GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in UVM-TP
Uveal Melanoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1P84B14
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in UVM-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1P84B14
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 in UVM-TP. 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: 187
Number of samples: 80
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 30
pheno.type: 2 - 3 :[ clus2 ] 15
pheno.type: 3 - 3 :[ clus3 ] 35

For the expression subtypes of 17361 genes in 81 samples, GSEA found enriched gene sets in each cluster using 80 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA BCR PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA TCR PATHWAY, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG PROTEASOME, KEGG HOMOLOGOUS RECOMBINATION, KEGG CELL CYCLE, KEGG OOCYTE MEIOSIS, KEGG P53 SIGNALING PATHWAY, KEGG ANTIGEN PROCESSING AND PRESENTATION

    • And common core enriched genes are IFNG, NFATC2, NFATC4, PPP3CA, VAV1, AIM2, CASP1, CCL4, CCL4L2, CCL5

  • clus2

    • Top enriched gene sets are BIOCARTA ALK PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA FMLP PATHWAY, BIOCARTA EDG1 PATHWAY, BIOCARTA MYOSIN PATHWAY, BIOCARTA CHREBP2 PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG PURINE METABOLISM

    • And common core enriched genes are CCND2, CXXC4, DKK1, FOSL1, FZD2, FZD5, FZD7, FZD8, LEF1, SFRP1

  • clus3

    • Top enriched gene sets are BIOCARTA RACCYCD PATHWAY, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG PYRUVATE METABOLISM, KEGG PROPANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM CYTOCHROME P450, KEGG RIBOSOME

    • And common core enriched genes are FAU, RPL10, RPL10A, RPL11, RPL12, RPL13, RPL13A, RPL14, RPL15, RPL17

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
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.53 1.5 0.07 1 0.78 0.42 0.22 0.33 0.75 0.41
BIOCARTA IL2RB PATHWAY 37 genes.ES.table 0.56 1.5 0.11 0.93 0.82 0.3 0.14 0.26 0.6 0.32
BIOCARTA TCR PATHWAY 43 genes.ES.table 0.59 1.5 0.1 0.97 0.8 0.35 0.14 0.3 0.61 0.34
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 42 genes.ES.table 0.38 1.4 0.13 0.7 0.88 0.6 0.41 0.35 0.47 0.23
KEGG PROTEASOME 42 genes.ES.table 0.5 1.6 0.066 1 0.62 0.64 0.38 0.4 0.88 0.47
KEGG HOMOLOGOUS RECOMBINATION 27 genes.ES.table 0.59 1.4 0.096 0.86 0.87 0.44 0.2 0.35 0.57 0.29
KEGG CELL CYCLE 123 genes.ES.table 0.48 1.5 0.077 1 0.78 0.37 0.23 0.29 0.62 0.35
KEGG OOCYTE MEIOSIS 103 genes.ES.table 0.43 1.4 0.1 0.57 0.88 0.34 0.23 0.26 0.38 0.16
KEGG P53 SIGNALING PATHWAY 66 genes.ES.table 0.44 1.4 0.049 0.59 0.88 0.3 0.16 0.26 0.4 0.18
KEGG ANTIGEN PROCESSING AND PRESENTATION 65 genes.ES.table 0.63 1.4 0.13 0.81 0.88 0.57 0.2 0.46 0.54 0.27
genes ES table in pathway: BIOCARTA BCR PATHWAY

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 CXCL10 CXCL10 CXCL10 222 0.54 0.069 YES
2 CCL4 CCL4 CCL4 305 0.51 0.14 YES
3 AIM2 AIM2 AIM2 360 0.48 0.21 YES
4 CASP1 CASP1 CASP1 478 0.45 0.27 YES
5 CCL5 CCL5 CCL5 500 0.44 0.34 YES
6 CCL4L2 CCL4L2 CCL4L2 550 0.43 0.4 YES
7 IL18 IL18 IL18 881 0.36 0.44 YES
8 IL1B IL1B IL1B 1051 0.34 0.48 YES
9 ZBP1 ZBP1 ZBP1 1277 0.31 0.52 YES
10 IL6 IL6 IL6 1453 0.29 0.55 YES
11 TMEM173 TMEM173 TMEM173 2242 0.22 0.54 YES
12 TBK1 TBK1 TBK1 2280 0.21 0.57 YES
13 RIPK3 RIPK3 RIPK3 2839 0.18 0.56 YES
14 DDX58 DDX58 DDX58 2879 0.17 0.58 YES
15 IRF7 IRF7 IRF7 2908 0.17 0.61 YES
16 IKBKE IKBKE IKBKE 3260 0.15 0.61 YES
17 POLR3G POLR3G POLR3G 3300 0.15 0.63 YES
18 NFKB1 NFKB1 NFKB1 5570 0.076 0.52 NO
19 CHUK CHUK CHUK 5832 0.069 0.51 NO
20 POLR3K POLR3K POLR3K 6045 0.064 0.51 NO
21 POLR3C POLR3C POLR3C 6340 0.058 0.5 NO
22 NFKBIA NFKBIA NFKBIA 6687 0.05 0.49 NO
23 POLR3B POLR3B POLR3B 7160 0.04 0.47 NO
24 POLR3A POLR3A POLR3A 8482 0.014 0.39 NO
25 POLR3GL POLR3GL POLR3GL 8717 0.0096 0.38 NO
26 ADAR ADAR ADAR 8867 0.0068 0.37 NO
27 POLR3H POLR3H POLR3H 9033 0.0034 0.36 NO
28 POLR3F POLR3F POLR3F 9073 0.0028 0.36 NO
29 POLR1C POLR1C POLR1C 9376 -0.0031 0.34 NO
30 IRF3 IRF3 IRF3 9465 -0.0049 0.34 NO
31 MAVS MAVS MAVS 9978 -0.015 0.31 NO
32 RIPK1 RIPK1 RIPK1 10381 -0.023 0.29 NO
33 IKBKB IKBKB IKBKB 10781 -0.031 0.28 NO
34 IKBKG IKBKG IKBKG 11553 -0.049 0.24 NO
35 TREX1 TREX1 TREX1 12187 -0.066 0.21 NO
36 NFKBIB NFKBIB NFKBIB 12425 -0.073 0.21 NO
37 RELA RELA RELA 12507 -0.076 0.22 NO
38 POLR3D POLR3D POLR3D 12740 -0.082 0.21 NO
39 POLR1D POLR1D POLR1D 13032 -0.093 0.21 NO
40 IL33 IL33 IL33 13500 -0.11 0.2 NO
41 PYCARD PYCARD PYCARD 14060 -0.14 0.19 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: BIOCARTA BCR PATHWAY.

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

genes ES table in pathway: BIOCARTA IL2RB 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 PSMB9 PSMB9 PSMB9 279 0.52 0.098 YES
2 IFNG IFNG IFNG 316 0.5 0.21 YES
3 PSMB8 PSMB8 PSMB8 1150 0.33 0.23 YES
4 PSMA3 PSMA3 PSMA3 2105 0.23 0.22 YES
5 PSME4 PSME4 PSME4 2202 0.22 0.27 YES
6 PSMD14 PSMD14 PSMD14 2907 0.17 0.27 YES
7 PSMA4 PSMA4 PSMA4 2979 0.17 0.3 YES
8 PSMA6 PSMA6 PSMA6 3512 0.14 0.3 YES
9 PSMD12 PSMD12 PSMD12 3627 0.14 0.32 YES
10 PSMC6 PSMC6 PSMC6 3819 0.13 0.34 YES
11 PSME2 PSME2 PSME2 3916 0.13 0.36 YES
12 PSMC1 PSMC1 PSMC1 4086 0.12 0.38 YES
13 PSMD11 PSMD11 PSMD11 4230 0.12 0.4 YES
14 PSMA7 PSMA7 PSMA7 4479 0.11 0.41 YES
15 PSMC2 PSMC2 PSMC2 4575 0.1 0.43 YES
16 PSMB3 PSMB3 PSMB3 4663 0.1 0.44 YES
17 POMP POMP POMP 4878 0.094 0.45 YES
18 PSMA2 PSMA2 PSMA2 5297 0.083 0.45 YES
19 PSMA5 PSMA5 PSMA5 5560 0.076 0.45 YES
20 PSMD7 PSMD7 PSMD7 5606 0.075 0.46 YES
21 PSMC4 PSMC4 PSMC4 5646 0.074 0.48 YES
22 PSMA1 PSMA1 PSMA1 5869 0.068 0.48 YES
23 PSMC3 PSMC3 PSMC3 6079 0.064 0.48 YES
24 PSME3 PSME3 PSME3 6312 0.058 0.48 YES
25 SHFM1 SHFM1 SHFM1 6372 0.057 0.49 YES
26 PSMC5 PSMC5 PSMC5 6448 0.055 0.5 YES
27 PSME1 PSME1 PSME1 6560 0.053 0.5 YES
28 PSMB5 PSMB5 PSMB5 6870 0.046 0.5 NO
29 PSMD8 PSMD8 PSMD8 6963 0.044 0.5 NO
30 PSMB6 PSMB6 PSMB6 7335 0.037 0.49 NO
31 PSMD3 PSMD3 PSMD3 7359 0.036 0.49 NO
32 PSMB2 PSMB2 PSMB2 7743 0.029 0.48 NO
33 PSMB1 PSMB1 PSMB1 7802 0.028 0.48 NO
34 PSMD13 PSMD13 PSMD13 8116 0.022 0.47 NO
35 PSMB4 PSMB4 PSMB4 8452 0.015 0.45 NO
36 PSMA8 PSMA8 PSMA8 8677 0.01 0.44 NO
37 PSMD4 PSMD4 PSMD4 8695 0.01 0.44 NO
38 PSMD1 PSMD1 PSMD1 8915 0.0057 0.43 NO
39 PSMB7 PSMB7 PSMB7 8951 0.0049 0.43 NO
40 PSMF1 PSMF1 PSMF1 12246 -0.068 0.25 NO
41 PSMD6 PSMD6 PSMD6 12612 -0.079 0.25 NO
42 PSMD2 PSMD2 PSMD2 13429 -0.11 0.23 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 IL2RB PATHWAY.

Figure S4.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA TCR 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 MMP1 MMP1 MMP1 534 0.43 0.046 YES
2 E2F2 E2F2 E2F2 700 0.4 0.11 YES
3 MMP9 MMP9 MMP9 771 0.38 0.17 YES
4 TYMP TYMP TYMP 1039 0.34 0.22 YES
5 CDH1 CDH1 CDH1 1367 0.3 0.25 YES
6 THBS1 THBS1 THBS1 1476 0.29 0.29 YES
7 EGF EGF EGF 1761 0.26 0.32 YES
8 FGFR3 FGFR3 FGFR3 1943 0.24 0.35 YES
9 MMP2 MMP2 MMP2 2030 0.23 0.39 YES
10 IL8 IL8 IL8 2118 0.22 0.42 YES
11 CDKN1A CDKN1A CDKN1A 2120 0.22 0.46 YES
12 DAPK2 DAPK2 DAPK2 2235 0.22 0.5 YES
13 MDM2 MDM2 MDM2 2733 0.18 0.5 YES
14 VEGFC VEGFC VEGFC 2795 0.18 0.53 YES
15 PGF PGF PGF 4013 0.12 0.48 NO
16 DAPK1 DAPK1 DAPK1 4037 0.12 0.5 NO
17 VEGFA VEGFA VEGFA 4700 0.099 0.48 NO
18 FIGF FIGF FIGF 4728 0.098 0.5 NO
19 KRAS KRAS KRAS 5083 0.089 0.49 NO
20 RPS6KA5 RPS6KA5 RPS6KA5 5171 0.086 0.5 NO
21 MAPK1 MAPK1 MAPK1 5232 0.085 0.51 NO
22 MAP2K1 MAP2K1 MAP2K1 6597 0.052 0.44 NO
23 NRAS NRAS NRAS 6926 0.045 0.43 NO
24 CDKN2A CDKN2A CDKN2A 7385 0.036 0.41 NO
25 RB1 RB1 RB1 7658 0.03 0.4 NO
26 CCND1 CCND1 CCND1 8162 0.02 0.38 NO
27 MAP2K2 MAP2K2 MAP2K2 8684 0.01 0.35 NO
28 ARAF ARAF ARAF 8716 0.0096 0.35 NO
29 TP53 TP53 TP53 9313 -0.002 0.31 NO
30 BRAF BRAF BRAF 9436 -0.0042 0.31 NO
31 DAPK3 DAPK3 DAPK3 10590 -0.027 0.25 NO
32 HRAS HRAS HRAS 10606 -0.028 0.25 NO
33 EGFR EGFR EGFR 11157 -0.04 0.22 NO
34 MAPK3 MAPK3 MAPK3 11383 -0.044 0.22 NO
35 ERBB2 ERBB2 ERBB2 11401 -0.045 0.23 NO
36 MYC MYC MYC 11677 -0.052 0.22 NO
37 CDK4 CDK4 CDK4 12218 -0.067 0.2 NO
38 E2F3 E2F3 E2F3 12618 -0.079 0.19 NO
39 VEGFB VEGFB VEGFB 13234 -0.1 0.17 NO
40 RASSF1 RASSF1 RASSF1 14073 -0.14 0.15 NO
41 RAF1 RAF1 RAF1 15355 -0.22 0.12 NO

Figure S5.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TCR PATHWAY.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TCR 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

Table S4.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CARD11 CARD11 CARD11 30 0.75 0.037 YES
2 PDCD1 PDCD1 PDCD1 232 0.54 0.052 YES
3 CD3D CD3D CD3D 245 0.53 0.079 YES
4 IFNG IFNG IFNG 316 0.5 0.1 YES
5 CD8B CD8B CD8B 359 0.48 0.12 YES
6 ICOS ICOS ICOS 375 0.48 0.15 YES
7 CD8A CD8A CD8A 389 0.47 0.17 YES
8 MAPK12 MAPK12 MAPK12 391 0.47 0.19 YES
9 CD3G CD3G CD3G 396 0.47 0.22 YES
10 GRAP2 GRAP2 GRAP2 407 0.47 0.24 YES
11 LCK LCK LCK 424 0.46 0.26 YES
12 TNF TNF TNF 463 0.45 0.29 YES
13 MAP3K8 MAP3K8 MAP3K8 518 0.44 0.3 YES
14 CTLA4 CTLA4 CTLA4 523 0.44 0.33 YES
15 ZAP70 ZAP70 ZAP70 551 0.43 0.35 YES
16 LCP2 LCP2 LCP2 572 0.42 0.37 YES
17 CD247 CD247 CD247 592 0.42 0.39 YES
18 CD3E CD3E CD3E 656 0.41 0.41 YES
19 NFATC4 NFATC4 NFATC4 658 0.41 0.43 YES
20 PTPRC PTPRC PTPRC 712 0.4 0.44 YES
21 NFATC2 NFATC2 NFATC2 851 0.37 0.46 YES
22 CD28 CD28 CD28 864 0.36 0.47 YES
23 PIK3CG PIK3CG PIK3CG 972 0.35 0.48 YES
24 RASGRP1 RASGRP1 RASGRP1 1046 0.34 0.5 YES
25 PDK1 PDK1 PDK1 1078 0.33 0.51 YES
26 LAT LAT LAT 1089 0.33 0.53 YES
27 ITK ITK ITK 1130 0.33 0.54 YES
28 PTPN6 PTPN6 PTPN6 1262 0.31 0.55 YES
29 CD40LG CD40LG CD40LG 1615 0.27 0.55 YES
30 PIK3R3 PIK3R3 PIK3R3 1735 0.26 0.55 YES
31 IL10 IL10 IL10 1767 0.26 0.56 YES
32 VAV1 VAV1 VAV1 1809 0.25 0.57 YES
33 PIK3R5 PIK3R5 PIK3R5 2056 0.23 0.57 YES
34 VAV2 VAV2 VAV2 2135 0.22 0.58 YES
35 PPP3CA PPP3CA PPP3CA 2146 0.22 0.59 YES
36 FOS FOS FOS 2448 0.2 0.58 NO
37 PAK6 PAK6 PAK6 3115 0.16 0.55 NO
38 PPP3CC PPP3CC PPP3CC 3248 0.16 0.55 NO
39 SOS1 SOS1 SOS1 3647 0.14 0.54 NO
40 NFAT5 NFAT5 NFAT5 3985 0.12 0.52 NO
41 BCL10 BCL10 BCL10 4132 0.12 0.52 NO
42 KRAS KRAS KRAS 5083 0.089 0.47 NO
43 MAPK1 MAPK1 MAPK1 5232 0.085 0.47 NO
44 NFKB1 NFKB1 NFKB1 5570 0.076 0.45 NO
45 CHUK CHUK CHUK 5832 0.069 0.44 NO
46 MAP2K1 MAP2K1 MAP2K1 6597 0.052 0.4 NO
47 NFKBIA NFKBIA NFKBIA 6687 0.05 0.39 NO
48 NRAS NRAS NRAS 6926 0.045 0.38 NO
49 PLCG1 PLCG1 PLCG1 6969 0.044 0.38 NO
50 MAP3K14 MAP3K14 MAP3K14 7030 0.043 0.38 NO
51 PIK3R1 PIK3R1 PIK3R1 7053 0.042 0.38 NO
52 CD4 CD4 CD4 7138 0.041 0.38 NO
53 PPP3CB PPP3CB PPP3CB 7244 0.039 0.38 NO
54 PPP3R1 PPP3R1 PPP3R1 7452 0.034 0.36 NO
55 MAP3K7 MAP3K7 MAP3K7 7465 0.034 0.37 NO
56 MAPK14 MAPK14 MAPK14 7906 0.026 0.34 NO
57 CDC42 CDC42 CDC42 8029 0.023 0.34 NO
58 MAPK9 MAPK9 MAPK9 8036 0.023 0.34 NO
59 NCK1 NCK1 NCK1 8113 0.022 0.33 NO
60 MAPK11 MAPK11 MAPK11 8221 0.019 0.33 NO
61 MAP2K2 MAP2K2 MAP2K2 8684 0.01 0.3 NO
62 CBL CBL CBL 8888 0.0062 0.29 NO
63 VAV3 VAV3 VAV3 9185 0.00062 0.27 NO
64 NFATC3 NFATC3 NFATC3 9334 -0.0024 0.26 NO
65 GRB2 GRB2 GRB2 9337 -0.0024 0.26 NO
66 PIK3CB PIK3CB PIK3CB 9642 -0.008 0.25 NO
67 MAP2K7 MAP2K7 MAP2K7 9651 -0.0081 0.25 NO
68 PIK3CA PIK3CA PIK3CA 10272 -0.021 0.21 NO
69 IKBKB IKBKB IKBKB 10781 -0.031 0.18 NO
70 AKT1 AKT1 AKT1 10801 -0.032 0.19 NO
71 NFKBIE NFKBIE NFKBIE 10819 -0.032 0.19 NO
72 CHP CHP CHP 10882 -0.033 0.18 NO
73 MALT1 MALT1 MALT1 11175 -0.04 0.17 NO
74 SOS2 SOS2 SOS2 11278 -0.042 0.17 NO
75 PIK3R2 PIK3R2 PIK3R2 11352 -0.044 0.16 NO
76 MAPK3 MAPK3 MAPK3 11383 -0.044 0.16 NO
77 IKBKG IKBKG IKBKG 11553 -0.049 0.16 NO
78 AKT2 AKT2 AKT2 12000 -0.06 0.13 NO
79 PAK2 PAK2 PAK2 12072 -0.063 0.13 NO
80 CDK4 CDK4 CDK4 12218 -0.067 0.13 NO
81 TEC TEC TEC 12368 -0.071 0.12 NO
82 GSK3B GSK3B GSK3B 12373 -0.072 0.13 NO
83 RHOA RHOA RHOA 12386 -0.072 0.13 NO
84 NFKBIB NFKBIB NFKBIB 12425 -0.073 0.13 NO
85 PAK1 PAK1 PAK1 12465 -0.074 0.13 NO
86 RELA RELA RELA 12507 -0.076 0.14 NO
87 DLG1 DLG1 DLG1 12575 -0.078 0.14 NO
88 PAK4 PAK4 PAK4 12649 -0.08 0.13 NO
89 NCK2 NCK2 NCK2 12770 -0.083 0.13 NO
90 PIK3CD PIK3CD PIK3CD 13042 -0.093 0.12 NO
91 AKT3 AKT3 AKT3 13073 -0.094 0.12 NO
92 JUN JUN JUN 13634 -0.12 0.097 NO
93 NFATC1 NFATC1 NFATC1 14080 -0.14 0.079 NO
94 CBLB CBLB CBLB 14836 -0.18 0.044 NO
95 FYN FYN FYN 14885 -0.19 0.051 NO
96 RAF1 RAF1 RAF1 15355 -0.22 0.035 NO
97 CHP2 CHP2 CHP2 15647 -0.25 0.031 NO
98 PAK7 PAK7 PAK7 15791 -0.27 0.037 NO
99 PRKCQ PRKCQ PRKCQ 15938 -0.29 0.043 NO
100 MAPK13 MAPK13 MAPK13 16047 -0.31 0.052 NO
101 PAK3 PAK3 PAK3 16691 -0.44 0.038 NO

