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

Prostate Adenocarcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

doi:10.7908/C19886GD

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 PRAD-TP. Broad Institute of MIT and Harvard. doi:10.7908/C19886GD

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 "PRAD-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: 717
Number of samples: 497
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 96
pheno.type: 2 - 4 :[ clus2 ] 142
pheno.type: 3 - 4 :[ clus3 ] 151
pheno.type: 4 - 4 :[ clus4 ] 108

For the expression subtypes of 18274 genes in 498 samples, GSEA found enriched gene sets in each cluster using 497 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG PROPANOATE METABOLISM, KEGG ADHERENS JUNCTION, KEGG INSULIN SIGNALING PATHWAY, KEGG THYROID CANCER, BIOCARTA AGR PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA MYOSIN PATHWAY

And common core enriched genes are ACTN1, ACTN2, ACTN3, MAPK1, VCL, ABAT, ACACB, ACAT2, ACSS2, ACSS3

clus2

Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG N GLYCAN BIOSYNTHESIS, KEGG UBIQUITIN MEDIATED PROTEOLYSIS, PID ECADHERIN NASCENTAJ PATHWAY, PID LIS1PATHWAY, REACTOME METABOLISM OF NON CODING RNA, REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER, REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM, REACTOME RNA POL II TRANSCRIPTION, REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES

And common core enriched genes are NCBP1, NUP107, NUP133, NUP153, NUP155, NUP188, NUP205, NUP210, NUP214, NUP37

clus3

Top enriched gene sets are KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG RIBOSOME, KEGG DNA REPLICATION, KEGG PROTEASOME, KEGG BASE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION, KEGG CELL CYCLE, KEGG PARKINSONS DISEASE

And common core enriched genes are MCM7, POLE2, PRIM2, RPA3, CDC45, CDC6, CDT1, DNA2, FEN1, MCM5

clus4

Top enriched gene sets are KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG LYSINE DEGRADATION, KEGG ARGININE AND PROLINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG GLYCEROLIPID METABOLISM, KEGG INOSITOL PHOSPHATE METABOLISM

And common core enriched genes are BDNF, BEX1, BIRC3, MMP7, NGFR, NTF3, NTF4, NTRK1, BBOX1, PIPOX

Results

Subtype clus1 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION	44	genes.ES.table	0.55	1.7	0.025	0.46	0.66	0.5	0.26	0.37	0.13	0.11
KEGG PROPANOATE METABOLISM	32	genes.ES.table	0.63	1.9	0.004	1	0.22	0.59	0.26	0.44	0	0.19
KEGG ADHERENS JUNCTION	73	genes.ES.table	0.51	1.8	0.002	0.64	0.47	0.33	0.24	0.25	0	0.14
KEGG INSULIN SIGNALING PATHWAY	133	genes.ES.table	0.42	1.7	0.0041	0.45	0.8	0.33	0.24	0.25	0.16	0.12
KEGG THYROID CANCER	29	genes.ES.table	0.54	1.7	0.014	0.41	0.75	0.17	0.11	0.15	0.14	0.11
BIOCARTA AGR PATHWAY	36	genes.ES.table	0.69	1.8	0	0.54	0.61	0.36	0.14	0.31	0.13	0.13
BIOCARTA HDAC PATHWAY	26	genes.ES.table	0.64	1.8	0	0.76	0.44	0.46	0.26	0.34	0	0.16
BIOCARTA INTEGRIN PATHWAY	38	genes.ES.table	0.59	1.9	0	0.64	0.33	0.37	0.24	0.28	0	0.14
BIOCARTA PYK2 PATHWAY	28	genes.ES.table	0.46	1.7	0.0078	0.51	0.62	0.29	0.26	0.21	0.12	0.13
BIOCARTA MYOSIN PATHWAY	29	genes.ES.table	0.61	1.8	0	0.57	0.58	0.45	0.19	0.36	0.13	0.14

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

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	ACSS3	ACSS3	ACSS3	181	0.44	0.14	YES
2	EHHADH	EHHADH	EHHADH	530	0.33	0.24	YES
3	LDHAL6A	LDHAL6A	LDHAL6A	1128	0.23	0.28	YES
4	ABAT	ABAT	ABAT	1442	0.2	0.34	YES
5	ACACB	ACACB	ACACB	2119	0.15	0.35	YES
6	ALDH2	ALDH2	ALDH2	2276	0.14	0.39	YES
7	ALDH6A1	ALDH6A1	ALDH6A1	2584	0.13	0.42	YES
8	LDHC	LDHC	LDHC	2901	0.11	0.44	YES
9	ALDH3A2	ALDH3A2	ALDH3A2	2986	0.11	0.47	YES
10	MLYCD	MLYCD	MLYCD	3265	0.095	0.49	YES
11	SUCLA2	SUCLA2	SUCLA2	3413	0.089	0.51	YES
12	LDHB	LDHB	LDHB	3498	0.086	0.54	YES
13	PCCA	PCCA	PCCA	3575	0.084	0.56	YES
14	ACAT2	ACAT2	ACAT2	3629	0.082	0.58	YES
15	ALDH1B1	ALDH1B1	ALDH1B1	3877	0.074	0.6	YES
16	MCEE	MCEE	MCEE	4352	0.062	0.59	YES
17	ALDH7A1	ALDH7A1	ALDH7A1	4437	0.06	0.61	YES
18	ACSS2	ACSS2	ACSS2	4528	0.058	0.62	YES
19	ALDH9A1	ALDH9A1	ALDH9A1	4797	0.052	0.62	YES
20	ACADM	ACADM	ACADM	5495	0.04	0.6	NO
21	SUCLG2	SUCLG2	SUCLG2	6439	0.027	0.56	NO
22	LDHAL6B	LDHAL6B	LDHAL6B	6950	0.02	0.54	NO
23	HIBCH	HIBCH	HIBCH	8274	0.0052	0.47	NO
24	MUT	MUT	MUT	9393	-0.0064	0.41	NO
25	HADHA	HADHA	HADHA	9777	-0.01	0.39	NO
26	ACACA	ACACA	ACACA	10658	-0.02	0.35	NO
27	PCCB	PCCB	PCCB	11114	-0.025	0.33	NO
28	ECHS1	ECHS1	ECHS1	11160	-0.025	0.34	NO
29	SUCLG1	SUCLG1	SUCLG1	11218	-0.026	0.34	NO
30	ACSS1	ACSS1	ACSS1	11326	-0.027	0.35	NO
31	ACAT1	ACAT1	ACAT1	12444	-0.04	0.3	NO
32	LDHA	LDHA	LDHA	13675	-0.056	0.25	NO

Figure S1. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S2. 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 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	PAK3	PAK3	PAK3	5	0.73	0.2	YES
2	FLNC	FLNC	FLNC	477	0.34	0.27	YES
3	MYLK	MYLK	MYLK	800	0.28	0.33	YES
4	MYH2	MYH2	MYH2	839	0.27	0.4	YES
5	ACTG2	ACTG2	ACTG2	1011	0.25	0.46	YES
6	PAK7	PAK7	PAK7	1189	0.23	0.51	YES
7	FLNA	FLNA	FLNA	1304	0.22	0.57	YES
8	ROCK2	ROCK2	ROCK2	1370	0.21	0.62	YES
9	CFL2	CFL2	CFL2	1528	0.2	0.67	YES
10	MYLK2	MYLK2	MYLK2	2881	0.11	0.62	NO
11	ROCK1	ROCK1	ROCK1	4263	0.064	0.56	NO
12	ANGPTL2	ANGPTL2	ANGPTL2	5020	0.049	0.54	NO
13	PAK1	PAK1	PAK1	6748	0.023	0.45	NO
14	ACTR2	ACTR2	ACTR2	7092	0.019	0.43	NO
15	PAK2	PAK2	PAK2	7954	0.0086	0.39	NO
16	ACTR3	ACTR3	ACTR3	8415	0.0039	0.36	NO
17	WASL	WASL	WASL	8438	0.0036	0.36	NO
18	VASP	VASP	VASP	8568	0.0023	0.36	NO
19	PFN2	PFN2	PFN2	8616	0.0018	0.36	NO
20	AKT1	AKT1	AKT1	8881	-0.0011	0.34	NO
21	CDC42	CDC42	CDC42	9838	-0.011	0.29	NO
22	PFN1	PFN1	PFN1	10331	-0.016	0.27	NO
23	FSCN3	FSCN3	FSCN3	10526	-0.018	0.26	NO
24	GDI2	GDI2	GDI2	10920	-0.022	0.25	NO
25	PAK4	PAK4	PAK4	10973	-0.023	0.25	NO
26	CFL1	CFL1	CFL1	11779	-0.032	0.22	NO
27	ACTG1	ACTG1	ACTG1	11852	-0.033	0.22	NO
28	GDI1	GDI1	GDI1	11911	-0.034	0.23	NO
29	RPS4X	RPS4X	RPS4X	12167	-0.036	0.22	NO
30	RHO	RHO	RHO	12182	-0.037	0.23	NO
31	FSCN1	FSCN1	FSCN1	12200	-0.037	0.24	NO
32	PAK6	PAK6	PAK6	13444	-0.053	0.19	NO
33	LIMK1	LIMK1	LIMK1	13799	-0.058	0.19	NO
34	WASF1	WASF1	WASF1	14340	-0.068	0.18	NO
35	FSCN2	FSCN2	FSCN2	16592	-0.15	0.091	NO

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

Figure S4. 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 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	ACTA1	ACTA1	ACTA1	204	0.43	0.12	YES
2	ACTN2	ACTN2	ACTN2	523	0.33	0.21	YES
3	CAV1	CAV1	CAV1	988	0.25	0.27	YES
4	ITGA1	ITGA1	ITGA1	1022	0.25	0.34	YES
5	VCL	VCL	VCL	1215	0.22	0.41	YES
6	ACTN3	ACTN3	ACTN3	1331	0.21	0.47	YES
7	PPP1R12B	PPP1R12B	PPP1R12B	1444	0.2	0.53	YES
8	TNS1	TNS1	TNS1	1505	0.2	0.59	YES
9	ACTN1	ACTN1	ACTN1	2592	0.12	0.57	YES
10	TLN1	TLN1	TLN1	3154	0.1	0.57	YES
11	JUN	JUN	JUN	3467	0.087	0.58	YES
12	SOS1	SOS1	SOS1	4197	0.066	0.56	YES
13	ROCK1	ROCK1	ROCK1	4263	0.064	0.57	YES
14	MAPK1	MAPK1	MAPK1	4310	0.063	0.59	YES
15	ITGB1	ITGB1	ITGB1	5128	0.047	0.56	NO
16	ZYX	ZYX	ZYX	5487	0.041	0.56	NO
17	RAP1A	RAP1A	RAP1A	5716	0.037	0.56	NO
18	MAPK8	MAPK8	MAPK8	6660	0.024	0.51	NO
19	MAP2K1	MAP2K1	MAP2K1	7035	0.019	0.5	NO
20	CRKL	CRKL	CRKL	7072	0.019	0.5	NO
21	RAPGEF1	RAPGEF1	RAPGEF1	7131	0.018	0.5	NO
22	GRB2	GRB2	GRB2	7569	0.013	0.48	NO
23	BCAR1	BCAR1	BCAR1	7759	0.011	0.48	NO
24	PXN	PXN	PXN	8011	0.008	0.46	NO
25	CAPNS2	CAPNS2	CAPNS2	8217	0.006	0.46	NO
26	FYN	FYN	FYN	8432	0.0037	0.44	NO
27	RHOA	RHOA	RHOA	8975	-0.0021	0.42	NO
28	RAF1	RAF1	RAF1	9259	-0.0051	0.4	NO
29	MAPK3	MAPK3	MAPK3	9285	-0.0054	0.4	NO
30	SHC1	SHC1	SHC1	9297	-0.0055	0.4	NO
31	CAPN1	CAPN1	CAPN1	9939	-0.012	0.37	NO
32	SRC	SRC	SRC	10220	-0.015	0.36	NO
33	CAPNS1	CAPNS1	CAPNS1	10615	-0.019	0.35	NO
34	MAP2K2	MAP2K2	MAP2K2	11396	-0.028	0.31	NO
35	PTK2	PTK2	PTK2	11585	-0.03	0.31	NO
36	CSK	CSK	CSK	12196	-0.037	0.29	NO
37	BCR	BCR	BCR	13098	-0.048	0.26	NO
38	HRAS	HRAS	HRAS	15206	-0.086	0.17	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: KEGG ADHERENS JUNCTION.

Figure S6. 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: KEGG INSULIN SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CAMK1G	CAMK1G	CAMK1G	201	0.43	0.2	YES
2	NFATC2	NFATC2	NFATC2	845	0.27	0.3	YES
3	IGF1	IGF1	IGF1	886	0.27	0.43	YES
4	MEF2C	MEF2C	MEF2C	1683	0.18	0.47	YES
5	PIK3CG	PIK3CG	PIK3CG	2292	0.14	0.51	YES
6	PIK3R1	PIK3R1	PIK3R1	2618	0.12	0.55	YES
7	CALM1	CALM1	CALM1	3402	0.089	0.55	YES
8	MEF2A	MEF2A	MEF2A	3535	0.085	0.59	YES
9	PIK3CA	PIK3CA	PIK3CA	3567	0.084	0.63	YES
10	MEF2D	MEF2D	MEF2D	4323	0.063	0.62	YES
11	PPP3CC	PPP3CC	PPP3CC	4350	0.062	0.64	YES
12	PPP3CB	PPP3CB	PPP3CB	4802	0.052	0.64	YES
13	MAPK7	MAPK7	MAPK7	5849	0.035	0.6	NO
14	INSR	INSR	INSR	6550	0.025	0.58	NO
15	IGF1R	IGF1R	IGF1R	6955	0.02	0.57	NO
16	NFATC1	NFATC1	NFATC1	7051	0.019	0.57	NO
17	CABIN1	CABIN1	CABIN1	7410	0.015	0.56	NO
18	CAMK1	CAMK1	CAMK1	7573	0.013	0.56	NO
19	HDAC5	HDAC5	HDAC5	8103	0.0069	0.53	NO
20	YWHAH	YWHAH	YWHAH	8264	0.0054	0.52	NO
21	CALM2	CALM2	CALM2	8591	0.0021	0.51	NO
22	AKT1	AKT1	AKT1	8881	-0.0011	0.49	NO
23	CALM3	CALM3	CALM3	8915	-0.0016	0.49	NO
24	MAPK14	MAPK14	MAPK14	9149	-0.004	0.48	NO
25	MAP2K6	MAP2K6	MAP2K6	9517	-0.0077	0.46	NO
26	PPP3CA	PPP3CA	PPP3CA	11885	-0.034	0.35	NO

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

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

genes ES table in pathway: KEGG THYROID CANCER

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	ACTN2	ACTN2	ACTN2	523	0.33	0.041	YES
2	SNAI2	SNAI2	SNAI2	685	0.3	0.094	YES
3	SORBS1	SORBS1	SORBS1	794	0.28	0.15	YES
4	VCL	VCL	VCL	1215	0.22	0.17	YES
5	ACTN3	ACTN3	ACTN3	1331	0.21	0.21	YES
6	FER	FER	FER	1571	0.19	0.24	YES
7	CTNNA3	CTNNA3	CTNNA3	1834	0.17	0.26	YES
8	PTPRM	PTPRM	PTPRM	1972	0.16	0.28	YES
9	TCF7	TCF7	TCF7	2000	0.16	0.32	YES
10	TCF7L1	TCF7L1	TCF7L1	2070	0.16	0.35	YES
11	LMO7	LMO7	LMO7	2182	0.15	0.37	YES
12	FGFR1	FGFR1	FGFR1	2200	0.15	0.4	YES
13	TGFBR2	TGFBR2	TGFBR2	2386	0.14	0.42	YES
14	EGFR	EGFR	EGFR	2471	0.13	0.44	YES
15	ACTN1	ACTN1	ACTN1	2592	0.12	0.46	YES
16	PTPRB	PTPRB	PTPRB	3429	0.088	0.44	YES
17	CTNNA2	CTNNA2	CTNNA2	3475	0.087	0.45	YES
18	SMAD4	SMAD4	SMAD4	3667	0.081	0.46	YES
19	SSX2IP	SSX2IP	SSX2IP	3705	0.079	0.47	YES
20	IQGAP1	IQGAP1	IQGAP1	3987	0.07	0.47	YES
21	TGFBR1	TGFBR1	TGFBR1	4126	0.067	0.48	YES
22	SNAI1	SNAI1	SNAI1	4182	0.066	0.49	YES
23	MAPK1	MAPK1	MAPK1	4310	0.063	0.5	YES
24	EP300	EP300	EP300	4311	0.063	0.51	YES
25	PVRL3	PVRL3	PVRL3	4775	0.053	0.49	NO
26	PTPN1	PTPN1	PTPN1	4921	0.05	0.5	NO
27	MET	MET	MET	5095	0.047	0.5	NO
28	SMAD3	SMAD3	SMAD3	5297	0.044	0.5	NO
29	BAIAP2	BAIAP2	BAIAP2	5544	0.04	0.49	NO
30	TCF7L2	TCF7L2	TCF7L2	5771	0.036	0.48	NO
31	CREBBP	CREBBP	CREBBP	5796	0.036	0.49	NO
32	CDH1	CDH1	CDH1	6263	0.029	0.47	NO
33	CTNNB1	CTNNB1	CTNNB1	6338	0.028	0.47	NO
34	WASF3	WASF3	WASF3	6392	0.028	0.48	NO
35	INSR	INSR	INSR	6550	0.025	0.47	NO
36	MAP3K7	MAP3K7	MAP3K7	6595	0.025	0.48	NO
37	ACTB	ACTB	ACTB	6663	0.024	0.48	NO
38	PARD3	PARD3	PARD3	6736	0.023	0.48	NO
39	CTNND1	CTNND1	CTNND1	6833	0.022	0.48	NO
40	IGF1R	IGF1R	IGF1R	6955	0.02	0.48	NO
41	MLLT4	MLLT4	MLLT4	7362	0.015	0.46	NO
42	ACTN4	ACTN4	ACTN4	7443	0.014	0.45	NO
43	TJP1	TJP1	TJP1	7533	0.013	0.45	NO
44	PTPRF	PTPRF	PTPRF	7577	0.013	0.45	NO
45	ERBB2	ERBB2	ERBB2	7804	0.01	0.44	NO
46	PVRL4	PVRL4	PVRL4	7846	0.0098	0.44	NO
47	WASF2	WASF2	WASF2	7854	0.0097	0.44	NO
48	CTNNA1	CTNNA1	CTNNA1	8219	0.006	0.42	NO
49	SMAD2	SMAD2	SMAD2	8250	0.0055	0.42	NO
50	FYN	FYN	FYN	8432	0.0037	0.42	NO
51	WASL	WASL	WASL	8438	0.0036	0.42	NO
52	CSNK2A2	CSNK2A2	CSNK2A2	8759	0.000045	0.4	NO
53	RHOA	RHOA	RHOA	8975	-0.0021	0.39	NO
54	NLK	NLK	NLK	9125	-0.0038	0.38	NO
55	PTPRJ	PTPRJ	PTPRJ	9267	-0.0052	0.37	NO
56	MAPK3	MAPK3	MAPK3	9285	-0.0054	0.37	NO
57	YES1	YES1	YES1	9462	-0.0073	0.36	NO
58	PTPN6	PTPN6	PTPN6	9756	-0.01	0.35	NO
59	PVRL2	PVRL2	PVRL2	9802	-0.01	0.35	NO
60	CDC42	CDC42	CDC42	9838	-0.011	0.35	NO
61	PVRL1	PVRL1	PVRL1	10036	-0.013	0.34	NO
62	SRC	SRC	SRC	10220	-0.015	0.34	NO
63	CSNK2A1	CSNK2A1	CSNK2A1	10443	-0.017	0.33	NO
64	RAC1	RAC1	RAC1	10867	-0.022	0.31	NO
65	RAC2	RAC2	RAC2	11154	-0.025	0.3	NO
66	ACP1	ACP1	ACP1	11562	-0.03	0.28	NO
67	LEF1	LEF1	LEF1	11583	-0.03	0.29	NO
68	ACTG1	ACTG1	ACTG1	11852	-0.033	0.28	NO
69	CSNK2B	CSNK2B	CSNK2B	12664	-0.042	0.24	NO
70	FARP2	FARP2	FARP2	13572	-0.055	0.2	NO
71	WAS	WAS	WAS	13892	-0.06	0.2	NO
72	WASF1	WASF1	WASF1	14340	-0.068	0.19	NO
73	RAC3	RAC3	RAC3	16208	-0.12	0.11	NO

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

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG THYROID 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: BIOCARTA AGR 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	PRKCB	PRKCB	PRKCB	152	0.46	0.099	YES
2	ITGB3	ITGB3	ITGB3	195	0.44	0.2	YES
3	CAV1	CAV1	CAV1	988	0.25	0.22	YES
4	VCL	VCL	VCL	1215	0.22	0.26	YES
5	PRKCA	PRKCA	PRKCA	1470	0.2	0.29	YES
6	KDR	KDR	KDR	1480	0.2	0.34	YES
7	NEDD4	NEDD4	NEDD4	1796	0.18	0.36	YES
8	MYOF	MYOF	MYOF	2017	0.16	0.39	YES
9	PRKAA2	PRKAA2	PRKAA2	2469	0.13	0.39	YES
10	PIK3R1	PIK3R1	PIK3R1	2618	0.12	0.41	YES
11	FLT1	FLT1	FLT1	2653	0.12	0.44	YES
12	PIK3CA	PIK3CA	PIK3CA	3567	0.084	0.41	YES
13	CDH5	CDH5	CDH5	3944	0.072	0.41	YES
14	IQGAP1	IQGAP1	IQGAP1	3987	0.07	0.42	YES
15	ITGAV	ITGAV	ITGAV	4029	0.069	0.44	YES
16	PTPN11	PTPN11	PTPN11	4205	0.065	0.44	YES
17	ROCK1	ROCK1	ROCK1	4263	0.064	0.45	YES
18	CBL	CBL	CBL	4265	0.064	0.47	YES
19	MAPK1	MAPK1	MAPK1	4310	0.063	0.48	YES
20	PTK2B	PTK2B	PTK2B	4747	0.054	0.47	NO
21	AKAP1	AKAP1	AKAP1	4835	0.052	0.48	NO
22	GAB1	GAB1	GAB1	5615	0.038	0.44	NO
23	FBXW11	FBXW11	FBXW11	5873	0.034	0.44	NO
24	GRB10	GRB10	GRB10	5994	0.033	0.44	NO
25	VEGFA	VEGFA	VEGFA	6160	0.03	0.44	NO
26	SHB	SHB	SHB	6186	0.03	0.44	NO
27	PDPK1	PDPK1	PDPK1	6296	0.029	0.44	NO
28	CTNNB1	CTNNB1	CTNNB1	6338	0.028	0.45	NO
29	NOS3	NOS3	NOS3	6518	0.026	0.44	NO
30	MAP2K1	MAP2K1	MAP2K1	7035	0.019	0.42	NO
31	HSP90AA1	HSP90AA1	HSP90AA1	7402	0.015	0.4	NO
32	PRKACA	PRKACA	PRKACA	7495	0.014	0.4	NO
33	GRB2	GRB2	GRB2	7569	0.013	0.4	NO
34	PAK2	PAK2	PAK2	7954	0.0086	0.38	NO
35	PXN	PXN	PXN	8011	0.008	0.38	NO
36	CTNNA1	CTNNA1	CTNNA1	8219	0.006	0.37	NO
37	CAMKK2	CAMKK2	CAMKK2	8411	0.0039	0.36	NO
38	FYN	FYN	FYN	8432	0.0037	0.36	NO
39	PRKAA1	PRKAA1	PRKAA1	8599	0.002	0.35	NO
40	DNM2	DNM2	DNM2	8717	0.00053	0.34	NO
41	AKT1	AKT1	AKT1	8881	-0.0011	0.34	NO
42	PRKAB1	PRKAB1	PRKAB1	8890	-0.0012	0.34	NO
43	RHOA	RHOA	RHOA	8975	-0.0021	0.33	NO
44	ARF1	ARF1	ARF1	9113	-0.0037	0.32	NO
45	MAPK14	MAPK14	MAPK14	9149	-0.004	0.32	NO
46	RAF1	RAF1	RAF1	9259	-0.0051	0.32	NO
47	PTPRJ	PTPRJ	PTPRJ	9267	-0.0052	0.32	NO
48	MAPK3	MAPK3	MAPK3	9285	-0.0054	0.32	NO
49	PRKAG1	PRKAG1	PRKAG1	9415	-0.0067	0.31	NO
50	MAP2K6	MAP2K6	MAP2K6	9517	-0.0077	0.31	NO
51	NCK2	NCK2	NCK2	9660	-0.0092	0.3	NO
52	PTPN6	PTPN6	PTPN6	9756	-0.01	0.3	NO
53	CDC42	CDC42	CDC42	9838	-0.011	0.3	NO
54	SRC	SRC	SRC	10220	-0.015	0.28	NO
55	HGS	HGS	HGS	10404	-0.017	0.28	NO
56	MAPK11	MAPK11	MAPK11	10414	-0.017	0.28	NO
57	FES	FES	FES	10497	-0.018	0.28	NO
58	MAP2K2	MAP2K2	MAP2K2	11396	-0.028	0.24	NO
59	PTK2	PTK2	PTK2	11585	-0.03	0.23	NO
60	MAP2K3	MAP2K3	MAP2K3	11737	-0.032	0.23	NO
61	NCK1	NCK1	NCK1	11856	-0.033	0.23	NO
62	MAPKAPK2	MAPKAPK2	MAPKAPK2	11941	-0.034	0.24	NO
63	PLCG1	PLCG1	PLCG1	12034	-0.035	0.24	NO
64	BRAF	BRAF	BRAF	12356	-0.039	0.23	NO
65	HSP90AB1	HSP90AB1	HSP90AB1	12818	-0.044	0.22	NO
66	PTPN2	PTPN2	PTPN2	14011	-0.062	0.17	NO
67	SH2D2A	SH2D2A	SH2D2A	14495	-0.07	0.16	NO
68	PRKCD	PRKCD	PRKCD	14667	-0.074	0.16	NO
69	VTN	VTN	VTN	16531	-0.14	0.095	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: BIOCARTA AGR PATHWAY.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AGR 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 HDAC PATHWAY

Table S7. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PRKCB	PRKCB	PRKCB	152	0.46	0.2	YES
2	CAMK2A	CAMK2A	CAMK2A	164	0.45	0.4	YES
3	PRKCA	PRKCA	PRKCA	1470	0.2	0.42	YES
4	PRKAR2A	PRKAR2A	PRKAR2A	1486	0.2	0.51	YES
5	CAMK2G	CAMK2G	CAMK2G	2549	0.13	0.51	YES
6	PIK3R1	PIK3R1	PIK3R1	2618	0.12	0.56	YES
7	PIK3CA	PIK3CA	PIK3CA	3567	0.084	0.55	YES
8	SOS1	SOS1	SOS1	4197	0.066	0.54	YES
9	PRKAR2B	PRKAR2B	PRKAR2B	4273	0.064	0.56	YES
10	MAPK1	MAPK1	MAPK1	4310	0.063	0.59	YES
11	RPS6KA5	RPS6KA5	RPS6KA5	5482	0.041	0.55	NO
12	PRKACB	PRKACB	PRKACB	5519	0.04	0.56	NO
13	PRKAR1A	PRKAR1A	PRKAR1A	6282	0.029	0.53	NO
14	CREB1	CREB1	CREB1	7163	0.018	0.49	NO
15	GRB2	GRB2	GRB2	7569	0.013	0.48	NO
16	CAMK2D	CAMK2D	CAMK2D	8838	-0.00074	0.41	NO
17	AKT1	AKT1	AKT1	8881	-0.0011	0.4	NO
18	MAPK14	MAPK14	MAPK14	9149	-0.004	0.39	NO
19	MAPK3	MAPK3	MAPK3	9285	-0.0054	0.39	NO
20	CAMK2B	CAMK2B	CAMK2B	9476	-0.0074	0.38	NO
21	ADCY1	ADCY1	ADCY1	10231	-0.015	0.34	NO
22	RAC1	RAC1	RAC1	10867	-0.022	0.32	NO
23	GNAS	GNAS	GNAS	11117	-0.025	0.32	NO
24	RPS6KA1	RPS6KA1	RPS6KA1	11294	-0.027	0.32	NO
25	PRKAR1B	PRKAR1B	PRKAR1B	13330	-0.052	0.23	NO
26	HRAS	HRAS	HRAS	15206	-0.086	0.17	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: BIOCARTA HDAC PATHWAY.

Figure S14. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HDAC 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 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	PRKCB	PRKCB	PRKCB	152	0.46	0.15	YES
2	MYL2	MYL2	MYL2	647	0.3	0.23	YES
3	MYLK	MYLK	MYLK	800	0.28	0.32	YES
4	PPP1R12B	PPP1R12B	PPP1R12B	1444	0.2	0.35	YES
5	PRKCA	PRKCA	PRKCA	1470	0.2	0.42	YES
6	ARHGEF4	ARHGEF4	ARHGEF4	2152	0.15	0.44	YES
7	ARHGEF7	ARHGEF7	ARHGEF7	2833	0.11	0.44	YES
8	ARHGEF17	ARHGEF17	ARHGEF17	2962	0.11	0.47	YES
9	ARHGEF6	ARHGEF6	ARHGEF6	3099	0.1	0.5	YES
10	ARHGEF9	ARHGEF9	ARHGEF9	3119	0.1	0.53	YES
11	ARHGEF10	ARHGEF10	ARHGEF10	3137	0.1	0.57	YES
12	PLCB1	PLCB1	PLCB1	3235	0.096	0.6	YES
13	ARHGEF15	ARHGEF15	ARHGEF15	3502	0.086	0.61	YES
14	ROCK1	ROCK1	ROCK1	4263	0.064	0.59	NO
15	ARHGEF2	ARHGEF2	ARHGEF2	5686	0.037	0.53	NO
16	ARHGEF12	ARHGEF12	ARHGEF12	5818	0.035	0.53	NO
17	GNAQ	GNAQ	GNAQ	5836	0.035	0.54	NO
18	GNA12	GNA12	GNA12	6515	0.026	0.52	NO
19	ARHGEF18	ARHGEF18	ARHGEF18	6644	0.024	0.52	NO
20	ARHGAP5	ARHGAP5	ARHGAP5	6675	0.024	0.52	NO
21	ARHGEF11	ARHGEF11	ARHGEF11	6677	0.024	0.53	NO
22	ARHGEF5	ARHGEF5	ARHGEF5	6996	0.02	0.52	NO
23	GNA13	GNA13	GNA13	8311	0.0049	0.45	NO
24	GNB1	GNB1	GNB1	8425	0.0038	0.44	NO
25	ARHGEF3	ARHGEF3	ARHGEF3	12361	-0.039	0.24	NO
26	ARHGEF1	ARHGEF1	ARHGEF1	12509	-0.04	0.25	NO
27	ARHGEF19	ARHGEF19	ARHGEF19	13032	-0.048	0.24	NO
28	ARHGEF16	ARHGEF16	ARHGEF16	13204	-0.05	0.24	NO
29	PKN1	PKN1	PKN1	15439	-0.093	0.16	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: BIOCARTA INTEGRIN PATHWAY.

