GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in PAAD-TP
Pancreatic Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1H70F83
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in PAAD-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1H70F83
Overview
Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes having more than three samples and the input expression file "PAAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:

  1. For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.

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

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

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

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

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

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 730
Number of samples: 178
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 5 :[ clus1 ] 39
pheno.type: 2 - 5 :[ clus2 ] 26
pheno.type: 3 - 5 :[ clus3 ] 43
pheno.type: 4 - 5 :[ clus4 ] 40
pheno.type: 5 - 5 :[ clus5 ] 30

For the expression subtypes of 18475 genes in 179 samples, GSEA found enriched gene sets in each cluster using 178 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG RETINOL METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM CYTOCHROME P450, KEGG DRUG METABOLISM OTHER ENZYMES, KEGG BASE EXCISION REPAIR

    • And common core enriched genes are UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT2A3, UGT2B10

  • clus2

    • Top enriched gene sets are KEGG LYSINE DEGRADATION, KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA CHREBP2 PATHWAY, SIG CD40PATHWAYMAP, PID P38 MKK3 6PATHWAY, PID LKB1 PATHWAY, PID LIS1PATHWAY, PID HEDGEHOG GLIPATHWAY, REACTOME TRANS GOLGI NETWORK VESICLE BUDDING

    • And common core enriched genes are MLXIPL, PKLR, PRKAR2B, OGDHL, PIPOX, GCK, PPP2R2B, PPP2R2C, PPP2R3B, CACNG2

  • clus3

    • Top enriched gene sets are KEGG DNA REPLICATION, KEGG CELL CYCLE, KEGG P53 SIGNALING PATHWAY, BIOCARTA RACCYCD PATHWAY, PID P73PATHWAY, PID E2F PATHWAY, PID ATR PATHWAY, PID FRA PATHWAY, PID MYC ACTIVPATHWAY, PID PLK1 PATHWAY

    • And common core enriched genes are CCNB1, CDK1, CDK2, CCNA2, CCNB2, PLK1, CCNE2, CDK6, CHEK1, AZI1

  • clus4

    • Top enriched gene sets are KEGG FATTY ACID METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG GLYCEROLIPID METABOLISM, KEGG PROPANOATE METABOLISM, KEGG ENDOCYTOSIS, SIG PIP3 SIGNALING IN CARDIAC MYOCTES, SIG CHEMOTAXIS, SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES, PID INSULIN PATHWAY

    • And common core enriched genes are ERBB4, F2RL2, CBS, CTH, GGT1, GGT6, MAT1A, EGF, FOXO3, NRG2

  • clus5

    • Top enriched gene sets are KEGG PURINE METABOLISM, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG ABC TRANSPORTERS, KEGG MAPK SIGNALING PATHWAY, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION, KEGG OOCYTE MEIOSIS, KEGG MTOR SIGNALING PATHWAY, KEGG APOPTOSIS

    • And common core enriched genes are FYN, HCK, LCK, PSMA8, SLC2A4, BLK, PIK3CD, AP1S2, APOBEC3G, CD247

Results
Subtype clus1 enriched pathways

Table 3.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS 26 genes.ES.table 0.81 1.7 0.0065 1 0.81 0.58 0.066 0.54 0.51 0.3
KEGG FRUCTOSE AND MANNOSE METABOLISM 34 genes.ES.table 0.44 1.4 0.1 1 1 0.32 0.16 0.27 0.95 0.47
KEGG STEROID HORMONE BIOSYNTHESIS 50 genes.ES.table 0.61 1.4 0.043 1 0.99 0.46 0.068 0.43 0.91 0.45
KEGG RETINOL METABOLISM 59 genes.ES.table 0.72 1.7 0 1 0.85 0.64 0.13 0.56 0.5 0.29
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 38 genes.ES.table 0.64 1.6 0.044 1 0.96 0.34 0.066 0.32 0.63 0.32
KEGG AMINOACYL TRNA BIOSYNTHESIS 41 genes.ES.table 0.41 1.5 0.13 1 0.99 1 0.59 0.41 0.82 0.4
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 65 genes.ES.table 0.67 1.5 0.015 0.86 0.97 0.58 0.14 0.51 0.53 0.26
KEGG DRUG METABOLISM CYTOCHROME P450 66 genes.ES.table 0.62 1.4 0.047 1 0.99 0.48 0.082 0.45 0.94 0.46
KEGG DRUG METABOLISM OTHER ENZYMES 47 genes.ES.table 0.71 1.7 0 1 0.78 0.47 0.066 0.44 0.68 0.39
KEGG BASE EXCISION REPAIR 33 genes.ES.table 0.58 1.7 0.054 1 0.76 0.46 0.24 0.35 1 0.56
genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

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 POLE2 POLE2 POLE2 996 0.22 0.051 YES
2 NTHL1 NTHL1 NTHL1 1367 0.18 0.12 YES
3 NEIL3 NEIL3 NEIL3 1476 0.17 0.19 YES
4 MUTYH MUTYH MUTYH 1666 0.15 0.25 YES
5 NEIL1 NEIL1 NEIL1 1958 0.13 0.3 YES
6 POLD4 POLD4 POLD4 1971 0.13 0.36 YES
7 PARP3 PARP3 PARP3 2038 0.13 0.41 YES
8 SMUG1 SMUG1 SMUG1 2457 0.11 0.44 YES
9 PARP4 PARP4 PARP4 2590 0.1 0.48 YES
10 POLD3 POLD3 POLD3 2637 0.098 0.52 YES
11 POLE POLE POLE 3224 0.078 0.53 YES
12 MPG MPG MPG 3485 0.071 0.55 YES
13 POLB POLB POLB 3556 0.069 0.58 YES
14 POLL POLL POLL 4057 0.056 0.57 YES
15 POLD2 POLD2 POLD2 4437 0.048 0.58 YES
16 POLE4 POLE4 POLE4 4846 0.04 0.57 NO
17 APEX2 APEX2 APEX2 5141 0.034 0.57 NO
18 OGG1 OGG1 OGG1 5434 0.029 0.57 NO
19 PCNA PCNA PCNA 6042 0.02 0.55 NO
20 MBD4 MBD4 MBD4 6332 0.016 0.54 NO
21 LIG3 LIG3 LIG3 6371 0.016 0.55 NO
22 POLD1 POLD1 POLD1 6586 0.012 0.54 NO
23 HMGB1 HMGB1 HMGB1 6914 0.0078 0.52 NO
24 UNG UNG UNG 6977 0.0071 0.52 NO
25 LIG1 LIG1 LIG1 7154 0.005 0.52 NO
26 APEX1 APEX1 APEX1 7626 -0.0017 0.49 NO
27 TDG TDG TDG 7780 -0.0037 0.49 NO
28 XRCC1 XRCC1 XRCC1 7956 -0.006 0.48 NO
29 FEN1 FEN1 FEN1 8038 -0.007 0.48 NO
30 PARP1 PARP1 PARP1 8813 -0.019 0.45 NO
31 POLE3 POLE3 POLE3 8921 -0.021 0.45 NO
32 PARP2 PARP2 PARP2 10309 -0.043 0.4 NO
33 NEIL2 NEIL2 NEIL2 12673 -0.1 0.31 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS.

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

Table 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 CYP3A7 CYP3A7 CYP3A7 70 0.56 0.055 YES
2 UGT1A1 UGT1A1 UGT1A1 78 0.55 0.11 YES
3 UGT1A9 UGT1A9 UGT1A9 145 0.48 0.16 YES
4 NAT2 NAT2 NAT2 156 0.47 0.21 YES
5 CYP3A5 CYP3A5 CYP3A5 236 0.42 0.25 YES
6 UGT1A3 UGT1A3 UGT1A3 246 0.41 0.29 YES
7 CYP3A4 CYP3A4 CYP3A4 274 0.4 0.33 YES
8 CYP2A7 CYP2A7 CYP2A7 296 0.39 0.37 YES
9 UGT1A8 UGT1A8 UGT1A8 367 0.36 0.4 YES
10 UGT2B7 UGT2B7 UGT2B7 412 0.34 0.44 YES
11 UGT1A10 UGT1A10 UGT1A10 450 0.33 0.47 YES
12 UGT1A4 UGT1A4 UGT1A4 470 0.33 0.5 YES
13 UGT2B10 UGT2B10 UGT2B10 624 0.29 0.52 YES
14 UGT1A6 UGT1A6 UGT1A6 751 0.27 0.55 YES
15 XDH XDH XDH 845 0.25 0.57 YES
16 UGT2A3 UGT2A3 UGT2A3 867 0.24 0.59 YES
17 CYP2A6 CYP2A6 CYP2A6 872 0.24 0.62 YES
18 UGT2B28 UGT2B28 UGT2B28 1015 0.22 0.63 YES
19 UGT1A7 UGT1A7 UGT1A7 1069 0.21 0.65 YES
20 NAT1 NAT1 NAT1 1080 0.21 0.67 YES
21 CES2 CES2 CES2 1134 0.2 0.69 YES
22 UGT2B15 UGT2B15 UGT2B15 1210 0.19 0.71 YES
23 UCK2 UCK2 UCK2 2189 0.12 0.67 NO
24 UGT2B11 UGT2B11 UGT2B11 2269 0.12 0.67 NO
25 TPMT TPMT TPMT 2272 0.11 0.69 NO
26 UGT2A1 UGT2A1 UGT2A1 2473 0.1 0.69 NO
27 TK1 TK1 TK1 2723 0.095 0.68 NO
28 ITPA ITPA ITPA 3059 0.083 0.67 NO
29 HPRT1 HPRT1 HPRT1 3611 0.068 0.65 NO
30 GUSB GUSB GUSB 3708 0.065 0.65 NO
31 UCKL1 UCKL1 UCKL1 4659 0.044 0.6 NO
32 UMPS UMPS UMPS 6016 0.02 0.53 NO
33 IMPDH2 IMPDH2 IMPDH2 6031 0.02 0.54 NO
34 GMPS GMPS GMPS 7038 0.0064 0.48 NO
35 TK2 TK2 TK2 7463 0.00044 0.46 NO
36 UPP1 UPP1 UPP1 7991 -0.0065 0.43 NO
37 UGT2B4 UGT2B4 UGT2B4 8130 -0.0082 0.42 NO
38 CYP3A43 CYP3A43 CYP3A43 9192 -0.024 0.37 NO
39 IMPDH1 IMPDH1 IMPDH1 10073 -0.039 0.32 NO
40 CDA CDA CDA 10342 -0.043 0.31 NO
41 UCK1 UCK1 UCK1 11628 -0.07 0.25 NO
42 TYMP TYMP TYMP 11639 -0.07 0.26 NO
43 CES1 CES1 CES1 13275 -0.12 0.18 NO
44 DPYD DPYD DPYD 14195 -0.17 0.15 NO
45 UPP2 UPP2 UPP2 14772 -0.2 0.14 NO
46 DPYS DPYS DPYS 15830 -0.27 0.11 NO
47 UPB1 UPB1 UPB1 16405 -0.3 0.11 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 FRUCTOSE AND MANNOSE METABOLISM.

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

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 UGT1A1 UGT1A1 UGT1A1 78 0.55 0.098 YES
2 UGT1A9 UGT1A9 UGT1A9 145 0.48 0.18 YES
3 UGT1A3 UGT1A3 UGT1A3 246 0.41 0.26 YES
4 UGT1A8 UGT1A8 UGT1A8 367 0.36 0.32 YES
5 UGT2B7 UGT2B7 UGT2B7 412 0.34 0.38 YES
6 UGT1A10 UGT1A10 UGT1A10 450 0.33 0.44 YES
7 UGT1A4 UGT1A4 UGT1A4 470 0.33 0.5 YES
8 UGT2B10 UGT2B10 UGT2B10 624 0.29 0.54 YES
9 UGT1A6 UGT1A6 UGT1A6 751 0.27 0.59 YES
10 XYLB XYLB XYLB 807 0.25 0.63 YES
11 UGT2A3 UGT2A3 UGT2A3 867 0.24 0.67 YES
12 UGT2B28 UGT2B28 UGT2B28 1015 0.22 0.71 YES
13 UGT1A7 UGT1A7 UGT1A7 1069 0.21 0.74 YES
14 CRYL1 CRYL1 CRYL1 1181 0.2 0.77 YES
15 UGT2B15 UGT2B15 UGT2B15 1210 0.19 0.81 YES
16 DHDH DHDH DHDH 2116 0.12 0.78 NO
17 UGT2B11 UGT2B11 UGT2B11 2269 0.12 0.8 NO
18 UGT2A1 UGT2A1 UGT2A1 2473 0.1 0.8 NO
19 GUSB GUSB GUSB 3708 0.065 0.75 NO
20 DCXR DCXR DCXR 4791 0.041 0.7 NO
21 RPE RPE RPE 6815 0.0092 0.59 NO
22 UGDH UGDH UGDH 7569 -0.00097 0.55 NO
23 UGT2B4 UGT2B4 UGT2B4 8130 -0.0082 0.52 NO
24 UGP2 UGP2 UGP2 9611 -0.032 0.45 NO
25 LOC729020 LOC729020 LOC729020 9741 -0.034 0.44 NO
26 AKR1B1 AKR1B1 AKR1B1 13744 -0.15 0.26 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 STEROID HORMONE BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RETINOL METABOLISM

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 CYP3A7 CYP3A7 CYP3A7 70 0.56 0.037 YES
2 CYP2B6 CYP2B6 CYP2B6 76 0.55 0.078 YES
3 UGT1A1 UGT1A1 UGT1A1 78 0.55 0.12 YES
4 CYP2C9 CYP2C9 CYP2C9 91 0.53 0.16 YES
5 CYP2C19 CYP2C19 CYP2C19 95 0.53 0.19 YES
6 CYP2C18 CYP2C18 CYP2C18 128 0.5 0.23 YES
7 UGT1A9 UGT1A9 UGT1A9 145 0.48 0.26 YES
8 BCMO1 BCMO1 BCMO1 150 0.48 0.3 YES
9 CYP3A5 CYP3A5 CYP3A5 236 0.42 0.32 YES
10 UGT1A3 UGT1A3 UGT1A3 246 0.41 0.35 YES
11 CYP3A4 CYP3A4 CYP3A4 274 0.4 0.38 YES
12 CYP2A7 CYP2A7 CYP2A7 296 0.39 0.41 YES
13 UGT1A8 UGT1A8 UGT1A8 367 0.36 0.43 YES
14 UGT2B7 UGT2B7 UGT2B7 412 0.34 0.45 YES
15 ADH6 ADH6 ADH6 441 0.33 0.48 YES
16 UGT1A10 UGT1A10 UGT1A10 450 0.33 0.5 YES
17 UGT1A4 UGT1A4 UGT1A4 470 0.33 0.52 YES
18 RDH5 RDH5 RDH5 515 0.32 0.54 YES
19 UGT2B10 UGT2B10 UGT2B10 624 0.29 0.56 YES
20 ADH1C ADH1C ADH1C 745 0.27 0.57 YES
21 UGT1A6 UGT1A6 UGT1A6 751 0.27 0.59 YES
22 DHRS9 DHRS9 DHRS9 811 0.25 0.6 YES
23 UGT2A3 UGT2A3 UGT2A3 867 0.24 0.62 YES
24 CYP2A6 CYP2A6 CYP2A6 872 0.24 0.64 YES
25 DGAT2 DGAT2 DGAT2 914 0.23 0.65 YES
26 RDH12 RDH12 RDH12 983 0.22 0.66 YES
27 UGT2B28 UGT2B28 UGT2B28 1015 0.22 0.68 YES
28 UGT1A7 UGT1A7 UGT1A7 1069 0.21 0.69 YES
29 UGT2B15 UGT2B15 UGT2B15 1210 0.19 0.7 YES
30 CYP26A1 CYP26A1 CYP26A1 1285 0.19 0.71 YES
31 DGAT1 DGAT1 DGAT1 1310 0.18 0.72 YES
32 RETSAT RETSAT RETSAT 1574 0.16 0.72 YES
33 CYP4A11 CYP4A11 CYP4A11 1697 0.15 0.72 YES
34 RDH10 RDH10 RDH10 1928 0.13 0.72 YES
35 RDH16 RDH16 RDH16 2263 0.12 0.71 YES
36 UGT2B11 UGT2B11 UGT2B11 2269 0.12 0.72 YES
37 DHRS3 DHRS3 DHRS3 2391 0.11 0.72 YES
38 UGT2A1 UGT2A1 UGT2A1 2473 0.1 0.72 YES
39 ADH4 ADH4 ADH4 2636 0.098 0.72 NO
40 CYP2C8 CYP2C8 CYP2C8 3908 0.06 0.66 NO
41 ALDH1A1 ALDH1A1 ALDH1A1 4300 0.05 0.64 NO
42 DHRS4L2 DHRS4L2 DHRS4L2 4918 0.038 0.61 NO
43 PNPLA4 PNPLA4 PNPLA4 5954 0.021 0.55 NO
44 CYP26C1 CYP26C1 CYP26C1 6699 0.011 0.51 NO
45 DHRS4 DHRS4 DHRS4 7310 0.0027 0.48 NO
46 RDH11 RDH11 RDH11 7621 -0.0016 0.46 NO
47 UGT2B4 UGT2B4 UGT2B4 8130 -0.0082 0.44 NO
48 ADH5 ADH5 ADH5 9149 -0.024 0.38 NO
49 CYP3A43 CYP3A43 CYP3A43 9192 -0.024 0.38 NO
50 ALDH1A2 ALDH1A2 ALDH1A2 10807 -0.052 0.3 NO
51 CYP1A1 CYP1A1 CYP1A1 12120 -0.084 0.23 NO
52 CYP1A2 CYP1A2 CYP1A2 12282 -0.089 0.23 NO
53 LRAT LRAT LRAT 12519 -0.096 0.22 NO
54 RDH8 RDH8 RDH8 12630 -0.1 0.23 NO
55 RPE65 RPE65 RPE65 13797 -0.15 0.17 NO
56 ADH1A ADH1A ADH1A 14031 -0.16 0.17 NO
57 AWAT2 AWAT2 AWAT2 14652 -0.19 0.15 NO
58 ADH1B ADH1B ADH1B 16672 -0.32 0.067 NO
59 CYP26B1 CYP26B1 CYP26B1 17689 -0.41 0.042 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 RETINOL METABOLISM.

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

genes ES table in pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM

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 NDUFA7 NDUFA7 NDUFA7 1899 0.14 -0.06 YES
2 COX5A COX5A COX5A 2205 0.12 -0.04 YES
3 COX5B COX5B COX5B 2369 0.11 -0.014 YES
4 COX7B COX7B COX7B 2730 0.094 -0.0035 YES
5 NDUFV2 NDUFV2 NDUFV2 3168 0.08 -0.002 YES
6 UQCRQ UQCRQ UQCRQ 3170 0.08 0.023 YES
7 COX6A1 COX6A1 COX6A1 3207 0.079 0.046 YES
8 NDUFS7 NDUFS7 NDUFS7 3278 0.077 0.067 YES
9 NDUFA4 NDUFA4 NDUFA4 3319 0.076 0.088 YES
10 CYCS CYCS CYCS 3354 0.074 0.11 YES
11 NDUFA3 NDUFA3 NDUFA3 3371 0.074 0.13 YES
12 NDUFB3 NDUFB3 NDUFB3 3418 0.072 0.15 YES
13 COX6B1 COX6B1 COX6B1 3420 0.072 0.18 YES
14 ETFB ETFB ETFB 3486 0.071 0.2 YES
15 ETFA ETFA ETFA 3508 0.07 0.22 YES
16 SDHA SDHA SDHA 3537 0.07 0.24 YES
17 NDUFC1 NDUFC1 NDUFC1 3598 0.068 0.26 YES
18 NDUFB7 NDUFB7 NDUFB7 3617 0.067 0.28 YES
19 UQCRHL UQCRHL UQCRHL 3669 0.066 0.29 YES
20 NDUFA1 NDUFA1 NDUFA1 3812 0.062 0.31 YES
21 NDUFA2 NDUFA2 NDUFA2 3856 0.061 0.32 YES
22 NDUFS3 NDUFS3 NDUFS3 3871 0.061 0.34 YES
23 COX6C COX6C COX6C 3880 0.061 0.36 YES
24 COX4I1 COX4I1 COX4I1 3891 0.06 0.38 YES
25 NDUFS6 NDUFS6 NDUFS6 3894 0.06 0.4 YES
26 UQCR11 UQCR11 UQCR11 3977 0.058 0.41 YES
27 CYC1 CYC1 CYC1 4096 0.055 0.42 YES
28 COX7C COX7C COX7C 4120 0.054 0.44 YES
29 NDUFS2 NDUFS2 NDUFS2 4135 0.054 0.46 YES
30 NDUFB10 NDUFB10 NDUFB10 4140 0.054 0.47 YES
31 NDUFA12 NDUFA12 NDUFA12 4144 0.054 0.49 YES
32 UQCRC1 UQCRC1 UQCRC1 4149 0.054 0.51 YES
33 SDHC SDHC SDHC 4375 0.049 0.51 YES
34 UQCRH UQCRH UQCRH 4384 0.049 0.52 YES
35 NDUFA13 NDUFA13 NDUFA13 4505 0.047 0.53 YES
36 NDUFS5 NDUFS5 NDUFS5 4632 0.044 0.54 YES
37 NDUFB1 NDUFB1 NDUFB1 4705 0.042 0.55 YES
38 COX8A COX8A COX8A 4748 0.042 0.56 YES
39 NDUFA10 NDUFA10 NDUFA10 4785 0.041 0.57 YES
40 NDUFAB1 NDUFAB1 NDUFAB1 4799 0.04 0.58 YES
41 ETFDH ETFDH ETFDH 4850 0.04 0.59 YES
42 NDUFB8 NDUFB8 NDUFB8 4891 0.039 0.6 YES
43 UQCRC2 UQCRC2 UQCRC2 4931 0.038 0.61 YES
44 NDUFA9 NDUFA9 NDUFA9 5109 0.035 0.62 YES
45 NDUFS8 NDUFS8 NDUFS8 5113 0.035 0.63 YES
46 NDUFA11 NDUFA11 NDUFA11 5127 0.035 0.64 YES
47 NDUFC2 NDUFC2 NDUFC2 5292 0.032 0.64 YES
48 NDUFV3 NDUFV3 NDUFV3 5327 0.031 0.64 YES
49 NDUFB9 NDUFB9 NDUFB9 5504 0.028 0.64 YES
50 NDUFB2 NDUFB2 NDUFB2 5854 0.023 0.63 YES
51 NDUFA8 NDUFA8 NDUFA8 5978 0.021 0.63 YES
52 NDUFB4 NDUFB4 NDUFB4 6072 0.019 0.63 YES
53 NDUFV1 NDUFV1 NDUFV1 6083 0.019 0.64 YES
54 UQCRFS1 UQCRFS1 UQCRFS1 6237 0.017 0.64 YES
55 NDUFA5 NDUFA5 NDUFA5 6290 0.016 0.64 YES
56 NDUFA6 NDUFA6 NDUFA6 6291 0.016 0.64 YES
57 NDUFS4 NDUFS4 NDUFS4 6338 0.016 0.65 YES
58 SDHD SDHD SDHD 6521 0.013 0.64 NO
59 NDUFB5 NDUFB5 NDUFB5 6528 0.013 0.64 NO
60 NDUFS1 NDUFS1 NDUFS1 7287 0.0031 0.6 NO
61 COX7A2L COX7A2L COX7A2L 7351 0.002 0.6 NO
62 NDUFB6 NDUFB6 NDUFB6 7440 0.00073 0.6 NO
63 SDHB SDHB SDHB 7647 -0.002 0.59 NO
64 UQCRB UQCRB UQCRB 7728 -0.0031 0.58 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 PORPHYRIN AND CHLOROPHYLL METABOLISM.

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

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 NDUFA7 NDUFA7 NDUFA7 1899 0.14 -0.068 YES
2 COX5A COX5A COX5A 2205 0.12 -0.055 YES
3 COX5B COX5B COX5B 2369 0.11 -0.035 YES
4 ATP5D ATP5D ATP5D 2440 0.11 -0.011 YES
5 COX7B COX7B COX7B 2730 0.094 -0.0028 YES
6 ATP5I ATP5I ATP5I 3092 0.082 -0.0012 YES
7 NDUFV2 NDUFV2 NDUFV2 3168 0.08 0.015 YES
8 UQCRQ UQCRQ UQCRQ 3170 0.08 0.036 YES
9 COX6A1 COX6A1 COX6A1 3207 0.079 0.054 YES
10 NDUFS7 NDUFS7 NDUFS7 3278 0.077 0.07 YES
11 NDUFA4 NDUFA4 NDUFA4 3319 0.076 0.088 YES
12 CYCS CYCS CYCS 3354 0.074 0.1 YES
13 NDUFA3 NDUFA3 NDUFA3 3371 0.074 0.12 YES
14 NDUFB3 NDUFB3 NDUFB3 3418 0.072 0.14 YES
15 COX6B1 COX6B1 COX6B1 3420 0.072 0.16 YES
16 ETFB ETFB ETFB 3486 0.071 0.17 YES
17 ETFA ETFA ETFA 3508 0.07 0.19 YES
18 SDHA SDHA SDHA 3537 0.07 0.21 YES
19 NDUFC1 NDUFC1 NDUFC1 3598 0.068 0.22 YES
20 NDUFB7 NDUFB7 NDUFB7 3617 0.067 0.24 YES
21 UQCRHL UQCRHL UQCRHL 3669 0.066 0.25 YES
22 NDUFA1 NDUFA1 NDUFA1 3812 0.062 0.26 YES
23 ATP5J2 ATP5J2 ATP5J2 3845 0.062 0.27 YES
24 NDUFA2 NDUFA2 NDUFA2 3856 0.061 0.29 YES
25 NDUFS3 NDUFS3 NDUFS3 3871 0.061 0.3 YES
26 COX6C COX6C COX6C 3880 0.061 0.32 YES
27 COX4I1 COX4I1 COX4I1 3891 0.06 0.33 YES
28 NDUFS6 NDUFS6 NDUFS6 3894 0.06 0.35 YES
29 UQCR11 UQCR11 UQCR11 3977 0.058 0.36 YES
30 ATP5G1 ATP5G1 ATP5G1 3990 0.058 0.38 YES
31 ATP5C1 ATP5C1 ATP5C1 4051 0.056 0.39 YES
32 CYC1 CYC1 CYC1 4096 0.055 0.4 YES
33 COX7C COX7C COX7C 4120 0.054 0.41 YES
34 NDUFS2 NDUFS2 NDUFS2 4135 0.054 0.42 YES
35 NDUFB10 NDUFB10 NDUFB10 4140 0.054 0.44 YES
36 NDUFA12 NDUFA12 NDUFA12 4144 0.054 0.45 YES
37 UQCRC1 UQCRC1 UQCRC1 4149 0.054 0.46 YES
38 SDHC SDHC SDHC 4375 0.049 0.46 YES
39 UQCRH UQCRH UQCRH 4384 0.049 0.48 YES
40 ATP5O ATP5O ATP5O 4493 0.047 0.48 YES
41 NDUFA13 NDUFA13 NDUFA13 4505 0.047 0.5 YES
42 NDUFS5 NDUFS5 NDUFS5 4632 0.044 0.5 YES
43 NDUFB1 NDUFB1 NDUFB1 4705 0.042 0.51 YES
44 COX8A COX8A COX8A 4748 0.042 0.52 YES
45 NDUFA10 NDUFA10 NDUFA10 4785 0.041 0.52 YES
46 NDUFAB1 NDUFAB1 NDUFAB1 4799 0.04 0.53 YES
47 ETFDH ETFDH ETFDH 4850 0.04 0.54 YES
48 NDUFB8 NDUFB8 NDUFB8 4891 0.039 0.55 YES
49 UQCRC2 UQCRC2 UQCRC2 4931 0.038 0.56 YES
50 NDUFA9 NDUFA9 NDUFA9 5109 0.035 0.56 YES
51 NDUFS8 NDUFS8 NDUFS8 5113 0.035 0.56 YES
52 NDUFA11 NDUFA11 NDUFA11 5127 0.035 0.57 YES
53 NDUFC2 NDUFC2 NDUFC2 5292 0.032 0.57 YES
54 NDUFV3 NDUFV3 NDUFV3 5327 0.031 0.58 YES
55 NDUFB9 NDUFB9 NDUFB9 5504 0.028 0.58 YES
56 NDUFB2 NDUFB2 NDUFB2 5854 0.023 0.56 YES
57 ATP5B ATP5B ATP5B 5903 0.022 0.57 YES
58 NDUFA8 NDUFA8 NDUFA8 5978 0.021 0.57 YES
59 ATP5E ATP5E ATP5E 6015 0.02 0.57 YES
60 NDUFB4 NDUFB4 NDUFB4 6072 0.019 0.57 YES
61 NDUFV1 NDUFV1 NDUFV1 6083 0.019 0.58 YES
62 UQCRFS1 UQCRFS1 UQCRFS1 6237 0.017 0.57 YES
63 ATP5L ATP5L ATP5L 6287 0.016 0.57 YES
64 NDUFA5 NDUFA5 NDUFA5 6290 0.016 0.58 YES
65 NDUFA6 NDUFA6 NDUFA6 6291 0.016 0.58 YES
66 NDUFS4 NDUFS4 NDUFS4 6338 0.016 0.58 YES
67 ATP5H ATP5H ATP5H 6352 0.016 0.59 YES
68 SDHD SDHD SDHD 6521 0.013 0.58 NO
69 NDUFB5 NDUFB5 NDUFB5 6528 0.013 0.59 NO
70 ATP5J ATP5J ATP5J 6625 0.012 0.58 NO
71 NDUFS1 NDUFS1 NDUFS1 7287 0.0031 0.55 NO
72 COX7A2L COX7A2L COX7A2L 7351 0.002 0.55 NO
73 NDUFB6 NDUFB6 NDUFB6 7440 0.00073 0.54 NO
74 SDHB SDHB SDHB 7647 -0.002 0.53 NO
75 UQCRB UQCRB UQCRB 7728 -0.0031 0.53 NO
76 ATP5F1 ATP5F1 ATP5F1 7993 -0.0065 0.51 NO
77 UCP2 UCP2 UCP2 8479 -0.014 0.49 NO
78 ATP5A1 ATP5A1 ATP5A1 10422 -0.045 0.4 NO
79 UCP3 UCP3 UCP3 13913 -0.15 0.25 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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450

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 SLC16A8 SLC16A8 SLC16A8 1404 0.18 -0.047 YES
2 SLC16A1 SLC16A1 SLC16A1 1803 0.14 -0.045 YES
3 D2HGDH D2HGDH D2HGDH 1859 0.14 -0.025 YES
4 NDUFA7 NDUFA7 NDUFA7 1899 0.14 -0.0047 YES
5 COX5A COX5A COX5A 2205 0.12 -0.0017 YES
6 COX5B COX5B COX5B 2369 0.11 0.0077 YES
7 SUCLG2 SUCLG2 SUCLG2 2433 0.11 0.022 YES
8 ATP5D ATP5D ATP5D 2440 0.11 0.04 YES
9 IDH1 IDH1 IDH1 2689 0.096 0.042 YES
10 COX7B COX7B COX7B 2730 0.094 0.056 YES
11 ATP5I ATP5I ATP5I 3092 0.082 0.05 YES
12 NDUFV2 NDUFV2 NDUFV2 3168 0.08 0.059 YES
13 UQCRQ UQCRQ UQCRQ 3170 0.08 0.072 YES
14 COX6A1 COX6A1 COX6A1 3207 0.079 0.084 YES
15 PDK2 PDK2 PDK2 3246 0.077 0.094 YES
16 NDUFS7 NDUFS7 NDUFS7 3278 0.077 0.11 YES
17 NDUFA4 NDUFA4 NDUFA4 3319 0.076 0.12 YES
18 CYCS CYCS CYCS 3354 0.074 0.13 YES
19 NDUFA3 NDUFA3 NDUFA3 3371 0.074 0.14 YES
20 FH FH FH 3389 0.073 0.15 YES
21 NDUFB3 NDUFB3 NDUFB3 3418 0.072 0.16 YES
22 COX6B1 COX6B1 COX6B1 3420 0.072 0.17 YES
23 ETFB ETFB ETFB 3486 0.071 0.18 YES
24 ETFA ETFA ETFA 3508 0.07 0.19 YES
25 SDHA SDHA SDHA 3537 0.07 0.2 YES
26 NDUFC1 NDUFC1 NDUFC1 3598 0.068 0.21 YES
27 NDUFB7 NDUFB7 NDUFB7 3617 0.067 0.22 YES
28 UQCRHL UQCRHL UQCRHL 3669 0.066 0.23 YES
29 NDUFA1 NDUFA1 NDUFA1 3812 0.062 0.23 YES
30 ATP5J2 ATP5J2 ATP5J2 3845 0.062 0.24 YES
31 NDUFA2 NDUFA2 NDUFA2 3856 0.061 0.25 YES
32 NDUFS3 NDUFS3 NDUFS3 3871 0.061 0.26 YES
33 COX6C COX6C COX6C 3880 0.061 0.27 YES
34 COX4I1 COX4I1 COX4I1 3891 0.06 0.28 YES
35 NDUFS6 NDUFS6 NDUFS6 3894 0.06 0.29 YES
36 UQCR11 UQCR11 UQCR11 3977 0.058 0.29 YES
37 ATP5G1 ATP5G1 ATP5G1 3990 0.058 0.3 YES
38 ATP5C1 ATP5C1 ATP5C1 4051 0.056 0.31 YES
39 CYC1 CYC1 CYC1 4096 0.055 0.31 YES
40 COX7C COX7C COX7C 4120 0.054 0.32 YES
41 NDUFS2 NDUFS2 NDUFS2 4135 0.054 0.33 YES
42 NDUFB10 NDUFB10 NDUFB10 4140 0.054 0.34 YES
43 NDUFA12 NDUFA12 NDUFA12 4144 0.054 0.35 YES
44 UQCRC1 UQCRC1 UQCRC1 4149 0.054 0.36 YES
45 SDHC SDHC SDHC 4375 0.049 0.35 YES
46 UQCRH UQCRH UQCRH 4384 0.049 0.36 YES
47 BSG BSG BSG 4418 0.048 0.37 YES
48 ATP5O ATP5O ATP5O 4493 0.047 0.37 YES
49 NDUFA13 NDUFA13 NDUFA13 4505 0.047 0.38 YES
50 MDH2 MDH2 MDH2 4525 0.046 0.38 YES
51 NDUFS5 NDUFS5 NDUFS5 4632 0.044 0.39 YES
52 NDUFB1 NDUFB1 NDUFB1 4705 0.042 0.39 YES
53 COX8A COX8A COX8A 4748 0.042 0.39 YES
54 NDUFA10 NDUFA10 NDUFA10 4785 0.041 0.4 YES
55 NDUFAB1 NDUFAB1 NDUFAB1 4799 0.04 0.4 YES
56 ETFDH ETFDH ETFDH 4850 0.04 0.41 YES
57 NDUFB8 NDUFB8 NDUFB8 4891 0.039 0.41 YES
58 UQCRC2 UQCRC2 UQCRC2 4931 0.038 0.42 YES
59 NDUFA9 NDUFA9 NDUFA9 5109 0.035 0.41 YES
60 NDUFS8 NDUFS8 NDUFS8 5113 0.035 0.42 YES
61 NDUFA11 NDUFA11 NDUFA11 5127 0.035 0.42 YES
62 NDUFC2 NDUFC2 NDUFC2 5292 0.032 0.42 YES
63 NDUFV3 NDUFV3 NDUFV3 5327 0.031 0.42 YES
64 SUCLG1 SUCLG1 SUCLG1 5369 0.03 0.43 YES
65 NDUFB9 NDUFB9 NDUFB9 5504 0.028 0.42 YES
66 OGDH OGDH OGDH 5597 0.027 0.42 YES
67 LDHA LDHA LDHA 5710 0.025 0.42 YES
68 IDH3B IDH3B IDH3B 5806 0.024 0.42 YES
69 NDUFB2 NDUFB2 NDUFB2 5854 0.023 0.42 YES
70 ATP5B ATP5B ATP5B 5903 0.022 0.42 YES
71 IDH3G IDH3G IDH3G 5925 0.022 0.43 YES
72 NDUFA8 NDUFA8 NDUFA8 5978 0.021 0.43 YES
73 ATP5E ATP5E ATP5E 6015 0.02 0.43 YES
74 NDUFB4 NDUFB4 NDUFB4 6072 0.019 0.43 YES
75 NDUFV1 NDUFV1 NDUFV1 6083 0.019 0.43 YES
76 PDHA1 PDHA1 PDHA1 6109 0.019 0.43 YES
77 UQCRFS1 UQCRFS1 UQCRFS1 6237 0.017 0.43 YES
78 ATP5L ATP5L ATP5L 6287 0.016 0.43 YES
79 NDUFA5 NDUFA5 NDUFA5 6290 0.016 0.43 YES
80 NDUFA6 NDUFA6 NDUFA6 6291 0.016 0.43 YES
81 NDUFS4 NDUFS4 NDUFS4 6338 0.016 0.43 YES
82 ATP5H ATP5H ATP5H 6352 0.016 0.44 YES
83 SDHD SDHD SDHD 6521 0.013 0.43 NO
84 NDUFB5 NDUFB5 NDUFB5 6528 0.013 0.43 NO
85 ACO2 ACO2 ACO2 6573 0.013 0.43 NO
86 ATP5J ATP5J ATP5J 6625 0.012 0.43 NO
87 SLC16A3 SLC16A3 SLC16A3 6653 0.012 0.43 NO
88 PDHX PDHX PDHX 6826 0.009 0.42 NO
89 DLST DLST DLST 7176 0.0046 0.4 NO
90 PDP2 PDP2 PDP2 7273 0.0034 0.4 NO
91 NDUFS1 NDUFS1 NDUFS1 7287 0.0031 0.4 NO
92 COX7A2L COX7A2L COX7A2L 7351 0.002 0.4 NO
93 CS CS CS 7379 0.0017 0.4 NO
94 NDUFB6 NDUFB6 NDUFB6 7440 0.00073 0.39 NO
95 SDHB SDHB SDHB 7647 -0.002 0.38 NO
96 UQCRB UQCRB UQCRB 7728 -0.0031 0.38 NO
97 DLD DLD DLD 7794 -0.0039 0.37 NO
98 ATP5F1 ATP5F1 ATP5F1 7993 -0.0065 0.36 NO
99 IDH3A IDH3A IDH3A 8205 -0.0093 0.35 NO
100 UCP2 UCP2 UCP2 8479 -0.014 0.34 NO
101 PDP1 PDP1 PDP1 8589 -0.015 0.34 NO
102 PDPR PDPR PDPR 9307 -0.026 0.3 NO
103 L2HGDH L2HGDH L2HGDH 9521 -0.03 0.3 NO
104 IDH2 IDH2 IDH2 9539 -0.03 0.3 NO
105 DLAT DLAT DLAT 9664 -0.032 0.3 NO
106 PDK1 PDK1 PDK1 9698 -0.033 0.3 NO
107 PDHB PDHB PDHB 10219 -0.041 0.28 NO
108 ATP5A1 ATP5A1 ATP5A1 10422 -0.045 0.28 NO
109 NNT NNT NNT 10538 -0.047 0.28 NO
110 SUCLA2 SUCLA2 SUCLA2 10972 -0.055 0.27 NO
111 PDK3 PDK3 PDK3 12744 -0.1 0.19 NO
112 UCP3 UCP3 UCP3 13913 -0.15 0.15 NO
113 LDHB LDHB LDHB 14519 -0.19 0.15 NO
114 ADHFE1 ADHFE1 ADHFE1 14531 -0.19 0.18 NO
115 PDK4 PDK4 PDK4 15059 -0.22 0.18 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: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG DRUG METABOLISM CYTOCHROME P450