Figure S7.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S8.  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: KEGG PROTEASOME

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 NFATC4 NFATC4 NFATC4 658 0.41 0.048 YES
2 NFATC2 NFATC2 NFATC2 851 0.37 0.12 YES
3 SYK SYK SYK 896 0.36 0.19 YES
4 CD79B CD79B CD79B 1184 0.32 0.24 YES
5 LYN LYN LYN 1338 0.3 0.29 YES
6 PRKCA PRKCA PRKCA 1395 0.3 0.35 YES
7 BLNK BLNK BLNK 1756 0.26 0.39 YES
8 VAV1 VAV1 VAV1 1809 0.25 0.44 YES
9 PPP3CA PPP3CA PPP3CA 2146 0.22 0.46 YES
10 FOS FOS FOS 2448 0.2 0.49 YES
11 PPP3CC PPP3CC PPP3CC 3248 0.16 0.48 YES
12 BTK BTK BTK 3456 0.14 0.5 YES
13 SOS1 SOS1 SOS1 3647 0.14 0.51 YES
14 SHC1 SHC1 SHC1 3784 0.13 0.53 YES
15 CALM2 CALM2 CALM2 4381 0.11 0.52 NO
16 CALM1 CALM1 CALM1 4950 0.092 0.51 NO
17 CD79A CD79A CD79A 5492 0.078 0.49 NO
18 MAP2K1 MAP2K1 MAP2K1 6597 0.052 0.44 NO
19 PLCG1 PLCG1 PLCG1 6969 0.044 0.43 NO
20 PPP3CB PPP3CB PPP3CB 7244 0.039 0.42 NO
21 MAPK14 MAPK14 MAPK14 7906 0.026 0.39 NO
22 MAPK8 MAPK8 MAPK8 8961 0.0046 0.33 NO
23 NFATC3 NFATC3 NFATC3 9334 -0.0024 0.31 NO
24 GRB2 GRB2 GRB2 9337 -0.0024 0.31 NO
25 MAP3K1 MAP3K1 MAP3K1 9845 -0.012 0.28 NO
26 RAC1 RAC1 RAC1 10017 -0.016 0.28 NO
27 CALM3 CALM3 CALM3 11298 -0.043 0.21 NO
28 ELK1 ELK1 ELK1 11340 -0.044 0.22 NO
29 MAPK3 MAPK3 MAPK3 11383 -0.044 0.22 NO
30 PRKCB PRKCB PRKCB 13013 -0.093 0.15 NO
31 JUN JUN JUN 13634 -0.12 0.14 NO
32 NFATC1 NFATC1 NFATC1 14080 -0.14 0.14 NO
33 RAF1 RAF1 RAF1 15355 -0.22 0.12 NO

Figure S9.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PROTEASOME.

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

genes ES table in pathway: KEGG HOMOLOGOUS RECOMBINATION

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 CCNE2 CCNE2 CCNE2 192 0.55 0.024 YES
2 GADD45G GADD45G GADD45G 233 0.53 0.055 YES
3 PTTG2 PTTG2 PTTG2 336 0.49 0.079 YES
4 CDC25C CDC25C CDC25C 495 0.44 0.098 YES
5 E2F2 E2F2 E2F2 700 0.4 0.11 YES
6 CDC6 CDC6 CDC6 748 0.39 0.13 YES
7 ORC6L ORC6L ORC6L 888 0.36 0.15 YES
8 E2F5 E2F5 E2F5 889 0.36 0.17 YES
9 CCNB2 CCNB2 CCNB2 936 0.35 0.19 YES
10 BUB1 BUB1 BUB1 1009 0.34 0.21 YES
11 CDC25B CDC25B CDC25B 1095 0.33 0.22 YES
12 SFN SFN SFN 1144 0.33 0.24 YES
13 CDK1 CDK1 CDK1 1238 0.31 0.25 YES
14 BUB1B BUB1B BUB1B 1267 0.31 0.27 YES
15 CDC45 CDC45 CDC45 1430 0.29 0.28 YES
16 CCNA2 CCNA2 CCNA2 1564 0.28 0.29 YES
17 TTK TTK TTK 1682 0.26 0.3 YES
18 ATM ATM ATM 1719 0.26 0.31 YES
19 PRKDC PRKDC PRKDC 1889 0.24 0.32 YES
20 CHEK2 CHEK2 CHEK2 2039 0.23 0.33 YES
21 MCM4 MCM4 MCM4 2040 0.23 0.34 YES
22 PLK1 PLK1 PLK1 2050 0.23 0.35 YES
23 CDKN1A CDKN1A CDKN1A 2120 0.22 0.36 YES
24 CDC7 CDC7 CDC7 2209 0.22 0.37 YES
25 CCNA1 CCNA1 CCNA1 2266 0.22 0.38 YES
26 ESPL1 ESPL1 ESPL1 2353 0.21 0.39 YES
27 CDC27 CDC27 CDC27 2582 0.19 0.39 YES
28 MDM2 MDM2 MDM2 2733 0.18 0.39 YES
29 CCND2 CCND2 CCND2 2746 0.18 0.4 YES
30 RBL1 RBL1 RBL1 2856 0.18 0.41 YES
31 CCNH CCNH CCNH 3094 0.16 0.4 YES
32 WEE1 WEE1 WEE1 3221 0.16 0.41 YES
33 ORC1L ORC1L ORC1L 3241 0.16 0.42 YES
34 MAD1L1 MAD1L1 MAD1L1 3263 0.15 0.42 YES
35 ANAPC4 ANAPC4 ANAPC4 3323 0.15 0.43 YES
36 PKMYT1 PKMYT1 PKMYT1 3336 0.15 0.44 YES
37 RAD21 RAD21 RAD21 3399 0.15 0.44 YES
38 MCM6 MCM6 MCM6 3428 0.14 0.45 YES
39 CDC20 CDC20 CDC20 3594 0.14 0.45 YES
40 PTTG1 PTTG1 PTTG1 3670 0.14 0.46 YES
41 ANAPC10 ANAPC10 ANAPC10 3676 0.14 0.46 YES
42 CCNB1 CCNB1 CCNB1 3787 0.13 0.46 YES
43 PCNA PCNA PCNA 3849 0.13 0.47 YES
44 CUL1 CUL1 CUL1 3928 0.13 0.47 YES
45 YWHAZ YWHAZ YWHAZ 3993 0.12 0.48 YES
46 CDKN2C CDKN2C CDKN2C 4048 0.12 0.48 YES
47 ORC5L ORC5L ORC5L 4421 0.11 0.47 NO
48 TGFB3 TGFB3 TGFB3 4756 0.098 0.45 NO
49 RBX1 RBX1 RBX1 4862 0.095 0.45 NO
50 ORC2L ORC2L ORC2L 4961 0.092 0.45 NO
51 CCNE1 CCNE1 CCNE1 5159 0.086 0.45 NO
52 MAD2L1 MAD2L1 MAD2L1 5356 0.081 0.44 NO
53 CDK6 CDK6 CDK6 5573 0.076 0.43 NO
54 TGFB1 TGFB1 TGFB1 5687 0.072 0.43 NO
55 SMC1B SMC1B SMC1B 5823 0.069 0.43 NO
56 STAG2 STAG2 STAG2 5891 0.068 0.43 NO
57 ANAPC7 ANAPC7 ANAPC7 6167 0.061 0.42 NO
58 CDC23 CDC23 CDC23 6353 0.058 0.41 NO
59 YWHAH YWHAH YWHAH 6427 0.056 0.41 NO
60 YWHAQ YWHAQ YWHAQ 6492 0.054 0.41 NO
61 CDK7 CDK7 CDK7 6669 0.05 0.4 NO
62 BUB3 BUB3 BUB3 6713 0.049 0.4 NO
63 TFDP1 TFDP1 TFDP1 6767 0.048 0.4 NO
64 HDAC1 HDAC1 HDAC1 6779 0.048 0.4 NO
65 GADD45B GADD45B GADD45B 6785 0.048 0.41 NO
66 YWHAB YWHAB YWHAB 6833 0.047 0.41 NO
67 CDC14A CDC14A CDC14A 6916 0.046 0.4 NO
68 ORC3L ORC3L ORC3L 6922 0.045 0.41 NO
69 CDKN1B CDKN1B CDKN1B 6947 0.045 0.41 NO
70 CDKN2A CDKN2A CDKN2A 7385 0.036 0.39 NO
71 YWHAG YWHAG YWHAG 7634 0.031 0.37 NO
72 RB1 RB1 RB1 7658 0.03 0.37 NO
73 GADD45A GADD45A GADD45A 7709 0.03 0.37 NO
74 CDC26 CDC26 CDC26 7836 0.027 0.37 NO
75 ABL1 ABL1 ABL1 7839 0.027 0.37 NO
76 ANAPC1 ANAPC1 ANAPC1 7876 0.026 0.37 NO
77 EP300 EP300 EP300 8144 0.021 0.35 NO
78 CCND1 CCND1 CCND1 8162 0.02 0.35 NO
79 SMAD4 SMAD4 SMAD4 8177 0.02 0.36 NO
80 TGFB2 TGFB2 TGFB2 8187 0.02 0.36 NO
81 SKP2 SKP2 SKP2 8272 0.018 0.35 NO
82 CDC16 CDC16 CDC16 8282 0.018 0.35 NO
83 ANAPC11 ANAPC11 ANAPC11 8346 0.017 0.35 NO
84 ORC4L ORC4L ORC4L 8476 0.014 0.34 NO
85 SKP1 SKP1 SKP1 8484 0.014 0.34 NO
86 SMC1A SMC1A SMC1A 8608 0.012 0.34 NO
87 E2F1 E2F1 E2F1 8617 0.012 0.34 NO
88 YWHAE YWHAE YWHAE 8630 0.012 0.34 NO
89 SMAD3 SMAD3 SMAD3 8653 0.011 0.34 NO
90 CDC14B CDC14B CDC14B 8662 0.011 0.34 NO
91 CDKN2B CDKN2B CDKN2B 8845 0.0072 0.33 NO
92 SMC3 SMC3 SMC3 9018 0.0037 0.32 NO
93 ANAPC5 ANAPC5 ANAPC5 9203 0.00029 0.31 NO
94 TP53 TP53 TP53 9313 -0.002 0.3 NO
95 CHEK1 CHEK1 CHEK1 9378 -0.0031 0.3 NO
96 MCM3 MCM3 MCM3 9570 -0.0068 0.29 NO
97 CREBBP CREBBP CREBBP 9702 -0.0095 0.28 NO
98 SMAD2 SMAD2 SMAD2 10370 -0.023 0.24 NO
99 RBL2 RBL2 RBL2 10459 -0.024 0.24 NO
100 ZBTB17 ZBTB17 ZBTB17 10666 -0.029 0.23 NO
101 MCM7 MCM7 MCM7 10727 -0.03 0.23 NO
102 HDAC2 HDAC2 HDAC2 11034 -0.037 0.21 NO
103 CDKN2D CDKN2D CDKN2D 11069 -0.038 0.21 NO
104 STAG1 STAG1 STAG1 11202 -0.041 0.21 NO
105 CDKN1C CDKN1C CDKN1C 11496 -0.047 0.19 NO
106 MYC MYC MYC 11677 -0.052 0.18 NO
107 ANAPC2 ANAPC2 ANAPC2 11851 -0.057 0.18 NO
108 MAD2L2 MAD2L2 MAD2L2 12002 -0.061 0.17 NO
109 E2F4 E2F4 E2F4 12154 -0.066 0.17 NO
110 FZR1 FZR1 FZR1 12210 -0.067 0.17 NO
111 CDK4 CDK4 CDK4 12218 -0.067 0.17 NO
112 GSK3B GSK3B GSK3B 12373 -0.072 0.17 NO
113 E2F3 E2F3 E2F3 12618 -0.079 0.16 NO
114 CCNB3 CCNB3 CCNB3 12654 -0.08 0.16 NO
115 ATR ATR ATR 12787 -0.084 0.16 NO
116 MCM5 MCM5 MCM5 12890 -0.088 0.16 NO
117 CCND3 CCND3 CCND3 13312 -0.1 0.14 NO
118 ANAPC13 ANAPC13 ANAPC13 14509 -0.16 0.083 NO
119 WEE2 WEE2 WEE2 15343 -0.22 0.049 NO
120 MCM2 MCM2 MCM2 15366 -0.22 0.061 NO
121 CDK2 CDK2 CDK2 15400 -0.23 0.074 NO
122 TFDP2 TFDP2 TFDP2 15667 -0.26 0.074 NO
123 CDC25A CDC25A CDC25A 16427 -0.37 0.053 NO

Figure S11.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HOMOLOGOUS RECOMBINATION.

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

genes ES table in pathway: KEGG CELL CYCLE

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 CD3D CD3D CD3D 245 0.53 0.055 YES
2 CD3G CD3G CD3G 396 0.47 0.11 YES
3 LCK LCK LCK 424 0.46 0.17 YES
4 ZAP70 ZAP70 ZAP70 551 0.43 0.22 YES
5 CD247 CD247 CD247 592 0.42 0.27 YES
6 PTPN7 PTPN7 PTPN7 623 0.41 0.32 YES
7 CD3E CD3E CD3E 656 0.41 0.37 YES
8 NFATC4 NFATC4 NFATC4 658 0.41 0.43 YES
9 NFATC2 NFATC2 NFATC2 851 0.37 0.46 YES
10 PIK3CG PIK3CG PIK3CG 972 0.35 0.5 YES
11 LAT LAT LAT 1089 0.33 0.54 YES
12 PRKCA PRKCA PRKCA 1395 0.3 0.56 YES
13 VAV1 VAV1 VAV1 1809 0.25 0.57 YES
14 PPP3CA PPP3CA PPP3CA 2146 0.22 0.58 YES
15 FOS FOS FOS 2448 0.2 0.59 YES
16 PPP3CC PPP3CC PPP3CC 3248 0.16 0.56 NO
17 SOS1 SOS1 SOS1 3647 0.14 0.56 NO
18 SHC1 SHC1 SHC1 3784 0.13 0.57 NO
19 CALM2 CALM2 CALM2 4381 0.11 0.55 NO
20 CALM1 CALM1 CALM1 4950 0.092 0.53 NO
21 NFKB1 NFKB1 NFKB1 5570 0.076 0.5 NO
22 MAP2K4 MAP2K4 MAP2K4 6522 0.054 0.45 NO
23 MAP2K1 MAP2K1 MAP2K1 6597 0.052 0.46 NO
24 NFKBIA NFKBIA NFKBIA 6687 0.05 0.46 NO
25 RASA1 RASA1 RASA1 6718 0.049 0.46 NO
26 PLCG1 PLCG1 PLCG1 6969 0.044 0.45 NO
27 PIK3R1 PIK3R1 PIK3R1 7053 0.042 0.46 NO
28 PPP3CB PPP3CB PPP3CB 7244 0.039 0.45 NO
29 MAPK8 MAPK8 MAPK8 8961 0.0046 0.35 NO
30 NFATC3 NFATC3 NFATC3 9334 -0.0024 0.33 NO
31 GRB2 GRB2 GRB2 9337 -0.0024 0.33 NO
32 MAP3K1 MAP3K1 MAP3K1 9845 -0.012 0.3 NO
33 RAC1 RAC1 RAC1 10017 -0.016 0.29 NO
34 PIK3CA PIK3CA PIK3CA 10272 -0.021 0.28 NO
35 CALM3 CALM3 CALM3 11298 -0.043 0.23 NO
36 ELK1 ELK1 ELK1 11340 -0.044 0.23 NO
37 MAPK3 MAPK3 MAPK3 11383 -0.044 0.24 NO
38 RELA RELA RELA 12507 -0.076 0.18 NO
39 PRKCB PRKCB PRKCB 13013 -0.093 0.16 NO
40 JUN JUN JUN 13634 -0.12 0.14 NO
41 NFATC1 NFATC1 NFATC1 14080 -0.14 0.14 NO
42 FYN FYN FYN 14885 -0.19 0.11 NO
43 RAF1 RAF1 RAF1 15355 -0.22 0.12 NO

Figure S13.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CELL CYCLE.

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

genes ES table in pathway: KEGG OOCYTE MEIOSIS

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 FASLG FASLG FASLG 321 0.5 0.079 YES
2 IL2RG IL2RG IL2RG 581 0.42 0.15 YES
3 SYK SYK SYK 896 0.36 0.2 YES
4 IKZF3 IKZF3 IKZF3 906 0.36 0.27 YES
5 IL2RB IL2RB IL2RB 914 0.36 0.34 YES
6 PIK3CG PIK3CG PIK3CG 972 0.35 0.4 YES
7 PTPN6 PTPN6 PTPN6 1262 0.31 0.45 YES
8 IL2RA IL2RA IL2RA 1478 0.29 0.49 YES
9 FAS FAS FAS 1757 0.26 0.53 YES
10 FOS FOS FOS 2448 0.2 0.53 YES
11 SOCS3 SOCS3 SOCS3 2513 0.2 0.56 YES
12 SOS1 SOS1 SOS1 3647 0.14 0.52 NO
13 SHC1 SHC1 SHC1 3784 0.13 0.54 NO
14 CFLAR CFLAR CFLAR 3902 0.13 0.56 NO
15 MAPK1 MAPK1 MAPK1 5232 0.085 0.5 NO
16 RPS6KB1 RPS6KB1 RPS6KB1 6282 0.059 0.45 NO
17 PIK3R1 PIK3R1 PIK3R1 7053 0.042 0.42 NO
18 NMI NMI NMI 7105 0.042 0.42 NO
19 BAD BAD BAD 7744 0.029 0.39 NO
20 PPIA PPIA PPIA 8016 0.024 0.38 NO
21 BCL2L1 BCL2L1 BCL2L1 8366 0.016 0.36 NO
22 CBL CBL CBL 8888 0.0062 0.33 NO
23 BCL2 BCL2 BCL2 9158 0.0012 0.32 NO
24 GRB2 GRB2 GRB2 9337 -0.0024 0.31 NO
25 JAK1 JAK1 JAK1 9428 -0.004 0.3 NO
26 STAT5B STAT5B STAT5B 9806 -0.011 0.28 NO
27 SOCS1 SOCS1 SOCS1 10267 -0.021 0.26 NO
28 PIK3CA PIK3CA PIK3CA 10272 -0.021 0.27 NO
29 HRAS HRAS HRAS 10606 -0.028 0.25 NO
30 AKT1 AKT1 AKT1 10801 -0.032 0.25 NO
31 CRKL CRKL CRKL 11178 -0.04 0.23 NO
32 MAPK3 MAPK3 MAPK3 11383 -0.044 0.23 NO
33 MYC MYC MYC 11677 -0.052 0.22 NO
34 STAT5A STAT5A STAT5A 12903 -0.089 0.17 NO
35 IRS1 IRS1 IRS1 13224 -0.1 0.17 NO
36 JAK3 JAK3 JAK3 13593 -0.12 0.17 NO
37 RAF1 RAF1 RAF1 15355 -0.22 0.12 NO

Figure S15.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OOCYTE MEIOSIS.

