GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in BRCA-TP

Breast Invasive Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in BRCA-TP. Broad Institute of MIT and Harvard. doi:10.7908/C11V5D9W

Overview

Introduction

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

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.
Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).
Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).
Checks if the top core genes are up-regulated or down-regulated.
Checks if the top core genes are high expressed or low expressed.
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: 711
Number of samples: 1093
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 7 :[ clus1 ] 267
pheno.type: 2 - 7 :[ clus2 ] 171
pheno.type: 3 - 7 :[ clus3 ] 147
pheno.type: 4 - 7 :[ clus4 ] 227
pheno.type: 5 - 7 :[ clus5 ] 209
pheno.type: 6 - 7 :[ clus6 ] 52
pheno.type: 7 - 7 :[ clus7 ] 20

For the expression subtypes of 18296 genes in 1094 samples, GSEA found enriched gene sets in each cluster using 1093 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, KEGG BASE EXCISION REPAIR, BIOCARTA CARM ER PATHWAY, BIOCARTA MPR PATHWAY, REACTOME METABOLISM OF VITAMINS AND COFACTORS, REACTOME GLUCONEOGENESIS, REACTOME TRANSCRIPTION COUPLED NER TC NER, REACTOME NUCLEOTIDE EXCISION REPAIR, REACTOME FORMATION OF RNA POL II ELONGATION COMPLEX , REACTOME POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS

And common core enriched genes are GPLD1, PGAP1, PIGF, PIGH, PIGL, PIGN, PIGO, PIGP, PIGQ, PIGS

clus2

Top enriched gene sets are KEGG STEROID HORMONE BIOSYNTHESIS, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG PROTEASOME, BIOCARTA PROTEASOME PATHWAY, BIOCARTA VEGF PATHWAY, PID INTEGRIN3 PATHWAY, REACTOME SIGNALING BY WNT, REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES, REACTOME ANTIGEN PROCESSING CROSS PRESENTATION, REACTOME ER PHAGOSOME PATHWAY

And common core enriched genes are PSMA2, PSMA3, PSMA4, PSMA6, PSMA7, PSMB1, PSMB3, PSMB5, PSMB7, PSMB9

clus3

Top enriched gene sets are KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG PURINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG GLYCEROPHOSPHOLIPID METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG ARACHIDONIC ACID METABOLISM, KEGG BUTANOATE METABOLISM

And common core enriched genes are AKT3, PIK3R1, PAK7, EGFR, NRG1, NRG2, JUN, PAK3, PIK3CD, PIK3CG

clus4

Top enriched gene sets are KEGG FATTY ACID METABOLISM, KEGG PURINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG PROPANOATE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG PEROXISOME, ST GA13 PATHWAY, PID AR PATHWAY, PID TRAIL PATHWAY

And common core enriched genes are ABAT, HMGCL, ACAA1, ACADS, ACAT1, ALDH3A2, ALDH9A1, HMGCS2, GAD1, DDO

clus5

Top enriched gene sets are KEGG LYSINE DEGRADATION, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG RNA POLYMERASE, KEGG CELL CYCLE, PID AURORA B PATHWAY, PID E2F PATHWAY, PID MYC ACTIVPATHWAY, PID LIS1PATHWAY, PID AURORA A PATHWAY, PID RB 1PATHWAY

And common core enriched genes are MAGOH, NCBP2, RBM8A, RNPS1, UPF3B, CCNB1, CDC25A, E2F3, MYC, CPSF1

clus6

Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG CITRATE CYCLE TCA CYCLE, KEGG FATTY ACID METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG ARGININE AND PROLINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG GLYCEROLIPID METABOLISM, KEGG GLYCEROPHOSPHOLIPID METABOLISM, KEGG ETHER LIPID METABOLISM

And common core enriched genes are PCK1, SLC2A4, ADIPOQ, CD36, LEP, PPARGC1A, ACACB, G6PC2, GYS2, IRS2

clus7

Top enriched gene sets are KEGG TRYPTOPHAN METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG RIBOSOME, KEGG PROTEASOME, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, KEGG UBIQUITIN MEDIATED PROTEOLYSIS

And common core enriched genes are PSMB8, FYN, PSMA8, PSMB10, PSMB9, PSME2, B2M, HCK, HLA-A, LCK

Results

Subtype clus1 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS	25	genes.ES.table	0.56	1.9	0.0063	0.46	0.26	0.6	0.21	0.47	0	0.1
KEGG BASE EXCISION REPAIR	33	genes.ES.table	0.41	1.4	0.16	1	1	0.48	0.32	0.33	0.8	0.4
BIOCARTA CARM ER PATHWAY	35	genes.ES.table	0.39	1.4	0.08	1	0.99	0.17	0.065	0.16	1	0.5
BIOCARTA MPR PATHWAY	33	genes.ES.table	0.49	1.6	0.02	1	0.9	0.39	0.19	0.32	0.59	0.33
REACTOME METABOLISM OF VITAMINS AND COFACTORS	50	genes.ES.table	0.43	1.7	0.014	1	0.82	0.36	0.15	0.31	0.46	0.27
REACTOME GLUCONEOGENESIS	30	genes.ES.table	0.46	1.4	0.081	1	1	0.3	0.16	0.25	0.85	0.42
REACTOME TRANSCRIPTION COUPLED NER TC NER	44	genes.ES.table	0.37	1.4	0.15	1	1	0.48	0.33	0.32	0.75	0.37
REACTOME NUCLEOTIDE EXCISION REPAIR	49	genes.ES.table	0.38	1.5	0.098	1	0.97	0.55	0.35	0.36	0.98	0.49
REACTOME FORMATION OF RNA POL II ELONGATION COMPLEX	43	genes.ES.table	0.41	1.7	0.027	1	0.72	0.33	0.25	0.24	0.43	0.26
REACTOME POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS	26	genes.ES.table	0.37	1.4	0.13	1	1	0.54	0.21	0.42	0.77	0.38

genes ES table in pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS

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	PIGP	PIGP	PIGP	1359	0.14	0.02	YES
2	PIGT	PIGT	PIGT	1920	0.11	0.062	YES
3	PIGW	PIGW	PIGW	1945	0.1	0.13	YES
4	PIGX	PIGX	PIGX	2558	0.084	0.16	YES
5	PIGS	PIGS	PIGS	2680	0.08	0.21	YES
6	PIGV	PIGV	PIGV	3111	0.069	0.23	YES
7	PIGO	PIGO	PIGO	3209	0.067	0.27	YES
8	PIGU	PIGU	PIGU	3241	0.066	0.32	YES
9	PIGQ	PIGQ	PIGQ	3251	0.066	0.36	YES
10	GPLD1	GPLD1	GPLD1	3562	0.059	0.38	YES
11	PIGL	PIGL	PIGL	3565	0.059	0.42	YES
12	PIGH	PIGH	PIGH	3601	0.058	0.46	YES
13	PGAP1	PGAP1	PGAP1	3759	0.055	0.49	YES
14	PIGN	PIGN	PIGN	3805	0.054	0.53	YES
15	PIGF	PIGF	PIGF	3900	0.052	0.56	YES
16	PIGG	PIGG	PIGG	4507	0.042	0.55	NO
17	PIGM	PIGM	PIGM	5395	0.03	0.53	NO
18	PIGB	PIGB	PIGB	5944	0.022	0.51	NO
19	DPM2	DPM2	DPM2	5959	0.022	0.52	NO
20	GPAA1	GPAA1	GPAA1	6172	0.019	0.53	NO
21	PIGY	PIGY	PIGY	8633	-0.0099	0.4	NO
22	PIGK	PIGK	PIGK	9865	-0.026	0.35	NO
23	PIGZ	PIGZ	PIGZ	10310	-0.032	0.35	NO
24	PIGC	PIGC	PIGC	10543	-0.036	0.36	NO
25	PIGA	PIGA	PIGA	13144	-0.093	0.28	NO

Figure S1. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS.

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

genes ES table in pathway: KEGG BASE EXCISION REPAIR

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	MNAT1	MNAT1	MNAT1	1672	0.12	-0.019	YES
2	SUPT4H1	SUPT4H1	SUPT4H1	1870	0.11	0.037	YES
3	POLR2K	POLR2K	POLR2K	1958	0.1	0.096	YES
4	CCNT1	CCNT1	CCNT1	2047	0.1	0.15	YES
5	GTF2H2	GTF2H2	GTF2H2	2139	0.097	0.21	YES
6	TCEB1	TCEB1	TCEB1	2292	0.092	0.26	YES
7	WHSC2	WHSC2	WHSC2	3118	0.068	0.25	YES
8	GTF2H3	GTF2H3	GTF2H3	3426	0.062	0.28	YES
9	CCNH	CCNH	CCNH	3467	0.061	0.31	YES
10	TH1L	TH1L	TH1L	3510	0.06	0.34	YES
11	TCEA1	TCEA1	TCEA1	3536	0.06	0.38	YES
12	GTF2H2B	GTF2H2B	GTF2H2B	3945	0.051	0.39	YES
13	SUPT16H	SUPT16H	SUPT16H	4397	0.044	0.39	YES
14	POLR2C	POLR2C	POLR2C	4594	0.041	0.41	YES
15	CDK7	CDK7	CDK7	5436	0.029	0.38	NO
16	ERCC3	ERCC3	ERCC3	5833	0.023	0.37	NO
17	POLR2E	POLR2E	POLR2E	5916	0.022	0.38	NO
18	POLR2I	POLR2I	POLR2I	5986	0.022	0.39	NO
19	TCEB2	TCEB2	TCEB2	6046	0.021	0.4	NO
20	POLR2G	POLR2G	POLR2G	6326	0.017	0.4	NO
21	POLR2B	POLR2B	POLR2B	6796	0.012	0.38	NO
22	POLR2A	POLR2A	POLR2A	6833	0.011	0.38	NO
23	GTF2F1	GTF2F1	GTF2F1	7115	0.008	0.37	NO
24	CCNT2	CCNT2	CCNT2	7168	0.0075	0.37	NO
25	NCBP2	NCBP2	NCBP2	7248	0.0066	0.37	NO
26	POLR2L	POLR2L	POLR2L	7368	0.0053	0.37	NO
27	POLR2H	POLR2H	POLR2H	7579	0.0029	0.36	NO
28	TCEB3	TCEB3	TCEB3	7584	0.0028	0.36	NO
29	POLR2J	POLR2J	POLR2J	7666	0.0018	0.36	NO
30	GTF2H1	GTF2H1	GTF2H1	7947	-0.0013	0.34	NO
31	RDBP	RDBP	RDBP	7954	-0.0014	0.34	NO
32	COBRA1	COBRA1	COBRA1	8791	-0.012	0.3	NO
33	POLR2D	POLR2D	POLR2D	8857	-0.012	0.31	NO
34	NCBP1	NCBP1	NCBP1	8873	-0.013	0.32	NO
35	CDK9	CDK9	CDK9	8905	-0.013	0.32	NO
36	ERCC2	ERCC2	ERCC2	9046	-0.015	0.32	NO
37	CTDP1	CTDP1	CTDP1	9990	-0.028	0.29	NO
38	SSRP1	SSRP1	SSRP1	10091	-0.029	0.3	NO
39	ELL	ELL	ELL	10340	-0.032	0.31	NO
40	GTF2F2	GTF2F2	GTF2F2	10857	-0.041	0.3	NO
41	SUPT5H	SUPT5H	SUPT5H	11335	-0.049	0.31	NO
42	POLR2F	POLR2F	POLR2F	11393	-0.05	0.34	NO
43	GTF2H4	GTF2H4	GTF2H4	12113	-0.066	0.34	NO

Figure S3. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BASE EXCISION REPAIR.

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

genes ES table in pathway: BIOCARTA CARM ER 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	SLC46A1	SLC46A1	SLC46A1	787	0.18	0.0048	YES
2	SLC19A2	SLC19A2	SLC19A2	878	0.18	0.046	YES
3	SLC23A1	SLC23A1	SLC23A1	999	0.16	0.081	YES
4	NMNAT3	NMNAT3	NMNAT3	1066	0.16	0.12	YES
5	GPHN	GPHN	GPHN	1077	0.16	0.16	YES
6	GSTO2	GSTO2	GSTO2	1135	0.15	0.2	YES
7	PNPO	PNPO	PNPO	1452	0.13	0.21	YES
8	ENPP1	ENPP1	ENPP1	1487	0.13	0.24	YES
9	DHFR	DHFR	DHFR	1538	0.12	0.27	YES
10	PANK3	PANK3	PANK3	1661	0.12	0.3	YES
11	NFS1	NFS1	NFS1	1817	0.11	0.32	YES
12	COASY	COASY	COASY	2083	0.099	0.33	YES
13	RFK	RFK	RFK	2204	0.095	0.35	YES
14	MOCS3	MOCS3	MOCS3	2235	0.094	0.37	YES
15	MOCS2	MOCS2	MOCS2	2331	0.09	0.39	YES
16	SLC19A1	SLC19A1	SLC19A1	2400	0.088	0.41	YES
17	THTPA	THTPA	THTPA	2517	0.084	0.42	YES
18	FASN	FASN	FASN	2666	0.08	0.43	YES
19	NADSYN1	NADSYN1	NADSYN1	3980	0.051	0.38	NO
20	NMNAT2	NMNAT2	NMNAT2	4009	0.05	0.39	NO
21	SLC25A32	SLC25A32	SLC25A32	4851	0.037	0.35	NO
22	MTHFD1	MTHFD1	MTHFD1	5240	0.031	0.34	NO
23	PPCS	PPCS	PPCS	5729	0.025	0.32	NO
24	PANK4	PANK4	PANK4	6013	0.021	0.31	NO
25	PPCDC	PPCDC	PPCDC	6045	0.021	0.31	NO
26	SLC2A1	SLC2A1	SLC2A1	6162	0.019	0.31	NO
27	MOCS1	MOCS1	MOCS1	6186	0.019	0.31	NO
28	ACP5	ACP5	ACP5	6485	0.016	0.3	NO
29	PANK1	PANK1	PANK1	6499	0.015	0.3	NO
30	AASDHPPT	AASDHPPT	AASDHPPT	7091	0.0083	0.27	NO
31	QPRT	QPRT	QPRT	7823	0.00012	0.23	NO
32	PANK2	PANK2	PANK2	8169	-0.004	0.22	NO
33	SHMT1	SHMT1	SHMT1	8463	-0.0079	0.2	NO
34	NADK	NADK	NADK	8594	-0.0094	0.2	NO
35	SLC23A2	SLC23A2	SLC23A2	8598	-0.0095	0.2	NO
36	MOCOS	MOCOS	MOCOS	9549	-0.022	0.15	NO
37	CYB5A	CYB5A	CYB5A	9771	-0.024	0.15	NO
38	NMNAT1	NMNAT1	NMNAT1	9798	-0.025	0.15	NO
39	GSTO1	GSTO1	GSTO1	9815	-0.025	0.16	NO
40	FLAD1	FLAD1	FLAD1	10724	-0.038	0.12	NO
41	MTHFR	MTHFR	MTHFR	11210	-0.047	0.1	NO
42	SLC25A16	SLC25A16	SLC25A16	11449	-0.051	0.1	NO
43	FPGS	FPGS	FPGS	11467	-0.052	0.12	NO
44	CYB5R3	CYB5R3	CYB5R3	11718	-0.057	0.12	NO
45	PDXK	PDXK	PDXK	13456	-0.1	0.049	NO
46	TPK1	TPK1	TPK1	14087	-0.12	0.047	NO
47	SLC5A6	SLC5A6	SLC5A6	14503	-0.14	0.06	NO
48	NAMPT	NAMPT	NAMPT	14532	-0.14	0.095	NO
49	SLC2A3	SLC2A3	SLC2A3	15037	-0.16	0.11	NO
50	SLC19A3	SLC19A3	SLC19A3	16832	-0.26	0.079	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 CARM ER PATHWAY.

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

genes ES table in pathway: BIOCARTA MPR PATHWAY

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	MYT1	MYT1	MYT1	3	0.63	0.2	YES
2	ADCY1	ADCY1	ADCY1	160	0.33	0.3	YES
3	CDC25C	CDC25C	CDC25C	514	0.23	0.35	YES
4	PGR	PGR	PGR	1008	0.16	0.37	YES
5	PAQR5	PAQR5	PAQR5	1136	0.15	0.41	YES
6	GNGT1	GNGT1	GNGT1	1745	0.11	0.41	YES
7	MAPK3	MAPK3	MAPK3	2050	0.1	0.43	YES
8	PRKAR1A	PRKAR1A	PRKAR1A	2274	0.092	0.45	YES
9	CDK1	CDK1	CDK1	2488	0.086	0.46	YES
10	HRAS	HRAS	HRAS	2624	0.082	0.48	YES
11	CCNB1	CCNB1	CCNB1	2922	0.073	0.49	YES
12	PRKAR2B	PRKAR2B	PRKAR2B	3279	0.065	0.49	YES
13	PAQR7	PAQR7	PAQR7	3531	0.06	0.49	YES
14	SRC	SRC	SRC	3958	0.051	0.48	NO
15	PIN1	PIN1	PIN1	4757	0.038	0.45	NO
16	GNB1	GNB1	GNB1	5608	0.026	0.42	NO
17	PRKAR2A	PRKAR2A	PRKAR2A	5614	0.026	0.42	NO
18	ARPC3	ARPC3	ARPC3	6076	0.02	0.4	NO
19	MAPK1	MAPK1	MAPK1	6839	0.011	0.37	NO
20	GNAS	GNAS	GNAS	7633	0.0022	0.32	NO
21	ARPC1A	ARPC1A	ARPC1A	8384	-0.0068	0.28	NO
22	PRKACB	PRKACB	PRKACB	9546	-0.022	0.23	NO
23	PRKAR1B	PRKAR1B	PRKAR1B	9578	-0.022	0.23	NO
24	ACTR2	ACTR2	ACTR2	9896	-0.026	0.22	NO
25	ARPC4	ARPC4	ARPC4	10090	-0.029	0.22	NO
26	CAP1	CAP1	CAP1	11743	-0.058	0.15	NO
27	ARPC2	ARPC2	ARPC2	11785	-0.058	0.17	NO
28	ARPC5	ARPC5	ARPC5	11910	-0.062	0.18	NO
29	ACTA1	ACTA1	ACTA1	12084	-0.066	0.19	NO
30	ACTR3	ACTR3	ACTR3	12458	-0.075	0.19	NO
31	ARPC1B	ARPC1B	ARPC1B	12874	-0.085	0.2	NO
32	RPS6KA1	RPS6KA1	RPS6KA1	13319	-0.098	0.2	NO
33	GNAI1	GNAI1	GNAI1	16152	-0.22	0.12	NO

Figure S7. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA MPR PATHWAY.

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

genes ES table in pathway: REACTOME METABOLISM OF VITAMINS AND COFACTORS

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	VPS37D	VPS37D	VPS37D	766	0.19	0.082	YES
2	CHMP4C	CHMP4C	CHMP4C	1729	0.12	0.1	YES
3	VPS25	VPS25	VPS25	1732	0.12	0.18	YES
4	CHMP5	CHMP5	CHMP5	2089	0.099	0.22	YES
5	TSG101	TSG101	TSG101	2189	0.095	0.28	YES
6	VPS28	VPS28	VPS28	2596	0.082	0.31	YES
7	VPS37A	VPS37A	VPS37A	2853	0.075	0.35	YES
8	CHMP2A	CHMP2A	CHMP2A	3716	0.056	0.34	YES
9	VPS37C	VPS37C	VPS37C	3781	0.054	0.37	YES
10	STAM2	STAM2	STAM2	3910	0.052	0.4	YES
11	VPS4A	VPS4A	VPS4A	4804	0.038	0.37	YES
12	CHMP6	CHMP6	CHMP6	4995	0.035	0.39	YES
13	SNF8	SNF8	SNF8	5007	0.035	0.41	YES
14	VPS4B	VPS4B	VPS4B	5231	0.032	0.42	YES
15	HGS	HGS	HGS	5615	0.026	0.41	YES
16	CHMP4B	CHMP4B	CHMP4B	5769	0.024	0.42	YES
17	STAM	STAM	STAM	5785	0.024	0.44	YES
18	CHMP4A	CHMP4A	CHMP4A	6085	0.02	0.43	NO
19	CHMP2B	CHMP2B	CHMP2B	6442	0.016	0.42	NO
20	VPS36	VPS36	VPS36	7251	0.0065	0.38	NO
21	VTA1	VTA1	VTA1	8915	-0.013	0.3	NO
22	CHMP7	CHMP7	CHMP7	10786	-0.039	0.23	NO
23	UBA52	UBA52	UBA52	11240	-0.048	0.23	NO
24	RPS27A	RPS27A	RPS27A	13191	-0.094	0.19	NO
25	VPS37B	VPS37B	VPS37B	14468	-0.14	0.21	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: REACTOME METABOLISM OF VITAMINS AND COFACTORS.

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

genes ES table in pathway: REACTOME GLUCONEOGENESIS

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	MNAT1	MNAT1	MNAT1	1672	0.12	-0.028	YES
2	POLR2K	POLR2K	POLR2K	1958	0.1	0.013	YES
3	GTF2H2	GTF2H2	GTF2H2	2139	0.097	0.056	YES
4	RFC5	RFC5	RFC5	2437	0.087	0.086	YES
5	ERCC4	ERCC4	ERCC4	2848	0.075	0.1	YES
6	POLD4	POLD4	POLD4	3023	0.071	0.13	YES
7	POLE2	POLE2	POLE2	3337	0.064	0.15	YES
8	GTF2H3	GTF2H3	GTF2H3	3426	0.062	0.18	YES
9	CCNH	CCNH	CCNH	3467	0.061	0.21	YES
10	TCEA1	TCEA1	TCEA1	3536	0.06	0.24	YES
11	LIG1	LIG1	LIG1	3921	0.052	0.25	YES
12	PCNA	PCNA	PCNA	3928	0.052	0.27	YES
13	GTF2H2B	GTF2H2B	GTF2H2B	3945	0.051	0.3	YES
14	XPC	XPC	XPC	4389	0.044	0.3	YES
15	DDB2	DDB2	DDB2	4400	0.044	0.32	YES
16	POLE	POLE	POLE	4410	0.043	0.35	YES
17	POLR2C	POLR2C	POLR2C	4594	0.041	0.36	YES
18	RPA3	RPA3	RPA3	5396	0.03	0.33	YES
19	CDK7	CDK7	CDK7	5436	0.029	0.34	YES
20	POLD2	POLD2	POLD2	5799	0.024	0.34	YES
21	ERCC3	ERCC3	ERCC3	5833	0.023	0.35	YES
22	POLR2E	POLR2E	POLR2E	5916	0.022	0.36	YES
23	POLR2I	POLR2I	POLR2I	5986	0.022	0.36	YES
24	DDB1	DDB1	DDB1	6190	0.019	0.36	YES
25	XPA	XPA	XPA	6277	0.018	0.37	YES
26	POLR2G	POLR2G	POLR2G	6326	0.017	0.38	YES
27	XAB2	XAB2	XAB2	6474	0.016	0.38	YES
28	RFC3	RFC3	RFC3	6704	0.013	0.37	NO
29	POLR2B	POLR2B	POLR2B	6796	0.012	0.37	NO
30	POLR2A	POLR2A	POLR2A	6833	0.011	0.38	NO
31	RAD23B	RAD23B	RAD23B	6994	0.0093	0.37	NO
32	ERCC6	ERCC6	ERCC6	7152	0.0076	0.37	NO
33	ERCC8	ERCC8	ERCC8	7364	0.0053	0.36	NO
34	POLR2L	POLR2L	POLR2L	7368	0.0053	0.36	NO
35	POLR2H	POLR2H	POLR2H	7579	0.0029	0.35	NO
36	POLR2J	POLR2J	POLR2J	7666	0.0018	0.35	NO
37	GTF2H1	GTF2H1	GTF2H1	7947	-0.0013	0.33	NO
38	POLR2D	POLR2D	POLR2D	8857	-0.012	0.29	NO
39	ERCC2	ERCC2	ERCC2	9046	-0.015	0.29	NO
40	RFC2	RFC2	RFC2	9931	-0.027	0.25	NO
41	POLD1	POLD1	POLD1	10076	-0.029	0.26	NO
42	POLD3	POLD3	POLD3	10107	-0.029	0.28	NO
43	RPA1	RPA1	RPA1	10482	-0.035	0.27	NO
44	RFC4	RFC4	RFC4	10811	-0.04	0.28	NO
45	RPA2	RPA2	RPA2	10848	-0.04	0.3	NO
46	ERCC5	ERCC5	ERCC5	10960	-0.043	0.31	NO
47	ERCC1	ERCC1	ERCC1	11035	-0.044	0.33	NO
48	POLR2F	POLR2F	POLR2F	11393	-0.05	0.34	NO
49	GTF2H4	GTF2H4	GTF2H4	12113	-0.066	0.34	NO

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

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME 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: REACTOME TRANSCRIPTION COUPLED NER TC NER

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	HIST4H4	HIST4H4	HIST4H4	49	0.43	0.074	YES
2	HIST1H2BD	HIST1H2BD	HIST1H2BD	463	0.24	0.094	YES
3	HIST1H2BF	HIST1H2BF	HIST1H2BF	474	0.24	0.14	YES
4	HIST1H2BL	HIST1H2BL	HIST1H2BL	493	0.23	0.18	YES
5	HIST1H4D	HIST1H4D	HIST1H4D	632	0.2	0.2	YES
6	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	665	0.2	0.24	YES
7	HIST1H2BC	HIST1H2BC	HIST1H2BC	673	0.2	0.28	YES
8	HIST2H2BE	HIST2H2BE	HIST2H2BE	677	0.2	0.31	YES
9	HIST2H4A	HIST2H4A	HIST2H4A	768	0.19	0.34	YES
10	HIST1H2BO	HIST1H2BO	HIST1H2BO	779	0.18	0.37	YES
11	HIST3H2BB	HIST3H2BB	HIST3H2BB	791	0.18	0.4	YES
12	HIST1H4I	HIST1H4I	HIST1H4I	797	0.18	0.44	YES
13	HIST1H4H	HIST1H4H	HIST1H4H	841	0.18	0.47	YES
14	HIST1H2AD	HIST1H2AD	HIST1H2AD	1020	0.16	0.48	YES
15	HIST1H2BN	HIST1H2BN	HIST1H2BN	1115	0.15	0.51	YES
16	HIST1H2BE	HIST1H2BE	HIST1H2BE	1162	0.15	0.53	YES
17	MLF1IP	MLF1IP	MLF1IP	1185	0.15	0.56	YES
18	CENPK	CENPK	CENPK	1229	0.14	0.58	YES
19	HIST1H4J	HIST1H4J	HIST1H4J	1474	0.13	0.59	YES
20	CASC5	CASC5	CASC5	1818	0.11	0.59	YES
21	CENPI	CENPI	CENPI	1868	0.11	0.61	YES
22	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1971	0.1	0.62	YES
23	HIST1H2AC	HIST1H2AC	HIST1H2AC	2026	0.1	0.64	YES
24	HIST1H4K	HIST1H4K	HIST1H4K	2058	0.1	0.65	YES
25	CENPQ	CENPQ	CENPQ	2130	0.097	0.66	YES
26	OIP5	OIP5	OIP5	2133	0.097	0.68	YES
27	HIST1H2BB	HIST1H2BB	HIST1H2BB	2362	0.09	0.69	YES
28	CENPA	CENPA	CENPA	2964	0.072	0.67	NO
29	HJURP	HJURP	HJURP	3013	0.071	0.68	NO
30	HIST1H2BM	HIST1H2BM	HIST1H2BM	3061	0.07	0.69	NO
31	CENPH	CENPH	CENPH	3435	0.062	0.68	NO
32	HIST1H2BK	HIST1H2BK	HIST1H2BK	3486	0.061	0.68	NO
33	RBBP7	RBBP7	RBBP7	3899	0.052	0.67	NO
34	HIST1H2AB	HIST1H2AB	HIST1H2AB	4158	0.048	0.67	NO
35	HIST2H2AC	HIST2H2AC	HIST2H2AC	4309	0.045	0.67	NO
36	H2AFZ	H2AFZ	H2AFZ	4569	0.041	0.66	NO
37	HIST1H4A	HIST1H4A	HIST1H4A	4709	0.039	0.66	NO
38	CENPO	CENPO	CENPO	4921	0.036	0.65	NO
39	HIST1H4E	HIST1H4E	HIST1H4E	5066	0.034	0.65	NO
40	SMARCA5	SMARCA5	SMARCA5	5122	0.033	0.65	NO
41	RBBP4	RBBP4	RBBP4	5350	0.03	0.65	NO
42	RUVBL1	RUVBL1	RUVBL1	5654	0.026	0.64	NO
43	RSF1	RSF1	RSF1	6007	0.022	0.62	NO
44	ITGB3BP	ITGB3BP	ITGB3BP	6054	0.021	0.62	NO
45	HIST1H4B	HIST1H4B	HIST1H4B	6981	0.0095	0.57	NO
46	HIST1H2BI	HIST1H2BI	HIST1H2BI	7003	0.0092	0.57	NO
47	NPM1	NPM1	NPM1	7024	0.009	0.57	NO
48	H2AFX	H2AFX	H2AFX	7655	0.0019	0.54	NO
49	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	7892	-0.00067	0.52	NO
50	CENPN	CENPN	CENPN	7985	-0.0017	0.52	NO
51	HIST1H4C	HIST1H4C	HIST1H4C	8047	-0.0025	0.52	NO
52	HIST1H2BG	HIST1H2BG	HIST1H2BG	8785	-0.012	0.48	NO
53	HIST1H2BH	HIST1H2BH	HIST1H2BH	11543	-0.053	0.34	NO
54	CENPP	CENPP	CENPP	12909	-0.086	0.28	NO
55	HIST1H2AE	HIST1H2AE	HIST1H2AE	13132	-0.092	0.28	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: REACTOME TRANSCRIPTION COUPLED NER TC NER.

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

genes ES table in pathway: REACTOME NUCLEOTIDE EXCISION REPAIR

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	HIST4H4	HIST4H4	HIST4H4	49	0.43	0.071	YES
2	HIST1H2BD	HIST1H2BD	HIST1H2BD	463	0.24	0.089	YES
3	HIST1H2BF	HIST1H2BF	HIST1H2BF	474	0.24	0.13	YES
4	HIST1H2BL	HIST1H2BL	HIST1H2BL	493	0.23	0.17	YES
5	HIST1H4D	HIST1H4D	HIST1H4D	632	0.2	0.2	YES
6	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	665	0.2	0.23	YES
7	HIST1H2BC	HIST1H2BC	HIST1H2BC	673	0.2	0.26	YES
8	HIST2H2BE	HIST2H2BE	HIST2H2BE	677	0.2	0.3	YES
9	HIST2H4A	HIST2H4A	HIST2H4A	768	0.19	0.32	YES
10	HIST1H2BO	HIST1H2BO	HIST1H2BO	779	0.18	0.36	YES
11	HIST3H2BB	HIST3H2BB	HIST3H2BB	791	0.18	0.39	YES
12	HIST1H4I	HIST1H4I	HIST1H4I	797	0.18	0.42	YES
13	HIST1H4H	HIST1H4H	HIST1H4H	841	0.18	0.44	YES
14	HIST1H2AD	HIST1H2AD	HIST1H2AD	1020	0.16	0.46	YES
15	HIST1H2BN	HIST1H2BN	HIST1H2BN	1115	0.15	0.48	YES
16	HIST1H2BE	HIST1H2BE	HIST1H2BE	1162	0.15	0.51	YES
17	PRIM1	PRIM1	PRIM1	1285	0.14	0.52	YES
18	HIST1H4J	HIST1H4J	HIST1H4J	1474	0.13	0.54	YES
19	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1971	0.1	0.53	YES
20	HIST1H2AC	HIST1H2AC	HIST1H2AC	2026	0.1	0.54	YES
21	HIST1H4K	HIST1H4K	HIST1H4K	2058	0.1	0.56	YES
22	HIST1H2BB	HIST1H2BB	HIST1H2BB	2362	0.09	0.56	YES
23	RFC5	RFC5	RFC5	2437	0.087	0.57	YES
24	TERF1	TERF1	TERF1	2471	0.086	0.58	YES
25	TERF2IP	TERF2IP	TERF2IP	2578	0.083	0.59	YES
26	POLA1	POLA1	POLA1	2916	0.073	0.58	YES
27	POLD4	POLD4	POLD4	3023	0.071	0.59	YES
28	HIST1H2BM	HIST1H2BM	HIST1H2BM	3061	0.07	0.6	YES
29	POLE2	POLE2	POLE2	3337	0.064	0.59	YES
30	HIST1H2BK	HIST1H2BK	HIST1H2BK	3486	0.061	0.6	YES
31	NHP2	NHP2	NHP2	3702	0.056	0.59	YES
32	ACD	ACD	ACD	3766	0.055	0.6	YES
33	LIG1	LIG1	LIG1	3921	0.052	0.6	YES
34	PCNA	PCNA	PCNA	3928	0.052	0.61	YES
35	HIST1H2AB	HIST1H2AB	HIST1H2AB	4158	0.048	0.6	YES
36	HIST2H2AC	HIST2H2AC	HIST2H2AC	4309	0.045	0.6	YES
37	POLE	POLE	POLE	4410	0.043	0.61	YES
38	TERF2	TERF2	TERF2	4555	0.041	0.6	YES
39	H2AFZ	H2AFZ	H2AFZ	4569	0.041	0.61	YES
40	HIST1H4A	HIST1H4A	HIST1H4A	4709	0.039	0.61	NO
41	POT1	POT1	POT1	5052	0.034	0.6	NO
42	HIST1H4E	HIST1H4E	HIST1H4E	5066	0.034	0.6	NO
43	TINF2	TINF2	TINF2	5284	0.031	0.6	NO
44	RUVBL2	RUVBL2	RUVBL2	5362	0.03	0.6	NO
45	RPA3	RPA3	RPA3	5396	0.03	0.6	NO
46	RUVBL1	RUVBL1	RUVBL1	5654	0.026	0.59	NO
47	POLD2	POLD2	POLD2	5799	0.024	0.59	NO
48	FEN1	FEN1	FEN1	5896	0.023	0.58	NO
49	RFC3	RFC3	RFC3	6704	0.013	0.54	NO
50	DNA2	DNA2	DNA2	6756	0.012	0.54	NO
51	POLA2	POLA2	POLA2	6962	0.0096	0.53	NO
52	HIST1H4B	HIST1H4B	HIST1H4B	6981	0.0095	0.53	NO
53	HIST1H2BI	HIST1H2BI	HIST1H2BI	7003	0.0092	0.53	NO
54	DKC1	DKC1	DKC1	7565	0.003	0.5	NO
55	H2AFX	H2AFX	H2AFX	7655	0.0019	0.5	NO
56	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	7892	-0.00067	0.49	NO
57	HIST1H4C	HIST1H4C	HIST1H4C	8047	-0.0025	0.48	NO
58	HIST1H2BG	HIST1H2BG	HIST1H2BG	8785	-0.012	0.44	NO
59	TERT	TERT	TERT	8786	-0.012	0.44	NO
60	WRAP53	WRAP53	WRAP53	9726	-0.024	0.39	NO
61	RFC2	RFC2	RFC2	9931	-0.027	0.39	NO
62	POLD1	POLD1	POLD1	10076	-0.029	0.38	NO
63	POLD3	POLD3	POLD3	10107	-0.029	0.39	NO
64	RPA1	RPA1	RPA1	10482	-0.035	0.37	NO
65	PRIM2	PRIM2	PRIM2	10493	-0.035	0.38	NO
66	RFC4	RFC4	RFC4	10811	-0.04	0.37	NO
67	RPA2	RPA2	RPA2	10848	-0.04	0.37	NO
68	HIST1H2BH	HIST1H2BH	HIST1H2BH	11543	-0.053	0.34	NO
69	HIST3H3	HIST3H3	HIST3H3	11741	-0.058	0.34	NO
70	HIST1H2AE	HIST1H2AE	HIST1H2AE	13132	-0.092	0.28	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: REACTOME NUCLEOTIDE EXCISION REPAIR.

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

genes ES table in pathway: REACTOME FORMATION OF RNA POL II ELONGATION COMPLEX

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	SUPT4H1	SUPT4H1	SUPT4H1	1870	0.11	-0.0016	YES
2	POLR2K	POLR2K	POLR2K	1958	0.1	0.09	YES
3	CCNT1	CCNT1	CCNT1	2047	0.1	0.18	YES
4	TCEB1	TCEB1	TCEB1	2292	0.092	0.25	YES
5	WHSC2	WHSC2	WHSC2	3118	0.068	0.27	YES
6	TH1L	TH1L	TH1L	3510	0.06	0.3	YES
7	TCEA1	TCEA1	TCEA1	3536	0.06	0.36	YES
8	SUPT16H	SUPT16H	SUPT16H	4397	0.044	0.35	YES
9	POLR2C	POLR2C	POLR2C	4594	0.041	0.38	YES
10	POLR2E	POLR2E	POLR2E	5916	0.022	0.32	YES
11	POLR2I	POLR2I	POLR2I	5986	0.022	0.34	YES
12	TCEB2	TCEB2	TCEB2	6046	0.021	0.36	YES
13	POLR2G	POLR2G	POLR2G	6326	0.017	0.36	YES
14	POLR2B	POLR2B	POLR2B	6796	0.012	0.34	YES
15	POLR2A	POLR2A	POLR2A	6833	0.011	0.35	YES
16	GTF2F1	GTF2F1	GTF2F1	7115	0.008	0.34	YES
17	CCNT2	CCNT2	CCNT2	7168	0.0075	0.35	YES
18	POLR2L	POLR2L	POLR2L	7368	0.0053	0.34	YES
19	POLR2H	POLR2H	POLR2H	7579	0.0029	0.33	YES
20	TCEB3	TCEB3	TCEB3	7584	0.0028	0.34	YES
21	POLR2J	POLR2J	POLR2J	7666	0.0018	0.33	YES
22	RDBP	RDBP	RDBP	7954	-0.0014	0.32	YES
23	COBRA1	COBRA1	COBRA1	8791	-0.012	0.28	YES
24	POLR2D	POLR2D	POLR2D	8857	-0.012	0.29	YES
25	CDK9	CDK9	CDK9	8905	-0.013	0.3	YES
26	CTDP1	CTDP1	CTDP1	9990	-0.028	0.27	YES
27	SSRP1	SSRP1	SSRP1	10091	-0.029	0.29	YES
28	ELL	ELL	ELL	10340	-0.032	0.3	YES
29	GTF2F2	GTF2F2	GTF2F2	10857	-0.041	0.31	YES
30	SUPT5H	SUPT5H	SUPT5H	11335	-0.049	0.33	YES
31	POLR2F	POLR2F	POLR2F	11393	-0.05	0.38	YES

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: REACTOME FORMATION OF RNA POL II ELONGATION COMPLEX .

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF RNA POL II ELONGATION COMPLEX , this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS

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	ESR1	ESR1	ESR1	30	0.46	0.14	YES
2	CCND1	CCND1	CCND1	311	0.27	0.21	YES
3	HDAC11	HDAC11	HDAC11	674	0.2	0.26	YES
4	BRCA1	BRCA1	BRCA1	739	0.19	0.31	YES
5	HIST2H3C	HIST2H3C	HIST2H3C	913	0.17	0.36	YES
6	NRIP1	NRIP1	NRIP1	1182	0.15	0.39	YES
7	HDAC10	HDAC10	HDAC10	3614	0.058	0.27	NO
8	NCOR2	NCOR2	NCOR2	3743	0.055	0.28	NO
9	NR0B1	NR0B1	NR0B1	3925	0.052	0.29	NO
10	HDAC6	HDAC6	HDAC6	4364	0.044	0.28	NO
11	HDAC5	HDAC5	HDAC5	4385	0.044	0.29	NO
12	HDAC1	HDAC1	HDAC1	4918	0.036	0.27	NO
13	GTF2A1	GTF2A1	GTF2A1	5133	0.033	0.27	NO
14	MED1	MED1	MED1	5679	0.025	0.25	NO
15	ERCC3	ERCC3	ERCC3	5833	0.023	0.25	NO
16	EP300	EP300	EP300	6140	0.02	0.24	NO
17	GTF2E1	GTF2E1	GTF2E1	6249	0.018	0.24	NO
18	SRA1	SRA1	SRA1	6585	0.014	0.22	NO
19	POLR2A	POLR2A	POLR2A	6833	0.011	0.22	NO
20	PELP1	PELP1	PELP1	7034	0.0089	0.21	NO
21	GTF2F1	GTF2F1	GTF2F1	7115	0.008	0.2	NO
22	CREBBP	CREBBP	CREBBP	7149	0.0077	0.21	NO
23	HDAC7	HDAC7	HDAC7	8399	-0.007	0.14	NO
24	HDAC8	HDAC8	HDAC8	8523	-0.0086	0.14	NO
25	SPEN	SPEN	SPEN	9012	-0.015	0.11	NO
26	TBP	TBP	TBP	9279	-0.018	0.1	NO
27	HDAC3	HDAC3	HDAC3	10021	-0.028	0.073	NO
28	PHB2	PHB2	PHB2	10874	-0.041	0.039	NO
29	CARM1	CARM1	CARM1	11005	-0.044	0.046	NO
30	HDAC2	HDAC2	HDAC2	11495	-0.052	0.035	NO
31	MEF2C	MEF2C	MEF2C	14271	-0.13	-0.076	NO
32	GRIP1	GRIP1	GRIP1	14456	-0.14	-0.042	NO
33	HDAC4	HDAC4	HDAC4	15078	-0.16	-0.025	NO
34	HDAC9	HDAC9	HDAC9	16578	-0.24	-0.03	NO
35	PPARGC1A	PPARGC1A	PPARGC1A	17922	-0.39	0.019	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: REACTOME POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS, 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
KEGG STEROID HORMONE BIOSYNTHESIS	41	genes.ES.table	0.68	1.7	0.0044	0.25	0.83	0.46	0.079	0.43	0.099	0.053
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM	29	genes.ES.table	0.63	1.8	0.021	0.2	0.69	0.24	0.054	0.23	0.068	0.043
KEGG PROTEASOME	43	genes.ES.table	0.62	1.8	0.02	0.16	0.5	0.74	0.31	0.52	0	0.038
BIOCARTA PROTEASOME PATHWAY	28	genes.ES.table	0.65	1.8	0	0.2	0.66	0.82	0.32	0.56	0.064	0.047
BIOCARTA VEGF PATHWAY	29	genes.ES.table	0.49	1.7	0.037	0.25	0.82	0.31	0.21	0.25	0.098	0.051
PID INTEGRIN3 PATHWAY	43	genes.ES.table	0.64	1.7	0.008	0.24	0.8	0.6	0.22	0.48	0.091	0.056
REACTOME SIGNALING BY WNT	63	genes.ES.table	0.48	1.9	0.02	0.22	0.27	0.59	0.31	0.41	0	0.057
REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES	47	genes.ES.table	0.56	1.8	0.021	0.2	0.66	0.62	0.24	0.47	0.065	0.048
REACTOME ANTIGEN PROCESSING CROSS PRESENTATION	72	genes.ES.table	0.55	1.8	0.012	0.19	0.67	0.71	0.32	0.49	0.064	0.044
REACTOME ER PHAGOSOME PATHWAY	58	genes.ES.table	0.59	1.8	0.018	0.18	0.59	0.67	0.32	0.46	0.049	0.043

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

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	NQO1	NQO1	NQO1	517	0.22	0.051	YES
2	PSMD3	PSMD3	PSMD3	564	0.22	0.12	YES
3	OAZ3	OAZ3	OAZ3	779	0.18	0.18	YES
4	PSMD5	PSMD5	PSMD5	1194	0.15	0.21	YES
5	PSMD12	PSMD12	PSMD12	1810	0.11	0.22	YES
6	PSMA3	PSMA3	PSMA3	2293	0.093	0.22	YES
7	PSME4	PSME4	PSME4	2353	0.091	0.25	YES
8	PSMD7	PSMD7	PSMD7	2399	0.089	0.28	YES
9	PSMC1	PSMC1	PSMC1	2534	0.085	0.3	YES
10	PSMD14	PSMD14	PSMD14	2554	0.085	0.33	YES
11	PSMB3	PSMB3	PSMB3	2605	0.083	0.36	YES
12	PSMA6	PSMA6	PSMA6	2683	0.081	0.38	YES
13	PSMD11	PSMD11	PSMD11	2814	0.078	0.4	YES
14	PSMA7	PSMA7	PSMA7	3137	0.07	0.41	YES
15	PSMB9	PSMB9	PSMB9	3292	0.067	0.43	YES
16	PSMD1	PSMD1	PSMD1	3309	0.066	0.45	YES
17	PSMC6	PSMC6	PSMC6	3326	0.066	0.47	YES
18	PSMB5	PSMB5	PSMB5	3633	0.06	0.48	YES
19	PSME2	PSME2	PSME2	3788	0.057	0.49	YES
20	PSMA2	PSMA2	PSMA2	3927	0.055	0.5	YES
21	PSMB1	PSMB1	PSMB1	4044	0.053	0.52	YES
22	PSMC5	PSMC5	PSMC5	4128	0.051	0.53	YES
23	PSMC2	PSMC2	PSMC2	4132	0.051	0.55	YES
24	PSMA4	PSMA4	PSMA4	4230	0.05	0.56	YES
25	PSMD10	PSMD10	PSMD10	4256	0.049	0.57	YES
26	PSMB7	PSMB7	PSMB7	4259	0.049	0.59	YES
27	PSMD2	PSMD2	PSMD2	4373	0.047	0.6	YES
28	PSMA5	PSMA5	PSMA5	4985	0.039	0.58	YES
29	PSMD6	PSMD6	PSMD6	5043	0.038	0.59	YES
30	PSMB2	PSMB2	PSMB2	5081	0.038	0.6	YES
31	PSMA1	PSMA1	PSMA1	5433	0.033	0.6	YES
32	PSMF1	PSMF1	PSMF1	5477	0.032	0.61	YES
33	PSMC4	PSMC4	PSMC4	5657	0.03	0.61	YES
34	PSMB10	PSMB10	PSMB10	6021	0.026	0.6	NO
35	AZIN1	AZIN1	AZIN1	6223	0.024	0.6	NO
36	PSMB8	PSMB8	PSMB8	6694	0.019	0.58	NO
37	PSMD13	PSMD13	PSMD13	6926	0.017	0.57	NO
38	ODC1	ODC1	ODC1	7140	0.014	0.56	NO
39	PSMD8	PSMD8	PSMD8	7460	0.011	0.55	NO
40	PSMC3	PSMC3	PSMC3	7604	0.0099	0.55	NO
41	PSME1	PSME1	PSME1	7765	0.0081	0.54	NO
42	PSMB4	PSMB4	PSMB4	8280	0.0028	0.51	NO
43	OAZ1	OAZ1	OAZ1	8554	-0.00018	0.5	NO
44	PSMD4	PSMD4	PSMD4	8572	-0.00038	0.5	NO
45	PSMB6	PSMB6	PSMB6	9012	-0.0046	0.47	NO
46	PSMD9	PSMD9	PSMD9	9236	-0.0071	0.46	NO
47	OAZ2	OAZ2	OAZ2	12133	-0.041	0.32	NO
48	PSMA8	PSMA8	PSMA8	12721	-0.05	0.3	NO

Figure S21. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS.

Figure S22. 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 PORPHYRIN AND CHLOROPHYLL METABOLISM

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	UNC5A	UNC5A	UNC5A	215	0.3	0.072	YES
2	PSMD3	PSMD3	PSMD3	564	0.22	0.11	YES
3	PSMD5	PSMD5	PSMD5	1194	0.15	0.12	YES
4	DAPK1	DAPK1	DAPK1	1567	0.12	0.13	YES
5	PSMD12	PSMD12	PSMD12	1810	0.11	0.15	YES
6	CASP3	CASP3	CASP3	2219	0.096	0.16	YES
7	PSMA3	PSMA3	PSMA3	2293	0.093	0.18	YES
8	PSME4	PSME4	PSME4	2353	0.091	0.2	YES
9	MAGED1	MAGED1	MAGED1	2398	0.089	0.22	YES
10	PSMD7	PSMD7	PSMD7	2399	0.089	0.25	YES
11	ARHGAP10	ARHGAP10	ARHGAP10	2432	0.088	0.27	YES
12	PSMC1	PSMC1	PSMC1	2534	0.085	0.29	YES
13	PSMD14	PSMD14	PSMD14	2554	0.085	0.31	YES
14	PSMB3	PSMB3	PSMB3	2605	0.083	0.33	YES
15	PSMA6	PSMA6	PSMA6	2683	0.081	0.35	YES
16	PSMD11	PSMD11	PSMD11	2814	0.078	0.36	YES
17	PSMA7	PSMA7	PSMA7	3137	0.07	0.37	YES
18	PSMB9	PSMB9	PSMB9	3292	0.067	0.38	YES
19	PSMD1	PSMD1	PSMD1	3309	0.066	0.39	YES
20	PSMC6	PSMC6	PSMC6	3326	0.066	0.41	YES
21	UNC5B	UNC5B	UNC5B	3434	0.064	0.42	YES
22	PSMB5	PSMB5	PSMB5	3633	0.06	0.43	YES
23	PSME2	PSME2	PSME2	3788	0.057	0.44	YES
24	PSMA2	PSMA2	PSMA2	3927	0.055	0.44	YES
25	PSMB1	PSMB1	PSMB1	4044	0.053	0.45	YES
26	PSMC5	PSMC5	PSMC5	4128	0.051	0.46	YES
27	PSMC2	PSMC2	PSMC2	4132	0.051	0.48	YES
28	PSMA4	PSMA4	PSMA4	4230	0.05	0.48	YES
29	PSMD10	PSMD10	PSMD10	4256	0.049	0.5	YES
30	PSMB7	PSMB7	PSMB7	4259	0.049	0.51	YES
31	PSMD2	PSMD2	PSMD2	4373	0.047	0.52	YES
32	PSMA5	PSMA5	PSMA5	4985	0.039	0.5	NO
33	PSMD6	PSMD6	PSMD6	5043	0.038	0.5	NO
34	PSMB2	PSMB2	PSMB2	5081	0.038	0.51	NO
35	PSMA1	PSMA1	PSMA1	5433	0.033	0.5	NO
36	PSMF1	PSMF1	PSMF1	5477	0.032	0.51	NO
37	PSMC4	PSMC4	PSMC4	5657	0.03	0.51	NO
38	DCC	DCC	DCC	5763	0.029	0.51	NO
39	PAK2	PAK2	PAK2	5983	0.027	0.5	NO
40	PSMB10	PSMB10	PSMB10	6021	0.026	0.51	NO
41	DAPK3	DAPK3	DAPK3	6635	0.02	0.48	NO
42	PSMB8	PSMB8	PSMB8	6694	0.019	0.48	NO
43	PSMD13	PSMD13	PSMD13	6926	0.017	0.48	NO
44	PSMD8	PSMD8	PSMD8	7460	0.011	0.45	NO
45	PSMC3	PSMC3	PSMC3	7604	0.0099	0.44	NO
46	PSME1	PSME1	PSME1	7765	0.0081	0.44	NO
47	PSMB4	PSMB4	PSMB4	8280	0.0028	0.41	NO
48	PSMD4	PSMD4	PSMD4	8572	-0.00038	0.39	NO
49	PSMB6	PSMB6	PSMB6	9012	-0.0046	0.37	NO
50	PSMD9	PSMD9	PSMD9	9236	-0.0071	0.36	NO
51	UBA52	UBA52	UBA52	10430	-0.02	0.3	NO
52	RPS27A	RPS27A	RPS27A	11335	-0.03	0.26	NO
53	CASP9	CASP9	CASP9	12270	-0.043	0.22	NO
54	PSMA8	PSMA8	PSMA8	12721	-0.05	0.21	NO
55	APPL1	APPL1	APPL1	13187	-0.057	0.2	NO
56	DAPK2	DAPK2	DAPK2	17824	-0.28	0.025	NO

Figure S23. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM.