Figure S16. 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: BIOCARTA PYK2 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	PAK3	PAK3	PAK3	5	0.73	0.17	YES
2	ACTA1	ACTA1	ACTA1	204	0.43	0.26	YES
3	NRG2	NRG2	NRG2	239	0.42	0.35	YES
4	NRG1	NRG1	NRG1	498	0.34	0.41	YES
5	DMD	DMD	DMD	775	0.28	0.46	YES
6	ITGA1	ITGA1	ITGA1	1022	0.25	0.5	YES
7	PAK7	PAK7	PAK7	1189	0.23	0.55	YES
8	MUSK	MUSK	MUSK	1340	0.21	0.59	YES
9	CHRM1	CHRM1	CHRM1	1544	0.19	0.62	YES
10	LAMA2	LAMA2	LAMA2	2010	0.16	0.63	YES
11	EGFR	EGFR	EGFR	2471	0.13	0.64	YES
12	LAMA4	LAMA4	LAMA4	2526	0.13	0.67	YES
13	CHRNA1	CHRNA1	CHRNA1	2598	0.12	0.69	YES
14	JUN	JUN	JUN	3467	0.087	0.66	NO
15	MAPK1	MAPK1	MAPK1	4310	0.063	0.63	NO
16	RAPSN	RAPSN	RAPSN	4534	0.058	0.63	NO
17	ITGB1	ITGB1	ITGB1	5128	0.047	0.61	NO
18	MAPK8	MAPK8	MAPK8	6660	0.024	0.53	NO
19	SP1	SP1	SP1	6700	0.024	0.54	NO
20	PAK1	PAK1	PAK1	6748	0.023	0.54	NO
21	DAG1	DAG1	DAG1	7036	0.019	0.53	NO
22	LAMA3	LAMA3	LAMA3	7428	0.014	0.51	NO
23	PAK2	PAK2	PAK2	7954	0.0086	0.48	NO
24	PXN	PXN	PXN	8011	0.008	0.48	NO
25	UTRN	UTRN	UTRN	8112	0.0069	0.48	NO
26	GIT2	GIT2	GIT2	8287	0.0051	0.47	NO
27	MAPK3	MAPK3	MAPK3	9285	-0.0054	0.42	NO
28	CTTN	CTTN	CTTN	9436	-0.0069	0.41	NO
29	CDC42	CDC42	CDC42	9838	-0.011	0.39	NO
30	SRC	SRC	SRC	10220	-0.015	0.37	NO
31	RAC1	RAC1	RAC1	10867	-0.022	0.34	NO
32	PAK4	PAK4	PAK4	10973	-0.023	0.34	NO
33	PTK2	PTK2	PTK2	11585	-0.03	0.31	NO
34	PAK6	PAK6	PAK6	13444	-0.053	0.22	NO
35	DVL1	DVL1	DVL1	14683	-0.074	0.17	NO
36	NRG3	NRG3	NRG3	15645	-0.1	0.14	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: BIOCARTA PYK2 PATHWAY.

Figure S18. 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 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	PRKCB	PRKCB	PRKCB	152	0.46	0.3	YES
2	PRKCA	PRKCA	PRKCA	1470	0.2	0.36	YES
3	CALM1	CALM1	CALM1	3402	0.089	0.31	YES
4	JUN	JUN	JUN	3467	0.087	0.37	YES
5	MAP2K4	MAP2K4	MAP2K4	4056	0.069	0.38	YES
6	SOS1	SOS1	SOS1	4197	0.066	0.42	YES
7	MAPK1	MAPK1	MAPK1	4310	0.063	0.45	YES
8	PTK2B	PTK2B	PTK2B	4747	0.054	0.46	YES
9	GNAQ	GNAQ	GNAQ	5836	0.035	0.43	NO
10	MAP3K1	MAP3K1	MAP3K1	6134	0.031	0.43	NO
11	MAPK8	MAPK8	MAPK8	6660	0.024	0.42	NO
12	PAK1	PAK1	PAK1	6748	0.023	0.43	NO
13	MAP2K1	MAP2K1	MAP2K1	7035	0.019	0.43	NO
14	CRKL	CRKL	CRKL	7072	0.019	0.44	NO
15	GRB2	GRB2	GRB2	7569	0.013	0.42	NO
16	BCAR1	BCAR1	BCAR1	7759	0.011	0.41	NO
17	CALM2	CALM2	CALM2	8591	0.0021	0.37	NO
18	CALM3	CALM3	CALM3	8915	-0.0016	0.35	NO
19	MAPK14	MAPK14	MAPK14	9149	-0.004	0.34	NO
20	RAF1	RAF1	RAF1	9259	-0.0051	0.34	NO
21	MAPK3	MAPK3	MAPK3	9285	-0.0054	0.34	NO
22	SHC1	SHC1	SHC1	9297	-0.0055	0.35	NO
23	SRC	SRC	SRC	10220	-0.015	0.3	NO
24	RAC1	RAC1	RAC1	10867	-0.022	0.28	NO
25	MAP2K2	MAP2K2	MAP2K2	11396	-0.028	0.27	NO
26	MAP2K3	MAP2K3	MAP2K3	11737	-0.032	0.28	NO
27	PLCG1	PLCG1	PLCG1	12034	-0.035	0.28	NO
28	HRAS	HRAS	HRAS	15206	-0.086	0.17	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: BIOCARTA MYOSIN PATHWAY.

Figure S20. 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 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 CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.51	1.7	0.029	0.44	0.75	0.034	0.00038	0.034	0.17	0.12
KEGG N GLYCAN BIOSYNTHESIS	46	genes.ES.table	0.49	1.6	0.031	0.55	0.9	0.46	0.29	0.32	0.26	0.15
KEGG UBIQUITIN MEDIATED PROTEOLYSIS	133	genes.ES.table	0.31	1.8	0.0019	0.71	0.56	0.44	0.3	0.32	0.17	0.16
PID ECADHERIN NASCENTAJ PATHWAY	39	genes.ES.table	0.38	1.6	0.032	0.54	0.9	0.33	0.24	0.25	0.27	0.16
PID LIS1PATHWAY	28	genes.ES.table	0.58	1.8	0.0063	0.43	0.62	0.21	0.087	0.2	0.12	0.1
REACTOME METABOLISM OF NON CODING RNA	47	genes.ES.table	0.5	1.8	0.042	0.55	0.57	0.68	0.37	0.43	0.14	0.14
REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER	36	genes.ES.table	0.55	1.6	0.016	0.57	0.89	0.5	0.25	0.38	0.27	0.16
REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM	44	genes.ES.table	0.53	1.9	0.004	0.55	0.36	0.61	0.33	0.41	0	0.12
REACTOME RNA POL II TRANSCRIPTION	93	genes.ES.table	0.34	1.6	0.066	0.6	0.94	0.38	0.32	0.26	0.33	0.18
REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES	59	genes.ES.table	0.41	1.6	0.089	0.62	0.95	0.32	0.22	0.25	0.37	0.18

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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	CCNT1	CCNT1	CCNT1	534	0.23	0.023	YES
2	TAF4B	TAF4B	TAF4B	808	0.18	0.05	YES
3	GTF2A1	GTF2A1	GTF2A1	845	0.18	0.088	YES
4	GTF2H2	GTF2H2	GTF2H2	1117	0.15	0.11	YES
5	NUP210	NUP210	NUP210	1167	0.15	0.14	YES
6	GTF2H3	GTF2H3	GTF2H3	1408	0.13	0.16	YES
7	RCC1	RCC1	RCC1	1622	0.12	0.17	YES
8	TAF1	TAF1	TAF1	1789	0.11	0.18	YES
9	GTF2E1	GTF2E1	GTF2E1	1841	0.11	0.21	YES
10	NUP155	NUP155	NUP155	2195	0.092	0.21	YES
11	RANBP2	RANBP2	RANBP2	2435	0.086	0.22	YES
12	CCNT2	CCNT2	CCNT2	2543	0.083	0.23	YES
13	TAF4	TAF4	TAF4	2743	0.077	0.23	YES
14	NUP54	NUP54	NUP54	2756	0.077	0.25	YES
15	TPR	TPR	TPR	2985	0.071	0.26	YES
16	NUPL1	NUPL1	NUPL1	3073	0.069	0.27	YES
17	CDK7	CDK7	CDK7	3142	0.068	0.28	YES
18	POM121	POM121	POM121	3241	0.065	0.29	YES
19	NUP133	NUP133	NUP133	3284	0.064	0.3	YES
20	NUP153	NUP153	NUP153	3387	0.062	0.31	YES
21	POLR2B	POLR2B	POLR2B	3577	0.059	0.31	YES
22	TAF9	TAF9	TAF9	3631	0.058	0.32	YES
23	XPO1	XPO1	XPO1	3662	0.057	0.33	YES
24	POLR2D	POLR2D	POLR2D	3706	0.056	0.34	YES
25	NUP205	NUP205	NUP205	3924	0.052	0.34	YES
26	SEH1L	SEH1L	SEH1L	3927	0.052	0.35	YES
27	RNGTT	RNGTT	RNGTT	4072	0.05	0.36	YES
28	TAF13	TAF13	TAF13	4226	0.048	0.36	YES
29	NCBP1	NCBP1	NCBP1	4246	0.048	0.37	YES
30	NUP188	NUP188	NUP188	4343	0.046	0.38	YES
31	NUP50	NUP50	NUP50	4709	0.041	0.36	YES
32	RNMT	RNMT	RNMT	4763	0.04	0.37	YES
33	GTF2H2B	GTF2H2B	GTF2H2B	4963	0.036	0.37	YES
34	SSRP1	SSRP1	SSRP1	5029	0.036	0.37	YES
35	ERCC3	ERCC3	ERCC3	5072	0.035	0.38	YES
36	TSG101	TSG101	TSG101	5236	0.033	0.38	YES
37	SUPT16H	SUPT16H	SUPT16H	5336	0.032	0.38	YES
38	NUP43	NUP43	NUP43	5341	0.032	0.38	YES
39	RANBP1	RANBP1	RANBP1	5423	0.03	0.39	YES
40	GTF2H1	GTF2H1	GTF2H1	5431	0.03	0.39	YES
41	NUP107	NUP107	NUP107	5505	0.029	0.4	YES
42	NUPL2	NUPL2	NUPL2	5570	0.028	0.4	YES
43	GTF2A2	GTF2A2	GTF2A2	5800	0.025	0.39	YES
44	NUP37	NUP37	NUP37	5914	0.023	0.39	YES
45	MNAT1	MNAT1	MNAT1	5965	0.022	0.39	YES
46	NUP214	NUP214	NUP214	6006	0.022	0.4	YES
47	VPS37A	VPS37A	VPS37A	6018	0.022	0.4	YES
48	RAN	RAN	RAN	6225	0.019	0.39	NO
49	RAE1	RAE1	RAE1	6332	0.018	0.39	NO
50	CCNH	CCNH	CCNH	6509	0.016	0.39	NO
51	NCBP2	NCBP2	NCBP2	6679	0.014	0.38	NO
52	NUP62	NUP62	NUP62	6823	0.012	0.38	NO
53	POLR2A	POLR2A	POLR2A	6936	0.01	0.37	NO
54	TCEA1	TCEA1	TCEA1	6953	0.0099	0.37	NO
55	TCEB3	TCEB3	TCEB3	7236	0.0065	0.36	NO
56	POLR2C	POLR2C	POLR2C	7468	0.0038	0.35	NO
57	GTF2E2	GTF2E2	GTF2E2	7543	0.0027	0.34	NO
58	WHSC2	WHSC2	WHSC2	7621	0.0017	0.34	NO
59	CTDP1	CTDP1	CTDP1	7891	-0.0016	0.32	NO
60	NMT1	NMT1	NMT1	7934	-0.0023	0.32	NO
61	COBRA1	COBRA1	COBRA1	7989	-0.0028	0.32	NO
62	TBP	TBP	TBP	8031	-0.0032	0.32	NO
63	ERCC2	ERCC2	ERCC2	8157	-0.005	0.31	NO
64	RANGAP1	RANGAP1	RANGAP1	8191	-0.0053	0.31	NO
65	NUP88	NUP88	NUP88	8218	-0.0057	0.31	NO
66	RPS27A	RPS27A	RPS27A	8342	-0.0071	0.31	NO
67	AAAS	AAAS	AAAS	8506	-0.0094	0.3	NO
68	VPS37D	VPS37D	VPS37D	8535	-0.0099	0.3	NO
69	TH1L	TH1L	TH1L	8562	-0.01	0.3	NO
70	POLR2H	POLR2H	POLR2H	8577	-0.01	0.3	NO
71	NMT2	NMT2	NMT2	8684	-0.012	0.3	NO
72	TAF5	TAF5	TAF5	8709	-0.012	0.3	NO
73	NUP35	NUP35	NUP35	8846	-0.014	0.3	NO
74	TAF12	TAF12	TAF12	8897	-0.014	0.3	NO
75	NUP93	NUP93	NUP93	9030	-0.016	0.3	NO
76	TCEB1	TCEB1	TCEB1	9057	-0.016	0.3	NO
77	TAF11	TAF11	TAF11	9111	-0.017	0.3	NO
78	NUP85	NUP85	NUP85	9155	-0.018	0.3	NO
79	GTF2F2	GTF2F2	GTF2F2	9403	-0.021	0.29	NO
80	GTF2F1	GTF2F1	GTF2F1	9438	-0.021	0.29	NO
81	POLR2K	POLR2K	POLR2K	9532	-0.022	0.29	NO
82	CDK9	CDK9	CDK9	9572	-0.023	0.3	NO
83	UBA52	UBA52	UBA52	9623	-0.024	0.3	NO
84	TAF6	TAF6	TAF6	9660	-0.024	0.3	NO
85	SUPT4H1	SUPT4H1	SUPT4H1	9920	-0.028	0.3	NO
86	GTF2H4	GTF2H4	GTF2H4	9932	-0.028	0.3	NO
87	ELL	ELL	ELL	9970	-0.029	0.3	NO
88	SUPT5H	SUPT5H	SUPT5H	9981	-0.029	0.31	NO
89	VPS37C	VPS37C	VPS37C	10056	-0.03	0.31	NO
90	POLR2F	POLR2F	POLR2F	10472	-0.036	0.3	NO
91	VPS37B	VPS37B	VPS37B	10562	-0.037	0.3	NO
92	RDBP	RDBP	RDBP	10609	-0.038	0.31	NO
93	POLR2E	POLR2E	POLR2E	10610	-0.038	0.32	NO
94	TAF10	TAF10	TAF10	10632	-0.039	0.33	NO
95	VPS28	VPS28	VPS28	11012	-0.044	0.32	NO
96	POLR2G	POLR2G	POLR2G	11172	-0.047	0.32	NO
97	GTF2B	GTF2B	GTF2B	11558	-0.054	0.31	NO
98	POLR2L	POLR2L	POLR2L	11891	-0.06	0.3	NO
99	POLR2I	POLR2I	POLR2I	12011	-0.063	0.31	NO
100	POLR2J	POLR2J	POLR2J	12325	-0.069	0.31	NO
101	TCEB2	TCEB2	TCEB2	12641	-0.076	0.31	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 CITRATE CYCLE TCA CYCLE.

Figure S22. 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 N GLYCAN BIOSYNTHESIS

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NUP210	NUP210	NUP210	1167	0.15	0.022	YES
2	CDC40	CDC40	CDC40	1643	0.12	0.064	YES
3	NUP155	NUP155	NUP155	2195	0.092	0.088	YES
4	RANBP2	RANBP2	RANBP2	2435	0.086	0.12	YES
5	NUP54	NUP54	NUP54	2756	0.077	0.15	YES
6	TPR	TPR	TPR	2985	0.071	0.18	YES
7	NUPL1	NUPL1	NUPL1	3073	0.069	0.22	YES
8	POM121	POM121	POM121	3241	0.065	0.25	YES
9	NUP133	NUP133	NUP133	3284	0.064	0.28	YES
10	NUP153	NUP153	NUP153	3387	0.062	0.31	YES
11	NUP205	NUP205	NUP205	3924	0.052	0.31	YES
12	SEH1L	SEH1L	SEH1L	3927	0.052	0.34	YES
13	CPSF2	CPSF2	CPSF2	4117	0.049	0.36	YES
14	NCBP1	NCBP1	NCBP1	4246	0.048	0.38	YES
15	NUP188	NUP188	NUP188	4343	0.046	0.41	YES
16	EIF4E	EIF4E	EIF4E	4414	0.045	0.43	YES
17	NUP50	NUP50	NUP50	4709	0.041	0.44	YES
18	CPSF3	CPSF3	CPSF3	5144	0.034	0.43	YES
19	NFX1	NFX1	NFX1	5163	0.034	0.45	YES
20	NUP43	NUP43	NUP43	5341	0.032	0.46	YES
21	NUP107	NUP107	NUP107	5505	0.029	0.47	YES
22	RBM8A	RBM8A	RBM8A	5565	0.028	0.48	YES
23	NUPL2	NUPL2	NUPL2	5570	0.028	0.5	YES
24	UPF3B	UPF3B	UPF3B	5751	0.026	0.5	YES
25	NUP37	NUP37	NUP37	5914	0.023	0.51	YES
26	NUP214	NUP214	NUP214	6006	0.022	0.52	YES
27	U2AF2	U2AF2	U2AF2	6014	0.022	0.53	YES
28	RAE1	RAE1	RAE1	6332	0.018	0.52	NO
29	NCBP2	NCBP2	NCBP2	6679	0.014	0.51	NO
30	NUP62	NUP62	NUP62	6823	0.012	0.51	NO
31	THOC4	THOC4	THOC4	7518	0.0031	0.47	NO
32	SLBP	SLBP	SLBP	7547	0.0027	0.47	NO
33	U2AF1	U2AF1	U2AF1	8180	-0.0052	0.44	NO
34	NUP88	NUP88	NUP88	8218	-0.0057	0.44	NO
35	MAGOH	MAGOH	MAGOH	8457	-0.0086	0.43	NO
36	AAAS	AAAS	AAAS	8506	-0.0094	0.44	NO
37	NUP35	NUP35	NUP35	8846	-0.014	0.43	NO
38	RNPS1	RNPS1	RNPS1	8939	-0.015	0.43	NO
39	NUP93	NUP93	NUP93	9030	-0.016	0.44	NO
40	NUP85	NUP85	NUP85	9155	-0.018	0.44	NO
41	SRRM1	SRRM1	SRRM1	9259	-0.019	0.44	NO
42	DHX38	DHX38	DHX38	9535	-0.023	0.44	NO
43	CPSF1	CPSF1	CPSF1	9996	-0.029	0.43	NO
44	NXF1	NXF1	NXF1	10311	-0.034	0.44	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 N GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS

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	CBLC	CBLC	CBLC	558	0.23	0.0016	YES
2	UBE2NL	UBE2NL	UBE2NL	826	0.18	0.012	YES
3	SKP2	SKP2	SKP2	852	0.18	0.036	YES
4	UBE2E3	UBE2E3	UBE2E3	884	0.17	0.06	YES
5	ANAPC1	ANAPC1	ANAPC1	1258	0.14	0.059	YES
6	NHLRC1	NHLRC1	NHLRC1	1270	0.14	0.078	YES
7	MID1	MID1	MID1	1860	0.11	0.061	YES
8	ERCC8	ERCC8	ERCC8	2067	0.098	0.063	YES
9	PARK2	PARK2	PARK2	2087	0.097	0.076	YES
10	TRIM37	TRIM37	TRIM37	2127	0.095	0.087	YES
11	WWP2	WWP2	WWP2	2320	0.089	0.09	YES
12	XIAP	XIAP	XIAP	2472	0.085	0.093	YES
13	CDC20	CDC20	CDC20	2547	0.083	0.1	YES
14	BIRC6	BIRC6	BIRC6	2578	0.082	0.11	YES
15	HERC2	HERC2	HERC2	2725	0.078	0.11	YES
16	HERC1	HERC1	HERC1	2770	0.077	0.12	YES
17	VHL	VHL	VHL	2777	0.076	0.13	YES
18	CUL7	CUL7	CUL7	2878	0.074	0.14	YES
19	ITCH	ITCH	ITCH	2905	0.073	0.15	YES
20	UBE2C	UBE2C	UBE2C	2975	0.072	0.15	YES
21	HERC3	HERC3	HERC3	2980	0.071	0.16	YES
22	CUL4B	CUL4B	CUL4B	3046	0.07	0.17	YES
23	UBE3C	UBE3C	UBE3C	3063	0.07	0.18	YES
24	RCHY1	RCHY1	RCHY1	3097	0.069	0.19	YES
25	UBE2J1	UBE2J1	UBE2J1	3170	0.067	0.19	YES
26	UBA2	UBA2	UBA2	3186	0.066	0.2	YES
27	PIAS2	PIAS2	PIAS2	3204	0.066	0.21	YES
28	KLHL9	KLHL9	KLHL9	3215	0.066	0.22	YES
29	UBE2G1	UBE2G1	UBE2G1	3255	0.065	0.22	YES
30	UBE2H	UBE2H	UBE2H	3314	0.064	0.23	YES
31	CBLB	CBLB	CBLB	3334	0.063	0.24	YES
32	SIAH1	SIAH1	SIAH1	3380	0.063	0.25	YES
33	UBE2W	UBE2W	UBE2W	3425	0.062	0.25	YES
34	BRCA1	BRCA1	BRCA1	3447	0.062	0.26	YES
35	PIAS3	PIAS3	PIAS3	3583	0.059	0.26	YES
36	TRIM32	TRIM32	TRIM32	3621	0.058	0.27	YES
37	UBR5	UBR5	UBR5	3931	0.052	0.26	YES
38	UBE2K	UBE2K	UBE2K	3952	0.052	0.26	YES
39	FBXW11	FBXW11	FBXW11	4042	0.05	0.27	YES
40	CUL5	CUL5	CUL5	4075	0.05	0.27	YES
41	UBE3A	UBE3A	UBE3A	4080	0.05	0.28	YES
42	NEDD4L	NEDD4L	NEDD4L	4218	0.048	0.28	YES
43	HUWE1	HUWE1	HUWE1	4249	0.048	0.28	YES
44	RFWD2	RFWD2	RFWD2	4555	0.043	0.27	YES
45	BIRC2	BIRC2	BIRC2	4594	0.043	0.28	YES
46	UBE2I	UBE2I	UBE2I	4608	0.042	0.28	YES
47	UBA3	UBA3	UBA3	4638	0.042	0.28	YES
48	UBE2Q2	UBE2Q2	UBE2Q2	4654	0.042	0.29	YES
49	TRIP12	TRIP12	TRIP12	4663	0.041	0.3	YES
50	UBE2N	UBE2N	UBE2N	4795	0.039	0.29	YES
51	PIAS1	PIAS1	PIAS1	4943	0.037	0.29	YES
52	MAP3K1	MAP3K1	MAP3K1	4967	0.036	0.3	YES
53	UBE2R2	UBE2R2	UBE2R2	5044	0.035	0.3	YES
54	DET1	DET1	DET1	5107	0.035	0.3	YES
55	TRAF6	TRAF6	TRAF6	5140	0.034	0.3	YES
56	UBE4B	UBE4B	UBE4B	5277	0.032	0.3	YES
57	FBXO4	FBXO4	FBXO4	5294	0.032	0.3	YES
58	HERC4	HERC4	HERC4	5360	0.031	0.3	YES
59	CDC27	CDC27	CDC27	5390	0.031	0.3	YES
60	UBE2Q1	UBE2Q1	UBE2Q1	5634	0.027	0.3	NO
61	ANAPC10	ANAPC10	ANAPC10	5668	0.027	0.3	NO
62	DDB1	DDB1	DDB1	5764	0.026	0.3	NO
63	CUL2	CUL2	CUL2	5831	0.025	0.3	NO
64	FBXW8	FBXW8	FBXW8	5855	0.024	0.3	NO
65	UBA6	UBA6	UBA6	5983	0.022	0.29	NO
66	CUL3	CUL3	CUL3	6239	0.019	0.28	NO
67	UBE2O	UBE2O	UBE2O	6255	0.019	0.28	NO
68	UBE2A	UBE2A	UBE2A	6258	0.019	0.29	NO
69	PIAS4	PIAS4	PIAS4	6262	0.019	0.29	NO
70	UBE2Z	UBE2Z	UBE2Z	6294	0.018	0.29	NO
71	SYVN1	SYVN1	SYVN1	6326	0.018	0.29	NO
72	UBE2E2	UBE2E2	UBE2E2	6508	0.016	0.28	NO
73	CUL4A	CUL4A	CUL4A	6575	0.015	0.28	NO
74	KEAP1	KEAP1	KEAP1	6625	0.014	0.28	NO
75	UBE2D3	UBE2D3	UBE2D3	6642	0.014	0.28	NO
76	CBL	CBL	CBL	6690	0.013	0.28	NO
77	MGRN1	MGRN1	MGRN1	6768	0.012	0.28	NO
78	UBE2E1	UBE2E1	UBE2E1	6876	0.011	0.28	NO
79	MDM2	MDM2	MDM2	6951	0.0099	0.27	NO
80	SMURF2	SMURF2	SMURF2	7018	0.0091	0.27	NO
81	UBE2J2	UBE2J2	UBE2J2	7092	0.0083	0.27	NO
82	UBE2D2	UBE2D2	UBE2D2	7171	0.0073	0.26	NO
83	FANCL	FANCL	FANCL	7210	0.0068	0.26	NO
84	UBE4A	UBE4A	UBE4A	7280	0.006	0.26	NO
85	CDC26	CDC26	CDC26	7302	0.0058	0.26	NO
86	WWP1	WWP1	WWP1	7322	0.0055	0.26	NO
87	SKP1	SKP1	SKP1	7451	0.0039	0.25	NO
88	BTRC	BTRC	BTRC	7719	0.00054	0.24	NO
89	CDC16	CDC16	CDC16	7966	-0.0026	0.22	NO
90	UBE2D1	UBE2D1	UBE2D1	7996	-0.0028	0.22	NO
91	PRPF19	PRPF19	PRPF19	8521	-0.0097	0.2	NO
92	UBE3B	UBE3B	UBE3B	8546	-0.01	0.2	NO
93	BIRC3	BIRC3	BIRC3	8609	-0.011	0.2	NO
94	ANAPC7	ANAPC7	ANAPC7	8617	-0.011	0.2	NO
95	PML	PML	PML	8764	-0.013	0.19	NO
96	UBA1	UBA1	UBA1	8784	-0.013	0.19	NO
97	FBXW7	FBXW7	FBXW7	8913	-0.015	0.18	NO
98	ANAPC5	ANAPC5	ANAPC5	8984	-0.016	0.18	NO
99	TCEB1	TCEB1	TCEB1	9057	-0.016	0.18	NO
100	UBE2B	UBE2B	UBE2B	9120	-0.017	0.18	NO
101	CUL1	CUL1	CUL1	9236	-0.019	0.18	NO
102	CDC23	CDC23	CDC23	9412	-0.021	0.17	NO
103	NEDD4	NEDD4	NEDD4	9875	-0.028	0.15	NO
104	RBX1	RBX1	RBX1	9961	-0.029	0.15	NO
105	RNF7	RNF7	RNF7	10044	-0.03	0.15	NO
106	PPIL2	PPIL2	PPIL2	10122	-0.031	0.15	NO
107	UBE2F	UBE2F	UBE2F	10212	-0.032	0.15	NO
108	UBE2L3	UBE2L3	UBE2L3	10504	-0.036	0.14	NO
109	ANAPC2	ANAPC2	ANAPC2	10747	-0.04	0.13	NO
110	UBE2M	UBE2M	UBE2M	10802	-0.041	0.13	NO
111	SAE1	SAE1	SAE1	10873	-0.042	0.14	NO
112	UBE2L6	UBE2L6	UBE2L6	11022	-0.044	0.13	NO
113	UBE2G2	UBE2G2	UBE2G2	11128	-0.047	0.13	NO
114	ANAPC13	ANAPC13	ANAPC13	11151	-0.047	0.14	NO
115	FZR1	FZR1	FZR1	11422	-0.051	0.13	NO
116	UBOX5	UBOX5	UBOX5	11439	-0.052	0.14	NO
117	UBE2S	UBE2S	UBE2S	11453	-0.052	0.14	NO
118	AIRE	AIRE	AIRE	11572	-0.054	0.15	NO
119	ANAPC4	ANAPC4	ANAPC4	11608	-0.055	0.15	NO
120	UBE2D4	UBE2D4	UBE2D4	11618	-0.055	0.16	NO
121	STUB1	STUB1	STUB1	12019	-0.063	0.15	NO
122	ANAPC11	ANAPC11	ANAPC11	12278	-0.068	0.14	NO
123	TCEB2	TCEB2	TCEB2	12641	-0.076	0.13	NO
124	SMURF1	SMURF1	SMURF1	12661	-0.076	0.14	NO
125	UBE2QL1	UBE2QL1	UBE2QL1	13276	-0.091	0.12	NO
126	CDC34	CDC34	CDC34	13327	-0.092	0.13	NO
127	RHOBTB2	RHOBTB2	RHOBTB2	13543	-0.098	0.13	NO
128	FBXO2	FBXO2	FBXO2	13998	-0.11	0.12	NO
129	KLHL13	KLHL13	KLHL13	14154	-0.12	0.13	NO
130	DDB2	DDB2	DDB2	14444	-0.13	0.14	NO
131	SOCS3	SOCS3	SOCS3	15311	-0.16	0.11	NO
132	UBA7	UBA7	UBA7	15887	-0.18	0.1	NO
133	SOCS1	SOCS1	SOCS1	15982	-0.19	0.12	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 UBIQUITIN MEDIATED PROTEOLYSIS.