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

genes ES table in pathway: KEGG P53 SIGNALING 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 IL3RA IL3RA IL3RA 37 0.72 0.037 YES
2 ANPEP ANPEP ANPEP 116 0.61 0.065 YES
3 ITGB3 ITGB3 ITGB3 168 0.57 0.093 YES
4 CSF2RA CSF2RA CSF2RA 177 0.57 0.12 YES
5 IL1R2 IL1R2 IL1R2 212 0.54 0.15 YES
6 CD3D CD3D CD3D 245 0.53 0.18 YES
7 CD7 CD7 CD7 300 0.51 0.2 YES
8 CD38 CD38 CD38 352 0.49 0.22 YES
9 CD8B CD8B CD8B 359 0.48 0.25 YES
10 CD8A CD8A CD8A 389 0.47 0.27 YES
11 CD3G CD3G CD3G 396 0.47 0.3 YES
12 CD2 CD2 CD2 412 0.47 0.32 YES
13 ITGA4 ITGA4 ITGA4 438 0.46 0.35 YES
14 TNF TNF TNF 463 0.45 0.37 YES
15 ITGA6 ITGA6 ITGA6 641 0.41 0.38 YES
16 CD3E CD3E CD3E 656 0.41 0.4 YES
17 ITGA2 ITGA2 ITGA2 695 0.4 0.42 YES
18 KIT KIT KIT 714 0.4 0.44 YES
19 IL11 IL11 IL11 922 0.36 0.45 YES
20 CD5 CD5 CD5 952 0.35 0.46 YES
21 FCER2 FCER2 FCER2 978 0.35 0.48 YES
22 ITGA5 ITGA5 ITGA5 994 0.34 0.5 YES
23 FCGR1A FCGR1A FCGR1A 1005 0.34 0.52 YES
24 IL1B IL1B IL1B 1051 0.34 0.53 YES
25 IL7 IL7 IL7 1139 0.33 0.55 YES
26 HLA-DRB1 HLA-DRB1 HLA-DRB1 1290 0.31 0.55 YES
27 ITGA1 ITGA1 ITGA1 1370 0.3 0.56 YES
28 ITGA2B ITGA2B ITGA2B 1405 0.3 0.58 YES
29 THPO THPO THPO 1431 0.29 0.59 YES
30 HLA-DRB5 HLA-DRB5 HLA-DRB5 1439 0.29 0.61 YES
31 IL6 IL6 IL6 1453 0.29 0.62 YES
32 IL2RA IL2RA IL2RA 1478 0.29 0.64 YES
33 HLA-DRA HLA-DRA HLA-DRA 1504 0.28 0.65 YES
34 IL7R IL7R IL7R 1546 0.28 0.66 YES
35 FLT3 FLT3 FLT3 1718 0.26 0.67 YES
36 CD9 CD9 CD9 2053 0.23 0.66 YES
37 KITLG KITLG KITLG 2082 0.23 0.67 YES
38 IL1R1 IL1R1 IL1R1 2113 0.23 0.68 YES
39 MS4A1 MS4A1 MS4A1 2190 0.22 0.69 YES
40 CD36 CD36 CD36 2442 0.2 0.68 YES
41 CD1D CD1D CD1D 2495 0.2 0.69 YES
42 TFRC TFRC TFRC 2918 0.17 0.68 NO
43 CD1E CD1E CD1E 3443 0.14 0.66 NO
44 CSF3R CSF3R CSF3R 3699 0.14 0.65 NO
45 IL6R IL6R IL6R 3774 0.13 0.65 NO
46 CD33 CD33 CD33 3815 0.13 0.66 NO
47 CD14 CD14 CD14 4124 0.12 0.64 NO
48 CSF1 CSF1 CSF1 4284 0.11 0.64 NO
49 CD37 CD37 CD37 4441 0.11 0.64 NO
50 CR1 CR1 CR1 4687 0.1 0.63 NO
51 CD19 CD19 CD19 4914 0.094 0.62 NO
52 CD55 CD55 CD55 5007 0.091 0.62 NO
53 CD1C CD1C CD1C 6131 0.062 0.56 NO
54 CSF1R CSF1R CSF1R 6207 0.061 0.56 NO
55 GP5 GP5 GP5 6397 0.057 0.55 NO
56 CD34 CD34 CD34 6599 0.052 0.54 NO
57 IL4R IL4R IL4R 6746 0.049 0.54 NO
58 CD4 CD4 CD4 7138 0.041 0.51 NO
59 GP1BA GP1BA GP1BA 7885 0.026 0.47 NO
60 IL5RA IL5RA IL5RA 9078 0.0027 0.4 NO
61 ITGA3 ITGA3 ITGA3 10741 -0.03 0.31 NO
62 EPO EPO EPO 10869 -0.033 0.3 NO
63 CD44 CD44 CD44 11139 -0.039 0.29 NO
64 CD59 CD59 CD59 11294 -0.043 0.28 NO
65 EPOR EPOR EPOR 13454 -0.11 0.16 NO
66 ITGAM ITGAM ITGAM 14009 -0.13 0.14 NO
67 CD22 CD22 CD22 14375 -0.15 0.13 NO
68 IL11RA IL11RA IL11RA 15473 -0.23 0.076 NO
69 FLT3LG FLT3LG FLT3LG 15546 -0.24 0.084 NO
70 MME MME MME 16408 -0.37 0.054 NO

Figure S17.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG P53 SIGNALING PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG P53 SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION

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 ULBP1 ULBP1 ULBP1 5 0.95 0.04 YES
2 GZMB GZMB GZMB 108 0.62 0.06 YES
3 SH2D1A SH2D1A SH2D1A 303 0.51 0.07 YES
4 IFNG IFNG IFNG 316 0.5 0.09 YES
5 FASLG FASLG FASLG 321 0.5 0.11 YES
6 CD48 CD48 CD48 366 0.48 0.13 YES
7 PRF1 PRF1 PRF1 377 0.48 0.15 YES
8 LCK LCK LCK 424 0.46 0.16 YES
9 FCGR3A FCGR3A FCGR3A 457 0.45 0.18 YES
10 TNF TNF TNF 463 0.45 0.2 YES
11 ZAP70 ZAP70 ZAP70 551 0.43 0.21 YES
12 RAC2 RAC2 RAC2 565 0.42 0.23 YES
13 LCP2 LCP2 LCP2 572 0.42 0.25 YES
14 CD247 CD247 CD247 592 0.42 0.26 YES
15 NFATC4 NFATC4 NFATC4 658 0.41 0.28 YES
16 ULBP2 ULBP2 ULBP2 672 0.4 0.29 YES
17 ITGAL ITGAL ITGAL 678 0.4 0.31 YES
18 KIR2DL4 KIR2DL4 KIR2DL4 731 0.39 0.32 YES
19 KLRK1 KLRK1 KLRK1 768 0.39 0.34 YES
20 NFATC2 NFATC2 NFATC2 851 0.37 0.35 YES
21 TNFRSF10C TNFRSF10C TNFRSF10C 857 0.37 0.36 YES
22 KIR2DL3 KIR2DL3 KIR2DL3 860 0.36 0.38 YES
23 SYK SYK SYK 896 0.36 0.39 YES
24 HLA-B HLA-B HLA-B 909 0.36 0.4 YES
25 PIK3CG PIK3CG PIK3CG 972 0.35 0.42 YES
26 LAT LAT LAT 1089 0.33 0.42 YES
27 KLRC3 KLRC3 KLRC3 1160 0.32 0.43 YES
28 PTPN6 PTPN6 PTPN6 1262 0.31 0.44 YES
29 PRKCA PRKCA PRKCA 1395 0.3 0.44 YES
30 KLRC1 KLRC1 KLRC1 1425 0.29 0.46 YES
31 NCR3 NCR3 NCR3 1498 0.28 0.46 YES
32 KLRC2 KLRC2 KLRC2 1592 0.27 0.47 YES
33 FCGR3B FCGR3B FCGR3B 1685 0.26 0.48 YES
34 PIK3R3 PIK3R3 PIK3R3 1735 0.26 0.48 YES
35 FAS FAS FAS 1757 0.26 0.49 YES
36 KLRD1 KLRD1 KLRD1 1774 0.26 0.5 YES
37 VAV1 VAV1 VAV1 1809 0.25 0.51 YES
38 IFNAR2 IFNAR2 IFNAR2 1820 0.25 0.52 YES
39 KIR2DS4 KIR2DS4 KIR2DS4 1833 0.25 0.53 YES
40 KIR3DL1 KIR3DL1 KIR3DL1 1950 0.24 0.53 YES
41 PIK3R5 PIK3R5 PIK3R5 2056 0.23 0.54 YES
42 HLA-C HLA-C HLA-C 2087 0.23 0.55 YES
43 VAV2 VAV2 VAV2 2135 0.22 0.55 YES
44 PPP3CA PPP3CA PPP3CA 2146 0.22 0.56 YES
45 FCER1G FCER1G FCER1G 2188 0.22 0.57 YES
46 TNFRSF10A TNFRSF10A TNFRSF10A 2269 0.22 0.57 YES
47 TNFSF10 TNFSF10 TNFSF10 2304 0.21 0.58 YES
48 TYROBP TYROBP TYROBP 2472 0.2 0.58 YES
49 HLA-E HLA-E HLA-E 2633 0.19 0.58 YES
50 KIR3DL2 KIR3DL2 KIR3DL2 2665 0.19 0.58 YES
51 IFNGR1 IFNGR1 IFNGR1 2904 0.17 0.58 YES
52 SH2D1B SH2D1B SH2D1B 2942 0.17 0.58 YES
53 ULBP3 ULBP3 ULBP3 3209 0.16 0.57 YES
54 HLA-A HLA-A HLA-A 3223 0.16 0.58 YES
55 PPP3CC PPP3CC PPP3CC 3248 0.16 0.58 YES
56 CASP3 CASP3 CASP3 3388 0.15 0.58 YES
57 KIR2DL1 KIR2DL1 KIR2DL1 3393 0.15 0.59 YES
58 TNFRSF10D TNFRSF10D TNFRSF10D 3398 0.15 0.59 YES
59 PLCG2 PLCG2 PLCG2 3497 0.14 0.59 YES
60 ITGB2 ITGB2 ITGB2 3615 0.14 0.59 YES
61 HLA-G HLA-G HLA-G 3640 0.14 0.6 YES
62 SOS1 SOS1 SOS1 3647 0.14 0.6 YES
63 SHC1 SHC1 SHC1 3784 0.13 0.6 NO
64 NFAT5 NFAT5 NFAT5 3985 0.12 0.59 NO
65 HCST HCST HCST 4005 0.12 0.6 NO
66 IFNAR1 IFNAR1 IFNAR1 4497 0.11 0.57 NO
67 ICAM1 ICAM1 ICAM1 4641 0.1 0.57 NO
68 KRAS KRAS KRAS 5083 0.089 0.55 NO
69 SH3BP2 SH3BP2 SH3BP2 5181 0.086 0.55 NO
70 RAET1E RAET1E RAET1E 5228 0.085 0.55 NO
71 MAPK1 MAPK1 MAPK1 5232 0.085 0.55 NO
72 SHC3 SHC3 SHC3 5299 0.083 0.55 NO
73 PTPN11 PTPN11 PTPN11 5306 0.083 0.55 NO
74 ICAM2 ICAM2 ICAM2 5507 0.077 0.54 NO
75 CD244 CD244 CD244 5801 0.07 0.53 NO
76 BID BID BID 6452 0.055 0.49 NO
77 MAP2K1 MAP2K1 MAP2K1 6597 0.052 0.49 NO
78 RAC3 RAC3 RAC3 6609 0.052 0.49 NO
79 NRAS NRAS NRAS 6926 0.045 0.47 NO
80 PLCG1 PLCG1 PLCG1 6969 0.044 0.47 NO
81 PIK3R1 PIK3R1 PIK3R1 7053 0.042 0.47 NO
82 PPP3CB PPP3CB PPP3CB 7244 0.039 0.46 NO
83 PPP3R1 PPP3R1 PPP3R1 7452 0.034 0.45 NO
84 MAP2K2 MAP2K2 MAP2K2 8684 0.01 0.38 NO
85 ARAF ARAF ARAF 8716 0.0096 0.38 NO
86 VAV3 VAV3 VAV3 9185 0.00062 0.35 NO
87 NFATC3 NFATC3 NFATC3 9334 -0.0024 0.34 NO
88 GRB2 GRB2 GRB2 9337 -0.0024 0.34 NO
89 NCR1 NCR1 NCR1 9341 -0.0026 0.34 NO
90 BRAF BRAF BRAF 9436 -0.0042 0.34 NO
91 PIK3CB PIK3CB PIK3CB 9642 -0.008 0.32 NO
92 RAC1 RAC1 RAC1 10017 -0.016 0.3 NO
93 IFNGR2 IFNGR2 IFNGR2 10041 -0.016 0.3 NO
94 PIK3CA PIK3CA PIK3CA 10272 -0.021 0.29 NO
95 SHC2 SHC2 SHC2 10470 -0.025 0.28 NO
96 HRAS HRAS HRAS 10606 -0.028 0.27 NO
97 CHP CHP CHP 10882 -0.033 0.26 NO
98 SOS2 SOS2 SOS2 11278 -0.042 0.24 NO
99 PIK3R2 PIK3R2 PIK3R2 11352 -0.044 0.24 NO
100 MAPK3 MAPK3 MAPK3 11383 -0.044 0.24 NO
101 TNFRSF10B TNFRSF10B TNFRSF10B 11884 -0.057 0.21 NO
102 PAK1 PAK1 PAK1 12465 -0.074 0.18 NO
103 PRKCB PRKCB PRKCB 13013 -0.093 0.15 NO
104 PIK3CD PIK3CD PIK3CD 13042 -0.093 0.15 NO
105 PRKCG PRKCG PRKCG 13544 -0.11 0.13 NO
106 PTK2B PTK2B PTK2B 14011 -0.13 0.11 NO
107 NFATC1 NFATC1 NFATC1 14080 -0.14 0.11 NO
108 FYN FYN FYN 14885 -0.19 0.07 NO
109 MICA MICA MICA 15082 -0.2 0.067 NO
110 RAF1 RAF1 RAF1 15355 -0.22 0.06 NO
111 CHP2 CHP2 CHP2 15647 -0.25 0.054 NO
112 RAET1G RAET1G RAET1G 16402 -0.37 0.026 NO
113 SHC4 SHC4 SHC4 17148 -0.7 0.012 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: KEGG ANTIGEN PROCESSING AND PRESENTATION.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION, 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
BIOCARTA ALK PATHWAY 32 genes.ES.table 0.55 1.6 0.037 0.13 0.63 0.31 0.18 0.26 0.066 0.011
BIOCARTA BIOPEPTIDES PATHWAY 38 genes.ES.table 0.46 1.6 0.024 0.14 0.63 0.34 0.29 0.24 0.068 0.011
BIOCARTA ERK PATHWAY 27 genes.ES.table 0.66 2.1 0 0.057 0.014 0.18 0.066 0.17 0 0.014
BIOCARTA FMLP PATHWAY 34 genes.ES.table 0.55 1.6 0.046 0.12 0.54 0.26 0.16 0.22 0.045 0.009
BIOCARTA EDG1 PATHWAY 26 genes.ES.table 0.57 1.5 0.055 0.17 0.76 0.35 0.2 0.28 0.1 0.014
BIOCARTA MYOSIN PATHWAY 28 genes.ES.table 0.52 1.6 0.027 0.13 0.6 0.25 0.16 0.21 0.065 0.01
BIOCARTA CHREBP2 PATHWAY 40 genes.ES.table 0.4 1.5 0.07 0.17 0.81 0.12 0.096 0.11 0.11 0.013
KEGG GLYCOLYSIS GLUCONEOGENESIS 54 genes.ES.table 0.44 1.5 0.033 0.17 0.78 0.59 0.38 0.37 0.1 0.015
KEGG STEROID HORMONE BIOSYNTHESIS 27 genes.ES.table 0.55 1.4 0.041 0.21 0.89 0.37 0.13 0.32 0.15 0.015
KEGG PURINE METABOLISM 150 genes.ES.table 0.37 1.5 0.02 0.17 0.8 0.2 0.19 0.16 0.11 0.013
genes ES table in pathway: BIOCARTA ALK PATHWAY

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 NGFR NGFR NGFR 24 1.1 0.24 YES
2 GNGT1 GNGT1 GNGT1 181 0.79 0.41 YES
3 PDGFRA PDGFRA PDGFRA 670 0.53 0.5 YES
4 NGF NGF NGF 987 0.43 0.58 YES
5 EGFR EGFR EGFR 1150 0.39 0.66 YES
6 MAPK3 MAPK3 MAPK3 4278 0.1 0.5 NO
7 SHC1 SHC1 SHC1 4812 0.088 0.49 NO
8 PTPRR PTPRR PTPRR 5870 0.063 0.44 NO
9 GNB1 GNB1 GNB1 6207 0.056 0.44 NO
10 MAP2K2 MAP2K2 MAP2K2 6504 0.05 0.43 NO
11 RPS6KA1 RPS6KA1 RPS6KA1 6520 0.05 0.44 NO
12 SRC SRC SRC 7184 0.038 0.41 NO
13 GNAS GNAS GNAS 8149 0.021 0.36 NO
14 STAT3 STAT3 STAT3 8169 0.02 0.36 NO
15 MKNK2 MKNK2 MKNK2 8421 0.016 0.35 NO
16 GRB2 GRB2 GRB2 9277 0.0032 0.3 NO
17 ELK1 ELK1 ELK1 9538 -0.0014 0.29 NO
18 MAPK1 MAPK1 MAPK1 9982 -0.009 0.26 NO
19 SOS1 SOS1 SOS1 10603 -0.02 0.23 NO
20 RAF1 RAF1 RAF1 10852 -0.025 0.22 NO
21 IGF1R IGF1R IGF1R 11440 -0.037 0.2 NO
22 PPP2CA PPP2CA PPP2CA 11621 -0.041 0.2 NO
23 ITGB1 ITGB1 ITGB1 11681 -0.042 0.2 NO
24 MAP2K1 MAP2K1 MAP2K1 11793 -0.045 0.21 NO
25 MKNK1 MKNK1 MKNK1 12757 -0.065 0.17 NO
26 MYC MYC MYC 13488 -0.085 0.14 NO
27 RPS6KA5 RPS6KA5 RPS6KA5 17228 -0.35 0.0068 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: BIOCARTA ALK PATHWAY.