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

genes ES table in pathway: KEGG PROTEASOME

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	PSMD3	PSMD3	PSMD3	564	0.22	0.051	YES
2	PSMD5	PSMD5	PSMD5	1194	0.15	0.072	YES
3	CDC25A	CDC25A	CDC25A	1285	0.14	0.12	YES
4	PSMD12	PSMD12	PSMD12	1810	0.11	0.13	YES
5	PSMA3	PSMA3	PSMA3	2293	0.093	0.14	YES
6	CHEK1	CHEK1	CHEK1	2299	0.093	0.18	YES
7	PSME4	PSME4	PSME4	2353	0.091	0.21	YES
8	PSMD7	PSMD7	PSMD7	2399	0.089	0.24	YES
9	PSMC1	PSMC1	PSMC1	2534	0.085	0.27	YES
10	PSMD14	PSMD14	PSMD14	2554	0.085	0.3	YES
11	PSMB3	PSMB3	PSMB3	2605	0.083	0.33	YES
12	PSMA6	PSMA6	PSMA6	2683	0.081	0.35	YES
13	PSMD11	PSMD11	PSMD11	2814	0.078	0.38	YES
14	PSMA7	PSMA7	PSMA7	3137	0.07	0.38	YES
15	PSMB9	PSMB9	PSMB9	3292	0.067	0.4	YES
16	PSMD1	PSMD1	PSMD1	3309	0.066	0.42	YES
17	PSMC6	PSMC6	PSMC6	3326	0.066	0.45	YES
18	PSMB5	PSMB5	PSMB5	3633	0.06	0.46	YES
19	PSME2	PSME2	PSME2	3788	0.057	0.47	YES
20	PSMA2	PSMA2	PSMA2	3927	0.055	0.48	YES
21	PSMB1	PSMB1	PSMB1	4044	0.053	0.5	YES
22	PSMC5	PSMC5	PSMC5	4128	0.051	0.51	YES
23	PSMC2	PSMC2	PSMC2	4132	0.051	0.53	YES
24	PSMA4	PSMA4	PSMA4	4230	0.05	0.54	YES
25	PSMD10	PSMD10	PSMD10	4256	0.049	0.56	YES
26	PSMB7	PSMB7	PSMB7	4259	0.049	0.58	YES
27	PSMD2	PSMD2	PSMD2	4373	0.047	0.59	YES
28	PSMA5	PSMA5	PSMA5	4985	0.039	0.57	YES
29	PSMD6	PSMD6	PSMD6	5043	0.038	0.58	YES
30	PSMB2	PSMB2	PSMB2	5081	0.038	0.6	YES
31	CHEK2	CHEK2	CHEK2	5278	0.035	0.6	YES
32	PSMA1	PSMA1	PSMA1	5433	0.033	0.6	YES
33	PSMF1	PSMF1	PSMF1	5477	0.032	0.61	YES
34	PSMC4	PSMC4	PSMC4	5657	0.03	0.61	YES
35	PSMB10	PSMB10	PSMB10	6021	0.026	0.6	NO
36	PSMB8	PSMB8	PSMB8	6694	0.019	0.57	NO
37	PSMD13	PSMD13	PSMD13	6926	0.017	0.57	NO
38	PSMD8	PSMD8	PSMD8	7460	0.011	0.54	NO
39	PSMC3	PSMC3	PSMC3	7604	0.0099	0.54	NO
40	PSME1	PSME1	PSME1	7765	0.0081	0.53	NO
41	PSMB4	PSMB4	PSMB4	8280	0.0028	0.5	NO
42	ATM	ATM	ATM	8447	0.001	0.5	NO
43	PSMD4	PSMD4	PSMD4	8572	-0.00038	0.49	NO
44	PSMB6	PSMB6	PSMB6	9012	-0.0046	0.47	NO
45	PSMD9	PSMD9	PSMD9	9236	-0.0071	0.46	NO
46	UBA52	UBA52	UBA52	10430	-0.02	0.4	NO
47	RPS27A	RPS27A	RPS27A	11335	-0.03	0.36	NO
48	PSMA8	PSMA8	PSMA8	12721	-0.05	0.3	NO

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

Figure S26. 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: BIOCARTA PROTEASOME 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	PSMD3	PSMD3	PSMD3	564	0.22	0.032	YES
2	PSMD5	PSMD5	PSMD5	1194	0.15	0.041	YES
3	PSMD12	PSMD12	PSMD12	1810	0.11	0.04	YES
4	AKT1	AKT1	AKT1	2021	0.1	0.058	YES
5	PSMA3	PSMA3	PSMA3	2293	0.093	0.071	YES
6	PSME4	PSME4	PSME4	2353	0.091	0.094	YES
7	PSMD7	PSMD7	PSMD7	2399	0.089	0.12	YES
8	PSMC1	PSMC1	PSMC1	2534	0.085	0.14	YES
9	PSMD14	PSMD14	PSMD14	2554	0.085	0.16	YES
10	PSMB3	PSMB3	PSMB3	2605	0.083	0.18	YES
11	PSMA6	PSMA6	PSMA6	2683	0.081	0.2	YES
12	PSMD11	PSMD11	PSMD11	2814	0.078	0.22	YES
13	PSMA7	PSMA7	PSMA7	3137	0.07	0.22	YES
14	PSMB9	PSMB9	PSMB9	3292	0.067	0.23	YES
15	PSMD1	PSMD1	PSMD1	3309	0.066	0.25	YES
16	PSMC6	PSMC6	PSMC6	3326	0.066	0.27	YES
17	PSMB5	PSMB5	PSMB5	3633	0.06	0.27	YES
18	PSME2	PSME2	PSME2	3788	0.057	0.28	YES
19	PSMA2	PSMA2	PSMA2	3927	0.055	0.28	YES
20	HSPA8	HSPA8	HSPA8	4034	0.053	0.3	YES
21	PSMB1	PSMB1	PSMB1	4044	0.053	0.31	YES
22	PSMC5	PSMC5	PSMC5	4128	0.051	0.32	YES
23	PSMC2	PSMC2	PSMC2	4132	0.051	0.34	YES
24	PSMA4	PSMA4	PSMA4	4230	0.05	0.34	YES
25	PSMD10	PSMD10	PSMD10	4256	0.049	0.36	YES
26	PSMB7	PSMB7	PSMB7	4259	0.049	0.37	YES
27	PSMD2	PSMD2	PSMD2	4373	0.047	0.38	YES
28	YWHAB	YWHAB	YWHAB	4652	0.043	0.38	YES
29	PSMA5	PSMA5	PSMA5	4985	0.039	0.37	YES
30	PSMD6	PSMD6	PSMD6	5043	0.038	0.38	YES
31	PSMB2	PSMB2	PSMB2	5081	0.038	0.39	YES
32	YWHAZ	YWHAZ	YWHAZ	5101	0.037	0.4	YES
33	PRKCD	PRKCD	PRKCD	5157	0.036	0.4	YES
34	MAPK14	MAPK14	MAPK14	5246	0.035	0.41	YES
35	EIF4G1	EIF4G1	EIF4G1	5370	0.034	0.41	YES
36	PSMA1	PSMA1	PSMA1	5433	0.033	0.42	YES
37	PSMF1	PSMF1	PSMF1	5477	0.032	0.43	YES
38	TNPO1	TNPO1	TNPO1	5483	0.032	0.44	YES
39	PABPC1	PABPC1	PABPC1	5564	0.031	0.44	YES
40	PSMC4	PSMC4	PSMC4	5657	0.03	0.44	YES
41	ZFP36L1	ZFP36L1	ZFP36L1	5984	0.027	0.43	YES
42	PSMB10	PSMB10	PSMB10	6021	0.026	0.44	YES
43	EXOSC2	EXOSC2	EXOSC2	6098	0.025	0.44	YES
44	TNFSF13	TNFSF13	TNFSF13	6324	0.023	0.44	YES
45	HSPB1	HSPB1	HSPB1	6350	0.022	0.44	YES
46	NUP214	NUP214	NUP214	6470	0.021	0.44	YES
47	EXOSC8	EXOSC8	EXOSC8	6472	0.021	0.45	YES
48	EXOSC6	EXOSC6	EXOSC6	6642	0.02	0.44	YES
49	PSMB8	PSMB8	PSMB8	6694	0.019	0.45	YES
50	MAPK11	MAPK11	MAPK11	6739	0.019	0.45	YES
51	PSMD13	PSMD13	PSMD13	6926	0.017	0.44	NO
52	XPO1	XPO1	XPO1	7119	0.015	0.44	NO
53	DCP2	DCP2	DCP2	7256	0.013	0.44	NO
54	PSMD8	PSMD8	PSMD8	7460	0.011	0.43	NO
55	XRN1	XRN1	XRN1	7490	0.011	0.43	NO
56	PSMC3	PSMC3	PSMC3	7604	0.0099	0.43	NO
57	PSME1	PSME1	PSME1	7765	0.0081	0.42	NO
58	EXOSC1	EXOSC1	EXOSC1	8122	0.0043	0.4	NO
59	PARN	PARN	PARN	8188	0.0036	0.4	NO
60	PSMB4	PSMB4	PSMB4	8280	0.0028	0.4	NO
61	DIS3	DIS3	DIS3	8337	0.0021	0.39	NO
62	PSMD4	PSMD4	PSMD4	8572	-0.00038	0.38	NO
63	EXOSC7	EXOSC7	EXOSC7	8574	-0.00041	0.38	NO
64	KHSRP	KHSRP	KHSRP	8998	-0.0045	0.36	NO
65	PSMB6	PSMB6	PSMB6	9012	-0.0046	0.36	NO
66	PRKCA	PRKCA	PRKCA	9148	-0.0063	0.35	NO
67	PSMD9	PSMD9	PSMD9	9236	-0.0071	0.35	NO
68	EXOSC9	EXOSC9	EXOSC9	9527	-0.01	0.34	NO
69	HNRNPD	HNRNPD	HNRNPD	9576	-0.011	0.34	NO
70	ELAVL1	ELAVL1	ELAVL1	9849	-0.014	0.33	NO
71	MAPKAPK2	MAPKAPK2	MAPKAPK2	9949	-0.015	0.33	NO
72	EXOSC4	EXOSC4	EXOSC4	10147	-0.017	0.32	NO
73	UBA52	UBA52	UBA52	10430	-0.02	0.31	NO
74	ANP32A	ANP32A	ANP32A	10744	-0.024	0.3	NO
75	HSPA1B	HSPA1B	HSPA1B	10865	-0.025	0.3	NO
76	RPS27A	RPS27A	RPS27A	11335	-0.03	0.28	NO
77	DCP1A	DCP1A	DCP1A	12652	-0.048	0.23	NO
78	PSMA8	PSMA8	PSMA8	12721	-0.05	0.24	NO
79	EXOSC3	EXOSC3	EXOSC3	12787	-0.05	0.25	NO
80	ZFP36	ZFP36	ZFP36	13563	-0.064	0.22	NO
81	EXOSC5	EXOSC5	EXOSC5	15644	-0.12	0.14	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 PROTEASOME PATHWAY.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PROTEASOME 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 VEGF 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	PSMD3	PSMD3	PSMD3	564	0.22	0.039	YES
2	PSMD5	PSMD5	PSMD5	1194	0.15	0.052	YES
3	PSMD12	PSMD12	PSMD12	1810	0.11	0.055	YES
4	PSMA3	PSMA3	PSMA3	2293	0.093	0.058	YES
5	PSME4	PSME4	PSME4	2353	0.091	0.085	YES
6	PSMD7	PSMD7	PSMD7	2399	0.089	0.11	YES
7	PSMC1	PSMC1	PSMC1	2534	0.085	0.13	YES
8	PSMD14	PSMD14	PSMD14	2554	0.085	0.16	YES
9	PSMB3	PSMB3	PSMB3	2605	0.083	0.18	YES
10	PSMA6	PSMA6	PSMA6	2683	0.081	0.2	YES
11	PPP2R5E	PPP2R5E	PPP2R5E	2705	0.081	0.23	YES
12	PSMD11	PSMD11	PSMD11	2814	0.078	0.25	YES
13	PSMA7	PSMA7	PSMA7	3137	0.07	0.26	YES
14	PSMB9	PSMB9	PSMB9	3292	0.067	0.27	YES
15	PSMD1	PSMD1	PSMD1	3309	0.066	0.29	YES
16	PSMC6	PSMC6	PSMC6	3326	0.066	0.31	YES
17	PSMB5	PSMB5	PSMB5	3633	0.06	0.31	YES
18	PSME2	PSME2	PSME2	3788	0.057	0.32	YES
19	PSMA2	PSMA2	PSMA2	3927	0.055	0.33	YES
20	PSMB1	PSMB1	PSMB1	4044	0.053	0.34	YES
21	PSMC5	PSMC5	PSMC5	4128	0.051	0.36	YES
22	PSMC2	PSMC2	PSMC2	4132	0.051	0.37	YES
23	PSMA4	PSMA4	PSMA4	4230	0.05	0.38	YES
24	PSMD10	PSMD10	PSMD10	4256	0.049	0.4	YES
25	PSMB7	PSMB7	PSMB7	4259	0.049	0.41	YES
26	PSMD2	PSMD2	PSMD2	4373	0.047	0.42	YES
27	PPP2R1B	PPP2R1B	PPP2R1B	4474	0.046	0.43	YES
28	APC	APC	APC	4494	0.046	0.44	YES
29	PSMA5	PSMA5	PSMA5	4985	0.039	0.43	YES
30	PSMD6	PSMD6	PSMD6	5043	0.038	0.44	YES
31	PSMB2	PSMB2	PSMB2	5081	0.038	0.45	YES
32	PPP2R5C	PPP2R5C	PPP2R5C	5366	0.034	0.45	YES
33	PSMA1	PSMA1	PSMA1	5433	0.033	0.45	YES
34	PSMF1	PSMF1	PSMF1	5477	0.032	0.46	YES
35	PPP2CA	PPP2CA	PPP2CA	5506	0.032	0.47	YES
36	CSNK1A1	CSNK1A1	CSNK1A1	5538	0.032	0.48	YES
37	PSMC4	PSMC4	PSMC4	5657	0.03	0.48	YES
38	PSMB10	PSMB10	PSMB10	6021	0.026	0.47	NO
39	FAM123B	FAM123B	FAM123B	6632	0.02	0.44	NO
40	FRAT2	FRAT2	FRAT2	6647	0.019	0.45	NO
41	PSMB8	PSMB8	PSMB8	6694	0.019	0.45	NO
42	PPP2R5B	PPP2R5B	PPP2R5B	6826	0.018	0.45	NO
43	PSMD13	PSMD13	PSMD13	6926	0.017	0.45	NO
44	PPP2R5D	PPP2R5D	PPP2R5D	6996	0.016	0.45	NO
45	PPP2R1A	PPP2R1A	PPP2R1A	7076	0.015	0.45	NO
46	PSMD8	PSMD8	PSMD8	7460	0.011	0.44	NO
47	PSMC3	PSMC3	PSMC3	7604	0.0099	0.43	NO
48	PPP2CB	PPP2CB	PPP2CB	7764	0.0081	0.42	NO
49	PSME1	PSME1	PSME1	7765	0.0081	0.43	NO
50	PSMB4	PSMB4	PSMB4	8280	0.0028	0.4	NO
51	PSMD4	PSMD4	PSMD4	8572	-0.00038	0.38	NO
52	PSMB6	PSMB6	PSMB6	9012	-0.0046	0.36	NO
53	SKP1	SKP1	SKP1	9192	-0.0066	0.35	NO
54	PSMD9	PSMD9	PSMD9	9236	-0.0071	0.35	NO
55	PPP2R5A	PPP2R5A	PPP2R5A	9369	-0.0086	0.35	NO
56	CUL1	CUL1	CUL1	9525	-0.01	0.34	NO
57	UBA52	UBA52	UBA52	10430	-0.02	0.3	NO
58	CTNNB1	CTNNB1	CTNNB1	10940	-0.026	0.28	NO
59	RPS27A	RPS27A	RPS27A	11335	-0.03	0.27	NO
60	PSMA8	PSMA8	PSMA8	12721	-0.05	0.21	NO
61	AXIN1	AXIN1	AXIN1	13391	-0.061	0.19	NO
62	BTRC	BTRC	BTRC	15434	-0.11	0.12	NO
63	FRAT1	FRAT1	FRAT1	15620	-0.12	0.15	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 VEGF PATHWAY.

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

genes ES table in pathway: PID INTEGRIN3 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	PSMD3	PSMD3	PSMD3	564	0.22	0.012	YES
2	PSMD5	PSMD5	PSMD5	1194	0.15	0.0073	YES
3	CD28	CD28	CD28	1692	0.12	0.0037	YES
4	PSMD12	PSMD12	PSMD12	1810	0.11	0.02	YES
5	DOCK2	DOCK2	DOCK2	2241	0.095	0.015	YES
6	PSMA3	PSMA3	PSMA3	2293	0.093	0.031	YES
7	PSME4	PSME4	PSME4	2353	0.091	0.046	YES
8	PSMD7	PSMD7	PSMD7	2399	0.089	0.062	YES
9	PSMC1	PSMC1	PSMC1	2534	0.085	0.072	YES
10	PSMD14	PSMD14	PSMD14	2554	0.085	0.088	YES
11	PSMB3	PSMB3	PSMB3	2605	0.083	0.1	YES
12	SLC25A5	SLC25A5	SLC25A5	2628	0.083	0.12	YES
13	PSMA6	PSMA6	PSMA6	2683	0.081	0.13	YES
14	PSMD11	PSMD11	PSMD11	2814	0.078	0.14	YES
15	PSMA7	PSMA7	PSMA7	3137	0.07	0.14	YES
16	AP1B1	AP1B1	AP1B1	3264	0.068	0.14	YES
17	PSMB9	PSMB9	PSMB9	3292	0.067	0.15	YES
18	PSMD1	PSMD1	PSMD1	3309	0.066	0.17	YES
19	PSMC6	PSMC6	PSMC6	3326	0.066	0.18	YES
20	PSMB5	PSMB5	PSMB5	3633	0.06	0.18	YES
21	PSME2	PSME2	PSME2	3788	0.057	0.18	YES
22	NUP93	NUP93	NUP93	3868	0.056	0.18	YES
23	LCK	LCK	LCK	3875	0.056	0.2	YES
24	NUP155	NUP155	NUP155	3911	0.055	0.2	YES
25	PSMA2	PSMA2	PSMA2	3927	0.055	0.22	YES
26	AP2S1	AP2S1	AP2S1	3997	0.054	0.22	YES
27	SLC25A4	SLC25A4	SLC25A4	4027	0.053	0.23	YES
28	PSMB1	PSMB1	PSMB1	4044	0.053	0.24	YES
29	CD4	CD4	CD4	4069	0.052	0.25	YES
30	KPNA1	KPNA1	KPNA1	4072	0.052	0.26	YES
31	B2M	B2M	B2M	4082	0.052	0.27	YES
32	PSMC5	PSMC5	PSMC5	4128	0.051	0.28	YES
33	PSMC2	PSMC2	PSMC2	4132	0.051	0.29	YES
34	AP1G1	AP1G1	AP1G1	4142	0.051	0.3	YES
35	CCNT1	CCNT1	CCNT1	4184	0.05	0.31	YES
36	PSMA4	PSMA4	PSMA4	4230	0.05	0.31	YES
37	PSMD10	PSMD10	PSMD10	4256	0.049	0.32	YES
38	PSMB7	PSMB7	PSMB7	4259	0.049	0.33	YES
39	PSMD2	PSMD2	PSMD2	4373	0.047	0.34	YES
40	RAC1	RAC1	RAC1	4504	0.046	0.34	YES
41	HMGA1	HMGA1	HMGA1	4615	0.044	0.34	YES
42	NUP188	NUP188	NUP188	4807	0.041	0.34	YES
43	RAE1	RAE1	RAE1	4856	0.04	0.34	YES
44	PPIA	PPIA	PPIA	4931	0.039	0.35	YES
45	CD247	CD247	CD247	4978	0.039	0.35	YES
46	RCC1	RCC1	RCC1	4980	0.039	0.36	YES
47	PSMA5	PSMA5	PSMA5	4985	0.039	0.37	YES
48	RBX1	RBX1	RBX1	5035	0.038	0.37	YES
49	PSMD6	PSMD6	PSMD6	5043	0.038	0.38	YES
50	PSMB2	PSMB2	PSMB2	5081	0.038	0.39	YES
51	NUP43	NUP43	NUP43	5111	0.037	0.39	YES
52	NUP50	NUP50	NUP50	5208	0.036	0.39	YES
53	AP1S2	AP1S2	AP1S2	5211	0.036	0.4	YES
54	BANF1	BANF1	BANF1	5243	0.035	0.41	YES
55	PACS1	PACS1	PACS1	5417	0.033	0.4	YES
56	PSMA1	PSMA1	PSMA1	5433	0.033	0.41	YES
57	RANBP1	RANBP1	RANBP1	5443	0.032	0.42	YES
58	PSMF1	PSMF1	PSMF1	5477	0.032	0.42	YES
59	ARF1	ARF1	ARF1	5539	0.032	0.42	YES
60	PSMC4	PSMC4	PSMC4	5657	0.03	0.42	YES
61	RAN	RAN	RAN	5713	0.03	0.42	YES
62	RANGAP1	RANGAP1	RANGAP1	5821	0.028	0.42	YES
63	TCEB1	TCEB1	TCEB1	5899	0.028	0.43	YES
64	AP1S1	AP1S1	AP1S1	5903	0.027	0.43	YES
65	RANBP2	RANBP2	RANBP2	5920	0.027	0.44	YES
66	PAK2	PAK2	PAK2	5983	0.027	0.44	YES
67	PSMB10	PSMB10	PSMB10	6021	0.026	0.44	YES
68	NUP205	NUP205	NUP205	6073	0.026	0.44	YES
69	CDK9	CDK9	CDK9	6088	0.026	0.45	YES
70	AP2M1	AP2M1	AP2M1	6328	0.023	0.44	NO
71	NUP214	NUP214	NUP214	6470	0.021	0.44	NO
72	PSMB8	PSMB8	PSMB8	6694	0.019	0.43	NO
73	PSMD13	PSMD13	PSMD13	6926	0.017	0.42	NO
74	NUP37	NUP37	NUP37	6978	0.016	0.42	NO
75	APOBEC3G	APOBEC3G	APOBEC3G	7003	0.016	0.42	NO
76	HCK	HCK	HCK	7044	0.016	0.42	NO
77	XPO1	XPO1	XPO1	7119	0.015	0.42	NO
78	HLA-A	HLA-A	HLA-A	7200	0.014	0.42	NO
79	NUP153	NUP153	NUP153	7328	0.013	0.42	NO
80	PSMD8	PSMD8	PSMD8	7460	0.011	0.41	NO
81	PSMC3	PSMC3	PSMC3	7604	0.0099	0.4	NO
82	PSME1	PSME1	PSME1	7765	0.0081	0.4	NO
83	AP1M2	AP1M2	AP1M2	7851	0.0071	0.39	NO
84	NUP107	NUP107	NUP107	7883	0.0068	0.39	NO
85	NUP85	NUP85	NUP85	7964	0.0058	0.39	NO
86	FYN	FYN	FYN	8113	0.0043	0.38	NO
87	NUP54	NUP54	NUP54	8272	0.0028	0.38	NO
88	AP2A1	AP2A1	AP2A1	8274	0.0028	0.38	NO
89	PSMB4	PSMB4	PSMB4	8280	0.0028	0.38	NO
90	AP1M1	AP1M1	AP1M1	8414	0.0015	0.37	NO
91	NPM1	NPM1	NPM1	8565	-0.00032	0.36	NO
92	PSMD4	PSMD4	PSMD4	8572	-0.00038	0.36	NO
93	CUL5	CUL5	CUL5	8576	-0.00042	0.36	NO
94	NUPL1	NUPL1	NUPL1	8615	-0.00082	0.36	NO
95	NUP35	NUP35	NUP35	8653	-0.0012	0.36	NO
96	PSMB6	PSMB6	PSMB6	9012	-0.0046	0.34	NO
97	TPR	TPR	TPR	9051	-0.0051	0.34	NO
98	ELMO1	ELMO1	ELMO1	9056	-0.0052	0.34	NO
99	SKP1	SKP1	SKP1	9192	-0.0066	0.33	NO
100	KPNB1	KPNB1	KPNB1	9203	-0.0068	0.33	NO
101	PSMD9	PSMD9	PSMD9	9236	-0.0071	0.33	NO
102	SLC25A6	SLC25A6	SLC25A6	9394	-0.0088	0.32	NO
103	TCEB2	TCEB2	TCEB2	9514	-0.01	0.32	NO
104	NUP133	NUP133	NUP133	9676	-0.012	0.31	NO
105	CD8B	CD8B	CD8B	9927	-0.015	0.3	NO
106	UBA52	UBA52	UBA52	10430	-0.02	0.28	NO
107	NUP62	NUP62	NUP62	10436	-0.02	0.28	NO
108	AAAS	AAAS	AAAS	11155	-0.028	0.25	NO
109	AP2A2	AP2A2	AP2A2	11297	-0.03	0.25	NO
110	RPS27A	RPS27A	RPS27A	11335	-0.03	0.25	NO
111	ATP6V1H	ATP6V1H	ATP6V1H	11373	-0.031	0.26	NO
112	POM121	POM121	POM121	11461	-0.032	0.26	NO
113	NUP88	NUP88	NUP88	11501	-0.032	0.26	NO
114	AP2B1	AP2B1	AP2B1	11731	-0.035	0.26	NO
115	PSMA8	PSMA8	PSMA8	12721	-0.05	0.21	NO
116	SEH1L	SEH1L	SEH1L	13047	-0.055	0.2	NO
117	NUPL2	NUPL2	NUPL2	14190	-0.077	0.16	NO
118	NUP210	NUP210	NUP210	14740	-0.091	0.15	NO
119	BTRC	BTRC	BTRC	15434	-0.11	0.13	NO
120	PSIP1	PSIP1	PSIP1	15898	-0.13	0.13	NO

Figure S31. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID INTEGRIN3 PATHWAY.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: PID INTEGRIN3 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME SIGNALING BY WNT

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	PSMD3	PSMD3	PSMD3	564	0.22	0.057	YES
2	PSMD5	PSMD5	PSMD5	1194	0.15	0.082	YES
3	PSMD12	PSMD12	PSMD12	1810	0.11	0.094	YES
4	PSMA3	PSMA3	PSMA3	2293	0.093	0.11	YES
5	PSME4	PSME4	PSME4	2353	0.091	0.14	YES
6	PSMD7	PSMD7	PSMD7	2399	0.089	0.17	YES
7	PSMC1	PSMC1	PSMC1	2534	0.085	0.2	YES
8	PSMD14	PSMD14	PSMD14	2554	0.085	0.24	YES
9	PSMB3	PSMB3	PSMB3	2605	0.083	0.27	YES
10	PSMA6	PSMA6	PSMA6	2683	0.081	0.3	YES
11	PSMD11	PSMD11	PSMD11	2814	0.078	0.32	YES
12	PSMA7	PSMA7	PSMA7	3137	0.07	0.33	YES
13	PSMB9	PSMB9	PSMB9	3292	0.067	0.35	YES
14	PSMD1	PSMD1	PSMD1	3309	0.066	0.38	YES
15	PSMC6	PSMC6	PSMC6	3326	0.066	0.4	YES
16	PSMB5	PSMB5	PSMB5	3633	0.06	0.41	YES
17	PSME2	PSME2	PSME2	3788	0.057	0.42	YES
18	PSMA2	PSMA2	PSMA2	3927	0.055	0.44	YES
19	PSMB1	PSMB1	PSMB1	4044	0.053	0.46	YES
20	PSMC5	PSMC5	PSMC5	4128	0.051	0.47	YES
21	PSMC2	PSMC2	PSMC2	4132	0.051	0.49	YES
22	PSMA4	PSMA4	PSMA4	4230	0.05	0.51	YES
23	PSMD10	PSMD10	PSMD10	4256	0.049	0.53	YES
24	PSMB7	PSMB7	PSMB7	4259	0.049	0.55	YES
25	PSMD2	PSMD2	PSMD2	4373	0.047	0.56	YES
26	PSMA5	PSMA5	PSMA5	4985	0.039	0.54	YES
27	PSMD6	PSMD6	PSMD6	5043	0.038	0.55	YES
28	PSMB2	PSMB2	PSMB2	5081	0.038	0.57	YES
29	RFWD2	RFWD2	RFWD2	5411	0.033	0.56	YES
30	PSMA1	PSMA1	PSMA1	5433	0.033	0.57	YES
31	PSMF1	PSMF1	PSMF1	5477	0.032	0.59	YES
32	PSMC4	PSMC4	PSMC4	5657	0.03	0.59	YES
33	PSMB10	PSMB10	PSMB10	6021	0.026	0.58	NO
34	PSMB8	PSMB8	PSMB8	6694	0.019	0.55	NO
35	PSMD13	PSMD13	PSMD13	6926	0.017	0.54	NO
36	PSMD8	PSMD8	PSMD8	7460	0.011	0.52	NO
37	PSMC3	PSMC3	PSMC3	7604	0.0099	0.52	NO
38	PSME1	PSME1	PSME1	7765	0.0081	0.51	NO
39	PSMB4	PSMB4	PSMB4	8280	0.0028	0.48	NO
40	ATM	ATM	ATM	8447	0.001	0.47	NO
41	PSMD4	PSMD4	PSMD4	8572	-0.00038	0.47	NO
42	PSMB6	PSMB6	PSMB6	9012	-0.0046	0.44	NO
43	PSMD9	PSMD9	PSMD9	9236	-0.0071	0.44	NO
44	UBA52	UBA52	UBA52	10430	-0.02	0.38	NO
45	RPS27A	RPS27A	RPS27A	11335	-0.03	0.34	NO
46	TP53	TP53	TP53	12514	-0.046	0.3	NO
47	PSMA8	PSMA8	PSMA8	12721	-0.05	0.3	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: REACTOME SIGNALING BY WNT.

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

genes ES table in pathway: REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES

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	CDC6	CDC6	CDC6	316	0.27	0.075	YES
2	PSMD3	PSMD3	PSMD3	564	0.22	0.14	YES
3	PSMD5	PSMD5	PSMD5	1194	0.15	0.15	YES
4	MCM8	MCM8	MCM8	1683	0.12	0.17	YES
5	PSMD12	PSMD12	PSMD12	1810	0.11	0.2	YES
6	PSMA3	PSMA3	PSMA3	2293	0.093	0.2	YES
7	PSME4	PSME4	PSME4	2353	0.091	0.23	YES
8	PSMD7	PSMD7	PSMD7	2399	0.089	0.26	YES
9	PSMC1	PSMC1	PSMC1	2534	0.085	0.28	YES
10	PSMD14	PSMD14	PSMD14	2554	0.085	0.31	YES
11	PSMB3	PSMB3	PSMB3	2605	0.083	0.34	YES
12	CDT1	CDT1	CDT1	2669	0.082	0.36	YES
13	PSMA6	PSMA6	PSMA6	2683	0.081	0.39	YES
14	PSMD11	PSMD11	PSMD11	2814	0.078	0.41	YES
15	PSMA7	PSMA7	PSMA7	3137	0.07	0.42	YES
16	PSMB9	PSMB9	PSMB9	3292	0.067	0.43	YES
17	PSMD1	PSMD1	PSMD1	3309	0.066	0.45	YES
18	PSMC6	PSMC6	PSMC6	3326	0.066	0.47	YES
19	GMNN	GMNN	GMNN	3584	0.061	0.48	YES
20	PSMB5	PSMB5	PSMB5	3633	0.06	0.5	YES
21	PSME2	PSME2	PSME2	3788	0.057	0.51	YES
22	PSMA2	PSMA2	PSMA2	3927	0.055	0.52	YES
23	PSMB1	PSMB1	PSMB1	4044	0.053	0.53	YES
24	PSMC5	PSMC5	PSMC5	4128	0.051	0.55	YES
25	PSMC2	PSMC2	PSMC2	4132	0.051	0.56	YES
26	PSMA4	PSMA4	PSMA4	4230	0.05	0.58	YES
27	PSMD10	PSMD10	PSMD10	4256	0.049	0.59	YES
28	PSMB7	PSMB7	PSMB7	4259	0.049	0.61	YES
29	PSMD2	PSMD2	PSMD2	4373	0.047	0.62	YES
30	PSMA5	PSMA5	PSMA5	4985	0.039	0.6	YES
31	PSMD6	PSMD6	PSMD6	5043	0.038	0.61	YES
32	PSMB2	PSMB2	PSMB2	5081	0.038	0.62	YES
33	PSMA1	PSMA1	PSMA1	5433	0.033	0.61	YES
34	PSMF1	PSMF1	PSMF1	5477	0.032	0.62	YES
35	PSMC4	PSMC4	PSMC4	5657	0.03	0.62	YES
36	PSMB10	PSMB10	PSMB10	6021	0.026	0.61	NO
37	PSMB8	PSMB8	PSMB8	6694	0.019	0.58	NO
38	PSMD13	PSMD13	PSMD13	6926	0.017	0.57	NO
39	PSMD8	PSMD8	PSMD8	7460	0.011	0.55	NO
40	PSMC3	PSMC3	PSMC3	7604	0.0099	0.54	NO
41	PSME1	PSME1	PSME1	7765	0.0081	0.54	NO
42	PSMB4	PSMB4	PSMB4	8280	0.0028	0.51	NO
43	PSMD4	PSMD4	PSMD4	8572	-0.00038	0.49	NO
44	PSMB6	PSMB6	PSMB6	9012	-0.0046	0.47	NO
45	PSMD9	PSMD9	PSMD9	9236	-0.0071	0.46	NO
46	UBA52	UBA52	UBA52	10430	-0.02	0.4	NO
47	RPS27A	RPS27A	RPS27A	11335	-0.03	0.36	NO
48	PSMA8	PSMA8	PSMA8	12721	-0.05	0.3	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: REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES.

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

genes ES table in pathway: REACTOME ANTIGEN PROCESSING CROSS PRESENTATION

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	CCNE2	CCNE2	CCNE2	401	0.25	0.059	YES
2	PSMD3	PSMD3	PSMD3	564	0.22	0.12	YES
3	CCNE1	CCNE1	CCNE1	911	0.17	0.16	YES
4	PSMD5	PSMD5	PSMD5	1194	0.15	0.19	YES
5	PSMD12	PSMD12	PSMD12	1810	0.11	0.19	YES
6	PSMA3	PSMA3	PSMA3	2293	0.093	0.2	YES
7	PSME4	PSME4	PSME4	2353	0.091	0.22	YES
8	PSMD7	PSMD7	PSMD7	2399	0.089	0.25	YES
9	PSMC1	PSMC1	PSMC1	2534	0.085	0.27	YES
10	PSMD14	PSMD14	PSMD14	2554	0.085	0.3	YES
11	PSMB3	PSMB3	PSMB3	2605	0.083	0.32	YES
12	PSMA6	PSMA6	PSMA6	2683	0.081	0.34	YES
13	PSMD11	PSMD11	PSMD11	2814	0.078	0.36	YES
14	PSMA7	PSMA7	PSMA7	3137	0.07	0.37	YES
15	PSMB9	PSMB9	PSMB9	3292	0.067	0.38	YES
16	PSMD1	PSMD1	PSMD1	3309	0.066	0.4	YES
17	PSMC6	PSMC6	PSMC6	3326	0.066	0.42	YES
18	PSMB5	PSMB5	PSMB5	3633	0.06	0.43	YES
19	PSME2	PSME2	PSME2	3788	0.057	0.44	YES
20	PSMA2	PSMA2	PSMA2	3927	0.055	0.45	YES
21	PSMB1	PSMB1	PSMB1	4044	0.053	0.46	YES
22	PSMC5	PSMC5	PSMC5	4128	0.051	0.47	YES
23	PSMC2	PSMC2	PSMC2	4132	0.051	0.49	YES
24	PSMA4	PSMA4	PSMA4	4230	0.05	0.5	YES
25	PSMD10	PSMD10	PSMD10	4256	0.049	0.51	YES
26	PSMB7	PSMB7	PSMB7	4259	0.049	0.53	YES
27	PSMD2	PSMD2	PSMD2	4373	0.047	0.54	YES
28	PSMA5	PSMA5	PSMA5	4985	0.039	0.52	YES
29	PSMD6	PSMD6	PSMD6	5043	0.038	0.53	YES
30	PSMB2	PSMB2	PSMB2	5081	0.038	0.54	YES
31	RFWD2	RFWD2	RFWD2	5411	0.033	0.53	YES
32	PSMA1	PSMA1	PSMA1	5433	0.033	0.54	YES
33	PSMF1	PSMF1	PSMF1	5477	0.032	0.55	YES
34	PSMC4	PSMC4	PSMC4	5657	0.03	0.55	YES
35	PSMB10	PSMB10	PSMB10	6021	0.026	0.54	NO
36	CDK2	CDK2	CDK2	6097	0.025	0.54	NO
37	PSMB8	PSMB8	PSMB8	6694	0.019	0.52	NO
38	PSMD13	PSMD13	PSMD13	6926	0.017	0.51	NO
39	PSMD8	PSMD8	PSMD8	7460	0.011	0.48	NO
40	PSMC3	PSMC3	PSMC3	7604	0.0099	0.48	NO
41	PSME1	PSME1	PSME1	7765	0.0081	0.47	NO
42	CDKN1A	CDKN1A	CDKN1A	8156	0.0039	0.45	NO
43	PSMB4	PSMB4	PSMB4	8280	0.0028	0.44	NO
44	ATM	ATM	ATM	8447	0.001	0.44	NO
45	PSMD4	PSMD4	PSMD4	8572	-0.00038	0.43	NO
46	PSMB6	PSMB6	PSMB6	9012	-0.0046	0.41	NO
47	PSMD9	PSMD9	PSMD9	9236	-0.0071	0.4	NO
48	UBA52	UBA52	UBA52	10430	-0.02	0.34	NO
49	RPS27A	RPS27A	RPS27A	11335	-0.03	0.3	NO
50	TP53	TP53	TP53	12514	-0.046	0.25	NO
51	PSMA8	PSMA8	PSMA8	12721	-0.05	0.25	NO
52	MDM2	MDM2	MDM2	13009	-0.054	0.26	NO
53	CDKN1B	CDKN1B	CDKN1B	15055	-0.1	0.18	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: REACTOME ANTIGEN PROCESSING CROSS PRESENTATION.

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

genes ES table in pathway: REACTOME ER PHAGOSOME PATHWAY

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	PSMD3	PSMD3	PSMD3	564	0.22	0.03	YES
2	UBE2C	UBE2C	UBE2C	1085	0.16	0.046	YES
3	PSMD5	PSMD5	PSMD5	1194	0.15	0.081	YES
4	CDK1	CDK1	CDK1	1353	0.14	0.11	YES
5	BUB1B	BUB1B	BUB1B	1455	0.13	0.14	YES
6	PTTG1	PTTG1	PTTG1	1744	0.11	0.16	YES
7	CDC20	CDC20	CDC20	1785	0.11	0.19	YES
8	PSMD12	PSMD12	PSMD12	1810	0.11	0.22	YES
9	CCNB1	CCNB1	CCNB1	1865	0.11	0.25	YES
10	PSMA3	PSMA3	PSMA3	2293	0.093	0.25	YES
11	PSME4	PSME4	PSME4	2353	0.091	0.27	YES
12	PSMD7	PSMD7	PSMD7	2399	0.089	0.3	YES
13	PSMC1	PSMC1	PSMC1	2534	0.085	0.31	YES
14	PSMD14	PSMD14	PSMD14	2554	0.085	0.34	YES
15	PSMB3	PSMB3	PSMB3	2605	0.083	0.36	YES
16	PSMA6	PSMA6	PSMA6	2683	0.081	0.38	YES
17	MAD2L1	MAD2L1	MAD2L1	2744	0.08	0.39	YES
18	PSMD11	PSMD11	PSMD11	2814	0.078	0.41	YES
19	UBE2D1	UBE2D1	UBE2D1	2840	0.078	0.43	YES
20	PSMA7	PSMA7	PSMA7	3137	0.07	0.44	YES
21	PSMB9	PSMB9	PSMB9	3292	0.067	0.45	YES
22	PSMD1	PSMD1	PSMD1	3309	0.066	0.46	YES
23	PSMC6	PSMC6	PSMC6	3326	0.066	0.48	YES
24	PSMB5	PSMB5	PSMB5	3633	0.06	0.48	YES
25	PSME2	PSME2	PSME2	3788	0.057	0.49	YES
26	PSMA2	PSMA2	PSMA2	3927	0.055	0.5	YES
27	PSMB1	PSMB1	PSMB1	4044	0.053	0.51	YES
28	PSMC5	PSMC5	PSMC5	4128	0.051	0.52	YES
29	PSMC2	PSMC2	PSMC2	4132	0.051	0.53	YES
30	PSMA4	PSMA4	PSMA4	4230	0.05	0.54	YES
31	PSMD10	PSMD10	PSMD10	4256	0.049	0.55	YES
32	PSMB7	PSMB7	PSMB7	4259	0.049	0.57	YES
33	PSMD2	PSMD2	PSMD2	4373	0.047	0.57	YES
34	CDC26	CDC26	CDC26	4833	0.041	0.56	YES
35	PSMA5	PSMA5	PSMA5	4985	0.039	0.56	YES
36	PSMD6	PSMD6	PSMD6	5043	0.038	0.57	YES
37	PSMB2	PSMB2	PSMB2	5081	0.038	0.58	YES
38	PSMA1	PSMA1	PSMA1	5433	0.033	0.57	NO
39	PSMF1	PSMF1	PSMF1	5477	0.032	0.58	NO
40	PSMC4	PSMC4	PSMC4	5657	0.03	0.57	NO
41	PSMB10	PSMB10	PSMB10	6021	0.026	0.56	NO
42	ANAPC7	ANAPC7	ANAPC7	6560	0.02	0.54	NO
43	PSMB8	PSMB8	PSMB8	6694	0.019	0.54	NO
44	PSMD13	PSMD13	PSMD13	6926	0.017	0.53	NO
45	PSMD8	PSMD8	PSMD8	7460	0.011	0.5	NO
46	ANAPC1	ANAPC1	ANAPC1	7526	0.011	0.5	NO
47	PSMC3	PSMC3	PSMC3	7604	0.0099	0.5	NO
48	UBE2E1	UBE2E1	UBE2E1	7718	0.0086	0.5	NO
49	PSME1	PSME1	PSME1	7765	0.0081	0.5	NO
50	CDC23	CDC23	CDC23	7774	0.0081	0.5	NO
51	BUB3	BUB3	BUB3	8144	0.004	0.48	NO
52	PSMB4	PSMB4	PSMB4	8280	0.0028	0.47	NO
53	PSMD4	PSMD4	PSMD4	8572	-0.00038	0.46	NO
54	ANAPC10	ANAPC10	ANAPC10	8764	-0.0024	0.45	NO
55	PSMB6	PSMB6	PSMB6	9012	-0.0046	0.44	NO
56	PSMD9	PSMD9	PSMD9	9236	-0.0071	0.42	NO
57	ANAPC2	ANAPC2	ANAPC2	9395	-0.0088	0.42	NO
58	ANAPC11	ANAPC11	ANAPC11	9719	-0.012	0.4	NO
59	ANAPC5	ANAPC5	ANAPC5	9905	-0.014	0.4	NO
60	UBA52	UBA52	UBA52	10430	-0.02	0.38	NO
61	CDC16	CDC16	CDC16	10883	-0.025	0.36	NO
62	RPS27A	RPS27A	RPS27A	11335	-0.03	0.34	NO
63	CDC27	CDC27	CDC27	11403	-0.031	0.35	NO
64	PSMA8	PSMA8	PSMA8	12721	-0.05	0.29	NO
65	ANAPC4	ANAPC4	ANAPC4	13444	-0.062	0.26	NO

Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ER PHAGOSOME PATHWAY.

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

Fold change

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

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
KEGG FATTY ACID METABOLISM	39	genes.ES.table	0.59	1.8	0	0.11	0.57	0.38	0.24	0.29	0.031	0.015
KEGG STEROID HORMONE BIOSYNTHESIS	41	genes.ES.table	0.57	1.4	0.076	0.22	1	0.63	0.29	0.45	0.16	0.002
KEGG PURINE METABOLISM	153	genes.ES.table	0.39	1.7	0.0021	0.13	0.85	0.18	0.17	0.15	0.053	0.01
KEGG TYROSINE METABOLISM	40	genes.ES.table	0.63	1.7	0.008	0.13	0.88	0.35	0.091	0.32	0.058	0.007
KEGG O GLYCAN BIOSYNTHESIS	28	genes.ES.table	0.57	1.5	0.033	0.17	0.98	0.46	0.24	0.36	0.11	0.001
KEGG INOSITOL PHOSPHATE METABOLISM	53	genes.ES.table	0.37	1.4	0.075	0.23	1	0.26	0.25	0.2	0.17	0.001
KEGG GLYCEROPHOSPHOLIPID METABOLISM	71	genes.ES.table	0.49	1.8	0	0.11	0.56	0.44	0.3	0.3	0.03	0.017
KEGG ETHER LIPID METABOLISM	28	genes.ES.table	0.52	1.5	0.052	0.18	0.99	0.57	0.3	0.4	0.12	0.001
KEGG ARACHIDONIC ACID METABOLISM	50	genes.ES.table	0.54	1.4	0.05	0.2	1	0.54	0.26	0.4	0.13	0.001
KEGG BUTANOATE METABOLISM	30	genes.ES.table	0.51	1.5	0.059	0.19	0.99	0.33	0.24	0.25	0.12	0.001

genes ES table in pathway: KEGG FATTY ACID METABOLISM

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	GFAP	GFAP	GFAP	18	0.85	0.089	YES
2	NRG1	NRG1	NRG1	94	0.7	0.16	YES
3	NRG2	NRG2	NRG2	253	0.55	0.21	YES
4	PGR	PGR	PGR	549	0.44	0.24	YES
5	EGFR	EGFR	EGFR	662	0.41	0.28	YES
6	S100B	S100B	S100B	999	0.35	0.3	YES
7	ERBB4	ERBB4	ERBB4	1109	0.33	0.32	YES
8	EGF	EGF	EGF	1694	0.26	0.32	YES
9	EREG	EREG	EREG	1695	0.26	0.35	YES
10	CXCL12	CXCL12	CXCL12	1996	0.24	0.36	YES
11	AKT3	AKT3	AKT3	2006	0.24	0.38	YES
12	FOXO1	FOXO1	FOXO1	2015	0.24	0.41	YES
13	GHR	GHR	GHR	2059	0.24	0.43	YES
14	NR4A1	NR4A1	NR4A1	2213	0.22	0.44	YES
15	PIK3R1	PIK3R1	PIK3R1	2460	0.21	0.45	YES
16	ESR1	ESR1	ESR1	2807	0.19	0.45	YES
17	FOXO4	FOXO4	FOXO4	3250	0.16	0.45	YES
18	GH1	GH1	GH1	3416	0.16	0.45	YES
19	NEDD4	NEDD4	NEDD4	3857	0.14	0.44	YES
20	STAT5A	STAT5A	STAT5A	3932	0.14	0.46	YES
21	HBEGF	HBEGF	HBEGF	3950	0.14	0.47	YES
22	YAP1	YAP1	YAP1	3961	0.14	0.48	YES
23	APH1B	APH1B	APH1B	3995	0.13	0.5	YES
24	BTC	BTC	BTC	4418	0.12	0.48	YES
25	STAT5B	STAT5B	STAT5B	4441	0.12	0.5	YES
26	JAK2	JAK2	JAK2	4537	0.12	0.5	YES
27	PRLR	PRLR	PRLR	4864	0.1	0.5	NO
28	FOXO3	FOXO3	FOXO3	5512	0.086	0.47	NO
29	RICTOR	RICTOR	RICTOR	5990	0.076	0.45	NO
30	BTRC	BTRC	BTRC	6249	0.07	0.44	NO
31	PTEN	PTEN	PTEN	6361	0.068	0.45	NO
32	CASP9	CASP9	CASP9	6428	0.067	0.45	NO
33	CDKN1B	CDKN1B	CDKN1B	6544	0.065	0.45	NO
34	ERBB3	ERBB3	ERBB3	6649	0.063	0.45	NO
35	CREB1	CREB1	CREB1	7195	0.053	0.43	NO
36	CDKN1A	CDKN1A	CDKN1A	7488	0.048	0.42	NO
37	PIK3CA	PIK3CA	PIK3CA	7603	0.047	0.41	NO
38	WWP1	WWP1	WWP1	7620	0.046	0.42	NO
39	NCOR1	NCOR1	NCOR1	7632	0.046	0.42	NO
40	PHLPP1	PHLPP1	PHLPP1	8131	0.038	0.4	NO
41	ADAM17	ADAM17	ADAM17	8389	0.034	0.39	NO
42	RPS27A	RPS27A	RPS27A	8555	0.032	0.38	NO
43	TAB2	TAB2	TAB2	8616	0.031	0.38	NO
44	PDPK1	PDPK1	PDPK1	8838	0.028	0.37	NO
45	MTOR	MTOR	MTOR	9043	0.026	0.37	NO
46	SHC1	SHC1	SHC1	9127	0.024	0.36	NO
47	SKP1	SKP1	SKP1	9199	0.024	0.36	NO
48	SH2B1	SH2B1	SH2B1	9406	0.021	0.35	NO
49	PSEN1	PSEN1	PSEN1	9697	0.018	0.34	NO
50	THEM4	THEM4	THEM4	10129	0.012	0.32	NO
51	TSC2	TSC2	TSC2	10208	0.011	0.31	NO
52	SOS1	SOS1	SOS1	10229	0.011	0.31	NO
53	MAPK1	MAPK1	MAPK1	10356	0.0092	0.31	NO
54	BAD	BAD	BAD	10804	0.004	0.28	NO
55	AKT2	AKT2	AKT2	10984	0.0022	0.27	NO
56	MAPK3	MAPK3	MAPK3	11179	-0.00013	0.26	NO
57	MDM2	MDM2	MDM2	11185	-0.00018	0.26	NO
58	WWOX	WWOX	WWOX	11421	-0.0031	0.25	NO
59	NRAS	NRAS	NRAS	11512	-0.0041	0.25	NO
60	MAPKAP1	MAPKAP1	MAPKAP1	11721	-0.0066	0.24	NO
61	GRB2	GRB2	GRB2	12115	-0.012	0.22	NO
62	RAF1	RAF1	RAF1	12270	-0.014	0.21	NO
63	UBA52	UBA52	UBA52	12325	-0.014	0.21	NO
64	AKT1	AKT1	AKT1	12363	-0.015	0.21	NO
65	CHUK	CHUK	CHUK	12459	-0.016	0.2	NO
66	MAP2K2	MAP2K2	MAP2K2	12523	-0.017	0.2	NO
67	KRAS	KRAS	KRAS	12738	-0.02	0.19	NO
68	PRL	PRL	PRL	12782	-0.02	0.19	NO
69	CUL1	CUL1	CUL1	12930	-0.022	0.18	NO
70	YWHAB	YWHAB	YWHAB	12933	-0.022	0.19	NO
71	NCSTN	NCSTN	NCSTN	13003	-0.023	0.19	NO
72	AKT1S1	AKT1S1	AKT1S1	13211	-0.026	0.18	NO
73	APH1A	APH1A	APH1A	13493	-0.03	0.16	NO
74	GSK3A	GSK3A	GSK3A	13784	-0.035	0.15	NO
75	PSEN2	PSEN2	PSEN2	14077	-0.039	0.14	NO
76	TRIB3	TRIB3	TRIB3	14364	-0.043	0.13	NO
77	MAP2K1	MAP2K1	MAP2K1	14607	-0.048	0.12	NO
78	NRG4	NRG4	NRG4	14668	-0.049	0.12	NO
79	PSENEN	PSENEN	PSENEN	14912	-0.053	0.12	NO
80	MLST8	MLST8	MLST8	15131	-0.056	0.11	NO
81	HRAS	HRAS	HRAS	16142	-0.081	0.062	NO
82	RBX1	RBX1	RBX1	16161	-0.082	0.07	NO
83	RPS6KB2	RPS6KB2	RPS6KB2	16368	-0.089	0.068	NO
84	CDK1	CDK1	CDK1	18137	-0.34	0.0076	NO

Figure S41. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FATTY ACID METABOLISM.

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

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	PAK7	PAK7	PAK7	2	1.3	0.38	YES
2	SLIT2	SLIT2	SLIT2	557	0.44	0.49	YES
3	ROBO3	ROBO3	ROBO3	559	0.43	0.62	YES
4	CAP2	CAP2	CAP2	4339	0.12	0.45	NO
5	SRGAP3	SRGAP3	SRGAP3	5012	0.1	0.44	NO
6	EVL	EVL	EVL	5077	0.098	0.47	NO
7	ROBO1	ROBO1	ROBO1	5099	0.098	0.5	NO
8	SOS2	SOS2	SOS2	6199	0.072	0.46	NO
9	GPC1	GPC1	GPC1	6282	0.07	0.48	NO
10	ABL1	ABL1	ABL1	6357	0.068	0.5	NO
11	PAK6	PAK6	PAK6	6807	0.06	0.49	NO
12	NCK2	NCK2	NCK2	8356	0.035	0.42	NO
13	SRGAP1	SRGAP1	SRGAP1	8417	0.034	0.42	NO
14	ROBO2	ROBO2	ROBO2	8574	0.032	0.42	NO
15	CDC42	CDC42	CDC42	9207	0.023	0.4	NO
16	CLASP1	CLASP1	CLASP1	9318	0.022	0.4	NO
17	ABL2	ABL2	ABL2	9721	0.017	0.38	NO
18	SOS1	SOS1	SOS1	10229	0.011	0.36	NO
19	ENAH	ENAH	ENAH	10728	0.0048	0.33	NO
20	CAP1	CAP1	CAP1	10794	0.0041	0.33	NO
21	VASP	VASP	VASP	11676	-0.0062	0.28	NO
22	NCK1	NCK1	NCK1	11706	-0.0064	0.28	NO
23	PAK2	PAK2	PAK2	12225	-0.013	0.26	NO
24	RAC1	RAC1	RAC1	12462	-0.016	0.25	NO
25	PAK4	PAK4	PAK4	13228	-0.026	0.22	NO
26	PAK1	PAK1	PAK1	13459	-0.03	0.21	NO
27	SRGAP2	SRGAP2	SRGAP2	14789	-0.05	0.16	NO
28	PFN2	PFN2	PFN2	14870	-0.052	0.17	NO
29	PFN1	PFN1	PFN1	15607	-0.066	0.15	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 STEROID HORMONE BIOSYNTHESIS.

