GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in GBMLGG-TP
Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C12Z14XG
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 GBMLGG-TP. Broad Institute of MIT and Harvard. doi:10.7908/C12Z14XG
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 "GBMLGG-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: 709
Number of samples: 669
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 250
pheno.type: 2 - 3 :[ clus2 ] 191
pheno.type: 3 - 3 :[ clus3 ] 228

For the expression subtypes of 18325 genes in 670 samples, GSEA found enriched gene sets in each cluster using 669 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, BIOCARTA HIVNEF PATHWAY, PID AURORA B PATHWAY, PID P73PATHWAY, PID E2F PATHWAY, PID MYC ACTIVPATHWAY, PID CASPASE PATHWAY, PID IL2 STAT5PATHWAY, PID AURORA A PATHWAY, PID BARD1PATHWAY

    • And common core enriched genes are BUB1, AURKB, BIRC5, CDCA8, CENPA, KIF2C, NDC80, SGOL1, NUP37, PLK1

  • clus2

    • Top enriched gene sets are KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG PYRUVATE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG MAPK SIGNALING PATHWAY, KEGG ERBB SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

    • And common core enriched genes are PRKACB, PRKACG, PRKAR1B, PRKAR2B, YWHAB, CALM1, CALM3, MAP2K1, PPP2R5D, PRKAR1A

  • clus3

    • Top enriched gene sets are KEGG RIBOSOME, BIOCARTA CARM ER PATHWAY, PID RET PATHWAY, PID HDAC CLASSI PATHWAY, PID ERA GENOMIC PATHWAY, PID AR NONGENOMIC PATHWAY, REACTOME TRANSLATION, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION, REACTOME SIGNALING BY NOTCH1

    • And common core enriched genes are RPS6, CREBBP, EP300, HDAC11, HDAC4, HDAC5, KAT2B, NCOR2, RPS27A, CAB39L

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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 44 genes.ES.table 0.53 1.6 0.045 0.81 0.88 0.52 0.28 0.38 0.43 0.24
BIOCARTA HIVNEF PATHWAY 58 genes.ES.table 0.49 1.6 0.032 1 0.86 0.41 0.25 0.31 0.6 0.34
PID AURORA B PATHWAY 39 genes.ES.table 0.79 1.7 0.01 1 0.79 0.44 0.095 0.4 1 0.66
PID P73PATHWAY 79 genes.ES.table 0.58 1.6 0.0062 1 0.83 0.4 0.2 0.32 1 0.52
PID E2F PATHWAY 69 genes.ES.table 0.61 1.6 0.035 1 0.84 0.38 0.17 0.31 0.77 0.41
PID MYC ACTIVPATHWAY 79 genes.ES.table 0.46 1.6 0.041 0.8 0.89 0.27 0.2 0.21 0.43 0.24
PID CASPASE PATHWAY 51 genes.ES.table 0.54 1.6 0.025 0.95 0.88 0.39 0.2 0.31 0.5 0.28
PID IL2 STAT5PATHWAY 28 genes.ES.table 0.68 1.6 0.017 1 0.86 0.39 0.15 0.33 0.66 0.37
PID AURORA A PATHWAY 31 genes.ES.table 0.64 1.6 0.044 0.99 0.87 0.29 0.089 0.26 0.51 0.3
PID BARD1PATHWAY 29 genes.ES.table 0.65 1.6 0.042 1 0.87 0.34 0.15 0.3 0.57 0.33
genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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 PLAUR PLAUR PLAUR 191 0.87 0.23 YES
2 PIGB PIGB PIGB 3215 0.24 0.14 YES
3 PIGL PIGL PIGL 3605 0.21 0.18 YES
4 DPM3 DPM3 DPM3 3724 0.2 0.22 YES
5 PIGT PIGT PIGT 3888 0.19 0.27 YES
6 PIGW PIGW PIGW 3901 0.19 0.32 YES
7 PIGC PIGC PIGC 4498 0.16 0.34 YES
8 DPM1 DPM1 DPM1 4731 0.15 0.36 YES
9 PIGF PIGF PIGF 4988 0.14 0.39 YES
10 PIGN PIGN PIGN 5151 0.13 0.42 YES
11 PIGK PIGK PIGK 5158 0.13 0.45 YES
12 PIGP PIGP PIGP 5283 0.12 0.48 YES
13 DPM2 DPM2 DPM2 5637 0.11 0.49 YES
14 PIGG PIGG PIGG 5664 0.11 0.52 YES
15 SEMA6D SEMA6D SEMA6D 5972 0.1 0.54 YES
16 PIGA PIGA PIGA 6100 0.096 0.56 YES
17 PIGU PIGU PIGU 6152 0.094 0.58 YES
18 PIGV PIGV PIGV 7155 0.064 0.54 NO
19 PIGH PIGH PIGH 8292 0.033 0.49 NO
20 PIGO PIGO PIGO 8322 0.033 0.5 NO
21 GPAA1 GPAA1 GPAA1 8623 0.026 0.49 NO
22 PIGQ PIGQ PIGQ 8976 0.017 0.47 NO
23 PIGS PIGS PIGS 9648 0.00056 0.44 NO
24 PIGX PIGX PIGX 10916 -0.031 0.38 NO
25 PGAP1 PGAP1 PGAP1 11228 -0.038 0.37 NO
26 PIGM PIGM PIGM 12143 -0.065 0.34 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S2.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR 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: BIOCARTA HIVNEF PATHWAY

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 CENPA CENPA CENPA 82 1 0.065 YES
2 CDCA8 CDCA8 CDCA8 117 0.94 0.13 YES
3 KIF23 KIF23 KIF23 133 0.92 0.19 YES
4 KIF20A KIF20A KIF20A 210 0.86 0.25 YES
5 KIF2C KIF2C KIF2C 217 0.86 0.3 YES
6 NDC80 NDC80 NDC80 270 0.81 0.36 YES
7 BIRC5 BIRC5 BIRC5 282 0.8 0.41 YES
8 BUB1 BUB1 BUB1 322 0.78 0.47 YES
9 SGOL1 SGOL1 SGOL1 339 0.77 0.52 YES
10 NCAPG NCAPG NCAPG 413 0.74 0.56 YES
11 AURKB AURKB AURKB 415 0.74 0.62 YES
12 AURKA AURKA AURKA 442 0.72 0.66 YES
13 DES DES DES 496 0.7 0.71 YES
14 NCAPH NCAPH NCAPH 525 0.7 0.76 YES
15 SMC4 SMC4 SMC4 1155 0.51 0.76 YES
16 VIM VIM VIM 1487 0.45 0.77 YES
17 AURKC AURKC AURKC 1735 0.41 0.78 YES
18 RACGAP1 RACGAP1 RACGAP1 2937 0.27 0.74 NO
19 SEPT1 SEPT1 SEPT1 3206 0.24 0.74 NO
20 NCAPD2 NCAPD2 NCAPD2 5025 0.14 0.65 NO
21 PSMA3 PSMA3 PSMA3 5530 0.12 0.63 NO
22 MYLK MYLK MYLK 5809 0.1 0.62 NO
23 SMC2 SMC2 SMC2 6485 0.084 0.59 NO
24 RHOA RHOA RHOA 6649 0.079 0.59 NO
25 PPP1CC PPP1CC PPP1CC 7783 0.047 0.53 NO
26 EVI5 EVI5 EVI5 8654 0.025 0.48 NO
27 NSUN2 NSUN2 NSUN2 9150 0.013 0.46 NO
28 KLHL13 KLHL13 KLHL13 9413 0.0063 0.44 NO
29 INCENP INCENP INCENP 10043 -0.0093 0.41 NO
30 CUL3 CUL3 CUL3 10084 -0.01 0.41 NO
31 PPP2R5D PPP2R5D PPP2R5D 10548 -0.022 0.38 NO
32 STMN1 STMN1 STMN1 10823 -0.029 0.37 NO
33 RASA1 RASA1 RASA1 10977 -0.032 0.36 NO
34 NPM1 NPM1 NPM1 11526 -0.047 0.34 NO
35 NCL NCL NCL 11618 -0.05 0.34 NO
36 CBX5 CBX5 CBX5 11620 -0.05 0.34 NO
37 PEBP1 PEBP1 PEBP1 12994 -0.091 0.27 NO
38 TACC1 TACC1 TACC1 13403 -0.1 0.26 NO
39 KLHL9 KLHL9 KLHL9 14970 -0.18 0.18 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: BIOCARTA HIVNEF PATHWAY.

Figure S4.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HIVNEF 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 AURORA B PATHWAY

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 CENPA CENPA CENPA 82 1 0.033 YES
2 KIF18A KIF18A KIF18A 99 0.96 0.069 YES
3 CDCA8 CDCA8 CDCA8 117 0.94 0.1 YES
4 CDC20 CDC20 CDC20 120 0.94 0.14 YES
5 SKA1 SKA1 SKA1 164 0.89 0.17 YES
6 CENPK CENPK CENPK 170 0.89 0.2 YES
7 KIF2C KIF2C KIF2C 217 0.86 0.23 YES
8 ERCC6L ERCC6L ERCC6L 239 0.83 0.26 YES
9 NDC80 NDC80 NDC80 270 0.81 0.29 YES
10 BIRC5 BIRC5 BIRC5 282 0.8 0.32 YES
11 BUB1 BUB1 BUB1 322 0.78 0.35 YES
12 SGOL1 SGOL1 SGOL1 339 0.77 0.38 YES
13 NUF2 NUF2 NUF2 352 0.77 0.41 YES
14 MLF1IP MLF1IP MLF1IP 361 0.76 0.44 YES
15 SPC24 SPC24 SPC24 393 0.75 0.46 YES
16 AURKB AURKB AURKB 415 0.74 0.49 YES
17 CENPM CENPM CENPM 549 0.68 0.51 YES
18 BUB1B BUB1B BUB1B 569 0.68 0.53 YES
19 CENPI CENPI CENPI 686 0.64 0.55 YES
20 PLK1 PLK1 PLK1 779 0.6 0.57 YES
21 CASC5 CASC5 CASC5 1224 0.49 0.56 YES
22 ITGB3BP ITGB3BP ITGB3BP 1235 0.49 0.58 YES
23 SGOL2 SGOL2 SGOL2 1247 0.49 0.6 YES
24 CENPN CENPN CENPN 1494 0.44 0.6 YES
25 CENPH CENPH CENPH 1496 0.44 0.62 YES
26 CENPL CENPL CENPL 1521 0.44 0.63 YES
27 SPC25 SPC25 SPC25 1631 0.42 0.64 YES
28 MAD2L1 MAD2L1 MAD2L1 1650 0.42 0.66 YES
29 ZWILCH ZWILCH ZWILCH 1750 0.4 0.67 YES
30 ZWINT ZWINT ZWINT 1859 0.39 0.68 YES
31 B9D2 B9D2 B9D2 1981 0.37 0.68 YES
32 DSN1 DSN1 DSN1 2027 0.37 0.7 YES
33 NUP37 NUP37 NUP37 2285 0.33 0.7 YES
34 KNTC1 KNTC1 KNTC1 2310 0.33 0.71 YES
35 APITD1 APITD1 APITD1 2436 0.32 0.71 YES
36 CENPP CENPP CENPP 2531 0.3 0.72 YES
37 CENPO CENPO CENPO 3292 0.24 0.68 NO
38 NUP107 NUP107 NUP107 4605 0.16 0.62 NO
39 NUP85 NUP85 NUP85 4661 0.15 0.62 NO
40 RPS27 RPS27 RPS27 5030 0.14 0.61 NO
41 RCC2 RCC2 RCC2 5244 0.13 0.6 NO
42 MIS12 MIS12 MIS12 5648 0.11 0.58 NO
43 CENPQ CENPQ CENPQ 5849 0.1 0.57 NO
44 CCDC99 CCDC99 CCDC99 6240 0.092 0.56 NO
45 SEC13 SEC13 SEC13 6492 0.084 0.55 NO
46 ZW10 ZW10 ZW10 7072 0.066 0.52 NO
47 NUP43 NUP43 NUP43 7296 0.06 0.51 NO
48 NSL1 NSL1 NSL1 7325 0.06 0.51 NO
49 MAD1L1 MAD1L1 MAD1L1 7480 0.055 0.5 NO
50 PMF1 PMF1 PMF1 7647 0.051 0.49 NO
51 PPP1CC PPP1CC PPP1CC 7783 0.047 0.49 NO
52 MAPRE1 MAPRE1 MAPRE1 8251 0.035 0.46 NO
53 PPP2R1B PPP2R1B PPP2R1B 8458 0.029 0.45 NO
54 XPO1 XPO1 XPO1 8545 0.027 0.45 NO
55 CLIP1 CLIP1 CLIP1 8651 0.025 0.44 NO
56 PPP2CA PPP2CA PPP2CA 8727 0.023 0.44 NO
57 SEH1L SEH1L SEH1L 8943 0.018 0.43 NO
58 SKA2 SKA2 SKA2 9145 0.013 0.42 NO
59 PPP2R5E PPP2R5E PPP2R5E 9197 0.012 0.42 NO
60 NDEL1 NDEL1 NDEL1 9454 0.0053 0.4 NO
61 PPP2R1A PPP2R1A PPP2R1A 9757 -0.0021 0.39 NO
62 PPP2CB PPP2CB PPP2CB 9919 -0.0062 0.38 NO
63 INCENP INCENP INCENP 10043 -0.0093 0.37 NO
64 PPP2R5D PPP2R5D PPP2R5D 10548 -0.022 0.35 NO
65 NUDC NUDC NUDC 10571 -0.022 0.35 NO
66 SMC1A SMC1A SMC1A 10910 -0.031 0.33 NO
67 CENPT CENPT CENPT 11002 -0.033 0.32 NO
68 NUP133 NUP133 NUP133 11243 -0.039 0.31 NO
69 STAG1 STAG1 STAG1 11392 -0.043 0.31 NO
70 STAG2 STAG2 STAG2 11478 -0.045 0.3 NO
71 RAD21 RAD21 RAD21 11750 -0.053 0.29 NO
72 BUB3 BUB3 BUB3 11880 -0.057 0.29 NO
73 CENPC1 CENPC1 CENPC1 12134 -0.065 0.27 NO
74 PPP2R5B PPP2R5B PPP2R5B 12272 -0.069 0.27 NO
75 CKAP5 CKAP5 CKAP5 12484 -0.075 0.26 NO
76 RANBP2 RANBP2 RANBP2 12747 -0.083 0.25 NO
77 AHCTF1 AHCTF1 AHCTF1 13161 -0.096 0.23 NO
78 PPP2R5C PPP2R5C PPP2R5C 13251 -0.1 0.23 NO
79 RANGAP1 RANGAP1 RANGAP1 13321 -0.1 0.23 NO
80 PAFAH1B1 PAFAH1B1 PAFAH1B1 13691 -0.12 0.21 NO
81 CLASP1 CLASP1 CLASP1 13859 -0.12 0.21 NO
82 KIF2A KIF2A KIF2A 14932 -0.18 0.16 NO
83 PPP2R5A PPP2R5A PPP2R5A 15425 -0.21 0.14 NO
84 SMC3 SMC3 SMC3 15459 -0.21 0.14 NO
85 TAOK1 TAOK1 TAOK1 16563 -0.32 0.096 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: PID AURORA B PATHWAY.

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

genes ES table in pathway: PID P73PATHWAY

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 CCR5 CCR5 CCR5 384 0.75 0.014 YES
2 APOBEC3G APOBEC3G APOBEC3G 426 0.74 0.046 YES
3 CD247 CD247 CD247 615 0.66 0.066 YES
4 LCK LCK LCK 647 0.65 0.095 YES
5 CD28 CD28 CD28 839 0.59 0.11 YES
6 RCC1 RCC1 RCC1 1362 0.47 0.1 YES
7 CXCR4 CXCR4 CXCR4 1584 0.43 0.11 YES
8 PSMB9 PSMB9 PSMB9 1686 0.42 0.13 YES
9 NUP37 NUP37 NUP37 2285 0.33 0.11 YES
10 PSMB8 PSMB8 PSMB8 2390 0.32 0.12 YES
11 HCK HCK HCK 2685 0.29 0.12 YES
12 TAF13 TAF13 TAF13 3015 0.26 0.11 YES
13 POLR2L POLR2L POLR2L 3035 0.26 0.12 YES
14 CD8B CD8B CD8B 3075 0.26 0.13 YES
15 HLA-A HLA-A HLA-A 3347 0.23 0.13 YES
16 AP2S1 AP2S1 AP2S1 3383 0.23 0.14 YES
17 B2M B2M B2M 3440 0.22 0.14 YES
18 CD4 CD4 CD4 3459 0.22 0.15 YES
19 AP1S2 AP1S2 AP1S2 3509 0.22 0.16 YES
20 NUP210 NUP210 NUP210 3533 0.22 0.17 YES
21 TAF12 TAF12 TAF12 3687 0.21 0.17 YES
22 DOCK2 DOCK2 DOCK2 3751 0.2 0.18 YES
23 LIG1 LIG1 LIG1 3922 0.19 0.18 YES
24 GTF2E2 GTF2E2 GTF2E2 3967 0.19 0.18 YES
25 PSMA5 PSMA5 PSMA5 3993 0.19 0.19 YES
26 PSMC2 PSMC2 PSMC2 4004 0.19 0.2 YES
27 PSMD5 PSMD5 PSMD5 4143 0.18 0.2 YES
28 PPIA PPIA PPIA 4172 0.18 0.2 YES
29 GTF2H2B GTF2H2B GTF2H2B 4242 0.17 0.21 YES
30 PSMD8 PSMD8 PSMD8 4258 0.17 0.22 YES
31 NUP54 NUP54 NUP54 4263 0.17 0.22 YES
32 PSMA2 PSMA2 PSMA2 4285 0.17 0.23 YES
33 GTF2H2 GTF2H2 GTF2H2 4420 0.16 0.23 YES
34 POLR2I POLR2I POLR2I 4421 0.16 0.24 YES
35 NUP107 NUP107 NUP107 4605 0.16 0.24 YES
36 PSMB10 PSMB10 PSMB10 4618 0.16 0.24 YES
37 NUP85 NUP85 NUP85 4661 0.15 0.25 YES
38 PSME2 PSME2 PSME2 4698 0.15 0.25 YES
39 PSMD9 PSMD9 PSMD9 4824 0.14 0.25 YES
40 PSMC4 PSMC4 PSMC4 4849 0.14 0.26 YES
41 PSMA7 PSMA7 PSMA7 4861 0.14 0.26 YES
42 HMGA1 HMGA1 HMGA1 4911 0.14 0.27 YES
43 TAF10 TAF10 TAF10 4962 0.14 0.27 YES
44 POLR2J POLR2J POLR2J 5032 0.14 0.27 YES
45 NUP205 NUP205 NUP205 5060 0.14 0.28 YES
46 PSMB3 PSMB3 PSMB3 5083 0.13 0.28 YES
47 PSMA8 PSMA8 PSMA8 5089 0.13 0.29 YES
48 POLR2H POLR2H POLR2H 5152 0.13 0.29 YES
49 POLR2D POLR2D POLR2D 5182 0.13 0.3 YES
50 NUP62 NUP62 NUP62 5249 0.13 0.3 YES
51 GTF2B GTF2B GTF2B 5256 0.13 0.3 YES
52 POLR2G POLR2G POLR2G 5321 0.12 0.31 YES
53 PSMA1 PSMA1 PSMA1 5334 0.12 0.31 YES
54 RAN RAN RAN 5424 0.12 0.31 YES
55 PSMB2 PSMB2 PSMB2 5454 0.12 0.32 YES
56 PSMA3 PSMA3 PSMA3 5530 0.12 0.32 YES
57 PSMB4 PSMB4 PSMB4 5831 0.1 0.31 YES
58 RAE1 RAE1 RAE1 5846 0.1 0.31 YES
59 FEN1 FEN1 FEN1 5848 0.1 0.32 YES
60 PSME1 PSME1 PSME1 5865 0.1 0.32 YES
61 PSMA4 PSMA4 PSMA4 5907 0.1 0.32 YES
62 PSMD12 PSMD12 PSMD12 5920 0.1 0.32 YES
63 PSMD14 PSMD14 PSMD14 5923 0.1 0.33 YES
64 CDK7 CDK7 CDK7 5925 0.1 0.33 YES
65 XRCC4 XRCC4 XRCC4 5940 0.1 0.34 YES
66 PSMB1 PSMB1 PSMB1 6023 0.098 0.34 YES
67 NUP35 NUP35 NUP35 6234 0.092 0.33 YES
68 PSMC1 PSMC1 PSMC1 6273 0.091 0.33 YES
69 TCEB1 TCEB1 TCEB1 6403 0.087 0.33 YES
70 GTF2E1 GTF2E1 GTF2E1 6447 0.085 0.33 YES
71 AP1S1 AP1S1 AP1S1 6536 0.082 0.33 YES
72 PSMD11 PSMD11 PSMD11 6562 0.082 0.33 YES
73 NUP93 NUP93 NUP93 6680 0.078 0.33 YES
74 TAF11 TAF11 TAF11 6698 0.077 0.33 YES
75 GTF2A2 GTF2A2 GTF2A2 6755 0.076 0.33 YES
76 NUP88 NUP88 NUP88 6848 0.073 0.33 YES
77 NUP155 NUP155 NUP155 7002 0.068 0.33 YES
78 UBA52 UBA52 UBA52 7022 0.067 0.33 YES
79 POLR2C POLR2C POLR2C 7023 0.067 0.33 YES
80 POLR2K POLR2K POLR2K 7046 0.067 0.33 YES
81 AP1M1 AP1M1 AP1M1 7180 0.063 0.33 YES
82 PSMD13 PSMD13 PSMD13 7186 0.063 0.33 YES
83 VPS37B VPS37B VPS37B 7195 0.063 0.33 YES
84 TAF9 TAF9 TAF9 7201 0.063 0.34 YES
85 PSMD6 PSMD6 PSMD6 7227 0.062 0.34 YES
86 NUPL2 NUPL2 NUPL2 7243 0.061 0.34 YES
87 NUP43 NUP43 NUP43 7296 0.06 0.34 YES
88 TCEB3 TCEB3 TCEB3 7332 0.059 0.34 YES
89 ARF1 ARF1 ARF1 7408 0.057 0.34 YES
90 PSME4 PSME4 PSME4 7499 0.055 0.34 YES
91 RBX1 RBX1 RBX1 7521 0.054 0.34 YES
92 GTF2H3 GTF2H3 GTF2H3 7540 0.053 0.34 YES
93 BANF1 BANF1 BANF1 7621 0.052 0.34 YES
94 SLC25A5 SLC25A5 SLC25A5 7718 0.049 0.34 YES
95 TCEB2 TCEB2 TCEB2 7723 0.049 0.34 YES
96 PSMD7 PSMD7 PSMD7 7752 0.048 0.34 YES
97 RAC1 RAC1 RAC1 7784 0.047 0.34 YES
98 ERCC2 ERCC2 ERCC2 7826 0.046 0.34 YES
99 POM121 POM121 POM121 7856 0.045 0.34 YES
100 PSMD2 PSMD2 PSMD2 7860 0.045 0.34 YES
101 NUP188 NUP188 NUP188 7906 0.044 0.34 YES
102 NCBP1 NCBP1 NCBP1 7908 0.044 0.34 YES
103 SUPT4H1 SUPT4H1 SUPT4H1 7923 0.044 0.34 YES
104 TH1L TH1L TH1L 7937 0.043 0.34 YES
105 TAF6 TAF6 TAF6 8018 0.041 0.34 NO
106 PSMF1 PSMF1 PSMF1 8114 0.038 0.34 NO
107 XRCC5 XRCC5 XRCC5 8453 0.029 0.32 NO
108 RANBP1 RANBP1 RANBP1 8491 0.028 0.32 NO
109 POLR2B POLR2B POLR2B 8520 0.028 0.32 NO
110 PSMB6 PSMB6 PSMB6 8526 0.028 0.32 NO
111 XPO1 XPO1 XPO1 8545 0.027 0.32 NO
112 PSMA6 PSMA6 PSMA6 8626 0.025 0.32 NO
113 CCNH CCNH CCNH 8732 0.023 0.31 NO
114 PSMD3 PSMD3 PSMD3 8794 0.021 0.31 NO
115 POLR2E POLR2E POLR2E 8802 0.021 0.31 NO
116 PSMC3 PSMC3 PSMC3 8822 0.021 0.31 NO
117 PSMB7 PSMB7 PSMB7 8831 0.02 0.31 NO
118 AAAS AAAS AAAS 8909 0.018 0.31 NO
119 SEH1L SEH1L SEH1L 8943 0.018 0.31 NO
120 GTF2H4 GTF2H4 GTF2H4 8977 0.017 0.31 NO
121 ELL ELL ELL 9057 0.015 0.3 NO
122 CTDP1 CTDP1 CTDP1 9120 0.013 0.3 NO
123 RDBP RDBP RDBP 9169 0.012 0.3 NO
124 PSMD1 PSMD1 PSMD1 9310 0.0088 0.29 NO
125 NUP153 NUP153 NUP153 9364 0.0073 0.29 NO
126 KPNA1 KPNA1 KPNA1 9406 0.0064 0.29 NO
127 PSMD10 PSMD10 PSMD10 9448 0.0055 0.28 NO
128 XRCC6 XRCC6 XRCC6 9468 0.005 0.28 NO
129 SLC25A6 SLC25A6 SLC25A6 9499 0.0042 0.28 NO
130 GTF2H1 GTF2H1 GTF2H1 9586 0.0021 0.28 NO
131 KPNB1 KPNB1 KPNB1 9588 0.002 0.28 NO
132 AP2M1 AP2M1 AP2M1 9613 0.0014 0.28 NO
133 SSRP1 SSRP1 SSRP1 9666 0.00012 0.27 NO
134 TCEA1 TCEA1 TCEA1 9690 -0.00043 0.27 NO
135 SKP1 SKP1 SKP1 9836 -0.0042 0.26 NO
136 VPS28 VPS28 VPS28 9994 -0.008 0.26 NO
137 MNAT1 MNAT1 MNAT1 10012 -0.0084 0.26 NO
138 SLC25A4 SLC25A4 SLC25A4 10121 -0.011 0.25 NO
139 COBRA1 COBRA1 COBRA1 10132 -0.011 0.25 NO
140 PAK2 PAK2 PAK2 10162 -0.012 0.25 NO
141 ERCC3 ERCC3 ERCC3 10165 -0.012 0.25 NO
142 VPS37C VPS37C VPS37C 10248 -0.014 0.25 NO
143 AP2A1 AP2A1 AP2A1 10275 -0.015 0.24 NO
144 PSMB5 PSMB5 PSMB5 10302 -0.016 0.24 NO
145 RNGTT RNGTT RNGTT 10326 -0.016 0.24 NO
146 TBP TBP TBP 10388 -0.018 0.24 NO
147 VPS37A VPS37A VPS37A 10395 -0.018 0.24 NO
148 NMT1 NMT1 NMT1 10397 -0.018 0.24 NO
149 NCBP2 NCBP2 NCBP2 10493 -0.021 0.24 NO
150 AP1B1 AP1B1 AP1B1 10645 -0.024 0.23 NO
151 PSMD4 PSMD4 PSMD4 10670 -0.025 0.23 NO
152 PACS1 PACS1 PACS1 10691 -0.026 0.23 NO
153 TSG101 TSG101 TSG101 10806 -0.028 0.23 NO
154 SUPT5H SUPT5H SUPT5H 10949 -0.032 0.22 NO
155 AP1G1 AP1G1 AP1G1 10971 -0.032 0.22 NO
156 WHSC2 WHSC2 WHSC2 11079 -0.035 0.22 NO
157 NUP50 NUP50 NUP50 11080 -0.035 0.22 NO
158 CCNT2 CCNT2 CCNT2 11121 -0.036 0.22 NO
159 LIG4 LIG4 LIG4 11154 -0.036 0.22 NO
160 NUPL1 NUPL1 NUPL1 11229 -0.038 0.22 NO
161 NUP133 NUP133 NUP133 11243 -0.039 0.22 NO
162 TAF4 TAF4 TAF4 11459 -0.045 0.21 NO
163 NPM1 NPM1 NPM1 11526 -0.047 0.2 NO
164 CUL5 CUL5 CUL5 11575 -0.048 0.2 NO
165 AP2A2 AP2A2 AP2A2 11630 -0.05 0.2 NO
166 NUP214 NUP214 NUP214 11714 -0.052 0.2 NO
167 PSMC5 PSMC5 PSMC5 11799 -0.055 0.2 NO
168 PSMC6 PSMC6 PSMC6 12000 -0.061 0.19 NO
169 GTF2F1 GTF2F1 GTF2F1 12017 -0.062 0.19 NO
170 TPR TPR TPR 12398 -0.073 0.18 NO
171 CDK9 CDK9 CDK9 12418 -0.074 0.18 NO
172 POLR2A POLR2A POLR2A 12442 -0.074 0.18 NO
173 RNMT RNMT RNMT 12449 -0.074 0.18 NO
174 VPS37D VPS37D VPS37D 12455 -0.075 0.19 NO
175 RANBP2 RANBP2 RANBP2 12747 -0.083 0.18 NO
176 FYN FYN FYN 12762 -0.084 0.18 NO
177 CCNT1 CCNT1 CCNT1 13156 -0.096 0.16 NO
178 ATP6V1H ATP6V1H ATP6V1H 13194 -0.097 0.16 NO
179 SUPT16H SUPT16H SUPT16H 13259 -0.1 0.16 NO
180 RANGAP1 RANGAP1 RANGAP1 13321 -0.1 0.17 NO
181 TAF1 TAF1 TAF1 13412 -0.11 0.16 NO
182 PSIP1 PSIP1 PSIP1 13793 -0.12 0.15 NO
183 AP2B1 AP2B1 AP2B1 13860 -0.12 0.15 NO
184 GTF2F2 GTF2F2 GTF2F2 13907 -0.12 0.16 NO
185 TAF5 TAF5 TAF5 14144 -0.14 0.15 NO
186 TAF4B TAF4B TAF4B 14249 -0.14 0.15 NO
187 RPS27A RPS27A RPS27A 14744 -0.16 0.13 NO
188 POLR2F POLR2F POLR2F 15357 -0.2 0.11 NO
189 AP1M2 AP1M2 AP1M2 15622 -0.22 0.1 NO
190 GTF2A1 GTF2A1 GTF2A1 15659 -0.23 0.11 NO
191 NMT2 NMT2 NMT2 15728 -0.23 0.12 NO
192 BTRC BTRC BTRC 15857 -0.25 0.12 NO
193 ELMO1 ELMO1 ELMO1 16203 -0.28 0.12 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: PID P73PATHWAY.