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 SULT1B1 SULT1B1 SULT1B1 16 0.7 0.058 YES
2 UGT1A1 UGT1A1 UGT1A1 78 0.55 0.1 YES
3 SULT1C2 SULT1C2 SULT1C2 122 0.5 0.14 YES
4 UGT1A9 UGT1A9 UGT1A9 145 0.48 0.18 YES
5 NAT2 NAT2 NAT2 156 0.47 0.22 YES
6 UGT1A3 UGT1A3 UGT1A3 246 0.41 0.25 YES
7 SULT1E1 SULT1E1 SULT1E1 308 0.38 0.28 YES
8 UGT1A8 UGT1A8 UGT1A8 367 0.36 0.3 YES
9 UGT2B7 UGT2B7 UGT2B7 412 0.34 0.33 YES
10 UGT1A4 UGT1A4 UGT1A4 470 0.33 0.35 YES
11 UGT2B10 UGT2B10 UGT2B10 624 0.29 0.37 YES
12 GSTA1 GSTA1 GSTA1 639 0.29 0.39 YES
13 SULT2B1 SULT2B1 SULT2B1 732 0.27 0.41 YES
14 UGT1A6 UGT1A6 UGT1A6 751 0.27 0.43 YES
15 ACSM1 ACSM1 ACSM1 774 0.26 0.45 YES
16 SULT1A2 SULT1A2 SULT1A2 809 0.25 0.47 YES
17 UGT2B28 UGT2B28 UGT2B28 1015 0.22 0.48 YES
18 UGT1A7 UGT1A7 UGT1A7 1069 0.21 0.49 YES
19 NAT1 NAT1 NAT1 1080 0.21 0.51 YES
20 OPLAH OPLAH OPLAH 1138 0.2 0.52 YES
21 SULT1A3 SULT1A3 SULT1A3 1235 0.19 0.53 YES
22 GSTO2 GSTO2 GSTO2 1358 0.18 0.54 YES
23 MGST2 MGST2 MGST2 1388 0.18 0.56 YES
24 SULT2A1 SULT2A1 SULT2A1 1447 0.17 0.57 YES
25 BPNT1 BPNT1 BPNT1 1495 0.17 0.58 YES
26 MGST3 MGST3 MGST3 1904 0.14 0.57 YES
27 GSTM4 GSTM4 GSTM4 1951 0.13 0.57 YES
28 SLC35D1 SLC35D1 SLC35D1 2167 0.12 0.57 YES
29 UGT2B11 UGT2B11 UGT2B11 2269 0.12 0.58 YES
30 TPMT TPMT TPMT 2272 0.11 0.59 YES
31 GSTP1 GSTP1 GSTP1 2357 0.11 0.59 YES
32 UGT2A1 UGT2A1 UGT2A1 2473 0.1 0.59 YES
33 MAT2A MAT2A MAT2A 2497 0.1 0.6 YES
34 GSS GSS GSS 2775 0.093 0.59 NO
35 SULT1A1 SULT1A1 SULT1A1 2892 0.089 0.6 NO
36 GGCT GGCT GGCT 3116 0.081 0.59 NO
37 AHCY AHCY AHCY 3256 0.077 0.59 NO
38 MGST1 MGST1 MGST1 3685 0.066 0.57 NO
39 GSTO1 GSTO1 GSTO1 3953 0.058 0.56 NO
40 GGT7 GGT7 GGT7 4210 0.053 0.55 NO
41 COMT COMT COMT 4540 0.046 0.54 NO
42 MAT2B MAT2B MAT2B 5099 0.035 0.51 NO
43 UGDH UGDH UGDH 7569 -0.00097 0.38 NO
44 UGT2B4 UGT2B4 UGT2B4 8130 -0.0082 0.35 NO
45 CNDP2 CNDP2 CNDP2 8278 -0.01 0.34 NO
46 GSTM1 GSTM1 GSTM1 8653 -0.016 0.32 NO
47 GGT1 GGT1 GGT1 9155 -0.024 0.29 NO
48 UGP2 UGP2 UGP2 9611 -0.032 0.27 NO
49 ACSM2B ACSM2B ACSM2B 9721 -0.033 0.27 NO
50 GSTA2 GSTA2 GSTA2 9771 -0.034 0.27 NO
51 GCLC GCLC GCLC 9860 -0.036 0.27 NO
52 PAPSS1 PAPSS1 PAPSS1 9927 -0.037 0.27 NO
53 MTR MTR MTR 11009 -0.056 0.21 NO
54 CYP1A2 CYP1A2 CYP1A2 12282 -0.089 0.15 NO
55 GSTA4 GSTA4 GSTA4 13453 -0.13 0.099 NO
56 GCLM GCLM GCLM 13783 -0.15 0.093 NO
57 PAPSS2 PAPSS2 PAPSS2 13796 -0.15 0.1 NO
58 GGT5 GGT5 GGT5 13987 -0.16 0.11 NO
59 NNMT NNMT NNMT 14243 -0.17 0.11 NO
60 MAT1A MAT1A MAT1A 14252 -0.17 0.12 NO
61 GLYAT GLYAT GLYAT 15516 -0.24 0.074 NO
62 GSTM5 GSTM5 GSTM5 16210 -0.29 0.06 NO
63 SULT4A1 SULT4A1 SULT4A1 17178 -0.36 0.038 NO
64 SULT1C4 SULT1C4 SULT1C4 17356 -0.38 0.06 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: KEGG DRUG METABOLISM CYTOCHROME P450.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG DRUG METABOLISM OTHER ENZYMES

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 UGT1A1 UGT1A1 UGT1A1 78 0.55 0.088 YES
2 UGT1A9 UGT1A9 UGT1A9 145 0.48 0.16 YES
3 UGT1A3 UGT1A3 UGT1A3 246 0.41 0.23 YES
4 UGT1A8 UGT1A8 UGT1A8 367 0.36 0.28 YES
5 UGT2B7 UGT2B7 UGT2B7 412 0.34 0.34 YES
6 UGT1A10 UGT1A10 UGT1A10 450 0.33 0.39 YES
7 UGT1A4 UGT1A4 UGT1A4 470 0.33 0.44 YES
8 UGT2B10 UGT2B10 UGT2B10 624 0.29 0.48 YES
9 UGT1A6 UGT1A6 UGT1A6 751 0.27 0.52 YES
10 UGT2A3 UGT2A3 UGT2A3 867 0.24 0.56 YES
11 UGT2B28 UGT2B28 UGT2B28 1015 0.22 0.59 YES
12 UGT1A7 UGT1A7 UGT1A7 1069 0.21 0.62 YES
13 UGT2B15 UGT2B15 UGT2B15 1210 0.19 0.64 YES
14 UGT2B11 UGT2B11 UGT2B11 2269 0.12 0.6 NO
15 BLVRB BLVRB BLVRB 2275 0.11 0.62 NO
16 UGT2A1 UGT2A1 UGT2A1 2473 0.1 0.63 NO
17 ALAS1 ALAS1 ALAS1 2960 0.086 0.62 NO
18 HCCS HCCS HCCS 3230 0.078 0.62 NO
19 COX15 COX15 COX15 3535 0.07 0.61 NO
20 GUSB GUSB GUSB 3708 0.065 0.61 NO
21 HMBS HMBS HMBS 3811 0.062 0.62 NO
22 MMAB MMAB MMAB 3958 0.058 0.62 NO
23 HMOX2 HMOX2 HMOX2 4348 0.05 0.61 NO
24 PPOX PPOX PPOX 5361 0.03 0.56 NO
25 ALAD ALAD ALAD 5415 0.03 0.56 NO
26 EPRS EPRS EPRS 6250 0.017 0.52 NO
27 EARS2 EARS2 EARS2 6592 0.012 0.5 NO
28 COX10 COX10 COX10 6690 0.011 0.5 NO
29 CPOX CPOX CPOX 7333 0.0024 0.46 NO
30 UROS UROS UROS 7925 -0.0054 0.43 NO
31 UGT2B4 UGT2B4 UGT2B4 8130 -0.0082 0.42 NO
32 BLVRA BLVRA BLVRA 8349 -0.011 0.41 NO
33 FTH1 FTH1 FTH1 10310 -0.043 0.31 NO
34 UROD UROD UROD 11369 -0.064 0.27 NO
35 CP CP CP 12122 -0.084 0.24 NO
36 FECH FECH FECH 14331 -0.18 0.15 NO
37 HMOX1 HMOX1 HMOX1 14733 -0.2 0.16 NO
38 ALAS2 ALAS2 ALAS2 15480 -0.24 0.16 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: KEGG DRUG METABOLISM OTHER ENZYMES.

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

genes ES table in pathway: KEGG BASE EXCISION REPAIR

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 LSM4 LSM4 LSM4 2543 0.1 -0.064 YES
2 C2orf29 C2orf29 C2orf29 2662 0.097 -0.00011 YES
3 EXOSC5 EXOSC5 EXOSC5 3152 0.08 0.032 YES
4 EXOSC1 EXOSC1 EXOSC1 3186 0.079 0.087 YES
5 EXOSC4 EXOSC4 EXOSC4 3661 0.066 0.11 YES
6 LSM5 LSM5 LSM5 4280 0.051 0.11 YES
7 EXOSC7 EXOSC7 EXOSC7 4680 0.043 0.12 YES
8 EXOSC8 EXOSC8 EXOSC8 5142 0.034 0.12 YES
9 PATL1 PATL1 PATL1 5207 0.033 0.14 YES
10 EXOSC3 EXOSC3 EXOSC3 5213 0.033 0.17 YES
11 PABPC1 PABPC1 PABPC1 5533 0.028 0.17 YES
12 DCPS DCPS DCPS 5554 0.027 0.19 YES
13 PARN PARN PARN 5627 0.026 0.2 YES
14 EDC4 EDC4 EDC4 5890 0.022 0.2 YES
15 EXOSC6 EXOSC6 EXOSC6 5967 0.021 0.22 YES
16 TNKS1BP1 TNKS1BP1 TNKS1BP1 6230 0.017 0.22 YES
17 EXOSC2 EXOSC2 EXOSC2 6403 0.015 0.22 YES
18 LSM2 LSM2 LSM2 6519 0.013 0.22 YES
19 LSM6 LSM6 LSM6 6877 0.0084 0.21 YES
20 CNOT2 CNOT2 CNOT2 6886 0.0083 0.21 YES
21 CNOT6 CNOT6 CNOT6 6915 0.0078 0.22 YES
22 DIS3 DIS3 DIS3 7043 0.0063 0.21 YES
23 LSM1 LSM1 LSM1 7112 0.0056 0.21 YES
24 CNOT3 CNOT3 CNOT3 7180 0.0046 0.21 YES
25 CNOT10 CNOT10 CNOT10 7298 0.003 0.21 YES
26 CNOT8 CNOT8 CNOT8 7358 0.002 0.21 YES
27 LSM3 LSM3 LSM3 8124 -0.0081 0.17 YES
28 PAIP1 PAIP1 PAIP1 8264 -0.01 0.17 YES
29 EIF4A1 EIF4A1 EIF4A1 8566 -0.015 0.17 YES
30 EIF4G1 EIF4G1 EIF4G1 8580 -0.015 0.18 YES
31 EIF4A2 EIF4A2 EIF4A2 8927 -0.021 0.17 YES
32 EXOSC9 EXOSC9 EXOSC9 8955 -0.021 0.19 YES
33 EDC3 EDC3 EDC3 9088 -0.023 0.2 YES
34 EIF4A3 EIF4A3 EIF4A3 9144 -0.024 0.21 YES
35 CNOT4 CNOT4 CNOT4 9159 -0.024 0.23 YES
36 EIF4E EIF4E EIF4E 9189 -0.024 0.24 YES
37 EIF4B EIF4B EIF4B 9394 -0.028 0.25 YES
38 DCP1A DCP1A DCP1A 9921 -0.036 0.25 YES
39 DCP1B DCP1B DCP1B 10237 -0.042 0.26 YES
40 DDX6 DDX6 DDX6 10508 -0.046 0.28 YES
41 RQCD1 RQCD1 RQCD1 10550 -0.047 0.31 YES
42 CNOT7 CNOT7 CNOT7 10695 -0.05 0.34 YES
43 DCP2 DCP2 DCP2 10863 -0.053 0.37 YES
44 XRN1 XRN1 XRN1 11038 -0.057 0.4 YES

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: KEGG BASE EXCISION REPAIR.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

Table 4.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus2. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG LYSINE DEGRADATION 44 genes.ES.table 0.45 1.9 0 0.84 0.27 0.046 0.0097 0.045 0 0.17
KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS 25 genes.ES.table 0.49 1.7 0.03 0.36 0.85 0.76 0.42 0.44 0.17 0.085
BIOCARTA BIOPEPTIDES PATHWAY 42 genes.ES.table 0.51 1.7 0.011 0.46 0.74 0.14 0.11 0.13 0.18 0.11
BIOCARTA CHREBP2 PATHWAY 40 genes.ES.table 0.55 1.9 0 0.49 0.3 0.18 0.11 0.16 0 0.1
SIG CD40PATHWAYMAP 33 genes.ES.table 0.49 1.7 0.024 0.38 0.8 0.15 0.089 0.14 0.16 0.091
PID P38 MKK3 6PATHWAY 26 genes.ES.table 0.45 1.7 0.015 0.41 0.79 0.15 0.14 0.13 0.17 0.097
PID LKB1 PATHWAY 47 genes.ES.table 0.38 1.7 0.033 0.45 0.77 0.11 0.056 0.1 0.18 0.11
PID LIS1PATHWAY 28 genes.ES.table 0.61 1.8 0.0042 0.41 0.54 0.25 0.11 0.22 0.1 0.097
PID HEDGEHOG GLIPATHWAY 48 genes.ES.table 0.43 1.6 0.024 0.38 0.9 0.15 0.11 0.13 0.2 0.087
REACTOME TRANS GOLGI NETWORK VESICLE BUDDING 59 genes.ES.table 0.33 1.7 0.023 0.42 0.77 0.034 0.013 0.034 0.17 0.098
genes ES table in pathway: KEGG LYSINE DEGRADATION

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 OGDHL OGDHL OGDHL 101 0.96 0.24 YES
2 PIPOX PIPOX PIPOX 179 0.85 0.45 YES
3 AADAT AADAT AADAT 2443 0.21 0.38 NO
4 ACAT1 ACAT1 ACAT1 3430 0.14 0.36 NO
5 HADH HADH HADH 3857 0.12 0.37 NO
6 SUV420H2 SUV420H2 SUV420H2 4021 0.11 0.39 NO
7 GCDH GCDH GCDH 5023 0.08 0.35 NO
8 AASDH AASDH AASDH 5360 0.071 0.35 NO
9 SUV39H1 SUV39H1 SUV39H1 5792 0.061 0.34 NO
10 SETMAR SETMAR SETMAR 6038 0.056 0.34 NO
11 ALDH9A1 ALDH9A1 ALDH9A1 6143 0.054 0.35 NO
12 SETDB2 SETDB2 SETDB2 7149 0.034 0.31 NO
13 AASDHPPT AASDHPPT AASDHPPT 7155 0.034 0.32 NO
14 DOT1L DOT1L DOT1L 7193 0.033 0.32 NO
15 ECHS1 ECHS1 ECHS1 7747 0.024 0.3 NO
16 NSD1 NSD1 NSD1 7801 0.023 0.3 NO
17 SETD1B SETD1B SETD1B 8109 0.018 0.29 NO
18 BBOX1 BBOX1 BBOX1 8393 0.014 0.28 NO
19 EHMT2 EHMT2 EHMT2 8910 0.0059 0.25 NO
20 PLOD3 PLOD3 PLOD3 8914 0.0057 0.25 NO
21 SETD1A SETD1A SETD1A 9193 0.0014 0.24 NO
22 OGDH OGDH OGDH 9314 -0.00048 0.23 NO
23 ALDH3A2 ALDH3A2 ALDH3A2 9355 -0.00097 0.23 NO
24 HADHA HADHA HADHA 9453 -0.0023 0.22 NO
25 EHHADH EHHADH EHHADH 9992 -0.011 0.2 NO
26 EHMT1 EHMT1 EHMT1 10429 -0.018 0.18 NO
27 SETD2 SETD2 SETD2 10541 -0.02 0.18 NO
28 AASS AASS AASS 10607 -0.021 0.18 NO
29 ASH1L ASH1L ASH1L 10659 -0.022 0.18 NO
30 WHSC1 WHSC1 WHSC1 11051 -0.028 0.17 NO
31 SETDB1 SETDB1 SETDB1 11060 -0.028 0.17 NO
32 SUV420H1 SUV420H1 SUV420H1 11146 -0.03 0.18 NO
33 DLST DLST DLST 11189 -0.031 0.18 NO
34 ACAT2 ACAT2 ACAT2 11659 -0.039 0.17 NO
35 SUV39H2 SUV39H2 SUV39H2 11981 -0.044 0.16 NO
36 TMLHE TMLHE TMLHE 12286 -0.051 0.16 NO
37 SETD7 SETD7 SETD7 12505 -0.055 0.16 NO
38 WHSC1L1 WHSC1L1 WHSC1L1 12770 -0.061 0.16 NO
39 SETD8 SETD8 SETD8 13264 -0.072 0.15 NO
40 PLOD1 PLOD1 PLOD1 13787 -0.086 0.14 NO
41 ALDH7A1 ALDH7A1 ALDH7A1 13791 -0.086 0.17 NO
42 ALDH2 ALDH2 ALDH2 13964 -0.092 0.18 NO
43 PLOD2 PLOD2 PLOD2 14884 -0.12 0.16 NO
44 ALDH1B1 ALDH1B1 ALDH1B1 15009 -0.13 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 LYSINE DEGRADATION.

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

genes ES table in pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS

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 GCK GCK GCK 73 1 0.2 YES
2 PPP2R2B PPP2R2B PPP2R2B 491 0.61 0.3 YES
3 MLXIPL MLXIPL MLXIPL 636 0.55 0.4 YES
4 PPP2R2C PPP2R2C PPP2R2C 1337 0.35 0.43 YES
5 PRKAR2B PRKAR2B PRKAR2B 1779 0.28 0.46 YES
6 PPP2R3B PPP2R3B PPP2R3B 2025 0.25 0.5 YES
7 PKLR PKLR PKLR 2033 0.25 0.55 YES
8 PRKAR1B PRKAR1B PRKAR1B 2731 0.19 0.55 NO
9 PPP2R5B PPP2R5B PPP2R5B 4189 0.11 0.49 NO
10 PRKACA PRKACA PRKACA 4439 0.098 0.5 NO
11 PRKAR1A PRKAR1A PRKAR1A 4780 0.087 0.5 NO
12 PRKACB PRKACB PRKACB 5572 0.066 0.46 NO
13 YWHAE YWHAE YWHAE 5835 0.06 0.46 NO
14 ACACA ACACA ACACA 5904 0.059 0.47 NO
15 PPP2R4 PPP2R4 PPP2R4 6604 0.045 0.44 NO
16 PPP2R1A PPP2R1A PPP2R1A 6624 0.044 0.45 NO
17 PRKAA2 PRKAA2 PRKAA2 6668 0.044 0.46 NO
18 PRKAG1 PRKAG1 PRKAG1 6859 0.04 0.45 NO
19 PRKAG2 PRKAG2 PRKAG2 7011 0.037 0.45 NO
20 FASN FASN FASN 7096 0.035 0.46 NO
21 YWHAQ YWHAQ YWHAQ 7103 0.035 0.46 NO
22 PPP2R1B PPP2R1B PPP2R1B 7342 0.031 0.46 NO
23 PPP2CB PPP2CB PPP2CB 8923 0.0056 0.37 NO
24 YWHAG YWHAG YWHAG 9307 -0.0004 0.35 NO
25 YWHAH YWHAH YWHAH 9428 -0.0018 0.34 NO
26 PPP2CA PPP2CA PPP2CA 9469 -0.0026 0.34 NO
27 PPP2R5D PPP2R5D PPP2R5D 9951 -0.01 0.32 NO
28 PPP2R5C PPP2R5C PPP2R5C 10091 -0.012 0.31 NO
29 MLX MLX MLX 10226 -0.014 0.31 NO
30 PPP2R2D PPP2R2D PPP2R2D 10708 -0.022 0.29 NO
31 PRKAB1 PRKAB1 PRKAB1 10795 -0.024 0.29 NO
32 YWHAB YWHAB YWHAB 11239 -0.032 0.27 NO
33 PPP2R5A PPP2R5A PPP2R5A 11528 -0.037 0.26 NO
34 PRKAB2 PRKAB2 PRKAB2 11955 -0.044 0.25 NO
35 PPP2R5E PPP2R5E PPP2R5E 12809 -0.062 0.21 NO
36 PRKAR2A PRKAR2A PRKAR2A 13258 -0.072 0.2 NO
37 PRKAA1 PRKAA1 PRKAA1 13550 -0.08 0.2 NO
38 PPP2R2A PPP2R2A PPP2R2A 13729 -0.084 0.21 NO
39 YWHAZ YWHAZ YWHAZ 14377 -0.1 0.2 NO
40 PPP2R3A PPP2R3A PPP2R3A 15136 -0.13 0.18 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 GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS.

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

genes ES table in pathway: BIOCARTA BIOPEPTIDES PATHWAY

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 GRIA2 GRIA2 GRIA2 17 1.2 0.18 YES
2 CAMK2B CAMK2B CAMK2B 19 1.2 0.35 YES
3 GRIA3 GRIA3 GRIA3 62 1 0.51 YES
4 CACNG2 CACNG2 CACNG2 413 0.66 0.59 YES
5 GRIA4 GRIA4 GRIA4 1088 0.4 0.62 YES
6 CACNG4 CACNG4 CACNG4 1146 0.38 0.67 YES
7 PRKCG PRKCG PRKCG 1259 0.36 0.72 YES
8 GRIA1 GRIA1 GRIA1 1644 0.3 0.75 YES
9 NSF NSF NSF 4298 0.1 0.62 NO
10 PICK1 PICK1 PICK1 4814 0.086 0.6 NO
11 CACNG8 CACNG8 CACNG8 5084 0.078 0.6 NO
12 CACNG3 CACNG3 CACNG3 5971 0.058 0.56 NO
13 AP2A2 AP2A2 AP2A2 7329 0.031 0.49 NO
14 AP2B1 AP2B1 AP2B1 8510 0.012 0.43 NO
15 AP2S1 AP2S1 AP2S1 8906 0.006 0.41 NO
16 CAMK2D CAMK2D CAMK2D 9257 0.00034 0.39 NO
17 AP2M1 AP2M1 AP2M1 10023 -0.011 0.35 NO
18 AP2A1 AP2A1 AP2A1 10106 -0.012 0.35 NO
19 MDM2 MDM2 MDM2 10122 -0.012 0.35 NO
20 GRIP2 GRIP2 GRIP2 10543 -0.02 0.33 NO
21 DLG1 DLG1 DLG1 12149 -0.048 0.25 NO
22 EPB41L1 EPB41L1 EPB41L1 12363 -0.053 0.25 NO
23 MYO6 MYO6 MYO6 12562 -0.056 0.25 NO
24 PRKCA PRKCA PRKCA 13493 -0.078 0.21 NO
25 CAMK2A CAMK2A CAMK2A 13497 -0.078 0.22 NO
26 PRKCB PRKCB PRKCB 13923 -0.091 0.21 NO
27 AKAP5 AKAP5 AKAP5 16902 -0.23 0.084 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: BIOCARTA BIOPEPTIDES PATHWAY.

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

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

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 CACNA1A CACNA1A CACNA1A 27 1.1 0.039 YES
2 SYT5 SYT5 SYT5 52 1.1 0.077 YES
3 SNAP25 SNAP25 SNAP25 97 0.97 0.11 YES
4 ABCC8 ABCC8 ABCC8 122 0.92 0.14 YES
5 KCNJ11 KCNJ11 KCNJ11 136 0.91 0.18 YES
6 PAX6 PAX6 PAX6 157 0.88 0.21 YES
7 ISL1 ISL1 ISL1 180 0.85 0.24 YES
8 GNG4 GNG4 GNG4 188 0.84 0.27 YES
9 PCSK1 PCSK1 PCSK1 189 0.84 0.3 YES
10 GPR119 GPR119 GPR119 191 0.83 0.33 YES
11 ADCY1 ADCY1 ADCY1 295 0.74 0.35 YES
12 FFAR1 FFAR1 FFAR1 306 0.73 0.38 YES
13 CACNB2 CACNB2 CACNB2 321 0.71 0.4 YES
14 GNAO1 GNAO1 GNAO1 352 0.69 0.42 YES
15 KCNC2 KCNC2 KCNC2 368 0.68 0.45 YES
16 KCNB1 KCNB1 KCNB1 451 0.63 0.47 YES
17 GCGR GCGR GCGR 536 0.59 0.48 YES
18 MLXIPL MLXIPL MLXIPL 636 0.55 0.5 YES
19 GNB3 GNB3 GNB3 654 0.53 0.52 YES
20 RAPGEF4 RAPGEF4 RAPGEF4 801 0.48 0.53 YES
21 ADCY2 ADCY2 ADCY2 956 0.43 0.54 YES
22 GNG2 GNG2 GNG2 986 0.43 0.55 YES
23 GNG7 GNG7 GNG7 1124 0.39 0.56 YES
24 GLP1R GLP1R GLP1R 1265 0.36 0.56 YES
25 STXBP1 STXBP1 STXBP1 1400 0.34 0.57 YES
26 SEC11C SEC11C SEC11C 1464 0.32 0.58 YES
27 STX1A STX1A STX1A 1666 0.3 0.58 YES
28 PRKAR2B PRKAR2B PRKAR2B 1779 0.28 0.58 YES
29 VAMP2 VAMP2 VAMP2 1921 0.26 0.58 YES
30 ACACB ACACB ACACB 1935 0.26 0.59 YES
31 GNAI1 GNAI1 GNAI1 1995 0.26 0.6 YES
32 PKLR PKLR PKLR 2033 0.25 0.6 YES
33 GCG GCG GCG 2049 0.25 0.61 YES
34 GNAS GNAS GNAS 2253 0.23 0.61 YES
35 GNG3 GNG3 GNG3 2256 0.23 0.62 YES
36 PFKFB1 PFKFB1 PFKFB1 2263 0.23 0.63 YES
37 INS INS INS 2335 0.22 0.63 YES
38 SLC25A4 SLC25A4 SLC25A4 2472 0.21 0.63 YES
39 ADCY8 ADCY8 ADCY8 2592 0.2 0.63 YES
40 PRKAR1B PRKAR1B PRKAR1B 2731 0.19 0.63 NO
41 DPP4 DPP4 DPP4 3762 0.12 0.58 NO
42 ACLY ACLY ACLY 3893 0.12 0.58 NO
43 PRKACA PRKACA PRKACA 4439 0.098 0.55 NO
44 KCNG2 KCNG2 KCNG2 4536 0.095 0.55 NO
45 GNB5 GNB5 GNB5 4540 0.095 0.55 NO
46 SLC2A2 SLC2A2 SLC2A2 4581 0.094 0.55 NO
47 LEP LEP LEP 4751 0.088 0.55 NO
48 PRKAR1A PRKAR1A PRKAR1A 4780 0.087 0.55 NO
49 ADCY4 ADCY4 ADCY4 5042 0.08 0.54 NO
50 GNG10 GNG10 GNG10 5122 0.078 0.54 NO
51 PLCB1 PLCB1 PLCB1 5349 0.072 0.53 NO
52 PRKACB PRKACB PRKACB 5572 0.066 0.52 NO
53 GNG11 GNG11 GNG11 5673 0.064 0.51 NO
54 STK11 STK11 STK11 5752 0.062 0.51 NO
55 ACACA ACACA ACACA 5904 0.059 0.51 NO
56 PPP2R1A PPP2R1A PPP2R1A 6624 0.044 0.47 NO
57 PRKAA2 PRKAA2 PRKAA2 6668 0.044 0.47 NO
58 GRP GRP GRP 6685 0.043 0.47 NO
59 GNA11 GNA11 GNA11 6709 0.043 0.47 NO
60 GNB2 GNB2 GNB2 6739 0.042 0.47 NO
61 ADCY6 ADCY6 ADCY6 6762 0.042 0.47 NO
62 PRKAG2 PRKAG2 PRKAG2 7011 0.037 0.46 NO
63 AGPAT1 AGPAT1 AGPAT1 7083 0.036 0.45 NO
64 FASN FASN FASN 7096 0.035 0.46 NO
65 PPP2R1B PPP2R1B PPP2R1B 7342 0.031 0.44 NO
66 SPCS1 SPCS1 SPCS1 7970 0.02 0.41 NO
67 ADCY3 ADCY3 ADCY3 8084 0.018 0.4 NO
68 GNAI2 GNAI2 GNAI2 8375 0.014 0.39 NO
69 MARCKS MARCKS MARCKS 8646 0.0096 0.37 NO
70 SPCS2 SPCS2 SPCS2 8857 0.0065 0.36 NO
71 PPP2CB PPP2CB PPP2CB 8923 0.0056 0.36 NO
72 SLC25A6 SLC25A6 SLC25A6 8971 0.0047 0.36 NO
73 LOC653566 LOC653566 LOC653566 8979 0.0046 0.36 NO
74 ADCY9 ADCY9 ADCY9 9024 0.0039 0.36 NO
75 GNA14 GNA14 GNA14 9367 -0.0011 0.34 NO
76 PPP2CA PPP2CA PPP2CA 9469 -0.0026 0.33 NO
77 GNAQ GNAQ GNAQ 9679 -0.0058 0.32 NO
78 GNB1 GNB1 GNB1 9761 -0.0071 0.32 NO
79 PPP2R5D PPP2R5D PPP2R5D 9951 -0.01 0.3 NO
80 MLX MLX MLX 10226 -0.014 0.29 NO
81 ADCY5 ADCY5 ADCY5 10580 -0.02 0.27 NO
82 SLC25A5 SLC25A5 SLC25A5 10602 -0.021 0.27 NO
83 GNG13 GNG13 GNG13 10804 -0.024 0.26 NO
84 SEC11A SEC11A SEC11A 10936 -0.026 0.26 NO
85 GNGT2 GNGT2 GNGT2 11817 -0.042 0.21 NO
86 CACNB3 CACNB3 CACNB3 11871 -0.043 0.21 NO
87 PRKAB2 PRKAB2 PRKAB2 11955 -0.044 0.2 NO
88 SPCS3 SPCS3 SPCS3 12103 -0.047 0.2 NO
89 KCNS3 KCNS3 KCNS3 12640 -0.058 0.17 NO
90 TALDO1 TALDO1 TALDO1 12752 -0.06 0.17 NO
91 RAP1B RAP1B RAP1B 12791 -0.061 0.17 NO
92 RAPGEF3 RAPGEF3 RAPGEF3 13109 -0.068 0.15 NO
93 PRKAR2A PRKAR2A PRKAR2A 13258 -0.072 0.15 NO
94 GNG8 GNG8 GNG8 13314 -0.073 0.15 NO
95 PRKCA PRKCA PRKCA 13493 -0.078 0.14 NO
96 GIP GIP GIP 13529 -0.079 0.14 NO
97 CTNNB1 CTNNB1 CTNNB1 13669 -0.083 0.14 NO
98 GNG5 GNG5 GNG5 13821 -0.087 0.13 NO
99 ADCY7 ADCY7 ADCY7 14137 -0.097 0.12 NO
100 RAP1A RAP1A RAP1A 14348 -0.1 0.11 NO
101 GNGT1 GNGT1 GNGT1 14480 -0.11 0.11 NO
102 GNB4 GNB4 GNB4 14597 -0.11 0.11 NO
103 GNG12 GNG12 GNG12 14695 -0.12 0.1 NO
104 TKT TKT TKT 14791 -0.12 0.1 NO
105 CDX2 CDX2 CDX2 14837 -0.12 0.11 NO
106 ITPR2 ITPR2 ITPR2 14944 -0.12 0.1 NO
107 IQGAP1 IQGAP1 IQGAP1 15360 -0.14 0.087 NO
108 PLCB2 PLCB2 PLCB2 15634 -0.15 0.078 NO
109 ADRA2A ADRA2A ADRA2A 15806 -0.16 0.075 NO
110 CHRM3 CHRM3 CHRM3 15883 -0.16 0.077 NO
111 SLC2A1 SLC2A1 SLC2A1 16445 -0.2 0.053 NO
112 PLCB3 PLCB3 PLCB3 16825 -0.23 0.041 NO
113 AKAP5 AKAP5 AKAP5 16902 -0.23 0.045 NO
114 ITPR3 ITPR3 ITPR3 17475 -0.28 0.024 NO
115 GNA15 GNA15 GNA15 18012 -0.35 0.0079 NO
116 GATA4 GATA4 GATA4 18374 -0.44 0.0045 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: BIOCARTA CHREBP2 PATHWAY.

Figure S28.  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

genes ES table in pathway: SIG CD40PATHWAYMAP

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 CDK5R2 CDK5R2 CDK5R2 11 1.2 0.24 YES
2 DCX DCX DCX 225 0.8 0.38 YES
3 CDK5R1 CDK5R1 CDK5R1 870 0.46 0.44 YES
4 RELN RELN RELN 1336 0.35 0.48 YES
5 MAP1B MAP1B MAP1B 1707 0.29 0.52 YES
6 DAB1 DAB1 DAB1 1780 0.28 0.57 YES
7 VLDLR VLDLR VLDLR 1986 0.26 0.61 YES
8 LRPAP1 LRPAP1 LRPAP1 3336 0.14 0.57 NO
9 CDK5 CDK5 CDK5 4604 0.093 0.52 NO
10 PAFAH1B1 PAFAH1B1 PAFAH1B1 4871 0.085 0.52 NO
11 YWHAE YWHAE YWHAE 5835 0.06 0.48 NO
12 PAFAH1B3 PAFAH1B3 PAFAH1B3 6079 0.055 0.48 NO
13 NDEL1 NDEL1 NDEL1 7916 0.021 0.38 NO
14 NUDC NUDC NUDC 9001 0.0042 0.32 NO
15 DYNC1H1 DYNC1H1 DYNC1H1 9142 0.002 0.32 NO
16 DYNLT1 DYNLT1 DYNLT1 9299 -0.00021 0.31 NO
17 ABL1 ABL1 ABL1 9316 -0.00051 0.31 NO
18 PPP2R5D PPP2R5D PPP2R5D 9951 -0.01 0.28 NO
19 CLIP1 CLIP1 CLIP1 10749 -0.023 0.24 NO
20 KATNA1 KATNA1 KATNA1 11331 -0.033 0.21 NO
21 RAC1 RAC1 RAC1 11759 -0.041 0.2 NO
22 CDC42 CDC42 CDC42 11766 -0.041 0.21 NO
23 CSNK2A1 CSNK2A1 CSNK2A1 12131 -0.048 0.2 NO
24 RHOA RHOA RHOA 12312 -0.052 0.2 NO
25 PAFAH1B2 PAFAH1B2 PAFAH1B2 14561 -0.11 0.096 NO
26 IQGAP1 IQGAP1 IQGAP1 15360 -0.14 0.081 NO
27 LRP8 LRP8 LRP8 16439 -0.2 0.062 NO
28 PLA2G7 PLA2G7 PLA2G7 17046 -0.24 0.077 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: SIG CD40PATHWAYMAP.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: SIG CD40PATHWAYMAP, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID P38 MKK3 6PATHWAY

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 SH3GL2 SH3GL2 SH3GL2 45 1.1 0.21 YES
2 DNAJC6 DNAJC6 DNAJC6 245 0.77 0.36 YES
3 VAMP2 VAMP2 VAMP2 1921 0.26 0.32 NO
4 OCRL OCRL OCRL 2734 0.19 0.31 NO
5 NECAP1 NECAP1 NECAP1 3536 0.14 0.3 NO
6 TPD52 TPD52 TPD52 3826 0.12 0.31 NO
7 AP1S2 AP1S2 AP1S2 4012 0.11 0.32 NO
8 NAPA NAPA NAPA 4328 0.1 0.32 NO
9 BLOC1S1 BLOC1S1 BLOC1S1 4367 0.1 0.34 NO
10 HIP1R HIP1R HIP1R 4734 0.089 0.34 NO
11 DTNBP1 DTNBP1 DTNBP1 5208 0.075 0.33 NO
12 AP1S1 AP1S1 AP1S1 6094 0.055 0.29 NO
13 AP1M1 AP1M1 AP1M1 6321 0.05 0.29 NO
14 PLDN PLDN PLDN 6695 0.043 0.28 NO
15 SORT1 SORT1 SORT1 6748 0.042 0.28 NO
16 AP3B1 AP3B1 AP3B1 7123 0.035 0.27 NO
17 AP1B1 AP1B1 AP1B1 7374 0.03 0.26 NO
18 CLTA CLTA CLTA 7460 0.029 0.26 NO
19 HSPA8 HSPA8 HSPA8 8218 0.016 0.23 NO
20 AP1M2 AP1M2 AP1M2 8438 0.013 0.22 NO
21 CLTC CLTC CLTC 8662 0.0093 0.21 NO
22 SNX2 SNX2 SNX2 8766 0.008 0.2 NO
23 TGOLN2 TGOLN2 TGOLN2 9572 -0.0042 0.16 NO
24 ARF1 ARF1 ARF1 9741 -0.0068 0.15 NO
25 BLOC1S3 BLOC1S3 BLOC1S3 9955 -0.01 0.14 NO
26 RAB5C RAB5C RAB5C 10012 -0.011 0.14 NO
27 CPD CPD CPD 10053 -0.012 0.14 NO
28 GAK GAK GAK 10366 -0.017 0.13 NO
29 AP1G1 AP1G1 AP1G1 10631 -0.021 0.12 NO
30 VAMP7 VAMP7 VAMP7 10665 -0.022 0.12 NO
31 IGF2R IGF2R IGF2R 10679 -0.022 0.12 NO
32 SNAPIN SNAPIN SNAPIN 10957 -0.027 0.12 NO
33 FTL FTL FTL 11227 -0.031 0.11 NO
34 PUM1 PUM1 PUM1 11344 -0.033 0.11 NO
35 YIPF6 YIPF6 YIPF6 11735 -0.04 0.094 NO
36 FTH1 FTH1 FTH1 11754 -0.041 0.1 NO
37 ARRB1 ARRB1 ARRB1 11866 -0.043 0.1 NO
38 AP4E1 AP4E1 AP4E1 12087 -0.047 0.1 NO
39 TPD52L1 TPD52L1 TPD52L1 12403 -0.053 0.094 NO
40 TXNDC5 TXNDC5 TXNDC5 12793 -0.061 0.086 NO
41 PICALM PICALM PICALM 12920 -0.064 0.092 NO
42 SNX5 SNX5 SNX5 13032 -0.066 0.099 NO
43 TBC1D8B TBC1D8B TBC1D8B 13111 -0.068 0.11 NO
44 SNX9 SNX9 SNX9 13112 -0.068 0.12 NO
45 DNM2 DNM2 DNM2 13160 -0.07 0.13 NO
46 PIK3C2A PIK3C2A PIK3C2A 13202 -0.071 0.15 NO
47 AP4B1 AP4B1 AP4B1 13471 -0.078 0.15 NO
48 CNO CNO CNO 13658 -0.083 0.15 NO
49 AP3S1 AP3S1 AP3S1 14002 -0.093 0.15 NO
50 SH3D19 SH3D19 SH3D19 15350 -0.14 0.11 NO
51 TFRC TFRC TFRC 15466 -0.15 0.13 NO
52 VAMP8 VAMP8 VAMP8 15544 -0.15 0.16 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 P38 MKK3 6PATHWAY.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: PID P38 MKK3 6PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID LKB1 PATHWAY