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

genes ES table in pathway: PID ECADHERIN NASCENTAJ PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	SMN1	SMN1	SMN1	501	0.24	0.093	YES
2	NUP210	NUP210	NUP210	1167	0.15	0.13	YES
3	NUP155	NUP155	NUP155	2195	0.092	0.12	YES
4	RANBP2	RANBP2	RANBP2	2435	0.086	0.15	YES
5	NUP54	NUP54	NUP54	2756	0.077	0.17	YES
6	TPR	TPR	TPR	2985	0.071	0.2	YES
7	NUPL1	NUPL1	NUPL1	3073	0.069	0.23	YES
8	POM121	POM121	POM121	3241	0.065	0.25	YES
9	NUP133	NUP133	NUP133	3284	0.064	0.28	YES
10	NUP153	NUP153	NUP153	3387	0.062	0.31	YES
11	SMN2	SMN2	SMN2	3840	0.054	0.31	YES
12	NUP205	NUP205	NUP205	3924	0.052	0.33	YES
13	SEH1L	SEH1L	SEH1L	3927	0.052	0.36	YES
14	NCBP1	NCBP1	NCBP1	4246	0.048	0.36	YES
15	PHAX	PHAX	PHAX	4260	0.047	0.39	YES
16	GEMIN5	GEMIN5	GEMIN5	4327	0.046	0.41	YES
17	NUP188	NUP188	NUP188	4343	0.046	0.43	YES
18	CLNS1A	CLNS1A	CLNS1A	4481	0.044	0.44	YES
19	NUP50	NUP50	NUP50	4709	0.041	0.45	YES
20	NUP43	NUP43	NUP43	5341	0.032	0.43	YES
21	NUP107	NUP107	NUP107	5505	0.029	0.44	YES
22	SNRPD3	SNRPD3	SNRPD3	5547	0.029	0.45	YES
23	PRMT5	PRMT5	PRMT5	5561	0.028	0.47	YES
24	NUPL2	NUPL2	NUPL2	5570	0.028	0.48	YES
25	TGS1	TGS1	TGS1	5582	0.028	0.49	YES
26	NUP37	NUP37	NUP37	5914	0.023	0.49	YES
27	NUP214	NUP214	NUP214	6006	0.022	0.49	YES
28	RAE1	RAE1	RAE1	6332	0.018	0.48	YES
29	SNRPE	SNRPE	SNRPE	6357	0.017	0.49	YES
30	SNRPG	SNRPG	SNRPG	6462	0.016	0.49	YES
31	GEMIN4	GEMIN4	GEMIN4	6669	0.014	0.49	YES
32	NCBP2	NCBP2	NCBP2	6679	0.014	0.5	YES
33	NUP62	NUP62	NUP62	6823	0.012	0.49	NO
34	SNRPD1	SNRPD1	SNRPD1	7272	0.0061	0.47	NO
35	SNRPF	SNRPF	SNRPF	7644	0.0014	0.45	NO
36	SNRPB	SNRPB	SNRPB	7963	-0.0026	0.44	NO
37	NUP88	NUP88	NUP88	8218	-0.0057	0.43	NO
38	DDX20	DDX20	DDX20	8490	-0.0092	0.42	NO
39	AAAS	AAAS	AAAS	8506	-0.0094	0.42	NO
40	NUP35	NUP35	NUP35	8846	-0.014	0.41	NO
41	SNRPD2	SNRPD2	SNRPD2	8965	-0.015	0.41	NO
42	NUP93	NUP93	NUP93	9030	-0.016	0.41	NO
43	NUP85	NUP85	NUP85	9155	-0.018	0.42	NO
44	SNUPN	SNUPN	SNUPN	9322	-0.02	0.42	NO
45	WDR77	WDR77	WDR77	9988	-0.029	0.4	NO
46	GEMIN6	GEMIN6	GEMIN6	10120	-0.031	0.4	NO
47	GEMIN7	GEMIN7	GEMIN7	13065	-0.086	0.28	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: PID ECADHERIN NASCENTAJ PATHWAY.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: PID ECADHERIN NASCENTAJ 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 LIS1PATHWAY

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	NUP210	NUP210	NUP210	1167	0.15	0.04	YES
2	NUP155	NUP155	NUP155	2195	0.092	0.049	YES
3	RANBP2	RANBP2	RANBP2	2435	0.086	0.097	YES
4	NUP54	NUP54	NUP54	2756	0.077	0.13	YES
5	TPR	TPR	TPR	2985	0.071	0.17	YES
6	NUPL1	NUPL1	NUPL1	3073	0.069	0.22	YES
7	POM121	POM121	POM121	3241	0.065	0.25	YES
8	NUP133	NUP133	NUP133	3284	0.064	0.3	YES
9	NUP153	NUP153	NUP153	3387	0.062	0.34	YES
10	NUP205	NUP205	NUP205	3924	0.052	0.34	YES
11	SEH1L	SEH1L	SEH1L	3927	0.052	0.38	YES
12	CPSF2	CPSF2	CPSF2	4117	0.049	0.41	YES
13	NCBP1	NCBP1	NCBP1	4246	0.048	0.43	YES
14	NUP188	NUP188	NUP188	4343	0.046	0.46	YES
15	EIF4E	EIF4E	EIF4E	4414	0.045	0.49	YES
16	NUP50	NUP50	NUP50	4709	0.041	0.5	YES
17	CPSF3	CPSF3	CPSF3	5144	0.034	0.5	YES
18	NUP43	NUP43	NUP43	5341	0.032	0.51	YES
19	NUP107	NUP107	NUP107	5505	0.029	0.52	YES
20	NUPL2	NUPL2	NUPL2	5570	0.028	0.54	YES
21	NUP37	NUP37	NUP37	5914	0.023	0.54	YES
22	NUP214	NUP214	NUP214	6006	0.022	0.55	YES
23	RAE1	RAE1	RAE1	6332	0.018	0.54	NO
24	NCBP2	NCBP2	NCBP2	6679	0.014	0.54	NO
25	NUP62	NUP62	NUP62	6823	0.012	0.54	NO
26	THOC4	THOC4	THOC4	7518	0.0031	0.5	NO
27	NUP88	NUP88	NUP88	8218	-0.0057	0.46	NO
28	AAAS	AAAS	AAAS	8506	-0.0094	0.46	NO
29	NUP35	NUP35	NUP35	8846	-0.014	0.45	NO
30	NUP93	NUP93	NUP93	9030	-0.016	0.45	NO
31	NUP85	NUP85	NUP85	9155	-0.018	0.46	NO
32	CPSF1	CPSF1	CPSF1	9996	-0.029	0.43	NO
33	NXF1	NXF1	NXF1	10311	-0.034	0.44	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: PID LIS1PATHWAY.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: PID LIS1PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME METABOLISM OF NON CODING RNA

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	PLA2G7	PLA2G7	PLA2G7	102	0.47	0.21	YES
2	CDK5R2	CDK5R2	CDK5R2	364	0.27	0.32	YES
3	VLDLR	VLDLR	VLDLR	385	0.27	0.45	YES
4	LRP8	LRP8	LRP8	877	0.17	0.5	YES
5	DAB1	DAB1	DAB1	1516	0.12	0.53	YES
6	PAFAH1B2	PAFAH1B2	PAFAH1B2	1590	0.12	0.58	YES
7	CSNK2A1	CSNK2A1	CSNK2A1	2648	0.08	0.56	NO
8	CDK5R1	CDK5R1	CDK5R1	3917	0.052	0.51	NO
9	DYNC1H1	DYNC1H1	DYNC1H1	5222	0.033	0.46	NO
10	KATNA1	KATNA1	KATNA1	5609	0.028	0.45	NO
11	ABL1	ABL1	ABL1	5611	0.028	0.46	NO
12	YWHAE	YWHAE	YWHAE	6543	0.015	0.42	NO
13	CDC42	CDC42	CDC42	6822	0.012	0.41	NO
14	RHOA	RHOA	RHOA	6939	0.01	0.4	NO
15	CLIP1	CLIP1	CLIP1	7066	0.0086	0.4	NO
16	IQGAP1	IQGAP1	IQGAP1	7593	0.002	0.37	NO
17	CDK5	CDK5	CDK5	7739	0.00029	0.37	NO
18	PAFAH1B1	PAFAH1B1	PAFAH1B1	8042	-0.0034	0.35	NO
19	PPP2R5D	PPP2R5D	PPP2R5D	8214	-0.0056	0.34	NO
20	RAC1	RAC1	RAC1	8754	-0.013	0.32	NO
21	DYNLT1	DYNLT1	DYNLT1	9729	-0.025	0.28	NO
22	LRPAP1	LRPAP1	LRPAP1	9788	-0.026	0.29	NO
23	MAP1B	MAP1B	MAP1B	10426	-0.035	0.27	NO
24	NUDC	NUDC	NUDC	10698	-0.04	0.27	NO
25	NDEL1	NDEL1	NDEL1	10752	-0.04	0.29	NO
26	PAFAH1B3	PAFAH1B3	PAFAH1B3	12142	-0.066	0.24	NO
27	DCX	DCX	DCX	12301	-0.068	0.27	NO
28	RELN	RELN	RELN	14501	-0.13	0.21	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: REACTOME METABOLISM OF NON CODING RNA.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME METABOLISM OF NON CODING RNA, 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 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER

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	NUP210	NUP210	NUP210	1167	0.15	0.056	YES
2	NUP155	NUP155	NUP155	2195	0.092	0.076	YES
3	RANBP2	RANBP2	RANBP2	2435	0.086	0.13	YES
4	NUP54	NUP54	NUP54	2756	0.077	0.18	YES
5	TPR	TPR	TPR	2985	0.071	0.22	YES
6	NUPL1	NUPL1	NUPL1	3073	0.069	0.28	YES
7	POM121	POM121	POM121	3241	0.065	0.32	YES
8	NUP133	NUP133	NUP133	3284	0.064	0.37	YES
9	NUP153	NUP153	NUP153	3387	0.062	0.42	YES
10	KPNB1	KPNB1	KPNB1	3464	0.061	0.46	YES
11	NUP205	NUP205	NUP205	3924	0.052	0.48	YES
12	SEH1L	SEH1L	SEH1L	3927	0.052	0.52	YES
13	NUP188	NUP188	NUP188	4343	0.046	0.54	YES
14	NUP50	NUP50	NUP50	4709	0.041	0.55	YES
15	NUP43	NUP43	NUP43	5341	0.032	0.54	YES
16	NUP107	NUP107	NUP107	5505	0.029	0.56	YES
17	NUPL2	NUPL2	NUPL2	5570	0.028	0.58	YES
18	NUP37	NUP37	NUP37	5914	0.023	0.58	YES
19	NUP214	NUP214	NUP214	6006	0.022	0.59	YES
20	RAE1	RAE1	RAE1	6332	0.018	0.59	NO
21	NUP62	NUP62	NUP62	6823	0.012	0.57	NO
22	KPNA1	KPNA1	KPNA1	7412	0.0044	0.54	NO
23	NUP88	NUP88	NUP88	8218	-0.0057	0.5	NO
24	AAAS	AAAS	AAAS	8506	-0.0094	0.5	NO
25	NUP35	NUP35	NUP35	8846	-0.014	0.49	NO
26	NUP93	NUP93	NUP93	9030	-0.016	0.49	NO
27	NUP85	NUP85	NUP85	9155	-0.018	0.5	NO

Figure S33. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER, 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 TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM

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	NUP210	NUP210	NUP210	1167	0.15	0.055	YES
2	NUP155	NUP155	NUP155	2195	0.092	0.074	YES
3	RANBP2	RANBP2	RANBP2	2435	0.086	0.13	YES
4	NUP54	NUP54	NUP54	2756	0.077	0.18	YES
5	TPR	TPR	TPR	2985	0.071	0.22	YES
6	NUPL1	NUPL1	NUPL1	3073	0.069	0.27	YES
7	POM121	POM121	POM121	3241	0.065	0.32	YES
8	NUP133	NUP133	NUP133	3284	0.064	0.37	YES
9	NUP153	NUP153	NUP153	3387	0.062	0.41	YES
10	XPO1	XPO1	XPO1	3662	0.057	0.44	YES
11	NUP205	NUP205	NUP205	3924	0.052	0.47	YES
12	SEH1L	SEH1L	SEH1L	3927	0.052	0.52	YES
13	NUP188	NUP188	NUP188	4343	0.046	0.53	YES
14	NUP50	NUP50	NUP50	4709	0.041	0.54	YES
15	NUP43	NUP43	NUP43	5341	0.032	0.53	YES
16	NUP107	NUP107	NUP107	5505	0.029	0.55	YES
17	NUPL2	NUPL2	NUPL2	5570	0.028	0.57	YES
18	NUP37	NUP37	NUP37	5914	0.023	0.57	YES
19	NUP214	NUP214	NUP214	6006	0.022	0.58	YES
20	RAN	RAN	RAN	6225	0.019	0.58	YES
21	RAE1	RAE1	RAE1	6332	0.018	0.59	YES
22	NUP62	NUP62	NUP62	6823	0.012	0.58	NO
23	NUP88	NUP88	NUP88	8218	-0.0057	0.5	NO
24	AAAS	AAAS	AAAS	8506	-0.0094	0.5	NO
25	NUP35	NUP35	NUP35	8846	-0.014	0.49	NO
26	NUP93	NUP93	NUP93	9030	-0.016	0.49	NO
27	NUP85	NUP85	NUP85	9155	-0.018	0.5	NO

Figure S35. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM, 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 II TRANSCRIPTION

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	OGDHL	OGDHL	OGDHL	7	0.82	0.51	YES
2	DLAT	DLAT	DLAT	1966	0.1	0.47	NO
3	CS	CS	CS	4658	0.042	0.35	NO
4	SDHD	SDHD	SDHD	5496	0.029	0.32	NO
5	ACLY	ACLY	ACLY	5839	0.024	0.32	NO
6	FH	FH	FH	6009	0.022	0.32	NO
7	DLD	DLD	DLD	6099	0.021	0.33	NO
8	MDH2	MDH2	MDH2	6129	0.021	0.34	NO
9	OGDH	OGDH	OGDH	6137	0.02	0.35	NO
10	SUCLG1	SUCLG1	SUCLG1	6351	0.018	0.35	NO
11	IDH1	IDH1	IDH1	6549	0.015	0.35	NO
12	PDHB	PDHB	PDHB	6709	0.013	0.35	NO
13	SDHC	SDHC	SDHC	6716	0.013	0.36	NO
14	SDHB	SDHB	SDHB	6725	0.013	0.37	NO
15	SUCLG2	SUCLG2	SUCLG2	6820	0.012	0.37	NO
16	PDHA1	PDHA1	PDHA1	6848	0.011	0.37	NO
17	ACO1	ACO1	ACO1	6976	0.0096	0.37	NO
18	ACO2	ACO2	ACO2	6988	0.0095	0.38	NO
19	SUCLA2	SUCLA2	SUCLA2	7439	0.0041	0.36	NO
20	MDH1	MDH1	MDH1	7680	0.0009	0.34	NO
21	SDHA	SDHA	SDHA	8712	-0.012	0.29	NO
22	DLST	DLST	DLST	9434	-0.021	0.27	NO
23	IDH3A	IDH3A	IDH3A	9488	-0.022	0.28	NO
24	IDH3G	IDH3G	IDH3G	9947	-0.028	0.27	NO
25	PCK2	PCK2	PCK2	10253	-0.033	0.28	NO
26	IDH2	IDH2	IDH2	10532	-0.037	0.28	NO
27	IDH3B	IDH3B	IDH3B	10880	-0.042	0.29	NO
28	PCK1	PCK1	PCK1	11708	-0.057	0.28	NO
29	PC	PC	PC	14460	-0.13	0.21	NO

Figure S37. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME RNA POL II TRANSCRIPTION.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME RNA POL II 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 RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES

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	GTF2H2	GTF2H2	GTF2H2	1117	0.15	-0.033	YES
2	NUP210	NUP210	NUP210	1167	0.15	-0.0076	YES
3	SNRNP40	SNRNP40	SNRNP40	1388	0.13	0.0053	YES
4	GTF2H3	GTF2H3	GTF2H3	1408	0.13	0.029	YES
5	CDC40	CDC40	CDC40	1643	0.12	0.038	YES
6	NUP155	NUP155	NUP155	2195	0.092	0.026	YES
7	ZNF473	ZNF473	ZNF473	2380	0.087	0.032	YES
8	RANBP2	RANBP2	RANBP2	2435	0.086	0.046	YES
9	NUP54	NUP54	NUP54	2756	0.077	0.043	YES
10	TPR	TPR	TPR	2985	0.071	0.044	YES
11	NUPL1	NUPL1	NUPL1	3073	0.069	0.052	YES
12	CDK7	CDK7	CDK7	3142	0.068	0.061	YES
13	CCAR1	CCAR1	CCAR1	3222	0.066	0.07	YES
14	POM121	POM121	POM121	3241	0.065	0.081	YES
15	NUP133	NUP133	NUP133	3284	0.064	0.091	YES
16	HNRNPR	HNRNPR	HNRNPR	3351	0.063	0.099	YES
17	NUP153	NUP153	NUP153	3387	0.062	0.11	YES
18	HNRNPUL1	HNRNPUL1	HNRNPUL1	3395	0.062	0.12	YES
19	NUDT21	NUDT21	NUDT21	3398	0.062	0.13	YES
20	POLR2B	POLR2B	POLR2B	3577	0.059	0.13	YES
21	CPSF7	CPSF7	CPSF7	3586	0.059	0.14	YES
22	DHX9	DHX9	DHX9	3634	0.058	0.15	YES
23	SNRPB2	SNRPB2	SNRPB2	3700	0.056	0.16	YES
24	POLR2D	POLR2D	POLR2D	3706	0.056	0.17	YES
25	HNRNPF	HNRNPF	HNRNPF	3842	0.054	0.17	YES
26	NUP205	NUP205	NUP205	3924	0.052	0.18	YES
27	SEH1L	SEH1L	SEH1L	3927	0.052	0.19	YES
28	PCF11	PCF11	PCF11	3947	0.052	0.2	YES
29	SNRNP200	SNRNP200	SNRNP200	4025	0.051	0.2	YES
30	RNGTT	RNGTT	RNGTT	4072	0.05	0.21	YES
31	CPSF2	CPSF2	CPSF2	4117	0.049	0.22	YES
32	NCBP1	NCBP1	NCBP1	4246	0.048	0.22	YES
33	NUP188	NUP188	NUP188	4343	0.046	0.22	YES
34	RBMX	RBMX	RBMX	4385	0.046	0.23	YES
35	EIF4E	EIF4E	EIF4E	4414	0.045	0.24	YES
36	HNRNPA0	HNRNPA0	HNRNPA0	4447	0.045	0.24	YES
37	HNRNPK	HNRNPK	HNRNPK	4513	0.044	0.25	YES
38	PAPOLA	PAPOLA	PAPOLA	4686	0.041	0.25	YES
39	NUP50	NUP50	NUP50	4709	0.041	0.25	YES
40	ADAR	ADAR	ADAR	4725	0.04	0.26	YES
41	RNMT	RNMT	RNMT	4763	0.04	0.27	YES
42	SF3B3	SF3B3	SF3B3	4824	0.039	0.27	YES
43	SF3A1	SF3A1	SF3A1	4849	0.038	0.28	YES
44	SMC1A	SMC1A	SMC1A	4859	0.038	0.28	YES
45	SF3B1	SF3B1	SF3B1	4879	0.038	0.29	YES
46	HNRNPL	HNRNPL	HNRNPL	4884	0.038	0.3	YES
47	PRPF8	PRPF8	PRPF8	4922	0.037	0.3	YES
48	GTF2H2B	GTF2H2B	GTF2H2B	4963	0.036	0.31	YES
49	PCBP2	PCBP2	PCBP2	4986	0.036	0.31	YES
50	ERCC3	ERCC3	ERCC3	5072	0.035	0.31	YES
51	CPSF3	CPSF3	CPSF3	5144	0.034	0.32	YES
52	NFX1	NFX1	NFX1	5163	0.034	0.32	YES
53	HNRNPU	HNRNPU	HNRNPU	5197	0.033	0.33	YES
54	NUP43	NUP43	NUP43	5341	0.032	0.32	YES
55	HNRNPH2	HNRNPH2	HNRNPH2	5370	0.031	0.33	YES
56	GTF2H1	GTF2H1	GTF2H1	5431	0.03	0.33	YES
57	HNRNPC	HNRNPC	HNRNPC	5468	0.03	0.34	YES
58	NUP107	NUP107	NUP107	5505	0.029	0.34	YES
59	SNRPD3	SNRPD3	SNRPD3	5547	0.029	0.34	YES
60	RBM8A	RBM8A	RBM8A	5565	0.028	0.35	YES
61	NUPL2	NUPL2	NUPL2	5570	0.028	0.35	YES
62	UPF3B	UPF3B	UPF3B	5751	0.026	0.35	YES
63	SNRPA1	SNRPA1	SNRPA1	5842	0.024	0.35	YES
64	NUP37	NUP37	NUP37	5914	0.023	0.35	YES
65	PCBP1	PCBP1	PCBP1	5917	0.023	0.35	YES
66	PTBP1	PTBP1	PTBP1	5926	0.023	0.36	YES
67	MNAT1	MNAT1	MNAT1	5965	0.022	0.36	YES
68	NUP214	NUP214	NUP214	6006	0.022	0.36	YES
69	U2AF2	U2AF2	U2AF2	6014	0.022	0.36	YES
70	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	6260	0.019	0.35	NO
71	SF3B14	SF3B14	SF3B14	6329	0.018	0.35	NO
72	RAE1	RAE1	RAE1	6332	0.018	0.36	NO
73	SNRPE	SNRPE	SNRPE	6357	0.017	0.36	NO
74	HNRNPD	HNRNPD	HNRNPD	6440	0.016	0.36	NO
75	SNRPG	SNRPG	SNRPG	6462	0.016	0.36	NO
76	CCNH	CCNH	CCNH	6509	0.016	0.36	NO
77	SF3B4	SF3B4	SF3B4	6581	0.015	0.36	NO
78	PRPF4	PRPF4	PRPF4	6649	0.014	0.36	NO
79	NCBP2	NCBP2	NCBP2	6679	0.014	0.36	NO
80	SF3A3	SF3A3	SF3A3	6781	0.012	0.35	NO
81	NUP62	NUP62	NUP62	6823	0.012	0.35	NO
82	HNRNPA1	HNRNPA1	HNRNPA1	6860	0.011	0.36	NO
83	CSTF3	CSTF3	CSTF3	6866	0.011	0.36	NO
84	POLR2A	POLR2A	POLR2A	6936	0.01	0.36	NO
85	DDX23	DDX23	DDX23	7051	0.0087	0.35	NO
86	HNRNPA3	HNRNPA3	HNRNPA3	7071	0.0085	0.35	NO
87	SF3B2	SF3B2	SF3B2	7248	0.0064	0.34	NO
88	SNRPD1	SNRPD1	SNRPD1	7272	0.0061	0.34	NO
89	FUS	FUS	FUS	7321	0.0055	0.34	NO
90	HNRNPH1	HNRNPH1	HNRNPH1	7403	0.0045	0.34	NO
91	PHF5A	PHF5A	PHF5A	7408	0.0044	0.34	NO
92	POLR2C	POLR2C	POLR2C	7468	0.0038	0.34	NO
93	THOC4	THOC4	THOC4	7518	0.0031	0.33	NO
94	SLBP	SLBP	SLBP	7547	0.0027	0.33	NO
95	YBX1	YBX1	YBX1	7557	0.0026	0.33	NO
96	CSTF1	CSTF1	CSTF1	7636	0.0015	0.33	NO
97	SNRPF	SNRPF	SNRPF	7644	0.0014	0.33	NO
98	SNRPB	SNRPB	SNRPB	7963	-0.0026	0.31	NO
99	PRPF6	PRPF6	PRPF6	7978	-0.0027	0.31	NO
100	ERCC2	ERCC2	ERCC2	8157	-0.005	0.3	NO
101	SF3A2	SF3A2	SF3A2	8178	-0.0052	0.3	NO
102	U2AF1	U2AF1	U2AF1	8180	-0.0052	0.3	NO
103	NUP88	NUP88	NUP88	8218	-0.0057	0.3	NO
104	CLP1	CLP1	CLP1	8224	-0.0058	0.3	NO
105	METTL3	METTL3	METTL3	8388	-0.0077	0.29	NO
106	MAGOH	MAGOH	MAGOH	8457	-0.0086	0.29	NO
107	AAAS	AAAS	AAAS	8506	-0.0094	0.29	NO
108	POLR2H	POLR2H	POLR2H	8577	-0.01	0.29	NO
109	HNRNPM	HNRNPM	HNRNPM	8666	-0.012	0.29	NO
110	EFTUD2	EFTUD2	EFTUD2	8708	-0.012	0.29	NO
111	DNAJC8	DNAJC8	DNAJC8	8820	-0.014	0.28	NO
112	NUP35	NUP35	NUP35	8846	-0.014	0.28	NO
113	PABPN1	PABPN1	PABPN1	8925	-0.015	0.28	NO
114	RNPS1	RNPS1	RNPS1	8939	-0.015	0.29	NO
115	SNRPD2	SNRPD2	SNRPD2	8965	-0.015	0.29	NO
116	LSM2	LSM2	LSM2	8999	-0.016	0.29	NO
117	NUP93	NUP93	NUP93	9030	-0.016	0.29	NO
118	NUP85	NUP85	NUP85	9155	-0.018	0.29	NO
119	SRRM1	SRRM1	SRRM1	9259	-0.019	0.28	NO
120	GTF2F2	GTF2F2	GTF2F2	9403	-0.021	0.28	NO
121	GTF2F1	GTF2F1	GTF2F1	9438	-0.021	0.28	NO
122	POLR2K	POLR2K	POLR2K	9532	-0.022	0.28	NO
123	DHX38	DHX38	DHX38	9535	-0.023	0.29	NO
124	RBM5	RBM5	RBM5	9545	-0.023	0.29	NO
125	TXNL4A	TXNL4A	TXNL4A	9885	-0.028	0.28	NO
126	GTF2H4	GTF2H4	GTF2H4	9932	-0.028	0.28	NO
127	A1CF	A1CF	A1CF	9948	-0.028	0.28	NO
128	SUPT5H	SUPT5H	SUPT5H	9981	-0.029	0.29	NO
129	CPSF1	CPSF1	CPSF1	9996	-0.029	0.29	NO
130	NHP2L1	NHP2L1	NHP2L1	10052	-0.03	0.3	NO
131	CSTF2	CSTF2	CSTF2	10089	-0.031	0.3	NO
132	NXF1	NXF1	NXF1	10311	-0.034	0.29	NO
133	SNRNP70	SNRNP70	SNRNP70	10372	-0.035	0.3	NO
134	POLR2F	POLR2F	POLR2F	10472	-0.036	0.3	NO
135	SNRPA	SNRPA	SNRPA	10526	-0.037	0.3	NO
136	POLR2E	POLR2E	POLR2E	10610	-0.038	0.3	NO
137	CD2BP2	CD2BP2	CD2BP2	11087	-0.046	0.29	NO
138	POLR2G	POLR2G	POLR2G	11172	-0.047	0.29	NO
139	POLR2L	POLR2L	POLR2L	11891	-0.06	0.26	NO
140	POLR2I	POLR2I	POLR2I	12011	-0.063	0.27	NO
141	POLR2J	POLR2J	POLR2J	12325	-0.069	0.26	NO
142	SF3B5	SF3B5	SF3B5	12331	-0.069	0.28	NO
143	LSM11	LSM11	LSM11	12433	-0.071	0.29	NO
144	LSM10	LSM10	LSM10	13311	-0.092	0.26	NO
145	ADARB1	ADARB1	ADARB1	13370	-0.094	0.27	NO

Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES, 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 OXIDATIVE PHOSPHORYLATION	114	genes.ES.table	0.52	1.6	0.036	0.21	0.88	0.64	0.28	0.46	0.11	0.031
KEGG PYRIMIDINE METABOLISM	98	genes.ES.table	0.38	1.7	0.013	0.18	0.78	0.44	0.27	0.32	0.078	0.034
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM	33	genes.ES.table	0.63	1.5	0.047	0.22	0.98	0.52	0.2	0.41	0.14	0.017
KEGG RIBOSOME	86	genes.ES.table	0.64	1.5	0.098	0.21	0.96	0.85	0.32	0.58	0.13	0.019
KEGG DNA REPLICATION	36	genes.ES.table	0.6	1.8	0.022	0.47	0.41	0.5	0.22	0.39	0	0.1
KEGG PROTEASOME	43	genes.ES.table	0.56	1.7	0.036	0.28	0.68	0.74	0.37	0.47	0.096	0.069
KEGG BASE EXCISION REPAIR	33	genes.ES.table	0.52	1.7	0.045	0.19	0.73	0.7	0.35	0.45	0.073	0.034
KEGG HOMOLOGOUS RECOMBINATION	26	genes.ES.table	0.64	1.5	0.074	0.21	0.98	0.58	0.22	0.45	0.14	0.014
KEGG CELL CYCLE	118	genes.ES.table	0.51	1.6	0.063	0.21	0.93	0.26	0.13	0.23	0.12	0.023
KEGG PARKINSONS DISEASE	111	genes.ES.table	0.42	1.5	0.12	0.23	0.98	0.63	0.28	0.45	0.16	0.012

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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	CDT1	CDT1	CDT1	59	0.43	0.067	YES
2	GINS2	GINS2	GINS2	248	0.32	0.11	YES
3	CDC6	CDC6	CDC6	376	0.29	0.15	YES
4	CCNA2	CCNA2	CCNA2	506	0.26	0.18	YES
5	CDC45	CDC45	CDC45	551	0.26	0.22	YES
6	POLE2	POLE2	POLE2	597	0.25	0.26	YES
7	GINS1	GINS1	GINS1	829	0.21	0.28	YES
8	DNA2	DNA2	DNA2	998	0.19	0.3	YES
9	PRIM2	PRIM2	PRIM2	1064	0.18	0.33	YES
10	RFC4	RFC4	RFC4	1169	0.17	0.35	YES
11	GINS4	GINS4	GINS4	1212	0.17	0.38	YES
12	RFC3	RFC3	RFC3	1654	0.14	0.38	YES
13	POLD4	POLD4	POLD4	1834	0.13	0.39	YES
14	RPA3	RPA3	RPA3	2175	0.11	0.39	YES
15	RFC2	RFC2	RFC2	2242	0.11	0.4	YES
16	PSMC1	PSMC1	PSMC1	2564	0.097	0.4	YES
17	PSME2	PSME2	PSME2	2596	0.096	0.41	YES
18	FEN1	FEN1	FEN1	2686	0.094	0.42	YES
19	PSMB7	PSMB7	PSMB7	2861	0.089	0.43	YES
20	PSMB3	PSMB3	PSMB3	2925	0.087	0.44	YES
21	POLD2	POLD2	POLD2	3118	0.082	0.44	YES
22	MCM7	MCM7	MCM7	3337	0.078	0.44	YES
23	PSMD9	PSMD9	PSMD9	3516	0.074	0.44	YES
24	PSMB4	PSMB4	PSMB4	3775	0.068	0.44	YES
25	UBA52	UBA52	UBA52	3903	0.065	0.44	YES
26	PCNA	PCNA	PCNA	3917	0.065	0.45	YES
27	PSMD4	PSMD4	PSMD4	3919	0.065	0.46	YES
28	PSMA3	PSMA3	PSMA3	3929	0.065	0.48	YES
29	POLD1	POLD1	POLD1	3948	0.064	0.48	YES
30	PSMB1	PSMB1	PSMB1	4032	0.063	0.49	YES
31	PSMB6	PSMB6	PSMB6	4124	0.061	0.5	YES
32	PSMA4	PSMA4	PSMA4	4132	0.06	0.5	YES
33	PSMA6	PSMA6	PSMA6	4173	0.06	0.51	YES
34	PSMB5	PSMB5	PSMB5	4332	0.057	0.51	YES
35	PSMA7	PSMA7	PSMA7	4443	0.055	0.52	YES
36	PSMA5	PSMA5	PSMA5	4474	0.054	0.52	YES
37	PSMA2	PSMA2	PSMA2	4513	0.053	0.53	YES
38	PSMD13	PSMD13	PSMD13	4563	0.052	0.54	YES
39	LIG1	LIG1	LIG1	4702	0.05	0.54	YES
40	CDKN1A	CDKN1A	CDKN1A	4721	0.05	0.54	YES
41	PSMC2	PSMC2	PSMC2	4913	0.046	0.54	YES
42	PSMB2	PSMB2	PSMB2	5057	0.044	0.54	YES
43	POLA2	POLA2	POLA2	5084	0.044	0.55	YES
44	RPS27A	RPS27A	RPS27A	5181	0.042	0.55	YES
45	PSMC3	PSMC3	PSMC3	5230	0.041	0.55	YES
46	MCM5	MCM5	MCM5	5318	0.04	0.55	YES
47	PSMC5	PSMC5	PSMC5	5584	0.036	0.54	NO
48	MCM2	MCM2	MCM2	5820	0.032	0.54	NO
49	PSME1	PSME1	PSME1	5831	0.032	0.54	NO
50	PSMC6	PSMC6	PSMC6	5960	0.031	0.54	NO
51	PSMD3	PSMD3	PSMD3	6167	0.027	0.53	NO
52	POLE	POLE	POLE	6400	0.024	0.52	NO
53	MCM4	MCM4	MCM4	6480	0.023	0.52	NO
54	RPA2	RPA2	RPA2	6548	0.022	0.52	NO
55	PSMD14	PSMD14	PSMD14	6592	0.021	0.52	NO
56	PSMC4	PSMC4	PSMC4	6606	0.021	0.52	NO
57	PSMD6	PSMD6	PSMD6	6652	0.02	0.53	NO
58	MCM3	MCM3	MCM3	6679	0.02	0.53	NO
59	PSMA1	PSMA1	PSMA1	6765	0.019	0.53	NO
60	RFC5	RFC5	RFC5	6768	0.019	0.53	NO
61	PSMD8	PSMD8	PSMD8	6780	0.019	0.53	NO
62	PSMD11	PSMD11	PSMD11	7003	0.016	0.52	NO
63	PSMB10	PSMB10	PSMB10	7416	0.0097	0.5	NO
64	PSMD12	PSMD12	PSMD12	7542	0.0078	0.5	NO
65	CDK2	CDK2	CDK2	7776	0.0047	0.48	NO
66	PSMF1	PSMF1	PSMF1	7778	0.0046	0.48	NO
67	PSMD2	PSMD2	PSMD2	8193	-0.0013	0.46	NO
68	PSME4	PSME4	PSME4	8241	-0.0018	0.46	NO
69	PSMB9	PSMB9	PSMB9	8664	-0.0073	0.44	NO
70	CCNA1	CCNA1	CCNA1	8702	-0.0077	0.44	NO
71	PSMD7	PSMD7	PSMD7	8770	-0.0086	0.43	NO
72	PSMD1	PSMD1	PSMD1	8998	-0.012	0.42	NO
73	POLD3	POLD3	POLD3	9619	-0.02	0.39	NO
74	PSMD10	PSMD10	PSMD10	9843	-0.023	0.38	NO
75	CDKN1B	CDKN1B	CDKN1B	10343	-0.031	0.36	NO
76	MCM6	MCM6	MCM6	10350	-0.031	0.37	NO
77	POLA1	POLA1	POLA1	10639	-0.035	0.36	NO
78	RPA1	RPA1	RPA1	10860	-0.039	0.35	NO
79	PRIM1	PRIM1	PRIM1	10904	-0.04	0.36	NO
80	PSMB8	PSMB8	PSMB8	11588	-0.05	0.32	NO
81	MCM8	MCM8	MCM8	11995	-0.057	0.31	NO
82	PSMD5	PSMD5	PSMD5	13662	-0.094	0.24	NO
83	RB1	RB1	RB1	14004	-0.1	0.23	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 OXIDATIVE PHOSPHORYLATION.