Figure S8.  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 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 GDF15 GDF15 GDF15 32 1.1 0.053 YES
2 SERPINE1 SERPINE1 SERPINE1 152 0.91 0.09 YES
3 RAD51 RAD51 RAD51 234 0.84 0.13 YES
4 CCNA2 CCNA2 CCNA2 284 0.8 0.16 YES
5 BUB1 BUB1 BUB1 322 0.78 0.2 YES
6 SERPINA1 SERPINA1 SERPINA1 405 0.74 0.23 YES
7 S100A2 S100A2 S100A2 483 0.71 0.26 YES
8 CDK1 CDK1 CDK1 576 0.68 0.29 YES
9 CCNB1 CCNB1 CCNB1 596 0.67 0.32 YES
10 BRCA2 BRCA2 BRCA2 711 0.63 0.34 YES
11 PLK1 PLK1 PLK1 779 0.6 0.37 YES
12 AFP AFP AFP 835 0.59 0.4 YES
13 IL1RAP IL1RAP IL1RAP 855 0.58 0.42 YES
14 FAS FAS FAS 1093 0.52 0.44 YES
15 TP73 TP73 TP73 1148 0.51 0.46 YES
16 CDK2 CDK2 CDK2 1196 0.5 0.48 YES
17 WT1 WT1 WT1 1250 0.49 0.5 YES
18 PLK3 PLK3 PLK3 1620 0.42 0.5 YES
19 SFN SFN SFN 1655 0.42 0.52 YES
20 CHEK1 CHEK1 CHEK1 1842 0.39 0.53 YES
21 TP63 TP63 TP63 2075 0.36 0.53 YES
22 AEN AEN AEN 2401 0.32 0.53 YES
23 TP53I3 TP53I3 TP53I3 2572 0.3 0.54 YES
24 CDK6 CDK6 CDK6 2821 0.28 0.54 YES
25 CDKN1A CDKN1A CDKN1A 3183 0.24 0.53 YES
26 IL4R IL4R IL4R 3200 0.24 0.54 YES
27 CCNE2 CCNE2 CCNE2 3445 0.22 0.54 YES
28 BAX BAX BAX 3450 0.22 0.55 YES
29 TP53AIP1 TP53AIP1 TP53AIP1 3569 0.21 0.55 YES
30 CASP2 CASP2 CASP2 3674 0.21 0.56 YES
31 NTRK1 NTRK1 NTRK1 3676 0.21 0.57 YES
32 BAK1 BAK1 BAK1 3677 0.21 0.58 YES
33 YAP1 YAP1 YAP1 3919 0.19 0.57 NO
34 MDM2 MDM2 MDM2 4382 0.16 0.56 NO
35 TUBA1A TUBA1A TUBA1A 4802 0.15 0.54 NO
36 PPAP2A PPAP2A PPAP2A 5236 0.13 0.52 NO
37 FLOT2 FLOT2 FLOT2 5386 0.12 0.52 NO
38 RB1 RB1 RB1 5577 0.11 0.52 NO
39 PML PML PML 6582 0.081 0.46 NO
40 ADA ADA ADA 6717 0.077 0.46 NO
41 DCP1B DCP1B DCP1B 6935 0.07 0.45 NO
42 PFDN5 PFDN5 PFDN5 6997 0.068 0.45 NO
43 MAPK14 MAPK14 MAPK14 7351 0.059 0.44 NO
44 BBC3 BBC3 BBC3 7758 0.048 0.42 NO
45 DEDD DEDD DEDD 7851 0.045 0.41 NO
46 GNB2L1 GNB2L1 GNB2L1 8774 0.022 0.36 NO
47 RCHY1 RCHY1 RCHY1 8907 0.018 0.36 NO
48 RELA RELA RELA 8998 0.016 0.35 NO
49 ITCH ITCH ITCH 9064 0.015 0.35 NO
50 NEDD4L NEDD4L NEDD4L 9270 0.01 0.34 NO
51 SP1 SP1 SP1 9384 0.0069 0.33 NO
52 PIN1 PIN1 PIN1 9450 0.0054 0.33 NO
53 HSF1 HSF1 HSF1 10211 -0.013 0.29 NO
54 BCL2L11 BCL2L11 BCL2L11 10277 -0.015 0.28 NO
55 NDUFS2 NDUFS2 NDUFS2 11201 -0.038 0.24 NO
56 GRAMD4 GRAMD4 GRAMD4 11427 -0.044 0.23 NO
57 JAK1 JAK1 JAK1 11660 -0.051 0.22 NO
58 BUB3 BUB3 BUB3 11880 -0.057 0.21 NO
59 UBE4B UBE4B UBE4B 11958 -0.06 0.21 NO
60 ABL1 ABL1 ABL1 12160 -0.066 0.2 NO
61 KAT5 KAT5 KAT5 12185 -0.067 0.2 NO
62 HAGH HAGH HAGH 12698 -0.082 0.18 NO
63 FBXO45 FBXO45 FBXO45 12960 -0.09 0.17 NO
64 PRKACB PRKACB PRKACB 13039 -0.092 0.17 NO
65 JAG2 JAG2 JAG2 13103 -0.094 0.17 NO
66 MAPK11 MAPK11 MAPK11 13302 -0.1 0.16 NO
67 MYC MYC MYC 13719 -0.12 0.14 NO
68 BIN1 BIN1 BIN1 14119 -0.13 0.13 NO
69 FOXO3 FOXO3 FOXO3 14402 -0.15 0.12 NO
70 D4S234E D4S234E D4S234E 14560 -0.16 0.12 NO
71 PEA15 PEA15 PEA15 14665 -0.16 0.12 NO
72 EP300 EP300 EP300 14679 -0.16 0.13 NO
73 GATA1 GATA1 GATA1 14972 -0.18 0.12 NO
74 CLCA2 CLCA2 CLCA2 15008 -0.18 0.13 NO
75 WWOX WWOX WWOX 15086 -0.18 0.13 NO
76 RNF43 RNF43 RNF43 15179 -0.19 0.14 NO
77 HEY2 HEY2 HEY2 15522 -0.22 0.13 NO
78 FASN FASN FASN 15742 -0.24 0.13 NO
79 SIRT1 SIRT1 SIRT1 15856 -0.25 0.13 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: PID E2F PATHWAY.

Figure S10.  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 MYC ACTIVPATHWAY

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 ALG6 ALG6 ALG6 2074 0.36 -0.018 YES
2 ALG14 ALG14 ALG14 2565 0.3 0.034 YES
3 PMM2 PMM2 PMM2 2640 0.29 0.11 YES
4 GMPPB GMPPB GMPPB 3249 0.24 0.14 YES
5 ALG3 ALG3 ALG3 3414 0.23 0.19 YES
6 DPM3 DPM3 DPM3 3724 0.2 0.23 YES
7 GMPPA GMPPA GMPPA 4003 0.19 0.26 YES
8 ALG1 ALG1 ALG1 4037 0.18 0.31 YES
9 ALG10 ALG10 ALG10 4373 0.17 0.33 YES
10 ALG5 ALG5 ALG5 4410 0.16 0.37 YES
11 ALG2 ALG2 ALG2 4454 0.16 0.41 YES
12 ALG12 ALG12 ALG12 4611 0.16 0.45 YES
13 DPAGT1 DPAGT1 DPAGT1 4622 0.16 0.49 YES
14 DPM1 DPM1 DPM1 4731 0.15 0.52 YES
15 ALG8 ALG8 ALG8 4857 0.14 0.55 YES
16 DPM2 DPM2 DPM2 5637 0.11 0.54 YES
17 RFT1 RFT1 RFT1 5906 0.1 0.55 YES
18 DOLK DOLK DOLK 6426 0.086 0.55 YES
19 GFPT2 GFPT2 GFPT2 6730 0.076 0.55 YES
20 GNPNAT1 GNPNAT1 GNPNAT1 6966 0.069 0.55 YES
21 ALG13 ALG13 ALG13 8501 0.028 0.48 NO
22 ALG11 ALG11 ALG11 8622 0.026 0.48 NO
23 ALG9 ALG9 ALG9 9058 0.015 0.46 NO
24 PGM3 PGM3 PGM3 9330 0.0081 0.44 NO
25 DOLPP1 DOLPP1 DOLPP1 9930 -0.0063 0.41 NO
26 PMM1 PMM1 PMM1 11736 -0.053 0.33 NO
27 MPI MPI MPI 11737 -0.053 0.34 NO
28 ALG10B ALG10B ALG10B 12055 -0.063 0.34 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: PID MYC ACTIVPATHWAY.

Figure S12.  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 CASPASE PATHWAY

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 PLAU PLAU PLAU 75 1 0.052 YES
2 E2F7 E2F7 E2F7 86 0.99 0.11 YES
3 SERPINE1 SERPINE1 SERPINE1 152 0.91 0.15 YES
4 TK1 TK1 TK1 268 0.81 0.19 YES
5 CCNA2 CCNA2 CCNA2 284 0.8 0.24 YES
6 MYBL2 MYBL2 MYBL2 286 0.8 0.28 YES
7 CDC6 CDC6 CDC6 300 0.8 0.32 YES
8 RRM2 RRM2 RRM2 314 0.79 0.37 YES
9 CDK1 CDK1 CDK1 576 0.68 0.39 YES
10 TYMS TYMS TYMS 743 0.62 0.42 YES
11 CDKN2C CDKN2C CDKN2C 900 0.57 0.44 YES
12 E2F2 E2F2 E2F2 992 0.55 0.46 YES
13 TP73 TP73 TP73 1148 0.51 0.48 YES
14 CDK2 CDK2 CDK2 1196 0.5 0.51 YES
15 HIC1 HIC1 HIC1 1417 0.46 0.52 YES
16 CDC25A CDC25A CDC25A 1884 0.39 0.52 YES
17 E2F1 E2F1 E2F1 1899 0.39 0.54 YES
18 CASP7 CASP7 CASP7 2229 0.34 0.54 YES
19 CCNE1 CCNE1 CCNE1 2232 0.34 0.56 YES
20 RBBP8 RBBP8 RBBP8 2340 0.33 0.57 YES
21 BRCA1 BRCA1 BRCA1 2689 0.29 0.57 YES
22 CEBPA CEBPA CEBPA 2710 0.29 0.58 YES
23 RBL1 RBL1 RBL1 3019 0.26 0.58 YES
24 HDAC1 HDAC1 HDAC1 3136 0.25 0.59 YES
25 CDKN1A CDKN1A CDKN1A 3183 0.24 0.6 YES
26 CES1 CES1 CES1 3185 0.24 0.61 YES
27 CCNE2 CCNE2 CCNE2 3445 0.22 0.61 NO
28 MCM3 MCM3 MCM3 4269 0.17 0.57 NO
29 DHFR DHFR DHFR 5430 0.12 0.52 NO
30 UXT UXT UXT 5487 0.12 0.52 NO
31 E2F6 E2F6 E2F6 5512 0.12 0.52 NO
32 RB1 RB1 RB1 5577 0.11 0.53 NO
33 HBP1 HBP1 HBP1 5707 0.11 0.53 NO
34 E2F4 E2F4 E2F4 6075 0.097 0.51 NO
35 RRM1 RRM1 RRM1 6089 0.097 0.52 NO
36 E2F5 E2F5 E2F5 6176 0.094 0.52 NO
37 MCL1 MCL1 MCL1 6543 0.082 0.5 NO
38 RBBP4 RBBP4 RBBP4 6682 0.078 0.5 NO
39 TRIM28 TRIM28 TRIM28 6873 0.072 0.49 NO
40 YY1 YY1 YY1 7391 0.058 0.47 NO
41 XRCC1 XRCC1 XRCC1 8002 0.042 0.44 NO
42 E2F3 E2F3 E2F3 8276 0.034 0.42 NO
43 POLA1 POLA1 POLA1 8370 0.031 0.42 NO
44 RANBP1 RANBP1 RANBP1 8491 0.028 0.41 NO
45 TFDP2 TFDP2 TFDP2 8780 0.022 0.4 NO
46 TFE3 TFE3 TFE3 8896 0.019 0.4 NO
47 RYBP RYBP RYBP 9023 0.016 0.39 NO
48 SP1 SP1 SP1 9384 0.0069 0.37 NO
49 CCND3 CCND3 CCND3 9750 -0.0019 0.35 NO
50 TFDP1 TFDP1 TFDP1 10151 -0.012 0.33 NO
51 APAF1 APAF1 APAF1 10339 -0.017 0.32 NO
52 TOPBP1 TOPBP1 TOPBP1 10380 -0.018 0.32 NO
53 TRRAP TRRAP TRRAP 10619 -0.024 0.31 NO
54 CDKN2A CDKN2A CDKN2A 10933 -0.031 0.29 NO
55 PRMT5 PRMT5 PRMT5 11380 -0.042 0.27 NO
56 CBX5 CBX5 CBX5 11620 -0.05 0.26 NO
57 CES2 CES2 CES2 11779 -0.054 0.25 NO
58 RBL2 RBL2 RBL2 12680 -0.081 0.21 NO
59 CDKN1B CDKN1B CDKN1B 13324 -0.1 0.18 NO
60 MYC MYC MYC 13719 -0.12 0.16 NO
61 KAT2A KAT2A KAT2A 13929 -0.13 0.16 NO
62 KAT2B KAT2B KAT2B 13949 -0.13 0.16 NO
63 ATM ATM ATM 14176 -0.14 0.16 NO
64 CREBBP CREBBP CREBBP 14341 -0.14 0.16 NO
65 SMARCA2 SMARCA2 SMARCA2 14425 -0.15 0.16 NO
66 EP300 EP300 EP300 14679 -0.16 0.16 NO
67 CES3 CES3 CES3 14705 -0.16 0.16 NO
68 SIRT1 SIRT1 SIRT1 15856 -0.25 0.12 NO
69 WASF1 WASF1 WASF1 16700 -0.34 0.088 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: PID CASPASE PATHWAY.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: PID CASPASE 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 IL2 STAT5PATHWAY