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

genes ES table in pathway: BIOCARTA BIOPEPTIDES PATHWAY

Table S12.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 APC2 APC2 APC2 44 1 0.046 YES
2 SFRP5 SFRP5 SFRP5 56 0.97 0.093 YES
3 SFRP2 SFRP2 SFRP2 64 0.95 0.14 YES
4 WNT5B WNT5B WNT5B 96 0.89 0.18 YES
5 WIF1 WIF1 WIF1 162 0.8 0.22 YES
6 WNT2B WNT2B WNT2B 235 0.75 0.25 YES
7 MAPK10 MAPK10 MAPK10 390 0.65 0.27 YES
8 FZD2 FZD2 FZD2 523 0.59 0.29 YES
9 SFRP4 SFRP4 SFRP4 572 0.57 0.32 YES
10 PRKCG PRKCG PRKCG 796 0.49 0.33 YES
11 WNT9B WNT9B WNT9B 858 0.47 0.35 YES
12 CAMK2B CAMK2B CAMK2B 885 0.46 0.37 YES
13 WNT2 WNT2 WNT2 966 0.44 0.39 YES
14 NFATC4 NFATC4 NFATC4 986 0.43 0.41 YES
15 DKK1 DKK1 DKK1 1089 0.41 0.42 YES
16 PRKCB PRKCB PRKCB 1424 0.34 0.42 YES
17 WNT5A WNT5A WNT5A 1484 0.34 0.43 YES
18 WNT10A WNT10A WNT10A 1650 0.31 0.44 YES
19 WNT6 WNT6 WNT6 1810 0.29 0.44 YES
20 FZD7 FZD7 FZD7 1937 0.27 0.45 YES
21 FOSL1 FOSL1 FOSL1 1953 0.27 0.46 YES
22 SOX17 SOX17 SOX17 1986 0.27 0.47 YES
23 CCND2 CCND2 CCND2 1994 0.27 0.48 YES
24 FZD8 FZD8 FZD8 2049 0.26 0.49 YES
25 LEF1 LEF1 LEF1 2562 0.21 0.47 YES
26 FZD5 FZD5 FZD5 2631 0.2 0.48 YES
27 WNT3A WNT3A WNT3A 2632 0.2 0.49 YES
28 PLCB1 PLCB1 PLCB1 2722 0.2 0.49 YES
29 NKD2 NKD2 NKD2 2815 0.19 0.5 YES
30 CXXC4 CXXC4 CXXC4 2835 0.19 0.51 YES
31 AXIN2 AXIN2 AXIN2 2907 0.18 0.51 YES
32 FZD10 FZD10 FZD10 2997 0.18 0.51 YES
33 SFRP1 SFRP1 SFRP1 3039 0.17 0.52 YES
34 WNT1 WNT1 WNT1 3172 0.16 0.52 YES
35 MMP7 MMP7 MMP7 3264 0.16 0.52 YES
36 PLCB2 PLCB2 PLCB2 3594 0.14 0.51 NO
37 CAMK2A CAMK2A CAMK2A 3920 0.12 0.5 NO
38 WNT7B WNT7B WNT7B 3975 0.12 0.5 NO
39 JUN JUN JUN 4120 0.11 0.5 NO
40 NFATC2 NFATC2 NFATC2 4461 0.098 0.48 NO
41 PORCN PORCN PORCN 4478 0.098 0.49 NO
42 FZD3 FZD3 FZD3 4542 0.096 0.49 NO
43 DKK2 DKK2 DKK2 4553 0.095 0.49 NO
44 SMAD3 SMAD3 SMAD3 4695 0.091 0.49 NO
45 VANGL2 VANGL2 VANGL2 4716 0.091 0.49 NO
46 TCF7L1 TCF7L1 TCF7L1 4919 0.085 0.48 NO
47 PRKACA PRKACA PRKACA 4951 0.084 0.48 NO
48 FZD4 FZD4 FZD4 4993 0.083 0.49 NO
49 PRICKLE1 PRICKLE1 PRICKLE1 5139 0.079 0.48 NO
50 NFATC3 NFATC3 NFATC3 5153 0.079 0.49 NO
51 WNT9A WNT9A WNT9A 5204 0.078 0.49 NO
52 CHP2 CHP2 CHP2 5617 0.068 0.47 NO
53 RAC2 RAC2 RAC2 5651 0.067 0.47 NO
54 DVL3 DVL3 DVL3 5749 0.066 0.46 NO
55 RAC3 RAC3 RAC3 5938 0.062 0.46 NO
56 CSNK1A1L CSNK1A1L CSNK1A1L 6108 0.058 0.45 NO
57 PPP2R1A PPP2R1A PPP2R1A 6201 0.056 0.45 NO
58 WNT3 WNT3 WNT3 6351 0.053 0.44 NO
59 TCF7 TCF7 TCF7 6353 0.053 0.44 NO
60 TP53 TP53 TP53 6479 0.05 0.44 NO
61 CSNK1E CSNK1E CSNK1E 6805 0.044 0.42 NO
62 PPP2R5A PPP2R5A PPP2R5A 6835 0.044 0.42 NO
63 DVL1 DVL1 DVL1 6988 0.041 0.42 NO
64 PPARD PPARD PPARD 7055 0.04 0.41 NO
65 PLCB3 PLCB3 PLCB3 7288 0.036 0.4 NO
66 CTNNBIP1 CTNNBIP1 CTNNBIP1 7597 0.03 0.39 NO
67 RBX1 RBX1 RBX1 7673 0.029 0.38 NO
68 RAC1 RAC1 RAC1 7831 0.026 0.38 NO
69 DVL2 DVL2 DVL2 7880 0.025 0.37 NO
70 CCND1 CCND1 CCND1 8012 0.023 0.37 NO
71 CHD8 CHD8 CHD8 8259 0.019 0.35 NO
72 LRP5 LRP5 LRP5 8296 0.018 0.35 NO
73 PRKX PRKX PRKX 8318 0.018 0.35 NO
74 TBL1X TBL1X TBL1X 8536 0.015 0.34 NO
75 PPP2CB PPP2CB PPP2CB 8582 0.014 0.34 NO
76 CTBP1 CTBP1 CTBP1 8614 0.014 0.34 NO
77 CAMK2G CAMK2G CAMK2G 8715 0.012 0.33 NO
78 NKD1 NKD1 NKD1 8793 0.011 0.33 NO
79 CREBBP CREBBP CREBBP 8844 0.01 0.33 NO
80 PPP3CB PPP3CB PPP3CB 8892 0.0093 0.32 NO
81 PPP3R1 PPP3R1 PPP3R1 9101 0.006 0.31 NO
82 WNT11 WNT11 WNT11 9218 0.0041 0.3 NO
83 CSNK2A1 CSNK2A1 CSNK2A1 9296 0.0029 0.3 NO
84 CAMK2D CAMK2D CAMK2D 9316 0.0026 0.3 NO
85 WNT10B WNT10B WNT10B 9343 0.0019 0.3 NO
86 PPP2R5D PPP2R5D PPP2R5D 9421 0.0006 0.29 NO
87 AXIN1 AXIN1 AXIN1 9428 0.00044 0.29 NO
88 RHOA RHOA RHOA 9478 -0.00042 0.29 NO
89 EP300 EP300 EP300 9541 -0.0014 0.29 NO
90 SMAD2 SMAD2 SMAD2 9560 -0.0017 0.29 NO
91 NFATC1 NFATC1 NFATC1 9568 -0.0019 0.29 NO
92 FZD1 FZD1 FZD1 9601 -0.0025 0.28 NO
93 CSNK2B CSNK2B CSNK2B 9633 -0.0029 0.28 NO
94 CSNK2A2 CSNK2A2 CSNK2A2 9635 -0.003 0.28 NO
95 CHP CHP CHP 9642 -0.0031 0.28 NO
96 PSEN1 PSEN1 PSEN1 9669 -0.0036 0.28 NO
97 PRKCA PRKCA PRKCA 9761 -0.0051 0.28 NO
98 CCND3 CCND3 CCND3 9845 -0.0066 0.27 NO
99 CUL1 CUL1 CUL1 10111 -0.011 0.26 NO
100 PRICKLE2 PRICKLE2 PRICKLE2 10133 -0.012 0.26 NO
101 PPP3CC PPP3CC PPP3CC 10145 -0.012 0.26 NO
102 FRAT2 FRAT2 FRAT2 10156 -0.012 0.26 NO
103 FRAT1 FRAT1 FRAT1 10269 -0.014 0.25 NO
104 BTRC BTRC BTRC 10302 -0.015 0.25 NO
105 RUVBL1 RUVBL1 RUVBL1 10562 -0.02 0.24 NO
106 NLK NLK NLK 10876 -0.026 0.22 NO
107 NFAT5 NFAT5 NFAT5 10899 -0.026 0.22 NO
108 PPP2R5C PPP2R5C PPP2R5C 11063 -0.029 0.21 NO
109 SKP1 SKP1 SKP1 11109 -0.03 0.21 NO
110 CACYBP CACYBP CACYBP 11461 -0.038 0.19 NO
111 CTBP2 CTBP2 CTBP2 11608 -0.041 0.18 NO
112 MAP3K7 MAP3K7 MAP3K7 11614 -0.041 0.18 NO
113 PPP2CA PPP2CA PPP2CA 11621 -0.041 0.19 NO
114 GSK3B GSK3B GSK3B 11850 -0.046 0.18 NO
115 CSNK1A1 CSNK1A1 CSNK1A1 11885 -0.046 0.18 NO
116 TBL1XR1 TBL1XR1 TBL1XR1 11990 -0.049 0.17 NO
117 WNT16 WNT16 WNT16 12038 -0.05 0.17 NO
118 FBXW11 FBXW11 FBXW11 12045 -0.05 0.17 NO
119 VANGL1 VANGL1 VANGL1 12080 -0.051 0.18 NO
120 SENP2 SENP2 SENP2 12431 -0.058 0.16 NO
121 MAPK9 MAPK9 MAPK9 12634 -0.063 0.15 NO
122 TCF7L2 TCF7L2 TCF7L2 12845 -0.068 0.14 NO
123 WNT4 WNT4 WNT4 12995 -0.071 0.14 NO
124 PPP3CA PPP3CA PPP3CA 13280 -0.078 0.12 NO
125 LRP6 LRP6 LRP6 13326 -0.08 0.12 NO
126 MYC MYC MYC 13488 -0.085 0.12 NO
127 PPP2R1B PPP2R1B PPP2R1B 13680 -0.09 0.11 NO
128 CTNNB1 CTNNB1 CTNNB1 13819 -0.094 0.11 NO
129 PPP2R5E PPP2R5E PPP2R5E 13834 -0.094 0.11 NO
130 SMAD4 SMAD4 SMAD4 13949 -0.097 0.11 NO
131 PRKACB PRKACB PRKACB 14001 -0.098 0.11 NO
132 APC APC APC 14501 -0.11 0.088 NO
133 SIAH1 SIAH1 SIAH1 15005 -0.13 0.066 NO
134 DAAM2 DAAM2 DAAM2 15064 -0.13 0.069 NO
135 FZD6 FZD6 FZD6 15087 -0.14 0.074 NO
136 PLCB4 PLCB4 PLCB4 15366 -0.15 0.065 NO
137 ROCK1 ROCK1 ROCK1 15380 -0.15 0.072 NO
138 ROCK2 ROCK2 ROCK2 15535 -0.16 0.07 NO
139 FZD9 FZD9 FZD9 15608 -0.16 0.074 NO
140 DAAM1 DAAM1 DAAM1 15631 -0.16 0.081 NO
141 WNT8B WNT8B WNT8B 16108 -0.19 0.062 NO
142 MAPK8 MAPK8 MAPK8 16177 -0.2 0.068 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: BIOCARTA BIOPEPTIDES PATHWAY.

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

genes ES table in pathway: BIOCARTA ERK PATHWAY

Table S13.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACTC1 ACTC1 ACTC1 2 1.4 0.093 YES
2 ATP1A3 ATP1A3 ATP1A3 23 1.1 0.16 YES
3 ATP1A2 ATP1A2 ATP1A2 43 1 0.22 YES
4 CACNG7 CACNG7 CACNG7 190 0.78 0.27 YES
5 CACNG3 CACNG3 CACNG3 239 0.75 0.31 YES
6 CACNA1S CACNA1S CACNA1S 276 0.72 0.36 YES
7 TNNC1 TNNC1 TNNC1 427 0.63 0.39 YES
8 CACNA2D4 CACNA2D4 CACNA2D4 499 0.6 0.42 YES
9 CACNA1C CACNA1C CACNA1C 583 0.56 0.45 YES
10 CACNG4 CACNG4 CACNG4 587 0.56 0.49 YES
11 SLC8A1 SLC8A1 SLC8A1 774 0.49 0.51 YES
12 CACNA1F CACNA1F CACNA1F 812 0.48 0.54 YES
13 CACNA1D CACNA1D CACNA1D 923 0.45 0.56 YES
14 CACNA2D3 CACNA2D3 CACNA2D3 939 0.45 0.59 YES
15 ATP1B2 ATP1B2 ATP1B2 1023 0.42 0.61 YES
16 CACNB1 CACNB1 CACNB1 1244 0.38 0.62 YES
17 COX4I2 COX4I2 COX4I2 1370 0.35 0.64 YES
18 CACNG5 CACNG5 CACNG5 1394 0.35 0.66 YES
19 RYR2 RYR2 RYR2 1510 0.33 0.68 YES
20 CACNB2 CACNB2 CACNB2 1715 0.3 0.68 YES
21 MYH7 MYH7 MYH7 1795 0.29 0.7 YES
22 MYL3 MYL3 MYL3 1846 0.28 0.71 YES
23 COX7A1 COX7A1 COX7A1 2219 0.24 0.71 YES
24 COX8C COX8C COX8C 2342 0.23 0.71 YES
25 CACNA2D2 CACNA2D2 CACNA2D2 2488 0.22 0.72 YES
26 TPM2 TPM2 TPM2 2848 0.19 0.71 NO
27 CACNB4 CACNB4 CACNB4 3340 0.15 0.69 NO
28 TPM1 TPM1 TPM1 4188 0.11 0.65 NO
29 COX6B2 COX6B2 COX6B2 4216 0.11 0.66 NO
30 FXYD2 FXYD2 FXYD2 4264 0.1 0.66 NO
31 CACNB3 CACNB3 CACNB3 4556 0.095 0.65 NO
32 ATP1B1 ATP1B1 ATP1B1 4646 0.093 0.65 NO
33 UQCR10 UQCR10 UQCR10 4682 0.092 0.65 NO
34 MYH6 MYH6 MYH6 4737 0.09 0.66 NO
35 TNNI3 TNNI3 TNNI3 5335 0.075 0.63 NO
36 COX6A1 COX6A1 COX6A1 5481 0.071 0.62 NO
37 SLC9A1 SLC9A1 SLC9A1 5612 0.068 0.62 NO
38 COX8A COX8A COX8A 5659 0.067 0.62 NO
39 COX5B COX5B COX5B 5724 0.066 0.62 NO
40 ATP1A4 ATP1A4 ATP1A4 5755 0.065 0.62 NO
41 COX4I1 COX4I1 COX4I1 5785 0.065 0.63 NO
42 COX6B1 COX6B1 COX6B1 5918 0.062 0.62 NO
43 UQCRC1 UQCRC1 UQCRC1 6533 0.049 0.59 NO
44 COX7A2 COX7A2 COX7A2 7333 0.035 0.55 NO
45 COX5A COX5A COX5A 7642 0.029 0.53 NO
46 TPM4 TPM4 TPM4 7891 0.025 0.52 NO
47 UQCRQ UQCRQ UQCRQ 8140 0.021 0.51 NO
48 CACNA2D1 CACNA2D1 CACNA2D1 8725 0.012 0.47 NO
49 TPM3 TPM3 TPM3 8829 0.01 0.47 NO
50 UQCRH UQCRH UQCRH 9026 0.0073 0.46 NO
51 COX6C COX6C COX6C 9166 0.0049 0.45 NO
52 UQCRHL UQCRHL UQCRHL 9217 0.0041 0.45 NO
53 COX7A2L COX7A2L COX7A2L 9246 0.0037 0.44 NO
54 ATP2A2 ATP2A2 ATP2A2 9658 -0.0033 0.42 NO
55 ATP1A1 ATP1A1 ATP1A1 10050 -0.01 0.4 NO
56 COX7C COX7C COX7C 10081 -0.011 0.4 NO
57 UQCR11 UQCR11 UQCR11 10118 -0.011 0.4 NO
58 CYC1 CYC1 CYC1 10159 -0.012 0.4 NO
59 UQCRB UQCRB UQCRB 11315 -0.034 0.33 NO
60 ATP1B3 ATP1B3 ATP1B3 11415 -0.037 0.33 NO
61 SLC9A6 SLC9A6 SLC9A6 11964 -0.048 0.3 NO
62 UQCRFS1 UQCRFS1 UQCRFS1 12206 -0.054 0.29 NO
63 COX6A2 COX6A2 COX6A2 12245 -0.055 0.29 NO
64 COX7B COX7B COX7B 13654 -0.089 0.21 NO

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

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

genes ES table in pathway: BIOCARTA FMLP PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACTC1 ACTC1 ACTC1 2 1.4 0.067 YES
2 CACNG7 CACNG7 CACNG7 190 0.78 0.093 YES
3 ADCY8 ADCY8 ADCY8 197 0.78 0.13 YES
4 CACNG3 CACNG3 CACNG3 239 0.75 0.16 YES
5 CACNA1S CACNA1S CACNA1S 276 0.72 0.19 YES
6 DES DES DES 277 0.72 0.23 YES
7 TGFB2 TGFB2 TGFB2 293 0.71 0.26 YES
8 SGCG SGCG SGCG 403 0.65 0.28 YES
9 TNNC1 TNNC1 TNNC1 427 0.63 0.31 YES
10 ADRB1 ADRB1 ADRB1 471 0.61 0.34 YES
11 CACNA2D4 CACNA2D4 CACNA2D4 499 0.6 0.36 YES
12 CACNA1C CACNA1C CACNA1C 583 0.56 0.38 YES
13 CACNG4 CACNG4 CACNG4 587 0.56 0.41 YES
14 ADCY5 ADCY5 ADCY5 758 0.5 0.42 YES
15 SLC8A1 SLC8A1 SLC8A1 774 0.49 0.45 YES
16 ITGA11 ITGA11 ITGA11 797 0.49 0.47 YES
17 CACNA1F CACNA1F CACNA1F 812 0.48 0.49 YES
18 CACNA1D CACNA1D CACNA1D 923 0.45 0.5 YES
19 CACNA2D3 CACNA2D3 CACNA2D3 939 0.45 0.52 YES
20 SGCA SGCA SGCA 1051 0.42 0.54 YES
21 CACNB1 CACNB1 CACNB1 1244 0.38 0.55 YES
22 ITGA7 ITGA7 ITGA7 1298 0.36 0.56 YES
23 PLN PLN PLN 1377 0.35 0.57 YES
24 CACNG5 CACNG5 CACNG5 1394 0.35 0.59 YES
25 LAMA2 LAMA2 LAMA2 1396 0.35 0.6 YES
26 ITGB4 ITGB4 ITGB4 1486 0.34 0.61 YES
27 RYR2 RYR2 RYR2 1510 0.33 0.63 YES
28 CACNB2 CACNB2 CACNB2 1715 0.3 0.63 YES
29 ITGA2B ITGA2B ITGA2B 1718 0.3 0.64 YES
30 ADCY1 ADCY1 ADCY1 1723 0.3 0.66 YES
31 ADCY2 ADCY2 ADCY2 1736 0.3 0.67 YES
32 ADCY4 ADCY4 ADCY4 1786 0.29 0.68 YES
33 MYH7 MYH7 MYH7 1795 0.29 0.69 YES
34 MYL3 MYL3 MYL3 1846 0.28 0.7 YES
35 ITGA5 ITGA5 ITGA5 1886 0.28 0.72 YES
36 TGFB3 TGFB3 TGFB3 2051 0.26 0.72 YES
37 ITGA2 ITGA2 ITGA2 2060 0.26 0.73 YES
38 TGFB1 TGFB1 TGFB1 2336 0.23 0.72 NO
39 CACNA2D2 CACNA2D2 CACNA2D2 2488 0.22 0.73 NO
40 TPM2 TPM2 TPM2 2848 0.19 0.71 NO
41 ITGB3 ITGB3 ITGB3 3186 0.16 0.7 NO
42 CACNB4 CACNB4 CACNB4 3340 0.15 0.7 NO
43 IGF1 IGF1 IGF1 3505 0.14 0.7 NO
44 DMD DMD DMD 3980 0.12 0.68 NO
45 TPM1 TPM1 TPM1 4188 0.11 0.67 NO
46 CACNB3 CACNB3 CACNB3 4556 0.095 0.65 NO
47 ITGB7 ITGB7 ITGB7 4661 0.092 0.65 NO
48 MYH6 MYH6 MYH6 4737 0.09 0.65 NO
49 ITGA8 ITGA8 ITGA8 4772 0.089 0.65 NO
50 ITGB8 ITGB8 ITGB8 4788 0.088 0.66 NO
51 PRKACA PRKACA PRKACA 4951 0.084 0.65 NO
52 EMD EMD EMD 5166 0.079 0.64 NO
53 TNNI3 TNNI3 TNNI3 5335 0.075 0.64 NO
54 ITGA3 ITGA3 ITGA3 5554 0.07 0.62 NO
55 ACTB ACTB ACTB 6607 0.048 0.57 NO
56 ITGA4 ITGA4 ITGA4 7253 0.036 0.53 NO
57 ITGA6 ITGA6 ITGA6 7480 0.032 0.52 NO
58 ACTG1 ACTG1 ACTG1 7560 0.03 0.52 NO
59 LMNA LMNA LMNA 7709 0.028 0.51 NO
60 TPM4 TPM4 TPM4 7891 0.025 0.5 NO
61 GNAS GNAS GNAS 8149 0.021 0.49 NO
62 PRKX PRKX PRKX 8318 0.018 0.48 NO
63 CACNA2D1 CACNA2D1 CACNA2D1 8725 0.012 0.45 NO
64 TPM3 TPM3 TPM3 8829 0.01 0.45 NO
65 SGCB SGCB SGCB 8993 0.0078 0.44 NO
66 MYBPC3 MYBPC3 MYBPC3 9067 0.0065 0.44 NO
67 ITGB5 ITGB5 ITGB5 9119 0.0057 0.43 NO
68 ADCY9 ADCY9 ADCY9 9188 0.0046 0.43 NO
69 ATP2A2 ATP2A2 ATP2A2 9658 -0.0033 0.4 NO
70 DAG1 DAG1 DAG1 11095 -0.03 0.32 NO
71 ADCY7 ADCY7 ADCY7 11120 -0.03 0.32 NO
72 TNF TNF TNF 11342 -0.035 0.31 NO
73 ITGA10 ITGA10 ITGA10 11656 -0.042 0.29 NO
74 ITGB1 ITGB1 ITGB1 11681 -0.042 0.29 NO
75 ADCY6 ADCY6 ADCY6 12003 -0.049 0.28 NO
76 SGCD SGCD SGCD 12529 -0.06 0.25 NO
77 ITGA1 ITGA1 ITGA1 12607 -0.062 0.25 NO
78 ITGAV ITGAV ITGAV 13222 -0.077 0.22 NO
79 PRKACB PRKACB PRKACB 14001 -0.098 0.18 NO
80 TTN TTN TTN 14715 -0.12 0.14 NO
81 ITGA9 ITGA9 ITGA9 16815 -0.26 0.031 NO