Figure S44. 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 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	PAK7	PAK7	PAK7	2	1.3	0.18	YES
2	FIGF	FIGF	FIGF	306	0.52	0.23	YES
3	PAK3	PAK3	PAK3	367	0.49	0.3	YES
4	HGF	HGF	HGF	524	0.44	0.35	YES
5	MET	MET	MET	867	0.37	0.38	YES
6	TGFB2	TGFB2	TGFB2	1427	0.29	0.39	YES
7	TGFB3	TGFB3	TGFB3	1768	0.26	0.41	YES
8	AKT3	AKT3	AKT3	2006	0.24	0.43	YES
9	PIK3R1	PIK3R1	PIK3R1	2460	0.21	0.44	YES
10	PIK3CG	PIK3CG	PIK3CG	2960	0.18	0.43	YES
11	VEGFC	VEGFC	VEGFC	3217	0.17	0.44	YES
12	PGF	PGF	PGF	3291	0.16	0.46	YES
13	EPAS1	EPAS1	EPAS1	3452	0.16	0.48	YES
14	PIK3CD	PIK3CD	PIK3CD	3458	0.16	0.5	YES
15	JUN	JUN	JUN	3526	0.15	0.51	YES
16	ETS1	ETS1	ETS1	3938	0.14	0.51	NO
17	TGFA	TGFA	TGFA	4468	0.12	0.5	NO
18	GAB1	GAB1	GAB1	4671	0.11	0.5	NO
19	TGFB1	TGFB1	TGFB1	5927	0.077	0.44	NO
20	SOS2	SOS2	SOS2	6199	0.072	0.44	NO
21	PAK6	PAK6	PAK6	6807	0.06	0.42	NO
22	FLCN	FLCN	FLCN	6928	0.058	0.42	NO
23	CREBBP	CREBBP	CREBBP	7238	0.052	0.41	NO
24	RAPGEF1	RAPGEF1	RAPGEF1	7252	0.052	0.41	NO
25	PIK3CA	PIK3CA	PIK3CA	7603	0.047	0.4	NO
26	CRK	CRK	CRK	7745	0.044	0.4	NO
27	EP300	EP300	EP300	8058	0.039	0.39	NO
28	ARNT2	ARNT2	ARNT2	8081	0.039	0.39	NO
29	ARNT	ARNT	ARNT	8460	0.033	0.38	NO
30	PIK3R5	PIK3R5	PIK3R5	8967	0.026	0.35	NO
31	PIK3R3	PIK3R3	PIK3R3	9088	0.025	0.35	NO
32	CDC42	CDC42	CDC42	9207	0.023	0.34	NO
33	EGLN3	EGLN3	EGLN3	9791	0.016	0.32	NO
34	VHL	VHL	VHL	9823	0.016	0.32	NO
35	RAP1A	RAP1A	RAP1A	10087	0.012	0.3	NO
36	SOS1	SOS1	SOS1	10229	0.011	0.3	NO
37	VEGFB	VEGFB	VEGFB	10330	0.0094	0.29	NO
38	MAPK1	MAPK1	MAPK1	10356	0.0092	0.29	NO
39	RAP1B	RAP1B	RAP1B	10462	0.0079	0.29	NO
40	BRAF	BRAF	BRAF	10508	0.0072	0.29	NO
41	PDGFB	PDGFB	PDGFB	10788	0.0042	0.27	NO
42	ARAF	ARAF	ARAF	10940	0.0027	0.26	NO
43	AKT2	AKT2	AKT2	10984	0.0022	0.26	NO
44	PIK3R2	PIK3R2	PIK3R2	11037	0.0017	0.26	NO
45	CRKL	CRKL	CRKL	11176	-0.000069	0.25	NO
46	MAPK3	MAPK3	MAPK3	11179	-0.00013	0.25	NO
47	NRAS	NRAS	NRAS	11512	-0.0041	0.23	NO
48	HIF1A	HIF1A	HIF1A	11868	-0.009	0.22	NO
49	GRB2	GRB2	GRB2	12115	-0.012	0.2	NO
50	PAK2	PAK2	PAK2	12225	-0.013	0.2	NO
51	PTPN11	PTPN11	PTPN11	12242	-0.013	0.2	NO
52	RAF1	RAF1	RAF1	12270	-0.014	0.2	NO
53	EGLN2	EGLN2	EGLN2	12289	-0.014	0.2	NO
54	AKT1	AKT1	AKT1	12363	-0.015	0.2	NO
55	RAC1	RAC1	RAC1	12462	-0.016	0.2	NO
56	MAP2K2	MAP2K2	MAP2K2	12523	-0.017	0.2	NO
57	KRAS	KRAS	KRAS	12738	-0.02	0.19	NO
58	PIK3CB	PIK3CB	PIK3CB	12931	-0.022	0.18	NO
59	PAK4	PAK4	PAK4	13228	-0.026	0.17	NO
60	PAK1	PAK1	PAK1	13459	-0.03	0.16	NO
61	EGLN1	EGLN1	EGLN1	13930	-0.037	0.14	NO
62	CUL2	CUL2	CUL2	14204	-0.041	0.13	NO
63	MAP2K1	MAP2K1	MAP2K1	14607	-0.048	0.11	NO
64	SLC2A1	SLC2A1	SLC2A1	15674	-0.068	0.064	NO
65	TCEB2	TCEB2	TCEB2	15817	-0.071	0.066	NO
66	FH	FH	FH	16132	-0.08	0.06	NO
67	HRAS	HRAS	HRAS	16142	-0.081	0.071	NO
68	RBX1	RBX1	RBX1	16161	-0.082	0.082	NO
69	VEGFA	VEGFA	VEGFA	16658	-0.1	0.068	NO
70	TCEB1	TCEB1	TCEB1	17292	-0.14	0.054	NO

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

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

genes ES table in pathway: KEGG TYROSINE 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	PAK7	PAK7	PAK7	2	1.3	0.2	YES
2	NRG1	NRG1	NRG1	94	0.7	0.3	YES
3	NRG2	NRG2	NRG2	253	0.55	0.38	YES
4	LAMA2	LAMA2	LAMA2	356	0.5	0.45	YES
5	PAK3	PAK3	PAK3	367	0.49	0.53	YES
6	DMD	DMD	DMD	372	0.49	0.61	YES
7	EGFR	EGFR	EGFR	662	0.41	0.66	YES
8	LAMA3	LAMA3	LAMA3	706	0.4	0.72	YES
9	UTRN	UTRN	UTRN	3068	0.17	0.62	NO
10	CHRM1	CHRM1	CHRM1	3404	0.16	0.62	NO
11	JUN	JUN	JUN	3526	0.15	0.64	NO
12	ITGA1	ITGA1	ITGA1	4890	0.1	0.58	NO
13	MAPK8	MAPK8	MAPK8	5445	0.088	0.57	NO
14	LAMA4	LAMA4	LAMA4	5988	0.076	0.55	NO
15	PAK6	PAK6	PAK6	6807	0.06	0.51	NO
16	PXN	PXN	PXN	7170	0.053	0.5	NO
17	SP1	SP1	SP1	7500	0.048	0.49	NO
18	GIT2	GIT2	GIT2	7735	0.044	0.48	NO
19	NRG3	NRG3	NRG3	8511	0.032	0.45	NO
20	ITGB1	ITGB1	ITGB1	8661	0.03	0.44	NO
21	CDC42	CDC42	CDC42	9207	0.023	0.42	NO
22	DAG1	DAG1	DAG1	9478	0.02	0.41	NO
23	MUSK	MUSK	MUSK	9919	0.015	0.38	NO
24	MAPK1	MAPK1	MAPK1	10356	0.0092	0.36	NO
25	MAPK3	MAPK3	MAPK3	11179	-0.00013	0.32	NO
26	ACTA1	ACTA1	ACTA1	11184	-0.00017	0.32	NO
27	DVL1	DVL1	DVL1	11459	-0.0035	0.3	NO
28	PAK2	PAK2	PAK2	12225	-0.013	0.26	NO
29	RAC1	RAC1	RAC1	12462	-0.016	0.25	NO
30	CTTN	CTTN	CTTN	12597	-0.018	0.25	NO
31	PAK4	PAK4	PAK4	13228	-0.026	0.22	NO
32	PAK1	PAK1	PAK1	13459	-0.03	0.21	NO
33	SRC	SRC	SRC	13795	-0.035	0.2	NO
34	PTK2	PTK2	PTK2	14263	-0.042	0.18	NO
35	RAPSN	RAPSN	RAPSN	16289	-0.086	0.08	NO
36	CHRNA1	CHRNA1	CHRNA1	17582	-0.18	0.038	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 TYROSINE METABOLISM.

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

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

Table 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	CALML3	CALML3	CALML3	30	0.8	0.061	YES
2	NGFR	NGFR	NGFR	69	0.73	0.12	YES
3	NTF4	NTF4	NTF4	78	0.72	0.17	YES
4	NTRK3	NTRK3	NTRK3	176	0.6	0.21	YES
5	NTRK2	NTRK2	NTRK2	276	0.54	0.25	YES
6	SHC4	SHC4	SHC4	1219	0.32	0.22	YES
7	IRAK3	IRAK3	IRAK3	1309	0.3	0.24	YES
8	NTF3	NTF3	NTF3	1337	0.3	0.26	YES
9	NTRK1	NTRK1	NTRK1	1804	0.25	0.26	YES
10	CAMK4	CAMK4	CAMK4	1829	0.25	0.28	YES
11	NGF	NGF	NGF	1838	0.25	0.3	YES
12	AKT3	AKT3	AKT3	2006	0.24	0.31	YES
13	IRS1	IRS1	IRS1	2040	0.24	0.32	YES
14	SHC2	SHC2	SHC2	2269	0.22	0.33	YES
15	PIK3R1	PIK3R1	PIK3R1	2460	0.21	0.33	YES
16	RPS6KA6	RPS6KA6	RPS6KA6	2527	0.2	0.35	YES
17	BDNF	BDNF	BDNF	2544	0.2	0.36	YES
18	RPS6KA5	RPS6KA5	RPS6KA5	2620	0.2	0.37	YES
19	MAP3K1	MAP3K1	MAP3K1	2660	0.2	0.39	YES
20	BCL2	BCL2	BCL2	2771	0.19	0.4	YES
21	RPS6KA2	RPS6KA2	RPS6KA2	2855	0.18	0.4	YES
22	CAMK2B	CAMK2B	CAMK2B	2923	0.18	0.42	YES
23	PIK3CG	PIK3CG	PIK3CG	2960	0.18	0.43	YES
24	IRS2	IRS2	IRS2	3297	0.16	0.42	YES
25	IRS4	IRS4	IRS4	3328	0.16	0.43	YES
26	PIK3CD	PIK3CD	PIK3CD	3458	0.16	0.44	YES
27	JUN	JUN	JUN	3526	0.15	0.44	YES
28	TP73	TP73	TP73	3602	0.15	0.45	YES
29	RPS6KA3	RPS6KA3	RPS6KA3	3638	0.15	0.46	YES
30	CAMK2A	CAMK2A	CAMK2A	3645	0.15	0.47	YES
31	MAPK10	MAPK10	MAPK10	4457	0.12	0.44	NO
32	IRAK2	IRAK2	IRAK2	4610	0.11	0.44	NO
33	PLCG2	PLCG2	PLCG2	4632	0.11	0.45	NO
34	GAB1	GAB1	GAB1	4671	0.11	0.45	NO
35	CAMK2D	CAMK2D	CAMK2D	5370	0.09	0.42	NO
36	MAPK8	MAPK8	MAPK8	5445	0.088	0.42	NO
37	MAP3K3	MAP3K3	MAP3K3	5455	0.088	0.43	NO
38	FRS2	FRS2	FRS2	5482	0.087	0.44	NO
39	FOXO3	FOXO3	FOXO3	5512	0.086	0.44	NO
40	MAP2K5	MAP2K5	MAP2K5	5730	0.082	0.44	NO
41	MAPK11	MAPK11	MAPK11	5795	0.08	0.44	NO
42	SOS2	SOS2	SOS2	6199	0.072	0.42	NO
43	ABL1	ABL1	ABL1	6357	0.068	0.42	NO
44	KIDINS220	KIDINS220	KIDINS220	6553	0.065	0.41	NO
45	SH2B3	SH2B3	SH2B3	6657	0.063	0.41	NO
46	ARHGDIB	ARHGDIB	ARHGDIB	6669	0.062	0.42	NO
47	ZNF274	ZNF274	ZNF274	6749	0.061	0.42	NO
48	TRAF6	TRAF6	TRAF6	6890	0.058	0.41	NO
49	MAP3K5	MAP3K5	MAP3K5	7048	0.056	0.41	NO
50	NFKB1	NFKB1	NFKB1	7062	0.055	0.41	NO
51	RAPGEF1	RAPGEF1	RAPGEF1	7252	0.052	0.41	NO
52	IKBKB	IKBKB	IKBKB	7374	0.05	0.4	NO
53	PIK3CA	PIK3CA	PIK3CA	7603	0.047	0.4	NO
54	CRK	CRK	CRK	7745	0.044	0.39	NO
55	PRDM4	PRDM4	PRDM4	7980	0.041	0.38	NO
56	FASLG	FASLG	FASLG	8037	0.04	0.38	NO
57	TP53	TP53	TP53	8372	0.035	0.37	NO
58	MAPK7	MAPK7	MAPK7	8554	0.032	0.36	NO
59	NGFRAP1	NGFRAP1	NGFRAP1	8781	0.029	0.35	NO
60	PIK3R5	PIK3R5	PIK3R5	8967	0.026	0.34	NO
61	NFKBIA	NFKBIA	NFKBIA	9018	0.026	0.34	NO
62	PIK3R3	PIK3R3	PIK3R3	9088	0.025	0.34	NO
63	SHC1	SHC1	SHC1	9127	0.024	0.34	NO
64	CDC42	CDC42	CDC42	9207	0.023	0.34	NO
65	SH2B1	SH2B1	SH2B1	9406	0.021	0.33	NO
66	CALML6	CALML6	CALML6	9523	0.02	0.32	NO
67	IRAK4	IRAK4	IRAK4	9603	0.019	0.32	NO
68	PSEN1	PSEN1	PSEN1	9697	0.018	0.31	NO
69	RPS6KA1	RPS6KA1	RPS6KA1	10002	0.014	0.3	NO
70	RAP1A	RAP1A	RAP1A	10087	0.012	0.3	NO
71	RELA	RELA	RELA	10108	0.012	0.3	NO
72	SOS1	SOS1	SOS1	10229	0.011	0.29	NO
73	MAPK1	MAPK1	MAPK1	10356	0.0092	0.28	NO
74	MAP2K7	MAP2K7	MAP2K7	10374	0.0091	0.28	NO
75	RAP1B	RAP1B	RAP1B	10462	0.0079	0.28	NO
76	BRAF	BRAF	BRAF	10508	0.0072	0.28	NO
77	BAD	BAD	BAD	10804	0.004	0.26	NO
78	MAPK14	MAPK14	MAPK14	10858	0.0034	0.26	NO
79	AKT2	AKT2	AKT2	10984	0.0022	0.25	NO
80	PIK3R2	PIK3R2	PIK3R2	11037	0.0017	0.25	NO
81	PLCG1	PLCG1	PLCG1	11071	0.0013	0.25	NO
82	CRKL	CRKL	CRKL	11176	-0.000069	0.24	NO
83	MAPK3	MAPK3	MAPK3	11179	-0.00013	0.24	NO
84	RHOA	RHOA	RHOA	11358	-0.0023	0.23	NO
85	CAMK2G	CAMK2G	CAMK2G	11456	-0.0035	0.23	NO
86	NRAS	NRAS	NRAS	11512	-0.0041	0.22	NO
87	RPS6KA4	RPS6KA4	RPS6KA4	12060	-0.011	0.19	NO
88	SORT1	SORT1	SORT1	12102	-0.012	0.19	NO
89	GRB2	GRB2	GRB2	12115	-0.012	0.19	NO
90	PTPN11	PTPN11	PTPN11	12242	-0.013	0.19	NO
91	MAPK9	MAPK9	MAPK9	12246	-0.013	0.19	NO
92	RAF1	RAF1	RAF1	12270	-0.014	0.19	NO
93	AKT1	AKT1	AKT1	12363	-0.015	0.18	NO
94	RAC1	RAC1	RAC1	12462	-0.016	0.18	NO
95	CALM3	CALM3	CALM3	12482	-0.016	0.18	NO
96	MAP2K2	MAP2K2	MAP2K2	12523	-0.017	0.18	NO
97	GSK3B	GSK3B	GSK3B	12638	-0.018	0.17	NO
98	MAPKAPK2	MAPKAPK2	MAPKAPK2	12646	-0.018	0.18	NO
99	KRAS	KRAS	KRAS	12738	-0.02	0.17	NO
100	PIK3CB	PIK3CB	PIK3CB	12931	-0.022	0.16	NO
101	YWHAB	YWHAB	YWHAB	12933	-0.022	0.16	NO
102	CALML5	CALML5	CALML5	13088	-0.024	0.16	NO
103	YWHAQ	YWHAQ	YWHAQ	13306	-0.028	0.15	NO
104	MAGED1	MAGED1	MAGED1	13329	-0.028	0.15	NO
105	YWHAE	YWHAE	YWHAE	13595	-0.032	0.14	NO
106	CALM1	CALM1	CALM1	13680	-0.033	0.14	NO
107	CSK	CSK	CSK	13805	-0.035	0.13	NO
108	CALM2	CALM2	CALM2	13837	-0.036	0.13	NO
109	ATF4	ATF4	ATF4	14131	-0.04	0.12	NO
110	PRKCD	PRKCD	PRKCD	14248	-0.042	0.12	NO
111	ARHGDIA	ARHGDIA	ARHGDIA	14258	-0.042	0.12	NO
112	MAP2K1	MAP2K1	MAP2K1	14607	-0.048	0.1	NO
113	YWHAH	YWHAH	YWHAH	14662	-0.048	0.1	NO
114	MAPK13	MAPK13	MAPK13	14963	-0.054	0.092	NO
115	YWHAG	YWHAG	YWHAG	15336	-0.06	0.076	NO
116	NFKBIB	NFKBIB	NFKBIB	15571	-0.066	0.068	NO
117	SHC3	SHC3	SHC3	15704	-0.069	0.066	NO
118	BAX	BAX	BAX	15784	-0.07	0.068	NO
119	IRAK1	IRAK1	IRAK1	15829	-0.072	0.071	NO
120	NFKBIE	NFKBIE	NFKBIE	15841	-0.072	0.076	NO
121	HRAS	HRAS	HRAS	16142	-0.081	0.066	NO
122	YWHAZ	YWHAZ	YWHAZ	16278	-0.086	0.065	NO
123	MAPK12	MAPK12	MAPK12	17127	-0.13	0.028	NO
124	RIPK2	RIPK2	RIPK2	17269	-0.14	0.032	NO
125	SH2B2	SH2B2	SH2B2	17326	-0.15	0.04	NO
126	PDK1	PDK1	PDK1	17340	-0.15	0.052	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 O GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG INOSITOL PHOSPHATE 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	ADCYAP1R1	ADCYAP1R1	ADCYAP1R1	179	0.6	0.04	YES
2	NTRK2	NTRK2	NTRK2	276	0.54	0.08	YES
3	PDE1A	PDE1A	PDE1A	325	0.51	0.12	YES
4	ADCY5	ADCY5	ADCY5	384	0.49	0.16	YES
5	ADCY4	ADCY4	ADCY4	921	0.36	0.16	YES
6	ADCY2	ADCY2	ADCY2	1301	0.31	0.16	YES
7	ADCYAP1	ADCYAP1	ADCYAP1	1431	0.29	0.18	YES
8	DUSP4	DUSP4	DUSP4	1525	0.28	0.2	YES
9	PRKCA	PRKCA	PRKCA	1614	0.27	0.22	YES
10	NTRK1	NTRK1	NTRK1	1804	0.25	0.23	YES
11	CAMK4	CAMK4	CAMK4	1829	0.25	0.25	YES
12	NGF	NGF	NGF	1838	0.25	0.27	YES
13	AKT3	AKT3	AKT3	2006	0.24	0.28	YES
14	FOXO1	FOXO1	FOXO1	2015	0.24	0.3	YES
15	IRS1	IRS1	IRS1	2040	0.24	0.32	YES
16	NR4A1	NR4A1	NR4A1	2213	0.22	0.32	YES
17	SHC2	SHC2	SHC2	2269	0.22	0.34	YES
18	PIK3R1	PIK3R1	PIK3R1	2460	0.21	0.35	YES
19	DUSP6	DUSP6	DUSP6	2610	0.2	0.36	YES
20	RPS6KA5	RPS6KA5	RPS6KA5	2620	0.2	0.37	YES
21	PDE1B	PDE1B	PDE1B	2713	0.19	0.38	YES
22	ADCY1	ADCY1	ADCY1	2804	0.19	0.39	YES
23	RPS6KA2	RPS6KA2	RPS6KA2	2855	0.18	0.4	YES
24	MEF2C	MEF2C	MEF2C	3018	0.18	0.41	YES
25	FOXO4	FOXO4	FOXO4	3250	0.16	0.41	YES
26	IRS2	IRS2	IRS2	3297	0.16	0.42	YES
27	DNM1	DNM1	DNM1	3342	0.16	0.43	YES
28	RPS6KA3	RPS6KA3	RPS6KA3	3638	0.15	0.43	NO
29	ITPR2	ITPR2	ITPR2	4508	0.12	0.39	NO
30	PRKCE	PRKCE	PRKCE	4553	0.11	0.4	NO
31	PRKAR1B	PRKAR1B	PRKAR1B	4825	0.11	0.39	NO
32	PRKACB	PRKACB	PRKACB	5133	0.097	0.38	NO
33	ADCY9	ADCY9	ADCY9	5391	0.09	0.38	NO
34	PRKAR2A	PRKAR2A	PRKAR2A	5422	0.089	0.38	NO
35	FRS2	FRS2	FRS2	5482	0.087	0.39	NO
36	FOXO3	FOXO3	FOXO3	5512	0.086	0.39	NO
37	MAP2K5	MAP2K5	MAP2K5	5730	0.082	0.39	NO
38	MAPK11	MAPK11	MAPK11	5795	0.08	0.39	NO
39	RICTOR	RICTOR	RICTOR	5990	0.076	0.39	NO
40	PTEN	PTEN	PTEN	6361	0.068	0.37	NO
41	CASP9	CASP9	CASP9	6428	0.067	0.37	NO
42	ADORA2A	ADORA2A	ADORA2A	6453	0.067	0.38	NO
43	CDKN1B	CDKN1B	CDKN1B	6544	0.065	0.38	NO
44	KIDINS220	KIDINS220	KIDINS220	6553	0.065	0.38	NO
45	ADCY6	ADCY6	ADCY6	6875	0.058	0.37	NO
46	MEF2A	MEF2A	MEF2A	6902	0.058	0.37	NO
47	PRKAR2B	PRKAR2B	PRKAR2B	7083	0.055	0.37	NO
48	ATF1	ATF1	ATF1	7123	0.054	0.37	NO
49	CREB1	CREB1	CREB1	7195	0.053	0.37	NO
50	RAPGEF1	RAPGEF1	RAPGEF1	7252	0.052	0.37	NO
51	PPP2CB	PPP2CB	PPP2CB	7290	0.051	0.38	NO
52	STAT3	STAT3	STAT3	7371	0.05	0.38	NO
53	CDKN1A	CDKN1A	CDKN1A	7488	0.048	0.37	NO
54	RALGDS	RALGDS	RALGDS	7537	0.048	0.37	NO
55	RALB	RALB	RALB	7553	0.048	0.38	NO
56	PIK3CA	PIK3CA	PIK3CA	7603	0.047	0.38	NO
57	DUSP7	DUSP7	DUSP7	7610	0.046	0.38	NO
58	CRK	CRK	CRK	7745	0.044	0.38	NO
59	PHLPP1	PHLPP1	PHLPP1	8131	0.038	0.36	NO
60	DUSP3	DUSP3	DUSP3	8351	0.035	0.35	NO
61	ADCY3	ADCY3	ADCY3	8385	0.034	0.35	NO
62	MAPK7	MAPK7	MAPK7	8554	0.032	0.34	NO
63	AP2B1	AP2B1	AP2B1	8688	0.03	0.34	NO
64	PRKAR1A	PRKAR1A	PRKAR1A	8730	0.03	0.34	NO
65	PDPK1	PDPK1	PDPK1	8838	0.028	0.34	NO
66	MTOR	MTOR	MTOR	9043	0.026	0.33	NO
67	SHC1	SHC1	SHC1	9127	0.024	0.32	NO
68	RPS6KA1	RPS6KA1	RPS6KA1	10002	0.014	0.28	NO
69	AP2A2	AP2A2	AP2A2	10046	0.013	0.28	NO
70	RAP1A	RAP1A	RAP1A	10087	0.012	0.28	NO
71	THEM4	THEM4	THEM4	10129	0.012	0.28	NO
72	TSC2	TSC2	TSC2	10208	0.011	0.27	NO
73	SOS1	SOS1	SOS1	10229	0.011	0.27	NO
74	MAPK1	MAPK1	MAPK1	10356	0.0092	0.26	NO
75	BRAF	BRAF	BRAF	10508	0.0072	0.26	NO
76	BAD	BAD	BAD	10804	0.004	0.24	NO
77	MAPK14	MAPK14	MAPK14	10858	0.0034	0.24	NO
78	AKT2	AKT2	AKT2	10984	0.0022	0.23	NO
79	PIK3R2	PIK3R2	PIK3R2	11037	0.0017	0.23	NO
80	PLCG1	PLCG1	PLCG1	11071	0.0013	0.23	NO
81	MAPK3	MAPK3	MAPK3	11179	-0.00013	0.22	NO
82	MDM2	MDM2	MDM2	11185	-0.00018	0.22	NO
83	RHOA	RHOA	RHOA	11358	-0.0023	0.21	NO
84	ADCY8	ADCY8	ADCY8	11495	-0.0039	0.2	NO
85	NRAS	NRAS	NRAS	11512	-0.0041	0.2	NO
86	RIT1	RIT1	RIT1	11533	-0.0044	0.2	NO
87	PPP2CA	PPP2CA	PPP2CA	11573	-0.0048	0.2	NO
88	MAPKAPK3	MAPKAPK3	MAPKAPK3	11594	-0.005	0.2	NO
89	MAPKAP1	MAPKAP1	MAPKAP1	11721	-0.0066	0.2	NO
90	PRKACA	PRKACA	PRKACA	11749	-0.007	0.19	NO
91	GRB2	GRB2	GRB2	12115	-0.012	0.18	NO
92	RALA	RALA	RALA	12188	-0.013	0.17	NO
93	RAF1	RAF1	RAF1	12270	-0.014	0.17	NO
94	DNAL4	DNAL4	DNAL4	12291	-0.014	0.17	NO
95	AKT1	AKT1	AKT1	12363	-0.015	0.17	NO
96	PPP2R1A	PPP2R1A	PPP2R1A	12413	-0.015	0.16	NO
97	CHUK	CHUK	CHUK	12459	-0.016	0.16	NO
98	CALM3	CALM3	CALM3	12482	-0.016	0.16	NO
99	MAP2K2	MAP2K2	MAP2K2	12523	-0.017	0.16	NO
100	DNM2	DNM2	DNM2	12561	-0.017	0.16	NO
101	ADRBK1	ADRBK1	ADRBK1	12603	-0.018	0.16	NO
102	MAPKAPK2	MAPKAPK2	MAPKAPK2	12646	-0.018	0.16	NO
103	KRAS	KRAS	KRAS	12738	-0.02	0.16	NO
104	AP2A1	AP2A1	AP2A1	12793	-0.02	0.16	NO
105	PIK3CB	PIK3CB	PIK3CB	12931	-0.022	0.15	NO
106	YWHAB	YWHAB	YWHAB	12933	-0.022	0.15	NO
107	ELK1	ELK1	ELK1	12985	-0.023	0.15	NO
108	AKT1S1	AKT1S1	AKT1S1	13211	-0.026	0.14	NO
109	CLTC	CLTC	CLTC	13430	-0.029	0.13	NO
110	AP2M1	AP2M1	AP2M1	13512	-0.031	0.13	NO
111	CALM1	CALM1	CALM1	13680	-0.033	0.12	NO
112	GSK3A	GSK3A	GSK3A	13784	-0.035	0.12	NO
113	SRC	SRC	SRC	13795	-0.035	0.12	NO
114	CALM2	CALM2	CALM2	13837	-0.036	0.12	NO
115	ADCY7	ADCY7	ADCY7	14085	-0.039	0.11	NO
116	PRKCD	PRKCD	PRKCD	14248	-0.042	0.11	NO
117	CLTA	CLTA	CLTA	14359	-0.043	0.1	NO
118	TRIB3	TRIB3	TRIB3	14364	-0.043	0.11	NO
119	ITPR3	ITPR3	ITPR3	14501	-0.046	0.1	NO
120	MAP2K1	MAP2K1	MAP2K1	14607	-0.048	0.1	NO
121	PPP2R1B	PPP2R1B	PPP2R1B	14690	-0.049	0.1	NO
122	PPP2R5D	PPP2R5D	PPP2R5D	14793	-0.05	0.1	NO
123	MAPK13	MAPK13	MAPK13	14963	-0.054	0.096	NO
124	MLST8	MLST8	MLST8	15131	-0.056	0.092	NO
125	AP2S1	AP2S1	AP2S1	15677	-0.068	0.067	NO
126	SHC3	SHC3	SHC3	15704	-0.069	0.072	NO
127	SH3GL2	SH3GL2	SH3GL2	15992	-0.077	0.062	NO
128	HRAS	HRAS	HRAS	16142	-0.081	0.061	NO
129	RPS6KB2	RPS6KB2	RPS6KB2	16368	-0.089	0.056	NO
130	PRKCG	PRKCG	PRKCG	16911	-0.12	0.035	NO
131	MAPK12	MAPK12	MAPK12	17127	-0.13	0.034	NO
132	CDK1	CDK1	CDK1	18137	-0.34	0.0077	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 INOSITOL PHOSPHATE METABOLISM.

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

genes ES table in pathway: KEGG GLYCEROPHOSPHOLIPID METABOLISM

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	WIF1	WIF1	WIF1	91	0.7	0.15	YES
2	SFRP1	SFRP1	SFRP1	195	0.59	0.28	YES
3	DKK2	DKK2	DKK2	1121	0.33	0.3	YES
4	NKD2	NKD2	NKD2	1192	0.32	0.37	YES
5	DKK3	DKK3	DKK3	1771	0.26	0.4	YES
6	AKT3	AKT3	AKT3	2006	0.24	0.44	YES
7	AXIN2	AXIN2	AXIN2	2062	0.23	0.49	YES
8	ANKRD6	ANKRD6	ANKRD6	2137	0.23	0.54	YES
9	NKD1	NKD1	NKD1	2632	0.2	0.56	YES
10	DACT1	DACT1	DACT1	2703	0.19	0.59	YES
11	CXXC4	CXXC4	CXXC4	2986	0.18	0.62	YES
12	LRP1	LRP1	LRP1	3332	0.16	0.64	YES
13	DKK4	DKK4	DKK4	3544	0.15	0.66	YES
14	FSTL1	FSTL1	FSTL1	3802	0.14	0.68	YES
15	FRAT1	FRAT1	FRAT1	6080	0.074	0.57	NO
16	CTNNB1	CTNNB1	CTNNB1	6678	0.062	0.55	NO
17	APC	APC	APC	6711	0.062	0.56	NO
18	DKK1	DKK1	DKK1	8182	0.037	0.49	NO
19	PTPRA	PTPRA	PTPRA	8256	0.036	0.49	NO
20	CSNK1A1	CSNK1A1	CSNK1A1	8435	0.034	0.49	NO
21	MVP	MVP	MVP	8446	0.033	0.5	NO
22	PSEN1	PSEN1	PSEN1	9697	0.018	0.44	NO
23	CBY1	CBY1	CBY1	10367	0.0091	0.4	NO
24	AKT2	AKT2	AKT2	10984	0.0022	0.37	NO
25	RPSA	RPSA	RPSA	11345	-0.0022	0.35	NO
26	DVL1	DVL1	DVL1	11459	-0.0035	0.34	NO
27	SENP2	SENP2	SENP2	11752	-0.0071	0.33	NO
28	AKT1	AKT1	AKT1	12363	-0.015	0.3	NO
29	PIN1	PIN1	PIN1	12582	-0.018	0.29	NO
30	GSK3B	GSK3B	GSK3B	12638	-0.018	0.29	NO
31	GSK3A	GSK3A	GSK3A	13784	-0.035	0.24	NO
32	AXIN1	AXIN1	AXIN1	14534	-0.046	0.2	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 GLYCEROPHOSPHOLIPID METABOLISM.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCEROPHOSPHOLIPID 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 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	PAK7	PAK7	PAK7	2	1.3	0.15	YES
2	IGF1	IGF1	IGF1	221	0.57	0.2	YES
3	F2RL2	F2RL2	F2RL2	344	0.5	0.26	YES
4	PAK3	PAK3	PAK3	367	0.49	0.32	YES
5	MET	MET	MET	867	0.37	0.33	YES
6	ERBB4	ERBB4	ERBB4	1109	0.33	0.36	YES
7	SLC2A4	SLC2A4	SLC2A4	1413	0.29	0.38	YES
8	CREB5	CREB5	CREB5	1569	0.28	0.4	YES
9	AKT3	AKT3	AKT3	2006	0.24	0.4	YES
10	IRS1	IRS1	IRS1	2040	0.24	0.43	YES
11	IGFBP1	IGFBP1	IGFBP1	2162	0.23	0.45	YES
12	RPS6KA2	RPS6KA2	RPS6KA2	2855	0.18	0.44	YES
13	IRS2	IRS2	IRS2	3297	0.16	0.43	YES
14	IRS4	IRS4	IRS4	3328	0.16	0.45	YES
15	PIK3CD	PIK3CD	PIK3CD	3458	0.16	0.46	YES
16	RPS6KA3	RPS6KA3	RPS6KA3	3638	0.15	0.47	YES
17	GADD45A	GADD45A	GADD45A	3760	0.14	0.48	YES
18	CYTH3	CYTH3	CYTH3	3842	0.14	0.49	YES
19	PREX1	PREX1	PREX1	3943	0.14	0.5	YES
20	GAB1	GAB1	GAB1	4671	0.11	0.47	NO
21	MYC	MYC	MYC	4873	0.1	0.48	NO
22	FOXO3	FOXO3	FOXO3	5512	0.086	0.45	NO
23	SOS2	SOS2	SOS2	6199	0.072	0.42	NO
24	PTEN	PTEN	PTEN	6361	0.068	0.42	NO
25	CDKN1B	CDKN1B	CDKN1B	6544	0.065	0.42	NO
26	PAK6	PAK6	PAK6	6807	0.06	0.41	NO
27	TSC1	TSC1	TSC1	6888	0.058	0.41	NO
28	PPP1R13B	PPP1R13B	PPP1R13B	7137	0.054	0.41	NO
29	CREB1	CREB1	CREB1	7195	0.053	0.41	NO
30	PIK3CA	PIK3CA	PIK3CA	7603	0.047	0.39	NO
31	PARD3	PARD3	PARD3	8254	0.036	0.36	NO
32	SFN	SFN	SFN	8773	0.029	0.34	NO
33	PIK3R5	PIK3R5	PIK3R5	8967	0.026	0.33	NO
34	MTOR	MTOR	MTOR	9043	0.026	0.33	NO
35	SHC1	SHC1	SHC1	9127	0.024	0.32	NO
36	CDC42	CDC42	CDC42	9207	0.023	0.32	NO
37	RPS6KA1	RPS6KA1	RPS6KA1	10002	0.014	0.28	NO
38	TSC2	TSC2	TSC2	10208	0.011	0.27	NO
39	SOS1	SOS1	SOS1	10229	0.011	0.27	NO
40	BCL2L1	BCL2L1	BCL2L1	10575	0.0064	0.25	NO
41	BAD	BAD	BAD	10804	0.004	0.24	NO
42	AKT2	AKT2	AKT2	10984	0.0022	0.23	NO
43	CREB3	CREB3	CREB3	11671	-0.0061	0.2	NO
44	RPS6KB1	RPS6KB1	RPS6KB1	11853	-0.0087	0.19	NO
45	INPPL1	INPPL1	INPPL1	11909	-0.0095	0.18	NO
46	GRB2	GRB2	GRB2	12115	-0.012	0.18	NO
47	PAK2	PAK2	PAK2	12225	-0.013	0.17	NO
48	AKT1	AKT1	AKT1	12363	-0.015	0.16	NO
49	GSK3B	GSK3B	GSK3B	12638	-0.018	0.15	NO
50	YWHAB	YWHAB	YWHAB	12933	-0.022	0.14	NO
51	PAK4	PAK4	PAK4	13228	-0.026	0.12	NO
52	YWHAQ	YWHAQ	YWHAQ	13306	-0.028	0.12	NO
53	PAK1	PAK1	PAK1	13459	-0.03	0.12	NO
54	YWHAE	YWHAE	YWHAE	13595	-0.032	0.12	NO
55	GSK3A	GSK3A	GSK3A	13784	-0.035	0.11	NO
56	NOLC1	NOLC1	NOLC1	14047	-0.038	0.1	NO
57	PTK2	PTK2	PTK2	14263	-0.042	0.093	NO
58	YWHAH	YWHAH	YWHAH	14662	-0.048	0.077	NO
59	PTPN1	PTPN1	PTPN1	14982	-0.054	0.066	NO
60	YWHAG	YWHAG	YWHAG	15336	-0.06	0.054	NO
61	CDK2	CDK2	CDK2	15530	-0.065	0.051	NO
62	YWHAZ	YWHAZ	YWHAZ	16278	-0.086	0.02	NO
63	PARD6A	PARD6A	PARD6A	16315	-0.087	0.028	NO
64	IFI27	IFI27	IFI27	17277	-0.14	-0.0075	NO
65	EBP	EBP	EBP	17317	-0.15	0.008	NO
66	PDK1	PDK1	PDK1	17340	-0.15	0.025	NO
67	CDKN2A	CDKN2A	CDKN2A	17841	-0.22	0.024	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 ETHER LIPID METABOLISM.

Figure S56. 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 ARACHIDONIC ACID METABOLISM

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	IGF1	IGF1	IGF1	221	0.57	0.11	YES
2	FIGF	FIGF	FIGF	306	0.52	0.22	YES
3	AKT3	AKT3	AKT3	2006	0.24	0.18	YES
4	PRKAA2	PRKAA2	PRKAA2	2256	0.22	0.22	YES
5	PIK3R1	PIK3R1	PIK3R1	2460	0.21	0.25	YES
6	RPS6KA6	RPS6KA6	RPS6KA6	2527	0.2	0.29	YES
7	CAB39L	CAB39L	CAB39L	2808	0.19	0.32	YES
8	RPS6KA2	RPS6KA2	RPS6KA2	2855	0.18	0.36	YES
9	PIK3CG	PIK3CG	PIK3CG	2960	0.18	0.39	YES
10	VEGFC	VEGFC	VEGFC	3217	0.17	0.41	YES
11	PGF	PGF	PGF	3291	0.16	0.44	YES
12	PIK3CD	PIK3CD	PIK3CD	3458	0.16	0.47	YES
13	RPS6KA3	RPS6KA3	RPS6KA3	3638	0.15	0.49	YES
14	PRKAA1	PRKAA1	PRKAA1	4699	0.11	0.46	NO
15	RICTOR	RICTOR	RICTOR	5990	0.076	0.4	NO
16	EIF4B	EIF4B	EIF4B	6819	0.059	0.37	NO
17	TSC1	TSC1	TSC1	6888	0.058	0.38	NO
18	RPS6	RPS6	RPS6	7516	0.048	0.36	NO
19	PIK3CA	PIK3CA	PIK3CA	7603	0.047	0.36	NO
20	CAB39	CAB39	CAB39	8441	0.033	0.32	NO
21	PDPK1	PDPK1	PDPK1	8838	0.028	0.31	NO
22	PIK3R5	PIK3R5	PIK3R5	8967	0.026	0.3	NO
23	MTOR	MTOR	MTOR	9043	0.026	0.31	NO
24	PIK3R3	PIK3R3	PIK3R3	9088	0.025	0.31	NO
25	STK11	STK11	STK11	9104	0.025	0.31	NO
26	RPS6KA1	RPS6KA1	RPS6KA1	10002	0.014	0.27	NO
27	TSC2	TSC2	TSC2	10208	0.011	0.26	NO
28	VEGFB	VEGFB	VEGFB	10330	0.0094	0.26	NO
29	MAPK1	MAPK1	MAPK1	10356	0.0092	0.26	NO
30	BRAF	BRAF	BRAF	10508	0.0072	0.25	NO
31	ULK2	ULK2	ULK2	10752	0.0046	0.24	NO
32	AKT2	AKT2	AKT2	10984	0.0022	0.22	NO
33	PIK3R2	PIK3R2	PIK3R2	11037	0.0017	0.22	NO
34	MAPK3	MAPK3	MAPK3	11179	-0.00013	0.21	NO
35	ULK1	ULK1	ULK1	11199	-0.00031	0.21	NO
36	STRADA	STRADA	STRADA	11419	-0.003	0.2	NO
37	DDIT4	DDIT4	DDIT4	11668	-0.006	0.19	NO
38	RPS6KB1	RPS6KB1	RPS6KB1	11853	-0.0087	0.18	NO
39	HIF1A	HIF1A	HIF1A	11868	-0.009	0.18	NO
40	RPTOR	RPTOR	RPTOR	12227	-0.013	0.17	NO
41	AKT1	AKT1	AKT1	12363	-0.015	0.16	NO
42	EIF4E	EIF4E	EIF4E	12655	-0.018	0.15	NO
43	EIF4E2	EIF4E2	EIF4E2	12811	-0.02	0.14	NO
44	ULK3	ULK3	ULK3	12883	-0.022	0.15	NO
45	PIK3CB	PIK3CB	PIK3CB	12931	-0.022	0.15	NO
46	MLST8	MLST8	MLST8	15131	-0.056	0.04	NO
47	RHEB	RHEB	RHEB	16150	-0.081	0.0021	NO
48	RPS6KB2	RPS6KB2	RPS6KB2	16368	-0.089	0.0097	NO
49	VEGFA	VEGFA	VEGFA	16658	-0.1	0.016	NO
50	EIF4E1B	EIF4E1B	EIF4E1B	17132	-0.13	0.019	NO
51	EIF4EBP1	EIF4EBP1	EIF4EBP1	17718	-0.2	0.031	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 ARACHIDONIC ACID METABOLISM.

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

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	PDE1A	PDE1A	PDE1A	325	0.51	0.025	YES
2	KL	KL	KL	328	0.51	0.068	YES
3	FGF2	FGF2	FGF2	361	0.5	0.11	YES
4	ADCY5	ADCY5	ADCY5	384	0.49	0.15	YES
5	FGF1	FGF1	FGF1	432	0.47	0.18	YES
6	SPRY2	SPRY2	SPRY2	567	0.43	0.21	YES
7	FGF19	FGF19	FGF19	578	0.43	0.25	YES
8	FGF18	FGF18	FGF18	611	0.42	0.28	YES
9	FGF7	FGF7	FGF7	869	0.37	0.3	YES
10	ADCY4	ADCY4	ADCY4	921	0.36	0.33	YES
11	IL17RD	IL17RD	IL17RD	938	0.36	0.36	YES
12	FGF9	FGF9	FGF9	1176	0.32	0.37	YES
13	ADCY2	ADCY2	ADCY2	1301	0.31	0.39	YES
14	PRKCA	PRKCA	PRKCA	1614	0.27	0.4	YES
15	CAMK4	CAMK4	CAMK4	1829	0.25	0.4	YES
16	AKT3	AKT3	AKT3	2006	0.24	0.42	YES
17	FOXO1	FOXO1	FOXO1	2015	0.24	0.43	YES
18	FGF20	FGF20	FGF20	2176	0.23	0.44	YES
19	NR4A1	NR4A1	NR4A1	2213	0.22	0.46	YES
20	FGF17	FGF17	FGF17	2347	0.22	0.47	YES
21	PIK3R1	PIK3R1	PIK3R1	2460	0.21	0.48	YES
22	PDE1B	PDE1B	PDE1B	2713	0.19	0.49	YES
23	ADCY1	ADCY1	ADCY1	2804	0.19	0.5	YES
24	FOXO4	FOXO4	FOXO4	3250	0.16	0.49	YES
25	KLB	KLB	KLB	3254	0.16	0.5	YES
26	FGF10	FGF10	FGF10	3335	0.16	0.51	YES
27	FGFR2	FGFR2	FGFR2	3834	0.14	0.49	NO
28	ITPR2	ITPR2	ITPR2	4508	0.12	0.47	NO
29	PRKCE	PRKCE	PRKCE	4553	0.11	0.47	NO
30	GAB1	GAB1	GAB1	4671	0.11	0.48	NO
31	FGFR1	FGFR1	FGFR1	4709	0.11	0.48	NO
32	PRKAR1B	PRKAR1B	PRKAR1B	4825	0.11	0.49	NO
33	PRKACB	PRKACB	PRKACB	5133	0.097	0.48	NO
34	ADCY9	ADCY9	ADCY9	5391	0.09	0.47	NO
35	PRKAR2A	PRKAR2A	PRKAR2A	5422	0.089	0.48	NO
36	FRS2	FRS2	FRS2	5482	0.087	0.48	NO
37	FOXO3	FOXO3	FOXO3	5512	0.086	0.49	NO
38	RICTOR	RICTOR	RICTOR	5990	0.076	0.47	NO
39	FGFR4	FGFR4	FGFR4	6337	0.069	0.45	NO
40	PTEN	PTEN	PTEN	6361	0.068	0.46	NO
41	CASP9	CASP9	CASP9	6428	0.067	0.46	NO
42	CDKN1B	CDKN1B	CDKN1B	6544	0.065	0.46	NO
43	ADCY6	ADCY6	ADCY6	6875	0.058	0.44	NO
44	FGFR3	FGFR3	FGFR3	6991	0.056	0.44	NO
45	PRKAR2B	PRKAR2B	PRKAR2B	7083	0.055	0.44	NO
46	CREB1	CREB1	CREB1	7195	0.053	0.44	NO
47	PPP2CB	PPP2CB	PPP2CB	7290	0.051	0.44	NO
48	CDKN1A	CDKN1A	CDKN1A	7488	0.048	0.43	NO
49	PIK3CA	PIK3CA	PIK3CA	7603	0.047	0.43	NO
50	CBL	CBL	CBL	7884	0.042	0.42	NO
51	PHLPP1	PHLPP1	PHLPP1	8131	0.038	0.41	NO
52	ADCY3	ADCY3	ADCY3	8385	0.034	0.4	NO
53	RPS27A	RPS27A	RPS27A	8555	0.032	0.39	NO
54	PRKAR1A	PRKAR1A	PRKAR1A	8730	0.03	0.38	NO
55	PDPK1	PDPK1	PDPK1	8838	0.028	0.38	NO
56	MKNK1	MKNK1	MKNK1	8976	0.026	0.38	NO
57	MTOR	MTOR	MTOR	9043	0.026	0.37	NO
58	SHC1	SHC1	SHC1	9127	0.024	0.37	NO
59	FGF22	FGF22	FGF22	9973	0.014	0.33	NO
60	THEM4	THEM4	THEM4	10129	0.012	0.32	NO
61	TSC2	TSC2	TSC2	10208	0.011	0.32	NO
62	SOS1	SOS1	SOS1	10229	0.011	0.32	NO
63	MAPK1	MAPK1	MAPK1	10356	0.0092	0.31	NO
64	BRAF	BRAF	BRAF	10508	0.0072	0.3	NO
65	BAD	BAD	BAD	10804	0.004	0.28	NO
66	AKT2	AKT2	AKT2	10984	0.0022	0.28	NO
67	PLCG1	PLCG1	PLCG1	11071	0.0013	0.27	NO
68	MAPK3	MAPK3	MAPK3	11179	-0.00013	0.26	NO
69	MDM2	MDM2	MDM2	11185	-0.00018	0.26	NO
70	ADCY8	ADCY8	ADCY8	11495	-0.0039	0.25	NO
71	NRAS	NRAS	NRAS	11512	-0.0041	0.25	NO
72	FRS3	FRS3	FRS3	11519	-0.0042	0.25	NO
73	PPP2CA	PPP2CA	PPP2CA	11573	-0.0048	0.24	NO
74	MAPKAP1	MAPKAP1	MAPKAP1	11721	-0.0066	0.24	NO
75	PRKACA	PRKACA	PRKACA	11749	-0.007	0.24	NO
76	GRB2	GRB2	GRB2	12115	-0.012	0.22	NO
77	RAF1	RAF1	RAF1	12270	-0.014	0.21	NO
78	UBA52	UBA52	UBA52	12325	-0.014	0.21	NO
79	AKT1	AKT1	AKT1	12363	-0.015	0.21	NO
80	PPP2R1A	PPP2R1A	PPP2R1A	12413	-0.015	0.21	NO
81	CHUK	CHUK	CHUK	12459	-0.016	0.2	NO
82	CALM3	CALM3	CALM3	12482	-0.016	0.21	NO
83	MAP2K2	MAP2K2	MAP2K2	12523	-0.017	0.2	NO
84	ADRBK1	ADRBK1	ADRBK1	12603	-0.018	0.2	NO
85	KRAS	KRAS	KRAS	12738	-0.02	0.2	NO
86	YWHAB	YWHAB	YWHAB	12933	-0.022	0.19	NO
87	AKT1S1	AKT1S1	AKT1S1	13211	-0.026	0.17	NO
88	CALM1	CALM1	CALM1	13680	-0.033	0.15	NO
89	GSK3A	GSK3A	GSK3A	13784	-0.035	0.15	NO
90	SRC	SRC	SRC	13795	-0.035	0.15	NO
91	CALM2	CALM2	CALM2	13837	-0.036	0.15	NO
92	ADCY7	ADCY7	ADCY7	14085	-0.039	0.14	NO
93	PRKCD	PRKCD	PRKCD	14248	-0.042	0.14	NO
94	TRIB3	TRIB3	TRIB3	14364	-0.043	0.13	NO
95	ITPR3	ITPR3	ITPR3	14501	-0.046	0.13	NO
96	MAP2K1	MAP2K1	MAP2K1	14607	-0.048	0.13	NO
97	MLST8	MLST8	MLST8	15131	-0.056	0.1	NO
98	HRAS	HRAS	HRAS	16142	-0.081	0.055	NO
99	FGF5	FGF5	FGF5	16154	-0.081	0.061	NO
100	RPS6KB2	RPS6KB2	RPS6KB2	16368	-0.089	0.057	NO
101	FGF8	FGF8	FGF8	16758	-0.11	0.045	NO
102	PRKCG	PRKCG	PRKCG	16911	-0.12	0.046	NO
103	CDK1	CDK1	CDK1	18137	-0.34	0.0076	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 BUTANOATE METABOLISM.

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

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 clus4 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG FATTY ACID METABOLISM	39	genes.ES.table	0.35	1.1	0.37	1	1	0.46	0.26	0.34	1	0.95
KEGG PURINE METABOLISM	153	genes.ES.table	0.27	1.2	0.21	1	1	0.18	0.15	0.15	1	0.95
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM	31	genes.ES.table	0.44	1.4	0.067	1	1	0.26	0.1	0.23	1	0.87
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION	44	genes.ES.table	0.45	1.7	0.028	1	0.8	0.36	0.19	0.3	0.94	0.48
KEGG PROPANOATE METABOLISM	32	genes.ES.table	0.37	1.3	0.22	1	1	0.41	0.27	0.3	1	0.9
KEGG BUTANOATE METABOLISM	30	genes.ES.table	0.53	1.6	0.029	1	0.93	0.43	0.19	0.35	1	0.55
KEGG PEROXISOME	76	genes.ES.table	0.39	1.5	0.062	1	0.99	0.36	0.21	0.28	1	0.74
ST GA13 PATHWAY	35	genes.ES.table	0.36	1.3	0.13	1	1	0.17	0.08	0.16	1	0.87
PID AR PATHWAY	61	genes.ES.table	0.27	1.1	0.37	1	1	0.28	0.26	0.21	1	0.96
PID TRAIL PATHWAY	28	genes.ES.table	0.39	1.3	0.22	1	1	0.32	0.22	0.25	1	0.88

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table S31. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ABAT	ABAT	ABAT	85	0.47	0.12	YES
2	HMGCS2	HMGCS2	HMGCS2	511	0.27	0.18	YES
3	ACADSB	ACADSB	ACADSB	766	0.23	0.22	YES
4	ALDH6A1	ALDH6A1	ALDH6A1	1090	0.19	0.26	YES
5	MCCC2	MCCC2	MCCC2	1339	0.16	0.29	YES
6	HMGCL	HMGCL	HMGCL	1856	0.13	0.3	YES
7	ACADS	ACADS	ACADS	2117	0.12	0.31	YES
8	IVD	IVD	IVD	2180	0.11	0.34	YES
9	BCAT2	BCAT2	BCAT2	2427	0.1	0.36	YES
10	AUH	AUH	AUH	2737	0.09	0.36	YES
11	ACAA1	ACAA1	ACAA1	2781	0.089	0.38	YES
12	ACAT1	ACAT1	ACAT1	2919	0.085	0.4	YES
13	BCKDHB	BCKDHB	BCKDHB	3302	0.075	0.4	YES
14	ALDH3A2	ALDH3A2	ALDH3A2	3326	0.074	0.42	YES
15	MCEE	MCEE	MCEE	3411	0.072	0.44	YES
16	ALDH9A1	ALDH9A1	ALDH9A1	3497	0.07	0.45	YES
17	ALDH2	ALDH2	ALDH2	4304	0.054	0.42	NO
18	PCCB	PCCB	PCCB	4544	0.049	0.42	NO
19	OXCT2	OXCT2	OXCT2	4559	0.049	0.43	NO
20	EHHADH	EHHADH	EHHADH	4805	0.045	0.43	NO
21	HIBCH	HIBCH	HIBCH	4942	0.042	0.44	NO
22	BCKDHA	BCKDHA	BCKDHA	5202	0.039	0.43	NO
23	PCCA	PCCA	PCCA	5461	0.035	0.43	NO
24	ACAD8	ACAD8	ACAD8	5470	0.035	0.44	NO
25	HADHB	HADHB	HADHB	5608	0.033	0.44	NO
26	HADH	HADH	HADH	6038	0.027	0.42	NO
27	ECHS1	ECHS1	ECHS1	6618	0.02	0.4	NO
28	AOX1	AOX1	AOX1	6794	0.018	0.39	NO
29	ACADM	ACADM	ACADM	6848	0.017	0.39	NO
30	HADHA	HADHA	HADHA	7273	0.012	0.37	NO
31	HIBADH	HIBADH	HIBADH	7416	0.01	0.37	NO
32	MUT	MUT	MUT	7882	0.0049	0.34	NO
33	DBT	DBT	DBT	8407	-0.00059	0.32	NO
34	ALDH7A1	ALDH7A1	ALDH7A1	9217	-0.0095	0.27	NO
35	ALDH1B1	ALDH1B1	ALDH1B1	10224	-0.02	0.22	NO
36	HSD17B10	HSD17B10	HSD17B10	10574	-0.025	0.21	NO
37	DLD	DLD	DLD	10914	-0.028	0.2	NO
38	HMGCS1	HMGCS1	HMGCS1	13371	-0.067	0.084	NO
39	BCAT1	BCAT1	BCAT1	13461	-0.068	0.098	NO
40	ACAA2	ACAA2	ACAA2	13519	-0.07	0.11	NO
41	ACAT2	ACAT2	ACAT2	14139	-0.084	0.1	NO
42	MCCC1	MCCC1	MCCC1	14588	-0.096	0.1	NO
43	OXCT1	OXCT1	OXCT1	16424	-0.17	0.05	NO
44	IL4I1	IL4I1	IL4I1	16760	-0.19	0.083	NO

Figure S61. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FATTY ACID METABOLISM.