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 HIST1H2BH HIST1H2BH HIST1H2BH 73 1 0.0076 YES
2 CENPA CENPA CENPA 82 1 0.019 YES
3 KIF18A KIF18A KIF18A 99 0.96 0.029 YES
4 CDCA8 CDCA8 CDCA8 117 0.94 0.038 YES
5 CDC20 CDC20 CDC20 120 0.94 0.049 YES
6 KIF23 KIF23 KIF23 133 0.92 0.059 YES
7 SKA1 SKA1 SKA1 164 0.89 0.068 YES
8 CENPK CENPK CENPK 170 0.89 0.077 YES
9 PTTG1 PTTG1 PTTG1 184 0.88 0.087 YES
10 POLE2 POLE2 POLE2 202 0.86 0.096 YES
11 KIF20A KIF20A KIF20A 210 0.86 0.1 YES
12 KIF2C KIF2C KIF2C 217 0.86 0.11 YES
13 OIP5 OIP5 OIP5 225 0.85 0.12 YES
14 ERCC6L ERCC6L ERCC6L 239 0.83 0.13 YES
15 CCNB2 CCNB2 CCNB2 261 0.82 0.14 YES
16 NDC80 NDC80 NDC80 270 0.81 0.15 YES
17 BIRC5 BIRC5 BIRC5 282 0.8 0.16 YES
18 CCNA2 CCNA2 CCNA2 284 0.8 0.17 YES
19 MYBL2 MYBL2 MYBL2 286 0.8 0.18 YES
20 CDC6 CDC6 CDC6 300 0.8 0.18 YES
21 CDC25C CDC25C CDC25C 303 0.79 0.19 YES
22 NEK2 NEK2 NEK2 307 0.79 0.2 YES
23 HJURP HJURP HJURP 309 0.79 0.21 YES
24 RRM2 RRM2 RRM2 314 0.79 0.22 YES
25 BUB1 BUB1 BUB1 322 0.78 0.23 YES
26 UBE2C UBE2C UBE2C 325 0.78 0.24 YES
27 SGOL1 SGOL1 SGOL1 339 0.77 0.24 YES
28 NUF2 NUF2 NUF2 352 0.77 0.25 YES
29 MLF1IP MLF1IP MLF1IP 361 0.76 0.26 YES
30 HIST1H2BJ HIST1H2BJ HIST1H2BJ 382 0.75 0.27 YES
31 CDC45 CDC45 CDC45 389 0.75 0.28 YES
32 SPC24 SPC24 SPC24 393 0.75 0.29 YES
33 AURKB AURKB AURKB 415 0.74 0.29 YES
34 AURKA AURKA AURKA 442 0.72 0.3 YES
35 CENPM CENPM CENPM 549 0.68 0.3 YES
36 BUB1B BUB1B BUB1B 569 0.68 0.31 YES
37 CDK1 CDK1 CDK1 576 0.68 0.32 YES
38 CCNB1 CCNB1 CCNB1 596 0.67 0.32 YES
39 CHEK2 CHEK2 CHEK2 641 0.65 0.33 YES
40 WEE1 WEE1 WEE1 659 0.65 0.33 YES
41 GINS2 GINS2 GINS2 677 0.64 0.34 YES
42 CENPI CENPI CENPI 686 0.64 0.35 YES
43 TYMS TYMS TYMS 743 0.62 0.35 YES
44 GINS4 GINS4 GINS4 744 0.62 0.36 YES
45 PLK1 PLK1 PLK1 779 0.6 0.36 YES
46 CDKN2C CDKN2C CDKN2C 900 0.57 0.36 YES
47 E2F2 E2F2 E2F2 992 0.55 0.36 YES
48 PLK4 PLK4 PLK4 999 0.55 0.37 YES
49 HIST1H4H HIST1H4H HIST1H4H 1094 0.52 0.37 YES
50 MCM10 MCM10 MCM10 1171 0.5 0.37 YES
51 CDK2 CDK2 CDK2 1196 0.5 0.38 YES
52 PKMYT1 PKMYT1 PKMYT1 1211 0.49 0.38 YES
53 HIST2H2AC HIST2H2AC HIST2H2AC 1217 0.49 0.39 YES
54 CASC5 CASC5 CASC5 1224 0.49 0.39 YES
55 ITGB3BP ITGB3BP ITGB3BP 1235 0.49 0.4 YES
56 SGOL2 SGOL2 SGOL2 1247 0.49 0.4 YES
57 HIST1H4J HIST1H4J HIST1H4J 1292 0.48 0.4 YES
58 GINS1 GINS1 GINS1 1312 0.48 0.41 YES
59 HIST1H2BK HIST1H2BK HIST1H2BK 1393 0.46 0.41 YES
60 HIST1H2AE HIST1H2AE HIST1H2AE 1406 0.46 0.42 YES
61 CENPN CENPN CENPN 1494 0.44 0.42 YES
62 CENPH CENPH CENPH 1496 0.44 0.42 YES
63 HIST1H2BG HIST1H2BG HIST1H2BG 1512 0.44 0.42 YES
64 CENPL CENPL CENPL 1521 0.44 0.43 YES
65 HIST1H2BO HIST1H2BO HIST1H2BO 1565 0.43 0.43 YES
66 SPC25 SPC25 SPC25 1631 0.42 0.43 YES
67 MCM2 MCM2 MCM2 1646 0.42 0.44 YES
68 MAD2L1 MAD2L1 MAD2L1 1650 0.42 0.44 YES
69 PSMB9 PSMB9 PSMB9 1686 0.42 0.44 YES
70 HIST4H4 HIST4H4 HIST4H4 1692 0.41 0.45 YES
71 ZWILCH ZWILCH ZWILCH 1750 0.4 0.45 YES
72 CKS1B CKS1B CKS1B 1751 0.4 0.45 YES
73 TERT TERT TERT 1755 0.4 0.46 YES
74 CEP135 CEP135 CEP135 1790 0.4 0.46 YES
75 RPA3 RPA3 RPA3 1833 0.39 0.46 YES
76 CHEK1 CHEK1 CHEK1 1842 0.39 0.47 YES
77 ZWINT ZWINT ZWINT 1859 0.39 0.47 YES
78 CDC25A CDC25A CDC25A 1884 0.39 0.47 YES
79 E2F1 E2F1 E2F1 1899 0.39 0.48 YES
80 CDT1 CDT1 CDT1 1931 0.38 0.48 YES
81 B9D2 B9D2 B9D2 1981 0.37 0.48 YES
82 DSN1 DSN1 DSN1 2027 0.37 0.48 YES
83 HIST1H4C HIST1H4C HIST1H4C 2067 0.36 0.49 YES
84 LMNB1 LMNB1 LMNB1 2110 0.35 0.49 YES
85 MCM8 MCM8 MCM8 2120 0.35 0.49 YES
86 HIST1H4D HIST1H4D HIST1H4D 2211 0.34 0.49 YES
87 CCNE1 CCNE1 CCNE1 2232 0.34 0.49 YES
88 HIST1H4A HIST1H4A HIST1H4A 2254 0.34 0.5 YES
89 NUP37 NUP37 NUP37 2285 0.33 0.5 YES
90 KNTC1 KNTC1 KNTC1 2310 0.33 0.5 YES
91 HIST1H2AB HIST1H2AB HIST1H2AB 2322 0.33 0.5 YES
92 HIST1H2BC HIST1H2BC HIST1H2BC 2331 0.33 0.51 YES
93 FBXO5 FBXO5 FBXO5 2338 0.33 0.51 YES
94 DBF4 DBF4 DBF4 2373 0.32 0.51 YES
95 PSMB8 PSMB8 PSMB8 2390 0.32 0.51 YES
96 APITD1 APITD1 APITD1 2436 0.32 0.52 YES
97 HIST1H4E HIST1H4E HIST1H4E 2464 0.31 0.52 YES
98 PCNA PCNA PCNA 2516 0.31 0.52 YES
99 CENPP CENPP CENPP 2531 0.3 0.52 YES
100 RFC2 RFC2 RFC2 2630 0.3 0.52 YES
101 BRCA1 BRCA1 BRCA1 2689 0.29 0.52 YES
102 HIST1H4B HIST1H4B HIST1H4B 2716 0.29 0.52 YES
103 CDK6 CDK6 CDK6 2821 0.28 0.52 YES
104 HIST2H2AA3 HIST2H2AA3 HIST2H2AA3 2895 0.27 0.52 YES
105 RFC3 RFC3 RFC3 2927 0.27 0.52 YES
106 SKP2 SKP2 SKP2 2942 0.27 0.52 YES
107 POLD1 POLD1 POLD1 3005 0.26 0.52 YES
108 RBL1 RBL1 RBL1 3019 0.26 0.52 YES
109 HIST1H4I HIST1H4I HIST1H4I 3030 0.26 0.52 YES
110 HIST1H2AD HIST1H2AD HIST1H2AD 3037 0.26 0.53 YES
111 PRIM2 PRIM2 PRIM2 3056 0.26 0.53 YES
112 CDK4 CDK4 CDK4 3066 0.26 0.53 YES
113 HDAC1 HDAC1 HDAC1 3136 0.25 0.53 YES
114 HIST1H2BD HIST1H2BD HIST1H2BD 3159 0.25 0.53 YES
115 HIST1H2AC HIST1H2AC HIST1H2AC 3162 0.25 0.54 YES
116 CDKN1A CDKN1A CDKN1A 3183 0.24 0.54 YES
117 RFC4 RFC4 RFC4 3242 0.24 0.54 YES
118 CENPO CENPO CENPO 3292 0.24 0.54 YES
119 CCNA1 CCNA1 CCNA1 3330 0.23 0.54 YES
120 CDC7 CDC7 CDC7 3349 0.23 0.54 YES
121 MCM5 MCM5 MCM5 3400 0.23 0.54 YES
122 LMNA LMNA LMNA 3408 0.23 0.54 YES
123 CCNE2 CCNE2 CCNE2 3445 0.22 0.54 YES
124 NEDD1 NEDD1 NEDD1 3452 0.22 0.54 YES
125 POLA2 POLA2 POLA2 3455 0.22 0.55 YES
126 MCM6 MCM6 MCM6 3465 0.22 0.55 YES
127 H2AFX H2AFX H2AFX 3618 0.21 0.54 NO
128 HUS1 HUS1 HUS1 3657 0.21 0.54 NO
129 PRIM1 PRIM1 PRIM1 3768 0.2 0.54 NO
130 HIST2H4A HIST2H4A HIST2H4A 3910 0.19 0.53 NO
131 SMC1B SMC1B SMC1B 3921 0.19 0.53 NO
132 LIG1 LIG1 LIG1 3922 0.19 0.54 NO
133 POLD3 POLD3 POLD3 3986 0.19 0.54 NO
134 PSMA5 PSMA5 PSMA5 3993 0.19 0.54 NO
135 PSMC2 PSMC2 PSMC2 4004 0.19 0.54 NO
136 FGFR1OP FGFR1OP FGFR1OP 4036 0.18 0.54 NO
137 PSMD5 PSMD5 PSMD5 4143 0.18 0.54 NO
138 MCM4 MCM4 MCM4 4218 0.17 0.53 NO
139 PSMD8 PSMD8 PSMD8 4258 0.17 0.53 NO
140 MCM3 MCM3 MCM3 4269 0.17 0.53 NO
141 PSMA2 PSMA2 PSMA2 4285 0.17 0.54 NO
142 MDM2 MDM2 MDM2 4382 0.16 0.53 NO
143 NUP107 NUP107 NUP107 4605 0.16 0.52 NO
144 PSMB10 PSMB10 PSMB10 4618 0.16 0.52 NO
145 NUP85 NUP85 NUP85 4661 0.15 0.52 NO
146 PSME2 PSME2 PSME2 4698 0.15 0.52 NO
147 H2AFZ H2AFZ H2AFZ 4764 0.15 0.52 NO
148 ANAPC10 ANAPC10 ANAPC10 4771 0.15 0.52 NO
149 LIN9 LIN9 LIN9 4794 0.15 0.52 NO
150 TUBA1A TUBA1A TUBA1A 4802 0.15 0.52 NO
151 HIST1H2BL HIST1H2BL HIST1H2BL 4813 0.15 0.52 NO
152 PSMD9 PSMD9 PSMD9 4824 0.14 0.52 NO
153 TP53 TP53 TP53 4841 0.14 0.52 NO
154 PSMC4 PSMC4 PSMC4 4849 0.14 0.53 NO
155 PSMA7 PSMA7 PSMA7 4861 0.14 0.53 NO
156 CETN2 CETN2 CETN2 4980 0.14 0.52 NO
157 RPS27 RPS27 RPS27 5030 0.14 0.52 NO
158 HIST2H2BE HIST2H2BE HIST2H2BE 5076 0.13 0.52 NO
159 PSMB3 PSMB3 PSMB3 5083 0.13 0.52 NO
160 PSMA8 PSMA8 PSMA8 5089 0.13 0.52 NO
161 POLD4 POLD4 POLD4 5145 0.13 0.52 NO
162 TUBB TUBB TUBB 5234 0.13 0.52 NO
163 RCC2 RCC2 RCC2 5244 0.13 0.52 NO
164 RPA2 RPA2 RPA2 5331 0.12 0.52 NO
165 PSMA1 PSMA1 PSMA1 5334 0.12 0.52 NO
166 RUVBL1 RUVBL1 RUVBL1 5419 0.12 0.51 NO
167 DHFR DHFR DHFR 5430 0.12 0.51 NO
168 ANAPC11 ANAPC11 ANAPC11 5449 0.12 0.51 NO
169 PSMB2 PSMB2 PSMB2 5454 0.12 0.52 NO
170 POT1 POT1 POT1 5471 0.12 0.52 NO
171 HIST1H2BN HIST1H2BN HIST1H2BN 5475 0.12 0.52 NO
172 SSNA1 SSNA1 SSNA1 5495 0.12 0.52 NO
173 CDC25B CDC25B CDC25B 5528 0.12 0.52 NO
174 PSMA3 PSMA3 PSMA3 5530 0.12 0.52 NO
175 RB1 RB1 RB1 5577 0.11 0.52 NO
176 POLE POLE POLE 5587 0.11 0.52 NO
177 RFC5 RFC5 RFC5 5610 0.11 0.52 NO
178 MIS12 MIS12 MIS12 5648 0.11 0.52 NO
179 TUBG1 TUBG1 TUBG1 5660 0.11 0.52 NO
180 UBE2I UBE2I UBE2I 5774 0.11 0.51 NO
181 PSMB4 PSMB4 PSMB4 5831 0.1 0.51 NO
182 FEN1 FEN1 FEN1 5848 0.1 0.51 NO
183 CENPQ CENPQ CENPQ 5849 0.1 0.51 NO
184 PSME1 PSME1 PSME1 5865 0.1 0.51 NO
185 WRAP53 WRAP53 WRAP53 5876 0.1 0.51 NO
186 PSMA4 PSMA4 PSMA4 5907 0.1 0.51 NO
187 PSMD12 PSMD12 PSMD12 5920 0.1 0.51 NO
188 PSMD14 PSMD14 PSMD14 5923 0.1 0.51 NO
189 CDK7 CDK7 CDK7 5925 0.1 0.52 NO
190 RUVBL2 RUVBL2 RUVBL2 5930 0.1 0.52 NO
191 TEX12 TEX12 TEX12 5995 0.099 0.51 NO
192 PSMB1 PSMB1 PSMB1 6023 0.098 0.51 NO
193 E2F4 E2F4 E2F4 6075 0.097 0.51 NO
194 E2F5 E2F5 E2F5 6176 0.094 0.51 NO
195 HAUS2 HAUS2 HAUS2 6196 0.093 0.51 NO
196 DYNLL1 DYNLL1 DYNLL1 6230 0.092 0.51 NO
197 CCDC99 CCDC99 CCDC99 6240 0.092 0.51 NO
198 POLD2 POLD2 POLD2 6246 0.091 0.51 NO
199 PSMC1 PSMC1 PSMC1 6273 0.091 0.51 NO
200 RAD1 RAD1 RAD1 6295 0.09 0.51 NO
201 ANAPC7 ANAPC7 ANAPC7 6425 0.086 0.5 NO
202 SEC13 SEC13 SEC13 6492 0.084 0.5 NO
203 RPA4 RPA4 RPA4 6494 0.084 0.5 NO
204 RAD9A RAD9A RAD9A 6526 0.083 0.5 NO
205 PRKACA PRKACA PRKACA 6557 0.082 0.5 NO
206 PSMD11 PSMD11 PSMD11 6562 0.082 0.5 NO
207 RBBP4 RBBP4 RBBP4 6682 0.078 0.49 NO
208 MCM7 MCM7 MCM7 6705 0.077 0.49 NO
209 LIN37 LIN37 LIN37 6720 0.077 0.49 NO
210 DKC1 DKC1 DKC1 6806 0.074 0.49 NO
211 CUL1 CUL1 CUL1 6901 0.071 0.48 NO
212 RPA1 RPA1 RPA1 6908 0.071 0.48 NO
213 CDC14A CDC14A CDC14A 6919 0.07 0.48 NO
214 DNA2 DNA2 DNA2 6993 0.068 0.48 NO
215 PPP2R2A PPP2R2A PPP2R2A 7005 0.068 0.48 NO
216 UBA52 UBA52 UBA52 7022 0.067 0.48 NO
217 ZW10 ZW10 ZW10 7072 0.066 0.48 NO
218 PSMD13 PSMD13 PSMD13 7186 0.063 0.47 NO
219 DCTN2 DCTN2 DCTN2 7188 0.063 0.47 NO
220 CEP76 CEP76 CEP76 7202 0.062 0.47 NO
221 PSMD6 PSMD6 PSMD6 7227 0.062 0.47 NO
222 CDC23 CDC23 CDC23 7235 0.062 0.47 NO
223 RFWD2 RFWD2 RFWD2 7277 0.06 0.47 NO
224 NUP43 NUP43 NUP43 7296 0.06 0.47 NO
225 NSL1 NSL1 NSL1 7325 0.06 0.47 NO
226 CCND2 CCND2 CCND2 7379 0.058 0.47 NO
227 MAD1L1 MAD1L1 MAD1L1 7480 0.055 0.46 NO
228 PSME4 PSME4 PSME4 7499 0.055 0.46 NO
229 ATR ATR ATR 7558 0.053 0.46 NO
230 PMF1 PMF1 PMF1 7647 0.051 0.46 NO
231 CDC16 CDC16 CDC16 7669 0.05 0.46 NO
232 UBE2E1 UBE2E1 UBE2E1 7700 0.05 0.46 NO
233 PSMD7 PSMD7 PSMD7 7752 0.048 0.45 NO
234 PPP1CC PPP1CC PPP1CC 7783 0.047 0.45 NO
235 PSMD2 PSMD2 PSMD2 7860 0.045 0.45 NO
236 GMNN GMNN GMNN 7934 0.043 0.44 NO
237 FKBP6 FKBP6 FKBP6 8113 0.038 0.43 NO
238 PSMF1 PSMF1 PSMF1 8114 0.038 0.44 NO
239 ANAPC4 ANAPC4 ANAPC4 8155 0.038 0.43 NO
240 ATRIP ATRIP ATRIP 8215 0.036 0.43 NO
241 MAPRE1 MAPRE1 MAPRE1 8251 0.035 0.43 NO
242 E2F3 E2F3 E2F3 8276 0.034 0.43 NO
243 TINF2 TINF2 TINF2 8359 0.032 0.42 NO
244 POLA1 POLA1 POLA1 8370 0.031 0.42 NO
245 HIST1H2BF HIST1H2BF HIST1H2BF 8378 0.031 0.42 NO
246 PPP2R1B PPP2R1B PPP2R1B 8458 0.029 0.42 NO
247 NINL NINL NINL 8507 0.028 0.42 NO
248 PSMB6 PSMB6 PSMB6 8526 0.028 0.42 NO
249 XPO1 XPO1 XPO1 8545 0.027 0.42 NO
250 PSMA6 PSMA6 PSMA6 8626 0.025 0.41 NO
251 CLIP1 CLIP1 CLIP1 8651 0.025 0.41 NO
252 PPP2CA PPP2CA PPP2CA 8727 0.023 0.41 NO
253 CCNH CCNH CCNH 8732 0.023 0.41 NO
254 PSMD3 PSMD3 PSMD3 8794 0.021 0.4 NO
255 PSMC3 PSMC3 PSMC3 8822 0.021 0.4 NO
256 PSMB7 PSMB7 PSMB7 8831 0.02 0.4 NO
257 ANAPC1 ANAPC1 ANAPC1 8843 0.02 0.4 NO
258 SEH1L SEH1L SEH1L 8943 0.018 0.4 NO
259 RBBP7 RBBP7 RBBP7 8988 0.016 0.39 NO
260 ANAPC5 ANAPC5 ANAPC5 9101 0.014 0.39 NO
261 SKA2 SKA2 SKA2 9145 0.013 0.38 NO
262 PPP2R5E PPP2R5E PPP2R5E 9197 0.012 0.38 NO
263 PSMD1 PSMD1 PSMD1 9310 0.0088 0.38 NO
264 CDC27 CDC27 CDC27 9311 0.0088 0.38 NO
265 LIN52 LIN52 LIN52 9375 0.0071 0.37 NO
266 PSMD10 PSMD10 PSMD10 9448 0.0055 0.37 NO
267 NDEL1 NDEL1 NDEL1 9454 0.0053 0.37 NO
268 NHP2 NHP2 NHP2 9635 0.00095 0.36 NO
269 DCTN3 DCTN3 DCTN3 9668 0.000069 0.36 NO
270 CEP70 CEP70 CEP70 9720 -0.0013 0.35 NO
271 CCND3 CCND3 CCND3 9750 -0.0019 0.35 NO
272 PPP2R1A PPP2R1A PPP2R1A 9757 -0.0021 0.35 NO
273 YWHAE YWHAE YWHAE 9813 -0.0035 0.35 NO
274 SKP1 SKP1 SKP1 9836 -0.0042 0.35 NO
275 CEP164 CEP164 CEP164 9892 -0.0056 0.34 NO
276 PPP2CB PPP2CB PPP2CB 9919 -0.0062 0.34 NO
277 CSNK1D CSNK1D CSNK1D 9971 -0.0073 0.34 NO
278 MNAT1 MNAT1 MNAT1 10012 -0.0084 0.34 NO
279 INCENP INCENP INCENP 10043 -0.0093 0.34 NO
280 RAD17 RAD17 RAD17 10047 -0.0093 0.34 NO
281 HSP90AA1 HSP90AA1 HSP90AA1 10127 -0.011 0.33 NO
282 TFDP1 TFDP1 TFDP1 10151 -0.012 0.33 NO
283 PSMB5 PSMB5 PSMB5 10302 -0.016 0.32 NO
284 SMARCA5 SMARCA5 SMARCA5 10365 -0.018 0.32 NO
285 YWHAG YWHAG YWHAG 10374 -0.018 0.32 NO
286 OFD1 OFD1 OFD1 10430 -0.019 0.32 NO
287 CEP72 CEP72 CEP72 10441 -0.02 0.32 NO
288 MAX MAX MAX 10542 -0.022 0.31 NO
289 PPP2R5D PPP2R5D PPP2R5D 10548 -0.022 0.31 NO
290 UBE2D1 UBE2D1 UBE2D1 10561 -0.022 0.31 NO
291 NUDC NUDC NUDC 10571 -0.022 0.31 NO
292 DIDO1 DIDO1 DIDO1 10648 -0.024 0.31 NO
293 PSMD4 PSMD4 PSMD4 10670 -0.025 0.31 NO
294 STAG3 STAG3 STAG3 10760 -0.027 0.3 NO
295 HIST1H2BE HIST1H2BE HIST1H2BE 10867 -0.03 0.3 NO
296 SMC1A SMC1A SMC1A 10910 -0.031 0.29 NO
297 CDKN2A CDKN2A CDKN2A 10933 -0.031 0.29 NO
298 CENPT CENPT CENPT 11002 -0.033 0.29 NO
299 SDCCAG8 SDCCAG8 SDCCAG8 11008 -0.033 0.29 NO
300 CDK5RAP2 CDK5RAP2 CDK5RAP2 11136 -0.036 0.28 NO
301 NUP133 NUP133 NUP133 11243 -0.039 0.28 NO
302 STAG1 STAG1 STAG1 11392 -0.043 0.27 NO
303 CEP63 CEP63 CEP63 11461 -0.045 0.27 NO
304 STAG2 STAG2 STAG2 11478 -0.045 0.27 NO
305 CCND1 CCND1 CCND1 11510 -0.046 0.26 NO
306 NPM1 NPM1 NPM1 11526 -0.047 0.26 NO
307 DYRK1A DYRK1A DYRK1A 11562 -0.048 0.26 NO
308 TERF1 TERF1 TERF1 11679 -0.052 0.26 NO
309 TK2 TK2 TK2 11700 -0.052 0.26 NO
310 RAD21 RAD21 RAD21 11750 -0.053 0.26 NO
311 PSMC5 PSMC5 PSMC5 11799 -0.055 0.25 NO
312 CEP57 CEP57 CEP57 11857 -0.057 0.25 NO
313 BUB3 BUB3 BUB3 11880 -0.057 0.25 NO
314 HIST3H3 HIST3H3 HIST3H3 11910 -0.058 0.25 NO
315 PSMC6 PSMC6 PSMC6 12000 -0.061 0.24 NO
316 CENPC1 CENPC1 CENPC1 12134 -0.065 0.24 NO
317 PPP2R5B PPP2R5B PPP2R5B 12272 -0.069 0.23 NO
318 ACD ACD ACD 12317 -0.07 0.23 NO
319 TUBGCP5 TUBGCP5 TUBGCP5 12326 -0.071 0.23 NO
320 CEP192 CEP192 CEP192 12348 -0.071 0.23 NO
321 TUBGCP3 TUBGCP3 TUBGCP3 12421 -0.074 0.23 NO
322 LIN54 LIN54 LIN54 12424 -0.074 0.23 NO
323 SUN2 SUN2 SUN2 12483 -0.075 0.22 NO
324 CKAP5 CKAP5 CKAP5 12484 -0.075 0.22 NO
325 PCM1 PCM1 PCM1 12570 -0.078 0.22 NO
326 GORASP1 GORASP1 GORASP1 12632 -0.079 0.22 NO
327 RBL2 RBL2 RBL2 12680 -0.081 0.22 NO
328 ANAPC2 ANAPC2 ANAPC2 12697 -0.082 0.22 NO
329 RANBP2 RANBP2 RANBP2 12747 -0.083 0.22 NO
330 CENPJ CENPJ CENPJ 12989 -0.091 0.2 NO
331 AHCTF1 AHCTF1 AHCTF1 13161 -0.096 0.2 NO
332 PPP2R5C PPP2R5C PPP2R5C 13251 -0.1 0.19 NO
333 DYNC1I2 DYNC1I2 DYNC1I2 13291 -0.1 0.19 NO
334 RANGAP1 RANGAP1 RANGAP1 13321 -0.1 0.19 NO
335 CDKN1B CDKN1B CDKN1B 13324 -0.1 0.19 NO
336 PRKAR2B PRKAR2B PRKAR2B 13464 -0.11 0.18 NO
337 DCTN1 DCTN1 DCTN1 13585 -0.11 0.18 NO
338 PAFAH1B1 PAFAH1B1 PAFAH1B1 13691 -0.12 0.17 NO
339 MYC MYC MYC 13719 -0.12 0.17 NO
340 ACTR1A ACTR1A ACTR1A 13720 -0.12 0.18 NO
341 CDKN2D CDKN2D CDKN2D 13798 -0.12 0.17 NO
342 CLASP1 CLASP1 CLASP1 13859 -0.12 0.17 NO
343 SYNE2 SYNE2 SYNE2 13990 -0.13 0.16 NO
344 AZI1 AZI1 AZI1 14018 -0.13 0.16 NO
345 HSPA2 HSPA2 HSPA2 14044 -0.13 0.16 NO
346 TERF2IP TERF2IP TERF2IP 14060 -0.13 0.16 NO
347 TERF2 TERF2 TERF2 14062 -0.13 0.17 NO
348 ALMS1 ALMS1 ALMS1 14156 -0.14 0.16 NO
349 ATM ATM ATM 14176 -0.14 0.16 NO
350 TUBGCP2 TUBGCP2 TUBGCP2 14292 -0.14 0.16 NO
351 PCNT PCNT PCNT 14616 -0.16 0.14 NO
352 CEP250 CEP250 CEP250 14640 -0.16 0.14 NO
353 PPP2R3B PPP2R3B PPP2R3B 14707 -0.16 0.14 NO
354 RPS27A RPS27A RPS27A 14744 -0.16 0.14 NO
355 TUBG2 TUBG2 TUBG2 14755 -0.17 0.14 NO
356 TUBGCP6 TUBGCP6 TUBGCP6 14761 -0.17 0.14 NO
357 KIF2A KIF2A KIF2A 14932 -0.18 0.14 NO
358 CSNK1E CSNK1E CSNK1E 14973 -0.18 0.14 NO
359 DYNC1H1 DYNC1H1 DYNC1H1 15062 -0.18 0.13 NO
360 TUBA4A TUBA4A TUBA4A 15231 -0.2 0.13 NO
361 PPP2R5A PPP2R5A PPP2R5A 15425 -0.21 0.12 NO
362 SMC3 SMC3 SMC3 15459 -0.21 0.12 NO
363 NUMA1 NUMA1 NUMA1 15472 -0.21 0.12 NO
364 CEP290 CEP290 CEP290 15544 -0.22 0.12 NO
365 AKAP9 AKAP9 AKAP9 15594 -0.22 0.12 NO
366 REC8 REC8 REC8 15704 -0.23 0.12 NO
367 RSF1 RSF1 RSF1 15768 -0.24 0.12 NO
368 BTRC BTRC BTRC 15857 -0.25 0.11 NO
369 CDKN2B CDKN2B CDKN2B 15897 -0.25 0.11 NO
370 SYNE1 SYNE1 SYNE1 16052 -0.26 0.11 NO
371 TAOK1 TAOK1 TAOK1 16563 -0.32 0.083 NO
372 HIST3H2BB HIST3H2BB HIST3H2BB 17078 -0.4 0.059 NO
373 SYCP2 SYCP2 SYCP2 17181 -0.42 0.058 NO
374 CDC26 CDC26 CDC26 17259 -0.43 0.058 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: PID IL2 STAT5PATHWAY.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: PID IL2 STAT5PATHWAY, 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 AURORA A PATHWAY

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 CCNA2 CCNA2 CCNA2 284 0.8 0.089 YES
2 IL2RG IL2RG IL2RG 333 0.78 0.19 YES
3 PRF1 PRF1 PRF1 341 0.77 0.29 YES
4 IL2RB IL2RB IL2RB 346 0.77 0.39 YES
5 IL2RA IL2RA IL2RA 610 0.66 0.46 YES
6 LCK LCK LCK 647 0.65 0.54 YES
7 FASLG FASLG FASLG 950 0.56 0.6 YES
8 JAK3 JAK3 JAK3 1062 0.53 0.66 YES
9 SHC1 SHC1 SHC1 2426 0.32 0.63 YES
10 STAT5A STAT5A STAT5A 2793 0.28 0.64 YES
11 CDK6 CDK6 CDK6 2821 0.28 0.68 YES
12 ELF1 ELF1 ELF1 6913 0.071 0.46 NO
13 CCND2 CCND2 CCND2 7379 0.058 0.45 NO
14 LTA LTA LTA 7842 0.046 0.43 NO
15 BCL2L1 BCL2L1 BCL2L1 8004 0.041 0.42 NO
16 SP1 SP1 SP1 9384 0.0069 0.35 NO
17 CCND3 CCND3 CCND3 9750 -0.0019 0.33 NO
18 FOXP3 FOXP3 FOXP3 10133 -0.011 0.31 NO
19 GRB2 GRB2 GRB2 10272 -0.015 0.3 NO
20 JAK1 JAK1 JAK1 11660 -0.051 0.24 NO
21 STAT5B STAT5B STAT5B 12592 -0.078 0.19 NO
22 SOS1 SOS1 SOS1 12719 -0.082 0.2 NO
23 PIK3CA PIK3CA PIK3CA 13098 -0.094 0.19 NO
24 MYC MYC MYC 13719 -0.12 0.17 NO
25 PTPN11 PTPN11 PTPN11 13893 -0.12 0.18 NO
26 BCL2 BCL2 BCL2 13976 -0.13 0.19 NO
27 GAB2 GAB2 GAB2 14199 -0.14 0.2 NO
28 PIK3R1 PIK3R1 PIK3R1 15566 -0.22 0.15 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: PID AURORA A PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AURORA A 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 BARD1PATHWAY