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 CACNA1A CACNA1A CACNA1A 27 1.1 0.046 YES
2 SYT5 SYT5 SYT5 52 1.1 0.09 YES
3 SNAP25 SNAP25 SNAP25 97 0.97 0.13 YES
4 ABCC8 ABCC8 ABCC8 122 0.92 0.17 YES
5 KCNJ11 KCNJ11 KCNJ11 136 0.91 0.21 YES
6 PAX6 PAX6 PAX6 157 0.88 0.24 YES
7 ISL1 ISL1 ISL1 180 0.85 0.28 YES
8 GNG4 GNG4 GNG4 188 0.84 0.31 YES
9 PCSK1 PCSK1 PCSK1 189 0.84 0.35 YES
10 GPR119 GPR119 GPR119 191 0.83 0.39 YES
11 FFAR1 FFAR1 FFAR1 306 0.73 0.41 YES
12 CACNB2 CACNB2 CACNB2 321 0.71 0.44 YES
13 GNAO1 GNAO1 GNAO1 352 0.69 0.47 YES
14 KCNC2 KCNC2 KCNC2 368 0.68 0.5 YES
15 KCNB1 KCNB1 KCNB1 451 0.63 0.52 YES
16 GNB3 GNB3 GNB3 654 0.53 0.53 YES
17 RAPGEF4 RAPGEF4 RAPGEF4 801 0.48 0.55 YES
18 GNG2 GNG2 GNG2 986 0.43 0.55 YES
19 GNG7 GNG7 GNG7 1124 0.39 0.56 YES
20 GLP1R GLP1R GLP1R 1265 0.36 0.57 YES
21 STXBP1 STXBP1 STXBP1 1400 0.34 0.58 YES
22 SEC11C SEC11C SEC11C 1464 0.32 0.59 YES
23 STX1A STX1A STX1A 1666 0.3 0.59 YES
24 PRKAR2B PRKAR2B PRKAR2B 1779 0.28 0.6 YES
25 VAMP2 VAMP2 VAMP2 1921 0.26 0.6 YES
26 GNAI1 GNAI1 GNAI1 1995 0.26 0.61 YES
27 GCG GCG GCG 2049 0.25 0.62 YES
28 GNAS GNAS GNAS 2253 0.23 0.61 YES
29 GNG3 GNG3 GNG3 2256 0.23 0.62 YES
30 INS INS INS 2335 0.22 0.63 YES
31 SLC25A4 SLC25A4 SLC25A4 2472 0.21 0.63 YES
32 ADCY8 ADCY8 ADCY8 2592 0.2 0.63 YES
33 PRKAR1B PRKAR1B PRKAR1B 2731 0.19 0.63 YES
34 DPP4 DPP4 DPP4 3762 0.12 0.58 NO
35 PRKACA PRKACA PRKACA 4439 0.098 0.55 NO
36 KCNG2 KCNG2 KCNG2 4536 0.095 0.55 NO
37 GNB5 GNB5 GNB5 4540 0.095 0.55 NO
38 SLC2A2 SLC2A2 SLC2A2 4581 0.094 0.55 NO
39 LEP LEP LEP 4751 0.088 0.55 NO
40 PRKAR1A PRKAR1A PRKAR1A 4780 0.087 0.55 NO
41 GNG10 GNG10 GNG10 5122 0.078 0.54 NO
42 PLCB1 PLCB1 PLCB1 5349 0.072 0.53 NO
43 PRKACB PRKACB PRKACB 5572 0.066 0.52 NO
44 GNG11 GNG11 GNG11 5673 0.064 0.51 NO
45 GRP GRP GRP 6685 0.043 0.46 NO
46 GNA11 GNA11 GNA11 6709 0.043 0.46 NO
47 GNB2 GNB2 GNB2 6739 0.042 0.46 NO
48 ADCY6 ADCY6 ADCY6 6762 0.042 0.46 NO
49 SPCS1 SPCS1 SPCS1 7970 0.02 0.4 NO
50 GNAI2 GNAI2 GNAI2 8375 0.014 0.38 NO
51 MARCKS MARCKS MARCKS 8646 0.0096 0.36 NO
52 SPCS2 SPCS2 SPCS2 8857 0.0065 0.35 NO
53 SLC25A6 SLC25A6 SLC25A6 8971 0.0047 0.34 NO
54 LOC653566 LOC653566 LOC653566 8979 0.0046 0.34 NO
55 GNA14 GNA14 GNA14 9367 -0.0011 0.32 NO
56 GNAQ GNAQ GNAQ 9679 -0.0058 0.31 NO
57 GNB1 GNB1 GNB1 9761 -0.0071 0.3 NO
58 ADCY5 ADCY5 ADCY5 10580 -0.02 0.26 NO
59 SLC25A5 SLC25A5 SLC25A5 10602 -0.021 0.26 NO
60 GNG13 GNG13 GNG13 10804 -0.024 0.25 NO
61 SEC11A SEC11A SEC11A 10936 -0.026 0.24 NO
62 GNGT2 GNGT2 GNGT2 11817 -0.042 0.2 NO
63 CACNB3 CACNB3 CACNB3 11871 -0.043 0.2 NO
64 SPCS3 SPCS3 SPCS3 12103 -0.047 0.18 NO
65 KCNS3 KCNS3 KCNS3 12640 -0.058 0.16 NO
66 RAP1B RAP1B RAP1B 12791 -0.061 0.15 NO
67 RAPGEF3 RAPGEF3 RAPGEF3 13109 -0.068 0.14 NO
68 PRKAR2A PRKAR2A PRKAR2A 13258 -0.072 0.13 NO
69 GNG8 GNG8 GNG8 13314 -0.073 0.13 NO
70 PRKCA PRKCA PRKCA 13493 -0.078 0.13 NO
71 GIP GIP GIP 13529 -0.079 0.13 NO
72 CTNNB1 CTNNB1 CTNNB1 13669 -0.083 0.12 NO
73 GNG5 GNG5 GNG5 13821 -0.087 0.12 NO
74 RAP1A RAP1A RAP1A 14348 -0.1 0.097 NO
75 GNGT1 GNGT1 GNGT1 14480 -0.11 0.094 NO
76 GNB4 GNB4 GNB4 14597 -0.11 0.093 NO
77 GNG12 GNG12 GNG12 14695 -0.12 0.092 NO
78 CDX2 CDX2 CDX2 14837 -0.12 0.09 NO
79 ITPR2 ITPR2 ITPR2 14944 -0.12 0.09 NO
80 IQGAP1 IQGAP1 IQGAP1 15360 -0.14 0.073 NO
81 PLCB2 PLCB2 PLCB2 15634 -0.15 0.065 NO
82 ADRA2A ADRA2A ADRA2A 15806 -0.16 0.063 NO
83 CHRM3 CHRM3 CHRM3 15883 -0.16 0.066 NO
84 SLC2A1 SLC2A1 SLC2A1 16445 -0.2 0.044 NO
85 PLCB3 PLCB3 PLCB3 16825 -0.23 0.033 NO
86 AKAP5 AKAP5 AKAP5 16902 -0.23 0.038 NO
87 ITPR3 ITPR3 ITPR3 17475 -0.28 0.019 NO
88 GNA15 GNA15 GNA15 18012 -0.35 0.0051 NO
89 GATA4 GATA4 GATA4 18374 -0.44 0.0045 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 LKB1 PATHWAY.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: PID LKB1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID LIS1PATHWAY

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 CAMK2B CAMK2B CAMK2B 19 1.2 0.22 YES
2 MAPT MAPT MAPT 293 0.74 0.35 YES
3 F2 F2 F2 1125 0.39 0.38 YES
4 STAT4 STAT4 STAT4 1222 0.37 0.44 YES
5 AGT AGT AGT 1465 0.32 0.49 YES
6 GNAI1 GNAI1 GNAI1 1995 0.26 0.52 YES
7 HRAS HRAS HRAS 3964 0.12 0.43 NO
8 CALM1 CALM1 CALM1 4065 0.11 0.45 NO
9 STAT5B STAT5B STAT5B 4469 0.097 0.44 NO
10 CDK5 CDK5 CDK5 4604 0.093 0.45 NO
11 AGTR2 AGTR2 AGTR2 5064 0.079 0.44 NO
12 MAP2K2 MAP2K2 MAP2K2 5877 0.06 0.41 NO
13 GNA11 GNA11 GNA11 6709 0.043 0.38 NO
14 CAMK2G CAMK2G CAMK2G 6825 0.041 0.38 NO
15 FYN FYN FYN 7710 0.024 0.33 NO
16 PLCG1 PLCG1 PLCG1 7924 0.021 0.33 NO
17 KNG1 KNG1 KNG1 8538 0.011 0.29 NO
18 STAT3 STAT3 STAT3 9147 0.002 0.26 NO
19 GRB2 GRB2 GRB2 9153 0.0018 0.26 NO
20 CALM3 CALM3 CALM3 9256 0.00036 0.26 NO
21 CAMK2D CAMK2D CAMK2D 9257 0.00034 0.26 NO
22 PTK2B PTK2B PTK2B 9410 -0.0016 0.25 NO
23 GNB1 GNB1 GNB1 9761 -0.0071 0.23 NO
24 JAK2 JAK2 JAK2 9781 -0.0076 0.23 NO
25 CALM2 CALM2 CALM2 10029 -0.011 0.22 NO
26 MAP2K1 MAP2K1 MAP2K1 10405 -0.017 0.2 NO
27 MAPK1 MAPK1 MAPK1 11224 -0.031 0.16 NO
28 MAPK8 MAPK8 MAPK8 11334 -0.033 0.16 NO
29 STAT2 STAT2 STAT2 11477 -0.036 0.16 NO
30 MAPK3 MAPK3 MAPK3 11548 -0.037 0.17 NO
31 STAT5A STAT5A STAT5A 11584 -0.038 0.17 NO
32 SOS1 SOS1 SOS1 11656 -0.039 0.18 NO
33 MAPK14 MAPK14 MAPK14 12779 -0.061 0.13 NO
34 RAF1 RAF1 RAF1 13211 -0.071 0.12 NO
35 PRKCA PRKCA PRKCA 13493 -0.078 0.12 NO
36 CAMK2A CAMK2A CAMK2A 13497 -0.078 0.13 NO
37 PRKCB PRKCB PRKCB 13923 -0.091 0.13 NO
38 SHC1 SHC1 SHC1 14292 -0.1 0.13 NO
39 GNGT1 GNGT1 GNGT1 14480 -0.11 0.14 NO
40 STAT1 STAT1 STAT1 14843 -0.12 0.14 NO
41 MYLK MYLK MYLK 15090 -0.13 0.15 NO
42 STAT6 STAT6 STAT6 15688 -0.16 0.15 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 LIS1PATHWAY.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: PID LIS1PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID HEDGEHOG GLIPATHWAY

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 MAPT MAPT MAPT 293 0.74 0.1 YES
2 BRSK1 BRSK1 BRSK1 509 0.6 0.19 YES
3 MAP2 MAP2 MAP2 681 0.52 0.26 YES
4 BRSK2 BRSK2 BRSK2 861 0.46 0.33 YES
5 ESR1 ESR1 ESR1 1043 0.41 0.38 YES
6 SMARCD3 SMARCD3 SMARCD3 2031 0.25 0.37 NO
7 SMAD4 SMAD4 SMAD4 3911 0.12 0.29 NO
8 SIK3 SIK3 SIK3 4185 0.11 0.29 NO
9 PRKACA PRKACA PRKACA 4439 0.098 0.29 NO
10 RPTOR RPTOR RPTOR 4847 0.085 0.28 NO
11 AKT1S1 AKT1S1 AKT1S1 5005 0.081 0.29 NO
12 PSEN2 PSEN2 PSEN2 5069 0.079 0.3 NO
13 STRADA STRADA STRADA 5167 0.076 0.3 NO
14 SIK2 SIK2 SIK2 5412 0.07 0.3 NO
15 MARK4 MARK4 MARK4 5642 0.065 0.3 NO
16 MLST8 MLST8 MLST8 5736 0.062 0.31 NO
17 STK11 STK11 STK11 5752 0.062 0.32 NO
18 YWHAE YWHAE YWHAE 5835 0.06 0.32 NO
19 TSC1 TSC1 TSC1 6062 0.056 0.32 NO
20 STK11IP STK11IP STK11IP 6560 0.046 0.3 NO
21 PRKAA2 PRKAA2 PRKAA2 6668 0.044 0.3 NO
22 PRKAG1 PRKAG1 PRKAG1 6859 0.04 0.3 NO
23 YWHAQ YWHAQ YWHAQ 7103 0.035 0.29 NO
24 TSC2 TSC2 TSC2 7346 0.031 0.28 NO
25 YWHAG YWHAG YWHAG 9307 -0.0004 0.17 NO
26 HSP90AA1 HSP90AA1 HSP90AA1 9328 -0.00067 0.17 NO
27 YWHAH YWHAH YWHAH 9428 -0.0018 0.17 NO
28 STRADB STRADB STRADB 9803 -0.0079 0.15 NO
29 CDC37 CDC37 CDC37 10041 -0.011 0.14 NO
30 PRKAB1 PRKAB1 PRKAB1 10795 -0.024 0.1 NO
31 YWHAB YWHAB YWHAB 11239 -0.032 0.081 NO
32 GSK3B GSK3B GSK3B 11461 -0.035 0.075 NO
33 MARK2 MARK2 MARK2 11476 -0.036 0.08 NO
34 CRTC2 CRTC2 CRTC2 11654 -0.039 0.076 NO
35 CTSD CTSD CTSD 11680 -0.04 0.082 NO
36 SIK1 SIK1 SIK1 11777 -0.041 0.083 NO
37 CREB1 CREB1 CREB1 12191 -0.049 0.068 NO
38 MTOR MTOR MTOR 12583 -0.057 0.056 NO
39 TP53 TP53 TP53 12788 -0.061 0.055 NO
40 PRKAA1 PRKAA1 PRKAA1 13550 -0.08 0.026 NO
41 YWHAZ YWHAZ YWHAZ 14377 -0.1 -0.0014 NO
42 CAB39 CAB39 CAB39 14723 -0.12 -0.0013 NO
43 MYC MYC MYC 15265 -0.14 -0.0085 NO
44 EZR EZR EZR 15827 -0.16 -0.013 NO
45 MST4 MST4 MST4 16706 -0.22 -0.026 NO
46 ETV4 ETV4 ETV4 17737 -0.31 -0.032 NO
47 SFN SFN SFN 18365 -0.44 0.005 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 HEDGEHOG GLIPATHWAY.

Figure S38.  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

genes ES table in pathway: REACTOME TRANS GOLGI NETWORK VESICLE BUDDING

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 SH3GL2 SH3GL2 SH3GL2 45 1.1 0.2 YES
2 DNAJC6 DNAJC6 DNAJC6 245 0.77 0.33 YES
3 VAMP2 VAMP2 VAMP2 1921 0.26 0.28 NO
4 OCRL OCRL OCRL 2734 0.19 0.28 NO
5 NECAP1 NECAP1 NECAP1 3536 0.14 0.26 NO
6 TPD52 TPD52 TPD52 3826 0.12 0.26 NO
7 AP1S2 AP1S2 AP1S2 4012 0.11 0.27 NO
8 NAPA NAPA NAPA 4328 0.1 0.28 NO
9 BLOC1S1 BLOC1S1 BLOC1S1 4367 0.1 0.29 NO
10 HIP1R HIP1R HIP1R 4734 0.089 0.29 NO
11 DTNBP1 DTNBP1 DTNBP1 5208 0.075 0.28 NO
12 AP1S1 AP1S1 AP1S1 6094 0.055 0.24 NO
13 AP1M1 AP1M1 AP1M1 6321 0.05 0.24 NO
14 PLDN PLDN PLDN 6695 0.043 0.22 NO
15 SORT1 SORT1 SORT1 6748 0.042 0.23 NO
16 GNS GNS GNS 6867 0.04 0.23 NO
17 AP3B1 AP3B1 AP3B1 7123 0.035 0.22 NO
18 AP1B1 AP1B1 AP1B1 7374 0.03 0.21 NO
19 DNASE2 DNASE2 DNASE2 7456 0.029 0.22 NO
20 CLTA CLTA CLTA 7460 0.029 0.22 NO
21 GBF1 GBF1 GBF1 7600 0.026 0.22 NO
22 HSPA8 HSPA8 HSPA8 8218 0.016 0.19 NO
23 AP1M2 AP1M2 AP1M2 8438 0.013 0.18 NO
24 CLTC CLTC CLTC 8662 0.0093 0.17 NO
25 SNX2 SNX2 SNX2 8766 0.008 0.16 NO
26 M6PR M6PR M6PR 9557 -0.0039 0.12 NO
27 TGOLN2 TGOLN2 TGOLN2 9572 -0.0042 0.12 NO
28 ARF1 ARF1 ARF1 9741 -0.0068 0.11 NO
29 BLOC1S3 BLOC1S3 BLOC1S3 9955 -0.01 0.1 NO
30 RAB5C RAB5C RAB5C 10012 -0.011 0.1 NO
31 CPD CPD CPD 10053 -0.012 0.1 NO
32 GAK GAK GAK 10366 -0.017 0.088 NO
33 AP1G1 AP1G1 AP1G1 10631 -0.021 0.078 NO
34 VAMP7 VAMP7 VAMP7 10665 -0.022 0.08 NO
35 IGF2R IGF2R IGF2R 10679 -0.022 0.084 NO
36 SNAPIN SNAPIN SNAPIN 10957 -0.027 0.073 NO
37 FTL FTL FTL 11227 -0.031 0.064 NO
38 PUM1 PUM1 PUM1 11344 -0.033 0.064 NO
39 YIPF6 YIPF6 YIPF6 11735 -0.04 0.051 NO
40 FTH1 FTH1 FTH1 11754 -0.041 0.057 NO
41 ARRB1 ARRB1 ARRB1 11866 -0.043 0.059 NO
42 AP4E1 AP4E1 AP4E1 12087 -0.047 0.056 NO
43 TPD52L1 TPD52L1 TPD52L1 12403 -0.053 0.048 NO
44 TXNDC5 TXNDC5 TXNDC5 12793 -0.061 0.039 NO
45 PICALM PICALM PICALM 12920 -0.064 0.044 NO
46 SNX5 SNX5 SNX5 13032 -0.066 0.05 NO
47 TBC1D8B TBC1D8B TBC1D8B 13111 -0.068 0.058 NO
48 SNX9 SNX9 SNX9 13112 -0.068 0.071 NO
49 DNM2 DNM2 DNM2 13160 -0.07 0.081 NO
50 PIK3C2A PIK3C2A PIK3C2A 13202 -0.071 0.092 NO
51 STX4 STX4 STX4 13280 -0.072 0.1 NO
52 AP4B1 AP4B1 AP4B1 13471 -0.078 0.1 NO
53 CNO CNO CNO 13658 -0.083 0.11 NO
54 AP3S1 AP3S1 AP3S1 14002 -0.093 0.11 NO
55 CTSZ CTSZ CTSZ 14131 -0.097 0.12 NO
56 SH3D19 SH3D19 SH3D19 15350 -0.14 0.08 NO
57 TFRC TFRC TFRC 15466 -0.15 0.1 NO
58 VAMP8 VAMP8 VAMP8 15544 -0.15 0.12 NO
59 SNAP23 SNAP23 SNAP23 16256 -0.19 0.12 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: REACTOME TRANS GOLGI NETWORK VESICLE BUDDING.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

Table 5.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus3. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG DNA REPLICATION 36 genes.ES.table 0.57 1.6 0.1 0.25 0.95 0.61 0.26 0.46 0.15 0.034
KEGG CELL CYCLE 118 genes.ES.table 0.54 1.7 0.035 0.35 0.73 0.4 0.2 0.32 0.12 0.084
KEGG P53 SIGNALING PATHWAY 67 genes.ES.table 0.54 1.8 0.004 0.48 0.58 0.42 0.15 0.36 0.13 0.1
BIOCARTA RACCYCD PATHWAY 26 genes.ES.table 0.5 1.7 0.023 0.32 0.73 0.58 0.33 0.39 0.11 0.075
PID P73PATHWAY 79 genes.ES.table 0.54 1.9 0.0041 0.7 0.41 0.33 0.13 0.29 0 0.16
PID E2F PATHWAY 70 genes.ES.table 0.49 1.6 0.07 0.25 0.94 0.29 0.15 0.24 0.14 0.04
PID ATR PATHWAY 39 genes.ES.table 0.57 1.6 0.08 0.24 0.94 0.38 0.14 0.33 0.14 0.038
PID FRA PATHWAY 37 genes.ES.table 0.65 1.6 0.008 0.24 0.9 0.35 0.086 0.32 0.12 0.044
PID MYC ACTIVPATHWAY 78 genes.ES.table 0.43 1.6 0.046 0.24 0.9 0.33 0.19 0.27 0.12 0.045
PID PLK1 PATHWAY 45 genes.ES.table 0.73 1.7 0.024 0.31 0.8 0.42 0.075 0.39 0.13 0.07
genes ES table in pathway: KEGG DNA REPLICATION

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 CDC25C CDC25C CDC25C 214 0.37 0.057 YES
2 NEK2 NEK2 NEK2 278 0.34 0.12 YES
3 PKMYT1 PKMYT1 PKMYT1 350 0.32 0.17 YES
4 CCNB2 CCNB2 CCNB2 440 0.3 0.22 YES
5 PLK4 PLK4 PLK4 542 0.27 0.27 YES
6 E2F1 E2F1 E2F1 659 0.25 0.31 YES
7 PLK1 PLK1 PLK1 672 0.25 0.35 YES
8 CDK1 CDK1 CDK1 888 0.22 0.38 YES
9 CCNA2 CCNA2 CCNA2 939 0.21 0.42 YES
10 CCNB1 CCNB1 CCNB1 1102 0.19 0.44 YES
11 CDC25A CDC25A CDC25A 2038 0.12 0.42 YES
12 WEE1 WEE1 WEE1 2106 0.11 0.43 YES
13 CDK2 CDK2 CDK2 2260 0.11 0.44 YES
14 MNAT1 MNAT1 MNAT1 2403 0.098 0.45 YES
15 TUBA4A TUBA4A TUBA4A 2427 0.097 0.47 YES
16 E2F3 E2F3 E2F3 2606 0.09 0.48 YES
17 CSNK1E CSNK1E CSNK1E 2670 0.087 0.49 YES
18 AZI1 AZI1 AZI1 2760 0.084 0.5 YES
19 CENPJ CENPJ CENPJ 2823 0.082 0.51 YES
20 TUBB TUBB TUBB 3374 0.067 0.5 YES
21 CKAP5 CKAP5 CKAP5 3467 0.065 0.5 YES
22 CDK7 CDK7 CDK7 3599 0.061 0.51 YES
23 XPO1 XPO1 XPO1 3930 0.054 0.5 YES
24 DYNC1I2 DYNC1I2 DYNC1I2 4015 0.052 0.5 YES
25 YWHAG YWHAG YWHAG 4091 0.05 0.51 YES
26 TUBG1 TUBG1 TUBG1 4092 0.05 0.52 YES
27 HSP90AA1 HSP90AA1 HSP90AA1 4138 0.05 0.52 YES
28 NUMA1 NUMA1 NUMA1 4615 0.041 0.51 NO
29 NEDD1 NEDD1 NEDD1 4879 0.037 0.5 NO
30 CETN2 CETN2 CETN2 4960 0.036 0.5 NO
31 CEP250 CEP250 CEP250 5045 0.035 0.5 NO
32 CEP70 CEP70 CEP70 5156 0.033 0.5 NO
33 CEP72 CEP72 CEP72 5180 0.033 0.51 NO
34 HAUS2 HAUS2 HAUS2 5457 0.029 0.5 NO
35 CDC25B CDC25B CDC25B 6043 0.021 0.47 NO
36 DYNC1H1 DYNC1H1 DYNC1H1 6188 0.02 0.47 NO
37 CLASP1 CLASP1 CLASP1 6661 0.014 0.44 NO
38 PPP2R1A PPP2R1A PPP2R1A 6745 0.014 0.44 NO
39 DYNLL1 DYNLL1 DYNLL1 6847 0.012 0.44 NO
40 MAPRE1 MAPRE1 MAPRE1 6962 0.011 0.43 NO
41 FGFR1OP FGFR1OP FGFR1OP 6971 0.011 0.44 NO
42 DCTN1 DCTN1 DCTN1 7237 0.0084 0.42 NO
43 CEP63 CEP63 CEP63 7355 0.0071 0.42 NO
44 CEP135 CEP135 CEP135 7416 0.0064 0.42 NO
45 TUBA1A TUBA1A TUBA1A 7597 0.0042 0.41 NO
46 CEP192 CEP192 CEP192 7810 0.0016 0.4 NO
47 CSNK1D CSNK1D CSNK1D 7864 0.001 0.39 NO
48 TUBGCP2 TUBGCP2 TUBGCP2 8056 -0.00092 0.38 NO
49 ALMS1 ALMS1 ALMS1 8154 -0.0019 0.38 NO
50 TUBGCP5 TUBGCP5 TUBGCP5 8299 -0.0037 0.37 NO
51 YWHAE YWHAE YWHAE 8418 -0.005 0.36 NO
52 CDK5RAP2 CDK5RAP2 CDK5RAP2 8452 -0.0054 0.36 NO
53 NINL NINL NINL 8485 -0.0057 0.36 NO
54 SDCCAG8 SDCCAG8 SDCCAG8 8760 -0.0086 0.35 NO
55 TUBG2 TUBG2 TUBG2 8762 -0.0086 0.35 NO
56 ACTR1A ACTR1A ACTR1A 8781 -0.0088 0.35 NO
57 CEP76 CEP76 CEP76 8956 -0.011 0.34 NO
58 SSNA1 SSNA1 SSNA1 9144 -0.013 0.34 NO
59 CEP164 CEP164 CEP164 9366 -0.015 0.33 NO
60 CCNH CCNH CCNH 9461 -0.016 0.33 NO
61 DCTN2 DCTN2 DCTN2 9995 -0.022 0.3 NO
62 OFD1 OFD1 OFD1 10006 -0.022 0.3 NO
63 CEP57 CEP57 CEP57 10044 -0.023 0.31 NO
64 CEP290 CEP290 CEP290 10516 -0.028 0.29 NO
65 TUBGCP3 TUBGCP3 TUBGCP3 11043 -0.036 0.26 NO
66 TUBGCP6 TUBGCP6 TUBGCP6 11074 -0.036 0.27 NO
67 PRKACA PRKACA PRKACA 11373 -0.04 0.26 NO
68 AKAP9 AKAP9 AKAP9 11420 -0.041 0.26 NO
69 DCTN3 DCTN3 DCTN3 12060 -0.052 0.24 NO
70 PCM1 PCM1 PCM1 12166 -0.054 0.24 NO
71 PAFAH1B1 PAFAH1B1 PAFAH1B1 12209 -0.055 0.25 NO
72 PCNT PCNT PCNT 12274 -0.057 0.26 NO
73 CCNA1 CCNA1 CCNA1 15153 -0.15 0.13 NO
74 PRKAR2B PRKAR2B PRKAR2B 16712 -0.26 0.095 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 DNA REPLICATION.

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

genes ES table in pathway: KEGG CELL CYCLE

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 S100A2 S100A2 S100A2 33 0.56 0.063 YES
2 TP73 TP73 TP73 54 0.5 0.12 YES
3 TP63 TP63 TP63 115 0.44 0.17 YES
4 BUB1 BUB1 BUB1 416 0.3 0.18 YES
5 SFN SFN SFN 450 0.29 0.22 YES
6 IL1RAP IL1RAP IL1RAP 465 0.29 0.25 YES
7 TP53AIP1 TP53AIP1 TP53AIP1 484 0.28 0.28 YES
8 RAD51 RAD51 RAD51 517 0.28 0.31 YES
9 PLK1 PLK1 PLK1 672 0.25 0.33 YES
10 WT1 WT1 WT1 773 0.23 0.35 YES
11 CDK1 CDK1 CDK1 888 0.22 0.37 YES
12 CCNA2 CCNA2 CCNA2 939 0.21 0.39 YES
13 ADA ADA ADA 1031 0.2 0.41 YES
14 CCNE2 CCNE2 CCNE2 1067 0.2 0.43 YES
15 CCNB1 CCNB1 CCNB1 1102 0.19 0.45 YES
16 CLCA2 CLCA2 CLCA2 1224 0.18 0.46 YES
17 CHEK1 CHEK1 CHEK1 1292 0.17 0.48 YES
18 BRCA2 BRCA2 BRCA2 1413 0.16 0.49 YES
19 SERPINE1 SERPINE1 SERPINE1 1486 0.16 0.5 YES
20 JAG2 JAG2 JAG2 1673 0.14 0.51 YES
21 CDK6 CDK6 CDK6 2115 0.11 0.5 YES
22 PLK3 PLK3 PLK3 2188 0.11 0.51 YES
23 BBC3 BBC3 BBC3 2198 0.11 0.52 YES
24 CDK2 CDK2 CDK2 2260 0.11 0.53 YES
25 YAP1 YAP1 YAP1 2287 0.1 0.54 YES
26 HSF1 HSF1 HSF1 2415 0.098 0.54 YES
27 FBXO45 FBXO45 FBXO45 2657 0.088 0.54 NO
28 PML PML PML 3179 0.072 0.52 NO
29 IL4R IL4R IL4R 3219 0.071 0.53 NO
30 TP53I3 TP53I3 TP53I3 3794 0.057 0.5 NO
31 CASP2 CASP2 CASP2 3859 0.055 0.5 NO
32 ITCH ITCH ITCH 3867 0.055 0.51 NO
33 RELA RELA RELA 4309 0.046 0.49 NO
34 SP1 SP1 SP1 4780 0.039 0.47 NO
35 MDM2 MDM2 MDM2 4867 0.037 0.47 NO
36 BCL2L11 BCL2L11 BCL2L11 5136 0.034 0.46 NO
37 BUB3 BUB3 BUB3 5218 0.032 0.46 NO
38 FASN FASN FASN 5233 0.032 0.46 NO
39 BAK1 BAK1 BAK1 5234 0.032 0.46 NO
40 CDKN1A CDKN1A CDKN1A 6056 0.021 0.42 NO
41 PEA15 PEA15 PEA15 6289 0.018 0.41 NO
42 MAPK14 MAPK14 MAPK14 6355 0.018 0.41 NO
43 DEDD DEDD DEDD 6409 0.017 0.41 NO
44 MYC MYC MYC 7176 0.009 0.37 NO
45 TUBA1A TUBA1A TUBA1A 7597 0.0042 0.35 NO
46 BAX BAX BAX 7713 0.0028 0.34 NO
47 FLOT2 FLOT2 FLOT2 7912 0.00052 0.33 NO
48 UBE4B UBE4B UBE4B 8001 -0.00039 0.32 NO
49 EP300 EP300 EP300 8021 -0.00054 0.32 NO
50 ABL1 ABL1 ABL1 8208 -0.0025 0.31 NO
51 FAS FAS FAS 8537 -0.0062 0.3 NO
52 AFP AFP AFP 8794 -0.0089 0.28 NO
53 GNB2L1 GNB2L1 GNB2L1 8862 -0.0097 0.28 NO
54 JAK1 JAK1 JAK1 9052 -0.012 0.27 NO
55 NDUFS2 NDUFS2 NDUFS2 9758 -0.02 0.24 NO
56 KAT5 KAT5 KAT5 9806 -0.02 0.24 NO
57 MAPK11 MAPK11 MAPK11 10045 -0.023 0.23 NO
58 RB1 RB1 RB1 10458 -0.027 0.21 NO
59 FOXO3 FOXO3 FOXO3 10875 -0.033 0.19 NO
60 BIN1 BIN1 BIN1 11231 -0.038 0.17 NO
61 RCHY1 RCHY1 RCHY1 11436 -0.042 0.17 NO
62 PFDN5 PFDN5 PFDN5 11597 -0.044 0.16 NO
63 AEN AEN AEN 11645 -0.045 0.16 NO
64 DCP1B DCP1B DCP1B 11652 -0.045 0.17 NO
65 RNF43 RNF43 RNF43 11700 -0.046 0.17 NO
66 PIN1 PIN1 PIN1 11995 -0.051 0.16 NO
67 GRAMD4 GRAMD4 GRAMD4 12007 -0.051 0.17 NO
68 SIRT1 SIRT1 SIRT1 12285 -0.057 0.16 NO
69 HEY2 HEY2 HEY2 12572 -0.063 0.15 NO
70 SERPINA1 SERPINA1 SERPINA1 12801 -0.068 0.15 NO
71 NEDD4L NEDD4L NEDD4L 12909 -0.07 0.15 NO
72 HAGH HAGH HAGH 13411 -0.083 0.13 NO
73 GDF15 GDF15 GDF15 13498 -0.086 0.14 NO
74 WWOX WWOX WWOX 13747 -0.093 0.13 NO
75 GATA1 GATA1 GATA1 14828 -0.14 0.09 NO
76 PRKACB PRKACB PRKACB 14965 -0.14 0.099 NO
77 PPAP2A PPAP2A PPAP2A 15049 -0.15 0.11 NO
78 NTRK1 NTRK1 NTRK1 16684 -0.26 0.052 NO
79 D4S234E D4S234E D4S234E 17796 -0.39 0.036 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: KEGG CELL CYCLE.