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

genes ES table in pathway: KEGG PURINE METABOLISM

Table S32. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ABAT	ABAT	ABAT	85	0.47	0.14	YES
2	GAD1	GAD1	GAD1	165	0.4	0.26	YES
3	ACSM1	ACSM1	ACSM1	255	0.35	0.36	YES
4	HMGCS2	HMGCS2	HMGCS2	511	0.27	0.42	YES
5	HMGCL	HMGCL	HMGCL	1856	0.13	0.39	YES
6	ACSM5	ACSM5	ACSM5	1960	0.12	0.42	YES
7	ACADS	ACADS	ACADS	2117	0.12	0.45	YES
8	BDH2	BDH2	BDH2	2377	0.1	0.47	YES
9	PDHB	PDHB	PDHB	2865	0.087	0.47	YES
10	ACAT1	ACAT1	ACAT1	2919	0.085	0.49	YES
11	BDH1	BDH1	BDH1	3227	0.077	0.5	YES
12	ALDH3A2	ALDH3A2	ALDH3A2	3326	0.074	0.51	YES
13	ALDH9A1	ALDH9A1	ALDH9A1	3497	0.07	0.52	YES
14	ALDH2	ALDH2	ALDH2	4304	0.054	0.5	NO
15	OXCT2	OXCT2	OXCT2	4559	0.049	0.5	NO
16	EHHADH	EHHADH	EHHADH	4805	0.045	0.5	NO
17	HADH	HADH	HADH	6038	0.027	0.44	NO
18	ECHS1	ECHS1	ECHS1	6618	0.02	0.41	NO
19	AACS	AACS	AACS	7246	0.012	0.38	NO
20	HADHA	HADHA	HADHA	7273	0.012	0.38	NO
21	ALDH7A1	ALDH7A1	ALDH7A1	9217	-0.0095	0.28	NO
22	L2HGDH	L2HGDH	L2HGDH	9589	-0.014	0.27	NO
23	ALDH1B1	ALDH1B1	ALDH1B1	10224	-0.02	0.24	NO
24	ACSM3	ACSM3	ACSM3	13366	-0.066	0.085	NO
25	HMGCS1	HMGCS1	HMGCS1	13371	-0.067	0.1	NO
26	ACAT2	ACAT2	ACAT2	14139	-0.084	0.089	NO
27	ALDH5A1	ALDH5A1	ALDH5A1	14484	-0.093	0.098	NO
28	PDHA1	PDHA1	PDHA1	14552	-0.095	0.12	NO
29	AKR1B10	AKR1B10	AKR1B10	14615	-0.096	0.15	NO
30	OXCT1	OXCT1	OXCT1	16424	-0.17	0.1	NO

Figure S63. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PURINE METABOLISM.

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

Table S33. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ACOX2	ACOX2	ACOX2	174	0.39	0.045	YES
2	DDO	DDO	DDO	213	0.37	0.094	YES
3	MPV17L	MPV17L	MPV17L	401	0.3	0.12	YES
4	CRAT	CRAT	CRAT	468	0.28	0.16	YES
5	EPHX2	EPHX2	EPHX2	481	0.28	0.2	YES
6	PEX11G	PEX11G	PEX11G	492	0.28	0.24	YES
7	SLC27A2	SLC27A2	SLC27A2	537	0.26	0.27	YES
8	NUDT12	NUDT12	NUDT12	918	0.21	0.28	YES
9	CROT	CROT	CROT	929	0.21	0.31	YES
10	PEX11A	PEX11A	PEX11A	1445	0.16	0.3	YES
11	PEX12	PEX12	PEX12	1759	0.13	0.3	YES
12	HMGCL	HMGCL	HMGCL	1856	0.13	0.32	YES
13	DECR2	DECR2	DECR2	1890	0.13	0.33	YES
14	PEX7	PEX7	PEX7	1986	0.12	0.34	YES
15	HSD17B4	HSD17B4	HSD17B4	2076	0.12	0.35	YES
16	PXMP4	PXMP4	PXMP4	2486	0.099	0.34	YES
17	PEX11B	PEX11B	PEX11B	2557	0.096	0.35	YES
18	PMVK	PMVK	PMVK	2577	0.096	0.37	YES
19	ACAA1	ACAA1	ACAA1	2781	0.089	0.37	YES
20	ABCD3	ABCD3	ABCD3	3142	0.079	0.36	YES
21	DHRS4	DHRS4	DHRS4	3183	0.078	0.37	YES
22	PEX19	PEX19	PEX19	3217	0.077	0.38	YES
23	PECR	PECR	PECR	3355	0.073	0.38	YES
24	PAOX	PAOX	PAOX	3470	0.071	0.38	YES
25	ACOX3	ACOX3	ACOX3	3596	0.068	0.38	YES
26	HACL1	HACL1	HACL1	3684	0.066	0.39	YES
27	ABCD4	ABCD4	ABCD4	3809	0.063	0.39	YES
28	GNPAT	GNPAT	GNPAT	4137	0.057	0.38	NO
29	AMACR	AMACR	AMACR	4219	0.055	0.38	NO
30	AGPS	AGPS	AGPS	4528	0.05	0.37	NO
31	ACSL5	ACSL5	ACSL5	4719	0.046	0.37	NO
32	EHHADH	EHHADH	EHHADH	4805	0.045	0.37	NO
33	PEX6	PEX6	PEX6	4970	0.042	0.37	NO
34	PEX10	PEX10	PEX10	4972	0.042	0.37	NO
35	CAT	CAT	CAT	5256	0.038	0.36	NO
36	SCP2	SCP2	SCP2	5271	0.038	0.37	NO
37	GSTK1	GSTK1	GSTK1	5548	0.034	0.36	NO
38	PXMP2	PXMP2	PXMP2	5583	0.033	0.36	NO
39	PEX16	PEX16	PEX16	5671	0.032	0.36	NO
40	MPV17	MPV17	MPV17	5738	0.031	0.36	NO
41	ECH1	ECH1	ECH1	6586	0.02	0.32	NO
42	PEX14	PEX14	PEX14	6703	0.019	0.31	NO
43	PEX1	PEX1	PEX1	7146	0.014	0.29	NO
44	PEX5	PEX5	PEX5	8437	-0.00086	0.22	NO
45	HAO2	HAO2	HAO2	9033	-0.0074	0.19	NO
46	PEX2	PEX2	PEX2	9377	-0.011	0.17	NO
47	FAR1	FAR1	FAR1	9653	-0.014	0.16	NO
48	PEX26	PEX26	PEX26	10110	-0.019	0.14	NO
49	MLYCD	MLYCD	MLYCD	10135	-0.019	0.14	NO
50	PRDX5	PRDX5	PRDX5	10235	-0.021	0.14	NO
51	SLC25A17	SLC25A17	SLC25A17	10312	-0.021	0.13	NO
52	ACOT8	ACOT8	ACOT8	10360	-0.022	0.13	NO
53	SOD1	SOD1	SOD1	10400	-0.022	0.14	NO
54	PHYH	PHYH	PHYH	10758	-0.026	0.12	NO
55	PEX3	PEX3	PEX3	10811	-0.027	0.12	NO
56	DAO	DAO	DAO	11256	-0.033	0.1	NO
57	PEX13	PEX13	PEX13	11370	-0.035	0.099	NO
58	ACSL3	ACSL3	ACSL3	11638	-0.038	0.089	NO
59	ACOX1	ACOX1	ACOX1	12017	-0.043	0.074	NO
60	PRDX1	PRDX1	PRDX1	12536	-0.051	0.053	NO
61	IDH2	IDH2	IDH2	12570	-0.052	0.058	NO
62	IDH1	IDH1	IDH1	12861	-0.057	0.05	NO
63	AGXT	AGXT	AGXT	12947	-0.059	0.054	NO
64	FAR2	FAR2	FAR2	13205	-0.063	0.048	NO
65	SOD2	SOD2	SOD2	13900	-0.078	0.021	NO
66	MVK	MVK	MVK	14015	-0.081	0.026	NO
67	XDH	XDH	XDH	14584	-0.096	0.008	NO
68	NOS2	NOS2	NOS2	14919	-0.11	0.0043	NO
69	ABCD1	ABCD1	ABCD1	15034	-0.11	0.013	NO
70	NUDT19	NUDT19	NUDT19	15145	-0.11	0.023	NO
71	PIPOX	PIPOX	PIPOX	16049	-0.15	-0.0062	NO
72	ACSL6	ACSL6	ACSL6	16179	-0.16	0.0082	NO
73	ACSL4	ACSL4	ACSL4	16294	-0.16	0.024	NO
74	ABCD2	ABCD2	ABCD2	16619	-0.18	0.031	NO
75	ACSL1	ACSL1	ACSL1	16970	-0.2	0.04	NO
76	BAAT	BAAT	BAAT	17271	-0.23	0.055	NO

Figure S65. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

genes ES table in pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION

Table S34. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ABAT	ABAT	ABAT	85	0.47	0.11	YES
2	GAD1	GAD1	GAD1	165	0.4	0.21	YES
3	DDO	DDO	DDO	213	0.37	0.3	YES
4	GLS2	GLS2	GLS2	327	0.32	0.37	YES
5	GPT	GPT	GPT	1006	0.2	0.38	YES
6	GLUL	GLUL	GLUL	1164	0.18	0.42	YES
7	ADSSL1	ADSSL1	ADSSL1	1593	0.14	0.43	YES
8	ASPA	ASPA	ASPA	1917	0.12	0.44	YES
9	AGXT2	AGXT2	AGXT2	2481	0.1	0.44	NO
10	ADSS	ADSS	ADSS	3432	0.072	0.4	NO
11	GLUD1	GLUD1	GLUD1	3801	0.064	0.4	NO
12	GLUD2	GLUD2	GLUD2	4069	0.058	0.4	NO
13	ASL	ASL	ASL	4385	0.052	0.39	NO
14	NIT2	NIT2	NIT2	7608	0.0082	0.22	NO
15	GOT2	GOT2	GOT2	9590	-0.014	0.11	NO
16	GFPT1	GFPT1	GFPT1	9872	-0.017	0.1	NO
17	CPS1	CPS1	CPS1	10000	-0.018	0.1	NO
18	ALDH4A1	ALDH4A1	ALDH4A1	10936	-0.029	0.056	NO
19	GOT1	GOT1	GOT1	11189	-0.032	0.05	NO
20	AGXT	AGXT	AGXT	12947	-0.059	-0.032	NO
21	CAD	CAD	CAD	13097	-0.061	-0.025	NO
22	ACY3	ACY3	ACY3	13483	-0.069	-0.029	NO
23	GFPT2	GFPT2	GFPT2	13497	-0.069	-0.012	NO
24	ADSL	ADSL	ADSL	13605	-0.071	-0.0004	NO
25	ALDH5A1	ALDH5A1	ALDH5A1	14484	-0.093	-0.026	NO
26	PPAT	PPAT	PPAT	14717	-0.099	-0.014	NO
27	ASS1	ASS1	ASS1	15152	-0.11	-0.0096	NO
28	GLS	GLS	GLS	15724	-0.14	-0.007	NO
29	IL4I1	IL4I1	IL4I1	16760	-0.19	-0.017	NO
30	ASNS	ASNS	ASNS	16806	-0.19	0.028	NO
31	GPT2	GPT2	GPT2	17115	-0.21	0.064	NO

Figure S67. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG PROPANOATE METABOLISM

Table S35. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	TFF1	TFF1	TFF1	120	0.43	0.089	YES
2	ESR1	ESR1	ESR1	135	0.42	0.18	YES
3	AR	AR	AR	344	0.32	0.24	YES
4	FOXA1	FOXA1	FOXA1	362	0.31	0.31	YES
5	NKX3-1	NKX3-1	NKX3-1	409	0.3	0.37	YES
6	SERPINA1	SERPINA1	SERPINA1	647	0.25	0.41	YES
7	NFIA	NFIA	NFIA	861	0.22	0.45	YES
8	XBP1	XBP1	XBP1	1233	0.17	0.47	YES
9	NR2F2	NR2F2	NR2F2	2357	0.1	0.43	NO
10	NRIP1	NRIP1	NRIP1	2513	0.098	0.44	NO
11	FOS	FOS	FOS	2622	0.094	0.46	NO
12	FOXA3	FOXA3	FOXA3	3232	0.076	0.44	NO
13	NFIC	NFIC	NFIC	3304	0.075	0.45	NO
14	CDKN1B	CDKN1B	CDKN1B	3830	0.063	0.44	NO
15	C4BPB	C4BPB	C4BPB	3943	0.06	0.44	NO
16	CREBBP	CREBBP	CREBBP	4640	0.047	0.42	NO
17	POU2F1	POU2F1	POU2F1	4797	0.045	0.42	NO
18	JUN	JUN	JUN	5067	0.041	0.41	NO
19	SP1	SP1	SP1	5716	0.031	0.38	NO
20	PISD	PISD	PISD	6275	0.024	0.36	NO
21	NDUFV3	NDUFV3	NDUFV3	7865	0.0052	0.27	NO
22	BRCA1	BRCA1	BRCA1	8060	0.0032	0.26	NO
23	SFTPD	SFTPD	SFTPD	8711	-0.0038	0.23	NO
24	EP300	EP300	EP300	9686	-0.015	0.18	NO
25	ATP5J	ATP5J	ATP5J	9747	-0.015	0.18	NO
26	AP1B1	AP1B1	AP1B1	10240	-0.021	0.16	NO
27	SOD1	SOD1	SOD1	10400	-0.022	0.15	NO
28	COL18A1	COL18A1	COL18A1	10481	-0.023	0.15	NO
29	PRDM15	PRDM15	PRDM15	11011	-0.03	0.13	NO
30	KLK3	KLK3	KLK3	11902	-0.042	0.09	NO
31	SHH	SHH	SHH	13935	-0.078	-0.004	NO
32	DSCAM	DSCAM	DSCAM	13943	-0.079	0.013	NO
33	APOB	APOB	APOB	14158	-0.084	0.02	NO
34	NCOA3	NCOA3	NCOA3	14415	-0.091	0.026	NO
35	SFTPA2	SFTPA2	SFTPA2	14788	-0.1	0.028	NO
36	VTN	VTN	VTN	14793	-0.1	0.05	NO
37	CEBPB	CEBPB	CEBPB	15469	-0.12	0.041	NO
38	NFIB	NFIB	NFIB	17388	-0.24	-0.012	NO
39	CYP2C18	CYP2C18	CYP2C18	17674	-0.27	0.033	NO

Figure S69. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PROPANOATE METABOLISM.

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

Table S36. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CFB	CFB	CFB	178	0.39	0.12	YES
2	BCL2	BCL2	BCL2	706	0.24	0.16	YES
3	SERPINA4	SERPINA4	SERPINA4	795	0.22	0.23	YES
4	DLG4	DLG4	DLG4	1109	0.19	0.28	YES
5	MAP3K1	MAP3K1	MAP3K1	1434	0.16	0.31	YES
6	MAP2K4	MAP2K4	MAP2K4	1461	0.15	0.36	YES
7	PLD2	PLD2	PLD2	3510	0.07	0.27	NO
8	NFKB1	NFKB1	NFKB1	4032	0.059	0.26	NO
9	ARHGEF11	ARHGEF11	ARHGEF11	5051	0.041	0.22	NO
10	NFKBIA	NFKBIA	NFKBIA	6212	0.025	0.16	NO
11	NFKBIL1	NFKBIL1	NFKBIL1	6975	0.016	0.12	NO
12	PHKA2	PHKA2	PHKA2	7030	0.015	0.13	NO
13	ROCK1	ROCK1	ROCK1	7982	0.004	0.076	NO
14	NFKB2	NFKB2	NFKB2	8274	0.001	0.061	NO
15	AKT1	AKT1	AKT1	8403	-0.00055	0.054	NO
16	CDC42	CDC42	CDC42	8405	-0.00056	0.054	NO
17	AKT2	AKT2	AKT2	9011	-0.0071	0.023	NO
18	IKBKG	IKBKG	IKBKG	9397	-0.011	0.0056	NO
19	NFKBIE	NFKBIE	NFKBIE	10213	-0.02	-0.032	NO
20	PIK3CB	PIK3CB	PIK3CB	10234	-0.021	-0.027	NO
21	TBXA2R	TBXA2R	TBXA2R	11026	-0.03	-0.06	NO
22	NFKBIB	NFKBIB	NFKBIB	11319	-0.034	-0.065	NO
23	PLD3	PLD3	PLD3	11655	-0.038	-0.071	NO
24	AKT3	AKT3	AKT3	11975	-0.042	-0.075	NO
25	MAPK8	MAPK8	MAPK8	12211	-0.046	-0.073	NO
26	SRF	SRF	SRF	12690	-0.054	-0.082	NO
27	RDX	RDX	RDX	12789	-0.056	-0.069	NO
28	PTK2	PTK2	PTK2	12857	-0.057	-0.054	NO
29	GNA13	GNA13	GNA13	13247	-0.064	-0.055	NO
30	MAP3K5	MAP3K5	MAP3K5	14033	-0.081	-0.071	NO
31	PRKD1	PRKD1	PRKD1	14628	-0.097	-0.072	NO
32	ROCK2	ROCK2	ROCK2	14680	-0.098	-0.043	NO
33	PDK1	PDK1	PDK1	15443	-0.12	-0.045	NO
34	PLD1	PLD1	PLD1	16427	-0.17	-0.044	NO
35	PI3	PI3	PI3	18251	-0.45	0.0014	NO

Figure S71. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BUTANOATE METABOLISM.

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

genes ES table in pathway: KEGG PEROXISOME

Table S37. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SEMA6D	SEMA6D	SEMA6D	1082	0.19	0.047	YES
2	PIGH	PIGH	PIGH	1788	0.13	0.082	YES
3	PIGQ	PIGQ	PIGQ	1791	0.13	0.16	YES
4	PIGV	PIGV	PIGV	1984	0.12	0.21	YES
5	PIGB	PIGB	PIGB	2103	0.12	0.27	YES
6	DPM3	DPM3	DPM3	3268	0.076	0.25	YES
7	PIGM	PIGM	PIGM	3652	0.067	0.27	YES
8	PIGN	PIGN	PIGN	3720	0.065	0.3	YES
9	PIGX	PIGX	PIGX	4222	0.055	0.3	YES
10	PIGC	PIGC	PIGC	4530	0.05	0.32	YES
11	PIGG	PIGG	PIGG	4729	0.046	0.33	YES
12	PIGL	PIGL	PIGL	4867	0.044	0.35	YES
13	PIGT	PIGT	PIGT	5084	0.04	0.36	YES
14	PIGK	PIGK	PIGK	5502	0.034	0.36	NO
15	PIGO	PIGO	PIGO	6486	0.022	0.31	NO
16	DPM2	DPM2	DPM2	6942	0.016	0.3	NO
17	PIGF	PIGF	PIGF	8619	-0.0029	0.21	NO
18	PIGS	PIGS	PIGS	9060	-0.0076	0.19	NO
19	PIGP	PIGP	PIGP	9128	-0.0083	0.19	NO
20	GPAA1	GPAA1	GPAA1	11850	-0.041	0.062	NO
21	PIGU	PIGU	PIGU	12123	-0.045	0.072	NO
22	PLAUR	PLAUR	PLAUR	12746	-0.055	0.069	NO
23	PIGA	PIGA	PIGA	13404	-0.067	0.071	NO
24	DPM1	DPM1	DPM1	14316	-0.088	0.07	NO
25	PIGW	PIGW	PIGW	15153	-0.11	0.088	NO
26	PGAP1	PGAP1	PGAP1	16003	-0.15	0.12	NO

Figure S73. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PEROXISOME.

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

genes ES table in pathway: ST GA13 PATHWAY

Table S38. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	TNFRSF10C	TNFRSF10C	TNFRSF10C	101	0.46	0.21	YES
2	MAP3K1	MAP3K1	MAP3K1	1434	0.16	0.22	YES
3	MAP2K4	MAP2K4	MAP2K4	1461	0.15	0.29	YES
4	IKBKB	IKBKB	IKBKB	1945	0.12	0.32	YES
5	TNFSF10	TNFSF10	TNFSF10	2062	0.12	0.37	YES
6	PIK3R3	PIK3R3	PIK3R3	3597	0.068	0.32	YES
7	SMPD1	SMPD1	SMPD1	3599	0.068	0.35	YES
8	TNFRSF10B	TNFRSF10B	TNFRSF10B	3770	0.064	0.38	YES
9	PIK3R1	PIK3R1	PIK3R1	4033	0.059	0.39	YES
10	CASP8	CASP8	CASP8	4750	0.046	0.37	NO
11	DAP3	DAP3	DAP3	5325	0.037	0.36	NO
12	MAPK3	MAPK3	MAPK3	6310	0.024	0.32	NO
13	PIK3R2	PIK3R2	PIK3R2	7214	0.013	0.27	NO
14	TRAF2	TRAF2	TRAF2	7450	0.01	0.26	NO
15	RIPK1	RIPK1	RIPK1	7523	0.0092	0.26	NO
16	CHUK	CHUK	CHUK	9164	-0.0088	0.18	NO
17	TNFRSF10A	TNFRSF10A	TNFRSF10A	9344	-0.011	0.18	NO
18	IKBKG	IKBKG	IKBKG	9397	-0.011	0.18	NO
19	PIK3CB	PIK3CB	PIK3CB	10234	-0.021	0.14	NO
20	TRADD	TRADD	TRADD	10674	-0.026	0.13	NO
21	FADD	FADD	FADD	11766	-0.04	0.089	NO
22	MAPK1	MAPK1	MAPK1	12089	-0.044	0.092	NO
23	MAPK8	MAPK8	MAPK8	12211	-0.046	0.11	NO
24	CFLAR	CFLAR	CFLAR	13056	-0.061	0.091	NO
25	PIK3CA	PIK3CA	PIK3CA	14148	-0.084	0.071	NO
26	TNFRSF10D	TNFRSF10D	TNFRSF10D	14375	-0.09	0.1	NO
27	PIK3CD	PIK3CD	PIK3CD	14726	-0.1	0.13	NO
28	CASP10	CASP10	CASP10	15610	-0.13	0.15	NO

Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST GA13 PATHWAY.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: ST GA13 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID AR PATHWAY

Table S39. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ABAT	ABAT	ABAT	85	0.47	0.22	YES
2	ALDH6A1	ALDH6A1	ALDH6A1	1090	0.19	0.25	YES
3	SUCLG2	SUCLG2	SUCLG2	2242	0.11	0.24	YES
4	ACAT1	ACAT1	ACAT1	2919	0.085	0.24	YES
5	ALDH3A2	ALDH3A2	ALDH3A2	3326	0.074	0.26	YES
6	MCEE	MCEE	MCEE	3411	0.072	0.29	YES
7	ALDH9A1	ALDH9A1	ALDH9A1	3497	0.07	0.32	YES
8	ALDH2	ALDH2	ALDH2	4304	0.054	0.3	YES
9	ACACB	ACACB	ACACB	4359	0.052	0.32	YES
10	PCCB	PCCB	PCCB	4544	0.049	0.33	YES
11	ACSS3	ACSS3	ACSS3	4760	0.045	0.34	YES
12	EHHADH	EHHADH	EHHADH	4805	0.045	0.36	YES
13	HIBCH	HIBCH	HIBCH	4942	0.042	0.37	YES
14	PCCA	PCCA	PCCA	5461	0.035	0.36	NO
15	ECHS1	ECHS1	ECHS1	6618	0.02	0.31	NO
16	ACADM	ACADM	ACADM	6848	0.017	0.3	NO
17	ACACA	ACACA	ACACA	7130	0.014	0.29	NO
18	HADHA	HADHA	HADHA	7273	0.012	0.29	NO
19	MUT	MUT	MUT	7882	0.0049	0.26	NO
20	SUCLA2	SUCLA2	SUCLA2	7996	0.0039	0.26	NO
21	ALDH7A1	ALDH7A1	ALDH7A1	9217	-0.0095	0.19	NO
22	LDHA	LDHA	LDHA	9351	-0.011	0.19	NO
23	SUCLG1	SUCLG1	SUCLG1	9567	-0.013	0.19	NO
24	ACSS2	ACSS2	ACSS2	9652	-0.014	0.19	NO
25	LDHC	LDHC	LDHC	9724	-0.015	0.19	NO
26	MLYCD	MLYCD	MLYCD	10135	-0.019	0.18	NO
27	ALDH1B1	ALDH1B1	ALDH1B1	10224	-0.02	0.18	NO
28	ACSS1	ACSS1	ACSS1	10927	-0.029	0.16	NO
29	LDHAL6A	LDHAL6A	LDHAL6A	11599	-0.037	0.14	NO
30	ACAT2	ACAT2	ACAT2	14139	-0.084	0.04	NO
31	LDHAL6B	LDHAL6B	LDHAL6B	15410	-0.12	0.029	NO
32	LDHB	LDHB	LDHB	17654	-0.27	0.034	NO

Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID AR PATHWAY.

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

genes ES table in pathway: PID TRAIL PATHWAY

Table S40. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PGR	PGR	PGR	17	0.59	0.1	YES
2	TFF1	TFF1	TFF1	120	0.43	0.17	YES
3	ESR1	ESR1	ESR1	135	0.42	0.24	YES
4	GREB1	GREB1	GREB1	464	0.28	0.27	YES
5	XBP1	XBP1	XBP1	1233	0.17	0.26	YES
6	ABCA3	ABCA3	ABCA3	1385	0.16	0.28	YES
7	APBB1	APBB1	APBB1	1501	0.15	0.3	YES
8	MPG	MPG	MPG	2392	0.1	0.26	NO
9	AXIN2	AXIN2	AXIN2	2404	0.1	0.28	NO
10	NRIP1	NRIP1	NRIP1	2513	0.098	0.29	NO
11	CALCOCO1	CALCOCO1	CALCOCO1	2741	0.09	0.3	NO
12	CCND1	CCND1	CCND1	3069	0.081	0.29	NO
13	LCOR	LCOR	LCOR	3362	0.073	0.29	NO
14	CTSD	CTSD	CTSD	3586	0.068	0.29	NO
15	STAT5A	STAT5A	STAT5A	3963	0.06	0.28	NO
16	NCOR1	NCOR1	NCOR1	4882	0.043	0.23	NO
17	JUN	JUN	JUN	5067	0.041	0.23	NO
18	DDX17	DDX17	DDX17	5242	0.038	0.23	NO
19	SMAD4	SMAD4	SMAD4	5402	0.036	0.22	NO
20	SRA1	SRA1	SRA1	5420	0.036	0.23	NO
21	MTA1	MTA1	MTA1	5424	0.036	0.24	NO
22	UBA3	UBA3	UBA3	6086	0.026	0.2	NO
23	C3	C3	C3	6500	0.022	0.18	NO
24	NCOA1	NCOA1	NCOA1	6645	0.02	0.18	NO
25	NEDD8	NEDD8	NEDD8	6933	0.016	0.17	NO
26	ANP32A	ANP32A	ANP32A	7568	0.0086	0.13	NO
27	NDUFV3	NDUFV3	NDUFV3	7865	0.0052	0.12	NO
28	BRCA1	BRCA1	BRCA1	8060	0.0032	0.11	NO
29	SAFB	SAFB	SAFB	8742	-0.0041	0.072	NO
30	DDX54	DDX54	DDX54	8785	-0.0047	0.071	NO
31	HDAC4	HDAC4	HDAC4	9110	-0.0081	0.054	NO
32	CHUK	CHUK	CHUK	9164	-0.0088	0.053	NO
33	NCOR2	NCOR2	NCOR2	9438	-0.012	0.04	NO
34	EP300	EP300	EP300	9686	-0.015	0.029	NO
35	ATP5J	ATP5J	ATP5J	9747	-0.015	0.028	NO
36	PHB2	PHB2	PHB2	10037	-0.018	0.015	NO
37	AP1B1	AP1B1	AP1B1	10240	-0.021	0.0078	NO
38	SOD1	SOD1	SOD1	10400	-0.022	0.0029	NO
39	HDAC1	HDAC1	HDAC1	10472	-0.023	0.003	NO
40	COL18A1	COL18A1	COL18A1	10481	-0.023	0.0065	NO
41	PRDM15	PRDM15	PRDM15	11011	-0.03	-0.017	NO
42	CD82	CD82	CD82	11045	-0.03	-0.014	NO
43	SET	SET	SET	11085	-0.031	-0.011	NO
44	TRIM59	TRIM59	TRIM59	11215	-0.032	-0.013	NO
45	EBAG9	EBAG9	EBAG9	12114	-0.044	-0.054	NO
46	HSF2	HSF2	HSF2	12269	-0.047	-0.055	NO
47	UBE2M	UBE2M	UBE2M	12358	-0.048	-0.051	NO
48	NCOA2	NCOA2	NCOA2	12736	-0.055	-0.063	NO
49	NR0B1	NR0B1	NR0B1	13052	-0.061	-0.07	NO
50	MED1	MED1	MED1	13392	-0.067	-0.077	NO
51	PRL	PRL	PRL	13531	-0.07	-0.072	NO
52	KLRC3	KLRC3	KLRC3	13908	-0.078	-0.08	NO
53	DSCAM	DSCAM	DSCAM	13943	-0.079	-0.068	NO
54	PCNA	PCNA	PCNA	14042	-0.081	-0.06	NO
55	NCOA3	NCOA3	NCOA3	14415	-0.091	-0.065	NO
56	CEBPB	CEBPB	CEBPB	15469	-0.12	-0.1	NO
57	PDIA2	PDIA2	PDIA2	15848	-0.14	-0.098	NO
58	MYC	MYC	MYC	15856	-0.14	-0.074	NO
59	LMO4	LMO4	LMO4	16348	-0.16	-0.073	NO
60	NCOA7	NCOA7	NCOA7	16979	-0.2	-0.073	NO
61	NR0B2	NR0B2	NR0B2	17181	-0.22	-0.046	NO
62	ESR2	ESR2	ESR2	17263	-0.23	-0.012	NO
63	POU4F1	POU4F1	POU4F1	18203	-0.39	0.004	NO

Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TRAIL PATHWAY.

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

Fold change

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

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 clus5 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG LYSINE DEGRADATION	44	genes.ES.table	0.39	1.7	0.024	1	0.82	0.2	0.19	0.17	0.53	0.32
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES	26	genes.ES.table	0.71	1.7	0.0062	0.87	0.88	0.5	0.17	0.42	0.4	0.24
KEGG RNA POLYMERASE	29	genes.ES.table	0.48	1.7	0.058	0.98	0.87	0.48	0.3	0.34	0.44	0.26
KEGG CELL CYCLE	118	genes.ES.table	0.56	1.8	0.01	1	0.53	0.39	0.16	0.33	0.45	0.34
PID AURORA B PATHWAY	39	genes.ES.table	0.66	1.6	0.049	0.88	0.92	0.41	0.12	0.36	0.44	0.25
PID E2F PATHWAY	69	genes.ES.table	0.52	1.7	0.063	0.91	0.88	0.35	0.18	0.28	0.42	0.25
PID MYC ACTIVPATHWAY	78	genes.ES.table	0.48	1.9	0.017	1	0.42	0.35	0.21	0.27	0	0.38
PID LIS1PATHWAY	28	genes.ES.table	0.54	1.7	0.032	1	0.85	0.25	0.17	0.21	0.57	0.34
PID AURORA A PATHWAY	31	genes.ES.table	0.57	1.7	0.044	1	0.81	0.26	0.12	0.23	0.62	0.37
PID RB 1PATHWAY	64	genes.ES.table	0.44	1.7	0.008	1	0.86	0.19	0.076	0.17	0.46	0.27

genes ES table in pathway: KEGG LYSINE DEGRADATION

Table S41. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CDCA7	CDCA7	CDCA7	43	0.88	0.07	YES
2	FOSL1	FOSL1	FOSL1	213	0.67	0.12	YES
3	TAF4B	TAF4B	TAF4B	354	0.59	0.16	YES
4	CDC25A	CDC25A	CDC25A	397	0.56	0.2	YES
5	BIRC5	BIRC5	BIRC5	520	0.51	0.24	YES
6	TERT	TERT	TERT	735	0.44	0.26	YES
7	ODC1	ODC1	ODC1	1126	0.36	0.27	YES
8	PIM1	PIM1	PIM1	1162	0.36	0.3	YES
9	SNAI1	SNAI1	SNAI1	1246	0.34	0.32	YES
10	E2F3	E2F3	E2F3	1395	0.32	0.34	YES
11	HMGA1	HMGA1	HMGA1	1508	0.31	0.36	YES
12	MMP9	MMP9	MMP9	1729	0.28	0.37	YES
13	MYC	MYC	MYC	1819	0.27	0.39	YES
14	KIR3DL1	KIR3DL1	KIR3DL1	2495	0.21	0.37	YES
15	ENO1	ENO1	ENO1	2515	0.21	0.38	YES
16	RCC1	RCC1	RCC1	2537	0.21	0.4	YES
17	TK1	TK1	TK1	2589	0.21	0.41	YES
18	BCAT1	BCAT1	BCAT1	2614	0.21	0.43	YES
19	CCNB1	CCNB1	CCNB1	2670	0.2	0.44	YES
20	SLC2A1	SLC2A1	SLC2A1	2769	0.19	0.45	YES
21	POLR3D	POLR3D	POLR3D	2925	0.18	0.46	YES
22	PEG10	PEG10	PEG10	3070	0.18	0.47	YES
23	CAD	CAD	CAD	3264	0.17	0.47	YES
24	GAPDH	GAPDH	GAPDH	3500	0.16	0.47	YES
25	SUPT3H	SUPT3H	SUPT3H	3661	0.15	0.47	YES
26	MINA	MINA	MINA	3753	0.14	0.48	YES
27	ACTL6A	ACTL6A	ACTL6A	3878	0.14	0.48	YES
28	TFRC	TFRC	TFRC	4168	0.13	0.48	NO
29	RUVBL1	RUVBL1	RUVBL1	4467	0.12	0.47	NO
30	BAX	BAX	BAX	4669	0.11	0.47	NO
31	CDK4	CDK4	CDK4	4899	0.1	0.47	NO
32	PTMA	PTMA	PTMA	4931	0.1	0.47	NO
33	HSPD1	HSPD1	HSPD1	5252	0.091	0.46	NO
34	DDX18	DDX18	DDX18	5325	0.089	0.46	NO
35	NCL	NCL	NCL	5849	0.075	0.44	NO
36	EIF4G1	EIF4G1	EIF4G1	6213	0.066	0.43	NO
37	PDCD10	PDCD10	PDCD10	6285	0.065	0.43	NO
38	NME1	NME1	NME1	6327	0.064	0.43	NO
39	SUPT7L	SUPT7L	SUPT7L	6402	0.062	0.43	NO
40	MTA1	MTA1	MTA1	6412	0.062	0.44	NO
41	TRRAP	TRRAP	TRRAP	6470	0.06	0.44	NO
42	EIF4A1	EIF4A1	EIF4A1	6589	0.057	0.44	NO
43	LDHA	LDHA	LDHA	6595	0.057	0.44	NO
44	NME2	NME2	NME2	6827	0.052	0.43	NO
45	RPL11	RPL11	RPL11	6843	0.051	0.44	NO
46	KAT2A	KAT2A	KAT2A	7060	0.046	0.43	NO
47	MTDH	MTDH	MTDH	7189	0.044	0.43	NO
48	HUWE1	HUWE1	HUWE1	7459	0.038	0.42	NO
49	RUVBL2	RUVBL2	RUVBL2	7498	0.037	0.42	NO
50	NPM1	NPM1	NPM1	7721	0.032	0.41	NO
51	TAF12	TAF12	TAF12	7747	0.031	0.41	NO
52	NDUFAF2	NDUFAF2	NDUFAF2	7993	0.026	0.4	NO
53	ID2	ID2	ID2	8582	0.014	0.36	NO
54	HSP90AA1	HSP90AA1	HSP90AA1	8608	0.013	0.36	NO
55	EIF2S1	EIF2S1	EIF2S1	8784	0.0088	0.36	NO
56	NBN	NBN	NBN	8878	0.007	0.35	NO
57	SMAD4	SMAD4	SMAD4	9030	0.0039	0.34	NO
58	SHMT1	SHMT1	SHMT1	9135	0.0018	0.34	NO
59	TAF10	TAF10	TAF10	9788	-0.011	0.3	NO
60	PMAIP1	PMAIP1	PMAIP1	10177	-0.02	0.28	NO
61	TP53	TP53	TP53	10310	-0.022	0.28	NO
62	KAT5	KAT5	KAT5	10765	-0.033	0.26	NO
63	CCND2	CCND2	CCND2	10905	-0.037	0.25	NO
64	IREB2	IREB2	IREB2	10988	-0.039	0.25	NO
65	EP300	EP300	EP300	11071	-0.041	0.25	NO
66	PFKM	PFKM	PFKM	11076	-0.041	0.25	NO
67	UBTF	UBTF	UBTF	11579	-0.053	0.23	NO
68	EIF4E	EIF4E	EIF4E	11900	-0.062	0.22	NO
69	HSPA4	HSPA4	HSPA4	11948	-0.063	0.22	NO
70	MAX	MAX	MAX	12238	-0.07	0.21	NO
71	CREBBP	CREBBP	CREBBP	12580	-0.079	0.2	NO
72	TAF9	TAF9	TAF9	13528	-0.11	0.15	NO
73	PRDX3	PRDX3	PRDX3	14127	-0.13	0.13	NO
74	GPAM	GPAM	GPAM	14507	-0.15	0.12	NO
75	SMAD3	SMAD3	SMAD3	14848	-0.16	0.12	NO
76	BMI1	BMI1	BMI1	15111	-0.18	0.12	NO
77	MYCT1	MYCT1	MYCT1	16540	-0.29	0.062	NO
78	SERPINI1	SERPINI1	SERPINI1	17358	-0.41	0.05	NO

Figure S81. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG LYSINE DEGRADATION.

Figure S82. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

Table S42. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCNE1	CCNE1	CCNE1	37	0.9	0.039	YES
2	SMC1B	SMC1B	SMC1B	235	0.66	0.057	YES
3	CDKN2A	CDKN2A	CDKN2A	380	0.57	0.075	YES
4	CDC25A	CDC25A	CDC25A	397	0.56	0.1	YES
5	CDC20	CDC20	CDC20	448	0.54	0.12	YES
6	TTK	TTK	TTK	462	0.53	0.14	YES
7	CDC45	CDC45	CDC45	472	0.53	0.17	YES
8	E2F2	E2F2	E2F2	568	0.5	0.18	YES
9	CCNA1	CCNA1	CCNA1	593	0.48	0.2	YES
10	CDK6	CDK6	CDK6	677	0.46	0.22	YES
11	PLK1	PLK1	PLK1	738	0.44	0.24	YES
12	SKP2	SKP2	SKP2	842	0.42	0.25	YES
13	CCNB2	CCNB2	CCNB2	846	0.42	0.27	YES
14	BUB1	BUB1	BUB1	874	0.41	0.29	YES
15	CCNA2	CCNA2	CCNA2	955	0.4	0.3	YES
16	PTTG1	PTTG1	PTTG1	970	0.39	0.32	YES
17	CHEK1	CHEK1	CHEK1	987	0.39	0.33	YES
18	CDC7	CDC7	CDC7	1159	0.36	0.34	YES
19	E2F1	E2F1	E2F1	1349	0.33	0.34	YES
20	E2F3	E2F3	E2F3	1395	0.32	0.36	YES
21	BUB1B	BUB1B	BUB1B	1468	0.32	0.37	YES
22	CDC25C	CDC25C	CDC25C	1473	0.31	0.38	YES
23	CHEK2	CHEK2	CHEK2	1572	0.3	0.39	YES
24	MAD2L1	MAD2L1	MAD2L1	1705	0.28	0.4	YES
25	PKMYT1	PKMYT1	PKMYT1	1809	0.27	0.4	YES
26	ESPL1	ESPL1	ESPL1	1817	0.27	0.41	YES
27	MYC	MYC	MYC	1819	0.27	0.43	YES
28	CDC25B	CDC25B	CDC25B	1844	0.27	0.44	YES
29	PTTG2	PTTG2	PTTG2	1906	0.26	0.44	YES
30	E2F5	E2F5	E2F5	1976	0.26	0.45	YES
31	MCM2	MCM2	MCM2	2047	0.25	0.46	YES
32	DBF4	DBF4	DBF4	2055	0.25	0.47	YES
33	CDK1	CDK1	CDK1	2078	0.25	0.48	YES
34	MCM5	MCM5	MCM5	2094	0.24	0.49	YES
35	CDKN2C	CDKN2C	CDKN2C	2097	0.24	0.5	YES
36	RBL1	RBL1	RBL1	2153	0.24	0.51	YES
37	MCM7	MCM7	MCM7	2167	0.24	0.52	YES
38	CDC6	CDC6	CDC6	2221	0.23	0.53	YES
39	SFN	SFN	SFN	2279	0.23	0.53	YES
40	MCM4	MCM4	MCM4	2488	0.21	0.53	YES
41	MCM6	MCM6	MCM6	2651	0.2	0.53	YES
42	CCNB1	CCNB1	CCNB1	2670	0.2	0.54	YES
43	MAD2L2	MAD2L2	MAD2L2	2774	0.19	0.54	YES
44	CDKN2D	CDKN2D	CDKN2D	2822	0.19	0.55	YES
45	TFDP1	TFDP1	TFDP1	2858	0.19	0.56	YES
46	HDAC2	HDAC2	HDAC2	2896	0.19	0.56	YES
47	CCNE2	CCNE2	CCNE2	3054	0.18	0.56	NO
48	MCM3	MCM3	MCM3	3320	0.16	0.56	NO
49	TFDP2	TFDP2	TFDP2	3336	0.16	0.56	NO
50	E2F4	E2F4	E2F4	3770	0.14	0.54	NO
51	TGFB2	TGFB2	TGFB2	3809	0.14	0.55	NO
52	PRKDC	PRKDC	PRKDC	4400	0.12	0.52	NO
53	PCNA	PCNA	PCNA	4535	0.11	0.52	NO
54	CDC14B	CDC14B	CDC14B	4542	0.11	0.52	NO
55	YWHAQ	YWHAQ	YWHAQ	4884	0.1	0.51	NO
56	CDK4	CDK4	CDK4	4899	0.1	0.51	NO
57	MAD1L1	MAD1L1	MAD1L1	5251	0.091	0.5	NO
58	RAD21	RAD21	RAD21	5345	0.088	0.5	NO
59	CCND3	CCND3	CCND3	5426	0.086	0.5	NO
60	CUL1	CUL1	CUL1	5502	0.084	0.5	NO
61	ANAPC1	ANAPC1	ANAPC1	5561	0.082	0.5	NO
62	RBX1	RBX1	RBX1	5782	0.077	0.49	NO
63	CDK2	CDK2	CDK2	5808	0.076	0.49	NO
64	CDKN1C	CDKN1C	CDKN1C	5890	0.074	0.49	NO
65	YWHAZ	YWHAZ	YWHAZ	5946	0.073	0.49	NO
66	YWHAH	YWHAH	YWHAH	6315	0.064	0.47	NO
67	CDKN2B	CDKN2B	CDKN2B	6386	0.062	0.47	NO
68	ANAPC11	ANAPC11	ANAPC11	6743	0.054	0.45	NO
69	CDC26	CDC26	CDC26	6759	0.053	0.46	NO
70	GADD45A	GADD45A	GADD45A	6948	0.049	0.45	NO
71	HDAC1	HDAC1	HDAC1	7007	0.047	0.45	NO
72	YWHAE	YWHAE	YWHAE	7086	0.046	0.44	NO
73	YWHAG	YWHAG	YWHAG	7333	0.041	0.43	NO
74	ATR	ATR	ATR	7502	0.037	0.42	NO
75	CDC16	CDC16	CDC16	7520	0.036	0.42	NO
76	SMC1A	SMC1A	SMC1A	7606	0.034	0.42	NO
77	SMC3	SMC3	SMC3	7649	0.033	0.42	NO
78	WEE2	WEE2	WEE2	7710	0.032	0.42	NO
79	ZBTB17	ZBTB17	ZBTB17	8110	0.024	0.4	NO
80	SMAD2	SMAD2	SMAD2	8140	0.023	0.4	NO
81	ANAPC5	ANAPC5	ANAPC5	8371	0.018	0.39	NO
82	STAG1	STAG1	STAG1	8470	0.016	0.38	NO
83	ANAPC10	ANAPC10	ANAPC10	8604	0.014	0.37	NO
84	ANAPC7	ANAPC7	ANAPC7	8997	0.0044	0.35	NO
85	SMAD4	SMAD4	SMAD4	9030	0.0039	0.35	NO
86	GSK3B	GSK3B	GSK3B	9737	-0.01	0.31	NO
87	ANAPC4	ANAPC4	ANAPC4	9755	-0.011	0.31	NO
88	CDC27	CDC27	CDC27	9975	-0.016	0.3	NO
89	CCNB3	CCNB3	CCNB3	10027	-0.017	0.3	NO
90	STAG2	STAG2	STAG2	10101	-0.018	0.3	NO
91	FZR1	FZR1	FZR1	10233	-0.021	0.29	NO
92	ATM	ATM	ATM	10302	-0.022	0.29	NO
93	TP53	TP53	TP53	10310	-0.022	0.29	NO
94	WEE1	WEE1	WEE1	10857	-0.036	0.26	NO
95	CCND2	CCND2	CCND2	10905	-0.037	0.26	NO
96	CDC23	CDC23	CDC23	11069	-0.041	0.25	NO
97	EP300	EP300	EP300	11071	-0.041	0.25	NO
98	YWHAB	YWHAB	YWHAB	11123	-0.042	0.25	NO
99	ABL1	ABL1	ABL1	11791	-0.059	0.22	NO
100	CDKN1B	CDKN1B	CDKN1B	12250	-0.071	0.2	NO
101	TGFB1	TGFB1	TGFB1	12268	-0.071	0.2	NO
102	GADD45B	GADD45B	GADD45B	12507	-0.078	0.19	NO
103	CREBBP	CREBBP	CREBBP	12580	-0.079	0.19	NO
104	BUB3	BUB3	BUB3	12619	-0.081	0.19	NO
105	ANAPC13	ANAPC13	ANAPC13	13115	-0.095	0.17	NO
106	CDKN1A	CDKN1A	CDKN1A	13116	-0.095	0.17	NO
107	CDK7	CDK7	CDK7	13409	-0.1	0.16	NO
108	RBL2	RBL2	RBL2	13519	-0.11	0.16	NO
109	ANAPC2	ANAPC2	ANAPC2	13571	-0.11	0.16	NO
110	MDM2	MDM2	MDM2	14050	-0.13	0.14	NO
111	SMAD3	SMAD3	SMAD3	14848	-0.16	0.1	NO
112	CDC14A	CDC14A	CDC14A	14854	-0.16	0.11	NO
113	SKP1	SKP1	SKP1	14867	-0.16	0.12	NO
114	CCNH	CCNH	CCNH	15454	-0.2	0.094	NO
115	RB1	RB1	RB1	15759	-0.22	0.087	NO
116	CCND1	CCND1	CCND1	16907	-0.34	0.039	NO
117	GADD45G	GADD45G	GADD45G	17251	-0.39	0.037	NO
118	TGFB3	TGFB3	TGFB3	17426	-0.42	0.047	NO

Figure S83. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

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

genes ES table in pathway: KEGG RNA POLYMERASE

Table S43. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MAGOH	MAGOH	MAGOH	1984	0.26	-0.015	YES
2	THOC4	THOC4	THOC4	2289	0.23	0.053	YES
3	UPF3B	UPF3B	UPF3B	2627	0.2	0.11	YES
4	SNRPG	SNRPG	SNRPG	3167	0.17	0.14	YES
5	U2AF1	U2AF1	U2AF1	4050	0.13	0.14	YES
6	CLP1	CLP1	CLP1	4269	0.12	0.18	YES
7	CPSF3	CPSF3	CPSF3	4485	0.12	0.21	YES
8	DHX38	DHX38	DHX38	4513	0.12	0.25	YES
9	CPSF1	CPSF1	CPSF1	4848	0.1	0.27	YES
10	SNRPF	SNRPF	SNRPF	5059	0.098	0.29	YES
11	LSM10	LSM10	LSM10	5172	0.094	0.32	YES
12	ZNF473	ZNF473	ZNF473	5471	0.084	0.34	YES
13	SNRPB	SNRPB	SNRPB	5684	0.079	0.35	YES
14	RBM8A	RBM8A	RBM8A	5714	0.079	0.38	YES
15	SLBP	SLBP	SLBP	5881	0.074	0.4	YES
16	CSTF3	CSTF3	CSTF3	5936	0.073	0.42	YES
17	SNRPD3	SNRPD3	SNRPD3	6117	0.069	0.44	YES
18	NUDT21	NUDT21	NUDT21	6172	0.067	0.46	YES
19	PABPN1	PABPN1	PABPN1	6583	0.058	0.46	YES
20	RNPS1	RNPS1	RNPS1	6691	0.055	0.47	YES
21	SNRPE	SNRPE	SNRPE	6849	0.051	0.48	YES
22	SRRM1	SRRM1	SRRM1	6923	0.049	0.5	YES
23	NCBP2	NCBP2	NCBP2	7213	0.043	0.5	YES
24	NCBP1	NCBP1	NCBP1	7583	0.035	0.49	YES
25	CPSF7	CPSF7	CPSF7	7626	0.034	0.5	YES
26	CSTF2	CSTF2	CSTF2	8203	0.022	0.48	NO
27	U2AF2	U2AF2	U2AF2	8892	0.0068	0.44	NO
28	CDC40	CDC40	CDC40	9410	-0.0037	0.42	NO
29	NFX1	NFX1	NFX1	9471	-0.0049	0.41	NO
30	PAPOLA	PAPOLA	PAPOLA	10118	-0.019	0.38	NO
31	CSTF1	CSTF1	CSTF1	10138	-0.019	0.39	NO
32	LSM11	LSM11	LSM11	10424	-0.025	0.38	NO
33	CPSF2	CPSF2	CPSF2	10841	-0.035	0.38	NO
34	PCF11	PCF11	PCF11	12894	-0.088	0.3	NO

Figure S85. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RNA POLYMERASE.

