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

Kidney Chromophobe (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 KICH-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1KH0MQC

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 "KICH-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: 701
Number of samples: 66
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 ] 17
pheno.type: 2 - 7 :[ clus2 ] 15
pheno.type: 3 - 7 :[ clus3 ] 5
pheno.type: 4 - 7 :[ clus4 ] 6
pheno.type: 5 - 7 :[ clus5 ] 14
pheno.type: 6 - 7 :[ clus6 ] 4
pheno.type: 7 - 7 :[ clus7 ] 5

For the expression subtypes of 17843 genes in 67 samples, GSEA found enriched gene sets in each cluster using 66 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are ST WNT BETA CATENIN PATHWAY, PID P38 MKK3 6PATHWAY, PID REELINPATHWAY, REACTOME MEIOSIS, REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS, REACTOME GENERIC TRANSCRIPTION PATHWAY, REACTOME RNA POL I TRANSCRIPTION, REACTOME GLUCONEOGENESIS, REACTOME OLFACTORY SIGNALING PATHWAY, REACTOME TRANSCRIPTION

And common core enriched genes are HIST1H2AC, HIST1H2AD, HIST1H2AE, HIST1H2BC, HIST1H2BD, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BJ, HIST1H2BK

clus2

Top enriched gene sets are KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG ANTIGEN PROCESSING AND PRESENTATION, KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY, KEGG PATHOGENIC ESCHERICHIA COLI INFECTION, KEGG NON SMALL CELL LUNG CANCER, KEGG GRAFT VERSUS HOST DISEASE, BIOCARTA DEATH PATHWAY, BIOCARTA KERATINOCYTE PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA MYOSIN PATHWAY

And common core enriched genes are BIRC3, CASP3, CASP6, CASP7, CFLAR, CYCS, FADD, MAP3K14, NFKB1, NFKBIA

clus3

Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG TYROSINE METABOLISM, BIOCARTA RACCYCD PATHWAY, BIOCARTA INTEGRIN PATHWAY, PID WNT NONCANONICAL PATHWAY, PID NECTIN PATHWAY, PID HNF3BPATHWAY, PID IGF1 PATHWAY, PID AR TF PATHWAY, PID ECADHERIN STABILIZATION PATHWAY

And common core enriched genes are CDKN1A, AKT2, AKT3, BAD, CASP9, FOXO1, FOXO3, FOXO4, GSK3A, PDPK1

clus4

Top enriched gene sets are KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG PROPANOATE METABOLISM, KEGG ADHERENS JUNCTION, BIOCARTA AT1R PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA PPARA PATHWAY, BIOCARTA PDGF PATHWAY, BIOCARTA VEGF PATHWAY, PID S1P S1P3 PATHWAY, PID AVB3 OPN PATHWAY

And common core enriched genes are AGTR1, ITGA5, MAPK8, PIK3CA, PLD2, STAT5A, STAT5B, EGFR, SOS1, ITGA1

clus5

Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG RNA DEGRADATION, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG NUCLEOTIDE EXCISION REPAIR, PID FANCONI PATHWAY, REACTOME TRANSLATION, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME MITOCHONDRIAL PROTEIN IMPORT, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

And common core enriched genes are FAM153A, RPL10, RPL10A, RPL11, RPL12, RPL13A, RPL14, RPL15, RPL17, RPL18

clus6

Top enriched gene sets are KEGG ARGININE AND PROLINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG GLYCEROLIPID METABOLISM, KEGG PROPANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, SIG CD40PATHWAYMAP, PID TRAIL PATHWAY, PID RET PATHWAY

And common core enriched genes are ALDH1B1, ALDH2, AHCYL1, CBS, CTH, GGT1, GGT5, GGT6, MARS2, MAT1A

clus7

Top enriched gene sets are BIOCARTA RACCYCD PATHWAY, PID ILK PATHWAY, REACTOME TRIF MEDIATED TLR3 SIGNALING, REACTOME ORC1 REMOVAL FROM CHROMATIN, REACTOME ACTIVATION OF NF KAPPAB IN B CELLS, REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT, REACTOME CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6, REACTOME REGULATION OF APOPTOSIS, REACTOME CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION , REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE

And common core enriched genes are PSMA1, PSMA4, PSMA5, PSMA6, PSMA7, PSMB1, PSMB10, PSMB2, PSMB3, PSMB4

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
ST WNT BETA CATENIN PATHWAY	33	genes.ES.table	0.47	1.4	0.1	1	1	0.18	0.086	0.17	1	0.8
PID P38 MKK3 6PATHWAY	26	genes.ES.table	0.54	2.1	0	0.11	0.043	0.12	0.041	0.11	0	0.028
PID REELINPATHWAY	28	genes.ES.table	0.44	1.4	0.14	1	1	0.14	0.049	0.14	1	0.78
REACTOME MEIOSIS	92	genes.ES.table	0.6	1.4	0.16	1	1	0.36	0.14	0.31	1	0.83
REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS	25	genes.ES.table	0.5	1.3	0.14	1	1	0.24	0.052	0.23	1	0.83
REACTOME GENERIC TRANSCRIPTION PATHWAY	337	genes.ES.table	0.37	1.4	0.16	1	0.99	0.42	0.27	0.31	1	0.87
REACTOME RNA POL I TRANSCRIPTION	71	genes.ES.table	0.61	1.4	0.16	1	1	0.38	0.14	0.33	1	0.81
REACTOME GLUCONEOGENESIS	30	genes.ES.table	0.45	1.3	0.12	1	1	0.27	0.11	0.24	1	0.73
REACTOME OLFACTORY SIGNALING PATHWAY	32	genes.ES.table	0.59	1.4	0.047	1	0.99	0.5	0.2	0.4	1	0.84
REACTOME TRANSCRIPTION	181	genes.ES.table	0.37	1.3	0.27	1	1	0.2	0.19	0.17	1	0.83

genes ES table in pathway: ST WNT BETA CATENIN PATHWAY

Table S1. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CAMK2B	CAMK2B	CAMK2B	244	0.46	0.24	YES
2	MAP2K6	MAP2K6	MAP2K6	720	0.3	0.38	YES
3	GADD45G	GADD45G	GADD45G	738	0.3	0.54	YES
4	TAB1	TAB1	TAB1	5096	0.06	0.33	NO
5	TXN	TXN	TXN	5148	0.058	0.36	NO
6	TAOK2	TAOK2	TAOK2	6791	0.031	0.29	NO
7	TAOK3	TAOK3	TAOK3	7302	0.023	0.27	NO
8	TAB2	TAB2	TAB2	8013	0.012	0.24	NO
9	MAP3K1	MAP3K1	MAP3K1	8534	0.0039	0.21	NO
10	MAP3K7	MAP3K7	MAP3K7	8743	0.00081	0.2	NO
11	TRAF2	TRAF2	TRAF2	8829	-0.00049	0.19	NO
12	MAP3K4	MAP3K4	MAP3K4	8877	-0.00098	0.19	NO
13	RAC1	RAC1	RAC1	9342	-0.0076	0.17	NO
14	GADD45B	GADD45B	GADD45B	9372	-0.0081	0.17	NO
15	MAP3K3	MAP3K3	MAP3K3	10111	-0.02	0.14	NO
16	CCM2	CCM2	CCM2	10112	-0.02	0.15	NO
17	MAPK14	MAPK14	MAPK14	10115	-0.02	0.16	NO
18	MAP3K10	MAP3K10	MAP3K10	10873	-0.031	0.14	NO
19	TAOK1	TAOK1	TAOK1	11018	-0.034	0.15	NO
20	TRAF6	TRAF6	TRAF6	11036	-0.034	0.17	NO
21	ATM	ATM	ATM	11637	-0.045	0.16	NO
22	GADD45A	GADD45A	GADD45A	11924	-0.05	0.17	NO
23	MAP3K5	MAP3K5	MAP3K5	12025	-0.052	0.19	NO
24	MAP2K3	MAP2K3	MAP2K3	12074	-0.052	0.22	NO
25	MAP3K6	MAP3K6	MAP3K6	12894	-0.07	0.21	NO
26	MAPK11	MAPK11	MAPK11	14495	-0.12	0.19	NO

Figure S1. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST WNT BETA CATENIN PATHWAY.

Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: ST WNT BETA CATENIN 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 P38 MKK3 6PATHWAY

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	HIST1H2AE	HIST1H2AE	HIST1H2AE	87	0.58	0.085	YES
2	HIST1H2BL	HIST1H2BL	HIST1H2BL	276	0.44	0.14	YES
3	HIST1H2BC	HIST1H2BC	HIST1H2BC	316	0.42	0.2	YES
4	HIST1H2BG	HIST1H2BG	HIST1H2BG	408	0.38	0.26	YES
5	HIST4H4	HIST4H4	HIST4H4	472	0.35	0.31	YES
6	HIST1H2BD	HIST1H2BD	HIST1H2BD	509	0.34	0.36	YES
7	HIST1H4E	HIST1H4E	HIST1H4E	567	0.33	0.41	YES
8	HIST1H4H	HIST1H4H	HIST1H4H	653	0.31	0.45	YES
9	HIST1H2BE	HIST1H2BE	HIST1H2BE	769	0.29	0.49	YES
10	HIST1H2BN	HIST1H2BN	HIST1H2BN	973	0.26	0.52	YES
11	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	1208	0.23	0.54	YES
12	HIST1H2BK	HIST1H2BK	HIST1H2BK	1281	0.22	0.57	YES
13	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1359	0.22	0.6	YES
14	HIST1H4D	HIST1H4D	HIST1H4D	1379	0.21	0.63	YES
15	HIST1H2AD	HIST1H2AD	HIST1H2AD	1386	0.21	0.66	YES
16	HIST1H2AC	HIST1H2AC	HIST1H2AC	1490	0.2	0.69	YES
17	HIST1H2BO	HIST1H2BO	HIST1H2BO	1552	0.2	0.72	YES
18	HIST1H2BF	HIST1H2BF	HIST1H2BF	1923	0.17	0.72	YES
19	HIST2H2BE	HIST2H2BE	HIST2H2BE	1942	0.17	0.75	YES
20	HIST1H4B	HIST1H4B	HIST1H4B	2312	0.14	0.75	YES
21	HIST1H4I	HIST1H4I	HIST1H4I	2488	0.14	0.76	YES
22	HIST1H2BH	HIST1H2BH	HIST1H2BH	5233	0.057	0.61	NO
23	HIST1H4C	HIST1H4C	HIST1H4C	5429	0.053	0.61	NO
24	HIST1H4A	HIST1H4A	HIST1H4A	5492	0.052	0.62	NO
25	HIST1H4J	HIST1H4J	HIST1H4J	5871	0.046	0.6	NO
26	HIST2H4A	HIST2H4A	HIST2H4A	6074	0.043	0.6	NO
27	H2AFX	H2AFX	H2AFX	6177	0.041	0.6	NO
28	TERF2IP	TERF2IP	TERF2IP	6561	0.035	0.58	NO
29	TERF2	TERF2	TERF2	7733	0.016	0.52	NO
30	H2AFZ	H2AFZ	H2AFZ	7926	0.013	0.51	NO
31	POT1	POT1	POT1	8565	0.0034	0.47	NO
32	HIST2H2AC	HIST2H2AC	HIST2H2AC	9110	-0.0042	0.44	NO
33	TINF2	TINF2	TINF2	9134	-0.0046	0.44	NO
34	ACD	ACD	ACD	9509	-0.01	0.42	NO
35	TERF1	TERF1	TERF1	10934	-0.032	0.35	NO
36	HIST3H2BB	HIST3H2BB	HIST3H2BB	14284	-0.11	0.18	NO
37	HIST1H2BI	HIST1H2BI	HIST1H2BI	15117	-0.15	0.15	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: PID P38 MKK3 6PATHWAY.

Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: PID P38 MKK3 6PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID REELINPATHWAY

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	HIST1H2AE	HIST1H2AE	HIST1H2AE	87	0.58	0.064	YES
2	HIST1H2BL	HIST1H2BL	HIST1H2BL	276	0.44	0.11	YES
3	HIST1H2BC	HIST1H2BC	HIST1H2BC	316	0.42	0.15	YES
4	HIST1H2BG	HIST1H2BG	HIST1H2BG	408	0.38	0.19	YES
5	TEX12	TEX12	TEX12	422	0.37	0.24	YES
6	HIST4H4	HIST4H4	HIST4H4	472	0.35	0.28	YES
7	HIST1H2BD	HIST1H2BD	HIST1H2BD	509	0.34	0.32	YES
8	HIST1H4E	HIST1H4E	HIST1H4E	567	0.33	0.35	YES
9	HIST1H4H	HIST1H4H	HIST1H4H	653	0.31	0.38	YES
10	HIST1H2BE	HIST1H2BE	HIST1H2BE	769	0.29	0.41	YES
11	HIST1H2BN	HIST1H2BN	HIST1H2BN	973	0.26	0.43	YES
12	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	1208	0.23	0.45	YES
13	HIST1H2BK	HIST1H2BK	HIST1H2BK	1281	0.22	0.47	YES
14	SYNE1	SYNE1	SYNE1	1358	0.22	0.49	YES
15	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1359	0.22	0.52	YES
16	HIST1H4D	HIST1H4D	HIST1H4D	1379	0.21	0.54	YES
17	HIST1H2AD	HIST1H2AD	HIST1H2AD	1386	0.21	0.57	YES
18	HIST1H2AC	HIST1H2AC	HIST1H2AC	1490	0.2	0.58	YES
19	HIST1H2BO	HIST1H2BO	HIST1H2BO	1552	0.2	0.6	YES
20	HIST1H2BF	HIST1H2BF	HIST1H2BF	1923	0.17	0.6	YES
21	HIST2H2BE	HIST2H2BE	HIST2H2BE	1942	0.17	0.62	YES
22	LMNB1	LMNB1	LMNB1	2242	0.15	0.62	YES
23	HIST1H4B	HIST1H4B	HIST1H4B	2312	0.14	0.64	YES
24	HIST1H4I	HIST1H4I	HIST1H4I	2488	0.14	0.64	YES
25	SMC1B	SMC1B	SMC1B	3201	0.11	0.62	NO
26	ATR	ATR	ATR	3285	0.1	0.62	NO
27	SUN2	SUN2	SUN2	4014	0.083	0.59	NO
28	SYNE2	SYNE2	SYNE2	4438	0.073	0.58	NO
29	STAG2	STAG2	STAG2	5127	0.059	0.55	NO
30	HIST1H2BH	HIST1H2BH	HIST1H2BH	5233	0.057	0.55	NO
31	DIDO1	DIDO1	DIDO1	5386	0.054	0.55	NO
32	HIST1H4C	HIST1H4C	HIST1H4C	5429	0.053	0.55	NO
33	HIST1H4A	HIST1H4A	HIST1H4A	5492	0.052	0.55	NO
34	HIST1H4J	HIST1H4J	HIST1H4J	5871	0.046	0.54	NO
35	HIST2H4A	HIST2H4A	HIST2H4A	6074	0.043	0.53	NO
36	H2AFX	H2AFX	H2AFX	6177	0.041	0.53	NO
37	SYCP2	SYCP2	SYCP2	6443	0.037	0.52	NO
38	UBE2I	UBE2I	UBE2I	6496	0.036	0.52	NO
39	TERF2IP	TERF2IP	TERF2IP	6561	0.035	0.52	NO
40	STAG1	STAG1	STAG1	6663	0.033	0.52	NO
41	TERF2	TERF2	TERF2	7733	0.016	0.46	NO
42	H2AFZ	H2AFZ	H2AFZ	7926	0.013	0.45	NO
43	SMC1A	SMC1A	SMC1A	7978	0.012	0.45	NO
44	POT1	POT1	POT1	8565	0.0034	0.42	NO
45	BRCA1	BRCA1	BRCA1	8613	0.0028	0.42	NO
46	HIST2H2AC	HIST2H2AC	HIST2H2AC	9110	-0.0042	0.39	NO
47	TINF2	TINF2	TINF2	9134	-0.0046	0.39	NO
48	ACD	ACD	ACD	9509	-0.01	0.37	NO
49	REC8	REC8	REC8	10081	-0.019	0.34	NO
50	TERF1	TERF1	TERF1	10934	-0.032	0.29	NO
51	RAD21	RAD21	RAD21	11252	-0.038	0.28	NO
52	LMNA	LMNA	LMNA	11958	-0.05	0.25	NO
53	SMC3	SMC3	SMC3	12439	-0.06	0.23	NO
54	HSPA2	HSPA2	HSPA2	13462	-0.084	0.18	NO
55	STAG3	STAG3	STAG3	13723	-0.091	0.18	NO
56	HIST3H2BB	HIST3H2BB	HIST3H2BB	14284	-0.11	0.16	NO
57	HIST1H2BI	HIST1H2BI	HIST1H2BI	15117	-0.15	0.13	NO
58	FKBP6	FKBP6	FKBP6	16130	-0.21	0.095	NO

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

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: PID REELINPATHWAY, 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 MEIOSIS

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	HIST1H2AE	HIST1H2AE	HIST1H2AE	87	0.58	0.065	YES
2	HIST1H2BL	HIST1H2BL	HIST1H2BL	276	0.44	0.11	YES
3	HIST1H2BC	HIST1H2BC	HIST1H2BC	316	0.42	0.16	YES
4	HIST1H2BG	HIST1H2BG	HIST1H2BG	408	0.38	0.2	YES
5	HIST4H4	HIST4H4	HIST4H4	472	0.35	0.23	YES
6	HIST1H2BD	HIST1H2BD	HIST1H2BD	509	0.34	0.27	YES
7	HIST1H4E	HIST1H4E	HIST1H4E	567	0.33	0.31	YES
8	CENPP	CENPP	CENPP	640	0.32	0.34	YES
9	HIST1H4H	HIST1H4H	HIST1H4H	653	0.31	0.38	YES
10	HIST1H2BE	HIST1H2BE	HIST1H2BE	769	0.29	0.41	YES
11	HIST1H2BN	HIST1H2BN	HIST1H2BN	973	0.26	0.43	YES
12	MLF1IP	MLF1IP	MLF1IP	995	0.26	0.46	YES
13	CENPH	CENPH	CENPH	997	0.26	0.49	YES
14	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	1208	0.23	0.5	YES
15	HJURP	HJURP	HJURP	1262	0.23	0.53	YES
16	HIST1H2BK	HIST1H2BK	HIST1H2BK	1281	0.22	0.56	YES
17	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1359	0.22	0.58	YES
18	HIST1H4D	HIST1H4D	HIST1H4D	1379	0.21	0.6	YES
19	HIST1H2AD	HIST1H2AD	HIST1H2AD	1386	0.21	0.63	YES
20	HIST1H2AC	HIST1H2AC	HIST1H2AC	1490	0.2	0.64	YES
21	HIST1H2BO	HIST1H2BO	HIST1H2BO	1552	0.2	0.66	YES
22	HIST1H2BF	HIST1H2BF	HIST1H2BF	1923	0.17	0.66	YES
23	HIST2H2BE	HIST2H2BE	HIST2H2BE	1942	0.17	0.68	YES
24	HIST1H4B	HIST1H4B	HIST1H4B	2312	0.14	0.68	YES
25	HIST1H4I	HIST1H4I	HIST1H4I	2488	0.14	0.69	YES
26	CENPK	CENPK	CENPK	2622	0.13	0.7	YES
27	CENPI	CENPI	CENPI	3327	0.1	0.67	NO
28	NPM1	NPM1	NPM1	3734	0.091	0.66	NO
29	RUVBL1	RUVBL1	RUVBL1	3847	0.087	0.66	NO
30	CENPA	CENPA	CENPA	4035	0.083	0.66	NO
31	HIST1H2BH	HIST1H2BH	HIST1H2BH	5233	0.057	0.6	NO
32	CENPN	CENPN	CENPN	5345	0.055	0.6	NO
33	HIST1H4C	HIST1H4C	HIST1H4C	5429	0.053	0.6	NO
34	HIST1H4A	HIST1H4A	HIST1H4A	5492	0.052	0.6	NO
35	HIST1H4J	HIST1H4J	HIST1H4J	5871	0.046	0.59	NO
36	HIST2H4A	HIST2H4A	HIST2H4A	6074	0.043	0.58	NO
37	H2AFX	H2AFX	H2AFX	6177	0.041	0.58	NO
38	RSF1	RSF1	RSF1	6838	0.03	0.55	NO
39	OIP5	OIP5	OIP5	7391	0.022	0.52	NO
40	ITGB3BP	ITGB3BP	ITGB3BP	7611	0.018	0.51	NO
41	H2AFZ	H2AFZ	H2AFZ	7926	0.013	0.49	NO
42	CENPQ	CENPQ	CENPQ	7988	0.012	0.49	NO
43	RBBP7	RBBP7	RBBP7	8769	0.00034	0.45	NO
44	HIST2H2AC	HIST2H2AC	HIST2H2AC	9110	-0.0042	0.43	NO
45	SMARCA5	SMARCA5	SMARCA5	9357	-0.0079	0.42	NO
46	RBBP4	RBBP4	RBBP4	11171	-0.036	0.32	NO
47	CASC5	CASC5	CASC5	11923	-0.05	0.28	NO
48	HIST3H2BB	HIST3H2BB	HIST3H2BB	14284	-0.11	0.16	NO
49	HIST1H2BI	HIST1H2BI	HIST1H2BI	15117	-0.15	0.13	NO
50	CENPO	CENPO	CENPO	15337	-0.16	0.14	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: REACTOME MEIOSIS.

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

genes ES table in pathway: REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS

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	HIST1H2AE	HIST1H2AE	HIST1H2AE	87	0.58	0.07	YES
2	HIST1H2BL	HIST1H2BL	HIST1H2BL	276	0.44	0.12	YES
3	HIST1H2BC	HIST1H2BC	HIST1H2BC	316	0.42	0.17	YES
4	HIST1H2BG	HIST1H2BG	HIST1H2BG	408	0.38	0.21	YES
5	HIST4H4	HIST4H4	HIST4H4	472	0.35	0.25	YES
6	HIST1H2BD	HIST1H2BD	HIST1H2BD	509	0.34	0.3	YES
7	HIST1H4E	HIST1H4E	HIST1H4E	567	0.33	0.34	YES
8	HIST1H4H	HIST1H4H	HIST1H4H	653	0.31	0.37	YES
9	HIST1H2BE	HIST1H2BE	HIST1H2BE	769	0.29	0.4	YES
10	HIST1H2BN	HIST1H2BN	HIST1H2BN	973	0.26	0.42	YES
11	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	1208	0.23	0.44	YES
12	HIST1H2BK	HIST1H2BK	HIST1H2BK	1281	0.22	0.46	YES
13	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1359	0.22	0.49	YES
14	HIST1H4D	HIST1H4D	HIST1H4D	1379	0.21	0.51	YES
15	HIST1H2AD	HIST1H2AD	HIST1H2AD	1386	0.21	0.54	YES
16	HIST1H2AC	HIST1H2AC	HIST1H2AC	1490	0.2	0.56	YES
17	HIST1H2BO	HIST1H2BO	HIST1H2BO	1552	0.2	0.58	YES
18	HIST1H2BF	HIST1H2BF	HIST1H2BF	1923	0.17	0.58	YES
19	HIST2H2BE	HIST2H2BE	HIST2H2BE	1942	0.17	0.61	YES
20	HIST1H4B	HIST1H4B	HIST1H4B	2312	0.14	0.6	YES
21	HIST1H4I	HIST1H4I	HIST1H4I	2488	0.14	0.61	YES
22	POLD4	POLD4	POLD4	2815	0.12	0.61	NO
23	POLA1	POLA1	POLA1	3495	0.097	0.58	NO
24	RPA3	RPA3	RPA3	3822	0.088	0.58	NO
25	RUVBL1	RUVBL1	RUVBL1	3847	0.087	0.59	NO
26	NHP2	NHP2	NHP2	3916	0.086	0.59	NO
27	RFC4	RFC4	RFC4	4125	0.08	0.59	NO
28	LIG1	LIG1	LIG1	5097	0.06	0.54	NO
29	HIST1H2BH	HIST1H2BH	HIST1H2BH	5233	0.057	0.54	NO
30	HIST1H4C	HIST1H4C	HIST1H4C	5429	0.053	0.54	NO
31	HIST1H4A	HIST1H4A	HIST1H4A	5492	0.052	0.54	NO
32	POLE2	POLE2	POLE2	5588	0.051	0.55	NO
33	RFC3	RFC3	RFC3	5731	0.048	0.54	NO
34	HIST1H4J	HIST1H4J	HIST1H4J	5871	0.046	0.54	NO
35	HIST2H4A	HIST2H4A	HIST2H4A	6074	0.043	0.54	NO
36	H2AFX	H2AFX	H2AFX	6177	0.041	0.54	NO
37	RUVBL2	RUVBL2	RUVBL2	6499	0.036	0.52	NO
38	POLD1	POLD1	POLD1	6501	0.036	0.53	NO
39	TERF2IP	TERF2IP	TERF2IP	6561	0.035	0.53	NO
40	POLA2	POLA2	POLA2	7005	0.028	0.51	NO
41	DKC1	DKC1	DKC1	7250	0.024	0.5	NO
42	RFC5	RFC5	RFC5	7494	0.02	0.48	NO
43	FEN1	FEN1	FEN1	7581	0.018	0.48	NO
44	PCNA	PCNA	PCNA	7710	0.017	0.48	NO
45	TERF2	TERF2	TERF2	7733	0.016	0.48	NO
46	DNA2	DNA2	DNA2	7917	0.013	0.47	NO
47	H2AFZ	H2AFZ	H2AFZ	7926	0.013	0.47	NO
48	POLE	POLE	POLE	8117	0.01	0.46	NO
49	RPA2	RPA2	RPA2	8171	0.0092	0.46	NO
50	POT1	POT1	POT1	8565	0.0034	0.44	NO
51	HIST2H2AC	HIST2H2AC	HIST2H2AC	9110	-0.0042	0.41	NO
52	TINF2	TINF2	TINF2	9134	-0.0046	0.41	NO
53	ACD	ACD	ACD	9509	-0.01	0.39	NO
54	RFC2	RFC2	RFC2	10565	-0.026	0.33	NO
55	RPA1	RPA1	RPA1	10805	-0.03	0.32	NO
56	TERF1	TERF1	TERF1	10934	-0.032	0.32	NO
57	PRIM2	PRIM2	PRIM2	11336	-0.039	0.3	NO
58	POLD2	POLD2	POLD2	11384	-0.04	0.3	NO
59	POLD3	POLD3	POLD3	11642	-0.045	0.29	NO
60	PRIM1	PRIM1	PRIM1	13188	-0.077	0.22	NO
61	WRAP53	WRAP53	WRAP53	13507	-0.085	0.21	NO
62	HIST3H2BB	HIST3H2BB	HIST3H2BB	14284	-0.11	0.18	NO
63	HIST1H2BI	HIST1H2BI	HIST1H2BI	15117	-0.15	0.15	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 A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS, 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 GENERIC TRANSCRIPTION PATHWAY

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	HIST1H3G	HIST1H3G	HIST1H3G	79	0.59	0.049	YES
2	HIST1H2AE	HIST1H2AE	HIST1H2AE	87	0.58	0.1	YES
3	HIST1H2BL	HIST1H2BL	HIST1H2BL	276	0.44	0.13	YES
4	HIST1H2BC	HIST1H2BC	HIST1H2BC	316	0.42	0.16	YES
5	TTR	TTR	TTR	351	0.4	0.2	YES
6	HIST1H2BG	HIST1H2BG	HIST1H2BG	408	0.38	0.23	YES
7	HIST4H4	HIST4H4	HIST4H4	472	0.35	0.26	YES
8	ODAM	ODAM	ODAM	494	0.35	0.29	YES
9	HIST1H2BD	HIST1H2BD	HIST1H2BD	509	0.34	0.32	YES
10	HIST1H3H	HIST1H3H	HIST1H3H	564	0.33	0.34	YES
11	HIST1H4E	HIST1H4E	HIST1H4E	567	0.33	0.38	YES
12	HIST1H3E	HIST1H3E	HIST1H3E	624	0.32	0.4	YES
13	HIST1H4H	HIST1H4H	HIST1H4H	653	0.31	0.43	YES
14	LTF	LTF	LTF	681	0.31	0.45	YES
15	HIST1H3D	HIST1H3D	HIST1H3D	748	0.29	0.48	YES
16	HIST1H2BE	HIST1H2BE	HIST1H2BE	769	0.29	0.5	YES
17	HIST1H2BN	HIST1H2BN	HIST1H2BN	973	0.26	0.51	YES
18	HIST2H3D	HIST2H3D	HIST2H3D	1037	0.25	0.53	YES
19	NPPA	NPPA	NPPA	1153	0.24	0.55	YES
20	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	1208	0.23	0.56	YES
21	HIST1H2BK	HIST1H2BK	HIST1H2BK	1281	0.22	0.58	YES
22	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1359	0.22	0.59	YES
23	HIST1H4D	HIST1H4D	HIST1H4D	1379	0.21	0.61	YES
24	HIST1H2AD	HIST1H2AD	HIST1H2AD	1386	0.21	0.63	YES
25	HIST1H2AC	HIST1H2AC	HIST1H2AC	1490	0.2	0.64	YES
26	HIST1H2BO	HIST1H2BO	HIST1H2BO	1552	0.2	0.66	YES
27	HIST1H2BF	HIST1H2BF	HIST1H2BF	1923	0.17	0.65	YES
28	HIST2H2BE	HIST2H2BE	HIST2H2BE	1942	0.17	0.67	YES
29	HIST1H4B	HIST1H4B	HIST1H4B	2312	0.14	0.66	NO
30	HIST1H4I	HIST1H4I	HIST1H4I	2488	0.14	0.66	NO
31	GSN	GSN	GSN	2981	0.11	0.64	NO
32	HIST2H3C	HIST2H3C	HIST2H3C	3400	0.1	0.63	NO
33	HIST1H3A	HIST1H3A	HIST1H3A	5149	0.058	0.54	NO
34	HIST1H2BH	HIST1H2BH	HIST1H2BH	5233	0.057	0.54	NO
35	HIST1H4C	HIST1H4C	HIST1H4C	5429	0.053	0.53	NO
36	HIST1H4A	HIST1H4A	HIST1H4A	5492	0.052	0.53	NO
37	HIST1H4J	HIST1H4J	HIST1H4J	5871	0.046	0.52	NO
38	HIST2H4A	HIST2H4A	HIST2H4A	6074	0.043	0.51	NO
39	H2AFX	H2AFX	H2AFX	6177	0.041	0.5	NO
40	HSPG2	HSPG2	HSPG2	7331	0.022	0.44	NO
41	SNCA	SNCA	SNCA	7476	0.02	0.44	NO
42	H2AFZ	H2AFZ	H2AFZ	7926	0.013	0.41	NO
43	B2M	B2M	B2M	8627	0.0026	0.37	NO
44	CST3	CST3	CST3	8970	-0.0023	0.35	NO
45	HIST2H2AC	HIST2H2AC	HIST2H2AC	9110	-0.0042	0.35	NO
46	H3F3A	H3F3A	H3F3A	9617	-0.012	0.32	NO
47	APOA1	APOA1	APOA1	10848	-0.031	0.25	NO
48	ITM2B	ITM2B	ITM2B	11185	-0.037	0.24	NO
49	LYZ	LYZ	LYZ	11673	-0.045	0.21	NO
50	H3F3B	H3F3B	H3F3B	12513	-0.062	0.17	NO
51	HIST1H3B	HIST1H3B	HIST1H3B	12723	-0.066	0.17	NO
52	HIST1H3C	HIST1H3C	HIST1H3C	13286	-0.08	0.14	NO
53	MFGE8	MFGE8	MFGE8	13561	-0.087	0.13	NO
54	FGA	FGA	FGA	14211	-0.11	0.11	NO
55	HIST3H2BB	HIST3H2BB	HIST3H2BB	14284	-0.11	0.11	NO
56	APP	APP	APP	14537	-0.12	0.11	NO
57	TGFBI	TGFBI	TGFBI	14580	-0.12	0.12	NO
58	HIST1H2BI	HIST1H2BI	HIST1H2BI	15117	-0.15	0.1	NO
59	SAA1	SAA1	SAA1	15487	-0.17	0.095	NO
60	CALCA	CALCA	CALCA	16023	-0.2	0.082	NO
61	HIST1H3J	HIST1H3J	HIST1H3J	16167	-0.21	0.093	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 GENERIC TRANSCRIPTION PATHWAY.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME GENERIC TRANSCRIPTION 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 RNA POL I TRANSCRIPTION

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	HIST1H3G	HIST1H3G	HIST1H3G	79	0.59	0.051	YES
2	HIST1H2AE	HIST1H2AE	HIST1H2AE	87	0.58	0.1	YES
3	HIST1H2BL	HIST1H2BL	HIST1H2BL	276	0.44	0.13	YES
4	HIST1H2BC	HIST1H2BC	HIST1H2BC	316	0.42	0.17	YES
5	MND1	MND1	MND1	350	0.4	0.21	YES
6	HIST1H2BG	HIST1H2BG	HIST1H2BG	408	0.38	0.24	YES
7	HIST4H4	HIST4H4	HIST4H4	472	0.35	0.27	YES
8	HIST1H2BD	HIST1H2BD	HIST1H2BD	509	0.34	0.3	YES
9	HIST1H3H	HIST1H3H	HIST1H3H	564	0.33	0.32	YES
10	HIST1H4E	HIST1H4E	HIST1H4E	567	0.33	0.36	YES
11	MSH4	MSH4	MSH4	599	0.32	0.38	YES
12	HIST1H3E	HIST1H3E	HIST1H3E	624	0.32	0.41	YES
13	HIST1H4H	HIST1H4H	HIST1H4H	653	0.31	0.44	YES
14	HIST1H3D	HIST1H3D	HIST1H3D	748	0.29	0.46	YES
15	HIST1H2BE	HIST1H2BE	HIST1H2BE	769	0.29	0.49	YES
16	HIST1H2BN	HIST1H2BN	HIST1H2BN	973	0.26	0.5	YES
17	HIST2H3D	HIST2H3D	HIST2H3D	1037	0.25	0.52	YES
18	TEX15	TEX15	TEX15	1160	0.24	0.53	YES
19	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	1208	0.23	0.55	YES
20	HIST1H2BK	HIST1H2BK	HIST1H2BK	1281	0.22	0.57	YES
21	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1359	0.22	0.58	YES
22	HIST1H4D	HIST1H4D	HIST1H4D	1379	0.21	0.6	YES
23	HIST1H2AD	HIST1H2AD	HIST1H2AD	1386	0.21	0.62	YES
24	HIST1H2AC	HIST1H2AC	HIST1H2AC	1490	0.2	0.64	YES
25	HIST1H2BO	HIST1H2BO	HIST1H2BO	1552	0.2	0.65	YES
26	HIST1H2BF	HIST1H2BF	HIST1H2BF	1923	0.17	0.64	YES
27	HIST2H2BE	HIST2H2BE	HIST2H2BE	1942	0.17	0.66	YES
28	HIST1H4B	HIST1H4B	HIST1H4B	2312	0.14	0.65	YES
29	HIST1H4I	HIST1H4I	HIST1H4I	2488	0.14	0.66	YES
30	RBBP8	RBBP8	RBBP8	2516	0.14	0.67	YES
31	HIST2H3C	HIST2H3C	HIST2H3C	3400	0.1	0.63	NO
32	RAD50	RAD50	RAD50	3430	0.099	0.63	NO
33	RPA3	RPA3	RPA3	3822	0.088	0.62	NO
34	DMC1	DMC1	DMC1	4715	0.067	0.57	NO
35	HIST1H3A	HIST1H3A	HIST1H3A	5149	0.058	0.56	NO
36	HIST1H2BH	HIST1H2BH	HIST1H2BH	5233	0.057	0.56	NO
37	HIST1H4C	HIST1H4C	HIST1H4C	5429	0.053	0.55	NO
38	HIST1H4A	HIST1H4A	HIST1H4A	5492	0.052	0.55	NO
39	RAD51	RAD51	RAD51	5778	0.048	0.54	NO
40	HIST1H4J	HIST1H4J	HIST1H4J	5871	0.046	0.54	NO
41	BRCA2	BRCA2	BRCA2	5918	0.045	0.54	NO
42	BLM	BLM	BLM	6051	0.043	0.54	NO
43	HIST2H4A	HIST2H4A	HIST2H4A	6074	0.043	0.54	NO
44	H2AFX	H2AFX	H2AFX	6177	0.041	0.54	NO
45	MLH1	MLH1	MLH1	7129	0.026	0.49	NO
46	H2AFZ	H2AFZ	H2AFZ	7926	0.013	0.44	NO
47	RPA2	RPA2	RPA2	8171	0.0092	0.43	NO
48	MRE11A	MRE11A	MRE11A	8381	0.0064	0.42	NO
49	BRCA1	BRCA1	BRCA1	8613	0.0028	0.41	NO
50	MLH3	MLH3	MLH3	9031	-0.0032	0.38	NO
51	HIST2H2AC	HIST2H2AC	HIST2H2AC	9110	-0.0042	0.38	NO
52	CDK4	CDK4	CDK4	9260	-0.0063	0.37	NO
53	H3F3A	H3F3A	H3F3A	9617	-0.012	0.35	NO
54	NBN	NBN	NBN	10415	-0.024	0.31	NO
55	RPA1	RPA1	RPA1	10805	-0.03	0.29	NO
56	TOP3A	TOP3A	TOP3A	11524	-0.043	0.26	NO
57	ATM	ATM	ATM	11637	-0.045	0.25	NO
58	CDK2	CDK2	CDK2	11937	-0.05	0.24	NO
59	H3F3B	H3F3B	H3F3B	12513	-0.062	0.21	NO
60	HIST1H3B	HIST1H3B	HIST1H3B	12723	-0.066	0.21	NO
61	HIST1H3C	HIST1H3C	HIST1H3C	13286	-0.08	0.18	NO
62	HIST3H2BB	HIST3H2BB	HIST3H2BB	14284	-0.11	0.14	NO
63	HIST1H2BI	HIST1H2BI	HIST1H2BI	15117	-0.15	0.1	NO
64	RAD51C	RAD51C	RAD51C	15118	-0.15	0.12	NO
65	MSH5	MSH5	MSH5	15370	-0.16	0.12	NO
66	HIST1H3J	HIST1H3J	HIST1H3J	16167	-0.21	0.093	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 RNA POL I TRANSCRIPTION.