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

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

genes ES table in pathway: BIOCARTA EDG1 PATHWAY

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 WNT5B WNT5B WNT5B 96 0.89 0.066 YES
2 FRZB FRZB FRZB 132 0.83 0.13 YES
3 WIF1 WIF1 WIF1 162 0.8 0.19 YES
4 WNT2B WNT2B WNT2B 235 0.75 0.25 YES
5 FZD2 FZD2 FZD2 523 0.59 0.28 YES
6 SFRP4 SFRP4 SFRP4 572 0.57 0.32 YES
7 WNT2 WNT2 WNT2 966 0.44 0.34 YES
8 DKK1 DKK1 DKK1 1089 0.41 0.36 YES
9 RHOU RHOU RHOU 1335 0.36 0.38 YES
10 WNT5A WNT5A WNT5A 1484 0.34 0.39 YES
11 WNT10A WNT10A WNT10A 1650 0.31 0.41 YES
12 WNT6 WNT6 WNT6 1810 0.29 0.42 YES
13 FZD7 FZD7 FZD7 1937 0.27 0.44 YES
14 FOSL1 FOSL1 FOSL1 1953 0.27 0.46 YES
15 SOX17 SOX17 SOX17 1986 0.27 0.48 YES
16 CCND2 CCND2 CCND2 1994 0.27 0.5 YES
17 FZD8 FZD8 FZD8 2049 0.26 0.52 YES
18 LEF1 LEF1 LEF1 2562 0.21 0.5 YES
19 FZD5 FZD5 FZD5 2631 0.2 0.52 YES
20 PITX2 PITX2 PITX2 2765 0.19 0.52 YES
21 CXXC4 CXXC4 CXXC4 2835 0.19 0.54 YES
22 SFRP1 SFRP1 SFRP1 3039 0.17 0.54 YES
23 WNT1 WNT1 WNT1 3172 0.16 0.54 YES
24 TLE2 TLE2 TLE2 3955 0.12 0.51 NO
25 WNT7B WNT7B WNT7B 3975 0.12 0.52 NO
26 JUN JUN JUN 4120 0.11 0.52 NO
27 TLE1 TLE1 TLE1 4243 0.1 0.52 NO
28 BCL9 BCL9 BCL9 4267 0.1 0.52 NO
29 PORCN PORCN PORCN 4478 0.098 0.52 NO
30 FZD3 FZD3 FZD3 4542 0.096 0.52 NO
31 TCF7L1 TCF7L1 TCF7L1 4919 0.085 0.51 NO
32 FZD4 FZD4 FZD4 4993 0.083 0.51 NO
33 WNT9A WNT9A WNT9A 5204 0.078 0.5 NO
34 GAPDH GAPDH GAPDH 5326 0.075 0.5 NO
35 GSK3A GSK3A GSK3A 5559 0.069 0.5 NO
36 PPP2R1A PPP2R1A PPP2R1A 6201 0.056 0.46 NO
37 WNT3 WNT3 WNT3 6351 0.053 0.46 NO
38 TCF7 TCF7 TCF7 6353 0.053 0.46 NO
39 FBXW4 FBXW4 FBXW4 6493 0.05 0.46 NO
40 ACTB ACTB ACTB 6607 0.048 0.46 NO
41 KREMEN1 KREMEN1 KREMEN1 6743 0.046 0.45 NO
42 DVL1 DVL1 DVL1 6988 0.041 0.44 NO
43 AES AES AES 7009 0.041 0.44 NO
44 SLC9A3R1 SLC9A3R1 SLC9A3R1 7397 0.034 0.42 NO
45 CTNNBIP1 CTNNBIP1 CTNNBIP1 7597 0.03 0.42 NO
46 DVL2 DVL2 DVL2 7880 0.025 0.4 NO
47 CCND1 CCND1 CCND1 8012 0.023 0.4 NO
48 LRP5 LRP5 LRP5 8296 0.018 0.38 NO
49 CTBP1 CTBP1 CTBP1 8614 0.014 0.36 NO
50 RPL13A RPL13A RPL13A 8638 0.013 0.36 NO
51 B2M B2M B2M 8654 0.013 0.36 NO
52 NKD1 NKD1 NKD1 8793 0.011 0.36 NO
53 WNT11 WNT11 WNT11 9218 0.0041 0.33 NO
54 CSNK1D CSNK1D CSNK1D 9229 0.004 0.33 NO
55 CSNK2A1 CSNK2A1 CSNK2A1 9296 0.0029 0.33 NO
56 AXIN1 AXIN1 AXIN1 9428 0.00044 0.32 NO
57 EP300 EP300 EP300 9541 -0.0014 0.31 NO
58 FZD1 FZD1 FZD1 9601 -0.0025 0.31 NO
59 CCND3 CCND3 CCND3 9845 -0.0066 0.3 NO
60 FRAT1 FRAT1 FRAT1 10269 -0.014 0.27 NO
61 BTRC BTRC BTRC 10302 -0.015 0.27 NO
62 CSNK1G1 CSNK1G1 CSNK1G1 10552 -0.02 0.26 NO
63 DIXDC1 DIXDC1 DIXDC1 10712 -0.022 0.25 NO
64 NLK NLK NLK 10876 -0.026 0.24 NO
65 HPRT1 HPRT1 HPRT1 11030 -0.028 0.24 NO
66 CTBP2 CTBP2 CTBP2 11608 -0.041 0.21 NO
67 PPP2CA PPP2CA PPP2CA 11621 -0.041 0.21 NO
68 GSK3B GSK3B GSK3B 11850 -0.046 0.2 NO
69 CSNK1A1 CSNK1A1 CSNK1A1 11885 -0.046 0.2 NO
70 WNT16 WNT16 WNT16 12038 -0.05 0.2 NO
71 FBXW11 FBXW11 FBXW11 12045 -0.05 0.2 NO
72 FBXW2 FBXW2 FBXW2 12218 -0.054 0.2 NO
73 SENP2 SENP2 SENP2 12431 -0.058 0.19 NO
74 WNT4 WNT4 WNT4 12995 -0.071 0.16 NO
75 LRP6 LRP6 LRP6 13326 -0.08 0.15 NO
76 MYC MYC MYC 13488 -0.085 0.15 NO
77 CTNNB1 CTNNB1 CTNNB1 13819 -0.094 0.14 NO
78 APC APC APC 14501 -0.11 0.1 NO
79 FZD6 FZD6 FZD6 15087 -0.14 0.081 NO
80 DAAM1 DAAM1 DAAM1 15631 -0.16 0.063 NO
81 WISP1 WISP1 WISP1 15934 -0.18 0.06 NO
82 PYGO1 PYGO1 PYGO1 16932 -0.28 0.024 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: BIOCARTA EDG1 PATHWAY.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EDG1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA MYOSIN PATHWAY

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 ACTC1 ACTC1 ACTC1 2 1.4 0.074 YES
2 CACNG7 CACNG7 CACNG7 190 0.78 0.1 YES
3 CACNG3 CACNG3 CACNG3 239 0.75 0.14 YES
4 CACNA1S CACNA1S CACNA1S 276 0.72 0.17 YES
5 DES DES DES 277 0.72 0.21 YES
6 TGFB2 TGFB2 TGFB2 293 0.71 0.25 YES
7 SGCG SGCG SGCG 403 0.65 0.27 YES
8 TNNC1 TNNC1 TNNC1 427 0.63 0.3 YES
9 CACNA2D4 CACNA2D4 CACNA2D4 499 0.6 0.33 YES
10 CACNA1C CACNA1C CACNA1C 583 0.56 0.36 YES
11 CACNG4 CACNG4 CACNG4 587 0.56 0.38 YES
12 ACE ACE ACE 770 0.49 0.4 YES
13 SLC8A1 SLC8A1 SLC8A1 774 0.49 0.42 YES
14 ITGA11 ITGA11 ITGA11 797 0.49 0.45 YES
15 CACNA1F CACNA1F CACNA1F 812 0.48 0.47 YES
16 CACNA1D CACNA1D CACNA1D 923 0.45 0.49 YES
17 CACNA2D3 CACNA2D3 CACNA2D3 939 0.45 0.51 YES
18 SGCA SGCA SGCA 1051 0.42 0.53 YES
19 CACNB1 CACNB1 CACNB1 1244 0.38 0.54 YES
20 ITGA7 ITGA7 ITGA7 1298 0.36 0.55 YES
21 IL6 IL6 IL6 1386 0.35 0.56 YES
22 CACNG5 CACNG5 CACNG5 1394 0.35 0.58 YES
23 LAMA2 LAMA2 LAMA2 1396 0.35 0.6 YES
24 ITGB4 ITGB4 ITGB4 1486 0.34 0.61 YES
25 RYR2 RYR2 RYR2 1510 0.33 0.63 YES
26 PRKAA2 PRKAA2 PRKAA2 1656 0.31 0.63 YES
27 CACNB2 CACNB2 CACNB2 1715 0.3 0.65 YES
28 ITGA2B ITGA2B ITGA2B 1718 0.3 0.66 YES
29 MYH7 MYH7 MYH7 1795 0.29 0.67 YES
30 MYL3 MYL3 MYL3 1846 0.28 0.68 YES
31 ITGA5 ITGA5 ITGA5 1886 0.28 0.7 YES
32 TGFB3 TGFB3 TGFB3 2051 0.26 0.7 YES
33 ITGA2 ITGA2 ITGA2 2060 0.26 0.71 YES
34 TGFB1 TGFB1 TGFB1 2336 0.23 0.71 NO
35 CACNA2D2 CACNA2D2 CACNA2D2 2488 0.22 0.71 NO
36 TPM2 TPM2 TPM2 2848 0.19 0.7 NO
37 ITGB3 ITGB3 ITGB3 3186 0.16 0.69 NO
38 CACNB4 CACNB4 CACNB4 3340 0.15 0.69 NO
39 IGF1 IGF1 IGF1 3505 0.14 0.69 NO
40 DMD DMD DMD 3980 0.12 0.66 NO
41 TPM1 TPM1 TPM1 4188 0.11 0.66 NO
42 CACNB3 CACNB3 CACNB3 4556 0.095 0.64 NO
43 ITGB7 ITGB7 ITGB7 4661 0.092 0.64 NO
44 MYH6 MYH6 MYH6 4737 0.09 0.64 NO
45 ITGA8 ITGA8 ITGA8 4772 0.089 0.64 NO
46 ITGB8 ITGB8 ITGB8 4788 0.088 0.65 NO
47 EMD EMD EMD 5166 0.079 0.63 NO
48 TNNI3 TNNI3 TNNI3 5335 0.075 0.62 NO
49 ITGA3 ITGA3 ITGA3 5554 0.07 0.62 NO
50 ACTB ACTB ACTB 6607 0.048 0.56 NO
51 ITGA4 ITGA4 ITGA4 7253 0.036 0.52 NO
52 ITGA6 ITGA6 ITGA6 7480 0.032 0.51 NO
53 ACTG1 ACTG1 ACTG1 7560 0.03 0.51 NO
54 LMNA LMNA LMNA 7709 0.028 0.5 NO
55 TPM4 TPM4 TPM4 7891 0.025 0.49 NO
56 CACNA2D1 CACNA2D1 CACNA2D1 8725 0.012 0.44 NO
57 TPM3 TPM3 TPM3 8829 0.01 0.44 NO
58 SGCB SGCB SGCB 8993 0.0078 0.43 NO
59 MYBPC3 MYBPC3 MYBPC3 9067 0.0065 0.42 NO
60 ITGB5 ITGB5 ITGB5 9119 0.0057 0.42 NO
61 ATP2A2 ATP2A2 ATP2A2 9658 -0.0033 0.39 NO
62 PRKAB1 PRKAB1 PRKAB1 10185 -0.013 0.36 NO
63 DAG1 DAG1 DAG1 11095 -0.03 0.31 NO
64 TNF TNF TNF 11342 -0.035 0.3 NO
65 ITGA10 ITGA10 ITGA10 11656 -0.042 0.28 NO
66 ITGB1 ITGB1 ITGB1 11681 -0.042 0.28 NO
67 PRKAG1 PRKAG1 PRKAG1 11812 -0.045 0.28 NO
68 PRKAB2 PRKAB2 PRKAB2 11926 -0.047 0.27 NO
69 SGCD SGCD SGCD 12529 -0.06 0.24 NO
70 ITGA1 ITGA1 ITGA1 12607 -0.062 0.24 NO
71 ITGAV ITGAV ITGAV 13222 -0.077 0.21 NO
72 PRKAG2 PRKAG2 PRKAG2 13848 -0.094 0.18 NO
73 PRKAA1 PRKAA1 PRKAA1 14525 -0.12 0.14 NO
74 TTN TTN TTN 14715 -0.12 0.14 NO
75 ITGA9 ITGA9 ITGA9 16815 -0.26 0.031 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: BIOCARTA MYOSIN PATHWAY.

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

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

Table 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 PLA2G2A PLA2G2A PLA2G2A 143 0.82 0.051 YES
2 PLA2G5 PLA2G5 PLA2G5 147 0.82 0.11 YES
3 ADCY8 ADCY8 ADCY8 197 0.78 0.16 YES
4 CACNA1S CACNA1S CACNA1S 276 0.72 0.21 YES
5 MAPK10 MAPK10 MAPK10 390 0.65 0.25 YES
6 CACNA1C CACNA1C CACNA1C 583 0.56 0.28 YES
7 MMP2 MMP2 MMP2 676 0.52 0.31 YES
8 ADCY5 ADCY5 ADCY5 758 0.5 0.34 YES
9 CACNA1F CACNA1F CACNA1F 812 0.48 0.38 YES
10 CAMK2B CAMK2B CAMK2B 885 0.46 0.4 YES
11 CACNA1D CACNA1D CACNA1D 923 0.45 0.44 YES
12 EGFR EGFR EGFR 1150 0.39 0.45 YES
13 PRKCB PRKCB PRKCB 1424 0.34 0.46 YES
14 LHB LHB LHB 1665 0.31 0.47 YES
15 ADCY1 ADCY1 ADCY1 1723 0.3 0.49 YES
16 ADCY2 ADCY2 ADCY2 1736 0.3 0.51 YES
17 ADCY4 ADCY4 ADCY4 1786 0.29 0.52 YES
18 PLCB1 PLCB1 PLCB1 2722 0.2 0.48 NO
19 MAP2K6 MAP2K6 MAP2K6 2752 0.2 0.5 NO
20 PLA2G2D PLA2G2D PLA2G2D 3194 0.16 0.48 NO
21 PLCB2 PLCB2 PLCB2 3594 0.14 0.47 NO
22 CAMK2A CAMK2A CAMK2A 3920 0.12 0.46 NO
23 MAPK11 MAPK11 MAPK11 4018 0.12 0.46 NO
24 HRAS HRAS HRAS 4025 0.12 0.47 NO
25 JUN JUN JUN 4120 0.11 0.47 NO
26 MAPK12 MAPK12 MAPK12 4229 0.11 0.47 NO
27 MAPK3 MAPK3 MAPK3 4278 0.1 0.48 NO
28 MAPK13 MAPK13 MAPK13 4364 0.1 0.48 NO
29 PTK2B PTK2B PTK2B 4436 0.1 0.48 NO
30 PRKACA PRKACA PRKACA 4951 0.084 0.46 NO
31 MAPK7 MAPK7 MAPK7 5191 0.078 0.45 NO
32 CALM3 CALM3 CALM3 5804 0.065 0.42 NO
33 MAP2K2 MAP2K2 MAP2K2 6504 0.05 0.38 NO
34 MAP2K3 MAP2K3 MAP2K3 6606 0.048 0.38 NO
35 MMP14 MMP14 MMP14 6823 0.044 0.37 NO
36 PLA2G10 PLA2G10 PLA2G10 6898 0.043 0.37 NO
37 ATF4 ATF4 ATF4 7004 0.041 0.37 NO
38 ITPR2 ITPR2 ITPR2 7171 0.038 0.36 NO
39 SRC SRC SRC 7184 0.038 0.36 NO
40 PLCB3 PLCB3 PLCB3 7288 0.036 0.36 NO
41 MAP2K7 MAP2K7 MAP2K7 7400 0.034 0.36 NO
42 CALM1 CALM1 CALM1 7505 0.032 0.35 NO
43 PLD2 PLD2 PLD2 7941 0.024 0.33 NO
44 GNAS GNAS GNAS 8149 0.021 0.32 NO
45 PRKX PRKX PRKX 8318 0.018 0.31 NO
46 HBEGF HBEGF HBEGF 8344 0.018 0.31 NO
47 CAMK2G CAMK2G CAMK2G 8715 0.012 0.29 NO
48 ADCY9 ADCY9 ADCY9 9188 0.0046 0.26 NO
49 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 9207 0.0043 0.26 NO
50 GRB2 GRB2 GRB2 9277 0.0032 0.26 NO
51 MAP3K4 MAP3K4 MAP3K4 9315 0.0026 0.26 NO
52 CAMK2D CAMK2D CAMK2D 9316 0.0026 0.26 NO
53 ELK1 ELK1 ELK1 9538 -0.0014 0.24 NO
54 PRKCA PRKCA PRKCA 9761 -0.0051 0.23 NO
55 MAPK1 MAPK1 MAPK1 9982 -0.009 0.22 NO
56 MAP3K3 MAP3K3 MAP3K3 10090 -0.011 0.21 NO
57 CALM2 CALM2 CALM2 10291 -0.014 0.2 NO
58 MAP2K4 MAP2K4 MAP2K4 10590 -0.02 0.19 NO
59 SOS1 SOS1 SOS1 10603 -0.02 0.19 NO
60 RAF1 RAF1 RAF1 10852 -0.025 0.18 NO
61 PLD1 PLD1 PLD1 10985 -0.028 0.17 NO
62 ADCY7 ADCY7 ADCY7 11120 -0.03 0.16 NO
63 CDC42 CDC42 CDC42 11328 -0.035 0.16 NO
64 GNA11 GNA11 GNA11 11500 -0.038 0.15 NO
65 GNAQ GNAQ GNAQ 11651 -0.042 0.14 NO
66 MAP2K1 MAP2K1 MAP2K1 11793 -0.045 0.14 NO
67 PRKCD PRKCD PRKCD 11857 -0.046 0.14 NO
68 ADCY6 ADCY6 ADCY6 12003 -0.049 0.13 NO
69 ITPR3 ITPR3 ITPR3 12597 -0.062 0.1 NO
70 PLA2G6 PLA2G6 PLA2G6 12627 -0.063 0.1 NO
71 MAPK9 MAPK9 MAPK9 12634 -0.063 0.11 NO
72 MAPK14 MAPK14 MAPK14 13522 -0.086 0.063 NO
73 PLA2G4A PLA2G4A PLA2G4A 13562 -0.087 0.067 NO
74 KRAS KRAS KRAS 13731 -0.091 0.064 NO
75 NRAS NRAS NRAS 13812 -0.093 0.066 NO
76 PRKACB PRKACB PRKACB 14001 -0.098 0.062 NO
77 PLA2G12A PLA2G12A PLA2G12A 14282 -0.11 0.054 NO
78 GNRH1 GNRH1 GNRH1 14961 -0.13 0.024 NO
79 SOS2 SOS2 SOS2 15099 -0.14 0.026 NO
80 MAP3K1 MAP3K1 MAP3K1 15172 -0.14 0.032 NO
81 MAP3K2 MAP3K2 MAP3K2 15216 -0.14 0.04 NO
82 PLCB4 PLCB4 PLCB4 15366 -0.15 0.042 NO
83 ITPR1 ITPR1 ITPR1 15695 -0.16 0.034 NO
84 PLA2G1B PLA2G1B PLA2G1B 15763 -0.17 0.043 NO
85 GNRHR GNRHR GNRHR 15809 -0.17 0.052 NO
86 MAPK8 MAPK8 MAPK8 16177 -0.2 0.045 NO
87 CALML6 CALML6 CALML6 17103 -0.31 0.014 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: BIOCARTA CHREBP2 PATHWAY.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 CACNG7 CACNG7 CACNG7 190 0.78 0.036 YES
2 CTNNA2 CTNNA2 CTNNA2 229 0.75 0.078 YES
3 CACNG3 CACNG3 CACNG3 239 0.75 0.12 YES
4 CACNA1S CACNA1S CACNA1S 276 0.72 0.16 YES
5 DES DES DES 277 0.72 0.2 YES
6 CDH2 CDH2 CDH2 296 0.7 0.25 YES
7 SGCG SGCG SGCG 403 0.65 0.28 YES
8 CACNA2D4 CACNA2D4 CACNA2D4 499 0.6 0.31 YES
9 CACNA1C CACNA1C CACNA1C 583 0.56 0.34 YES
10 CACNG4 CACNG4 CACNG4 587 0.56 0.37 YES
11 SLC8A1 SLC8A1 SLC8A1 774 0.49 0.39 YES
12 ITGA11 ITGA11 ITGA11 797 0.49 0.42 YES
13 CACNA1F CACNA1F CACNA1F 812 0.48 0.44 YES
14 CACNA1D CACNA1D CACNA1D 923 0.45 0.46 YES
15 CACNA2D3 CACNA2D3 CACNA2D3 939 0.45 0.49 YES
16 SGCA SGCA SGCA 1051 0.42 0.51 YES
17 CACNB1 CACNB1 CACNB1 1244 0.38 0.52 YES
18 ITGA7 ITGA7 ITGA7 1298 0.36 0.54 YES
19 CACNG5 CACNG5 CACNG5 1394 0.35 0.55 YES
20 LAMA2 LAMA2 LAMA2 1396 0.35 0.57 YES
21 ITGB4 ITGB4 ITGB4 1486 0.34 0.59 YES
22 RYR2 RYR2 RYR2 1510 0.33 0.61 YES
23 CACNB2 CACNB2 CACNB2 1715 0.3 0.61 YES
24 ITGA2B ITGA2B ITGA2B 1718 0.3 0.63 YES
25 DSP DSP DSP 1735 0.3 0.65 YES
26 ITGA5 ITGA5 ITGA5 1886 0.28 0.66 YES
27 GJA1 GJA1 GJA1 1949 0.27 0.67 YES
28 ITGA2 ITGA2 ITGA2 2060 0.26 0.68 YES
29 CACNA2D2 CACNA2D2 CACNA2D2 2488 0.22 0.67 NO
30 LEF1 LEF1 LEF1 2562 0.21 0.67 NO
31 ITGB3 ITGB3 ITGB3 3186 0.16 0.65 NO
32 CACNB4 CACNB4 CACNB4 3340 0.15 0.65 NO
33 ACTN3 ACTN3 ACTN3 3396 0.15 0.65 NO
34 PKP2 PKP2 PKP2 3583 0.14 0.65 NO
35 DSC2 DSC2 DSC2 3600 0.14 0.66 NO
36 DMD DMD DMD 3980 0.12 0.64 NO
37 CACNB3 CACNB3 CACNB3 4556 0.095 0.62 NO
38 ITGB7 ITGB7 ITGB7 4661 0.092 0.62 NO
39 ITGA8 ITGA8 ITGA8 4772 0.089 0.61 NO
40 ITGB8 ITGB8 ITGB8 4788 0.088 0.62 NO
41 TCF7L1 TCF7L1 TCF7L1 4919 0.085 0.62 NO
42 EMD EMD EMD 5166 0.079 0.61 NO
43 ITGA3 ITGA3 ITGA3 5554 0.07 0.59 NO
44 TCF7 TCF7 TCF7 6353 0.053 0.55 NO
45 ACTB ACTB ACTB 6607 0.048 0.53 NO
46 JUP JUP JUP 7167 0.038 0.5 NO
47 ITGA4 ITGA4 ITGA4 7253 0.036 0.5 NO
48 ITGA6 ITGA6 ITGA6 7480 0.032 0.49 NO
49 ACTG1 ACTG1 ACTG1 7560 0.03 0.49 NO
50 LMNA LMNA LMNA 7709 0.028 0.48 NO
51 CACNA2D1 CACNA2D1 CACNA2D1 8725 0.012 0.42 NO
52 ACTN4 ACTN4 ACTN4 8986 0.0079 0.41 NO
53 SGCB SGCB SGCB 8993 0.0078 0.41 NO
54 ITGB5 ITGB5 ITGB5 9119 0.0057 0.4 NO
55 ACTN1 ACTN1 ACTN1 9448 6e-05 0.38 NO
56 ATP2A2 ATP2A2 ATP2A2 9658 -0.0033 0.37 NO
57 CTNNA1 CTNNA1 CTNNA1 10717 -0.022 0.31 NO
58 DAG1 DAG1 DAG1 11095 -0.03 0.29 NO
59 ITGA10 ITGA10 ITGA10 11656 -0.042 0.26 NO
60 ITGB1 ITGB1 ITGB1 11681 -0.042 0.26 NO
61 SGCD SGCD SGCD 12529 -0.06 0.22 NO
62 ITGA1 ITGA1 ITGA1 12607 -0.062 0.21 NO
63 TCF7L2 TCF7L2 TCF7L2 12845 -0.068 0.2 NO
64 ACTN2 ACTN2 ACTN2 13010 -0.072 0.2 NO
65 ITGAV ITGAV ITGAV 13222 -0.077 0.19 NO
66 CTNNB1 CTNNB1 CTNNB1 13819 -0.094 0.16 NO
67 CTNNA3 CTNNA3 CTNNA3 15916 -0.18 0.052 NO
68 DSG2 DSG2 DSG2 16773 -0.25 0.018 NO
69 ITGA9 ITGA9 ITGA9 16815 -0.26 0.031 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 GLYCOLYSIS GLUCONEOGENESIS.