Figure S86. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA POLYMERASE, 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 S44. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PRKCA	PRKCA	PRKCA	1074	0.37	-0.039	YES
2	RPL36A	RPL36A	RPL36A	1325	0.33	-0.034	YES
3	PSMA8	PSMA8	PSMA8	1956	0.26	-0.055	YES
4	MAGOH	MAGOH	MAGOH	1984	0.26	-0.042	YES
5	DCPS	DCPS	DCPS	2107	0.24	-0.035	YES
6	NUP93	NUP93	NUP93	2349	0.22	-0.036	YES
7	RPL21	RPL21	RPL21	2547	0.21	-0.036	YES
8	LSM2	LSM2	LSM2	2565	0.21	-0.025	YES
9	LSM6	LSM6	LSM6	2576	0.21	-0.014	YES
10	PSMB9	PSMB9	PSMB9	2620	0.21	-0.0047	YES
11	UPF3B	UPF3B	UPF3B	2627	0.2	0.0064	YES
12	PSME4	PSME4	PSME4	2949	0.18	-0.0013	YES
13	SNRPD1	SNRPD1	SNRPD1	3024	0.18	0.0046	YES
14	WDR77	WDR77	WDR77	3122	0.17	0.0088	YES
15	EXOSC4	EXOSC4	EXOSC4	3149	0.17	0.017	YES
16	SEH1L	SEH1L	SEH1L	3159	0.17	0.026	YES
17	SNRPG	SNRPG	SNRPG	3167	0.17	0.035	YES
18	PSMB2	PSMB2	PSMB2	3242	0.17	0.04	YES
19	RPS7	RPS7	RPS7	3430	0.16	0.039	YES
20	SMG5	SMG5	SMG5	3575	0.15	0.039	YES
21	RPS19	RPS19	RPS19	3626	0.15	0.045	YES
22	PSMB4	PSMB4	PSMB4	3647	0.15	0.052	YES
23	EXOSC5	EXOSC5	EXOSC5	3718	0.14	0.056	YES
24	EXOSC8	EXOSC8	EXOSC8	3725	0.14	0.064	YES
25	PATL1	PATL1	PATL1	3730	0.14	0.072	YES
26	PSMD7	PSMD7	PSMD7	3791	0.14	0.076	YES
27	RPL18A	RPL18A	RPL18A	3836	0.14	0.081	YES
28	NUP205	NUP205	NUP205	3912	0.14	0.085	YES
29	GEMIN4	GEMIN4	GEMIN4	3919	0.14	0.092	YES
30	TGS1	TGS1	TGS1	3976	0.14	0.097	YES
31	EXOSC6	EXOSC6	EXOSC6	4072	0.13	0.099	YES
32	NUPL2	NUPL2	NUPL2	4195	0.13	0.099	YES
33	RPL39	RPL39	RPL39	4202	0.13	0.1	YES
34	GSPT2	GSPT2	GSPT2	4210	0.13	0.11	YES
35	PABPC1	PABPC1	PABPC1	4246	0.12	0.12	YES
36	RPS27A	RPS27A	RPS27A	4273	0.12	0.12	YES
37	UPF2	UPF2	UPF2	4311	0.12	0.13	YES
38	NUP88	NUP88	NUP88	4426	0.12	0.13	YES
39	PSMA7	PSMA7	PSMA7	4451	0.12	0.13	YES
40	RPS10	RPS10	RPS10	4462	0.12	0.14	YES
41	RPS20	RPS20	RPS20	4518	0.12	0.14	YES
42	RPS16	RPS16	RPS16	4563	0.11	0.15	YES
43	RPS12	RPS12	RPS12	4605	0.11	0.15	YES
44	RQCD1	RQCD1	RQCD1	4641	0.11	0.15	YES
45	NUP85	NUP85	NUP85	4679	0.11	0.16	YES
46	RPS27	RPS27	RPS27	4778	0.11	0.16	YES
47	KHSRP	KHSRP	KHSRP	4785	0.11	0.16	YES
48	RPL13	RPL13	RPL13	4918	0.1	0.16	YES
49	LSM4	LSM4	LSM4	4982	0.1	0.16	YES
50	RPSAP9	RPSAP9	RPSAP9	4987	0.1	0.17	YES
51	RPS21	RPS21	RPS21	5018	0.099	0.17	YES
52	SNRPF	SNRPF	SNRPF	5059	0.098	0.18	YES
53	NUP155	NUP155	NUP155	5071	0.097	0.18	YES
54	RPL30	RPL30	RPL30	5187	0.093	0.18	YES
55	RPL35A	RPL35A	RPL35A	5229	0.092	0.18	YES
56	PSMB8	PSMB8	PSMB8	5272	0.091	0.19	YES
57	PSMD2	PSMD2	PSMD2	5278	0.091	0.19	YES
58	NUP153	NUP153	NUP153	5344	0.088	0.19	YES
59	RPL5	RPL5	RPL5	5361	0.088	0.2	YES
60	RPL7	RPL7	RPL7	5368	0.088	0.2	YES
61	RPLP2	RPLP2	RPLP2	5370	0.088	0.2	YES
62	EXOSC3	EXOSC3	EXOSC3	5405	0.086	0.21	YES
63	PSMD14	PSMD14	PSMD14	5453	0.085	0.21	YES
64	RPS17	RPS17	RPS17	5499	0.084	0.21	YES
65	NUP62	NUP62	NUP62	5503	0.084	0.22	YES
66	PSMC3	PSMC3	PSMC3	5532	0.083	0.22	YES
67	RPL8	RPL8	RPL8	5543	0.083	0.22	YES
68	GEMIN6	GEMIN6	GEMIN6	5567	0.082	0.23	YES
69	PSMB10	PSMB10	PSMB10	5604	0.081	0.23	YES
70	UBA52	UBA52	UBA52	5614	0.081	0.23	YES
71	PSMC2	PSMC2	PSMC2	5622	0.081	0.24	YES
72	RPS18	RPS18	RPS18	5638	0.08	0.24	YES
73	RPL38	RPL38	RPL38	5651	0.08	0.25	YES
74	RPL37	RPL37	RPL37	5653	0.08	0.25	YES
75	PSMD4	PSMD4	PSMD4	5677	0.08	0.25	YES
76	SNRPB	SNRPB	SNRPB	5684	0.079	0.26	YES
77	RBM8A	RBM8A	RBM8A	5714	0.079	0.26	YES
78	PSMA4	PSMA4	PSMA4	5737	0.078	0.26	YES
79	ELAVL1	ELAVL1	ELAVL1	5785	0.077	0.26	YES
80	RPSA	RPSA	RPSA	5809	0.076	0.27	YES
81	PSMC4	PSMC4	PSMC4	5810	0.076	0.27	YES
82	SNRPD2	SNRPD2	SNRPD2	5820	0.076	0.28	YES
83	RPS6	RPS6	RPS6	5851	0.075	0.28	YES
84	FAM153A	FAM153A	FAM153A	5862	0.075	0.28	YES
85	RPS25	RPS25	RPS25	5868	0.075	0.29	YES
86	RPL27A	RPL27A	RPL27A	5927	0.073	0.29	YES
87	RPS8	RPS8	RPS8	5931	0.073	0.29	YES
88	YWHAZ	YWHAZ	YWHAZ	5946	0.073	0.29	YES
89	RPL36	RPL36	RPL36	5970	0.072	0.3	YES
90	RPS3	RPS3	RPS3	5994	0.072	0.3	YES
91	HNRNPD	HNRNPD	HNRNPD	6014	0.071	0.3	YES
92	SNRPD3	SNRPD3	SNRPD3	6117	0.069	0.3	YES
93	NUP37	NUP37	NUP37	6156	0.068	0.3	YES
94	PSMD12	PSMD12	PSMD12	6165	0.068	0.3	YES
95	NUP50	NUP50	NUP50	6194	0.067	0.31	YES
96	PSMB6	PSMB6	PSMB6	6209	0.067	0.31	YES
97	EIF4G1	EIF4G1	EIF4G1	6213	0.066	0.31	YES
98	PSMA5	PSMA5	PSMA5	6227	0.066	0.32	YES
99	NUP54	NUP54	NUP54	6230	0.066	0.32	YES
100	XPO1	XPO1	XPO1	6293	0.065	0.32	YES
101	EXOSC2	EXOSC2	EXOSC2	6310	0.064	0.32	YES
102	PSMB7	PSMB7	PSMB7	6434	0.061	0.32	YES
103	PSMB1	PSMB1	PSMB1	6453	0.061	0.32	YES
104	PSMC1	PSMC1	PSMC1	6456	0.061	0.32	YES
105	NUP107	NUP107	NUP107	6477	0.06	0.33	YES
106	RPL35	RPL35	RPL35	6492	0.059	0.33	YES
107	RPL24	RPL24	RPL24	6504	0.059	0.33	YES
108	POM121	POM121	POM121	6510	0.059	0.34	YES
109	PSMD8	PSMD8	PSMD8	6549	0.058	0.34	YES
110	EIF4A1	EIF4A1	EIF4A1	6589	0.057	0.34	YES
111	EDC4	EDC4	EDC4	6629	0.056	0.34	YES
112	FAU	FAU	FAU	6649	0.056	0.34	YES
113	SNUPN	SNUPN	SNUPN	6655	0.056	0.34	YES
114	RNPS1	RNPS1	RNPS1	6691	0.055	0.34	YES
115	PSMB5	PSMB5	PSMB5	6699	0.055	0.35	YES
116	PSMD13	PSMD13	PSMD13	6728	0.054	0.35	YES
117	LSM5	LSM5	LSM5	6814	0.052	0.35	YES
118	RPL4	RPL4	RPL4	6820	0.052	0.35	YES
119	RPL11	RPL11	RPL11	6843	0.051	0.35	YES
120	SNRPE	SNRPE	SNRPE	6849	0.051	0.35	YES
121	RPL27	RPL27	RPL27	6875	0.051	0.36	YES
122	RPS24	RPS24	RPS24	6896	0.05	0.36	YES
123	RPL32	RPL32	RPL32	6988	0.048	0.36	YES
124	CLNS1A	CLNS1A	CLNS1A	6990	0.048	0.36	YES
125	RPL37A	RPL37A	RPL37A	7003	0.048	0.36	YES
126	PSMA2	PSMA2	PSMA2	7054	0.046	0.36	YES
127	EXOSC9	EXOSC9	EXOSC9	7067	0.046	0.36	YES
128	RPL28	RPL28	RPL28	7076	0.046	0.36	YES
129	CNOT7	CNOT7	CNOT7	7111	0.045	0.36	YES
130	PSMD11	PSMD11	PSMD11	7122	0.045	0.37	YES
131	EXOSC7	EXOSC7	EXOSC7	7176	0.044	0.36	YES
132	NCBP2	NCBP2	NCBP2	7213	0.043	0.37	YES
133	RPS2	RPS2	RPS2	7227	0.043	0.37	YES
134	EIF4A3	EIF4A3	EIF4A3	7274	0.042	0.37	YES
135	NUP35	NUP35	NUP35	7314	0.041	0.37	YES
136	CNOT3	CNOT3	CNOT3	7315	0.041	0.37	YES
137	RPL31	RPL31	RPL31	7327	0.041	0.37	YES
138	RPL17	RPL17	RPL17	7342	0.04	0.37	YES
139	MAPK14	MAPK14	MAPK14	7400	0.039	0.37	YES
140	XRN1	XRN1	XRN1	7521	0.036	0.37	YES
141	RPS11	RPS11	RPS11	7557	0.036	0.37	YES
142	NCBP1	NCBP1	NCBP1	7583	0.035	0.37	YES
143	RPL26	RPL26	RPL26	7591	0.035	0.37	YES
144	HSPA1B	HSPA1B	HSPA1B	7611	0.034	0.37	YES
145	PSMB3	PSMB3	PSMB3	7612	0.034	0.37	YES
146	PSMA1	PSMA1	PSMA1	7614	0.034	0.37	YES
147	RPLP0	RPLP0	RPLP0	7619	0.034	0.38	YES
148	RPS9	RPS9	RPS9	7627	0.034	0.38	YES
149	RPL18	RPL18	RPL18	7655	0.033	0.38	YES
150	DDX20	DDX20	DDX20	7659	0.033	0.38	YES
151	RPS29	RPS29	RPS29	7693	0.032	0.38	NO
152	PSMA3	PSMA3	PSMA3	7754	0.031	0.38	NO
153	CNOT10	CNOT10	CNOT10	7767	0.031	0.38	NO
154	GEMIN7	GEMIN7	GEMIN7	7816	0.03	0.38	NO
155	RPL12	RPL12	RPL12	7930	0.027	0.37	NO
156	PSMD1	PSMD1	PSMD1	7948	0.027	0.37	NO
157	RPS13	RPS13	RPS13	7982	0.026	0.37	NO
158	RPS15A	RPS15A	RPS15A	7989	0.026	0.37	NO
159	TPR	TPR	TPR	8031	0.026	0.37	NO
160	EXOSC1	EXOSC1	EXOSC1	8082	0.024	0.37	NO
161	RPS28	RPS28	RPS28	8084	0.024	0.37	NO
162	PAIP1	PAIP1	PAIP1	8109	0.024	0.37	NO
163	RPL6	RPL6	RPL6	8175	0.022	0.37	NO
164	PSMD10	PSMD10	PSMD10	8181	0.022	0.37	NO
165	RPL22	RPL22	RPL22	8237	0.021	0.37	NO
166	NUP188	NUP188	NUP188	8244	0.021	0.37	NO
167	DIS3	DIS3	DIS3	8260	0.021	0.37	NO
168	RPL10A	RPL10A	RPL10A	8316	0.019	0.37	NO
169	RPS5	RPS5	RPS5	8435	0.017	0.36	NO
170	RPLP1	RPLP1	RPLP1	8483	0.016	0.36	NO
171	NUP210	NUP210	NUP210	8517	0.015	0.36	NO
172	RPL14	RPL14	RPL14	8522	0.015	0.36	NO
173	UPF3A	UPF3A	UPF3A	8541	0.015	0.36	NO
174	RAE1	RAE1	RAE1	8643	0.013	0.36	NO
175	RPL9	RPL9	RPL9	8655	0.012	0.36	NO
176	HSPA8	HSPA8	HSPA8	8663	0.012	0.36	NO
177	LSM3	LSM3	LSM3	8664	0.012	0.36	NO
178	SMG7	SMG7	SMG7	8677	0.012	0.36	NO
179	C2orf29	C2orf29	C2orf29	8715	0.011	0.36	NO
180	RPL34	RPL34	RPL34	8793	0.0086	0.35	NO
181	RPL10	RPL10	RPL10	8928	0.006	0.34	NO
182	ZFP36L1	ZFP36L1	ZFP36L1	9004	0.0043	0.34	NO
183	PSME2	PSME2	PSME2	9069	0.0032	0.34	NO
184	NUPL1	NUPL1	NUPL1	9189	0.00094	0.33	NO
185	RPL13A	RPL13A	RPL13A	9221	0.000071	0.33	NO
186	EDC3	EDC3	EDC3	9269	-0.00078	0.33	NO
187	DDX6	DDX6	DDX6	9306	-0.0016	0.32	NO
188	RANBP2	RANBP2	RANBP2	9318	-0.0019	0.32	NO
189	LSM1	LSM1	LSM1	9353	-0.0026	0.32	NO
190	RPL23	RPL23	RPL23	9382	-0.0032	0.32	NO
191	CNOT4	CNOT4	CNOT4	9401	-0.0036	0.32	NO
192	RPL3	RPL3	RPL3	9430	-0.0041	0.32	NO
193	RPL29	RPL29	RPL29	9473	-0.0049	0.32	NO
194	RPL19	RPL19	RPL19	9513	-0.0057	0.32	NO
195	EIF4A2	EIF4A2	EIF4A2	9546	-0.0062	0.31	NO
196	RPS4X	RPS4X	RPS4X	9578	-0.0069	0.31	NO
197	PSMD9	PSMD9	PSMD9	9583	-0.007	0.31	NO
198	RPS3A	RPS3A	RPS3A	9626	-0.008	0.31	NO
199	NUP43	NUP43	NUP43	9709	-0.0097	0.31	NO
200	RPL26L1	RPL26L1	RPL26L1	9749	-0.01	0.3	NO
201	RPL7A	RPL7A	RPL7A	9774	-0.011	0.3	NO
202	TNKS1BP1	TNKS1BP1	TNKS1BP1	9792	-0.011	0.3	NO
203	ETF1	ETF1	ETF1	9800	-0.012	0.3	NO
204	ANP32A	ANP32A	ANP32A	9840	-0.013	0.3	NO
205	RPS26	RPS26	RPS26	9883	-0.014	0.3	NO
206	PPP2R2A	PPP2R2A	PPP2R2A	9910	-0.014	0.3	NO
207	NUP133	NUP133	NUP133	9947	-0.015	0.3	NO
208	PSMD6	PSMD6	PSMD6	9965	-0.015	0.3	NO
209	RPL15	RPL15	RPL15	10006	-0.016	0.3	NO
210	PRMT5	PRMT5	PRMT5	10009	-0.016	0.3	NO
211	RPL23A	RPL23A	RPL23A	10028	-0.017	0.3	NO
212	PPP2R1A	PPP2R1A	PPP2R1A	10082	-0.018	0.3	NO
213	NUP214	NUP214	NUP214	10113	-0.018	0.3	NO
214	PSMF1	PSMF1	PSMF1	10217	-0.021	0.29	NO
215	RPS15	RPS15	RPS15	10220	-0.021	0.29	NO
216	PSMA6	PSMA6	PSMA6	10428	-0.026	0.28	NO
217	MAPK11	MAPK11	MAPK11	10463	-0.026	0.28	NO
218	RPS14	RPS14	RPS14	10475	-0.027	0.28	NO
219	RPS23	RPS23	RPS23	10555	-0.028	0.28	NO
220	MAPKAPK2	MAPKAPK2	MAPKAPK2	10754	-0.033	0.27	NO
221	GEMIN5	GEMIN5	GEMIN5	10978	-0.038	0.26	NO
222	PSMC5	PSMC5	PSMC5	11075	-0.041	0.26	NO
223	YWHAB	YWHAB	YWHAB	11123	-0.042	0.26	NO
224	PSMD3	PSMD3	PSMD3	11163	-0.043	0.26	NO
225	SMN2	SMN2	SMN2	11178	-0.043	0.26	NO
226	SMG1	SMG1	SMG1	11286	-0.046	0.26	NO
227	DCP1A	DCP1A	DCP1A	11388	-0.048	0.25	NO
228	PARN	PARN	PARN	11426	-0.049	0.25	NO
229	DCP1B	DCP1B	DCP1B	11642	-0.055	0.24	NO
230	CNOT2	CNOT2	CNOT2	11808	-0.06	0.24	NO
231	SMG6	SMG6	SMG6	11815	-0.06	0.24	NO
232	EIF4E	EIF4E	EIF4E	11900	-0.062	0.24	NO
233	ZFP36	ZFP36	ZFP36	11931	-0.063	0.24	NO
234	PSMC6	PSMC6	PSMC6	11949	-0.063	0.24	NO
235	TNPO1	TNPO1	TNPO1	11976	-0.064	0.25	NO
236	CASC3	CASC3	CASC3	11996	-0.065	0.25	NO
237	RPL41	RPL41	RPL41	12043	-0.066	0.25	NO
238	AKT1	AKT1	AKT1	12078	-0.066	0.25	NO
239	CNOT6	CNOT6	CNOT6	12087	-0.067	0.26	NO
240	PSMD5	PSMD5	PSMD5	12552	-0.079	0.24	NO
241	CNOT8	CNOT8	CNOT8	12906	-0.088	0.22	NO
242	AAAS	AAAS	AAAS	12962	-0.09	0.22	NO
243	DCP2	DCP2	DCP2	13135	-0.096	0.22	NO
244	EIF4B	EIF4B	EIF4B	13168	-0.097	0.22	NO
245	PPP2CA	PPP2CA	PPP2CA	13462	-0.11	0.21	NO
246	PHAX	PHAX	PHAX	13598	-0.11	0.21	NO
247	PSME1	PSME1	PSME1	14033	-0.13	0.19	NO
248	PRKCD	PRKCD	PRKCD	14833	-0.16	0.16	NO
249	SMN1	SMN1	SMN1	15237	-0.19	0.14	NO
250	TNFSF13	TNFSF13	TNFSF13	15510	-0.2	0.14	NO
251	HSPB1	HSPB1	HSPB1	15730	-0.22	0.14	NO

Figure S87. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CELL CYCLE.

Figure S88. 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: PID AURORA B PATHWAY

Table S45. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MAGOH	MAGOH	MAGOH	1984	0.26	-0.032	YES
2	THOC4	THOC4	THOC4	2289	0.23	0.02	YES
3	NUP93	NUP93	NUP93	2349	0.22	0.084	YES
4	UPF3B	UPF3B	UPF3B	2627	0.2	0.13	YES
5	SEH1L	SEH1L	SEH1L	3159	0.17	0.15	YES
6	NUP205	NUP205	NUP205	3912	0.14	0.15	YES
7	U2AF1	U2AF1	U2AF1	4050	0.13	0.18	YES
8	NUPL2	NUPL2	NUPL2	4195	0.13	0.22	YES
9	NUP88	NUP88	NUP88	4426	0.12	0.24	YES
10	CPSF3	CPSF3	CPSF3	4485	0.12	0.27	YES
11	DHX38	DHX38	DHX38	4513	0.12	0.3	YES
12	NUP85	NUP85	NUP85	4679	0.11	0.33	YES
13	CPSF1	CPSF1	CPSF1	4848	0.1	0.35	YES
14	NUP155	NUP155	NUP155	5071	0.097	0.36	YES
15	NUP153	NUP153	NUP153	5344	0.088	0.38	YES
16	NUP62	NUP62	NUP62	5503	0.084	0.39	YES
17	RBM8A	RBM8A	RBM8A	5714	0.079	0.4	YES
18	SLBP	SLBP	SLBP	5881	0.074	0.42	YES
19	NUP37	NUP37	NUP37	6156	0.068	0.42	YES
20	NUP50	NUP50	NUP50	6194	0.067	0.44	YES
21	NUP54	NUP54	NUP54	6230	0.066	0.46	YES
22	NUP107	NUP107	NUP107	6477	0.06	0.46	YES
23	POM121	POM121	POM121	6510	0.059	0.48	YES
24	RNPS1	RNPS1	RNPS1	6691	0.055	0.49	YES
25	SRRM1	SRRM1	SRRM1	6923	0.049	0.49	YES
26	NCBP2	NCBP2	NCBP2	7213	0.043	0.49	YES
27	NUP35	NUP35	NUP35	7314	0.041	0.49	YES
28	NCBP1	NCBP1	NCBP1	7583	0.035	0.49	NO
29	TPR	TPR	TPR	8031	0.026	0.47	NO
30	NUP188	NUP188	NUP188	8244	0.021	0.47	NO
31	NUP210	NUP210	NUP210	8517	0.015	0.46	NO
32	RAE1	RAE1	RAE1	8643	0.013	0.45	NO
33	U2AF2	U2AF2	U2AF2	8892	0.0068	0.44	NO
34	NUPL1	NUPL1	NUPL1	9189	0.00094	0.43	NO
35	NXF1	NXF1	NXF1	9233	-0.00012	0.42	NO
36	RANBP2	RANBP2	RANBP2	9318	-0.0019	0.42	NO
37	CDC40	CDC40	CDC40	9410	-0.0037	0.42	NO
38	NFX1	NFX1	NFX1	9471	-0.0049	0.41	NO
39	NUP43	NUP43	NUP43	9709	-0.0097	0.4	NO
40	NUP133	NUP133	NUP133	9947	-0.015	0.4	NO
41	NUP214	NUP214	NUP214	10113	-0.018	0.39	NO
42	CPSF2	CPSF2	CPSF2	10841	-0.035	0.36	NO
43	EIF4E	EIF4E	EIF4E	11900	-0.062	0.32	NO
44	AAAS	AAAS	AAAS	12962	-0.09	0.29	NO

Figure S89. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID AURORA B PATHWAY.

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

genes ES table in pathway: PID E2F PATHWAY

Table S46. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CENPA	CENPA	CENPA	202	0.68	0.13	YES
2	AURKB	AURKB	AURKB	246	0.64	0.26	YES
3	BIRC5	BIRC5	BIRC5	520	0.51	0.34	YES
4	DLGAP5	DLGAP5	DLGAP5	873	0.41	0.41	YES
5	TPX2	TPX2	TPX2	1175	0.35	0.46	YES
6	AURKA	AURKA	AURKA	1464	0.32	0.51	YES
7	CDC25B	CDC25B	CDC25B	1844	0.27	0.55	YES
8	TACC3	TACC3	TACC3	2232	0.23	0.57	YES
9	PPP2R5D	PPP2R5D	PPP2R5D	4526	0.11	0.47	NO
10	RAN	RAN	RAN	4936	0.1	0.47	NO
11	NDEL1	NDEL1	NDEL1	5412	0.086	0.46	NO
12	CKAP5	CKAP5	CKAP5	5590	0.081	0.47	NO
13	GIT1	GIT1	GIT1	5914	0.074	0.46	NO
14	AURKAIP1	AURKAIP1	AURKAIP1	6540	0.058	0.44	NO
15	ARHGEF7	ARHGEF7	ARHGEF7	6818	0.052	0.44	NO
16	GADD45A	GADD45A	GADD45A	6948	0.049	0.44	NO
17	PAK1	PAK1	PAK1	8449	0.017	0.36	NO
18	PRKACA	PRKACA	PRKACA	8992	0.0045	0.33	NO
19	OAZ1	OAZ1	OAZ1	9377	-0.0031	0.31	NO
20	NFKBIA	NFKBIA	NFKBIA	9446	-0.0045	0.31	NO
21	GSK3B	GSK3B	GSK3B	9737	-0.01	0.3	NO
22	JUB	JUB	JUB	10166	-0.02	0.28	NO
23	FZR1	FZR1	FZR1	10233	-0.021	0.28	NO
24	TP53	TP53	TP53	10310	-0.022	0.28	NO
25	AKT1	AKT1	AKT1	12078	-0.066	0.2	NO
26	BRCA1	BRCA1	BRCA1	12728	-0.084	0.18	NO
27	TDRD7	TDRD7	TDRD7	12795	-0.085	0.19	NO
28	CPEB1	CPEB1	CPEB1	13647	-0.11	0.17	NO
29	TACC1	TACC1	TACC1	13732	-0.12	0.18	NO
30	MDM2	MDM2	MDM2	14050	-0.13	0.19	NO
31	RASA1	RASA1	RASA1	15256	-0.19	0.17	NO

Figure S91. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID E2F PATHWAY.

Figure S92. Get High-res Image For the top 5 core enriched genes in the pathway: PID E2F PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID MYC ACTIVPATHWAY

Table S47. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	BBOX1	BBOX1	BBOX1	217	0.67	0.12	YES
2	AADAT	AADAT	AADAT	440	0.55	0.21	YES
3	OGDHL	OGDHL	OGDHL	1025	0.38	0.26	YES
4	SUV39H2	SUV39H2	SUV39H2	1094	0.37	0.32	YES
5	PLOD1	PLOD1	PLOD1	1857	0.27	0.33	YES
6	PLOD3	PLOD3	PLOD3	2296	0.23	0.35	YES
7	PLOD2	PLOD2	PLOD2	2692	0.2	0.37	YES
8	ACAT2	ACAT2	ACAT2	3153	0.17	0.38	YES
9	SUV39H1	SUV39H1	SUV39H1	3501	0.16	0.39	YES
10	ALDH1B1	ALDH1B1	ALDH1B1	4593	0.11	0.35	NO
11	EHMT2	EHMT2	EHMT2	5140	0.095	0.34	NO
12	SETD8	SETD8	SETD8	5224	0.092	0.36	NO
13	DOT1L	DOT1L	DOT1L	5741	0.078	0.34	NO
14	SETDB1	SETDB1	SETDB1	5981	0.072	0.34	NO
15	TMLHE	TMLHE	TMLHE	6466	0.06	0.33	NO
16	WHSC1	WHSC1	WHSC1	7006	0.047	0.31	NO
17	PIPOX	PIPOX	PIPOX	7431	0.038	0.29	NO
18	ALDH7A1	ALDH7A1	ALDH7A1	7976	0.026	0.27	NO
19	HADHA	HADHA	HADHA	8412	0.018	0.25	NO
20	SETD1A	SETD1A	SETD1A	8835	0.0077	0.22	NO
21	OGDH	OGDH	OGDH	9244	-0.00032	0.2	NO
22	GCDH	GCDH	GCDH	9600	-0.0075	0.18	NO
23	EHHADH	EHHADH	EHHADH	9836	-0.013	0.17	NO
24	HADH	HADH	HADH	9893	-0.014	0.17	NO
25	SUV420H1	SUV420H1	SUV420H1	9929	-0.015	0.18	NO
26	ALDH9A1	ALDH9A1	ALDH9A1	10127	-0.019	0.17	NO
27	DLST	DLST	DLST	10194	-0.02	0.17	NO
28	AASDHPPT	AASDHPPT	AASDHPPT	10490	-0.027	0.16	NO
29	NSD1	NSD1	NSD1	10741	-0.033	0.15	NO
30	ACAT1	ACAT1	ACAT1	11061	-0.04	0.14	NO
31	ECHS1	ECHS1	ECHS1	11378	-0.048	0.13	NO
32	SETD2	SETD2	SETD2	11611	-0.054	0.13	NO
33	SUV420H2	SUV420H2	SUV420H2	11612	-0.054	0.14	NO
34	SETD1B	SETD1B	SETD1B	11635	-0.055	0.15	NO
35	SETMAR	SETMAR	SETMAR	11884	-0.061	0.15	NO
36	ASH1L	ASH1L	ASH1L	11985	-0.064	0.16	NO
37	WHSC1L1	WHSC1L1	WHSC1L1	12468	-0.077	0.14	NO
38	AASDH	AASDH	AASDH	13195	-0.098	0.12	NO
39	EHMT1	EHMT1	EHMT1	13339	-0.1	0.14	NO
40	ALDH2	ALDH2	ALDH2	13392	-0.1	0.15	NO
41	SETDB2	SETDB2	SETDB2	13630	-0.11	0.16	NO
42	ALDH3A2	ALDH3A2	ALDH3A2	14419	-0.14	0.15	NO
43	AASS	AASS	AASS	14899	-0.16	0.15	NO
44	SETD7	SETD7	SETD7	14989	-0.17	0.18	NO

Figure S93. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID MYC ACTIVPATHWAY.

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

genes ES table in pathway: PID LIS1PATHWAY

Table S48. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	LRP8	LRP8	LRP8	253	0.64	0.2	YES
2	PLA2G7	PLA2G7	PLA2G7	974	0.39	0.29	YES
3	VLDLR	VLDLR	VLDLR	1368	0.33	0.38	YES
4	DCX	DCX	DCX	2456	0.22	0.39	YES
5	KATNA1	KATNA1	KATNA1	2657	0.2	0.44	YES
6	CDK5R1	CDK5R1	CDK5R1	3021	0.18	0.48	YES
7	CDK5R2	CDK5R2	CDK5R2	3073	0.18	0.54	YES
8	PPP2R5D	PPP2R5D	PPP2R5D	4526	0.11	0.5	NO
9	NDEL1	NDEL1	NDEL1	5412	0.086	0.48	NO
10	MAP1B	MAP1B	MAP1B	6605	0.057	0.43	NO
11	YWHAE	YWHAE	YWHAE	7086	0.046	0.42	NO
12	NUDC	NUDC	NUDC	7774	0.031	0.39	NO
13	CSNK2A1	CSNK2A1	CSNK2A1	8148	0.023	0.38	NO
14	DYNLT1	DYNLT1	DYNLT1	8446	0.017	0.37	NO
15	DYNC1H1	DYNC1H1	DYNC1H1	8783	0.0088	0.35	NO
16	PAFAH1B1	PAFAH1B1	PAFAH1B1	9090	0.0028	0.34	NO
17	RELN	RELN	RELN	9180	0.0011	0.33	NO
18	RAC1	RAC1	RAC1	9523	-0.0059	0.31	NO
19	CDK5	CDK5	CDK5	9587	-0.0071	0.31	NO
20	IQGAP1	IQGAP1	IQGAP1	9977	-0.016	0.3	NO
21	PAFAH1B2	PAFAH1B2	PAFAH1B2	10301	-0.022	0.29	NO
22	RHOA	RHOA	RHOA	10950	-0.038	0.26	NO
23	CLIP1	CLIP1	CLIP1	11135	-0.042	0.27	NO
24	LRPAP1	LRPAP1	LRPAP1	11275	-0.046	0.28	NO
25	CDC42	CDC42	CDC42	11321	-0.046	0.29	NO
26	ABL1	ABL1	ABL1	11791	-0.059	0.28	NO
27	PAFAH1B3	PAFAH1B3	PAFAH1B3	11913	-0.062	0.3	NO
28	DAB1	DAB1	DAB1	14831	-0.16	0.19	NO

Figure S95. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID LIS1PATHWAY.

Figure S96. Get High-res Image For the top 5 core enriched genes in the pathway: PID LIS1PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID AURORA A PATHWAY

Table S49. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HMGA1	HMGA1	HMGA1	1508	0.31	0.038	YES
2	NUP93	NUP93	NUP93	2349	0.22	0.08	YES
3	PSIP1	PSIP1	PSIP1	2688	0.2	0.14	YES
4	SEH1L	SEH1L	SEH1L	3159	0.17	0.18	YES
5	NUP205	NUP205	NUP205	3912	0.14	0.19	YES
6	NUPL2	NUPL2	NUPL2	4195	0.13	0.23	YES
7	NUP88	NUP88	NUP88	4426	0.12	0.26	YES
8	NUP85	NUP85	NUP85	4679	0.11	0.29	YES
9	NUP155	NUP155	NUP155	5071	0.097	0.31	YES
10	NUP153	NUP153	NUP153	5344	0.088	0.33	YES
11	SLC25A5	SLC25A5	SLC25A5	5487	0.084	0.35	YES
12	NUP62	NUP62	NUP62	5503	0.084	0.38	YES
13	BANF1	BANF1	BANF1	5973	0.072	0.39	YES
14	NUP37	NUP37	NUP37	6156	0.068	0.4	YES
15	NUP50	NUP50	NUP50	6194	0.067	0.43	YES
16	NUP54	NUP54	NUP54	6230	0.066	0.45	YES
17	NUP107	NUP107	NUP107	6477	0.06	0.46	YES
18	POM121	POM121	POM121	6510	0.059	0.48	YES
19	NUP35	NUP35	NUP35	7314	0.041	0.45	NO
20	SLC25A6	SLC25A6	SLC25A6	7692	0.032	0.45	NO
21	TPR	TPR	TPR	8031	0.026	0.44	NO
22	NUP188	NUP188	NUP188	8244	0.021	0.43	NO
23	NUP210	NUP210	NUP210	8517	0.015	0.42	NO
24	RAE1	RAE1	RAE1	8643	0.013	0.42	NO
25	NUPL1	NUPL1	NUPL1	9189	0.00094	0.39	NO
26	RANBP2	RANBP2	RANBP2	9318	-0.0019	0.39	NO
27	NUP43	NUP43	NUP43	9709	-0.0097	0.37	NO
28	NUP133	NUP133	NUP133	9947	-0.015	0.36	NO
29	NUP214	NUP214	NUP214	10113	-0.018	0.36	NO
30	KPNA1	KPNA1	KPNA1	10227	-0.021	0.36	NO
31	AAAS	AAAS	AAAS	12962	-0.09	0.25	NO
32	SLC25A4	SLC25A4	SLC25A4	13588	-0.11	0.26	NO

Figure S97. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID AURORA A PATHWAY.

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

genes ES table in pathway: PID RB 1PATHWAY

Table S50. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCNE1	CCNE1	CCNE1	37	0.9	0.043	YES
2	MCM10	MCM10	MCM10	359	0.58	0.054	YES
3	CDKN2A	CDKN2A	CDKN2A	380	0.57	0.081	YES
4	CDC25A	CDC25A	CDC25A	397	0.56	0.11	YES
5	CDC45	CDC45	CDC45	472	0.53	0.13	YES
6	E2F2	E2F2	E2F2	568	0.5	0.15	YES
7	MYBL2	MYBL2	MYBL2	577	0.49	0.17	YES
8	CCNA1	CCNA1	CCNA1	593	0.48	0.2	YES
9	CDK6	CDK6	CDK6	677	0.46	0.22	YES
10	CDT1	CDT1	CDT1	683	0.46	0.24	YES
11	SKP2	SKP2	SKP2	842	0.42	0.25	YES
12	RPA4	RPA4	RPA4	931	0.4	0.26	YES
13	CCNA2	CCNA2	CCNA2	955	0.4	0.28	YES
14	CDC7	CDC7	CDC7	1159	0.36	0.29	YES
15	TYMS	TYMS	TYMS	1327	0.33	0.3	YES
16	E2F1	E2F1	E2F1	1349	0.33	0.31	YES
17	E2F3	E2F3	E2F3	1395	0.32	0.32	YES
18	CKS1B	CKS1B	CKS1B	1745	0.28	0.32	YES
19	PKMYT1	PKMYT1	PKMYT1	1809	0.27	0.33	YES
20	MYC	MYC	MYC	1819	0.27	0.34	YES
21	LIN9	LIN9	LIN9	1900	0.26	0.35	YES
22	FBXO5	FBXO5	FBXO5	1964	0.26	0.36	YES
23	E2F5	E2F5	E2F5	1976	0.26	0.37	YES
24	PRIM2	PRIM2	PRIM2	1995	0.25	0.38	YES
25	MCM2	MCM2	MCM2	2047	0.25	0.39	YES
26	DBF4	DBF4	DBF4	2055	0.25	0.4	YES
27	CDK1	CDK1	CDK1	2078	0.25	0.42	YES
28	MCM5	MCM5	MCM5	2094	0.24	0.43	YES
29	CDKN2C	CDKN2C	CDKN2C	2097	0.24	0.44	YES
30	RRM2	RRM2	RRM2	2110	0.24	0.45	YES
31	RBL1	RBL1	RBL1	2153	0.24	0.46	YES
32	MCM7	MCM7	MCM7	2167	0.24	0.47	YES
33	CDC6	CDC6	CDC6	2221	0.23	0.48	YES
34	MCM4	MCM4	MCM4	2488	0.21	0.48	YES
35	PSMB9	PSMB9	PSMB9	2620	0.21	0.48	YES
36	MCM6	MCM6	MCM6	2651	0.2	0.49	YES
37	CCNB1	CCNB1	CCNB1	2670	0.2	0.5	YES
38	CDKN2D	CDKN2D	CDKN2D	2822	0.19	0.5	YES
39	TFDP1	TFDP1	TFDP1	2858	0.19	0.5	YES
40	CCNE2	CCNE2	CCNE2	3054	0.18	0.5	YES
41	PSMB2	PSMB2	PSMB2	3242	0.17	0.5	YES
42	MCM3	MCM3	MCM3	3320	0.16	0.5	YES
43	PPP2R3B	PPP2R3B	PPP2R3B	3606	0.15	0.5	YES
44	LIN37	LIN37	LIN37	3609	0.15	0.5	YES
45	PSMB4	PSMB4	PSMB4	3647	0.15	0.51	YES
46	POLE2	POLE2	POLE2	3681	0.15	0.51	YES
47	E2F4	E2F4	E2F4	3770	0.14	0.52	YES
48	PSMD7	PSMD7	PSMD7	3791	0.14	0.52	YES
49	POLA2	POLA2	POLA2	4163	0.13	0.51	NO
50	MCM8	MCM8	MCM8	4238	0.12	0.51	NO
51	RPS27A	RPS27A	RPS27A	4273	0.12	0.52	NO
52	PSMA7	PSMA7	PSMA7	4451	0.12	0.51	NO
53	PCNA	PCNA	PCNA	4535	0.11	0.51	NO
54	CDK4	CDK4	CDK4	4899	0.1	0.5	NO
55	PSMB8	PSMB8	PSMB8	5272	0.091	0.48	NO
56	PSMD2	PSMD2	PSMD2	5278	0.091	0.48	NO
57	RPA1	RPA1	RPA1	5409	0.086	0.48	NO
58	CCND3	CCND3	CCND3	5426	0.086	0.49	NO
59	PSMD14	PSMD14	PSMD14	5453	0.085	0.49	NO
60	CUL1	CUL1	CUL1	5502	0.084	0.49	NO
61	PSMC3	PSMC3	PSMC3	5532	0.083	0.49	NO
62	PSMB10	PSMB10	PSMB10	5604	0.081	0.49	NO
63	UBA52	UBA52	UBA52	5614	0.081	0.5	NO
64	PSMC2	PSMC2	PSMC2	5622	0.081	0.5	NO
65	PSMD4	PSMD4	PSMD4	5677	0.08	0.5	NO
66	PSMA4	PSMA4	PSMA4	5737	0.078	0.5	NO
67	CDK2	CDK2	CDK2	5808	0.076	0.5	NO
68	PSMC4	PSMC4	PSMC4	5810	0.076	0.5	NO
69	PSMD12	PSMD12	PSMD12	6165	0.068	0.49	NO
70	PSMB6	PSMB6	PSMB6	6209	0.067	0.49	NO
71	PSMA5	PSMA5	PSMA5	6227	0.066	0.49	NO
72	CDKN2B	CDKN2B	CDKN2B	6386	0.062	0.49	NO
73	PSMB7	PSMB7	PSMB7	6434	0.061	0.49	NO
74	PSMB1	PSMB1	PSMB1	6453	0.061	0.49	NO
75	PSMC1	PSMC1	PSMC1	6456	0.061	0.49	NO
76	PSMD8	PSMD8	PSMD8	6549	0.058	0.49	NO
77	RPA2	RPA2	RPA2	6636	0.056	0.49	NO
78	PPP2R1B	PPP2R1B	PPP2R1B	6662	0.055	0.49	NO
79	PSMB5	PSMB5	PSMB5	6699	0.055	0.49	NO
80	PSMD13	PSMD13	PSMD13	6728	0.054	0.49	NO
81	HDAC1	HDAC1	HDAC1	7007	0.047	0.48	NO
82	PSMA2	PSMA2	PSMA2	7054	0.046	0.48	NO
83	PSMD11	PSMD11	PSMD11	7122	0.045	0.48	NO
84	POLE	POLE	POLE	7292	0.042	0.47	NO
85	PSMB3	PSMB3	PSMB3	7612	0.034	0.45	NO
86	PSMA1	PSMA1	PSMA1	7614	0.034	0.46	NO
87	PSMA3	PSMA3	PSMA3	7754	0.031	0.45	NO
88	PSMD1	PSMD1	PSMD1	7948	0.027	0.44	NO
89	PSMD10	PSMD10	PSMD10	8181	0.022	0.43	NO
90	RBBP4	RBBP4	RBBP4	8392	0.018	0.42	NO
91	POLA1	POLA1	POLA1	8466	0.016	0.41	NO
92	DYRK1A	DYRK1A	DYRK1A	8698	0.011	0.4	NO
93	PSME2	PSME2	PSME2	9069	0.0032	0.38	NO
94	PRIM1	PRIM1	PRIM1	9465	-0.0048	0.36	NO
95	PSMD9	PSMD9	PSMD9	9583	-0.007	0.35	NO
96	LIN54	LIN54	LIN54	9734	-0.01	0.35	NO
97	PPP2R2A	PPP2R2A	PPP2R2A	9910	-0.014	0.34	NO
98	PSMD6	PSMD6	PSMD6	9965	-0.015	0.34	NO
99	PPP2R1A	PPP2R1A	PPP2R1A	10082	-0.018	0.33	NO
100	PSMF1	PSMF1	PSMF1	10217	-0.021	0.32	NO
101	DHFR	DHFR	DHFR	10369	-0.024	0.32	NO
102	PSMA6	PSMA6	PSMA6	10428	-0.026	0.31	NO
103	PPP2CB	PPP2CB	PPP2CB	10590	-0.029	0.31	NO
104	WEE1	WEE1	WEE1	10857	-0.036	0.29	NO
105	CCND2	CCND2	CCND2	10905	-0.037	0.29	NO
106	RPA3	RPA3	RPA3	10961	-0.038	0.29	NO
107	PSMC5	PSMC5	PSMC5	11075	-0.041	0.29	NO
108	PSMD3	PSMD3	PSMD3	11163	-0.043	0.28	NO
109	PSMC6	PSMC6	PSMC6	11949	-0.063	0.24	NO
110	MAX	MAX	MAX	12238	-0.07	0.23	NO
111	CDKN1B	CDKN1B	CDKN1B	12250	-0.071	0.24	NO
112	PSMD5	PSMD5	PSMD5	12552	-0.079	0.22	NO
113	CDKN1A	CDKN1A	CDKN1A	13116	-0.095	0.2	NO
114	CDK7	CDK7	CDK7	13409	-0.1	0.18	NO
115	PPP2CA	PPP2CA	PPP2CA	13462	-0.11	0.19	NO
116	RBL2	RBL2	RBL2	13519	-0.11	0.19	NO
117	PSME1	PSME1	PSME1	14033	-0.13	0.17	NO
118	TK2	TK2	TK2	14256	-0.14	0.16	NO
119	MNAT1	MNAT1	MNAT1	14296	-0.14	0.17	NO
120	LIN52	LIN52	LIN52	14377	-0.14	0.17	NO
121	SKP1	SKP1	SKP1	14867	-0.16	0.15	NO
122	CCNH	CCNH	CCNH	15454	-0.2	0.13	NO
123	RB1	RB1	RB1	15759	-0.22	0.12	NO
124	CCND1	CCND1	CCND1	16907	-0.34	0.075	NO

Figure S99. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID RB 1PATHWAY.

Figure S100. Get High-res Image For the top 5 core enriched genes in the pathway: PID RB 1PATHWAY, 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 clus6 enriched pathways

Table 8. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus6. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG GLYCOLYSIS GLUCONEOGENESIS	59	genes.ES.table	0.5	1.7	0.0043	0.16	0.85	0.12	0.082	0.11	0.07	0.018
KEGG CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.49	1.8	0.046	0.16	0.62	0.034	0.00077	0.034	0.051	0.034
KEGG FATTY ACID METABOLISM	39	genes.ES.table	0.66	2	0	0.19	0.18	0.33	0.17	0.28	0	0.042
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM	31	genes.ES.table	0.44	1.3	0.09	0.23	1	0.36	0.24	0.27	0.18	0
KEGG GLYCINE SERINE AND THREONINE METABOLISM	31	genes.ES.table	0.59	1.6	0.012	0.15	0.93	0.36	0.1	0.32	0.078	0.005
KEGG ARGININE AND PROLINE METABOLISM	52	genes.ES.table	0.39	1.3	0.12	0.25	1	0.25	0.2	0.2	0.2	0
KEGG TYROSINE METABOLISM	40	genes.ES.table	0.7	1.9	0	0.18	0.49	0.25	0.044	0.24	0	0.04
KEGG GLYCEROLIPID METABOLISM	45	genes.ES.table	0.55	1.8	0.0021	0.16	0.7	0.42	0.24	0.32	0.056	0.031
KEGG GLYCEROPHOSPHOLIPID METABOLISM	71	genes.ES.table	0.49	1.8	0	0.16	0.61	0.38	0.27	0.28	0.052	0.031
KEGG ETHER LIPID METABOLISM	28	genes.ES.table	0.58	1.6	0.0042	0.15	0.89	0.54	0.3	0.38	0.073	0.011

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

Table S51. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	LEP	LEP	LEP	12	1.2	0.085	YES
2	PCK1	PCK1	PCK1	14	1.1	0.17	YES
3	PLIN1	PLIN1	PLIN1	27	1	0.24	YES
4	ADIPOQ	ADIPOQ	ADIPOQ	40	0.94	0.31	YES
5	FABP4	FABP4	FABP4	50	0.89	0.38	YES
6	SLC2A4	SLC2A4	SLC2A4	62	0.87	0.44	YES
7	CD36	CD36	CD36	101	0.75	0.5	YES
8	LPL	LPL	LPL	107	0.74	0.55	YES
9	PPARG	PPARG	PPARG	193	0.62	0.59	YES
10	ANGPTL4	ANGPTL4	ANGPTL4	287	0.54	0.63	YES
11	EBF1	EBF1	EBF1	353	0.5	0.66	YES
12	WNT1	WNT1	WNT1	485	0.43	0.68	YES
13	EGR2	EGR2	EGR2	766	0.36	0.7	YES
14	WNT10B	WNT10B	WNT10B	923	0.34	0.71	YES
15	KLF4	KLF4	KLF4	1090	0.31	0.73	YES
16	CEBPD	CEBPD	CEBPD	1860	0.23	0.7	NO
17	NR2F2	NR2F2	NR2F2	2411	0.19	0.68	NO
18	PPARGC1A	PPARGC1A	PPARGC1A	2822	0.17	0.68	NO
19	TGFB1	TGFB1	TGFB1	3281	0.15	0.66	NO
20	RXRA	RXRA	RXRA	3791	0.13	0.64	NO
21	SMARCD3	SMARCD3	SMARCD3	4854	0.092	0.59	NO
22	MED16	MED16	MED16	5785	0.069	0.55	NO
23	MED22	MED22	MED22	6490	0.053	0.51	NO
24	MED15	MED15	MED15	6849	0.047	0.49	NO
25	PPARA	PPARA	PPARA	6932	0.045	0.49	NO
26	PRIC285	PRIC285	PRIC285	7140	0.042	0.48	NO
27	MED26	MED26	MED26	7653	0.033	0.46	NO
28	NCOR2	NCOR2	NCOR2	8094	0.027	0.44	NO
29	MED7	MED7	MED7	8349	0.023	0.42	NO
30	CREBBP	CREBBP	CREBBP	8571	0.02	0.41	NO
31	MED11	MED11	MED11	8600	0.02	0.41	NO
32	MED10	MED10	MED10	9093	0.013	0.39	NO
33	CCND3	CCND3	CCND3	9162	0.012	0.38	NO
34	MED25	MED25	MED25	9488	0.0084	0.37	NO
35	HDAC3	HDAC3	HDAC3	9504	0.0082	0.37	NO
36	NCOA1	NCOA1	NCOA1	9715	0.0056	0.36	NO
37	MED4	MED4	MED4	9754	0.0051	0.36	NO
38	TNF	TNF	TNF	9769	0.0049	0.36	NO
39	CEBPB	CEBPB	CEBPB	10169	-0.00022	0.33	NO
40	MED9	MED9	MED9	10226	-0.00084	0.33	NO
41	MED13L	MED13L	MED13L	10376	-0.0026	0.32	NO
42	MED23	MED23	MED23	10642	-0.0055	0.31	NO
43	MED12	MED12	MED12	10745	-0.0068	0.3	NO
44	MED29	MED29	MED29	11117	-0.011	0.28	NO
45	MED6	MED6	MED6	11391	-0.014	0.27	NO
46	MED8	MED8	MED8	11545	-0.016	0.26	NO
47	RELA	RELA	RELA	11817	-0.018	0.25	NO
48	NCOR1	NCOR1	NCOR1	12502	-0.026	0.21	NO
49	MED19	MED19	MED19	12567	-0.027	0.21	NO
50	TBL1X	TBL1X	TBL1X	12661	-0.028	0.21	NO
51	MED18	MED18	MED18	12665	-0.028	0.21	NO
52	NCOA3	NCOA3	NCOA3	12710	-0.029	0.21	NO
53	KLF5	KLF5	KLF5	13016	-0.033	0.2	NO
54	EP300	EP300	EP300	13136	-0.034	0.19	NO
55	MED27	MED27	MED27	13167	-0.034	0.19	NO
56	MED31	MED31	MED31	13264	-0.036	0.19	NO
57	TBL1XR1	TBL1XR1	TBL1XR1	13478	-0.039	0.18	NO
58	CDK19	CDK19	CDK19	13643	-0.041	0.18	NO
59	MED17	MED17	MED17	13718	-0.042	0.17	NO
60	MED21	MED21	MED21	13761	-0.042	0.18	NO
61	MED24	MED24	MED24	14286	-0.051	0.15	NO
62	CDK4	CDK4	CDK4	14491	-0.054	0.14	NO
63	CCNC	CCNC	CCNC	14775	-0.058	0.13	NO
64	SREBF1	SREBF1	SREBF1	15069	-0.064	0.12	NO
65	NCOA6	NCOA6	NCOA6	15588	-0.075	0.097	NO
66	MED20	MED20	MED20	15731	-0.078	0.095	NO
67	MED14	MED14	MED14	15883	-0.082	0.093	NO
68	TGS1	TGS1	TGS1	16313	-0.095	0.076	NO
69	MED30	MED30	MED30	16321	-0.095	0.083	NO
70	NCOA2	NCOA2	NCOA2	16398	-0.097	0.086	NO
71	CDK8	CDK8	CDK8	16731	-0.11	0.076	NO
72	MED1	MED1	MED1	16770	-0.12	0.083	NO

Figure S101. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS.