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

genes ES table in pathway: REACTOME GLUCONEOGENESIS

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	AR	AR	AR	119	0.54	0.0088	YES
2	ZNF483	ZNF483	ZNF483	151	0.51	0.022	YES
3	RORB	RORB	RORB	249	0.46	0.029	YES
4	ZNF221	ZNF221	ZNF221	251	0.45	0.042	YES
5	NR4A2	NR4A2	NR4A2	255	0.45	0.055	YES
6	ZNF154	ZNF154	ZNF154	362	0.4	0.06	YES
7	ZNF540	ZNF540	ZNF540	388	0.39	0.07	YES
8	NR4A3	NR4A3	NR4A3	389	0.39	0.081	YES
9	ZNF439	ZNF439	ZNF439	523	0.34	0.083	YES
10	ZNF418	ZNF418	ZNF418	538	0.34	0.092	YES
11	NR4A1	NR4A1	NR4A1	586	0.33	0.099	YES
12	ZNF208	ZNF208	ZNF208	637	0.32	0.1	YES
13	ZNF311	ZNF311	ZNF311	686	0.3	0.11	YES
14	MAMLD1	MAMLD1	MAMLD1	698	0.3	0.12	YES
15	ZIM2	ZIM2	ZIM2	813	0.28	0.12	YES
16	ZNF492	ZNF492	ZNF492	814	0.28	0.13	YES
17	ZNF331	ZNF331	ZNF331	833	0.28	0.14	YES
18	NR2E3	NR2E3	NR2E3	836	0.28	0.14	YES
19	ZNF620	ZNF620	ZNF620	957	0.26	0.14	YES
20	ZNF285	ZNF285	ZNF285	1006	0.26	0.15	YES
21	ZNF334	ZNF334	ZNF334	1011	0.25	0.16	YES
22	ZNF167	ZNF167	ZNF167	1033	0.25	0.16	YES
23	NR5A2	NR5A2	NR5A2	1038	0.25	0.17	YES
24	VDR	VDR	VDR	1045	0.25	0.18	YES
25	ZNF547	ZNF547	ZNF547	1090	0.24	0.18	YES
26	ZNF563	ZNF563	ZNF563	1105	0.24	0.19	YES
27	NPPA	NPPA	NPPA	1153	0.24	0.19	YES
28	ZNF98	ZNF98	ZNF98	1241	0.23	0.19	YES
29	ZNF10	ZNF10	ZNF10	1283	0.22	0.2	YES
30	ZNF610	ZNF610	ZNF610	1327	0.22	0.2	YES
31	ZNF19	ZNF19	ZNF19	1343	0.22	0.2	YES
32	ZIK1	ZIK1	ZIK1	1451	0.21	0.2	YES
33	ZNF442	ZNF442	ZNF442	1462	0.21	0.21	YES
34	ZNF493	ZNF493	ZNF493	1531	0.2	0.21	YES
35	ZNF546	ZNF546	ZNF546	1540	0.2	0.22	YES
36	ZNF658	ZNF658	ZNF658	1546	0.2	0.22	YES
37	ZNF256	ZNF256	ZNF256	1587	0.2	0.22	YES
38	ZNF169	ZNF169	ZNF169	1730	0.18	0.22	YES
39	ESRRB	ESRRB	ESRRB	1746	0.18	0.23	YES
40	ZNF530	ZNF530	ZNF530	1810	0.18	0.23	YES
41	ZNF582	ZNF582	ZNF582	1818	0.18	0.23	YES
42	MAML3	MAML3	MAML3	1831	0.18	0.24	YES
43	ZNF597	ZNF597	ZNF597	1839	0.18	0.24	YES
44	ZNF619	ZNF619	ZNF619	1937	0.17	0.24	YES
45	ZNF274	ZNF274	ZNF274	1943	0.17	0.25	YES
46	ZNF226	ZNF226	ZNF226	2020	0.16	0.25	YES
47	ZNF551	ZNF551	ZNF551	2057	0.16	0.25	YES
48	ZNF141	ZNF141	ZNF141	2067	0.16	0.25	YES
49	ZNF43	ZNF43	ZNF43	2164	0.15	0.25	YES
50	ZNF510	ZNF510	ZNF510	2265	0.15	0.25	YES
51	ZNF431	ZNF431	ZNF431	2280	0.15	0.25	YES
52	ZNF354B	ZNF354B	ZNF354B	2346	0.14	0.25	YES
53	ZNF23	ZNF23	ZNF23	2367	0.14	0.26	YES
54	ZNF585B	ZNF585B	ZNF585B	2378	0.14	0.26	YES
55	ZNF528	ZNF528	ZNF528	2405	0.14	0.26	YES
56	ZNF224	ZNF224	ZNF224	2413	0.14	0.27	YES
57	THRB	THRB	THRB	2419	0.14	0.27	YES
58	ZNF417	ZNF417	ZNF417	2430	0.14	0.27	YES
59	ZNF571	ZNF571	ZNF571	2443	0.14	0.28	YES
60	ZNF197	ZNF197	ZNF197	2455	0.14	0.28	YES
61	ZNF304	ZNF304	ZNF304	2501	0.14	0.28	YES
62	ZNF441	ZNF441	ZNF441	2536	0.13	0.28	YES
63	ZNF223	ZNF223	ZNF223	2539	0.13	0.29	YES
64	ZNF101	ZNF101	ZNF101	2617	0.13	0.29	YES
65	SKIL	SKIL	SKIL	2644	0.13	0.29	YES
66	ZNF138	ZNF138	ZNF138	2711	0.13	0.29	YES
67	PPARG	PPARG	PPARG	2717	0.13	0.29	YES
68	ZNF157	ZNF157	ZNF157	2744	0.12	0.29	YES
69	NR3C1	NR3C1	NR3C1	2747	0.12	0.3	YES
70	NR1D2	NR1D2	NR1D2	2752	0.12	0.3	YES
71	ZNF440	ZNF440	ZNF440	2785	0.12	0.3	YES
72	CDK9	CDK9	CDK9	2786	0.12	0.31	YES
73	SMAD3	SMAD3	SMAD3	2810	0.12	0.31	YES
74	ZNF155	ZNF155	ZNF155	2848	0.12	0.31	YES
75	ZNF14	ZNF14	ZNF14	2861	0.12	0.31	YES
76	ZNF548	ZNF548	ZNF548	2988	0.11	0.31	YES
77	CCNT1	CCNT1	CCNT1	2990	0.11	0.31	YES
78	ZNF606	ZNF606	ZNF606	2991	0.11	0.32	YES
79	MED7	MED7	MED7	3003	0.11	0.32	YES
80	ZNF426	ZNF426	ZNF426	3024	0.11	0.32	YES
81	ZNF471	ZNF471	ZNF471	3051	0.11	0.32	YES
82	ZNF708	ZNF708	ZNF708	3055	0.11	0.32	YES
83	ZNF566	ZNF566	ZNF566	3119	0.11	0.32	YES
84	ZNF394	ZNF394	ZNF394	3142	0.11	0.33	YES
85	ZNF420	ZNF420	ZNF420	3166	0.11	0.33	YES
86	ZNF595	ZNF595	ZNF595	3196	0.11	0.33	YES
87	PPM1A	PPM1A	PPM1A	3234	0.1	0.33	YES
88	ZNF627	ZNF627	ZNF627	3244	0.1	0.33	YES
89	ZNF589	ZNF589	ZNF589	3251	0.1	0.34	YES
90	PPARD	PPARD	PPARD	3262	0.1	0.34	YES
91	ZNF136	ZNF136	ZNF136	3365	0.1	0.33	YES
92	ZNF773	ZNF773	ZNF773	3432	0.099	0.33	YES
93	ZNF230	ZNF230	ZNF230	3442	0.099	0.34	YES
94	ZNF227	ZNF227	ZNF227	3464	0.098	0.34	YES
95	ZNF354A	ZNF354A	ZNF354A	3500	0.097	0.34	YES
96	NR3C2	NR3C2	NR3C2	3542	0.096	0.34	YES
97	ZNF484	ZNF484	ZNF484	3550	0.096	0.34	YES
98	ZNF184	ZNF184	ZNF184	3579	0.095	0.34	YES
99	MED27	MED27	MED27	3617	0.094	0.34	YES
100	ZNF189	ZNF189	ZNF189	3629	0.094	0.34	YES
101	ZNF100	ZNF100	ZNF100	3659	0.093	0.34	YES
102	ZNF266	ZNF266	ZNF266	3681	0.092	0.35	YES
103	ZNF506	ZNF506	ZNF506	3683	0.092	0.35	YES
104	NR6A1	NR6A1	NR6A1	3692	0.092	0.35	YES
105	ZNF92	ZNF92	ZNF92	3774	0.09	0.35	YES
106	ZNF544	ZNF544	ZNF544	3801	0.089	0.35	YES
107	ZNF621	ZNF621	ZNF621	3938	0.085	0.34	YES
108	ZNF587	ZNF587	ZNF587	3976	0.084	0.35	YES
109	RORA	RORA	RORA	3982	0.084	0.35	YES
110	ZNF45	ZNF45	ZNF45	4010	0.083	0.35	YES
111	ZNF570	ZNF570	ZNF570	4021	0.083	0.35	YES
112	ZNF596	ZNF596	ZNF596	4040	0.082	0.35	YES
113	ZNF254	ZNF254	ZNF254	4108	0.08	0.35	YES
114	ZNF616	ZNF616	ZNF616	4196	0.078	0.35	YES
115	ZNF543	ZNF543	ZNF543	4214	0.078	0.35	YES
116	ZNF607	ZNF607	ZNF607	4242	0.077	0.35	YES
117	RBPJ	RBPJ	RBPJ	4251	0.077	0.35	YES
118	ZNF234	ZNF234	ZNF234	4254	0.077	0.35	YES
119	ZNF500	ZNF500	ZNF500	4260	0.077	0.36	YES
120	NR1H2	NR1H2	NR1H2	4310	0.076	0.36	YES
121	ZNF443	ZNF443	ZNF443	4331	0.075	0.36	YES
122	ZNF557	ZNF557	ZNF557	4332	0.075	0.36	YES
123	ZNF350	ZNF350	ZNF350	4347	0.075	0.36	YES
124	ZNF211	ZNF211	ZNF211	4363	0.075	0.36	YES
125	TGIF1	TGIF1	TGIF1	4412	0.074	0.36	YES
126	ZNF212	ZNF212	ZNF212	4425	0.074	0.36	YES
127	ZNF485	ZNF485	ZNF485	4444	0.073	0.36	YES
128	ZNF446	ZNF446	ZNF446	4471	0.072	0.36	YES
129	MED10	MED10	MED10	4522	0.071	0.36	YES
130	ZNF564	ZNF564	ZNF564	4535	0.071	0.36	YES
131	ZNF419	ZNF419	ZNF419	4576	0.07	0.36	YES
132	KAT2B	KAT2B	KAT2B	4611	0.069	0.36	YES
133	ZNF287	ZNF287	ZNF287	4616	0.069	0.36	YES
134	ZNF565	ZNF565	ZNF565	4740	0.066	0.36	YES
135	ZNF17	ZNF17	ZNF17	4782	0.066	0.36	YES
136	NOTCH4	NOTCH4	NOTCH4	4797	0.066	0.36	YES
137	MED6	MED6	MED6	4811	0.066	0.36	YES
138	ZNF561	ZNF561	ZNF561	4831	0.065	0.36	YES
139	ZNF445	ZNF445	ZNF445	4843	0.065	0.36	YES
140	ZNF347	ZNF347	ZNF347	4862	0.064	0.36	YES
141	NCOR2	NCOR2	NCOR2	4871	0.064	0.37	YES
142	ZNF416	ZNF416	ZNF416	4907	0.064	0.36	NO
143	ZNF613	ZNF613	ZNF613	4987	0.062	0.36	NO
144	ZNF641	ZNF641	ZNF641	5038	0.061	0.36	NO
145	RARG	RARG	RARG	5043	0.061	0.36	NO
146	ZNF317	ZNF317	ZNF317	5117	0.059	0.36	NO
147	ZNF490	ZNF490	ZNF490	5135	0.059	0.36	NO
148	MAML1	MAML1	MAML1	5191	0.058	0.36	NO
149	RORC	RORC	RORC	5315	0.056	0.35	NO
150	TEAD1	TEAD1	TEAD1	5352	0.055	0.35	NO
151	ZFP2	ZFP2	ZFP2	5359	0.055	0.36	NO
152	TRIM28	TRIM28	TRIM28	5394	0.054	0.36	NO
153	ZNF37A	ZNF37A	ZNF37A	5407	0.054	0.36	NO
154	ZNF337	ZNF337	ZNF337	5415	0.054	0.36	NO
155	ZNF222	ZNF222	ZNF222	5428	0.053	0.36	NO
156	ZNF320	ZNF320	ZNF320	5495	0.052	0.36	NO
157	ZNF175	ZNF175	ZNF175	5553	0.051	0.35	NO
158	ZNF3	ZNF3	ZNF3	5671	0.049	0.35	NO
159	ZNF263	ZNF263	ZNF263	5718	0.048	0.35	NO
160	ZKSCAN1	ZKSCAN1	ZKSCAN1	5735	0.048	0.35	NO
161	ZNF577	ZNF577	ZNF577	5748	0.048	0.35	NO
162	NR2C2AP	NR2C2AP	NR2C2AP	5766	0.048	0.35	NO
163	ZNF433	ZNF433	ZNF433	5792	0.048	0.35	NO
164	NR1D1	NR1D1	NR1D1	5801	0.047	0.35	NO
165	ZNF585A	ZNF585A	ZNF585A	5843	0.047	0.35	NO
166	ZFP28	ZFP28	ZFP28	5875	0.046	0.35	NO
167	NR1I2	NR1I2	NR1I2	5963	0.045	0.34	NO
168	ZFP112	ZFP112	ZFP112	6027	0.044	0.34	NO
169	E2F4	E2F4	E2F4	6029	0.044	0.34	NO
170	ZFP1	ZFP1	ZFP1	6044	0.043	0.34	NO
171	ZNF213	ZNF213	ZNF213	6065	0.043	0.34	NO
172	ZNF225	ZNF225	ZNF225	6119	0.042	0.34	NO
173	ZNF192	ZNF192	ZNF192	6131	0.042	0.34	NO
174	ZNF605	ZNF605	ZNF605	6141	0.042	0.34	NO
175	ZNF583	ZNF583	ZNF583	6181	0.041	0.34	NO
176	ZNF558	ZNF558	ZNF558	6209	0.04	0.34	NO
177	ZNF614	ZNF614	ZNF614	6272	0.039	0.34	NO
178	ZNF430	ZNF430	ZNF430	6388	0.038	0.33	NO
179	ZNF415	ZNF415	ZNF415	6398	0.037	0.33	NO
180	ZNF559	ZNF559	ZNF559	6399	0.037	0.34	NO
181	RXRA	RXRA	RXRA	6419	0.037	0.34	NO
182	ZNF552	ZNF552	ZNF552	6538	0.035	0.33	NO
183	ZNF160	ZNF160	ZNF160	6550	0.035	0.33	NO
184	ZKSCAN5	ZKSCAN5	ZKSCAN5	6596	0.034	0.33	NO
185	ZNF611	ZNF611	ZNF611	6701	0.032	0.32	NO
186	UBE2D3	UBE2D3	UBE2D3	6759	0.032	0.32	NO
187	ZNF398	ZNF398	ZNF398	6865	0.03	0.32	NO
188	TBL1X	TBL1X	TBL1X	6937	0.029	0.31	NO
189	ZNF333	ZNF333	ZNF333	6946	0.029	0.31	NO
190	HNF4A	HNF4A	HNF4A	6992	0.028	0.31	NO
191	ZNF33A	ZNF33A	ZNF33A	7025	0.027	0.31	NO
192	THRA	THRA	THRA	7143	0.025	0.3	NO
193	ZNF20	ZNF20	ZNF20	7158	0.025	0.3	NO
194	ZNF600	ZNF600	ZNF600	7216	0.024	0.3	NO
195	ZNF514	ZNF514	ZNF514	7226	0.024	0.3	NO
196	SMAD2	SMAD2	SMAD2	7237	0.024	0.3	NO
197	CDKN2B	CDKN2B	CDKN2B	7283	0.023	0.3	NO
198	UBA52	UBA52	UBA52	7294	0.023	0.3	NO
199	ZNF140	ZNF140	ZNF140	7333	0.022	0.3	NO
200	ZNF273	ZNF273	ZNF273	7422	0.021	0.29	NO
201	CCNT2	CCNT2	CCNT2	7438	0.021	0.29	NO
202	ZNF480	ZNF480	ZNF480	7474	0.02	0.29	NO
203	ZNF26	ZNF26	ZNF26	7512	0.02	0.29	NO
204	ZKSCAN4	ZKSCAN4	ZKSCAN4	7542	0.019	0.29	NO
205	ZNF382	ZNF382	ZNF382	7567	0.019	0.29	NO
206	ZNF180	ZNF180	ZNF180	7591	0.018	0.29	NO
207	ZNF569	ZNF569	ZNF569	7600	0.018	0.29	NO
208	SMAD4	SMAD4	SMAD4	7605	0.018	0.29	NO
209	JUNB	JUNB	JUNB	7635	0.018	0.29	NO
210	ZNF12	ZNF12	ZNF12	7667	0.017	0.29	NO
211	NR2F6	NR2F6	NR2F6	7738	0.016	0.28	NO
212	ZNF460	ZNF460	ZNF460	7761	0.016	0.28	NO
213	ZNF567	ZNF567	ZNF567	7844	0.014	0.28	NO
214	CREBBP	CREBBP	CREBBP	7907	0.013	0.27	NO
215	ZNF205	ZNF205	ZNF205	7909	0.013	0.27	NO
216	ZNF28	ZNF28	ZNF28	7955	0.013	0.27	NO
217	MED16	MED16	MED16	7987	0.012	0.27	NO
218	PPARA	PPARA	PPARA	8018	0.012	0.27	NO
219	ZNF529	ZNF529	ZNF529	8083	0.01	0.27	NO
220	MED15	MED15	MED15	8107	0.01	0.26	NO
221	ZNF383	ZNF383	ZNF383	8115	0.01	0.26	NO
222	ZNF324	ZNF324	ZNF324	8192	0.0089	0.26	NO
223	ZNF434	ZNF434	ZNF434	8229	0.0084	0.26	NO
224	ZNF498	ZNF498	ZNF498	8384	0.0064	0.25	NO
225	ZNF649	ZNF649	ZNF649	8414	0.0058	0.25	NO
226	ZNF432	ZNF432	ZNF432	8431	0.0056	0.25	NO
227	MED12	MED12	MED12	8541	0.0038	0.24	NO
228	MED25	MED25	MED25	8629	0.0025	0.24	NO
229	MED14	MED14	MED14	8672	0.0018	0.24	NO
230	ZNF615	ZNF615	ZNF615	8819	-0.00038	0.23	NO
231	WWTR1	WWTR1	WWTR1	8870	-0.00094	0.22	NO
232	USP9X	USP9X	USP9X	8922	-0.0017	0.22	NO
233	ZNF584	ZNF584	ZNF584	8992	-0.0027	0.22	NO
234	MEN1	MEN1	MEN1	9003	-0.0029	0.22	NO
235	ZNF655	ZNF655	ZNF655	9013	-0.003	0.22	NO
236	ZNF282	ZNF282	ZNF282	9045	-0.0033	0.21	NO
237	NCOA3	NCOA3	NCOA3	9118	-0.0044	0.21	NO
238	ZNF468	ZNF468	ZNF468	9135	-0.0046	0.21	NO
239	MED23	MED23	MED23	9195	-0.0053	0.21	NO
240	ZNF235	ZNF235	ZNF235	9206	-0.0055	0.21	NO
241	NOTCH3	NOTCH3	NOTCH3	9264	-0.0064	0.2	NO
242	ZNF264	ZNF264	ZNF264	9341	-0.0076	0.2	NO
243	TRIM33	TRIM33	TRIM33	9502	-0.01	0.19	NO
244	MED4	MED4	MED4	9583	-0.011	0.18	NO
245	SP1	SP1	SP1	9635	-0.012	0.18	NO
246	SNW1	SNW1	SNW1	9783	-0.014	0.18	NO
247	E2F5	E2F5	E2F5	9886	-0.016	0.17	NO
248	ZNF425	ZNF425	ZNF425	9934	-0.016	0.17	NO
249	NCOA6	NCOA6	NCOA6	9964	-0.017	0.17	NO
250	CCNC	CCNC	CCNC	9984	-0.017	0.16	NO
251	ZNF599	ZNF599	ZNF599	9996	-0.017	0.16	NO
252	ZNF200	ZNF200	ZNF200	10042	-0.018	0.16	NO
253	TBL1XR1	TBL1XR1	TBL1XR1	10049	-0.018	0.16	NO
254	NCOA2	NCOA2	NCOA2	10104	-0.019	0.16	NO
255	KAT2A	KAT2A	KAT2A	10121	-0.02	0.16	NO
256	YAP1	YAP1	YAP1	10179	-0.02	0.16	NO
257	MED26	MED26	MED26	10190	-0.021	0.16	NO
258	ZNF250	ZNF250	ZNF250	10191	-0.021	0.16	NO
259	ESRRA	ESRRA	ESRRA	10292	-0.022	0.15	NO
260	HDAC1	HDAC1	HDAC1	10502	-0.025	0.14	NO
261	ZFP90	ZFP90	ZFP90	10601	-0.027	0.14	NO
262	TGS1	TGS1	TGS1	10750	-0.029	0.13	NO
263	MED31	MED31	MED31	10761	-0.03	0.13	NO
264	TFDP1	TFDP1	TFDP1	10764	-0.03	0.13	NO
265	RXRB	RXRB	RXRB	10959	-0.032	0.12	NO
266	ZNF33B	ZNF33B	ZNF33B	11015	-0.034	0.12	NO
267	ZNF114	ZNF114	ZNF114	11184	-0.037	0.11	NO
268	NRBF2	NRBF2	NRBF2	11214	-0.037	0.11	NO
269	ZNF248	ZNF248	ZNF248	11235	-0.038	0.11	NO
270	ZNF18	ZNF18	ZNF18	11350	-0.04	0.1	NO
271	ZNF343	ZNF343	ZNF343	11373	-0.04	0.1	NO
272	ZNF624	ZNF624	ZNF624	11378	-0.04	0.1	NO
273	NR1H3	NR1H3	NR1H3	11418	-0.041	0.1	NO
274	MED24	MED24	MED24	11439	-0.041	0.1	NO
275	SMARCD3	SMARCD3	SMARCD3	11564	-0.043	0.098	NO
276	MED1	MED1	MED1	11692	-0.046	0.092	NO
277	ESR1	ESR1	ESR1	11851	-0.048	0.084	NO
278	ZNF202	ZNF202	ZNF202	11882	-0.049	0.084	NO
279	ZNF496	ZNF496	ZNF496	11891	-0.049	0.085	NO
280	SKI	SKI	SKI	11978	-0.051	0.081	NO
281	MED17	MED17	MED17	12012	-0.051	0.081	NO
282	ZNF267	ZNF267	ZNF267	12100	-0.053	0.077	NO
283	NCOR1	NCOR1	NCOR1	12174	-0.054	0.075	NO
284	NCOA1	NCOA1	NCOA1	12346	-0.058	0.067	NO
285	RPS27A	RPS27A	RPS27A	12398	-0.059	0.065	NO
286	ZNF560	ZNF560	ZNF560	12591	-0.063	0.056	NO
287	RARA	RARA	RARA	12675	-0.065	0.053	NO
288	PRIC285	PRIC285	PRIC285	12786	-0.068	0.049	NO
289	MED8	MED8	MED8	13077	-0.075	0.035	NO
290	ZNF555	ZNF555	ZNF555	13100	-0.076	0.036	NO
291	NRBP1	NRBP1	NRBP1	13161	-0.077	0.034	NO
292	RBL1	RBL1	RBL1	13274	-0.08	0.03	NO
293	ZNF454	ZNF454	ZNF454	13287	-0.08	0.032	NO
294	ZNF354C	ZNF354C	ZNF354C	13322	-0.081	0.032	NO
295	ZNF436	ZNF436	ZNF436	13392	-0.082	0.03	NO
296	ZNF214	ZNF214	ZNF214	13478	-0.085	0.028	NO
297	MYC	MYC	MYC	13518	-0.086	0.028	NO
298	ZNF473	ZNF473	ZNF473	13539	-0.086	0.03	NO
299	ZNF556	ZNF556	ZNF556	13579	-0.087	0.03	NO
300	SMAD7	SMAD7	SMAD7	13709	-0.091	0.025	NO
301	MED30	MED30	MED30	13727	-0.091	0.027	NO
302	MED20	MED20	MED20	13867	-0.096	0.022	NO
303	PARP1	PARP1	PARP1	13955	-0.098	0.019	NO
304	ZNF625	ZNF625	ZNF625	13962	-0.098	0.022	NO
305	ZNF517	ZNF517	ZNF517	13989	-0.099	0.023	NO
306	CTGF	CTGF	CTGF	14004	-0.099	0.025	NO
307	CDK8	CDK8	CDK8	14031	-0.1	0.027	NO
308	MAML2	MAML2	MAML2	14107	-0.1	0.025	NO
309	NR0B2	NR0B2	NR0B2	14179	-0.1	0.024	NO
310	TGIF2	TGIF2	TGIF2	14501	-0.12	0.0092	NO
311	ZKSCAN3	ZKSCAN3	ZKSCAN3	14530	-0.12	0.011	NO
312	ZNF2	ZNF2	ZNF2	14585	-0.12	0.011	NO
313	ZNF286A	ZNF286A	ZNF286A	14781	-0.13	0.0039	NO
314	ZFP37	ZFP37	ZFP37	14867	-0.13	0.0029	NO
315	SMURF2	SMURF2	SMURF2	14884	-0.14	0.0058	NO
316	ESR2	ESR2	ESR2	14913	-0.14	0.0081	NO
317	ZNF25	ZNF25	ZNF25	15044	-0.14	0.0048	NO
318	TEAD2	TEAD2	TEAD2	15144	-0.15	0.0033	NO
319	ZNF642	ZNF642	ZNF642	15164	-0.15	0.0065	NO
320	UBE2D1	UBE2D1	UBE2D1	15291	-0.16	0.0038	NO
321	ESRRG	ESRRG	ESRRG	15418	-0.16	0.0012	NO
322	NR2F1	NR2F1	NR2F1	15668	-0.18	-0.008	NO
323	TEAD3	TEAD3	TEAD3	15889	-0.19	-0.015	NO
324	ZNF300	ZNF300	ZNF300	15986	-0.2	-0.015	NO
325	ZNF519	ZNF519	ZNF519	16150	-0.21	-0.018	NO
326	ZNF215	ZNF215	ZNF215	16156	-0.21	-0.013	NO
327	TEAD4	TEAD4	TEAD4	16483	-0.24	-0.024	NO
328	ZNF30	ZNF30	ZNF30	16519	-0.24	-0.02	NO
329	ZNF643	ZNF643	ZNF643	16788	-0.26	-0.027	NO
330	SERPINE1	SERPINE1	SERPINE1	16978	-0.29	-0.03	NO
331	NR1I3	NR1I3	NR1I3	17001	-0.29	-0.023	NO
332	RUNX2	RUNX2	RUNX2	17072	-0.3	-0.018	NO
333	NOTCH2	NOTCH2	NOTCH2	17290	-0.34	-0.021	NO
334	HNF4G	HNF4G	HNF4G	17362	-0.36	-0.014	NO
335	NR0B1	NR0B1	NR0B1	17559	-0.42	-0.013	NO
336	RXRG	RXRG	RXRG	17627	-0.46	-0.0042	NO
337	PGR	PGR	PGR	17729	-0.54	0.0054	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 GLUCONEOGENESIS.

Figure S16. 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 OLFACTORY SIGNALING PATHWAY

Table S9. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	OR1N1	OR1N1	OR1N1	7	1	0.16	YES
2	OR1L8	OR1L8	OR1L8	37	0.76	0.27	YES
3	OR1N2	OR1N2	OR1N2	73	0.62	0.37	YES
4	OR5B12	OR5B12	OR5B12	77	0.6	0.46	YES
5	OR1B1	OR1B1	OR1B1	105	0.56	0.54	YES
6	OR2A1	OR2A1	OR2A1	1159	0.24	0.52	YES
7	OR1J1	OR1J1	OR1J1	1606	0.2	0.53	YES
8	OR51E1	OR51E1	OR51E1	1842	0.18	0.54	YES
9	OR2A5	OR2A5	OR2A5	2313	0.14	0.54	YES
10	OR1J2	OR1J2	OR1J2	2438	0.14	0.55	YES
11	GNGT1	GNGT1	GNGT1	2467	0.14	0.57	YES
12	OR2A25	OR2A25	OR2A25	2529	0.13	0.59	YES
13	OR7D2	OR7D2	OR7D2	2946	0.12	0.58	YES
14	OR6T1	OR6T1	OR6T1	3222	0.11	0.58	YES
15	OR2A4	OR2A4	OR2A4	3592	0.094	0.58	YES
16	OR1Q1	OR1Q1	OR1Q1	3644	0.093	0.59	YES
17	OR2A7	OR2A7	OR2A7	4156	0.079	0.57	NO
18	OR2W3	OR2W3	OR2W3	4850	0.065	0.54	NO
19	OR56B4	OR56B4	OR56B4	5956	0.045	0.49	NO
20	OR3A2	OR3A2	OR3A2	7187	0.025	0.42	NO
21	OR51E2	OR51E2	OR51E2	8167	0.0093	0.37	NO
22	OR5K2	OR5K2	OR5K2	8869	-0.00093	0.33	NO
23	OR2A14	OR2A14	OR2A14	10457	-0.024	0.24	NO
24	OR10AD1	OR10AD1	OR10AD1	10523	-0.026	0.24	NO
25	OR2A2	OR2A2	OR2A2	10703	-0.028	0.24	NO
26	OR4F29	OR4F29	OR4F29	12210	-0.055	0.16	NO
27	OR2C1	OR2C1	OR2C1	12242	-0.056	0.17	NO
28	GNB1	GNB1	GNB1	13489	-0.085	0.11	NO
29	GNAL	GNAL	GNAL	14479	-0.12	0.074	NO
30	OR52R1	OR52R1	OR52R1	15778	-0.18	0.029	NO
31	OR52N4	OR52N4	OR52N4	16650	-0.25	0.019	NO
32	OR51T1	OR51T1	OR51T1	17094	-0.31	0.041	NO

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

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME OLFACTORY 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: REACTOME TRANSCRIPTION

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	HIST1H3G	HIST1H3G	HIST1H3G	79	0.59	0.042	YES
2	HIST1H2AE	HIST1H2AE	HIST1H2AE	87	0.58	0.087	YES
3	HIST1H2BL	HIST1H2BL	HIST1H2BL	276	0.44	0.11	YES
4	HIST1H2BC	HIST1H2BC	HIST1H2BC	316	0.42	0.14	YES
5	MND1	MND1	MND1	350	0.4	0.17	YES
6	HIST1H2BG	HIST1H2BG	HIST1H2BG	408	0.38	0.2	YES
7	TEX12	TEX12	TEX12	422	0.37	0.22	YES
8	HIST4H4	HIST4H4	HIST4H4	472	0.35	0.25	YES
9	HIST1H2BD	HIST1H2BD	HIST1H2BD	509	0.34	0.28	YES
10	HIST1H3H	HIST1H3H	HIST1H3H	564	0.33	0.3	YES
11	HIST1H4E	HIST1H4E	HIST1H4E	567	0.33	0.32	YES
12	MSH4	MSH4	MSH4	599	0.32	0.35	YES
13	HIST1H3E	HIST1H3E	HIST1H3E	624	0.32	0.37	YES
14	HIST1H4H	HIST1H4H	HIST1H4H	653	0.31	0.39	YES
15	HIST1H3D	HIST1H3D	HIST1H3D	748	0.29	0.41	YES
16	HIST1H2BE	HIST1H2BE	HIST1H2BE	769	0.29	0.43	YES
17	HIST1H2BN	HIST1H2BN	HIST1H2BN	973	0.26	0.44	YES
18	HIST2H3D	HIST2H3D	HIST2H3D	1037	0.25	0.46	YES
19	TEX15	TEX15	TEX15	1160	0.24	0.47	YES
20	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	1208	0.23	0.48	YES
21	HIST1H2BK	HIST1H2BK	HIST1H2BK	1281	0.22	0.5	YES
22	SYNE1	SYNE1	SYNE1	1358	0.22	0.51	YES
23	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1359	0.22	0.53	YES
24	HIST1H4D	HIST1H4D	HIST1H4D	1379	0.21	0.54	YES
25	HIST1H2AD	HIST1H2AD	HIST1H2AD	1386	0.21	0.56	YES
26	HIST1H2AC	HIST1H2AC	HIST1H2AC	1490	0.2	0.57	YES
27	HIST1H2BO	HIST1H2BO	HIST1H2BO	1552	0.2	0.58	YES
28	HIST1H2BF	HIST1H2BF	HIST1H2BF	1923	0.17	0.57	YES
29	HIST2H2BE	HIST2H2BE	HIST2H2BE	1942	0.17	0.59	YES
30	LMNB1	LMNB1	LMNB1	2242	0.15	0.58	YES
31	HIST1H4B	HIST1H4B	HIST1H4B	2312	0.14	0.59	YES
32	HIST1H4I	HIST1H4I	HIST1H4I	2488	0.14	0.59	YES
33	RBBP8	RBBP8	RBBP8	2516	0.14	0.6	YES
34	SMC1B	SMC1B	SMC1B	3201	0.11	0.57	NO
35	ATR	ATR	ATR	3285	0.1	0.57	NO
36	HIST2H3C	HIST2H3C	HIST2H3C	3400	0.1	0.57	NO
37	RAD50	RAD50	RAD50	3430	0.099	0.58	NO
38	RPA3	RPA3	RPA3	3822	0.088	0.56	NO
39	SUN2	SUN2	SUN2	4014	0.083	0.56	NO
40	SYNE2	SYNE2	SYNE2	4438	0.073	0.54	NO
41	DMC1	DMC1	DMC1	4715	0.067	0.53	NO
42	STAG2	STAG2	STAG2	5127	0.059	0.51	NO
43	HIST1H3A	HIST1H3A	HIST1H3A	5149	0.058	0.52	NO
44	HIST1H2BH	HIST1H2BH	HIST1H2BH	5233	0.057	0.52	NO
45	DIDO1	DIDO1	DIDO1	5386	0.054	0.51	NO
46	HIST1H4C	HIST1H4C	HIST1H4C	5429	0.053	0.51	NO
47	HIST1H4A	HIST1H4A	HIST1H4A	5492	0.052	0.51	NO
48	RAD51	RAD51	RAD51	5778	0.048	0.5	NO
49	HIST1H4J	HIST1H4J	HIST1H4J	5871	0.046	0.5	NO
50	BRCA2	BRCA2	BRCA2	5918	0.045	0.5	NO
51	BLM	BLM	BLM	6051	0.043	0.5	NO
52	HIST2H4A	HIST2H4A	HIST2H4A	6074	0.043	0.5	NO
53	H2AFX	H2AFX	H2AFX	6177	0.041	0.5	NO
54	SYCP2	SYCP2	SYCP2	6443	0.037	0.48	NO
55	UBE2I	UBE2I	UBE2I	6496	0.036	0.48	NO
56	TERF2IP	TERF2IP	TERF2IP	6561	0.035	0.48	NO
57	STAG1	STAG1	STAG1	6663	0.033	0.48	NO
58	MLH1	MLH1	MLH1	7129	0.026	0.46	NO
59	TERF2	TERF2	TERF2	7733	0.016	0.42	NO
60	H2AFZ	H2AFZ	H2AFZ	7926	0.013	0.41	NO
61	SMC1A	SMC1A	SMC1A	7978	0.012	0.41	NO
62	RPA2	RPA2	RPA2	8171	0.0092	0.4	NO
63	MRE11A	MRE11A	MRE11A	8381	0.0064	0.39	NO
64	POT1	POT1	POT1	8565	0.0034	0.38	NO
65	BRCA1	BRCA1	BRCA1	8613	0.0028	0.38	NO
66	MLH3	MLH3	MLH3	9031	-0.0032	0.35	NO
67	HIST2H2AC	HIST2H2AC	HIST2H2AC	9110	-0.0042	0.35	NO
68	TINF2	TINF2	TINF2	9134	-0.0046	0.35	NO
69	CDK4	CDK4	CDK4	9260	-0.0063	0.34	NO
70	ACD	ACD	ACD	9509	-0.01	0.33	NO
71	H3F3A	H3F3A	H3F3A	9617	-0.012	0.32	NO
72	REC8	REC8	REC8	10081	-0.019	0.3	NO
73	NBN	NBN	NBN	10415	-0.024	0.28	NO
74	RPA1	RPA1	RPA1	10805	-0.03	0.26	NO
75	TERF1	TERF1	TERF1	10934	-0.032	0.26	NO
76	RAD21	RAD21	RAD21	11252	-0.038	0.24	NO
77	TOP3A	TOP3A	TOP3A	11524	-0.043	0.23	NO
78	ATM	ATM	ATM	11637	-0.045	0.23	NO
79	CDK2	CDK2	CDK2	11937	-0.05	0.22	NO
80	LMNA	LMNA	LMNA	11958	-0.05	0.22	NO
81	SMC3	SMC3	SMC3	12439	-0.06	0.2	NO
82	H3F3B	H3F3B	H3F3B	12513	-0.062	0.2	NO
83	HIST1H3B	HIST1H3B	HIST1H3B	12723	-0.066	0.19	NO
84	HIST1H3C	HIST1H3C	HIST1H3C	13286	-0.08	0.16	NO
85	HSPA2	HSPA2	HSPA2	13462	-0.084	0.16	NO
86	STAG3	STAG3	STAG3	13723	-0.091	0.15	NO
87	HIST3H2BB	HIST3H2BB	HIST3H2BB	14284	-0.11	0.13	NO
88	HIST1H2BI	HIST1H2BI	HIST1H2BI	15117	-0.15	0.096	NO
89	RAD51C	RAD51C	RAD51C	15118	-0.15	0.11	NO
90	MSH5	MSH5	MSH5	15370	-0.16	0.11	NO
91	FKBP6	FKBP6	FKBP6	16130	-0.21	0.079	NO
92	HIST1H3J	HIST1H3J	HIST1H3J	16167	-0.21	0.093	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 TRANSCRIPTION.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSCRIPTION, 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES	26	genes.ES.table	0.52	1.4	0.03	1	0.99	0.31	0.1	0.28	1	0.92
KEGG ANTIGEN PROCESSING AND PRESENTATION	67	genes.ES.table	0.56	1.4	0.16	1	1	0.4	0.19	0.33	1	0.89
KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY	116	genes.ES.table	0.54	1.4	0.14	1	1	0.4	0.19	0.33	1	0.91
KEGG PATHOGENIC ESCHERICHIA COLI INFECTION	50	genes.ES.table	0.39	1.3	0.13	1	1	0.14	0.11	0.12	1	0.86
KEGG NON SMALL CELL LUNG CANCER	54	genes.ES.table	0.35	1.3	0.13	1	1	0.39	0.28	0.28	1	0.88
KEGG GRAFT VERSUS HOST DISEASE	36	genes.ES.table	0.71	1.3	0.16	1	1	0.64	0.19	0.52	1	0.89
BIOCARTA DEATH PATHWAY	33	genes.ES.table	0.51	1.6	0.024	1	0.85	0.58	0.34	0.38	1	0.8
BIOCARTA KERATINOCYTE PATHWAY	46	genes.ES.table	0.42	1.4	0.12	1	1	0.48	0.29	0.34	1	0.93
BIOCARTA PYK2 PATHWAY	28	genes.ES.table	0.31	1.3	0.13	1	1	0.32	0.28	0.23	1	0.9
BIOCARTA MYOSIN PATHWAY	29	genes.ES.table	0.42	1.4	0.075	1	0.99	0.31	0.21	0.25	1	0.93

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

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	GAS2	GAS2	GAS2	618	0.32	0.095	YES
2	BIRC3	BIRC3	BIRC3	1020	0.26	0.18	YES
3	TNFRSF10A	TNFRSF10A	TNFRSF10A	1812	0.18	0.21	YES
4	CASP3	CASP3	CASP3	2087	0.17	0.26	YES
5	CASP6	CASP6	CASP6	2257	0.16	0.32	YES
6	TNFSF12	TNFSF12	TNFSF12	2768	0.13	0.34	YES
7	NFKBIA	NFKBIA	NFKBIA	3839	0.094	0.32	YES
8	TRADD	TRADD	TRADD	3983	0.09	0.35	YES
9	CASP7	CASP7	CASP7	4119	0.086	0.38	YES
10	TNFRSF10B	TNFRSF10B	TNFRSF10B	4479	0.076	0.39	YES
11	RELA	RELA	RELA	4607	0.074	0.41	YES
12	NFKB1	NFKB1	NFKB1	4850	0.068	0.43	YES
13	TRAF2	TRAF2	TRAF2	5248	0.06	0.43	YES
14	FADD	FADD	FADD	5544	0.054	0.43	YES
15	CFLAR	CFLAR	CFLAR	5632	0.052	0.45	YES
16	SPTAN1	SPTAN1	SPTAN1	5658	0.052	0.47	YES
17	BIRC2	BIRC2	BIRC2	5780	0.049	0.48	YES
18	CYCS	CYCS	CYCS	5997	0.045	0.49	YES
19	MAP3K14	MAP3K14	MAP3K14	6034	0.044	0.51	YES
20	TNFRSF25	TNFRSF25	TNFRSF25	6477	0.036	0.5	NO
21	XIAP	XIAP	XIAP	7613	0.017	0.44	NO
22	RIPK1	RIPK1	RIPK1	7748	0.016	0.44	NO
23	APAF1	APAF1	APAF1	8392	0.0058	0.4	NO
24	CHUK	CHUK	CHUK	8682	0.0018	0.39	NO
25	BCL2	BCL2	BCL2	8698	0.0016	0.39	NO
26	TNFSF10	TNFSF10	TNFSF10	9639	-0.012	0.34	NO
27	CASP10	CASP10	CASP10	10076	-0.019	0.32	NO
28	LMNA	LMNA	LMNA	10212	-0.021	0.32	NO
29	DFFA	DFFA	DFFA	10297	-0.022	0.33	NO
30	CASP9	CASP9	CASP9	11394	-0.041	0.28	NO
31	BID	BID	BID	11439	-0.042	0.3	NO
32	DFFB	DFFB	DFFB	11798	-0.049	0.3	NO
33	CASP8	CASP8	CASP8	13773	-0.097	0.23	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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

Figure S22. 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 ANTIGEN PROCESSING AND PRESENTATION

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	FASLG	FASLG	FASLG	191	0.46	0.15	YES
2	CD247	CD247	CD247	479	0.35	0.25	YES
3	BIRC3	BIRC3	BIRC3	1020	0.26	0.31	YES
4	CASP3	CASP3	CASP3	2087	0.17	0.31	YES
5	CASP6	CASP6	CASP6	2257	0.16	0.35	YES
6	FAS	FAS	FAS	2971	0.12	0.36	YES
7	NFKBIA	NFKBIA	NFKBIA	3839	0.094	0.34	YES
8	TRADD	TRADD	TRADD	3983	0.09	0.36	YES
9	CASP7	CASP7	CASP7	4119	0.086	0.38	YES
10	TRAF1	TRAF1	TRAF1	4495	0.076	0.39	YES
11	RELA	RELA	RELA	4607	0.074	0.41	YES
12	TNF	TNF	TNF	4741	0.07	0.43	YES
13	NFKB1	NFKB1	NFKB1	4850	0.068	0.44	YES
14	MAPK8	MAPK8	MAPK8	5041	0.064	0.46	YES
15	MAP2K7	MAP2K7	MAP2K7	5076	0.064	0.48	YES
16	TRAF2	TRAF2	TRAF2	5248	0.06	0.49	YES
17	FADD	FADD	FADD	5544	0.054	0.49	YES
18	CFLAR	CFLAR	CFLAR	5632	0.052	0.5	YES
19	CYCS	CYCS	CYCS	5997	0.045	0.5	YES
20	MAP3K14	MAP3K14	MAP3K14	6034	0.044	0.51	YES
21	CRADD	CRADD	CRADD	7541	0.018	0.43	NO
22	MAP3K5	MAP3K5	MAP3K5	7628	0.017	0.43	NO
23	DAXX	DAXX	DAXX	7721	0.016	0.43	NO
24	RIPK1	RIPK1	RIPK1	7748	0.016	0.44	NO
25	APAF1	APAF1	APAF1	8392	0.0058	0.4	NO
26	CHUK	CHUK	CHUK	8682	0.0018	0.39	NO
27	BCL2	BCL2	BCL2	8698	0.0016	0.39	NO
28	CASP2	CASP2	CASP2	9189	-0.0056	0.36	NO
29	DFFA	DFFA	DFFA	10297	-0.022	0.31	NO
30	TNFRSF1A	TNFRSF1A	TNFRSF1A	10598	-0.027	0.3	NO
31	CASP9	CASP9	CASP9	11394	-0.041	0.27	NO
32	BID	BID	BID	11439	-0.042	0.28	NO
33	DFFB	DFFB	DFFB	11798	-0.049	0.28	NO
34	BAG4	BAG4	BAG4	12987	-0.075	0.24	NO
35	CASP8	CASP8	CASP8	13773	-0.097	0.23	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 ANTIGEN PROCESSING AND PRESENTATION.

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

genes ES table in pathway: KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY

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	ITGA2B	ITGA2B	ITGA2B	710	0.3	0.084	YES
2	APBB1IP	APBB1IP	APBB1IP	993	0.26	0.18	YES
3	FGB	FGB	FGB	1833	0.18	0.2	YES
4	RAPGEF3	RAPGEF3	RAPGEF3	1947	0.18	0.27	YES
5	RASGRP2	RASGRP2	RASGRP2	2016	0.17	0.34	YES
6	SYK	SYK	SYK	2455	0.15	0.37	YES
7	AKT1	AKT1	AKT1	2514	0.14	0.43	YES
8	BCAR1	BCAR1	BCAR1	3508	0.1	0.42	YES
9	SRC	SRC	SRC	3808	0.095	0.44	YES
10	CSK	CSK	CSK	4065	0.087	0.46	YES
11	PDPK1	PDPK1	PDPK1	4713	0.071	0.45	YES
12	RAPGEF4	RAPGEF4	RAPGEF4	4727	0.071	0.48	YES
13	FGG	FGG	FGG	4839	0.068	0.5	YES
14	VWF	VWF	VWF	5109	0.063	0.52	YES
15	FGA	FGA	FGA	5303	0.059	0.53	YES
16	RASGRP1	RASGRP1	RASGRP1	5732	0.05	0.52	NO
17	PTK2	PTK2	PTK2	6348	0.038	0.51	NO
18	ITGB3	ITGB3	ITGB3	6934	0.028	0.48	NO
19	SHC1	SHC1	SHC1	8444	0.0052	0.4	NO
20	SOS1	SOS1	SOS1	9833	-0.015	0.33	NO
21	PTPN1	PTPN1	PTPN1	9892	-0.016	0.33	NO
22	RAP1B	RAP1B	RAP1B	10117	-0.019	0.33	NO
23	RAP1A	RAP1A	RAP1A	10469	-0.025	0.32	NO
24	GRB2	GRB2	GRB2	10636	-0.028	0.32	NO
25	TLN1	TLN1	TLN1	11153	-0.036	0.31	NO
26	CRK	CRK	CRK	12788	-0.07	0.24	NO
27	FN1	FN1	FN1	13603	-0.092	0.24	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 NATURAL KILLER CELL MEDIATED CYTOTOXICITY.