Figure S42. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, 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 PYRIMIDINE 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	POLE2	POLE2	POLE2	597	0.25	0.058	YES
2	DNA2	DNA2	DNA2	998	0.19	0.1	YES
3	PRIM2	PRIM2	PRIM2	1064	0.18	0.17	YES
4	RFC4	RFC4	RFC4	1169	0.17	0.22	YES
5	RNASEH2A	RNASEH2A	RNASEH2A	1356	0.16	0.27	YES
6	RPA4	RPA4	RPA4	1444	0.15	0.32	YES
7	RFC3	RFC3	RFC3	1654	0.14	0.36	YES
8	POLE4	POLE4	POLE4	1741	0.13	0.4	YES
9	POLD4	POLD4	POLD4	1834	0.13	0.44	YES
10	RPA3	RPA3	RPA3	2175	0.11	0.47	YES
11	RFC2	RFC2	RFC2	2242	0.11	0.5	YES
12	FEN1	FEN1	FEN1	2686	0.094	0.51	YES
13	POLD2	POLD2	POLD2	3118	0.082	0.52	YES
14	MCM7	MCM7	MCM7	3337	0.078	0.54	YES
15	SSBP1	SSBP1	SSBP1	3395	0.076	0.56	YES
16	RNASEH2C	RNASEH2C	RNASEH2C	3652	0.071	0.57	YES
17	PCNA	PCNA	PCNA	3917	0.065	0.58	YES
18	POLD1	POLD1	POLD1	3948	0.064	0.6	YES
19	LIG1	LIG1	LIG1	4702	0.05	0.58	NO
20	POLA2	POLA2	POLA2	5084	0.044	0.57	NO
21	MCM5	MCM5	MCM5	5318	0.04	0.58	NO
22	MCM2	MCM2	MCM2	5820	0.032	0.56	NO
23	POLE	POLE	POLE	6400	0.024	0.54	NO
24	MCM4	MCM4	MCM4	6480	0.023	0.54	NO
25	RPA2	RPA2	RPA2	6548	0.022	0.55	NO
26	MCM3	MCM3	MCM3	6679	0.02	0.55	NO
27	RFC5	RFC5	RFC5	6768	0.019	0.55	NO
28	POLE3	POLE3	POLE3	7804	0.0042	0.49	NO
29	RNASEH1	RNASEH1	RNASEH1	8463	-0.0048	0.46	NO
30	RNASEH2B	RNASEH2B	RNASEH2B	9600	-0.02	0.4	NO
31	POLD3	POLD3	POLD3	9619	-0.02	0.41	NO
32	RFC1	RFC1	RFC1	10184	-0.028	0.39	NO
33	MCM6	MCM6	MCM6	10350	-0.031	0.39	NO
34	POLA1	POLA1	POLA1	10639	-0.035	0.39	NO
35	RPA1	RPA1	RPA1	10860	-0.039	0.39	NO
36	PRIM1	PRIM1	PRIM1	10904	-0.04	0.4	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 PYRIMIDINE METABOLISM.

Figure S44. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRIMIDINE 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 PORPHYRIN AND CHLOROPHYLL METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CDT1	CDT1	CDT1	59	0.43	0.056	YES
2	GINS2	GINS2	GINS2	248	0.32	0.09	YES
3	CDC6	CDC6	CDC6	376	0.29	0.12	YES
4	CCNA2	CCNA2	CCNA2	506	0.26	0.15	YES
5	CDC45	CDC45	CDC45	551	0.26	0.18	YES
6	POLE2	POLE2	POLE2	597	0.25	0.22	YES
7	CCNE1	CCNE1	CCNE1	772	0.22	0.24	YES
8	GINS1	GINS1	GINS1	829	0.21	0.26	YES
9	CDC25A	CDC25A	CDC25A	872	0.21	0.29	YES
10	CCNE2	CCNE2	CCNE2	920	0.2	0.31	YES
11	DNA2	DNA2	DNA2	998	0.19	0.33	YES
12	PRIM2	PRIM2	PRIM2	1064	0.18	0.36	YES
13	RFC4	RFC4	RFC4	1169	0.17	0.37	YES
14	GINS4	GINS4	GINS4	1212	0.17	0.39	YES
15	RFC3	RFC3	RFC3	1654	0.14	0.39	YES
16	POLD4	POLD4	POLD4	1834	0.13	0.4	YES
17	RPA3	RPA3	RPA3	2175	0.11	0.39	YES
18	RFC2	RFC2	RFC2	2242	0.11	0.4	YES
19	PSMC1	PSMC1	PSMC1	2564	0.097	0.4	YES
20	PSME2	PSME2	PSME2	2596	0.096	0.41	YES
21	FEN1	FEN1	FEN1	2686	0.094	0.42	YES
22	PSMB7	PSMB7	PSMB7	2861	0.089	0.42	YES
23	PSMB3	PSMB3	PSMB3	2925	0.087	0.43	YES
24	POLD2	POLD2	POLD2	3118	0.082	0.43	YES
25	CKS1B	CKS1B	CKS1B	3330	0.078	0.43	YES
26	MCM7	MCM7	MCM7	3337	0.078	0.44	YES
27	PSMD9	PSMD9	PSMD9	3516	0.074	0.44	YES
28	PSMB4	PSMB4	PSMB4	3775	0.068	0.44	YES
29	UBA52	UBA52	UBA52	3903	0.065	0.44	YES
30	PCNA	PCNA	PCNA	3917	0.065	0.45	YES
31	PSMD4	PSMD4	PSMD4	3919	0.065	0.46	YES
32	PSMA3	PSMA3	PSMA3	3929	0.065	0.46	YES
33	CDC25B	CDC25B	CDC25B	3945	0.064	0.47	YES
34	POLD1	POLD1	POLD1	3948	0.064	0.48	YES
35	PSMB1	PSMB1	PSMB1	4032	0.063	0.48	YES
36	PSMB6	PSMB6	PSMB6	4124	0.061	0.49	YES
37	PSMA4	PSMA4	PSMA4	4132	0.06	0.5	YES
38	PSMA6	PSMA6	PSMA6	4173	0.06	0.5	YES
39	PSMB5	PSMB5	PSMB5	4332	0.057	0.5	YES
40	PSMA7	PSMA7	PSMA7	4443	0.055	0.5	YES
41	PSMA5	PSMA5	PSMA5	4474	0.054	0.51	YES
42	PSMA2	PSMA2	PSMA2	4513	0.053	0.51	YES
43	PSMD13	PSMD13	PSMD13	4563	0.052	0.52	YES
44	LIG1	LIG1	LIG1	4702	0.05	0.52	YES
45	CDKN1A	CDKN1A	CDKN1A	4721	0.05	0.52	YES
46	MNAT1	MNAT1	MNAT1	4796	0.048	0.52	YES
47	PSMC2	PSMC2	PSMC2	4913	0.046	0.52	YES
48	PSMB2	PSMB2	PSMB2	5057	0.044	0.52	YES
49	POLA2	POLA2	POLA2	5084	0.044	0.53	YES
50	RPS27A	RPS27A	RPS27A	5181	0.042	0.53	YES
51	PSMC3	PSMC3	PSMC3	5230	0.041	0.53	YES
52	MCM5	MCM5	MCM5	5318	0.04	0.53	YES
53	PSMC5	PSMC5	PSMC5	5584	0.036	0.52	NO
54	CCND1	CCND1	CCND1	5735	0.034	0.52	NO
55	MCM2	MCM2	MCM2	5820	0.032	0.52	NO
56	PSME1	PSME1	PSME1	5831	0.032	0.52	NO
57	CDK4	CDK4	CDK4	5865	0.032	0.52	NO
58	PSMC6	PSMC6	PSMC6	5960	0.031	0.52	NO
59	PSMD3	PSMD3	PSMD3	6167	0.027	0.52	NO
60	POLE	POLE	POLE	6400	0.024	0.51	NO
61	MCM4	MCM4	MCM4	6480	0.023	0.5	NO
62	RPA2	RPA2	RPA2	6548	0.022	0.5	NO
63	PSMD14	PSMD14	PSMD14	6592	0.021	0.5	NO
64	PSMC4	PSMC4	PSMC4	6606	0.021	0.51	NO
65	PSMD6	PSMD6	PSMD6	6652	0.02	0.51	NO
66	MCM3	MCM3	MCM3	6679	0.02	0.51	NO
67	PSMA1	PSMA1	PSMA1	6765	0.019	0.51	NO
68	RFC5	RFC5	RFC5	6768	0.019	0.51	NO
69	PSMD8	PSMD8	PSMD8	6780	0.019	0.51	NO
70	PSMD11	PSMD11	PSMD11	7003	0.016	0.5	NO
71	PSMB10	PSMB10	PSMB10	7416	0.0097	0.48	NO
72	CCNH	CCNH	CCNH	7441	0.0094	0.48	NO
73	MAX	MAX	MAX	7448	0.0093	0.48	NO
74	PSMD12	PSMD12	PSMD12	7542	0.0078	0.48	NO
75	CDK2	CDK2	CDK2	7776	0.0047	0.46	NO
76	PSMF1	PSMF1	PSMF1	7778	0.0046	0.46	NO
77	CUL1	CUL1	CUL1	7921	0.0026	0.46	NO
78	SKP1	SKP1	SKP1	7936	0.0023	0.46	NO
79	PSMD2	PSMD2	PSMD2	8193	-0.0013	0.44	NO
80	PSME4	PSME4	PSME4	8241	-0.0018	0.44	NO
81	CDK7	CDK7	CDK7	8495	-0.0054	0.43	NO
82	PSMB9	PSMB9	PSMB9	8664	-0.0073	0.42	NO
83	CCNA1	CCNA1	CCNA1	8702	-0.0077	0.42	NO
84	PSMD7	PSMD7	PSMD7	8770	-0.0086	0.42	NO
85	PSMD1	PSMD1	PSMD1	8998	-0.012	0.4	NO
86	MYC	MYC	MYC	9306	-0.016	0.39	NO
87	POLD3	POLD3	POLD3	9619	-0.02	0.38	NO
88	PSMD10	PSMD10	PSMD10	9843	-0.023	0.37	NO
89	CDKN1B	CDKN1B	CDKN1B	10343	-0.031	0.34	NO
90	MCM6	MCM6	MCM6	10350	-0.031	0.35	NO
91	POLA1	POLA1	POLA1	10639	-0.035	0.34	NO
92	RPA1	RPA1	RPA1	10860	-0.039	0.33	NO
93	PRIM1	PRIM1	PRIM1	10904	-0.04	0.33	NO
94	PSMB8	PSMB8	PSMB8	11588	-0.05	0.3	NO
95	MCM8	MCM8	MCM8	11995	-0.057	0.29	NO
96	PSMD5	PSMD5	PSMD5	13662	-0.094	0.21	NO
97	WEE1	WEE1	WEE1	13681	-0.094	0.22	NO
98	RB1	RB1	RB1	14004	-0.1	0.22	NO
99	SKP2	SKP2	SKP2	14650	-0.12	0.2	NO

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

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

genes ES table in pathway: KEGG RIBOSOME

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	COX17	COX17	COX17	1351	0.16	-0.023	YES
2	LDHD	LDHD	LDHD	1381	0.15	0.026	YES
3	TAZ	TAZ	TAZ	1886	0.12	0.039	YES
4	MTX1	MTX1	MTX1	1887	0.12	0.079	YES
5	TIMM10	TIMM10	TIMM10	1888	0.12	0.12	YES
6	BCS1L	BCS1L	BCS1L	2150	0.11	0.14	YES
7	TIMM8B	TIMM8B	TIMM8B	2160	0.11	0.18	YES
8	TIMM13	TIMM13	TIMM13	2227	0.11	0.21	YES
9	GFER	GFER	GFER	2237	0.11	0.25	YES
10	TIMM8A	TIMM8A	TIMM8A	2295	0.11	0.28	YES
11	ATP5G1	ATP5G1	ATP5G1	2382	0.1	0.31	YES
12	TOMM7	TOMM7	TOMM7	2696	0.093	0.32	YES
13	TOMM5	TOMM5	TOMM5	2798	0.091	0.35	YES
14	TIMM50	TIMM50	TIMM50	2974	0.086	0.36	YES
15	DNAJC19	DNAJC19	DNAJC19	2982	0.086	0.39	YES
16	TIMM17B	TIMM17B	TIMM17B	3091	0.083	0.41	YES
17	TOMM40	TOMM40	TOMM40	3513	0.074	0.42	YES
18	CYC1	CYC1	CYC1	3728	0.069	0.43	YES
19	TIMM44	TIMM44	TIMM44	3729	0.069	0.45	YES
20	PMPCB	PMPCB	PMPCB	4063	0.062	0.45	YES
21	PMPCA	PMPCA	PMPCA	4076	0.062	0.47	YES
22	GRPEL1	GRPEL1	GRPEL1	4097	0.061	0.49	YES
23	TIMM9	TIMM9	TIMM9	4264	0.058	0.5	YES
24	HSPD1	HSPD1	HSPD1	4270	0.058	0.52	YES
25	CHCHD4	CHCHD4	CHCHD4	4295	0.057	0.54	YES
26	MTX2	MTX2	MTX2	4564	0.052	0.54	YES
27	IDH3G	IDH3G	IDH3G	4642	0.051	0.55	YES
28	COQ2	COQ2	COQ2	4704	0.05	0.56	YES
29	TIMM17A	TIMM17A	TIMM17A	4844	0.048	0.57	YES
30	HSCB	HSCB	HSCB	4881	0.047	0.58	YES
31	TOMM70A	TOMM70A	TOMM70A	5149	0.042	0.58	YES
32	GRPEL2	GRPEL2	GRPEL2	5415	0.038	0.58	YES
33	VDAC1	VDAC1	VDAC1	5485	0.037	0.59	YES
34	FXN	FXN	FXN	5673	0.035	0.59	YES
35	TOMM22	TOMM22	TOMM22	5697	0.034	0.6	YES
36	TIMM22	TIMM22	TIMM22	5904	0.032	0.6	NO
37	HSPA9	HSPA9	HSPA9	7104	0.014	0.54	NO
38	ATP5B	ATP5B	ATP5B	7312	0.011	0.53	NO
39	SLC25A13	SLC25A13	SLC25A13	7588	0.0072	0.52	NO
40	SLC25A6	SLC25A6	SLC25A6	7790	0.0045	0.51	NO
41	CS	CS	CS	8126	-0.00031	0.49	NO
42	SLC25A4	SLC25A4	SLC25A4	8247	-0.0019	0.49	NO
43	TOMM20	TOMM20	TOMM20	8290	-0.0024	0.48	NO
44	ATP5A1	ATP5A1	ATP5A1	8296	-0.0024	0.48	NO
45	ACO2	ACO2	ACO2	8473	-0.005	0.48	NO
46	SAMM50	SAMM50	SAMM50	8903	-0.01	0.46	NO
47	C18orf55	C18orf55	C18orf55	9386	-0.017	0.44	NO
48	FXC1	FXC1	FXC1	12117	-0.06	0.31	NO
49	SLC25A12	SLC25A12	SLC25A12	13750	-0.096	0.25	NO

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

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

genes ES table in pathway: KEGG DNA REPLICATION

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	CDT1	CDT1	CDT1	59	0.43	0.082	YES
2	E2F1	E2F1	E2F1	274	0.32	0.13	YES
3	E2F2	E2F2	E2F2	313	0.3	0.19	YES
4	CDC6	CDC6	CDC6	376	0.29	0.24	YES
5	CDC45	CDC45	CDC45	551	0.26	0.28	YES
6	POLE2	POLE2	POLE2	597	0.25	0.33	YES
7	MCM10	MCM10	MCM10	648	0.24	0.37	YES
8	PRIM2	PRIM2	PRIM2	1064	0.18	0.39	YES
9	RPA4	RPA4	RPA4	1444	0.15	0.4	YES
10	RPA3	RPA3	RPA3	2175	0.11	0.38	YES
11	PSMC1	PSMC1	PSMC1	2564	0.097	0.38	YES
12	PSME2	PSME2	PSME2	2596	0.096	0.39	YES
13	DBF4	DBF4	DBF4	2852	0.089	0.4	YES
14	PSMB7	PSMB7	PSMB7	2861	0.089	0.41	YES
15	PSMB3	PSMB3	PSMB3	2925	0.087	0.43	YES
16	MCM7	MCM7	MCM7	3337	0.078	0.42	YES
17	CDC7	CDC7	CDC7	3448	0.075	0.43	YES
18	PSMD9	PSMD9	PSMD9	3516	0.074	0.44	YES
19	PSMB4	PSMB4	PSMB4	3775	0.068	0.44	YES
20	UBA52	UBA52	UBA52	3903	0.065	0.44	YES
21	PSMD4	PSMD4	PSMD4	3919	0.065	0.46	YES
22	PSMA3	PSMA3	PSMA3	3929	0.065	0.47	YES
23	PSMB1	PSMB1	PSMB1	4032	0.063	0.48	YES
24	PSMB6	PSMB6	PSMB6	4124	0.061	0.48	YES
25	PSMA4	PSMA4	PSMA4	4132	0.06	0.49	YES
26	PSMA6	PSMA6	PSMA6	4173	0.06	0.5	YES
27	PSMB5	PSMB5	PSMB5	4332	0.057	0.5	YES
28	PSMA7	PSMA7	PSMA7	4443	0.055	0.51	YES
29	PSMA5	PSMA5	PSMA5	4474	0.054	0.52	YES
30	PSMA2	PSMA2	PSMA2	4513	0.053	0.53	YES
31	PSMD13	PSMD13	PSMD13	4563	0.052	0.54	YES
32	PSMC2	PSMC2	PSMC2	4913	0.046	0.52	YES
33	PSMB2	PSMB2	PSMB2	5057	0.044	0.53	YES
34	POLA2	POLA2	POLA2	5084	0.044	0.53	YES
35	RPS27A	RPS27A	RPS27A	5181	0.042	0.54	YES
36	PSMC3	PSMC3	PSMC3	5230	0.041	0.54	YES
37	MCM5	MCM5	MCM5	5318	0.04	0.54	YES
38	GMNN	GMNN	GMNN	5386	0.039	0.55	YES
39	PSMC5	PSMC5	PSMC5	5584	0.036	0.54	NO
40	MCM2	MCM2	MCM2	5820	0.032	0.54	NO
41	PSME1	PSME1	PSME1	5831	0.032	0.54	NO
42	PSMC6	PSMC6	PSMC6	5960	0.031	0.54	NO
43	PSMD3	PSMD3	PSMD3	6167	0.027	0.54	NO
44	POLE	POLE	POLE	6400	0.024	0.53	NO
45	MCM4	MCM4	MCM4	6480	0.023	0.53	NO
46	RPA2	RPA2	RPA2	6548	0.022	0.53	NO
47	PSMD14	PSMD14	PSMD14	6592	0.021	0.53	NO
48	PSMC4	PSMC4	PSMC4	6606	0.021	0.54	NO
49	PSMD6	PSMD6	PSMD6	6652	0.02	0.54	NO
50	MCM3	MCM3	MCM3	6679	0.02	0.54	NO
51	PSMA1	PSMA1	PSMA1	6765	0.019	0.54	NO
52	PSMD8	PSMD8	PSMD8	6780	0.019	0.54	NO
53	PSMD11	PSMD11	PSMD11	7003	0.016	0.53	NO
54	PSMB10	PSMB10	PSMB10	7416	0.0097	0.51	NO
55	PSMD12	PSMD12	PSMD12	7542	0.0078	0.5	NO
56	CDK2	CDK2	CDK2	7776	0.0047	0.49	NO
57	PSMF1	PSMF1	PSMF1	7778	0.0046	0.49	NO
58	PSMD2	PSMD2	PSMD2	8193	-0.0013	0.47	NO
59	PSME4	PSME4	PSME4	8241	-0.0018	0.47	NO
60	PSMB9	PSMB9	PSMB9	8664	-0.0073	0.45	NO
61	PSMD7	PSMD7	PSMD7	8770	-0.0086	0.44	NO
62	E2F3	E2F3	E2F3	8991	-0.012	0.43	NO
63	PSMD1	PSMD1	PSMD1	8998	-0.012	0.44	NO
64	PSMD10	PSMD10	PSMD10	9843	-0.023	0.39	NO
65	MCM6	MCM6	MCM6	10350	-0.031	0.37	NO
66	POLA1	POLA1	POLA1	10639	-0.035	0.36	NO
67	RPA1	RPA1	RPA1	10860	-0.039	0.36	NO
68	PRIM1	PRIM1	PRIM1	10904	-0.04	0.36	NO
69	PSMB8	PSMB8	PSMB8	11588	-0.05	0.34	NO
70	MCM8	MCM8	MCM8	11995	-0.057	0.33	NO
71	PSMD5	PSMD5	PSMD5	13662	-0.094	0.25	NO

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

Figure S50. 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 PROTEASOME

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	CDT1	CDT1	CDT1	59	0.43	0.13	YES
2	CDC6	CDC6	CDC6	376	0.29	0.2	YES
3	CCNA2	CCNA2	CCNA2	506	0.26	0.27	YES
4	PSMC1	PSMC1	PSMC1	2564	0.097	0.19	YES
5	PSME2	PSME2	PSME2	2596	0.096	0.21	YES
6	PSMB7	PSMB7	PSMB7	2861	0.089	0.22	YES
7	PSMB3	PSMB3	PSMB3	2925	0.087	0.25	YES
8	MCM7	MCM7	MCM7	3337	0.078	0.25	YES
9	PSMD9	PSMD9	PSMD9	3516	0.074	0.26	YES
10	PSMB4	PSMB4	PSMB4	3775	0.068	0.27	YES
11	UBA52	UBA52	UBA52	3903	0.065	0.28	YES
12	PSMD4	PSMD4	PSMD4	3919	0.065	0.3	YES
13	PSMA3	PSMA3	PSMA3	3929	0.065	0.32	YES
14	PSMB1	PSMB1	PSMB1	4032	0.063	0.33	YES
15	PSMB6	PSMB6	PSMB6	4124	0.061	0.34	YES
16	PSMA4	PSMA4	PSMA4	4132	0.06	0.36	YES
17	PSMA6	PSMA6	PSMA6	4173	0.06	0.38	YES
18	PSMB5	PSMB5	PSMB5	4332	0.057	0.39	YES
19	PSMA7	PSMA7	PSMA7	4443	0.055	0.4	YES
20	PSMA5	PSMA5	PSMA5	4474	0.054	0.41	YES
21	PSMA2	PSMA2	PSMA2	4513	0.053	0.42	YES
22	PSMD13	PSMD13	PSMD13	4563	0.052	0.44	YES
23	CDKN1A	CDKN1A	CDKN1A	4721	0.05	0.44	YES
24	PSMC2	PSMC2	PSMC2	4913	0.046	0.45	YES
25	PSMB2	PSMB2	PSMB2	5057	0.044	0.45	YES
26	RPS27A	RPS27A	RPS27A	5181	0.042	0.46	YES
27	PSMC3	PSMC3	PSMC3	5230	0.041	0.47	YES
28	MCM5	MCM5	MCM5	5318	0.04	0.48	YES
29	PSMC5	PSMC5	PSMC5	5584	0.036	0.47	YES
30	MCM2	MCM2	MCM2	5820	0.032	0.47	YES
31	PSME1	PSME1	PSME1	5831	0.032	0.48	YES
32	PSMC6	PSMC6	PSMC6	5960	0.031	0.48	YES
33	PSMD3	PSMD3	PSMD3	6167	0.027	0.48	YES
34	MCM4	MCM4	MCM4	6480	0.023	0.47	YES
35	PSMD14	PSMD14	PSMD14	6592	0.021	0.47	YES
36	PSMC4	PSMC4	PSMC4	6606	0.021	0.47	YES
37	PSMD6	PSMD6	PSMD6	6652	0.02	0.48	YES
38	MCM3	MCM3	MCM3	6679	0.02	0.48	YES
39	PSMA1	PSMA1	PSMA1	6765	0.019	0.48	YES
40	PSMD8	PSMD8	PSMD8	6780	0.019	0.49	YES
41	PSMD11	PSMD11	PSMD11	7003	0.016	0.48	NO
42	PSMB10	PSMB10	PSMB10	7416	0.0097	0.46	NO
43	PSMD12	PSMD12	PSMD12	7542	0.0078	0.46	NO
44	CDK2	CDK2	CDK2	7776	0.0047	0.44	NO
45	PSMF1	PSMF1	PSMF1	7778	0.0046	0.45	NO
46	PSMD2	PSMD2	PSMD2	8193	-0.0013	0.42	NO
47	PSME4	PSME4	PSME4	8241	-0.0018	0.42	NO
48	PSMB9	PSMB9	PSMB9	8664	-0.0073	0.4	NO
49	CCNA1	CCNA1	CCNA1	8702	-0.0077	0.4	NO
50	PSMD7	PSMD7	PSMD7	8770	-0.0086	0.4	NO
51	PSMD1	PSMD1	PSMD1	8998	-0.012	0.39	NO
52	PSMD10	PSMD10	PSMD10	9843	-0.023	0.35	NO
53	CDKN1B	CDKN1B	CDKN1B	10343	-0.031	0.33	NO
54	MCM6	MCM6	MCM6	10350	-0.031	0.34	NO
55	PSMB8	PSMB8	PSMB8	11588	-0.05	0.29	NO
56	MCM8	MCM8	MCM8	11995	-0.057	0.28	NO
57	PSMD5	PSMD5	PSMD5	13662	-0.094	0.22	NO
58	RB1	RB1	RB1	14004	-0.1	0.23	NO