Figure S102. 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 CITRATE CYCLE TCA CYCLE

Table S52. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PCK1	PCK1	PCK1	14	1.1	0.069	YES
2	LIPE	LIPE	LIPE	57	0.88	0.12	YES
3	SLC2A4	SLC2A4	SLC2A4	62	0.87	0.18	YES
4	PYGM	PYGM	PYGM	63	0.85	0.23	YES
5	PDE3B	PDE3B	PDE3B	165	0.64	0.26	YES
6	PHKG1	PHKG1	PHKG1	186	0.62	0.3	YES
7	GYS2	GYS2	GYS2	195	0.62	0.34	YES
8	ACACB	ACACB	ACACB	318	0.52	0.36	YES
9	SOCS2	SOCS2	SOCS2	517	0.42	0.38	YES
10	SORBS1	SORBS1	SORBS1	551	0.42	0.4	YES
11	MAPK10	MAPK10	MAPK10	761	0.36	0.41	YES
12	G6PC2	G6PC2	G6PC2	1025	0.32	0.42	YES
13	SHC2	SHC2	SHC2	1102	0.31	0.43	YES
14	PIK3R5	PIK3R5	PIK3R5	1417	0.27	0.43	YES
15	SOCS3	SOCS3	SOCS3	1697	0.25	0.43	YES
16	SOCS1	SOCS1	SOCS1	1795	0.24	0.44	YES
17	INPP5D	INPP5D	INPP5D	1880	0.23	0.45	YES
18	IRS2	IRS2	IRS2	1967	0.22	0.46	YES
19	PIK3CD	PIK3CD	PIK3CD	2032	0.22	0.47	YES
20	PRKAR2B	PRKAR2B	PRKAR2B	2211	0.2	0.47	YES
21	GCK	GCK	GCK	2229	0.2	0.48	YES
22	FOXO1	FOXO1	FOXO1	2452	0.19	0.48	YES
23	PIK3CG	PIK3CG	PIK3CG	2637	0.18	0.48	YES
24	FBP1	FBP1	FBP1	2723	0.17	0.49	YES
25	FBP2	FBP2	FBP2	2732	0.17	0.5	YES
26	PPARGC1A	PPARGC1A	PPARGC1A	2822	0.17	0.51	YES
27	IRS1	IRS1	IRS1	3985	0.12	0.45	NO
28	PDE3A	PDE3A	PDE3A	4051	0.12	0.45	NO
29	TRIP10	TRIP10	TRIP10	4083	0.12	0.46	NO
30	HK3	HK3	HK3	4136	0.11	0.46	NO
31	PRKAA2	PRKAA2	PRKAA2	4191	0.11	0.47	NO
32	CALML6	CALML6	CALML6	4194	0.11	0.47	NO
33	AKT3	AKT3	AKT3	4331	0.11	0.47	NO
34	PPP1R3C	PPP1R3C	PPP1R3C	4359	0.11	0.48	NO
35	PRKAR1B	PRKAR1B	PRKAR1B	4395	0.1	0.48	NO
36	PYGL	PYGL	PYGL	4502	0.1	0.48	NO
37	CALML3	CALML3	CALML3	4640	0.098	0.48	NO
38	MKNK2	MKNK2	MKNK2	4847	0.092	0.48	NO
39	PIK3R1	PIK3R1	PIK3R1	4989	0.088	0.47	NO
40	RHOQ	RHOQ	RHOQ	5485	0.075	0.45	NO
41	PPP1R3B	PPP1R3B	PPP1R3B	5666	0.071	0.45	NO
42	RAPGEF1	RAPGEF1	RAPGEF1	5680	0.071	0.45	NO
43	IKBKB	IKBKB	IKBKB	5872	0.066	0.44	NO
44	MKNK1	MKNK1	MKNK1	6060	0.063	0.44	NO
45	CBLC	CBLC	CBLC	6205	0.059	0.43	NO
46	PKLR	PKLR	PKLR	6250	0.058	0.43	NO
47	PRKAA1	PRKAA1	PRKAA1	6448	0.054	0.43	NO
48	BAD	BAD	BAD	6535	0.052	0.42	NO
49	TSC1	TSC1	TSC1	6636	0.051	0.42	NO
50	PRKACB	PRKACB	PRKACB	6648	0.05	0.42	NO
51	INPP5K	INPP5K	INPP5K	6680	0.05	0.43	NO
52	AKT2	AKT2	AKT2	7031	0.043	0.41	NO
53	ARAF	ARAF	ARAF	7387	0.037	0.39	NO
54	TSC2	TSC2	TSC2	7401	0.037	0.39	NO
55	PRKAG2	PRKAG2	PRKAG2	7508	0.035	0.39	NO
56	MAPK3	MAPK3	MAPK3	7546	0.035	0.39	NO
57	PRKAB1	PRKAB1	PRKAB1	7602	0.034	0.39	NO
58	FLOT1	FLOT1	FLOT1	7608	0.034	0.39	NO
59	MAP2K2	MAP2K2	MAP2K2	7776	0.031	0.38	NO
60	RPS6	RPS6	RPS6	7886	0.029	0.38	NO
61	SHC3	SHC3	SHC3	7939	0.029	0.38	NO
62	PHKA2	PHKA2	PHKA2	8142	0.026	0.37	NO
63	INSR	INSR	INSR	8473	0.022	0.35	NO
64	AKT1	AKT1	AKT1	8539	0.021	0.35	NO
65	CALM3	CALM3	CALM3	8542	0.021	0.35	NO
66	PHKG2	PHKG2	PHKG2	8558	0.02	0.35	NO
67	SHC1	SHC1	SHC1	8717	0.018	0.34	NO
68	CBLB	CBLB	CBLB	9356	0.01	0.31	NO
69	PDPK1	PDPK1	PDPK1	9426	0.0092	0.31	NO
70	CBL	CBL	CBL	9623	0.0068	0.3	NO
71	EXOC7	EXOC7	EXOC7	9654	0.0065	0.3	NO
72	RPS6KB2	RPS6KB2	RPS6KB2	9870	0.0034	0.28	NO
73	PIK3R2	PIK3R2	PIK3R2	9981	0.0021	0.28	NO
74	HK1	HK1	HK1	10297	-0.0017	0.26	NO
75	SOS2	SOS2	SOS2	10362	-0.0025	0.26	NO
76	CALM1	CALM1	CALM1	10674	-0.0059	0.24	NO
77	PIK3R3	PIK3R3	PIK3R3	10725	-0.0066	0.24	NO
78	HK2	HK2	HK2	10727	-0.0066	0.24	NO
79	MAP2K1	MAP2K1	MAP2K1	10791	-0.0072	0.24	NO
80	PRKACA	PRKACA	PRKACA	10883	-0.0081	0.23	NO
81	FLOT2	FLOT2	FLOT2	10941	-0.0087	0.23	NO
82	PCK2	PCK2	PCK2	11001	-0.0094	0.22	NO
83	EIF4E2	EIF4E2	EIF4E2	11085	-0.01	0.22	NO
84	KRAS	KRAS	KRAS	11114	-0.011	0.22	NO
85	GYS1	GYS1	GYS1	11268	-0.012	0.21	NO
86	CALML5	CALML5	CALML5	11417	-0.014	0.2	NO
87	PRKAR1A	PRKAR1A	PRKAR1A	11430	-0.014	0.2	NO
88	PRKAB2	PRKAB2	PRKAB2	11522	-0.015	0.2	NO
89	HRAS	HRAS	HRAS	11537	-0.015	0.2	NO
90	RPTOR	RPTOR	RPTOR	11666	-0.017	0.2	NO
91	GRB2	GRB2	GRB2	11676	-0.017	0.2	NO
92	PPP1CA	PPP1CA	PPP1CA	11883	-0.019	0.19	NO
93	EIF4E1B	EIF4E1B	EIF4E1B	12035	-0.021	0.18	NO
94	SOCS4	SOCS4	SOCS4	12134	-0.022	0.18	NO
95	PRKAG1	PRKAG1	PRKAG1	12152	-0.022	0.18	NO
96	SOS1	SOS1	SOS1	12156	-0.022	0.18	NO
97	RAF1	RAF1	RAF1	12185	-0.023	0.18	NO
98	CRKL	CRKL	CRKL	12528	-0.026	0.16	NO
99	PRKX	PRKX	PRKX	12563	-0.027	0.16	NO
100	IRS4	IRS4	IRS4	12760	-0.03	0.15	NO
101	FASN	FASN	FASN	12947	-0.032	0.14	NO
102	CRK	CRK	CRK	13026	-0.033	0.14	NO
103	PPP1CC	PPP1CC	PPP1CC	13041	-0.033	0.14	NO
104	NRAS	NRAS	NRAS	13068	-0.033	0.14	NO
105	PHKB	PHKB	PHKB	13168	-0.034	0.14	NO
106	PYGB	PYGB	PYGB	13196	-0.035	0.14	NO
107	MAPK1	MAPK1	MAPK1	13399	-0.038	0.13	NO
108	MAPK9	MAPK9	MAPK9	13436	-0.038	0.13	NO
109	ELK1	ELK1	ELK1	13556	-0.04	0.13	NO
110	PTPRF	PTPRF	PTPRF	13585	-0.04	0.13	NO
111	SH2B2	SH2B2	SH2B2	13649	-0.041	0.13	NO
112	CALM2	CALM2	CALM2	13769	-0.043	0.12	NO
113	PTPN1	PTPN1	PTPN1	13781	-0.043	0.12	NO
114	RPS6KB1	RPS6KB1	RPS6KB1	13782	-0.043	0.13	NO
115	PRKCZ	PRKCZ	PRKCZ	14029	-0.047	0.12	NO
116	EIF4E	EIF4E	EIF4E	14084	-0.047	0.12	NO
117	PIK3CA	PIK3CA	PIK3CA	14366	-0.052	0.1	NO
118	RHEB	RHEB	RHEB	14651	-0.056	0.092	NO
119	PIK3CB	PIK3CB	PIK3CB	15058	-0.063	0.073	NO
120	MTOR	MTOR	MTOR	15061	-0.063	0.077	NO
121	SREBF1	SREBF1	SREBF1	15069	-0.064	0.08	NO
122	PPP1CB	PPP1CB	PPP1CB	15265	-0.068	0.074	NO
123	PPP1R3D	PPP1R3D	PPP1R3D	15558	-0.074	0.062	NO
124	PRKAR2A	PRKAR2A	PRKAR2A	15878	-0.082	0.05	NO
125	EIF4EBP1	EIF4EBP1	EIF4EBP1	15902	-0.083	0.054	NO
126	GSK3B	GSK3B	GSK3B	15904	-0.083	0.059	NO
127	PRKCI	PRKCI	PRKCI	16325	-0.095	0.042	NO
128	ACACA	ACACA	ACACA	16363	-0.096	0.045	NO
129	MAPK8	MAPK8	MAPK8	16664	-0.11	0.036	NO
130	BRAF	BRAF	BRAF	16924	-0.12	0.029	NO
131	PHKA1	PHKA1	PHKA1	17192	-0.14	0.023	NO
132	PRKAG3	PRKAG3	PRKAG3	18091	-0.28	-0.0095	NO
133	SHC4	SHC4	SHC4	18188	-0.32	0.0048	NO

Figure S103. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CITRATE CYCLE TCA CYCLE.

Figure S104. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CITRATE CYCLE TCA 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 FATTY ACID METABOLISM

Table S53. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PCK1	PCK1	PCK1	14	1.1	0.14	YES
2	PYGM	PYGM	PYGM	63	0.85	0.24	YES
3	PFKFB1	PFKFB1	PFKFB1	86	0.78	0.34	YES
4	PHKG1	PHKG1	PHKG1	186	0.62	0.41	YES
5	GYS2	GYS2	GYS2	195	0.62	0.49	YES
6	GYG2	GYG2	GYG2	259	0.56	0.55	YES
7	PFKFB3	PFKFB3	PFKFB3	2660	0.18	0.44	NO
8	FBP1	FBP1	FBP1	2723	0.17	0.46	NO
9	FBP2	FBP2	FBP2	2732	0.17	0.48	NO
10	PC	PC	PC	3680	0.13	0.45	NO
11	ENO3	ENO3	ENO3	4411	0.1	0.42	NO
12	PGAM2	PGAM2	PGAM2	4447	0.1	0.43	NO
13	PYGL	PYGL	PYGL	4502	0.1	0.44	NO
14	ALDOB	ALDOB	ALDOB	4521	0.1	0.45	NO
15	ALDOC	ALDOC	ALDOC	5127	0.084	0.43	NO
16	PPP2R1B	PPP2R1B	PPP2R1B	5928	0.065	0.4	NO
17	GBE1	GBE1	GBE1	6228	0.059	0.39	NO
18	PKLR	PKLR	PKLR	6250	0.058	0.39	NO
19	PRKACB	PRKACB	PRKACB	6648	0.05	0.38	NO
20	GAPDHS	GAPDHS	GAPDHS	6867	0.046	0.37	NO
21	PHKA2	PHKA2	PHKA2	8142	0.026	0.3	NO
22	CALM3	CALM3	CALM3	8542	0.021	0.28	NO
23	PHKG2	PHKG2	PHKG2	8558	0.02	0.29	NO
24	SLC25A12	SLC25A12	SLC25A12	8708	0.018	0.28	NO
25	PPP2CB	PPP2CB	PPP2CB	8995	0.014	0.27	NO
26	PGM1	PGM1	PGM1	9550	0.0077	0.24	NO
27	SLC25A1	SLC25A1	SLC25A1	9615	0.0069	0.23	NO
28	PFKM	PFKM	PFKM	9624	0.0068	0.23	NO
29	UGP2	UGP2	UGP2	9676	0.0061	0.23	NO
30	PFKL	PFKL	PFKL	9836	0.0039	0.22	NO
31	PPP2R1A	PPP2R1A	PPP2R1A	10629	-0.0053	0.18	NO
32	CALM1	CALM1	CALM1	10674	-0.0059	0.18	NO
33	PRKACA	PRKACA	PRKACA	10883	-0.0081	0.17	NO
34	PCK2	PCK2	PCK2	11001	-0.0094	0.16	NO
35	GYS1	GYS1	GYS1	11268	-0.012	0.15	NO
36	AGL	AGL	AGL	11546	-0.016	0.14	NO
37	PPP2CA	PPP2CA	PPP2CA	12131	-0.022	0.11	NO
38	SLC25A11	SLC25A11	SLC25A11	12366	-0.025	0.098	NO
39	MDH1	MDH1	MDH1	12994	-0.032	0.068	NO
40	PHKB	PHKB	PHKB	13168	-0.034	0.063	NO
41	PYGB	PYGB	PYGB	13196	-0.035	0.066	NO
42	CALM2	CALM2	CALM2	13769	-0.043	0.04	NO
43	ALDOA	ALDOA	ALDOA	13928	-0.045	0.036	NO
44	PKM2	PKM2	PKM2	14047	-0.047	0.036	NO
45	GYG1	GYG1	GYG1	14151	-0.048	0.036	NO
46	PGM2	PGM2	PGM2	14251	-0.05	0.037	NO
47	GOT1	GOT1	GOT1	14280	-0.05	0.042	NO
48	PGAM1	PGAM1	PGAM1	14480	-0.054	0.038	NO
49	GPI	GPI	GPI	14486	-0.054	0.044	NO
50	MDH2	MDH2	MDH2	14762	-0.058	0.036	NO
51	PPP2R5D	PPP2R5D	PPP2R5D	15110	-0.064	0.025	NO
52	ENO2	ENO2	ENO2	15198	-0.066	0.028	NO
53	SLC25A10	SLC25A10	SLC25A10	15303	-0.068	0.031	NO
54	PGK1	PGK1	PGK1	15631	-0.076	0.023	NO
55	TPI1	TPI1	TPI1	15737	-0.079	0.027	NO
56	GAPDH	GAPDH	GAPDH	16063	-0.087	0.02	NO
57	GOT2	GOT2	GOT2	16067	-0.087	0.031	NO
58	ENO1	ENO1	ENO1	16173	-0.09	0.036	NO
59	PFKP	PFKP	PFKP	16464	-0.1	0.033	NO
60	PFKFB4	PFKFB4	PFKFB4	16909	-0.12	0.023	NO
61	SLC25A13	SLC25A13	SLC25A13	17083	-0.13	0.03	NO
62	PHKA1	PHKA1	PHKA1	17192	-0.14	0.042	NO
63	PFKFB2	PFKFB2	PFKFB2	17193	-0.14	0.06	NO

Figure S105. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FATTY ACID METABOLISM.

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

Table S54. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ADH1A	ADH1A	ADH1A	13	1.1	0.16	YES
2	ADH1B	ADH1B	ADH1B	49	0.89	0.29	YES
3	ADH1C	ADH1C	ADH1C	66	0.85	0.41	YES
4	ACADL	ACADL	ACADL	80	0.79	0.52	YES
5	ADH4	ADH4	ADH4	732	0.37	0.54	YES
6	CYP4A22	CYP4A22	CYP4A22	1481	0.26	0.54	YES
7	ACADS	ACADS	ACADS	1483	0.26	0.58	YES
8	ALDH2	ALDH2	ALDH2	1499	0.26	0.61	YES
9	ACSL1	ACSL1	ACSL1	2394	0.19	0.59	YES
10	CYP4A11	CYP4A11	CYP4A11	2427	0.19	0.62	YES
11	CPT1C	CPT1C	CPT1C	2656	0.18	0.63	YES
12	CPT1B	CPT1B	CPT1B	2667	0.18	0.66	YES
13	ACSL5	ACSL5	ACSL5	3029	0.16	0.66	YES
14	CPT1A	CPT1A	CPT1A	4066	0.12	0.62	NO
15	ACSL4	ACSL4	ACSL4	4399	0.1	0.62	NO
16	ACADVL	ACADVL	ACADVL	5332	0.079	0.58	NO
17	ACADSB	ACADSB	ACADSB	5503	0.075	0.58	NO
18	ADH6	ADH6	ADH6	5616	0.072	0.58	NO
19	ACAA2	ACAA2	ACAA2	6179	0.06	0.56	NO
20	ACAA1	ACAA1	ACAA1	6181	0.06	0.57	NO
21	EHHADH	EHHADH	EHHADH	6454	0.054	0.56	NO
22	HADH	HADH	HADH	7427	0.036	0.51	NO
23	ALDH3A2	ALDH3A2	ALDH3A2	7442	0.036	0.52	NO
24	GCDH	GCDH	GCDH	7464	0.036	0.52	NO
25	ACADM	ACADM	ACADM	7741	0.032	0.51	NO
26	ECHS1	ECHS1	ECHS1	8110	0.026	0.5	NO
27	ADH5	ADH5	ADH5	8493	0.021	0.48	NO
28	HADHB	HADHB	HADHB	9533	0.0079	0.42	NO
29	HADHA	HADHA	HADHA	9593	0.0072	0.42	NO
30	ACOX1	ACOX1	ACOX1	9955	0.0023	0.4	NO
31	ACOX3	ACOX3	ACOX3	10676	-0.0059	0.36	NO
32	ALDH9A1	ALDH9A1	ALDH9A1	11301	-0.013	0.33	NO
33	ACSL6	ACSL6	ACSL6	12059	-0.021	0.29	NO
34	ACSL3	ACSL3	ACSL3	12345	-0.024	0.28	NO
35	CPT2	CPT2	CPT2	12585	-0.027	0.27	NO
36	ACAT1	ACAT1	ACAT1	12671	-0.028	0.27	NO
37	ALDH1B1	ALDH1B1	ALDH1B1	14444	-0.053	0.18	NO
38	ALDH7A1	ALDH7A1	ALDH7A1	15812	-0.08	0.12	NO
39	ACAT2	ACAT2	ACAT2	17142	-0.14	0.062	NO

Figure S107. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

genes ES table in pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM

Table S55. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	LEP	LEP	LEP	12	1.2	0.096	YES
2	PCK1	PCK1	PCK1	14	1.1	0.19	YES
3	ADIPOQ	ADIPOQ	ADIPOQ	40	0.94	0.27	YES
4	SLC2A4	SLC2A4	SLC2A4	62	0.87	0.34	YES
5	CD36	CD36	CD36	101	0.75	0.4	YES
6	RXRG	RXRG	RXRG	285	0.54	0.44	YES
7	ACACB	ACACB	ACACB	318	0.52	0.48	YES
8	LEPR	LEPR	LEPR	522	0.42	0.51	YES
9	MAPK10	MAPK10	MAPK10	761	0.36	0.52	YES
10	G6PC2	G6PC2	G6PC2	1025	0.32	0.54	YES
11	POMC	POMC	POMC	1443	0.27	0.54	YES
12	PRKCQ	PRKCQ	PRKCQ	1478	0.26	0.56	YES
13	TNFRSF1B	TNFRSF1B	TNFRSF1B	1532	0.26	0.58	YES
14	SOCS3	SOCS3	SOCS3	1697	0.25	0.59	YES
15	IRS2	IRS2	IRS2	1967	0.22	0.59	YES
16	ACSL1	ACSL1	ACSL1	2394	0.19	0.58	YES
17	CPT1C	CPT1C	CPT1C	2656	0.18	0.59	YES
18	CPT1B	CPT1B	CPT1B	2667	0.18	0.6	YES
19	PPARGC1A	PPARGC1A	PPARGC1A	2822	0.17	0.61	YES
20	ACSL5	ACSL5	ACSL5	3029	0.16	0.61	YES
21	RXRA	RXRA	RXRA	3791	0.13	0.58	NO
22	IRS1	IRS1	IRS1	3985	0.12	0.58	NO
23	CPT1A	CPT1A	CPT1A	4066	0.12	0.58	NO
24	PRKAA2	PRKAA2	PRKAA2	4191	0.11	0.58	NO
25	AKT3	AKT3	AKT3	4331	0.11	0.59	NO
26	ACSL4	ACSL4	ACSL4	4399	0.1	0.59	NO
27	TRADD	TRADD	TRADD	4556	0.1	0.59	NO
28	JAK2	JAK2	JAK2	5018	0.087	0.57	NO
29	STK11	STK11	STK11	5044	0.086	0.58	NO
30	IKBKG	IKBKG	IKBKG	5344	0.079	0.57	NO
31	AGRP	AGRP	AGRP	5538	0.074	0.57	NO
32	CAMKK1	CAMKK1	CAMKK1	5827	0.068	0.56	NO
33	IKBKB	IKBKB	IKBKB	5872	0.066	0.56	NO
34	NFKBIA	NFKBIA	NFKBIA	6281	0.058	0.54	NO
35	PRKAA1	PRKAA1	PRKAA1	6448	0.054	0.54	NO
36	TNFRSF1A	TNFRSF1A	TNFRSF1A	6631	0.051	0.53	NO
37	TRAF2	TRAF2	TRAF2	6783	0.048	0.53	NO
38	PPARA	PPARA	PPARA	6932	0.045	0.52	NO
39	NFKB1	NFKB1	NFKB1	6947	0.045	0.52	NO
40	AKT2	AKT2	AKT2	7031	0.043	0.52	NO
41	NFKBIB	NFKBIB	NFKBIB	7106	0.042	0.52	NO
42	PRKAG2	PRKAG2	PRKAG2	7508	0.035	0.5	NO
43	PRKAB1	PRKAB1	PRKAB1	7602	0.034	0.5	NO
44	AKT1	AKT1	AKT1	8539	0.021	0.45	NO
45	RXRB	RXRB	RXRB	8873	0.016	0.44	NO
46	CAMKK2	CAMKK2	CAMKK2	9391	0.0096	0.41	NO
47	TNF	TNF	TNF	9769	0.0049	0.39	NO
48	NFKBIE	NFKBIE	NFKBIE	9829	0.004	0.39	NO
49	PCK2	PCK2	PCK2	11001	-0.0094	0.32	NO
50	STAT3	STAT3	STAT3	11374	-0.014	0.3	NO
51	PRKAB2	PRKAB2	PRKAB2	11522	-0.015	0.3	NO
52	RELA	RELA	RELA	11817	-0.018	0.28	NO
53	ACSL6	ACSL6	ACSL6	12059	-0.021	0.27	NO
54	PRKAG1	PRKAG1	PRKAG1	12152	-0.022	0.27	NO
55	ACSL3	ACSL3	ACSL3	12345	-0.024	0.26	NO
56	ADIPOR1	ADIPOR1	ADIPOR1	12657	-0.028	0.24	NO
57	IRS4	IRS4	IRS4	12760	-0.03	0.24	NO
58	MAPK9	MAPK9	MAPK9	13436	-0.038	0.21	NO
59	CHUK	CHUK	CHUK	13509	-0.039	0.21	NO
60	ADIPOR2	ADIPOR2	ADIPOR2	13629	-0.041	0.2	NO
61	PTPN11	PTPN11	PTPN11	14096	-0.048	0.18	NO
62	MTOR	MTOR	MTOR	15061	-0.063	0.13	NO
63	MAPK8	MAPK8	MAPK8	16664	-0.11	0.055	NO
64	SLC2A1	SLC2A1	SLC2A1	16832	-0.12	0.056	NO
65	PRKAG3	PRKAG3	PRKAG3	18091	-0.28	0.01	NO

Figure S109. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM.

Figure S110. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCINE SERINE AND THREONINE 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 ARGININE AND PROLINE METABOLISM

Table S56. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SAA1	SAA1	SAA1	122	0.72	0.11	YES
2	S100B	S100B	S100B	288	0.54	0.18	YES
3	MAPK10	MAPK10	MAPK10	761	0.36	0.21	YES
4	FOS	FOS	FOS	888	0.34	0.26	YES
5	AGER	AGER	AGER	1309	0.28	0.28	YES
6	MAPK11	MAPK11	MAPK11	1587	0.26	0.3	YES
7	DUSP4	DUSP4	DUSP4	1884	0.23	0.32	YES
8	LY96	LY96	LY96	2212	0.2	0.34	YES
9	TLR4	TLR4	TLR4	2237	0.2	0.37	YES
10	JUN	JUN	JUN	2531	0.18	0.38	YES
11	MEF2C	MEF2C	MEF2C	2543	0.18	0.41	YES
12	IRAK2	IRAK2	IRAK2	2959	0.16	0.41	YES
13	DUSP6	DUSP6	DUSP6	3232	0.15	0.42	YES
14	RPS6KA2	RPS6KA2	RPS6KA2	3302	0.15	0.44	YES
15	TLR3	TLR3	TLR3	3307	0.15	0.46	YES
16	NOD1	NOD1	NOD1	3511	0.14	0.47	YES
17	TICAM2	TICAM2	TICAM2	3647	0.13	0.49	YES
18	CD14	CD14	CD14	4517	0.1	0.46	NO
19	RPS6KA3	RPS6KA3	RPS6KA3	4935	0.09	0.45	NO
20	IKBKG	IKBKG	IKBKG	5344	0.079	0.44	NO
21	IKBKB	IKBKB	IKBKB	5872	0.066	0.42	NO
22	PPP2R1B	PPP2R1B	PPP2R1B	5928	0.065	0.42	NO
23	NFKB2	NFKB2	NFKB2	5959	0.065	0.43	NO
24	MAP2K7	MAP2K7	MAP2K7	6072	0.062	0.44	NO
25	MAPK7	MAPK7	MAPK7	6119	0.061	0.44	NO
26	NFKBIA	NFKBIA	NFKBIA	6281	0.058	0.44	NO
27	NFKBIB	NFKBIB	NFKBIB	7106	0.042	0.4	NO
28	S100A12	S100A12	S100A12	7227	0.04	0.4	NO
29	MAPK3	MAPK3	MAPK3	7546	0.035	0.39	NO
30	DUSP7	DUSP7	DUSP7	7753	0.032	0.39	NO
31	MAP2K2	MAP2K2	MAP2K2	7776	0.031	0.39	NO
32	RPS6KA5	RPS6KA5	RPS6KA5	8320	0.024	0.36	NO
33	RIPK1	RIPK1	RIPK1	8513	0.021	0.36	NO
34	MEF2A	MEF2A	MEF2A	8528	0.021	0.36	NO
35	TICAM1	TICAM1	TICAM1	8691	0.018	0.35	NO
36	MAP2K6	MAP2K6	MAP2K6	8728	0.018	0.35	NO
37	DUSP3	DUSP3	DUSP3	8762	0.018	0.36	NO
38	TAB1	TAB1	TAB1	8864	0.016	0.35	NO
39	UBA52	UBA52	UBA52	8895	0.016	0.35	NO
40	PPP2CB	PPP2CB	PPP2CB	8995	0.014	0.35	NO
41	ATF1	ATF1	ATF1	9332	0.01	0.33	NO
42	MAP2K3	MAP2K3	MAP2K3	9837	0.0039	0.3	NO
43	MAPKAPK3	MAPKAPK3	MAPKAPK3	10148	0.000022	0.29	NO
44	RPS27A	RPS27A	RPS27A	10171	-0.00023	0.29	NO
45	CREB1	CREB1	CREB1	10607	-0.005	0.26	NO
46	PPP2R1A	PPP2R1A	PPP2R1A	10629	-0.0053	0.26	NO
47	MAP2K1	MAP2K1	MAP2K1	10791	-0.0072	0.26	NO
48	RPS6KA1	RPS6KA1	RPS6KA1	10810	-0.0073	0.26	NO
49	MAPKAPK2	MAPKAPK2	MAPKAPK2	11065	-0.01	0.24	NO
50	MAPK14	MAPK14	MAPK14	11533	-0.015	0.22	NO
51	HMGB1	HMGB1	HMGB1	11691	-0.017	0.22	NO
52	TRAF6	TRAF6	TRAF6	11721	-0.017	0.22	NO
53	TAB3	TAB3	TAB3	11756	-0.018	0.22	NO
54	NOD2	NOD2	NOD2	11761	-0.018	0.22	NO
55	RELA	RELA	RELA	11817	-0.018	0.22	NO
56	MAP2K4	MAP2K4	MAP2K4	12043	-0.021	0.21	NO
57	PPP2CA	PPP2CA	PPP2CA	12131	-0.022	0.21	NO
58	MAP3K7	MAP3K7	MAP3K7	12987	-0.032	0.17	NO
59	MAPK1	MAPK1	MAPK1	13399	-0.038	0.15	NO
60	MAPK9	MAPK9	MAPK9	13436	-0.038	0.15	NO
61	CHUK	CHUK	CHUK	13509	-0.039	0.16	NO
62	ELK1	ELK1	ELK1	13556	-0.04	0.16	NO
63	APP	APP	APP	13577	-0.04	0.16	NO
64	ATF2	ATF2	ATF2	13924	-0.045	0.15	NO
65	TAB2	TAB2	TAB2	13966	-0.046	0.16	NO
66	IRAK1	IRAK1	IRAK1	13980	-0.046	0.16	NO
67	PPP2R5D	PPP2R5D	PPP2R5D	15110	-0.064	0.11	NO
68	RIPK2	RIPK2	RIPK2	16491	-0.1	0.053	NO
69	MAPK8	MAPK8	MAPK8	16664	-0.11	0.06	NO
70	CDK1	CDK1	CDK1	17603	-0.18	0.037	NO

Figure S111. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ARGININE AND PROLINE METABOLISM.

Figure S112. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ARGININE AND PROLINE 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 TYROSINE METABOLISM

Table S57. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SAA1	SAA1	SAA1	122	0.72	0.098	YES
2	S100B	S100B	S100B	288	0.54	0.17	YES
3	MAPK10	MAPK10	MAPK10	761	0.36	0.19	YES
4	FOS	FOS	FOS	888	0.34	0.24	YES
5	AGER	AGER	AGER	1309	0.28	0.25	YES
6	PELI2	PELI2	PELI2	1524	0.26	0.28	YES
7	MAPK11	MAPK11	MAPK11	1587	0.26	0.31	YES
8	TLR8	TLR8	TLR8	1656	0.25	0.35	YES
9	DUSP4	DUSP4	DUSP4	1884	0.23	0.37	YES
10	TLR9	TLR9	TLR9	2140	0.21	0.38	YES
11	JUN	JUN	JUN	2531	0.18	0.39	YES
12	MEF2C	MEF2C	MEF2C	2543	0.18	0.42	YES
13	TLR7	TLR7	TLR7	2925	0.16	0.42	YES
14	IRAK2	IRAK2	IRAK2	2959	0.16	0.44	YES
15	DUSP6	DUSP6	DUSP6	3232	0.15	0.45	YES
16	RPS6KA2	RPS6KA2	RPS6KA2	3302	0.15	0.46	YES
17	NOD1	NOD1	NOD1	3511	0.14	0.47	YES
18	RPS6KA3	RPS6KA3	RPS6KA3	4935	0.09	0.41	NO
19	MAP3K1	MAP3K1	MAP3K1	5155	0.083	0.41	NO
20	IKBKG	IKBKG	IKBKG	5344	0.079	0.41	NO
21	IKBKB	IKBKB	IKBKB	5872	0.066	0.39	NO
22	PPP2R1B	PPP2R1B	PPP2R1B	5928	0.065	0.4	NO
23	NFKB2	NFKB2	NFKB2	5959	0.065	0.4	NO
24	MAP2K7	MAP2K7	MAP2K7	6072	0.062	0.41	NO
25	MAPK7	MAPK7	MAPK7	6119	0.061	0.41	NO
26	NFKBIA	NFKBIA	NFKBIA	6281	0.058	0.41	NO
27	PELI3	PELI3	PELI3	6598	0.051	0.4	NO
28	ECSIT	ECSIT	ECSIT	7071	0.043	0.38	NO
29	NFKBIB	NFKBIB	NFKBIB	7106	0.042	0.39	NO
30	S100A12	S100A12	S100A12	7227	0.04	0.39	NO
31	MAPK3	MAPK3	MAPK3	7546	0.035	0.38	NO
32	DUSP7	DUSP7	DUSP7	7753	0.032	0.37	NO
33	MAP2K2	MAP2K2	MAP2K2	7776	0.031	0.37	NO
34	RPS6KA5	RPS6KA5	RPS6KA5	8320	0.024	0.34	NO
35	MEF2A	MEF2A	MEF2A	8528	0.021	0.34	NO
36	MAP2K6	MAP2K6	MAP2K6	8728	0.018	0.33	NO
37	DUSP3	DUSP3	DUSP3	8762	0.018	0.33	NO
38	IRAK4	IRAK4	IRAK4	8778	0.017	0.33	NO
39	TAB1	TAB1	TAB1	8864	0.016	0.33	NO
40	PELI1	PELI1	PELI1	8889	0.016	0.33	NO
41	UBA52	UBA52	UBA52	8895	0.016	0.33	NO
42	PPP2CB	PPP2CB	PPP2CB	8995	0.014	0.33	NO
43	ATF1	ATF1	ATF1	9332	0.01	0.31	NO
44	MAP2K3	MAP2K3	MAP2K3	9837	0.0039	0.28	NO
45	MAPKAPK3	MAPKAPK3	MAPKAPK3	10148	0.000022	0.27	NO
46	RPS27A	RPS27A	RPS27A	10171	-0.00023	0.27	NO
47	MYD88	MYD88	MYD88	10374	-0.0026	0.26	NO
48	CREB1	CREB1	CREB1	10607	-0.005	0.24	NO
49	PPP2R1A	PPP2R1A	PPP2R1A	10629	-0.0053	0.24	NO
50	MAP2K1	MAP2K1	MAP2K1	10791	-0.0072	0.24	NO
51	RPS6KA1	RPS6KA1	RPS6KA1	10810	-0.0073	0.24	NO
52	MAPKAPK2	MAPKAPK2	MAPKAPK2	11065	-0.01	0.22	NO
53	MAPK14	MAPK14	MAPK14	11533	-0.015	0.2	NO
54	HMGB1	HMGB1	HMGB1	11691	-0.017	0.19	NO
55	TRAF6	TRAF6	TRAF6	11721	-0.017	0.19	NO
56	TAB3	TAB3	TAB3	11756	-0.018	0.2	NO
57	NOD2	NOD2	NOD2	11761	-0.018	0.2	NO
58	RELA	RELA	RELA	11817	-0.018	0.2	NO
59	MAP2K4	MAP2K4	MAP2K4	12043	-0.021	0.19	NO
60	PPP2CA	PPP2CA	PPP2CA	12131	-0.022	0.19	NO
61	MAP3K7	MAP3K7	MAP3K7	12987	-0.032	0.14	NO
62	MAPK1	MAPK1	MAPK1	13399	-0.038	0.13	NO
63	MAPK9	MAPK9	MAPK9	13436	-0.038	0.13	NO
64	CHUK	CHUK	CHUK	13509	-0.039	0.13	NO
65	ELK1	ELK1	ELK1	13556	-0.04	0.14	NO
66	APP	APP	APP	13577	-0.04	0.14	NO
67	UBE2N	UBE2N	UBE2N	13831	-0.043	0.13	NO
68	ATF2	ATF2	ATF2	13924	-0.045	0.13	NO
69	TAB2	TAB2	TAB2	13966	-0.046	0.14	NO
70	IRAK1	IRAK1	IRAK1	13980	-0.046	0.14	NO
71	PPP2R5D	PPP2R5D	PPP2R5D	15110	-0.064	0.092	NO
72	RIPK2	RIPK2	RIPK2	16491	-0.1	0.031	NO
73	MAPK8	MAPK8	MAPK8	16664	-0.11	0.037	NO
74	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	17564	-0.18	0.013	NO
75	CDK1	CDK1	CDK1	17603	-0.18	0.037	NO

Figure S113. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TYROSINE METABOLISM.

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

genes ES table in pathway: KEGG GLYCEROLIPID METABOLISM

Table S58. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GPD1	GPD1	GPD1	23	1	0.058	YES
2	G0S2	G0S2	G0S2	51	0.89	0.11	YES
3	ACADL	ACADL	ACADL	80	0.79	0.15	YES
4	CD36	CD36	CD36	101	0.75	0.19	YES
5	PPARG	PPARG	PPARG	193	0.62	0.22	YES
6	ANGPTL4	ANGPTL4	ANGPTL4	287	0.54	0.25	YES
7	ACACB	ACACB	ACACB	318	0.52	0.28	YES
8	DGAT2	DGAT2	DGAT2	385	0.48	0.3	YES
9	GPAM	GPAM	GPAM	442	0.45	0.32	YES
10	HMGCS2	HMGCS2	HMGCS2	638	0.39	0.33	YES
11	CYP7A1	CYP7A1	CYP7A1	696	0.38	0.35	YES
12	ELOVL3	ELOVL3	ELOVL3	789	0.36	0.37	YES
13	AGPAT9	AGPAT9	AGPAT9	1064	0.32	0.37	YES
14	GPAT2	GPAT2	GPAT2	1080	0.31	0.39	YES
15	ACADS	ACADS	ACADS	1483	0.26	0.38	YES
16	ABCB4	ABCB4	ABCB4	1659	0.25	0.38	YES
17	AGPAT2	AGPAT2	AGPAT2	1705	0.24	0.4	YES
18	ELOVL2	ELOVL2	ELOVL2	2199	0.21	0.38	YES
19	ACSL1	ACSL1	ACSL1	2394	0.19	0.38	YES
20	CYP4A11	CYP4A11	CYP4A11	2427	0.19	0.39	YES
21	CTGF	CTGF	CTGF	2582	0.18	0.39	YES
22	CPT1B	CPT1B	CPT1B	2667	0.18	0.4	YES
23	PPARGC1A	PPARGC1A	PPARGC1A	2822	0.17	0.4	YES
24	ACSL5	ACSL5	ACSL5	3029	0.16	0.4	YES
25	APOA1	APOA1	APOA1	3082	0.16	0.4	YES
26	PLIN2	PLIN2	PLIN2	3093	0.16	0.41	YES
27	SLC27A1	SLC27A1	SLC27A1	3100	0.16	0.42	YES
28	PPARGC1B	PPARGC1B	PPARGC1B	3252	0.15	0.42	YES
29	CYP1A1	CYP1A1	CYP1A1	3479	0.14	0.42	YES
30	ABCA1	ABCA1	ABCA1	3726	0.13	0.41	YES
31	PCCA	PCCA	PCCA	3741	0.13	0.42	YES
32	RXRA	RXRA	RXRA	3791	0.13	0.42	YES
33	RORA	RORA	RORA	3893	0.12	0.42	YES
34	CPT1A	CPT1A	CPT1A	4066	0.12	0.42	YES
35	GLIPR1	GLIPR1	GLIPR1	4077	0.12	0.42	YES
36	PRKAA2	PRKAA2	PRKAA2	4191	0.11	0.42	YES
37	SLC25A20	SLC25A20	SLC25A20	4386	0.11	0.42	YES
38	ACSL4	ACSL4	ACSL4	4399	0.1	0.42	YES
39	AGPAT4	AGPAT4	AGPAT4	4828	0.092	0.41	NO
40	NPAS2	NPAS2	NPAS2	4835	0.092	0.41	NO
41	SMARCD3	SMARCD3	SMARCD3	4854	0.092	0.42	NO
42	LPCAT4	LPCAT4	LPCAT4	4881	0.091	0.42	NO
43	PEX11A	PEX11A	PEX11A	5135	0.084	0.41	NO
44	ACADVL	ACADVL	ACADVL	5332	0.079	0.4	NO
45	SIN3B	SIN3B	SIN3B	5422	0.077	0.4	NO
46	AGT	AGT	AGT	5637	0.072	0.4	NO
47	MED16	MED16	MED16	5785	0.069	0.39	NO
48	MED22	MED22	MED22	6490	0.053	0.36	NO
49	ESRRA	ESRRA	ESRRA	6689	0.05	0.35	NO
50	MED15	MED15	MED15	6849	0.047	0.34	NO
51	PPARA	PPARA	PPARA	6932	0.045	0.34	NO
52	LPIN3	LPIN3	LPIN3	7092	0.042	0.33	NO
53	PRIC285	PRIC285	PRIC285	7140	0.042	0.33	NO
54	GPD1L	GPD1L	GPD1L	7202	0.04	0.33	NO
55	HADH	HADH	HADH	7427	0.036	0.32	NO
56	HMGCL	HMGCL	HMGCL	7455	0.036	0.32	NO
57	DGAT1	DGAT1	DGAT1	7463	0.036	0.32	NO
58	PRKAG2	PRKAG2	PRKAG2	7508	0.035	0.32	NO
59	ME1	ME1	ME1	7612	0.034	0.32	NO
60	MED26	MED26	MED26	7653	0.033	0.32	NO
61	NR1D1	NR1D1	NR1D1	7726	0.032	0.32	NO
62	ACADM	ACADM	ACADM	7741	0.032	0.32	NO
63	TEAD2	TEAD2	TEAD2	8078	0.027	0.3	NO
64	NCOR2	NCOR2	NCOR2	8094	0.027	0.3	NO
65	ECHS1	ECHS1	ECHS1	8110	0.026	0.3	NO
66	LPIN2	LPIN2	LPIN2	8254	0.024	0.3	NO
67	MED7	MED7	MED7	8349	0.023	0.29	NO
68	YAP1	YAP1	YAP1	8397	0.023	0.29	NO
69	ELOVL5	ELOVL5	ELOVL5	8464	0.022	0.29	NO
70	CREBBP	CREBBP	CREBBP	8571	0.02	0.28	NO
71	MED11	MED11	MED11	8600	0.02	0.28	NO
72	ARNTL	ARNTL	ARNTL	8743	0.018	0.28	NO
73	TEAD1	TEAD1	TEAD1	8846	0.016	0.27	NO
74	NRF1	NRF1	NRF1	9010	0.014	0.26	NO
75	MED10	MED10	MED10	9093	0.013	0.26	NO
76	MCEE	MCEE	MCEE	9136	0.013	0.26	NO
77	LPCAT1	LPCAT1	LPCAT1	9229	0.012	0.25	NO
78	MED25	MED25	MED25	9488	0.0084	0.24	NO
79	HDAC3	HDAC3	HDAC3	9504	0.0082	0.24	NO
80	HADHB	HADHB	HADHB	9533	0.0079	0.24	NO
81	HADHA	HADHA	HADHA	9593	0.0072	0.24	NO
82	SLC25A1	SLC25A1	SLC25A1	9615	0.0069	0.24	NO
83	TNFRSF21	TNFRSF21	TNFRSF21	9673	0.0062	0.23	NO
84	NCOA1	NCOA1	NCOA1	9715	0.0056	0.23	NO
85	MED4	MED4	MED4	9754	0.0051	0.23	NO
86	ACOX1	ACOX1	ACOX1	9955	0.0023	0.22	NO
87	AGPAT3	AGPAT3	AGPAT3	10094	0.00066	0.21	NO
88	WWTR1	WWTR1	WWTR1	10207	-0.0006	0.2	NO
89	MED9	MED9	MED9	10226	-0.00084	0.2	NO
90	SIN3A	SIN3A	SIN3A	10361	-0.0025	0.2	NO
91	MED13L	MED13L	MED13L	10376	-0.0026	0.2	NO
92	ALAS1	ALAS1	ALAS1	10597	-0.0049	0.18	NO
93	MED23	MED23	MED23	10642	-0.0055	0.18	NO
94	MED12	MED12	MED12	10745	-0.0068	0.18	NO
95	TEAD3	TEAD3	TEAD3	10816	-0.0074	0.17	NO
96	GK	GK	GK	11055	-0.01	0.16	NO
97	DECR1	DECR1	DECR1	11080	-0.01	0.16	NO
98	MED29	MED29	MED29	11117	-0.011	0.16	NO
99	ELOVL7	ELOVL7	ELOVL7	11146	-0.011	0.16	NO
100	NFYB	NFYB	NFYB	11230	-0.012	0.15	NO
101	MED6	MED6	MED6	11391	-0.014	0.14	NO
102	PRKAB2	PRKAB2	PRKAB2	11522	-0.015	0.14	NO
103	MED8	MED8	MED8	11545	-0.016	0.14	NO
104	ACSL6	ACSL6	ACSL6	12059	-0.021	0.11	NO
105	ACSL3	ACSL3	ACSL3	12345	-0.024	0.097	NO
106	NCOR1	NCOR1	NCOR1	12502	-0.026	0.09	NO
107	TECR	TECR	TECR	12551	-0.027	0.088	NO
108	MED19	MED19	MED19	12567	-0.027	0.089	NO
109	AGPAT6	AGPAT6	AGPAT6	12580	-0.027	0.09	NO
110	CPT2	CPT2	CPT2	12585	-0.027	0.091	NO
111	TBL1X	TBL1X	TBL1X	12661	-0.028	0.089	NO
112	MED18	MED18	MED18	12665	-0.028	0.09	NO
113	ACAT1	ACAT1	ACAT1	12671	-0.028	0.092	NO
114	NCOA3	NCOA3	NCOA3	12710	-0.029	0.091	NO
115	FHL2	FHL2	FHL2	12764	-0.03	0.09	NO
116	FASN	FASN	FASN	12947	-0.032	0.082	NO
117	EP300	EP300	EP300	13136	-0.034	0.073	NO
118	MED27	MED27	MED27	13167	-0.034	0.073	NO
119	MED31	MED31	MED31	13264	-0.036	0.07	NO
120	AGPAT1	AGPAT1	AGPAT1	13420	-0.038	0.064	NO
121	TBL1XR1	TBL1XR1	TBL1XR1	13478	-0.039	0.063	NO
122	LPIN1	LPIN1	LPIN1	13609	-0.041	0.058	NO
123	CDK19	CDK19	CDK19	13643	-0.041	0.058	NO
124	ELOVL1	ELOVL1	ELOVL1	13651	-0.041	0.06	NO
125	MED17	MED17	MED17	13718	-0.042	0.059	NO
126	FDFT1	FDFT1	FDFT1	13750	-0.042	0.06	NO
127	MED21	MED21	MED21	13761	-0.042	0.062	NO
128	SREBF2	SREBF2	SREBF2	13772	-0.043	0.064	NO
129	MUT	MUT	MUT	13882	-0.044	0.06	NO
130	PCCB	PCCB	PCCB	13937	-0.045	0.06	NO
131	OXCT1	OXCT1	OXCT1	14113	-0.048	0.053	NO
132	BDH1	BDH1	BDH1	14234	-0.05	0.049	NO
133	MED24	MED24	MED24	14286	-0.051	0.049	NO
134	HSD17B12	HSD17B12	HSD17B12	14560	-0.055	0.037	NO
135	HMGCS1	HMGCS1	HMGCS1	14617	-0.056	0.037	NO
136	APOA5	APOA5	APOA5	14702	-0.057	0.036	NO
137	CCNC	CCNC	CCNC	14775	-0.058	0.035	NO
138	AGPAT5	AGPAT5	AGPAT5	14818	-0.058	0.036	NO
139	SREBF1	SREBF1	SREBF1	15069	-0.064	0.026	NO
140	HMGCR	HMGCR	HMGCR	15080	-0.064	0.029	NO
141	TEAD4	TEAD4	TEAD4	15218	-0.067	0.025	NO
142	TXNRD1	TXNRD1	TXNRD1	15237	-0.067	0.028	NO
143	NCOA6	NCOA6	NCOA6	15588	-0.075	0.013	NO
144	MED20	MED20	MED20	15731	-0.078	0.0096	NO
145	ACLY	ACLY	ACLY	15872	-0.082	0.0065	NO
146	MED14	MED14	MED14	15883	-0.082	0.011	NO
147	ELOVL4	ELOVL4	ELOVL4	15978	-0.085	0.01	NO
148	GRHL1	GRHL1	GRHL1	16303	-0.095	-0.0022	NO
149	GPD2	GPD2	GPD2	16311	-0.095	0.0028	NO
150	TGS1	TGS1	TGS1	16313	-0.095	0.0082	NO
151	MED30	MED30	MED30	16321	-0.095	0.013	NO
152	ACACA	ACACA	ACACA	16363	-0.096	0.016	NO
153	NCOA2	NCOA2	NCOA2	16398	-0.097	0.02	NO
154	TIAM2	TIAM2	TIAM2	16427	-0.098	0.024	NO
155	LCLAT1	LCLAT1	LCLAT1	16494	-0.1	0.026	NO
156	NFYA	NFYA	NFYA	16500	-0.1	0.032	NO
157	TRIB3	TRIB3	TRIB3	16546	-0.1	0.035	NO
158	CDK8	CDK8	CDK8	16731	-0.11	0.032	NO
159	MED1	MED1	MED1	16770	-0.12	0.036	NO
160	CLOCK	CLOCK	CLOCK	17178	-0.14	0.022	NO
161	ELOVL6	ELOVL6	ELOVL6	17461	-0.16	0.015	NO
162	FADS1	FADS1	FADS1	17758	-0.2	0.01	NO
163	ANKRD1	ANKRD1	ANKRD1	18202	-0.32	0.0041	NO

Figure S115. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCEROLIPID METABOLISM.

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

genes ES table in pathway: KEGG GLYCEROPHOSPHOLIPID METABOLISM

Table S59. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FIGF	FIGF	FIGF	42	0.93	0.034	YES
2	CD36	CD36	CD36	101	0.75	0.061	YES
3	CFD	CFD	CFD	125	0.71	0.088	YES
4	LEFTY2	LEFTY2	LEFTY2	173	0.64	0.11	YES
5	SELP	SELP	SELP	214	0.6	0.13	YES
6	RASGRP2	RASGRP2	RASGRP2	244	0.57	0.15	YES
7	MMRN1	MMRN1	MMRN1	256	0.56	0.17	YES
8	TF	TF	TF	269	0.55	0.2	YES
9	P2RY12	P2RY12	P2RY12	401	0.47	0.21	YES
10	RAPGEF3	RAPGEF3	RAPGEF3	500	0.43	0.22	YES
11	F2RL2	F2RL2	F2RL2	649	0.39	0.22	YES
12	LAT	LAT	LAT	721	0.37	0.24	YES
13	PIK3R6	PIK3R6	PIK3R6	744	0.37	0.25	YES
14	PRKCB	PRKCB	PRKCB	776	0.36	0.26	YES
15	ADRA2A	ADRA2A	ADRA2A	838	0.35	0.27	YES
16	GNG11	GNG11	GNG11	856	0.35	0.28	YES
17	HGF	HGF	HGF	867	0.34	0.3	YES
18	LCK	LCK	LCK	917	0.34	0.31	YES
19	GNA14	GNA14	GNA14	1060	0.32	0.31	YES
20	VWF	VWF	VWF	1125	0.31	0.32	YES
21	APBB1IP	APBB1IP	APBB1IP	1137	0.3	0.33	YES
22	GP5	GP5	GP5	1138	0.3	0.34	YES
23	GNG2	GNG2	GNG2	1177	0.3	0.35	YES
24	F2RL3	F2RL3	F2RL3	1210	0.3	0.36	YES
25	GNAI1	GNAI1	GNAI1	1283	0.29	0.37	YES
26	TRPC3	TRPC3	TRPC3	1315	0.28	0.38	YES
27	MGLL	MGLL	MGLL	1333	0.28	0.39	YES
28	GP1BA	GP1BA	GP1BA	1349	0.28	0.4	YES
29	PIK3R5	PIK3R5	PIK3R5	1417	0.27	0.41	YES
30	PECAM1	PECAM1	PECAM1	1436	0.27	0.42	YES
31	PRKCQ	PRKCQ	PRKCQ	1478	0.26	0.42	YES
32	PROS1	PROS1	PROS1	1508	0.26	0.43	YES
33	SERPINE1	SERPINE1	SERPINE1	1601	0.25	0.44	YES
34	VAV1	VAV1	VAV1	1644	0.25	0.45	YES
35	SERPINF2	SERPINF2	SERPINF2	1711	0.24	0.45	YES
36	TBXA2R	TBXA2R	TBXA2R	1789	0.24	0.46	YES
37	ADRA2B	ADRA2B	ADRA2B	1833	0.23	0.46	YES
38	F13A1	F13A1	F13A1	1916	0.23	0.47	YES
39	GNGT2	GNGT2	GNGT2	1949	0.22	0.48	YES
40	PLA2G4A	PLA2G4A	PLA2G4A	1985	0.22	0.48	YES
41	GNB3	GNB3	GNB3	1988	0.22	0.49	YES
42	TRPC6	TRPC6	TRPC6	2166	0.21	0.49	YES
43	F2R	F2R	F2R	2259	0.2	0.49	YES
44	F2	F2	F2	2298	0.2	0.5	YES
45	VEGFC	VEGFC	VEGFC	2332	0.2	0.5	YES
46	FYN	FYN	FYN	2388	0.19	0.51	YES
47	TGFB3	TGFB3	TGFB3	2420	0.19	0.51	YES
48	DGKB	DGKB	DGKB	2464	0.19	0.52	YES
49	PIK3CG	PIK3CG	PIK3CG	2637	0.18	0.52	YES
50	SRGN	SRGN	SRGN	2658	0.18	0.52	YES
51	PLEK	PLEK	PLEK	2764	0.17	0.52	YES
52	RAPGEF4	RAPGEF4	RAPGEF4	2891	0.16	0.52	YES
53	F8	F8	F8	2963	0.16	0.53	YES
54	LCP2	LCP2	LCP2	2982	0.16	0.53	YES
55	APOA1	APOA1	APOA1	3082	0.16	0.53	YES
56	RAC2	RAC2	RAC2	3108	0.16	0.54	YES
57	PRKCA	PRKCA	PRKCA	3223	0.15	0.54	YES
58	RHOB	RHOB	RHOB	3245	0.15	0.54	YES
59	TGFB1	TGFB1	TGFB1	3281	0.15	0.55	YES
60	DGKA	DGKA	DGKA	3311	0.15	0.55	YES
61	SERPING1	SERPING1	SERPING1	3320	0.15	0.55	YES
62	PLCG2	PLCG2	PLCG2	3365	0.14	0.56	YES
63	HABP4	HABP4	HABP4	3433	0.14	0.56	YES
64	GNG7	GNG7	GNG7	3455	0.14	0.56	YES
65	DGKD	DGKD	DGKD	3670	0.13	0.56	YES
66	ALB	ALB	ALB	3777	0.13	0.56	YES
67	PRKCH	PRKCH	PRKCH	3842	0.12	0.56	YES
68	VEGFB	VEGFB	VEGFB	3847	0.12	0.56	YES
69	DGKI	DGKI	DGKI	4087	0.12	0.55	YES
70	ARRB1	ARRB1	ARRB1	4220	0.11	0.55	YES
71	A2M	A2M	A2M	4227	0.11	0.56	YES
72	COL1A1	COL1A1	COL1A1	4255	0.11	0.56	YES
73	VAV3	VAV3	VAV3	4314	0.11	0.56	YES
74	DGKQ	DGKQ	DGKQ	4316	0.11	0.56	YES
75	AKT3	AKT3	AKT3	4331	0.11	0.57	YES
76	CLU	CLU	CLU	4422	0.1	0.57	NO
77	THPO	THPO	THPO	4614	0.098	0.56	NO
78	COL1A2	COL1A2	COL1A2	4736	0.095	0.56	NO
79	ITGB3	ITGB3	ITGB3	4809	0.093	0.56	NO
80	PRKCE	PRKCE	PRKCE	4825	0.092	0.56	NO
81	P2RY1	P2RY1	P2RY1	4860	0.092	0.56	NO
82	SPARC	SPARC	SPARC	4921	0.09	0.56	NO
83	PIK3R1	PIK3R1	PIK3R1	4989	0.088	0.56	NO
84	GNAI2	GNAI2	GNAI2	5744	0.07	0.52	NO
85	TIMP1	TIMP1	TIMP1	5831	0.068	0.52	NO
86	STX4	STX4	STX4	5838	0.067	0.52	NO
87	ARRB2	ARRB2	ARRB2	5861	0.067	0.52	NO
88	GNB5	GNB5	GNB5	6009	0.064	0.52	NO
89	GNG12	GNG12	GNG12	6169	0.06	0.51	NO
90	DGKG	DGKG	DGKG	6218	0.059	0.51	NO
91	RHOG	RHOG	RHOG	6358	0.056	0.5	NO
92	FCER1G	FCER1G	FCER1G	6488	0.053	0.5	NO
93	GNA11	GNA11	GNA11	6524	0.053	0.5	NO
94	SYK	SYK	SYK	6577	0.052	0.5	NO
95	CD63	CD63	CD63	6650	0.05	0.5	NO
96	CSK	CSK	CSK	6721	0.049	0.5	NO
97	TLN1	TLN1	TLN1	6724	0.049	0.5	NO
98	F5	F5	F5	6731	0.049	0.5	NO
99	PDGFB	PDGFB	PDGFB	6807	0.048	0.5	NO
100	ITPR2	ITPR2	ITPR2	6817	0.047	0.5	NO
101	RAP1A	RAP1A	RAP1A	6899	0.046	0.5	NO
102	AKT2	AKT2	AKT2	7031	0.043	0.49	NO
103	LYN	LYN	LYN	7046	0.043	0.49	NO
104	TGFB2	TGFB2	TGFB2	7084	0.042	0.49	NO
105	DAGLB	DAGLB	DAGLB	7122	0.042	0.49	NO
106	EGF	EGF	EGF	7123	0.042	0.49	NO
107	DAGLA	DAGLA	DAGLA	7125	0.042	0.49	NO
108	FGA	FGA	FGA	7151	0.042	0.49	NO
109	GNG10	GNG10	GNG10	7254	0.039	0.49	NO
110	MAPK3	MAPK3	MAPK3	7546	0.035	0.47	NO
111	THBS1	THBS1	THBS1	7725	0.032	0.47	NO
112	GNA15	GNA15	GNA15	7928	0.029	0.46	NO
113	BCAR1	BCAR1	BCAR1	7934	0.029	0.46	NO
114	PSAP	PSAP	PSAP	8145	0.026	0.45	NO
115	RAP1B	RAP1B	RAP1B	8258	0.024	0.44	NO
116	AKT1	AKT1	AKT1	8539	0.021	0.43	NO
117	CALM3	CALM3	CALM3	8542	0.021	0.43	NO
118	GNA12	GNA12	GNA12	8650	0.019	0.42	NO
119	SHC1	SHC1	SHC1	8717	0.018	0.42	NO
120	MPL	MPL	MPL	8798	0.017	0.42	NO
121	RHOA	RHOA	RHOA	8904	0.016	0.41	NO
122	PRKCD	PRKCD	PRKCD	9308	0.011	0.39	NO
123	PDPK1	PDPK1	PDPK1	9426	0.0092	0.38	NO
124	GNAQ	GNAQ	GNAQ	9542	0.0078	0.38	NO
125	PDGFA	PDGFA	PDGFA	9807	0.0043	0.36	NO
126	WDR1	WDR1	WDR1	9868	0.0034	0.36	NO
127	ACTN2	ACTN2	ACTN2	9945	0.0023	0.35	NO
128	ABCC4	ABCC4	ABCC4	9959	0.0022	0.35	NO
129	PIK3R2	PIK3R2	PIK3R2	9981	0.0021	0.35	NO
130	GNB2	GNB2	GNB2	10153	-0.000068	0.34	NO
131	SCG3	SCG3	SCG3	10223	-0.0008	0.34	NO
132	VCL	VCL	VCL	10271	-0.0014	0.34	NO
133	CALM1	CALM1	CALM1	10674	-0.0059	0.32	NO
134	PIK3R3	PIK3R3	PIK3R3	10725	-0.0066	0.31	NO
135	ACTN1	ACTN1	ACTN1	11011	-0.0096	0.3	NO
136	CDC42	CDC42	CDC42	11049	-0.01	0.3	NO
137	ACTN4	ACTN4	ACTN4	11072	-0.01	0.29	NO
138	CAP1	CAP1	CAP1	11106	-0.011	0.29	NO
139	DGKE	DGKE	DGKE	11288	-0.013	0.28	NO
140	GNG5	GNG5	GNG5	11320	-0.013	0.28	NO
141	PFN1	PFN1	PFN1	11456	-0.014	0.28	NO
142	MAPK14	MAPK14	MAPK14	11533	-0.015	0.27	NO
143	GNG13	GNG13	GNG13	11672	-0.017	0.26	NO
144	GRB2	GRB2	GRB2	11676	-0.017	0.26	NO
145	RAC1	RAC1	RAC1	11763	-0.018	0.26	NO
146	GNA13	GNA13	GNA13	11961	-0.02	0.25	NO
147	SOS1	SOS1	SOS1	12156	-0.022	0.24	NO
148	STXBP3	STXBP3	STXBP3	12167	-0.022	0.24	NO
149	RAF1	RAF1	RAF1	12185	-0.023	0.24	NO
150	GNGT1	GNGT1	GNGT1	12664	-0.028	0.22	NO
151	CFL1	CFL1	CFL1	12735	-0.029	0.21	NO
152	CD9	CD9	CD9	12767	-0.03	0.21	NO
153	BRPF3	BRPF3	BRPF3	12982	-0.032	0.2	NO
154	CRK	CRK	CRK	13026	-0.033	0.2	NO
155	GNB1	GNB1	GNB1	13110	-0.034	0.2	NO
156	ITGA2B	ITGA2B	ITGA2B	13262	-0.036	0.19	NO
157	GNAI3	GNAI3	GNAI3	13281	-0.036	0.19	NO
158	MAPK1	MAPK1	MAPK1	13399	-0.038	0.19	NO
159	FN1	FN1	FN1	13507	-0.039	0.18	NO
160	APP	APP	APP	13577	-0.04	0.18	NO
161	HSPA5	HSPA5	HSPA5	13723	-0.042	0.17	NO
162	CALM2	CALM2	CALM2	13769	-0.043	0.17	NO
163	PTPN1	PTPN1	PTPN1	13781	-0.043	0.17	NO
164	TUBA4A	TUBA4A	TUBA4A	13804	-0.043	0.17	NO
165	ALDOA	ALDOA	ALDOA	13928	-0.045	0.17	NO
166	PRKCZ	PRKCZ	PRKCZ	14029	-0.047	0.17	NO
167	LAMP2	LAMP2	LAMP2	14200	-0.049	0.16	NO
168	RASGRP1	RASGRP1	RASGRP1	14293	-0.051	0.16	NO
169	PIK3CA	PIK3CA	PIK3CA	14366	-0.052	0.15	NO
170	PRKCG	PRKCG	PRKCG	14402	-0.052	0.15	NO
171	CALU	CALU	CALU	14689	-0.057	0.14	NO
172	GNB4	GNB4	GNB4	15052	-0.063	0.12	NO
173	PIK3CB	PIK3CB	PIK3CB	15058	-0.063	0.12	NO
174	SOD1	SOD1	SOD1	15281	-0.068	0.12	NO
175	ITPR3	ITPR3	ITPR3	15462	-0.072	0.11	NO
176	PPIA	PPIA	PPIA	15508	-0.073	0.11	NO
177	SRC	SRC	SRC	15973	-0.085	0.086	NO
178	PPBP	PPBP	PPBP	16015	-0.086	0.087	NO
179	PTK2	PTK2	PTK2	16022	-0.086	0.09	NO
180	GNG3	GNG3	GNG3	16050	-0.087	0.092	NO
181	SERPINA1	SERPINA1	SERPINA1	16068	-0.087	0.094	NO
182	VEGFA	VEGFA	VEGFA	16166	-0.09	0.092	NO
183	GNG4	GNG4	GNG4	16203	-0.091	0.094	NO
184	FGG	FGG	FGG	16385	-0.097	0.088	NO
185	FGB	FGB	FGB	16419	-0.098	0.09	NO
186	YWHAZ	YWHAZ	YWHAZ	16590	-0.11	0.084	NO
187	DGKH	DGKH	DGKH	17873	-0.22	0.022	NO

Figure S117. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCEROPHOSPHOLIPID METABOLISM.