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY, 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 PATHOGENIC ESCHERICHIA COLI INFECTION

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	KIR2DL3	KIR2DL3	KIR2DL3	133	0.5	0.036	YES
2	ULBP3	ULBP3	ULBP3	156	0.47	0.076	YES
3	ICAM4	ICAM4	ICAM4	204	0.45	0.11	YES
4	CD160	CD160	CD160	238	0.43	0.15	YES
5	KLRK1	KLRK1	KLRK1	246	0.43	0.18	YES
6	KIR2DL4	KIR2DL4	KIR2DL4	337	0.39	0.21	YES
7	CD247	CD247	CD247	479	0.35	0.24	YES
8	KIR3DL1	KIR3DL1	KIR3DL1	494	0.34	0.26	YES
9	ITGB7	ITGB7	ITGB7	573	0.33	0.29	YES
10	CD3D	CD3D	CD3D	607	0.32	0.32	YES
11	ITGAL	ITGAL	ITGAL	640	0.31	0.34	YES
12	CD96	CD96	CD96	652	0.31	0.37	YES
13	CD40LG	CD40LG	CD40LG	685	0.3	0.39	YES
14	CD3E	CD3E	CD3E	689	0.3	0.42	YES
15	KLRC1	KLRC1	KLRC1	700	0.3	0.44	YES
16	ULBP1	ULBP1	ULBP1	725	0.3	0.47	YES
17	CD8A	CD8A	CD8A	860	0.28	0.48	YES
18	KIR2DL1	KIR2DL1	KIR2DL1	888	0.27	0.51	YES
19	C3	C3	C3	979	0.26	0.52	YES
20	KIR3DL2	KIR3DL2	KIR3DL2	1142	0.24	0.54	YES
21	CRTAM	CRTAM	CRTAM	1210	0.23	0.55	YES
22	CD19	CD19	CD19	1307	0.22	0.57	YES
23	AMICA1	AMICA1	AMICA1	1328	0.22	0.59	YES
24	FCGR3A	FCGR3A	FCGR3A	1350	0.22	0.6	YES
25	FCGR2B	FCGR2B	FCGR2B	1393	0.22	0.62	YES
26	LILRA1	LILRA1	LILRA1	1592	0.2	0.63	YES
27	LILRB2	LILRB2	LILRB2	1627	0.2	0.64	YES
28	ICAM3	ICAM3	ICAM3	1665	0.2	0.66	YES
29	CD3G	CD3G	CD3G	1732	0.19	0.67	YES
30	CDH1	CDH1	CDH1	2008	0.17	0.67	YES
31	LILRB1	LILRB1	LILRB1	2378	0.15	0.66	YES
32	VCAM1	VCAM1	VCAM1	2649	0.14	0.66	YES
33	ITGB2	ITGB2	ITGB2	2660	0.14	0.67	YES
34	TYROBP	TYROBP	TYROBP	2672	0.14	0.68	YES
35	HCST	HCST	HCST	2706	0.14	0.69	YES
36	SELL	SELL	SELL	2782	0.13	0.7	YES
37	CD8B	CD8B	CD8B	2942	0.12	0.7	YES
38	HLA-F	HLA-F	HLA-F	3183	0.12	0.7	YES
39	LILRB4	LILRB4	LILRB4	3215	0.11	0.71	YES
40	IFITM1	IFITM1	IFITM1	3281	0.11	0.71	YES
41	PVRL2	PVRL2	PVRL2	3328	0.11	0.72	YES
42	CD34	CD34	CD34	3779	0.096	0.7	NO
43	ICAM2	ICAM2	ICAM2	3826	0.094	0.71	NO
44	CD226	CD226	CD226	4301	0.081	0.69	NO
45	CD81	CD81	CD81	4323	0.08	0.69	NO
46	ICAM1	ICAM1	ICAM1	4716	0.071	0.68	NO
47	ULBP2	ULBP2	ULBP2	4941	0.066	0.67	NO
48	HLA-C	HLA-C	HLA-C	5004	0.065	0.67	NO
49	PVR	PVR	PVR	5383	0.057	0.66	NO
50	HLA-B	HLA-B	HLA-B	5458	0.056	0.66	NO
51	CD200R1	CD200R1	CD200R1	5785	0.049	0.64	NO
52	HLA-A	HLA-A	HLA-A	6203	0.041	0.62	NO
53	B2M	B2M	B2M	7908	0.013	0.53	NO
54	RAET1E	RAET1E	RAET1E	8420	0.0055	0.5	NO
55	LILRB3	LILRB3	LILRB3	8425	0.0054	0.5	NO
56	KLRD1	KLRD1	KLRD1	8491	0.0046	0.5	NO
57	LILRB5	LILRB5	LILRB5	8848	-0.00054	0.48	NO
58	ITGB1	ITGB1	ITGB1	9668	-0.013	0.43	NO
59	HLA-G	HLA-G	HLA-G	11435	-0.042	0.34	NO
60	CD40	CD40	CD40	12023	-0.053	0.31	NO
61	CXADR	CXADR	CXADR	15994	-0.2	0.1	NO

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

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PATHOGENIC ESCHERICHIA COLI INFECTION, 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 NON SMALL CELL LUNG CANCER

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	ARHGEF19	ARHGEF19	ARHGEF19	115	0.52	0.19	YES
2	ARHGEF16	ARHGEF16	ARHGEF16	1310	0.22	0.21	YES
3	PLCB1	PLCB1	PLCB1	1445	0.21	0.29	YES
4	ARHGEF15	ARHGEF15	ARHGEF15	2626	0.14	0.28	YES
5	PRKCB	PRKCB	PRKCB	3235	0.11	0.29	YES
6	ARHGEF18	ARHGEF18	ARHGEF18	3341	0.11	0.32	YES
7	MYLK	MYLK	MYLK	3410	0.11	0.36	YES
8	PKN1	PKN1	PKN1	3603	0.1	0.39	YES
9	GNGT1	GNGT1	GNGT1	3720	0.097	0.42	YES
10	ARHGEF9	ARHGEF9	ARHGEF9	5550	0.054	0.34	NO
11	ARHGEF12	ARHGEF12	ARHGEF12	5846	0.048	0.34	NO
12	ARHGEF1	ARHGEF1	ARHGEF1	5871	0.047	0.36	NO
13	ARHGEF5	ARHGEF5	ARHGEF5	5935	0.046	0.37	NO
14	ARHGEF11	ARHGEF11	ARHGEF11	6776	0.031	0.34	NO
15	ARHGEF17	ARHGEF17	ARHGEF17	7077	0.025	0.33	NO
16	GNB1	GNB1	GNB1	7089	0.025	0.34	NO
17	PRKCA	PRKCA	PRKCA	7164	0.024	0.34	NO
18	PPP1R12B	PPP1R12B	PPP1R12B	7388	0.02	0.34	NO
19	GNA12	GNA12	GNA12	7652	0.017	0.33	NO
20	ARHGAP5	ARHGAP5	ARHGAP5	7964	0.012	0.32	NO
21	ARHGEF2	ARHGEF2	ARHGEF2	9232	-0.0062	0.25	NO
22	ARHGEF6	ARHGEF6	ARHGEF6	9556	-0.011	0.24	NO
23	ROCK1	ROCK1	ROCK1	11258	-0.038	0.16	NO
24	ARHGEF7	ARHGEF7	ARHGEF7	11358	-0.04	0.16	NO
25	ARHGEF10	ARHGEF10	ARHGEF10	12167	-0.056	0.14	NO
26	GNA13	GNA13	GNA13	13592	-0.092	0.096	NO
27	ARHGEF3	ARHGEF3	ARHGEF3	14226	-0.11	0.1	NO
28	GNAQ	GNAQ	GNAQ	14506	-0.12	0.14	NO
29	ARHGEF4	ARHGEF4	ARHGEF4	14571	-0.13	0.18	NO

Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NON SMALL CELL LUNG CANCER.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NON SMALL CELL LUNG CANCER, 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 GRAFT VERSUS HOST DISEASE

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	FUT2	FUT2	FUT2	140	0.48	0.11	YES
2	FUT1	FUT1	FUT1	176	0.46	0.21	YES
3	FUT5	FUT5	FUT5	366	0.38	0.29	YES
4	ABO	ABO	ABO	390	0.37	0.37	YES
5	B3GNT4	B3GNT4	B3GNT4	737	0.3	0.42	YES
6	FUT3	FUT3	FUT3	853	0.28	0.48	YES
7	FUT7	FUT7	FUT7	1729	0.19	0.48	YES
8	GCNT2	GCNT2	GCNT2	1814	0.18	0.52	YES
9	FUT4	FUT4	FUT4	2883	0.13	0.48	NO
10	FUT6	FUT6	FUT6	3519	0.1	0.47	NO
11	B4GALT2	B4GALT2	B4GALT2	5601	0.053	0.37	NO
12	ST3GAL3	ST3GAL3	ST3GAL3	6811	0.03	0.31	NO
13	B3GNT3	B3GNT3	B3GNT3	7293	0.022	0.29	NO
14	B3GALT1	B3GALT1	B3GALT1	9324	-0.0076	0.17	NO
15	B3GALT5	B3GALT5	B3GALT5	9679	-0.013	0.16	NO
16	B3GNT1	B3GNT1	B3GNT1	10007	-0.018	0.14	NO
17	B4GALT3	B4GALT3	B4GALT3	10201	-0.021	0.14	NO
18	B3GNT5	B3GNT5	B3GNT5	10266	-0.022	0.14	NO
19	FUT9	FUT9	FUT9	12910	-0.073	0.0068	NO
20	B3GNT2	B3GNT2	B3GNT2	13088	-0.077	0.015	NO
21	B3GALT2	B3GALT2	B3GALT2	13767	-0.097	-0.00041	NO
22	B4GALT1	B4GALT1	B4GALT1	14053	-0.11	0.0086	NO
23	ST3GAL6	ST3GAL6	ST3GAL6	15622	-0.18	-0.038	NO
24	B4GALT4	B4GALT4	B4GALT4	16213	-0.22	-0.019	NO
25	ST8SIA1	ST8SIA1	ST8SIA1	16252	-0.23	0.032	NO
26	ST3GAL4	ST3GAL4	ST3GAL4	16380	-0.24	0.081	NO

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

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GRAFT VERSUS HOST DISEASE, 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 DEATH PATHWAY

Table S17. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FASLG	FASLG	FASLG	191	0.46	0.093	YES
2	PRKCG	PRKCG	PRKCG	262	0.42	0.18	YES
3	JUN	JUN	JUN	901	0.27	0.21	YES
4	CEBPA	CEBPA	CEBPA	1242	0.23	0.24	YES
5	HOXA7	HOXA7	HOXA7	1371	0.22	0.29	YES
6	EGF	EGF	EGF	1728	0.19	0.31	YES
7	FAS	FAS	FAS	2971	0.12	0.27	YES
8	MAPK13	MAPK13	MAPK13	3220	0.11	0.28	YES
9	PRKCB	PRKCB	PRKCB	3235	0.11	0.3	YES
10	MAP2K1	MAP2K1	MAP2K1	3579	0.1	0.31	YES
11	EGFR	EGFR	EGFR	3728	0.097	0.32	YES
12	NFKBIA	NFKBIA	NFKBIA	3839	0.094	0.34	YES
13	TNFRSF1B	TNFRSF1B	TNFRSF1B	4025	0.088	0.35	YES
14	HRAS	HRAS	HRAS	4452	0.077	0.34	YES
15	RELA	RELA	RELA	4607	0.074	0.35	YES
16	TNF	TNF	TNF	4741	0.07	0.36	YES
17	MAPK3	MAPK3	MAPK3	4805	0.069	0.37	YES
18	NFKB1	NFKB1	NFKB1	4850	0.068	0.38	YES
19	PRKCE	PRKCE	PRKCE	4929	0.066	0.39	YES
20	MAPK8	MAPK8	MAPK8	5041	0.064	0.4	YES
21	MAP2K7	MAP2K7	MAP2K7	5076	0.064	0.41	YES
22	TRAF2	TRAF2	TRAF2	5248	0.06	0.42	YES
23	ETS1	ETS1	ETS1	5648	0.052	0.41	NO
24	MAP3K14	MAP3K14	MAP3K14	6034	0.044	0.39	NO
25	SP1	SP1	SP1	6406	0.037	0.38	NO
26	PRKCA	PRKCA	PRKCA	7164	0.024	0.34	NO
27	PRKCD	PRKCD	PRKCD	7482	0.019	0.33	NO
28	MAP3K5	MAP3K5	MAP3K5	7628	0.017	0.33	NO
29	DAXX	DAXX	DAXX	7721	0.016	0.32	NO
30	RIPK1	RIPK1	RIPK1	7748	0.016	0.33	NO
31	MAPK1	MAPK1	MAPK1	8530	0.004	0.28	NO
32	CHUK	CHUK	CHUK	8682	0.0018	0.28	NO
33	BCL2	BCL2	BCL2	8698	0.0016	0.28	NO
34	IKBKB	IKBKB	IKBKB	9005	-0.0029	0.26	NO
35	TNFRSF1A	TNFRSF1A	TNFRSF1A	10598	-0.027	0.18	NO
36	MAPK14	MAPK14	MAPK14	11005	-0.033	0.16	NO
37	MAP2K3	MAP2K3	MAP2K3	11150	-0.036	0.16	NO
38	MAP2K4	MAP2K4	MAP2K4	11956	-0.052	0.13	NO
39	MAP3K1	MAP3K1	MAP3K1	12198	-0.057	0.13	NO
40	PRKCH	PRKCH	PRKCH	12694	-0.068	0.11	NO
41	RAF1	RAF1	RAF1	13287	-0.083	0.1	NO
42	FOS	FOS	FOS	13683	-0.094	0.099	NO
43	ETS2	ETS2	ETS2	13800	-0.098	0.12	NO
44	PPP2CA	PPP2CA	PPP2CA	14644	-0.13	0.097	NO
45	PRKCQ	PRKCQ	PRKCQ	15517	-0.17	0.086	NO
46	MAP2K6	MAP2K6	MAP2K6	15845	-0.19	0.11	NO

Figure S33. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA DEATH PATHWAY.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA DEATH 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 KERATINOCYTE PATHWAY

Table S18. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NCR1	NCR1	NCR1	123	0.5	0.024	YES
2	KIR2DL3	KIR2DL3	KIR2DL3	133	0.5	0.053	YES
3	ULBP3	ULBP3	ULBP3	156	0.47	0.081	YES
4	FASLG	FASLG	FASLG	191	0.46	0.11	YES
5	KLRK1	KLRK1	KLRK1	246	0.43	0.13	YES
6	PRKCG	PRKCG	PRKCG	262	0.42	0.15	YES
7	KLRC3	KLRC3	KLRC3	329	0.39	0.17	YES
8	KIR2DL4	KIR2DL4	KIR2DL4	337	0.39	0.2	YES
9	KIR2DS4	KIR2DS4	KIR2DS4	362	0.38	0.22	YES
10	CD244	CD244	CD244	437	0.36	0.24	YES
11	LCK	LCK	LCK	446	0.36	0.26	YES
12	ZAP70	ZAP70	ZAP70	463	0.35	0.28	YES
13	CD247	CD247	CD247	479	0.35	0.3	YES
14	KIR3DL1	KIR3DL1	KIR3DL1	494	0.34	0.32	YES
15	NCR3	NCR3	NCR3	555	0.33	0.33	YES
16	ITGAL	ITGAL	ITGAL	640	0.31	0.35	YES
17	KLRC1	KLRC1	KLRC1	700	0.3	0.36	YES
18	ULBP1	ULBP1	ULBP1	725	0.3	0.38	YES
19	PRF1	PRF1	PRF1	789	0.29	0.39	YES
20	SH2D1A	SH2D1A	SH2D1A	814	0.28	0.41	YES
21	KIR2DL1	KIR2DL1	KIR2DL1	888	0.27	0.42	YES
22	CD48	CD48	CD48	1119	0.24	0.42	YES
23	KIR3DL2	KIR3DL2	KIR3DL2	1142	0.24	0.44	YES
24	FCGR3B	FCGR3B	FCGR3B	1192	0.24	0.45	YES
25	PIK3R5	PIK3R5	PIK3R5	1222	0.23	0.46	YES
26	FCGR3A	FCGR3A	FCGR3A	1350	0.22	0.47	YES
27	GZMB	GZMB	GZMB	1421	0.22	0.48	YES
28	VAV1	VAV1	VAV1	1468	0.21	0.49	YES
29	KLRC2	KLRC2	KLRC2	1552	0.2	0.5	YES
30	TNFRSF10A	TNFRSF10A	TNFRSF10A	1812	0.18	0.49	YES
31	CASP3	CASP3	CASP3	2087	0.17	0.49	YES
32	PIK3CG	PIK3CG	PIK3CG	2098	0.17	0.5	YES
33	RAET1G	RAET1G	RAET1G	2185	0.16	0.5	YES
34	SYK	SYK	SYK	2455	0.15	0.49	YES
35	RAC2	RAC2	RAC2	2590	0.14	0.5	YES
36	ITGB2	ITGB2	ITGB2	2660	0.14	0.5	YES
37	TYROBP	TYROBP	TYROBP	2672	0.14	0.51	YES
38	IFNG	IFNG	IFNG	2684	0.14	0.52	YES
39	HCST	HCST	HCST	2706	0.14	0.52	YES
40	TNFRSF10C	TNFRSF10C	TNFRSF10C	2757	0.13	0.53	YES
41	RAC3	RAC3	RAC3	2801	0.13	0.53	YES
42	FAS	FAS	FAS	2971	0.12	0.53	YES
43	RAET1L	RAET1L	RAET1L	3058	0.12	0.53	YES
44	PRKCB	PRKCB	PRKCB	3235	0.11	0.53	YES
45	PAK1	PAK1	PAK1	3247	0.11	0.54	YES
46	PIK3CD	PIK3CD	PIK3CD	3346	0.11	0.54	YES
47	FCER1G	FCER1G	FCER1G	3353	0.11	0.54	YES
48	MAP2K1	MAP2K1	MAP2K1	3579	0.1	0.54	NO
49	ICAM2	ICAM2	ICAM2	3826	0.094	0.53	NO
50	SHC2	SHC2	SHC2	3993	0.089	0.52	NO
51	NFAT5	NFAT5	NFAT5	4001	0.089	0.53	NO
52	LCP2	LCP2	LCP2	4051	0.088	0.53	NO
53	SH2D1B	SH2D1B	SH2D1B	4394	0.079	0.52	NO
54	PPP3CC	PPP3CC	PPP3CC	4420	0.078	0.52	NO
55	HRAS	HRAS	HRAS	4452	0.077	0.52	NO
56	TNFRSF10B	TNFRSF10B	TNFRSF10B	4479	0.076	0.53	NO
57	LAT	LAT	LAT	4518	0.076	0.53	NO
58	HLA-E	HLA-E	HLA-E	4714	0.071	0.52	NO
59	ICAM1	ICAM1	ICAM1	4716	0.071	0.53	NO
60	TNF	TNF	TNF	4741	0.07	0.53	NO
61	MAPK3	MAPK3	MAPK3	4805	0.069	0.53	NO
62	VAV3	VAV3	VAV3	4834	0.068	0.53	NO
63	ULBP2	ULBP2	ULBP2	4941	0.066	0.53	NO
64	HLA-C	HLA-C	HLA-C	5004	0.065	0.53	NO
65	NFATC3	NFATC3	NFATC3	5254	0.06	0.52	NO
66	NCR2	NCR2	NCR2	5366	0.058	0.52	NO
67	HLA-B	HLA-B	HLA-B	5458	0.056	0.52	NO
68	MAP2K2	MAP2K2	MAP2K2	5799	0.049	0.5	NO
69	FYN	FYN	FYN	5807	0.048	0.5	NO
70	HLA-A	HLA-A	HLA-A	6203	0.041	0.48	NO
71	PTPN6	PTPN6	PTPN6	6208	0.041	0.49	NO
72	PTK2B	PTK2B	PTK2B	6210	0.041	0.49	NO
73	KRAS	KRAS	KRAS	6233	0.041	0.49	NO
74	SH3BP2	SH3BP2	SH3BP2	6514	0.035	0.48	NO
75	PLCG1	PLCG1	PLCG1	6727	0.031	0.46	NO
76	ARAF	ARAF	ARAF	6732	0.031	0.47	NO
77	SOS2	SOS2	SOS2	6817	0.03	0.46	NO
78	PRKCA	PRKCA	PRKCA	7164	0.024	0.45	NO
79	VAV2	VAV2	VAV2	7817	0.014	0.41	NO
80	RAET1E	RAET1E	RAET1E	8420	0.0055	0.38	NO
81	PIK3R3	PIK3R3	PIK3R3	8442	0.0052	0.38	NO
82	SHC1	SHC1	SHC1	8444	0.0052	0.38	NO
83	KLRD1	KLRD1	KLRD1	8491	0.0046	0.37	NO
84	MAPK1	MAPK1	MAPK1	8530	0.004	0.37	NO
85	PPP3CB	PPP3CB	PPP3CB	8599	0.0031	0.37	NO
86	RAC1	RAC1	RAC1	8732	0.0011	0.36	NO
87	PTPN11	PTPN11	PTPN11	8957	-0.0023	0.35	NO
88	NRAS	NRAS	NRAS	9274	-0.0068	0.33	NO
89	PLCG2	PLCG2	PLCG2	9317	-0.0075	0.33	NO
90	TNFSF10	TNFSF10	TNFSF10	9639	-0.012	0.31	NO
91	SOS1	SOS1	SOS1	9833	-0.015	0.3	NO
92	PIK3R2	PIK3R2	PIK3R2	9949	-0.017	0.3	NO
93	IFNAR2	IFNAR2	IFNAR2	10013	-0.018	0.29	NO
94	IFNGR1	IFNGR1	IFNGR1	10291	-0.022	0.28	NO
95	PPP3CA	PPP3CA	PPP3CA	10398	-0.024	0.28	NO
96	GRB2	GRB2	GRB2	10636	-0.028	0.26	NO
97	CHP	CHP	CHP	11423	-0.041	0.22	NO
98	HLA-G	HLA-G	HLA-G	11435	-0.042	0.22	NO
99	BID	BID	BID	11439	-0.042	0.22	NO
100	IFNAR1	IFNAR1	IFNAR1	12086	-0.054	0.19	NO
101	MICA	MICA	MICA	12491	-0.063	0.17	NO
102	IFNGR2	IFNGR2	IFNGR2	12642	-0.067	0.17	NO
103	MICB	MICB	MICB	12758	-0.07	0.17	NO
104	PPP3R1	PPP3R1	PPP3R1	13122	-0.078	0.15	NO
105	PPP3R2	PPP3R2	PPP3R2	13200	-0.081	0.15	NO
106	RAF1	RAF1	RAF1	13287	-0.083	0.15	NO
107	PIK3R1	PIK3R1	PIK3R1	13471	-0.088	0.15	NO
108	BRAF	BRAF	BRAF	14082	-0.11	0.12	NO
109	NFATC1	NFATC1	NFATC1	14264	-0.12	0.12	NO
110	TNFRSF10D	TNFRSF10D	TNFRSF10D	14511	-0.12	0.11	NO
111	PIK3CB	PIK3CB	PIK3CB	14975	-0.14	0.091	NO
112	NFATC4	NFATC4	NFATC4	15202	-0.15	0.088	NO
113	SHC4	SHC4	SHC4	15519	-0.17	0.08	NO
114	SHC3	SHC3	SHC3	16171	-0.22	0.057	NO
115	PIK3CA	PIK3CA	PIK3CA	16354	-0.24	0.061	NO
116	NFATC2	NFATC2	NFATC2	17224	-0.36	0.034	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: BIOCARTA KERATINOCYTE PATHWAY.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA KERATINOCYTE 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 PYK2 PATHWAY

Table S19. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	KIR2DL3	KIR2DL3	KIR2DL3	133	0.5	0.049	YES
2	HLA-DOB	HLA-DOB	HLA-DOB	242	0.43	0.092	YES
3	KLRC3	KLRC3	KLRC3	329	0.39	0.13	YES
4	KIR2DL4	KIR2DL4	KIR2DL4	337	0.39	0.18	YES
5	KIR2DS4	KIR2DS4	KIR2DS4	362	0.38	0.22	YES
6	KIR3DL1	KIR3DL1	KIR3DL1	494	0.34	0.25	YES
7	KLRC4	KLRC4	KLRC4	620	0.32	0.28	YES
8	KLRC1	KLRC1	KLRC1	700	0.3	0.31	YES
9	HLA-DQA2	HLA-DQA2	HLA-DQA2	774	0.29	0.34	YES
10	CD8A	CD8A	CD8A	860	0.28	0.37	YES
11	KIR2DL1	KIR2DL1	KIR2DL1	888	0.27	0.4	YES
12	HLA-DOA	HLA-DOA	HLA-DOA	984	0.26	0.42	YES
13	KIR3DL2	KIR3DL2	KIR3DL2	1142	0.24	0.44	YES
14	HLA-DQA1	HLA-DQA1	HLA-DQA1	1407	0.22	0.45	YES
15	HSPA6	HSPA6	HSPA6	1408	0.22	0.47	YES
16	KLRC2	KLRC2	KLRC2	1552	0.2	0.49	YES
17	CIITA	CIITA	CIITA	1698	0.19	0.5	YES
18	HSPA2	HSPA2	HSPA2	2314	0.16	0.49	YES
19	HLA-DPB1	HLA-DPB1	HLA-DPB1	2384	0.15	0.5	YES
20	HLA-DMA	HLA-DMA	HLA-DMA	2441	0.15	0.51	YES
21	HLA-DMB	HLA-DMB	HLA-DMB	2659	0.14	0.52	YES
22	HLA-DPA1	HLA-DPA1	HLA-DPA1	2787	0.13	0.52	YES
23	HLA-DRA	HLA-DRA	HLA-DRA	2851	0.13	0.54	YES
24	CD8B	CD8B	CD8B	2942	0.12	0.55	YES
25	HLA-DRB5	HLA-DRB5	HLA-DRB5	3005	0.12	0.56	YES
26	HLA-F	HLA-F	HLA-F	3183	0.12	0.56	YES
27	HLA-DRB1	HLA-DRB1	HLA-DRB1	3396	0.11	0.56	YES
28	CD4	CD4	CD4	4587	0.074	0.5	NO
29	LTA	LTA	LTA	4600	0.074	0.51	NO
30	HLA-E	HLA-E	HLA-E	4714	0.071	0.51	NO
31	HLA-C	HLA-C	HLA-C	5004	0.065	0.5	NO
32	HLA-DQB1	HLA-DQB1	HLA-DQB1	5073	0.064	0.5	NO
33	CD74	CD74	CD74	5321	0.058	0.5	NO
34	HLA-B	HLA-B	HLA-B	5458	0.056	0.5	NO
35	LGMN	LGMN	LGMN	5517	0.054	0.5	NO
36	NFYC	NFYC	NFYC	5584	0.053	0.5	NO
37	PSME1	PSME1	PSME1	5664	0.052	0.5	NO
38	HLA-A	HLA-A	HLA-A	6203	0.041	0.48	NO
39	NFYB	NFYB	NFYB	6434	0.037	0.47	NO
40	CTSS	CTSS	CTSS	6546	0.035	0.47	NO
41	TAP2	TAP2	TAP2	6766	0.031	0.46	NO
42	TAP1	TAP1	TAP1	6891	0.029	0.45	NO
43	TAPBP	TAPBP	TAPBP	6896	0.028	0.46	NO
44	PSME2	PSME2	PSME2	7213	0.023	0.44	NO
45	HSPA8	HSPA8	HSPA8	7449	0.02	0.43	NO
46	B2M	B2M	B2M	7908	0.013	0.41	NO
47	RFXANK	RFXANK	RFXANK	8066	0.01	0.4	NO
48	PSME3	PSME3	PSME3	8208	0.0083	0.39	NO
49	KLRD1	KLRD1	KLRD1	8491	0.0046	0.38	NO
50	CALR	CALR	CALR	8569	0.0036	0.37	NO
51	CREB1	CREB1	CREB1	9432	-0.0091	0.32	NO
52	RFX5	RFX5	RFX5	10190	-0.02	0.28	NO
53	NFYA	NFYA	NFYA	10280	-0.022	0.28	NO
54	HLA-G	HLA-G	HLA-G	11435	-0.042	0.22	NO
55	HSP90AB1	HSP90AB1	HSP90AB1	11735	-0.048	0.21	NO
56	HSP90AA1	HSP90AA1	HSP90AA1	11874	-0.05	0.21	NO
57	PDIA3	PDIA3	PDIA3	11949	-0.052	0.21	NO
58	CTSL1	CTSL1	CTSL1	12282	-0.059	0.2	NO
59	HSPA1A	HSPA1A	HSPA1A	12458	-0.062	0.2	NO
60	HSPA5	HSPA5	HSPA5	13179	-0.08	0.16	NO
61	HSPA1B	HSPA1B	HSPA1B	13369	-0.085	0.16	NO
62	CTSB	CTSB	CTSB	13827	-0.099	0.15	NO
63	HSPA1L	HSPA1L	HSPA1L	13905	-0.1	0.16	NO
64	CANX	CANX	CANX	13918	-0.1	0.17	NO
65	IFI30	IFI30	IFI30	14836	-0.14	0.13	NO
66	HSPA4	HSPA4	HSPA4	15203	-0.15	0.13	NO
67	RFXAP	RFXAP	RFXAP	15442	-0.17	0.13	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: BIOCARTA PYK2 PATHWAY.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA MYOSIN PATHWAY

Table 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	SPON2	SPON2	SPON2	80	0.55	0.12	YES
2	ICAM4	ICAM4	ICAM4	204	0.45	0.21	YES
3	ITGAL	ITGAL	ITGAL	640	0.31	0.26	YES
4	CD40LG	CD40LG	CD40LG	685	0.3	0.32	YES
5	PROC	PROC	PROC	818	0.28	0.38	YES
6	C3	C3	C3	979	0.26	0.43	YES
7	ICAM3	ICAM3	ICAM3	1665	0.2	0.43	YES
8	FGB	FGB	FGB	1833	0.18	0.46	YES
9	PLAT	PLAT	PLAT	2029	0.17	0.49	YES
10	ITGAD	ITGAD	ITGAD	2312	0.16	0.51	YES
11	KNG1	KNG1	KNG1	2373	0.15	0.54	YES
12	ITGAM	ITGAM	ITGAM	2410	0.15	0.57	YES
13	F10	F10	F10	2604	0.14	0.59	YES
14	VCAM1	VCAM1	VCAM1	2649	0.14	0.62	YES
15	ITGB2	ITGB2	ITGB2	2660	0.14	0.65	YES
16	ITGAX	ITGAX	ITGAX	3254	0.11	0.64	YES
17	GP1BA	GP1BA	GP1BA	3674	0.099	0.64	YES
18	ICAM2	ICAM2	ICAM2	3826	0.094	0.66	YES
19	ICAM1	ICAM1	ICAM1	4716	0.071	0.62	NO
20	FGG	FGG	FGG	4839	0.068	0.63	NO
21	FGA	FGA	FGA	5303	0.059	0.62	NO
22	FCGR2A	FCGR2A	FCGR2A	5467	0.055	0.62	NO
23	F11R	F11R	F11R	6457	0.036	0.57	NO
24	JAM3	JAM3	JAM3	7705	0.016	0.5	NO
25	THY1	THY1	THY1	9644	-0.012	0.4	NO
26	CYR61	CYR61	CYR61	10135	-0.02	0.38	NO
27	PLAUR	PLAUR	PLAUR	12203	-0.057	0.27	NO
28	PLAU	PLAU	PLAU	12769	-0.07	0.26	NO
29	TGFBI	TGFBI	TGFBI	14484	-0.12	0.19	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: BIOCARTA MYOSIN PATHWAY.

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

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 GLYCOLYSIS GLUCONEOGENESIS	59	genes.ES.table	0.52	1.6	0.017	0.75	0.88	0.25	0.096	0.23	0.4	0.21
KEGG TYROSINE METABOLISM	41	genes.ES.table	0.65	1.8	0.0074	0.27	0.59	0.37	0.089	0.33	0.095	0.062
BIOCARTA RACCYCD PATHWAY	26	genes.ES.table	0.59	2.3	0	0.0062	0.006	0.5	0.23	0.38	0	0.003
BIOCARTA INTEGRIN PATHWAY	38	genes.ES.table	0.37	1.5	0.086	0.98	0.96	0.34	0.25	0.26	0.64	0.32
PID WNT NONCANONICAL PATHWAY	32	genes.ES.table	0.44	1.5	0.041	0.95	0.97	0.34	0.22	0.27	0.62	0.31
PID NECTIN PATHWAY	30	genes.ES.table	0.56	1.9	0.0039	0.07	0.22	0.47	0.25	0.35	0	0.011
PID HNF3BPATHWAY	41	genes.ES.table	0.57	1.6	0.011	0.68	0.9	0.39	0.1	0.35	0.38	0.19
PID IGF1 PATHWAY	30	genes.ES.table	0.48	2	0.0062	0.06	0.18	0.57	0.32	0.38	0	0.011
PID AR TF PATHWAY	51	genes.ES.table	0.42	1.5	0.06	0.88	0.95	0.22	0.15	0.18	0.56	0.28
PID ECADHERIN STABILIZATION PATHWAY	40	genes.ES.table	0.44	1.5	0.093	0.99	0.97	0.4	0.25	0.3	0.65	0.33

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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	PHLPP1	PHLPP1	PHLPP1	1540	0.19	0.026	YES
2	FOXO1	FOXO1	FOXO1	2165	0.14	0.074	YES
3	AKT2	AKT2	AKT2	2199	0.14	0.15	YES
4	AKT3	AKT3	AKT3	2426	0.13	0.21	YES
5	CDKN1A	CDKN1A	CDKN1A	2644	0.12	0.27	YES
6	NR4A1	NR4A1	NR4A1	3112	0.094	0.3	YES
7	THEM4	THEM4	THEM4	3153	0.093	0.35	YES
8	RPS6KB2	RPS6KB2	RPS6KB2	3535	0.081	0.37	YES
9	TRIB3	TRIB3	TRIB3	3751	0.074	0.4	YES
10	BAD	BAD	BAD	3783	0.073	0.44	YES
11	FOXO3	FOXO3	FOXO3	3908	0.07	0.48	YES
12	GSK3A	GSK3A	GSK3A	4236	0.062	0.5	YES
13	FOXO4	FOXO4	FOXO4	4364	0.059	0.52	YES
14	MDM2	MDM2	MDM2	4381	0.059	0.56	YES
15	CASP9	CASP9	CASP9	4393	0.058	0.59	YES
16	PDPK1	PDPK1	PDPK1	4556	0.054	0.61	YES
17	TSC2	TSC2	TSC2	5497	0.035	0.58	NO
18	PTEN	PTEN	PTEN	5556	0.034	0.6	NO
19	AKT1	AKT1	AKT1	5795	0.03	0.6	NO
20	CREB1	CREB1	CREB1	6225	0.023	0.59	NO
21	AKT1S1	AKT1S1	AKT1S1	6427	0.019	0.59	NO
22	MTOR	MTOR	MTOR	6458	0.019	0.6	NO
23	RICTOR	RICTOR	RICTOR	7205	0.0066	0.56	NO
24	CHUK	CHUK	CHUK	7834	-0.0029	0.53	NO
25	MAPKAP1	MAPKAP1	MAPKAP1	8359	-0.011	0.5	NO
26	CDKN1B	CDKN1B	CDKN1B	8790	-0.017	0.49	NO
27	MLST8	MLST8	MLST8	9650	-0.031	0.46	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 GLYCOLYSIS GLUCONEOGENESIS.

Figure S42. 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 TYROSINE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCNE1	CCNE1	CCNE1	864	0.29	0.1	YES
2	RAF1	RAF1	RAF1	1440	0.2	0.18	YES
3	PIK3CA	PIK3CA	PIK3CA	1702	0.18	0.26	YES
4	IKBKB	IKBKB	IKBKB	2548	0.12	0.28	YES
5	NFKB1	NFKB1	NFKB1	2602	0.12	0.34	YES
6	CDKN1A	CDKN1A	CDKN1A	2644	0.12	0.4	YES
7	PAK1	PAK1	PAK1	3073	0.096	0.42	YES
8	CCND1	CCND1	CCND1	3619	0.078	0.44	YES
9	NFKBIA	NFKBIA	NFKBIA	3634	0.078	0.48	YES
10	RELA	RELA	RELA	3807	0.073	0.5	YES
11	CDK2	CDK2	CDK2	4092	0.066	0.52	YES
12	E2F1	E2F1	E2F1	4106	0.065	0.56	YES
13	MAPK1	MAPK1	MAPK1	4117	0.065	0.59	YES
14	PIK3R1	PIK3R1	PIK3R1	5107	0.043	0.56	NO
15	RHOA	RHOA	RHOA	5411	0.036	0.56	NO
16	AKT1	AKT1	AKT1	5795	0.03	0.56	NO
17	CDK6	CDK6	CDK6	7279	0.0054	0.48	NO
18	MAPK3	MAPK3	MAPK3	7402	0.0036	0.47	NO
19	CHUK	CHUK	CHUK	7834	-0.0029	0.45	NO
20	CDK4	CDK4	CDK4	7868	-0.0033	0.45	NO
21	RAC1	RAC1	RAC1	7880	-0.0035	0.45	NO
22	CDKN1B	CDKN1B	CDKN1B	8790	-0.017	0.41	NO
23	HRAS	HRAS	HRAS	9542	-0.03	0.38	NO
24	IKBKG	IKBKG	IKBKG	10660	-0.048	0.34	NO
25	RB1	RB1	RB1	10703	-0.049	0.37	NO
26	TFDP1	TFDP1	TFDP1	11395	-0.062	0.36	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 TYROSINE METABOLISM.

Figure S44. 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: BIOCARTA RACCYCD PATHWAY

Table S23. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	EGFR	EGFR	EGFR	776	0.31	0.07	YES
2	PHLPP1	PHLPP1	PHLPP1	1540	0.19	0.1	YES
3	SRC	SRC	SRC	1612	0.19	0.17	YES
4	PIK3CA	PIK3CA	PIK3CA	1702	0.18	0.23	YES
5	FOXO1	FOXO1	FOXO1	2165	0.14	0.26	YES
6	AKT2	AKT2	AKT2	2199	0.14	0.3	YES
7	AKT3	AKT3	AKT3	2426	0.13	0.34	YES
8	CDKN1A	CDKN1A	CDKN1A	2644	0.12	0.37	YES
9	NR4A1	NR4A1	NR4A1	3112	0.094	0.38	YES
10	THEM4	THEM4	THEM4	3153	0.093	0.41	YES
11	RPS6KB2	RPS6KB2	RPS6KB2	3535	0.081	0.42	YES
12	TRIB3	TRIB3	TRIB3	3751	0.074	0.44	YES
13	BAD	BAD	BAD	3783	0.073	0.46	YES
14	FOXO3	FOXO3	FOXO3	3908	0.07	0.48	YES
15	GSK3A	GSK3A	GSK3A	4236	0.062	0.48	YES
16	FOXO4	FOXO4	FOXO4	4364	0.059	0.5	YES
17	MDM2	MDM2	MDM2	4381	0.059	0.52	YES
18	CASP9	CASP9	CASP9	4393	0.058	0.54	YES
19	PDPK1	PDPK1	PDPK1	4556	0.054	0.55	YES
20	PIK3R1	PIK3R1	PIK3R1	5107	0.043	0.54	NO
21	TSC2	TSC2	TSC2	5497	0.035	0.53	NO
22	PTEN	PTEN	PTEN	5556	0.034	0.54	NO
23	AKT1	AKT1	AKT1	5795	0.03	0.54	NO
24	CSK	CSK	CSK	6185	0.024	0.52	NO
25	CREB1	CREB1	CREB1	6225	0.023	0.53	NO
26	AKT1S1	AKT1S1	AKT1S1	6427	0.019	0.53	NO
27	MTOR	MTOR	MTOR	6458	0.019	0.53	NO
28	RICTOR	RICTOR	RICTOR	7205	0.0066	0.49	NO
29	EGF	EGF	EGF	7468	0.0023	0.48	NO
30	CHUK	CHUK	CHUK	7834	-0.0029	0.46	NO
31	MAPKAP1	MAPKAP1	MAPKAP1	8359	-0.011	0.43	NO
32	GRB2	GRB2	GRB2	8736	-0.016	0.42	NO
33	CDKN1B	CDKN1B	CDKN1B	8790	-0.017	0.42	NO
34	MLST8	MLST8	MLST8	9650	-0.031	0.38	NO
35	GAB1	GAB1	GAB1	10145	-0.04	0.37	NO
36	PAG1	PAG1	PAG1	14521	-0.16	0.19	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: BIOCARTA RACCYCD PATHWAY.

