 | 0.14 | NO |
46 | DTX4 | DTX4 | DTX4 | 15330 | -0.11 | 0.15 | NO |
47 | DLL4 | DLL4 | DLL4 | 16297 | -0.14 | 0.13 | NO |
Figure S115. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MAPKTRKPATHWAY.

Figure S116. Get High-res Image For the top 5 core enriched genes in the pathway: PID MAPKTRKPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Table S59. 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 | PLA2G3 | PLA2G3 | PLA2G3 | 123 | 0.87 | 0.081 | YES |
2 | PLA2G4D | PLA2G4D | PLA2G4D | 387 | 0.56 | 0.12 | YES |
3 | PLA2G4F | PLA2G4F | PLA2G4F | 566 | 0.47 | 0.16 | YES |
4 | MBOAT2 | MBOAT2 | MBOAT2 | 935 | 0.34 | 0.18 | YES |
5 | MGLL | MGLL | MGLL | 1022 | 0.32 | 0.2 | YES |
6 | PLD2 | PLD2 | PLD2 | 1034 | 0.32 | 0.24 | YES |
7 | DGAT2 | DGAT2 | DGAT2 | 1279 | 0.28 | 0.25 | YES |
8 | AGPAT9 | AGPAT9 | AGPAT9 | 1413 | 0.26 | 0.27 | YES |
9 | LPIN1 | LPIN1 | LPIN1 | 1487 | 0.25 | 0.29 | YES |
10 | PLD1 | PLD1 | PLD1 | 1535 | 0.24 | 0.31 | YES |
11 | ETNK2 | ETNK2 | ETNK2 | 1594 | 0.23 | 0.33 | YES |
12 | PLD4 | PLD4 | PLD4 | 1634 | 0.23 | 0.35 | YES |
13 | GPD1L | GPD1L | GPD1L | 1912 | 0.2 | 0.36 | YES |
14 | GPCPD1 | GPCPD1 | GPCPD1 | 1970 | 0.19 | 0.37 | YES |
15 | CDS1 | CDS1 | CDS1 | 2053 | 0.19 | 0.39 | YES |
16 | PLA2G2F | PLA2G2F | PLA2G2F | 2107 | 0.18 | 0.4 | YES |
17 | PNPLA3 | PNPLA3 | PNPLA3 | 2376 | 0.16 | 0.41 | YES |
18 | PHOSPHO1 | PHOSPHO1 | PHOSPHO1 | 2401 | 0.16 | 0.42 | YES |
19 | SLC44A3 | SLC44A3 | SLC44A3 | 2465 | 0.16 | 0.44 | YES |
20 | AGPAT4 | AGPAT4 | AGPAT4 | 2658 | 0.15 | 0.44 | YES |
21 | CHKB | CHKB | CHKB | 2662 | 0.15 | 0.45 | YES |
22 | PLBD1 | PLBD1 | PLBD1 | 2675 | 0.15 | 0.47 | YES |
23 | PLA2G2D | PLA2G2D | PLA2G2D | 2744 | 0.14 | 0.48 | YES |
24 | SLC44A5 | SLC44A5 | SLC44A5 | 3244 | 0.12 | 0.46 | YES |
25 | PLA2G2A | PLA2G2A | PLA2G2A | 3259 | 0.12 | 0.48 | YES |
26 | SLC44A2 | SLC44A2 | SLC44A2 | 3338 | 0.11 | 0.48 | YES |
27 | PNPLA8 | PNPLA8 | PNPLA8 | 4159 | 0.084 | 0.45 | NO |
28 | AGPAT3 | AGPAT3 | AGPAT3 | 4464 | 0.074 | 0.44 | NO |
29 | PLA2G12A | PLA2G12A | PLA2G12A | 4759 | 0.065 | 0.43 | NO |
30 | GPAT2 | GPAT2 | GPAT2 | 5151 | 0.055 | 0.41 | NO |
31 | LPCAT2 | LPCAT2 | LPCAT2 | 5626 | 0.045 | 0.39 | NO |
32 | PLA2G4A | PLA2G4A | PLA2G4A | 5962 | 0.039 | 0.38 | NO |
33 | HADHB | HADHB | HADHB | 6285 | 0.032 | 0.36 | NO |
34 | CEPT1 | CEPT1 | CEPT1 | 6554 | 0.028 | 0.35 | NO |