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

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

genes ES table in pathway: KEGG BASE EXCISION REPAIR

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	UBE2C	UBE2C	UBE2C	22	0.5	0.057	YES
2	CDC25C	CDC25C	CDC25C	36	0.46	0.11	YES
3	CDC20	CDC20	CDC20	97	0.4	0.15	YES
4	CDK1	CDK1	CDK1	139	0.37	0.2	YES
5	CDC6	CDC6	CDC6	376	0.29	0.22	YES
6	BUB1B	BUB1B	BUB1B	522	0.26	0.24	YES
7	CDC45	CDC45	CDC45	551	0.26	0.27	YES
8	MCM10	MCM10	MCM10	648	0.24	0.29	YES
9	CCNE1	CCNE1	CCNE1	772	0.22	0.31	YES
10	CCNB2	CCNB2	CCNB2	852	0.21	0.33	YES
11	CDC25A	CDC25A	CDC25A	872	0.21	0.35	YES
12	CCNE2	CCNE2	CCNE2	920	0.2	0.37	YES
13	CHEK1	CHEK1	CHEK1	1041	0.18	0.39	YES
14	RFC4	RFC4	RFC4	1169	0.17	0.4	YES
15	CCNB1	CCNB1	CCNB1	1228	0.16	0.42	YES
16	MAD1L1	MAD1L1	MAD1L1	1409	0.15	0.42	YES
17	RAD9A	RAD9A	RAD9A	1545	0.14	0.43	YES
18	RFC3	RFC3	RFC3	1654	0.14	0.44	YES
19	ANAPC11	ANAPC11	ANAPC11	1776	0.13	0.45	YES
20	RPA3	RPA3	RPA3	2175	0.11	0.44	YES
21	RFC2	RFC2	RFC2	2242	0.11	0.45	YES
22	MAD2L1	MAD2L1	MAD2L1	2404	0.1	0.46	YES
23	PSMC1	PSMC1	PSMC1	2564	0.097	0.46	YES
24	PSME2	PSME2	PSME2	2596	0.096	0.47	YES
25	DBF4	DBF4	DBF4	2852	0.089	0.46	YES
26	PSMB7	PSMB7	PSMB7	2861	0.089	0.48	YES
27	CHEK2	CHEK2	CHEK2	2893	0.088	0.48	YES
28	PSMB3	PSMB3	PSMB3	2925	0.087	0.49	YES
29	MCM7	MCM7	MCM7	3337	0.078	0.48	YES
30	CDC7	CDC7	CDC7	3448	0.075	0.48	YES
31	PSMD9	PSMD9	PSMD9	3516	0.074	0.49	YES
32	ATRIP	ATRIP	ATRIP	3595	0.072	0.49	YES
33	ANAPC5	ANAPC5	ANAPC5	3622	0.072	0.5	YES
34	PSMB4	PSMB4	PSMB4	3775	0.068	0.5	YES
35	UBA52	UBA52	UBA52	3903	0.065	0.5	YES
36	PSMD4	PSMD4	PSMD4	3919	0.065	0.5	YES
37	PSMA3	PSMA3	PSMA3	3929	0.065	0.51	YES
38	PSMB1	PSMB1	PSMB1	4032	0.063	0.51	YES
39	PSMB6	PSMB6	PSMB6	4124	0.061	0.52	YES
40	PSMA4	PSMA4	PSMA4	4132	0.06	0.52	YES
41	PSMA6	PSMA6	PSMA6	4173	0.06	0.53	YES
42	PSMB5	PSMB5	PSMB5	4332	0.057	0.52	YES
43	PSMA7	PSMA7	PSMA7	4443	0.055	0.52	YES
44	PSMA5	PSMA5	PSMA5	4474	0.054	0.53	YES
45	HUS1	HUS1	HUS1	4506	0.054	0.53	YES
46	PSMA2	PSMA2	PSMA2	4513	0.053	0.54	YES
47	PSMD13	PSMD13	PSMD13	4563	0.052	0.54	YES
48	CDKN1A	CDKN1A	CDKN1A	4721	0.05	0.54	YES
49	UBE2E1	UBE2E1	UBE2E1	4842	0.048	0.54	YES
50	PSMC2	PSMC2	PSMC2	4913	0.046	0.54	YES
51	ANAPC2	ANAPC2	ANAPC2	4945	0.046	0.55	YES
52	PSMB2	PSMB2	PSMB2	5057	0.044	0.54	YES
53	UBE2D1	UBE2D1	UBE2D1	5112	0.043	0.55	YES
54	RPS27A	RPS27A	RPS27A	5181	0.042	0.55	YES
55	PSMC3	PSMC3	PSMC3	5230	0.041	0.55	YES
56	MCM5	MCM5	MCM5	5318	0.04	0.55	NO
57	PSMC5	PSMC5	PSMC5	5584	0.036	0.54	NO
58	MCM2	MCM2	MCM2	5820	0.032	0.53	NO
59	PSME1	PSME1	PSME1	5831	0.032	0.53	NO
60	CDC26	CDC26	CDC26	5946	0.031	0.53	NO
61	PSMC6	PSMC6	PSMC6	5960	0.031	0.53	NO
62	PSMD3	PSMD3	PSMD3	6167	0.027	0.52	NO
63	ANAPC7	ANAPC7	ANAPC7	6221	0.027	0.52	NO
64	MCM4	MCM4	MCM4	6480	0.023	0.51	NO
65	RPA2	RPA2	RPA2	6548	0.022	0.51	NO
66	PSMD14	PSMD14	PSMD14	6592	0.021	0.51	NO
67	PSMC4	PSMC4	PSMC4	6606	0.021	0.52	NO
68	PSMD6	PSMD6	PSMD6	6652	0.02	0.51	NO
69	MCM3	MCM3	MCM3	6679	0.02	0.52	NO
70	PSMA1	PSMA1	PSMA1	6765	0.019	0.51	NO
71	RFC5	RFC5	RFC5	6768	0.019	0.52	NO
72	PSMD8	PSMD8	PSMD8	6780	0.019	0.52	NO
73	PSMD11	PSMD11	PSMD11	7003	0.016	0.51	NO
74	BUB3	BUB3	BUB3	7267	0.012	0.49	NO
75	PSMB10	PSMB10	PSMB10	7416	0.0097	0.49	NO
76	PSMD12	PSMD12	PSMD12	7542	0.0078	0.48	NO
77	RAD1	RAD1	RAD1	7607	0.007	0.48	NO
78	CDK2	CDK2	CDK2	7776	0.0047	0.47	NO
79	PSMF1	PSMF1	PSMF1	7778	0.0046	0.47	NO
80	CDC16	CDC16	CDC16	7795	0.0044	0.47	NO
81	CDC23	CDC23	CDC23	8158	-0.00084	0.45	NO
82	PSMD2	PSMD2	PSMD2	8193	-0.0013	0.45	NO
83	PSME4	PSME4	PSME4	8241	-0.0018	0.44	NO
84	RFWD2	RFWD2	RFWD2	8568	-0.0062	0.43	NO
85	PSMB9	PSMB9	PSMB9	8664	-0.0073	0.42	NO
86	ANAPC4	ANAPC4	ANAPC4	8740	-0.0082	0.42	NO
87	ANAPC10	ANAPC10	ANAPC10	8767	-0.0086	0.42	NO
88	PSMD7	PSMD7	PSMD7	8770	-0.0086	0.42	NO
89	PSMD1	PSMD1	PSMD1	8998	-0.012	0.41	NO
90	MDM2	MDM2	MDM2	9104	-0.013	0.4	NO
91	TP53	TP53	TP53	9333	-0.016	0.4	NO
92	PSMD10	PSMD10	PSMD10	9843	-0.023	0.37	NO
93	CDKN1B	CDKN1B	CDKN1B	10343	-0.031	0.34	NO
94	MCM6	MCM6	MCM6	10350	-0.031	0.35	NO
95	RPA1	RPA1	RPA1	10860	-0.039	0.32	NO
96	CDC27	CDC27	CDC27	11105	-0.042	0.32	NO
97	PSMB8	PSMB8	PSMB8	11588	-0.05	0.3	NO
98	RAD17	RAD17	RAD17	11702	-0.052	0.3	NO
99	MCM8	MCM8	MCM8	11995	-0.057	0.29	NO
100	ATR	ATR	ATR	12371	-0.064	0.27	NO
101	PSMD5	PSMD5	PSMD5	13662	-0.094	0.21	NO
102	WEE1	WEE1	WEE1	13681	-0.094	0.22	NO
103	ATM	ATM	ATM	14535	-0.12	0.19	NO
104	ANAPC1	ANAPC1	ANAPC1	14683	-0.12	0.2	NO

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

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

genes ES table in pathway: KEGG HOMOLOGOUS RECOMBINATION

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	SHFM1	SHFM1	SHFM1	1315	0.16	0.008	YES
2	PSMB11	PSMB11	PSMB11	1687	0.14	0.056	YES
3	PSMC1	PSMC1	PSMC1	2564	0.097	0.057	YES
4	PSME2	PSME2	PSME2	2596	0.096	0.1	YES
5	PSMB7	PSMB7	PSMB7	2861	0.089	0.13	YES
6	PSMB3	PSMB3	PSMB3	2925	0.087	0.18	YES
7	PSMB4	PSMB4	PSMB4	3775	0.068	0.16	YES
8	PSMD4	PSMD4	PSMD4	3919	0.065	0.19	YES
9	PSMA3	PSMA3	PSMA3	3929	0.065	0.22	YES
10	PSMB1	PSMB1	PSMB1	4032	0.063	0.25	YES
11	POMP	POMP	POMP	4114	0.061	0.27	YES
12	PSMB6	PSMB6	PSMB6	4124	0.061	0.3	YES
13	PSMA4	PSMA4	PSMA4	4132	0.06	0.33	YES
14	PSMA6	PSMA6	PSMA6	4173	0.06	0.36	YES
15	PSMB5	PSMB5	PSMB5	4332	0.057	0.38	YES
16	IFNG	IFNG	IFNG	4423	0.055	0.4	YES
17	PSMA7	PSMA7	PSMA7	4443	0.055	0.43	YES
18	PSMA5	PSMA5	PSMA5	4474	0.054	0.46	YES
19	PSMA2	PSMA2	PSMA2	4513	0.053	0.48	YES
20	PSMD13	PSMD13	PSMD13	4563	0.052	0.5	YES
21	PSMC2	PSMC2	PSMC2	4913	0.046	0.51	YES
22	PSMB2	PSMB2	PSMB2	5057	0.044	0.52	YES
23	PSMC3	PSMC3	PSMC3	5230	0.041	0.54	YES
24	PSMC5	PSMC5	PSMC5	5584	0.036	0.53	YES
25	PSME1	PSME1	PSME1	5831	0.032	0.54	YES
26	PSMC6	PSMC6	PSMC6	5960	0.031	0.55	YES
27	PSMD3	PSMD3	PSMD3	6167	0.027	0.55	YES
28	PSMD14	PSMD14	PSMD14	6592	0.021	0.54	YES
29	PSMC4	PSMC4	PSMC4	6606	0.021	0.55	YES
30	PSMD6	PSMD6	PSMD6	6652	0.02	0.55	YES
31	PSMA1	PSMA1	PSMA1	6765	0.019	0.56	YES
32	PSMD8	PSMD8	PSMD8	6780	0.019	0.56	YES
33	PSMD11	PSMD11	PSMD11	7003	0.016	0.56	NO
34	PSMB10	PSMB10	PSMB10	7416	0.0097	0.54	NO
35	PSMD12	PSMD12	PSMD12	7542	0.0078	0.54	NO
36	PSMF1	PSMF1	PSMF1	7778	0.0046	0.53	NO
37	PSMD2	PSMD2	PSMD2	8193	-0.0013	0.51	NO
38	PSME4	PSME4	PSME4	8241	-0.0018	0.5	NO
39	PSMB9	PSMB9	PSMB9	8664	-0.0073	0.49	NO
40	PSMD7	PSMD7	PSMD7	8770	-0.0086	0.48	NO
41	PSME3	PSME3	PSME3	8840	-0.0097	0.48	NO
42	PSMD1	PSMD1	PSMD1	8998	-0.012	0.48	NO
43	PSMB8	PSMB8	PSMB8	11588	-0.05	0.37	NO

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

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

genes ES table in pathway: KEGG CELL CYCLE

Table 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	AURKB	AURKB	AURKB	3	0.58	0.09	YES
2	UBE2C	UBE2C	UBE2C	22	0.5	0.17	YES
3	PTTG1	PTTG1	PTTG1	39	0.46	0.24	YES
4	CDC20	CDC20	CDC20	97	0.4	0.29	YES
5	CDK1	CDK1	CDK1	139	0.37	0.35	YES
6	PLK1	PLK1	PLK1	165	0.36	0.4	YES
7	AURKA	AURKA	AURKA	309	0.3	0.44	YES
8	CCNA2	CCNA2	CCNA2	506	0.26	0.47	YES
9	BUB1B	BUB1B	BUB1B	522	0.26	0.51	YES
10	CCNB1	CCNB1	CCNB1	1228	0.16	0.5	YES
11	ANAPC11	ANAPC11	ANAPC11	1776	0.13	0.49	YES
12	MAD2L1	MAD2L1	MAD2L1	2404	0.1	0.47	YES
13	PSMC1	PSMC1	PSMC1	2564	0.097	0.48	YES
14	PSME2	PSME2	PSME2	2596	0.096	0.49	YES
15	PSMB7	PSMB7	PSMB7	2861	0.089	0.49	YES
16	PSMB3	PSMB3	PSMB3	2925	0.087	0.5	YES
17	PSMD9	PSMD9	PSMD9	3516	0.074	0.48	YES
18	ANAPC5	ANAPC5	ANAPC5	3622	0.072	0.48	YES
19	PSMB4	PSMB4	PSMB4	3775	0.068	0.48	YES
20	UBA52	UBA52	UBA52	3903	0.065	0.49	YES
21	PSMD4	PSMD4	PSMD4	3919	0.065	0.5	YES
22	PSMA3	PSMA3	PSMA3	3929	0.065	0.51	YES
23	PSMB1	PSMB1	PSMB1	4032	0.063	0.51	YES
24	PSMB6	PSMB6	PSMB6	4124	0.061	0.52	YES
25	PSMA4	PSMA4	PSMA4	4132	0.06	0.52	YES
26	PSMA6	PSMA6	PSMA6	4173	0.06	0.53	YES
27	PSMB5	PSMB5	PSMB5	4332	0.057	0.53	YES
28	PSMA7	PSMA7	PSMA7	4443	0.055	0.53	YES
29	PSMA5	PSMA5	PSMA5	4474	0.054	0.54	YES
30	PSMA2	PSMA2	PSMA2	4513	0.053	0.55	YES
31	PSMD13	PSMD13	PSMD13	4563	0.052	0.55	YES
32	UBE2E1	UBE2E1	UBE2E1	4842	0.048	0.54	YES
33	PSMC2	PSMC2	PSMC2	4913	0.046	0.55	YES
34	ANAPC2	ANAPC2	ANAPC2	4945	0.046	0.55	YES
35	PSMB2	PSMB2	PSMB2	5057	0.044	0.55	YES
36	UBE2D1	UBE2D1	UBE2D1	5112	0.043	0.56	YES
37	RPS27A	RPS27A	RPS27A	5181	0.042	0.56	YES
38	PSMC3	PSMC3	PSMC3	5230	0.041	0.56	YES
39	PSMC5	PSMC5	PSMC5	5584	0.036	0.55	NO
40	PSME1	PSME1	PSME1	5831	0.032	0.54	NO
41	CDC26	CDC26	CDC26	5946	0.031	0.54	NO
42	PSMC6	PSMC6	PSMC6	5960	0.031	0.54	NO
43	PSMD3	PSMD3	PSMD3	6167	0.027	0.54	NO
44	ANAPC7	ANAPC7	ANAPC7	6221	0.027	0.54	NO
45	PSMD14	PSMD14	PSMD14	6592	0.021	0.52	NO
46	PSMC4	PSMC4	PSMC4	6606	0.021	0.52	NO
47	PSMD6	PSMD6	PSMD6	6652	0.02	0.52	NO
48	PSMA1	PSMA1	PSMA1	6765	0.019	0.52	NO
49	PSMD8	PSMD8	PSMD8	6780	0.019	0.52	NO
50	PSMD11	PSMD11	PSMD11	7003	0.016	0.51	NO
51	BUB3	BUB3	BUB3	7267	0.012	0.5	NO
52	FBXO5	FBXO5	FBXO5	7322	0.011	0.5	NO
53	PSMB10	PSMB10	PSMB10	7416	0.0097	0.5	NO
54	PSMD12	PSMD12	PSMD12	7542	0.0078	0.49	NO
55	CDK2	CDK2	CDK2	7776	0.0047	0.48	NO
56	PSMF1	PSMF1	PSMF1	7778	0.0046	0.48	NO
57	CDC16	CDC16	CDC16	7795	0.0044	0.48	NO
58	CUL1	CUL1	CUL1	7921	0.0026	0.47	NO
59	SKP1	SKP1	SKP1	7936	0.0023	0.47	NO
60	CDC23	CDC23	CDC23	8158	-0.00084	0.46	NO
61	PSMD2	PSMD2	PSMD2	8193	-0.0013	0.46	NO
62	PSME4	PSME4	PSME4	8241	-0.0018	0.46	NO
63	PSMB9	PSMB9	PSMB9	8664	-0.0073	0.43	NO
64	CCNA1	CCNA1	CCNA1	8702	-0.0077	0.43	NO
65	ANAPC4	ANAPC4	ANAPC4	8740	-0.0082	0.43	NO
66	ANAPC10	ANAPC10	ANAPC10	8767	-0.0086	0.43	NO
67	PSMD7	PSMD7	PSMD7	8770	-0.0086	0.43	NO
68	PSMD1	PSMD1	PSMD1	8998	-0.012	0.42	NO
69	PSMD10	PSMD10	PSMD10	9843	-0.023	0.38	NO
70	BTRC	BTRC	BTRC	10644	-0.036	0.34	NO
71	CDC27	CDC27	CDC27	11105	-0.042	0.32	NO
72	PSMB8	PSMB8	PSMB8	11588	-0.05	0.3	NO
73	CDC14A	CDC14A	CDC14A	12656	-0.07	0.26	NO
74	PSMD5	PSMD5	PSMD5	13662	-0.094	0.21	NO
75	SKP2	SKP2	SKP2	14650	-0.12	0.18	NO
76	ANAPC1	ANAPC1	ANAPC1	14683	-0.12	0.2	NO

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

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

genes ES table in pathway: KEGG PARKINSONS DISEASE

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	UCP3	UCP3	UCP3	889	0.2	-0.025	YES
2	COX6C	COX6C	COX6C	1303	0.16	-0.028	YES
3	ATP5I	ATP5I	ATP5I	1515	0.14	-0.023	YES
4	NDUFA3	NDUFA3	NDUFA3	1523	0.14	-0.0061	YES
5	NDUFB9	NDUFB9	NDUFB9	1671	0.14	0.002	YES
6	ATP5J2	ATP5J2	ATP5J2	1701	0.13	0.016	YES
7	NDUFB1	NDUFB1	NDUFB1	1712	0.13	0.032	YES
8	COX6A1	COX6A1	COX6A1	1757	0.13	0.045	YES
9	UQCRHL	UQCRHL	UQCRHL	1774	0.13	0.06	YES
10	ATP5D	ATP5D	ATP5D	1786	0.13	0.074	YES
11	NDUFB7	NDUFB7	NDUFB7	1839	0.13	0.087	YES
12	COX5B	COX5B	COX5B	1854	0.12	0.1	YES
13	UQCR11	UQCR11	UQCR11	1969	0.12	0.11	YES
14	NDUFA2	NDUFA2	NDUFA2	1978	0.12	0.12	YES
15	NDUFB10	NDUFB10	NDUFB10	2082	0.12	0.13	YES
16	UQCRB	UQCRB	UQCRB	2091	0.12	0.14	YES
17	NDUFA13	NDUFA13	NDUFA13	2095	0.12	0.16	YES
18	NDUFS8	NDUFS8	NDUFS8	2134	0.11	0.17	YES
19	UQCRQ	UQCRQ	UQCRQ	2165	0.11	0.18	YES
20	NDUFA7	NDUFA7	NDUFA7	2185	0.11	0.19	YES
21	COX7B	COX7B	COX7B	2217	0.11	0.21	YES
22	NDUFA1	NDUFA1	NDUFA1	2361	0.1	0.21	YES
23	D2HGDH	D2HGDH	D2HGDH	2379	0.1	0.22	YES
24	ATP5G1	ATP5G1	ATP5G1	2382	0.1	0.23	YES
25	SLC16A1	SLC16A1	SLC16A1	2394	0.1	0.25	YES
26	NDUFS6	NDUFS6	NDUFS6	2409	0.1	0.26	YES
27	ADHFE1	ADHFE1	ADHFE1	2468	0.1	0.27	YES
28	NDUFC2	NDUFC2	NDUFC2	2577	0.097	0.27	YES
29	ATP5E	ATP5E	ATP5E	2667	0.094	0.28	YES
30	COX6B1	COX6B1	COX6B1	2672	0.094	0.29	YES
31	UQCRH	UQCRH	UQCRH	2744	0.092	0.3	YES
32	COX8A	COX8A	COX8A	2764	0.092	0.31	YES
33	NDUFV3	NDUFV3	NDUFV3	2766	0.091	0.32	YES
34	NDUFV1	NDUFV1	NDUFV1	2838	0.09	0.32	YES
35	NDUFA11	NDUFA11	NDUFA11	2946	0.086	0.33	YES
36	NDUFB2	NDUFB2	NDUFB2	2954	0.086	0.34	YES
37	NDUFV2	NDUFV2	NDUFV2	2958	0.086	0.35	YES
38	NDUFA8	NDUFA8	NDUFA8	2986	0.085	0.36	YES
39	NDUFB3	NDUFB3	NDUFB3	3038	0.084	0.36	YES
40	NDUFB6	NDUFB6	NDUFB6	3060	0.084	0.37	YES
41	NDUFS7	NDUFS7	NDUFS7	3074	0.083	0.38	YES
42	COX5A	COX5A	COX5A	3143	0.082	0.39	YES
43	NDUFAB1	NDUFAB1	NDUFAB1	3509	0.074	0.38	YES
44	UCP2	UCP2	UCP2	3533	0.073	0.38	YES
45	CYC1	CYC1	CYC1	3728	0.069	0.38	YES
46	NDUFC1	NDUFC1	NDUFC1	3763	0.068	0.39	YES
47	NDUFB8	NDUFB8	NDUFB8	3856	0.066	0.39	YES
48	NDUFA12	NDUFA12	NDUFA12	3865	0.066	0.4	YES
49	BSG	BSG	BSG	3958	0.064	0.4	YES
50	NDUFS5	NDUFS5	NDUFS5	4059	0.062	0.4	YES
51	NDUFB4	NDUFB4	NDUFB4	4123	0.061	0.41	YES
52	COX4I1	COX4I1	COX4I1	4178	0.06	0.41	YES
53	ATP5H	ATP5H	ATP5H	4182	0.06	0.42	YES
54	ATP5L	ATP5L	ATP5L	4319	0.057	0.42	YES
55	NDUFA10	NDUFA10	NDUFA10	4487	0.054	0.42	YES
56	ATP5O	ATP5O	ATP5O	4511	0.053	0.42	YES
57	UQCRC1	UQCRC1	UQCRC1	4523	0.053	0.43	YES
58	SLC16A8	SLC16A8	SLC16A8	4546	0.053	0.43	YES
59	NDUFA6	NDUFA6	NDUFA6	4560	0.052	0.44	YES
60	IDH3B	IDH3B	IDH3B	4629	0.051	0.44	YES
61	IDH3G	IDH3G	IDH3G	4642	0.051	0.44	YES
62	IDH2	IDH2	IDH2	4771	0.049	0.44	YES
63	NDUFA4	NDUFA4	NDUFA4	4831	0.048	0.45	YES
64	NDUFS3	NDUFS3	NDUFS3	4903	0.047	0.45	YES
65	COX7C	COX7C	COX7C	4952	0.046	0.45	YES
66	NDUFA9	NDUFA9	NDUFA9	5016	0.044	0.45	YES
67	MDH2	MDH2	MDH2	5054	0.044	0.46	YES
68	ATP5J	ATP5J	ATP5J	5091	0.043	0.46	YES
69	CYCS	CYCS	CYCS	5196	0.042	0.46	YES
70	ATP5C1	ATP5C1	ATP5C1	5197	0.042	0.46	YES
71	FH	FH	FH	5227	0.041	0.47	YES
72	NDUFB5	NDUFB5	NDUFB5	5436	0.038	0.46	NO
73	SDHB	SDHB	SDHB	5896	0.032	0.44	NO
74	PDHX	PDHX	PDHX	5981	0.03	0.44	NO
75	NDUFA5	NDUFA5	NDUFA5	6139	0.028	0.43	NO
76	COX7A2L	COX7A2L	COX7A2L	6258	0.026	0.43	NO
77	PDHA1	PDHA1	PDHA1	6466	0.023	0.42	NO
78	ETFB	ETFB	ETFB	6671	0.02	0.41	NO
79	ETFA	ETFA	ETFA	6681	0.02	0.41	NO
80	SDHA	SDHA	SDHA	6718	0.02	0.41	NO
81	UQCRFS1	UQCRFS1	UQCRFS1	6745	0.019	0.41	NO
82	NDUFS2	NDUFS2	NDUFS2	7008	0.015	0.4	NO
83	DLST	DLST	DLST	7208	0.013	0.39	NO
84	L2HGDH	L2HGDH	L2HGDH	7214	0.013	0.39	NO
85	SDHC	SDHC	SDHC	7220	0.013	0.4	NO
86	ATP5B	ATP5B	ATP5B	7312	0.011	0.39	NO
87	NDUFS4	NDUFS4	NDUFS4	7614	0.0069	0.38	NO
88	SUCLG1	SUCLG1	SUCLG1	7620	0.0069	0.38	NO
89	PDHB	PDHB	PDHB	7869	0.0033	0.36	NO
90	ATP5F1	ATP5F1	ATP5F1	7890	0.003	0.36	NO
91	IDH1	IDH1	IDH1	8077	0.00017	0.35	NO
92	CS	CS	CS	8126	-0.00031	0.35	NO
93	PDK1	PDK1	PDK1	8176	-0.0011	0.35	NO
94	DLD	DLD	DLD	8206	-0.0014	0.34	NO
95	ETFDH	ETFDH	ETFDH	8223	-0.0016	0.34	NO
96	SUCLG2	SUCLG2	SUCLG2	8257	-0.002	0.34	NO
97	SLC16A3	SLC16A3	SLC16A3	8279	-0.0023	0.34	NO
98	ATP5A1	ATP5A1	ATP5A1	8296	-0.0024	0.34	NO
99	LDHA	LDHA	LDHA	8332	-0.0029	0.34	NO
100	ACO2	ACO2	ACO2	8473	-0.005	0.33	NO
101	IDH3A	IDH3A	IDH3A	9758	-0.022	0.26	NO
102	UQCRC2	UQCRC2	UQCRC2	10390	-0.031	0.23	NO
103	OGDH	OGDH	OGDH	11054	-0.042	0.2	NO
104	DLAT	DLAT	DLAT	11814	-0.054	0.17	NO
105	SDHD	SDHD	SDHD	12065	-0.059	0.16	NO
106	PDP1	PDP1	PDP1	12402	-0.065	0.15	NO
107	NDUFS1	NDUFS1	NDUFS1	12526	-0.067	0.15	NO
108	PDK2	PDK2	PDK2	12617	-0.069	0.15	NO
109	SUCLA2	SUCLA2	SUCLA2	13068	-0.078	0.14	NO
110	PDK3	PDK3	PDK3	14597	-0.12	0.068	NO
111	PDP2	PDP2	PDP2	15888	-0.18	0.019	NO
112	LDHB	LDHB	LDHB	16386	-0.21	0.017	NO
113	NNT	NNT	NNT	16414	-0.21	0.041	NO
114	PDPR	PDPR	PDPR	16526	-0.22	0.061	NO
115	PDK4	PDK4	PDK4	17262	-0.28	0.055	NO

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

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PARKINSONS DISEASE, 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM	30	genes.ES.table	0.52	1.6	0.024	0.2	0.93	0.43	0.29	0.31	0.11	0.015
KEGG LYSINE DEGRADATION	44	genes.ES.table	0.46	1.9	0.0061	0.91	0.32	0.068	0.059	0.064	0	0.19
KEGG ARGININE AND PROLINE METABOLISM	51	genes.ES.table	0.44	1.4	0.11	0.22	1	0.2	0.13	0.17	0.16	0.001
KEGG HISTIDINE METABOLISM	29	genes.ES.table	0.58	1.5	0.029	0.19	0.98	0.34	0.2	0.28	0.13	0.004
KEGG TRYPTOPHAN METABOLISM	38	genes.ES.table	0.59	1.6	0.0021	0.21	0.82	0.34	0.19	0.28	0.097	0.033
KEGG SELENOAMINO ACID METABOLISM	26	genes.ES.table	0.47	1.6	0.04	0.21	0.86	0.077	0.019	0.076	0.1	0.031
KEGG GLUTATHIONE METABOLISM	48	genes.ES.table	0.55	1.6	0.037	0.2	0.93	0.31	0.21	0.25	0.11	0.014
KEGG O GLYCAN BIOSYNTHESIS	29	genes.ES.table	0.57	1.4	0.06	0.19	0.99	0.21	0.08	0.19	0.13	0.002
KEGG GLYCEROLIPID METABOLISM	44	genes.ES.table	0.44	1.4	0.098	0.22	1	0.41	0.29	0.29	0.17	0.001
KEGG INOSITOL PHOSPHATE METABOLISM	53	genes.ES.table	0.46	1.6	0.022	0.2	0.93	0.26	0.23	0.2	0.11	0.014

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

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NTF4	NTF4	NTF4	23	0.81	0.14	YES
2	NTF3	NTF3	NTF3	436	0.46	0.2	YES
3	MMP7	MMP7	MMP7	616	0.42	0.26	YES
4	NGFR	NGFR	NGFR	633	0.41	0.34	YES
5	BEX1	BEX1	BEX1	718	0.4	0.4	YES
6	BDNF	BDNF	BDNF	905	0.37	0.46	YES
7	NTRK1	NTRK1	NTRK1	1592	0.28	0.47	YES
8	BIRC3	BIRC3	BIRC3	1715	0.28	0.51	YES
9	OMG	OMG	OMG	3031	0.18	0.47	NO
10	RHOB	RHOB	RHOB	4168	0.13	0.43	NO
11	NGF	NGF	NGF	4673	0.1	0.42	NO
12	NDN	NDN	NDN	4904	0.097	0.42	NO
13	MAG	MAG	MAG	5279	0.085	0.42	NO
14	PIK3R1	PIK3R1	PIK3R1	5289	0.085	0.43	NO
15	IKBKB	IKBKB	IKBKB	5888	0.067	0.41	NO
16	TRAF6	TRAF6	TRAF6	5933	0.065	0.42	NO
17	PLG	PLG	PLG	6634	0.049	0.39	NO
18	SQSTM1	SQSTM1	SQSTM1	7190	0.038	0.37	NO
19	IKBKG	IKBKG	IKBKG	7285	0.037	0.37	NO
20	SHC1	SHC1	SHC1	7466	0.034	0.36	NO
21	NDNL2	NDNL2	NDNL2	7564	0.032	0.36	NO
22	CASP9	CASP9	CASP9	7837	0.029	0.36	NO
23	FURIN	FURIN	FURIN	7914	0.028	0.36	NO
24	ZNF274	ZNF274	ZNF274	8071	0.026	0.35	NO
25	APP	APP	APP	8575	0.019	0.33	NO
26	TP53	TP53	TP53	8592	0.019	0.33	NO
27	MYD88	MYD88	MYD88	8650	0.018	0.33	NO
28	ADAM17	ADAM17	ADAM17	8674	0.018	0.33	NO
29	CASP3	CASP3	CASP3	8703	0.018	0.33	NO
30	MAPK10	MAPK10	MAPK10	8765	0.017	0.33	NO
31	BIRC2	BIRC2	BIRC2	8806	0.016	0.33	NO
32	RTN4R	RTN4R	RTN4R	8863	0.016	0.33	NO
33	RTN4	RTN4	RTN4	9098	0.013	0.32	NO
34	DIABLO	DIABLO	DIABLO	9538	0.0092	0.3	NO
35	BCL2L11	BCL2L11	BCL2L11	9762	0.0069	0.29	NO
36	PRDM4	PRDM4	PRDM4	9767	0.0069	0.29	NO
37	RHOC	RHOC	RHOC	10018	0.0044	0.28	NO
38	RHOA	RHOA	RHOA	10188	0.0027	0.27	NO
39	CASP6	CASP6	CASP6	10357	0.0013	0.26	NO
40	NGFRAP1	NGFRAP1	NGFRAP1	10549	-0.00028	0.25	NO
41	APH1A	APH1A	APH1A	10643	-0.0011	0.24	NO
42	SORT1	SORT1	SORT1	10677	-0.0014	0.24	NO
43	PRKCZ	PRKCZ	PRKCZ	10679	-0.0014	0.24	NO
44	RAC1	RAC1	RAC1	10712	-0.0017	0.24	NO
45	APAF1	APAF1	APAF1	10827	-0.0028	0.24	NO
46	PIK3CA	PIK3CA	PIK3CA	10930	-0.0038	0.23	NO
47	PSENEN	PSENEN	PSENEN	11199	-0.0059	0.22	NO
48	PSEN1	PSEN1	PSEN1	11543	-0.0086	0.2	NO
49	CHUK	CHUK	CHUK	11656	-0.0095	0.2	NO
50	MAGEH1	MAGEH1	MAGEH1	11701	-0.0099	0.2	NO
51	SMPD2	SMPD2	SMPD2	11832	-0.011	0.19	NO
52	BAD	BAD	BAD	12165	-0.014	0.17	NO
53	ARHGDIA	ARHGDIA	ARHGDIA	12922	-0.02	0.14	NO
54	APH1B	APH1B	APH1B	12943	-0.02	0.14	NO
55	NCSTN	NCSTN	NCSTN	13585	-0.026	0.11	NO
56	AKT1	AKT1	AKT1	13643	-0.027	0.11	NO
57	MMP3	MMP3	MMP3	13790	-0.028	0.11	NO
58	YWHAE	YWHAE	YWHAE	13820	-0.029	0.11	NO
59	PRKCI	PRKCI	PRKCI	14097	-0.032	0.1	NO
60	IRAK1	IRAK1	IRAK1	14719	-0.038	0.072	NO
61	MAPK8	MAPK8	MAPK8	14780	-0.039	0.076	NO
62	XIAP	XIAP	XIAP	15262	-0.045	0.057	NO
63	MAPK9	MAPK9	MAPK9	15445	-0.049	0.056	NO
64	CYCS	CYCS	CYCS	15484	-0.05	0.063	NO
65	PRKACB	PRKACB	PRKACB	15832	-0.056	0.053	NO
66	MAGED1	MAGED1	MAGED1	15984	-0.06	0.056	NO
67	RIPK2	RIPK2	RIPK2	17175	-0.1	0.0083	NO
68	E2F1	E2F1	E2F1	17486	-0.12	0.013	NO
69	LINGO1	LINGO1	LINGO1	17827	-0.16	0.024	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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