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

genes ES table in pathway: BIOCARTA INTEGRIN PATHWAY

Table S24. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NTRK1	NTRK1	NTRK1	755	0.31	0.069	YES
2	PHLPP1	PHLPP1	PHLPP1	1540	0.19	0.094	YES
3	PIK3CA	PIK3CA	PIK3CA	1702	0.18	0.15	YES
4	FOXO1	FOXO1	FOXO1	2165	0.14	0.17	YES
5	AKT2	AKT2	AKT2	2199	0.14	0.22	YES
6	AKT3	AKT3	AKT3	2426	0.13	0.26	YES
7	CDKN1A	CDKN1A	CDKN1A	2644	0.12	0.28	YES
8	PIK3CB	PIK3CB	PIK3CB	2837	0.11	0.31	YES
9	NR4A1	NR4A1	NR4A1	3112	0.094	0.33	YES
10	THEM4	THEM4	THEM4	3153	0.093	0.36	YES
11	RPS6KB2	RPS6KB2	RPS6KB2	3535	0.081	0.37	YES
12	TRIB3	TRIB3	TRIB3	3751	0.074	0.38	YES
13	BAD	BAD	BAD	3783	0.073	0.41	YES
14	FOXO3	FOXO3	FOXO3	3908	0.07	0.42	YES
15	GSK3A	GSK3A	GSK3A	4236	0.062	0.43	YES
16	FOXO4	FOXO4	FOXO4	4364	0.059	0.44	YES
17	MDM2	MDM2	MDM2	4381	0.059	0.46	YES
18	CASP9	CASP9	CASP9	4393	0.058	0.48	YES
19	IRS1	IRS1	IRS1	4411	0.058	0.5	YES
20	PDPK1	PDPK1	PDPK1	4556	0.054	0.51	YES
21	IRS2	IRS2	IRS2	5094	0.043	0.5	YES
22	PIK3R1	PIK3R1	PIK3R1	5107	0.043	0.51	YES
23	RHOA	RHOA	RHOA	5411	0.036	0.51	YES
24	TSC2	TSC2	TSC2	5497	0.035	0.52	YES
25	PTEN	PTEN	PTEN	5556	0.034	0.53	YES
26	AKT1	AKT1	AKT1	5795	0.03	0.52	NO
27	CREB1	CREB1	CREB1	6225	0.023	0.51	NO
28	AKT1S1	AKT1S1	AKT1S1	6427	0.019	0.5	NO
29	MTOR	MTOR	MTOR	6458	0.019	0.51	NO
30	RICTOR	RICTOR	RICTOR	7205	0.0066	0.47	NO
31	PIK3R2	PIK3R2	PIK3R2	7497	0.002	0.45	NO
32	CHUK	CHUK	CHUK	7834	-0.0029	0.44	NO
33	MAPKAP1	MAPKAP1	MAPKAP1	8359	-0.011	0.41	NO
34	CDKN1B	CDKN1B	CDKN1B	8790	-0.017	0.39	NO
35	MLST8	MLST8	MLST8	9650	-0.031	0.36	NO
36	NGF	NGF	NGF	16337	-0.29	0.084	NO

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

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA INTEGRIN 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 WNT NONCANONICAL PATHWAY

Table S25. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	RAF1	RAF1	RAF1	1440	0.2	0.0097	YES
2	SRC	SRC	SRC	1612	0.19	0.083	YES
3	FOXO1	FOXO1	FOXO1	2165	0.14	0.12	YES
4	AKT2	AKT2	AKT2	2199	0.14	0.18	YES
5	AKT3	AKT3	AKT3	2426	0.13	0.22	YES
6	CDKN1A	CDKN1A	CDKN1A	2644	0.12	0.26	YES
7	SFN	SFN	SFN	2674	0.11	0.31	YES
8	YWHAH	YWHAH	YWHAH	3610	0.079	0.29	YES
9	BAD	BAD	BAD	3783	0.073	0.31	YES
10	FOXO3	FOXO3	FOXO3	3908	0.07	0.34	YES
11	KPNA1	KPNA1	KPNA1	3984	0.068	0.36	YES
12	GSK3A	GSK3A	GSK3A	4236	0.062	0.38	YES
13	FOXO4	FOXO4	FOXO4	4364	0.059	0.39	YES
14	CASP9	CASP9	CASP9	4393	0.058	0.42	YES
15	PDPK1	PDPK1	PDPK1	4556	0.054	0.43	YES
16	GSK3B	GSK3B	GSK3B	4790	0.05	0.44	YES
17	BCL2L1	BCL2L1	BCL2L1	5117	0.042	0.44	YES
18	YWHAB	YWHAB	YWHAB	5205	0.04	0.46	YES
19	PRKDC	PRKDC	PRKDC	5464	0.036	0.46	YES
20	AKT1	AKT1	AKT1	5795	0.03	0.45	NO
21	HSP90AA1	HSP90AA1	HSP90AA1	6073	0.025	0.45	NO
22	MAP3K5	MAP3K5	MAP3K5	6131	0.024	0.46	NO
23	MTOR	MTOR	MTOR	6458	0.019	0.44	NO
24	PRKACA	PRKACA	PRKACA	6580	0.017	0.45	NO
25	RICTOR	RICTOR	RICTOR	7205	0.0066	0.41	NO
26	YWHAG	YWHAG	YWHAG	7769	-0.002	0.38	NO
27	CHUK	CHUK	CHUK	7834	-0.0029	0.38	NO
28	YWHAZ	YWHAZ	YWHAZ	7967	-0.0049	0.38	NO
29	MAPKAP1	MAPKAP1	MAPKAP1	8359	-0.011	0.36	NO
30	CDKN1B	CDKN1B	CDKN1B	8790	-0.017	0.34	NO
31	MLST8	MLST8	MLST8	9650	-0.031	0.31	NO
32	YWHAE	YWHAE	YWHAE	10444	-0.045	0.28	NO
33	TBC1D4	TBC1D4	TBC1D4	10612	-0.047	0.29	NO
34	YWHAQ	YWHAQ	YWHAQ	10900	-0.052	0.3	NO
35	SLC2A4	SLC2A4	SLC2A4	15191	-0.2	0.15	NO

Figure S49. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID WNT NONCANONICAL PATHWAY.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: PID WNT NONCANONICAL 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 NECTIN PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IGF1	IGF1	IGF1	64	0.69	0.28	YES
2	RAF1	RAF1	RAF1	1440	0.2	0.29	YES
3	PIK3CA	PIK3CA	PIK3CA	1702	0.18	0.35	YES
4	PRKD1	PRKD1	PRKD1	2259	0.14	0.38	YES
5	PRKCD	PRKCD	PRKCD	3311	0.087	0.36	YES
6	GRB10	GRB10	GRB10	3719	0.075	0.36	YES
7	BAD	BAD	BAD	3783	0.073	0.39	YES
8	PXN	PXN	PXN	4039	0.067	0.4	YES
9	CRKL	CRKL	CRKL	4069	0.066	0.43	YES
10	IGF1R	IGF1R	IGF1R	4404	0.058	0.44	YES
11	IRS1	IRS1	IRS1	4411	0.058	0.46	YES
12	PDPK1	PDPK1	PDPK1	4556	0.054	0.47	YES
13	IRS2	IRS2	IRS2	5094	0.043	0.46	YES
14	PIK3R1	PIK3R1	PIK3R1	5107	0.043	0.48	YES
15	PTPN11	PTPN11	PTPN11	5355	0.038	0.48	YES
16	BCAR1	BCAR1	BCAR1	5608	0.033	0.48	YES
17	AKT1	AKT1	AKT1	5795	0.03	0.48	YES
18	PTPN1	PTPN1	PTPN1	6234	0.023	0.47	NO
19	PTK2	PTK2	PTK2	6299	0.022	0.47	NO
20	PRKCZ	PRKCZ	PRKCZ	6347	0.021	0.48	NO
21	YWHAZ	YWHAZ	YWHAZ	7967	-0.0049	0.39	NO
22	CRK	CRK	CRK	8318	-0.01	0.38	NO
23	SOS1	SOS1	SOS1	8339	-0.01	0.38	NO
24	GRB2	GRB2	GRB2	8736	-0.016	0.36	NO
25	RPS6KB1	RPS6KB1	RPS6KB1	9032	-0.021	0.36	NO
26	HRAS	HRAS	HRAS	9542	-0.03	0.34	NO
27	SHC1	SHC1	SHC1	10200	-0.04	0.32	NO
28	YWHAE	YWHAE	YWHAE	10444	-0.045	0.32	NO
29	GNB2L1	GNB2L1	GNB2L1	11270	-0.06	0.3	NO
30	NCK2	NCK2	NCK2	14438	-0.16	0.19	NO

Figure S51. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID NECTIN PATHWAY.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: PID NECTIN 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 HNF3BPATHWAY

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	CLDN1	CLDN1	CLDN1	457	0.39	0.14	YES
2	SRC	SRC	SRC	1612	0.19	0.16	YES
3	PIK3CA	PIK3CA	PIK3CA	1702	0.18	0.23	YES
4	CDH1	CDH1	CDH1	1775	0.17	0.3	YES
5	PVRL1	PVRL1	PVRL1	1961	0.16	0.36	YES
6	ITGAV	ITGAV	ITGAV	2533	0.12	0.38	YES
7	PVRL2	PVRL2	PVRL2	2694	0.11	0.42	YES
8	PVR	PVR	PVR	2929	0.1	0.45	YES
9	FARP2	FARP2	FARP2	3040	0.098	0.49	YES
10	ITGB3	ITGB3	ITGB3	3136	0.094	0.52	YES
11	MLLT4	MLLT4	MLLT4	3646	0.077	0.53	YES
12	CTNNB1	CTNNB1	CTNNB1	3792	0.073	0.55	YES
13	RAPGEF1	RAPGEF1	RAPGEF1	4406	0.058	0.54	YES
14	PIP5K1C	PIP5K1C	PIP5K1C	4508	0.055	0.56	YES
15	PIK3R1	PIK3R1	PIK3R1	5107	0.043	0.55	NO
16	RAP1B	RAP1B	RAP1B	6176	0.024	0.5	NO
17	PTK2	PTK2	PTK2	6299	0.022	0.5	NO
18	CDC42	CDC42	CDC42	6967	0.011	0.47	NO
19	CTNNA1	CTNNA1	CTNNA1	7168	0.0071	0.46	NO
20	F11R	F11R	F11R	7466	0.0023	0.44	NO
21	PTPRM	PTPRM	PTPRM	7491	0.0021	0.44	NO
22	IQGAP1	IQGAP1	IQGAP1	7666	-0.00048	0.43	NO
23	RAC1	RAC1	RAC1	7880	-0.0035	0.42	NO
24	CRK	CRK	CRK	8318	-0.01	0.4	NO
25	RAP1A	RAP1A	RAP1A	8609	-0.014	0.39	NO
26	PVRL3	PVRL3	PVRL3	9645	-0.031	0.35	NO
27	PDGFB	PDGFB	PDGFB	9853	-0.034	0.35	NO
28	VAV2	VAV2	VAV2	10197	-0.04	0.35	NO
29	TLN1	TLN1	TLN1	11253	-0.059	0.31	NO
30	PDGFRB	PDGFRB	PDGFRB	13692	-0.13	0.23	NO

Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID HNF3BPATHWAY.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: PID HNF3BPATHWAY, 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 IGF1 PATHWAY

Table S28. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	DDC	DDC	DDC	62	0.69	0.098	YES
2	TAT	TAT	TAT	109	0.62	0.19	YES
3	ADH6	ADH6	ADH6	191	0.53	0.26	YES
4	ALDH1A3	ALDH1A3	ALDH1A3	385	0.43	0.31	YES
5	ADH1C	ADH1C	ADH1C	400	0.42	0.37	YES
6	TH	TH	TH	629	0.34	0.41	YES
7	ALDH3B2	ALDH3B2	ALDH3B2	927	0.28	0.43	YES
8	MAOA	MAOA	MAOA	939	0.28	0.47	YES
9	TYR	TYR	TYR	1051	0.26	0.5	YES
10	ADH1A	ADH1A	ADH1A	1294	0.22	0.52	YES
11	ADH4	ADH4	ADH4	1314	0.22	0.55	YES
12	MAOB	MAOB	MAOB	1433	0.21	0.58	YES
13	ADH7	ADH7	ADH7	1491	0.2	0.6	YES
14	PNMT	PNMT	PNMT	1564	0.19	0.63	YES
15	DBH	DBH	DBH	1585	0.19	0.65	YES
16	AOC2	AOC2	AOC2	1999	0.15	0.65	NO
17	METTL6	METTL6	METTL6	3316	0.087	0.59	NO
18	HPD	HPD	HPD	3980	0.068	0.56	NO
19	HGD	HGD	HGD	3992	0.068	0.57	NO
20	COMT	COMT	COMT	5452	0.036	0.5	NO
21	LCMT2	LCMT2	LCMT2	5807	0.03	0.48	NO
22	NAT6	NAT6	NAT6	6326	0.021	0.46	NO
23	HEMK1	HEMK1	HEMK1	6392	0.02	0.45	NO
24	ADH5	ADH5	ADH5	6657	0.016	0.44	NO
25	AOX1	AOX1	AOX1	7039	0.0093	0.42	NO
26	GSTZ1	GSTZ1	GSTZ1	7519	0.0016	0.4	NO
27	ALDH3B1	ALDH3B1	ALDH3B1	7652	-0.00023	0.39	NO
28	LCMT1	LCMT1	LCMT1	7723	-0.0014	0.38	NO
29	GOT2	GOT2	GOT2	7827	-0.0028	0.38	NO
30	FAH	FAH	FAH	8147	-0.0076	0.36	NO
31	GOT1	GOT1	GOT1	8759	-0.016	0.33	NO
32	MIF	MIF	MIF	8808	-0.017	0.33	NO
33	WBSCR22	WBSCR22	WBSCR22	10456	-0.045	0.24	NO
34	AOC3	AOC3	AOC3	11335	-0.061	0.2	NO
35	METTL2B	METTL2B	METTL2B	12628	-0.091	0.14	NO
36	ALDH3A1	ALDH3A1	ALDH3A1	12745	-0.095	0.15	NO
37	IL4I1	IL4I1	IL4I1	13512	-0.12	0.13	NO
38	TRMT11	TRMT11	TRMT11	14283	-0.15	0.1	NO
39	DCT	DCT	DCT	14585	-0.16	0.11	NO
40	TYRP1	TYRP1	TYRP1	14738	-0.17	0.13	NO
41	ADH1B	ADH1B	ADH1B	16508	-0.31	0.074	NO

Figure S55. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID IGF1 PATHWAY.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: PID IGF1 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 TF PATHWAY

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	EGFR	EGFR	EGFR	776	0.31	0.052	YES
2	ERBB4	ERBB4	ERBB4	1285	0.22	0.093	YES
3	ERBB3	ERBB3	ERBB3	1536	0.2	0.14	YES
4	PHLPP1	PHLPP1	PHLPP1	1540	0.19	0.2	YES
5	PIK3CA	PIK3CA	PIK3CA	1702	0.18	0.25	YES
6	FOXO1	FOXO1	FOXO1	2165	0.14	0.26	YES
7	AKT2	AKT2	AKT2	2199	0.14	0.31	YES
8	AKT3	AKT3	AKT3	2426	0.13	0.33	YES
9	CDKN1A	CDKN1A	CDKN1A	2644	0.12	0.36	YES
10	NR4A1	NR4A1	NR4A1	3112	0.094	0.36	YES
11	THEM4	THEM4	THEM4	3153	0.093	0.39	YES
12	RPS6KB2	RPS6KB2	RPS6KB2	3535	0.081	0.39	YES
13	TRIB3	TRIB3	TRIB3	3751	0.074	0.4	YES
14	BAD	BAD	BAD	3783	0.073	0.42	YES
15	FOXO3	FOXO3	FOXO3	3908	0.07	0.44	YES
16	ERBB2	ERBB2	ERBB2	3942	0.069	0.46	YES
17	GSK3A	GSK3A	GSK3A	4236	0.062	0.46	YES
18	FOXO4	FOXO4	FOXO4	4364	0.059	0.47	YES
19	MDM2	MDM2	MDM2	4381	0.059	0.49	YES
20	CASP9	CASP9	CASP9	4393	0.058	0.51	YES
21	PDPK1	PDPK1	PDPK1	4556	0.054	0.51	YES
22	PIK3R1	PIK3R1	PIK3R1	5107	0.043	0.5	NO
23	NRG2	NRG2	NRG2	5156	0.042	0.51	NO
24	TSC2	TSC2	TSC2	5497	0.035	0.5	NO
25	PTEN	PTEN	PTEN	5556	0.034	0.5	NO
26	AKT1	AKT1	AKT1	5795	0.03	0.5	NO
27	CREB1	CREB1	CREB1	6225	0.023	0.48	NO
28	AKT1S1	AKT1S1	AKT1S1	6427	0.019	0.48	NO
29	MTOR	MTOR	MTOR	6458	0.019	0.48	NO
30	EREG	EREG	EREG	6935	0.011	0.46	NO
31	RICTOR	RICTOR	RICTOR	7205	0.0066	0.45	NO
32	HBEGF	HBEGF	HBEGF	7265	0.0057	0.44	NO
33	EGF	EGF	EGF	7468	0.0023	0.44	NO
34	CHUK	CHUK	CHUK	7834	-0.0029	0.42	NO
35	MAPKAP1	MAPKAP1	MAPKAP1	8359	-0.011	0.39	NO
36	GRB2	GRB2	GRB2	8736	-0.016	0.37	NO
37	CDKN1B	CDKN1B	CDKN1B	8790	-0.017	0.38	NO
38	MLST8	MLST8	MLST8	9650	-0.031	0.34	NO
39	GAB1	GAB1	GAB1	10145	-0.04	0.32	NO
40	NRG4	NRG4	NRG4	10399	-0.044	0.32	NO
41	NRG1	NRG1	NRG1	11906	-0.074	0.26	NO
42	BTC	BTC	BTC	15722	-0.24	0.12	NO

Figure S57. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID AR TF PATHWAY.

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: PID AR TF 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 ECADHERIN STABILIZATION PATHWAY

Table S30. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	G6PC	G6PC	G6PC	171	0.54	0.056	YES
2	ADH6	ADH6	ADH6	191	0.53	0.12	YES
3	PKLR	PKLR	PKLR	230	0.5	0.18	YES
4	ALDOB	ALDOB	ALDOB	247	0.5	0.24	YES
5	ALDH1A3	ALDH1A3	ALDH1A3	385	0.43	0.28	YES
6	ADH1C	ADH1C	ADH1C	400	0.42	0.33	YES
7	ALDOC	ALDOC	ALDOC	484	0.38	0.37	YES
8	ALDH3B2	ALDH3B2	ALDH3B2	927	0.28	0.38	YES
9	PCK1	PCK1	PCK1	967	0.27	0.41	YES
10	G6PC2	G6PC2	G6PC2	1130	0.24	0.43	YES
11	ADH1A	ADH1A	ADH1A	1294	0.22	0.45	YES
12	ADH4	ADH4	ADH4	1314	0.22	0.48	YES
13	ADH7	ADH7	ADH7	1491	0.2	0.49	YES
14	GCK	GCK	GCK	1556	0.19	0.51	YES
15	FBP1	FBP1	FBP1	1715	0.18	0.52	YES
16	GALM	GALM	GALM	2380	0.13	0.5	NO
17	LDHAL6A	LDHAL6A	LDHAL6A	2716	0.11	0.5	NO
18	ENO2	ENO2	ENO2	2777	0.11	0.51	NO
19	PGM2	PGM2	PGM2	4174	0.063	0.44	NO
20	ALDH9A1	ALDH9A1	ALDH9A1	4488	0.056	0.42	NO
21	HK2	HK2	HK2	4761	0.05	0.42	NO
22	HK1	HK1	HK1	5108	0.043	0.4	NO
23	PKM2	PKM2	PKM2	5111	0.043	0.41	NO
24	PGK1	PGK1	PGK1	5914	0.028	0.36	NO
25	PDHB	PDHB	PDHB	5917	0.028	0.37	NO
26	LDHB	LDHB	LDHB	5919	0.028	0.37	NO
27	TPI1	TPI1	TPI1	5980	0.027	0.37	NO
28	PFKL	PFKL	PFKL	6320	0.022	0.36	NO
29	GAPDH	GAPDH	GAPDH	6529	0.018	0.34	NO
30	ADH5	ADH5	ADH5	6657	0.016	0.34	NO
31	LDHA	LDHA	LDHA	6718	0.015	0.34	NO
32	PGM1	PGM1	PGM1	6983	0.01	0.32	NO
33	ALDOA	ALDOA	ALDOA	7394	0.0037	0.3	NO
34	AKR1A1	AKR1A1	AKR1A1	7503	0.0018	0.3	NO
35	ALDH3B1	ALDH3B1	ALDH3B1	7652	-0.00023	0.29	NO
36	GPI	GPI	GPI	8019	-0.0056	0.27	NO
37	BPGM	BPGM	BPGM	8063	-0.0063	0.27	NO
38	ENO1	ENO1	ENO1	8302	-0.0099	0.25	NO
39	PGAM1	PGAM1	PGAM1	8314	-0.01	0.26	NO
40	ALDH3A2	ALDH3A2	ALDH3A2	8892	-0.019	0.22	NO
41	PFKM	PFKM	PFKM	8899	-0.019	0.23	NO
42	LDHC	LDHC	LDHC	9456	-0.028	0.2	NO
43	DLD	DLD	DLD	9726	-0.032	0.19	NO
44	PGAM4	PGAM4	PGAM4	9922	-0.036	0.18	NO
45	ACSS1	ACSS1	ACSS1	10501	-0.046	0.15	NO
46	PFKP	PFKP	PFKP	10507	-0.046	0.16	NO
47	ALDH7A1	ALDH7A1	ALDH7A1	10528	-0.046	0.16	NO
48	ACSS2	ACSS2	ACSS2	10783	-0.05	0.16	NO
49	DLAT	DLAT	DLAT	11829	-0.072	0.1	NO
50	PDHA1	PDHA1	PDHA1	12356	-0.084	0.086	NO
51	ALDH3A1	ALDH3A1	ALDH3A1	12745	-0.095	0.075	NO
52	PCK2	PCK2	PCK2	13119	-0.11	0.067	NO
53	PGAM2	PGAM2	PGAM2	14264	-0.15	0.021	NO
54	ALDH2	ALDH2	ALDH2	14278	-0.15	0.039	NO
55	LDHAL6B	LDHAL6B	LDHAL6B	14289	-0.15	0.057	NO
56	ENO3	ENO3	ENO3	15030	-0.19	0.038	NO
57	ALDH1B1	ALDH1B1	ALDH1B1	15055	-0.19	0.06	NO
58	ADH1B	ADH1B	ADH1B	16508	-0.31	0.016	NO
59	HK3	HK3	HK3	17461	-0.48	0.02	NO

Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ECADHERIN STABILIZATION PATHWAY.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: PID ECADHERIN STABILIZATION 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 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION	44	genes.ES.table	0.48	1.5	0.071	1	0.93	0.52	0.26	0.39	0.88	0.44
KEGG PROPANOATE METABOLISM	32	genes.ES.table	0.59	1.7	0.039	1	0.83	0.59	0.27	0.43	0.8	0.42
KEGG ADHERENS JUNCTION	73	genes.ES.table	0.36	1.5	0.041	1	0.96	0.29	0.2	0.23	0.87	0.44
BIOCARTA AT1R PATHWAY	32	genes.ES.table	0.45	1.8	0.016	1	0.55	0.31	0.17	0.26	0.49	0.34
BIOCARTA EGF PATHWAY	31	genes.ES.table	0.47	1.6	0.024	1	0.86	0.39	0.22	0.3	0.62	0.34
BIOCARTA PPARA PATHWAY	55	genes.ES.table	0.44	1.5	0.04	1	0.96	0.42	0.22	0.33	0.85	0.43
BIOCARTA PDGF PATHWAY	32	genes.ES.table	0.54	1.6	0.01	1	0.84	0.44	0.22	0.34	0.76	0.41
BIOCARTA VEGF PATHWAY	29	genes.ES.table	0.46	1.5	0.063	1	0.94	0.34	0.23	0.27	0.86	0.42
PID S1P S1P3 PATHWAY	29	genes.ES.table	0.53	1.6	0.023	1	0.85	0.45	0.26	0.33	0.67	0.37
PID AVB3 OPN PATHWAY	31	genes.ES.table	0.49	1.5	0.055	1	0.94	0.29	0.17	0.24	0.84	0.42

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

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	NOS3	NOS3	NOS3	661	0.36	0.019	YES
2	PLD2	PLD2	PLD2	783	0.34	0.064	YES
3	TEK	TEK	TEK	798	0.34	0.12	YES
4	GRB14	GRB14	GRB14	917	0.32	0.16	YES
5	ANGPT2	ANGPT2	ANGPT2	1235	0.27	0.18	YES
6	AGTR1	AGTR1	AGTR1	1501	0.25	0.21	YES
7	ETS1	ETS1	ETS1	1713	0.23	0.23	YES
8	ANGPT4	ANGPT4	ANGPT4	1885	0.22	0.25	YES
9	TNF	TNF	TNF	1901	0.22	0.29	YES
10	ELF1	ELF1	ELF1	1959	0.21	0.32	YES
11	MAPK8	MAPK8	MAPK8	2252	0.19	0.33	YES
12	CRK	CRK	CRK	2258	0.19	0.36	YES
13	FES	FES	FES	2454	0.18	0.38	YES
14	PIK3CA	PIK3CA	PIK3CA	2559	0.18	0.4	YES
15	RPS6KB1	RPS6KB1	RPS6KB1	2627	0.18	0.42	YES
16	STAT5B	STAT5B	STAT5B	2658	0.17	0.45	YES
17	BMX	BMX	BMX	2766	0.17	0.47	YES
18	FGF2	FGF2	FGF2	2860	0.16	0.49	YES
19	FOXO1	FOXO1	FOXO1	2923	0.16	0.51	YES
20	GRB7	GRB7	GRB7	3149	0.15	0.52	YES
21	PLG	PLG	PLG	3295	0.14	0.53	YES
22	ITGA5	ITGA5	ITGA5	3545	0.13	0.54	YES
23	FYN	FYN	FYN	3590	0.13	0.56	YES
24	CDKN1A	CDKN1A	CDKN1A	3792	0.12	0.57	YES
25	STAT5A	STAT5A	STAT5A	3928	0.12	0.58	YES
26	FN1	FN1	FN1	4308	0.1	0.57	NO
27	ITGB1	ITGB1	ITGB1	4833	0.088	0.56	NO
28	PTK2	PTK2	PTK2	5146	0.078	0.55	NO
29	PTPN11	PTPN11	PTPN11	5284	0.074	0.55	NO
30	MMP2	MMP2	MMP2	5497	0.068	0.55	NO
31	GRB2	GRB2	GRB2	5671	0.062	0.55	NO
32	MAPK14	MAPK14	MAPK14	6505	0.041	0.51	NO
33	MAPK1	MAPK1	MAPK1	6728	0.036	0.5	NO
34	RAC1	RAC1	RAC1	6796	0.034	0.51	NO
35	MAPK3	MAPK3	MAPK3	6903	0.032	0.5	NO
36	SHC1	SHC1	SHC1	7427	0.019	0.48	NO
37	RASA1	RASA1	RASA1	7450	0.019	0.48	NO
38	PXN	PXN	PXN	7485	0.018	0.48	NO
39	PIK3R1	PIK3R1	PIK3R1	8099	0.0029	0.45	NO
40	TNIP2	TNIP2	TNIP2	8243	-0.00061	0.44	NO
41	NFKB1	NFKB1	NFKB1	8782	-0.014	0.41	NO
42	ELF2	ELF2	ELF2	9149	-0.022	0.39	NO
43	RELA	RELA	RELA	9780	-0.037	0.36	NO
44	PAK1	PAK1	PAK1	9861	-0.039	0.37	NO
45	NCK1	NCK1	NCK1	10543	-0.055	0.34	NO
46	ELK1	ELK1	ELK1	11836	-0.09	0.28	NO
47	DOK2	DOK2	DOK2	11953	-0.093	0.28	NO
48	AKT1	AKT1	AKT1	11975	-0.094	0.3	NO
49	ANGPT1	ANGPT1	ANGPT1	14613	-0.2	0.18	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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S62. 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 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	AGT	AGT	AGT	458	0.42	0.091	YES
2	ATF2	ATF2	ATF2	815	0.33	0.16	YES
3	AGTR1	AGTR1	AGTR1	1501	0.25	0.2	YES
4	MAP2K4	MAP2K4	MAP2K4	2035	0.21	0.22	YES
5	MAPK8	MAPK8	MAPK8	2252	0.19	0.27	YES
6	PRKCA	PRKCA	PRKCA	2439	0.18	0.31	YES
7	SOS1	SOS1	SOS1	2646	0.17	0.34	YES
8	MEF2C	MEF2C	MEF2C	2777	0.17	0.38	YES
9	MEF2D	MEF2D	MEF2D	3008	0.16	0.42	YES
10	EGFR	EGFR	EGFR	3098	0.15	0.45	YES
11	PTK2	PTK2	PTK2	5146	0.078	0.36	NO
12	CALM2	CALM2	CALM2	5626	0.064	0.35	NO
13	GRB2	GRB2	GRB2	5671	0.062	0.36	NO
14	JUN	JUN	JUN	5906	0.056	0.37	NO
15	PRKCB	PRKCB	PRKCB	6098	0.051	0.37	NO
16	MAPK1	MAPK1	MAPK1	6728	0.036	0.35	NO
17	RAC1	RAC1	RAC1	6796	0.034	0.35	NO
18	MAPK3	MAPK3	MAPK3	6903	0.032	0.36	NO
19	MEF2A	MEF2A	MEF2A	7266	0.023	0.34	NO
20	GNAQ	GNAQ	GNAQ	7331	0.021	0.34	NO
21	SHC1	SHC1	SHC1	7427	0.019	0.34	NO
22	MAP2K1	MAP2K1	MAP2K1	8196	0.00046	0.3	NO
23	SRC	SRC	SRC	8213	0.000058	0.3	NO
24	MAP3K1	MAP3K1	MAP3K1	8592	-0.0086	0.28	NO
25	PAK1	PAK1	PAK1	9861	-0.039	0.22	NO
26	CALM1	CALM1	CALM1	11136	-0.071	0.17	NO
27	ELK1	ELK1	ELK1	11836	-0.09	0.15	NO
28	PTK2B	PTK2B	PTK2B	11881	-0.091	0.18	NO
29	HRAS	HRAS	HRAS	13120	-0.13	0.14	NO
30	RAF1	RAF1	RAF1	13125	-0.13	0.18	NO
31	MAP2K2	MAP2K2	MAP2K2	13425	-0.14	0.2	NO
32	CALM3	CALM3	CALM3	13813	-0.16	0.22	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 PROPANOATE METABOLISM.

Figure S64. 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 ADHERENS JUNCTION

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	EDNRB	EDNRB	EDNRB	242	0.5	0.053	YES
2	TSHR	TSHR	TSHR	308	0.47	0.11	YES
3	ITGA11	ITGA11	ITGA11	398	0.44	0.16	YES
4	ITGA8	ITGA8	ITGA8	552	0.39	0.21	YES
5	PLD2	PLD2	PLD2	783	0.34	0.24	YES
6	SPAG9	SPAG9	SPAG9	893	0.32	0.28	YES
7	IL2RA	IL2RA	IL2RA	1131	0.28	0.3	YES
8	ITGA4	ITGA4	ITGA4	1148	0.28	0.34	YES
9	ITGA10	ITGA10	ITGA10	1284	0.27	0.36	YES
10	CPE	CPE	CPE	1390	0.26	0.39	YES
11	AGTR1	AGTR1	AGTR1	1501	0.25	0.42	YES
12	ITGA2	ITGA2	ITGA2	1853	0.22	0.43	YES
13	CLTC	CLTC	CLTC	2078	0.21	0.44	YES
14	ITGA1	ITGA1	ITGA1	2095	0.2	0.47	YES
15	EXOC6	EXOC6	EXOC6	2688	0.17	0.46	YES
16	ITGA6	ITGA6	ITGA6	2927	0.16	0.47	YES
17	ITGAV	ITGAV	ITGAV	3086	0.15	0.48	YES
18	ASAP2	ASAP2	ASAP2	3088	0.15	0.5	YES
19	EXOC2	EXOC2	EXOC2	3442	0.14	0.5	YES
20	ITGA5	ITGA5	ITGA5	3545	0.13	0.51	YES
21	PLD1	PLD1	PLD1	3602	0.13	0.52	YES
22	ITGB1	ITGB1	ITGB1	4833	0.088	0.47	NO
23	NME1	NME1	NME1	5209	0.076	0.46	NO
24	EXOC5	EXOC5	EXOC5	6112	0.051	0.41	NO
25	EXOC1	EXOC1	EXOC1	6182	0.049	0.41	NO
26	ITGA9	ITGA9	ITGA9	6329	0.045	0.41	NO
27	EXOC7	EXOC7	EXOC7	6672	0.037	0.4	NO
28	ITGA7	ITGA7	ITGA7	6673	0.037	0.4	NO
29	VAMP3	VAMP3	VAMP3	6729	0.036	0.4	NO
30	ITGA3	ITGA3	ITGA3	6759	0.035	0.41	NO
31	EXOC4	EXOC4	EXOC4	7162	0.025	0.39	NO
32	CTNNB1	CTNNB1	CTNNB1	7629	0.014	0.36	NO
33	CTNNA1	CTNNA1	CTNNA1	7672	0.013	0.36	NO
34	CTNND1	CTNND1	CTNND1	7757	0.011	0.36	NO
35	RALA	RALA	RALA	8033	0.0045	0.34	NO
36	ADRB2	ADRB2	ADRB2	8690	-0.011	0.31	NO
37	EXOC3	EXOC3	EXOC3	8828	-0.015	0.3	NO
38	KLC1	KLC1	KLC1	10175	-0.046	0.23	NO
39	CDH1	CDH1	CDH1	10832	-0.063	0.21	NO
40	DNM2	DNM2	DNM2	11748	-0.088	0.17	NO
41	ARF6	ARF6	ARF6	12004	-0.094	0.16	NO
42	SCAMP2	SCAMP2	SCAMP2	12037	-0.095	0.18	NO
43	BIN1	BIN1	BIN1	12422	-0.11	0.17	NO
44	PIP5K1C	PIP5K1C	PIP5K1C	12870	-0.12	0.16	NO
45	SLC2A4	SLC2A4	SLC2A4	14180	-0.17	0.11	NO
46	MAPK8IP3	MAPK8IP3	MAPK8IP3	14408	-0.18	0.12	NO
47	AVPR2	AVPR2	AVPR2	15498	-0.26	0.092	NO
48	ACAP1	ACAP1	ACAP1	15857	-0.29	0.11	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 ADHERENS JUNCTION.

Figure S66. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ADHERENS JUNCTION, 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 AT1R PATHWAY

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	PDGFB	PDGFB	PDGFB	1286	0.27	-0.0081	YES
2	EIF2AK2	EIF2AK2	EIF2AK2	1370	0.26	0.05	YES
3	PDGFRB	PDGFRB	PDGFRB	1429	0.26	0.11	YES
4	KDR	KDR	KDR	1470	0.25	0.16	YES
5	ITGA1	ITGA1	ITGA1	2095	0.2	0.18	YES
6	CSF1	CSF1	CSF1	2150	0.2	0.22	YES
7	PIK3CA	PIK3CA	PIK3CA	2559	0.18	0.24	YES
8	SOS1	SOS1	SOS1	2646	0.17	0.28	YES
9	STAT5B	STAT5B	STAT5B	2658	0.17	0.32	YES
10	EGFR	EGFR	EGFR	3098	0.15	0.33	YES
11	STAT1	STAT1	STAT1	3105	0.15	0.37	YES
12	JAK1	JAK1	JAK1	3249	0.15	0.4	YES
13	VEGFA	VEGFA	VEGFA	3425	0.14	0.42	YES
14	STAT3	STAT3	STAT3	3717	0.13	0.43	YES
15	STAT5A	STAT5A	STAT5A	3928	0.12	0.45	YES
16	KPNB1	KPNB1	KPNB1	3976	0.12	0.48	YES
17	EIF2A	EIF2A	EIF2A	4004	0.12	0.5	YES
18	HGF	HGF	HGF	4649	0.094	0.49	NO
19	ITGB1	ITGB1	ITGB1	4833	0.088	0.5	NO
20	RAB4A	RAB4A	RAB4A	5298	0.073	0.49	NO
21	GRB2	GRB2	GRB2	5671	0.062	0.48	NO
22	PIK3CB	PIK3CB	PIK3CB	5674	0.062	0.5	NO
23	MET	MET	MET	5953	0.055	0.5	NO
24	PTPN2	PTPN2	PTPN2	6317	0.046	0.49	NO
25	PIAS1	PIAS1	PIAS1	6410	0.043	0.49	NO
26	SHC1	SHC1	SHC1	7427	0.019	0.44	NO
27	STAT6	STAT6	STAT6	7804	0.0098	0.42	NO
28	GAB1	GAB1	GAB1	7862	0.0086	0.42	NO
29	KPNA2	KPNA2	KPNA2	8002	0.005	0.41	NO
30	CSF1R	CSF1R	CSF1R	8039	0.0044	0.41	NO
31	PIK3R1	PIK3R1	PIK3R1	8099	0.0029	0.41	NO
32	SRC	SRC	SRC	8213	0.000058	0.4	NO
33	EGF	EGF	EGF	8422	-0.0048	0.39	NO
34	INSR	INSR	INSR	8601	-0.0088	0.38	NO
35	LMAN1	LMAN1	LMAN1	8733	-0.012	0.38	NO
36	PIK3CD	PIK3CD	PIK3CD	8893	-0.016	0.37	NO
37	ATR	ATR	ATR	8974	-0.018	0.37	NO
38	CREBBP	CREBBP	CREBBP	10520	-0.055	0.3	NO
39	PIK3R3	PIK3R3	PIK3R3	11135	-0.071	0.28	NO
40	PTPN1	PTPN1	PTPN1	11520	-0.082	0.28	NO
41	PIK3R2	PIK3R2	PIK3R2	13241	-0.13	0.22	NO
42	JAK3	JAK3	JAK3	14228	-0.18	0.2	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: BIOCARTA AT1R PATHWAY.

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R 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 EGF PATHWAY

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	ALDH2	ALDH2	ALDH2	655	0.36	0.06	YES
2	HIBCH	HIBCH	HIBCH	983	0.3	0.12	YES
3	ACADM	ACADM	ACADM	1674	0.24	0.14	YES
4	SUCLA2	SUCLA2	SUCLA2	1681	0.24	0.21	YES
5	MUT	MUT	MUT	1774	0.23	0.26	YES
6	PCCA	PCCA	PCCA	1800	0.22	0.32	YES
7	MCEE	MCEE	MCEE	1829	0.22	0.38	YES
8	ALDH3A2	ALDH3A2	ALDH3A2	2650	0.17	0.38	YES
9	SUCLG1	SUCLG1	SUCLG1	2770	0.17	0.41	YES
10	HADHA	HADHA	HADHA	3342	0.14	0.42	YES
11	ALDH6A1	ALDH6A1	ALDH6A1	3684	0.13	0.43	YES
12	EHHADH	EHHADH	EHHADH	3788	0.12	0.46	YES
13	PCCB	PCCB	PCCB	3859	0.12	0.49	YES
14	ECHS1	ECHS1	ECHS1	4162	0.11	0.5	YES
15	ALDH9A1	ALDH9A1	ALDH9A1	4287	0.11	0.52	YES
16	ALDH1B1	ALDH1B1	ALDH1B1	4474	0.099	0.54	YES
17	LDHA	LDHA	LDHA	4500	0.098	0.56	YES
18	ACAT1	ACAT1	ACAT1	4616	0.095	0.58	YES
19	LDHAL6B	LDHAL6B	LDHAL6B	4838	0.088	0.59	YES
20	ALDH7A1	ALDH7A1	ALDH7A1	6206	0.048	0.53	NO
21	SUCLG2	SUCLG2	SUCLG2	6533	0.04	0.52	NO
22	ACSS3	ACSS3	ACSS3	7274	0.022	0.48	NO
23	ACACB	ACACB	ACACB	7277	0.022	0.49	NO
24	ACAT2	ACAT2	ACAT2	7559	0.016	0.48	NO
25	ACACA	ACACA	ACACA	7630	0.014	0.48	NO
26	LDHB	LDHB	LDHB	8491	-0.0059	0.43	NO
27	ACSS1	ACSS1	ACSS1	9452	-0.03	0.39	NO
28	MLYCD	MLYCD	MLYCD	9966	-0.042	0.37	NO
29	ABAT	ABAT	ABAT	10085	-0.044	0.37	NO
30	LDHAL6A	LDHAL6A	LDHAL6A	10649	-0.058	0.36	NO
31	ACSS2	ACSS2	ACSS2	10676	-0.059	0.37	NO
32	LDHC	LDHC	LDHC	12676	-0.12	0.29	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: BIOCARTA EGF PATHWAY.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EGF 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 PPARA PATHWAY

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	PDGFRA	PDGFRA	PDGFRA	58	0.76	0.19	YES
2	FOS	FOS	FOS	1154	0.28	0.2	YES
3	MAP2K4	MAP2K4	MAP2K4	2035	0.21	0.21	YES
4	MAPK8	MAPK8	MAPK8	2252	0.19	0.25	YES
5	PRKCA	PRKCA	PRKCA	2439	0.18	0.28	YES
6	PIK3CA	PIK3CA	PIK3CA	2559	0.18	0.32	YES
7	SOS1	SOS1	SOS1	2646	0.17	0.36	YES
8	STAT5B	STAT5B	STAT5B	2658	0.17	0.41	YES
9	STAT1	STAT1	STAT1	3105	0.15	0.42	YES
10	JAK1	JAK1	JAK1	3249	0.15	0.45	YES
11	PDGFA	PDGFA	PDGFA	3610	0.13	0.46	YES
12	STAT3	STAT3	STAT3	3717	0.13	0.49	YES
13	PIK3CG	PIK3CG	PIK3CG	3728	0.13	0.52	YES
14	STAT5A	STAT5A	STAT5A	3928	0.12	0.54	YES
15	STAT4	STAT4	STAT4	4942	0.085	0.51	NO
16	GRB2	GRB2	GRB2	5671	0.062	0.48	NO
17	SRF	SRF	SRF	5852	0.057	0.48	NO
18	JUN	JUN	JUN	5906	0.056	0.5	NO
19	PRKCB	PRKCB	PRKCB	6098	0.051	0.5	NO
20	MAPK3	MAPK3	MAPK3	6903	0.032	0.46	NO
21	SHC1	SHC1	SHC1	7427	0.019	0.44	NO
22	RASA1	RASA1	RASA1	7450	0.019	0.44	NO
23	STAT6	STAT6	STAT6	7804	0.0098	0.42	NO
24	PIK3R1	PIK3R1	PIK3R1	8099	0.0029	0.41	NO
25	MAP2K1	MAP2K1	MAP2K1	8196	0.00046	0.4	NO
26	MAP3K1	MAP3K1	MAP3K1	8592	-0.0086	0.38	NO
27	CSNK2A1	CSNK2A1	CSNK2A1	8707	-0.011	0.38	NO
28	PLCG1	PLCG1	PLCG1	11345	-0.077	0.25	NO
29	STAT2	STAT2	STAT2	11707	-0.087	0.25	NO
30	ELK1	ELK1	ELK1	11836	-0.09	0.27	NO
31	HRAS	HRAS	HRAS	13120	-0.13	0.23	NO
32	RAF1	RAF1	RAF1	13125	-0.13	0.26	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: BIOCARTA PPARA PATHWAY.