35 | LPIN3 | LPIN3 | LPIN3 | 6570 | 0.028 | 0.36 | NO |
36 | PCYT1A | PCYT1A | PCYT1A | 6800 | 0.024 | 0.34 | NO |
37 | LPCAT4 | LPCAT4 | LPCAT4 | 6844 | 0.023 | 0.34 | NO |
38 | PITPNB | PITPNB | PITPNB | 7100 | 0.02 | 0.33 | NO |
39 | PLA2G6 | PLA2G6 | PLA2G6 | 7137 | 0.019 | 0.33 | NO |
40 | MBOAT1 | MBOAT1 | MBOAT1 | 7152 | 0.019 | 0.33 | NO |
41 | HADHA | HADHA | HADHA | 7583 | 0.012 | 0.31 | NO |
42 | CHPT1 | CHPT1 | CHPT1 | 7610 | 0.012 | 0.31 | NO |
43 | PLA2G5 | PLA2G5 | PLA2G5 | 8178 | 0.0036 | 0.28 | NO |
44 | PEMT | PEMT | PEMT | 8526 | -0.0012 | 0.26 | NO |
45 | PCYT1B | PCYT1B | PCYT1B | 8553 | -0.0015 | 0.26 | NO |
46 | SLC44A4 | SLC44A4 | SLC44A4 | 9097 | -0.0086 | 0.23 | NO |
47 | PNPLA2 | PNPLA2 | PNPLA2 | 9175 | -0.0095 | 0.23 | NO |
48 | EPT1 | EPT1 | EPT1 | 9466 | -0.013 | 0.22 | NO |
49 | GPAM | GPAM | GPAM | 9589 | -0.015 | 0.21 | NO |
50 | MBOAT7 | MBOAT7 | MBOAT7 | 10234 | -0.023 | 0.18 | NO |
51 | ACHE | ACHE | ACHE | 10488 | -0.026 | 0.17 | NO |
52 | PLD3 | PLD3 | PLD3 | 10527 | -0.027 | 0.17 | NO |
53 | TAZ | TAZ | TAZ | 10892 | -0.032 | 0.15 | NO |
54 | LPGAT1 | LPGAT1 | LPGAT1 | 11024 | -0.034 | 0.15 | NO |
55 | GNPAT | GNPAT | GNPAT | 11518 | -0.04 | 0.13 | NO |
56 | AGPAT6 | AGPAT6 | AGPAT6 | 11549 | -0.041 | 0.13 | NO |
57 | ETNK1 | ETNK1 | ETNK1 | 11633 | -0.042 | 0.13 | NO |
58 | LCLAT1 | LCLAT1 | LCLAT1 | 11787 | -0.044 | 0.13 | NO |
59 | DGAT1 | DGAT1 | DGAT1 | 12093 | -0.049 | 0.11 | NO |
60 | PTDSS2 | PTDSS2 | PTDSS2 | 12272 | -0.051 | 0.11 | NO |
61 | LPCAT3 | LPCAT3 | LPCAT3 | 12381 | -0.053 | 0.11 | NO |
62 | LPIN2 | LPIN2 | LPIN2 | 12560 | -0.055 | 0.11 | NO |
63 | CDIPT | CDIPT | CDIPT | 12693 | -0.057 | 0.1 | NO |
64 | SLC44A1 | SLC44A1 | SLC44A1 | 12696 | -0.057 | 0.11 | NO |
65 | PCYT2 | PCYT2 | PCYT2 | 12724 | -0.058 | 0.11 | NO |
66 | AGPAT5 | AGPAT5 | AGPAT5 | 13069 | -0.063 | 0.1 | NO |
67 | CDS2 | CDS2 | CDS2 | 13388 | -0.068 | 0.092 | NO |
68 | CHKA | CHKA | CHKA | 13554 | -0.07 | 0.09 | NO |
69 | CRLS1 | CRLS1 | CRLS1 | 14190 | -0.083 | 0.065 | NO |
70 | AGPAT1 | AGPAT1 | AGPAT1 | 14217 | -0.084 | 0.072 | NO |
71 | PLA2G4C | PLA2G4C | PLA2G4C | 14668 | -0.093 | 0.057 | NO |
72 | PGS1 | PGS1 | PGS1 | 15522 | -0.12 | 0.023 | NO |
73 | PTDSS1 | PTDSS1 | PTDSS1 | 15901 | -0.13 | 0.016 | NO |
74 | AGPAT2 | AGPAT2 | AGPAT2 | 16066 | -0.13 | 0.02 | NO |
75 | GPD1 | GPD1 | GPD1 | 16362 | -0.15 | 0.019 | NO |