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

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 DPYSL5 DPYSL5 DPYSL5 62 0.95 0.04 YES
2 LRRC4C LRRC4C LRRC4C 209 0.77 0.067 YES
3 NGEF NGEF NGEF 257 0.73 0.098 YES
4 SEMA5B SEMA5B SEMA5B 267 0.72 0.13 YES
5 UNC5A UNC5A UNC5A 271 0.72 0.16 YES
6 SLIT3 SLIT3 SLIT3 353 0.67 0.19 YES
7 ABLIM3 ABLIM3 ABLIM3 548 0.58 0.2 YES
8 NTN1 NTN1 NTN1 636 0.54 0.22 YES
9 EPHB2 EPHB2 EPHB2 672 0.52 0.25 YES
10 PAK7 PAK7 PAK7 699 0.52 0.27 YES
11 UNC5C UNC5C UNC5C 778 0.49 0.29 YES
12 EPHA7 EPHA7 EPHA7 918 0.45 0.3 YES
13 NFATC4 NFATC4 NFATC4 986 0.43 0.32 YES
14 SEMA3F SEMA3F SEMA3F 1122 0.4 0.33 YES
15 EPHB6 EPHB6 EPHB6 1172 0.39 0.34 YES
16 SEMA6B SEMA6B SEMA6B 1231 0.38 0.36 YES
17 SEMA6D SEMA6D SEMA6D 1390 0.35 0.36 YES
18 CXCR4 CXCR4 CXCR4 1429 0.34 0.38 YES
19 SEMA3A SEMA3A SEMA3A 1528 0.33 0.38 YES
20 SEMA3G SEMA3G SEMA3G 1548 0.33 0.4 YES
21 SEMA6C SEMA6C SEMA6C 1578 0.32 0.41 YES
22 EPHB3 EPHB3 EPHB3 1605 0.32 0.42 YES
23 UNC5D UNC5D UNC5D 1614 0.31 0.44 YES
24 EFNB2 EFNB2 EFNB2 1693 0.3 0.45 YES
25 SLIT2 SLIT2 SLIT2 1799 0.29 0.46 YES
26 CXCL12 CXCL12 CXCL12 1845 0.28 0.47 YES
27 EFNA3 EFNA3 EFNA3 1894 0.28 0.48 YES
28 EPHA4 EPHA4 EPHA4 1983 0.27 0.48 YES
29 EFNA5 EFNA5 EFNA5 1988 0.27 0.5 YES
30 SEMA3B SEMA3B SEMA3B 2109 0.25 0.5 YES
31 UNC5B UNC5B UNC5B 2191 0.24 0.51 YES
32 SEMA3D SEMA3D SEMA3D 2204 0.24 0.52 YES
33 EPHA8 EPHA8 EPHA8 2235 0.24 0.53 YES
34 EPHB1 EPHB1 EPHB1 2338 0.23 0.53 YES
35 ROBO2 ROBO2 ROBO2 2383 0.23 0.54 YES
36 RND1 RND1 RND1 2636 0.2 0.53 YES
37 NRP1 NRP1 NRP1 2965 0.18 0.52 YES
38 ABLIM2 ABLIM2 ABLIM2 3110 0.17 0.52 YES
39 SEMA7A SEMA7A SEMA7A 3230 0.16 0.52 YES
40 SEMA5A SEMA5A SEMA5A 3237 0.16 0.53 YES
41 SRGAP3 SRGAP3 SRGAP3 3345 0.15 0.53 YES
42 SEMA3E SEMA3E SEMA3E 3469 0.14 0.53 YES
43 LIMK2 LIMK2 LIMK2 3569 0.14 0.53 YES
44 CDK5 CDK5 CDK5 3586 0.14 0.54 YES
45 EPHA5 EPHA5 EPHA5 3624 0.14 0.54 YES
46 FYN FYN FYN 3711 0.13 0.54 YES
47 EFNA2 EFNA2 EFNA2 3820 0.12 0.54 YES
48 NTN3 NTN3 NTN3 3940 0.12 0.54 YES
49 SEMA4F SEMA4F SEMA4F 3996 0.12 0.54 YES
50 EFNB3 EFNB3 EFNB3 3999 0.12 0.55 YES
51 SEMA4B SEMA4B SEMA4B 4007 0.12 0.55 YES
52 EPHA3 EPHA3 EPHA3 4155 0.11 0.55 YES
53 RHOD RHOD RHOD 4201 0.11 0.55 YES
54 SEMA4A SEMA4A SEMA4A 4272 0.1 0.55 YES
55 MAPK3 MAPK3 MAPK3 4278 0.1 0.56 YES
56 NFATC2 NFATC2 NFATC2 4461 0.098 0.55 NO
57 LIMK1 LIMK1 LIMK1 4619 0.093 0.55 NO
58 PLXNA3 PLXNA3 PLXNA3 4665 0.092 0.55 NO
59 DPYSL2 DPYSL2 DPYSL2 4809 0.088 0.54 NO
60 PLXNB2 PLXNB2 PLXNB2 4851 0.086 0.54 NO
61 PAK6 PAK6 PAK6 4886 0.086 0.55 NO
62 GNAI2 GNAI2 GNAI2 5081 0.081 0.54 NO
63 NFATC3 NFATC3 NFATC3 5153 0.079 0.54 NO
64 SRGAP2 SRGAP2 SRGAP2 5469 0.072 0.52 NO
65 CFL1 CFL1 CFL1 5492 0.071 0.52 NO
66 CHP2 CHP2 CHP2 5617 0.068 0.52 NO
67 PAK4 PAK4 PAK4 5641 0.068 0.52 NO
68 RAC2 RAC2 RAC2 5651 0.067 0.52 NO
69 ABLIM1 ABLIM1 ABLIM1 5846 0.064 0.52 NO
70 RAC3 RAC3 RAC3 5938 0.062 0.51 NO
71 SRGAP1 SRGAP1 SRGAP1 6053 0.059 0.51 NO
72 SEMA6A SEMA6A SEMA6A 6266 0.055 0.5 NO
73 EFNB1 EFNB1 EFNB1 6376 0.052 0.5 NO
74 EPHA1 EPHA1 EPHA1 6476 0.05 0.49 NO
75 EFNA4 EFNA4 EFNA4 6831 0.044 0.47 NO
76 SEMA4D SEMA4D SEMA4D 6975 0.041 0.47 NO
77 EPHB4 EPHB4 EPHB4 7155 0.038 0.46 NO
78 SLIT1 SLIT1 SLIT1 7412 0.034 0.45 NO
79 FES FES FES 7509 0.032 0.44 NO
80 PAK1 PAK1 PAK1 7604 0.03 0.44 NO
81 MET MET MET 7608 0.03 0.44 NO
82 RAC1 RAC1 RAC1 7831 0.026 0.43 NO
83 SEMA4G SEMA4G SEMA4G 7932 0.024 0.42 NO
84 NTNG1 NTNG1 NTNG1 7949 0.024 0.42 NO
85 ABL1 ABL1 ABL1 8146 0.021 0.41 NO
86 EPHA2 EPHA2 EPHA2 8391 0.017 0.4 NO
87 PPP3CB PPP3CB PPP3CB 8892 0.0093 0.37 NO
88 PPP3R1 PPP3R1 PPP3R1 9101 0.006 0.36 NO
89 RHOA RHOA RHOA 9478 -0.00042 0.34 NO
90 NFATC1 NFATC1 NFATC1 9568 -0.0019 0.33 NO
91 CHP CHP CHP 9642 -0.0031 0.33 NO
92 CFL2 CFL2 CFL2 9838 -0.0065 0.32 NO
93 MAPK1 MAPK1 MAPK1 9982 -0.009 0.31 NO
94 PPP3CC PPP3CC PPP3CC 10145 -0.012 0.3 NO
95 ARHGEF12 ARHGEF12 ARHGEF12 10192 -0.013 0.3 NO
96 L1CAM L1CAM L1CAM 10279 -0.014 0.29 NO
97 NCK2 NCK2 NCK2 10842 -0.025 0.26 NO
98 SEMA3C SEMA3C SEMA3C 10880 -0.026 0.26 NO
99 NFAT5 NFAT5 NFAT5 10899 -0.026 0.26 NO
100 CDC42 CDC42 CDC42 11328 -0.035 0.24 NO
101 GNAI3 GNAI3 GNAI3 11407 -0.036 0.24 NO
102 ITGB1 ITGB1 ITGB1 11681 -0.042 0.22 NO
103 ROBO1 ROBO1 ROBO1 11814 -0.045 0.22 NO
104 PAK2 PAK2 PAK2 11827 -0.045 0.22 NO
105 GSK3B GSK3B GSK3B 11850 -0.046 0.22 NO
106 PLXNA1 PLXNA1 PLXNA1 11884 -0.046 0.22 NO
107 SEMA4C SEMA4C SEMA4C 11994 -0.049 0.21 NO
108 PLXNB1 PLXNB1 PLXNB1 12107 -0.051 0.21 NO
109 PTK2 PTK2 PTK2 12364 -0.057 0.2 NO
110 RGS3 RGS3 RGS3 12659 -0.063 0.18 NO
111 GNAI1 GNAI1 GNAI1 13235 -0.077 0.15 NO
112 PPP3CA PPP3CA PPP3CA 13280 -0.078 0.15 NO
113 PAK3 PAK3 PAK3 13617 -0.088 0.14 NO
114 PLXNA2 PLXNA2 PLXNA2 13672 -0.089 0.14 NO
115 KRAS KRAS KRAS 13731 -0.091 0.14 NO
116 ROBO3 ROBO3 ROBO3 13734 -0.091 0.14 NO
117 NRAS NRAS NRAS 13812 -0.093 0.14 NO
118 EFNA1 EFNA1 EFNA1 14008 -0.099 0.14 NO
119 PLXNC1 PLXNC1 PLXNC1 14055 -0.1 0.14 NO
120 RASA1 RASA1 RASA1 15028 -0.13 0.089 NO
121 ROCK1 ROCK1 ROCK1 15380 -0.15 0.076 NO
122 ROCK2 ROCK2 ROCK2 15535 -0.16 0.074 NO
123 PLXNB3 PLXNB3 PLXNB3 15565 -0.16 0.08 NO
124 NCK1 NCK1 NCK1 16127 -0.19 0.056 NO
125 NTN4 NTN4 NTN4 17142 -0.32 0.012 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 STEROID HORMONE BIOSYNTHESIS.

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

genes ES table in pathway: KEGG PURINE METABOLISM

Table 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 MAOB MAOB MAOB 13 1.2 0.18 YES
2 MAOA MAOA MAOA 799 0.49 0.21 YES
3 CKMT1B CKMT1B CKMT1B 1974 0.27 0.19 YES
4 CKM CKM CKM 2058 0.26 0.22 YES
5 ALDH2 ALDH2 ALDH2 2068 0.26 0.26 YES
6 CKMT1A CKMT1A CKMT1A 2145 0.25 0.3 YES
7 NOS3 NOS3 NOS3 2299 0.23 0.33 YES
8 CKB CKB CKB 2565 0.21 0.34 YES
9 NOS2 NOS2 NOS2 2572 0.21 0.38 YES
10 DAO DAO DAO 2639 0.2 0.4 YES
11 PRODH PRODH PRODH 2720 0.2 0.43 YES
12 P4HA3 P4HA3 P4HA3 3197 0.16 0.43 YES
13 P4HA2 P4HA2 P4HA2 3234 0.16 0.45 YES
14 GLS2 GLS2 GLS2 3514 0.14 0.46 YES
15 ALDH4A1 ALDH4A1 ALDH4A1 3608 0.14 0.47 YES
16 ABP1 ABP1 ABP1 3681 0.13 0.49 YES
17 ASS1 ASS1 ASS1 3843 0.12 0.5 YES
18 GLUL GLUL GLUL 3947 0.12 0.51 YES
19 SRM SRM SRM 4435 0.1 0.5 NO
20 GAMT GAMT GAMT 4775 0.089 0.5 NO
21 GOT2 GOT2 GOT2 5891 0.063 0.44 NO
22 PYCR2 PYCR2 PYCR2 5986 0.061 0.44 NO
23 GOT1 GOT1 GOT1 7000 0.041 0.39 NO
24 NAGS NAGS NAGS 7290 0.036 0.38 NO
25 ACY1 ACY1 ACY1 7318 0.035 0.38 NO
26 ODC1 ODC1 ODC1 7527 0.031 0.38 NO
27 SAT2 SAT2 SAT2 7879 0.025 0.36 NO
28 CKMT2 CKMT2 CKMT2 8322 0.018 0.34 NO
29 ASL ASL ASL 8690 0.012 0.32 NO
30 PYCRL PYCRL PYCRL 9181 0.0047 0.29 NO
31 ALDH1B1 ALDH1B1 ALDH1B1 9264 0.0034 0.29 NO
32 ARG2 ARG2 ARG2 9275 0.0033 0.29 NO
33 ALDH18A1 ALDH18A1 ALDH18A1 9477 -0.00038 0.28 NO
34 PYCR1 PYCR1 PYCR1 9605 -0.0026 0.27 NO
35 ALDH9A1 ALDH9A1 ALDH9A1 9829 -0.0064 0.26 NO
36 SMS SMS SMS 10976 -0.027 0.2 NO
37 ADC ADC ADC 11010 -0.028 0.2 NO
38 GLUD1 GLUD1 GLUD1 11176 -0.031 0.19 NO
39 ALDH3A2 ALDH3A2 ALDH3A2 11859 -0.046 0.16 NO
40 P4HA1 P4HA1 P4HA1 11907 -0.047 0.16 NO
41 OAT OAT OAT 12163 -0.052 0.16 NO
42 ALDH7A1 ALDH7A1 ALDH7A1 12180 -0.053 0.17 NO
43 AMD1 AMD1 AMD1 12250 -0.055 0.17 NO
44 AGMAT AGMAT AGMAT 12450 -0.059 0.17 NO
45 GATM GATM GATM 14217 -0.1 0.083 NO
46 CPS1 CPS1 CPS1 14938 -0.13 0.062 NO
47 GLUD2 GLUD2 GLUD2 15357 -0.15 0.06 NO
48 LAP3 LAP3 LAP3 15567 -0.16 0.073 NO
49 GLS GLS GLS 16097 -0.19 0.072 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 PURINE METABOLISM.