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 CASP8 CASP8 CASP8 628 0.66 0.03 YES
2 CASP6 CASP6 CASP6 731 0.62 0.085 YES
3 FASLG FASLG FASLG 950 0.56 0.13 YES
4 BIRC3 BIRC3 BIRC3 993 0.55 0.18 YES
5 FAS FAS FAS 1093 0.52 0.22 YES
6 TNFRSF1A TNFRSF1A TNFRSF1A 1824 0.4 0.22 YES
7 TRADD TRADD TRADD 2065 0.36 0.25 YES
8 LMNB1 LMNB1 LMNB1 2110 0.35 0.28 YES
9 CASP7 CASP7 CASP7 2229 0.34 0.3 YES
10 ARHGDIB ARHGDIB ARHGDIB 2554 0.3 0.32 YES
11 CASP3 CASP3 CASP3 2748 0.28 0.33 YES
12 TRAF1 TRAF1 TRAF1 2929 0.27 0.35 YES
13 LMNA LMNA LMNA 3408 0.23 0.35 YES
14 FADD FADD FADD 3449 0.22 0.37 YES
15 RIPK1 RIPK1 RIPK1 3534 0.22 0.38 YES
16 TNFRSF1B TNFRSF1B TNFRSF1B 3557 0.22 0.4 YES
17 CASP2 CASP2 CASP2 3674 0.21 0.42 YES
18 CFLAR CFLAR CFLAR 3762 0.2 0.43 YES
19 MAP3K1 MAP3K1 MAP3K1 3973 0.19 0.44 YES
20 MAP3K14 MAP3K14 MAP3K14 4153 0.18 0.45 YES
21 PSEN2 PSEN2 PSEN2 4288 0.17 0.46 YES
22 MDM2 MDM2 MDM2 4382 0.16 0.47 YES
23 PRKCD PRKCD PRKCD 4445 0.16 0.48 YES
24 LMNB2 LMNB2 LMNB2 4588 0.16 0.49 YES
25 NFKB1 NFKB1 NFKB1 4983 0.14 0.48 NO
26 RB1 RB1 RB1 5577 0.11 0.46 NO
27 DFFB DFFB DFFB 6048 0.098 0.44 NO
28 CYCS CYCS CYCS 6054 0.098 0.45 NO
29 ACTG1 ACTG1 ACTG1 6546 0.082 0.43 NO
30 BIRC2 BIRC2 BIRC2 7365 0.058 0.39 NO
31 DAXX DAXX DAXX 7538 0.053 0.39 NO
32 GSN GSN GSN 7604 0.052 0.39 NO
33 DFFA DFFA DFFA 7611 0.052 0.4 NO
34 TRAF2 TRAF2 TRAF2 8348 0.032 0.36 NO
35 CRADD CRADD CRADD 8892 0.019 0.33 NO
36 RELA RELA RELA 8998 0.016 0.32 NO
37 CDK11A CDK11A CDK11A 9535 0.0035 0.3 NO
38 CDK11B CDK11B CDK11B 9585 0.0021 0.29 NO
39 PAK2 PAK2 PAK2 10162 -0.012 0.26 NO
40 PSEN1 PSEN1 PSEN1 10177 -0.012 0.26 NO
41 PRKDC PRKDC PRKDC 10205 -0.013 0.26 NO
42 APAF1 APAF1 APAF1 10339 -0.017 0.26 NO
43 PARP1 PARP1 PARP1 10572 -0.023 0.25 NO
44 RASA1 RASA1 RASA1 10977 -0.032 0.23 NO
45 TNF TNF TNF 11029 -0.034 0.23 NO
46 NFKBIA NFKBIA NFKBIA 11169 -0.037 0.22 NO
47 MAP2K7 MAP2K7 MAP2K7 11525 -0.047 0.21 NO
48 XIAP XIAP XIAP 12009 -0.061 0.19 NO
49 PTK2 PTK2 PTK2 12209 -0.067 0.19 NO
50 CHUK CHUK CHUK 12233 -0.068 0.19 NO
51 BAG4 BAG4 BAG4 12519 -0.076 0.18 NO
52 BCL2 BCL2 BCL2 13976 -0.13 0.12 NO
53 SPTAN1 SPTAN1 SPTAN1 14557 -0.16 0.099 NO
54 CASP9 CASP9 CASP9 14626 -0.16 0.11 NO
55 BID BID BID 15028 -0.18 0.11 NO
56 NUMA1 NUMA1 NUMA1 15472 -0.21 0.1 NO
57 MAP3K5 MAP3K5 MAP3K5 15829 -0.24 0.11 NO
58 MAPK8 MAPK8 MAPK8 16268 -0.29 0.11 NO

Figure S19.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID BARD1PATHWAY.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: PID BARD1PATHWAY, 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM 30 genes.ES.table 0.56 1.6 0.022 0.18 0.94 0.37 0.17 0.3 0.11 0.009
KEGG O GLYCAN BIOSYNTHESIS 30 genes.ES.table 0.57 1.5 0.029 0.23 0.99 0.3 0.12 0.26 0.16 0.009
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE 26 genes.ES.table 0.63 1.6 0.0063 0.17 0.84 0.38 0.18 0.32 0.088 0.015
KEGG INOSITOL PHOSPHATE METABOLISM 52 genes.ES.table 0.47 1.5 0.063 0.2 0.96 0.44 0.26 0.33 0.13 0.008
KEGG PYRUVATE METABOLISM 39 genes.ES.table 0.47 1.6 0.041 0.18 0.95 0.41 0.25 0.31 0.11 0.009
KEGG BUTANOATE METABOLISM 31 genes.ES.table 0.54 1.6 0.031 0.18 0.94 0.39 0.23 0.3 0.11 0.009
KEGG MAPK SIGNALING PATHWAY 254 genes.ES.table 0.42 1.5 0.025 0.21 0.97 0.27 0.17 0.23 0.15 0.008
KEGG ERBB SIGNALING PATHWAY 86 genes.ES.table 0.44 1.6 0.019 0.19 0.92 0.23 0.17 0.19 0.11 0.011
KEGG CALCIUM SIGNALING PATHWAY 175 genes.ES.table 0.69 1.8 0 0.27 0.5 0.43 0.13 0.38 0 0.06
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM 74 genes.ES.table 0.56 1.7 0.0041 0.18 0.71 0.43 0.22 0.34 0.08 0.025
genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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 PPP2R2C PPP2R2C PPP2R2C 445 0.71 0.13 YES
2 PKLR PKLR PKLR 973 0.48 0.2 YES
3 PRKAR1B PRKAR1B PRKAR1B 1317 0.39 0.27 YES
4 PRKAR2B PRKAR2B PRKAR2B 1677 0.32 0.32 YES
5 YWHAH YWHAH YWHAH 2279 0.24 0.34 YES
6 YWHAG YWHAG YWHAG 2957 0.18 0.34 YES
7 PRKAA2 PRKAA2 PRKAA2 3003 0.18 0.38 YES
8 FASN FASN FASN 3712 0.13 0.36 YES
9 PRKACB PRKACB PRKACB 3826 0.12 0.39 YES
10 MLXIPL MLXIPL MLXIPL 3989 0.12 0.4 YES
11 ACACA ACACA ACACA 4066 0.12 0.42 YES
12 PPP2R2D PPP2R2D PPP2R2D 4112 0.11 0.44 YES
13 PPP2R2B PPP2R2B PPP2R2B 4113 0.11 0.47 YES
14 PRKAG2 PRKAG2 PRKAG2 4199 0.11 0.49 YES
15 PRKACG PRKACG PRKACG 4422 0.099 0.5 YES
16 PPP2R5B PPP2R5B PPP2R5B 4498 0.096 0.51 YES
17 PPP2R3A PPP2R3A PPP2R3A 4787 0.086 0.52 YES
18 YWHAB YWHAB YWHAB 4950 0.081 0.53 YES
19 PPP2R5A PPP2R5A PPP2R5A 5589 0.06 0.5 YES
20 YWHAZ YWHAZ YWHAZ 5668 0.058 0.51 YES
21 PPP2R5D PPP2R5D PPP2R5D 5728 0.056 0.52 YES
22 PRKAR1A PRKAR1A PRKAR1A 5740 0.056 0.53 YES
23 PRKAB2 PRKAB2 PRKAB2 5798 0.055 0.54 YES
24 PPP2R5C PPP2R5C PPP2R5C 5853 0.053 0.55 YES
25 PPP2R4 PPP2R4 PPP2R4 6579 0.036 0.52 NO
26 PPP2R1A PPP2R1A PPP2R1A 6924 0.029 0.51 NO
27 PPP2CA PPP2CA PPP2CA 7430 0.02 0.48 NO
28 PRKACA PRKACA PRKACA 7885 0.011 0.46 NO
29 PPP2R5E PPP2R5E PPP2R5E 8028 0.0091 0.45 NO
30 PPP2CB PPP2CB PPP2CB 8482 0.0016 0.43 NO
31 YWHAE YWHAE YWHAE 9072 -0.0086 0.4 NO
32 PPP2R3B PPP2R3B PPP2R3B 9326 -0.013 0.39 NO
33 YWHAQ YWHAQ YWHAQ 10198 -0.027 0.35 NO
34 PPP2R2A PPP2R2A PPP2R2A 10561 -0.033 0.33 NO
35 PPP2R1B PPP2R1B PPP2R1B 10836 -0.038 0.33 NO
36 PRKAR2A PRKAR2A PRKAR2A 11300 -0.045 0.31 NO
37 GCK GCK GCK 11359 -0.046 0.32 NO
38 PRKAG1 PRKAG1 PRKAG1 11469 -0.048 0.32 NO
39 PRKAA1 PRKAA1 PRKAA1 12055 -0.059 0.3 NO
40 PRKAB1 PRKAB1 PRKAB1 12278 -0.063 0.3 NO
41 MLX MLX MLX 14577 -0.12 0.2 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

genes ES table in pathway: KEGG O GLYCAN 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 TNNT2 TNNT2 TNNT2 28 1.2 0.073 YES
2 CACNG3 CACNG3 CACNG3 39 1.2 0.15 YES
3 RYR2 RYR2 RYR2 46 1.2 0.22 YES
4 CACNA2D3 CACNA2D3 CACNA2D3 317 0.82 0.25 YES
5 CACNA1F CACNA1F CACNA1F 393 0.75 0.29 YES
6 CACNG2 CACNG2 CACNG2 405 0.74 0.34 YES
7 CACNG8 CACNG8 CACNG8 452 0.71 0.38 YES
8 CACNA1S CACNA1S CACNA1S 718 0.57 0.4 YES
9 CACNA2D1 CACNA2D1 CACNA2D1 865 0.51 0.42 YES
10 CACNA2D2 CACNA2D2 CACNA2D2 867 0.51 0.45 YES
11 CACNB2 CACNB2 CACNB2 1026 0.46 0.47 YES
12 ATP1A3 ATP1A3 ATP1A3 1126 0.44 0.49 YES
13 COX7A1 COX7A1 COX7A1 1180 0.42 0.52 YES
14 CACNB1 CACNB1 CACNB1 1195 0.42 0.54 YES
15 CACNB4 CACNB4 CACNB4 1327 0.38 0.56 YES
16 CACNA1C CACNA1C CACNA1C 1445 0.36 0.57 YES
17 CACNA1D CACNA1D CACNA1D 1469 0.35 0.59 YES
18 MYL3 MYL3 MYL3 1578 0.34 0.61 YES
19 ATP1B1 ATP1B1 ATP1B1 1710 0.32 0.62 YES
20 CACNB3 CACNB3 CACNB3 1725 0.32 0.64 YES
21 MYH6 MYH6 MYH6 2053 0.27 0.64 YES
22 MYH7 MYH7 MYH7 2259 0.24 0.64 YES
23 ACTC1 ACTC1 ACTC1 2297 0.24 0.65 YES
24 ATP1A2 ATP1A2 ATP1A2 2413 0.23 0.66 YES
25 SLC9A6 SLC9A6 SLC9A6 2508 0.22 0.67 YES
26 ATP1A4 ATP1A4 ATP1A4 2510 0.22 0.68 YES
27 TNNI3 TNNI3 TNNI3 4046 0.12 0.6 NO
28 CACNG7 CACNG7 CACNG7 4236 0.11 0.6 NO
29 CACNG5 CACNG5 CACNG5 4264 0.11 0.6 NO
30 ATP1B4 ATP1B4 ATP1B4 4630 0.092 0.59 NO
31 ATP2A2 ATP2A2 ATP2A2 4870 0.083 0.58 NO
32 UQCRB UQCRB UQCRB 5398 0.066 0.56 NO
33 UQCRC2 UQCRC2 UQCRC2 5628 0.06 0.55 NO
34 SLC8A1 SLC8A1 SLC8A1 5947 0.051 0.53 NO
35 SLC9A1 SLC9A1 SLC9A1 6080 0.048 0.53 NO
36 CACNG4 CACNG4 CACNG4 6165 0.045 0.53 NO
37 TNNC1 TNNC1 TNNC1 6272 0.043 0.52 NO
38 ATP1A1 ATP1A1 ATP1A1 6304 0.042 0.52 NO
39 ATP1B2 ATP1B2 ATP1B2 6552 0.036 0.51 NO
40 COX4I1 COX4I1 COX4I1 6682 0.033 0.51 NO
41 COX7C COX7C COX7C 6845 0.031 0.5 NO
42 COX7A2L COX7A2L COX7A2L 6902 0.03 0.5 NO
43 COX6A1 COX6A1 COX6A1 7380 0.021 0.48 NO
44 UQCRC1 UQCRC1 UQCRC1 7645 0.016 0.46 NO
45 COX6C COX6C COX6C 8011 0.0093 0.44 NO
46 UQCRH UQCRH UQCRH 8022 0.0092 0.44 NO
47 TPM1 TPM1 TPM1 8430 0.0025 0.42 NO
48 COX5A COX5A COX5A 8669 -0.0018 0.41 NO
49 UQCR10 UQCR10 UQCR10 9327 -0.013 0.37 NO
50 COX7A2 COX7A2 COX7A2 9406 -0.014 0.37 NO
51 CACNG1 CACNG1 CACNG1 9559 -0.016 0.36 NO
52 CYC1 CYC1 CYC1 9622 -0.017 0.36 NO
53 COX6A2 COX6A2 COX6A2 9878 -0.022 0.35 NO
54 COX5B COX5B COX5B 9891 -0.022 0.35 NO
55 UQCRFS1 UQCRFS1 UQCRFS1 10180 -0.026 0.33 NO
56 COX8A COX8A COX8A 10807 -0.037 0.3 NO
57 TPM3 TPM3 TPM3 11109 -0.042 0.29 NO
58 COX7B COX7B COX7B 11693 -0.052 0.26 NO
59 COX6B1 COX6B1 COX6B1 12053 -0.058 0.24 NO
60 CACNG6 CACNG6 CACNG6 12200 -0.062 0.24 NO
61 UQCR11 UQCR11 UQCR11 12400 -0.066 0.23 NO
62 ATP1B3 ATP1B3 ATP1B3 12649 -0.071 0.22 NO
63 UQCRHL UQCRHL UQCRHL 13377 -0.086 0.19 NO
64 UQCRQ UQCRQ UQCRQ 13483 -0.088 0.18 NO
65 TPM2 TPM2 TPM2 13716 -0.095 0.18 NO
66 FXYD2 FXYD2 FXYD2 13950 -0.1 0.17 NO
67 COX8C COX8C COX8C 14379 -0.11 0.16 NO
68 COX4I2 COX4I2 COX4I2 15077 -0.14 0.13 NO
69 TPM4 TPM4 TPM4 15478 -0.16 0.11 NO
70 COX6B2 COX6B2 COX6B2 16142 -0.2 0.09 NO
71 CACNA2D4 CACNA2D4 CACNA2D4 18056 -0.48 0.014 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 O GLYCAN BIOSYNTHESIS.

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG O GLYCAN 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 GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

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 CAMK2A CAMK2A CAMK2A 123 1 0.16 YES
2 STAT4 STAT4 STAT4 243 0.88 0.29 YES
3 PRKCB PRKCB PRKCB 619 0.61 0.36 YES
4 CAMK2B CAMK2B CAMK2B 726 0.56 0.45 YES
5 PTK2B PTK2B PTK2B 1920 0.29 0.43 YES
6 CAMK2G CAMK2G CAMK2G 2362 0.23 0.44 YES
7 GNAI1 GNAI1 GNAI1 2525 0.22 0.46 YES
8 CALM3 CALM3 CALM3 2778 0.19 0.48 YES
9 MAPK8 MAPK8 MAPK8 2782 0.19 0.51 YES
10 MAPT MAPT MAPT 3066 0.17 0.52 YES
11 MAP2K1 MAP2K1 MAP2K1 3142 0.17 0.55 YES
12 CALM1 CALM1 CALM1 3228 0.16 0.57 YES
13 F2 F2 F2 3966 0.12 0.55 NO
14 PRKCA PRKCA PRKCA 3969 0.12 0.56 NO
15 MAPK3 MAPK3 MAPK3 4559 0.095 0.55 NO
16 MAPK1 MAPK1 MAPK1 4939 0.081 0.54 NO
17 CDK5 CDK5 CDK5 5202 0.073 0.54 NO
18 GNA11 GNA11 GNA11 5486 0.064 0.53 NO
19 CALM2 CALM2 CALM2 6291 0.042 0.49 NO
20 HRAS HRAS HRAS 6513 0.037 0.49 NO
21 MYLK MYLK MYLK 7385 0.02 0.44 NO
22 SOS1 SOS1 SOS1 7550 0.018 0.44 NO
23 GNB1 GNB1 GNB1 7711 0.014 0.43 NO
24 STAT5B STAT5B STAT5B 7866 0.012 0.42 NO
25 GRB2 GRB2 GRB2 8294 0.0048 0.4 NO
26 FYN FYN FYN 8312 0.0045 0.4 NO
27 AGT AGT AGT 8416 0.0027 0.4 NO
28 STAT6 STAT6 STAT6 8648 -0.0015 0.38 NO
29 MAP2K2 MAP2K2 MAP2K2 9076 -0.0087 0.36 NO
30 JAK2 JAK2 JAK2 9872 -0.022 0.32 NO
31 MAPK14 MAPK14 MAPK14 10332 -0.029 0.3 NO
32 CAMK2D CAMK2D CAMK2D 10553 -0.033 0.29 NO
33 PLCG1 PLCG1 PLCG1 10845 -0.038 0.28 NO
34 RAF1 RAF1 RAF1 11154 -0.042 0.27 NO
35 STAT2 STAT2 STAT2 13103 -0.08 0.18 NO
36 STAT3 STAT3 STAT3 13980 -0.1 0.15 NO
37 STAT1 STAT1 STAT1 14614 -0.12 0.13 NO
38 SHC1 SHC1 SHC1 15985 -0.19 0.087 NO
39 STAT5A STAT5A STAT5A 16723 -0.26 0.087 NO

Figure S25.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.

Figure S26.  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 INOSITOL PHOSPHATE METABOLISM

Table S14.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 73 1.1 0.058 YES
2 CAMK4 CAMK4 CAMK4 354 0.78 0.087 YES
3 DNM1 DNM1 DNM1 553 0.64 0.11 YES
4 PDE1A PDE1A PDE1A 587 0.63 0.15 YES
5 PDE1B PDE1B PDE1B 633 0.6 0.18 YES
6 ADCY1 ADCY1 ADCY1 649 0.59 0.21 YES
7 ADCYAP1 ADCYAP1 ADCYAP1 970 0.48 0.22 YES
8 SH3GL2 SH3GL2 SH3GL2 1016 0.46 0.24 YES
9 RIT2 RIT2 RIT2 1101 0.44 0.26 YES
10 SHC3 SHC3 SHC3 1169 0.42 0.28 YES
11 ADCY5 ADCY5 ADCY5 1244 0.4 0.3 YES
12 PRKCE PRKCE PRKCE 1284 0.39 0.32 YES
13 PRKAR1B PRKAR1B PRKAR1B 1317 0.39 0.34 YES
14 NGF NGF NGF 1452 0.36 0.35 YES
15 PRKAR2B PRKAR2B PRKAR2B 1677 0.32 0.36 YES
16 MEF2C MEF2C MEF2C 1995 0.28 0.36 YES
17 RPS6KA5 RPS6KA5 RPS6KA5 1997 0.28 0.37 YES
18 ADCYAP1R1 ADCYAP1R1 ADCYAP1R1 2432 0.22 0.36 YES
19 CALM3 CALM3 CALM3 2778 0.19 0.35 YES
20 MAPK11 MAPK11 MAPK11 2833 0.19 0.36 YES
21 AKT3 AKT3 AKT3 3008 0.18 0.36 YES
22 MAP2K1 MAP2K1 MAP2K1 3142 0.17 0.36 YES
23 CALM1 CALM1 CALM1 3228 0.16 0.37 YES
24 ADCY2 ADCY2 ADCY2 3297 0.16 0.37 YES
25 FOXO4 FOXO4 FOXO4 3329 0.15 0.38 YES
26 DUSP7 DUSP7 DUSP7 3512 0.14 0.38 YES
27 RPS6KA2 RPS6KA2 RPS6KA2 3588 0.14 0.38 YES
28 PDPK1 PDPK1 PDPK1 3608 0.14 0.39 YES
29 NTRK2 NTRK2 NTRK2 3625 0.14 0.39 YES
30 PRKACB PRKACB PRKACB 3826 0.12 0.39 YES
31 PIK3CB PIK3CB PIK3CB 3849 0.12 0.4 YES
32 RICTOR RICTOR RICTOR 3860 0.12 0.4 YES
33 ELK1 ELK1 ELK1 3917 0.12 0.4 YES
34 PRKCA PRKCA PRKCA 3969 0.12 0.41 YES
35 IRS1 IRS1 IRS1 4244 0.11 0.4 YES
36 PIK3R1 PIK3R1 PIK3R1 4256 0.11 0.4 YES
37 PRKACG PRKACG PRKACG 4422 0.099 0.4 YES
38 MAPK3 MAPK3 MAPK3 4559 0.095 0.4 YES
39 BRAF BRAF BRAF 4716 0.089 0.4 YES
40 DUSP3 DUSP3 DUSP3 4734 0.088 0.4 YES
41 THEM4 THEM4 THEM4 4741 0.088 0.4 YES
42 PTEN PTEN PTEN 4779 0.086 0.41 YES
43 ADRBK1 ADRBK1 ADRBK1 4839 0.084 0.41 YES
44 FOXO3 FOXO3 FOXO3 4847 0.084 0.41 YES
45 MAPK1 MAPK1 MAPK1 4939 0.081 0.41 YES
46 YWHAB YWHAB YWHAB 4950 0.081 0.42 YES
47 PHLPP1 PHLPP1 PHLPP1 5040 0.078 0.42 YES
48 MEF2A MEF2A MEF2A 5140 0.075 0.42 YES
49 AP2A2 AP2A2 AP2A2 5168 0.074 0.42 YES
50 NR4A1 NR4A1 NR4A1 5183 0.073 0.42 YES
51 KRAS KRAS KRAS 5193 0.073 0.42 YES
52 KIDINS220 KIDINS220 KIDINS220 5323 0.069 0.42 YES
53 AP2A1 AP2A1 AP2A1 5415 0.066 0.42 YES
54 MAPK12 MAPK12 MAPK12 5455 0.065 0.42 YES
55 ADCY9 ADCY9 ADCY9 5643 0.059 0.41 YES
56 AP2B1 AP2B1 AP2B1 5651 0.059 0.42 YES
57 MAPK13 MAPK13 MAPK13 5657 0.059 0.42 YES
58 DNAL4 DNAL4 DNAL4 5658 0.059 0.42 YES
59 ADCY3 ADCY3 ADCY3 5700 0.058 0.42 YES
60 PPP2R5D PPP2R5D PPP2R5D 5728 0.056 0.43 YES
61 PRKAR1A PRKAR1A PRKAR1A 5740 0.056 0.43 YES
62 SHC2 SHC2 SHC2 5751 0.056 0.43 YES
63 GSK3A GSK3A GSK3A 6040 0.048 0.42 NO
64 SRC SRC SRC 6043 0.048 0.42 NO
65 RALB RALB RALB 6179 0.045 0.42 NO
66 AP2M1 AP2M1 AP2M1 6188 0.045 0.42 NO
67 TSC2 TSC2 TSC2 6261 0.043 0.42 NO
68 CALM2 CALM2 CALM2 6291 0.042 0.42 NO
69 CLTC CLTC CLTC 6306 0.042 0.42 NO
70 ADCY8 ADCY8 ADCY8 6373 0.04 0.42 NO
71 HRAS HRAS HRAS 6513 0.037 0.41 NO
72 ITPR2 ITPR2 ITPR2 6818 0.031 0.4 NO
73 CDKN1B CDKN1B CDKN1B 6859 0.03 0.4 NO
74 PPP2R1A PPP2R1A PPP2R1A 6924 0.029 0.39 NO
75 PIK3CA PIK3CA PIK3CA 7196 0.024 0.38 NO
76 PIK3R2 PIK3R2 PIK3R2 7327 0.022 0.38 NO
77 PRKCD PRKCD PRKCD 7382 0.021 0.37 NO
78 PPP2CA PPP2CA PPP2CA 7430 0.02 0.37 NO
79 ADORA2A ADORA2A ADORA2A 7433 0.02 0.37 NO
80 MTOR MTOR MTOR 7479 0.019 0.37 NO
81 MAP2K5 MAP2K5 MAP2K5 7497 0.018 0.37 NO
82 SOS1 SOS1 SOS1 7550 0.018 0.37 NO
83 RAPGEF1 RAPGEF1 RAPGEF1 7657 0.015 0.36 NO
84 CHUK CHUK CHUK 7752 0.014 0.36 NO
85 RALGDS RALGDS RALGDS 7782 0.013 0.36 NO
86 ITPR3 ITPR3 ITPR3 7839 0.012 0.36 NO
87 PRKACA PRKACA PRKACA 7885 0.011 0.36 NO
88 GRB2 GRB2 GRB2 8294 0.0048 0.33 NO
89 ADCY6 ADCY6 ADCY6 8417 0.0027 0.33 NO
90 PPP2CB PPP2CB PPP2CB 8482 0.0016 0.32 NO
91 FRS2 FRS2 FRS2 8556 0.00035 0.32 NO
92 MLST8 MLST8 MLST8 8840 -0.0049 0.3 NO
93 MAP2K2 MAP2K2 MAP2K2 9076 -0.0087 0.29 NO
94 CLTA CLTA CLTA 9604 -0.017 0.26 NO
95 CASP9 CASP9 CASP9 9841 -0.021 0.25 NO
96 CRK CRK CRK 9922 -0.022 0.25 NO
97 CREB1 CREB1 CREB1 9966 -0.023 0.25 NO
98 RPS6KA3 RPS6KA3 RPS6KA3 10206 -0.027 0.24 NO
99 IRS2 IRS2 IRS2 10230 -0.027 0.24 NO
100 MAPK14 MAPK14 MAPK14 10332 -0.029 0.23 NO
101 ADCY4 ADCY4 ADCY4 10399 -0.03 0.23 NO
102 PPP2R1B PPP2R1B PPP2R1B 10836 -0.038 0.21 NO
103 PLCG1 PLCG1 PLCG1 10845 -0.038 0.21 NO
104 BAD BAD BAD 11021 -0.04 0.2 NO
105 RAF1 RAF1 RAF1 11154 -0.042 0.2 NO
106 MAPKAP1 MAPKAP1 MAPKAP1 11280 -0.045 0.19 NO
107 PRKAR2A PRKAR2A PRKAR2A 11300 -0.045 0.19 NO
108 DNM2 DNM2 DNM2 11554 -0.049 0.18 NO
109 AKT1 AKT1 AKT1 11659 -0.051 0.18 NO
110 FOXO1 FOXO1 FOXO1 11754 -0.053 0.18 NO
111 RALA RALA RALA 11961 -0.057 0.17 NO
112 ADCY7 ADCY7 ADCY7 11992 -0.057 0.17 NO
113 DUSP4 DUSP4 DUSP4 12081 -0.059 0.17 NO
114 AP2S1 AP2S1 AP2S1 12197 -0.061 0.17 NO
115 RHOA RHOA RHOA 12790 -0.074 0.14 NO
116 CDKN1A CDKN1A CDKN1A 12857 -0.075 0.14 NO
117 AKT1S1 AKT1S1 AKT1S1 13194 -0.082 0.12 NO
118 AKT2 AKT2 AKT2 13755 -0.096 0.1 NO
119 MAPK7 MAPK7 MAPK7 13960 -0.1 0.094 NO
120 MDM2 MDM2 MDM2 13963 -0.1 0.1 NO
121 STAT3 STAT3 STAT3 13980 -0.1 0.1 NO
122 ATF1 ATF1 ATF1 14023 -0.1 0.11 NO
123 MAPKAPK2 MAPKAPK2 MAPKAPK2 14442 -0.12 0.092 NO
124 RPS6KB2 RPS6KB2 RPS6KB2 14449 -0.12 0.098 NO
125 RAP1A RAP1A RAP1A 14826 -0.13 0.084 NO
126 NRAS NRAS NRAS 14931 -0.14 0.086 NO
127 DUSP6 DUSP6 DUSP6 15018 -0.14 0.089 NO
128 MAPKAPK3 MAPKAPK3 MAPKAPK3 15468 -0.16 0.073 NO
129 RIT1 RIT1 RIT1 15671 -0.17 0.072 NO
130 TRIB3 TRIB3 TRIB3 15732 -0.18 0.078 NO
131 SHC1 SHC1 SHC1 15985 -0.19 0.075 NO
132 NTRK1 NTRK1 NTRK1 16480 -0.23 0.061 NO
133 RPS6KA1 RPS6KA1 RPS6KA1 16956 -0.28 0.051 NO
134 CDK1 CDK1 CDK1 17840 -0.42 0.026 NO