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	TMLHE	TMLHE	TMLHE	401	0.47	0.18	YES
2	PIPOX	PIPOX	PIPOX	737	0.39	0.33	YES
3	BBOX1	BBOX1	BBOX1	1070	0.34	0.46	YES
4	ALDH2	ALDH2	ALDH2	3386	0.16	0.4	NO
5	ALDH3A2	ALDH3A2	ALDH3A2	5278	0.085	0.33	NO
6	SUV420H2	SUV420H2	SUV420H2	7311	0.036	0.23	NO
7	WHSC1L1	WHSC1L1	WHSC1L1	7611	0.032	0.23	NO
8	SETDB2	SETDB2	SETDB2	7694	0.031	0.24	NO
9	ALDH1B1	ALDH1B1	ALDH1B1	8327	0.022	0.22	NO
10	SETD1A	SETD1A	SETD1A	8356	0.022	0.22	NO
11	AASS	AASS	AASS	8377	0.022	0.23	NO
12	EHMT2	EHMT2	EHMT2	8565	0.019	0.23	NO
13	AASDH	AASDH	AASDH	9722	0.0073	0.17	NO
14	SUV39H1	SUV39H1	SUV39H1	10183	0.0027	0.14	NO
15	HADHA	HADHA	HADHA	10219	0.0024	0.14	NO
16	DOT1L	DOT1L	DOT1L	10235	0.0022	0.14	NO
17	SETD1B	SETD1B	SETD1B	10653	-0.0012	0.12	NO
18	SETDB1	SETDB1	SETDB1	10965	-0.004	0.11	NO
19	SETMAR	SETMAR	SETMAR	11132	-0.0053	0.099	NO
20	DLST	DLST	DLST	11273	-0.0064	0.094	NO
21	OGDH	OGDH	OGDH	11493	-0.0082	0.085	NO
22	ALDH7A1	ALDH7A1	ALDH7A1	11576	-0.0089	0.085	NO
23	GCDH	GCDH	GCDH	11719	-0.01	0.081	NO
24	EHMT1	EHMT1	EHMT1	12044	-0.013	0.069	NO
25	SETD8	SETD8	SETD8	12220	-0.014	0.065	NO
26	PLOD1	PLOD1	PLOD1	12251	-0.014	0.07	NO
27	ASH1L	ASH1L	ASH1L	12336	-0.015	0.072	NO
28	SUV420H1	SUV420H1	SUV420H1	12352	-0.015	0.077	NO
29	ALDH9A1	ALDH9A1	ALDH9A1	12358	-0.015	0.083	NO
30	SETD2	SETD2	SETD2	12361	-0.015	0.09	NO
31	OGDHL	OGDHL	OGDHL	12417	-0.016	0.094	NO
32	HADH	HADH	HADH	12793	-0.019	0.081	NO
33	NSD1	NSD1	NSD1	12907	-0.02	0.083	NO
34	PLOD3	PLOD3	PLOD3	13717	-0.028	0.051	NO
35	AASDHPPT	AASDHPPT	AASDHPPT	14000	-0.03	0.048	NO
36	ECHS1	ECHS1	ECHS1	14050	-0.031	0.059	NO
37	ACAT2	ACAT2	ACAT2	14226	-0.033	0.063	NO
38	PLOD2	PLOD2	PLOD2	14648	-0.038	0.056	NO
39	SUV39H2	SUV39H2	SUV39H2	15417	-0.048	0.034	NO
40	ACAT1	ACAT1	ACAT1	15682	-0.053	0.042	NO
41	SETD7	SETD7	SETD7	15807	-0.055	0.059	NO
42	EHHADH	EHHADH	EHHADH	15856	-0.056	0.08	NO
43	AADAT	AADAT	AADAT	15949	-0.059	0.1	NO
44	WHSC1	WHSC1	WHSC1	16147	-0.063	0.12	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 LYSINE DEGRADATION.

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

genes ES table in pathway: KEGG ARGININE AND PROLINE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MUC4	MUC4	MUC4	8	0.88	0.047	YES
2	B3GNT8	B3GNT8	B3GNT8	87	0.69	0.08	YES
3	MUC15	MUC15	MUC15	121	0.65	0.11	YES
4	ST6GALNAC2	ST6GALNAC2	ST6GALNAC2	133	0.64	0.15	YES
5	B3GNT3	B3GNT3	B3GNT3	139	0.64	0.18	YES
6	MUC16	MUC16	MUC16	158	0.62	0.21	YES
7	GALNT5	GALNT5	GALNT5	238	0.55	0.24	YES
8	GCNT3	GCNT3	GCNT3	272	0.53	0.26	YES
9	GALNT14	GALNT14	GALNT14	284	0.52	0.29	YES
10	GALNT6	GALNT6	GALNT6	479	0.45	0.31	YES
11	SEMA6D	SEMA6D	SEMA6D	634	0.41	0.32	YES
12	ST8SIA3	ST8SIA3	ST8SIA3	710	0.4	0.34	YES
13	MUC21	MUC21	MUC21	772	0.39	0.36	YES
14	MGAT3	MGAT3	MGAT3	827	0.38	0.37	YES
15	GALNT9	GALNT9	GALNT9	1008	0.35	0.38	YES
16	MUC12	MUC12	MUC12	1030	0.35	0.4	YES
17	MUC5B	MUC5B	MUC5B	1034	0.35	0.42	YES
18	ST6GALNAC4	ST6GALNAC4	ST6GALNAC4	1190	0.33	0.43	YES
19	ARSE	ARSE	ARSE	1212	0.32	0.44	YES
20	GCNT4	GCNT4	GCNT4	1469	0.3	0.44	YES
21	MUC13	MUC13	MUC13	1623	0.28	0.45	YES
22	MGAT4C	MGAT4C	MGAT4C	1892	0.26	0.45	YES
23	ARSJ	ARSJ	ARSJ	1959	0.26	0.46	YES
24	B3GNT9	B3GNT9	B3GNT9	2067	0.25	0.47	YES
25	B3GNT7	B3GNT7	B3GNT7	2274	0.23	0.47	YES
26	ARSF	ARSF	ARSF	2357	0.22	0.48	YES
27	B3GNT5	B3GNT5	B3GNT5	2434	0.22	0.48	YES
28	PLAUR	PLAUR	PLAUR	2553	0.21	0.49	YES
29	F10	F10	F10	2715	0.2	0.49	YES
30	F7	F7	F7	2739	0.2	0.5	YES
31	GALNT8	GALNT8	GALNT8	2745	0.2	0.51	YES
32	MUC17	MUC17	MUC17	3037	0.18	0.5	YES
33	GFPT2	GFPT2	GFPT2	3042	0.18	0.51	YES
34	ST6GALNAC3	ST6GALNAC3	ST6GALNAC3	3201	0.17	0.51	YES
35	PGAP1	PGAP1	PGAP1	3492	0.16	0.51	NO
36	ARSI	ARSI	ARSI	3971	0.14	0.49	NO
37	ST3GAL2	ST3GAL2	ST3GAL2	4438	0.12	0.47	NO
38	ST6GAL1	ST6GAL1	ST6GAL1	5397	0.082	0.42	NO
39	MAN1A1	MAN1A1	MAN1A1	5489	0.078	0.42	NO
40	SEC23A	SEC23A	SEC23A	5601	0.074	0.42	NO
41	B4GALT1	B4GALT1	B4GALT1	5816	0.068	0.41	NO
42	GALNTL1	GALNTL1	GALNTL1	5853	0.068	0.41	NO
43	WBSCR17	WBSCR17	WBSCR17	6039	0.062	0.4	NO
44	B3GNT2	B3GNT2	B3GNT2	6074	0.062	0.4	NO
45	PROS1	PROS1	PROS1	6083	0.061	0.41	NO
46	GALNTL4	GALNTL4	GALNTL4	6347	0.055	0.4	NO
47	GALNT12	GALNT12	GALNT12	6605	0.049	0.38	NO
48	B4GALT5	B4GALT5	B4GALT5	6683	0.048	0.38	NO
49	STS	STS	STS	6830	0.045	0.38	NO
50	EIF5A2	EIF5A2	EIF5A2	6998	0.042	0.37	NO
51	MGAT1	MGAT1	MGAT1	7055	0.041	0.37	NO
52	ST3GAL1	ST3GAL1	ST3GAL1	7145	0.039	0.37	NO
53	FUT8	FUT8	FUT8	7250	0.037	0.36	NO
54	C1GALT1	C1GALT1	C1GALT1	7499	0.034	0.35	NO
55	FURIN	FURIN	FURIN	7914	0.028	0.33	NO
56	PROC	PROC	PROC	7953	0.027	0.33	NO
57	MAN1C1	MAN1C1	MAN1C1	8166	0.024	0.32	NO
58	B4GALT4	B4GALT4	B4GALT4	8211	0.024	0.32	NO
59	PIGB	PIGB	PIGB	8258	0.023	0.32	NO
60	ARSK	ARSK	ARSK	8264	0.023	0.32	NO
61	PIGC	PIGC	PIGC	8595	0.019	0.3	NO
62	DOHH	DOHH	DOHH	8759	0.017	0.29	NO
63	B4GALT6	B4GALT6	B4GALT6	8924	0.015	0.28	NO
64	PIGS	PIGS	PIGS	8985	0.015	0.28	NO
65	ARSB	ARSB	ARSB	9029	0.014	0.28	NO
66	GALNT2	GALNT2	GALNT2	9195	0.012	0.27	NO
67	DPM1	DPM1	DPM1	9519	0.0093	0.25	NO
68	GALNTL2	GALNTL2	GALNTL2	9572	0.0088	0.25	NO
69	PIGQ	PIGQ	PIGQ	9591	0.0085	0.25	NO
70	B3GNT4	B3GNT4	B3GNT4	9797	0.0066	0.24	NO
71	GMPPA	GMPPA	GMPPA	9959	0.0049	0.23	NO
72	PIGA	PIGA	PIGA	10016	0.0044	0.23	NO
73	ALG5	ALG5	ALG5	10055	0.004	0.23	NO
74	EDEM2	EDEM2	EDEM2	10498	0.00026	0.2	NO
75	VKORC1	VKORC1	VKORC1	10620	-0.00091	0.2	NO
76	SUMF2	SUMF2	SUMF2	10666	-0.0013	0.19	NO
77	F2	F2	F2	10700	-0.0016	0.19	NO
78	DPM3	DPM3	DPM3	10715	-0.0017	0.19	NO
79	PIGT	PIGT	PIGT	11070	-0.0048	0.17	NO
80	RFT1	RFT1	RFT1	11171	-0.0056	0.16	NO
81	PIGL	PIGL	PIGL	11335	-0.0068	0.16	NO
82	MAN1B1	MAN1B1	MAN1B1	11427	-0.0076	0.15	NO
83	ALG12	ALG12	ALG12	11510	-0.0083	0.15	NO
84	DAD1	DAD1	DAD1	11511	-0.0083	0.15	NO
85	PRKCSH	PRKCSH	PRKCSH	11895	-0.012	0.13	NO
86	ALG1	ALG1	ALG1	11995	-0.012	0.12	NO
87	B4GALT2	B4GALT2	B4GALT2	12101	-0.013	0.12	NO
88	PIGG	PIGG	PIGG	12110	-0.013	0.12	NO
89	ALG13	ALG13	ALG13	12155	-0.014	0.12	NO
90	UGGT1	UGGT1	UGGT1	12234	-0.014	0.11	NO
91	SEC13	SEC13	SEC13	12403	-0.016	0.1	NO
92	EIF5A	EIF5A	EIF5A	12422	-0.016	0.1	NO
93	GALNT10	GALNT10	GALNT10	12428	-0.016	0.1	NO
94	DOLK	DOLK	DOLK	12587	-0.017	0.097	NO
95	ARSA	ARSA	ARSA	12596	-0.017	0.097	NO
96	GMPPB	GMPPB	GMPPB	12629	-0.018	0.097	NO
97	PIGF	PIGF	PIGF	12655	-0.018	0.096	NO
98	GPAA1	GPAA1	GPAA1	12713	-0.018	0.094	NO
99	PREB	PREB	PREB	12729	-0.018	0.094	NO
100	ALG2	ALG2	ALG2	12741	-0.019	0.095	NO
101	PROZ	PROZ	PROZ	12850	-0.02	0.09	NO
102	MOGS	MOGS	MOGS	12859	-0.02	0.09	NO
103	MCFD2	MCFD2	MCFD2	12888	-0.02	0.09	NO
104	PIGV	PIGV	PIGV	12906	-0.02	0.09	NO
105	RPN1	RPN1	RPN1	12916	-0.02	0.09	NO
106	DPM2	DPM2	DPM2	12926	-0.02	0.091	NO
107	PIGU	PIGU	PIGU	13023	-0.021	0.087	NO
108	SEC24B	SEC24B	SEC24B	13029	-0.021	0.088	NO
109	PIGN	PIGN	PIGN	13228	-0.023	0.078	NO
110	GGCX	GGCX	GGCX	13312	-0.024	0.075	NO
111	LMAN1	LMAN1	LMAN1	13333	-0.024	0.075	NO
112	EDEM1	EDEM1	EDEM1	13359	-0.024	0.075	NO
113	RPN2	RPN2	RPN2	13404	-0.025	0.074	NO
114	GALNT1	GALNT1	GALNT1	13436	-0.025	0.073	NO
115	MUCL1	MUCL1	MUCL1	13486	-0.025	0.072	NO
116	ST3GAL3	ST3GAL3	ST3GAL3	13513	-0.026	0.072	NO
117	PIGO	PIGO	PIGO	13543	-0.026	0.072	NO
118	GANAB	GANAB	GANAB	13598	-0.026	0.07	NO
119	DPAGT1	DPAGT1	DPAGT1	13674	-0.027	0.068	NO
120	SEC24C	SEC24C	SEC24C	13840	-0.029	0.06	NO
121	SEC24D	SEC24D	SEC24D	13875	-0.029	0.06	NO
122	UGGT2	UGGT2	UGGT2	14058	-0.031	0.051	NO
123	ALG9	ALG9	ALG9	14090	-0.031	0.051	NO
124	SEC31A	SEC31A	SEC31A	14122	-0.032	0.051	NO
125	DHPS	DHPS	DHPS	14153	-0.032	0.051	NO
126	MAN2A1	MAN2A1	MAN2A1	14222	-0.033	0.049	NO
127	SUMF1	SUMF1	SUMF1	14350	-0.034	0.044	NO
128	C1GALT1C1	C1GALT1C1	C1GALT1C1	14357	-0.034	0.046	NO
129	ALG3	ALG3	ALG3	14378	-0.034	0.046	NO
130	MGAT5	MGAT5	MGAT5	14400	-0.035	0.047	NO
131	DDOST	DDOST	DDOST	14532	-0.036	0.042	NO
132	DOLPP1	DOLPP1	DOLPP1	14574	-0.037	0.041	NO
133	MLEC	MLEC	MLEC	14622	-0.037	0.041	NO
134	PMM1	PMM1	PMM1	14742	-0.039	0.036	NO
135	B3GNTL1	B3GNTL1	B3GNTL1	14743	-0.039	0.038	NO
136	MPI	MPI	MPI	14758	-0.039	0.04	NO
137	MGAT4B	MGAT4B	MGAT4B	14829	-0.04	0.038	NO
138	PMM2	PMM2	PMM2	14874	-0.04	0.038	NO
139	PDIA3	PDIA3	PDIA3	14892	-0.04	0.039	NO
140	CALR	CALR	CALR	14930	-0.041	0.039	NO
141	ALG11	ALG11	ALG11	14934	-0.041	0.041	NO
142	MGAT2	MGAT2	MGAT2	14993	-0.042	0.04	NO
143	STT3A	STT3A	STT3A	15111	-0.043	0.036	NO
144	MUC6	MUC6	MUC6	15132	-0.043	0.037	NO
145	CANX	CANX	CANX	15133	-0.043	0.039	NO
146	MUC2	MUC2	MUC2	15206	-0.044	0.038	NO
147	MAN1A2	MAN1A2	MAN1A2	15212	-0.044	0.04	NO
148	PIGK	PIGK	PIGK	15502	-0.05	0.027	NO
149	ST8SIA6	ST8SIA6	ST8SIA6	15511	-0.05	0.029	NO
150	B4GALT3	B4GALT3	B4GALT3	15532	-0.051	0.03	NO
151	GALNT11	GALNT11	GALNT11	15599	-0.052	0.03	NO
152	PIGX	PIGX	PIGX	15689	-0.053	0.028	NO
153	PIGH	PIGH	PIGH	15744	-0.054	0.028	NO
154	MANEA	MANEA	MANEA	15803	-0.055	0.027	NO
155	PIGM	PIGM	PIGM	15847	-0.056	0.028	NO
156	PIGP	PIGP	PIGP	15887	-0.057	0.029	NO
157	ALG8	ALG8	ALG8	15983	-0.059	0.027	NO
158	ARSG	ARSG	ARSG	16018	-0.06	0.028	NO
159	ALG14	ALG14	ALG14	16104	-0.062	0.027	NO
160	PGM3	PGM3	PGM3	16224	-0.065	0.024	NO
161	ALG10B	ALG10B	ALG10B	16299	-0.067	0.023	NO
162	ALG10	ALG10	ALG10	16367	-0.069	0.023	NO
163	MGAT4A	MGAT4A	MGAT4A	16383	-0.07	0.026	NO
164	ALG6	ALG6	ALG6	16519	-0.074	0.023	NO
165	TUSC3	TUSC3	TUSC3	16671	-0.08	0.018	NO
166	GALNTL6	GALNTL6	GALNTL6	16719	-0.082	0.02	NO
167	SAR1B	SAR1B	SAR1B	16732	-0.082	0.024	NO
168	GCNT1	GCNT1	GCNT1	16786	-0.084	0.026	NO
169	GNPNAT1	GNPNAT1	GNPNAT1	17066	-0.098	0.016	NO
170	GALNT13	GALNT13	GALNT13	17084	-0.099	0.02	NO
171	PIGW	PIGW	PIGW	17123	-0.1	0.023	NO
172	GALNT7	GALNT7	GALNT7	17125	-0.1	0.029	NO
173	GALNT3	GALNT3	GALNT3	17130	-0.1	0.034	NO
174	ST8SIA2	ST8SIA2	ST8SIA2	17230	-0.11	0.034	NO
175	EDEM3	EDEM3	EDEM3	17448	-0.12	0.029	NO
176	B3GNT6	B3GNT6	B3GNT6	17531	-0.13	0.031	NO
177	ARSH	ARSH	ARSH	17836	-0.17	0.023	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 ARGININE AND PROLINE METABOLISM.

Figure S66. 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 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	CXCL1	CXCL1	CXCL1	106	0.67	0.085	YES
2	CXCR2	CXCR2	CXCR2	118	0.66	0.17	YES
3	ATP6V0A4	ATP6V0A4	ATP6V0A4	293	0.52	0.23	YES
4	PTPRZ1	PTPRZ1	PTPRZ1	375	0.48	0.29	YES
5	MET	MET	MET	636	0.41	0.33	YES
6	ATP6V0D2	ATP6V0D2	ATP6V0D2	692	0.4	0.38	YES
7	ATP6V1G3	ATP6V1G3	ATP6V1G3	856	0.38	0.43	YES
8	CCL5	CCL5	CCL5	1260	0.32	0.45	YES
9	IL8	IL8	IL8	1498	0.3	0.47	YES
10	ATP6V1B1	ATP6V1B1	ATP6V1B1	1542	0.29	0.51	YES
11	PLCG2	PLCG2	PLCG2	2173	0.24	0.51	YES
12	MAP3K14	MAP3K14	MAP3K14	2348	0.22	0.53	YES
13	TCIRG1	TCIRG1	TCIRG1	3061	0.18	0.51	YES
14	HBEGF	HBEGF	HBEGF	3229	0.17	0.53	YES
15	JAM2	JAM2	JAM2	3631	0.15	0.53	YES
16	ATP6V1C2	ATP6V1C2	ATP6V1C2	4407	0.12	0.5	YES
17	PAK1	PAK1	PAK1	4428	0.12	0.51	YES
18	JAM3	JAM3	JAM3	4504	0.11	0.52	YES
19	NOD1	NOD1	NOD1	4755	0.1	0.52	YES
20	EGFR	EGFR	EGFR	4956	0.095	0.53	YES
21	NFKBIA	NFKBIA	NFKBIA	5062	0.092	0.53	YES
22	CXCR1	CXCR1	CXCR1	5203	0.088	0.54	YES
23	NFKB1	NFKB1	NFKB1	5246	0.086	0.55	YES
24	F11R	F11R	F11R	5538	0.077	0.54	NO
25	JUN	JUN	JUN	5829	0.068	0.53	NO
26	IKBKB	IKBKB	IKBKB	5888	0.067	0.54	NO
27	MAPK11	MAPK11	MAPK11	6844	0.045	0.49	NO
28	MAPK13	MAPK13	MAPK13	7133	0.039	0.48	NO
29	IKBKG	IKBKG	IKBKG	7285	0.037	0.48	NO
30	LYN	LYN	LYN	7496	0.034	0.47	NO
31	SRC	SRC	SRC	7608	0.032	0.47	NO
32	ATP6V0D1	ATP6V0D1	ATP6V0D1	7803	0.029	0.46	NO
33	ADAM17	ADAM17	ADAM17	8674	0.018	0.42	NO
34	CASP3	CASP3	CASP3	8703	0.018	0.42	NO
35	MAPK10	MAPK10	MAPK10	8765	0.017	0.42	NO
36	MAPK14	MAPK14	MAPK14	9039	0.014	0.4	NO
37	RELA	RELA	RELA	9076	0.014	0.4	NO
38	PLCG1	PLCG1	PLCG1	9371	0.011	0.39	NO
39	GIT1	GIT1	GIT1	9760	0.0069	0.37	NO
40	ATP6V0E1	ATP6V0E1	ATP6V0E1	9814	0.0063	0.37	NO
41	ATP6V1G2	ATP6V1G2	ATP6V1G2	10216	0.0024	0.35	NO
42	ATP6V0A2	ATP6V0A2	ATP6V0A2	10245	0.0022	0.34	NO
43	ATP6V1B2	ATP6V1B2	ATP6V1B2	10254	0.0021	0.34	NO
44	CSK	CSK	CSK	10302	0.0017	0.34	NO
45	RAC1	RAC1	RAC1	10712	-0.0017	0.32	NO
46	CDC42	CDC42	CDC42	10947	-0.0039	0.31	NO
47	ATP6V1E1	ATP6V1E1	ATP6V1E1	11183	-0.0058	0.3	NO
48	ATP6V0A1	ATP6V0A1	ATP6V0A1	11635	-0.0094	0.27	NO
49	CHUK	CHUK	CHUK	11656	-0.0095	0.27	NO
50	ATP6V0C	ATP6V0C	ATP6V0C	11972	-0.012	0.26	NO
51	MAP2K4	MAP2K4	MAP2K4	12025	-0.013	0.26	NO
52	IGSF5	IGSF5	IGSF5	12320	-0.015	0.24	NO
53	ATP6V1H	ATP6V1H	ATP6V1H	12383	-0.016	0.24	NO
54	ATP6V1E2	ATP6V1E2	ATP6V1E2	12592	-0.017	0.23	NO
55	ATP6V1F	ATP6V1F	ATP6V1F	12933	-0.02	0.21	NO
56	ATP6V0B	ATP6V0B	ATP6V0B	13174	-0.022	0.2	NO
57	ATP6V1D	ATP6V1D	ATP6V1D	13366	-0.024	0.2	NO
58	PTPN11	PTPN11	PTPN11	13442	-0.025	0.2	NO
59	ATP6AP1	ATP6AP1	ATP6AP1	14343	-0.034	0.15	NO
60	ADAM10	ADAM10	ADAM10	14715	-0.038	0.14	NO
61	ATP6V1C1	ATP6V1C1	ATP6V1C1	14746	-0.039	0.14	NO
62	MAPK8	MAPK8	MAPK8	14780	-0.039	0.14	NO
63	MAPK9	MAPK9	MAPK9	15445	-0.049	0.11	NO
64	MAPK12	MAPK12	MAPK12	15636	-0.052	0.11	NO
65	ATP6V1A	ATP6V1A	ATP6V1A	15991	-0.06	0.098	NO
66	ATP6V1G1	ATP6V1G1	ATP6V1G1	16050	-0.061	0.1	NO
67	TJP1	TJP1	TJP1	16055	-0.061	0.11	NO
68	ATP6V0E2	ATP6V0E2	ATP6V0E2	16504	-0.073	0.096	NO

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

Figure S68. 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 TRYPTOPHAN METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PPARGC1A	PPARGC1A	PPARGC1A	489	0.45	0.055	YES
2	ANGPTL4	ANGPTL4	ANGPTL4	984	0.36	0.092	YES
3	SLC2A4	SLC2A4	SLC2A4	1037	0.35	0.15	YES
4	TNF	TNF	TNF	1148	0.33	0.21	YES
5	WNT1	WNT1	WNT1	1172	0.33	0.27	YES
6	FABP4	FABP4	FABP4	1237	0.32	0.32	YES
7	SMARCD3	SMARCD3	SMARCD3	1303	0.32	0.37	YES
8	KLF5	KLF5	KLF5	1405	0.3	0.42	YES
9	PCK1	PCK1	PCK1	2062	0.25	0.43	YES
10	CEBPB	CEBPB	CEBPB	2225	0.23	0.47	YES
11	CEBPD	CEBPD	CEBPD	2501	0.21	0.49	YES
12	TGFB1	TGFB1	TGFB1	3672	0.15	0.45	YES
13	PPARG	PPARG	PPARG	3768	0.15	0.47	YES
14	KLF4	KLF4	KLF4	4637	0.11	0.44	YES
15	EBF1	EBF1	EBF1	4644	0.11	0.46	YES
16	EGR2	EGR2	EGR2	4657	0.11	0.48	YES
17	CCND3	CCND3	CCND3	4822	0.1	0.49	YES
18	WNT10B	WNT10B	WNT10B	4835	0.1	0.51	YES
19	MED30	MED30	MED30	6260	0.057	0.44	NO
20	RXRA	RXRA	RXRA	6438	0.053	0.44	NO
21	MED21	MED21	MED21	6571	0.05	0.44	NO
22	MED4	MED4	MED4	7002	0.042	0.43	NO
23	MED15	MED15	MED15	7131	0.039	0.43	NO
24	MED11	MED11	MED11	7942	0.027	0.39	NO
25	NCOR2	NCOR2	NCOR2	8370	0.022	0.37	NO
26	MED9	MED9	MED9	8395	0.021	0.37	NO
27	MED24	MED24	MED24	8409	0.021	0.37	NO
28	MED10	MED10	MED10	8427	0.021	0.38	NO
29	MED12	MED12	MED12	8544	0.02	0.37	NO
30	MED6	MED6	MED6	8562	0.019	0.38	NO
31	TBL1X	TBL1X	TBL1X	8582	0.019	0.38	NO
32	MED16	MED16	MED16	8725	0.017	0.37	NO
33	MED7	MED7	MED7	8873	0.016	0.37	NO
34	MED20	MED20	MED20	8887	0.016	0.37	NO
35	RELA	RELA	RELA	9076	0.014	0.36	NO
36	CREBBP	CREBBP	CREBBP	9162	0.013	0.36	NO
37	TGS1	TGS1	TGS1	9199	0.012	0.36	NO
38	MED31	MED31	MED31	9446	0.01	0.35	NO
39	MED25	MED25	MED25	9492	0.0095	0.35	NO
40	PRIC285	PRIC285	PRIC285	9632	0.0081	0.34	NO
41	MED18	MED18	MED18	10068	0.0039	0.32	NO
42	HDAC3	HDAC3	HDAC3	10105	0.0035	0.32	NO
43	PPARA	PPARA	PPARA	10226	0.0023	0.31	NO
44	MED26	MED26	MED26	10488	0.00031	0.3	NO
45	MED22	MED22	MED22	10556	-0.00034	0.29	NO
46	NR2F2	NR2F2	NR2F2	10698	-0.0016	0.29	NO
47	MED13L	MED13L	MED13L	10958	-0.004	0.27	NO
48	LEP	LEP	LEP	10977	-0.0041	0.27	NO
49	MED27	MED27	MED27	11133	-0.0053	0.26	NO
50	MED8	MED8	MED8	11860	-0.011	0.23	NO
51	NCOA3	NCOA3	NCOA3	11962	-0.012	0.22	NO
52	MED29	MED29	MED29	12126	-0.014	0.22	NO
53	MED17	MED17	MED17	12235	-0.014	0.21	NO
54	MED19	MED19	MED19	12307	-0.015	0.21	NO
55	CDK8	CDK8	CDK8	12348	-0.015	0.21	NO
56	LPL	LPL	LPL	12366	-0.016	0.22	NO
57	NCOA1	NCOA1	NCOA1	12491	-0.017	0.21	NO
58	NCOR1	NCOR1	NCOR1	12647	-0.018	0.21	NO
59	CCNC	CCNC	CCNC	12773	-0.019	0.2	NO
60	CDK4	CDK4	CDK4	12785	-0.019	0.2	NO
61	MED23	MED23	MED23	12885	-0.02	0.2	NO
62	CDK19	CDK19	CDK19	13209	-0.023	0.19	NO
63	MED1	MED1	MED1	13886	-0.029	0.16	NO
64	MED14	MED14	MED14	14168	-0.032	0.15	NO
65	EP300	EP300	EP300	14397	-0.034	0.14	NO
66	NCOA6	NCOA6	NCOA6	14709	-0.038	0.13	NO
67	TBL1XR1	TBL1XR1	TBL1XR1	15247	-0.045	0.11	NO
68	PLIN1	PLIN1	PLIN1	15882	-0.057	0.086	NO
69	CD36	CD36	CD36	16031	-0.061	0.089	NO
70	SREBF1	SREBF1	SREBF1	16518	-0.074	0.076	NO
71	NCOA2	NCOA2	NCOA2	17278	-0.11	0.054	NO

