GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in UVM-TP
Uveal Melanoma (Primary solid tumor)
21 August 2015 | analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1ZP45F2
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/C1ZP45F2
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

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

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

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

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

Significant gene list

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

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

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

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

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

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

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

Significant gene list

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

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

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

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

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

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

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

Significant gene list

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

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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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