Figure S72. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PPARA 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 PDGF PATHWAY

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	ITGB3	ITGB3	ITGB3	116	0.62	0.15	YES
2	S1PR3	S1PR3	S1PR3	345	0.45	0.24	YES
3	FLT1	FLT1	FLT1	903	0.32	0.29	YES
4	PDGFB	PDGFB	PDGFB	1286	0.27	0.34	YES
5	GNA13	GNA13	GNA13	1368	0.26	0.4	YES
6	PDGFRB	PDGFRB	PDGFRB	1429	0.26	0.46	YES
7	S1PR1	S1PR1	S1PR1	1791	0.23	0.49	YES
8	CXCR4	CXCR4	CXCR4	2489	0.18	0.5	YES
9	ITGAV	ITGAV	ITGAV	3086	0.15	0.5	YES
10	VEGFA	VEGFA	VEGFA	3425	0.14	0.52	YES
11	GNA14	GNA14	GNA14	3971	0.12	0.51	YES
12	GNAI3	GNAI3	GNAI3	4574	0.096	0.5	YES
13	GNA15	GNA15	GNA15	4576	0.096	0.53	YES
14	GNAI1	GNAI1	GNAI1	5173	0.077	0.51	NO
15	JAK2	JAK2	JAK2	5672	0.062	0.5	NO
16	AKT3	AKT3	AKT3	6584	0.039	0.46	NO
17	MAPK1	MAPK1	MAPK1	6728	0.036	0.46	NO
18	RAC1	RAC1	RAC1	6796	0.034	0.46	NO
19	MAPK3	MAPK3	MAPK3	6903	0.032	0.47	NO
20	GNAZ	GNAZ	GNAZ	6950	0.03	0.47	NO
21	GNAQ	GNAQ	GNAQ	7331	0.021	0.46	NO
22	GNAI2	GNAI2	GNAI2	7699	0.012	0.44	NO
23	RHOA	RHOA	RHOA	7875	0.0082	0.43	NO
24	SRC	SRC	SRC	8213	0.000058	0.41	NO
25	GNA12	GNA12	GNA12	9025	-0.019	0.37	NO
26	GNA11	GNA11	GNA11	9599	-0.033	0.34	NO
27	AKT1	AKT1	AKT1	11975	-0.094	0.24	NO
28	GNAO1	GNAO1	GNAO1	13706	-0.15	0.18	NO
29	S1PR2	S1PR2	S1PR2	15107	-0.23	0.15	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: BIOCARTA PDGF PATHWAY.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PDGF 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 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	FOS	FOS	FOS	1154	0.28	0.028	YES
2	MAP2K4	MAP2K4	MAP2K4	2035	0.21	0.048	YES
3	MAPK8	MAPK8	MAPK8	2252	0.19	0.1	YES
4	PRKCA	PRKCA	PRKCA	2439	0.18	0.15	YES
5	PIK3CA	PIK3CA	PIK3CA	2559	0.18	0.2	YES
6	SOS1	SOS1	SOS1	2646	0.17	0.26	YES
7	STAT5B	STAT5B	STAT5B	2658	0.17	0.31	YES
8	EGFR	EGFR	EGFR	3098	0.15	0.34	YES
9	STAT1	STAT1	STAT1	3105	0.15	0.39	YES
10	JAK1	JAK1	JAK1	3249	0.15	0.43	YES
11	STAT3	STAT3	STAT3	3717	0.13	0.44	YES
12	STAT5A	STAT5A	STAT5A	3928	0.12	0.47	YES
13	STAT4	STAT4	STAT4	4942	0.085	0.44	NO
14	GRB2	GRB2	GRB2	5671	0.062	0.42	NO
15	SRF	SRF	SRF	5852	0.057	0.43	NO
16	JUN	JUN	JUN	5906	0.056	0.45	NO
17	PRKCB	PRKCB	PRKCB	6098	0.051	0.45	NO
18	MAPK3	MAPK3	MAPK3	6903	0.032	0.42	NO
19	SHC1	SHC1	SHC1	7427	0.019	0.4	NO
20	RASA1	RASA1	RASA1	7450	0.019	0.4	NO
21	STAT6	STAT6	STAT6	7804	0.0098	0.38	NO
22	PIK3R1	PIK3R1	PIK3R1	8099	0.0029	0.37	NO
23	MAP2K1	MAP2K1	MAP2K1	8196	0.00046	0.36	NO
24	EGF	EGF	EGF	8422	-0.0048	0.35	NO
25	MAP3K1	MAP3K1	MAP3K1	8592	-0.0086	0.34	NO
26	CSNK2A1	CSNK2A1	CSNK2A1	8707	-0.011	0.34	NO
27	PLCG1	PLCG1	PLCG1	11345	-0.077	0.22	NO
28	STAT2	STAT2	STAT2	11707	-0.087	0.23	NO
29	ELK1	ELK1	ELK1	11836	-0.09	0.25	NO
30	HRAS	HRAS	HRAS	13120	-0.13	0.22	NO
31	RAF1	RAF1	RAF1	13125	-0.13	0.26	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: BIOCARTA VEGF PATHWAY.

Figure S76. 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 S1P S1P3 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	COL9A2	COL9A2	COL9A2	16	0.95	0.052	YES
2	PDGFRA	PDGFRA	PDGFRA	58	0.76	0.091	YES
3	ADCY5	ADCY5	ADCY5	224	0.52	0.11	YES
4	ITPR3	ITPR3	ITPR3	469	0.41	0.12	YES
5	PDGFD	PDGFD	PDGFD	733	0.35	0.12	YES
6	THBS2	THBS2	THBS2	830	0.33	0.14	YES
7	CAMK4	CAMK4	CAMK4	867	0.32	0.15	YES
8	COL4A3	COL4A3	COL4A3	887	0.32	0.17	YES
9	THBS4	THBS4	THBS4	1032	0.3	0.18	YES
10	COL6A3	COL6A3	COL6A3	1074	0.29	0.19	YES
11	PDGFB	PDGFB	PDGFB	1286	0.27	0.19	YES
12	ADCY3	ADCY3	ADCY3	1342	0.26	0.2	YES
13	ADCY4	ADCY4	ADCY4	1383	0.26	0.22	YES
14	PDGFRB	PDGFRB	PDGFRB	1429	0.26	0.23	YES
15	PLAT	PLAT	PLAT	1525	0.25	0.24	YES
16	COL5A1	COL5A1	COL5A1	1601	0.24	0.24	YES
17	PDE1B	PDE1B	PDE1B	1751	0.23	0.25	YES
18	ADCY2	ADCY2	ADCY2	1793	0.23	0.26	YES
19	COL4A4	COL4A4	COL4A4	1869	0.22	0.27	YES
20	CHUK	CHUK	CHUK	1880	0.22	0.28	YES
21	COL9A3	COL9A3	COL9A3	2160	0.2	0.27	YES
22	COL4A1	COL4A1	COL4A1	2206	0.2	0.28	YES
23	CRK	CRK	CRK	2258	0.19	0.29	YES
24	PRKAR1A	PRKAR1A	PRKAR1A	2300	0.19	0.3	YES
25	COL3A1	COL3A1	COL3A1	2380	0.19	0.3	YES
26	COL5A2	COL5A2	COL5A2	2387	0.19	0.31	YES
27	PRKCA	PRKCA	PRKCA	2439	0.18	0.32	YES
28	PIK3CA	PIK3CA	PIK3CA	2559	0.18	0.32	YES
29	SOS1	SOS1	SOS1	2646	0.17	0.33	YES
30	STAT5B	STAT5B	STAT5B	2658	0.17	0.34	YES
31	COL6A2	COL6A2	COL6A2	2673	0.17	0.35	YES
32	COL4A2	COL4A2	COL4A2	2678	0.17	0.36	YES
33	FOXO1	FOXO1	FOXO1	2923	0.16	0.35	YES
34	SPP1	SPP1	SPP1	2932	0.16	0.36	YES
35	THEM4	THEM4	THEM4	2979	0.16	0.36	YES
36	PDE1A	PDE1A	PDE1A	3064	0.15	0.37	YES
37	STAT1	STAT1	STAT1	3105	0.15	0.38	YES
38	GRB7	GRB7	GRB7	3149	0.15	0.38	YES
39	PLG	PLG	PLG	3295	0.14	0.38	YES
40	COL1A2	COL1A2	COL1A2	3521	0.13	0.38	YES
41	PDGFA	PDGFA	PDGFA	3610	0.13	0.38	YES
42	COL1A1	COL1A1	COL1A1	3708	0.13	0.38	YES
43	STAT3	STAT3	STAT3	3717	0.13	0.39	YES
44	CDKN1A	CDKN1A	CDKN1A	3792	0.12	0.39	YES
45	CREB1	CREB1	CREB1	3794	0.12	0.4	YES
46	STAT5A	STAT5A	STAT5A	3928	0.12	0.39	NO
47	THBS1	THBS1	THBS1	4344	0.1	0.38	NO
48	COL4A5	COL4A5	COL4A5	4350	0.1	0.38	NO
49	FOXO3	FOXO3	FOXO3	4689	0.093	0.37	NO
50	NRAS	NRAS	NRAS	4714	0.092	0.37	NO
51	PTEN	PTEN	PTEN	4801	0.09	0.37	NO
52	ITPR2	ITPR2	ITPR2	4884	0.086	0.37	NO
53	ADCY9	ADCY9	ADCY9	5272	0.074	0.35	NO
54	FOXO4	FOXO4	FOXO4	5485	0.068	0.34	NO
55	MDM2	MDM2	MDM2	5512	0.067	0.35	NO
56	COL9A1	COL9A1	COL9A1	5524	0.066	0.35	NO
57	CALM2	CALM2	CALM2	5626	0.064	0.35	NO
58	GRB2	GRB2	GRB2	5671	0.062	0.35	NO
59	PIK3CB	PIK3CB	PIK3CB	5674	0.062	0.35	NO
60	NCK2	NCK2	NCK2	5821	0.058	0.35	NO
61	AKT3	AKT3	AKT3	6584	0.039	0.31	NO
62	MAPK1	MAPK1	MAPK1	6728	0.036	0.3	NO
63	MAPK3	MAPK3	MAPK3	6903	0.032	0.29	NO
64	PRKAR2A	PRKAR2A	PRKAR2A	7029	0.029	0.29	NO
65	KRAS	KRAS	KRAS	7072	0.028	0.29	NO
66	RICTOR	RICTOR	RICTOR	7232	0.024	0.28	NO
67	RASA1	RASA1	RASA1	7450	0.019	0.27	NO
68	MTOR	MTOR	MTOR	7462	0.018	0.27	NO
69	YWHAB	YWHAB	YWHAB	7651	0.014	0.26	NO
70	CDKN1B	CDKN1B	CDKN1B	7724	0.012	0.25	NO
71	PRKACB	PRKACB	PRKACB	7789	0.01	0.25	NO
72	STAT6	STAT6	STAT6	7804	0.0098	0.25	NO
73	NR4A1	NR4A1	NR4A1	7868	0.0085	0.25	NO
74	PIK3R1	PIK3R1	PIK3R1	8099	0.0029	0.24	NO
75	MAP2K1	MAP2K1	MAP2K1	8196	0.00046	0.23	NO
76	SRC	SRC	SRC	8213	0.000058	0.23	NO
77	PRKAR2B	PRKAR2B	PRKAR2B	8581	-0.0083	0.21	NO
78	RAPGEF1	RAPGEF1	RAPGEF1	8655	-0.01	0.2	NO
79	PRKCE	PRKCE	PRKCE	8831	-0.015	0.2	NO
80	COL6A1	COL6A1	COL6A1	8902	-0.016	0.19	NO
81	CASP9	CASP9	CASP9	9889	-0.04	0.14	NO
82	THBS3	THBS3	THBS3	9963	-0.042	0.14	NO
83	PHLPP1	PHLPP1	PHLPP1	10053	-0.044	0.14	NO
84	PDPK1	PDPK1	PDPK1	10065	-0.044	0.14	NO
85	PDGFC	PDGFC	PDGFC	10078	-0.044	0.14	NO
86	CRKL	CRKL	CRKL	10161	-0.046	0.14	NO
87	FURIN	FURIN	FURIN	10300	-0.05	0.13	NO
88	NCK1	NCK1	NCK1	10543	-0.055	0.12	NO
89	RPS6KB2	RPS6KB2	RPS6KB2	11052	-0.069	0.096	NO
90	CALM1	CALM1	CALM1	11136	-0.071	0.095	NO
91	PRKCD	PRKCD	PRKCD	11230	-0.074	0.094	NO
92	ADCY1	ADCY1	ADCY1	11267	-0.075	0.096	NO
93	PLCG1	PLCG1	PLCG1	11345	-0.077	0.096	NO
94	PRKAR1B	PRKAR1B	PRKAR1B	11384	-0.078	0.098	NO
95	TSC2	TSC2	TSC2	11575	-0.083	0.092	NO
96	GSK3A	GSK3A	GSK3A	11917	-0.092	0.078	NO
97	AKT1	AKT1	AKT1	11975	-0.094	0.08	NO
98	MAPKAP1	MAPKAP1	MAPKAP1	12205	-0.1	0.072	NO
99	ADCY6	ADCY6	ADCY6	12207	-0.1	0.078	NO
100	BCAR1	BCAR1	BCAR1	12587	-0.11	0.062	NO
101	BAD	BAD	BAD	12624	-0.11	0.067	NO
102	HRAS	HRAS	HRAS	13120	-0.13	0.046	NO
103	RAF1	RAF1	RAF1	13125	-0.13	0.053	NO
104	PIK3R2	PIK3R2	PIK3R2	13241	-0.13	0.054	NO
105	AKT2	AKT2	AKT2	13301	-0.14	0.058	NO
106	MLST8	MLST8	MLST8	13406	-0.14	0.06	NO
107	MAP2K2	MAP2K2	MAP2K2	13425	-0.14	0.066	NO
108	ADRBK1	ADRBK1	ADRBK1	13717	-0.15	0.058	NO
109	CALM3	CALM3	CALM3	13813	-0.16	0.062	NO
110	AKT1S1	AKT1S1	AKT1S1	14032	-0.16	0.058	NO
111	PRKACA	PRKACA	PRKACA	14048	-0.17	0.067	NO
112	ADCY7	ADCY7	ADCY7	14634	-0.2	0.044	NO
113	CDK1	CDK1	CDK1	15268	-0.24	0.022	NO
114	PRKACG	PRKACG	PRKACG	15839	-0.29	0.0056	NO
115	COL2A1	COL2A1	COL2A1	16283	-0.34	-0.00058	NO
116	PRKCG	PRKCG	PRKCG	16890	-0.45	-0.01	NO
117	TRIB3	TRIB3	TRIB3	17116	-0.52	0.0057	NO
118	ADCY8	ADCY8	ADCY8	17403	-0.62	0.024	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 S1P S1P3 PATHWAY.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: PID S1P S1P3 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 AVB3 OPN 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	DOCK1	DOCK1	DOCK1	1072	0.29	-0.0093	YES
2	ROCK2	ROCK2	ROCK2	1276	0.27	0.026	YES
3	ETS1	ETS1	ETS1	1713	0.23	0.042	YES
4	RGNEF	RGNEF	RGNEF	1747	0.23	0.081	YES
5	MAP2K4	MAP2K4	MAP2K4	2035	0.21	0.1	YES
6	ARHGEF7	ARHGEF7	ARHGEF7	2127	0.2	0.13	YES
7	MAPK8	MAPK8	MAPK8	2252	0.19	0.16	YES
8	CRK	CRK	CRK	2258	0.19	0.19	YES
9	ELMO1	ELMO1	ELMO1	2285	0.19	0.22	YES
10	WASL	WASL	WASL	2552	0.18	0.24	YES
11	PIK3CA	PIK3CA	PIK3CA	2559	0.18	0.27	YES
12	SOS1	SOS1	SOS1	2646	0.17	0.3	YES
13	BMX	BMX	BMX	2766	0.17	0.32	YES
14	ITGAV	ITGAV	ITGAV	3086	0.15	0.33	YES
15	GRB7	GRB7	GRB7	3149	0.15	0.35	YES
16	BRAF	BRAF	BRAF	3373	0.14	0.36	YES
17	ITGA5	ITGA5	ITGA5	3545	0.13	0.38	YES
18	FYN	FYN	FYN	3590	0.13	0.4	YES
19	ASAP1	ASAP1	ASAP1	4036	0.12	0.39	YES
20	ARHGAP26	ARHGAP26	ARHGAP26	4551	0.097	0.38	YES
21	ITGB5	ITGB5	ITGB5	4809	0.089	0.38	YES
22	ITGB1	ITGB1	ITGB1	4833	0.088	0.4	YES
23	CAPN2	CAPN2	CAPN2	4888	0.086	0.41	YES
24	PTK2	PTK2	PTK2	5146	0.078	0.41	YES
25	YES1	YES1	YES1	5317	0.072	0.41	YES
26	KLF8	KLF8	KLF8	5469	0.068	0.41	YES
27	VCL	VCL	VCL	5552	0.066	0.42	YES
28	GRB2	GRB2	GRB2	5671	0.062	0.42	YES
29	RAP1B	RAP1B	RAP1B	5709	0.061	0.43	YES
30	NCK2	NCK2	NCK2	5821	0.058	0.44	YES
31	JUN	JUN	JUN	5906	0.056	0.44	YES
32	ACTN1	ACTN1	ACTN1	6163	0.05	0.44	NO
33	RAP1A	RAP1A	RAP1A	6242	0.048	0.44	NO
34	MMP14	MMP14	MMP14	6670	0.037	0.42	NO
35	MAPK1	MAPK1	MAPK1	6728	0.036	0.42	NO
36	RAC1	RAC1	RAC1	6796	0.034	0.43	NO
37	MAPK9	MAPK9	MAPK9	7413	0.019	0.4	NO
38	RASA1	RASA1	RASA1	7450	0.019	0.4	NO
39	PXN	PXN	PXN	7485	0.018	0.4	NO
40	GIT2	GIT2	GIT2	7719	0.012	0.39	NO
41	RRAS	RRAS	RRAS	7801	0.0099	0.38	NO
42	RHOA	RHOA	RHOA	7875	0.0082	0.38	NO
43	ARHGEF11	ARHGEF11	ARHGEF11	7953	0.0063	0.38	NO
44	TLN1	TLN1	TLN1	8081	0.0035	0.37	NO
45	PIK3R1	PIK3R1	PIK3R1	8099	0.0029	0.37	NO
46	MAP2K1	MAP2K1	MAP2K1	8196	0.00046	0.37	NO
47	SRC	SRC	SRC	8213	0.000058	0.36	NO
48	RAPGEF1	RAPGEF1	RAPGEF1	8655	-0.01	0.34	NO
49	CCND1	CCND1	CCND1	9670	-0.035	0.29	NO
50	PAK1	PAK1	PAK1	9861	-0.039	0.29	NO
51	PTPN21	PTPN21	PTPN21	10267	-0.049	0.27	NO
52	NCK1	NCK1	NCK1	10543	-0.055	0.27	NO
53	PLCG1	PLCG1	PLCG1	11345	-0.077	0.24	NO
54	SH3GL1	SH3GL1	SH3GL1	12482	-0.11	0.19	NO
55	BCAR1	BCAR1	BCAR1	12587	-0.11	0.2	NO
56	RAF1	RAF1	RAF1	13125	-0.13	0.2	NO
57	MAPK8IP3	MAPK8IP3	MAPK8IP3	14408	-0.18	0.16	NO
58	ACTA1	ACTA1	ACTA1	14698	-0.2	0.18	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 AVB3 OPN PATHWAY.

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: PID AVB3 OPN 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 CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.5	1.5	0.13	0.25	0.98	0.83	0.46	0.45	0.17	0.024
KEGG RNA DEGRADATION	57	genes.ES.table	0.37	1.7	0.058	0.25	0.82	0.4	0.26	0.3	0.12	0.052
KEGG DNA REPLICATION	36	genes.ES.table	0.64	1.8	0.029	0.39	0.63	0.67	0.24	0.51	0.13	0.087
KEGG SPLICEOSOME	114	genes.ES.table	0.35	1.5	0.13	0.25	0.97	0.6	0.42	0.35	0.16	0.027
KEGG NUCLEOTIDE EXCISION REPAIR	44	genes.ES.table	0.45	1.6	0.059	0.28	0.85	0.52	0.3	0.37	0.14	0.06
PID FANCONI PATHWAY	46	genes.ES.table	0.64	1.7	0.018	0.26	0.76	0.63	0.23	0.48	0.11	0.058
REACTOME TRANSLATION	146	genes.ES.table	0.54	1.9	0.041	0.87	0.33	0.73	0.35	0.48	0	0.17
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE	109	genes.ES.table	0.56	1.7	0.069	0.31	0.71	0.78	0.35	0.51	0.12	0.075
REACTOME MITOCHONDRIAL PROTEIN IMPORT	49	genes.ES.table	0.52	1.8	0.039	0.34	0.64	0.71	0.35	0.47	0.12	0.084
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S	57	genes.ES.table	0.57	1.7	0.057	0.33	0.7	0.74	0.31	0.51	0.12	0.08

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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	FAM153A	FAM153A	FAM153A	296	0.38	0.021	YES
2	RPSAP9	RPSAP9	RPSAP9	1115	0.23	-0.0026	YES
3	RPL9	RPL9	RPL9	1677	0.17	-0.018	YES
4	RPS26	RPS26	RPS26	1725	0.17	-0.0037	YES
5	RPL7	RPL7	RPL7	1751	0.16	0.011	YES
6	RPL36A	RPL36A	RPL36A	1800	0.16	0.024	YES
7	EIF4EBP1	EIF4EBP1	EIF4EBP1	1930	0.15	0.032	YES
8	RPSA	RPSA	RPSA	1975	0.15	0.044	YES
9	RPS17	RPS17	RPS17	2327	0.13	0.037	YES
10	RPL24	RPL24	RPL24	2336	0.13	0.05	YES
11	RPS27	RPS27	RPS27	2342	0.13	0.062	YES
12	RPL15	RPL15	RPL15	2568	0.12	0.061	YES
13	RPS5	RPS5	RPS5	2600	0.12	0.071	YES
14	RPS14	RPS14	RPS14	2637	0.12	0.08	YES
15	RPL32	RPL32	RPL32	2666	0.12	0.09	YES
16	RPL7A	RPL7A	RPL7A	2770	0.11	0.095	YES
17	RPS23	RPS23	RPS23	2791	0.11	0.1	YES
18	RPL41	RPL41	RPL41	2880	0.11	0.11	YES
19	RPS6	RPS6	RPS6	2885	0.11	0.12	YES
20	RPS3A	RPS3A	RPS3A	2945	0.1	0.13	YES
21	RPL18A	RPL18A	RPL18A	2949	0.1	0.14	YES
22	RPL17	RPL17	RPL17	3057	0.1	0.14	YES
23	RPL35A	RPL35A	RPL35A	3066	0.1	0.15	YES
24	RPL35	RPL35	RPL35	3075	0.1	0.16	YES
25	RPL14	RPL14	RPL14	3078	0.1	0.17	YES
26	RPS15	RPS15	RPS15	3084	0.1	0.18	YES
27	RPL6	RPL6	RPL6	3095	0.1	0.19	YES
28	RPL29	RPL29	RPL29	3150	0.098	0.2	YES
29	EIF4A2	EIF4A2	EIF4A2	3178	0.097	0.2	YES
30	SEC61G	SEC61G	SEC61G	3309	0.093	0.21	YES
31	RPL37	RPL37	RPL37	3390	0.091	0.21	YES
32	RPLP0	RPLP0	RPLP0	3439	0.09	0.22	YES
33	SPCS1	SPCS1	SPCS1	3495	0.088	0.22	YES
34	RPS16	RPS16	RPS16	3497	0.088	0.23	YES
35	EIF3K	EIF3K	EIF3K	3504	0.088	0.24	YES
36	RPL38	RPL38	RPL38	3522	0.087	0.25	YES
37	EIF3E	EIF3E	EIF3E	3570	0.086	0.25	YES
38	RPS29	RPS29	RPS29	3572	0.085	0.26	YES
39	UBA52	UBA52	UBA52	3677	0.083	0.26	YES
40	RPL8	RPL8	RPL8	3707	0.082	0.27	YES
41	EEF1B2	EEF1B2	EEF1B2	3716	0.082	0.28	YES
42	RPL18	RPL18	RPL18	3747	0.081	0.28	YES
43	EIF3G	EIF3G	EIF3G	3806	0.08	0.29	YES
44	RPL3	RPL3	RPL3	3819	0.08	0.3	YES
45	EEF2	EEF2	EEF2	3820	0.08	0.3	YES
46	RPS8	RPS8	RPS8	3844	0.079	0.31	YES
47	SRPRB	SRPRB	SRPRB	3872	0.078	0.32	YES
48	RPS10	RPS10	RPS10	3960	0.076	0.32	YES
49	RPS9	RPS9	RPS9	3971	0.076	0.33	YES
50	EIF4B	EIF4B	EIF4B	3995	0.076	0.33	YES
51	RPL28	RPL28	RPL28	4029	0.075	0.34	YES
52	EEF1G	EEF1G	EEF1G	4095	0.074	0.34	YES
53	RPS4Y1	RPS4Y1	RPS4Y1	4122	0.073	0.35	YES
54	RPL4	RPL4	RPL4	4127	0.073	0.35	YES
55	RPL39	RPL39	RPL39	4144	0.072	0.36	YES
56	RPL10	RPL10	RPL10	4189	0.072	0.36	YES
57	RPL5	RPL5	RPL5	4233	0.071	0.37	YES
58	RPS3	RPS3	RPS3	4244	0.07	0.38	YES
59	EIF3H	EIF3H	EIF3H	4308	0.069	0.38	YES
60	ETF1	ETF1	ETF1	4324	0.069	0.38	YES
61	EIF3D	EIF3D	EIF3D	4334	0.068	0.39	YES
62	PABPC1	PABPC1	PABPC1	4344	0.068	0.4	YES
63	RPS11	RPS11	RPS11	4361	0.068	0.4	YES
64	RPS25	RPS25	RPS25	4404	0.067	0.41	YES
65	RPL36	RPL36	RPL36	4410	0.067	0.41	YES
66	SEC61B	SEC61B	SEC61B	4430	0.067	0.42	YES
67	RPL34	RPL34	RPL34	4431	0.067	0.43	YES
68	RPL30	RPL30	RPL30	4433	0.067	0.43	YES
69	RPS18	RPS18	RPS18	4439	0.067	0.44	YES
70	RPL13A	RPL13A	RPL13A	4450	0.066	0.44	YES
71	EIF5	EIF5	EIF5	4451	0.066	0.45	YES
72	RPS4X	RPS4X	RPS4X	4468	0.066	0.46	YES
73	RPL22	RPL22	RPL22	4521	0.065	0.46	YES
74	RPL10A	RPL10A	RPL10A	4581	0.064	0.46	YES
75	RPS2	RPS2	RPS2	4614	0.063	0.47	YES
76	RPL26	RPL26	RPL26	4625	0.063	0.47	YES
77	RPL11	RPL11	RPL11	4651	0.063	0.48	YES
78	RPN1	RPN1	RPN1	4783	0.06	0.48	YES
79	SPCS3	SPCS3	SPCS3	4910	0.058	0.48	YES
80	EIF1AX	EIF1AX	EIF1AX	4914	0.058	0.48	YES
81	RPL26L1	RPL26L1	RPL26L1	5000	0.057	0.48	YES
82	RPL12	RPL12	RPL12	5003	0.057	0.49	YES
83	EIF2B5	EIF2B5	EIF2B5	5004	0.057	0.49	YES
84	RPS15A	RPS15A	RPS15A	5021	0.056	0.5	YES
85	SEC11A	SEC11A	SEC11A	5041	0.056	0.5	YES
86	RPS21	RPS21	RPS21	5098	0.055	0.5	YES
87	EIF2S1	EIF2S1	EIF2S1	5108	0.055	0.51	YES
88	RPLP1	RPLP1	RPLP1	5146	0.054	0.51	YES
89	RPL27	RPL27	RPL27	5166	0.054	0.52	YES
90	EIF4H	EIF4H	EIF4H	5209	0.053	0.52	YES
91	EIF3B	EIF3B	EIF3B	5228	0.053	0.52	YES
92	EIF2S3	EIF2S3	EIF2S3	5356	0.051	0.52	YES
93	SRP54	SRP54	SRP54	5421	0.05	0.52	YES
94	SEC11C	SEC11C	SEC11C	5527	0.048	0.52	YES
95	RPS13	RPS13	RPS13	5587	0.047	0.52	YES
96	RPS19	RPS19	RPS19	5593	0.047	0.53	YES
97	RPS20	RPS20	RPS20	5601	0.047	0.53	YES
98	RPL23	RPL23	RPL23	5675	0.046	0.53	YES
99	EIF2B3	EIF2B3	EIF2B3	5699	0.045	0.54	YES
100	SRP14	SRP14	SRP14	5872	0.043	0.53	YES
101	RPL37A	RPL37A	RPL37A	5882	0.042	0.53	YES
102	TRAM1	TRAM1	TRAM1	5945	0.042	0.54	YES
103	RPS24	RPS24	RPS24	5985	0.041	0.54	YES
104	EEF1D	EEF1D	EEF1D	6113	0.039	0.53	YES
105	SSR4	SSR4	SSR4	6116	0.039	0.54	YES
106	RPL31	RPL31	RPL31	6158	0.038	0.54	YES
107	FAU	FAU	FAU	6177	0.038	0.54	YES
108	EEF1A1	EEF1A1	EEF1A1	6320	0.036	0.54	NO
109	RPS12	RPS12	RPS12	6360	0.036	0.54	NO
110	RPS7	RPS7	RPS7	6372	0.035	0.54	NO
111	SEC61A1	SEC61A1	SEC61A1	6437	0.034	0.54	NO
112	RPN2	RPN2	RPN2	6512	0.033	0.54	NO
113	SRP68	SRP68	SRP68	6709	0.03	0.53	NO
114	RPL27A	RPL27A	RPL27A	6741	0.03	0.53	NO
115	RPL13	RPL13	RPL13	6809	0.029	0.53	NO
116	RPS27A	RPS27A	RPS27A	6817	0.029	0.54	NO
117	SRP19	SRP19	SRP19	6857	0.029	0.54	NO
118	RPLP2	RPLP2	RPLP2	7042	0.026	0.53	NO
119	DDOST	DDOST	DDOST	7090	0.025	0.53	NO
120	EIF3J	EIF3J	EIF3J	7255	0.023	0.52	NO
121	EIF3I	EIF3I	EIF3I	7331	0.022	0.52	NO
122	RPL23A	RPL23A	RPL23A	7349	0.022	0.52	NO
123	SRP9	SRP9	SRP9	7359	0.022	0.52	NO
124	EIF3F	EIF3F	EIF3F	7628	0.018	0.51	NO
125	RPL19	RPL19	RPL19	7648	0.018	0.51	NO
126	SRP72	SRP72	SRP72	7680	0.018	0.51	NO
127	LOC653566	LOC653566	LOC653566	7778	0.016	0.5	NO
128	SPCS2	SPCS2	SPCS2	7899	0.014	0.5	NO
129	EIF4E	EIF4E	EIF4E	8157	0.011	0.49	NO
130	SSR2	SSR2	SSR2	8393	0.0077	0.47	NO
131	EIF2S2	EIF2S2	EIF2S2	8475	0.0067	0.47	NO
132	EIF2B1	EIF2B1	EIF2B1	8626	0.0046	0.46	NO
133	SSR3	SSR3	SSR3	8693	0.0037	0.46	NO
134	EIF4G1	EIF4G1	EIF4G1	8749	0.003	0.46	NO
135	EIF2B2	EIF2B2	EIF2B2	9421	-0.0068	0.42	NO
136	EIF3A	EIF3A	EIF3A	10022	-0.016	0.39	NO
137	SRPR	SRPR	SRPR	10807	-0.028	0.34	NO
138	RPL21	RPL21	RPL21	11119	-0.033	0.33	NO
139	GSPT2	GSPT2	GSPT2	11167	-0.034	0.33	NO
140	SSR1	SSR1	SSR1	11189	-0.035	0.33	NO
141	EIF3C	EIF3C	EIF3C	11377	-0.038	0.33	NO
142	EIF4A1	EIF4A1	EIF4A1	11387	-0.038	0.33	NO
143	EIF5B	EIF5B	EIF5B	12085	-0.052	0.3	NO
144	EIF2B4	EIF2B4	EIF2B4	12217	-0.055	0.29	NO
145	SEC61A2	SEC61A2	SEC61A2	13952	-0.1	0.2	NO
146	RPS28	RPS28	RPS28	14788	-0.14	0.17	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 CITRATE CYCLE TCA CYCLE.

Figure S82. 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 RNA DEGRADATION

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	GTF2H2B	GTF2H2B	GTF2H2B	1048	0.24	0.087	YES
2	GTF2H2	GTF2H2	GTF2H2	1085	0.23	0.23	YES
3	POLR2I	POLR2I	POLR2I	3605	0.085	0.14	YES
4	NCBP1	NCBP1	NCBP1	3885	0.078	0.17	YES
5	ERCC2	ERCC2	ERCC2	4646	0.063	0.17	YES
6	MNAT1	MNAT1	MNAT1	4659	0.063	0.2	YES
7	POLR2K	POLR2K	POLR2K	4749	0.061	0.24	YES
8	GTF2H3	GTF2H3	GTF2H3	4983	0.057	0.26	YES
9	POLR2L	POLR2L	POLR2L	5026	0.056	0.29	YES
10	POLR2F	POLR2F	POLR2F	5103	0.055	0.32	YES
11	POLR2E	POLR2E	POLR2E	5297	0.052	0.34	YES
12	GTF2F1	GTF2F1	GTF2F1	5417	0.05	0.37	YES
13	POLR2J	POLR2J	POLR2J	5621	0.047	0.38	YES
14	CDK7	CDK7	CDK7	5742	0.044	0.41	YES
15	POLR2H	POLR2H	POLR2H	5774	0.044	0.43	YES
16	RNGTT	RNGTT	RNGTT	5839	0.043	0.45	YES
17	POLR2B	POLR2B	POLR2B	6052	0.04	0.47	YES
18	SUPT5H	SUPT5H	SUPT5H	6252	0.037	0.48	YES
19	NCBP2	NCBP2	NCBP2	7028	0.026	0.45	NO
20	POLR2C	POLR2C	POLR2C	7355	0.022	0.45	NO
21	CCNH	CCNH	CCNH	7584	0.019	0.44	NO
22	RNMT	RNMT	RNMT	8199	0.01	0.42	NO
23	POLR2G	POLR2G	POLR2G	8620	0.0047	0.4	NO
24	GTF2F2	GTF2F2	GTF2F2	9458	-0.0074	0.35	NO
25	ERCC3	ERCC3	ERCC3	9516	-0.0082	0.36	NO
26	POLR2A	POLR2A	POLR2A	10858	-0.029	0.3	NO
27	POLR2D	POLR2D	POLR2D	11662	-0.043	0.28	NO
28	GTF2H1	GTF2H1	GTF2H1	11807	-0.046	0.3	NO
29	GTF2H4	GTF2H4	GTF2H4	12481	-0.061	0.3	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 RNA DEGRADATION.

Figure S84. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA 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 DNA REPLICATION

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	FAM153A	FAM153A	FAM153A	296	0.38	0.024	YES
2	RPSAP9	RPSAP9	RPSAP9	1115	0.23	0.0023	YES
3	NUP155	NUP155	NUP155	1373	0.2	0.0091	YES
4	RPL9	RPL9	RPL9	1677	0.17	0.01	YES
5	NUP210	NUP210	NUP210	1697	0.17	0.027	YES
6	RPS26	RPS26	RPS26	1725	0.17	0.043	YES
7	RPL7	RPL7	RPL7	1751	0.16	0.06	YES
8	RPL36A	RPL36A	RPL36A	1800	0.16	0.074	YES
9	RPSA	RPSA	RPSA	1975	0.15	0.08	YES
10	RPS17	RPS17	RPS17	2327	0.13	0.074	YES
11	RPL24	RPL24	RPL24	2336	0.13	0.087	YES
12	RPS27	RPS27	RPS27	2342	0.13	0.1	YES
13	RPL15	RPL15	RPL15	2568	0.12	0.1	YES
14	RPS5	RPS5	RPS5	2600	0.12	0.11	YES
15	RPS14	RPS14	RPS14	2637	0.12	0.12	YES
16	RPL32	RPL32	RPL32	2666	0.12	0.13	YES
17	RPL7A	RPL7A	RPL7A	2770	0.11	0.14	YES
18	RPS23	RPS23	RPS23	2791	0.11	0.15	YES
19	RPL41	RPL41	RPL41	2880	0.11	0.16	YES
20	RPS6	RPS6	RPS6	2885	0.11	0.17	YES
21	RPS3A	RPS3A	RPS3A	2945	0.1	0.18	YES
22	RPL18A	RPL18A	RPL18A	2949	0.1	0.19	YES
23	RPL17	RPL17	RPL17	3057	0.1	0.19	YES
24	RPL35A	RPL35A	RPL35A	3066	0.1	0.2	YES
25	RPL35	RPL35	RPL35	3075	0.1	0.21	YES
26	RPL14	RPL14	RPL14	3078	0.1	0.22	YES
27	RPS15	RPS15	RPS15	3084	0.1	0.23	YES
28	RPL6	RPL6	RPL6	3095	0.1	0.24	YES
29	RPL29	RPL29	RPL29	3150	0.098	0.25	YES
30	RPL37	RPL37	RPL37	3390	0.091	0.25	YES
31	RPLP0	RPLP0	RPLP0	3439	0.09	0.25	YES
32	RPS16	RPS16	RPS16	3497	0.088	0.26	YES
33	RPL38	RPL38	RPL38	3522	0.087	0.27	YES
34	RPS29	RPS29	RPS29	3572	0.085	0.27	YES
35	NUP205	NUP205	NUP205	3603	0.085	0.28	YES
36	POLR2I	POLR2I	POLR2I	3605	0.085	0.29	YES
37	CANX	CANX	CANX	3606	0.085	0.3	YES
38	NUP37	NUP37	NUP37	3623	0.084	0.31	YES
39	UBA52	UBA52	UBA52	3677	0.083	0.31	YES
40	RPL8	RPL8	RPL8	3707	0.082	0.32	YES
41	NUP107	NUP107	NUP107	3743	0.081	0.33	YES
42	RPL18	RPL18	RPL18	3747	0.081	0.34	YES
43	RPL3	RPL3	RPL3	3819	0.08	0.34	YES
44	RPS8	RPS8	RPS8	3844	0.079	0.35	YES
45	AAAS	AAAS	AAAS	3877	0.078	0.35	YES
46	RPS10	RPS10	RPS10	3960	0.076	0.36	YES
47	RPS9	RPS9	RPS9	3971	0.076	0.36	YES
48	RPL28	RPL28	RPL28	4029	0.075	0.37	YES
49	RPS4Y1	RPS4Y1	RPS4Y1	4122	0.073	0.37	YES
50	RPL4	RPL4	RPL4	4127	0.073	0.38	YES
51	RPL39	RPL39	RPL39	4144	0.072	0.39	YES
52	RPL10	RPL10	RPL10	4189	0.072	0.39	YES
53	RPL5	RPL5	RPL5	4233	0.071	0.4	YES
54	RPS3	RPS3	RPS3	4244	0.07	0.4	YES
55	RPS11	RPS11	RPS11	4361	0.068	0.4	YES
56	RPS25	RPS25	RPS25	4404	0.067	0.41	YES
57	RPL36	RPL36	RPL36	4410	0.067	0.42	YES
58	RPL34	RPL34	RPL34	4431	0.067	0.42	YES
59	RPL30	RPL30	RPL30	4433	0.067	0.43	YES
60	RPS18	RPS18	RPS18	4439	0.067	0.44	YES
61	RPL13A	RPL13A	RPL13A	4450	0.066	0.44	YES
62	RPS4X	RPS4X	RPS4X	4468	0.066	0.45	YES
63	NUP35	NUP35	NUP35	4478	0.066	0.46	YES
64	CLTA	CLTA	CLTA	4509	0.065	0.46	YES
65	RPL22	RPL22	RPL22	4521	0.065	0.47	YES
66	RPL10A	RPL10A	RPL10A	4581	0.064	0.47	YES
67	RPS2	RPS2	RPS2	4614	0.063	0.48	YES
68	RPL26	RPL26	RPL26	4625	0.063	0.48	YES
69	RPL11	RPL11	RPL11	4651	0.063	0.49	YES
70	POLR2K	POLR2K	POLR2K	4749	0.061	0.49	YES
71	POM121	POM121	POM121	4973	0.057	0.48	YES
72	RPL26L1	RPL26L1	RPL26L1	5000	0.057	0.49	YES
73	RPL12	RPL12	RPL12	5003	0.057	0.49	YES
74	RPS15A	RPS15A	RPS15A	5021	0.056	0.5	YES
75	POLR2L	POLR2L	POLR2L	5026	0.056	0.5	YES
76	RPS21	RPS21	RPS21	5098	0.055	0.5	YES
77	POLR2F	POLR2F	POLR2F	5103	0.055	0.51	YES
78	RPLP1	RPLP1	RPLP1	5146	0.054	0.51	YES
79	RPL27	RPL27	RPL27	5166	0.054	0.52	YES
80	POLR2E	POLR2E	POLR2E	5297	0.052	0.52	YES
81	GTF2F1	GTF2F1	GTF2F1	5417	0.05	0.52	YES
82	RPS13	RPS13	RPS13	5587	0.047	0.51	YES
83	RPS19	RPS19	RPS19	5593	0.047	0.52	YES
84	RPS20	RPS20	RPS20	5601	0.047	0.52	YES
85	POLR2J	POLR2J	POLR2J	5621	0.047	0.52	YES
86	RPL23	RPL23	RPL23	5675	0.046	0.53	YES
87	POLR2H	POLR2H	POLR2H	5774	0.044	0.52	YES
88	IPO5	IPO5	IPO5	5781	0.044	0.53	YES
89	HSP90AA1	HSP90AA1	HSP90AA1	5827	0.043	0.53	YES
90	RPL37A	RPL37A	RPL37A	5882	0.042	0.53	YES
91	RPS24	RPS24	RPS24	5985	0.041	0.53	YES
92	POLR2B	POLR2B	POLR2B	6052	0.04	0.53	YES
93	RPL31	RPL31	RPL31	6158	0.038	0.53	YES
94	NUP54	NUP54	NUP54	6163	0.038	0.53	YES
95	FAU	FAU	FAU	6177	0.038	0.54	YES
96	RAE1	RAE1	RAE1	6272	0.037	0.54	YES
97	NUP214	NUP214	NUP214	6348	0.036	0.54	YES
98	RPS12	RPS12	RPS12	6360	0.036	0.54	YES
99	RPS7	RPS7	RPS7	6372	0.035	0.54	YES
100	XPO1	XPO1	XPO1	6438	0.034	0.54	NO
101	NUP133	NUP133	NUP133	6586	0.032	0.54	NO
102	NUPL2	NUPL2	NUPL2	6591	0.032	0.54	NO
103	GRSF1	GRSF1	GRSF1	6658	0.031	0.54	NO
104	RPL27A	RPL27A	RPL27A	6741	0.03	0.54	NO
105	RPL13	RPL13	RPL13	6809	0.029	0.54	NO
106	RPS27A	RPS27A	RPS27A	6817	0.029	0.54	NO
107	RPLP2	RPLP2	RPLP2	7042	0.026	0.53	NO
108	NUP62	NUP62	NUP62	7167	0.024	0.53	NO
109	RPL23A	RPL23A	RPL23A	7349	0.022	0.52	NO
110	POLR2C	POLR2C	POLR2C	7355	0.022	0.52	NO
111	TPR	TPR	TPR	7544	0.019	0.51	NO
112	RPL19	RPL19	RPL19	7648	0.018	0.51	NO
113	RAN	RAN	RAN	7723	0.017	0.51	NO
114	NUP188	NUP188	NUP188	7785	0.016	0.5	NO
115	CALR	CALR	CALR	7895	0.014	0.5	NO
116	POLR2G	POLR2G	POLR2G	8620	0.0047	0.46	NO
117	KPNA1	KPNA1	KPNA1	8666	0.0041	0.46	NO
118	DNAJC3	DNAJC3	DNAJC3	8874	0.0011	0.44	NO
119	NUP85	NUP85	NUP85	9040	-0.0014	0.44	NO
120	SEH1L	SEH1L	SEH1L	9202	-0.0037	0.43	NO
121	RANBP2	RANBP2	RANBP2	9220	-0.004	0.43	NO
122	GTF2F2	GTF2F2	GTF2F2	9458	-0.0074	0.41	NO
123	NUPL1	NUPL1	NUPL1	9477	-0.0077	0.41	NO
124	KPNB1	KPNB1	KPNB1	10197	-0.018	0.38	NO
125	NUP50	NUP50	NUP50	10381	-0.021	0.37	NO
126	CLTC	CLTC	CLTC	10463	-0.023	0.36	NO
127	NUP93	NUP93	NUP93	10715	-0.027	0.35	NO
128	POLR2A	POLR2A	POLR2A	10858	-0.029	0.35	NO
129	NUP43	NUP43	NUP43	10877	-0.029	0.35	NO
130	NUP153	NUP153	NUP153	11036	-0.032	0.34	NO
131	RPL21	RPL21	RPL21	11119	-0.033	0.34	NO
132	POLR2D	POLR2D	POLR2D	11662	-0.043	0.32	NO
133	NUP88	NUP88	NUP88	12612	-0.065	0.27	NO
134	HSPA1B	HSPA1B	HSPA1B	13008	-0.074	0.26	NO
135	RPS28	RPS28	RPS28	14788	-0.14	0.17	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 DNA REPLICATION.