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

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

genes ES table in pathway: KEGG SELENOAMINO ACID METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MUC4	MUC4	MUC4	8	0.88	0.034	YES
2	B3GNT8	B3GNT8	B3GNT8	87	0.69	0.056	YES
3	MUC15	MUC15	MUC15	121	0.65	0.079	YES
4	ST6GALNAC2	ST6GALNAC2	ST6GALNAC2	133	0.64	0.1	YES
5	B3GNT3	B3GNT3	B3GNT3	139	0.64	0.13	YES
6	MUC16	MUC16	MUC16	158	0.62	0.15	YES
7	GALNT5	GALNT5	GALNT5	238	0.55	0.17	YES
8	GCNT3	GCNT3	GCNT3	272	0.53	0.18	YES
9	GALNT14	GALNT14	GALNT14	284	0.52	0.2	YES
10	FAM153A	FAM153A	FAM153A	473	0.45	0.21	YES
11	GALNT6	GALNT6	GALNT6	479	0.45	0.23	YES
12	SEMA6D	SEMA6D	SEMA6D	634	0.41	0.24	YES
13	ST8SIA3	ST8SIA3	ST8SIA3	710	0.4	0.25	YES
14	MUC21	MUC21	MUC21	772	0.39	0.26	YES
15	MGAT3	MGAT3	MGAT3	827	0.38	0.27	YES
16	GALNT9	GALNT9	GALNT9	1008	0.35	0.27	YES
17	MUC12	MUC12	MUC12	1030	0.35	0.28	YES
18	MUC5B	MUC5B	MUC5B	1034	0.35	0.3	YES
19	ST6GALNAC4	ST6GALNAC4	ST6GALNAC4	1190	0.33	0.3	YES
20	ARSE	ARSE	ARSE	1212	0.32	0.31	YES
21	GCNT4	GCNT4	GCNT4	1469	0.3	0.31	YES
22	MUC13	MUC13	MUC13	1623	0.28	0.31	YES
23	KIFC3	KIFC3	KIFC3	1678	0.28	0.32	YES
24	MGAT4C	MGAT4C	MGAT4C	1892	0.26	0.32	YES
25	ARSJ	ARSJ	ARSJ	1959	0.26	0.32	YES
26	TUBA4A	TUBA4A	TUBA4A	1963	0.26	0.33	YES
27	B3GNT9	B3GNT9	B3GNT9	2067	0.25	0.34	YES
28	B3GNT7	B3GNT7	B3GNT7	2274	0.23	0.34	YES
29	ARSF	ARSF	ARSF	2357	0.22	0.34	YES
30	B3GNT5	B3GNT5	B3GNT5	2434	0.22	0.34	YES
31	PLAUR	PLAUR	PLAUR	2553	0.21	0.34	YES
32	SPHK1	SPHK1	SPHK1	2676	0.2	0.35	YES
33	F10	F10	F10	2715	0.2	0.35	YES
34	F7	F7	F7	2739	0.2	0.36	YES
35	GALNT8	GALNT8	GALNT8	2745	0.2	0.36	YES
36	MUC17	MUC17	MUC17	3037	0.18	0.36	NO
37	GFPT2	GFPT2	GFPT2	3042	0.18	0.36	NO
38	ST6GALNAC3	ST6GALNAC3	ST6GALNAC3	3201	0.17	0.36	NO
39	TUBB2B	TUBB2B	TUBB2B	3434	0.16	0.35	NO
40	PGAP1	PGAP1	PGAP1	3492	0.16	0.36	NO
41	ARSI	ARSI	ARSI	3971	0.14	0.33	NO
42	ST3GAL2	ST3GAL2	ST3GAL2	4438	0.12	0.31	NO
43	RPL21	RPL21	RPL21	4589	0.11	0.31	NO
44	SLC25A12	SLC25A12	SLC25A12	4728	0.1	0.3	NO
45	TUBB6	TUBB6	TUBB6	4794	0.1	0.3	NO
46	TUBA1A	TUBA1A	TUBA1A	5119	0.09	0.29	NO
47	ST6GAL1	ST6GAL1	ST6GAL1	5397	0.082	0.28	NO
48	MAN1A1	MAN1A1	MAN1A1	5489	0.078	0.28	NO
49	SEC23A	SEC23A	SEC23A	5601	0.074	0.27	NO
50	B4GALT1	B4GALT1	B4GALT1	5816	0.068	0.26	NO
51	GALNTL1	GALNTL1	GALNTL1	5853	0.068	0.26	NO
52	RPS27	RPS27	RPS27	5951	0.065	0.26	NO
53	WBSCR17	WBSCR17	WBSCR17	6039	0.062	0.26	NO
54	B3GNT2	B3GNT2	B3GNT2	6074	0.062	0.26	NO
55	PROS1	PROS1	PROS1	6083	0.061	0.26	NO
56	USP11	USP11	USP11	6106	0.061	0.26	NO
57	TAZ	TAZ	TAZ	6114	0.06	0.26	NO
58	GALNTL4	GALNTL4	GALNTL4	6347	0.055	0.25	NO
59	GSPT2	GSPT2	GSPT2	6452	0.052	0.25	NO
60	GALNT12	GALNT12	GALNT12	6605	0.049	0.24	NO
61	B4GALT5	B4GALT5	B4GALT5	6683	0.048	0.24	NO
62	STS	STS	STS	6830	0.045	0.23	NO
63	ACTB	ACTB	ACTB	6909	0.043	0.23	NO
64	LDHD	LDHD	LDHD	6949	0.042	0.23	NO
65	EIF5A2	EIF5A2	EIF5A2	6998	0.042	0.23	NO
66	MGAT1	MGAT1	MGAT1	7055	0.041	0.23	NO
67	ST3GAL1	ST3GAL1	ST3GAL1	7145	0.039	0.22	NO
68	PFDN5	PFDN5	PFDN5	7183	0.038	0.22	NO
69	TUBB1	TUBB1	TUBB1	7215	0.038	0.22	NO
70	FUT8	FUT8	FUT8	7250	0.037	0.22	NO
71	FBXW7	FBXW7	FBXW7	7320	0.036	0.22	NO
72	C1GALT1	C1GALT1	C1GALT1	7499	0.034	0.21	NO
73	FBXW4	FBXW4	FBXW4	7638	0.032	0.2	NO
74	TUBA3D	TUBA3D	TUBA3D	7862	0.028	0.19	NO
75	FURIN	FURIN	FURIN	7914	0.028	0.19	NO
76	PROC	PROC	PROC	7953	0.027	0.19	NO
77	EIF3G	EIF3G	EIF3G	7972	0.027	0.19	NO
78	RPS28	RPS28	RPS28	8002	0.027	0.19	NO
79	MAN1C1	MAN1C1	MAN1C1	8166	0.024	0.18	NO
80	B4GALT4	B4GALT4	B4GALT4	8211	0.024	0.18	NO
81	PIGB	PIGB	PIGB	8258	0.023	0.18	NO
82	ARSK	ARSK	ARSK	8264	0.023	0.18	NO
83	HSCB	HSCB	HSCB	8316	0.022	0.18	NO
84	RPS12	RPS12	RPS12	8385	0.021	0.17	NO
85	PIGC	PIGC	PIGC	8595	0.019	0.16	NO
86	RPL13	RPL13	RPL13	8601	0.019	0.16	NO
87	EIF3K	EIF3K	EIF3K	8606	0.019	0.16	NO
88	TUBA3C	TUBA3C	TUBA3C	8633	0.018	0.16	NO
89	EEF1B2	EEF1B2	EEF1B2	8649	0.018	0.16	NO
90	DOHH	DOHH	DOHH	8759	0.017	0.16	NO
91	RPS9	RPS9	RPS9	8767	0.017	0.16	NO
92	ETF1	ETF1	ETF1	8832	0.016	0.16	NO
93	B4GALT6	B4GALT6	B4GALT6	8924	0.015	0.15	NO
94	RPL34	RPL34	RPL34	8977	0.015	0.15	NO
95	PIGS	PIGS	PIGS	8985	0.015	0.15	NO
96	FAU	FAU	FAU	9025	0.014	0.15	NO
97	ARSB	ARSB	ARSB	9029	0.014	0.15	NO
98	EIF3F	EIF3F	EIF3F	9070	0.014	0.14	NO
99	EEF1D	EEF1D	EEF1D	9131	0.013	0.14	NO
100	SLC25A4	SLC25A4	SLC25A4	9137	0.013	0.14	NO
101	GALNT2	GALNT2	GALNT2	9195	0.012	0.14	NO
102	FXC1	FXC1	FXC1	9204	0.012	0.14	NO
103	EEF1A1	EEF1A1	EEF1A1	9227	0.012	0.14	NO
104	RPL11	RPL11	RPL11	9236	0.012	0.14	NO
105	TBCC	TBCC	TBCC	9269	0.012	0.14	NO
106	FBXL3	FBXL3	FBXL3	9273	0.012	0.14	NO
107	FKBP9	FKBP9	FKBP9	9303	0.011	0.14	NO
108	RPL10A	RPL10A	RPL10A	9456	0.0099	0.13	NO
109	RPS20	RPS20	RPS20	9461	0.0098	0.13	NO
110	DPM1	DPM1	DPM1	9519	0.0093	0.13	NO
111	GALNTL2	GALNTL2	GALNTL2	9572	0.0088	0.12	NO
112	PIGQ	PIGQ	PIGQ	9591	0.0085	0.12	NO
113	RPS19	RPS19	RPS19	9640	0.008	0.12	NO
114	RPL17	RPL17	RPL17	9667	0.0078	0.12	NO
115	RPL10	RPL10	RPL10	9748	0.007	0.12	NO
116	RPLP1	RPLP1	RPLP1	9750	0.007	0.12	NO
117	C18orf55	C18orf55	C18orf55	9751	0.007	0.12	NO
118	B3GNT4	B3GNT4	B3GNT4	9797	0.0066	0.11	NO
119	RPLP2	RPLP2	RPLP2	9850	0.006	0.11	NO
120	RPS27A	RPS27A	RPS27A	9873	0.0058	0.11	NO
121	TOMM7	TOMM7	TOMM7	9899	0.0055	0.11	NO
122	GMPPA	GMPPA	GMPPA	9959	0.0049	0.1	NO
123	PIGA	PIGA	PIGA	10016	0.0044	0.1	NO
124	ALG5	ALG5	ALG5	10055	0.004	0.1	NO
125	SEC61A2	SEC61A2	SEC61A2	10062	0.004	0.1	NO
126	TIMM22	TIMM22	TIMM22	10117	0.0034	0.097	NO
127	FBXW5	FBXW5	FBXW5	10236	0.0022	0.091	NO
128	TIMM44	TIMM44	TIMM44	10249	0.0021	0.09	NO
129	UBA52	UBA52	UBA52	10270	0.002	0.089	NO
130	RPS3	RPS3	RPS3	10282	0.0019	0.088	NO
131	RPS14	RPS14	RPS14	10352	0.0014	0.085	NO
132	RPL5	RPL5	RPL5	10366	0.0012	0.084	NO
133	EIF3D	EIF3D	EIF3D	10387	0.0011	0.083	NO
134	EIF5	EIF5	EIF5	10423	0.00084	0.081	NO
135	SRP68	SRP68	SRP68	10431	0.00078	0.08	NO
136	RPS21	RPS21	RPS21	10465	0.00048	0.079	NO
137	RPS23	RPS23	RPS23	10485	0.00033	0.078	NO
138	GFER	GFER	GFER	10496	0.00028	0.077	NO
139	EDEM2	EDEM2	EDEM2	10498	0.00026	0.077	NO
140	RPS4X	RPS4X	RPS4X	10519	0.000026	0.076	NO
141	RPL35	RPL35	RPL35	10531	-0.00014	0.075	NO
142	RPS11	RPS11	RPS11	10613	-0.00085	0.071	NO
143	VKORC1	VKORC1	VKORC1	10620	-0.00091	0.07	NO
144	RPL22	RPL22	RPL22	10665	-0.0013	0.068	NO
145	SUMF2	SUMF2	SUMF2	10666	-0.0013	0.068	NO
146	RPL27A	RPL27A	RPL27A	10669	-0.0013	0.068	NO
147	EEF1G	EEF1G	EEF1G	10693	-0.0016	0.067	NO
148	F2	F2	F2	10700	-0.0016	0.067	NO
149	DPM3	DPM3	DPM3	10715	-0.0017	0.066	NO
150	ATP5A1	ATP5A1	ATP5A1	10722	-0.0018	0.066	NO
151	RPL18	RPL18	RPL18	10741	-0.002	0.065	NO
152	RPL18A	RPL18A	RPL18A	10773	-0.0023	0.063	NO
153	RPS3A	RPS3A	RPS3A	10832	-0.0029	0.06	NO
154	RPS29	RPS29	RPS29	10848	-0.003	0.059	NO
155	SRP14	SRP14	SRP14	10873	-0.0033	0.058	NO
156	RPL23A	RPL23A	RPL23A	10931	-0.0038	0.055	NO
157	RPL3	RPL3	RPL3	10991	-0.0042	0.052	NO
158	RPS16	RPS16	RPS16	10993	-0.0042	0.052	NO
159	RPL26	RPL26	RPL26	10997	-0.0043	0.052	NO
160	RPS5	RPS5	RPS5	11010	-0.0044	0.051	NO
161	RPL41	RPL41	RPL41	11046	-0.0046	0.05	NO
162	TBCB	TBCB	TBCB	11050	-0.0046	0.05	NO
163	PIGT	PIGT	PIGT	11070	-0.0048	0.049	NO
164	EIF2B2	EIF2B2	EIF2B2	11114	-0.0051	0.046	NO
165	RPS10	RPS10	RPS10	11131	-0.0052	0.046	NO
166	EIF4A2	EIF4A2	EIF4A2	11163	-0.0056	0.044	NO
167	RPS25	RPS25	RPS25	11170	-0.0056	0.044	NO
168	RFT1	RFT1	RFT1	11171	-0.0056	0.044	NO
169	RPS24	RPS24	RPS24	11247	-0.0062	0.04	NO
170	RPS17	RPS17	RPS17	11249	-0.0063	0.04	NO
171	PIGL	PIGL	PIGL	11335	-0.0068	0.036	NO
172	RPL13A	RPL13A	RPL13A	11370	-0.0072	0.034	NO
173	SEC11C	SEC11C	SEC11C	11408	-0.0075	0.033	NO
174	RPS8	RPS8	RPS8	11412	-0.0075	0.033	NO
175	EIF4H	EIF4H	EIF4H	11414	-0.0076	0.033	NO
176	MAN1B1	MAN1B1	MAN1B1	11427	-0.0076	0.033	NO
177	RPL15	RPL15	RPL15	11450	-0.0078	0.032	NO
178	RPL4	RPL4	RPL4	11484	-0.0081	0.03	NO
179	RPL19	RPL19	RPL19	11487	-0.0081	0.03	NO
180	TUBA1B	TUBA1B	TUBA1B	11497	-0.0082	0.03	NO
181	RPL35A	RPL35A	RPL35A	11505	-0.0082	0.03	NO
182	ALG12	ALG12	ALG12	11510	-0.0083	0.03	NO
183	DAD1	DAD1	DAD1	11511	-0.0083	0.03	NO
184	RPS4Y1	RPS4Y1	RPS4Y1	11518	-0.0084	0.03	NO
185	RPL38	RPL38	RPL38	11540	-0.0086	0.03	NO
186	RPL8	RPL8	RPL8	11599	-0.0091	0.027	NO
187	PMPCA	PMPCA	PMPCA	11620	-0.0093	0.026	NO
188	RPS15	RPS15	RPS15	11651	-0.0095	0.025	NO
189	FXN	FXN	FXN	11675	-0.0097	0.024	NO
190	RPL32	RPL32	RPL32	11678	-0.0097	0.024	NO
191	SRP19	SRP19	SRP19	11681	-0.0097	0.024	NO
192	EIF2B1	EIF2B1	EIF2B1	11687	-0.0098	0.024	NO
193	IDH3G	IDH3G	IDH3G	11756	-0.01	0.021	NO
194	SAMM50	SAMM50	SAMM50	11802	-0.011	0.019	NO
195	RPL36	RPL36	RPL36	11842	-0.011	0.017	NO
196	RPL28	RPL28	RPL28	11863	-0.011	0.016	NO
197	RPL24	RPL24	RPL24	11879	-0.012	0.016	NO
198	EIF2B5	EIF2B5	EIF2B5	11892	-0.012	0.016	NO
199	PRKCSH	PRKCSH	PRKCSH	11895	-0.012	0.016	NO
200	RPSAP9	RPSAP9	RPSAP9	11929	-0.012	0.015	NO
201	RPS13	RPS13	RPS13	11956	-0.012	0.014	NO
202	RPS6	RPS6	RPS6	11974	-0.012	0.013	NO
203	RPS15A	RPS15A	RPS15A	11991	-0.012	0.013	NO
204	RPL31	RPL31	RPL31	11993	-0.012	0.013	NO
205	ALG1	ALG1	ALG1	11995	-0.012	0.014	NO
206	SPCS2	SPCS2	SPCS2	12039	-0.013	0.012	NO
207	B4GALT2	B4GALT2	B4GALT2	12101	-0.013	0.0087	NO
208	PIGG	PIGG	PIGG	12110	-0.013	0.0088	NO
209	ALG13	ALG13	ALG13	12155	-0.014	0.0069	NO
210	RPL6	RPL6	RPL6	12216	-0.014	0.004	NO
211	RPL14	RPL14	RPL14	12222	-0.014	0.0043	NO
212	UGGT1	UGGT1	UGGT1	12234	-0.014	0.0042	NO
213	LOC653566	LOC653566	LOC653566	12299	-0.015	0.0012	NO
214	RPSA	RPSA	RPSA	12329	-0.015	0.00018	NO
215	TOMM22	TOMM22	TOMM22	12330	-0.015	0.00076	NO
216	TIMM9	TIMM9	TIMM9	12335	-0.015	0.0011	NO
217	RPL37	RPL37	RPL37	12365	-0.016	0.000082	NO
218	SEC13	SEC13	SEC13	12403	-0.016	-0.0014	NO
219	SEC11A	SEC11A	SEC11A	12420	-0.016	-0.0017	NO
220	EIF5A	EIF5A	EIF5A	12422	-0.016	-0.0011	NO
221	GALNT10	GALNT10	GALNT10	12428	-0.016	-0.00079	NO
222	TIMM17A	TIMM17A	TIMM17A	12447	-0.016	-0.0012	NO
223	TIMM50	TIMM50	TIMM50	12463	-0.016	-0.0014	NO
224	EIF4B	EIF4B	EIF4B	12474	-0.016	-0.0013	NO
225	RPL37A	RPL37A	RPL37A	12485	-0.016	-0.0012	NO
226	BCS1L	BCS1L	BCS1L	12529	-0.017	-0.003	NO
227	PFDN1	PFDN1	PFDN1	12544	-0.017	-0.0032	NO
228	DOLK	DOLK	DOLK	12587	-0.017	-0.0048	NO
229	ARSA	ARSA	ARSA	12596	-0.017	-0.0046	NO
230	RPL12	RPL12	RPL12	12610	-0.018	-0.0047	NO
231	RPL27	RPL27	RPL27	12627	-0.018	-0.0049	NO
232	GMPPB	GMPPB	GMPPB	12629	-0.018	-0.0043	NO
233	TBCD	TBCD	TBCD	12646	-0.018	-0.0045	NO
234	PIGF	PIGF	PIGF	12655	-0.018	-0.0043	NO
235	RPL39	RPL39	RPL39	12666	-0.018	-0.0041	NO
236	SPCS3	SPCS3	SPCS3	12694	-0.018	-0.005	NO
237	MTX1	MTX1	MTX1	12698	-0.018	-0.0044	NO
238	SSR4	SSR4	SSR4	12703	-0.018	-0.004	NO
239	GPAA1	GPAA1	GPAA1	12713	-0.018	-0.0038	NO
240	RPS2	RPS2	RPS2	12721	-0.018	-0.0034	NO
241	PREB	PREB	PREB	12729	-0.018	-0.0031	NO
242	RPLP0	RPLP0	RPLP0	12732	-0.018	-0.0025	NO
243	ALG2	ALG2	ALG2	12741	-0.019	-0.0022	NO
244	COQ2	COQ2	COQ2	12775	-0.019	-0.0034	NO
245	RPL23	RPL23	RPL23	12783	-0.019	-0.003	NO
246	CHCHD4	CHCHD4	CHCHD4	12795	-0.019	-0.0029	NO
247	ARFGEF2	ARFGEF2	ARFGEF2	12799	-0.019	-0.0024	NO
248	EIF2S2	EIF2S2	EIF2S2	12829	-0.019	-0.0033	NO
249	PROZ	PROZ	PROZ	12850	-0.02	-0.0036	NO
250	MOGS	MOGS	MOGS	12859	-0.02	-0.0033	NO
251	MCFD2	MCFD2	MCFD2	12888	-0.02	-0.0041	NO
252	PIGV	PIGV	PIGV	12906	-0.02	-0.0043	NO
253	RPN1	RPN1	RPN1	12916	-0.02	-0.0041	NO
254	PFDN2	PFDN2	PFDN2	12918	-0.02	-0.0034	NO
255	DPM2	DPM2	DPM2	12926	-0.02	-0.003	NO
256	FBXO6	FBXO6	FBXO6	12977	-0.021	-0.005	NO
257	RPL30	RPL30	RPL30	13017	-0.021	-0.0064	NO
258	PIGU	PIGU	PIGU	13023	-0.021	-0.0058	NO
259	SEC24B	SEC24B	SEC24B	13029	-0.021	-0.0053	NO
260	TIMM17B	TIMM17B	TIMM17B	13041	-0.021	-0.0051	NO
261	ACO2	ACO2	ACO2	13049	-0.021	-0.0047	NO
262	RPL29	RPL29	RPL29	13063	-0.021	-0.0046	NO
263	TUBA1C	TUBA1C	TUBA1C	13064	-0.021	-0.0038	NO
264	FBXL5	FBXL5	FBXL5	13096	-0.022	-0.0047	NO
265	FBXW2	FBXW2	FBXW2	13105	-0.022	-0.0043	NO
266	EIF2B3	EIF2B3	EIF2B3	13143	-0.022	-0.0055	NO
267	EIF3E	EIF3E	EIF3E	13156	-0.022	-0.0054	NO
268	XRN2	XRN2	XRN2	13168	-0.022	-0.0051	NO
269	RPL7	RPL7	RPL7	13170	-0.022	-0.0043	NO
270	PIGN	PIGN	PIGN	13228	-0.023	-0.0066	NO
271	EIF2S1	EIF2S1	EIF2S1	13279	-0.023	-0.0086	NO
272	RPS18	RPS18	RPS18	13301	-0.024	-0.0088	NO
273	SSR1	SSR1	SSR1	13311	-0.024	-0.0084	NO
274	GGCX	GGCX	GGCX	13312	-0.024	-0.0075	NO
275	LMAN1	LMAN1	LMAN1	13333	-0.024	-0.0077	NO
276	EDEM1	EDEM1	EDEM1	13359	-0.024	-0.0082	NO
277	EIF3H	EIF3H	EIF3H	13391	-0.024	-0.009	NO
278	GRPEL1	GRPEL1	GRPEL1	13402	-0.025	-0.0086	NO
279	TRAM1	TRAM1	TRAM1	13403	-0.025	-0.0077	NO
280	RPN2	RPN2	RPN2	13404	-0.025	-0.0067	NO
281	EIF2S3	EIF2S3	EIF2S3	13420	-0.025	-0.0066	NO
282	RPS7	RPS7	RPS7	13428	-0.025	-0.0061	NO
283	GALNT1	GALNT1	GALNT1	13436	-0.025	-0.0055	NO
284	MUCL1	MUCL1	MUCL1	13486	-0.025	-0.0073	NO
285	ST3GAL3	ST3GAL3	ST3GAL3	13513	-0.026	-0.0078	NO
286	PIGO	PIGO	PIGO	13543	-0.026	-0.0084	NO
287	SEC61A1	SEC61A1	SEC61A1	13575	-0.026	-0.0091	NO
288	GANAB	GANAB	GANAB	13598	-0.026	-0.0093	NO
289	KIF13A	KIF13A	KIF13A	13601	-0.026	-0.0084	NO
290	SSR2	SSR2	SSR2	13606	-0.027	-0.0076	NO
291	FBXO4	FBXO4	FBXO4	13641	-0.027	-0.0085	NO
292	DPAGT1	DPAGT1	DPAGT1	13674	-0.027	-0.0092	NO
293	EIF2B4	EIF2B4	EIF2B4	13676	-0.027	-0.0083	NO
294	SRPR	SRPR	SRPR	13687	-0.028	-0.0078	NO
295	CS	CS	CS	13703	-0.028	-0.0076	NO
296	NOP56	NOP56	NOP56	13718	-0.028	-0.0073	NO
297	SPCS1	SPCS1	SPCS1	13733	-0.028	-0.007	NO
298	EIF1AX	EIF1AX	EIF1AX	13757	-0.028	-0.0072	NO
299	EIF3A	EIF3A	EIF3A	13764	-0.028	-0.0065	NO
300	EIF4A1	EIF4A1	EIF4A1	13768	-0.028	-0.0056	NO
301	CCT4	CCT4	CCT4	13777	-0.028	-0.0049	NO
302	TIMM13	TIMM13	TIMM13	13782	-0.028	-0.004	NO
303	SEC24C	SEC24C	SEC24C	13840	-0.029	-0.0062	NO
304	SRP9	SRP9	SRP9	13854	-0.029	-0.0058	NO
305	SEC24D	SEC24D	SEC24D	13875	-0.029	-0.0058	NO
306	RPS26	RPS26	RPS26	13891	-0.029	-0.0055	NO
307	TOMM5	TOMM5	TOMM5	13928	-0.03	-0.0064	NO
308	TBCA	TBCA	TBCA	13962	-0.03	-0.0071	NO
309	EIF5B	EIF5B	EIF5B	13965	-0.03	-0.006	NO
310	RPL7A	RPL7A	RPL7A	13970	-0.03	-0.0051	NO
311	EIF3B	EIF3B	EIF3B	13983	-0.03	-0.0046	NO
312	SLC25A6	SLC25A6	SLC25A6	14006	-0.031	-0.0047	NO
313	VDAC1	VDAC1	VDAC1	14007	-0.031	-0.0035	NO
314	TOMM40	TOMM40	TOMM40	14038	-0.031	-0.004	NO
315	PFDN6	PFDN6	PFDN6	14054	-0.031	-0.0036	NO
316	UGGT2	UGGT2	UGGT2	14058	-0.031	-0.0026	NO
317	ALG9	ALG9	ALG9	14090	-0.031	-0.0032	NO
318	CCT7	CCT7	CCT7	14099	-0.032	-0.0024	NO
319	PFDN4	PFDN4	PFDN4	14113	-0.032	-0.0019	NO
320	SEC31A	SEC31A	SEC31A	14122	-0.032	-0.0011	NO
321	DHPS	DHPS	DHPS	14153	-0.032	-0.0016	NO
322	EIF3I	EIF3I	EIF3I	14181	-0.032	-0.0019	NO
323	AP3M1	AP3M1	AP3M1	14183	-0.032	-0.00069	NO
324	MAN2A1	MAN2A1	MAN2A1	14222	-0.033	-0.0016	NO
325	EEF2	EEF2	EEF2	14263	-0.033	-0.0025	NO
326	SEC61B	SEC61B	SEC61B	14286	-0.033	-0.0025	NO
327	ATP5B	ATP5B	ATP5B	14298	-0.034	-0.0018	NO
328	SUMF1	SUMF1	SUMF1	14350	-0.034	-0.0034	NO
329	C1GALT1C1	C1GALT1C1	C1GALT1C1	14357	-0.034	-0.0024	NO
330	ALG3	ALG3	ALG3	14378	-0.034	-0.0022	NO
331	MGAT5	MGAT5	MGAT5	14400	-0.035	-0.002	NO
332	EIF4G1	EIF4G1	EIF4G1	14404	-0.035	-0.00089	NO
333	TOMM20	TOMM20	TOMM20	14415	-0.035	-0.00012	NO
334	DDOST	DDOST	DDOST	14532	-0.036	-0.0052	NO
335	DOLPP1	DOLPP1	DOLPP1	14574	-0.037	-0.0061	NO
336	CYC1	CYC1	CYC1	14581	-0.037	-0.0051	NO
337	MLEC	MLEC	MLEC	14622	-0.037	-0.0059	NO
338	ATP5G1	ATP5G1	ATP5G1	14736	-0.038	-0.011	NO
339	PMM1	PMM1	PMM1	14742	-0.039	-0.0095	NO
340	B3GNTL1	B3GNTL1	B3GNTL1	14743	-0.039	-0.0081	NO
341	MPI	MPI	MPI	14758	-0.039	-0.0074	NO
342	MGAT4B	MGAT4B	MGAT4B	14829	-0.04	-0.0098	NO
343	TIMM10	TIMM10	TIMM10	14847	-0.04	-0.0092	NO
344	PMM2	PMM2	PMM2	14874	-0.04	-0.0091	NO
345	PDIA3	PDIA3	PDIA3	14892	-0.04	-0.0085	NO
346	CALR	CALR	CALR	14930	-0.041	-0.009	NO
347	ALG11	ALG11	ALG11	14934	-0.041	-0.0076	NO
348	HSPA9	HSPA9	HSPA9	14982	-0.041	-0.0087	NO
349	MGAT2	MGAT2	MGAT2	14993	-0.042	-0.0076	NO
350	EIF4E	EIF4E	EIF4E	15074	-0.043	-0.01	NO
351	STT3A	STT3A	STT3A	15111	-0.043	-0.011	NO
352	DNAJC19	DNAJC19	DNAJC19	15121	-0.043	-0.0097	NO
353	MUC6	MUC6	MUC6	15132	-0.043	-0.0086	NO
354	CANX	CANX	CANX	15133	-0.043	-0.007	NO
355	PMPCB	PMPCB	PMPCB	15137	-0.043	-0.0055	NO
356	SSR3	SSR3	SSR3	15165	-0.044	-0.0053	NO
357	SRP72	SRP72	SRP72	15171	-0.044	-0.0039	NO
358	CCT3	CCT3	CCT3	15182	-0.044	-0.0028	NO
359	MUC2	MUC2	MUC2	15206	-0.044	-0.0024	NO
360	MAN1A2	MAN1A2	MAN1A2	15212	-0.044	-0.00092	NO
361	TIMM8A	TIMM8A	TIMM8A	15307	-0.046	-0.0044	NO
362	VBP1	VBP1	VBP1	15337	-0.046	-0.0043	NO
363	SEC61G	SEC61G	SEC61G	15351	-0.047	-0.0032	NO
364	TCP1	TCP1	TCP1	15390	-0.048	-0.0035	NO
365	CCT6A	CCT6A	CCT6A	15403	-0.048	-0.0024	NO
366	TBCE	TBCE	TBCE	15457	-0.049	-0.0034	NO
367	TIMM8B	TIMM8B	TIMM8B	15492	-0.05	-0.0034	NO
368	PIGK	PIGK	PIGK	15502	-0.05	-0.002	NO
369	ST8SIA6	ST8SIA6	ST8SIA6	15511	-0.05	-0.00055	NO
370	B4GALT3	B4GALT3	B4GALT3	15532	-0.051	0.00027	NO
371	SRPRB	SRPRB	SRPRB	15533	-0.051	0.0022	NO
372	EIF4EBP1	EIF4EBP1	EIF4EBP1	15543	-0.051	0.0036	NO
373	SRP54	SRP54	SRP54	15575	-0.051	0.0039	NO
374	CCT5	CCT5	CCT5	15582	-0.051	0.0055	NO
375	GALNT11	GALNT11	GALNT11	15599	-0.052	0.0066	NO
376	RPL26L1	RPL26L1	RPL26L1	15623	-0.052	0.0073	NO
377	RPL9	RPL9	RPL9	15651	-0.052	0.0078	NO
378	CCT8	CCT8	CCT8	15660	-0.053	0.0094	NO
379	PIGX	PIGX	PIGX	15689	-0.053	0.0098	NO
380	PIGH	PIGH	PIGH	15744	-0.054	0.0089	NO
381	PABPC1	PABPC1	PABPC1	15745	-0.054	0.011	NO
382	EIF3J	EIF3J	EIF3J	15766	-0.054	0.012	NO
383	MANEA	MANEA	MANEA	15803	-0.055	0.012	NO
384	PIGM	PIGM	PIGM	15847	-0.056	0.012	NO
385	PIGP	PIGP	PIGP	15887	-0.057	0.012	NO
386	CCT2	CCT2	CCT2	15905	-0.057	0.013	NO
387	ALG8	ALG8	ALG8	15983	-0.059	0.011	NO
388	ARSG	ARSG	ARSG	16018	-0.06	0.011	NO
389	LONP2	LONP2	LONP2	16075	-0.062	0.011	NO
390	ALG14	ALG14	ALG14	16104	-0.062	0.011	NO
391	TOMM70A	TOMM70A	TOMM70A	16149	-0.063	0.011	NO
392	PGM3	PGM3	PGM3	16224	-0.065	0.0097	NO
393	GRPEL2	GRPEL2	GRPEL2	16268	-0.066	0.0098	NO
394	COX17	COX17	COX17	16278	-0.066	0.012	NO
395	ALG10B	ALG10B	ALG10B	16299	-0.067	0.013	NO
396	MTX2	MTX2	MTX2	16308	-0.068	0.015	NO
397	ALG10	ALG10	ALG10	16367	-0.069	0.015	NO
398	MGAT4A	MGAT4A	MGAT4A	16383	-0.07	0.017	NO
399	SLC25A13	SLC25A13	SLC25A13	16465	-0.072	0.015	NO
400	ALG6	ALG6	ALG6	16519	-0.074	0.015	NO
401	HSPD1	HSPD1	HSPD1	16528	-0.074	0.017	NO
402	TUSC3	TUSC3	TUSC3	16671	-0.08	0.012	NO
403	GALNTL6	GALNTL6	GALNTL6	16719	-0.082	0.013	NO
404	SAR1B	SAR1B	SAR1B	16732	-0.082	0.015	NO
405	GCNT1	GCNT1	GCNT1	16786	-0.084	0.016	NO
406	EIF3C	EIF3C	EIF3C	17052	-0.097	0.0044	NO
407	GNPNAT1	GNPNAT1	GNPNAT1	17066	-0.098	0.0074	NO
408	GALNT13	GALNT13	GALNT13	17084	-0.099	0.01	NO
409	PIGW	PIGW	PIGW	17123	-0.1	0.012	NO
410	GALNT7	GALNT7	GALNT7	17125	-0.1	0.016	NO
411	GALNT3	GALNT3	GALNT3	17130	-0.1	0.02	NO
412	ST8SIA2	ST8SIA2	ST8SIA2	17230	-0.11	0.018	NO
413	RPL36A	RPL36A	RPL36A	17239	-0.11	0.022	NO
414	TUBB3	TUBB3	TUBB3	17259	-0.11	0.025	NO
415	EDEM3	EDEM3	EDEM3	17448	-0.12	0.019	NO
416	B3GNT6	B3GNT6	B3GNT6	17531	-0.13	0.019	NO
417	TUBB2A	TUBB2A	TUBB2A	17662	-0.14	0.018	NO
418	ARSH	ARSH	ARSH	17836	-0.17	0.014	NO
419	RPL3L	RPL3L	RPL3L	18160	-0.24	0.0054	NO