Figure S118. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCEROPHOSPHOLIPID 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 S60. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ADCY5	ADCY5	ADCY5	243	0.57	0.036	YES
2	ADCY4	ADCY4	ADCY4	321	0.51	0.077	YES
3	PDE1B	PDE1B	PDE1B	340	0.51	0.12	YES
4	PDE1A	PDE1A	PDE1A	344	0.5	0.16	YES
5	ADCYAP1R1	ADCYAP1R1	ADCYAP1R1	676	0.38	0.18	YES
6	NTRK1	NTRK1	NTRK1	829	0.35	0.2	YES
7	NGF	NGF	NGF	906	0.34	0.23	YES
8	NR4A1	NR4A1	NR4A1	947	0.33	0.26	YES
9	SHC2	SHC2	SHC2	1102	0.31	0.27	YES
10	NTRK2	NTRK2	NTRK2	1237	0.29	0.29	YES
11	ADCYAP1	ADCYAP1	ADCYAP1	1379	0.27	0.31	YES
12	MAPK11	MAPK11	MAPK11	1587	0.26	0.32	YES
13	DUSP4	DUSP4	DUSP4	1884	0.23	0.32	YES
14	CAMK4	CAMK4	CAMK4	1961	0.22	0.34	YES
15	IRS2	IRS2	IRS2	1967	0.22	0.36	YES
16	PRKAR2B	PRKAR2B	PRKAR2B	2211	0.2	0.36	YES
17	FOXO1	FOXO1	FOXO1	2452	0.19	0.36	YES
18	DNM1	DNM1	DNM1	2520	0.19	0.38	YES
19	MEF2C	MEF2C	MEF2C	2543	0.18	0.39	YES
20	ADORA2A	ADORA2A	ADORA2A	2744	0.17	0.4	YES
21	PRKCA	PRKCA	PRKCA	3223	0.15	0.38	YES
22	DUSP6	DUSP6	DUSP6	3232	0.15	0.4	YES
23	RPS6KA2	RPS6KA2	RPS6KA2	3302	0.15	0.4	YES
24	ADCY1	ADCY1	ADCY1	3329	0.15	0.42	YES
25	MAPK12	MAPK12	MAPK12	3731	0.13	0.41	NO
26	IRS1	IRS1	IRS1	3985	0.12	0.4	NO
27	AKT3	AKT3	AKT3	4331	0.11	0.39	NO
28	PRKAR1B	PRKAR1B	PRKAR1B	4395	0.1	0.4	NO
29	ADCY2	ADCY2	ADCY2	4778	0.094	0.39	NO
30	PRKCE	PRKCE	PRKCE	4825	0.092	0.39	NO
31	ADCY6	ADCY6	ADCY6	4877	0.091	0.4	NO
32	RPS6KA3	RPS6KA3	RPS6KA3	4935	0.09	0.4	NO
33	FOXO4	FOXO4	FOXO4	4954	0.089	0.41	NO
34	PIK3R1	PIK3R1	PIK3R1	4989	0.088	0.41	NO
35	ADCY9	ADCY9	ADCY9	5385	0.078	0.4	NO
36	RAPGEF1	RAPGEF1	RAPGEF1	5680	0.071	0.39	NO
37	ADCY7	ADCY7	ADCY7	5894	0.066	0.38	NO
38	PPP2R1B	PPP2R1B	PPP2R1B	5928	0.065	0.39	NO
39	ADRBK1	ADRBK1	ADRBK1	6110	0.062	0.38	NO
40	MAPK7	MAPK7	MAPK7	6119	0.061	0.39	NO
41	MAP2K5	MAP2K5	MAP2K5	6193	0.06	0.39	NO
42	RALGDS	RALGDS	RALGDS	6305	0.057	0.39	NO
43	BAD	BAD	BAD	6535	0.052	0.38	NO
44	CDKN1B	CDKN1B	CDKN1B	6564	0.052	0.38	NO
45	ADCY3	ADCY3	ADCY3	6610	0.051	0.38	NO
46	PRKACB	PRKACB	PRKACB	6648	0.05	0.39	NO
47	PTEN	PTEN	PTEN	6785	0.048	0.38	NO
48	ITPR2	ITPR2	ITPR2	6817	0.047	0.39	NO
49	RAP1A	RAP1A	RAP1A	6899	0.046	0.38	NO
50	AKT2	AKT2	AKT2	7031	0.043	0.38	NO
51	RALB	RALB	RALB	7061	0.043	0.38	NO
52	CASP9	CASP9	CASP9	7300	0.039	0.37	NO
53	CDKN1A	CDKN1A	CDKN1A	7366	0.038	0.37	NO
54	TSC2	TSC2	TSC2	7401	0.037	0.38	NO
55	MAPK3	MAPK3	MAPK3	7546	0.035	0.37	NO
56	DUSP7	DUSP7	DUSP7	7753	0.032	0.36	NO
57	MAP2K2	MAP2K2	MAP2K2	7776	0.031	0.36	NO
58	AP2A2	AP2A2	AP2A2	7789	0.031	0.36	NO
59	PLCG1	PLCG1	PLCG1	7820	0.03	0.37	NO
60	SHC3	SHC3	SHC3	7939	0.029	0.36	NO
61	RPS6KA5	RPS6KA5	RPS6KA5	8320	0.024	0.34	NO
62	MEF2A	MEF2A	MEF2A	8528	0.021	0.33	NO
63	AKT1	AKT1	AKT1	8539	0.021	0.34	NO
64	CALM3	CALM3	CALM3	8542	0.021	0.34	NO
65	THEM4	THEM4	THEM4	8642	0.019	0.33	NO
66	SHC1	SHC1	SHC1	8717	0.018	0.33	NO
67	DUSP3	DUSP3	DUSP3	8762	0.018	0.33	NO
68	AP2A1	AP2A1	AP2A1	8819	0.017	0.33	NO
69	FOXO3	FOXO3	FOXO3	8891	0.016	0.33	NO
70	RHOA	RHOA	RHOA	8904	0.016	0.33	NO
71	PPP2CB	PPP2CB	PPP2CB	8995	0.014	0.32	NO
72	DNM2	DNM2	DNM2	9139	0.013	0.32	NO
73	AKT1S1	AKT1S1	AKT1S1	9191	0.012	0.31	NO
74	PRKCD	PRKCD	PRKCD	9308	0.011	0.31	NO
75	ATF1	ATF1	ATF1	9332	0.01	0.31	NO
76	PDPK1	PDPK1	PDPK1	9426	0.0092	0.3	NO
77	MLST8	MLST8	MLST8	9755	0.0051	0.29	NO
78	RPS6KB2	RPS6KB2	RPS6KB2	9870	0.0034	0.28	NO
79	PIK3R2	PIK3R2	PIK3R2	9981	0.0021	0.28	NO
80	RICTOR	RICTOR	RICTOR	10067	0.0011	0.27	NO
81	MAPKAPK3	MAPKAPK3	MAPKAPK3	10148	0.000022	0.27	NO
82	FRS2	FRS2	FRS2	10440	-0.0032	0.25	NO
83	CREB1	CREB1	CREB1	10607	-0.005	0.24	NO
84	PPP2R1A	PPP2R1A	PPP2R1A	10629	-0.0053	0.24	NO
85	CALM1	CALM1	CALM1	10674	-0.0059	0.24	NO
86	MAP2K1	MAP2K1	MAP2K1	10791	-0.0072	0.23	NO
87	RPS6KA1	RPS6KA1	RPS6KA1	10810	-0.0073	0.23	NO
88	PRKACA	PRKACA	PRKACA	10883	-0.0081	0.23	NO
89	MAPKAP1	MAPKAP1	MAPKAP1	10933	-0.0086	0.23	NO
90	MAPKAPK2	MAPKAPK2	MAPKAPK2	11065	-0.01	0.22	NO
91	KRAS	KRAS	KRAS	11114	-0.011	0.22	NO
92	STAT3	STAT3	STAT3	11374	-0.014	0.21	NO
93	PRKAR1A	PRKAR1A	PRKAR1A	11430	-0.014	0.2	NO
94	MAPK14	MAPK14	MAPK14	11533	-0.015	0.2	NO
95	HRAS	HRAS	HRAS	11537	-0.015	0.2	NO
96	AP2S1	AP2S1	AP2S1	11596	-0.016	0.2	NO
97	GRB2	GRB2	GRB2	11676	-0.017	0.2	NO
98	CLTA	CLTA	CLTA	11679	-0.017	0.2	NO
99	AP2M1	AP2M1	AP2M1	11804	-0.018	0.19	NO
100	KIDINS220	KIDINS220	KIDINS220	11806	-0.018	0.19	NO
101	PPP2CA	PPP2CA	PPP2CA	12131	-0.022	0.18	NO
102	SOS1	SOS1	SOS1	12156	-0.022	0.18	NO
103	RIT1	RIT1	RIT1	12157	-0.022	0.18	NO
104	RAF1	RAF1	RAF1	12185	-0.023	0.18	NO
105	YWHAB	YWHAB	YWHAB	12414	-0.025	0.17	NO
106	MDM2	MDM2	MDM2	12697	-0.028	0.16	NO
107	CRK	CRK	CRK	13026	-0.033	0.14	NO
108	NRAS	NRAS	NRAS	13068	-0.033	0.14	NO
109	MAPK13	MAPK13	MAPK13	13089	-0.034	0.14	NO
110	GSK3A	GSK3A	GSK3A	13140	-0.034	0.14	NO
111	DNAL4	DNAL4	DNAL4	13159	-0.034	0.15	NO
112	MAPK1	MAPK1	MAPK1	13399	-0.038	0.14	NO
113	CHUK	CHUK	CHUK	13509	-0.039	0.14	NO
114	RALA	RALA	RALA	13531	-0.039	0.14	NO
115	ELK1	ELK1	ELK1	13556	-0.04	0.14	NO
116	CALM2	CALM2	CALM2	13769	-0.043	0.13	NO
117	AP2B1	AP2B1	AP2B1	14166	-0.049	0.11	NO
118	PIK3CA	PIK3CA	PIK3CA	14366	-0.052	0.11	NO
119	PRKCG	PRKCG	PRKCG	14402	-0.052	0.11	NO
120	CLTC	CLTC	CLTC	14642	-0.056	0.1	NO
121	PIK3CB	PIK3CB	PIK3CB	15058	-0.063	0.085	NO
122	MTOR	MTOR	MTOR	15061	-0.063	0.09	NO
123	PPP2R5D	PPP2R5D	PPP2R5D	15110	-0.064	0.093	NO
124	ADCY8	ADCY8	ADCY8	15456	-0.072	0.08	NO
125	ITPR3	ITPR3	ITPR3	15462	-0.072	0.086	NO
126	PRKAR2A	PRKAR2A	PRKAR2A	15878	-0.082	0.071	NO
127	SRC	SRC	SRC	15973	-0.085	0.073	NO
128	PHLPP1	PHLPP1	PHLPP1	16446	-0.099	0.056	NO
129	TRIB3	TRIB3	TRIB3	16546	-0.1	0.059	NO
130	SH3GL2	SH3GL2	SH3GL2	16676	-0.11	0.062	NO
131	BRAF	BRAF	BRAF	16924	-0.12	0.059	NO
132	CDK1	CDK1	CDK1	17603	-0.18	0.037	NO

Figure S119. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ETHER LIPID METABOLISM.

Figure S120. 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

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 clus7 enriched pathways

Table 9. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus7. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG TRYPTOPHAN METABOLISM	38	genes.ES.table	0.62	1.7	0	0.054	0.73	0.4	0.14	0.34	0.02	0
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	43	genes.ES.table	0.41	1.5	0.069	0.14	0.97	0.093	0.064	0.087	0.085	0.001
KEGG INOSITOL PHOSPHATE METABOLISM	53	genes.ES.table	0.39	1.5	0.06	0.18	0.99	0.17	0.14	0.15	0.12	0.002
KEGG ETHER LIPID METABOLISM	28	genes.ES.table	0.51	1.4	0.047	0.2	0.99	0.11	0.054	0.1	0.14	0.003
KEGG RIBOSOME	84	genes.ES.table	0.6	1.6	0.085	0.11	0.94	0.86	0.35	0.56	0.058	0.001
KEGG PROTEASOME	43	genes.ES.table	0.65	1.9	0.0041	0.022	0.35	0.16	0.12	0.14	0	0
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION	238	genes.ES.table	0.74	1.8	0	0.04	0.6	0.54	0.12	0.48	0.013	0
KEGG CHEMOKINE SIGNALING PATHWAY	183	genes.ES.table	0.72	2	0	0.011	0.15	0.44	0.13	0.39	0	0
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM	75	genes.ES.table	0.44	1.6	0.016	0.12	0.95	0.17	0.11	0.15	0.068	0.001
KEGG UBIQUITIN MEDIATED PROTEOLYSIS	133	genes.ES.table	0.24	1.5	0.077	0.19	0.99	0.25	0.31	0.17	0.13	0.002

genes ES table in pathway: KEGG TRYPTOPHAN METABOLISM

Table S61. 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	CD247	CD247	CD247	95	0.86	0.074	YES
2	CD28	CD28	CD28	129	0.82	0.15	YES
3	CD8B	CD8B	CD8B	130	0.82	0.22	YES
4	LCK	LCK	LCK	159	0.8	0.3	YES
5	APOBEC3G	APOBEC3G	APOBEC3G	452	0.56	0.33	YES
6	DOCK2	DOCK2	DOCK2	477	0.53	0.38	YES
7	PSMB9	PSMB9	PSMB9	652	0.45	0.41	YES
8	PSMA8	PSMA8	PSMA8	713	0.42	0.45	YES
9	CD4	CD4	CD4	850	0.37	0.48	YES
10	HCK	HCK	HCK	950	0.34	0.5	YES
11	ELMO1	ELMO1	ELMO1	976	0.34	0.53	YES
12	FYN	FYN	FYN	1084	0.31	0.55	YES
13	PSMB8	PSMB8	PSMB8	1276	0.27	0.57	YES
14	AP1S2	AP1S2	AP1S2	1559	0.22	0.57	YES
15	HLA-A	HLA-A	HLA-A	1573	0.22	0.59	YES
16	PSMB10	PSMB10	PSMB10	1580	0.22	0.61	YES
17	B2M	B2M	B2M	1616	0.21	0.63	YES
18	PSME2	PSME2	PSME2	1644	0.21	0.65	YES
19	PSME1	PSME1	PSME1	2162	0.15	0.64	NO
20	NUP93	NUP93	NUP93	3658	0.078	0.56	NO
21	PSMA5	PSMA5	PSMA5	3693	0.077	0.56	NO
22	SLC25A6	SLC25A6	SLC25A6	3841	0.072	0.56	NO
23	AP1M1	AP1M1	AP1M1	3929	0.07	0.56	NO
24	NUP62	NUP62	NUP62	3942	0.069	0.57	NO
25	NUP210	NUP210	NUP210	4140	0.064	0.57	NO
26	HMGA1	HMGA1	HMGA1	4225	0.063	0.57	NO
27	NUP54	NUP54	NUP54	4550	0.056	0.55	NO
28	PSMA6	PSMA6	PSMA6	4648	0.054	0.55	NO
29	TCEB1	TCEB1	TCEB1	4653	0.054	0.56	NO
30	SLC25A5	SLC25A5	SLC25A5	4659	0.054	0.56	NO
31	UBA52	UBA52	UBA52	5070	0.046	0.55	NO
32	AP1B1	AP1B1	AP1B1	5078	0.046	0.55	NO
33	PSIP1	PSIP1	PSIP1	5085	0.046	0.55	NO
34	PSMA2	PSMA2	PSMA2	5176	0.044	0.55	NO
35	NUPL2	NUPL2	NUPL2	5344	0.041	0.55	NO
36	RPS27A	RPS27A	RPS27A	5423	0.04	0.55	NO
37	PSMF1	PSMF1	PSMF1	5516	0.038	0.55	NO
38	AP2A1	AP2A1	AP2A1	5517	0.038	0.55	NO
39	KPNB1	KPNB1	KPNB1	5631	0.037	0.55	NO
40	PSMA4	PSMA4	PSMA4	5696	0.036	0.55	NO
41	ATP6V1H	ATP6V1H	ATP6V1H	6002	0.032	0.53	NO
42	PSMA3	PSMA3	PSMA3	6017	0.031	0.53	NO
43	NUP153	NUP153	NUP153	6113	0.03	0.53	NO
44	PSMD13	PSMD13	PSMD13	6142	0.03	0.53	NO
45	PSMB1	PSMB1	PSMB1	6196	0.029	0.53	NO
46	RAN	RAN	RAN	6348	0.027	0.53	NO
47	PSMB2	PSMB2	PSMB2	6363	0.027	0.53	NO
48	RCC1	RCC1	RCC1	6576	0.024	0.52	NO
49	PSMD1	PSMD1	PSMD1	6600	0.024	0.52	NO
50	NUP85	NUP85	NUP85	6601	0.024	0.52	NO
51	AP2S1	AP2S1	AP2S1	6639	0.024	0.52	NO
52	NUP43	NUP43	NUP43	6779	0.022	0.52	NO
53	KPNA1	KPNA1	KPNA1	6834	0.021	0.52	NO
54	PSMC4	PSMC4	PSMC4	6856	0.021	0.52	NO
55	AAAS	AAAS	AAAS	6925	0.02	0.51	NO
56	PSMD11	PSMD11	PSMD11	6929	0.02	0.52	NO
57	RANBP1	RANBP1	RANBP1	7080	0.018	0.51	NO
58	PAK2	PAK2	PAK2	7128	0.018	0.51	NO
59	NPM1	NPM1	NPM1	7172	0.018	0.51	NO
60	PSMD14	PSMD14	PSMD14	7175	0.018	0.51	NO
61	NUP35	NUP35	NUP35	7178	0.018	0.51	NO
62	CDK9	CDK9	CDK9	7179	0.018	0.51	NO
63	PSMD7	PSMD7	PSMD7	7190	0.017	0.51	NO
64	PSMB6	PSMB6	PSMB6	7589	0.013	0.49	NO
65	NUP188	NUP188	NUP188	7687	0.012	0.49	NO
66	NUP88	NUP88	NUP88	7717	0.011	0.49	NO
67	PSMD2	PSMD2	PSMD2	7871	0.0098	0.48	NO
68	RANGAP1	RANGAP1	RANGAP1	7894	0.0096	0.48	NO
69	NUP107	NUP107	NUP107	7908	0.0094	0.48	NO
70	PSMC5	PSMC5	PSMC5	7970	0.0088	0.48	NO
71	PSMD12	PSMD12	PSMD12	7986	0.0087	0.48	NO
72	NUP37	NUP37	NUP37	8005	0.0085	0.48	NO
73	PSMA1	PSMA1	PSMA1	8113	0.0073	0.47	NO
74	PSMD6	PSMD6	PSMD6	8119	0.0072	0.47	NO
75	NUP155	NUP155	NUP155	8137	0.007	0.47	NO
76	PSMD10	PSMD10	PSMD10	8153	0.0069	0.47	NO
77	RBX1	RBX1	RBX1	8163	0.0068	0.47	NO
78	PSMB7	PSMB7	PSMB7	8251	0.0059	0.47	NO
79	RAE1	RAE1	RAE1	8297	0.0055	0.47	NO
80	NUP50	NUP50	NUP50	8415	0.0042	0.46	NO
81	PSMA7	PSMA7	PSMA7	8557	0.0027	0.45	NO
82	PSMD8	PSMD8	PSMD8	8638	0.0016	0.45	NO
83	PPIA	PPIA	PPIA	8651	0.0015	0.45	NO
84	POM121	POM121	POM121	8658	0.0014	0.45	NO
85	PSMC3	PSMC3	PSMC3	8679	0.0012	0.45	NO
86	PSME4	PSME4	PSME4	8840	-0.00024	0.44	NO
87	PSMD9	PSMD9	PSMD9	8841	-0.00024	0.44	NO
88	PSMB5	PSMB5	PSMB5	8900	-0.00083	0.43	NO
89	BTRC	BTRC	BTRC	8924	-0.001	0.43	NO
90	NUP214	NUP214	NUP214	9409	-0.0059	0.41	NO
91	XPO1	XPO1	XPO1	9416	-0.006	0.41	NO
92	AP2A2	AP2A2	AP2A2	9436	-0.0062	0.41	NO
93	PACS1	PACS1	PACS1	9622	-0.0082	0.4	NO
94	NUP205	NUP205	NUP205	9626	-0.0082	0.4	NO
95	TPR	TPR	TPR	9700	-0.009	0.4	NO
96	RANBP2	RANBP2	RANBP2	9850	-0.01	0.39	NO
97	BANF1	BANF1	BANF1	9876	-0.01	0.39	NO
98	AP2M1	AP2M1	AP2M1	10000	-0.012	0.38	NO
99	NUP133	NUP133	NUP133	10062	-0.013	0.38	NO
100	PSMB3	PSMB3	PSMB3	10223	-0.014	0.37	NO
101	PSMC2	PSMC2	PSMC2	10488	-0.017	0.36	NO
102	PSMB4	PSMB4	PSMB4	10694	-0.019	0.35	NO
103	RAC1	RAC1	RAC1	11074	-0.024	0.33	NO
104	PSMD4	PSMD4	PSMD4	11111	-0.024	0.33	NO
105	SKP1	SKP1	SKP1	11147	-0.024	0.33	NO
106	CUL5	CUL5	CUL5	11162	-0.024	0.33	NO
107	ARF1	ARF1	ARF1	11184	-0.025	0.33	NO
108	PSMD5	PSMD5	PSMD5	11318	-0.026	0.33	NO
109	TCEB2	TCEB2	TCEB2	11325	-0.026	0.33	NO
110	AP1G1	AP1G1	AP1G1	11477	-0.028	0.33	NO
111	AP2B1	AP2B1	AP2B1	12045	-0.035	0.3	NO
112	PSMC1	PSMC1	PSMC1	12144	-0.036	0.3	NO
113	PSMD3	PSMD3	PSMD3	12250	-0.038	0.29	NO
114	PSMC6	PSMC6	PSMC6	12403	-0.04	0.29	NO
115	SLC25A4	SLC25A4	SLC25A4	12754	-0.046	0.27	NO
116	CCNT1	CCNT1	CCNT1	12953	-0.049	0.27	NO
117	SEH1L	SEH1L	SEH1L	12977	-0.049	0.27	NO
118	AP1M2	AP1M2	AP1M2	13282	-0.054	0.26	NO
119	NUPL1	NUPL1	NUPL1	14404	-0.077	0.2	NO
120	AP1S1	AP1S1	AP1S1	15148	-0.099	0.17	NO

Figure S121. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TRYPTOPHAN METABOLISM.

Figure S122. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TRYPTOPHAN METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

Table S62. 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	CD19	CD19	CD19	8	1	0.069	YES
2	BLK	BLK	BLK	62	0.9	0.13	YES
3	CD79A	CD79A	CD79A	85	0.87	0.19	YES
4	PRKCB	PRKCB	PRKCB	114	0.84	0.24	YES
5	CD79B	CD79B	CD79B	148	0.81	0.3	YES
6	CARD11	CARD11	CARD11	234	0.73	0.34	YES
7	BTK	BTK	BTK	475	0.53	0.37	YES
8	VAV1	VAV1	VAV1	507	0.52	0.4	YES
9	PIK3CD	PIK3CD	PIK3CD	635	0.46	0.42	YES
10	PSMB9	PSMB9	PSMB9	652	0.45	0.46	YES
11	PSMA8	PSMA8	PSMA8	713	0.42	0.48	YES
12	PIK3AP1	PIK3AP1	PIK3AP1	827	0.38	0.5	YES
13	PLCG2	PLCG2	PLCG2	966	0.34	0.52	YES
14	FYN	FYN	FYN	1084	0.31	0.53	YES
15	PSMB8	PSMB8	PSMB8	1276	0.27	0.54	YES
16	SYK	SYK	SYK	1283	0.27	0.56	YES
17	RASGRP1	RASGRP1	RASGRP1	1321	0.26	0.57	YES
18	BLNK	BLNK	BLNK	1327	0.26	0.59	YES
19	LYN	LYN	LYN	1413	0.24	0.6	YES
20	PSMB10	PSMB10	PSMB10	1580	0.22	0.61	YES
21	RASGRP3	RASGRP3	RASGRP3	1615	0.22	0.62	YES
22	PSME2	PSME2	PSME2	1644	0.21	0.64	YES
23	FOXO1	FOXO1	FOXO1	1796	0.19	0.64	YES
24	SH3KBP1	SH3KBP1	SH3KBP1	1958	0.17	0.64	YES
25	NFKBIE	NFKBIE	NFKBIE	2014	0.17	0.65	YES
26	PSME1	PSME1	PSME1	2162	0.15	0.65	YES
27	GRB2	GRB2	GRB2	2705	0.12	0.63	NO
28	MALT1	MALT1	MALT1	2846	0.11	0.63	NO
29	PLCG1	PLCG1	PLCG1	3008	0.1	0.63	NO
30	FOXO4	FOXO4	FOXO4	3063	0.098	0.63	NO
31	NFKBIA	NFKBIA	NFKBIA	3283	0.09	0.63	NO
32	CHUK	CHUK	CHUK	3492	0.083	0.62	NO
33	NFKBIB	NFKBIB	NFKBIB	3513	0.083	0.63	NO
34	RPS6KB2	RPS6KB2	RPS6KB2	3634	0.079	0.62	NO
35	ORAI1	ORAI1	ORAI1	3678	0.078	0.63	NO
36	PSMA5	PSMA5	PSMA5	3693	0.077	0.63	NO
37	FOXO3	FOXO3	FOXO3	4265	0.062	0.6	NO
38	NCK1	NCK1	NCK1	4391	0.059	0.6	NO
39	CBLB	CBLB	CBLB	4456	0.057	0.6	NO
40	PSMA6	PSMA6	PSMA6	4648	0.054	0.6	NO
41	NRAS	NRAS	NRAS	4699	0.053	0.6	NO
42	CBL	CBL	CBL	4701	0.053	0.6	NO
43	CALM3	CALM3	CALM3	4858	0.05	0.6	NO
44	UBA52	UBA52	UBA52	5070	0.046	0.59	NO
45	PSMA2	PSMA2	PSMA2	5176	0.044	0.58	NO
46	IKBKG	IKBKG	IKBKG	5202	0.043	0.58	NO
47	RPS27A	RPS27A	RPS27A	5423	0.04	0.58	NO
48	PSMF1	PSMF1	PSMF1	5516	0.038	0.57	NO
49	PSMA4	PSMA4	PSMA4	5696	0.036	0.57	NO
50	PSMA3	PSMA3	PSMA3	6017	0.031	0.55	NO
51	PSMD13	PSMD13	PSMD13	6142	0.03	0.55	NO
52	PSMB1	PSMB1	PSMB1	6196	0.029	0.55	NO
53	MTOR	MTOR	MTOR	6262	0.028	0.54	NO
54	PSMB2	PSMB2	PSMB2	6363	0.027	0.54	NO
55	SOS1	SOS1	SOS1	6448	0.026	0.54	NO
56	PSMD1	PSMD1	PSMD1	6600	0.024	0.53	NO
57	CASP9	CASP9	CASP9	6616	0.024	0.53	NO
58	AKT2	AKT2	AKT2	6736	0.022	0.53	NO
59	TRIB3	TRIB3	TRIB3	6793	0.022	0.52	NO
60	PSMC4	PSMC4	PSMC4	6856	0.021	0.52	NO
61	PSMD11	PSMD11	PSMD11	6929	0.02	0.52	NO
62	THEM4	THEM4	THEM4	7144	0.018	0.51	NO
63	PSMD14	PSMD14	PSMD14	7175	0.018	0.51	NO
64	PSMD7	PSMD7	PSMD7	7190	0.017	0.51	NO
65	AKT3	AKT3	AKT3	7335	0.016	0.5	NO
66	PSMB6	PSMB6	PSMB6	7589	0.013	0.49	NO
67	AKT1S1	AKT1S1	AKT1S1	7629	0.012	0.49	NO
68	RICTOR	RICTOR	RICTOR	7667	0.012	0.49	NO
69	PSMD2	PSMD2	PSMD2	7871	0.0098	0.48	NO
70	CDKN1B	CDKN1B	CDKN1B	7909	0.0094	0.48	NO
71	PSMC5	PSMC5	PSMC5	7970	0.0088	0.47	NO
72	PSMD12	PSMD12	PSMD12	7986	0.0087	0.47	NO
73	CREB1	CREB1	CREB1	8094	0.0075	0.47	NO
74	PSMA1	PSMA1	PSMA1	8113	0.0073	0.47	NO
75	PSMD6	PSMD6	PSMD6	8119	0.0072	0.47	NO
76	PSMD10	PSMD10	PSMD10	8153	0.0069	0.46	NO
77	BCL10	BCL10	BCL10	8236	0.0061	0.46	NO
78	PSMB7	PSMB7	PSMB7	8251	0.0059	0.46	NO
79	CALM1	CALM1	CALM1	8400	0.0044	0.45	NO
80	PSMA7	PSMA7	PSMA7	8557	0.0027	0.44	NO
81	MAPKAP1	MAPKAP1	MAPKAP1	8600	0.0021	0.44	NO
82	PSMD8	PSMD8	PSMD8	8638	0.0016	0.44	NO
83	PSMC3	PSMC3	PSMC3	8679	0.0012	0.44	NO
84	MAP3K7	MAP3K7	MAP3K7	8695	0.0011	0.44	NO
85	PSME4	PSME4	PSME4	8840	-0.00024	0.43	NO
86	PSMD9	PSMD9	PSMD9	8841	-0.00024	0.43	NO
87	PSMB5	PSMB5	PSMB5	8900	-0.00083	0.43	NO
88	BTRC	BTRC	BTRC	8924	-0.001	0.42	NO
89	RELA	RELA	RELA	8928	-0.001	0.42	NO
90	CUL1	CUL1	CUL1	8957	-0.0014	0.42	NO
91	REL	REL	REL	9239	-0.0043	0.41	NO
92	GSK3A	GSK3A	GSK3A	9513	-0.0068	0.39	NO
93	PSMB3	PSMB3	PSMB3	10223	-0.014	0.36	NO
94	FBXW11	FBXW11	FBXW11	10432	-0.017	0.35	NO
95	NR4A1	NR4A1	NR4A1	10434	-0.017	0.35	NO
96	PSMC2	PSMC2	PSMC2	10488	-0.017	0.34	NO
97	TSC2	TSC2	TSC2	10497	-0.017	0.35	NO
98	PSMB4	PSMB4	PSMB4	10694	-0.019	0.34	NO
99	PSMD4	PSMD4	PSMD4	11111	-0.024	0.32	NO
100	SKP1	SKP1	SKP1	11147	-0.024	0.32	NO
101	ITPR3	ITPR3	ITPR3	11251	-0.026	0.31	NO
102	PSMD5	PSMD5	PSMD5	11318	-0.026	0.31	NO
103	PTEN	PTEN	PTEN	11984	-0.034	0.28	NO
104	PDPK1	PDPK1	PDPK1	12034	-0.035	0.27	NO
105	PSMC1	PSMC1	PSMC1	12144	-0.036	0.27	NO
106	CALM2	CALM2	CALM2	12171	-0.037	0.27	NO
107	IKBKB	IKBKB	IKBKB	12216	-0.037	0.27	NO
108	PSMD3	PSMD3	PSMD3	12250	-0.038	0.27	NO
109	PIK3R1	PIK3R1	PIK3R1	12279	-0.038	0.27	NO
110	HRAS	HRAS	HRAS	12316	-0.039	0.28	NO
111	PSMC6	PSMC6	PSMC6	12403	-0.04	0.27	NO
112	MLST8	MLST8	MLST8	12408	-0.04	0.28	NO
113	KRAS	KRAS	KRAS	13082	-0.05	0.24	NO
114	AKT1	AKT1	AKT1	13673	-0.061	0.21	NO
115	STIM1	STIM1	STIM1	13675	-0.061	0.22	NO
116	BAD	BAD	BAD	13941	-0.066	0.21	NO
117	MDM2	MDM2	MDM2	14057	-0.069	0.21	NO
118	SHC1	SHC1	SHC1	14128	-0.07	0.21	NO
119	CDKN1A	CDKN1A	CDKN1A	14521	-0.08	0.19	NO
120	ITPR2	ITPR2	ITPR2	14939	-0.092	0.17	NO
121	PHLPP1	PHLPP1	PHLPP1	16100	-0.14	0.12	NO

Figure S123. 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 S124. 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 INOSITOL PHOSPHATE METABOLISM

Table S63. 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	CD247	CD247	CD247	95	0.86	0.054	YES
2	CD28	CD28	CD28	129	0.82	0.11	YES
3	CD8B	CD8B	CD8B	130	0.82	0.16	YES
4	LCK	LCK	LCK	159	0.8	0.22	YES
5	CCR5	CCR5	CCR5	260	0.7	0.26	YES
6	APOBEC3G	APOBEC3G	APOBEC3G	452	0.56	0.29	YES
7	DOCK2	DOCK2	DOCK2	477	0.53	0.32	YES
8	PSMB9	PSMB9	PSMB9	652	0.45	0.34	YES
9	PSMA8	PSMA8	PSMA8	713	0.42	0.37	YES
10	CXCR4	CXCR4	CXCR4	814	0.38	0.39	YES
11	CD4	CD4	CD4	850	0.37	0.42	YES
12	HCK	HCK	HCK	950	0.34	0.43	YES
13	ELMO1	ELMO1	ELMO1	976	0.34	0.46	YES
14	FYN	FYN	FYN	1084	0.31	0.47	YES
15	PSMB8	PSMB8	PSMB8	1276	0.27	0.48	YES
16	AP1S2	AP1S2	AP1S2	1559	0.22	0.48	YES
17	HLA-A	HLA-A	HLA-A	1573	0.22	0.49	YES
18	PSMB10	PSMB10	PSMB10	1580	0.22	0.51	YES
19	B2M	B2M	B2M	1616	0.21	0.52	YES
20	PSME2	PSME2	PSME2	1644	0.21	0.53	YES
21	TAF4B	TAF4B	TAF4B	2026	0.16	0.52	YES
22	TAF5	TAF5	TAF5	2117	0.16	0.53	YES
23	PSME1	PSME1	PSME1	2162	0.15	0.54	YES
24	LIG1	LIG1	LIG1	2931	0.1	0.5	NO
25	GTF2E1	GTF2E1	GTF2E1	3348	0.087	0.48	NO
26	NUP93	NUP93	NUP93	3658	0.078	0.47	NO
27	PSMA5	PSMA5	PSMA5	3693	0.077	0.48	NO
28	SLC25A6	SLC25A6	SLC25A6	3841	0.072	0.47	NO
29	POLR2K	POLR2K	POLR2K	3870	0.071	0.48	NO
30	AP1M1	AP1M1	AP1M1	3929	0.07	0.48	NO
31	NUP62	NUP62	NUP62	3942	0.069	0.48	NO
32	NUP210	NUP210	NUP210	4140	0.064	0.48	NO
33	ELL	ELL	ELL	4188	0.063	0.48	NO
34	HMGA1	HMGA1	HMGA1	4225	0.063	0.48	NO
35	NUP54	NUP54	NUP54	4550	0.056	0.47	NO
36	RNGTT	RNGTT	RNGTT	4635	0.054	0.46	NO
37	PSMA6	PSMA6	PSMA6	4648	0.054	0.47	NO
38	TCEB1	TCEB1	TCEB1	4653	0.054	0.47	NO
39	SLC25A5	SLC25A5	SLC25A5	4659	0.054	0.48	NO
40	POLR2D	POLR2D	POLR2D	4882	0.049	0.47	NO
41	NMT2	NMT2	NMT2	4983	0.047	0.46	NO
42	UBA52	UBA52	UBA52	5070	0.046	0.46	NO
43	AP1B1	AP1B1	AP1B1	5078	0.046	0.46	NO
44	PSIP1	PSIP1	PSIP1	5085	0.046	0.47	NO
45	NCBP2	NCBP2	NCBP2	5129	0.045	0.47	NO
46	GTF2B	GTF2B	GTF2B	5150	0.044	0.47	NO
47	PSMA2	PSMA2	PSMA2	5176	0.044	0.47	NO
48	NUPL2	NUPL2	NUPL2	5344	0.041	0.47	NO
49	VPS28	VPS28	VPS28	5389	0.041	0.47	NO
50	RPS27A	RPS27A	RPS27A	5423	0.04	0.47	NO
51	FEN1	FEN1	FEN1	5470	0.039	0.47	NO
52	PSMF1	PSMF1	PSMF1	5516	0.038	0.47	NO
53	AP2A1	AP2A1	AP2A1	5517	0.038	0.47	NO
54	POLR2H	POLR2H	POLR2H	5534	0.038	0.47	NO
55	KPNB1	KPNB1	KPNB1	5631	0.037	0.47	NO
56	TAF11	TAF11	TAF11	5664	0.036	0.47	NO
57	PSMA4	PSMA4	PSMA4	5696	0.036	0.47	NO
58	SUPT5H	SUPT5H	SUPT5H	5778	0.035	0.47	NO
59	SUPT4H1	SUPT4H1	SUPT4H1	5825	0.034	0.47	NO
60	NMT1	NMT1	NMT1	5985	0.032	0.46	NO
61	ATP6V1H	ATP6V1H	ATP6V1H	6002	0.032	0.46	NO
62	PSMA3	PSMA3	PSMA3	6017	0.031	0.46	NO
63	XRCC5	XRCC5	XRCC5	6053	0.031	0.46	NO
64	NUP153	NUP153	NUP153	6113	0.03	0.46	NO
65	PSMD13	PSMD13	PSMD13	6142	0.03	0.46	NO
66	GTF2H4	GTF2H4	GTF2H4	6143	0.03	0.47	NO
67	PSMB1	PSMB1	PSMB1	6196	0.029	0.46	NO
68	CTDP1	CTDP1	CTDP1	6336	0.027	0.46	NO
69	RAN	RAN	RAN	6348	0.027	0.46	NO
70	PSMB2	PSMB2	PSMB2	6363	0.027	0.46	NO
71	TCEB3	TCEB3	TCEB3	6482	0.025	0.46	NO
72	TCEA1	TCEA1	TCEA1	6569	0.024	0.45	NO
73	RCC1	RCC1	RCC1	6576	0.024	0.46	NO
74	CDK7	CDK7	CDK7	6586	0.024	0.46	NO
75	PSMD1	PSMD1	PSMD1	6600	0.024	0.46	NO
76	NUP85	NUP85	NUP85	6601	0.024	0.46	NO
77	TH1L	TH1L	TH1L	6630	0.024	0.46	NO
78	AP2S1	AP2S1	AP2S1	6639	0.024	0.46	NO
79	NUP43	NUP43	NUP43	6779	0.022	0.45	NO
80	KPNA1	KPNA1	KPNA1	6834	0.021	0.45	NO
81	PSMC4	PSMC4	PSMC4	6856	0.021	0.45	NO
82	TAF12	TAF12	TAF12	6867	0.021	0.45	NO
83	AAAS	AAAS	AAAS	6925	0.02	0.45	NO
84	PSMD11	PSMD11	PSMD11	6929	0.02	0.45	NO
85	TBP	TBP	TBP	7004	0.019	0.45	NO
86	GTF2H3	GTF2H3	GTF2H3	7052	0.019	0.45	NO
87	RANBP1	RANBP1	RANBP1	7080	0.018	0.45	NO
88	POLR2C	POLR2C	POLR2C	7126	0.018	0.45	NO
89	PAK2	PAK2	PAK2	7128	0.018	0.45	NO
90	NPM1	NPM1	NPM1	7172	0.018	0.45	NO
91	PSMD14	PSMD14	PSMD14	7175	0.018	0.45	NO
92	NUP35	NUP35	NUP35	7178	0.018	0.45	NO
93	CDK9	CDK9	CDK9	7179	0.018	0.45	NO
94	PSMD7	PSMD7	PSMD7	7190	0.017	0.45	NO
95	TAF10	TAF10	TAF10	7311	0.016	0.45	NO
96	XRCC6	XRCC6	XRCC6	7442	0.014	0.44	NO
97	PSMB6	PSMB6	PSMB6	7589	0.013	0.43	NO
98	NUP188	NUP188	NUP188	7687	0.012	0.43	NO
99	NUP88	NUP88	NUP88	7717	0.011	0.43	NO
100	PSMD2	PSMD2	PSMD2	7871	0.0098	0.42	NO
101	RANGAP1	RANGAP1	RANGAP1	7894	0.0096	0.42	NO
102	NUP107	NUP107	NUP107	7908	0.0094	0.42	NO
103	PSMC5	PSMC5	PSMC5	7970	0.0088	0.42	NO
104	PSMD12	PSMD12	PSMD12	7986	0.0087	0.42	NO
105	NUP37	NUP37	NUP37	8005	0.0085	0.42	NO
106	TAF1	TAF1	TAF1	8026	0.0083	0.42	NO
107	PSMA1	PSMA1	PSMA1	8113	0.0073	0.41	NO
108	PSMD6	PSMD6	PSMD6	8119	0.0072	0.41	NO
109	NUP155	NUP155	NUP155	8137	0.007	0.41	NO
110	PSMD10	PSMD10	PSMD10	8153	0.0069	0.41	NO
111	RBX1	RBX1	RBX1	8163	0.0068	0.41	NO
112	PSMB7	PSMB7	PSMB7	8251	0.0059	0.41	NO
113	TAF9	TAF9	TAF9	8293	0.0055	0.4	NO
114	RAE1	RAE1	RAE1	8297	0.0055	0.4	NO
115	ERCC2	ERCC2	ERCC2	8306	0.0054	0.4	NO
116	NUP50	NUP50	NUP50	8415	0.0042	0.4	NO
117	POLR2B	POLR2B	POLR2B	8416	0.0042	0.4	NO
118	PSMA7	PSMA7	PSMA7	8557	0.0027	0.39	NO
119	PSMD8	PSMD8	PSMD8	8638	0.0016	0.39	NO
120	POLR2G	POLR2G	POLR2G	8649	0.0015	0.39	NO
121	PPIA	PPIA	PPIA	8651	0.0015	0.39	NO
122	SUPT16H	SUPT16H	SUPT16H	8654	0.0014	0.39	NO
123	POM121	POM121	POM121	8658	0.0014	0.39	NO
124	PSMC3	PSMC3	PSMC3	8679	0.0012	0.38	NO
125	ERCC3	ERCC3	ERCC3	8715	0.00096	0.38	NO
126	RDBP	RDBP	RDBP	8800	0.00016	0.38	NO
127	SSRP1	SSRP1	SSRP1	8834	-0.00019	0.38	NO
128	PSME4	PSME4	PSME4	8840	-0.00024	0.38	NO
129	PSMD9	PSMD9	PSMD9	8841	-0.00024	0.38	NO
130	PSMB5	PSMB5	PSMB5	8900	-0.00083	0.37	NO
131	BTRC	BTRC	BTRC	8924	-0.001	0.37	NO
132	POLR2A	POLR2A	POLR2A	9019	-0.002	0.37	NO
133	POLR2F	POLR2F	POLR2F	9230	-0.0042	0.36	NO
134	NUP214	NUP214	NUP214	9409	-0.0059	0.35	NO
135	XPO1	XPO1	XPO1	9416	-0.006	0.35	NO
136	AP2A2	AP2A2	AP2A2	9436	-0.0062	0.35	NO
137	COBRA1	COBRA1	COBRA1	9541	-0.007	0.34	NO
138	TAF4	TAF4	TAF4	9577	-0.0076	0.34	NO
139	PACS1	PACS1	PACS1	9622	-0.0082	0.34	NO
140	NUP205	NUP205	NUP205	9626	-0.0082	0.34	NO
141	TPR	TPR	TPR	9700	-0.009	0.33	NO
142	WHSC2	WHSC2	WHSC2	9776	-0.0096	0.33	NO
143	GTF2H1	GTF2H1	GTF2H1	9846	-0.01	0.33	NO
144	RANBP2	RANBP2	RANBP2	9850	-0.01	0.33	NO
145	BANF1	BANF1	BANF1	9876	-0.01	0.33	NO
146	CCNT2	CCNT2	CCNT2	9979	-0.012	0.32	NO
147	NCBP1	NCBP1	NCBP1	9989	-0.012	0.32	NO
148	AP2M1	AP2M1	AP2M1	10000	-0.012	0.32	NO
149	NUP133	NUP133	NUP133	10062	-0.013	0.32	NO
150	GTF2E2	GTF2E2	GTF2E2	10116	-0.013	0.32	NO
151	PSMB3	PSMB3	PSMB3	10223	-0.014	0.31	NO
152	GTF2A2	GTF2A2	GTF2A2	10450	-0.017	0.3	NO
153	PSMC2	PSMC2	PSMC2	10488	-0.017	0.3	NO
154	GTF2F1	GTF2F1	GTF2F1	10542	-0.018	0.3	NO
155	XRCC4	XRCC4	XRCC4	10626	-0.019	0.3	NO
156	PSMB4	PSMB4	PSMB4	10694	-0.019	0.29	NO
157	LIG4	LIG4	LIG4	10724	-0.02	0.29	NO
158	POLR2L	POLR2L	POLR2L	10776	-0.02	0.29	NO
159	TAF13	TAF13	TAF13	10893	-0.022	0.29	NO
160	POLR2I	POLR2I	POLR2I	11015	-0.023	0.28	NO
161	RAC1	RAC1	RAC1	11074	-0.024	0.28	NO
162	PSMD4	PSMD4	PSMD4	11111	-0.024	0.28	NO
163	SKP1	SKP1	SKP1	11147	-0.024	0.28	NO
164	CUL5	CUL5	CUL5	11162	-0.024	0.28	NO
165	ARF1	ARF1	ARF1	11184	-0.025	0.28	NO
166	PSMD5	PSMD5	PSMD5	11318	-0.026	0.28	NO
167	TCEB2	TCEB2	TCEB2	11325	-0.026	0.28	NO
168	RNMT	RNMT	RNMT	11428	-0.028	0.27	NO
169	AP1G1	AP1G1	AP1G1	11477	-0.028	0.27	NO
170	GTF2F2	GTF2F2	GTF2F2	11512	-0.029	0.27	NO
171	VPS37C	VPS37C	VPS37C	11545	-0.029	0.27	NO
172	VPS37B	VPS37B	VPS37B	11648	-0.03	0.27	NO
173	POLR2E	POLR2E	POLR2E	11674	-0.031	0.27	NO
174	POLR2J	POLR2J	POLR2J	12027	-0.035	0.25	NO
175	AP2B1	AP2B1	AP2B1	12045	-0.035	0.26	NO
176	CCNH	CCNH	CCNH	12075	-0.036	0.26	NO
177	PSMC1	PSMC1	PSMC1	12144	-0.036	0.26	NO
178	PSMD3	PSMD3	PSMD3	12250	-0.038	0.25	NO
179	PSMC6	PSMC6	PSMC6	12403	-0.04	0.25	NO
180	SLC25A4	SLC25A4	SLC25A4	12754	-0.046	0.23	NO
181	CCNT1	CCNT1	CCNT1	12953	-0.049	0.22	NO
182	SEH1L	SEH1L	SEH1L	12977	-0.049	0.22	NO
183	TSG101	TSG101	TSG101	13096	-0.051	0.22	NO
184	GTF2A1	GTF2A1	GTF2A1	13131	-0.051	0.22	NO
185	AP1M2	AP1M2	AP1M2	13282	-0.054	0.22	NO
186	TAF6	TAF6	TAF6	13693	-0.062	0.2	NO
187	NUPL1	NUPL1	NUPL1	14404	-0.077	0.17	NO
188	GTF2H2B	GTF2H2B	GTF2H2B	14628	-0.082	0.16	NO
189	MNAT1	MNAT1	MNAT1	14967	-0.093	0.15	NO
190	AP1S1	AP1S1	AP1S1	15148	-0.099	0.14	NO
191	VPS37A	VPS37A	VPS37A	15636	-0.12	0.12	NO
192	GTF2H2	GTF2H2	GTF2H2	15646	-0.12	0.13	NO
193	VPS37D	VPS37D	VPS37D	16872	-0.19	0.078	NO

Figure S125. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG INOSITOL PHOSPHATE METABOLISM.