Figure S86. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DNA REPLICATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG SPLICEOSOME

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	GTF2H2B	GTF2H2B	GTF2H2B	1048	0.24	0.043	YES
2	GTF2H2	GTF2H2	GTF2H2	1085	0.23	0.14	YES
3	CCNT1	CCNT1	CCNT1	1694	0.17	0.18	YES
4	POLR2I	POLR2I	POLR2I	3605	0.085	0.11	YES
5	NCBP1	NCBP1	NCBP1	3885	0.078	0.13	YES
6	TCEB1	TCEB1	TCEB1	4290	0.069	0.14	YES
7	ERCC2	ERCC2	ERCC2	4646	0.063	0.14	YES
8	MNAT1	MNAT1	MNAT1	4659	0.063	0.17	YES
9	SUPT16H	SUPT16H	SUPT16H	4669	0.062	0.2	YES
10	POLR2K	POLR2K	POLR2K	4749	0.061	0.22	YES
11	GTF2H3	GTF2H3	GTF2H3	4983	0.057	0.23	YES
12	POLR2L	POLR2L	POLR2L	5026	0.056	0.25	YES
13	SSRP1	SSRP1	SSRP1	5089	0.055	0.27	YES
14	POLR2F	POLR2F	POLR2F	5103	0.055	0.3	YES
15	POLR2E	POLR2E	POLR2E	5297	0.052	0.31	YES
16	GTF2F1	GTF2F1	GTF2F1	5417	0.05	0.32	YES
17	POLR2J	POLR2J	POLR2J	5621	0.047	0.33	YES
18	CDK7	CDK7	CDK7	5742	0.044	0.34	YES
19	POLR2H	POLR2H	POLR2H	5774	0.044	0.36	YES
20	TCEB2	TCEB2	TCEB2	5907	0.042	0.37	YES
21	COBRA1	COBRA1	COBRA1	6043	0.04	0.38	YES
22	POLR2B	POLR2B	POLR2B	6052	0.04	0.4	YES
23	SUPT5H	SUPT5H	SUPT5H	6252	0.037	0.4	YES
24	TCEA1	TCEA1	TCEA1	6355	0.036	0.41	YES
25	NCBP2	NCBP2	NCBP2	7028	0.026	0.39	NO
26	POLR2C	POLR2C	POLR2C	7355	0.022	0.38	NO
27	SUPT4H1	SUPT4H1	SUPT4H1	7357	0.022	0.39	NO
28	CCNH	CCNH	CCNH	7584	0.019	0.38	NO
29	ELL	ELL	ELL	8531	0.0058	0.33	NO
30	POLR2G	POLR2G	POLR2G	8620	0.0047	0.33	NO
31	GTF2F2	GTF2F2	GTF2F2	9458	-0.0074	0.28	NO
32	ERCC3	ERCC3	ERCC3	9516	-0.0082	0.28	NO
33	CCNT2	CCNT2	CCNT2	10134	-0.017	0.26	NO
34	WHSC2	WHSC2	WHSC2	10323	-0.02	0.26	NO
35	TH1L	TH1L	TH1L	10328	-0.02	0.26	NO
36	RDBP	RDBP	RDBP	10443	-0.022	0.27	NO
37	CDK9	CDK9	CDK9	10700	-0.026	0.26	NO
38	POLR2A	POLR2A	POLR2A	10858	-0.029	0.27	NO
39	POLR2D	POLR2D	POLR2D	11662	-0.043	0.24	NO
40	GTF2H1	GTF2H1	GTF2H1	11807	-0.046	0.25	NO
41	GTF2H4	GTF2H4	GTF2H4	12481	-0.061	0.24	NO
42	TCEB3	TCEB3	TCEB3	12698	-0.067	0.26	NO
43	CTDP1	CTDP1	CTDP1	12744	-0.068	0.29	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 SPLICEOSOME.

Figure S88. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPLICEOSOME, 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 NUCLEOTIDE EXCISION REPAIR

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	FAM153A	FAM153A	FAM153A	296	0.38	0.033	YES
2	RPSAP9	RPSAP9	RPSAP9	1115	0.23	0.016	YES
3	RPL9	RPL9	RPL9	1677	0.17	0.0069	YES
4	RPS26	RPS26	RPS26	1725	0.17	0.026	YES
5	RPL7	RPL7	RPL7	1751	0.16	0.046	YES
6	RPL36A	RPL36A	RPL36A	1800	0.16	0.064	YES
7	RPSA	RPSA	RPSA	1975	0.15	0.074	YES
8	RPS17	RPS17	RPS17	2327	0.13	0.071	YES
9	RPL24	RPL24	RPL24	2336	0.13	0.087	YES
10	RPS27	RPS27	RPS27	2342	0.13	0.1	YES
11	RPL15	RPL15	RPL15	2568	0.12	0.11	YES
12	RPS5	RPS5	RPS5	2600	0.12	0.12	YES
13	RPS14	RPS14	RPS14	2637	0.12	0.13	YES
14	RPL32	RPL32	RPL32	2666	0.12	0.15	YES
15	RPL7A	RPL7A	RPL7A	2770	0.11	0.16	YES
16	RPS23	RPS23	RPS23	2791	0.11	0.17	YES
17	RPL41	RPL41	RPL41	2880	0.11	0.18	YES
18	RPS6	RPS6	RPS6	2885	0.11	0.19	YES
19	RPS3A	RPS3A	RPS3A	2945	0.1	0.2	YES
20	RPL18A	RPL18A	RPL18A	2949	0.1	0.21	YES
21	RPL17	RPL17	RPL17	3057	0.1	0.22	YES
22	RPL35A	RPL35A	RPL35A	3066	0.1	0.23	YES
23	RPL35	RPL35	RPL35	3075	0.1	0.25	YES
24	RPL14	RPL14	RPL14	3078	0.1	0.26	YES
25	RPS15	RPS15	RPS15	3084	0.1	0.27	YES
26	RPL6	RPL6	RPL6	3095	0.1	0.28	YES
27	RPL29	RPL29	RPL29	3150	0.098	0.29	YES
28	RPL37	RPL37	RPL37	3390	0.091	0.29	YES
29	RPLP0	RPLP0	RPLP0	3439	0.09	0.3	YES
30	RPS16	RPS16	RPS16	3497	0.088	0.31	YES
31	RPL38	RPL38	RPL38	3522	0.087	0.32	YES
32	RPS29	RPS29	RPS29	3572	0.085	0.33	YES
33	PPP2R2A	PPP2R2A	PPP2R2A	3593	0.085	0.34	YES
34	UBA52	UBA52	UBA52	3677	0.083	0.34	YES
35	RPL8	RPL8	RPL8	3707	0.082	0.35	YES
36	RPL18	RPL18	RPL18	3747	0.081	0.36	YES
37	RPL3	RPL3	RPL3	3819	0.08	0.37	YES
38	RPS8	RPS8	RPS8	3844	0.079	0.38	YES
39	NCBP1	NCBP1	NCBP1	3885	0.078	0.38	YES
40	RPS10	RPS10	RPS10	3960	0.076	0.39	YES
41	RPS9	RPS9	RPS9	3971	0.076	0.4	YES
42	RPL28	RPL28	RPL28	4029	0.075	0.41	YES
43	RPS4Y1	RPS4Y1	RPS4Y1	4122	0.073	0.41	YES
44	RPL4	RPL4	RPL4	4127	0.073	0.42	YES
45	RPL39	RPL39	RPL39	4144	0.072	0.43	YES
46	RPL10	RPL10	RPL10	4189	0.072	0.44	YES
47	RPL5	RPL5	RPL5	4233	0.071	0.44	YES
48	RPS3	RPS3	RPS3	4244	0.07	0.45	YES
49	ETF1	ETF1	ETF1	4324	0.069	0.46	YES
50	PABPC1	PABPC1	PABPC1	4344	0.068	0.46	YES
51	RPS11	RPS11	RPS11	4361	0.068	0.47	YES
52	RPS25	RPS25	RPS25	4404	0.067	0.48	YES
53	RPL36	RPL36	RPL36	4410	0.067	0.48	YES
54	RPL34	RPL34	RPL34	4431	0.067	0.49	YES
55	RPL30	RPL30	RPL30	4433	0.067	0.5	YES
56	RPS18	RPS18	RPS18	4439	0.067	0.51	YES
57	RPL13A	RPL13A	RPL13A	4450	0.066	0.52	YES
58	RPS4X	RPS4X	RPS4X	4468	0.066	0.52	YES
59	RPL22	RPL22	RPL22	4521	0.065	0.53	YES
60	RPL10A	RPL10A	RPL10A	4581	0.064	0.54	YES
61	RPS2	RPS2	RPS2	4614	0.063	0.54	YES
62	RPL26	RPL26	RPL26	4625	0.063	0.55	YES
63	RPL11	RPL11	RPL11	4651	0.063	0.56	YES
64	RPL26L1	RPL26L1	RPL26L1	5000	0.057	0.55	YES
65	RPL12	RPL12	RPL12	5003	0.057	0.55	YES
66	RPS15A	RPS15A	RPS15A	5021	0.056	0.56	YES
67	RPS21	RPS21	RPS21	5098	0.055	0.56	YES
68	UPF3B	UPF3B	UPF3B	5132	0.055	0.57	YES
69	RPLP1	RPLP1	RPLP1	5146	0.054	0.57	YES
70	RPL27	RPL27	RPL27	5166	0.054	0.58	YES
71	RPS13	RPS13	RPS13	5587	0.047	0.56	NO
72	RPS19	RPS19	RPS19	5593	0.047	0.57	NO
73	RPS20	RPS20	RPS20	5601	0.047	0.57	NO
74	RPL23	RPL23	RPL23	5675	0.046	0.57	NO
75	PPP2CA	PPP2CA	PPP2CA	5881	0.042	0.57	NO
76	RPL37A	RPL37A	RPL37A	5882	0.042	0.57	NO
77	RPS24	RPS24	RPS24	5985	0.041	0.57	NO
78	RPL31	RPL31	RPL31	6158	0.038	0.57	NO
79	FAU	FAU	FAU	6177	0.038	0.57	NO
80	RPS12	RPS12	RPS12	6360	0.036	0.57	NO
81	RPS7	RPS7	RPS7	6372	0.035	0.57	NO
82	RPL27A	RPL27A	RPL27A	6741	0.03	0.55	NO
83	RPL13	RPL13	RPL13	6809	0.029	0.55	NO
84	RPS27A	RPS27A	RPS27A	6817	0.029	0.56	NO
85	SMG7	SMG7	SMG7	6882	0.028	0.56	NO
86	NCBP2	NCBP2	NCBP2	7028	0.026	0.55	NO
87	RPLP2	RPLP2	RPLP2	7042	0.026	0.56	NO
88	RPL23A	RPL23A	RPL23A	7349	0.022	0.54	NO
89	RNPS1	RNPS1	RNPS1	7386	0.021	0.54	NO
90	SMG5	SMG5	SMG5	7421	0.021	0.54	NO
91	EIF4A3	EIF4A3	EIF4A3	7460	0.021	0.54	NO
92	RPL19	RPL19	RPL19	7648	0.018	0.54	NO
93	EIF4G1	EIF4G1	EIF4G1	8749	0.003	0.47	NO
94	SMG1	SMG1	SMG1	8822	0.0019	0.47	NO
95	MAGOH	MAGOH	MAGOH	8832	0.0018	0.47	NO
96	RBM8A	RBM8A	RBM8A	8866	0.0012	0.47	NO
97	UPF3A	UPF3A	UPF3A	9649	-0.01	0.42	NO
98	SMG6	SMG6	SMG6	9951	-0.015	0.41	NO
99	PPP2R1A	PPP2R1A	PPP2R1A	9980	-0.015	0.41	NO
100	CASC3	CASC3	CASC3	10271	-0.02	0.4	NO
101	UPF2	UPF2	UPF2	10380	-0.021	0.39	NO
102	RPL21	RPL21	RPL21	11119	-0.033	0.36	NO
103	GSPT2	GSPT2	GSPT2	11167	-0.034	0.36	NO
104	RPS28	RPS28	RPS28	14788	-0.14	0.17	NO

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

Figure S90. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG 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: PID FANCONI 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	POLE2	POLE2	POLE2	1042	0.24	0.007	YES
2	PRIM1	PRIM1	PRIM1	1165	0.22	0.061	YES
3	MCM2	MCM2	MCM2	1240	0.21	0.12	YES
4	RFC4	RFC4	RFC4	1427	0.19	0.16	YES
5	RNASEH2A	RNASEH2A	RNASEH2A	1507	0.18	0.21	YES
6	FEN1	FEN1	FEN1	2015	0.15	0.22	YES
7	LIG1	LIG1	LIG1	2101	0.14	0.25	YES
8	POLA1	POLA1	POLA1	2145	0.14	0.29	YES
9	RPA3	RPA3	RPA3	2165	0.14	0.32	YES
10	MCM4	MCM4	MCM4	2220	0.13	0.36	YES
11	RFC5	RFC5	RFC5	2341	0.13	0.39	YES
12	POLE3	POLE3	POLE3	2456	0.12	0.42	YES
13	POLD2	POLD2	POLD2	2559	0.12	0.44	YES
14	MCM7	MCM7	MCM7	2592	0.12	0.47	YES
15	POLA2	POLA2	POLA2	2650	0.12	0.5	YES
16	POLD1	POLD1	POLD1	2658	0.12	0.54	YES
17	PRIM2	PRIM2	PRIM2	2776	0.11	0.56	YES
18	RFC1	RFC1	RFC1	2886	0.11	0.58	YES
19	RFC2	RFC2	RFC2	3360	0.092	0.58	YES
20	POLE4	POLE4	POLE4	3420	0.09	0.6	YES
21	RNASEH2C	RNASEH2C	RNASEH2C	3713	0.082	0.61	YES
22	SSBP1	SSBP1	SSBP1	3917	0.077	0.62	YES
23	RFC3	RFC3	RFC3	4175	0.072	0.62	YES
24	MCM6	MCM6	MCM6	4187	0.072	0.64	YES
25	PCNA	PCNA	PCNA	4546	0.065	0.64	NO
26	MCM5	MCM5	MCM5	5629	0.047	0.59	NO
27	RPA1	RPA1	RPA1	6739	0.03	0.54	NO
28	POLD3	POLD3	POLD3	6947	0.028	0.54	NO
29	MCM3	MCM3	MCM3	7012	0.026	0.54	NO
30	POLE	POLE	POLE	7690	0.017	0.51	NO
31	RPA2	RPA2	RPA2	7759	0.016	0.51	NO
32	RNASEH1	RNASEH1	RNASEH1	8032	0.012	0.5	NO
33	DNA2	DNA2	DNA2	8038	0.012	0.5	NO
34	RPA4	RPA4	RPA4	10611	-0.025	0.36	NO
35	RNASEH2B	RNASEH2B	RNASEH2B	10999	-0.031	0.35	NO
36	POLD4	POLD4	POLD4	14539	-0.13	0.18	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 FANCONI PATHWAY.

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

genes ES table in pathway: REACTOME TRANSLATION

Table 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	TIMM10	TIMM10	TIMM10	1983	0.15	-0.062	YES
2	CHCHD4	CHCHD4	CHCHD4	2352	0.13	-0.04	YES
3	GRPEL2	GRPEL2	GRPEL2	2433	0.12	-0.0029	YES
4	HSPA9	HSPA9	HSPA9	2491	0.12	0.035	YES
5	TOMM7	TOMM7	TOMM7	2741	0.11	0.058	YES
6	COX17	COX17	COX17	2973	0.1	0.08	YES
7	SLC25A4	SLC25A4	SLC25A4	2998	0.1	0.11	YES
8	COQ2	COQ2	COQ2	3272	0.094	0.13	YES
9	PMPCB	PMPCB	PMPCB	3274	0.094	0.16	YES
10	DNAJC19	DNAJC19	DNAJC19	3400	0.091	0.18	YES
11	TOMM20	TOMM20	TOMM20	3624	0.084	0.2	YES
12	HSCB	HSCB	HSCB	3694	0.082	0.22	YES
13	TIMM8A	TIMM8A	TIMM8A	3712	0.082	0.25	YES
14	VDAC1	VDAC1	VDAC1	3777	0.081	0.27	YES
15	GRPEL1	GRPEL1	GRPEL1	4058	0.074	0.28	YES
16	SAMM50	SAMM50	SAMM50	4138	0.073	0.3	YES
17	TOMM70A	TOMM70A	TOMM70A	4190	0.072	0.32	YES
18	TOMM5	TOMM5	TOMM5	4212	0.071	0.34	YES
19	TIMM9	TIMM9	TIMM9	4214	0.071	0.37	YES
20	TIMM17B	TIMM17B	TIMM17B	4675	0.062	0.36	YES
21	TIMM50	TIMM50	TIMM50	4709	0.062	0.38	YES
22	ATP5G1	ATP5G1	ATP5G1	4780	0.06	0.4	YES
23	HSPD1	HSPD1	HSPD1	4906	0.058	0.41	YES
24	TOMM40	TOMM40	TOMM40	4932	0.058	0.43	YES
25	PMPCA	PMPCA	PMPCA	5280	0.052	0.43	YES
26	CYC1	CYC1	CYC1	5285	0.052	0.44	YES
27	C18orf55	C18orf55	C18orf55	5287	0.052	0.46	YES
28	ATP5B	ATP5B	ATP5B	5563	0.048	0.46	YES
29	CS	CS	CS	5663	0.046	0.47	YES
30	TOMM22	TOMM22	TOMM22	5764	0.044	0.48	YES
31	TIMM13	TIMM13	TIMM13	5995	0.041	0.48	YES
32	SLC25A12	SLC25A12	SLC25A12	6053	0.04	0.49	YES
33	ACO2	ACO2	ACO2	6071	0.039	0.5	YES
34	FXC1	FXC1	FXC1	6099	0.039	0.51	YES
35	FXN	FXN	FXN	6202	0.038	0.52	YES
36	ATP5A1	ATP5A1	ATP5A1	6903	0.028	0.49	NO
37	TIMM17A	TIMM17A	TIMM17A	7044	0.026	0.49	NO
38	SLC25A6	SLC25A6	SLC25A6	7985	0.013	0.44	NO
39	TIMM44	TIMM44	TIMM44	8384	0.0077	0.42	NO
40	GFER	GFER	GFER	8497	0.0064	0.42	NO
41	MTX2	MTX2	MTX2	9427	-0.0069	0.37	NO
42	SLC25A13	SLC25A13	SLC25A13	9521	-0.0083	0.37	NO
43	TIMM8B	TIMM8B	TIMM8B	10050	-0.016	0.34	NO
44	TAZ	TAZ	TAZ	10292	-0.02	0.34	NO
45	IDH3G	IDH3G	IDH3G	10820	-0.028	0.32	NO
46	MTX1	MTX1	MTX1	11861	-0.047	0.27	NO
47	LDHD	LDHD	LDHD	12482	-0.061	0.26	NO
48	TIMM22	TIMM22	TIMM22	12508	-0.062	0.28	NO
49	BCS1L	BCS1L	BCS1L	12717	-0.067	0.29	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: REACTOME TRANSLATION.

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

genes ES table in pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE

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	FAM153A	FAM153A	FAM153A	296	0.38	0.03	YES
2	RPSAP9	RPSAP9	RPSAP9	1115	0.23	0.012	YES
3	RPL9	RPL9	RPL9	1677	0.17	0.0014	YES
4	RPS26	RPS26	RPS26	1725	0.17	0.019	YES
5	RPL7	RPL7	RPL7	1751	0.16	0.038	YES
6	RPL36A	RPL36A	RPL36A	1800	0.16	0.055	YES
7	RPSA	RPSA	RPSA	1975	0.15	0.064	YES
8	RPS17	RPS17	RPS17	2327	0.13	0.06	YES
9	RPL24	RPL24	RPL24	2336	0.13	0.075	YES
10	RPS27	RPS27	RPS27	2342	0.13	0.091	YES
11	RPL15	RPL15	RPL15	2568	0.12	0.093	YES
12	RPS5	RPS5	RPS5	2600	0.12	0.1	YES
13	RPS14	RPS14	RPS14	2637	0.12	0.12	YES
14	RPL32	RPL32	RPL32	2666	0.12	0.13	YES
15	RPL7A	RPL7A	RPL7A	2770	0.11	0.14	YES
16	RPS23	RPS23	RPS23	2791	0.11	0.15	YES
17	RPL41	RPL41	RPL41	2880	0.11	0.16	YES
18	RPS6	RPS6	RPS6	2885	0.11	0.17	YES
19	RPS3A	RPS3A	RPS3A	2945	0.1	0.18	YES
20	RPL18A	RPL18A	RPL18A	2949	0.1	0.19	YES
21	RPL17	RPL17	RPL17	3057	0.1	0.2	YES
22	RPL35A	RPL35A	RPL35A	3066	0.1	0.21	YES
23	RPL35	RPL35	RPL35	3075	0.1	0.22	YES
24	RPL14	RPL14	RPL14	3078	0.1	0.24	YES
25	RPS15	RPS15	RPS15	3084	0.1	0.25	YES
26	RPL6	RPL6	RPL6	3095	0.1	0.26	YES
27	RPL29	RPL29	RPL29	3150	0.098	0.27	YES
28	EIF4A2	EIF4A2	EIF4A2	3178	0.097	0.28	YES
29	RPL37	RPL37	RPL37	3390	0.091	0.28	YES
30	RPLP0	RPLP0	RPLP0	3439	0.09	0.29	YES
31	RPS16	RPS16	RPS16	3497	0.088	0.29	YES
32	EIF3K	EIF3K	EIF3K	3504	0.088	0.3	YES
33	RPL38	RPL38	RPL38	3522	0.087	0.31	YES
34	EIF3E	EIF3E	EIF3E	3570	0.086	0.32	YES
35	RPS29	RPS29	RPS29	3572	0.085	0.33	YES
36	UBA52	UBA52	UBA52	3677	0.083	0.34	YES
37	RPL8	RPL8	RPL8	3707	0.082	0.35	YES
38	RPL18	RPL18	RPL18	3747	0.081	0.35	YES
39	EIF3G	EIF3G	EIF3G	3806	0.08	0.36	YES
40	RPL3	RPL3	RPL3	3819	0.08	0.37	YES
41	RPS8	RPS8	RPS8	3844	0.079	0.38	YES
42	RPS10	RPS10	RPS10	3960	0.076	0.38	YES
43	RPS9	RPS9	RPS9	3971	0.076	0.39	YES
44	EIF4B	EIF4B	EIF4B	3995	0.076	0.4	YES
45	RPL28	RPL28	RPL28	4029	0.075	0.4	YES
46	RPS4Y1	RPS4Y1	RPS4Y1	4122	0.073	0.41	YES
47	RPL4	RPL4	RPL4	4127	0.073	0.42	YES
48	RPL39	RPL39	RPL39	4144	0.072	0.42	YES
49	RPL10	RPL10	RPL10	4189	0.072	0.43	YES
50	RPL5	RPL5	RPL5	4233	0.071	0.44	YES
51	RPS3	RPS3	RPS3	4244	0.07	0.44	YES
52	EIF3H	EIF3H	EIF3H	4308	0.069	0.45	YES
53	EIF3D	EIF3D	EIF3D	4334	0.068	0.46	YES
54	PABPC1	PABPC1	PABPC1	4344	0.068	0.46	YES
55	RPS11	RPS11	RPS11	4361	0.068	0.47	YES
56	RPS25	RPS25	RPS25	4404	0.067	0.48	YES
57	RPL36	RPL36	RPL36	4410	0.067	0.49	YES
58	RPL34	RPL34	RPL34	4431	0.067	0.49	YES
59	RPL30	RPL30	RPL30	4433	0.067	0.5	YES
60	RPS18	RPS18	RPS18	4439	0.067	0.51	YES
61	RPL13A	RPL13A	RPL13A	4450	0.066	0.52	YES
62	RPS4X	RPS4X	RPS4X	4468	0.066	0.52	YES
63	RPL22	RPL22	RPL22	4521	0.065	0.53	YES
64	RPL10A	RPL10A	RPL10A	4581	0.064	0.53	YES
65	RPS2	RPS2	RPS2	4614	0.063	0.54	YES
66	RPL26	RPL26	RPL26	4625	0.063	0.55	YES
67	RPL11	RPL11	RPL11	4651	0.063	0.55	YES
68	EIF1AX	EIF1AX	EIF1AX	4914	0.058	0.55	YES
69	RPL26L1	RPL26L1	RPL26L1	5000	0.057	0.55	YES
70	RPL12	RPL12	RPL12	5003	0.057	0.56	YES
71	RPS15A	RPS15A	RPS15A	5021	0.056	0.56	YES
72	RPS21	RPS21	RPS21	5098	0.055	0.56	YES
73	EIF2S1	EIF2S1	EIF2S1	5108	0.055	0.57	YES
74	RPLP1	RPLP1	RPLP1	5146	0.054	0.57	YES
75	RPL27	RPL27	RPL27	5166	0.054	0.58	YES
76	EIF4H	EIF4H	EIF4H	5209	0.053	0.58	YES
77	EIF3B	EIF3B	EIF3B	5228	0.053	0.59	YES
78	EIF2S3	EIF2S3	EIF2S3	5356	0.051	0.59	YES
79	RPS13	RPS13	RPS13	5587	0.047	0.58	YES
80	RPS19	RPS19	RPS19	5593	0.047	0.59	YES
81	RPS20	RPS20	RPS20	5601	0.047	0.59	YES
82	RPL23	RPL23	RPL23	5675	0.046	0.59	YES
83	RPL37A	RPL37A	RPL37A	5882	0.042	0.59	NO
84	RPS24	RPS24	RPS24	5985	0.041	0.59	NO
85	RPL31	RPL31	RPL31	6158	0.038	0.58	NO
86	FAU	FAU	FAU	6177	0.038	0.58	NO
87	RPS12	RPS12	RPS12	6360	0.036	0.58	NO
88	RPS7	RPS7	RPS7	6372	0.035	0.58	NO
89	RPL27A	RPL27A	RPL27A	6741	0.03	0.57	NO
90	RPL13	RPL13	RPL13	6809	0.029	0.57	NO
91	RPS27A	RPS27A	RPS27A	6817	0.029	0.57	NO
92	RPLP2	RPLP2	RPLP2	7042	0.026	0.56	NO
93	EIF3J	EIF3J	EIF3J	7255	0.023	0.55	NO
94	EIF3I	EIF3I	EIF3I	7331	0.022	0.55	NO
95	RPL23A	RPL23A	RPL23A	7349	0.022	0.55	NO
96	EIF3F	EIF3F	EIF3F	7628	0.018	0.54	NO
97	RPL19	RPL19	RPL19	7648	0.018	0.54	NO
98	EIF4E	EIF4E	EIF4E	8157	0.011	0.51	NO
99	EIF2S2	EIF2S2	EIF2S2	8475	0.0067	0.49	NO
100	EIF4G1	EIF4G1	EIF4G1	8749	0.003	0.48	NO
101	EIF3A	EIF3A	EIF3A	10022	-0.016	0.41	NO
102	RPL21	RPL21	RPL21	11119	-0.033	0.35	NO
103	EIF3C	EIF3C	EIF3C	11377	-0.038	0.34	NO
104	EIF4A1	EIF4A1	EIF4A1	11387	-0.038	0.35	NO
105	RPS28	RPS28	RPS28	14788	-0.14	0.17	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: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S96. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, 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 MITOCHONDRIAL PROTEIN IMPORT

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	RPSAP9	RPSAP9	RPSAP9	1115	0.23	-0.0078	YES
2	RPS26	RPS26	RPS26	1725	0.17	-0.0019	YES
3	EIF4EBP1	EIF4EBP1	EIF4EBP1	1930	0.15	0.023	YES
4	RPSA	RPSA	RPSA	1975	0.15	0.057	YES
5	RPS17	RPS17	RPS17	2327	0.13	0.068	YES
6	RPS27	RPS27	RPS27	2342	0.13	0.099	YES
7	RPS5	RPS5	RPS5	2600	0.12	0.11	YES
8	RPS14	RPS14	RPS14	2637	0.12	0.14	YES
9	RPS23	RPS23	RPS23	2791	0.11	0.16	YES
10	RPS6	RPS6	RPS6	2885	0.11	0.18	YES
11	RPS3A	RPS3A	RPS3A	2945	0.1	0.2	YES
12	RPS15	RPS15	RPS15	3084	0.1	0.22	YES
13	EIF4A2	EIF4A2	EIF4A2	3178	0.097	0.23	YES
14	RPS16	RPS16	RPS16	3497	0.088	0.24	YES
15	EIF3K	EIF3K	EIF3K	3504	0.088	0.26	YES
16	EIF3E	EIF3E	EIF3E	3570	0.086	0.28	YES
17	RPS29	RPS29	RPS29	3572	0.085	0.3	YES
18	EIF3G	EIF3G	EIF3G	3806	0.08	0.3	YES
19	RPS8	RPS8	RPS8	3844	0.079	0.32	YES
20	RPS10	RPS10	RPS10	3960	0.076	0.33	YES
21	RPS9	RPS9	RPS9	3971	0.076	0.35	YES
22	EIF4B	EIF4B	EIF4B	3995	0.076	0.37	YES
23	RPS4Y1	RPS4Y1	RPS4Y1	4122	0.073	0.38	YES
24	RPS3	RPS3	RPS3	4244	0.07	0.39	YES
25	EIF3H	EIF3H	EIF3H	4308	0.069	0.4	YES
26	EIF3D	EIF3D	EIF3D	4334	0.068	0.42	YES
27	PABPC1	PABPC1	PABPC1	4344	0.068	0.43	YES
28	RPS11	RPS11	RPS11	4361	0.068	0.45	YES
29	RPS25	RPS25	RPS25	4404	0.067	0.46	YES
30	RPS18	RPS18	RPS18	4439	0.067	0.47	YES
31	RPS4X	RPS4X	RPS4X	4468	0.066	0.49	YES
32	RPS2	RPS2	RPS2	4614	0.063	0.5	YES
33	EIF1AX	EIF1AX	EIF1AX	4914	0.058	0.49	YES
34	RPS15A	RPS15A	RPS15A	5021	0.056	0.5	YES
35	RPS21	RPS21	RPS21	5098	0.055	0.51	YES
36	EIF2S1	EIF2S1	EIF2S1	5108	0.055	0.52	YES
37	EIF4H	EIF4H	EIF4H	5209	0.053	0.53	YES
38	EIF3B	EIF3B	EIF3B	5228	0.053	0.54	YES
39	EIF2S3	EIF2S3	EIF2S3	5356	0.051	0.55	YES
40	RPS13	RPS13	RPS13	5587	0.047	0.55	YES
41	RPS19	RPS19	RPS19	5593	0.047	0.56	YES
42	RPS20	RPS20	RPS20	5601	0.047	0.57	YES
43	RPS24	RPS24	RPS24	5985	0.041	0.56	NO
44	FAU	FAU	FAU	6177	0.038	0.55	NO
45	RPS12	RPS12	RPS12	6360	0.036	0.55	NO
46	RPS7	RPS7	RPS7	6372	0.035	0.56	NO
47	RPS27A	RPS27A	RPS27A	6817	0.029	0.54	NO
48	EIF3J	EIF3J	EIF3J	7255	0.023	0.52	NO
49	EIF3I	EIF3I	EIF3I	7331	0.022	0.52	NO
50	EIF3F	EIF3F	EIF3F	7628	0.018	0.51	NO
51	EIF4E	EIF4E	EIF4E	8157	0.011	0.48	NO
52	EIF2S2	EIF2S2	EIF2S2	8475	0.0067	0.47	NO
53	EIF4G1	EIF4G1	EIF4G1	8749	0.003	0.45	NO
54	EIF3A	EIF3A	EIF3A	10022	-0.016	0.39	NO
55	EIF3C	EIF3C	EIF3C	11377	-0.038	0.32	NO
56	EIF4A1	EIF4A1	EIF4A1	11387	-0.038	0.33	NO
57	RPS28	RPS28	RPS28	14788	-0.14	0.17	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: REACTOME MITOCHONDRIAL PROTEIN IMPORT.

Figure S98. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MITOCHONDRIAL PROTEIN IMPORT, 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 ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

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	FAM153A	FAM153A	FAM153A	296	0.38	0.03	YES
2	RPSAP9	RPSAP9	RPSAP9	1115	0.23	0.012	YES
3	RPL9	RPL9	RPL9	1677	0.17	0.00087	YES
4	RPS26	RPS26	RPS26	1725	0.17	0.019	YES
5	RPL7	RPL7	RPL7	1751	0.16	0.037	YES
6	RPL36A	RPL36A	RPL36A	1800	0.16	0.054	YES
7	RPSA	RPSA	RPSA	1975	0.15	0.063	YES
8	RPS17	RPS17	RPS17	2327	0.13	0.059	YES
9	RPL24	RPL24	RPL24	2336	0.13	0.074	YES
10	RPS27	RPS27	RPS27	2342	0.13	0.089	YES
11	RPL15	RPL15	RPL15	2568	0.12	0.091	YES
12	RPS5	RPS5	RPS5	2600	0.12	0.1	YES
13	RPS14	RPS14	RPS14	2637	0.12	0.12	YES
14	RPL32	RPL32	RPL32	2666	0.12	0.13	YES
15	RPL7A	RPL7A	RPL7A	2770	0.11	0.14	YES
16	RPS23	RPS23	RPS23	2791	0.11	0.15	YES
17	RPL41	RPL41	RPL41	2880	0.11	0.16	YES
18	RPS6	RPS6	RPS6	2885	0.11	0.17	YES
19	RPS3A	RPS3A	RPS3A	2945	0.1	0.18	YES
20	RPL18A	RPL18A	RPL18A	2949	0.1	0.19	YES
21	RPL17	RPL17	RPL17	3057	0.1	0.2	YES
22	RPL35A	RPL35A	RPL35A	3066	0.1	0.21	YES
23	RPL35	RPL35	RPL35	3075	0.1	0.22	YES
24	RPL14	RPL14	RPL14	3078	0.1	0.23	YES
25	RPS15	RPS15	RPS15	3084	0.1	0.25	YES
26	RPL6	RPL6	RPL6	3095	0.1	0.26	YES
27	RPL29	RPL29	RPL29	3150	0.098	0.27	YES
28	SEC61G	SEC61G	SEC61G	3309	0.093	0.27	YES
29	RPL37	RPL37	RPL37	3390	0.091	0.28	YES
30	RPLP0	RPLP0	RPLP0	3439	0.09	0.28	YES
31	SPCS1	SPCS1	SPCS1	3495	0.088	0.29	YES
32	RPS16	RPS16	RPS16	3497	0.088	0.3	YES
33	RPL38	RPL38	RPL38	3522	0.087	0.31	YES
34	RPS29	RPS29	RPS29	3572	0.085	0.32	YES
35	UBA52	UBA52	UBA52	3677	0.083	0.32	YES
36	RPL8	RPL8	RPL8	3707	0.082	0.33	YES
37	RPL18	RPL18	RPL18	3747	0.081	0.34	YES
38	RPL3	RPL3	RPL3	3819	0.08	0.34	YES
39	RPS8	RPS8	RPS8	3844	0.079	0.35	YES
40	SRPRB	SRPRB	SRPRB	3872	0.078	0.36	YES
41	RPS10	RPS10	RPS10	3960	0.076	0.37	YES
42	RPS9	RPS9	RPS9	3971	0.076	0.38	YES
43	RPL28	RPL28	RPL28	4029	0.075	0.38	YES
44	RPS4Y1	RPS4Y1	RPS4Y1	4122	0.073	0.38	YES
45	RPL4	RPL4	RPL4	4127	0.073	0.39	YES
46	RPL39	RPL39	RPL39	4144	0.072	0.4	YES
47	RPL10	RPL10	RPL10	4189	0.072	0.41	YES
48	RPL5	RPL5	RPL5	4233	0.071	0.41	YES
49	RPS3	RPS3	RPS3	4244	0.07	0.42	YES
50	RPS11	RPS11	RPS11	4361	0.068	0.42	YES
51	RPS25	RPS25	RPS25	4404	0.067	0.43	YES
52	RPL36	RPL36	RPL36	4410	0.067	0.44	YES
53	SEC61B	SEC61B	SEC61B	4430	0.067	0.44	YES
54	RPL34	RPL34	RPL34	4431	0.067	0.45	YES
55	RPL30	RPL30	RPL30	4433	0.067	0.46	YES
56	RPS18	RPS18	RPS18	4439	0.067	0.47	YES
57	RPL13A	RPL13A	RPL13A	4450	0.066	0.48	YES
58	RPS4X	RPS4X	RPS4X	4468	0.066	0.48	YES
59	RPL22	RPL22	RPL22	4521	0.065	0.49	YES
60	RPL10A	RPL10A	RPL10A	4581	0.064	0.49	YES
61	RPS2	RPS2	RPS2	4614	0.063	0.5	YES
62	RPL26	RPL26	RPL26	4625	0.063	0.5	YES
63	RPL11	RPL11	RPL11	4651	0.063	0.51	YES
64	RPN1	RPN1	RPN1	4783	0.06	0.51	YES
65	SPCS3	SPCS3	SPCS3	4910	0.058	0.51	YES
66	RPL26L1	RPL26L1	RPL26L1	5000	0.057	0.51	YES
67	RPL12	RPL12	RPL12	5003	0.057	0.52	YES
68	RPS15A	RPS15A	RPS15A	5021	0.056	0.53	YES
69	SEC11A	SEC11A	SEC11A	5041	0.056	0.53	YES
70	RPS21	RPS21	RPS21	5098	0.055	0.54	YES
71	RPLP1	RPLP1	RPLP1	5146	0.054	0.54	YES
72	RPL27	RPL27	RPL27	5166	0.054	0.55	YES
73	SRP54	SRP54	SRP54	5421	0.05	0.54	YES
74	SEC11C	SEC11C	SEC11C	5527	0.048	0.54	YES
75	RPS13	RPS13	RPS13	5587	0.047	0.54	YES
76	RPS19	RPS19	RPS19	5593	0.047	0.55	YES
77	RPS20	RPS20	RPS20	5601	0.047	0.55	YES
78	RPL23	RPL23	RPL23	5675	0.046	0.55	YES
79	SRP14	SRP14	SRP14	5872	0.043	0.55	YES
80	RPL37A	RPL37A	RPL37A	5882	0.042	0.55	YES
81	TRAM1	TRAM1	TRAM1	5945	0.042	0.55	YES
82	RPS24	RPS24	RPS24	5985	0.041	0.56	YES
83	SSR4	SSR4	SSR4	6116	0.039	0.55	YES
84	RPL31	RPL31	RPL31	6158	0.038	0.56	YES
85	FAU	FAU	FAU	6177	0.038	0.56	YES
86	RPS12	RPS12	RPS12	6360	0.036	0.55	NO
87	RPS7	RPS7	RPS7	6372	0.035	0.56	NO
88	SEC61A1	SEC61A1	SEC61A1	6437	0.034	0.56	NO
89	RPN2	RPN2	RPN2	6512	0.033	0.56	NO
90	SRP68	SRP68	SRP68	6709	0.03	0.55	NO
91	RPL27A	RPL27A	RPL27A	6741	0.03	0.55	NO
92	RPL13	RPL13	RPL13	6809	0.029	0.55	NO
93	RPS27A	RPS27A	RPS27A	6817	0.029	0.55	NO
94	SRP19	SRP19	SRP19	6857	0.029	0.56	NO
95	RPLP2	RPLP2	RPLP2	7042	0.026	0.55	NO
96	DDOST	DDOST	DDOST	7090	0.025	0.55	NO
97	RPL23A	RPL23A	RPL23A	7349	0.022	0.54	NO
98	SRP9	SRP9	SRP9	7359	0.022	0.54	NO
99	RPL19	RPL19	RPL19	7648	0.018	0.52	NO
100	SRP72	SRP72	SRP72	7680	0.018	0.52	NO
101	LOC653566	LOC653566	LOC653566	7778	0.016	0.52	NO
102	SPCS2	SPCS2	SPCS2	7899	0.014	0.52	NO
103	SSR2	SSR2	SSR2	8393	0.0077	0.49	NO
104	SSR3	SSR3	SSR3	8693	0.0037	0.47	NO
105	SRPR	SRPR	SRPR	10807	-0.028	0.36	NO
106	RPL21	RPL21	RPL21	11119	-0.033	0.34	NO
107	SSR1	SSR1	SSR1	11189	-0.035	0.34	NO
108	SEC61A2	SEC61A2	SEC61A2	13952	-0.1	0.2	NO
109	RPS28	RPS28	RPS28	14788	-0.14	0.17	NO

Figure S99. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S100. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, 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 ARGININE AND PROLINE METABOLISM	54	genes.ES.table	0.44	1.5	0.029	1	0.98	0.39	0.22	0.31	0.93	0.46
KEGG HISTIDINE METABOLISM	29	genes.ES.table	0.64	1.6	0.016	1	0.91	0.41	0.076	0.38	1	0.68
KEGG SELENOAMINO ACID METABOLISM	26	genes.ES.table	0.59	1.7	0.024	1	0.73	0.42	0.2	0.34	1	0.64
KEGG GLUTATHIONE METABOLISM	47	genes.ES.table	0.52	1.5	0.062	1	0.96	0.32	0.13	0.28	0.91	0.46
KEGG GLYCEROLIPID METABOLISM	44	genes.ES.table	0.51	1.5	0.03	1	0.95	0.36	0.15	0.31	1	0.66
KEGG PROPANOATE METABOLISM	32	genes.ES.table	0.51	1.4	0.11	1	0.98	0.47	0.18	0.39	0.91	0.46
KEGG AMINOACYL TRNA BIOSYNTHESIS	41	genes.ES.table	0.41	1.4	0.12	1	0.98	0.58	0.37	0.37	0.87	0.44
SIG CD40PATHWAYMAP	33	genes.ES.table	0.49	1.6	0.018	1	0.89	0.18	0.062	0.17	1	0.72
PID TRAIL PATHWAY	28	genes.ES.table	0.49	1.5	0.056	1	0.96	0.5	0.33	0.34	1	0.65
PID RET PATHWAY	38	genes.ES.table	0.45	1.5	0.062	1	0.96	0.1	0.052	0.1	1	0.6

genes ES table in pathway: KEGG ARGININE AND PROLINE METABOLISM

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	MAT1A	MAT1A	MAT1A	308	1.1	0.13	YES
2	CBS	CBS	CBS	646	0.8	0.22	YES
3	CTH	CTH	CTH	827	0.71	0.3	YES
4	GGT1	GGT1	GGT1	930	0.67	0.38	YES
5	GGT5	GGT5	GGT5	1241	0.56	0.44	YES
6	SCLY	SCLY	SCLY	1350	0.53	0.5	YES
7	GGT6	GGT6	GGT6	1549	0.48	0.55	YES
8	SEPHS2	SEPHS2	SEPHS2	1844	0.42	0.59	YES
9	PAPSS2	PAPSS2	PAPSS2	2584	0.32	0.59	YES
10	MARS2	MARS2	MARS2	3520	0.24	0.57	YES
11	AHCYL1	AHCYL1	AHCYL1	3650	0.23	0.59	YES
12	PAPSS1	PAPSS1	PAPSS1	5446	0.13	0.51	NO
13	TRMT11	TRMT11	TRMT11	5496	0.13	0.52	NO
14	MAT2A	MAT2A	MAT2A	5546	0.12	0.54	NO
15	SEPHS1	SEPHS1	SEPHS1	5552	0.12	0.55	NO
16	METTL6	METTL6	METTL6	5678	0.12	0.56	NO
17	LCMT2	LCMT2	LCMT2	7138	0.055	0.48	NO
18	HEMK1	HEMK1	HEMK1	7603	0.038	0.46	NO
19	GGT7	GGT7	GGT7	8517	0.0026	0.41	NO
20	MARS	MARS	MARS	10022	-0.051	0.34	NO
21	MAT2B	MAT2B	MAT2B	10802	-0.078	0.3	NO
22	LCMT1	LCMT1	LCMT1	10844	-0.08	0.31	NO
23	METTL2B	METTL2B	METTL2B	10980	-0.085	0.31	NO
24	WBSCR22	WBSCR22	WBSCR22	12568	-0.15	0.24	NO
25	AHCY	AHCY	AHCY	13024	-0.17	0.24	NO
26	AHCYL2	AHCYL2	AHCYL2	13731	-0.22	0.23	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 ARGININE AND PROLINE METABOLISM.