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

genes ES table in pathway: KEGG P53 SIGNALING PATHWAY

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 KIF18A KIF18A KIF18A 148 0.41 0.0039 YES
2 SPC24 SPC24 SPC24 165 0.4 0.015 YES
3 CDC25C CDC25C CDC25C 214 0.37 0.023 YES
4 BIRC5 BIRC5 BIRC5 220 0.37 0.034 YES
5 MCM10 MCM10 MCM10 250 0.35 0.042 YES
6 CENPA CENPA CENPA 263 0.35 0.052 YES
7 CENPI CENPI CENPI 269 0.34 0.062 YES
8 HJURP HJURP HJURP 273 0.34 0.072 YES
9 NEK2 NEK2 NEK2 278 0.34 0.082 YES
10 OIP5 OIP5 OIP5 280 0.34 0.092 YES
11 KIF20A KIF20A KIF20A 300 0.34 0.1 YES
12 HIST1H2BC HIST1H2BC HIST1H2BC 319 0.33 0.11 YES
13 UBE2C UBE2C UBE2C 333 0.32 0.12 YES
14 SGOL1 SGOL1 SGOL1 335 0.32 0.13 YES
15 PKMYT1 PKMYT1 PKMYT1 350 0.32 0.14 YES
16 HIST1H2BO HIST1H2BO HIST1H2BO 351 0.32 0.15 YES
17 KIF23 KIF23 KIF23 354 0.32 0.16 YES
18 CDC45 CDC45 CDC45 373 0.31 0.16 YES
19 CDC20 CDC20 CDC20 395 0.3 0.17 YES
20 KIF2C KIF2C KIF2C 401 0.3 0.18 YES
21 ERCC6L ERCC6L ERCC6L 407 0.3 0.19 YES
22 HIST1H2BJ HIST1H2BJ HIST1H2BJ 410 0.3 0.2 YES
23 BUB1 BUB1 BUB1 416 0.3 0.21 YES
24 CCNB2 CCNB2 CCNB2 440 0.3 0.21 YES
25 CENPK CENPK CENPK 449 0.29 0.22 YES
26 HIST1H2BD HIST1H2BD HIST1H2BD 469 0.29 0.23 YES
27 PLK4 PLK4 PLK4 542 0.27 0.23 YES
28 CASC5 CASC5 CASC5 584 0.27 0.24 YES
29 HIST1H4E HIST1H4E HIST1H4E 587 0.27 0.25 YES
30 HIST1H4I HIST1H4I HIST1H4I 597 0.26 0.25 YES
31 BUB1B BUB1B BUB1B 608 0.26 0.26 YES
32 AURKB AURKB AURKB 625 0.26 0.27 YES
33 MYBL2 MYBL2 MYBL2 632 0.26 0.28 YES
34 E2F1 E2F1 E2F1 659 0.25 0.28 YES
35 NUF2 NUF2 NUF2 664 0.25 0.29 YES
36 PLK1 PLK1 PLK1 672 0.25 0.3 YES
37 SMC1B SMC1B SMC1B 685 0.25 0.3 YES
38 HIST3H2BB HIST3H2BB HIST3H2BB 713 0.24 0.31 YES
39 CDC6 CDC6 CDC6 762 0.24 0.31 YES
40 HIST1H2BG HIST1H2BG HIST1H2BG 767 0.23 0.32 YES
41 CDT1 CDT1 CDT1 771 0.23 0.32 YES
42 HIST1H2AJ HIST1H2AJ HIST1H2AJ 818 0.23 0.33 YES
43 HIST1H2BF HIST1H2BF HIST1H2BF 843 0.22 0.33 YES
44 POLE2 POLE2 POLE2 857 0.22 0.34 YES
45 HIST1H2AD HIST1H2AD HIST1H2AD 874 0.22 0.34 YES
46 GINS4 GINS4 GINS4 875 0.22 0.35 YES
47 HIST1H2BM HIST1H2BM HIST1H2BM 876 0.22 0.36 YES
48 AURKA AURKA AURKA 877 0.22 0.36 YES
49 PTTG1 PTTG1 PTTG1 884 0.22 0.37 YES
50 CDK1 CDK1 CDK1 888 0.22 0.38 YES
51 CCNE1 CCNE1 CCNE1 930 0.22 0.38 YES
52 CCNA2 CCNA2 CCNA2 939 0.21 0.39 YES
53 HIST1H2AE HIST1H2AE HIST1H2AE 971 0.21 0.39 YES
54 NDC80 NDC80 NDC80 979 0.21 0.4 YES
55 HIST2H2AA3 HIST2H2AA3 HIST2H2AA3 988 0.21 0.4 YES
56 SKA1 SKA1 SKA1 993 0.21 0.41 YES
57 MCM2 MCM2 MCM2 1030 0.2 0.41 YES
58 HIST1H2BN HIST1H2BN HIST1H2BN 1032 0.2 0.42 YES
59 RRM2 RRM2 RRM2 1040 0.2 0.42 YES
60 CCNE2 CCNE2 CCNE2 1067 0.2 0.43 YES
61 HIST1H4H HIST1H4H HIST1H4H 1084 0.19 0.43 YES
62 GINS2 GINS2 GINS2 1087 0.19 0.44 YES
63 MCM4 MCM4 MCM4 1089 0.19 0.44 YES
64 MAD2L1 MAD2L1 MAD2L1 1091 0.19 0.45 YES
65 HIST1H4B HIST1H4B HIST1H4B 1096 0.19 0.46 YES
66 CCNB1 CCNB1 CCNB1 1102 0.19 0.46 YES
67 GINS1 GINS1 GINS1 1126 0.19 0.47 YES
68 CDCA8 CDCA8 CDCA8 1135 0.19 0.47 YES
69 HIST1H2BE HIST1H2BE HIST1H2BE 1175 0.18 0.47 YES
70 CENPM CENPM CENPM 1250 0.18 0.48 YES
71 HIST1H2BL HIST1H2BL HIST1H2BL 1280 0.18 0.48 YES
72 CHEK1 CHEK1 CHEK1 1292 0.17 0.48 YES
73 HIST1H4D HIST1H4D HIST1H4D 1296 0.17 0.49 YES
74 KNTC1 KNTC1 KNTC1 1299 0.17 0.49 YES
75 HIST2H4A HIST2H4A HIST2H4A 1312 0.17 0.5 YES
76 SGOL2 SGOL2 SGOL2 1338 0.17 0.5 YES
77 RFC4 RFC4 RFC4 1365 0.17 0.5 YES
78 MLF1IP MLF1IP MLF1IP 1380 0.16 0.51 YES
79 CENPH CENPH CENPH 1442 0.16 0.51 YES
80 HIST2H2BE HIST2H2BE HIST2H2BE 1457 0.16 0.51 YES
81 CCND1 CCND1 CCND1 1526 0.15 0.52 YES
82 ZWINT ZWINT ZWINT 1606 0.15 0.52 YES
83 CKS1B CKS1B CKS1B 1615 0.14 0.52 YES
84 SYCP2 SYCP2 SYCP2 1632 0.14 0.52 YES
85 TYMS TYMS TYMS 1647 0.14 0.52 YES
86 SPC25 SPC25 SPC25 1784 0.13 0.52 YES
87 TERT TERT TERT 1979 0.12 0.51 YES
88 DNA2 DNA2 DNA2 2018 0.12 0.52 YES
89 CDC25A CDC25A CDC25A 2038 0.12 0.52 YES
90 INCENP INCENP INCENP 2105 0.11 0.52 YES
91 WEE1 WEE1 WEE1 2106 0.11 0.52 YES
92 CDK6 CDK6 CDK6 2115 0.11 0.52 YES
93 CCDC99 CCDC99 CCDC99 2153 0.11 0.52 YES
94 CENPN CENPN CENPN 2235 0.11 0.52 YES
95 CDK2 CDK2 CDK2 2260 0.11 0.53 YES
96 LMNB1 LMNB1 LMNB1 2264 0.11 0.53 YES
97 E2F2 E2F2 E2F2 2298 0.1 0.53 YES
98 HIST1H4J HIST1H4J HIST1H4J 2300 0.1 0.53 YES
99 HIST1H2BK HIST1H2BK HIST1H2BK 2354 0.1 0.53 YES
100 ZWILCH ZWILCH ZWILCH 2371 0.1 0.54 YES
101 MNAT1 MNAT1 MNAT1 2403 0.098 0.54 YES
102 CENPO CENPO CENPO 2424 0.097 0.54 YES
103 TUBA4A TUBA4A TUBA4A 2427 0.097 0.54 YES
104 RFC2 RFC2 RFC2 2435 0.097 0.54 YES
105 H2AFX H2AFX H2AFX 2484 0.095 0.54 YES
106 HIST1H2AC HIST1H2AC HIST1H2AC 2490 0.094 0.55 YES
107 RUVBL1 RUVBL1 RUVBL1 2507 0.094 0.55 YES
108 POLD1 POLD1 POLD1 2510 0.094 0.55 YES
109 NUP107 NUP107 NUP107 2554 0.092 0.55 YES
110 LIN9 LIN9 LIN9 2577 0.09 0.55 YES
111 E2F3 E2F3 E2F3 2606 0.09 0.55 YES
112 PSMD2 PSMD2 PSMD2 2609 0.089 0.56 YES
113 RBL1 RBL1 RBL1 2663 0.087 0.56 YES
114 CSNK1E CSNK1E CSNK1E 2670 0.087 0.56 YES
115 MCM7 MCM7 MCM7 2678 0.087 0.56 YES
116 CDC7 CDC7 CDC7 2696 0.086 0.56 YES
117 CHEK2 CHEK2 CHEK2 2710 0.086 0.56 YES
118 RCC2 RCC2 RCC2 2753 0.084 0.56 YES
119 AZI1 AZI1 AZI1 2760 0.084 0.57 YES
120 HIST4H4 HIST4H4 HIST4H4 2765 0.084 0.57 YES
121 FEN1 FEN1 FEN1 2771 0.084 0.57 YES
122 CENPJ CENPJ CENPJ 2823 0.082 0.57 YES
123 DSN1 DSN1 DSN1 2848 0.082 0.57 YES
124 PSMD14 PSMD14 PSMD14 2871 0.081 0.57 YES
125 MCM6 MCM6 MCM6 2932 0.079 0.57 YES
126 CDKN2B CDKN2B CDKN2B 2966 0.078 0.57 YES
127 RUVBL2 RUVBL2 RUVBL2 3055 0.075 0.57 YES
128 NUP85 NUP85 NUP85 3129 0.073 0.57 YES
129 HIST3H3 HIST3H3 HIST3H3 3140 0.073 0.57 YES
130 FKBP6 FKBP6 FKBP6 3166 0.072 0.57 YES
131 PRIM2 PRIM2 PRIM2 3200 0.071 0.57 YES
132 MCM8 MCM8 MCM8 3214 0.071 0.57 YES
133 CENPL CENPL CENPL 3241 0.07 0.57 YES
134 CENPP CENPP CENPP 3309 0.068 0.57 YES
135 PSMD12 PSMD12 PSMD12 3311 0.068 0.57 YES
136 TUBB TUBB TUBB 3374 0.067 0.57 YES
137 CDKN2D CDKN2D CDKN2D 3379 0.067 0.57 YES
138 RPA3 RPA3 RPA3 3390 0.067 0.57 YES
139 MCM5 MCM5 MCM5 3395 0.067 0.57 YES
140 CKAP5 CKAP5 CKAP5 3467 0.065 0.57 YES
141 SKP2 SKP2 SKP2 3471 0.065 0.57 YES
142 H2AFZ H2AFZ H2AFZ 3541 0.063 0.57 YES
143 RANGAP1 RANGAP1 RANGAP1 3562 0.062 0.57 YES
144 RFC5 RFC5 RFC5 3577 0.062 0.57 YES
145 PPP2R2A PPP2R2A PPP2R2A 3596 0.061 0.58 YES
146 CDK7 CDK7 CDK7 3599 0.061 0.58 YES
147 PSMD7 PSMD7 PSMD7 3660 0.06 0.58 YES
148 UBE2E1 UBE2E1 UBE2E1 3695 0.059 0.58 YES
149 HSPA2 HSPA2 HSPA2 3698 0.059 0.58 YES
150 PSMD11 PSMD11 PSMD11 3713 0.058 0.58 YES
151 TAOK1 TAOK1 TAOK1 3723 0.058 0.58 YES
152 NUP37 NUP37 NUP37 3731 0.058 0.58 YES
153 LIG1 LIG1 LIG1 3804 0.056 0.58 NO
154 XPO1 XPO1 XPO1 3930 0.054 0.57 NO
155 BRCA1 BRCA1 BRCA1 3945 0.053 0.57 NO
156 LMNA LMNA LMNA 4005 0.052 0.57 NO
157 DYNC1I2 DYNC1I2 DYNC1I2 4015 0.052 0.57 NO
158 UBE2I UBE2I UBE2I 4038 0.052 0.57 NO
159 RSF1 RSF1 RSF1 4047 0.051 0.57 NO
160 PSMA1 PSMA1 PSMA1 4051 0.051 0.58 NO
161 ZW10 ZW10 ZW10 4053 0.051 0.58 NO
162 ANAPC11 ANAPC11 ANAPC11 4073 0.051 0.58 NO
163 YWHAG YWHAG YWHAG 4091 0.05 0.58 NO
164 TUBG1 TUBG1 TUBG1 4092 0.05 0.58 NO
165 HSP90AA1 HSP90AA1 HSP90AA1 4138 0.05 0.58 NO
166 POLD4 POLD4 POLD4 4167 0.049 0.58 NO
167 PCNA PCNA PCNA 4202 0.048 0.58 NO
168 TK2 TK2 TK2 4225 0.048 0.58 NO
169 PSMB2 PSMB2 PSMB2 4258 0.047 0.58 NO
170 PSMA7 PSMA7 PSMA7 4327 0.046 0.58 NO
171 DBF4 DBF4 DBF4 4330 0.046 0.58 NO
172 TEX12 TEX12 TEX12 4343 0.046 0.58 NO
173 RFC3 RFC3 RFC3 4368 0.045 0.58 NO
174 ANAPC1 ANAPC1 ANAPC1 4384 0.045 0.58 NO
175 PSMA5 PSMA5 PSMA5 4401 0.045 0.58 NO
176 ACD ACD ACD 4432 0.044 0.58 NO
177 CENPQ CENPQ CENPQ 4447 0.044 0.58 NO
178 LIN37 LIN37 LIN37 4497 0.043 0.58 NO
179 RAD21 RAD21 RAD21 4525 0.043 0.58 NO
180 HIST1H2AB HIST1H2AB HIST1H2AB 4553 0.042 0.58 NO
181 PSMA6 PSMA6 PSMA6 4582 0.042 0.58 NO
182 NUMA1 NUMA1 NUMA1 4615 0.041 0.58 NO
183 UBE2D1 UBE2D1 UBE2D1 4616 0.041 0.58 NO
184 MAD1L1 MAD1L1 MAD1L1 4667 0.04 0.58 NO
185 CLIP1 CLIP1 CLIP1 4673 0.04 0.58 NO
186 ATR ATR ATR 4674 0.04 0.58 NO
187 PPP2R5E PPP2R5E PPP2R5E 4701 0.04 0.58 NO
188 POLA2 POLA2 POLA2 4740 0.039 0.58 NO
189 PSMD8 PSMD8 PSMD8 4821 0.038 0.57 NO
190 STAG1 STAG1 STAG1 4835 0.038 0.57 NO
191 MDM2 MDM2 MDM2 4867 0.037 0.57 NO
192 NEDD1 NEDD1 NEDD1 4879 0.037 0.57 NO
193 ITGB3BP ITGB3BP ITGB3BP 4881 0.037 0.57 NO
194 CETN2 CETN2 CETN2 4960 0.036 0.57 NO
195 CEP250 CEP250 CEP250 5045 0.035 0.57 NO
196 PSMD13 PSMD13 PSMD13 5082 0.034 0.57 NO
197 POLE POLE POLE 5120 0.034 0.57 NO
198 CEP70 CEP70 CEP70 5156 0.033 0.56 NO
199 CEP72 CEP72 CEP72 5180 0.033 0.56 NO
200 PSMC3 PSMC3 PSMC3 5187 0.033 0.56 NO
201 BUB3 BUB3 BUB3 5218 0.032 0.56 NO
202 PSMC1 PSMC1 PSMC1 5255 0.032 0.56 NO
203 RAD9A RAD9A RAD9A 5260 0.032 0.56 NO
204 PSMD1 PSMD1 PSMD1 5280 0.032 0.56 NO
205 POT1 POT1 POT1 5412 0.03 0.56 NO
206 PSMC6 PSMC6 PSMC6 5442 0.029 0.56 NO
207 HAUS2 HAUS2 HAUS2 5457 0.029 0.56 NO
208 CDC23 CDC23 CDC23 5505 0.028 0.56 NO
209 KIF2A KIF2A KIF2A 5545 0.028 0.55 NO
210 PSMD5 PSMD5 PSMD5 5561 0.028 0.55 NO
211 PSME4 PSME4 PSME4 5630 0.027 0.55 NO
212 ANAPC10 ANAPC10 ANAPC10 5665 0.026 0.55 NO
213 PSMC4 PSMC4 PSMC4 5669 0.026 0.55 NO
214 DHFR DHFR DHFR 5672 0.026 0.55 NO
215 TFDP1 TFDP1 TFDP1 5771 0.025 0.55 NO
216 PSMA3 PSMA3 PSMA3 5831 0.024 0.54 NO
217 PSMD4 PSMD4 PSMD4 5878 0.024 0.54 NO
218 CENPT CENPT CENPT 5884 0.023 0.54 NO
219 CDK4 CDK4 CDK4 5928 0.023 0.54 NO
220 CDC25B CDC25B CDC25B 6043 0.021 0.54 NO
221 PSMD10 PSMD10 PSMD10 6055 0.021 0.54 NO
222 CDKN1A CDKN1A CDKN1A 6056 0.021 0.54 NO
223 SKA2 SKA2 SKA2 6077 0.021 0.54 NO
224 CDKN2A CDKN2A CDKN2A 6115 0.021 0.53 NO
225 SEC13 SEC13 SEC13 6170 0.02 0.53 NO
226 PPP2R5B PPP2R5B PPP2R5B 6173 0.02 0.53 NO
227 DYNC1H1 DYNC1H1 DYNC1H1 6188 0.02 0.53 NO
228 PSMD3 PSMD3 PSMD3 6194 0.02 0.53 NO
229 NUDC NUDC NUDC 6225 0.019 0.53 NO
230 CDC27 CDC27 CDC27 6249 0.019 0.53 NO
231 PSMA2 PSMA2 PSMA2 6271 0.019 0.53 NO
232 PSMA4 PSMA4 PSMA4 6379 0.018 0.52 NO
233 PSMB5 PSMB5 PSMB5 6385 0.018 0.52 NO
234 PSMB3 PSMB3 PSMB3 6437 0.017 0.52 NO
235 SUN2 SUN2 SUN2 6458 0.017 0.52 NO
236 NPM1 NPM1 NPM1 6558 0.016 0.52 NO
237 NDEL1 NDEL1 NDEL1 6654 0.014 0.51 NO
238 CLASP1 CLASP1 CLASP1 6661 0.014 0.51 NO
239 HDAC1 HDAC1 HDAC1 6671 0.014 0.51 NO
240 PSMB9 PSMB9 PSMB9 6695 0.014 0.51 NO
241 E2F4 E2F4 E2F4 6720 0.014 0.51 NO
242 PPP2R1A PPP2R1A PPP2R1A 6745 0.014 0.51 NO
243 PPP2CA PPP2CA PPP2CA 6752 0.014 0.51 NO
244 PSMB7 PSMB7 PSMB7 6763 0.013 0.51 NO
245 SEH1L SEH1L SEH1L 6823 0.013 0.51 NO
246 DYNLL1 DYNLL1 DYNLL1 6847 0.012 0.5 NO
247 PSMB4 PSMB4 PSMB4 6883 0.012 0.5 NO
248 MAPRE1 MAPRE1 MAPRE1 6962 0.011 0.5 NO
249 FGFR1OP FGFR1OP FGFR1OP 6971 0.011 0.5 NO
250 POLD2 POLD2 POLD2 7077 0.01 0.49 NO
251 RBBP4 RBBP4 RBBP4 7143 0.0094 0.49 NO
252 PSMD9 PSMD9 PSMD9 7162 0.0092 0.49 NO
253 MYC MYC MYC 7176 0.009 0.49 NO
254 PSMC2 PSMC2 PSMC2 7201 0.0088 0.49 NO
255 DCTN1 DCTN1 DCTN1 7237 0.0084 0.49 NO
256 SMARCA5 SMARCA5 SMARCA5 7244 0.0083 0.49 NO
257 RBBP7 RBBP7 RBBP7 7338 0.0073 0.48 NO
258 CEP63 CEP63 CEP63 7355 0.0071 0.48 NO
259 RAD1 RAD1 RAD1 7386 0.0068 0.48 NO
260 PSMB8 PSMB8 PSMB8 7411 0.0065 0.48 NO
261 CEP135 CEP135 CEP135 7416 0.0064 0.48 NO
262 PSMC5 PSMC5 PSMC5 7439 0.0062 0.48 NO
263 DKC1 DKC1 DKC1 7446 0.0061 0.48 NO
264 HIST1H4A HIST1H4A HIST1H4A 7530 0.0051 0.47 NO
265 TUBA1A TUBA1A TUBA1A 7597 0.0042 0.47 NO
266 PRIM1 PRIM1 PRIM1 7684 0.0032 0.46 NO
267 PPP2CB PPP2CB PPP2CB 7803 0.0017 0.46 NO
268 CEP192 CEP192 CEP192 7810 0.0016 0.46 NO
269 SYNE2 SYNE2 SYNE2 7846 0.0012 0.46 NO
270 CSNK1D CSNK1D CSNK1D 7864 0.001 0.46 NO
271 MCM3 MCM3 MCM3 8011 -0.00046 0.45 NO
272 TUBGCP2 TUBGCP2 TUBGCP2 8056 -0.00092 0.44 NO
273 PPP2R5C PPP2R5C PPP2R5C 8066 -0.00098 0.44 NO
274 PSME2 PSME2 PSME2 8112 -0.0015 0.44 NO
275 ALMS1 ALMS1 ALMS1 8154 -0.0019 0.44 NO
276 LIN54 LIN54 LIN54 8197 -0.0024 0.44 NO
277 AHCTF1 AHCTF1 AHCTF1 8198 -0.0024 0.44 NO
278 PSMF1 PSMF1 PSMF1 8251 -0.003 0.43 NO
279 SKP1 SKP1 SKP1 8277 -0.0034 0.43 NO
280 TUBGCP5 TUBGCP5 TUBGCP5 8299 -0.0037 0.43 NO
281 NHP2 NHP2 NHP2 8360 -0.0044 0.43 NO
282 YWHAE YWHAE YWHAE 8418 -0.005 0.43 NO
283 PSME1 PSME1 PSME1 8420 -0.005 0.43 NO
284 CDK5RAP2 CDK5RAP2 CDK5RAP2 8452 -0.0054 0.42 NO
285 NINL NINL NINL 8485 -0.0057 0.42 NO
286 TERF1 TERF1 TERF1 8486 -0.0057 0.42 NO
287 E2F5 E2F5 E2F5 8487 -0.0058 0.42 NO
288 ATRIP ATRIP ATRIP 8697 -0.0079 0.41 NO
289 SDCCAG8 SDCCAG8 SDCCAG8 8760 -0.0086 0.41 NO
290 TUBG2 TUBG2 TUBG2 8762 -0.0086 0.41 NO
291 ACTR1A ACTR1A ACTR1A 8781 -0.0088 0.41 NO
292 FBXO5 FBXO5 FBXO5 8887 -0.01 0.4 NO
293 SMC3 SMC3 SMC3 8889 -0.01 0.4 NO
294 HUS1 HUS1 HUS1 8899 -0.01 0.4 NO
295 STAG2 STAG2 STAG2 8921 -0.01 0.4 NO
296 RPS27A RPS27A RPS27A 8932 -0.01 0.4 NO
297 CEP76 CEP76 CEP76 8956 -0.011 0.4 NO
298 PPP2R5D PPP2R5D PPP2R5D 8989 -0.011 0.4 NO
299 DIDO1 DIDO1 DIDO1 9010 -0.011 0.4 NO
300 CUL1 CUL1 CUL1 9026 -0.012 0.4 NO
301 RPA2 RPA2 RPA2 9089 -0.012 0.39 NO
302 CDKN1B CDKN1B CDKN1B 9103 -0.012 0.39 NO
303 SSNA1 SSNA1 SSNA1 9144 -0.013 0.39 NO
304 PSMB10 PSMB10 PSMB10 9206 -0.014 0.39 NO
305 TINF2 TINF2 TINF2 9237 -0.014 0.39 NO
306 RFWD2 RFWD2 RFWD2 9287 -0.015 0.39 NO
307 PSMB1 PSMB1 PSMB1 9317 -0.015 0.38 NO
308 ANAPC7 ANAPC7 ANAPC7 9353 -0.015 0.38 NO
309 CEP164 CEP164 CEP164 9366 -0.015 0.38 NO
310 CDC16 CDC16 CDC16 9441 -0.016 0.38 NO
311 CCNH CCNH CCNH 9461 -0.016 0.38 NO
312 POLA1 POLA1 POLA1 9488 -0.017 0.38 NO
313 NUP133 NUP133 NUP133 9516 -0.017 0.38 NO
314 GORASP1 GORASP1 GORASP1 9521 -0.017 0.38 NO
315 ANAPC4 ANAPC4 ANAPC4 9667 -0.019 0.37 NO
316 TP53 TP53 TP53 9714 -0.019 0.37 NO
317 POLD3 POLD3 POLD3 9730 -0.019 0.37 NO
318 PPP2R3B PPP2R3B PPP2R3B 9864 -0.021 0.36 NO
319 PSMD6 PSMD6 PSMD6 9911 -0.021 0.36 NO
320 DCTN2 DCTN2 DCTN2 9995 -0.022 0.36 NO
321 OFD1 OFD1 OFD1 10006 -0.022 0.36 NO
322 CEP57 CEP57 CEP57 10044 -0.023 0.35 NO
323 PMF1 PMF1 PMF1 10065 -0.023 0.35 NO
324 PPP1CC PPP1CC PPP1CC 10091 -0.023 0.35 NO
325 SMC1A SMC1A SMC1A 10363 -0.026 0.34 NO
326 PSMB6 PSMB6 PSMB6 10392 -0.026 0.34 NO
327 RB1 RB1 RB1 10458 -0.027 0.34 NO
328 RBL2 RBL2 RBL2 10469 -0.028 0.34 NO
329 ANAPC5 ANAPC5 ANAPC5 10493 -0.028 0.33 NO
330 GMNN GMNN GMNN 10506 -0.028 0.34 NO
331 LIN52 LIN52 LIN52 10507 -0.028 0.34 NO
332 CEP290 CEP290 CEP290 10516 -0.028 0.34 NO
333 RPA1 RPA1 RPA1 10536 -0.028 0.34 NO
334 MAX MAX MAX 10558 -0.029 0.34 NO
335 HIST2H2AC HIST2H2AC HIST2H2AC 10616 -0.03 0.33 NO
336 NUP43 NUP43 NUP43 10721 -0.031 0.33 NO
337 RANBP2 RANBP2 RANBP2 10769 -0.032 0.33 NO
338 TUBGCP3 TUBGCP3 TUBGCP3 11043 -0.036 0.31 NO
339 TUBGCP6 TUBGCP6 TUBGCP6 11074 -0.036 0.31 NO
340 CDKN2C CDKN2C CDKN2C 11098 -0.036 0.31 NO
341 TERF2 TERF2 TERF2 11185 -0.038 0.31 NO
342 HIST1H4C HIST1H4C HIST1H4C 11308 -0.04 0.3 NO
343 CDC26 CDC26 CDC26 11351 -0.04 0.3 NO
344 PRKACA PRKACA PRKACA 11373 -0.04 0.3 NO
345 AKAP9 AKAP9 AKAP9 11420 -0.041 0.3 NO
346 ANAPC2 ANAPC2 ANAPC2 11466 -0.042 0.3 NO
347 UBA52 UBA52 UBA52 11476 -0.042 0.3 NO
348 DYRK1A DYRK1A DYRK1A 11509 -0.043 0.3 NO
349 CENPC1 CENPC1 CENPC1 11513 -0.043 0.3 NO
350 TERF2IP TERF2IP TERF2IP 11591 -0.044 0.3 NO
351 RAD17 RAD17 RAD17 11596 -0.044 0.3 NO
352 ATM ATM ATM 11624 -0.045 0.3 NO
353 HIST1H2BH HIST1H2BH HIST1H2BH 11661 -0.045 0.3 NO
354 PPP2R1B PPP2R1B PPP2R1B 11667 -0.046 0.3 NO
355 APITD1 APITD1 APITD1 11910 -0.05 0.29 NO
356 CCND3 CCND3 CCND3 11961 -0.051 0.28 NO
357 DCTN3 DCTN3 DCTN3 12060 -0.052 0.28 NO
358 BTRC BTRC BTRC 12104 -0.053 0.28 NO
359 PCM1 PCM1 PCM1 12166 -0.054 0.28 NO
360 PAFAH1B1 PAFAH1B1 PAFAH1B1 12209 -0.055 0.28 NO
361 PCNT PCNT PCNT 12274 -0.057 0.28 NO
362 WRAP53 WRAP53 WRAP53 12445 -0.06 0.27 NO
363 PPP2R5A PPP2R5A PPP2R5A 13073 -0.074 0.24 NO
364 B9D2 B9D2 B9D2 13178 -0.077 0.23 NO
365 NSL1 NSL1 NSL1 13249 -0.079 0.23 NO
366 CDC14A CDC14A CDC14A 13905 -0.099 0.2 NO
367 MIS12 MIS12 MIS12 14114 -0.11 0.19 NO
368 RPA4 RPA4 RPA4 14716 -0.13 0.16 NO
369 RPS27 RPS27 RPS27 15001 -0.14 0.15 NO
370 CCNA1 CCNA1 CCNA1 15153 -0.15 0.14 NO
371 CCND2 CCND2 CCND2 15348 -0.16 0.14 NO
372 SYNE1 SYNE1 SYNE1 15352 -0.16 0.14 NO
373 STAG3 STAG3 STAG3 15363 -0.16 0.15 NO
374 PSMA8 PSMA8 PSMA8 16164 -0.22 0.11 NO
375 PRKAR2B PRKAR2B PRKAR2B 16712 -0.26 0.088 NO
376 REC8 REC8 REC8 17109 -0.3 0.075 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: KEGG P53 SIGNALING PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG P53 SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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 IL8 IL8 IL8 730 0.24 0.04 YES
2 LAMA3 LAMA3 LAMA3 797 0.23 0.11 YES
3 FN1 FN1 FN1 841 0.22 0.19 YES
4 EPHB2 EPHB2 EPHB2 1034 0.2 0.24 YES
5 LAMA1 LAMA1 LAMA1 1036 0.2 0.31 YES
6 ITGA2 ITGA2 ITGA2 1085 0.19 0.37 YES
7 CAV2 CAV2 CAV2 1377 0.16 0.41 YES
8 CSF2 CSF2 CSF2 1392 0.16 0.46 YES
9 MMP2 MMP2 MMP2 1406 0.16 0.52 YES
10 ITGA5 ITGA5 ITGA5 1466 0.16 0.57 YES
11 RASA1 RASA1 RASA1 2308 0.1 0.56 YES
12 EZR EZR EZR 2420 0.097 0.58 YES
13 ITGB1 ITGB1 ITGB1 2633 0.089 0.6 YES
14 TGFB1 TGFB1 TGFB1 2669 0.087 0.63 YES
15 SRC SRC SRC 4208 0.048 0.56 NO
16 HRAS HRAS HRAS 4413 0.045 0.56 NO
17 MAPK8 MAPK8 MAPK8 5036 0.035 0.54 NO
18 NF1 NF1 NF1 5659 0.026 0.52 NO
19 RHOA RHOA RHOA 5695 0.026 0.52 NO
20 CASK CASK CASK 5952 0.022 0.52 NO
21 KNG1 KNG1 KNG1 6407 0.017 0.5 NO
22 MAPK3 MAPK3 MAPK3 7034 0.011 0.47 NO
23 CASP3 CASP3 CASP3 7174 0.009 0.46 NO
24 BAX BAX BAX 7713 0.0028 0.44 NO
25 MAPK1 MAPK1 MAPK1 8193 -0.0023 0.41 NO
26 SDCBP SDCBP SDCBP 8262 -0.0031 0.41 NO
27 GNB2L1 GNB2L1 GNB2L1 8862 -0.0097 0.38 NO
28 SDC2 SDC2 SDC2 10818 -0.032 0.28 NO
29 PRKCD PRKCD PRKCD 10892 -0.034 0.29 NO
30 PRKACA PRKACA PRKACA 11373 -0.04 0.28 NO
31 TRAPPC4 TRAPPC4 TRAPPC4 11782 -0.048 0.27 NO
32 EPB41 EPB41 EPB41 13870 -0.098 0.19 NO
33 TNFRSF13B TNFRSF13B TNFRSF13B 15544 -0.18 0.16 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: BIOCARTA RACCYCD PATHWAY.

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

genes ES table in pathway: PID P73PATHWAY

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 TP73 TP73 TP73 54 0.5 0.062 YES
2 SERPINB5 SERPINB5 SERPINB5 281 0.34 0.094 YES
3 CCNB2 CCNB2 CCNB2 440 0.3 0.12 YES
4 SFN SFN SFN 450 0.29 0.16 YES
5 TP53AIP1 TP53AIP1 TP53AIP1 484 0.28 0.2 YES
6 PMAIP1 PMAIP1 PMAIP1 524 0.28 0.23 YES
7 GTSE1 GTSE1 GTSE1 752 0.24 0.25 YES
8 CDK1 CDK1 CDK1 888 0.22 0.27 YES
9 CCNE1 CCNE1 CCNE1 930 0.22 0.29 YES
10 STEAP3 STEAP3 STEAP3 989 0.21 0.32 YES
11 RRM2 RRM2 RRM2 1040 0.2 0.34 YES
12 CCNE2 CCNE2 CCNE2 1067 0.2 0.36 YES
13 CCNB1 CCNB1 CCNB1 1102 0.19 0.39 YES
14 IGFBP3 IGFBP3 IGFBP3 1206 0.18 0.41 YES
15 CHEK1 CHEK1 CHEK1 1292 0.17 0.42 YES
16 SERPINE1 SERPINE1 SERPINE1 1486 0.16 0.43 YES
17 CCND1 CCND1 CCND1 1526 0.15 0.45 YES
18 TNFRSF10B TNFRSF10B TNFRSF10B 1869 0.13 0.45 YES
19 PERP PERP PERP 1900 0.12 0.46 YES
20 CCNG2 CCNG2 CCNG2 2013 0.12 0.47 YES
21 CDK6 CDK6 CDK6 2115 0.11 0.48 YES
22 BBC3 BBC3 BBC3 2198 0.11 0.49 YES
23 THBS1 THBS1 THBS1 2218 0.11 0.5 YES
24 CDK2 CDK2 CDK2 2260 0.11 0.52 YES
25 BID BID BID 2271 0.1 0.53 YES
26 CASP8 CASP8 CASP8 2423 0.097 0.53 YES
27 CD82 CD82 CD82 2646 0.088 0.53 YES
28 CHEK2 CHEK2 CHEK2 2710 0.086 0.54 YES
29 TP53I3 TP53I3 TP53I3 3794 0.057 0.49 NO
30 ATR ATR ATR 4674 0.04 0.45 NO
31 SIAH1 SIAH1 SIAH1 4688 0.04 0.45 NO
32 MDM2 MDM2 MDM2 4867 0.037 0.44 NO
33 EI24 EI24 EI24 5445 0.029 0.42 NO
34 SHISA5 SHISA5 SHISA5 5744 0.025 0.4 NO
35 DDB2 DDB2 DDB2 5915 0.023 0.4 NO
36 CDK4 CDK4 CDK4 5928 0.023 0.4 NO
37 CDKN1A CDKN1A CDKN1A 6056 0.021 0.4 NO
38 CDKN2A CDKN2A CDKN2A 6115 0.021 0.4 NO
39 GADD45A GADD45A GADD45A 6614 0.015 0.37 NO
40 CASP3 CASP3 CASP3 7174 0.009 0.34 NO
41 BAX BAX BAX 7713 0.0028 0.31 NO
42 ZMAT3 ZMAT3 ZMAT3 7967 -0.000038 0.3 NO
43 FAS FAS FAS 8537 -0.0062 0.27 NO
44 GADD45B GADD45B GADD45B 8631 -0.0072 0.26 NO
45 TSC2 TSC2 TSC2 8937 -0.011 0.25 NO
46 CYCS CYCS CYCS 9285 -0.015 0.23 NO
47 RFWD2 RFWD2 RFWD2 9287 -0.015 0.23 NO
48 RRM2B RRM2B RRM2B 9396 -0.016 0.23 NO
49 TP53 TP53 TP53 9714 -0.019 0.22 NO
50 PTEN PTEN PTEN 9804 -0.02 0.21 NO
51 BAI1 BAI1 BAI1 9851 -0.02 0.21 NO
52 CASP9 CASP9 CASP9 10248 -0.025 0.2 NO
53 RCHY1 RCHY1 RCHY1 11436 -0.042 0.14 NO
54 ATM ATM ATM 11624 -0.045 0.13 NO
55 SESN3 SESN3 SESN3 11947 -0.05 0.12 NO
56 CCND3 CCND3 CCND3 11961 -0.051 0.13 NO
57 MDM4 MDM4 MDM4 12605 -0.063 0.1 NO
58 CCNG1 CCNG1 CCNG1 13254 -0.079 0.075 NO
59 APAF1 APAF1 APAF1 13974 -0.1 0.049 NO
60 SESN2 SESN2 SESN2 14505 -0.12 0.036 NO
61 PPM1D PPM1D PPM1D 14671 -0.13 0.044 NO
62 CCND2 CCND2 CCND2 15348 -0.16 0.028 NO
63 CCNB3 CCNB3 CCNB3 15614 -0.18 0.037 NO
64 IGF1 IGF1 IGF1 15695 -0.18 0.057 NO
65 RPRM RPRM RPRM 15727 -0.19 0.079 NO
66 SESN1 SESN1 SESN1 16201 -0.22 0.082 NO
67 GADD45G GADD45G GADD45G 17256 -0.32 0.065 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 P73PATHWAY.