Figure S126. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG INOSITOL PHOSPHATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ETHER LIPID METABOLISM

Table S64. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PRKCB	PRKCB	PRKCB	114	0.84	0.12	YES
2	CARD11	CARD11	CARD11	234	0.73	0.22	YES
3	PSMB9	PSMB9	PSMB9	652	0.45	0.27	YES
4	PSMA8	PSMA8	PSMA8	713	0.42	0.33	YES
5	PSMB8	PSMB8	PSMB8	1276	0.27	0.34	YES
6	RASGRP1	RASGRP1	RASGRP1	1321	0.26	0.38	YES
7	PSMB10	PSMB10	PSMB10	1580	0.22	0.4	YES
8	RASGRP3	RASGRP3	RASGRP3	1615	0.22	0.43	YES
9	PSME2	PSME2	PSME2	1644	0.21	0.46	YES
10	FOXO1	FOXO1	FOXO1	1796	0.19	0.48	YES
11	NFKBIE	NFKBIE	NFKBIE	2014	0.17	0.49	YES
12	PSME1	PSME1	PSME1	2162	0.15	0.51	YES
13	MALT1	MALT1	MALT1	2846	0.11	0.49	YES
14	FOXO4	FOXO4	FOXO4	3063	0.098	0.49	YES
15	NFKBIA	NFKBIA	NFKBIA	3283	0.09	0.49	YES
16	CHUK	CHUK	CHUK	3492	0.083	0.49	YES
17	NFKBIB	NFKBIB	NFKBIB	3513	0.083	0.5	YES
18	RPS6KB2	RPS6KB2	RPS6KB2	3634	0.079	0.51	YES
19	PSMA5	PSMA5	PSMA5	3693	0.077	0.52	YES
20	FOXO3	FOXO3	FOXO3	4265	0.062	0.5	NO
21	PSMA6	PSMA6	PSMA6	4648	0.054	0.48	NO
22	NRAS	NRAS	NRAS	4699	0.053	0.49	NO
23	UBA52	UBA52	UBA52	5070	0.046	0.48	NO
24	PSMA2	PSMA2	PSMA2	5176	0.044	0.48	NO
25	IKBKG	IKBKG	IKBKG	5202	0.043	0.48	NO
26	RPS27A	RPS27A	RPS27A	5423	0.04	0.48	NO
27	PSMF1	PSMF1	PSMF1	5516	0.038	0.48	NO
28	PSMA4	PSMA4	PSMA4	5696	0.036	0.47	NO
29	PSMA3	PSMA3	PSMA3	6017	0.031	0.46	NO
30	PSMD13	PSMD13	PSMD13	6142	0.03	0.46	NO
31	PSMB1	PSMB1	PSMB1	6196	0.029	0.46	NO
32	MTOR	MTOR	MTOR	6262	0.028	0.46	NO
33	PSMB2	PSMB2	PSMB2	6363	0.027	0.46	NO
34	PSMD1	PSMD1	PSMD1	6600	0.024	0.45	NO
35	CASP9	CASP9	CASP9	6616	0.024	0.45	NO
36	AKT2	AKT2	AKT2	6736	0.022	0.45	NO
37	TRIB3	TRIB3	TRIB3	6793	0.022	0.45	NO
38	PSMC4	PSMC4	PSMC4	6856	0.021	0.45	NO
39	PSMD11	PSMD11	PSMD11	6929	0.02	0.45	NO
40	THEM4	THEM4	THEM4	7144	0.018	0.44	NO
41	PSMD14	PSMD14	PSMD14	7175	0.018	0.44	NO
42	PSMD7	PSMD7	PSMD7	7190	0.017	0.44	NO
43	AKT3	AKT3	AKT3	7335	0.016	0.44	NO
44	PSMB6	PSMB6	PSMB6	7589	0.013	0.42	NO
45	AKT1S1	AKT1S1	AKT1S1	7629	0.012	0.42	NO
46	RICTOR	RICTOR	RICTOR	7667	0.012	0.42	NO
47	PSMD2	PSMD2	PSMD2	7871	0.0098	0.41	NO
48	CDKN1B	CDKN1B	CDKN1B	7909	0.0094	0.41	NO
49	PSMC5	PSMC5	PSMC5	7970	0.0088	0.41	NO
50	PSMD12	PSMD12	PSMD12	7986	0.0087	0.41	NO
51	CREB1	CREB1	CREB1	8094	0.0075	0.41	NO
52	PSMA1	PSMA1	PSMA1	8113	0.0073	0.41	NO
53	PSMD6	PSMD6	PSMD6	8119	0.0072	0.41	NO
54	PSMD10	PSMD10	PSMD10	8153	0.0069	0.41	NO
55	BCL10	BCL10	BCL10	8236	0.0061	0.4	NO
56	PSMB7	PSMB7	PSMB7	8251	0.0059	0.4	NO
57	PSMA7	PSMA7	PSMA7	8557	0.0027	0.39	NO
58	MAPKAP1	MAPKAP1	MAPKAP1	8600	0.0021	0.38	NO
59	PSMD8	PSMD8	PSMD8	8638	0.0016	0.38	NO
60	PSMC3	PSMC3	PSMC3	8679	0.0012	0.38	NO
61	MAP3K7	MAP3K7	MAP3K7	8695	0.0011	0.38	NO
62	PSME4	PSME4	PSME4	8840	-0.00024	0.37	NO
63	PSMD9	PSMD9	PSMD9	8841	-0.00024	0.37	NO
64	PSMB5	PSMB5	PSMB5	8900	-0.00083	0.37	NO
65	BTRC	BTRC	BTRC	8924	-0.001	0.37	NO
66	RELA	RELA	RELA	8928	-0.001	0.37	NO
67	CUL1	CUL1	CUL1	8957	-0.0014	0.37	NO
68	REL	REL	REL	9239	-0.0043	0.35	NO
69	GSK3A	GSK3A	GSK3A	9513	-0.0068	0.34	NO
70	PSMB3	PSMB3	PSMB3	10223	-0.014	0.3	NO
71	FBXW11	FBXW11	FBXW11	10432	-0.017	0.29	NO
72	NR4A1	NR4A1	NR4A1	10434	-0.017	0.29	NO
73	PSMC2	PSMC2	PSMC2	10488	-0.017	0.29	NO
74	TSC2	TSC2	TSC2	10497	-0.017	0.3	NO
75	PSMB4	PSMB4	PSMB4	10694	-0.019	0.29	NO
76	PSMD4	PSMD4	PSMD4	11111	-0.024	0.27	NO
77	SKP1	SKP1	SKP1	11147	-0.024	0.27	NO
78	PSMD5	PSMD5	PSMD5	11318	-0.026	0.27	NO
79	PTEN	PTEN	PTEN	11984	-0.034	0.23	NO
80	PDPK1	PDPK1	PDPK1	12034	-0.035	0.24	NO
81	PSMC1	PSMC1	PSMC1	12144	-0.036	0.24	NO
82	IKBKB	IKBKB	IKBKB	12216	-0.037	0.24	NO
83	PSMD3	PSMD3	PSMD3	12250	-0.038	0.24	NO
84	HRAS	HRAS	HRAS	12316	-0.039	0.24	NO
85	PSMC6	PSMC6	PSMC6	12403	-0.04	0.25	NO
86	MLST8	MLST8	MLST8	12408	-0.04	0.25	NO
87	KRAS	KRAS	KRAS	13082	-0.05	0.22	NO
88	AKT1	AKT1	AKT1	13673	-0.061	0.2	NO
89	BAD	BAD	BAD	13941	-0.066	0.2	NO
90	MDM2	MDM2	MDM2	14057	-0.069	0.2	NO
91	CDKN1A	CDKN1A	CDKN1A	14521	-0.08	0.18	NO
92	PHLPP1	PHLPP1	PHLPP1	16100	-0.14	0.12	NO

Figure S127. 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 S128. 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 RIBOSOME

Table S65. 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	IFNG	IFNG	IFNG	32	0.95	0.02	YES
2	IRF4	IRF4	IRF4	122	0.83	0.034	YES
3	IL2RA	IL2RA	IL2RA	151	0.8	0.05	YES
4	LCK	LCK	LCK	159	0.8	0.068	YES
5	IL7R	IL7R	IL7R	224	0.74	0.082	YES
6	GBP7	GBP7	GBP7	263	0.7	0.095	YES
7	IL2RB	IL2RB	IL2RB	273	0.69	0.11	YES
8	GBP5	GBP5	GBP5	274	0.69	0.13	YES
9	IL2RG	IL2RG	IL2RG	276	0.69	0.14	YES
10	IL2	IL2	IL2	291	0.67	0.16	YES
11	JAK3	JAK3	JAK3	319	0.65	0.17	YES
12	SOCS1	SOCS1	SOCS1	412	0.58	0.18	YES
13	IRF8	IRF8	IRF8	418	0.58	0.19	YES
14	GBP4	GBP4	GBP4	428	0.57	0.2	YES
15	IL1R2	IL1R2	IL1R2	435	0.57	0.22	YES
16	CIITA	CIITA	CIITA	453	0.56	0.23	YES
17	OASL	OASL	OASL	457	0.55	0.24	YES
18	CSF2RB	CSF2RB	CSF2RB	476	0.53	0.25	YES
19	VAV1	VAV1	VAV1	507	0.52	0.26	YES
20	IL7	IL7	IL7	518	0.51	0.27	YES
21	GBP6	GBP6	GBP6	531	0.5	0.28	YES
22	PTAFR	PTAFR	PTAFR	538	0.5	0.29	YES
23	CSF2RA	CSF2RA	CSF2RA	576	0.48	0.3	YES
24	HLA-DQA1	HLA-DQA1	HLA-DQA1	627	0.46	0.31	YES
25	PIK3CD	PIK3CD	PIK3CD	635	0.46	0.32	YES
26	GBP1	GBP1	GBP1	689	0.43	0.33	YES
27	IL18	IL18	IL18	694	0.43	0.34	YES
28	HLA-DQA2	HLA-DQA2	HLA-DQA2	695	0.43	0.35	YES
29	ISG20	ISG20	ISG20	702	0.43	0.36	YES
30	IFIT3	IFIT3	IFIT3	710	0.42	0.36	YES
31	IL6R	IL6R	IL6R	725	0.41	0.37	YES
32	IL5RA	IL5RA	IL5RA	740	0.41	0.38	YES
33	HERC5	HERC5	HERC5	770	0.4	0.39	YES
34	IFIT2	IFIT2	IFIT2	791	0.39	0.4	YES
35	XAF1	XAF1	XAF1	800	0.39	0.4	YES
36	IFIT1	IFIT1	IFIT1	815	0.38	0.41	YES
37	CASP1	CASP1	CASP1	826	0.38	0.42	YES
38	HLA-DRB5	HLA-DRB5	HLA-DRB5	832	0.38	0.43	YES
39	FCGR1A	FCGR1A	FCGR1A	841	0.37	0.44	YES
40	MX1	MX1	MX1	847	0.37	0.45	YES
41	GH1	GH1	GH1	857	0.37	0.45	YES
42	VCAM1	VCAM1	VCAM1	874	0.36	0.46	YES
43	IL3RA	IL3RA	IL3RA	885	0.36	0.47	YES
44	OAS2	OAS2	OAS2	904	0.36	0.48	YES
45	HLA-F	HLA-F	HLA-F	917	0.35	0.48	YES
46	ISG15	ISG15	ISG15	921	0.35	0.49	YES
47	MX2	MX2	MX2	937	0.34	0.5	YES
48	FCGR1B	FCGR1B	FCGR1B	939	0.34	0.5	YES
49	HLA-G	HLA-G	HLA-G	947	0.34	0.51	YES
50	HLA-DRB1	HLA-DRB1	HLA-DRB1	949	0.34	0.52	YES
51	HCK	HCK	HCK	950	0.34	0.53	YES
52	IL6	IL6	IL6	1005	0.33	0.53	YES
53	IFNB1	IFNB1	IFNB1	1052	0.32	0.54	YES
54	STAT1	STAT1	STAT1	1064	0.31	0.54	YES
55	IRF1	IRF1	IRF1	1073	0.31	0.55	YES
56	GBP2	GBP2	GBP2	1077	0.31	0.56	YES
57	OAS1	OAS1	OAS1	1079	0.31	0.56	YES
58	FYN	FYN	FYN	1084	0.31	0.57	YES
59	HLA-DPA1	HLA-DPA1	HLA-DPA1	1103	0.3	0.58	YES
60	HLA-DPB1	HLA-DPB1	HLA-DPB1	1122	0.3	0.58	YES
61	NOD2	NOD2	NOD2	1126	0.3	0.59	YES
62	IFI6	IFI6	IFI6	1185	0.28	0.59	YES
63	PTK2B	PTK2B	PTK2B	1204	0.28	0.6	YES
64	IFI27	IFI27	IFI27	1257	0.27	0.6	YES
65	TEC	TEC	TEC	1261	0.27	0.61	YES
66	IRF7	IRF7	IRF7	1268	0.27	0.61	YES
67	PSMB8	PSMB8	PSMB8	1276	0.27	0.62	YES
68	SYK	SYK	SYK	1283	0.27	0.62	YES
69	UBE2L6	UBE2L6	UBE2L6	1298	0.27	0.63	YES
70	BLNK	BLNK	BLNK	1327	0.26	0.63	YES
71	IFITM1	IFITM1	IFITM1	1335	0.26	0.64	YES
72	HGF	HGF	HGF	1343	0.26	0.64	YES
73	IRAK2	IRAK2	IRAK2	1388	0.25	0.65	YES
74	CSF2	CSF2	CSF2	1391	0.25	0.65	YES
75	UBA7	UBA7	UBA7	1396	0.25	0.66	YES
76	LYN	LYN	LYN	1413	0.24	0.66	YES
77	HLA-B	HLA-B	HLA-B	1427	0.24	0.67	YES
78	OAS3	OAS3	OAS3	1446	0.24	0.67	YES
79	USP18	USP18	USP18	1465	0.24	0.68	YES
80	IFI35	IFI35	IFI35	1497	0.23	0.68	YES
81	DDX58	DDX58	DDX58	1503	0.23	0.69	YES
82	IL1RN	IL1RN	IL1RN	1509	0.23	0.69	YES
83	IRF9	IRF9	IRF9	1569	0.22	0.69	YES
84	HLA-A	HLA-A	HLA-A	1573	0.22	0.7	YES
85	STAT5A	STAT5A	STAT5A	1606	0.22	0.7	YES
86	B2M	B2M	B2M	1616	0.21	0.71	YES
87	PTPN6	PTPN6	PTPN6	1636	0.21	0.71	YES
88	JAK2	JAK2	JAK2	1657	0.21	0.71	YES
89	IL1B	IL1B	IL1B	1706	0.2	0.72	YES
90	SP100	SP100	SP100	1723	0.2	0.72	YES
91	IFNAR2	IFNAR2	IFNAR2	1734	0.2	0.72	YES
92	HLA-C	HLA-C	HLA-C	1755	0.2	0.73	YES
93	ICAM1	ICAM1	ICAM1	1764	0.2	0.73	YES
94	IRF5	IRF5	IRF5	1872	0.18	0.73	YES
95	NFKB2	NFKB2	NFKB2	1884	0.18	0.73	YES
96	IRAK3	IRAK3	IRAK3	1936	0.17	0.73	YES
97	STAT2	STAT2	STAT2	1971	0.17	0.74	YES
98	MAP3K8	MAP3K8	MAP3K8	2032	0.16	0.74	YES
99	IRF3	IRF3	IRF3	2131	0.16	0.73	NO
100	MT2A	MT2A	MT2A	2319	0.14	0.73	NO
101	EIF2AK2	EIF2AK2	EIF2AK2	2335	0.14	0.73	NO
102	GHR	GHR	GHR	2392	0.14	0.73	NO
103	NOD1	NOD1	NOD1	2578	0.12	0.72	NO
104	KPNA5	KPNA5	KPNA5	2584	0.12	0.72	NO
105	IFITM3	IFITM3	IFITM3	2678	0.12	0.72	NO
106	GRB2	GRB2	GRB2	2705	0.12	0.72	NO
107	SOCS3	SOCS3	SOCS3	2829	0.11	0.72	NO
108	PML	PML	PML	2850	0.11	0.72	NO
109	CAMK2D	CAMK2D	CAMK2D	2903	0.11	0.72	NO
110	STAT5B	STAT5B	STAT5B	2946	0.1	0.72	NO
111	MAP2K6	MAP2K6	MAP2K6	2961	0.1	0.72	NO
112	RAPGEF1	RAPGEF1	RAPGEF1	2991	0.1	0.72	NO
113	PLCG1	PLCG1	PLCG1	3008	0.1	0.72	NO
114	IL1R1	IL1R1	IL1R1	3079	0.098	0.72	NO
115	PRKACB	PRKACB	PRKACB	3211	0.093	0.72	NO
116	MYD88	MYD88	MYD88	3303	0.089	0.71	NO
117	PTPN2	PTPN2	PTPN2	3446	0.084	0.71	NO
118	CHUK	CHUK	CHUK	3492	0.083	0.71	NO
119	IRF2	IRF2	IRF2	3591	0.08	0.7	NO
120	NUP93	NUP93	NUP93	3658	0.078	0.7	NO
121	TYK2	TYK2	TYK2	3674	0.078	0.7	NO
122	CDK1	CDK1	CDK1	3723	0.076	0.7	NO
123	SOCS2	SOCS2	SOCS2	3814	0.073	0.7	NO
124	TAB2	TAB2	TAB2	3865	0.071	0.7	NO
125	NUP62	NUP62	NUP62	3942	0.069	0.69	NO
126	NUP210	NUP210	NUP210	4140	0.064	0.68	NO
127	NUP54	NUP54	NUP54	4550	0.056	0.66	NO
128	TRIM25	TRIM25	TRIM25	4560	0.056	0.66	NO
129	MAP3K3	MAP3K3	MAP3K3	4640	0.054	0.66	NO
130	GAB2	GAB2	GAB2	4649	0.054	0.66	NO
131	NRAS	NRAS	NRAS	4699	0.053	0.66	NO
132	CISH	CISH	CISH	4700	0.053	0.66	NO
133	CBL	CBL	CBL	4701	0.053	0.66	NO
134	RIPK2	RIPK2	RIPK2	4814	0.051	0.66	NO
135	PTPN1	PTPN1	PTPN1	4816	0.05	0.66	NO
136	MAP2K1	MAP2K1	MAP2K1	4916	0.049	0.65	NO
137	ADAR	ADAR	ADAR	5046	0.046	0.65	NO
138	UBA52	UBA52	UBA52	5070	0.046	0.65	NO
139	IFNGR1	IFNGR1	IFNGR1	5093	0.046	0.65	NO
140	TNIP2	TNIP2	TNIP2	5113	0.045	0.65	NO
141	IRAK4	IRAK4	IRAK4	5160	0.044	0.64	NO
142	IKBKG	IKBKG	IKBKG	5202	0.043	0.64	NO
143	YWHAZ	YWHAZ	YWHAZ	5235	0.043	0.64	NO
144	NUPL2	NUPL2	NUPL2	5344	0.041	0.64	NO
145	JAK1	JAK1	JAK1	5416	0.04	0.64	NO
146	RPS27A	RPS27A	RPS27A	5423	0.04	0.64	NO
147	KPNA2	KPNA2	KPNA2	5437	0.04	0.64	NO
148	EIF4E3	EIF4E3	EIF4E3	5578	0.038	0.63	NO
149	UBE2N	UBE2N	UBE2N	5621	0.037	0.63	NO
150	KPNB1	KPNB1	KPNB1	5631	0.037	0.63	NO
151	RNASEL	RNASEL	RNASEL	5705	0.036	0.62	NO
152	IFNGR2	IFNGR2	IFNGR2	5715	0.036	0.62	NO
153	CD44	CD44	CD44	5733	0.035	0.62	NO
154	PRKCD	PRKCD	PRKCD	5815	0.034	0.62	NO
155	NUP153	NUP153	NUP153	6113	0.03	0.6	NO
156	PRLR	PRLR	PRLR	6351	0.027	0.59	NO
157	EIF4A3	EIF4A3	EIF4A3	6444	0.026	0.59	NO
158	IFITM2	IFITM2	IFITM2	6445	0.026	0.59	NO
159	SOS1	SOS1	SOS1	6448	0.026	0.59	NO
160	IL6ST	IL6ST	IL6ST	6450	0.026	0.59	NO
161	PIK3CA	PIK3CA	PIK3CA	6468	0.026	0.59	NO
162	PIAS1	PIAS1	PIAS1	6546	0.025	0.59	NO
163	NUP85	NUP85	NUP85	6601	0.024	0.58	NO
164	EIF4E	EIF4E	EIF4E	6700	0.023	0.58	NO
165	NUP43	NUP43	NUP43	6779	0.022	0.57	NO
166	MAPK1	MAPK1	MAPK1	6797	0.022	0.57	NO
167	KPNA1	KPNA1	KPNA1	6834	0.021	0.57	NO
168	AAAS	AAAS	AAAS	6925	0.02	0.57	NO
169	CRKL	CRKL	CRKL	6965	0.02	0.57	NO
170	EIF4E2	EIF4E2	EIF4E2	6975	0.02	0.57	NO
171	EIF4A1	EIF4A1	EIF4A1	6996	0.019	0.57	NO
172	NUP35	NUP35	NUP35	7178	0.018	0.56	NO
173	YWHAB	YWHAB	YWHAB	7269	0.016	0.55	NO
174	PIN1	PIN1	PIN1	7305	0.016	0.55	NO
175	TAB3	TAB3	TAB3	7339	0.016	0.55	NO
176	IFNAR1	IFNAR1	IFNAR1	7344	0.016	0.55	NO
177	PIK3R3	PIK3R3	PIK3R3	7443	0.014	0.54	NO
178	EIF4G1	EIF4G1	EIF4G1	7521	0.014	0.54	NO
179	NUP188	NUP188	NUP188	7687	0.012	0.53	NO
180	NUP88	NUP88	NUP88	7717	0.011	0.53	NO
181	SUMO1	SUMO1	SUMO1	7809	0.01	0.52	NO
182	NUP107	NUP107	NUP107	7908	0.0094	0.52	NO
183	EIF4A2	EIF4A2	EIF4A2	7972	0.0088	0.52	NO
184	NUP37	NUP37	NUP37	8005	0.0085	0.51	NO
185	STAT3	STAT3	STAT3	8028	0.0083	0.51	NO
186	NUP155	NUP155	NUP155	8137	0.007	0.51	NO
187	TAB1	TAB1	TAB1	8158	0.0068	0.51	NO
188	RBX1	RBX1	RBX1	8163	0.0068	0.51	NO
189	EIF4G2	EIF4G2	EIF4G2	8192	0.0065	0.5	NO
190	PPM1B	PPM1B	PPM1B	8275	0.0056	0.5	NO
191	RAE1	RAE1	RAE1	8297	0.0055	0.5	NO
192	NUP50	NUP50	NUP50	8415	0.0042	0.49	NO
193	NCAM1	NCAM1	NCAM1	8432	0.004	0.49	NO
194	RAF1	RAF1	RAF1	8483	0.0035	0.49	NO
195	PELI1	PELI1	PELI1	8603	0.0021	0.48	NO
196	POM121	POM121	POM121	8658	0.0014	0.48	NO
197	MAP3K7	MAP3K7	MAP3K7	8695	0.0011	0.48	NO
198	MAP2K2	MAP2K2	MAP2K2	8807	0.000046	0.47	NO
199	KPNA3	KPNA3	KPNA3	8853	-0.00034	0.47	NO
200	KPNA4	KPNA4	KPNA4	8880	-0.00064	0.47	NO
201	BTRC	BTRC	BTRC	8924	-0.001	0.47	NO
202	RELA	RELA	RELA	8928	-0.001	0.46	NO
203	IRAK1	IRAK1	IRAK1	8933	-0.0011	0.46	NO
204	CUL1	CUL1	CUL1	8957	-0.0014	0.46	NO
205	INPPL1	INPPL1	INPPL1	9282	-0.0048	0.45	NO
206	NUP214	NUP214	NUP214	9409	-0.0059	0.44	NO
207	UBE2E1	UBE2E1	UBE2E1	9450	-0.0063	0.44	NO
208	EIF4G3	EIF4G3	EIF4G3	9543	-0.0071	0.43	NO
209	NUP205	NUP205	NUP205	9626	-0.0082	0.43	NO
210	EGR1	EGR1	EGR1	9643	-0.0084	0.43	NO
211	TPR	TPR	TPR	9700	-0.009	0.42	NO
212	RANBP2	RANBP2	RANBP2	9850	-0.01	0.42	NO
213	PIK3CB	PIK3CB	PIK3CB	9877	-0.01	0.42	NO
214	NUP133	NUP133	NUP133	10062	-0.013	0.4	NO
215	TRAF6	TRAF6	TRAF6	10201	-0.014	0.4	NO
216	IRS1	IRS1	IRS1	10273	-0.015	0.39	NO
217	IP6K2	IP6K2	IP6K2	10334	-0.016	0.39	NO
218	IL1A	IL1A	IL1A	10436	-0.017	0.39	NO
219	PIK3R2	PIK3R2	PIK3R2	10442	-0.017	0.39	NO
220	ARIH1	ARIH1	ARIH1	10859	-0.021	0.36	NO
221	SKP1	SKP1	SKP1	11147	-0.024	0.35	NO
222	SQSTM1	SQSTM1	SQSTM1	11279	-0.026	0.34	NO
223	MAPK3	MAPK3	MAPK3	11362	-0.027	0.34	NO
224	TOLLIP	TOLLIP	TOLLIP	11600	-0.03	0.32	NO
225	ADAM17	ADAM17	ADAM17	11677	-0.031	0.32	NO
226	IKBKB	IKBKB	IKBKB	12216	-0.037	0.29	NO
227	PIK3R1	PIK3R1	PIK3R1	12279	-0.038	0.29	NO
228	HRAS	HRAS	HRAS	12316	-0.039	0.29	NO
229	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	12412	-0.04	0.28	NO
230	FLNB	FLNB	FLNB	12847	-0.047	0.26	NO
231	SH2B1	SH2B1	SH2B1	12864	-0.047	0.26	NO
232	CRK	CRK	CRK	12877	-0.048	0.26	NO
233	SEH1L	SEH1L	SEH1L	12977	-0.049	0.26	NO
234	KRAS	KRAS	KRAS	13082	-0.05	0.25	NO
235	CAMK2B	CAMK2B	CAMK2B	13685	-0.061	0.22	NO
236	NEDD4	NEDD4	NEDD4	14123	-0.07	0.2	NO
237	SHC1	SHC1	SHC1	14128	-0.07	0.2	NO
238	YES1	YES1	YES1	14385	-0.076	0.19	NO
239	NUPL1	NUPL1	NUPL1	14404	-0.077	0.19	NO
240	MAP2K4	MAP2K4	MAP2K4	14585	-0.081	0.18	NO
241	PELI3	PELI3	PELI3	14640	-0.083	0.18	NO
242	CAMK2A	CAMK2A	CAMK2A	14696	-0.084	0.18	NO
243	PELI2	PELI2	PELI2	14933	-0.092	0.17	NO
244	IL1RAP	IL1RAP	IL1RAP	15767	-0.12	0.12	NO
245	PRL	PRL	PRL	16856	-0.18	0.067	NO
246	IRF6	IRF6	IRF6	17399	-0.23	0.042	NO
247	IRS2	IRS2	IRS2	17718	-0.27	0.031	NO

Figure S129. 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 S130. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIBOSOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PROTEASOME

Table S66. 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	NLRC5	NLRC5	NLRC5	582	0.48	0.032	YES
2	HERC5	HERC5	HERC5	770	0.4	0.076	YES
3	AGER	AGER	AGER	797	0.39	0.13	YES
4	TNFAIP3	TNFAIP3	TNFAIP3	905	0.35	0.17	YES
5	ISG15	ISG15	ISG15	921	0.35	0.22	YES
6	CASP10	CASP10	CASP10	924	0.35	0.26	YES
7	IFNB1	IFNB1	IFNB1	1052	0.32	0.3	YES
8	IRF1	IRF1	IRF1	1073	0.31	0.34	YES
9	IFIH1	IFIH1	IFIH1	1134	0.3	0.37	YES
10	IRF7	IRF7	IRF7	1268	0.27	0.4	YES
11	UBE2L6	UBE2L6	UBE2L6	1298	0.27	0.44	YES
12	UBA7	UBA7	UBA7	1396	0.25	0.46	YES
13	DDX58	DDX58	DDX58	1503	0.23	0.49	YES
14	S100A12	S100A12	S100A12	1517	0.23	0.52	YES
15	DHX58	DHX58	DHX58	1574	0.22	0.55	YES
16	NFKB2	NFKB2	NFKB2	1884	0.18	0.55	YES
17	RNF125	RNF125	RNF125	1908	0.18	0.58	YES
18	CYLD	CYLD	CYLD	1916	0.18	0.6	YES
19	S100B	S100B	S100B	2040	0.16	0.62	YES
20	IRF3	IRF3	IRF3	2131	0.16	0.63	YES
21	CASP8	CASP8	CASP8	2159	0.15	0.65	YES
22	IKBKE	IKBKE	IKBKE	2289	0.14	0.66	YES
23	TRAF3	TRAF3	TRAF3	2566	0.12	0.66	YES
24	NFKBIA	NFKBIA	NFKBIA	3283	0.09	0.64	NO
25	CHUK	CHUK	CHUK	3492	0.083	0.64	NO
26	NFKBIB	NFKBIB	NFKBIB	3513	0.083	0.65	NO
27	IRF2	IRF2	IRF2	3591	0.08	0.65	NO
28	UBE2D1	UBE2D1	UBE2D1	4214	0.063	0.63	NO
29	ATG5	ATG5	ATG5	4426	0.058	0.62	NO
30	TRAF2	TRAF2	TRAF2	4429	0.058	0.63	NO
31	TRIM25	TRIM25	TRIM25	4560	0.056	0.63	NO
32	MAP3K1	MAP3K1	MAP3K1	4937	0.048	0.62	NO
33	UBA52	UBA52	UBA52	5070	0.046	0.62	NO
34	FADD	FADD	FADD	5194	0.044	0.62	NO
35	IKBKG	IKBKG	IKBKG	5202	0.043	0.62	NO
36	RIPK1	RIPK1	RIPK1	5254	0.043	0.62	NO
37	TBK1	TBK1	TBK1	5383	0.041	0.62	NO
38	RPS27A	RPS27A	RPS27A	5423	0.04	0.62	NO
39	HMGB1	HMGB1	HMGB1	5726	0.036	0.61	NO
40	OTUD5	OTUD5	OTUD5	6355	0.027	0.58	NO
41	PIN1	PIN1	PIN1	7305	0.016	0.53	NO
42	UBE2D3	UBE2D3	UBE2D3	7449	0.014	0.53	NO
43	TANK	TANK	TANK	7502	0.014	0.53	NO
44	UBE2K	UBE2K	UBE2K	7801	0.011	0.51	NO
45	PCBP2	PCBP2	PCBP2	8140	0.007	0.49	NO
46	MAVS	MAVS	MAVS	8406	0.0043	0.48	NO
47	RELA	RELA	RELA	8928	-0.001	0.45	NO
48	UBE2D2	UBE2D2	UBE2D2	9144	-0.0033	0.44	NO
49	SIKE1	SIKE1	SIKE1	9482	-0.0066	0.42	NO
50	ATG12	ATG12	ATG12	9727	-0.0091	0.41	NO
51	EP300	EP300	EP300	9770	-0.0095	0.41	NO
52	TRAF6	TRAF6	TRAF6	10201	-0.014	0.39	NO
53	CREBBP	CREBBP	CREBBP	10283	-0.015	0.38	NO
54	RNF135	RNF135	RNF135	10345	-0.016	0.38	NO
55	DAK	DAK	DAK	11167	-0.024	0.34	NO
56	IKBKB	IKBKB	IKBKB	12216	-0.037	0.29	NO
57	TAX1BP1	TAX1BP1	TAX1BP1	12718	-0.045	0.27	NO
58	APP	APP	APP	13187	-0.052	0.25	NO
59	NLRX1	NLRX1	NLRX1	15111	-0.098	0.16	NO
60	SAA1	SAA1	SAA1	15943	-0.13	0.13	NO

Figure S131. 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 S132. 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 CYTOKINE CYTOKINE RECEPTOR INTERACTION

Table S67. 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	IFNG	IFNG	IFNG	32	0.95	0.036	YES
2	IRF4	IRF4	IRF4	122	0.83	0.063	YES
3	GBP7	GBP7	GBP7	263	0.7	0.083	YES
4	GBP5	GBP5	GBP5	274	0.69	0.11	YES
5	SOCS1	SOCS1	SOCS1	412	0.58	0.12	YES
6	IRF8	IRF8	IRF8	418	0.58	0.15	YES
7	GBP4	GBP4	GBP4	428	0.57	0.17	YES
8	CIITA	CIITA	CIITA	453	0.56	0.19	YES
9	OASL	OASL	OASL	457	0.55	0.21	YES
10	GBP6	GBP6	GBP6	531	0.5	0.23	YES
11	PTAFR	PTAFR	PTAFR	538	0.5	0.24	YES
12	HLA-DQA1	HLA-DQA1	HLA-DQA1	627	0.46	0.26	YES
13	GBP1	GBP1	GBP1	689	0.43	0.27	YES
14	HLA-DQA2	HLA-DQA2	HLA-DQA2	695	0.43	0.29	YES
15	ISG20	ISG20	ISG20	702	0.43	0.3	YES
16	IFIT3	IFIT3	IFIT3	710	0.42	0.32	YES
17	HERC5	HERC5	HERC5	770	0.4	0.33	YES
18	IFIT2	IFIT2	IFIT2	791	0.39	0.35	YES
19	XAF1	XAF1	XAF1	800	0.39	0.36	YES
20	IFIT1	IFIT1	IFIT1	815	0.38	0.38	YES
21	HLA-DRB5	HLA-DRB5	HLA-DRB5	832	0.38	0.39	YES
22	FCGR1A	FCGR1A	FCGR1A	841	0.37	0.4	YES
23	MX1	MX1	MX1	847	0.37	0.42	YES
24	VCAM1	VCAM1	VCAM1	874	0.36	0.43	YES
25	OAS2	OAS2	OAS2	904	0.36	0.44	YES
26	HLA-F	HLA-F	HLA-F	917	0.35	0.46	YES
27	ISG15	ISG15	ISG15	921	0.35	0.47	YES
28	MX2	MX2	MX2	937	0.34	0.48	YES
29	FCGR1B	FCGR1B	FCGR1B	939	0.34	0.5	YES
30	HLA-G	HLA-G	HLA-G	947	0.34	0.51	YES
31	HLA-DRB1	HLA-DRB1	HLA-DRB1	949	0.34	0.52	YES
32	IFNB1	IFNB1	IFNB1	1052	0.32	0.53	YES
33	STAT1	STAT1	STAT1	1064	0.31	0.54	YES
34	IRF1	IRF1	IRF1	1073	0.31	0.55	YES
35	GBP2	GBP2	GBP2	1077	0.31	0.56	YES
36	OAS1	OAS1	OAS1	1079	0.31	0.58	YES
37	HLA-DPA1	HLA-DPA1	HLA-DPA1	1103	0.3	0.59	YES
38	HLA-DPB1	HLA-DPB1	HLA-DPB1	1122	0.3	0.6	YES
39	IFI6	IFI6	IFI6	1185	0.28	0.61	YES
40	IFI27	IFI27	IFI27	1257	0.27	0.61	YES
41	IRF7	IRF7	IRF7	1268	0.27	0.62	YES
42	PSMB8	PSMB8	PSMB8	1276	0.27	0.63	YES
43	UBE2L6	UBE2L6	UBE2L6	1298	0.27	0.64	YES
44	IFITM1	IFITM1	IFITM1	1335	0.26	0.65	YES
45	UBA7	UBA7	UBA7	1396	0.25	0.66	YES
46	HLA-B	HLA-B	HLA-B	1427	0.24	0.66	YES
47	OAS3	OAS3	OAS3	1446	0.24	0.67	YES
48	USP18	USP18	USP18	1465	0.24	0.68	YES
49	IFI35	IFI35	IFI35	1497	0.23	0.69	YES
50	DDX58	DDX58	DDX58	1503	0.23	0.7	YES
51	IRF9	IRF9	IRF9	1569	0.22	0.7	YES
52	HLA-A	HLA-A	HLA-A	1573	0.22	0.71	YES
53	B2M	B2M	B2M	1616	0.21	0.72	YES
54	PTPN6	PTPN6	PTPN6	1636	0.21	0.72	YES
55	JAK2	JAK2	JAK2	1657	0.21	0.73	YES
56	SP100	SP100	SP100	1723	0.2	0.74	YES
57	IFNAR2	IFNAR2	IFNAR2	1734	0.2	0.74	YES
58	HLA-C	HLA-C	HLA-C	1755	0.2	0.75	YES
59	ICAM1	ICAM1	ICAM1	1764	0.2	0.76	YES
60	IRF5	IRF5	IRF5	1872	0.18	0.76	YES
61	STAT2	STAT2	STAT2	1971	0.17	0.76	YES
62	IRF3	IRF3	IRF3	2131	0.16	0.76	NO
63	MT2A	MT2A	MT2A	2319	0.14	0.75	NO
64	EIF2AK2	EIF2AK2	EIF2AK2	2335	0.14	0.76	NO
65	KPNA5	KPNA5	KPNA5	2584	0.12	0.75	NO
66	IFITM3	IFITM3	IFITM3	2678	0.12	0.75	NO
67	SOCS3	SOCS3	SOCS3	2829	0.11	0.74	NO
68	PML	PML	PML	2850	0.11	0.75	NO
69	CAMK2D	CAMK2D	CAMK2D	2903	0.11	0.75	NO
70	PLCG1	PLCG1	PLCG1	3008	0.1	0.75	NO
71	PTPN2	PTPN2	PTPN2	3446	0.084	0.73	NO
72	IRF2	IRF2	IRF2	3591	0.08	0.72	NO
73	NUP93	NUP93	NUP93	3658	0.078	0.72	NO
74	TYK2	TYK2	TYK2	3674	0.078	0.72	NO
75	NUP62	NUP62	NUP62	3942	0.069	0.71	NO
76	NUP210	NUP210	NUP210	4140	0.064	0.7	NO
77	NUP54	NUP54	NUP54	4550	0.056	0.68	NO
78	TRIM25	TRIM25	TRIM25	4560	0.056	0.68	NO
79	PTPN1	PTPN1	PTPN1	4816	0.05	0.67	NO
80	ADAR	ADAR	ADAR	5046	0.046	0.66	NO
81	UBA52	UBA52	UBA52	5070	0.046	0.66	NO
82	IFNGR1	IFNGR1	IFNGR1	5093	0.046	0.66	NO
83	NUPL2	NUPL2	NUPL2	5344	0.041	0.65	NO
84	JAK1	JAK1	JAK1	5416	0.04	0.65	NO
85	RPS27A	RPS27A	RPS27A	5423	0.04	0.65	NO
86	KPNA2	KPNA2	KPNA2	5437	0.04	0.65	NO
87	EIF4E3	EIF4E3	EIF4E3	5578	0.038	0.64	NO
88	UBE2N	UBE2N	UBE2N	5621	0.037	0.64	NO
89	KPNB1	KPNB1	KPNB1	5631	0.037	0.64	NO
90	RNASEL	RNASEL	RNASEL	5705	0.036	0.64	NO
91	IFNGR2	IFNGR2	IFNGR2	5715	0.036	0.64	NO
92	CD44	CD44	CD44	5733	0.035	0.64	NO
93	PRKCD	PRKCD	PRKCD	5815	0.034	0.64	NO
94	NUP153	NUP153	NUP153	6113	0.03	0.62	NO
95	EIF4A3	EIF4A3	EIF4A3	6444	0.026	0.61	NO
96	IFITM2	IFITM2	IFITM2	6445	0.026	0.61	NO
97	PIAS1	PIAS1	PIAS1	6546	0.025	0.6	NO
98	NUP85	NUP85	NUP85	6601	0.024	0.6	NO
99	EIF4E	EIF4E	EIF4E	6700	0.023	0.6	NO
100	NUP43	NUP43	NUP43	6779	0.022	0.59	NO
101	KPNA1	KPNA1	KPNA1	6834	0.021	0.59	NO
102	AAAS	AAAS	AAAS	6925	0.02	0.59	NO
103	EIF4E2	EIF4E2	EIF4E2	6975	0.02	0.58	NO
104	EIF4A1	EIF4A1	EIF4A1	6996	0.019	0.58	NO
105	NUP35	NUP35	NUP35	7178	0.018	0.57	NO
106	PIN1	PIN1	PIN1	7305	0.016	0.57	NO
107	IFNAR1	IFNAR1	IFNAR1	7344	0.016	0.57	NO
108	EIF4G1	EIF4G1	EIF4G1	7521	0.014	0.56	NO
109	NUP188	NUP188	NUP188	7687	0.012	0.55	NO
110	NUP88	NUP88	NUP88	7717	0.011	0.55	NO
111	SUMO1	SUMO1	SUMO1	7809	0.01	0.54	NO
112	NUP107	NUP107	NUP107	7908	0.0094	0.54	NO
113	EIF4A2	EIF4A2	EIF4A2	7972	0.0088	0.54	NO
114	NUP37	NUP37	NUP37	8005	0.0085	0.53	NO
115	NUP155	NUP155	NUP155	8137	0.007	0.53	NO
116	EIF4G2	EIF4G2	EIF4G2	8192	0.0065	0.52	NO
117	PPM1B	PPM1B	PPM1B	8275	0.0056	0.52	NO
118	RAE1	RAE1	RAE1	8297	0.0055	0.52	NO
119	NUP50	NUP50	NUP50	8415	0.0042	0.51	NO
120	NCAM1	NCAM1	NCAM1	8432	0.004	0.51	NO
121	POM121	POM121	POM121	8658	0.0014	0.5	NO
122	KPNA3	KPNA3	KPNA3	8853	-0.00034	0.49	NO
123	KPNA4	KPNA4	KPNA4	8880	-0.00064	0.49	NO
124	NUP214	NUP214	NUP214	9409	-0.0059	0.46	NO
125	UBE2E1	UBE2E1	UBE2E1	9450	-0.0063	0.46	NO
126	EIF4G3	EIF4G3	EIF4G3	9543	-0.0071	0.45	NO
127	NUP205	NUP205	NUP205	9626	-0.0082	0.45	NO
128	EGR1	EGR1	EGR1	9643	-0.0084	0.45	NO
129	TPR	TPR	TPR	9700	-0.009	0.44	NO
130	RANBP2	RANBP2	RANBP2	9850	-0.01	0.44	NO
131	NUP133	NUP133	NUP133	10062	-0.013	0.43	NO
132	IP6K2	IP6K2	IP6K2	10334	-0.016	0.41	NO
133	ARIH1	ARIH1	ARIH1	10859	-0.021	0.38	NO
134	MAPK3	MAPK3	MAPK3	11362	-0.027	0.36	NO
135	FLNB	FLNB	FLNB	12847	-0.047	0.28	NO
136	SEH1L	SEH1L	SEH1L	12977	-0.049	0.27	NO
137	CAMK2B	CAMK2B	CAMK2B	13685	-0.061	0.24	NO
138	NEDD4	NEDD4	NEDD4	14123	-0.07	0.21	NO
139	NUPL1	NUPL1	NUPL1	14404	-0.077	0.2	NO
140	CAMK2A	CAMK2A	CAMK2A	14696	-0.084	0.19	NO
141	IRF6	IRF6	IRF6	17399	-0.23	0.048	NO

Figure S133. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION.

Figure S134. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

Table S68. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PRKCB	PRKCB	PRKCB	114	0.84	0.17	YES
2	CARD11	CARD11	CARD11	234	0.73	0.31	YES
3	PSMB9	PSMB9	PSMB9	652	0.45	0.38	YES
4	PSMA8	PSMA8	PSMA8	713	0.42	0.47	YES
5	PSMB8	PSMB8	PSMB8	1276	0.27	0.49	YES
6	PSMB10	PSMB10	PSMB10	1580	0.22	0.52	YES
7	PSME2	PSME2	PSME2	1644	0.21	0.56	YES
8	NFKBIE	NFKBIE	NFKBIE	2014	0.17	0.58	YES
9	PSME1	PSME1	PSME1	2162	0.15	0.6	YES
10	MALT1	MALT1	MALT1	2846	0.11	0.59	YES
11	NFKBIA	NFKBIA	NFKBIA	3283	0.09	0.58	YES
12	CHUK	CHUK	CHUK	3492	0.083	0.59	YES
13	NFKBIB	NFKBIB	NFKBIB	3513	0.083	0.6	YES
14	PSMA5	PSMA5	PSMA5	3693	0.077	0.61	YES
15	PSMA6	PSMA6	PSMA6	4648	0.054	0.57	NO
16	UBA52	UBA52	UBA52	5070	0.046	0.56	NO
17	PSMA2	PSMA2	PSMA2	5176	0.044	0.56	NO
18	IKBKG	IKBKG	IKBKG	5202	0.043	0.57	NO
19	RPS27A	RPS27A	RPS27A	5423	0.04	0.56	NO
20	PSMF1	PSMF1	PSMF1	5516	0.038	0.57	NO
21	PSMA4	PSMA4	PSMA4	5696	0.036	0.56	NO
22	PSMA3	PSMA3	PSMA3	6017	0.031	0.55	NO
23	PSMD13	PSMD13	PSMD13	6142	0.03	0.55	NO
24	PSMB1	PSMB1	PSMB1	6196	0.029	0.56	NO
25	PSMB2	PSMB2	PSMB2	6363	0.027	0.55	NO
26	PSMD1	PSMD1	PSMD1	6600	0.024	0.54	NO
27	PSMC4	PSMC4	PSMC4	6856	0.021	0.53	NO
28	PSMD11	PSMD11	PSMD11	6929	0.02	0.53	NO
29	PSMD14	PSMD14	PSMD14	7175	0.018	0.52	NO
30	PSMD7	PSMD7	PSMD7	7190	0.017	0.53	NO
31	PSMB6	PSMB6	PSMB6	7589	0.013	0.51	NO
32	PSMD2	PSMD2	PSMD2	7871	0.0098	0.5	NO
33	PSMC5	PSMC5	PSMC5	7970	0.0088	0.49	NO
34	PSMD12	PSMD12	PSMD12	7986	0.0087	0.49	NO
35	PSMA1	PSMA1	PSMA1	8113	0.0073	0.49	NO
36	PSMD6	PSMD6	PSMD6	8119	0.0072	0.49	NO
37	PSMD10	PSMD10	PSMD10	8153	0.0069	0.49	NO
38	BCL10	BCL10	BCL10	8236	0.0061	0.48	NO
39	PSMB7	PSMB7	PSMB7	8251	0.0059	0.48	NO
40	PSMA7	PSMA7	PSMA7	8557	0.0027	0.47	NO
41	PSMD8	PSMD8	PSMD8	8638	0.0016	0.46	NO
42	PSMC3	PSMC3	PSMC3	8679	0.0012	0.46	NO
43	MAP3K7	MAP3K7	MAP3K7	8695	0.0011	0.46	NO
44	PSME4	PSME4	PSME4	8840	-0.00024	0.45	NO
45	PSMD9	PSMD9	PSMD9	8841	-0.00024	0.45	NO
46	PSMB5	PSMB5	PSMB5	8900	-0.00083	0.45	NO
47	BTRC	BTRC	BTRC	8924	-0.001	0.45	NO
48	RELA	RELA	RELA	8928	-0.001	0.45	NO
49	CUL1	CUL1	CUL1	8957	-0.0014	0.45	NO
50	REL	REL	REL	9239	-0.0043	0.43	NO
51	PSMB3	PSMB3	PSMB3	10223	-0.014	0.38	NO
52	FBXW11	FBXW11	FBXW11	10432	-0.017	0.38	NO
53	PSMC2	PSMC2	PSMC2	10488	-0.017	0.38	NO
54	PSMB4	PSMB4	PSMB4	10694	-0.019	0.37	NO
55	PSMD4	PSMD4	PSMD4	11111	-0.024	0.35	NO
56	SKP1	SKP1	SKP1	11147	-0.024	0.35	NO
57	PSMD5	PSMD5	PSMD5	11318	-0.026	0.35	NO
58	PSMC1	PSMC1	PSMC1	12144	-0.036	0.31	NO
59	IKBKB	IKBKB	IKBKB	12216	-0.037	0.32	NO
60	PSMD3	PSMD3	PSMD3	12250	-0.038	0.32	NO
61	PSMC6	PSMC6	PSMC6	12403	-0.04	0.32	NO

Figure S135. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY.

Figure S136. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

Table S69. 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	IL2RA	IL2RA	IL2RA	151	0.8	0.14	YES
2	LCK	LCK	LCK	159	0.8	0.29	YES
3	IL2RB	IL2RB	IL2RB	273	0.69	0.41	YES
4	IL2RG	IL2RG	IL2RG	276	0.69	0.54	YES
5	IL2	IL2	IL2	291	0.67	0.66	YES
6	JAK3	JAK3	JAK3	319	0.65	0.78	YES
7	GRB2	GRB2	GRB2	2705	0.12	0.67	NO
8	UGCG	UGCG	UGCG	3020	0.1	0.67	NO
9	MYC	MYC	MYC	3120	0.096	0.68	NO
10	FOXO3	FOXO3	FOXO3	4265	0.062	0.63	NO
11	NFKB1	NFKB1	NFKB1	4336	0.06	0.64	NO
12	GAB2	GAB2	GAB2	4649	0.054	0.63	NO
13	BCL2	BCL2	BCL2	5155	0.044	0.61	NO
14	E2F1	E2F1	E2F1	5214	0.043	0.62	NO
15	JAK1	JAK1	JAK1	5416	0.04	0.61	NO
16	MTOR	MTOR	MTOR	6262	0.028	0.57	NO
17	EIF3A	EIF3A	EIF3A	6321	0.028	0.57	NO
18	SOS1	SOS1	SOS1	6448	0.026	0.57	NO
19	PIK3CA	PIK3CA	PIK3CA	6468	0.026	0.57	NO
20	RPS6	RPS6	RPS6	7013	0.019	0.55	NO
21	MYB	MYB	MYB	8082	0.0077	0.49	NO
22	RELA	RELA	RELA	8928	-0.001	0.44	NO
23	BCL2L1	BCL2L1	BCL2L1	9215	-0.0041	0.43	NO
24	SMPD1	SMPD1	SMPD1	9480	-0.0066	0.42	NO
25	PRKCZ	PRKCZ	PRKCZ	9750	-0.0094	0.4	NO
26	RPS6KB1	RPS6KB1	RPS6KB1	10076	-0.013	0.39	NO
27	TERT	TERT	TERT	10293	-0.015	0.38	NO
28	PTPN11	PTPN11	PTPN11	10425	-0.016	0.38	NO
29	RAC1	RAC1	RAC1	11074	-0.024	0.34	NO
30	PIK3R1	PIK3R1	PIK3R1	12279	-0.038	0.28	NO
31	HSP90AA1	HSP90AA1	HSP90AA1	12325	-0.039	0.29	NO
32	AKT1	AKT1	AKT1	13673	-0.061	0.23	NO
33	SGMS1	SGMS1	SGMS1	14033	-0.068	0.22	NO
34	SHC1	SHC1	SHC1	14128	-0.07	0.23	NO

Figure S137. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM.

Figure S138. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS

Table S70. 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	NLRC5	NLRC5	NLRC5	582	0.48	0.089	YES
2	HERC5	HERC5	HERC5	770	0.4	0.18	YES
3	TNFAIP3	TNFAIP3	TNFAIP3	905	0.35	0.26	YES
4	ISG15	ISG15	ISG15	921	0.35	0.35	YES
5	IFIH1	IFIH1	IFIH1	1134	0.3	0.41	YES
6	UBE2L6	UBE2L6	UBE2L6	1298	0.27	0.47	YES
7	UBA7	UBA7	UBA7	1396	0.25	0.53	YES
8	DDX58	DDX58	DDX58	1503	0.23	0.58	YES
9	RNF125	RNF125	RNF125	1908	0.18	0.6	YES
10	CYLD	CYLD	CYLD	1916	0.18	0.65	YES
11	IRF3	IRF3	IRF3	2131	0.16	0.68	YES
12	IKBKE	IKBKE	IKBKE	2289	0.14	0.7	YES
13	TRAF3	TRAF3	TRAF3	2566	0.12	0.72	YES
14	UBE2D1	UBE2D1	UBE2D1	4214	0.063	0.65	NO
15	ATG5	ATG5	ATG5	4426	0.058	0.65	NO
16	TRIM25	TRIM25	TRIM25	4560	0.056	0.66	NO
17	UBA52	UBA52	UBA52	5070	0.046	0.64	NO
18	TBK1	TBK1	TBK1	5383	0.041	0.63	NO
19	RPS27A	RPS27A	RPS27A	5423	0.04	0.64	NO
20	OTUD5	OTUD5	OTUD5	6355	0.027	0.6	NO
21	PIN1	PIN1	PIN1	7305	0.016	0.55	NO
22	UBE2D3	UBE2D3	UBE2D3	7449	0.014	0.54	NO
23	UBE2K	UBE2K	UBE2K	7801	0.011	0.53	NO
24	PCBP2	PCBP2	PCBP2	8140	0.007	0.51	NO
25	MAVS	MAVS	MAVS	8406	0.0043	0.5	NO
26	UBE2D2	UBE2D2	UBE2D2	9144	-0.0033	0.46	NO
27	ATG12	ATG12	ATG12	9727	-0.0091	0.43	NO
28	RNF135	RNF135	RNF135	10345	-0.016	0.4	NO
29	TAX1BP1	TAX1BP1	TAX1BP1	12718	-0.045	0.28	NO
30	NLRX1	NLRX1	NLRX1	15111	-0.098	0.17	NO

Figure S139. 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 UBIQUITIN MEDIATED PROTEOLYSIS.

Figure S140. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS, 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.v4.0.symbols.gmt
Expression data file = BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = BRCA-TP.mergedcluster.txt

GSEA analysis

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

Download Results

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

References

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

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