Figure S27.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG INOSITOL PHOSPHATE METABOLISM.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG INOSITOL PHOSPHATE 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 PYRUVATE METABOLISM

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 PRKCG PRKCG PRKCG 73 1.1 0.071 YES
2 CAMK4 CAMK4 CAMK4 354 0.78 0.11 YES
3 PDE1A PDE1A PDE1A 587 0.63 0.14 YES
4 KLB KLB KLB 598 0.62 0.18 YES
5 FGF9 FGF9 FGF9 609 0.62 0.22 YES
6 PDE1B PDE1B PDE1B 633 0.6 0.26 YES
7 ADCY1 ADCY1 ADCY1 649 0.59 0.3 YES
8 FGF5 FGF5 FGF5 719 0.57 0.33 YES
9 FGF18 FGF18 FGF18 1239 0.41 0.33 YES
10 ADCY5 ADCY5 ADCY5 1244 0.4 0.36 YES
11 PRKCE PRKCE PRKCE 1284 0.39 0.38 YES
12 PRKAR1B PRKAR1B PRKAR1B 1317 0.39 0.4 YES
13 FGF8 FGF8 FGF8 1522 0.35 0.42 YES
14 FGF22 FGF22 FGF22 1524 0.35 0.44 YES
15 KL KL KL 1643 0.32 0.46 YES
16 PRKAR2B PRKAR2B PRKAR2B 1677 0.32 0.48 YES
17 FGF7 FGF7 FGF7 1784 0.31 0.49 YES
18 FGFR3 FGFR3 FGFR3 2481 0.22 0.47 YES
19 FGF17 FGF17 FGF17 2553 0.21 0.48 YES
20 CALM3 CALM3 CALM3 2778 0.19 0.48 YES
21 AKT3 AKT3 AKT3 3008 0.18 0.48 YES
22 FRS3 FRS3 FRS3 3083 0.17 0.48 YES
23 MAP2K1 MAP2K1 MAP2K1 3142 0.17 0.49 YES
24 CALM1 CALM1 CALM1 3228 0.16 0.5 YES
25 ADCY2 ADCY2 ADCY2 3297 0.16 0.5 YES
26 FOXO4 FOXO4 FOXO4 3329 0.15 0.51 YES
27 PDPK1 PDPK1 PDPK1 3608 0.14 0.51 YES
28 PRKACB PRKACB PRKACB 3826 0.12 0.5 YES
29 RICTOR RICTOR RICTOR 3860 0.12 0.51 YES
30 PRKCA PRKCA PRKCA 3969 0.12 0.51 YES
31 PIK3R1 PIK3R1 PIK3R1 4256 0.11 0.5 YES
32 PRKACG PRKACG PRKACG 4422 0.099 0.5 YES
33 FGFR2 FGFR2 FGFR2 4555 0.095 0.5 YES
34 MAPK3 MAPK3 MAPK3 4559 0.095 0.51 YES
35 THEM4 THEM4 THEM4 4741 0.088 0.5 YES
36 PTEN PTEN PTEN 4779 0.086 0.51 YES
37 ADRBK1 ADRBK1 ADRBK1 4839 0.084 0.51 YES
38 FOXO3 FOXO3 FOXO3 4847 0.084 0.51 YES
39 MAPK1 MAPK1 MAPK1 4939 0.081 0.51 YES
40 YWHAB YWHAB YWHAB 4950 0.081 0.52 YES
41 FGF10 FGF10 FGF10 5003 0.08 0.52 YES
42 PHLPP1 PHLPP1 PHLPP1 5040 0.078 0.52 YES
43 NR4A1 NR4A1 NR4A1 5183 0.073 0.52 YES
44 KRAS KRAS KRAS 5193 0.073 0.53 YES
45 ADCY9 ADCY9 ADCY9 5643 0.059 0.51 NO
46 ADCY3 ADCY3 ADCY3 5700 0.058 0.51 NO
47 PRKAR1A PRKAR1A PRKAR1A 5740 0.056 0.51 NO
48 GSK3A GSK3A GSK3A 6040 0.048 0.5 NO
49 TSC2 TSC2 TSC2 6261 0.043 0.49 NO
50 CALM2 CALM2 CALM2 6291 0.042 0.49 NO
51 ADCY8 ADCY8 ADCY8 6373 0.04 0.48 NO
52 HRAS HRAS HRAS 6513 0.037 0.48 NO
53 ITPR2 ITPR2 ITPR2 6818 0.031 0.47 NO
54 FGF1 FGF1 FGF1 6847 0.031 0.47 NO
55 CDKN1B CDKN1B CDKN1B 6859 0.03 0.47 NO
56 PIK3CA PIK3CA PIK3CA 7196 0.024 0.45 NO
57 PRKCD PRKCD PRKCD 7382 0.021 0.44 NO
58 MTOR MTOR MTOR 7479 0.019 0.44 NO
59 SOS1 SOS1 SOS1 7550 0.018 0.44 NO
60 CHUK CHUK CHUK 7752 0.014 0.42 NO
61 ITPR3 ITPR3 ITPR3 7839 0.012 0.42 NO
62 FGF2 FGF2 FGF2 7848 0.012 0.42 NO
63 PRKACA PRKACA PRKACA 7885 0.011 0.42 NO
64 GRB2 GRB2 GRB2 8294 0.0048 0.4 NO
65 ADCY6 ADCY6 ADCY6 8417 0.0027 0.39 NO
66 FRS2 FRS2 FRS2 8556 0.00035 0.38 NO
67 MLST8 MLST8 MLST8 8840 -0.0049 0.37 NO
68 MAP2K2 MAP2K2 MAP2K2 9076 -0.0087 0.36 NO
69 CASP9 CASP9 CASP9 9841 -0.021 0.32 NO
70 CREB1 CREB1 CREB1 9966 -0.023 0.31 NO
71 FGFR1 FGFR1 FGFR1 10270 -0.028 0.3 NO
72 ADCY4 ADCY4 ADCY4 10399 -0.03 0.29 NO
73 PLCG1 PLCG1 PLCG1 10845 -0.038 0.27 NO
74 BAD BAD BAD 11021 -0.04 0.26 NO
75 RAF1 RAF1 RAF1 11154 -0.042 0.26 NO
76 MAPKAP1 MAPKAP1 MAPKAP1 11280 -0.045 0.25 NO
77 PRKAR2A PRKAR2A PRKAR2A 11300 -0.045 0.26 NO
78 GAB1 GAB1 GAB1 11613 -0.05 0.24 NO
79 AKT1 AKT1 AKT1 11659 -0.051 0.24 NO
80 FOXO1 FOXO1 FOXO1 11754 -0.053 0.24 NO
81 ADCY7 ADCY7 ADCY7 11992 -0.057 0.23 NO
82 CDKN1A CDKN1A CDKN1A 12857 -0.075 0.19 NO
83 AKT1S1 AKT1S1 AKT1S1 13194 -0.082 0.18 NO
84 FGFR4 FGFR4 FGFR4 13726 -0.095 0.15 NO
85 AKT2 AKT2 AKT2 13755 -0.096 0.16 NO
86 MDM2 MDM2 MDM2 13963 -0.1 0.15 NO
87 RPS6KB2 RPS6KB2 RPS6KB2 14449 -0.12 0.14 NO
88 NRAS NRAS NRAS 14931 -0.14 0.12 NO
89 TRIB3 TRIB3 TRIB3 15732 -0.18 0.086 NO
90 SHC1 SHC1 SHC1 15985 -0.19 0.085 NO
91 FGF20 FGF20 FGF20 16226 -0.21 0.086 NO
92 CDK1 CDK1 CDK1 17840 -0.42 0.026 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: KEGG PYRUVATE METABOLISM.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRUVATE 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 BUTANOATE METABOLISM

Table S16.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HTR5A HTR5A HTR5A 4 1.4 0.026 YES
2 CCKBR CCKBR CCKBR 31 1.2 0.047 YES
3 RYR2 RYR2 RYR2 46 1.2 0.069 YES
4 DRD5 DRD5 DRD5 62 1.1 0.089 YES
5 PRKCG PRKCG PRKCG 73 1.1 0.11 YES
6 DRD1 DRD1 DRD1 102 1.1 0.13 YES
7 CAMK2A CAMK2A CAMK2A 123 1 0.14 YES
8 ATP2B3 ATP2B3 ATP2B3 137 1 0.16 YES
9 CACNA1I CACNA1I CACNA1I 199 0.92 0.18 YES
10 CHRM1 CHRM1 CHRM1 225 0.9 0.19 YES
11 CHRM2 CHRM2 CHRM2 246 0.88 0.21 YES
12 CACNA1B CACNA1B CACNA1B 247 0.88 0.22 YES
13 GRIN1 GRIN1 GRIN1 260 0.87 0.24 YES
14 HTR2C HTR2C HTR2C 294 0.84 0.25 YES
15 HTR2A HTR2A HTR2A 302 0.83 0.27 YES
16 HTR6 HTR6 HTR6 318 0.82 0.28 YES
17 SLC8A2 SLC8A2 SLC8A2 336 0.8 0.3 YES
18 CAMK4 CAMK4 CAMK4 354 0.78 0.31 YES
19 GRIN2A GRIN2A GRIN2A 367 0.78 0.32 YES
20 GRM1 GRM1 GRM1 391 0.75 0.34 YES
21 CACNA1F CACNA1F CACNA1F 393 0.75 0.35 YES
22 GRM5 GRM5 GRM5 395 0.75 0.36 YES
23 ADRA1B ADRA1B ADRA1B 406 0.74 0.38 YES
24 HTR4 HTR4 HTR4 508 0.67 0.38 YES
25 PTGER3 PTGER3 PTGER3 524 0.66 0.4 YES
26 ADRB3 ADRB3 ADRB3 526 0.66 0.41 YES
27 NTSR1 NTSR1 NTSR1 547 0.65 0.42 YES
28 ITPKA ITPKA ITPKA 573 0.64 0.43 YES
29 PDE1A PDE1A PDE1A 587 0.63 0.44 YES
30 CHRM3 CHRM3 CHRM3 605 0.62 0.45 YES
31 PRKCB PRKCB PRKCB 619 0.61 0.46 YES
32 PDE1B PDE1B PDE1B 633 0.6 0.47 YES
33 NOS1 NOS1 NOS1 648 0.59 0.48 YES
34 ADCY1 ADCY1 ADCY1 649 0.59 0.49 YES
35 ADRB1 ADRB1 ADRB1 679 0.58 0.5 YES
36 GNAL GNAL GNAL 686 0.58 0.51 YES
37 TACR3 TACR3 TACR3 709 0.57 0.52 YES
38 CACNA1S CACNA1S CACNA1S 718 0.57 0.53 YES
39 CAMK2B CAMK2B CAMK2B 726 0.56 0.54 YES
40 CACNA1E CACNA1E CACNA1E 774 0.54 0.55 YES
41 HRH2 HRH2 HRH2 787 0.53 0.56 YES
42 ITPR1 ITPR1 ITPR1 821 0.52 0.57 YES
43 CACNA1G CACNA1G CACNA1G 931 0.49 0.57 YES
44 CALML3 CALML3 CALML3 1009 0.46 0.58 YES
45 CHRNA7 CHRNA7 CHRNA7 1025 0.46 0.58 YES
46 PTGFR PTGFR PTGFR 1122 0.44 0.59 YES
47 ATP2B2 ATP2B2 ATP2B2 1148 0.43 0.59 YES
48 HTR7 HTR7 HTR7 1185 0.42 0.6 YES
49 P2RX2 P2RX2 P2RX2 1194 0.42 0.61 YES
50 TACR2 TACR2 TACR2 1257 0.4 0.61 YES
51 ADRA1A ADRA1A ADRA1A 1322 0.38 0.61 YES
52 GRIN2C GRIN2C GRIN2C 1353 0.38 0.62 YES
53 CACNA1A CACNA1A CACNA1A 1383 0.37 0.62 YES
54 CACNA1C CACNA1C CACNA1C 1445 0.36 0.63 YES
55 CACNA1D CACNA1D CACNA1D 1469 0.35 0.63 YES
56 GNA14 GNA14 GNA14 1539 0.34 0.64 YES
57 CHP2 CHP2 CHP2 1575 0.34 0.64 YES
58 P2RX5 P2RX5 P2RX5 1623 0.33 0.64 YES
59 PPP3R2 PPP3R2 PPP3R2 1628 0.33 0.65 YES
60 PLCB4 PLCB4 PLCB4 1664 0.32 0.65 YES
61 SLC8A3 SLC8A3 SLC8A3 1701 0.32 0.66 YES
62 PLCB1 PLCB1 PLCB1 1723 0.32 0.66 YES
63 ERBB4 ERBB4 ERBB4 1733 0.31 0.67 YES
64 TACR1 TACR1 TACR1 1872 0.29 0.67 YES
65 TNNC2 TNNC2 TNNC2 1917 0.29 0.67 YES
66 PTK2B PTK2B PTK2B 1920 0.29 0.67 YES
67 P2RX6 P2RX6 P2RX6 1984 0.28 0.68 YES
68 PPP3CB PPP3CB PPP3CB 2087 0.26 0.68 YES
69 ATP2B1 ATP2B1 ATP2B1 2131 0.26 0.68 YES
70 CHRM5 CHRM5 CHRM5 2224 0.25 0.68 YES
71 CAMK2G CAMK2G CAMK2G 2362 0.23 0.67 YES
72 MYLK3 MYLK3 MYLK3 2386 0.23 0.68 YES
73 PPP3CA PPP3CA PPP3CA 2421 0.22 0.68 YES
74 CACNA1H CACNA1H CACNA1H 2448 0.22 0.68 YES
75 AVPR1B AVPR1B AVPR1B 2450 0.22 0.68 YES
76 TRHR TRHR TRHR 2656 0.2 0.68 NO
77 ADORA2B ADORA2B ADORA2B 2677 0.2 0.68 NO
78 PPP3R1 PPP3R1 PPP3R1 2713 0.2 0.68 NO
79 CALM3 CALM3 CALM3 2778 0.19 0.68 NO
80 RYR1 RYR1 RYR1 2868 0.19 0.68 NO
81 GRIN2D GRIN2D GRIN2D 3078 0.17 0.67 NO
82 CALM1 CALM1 CALM1 3228 0.16 0.67 NO
83 ADCY2 ADCY2 ADCY2 3297 0.16 0.67 NO
84 RYR3 RYR3 RYR3 3397 0.15 0.66 NO
85 TRPC1 TRPC1 TRPC1 3573 0.14 0.66 NO
86 SLC25A31 SLC25A31 SLC25A31 3711 0.13 0.65 NO
87 ERBB3 ERBB3 ERBB3 3754 0.13 0.65 NO
88 PRKACB PRKACB PRKACB 3826 0.12 0.65 NO
89 PRKCA PRKCA PRKCA 3969 0.12 0.64 NO
90 PRKACG PRKACG PRKACG 4422 0.099 0.62 NO
91 CD38 CD38 CD38 4447 0.099 0.62 NO
92 P2RX7 P2RX7 P2RX7 4578 0.094 0.62 NO
93 GNAQ GNAQ GNAQ 4671 0.09 0.61 NO
94 SLC25A4 SLC25A4 SLC25A4 4772 0.086 0.61 NO
95 ATP2A2 ATP2A2 ATP2A2 4870 0.083 0.61 NO
96 AVPR1A AVPR1A AVPR1A 4904 0.082 0.6 NO
97 LHCGR LHCGR LHCGR 5075 0.077 0.6 NO
98 ADRA1D ADRA1D ADRA1D 5318 0.069 0.58 NO
99 PDGFRA PDGFRA PDGFRA 5375 0.067 0.58 NO
100 VDAC2 VDAC2 VDAC2 5402 0.066 0.58 NO
101 PDE1C PDE1C PDE1C 5442 0.065 0.58 NO
102 NOS2 NOS2 NOS2 5485 0.064 0.58 NO
103 GNA11 GNA11 GNA11 5486 0.064 0.58 NO
104 CHP CHP CHP 5511 0.063 0.58 NO
105 ADCY9 ADCY9 ADCY9 5643 0.059 0.58 NO
106 ADCY3 ADCY3 ADCY3 5700 0.058 0.57 NO
107 GRPR GRPR GRPR 5768 0.055 0.57 NO
108 PLN PLN PLN 5786 0.055 0.57 NO
109 SLC8A1 SLC8A1 SLC8A1 5947 0.051 0.56 NO
110 ATP2B4 ATP2B4 ATP2B4 6026 0.049 0.56 NO
111 PLCD4 PLCD4 PLCD4 6172 0.045 0.55 NO
112 ADRB2 ADRB2 ADRB2 6181 0.045 0.55 NO
113 TNNC1 TNNC1 TNNC1 6272 0.043 0.55 NO
114 CALM2 CALM2 CALM2 6291 0.042 0.55 NO
115 ADCY8 ADCY8 ADCY8 6373 0.04 0.55 NO
116 VDAC3 VDAC3 VDAC3 6457 0.038 0.54 NO
117 ITPR2 ITPR2 ITPR2 6818 0.031 0.52 NO
118 CYSLTR2 CYSLTR2 CYSLTR2 6830 0.031 0.52 NO
119 EDNRB EDNRB EDNRB 6954 0.028 0.52 NO
120 MYLK MYLK MYLK 7385 0.02 0.49 NO
121 PPID PPID PPID 7432 0.02 0.49 NO
122 ADORA2A ADORA2A ADORA2A 7433 0.02 0.49 NO
123 VDAC1 VDAC1 VDAC1 7507 0.018 0.49 NO
124 PRKX PRKX PRKX 7668 0.015 0.48 NO
125 ITPR3 ITPR3 ITPR3 7839 0.012 0.47 NO
126 PRKACA PRKACA PRKACA 7885 0.011 0.47 NO
127 GNAS GNAS GNAS 7963 0.01 0.46 NO
128 OXTR OXTR OXTR 8036 0.009 0.46 NO
129 SPHK2 SPHK2 SPHK2 8049 0.0087 0.46 NO
130 PHKA1 PHKA1 PHKA1 8080 0.0082 0.46 NO
131 PHKG2 PHKG2 PHKG2 8234 0.0058 0.45 NO
132 P2RX3 P2RX3 P2RX3 8314 0.0044 0.44 NO
133 NOS3 NOS3 NOS3 8531 0.00074 0.43 NO
134 ITPKB ITPKB ITPKB 8576 -0.00018 0.43 NO
135 CCKAR CCKAR CCKAR 8770 -0.0036 0.42 NO
136 P2RX1 P2RX1 P2RX1 8899 -0.0059 0.41 NO
137 SLC25A6 SLC25A6 SLC25A6 9061 -0.0085 0.4 NO
138 PPP3CC PPP3CC PPP3CC 9420 -0.014 0.38 NO
139 SLC25A5 SLC25A5 SLC25A5 10277 -0.028 0.34 NO
140 ADCY4 ADCY4 ADCY4 10399 -0.03 0.33 NO
141 BDKRB1 BDKRB1 BDKRB1 10422 -0.03 0.33 NO
142 PHKB PHKB PHKB 10440 -0.031 0.33 NO
143 CAMK2D CAMK2D CAMK2D 10553 -0.033 0.32 NO
144 PLCD3 PLCD3 PLCD3 10742 -0.036 0.32 NO
145 PLCG1 PLCG1 PLCG1 10845 -0.038 0.31 NO
146 PLCB3 PLCB3 PLCB3 11061 -0.041 0.3 NO
147 PHKA2 PHKA2 PHKA2 11713 -0.052 0.26 NO
148 MYLK2 MYLK2 MYLK2 11916 -0.056 0.26 NO
149 ADCY7 ADCY7 ADCY7 11992 -0.057 0.25 NO
150 PLCD1 PLCD1 PLCD1 12148 -0.06 0.24 NO
151 PDGFRB PDGFRB PDGFRB 12331 -0.064 0.24 NO
152 ATP2A3 ATP2A3 ATP2A3 12859 -0.075 0.21 NO
153 ERBB2 ERBB2 ERBB2 13510 -0.089 0.17 NO
154 CALML6 CALML6 CALML6 14021 -0.1 0.15 NO
155 EGFR EGFR EGFR 14278 -0.11 0.14 NO
156 HRH1 HRH1 HRH1 14540 -0.12 0.12 NO
157 PHKG1 PHKG1 PHKG1 14694 -0.12 0.12 NO
158 HTR2B HTR2B HTR2B 14749 -0.13 0.12 NO
159 LTB4R2 LTB4R2 LTB4R2 14982 -0.14 0.11 NO
160 BDKRB2 BDKRB2 BDKRB2 15165 -0.14 0.099 NO
161 PLCE1 PLCE1 PLCE1 15622 -0.17 0.077 NO
162 ATP2A1 ATP2A1 ATP2A1 15700 -0.17 0.076 NO
163 PLCB2 PLCB2 PLCB2 15839 -0.18 0.072 NO
164 P2RX4 P2RX4 P2RX4 16054 -0.2 0.063 NO
165 F2R F2R F2R 16197 -0.21 0.059 NO
166 AGTR1 AGTR1 AGTR1 16380 -0.22 0.054 NO
167 CYSLTR1 CYSLTR1 CYSLTR1 16418 -0.23 0.056 NO
168 SPHK1 SPHK1 SPHK1 16467 -0.23 0.057 NO
169 PLCG2 PLCG2 PLCG2 16567 -0.24 0.056 NO
170 GNA15 GNA15 GNA15 16789 -0.26 0.049 NO
171 EDNRA EDNRA EDNRA 16801 -0.26 0.053 NO
172 PTGER1 PTGER1 PTGER1 17152 -0.31 0.04 NO
173 PTAFR PTAFR PTAFR 17419 -0.34 0.031 NO
174 TBXA2R TBXA2R TBXA2R 17546 -0.37 0.031 NO
175 BST1 BST1 BST1 18249 -0.57 0.0032 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: KEGG BUTANOATE METABOLISM.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BUTANOATE 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 MAPK SIGNALING 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 PRKCG PRKCG PRKCG 73 1.1 0.068 YES
2 CAMK4 CAMK4 CAMK4 354 0.78 0.1 YES
3 PDE1A PDE1A PDE1A 587 0.63 0.13 YES
4 KLB KLB KLB 598 0.62 0.17 YES
5 FGF9 FGF9 FGF9 609 0.62 0.21 YES
6 PDE1B PDE1B PDE1B 633 0.6 0.25 YES
7 ADCY1 ADCY1 ADCY1 649 0.59 0.28 YES
8 FGF5 FGF5 FGF5 719 0.57 0.32 YES
9 FGF18 FGF18 FGF18 1239 0.41 0.32 YES
10 ADCY5 ADCY5 ADCY5 1244 0.4 0.34 YES
11 PRKCE PRKCE PRKCE 1284 0.39 0.36 YES
12 PRKAR1B PRKAR1B PRKAR1B 1317 0.39 0.39 YES
13 FGF8 FGF8 FGF8 1522 0.35 0.4 YES
14 FGF22 FGF22 FGF22 1524 0.35 0.42 YES
15 KL KL KL 1643 0.32 0.44 YES
16 PRKAR2B PRKAR2B PRKAR2B 1677 0.32 0.46 YES
17 FGF7 FGF7 FGF7 1784 0.31 0.47 YES
18 FGFR3 FGFR3 FGFR3 2481 0.22 0.44 YES
19 FGF17 FGF17 FGF17 2553 0.21 0.46 YES
20 CALM3 CALM3 CALM3 2778 0.19 0.46 YES
21 AKT3 AKT3 AKT3 3008 0.18 0.45 YES
22 FRS3 FRS3 FRS3 3083 0.17 0.46 YES
23 MAP2K1 MAP2K1 MAP2K1 3142 0.17 0.47 YES
24 CALM1 CALM1 CALM1 3228 0.16 0.47 YES
25 ADCY2 ADCY2 ADCY2 3297 0.16 0.48 YES
26 FOXO4 FOXO4 FOXO4 3329 0.15 0.49 YES
27 PDPK1 PDPK1 PDPK1 3608 0.14 0.48 YES
28 PRKACB PRKACB PRKACB 3826 0.12 0.48 YES
29 RICTOR RICTOR RICTOR 3860 0.12 0.48 YES
30 PRKCA PRKCA PRKCA 3969 0.12 0.49 YES
31 PIK3R1 PIK3R1 PIK3R1 4256 0.11 0.48 YES
32 PRKACG PRKACG PRKACG 4422 0.099 0.48 YES
33 FGFR2 FGFR2 FGFR2 4555 0.095 0.47 YES
34 MAPK3 MAPK3 MAPK3 4559 0.095 0.48 YES
35 BRAF BRAF BRAF 4716 0.089 0.48 YES
36 THEM4 THEM4 THEM4 4741 0.088 0.48 YES
37 PTEN PTEN PTEN 4779 0.086 0.48 YES
38 ADRBK1 ADRBK1 ADRBK1 4839 0.084 0.49 YES
39 FOXO3 FOXO3 FOXO3 4847 0.084 0.49 YES
40 MAPK1 MAPK1 MAPK1 4939 0.081 0.49 YES
41 YWHAB YWHAB YWHAB 4950 0.081 0.5 YES
42 FGF10 FGF10 FGF10 5003 0.08 0.5 YES
43 PHLPP1 PHLPP1 PHLPP1 5040 0.078 0.5 YES
44 NR4A1 NR4A1 NR4A1 5183 0.073 0.5 YES
45 KRAS KRAS KRAS 5193 0.073 0.5 YES
46 ADCY9 ADCY9 ADCY9 5643 0.059 0.48 NO
47 ADCY3 ADCY3 ADCY3 5700 0.058 0.48 NO
48 PRKAR1A PRKAR1A PRKAR1A 5740 0.056 0.48 NO
49 GSK3A GSK3A GSK3A 6040 0.048 0.47 NO
50 SRC SRC SRC 6043 0.048 0.47 NO
51 TSC2 TSC2 TSC2 6261 0.043 0.46 NO
52 CALM2 CALM2 CALM2 6291 0.042 0.47 NO
53 ADCY8 ADCY8 ADCY8 6373 0.04 0.46 NO
54 HRAS HRAS HRAS 6513 0.037 0.46 NO
55 RPS27A RPS27A RPS27A 6750 0.032 0.45 NO
56 ITPR2 ITPR2 ITPR2 6818 0.031 0.45 NO
57 FGF1 FGF1 FGF1 6847 0.031 0.45 NO
58 CDKN1B CDKN1B CDKN1B 6859 0.03 0.45 NO
59 PPP2R1A PPP2R1A PPP2R1A 6924 0.029 0.45 NO
60 CBL CBL CBL 7076 0.026 0.44 NO
61 PIK3CA PIK3CA PIK3CA 7196 0.024 0.44 NO
62 PRKCD PRKCD PRKCD 7382 0.021 0.43 NO
63 PPP2CA PPP2CA PPP2CA 7430 0.02 0.42 NO
64 MTOR MTOR MTOR 7479 0.019 0.42 NO
65 SOS1 SOS1 SOS1 7550 0.018 0.42 NO
66 CHUK CHUK CHUK 7752 0.014 0.41 NO
67 ITPR3 ITPR3 ITPR3 7839 0.012 0.41 NO
68 FGF2 FGF2 FGF2 7848 0.012 0.41 NO
69 PRKACA PRKACA PRKACA 7885 0.011 0.41 NO
70 GRB2 GRB2 GRB2 8294 0.0048 0.38 NO
71 ADCY6 ADCY6 ADCY6 8417 0.0027 0.38 NO
72 PPP2CB PPP2CB PPP2CB 8482 0.0016 0.37 NO
73 FRS2 FRS2 FRS2 8556 0.00035 0.37 NO
74 MLST8 MLST8 MLST8 8840 -0.0049 0.36 NO
75 MAP2K2 MAP2K2 MAP2K2 9076 -0.0087 0.34 NO
76 IL17RD IL17RD IL17RD 9677 -0.018 0.31 NO
77 CASP9 CASP9 CASP9 9841 -0.021 0.3 NO
78 CREB1 CREB1 CREB1 9966 -0.023 0.3 NO
79 FGFR1 FGFR1 FGFR1 10270 -0.028 0.28 NO
80 ADCY4 ADCY4 ADCY4 10399 -0.03 0.28 NO
81 PLCG1 PLCG1 PLCG1 10845 -0.038 0.26 NO
82 BAD BAD BAD 11021 -0.04 0.25 NO
83 RAF1 RAF1 RAF1 11154 -0.042 0.24 NO
84 MAPKAP1 MAPKAP1 MAPKAP1 11280 -0.045 0.24 NO
85 PRKAR2A PRKAR2A PRKAR2A 11300 -0.045 0.24 NO
86 GAB1 GAB1 GAB1 11613 -0.05 0.23 NO
87 AKT1 AKT1 AKT1 11659 -0.051 0.23 NO
88 FOXO1 FOXO1 FOXO1 11754 -0.053 0.23 NO
89 ADCY7 ADCY7 ADCY7 11992 -0.057 0.22 NO
90 UBA52 UBA52 UBA52 12825 -0.074 0.18 NO
91 CDKN1A CDKN1A CDKN1A 12857 -0.075 0.18 NO
92 AKT1S1 AKT1S1 AKT1S1 13194 -0.082 0.17 NO
93 FGFR4 FGFR4 FGFR4 13726 -0.095 0.14 NO
94 AKT2 AKT2 AKT2 13755 -0.096 0.15 NO
95 SPRY2 SPRY2 SPRY2 13845 -0.099 0.15 NO
96 MDM2 MDM2 MDM2 13963 -0.1 0.15 NO
97 MKNK1 MKNK1 MKNK1 14319 -0.11 0.14 NO
98 RPS6KB2 RPS6KB2 RPS6KB2 14449 -0.12 0.14 NO
99 NRAS NRAS NRAS 14931 -0.14 0.12 NO
100 TRIB3 TRIB3 TRIB3 15732 -0.18 0.088 NO
101 SHC1 SHC1 SHC1 15985 -0.19 0.087 NO
102 FGF20 FGF20 FGF20 16226 -0.21 0.087 NO
103 CDK1 CDK1 CDK1 17840 -0.42 0.026 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: KEGG MAPK SIGNALING PATHWAY.