Figure S50.  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

genes ES table in pathway: PID E2F PATHWAY

Table S26.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 KIF18A KIF18A KIF18A 148 0.41 0.0084 YES
2 SPC24 SPC24 SPC24 165 0.4 0.024 YES
3 CDC25C CDC25C CDC25C 214 0.37 0.036 YES
4 BIRC5 BIRC5 BIRC5 220 0.37 0.05 YES
5 MCM10 MCM10 MCM10 250 0.35 0.063 YES
6 CENPA CENPA CENPA 263 0.35 0.076 YES
7 CENPI CENPI CENPI 269 0.34 0.09 YES
8 NEK2 NEK2 NEK2 278 0.34 0.1 YES
9 KIF20A KIF20A KIF20A 300 0.34 0.12 YES
10 UBE2C UBE2C UBE2C 333 0.32 0.13 YES
11 SGOL1 SGOL1 SGOL1 335 0.32 0.14 YES
12 PKMYT1 PKMYT1 PKMYT1 350 0.32 0.15 YES
13 KIF23 KIF23 KIF23 354 0.32 0.16 YES
14 CDC45 CDC45 CDC45 373 0.31 0.18 YES
15 CDC20 CDC20 CDC20 395 0.3 0.19 YES
16 KIF2C KIF2C KIF2C 401 0.3 0.2 YES
17 ERCC6L ERCC6L ERCC6L 407 0.3 0.21 YES
18 BUB1 BUB1 BUB1 416 0.3 0.22 YES
19 CCNB2 CCNB2 CCNB2 440 0.3 0.23 YES
20 CENPK CENPK CENPK 449 0.29 0.24 YES
21 PLK4 PLK4 PLK4 542 0.27 0.25 YES
22 CASC5 CASC5 CASC5 584 0.27 0.26 YES
23 BUB1B BUB1B BUB1B 608 0.26 0.27 YES
24 AURKB AURKB AURKB 625 0.26 0.28 YES
25 MYBL2 MYBL2 MYBL2 632 0.26 0.29 YES
26 E2F1 E2F1 E2F1 659 0.25 0.3 YES
27 NUF2 NUF2 NUF2 664 0.25 0.31 YES
28 PLK1 PLK1 PLK1 672 0.25 0.32 YES
29 CDC6 CDC6 CDC6 762 0.24 0.32 YES
30 CDT1 CDT1 CDT1 771 0.23 0.33 YES
31 POLE2 POLE2 POLE2 857 0.22 0.33 YES
32 GINS4 GINS4 GINS4 875 0.22 0.34 YES
33 AURKA AURKA AURKA 877 0.22 0.35 YES
34 PTTG1 PTTG1 PTTG1 884 0.22 0.36 YES
35 CDK1 CDK1 CDK1 888 0.22 0.37 YES
36 CCNE1 CCNE1 CCNE1 930 0.22 0.37 YES
37 CCNA2 CCNA2 CCNA2 939 0.21 0.38 YES
38 NDC80 NDC80 NDC80 979 0.21 0.39 YES
39 SKA1 SKA1 SKA1 993 0.21 0.4 YES
40 MCM2 MCM2 MCM2 1030 0.2 0.4 YES
41 RRM2 RRM2 RRM2 1040 0.2 0.41 YES
42 CCNE2 CCNE2 CCNE2 1067 0.2 0.42 YES
43 GINS2 GINS2 GINS2 1087 0.19 0.42 YES
44 MCM4 MCM4 MCM4 1089 0.19 0.43 YES
45 MAD2L1 MAD2L1 MAD2L1 1091 0.19 0.44 YES
46 CCNB1 CCNB1 CCNB1 1102 0.19 0.45 YES
47 GINS1 GINS1 GINS1 1126 0.19 0.45 YES
48 CDCA8 CDCA8 CDCA8 1135 0.19 0.46 YES
49 CENPM CENPM CENPM 1250 0.18 0.46 YES
50 KNTC1 KNTC1 KNTC1 1299 0.17 0.46 YES
51 SGOL2 SGOL2 SGOL2 1338 0.17 0.47 YES
52 RFC4 RFC4 RFC4 1365 0.17 0.48 YES
53 MLF1IP MLF1IP MLF1IP 1380 0.16 0.48 YES
54 CENPH CENPH CENPH 1442 0.16 0.48 YES
55 CCND1 CCND1 CCND1 1526 0.15 0.48 YES
56 ZWINT ZWINT ZWINT 1606 0.15 0.49 YES
57 CKS1B CKS1B CKS1B 1615 0.14 0.49 YES
58 TYMS TYMS TYMS 1647 0.14 0.5 YES
59 SPC25 SPC25 SPC25 1784 0.13 0.49 YES
60 DNA2 DNA2 DNA2 2018 0.12 0.49 YES
61 CDC25A CDC25A CDC25A 2038 0.12 0.49 YES
62 INCENP INCENP INCENP 2105 0.11 0.49 YES
63 WEE1 WEE1 WEE1 2106 0.11 0.5 YES
64 CDK6 CDK6 CDK6 2115 0.11 0.5 YES
65 CCDC99 CCDC99 CCDC99 2153 0.11 0.5 YES
66 CENPN CENPN CENPN 2235 0.11 0.5 YES
67 CDK2 CDK2 CDK2 2260 0.11 0.5 YES
68 E2F2 E2F2 E2F2 2298 0.1 0.51 YES
69 ZWILCH ZWILCH ZWILCH 2371 0.1 0.51 YES
70 MNAT1 MNAT1 MNAT1 2403 0.098 0.51 YES
71 CENPO CENPO CENPO 2424 0.097 0.51 YES
72 TUBA4A TUBA4A TUBA4A 2427 0.097 0.52 YES
73 RFC2 RFC2 RFC2 2435 0.097 0.52 YES
74 POLD1 POLD1 POLD1 2510 0.094 0.52 YES
75 NUP107 NUP107 NUP107 2554 0.092 0.52 YES
76 LIN9 LIN9 LIN9 2577 0.09 0.52 YES
77 E2F3 E2F3 E2F3 2606 0.09 0.52 YES
78 PSMD2 PSMD2 PSMD2 2609 0.089 0.53 YES
79 RBL1 RBL1 RBL1 2663 0.087 0.53 YES
80 CSNK1E CSNK1E CSNK1E 2670 0.087 0.53 YES
81 MCM7 MCM7 MCM7 2678 0.087 0.54 YES
82 CDC7 CDC7 CDC7 2696 0.086 0.54 YES
83 RCC2 RCC2 RCC2 2753 0.084 0.54 YES
84 AZI1 AZI1 AZI1 2760 0.084 0.54 YES
85 FEN1 FEN1 FEN1 2771 0.084 0.54 YES
86 CENPJ CENPJ CENPJ 2823 0.082 0.54 YES
87 DSN1 DSN1 DSN1 2848 0.082 0.55 YES
88 PSMD14 PSMD14 PSMD14 2871 0.081 0.55 YES
89 MCM6 MCM6 MCM6 2932 0.079 0.55 YES
90 CDKN2B CDKN2B CDKN2B 2966 0.078 0.55 YES
91 NUP85 NUP85 NUP85 3129 0.073 0.54 YES
92 PRIM2 PRIM2 PRIM2 3200 0.071 0.54 YES
93 MCM8 MCM8 MCM8 3214 0.071 0.55 YES
94 CENPL CENPL CENPL 3241 0.07 0.55 YES
95 CENPP CENPP CENPP 3309 0.068 0.55 YES
96 PSMD12 PSMD12 PSMD12 3311 0.068 0.55 YES
97 TUBB TUBB TUBB 3374 0.067 0.55 YES
98 CDKN2D CDKN2D CDKN2D 3379 0.067 0.55 YES
99 RPA3 RPA3 RPA3 3390 0.067 0.55 YES
100 MCM5 MCM5 MCM5 3395 0.067 0.55 YES
101 CKAP5 CKAP5 CKAP5 3467 0.065 0.55 YES
102 SKP2 SKP2 SKP2 3471 0.065 0.56 YES
103 RANGAP1 RANGAP1 RANGAP1 3562 0.062 0.55 YES
104 RFC5 RFC5 RFC5 3577 0.062 0.56 YES
105 PPP2R2A PPP2R2A PPP2R2A 3596 0.061 0.56 YES
106 CDK7 CDK7 CDK7 3599 0.061 0.56 YES
107 PSMD7 PSMD7 PSMD7 3660 0.06 0.56 YES
108 UBE2E1 UBE2E1 UBE2E1 3695 0.059 0.56 YES
109 PSMD11 PSMD11 PSMD11 3713 0.058 0.56 YES
110 TAOK1 TAOK1 TAOK1 3723 0.058 0.56 YES
111 NUP37 NUP37 NUP37 3731 0.058 0.56 YES
112 LIG1 LIG1 LIG1 3804 0.056 0.56 NO
113 XPO1 XPO1 XPO1 3930 0.054 0.56 NO
114 DYNC1I2 DYNC1I2 DYNC1I2 4015 0.052 0.55 NO
115 PSMA1 PSMA1 PSMA1 4051 0.051 0.55 NO
116 ZW10 ZW10 ZW10 4053 0.051 0.56 NO
117 ANAPC11 ANAPC11 ANAPC11 4073 0.051 0.56 NO
118 YWHAG YWHAG YWHAG 4091 0.05 0.56 NO
119 TUBG1 TUBG1 TUBG1 4092 0.05 0.56 NO
120 HSP90AA1 HSP90AA1 HSP90AA1 4138 0.05 0.56 NO
121 POLD4 POLD4 POLD4 4167 0.049 0.56 NO
122 PCNA PCNA PCNA 4202 0.048 0.56 NO
123 TK2 TK2 TK2 4225 0.048 0.56 NO
124 PSMB2 PSMB2 PSMB2 4258 0.047 0.56 NO
125 PSMA7 PSMA7 PSMA7 4327 0.046 0.56 NO
126 DBF4 DBF4 DBF4 4330 0.046 0.56 NO
127 RFC3 RFC3 RFC3 4368 0.045 0.56 NO
128 ANAPC1 ANAPC1 ANAPC1 4384 0.045 0.56 NO
129 PSMA5 PSMA5 PSMA5 4401 0.045 0.56 NO
130 CENPQ CENPQ CENPQ 4447 0.044 0.56 NO
131 LIN37 LIN37 LIN37 4497 0.043 0.56 NO
132 RAD21 RAD21 RAD21 4525 0.043 0.56 NO
133 PSMA6 PSMA6 PSMA6 4582 0.042 0.56 NO
134 NUMA1 NUMA1 NUMA1 4615 0.041 0.56 NO
135 UBE2D1 UBE2D1 UBE2D1 4616 0.041 0.56 NO
136 MAD1L1 MAD1L1 MAD1L1 4667 0.04 0.56 NO
137 CLIP1 CLIP1 CLIP1 4673 0.04 0.56 NO
138 PPP2R5E PPP2R5E PPP2R5E 4701 0.04 0.56 NO
139 POLA2 POLA2 POLA2 4740 0.039 0.56 NO
140 PSMD8 PSMD8 PSMD8 4821 0.038 0.56 NO
141 STAG1 STAG1 STAG1 4835 0.038 0.56 NO
142 NEDD1 NEDD1 NEDD1 4879 0.037 0.56 NO
143 ITGB3BP ITGB3BP ITGB3BP 4881 0.037 0.56 NO
144 CETN2 CETN2 CETN2 4960 0.036 0.56 NO
145 CEP250 CEP250 CEP250 5045 0.035 0.55 NO
146 PSMD13 PSMD13 PSMD13 5082 0.034 0.55 NO
147 POLE POLE POLE 5120 0.034 0.55 NO
148 CEP70 CEP70 CEP70 5156 0.033 0.55 NO
149 CEP72 CEP72 CEP72 5180 0.033 0.55 NO
150 PSMC3 PSMC3 PSMC3 5187 0.033 0.55 NO
151 BUB3 BUB3 BUB3 5218 0.032 0.55 NO
152 PSMC1 PSMC1 PSMC1 5255 0.032 0.55 NO
153 PSMD1 PSMD1 PSMD1 5280 0.032 0.55 NO
154 PSMC6 PSMC6 PSMC6 5442 0.029 0.54 NO
155 HAUS2 HAUS2 HAUS2 5457 0.029 0.55 NO
156 CDC23 CDC23 CDC23 5505 0.028 0.54 NO
157 KIF2A KIF2A KIF2A 5545 0.028 0.54 NO
158 PSMD5 PSMD5 PSMD5 5561 0.028 0.54 NO
159 PSME4 PSME4 PSME4 5630 0.027 0.54 NO
160 ANAPC10 ANAPC10 ANAPC10 5665 0.026 0.54 NO
161 PSMC4 PSMC4 PSMC4 5669 0.026 0.54 NO
162 DHFR DHFR DHFR 5672 0.026 0.54 NO
163 TFDP1 TFDP1 TFDP1 5771 0.025 0.54 NO
164 PSMA3 PSMA3 PSMA3 5831 0.024 0.53 NO
165 PSMD4 PSMD4 PSMD4 5878 0.024 0.53 NO
166 CENPT CENPT CENPT 5884 0.023 0.53 NO
167 CDK4 CDK4 CDK4 5928 0.023 0.53 NO
168 CDC25B CDC25B CDC25B 6043 0.021 0.53 NO
169 PSMD10 PSMD10 PSMD10 6055 0.021 0.53 NO
170 CDKN1A CDKN1A CDKN1A 6056 0.021 0.53 NO
171 SKA2 SKA2 SKA2 6077 0.021 0.53 NO
172 CDKN2A CDKN2A CDKN2A 6115 0.021 0.53 NO
173 SEC13 SEC13 SEC13 6170 0.02 0.52 NO
174 PPP2R5B PPP2R5B PPP2R5B 6173 0.02 0.52 NO
175 DYNC1H1 DYNC1H1 DYNC1H1 6188 0.02 0.52 NO
176 PSMD3 PSMD3 PSMD3 6194 0.02 0.52 NO
177 NUDC NUDC NUDC 6225 0.019 0.52 NO
178 CDC27 CDC27 CDC27 6249 0.019 0.52 NO
179 PSMA2 PSMA2 PSMA2 6271 0.019 0.52 NO
180 PSMA4 PSMA4 PSMA4 6379 0.018 0.52 NO
181 PSMB5 PSMB5 PSMB5 6385 0.018 0.52 NO
182 PSMB3 PSMB3 PSMB3 6437 0.017 0.52 NO
183 NDEL1 NDEL1 NDEL1 6654 0.014 0.5 NO
184 CLASP1 CLASP1 CLASP1 6661 0.014 0.5 NO
185 HDAC1 HDAC1 HDAC1 6671 0.014 0.5 NO
186 PSMB9 PSMB9 PSMB9 6695 0.014 0.5 NO
187 E2F4 E2F4 E2F4 6720 0.014 0.5 NO
188 PPP2R1A PPP2R1A PPP2R1A 6745 0.014 0.5 NO
189 PPP2CA PPP2CA PPP2CA 6752 0.014 0.5 NO
190 PSMB7 PSMB7 PSMB7 6763 0.013 0.5 NO
191 SEH1L SEH1L SEH1L 6823 0.013 0.5 NO
192 DYNLL1 DYNLL1 DYNLL1 6847 0.012 0.5 NO
193 PSMB4 PSMB4 PSMB4 6883 0.012 0.5 NO
194 MAPRE1 MAPRE1 MAPRE1 6962 0.011 0.5 NO
195 FGFR1OP FGFR1OP FGFR1OP 6971 0.011 0.5 NO
196 POLD2 POLD2 POLD2 7077 0.01 0.49 NO
197 RBBP4 RBBP4 RBBP4 7143 0.0094 0.49 NO
198 PSMD9 PSMD9 PSMD9 7162 0.0092 0.48 NO
199 MYC MYC MYC 7176 0.009 0.48 NO
200 PSMC2 PSMC2 PSMC2 7201 0.0088 0.48 NO
201 DCTN1 DCTN1 DCTN1 7237 0.0084 0.48 NO
202 CEP63 CEP63 CEP63 7355 0.0071 0.48 NO
203 PSMB8 PSMB8 PSMB8 7411 0.0065 0.47 NO
204 CEP135 CEP135 CEP135 7416 0.0064 0.47 NO
205 PSMC5 PSMC5 PSMC5 7439 0.0062 0.47 NO
206 TUBA1A TUBA1A TUBA1A 7597 0.0042 0.46 NO
207 PRIM1 PRIM1 PRIM1 7684 0.0032 0.46 NO
208 PPP2CB PPP2CB PPP2CB 7803 0.0017 0.45 NO
209 CEP192 CEP192 CEP192 7810 0.0016 0.45 NO
210 CSNK1D CSNK1D CSNK1D 7864 0.001 0.45 NO
211 MCM3 MCM3 MCM3 8011 -0.00046 0.44 NO
212 TUBGCP2 TUBGCP2 TUBGCP2 8056 -0.00092 0.44 NO
213 PPP2R5C PPP2R5C PPP2R5C 8066 -0.00098 0.44 NO
214 PSME2 PSME2 PSME2 8112 -0.0015 0.44 NO
215 ALMS1 ALMS1 ALMS1 8154 -0.0019 0.44 NO
216 LIN54 LIN54 LIN54 8197 -0.0024 0.43 NO
217 AHCTF1 AHCTF1 AHCTF1 8198 -0.0024 0.43 NO
218 PSMF1 PSMF1 PSMF1 8251 -0.003 0.43 NO
219 SKP1 SKP1 SKP1 8277 -0.0034 0.43 NO
220 TUBGCP5 TUBGCP5 TUBGCP5 8299 -0.0037 0.43 NO
221 YWHAE YWHAE YWHAE 8418 -0.005 0.42 NO
222 PSME1 PSME1 PSME1 8420 -0.005 0.42 NO
223 CDK5RAP2 CDK5RAP2 CDK5RAP2 8452 -0.0054 0.42 NO
224 NINL NINL NINL 8485 -0.0057 0.42 NO
225 E2F5 E2F5 E2F5 8487 -0.0058 0.42 NO
226 SDCCAG8 SDCCAG8 SDCCAG8 8760 -0.0086 0.4 NO
227 TUBG2 TUBG2 TUBG2 8762 -0.0086 0.4 NO
228 ACTR1A ACTR1A ACTR1A 8781 -0.0088 0.4 NO
229 FBXO5 FBXO5 FBXO5 8887 -0.01 0.4 NO
230 SMC3 SMC3 SMC3 8889 -0.01 0.4 NO
231 STAG2 STAG2 STAG2 8921 -0.01 0.4 NO
232 RPS27A RPS27A RPS27A 8932 -0.01 0.4 NO
233 CEP76 CEP76 CEP76 8956 -0.011 0.4 NO
234 PPP2R5D PPP2R5D PPP2R5D 8989 -0.011 0.4 NO
235 CUL1 CUL1 CUL1 9026 -0.012 0.39 NO
236 RPA2 RPA2 RPA2 9089 -0.012 0.39 NO
237 CDKN1B CDKN1B CDKN1B 9103 -0.012 0.39 NO
238 SSNA1 SSNA1 SSNA1 9144 -0.013 0.39 NO
239 PSMB10 PSMB10 PSMB10 9206 -0.014 0.39 NO
240 PSMB1 PSMB1 PSMB1 9317 -0.015 0.38 NO
241 ANAPC7 ANAPC7 ANAPC7 9353 -0.015 0.38 NO
242 CEP164 CEP164 CEP164 9366 -0.015 0.38 NO
243 CDC16 CDC16 CDC16 9441 -0.016 0.38 NO
244 CCNH CCNH CCNH 9461 -0.016 0.38 NO
245 POLA1 POLA1 POLA1 9488 -0.017 0.37 NO
246 NUP133 NUP133 NUP133 9516 -0.017 0.37 NO
247 GORASP1 GORASP1 GORASP1 9521 -0.017 0.37 NO
248 ANAPC4 ANAPC4 ANAPC4 9667 -0.019 0.37 NO
249 POLD3 POLD3 POLD3 9730 -0.019 0.36 NO
250 PPP2R3B PPP2R3B PPP2R3B 9864 -0.021 0.36 NO
251 PSMD6 PSMD6 PSMD6 9911 -0.021 0.36 NO
252 DCTN2 DCTN2 DCTN2 9995 -0.022 0.35 NO
253 OFD1 OFD1 OFD1 10006 -0.022 0.35 NO
254 CEP57 CEP57 CEP57 10044 -0.023 0.35 NO
255 PMF1 PMF1 PMF1 10065 -0.023 0.35 NO
256 PPP1CC PPP1CC PPP1CC 10091 -0.023 0.35 NO
257 SMC1A SMC1A SMC1A 10363 -0.026 0.34 NO
258 PSMB6 PSMB6 PSMB6 10392 -0.026 0.34 NO
259 RB1 RB1 RB1 10458 -0.027 0.33 NO
260 RBL2 RBL2 RBL2 10469 -0.028 0.34 NO
261 ANAPC5 ANAPC5 ANAPC5 10493 -0.028 0.34 NO
262 GMNN GMNN GMNN 10506 -0.028 0.34 NO
263 LIN52 LIN52 LIN52 10507 -0.028 0.34 NO
264 CEP290 CEP290 CEP290 10516 -0.028 0.34 NO
265 RPA1 RPA1 RPA1 10536 -0.028 0.34 NO
266 MAX MAX MAX 10558 -0.029 0.34 NO
267 NUP43 NUP43 NUP43 10721 -0.031 0.33 NO
268 RANBP2 RANBP2 RANBP2 10769 -0.032 0.33 NO
269 TUBGCP3 TUBGCP3 TUBGCP3 11043 -0.036 0.31 NO
270 TUBGCP6 TUBGCP6 TUBGCP6 11074 -0.036 0.31 NO
271 CDKN2C CDKN2C CDKN2C 11098 -0.036 0.31 NO
272 CDC26 CDC26 CDC26 11351 -0.04 0.3 NO
273 PRKACA PRKACA PRKACA 11373 -0.04 0.3 NO
274 AKAP9 AKAP9 AKAP9 11420 -0.041 0.3 NO
275 ANAPC2 ANAPC2 ANAPC2 11466 -0.042 0.3 NO
276 UBA52 UBA52 UBA52 11476 -0.042 0.3 NO
277 DYRK1A DYRK1A DYRK1A 11509 -0.043 0.3 NO
278 CENPC1 CENPC1 CENPC1 11513 -0.043 0.3 NO
279 PPP2R1B PPP2R1B PPP2R1B 11667 -0.046 0.3 NO
280 APITD1 APITD1 APITD1 11910 -0.05 0.29 NO
281 CCND3 CCND3 CCND3 11961 -0.051 0.28 NO
282 DCTN3 DCTN3 DCTN3 12060 -0.052 0.28 NO
283 BTRC BTRC BTRC 12104 -0.053 0.28 NO
284 PCM1 PCM1 PCM1 12166 -0.054 0.28 NO
285 PAFAH1B1 PAFAH1B1 PAFAH1B1 12209 -0.055 0.28 NO
286 PCNT PCNT PCNT 12274 -0.057 0.28 NO
287 PPP2R5A PPP2R5A PPP2R5A 13073 -0.074 0.24 NO
288 B9D2 B9D2 B9D2 13178 -0.077 0.24 NO
289 NSL1 NSL1 NSL1 13249 -0.079 0.24 NO
290 CDC14A CDC14A CDC14A 13905 -0.099 0.2 NO
291 MIS12 MIS12 MIS12 14114 -0.11 0.2 NO
292 RPA4 RPA4 RPA4 14716 -0.13 0.17 NO
293 RPS27 RPS27 RPS27 15001 -0.14 0.16 NO
294 CCNA1 CCNA1 CCNA1 15153 -0.15 0.16 NO
295 CCND2 CCND2 CCND2 15348 -0.16 0.15 NO
296 PSMA8 PSMA8 PSMA8 16164 -0.22 0.12 NO
297 PRKAR2B PRKAR2B PRKAR2B 16712 -0.26 0.096 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 E2F PATHWAY.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: PID E2F PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID ATR PATHWAY

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 NEK2 NEK2 NEK2 278 0.34 0.094 YES
2 PLK4 PLK4 PLK4 542 0.27 0.17 YES
3 PLK1 PLK1 PLK1 672 0.25 0.24 YES
4 CDK1 CDK1 CDK1 888 0.22 0.3 YES
5 CCNB1 CCNB1 CCNB1 1102 0.19 0.35 YES
6 TUBA4A TUBA4A TUBA4A 2427 0.097 0.31 YES
7 CSNK1E CSNK1E CSNK1E 2670 0.087 0.32 YES
8 AZI1 AZI1 AZI1 2760 0.084 0.34 YES
9 CENPJ CENPJ CENPJ 2823 0.082 0.37 YES
10 TUBB TUBB TUBB 3374 0.067 0.36 YES
11 CKAP5 CKAP5 CKAP5 3467 0.065 0.37 YES
12 DYNC1I2 DYNC1I2 DYNC1I2 4015 0.052 0.36 YES
13 YWHAG YWHAG YWHAG 4091 0.05 0.37 YES
14 TUBG1 TUBG1 TUBG1 4092 0.05 0.39 YES
15 HSP90AA1 HSP90AA1 HSP90AA1 4138 0.05 0.4 YES
16 NUMA1 NUMA1 NUMA1 4615 0.041 0.39 YES
17 NEDD1 NEDD1 NEDD1 4879 0.037 0.39 YES
18 CETN2 CETN2 CETN2 4960 0.036 0.39 YES
19 CEP250 CEP250 CEP250 5045 0.035 0.4 YES
20 CEP70 CEP70 CEP70 5156 0.033 0.4 YES
21 CEP72 CEP72 CEP72 5180 0.033 0.41 YES
22 HAUS2 HAUS2 HAUS2 5457 0.029 0.41 NO
23 DYNC1H1 DYNC1H1 DYNC1H1 6188 0.02 0.37 NO
24 CLASP1 CLASP1 CLASP1 6661 0.014 0.35 NO
25 PPP2R1A PPP2R1A PPP2R1A 6745 0.014 0.35 NO
26 DYNLL1 DYNLL1 DYNLL1 6847 0.012 0.35 NO
27 MAPRE1 MAPRE1 MAPRE1 6962 0.011 0.35 NO
28 FGFR1OP FGFR1OP FGFR1OP 6971 0.011 0.35 NO
29 DCTN1 DCTN1 DCTN1 7237 0.0084 0.34 NO
30 CEP63 CEP63 CEP63 7355 0.0071 0.34 NO
31 CEP135 CEP135 CEP135 7416 0.0064 0.34 NO
32 TUBA1A TUBA1A TUBA1A 7597 0.0042 0.33 NO
33 CEP192 CEP192 CEP192 7810 0.0016 0.32 NO
34 CSNK1D CSNK1D CSNK1D 7864 0.001 0.31 NO
35 TUBGCP2 TUBGCP2 TUBGCP2 8056 -0.00092 0.3 NO
36 ALMS1 ALMS1 ALMS1 8154 -0.0019 0.3 NO
37 TUBGCP5 TUBGCP5 TUBGCP5 8299 -0.0037 0.29 NO
38 YWHAE YWHAE YWHAE 8418 -0.005 0.29 NO
39 CDK5RAP2 CDK5RAP2 CDK5RAP2 8452 -0.0054 0.29 NO
40 NINL NINL NINL 8485 -0.0057 0.29 NO
41 SDCCAG8 SDCCAG8 SDCCAG8 8760 -0.0086 0.28 NO
42 TUBG2 TUBG2 TUBG2 8762 -0.0086 0.28 NO
43 ACTR1A ACTR1A ACTR1A 8781 -0.0088 0.28 NO
44 CEP76 CEP76 CEP76 8956 -0.011 0.27 NO
45 SSNA1 SSNA1 SSNA1 9144 -0.013 0.27 NO
46 CEP164 CEP164 CEP164 9366 -0.015 0.26 NO
47 DCTN2 DCTN2 DCTN2 9995 -0.022 0.23 NO
48 OFD1 OFD1 OFD1 10006 -0.022 0.24 NO
49 CEP57 CEP57 CEP57 10044 -0.023 0.24 NO
50 CEP290 CEP290 CEP290 10516 -0.028 0.23 NO
51 TUBGCP3 TUBGCP3 TUBGCP3 11043 -0.036 0.21 NO
52 TUBGCP6 TUBGCP6 TUBGCP6 11074 -0.036 0.22 NO
53 PRKACA PRKACA PRKACA 11373 -0.04 0.22 NO
54 AKAP9 AKAP9 AKAP9 11420 -0.041 0.23 NO
55 DCTN3 DCTN3 DCTN3 12060 -0.052 0.21 NO
56 PCM1 PCM1 PCM1 12166 -0.054 0.22 NO
57 PAFAH1B1 PAFAH1B1 PAFAH1B1 12209 -0.055 0.24 NO
58 PCNT PCNT PCNT 12274 -0.057 0.25 NO
59 PRKAR2B PRKAR2B PRKAR2B 16712 -0.26 0.095 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 ATR PATHWAY.

Figure S54.  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

genes ES table in pathway: PID FRA PATHWAY

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 MCM10 MCM10 MCM10 250 0.35 0.028 YES
2 PKMYT1 PKMYT1 PKMYT1 350 0.32 0.059 YES
3 CDC45 CDC45 CDC45 373 0.31 0.094 YES
4 MYBL2 MYBL2 MYBL2 632 0.26 0.11 YES
5 E2F1 E2F1 E2F1 659 0.25 0.14 YES
6 CDC6 CDC6 CDC6 762 0.24 0.16 YES
7 CDT1 CDT1 CDT1 771 0.23 0.19 YES
8 POLE2 POLE2 POLE2 857 0.22 0.21 YES
9 CDK1 CDK1 CDK1 888 0.22 0.23 YES
10 CCNE1 CCNE1 CCNE1 930 0.22 0.26 YES
11 CCNA2 CCNA2 CCNA2 939 0.21 0.28 YES
12 MCM2 MCM2 MCM2 1030 0.2 0.3 YES
13 RRM2 RRM2 RRM2 1040 0.2 0.32 YES
14 CCNE2 CCNE2 CCNE2 1067 0.2 0.34 YES
15 MCM4 MCM4 MCM4 1089 0.19 0.36 YES
16 CCNB1 CCNB1 CCNB1 1102 0.19 0.39 YES
17 CCND1 CCND1 CCND1 1526 0.15 0.38 YES
18 CKS1B CKS1B CKS1B 1615 0.14 0.39 YES
19 TYMS TYMS TYMS 1647 0.14 0.41 YES
20 CDC25A CDC25A CDC25A 2038 0.12 0.4 YES
21 WEE1 WEE1 WEE1 2106 0.11 0.41 YES
22 CDK6 CDK6 CDK6 2115 0.11 0.42 YES
23 CDK2 CDK2 CDK2 2260 0.11 0.43 YES
24 E2F2 E2F2 E2F2 2298 0.1 0.44 YES
25 MNAT1 MNAT1 MNAT1 2403 0.098 0.44 YES
26 LIN9 LIN9 LIN9 2577 0.09 0.44 YES
27 E2F3 E2F3 E2F3 2606 0.09 0.45 YES
28 PSMD2 PSMD2 PSMD2 2609 0.089 0.46 YES
29 RBL1 RBL1 RBL1 2663 0.087 0.47 YES
30 MCM7 MCM7 MCM7 2678 0.087 0.48 YES
31 CDC7 CDC7 CDC7 2696 0.086 0.49 YES
32 PSMD14 PSMD14 PSMD14 2871 0.081 0.49 YES
33 MCM6 MCM6 MCM6 2932 0.079 0.5 YES
34 CDKN2B CDKN2B CDKN2B 2966 0.078 0.5 YES
35 PRIM2 PRIM2 PRIM2 3200 0.071 0.5 YES
36 MCM8 MCM8 MCM8 3214 0.071 0.5 YES
37 PSMD12 PSMD12 PSMD12 3311 0.068 0.51 YES
38 CDKN2D CDKN2D CDKN2D 3379 0.067 0.51 YES
39 RPA3 RPA3 RPA3 3390 0.067 0.52 YES
40 MCM5 MCM5 MCM5 3395 0.067 0.53 YES
41 SKP2 SKP2 SKP2 3471 0.065 0.53 YES
42 PPP2R2A PPP2R2A PPP2R2A 3596 0.061 0.53 YES
43 CDK7 CDK7 CDK7 3599 0.061 0.54 YES
44 PSMD7 PSMD7 PSMD7 3660 0.06 0.54 YES
45 PSMD11 PSMD11 PSMD11 3713 0.058 0.55 YES
46 PSMA1 PSMA1 PSMA1 4051 0.051 0.53 YES
47 PCNA PCNA PCNA 4202 0.048 0.53 YES
48 TK2 TK2 TK2 4225 0.048 0.54 YES
49 PSMB2 PSMB2 PSMB2 4258 0.047 0.54 YES
50 PSMA7 PSMA7 PSMA7 4327 0.046 0.54 YES
51 DBF4 DBF4 DBF4 4330 0.046 0.55 YES
52 PSMA5 PSMA5 PSMA5 4401 0.045 0.55 YES
53 LIN37 LIN37 LIN37 4497 0.043 0.55 YES
54 PSMA6 PSMA6 PSMA6 4582 0.042 0.55 YES
55 POLA2 POLA2 POLA2 4740 0.039 0.54 NO
56 PSMD8 PSMD8 PSMD8 4821 0.038 0.54 NO
57 PSMD13 PSMD13 PSMD13 5082 0.034 0.53 NO
58 POLE POLE POLE 5120 0.034 0.54 NO
59 PSMC3 PSMC3 PSMC3 5187 0.033 0.54 NO
60 PSMC1 PSMC1 PSMC1 5255 0.032 0.54 NO
61 PSMD1 PSMD1 PSMD1 5280 0.032 0.54 NO
62 PSMC6 PSMC6 PSMC6 5442 0.029 0.53 NO
63 PSMD5 PSMD5 PSMD5 5561 0.028 0.53 NO
64 PSMC4 PSMC4 PSMC4 5669 0.026 0.53 NO
65 DHFR DHFR DHFR 5672 0.026 0.53 NO
66 TFDP1 TFDP1 TFDP1 5771 0.025 0.53 NO
67 PSMA3 PSMA3 PSMA3 5831 0.024 0.53 NO
68 PSMD4 PSMD4 PSMD4 5878 0.024 0.53 NO
69 CDK4 CDK4 CDK4 5928 0.023 0.53 NO
70 PSMD10 PSMD10 PSMD10 6055 0.021 0.52 NO
71 CDKN1A CDKN1A CDKN1A 6056 0.021 0.52 NO
72 CDKN2A CDKN2A CDKN2A 6115 0.021 0.52 NO
73 PSMD3 PSMD3 PSMD3 6194 0.02 0.52 NO
74 PSMA2 PSMA2 PSMA2 6271 0.019 0.52 NO
75 PSMA4 PSMA4 PSMA4 6379 0.018 0.52 NO
76 PSMB5 PSMB5 PSMB5 6385 0.018 0.52 NO
77 PSMB3 PSMB3 PSMB3 6437 0.017 0.52 NO
78 HDAC1 HDAC1 HDAC1 6671 0.014 0.51 NO
79 PSMB9 PSMB9 PSMB9 6695 0.014 0.51 NO
80 E2F4 E2F4 E2F4 6720 0.014 0.51 NO
81 PPP2R1A PPP2R1A PPP2R1A 6745 0.014 0.51 NO
82 PPP2CA PPP2CA PPP2CA 6752 0.014 0.51 NO
83 PSMB7 PSMB7 PSMB7 6763 0.013 0.51 NO
84 PSMB4 PSMB4 PSMB4 6883 0.012 0.5 NO
85 RBBP4 RBBP4 RBBP4 7143 0.0094 0.49 NO
86 PSMD9 PSMD9 PSMD9 7162 0.0092 0.49 NO
87 MYC MYC MYC 7176 0.009 0.49 NO
88 PSMC2 PSMC2 PSMC2 7201 0.0088 0.49 NO
89 PSMB8 PSMB8 PSMB8 7411 0.0065 0.48 NO
90 PSMC5 PSMC5 PSMC5 7439 0.0062 0.48 NO
91 PRIM1 PRIM1 PRIM1 7684 0.0032 0.47 NO
92 PPP2CB PPP2CB PPP2CB 7803 0.0017 0.46 NO
93 MCM3 MCM3 MCM3 8011 -0.00046 0.45 NO
94 PSME2 PSME2 PSME2 8112 -0.0015 0.44 NO
95 LIN54 LIN54 LIN54 8197 -0.0024 0.44 NO
96 PSMF1 PSMF1 PSMF1 8251 -0.003 0.44 NO
97 SKP1 SKP1 SKP1 8277 -0.0034 0.44 NO
98 PSME1 PSME1 PSME1 8420 -0.005 0.43 NO
99 E2F5 E2F5 E2F5 8487 -0.0058 0.43 NO
100 FBXO5 FBXO5 FBXO5 8887 -0.01 0.41 NO
101 RPS27A RPS27A RPS27A 8932 -0.01 0.4 NO
102 CUL1 CUL1 CUL1 9026 -0.012 0.4 NO
103 RPA2 RPA2 RPA2 9089 -0.012 0.4 NO
104 CDKN1B CDKN1B CDKN1B 9103 -0.012 0.4 NO
105 PSMB10 PSMB10 PSMB10 9206 -0.014 0.4 NO
106 PSMB1 PSMB1 PSMB1 9317 -0.015 0.39 NO
107 CCNH CCNH CCNH 9461 -0.016 0.39 NO
108 POLA1 POLA1 POLA1 9488 -0.017 0.39 NO
109 PPP2R3B PPP2R3B PPP2R3B 9864 -0.021 0.37 NO
110 PSMD6 PSMD6 PSMD6 9911 -0.021 0.37 NO
111 PSMB6 PSMB6 PSMB6 10392 -0.026 0.34 NO
112 RB1 RB1 RB1 10458 -0.027 0.34 NO
113 RBL2 RBL2 RBL2 10469 -0.028 0.35 NO
114 LIN52 LIN52 LIN52 10507 -0.028 0.35 NO
115 RPA1 RPA1 RPA1 10536 -0.028 0.35 NO
116 MAX MAX MAX 10558 -0.029 0.35 NO
117 CDKN2C CDKN2C CDKN2C 11098 -0.036 0.33 NO
118 UBA52 UBA52 UBA52 11476 -0.042 0.31 NO
119 DYRK1A DYRK1A DYRK1A 11509 -0.043 0.32 NO
120 PPP2R1B PPP2R1B PPP2R1B 11667 -0.046 0.31 NO
121 CCND3 CCND3 CCND3 11961 -0.051 0.3 NO
122 RPA4 RPA4 RPA4 14716 -0.13 0.17 NO
123 CCNA1 CCNA1 CCNA1 15153 -0.15 0.16 NO
124 CCND2 CCND2 CCND2 15348 -0.16 0.17 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 FRA PATHWAY.

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

genes ES table in pathway: PID MYC ACTIVPATHWAY

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 KRT14 KRT14 KRT14 42 0.54 0.075 YES
2 KRT5 KRT5 KRT5 63 0.5 0.15 YES
3 TP63 TP63 TP63 115 0.44 0.21 YES
4 DLX5 DLX5 DLX5 257 0.35 0.25 YES
5 IL1A IL1A IL1A 383 0.31 0.29 YES
6 CCNB2 CCNB2 CCNB2 440 0.3 0.33 YES
7 SFN SFN SFN 450 0.29 0.37 YES
8 RAB38 RAB38 RAB38 688 0.25 0.39 YES
9 TOP2A TOP2A TOP2A 735 0.24 0.42 YES
10 RRAD RRAD RRAD 751 0.24 0.46 YES
11 ITGA3 ITGA3 ITGA3 777 0.23 0.49 YES
12 HELLS HELLS HELLS 879 0.22 0.51 YES
13 AXL AXL AXL 985 0.21 0.54 YES
14 ADA ADA ADA 1031 0.2 0.56 YES
15 IGFBP3 IGFBP3 IGFBP3 1206 0.18 0.58 YES
16 COL5A1 COL5A1 COL5A1 1209 0.18 0.61 YES
17 DLX6 DLX6 DLX6 1360 0.17 0.62 YES
18 BRCA2 BRCA2 BRCA2 1413 0.16 0.64 YES
19 SEC14L2 SEC14L2 SEC14L2 1572 0.15 0.66 YES
20 PERP PERP PERP 1900 0.12 0.66 YES
21 RUNX1 RUNX1 RUNX1 2147 0.11 0.66 YES
22 VDR VDR VDR 2157 0.11 0.68 YES
23 YAP1 YAP1 YAP1 2287 0.1 0.68 YES
24 FOSL2 FOSL2 FOSL2 2648 0.088 0.68 NO
25 TCF7L1 TCF7L1 TCF7L1 3111 0.074 0.66 NO
26 ITCH ITCH ITCH 3867 0.055 0.63 NO
27 MRE11A MRE11A MRE11A 4172 0.049 0.62 NO
28 ADRM1 ADRM1 ADRM1 4338 0.046 0.62 NO
29 GSK3B GSK3B GSK3B 4390 0.045 0.62 NO
30 MDM2 MDM2 MDM2 4867 0.037 0.6 NO
31 HES1 HES1 HES1 5042 0.035 0.6 NO
32 FASN FASN FASN 5233 0.032 0.59 NO
33 NOTCH1 NOTCH1 NOTCH1 6007 0.022 0.55 NO
34 HBP1 HBP1 HBP1 6017 0.022 0.55 NO
35 CDKN2A CDKN2A CDKN2A 6115 0.021 0.55 NO
36 WWP1 WWP1 WWP1 7205 0.0088 0.49 NO
37 CEBPD CEBPD CEBPD 7371 0.007 0.48 NO
38 GNB2L1 GNB2L1 GNB2L1 8862 -0.0097 0.41 NO
39 NRG1 NRG1 NRG1 10870 -0.033 0.3 NO
40 BDKRB2 BDKRB2 BDKRB2 11491 -0.043 0.27 NO
41 ATM ATM ATM 11624 -0.045 0.27 NO
42 FBXW7 FBXW7 FBXW7 12894 -0.07 0.22 NO
43 PPP2R5A PPP2R5A PPP2R5A 13073 -0.074 0.22 NO
44 STXBP4 STXBP4 STXBP4 15143 -0.15 0.12 NO
45 GPX2 GPX2 GPX2 15298 -0.16 0.14 NO
46 POU2F2 POU2F2 POU2F2 16209 -0.22 0.12 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 MYC ACTIVPATHWAY.

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

genes ES table in pathway: PID PLK1 PATHWAY

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 FANCB FANCB FANCB 357 0.32 0.031 YES
2 FANCA FANCA FANCA 397 0.3 0.077 YES
3 BRIP1 BRIP1 BRIP1 412 0.3 0.12 YES
4 RAD51 RAD51 RAD51 517 0.28 0.16 YES
5 POLE2 POLE2 POLE2 857 0.22 0.18 YES
6 C19orf40 C19orf40 C19orf40 1068 0.2 0.2 YES
7 UBE2T UBE2T UBE2T 1300 0.17 0.21 YES
8 RFC4 RFC4 RFC4 1365 0.17 0.24 YES
9 BRCA2 BRCA2 BRCA2 1413 0.16 0.26 YES
10 FANCD2 FANCD2 FANCD2 1459 0.16 0.28 YES
11 FANCE FANCE FANCE 2041 0.12 0.27 YES
12 POLB POLB POLB 2094 0.11 0.28 YES
13 MNAT1 MNAT1 MNAT1 2403 0.098 0.28 YES
14 RFC2 RFC2 RFC2 2435 0.097 0.3 YES
15 H2AFX H2AFX H2AFX 2484 0.095 0.31 YES
16 POLD1 POLD1 POLD1 2510 0.094 0.32 YES
17 POLR2H POLR2H POLR2H 2538 0.092 0.34 YES
18 FEN1 FEN1 FEN1 2771 0.084 0.34 YES
19 FANCG FANCG FANCG 3126 0.073 0.33 YES
20 PALB2 PALB2 PALB2 3264 0.07 0.33 YES
21 RPA3 RPA3 RPA3 3390 0.067 0.34 YES
22 GTF2H3 GTF2H3 GTF2H3 3447 0.066 0.34 YES
23 RFC5 RFC5 RFC5 3577 0.062 0.35 YES
24 CDK7 CDK7 CDK7 3599 0.061 0.36 YES
25 PRKDC PRKDC PRKDC 3620 0.061 0.36 YES
26 POLR2D POLR2D POLR2D 3787 0.057 0.36 YES
27 LIG1 LIG1 LIG1 3804 0.056 0.37 YES
28 MPG MPG MPG 3839 0.056 0.38 YES
29 MAD2L2 MAD2L2 MAD2L2 3847 0.056 0.39 YES
30 TCEA1 TCEA1 TCEA1 3929 0.054 0.39 YES
31 BRCA1 BRCA1 BRCA1 3945 0.053 0.4 YES
32 POLD4 POLD4 POLD4 4167 0.049 0.4 YES
33 MRE11A MRE11A MRE11A 4172 0.049 0.4 YES
34 PCNA PCNA PCNA 4202 0.048 0.41 YES
35 ERCC3 ERCC3 ERCC3 4346 0.046 0.41 YES
36 RFC3 RFC3 RFC3 4368 0.045 0.42 YES
37 ERCC2 ERCC2 ERCC2 4370 0.045 0.42 YES
38 C17orf70 C17orf70 C17orf70 4403 0.045 0.43 YES
39 GTF2H4 GTF2H4 GTF2H4 4543 0.042 0.43 NO
40 ATR ATR ATR 4674 0.04 0.43 NO
41 XRCC5 XRCC5 XRCC5 4870 0.037 0.42 NO
42 POLR2K POLR2K POLR2K 4930 0.036 0.42 NO
43 POLE POLE POLE 5120 0.034 0.42 NO
44 TP53BP1 TP53BP1 TP53BP1 5273 0.032 0.42 NO
45 MGMT MGMT MGMT 5379 0.03 0.41 NO
46 TDP1 TDP1 TDP1 5678 0.026 0.4 NO
47 FANCL FANCL FANCL 5823 0.024 0.4 NO
48 XRCC1 XRCC1 XRCC1 5868 0.024 0.4 NO
49 USP1 USP1 USP1 5885 0.023 0.4 NO
50 NBN NBN NBN 5912 0.023 0.4 NO
51 DDB2 DDB2 DDB2 5915 0.023 0.41 NO
52 APEX1 APEX1 APEX1 5981 0.022 0.41 NO
53 POLR2G POLR2G POLR2G 6039 0.022 0.41 NO
54 XRCC6 XRCC6 XRCC6 6049 0.021 0.41 NO
55 TDG TDG TDG 6266 0.019 0.4 NO
56 POLR2I POLR2I POLR2I 6411 0.017 0.4 NO
57 ALKBH2 ALKBH2 ALKBH2 6451 0.017 0.4 NO
58 RAD23B RAD23B RAD23B 6561 0.015 0.4 NO
59 ERCC1 ERCC1 ERCC1 6578 0.015 0.4 NO
60 REV1 REV1 REV1 6649 0.014 0.4 NO
61 GTF2H2 GTF2H2 GTF2H2 6864 0.012 0.38 NO
62 NTHL1 NTHL1 NTHL1 7003 0.011 0.38 NO
63 POLD2 POLD2 POLD2 7077 0.01 0.38 NO
64 DDB1 DDB1 DDB1 7222 0.0086 0.37 NO
65 LIG3 LIG3 LIG3 7262 0.0082 0.37 NO
66 POLR2L POLR2L POLR2L 7504 0.0054 0.36 NO
67 POLR2C POLR2C POLR2C 7549 0.0049 0.36 NO
68 ERCC6 ERCC6 ERCC6 7603 0.0041 0.35 NO
69 POLR2F POLR2F POLR2F 7642 0.0036 0.35 NO
70 MUTYH MUTYH MUTYH 7671 0.0033 0.35 NO
71 CCNO CCNO CCNO 7685 0.0031 0.35 NO
72 POLR2E POLR2E POLR2E 7829 0.0014 0.34 NO
73 SMUG1 SMUG1 SMUG1 8241 -0.003 0.32 NO
74 GTF2H1 GTF2H1 GTF2H1 8344 -0.0042 0.32 NO
75 MBD4 MBD4 MBD4 8705 -0.008 0.3 NO
76 RPS27A RPS27A RPS27A 8932 -0.01 0.29 NO
77 RAD50 RAD50 RAD50 9044 -0.012 0.28 NO
78 RPA2 RPA2 RPA2 9089 -0.012 0.28 NO
79 POLR2A POLR2A POLR2A 9134 -0.013 0.28 NO
80 FANCM FANCM FANCM 9186 -0.014 0.28 NO
81 XAB2 XAB2 XAB2 9309 -0.015 0.28 NO
82 POLR2B POLR2B POLR2B 9455 -0.016 0.27 NO
83 CCNH CCNH CCNH 9461 -0.016 0.27 NO
84 POLR2J POLR2J POLR2J 9639 -0.018 0.27 NO
85 POLD3 POLD3 POLD3 9730 -0.019 0.27 NO
86 ERCC8 ERCC8 ERCC8 9949 -0.022 0.26 NO
87 FANCF FANCF FANCF 9983 -0.022 0.26 NO
88 RPA1 RPA1 RPA1 10536 -0.028 0.23 NO
89 MDC1 MDC1 MDC1 10550 -0.029 0.24 NO
90 OGG1 OGG1 OGG1 10623 -0.03 0.24 NO
91 ALKBH3 ALKBH3 ALKBH3 10981 -0.035 0.22 NO
92 RAD52 RAD52 RAD52 11343 -0.04 0.21 NO
93 UBA52 UBA52 UBA52 11476 -0.042 0.21 NO
94 XPC XPC XPC 11488 -0.043 0.22 NO
95 ATM ATM ATM 11624 -0.045 0.22 NO
96 ERCC5 ERCC5 ERCC5 11723 -0.046 0.22 NO
97 POLH POLH POLH 12317 -0.058 0.2 NO
98 ERCC4 ERCC4 ERCC4 12330 -0.058 0.2 NO
99 LIG4 LIG4 LIG4 13015 -0.073 0.18 NO
100 FANCC FANCC FANCC 13242 -0.079 0.18 NO
101 XPA XPA XPA 13539 -0.087 0.18 NO
102 XRCC4 XRCC4 XRCC4 14442 -0.12 0.15 NO
103 ZBTB32 ZBTB32 ZBTB32 14587 -0.13 0.16 NO
104 REV3L REV3L REV3L 14756 -0.13 0.17 NO
105 GTF2H2B GTF2H2B GTF2H2B 15863 -0.2 0.14 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 PLK1 PATHWAY.