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

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
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.26 1.1 0.35 1 1 0.12 0.11 0.11 1 0.84
KEGG CYSTEINE AND METHIONINE METABOLISM 32 genes.ES.table 0.3 0.97 0.47 1 1 0.16 0.11 0.14 1 0.8
KEGG HISTIDINE METABOLISM 28 genes.ES.table 0.32 0.84 0.72 1 1 0.29 0.12 0.25 1 0.56
KEGG ETHER LIPID METABOLISM 25 genes.ES.table 0.33 0.96 0.52 1 1 0.08 0.021 0.078 1 0.74
KEGG PYRUVATE METABOLISM 38 genes.ES.table 0.25 0.93 0.54 1 1 0.18 0.14 0.16 1 0.72
KEGG PROPANOATE METABOLISM 31 genes.ES.table 0.24 0.77 0.74 1 1 0.29 0.25 0.22 1 0.63
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.18 0.72 0.75 0.98 1 0.28 0.28 0.2 1 0.51
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 38 genes.ES.table 0.27 0.72 0.92 1 1 0.34 0.17 0.28 1 0.71
KEGG DRUG METABOLISM CYTOCHROME P450 39 genes.ES.table 0.37 0.97 0.51 1 1 0.38 0.17 0.32 1 0.87
KEGG RIBOSOME 85 genes.ES.table 0.64 1.6 0.082 0.47 0.56 0.85 0.28 0.61 0.18 0.14
genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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 RPL21 RPL21 RPL21 771 0.36 -0.0057 YES
2 RPL3L RPL3L RPL3L 816 0.35 0.03 YES
3 RPL35A RPL35A RPL35A 1265 0.27 0.033 YES
4 RPSA RPSA RPSA 1522 0.24 0.044 YES
5 RPL15 RPL15 RPL15 1652 0.22 0.06 YES
6 RPL24 RPL24 RPL24 1655 0.22 0.084 YES
7 RPL32 RPL32 RPL32 1745 0.21 0.1 YES
8 RPL14 RPL14 RPL14 1822 0.2 0.12 YES
9 RPS10 RPS10 RPS10 2090 0.18 0.12 YES
10 RPS4Y1 RPS4Y1 RPS4Y1 2197 0.17 0.14 YES
11 RPS18 RPS18 RPS18 2217 0.17 0.15 YES
12 RPL10A RPL10A RPL10A 2264 0.17 0.17 YES
13 RPL29 RPL29 RPL29 2303 0.16 0.19 YES
14 RPS12 RPS12 RPS12 2334 0.16 0.2 YES
15 RPL22L1 RPL22L1 RPL22L1 2345 0.16 0.22 YES
16 RPS3A RPS3A RPS3A 2523 0.15 0.22 YES
17 RPL36A RPL36A RPL36A 2789 0.14 0.22 YES
18 RPL5 RPL5 RPL5 2961 0.13 0.23 YES
19 RPL22 RPL22 RPL22 3071 0.12 0.24 YES
20 RPL34 RPL34 RPL34 3088 0.12 0.25 YES
21 RPL39 RPL39 RPL39 3188 0.12 0.25 YES
22 RPS29 RPS29 RPS29 3237 0.11 0.26 YES
23 RPL17 RPL17 RPL17 3271 0.11 0.27 YES
24 RPS8 RPS8 RPS8 3274 0.11 0.29 YES
25 RPL26 RPL26 RPL26 3302 0.11 0.3 YES
26 RPS6 RPS6 RPS6 3331 0.11 0.31 YES
27 RPS3 RPS3 RPS3 3355 0.11 0.32 YES
28 RPS23 RPS23 RPS23 3363 0.11 0.33 YES
29 RPS27A RPS27A RPS27A 3382 0.11 0.34 YES
30 RPL18A RPL18A RPL18A 3387 0.11 0.35 YES
31 RPL12 RPL12 RPL12 3391 0.11 0.36 YES
32 RPL11 RPL11 RPL11 3396 0.11 0.37 YES
33 RPS17 RPS17 RPS17 3418 0.1 0.38 YES
34 RPS7 RPS7 RPS7 3420 0.1 0.39 YES
35 RPS15A RPS15A RPS15A 3449 0.1 0.4 YES
36 RPS19 RPS19 RPS19 3483 0.1 0.41 YES
37 RPL3 RPL3 RPL3 3487 0.1 0.42 YES
38 RPL23 RPL23 RPL23 3527 0.1 0.43 YES
39 RPL31 RPL31 RPL31 3538 0.1 0.44 YES
40 RPS9 RPS9 RPS9 3567 0.098 0.45 YES
41 RPS25 RPS25 RPS25 3586 0.098 0.46 YES
42 RPL38 RPL38 RPL38 3596 0.098 0.47 YES
43 RPS28 RPS28 RPS28 3651 0.096 0.48 YES
44 RPLP1 RPLP1 RPLP1 3705 0.094 0.48 YES
45 RPL9 RPL9 RPL9 3746 0.093 0.49 YES
46 RSL24D1 RSL24D1 RSL24D1 3755 0.092 0.5 YES
47 RPS5 RPS5 RPS5 3817 0.09 0.51 YES
48 RPL13A RPL13A RPL13A 3819 0.09 0.52 YES
49 RPS27 RPS27 RPS27 3824 0.089 0.53 YES
50 RPS24 RPS24 RPS24 3870 0.088 0.54 YES
51 RPS2 RPS2 RPS2 3927 0.086 0.54 YES
52 RPS13 RPS13 RPS13 3959 0.085 0.55 YES
53 RPL10 RPL10 RPL10 3965 0.085 0.56 YES
54 RPL7A RPL7A RPL7A 4122 0.08 0.56 YES
55 RPS21 RPS21 RPS21 4170 0.078 0.56 YES
56 RPS4X RPS4X RPS4X 4233 0.076 0.57 YES
57 RPLP2 RPLP2 RPLP2 4235 0.076 0.58 YES
58 RPL27 RPL27 RPL27 4313 0.073 0.58 YES
59 RPL37A RPL37A RPL37A 4323 0.073 0.59 YES
60 RPL41 RPL41 RPL41 4346 0.072 0.59 YES
61 RPL37 RPL37 RPL37 4382 0.071 0.6 YES
62 RPL35 RPL35 RPL35 4411 0.07 0.6 YES
63 RPL13 RPL13 RPL13 4454 0.069 0.61 YES
64 RPLP0 RPLP0 RPLP0 4480 0.068 0.62 YES
65 RPS15 RPS15 RPS15 4499 0.067 0.62 YES
66 RPL27A RPL27A RPL27A 4541 0.066 0.63 YES
67 FAU FAU FAU 4604 0.064 0.63 YES
68 RPL36 RPL36 RPL36 4747 0.06 0.63 YES
69 RPS11 RPS11 RPS11 4853 0.057 0.63 YES
70 RPL4 RPL4 RPL4 4866 0.057 0.63 YES
71 RPS16 RPS16 RPS16 4884 0.056 0.64 YES
72 RPL6 RPL6 RPL6 4905 0.056 0.64 YES
73 UBA52 UBA52 UBA52 5034 0.053 0.64 NO
74 RPL36AL RPL36AL RPL36AL 5232 0.047 0.64 NO
75 RPL23A RPL23A RPL23A 5255 0.046 0.64 NO
76 RPL19 RPL19 RPL19 5526 0.039 0.63 NO
77 RPL28 RPL28 RPL28 5668 0.036 0.62 NO
78 RPL8 RPL8 RPL8 6116 0.026 0.6 NO
79 RPL30 RPL30 RPL30 6159 0.025 0.6 NO
80 RPS26 RPS26 RPS26 6980 0.0094 0.56 NO
81 RPL7 RPL7 RPL7 6981 0.0093 0.56 NO
82 RPS20 RPS20 RPS20 8831 -0.025 0.45 NO
83 RPS27L RPS27L RPS27L 10347 -0.054 0.37 NO
84 RPL26L1 RPL26L1 RPL26L1 12174 -0.11 0.28 NO
85 MRPL13 MRPL13 MRPL13 14169 -0.22 0.18 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: BIOCARTA RACCYCD PATHWAY.

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

genes ES table in pathway: KEGG CYSTEINE AND METHIONINE METABOLISM

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 HSPA1L HSPA1L HSPA1L 741 0.37 0.018 YES
2 ISY1 ISY1 ISY1 1885 0.2 -0.016 YES
3 LSM3 LSM3 LSM3 2014 0.19 0.0073 YES
4 LSM2 LSM2 LSM2 2311 0.16 0.017 YES
5 LSM5 LSM5 LSM5 2539 0.15 0.029 YES
6 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 2611 0.15 0.049 YES
7 CCDC12 CCDC12 CCDC12 2820 0.13 0.059 YES
8 DHX16 DHX16 DHX16 2866 0.13 0.078 YES
9 PPIL1 PPIL1 PPIL1 2881 0.13 0.099 YES
10 LSM6 LSM6 LSM6 2931 0.13 0.12 YES
11 HNRNPA1 HNRNPA1 HNRNPA1 3123 0.12 0.13 YES
12 HSPA1B HSPA1B HSPA1B 3303 0.11 0.13 YES
13 SR140 SR140 SR140 3364 0.11 0.15 YES
14 BAT1 BAT1 BAT1 3366 0.11 0.16 YES
15 RBMX RBMX RBMX 3821 0.089 0.15 YES
16 PRPF38A PRPF38A PRPF38A 3864 0.088 0.17 YES
17 SYF2 SYF2 SYF2 4192 0.078 0.16 YES
18 HSPA1A HSPA1A HSPA1A 4324 0.073 0.16 YES
19 SNRPA SNRPA SNRPA 4654 0.063 0.16 YES
20 SF3B3 SF3B3 SF3B3 4680 0.062 0.16 YES
21 HSPA6 HSPA6 HSPA6 4787 0.059 0.17 YES
22 SNRPC SNRPC SNRPC 4793 0.059 0.18 YES
23 SF3A2 SF3A2 SF3A2 4882 0.056 0.18 YES
24 CDC5L CDC5L CDC5L 4897 0.056 0.19 YES
25 PPIH PPIH PPIH 4915 0.056 0.2 YES
26 SF3B14 SF3B14 SF3B14 4917 0.056 0.21 YES
27 HSPA2 HSPA2 HSPA2 5012 0.053 0.21 YES
28 XAB2 XAB2 XAB2 5130 0.05 0.21 YES
29 SFRS5 SFRS5 SFRS5 5204 0.048 0.22 YES
30 DDX46 DDX46 DDX46 5523 0.039 0.2 YES
31 TRA2B TRA2B TRA2B 5569 0.038 0.21 YES
32 HNRNPM HNRNPM HNRNPM 5574 0.038 0.21 YES
33 SMNDC1 SMNDC1 SMNDC1 5605 0.038 0.22 YES
34 SNRPE SNRPE SNRPE 5730 0.035 0.22 YES
35 SF3A1 SF3A1 SF3A1 5772 0.034 0.22 YES
36 SLU7 SLU7 SLU7 5842 0.032 0.22 YES
37 RBM8A RBM8A RBM8A 5937 0.03 0.22 YES
38 SF3B5 SF3B5 SF3B5 6026 0.028 0.22 YES
39 CHERP CHERP CHERP 6031 0.028 0.22 YES
40 PRPF38B PRPF38B PRPF38B 6101 0.027 0.22 YES
41 SFRS2B SFRS2B SFRS2B 6311 0.022 0.22 YES
42 CRNKL1 CRNKL1 CRNKL1 6324 0.022 0.22 YES
43 PRPF6 PRPF6 PRPF6 6483 0.018 0.21 YES
44 DHX38 DHX38 DHX38 6484 0.018 0.22 YES
45 SFRS3 SFRS3 SFRS3 6655 0.015 0.21 YES
46 PRPF40A PRPF40A PRPF40A 6739 0.014 0.21 YES
47 SF3B4 SF3B4 SF3B4 6748 0.014 0.21 YES
48 HNRNPA3 HNRNPA3 HNRNPA3 6765 0.013 0.21 YES
49 U2AF1 U2AF1 U2AF1 6844 0.012 0.21 YES
50 PRPF18 PRPF18 PRPF18 6859 0.012 0.21 YES
51 BUD31 BUD31 BUD31 6920 0.01 0.21 YES
52 NAA38 NAA38 NAA38 6942 0.01 0.21 YES
53 SNRPB2 SNRPB2 SNRPB2 6943 0.01 0.21 YES
54 HNRNPC HNRNPC HNRNPC 6961 0.0098 0.21 YES
55 SF3A3 SF3A3 SF3A3 6962 0.0098 0.21 YES
56 HNRNPK HNRNPK HNRNPK 6969 0.0097 0.21 YES
57 PRPF19 PRPF19 PRPF19 7024 0.0084 0.21 YES
58 SNRPF SNRPF SNRPF 7031 0.0082 0.21 YES
59 PRPF40B PRPF40B PRPF40B 7106 0.0068 0.21 YES
60 SART1 SART1 SART1 7108 0.0067 0.21 YES
61 HNRNPU HNRNPU HNRNPU 7166 0.0056 0.21 YES
62 PHF5A PHF5A PHF5A 7266 0.004 0.2 YES
63 SNRNP200 SNRNP200 SNRNP200 7308 0.0033 0.2 YES
64 PCBP1 PCBP1 PCBP1 7319 0.0031 0.2 YES
65 DDX42 DDX42 DDX42 7333 0.0029 0.2 YES
66 WBP11 WBP11 WBP11 7405 0.0016 0.2 YES
67 THOC4 THOC4 THOC4 7529 -0.00054 0.19 YES
68 ZMAT2 ZMAT2 ZMAT2 7573 -0.0011 0.19 YES
69 SNRPD2 SNRPD2 SNRPD2 7589 -0.0015 0.18 YES
70 DHX15 DHX15 DHX15 7592 -0.0015 0.18 YES
71 HSPA8 HSPA8 HSPA8 7634 -0.0022 0.18 YES
72 THOC3 THOC3 THOC3 7660 -0.0026 0.18 YES
73 DDX5 DDX5 DDX5 7749 -0.004 0.18 YES
74 RBM17 RBM17 RBM17 7754 -0.0041 0.18 YES
75 SF3B1 SF3B1 SF3B1 7864 -0.0062 0.17 YES
76 RBM22 RBM22 RBM22 7881 -0.0066 0.17 YES
77 PLRG1 PLRG1 PLRG1 8023 -0.0091 0.17 YES
78 PRPF8 PRPF8 PRPF8 8029 -0.0092 0.17 YES
79 SF3B2 SF3B2 SF3B2 8039 -0.0093 0.17 YES
80 SNRNP40 SNRNP40 SNRNP40 8158 -0.012 0.16 YES
81 CWC15 CWC15 CWC15 8182 -0.012 0.16 YES
82 USP39 USP39 USP39 8327 -0.015 0.16 YES
83 SNRNP70 SNRNP70 SNRNP70 8379 -0.016 0.16 YES
84 SFRS6 SFRS6 SFRS6 8411 -0.017 0.16 YES
85 SFRS4 SFRS4 SFRS4 8417 -0.017 0.16 YES
86 U2AF2 U2AF2 U2AF2 8534 -0.02 0.16 YES
87 SFRS2 SFRS2 SFRS2 8697 -0.022 0.15 YES
88 NHP2L1 NHP2L1 NHP2L1 8751 -0.023 0.15 YES
89 PQBP1 PQBP1 PQBP1 8755 -0.023 0.16 YES
90 PRPF4 PRPF4 PRPF4 8762 -0.024 0.16 YES
91 TCERG1 TCERG1 TCERG1 8795 -0.024 0.16 YES
92 MAGOH MAGOH MAGOH 8811 -0.024 0.17 YES
93 PPIE PPIE PPIE 8900 -0.026 0.16 YES
94 CTNNBL1 CTNNBL1 CTNNBL1 8909 -0.026 0.17 YES
95 SNRNP27 SNRNP27 SNRNP27 8935 -0.027 0.17 YES
96 LSM7 LSM7 LSM7 9045 -0.028 0.17 YES
97 PRPF31 PRPF31 PRPF31 9228 -0.032 0.16 YES
98 SNRPA1 SNRPA1 SNRPA1 9524 -0.037 0.15 YES
99 EFTUD2 EFTUD2 EFTUD2 9568 -0.038 0.16 YES
100 PRPF3 PRPF3 PRPF3 9691 -0.04 0.16 YES
101 BCAS2 BCAS2 BCAS2 9722 -0.04 0.16 YES
102 SFRS1 SFRS1 SFRS1 9929 -0.044 0.16 YES
103 ACIN1 ACIN1 ACIN1 9945 -0.044 0.16 YES
104 SNRPB SNRPB SNRPB 9994 -0.045 0.17 YES
105 SFRS13A SFRS13A SFRS13A 10015 -0.046 0.18 YES
106 LSM4 LSM4 LSM4 10017 -0.046 0.18 YES
107 DHX8 DHX8 DHX8 10096 -0.048 0.19 YES
108 CDC40 CDC40 CDC40 10127 -0.048 0.19 YES
109 SNRPD3 SNRPD3 SNRPD3 10141 -0.049 0.2 YES
110 SNRPD1 SNRPD1 SNRPD1 10196 -0.05 0.2 YES
111 EIF4A3 EIF4A3 EIF4A3 10243 -0.051 0.21 YES
112 SFRS7 SFRS7 SFRS7 10495 -0.057 0.2 YES
113 PUF60 PUF60 PUF60 10519 -0.058 0.21 YES
114 TXNL4A TXNL4A TXNL4A 10609 -0.06 0.22 YES
115 DDX23 DDX23 DDX23 10639 -0.061 0.23 YES
116 SFRS9 SFRS9 SFRS9 10786 -0.064 0.23 YES
117 AQR AQR AQR 10798 -0.065 0.24 YES
118 THOC2 THOC2 THOC2 10853 -0.066 0.25 YES
119 THOC1 THOC1 THOC1 11089 -0.072 0.24 YES
120 SNW1 SNW1 SNW1 11259 -0.076 0.25 YES
121 RBM25 RBM25 RBM25 11425 -0.081 0.25 YES
122 NCBP1 NCBP1 NCBP1 11780 -0.093 0.24 NO
123 SNRPG SNRPG SNRPG 13061 -0.14 0.2 NO
124 MAGOHB MAGOHB MAGOHB 13079 -0.15 0.22 NO
125 TRA2A TRA2A TRA2A 13583 -0.18 0.22 NO

Figure S43.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CYSTEINE AND METHIONINE METABOLISM.