Figure S102. 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 HISTIDINE METABOLISM

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	SYT1	SYT1	SYT1	63	1.7	0.18	YES
2	MAPK10	MAPK10	MAPK10	579	0.85	0.24	YES
3	PIK3R1	PIK3R1	PIK3R1	894	0.68	0.3	YES
4	PIK3CD	PIK3CD	PIK3CD	971	0.66	0.37	YES
5	TRAF5	TRAF5	TRAF5	1080	0.61	0.43	YES
6	MAPK12	MAPK12	MAPK12	1112	0.6	0.49	YES
7	NFKBIE	NFKBIE	NFKBIE	2643	0.32	0.44	NO
8	MAPK11	MAPK11	MAPK11	2888	0.29	0.46	NO
9	NFKBIL1	NFKBIL1	NFKBIL1	3978	0.2	0.42	NO
10	MAP2K4	MAP2K4	MAP2K4	4989	0.15	0.38	NO
11	MAPK14	MAPK14	MAPK14	5153	0.14	0.39	NO
12	MAPK8	MAPK8	MAPK8	5477	0.13	0.38	NO
13	MAPK8IP2	MAPK8IP2	MAPK8IP2	5663	0.12	0.39	NO
14	NFKB2	NFKB2	NFKB2	5772	0.11	0.39	NO
15	NFKBIB	NFKBIB	NFKBIB	6109	0.099	0.38	NO
16	TRAF6	TRAF6	TRAF6	6246	0.093	0.39	NO
17	MAPK9	MAPK9	MAPK9	8430	0.0059	0.26	NO
18	NFKBIA	NFKBIA	NFKBIA	8592	-0.00021	0.26	NO
19	MAPK1	MAPK1	MAPK1	9469	-0.033	0.21	NO
20	NFKB1	NFKB1	NFKB1	9756	-0.042	0.2	NO
21	TRAF2	TRAF2	TRAF2	10126	-0.054	0.18	NO
22	MAP2K7	MAP2K7	MAP2K7	10402	-0.064	0.18	NO
23	PIK3CA	PIK3CA	PIK3CA	10811	-0.079	0.16	NO
24	MAPK8IP1	MAPK8IP1	MAPK8IP1	10820	-0.079	0.17	NO
25	MAPK3	MAPK3	MAPK3	11036	-0.087	0.17	NO
26	MAPK8IP3	MAPK8IP3	MAPK8IP3	11298	-0.097	0.16	NO
27	IKBKG	IKBKG	IKBKG	11577	-0.11	0.16	NO
28	MAPK13	MAPK13	MAPK13	12496	-0.15	0.12	NO
29	MAPKAPK5	MAPKAPK5	MAPKAPK5	12923	-0.17	0.12	NO
30	GORASP1	GORASP1	GORASP1	13134	-0.18	0.12	NO
31	TRAF3	TRAF3	TRAF3	13871	-0.23	0.11	NO
32	DUSP1	DUSP1	DUSP1	14670	-0.3	0.096	NO
33	CD40	CD40	CD40	16823	-0.74	0.056	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 HISTIDINE METABOLISM.

Figure S104. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HISTIDINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG SELENOAMINO 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	ABP1	ABP1	ABP1	82	1.6	0.11	YES
2	UROC1	UROC1	UROC1	298	1.1	0.18	YES
3	MAOB	MAOB	MAOB	304	1.1	0.26	YES
4	CNDP1	CNDP1	CNDP1	431	0.98	0.33	YES
5	HDC	HDC	HDC	564	0.86	0.38	YES
6	HAL	HAL	HAL	834	0.71	0.42	YES
7	ALDH3B2	ALDH3B2	ALDH3B2	1091	0.61	0.45	YES
8	ALDH2	ALDH2	ALDH2	1097	0.61	0.49	YES
9	ALDH1B1	ALDH1B1	ALDH1B1	1196	0.57	0.53	YES
10	ALDH3B1	ALDH3B1	ALDH3B1	1221	0.57	0.57	YES
11	ASPA	ASPA	ASPA	1238	0.56	0.61	YES
12	ACY3	ACY3	ACY3	1348	0.53	0.64	YES
13	AMDHD1	AMDHD1	AMDHD1	2603	0.32	0.59	NO
14	ALDH9A1	ALDH9A1	ALDH9A1	2677	0.31	0.61	NO
15	ALDH3A2	ALDH3A2	ALDH3A2	4739	0.16	0.51	NO
16	TRMT11	TRMT11	TRMT11	5496	0.13	0.48	NO
17	ALDH7A1	ALDH7A1	ALDH7A1	5662	0.12	0.48	NO
18	METTL6	METTL6	METTL6	5678	0.12	0.48	NO
19	HNMT	HNMT	HNMT	6918	0.065	0.42	NO
20	LCMT2	LCMT2	LCMT2	7138	0.055	0.41	NO
21	HEMK1	HEMK1	HEMK1	7603	0.038	0.39	NO
22	LCMT1	LCMT1	LCMT1	10844	-0.08	0.21	NO
23	METTL2B	METTL2B	METTL2B	10980	-0.085	0.21	NO
24	WBSCR22	WBSCR22	WBSCR22	12568	-0.15	0.13	NO
25	MAOA	MAOA	MAOA	13198	-0.18	0.11	NO
26	DDC	DDC	DDC	14498	-0.28	0.056	NO
27	ALDH3A1	ALDH3A1	ALDH3A1	16054	-0.53	0.0073	NO
28	ALDH1A3	ALDH1A3	ALDH1A3	16306	-0.59	0.036	NO
29	FTCD	FTCD	FTCD	16624	-0.67	0.067	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 SELENOAMINO ACID METABOLISM.

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

genes ES table in pathway: KEGG GLUTATHIONE METABOLISM

Table 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	SLC19A3	SLC19A3	SLC19A3	62	1.7	0.13	YES
2	SHMT1	SHMT1	SHMT1	667	0.79	0.16	YES
3	TPK1	TPK1	TPK1	748	0.75	0.21	YES
4	QPRT	QPRT	QPRT	1086	0.61	0.24	YES
5	SLC25A16	SLC25A16	SLC25A16	1417	0.51	0.26	YES
6	MOCS1	MOCS1	MOCS1	1528	0.49	0.29	YES
7	SLC2A1	SLC2A1	SLC2A1	1532	0.48	0.33	YES
8	GSTO2	GSTO2	GSTO2	1655	0.46	0.36	YES
9	PANK1	PANK1	PANK1	2066	0.39	0.36	YES
10	DHFR	DHFR	DHFR	2341	0.35	0.38	YES
11	MOCOS	MOCOS	MOCOS	2374	0.35	0.4	YES
12	GPHN	GPHN	GPHN	3018	0.28	0.39	NO
13	NMNAT1	NMNAT1	NMNAT1	3166	0.27	0.4	NO
14	COASY	COASY	COASY	4043	0.2	0.36	NO
15	PPCS	PPCS	PPCS	4786	0.16	0.34	NO
16	PNPO	PNPO	PNPO	4855	0.16	0.34	NO
17	MTHFR	MTHFR	MTHFR	5039	0.15	0.34	NO
18	SLC2A3	SLC2A3	SLC2A3	5540	0.12	0.33	NO
19	MOCS2	MOCS2	MOCS2	5682	0.12	0.33	NO
20	MTHFD1	MTHFD1	MTHFD1	5809	0.11	0.33	NO
21	FLAD1	FLAD1	FLAD1	6237	0.093	0.31	NO
22	THTPA	THTPA	THTPA	6603	0.078	0.3	NO
23	SLC5A6	SLC5A6	SLC5A6	6795	0.07	0.29	NO
24	SLC19A1	SLC19A1	SLC19A1	6915	0.065	0.29	NO
25	AASDHPPT	AASDHPPT	AASDHPPT	7013	0.061	0.29	NO
26	NADK	NADK	NADK	7128	0.056	0.29	NO
27	PANK3	PANK3	PANK3	7154	0.055	0.29	NO
28	PDXK	PDXK	PDXK	7166	0.054	0.3	NO
29	CYB5A	CYB5A	CYB5A	7560	0.039	0.28	NO
30	PANK4	PANK4	PANK4	8219	0.014	0.24	NO
31	SLC46A1	SLC46A1	SLC46A1	8248	0.012	0.24	NO
32	NMNAT3	NMNAT3	NMNAT3	8263	0.012	0.24	NO
33	PANK2	PANK2	PANK2	8576	0.00036	0.22	NO
34	PPCDC	PPCDC	PPCDC	8585	0.000016	0.22	NO
35	GSTO1	GSTO1	GSTO1	9354	-0.028	0.18	NO
36	NFS1	NFS1	NFS1	9384	-0.03	0.18	NO
37	SLC19A2	SLC19A2	SLC19A2	10341	-0.062	0.13	NO
38	SLC23A2	SLC23A2	SLC23A2	10384	-0.063	0.14	NO
39	FPGS	FPGS	FPGS	11817	-0.12	0.063	NO
40	CYB5R3	CYB5R3	CYB5R3	12838	-0.16	0.018	NO
41	MOCS3	MOCS3	MOCS3	13073	-0.18	0.019	NO
42	NAMPT	NAMPT	NAMPT	13451	-0.2	0.013	NO
43	FASN	FASN	FASN	13596	-0.21	0.021	NO
44	SLC25A32	SLC25A32	SLC25A32	13682	-0.22	0.033	NO
45	SLC23A1	SLC23A1	SLC23A1	14605	-0.29	0.0038	NO
46	NADSYN1	NADSYN1	NADSYN1	14941	-0.33	0.011	NO
47	RFK	RFK	RFK	14964	-0.34	0.035	NO
48	ENPP1	ENPP1	ENPP1	15111	-0.36	0.055	NO
49	NMNAT2	NMNAT2	NMNAT2	15487	-0.42	0.066	NO
50	ACP5	ACP5	ACP5	17052	-0.85	0.043	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 GLUTATHIONE METABOLISM.

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

genes ES table in pathway: KEGG GLYCEROLIPID METABOLISM

Table 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	LIPF	LIPF	LIPF	80	1.6	0.09	YES
2	DGAT2	DGAT2	DGAT2	176	1.3	0.16	YES
3	CEL	CEL	CEL	474	0.93	0.2	YES
4	AGPAT4	AGPAT4	AGPAT4	480	0.93	0.25	YES
5	LPL	LPL	LPL	573	0.85	0.3	YES
6	PPAP2C	PPAP2C	PPAP2C	608	0.83	0.35	YES
7	PNPLA3	PNPLA3	PNPLA3	677	0.79	0.39	YES
8	ALDH2	ALDH2	ALDH2	1097	0.61	0.4	YES
9	ALDH1B1	ALDH1B1	ALDH1B1	1196	0.57	0.43	YES
10	MBOAT2	MBOAT2	MBOAT2	1304	0.54	0.45	YES
11	LIPC	LIPC	LIPC	1380	0.52	0.48	YES
12	GPAM	GPAM	GPAM	1707	0.45	0.49	YES
13	DGKA	DGKA	DGKA	2437	0.34	0.47	YES
14	LIPG	LIPG	LIPG	2600	0.32	0.48	YES
15	DGKG	DGKG	DGKG	2622	0.32	0.49	YES
16	ALDH9A1	ALDH9A1	ALDH9A1	2677	0.31	0.51	YES
17	DAK	DAK	DAK	4152	0.2	0.44	NO
18	PPAP2B	PPAP2B	PPAP2B	4467	0.18	0.43	NO
19	ALDH3A2	ALDH3A2	ALDH3A2	4739	0.16	0.42	NO
20	DGKE	DGKE	DGKE	5255	0.14	0.4	NO
21	DGKQ	DGKQ	DGKQ	5300	0.14	0.41	NO
22	AGPAT6	AGPAT6	AGPAT6	5337	0.13	0.41	NO
23	GPAT2	GPAT2	GPAT2	5466	0.13	0.42	NO
24	AGPAT1	AGPAT1	AGPAT1	5491	0.13	0.42	NO
25	ALDH7A1	ALDH7A1	ALDH7A1	5662	0.12	0.42	NO
26	AGPAT3	AGPAT3	AGPAT3	7210	0.053	0.33	NO
27	AKR1A1	AKR1A1	AKR1A1	7553	0.039	0.32	NO
28	AGK	AGK	AGK	7630	0.036	0.32	NO
29	DGKD	DGKD	DGKD	8884	-0.011	0.24	NO
30	GLYCTK	GLYCTK	GLYCTK	8927	-0.013	0.24	NO
31	LCLAT1	LCLAT1	LCLAT1	8982	-0.015	0.24	NO
32	DGKH	DGKH	DGKH	9448	-0.032	0.22	NO
33	MBOAT1	MBOAT1	MBOAT1	9561	-0.036	0.21	NO
34	PPAP2A	PPAP2A	PPAP2A	9732	-0.041	0.21	NO
35	AKR1B1	AKR1B1	AKR1B1	10026	-0.051	0.19	NO
36	DGAT1	DGAT1	DGAT1	11012	-0.086	0.14	NO
37	GLA	GLA	GLA	13029	-0.17	0.039	NO
38	GK	GK	GK	13916	-0.23	0.0026	NO
39	AGPAT9	AGPAT9	AGPAT9	14143	-0.25	0.0044	NO
40	DGKZ	DGKZ	DGKZ	14349	-0.27	0.0085	NO
41	AGPAT2	AGPAT2	AGPAT2	14381	-0.27	0.023	NO
42	MGLL	MGLL	MGLL	15608	-0.44	-0.021	NO
43	DGKB	DGKB	DGKB	16848	-0.75	-0.046	NO
44	DGKI	DGKI	DGKI	17717	-1.7	0.006	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 GLYCEROLIPID METABOLISM.

Figure S110. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCEROLIPID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PROPANOATE METABOLISM

Table 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	PIK3R1	PIK3R1	PIK3R1	894	0.68	0.084	YES
2	PIK3CD	PIK3CD	PIK3CD	971	0.66	0.21	YES
3	CASP10	CASP10	CASP10	1266	0.55	0.3	YES
4	TNFRSF10A	TNFRSF10A	TNFRSF10A	1623	0.47	0.37	YES
5	TNFRSF10C	TNFRSF10C	TNFRSF10C	2190	0.37	0.41	YES
6	PIK3R3	PIK3R3	PIK3R3	2851	0.3	0.43	YES
7	TNFRSF10D	TNFRSF10D	TNFRSF10D	4379	0.18	0.38	YES
8	CHUK	CHUK	CHUK	4431	0.18	0.41	YES
9	DAP3	DAP3	DAP3	4587	0.17	0.44	YES
10	PIK3R2	PIK3R2	PIK3R2	4752	0.16	0.46	YES
11	MAP2K4	MAP2K4	MAP2K4	4989	0.15	0.48	YES
12	MAPK8	MAPK8	MAPK8	5477	0.13	0.48	YES
13	CASP8	CASP8	CASP8	5764	0.11	0.48	YES
14	RIPK1	RIPK1	RIPK1	5905	0.11	0.5	YES
15	PIK3CB	PIK3CB	PIK3CB	7005	0.062	0.44	NO
16	CFLAR	CFLAR	CFLAR	7242	0.051	0.44	NO
17	SMPD1	SMPD1	SMPD1	7629	0.036	0.43	NO
18	MAP3K1	MAP3K1	MAP3K1	7684	0.034	0.43	NO
19	FADD	FADD	FADD	8330	0.0095	0.4	NO
20	TNFRSF10B	TNFRSF10B	TNFRSF10B	9423	-0.031	0.34	NO
21	MAPK1	MAPK1	MAPK1	9469	-0.033	0.34	NO
22	TNFSF10	TNFSF10	TNFSF10	9560	-0.036	0.35	NO
23	TRAF2	TRAF2	TRAF2	10126	-0.054	0.33	NO
24	PIK3CA	PIK3CA	PIK3CA	10811	-0.079	0.3	NO
25	MAPK3	MAPK3	MAPK3	11036	-0.087	0.31	NO
26	IKBKB	IKBKB	IKBKB	11387	-0.1	0.31	NO
27	IKBKG	IKBKG	IKBKG	11577	-0.11	0.32	NO
28	TRADD	TRADD	TRADD	12907	-0.17	0.28	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 PROPANOATE METABOLISM.

Figure S112. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PROPANOATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

Table 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	DOK5	DOK5	DOK5	107	1.5	0.21	YES
2	GFRA1	GFRA1	GFRA1	859	0.7	0.26	YES
3	PIK3R1	PIK3R1	PIK3R1	894	0.68	0.36	YES
4	DOK6	DOK6	DOK6	933	0.67	0.45	YES
5	GAB1	GAB1	GAB1	2306	0.36	0.42	NO
6	CRK	CRK	CRK	3923	0.21	0.36	NO
7	MAPK8	MAPK8	MAPK8	5477	0.13	0.29	NO
8	FRS2	FRS2	FRS2	5865	0.11	0.28	NO
9	DOK1	DOK1	DOK1	5906	0.11	0.3	NO
10	GRB2	GRB2	GRB2	5908	0.11	0.31	NO
11	SRC	SRC	SRC	6192	0.095	0.31	NO
12	PRKCA	PRKCA	PRKCA	6768	0.071	0.29	NO
13	RAP1A	RAP1A	RAP1A	7369	0.046	0.26	NO
14	HRAS	HRAS	HRAS	7821	0.03	0.24	NO
15	SHC1	SHC1	SHC1	7925	0.026	0.24	NO
16	SOS1	SOS1	SOS1	8191	0.015	0.22	NO
17	NCK1	NCK1	NCK1	8297	0.011	0.22	NO
18	RHOA	RHOA	RHOA	8460	0.0049	0.21	NO
19	PRKACA	PRKACA	PRKACA	8493	0.0037	0.21	NO
20	PTPN11	PTPN11	PTPN11	9049	-0.017	0.18	NO
21	MAPK1	MAPK1	MAPK1	9469	-0.033	0.16	NO
22	PDLIM7	PDLIM7	PDLIM7	9480	-0.033	0.17	NO
23	CREB1	CREB1	CREB1	9510	-0.034	0.17	NO
24	RASA1	RASA1	RASA1	9611	-0.038	0.17	NO
25	SHANK3	SHANK3	SHANK3	9852	-0.045	0.16	NO
26	RAC1	RAC1	RAC1	10523	-0.068	0.13	NO
27	DOK4	DOK4	DOK4	10780	-0.078	0.13	NO
28	PIK3CA	PIK3CA	PIK3CA	10811	-0.079	0.14	NO
29	PTK2	PTK2	PTK2	10841	-0.08	0.15	NO
30	BCAR1	BCAR1	BCAR1	11023	-0.087	0.15	NO
31	MAPK3	MAPK3	MAPK3	11036	-0.087	0.16	NO
32	JUN	JUN	JUN	11189	-0.093	0.17	NO
33	RET	RET	RET	11398	-0.1	0.17	NO
34	GRB7	GRB7	GRB7	13003	-0.17	0.1	NO
35	PXN	PXN	PXN	13264	-0.19	0.12	NO
36	GRB10	GRB10	GRB10	13322	-0.19	0.14	NO
37	IRS1	IRS1	IRS1	14800	-0.31	0.1	NO
38	IRS2	IRS2	IRS2	15877	-0.49	0.11	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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: SIG CD40PATHWAYMAP

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	KCNJ16	KCNJ16	KCNJ16	10	2.4	0.14	YES
2	KCNJ10	KCNJ10	KCNJ10	39	1.8	0.24	YES
3	KCNJ3	KCNJ3	KCNJ3	202	1.3	0.31	YES
4	GABRB3	GABRB3	GABRB3	248	1.2	0.37	YES
5	GABRB1	GABRB1	GABRB1	544	0.87	0.4	YES
6	KCNJ5	KCNJ5	KCNJ5	845	0.7	0.43	YES
7	KCNJ9	KCNJ9	KCNJ9	957	0.66	0.46	YES
8	KCNJ15	KCNJ15	KCNJ15	1370	0.52	0.47	YES
9	GNAL	GNAL	GNAL	1562	0.48	0.48	YES
10	GABBR1	GABBR1	GABBR1	1855	0.42	0.49	YES
11	GABRR2	GABRR2	GABRR2	1987	0.4	0.51	YES
12	GNG7	GNG7	GNG7	2428	0.34	0.5	YES
13	GNAI3	GNAI3	GNAI3	2450	0.34	0.52	YES
14	KCNJ2	KCNJ2	KCNJ2	2563	0.33	0.53	YES
15	ADCY5	ADCY5	ADCY5	2613	0.32	0.55	YES
16	GABBR2	GABBR2	GABBR2	3689	0.23	0.5	NO
17	ARHGEF9	ARHGEF9	ARHGEF9	4642	0.17	0.46	NO
18	ADCY9	ADCY9	ADCY9	4848	0.16	0.45	NO
19	GNG5	GNG5	GNG5	5484	0.13	0.42	NO
20	GNB1	GNB1	GNB1	6171	0.096	0.39	NO
21	GNAI2	GNAI2	GNAI2	7515	0.04	0.32	NO
22	ADCY2	ADCY2	ADCY2	7541	0.04	0.32	NO
23	KCNJ12	KCNJ12	KCNJ12	7775	0.031	0.31	NO
24	GNAI1	GNAI1	GNAI1	8101	0.018	0.29	NO
25	GNG2	GNG2	GNG2	8117	0.018	0.29	NO
26	ADCY6	ADCY6	ADCY6	8185	0.015	0.29	NO
27	GABRB2	GABRB2	GABRB2	8662	-0.0029	0.26	NO
28	GNGT2	GNGT2	GNGT2	10236	-0.058	0.18	NO
29	GNG12	GNG12	GNG12	10823	-0.079	0.15	NO
30	GNG10	GNG10	GNG10	10918	-0.082	0.15	NO
31	GNB3	GNB3	GNB3	11046	-0.088	0.14	NO
32	ADCY1	ADCY1	ADCY1	11911	-0.12	0.1	NO
33	ADCY4	ADCY4	ADCY4	12047	-0.13	0.1	NO
34	GNB2	GNB2	GNB2	12066	-0.13	0.11	NO
35	ADCY7	ADCY7	ADCY7	12204	-0.14	0.11	NO
36	ADCY3	ADCY3	ADCY3	13078	-0.18	0.07	NO
37	GABRR1	GABRR1	GABRR1	15083	-0.35	-0.023	NO
38	GNG4	GNG4	GNG4	16110	-0.54	-0.05	NO
39	KCNJ6	KCNJ6	KCNJ6	16149	-0.56	-0.02	NO
40	ADCY8	ADCY8	ADCY8	16385	-0.61	0.0015	NO
41	GNG3	GNG3	GNG3	16572	-0.65	0.028	NO
42	GNGT1	GNGT1	GNGT1	16816	-0.74	0.057	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: SIG CD40PATHWAYMAP.

Figure S116. Get High-res Image For the top 5 core enriched genes in the pathway: SIG CD40PATHWAYMAP, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID TRAIL PATHWAY

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	PARS2	PARS2	PARS2	1529	0.49	0.0034	YES
2	EEF1E1	EEF1E1	EEF1E1	2366	0.35	0.021	YES
3	WARS2	WARS2	WARS2	2792	0.3	0.052	YES
4	DARS2	DARS2	DARS2	3038	0.28	0.089	YES
5	MARS2	MARS2	MARS2	3520	0.24	0.11	YES
6	FARSB	FARSB	FARSB	3904	0.21	0.12	YES
7	NARS	NARS	NARS	4364	0.18	0.13	YES
8	WARS	WARS	WARS	4470	0.18	0.16	YES
9	RARS2	RARS2	RARS2	4503	0.18	0.19	YES
10	YARS	YARS	YARS	4524	0.17	0.22	YES
11	GARS	GARS	GARS	4593	0.17	0.25	YES
12	SARS	SARS	SARS	4753	0.16	0.27	YES
13	EPRS	EPRS	EPRS	4771	0.16	0.3	YES
14	SARS2	SARS2	SARS2	5056	0.15	0.31	YES
15	AARS2	AARS2	AARS2	5155	0.14	0.33	YES
16	IARS2	IARS2	IARS2	5181	0.14	0.35	YES
17	PPA1	PPA1	PPA1	5660	0.12	0.35	YES
18	NARS2	NARS2	NARS2	5688	0.12	0.37	YES
19	IARS	IARS	IARS	5847	0.11	0.38	YES
20	HARS2	HARS2	HARS2	5863	0.11	0.4	YES
21	TARS2	TARS2	TARS2	5965	0.1	0.41	YES
22	TARS	TARS	TARS	6406	0.086	0.4	YES
23	VARS2	VARS2	VARS2	6530	0.082	0.41	YES
24	VARS	VARS	VARS	6615	0.078	0.42	YES
25	DARS	DARS	DARS	6620	0.078	0.44	YES
26	FARS2	FARS2	FARS2	7232	0.052	0.41	NO
27	AIMP2	AIMP2	AIMP2	7529	0.04	0.4	NO
28	LARS2	LARS2	LARS2	7590	0.038	0.4	NO
29	AARS	AARS	AARS	8406	0.0067	0.36	NO
30	YARS2	YARS2	YARS2	8894	-0.011	0.34	NO
31	CARS2	CARS2	CARS2	9424	-0.031	0.31	NO
32	HARS	HARS	HARS	9991	-0.05	0.29	NO
33	MARS	MARS	MARS	10022	-0.051	0.3	NO
34	AIMP1	AIMP1	AIMP1	10164	-0.055	0.3	NO
35	PPA2	PPA2	PPA2	10194	-0.056	0.31	NO
36	CARS	CARS	CARS	10207	-0.057	0.32	NO
37	QARS	QARS	QARS	10454	-0.066	0.32	NO
38	LARS	LARS	LARS	10583	-0.071	0.32	NO
39	KARS	KARS	KARS	10744	-0.076	0.33	NO
40	RARS	RARS	RARS	11659	-0.11	0.3	NO
41	FARSA	FARSA	FARSA	11975	-0.12	0.3	NO
42	EARS2	EARS2	EARS2	12723	-0.16	0.29	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: PID TRAIL PATHWAY.

Figure S118. 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

genes ES table in pathway: PID RET PATHWAY

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	MAPK10	MAPK10	MAPK10	579	0.85	0.069	YES
2	PIK3R1	PIK3R1	PIK3R1	894	0.68	0.13	YES
3	FAIM2	FAIM2	FAIM2	941	0.67	0.21	YES
4	MAP2K6	MAP2K6	MAP2K6	952	0.67	0.29	YES
5	PIK3CD	PIK3CD	PIK3CD	971	0.66	0.37	YES
6	FAS	FAS	FAS	1034	0.63	0.44	YES
7	CASP10	CASP10	CASP10	1266	0.55	0.49	YES
8	PIK3R3	PIK3R3	PIK3R3	2851	0.3	0.44	NO
9	MAPK11	MAPK11	MAPK11	2888	0.29	0.47	NO
10	BTK	BTK	BTK	3945	0.21	0.44	NO
11	CLTC	CLTC	CLTC	4262	0.19	0.44	NO
12	EZR	EZR	EZR	4354	0.18	0.46	NO
13	CHUK	CHUK	CHUK	4431	0.18	0.48	NO
14	PIK3R2	PIK3R2	PIK3R2	4752	0.16	0.48	NO
15	MAPK14	MAPK14	MAPK14	5153	0.14	0.47	NO
16	MAPK8	MAPK8	MAPK8	5477	0.13	0.47	NO
17	CASP8	CASP8	CASP8	5764	0.11	0.47	NO
18	RIPK1	RIPK1	RIPK1	5905	0.11	0.47	NO
19	SRC	SRC	SRC	6192	0.095	0.47	NO
20	BIRC2	BIRC2	BIRC2	6989	0.062	0.43	NO
21	PIK3CB	PIK3CB	PIK3CB	7005	0.062	0.44	NO
22	CFLAR	CFLAR	CFLAR	7242	0.051	0.43	NO
23	FASLG	FASLG	FASLG	7532	0.04	0.42	NO
24	SMPD1	SMPD1	SMPD1	7629	0.036	0.42	NO
25	MAP3K1	MAP3K1	MAP3K1	7684	0.034	0.42	NO
26	BIRC3	BIRC3	BIRC3	8070	0.02	0.4	NO
27	FADD	FADD	FADD	8330	0.0095	0.38	NO
28	MAPK9	MAPK9	MAPK9	8430	0.0059	0.38	NO
29	MAP2K7	MAP2K7	MAP2K7	10402	-0.064	0.28	NO
30	PIK3CA	PIK3CA	PIK3CA	10811	-0.079	0.26	NO
31	IKBKB	IKBKB	IKBKB	11387	-0.1	0.24	NO
32	IKBKG	IKBKG	IKBKG	11577	-0.11	0.25	NO
33	RFC1	RFC1	RFC1	11751	-0.12	0.25	NO
34	SYK	SYK	SYK	11774	-0.12	0.26	NO
35	CASP3	CASP3	CASP3	12232	-0.14	0.25	NO
36	PDPK1	PDPK1	PDPK1	12284	-0.14	0.27	NO
37	AKT1	AKT1	AKT1	12861	-0.16	0.25	NO
38	BID	BID	BID	13620	-0.21	0.24	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: PID RET PATHWAY.

Figure S120. Get High-res Image For the top 5 core enriched genes in the pathway: PID RET PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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
BIOCARTA RACCYCD PATHWAY	26	genes.ES.table	0.47	1.8	0.011	0.35	0.5	0.46	0.32	0.31	0.089	0.082
PID ILK PATHWAY	45	genes.ES.table	0.47	1.9	0.0041	0.33	0.39	0.44	0.37	0.28	0	0.073
REACTOME TRIF MEDIATED TLR3 SIGNALING	72	genes.ES.table	0.5	1.8	0.0061	0.35	0.59	0.26	0.22	0.21	0.11	0.084
REACTOME ORC1 REMOVAL FROM CHROMATIN	58	genes.ES.table	0.48	1.9	0.015	0.47	0.29	0.78	0.45	0.42	0	0.11
REACTOME ACTIVATION OF NF KAPPAB IN B CELLS	60	genes.ES.table	0.44	1.9	0	0.73	0.23	0.67	0.45	0.36	0	0.14
REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT	47	genes.ES.table	0.47	1.9	0.011	0.41	0.32	0.74	0.45	0.41	0	0.096
REACTOME CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6	45	genes.ES.table	0.46	1.7	0.024	0.34	0.63	0.78	0.46	0.42	0.12	0.079
REACTOME REGULATION OF APOPTOSIS	55	genes.ES.table	0.44	1.9	0.011	0.34	0.36	0.73	0.45	0.4	0	0.075
REACTOME CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION	62	genes.ES.table	0.47	1.7	0.019	0.37	0.69	0.74	0.45	0.41	0.15	0.086
REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE	52	genes.ES.table	0.46	1.9	0.014	0.62	0.29	0.75	0.46	0.4	0	0.14

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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	CCR5	CCR5	CCR5	379	0.75	0.015	YES
2	DOCK2	DOCK2	DOCK2	792	0.62	0.021	YES
3	APOBEC3G	APOBEC3G	APOBEC3G	925	0.59	0.042	YES
4	CD28	CD28	CD28	1182	0.53	0.053	YES
5	LCK	LCK	LCK	1186	0.53	0.078	YES
6	CD4	CD4	CD4	1361	0.5	0.092	YES
7	CD247	CD247	CD247	1408	0.49	0.11	YES
8	CD8B	CD8B	CD8B	1917	0.41	0.1	YES
9	HCK	HCK	HCK	2222	0.37	0.1	YES
10	CXCR4	CXCR4	CXCR4	2414	0.34	0.11	YES
11	HMGA1	HMGA1	HMGA1	2596	0.32	0.12	YES
12	RCC1	RCC1	RCC1	2767	0.3	0.12	YES
13	TAF5	TAF5	TAF5	3007	0.28	0.12	YES
14	FYN	FYN	FYN	3155	0.27	0.12	YES
15	AP1S2	AP1S2	AP1S2	3163	0.26	0.14	YES
16	TAF12	TAF12	TAF12	3285	0.25	0.14	YES
17	PSMB9	PSMB9	PSMB9	3583	0.23	0.14	YES
18	GTF2E2	GTF2E2	GTF2E2	3592	0.23	0.15	YES
19	ELMO1	ELMO1	ELMO1	3841	0.21	0.14	YES
20	GTF2F2	GTF2F2	GTF2F2	3976	0.2	0.14	YES
21	NUP85	NUP85	NUP85	4054	0.19	0.15	YES
22	POLR2D	POLR2D	POLR2D	4060	0.19	0.16	YES
23	GTF2E1	GTF2E1	GTF2E1	4213	0.18	0.16	YES
24	CDK7	CDK7	CDK7	4244	0.18	0.16	YES
25	RPS27A	RPS27A	RPS27A	4385	0.17	0.16	YES
26	PSMD4	PSMD4	PSMD4	4433	0.17	0.17	YES
27	PSMB10	PSMB10	PSMB10	4455	0.17	0.18	YES
28	TAF10	TAF10	TAF10	4695	0.16	0.17	YES
29	RANGAP1	RANGAP1	RANGAP1	4727	0.15	0.18	YES
30	RDBP	RDBP	RDBP	4887	0.15	0.18	YES
31	PSMB3	PSMB3	PSMB3	4974	0.14	0.18	YES
32	PSMD14	PSMD14	PSMD14	5003	0.14	0.18	YES
33	PSMB2	PSMB2	PSMB2	5045	0.14	0.19	YES
34	GTF2H4	GTF2H4	GTF2H4	5056	0.14	0.19	YES
35	GTF2H1	GTF2H1	GTF2H1	5078	0.14	0.2	YES
36	PSMA5	PSMA5	PSMA5	5096	0.14	0.2	YES
37	XRCC4	XRCC4	XRCC4	5109	0.14	0.21	YES
38	RANBP1	RANBP1	RANBP1	5122	0.14	0.22	YES
39	PSMD13	PSMD13	PSMD13	5319	0.13	0.21	YES
40	NUP62	NUP62	NUP62	5334	0.12	0.22	YES
41	AP2A1	AP2A1	AP2A1	5357	0.12	0.22	YES
42	AP1M1	AP1M1	AP1M1	5441	0.12	0.22	YES
43	LIG1	LIG1	LIG1	5461	0.12	0.23	YES
44	NUPL1	NUPL1	NUPL1	5490	0.12	0.23	YES
45	AP2S1	AP2S1	AP2S1	5526	0.12	0.23	YES
46	TCEB1	TCEB1	TCEB1	5591	0.12	0.24	YES
47	KPNB1	KPNB1	KPNB1	5684	0.11	0.24	YES
48	PSME4	PSME4	PSME4	5697	0.11	0.24	YES
49	PSMD12	PSMD12	PSMD12	5708	0.11	0.24	YES
50	TCEA1	TCEA1	TCEA1	5852	0.1	0.24	YES
51	PSMB4	PSMB4	PSMB4	5929	0.1	0.24	YES
52	NUP93	NUP93	NUP93	5963	0.1	0.24	YES
53	BANF1	BANF1	BANF1	6018	0.099	0.25	YES
54	CCNH	CCNH	CCNH	6021	0.098	0.25	YES
55	AP2M1	AP2M1	AP2M1	6075	0.096	0.25	YES
56	AP1S1	AP1S1	AP1S1	6103	0.095	0.26	YES
57	PSMB6	PSMB6	PSMB6	6126	0.094	0.26	YES
58	XPO1	XPO1	XPO1	6155	0.093	0.26	YES
59	PSMC1	PSMC1	PSMC1	6166	0.093	0.27	YES
60	PSMC3	PSMC3	PSMC3	6255	0.09	0.27	YES
61	RAN	RAN	RAN	6278	0.089	0.27	YES
62	PSMC5	PSMC5	PSMC5	6287	0.089	0.27	YES
63	GTF2B	GTF2B	GTF2B	6376	0.086	0.27	YES
64	NPM1	NPM1	NPM1	6393	0.085	0.28	YES
65	PAK2	PAK2	PAK2	6423	0.084	0.28	YES
66	RAC1	RAC1	RAC1	6566	0.081	0.27	YES
67	TAF9	TAF9	TAF9	6593	0.08	0.28	YES
68	PSMD11	PSMD11	PSMD11	6652	0.078	0.28	YES
69	UBA52	UBA52	UBA52	6667	0.078	0.28	YES
70	PSMD3	PSMD3	PSMD3	6694	0.077	0.28	YES
71	ELL	ELL	ELL	6705	0.076	0.28	YES
72	NUP107	NUP107	NUP107	6773	0.074	0.28	YES
73	PSMB1	PSMB1	PSMB1	6784	0.074	0.29	YES
74	POLR2L	POLR2L	POLR2L	6805	0.073	0.29	YES
75	SEH1L	SEH1L	SEH1L	6816	0.073	0.29	YES
76	GTF2H2	GTF2H2	GTF2H2	6890	0.071	0.29	YES
77	NUP188	NUP188	NUP188	6995	0.068	0.29	YES
78	POLR2J	POLR2J	POLR2J	7049	0.066	0.29	YES
79	PSMA4	PSMA4	PSMA4	7102	0.064	0.29	YES
80	POLR2H	POLR2H	POLR2H	7155	0.063	0.29	YES
81	HLA-A	HLA-A	HLA-A	7191	0.062	0.29	YES
82	PSME2	PSME2	PSME2	7203	0.062	0.29	YES
83	PSMD2	PSMD2	PSMD2	7217	0.062	0.3	YES
84	VPS28	VPS28	VPS28	7282	0.06	0.29	YES
85	NMT2	NMT2	NMT2	7311	0.059	0.3	YES
86	ERCC2	ERCC2	ERCC2	7312	0.059	0.3	YES
87	TCEB2	TCEB2	TCEB2	7313	0.059	0.3	YES
88	NUP35	NUP35	NUP35	7328	0.058	0.3	YES
89	FEN1	FEN1	FEN1	7333	0.058	0.3	YES
90	NUP43	NUP43	NUP43	7369	0.057	0.31	YES
91	POLR2G	POLR2G	POLR2G	7378	0.057	0.31	YES
92	TAF6	TAF6	TAF6	7381	0.057	0.31	YES
93	TH1L	TH1L	TH1L	7419	0.056	0.31	YES
94	PPIA	PPIA	PPIA	7461	0.055	0.31	YES
95	NUP88	NUP88	NUP88	7499	0.054	0.31	YES
96	PSMD7	PSMD7	PSMD7	7536	0.052	0.31	YES
97	PSMA1	PSMA1	PSMA1	7543	0.052	0.32	YES
98	PSMC2	PSMC2	PSMC2	7551	0.052	0.32	YES
99	AP2A2	AP2A2	AP2A2	7603	0.051	0.32	YES
100	PSMB8	PSMB8	PSMB8	7623	0.05	0.32	YES
101	TCEB3	TCEB3	TCEB3	7688	0.048	0.32	YES
102	PSMA6	PSMA6	PSMA6	7727	0.048	0.32	YES
103	TAF11	TAF11	TAF11	7764	0.046	0.32	YES
104	TAF4	TAF4	TAF4	7803	0.046	0.32	YES
105	NUP153	NUP153	NUP153	7867	0.044	0.32	YES
106	POLR2F	POLR2F	POLR2F	7885	0.043	0.32	YES
107	RAE1	RAE1	RAE1	7938	0.042	0.32	YES
108	TAF4B	TAF4B	TAF4B	7969	0.041	0.32	YES
109	PSMB7	PSMB7	PSMB7	7970	0.041	0.32	YES
110	RBX1	RBX1	RBX1	7976	0.041	0.32	YES
111	XRCC6	XRCC6	XRCC6	7995	0.04	0.32	YES
112	PSMF1	PSMF1	PSMF1	8065	0.038	0.32	YES
113	PSMA7	PSMA7	PSMA7	8086	0.038	0.32	YES
114	PSMD5	PSMD5	PSMD5	8091	0.038	0.32	YES
115	NCBP2	NCBP2	NCBP2	8109	0.037	0.32	YES
116	LIG4	LIG4	LIG4	8210	0.035	0.32	NO
117	PSMB5	PSMB5	PSMB5	8246	0.034	0.32	NO
118	XRCC5	XRCC5	XRCC5	8269	0.033	0.32	NO
119	ARF1	ARF1	ARF1	8290	0.033	0.32	NO
120	NMT1	NMT1	NMT1	8336	0.031	0.32	NO
121	VPS37B	VPS37B	VPS37B	8377	0.03	0.32	NO
122	SSRP1	SSRP1	SSRP1	8390	0.03	0.32	NO
123	SUPT4H1	SUPT4H1	SUPT4H1	8455	0.028	0.32	NO
124	PSMA3	PSMA3	PSMA3	8564	0.025	0.31	NO
125	PSMC4	PSMC4	PSMC4	8613	0.024	0.31	NO
126	BTRC	BTRC	BTRC	8756	0.02	0.3	NO
127	POLR2E	POLR2E	POLR2E	8785	0.02	0.3	NO
128	VPS37A	VPS37A	VPS37A	8822	0.019	0.3	NO
129	PSMD9	PSMD9	PSMD9	8908	0.016	0.3	NO
130	PSMA2	PSMA2	PSMA2	8985	0.014	0.29	NO
131	RNMT	RNMT	RNMT	8986	0.014	0.29	NO
132	GTF2F1	GTF2F1	GTF2F1	8997	0.014	0.29	NO
133	ERCC3	ERCC3	ERCC3	9040	0.013	0.29	NO
134	PACS1	PACS1	PACS1	9057	0.012	0.29	NO
135	CDK9	CDK9	CDK9	9064	0.012	0.29	NO
136	TAF13	TAF13	TAF13	9106	0.011	0.29	NO
137	NUP37	NUP37	NUP37	9183	0.0091	0.28	NO
138	NUP54	NUP54	NUP54	9188	0.009	0.28	NO
139	PSMD1	PSMD1	PSMD1	9306	0.0062	0.28	NO
140	NUP50	NUP50	NUP50	9312	0.006	0.28	NO
141	TBP	TBP	TBP	9335	0.0053	0.28	NO
142	SUPT16H	SUPT16H	SUPT16H	9379	0.004	0.28	NO
143	SLC25A6	SLC25A6	SLC25A6	9497	0.00083	0.27	NO
144	KPNA1	KPNA1	KPNA1	9550	-0.0002	0.27	NO
145	POLR2B	POLR2B	POLR2B	9668	-0.0033	0.26	NO
146	TSG101	TSG101	TSG101	9706	-0.004	0.26	NO
147	NUP155	NUP155	NUP155	9708	-0.0041	0.26	NO
148	POLR2K	POLR2K	POLR2K	9743	-0.0049	0.26	NO
149	AP1B1	AP1B1	AP1B1	9782	-0.0058	0.25	NO
150	CTDP1	CTDP1	CTDP1	9795	-0.0062	0.25	NO
151	NUP133	NUP133	NUP133	9846	-0.0073	0.25	NO
152	RANBP2	RANBP2	RANBP2	9922	-0.0091	0.25	NO
153	GTF2A2	GTF2A2	GTF2A2	9971	-0.01	0.24	NO
154	B2M	B2M	B2M	10039	-0.012	0.24	NO
155	AAAS	AAAS	AAAS	10081	-0.014	0.24	NO
156	TPR	TPR	TPR	10114	-0.014	0.24	NO
157	AP2B1	AP2B1	AP2B1	10278	-0.019	0.23	NO
158	POLR2I	POLR2I	POLR2I	10360	-0.021	0.23	NO
159	RNGTT	RNGTT	RNGTT	10363	-0.021	0.23	NO
160	CCNT2	CCNT2	CCNT2	10492	-0.025	0.22	NO
161	NCBP1	NCBP1	NCBP1	10503	-0.025	0.22	NO
162	PSMC6	PSMC6	PSMC6	10607	-0.028	0.22	NO
163	COBRA1	COBRA1	COBRA1	10682	-0.03	0.22	NO
164	PSMD6	PSMD6	PSMD6	10711	-0.03	0.22	NO
165	POM121	POM121	POM121	10760	-0.032	0.21	NO
166	PSME1	PSME1	PSME1	10788	-0.032	0.21	NO
167	TAF1	TAF1	TAF1	10830	-0.033	0.21	NO
168	WHSC2	WHSC2	WHSC2	10918	-0.036	0.21	NO
169	MNAT1	MNAT1	MNAT1	11050	-0.04	0.2	NO
170	SUPT5H	SUPT5H	SUPT5H	11248	-0.045	0.2	NO
171	PSMD8	PSMD8	PSMD8	11299	-0.046	0.2	NO
172	GTF2H3	GTF2H3	GTF2H3	11339	-0.047	0.2	NO
173	NUPL2	NUPL2	NUPL2	11394	-0.048	0.19	NO
174	VPS37C	VPS37C	VPS37C	11502	-0.051	0.19	NO
175	PSMD10	PSMD10	PSMD10	11913	-0.064	0.17	NO
176	NUP205	NUP205	NUP205	12122	-0.069	0.16	NO
177	SKP1	SKP1	SKP1	12367	-0.078	0.15	NO
178	POLR2C	POLR2C	POLR2C	12506	-0.083	0.15	NO
179	POLR2A	POLR2A	POLR2A	13317	-0.11	0.11	NO
180	NUP214	NUP214	NUP214	13322	-0.11	0.11	NO
181	AP1G1	AP1G1	AP1G1	13566	-0.12	0.1	NO
182	PSIP1	PSIP1	PSIP1	13654	-0.13	0.11	NO
183	ATP6V1H	ATP6V1H	ATP6V1H	14441	-0.16	0.069	NO
184	GTF2A1	GTF2A1	GTF2A1	14681	-0.18	0.064	NO
185	CUL5	CUL5	CUL5	15244	-0.21	0.042	NO
186	SLC25A5	SLC25A5	SLC25A5	15457	-0.23	0.042	NO
187	VPS37D	VPS37D	VPS37D	15499	-0.24	0.05	NO
188	GTF2H2B	GTF2H2B	GTF2H2B	15751	-0.26	0.049	NO
189	CCNT1	CCNT1	CCNT1	15879	-0.27	0.054	NO
190	AP1M2	AP1M2	AP1M2	16542	-0.35	0.033	NO
191	SLC25A4	SLC25A4	SLC25A4	16839	-0.39	0.035	NO
192	NUP210	NUP210	NUP210	17097	-0.43	0.041	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: BIOCARTA RACCYCD PATHWAY.