Figure S60.  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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus4 enriched pathways

Table 6.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus4. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG FATTY ACID METABOLISM 38 genes.ES.table 0.6 1.8 0.004 0.26 0.6 0.21 0.093 0.19 0.088 0.069
KEGG SELENOAMINO ACID METABOLISM 26 genes.ES.table 0.76 2.3 0 0.082 0.021 0.19 0.03 0.19 0 0.021
KEGG GLUTATHIONE METABOLISM 46 genes.ES.table 0.6 1.9 0 0.2 0.36 0.11 0.028 0.11 0 0.049
KEGG GLYCEROLIPID METABOLISM 48 genes.ES.table 0.65 2 0 0.2 0.11 0.1 0.014 0.1 0 0.05
KEGG PROPANOATE METABOLISM 32 genes.ES.table 0.56 1.9 0.0041 0.22 0.35 0.56 0.28 0.41 0 0.055
KEGG ENDOCYTOSIS 179 genes.ES.table 0.39 1.8 0 0.24 0.5 0.26 0.25 0.2 0 0.06
SIG PIP3 SIGNALING IN CARDIAC MYOCTES 67 genes.ES.table 0.52 2 0 0.18 0.13 0.12 0.086 0.11 0 0.047
SIG CHEMOTAXIS 44 genes.ES.table 0.59 1.8 0.0021 0.23 0.51 0.16 0.086 0.15 0.059 0.059
SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES 35 genes.ES.table 0.61 1.9 0 0.26 0.28 0.086 0.018 0.084 0 0.06
PID INSULIN PATHWAY 45 genes.ES.table 0.49 1.9 0.0021 0.25 0.23 0.31 0.26 0.23 0 0.06
genes ES table in pathway: KEGG FATTY ACID METABOLISM

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 MAT1A MAT1A MAT1A 158 0.63 0.2 YES
2 CBS CBS CBS 191 0.58 0.4 YES
3 GGT6 GGT6 GGT6 412 0.41 0.52 YES
4 GGT1 GGT1 GGT1 518 0.36 0.64 YES
5 CTH CTH CTH 554 0.35 0.76 YES
6 SCLY SCLY SCLY 1937 0.17 0.74 NO
7 GGT7 GGT7 GGT7 4489 0.066 0.62 NO
8 AHCYL1 AHCYL1 AHCYL1 4679 0.062 0.63 NO
9 LCMT2 LCMT2 LCMT2 5585 0.046 0.6 NO
10 PAPSS1 PAPSS1 PAPSS1 6214 0.037 0.57 NO
11 MARS2 MARS2 MARS2 6606 0.032 0.56 NO
12 PAPSS2 PAPSS2 PAPSS2 7018 0.027 0.55 NO
13 MAT2B MAT2B MAT2B 7088 0.026 0.56 NO
14 MAT2A MAT2A MAT2A 7577 0.022 0.54 NO
15 AHCYL2 AHCYL2 AHCYL2 7628 0.021 0.54 NO
16 GGT5 GGT5 GGT5 8136 0.016 0.52 NO
17 LCMT1 LCMT1 LCMT1 8321 0.014 0.51 NO
18 SEPHS1 SEPHS1 SEPHS1 8626 0.011 0.5 NO
19 METTL2B METTL2B METTL2B 9346 0.0041 0.46 NO
20 METTL6 METTL6 METTL6 9688 0.0012 0.44 NO
21 SEPHS2 SEPHS2 SEPHS2 9778 0.00046 0.44 NO
22 HEMK1 HEMK1 HEMK1 9934 -0.00073 0.43 NO
23 MARS MARS MARS 10468 -0.0054 0.41 NO
24 AHCY AHCY AHCY 10508 -0.0057 0.4 NO
25 TRMT11 TRMT11 TRMT11 12457 -0.024 0.31 NO
26 WBSCR22 WBSCR22 WBSCR22 14632 -0.053 0.21 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 FATTY ACID METABOLISM.

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

genes ES table in pathway: KEGG SELENOAMINO ACID METABOLISM

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 EGF EGF EGF 52 1 0.22 YES
2 ERBB4 ERBB4 ERBB4 74 0.86 0.42 YES
3 NRG4 NRG4 NRG4 144 0.64 0.56 YES
4 NRG2 NRG2 NRG2 674 0.32 0.6 YES
5 PHLPP1 PHLPP1 PHLPP1 2165 0.15 0.55 NO
6 EGFR EGFR EGFR 2872 0.12 0.54 NO
7 FOXO3 FOXO3 FOXO3 3797 0.084 0.51 NO
8 CASP9 CASP9 CASP9 3916 0.08 0.52 NO
9 GAB1 GAB1 GAB1 4477 0.066 0.5 NO
10 PIK3R1 PIK3R1 PIK3R1 4539 0.065 0.51 NO
11 AKT3 AKT3 AKT3 4561 0.065 0.53 NO
12 FOXO4 FOXO4 FOXO4 4886 0.058 0.52 NO
13 PIK3CA PIK3CA PIK3CA 5589 0.046 0.5 NO
14 FOXO1 FOXO1 FOXO1 5701 0.044 0.5 NO
15 PDPK1 PDPK1 PDPK1 5702 0.044 0.51 NO
16 THEM4 THEM4 THEM4 5835 0.042 0.51 NO
17 PTEN PTEN PTEN 6302 0.036 0.49 NO
18 MTOR MTOR MTOR 6342 0.035 0.5 NO
19 ERBB3 ERBB3 ERBB3 6719 0.03 0.48 NO
20 MAPKAP1 MAPKAP1 MAPKAP1 6993 0.028 0.48 NO
21 BTC BTC BTC 7279 0.024 0.47 NO
22 CREB1 CREB1 CREB1 7490 0.022 0.46 NO
23 TRIB3 TRIB3 TRIB3 7930 0.018 0.44 NO
24 RICTOR RICTOR RICTOR 9171 0.0059 0.37 NO
25 CHUK CHUK CHUK 9228 0.0054 0.37 NO
26 CDKN1B CDKN1B CDKN1B 9491 0.0028 0.36 NO
27 GRB2 GRB2 GRB2 9686 0.0012 0.35 NO
28 NRG1 NRG1 NRG1 9829 0.000096 0.34 NO
29 MDM2 MDM2 MDM2 10293 -0.0039 0.32 NO
30 AKT1 AKT1 AKT1 11563 -0.015 0.25 NO
31 ERBB2 ERBB2 ERBB2 11821 -0.018 0.24 NO
32 MLST8 MLST8 MLST8 11860 -0.018 0.24 NO
33 TSC2 TSC2 TSC2 12129 -0.02 0.23 NO
34 AKT2 AKT2 AKT2 12227 -0.021 0.23 NO
35 RPS6KB2 RPS6KB2 RPS6KB2 12422 -0.023 0.23 NO
36 HBEGF HBEGF HBEGF 13015 -0.029 0.2 NO
37 GSK3A GSK3A GSK3A 13311 -0.033 0.19 NO
38 AKT1S1 AKT1S1 AKT1S1 13907 -0.041 0.17 NO
39 CDKN1A CDKN1A CDKN1A 14113 -0.044 0.17 NO
40 BAD BAD BAD 14636 -0.053 0.15 NO
41 NR4A1 NR4A1 NR4A1 15984 -0.087 0.098 NO
42 EREG EREG EREG 17401 -0.16 0.057 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 SELENOAMINO ACID METABOLISM.

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

genes ES table in pathway: KEGG GLUTATHIONE METABOLISM

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 PNLIPRP1 PNLIPRP1 PNLIPRP1 10 1.3 0.16 YES
2 PNLIPRP2 PNLIPRP2 PNLIPRP2 18 1.3 0.31 YES
3 PNLIP PNLIP PNLIP 23 1.2 0.46 YES
4 CEL CEL CEL 26 1.2 0.6 YES
5 LIPC LIPC LIPC 251 0.52 0.65 YES
6 ALDH3A2 ALDH3A2 ALDH3A2 1453 0.2 0.61 NO
7 DGKB DGKB DGKB 2077 0.16 0.6 NO
8 LIPG LIPG LIPG 2570 0.13 0.59 NO
9 PPAP2C PPAP2C PPAP2C 2984 0.11 0.58 NO
10 GPAM GPAM GPAM 3004 0.11 0.59 NO
11 PPAP2B PPAP2B PPAP2B 3329 0.098 0.58 NO
12 LPL LPL LPL 4268 0.071 0.54 NO
13 AGPAT3 AGPAT3 AGPAT3 4855 0.058 0.52 NO
14 ALDH7A1 ALDH7A1 ALDH7A1 4860 0.058 0.52 NO
15 MBOAT1 MBOAT1 MBOAT1 5043 0.055 0.52 NO
16 LIPF LIPF LIPF 5592 0.046 0.5 NO
17 AGPAT4 AGPAT4 AGPAT4 5872 0.042 0.48 NO
18 PPAP2A PPAP2A PPAP2A 6219 0.037 0.47 NO
19 AKR1B1 AKR1B1 AKR1B1 6318 0.035 0.47 NO
20 AGPAT6 AGPAT6 AGPAT6 6338 0.035 0.47 NO
21 ALDH9A1 ALDH9A1 ALDH9A1 7998 0.017 0.38 NO
22 AKR1A1 AKR1A1 AKR1A1 8352 0.014 0.37 NO
23 GK GK GK 8753 0.0099 0.35 NO
24 ALDH2 ALDH2 ALDH2 9447 0.0032 0.31 NO
25 DAK DAK DAK 9669 0.0014 0.3 NO
26 GLA GLA GLA 10171 -0.0029 0.27 NO
27 AGPAT1 AGPAT1 AGPAT1 10273 -0.0038 0.27 NO
28 LCLAT1 LCLAT1 LCLAT1 11416 -0.014 0.2 NO
29 ALDH1B1 ALDH1B1 ALDH1B1 11559 -0.015 0.2 NO
30 DGKH DGKH DGKH 12028 -0.019 0.18 NO
31 AGPAT2 AGPAT2 AGPAT2 12167 -0.021 0.17 NO
32 PNPLA3 PNPLA3 PNPLA3 12519 -0.024 0.16 NO
33 DGKE DGKE DGKE 12555 -0.025 0.16 NO
34 AGPAT9 AGPAT9 AGPAT9 12725 -0.026 0.15 NO
35 AWAT2 AWAT2 AWAT2 12755 -0.027 0.15 NO
36 AGK AGK AGK 13908 -0.041 0.094 NO
37 GPAT2 GPAT2 GPAT2 13929 -0.041 0.098 NO
38 DGKG DGKG DGKG 14708 -0.055 0.062 NO
39 DGKZ DGKZ DGKZ 14838 -0.057 0.062 NO
40 DGKD DGKD DGKD 15064 -0.062 0.057 NO
41 MGLL MGLL MGLL 15674 -0.077 0.034 NO
42 DGKQ DGKQ DGKQ 16006 -0.088 0.026 NO
43 DGKA DGKA DGKA 16532 -0.11 0.011 NO
44 DGAT1 DGAT1 DGAT1 16625 -0.12 0.019 NO
45 GLYCTK GLYCTK GLYCTK 16755 -0.12 0.027 NO
46 DGKI DGKI DGKI 17095 -0.14 0.025 NO
47 MBOAT2 MBOAT2 MBOAT2 17495 -0.17 0.024 NO
48 DGAT2 DGAT2 DGAT2 18086 -0.24 0.02 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 GLUTATHIONE METABOLISM.

Figure S66.  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

genes ES table in pathway: KEGG GLYCEROLIPID METABOLISM

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 ERBB4 ERBB4 ERBB4 74 0.86 0.15 YES
2 PAK7 PAK7 PAK7 81 0.83 0.3 YES
3 PAK3 PAK3 PAK3 325 0.45 0.37 YES
4 F2RL2 F2RL2 F2RL2 662 0.32 0.41 YES
5 IGF1 IGF1 IGF1 1038 0.25 0.44 YES
6 CREB5 CREB5 CREB5 1291 0.22 0.46 YES
7 IRS4 IRS4 IRS4 1379 0.21 0.5 YES
8 PIK3R5 PIK3R5 PIK3R5 1584 0.19 0.52 YES
9 PARD6A PARD6A PARD6A 3019 0.11 0.46 NO
10 PIK3CD PIK3CD PIK3CD 3035 0.11 0.48 NO
11 PREX1 PREX1 PREX1 3448 0.094 0.47 NO
12 FOXO3 FOXO3 FOXO3 3797 0.084 0.47 NO
13 RPS6KA2 RPS6KA2 RPS6KA2 4361 0.069 0.45 NO
14 PARD3 PARD3 PARD3 4458 0.067 0.46 NO
15 PPP1R13B PPP1R13B PPP1R13B 4465 0.067 0.47 NO
16 GAB1 GAB1 GAB1 4477 0.066 0.48 NO
17 SOS2 SOS2 SOS2 4531 0.065 0.49 NO
18 AKT3 AKT3 AKT3 4561 0.065 0.5 NO
19 PIK3CA PIK3CA PIK3CA 5589 0.046 0.45 NO
20 CYTH3 CYTH3 CYTH3 6247 0.036 0.42 NO
21 PTEN PTEN PTEN 6302 0.036 0.43 NO
22 MTOR MTOR MTOR 6342 0.035 0.43 NO
23 MYC MYC MYC 6349 0.035 0.44 NO
24 SOS1 SOS1 SOS1 6382 0.034 0.44 NO
25 RPS6KB1 RPS6KB1 RPS6KB1 7477 0.022 0.39 NO
26 CREB1 CREB1 CREB1 7490 0.022 0.39 NO
27 YWHAQ YWHAQ YWHAQ 8541 0.012 0.34 NO
28 PTK2 PTK2 PTK2 8715 0.01 0.33 NO
29 PAK6 PAK6 PAK6 8949 0.008 0.32 NO
30 RPS6KA3 RPS6KA3 RPS6KA3 9062 0.007 0.31 NO
31 YWHAE YWHAE YWHAE 9253 0.0052 0.3 NO
32 CDKN1B CDKN1B CDKN1B 9491 0.0028 0.29 NO
33 GRB2 GRB2 GRB2 9686 0.0012 0.28 NO
34 MET MET MET 9731 0.00083 0.28 NO
35 TSC1 TSC1 TSC1 9983 -0.0011 0.26 NO
36 GSK3B GSK3B GSK3B 10067 -0.0019 0.26 NO
37 PAK2 PAK2 PAK2 10118 -0.0025 0.26 NO
38 IRS1 IRS1 IRS1 10266 -0.0037 0.25 NO
39 CDK2 CDK2 CDK2 10557 -0.0062 0.24 NO
40 CDC42 CDC42 CDC42 10625 -0.0068 0.23 NO
41 CREB3 CREB3 CREB3 10787 -0.0081 0.23 NO
42 SHC1 SHC1 SHC1 11438 -0.014 0.19 NO
43 AKT1 AKT1 AKT1 11563 -0.015 0.19 NO
44 YWHAB YWHAB YWHAB 11921 -0.018 0.17 NO
45 YWHAZ YWHAZ YWHAZ 11942 -0.019 0.18 NO
46 INPPL1 INPPL1 INPPL1 11969 -0.019 0.18 NO
47 TSC2 TSC2 TSC2 12129 -0.02 0.17 NO
48 NOLC1 NOLC1 NOLC1 12226 -0.021 0.17 NO
49 AKT2 AKT2 AKT2 12227 -0.021 0.18 NO
50 YWHAG YWHAG YWHAG 12250 -0.022 0.18 NO
51 SLC2A4 SLC2A4 SLC2A4 12270 -0.022 0.18 NO
52 YWHAH YWHAH YWHAH 12338 -0.022 0.18 NO
53 RPS6KA1 RPS6KA1 RPS6KA1 12660 -0.026 0.17 NO
54 PAK1 PAK1 PAK1 13035 -0.03 0.15 NO
55 PTPN1 PTPN1 PTPN1 13058 -0.03 0.16 NO
56 GADD45A GADD45A GADD45A 13140 -0.031 0.16 NO
57 IRS2 IRS2 IRS2 13175 -0.031 0.16 NO
58 GSK3A GSK3A GSK3A 13311 -0.033 0.16 NO
59 CDKN2A CDKN2A CDKN2A 13653 -0.037 0.15 NO
60 BCL2L1 BCL2L1 BCL2L1 13777 -0.039 0.15 NO
61 EBP EBP EBP 14622 -0.053 0.11 NO
62 BAD BAD BAD 14636 -0.053 0.12 NO
63 PAK4 PAK4 PAK4 15578 -0.074 0.084 NO
64 PDK1 PDK1 PDK1 15601 -0.075 0.097 NO
65 SFN SFN SFN 16074 -0.09 0.087 NO
66 IFI27 IFI27 IFI27 16617 -0.11 0.078 NO
67 IGFBP1 IGFBP1 IGFBP1 16752 -0.12 0.093 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: KEGG GLYCEROLIPID METABOLISM.

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

genes ES table in pathway: KEGG PROPANOATE METABOLISM

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 GRB14 GRB14 GRB14 113 0.72 0.2 YES
2 INS INS INS 648 0.33 0.27 YES
3 F2RL2 F2RL2 F2RL2 662 0.32 0.36 YES
4 GRB10 GRB10 GRB10 1187 0.23 0.4 YES
5 SGK1 SGK1 SGK1 1487 0.2 0.45 YES
6 EIF4EBP1 EIF4EBP1 EIF4EBP1 2127 0.15 0.46 YES
7 INSR INSR INSR 2848 0.12 0.45 YES
8 PARD6A PARD6A PARD6A 3019 0.11 0.48 YES
9 FOXO3 FOXO3 FOXO3 3797 0.084 0.46 YES
10 EXOC6 EXOC6 EXOC6 4313 0.07 0.45 YES
11 CRK CRK CRK 4370 0.069 0.47 YES
12 PIK3R1 PIK3R1 PIK3R1 4539 0.065 0.48 YES
13 INPP5D INPP5D INPP5D 4844 0.059 0.48 YES
14 NCK2 NCK2 NCK2 4877 0.058 0.49 YES
15 RAPGEF1 RAPGEF1 RAPGEF1 5432 0.048 0.48 NO
16 PIK3CA PIK3CA PIK3CA 5589 0.046 0.48 NO
17 PDPK1 PDPK1 PDPK1 5702 0.044 0.49 NO
18 RHOQ RHOQ RHOQ 6001 0.04 0.49 NO
19 SOS1 SOS1 SOS1 6382 0.034 0.48 NO
20 EXOC2 EXOC2 EXOC2 7374 0.023 0.43 NO
21 RPS6KB1 RPS6KB1 RPS6KB1 7477 0.022 0.43 NO
22 CBL CBL CBL 7570 0.022 0.43 NO
23 DOK1 DOK1 DOK1 7856 0.019 0.42 NO
24 PTPN11 PTPN11 PTPN11 7867 0.019 0.42 NO
25 EXOC5 EXOC5 EXOC5 8271 0.015 0.41 NO
26 EXOC4 EXOC4 EXOC4 8364 0.014 0.41 NO
27 GRB2 GRB2 GRB2 9686 0.0012 0.34 NO
28 PTPRA PTPRA PTPRA 9694 0.0011 0.34 NO
29 EXOC7 EXOC7 EXOC7 9770 0.0005 0.33 NO
30 CAV1 CAV1 CAV1 9793 0.00038 0.33 NO
31 EXOC3 EXOC3 EXOC3 10055 -0.0018 0.32 NO
32 SORBS1 SORBS1 SORBS1 10122 -0.0025 0.31 NO
33 RASA1 RASA1 RASA1 10242 -0.0035 0.31 NO
34 IRS1 IRS1 IRS1 10266 -0.0037 0.31 NO
35 SHC1 SHC1 SHC1 11438 -0.014 0.25 NO
36 AKT1 AKT1 AKT1 11563 -0.015 0.25 NO
37 NCK1 NCK1 NCK1 12224 -0.021 0.22 NO
38 AKT2 AKT2 AKT2 12227 -0.021 0.22 NO
39 PTPN1 PTPN1 PTPN1 13058 -0.03 0.19 NO
40 EXOC1 EXOC1 EXOC1 13554 -0.036 0.17 NO
41 PRKCZ PRKCZ PRKCZ 13864 -0.04 0.16 NO
42 TRIP10 TRIP10 TRIP10 14310 -0.047 0.16 NO
43 PRKCI PRKCI PRKCI 14887 -0.058 0.14 NO
44 HRAS HRAS HRAS 15637 -0.076 0.12 NO
45 SH2B2 SH2B2 SH2B2 16433 -0.1 0.11 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: KEGG PROPANOATE METABOLISM.

Figure S70.  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

genes ES table in pathway: KEGG ENDOCYTOSIS

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 MYLK2 MYLK2 MYLK2 12 1.3 0.32 YES
2 PAK7 PAK7 PAK7 81 0.83 0.52 YES
3 PAK3 PAK3 PAK3 325 0.45 0.61 YES
4 FSCN2 FSCN2 FSCN2 1848 0.17 0.57 NO
5 ROCK2 ROCK2 ROCK2 5024 0.056 0.41 NO
6 WASF1 WASF1 WASF1 6380 0.034 0.35 NO
7 CFL2 CFL2 CFL2 6737 0.03 0.34 NO
8 RPS4X RPS4X RPS4X 7136 0.026 0.32 NO
9 ROCK1 ROCK1 ROCK1 7349 0.024 0.32 NO
10 FLNA FLNA FLNA 8294 0.014 0.27 NO
11 GDI2 GDI2 GDI2 8847 0.009 0.24 NO
12 PAK6 PAK6 PAK6 8949 0.008 0.24 NO
13 ACTR2 ACTR2 ACTR2 9160 0.0061 0.23 NO
14 PFN2 PFN2 PFN2 9997 -0.0013 0.18 NO
15 PAK2 PAK2 PAK2 10118 -0.0025 0.18 NO
16 CDC42 CDC42 CDC42 10625 -0.0068 0.15 NO
17 MYLK MYLK MYLK 10773 -0.0079 0.14 NO
18 WASL WASL WASL 10779 -0.008 0.14 NO
19 ACTR3 ACTR3 ACTR3 10899 -0.009 0.14 NO
20 LIMK1 LIMK1 LIMK1 11083 -0.011 0.13 NO
21 AKT1 AKT1 AKT1 11563 -0.015 0.11 NO
22 ACTG1 ACTG1 ACTG1 11818 -0.018 0.1 NO
23 PFN1 PFN1 PFN1 12658 -0.026 0.062 NO
24 PAK1 PAK1 PAK1 13035 -0.03 0.049 NO
25 CFL1 CFL1 CFL1 14741 -0.055 -0.031 NO
26 MYH2 MYH2 MYH2 14749 -0.055 -0.018 NO
27 ANGPTL2 ANGPTL2 ANGPTL2 14873 -0.058 -0.01 NO
28 GDI1 GDI1 GDI1 14954 -0.06 -0.000011 NO
29 FSCN3 FSCN3 FSCN3 15084 -0.062 0.0081 NO
30 VASP VASP VASP 15509 -0.072 0.0026 NO
31 PAK4 PAK4 PAK4 15578 -0.074 0.017 NO
32 RHO RHO RHO 16307 -0.1 0.0016 NO
33 FSCN1 FSCN1 FSCN1 16418 -0.1 0.021 NO
34 FLNC FLNC FLNC 16457 -0.11 0.044 NO
35 ACTG2 ACTG2 ACTG2 18237 -0.26 0.012 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: KEGG ENDOCYTOSIS.

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

genes ES table in pathway: SIG PIP3 SIGNALING IN CARDIAC MYOCTES

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 CLPS CLPS CLPS 17 1.3 0.16 YES
2 PNLIPRP2 PNLIPRP2 PNLIPRP2 18 1.3 0.32 YES
3 PNLIP PNLIP PNLIP 23 1.2 0.47 YES
4 ALB ALB ALB 65 0.92 0.58 YES
5 LPA LPA LPA 135 0.66 0.66 YES
6 LIPC LIPC LIPC 251 0.52 0.72 YES
7 FABP4 FABP4 FABP4 1494 0.2 0.67 NO
8 APOC2 APOC2 APOC2 2291 0.14 0.65 NO
9 CUBN CUBN CUBN 2718 0.12 0.64 NO
10 PLTP PLTP PLTP 2830 0.12 0.65 NO
11 PLIN1 PLIN1 PLIN1 3084 0.11 0.65 NO
12 A2M A2M A2M 3101 0.11 0.66 NO
13 LPL LPL LPL 4268 0.071 0.61 NO
14 P4HB P4HB P4HB 4280 0.071 0.61 NO
15 APOE APOE APOE 4325 0.07 0.62 NO
16 PRKACB PRKACB PRKACB 5318 0.05 0.57 NO
17 APOA5 APOA5 APOA5 5472 0.047 0.57 NO
18 ABHD5 ABHD5 ABHD5 5724 0.044 0.56 NO
19 ABCA1 ABCA1 ABCA1 6073 0.039 0.55 NO
20 PPP1CB PPP1CB PPP1CB 6536 0.032 0.53 NO
21 HSPG2 HSPG2 HSPG2 7647 0.021 0.47 NO
22 ABCG5 ABCG5 ABCG5 8343 0.014 0.43 NO
23 PPP1CC PPP1CC PPP1CC 8840 0.0091 0.41 NO
24 PRKACA PRKACA PRKACA 8982 0.0077 0.4 NO
25 CAV1 CAV1 CAV1 9793 0.00038 0.36 NO
26 SAR1B SAR1B SAR1B 10336 -0.0042 0.33 NO
27 PPP1CA PPP1CA PPP1CA 10362 -0.0044 0.33 NO
28 CETP CETP CETP 11153 -0.011 0.29 NO
29 LDLRAP1 LDLRAP1 LDLRAP1 11293 -0.013 0.28 NO
30 LDLR LDLR LDLR 11543 -0.015 0.27 NO
31 MTTP MTTP MTTP 11585 -0.015 0.27 NO
32 APOB APOB APOB 11737 -0.017 0.26 NO
33 APOA1 APOA1 APOA1 12308 -0.022 0.23 NO
34 ABCG8 ABCG8 ABCG8 12608 -0.025 0.22 NO
35 BMP1 BMP1 BMP1 14781 -0.056 0.11 NO
36 SCARB1 SCARB1 SCARB1 14900 -0.059 0.11 NO
37 MGLL MGLL MGLL 15674 -0.077 0.078 NO
38 APOC3 APOC3 APOC3 15683 -0.077 0.087 NO
39 LIPE LIPE LIPE 15727 -0.078 0.094 NO
40 LCAT LCAT LCAT 15845 -0.082 0.098 NO
41 ABCG1 ABCG1 ABCG1 16228 -0.096 0.089 NO
42 SDC1 SDC1 SDC1 16350 -0.1 0.095 NO
43 AMN AMN AMN 17312 -0.15 0.062 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 PIP3 SIGNALING IN CARDIAC MYOCTES.

Figure S74.  Get High-res Image For the top 5 core enriched genes in the pathway: SIG PIP3 SIGNALING IN CARDIAC MYOCTES, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: SIG CHEMOTAXIS

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 EGF EGF EGF 52 1 0.12 YES
2 ERBB4 ERBB4 ERBB4 74 0.86 0.22 YES
3 NRG4 NRG4 NRG4 144 0.64 0.3 YES
4 ADCY5 ADCY5 ADCY5 276 0.5 0.35 YES
5 NRG2 NRG2 NRG2 674 0.32 0.37 YES
6 PRKAR2B PRKAR2B PRKAR2B 755 0.3 0.4 YES
7 ITPR2 ITPR2 ITPR2 1041 0.25 0.41 YES
8 MATK MATK MATK 1835 0.17 0.39 YES
9 PDE1A PDE1A PDE1A 2017 0.16 0.4 YES
10 PHLPP1 PHLPP1 PHLPP1 2165 0.15 0.41 YES
11 ADCY1 ADCY1 ADCY1 2169 0.15 0.43 YES
12 ADCY9 ADCY9 ADCY9 2342 0.14 0.44 YES
13 ADCY8 ADCY8 ADCY8 2582 0.13 0.44 YES
14 EGFR EGFR EGFR 2872 0.12 0.44 YES
15 PRKAR2A PRKAR2A PRKAR2A 2945 0.11 0.45 YES
16 CAMK4 CAMK4 CAMK4 3461 0.094 0.43 NO
17 FOXO3 FOXO3 FOXO3 3797 0.084 0.42 NO
18 CASP9 CASP9 CASP9 3916 0.08 0.42 NO
19 GAB1 GAB1 GAB1 4477 0.066 0.4 NO
20 PIK3R1 PIK3R1 PIK3R1 4539 0.065 0.41 NO
21 AKT3 AKT3 AKT3 4561 0.065 0.41 NO
22 FOXO4 FOXO4 FOXO4 4886 0.058 0.4 NO
23 PDE1B PDE1B PDE1B 5112 0.054 0.4 NO
24 PRKACB PRKACB PRKACB 5318 0.05 0.39 NO
25 ADCY4 ADCY4 ADCY4 5446 0.048 0.39 NO
26 PRKCA PRKCA PRKCA 5456 0.048 0.4 NO
27 PIK3CA PIK3CA PIK3CA 5589 0.046 0.39 NO
28 FOXO1 FOXO1 FOXO1 5701 0.044 0.39 NO
29 PDPK1 PDPK1 PDPK1 5702 0.044 0.4 NO
30 CUL5 CUL5 CUL5 5805 0.043 0.4 NO
31 THEM4 THEM4 THEM4 5835 0.042 0.4 NO
32 MAPK1 MAPK1 MAPK1 6112 0.038 0.39 NO
33 USP8 USP8 USP8 6228 0.036 0.39 NO
34 PRKCE PRKCE PRKCE 6252 0.036 0.39 NO
35 PTEN PTEN PTEN 6302 0.036 0.39 NO
36 MTOR MTOR MTOR 6342 0.035 0.4 NO
37 SOS1 SOS1 SOS1 6382 0.034 0.4 NO
38 ERBB3 ERBB3 ERBB3 6719 0.03 0.38 NO
39 ADCY3 ADCY3 ADCY3 6827 0.029 0.38 NO
40 MAPKAP1 MAPKAP1 MAPKAP1 6993 0.028 0.38 NO
41 RAF1 RAF1 RAF1 7098 0.026 0.37 NO
42 BTC BTC BTC 7279 0.024 0.37 NO
43 CREB1 CREB1 CREB1 7490 0.022 0.36 NO
44 TRIB3 TRIB3 TRIB3 7930 0.018 0.34 NO
45 NRAS NRAS NRAS 7956 0.018 0.34 NO
46 PRKAR1A PRKAR1A PRKAR1A 8087 0.016 0.33 NO
47 YES1 YES1 YES1 8109 0.016 0.33 NO
48 RPS27A RPS27A RPS27A 8550 0.012 0.31 NO
49 UBA52 UBA52 UBA52 8864 0.0089 0.29 NO
50 PRKACA PRKACA PRKACA 8982 0.0077 0.29 NO
51 GRB7 GRB7 GRB7 9108 0.0066 0.28 NO
52 CALM3 CALM3 CALM3 9151 0.0062 0.28 NO
53 RICTOR RICTOR RICTOR 9171 0.0059 0.28 NO
54 PRKCD PRKCD PRKCD 9204 0.0056 0.28 NO
55 CHUK CHUK CHUK 9228 0.0054 0.28 NO
56 CDKN1B CDKN1B CDKN1B 9491 0.0028 0.26 NO
57 GRB2 GRB2 GRB2 9686 0.0012 0.26 NO
58 NRG1 NRG1 NRG1 9829 0.000096 0.25 NO
59 MAP2K1 MAP2K1 MAP2K1 9880 -0.00028 0.24 NO
60 FYN FYN FYN 9965 -0.0011 0.24 NO
61 MDM2 MDM2 MDM2 10293 -0.0039 0.22 NO
62 ITPR3 ITPR3 ITPR3 10309 -0.004 0.22 NO
63 RNF41 RNF41 RNF41 10780 -0.008 0.2 NO
64 HSP90AA1 HSP90AA1 HSP90AA1 11007 -0.01 0.19 NO
65 SHC1 SHC1 SHC1 11438 -0.014 0.16 NO
66 AKT1 AKT1 AKT1 11563 -0.015 0.16 NO
67 ERBB2 ERBB2 ERBB2 11821 -0.018 0.15 NO
68 MLST8 MLST8 MLST8 11860 -0.018 0.15 NO
69 YWHAB YWHAB YWHAB 11921 -0.018 0.15 NO
70 TSC2 TSC2 TSC2 12129 -0.02 0.14 NO
71 AKT2 AKT2 AKT2 12227 -0.021 0.14 NO
72 CALM1 CALM1 CALM1 12387 -0.023 0.13 NO
73 RPS6KB2 RPS6KB2 RPS6KB2 12422 -0.023 0.13 NO
74 KRAS KRAS KRAS 12583 -0.025 0.12 NO
75 HBEGF HBEGF HBEGF 13015 -0.029 0.1 NO
76 PLCG1 PLCG1 PLCG1 13023 -0.03 0.11 NO
77 GSK3A GSK3A GSK3A 13311 -0.033 0.096 NO
78 MAP2K2 MAP2K2 MAP2K2 13703 -0.038 0.08 NO
79 SRC SRC SRC 13791 -0.039 0.08 NO
80 CDC37 CDC37 CDC37 13851 -0.04 0.081 NO
81 ADCY7 ADCY7 ADCY7 13855 -0.04 0.086 NO
82 AKT1S1 AKT1S1 AKT1S1 13907 -0.041 0.088 NO
83 CDKN1A CDKN1A CDKN1A 14113 -0.044 0.082 NO
84 STUB1 STUB1 STUB1 14167 -0.045 0.085 NO
85 ADCY6 ADCY6 ADCY6 14221 -0.046 0.088 NO
86 CALM2 CALM2 CALM2 14516 -0.051 0.078 NO
87 BAD BAD BAD 14636 -0.053 0.078 NO
88 ADRBK1 ADRBK1 ADRBK1 15466 -0.071 0.041 NO
89 HRAS HRAS HRAS 15637 -0.076 0.041 NO
90 ADCY2 ADCY2 ADCY2 15735 -0.078 0.045 NO
91 NR4A1 NR4A1 NR4A1 15984 -0.087 0.042 NO
92 MAPK3 MAPK3 MAPK3 16243 -0.097 0.04 NO
93 PRKAR1B PRKAR1B PRKAR1B 16599 -0.11 0.034 NO
94 CDK1 CDK1 CDK1 17367 -0.16 0.012 NO
95 EREG EREG EREG 17401 -0.16 0.029 NO
96 PRKCG PRKCG PRKCG 18077 -0.23 0.021 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: SIG CHEMOTAXIS.

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

genes ES table in pathway: SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES

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 EGF EGF EGF 52 1 0.4 YES
2 PHLPP1 PHLPP1 PHLPP1 2165 0.15 0.34 YES
3 EGFR EGFR EGFR 2872 0.12 0.35 YES
4 FOXO3 FOXO3 FOXO3 3797 0.084 0.34 YES
5 CASP9 CASP9 CASP9 3916 0.08 0.36 YES
6 PAG1 PAG1 PAG1 4387 0.068 0.36 YES
7 GAB1 GAB1 GAB1 4477 0.066 0.38 YES
8 PIK3R1 PIK3R1 PIK3R1 4539 0.065 0.41 YES
9 AKT3 AKT3 AKT3 4561 0.065 0.43 YES
10 FOXO4 FOXO4 FOXO4 4886 0.058 0.44 YES
11 PIK3CA PIK3CA PIK3CA 5589 0.046 0.42 YES
12 FOXO1 FOXO1 FOXO1 5701 0.044 0.43 YES
13 PDPK1 PDPK1 PDPK1 5702 0.044 0.45 YES
14 THEM4 THEM4 THEM4 5835 0.042 0.46 YES
15 PTEN PTEN PTEN 6302 0.036 0.44 YES
16 MTOR MTOR MTOR 6342 0.035 0.46 YES
17 MAPKAP1 MAPKAP1 MAPKAP1 6993 0.028 0.43 NO
18 CREB1 CREB1 CREB1 7490 0.022 0.41 NO
19 TRIB3 TRIB3 TRIB3 7930 0.018 0.4 NO
20 RICTOR RICTOR RICTOR 9171 0.0059 0.33 NO
21 CHUK CHUK CHUK 9228 0.0054 0.33 NO
22 CDKN1B CDKN1B CDKN1B 9491 0.0028 0.32 NO
23 GRB2 GRB2 GRB2 9686 0.0012 0.31 NO
24 MDM2 MDM2 MDM2 10293 -0.0039 0.28 NO
25 AKT1 AKT1 AKT1 11563 -0.015 0.21 NO
26 MLST8 MLST8 MLST8 11860 -0.018 0.2 NO
27 TSC2 TSC2 TSC2 12129 -0.02 0.2 NO
28 AKT2 AKT2 AKT2 12227 -0.021 0.2 NO
29 RPS6KB2 RPS6KB2 RPS6KB2 12422 -0.023 0.2 NO
30 CSK CSK CSK 12505 -0.024 0.2 NO
31 GSK3A GSK3A GSK3A 13311 -0.033 0.17 NO
32 SRC SRC SRC 13791 -0.039 0.16 NO
33 AKT1S1 AKT1S1 AKT1S1 13907 -0.041 0.17 NO
34 CDKN1A CDKN1A CDKN1A 14113 -0.044 0.18 NO
35 BAD BAD BAD 14636 -0.053 0.17 NO
36 NR4A1 NR4A1 NR4A1 15984 -0.087 0.13 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: SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES.