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

genes ES table in pathway: KEGG HISTIDINE METABOLISM

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 ZNRD1 ZNRD1 ZNRD1 3339 0.11 -0.12 YES
2 POLR2J3 POLR2J3 POLR2J3 3466 0.1 -0.063 YES
3 POLR1E POLR1E POLR1E 3526 0.1 -0.0013 YES
4 POLR1B POLR1B POLR1B 3647 0.096 0.054 YES
5 POLR1D POLR1D POLR1D 3775 0.092 0.11 YES
6 POLR2J2 POLR2J2 POLR2J2 4249 0.076 0.13 YES
7 POLR3F POLR3F POLR3F 4617 0.064 0.15 YES
8 POLR3D POLR3D POLR3D 5177 0.049 0.15 YES
9 POLR1C POLR1C POLR1C 5256 0.046 0.17 YES
10 POLR3GL POLR3GL POLR3GL 6113 0.026 0.14 YES
11 POLR1A POLR1A POLR1A 6208 0.024 0.15 YES
12 POLR2G POLR2G POLR2G 6608 0.016 0.14 YES
13 POLR2F POLR2F POLR2F 6831 0.012 0.14 YES
14 POLR3G POLR3G POLR3G 7007 0.0089 0.13 YES
15 POLR2C POLR2C POLR2C 7286 0.0037 0.12 YES
16 POLR3B POLR3B POLR3B 8110 -0.011 0.076 YES
17 POLR2L POLR2L POLR2L 8351 -0.016 0.073 YES
18 POLR3A POLR3A POLR3A 8749 -0.023 0.065 YES
19 POLR2B POLR2B POLR2B 8930 -0.026 0.072 YES
20 POLR2I POLR2I POLR2I 10175 -0.049 0.032 YES
21 POLR2J POLR2J POLR2J 10377 -0.054 0.056 YES
22 POLR3H POLR3H POLR3H 10601 -0.06 0.082 YES
23 POLR2E POLR2E POLR2E 10676 -0.061 0.12 YES
24 POLR2A POLR2A POLR2A 10730 -0.063 0.16 YES
25 POLR3K POLR3K POLR3K 10884 -0.066 0.19 YES
26 POLR2D POLR2D POLR2D 11158 -0.074 0.22 YES
27 POLR3C POLR3C POLR3C 11948 -0.098 0.24 YES
28 POLR2K POLR2K POLR2K 12281 -0.11 0.29 YES

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

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

genes ES table in pathway: KEGG ETHER LIPID METABOLISM

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 RAF1 RAF1 RAF1 1610 0.22 0.039 YES
2 CDK2 CDK2 CDK2 1818 0.2 0.15 YES
3 PIK3CA PIK3CA PIK3CA 1876 0.2 0.26 YES
4 RHOA RHOA RHOA 4460 0.068 0.15 NO
5 PAK1 PAK1 PAK1 5056 0.052 0.14 NO
6 IKBKG IKBKG IKBKG 5159 0.049 0.17 NO
7 CDK6 CDK6 CDK6 5225 0.047 0.19 NO
8 RELA RELA RELA 5602 0.038 0.19 NO
9 CDK4 CDK4 CDK4 5688 0.036 0.21 NO
10 IKBKB IKBKB IKBKB 6191 0.024 0.19 NO
11 RB1 RB1 RB1 6264 0.023 0.2 NO
12 PIK3R1 PIK3R1 PIK3R1 7414 0.0014 0.14 NO
13 CDKN1B CDKN1B CDKN1B 7477 0.00039 0.14 NO
14 RAC1 RAC1 RAC1 7584 -0.0014 0.13 NO
15 AKT1 AKT1 AKT1 7636 -0.0022 0.13 NO
16 CHUK CHUK CHUK 8159 -0.012 0.1 NO
17 MAPK3 MAPK3 MAPK3 8744 -0.023 0.084 NO
18 CCNE1 CCNE1 CCNE1 9024 -0.028 0.084 NO
19 CCND1 CCND1 CCND1 9352 -0.034 0.085 NO
20 NFKB1 NFKB1 NFKB1 9912 -0.044 0.079 NO
21 HRAS HRAS HRAS 10012 -0.046 0.1 NO
22 TFDP1 TFDP1 TFDP1 10401 -0.055 0.11 NO
23 NFKBIA NFKBIA NFKBIA 10610 -0.06 0.13 NO
24 MAPK1 MAPK1 MAPK1 11227 -0.076 0.14 NO
25 CDKN1A CDKN1A CDKN1A 15676 -0.36 0.096 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: KEGG ETHER LIPID METABOLISM.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ETHER LIPID 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 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 GNAL GNAL GNAL 249 0.58 0.045 YES
2 OR2W3 OR2W3 OR2W3 340 0.52 0.093 YES
3 CLCA2 CLCA2 CLCA2 501 0.45 0.13 YES
4 OR2T8 OR2T8 OR2T8 553 0.42 0.17 YES
5 OR2A4 OR2A4 OR2A4 638 0.4 0.2 YES
6 OR2A1 OR2A1 OR2A1 727 0.37 0.24 YES
7 OR10AD1 OR10AD1 OR10AD1 748 0.36 0.27 YES
8 OR2C3 OR2C3 OR2C3 827 0.35 0.3 YES
9 OR2A7 OR2A7 OR2A7 850 0.34 0.34 YES
10 OR2C1 OR2C1 OR2C1 927 0.33 0.37 YES
11 OR2L13 OR2L13 OR2L13 1182 0.28 0.38 YES
12 OR2A25 OR2A25 OR2A25 1204 0.28 0.41 YES
13 OR3A2 OR3A2 OR3A2 1914 0.2 0.39 NO
14 OR7A5 OR7A5 OR7A5 2320 0.16 0.38 NO
15 OR2H2 OR2H2 OR2H2 2422 0.16 0.39 NO
16 PRKACB PRKACB PRKACB 3320 0.11 0.35 NO
17 CAMK2G CAMK2G CAMK2G 3348 0.11 0.36 NO
18 PRKG1 PRKG1 PRKG1 3435 0.1 0.37 NO
19 CAMK2B CAMK2B CAMK2B 4301 0.074 0.32 NO
20 CNGA4 CNGA4 CNGA4 4732 0.061 0.3 NO
21 CAMK2D CAMK2D CAMK2D 6642 0.016 0.2 NO
22 OR7D2 OR7D2 OR7D2 7174 0.0054 0.17 NO
23 CALM3 CALM3 CALM3 7488 0.00028 0.15 NO
24 OR13A1 OR13A1 OR13A1 7493 0.00022 0.15 NO
25 OR1L8 OR1L8 OR1L8 7533 -0.00059 0.15 NO
26 PRKG2 PRKG2 PRKG2 7705 -0.0031 0.14 NO
27 CALML6 CALML6 CALML6 8627 -0.021 0.085 NO
28 OR7C1 OR7C1 OR7C1 8999 -0.028 0.066 NO
29 OR52N4 OR52N4 OR52N4 9988 -0.045 0.014 NO
30 PRKACA PRKACA PRKACA 11139 -0.073 -0.045 NO
31 PRKX PRKX PRKX 11296 -0.077 -0.046 NO
32 ADRBK2 ADRBK2 ADRBK2 11566 -0.085 -0.053 NO
33 GUCA1B GUCA1B GUCA1B 11626 -0.088 -0.048 NO
34 CALM2 CALM2 CALM2 11927 -0.097 -0.055 NO
35 CALM1 CALM1 CALM1 12247 -0.11 -0.062 NO
36 ARRB2 ARRB2 ARRB2 13279 -0.16 -0.11 NO
37 PDE1C PDE1C PDE1C 14120 -0.22 -0.13 NO
38 GUCA1A GUCA1A GUCA1A 14125 -0.22 -0.11 NO
39 ADCY3 ADCY3 ADCY3 14159 -0.22 -0.09 NO
40 OR51E2 OR51E2 OR51E2 15564 -0.35 -0.14 NO
41 PDC PDC PDC 15787 -0.37 -0.11 NO
42 CNGB1 CNGB1 CNGB1 15866 -0.38 -0.076 NO
43 GUCY2D GUCY2D GUCY2D 16186 -0.43 -0.05 NO
44 CAMK2A CAMK2A CAMK2A 16539 -0.5 -0.02 NO
45 OR51E1 OR51E1 OR51E1 17031 -0.65 0.018 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: KEGG PYRUVATE METABOLISM.

Figure S50.  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 PROPANOATE METABOLISM

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 GSTA3 GSTA3 GSTA3 137 0.68 0.088 YES
2 GSTO2 GSTO2 GSTO2 272 0.56 0.16 YES
3 FMO4 FMO4 FMO4 958 0.32 0.16 YES
4 GSTA2 GSTA2 GSTA2 1123 0.29 0.2 YES
5 ALDH1A3 ALDH1A3 ALDH1A3 1208 0.28 0.23 YES
6 MAOA MAOA MAOA 1305 0.26 0.26 YES
7 GSTT2 GSTT2 GSTT2 1483 0.24 0.29 YES
8 GSTT1 GSTT1 GSTT1 1592 0.23 0.31 YES
9 GSTM2 GSTM2 GSTM2 2564 0.15 0.28 YES
10 GSTA1 GSTA1 GSTA1 2566 0.15 0.3 YES
11 ADH1B ADH1B ADH1B 2664 0.14 0.31 YES
12 GSTP1 GSTP1 GSTP1 2667 0.14 0.33 YES
13 CYP3A5 CYP3A5 CYP3A5 2733 0.14 0.35 YES
14 CYP2C8 CYP2C8 CYP2C8 2753 0.14 0.36 YES
15 GSTM3 GSTM3 GSTM3 2944 0.13 0.37 YES
16 ADH1C ADH1C ADH1C 3337 0.11 0.36 NO
17 FMO5 FMO5 FMO5 3645 0.096 0.36 NO
18 ALDH3B2 ALDH3B2 ALDH3B2 4512 0.067 0.32 NO
19 ALDH3B1 ALDH3B1 ALDH3B1 5026 0.053 0.3 NO
20 ADH5 ADH5 ADH5 5450 0.041 0.28 NO
21 FMO2 FMO2 FMO2 5580 0.038 0.28 NO
22 CYP2D6 CYP2D6 CYP2D6 6653 0.016 0.22 NO
23 GSTM1 GSTM1 GSTM1 7393 0.0018 0.17 NO
24 GSTM4 GSTM4 GSTM4 7727 -0.0035 0.16 NO
25 GSTA4 GSTA4 GSTA4 8799 -0.024 0.097 NO
26 GSTZ1 GSTZ1 GSTZ1 8978 -0.027 0.091 NO
27 CYP3A43 CYP3A43 CYP3A43 10047 -0.047 0.036 NO
28 MGST3 MGST3 MGST3 10354 -0.054 0.025 NO
29 GSTK1 GSTK1 GSTK1 11313 -0.078 -0.019 NO
30 CYP2E1 CYP2E1 CYP2E1 11329 -0.078 -0.0088 NO
31 GSTO1 GSTO1 GSTO1 12225 -0.11 -0.045 NO
32 AOX1 AOX1 AOX1 12372 -0.11 -0.038 NO
33 GSTM5 GSTM5 GSTM5 14747 -0.27 -0.14 NO
34 FMO3 FMO3 FMO3 14897 -0.28 -0.11 NO
35 MGST2 MGST2 MGST2 15001 -0.29 -0.072 NO
36 ALDH3A1 ALDH3A1 ALDH3A1 15016 -0.29 -0.032 NO
37 FMO1 FMO1 FMO1 15444 -0.34 -0.0096 NO
38 MAOB MAOB MAOB 16095 -0.42 0.012 NO
39 MGST1 MGST1 MGST1 16188 -0.43 0.067 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: KEGG PROPANOATE METABOLISM.

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

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 CTH CTH CTH 479 0.45 0.081 YES
2 AHCYL2 AHCYL2 AHCYL2 509 0.44 0.19 YES
3 CDO1 CDO1 CDO1 838 0.34 0.25 YES
4 DNMT3L DNMT3L DNMT3L 1296 0.27 0.29 YES
5 LDHAL6A LDHAL6A LDHAL6A 1874 0.2 0.3 YES
6 TRDMT1 TRDMT1 TRDMT1 2884 0.13 0.27 NO
7 MAT2B MAT2B MAT2B 3223 0.11 0.28 NO
8 AMD1 AMD1 AMD1 3696 0.095 0.28 NO
9 MPST MPST MPST 4200 0.078 0.27 NO
10 MTAP MTAP MTAP 4561 0.065 0.26 NO
11 APIP APIP APIP 5433 0.041 0.22 NO
12 MAT2A MAT2A MAT2A 6033 0.028 0.19 NO
13 LDHB LDHB LDHB 6080 0.027 0.2 NO
14 ENOPH1 ENOPH1 ENOPH1 6148 0.026 0.2 NO
15 AHCY AHCY AHCY 6708 0.014 0.17 NO
16 LDHA LDHA LDHA 6931 0.01 0.16 NO
17 GOT2 GOT2 GOT2 7399 0.0017 0.13 NO
18 SMS SMS SMS 7997 -0.0086 0.1 NO
19 DNMT3B DNMT3B DNMT3B 8451 -0.018 0.079 NO
20 MTR MTR MTR 8626 -0.021 0.074 NO
21 LDHAL6B LDHAL6B LDHAL6B 9350 -0.034 0.04 NO
22 AHCYL1 AHCYL1 AHCYL1 9464 -0.036 0.042 NO
23 GOT1 GOT1 GOT1 9580 -0.038 0.045 NO
24 ADI1 ADI1 ADI1 9797 -0.042 0.042 NO
25 SRM SRM SRM 10437 -0.056 0.019 NO
26 DNMT3A DNMT3A DNMT3A 11642 -0.088 -0.029 NO
27 DNMT1 DNMT1 DNMT1 11673 -0.089 -0.0098 NO
28 BHMT BHMT BHMT 12169 -0.11 -0.013 NO
29 CBS CBS CBS 13751 -0.19 -0.059 NO
30 MAT1A MAT1A MAT1A 14494 -0.24 -0.043 NO
31 IL4I1 IL4I1 IL4I1 15560 -0.35 -0.021 NO
32 SDS SDS SDS 16638 -0.52 0.041 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: KEGG AMINOACYL TRNA BIOSYNTHESIS.

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

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

Table 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 ENPP2 ENPP2 ENPP2 78 0.77 0.21 YES
2 PLA2G1B PLA2G1B PLA2G1B 368 0.5 0.33 YES
3 PLA2G10 PLA2G10 PLA2G10 4096 0.081 0.14 NO
4 AGPS AGPS AGPS 5326 0.044 0.083 NO
5 PLD1 PLD1 PLD1 5684 0.036 0.072 NO
6 PPAP2A PPAP2A PPAP2A 6373 0.021 0.038 NO
7 PAFAH2 PAFAH2 PAFAH2 6733 0.014 0.021 NO
8 PAFAH1B2 PAFAH1B2 PAFAH1B2 6949 0.01 0.012 NO
9 LPCAT4 LPCAT4 LPCAT4 7159 0.0058 0.0012 NO
10 PLA2G12A PLA2G12A PLA2G12A 7601 -0.0017 -0.024 NO
11 PLD2 PLD2 PLD2 7800 -0.0051 -0.034 NO
12 LPCAT2 LPCAT2 LPCAT2 8439 -0.018 -0.066 NO
13 PAFAH1B3 PAFAH1B3 PAFAH1B3 8802 -0.024 -0.08 NO
14 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 9772 -0.041 -0.12 NO
15 PLA2G6 PLA2G6 PLA2G6 10567 -0.059 -0.15 NO
16 LPCAT1 LPCAT1 LPCAT1 10927 -0.068 -0.16 NO
17 PAFAH1B1 PAFAH1B1 PAFAH1B1 11544 -0.084 -0.17 NO
18 PLA2G4A PLA2G4A PLA2G4A 12125 -0.1 -0.17 NO
19 PLA2G5 PLA2G5 PLA2G5 12518 -0.12 -0.16 NO
20 CHPT1 CHPT1 CHPT1 12548 -0.12 -0.13 NO
21 PPAP2C PPAP2C PPAP2C 13820 -0.19 -0.15 NO
22 PLA2G2D PLA2G2D PLA2G2D 13878 -0.2 -0.096 NO
23 PLA2G2A PLA2G2A PLA2G2A 15186 -0.31 -0.086 NO
24 PLA2G7 PLA2G7 PLA2G7 15735 -0.37 -0.014 NO
25 PPAP2B PPAP2B PPAP2B 15867 -0.38 0.085 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: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG DRUG METABOLISM CYTOCHROME P450

Table 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 ACOT12 ACOT12 ACOT12 81 0.77 0.12 YES
2 ME3 ME3 ME3 587 0.41 0.16 YES
3 PKLR PKLR PKLR 723 0.37 0.21 YES
4 LDHD LDHD LDHD 906 0.33 0.25 YES
5 LDHAL6A LDHAL6A LDHAL6A 1874 0.2 0.23 YES
6 PC PC PC 2181 0.17 0.24 YES
7 GLO1 GLO1 GLO1 2395 0.16 0.25 YES
8 ACYP1 ACYP1 ACYP1 3633 0.096 0.2 NO
9 ALDH9A1 ALDH9A1 ALDH9A1 3780 0.092 0.2 NO
10 PDHB PDHB PDHB 3874 0.088 0.21 NO
11 ALDH1B1 ALDH1B1 ALDH1B1 3954 0.085 0.22 NO
12 ALDH3A2 ALDH3A2 ALDH3A2 4303 0.074 0.21 NO
13 AKR1B1 AKR1B1 AKR1B1 5317 0.044 0.16 NO
14 ACAT1 ACAT1 ACAT1 5993 0.029 0.13 NO
15 LDHB LDHB LDHB 6080 0.027 0.13 NO
16 LDHA LDHA LDHA 6931 0.01 0.079 NO
17 ACSS2 ACSS2 ACSS2 7034 0.0082 0.074 NO
18 GRHPR GRHPR GRHPR 7281 0.0038 0.06 NO
19 ALDH7A1 ALDH7A1 ALDH7A1 7313 0.0033 0.059 NO
20 ACSS1 ACSS1 ACSS1 8727 -0.023 -0.019 NO
21 MDH2 MDH2 MDH2 9145 -0.03 -0.038 NO
22 LDHAL6B LDHAL6B LDHAL6B 9350 -0.034 -0.044 NO
23 PCK2 PCK2 PCK2 10442 -0.056 -0.098 NO
24 PDHA1 PDHA1 PDHA1 10672 -0.061 -0.1 NO
25 HAGHL HAGHL HAGHL 10896 -0.067 -0.1 NO
26 ACYP2 ACYP2 ACYP2 11153 -0.074 -0.11 NO
27 MDH1 MDH1 MDH1 11163 -0.074 -0.095 NO
28 DLAT DLAT DLAT 11279 -0.077 -0.09 NO
29 HAGH HAGH HAGH 11349 -0.079 -0.081 NO
30 DLD DLD DLD 11717 -0.09 -0.087 NO
31 ACACA ACACA ACACA 12693 -0.13 -0.12 NO
32 PKM2 PKM2 PKM2 12939 -0.14 -0.12 NO
33 ALDH2 ALDH2 ALDH2 13552 -0.18 -0.12 NO
34 ME2 ME2 ME2 13832 -0.2 -0.11 NO
35 ACAT2 ACAT2 ACAT2 14005 -0.21 -0.083 NO
36 ACACB ACACB ACACB 14469 -0.24 -0.071 NO
37 PCK1 PCK1 PCK1 17117 -0.7 -0.11 NO
38 ME1 ME1 ME1 17199 -0.76 0.0085 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: KEGG DRUG METABOLISM CYTOCHROME P450.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG RIBOSOME

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 PPARG PPARG PPARG 310 0.54 0.12 YES
2 CTNNB1 CTNNB1 CTNNB1 1198 0.28 0.15 YES
3 RXRB RXRB RXRB 1900 0.2 0.16 YES
4 RXRG RXRG RXRG 2129 0.18 0.19 YES
5 TCF7L2 TCF7L2 TCF7L2 2227 0.17 0.23 YES
6 TFG TFG TFG 2391 0.16 0.26 YES
7 MYC MYC MYC 3485 0.1 0.23 NO
8 TCF7L1 TCF7L1 TCF7L1 3759 0.092 0.24 NO
9 BRAF BRAF BRAF 3917 0.087 0.25 NO
10 NCOA4 NCOA4 NCOA4 4802 0.058 0.21 NO
11 TCF7 TCF7 TCF7 6011 0.028 0.15 NO
12 CCDC6 CCDC6 CCDC6 6057 0.028 0.16 NO
13 RET RET RET 6628 0.016 0.13 NO
14 NRAS NRAS NRAS 6736 0.014 0.12 NO
15 RXRA RXRA RXRA 7027 0.0084 0.11 NO
16 PAX8 PAX8 PAX8 7681 -0.0029 0.072 NO
17 MAP2K1 MAP2K1 MAP2K1 8695 -0.022 0.02 NO
18 MAPK3 MAPK3 MAPK3 8744 -0.023 0.023 NO
19 KRAS KRAS KRAS 9099 -0.029 0.01 NO
20 TP53 TP53 TP53 9118 -0.03 0.017 NO
21 CCND1 CCND1 CCND1 9352 -0.034 0.013 NO
22 TPM3 TPM3 TPM3 9507 -0.036 0.013 NO
23 MAP2K2 MAP2K2 MAP2K2 9753 -0.041 0.0099 NO
24 MAPK1 MAPK1 MAPK1 11227 -0.076 -0.055 NO
25 TPR TPR TPR 13812 -0.19 -0.15 NO
26 CDH1 CDH1 CDH1 15636 -0.36 -0.16 NO
27 LEF1 LEF1 LEF1 15960 -0.4 -0.08 NO
28 NTRK1 NTRK1 NTRK1 16927 -0.61 0.024 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: KEGG RIBOSOME.

Figure S60.  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

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.v3.0-2.symbols.gmt

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

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

GSEA analysis

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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