76 | PLD6 | PLD6 | PLD6 | 16645 | -0.16 | 0.02 | NO |
77 | PLA2G16 | PLA2G16 | PLA2G16 | 17234 | -0.19 | 0.0075 | NO |
78 | PLA2G1B | PLA2G1B | PLA2G1B | 17606 | -0.21 | 0.0092 | NO |
79 | LPCAT1 | LPCAT1 | LPCAT1 | 17941 | -0.24 | 0.016 | NO |
80 | PLA2G10 | PLA2G10 | PLA2G10 | 18140 | -0.27 | 0.033 | NO |
Figure S117. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS.
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Figure S118. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit
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Table S60. 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 | KAT2B | KAT2B | KAT2B | 733 | 0.4 | 0.078 | YES |
2 | SFN | SFN | SFN | 835 | 0.37 | 0.18 | YES |
3 | G6PC | G6PC | G6PC | 1505 | 0.25 | 0.22 | YES |
4 | SGK1 | SGK1 | SGK1 | 1748 | 0.22 | 0.27 | YES |
5 | FBXO32 | FBXO32 | FBXO32 | 2328 | 0.17 | 0.28 | YES |
6 | MAPK10 | MAPK10 | MAPK10 | 2583 | 0.15 | 0.32 | YES |
7 | FASLG | FASLG | FASLG | 3566 | 0.1 | 0.29 | YES |
8 | RALA | RALA | RALA | 3817 | 0.095 | 0.31 | YES |
9 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 3969 | 0.09 | 0.33 | YES |
10 | CSNK1G1 | CSNK1G1 | CSNK1G1 | 4213 | 0.082 | 0.34 | YES |
11 | IKBKB | IKBKB | IKBKB | 4796 | 0.064 | 0.33 | YES |
12 | BCL6 | BCL6 | BCL6 | 5080 | 0.057 | 0.33 | YES |
13 | YWHAQ | YWHAQ | YWHAQ | 5159 | 0.055 | 0.34 | YES |
14 | YWHAZ | YWHAZ | YWHAZ | 5560 | 0.046 | 0.33 | YES |
15 | FOXO3 | FOXO3 | FOXO3 | 5685 | 0.044 | 0.34 | YES |
16 | FOXO1 | FOXO1 | FOXO1 | 5777 | 0.042 | 0.34 | YES |
17 | EP300 | EP300 | EP300 | 5848 | 0.04 | 0.35 | YES |
18 | FOXO4 | FOXO4 | FOXO4 | 5911 | 0.04 | 0.36 | YES |
19 | RALB | RALB | RALB | 5936 | 0.039 | 0.37 | YES |
20 | USP7 | USP7 | USP7 | 6917 | 0.022 | 0.33 | NO |
21 | CDKN1B | CDKN1B | CDKN1B | 7113 | 0.019 | 0.32 | NO |
22 | CSNK1E | CSNK1E | CSNK1E | 7369 | 0.015 | 0.31 | NO |
23 | MAPK8 | MAPK8 | MAPK8 | 7737 | 0.01 | 0.3 | NO |
24 | ZFAND5 | ZFAND5 | ZFAND5 | 7829 | 0.0088 | 0.29 | NO |
25 | CSNK1G3 | CSNK1G3 | CSNK1G3 | 8096 | 0.0048 | 0.28 | NO |
26 | YWHAB | YWHAB | YWHAB | 8192 | 0.0035 | 0.28 | NO |
27 | BCL2L11 | BCL2L11 | BCL2L11 | 8228 | 0.003 | 0.28 | NO |
28 | YWHAE | YWHAE | YWHAE | 8267 | 0.0023 | 0.27 | NO |
29 | CREBBP | CREBBP | CREBBP | 8347 | 0.0012 | 0.27 | NO |
30 | RBL2 | RBL2 | RBL2 | 8356 | 0.0011 | 0.27 | NO |