Figure S78.  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

genes ES table in pathway: PID INSULIN PATHWAY

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 ACSS3 ACSS3 ACSS3 507 0.37 0.11 YES
2 ACSS1 ACSS1 ACSS1 1204 0.23 0.15 YES
3 ALDH3A2 ALDH3A2 ALDH3A2 1453 0.2 0.21 YES
4 ACAT1 ACAT1 ACAT1 1714 0.18 0.27 YES
5 PCCA PCCA PCCA 1972 0.16 0.31 YES
6 ABAT ABAT ABAT 2215 0.15 0.35 YES
7 ALDH6A1 ALDH6A1 ALDH6A1 2327 0.14 0.4 YES
8 ACACB ACACB ACACB 2781 0.12 0.42 YES
9 MLYCD MLYCD MLYCD 3100 0.11 0.44 YES
10 LDHB LDHB LDHB 3534 0.092 0.45 YES
11 MCEE MCEE MCEE 3743 0.085 0.47 YES
12 HIBCH HIBCH HIBCH 3890 0.081 0.49 YES
13 ACADM ACADM ACADM 3899 0.081 0.52 YES
14 MUT MUT MUT 4345 0.07 0.52 YES
15 ALDH7A1 ALDH7A1 ALDH7A1 4860 0.058 0.52 YES
16 ACAT2 ACAT2 ACAT2 4991 0.056 0.53 YES
17 SUCLG1 SUCLG1 SUCLG1 5039 0.055 0.55 YES
18 SUCLG2 SUCLG2 SUCLG2 5154 0.053 0.56 YES
19 LDHAL6A LDHAL6A LDHAL6A 6766 0.03 0.48 NO
20 PCCB PCCB PCCB 7399 0.023 0.46 NO
21 HADHA HADHA HADHA 7796 0.019 0.44 NO
22 ALDH9A1 ALDH9A1 ALDH9A1 7998 0.017 0.44 NO
23 EHHADH EHHADH EHHADH 8090 0.016 0.44 NO
24 SUCLA2 SUCLA2 SUCLA2 8531 0.012 0.42 NO
25 ALDH2 ALDH2 ALDH2 9447 0.0032 0.37 NO
26 ALDH1B1 ALDH1B1 ALDH1B1 11559 -0.015 0.26 NO
27 ACACA ACACA ACACA 12950 -0.029 0.2 NO
28 ACSS2 ACSS2 ACSS2 13515 -0.035 0.18 NO
29 ECHS1 ECHS1 ECHS1 13715 -0.038 0.18 NO
30 LDHA LDHA LDHA 13740 -0.039 0.2 NO
31 LDHAL6B LDHAL6B LDHAL6B 15285 -0.067 0.14 NO
32 LDHC LDHC LDHC 16303 -0.099 0.12 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 INSULIN PATHWAY.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus5 enriched pathways

Table 7.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG PURINE METABOLISM 155 genes.ES.table 0.34 1.4 0.026 0.25 1 0.22 0.22 0.17 0.19 0.004
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE 25 genes.ES.table 0.52 1.4 0.054 0.22 0.99 0.48 0.29 0.34 0.16 0.004
KEGG ABC TRANSPORTERS 43 genes.ES.table 0.58 1.5 0.048 0.2 0.98 0.3 0.16 0.26 0.14 0.004
KEGG MAPK SIGNALING PATHWAY 257 genes.ES.table 0.43 1.6 0 0.19 0.93 0.32 0.24 0.24 0.11 0.022
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION 240 genes.ES.table 0.68 1.6 0.0039 0.2 0.92 0.5 0.15 0.43 0.11 0.029
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM 75 genes.ES.table 0.42 1.5 0.038 0.19 0.97 0.31 0.25 0.23 0.12 0.009
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION 243 genes.ES.table 0.59 1.5 0.004 0.19 0.98 0.43 0.14 0.37 0.13 0.008
KEGG OOCYTE MEIOSIS 109 genes.ES.table 0.42 1.5 0.044 0.18 0.96 0.26 0.3 0.18 0.11 0.01
KEGG MTOR SIGNALING PATHWAY 52 genes.ES.table 0.43 1.5 0.052 0.19 0.98 0.25 0.25 0.19 0.13 0.005
KEGG APOPTOSIS 85 genes.ES.table 0.49 1.7 0.027 0.24 0.85 0.33 0.25 0.25 0.11 0.039
genes ES table in pathway: KEGG PURINE METABOLISM

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 CD28 CD28 CD28 64 0.76 0.09 YES
2 CD247 CD247 CD247 210 0.62 0.16 YES
3 CD8B CD8B CD8B 261 0.6 0.23 YES
4 PSMA8 PSMA8 PSMA8 519 0.5 0.28 YES
5 DOCK2 DOCK2 DOCK2 575 0.49 0.34 YES
6 LCK LCK LCK 951 0.41 0.37 YES
7 AP1S2 AP1S2 AP1S2 1467 0.32 0.38 YES
8 HCK HCK HCK 1771 0.29 0.4 YES
9 ELMO1 ELMO1 ELMO1 1850 0.28 0.43 YES
10 CD4 CD4 CD4 1968 0.27 0.46 YES
11 FYN FYN FYN 2277 0.24 0.47 YES
12 APOBEC3G APOBEC3G APOBEC3G 2730 0.21 0.47 YES
13 PSIP1 PSIP1 PSIP1 3671 0.15 0.44 NO
14 CCNT1 CCNT1 CCNT1 3868 0.14 0.44 NO
15 NUP153 NUP153 NUP153 4779 0.099 0.41 NO
16 PSMB9 PSMB9 PSMB9 5213 0.085 0.39 NO
17 AP1B1 AP1B1 AP1B1 5627 0.073 0.38 NO
18 NUP210 NUP210 NUP210 5664 0.072 0.39 NO
19 NUP50 NUP50 NUP50 5738 0.07 0.39 NO
20 AP1M1 AP1M1 AP1M1 6218 0.059 0.37 NO
21 NUP88 NUP88 NUP88 6415 0.054 0.37 NO
22 PACS1 PACS1 PACS1 6975 0.043 0.34 NO
23 NUP43 NUP43 NUP43 7120 0.041 0.34 NO
24 PAK2 PAK2 PAK2 7151 0.04 0.34 NO
25 RANBP2 RANBP2 RANBP2 7191 0.039 0.35 NO
26 B2M B2M B2M 7205 0.039 0.35 NO
27 PSME4 PSME4 PSME4 7382 0.036 0.35 NO
28 NUP188 NUP188 NUP188 7525 0.034 0.34 NO
29 PSMD5 PSMD5 PSMD5 7724 0.031 0.34 NO
30 CUL5 CUL5 CUL5 7783 0.03 0.34 NO
31 PSMB8 PSMB8 PSMB8 7798 0.03 0.34 NO
32 NUP93 NUP93 NUP93 7850 0.029 0.34 NO
33 NUP107 NUP107 NUP107 7999 0.027 0.34 NO
34 NUP155 NUP155 NUP155 8087 0.026 0.34 NO
35 NUP205 NUP205 NUP205 8092 0.026 0.34 NO
36 KPNA1 KPNA1 KPNA1 8241 0.024 0.33 NO
37 AP2M1 AP2M1 AP2M1 8816 0.017 0.3 NO
38 RBX1 RBX1 RBX1 8819 0.017 0.3 NO
39 PSMC2 PSMC2 PSMC2 9004 0.014 0.3 NO
40 UBA52 UBA52 UBA52 9019 0.014 0.3 NO
41 NUPL1 NUPL1 NUPL1 9057 0.014 0.3 NO
42 RPS27A RPS27A RPS27A 9064 0.014 0.3 NO
43 KPNB1 KPNB1 KPNB1 9084 0.014 0.3 NO
44 PSMC4 PSMC4 PSMC4 9111 0.013 0.3 NO
45 PSMD11 PSMD11 PSMD11 9198 0.012 0.3 NO
46 TPR TPR TPR 9255 0.012 0.3 NO
47 PSMA1 PSMA1 PSMA1 9453 0.0091 0.28 NO
48 BTRC BTRC BTRC 9479 0.0087 0.28 NO
49 RANBP1 RANBP1 RANBP1 9535 0.0081 0.28 NO
50 PSMD2 PSMD2 PSMD2 9603 0.0074 0.28 NO
51 RAN RAN RAN 9615 0.0073 0.28 NO
52 AP2A1 AP2A1 AP2A1 9619 0.0072 0.28 NO
53 PSMB1 PSMB1 PSMB1 9723 0.006 0.28 NO
54 SLC25A6 SLC25A6 SLC25A6 9813 0.005 0.27 NO
55 PSMD7 PSMD7 PSMD7 9846 0.0047 0.27 NO
56 NUP62 NUP62 NUP62 9880 0.0042 0.27 NO
57 PSMC5 PSMC5 PSMC5 9919 0.0037 0.27 NO
58 HLA-A HLA-A HLA-A 9949 0.0034 0.27 NO
59 PSMB2 PSMB2 PSMB2 10007 0.0026 0.26 NO
60 PSMA4 PSMA4 PSMA4 10034 0.0023 0.26 NO
61 NUP214 NUP214 NUP214 10042 0.0022 0.26 NO
62 PSMC1 PSMC1 PSMC1 10049 0.0021 0.26 NO
63 PSMB6 PSMB6 PSMB6 10144 0.0011 0.26 NO
64 NUPL2 NUPL2 NUPL2 10145 0.0011 0.26 NO
65 NUP133 NUP133 NUP133 10155 0.00099 0.26 NO
66 AP2A2 AP2A2 AP2A2 10192 0.0003 0.26 NO
67 XPO1 XPO1 XPO1 10221 -0.000073 0.25 NO
68 PSMD1 PSMD1 PSMD1 10267 -0.00062 0.25 NO
69 PSMD14 PSMD14 PSMD14 10334 -0.0012 0.25 NO
70 PSMA7 PSMA7 PSMA7 10358 -0.0015 0.25 NO
71 POM121 POM121 POM121 10368 -0.0016 0.25 NO
72 PSMA3 PSMA3 PSMA3 10432 -0.0025 0.24 NO
73 NUP37 NUP37 NUP37 10473 -0.003 0.24 NO
74 NUP85 NUP85 NUP85 10634 -0.0047 0.23 NO
75 NUP54 NUP54 NUP54 10715 -0.0055 0.23 NO
76 PSMC3 PSMC3 PSMC3 10778 -0.0061 0.23 NO
77 PSMD12 PSMD12 PSMD12 10810 -0.0065 0.23 NO
78 PSMD10 PSMD10 PSMD10 10820 -0.0066 0.23 NO
79 PSMA6 PSMA6 PSMA6 10958 -0.0083 0.22 NO
80 RAE1 RAE1 RAE1 11046 -0.0094 0.22 NO
81 AP1G1 AP1G1 AP1G1 11047 -0.0094 0.22 NO
82 PSMD13 PSMD13 PSMD13 11051 -0.0094 0.22 NO
83 AP2S1 AP2S1 AP2S1 11253 -0.012 0.21 NO
84 PSMA2 PSMA2 PSMA2 11262 -0.012 0.21 NO
85 PSMA5 PSMA5 PSMA5 11294 -0.012 0.21 NO
86 PSMD8 PSMD8 PSMD8 11503 -0.015 0.2 NO
87 NPM1 NPM1 NPM1 11555 -0.015 0.2 NO
88 TCEB1 TCEB1 TCEB1 11605 -0.016 0.2 NO
89 CDK9 CDK9 CDK9 11663 -0.017 0.2 NO
90 PSMB3 PSMB3 PSMB3 11695 -0.017 0.2 NO
91 PSMB4 PSMB4 PSMB4 11819 -0.019 0.2 NO
92 ATP6V1H ATP6V1H ATP6V1H 11834 -0.019 0.2 NO
93 AP2B1 AP2B1 AP2B1 11927 -0.02 0.19 NO
94 PSMC6 PSMC6 PSMC6 11954 -0.02 0.2 NO
95 PSMF1 PSMF1 PSMF1 11970 -0.02 0.2 NO
96 PSMD3 PSMD3 PSMD3 11986 -0.021 0.2 NO
97 PSMD9 PSMD9 PSMD9 12003 -0.021 0.2 NO
98 SEH1L SEH1L SEH1L 12051 -0.022 0.2 NO
99 PSMB5 PSMB5 PSMB5 12193 -0.024 0.2 NO
100 SKP1 SKP1 SKP1 12318 -0.025 0.19 NO
101 PSMD6 PSMD6 PSMD6 12380 -0.026 0.19 NO
102 PSMD4 PSMD4 PSMD4 12521 -0.028 0.19 NO
103 PSMB7 PSMB7 PSMB7 12649 -0.03 0.18 NO
104 PSME1 PSME1 PSME1 12893 -0.033 0.18 NO
105 AAAS AAAS AAAS 12917 -0.034 0.18 NO
106 RCC1 RCC1 RCC1 12933 -0.034 0.18 NO
107 PPIA PPIA PPIA 13030 -0.035 0.18 NO
108 SLC25A5 SLC25A5 SLC25A5 13058 -0.036 0.18 NO
109 PSME2 PSME2 PSME2 13073 -0.036 0.19 NO
110 ARF1 ARF1 ARF1 13134 -0.037 0.19 NO
111 SLC25A4 SLC25A4 SLC25A4 13190 -0.038 0.19 NO
112 BANF1 BANF1 BANF1 13207 -0.038 0.19 NO
113 PSMB10 PSMB10 PSMB10 13216 -0.038 0.2 NO
114 RANGAP1 RANGAP1 RANGAP1 13476 -0.042 0.19 NO
115 NUP35 NUP35 NUP35 13612 -0.044 0.19 NO
116 RAC1 RAC1 RAC1 14257 -0.056 0.16 NO
117 TCEB2 TCEB2 TCEB2 14921 -0.07 0.13 NO
118 HMGA1 HMGA1 HMGA1 15972 -0.1 0.088 NO
119 AP1S1 AP1S1 AP1S1 16146 -0.11 0.092 NO
120 AP1M2 AP1M2 AP1M2 18072 -0.28 0.021 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.

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

genes ES table in pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

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 SLC2A4 SLC2A4 SLC2A4 241 0.61 0.063 YES
2 FABP4 FABP4 FABP4 323 0.57 0.13 YES
3 WNT10B WNT10B WNT10B 356 0.56 0.2 YES
4 LEP LEP LEP 429 0.53 0.26 YES
5 WNT1 WNT1 WNT1 434 0.53 0.33 YES
6 ADIPOQ ADIPOQ ADIPOQ 492 0.51 0.39 YES
7 CD36 CD36 CD36 730 0.45 0.43 YES
8 PLIN1 PLIN1 PLIN1 985 0.41 0.47 YES
9 EBF1 EBF1 EBF1 1006 0.4 0.52 YES
10 LPL LPL LPL 1160 0.37 0.56 YES
11 TNF TNF TNF 1523 0.32 0.58 YES
12 PCK1 PCK1 PCK1 2243 0.25 0.57 NO
13 EGR2 EGR2 EGR2 2729 0.21 0.57 NO
14 MED13L MED13L MED13L 4644 0.1 0.48 NO
15 TGFB1 TGFB1 TGFB1 4995 0.092 0.47 NO
16 NCOA3 NCOA3 NCOA3 5544 0.076 0.45 NO
17 CEBPD CEBPD CEBPD 5666 0.072 0.45 NO
18 CDK8 CDK8 CDK8 5720 0.071 0.46 NO
19 CCND3 CCND3 CCND3 5803 0.068 0.46 NO
20 NCOA2 NCOA2 NCOA2 5822 0.068 0.47 NO
21 NR2F2 NR2F2 NR2F2 5963 0.064 0.47 NO
22 CDK19 CDK19 CDK19 6034 0.063 0.48 NO
23 NCOA1 NCOA1 NCOA1 6433 0.054 0.46 NO
24 MED27 MED27 MED27 6639 0.05 0.46 NO
25 TGS1 TGS1 TGS1 6787 0.047 0.45 NO
26 EP300 EP300 EP300 7110 0.041 0.44 NO
27 MED23 MED23 MED23 7371 0.036 0.43 NO
28 MED26 MED26 MED26 7583 0.033 0.42 NO
29 CREBBP CREBBP CREBBP 7609 0.033 0.43 NO
30 TBL1X TBL1X TBL1X 7683 0.032 0.43 NO
31 MED1 MED1 MED1 7900 0.029 0.42 NO
32 MED8 MED8 MED8 7994 0.027 0.42 NO
33 MED10 MED10 MED10 8097 0.026 0.41 NO
34 NCOR1 NCOR1 NCOR1 8410 0.022 0.4 NO
35 KLF4 KLF4 KLF4 8711 0.018 0.39 NO
36 MED4 MED4 MED4 8748 0.018 0.39 NO
37 MED17 MED17 MED17 8875 0.016 0.38 NO
38 MED31 MED31 MED31 8933 0.015 0.38 NO
39 MED12 MED12 MED12 9117 0.013 0.37 NO
40 MED22 MED22 MED22 9184 0.012 0.37 NO
41 MED14 MED14 MED14 9314 0.011 0.36 NO
42 MED15 MED15 MED15 9527 0.0081 0.35 NO
43 PPARA PPARA PPARA 9552 0.0079 0.35 NO
44 MED30 MED30 MED30 9578 0.0076 0.35 NO
45 MED18 MED18 MED18 9632 0.0071 0.35 NO
46 TBL1XR1 TBL1XR1 TBL1XR1 10002 0.0027 0.33 NO
47 CDK4 CDK4 CDK4 10053 0.002 0.33 NO
48 SMARCD3 SMARCD3 SMARCD3 10208 0.000052 0.32 NO
49 MED6 MED6 MED6 10259 -0.00046 0.32 NO
50 HDAC3 HDAC3 HDAC3 10538 -0.0036 0.3 NO
51 CEBPB CEBPB CEBPB 10592 -0.0042 0.3 NO
52 RXRA RXRA RXRA 10945 -0.0081 0.28 NO
53 MED11 MED11 MED11 11147 -0.01 0.27 NO
54 NCOR2 NCOR2 NCOR2 11190 -0.011 0.27 NO
55 RELA RELA RELA 11368 -0.013 0.26 NO
56 CCNC CCNC CCNC 11370 -0.013 0.27 NO
57 MED20 MED20 MED20 11750 -0.018 0.25 NO
58 MED29 MED29 MED29 11784 -0.018 0.25 NO
59 MED9 MED9 MED9 12348 -0.026 0.22 NO
60 MED24 MED24 MED24 12575 -0.029 0.21 NO
61 PRIC285 PRIC285 PRIC285 12710 -0.03 0.21 NO
62 NCOA6 NCOA6 NCOA6 13092 -0.036 0.19 NO
63 MED7 MED7 MED7 13197 -0.038 0.19 NO
64 SREBF1 SREBF1 SREBF1 13652 -0.045 0.17 NO
65 ANGPTL4 ANGPTL4 ANGPTL4 13784 -0.047 0.17 NO
66 PPARGC1A PPARGC1A PPARGC1A 14122 -0.053 0.16 NO
67 MED16 MED16 MED16 14787 -0.066 0.13 NO
68 MED21 MED21 MED21 14797 -0.067 0.14 NO
69 MED19 MED19 MED19 14919 -0.07 0.14 NO
70 MED25 MED25 MED25 15792 -0.097 0.11 NO
71 PPARG PPARG PPARG 16636 -0.14 0.078 NO
72 KLF5 KLF5 KLF5 17131 -0.17 0.072 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 GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.

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

genes ES table in pathway: KEGG ABC TRANSPORTERS

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 PRKCB PRKCB PRKCB 15 0.83 0.074 YES
2 CD79B CD79B CD79B 28 0.8 0.15 YES
3 CD19 CD19 CD19 66 0.75 0.21 YES
4 CD79A CD79A CD79A 85 0.73 0.28 YES
5 BLK BLK BLK 89 0.73 0.34 YES
6 BTK BTK BTK 300 0.58 0.39 YES
7 PSMA8 PSMA8 PSMA8 519 0.5 0.42 YES
8 PIK3CD PIK3CD PIK3CD 1288 0.35 0.41 YES
9 VAV1 VAV1 VAV1 1686 0.3 0.42 YES
10 PLCG2 PLCG2 PLCG2 1979 0.27 0.42 YES
11 RASGRP3 RASGRP3 RASGRP3 2155 0.25 0.44 YES
12 FYN FYN FYN 2277 0.24 0.45 YES
13 REL REL REL 2381 0.23 0.47 YES
14 MALT1 MALT1 MALT1 3005 0.18 0.45 YES
15 RASGRP1 RASGRP1 RASGRP1 3107 0.18 0.46 YES
16 FOXO1 FOXO1 FOXO1 3117 0.18 0.48 YES
17 AKT3 AKT3 AKT3 3143 0.18 0.49 YES
18 PIK3R1 PIK3R1 PIK3R1 3665 0.15 0.48 NO
19 NR4A1 NR4A1 NR4A1 4043 0.13 0.47 NO
20 ITPR2 ITPR2 ITPR2 4194 0.12 0.47 NO
21 CBL CBL CBL 4321 0.12 0.47 NO
22 PLCG1 PLCG1 PLCG1 4382 0.11 0.48 NO
23 SYK SYK SYK 4661 0.1 0.48 NO
24 LYN LYN LYN 4662 0.1 0.48 NO
25 CBLB CBLB CBLB 5043 0.091 0.47 NO
26 PSMB9 PSMB9 PSMB9 5213 0.085 0.47 NO
27 MAP3K7 MAP3K7 MAP3K7 5286 0.083 0.48 NO
28 CDKN1B CDKN1B CDKN1B 5586 0.074 0.46 NO
29 GRB2 GRB2 GRB2 5637 0.073 0.47 NO
30 SH3KBP1 SH3KBP1 SH3KBP1 5693 0.071 0.47 NO
31 FOXO3 FOXO3 FOXO3 5769 0.069 0.48 NO
32 NFKBIA NFKBIA NFKBIA 5933 0.065 0.47 NO
33 BLNK BLNK BLNK 5987 0.064 0.47 NO
34 ORAI1 ORAI1 ORAI1 6075 0.062 0.48 NO
35 SOS1 SOS1 SOS1 6304 0.057 0.47 NO
36 IKBKG IKBKG IKBKG 6342 0.056 0.47 NO
37 PTEN PTEN PTEN 6359 0.055 0.48 NO
38 MTOR MTOR MTOR 6475 0.053 0.47 NO
39 MAPKAP1 MAPKAP1 MAPKAP1 6615 0.05 0.47 NO
40 NRAS NRAS NRAS 6666 0.049 0.47 NO
41 AKT2 AKT2 AKT2 7088 0.041 0.45 NO
42 SHC1 SHC1 SHC1 7113 0.041 0.46 NO
43 STIM1 STIM1 STIM1 7183 0.04 0.46 NO
44 THEM4 THEM4 THEM4 7336 0.037 0.45 NO
45 PSME4 PSME4 PSME4 7382 0.036 0.45 NO
46 PDPK1 PDPK1 PDPK1 7413 0.036 0.45 NO
47 RICTOR RICTOR RICTOR 7449 0.035 0.45 NO
48 CALM1 CALM1 CALM1 7462 0.035 0.46 NO
49 PSMD5 PSMD5 PSMD5 7724 0.031 0.44 NO
50 CREB1 CREB1 CREB1 7776 0.03 0.44 NO
51 CHUK CHUK CHUK 7788 0.03 0.45 NO
52 PSMB8 PSMB8 PSMB8 7798 0.03 0.45 NO
53 CUL1 CUL1 CUL1 7813 0.03 0.45 NO
54 PIK3AP1 PIK3AP1 PIK3AP1 8181 0.025 0.43 NO
55 NCK1 NCK1 NCK1 8765 0.018 0.4 NO
56 CDKN1A CDKN1A CDKN1A 8818 0.017 0.4 NO
57 PSMC2 PSMC2 PSMC2 9004 0.014 0.39 NO
58 UBA52 UBA52 UBA52 9019 0.014 0.39 NO
59 RPS27A RPS27A RPS27A 9064 0.014 0.39 NO
60 PSMC4 PSMC4 PSMC4 9111 0.013 0.39 NO
61 NFKBIE NFKBIE NFKBIE 9166 0.013 0.39 NO
62 PSMD11 PSMD11 PSMD11 9198 0.012 0.39 NO
63 PSMA1 PSMA1 PSMA1 9453 0.0091 0.38 NO
64 BTRC BTRC BTRC 9479 0.0087 0.38 NO
65 PSMD2 PSMD2 PSMD2 9603 0.0074 0.37 NO
66 CALM3 CALM3 CALM3 9699 0.0063 0.36 NO
67 PSMB1 PSMB1 PSMB1 9723 0.006 0.36 NO
68 CASP9 CASP9 CASP9 9764 0.0056 0.36 NO
69 PSMD7 PSMD7 PSMD7 9846 0.0047 0.36 NO
70 PSMC5 PSMC5 PSMC5 9919 0.0037 0.36 NO
71 PSMB2 PSMB2 PSMB2 10007 0.0026 0.35 NO
72 PSMA4 PSMA4 PSMA4 10034 0.0023 0.35 NO
73 PSMC1 PSMC1 PSMC1 10049 0.0021 0.35 NO
74 PSMB6 PSMB6 PSMB6 10144 0.0011 0.34 NO
75 CARD11 CARD11 CARD11 10190 0.00031 0.34 NO
76 MDM2 MDM2 MDM2 10253 -0.00038 0.34 NO
77 PSMD1 PSMD1 PSMD1 10267 -0.00062 0.34 NO
78 PSMD14 PSMD14 PSMD14 10334 -0.0012 0.33 NO
79 PSMA7 PSMA7 PSMA7 10358 -0.0015 0.33 NO
80 PSMA3 PSMA3 PSMA3 10432 -0.0025 0.33 NO
81 IKBKB IKBKB IKBKB 10433 -0.0025 0.33 NO
82 RPS6KB2 RPS6KB2 RPS6KB2 10492 -0.0032 0.33 NO
83 PSMC3 PSMC3 PSMC3 10778 -0.0061 0.31 NO
84 PSMD12 PSMD12 PSMD12 10810 -0.0065 0.31 NO
85 PSMD10 PSMD10 PSMD10 10820 -0.0066 0.31 NO
86 PSMA6 PSMA6 PSMA6 10958 -0.0083 0.3 NO
87 PSMD13 PSMD13 PSMD13 11051 -0.0094 0.3 NO
88 NFKBIB NFKBIB NFKBIB 11160 -0.011 0.3 NO
89 FBXW11 FBXW11 FBXW11 11210 -0.011 0.29 NO
90 CALM2 CALM2 CALM2 11223 -0.011 0.29 NO
91 PSMA2 PSMA2 PSMA2 11262 -0.012 0.29 NO
92 PSMA5 PSMA5 PSMA5 11294 -0.012 0.29 NO
93 RELA RELA RELA 11368 -0.013 0.29 NO
94 AKT1 AKT1 AKT1 11471 -0.014 0.28 NO
95 PSMD8 PSMD8 PSMD8 11503 -0.015 0.28 NO
96 PSMB3 PSMB3 PSMB3 11695 -0.017 0.28 NO
97 PSMB4 PSMB4 PSMB4 11819 -0.019 0.27 NO
98 FOXO4 FOXO4 FOXO4 11946 -0.02 0.26 NO
99 PSMC6 PSMC6 PSMC6 11954 -0.02 0.27 NO
100 PSMF1 PSMF1 PSMF1 11970 -0.02 0.27 NO
101 PSMD3 PSMD3 PSMD3 11986 -0.021 0.27 NO
102 PSMD9 PSMD9 PSMD9 12003 -0.021 0.27 NO
103 PSMB5 PSMB5 PSMB5 12193 -0.024 0.26 NO
104 SKP1 SKP1 SKP1 12318 -0.025 0.26 NO
105 KRAS KRAS KRAS 12329 -0.025 0.26 NO
106 PSMD6 PSMD6 PSMD6 12380 -0.026 0.26 NO
107 TSC2 TSC2 TSC2 12427 -0.027 0.26 NO
108 PSMD4 PSMD4 PSMD4 12521 -0.028 0.26 NO
109 PSMB7 PSMB7 PSMB7 12649 -0.03 0.25 NO
110 PSME1 PSME1 PSME1 12893 -0.033 0.24 NO
111 PSME2 PSME2 PSME2 13073 -0.036 0.24 NO
112 PSMB10 PSMB10 PSMB10 13216 -0.038 0.23 NO
113 AKT1S1 AKT1S1 AKT1S1 13279 -0.039 0.23 NO
114 ITPR3 ITPR3 ITPR3 13384 -0.041 0.23 NO
115 BCL10 BCL10 BCL10 13421 -0.041 0.23 NO
116 GSK3A GSK3A GSK3A 13552 -0.043 0.23 NO
117 PHLPP1 PHLPP1 PHLPP1 14183 -0.054 0.2 NO
118 MLST8 MLST8 MLST8 14428 -0.059 0.19 NO
119 BAD BAD BAD 15149 -0.076 0.16 NO
120 HRAS HRAS HRAS 15336 -0.081 0.16 NO
121 TRIB3 TRIB3 TRIB3 17025 -0.16 0.078 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

genes ES table in pathway: KEGG MAPK SIGNALING PATHWAY

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 BLK BLK BLK 89 0.73 0.051 YES
2 MYOCD MYOCD MYOCD 456 0.52 0.072 YES
3 PIK3R5 PIK3R5 PIK3R5 601 0.48 0.1 YES
4 PIK3CG PIK3CG PIK3CG 646 0.47 0.13 YES
5 SLA SLA SLA 939 0.42 0.15 YES
6 LCK LCK LCK 951 0.41 0.18 YES
7 PIK3R6 PIK3R6 PIK3R6 975 0.41 0.21 YES
8 S1PR1 S1PR1 S1PR1 1249 0.36 0.22 YES
9 FGR FGR FGR 1275 0.36 0.25 YES
10 PIK3CD PIK3CD PIK3CD 1288 0.35 0.28 YES
11 ITGB3 ITGB3 ITGB3 1650 0.3 0.28 YES
12 HCK HCK HCK 1771 0.29 0.3 YES
13 MAPK10 MAPK10 MAPK10 1784 0.29 0.32 YES
14 FYN FYN FYN 2277 0.24 0.31 YES
15 CYFIP2 CYFIP2 CYFIP2 2422 0.23 0.32 YES
16 TAGLN TAGLN TAGLN 2718 0.21 0.32 YES
17 PAG1 PAG1 PAG1 2851 0.2 0.33 YES
18 ACTA2 ACTA2 ACTA2 3066 0.18 0.33 YES
19 DOCK4 DOCK4 DOCK4 3075 0.18 0.34 YES
20 PIK3R3 PIK3R3 PIK3R3 3095 0.18 0.36 YES
21 PPP2R2B PPP2R2B PPP2R2B 3391 0.16 0.35 YES
22 JAK2 JAK2 JAK2 3442 0.16 0.36 YES
23 SIPA1 SIPA1 SIPA1 3559 0.15 0.37 YES
24 PIK3R1 PIK3R1 PIK3R1 3665 0.15 0.37 YES
25 STAT5A STAT5A STAT5A 3679 0.15 0.38 YES
26 MYC MYC MYC 4023 0.13 0.37 YES
27 RAPGEF1 RAPGEF1 RAPGEF1 4053 0.13 0.38 YES
28 RAP1A RAP1A RAP1A 4170 0.12 0.38 YES
29 LRP1 LRP1 LRP1 4205 0.12 0.39 YES
30 ABL1 ABL1 ABL1 4232 0.12 0.4 YES
31 STAT5B STAT5B STAT5B 4237 0.12 0.41 YES
32 SRF SRF SRF 4316 0.12 0.41 YES
33 CBL CBL CBL 4321 0.12 0.42 YES
34 PLCG1 PLCG1 PLCG1 4382 0.11 0.43 YES
35 PDGFRB PDGFRB PDGFRB 4426 0.11 0.43 YES
36 CSK CSK CSK 4562 0.11 0.44 YES
37 PIK3CA PIK3CA PIK3CA 4566 0.11 0.44 YES
38 SPHK1 SPHK1 SPHK1 4572 0.11 0.45 YES
39 KSR1 KSR1 KSR1 4610 0.1 0.46 YES
40 PTPN1 PTPN1 PTPN1 4631 0.1 0.46 YES
41 LYN LYN LYN 4662 0.1 0.47 YES
42 WASF2 WASF2 WASF2 4822 0.098 0.47 YES
43 GAB1 GAB1 GAB1 4878 0.096 0.47 YES
44 DOK1 DOK1 DOK1 5240 0.084 0.46 NO
45 PRKCE PRKCE PRKCE 5301 0.082 0.46 NO
46 GRB2 GRB2 GRB2 5637 0.073 0.45 NO
47 MAP2K4 MAP2K4 MAP2K4 5776 0.069 0.45 NO
48 CRK CRK CRK 5971 0.064 0.44 NO
49 ITGAV ITGAV ITGAV 6018 0.063 0.44 NO
50 PDGFB PDGFB PDGFB 6113 0.061 0.44 NO
51 ARAP1 ARAP1 ARAP1 6220 0.059 0.44 NO
52 ACTR2 ACTR2 ACTR2 6302 0.057 0.44 NO
53 SOS1 SOS1 SOS1 6304 0.057 0.45 NO
54 ELK1 ELK1 ELK1 6322 0.056 0.45 NO
55 STAT3 STAT3 STAT3 6325 0.056 0.46 NO
56 RAP1B RAP1B RAP1B 6335 0.056 0.46 NO
57 PTEN PTEN PTEN 6359 0.055 0.46 NO
58 ACTR3 ACTR3 ACTR3 6368 0.055 0.47 NO
59 STAT1 STAT1 STAT1 6391 0.055 0.47 NO
60 NRAS NRAS NRAS 6666 0.049 0.46 NO
61 MAPK1 MAPK1 MAPK1 6760 0.048 0.46 NO
62 PTPN11 PTPN11 PTPN11 6857 0.046 0.46 NO
63 SHC1 SHC1 SHC1 7113 0.041 0.44 NO
64 ARPC2 ARPC2 ARPC2 7180 0.04 0.44 NO
65 RPS6KA3 RPS6KA3 RPS6KA3 7475 0.035 0.43 NO
66 MAP2K1 MAP2K1 MAP2K1 7825 0.03 0.41 NO
67 ARPC1B ARPC1B ARPC1B 7924 0.028 0.41 NO
68 MAPK8 MAPK8 MAPK8 8009 0.027 0.41 NO
69 RHOA RHOA RHOA 8044 0.026 0.41 NO
70 JUN JUN JUN 8203 0.024 0.4 NO
71 ARPC4 ARPC4 ARPC4 8661 0.019 0.38 NO
72 NCK1 NCK1 NCK1 8765 0.018 0.37 NO
73 RAF1 RAF1 RAF1 8915 0.016 0.37 NO
74 ABI1 ABI1 ABI1 8982 0.015 0.36 NO
75 YWHAB YWHAB YWHAB 9231 0.012 0.35 NO
76 YWHAQ YWHAQ YWHAQ 9301 0.011 0.35 NO
77 IQGAP1 IQGAP1 IQGAP1 9331 0.011 0.35 NO
78 USP6NL USP6NL USP6NL 9446 0.0091 0.34 NO
79 ARPC5 ARPC5 ARPC5 9733 0.0059 0.33 NO
80 YWHAG YWHAG YWHAG 9865 0.0044 0.32 NO
81 NCK2 NCK2 NCK2 10153 0.001 0.3 NO
82 JUND JUND JUND 10350 -0.0014 0.29 NO
83 FOS FOS FOS 10406 -0.002 0.29 NO
84 PRKCA PRKCA PRKCA 10424 -0.0024 0.29 NO
85 YWHAH YWHAH YWHAH 10537 -0.0036 0.28 NO
86 ARPC3 ARPC3 ARPC3 10915 -0.0078 0.26 NO
87 PPP2CA PPP2CA PPP2CA 10982 -0.0085 0.26 NO
88 PTPRJ PTPRJ PTPRJ 10991 -0.0086 0.26 NO
89 BRAF BRAF BRAF 11009 -0.0088 0.26 NO
90 ARHGDIA ARHGDIA ARHGDIA 11338 -0.013 0.24 NO
91 MAPK9 MAPK9 MAPK9 11534 -0.015 0.24 NO
92 PTPN2 PTPN2 PTPN2 11642 -0.016 0.23 NO
93 EIF2AK2 EIF2AK2 EIF2AK2 12043 -0.022 0.21 NO
94 PIN1 PIN1 PIN1 12148 -0.023 0.21 NO
95 GRB10 GRB10 GRB10 12172 -0.023 0.21 NO
96 EPS8 EPS8 EPS8 12191 -0.023 0.21 NO
97 RAB5A RAB5A RAB5A 12258 -0.024 0.21 NO
98 KRAS KRAS KRAS 12329 -0.025 0.2 NO
99 NCKAP1 NCKAP1 NCKAP1 12462 -0.028 0.2 NO
100 YWHAE YWHAE YWHAE 12536 -0.028 0.2 NO
101 RASA1 RASA1 RASA1 12790 -0.032 0.19 NO
102 ACTN4 ACTN4 ACTN4 12818 -0.032 0.19 NO
103 PPP2R1A PPP2R1A PPP2R1A 12853 -0.033 0.19 NO
104 YWHAZ YWHAZ YWHAZ 12968 -0.034 0.18 NO
105 MAP2K7 MAP2K7 MAP2K7 13008 -0.035 0.18 NO
106 PIK3R2 PIK3R2 PIK3R2 13595 -0.044 0.16 NO
107 PLA2G4A PLA2G4A PLA2G4A 13643 -0.045 0.16 NO
108 MAP2K2 MAP2K2 MAP2K2 13732 -0.046 0.16 NO
109 MAPK3 MAPK3 MAPK3 13954 -0.05 0.15 NO
110 DNM2 DNM2 DNM2 13970 -0.05 0.15 NO
111 RAB4A RAB4A RAB4A 14030 -0.051 0.15 NO
112 PIK3CB PIK3CB PIK3CB 14087 -0.053 0.15 NO
113 CTTN CTTN CTTN 14118 -0.053 0.16 NO
114 YES1 YES1 YES1 14159 -0.054 0.16 NO
115 MLLT4 MLLT4 MLLT4 14249 -0.056 0.16 NO
116 RAC1 RAC1 RAC1 14257 -0.056 0.16 NO
117 VAV2 VAV2 VAV2 14315 -0.057 0.16 NO
118 PRKCD PRKCD PRKCD 14668 -0.064 0.15 NO
119 BAIAP2 BAIAP2 BAIAP2 14695 -0.064 0.15 NO
120 WASL WASL WASL 14725 -0.065 0.15 NO
121 HRAS HRAS HRAS 15336 -0.081 0.13 NO
122 BCAR1 BCAR1 BCAR1 15338 -0.081 0.13 NO
123 SLC9A3R2 SLC9A3R2 SLC9A3R2 15395 -0.083 0.14 NO
124 SRC SRC SRC 15811 -0.098 0.12 NO
125 PAK1 PAK1 PAK1 15818 -0.098 0.13 NO
126 SFN SFN SFN 15853 -0.099 0.13 NO
127 SLC9A3R1 SLC9A3R1 SLC9A3R1 15897 -0.1 0.14 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

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

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 ACAP1 ACAP1 ACAP1 219 0.62 0.064 YES
2 SLC2A4 SLC2A4 SLC2A4 241 0.61 0.14 YES
3 ITGA8 ITGA8 ITGA8 251 0.6 0.21 YES
4 IL2RA IL2RA IL2RA 513 0.5 0.26 YES
5 ADRB2 ADRB2 ADRB2 563 0.49 0.32 YES
6 TSHR TSHR TSHR 651 0.47 0.37 YES
7 ITGA4 ITGA4 ITGA4 738 0.45 0.42 YES
8 AGTR1 AGTR1 AGTR1 773 0.44 0.47 YES
9 ITGA9 ITGA9 ITGA9 886 0.43 0.52 YES
10 AVPR2 AVPR2 AVPR2 911 0.42 0.57 YES
11 ITGA7 ITGA7 ITGA7 927 0.42 0.62 YES
12 EDNRB EDNRB EDNRB 1158 0.37 0.65 YES
13 ITGA5 ITGA5 ITGA5 3199 0.17 0.56 NO
14 ITGA11 ITGA11 ITGA11 3666 0.15 0.55 NO
15 ITGA1 ITGA1 ITGA1 3674 0.15 0.57 NO
16 ITGA10 ITGA10 ITGA10 4073 0.13 0.56 NO
17 BIN1 BIN1 BIN1 5191 0.086 0.51 NO
18 EXOC2 EXOC2 EXOC2 5791 0.069 0.49 NO
19 ITGAV ITGAV ITGAV 6018 0.063 0.49 NO
20 EXOC5 EXOC5 EXOC5 6057 0.062 0.49 NO
21 SPAG9 SPAG9 SPAG9 6298 0.057 0.48 NO
22 CPE CPE CPE 7002 0.043 0.45 NO
23 PIP5K1C PIP5K1C PIP5K1C 7422 0.036 0.43 NO
24 KLC1 KLC1 KLC1 8305 0.023 0.39 NO
25 ITGB1 ITGB1 ITGB1 8861 0.016 0.36 NO
26 VAMP3 VAMP3 VAMP3 9010 0.014 0.35 NO
27 PLD2 PLD2 PLD2 9273 0.012 0.34 NO
28 CLTC CLTC CLTC 9478 0.0087 0.33 NO
29 CTNNB1 CTNNB1 CTNNB1 10027 0.0024 0.3 NO
30 ARF6 ARF6 ARF6 10206 0.000091 0.29 NO
31 EXOC3 EXOC3 EXOC3 10652 -0.0049 0.27 NO
32 EXOC7 EXOC7 EXOC7 10738 -0.0057 0.26 NO
33 RALA RALA RALA 11202 -0.011 0.24 NO
34 EXOC1 EXOC1 EXOC1 11486 -0.015 0.23 NO
35 SCAMP2 SCAMP2 SCAMP2 12551 -0.028 0.17 NO
36 EXOC6 EXOC6 EXOC6 12787 -0.032 0.16 NO
37 MAPK8IP3 MAPK8IP3 MAPK8IP3 13428 -0.042 0.14 NO
38 NME1 NME1 NME1 13661 -0.045 0.13 NO
39 EXOC4 EXOC4 EXOC4 13714 -0.046 0.13 NO
40 CTNNA1 CTNNA1 CTNNA1 13909 -0.049 0.13 NO
41 DNM2 DNM2 DNM2 13970 -0.05 0.13 NO
42 ITGA6 ITGA6 ITGA6 15136 -0.076 0.075 NO
43 PLD1 PLD1 PLD1 15247 -0.079 0.078 NO
44 CTNND1 CTNND1 CTNND1 15597 -0.09 0.07 NO
45 ASAP2 ASAP2 ASAP2 16053 -0.11 0.059 NO
46 INS INS INS 16363 -0.12 0.057 NO
47 ITGA2 ITGA2 ITGA2 16476 -0.13 0.066 NO
48 ITGA3 ITGA3 ITGA3 17082 -0.17 0.054 NO
49 CDH1 CDH1 CDH1 17168 -0.17 0.07 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 CYTOKINE CYTOKINE RECEPTOR INTERACTION.