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

Figure S72. 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 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	GJB4	GJB4	GJB4	5	0.93	0.11	YES
2	GJB5	GJB5	GJB5	10	0.87	0.22	YES
3	GJB3	GJB3	GJB3	25	0.81	0.32	YES
4	GJC2	GJC2	GJC2	381	0.48	0.36	YES
5	GJA1	GJA1	GJA1	1672	0.28	0.32	NO
6	GJA9	GJA9	GJA9	2597	0.21	0.3	NO
7	DNM1	DNM1	DNM1	3307	0.17	0.28	NO
8	GJB6	GJB6	GJB6	3515	0.16	0.29	NO
9	CLTCL1	CLTCL1	CLTCL1	3829	0.14	0.29	NO
10	GJC1	GJC1	GJC1	4216	0.12	0.28	NO
11	VPS37D	VPS37D	VPS37D	4585	0.11	0.27	NO
12	TFRC	TFRC	TFRC	4608	0.11	0.28	NO
13	DNASE2	DNASE2	DNASE2	5104	0.091	0.27	NO
14	GJB2	GJB2	GJB2	5191	0.088	0.28	NO
15	SH3GL2	SH3GL2	SH3GL2	5368	0.082	0.28	NO
16	GJB7	GJB7	GJB7	5544	0.077	0.28	NO
17	SEC23A	SEC23A	SEC23A	5601	0.074	0.28	NO
18	AP1S2	AP1S2	AP1S2	5721	0.071	0.28	NO
19	STX4	STX4	STX4	6036	0.063	0.27	NO
20	ARRB1	ARRB1	ARRB1	6109	0.061	0.28	NO
21	M6PR	M6PR	M6PR	6149	0.06	0.28	NO
22	CHMP4A	CHMP4A	CHMP4A	6263	0.057	0.28	NO
23	HIP1R	HIP1R	HIP1R	6390	0.054	0.28	NO
24	VAMP8	VAMP8	VAMP8	6632	0.049	0.28	NO
25	CHMP7	CHMP7	CHMP7	6798	0.046	0.27	NO
26	VPS36	VPS36	VPS36	6922	0.043	0.27	NO
27	CHMP6	CHMP6	CHMP6	6939	0.043	0.28	NO
28	GJA4	GJA4	GJA4	6970	0.042	0.28	NO
29	FTH1	FTH1	FTH1	7136	0.039	0.27	NO
30	AP4B1	AP4B1	AP4B1	7256	0.037	0.27	NO
31	VAMP2	VAMP2	VAMP2	7459	0.034	0.26	NO
32	SRC	SRC	SRC	7608	0.032	0.26	NO
33	CLTB	CLTB	CLTB	7640	0.032	0.26	NO
34	AP4E1	AP4E1	AP4E1	7648	0.031	0.27	NO
35	DTNBP1	DTNBP1	DTNBP1	7825	0.029	0.26	NO
36	GJA5	GJA5	GJA5	8215	0.024	0.24	NO
37	ARFGAP1	ARFGAP1	ARFGAP1	8216	0.024	0.24	NO
38	CTSZ	CTSZ	CTSZ	8230	0.024	0.25	NO
39	AP1B1	AP1B1	AP1B1	8357	0.022	0.24	NO
40	BLOC1S1	BLOC1S1	BLOC1S1	8400	0.021	0.24	NO
41	CHMP4B	CHMP4B	CHMP4B	8438	0.021	0.24	NO
42	VPS4B	VPS4B	VPS4B	9033	0.014	0.21	NO
43	VPS37B	VPS37B	VPS37B	9144	0.013	0.21	NO
44	GJA3	GJA3	GJA3	9237	0.012	0.2	NO
45	TGOLN2	TGOLN2	TGOLN2	9284	0.012	0.2	NO
46	VPS4A	VPS4A	VPS4A	9414	0.01	0.2	NO
47	FTL	FTL	FTL	9520	0.0093	0.19	NO
48	TPD52L1	TPD52L1	TPD52L1	9593	0.0085	0.19	NO
49	AP2M1	AP2M1	AP2M1	9612	0.0082	0.19	NO
50	AP1M1	AP1M1	AP1M1	9793	0.0066	0.18	NO
51	RPS27A	RPS27A	RPS27A	9873	0.0058	0.18	NO
52	SNF8	SNF8	SNF8	10044	0.0041	0.17	NO
53	SNX2	SNX2	SNX2	10174	0.0028	0.16	NO
54	UBA52	UBA52	UBA52	10270	0.002	0.16	NO
55	CHMP2A	CHMP2A	CHMP2A	10367	0.0012	0.15	NO
56	RAB5C	RAB5C	RAB5C	10462	0.0005	0.15	NO
57	DNM2	DNM2	DNM2	10508	0.00016	0.14	NO
58	VPS28	VPS28	VPS28	10560	-0.00038	0.14	NO
59	SORT1	SORT1	SORT1	10677	-0.0014	0.14	NO
60	VPS37A	VPS37A	VPS37A	10707	-0.0017	0.13	NO
61	HGS	HGS	HGS	10726	-0.0018	0.13	NO
62	GAK	GAK	GAK	10764	-0.0022	0.13	NO
63	CHMP2B	CHMP2B	CHMP2B	10839	-0.0029	0.13	NO
64	CLTA	CLTA	CLTA	10849	-0.003	0.13	NO
65	VPS25	VPS25	VPS25	10872	-0.0033	0.13	NO
66	SNX5	SNX5	SNX5	11032	-0.0045	0.12	NO
67	AP1G1	AP1G1	AP1G1	11091	-0.005	0.12	NO
68	CNO	CNO	CNO	11292	-0.0065	0.1	NO
69	NAPA	NAPA	NAPA	11564	-0.0088	0.091	NO
70	SH3D19	SH3D19	SH3D19	11566	-0.0089	0.092	NO
71	SNX9	SNX9	SNX9	11586	-0.009	0.092	NO
72	CHMP5	CHMP5	CHMP5	11696	-0.0098	0.087	NO
73	AP3B1	AP3B1	AP3B1	12199	-0.014	0.061	NO
74	SNAPIN	SNAPIN	SNAPIN	12267	-0.015	0.06	NO
75	GNS	GNS	GNS	12392	-0.016	0.055	NO
76	SEC13	SEC13	SEC13	12403	-0.016	0.056	NO
77	VTA1	VTA1	VTA1	12446	-0.016	0.056	NO
78	PUM1	PUM1	PUM1	12489	-0.016	0.055	NO
79	BLOC1S3	BLOC1S3	BLOC1S3	12499	-0.017	0.057	NO
80	PLDN	PLDN	PLDN	12550	-0.017	0.056	NO
81	DAB2	DAB2	DAB2	12569	-0.017	0.057	NO
82	GBF1	GBF1	GBF1	12599	-0.017	0.058	NO
83	STAM2	STAM2	STAM2	12611	-0.018	0.059	NO
84	PREB	PREB	PREB	12729	-0.018	0.055	NO
85	CPD	CPD	CPD	12764	-0.019	0.056	NO
86	SEC24B	SEC24B	SEC24B	13029	-0.021	0.044	NO
87	COPE	COPE	COPE	13073	-0.022	0.044	NO
88	COPZ1	COPZ1	COPZ1	13079	-0.022	0.046	NO
89	IGF2R	IGF2R	IGF2R	13120	-0.022	0.047	NO
90	AP3S1	AP3S1	AP3S1	13189	-0.022	0.046	NO
91	NECAP1	NECAP1	NECAP1	13356	-0.024	0.04	NO
92	SNAP23	SNAP23	SNAP23	13500	-0.026	0.035	NO
93	PIK3C2A	PIK3C2A	PIK3C2A	13627	-0.027	0.031	NO
94	SEC24C	SEC24C	SEC24C	13840	-0.029	0.023	NO
95	SEC24D	SEC24D	SEC24D	13875	-0.029	0.025	NO
96	PICALM	PICALM	PICALM	14010	-0.031	0.021	NO
97	TSG101	TSG101	TSG101	14053	-0.031	0.023	NO
98	SEC31A	SEC31A	SEC31A	14122	-0.032	0.023	NO
99	ARF1	ARF1	ARF1	14179	-0.032	0.024	NO
100	ARCN1	ARCN1	ARCN1	14708	-0.038	-0.00082	NO
101	STAM	STAM	STAM	14790	-0.039	-0.00048	NO
102	TBC1D8B	TBC1D8B	TBC1D8B	14793	-0.039	0.0042	NO
103	GJD4	GJD4	GJD4	14990	-0.042	-0.0015	NO
104	COPB1	COPB1	COPB1	15048	-0.042	0.00053	NO
105	TXNDC5	TXNDC5	TXNDC5	15119	-0.043	0.002	NO
106	AP1S1	AP1S1	AP1S1	15145	-0.044	0.0059	NO
107	HSPA8	HSPA8	HSPA8	15207	-0.044	0.008	NO
108	COPA	COPA	COPA	15223	-0.045	0.013	NO
109	CLTC	CLTC	CLTC	15447	-0.049	0.0064	NO
110	COPG	COPG	COPG	15693	-0.053	-0.00062	NO
111	COPB2	COPB2	COPB2	15844	-0.056	-0.002	NO
112	VAMP7	VAMP7	VAMP7	16021	-0.06	-0.0043	NO
113	TJP1	TJP1	TJP1	16055	-0.061	0.0013	NO
114	AP1M2	AP1M2	AP1M2	16195	-0.064	0.0015	NO
115	VPS37C	VPS37C	VPS37C	16441	-0.071	-0.0032	NO
116	OCRL	OCRL	OCRL	16570	-0.076	-0.00099	NO
117	SAR1B	SAR1B	SAR1B	16732	-0.082	0.00021	NO
118	TPD52	TPD52	TPD52	16910	-0.09	0.0015	NO
119	MYO6	MYO6	MYO6	16995	-0.094	0.0085	NO
120	YIPF6	YIPF6	YIPF6	17269	-0.11	0.007	NO
121	CHMP4C	CHMP4C	CHMP4C	17297	-0.11	0.019	NO
122	DNAJC6	DNAJC6	DNAJC6	17502	-0.13	0.024	NO
123	GJB1	GJB1	GJB1	17704	-0.15	0.03	NO

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

Figure S74. 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 O GLYCAN BIOSYNTHESIS

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	CFTR	CFTR	CFTR	39	0.77	0.16	YES
2	ATP6V0A4	ATP6V0A4	ATP6V0A4	293	0.52	0.26	YES
3	ATP6V0D2	ATP6V0D2	ATP6V0D2	692	0.4	0.32	YES
4	ATP6V1G3	ATP6V1G3	ATP6V1G3	856	0.38	0.39	YES
5	ATP6V1B1	ATP6V1B1	ATP6V1B1	1542	0.29	0.42	YES
6	PRKCB	PRKCB	PRKCB	1561	0.29	0.48	YES
7	PLCG2	PLCG2	PLCG2	2173	0.24	0.49	YES
8	TCIRG1	TCIRG1	TCIRG1	3061	0.18	0.48	YES
9	ADCY3	ADCY3	ADCY3	3484	0.16	0.49	YES
10	KCNQ1	KCNQ1	KCNQ1	4048	0.13	0.49	YES
11	ATP6V1C2	ATP6V1C2	ATP6V1C2	4407	0.12	0.5	YES
12	PRKCA	PRKCA	PRKCA	5217	0.087	0.47	NO
13	ADCY9	ADCY9	ADCY9	5813	0.068	0.45	NO
14	ACTB	ACTB	ACTB	6909	0.043	0.4	NO
15	PRKX	PRKX	PRKX	7390	0.035	0.38	NO
16	PRKCG	PRKCG	PRKCG	7416	0.035	0.39	NO
17	ATP6V0D1	ATP6V0D1	ATP6V0D1	7803	0.029	0.37	NO
18	ERO1L	ERO1L	ERO1L	8317	0.022	0.35	NO
19	PLCG1	PLCG1	PLCG1	9371	0.011	0.3	NO
20	TJP2	TJP2	TJP2	9487	0.0096	0.29	NO
21	ATP6V0E1	ATP6V0E1	ATP6V0E1	9814	0.0063	0.27	NO
22	SEC61A2	SEC61A2	SEC61A2	10062	0.004	0.26	NO
23	ATP6V1G2	ATP6V1G2	ATP6V1G2	10216	0.0024	0.25	NO
24	ATP6V0A2	ATP6V0A2	ATP6V0A2	10245	0.0022	0.25	NO
25	ATP6V1B2	ATP6V1B2	ATP6V1B2	10254	0.0021	0.25	NO
26	PRKACA	PRKACA	PRKACA	10454	0.00057	0.24	NO
27	KDELR3	KDELR3	KDELR3	10631	-0.00099	0.23	NO
28	ATP6V1E1	ATP6V1E1	ATP6V1E1	11183	-0.0058	0.2	NO
29	ATP6V0A1	ATP6V0A1	ATP6V0A1	11635	-0.0094	0.18	NO
30	KDELR1	KDELR1	KDELR1	11875	-0.011	0.17	NO
31	ATP6V0C	ATP6V0C	ATP6V0C	11972	-0.012	0.17	NO
32	ACTG1	ACTG1	ACTG1	12237	-0.014	0.16	NO
33	ATP6V1H	ATP6V1H	ATP6V1H	12383	-0.016	0.15	NO
34	ATP6V1E2	ATP6V1E2	ATP6V1E2	12592	-0.017	0.14	NO
35	ATP6V1F	ATP6V1F	ATP6V1F	12933	-0.02	0.13	NO
36	ATP6V0B	ATP6V0B	ATP6V0B	13174	-0.022	0.12	NO
37	ATP6V1D	ATP6V1D	ATP6V1D	13366	-0.024	0.12	NO
38	SEC61A1	SEC61A1	SEC61A1	13575	-0.026	0.11	NO
39	SLC12A2	SLC12A2	SLC12A2	13623	-0.027	0.11	NO
40	ARF1	ARF1	ARF1	14179	-0.032	0.088	NO
41	GNAS	GNAS	GNAS	14260	-0.033	0.091	NO
42	SEC61B	SEC61B	SEC61B	14286	-0.033	0.097	NO
43	ATP6AP1	ATP6AP1	ATP6AP1	14343	-0.034	0.1	NO
44	ATP6V1C1	ATP6V1C1	ATP6V1C1	14746	-0.039	0.087	NO
45	MUC2	MUC2	MUC2	15206	-0.044	0.071	NO
46	PDIA4	PDIA4	PDIA4	15322	-0.046	0.075	NO
47	SEC61G	SEC61G	SEC61G	15351	-0.047	0.083	NO
48	KDELR2	KDELR2	KDELR2	15361	-0.047	0.093	NO
49	PRKACB	PRKACB	PRKACB	15832	-0.056	0.079	NO
50	ATP6V1A	ATP6V1A	ATP6V1A	15991	-0.06	0.083	NO
51	ATP6V1G1	ATP6V1G1	ATP6V1G1	16050	-0.061	0.092	NO
52	TJP1	TJP1	TJP1	16055	-0.061	0.1	NO
53	ATP6V0E2	ATP6V0E2	ATP6V0E2	16504	-0.073	0.096	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: KEGG O GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG GLYCEROLIPID METABOLISM

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	SAA1	SAA1	SAA1	285	0.52	0.1	YES
2	S100B	S100B	S100B	615	0.42	0.18	YES
3	IKBKE	IKBKE	IKBKE	960	0.36	0.24	YES
4	AGER	AGER	AGER	1310	0.31	0.29	YES
5	UBA7	UBA7	UBA7	2009	0.25	0.31	YES
6	CASP10	CASP10	CASP10	2344	0.22	0.34	YES
7	TNFAIP3	TNFAIP3	TNFAIP3	2444	0.22	0.38	YES
8	NLRC5	NLRC5	NLRC5	2511	0.21	0.43	YES
9	IRF1	IRF1	IRF1	2747	0.2	0.46	YES
10	UBE2L6	UBE2L6	UBE2L6	4057	0.13	0.42	YES
11	IRF3	IRF3	IRF3	4945	0.096	0.39	YES
12	NFKBIA	NFKBIA	NFKBIA	5062	0.092	0.4	YES
13	MAP3K1	MAP3K1	MAP3K1	5110	0.091	0.42	YES
14	S100A12	S100A12	S100A12	5515	0.078	0.42	YES
15	HERC5	HERC5	HERC5	5626	0.074	0.43	YES
16	IKBKB	IKBKB	IKBKB	5888	0.067	0.43	YES
17	DHX58	DHX58	DHX58	5893	0.066	0.44	YES
18	TRAF6	TRAF6	TRAF6	5933	0.065	0.45	YES
19	NFKB2	NFKB2	NFKB2	6151	0.06	0.46	YES
20	TRAF3	TRAF3	TRAF3	6471	0.052	0.45	YES
21	CYLD	CYLD	CYLD	6476	0.052	0.46	YES
22	IRF2	IRF2	IRF2	6682	0.048	0.46	YES
23	ATG5	ATG5	ATG5	6721	0.047	0.47	YES
24	DDX58	DDX58	DDX58	6750	0.046	0.48	YES
25	NFKBIB	NFKBIB	NFKBIB	6898	0.044	0.48	YES
26	ISG15	ISG15	ISG15	6929	0.043	0.49	YES
27	IRF7	IRF7	IRF7	7219	0.038	0.48	YES
28	RIPK1	RIPK1	RIPK1	7223	0.038	0.49	YES
29	IKBKG	IKBKG	IKBKG	7285	0.037	0.49	YES
30	TRAF2	TRAF2	TRAF2	7510	0.033	0.49	NO
31	FADD	FADD	FADD	8190	0.024	0.46	NO
32	APP	APP	APP	8575	0.019	0.44	NO
33	TANK	TANK	TANK	8687	0.018	0.44	NO
34	RELA	RELA	RELA	9076	0.014	0.42	NO
35	NLRX1	NLRX1	NLRX1	9103	0.013	0.42	NO
36	OTUD5	OTUD5	OTUD5	9106	0.013	0.42	NO
37	CREBBP	CREBBP	CREBBP	9162	0.013	0.42	NO
38	HMGB1	HMGB1	HMGB1	9344	0.011	0.42	NO
39	RPS27A	RPS27A	RPS27A	9873	0.0058	0.39	NO
40	IFIH1	IFIH1	IFIH1	10091	0.0036	0.38	NO
41	UBE2D3	UBE2D3	UBE2D3	10100	0.0035	0.38	NO
42	ATG12	ATG12	ATG12	10239	0.0022	0.37	NO
43	UBA52	UBA52	UBA52	10270	0.002	0.37	NO
44	RNF125	RNF125	RNF125	10763	-0.0022	0.34	NO
45	PIN1	PIN1	PIN1	11118	-0.0051	0.32	NO
46	CASP8	CASP8	CASP8	11160	-0.0056	0.32	NO
47	TBK1	TBK1	TBK1	11306	-0.0067	0.32	NO
48	RNF135	RNF135	RNF135	11405	-0.0075	0.31	NO
49	TRIM25	TRIM25	TRIM25	11437	-0.0077	0.31	NO
50	PCBP2	PCBP2	PCBP2	11580	-0.0089	0.31	NO
51	CHUK	CHUK	CHUK	11656	-0.0095	0.3	NO
52	UBE2D2	UBE2D2	UBE2D2	12532	-0.017	0.26	NO
53	MAVS	MAVS	MAVS	13485	-0.025	0.21	NO
54	UBE2D1	UBE2D1	UBE2D1	13911	-0.03	0.2	NO
55	DAK	DAK	DAK	14270	-0.033	0.18	NO
56	EP300	EP300	EP300	14397	-0.034	0.19	NO
57	SIKE1	SIKE1	SIKE1	14606	-0.037	0.18	NO
58	UBE2K	UBE2K	UBE2K	14660	-0.038	0.19	NO
59	TAX1BP1	TAX1BP1	TAX1BP1	15034	-0.042	0.18	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: KEGG GLYCEROLIPID METABOLISM.

Figure S78. 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 INOSITOL PHOSPHATE METABOLISM

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	CD7	CD7	CD7	392	0.48	0.07	YES
2	MET	MET	MET	636	0.41	0.14	YES
3	NR0B2	NR0B2	NR0B2	1165	0.33	0.17	YES
4	TNFRSF6B	TNFRSF6B	TNFRSF6B	1340	0.31	0.22	YES
5	IL8	IL8	IL8	1498	0.3	0.27	YES
6	BTK	BTK	BTK	1624	0.28	0.31	YES
7	FAIM2	FAIM2	FAIM2	1845	0.26	0.35	YES
8	CASP10	CASP10	CASP10	2344	0.22	0.37	YES
9	IL1A	IL1A	IL1A	2421	0.22	0.41	YES
10	FAS	FAS	FAS	3385	0.16	0.38	YES
11	NCS1	NCS1	NCS1	3795	0.14	0.39	YES
12	NFKBIE	NFKBIE	NFKBIE	4052	0.13	0.4	YES
13	HSPB1	HSPB1	HSPB1	4645	0.11	0.39	YES
14	EGFR	EGFR	EGFR	4956	0.095	0.39	YES
15	NFKBIA	NFKBIA	NFKBIA	5062	0.092	0.4	YES
16	MAP3K1	MAP3K1	MAP3K1	5110	0.091	0.42	YES
17	NFKB1	NFKB1	NFKB1	5246	0.086	0.42	YES
18	EPHB2	EPHB2	EPHB2	5255	0.086	0.44	YES
19	MAPK8IP3	MAPK8IP3	MAPK8IP3	5340	0.083	0.45	YES
20	NFKB2	NFKB2	NFKB2	6151	0.06	0.42	NO
21	MAP3K5	MAP3K5	MAP3K5	6454	0.052	0.41	NO
22	NFKBIB	NFKBIB	NFKBIB	6898	0.044	0.4	NO
23	NFAT5	NFAT5	NFAT5	6993	0.042	0.4	NO
24	RIPK1	RIPK1	RIPK1	7223	0.038	0.39	NO
25	TRAF2	TRAF2	TRAF2	7510	0.033	0.38	NO
26	DEDD2	DEDD2	DEDD2	7673	0.031	0.38	NO
27	BAK1	BAK1	BAK1	7801	0.03	0.38	NO
28	FADD	FADD	FADD	8190	0.024	0.36	NO
29	MAP2K7	MAP2K7	MAP2K7	8366	0.022	0.36	NO
30	PFN1	PFN1	PFN1	8458	0.021	0.36	NO
31	TP53	TP53	TP53	8592	0.019	0.35	NO
32	CASP3	CASP3	CASP3	8703	0.018	0.35	NO
33	MAPK10	MAPK10	MAPK10	8765	0.017	0.35	NO
34	DAXX	DAXX	DAXX	9209	0.012	0.33	NO
35	DIABLO	DIABLO	DIABLO	9538	0.0092	0.31	NO
36	CASP8AP2	CASP8AP2	CASP8AP2	9556	0.0089	0.31	NO
37	EZR	EZR	EZR	9836	0.0061	0.3	NO
38	CAD	CAD	CAD	10421	0.00087	0.27	NO
39	DFFA	DFFA	DFFA	10923	-0.0038	0.24	NO
40	BAX	BAX	BAX	11043	-0.0046	0.23	NO
41	SMPD1	SMPD1	SMPD1	11121	-0.0051	0.23	NO
42	CASP8	CASP8	CASP8	11160	-0.0056	0.23	NO
43	TUFM	TUFM	TUFM	11456	-0.0079	0.22	NO
44	DEDD	DEDD	DEDD	11579	-0.0089	0.21	NO
45	NFKBIL1	NFKBIL1	NFKBIL1	11986	-0.012	0.19	NO
46	MAP2K4	MAP2K4	MAP2K4	12025	-0.013	0.19	NO
47	PARP1	PARP1	PARP1	12305	-0.015	0.18	NO
48	FAF1	FAF1	FAF1	12332	-0.015	0.18	NO
49	BFAR	BFAR	BFAR	12350	-0.015	0.18	NO
50	AGFG1	AGFG1	AGFG1	12395	-0.016	0.18	NO
51	ROCK1	ROCK1	ROCK1	12623	-0.018	0.17	NO
52	ALG2	ALG2	ALG2	12741	-0.019	0.17	NO
53	CSNK1A1	CSNK1A1	CSNK1A1	13225	-0.023	0.15	NO
54	CDK2AP1	CDK2AP1	CDK2AP1	13444	-0.025	0.14	NO
55	RALBP1	RALBP1	RALBP1	13753	-0.028	0.13	NO
56	MAPK1	MAPK1	MAPK1	13960	-0.03	0.12	NO
57	MAPK8IP1	MAPK8IP1	MAPK8IP1	14288	-0.034	0.11	NO
58	MAPK8	MAPK8	MAPK8	14780	-0.039	0.093	NO
59	PFN2	PFN2	PFN2	15076	-0.043	0.085	NO
60	XIAP	XIAP	XIAP	15262	-0.045	0.083	NO
61	MAPK9	MAPK9	MAPK9	15445	-0.049	0.082	NO
62	PTPN13	PTPN13	PTPN13	15585	-0.052	0.085	NO
63	MAPK8IP2	MAPK8IP2	MAPK8IP2	16406	-0.07	0.053	NO
64	TPX2	TPX2	TPX2	18189	-0.26	0.0037	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: KEGG INOSITOL PHOSPHATE METABOLISM.

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

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 = PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = PRAD-TP.mergedcluster.txt

GSEA analysis

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

Download Results

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

References

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

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