Figure S34.  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 ERBB SIGNALING PATHWAY

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 NEFM NEFM NEFM 63 1.1 0.082 YES
2 NEFL NEFL NEFL 145 1 0.15 YES
3 NEFH NEFH NEFH 159 0.98 0.22 YES
4 PRPH2 PRPH2 PRPH2 183 0.94 0.3 YES
5 GRIN1 GRIN1 GRIN1 260 0.87 0.36 YES
6 GRIN2A GRIN2A GRIN2A 367 0.78 0.41 YES
7 GRIN2B GRIN2B GRIN2B 379 0.76 0.46 YES
8 NOS1 NOS1 NOS1 648 0.59 0.5 YES
9 GRIN2C GRIN2C GRIN2C 1353 0.38 0.48 YES
10 SLC1A2 SLC1A2 SLC1A2 1536 0.34 0.5 YES
11 CHP2 CHP2 CHP2 1575 0.34 0.52 YES
12 PPP3R2 PPP3R2 PPP3R2 1628 0.33 0.55 YES
13 GRIA1 GRIA1 GRIA1 1878 0.29 0.55 YES
14 GRIA2 GRIA2 GRIA2 1942 0.28 0.57 YES
15 PPP3CB PPP3CB PPP3CB 2087 0.26 0.58 YES
16 PPP3CA PPP3CA PPP3CA 2421 0.22 0.58 YES
17 PPP3R1 PPP3R1 PPP3R1 2713 0.2 0.58 YES
18 MAPK11 MAPK11 MAPK11 2833 0.19 0.59 YES
19 GRIN2D GRIN2D GRIN2D 3078 0.17 0.59 NO
20 MAP3K5 MAP3K5 MAP3K5 4566 0.094 0.52 NO
21 BCL2 BCL2 BCL2 5264 0.071 0.48 NO
22 MAPK12 MAPK12 MAPK12 5455 0.065 0.48 NO
23 CHP CHP CHP 5511 0.063 0.48 NO
24 ALS2 ALS2 ALS2 5565 0.061 0.48 NO
25 MAPK13 MAPK13 MAPK13 5657 0.059 0.48 NO
26 BID BID BID 5954 0.051 0.47 NO
27 TOMM40L TOMM40L TOMM40L 6025 0.049 0.47 NO
28 APAF1 APAF1 APAF1 6299 0.042 0.46 NO
29 SOD1 SOD1 SOD1 6512 0.037 0.45 NO
30 CYCS CYCS CYCS 7152 0.024 0.41 NO
31 RAB5A RAB5A RAB5A 8046 0.0088 0.36 NO
32 CCS CCS CCS 8990 -0.0073 0.31 NO
33 PPP3CC PPP3CC PPP3CC 9420 -0.014 0.29 NO
34 CASP9 CASP9 CASP9 9841 -0.021 0.27 NO
35 MAPK14 MAPK14 MAPK14 10332 -0.029 0.24 NO
36 RAC1 RAC1 RAC1 10453 -0.031 0.24 NO
37 BCL2L1 BCL2L1 BCL2L1 10862 -0.038 0.22 NO
38 BAD BAD BAD 11021 -0.04 0.22 NO
39 DERL1 DERL1 DERL1 11437 -0.047 0.2 NO
40 MAP2K6 MAP2K6 MAP2K6 11909 -0.056 0.18 NO
41 CAT CAT CAT 12035 -0.058 0.17 NO
42 TOMM40 TOMM40 TOMM40 12159 -0.061 0.17 NO
43 TNF TNF TNF 12356 -0.065 0.16 NO
44 DAXX DAXX DAXX 12547 -0.069 0.16 NO
45 TP53 TP53 TP53 14967 -0.14 0.037 NO
46 CASP3 CASP3 CASP3 15263 -0.15 0.032 NO
47 GPX1 GPX1 GPX1 15551 -0.16 0.029 NO
48 MAP2K3 MAP2K3 MAP2K3 15639 -0.17 0.037 NO
49 PRPH PRPH PRPH 16069 -0.2 0.028 NO
50 BAX BAX BAX 16081 -0.2 0.042 NO
51 TNFRSF1B TNFRSF1B TNFRSF1B 16758 -0.26 0.025 NO
52 TNFRSF1A TNFRSF1A TNFRSF1A 16915 -0.28 0.037 NO
53 CASP1 CASP1 CASP1 18156 -0.52 0.0083 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: KEGG ERBB SIGNALING PATHWAY.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ERBB 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 CALCIUM SIGNALING PATHWAY

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 PRKCG PRKCG PRKCG 73 1.1 0.064 YES
2 CAMK4 CAMK4 CAMK4 354 0.78 0.096 YES
3 PDE1A PDE1A PDE1A 587 0.63 0.12 YES
4 KLB KLB KLB 598 0.62 0.16 YES
5 FGF9 FGF9 FGF9 609 0.62 0.2 YES
6 PDE1B PDE1B PDE1B 633 0.6 0.23 YES
7 ADCY1 ADCY1 ADCY1 649 0.59 0.26 YES
8 FGF5 FGF5 FGF5 719 0.57 0.3 YES
9 FGF18 FGF18 FGF18 1239 0.41 0.29 YES
10 ADCY5 ADCY5 ADCY5 1244 0.4 0.32 YES
11 PRKCE PRKCE PRKCE 1284 0.39 0.34 YES
12 PRKAR1B PRKAR1B PRKAR1B 1317 0.39 0.36 YES
13 FGF8 FGF8 FGF8 1522 0.35 0.37 YES
14 FGF22 FGF22 FGF22 1524 0.35 0.39 YES
15 KL KL KL 1643 0.32 0.4 YES
16 PRKAR2B PRKAR2B PRKAR2B 1677 0.32 0.42 YES
17 FGF7 FGF7 FGF7 1784 0.31 0.43 YES
18 FGFR3 FGFR3 FGFR3 2481 0.22 0.41 YES
19 FGF17 FGF17 FGF17 2553 0.21 0.42 YES
20 CALM3 CALM3 CALM3 2778 0.19 0.42 YES
21 AKT3 AKT3 AKT3 3008 0.18 0.42 YES
22 FRS3 FRS3 FRS3 3083 0.17 0.42 YES
23 MAP2K1 MAP2K1 MAP2K1 3142 0.17 0.43 YES
24 CALM1 CALM1 CALM1 3228 0.16 0.43 YES
25 ADCY2 ADCY2 ADCY2 3297 0.16 0.44 YES
26 FOXO4 FOXO4 FOXO4 3329 0.15 0.45 YES
27 PDPK1 PDPK1 PDPK1 3608 0.14 0.44 YES
28 PRKACB PRKACB PRKACB 3826 0.12 0.44 YES
29 RICTOR RICTOR RICTOR 3860 0.12 0.44 YES
30 PRKCA PRKCA PRKCA 3969 0.12 0.44 YES
31 BCR BCR BCR 4062 0.12 0.44 YES
32 MYO18A MYO18A MYO18A 4105 0.11 0.45 YES
33 PIK3R1 PIK3R1 PIK3R1 4256 0.11 0.45 YES
34 PRKACG PRKACG PRKACG 4422 0.099 0.44 YES
35 FGFR2 FGFR2 FGFR2 4555 0.095 0.44 YES
36 MAPK3 MAPK3 MAPK3 4559 0.095 0.45 YES
37 BRAF BRAF BRAF 4716 0.089 0.44 YES
38 THEM4 THEM4 THEM4 4741 0.088 0.45 YES
39 PTEN PTEN PTEN 4779 0.086 0.45 YES
40 ADRBK1 ADRBK1 ADRBK1 4839 0.084 0.45 YES
41 FOXO3 FOXO3 FOXO3 4847 0.084 0.46 YES
42 MAPK1 MAPK1 MAPK1 4939 0.081 0.46 YES
43 YWHAB YWHAB YWHAB 4950 0.081 0.46 YES
44 FGF10 FGF10 FGF10 5003 0.08 0.46 YES
45 PHLPP1 PHLPP1 PHLPP1 5040 0.078 0.47 YES
46 NR4A1 NR4A1 NR4A1 5183 0.073 0.46 YES
47 KRAS KRAS KRAS 5193 0.073 0.47 YES
48 FGFR1OP2 FGFR1OP2 FGFR1OP2 5337 0.068 0.46 NO
49 ADCY9 ADCY9 ADCY9 5643 0.059 0.45 NO
50 ADCY3 ADCY3 ADCY3 5700 0.058 0.45 NO
51 ZMYM2 ZMYM2 ZMYM2 5734 0.056 0.45 NO
52 PRKAR1A PRKAR1A PRKAR1A 5740 0.056 0.46 NO
53 GSK3A GSK3A GSK3A 6040 0.048 0.44 NO
54 SRC SRC SRC 6043 0.048 0.45 NO
55 TSC2 TSC2 TSC2 6261 0.043 0.44 NO
56 CALM2 CALM2 CALM2 6291 0.042 0.44 NO
57 ADCY8 ADCY8 ADCY8 6373 0.04 0.44 NO
58 HRAS HRAS HRAS 6513 0.037 0.43 NO
59 RPS27A RPS27A RPS27A 6750 0.032 0.42 NO
60 ITPR2 ITPR2 ITPR2 6818 0.031 0.42 NO
61 FGF1 FGF1 FGF1 6847 0.031 0.42 NO
62 CDKN1B CDKN1B CDKN1B 6859 0.03 0.42 NO
63 PPP2R1A PPP2R1A PPP2R1A 6924 0.029 0.42 NO
64 CBL CBL CBL 7076 0.026 0.41 NO
65 PIK3CA PIK3CA PIK3CA 7196 0.024 0.4 NO
66 PRKCD PRKCD PRKCD 7382 0.021 0.4 NO
67 PPP2CA PPP2CA PPP2CA 7430 0.02 0.4 NO
68 MTOR MTOR MTOR 7479 0.019 0.39 NO
69 SOS1 SOS1 SOS1 7550 0.018 0.39 NO
70 CUX1 CUX1 CUX1 7737 0.014 0.38 NO
71 CHUK CHUK CHUK 7752 0.014 0.38 NO
72 CPSF6 CPSF6 CPSF6 7756 0.014 0.38 NO
73 ITPR3 ITPR3 ITPR3 7839 0.012 0.38 NO
74 FGF2 FGF2 FGF2 7848 0.012 0.38 NO
75 STAT5B STAT5B STAT5B 7866 0.012 0.38 NO
76 PRKACA PRKACA PRKACA 7885 0.011 0.38 NO
77 GAB2 GAB2 GAB2 8245 0.0056 0.36 NO
78 GRB2 GRB2 GRB2 8294 0.0048 0.36 NO
79 ADCY6 ADCY6 ADCY6 8417 0.0027 0.35 NO
80 PPP2CB PPP2CB PPP2CB 8482 0.0016 0.35 NO
81 FRS2 FRS2 FRS2 8556 0.00035 0.34 NO
82 MLST8 MLST8 MLST8 8840 -0.0049 0.33 NO
83 MAP2K2 MAP2K2 MAP2K2 9076 -0.0087 0.32 NO
84 IL17RD IL17RD IL17RD 9677 -0.018 0.28 NO
85 CASP9 CASP9 CASP9 9841 -0.021 0.28 NO
86 CREB1 CREB1 CREB1 9966 -0.023 0.27 NO
87 FGFR1 FGFR1 FGFR1 10270 -0.028 0.26 NO
88 ADCY4 ADCY4 ADCY4 10399 -0.03 0.25 NO
89 PLCG1 PLCG1 PLCG1 10845 -0.038 0.23 NO
90 BAD BAD BAD 11021 -0.04 0.22 NO
91 RAF1 RAF1 RAF1 11154 -0.042 0.22 NO
92 MAPKAP1 MAPKAP1 MAPKAP1 11280 -0.045 0.21 NO
93 PRKAR2A PRKAR2A PRKAR2A 11300 -0.045 0.21 NO
94 GAB1 GAB1 GAB1 11613 -0.05 0.2 NO
95 AKT1 AKT1 AKT1 11659 -0.051 0.2 NO
96 FOXO1 FOXO1 FOXO1 11754 -0.053 0.2 NO
97 ADCY7 ADCY7 ADCY7 11992 -0.057 0.19 NO
98 FGFR1OP FGFR1OP FGFR1OP 12306 -0.064 0.17 NO
99 UBA52 UBA52 UBA52 12825 -0.074 0.15 NO
100 CDKN1A CDKN1A CDKN1A 12857 -0.075 0.15 NO
101 AKT1S1 AKT1S1 AKT1S1 13194 -0.082 0.14 NO
102 TRIM24 TRIM24 TRIM24 13303 -0.084 0.14 NO
103 FGFR4 FGFR4 FGFR4 13726 -0.095 0.12 NO
104 AKT2 AKT2 AKT2 13755 -0.096 0.13 NO
105 SPRY2 SPRY2 SPRY2 13845 -0.099 0.13 NO
106 MDM2 MDM2 MDM2 13963 -0.1 0.13 NO
107 STAT3 STAT3 STAT3 13980 -0.1 0.13 NO
108 MKNK1 MKNK1 MKNK1 14319 -0.11 0.12 NO
109 RPS6KB2 RPS6KB2 RPS6KB2 14449 -0.12 0.12 NO
110 STAT1 STAT1 STAT1 14614 -0.12 0.12 NO
111 NRAS NRAS NRAS 14931 -0.14 0.11 NO
112 TRIB3 TRIB3 TRIB3 15732 -0.18 0.076 NO
113 SHC1 SHC1 SHC1 15985 -0.19 0.074 NO
114 FGF20 FGF20 FGF20 16226 -0.21 0.073 NO
115 STAT5A STAT5A STAT5A 16723 -0.26 0.061 NO
116 CDK1 CDK1 CDK1 17840 -0.42 0.026 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: KEGG CALCIUM SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

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 PRKCG PRKCG PRKCG 73 1.1 0.076 YES
2 MATK MATK MATK 331 0.81 0.12 YES
3 CAMK4 CAMK4 CAMK4 354 0.78 0.17 YES
4 PDE1A PDE1A PDE1A 587 0.63 0.21 YES
5 PDE1B PDE1B PDE1B 633 0.6 0.25 YES
6 ADCY1 ADCY1 ADCY1 649 0.59 0.29 YES
7 NRG1 NRG1 NRG1 797 0.53 0.32 YES
8 NRG4 NRG4 NRG4 933 0.49 0.34 YES
9 ADCY5 ADCY5 ADCY5 1244 0.4 0.36 YES
10 PRKCE PRKCE PRKCE 1284 0.39 0.38 YES
11 PRKAR1B PRKAR1B PRKAR1B 1317 0.39 0.41 YES
12 PRKAR2B PRKAR2B PRKAR2B 1677 0.32 0.41 YES
13 ERBB4 ERBB4 ERBB4 1733 0.31 0.43 YES
14 GRB7 GRB7 GRB7 2113 0.26 0.43 YES
15 CALM3 CALM3 CALM3 2778 0.19 0.41 YES
16 AKT3 AKT3 AKT3 3008 0.18 0.41 YES
17 MAP2K1 MAP2K1 MAP2K1 3142 0.17 0.41 YES
18 CALM1 CALM1 CALM1 3228 0.16 0.42 YES
19 ADCY2 ADCY2 ADCY2 3297 0.16 0.42 YES
20 FOXO4 FOXO4 FOXO4 3329 0.15 0.43 YES
21 PDPK1 PDPK1 PDPK1 3608 0.14 0.43 YES
22 ERBB3 ERBB3 ERBB3 3754 0.13 0.43 YES
23 PRKACB PRKACB PRKACB 3826 0.12 0.44 YES
24 RICTOR RICTOR RICTOR 3860 0.12 0.44 YES
25 PRKCA PRKCA PRKCA 3969 0.12 0.44 YES
26 PIK3R1 PIK3R1 PIK3R1 4256 0.11 0.44 YES
27 PRKACG PRKACG PRKACG 4422 0.099 0.44 YES
28 MAPK3 MAPK3 MAPK3 4559 0.095 0.43 YES
29 THEM4 THEM4 THEM4 4741 0.088 0.43 YES
30 PTEN PTEN PTEN 4779 0.086 0.43 YES
31 ADRBK1 ADRBK1 ADRBK1 4839 0.084 0.44 YES
32 FOXO3 FOXO3 FOXO3 4847 0.084 0.44 YES
33 MAPK1 MAPK1 MAPK1 4939 0.081 0.44 YES
34 YWHAB YWHAB YWHAB 4950 0.081 0.45 YES
35 PHLPP1 PHLPP1 PHLPP1 5040 0.078 0.45 YES
36 NR4A1 NR4A1 NR4A1 5183 0.073 0.45 YES
37 KRAS KRAS KRAS 5193 0.073 0.45 YES
38 RNF41 RNF41 RNF41 5213 0.072 0.46 YES
39 BTC BTC BTC 5231 0.072 0.46 YES
40 ADCY9 ADCY9 ADCY9 5643 0.059 0.44 NO
41 ADCY3 ADCY3 ADCY3 5700 0.058 0.44 NO
42 PRKAR1A PRKAR1A PRKAR1A 5740 0.056 0.44 NO
43 NRG2 NRG2 NRG2 5807 0.054 0.44 NO
44 STUB1 STUB1 STUB1 6038 0.048 0.44 NO
45 GSK3A GSK3A GSK3A 6040 0.048 0.44 NO
46 SRC SRC SRC 6043 0.048 0.44 NO
47 HSP90AA1 HSP90AA1 HSP90AA1 6174 0.045 0.44 NO
48 TSC2 TSC2 TSC2 6261 0.043 0.44 NO
49 CALM2 CALM2 CALM2 6291 0.042 0.44 NO
50 ADCY8 ADCY8 ADCY8 6373 0.04 0.44 NO
51 HRAS HRAS HRAS 6513 0.037 0.43 NO
52 RPS27A RPS27A RPS27A 6750 0.032 0.42 NO
53 ITPR2 ITPR2 ITPR2 6818 0.031 0.42 NO
54 CDKN1B CDKN1B CDKN1B 6859 0.03 0.42 NO
55 PIK3CA PIK3CA PIK3CA 7196 0.024 0.4 NO
56 CUL5 CUL5 CUL5 7247 0.023 0.4 NO
57 PRKCD PRKCD PRKCD 7382 0.021 0.4 NO
58 MTOR MTOR MTOR 7479 0.019 0.39 NO
59 SOS1 SOS1 SOS1 7550 0.018 0.39 NO
60 CHUK CHUK CHUK 7752 0.014 0.38 NO
61 ITPR3 ITPR3 ITPR3 7839 0.012 0.38 NO
62 PRKACA PRKACA PRKACA 7885 0.011 0.37 NO
63 GRB2 GRB2 GRB2 8294 0.0048 0.35 NO
64 FYN FYN FYN 8312 0.0045 0.35 NO
65 USP8 USP8 USP8 8409 0.0028 0.35 NO
66 ADCY6 ADCY6 ADCY6 8417 0.0027 0.35 NO
67 MLST8 MLST8 MLST8 8840 -0.0049 0.32 NO
68 MAP2K2 MAP2K2 MAP2K2 9076 -0.0087 0.31 NO
69 CDC37 CDC37 CDC37 9155 -0.01 0.31 NO
70 CASP9 CASP9 CASP9 9841 -0.021 0.27 NO
71 CREB1 CREB1 CREB1 9966 -0.023 0.27 NO
72 ADCY4 ADCY4 ADCY4 10399 -0.03 0.24 NO
73 PLCG1 PLCG1 PLCG1 10845 -0.038 0.22 NO
74 BAD BAD BAD 11021 -0.04 0.22 NO
75 RAF1 RAF1 RAF1 11154 -0.042 0.21 NO
76 MAPKAP1 MAPKAP1 MAPKAP1 11280 -0.045 0.21 NO
77 PRKAR2A PRKAR2A PRKAR2A 11300 -0.045 0.21 NO
78 GAB1 GAB1 GAB1 11613 -0.05 0.2 NO
79 AKT1 AKT1 AKT1 11659 -0.051 0.2 NO
80 FOXO1 FOXO1 FOXO1 11754 -0.053 0.2 NO
81 YES1 YES1 YES1 11982 -0.057 0.19 NO
82 ADCY7 ADCY7 ADCY7 11992 -0.057 0.19 NO
83 UBA52 UBA52 UBA52 12825 -0.074 0.15 NO
84 CDKN1A CDKN1A CDKN1A 12857 -0.075 0.15 NO
85 AKT1S1 AKT1S1 AKT1S1 13194 -0.082 0.14 NO
86 ERBB2 ERBB2 ERBB2 13510 -0.089 0.13 NO
87 EREG EREG EREG 13694 -0.094 0.13 NO
88 AKT2 AKT2 AKT2 13755 -0.096 0.13 NO
89 MDM2 MDM2 MDM2 13963 -0.1 0.13 NO
90 EGFR EGFR EGFR 14278 -0.11 0.12 NO
91 RPS6KB2 RPS6KB2 RPS6KB2 14449 -0.12 0.12 NO
92 NRAS NRAS NRAS 14931 -0.14 0.1 NO
93 HBEGF HBEGF HBEGF 15252 -0.15 0.093 NO
94 TRIB3 TRIB3 TRIB3 15732 -0.18 0.079 NO
95 SHC1 SHC1 SHC1 15985 -0.19 0.079 NO
96 EGF EGF EGF 16731 -0.26 0.056 NO
97 CDK1 CDK1 CDK1 17840 -0.42 0.026 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: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM.