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

genes ES table in pathway: PID ILK PATHWAY

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	PRKCB	PRKCB	PRKCB	571	0.68	0.091	YES
2	CARD11	CARD11	CARD11	1849	0.42	0.095	YES
3	NFKBIE	NFKBIE	NFKBIE	3141	0.27	0.07	YES
4	PSMB9	PSMB9	PSMB9	3583	0.23	0.087	YES
5	MALT1	MALT1	MALT1	4326	0.18	0.077	YES
6	RPS27A	RPS27A	RPS27A	4385	0.17	0.1	YES
7	PSMD4	PSMD4	PSMD4	4433	0.17	0.13	YES
8	PSMB10	PSMB10	PSMB10	4455	0.17	0.16	YES
9	PSMB3	PSMB3	PSMB3	4974	0.14	0.16	YES
10	PSMD14	PSMD14	PSMD14	5003	0.14	0.18	YES
11	PSMB2	PSMB2	PSMB2	5045	0.14	0.2	YES
12	PSMA5	PSMA5	PSMA5	5096	0.14	0.23	YES
13	PSMD13	PSMD13	PSMD13	5319	0.13	0.24	YES
14	IKBKB	IKBKB	IKBKB	5648	0.11	0.24	YES
15	NFKBIA	NFKBIA	NFKBIA	5672	0.11	0.26	YES
16	PSME4	PSME4	PSME4	5697	0.11	0.28	YES
17	PSMD12	PSMD12	PSMD12	5708	0.11	0.3	YES
18	BCL10	BCL10	BCL10	5747	0.11	0.31	YES
19	PSMB4	PSMB4	PSMB4	5929	0.1	0.32	YES
20	PSMB6	PSMB6	PSMB6	6126	0.094	0.33	YES
21	PSMC1	PSMC1	PSMC1	6166	0.093	0.34	YES
22	PSMC3	PSMC3	PSMC3	6255	0.09	0.35	YES
23	PSMC5	PSMC5	PSMC5	6287	0.089	0.37	YES
24	PSMD11	PSMD11	PSMD11	6652	0.078	0.36	YES
25	UBA52	UBA52	UBA52	6667	0.078	0.38	YES
26	PSMD3	PSMD3	PSMD3	6694	0.077	0.39	YES
27	PSMB1	PSMB1	PSMB1	6784	0.074	0.4	YES
28	REL	REL	REL	6990	0.068	0.4	YES
29	PSMA4	PSMA4	PSMA4	7102	0.064	0.4	YES
30	PSME2	PSME2	PSME2	7203	0.062	0.41	YES
31	PSMD2	PSMD2	PSMD2	7217	0.062	0.42	YES
32	PSMD7	PSMD7	PSMD7	7536	0.052	0.41	YES
33	PSMA1	PSMA1	PSMA1	7543	0.052	0.42	YES
34	PSMC2	PSMC2	PSMC2	7551	0.052	0.43	YES
35	PSMB8	PSMB8	PSMB8	7623	0.05	0.43	YES
36	PSMA6	PSMA6	PSMA6	7727	0.048	0.44	YES
37	PSMB7	PSMB7	PSMB7	7970	0.041	0.43	YES
38	PSMF1	PSMF1	PSMF1	8065	0.038	0.43	YES
39	PSMA7	PSMA7	PSMA7	8086	0.038	0.44	YES
40	PSMD5	PSMD5	PSMD5	8091	0.038	0.44	YES
41	PSMB5	PSMB5	PSMB5	8246	0.034	0.44	NO
42	PSMA3	PSMA3	PSMA3	8564	0.025	0.43	NO
43	PSMC4	PSMC4	PSMC4	8613	0.024	0.43	NO
44	BTRC	BTRC	BTRC	8756	0.02	0.42	NO
45	PSMD9	PSMD9	PSMD9	8908	0.016	0.42	NO
46	RELA	RELA	RELA	8914	0.016	0.42	NO
47	PSMA2	PSMA2	PSMA2	8985	0.014	0.42	NO
48	PSMD1	PSMD1	PSMD1	9306	0.0062	0.4	NO
49	IKBKG	IKBKG	IKBKG	9634	-0.0024	0.39	NO
50	MAP3K7	MAP3K7	MAP3K7	9876	-0.0078	0.37	NO
51	NFKBIB	NFKBIB	NFKBIB	10545	-0.026	0.34	NO
52	PSMC6	PSMC6	PSMC6	10607	-0.028	0.34	NO
53	CUL1	CUL1	CUL1	10653	-0.029	0.34	NO
54	PSMD6	PSMD6	PSMD6	10711	-0.03	0.35	NO
55	FBXW11	FBXW11	FBXW11	10747	-0.031	0.35	NO
56	PSME1	PSME1	PSME1	10788	-0.032	0.36	NO
57	CHUK	CHUK	CHUK	11084	-0.04	0.34	NO
58	PSMD8	PSMD8	PSMD8	11299	-0.046	0.34	NO
59	PSMD10	PSMD10	PSMD10	11913	-0.064	0.32	NO
60	SKP1	SKP1	SKP1	12367	-0.078	0.31	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: PID ILK PATHWAY.

Figure S124. Get High-res Image For the top 5 core enriched genes in the pathway: PID ILK 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 TRIF MEDIATED TLR3 SIGNALING

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	CCNE1	CCNE1	CCNE1	1091	0.55	0.057	YES
2	CCNE2	CCNE2	CCNE2	2912	0.29	0.016	YES
3	PSMB9	PSMB9	PSMB9	3583	0.23	0.028	YES
4	CDKN1A	CDKN1A	CDKN1A	4114	0.19	0.039	YES
5	RPS27A	RPS27A	RPS27A	4385	0.17	0.061	YES
6	PSMD4	PSMD4	PSMD4	4433	0.17	0.095	YES
7	PSMB10	PSMB10	PSMB10	4455	0.17	0.13	YES
8	PSMB3	PSMB3	PSMB3	4974	0.14	0.13	YES
9	PSMD14	PSMD14	PSMD14	5003	0.14	0.16	YES
10	PSMB2	PSMB2	PSMB2	5045	0.14	0.19	YES
11	PSMA5	PSMA5	PSMA5	5096	0.14	0.21	YES
12	PSMD13	PSMD13	PSMD13	5319	0.13	0.23	YES
13	PSME4	PSME4	PSME4	5697	0.11	0.23	YES
14	PSMD12	PSMD12	PSMD12	5708	0.11	0.25	YES
15	CDK2	CDK2	CDK2	5719	0.11	0.28	YES
16	PSMB4	PSMB4	PSMB4	5929	0.1	0.29	YES
17	PSMB6	PSMB6	PSMB6	6126	0.094	0.3	YES
18	PSMC1	PSMC1	PSMC1	6166	0.093	0.31	YES
19	PSMC3	PSMC3	PSMC3	6255	0.09	0.33	YES
20	PSMC5	PSMC5	PSMC5	6287	0.089	0.35	YES
21	PSMD11	PSMD11	PSMD11	6652	0.078	0.34	YES
22	UBA52	UBA52	UBA52	6667	0.078	0.36	YES
23	PSMD3	PSMD3	PSMD3	6694	0.077	0.37	YES
24	PSMB1	PSMB1	PSMB1	6784	0.074	0.38	YES
25	PSMA4	PSMA4	PSMA4	7102	0.064	0.38	YES
26	PSME2	PSME2	PSME2	7203	0.062	0.39	YES
27	PSMD2	PSMD2	PSMD2	7217	0.062	0.4	YES
28	RFWD2	RFWD2	RFWD2	7436	0.055	0.4	YES
29	PSMD7	PSMD7	PSMD7	7536	0.052	0.41	YES
30	PSMA1	PSMA1	PSMA1	7543	0.052	0.42	YES
31	PSMC2	PSMC2	PSMC2	7551	0.052	0.43	YES
32	PSMB8	PSMB8	PSMB8	7623	0.05	0.44	YES
33	PSMA6	PSMA6	PSMA6	7727	0.048	0.44	YES
34	PSMB7	PSMB7	PSMB7	7970	0.041	0.43	YES
35	PSMF1	PSMF1	PSMF1	8065	0.038	0.44	YES
36	PSMA7	PSMA7	PSMA7	8086	0.038	0.44	YES
37	PSMD5	PSMD5	PSMD5	8091	0.038	0.45	YES
38	TP53	TP53	TP53	8191	0.035	0.45	YES
39	PSMB5	PSMB5	PSMB5	8246	0.034	0.46	YES
40	PSMA3	PSMA3	PSMA3	8564	0.025	0.45	NO
41	PSMC4	PSMC4	PSMC4	8613	0.024	0.45	NO
42	PSMD9	PSMD9	PSMD9	8908	0.016	0.44	NO
43	PSMA2	PSMA2	PSMA2	8985	0.014	0.43	NO
44	PSMD1	PSMD1	PSMD1	9306	0.0062	0.42	NO
45	ATM	ATM	ATM	9751	-0.0051	0.39	NO
46	MDM2	MDM2	MDM2	10294	-0.02	0.37	NO
47	PSMC6	PSMC6	PSMC6	10607	-0.028	0.36	NO
48	PSMD6	PSMD6	PSMD6	10711	-0.03	0.36	NO
49	PSME1	PSME1	PSME1	10788	-0.032	0.36	NO
50	PSMD8	PSMD8	PSMD8	11299	-0.046	0.34	NO
51	CDKN1B	CDKN1B	CDKN1B	11800	-0.06	0.32	NO
52	PSMD10	PSMD10	PSMD10	11913	-0.064	0.33	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: REACTOME TRIF MEDIATED TLR3 SIGNALING.

Figure S126. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRIF MEDIATED TLR3 SIGNALING, 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 ORC1 REMOVAL FROM CHROMATIN

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	CDC6	CDC6	CDC6	1639	0.45	-0.018	YES
2	CDT1	CDT1	CDT1	1897	0.41	0.035	YES
3	CCNA2	CCNA2	CCNA2	2176	0.37	0.08	YES
4	PSMB9	PSMB9	PSMB9	3583	0.23	0.038	YES
5	CCNA1	CCNA1	CCNA1	3632	0.22	0.072	YES
6	MCM5	MCM5	MCM5	3703	0.22	0.1	YES
7	MCM6	MCM6	MCM6	3775	0.21	0.13	YES
8	CDKN1A	CDKN1A	CDKN1A	4114	0.19	0.15	YES
9	RPS27A	RPS27A	RPS27A	4385	0.17	0.16	YES
10	PSMD4	PSMD4	PSMD4	4433	0.17	0.18	YES
11	PSMB10	PSMB10	PSMB10	4455	0.17	0.21	YES
12	RB1	RB1	RB1	4501	0.17	0.24	YES
13	MCM7	MCM7	MCM7	4908	0.14	0.24	YES
14	PSMB3	PSMB3	PSMB3	4974	0.14	0.26	YES
15	PSMD14	PSMD14	PSMD14	5003	0.14	0.28	YES
16	PSMB2	PSMB2	PSMB2	5045	0.14	0.3	YES
17	PSMA5	PSMA5	PSMA5	5096	0.14	0.32	YES
18	PSMD13	PSMD13	PSMD13	5319	0.13	0.32	YES
19	PSME4	PSME4	PSME4	5697	0.11	0.32	YES
20	PSMD12	PSMD12	PSMD12	5708	0.11	0.34	YES
21	CDK2	CDK2	CDK2	5719	0.11	0.36	YES
22	PSMB4	PSMB4	PSMB4	5929	0.1	0.36	YES
23	PSMB6	PSMB6	PSMB6	6126	0.094	0.37	YES
24	PSMC1	PSMC1	PSMC1	6166	0.093	0.38	YES
25	MCM2	MCM2	MCM2	6176	0.093	0.39	YES
26	PSMC3	PSMC3	PSMC3	6255	0.09	0.4	YES
27	PSMC5	PSMC5	PSMC5	6287	0.089	0.42	YES
28	PSMD11	PSMD11	PSMD11	6652	0.078	0.41	YES
29	UBA52	UBA52	UBA52	6667	0.078	0.42	YES
30	PSMD3	PSMD3	PSMD3	6694	0.077	0.43	YES
31	PSMB1	PSMB1	PSMB1	6784	0.074	0.44	YES
32	MCM4	MCM4	MCM4	7029	0.067	0.44	YES
33	PSMA4	PSMA4	PSMA4	7102	0.064	0.44	YES
34	PSME2	PSME2	PSME2	7203	0.062	0.45	YES
35	PSMD2	PSMD2	PSMD2	7217	0.062	0.46	YES
36	PSMD7	PSMD7	PSMD7	7536	0.052	0.45	YES
37	PSMA1	PSMA1	PSMA1	7543	0.052	0.46	YES
38	PSMC2	PSMC2	PSMC2	7551	0.052	0.46	YES
39	PSMB8	PSMB8	PSMB8	7623	0.05	0.47	YES
40	PSMA6	PSMA6	PSMA6	7727	0.048	0.47	YES
41	PSMB7	PSMB7	PSMB7	7970	0.041	0.46	YES
42	PSMF1	PSMF1	PSMF1	8065	0.038	0.46	YES
43	MCM3	MCM3	MCM3	8067	0.038	0.47	YES
44	PSMA7	PSMA7	PSMA7	8086	0.038	0.48	YES
45	PSMD5	PSMD5	PSMD5	8091	0.038	0.48	YES
46	PSMB5	PSMB5	PSMB5	8246	0.034	0.48	NO
47	PSMA3	PSMA3	PSMA3	8564	0.025	0.46	NO
48	PSMC4	PSMC4	PSMC4	8613	0.024	0.47	NO
49	MCM8	MCM8	MCM8	8774	0.02	0.46	NO
50	PSMD9	PSMD9	PSMD9	8908	0.016	0.46	NO
51	PSMA2	PSMA2	PSMA2	8985	0.014	0.45	NO
52	PSMD1	PSMD1	PSMD1	9306	0.0062	0.44	NO
53	PSMC6	PSMC6	PSMC6	10607	-0.028	0.37	NO
54	PSMD6	PSMD6	PSMD6	10711	-0.03	0.37	NO
55	PSME1	PSME1	PSME1	10788	-0.032	0.37	NO
56	PSMD8	PSMD8	PSMD8	11299	-0.046	0.35	NO
57	CDKN1B	CDKN1B	CDKN1B	11800	-0.06	0.33	NO
58	PSMD10	PSMD10	PSMD10	11913	-0.064	0.33	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: REACTOME ORC1 REMOVAL FROM CHROMATIN.

Figure S128. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ORC1 REMOVAL FROM CHROMATIN, 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 ACTIVATION OF NF KAPPAB IN B CELLS

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	CHEK2	CHEK2	CHEK2	1287	0.51	0.054	YES
2	PSMB9	PSMB9	PSMB9	3583	0.23	-0.019	YES
3	RPS27A	RPS27A	RPS27A	4385	0.17	-0.021	YES
4	PSMD4	PSMD4	PSMD4	4433	0.17	0.018	YES
5	PSMB10	PSMB10	PSMB10	4455	0.17	0.059	YES
6	CDC25A	CDC25A	CDC25A	4815	0.15	0.075	YES
7	PSMB3	PSMB3	PSMB3	4974	0.14	0.1	YES
8	PSMD14	PSMD14	PSMD14	5003	0.14	0.14	YES
9	PSMB2	PSMB2	PSMB2	5045	0.14	0.17	YES
10	PSMA5	PSMA5	PSMA5	5096	0.14	0.2	YES
11	PSMD13	PSMD13	PSMD13	5319	0.13	0.22	YES
12	PSME4	PSME4	PSME4	5697	0.11	0.22	YES
13	PSMD12	PSMD12	PSMD12	5708	0.11	0.25	YES
14	PSMB4	PSMB4	PSMB4	5929	0.1	0.26	YES
15	PSMB6	PSMB6	PSMB6	6126	0.094	0.27	YES
16	PSMC1	PSMC1	PSMC1	6166	0.093	0.3	YES
17	PSMC3	PSMC3	PSMC3	6255	0.09	0.31	YES
18	PSMC5	PSMC5	PSMC5	6287	0.089	0.33	YES
19	PSMD11	PSMD11	PSMD11	6652	0.078	0.33	YES
20	UBA52	UBA52	UBA52	6667	0.078	0.35	YES
21	PSMD3	PSMD3	PSMD3	6694	0.077	0.37	YES
22	PSMB1	PSMB1	PSMB1	6784	0.074	0.38	YES
23	PSMA4	PSMA4	PSMA4	7102	0.064	0.38	YES
24	PSME2	PSME2	PSME2	7203	0.062	0.39	YES
25	PSMD2	PSMD2	PSMD2	7217	0.062	0.4	YES
26	PSMD7	PSMD7	PSMD7	7536	0.052	0.4	YES
27	PSMA1	PSMA1	PSMA1	7543	0.052	0.41	YES
28	PSMC2	PSMC2	PSMC2	7551	0.052	0.42	YES
29	PSMB8	PSMB8	PSMB8	7623	0.05	0.43	YES
30	PSMA6	PSMA6	PSMA6	7727	0.048	0.44	YES
31	CHEK1	CHEK1	CHEK1	7853	0.044	0.44	YES
32	PSMB7	PSMB7	PSMB7	7970	0.041	0.44	YES
33	PSMF1	PSMF1	PSMF1	8065	0.038	0.45	YES
34	PSMA7	PSMA7	PSMA7	8086	0.038	0.46	YES
35	PSMD5	PSMD5	PSMD5	8091	0.038	0.47	YES
36	PSMB5	PSMB5	PSMB5	8246	0.034	0.47	NO
37	PSMA3	PSMA3	PSMA3	8564	0.025	0.46	NO
38	PSMC4	PSMC4	PSMC4	8613	0.024	0.46	NO
39	PSMD9	PSMD9	PSMD9	8908	0.016	0.44	NO
40	PSMA2	PSMA2	PSMA2	8985	0.014	0.44	NO
41	PSMD1	PSMD1	PSMD1	9306	0.0062	0.43	NO
42	ATM	ATM	ATM	9751	-0.0051	0.4	NO
43	PSMC6	PSMC6	PSMC6	10607	-0.028	0.36	NO
44	PSMD6	PSMD6	PSMD6	10711	-0.03	0.36	NO
45	PSME1	PSME1	PSME1	10788	-0.032	0.37	NO
46	PSMD8	PSMD8	PSMD8	11299	-0.046	0.35	NO
47	PSMD10	PSMD10	PSMD10	11913	-0.064	0.33	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: REACTOME ACTIVATION OF NF KAPPAB IN B CELLS.

Figure S130. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF NF KAPPAB IN B CELLS, 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 P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT

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	CDC6	CDC6	CDC6	1639	0.45	0.013	YES
2	CDT1	CDT1	CDT1	1897	0.41	0.094	YES
3	PSMB9	PSMB9	PSMB9	3583	0.23	0.052	YES
4	RPS27A	RPS27A	RPS27A	4385	0.17	0.048	YES
5	PSMD4	PSMD4	PSMD4	4433	0.17	0.084	YES
6	PSMB10	PSMB10	PSMB10	4455	0.17	0.12	YES
7	PSMB3	PSMB3	PSMB3	4974	0.14	0.13	YES
8	PSMD14	PSMD14	PSMD14	5003	0.14	0.16	YES
9	PSMB2	PSMB2	PSMB2	5045	0.14	0.19	YES
10	PSMA5	PSMA5	PSMA5	5096	0.14	0.22	YES
11	PSMD13	PSMD13	PSMD13	5319	0.13	0.23	YES
12	PSME4	PSME4	PSME4	5697	0.11	0.24	YES
13	PSMD12	PSMD12	PSMD12	5708	0.11	0.26	YES
14	PSMB4	PSMB4	PSMB4	5929	0.1	0.27	YES
15	PSMB6	PSMB6	PSMB6	6126	0.094	0.28	YES
16	PSMC1	PSMC1	PSMC1	6166	0.093	0.3	YES
17	PSMC3	PSMC3	PSMC3	6255	0.09	0.32	YES
18	PSMC5	PSMC5	PSMC5	6287	0.089	0.34	YES
19	GMNN	GMNN	GMNN	6291	0.089	0.36	YES
20	PSMD11	PSMD11	PSMD11	6652	0.078	0.36	YES
21	UBA52	UBA52	UBA52	6667	0.078	0.37	YES
22	PSMD3	PSMD3	PSMD3	6694	0.077	0.39	YES
23	PSMB1	PSMB1	PSMB1	6784	0.074	0.4	YES
24	PSMA4	PSMA4	PSMA4	7102	0.064	0.4	YES
25	PSME2	PSME2	PSME2	7203	0.062	0.41	YES
26	PSMD2	PSMD2	PSMD2	7217	0.062	0.42	YES
27	PSMD7	PSMD7	PSMD7	7536	0.052	0.42	YES
28	PSMA1	PSMA1	PSMA1	7543	0.052	0.43	YES
29	PSMC2	PSMC2	PSMC2	7551	0.052	0.44	YES
30	PSMB8	PSMB8	PSMB8	7623	0.05	0.45	YES
31	PSMA6	PSMA6	PSMA6	7727	0.048	0.45	YES
32	PSMB7	PSMB7	PSMB7	7970	0.041	0.45	YES
33	PSMF1	PSMF1	PSMF1	8065	0.038	0.45	YES
34	PSMA7	PSMA7	PSMA7	8086	0.038	0.46	YES
35	PSMD5	PSMD5	PSMD5	8091	0.038	0.47	YES
36	PSMB5	PSMB5	PSMB5	8246	0.034	0.47	NO
37	PSMA3	PSMA3	PSMA3	8564	0.025	0.46	NO
38	PSMC4	PSMC4	PSMC4	8613	0.024	0.46	NO
39	MCM8	MCM8	MCM8	8774	0.02	0.45	NO
40	PSMD9	PSMD9	PSMD9	8908	0.016	0.45	NO
41	PSMA2	PSMA2	PSMA2	8985	0.014	0.45	NO
42	PSMD1	PSMD1	PSMD1	9306	0.0062	0.43	NO
43	PSMC6	PSMC6	PSMC6	10607	-0.028	0.37	NO
44	PSMD6	PSMD6	PSMD6	10711	-0.03	0.37	NO
45	PSME1	PSME1	PSME1	10788	-0.032	0.37	NO
46	PSMD8	PSMD8	PSMD8	11299	-0.046	0.35	NO
47	PSMD10	PSMD10	PSMD10	11913	-0.064	0.33	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: REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT.

Figure S132. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT, 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 CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6

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	ARHGAP10	ARHGAP10	ARHGAP10	212	0.84	0.14	YES
2	UNC5A	UNC5A	UNC5A	2763	0.3	0.045	YES
3	DAPK1	DAPK1	DAPK1	2864	0.29	0.091	YES
4	PSMB9	PSMB9	PSMB9	3583	0.23	0.091	YES
5	RPS27A	RPS27A	RPS27A	4385	0.17	0.076	YES
6	PSMD4	PSMD4	PSMD4	4433	0.17	0.1	YES
7	PSMB10	PSMB10	PSMB10	4455	0.17	0.13	YES
8	DCC	DCC	DCC	4530	0.16	0.16	YES
9	UNC5B	UNC5B	UNC5B	4875	0.15	0.16	YES
10	CASP3	CASP3	CASP3	4888	0.15	0.19	YES
11	PSMB3	PSMB3	PSMB3	4974	0.14	0.21	YES
12	PSMD14	PSMD14	PSMD14	5003	0.14	0.23	YES
13	PSMB2	PSMB2	PSMB2	5045	0.14	0.25	YES
14	PSMA5	PSMA5	PSMA5	5096	0.14	0.28	YES
15	PSMD13	PSMD13	PSMD13	5319	0.13	0.28	YES
16	PSME4	PSME4	PSME4	5697	0.11	0.28	YES
17	PSMD12	PSMD12	PSMD12	5708	0.11	0.3	YES
18	PSMB4	PSMB4	PSMB4	5929	0.1	0.31	YES
19	PSMB6	PSMB6	PSMB6	6126	0.094	0.31	YES
20	PSMC1	PSMC1	PSMC1	6166	0.093	0.33	YES
21	PSMC3	PSMC3	PSMC3	6255	0.09	0.34	YES
22	PSMC5	PSMC5	PSMC5	6287	0.089	0.35	YES
23	DAPK3	DAPK3	DAPK3	6340	0.087	0.36	YES
24	PAK2	PAK2	PAK2	6423	0.084	0.38	YES
25	PSMD11	PSMD11	PSMD11	6652	0.078	0.38	YES
26	UBA52	UBA52	UBA52	6667	0.078	0.39	YES
27	PSMD3	PSMD3	PSMD3	6694	0.077	0.4	YES
28	PSMB1	PSMB1	PSMB1	6784	0.074	0.41	YES
29	PSMA4	PSMA4	PSMA4	7102	0.064	0.4	YES
30	PSME2	PSME2	PSME2	7203	0.062	0.41	YES
31	PSMD2	PSMD2	PSMD2	7217	0.062	0.42	YES
32	PSMD7	PSMD7	PSMD7	7536	0.052	0.41	YES
33	PSMA1	PSMA1	PSMA1	7543	0.052	0.42	YES
34	PSMC2	PSMC2	PSMC2	7551	0.052	0.43	YES
35	PSMB8	PSMB8	PSMB8	7623	0.05	0.43	YES
36	PSMA6	PSMA6	PSMA6	7727	0.048	0.43	YES
37	PSMB7	PSMB7	PSMB7	7970	0.041	0.43	YES
38	PSMF1	PSMF1	PSMF1	8065	0.038	0.43	YES
39	PSMA7	PSMA7	PSMA7	8086	0.038	0.44	YES
40	PSMD5	PSMD5	PSMD5	8091	0.038	0.44	YES
41	PSMB5	PSMB5	PSMB5	8246	0.034	0.44	NO
42	PSMA3	PSMA3	PSMA3	8564	0.025	0.42	NO
43	PSMC4	PSMC4	PSMC4	8613	0.024	0.43	NO
44	MAGED1	MAGED1	MAGED1	8619	0.024	0.43	NO
45	PSMD9	PSMD9	PSMD9	8908	0.016	0.42	NO
46	PSMA2	PSMA2	PSMA2	8985	0.014	0.42	NO
47	CASP9	CASP9	CASP9	9154	0.0099	0.41	NO
48	PSMD1	PSMD1	PSMD1	9306	0.0062	0.4	NO
49	PSMC6	PSMC6	PSMC6	10607	-0.028	0.33	NO
50	PSMD6	PSMD6	PSMD6	10711	-0.03	0.33	NO
51	PSME1	PSME1	PSME1	10788	-0.032	0.33	NO
52	PSMD8	PSMD8	PSMD8	11299	-0.046	0.31	NO
53	PSMD10	PSMD10	PSMD10	11913	-0.064	0.29	NO
54	APPL1	APPL1	APPL1	12571	-0.085	0.27	NO
55	DAPK2	DAPK2	DAPK2	14413	-0.16	0.19	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: REACTOME CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6.

Figure S134. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6, 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 REGULATION OF APOPTOSIS

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	PARVG	PARVG	PARVG	254	0.82	0.11	YES
2	SNAI1	SNAI1	SNAI1	459	0.72	0.2	YES
3	PPP1R14C	PPP1R14C	PPP1R14C	843	0.61	0.28	YES
4	ACTN1	ACTN1	ACTN1	1597	0.46	0.3	YES
5	ZYX	ZYX	ZYX	1720	0.44	0.36	YES
6	MYL9	MYL9	MYL9	1828	0.42	0.42	YES
7	TACC3	TACC3	TACC3	2531	0.33	0.43	YES
8	RHOG	RHOG	RHOG	3270	0.26	0.43	YES
9	PPP1R14B	PPP1R14B	PPP1R14B	3843	0.21	0.43	YES
10	AURKA	AURKA	AURKA	4263	0.18	0.43	YES
11	ZEB1	ZEB1	ZEB1	4324	0.18	0.45	YES
12	NCK2	NCK2	NCK2	4793	0.15	0.45	YES
13	PARVA	PARVA	PARVA	5352	0.12	0.44	YES
14	ILK	ILK	ILK	5400	0.12	0.45	YES
15	PPP1R14A	PPP1R14A	PPP1R14A	5722	0.11	0.45	YES
16	JUN	JUN	JUN	6043	0.098	0.45	YES
17	XPO1	XPO1	XPO1	6155	0.093	0.46	YES
18	ILKAP	ILKAP	ILKAP	6228	0.091	0.46	YES
19	RUVBL2	RUVBL2	RUVBL2	6482	0.083	0.46	YES
20	RAC1	RAC1	RAC1	6566	0.081	0.47	YES
21	ELMO2	ELMO2	ELMO2	6868	0.072	0.46	NO
22	CDC37	CDC37	CDC37	7288	0.06	0.45	NO
23	CDC42	CDC42	CDC42	7685	0.048	0.44	NO
24	PARP1	PARP1	PARP1	8214	0.035	0.41	NO
25	IQGAP1	IQGAP1	IQGAP1	8389	0.03	0.4	NO
26	NACA	NACA	NACA	8498	0.027	0.4	NO
27	RUVBL1	RUVBL1	RUVBL1	8541	0.026	0.4	NO
28	CREB1	CREB1	CREB1	8797	0.019	0.39	NO
29	LIMS2	LIMS2	LIMS2	9107	0.011	0.38	NO
30	CKAP5	CKAP5	CKAP5	9124	0.01	0.38	NO
31	PPP1R12A	PPP1R12A	PPP1R12A	9509	0.00056	0.36	NO
32	GIT2	GIT2	GIT2	9516	0.00045	0.36	NO
33	CTNNB1	CTNNB1	CTNNB1	9851	-0.0074	0.34	NO
34	PXN	PXN	PXN	10032	-0.012	0.33	NO
35	LIMS1	LIMS1	LIMS1	10206	-0.017	0.32	NO
36	CCND1	CCND1	CCND1	10392	-0.022	0.32	NO
37	AKT1	AKT1	AKT1	10438	-0.023	0.32	NO
38	ARHGEF6	ARHGEF6	ARHGEF6	10852	-0.034	0.3	NO
39	DIAPH1	DIAPH1	DIAPH1	11220	-0.044	0.28	NO
40	ARHGEF7	ARHGEF7	ARHGEF7	11423	-0.049	0.28	NO
41	GSK3B	GSK3B	GSK3B	11561	-0.053	0.28	NO
42	HSP90AA1	HSP90AA1	HSP90AA1	11945	-0.065	0.27	NO
43	PARVB	PARVB	PARVB	12626	-0.087	0.24	NO
44	RICTOR	RICTOR	RICTOR	12708	-0.09	0.25	NO
45	TNS1	TNS1	TNS1	15419	-0.23	0.14	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: REACTOME REGULATION OF APOPTOSIS.

Figure S136. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME REGULATION OF APOPTOSIS, 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 CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION

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	KDELR3	KDELR3	KDELR3	439	0.72	0.15	YES
2	PDIA5	PDIA5	PDIA5	3147	0.27	0.058	YES
3	SHC1	SHC1	SHC1	3268	0.26	0.11	YES
4	WIPI1	WIPI1	WIPI1	3565	0.23	0.15	YES
5	HDGF	HDGF	HDGF	3599	0.23	0.2	YES
6	LMNA	LMNA	LMNA	3657	0.22	0.25	YES
7	FKBP14	FKBP14	FKBP14	4542	0.16	0.24	YES
8	ARFGAP1	ARFGAP1	ARFGAP1	4645	0.16	0.27	YES
9	DDX11	DDX11	DDX11	4902	0.14	0.29	YES
10	SULT1A3	SULT1A3	SULT1A3	5161	0.13	0.31	YES
11	TPP1	TPP1	TPP1	5662	0.11	0.31	YES
12	C19orf10	C19orf10	C19orf10	5830	0.11	0.32	YES
13	PDIA6	PDIA6	PDIA6	6063	0.097	0.33	YES
14	SSR1	SSR1	SSR1	6073	0.096	0.35	YES
15	PREB	PREB	PREB	6288	0.089	0.36	YES
16	DNAJB11	DNAJB11	DNAJB11	6559	0.081	0.37	YES
17	ZBTB17	ZBTB17	ZBTB17	6621	0.079	0.38	YES
18	YIF1A	YIF1A	YIF1A	6677	0.077	0.4	YES
19	EXTL3	EXTL3	EXTL3	6722	0.076	0.41	YES
20	SEC31A	SEC31A	SEC31A	6937	0.07	0.42	YES
21	KLHDC3	KLHDC3	KLHDC3	7272	0.06	0.41	YES
22	DCTN1	DCTN1	DCTN1	7350	0.058	0.42	YES
23	EDEM1	EDEM1	EDEM1	7384	0.057	0.43	YES
24	SRPRB	SRPRB	SRPRB	8001	0.04	0.41	NO
25	GOSR2	GOSR2	GOSR2	8598	0.025	0.38	NO
26	PPP2R5B	PPP2R5B	PPP2R5B	8793	0.02	0.38	NO
27	TATDN2	TATDN2	TATDN2	8837	0.018	0.38	NO
28	TLN1	TLN1	TLN1	8875	0.017	0.38	NO
29	CXXC1	CXXC1	CXXC1	9140	0.01	0.37	NO
30	ACADVL	ACADVL	ACADVL	9579	-0.0011	0.34	NO
31	XBP1	XBP1	XBP1	9632	-0.0024	0.34	NO
32	HYOU1	HYOU1	HYOU1	9802	-0.0063	0.33	NO
33	CUL7	CUL7	CUL7	9947	-0.0098	0.33	NO
34	ADD1	ADD1	ADD1	9980	-0.011	0.33	NO
35	DNAJC3	DNAJC3	DNAJC3	10052	-0.013	0.33	NO
36	WFS1	WFS1	WFS1	10073	-0.013	0.33	NO
37	SRPR	SRPR	SRPR	10171	-0.016	0.33	NO
38	SERP1	SERP1	SERP1	10271	-0.018	0.32	NO
39	ATP6V0D1	ATP6V0D1	ATP6V0D1	10326	-0.02	0.33	NO
40	TSPYL2	TSPYL2	TSPYL2	10919	-0.036	0.3	NO
41	CTDSP2	CTDSP2	CTDSP2	11603	-0.054	0.28	NO
42	GSK3A	GSK3A	GSK3A	11854	-0.062	0.28	NO
43	SYVN1	SYVN1	SYVN1	12031	-0.067	0.28	NO
44	DNAJB9	DNAJB9	DNAJB9	14786	-0.18	0.17	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: REACTOME CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION .

Figure S138. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION , 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 P53 DEPENDENT G1 DNA DAMAGE RESPONSE

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	CDC6	CDC6	CDC6	1639	0.45	-0.013	YES
2	CDT1	CDT1	CDT1	1897	0.41	0.044	YES
3	E2F2	E2F2	E2F2	2552	0.33	0.064	YES
4	PSMB9	PSMB9	PSMB9	3583	0.23	0.046	YES
5	MCM5	MCM5	MCM5	3703	0.22	0.077	YES
6	MCM6	MCM6	MCM6	3775	0.21	0.11	YES
7	E2F1	E2F1	E2F1	3827	0.21	0.14	YES
8	RPS27A	RPS27A	RPS27A	4385	0.17	0.14	YES
9	PSMD4	PSMD4	PSMD4	4433	0.17	0.17	YES
10	PSMB10	PSMB10	PSMB10	4455	0.17	0.2	YES
11	MCM7	MCM7	MCM7	4908	0.14	0.2	YES
12	PSMB3	PSMB3	PSMB3	4974	0.14	0.22	YES
13	PSMD14	PSMD14	PSMD14	5003	0.14	0.24	YES
14	PSMB2	PSMB2	PSMB2	5045	0.14	0.26	YES
15	PSMA5	PSMA5	PSMA5	5096	0.14	0.28	YES
16	E2F3	E2F3	E2F3	5259	0.13	0.3	YES
17	PSMD13	PSMD13	PSMD13	5319	0.13	0.32	YES
18	PSME4	PSME4	PSME4	5697	0.11	0.31	YES
19	PSMD12	PSMD12	PSMD12	5708	0.11	0.33	YES
20	PSMB4	PSMB4	PSMB4	5929	0.1	0.34	YES
21	PSMB6	PSMB6	PSMB6	6126	0.094	0.34	YES
22	PSMC1	PSMC1	PSMC1	6166	0.093	0.36	YES
23	MCM2	MCM2	MCM2	6176	0.093	0.37	YES
24	PSMC3	PSMC3	PSMC3	6255	0.09	0.38	YES
25	PSMC5	PSMC5	PSMC5	6287	0.089	0.4	YES
26	GMNN	GMNN	GMNN	6291	0.089	0.41	YES
27	PSMD11	PSMD11	PSMD11	6652	0.078	0.41	YES
28	UBA52	UBA52	UBA52	6667	0.078	0.42	YES
29	PSMD3	PSMD3	PSMD3	6694	0.077	0.43	YES
30	PSMB1	PSMB1	PSMB1	6784	0.074	0.44	YES
31	MCM4	MCM4	MCM4	7029	0.067	0.44	YES
32	PSMA4	PSMA4	PSMA4	7102	0.064	0.44	YES
33	PSME2	PSME2	PSME2	7203	0.062	0.45	YES
34	PSMD2	PSMD2	PSMD2	7217	0.062	0.46	YES
35	PSMD7	PSMD7	PSMD7	7536	0.052	0.45	YES
36	PSMA1	PSMA1	PSMA1	7543	0.052	0.46	YES
37	PSMC2	PSMC2	PSMC2	7551	0.052	0.47	YES
38	PSMB8	PSMB8	PSMB8	7623	0.05	0.47	YES
39	PSMA6	PSMA6	PSMA6	7727	0.048	0.48	YES
40	PSMB7	PSMB7	PSMB7	7970	0.041	0.47	YES
41	PSMF1	PSMF1	PSMF1	8065	0.038	0.47	YES
42	MCM3	MCM3	MCM3	8067	0.038	0.48	YES
43	PSMA7	PSMA7	PSMA7	8086	0.038	0.48	YES
44	PSMD5	PSMD5	PSMD5	8091	0.038	0.49	YES
45	PSMB5	PSMB5	PSMB5	8246	0.034	0.48	NO
46	PSMA3	PSMA3	PSMA3	8564	0.025	0.47	NO
47	PSMC4	PSMC4	PSMC4	8613	0.024	0.47	NO
48	MCM8	MCM8	MCM8	8774	0.02	0.47	NO
49	PSMD9	PSMD9	PSMD9	8908	0.016	0.46	NO
50	PSMA2	PSMA2	PSMA2	8985	0.014	0.46	NO
51	PSMD1	PSMD1	PSMD1	9306	0.0062	0.44	NO
52	PSMC6	PSMC6	PSMC6	10607	-0.028	0.38	NO
53	PSMD6	PSMD6	PSMD6	10711	-0.03	0.38	NO
54	PSME1	PSME1	PSME1	10788	-0.032	0.38	NO
55	PSMD8	PSMD8	PSMD8	11299	-0.046	0.36	NO
56	PSMD10	PSMD10	PSMD10	11913	-0.064	0.33	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: REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE.

Figure S140. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE, 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 = KICH-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = KICH-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)

Made with Nozzle