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

genes ES table in pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

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 CD28 CD28 CD28 64 0.76 0.056 YES
2 CD247 CD247 CD247 210 0.62 0.098 YES
3 CD8B CD8B CD8B 261 0.6 0.14 YES
4 CCR5 CCR5 CCR5 473 0.52 0.17 YES
5 PSMA8 PSMA8 PSMA8 519 0.5 0.21 YES
6 DOCK2 DOCK2 DOCK2 575 0.49 0.24 YES
7 LCK LCK LCK 951 0.41 0.26 YES
8 CXCR4 CXCR4 CXCR4 1355 0.34 0.26 YES
9 AP1S2 AP1S2 AP1S2 1467 0.32 0.28 YES
10 HCK HCK HCK 1771 0.29 0.29 YES
11 ELMO1 ELMO1 ELMO1 1850 0.28 0.31 YES
12 CD4 CD4 CD4 1968 0.27 0.32 YES
13 TAF4B TAF4B TAF4B 2025 0.26 0.34 YES
14 FYN FYN FYN 2277 0.24 0.34 YES
15 APOBEC3G APOBEC3G APOBEC3G 2730 0.21 0.34 YES
16 RNGTT RNGTT RNGTT 2951 0.19 0.34 YES
17 PSIP1 PSIP1 PSIP1 3671 0.15 0.31 YES
18 TAF13 TAF13 TAF13 3699 0.14 0.32 YES
19 GTF2H2B GTF2H2B GTF2H2B 3725 0.14 0.33 YES
20 GTF2H2 GTF2H2 GTF2H2 3759 0.14 0.34 YES
21 CCNT1 CCNT1 CCNT1 3868 0.14 0.35 YES
22 TAF5 TAF5 TAF5 4565 0.11 0.32 NO
23 NUP153 NUP153 NUP153 4779 0.099 0.31 NO
24 GTF2E1 GTF2E1 GTF2E1 5075 0.089 0.3 NO
25 PSMB9 PSMB9 PSMB9 5213 0.085 0.3 NO
26 GTF2A1 GTF2A1 GTF2A1 5255 0.084 0.31 NO
27 GTF2H3 GTF2H3 GTF2H3 5597 0.074 0.3 NO
28 AP1B1 AP1B1 AP1B1 5627 0.073 0.3 NO
29 NUP210 NUP210 NUP210 5664 0.072 0.3 NO
30 NUP50 NUP50 NUP50 5738 0.07 0.3 NO
31 TBP TBP TBP 5990 0.064 0.3 NO
32 ELL ELL ELL 6040 0.063 0.3 NO
33 AP1M1 AP1M1 AP1M1 6218 0.059 0.29 NO
34 CTDP1 CTDP1 CTDP1 6236 0.058 0.3 NO
35 NUP88 NUP88 NUP88 6415 0.054 0.29 NO
36 LIG4 LIG4 LIG4 6438 0.054 0.29 NO
37 GTF2H1 GTF2H1 GTF2H1 6885 0.045 0.27 NO
38 TAF12 TAF12 TAF12 6911 0.044 0.28 NO
39 PACS1 PACS1 PACS1 6975 0.043 0.28 NO
40 TAF1 TAF1 TAF1 7095 0.041 0.27 NO
41 NUP43 NUP43 NUP43 7120 0.041 0.27 NO
42 PAK2 PAK2 PAK2 7151 0.04 0.28 NO
43 RANBP2 RANBP2 RANBP2 7191 0.039 0.28 NO
44 B2M B2M B2M 7205 0.039 0.28 NO
45 POLR2B POLR2B POLR2B 7268 0.038 0.28 NO
46 PSME4 PSME4 PSME4 7382 0.036 0.28 NO
47 TAF11 TAF11 TAF11 7444 0.035 0.28 NO
48 NUP188 NUP188 NUP188 7525 0.034 0.27 NO
49 PSMD5 PSMD5 PSMD5 7724 0.031 0.26 NO
50 CUL5 CUL5 CUL5 7783 0.03 0.26 NO
51 PSMB8 PSMB8 PSMB8 7798 0.03 0.26 NO
52 VPS37A VPS37A VPS37A 7815 0.03 0.27 NO
53 NUP93 NUP93 NUP93 7850 0.029 0.27 NO
54 POLR2A POLR2A POLR2A 7855 0.029 0.27 NO
55 SUPT16H SUPT16H SUPT16H 7920 0.028 0.27 NO
56 TCEB3 TCEB3 TCEB3 7960 0.028 0.27 NO
57 NUP107 NUP107 NUP107 7999 0.027 0.27 NO
58 NUP155 NUP155 NUP155 8087 0.026 0.27 NO
59 NUP205 NUP205 NUP205 8092 0.026 0.27 NO
60 KPNA1 KPNA1 KPNA1 8241 0.024 0.26 NO
61 RNMT RNMT RNMT 8299 0.023 0.26 NO
62 NMT2 NMT2 NMT2 8682 0.018 0.24 NO
63 NCBP2 NCBP2 NCBP2 8736 0.018 0.24 NO
64 FEN1 FEN1 FEN1 8791 0.017 0.24 NO
65 AP2M1 AP2M1 AP2M1 8816 0.017 0.24 NO
66 RBX1 RBX1 RBX1 8819 0.017 0.24 NO
67 CCNH CCNH CCNH 8948 0.015 0.23 NO
68 PSMC2 PSMC2 PSMC2 9004 0.014 0.23 NO
69 SUPT4H1 SUPT4H1 SUPT4H1 9016 0.014 0.23 NO
70 UBA52 UBA52 UBA52 9019 0.014 0.23 NO
71 POLR2D POLR2D POLR2D 9042 0.014 0.23 NO
72 NUPL1 NUPL1 NUPL1 9057 0.014 0.23 NO
73 RPS27A RPS27A RPS27A 9064 0.014 0.23 NO
74 KPNB1 KPNB1 KPNB1 9084 0.014 0.23 NO
75 PSMC4 PSMC4 PSMC4 9111 0.013 0.23 NO
76 POLR2G POLR2G POLR2G 9186 0.012 0.23 NO
77 NMT1 NMT1 NMT1 9193 0.012 0.23 NO
78 PSMD11 PSMD11 PSMD11 9198 0.012 0.23 NO
79 ERCC3 ERCC3 ERCC3 9211 0.012 0.23 NO
80 TPR TPR TPR 9255 0.012 0.23 NO
81 PSMA1 PSMA1 PSMA1 9453 0.0091 0.22 NO
82 BTRC BTRC BTRC 9479 0.0087 0.22 NO
83 RANBP1 RANBP1 RANBP1 9535 0.0081 0.22 NO
84 NCBP1 NCBP1 NCBP1 9543 0.008 0.22 NO
85 PSMD2 PSMD2 PSMD2 9603 0.0074 0.22 NO
86 XRCC6 XRCC6 XRCC6 9614 0.0073 0.22 NO
87 RAN RAN RAN 9615 0.0073 0.22 NO
88 AP2A1 AP2A1 AP2A1 9619 0.0072 0.22 NO
89 PSMB1 PSMB1 PSMB1 9723 0.006 0.21 NO
90 CCNT2 CCNT2 CCNT2 9784 0.0054 0.21 NO
91 SLC25A6 SLC25A6 SLC25A6 9813 0.005 0.21 NO
92 PSMD7 PSMD7 PSMD7 9846 0.0047 0.2 NO
93 NUP62 NUP62 NUP62 9880 0.0042 0.2 NO
94 PSMC5 PSMC5 PSMC5 9919 0.0037 0.2 NO
95 HLA-A HLA-A HLA-A 9949 0.0034 0.2 NO
96 PSMB2 PSMB2 PSMB2 10007 0.0026 0.2 NO
97 PSMA4 PSMA4 PSMA4 10034 0.0023 0.2 NO
98 NUP214 NUP214 NUP214 10042 0.0022 0.2 NO
99 PSMC1 PSMC1 PSMC1 10049 0.0021 0.2 NO
100 PSMB6 PSMB6 PSMB6 10144 0.0011 0.19 NO
101 NUPL2 NUPL2 NUPL2 10145 0.0011 0.19 NO
102 NUP133 NUP133 NUP133 10155 0.00099 0.19 NO
103 GTF2B GTF2B GTF2B 10183 0.00041 0.19 NO
104 AP2A2 AP2A2 AP2A2 10192 0.0003 0.19 NO
105 XPO1 XPO1 XPO1 10221 -0.000073 0.19 NO
106 PSMD1 PSMD1 PSMD1 10267 -0.00062 0.18 NO
107 TCEA1 TCEA1 TCEA1 10272 -0.00067 0.18 NO
108 PSMD14 PSMD14 PSMD14 10334 -0.0012 0.18 NO
109 PSMA7 PSMA7 PSMA7 10358 -0.0015 0.18 NO
110 POM121 POM121 POM121 10368 -0.0016 0.18 NO
111 PSMA3 PSMA3 PSMA3 10432 -0.0025 0.18 NO
112 NUP37 NUP37 NUP37 10473 -0.003 0.18 NO
113 NUP85 NUP85 NUP85 10634 -0.0047 0.17 NO
114 NUP54 NUP54 NUP54 10715 -0.0055 0.16 NO
115 PSMC3 PSMC3 PSMC3 10778 -0.0061 0.16 NO
116 PSMD12 PSMD12 PSMD12 10810 -0.0065 0.16 NO
117 PSMD10 PSMD10 PSMD10 10820 -0.0066 0.16 NO
118 POLR2E POLR2E POLR2E 10838 -0.0068 0.16 NO
119 SUPT5H SUPT5H SUPT5H 10883 -0.0074 0.16 NO
120 PSMA6 PSMA6 PSMA6 10958 -0.0083 0.15 NO
121 RAE1 RAE1 RAE1 11046 -0.0094 0.15 NO
122 AP1G1 AP1G1 AP1G1 11047 -0.0094 0.15 NO
123 PSMD13 PSMD13 PSMD13 11051 -0.0094 0.15 NO
124 XRCC5 XRCC5 XRCC5 11121 -0.01 0.15 NO
125 AP2S1 AP2S1 AP2S1 11253 -0.012 0.14 NO
126 PSMA2 PSMA2 PSMA2 11262 -0.012 0.14 NO
127 PSMA5 PSMA5 PSMA5 11294 -0.012 0.14 NO
128 XRCC4 XRCC4 XRCC4 11438 -0.014 0.13 NO
129 POLR2F POLR2F POLR2F 11456 -0.014 0.13 NO
130 TAF9 TAF9 TAF9 11462 -0.014 0.14 NO
131 POLR2K POLR2K POLR2K 11485 -0.015 0.14 NO
132 PSMD8 PSMD8 PSMD8 11503 -0.015 0.14 NO
133 NPM1 NPM1 NPM1 11555 -0.015 0.13 NO
134 TCEB1 TCEB1 TCEB1 11605 -0.016 0.13 NO
135 CDK9 CDK9 CDK9 11663 -0.017 0.13 NO
136 PSMB3 PSMB3 PSMB3 11695 -0.017 0.13 NO
137 ERCC2 ERCC2 ERCC2 11764 -0.018 0.13 NO
138 GTF2A2 GTF2A2 GTF2A2 11772 -0.018 0.13 NO
139 GTF2H4 GTF2H4 GTF2H4 11781 -0.018 0.13 NO
140 PSMB4 PSMB4 PSMB4 11819 -0.019 0.13 NO
141 ATP6V1H ATP6V1H ATP6V1H 11834 -0.019 0.13 NO
142 AP2B1 AP2B1 AP2B1 11927 -0.02 0.13 NO
143 PSMC6 PSMC6 PSMC6 11954 -0.02 0.13 NO
144 PSMF1 PSMF1 PSMF1 11970 -0.02 0.13 NO
145 PSMD3 PSMD3 PSMD3 11986 -0.021 0.13 NO
146 PSMD9 PSMD9 PSMD9 12003 -0.021 0.13 NO
147 SEH1L SEH1L SEH1L 12051 -0.022 0.13 NO
148 PSMB5 PSMB5 PSMB5 12193 -0.024 0.12 NO
149 LIG1 LIG1 LIG1 12246 -0.024 0.12 NO
150 SSRP1 SSRP1 SSRP1 12313 -0.025 0.12 NO
151 SKP1 SKP1 SKP1 12318 -0.025 0.12 NO
152 GTF2F2 GTF2F2 GTF2F2 12340 -0.026 0.12 NO
153 PSMD6 PSMD6 PSMD6 12380 -0.026 0.12 NO
154 GTF2F1 GTF2F1 GTF2F1 12504 -0.028 0.12 NO
155 PSMD4 PSMD4 PSMD4 12521 -0.028 0.12 NO
156 TAF6 TAF6 TAF6 12625 -0.03 0.12 NO
157 PSMB7 PSMB7 PSMB7 12649 -0.03 0.12 NO
158 PSME1 PSME1 PSME1 12893 -0.033 0.11 NO
159 AAAS AAAS AAAS 12917 -0.034 0.11 NO
160 POLR2C POLR2C POLR2C 12930 -0.034 0.11 NO
161 RCC1 RCC1 RCC1 12933 -0.034 0.11 NO
162 TH1L TH1L TH1L 12944 -0.034 0.12 NO
163 VPS37C VPS37C VPS37C 12974 -0.035 0.12 NO
164 PPIA PPIA PPIA 13030 -0.035 0.12 NO
165 SLC25A5 SLC25A5 SLC25A5 13058 -0.036 0.12 NO
166 PSME2 PSME2 PSME2 13073 -0.036 0.12 NO
167 ARF1 ARF1 ARF1 13134 -0.037 0.12 NO
168 SLC25A4 SLC25A4 SLC25A4 13190 -0.038 0.12 NO
169 BANF1 BANF1 BANF1 13207 -0.038 0.12 NO
170 PSMB10 PSMB10 PSMB10 13216 -0.038 0.12 NO
171 RANGAP1 RANGAP1 RANGAP1 13476 -0.042 0.11 NO
172 COBRA1 COBRA1 COBRA1 13480 -0.042 0.12 NO
173 RDBP RDBP RDBP 13512 -0.043 0.12 NO
174 NUP35 NUP35 NUP35 13612 -0.044 0.12 NO
175 GTF2E2 GTF2E2 GTF2E2 13727 -0.046 0.11 NO
176 TAF4 TAF4 TAF4 13745 -0.047 0.12 NO
177 TAF10 TAF10 TAF10 13812 -0.048 0.12 NO
178 TSG101 TSG101 TSG101 14080 -0.052 0.11 NO
179 RAC1 RAC1 RAC1 14257 -0.056 0.1 NO
180 VPS28 VPS28 VPS28 14480 -0.06 0.093 NO
181 WHSC2 WHSC2 WHSC2 14571 -0.062 0.093 NO
182 VPS37B VPS37B VPS37B 14836 -0.068 0.084 NO
183 TCEB2 TCEB2 TCEB2 14921 -0.07 0.085 NO
184 POLR2L POLR2L POLR2L 14979 -0.072 0.087 NO
185 POLR2J POLR2J POLR2J 15195 -0.077 0.082 NO
186 CDK7 CDK7 CDK7 15298 -0.08 0.082 NO
187 MNAT1 MNAT1 MNAT1 15476 -0.086 0.08 NO
188 POLR2H POLR2H POLR2H 15663 -0.092 0.077 NO
189 POLR2I POLR2I POLR2I 15801 -0.097 0.077 NO
190 HMGA1 HMGA1 HMGA1 15972 -0.1 0.076 NO
191 AP1S1 AP1S1 AP1S1 16146 -0.11 0.075 NO
192 AP1M2 AP1M2 AP1M2 18072 -0.28 -0.0085 NO
193 VPS37D VPS37D VPS37D 18359 -0.37 0.0054 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 PHOSPHATIDYLINOSITOL SIGNALING SYSTEM.

Figure S92.  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

genes ES table in pathway: KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION

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 CD28 CD28 CD28 64 0.76 0.14 YES
2 CD247 CD247 CD247 210 0.62 0.26 YES
3 CD8B CD8B CD8B 261 0.6 0.37 YES
4 DOCK2 DOCK2 DOCK2 575 0.49 0.45 YES
5 LCK LCK LCK 951 0.41 0.51 YES
6 AP1S2 AP1S2 AP1S2 1467 0.32 0.55 YES
7 HCK HCK HCK 1771 0.29 0.59 YES
8 ELMO1 ELMO1 ELMO1 1850 0.28 0.64 YES
9 CD4 CD4 CD4 1968 0.27 0.68 YES
10 FYN FYN FYN 2277 0.24 0.72 YES
11 AP1B1 AP1B1 AP1B1 5627 0.073 0.55 NO
12 AP1M1 AP1M1 AP1M1 6218 0.059 0.53 NO
13 PACS1 PACS1 PACS1 6975 0.043 0.5 NO
14 PAK2 PAK2 PAK2 7151 0.04 0.49 NO
15 B2M B2M B2M 7205 0.039 0.5 NO
16 AP2M1 AP2M1 AP2M1 8816 0.017 0.42 NO
17 AP2A1 AP2A1 AP2A1 9619 0.0072 0.37 NO
18 HLA-A HLA-A HLA-A 9949 0.0034 0.36 NO
19 AP2A2 AP2A2 AP2A2 10192 0.0003 0.34 NO
20 AP1G1 AP1G1 AP1G1 11047 -0.0094 0.3 NO
21 AP2S1 AP2S1 AP2S1 11253 -0.012 0.29 NO
22 ATP6V1H ATP6V1H ATP6V1H 11834 -0.019 0.26 NO
23 AP2B1 AP2B1 AP2B1 11927 -0.02 0.26 NO
24 ARF1 ARF1 ARF1 13134 -0.037 0.2 NO
25 RAC1 RAC1 RAC1 14257 -0.056 0.15 NO
26 AP1S1 AP1S1 AP1S1 16146 -0.11 0.071 NO
27 AP1M2 AP1M2 AP1M2 18072 -0.28 0.021 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 NEUROACTIVE LIGAND RECEPTOR INTERACTION.

Figure S94.  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

genes ES table in pathway: KEGG OOCYTE MEIOSIS

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 NTRK3 NTRK3 NTRK3 117 0.7 0.044 YES
2 NGF NGF NGF 287 0.59 0.078 YES
3 CAMK2A CAMK2A CAMK2A 330 0.57 0.12 YES
4 NGFR NGFR NGFR 482 0.51 0.14 YES
5 FASLG FASLG FASLG 493 0.51 0.18 YES
6 PIK3R5 PIK3R5 PIK3R5 601 0.48 0.21 YES
7 PIK3CG PIK3CG PIK3CG 646 0.47 0.24 YES
8 CAMK4 CAMK4 CAMK4 767 0.44 0.27 YES
9 BCL2 BCL2 BCL2 824 0.44 0.3 YES
10 SHC4 SHC4 SHC4 826 0.44 0.33 YES
11 PIK3CD PIK3CD PIK3CD 1288 0.35 0.33 YES
12 NTRK1 NTRK1 NTRK1 1397 0.34 0.35 YES
13 MAPK10 MAPK10 MAPK10 1784 0.29 0.35 YES
14 RPS6KA5 RPS6KA5 RPS6KA5 1839 0.28 0.36 YES
15 PLCG2 PLCG2 PLCG2 1979 0.27 0.38 YES
16 NTF3 NTF3 NTF3 2349 0.24 0.37 YES
17 SH2B2 SH2B2 SH2B2 2596 0.22 0.38 YES
18 MAPK11 MAPK11 MAPK11 2800 0.2 0.38 YES
19 MAP3K3 MAP3K3 MAP3K3 3041 0.18 0.38 YES
20 PIK3R3 PIK3R3 PIK3R3 3095 0.18 0.39 YES
21 ARHGDIB ARHGDIB ARHGDIB 3119 0.18 0.4 YES
22 SH2B3 SH2B3 SH2B3 3131 0.18 0.41 YES
23 AKT3 AKT3 AKT3 3143 0.18 0.42 YES
24 NTRK2 NTRK2 NTRK2 3150 0.18 0.44 YES
25 MAPK12 MAPK12 MAPK12 3158 0.18 0.45 YES
26 IRAK3 IRAK3 IRAK3 3440 0.16 0.45 NO
27 PIK3R1 PIK3R1 PIK3R1 3665 0.15 0.44 NO
28 RAPGEF1 RAPGEF1 RAPGEF1 4053 0.13 0.43 NO
29 RAP1A RAP1A RAP1A 4170 0.12 0.44 NO
30 ABL1 ABL1 ABL1 4232 0.12 0.44 NO
31 PLCG1 PLCG1 PLCG1 4382 0.11 0.44 NO
32 CSK CSK CSK 4562 0.11 0.44 NO
33 PIK3CA PIK3CA PIK3CA 4566 0.11 0.45 NO
34 GAB1 GAB1 GAB1 4878 0.096 0.44 NO
35 BDNF BDNF BDNF 4917 0.095 0.44 NO
36 IRAK4 IRAK4 IRAK4 5169 0.086 0.43 NO
37 GRB2 GRB2 GRB2 5637 0.073 0.41 NO
38 FOXO3 FOXO3 FOXO3 5769 0.069 0.41 NO
39 NFKBIA NFKBIA NFKBIA 5933 0.065 0.41 NO
40 CRK CRK CRK 5971 0.064 0.41 NO
41 PDK1 PDK1 PDK1 6033 0.063 0.41 NO
42 MAPK7 MAPK7 MAPK7 6234 0.058 0.4 NO
43 SOS1 SOS1 SOS1 6304 0.057 0.4 NO
44 NFKB1 NFKB1 NFKB1 6320 0.056 0.41 NO
45 RAP1B RAP1B RAP1B 6335 0.056 0.41 NO
46 MAP3K1 MAP3K1 MAP3K1 6339 0.056 0.42 NO
47 TP53 TP53 TP53 6618 0.05 0.4 NO
48 NRAS NRAS NRAS 6666 0.049 0.4 NO
49 MAPK1 MAPK1 MAPK1 6760 0.048 0.4 NO
50 RPS6KA6 RPS6KA6 RPS6KA6 6794 0.047 0.4 NO
51 PTPN11 PTPN11 PTPN11 6857 0.046 0.4 NO
52 RPS6KA2 RPS6KA2 RPS6KA2 6858 0.046 0.41 NO
53 TRAF6 TRAF6 TRAF6 6878 0.045 0.41 NO
54 CAMK2G CAMK2G CAMK2G 6893 0.045 0.41 NO
55 FRS2 FRS2 FRS2 6932 0.044 0.41 NO
56 PRDM4 PRDM4 PRDM4 7012 0.043 0.41 NO
57 MAPKAPK2 MAPKAPK2 MAPKAPK2 7057 0.042 0.41 NO
58 AKT2 AKT2 AKT2 7088 0.041 0.41 NO
59 SHC1 SHC1 SHC1 7113 0.041 0.42 NO
60 MAPK14 MAPK14 MAPK14 7186 0.039 0.42 NO
61 MAP2K5 MAP2K5 MAP2K5 7204 0.039 0.42 NO
62 KIDINS220 KIDINS220 KIDINS220 7247 0.038 0.42 NO
63 CRKL CRKL CRKL 7369 0.036 0.41 NO
64 CALM1 CALM1 CALM1 7462 0.035 0.41 NO
65 RPS6KA3 RPS6KA3 RPS6KA3 7475 0.035 0.41 NO
66 CAMK2D CAMK2D CAMK2D 7560 0.034 0.41 NO
67 CDC42 CDC42 CDC42 7621 0.032 0.41 NO
68 MAP2K1 MAP2K1 MAP2K1 7825 0.03 0.4 NO
69 MAPK8 MAPK8 MAPK8 8009 0.027 0.39 NO
70 RHOA RHOA RHOA 8044 0.026 0.39 NO
71 SOS2 SOS2 SOS2 8100 0.026 0.39 NO
72 JUN JUN JUN 8203 0.024 0.39 NO
73 RIPK2 RIPK2 RIPK2 8274 0.024 0.39 NO
74 IRS2 IRS2 IRS2 8551 0.02 0.37 NO
75 RPS6KA1 RPS6KA1 RPS6KA1 8864 0.016 0.36 NO
76 RAF1 RAF1 RAF1 8915 0.016 0.36 NO
77 NFKBIE NFKBIE NFKBIE 9166 0.013 0.34 NO
78 YWHAB YWHAB YWHAB 9231 0.012 0.34 NO
79 YWHAQ YWHAQ YWHAQ 9301 0.011 0.34 NO
80 CALM3 CALM3 CALM3 9699 0.0063 0.32 NO
81 MAGED1 MAGED1 MAGED1 9831 0.0049 0.31 NO
82 YWHAG YWHAG YWHAG 9865 0.0044 0.31 NO
83 ZNF274 ZNF274 ZNF274 9904 0.004 0.3 NO
84 IKBKB IKBKB IKBKB 10433 -0.0025 0.28 NO
85 GSK3B GSK3B GSK3B 10472 -0.003 0.28 NO
86 YWHAH YWHAH YWHAH 10537 -0.0036 0.27 NO
87 CALML5 CALML5 CALML5 10748 -0.0058 0.26 NO
88 ATF4 ATF4 ATF4 10955 -0.0082 0.25 NO
89 BRAF BRAF BRAF 11009 -0.0088 0.25 NO
90 IRS1 IRS1 IRS1 11125 -0.01 0.24 NO
91 NFKBIB NFKBIB NFKBIB 11160 -0.011 0.24 NO
92 CALM2 CALM2 CALM2 11223 -0.011 0.24 NO
93 ARHGDIA ARHGDIA ARHGDIA 11338 -0.013 0.23 NO
94 IRAK1 IRAK1 IRAK1 11360 -0.013 0.23 NO
95 RELA RELA RELA 11368 -0.013 0.23 NO
96 AKT1 AKT1 AKT1 11471 -0.014 0.23 NO
97 MAPK9 MAPK9 MAPK9 11534 -0.015 0.23 NO
98 NGFRAP1 NGFRAP1 NGFRAP1 11568 -0.015 0.23 NO
99 SORT1 SORT1 SORT1 11681 -0.017 0.22 NO
100 BAX BAX BAX 12198 -0.024 0.2 NO
101 KRAS KRAS KRAS 12329 -0.025 0.19 NO
102 SH2B1 SH2B1 SH2B1 12361 -0.026 0.19 NO
103 RPS6KA4 RPS6KA4 RPS6KA4 12461 -0.027 0.19 NO
104 YWHAE YWHAE YWHAE 12536 -0.028 0.18 NO
105 YWHAZ YWHAZ YWHAZ 12968 -0.034 0.16 NO
106 MAP2K7 MAP2K7 MAP2K7 13008 -0.035 0.16 NO
107 MAP3K5 MAP3K5 MAP3K5 13086 -0.036 0.16 NO
108 CAMK2B CAMK2B CAMK2B 13138 -0.037 0.16 NO
109 PSEN1 PSEN1 PSEN1 13331 -0.04 0.15 NO
110 PIK3R2 PIK3R2 PIK3R2 13595 -0.044 0.14 NO
111 MAP2K2 MAP2K2 MAP2K2 13732 -0.046 0.14 NO
112 IRAK2 IRAK2 IRAK2 13762 -0.047 0.14 NO
113 MAPK3 MAPK3 MAPK3 13954 -0.05 0.13 NO
114 PIK3CB PIK3CB PIK3CB 14087 -0.053 0.13 NO
115 RAC1 RAC1 RAC1 14257 -0.056 0.12 NO
116 CALML3 CALML3 CALML3 14663 -0.064 0.11 NO
117 PRKCD PRKCD PRKCD 14668 -0.064 0.11 NO
118 BAD BAD BAD 15149 -0.076 0.092 NO
119 HRAS HRAS HRAS 15336 -0.081 0.087 NO
120 TP73 TP73 TP73 15409 -0.084 0.09 NO
121 IRS4 IRS4 IRS4 15884 -0.1 0.071 NO
122 MAPK13 MAPK13 MAPK13 16305 -0.12 0.056 NO
123 CALML6 CALML6 CALML6 16403 -0.12 0.06 NO
124 SHC2 SHC2 SHC2 17019 -0.16 0.038 NO
125 SHC3 SHC3 SHC3 17492 -0.2 0.027 NO
126 NTF4 NTF4 NTF4 18335 -0.35 0.0067 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 OOCYTE MEIOSIS.

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

genes ES table in pathway: KEGG MTOR SIGNALING PATHWAY

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 BTK BTK BTK 300 0.58 0.064 YES
2 TLR6 TLR6 TLR6 653 0.47 0.11 YES
3 S100A12 S100A12 S100A12 793 0.44 0.16 YES
4 LY96 LY96 LY96 1091 0.39 0.2 YES
5 S100B S100B S100B 1308 0.35 0.24 YES
6 MEF2C MEF2C MEF2C 1509 0.32 0.27 YES
7 SAA1 SAA1 SAA1 1515 0.32 0.31 YES
8 MAPK10 MAPK10 MAPK10 1784 0.29 0.34 YES
9 RPS6KA5 RPS6KA5 RPS6KA5 1839 0.28 0.37 YES
10 TLR4 TLR4 TLR4 2013 0.26 0.4 YES
11 MAPK11 MAPK11 MAPK11 2800 0.2 0.38 YES
12 TLR1 TLR1 TLR1 3234 0.17 0.38 YES
13 NOD1 NOD1 NOD1 3323 0.17 0.4 YES
14 NOD2 NOD2 NOD2 3436 0.16 0.42 YES
15 IRAK3 IRAK3 IRAK3 3440 0.16 0.44 YES
16 AGER AGER AGER 3558 0.15 0.45 YES
17 TLR2 TLR2 TLR2 3650 0.15 0.47 YES
18 MEF2A MEF2A MEF2A 5120 0.088 0.4 NO
19 IRAK4 IRAK4 IRAK4 5169 0.086 0.41 NO
20 MAP3K7 MAP3K7 MAP3K7 5286 0.083 0.42 NO
21 TMEM189-UBE2V1 TMEM189-UBE2V1 TMEM189-UBE2V1 5410 0.079 0.42 NO
22 MAP2K4 MAP2K4 MAP2K4 5776 0.069 0.41 NO
23 NFKBIA NFKBIA NFKBIA 5933 0.065 0.41 NO
24 TAB2 TAB2 TAB2 5994 0.064 0.42 NO
25 MAPK7 MAPK7 MAPK7 6234 0.058 0.41 NO
26 ELK1 ELK1 ELK1 6322 0.056 0.41 NO
27 MAP3K1 MAP3K1 MAP3K1 6339 0.056 0.42 NO
28 IKBKG IKBKG IKBKG 6342 0.056 0.43 NO
29 ATF2 ATF2 ATF2 6738 0.048 0.41 NO
30 MAPK1 MAPK1 MAPK1 6760 0.048 0.42 NO
31 RPS6KA2 RPS6KA2 RPS6KA2 6858 0.046 0.42 NO
32 TRAF6 TRAF6 TRAF6 6878 0.045 0.42 NO
33 DUSP3 DUSP3 DUSP3 6978 0.043 0.42 NO
34 PELI2 PELI2 PELI2 6986 0.043 0.43 NO
35 MAPKAPK2 MAPKAPK2 MAPKAPK2 7057 0.042 0.43 NO
36 MAPK14 MAPK14 MAPK14 7186 0.039 0.43 NO
37 NFKB2 NFKB2 NFKB2 7352 0.036 0.43 NO
38 RPS6KA3 RPS6KA3 RPS6KA3 7475 0.035 0.43 NO
39 ATF1 ATF1 ATF1 7499 0.034 0.43 NO
40 UBE2N UBE2N UBE2N 7537 0.034 0.43 NO
41 CREB1 CREB1 CREB1 7776 0.03 0.42 NO
42 CHUK CHUK CHUK 7788 0.03 0.43 NO
43 MAP2K1 MAP2K1 MAP2K1 7825 0.03 0.43 NO
44 MAPK8 MAPK8 MAPK8 8009 0.027 0.42 NO
45 JUN JUN JUN 8203 0.024 0.42 NO
46 RIPK2 RIPK2 RIPK2 8274 0.024 0.42 NO
47 PELI1 PELI1 PELI1 8393 0.022 0.41 NO
48 PPP2R5D PPP2R5D PPP2R5D 8425 0.022 0.41 NO
49 MAP2K6 MAP2K6 MAP2K6 8745 0.018 0.4 NO
50 RPS6KA1 RPS6KA1 RPS6KA1 8864 0.016 0.39 NO
51 HMGB1 HMGB1 HMGB1 8968 0.015 0.39 NO
52 UBA52 UBA52 UBA52 9019 0.014 0.39 NO
53 DUSP7 DUSP7 DUSP7 9062 0.014 0.39 NO
54 RPS27A RPS27A RPS27A 9064 0.014 0.39 NO
55 MYD88 MYD88 MYD88 9357 0.01 0.38 NO
56 PELI3 PELI3 PELI3 9551 0.0079 0.37 NO
57 TAB1 TAB1 TAB1 10204 0.00013 0.33 NO
58 FOS FOS FOS 10406 -0.002 0.32 NO
59 IKBKB IKBKB IKBKB 10433 -0.0025 0.32 NO
60 PPP2CA PPP2CA PPP2CA 10982 -0.0085 0.29 NO
61 TIRAP TIRAP TIRAP 11064 -0.0096 0.29 NO
62 NFKBIB NFKBIB NFKBIB 11160 -0.011 0.28 NO
63 MAPKAPK3 MAPKAPK3 MAPKAPK3 11355 -0.013 0.28 NO
64 IRAK1 IRAK1 IRAK1 11360 -0.013 0.28 NO
65 RELA RELA RELA 11368 -0.013 0.28 NO
66 MAPK9 MAPK9 MAPK9 11534 -0.015 0.27 NO
67 MAP2K3 MAP2K3 MAP2K3 11658 -0.017 0.27 NO
68 PPP2CB PPP2CB PPP2CB 11691 -0.017 0.27 NO
69 APP APP APP 12038 -0.022 0.25 NO
70 PPP2R1B PPP2R1B PPP2R1B 12210 -0.024 0.25 NO
71 TAB3 TAB3 TAB3 12391 -0.026 0.24 NO
72 CDK1 CDK1 CDK1 12606 -0.029 0.23 NO
73 PPP2R1A PPP2R1A PPP2R1A 12853 -0.033 0.22 NO
74 MAP2K7 MAP2K7 MAP2K7 13008 -0.035 0.22 NO
75 MAP2K2 MAP2K2 MAP2K2 13732 -0.046 0.19 NO
76 IRAK2 IRAK2 IRAK2 13762 -0.047 0.19 NO
77 MAPK3 MAPK3 MAPK3 13954 -0.05 0.19 NO
78 DUSP6 DUSP6 DUSP6 14667 -0.064 0.16 NO
79 ECSIT ECSIT ECSIT 14937 -0.071 0.15 NO
80 SIGIRR SIGIRR SIGIRR 15862 -0.099 0.12 NO
81 DUSP4 DUSP4 DUSP4 17300 -0.18 0.063 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 MTOR SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG APOPTOSIS

Table 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 PRKCB PRKCB PRKCB 15 0.83 0.1 YES
2 IKZF3 IKZF3 IKZF3 77 0.74 0.19 YES
3 IL2RA IL2RA IL2RA 513 0.5 0.23 YES
4 IL2RB IL2RB IL2RB 744 0.45 0.27 YES
5 BCL2 BCL2 BCL2 824 0.44 0.32 YES
6 LCK LCK LCK 951 0.41 0.37 YES
7 DOK2 DOK2 DOK2 1123 0.38 0.4 YES
8 JAK3 JAK3 JAK3 1354 0.34 0.43 YES
9 IL2 IL2 IL2 1386 0.34 0.48 YES
10 SOCS2 SOCS2 SOCS2 2246 0.25 0.46 YES
11 FYN FYN FYN 2277 0.24 0.49 YES
12 SOCS1 SOCS1 SOCS1 2434 0.23 0.51 YES
13 IFNG IFNG IFNG 2446 0.23 0.54 YES
14 MAPK11 MAPK11 MAPK11 2800 0.2 0.54 YES
15 SOCS3 SOCS3 SOCS3 3138 0.18 0.54 YES
16 PIK3R1 PIK3R1 PIK3R1 3665 0.15 0.53 YES
17 STAT5A STAT5A STAT5A 3679 0.15 0.55 YES
18 PTK2B PTK2B PTK2B 3807 0.14 0.56 YES
19 IL2RG IL2RG IL2RG 3820 0.14 0.58 YES
20 MYC MYC MYC 4023 0.13 0.58 YES
21 GAB2 GAB2 GAB2 4222 0.12 0.59 YES
22 STAT5B STAT5B STAT5B 4237 0.12 0.6 YES
23 PIK3CA PIK3CA PIK3CA 4566 0.11 0.6 YES
24 SYK SYK SYK 4661 0.1 0.6 YES
25 JAK1 JAK1 JAK1 5221 0.084 0.58 NO
26 PRKCE PRKCE PRKCE 5301 0.082 0.59 NO
27 GRB2 GRB2 GRB2 5637 0.073 0.58 NO
28 SOS1 SOS1 SOS1 6304 0.057 0.55 NO
29 STAT3 STAT3 STAT3 6325 0.056 0.56 NO
30 STAT1 STAT1 STAT1 6391 0.055 0.56 NO
31 NRAS NRAS NRAS 6666 0.049 0.55 NO
32 MAPK1 MAPK1 MAPK1 6760 0.048 0.55 NO
33 PTPN11 PTPN11 PTPN11 6857 0.046 0.55 NO
34 MAPKAPK2 MAPKAPK2 MAPKAPK2 7057 0.042 0.55 NO
35 SHC1 SHC1 SHC1 7113 0.041 0.55 NO
36 MAPK14 MAPK14 MAPK14 7186 0.039 0.55 NO
37 CISH CISH CISH 7756 0.031 0.52 NO
38 MAP2K1 MAP2K1 MAP2K1 7825 0.03 0.52 NO
39 MAPK8 MAPK8 MAPK8 8009 0.027 0.52 NO
40 RHOA RHOA RHOA 8044 0.026 0.52 NO
41 JUN JUN JUN 8203 0.024 0.51 NO
42 PPP2R5D PPP2R5D PPP2R5D 8425 0.022 0.5 NO
43 IRS2 IRS2 IRS2 8551 0.02 0.5 NO
44 CDK2 CDK2 CDK2 8580 0.02 0.5 NO
45 RAF1 RAF1 RAF1 8915 0.016 0.48 NO
46 STAM STAM STAM 9189 0.012 0.47 NO
47 STAM2 STAM2 STAM2 10230 -0.00015 0.41 NO
48 FOS FOS FOS 10406 -0.002 0.4 NO
49 IRS1 IRS1 IRS1 11125 -0.01 0.37 NO
50 MAPK9 MAPK9 MAPK9 11534 -0.015 0.35 NO
51 KRAS KRAS KRAS 12329 -0.025 0.31 NO
52 RASA1 RASA1 RASA1 12790 -0.032 0.29 NO
53 MAP2K2 MAP2K2 MAP2K2 13732 -0.046 0.24 NO
54 MAPK3 MAPK3 MAPK3 13954 -0.05 0.24 NO
55 HRAS HRAS HRAS 15336 -0.081 0.17 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 APOPTOSIS.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input

  • Gene set database = c2.cp.v4.0.symbols.gmt

  • Expression data file = PAAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = PAAD-TP.mergedcluster.txt

GSEA analysis

For the Gene Set Enrichment Analysis (GSEA), Broad GSEA-P-R.1.0 version is used with class2: canonical pathways geneses from MSigDB. Further details about statistics are available inThe Broad GSEA website.

Download Results

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.

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