Figure S40.  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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG RIBOSOME 86 genes.ES.table 0.64 1.6 0.091 0.72 0.94 0.69 0.26 0.51 0.44 0.21
BIOCARTA CARM ER PATHWAY 35 genes.ES.table 0.38 1.3 0.15 0.91 1 0.4 0.21 0.32 0.77 0.38
PID RET PATHWAY 39 genes.ES.table 0.37 1.4 0.15 0.96 1 0.41 0.22 0.32 0.8 0.4
PID HDAC CLASSI PATHWAY 65 genes.ES.table 0.36 1.7 0.04 0.59 0.69 0.48 0.31 0.33 0.24 0.15
PID ERA GENOMIC PATHWAY 62 genes.ES.table 0.38 1.4 0.085 0.74 1 0.52 0.28 0.38 0.57 0.24
PID AR NONGENOMIC PATHWAY 31 genes.ES.table 0.47 1.6 0.046 0.64 0.88 0.45 0.28 0.32 0.35 0.17
REACTOME TRANSLATION 146 genes.ES.table 0.44 1.3 0.28 0.9 1 0.49 0.26 0.36 0.78 0.37
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 49 genes.ES.table 0.57 1.5 0.13 0.61 0.98 0.67 0.31 0.46 0.43 0.16
REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 44 genes.ES.table 0.41 1.6 0.036 0.75 0.85 0.41 0.2 0.33 0.39 0.19
REACTOME SIGNALING BY NOTCH1 68 genes.ES.table 0.32 1.3 0.14 0.91 1 0.28 0.15 0.24 0.76 0.37
genes ES table in pathway: KEGG RIBOSOME

Table S21.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 EIF4B EIF4B EIF4B 2139 0.12 -0.015 YES
2 CAB39L CAB39L CAB39L 2652 0.1 0.042 YES
3 TSC1 TSC1 TSC1 2745 0.1 0.12 YES
4 PDE3B PDE3B PDE3B 2805 0.099 0.2 YES
5 PRKAG2 PRKAG2 PRKAG2 3442 0.082 0.23 YES
6 RPS6 RPS6 RPS6 3464 0.081 0.29 YES
7 TSC2 TSC2 TSC2 3702 0.075 0.34 YES
8 STRADB STRADB STRADB 3802 0.072 0.4 YES
9 RPTOR RPTOR RPTOR 4891 0.05 0.38 YES
10 RPS6KB1 RPS6KB1 RPS6KB1 5597 0.037 0.37 YES
11 PRKAB2 PRKAB2 PRKAB2 5646 0.036 0.4 YES
12 MLST8 MLST8 MLST8 5872 0.033 0.41 YES
13 PPM1A PPM1A PPM1A 6523 0.023 0.39 YES
14 STK11 STK11 STK11 6683 0.02 0.4 YES
15 STRADA STRADA STRADA 6742 0.02 0.41 YES
16 EIF4EBP1 EIF4EBP1 EIF4EBP1 7266 0.012 0.4 NO
17 EIF4G1 EIF4G1 EIF4G1 8205 -0.0013 0.34 NO
18 MTOR MTOR MTOR 8234 -0.0017 0.34 NO
19 RHEB RHEB RHEB 8304 -0.0026 0.34 NO
20 PRKAB1 PRKAB1 PRKAB1 8333 -0.003 0.34 NO
21 EEF2K EEF2K EEF2K 9236 -0.017 0.31 NO
22 PRKAG1 PRKAG1 PRKAG1 9260 -0.017 0.32 NO
23 CAB39 CAB39 CAB39 9750 -0.025 0.31 NO
24 PRKAA1 PRKAA1 PRKAA1 10266 -0.034 0.31 NO
25 AKT2 AKT2 AKT2 10556 -0.039 0.33 NO
26 PRKAA2 PRKAA2 PRKAA2 11175 -0.051 0.34 NO
27 EIF4E EIF4E EIF4E 11844 -0.064 0.35 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 RIBOSOME.

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

genes ES table in pathway: BIOCARTA CARM ER PATHWAY

Table S22.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SSPO SSPO SSPO 140 0.42 0.077 YES
2 GATA2 GATA2 GATA2 510 0.29 0.12 YES
3 HDAC4 HDAC4 HDAC4 890 0.22 0.14 YES
4 SMAD7 SMAD7 SMAD7 1106 0.2 0.17 YES
5 SIRT1 SIRT1 SIRT1 1286 0.18 0.2 YES
6 GATA1 GATA1 GATA1 1482 0.17 0.22 YES
7 SIRT2 SIRT2 SIRT2 2324 0.12 0.2 YES
8 HDAC5 HDAC5 HDAC5 2509 0.11 0.21 YES
9 NCOR2 NCOR2 NCOR2 2510 0.11 0.23 YES
10 EP300 EP300 EP300 2522 0.11 0.25 YES
11 CREBBP CREBBP CREBBP 2640 0.1 0.27 YES
12 CHD4 CHD4 CHD4 3088 0.091 0.26 YES
13 TNF TNF TNF 3154 0.089 0.28 YES
14 CHD3 CHD3 CHD3 3246 0.087 0.29 YES
15 HDAC11 HDAC11 HDAC11 3463 0.081 0.3 YES
16 SIRT4 SIRT4 SIRT4 3496 0.08 0.31 YES
17 KAT2B KAT2B KAT2B 3497 0.08 0.33 YES
18 NFKBIA NFKBIA NFKBIA 3720 0.074 0.33 YES
19 GATAD2B GATAD2B GATAD2B 3826 0.072 0.34 YES
20 PRMT5 PRMT5 PRMT5 4151 0.065 0.33 YES
21 HDAC6 HDAC6 HDAC6 4199 0.064 0.34 YES
22 TFCP2 TFCP2 TFCP2 4466 0.058 0.34 YES
23 NR2C1 NR2C1 NR2C1 4576 0.056 0.35 YES
24 MTA2 MTA2 MTA2 4624 0.055 0.36 YES
25 MXD1 MXD1 MXD1 4892 0.05 0.35 YES
26 SAP18 SAP18 SAP18 5023 0.047 0.35 YES
27 RELA RELA RELA 5172 0.045 0.35 YES
28 NCOR1 NCOR1 NCOR1 5254 0.043 0.36 YES
29 SIN3A SIN3A SIN3A 5448 0.04 0.36 YES
30 SIRT6 SIRT6 SIRT6 5591 0.038 0.36 YES
31 MAX MAX MAX 5676 0.036 0.36 YES
32 RANBP2 RANBP2 RANBP2 5980 0.031 0.35 NO
33 SIRT7 SIRT7 SIRT7 6491 0.023 0.32 NO
34 SIRT3 SIRT3 SIRT3 6681 0.02 0.32 NO
35 HDAC10 HDAC10 HDAC10 6781 0.019 0.32 NO
36 GATAD2A GATAD2A GATAD2A 6809 0.019 0.32 NO
37 RBBP7 RBBP7 RBBP7 6880 0.018 0.32 NO
38 HDAC2 HDAC2 HDAC2 6974 0.016 0.32 NO
39 HDAC8 HDAC8 HDAC8 7170 0.014 0.31 NO
40 MBD3 MBD3 MBD3 7409 0.01 0.3 NO
41 RANGAP1 RANGAP1 RANGAP1 7838 0.0041 0.28 NO
42 XPO1 XPO1 XPO1 7847 0.004 0.28 NO
43 SMG5 SMG5 SMG5 8625 -0.0072 0.24 NO
44 ZFPM1 ZFPM1 ZFPM1 8696 -0.0082 0.23 NO
45 YY1 YY1 YY1 9068 -0.014 0.22 NO
46 RBBP4 RBBP4 RBBP4 9343 -0.019 0.2 NO
47 FKBP3 FKBP3 FKBP3 9355 -0.019 0.21 NO
48 SUMO1 SUMO1 SUMO1 9515 -0.021 0.2 NO
49 STAT3 STAT3 STAT3 9806 -0.026 0.19 NO
50 NFKB1 NFKB1 NFKB1 9809 -0.026 0.2 NO
51 SAP30 SAP30 SAP30 9829 -0.026 0.2 NO
52 SMURF1 SMURF1 SMURF1 10051 -0.03 0.2 NO
53 SIRT5 SIRT5 SIRT5 10184 -0.032 0.2 NO
54 UBE2I UBE2I UBE2I 10327 -0.035 0.2 NO
55 SIN3B SIN3B SIN3B 10746 -0.043 0.18 NO
56 HDAC7 HDAC7 HDAC7 11333 -0.054 0.16 NO
57 RAN RAN RAN 11928 -0.066 0.14 NO
58 HDAC1 HDAC1 HDAC1 12122 -0.071 0.14 NO
59 HDAC3 HDAC3 HDAC3 12467 -0.08 0.14 NO
60 HDAC9 HDAC9 HDAC9 12669 -0.086 0.15 NO
61 PRKACA PRKACA PRKACA 13016 -0.096 0.15 NO
62 WDR77 WDR77 WDR77 13067 -0.098 0.17 NO
63 MBD2 MBD2 MBD2 13345 -0.11 0.17 NO
64 TNFRSF1A TNFRSF1A TNFRSF1A 14737 -0.18 0.13 NO
65 PPARG PPARG PPARG 16361 -0.31 0.11 NO

Figure S43.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CARM ER PATHWAY.

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CARM ER 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 RET 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 HES5 HES5 HES5 453 0.3 0.045 YES
2 HEY2 HEY2 HEY2 803 0.24 0.08 YES
3 MAML2 MAML2 MAML2 848 0.23 0.13 YES
4 HDAC4 HDAC4 HDAC4 890 0.22 0.18 YES
5 MYC MYC MYC 1060 0.2 0.22 YES
6 RBPJ RBPJ RBPJ 1633 0.16 0.22 YES
7 TLE3 TLE3 TLE3 1756 0.15 0.25 YES
8 RPS27A RPS27A RPS27A 1853 0.14 0.28 YES
9 HEY1 HEY1 HEY1 1923 0.14 0.31 YES
10 HDAC5 HDAC5 HDAC5 2509 0.11 0.3 YES
11 NCOR2 NCOR2 NCOR2 2510 0.11 0.33 YES
12 EP300 EP300 EP300 2522 0.11 0.35 YES
13 CREBBP CREBBP CREBBP 2640 0.1 0.37 YES
14 KAT2A KAT2A KAT2A 2704 0.1 0.39 YES
15 CDK8 CDK8 CDK8 3120 0.09 0.39 YES
16 HDAC11 HDAC11 HDAC11 3463 0.081 0.39 YES
17 KAT2B KAT2B KAT2B 3497 0.08 0.4 YES
18 MAMLD1 MAMLD1 MAMLD1 3651 0.076 0.41 YES
19 HDAC6 HDAC6 HDAC6 4199 0.064 0.4 NO
20 MAML1 MAML1 MAML1 4809 0.052 0.38 NO
21 NCOR1 NCOR1 NCOR1 5254 0.043 0.36 NO
22 TBL1X TBL1X TBL1X 5832 0.034 0.34 NO
23 SNW1 SNW1 SNW1 6739 0.02 0.29 NO
24 HIF1A HIF1A HIF1A 6745 0.02 0.3 NO
25 HDAC10 HDAC10 HDAC10 6781 0.019 0.3 NO
26 HDAC2 HDAC2 HDAC2 6974 0.016 0.29 NO
27 TBL1XR1 TBL1XR1 TBL1XR1 6998 0.016 0.3 NO
28 HDAC8 HDAC8 HDAC8 7170 0.014 0.29 NO
29 TLE1 TLE1 TLE1 8287 -0.0024 0.23 NO
30 UBA52 UBA52 UBA52 8360 -0.0033 0.23 NO
31 SKP1 SKP1 SKP1 9182 -0.016 0.19 NO
32 RBX1 RBX1 RBX1 9298 -0.018 0.18 NO
33 TLE2 TLE2 TLE2 10520 -0.039 0.13 NO
34 TLE4 TLE4 TLE4 10738 -0.042 0.12 NO
35 HDAC7 HDAC7 HDAC7 11333 -0.054 0.1 NO
36 CCNC CCNC CCNC 11455 -0.056 0.11 NO
37 CUL1 CUL1 CUL1 11766 -0.062 0.11 NO
38 HDAC1 HDAC1 HDAC1 12122 -0.071 0.1 NO
39 HDAC3 HDAC3 HDAC3 12467 -0.08 0.1 NO
40 HDAC9 HDAC9 HDAC9 12669 -0.086 0.11 NO
41 HES1 HES1 HES1 13228 -0.1 0.11 NO
42 MAML3 MAML3 MAML3 14055 -0.14 0.094 NO
43 FBXW7 FBXW7 FBXW7 15246 -0.21 0.078 NO
44 HEYL HEYL HEYL 17075 -0.39 0.068 NO

Figure S45.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID RET PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: PID RET 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 HDAC CLASSI 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 PLCB1 PLCB1 PLCB1 716 0.25 0.08 YES
2 GNAI1 GNAI1 GNAI1 1249 0.18 0.14 YES
3 SHBG SHBG SHBG 1357 0.18 0.22 YES
4 GNAO1 GNAO1 GNAO1 1716 0.15 0.27 YES
5 PLCB3 PLCB3 PLCB3 1955 0.13 0.32 YES
6 PIK3R1 PIK3R1 PIK3R1 2054 0.13 0.38 YES
7 GNRH1 GNRH1 GNRH1 2791 0.099 0.39 YES
8 PELP1 PELP1 PELP1 2979 0.094 0.42 YES
9 SRC SRC SRC 3494 0.08 0.43 YES
10 PIK3CA PIK3CA PIK3CA 3672 0.076 0.46 YES
11 GNAZ GNAZ GNAZ 4444 0.059 0.44 YES
12 AR AR AR 4673 0.054 0.46 YES
13 PTK2 PTK2 PTK2 4839 0.051 0.47 YES
14 RAF1 RAF1 RAF1 5216 0.044 0.47 YES
15 CREB1 CREB1 CREB1 6912 0.017 0.39 NO
16 MAPK1 MAPK1 MAPK1 7578 0.008 0.36 NO
17 GNAI2 GNAI2 GNAI2 7895 0.0033 0.34 NO
18 MAPK3 MAPK3 MAPK3 8145 -0.00034 0.33 NO
19 PLCG2 PLCG2 PLCG2 8258 -0.002 0.32 NO
20 MAP2K2 MAP2K2 MAP2K2 8323 -0.0029 0.32 NO
21 PLCB2 PLCB2 PLCB2 8416 -0.004 0.32 NO
22 AKT1 AKT1 AKT1 8464 -0.0046 0.32 NO
23 GNG2 GNG2 GNG2 9428 -0.02 0.27 NO
24 RAC1 RAC1 RAC1 9552 -0.022 0.28 NO
25 PLCG1 PLCG1 PLCG1 9579 -0.022 0.29 NO
26 HRAS HRAS HRAS 10007 -0.029 0.28 NO
27 GNAI3 GNAI3 GNAI3 10722 -0.042 0.26 NO
28 GNB1 GNB1 GNB1 10859 -0.045 0.27 NO
29 MAP2K1 MAP2K1 MAP2K1 12839 -0.091 0.21 NO
30 CDC42 CDC42 CDC42 12881 -0.092 0.25 NO
31 FOS FOS FOS 13047 -0.098 0.29 NO

Figure S47.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID HDAC CLASSI PATHWAY.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: PID HDAC CLASSI 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 ERA GENOMIC PATHWAY

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 RPL21 RPL21 RPL21 42 0.5 0.07 YES
2 RPL17 RPL17 RPL17 703 0.25 0.069 YES
3 RPL7 RPL7 RPL7 797 0.24 0.098 YES
4 RPS28 RPS28 RPS28 1000 0.21 0.12 YES
5 RPL9 RPL9 RPL9 1070 0.2 0.14 YES
6 RPL18A RPL18A RPL18A 1314 0.18 0.15 YES
7 RPL12 RPL12 RPL12 1385 0.17 0.18 YES
8 RPL13A RPL13A RPL13A 1475 0.17 0.19 YES
9 RPS25 RPS25 RPS25 1831 0.14 0.2 YES
10 RPS27A RPS27A RPS27A 1853 0.14 0.21 YES
11 RPL3 RPL3 RPL3 1867 0.14 0.23 YES
12 RPS12 RPS12 RPS12 1876 0.14 0.25 YES
13 RPL4 RPL4 RPL4 1948 0.14 0.27 YES
14 RPL7A RPL7A RPL7A 1954 0.13 0.29 YES
15 RPS24 RPS24 RPS24 2105 0.13 0.3 YES
16 RPL10L RPL10L RPL10L 2246 0.12 0.31 YES
17 RPL10 RPL10 RPL10 2270 0.12 0.32 YES
18 RPL6 RPL6 RPL6 2382 0.12 0.33 YES
19 RPL22 RPL22 RPL22 2571 0.11 0.34 YES
20 RPSA RPSA RPSA 2701 0.1 0.34 YES
21 RPS18 RPS18 RPS18 2807 0.099 0.35 YES
22 RPS3 RPS3 RPS3 2860 0.098 0.36 YES
23 RPS13 RPS13 RPS13 3005 0.094 0.37 YES
24 RPL34 RPL34 RPL34 3051 0.092 0.38 YES
25 RPS7 RPS7 RPS7 3092 0.091 0.39 YES
26 RPL27A RPL27A RPL27A 3138 0.09 0.4 YES
27 RPL30 RPL30 RPL30 3151 0.089 0.41 YES
28 RPS23 RPS23 RPS23 3254 0.087 0.42 YES
29 RPL24 RPL24 RPL24 3291 0.086 0.43 YES
30 RPL26 RPL26 RPL26 3295 0.086 0.44 YES
31 RPL19 RPL19 RPL19 3368 0.083 0.45 YES
32 RPL5 RPL5 RPL5 3376 0.083 0.46 YES
33 RPL13 RPL13 RPL13 3377 0.083 0.47 YES
34 RPS6 RPS6 RPS6 3464 0.081 0.48 YES
35 RPL37 RPL37 RPL37 3466 0.081 0.49 YES
36 RPS20 RPS20 RPS20 3511 0.08 0.5 YES
37 RPS10 RPS10 RPS10 3561 0.078 0.51 YES
38 RPLP0 RPLP0 RPLP0 3596 0.077 0.52 YES
39 RPL23 RPL23 RPL23 3618 0.077 0.53 YES
40 FAU FAU FAU 3743 0.074 0.53 YES
41 RPL15 RPL15 RPL15 3924 0.07 0.53 YES
42 RPLP1 RPLP1 RPLP1 3949 0.069 0.54 YES
43 RPS2 RPS2 RPS2 3997 0.068 0.55 YES
44 RPS4X RPS4X RPS4X 4098 0.066 0.55 YES
45 RPS17 RPS17 RPS17 4116 0.066 0.56 YES
46 RPL36AL RPL36AL RPL36AL 4131 0.066 0.57 YES
47 RPL11 RPL11 RPL11 4133 0.066 0.58 YES
48 RPS16 RPS16 RPS16 4242 0.063 0.58 YES
49 RPL14 RPL14 RPL14 4308 0.062 0.59 YES
50 RPL29 RPL29 RPL29 4355 0.061 0.59 YES
51 RPS8 RPS8 RPS8 4485 0.058 0.59 YES
52 RPLP2 RPLP2 RPLP2 4563 0.056 0.6 YES
53 RPL8 RPL8 RPL8 4636 0.055 0.6 YES
54 RPL32 RPL32 RPL32 4654 0.054 0.61 YES
55 RPL37A RPL37A RPL37A 4678 0.054 0.62 YES
56 RPS9 RPS9 RPS9 4751 0.053 0.62 YES
57 RPL18 RPL18 RPL18 4766 0.052 0.62 YES
58 RPS29 RPS29 RPS29 4801 0.052 0.63 YES
59 RPS3A RPS3A RPS3A 4837 0.051 0.64 YES
60 RPS15A RPS15A RPS15A 5024 0.047 0.63 NO
61 RPL10A RPL10A RPL10A 5175 0.045 0.63 NO
62 RSL24D1 RSL24D1 RSL24D1 5276 0.043 0.63 NO
63 RPL31 RPL31 RPL31 5476 0.04 0.63 NO
64 RPL39 RPL39 RPL39 5671 0.036 0.62 NO
65 RPS21 RPS21 RPS21 5681 0.036 0.62 NO
66 RPS11 RPS11 RPS11 5729 0.035 0.63 NO
67 RPS15 RPS15 RPS15 5967 0.032 0.62 NO
68 RPL35 RPL35 RPL35 6192 0.028 0.61 NO
69 RPS27 RPS27 RPS27 6363 0.026 0.6 NO
70 RPL35A RPL35A RPL35A 6392 0.025 0.61 NO
71 RPL38 RPL38 RPL38 6493 0.023 0.6 NO
72 RPL36A RPL36A RPL36A 6585 0.022 0.6 NO
73 RPS19 RPS19 RPS19 6774 0.019 0.6 NO
74 RPL36 RPL36 RPL36 6821 0.018 0.6 NO
75 RPL23A RPL23A RPL23A 7135 0.014 0.58 NO
76 RPL28 RPL28 RPL28 7407 0.01 0.57 NO
77 RPL22L1 RPL22L1 RPL22L1 7708 0.006 0.55 NO
78 RPL26L1 RPL26L1 RPL26L1 8215 -0.0015 0.52 NO
79 RPL27 RPL27 RPL27 8240 -0.0017 0.52 NO
80 RPS4Y1 RPS4Y1 RPS4Y1 8242 -0.0018 0.52 NO
81 RPS5 RPS5 RPS5 8249 -0.0019 0.52 NO
82 UBA52 UBA52 UBA52 8360 -0.0033 0.52 NO
83 RPL41 RPL41 RPL41 9888 -0.027 0.44 NO
84 RPS26 RPS26 RPS26 10383 -0.036 0.42 NO
85 RPS27L RPS27L RPS27L 10914 -0.046 0.39 NO
86 MRPL13 MRPL13 MRPL13 12674 -0.086 0.31 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 ERA GENOMIC PATHWAY.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ERA GENOMIC 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 AR NONGENOMIC 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 RPL21 RPL21 RPL21 42 0.5 0.059 YES
2 RPL17 RPL17 RPL17 703 0.25 0.053 YES
3 RPL7 RPL7 RPL7 797 0.24 0.076 YES
4 RPS28 RPS28 RPS28 1000 0.21 0.091 YES
5 RPL9 RPL9 RPL9 1070 0.2 0.11 YES
6 RPL18A RPL18A RPL18A 1314 0.18 0.12 YES
7 RPL12 RPL12 RPL12 1385 0.17 0.14 YES
8 RPL13A RPL13A RPL13A 1475 0.17 0.15 YES
9 UPF2 UPF2 UPF2 1665 0.15 0.16 YES
10 RPS25 RPS25 RPS25 1831 0.14 0.17 YES
11 RPS27A RPS27A RPS27A 1853 0.14 0.18 YES
12 RPL3 RPL3 RPL3 1867 0.14 0.2 YES
13 RPS12 RPS12 RPS12 1876 0.14 0.22 YES
14 RPL4 RPL4 RPL4 1948 0.14 0.23 YES
15 RPL7A RPL7A RPL7A 1954 0.13 0.25 YES
16 PABPC1 PABPC1 PABPC1 1993 0.13 0.26 YES
17 RPS24 RPS24 RPS24 2105 0.13 0.27 YES
18 RPL10 RPL10 RPL10 2270 0.12 0.27 YES
19 RPL6 RPL6 RPL6 2382 0.12 0.28 YES
20 RPL22 RPL22 RPL22 2571 0.11 0.28 YES
21 RPSA RPSA RPSA 2701 0.1 0.29 YES
22 RPS18 RPS18 RPS18 2807 0.099 0.3 YES
23 RPS3 RPS3 RPS3 2860 0.098 0.3 YES
24 RPS13 RPS13 RPS13 3005 0.094 0.31 YES
25 RPL34 RPL34 RPL34 3051 0.092 0.32 YES
26 RPS7 RPS7 RPS7 3092 0.091 0.33 YES
27 RPL27A RPL27A RPL27A 3138 0.09 0.34 YES
28 RPL30 RPL30 RPL30 3151 0.089 0.34 YES
29 UPF3A UPF3A UPF3A 3164 0.089 0.36 YES
30 CASC3 CASC3 CASC3 3198 0.088 0.36 YES
31 RPS23 RPS23 RPS23 3254 0.087 0.37 YES
32 RPL24 RPL24 RPL24 3291 0.086 0.38 YES
33 RPL26 RPL26 RPL26 3295 0.086 0.39 YES
34 RPL19 RPL19 RPL19 3368 0.083 0.4 YES
35 RPL5 RPL5 RPL5 3376 0.083 0.41 YES
36 RPL13 RPL13 RPL13 3377 0.083 0.42 YES
37 RPS6 RPS6 RPS6 3464 0.081 0.42 YES
38 RPL37 RPL37 RPL37 3466 0.081 0.43 YES
39 RPS20 RPS20 RPS20 3511 0.08 0.44 YES
40 RPS10 RPS10 RPS10 3561 0.078 0.44 YES
41 RPLP0 RPLP0 RPLP0 3596 0.077 0.45 YES
42 RPL23 RPL23 RPL23 3618 0.077 0.46 YES
43 SMG1 SMG1 SMG1 3694 0.075 0.46 YES
44 FAU FAU FAU 3743 0.074 0.47 YES
45 RPL15 RPL15 RPL15 3924 0.07 0.47 YES
46 RPLP1 RPLP1 RPLP1 3949 0.069 0.48 YES
47 RPS2 RPS2 RPS2 3997 0.068 0.48 YES
48 SMG6 SMG6 SMG6 4030 0.067 0.49 YES
49 RPS4X RPS4X RPS4X 4098 0.066 0.49 YES
50 RPS17 RPS17 RPS17 4116 0.066 0.5 YES
51 RPL11 RPL11 RPL11 4133 0.066 0.51 YES
52 RPS16 RPS16 RPS16 4242 0.063 0.51 YES
53 RPL14 RPL14 RPL14 4308 0.062 0.51 YES
54 RPL29 RPL29 RPL29 4355 0.061 0.52 YES
55 RPS8 RPS8 RPS8 4485 0.058 0.52 YES
56 RPLP2 RPLP2 RPLP2 4563 0.056 0.52 YES
57 UPF3B UPF3B UPF3B 4601 0.056 0.53 YES
58 RPL8 RPL8 RPL8 4636 0.055 0.53 YES
59 RPL32 RPL32 RPL32 4654 0.054 0.54 YES
60 RPL37A RPL37A RPL37A 4678 0.054 0.54 YES
61 RPS9 RPS9 RPS9 4751 0.053 0.54 YES
62 RPL18 RPL18 RPL18 4766 0.052 0.55 YES
63 RPS29 RPS29 RPS29 4801 0.052 0.55 YES
64 RPS3A RPS3A RPS3A 4837 0.051 0.56 YES
65 RPS15A RPS15A RPS15A 5024 0.047 0.55 NO
66 RPL10A RPL10A RPL10A 5175 0.045 0.55 NO
67 RBM8A RBM8A RBM8A 5463 0.04 0.54 NO
68 RPL31 RPL31 RPL31 5476 0.04 0.54 NO
69 NCBP2 NCBP2 NCBP2 5563 0.038 0.54 NO
70 RPL39 RPL39 RPL39 5671 0.036 0.54 NO
71 RPS21 RPS21 RPS21 5681 0.036 0.55 NO
72 RPS11 RPS11 RPS11 5729 0.035 0.55 NO
73 RPS15 RPS15 RPS15 5967 0.032 0.54 NO
74 SMG7 SMG7 SMG7 6120 0.029 0.53 NO
75 RPL35 RPL35 RPL35 6192 0.028 0.53 NO
76 GSPT2 GSPT2 GSPT2 6330 0.026 0.53 NO
77 RPS27 RPS27 RPS27 6363 0.026 0.53 NO
78 RPL35A RPL35A RPL35A 6392 0.025 0.53 NO
79 RPL38 RPL38 RPL38 6493 0.023 0.53 NO
80 RPL36A RPL36A RPL36A 6585 0.022 0.53 NO
81 RPS14 RPS14 RPS14 6691 0.02 0.52 NO
82 RPS19 RPS19 RPS19 6774 0.019 0.52 NO
83 RPL36 RPL36 RPL36 6821 0.018 0.52 NO
84 RPL23A RPL23A RPL23A 7135 0.014 0.51 NO
85 RPL28 RPL28 RPL28 7407 0.01 0.49 NO
86 RNPS1 RNPS1 RNPS1 7814 0.0045 0.47 NO
87 EIF4G1 EIF4G1 EIF4G1 8205 -0.0013 0.45 NO
88 RPL26L1 RPL26L1 RPL26L1 8215 -0.0015 0.45 NO
89 RPL27 RPL27 RPL27 8240 -0.0017 0.45 NO
90 RPS4Y1 RPS4Y1 RPS4Y1 8242 -0.0018 0.45 NO
91 EIF4A3 EIF4A3 EIF4A3 8243 -0.0018 0.45 NO
92 RPS5 RPS5 RPS5 8249 -0.0019 0.45 NO
93 UBA52 UBA52 UBA52 8360 -0.0033 0.44 NO
94 SMG5 SMG5 SMG5 8625 -0.0072 0.43 NO
95 NCBP1 NCBP1 NCBP1 8865 -0.011 0.42 NO
96 PPP2R1A PPP2R1A PPP2R1A 9710 -0.024 0.37 NO
97 RPSAP9 RPSAP9 RPSAP9 9743 -0.025 0.38 NO
98 RPL41 RPL41 RPL41 9888 -0.027 0.37 NO
99 RPS26 RPS26 RPS26 10383 -0.036 0.35 NO
100 PPP2R2A PPP2R2A PPP2R2A 10669 -0.041 0.34 NO
101 PPP2CA PPP2CA PPP2CA 10705 -0.042 0.34 NO
102 ETF1 ETF1 ETF1 10928 -0.046 0.33 NO
103 MAGOH MAGOH MAGOH 13713 -0.12 0.2 NO
104 FAM153A FAM153A FAM153A 17552 -0.47 0.042 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 AR NONGENOMIC PATHWAY.