31 | SIRT1 | SIRT1 | SIRT1 | 8461 | -0.00038 | 0.26 | NO |
32 | CSNK1G2 | CSNK1G2 | CSNK1G2 | 9140 | -0.0091 | 0.23 | NO |
33 | SOD2 | SOD2 | SOD2 | 9181 | -0.0096 | 0.23 | NO |
34 | CTNNB1 | CTNNB1 | CTNNB1 | 9385 | -0.012 | 0.22 | NO |
35 | GADD45A | GADD45A | GADD45A | 9732 | -0.017 | 0.21 | NO |
36 | CSNK1D | CSNK1D | CSNK1D | 10014 | -0.02 | 0.2 | NO |
37 | SKP2 | SKP2 | SKP2 | 10037 | -0.021 | 0.21 | NO |
38 | RAN | RAN | RAN | 11339 | -0.038 | 0.15 | NO |
39 | CHUK | CHUK | CHUK | 11405 | -0.039 | 0.16 | NO |
40 | XPO1 | XPO1 | XPO1 | 12004 | -0.048 | 0.14 | NO |
41 | YWHAG | YWHAG | YWHAG | 12055 | -0.048 | 0.15 | NO |
42 | AKT1 | AKT1 | AKT1 | 12218 | -0.05 | 0.16 | NO |
43 | MST1 | MST1 | MST1 | 13172 | -0.064 | 0.12 | NO |
44 | YWHAH | YWHAH | YWHAH | 13983 | -0.079 | 0.1 | NO |
45 | CAT | CAT | CAT | 14657 | -0.093 | 0.095 | NO |
46 | CCNB1 | CCNB1 | CCNB1 | 14713 | -0.094 | 0.12 | NO |
47 | MAPK9 | MAPK9 | MAPK9 | 14790 | -0.096 | 0.14 | NO |
48 | CDK2 | CDK2 | CDK2 | 14956 | -0.1 | 0.16 | NO |
49 | PLK1 | PLK1 | PLK1 | 16023 | -0.13 | 0.15 | NO |
Figure S119. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRIF MEDIATED TLR3 SIGNALING.

Figure S120. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRIF MEDIATED TLR3 SIGNALING, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

For the top enriched genes, if you want to check whether they are
-
up-regulated, please check the list of up-regulated genes
-
down-regulated, please check the list of down-regulated genes
For the top enriched genes, if you want to check whether they are
-
highly expressed genes, please check the list of high (top 30%) expressed genes
-
low expressed genes, please check the list of low (bottom 30%) expressed genes
An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap
For the top enriched genes, if you want to check whether they are
-
significantly differently expressed genes by eBayes lm fit, please check the list of significant genes
-
Gene set database = c2.cp.v4.0.symbols.gmt
-
Expression data file = ESCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
-
Phenotype data file = ESCA-TP.mergedcluster.txt
For the Gene Set Enrichment Analysis (GSEA), Broad GSEA-P-R.1.0 version is used with class2: canonical pathways geneses from MSigDB. Further details about statistics are available inThe Broad GSEA website.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.