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

genes ES table in pathway: REACTOME TRANSLATION

Table 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 RICTOR RICTOR RICTOR 708 0.25 0.053 YES
2 FOXO4 FOXO4 FOXO4 1180 0.19 0.097 YES
3 CASP9 CASP9 CASP9 1285 0.18 0.16 YES
4 PHLPP1 PHLPP1 PHLPP1 1718 0.15 0.19 YES
5 PIK3R1 PIK3R1 PIK3R1 2054 0.13 0.22 YES
6 PAG1 PAG1 PAG1 2321 0.12 0.25 YES
7 AKT3 AKT3 AKT3 3009 0.094 0.24 YES
8 SRC SRC SRC 3494 0.08 0.25 YES
9 GAB1 GAB1 GAB1 3553 0.078 0.27 YES
10 CDKN1B CDKN1B CDKN1B 3582 0.078 0.3 YES
11 PIK3CA PIK3CA PIK3CA 3672 0.076 0.32 YES
12 FOXO3 FOXO3 FOXO3 3674 0.076 0.35 YES
13 TSC2 TSC2 TSC2 3702 0.075 0.38 YES
14 THEM4 THEM4 THEM4 4158 0.065 0.38 YES
15 NR4A1 NR4A1 NR4A1 4396 0.06 0.38 YES
16 CHUK CHUK CHUK 4486 0.058 0.4 YES
17 PTEN PTEN PTEN 5406 0.041 0.37 NO
18 CSK CSK CSK 5686 0.036 0.36 NO
19 MLST8 MLST8 MLST8 5872 0.033 0.37 NO
20 CREB1 CREB1 CREB1 6912 0.017 0.32 NO
21 GRB2 GRB2 GRB2 7342 0.011 0.3 NO
22 PDPK1 PDPK1 PDPK1 7441 0.01 0.29 NO
23 MTOR MTOR MTOR 8234 -0.0017 0.25 NO
24 AKT1 AKT1 AKT1 8464 -0.0046 0.24 NO
25 AKT1S1 AKT1S1 AKT1S1 8543 -0.0059 0.24 NO
26 RPS6KB2 RPS6KB2 RPS6KB2 8750 -0.0091 0.23 NO
27 BAD BAD BAD 8783 -0.0096 0.23 NO
28 AKT2 AKT2 AKT2 10556 -0.039 0.15 NO
29 MAPKAP1 MAPKAP1 MAPKAP1 10661 -0.041 0.16 NO
30 EGFR EGFR EGFR 10988 -0.047 0.16 NO
31 FOXO1 FOXO1 FOXO1 11890 -0.065 0.13 NO
32 GSK3A GSK3A GSK3A 12125 -0.071 0.15 NO
33 MDM2 MDM2 MDM2 12560 -0.083 0.15 NO
34 EGF EGF EGF 13061 -0.098 0.16 NO
35 TRIB3 TRIB3 TRIB3 14193 -0.14 0.15 NO
36 CDKN1A CDKN1A CDKN1A 15008 -0.19 0.18 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: REACTOME TRANSLATION.

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

genes ES table in pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX

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 RPL21 RPL21 RPL21 42 0.5 0.058 YES
2 RPL17 RPL17 RPL17 703 0.25 0.052 YES
3 RPL7 RPL7 RPL7 797 0.24 0.076 YES
4 RPS28 RPS28 RPS28 1000 0.21 0.09 YES
5 RPL9 RPL9 RPL9 1070 0.2 0.11 YES
6 RPL18A RPL18A RPL18A 1314 0.18 0.12 YES
7 RPL12 RPL12 RPL12 1385 0.17 0.14 YES
8 RPL13A RPL13A RPL13A 1475 0.17 0.15 YES
9 RPS25 RPS25 RPS25 1831 0.14 0.15 YES
10 RPS27A RPS27A RPS27A 1853 0.14 0.16 YES
11 RPL3 RPL3 RPL3 1867 0.14 0.18 YES
12 RPS12 RPS12 RPS12 1876 0.14 0.2 YES
13 RPL4 RPL4 RPL4 1948 0.14 0.21 YES
14 RPL7A RPL7A RPL7A 1954 0.13 0.22 YES
15 PABPC1 PABPC1 PABPC1 1993 0.13 0.24 YES
16 RPS24 RPS24 RPS24 2105 0.13 0.25 YES
17 EIF4B EIF4B EIF4B 2139 0.12 0.26 YES
18 EIF3A EIF3A EIF3A 2185 0.12 0.27 YES
19 RPL10 RPL10 RPL10 2270 0.12 0.28 YES
20 RPL6 RPL6 RPL6 2382 0.12 0.29 YES
21 EIF3E EIF3E EIF3E 2495 0.11 0.3 YES
22 RPL22 RPL22 RPL22 2571 0.11 0.31 YES
23 EIF3F EIF3F EIF3F 2584 0.11 0.32 YES
24 RPSA RPSA RPSA 2701 0.1 0.32 YES
25 RPS18 RPS18 RPS18 2807 0.099 0.33 YES
26 RPS3 RPS3 RPS3 2860 0.098 0.34 YES
27 RPS13 RPS13 RPS13 3005 0.094 0.34 YES
28 RPL34 RPL34 RPL34 3051 0.092 0.35 YES
29 RPS7 RPS7 RPS7 3092 0.091 0.36 YES
30 RPL27A RPL27A RPL27A 3138 0.09 0.37 YES
31 RPL30 RPL30 RPL30 3151 0.089 0.38 YES
32 EIF3H EIF3H EIF3H 3197 0.088 0.39 YES
33 RPS23 RPS23 RPS23 3254 0.087 0.39 YES
34 RPL24 RPL24 RPL24 3291 0.086 0.4 YES
35 RPL26 RPL26 RPL26 3295 0.086 0.41 YES
36 RPL19 RPL19 RPL19 3368 0.083 0.42 YES
37 RPL5 RPL5 RPL5 3376 0.083 0.43 YES
38 RPL13 RPL13 RPL13 3377 0.083 0.44 YES
39 RPS6 RPS6 RPS6 3464 0.081 0.44 YES
40 RPL37 RPL37 RPL37 3466 0.081 0.45 YES
41 RPS20 RPS20 RPS20 3511 0.08 0.46 YES
42 RPS10 RPS10 RPS10 3561 0.078 0.47 YES
43 RPLP0 RPLP0 RPLP0 3596 0.077 0.48 YES
44 RPL23 RPL23 RPL23 3618 0.077 0.48 YES
45 FAU FAU FAU 3743 0.074 0.48 YES
46 RPL15 RPL15 RPL15 3924 0.07 0.48 YES
47 RPLP1 RPLP1 RPLP1 3949 0.069 0.49 YES
48 RPS2 RPS2 RPS2 3997 0.068 0.5 YES
49 RPS4X RPS4X RPS4X 4098 0.066 0.5 YES
50 RPS17 RPS17 RPS17 4116 0.066 0.5 YES
51 EIF3D EIF3D EIF3D 4117 0.066 0.51 YES
52 RPL11 RPL11 RPL11 4133 0.066 0.52 YES
53 RPS16 RPS16 RPS16 4242 0.063 0.52 YES
54 RPL14 RPL14 RPL14 4308 0.062 0.53 YES
55 RPL29 RPL29 RPL29 4355 0.061 0.53 YES
56 RPS8 RPS8 RPS8 4485 0.058 0.53 YES
57 RPLP2 RPLP2 RPLP2 4563 0.056 0.53 YES
58 RPL8 RPL8 RPL8 4636 0.055 0.54 YES
59 RPL32 RPL32 RPL32 4654 0.054 0.54 YES
60 RPL37A RPL37A RPL37A 4678 0.054 0.55 YES
61 RPS9 RPS9 RPS9 4751 0.053 0.55 YES
62 RPL18 RPL18 RPL18 4766 0.052 0.55 YES
63 RPS29 RPS29 RPS29 4801 0.052 0.56 YES
64 RPS3A RPS3A RPS3A 4837 0.051 0.56 YES
65 RPS15A RPS15A RPS15A 5024 0.047 0.56 NO
66 RPL10A RPL10A RPL10A 5175 0.045 0.56 NO
67 RPL31 RPL31 RPL31 5476 0.04 0.54 NO
68 EIF3G EIF3G EIF3G 5490 0.04 0.55 NO
69 EIF3J EIF3J EIF3J 5539 0.038 0.55 NO
70 RPL39 RPL39 RPL39 5671 0.036 0.55 NO
71 RPS21 RPS21 RPS21 5681 0.036 0.55 NO
72 RPS11 RPS11 RPS11 5729 0.035 0.55 NO
73 RPS15 RPS15 RPS15 5967 0.032 0.54 NO
74 RPL35 RPL35 RPL35 6192 0.028 0.53 NO
75 EIF2S3 EIF2S3 EIF2S3 6339 0.026 0.53 NO
76 RPS27 RPS27 RPS27 6363 0.026 0.53 NO
77 RPL35A RPL35A RPL35A 6392 0.025 0.53 NO
78 RPL38 RPL38 RPL38 6493 0.023 0.53 NO
79 RPL36A RPL36A RPL36A 6585 0.022 0.53 NO
80 RPS14 RPS14 RPS14 6691 0.02 0.52 NO
81 RPS19 RPS19 RPS19 6774 0.019 0.52 NO
82 RPL36 RPL36 RPL36 6821 0.018 0.52 NO
83 EIF1AX EIF1AX EIF1AX 7024 0.016 0.51 NO
84 EIF2S2 EIF2S2 EIF2S2 7081 0.015 0.51 NO
85 RPL23A RPL23A RPL23A 7135 0.014 0.51 NO
86 EIF4A1 EIF4A1 EIF4A1 7283 0.012 0.5 NO
87 RPL28 RPL28 RPL28 7407 0.01 0.5 NO
88 EIF4A2 EIF4A2 EIF4A2 7553 0.0084 0.49 NO
89 EIF3B EIF3B EIF3B 7779 0.0051 0.48 NO
90 EIF4G1 EIF4G1 EIF4G1 8205 -0.0013 0.46 NO
91 RPL26L1 RPL26L1 RPL26L1 8215 -0.0015 0.46 NO
92 RPL27 RPL27 RPL27 8240 -0.0017 0.46 NO
93 RPS4Y1 RPS4Y1 RPS4Y1 8242 -0.0018 0.46 NO
94 RPS5 RPS5 RPS5 8249 -0.0019 0.46 NO
95 UBA52 UBA52 UBA52 8360 -0.0033 0.45 NO
96 EIF4H EIF4H EIF4H 8899 -0.011 0.42 NO
97 EIF2S1 EIF2S1 EIF2S1 8949 -0.012 0.42 NO
98 RPSAP9 RPSAP9 RPSAP9 9743 -0.025 0.38 NO
99 RPL41 RPL41 RPL41 9888 -0.027 0.38 NO
100 EIF3C EIF3C EIF3C 10194 -0.033 0.36 NO
101 RPS26 RPS26 RPS26 10383 -0.036 0.36 NO
102 EIF3K EIF3K EIF3K 11696 -0.061 0.29 NO
103 EIF3I EIF3I EIF3I 11742 -0.062 0.3 NO
104 EIF4E EIF4E EIF4E 11844 -0.064 0.3 NO
105 FAM153A FAM153A FAM153A 17552 -0.47 0.042 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: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, 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 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION

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 RPS28 RPS28 RPS28 1000 0.21 0.0043 YES
2 RPS25 RPS25 RPS25 1831 0.14 -0.0014 YES
3 RPS27A RPS27A RPS27A 1853 0.14 0.037 YES
4 RPS12 RPS12 RPS12 1876 0.14 0.074 YES
5 PABPC1 PABPC1 PABPC1 1993 0.13 0.1 YES
6 RPS24 RPS24 RPS24 2105 0.13 0.14 YES
7 EIF4B EIF4B EIF4B 2139 0.12 0.17 YES
8 EIF3A EIF3A EIF3A 2185 0.12 0.2 YES
9 EIF3E EIF3E EIF3E 2495 0.11 0.21 YES
10 EIF3F EIF3F EIF3F 2584 0.11 0.24 YES
11 RPSA RPSA RPSA 2701 0.1 0.26 YES
12 RPS18 RPS18 RPS18 2807 0.099 0.28 YES
13 RPS3 RPS3 RPS3 2860 0.098 0.31 YES
14 RPS13 RPS13 RPS13 3005 0.094 0.33 YES
15 RPS7 RPS7 RPS7 3092 0.091 0.35 YES
16 EIF3H EIF3H EIF3H 3197 0.088 0.37 YES
17 RPS23 RPS23 RPS23 3254 0.087 0.39 YES
18 RPS6 RPS6 RPS6 3464 0.081 0.4 YES
19 RPS20 RPS20 RPS20 3511 0.08 0.42 YES
20 RPS10 RPS10 RPS10 3561 0.078 0.44 YES
21 FAU FAU FAU 3743 0.074 0.45 YES
22 RPS2 RPS2 RPS2 3997 0.068 0.45 YES
23 RPS4X RPS4X RPS4X 4098 0.066 0.47 YES
24 RPS17 RPS17 RPS17 4116 0.066 0.48 YES
25 EIF3D EIF3D EIF3D 4117 0.066 0.5 YES
26 RPS16 RPS16 RPS16 4242 0.063 0.51 YES
27 RPS8 RPS8 RPS8 4485 0.058 0.52 YES
28 RPS9 RPS9 RPS9 4751 0.053 0.52 YES
29 RPS29 RPS29 RPS29 4801 0.052 0.53 YES
30 RPS3A RPS3A RPS3A 4837 0.051 0.54 YES
31 RPS15A RPS15A RPS15A 5024 0.047 0.54 YES
32 EIF3G EIF3G EIF3G 5490 0.04 0.53 YES
33 EIF3J EIF3J EIF3J 5539 0.038 0.54 YES
34 RPS21 RPS21 RPS21 5681 0.036 0.54 YES
35 RPS11 RPS11 RPS11 5729 0.035 0.55 YES
36 RPS15 RPS15 RPS15 5967 0.032 0.54 NO
37 EIF2S3 EIF2S3 EIF2S3 6339 0.026 0.53 NO
38 RPS27 RPS27 RPS27 6363 0.026 0.54 NO
39 RPS14 RPS14 RPS14 6691 0.02 0.52 NO
40 RPS19 RPS19 RPS19 6774 0.019 0.52 NO
41 EIF1AX EIF1AX EIF1AX 7024 0.016 0.52 NO
42 EIF2S2 EIF2S2 EIF2S2 7081 0.015 0.52 NO
43 EIF4EBP1 EIF4EBP1 EIF4EBP1 7266 0.012 0.51 NO
44 EIF4A1 EIF4A1 EIF4A1 7283 0.012 0.51 NO
45 EIF4A2 EIF4A2 EIF4A2 7553 0.0084 0.5 NO
46 EIF3B EIF3B EIF3B 7779 0.0051 0.49 NO
47 EIF4G1 EIF4G1 EIF4G1 8205 -0.0013 0.47 NO
48 RPS4Y1 RPS4Y1 RPS4Y1 8242 -0.0018 0.46 NO
49 RPS5 RPS5 RPS5 8249 -0.0019 0.46 NO
50 EIF4H EIF4H EIF4H 8899 -0.011 0.43 NO
51 EIF2S1 EIF2S1 EIF2S1 8949 -0.012 0.43 NO
52 RPSAP9 RPSAP9 RPSAP9 9743 -0.025 0.4 NO
53 EIF3C EIF3C EIF3C 10194 -0.033 0.38 NO
54 RPS26 RPS26 RPS26 10383 -0.036 0.38 NO
55 EIF3K EIF3K EIF3K 11696 -0.061 0.33 NO
56 EIF3I EIF3I EIF3I 11742 -0.062 0.34 NO
57 EIF4E EIF4E EIF4E 11844 -0.064 0.35 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: REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION, 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 SIGNALING BY NOTCH1

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 RPS28 RPS28 RPS28 1000 0.21 0.011 YES
2 RPS25 RPS25 RPS25 1831 0.14 0.01 YES
3 RPS27A RPS27A RPS27A 1853 0.14 0.053 YES
4 RPS12 RPS12 RPS12 1876 0.14 0.095 YES
5 RPS24 RPS24 RPS24 2105 0.13 0.12 YES
6 EIF3A EIF3A EIF3A 2185 0.12 0.16 YES
7 EIF3E EIF3E EIF3E 2495 0.11 0.17 YES
8 EIF3F EIF3F EIF3F 2584 0.11 0.2 YES
9 RPSA RPSA RPSA 2701 0.1 0.23 YES
10 RPS18 RPS18 RPS18 2807 0.099 0.25 YES
11 RPS3 RPS3 RPS3 2860 0.098 0.28 YES
12 RPS13 RPS13 RPS13 3005 0.094 0.3 YES
13 RPS7 RPS7 RPS7 3092 0.091 0.33 YES
14 EIF3H EIF3H EIF3H 3197 0.088 0.35 YES
15 RPS23 RPS23 RPS23 3254 0.087 0.37 YES
16 RPS6 RPS6 RPS6 3464 0.081 0.39 YES
17 RPS20 RPS20 RPS20 3511 0.08 0.41 YES
18 RPS10 RPS10 RPS10 3561 0.078 0.43 YES
19 FAU FAU FAU 3743 0.074 0.44 YES
20 RPS2 RPS2 RPS2 3997 0.068 0.45 YES
21 RPS4X RPS4X RPS4X 4098 0.066 0.46 YES
22 RPS17 RPS17 RPS17 4116 0.066 0.48 YES
23 EIF3D EIF3D EIF3D 4117 0.066 0.51 YES
24 RPS16 RPS16 RPS16 4242 0.063 0.52 YES
25 RPS8 RPS8 RPS8 4485 0.058 0.52 YES
26 RPS9 RPS9 RPS9 4751 0.053 0.52 YES
27 RPS29 RPS29 RPS29 4801 0.052 0.54 YES
28 RPS3A RPS3A RPS3A 4837 0.051 0.55 YES
29 RPS15A RPS15A RPS15A 5024 0.047 0.56 YES
30 EIF3G EIF3G EIF3G 5490 0.04 0.54 YES
31 EIF3J EIF3J EIF3J 5539 0.038 0.55 YES
32 RPS21 RPS21 RPS21 5681 0.036 0.56 YES
33 RPS11 RPS11 RPS11 5729 0.035 0.57 YES
34 RPS15 RPS15 RPS15 5967 0.032 0.56 NO
35 EIF2S3 EIF2S3 EIF2S3 6339 0.026 0.55 NO
36 RPS27 RPS27 RPS27 6363 0.026 0.56 NO
37 RPS14 RPS14 RPS14 6691 0.02 0.55 NO
38 RPS19 RPS19 RPS19 6774 0.019 0.55 NO
39 EIF1AX EIF1AX EIF1AX 7024 0.016 0.54 NO
40 EIF2S2 EIF2S2 EIF2S2 7081 0.015 0.54 NO
41 EIF3B EIF3B EIF3B 7779 0.0051 0.5 NO
42 RPS4Y1 RPS4Y1 RPS4Y1 8242 -0.0018 0.48 NO
43 RPS5 RPS5 RPS5 8249 -0.0019 0.48 NO
44 EIF2S1 EIF2S1 EIF2S1 8949 -0.012 0.44 NO
45 RPSAP9 RPSAP9 RPSAP9 9743 -0.025 0.41 NO
46 EIF3C EIF3C EIF3C 10194 -0.033 0.39 NO
47 RPS26 RPS26 RPS26 10383 -0.036 0.4 NO
48 EIF3K EIF3K EIF3K 11696 -0.061 0.34 NO
49 EIF3I EIF3I EIF3I 11742 -0.062 0.36 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: REACTOME SIGNALING BY NOTCH1.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SIGNALING BY NOTCH1, 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 = GBMLGG-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = GBMLGG-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)
Copyright © 2016 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle