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

Colorectal Adenocarcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in COADREAD-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1TB168D

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 "COADREAD-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: 712
Number of samples: 623
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 ] 159
pheno.type: 2 - 4 :[ clus2 ] 129
pheno.type: 3 - 4 :[ clus3 ] 132
pheno.type: 4 - 4 :[ clus4 ] 203

For the expression subtypes of 18041 genes in 624 samples, GSEA found enriched gene sets in each cluster using 623 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG LYSINE DEGRADATION, KEGG RNA DEGRADATION, KEGG SPLICEOSOME, PID FANCONI PATHWAY, PID ATM PATHWAY, PID BARD1PATHWAY, REACTOME METABOLISM OF NON CODING RNA, REACTOME METABOLISM OF VITAMINS AND COFACTORS, REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA, REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM

And common core enriched genes are CDC40, CPSF3, MAGOH, NCBP1, NCBP2, UPF3B, CSTF1, CSTF2, CSTF3, NUDT21

clus2

Top enriched gene sets are KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG SPHINGOLIPID METABOLISM, KEGG RETINOL METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG DRUG METABOLISM OTHER ENZYMES, BIOCARTA FAS PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA KERATINOCYTE PATHWAY, BIOCARTA PYK2 PATHWAY

And common core enriched genes are MAPK8, CASP3, CASP8, LMNA, LMNB1, MAP3K1, MDM2, PAK2, PARP1, RB1

clus3

Top enriched gene sets are KEGG TRYPTOPHAN METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG ABC TRANSPORTERS, KEGG MAPK SIGNALING PATHWAY, KEGG ERBB SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY

And common core enriched genes are PIK3CA, AKT3, RAPGEF1, SOS1, ADCY1, ADCY2, ADCY4, ADCY5, ADCY7, ADCYAP1

clus4

Top enriched gene sets are KEGG PATHOGENIC ESCHERICHIA COLI INFECTION, KEGG SYSTEMIC LUPUS ERYTHEMATOSUS, REACTOME TRANSLATION, REACTOME MEIOSIS, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME RNA POL I TRANSCRIPTION, REACTOME PEPTIDE CHAIN ELONGATION, REACTOME METABOLISM OF PROTEINS, REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION, REACTOME TRANSCRIPTION

And common core enriched genes are H2AFX, HIST1H2AB, HIST1H2AJ, HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BH, HIST1H2BI, HIST1H2BJ

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 LYSINE DEGRADATION	44	genes.ES.table	0.51	2	0.004	0.28	0.14	0.43	0.26	0.32	0	0.046
KEGG RNA DEGRADATION	57	genes.ES.table	0.41	1.6	0.057	0.59	0.85	0.61	0.35	0.4	0.23	0.15
KEGG SPLICEOSOME	114	genes.ES.table	0.37	1.7	0.089	0.67	0.85	0.51	0.32	0.35	0.26	0.17
PID FANCONI PATHWAY	46	genes.ES.table	0.54	1.6	0.092	0.58	0.9	0.52	0.26	0.39	0.26	0.15
PID ATM PATHWAY	34	genes.ES.table	0.53	1.6	0.033	0.55	0.86	0.56	0.27	0.41	0.22	0.15
PID BARD1PATHWAY	29	genes.ES.table	0.51	1.6	0.099	0.47	0.94	0.48	0.26	0.36	0.24	0.13
REACTOME METABOLISM OF NON CODING RNA	47	genes.ES.table	0.44	1.5	0.1	0.48	0.96	0.7	0.36	0.45	0.27	0.14
REACTOME METABOLISM OF VITAMINS AND COFACTORS	50	genes.ES.table	0.4	1.6	0.039	0.51	0.93	0.24	0.12	0.21	0.25	0.14
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA	126	genes.ES.table	0.42	1.7	0.071	0.61	0.77	0.59	0.39	0.36	0.21	0.14
REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM	44	genes.ES.table	0.49	1.7	0.04	0.68	0.75	0.64	0.38	0.39	0.22	0.16

genes ES table in pathway: KEGG LYSINE 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	PIPOX	PIPOX	PIPOX	42	0.41	0.15	YES
2	OGDHL	OGDHL	OGDHL	205	0.28	0.25	YES
3	SETDB2	SETDB2	SETDB2	968	0.16	0.27	YES
4	AASDHPPT	AASDHPPT	AASDHPPT	1917	0.11	0.26	YES
5	AASS	AASS	AASS	2175	0.1	0.28	YES
6	SETMAR	SETMAR	SETMAR	2374	0.093	0.3	YES
7	PLOD2	PLOD2	PLOD2	2608	0.088	0.32	YES
8	ALDH7A1	ALDH7A1	ALDH7A1	2828	0.082	0.34	YES
9	SETD2	SETD2	SETD2	3123	0.076	0.36	YES
10	WHSC1L1	WHSC1L1	WHSC1L1	3149	0.076	0.38	YES
11	ASH1L	ASH1L	ASH1L	3266	0.073	0.41	YES
12	SUV39H2	SUV39H2	SUV39H2	3499	0.068	0.42	YES
13	AADAT	AADAT	AADAT	3610	0.066	0.44	YES
14	SUV420H1	SUV420H1	SUV420H1	3664	0.065	0.46	YES
15	TMLHE	TMLHE	TMLHE	3705	0.064	0.48	YES
16	ACAT1	ACAT1	ACAT1	3853	0.062	0.5	YES
17	ALDH1B1	ALDH1B1	ALDH1B1	4464	0.051	0.48	YES
18	ACAT2	ACAT2	ACAT2	4634	0.048	0.49	YES
19	AASDH	AASDH	AASDH	4646	0.048	0.51	YES
20	ALDH2	ALDH2	ALDH2	5919	0.03	0.45	NO
21	SETD1A	SETD1A	SETD1A	6184	0.026	0.45	NO
22	SUV39H1	SUV39H1	SUV39H1	6325	0.025	0.45	NO
23	SETDB1	SETDB1	SETDB1	6538	0.023	0.44	NO
24	EHMT2	EHMT2	EHMT2	6836	0.019	0.44	NO
25	ALDH9A1	ALDH9A1	ALDH9A1	6898	0.018	0.44	NO
26	PLOD3	PLOD3	PLOD3	6955	0.017	0.44	NO
27	HADHA	HADHA	HADHA	7084	0.016	0.44	NO
28	WHSC1	WHSC1	WHSC1	7164	0.015	0.44	NO
29	EHHADH	EHHADH	EHHADH	7288	0.013	0.44	NO
30	NSD1	NSD1	NSD1	7322	0.013	0.44	NO
31	GCDH	GCDH	GCDH	7882	0.0064	0.42	NO
32	HADH	HADH	HADH	8109	0.0035	0.4	NO
33	BBOX1	BBOX1	BBOX1	8258	0.0017	0.4	NO
34	SETD1B	SETD1B	SETD1B	8923	-0.0067	0.36	NO
35	SUV420H2	SUV420H2	SUV420H2	9055	-0.0083	0.36	NO
36	SETD8	SETD8	SETD8	9760	-0.018	0.33	NO
37	OGDH	OGDH	OGDH	9761	-0.018	0.33	NO
38	SETD7	SETD7	SETD7	9936	-0.021	0.33	NO
39	ECHS1	ECHS1	ECHS1	10935	-0.035	0.29	NO
40	ALDH3A2	ALDH3A2	ALDH3A2	11029	-0.037	0.3	NO
41	EHMT1	EHMT1	EHMT1	11255	-0.041	0.3	NO
42	PLOD1	PLOD1	PLOD1	11899	-0.054	0.29	NO
43	DOT1L	DOT1L	DOT1L	12385	-0.065	0.28	NO
44	DLST	DLST	DLST	12935	-0.079	0.28	NO

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

Figure S2. 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 RNA DEGRADATION

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	CAB39L	CAB39L	CAB39L	151	0.3	0.22	YES
2	PRKAA2	PRKAA2	PRKAA2	1807	0.11	0.21	YES
3	RHEB	RHEB	RHEB	1864	0.11	0.3	YES
4	STRADB	STRADB	STRADB	1882	0.11	0.38	YES
5	PDE3B	PDE3B	PDE3B	1890	0.11	0.46	YES
6	RPS6KB1	RPS6KB1	RPS6KB1	3816	0.062	0.4	NO
7	PRKAA1	PRKAA1	PRKAA1	4274	0.054	0.42	NO
8	EEF2K	EEF2K	EEF2K	4965	0.044	0.41	NO
9	PRKAB1	PRKAB1	PRKAB1	5122	0.041	0.43	NO
10	TSC1	TSC1	TSC1	6062	0.028	0.4	NO
11	CAB39	CAB39	CAB39	6283	0.025	0.41	NO
12	RPS6	RPS6	RPS6	6724	0.02	0.4	NO
13	PRKAB2	PRKAB2	PRKAB2	7017	0.017	0.4	NO
14	RPTOR	RPTOR	RPTOR	7078	0.016	0.41	NO
15	EIF4B	EIF4B	EIF4B	7560	0.01	0.39	NO
16	EIF4G1	EIF4G1	EIF4G1	8218	0.0022	0.35	NO
17	PRKAG2	PRKAG2	PRKAG2	8275	0.0015	0.35	NO
18	TSC2	TSC2	TSC2	8744	-0.0044	0.33	NO
19	PRKAG1	PRKAG1	PRKAG1	9229	-0.011	0.31	NO
20	AKT2	AKT2	AKT2	9254	-0.011	0.32	NO
21	EIF4E	EIF4E	EIF4E	9319	-0.012	0.32	NO
22	PPM1A	PPM1A	PPM1A	10033	-0.022	0.3	NO
23	STK11	STK11	STK11	10526	-0.029	0.29	NO
24	MTOR	MTOR	MTOR	10573	-0.03	0.31	NO
25	EIF4EBP1	EIF4EBP1	EIF4EBP1	11181	-0.04	0.31	NO
26	MLST8	MLST8	MLST8	11423	-0.044	0.33	NO
27	STRADA	STRADA	STRADA	11673	-0.049	0.35	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 RNA DEGRADATION.

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

genes ES table in pathway: KEGG SPLICEOSOME

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	UPF3B	UPF3B	UPF3B	1031	0.15	0.044	YES
2	NCBP2	NCBP2	NCBP2	1547	0.12	0.097	YES
3	SNRPE	SNRPE	SNRPE	2454	0.091	0.11	YES
4	CSTF3	CSTF3	CSTF3	2817	0.083	0.14	YES
5	PCF11	PCF11	PCF11	3013	0.078	0.18	YES
6	LSM11	LSM11	LSM11	3530	0.067	0.2	YES
7	SNRPG	SNRPG	SNRPG	3615	0.066	0.24	YES
8	CSTF1	CSTF1	CSTF1	3667	0.065	0.28	YES
9	CPSF3	CPSF3	CPSF3	3739	0.063	0.32	YES
10	NUDT21	NUDT21	NUDT21	3793	0.063	0.36	YES
11	CDC40	CDC40	CDC40	3851	0.062	0.4	YES
12	MAGOH	MAGOH	MAGOH	3903	0.061	0.43	YES
13	ZNF473	ZNF473	ZNF473	4403	0.052	0.44	YES
14	PAPOLA	PAPOLA	PAPOLA	4579	0.049	0.46	YES
15	CSTF2	CSTF2	CSTF2	4581	0.049	0.5	YES
16	NCBP1	NCBP1	NCBP1	5165	0.041	0.49	YES
17	SNRPF	SNRPF	SNRPF	5206	0.04	0.52	YES
18	SNRPD3	SNRPD3	SNRPD3	5360	0.038	0.53	YES
19	SLBP	SLBP	SLBP	5956	0.03	0.52	NO
20	CPSF7	CPSF7	CPSF7	6104	0.028	0.53	NO
21	CPSF2	CPSF2	CPSF2	6566	0.022	0.52	NO
22	CPSF1	CPSF1	CPSF1	6866	0.019	0.52	NO
23	CLP1	CLP1	CLP1	6901	0.018	0.53	NO
24	PABPN1	PABPN1	PABPN1	7372	0.012	0.51	NO
25	THOC4	THOC4	THOC4	7476	0.011	0.51	NO
26	NFX1	NFX1	NFX1	7538	0.01	0.51	NO
27	U2AF2	U2AF2	U2AF2	7667	0.0088	0.51	NO
28	DHX38	DHX38	DHX38	7668	0.0088	0.52	NO
29	U2AF1	U2AF1	U2AF1	7789	0.0075	0.52	NO
30	SRRM1	SRRM1	SRRM1	7889	0.0063	0.52	NO
31	RNPS1	RNPS1	RNPS1	7921	0.0058	0.52	NO
32	SNRPB	SNRPB	SNRPB	8126	0.0034	0.51	NO
33	RBM8A	RBM8A	RBM8A	8142	0.0032	0.51	NO
34	LSM10	LSM10	LSM10	12123	-0.058	0.33	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 SPLICEOSOME.

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

genes ES table in pathway: PID FANCONI 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	UPF3B	UPF3B	UPF3B	1031	0.15	0.088	YES
2	NCBP2	NCBP2	NCBP2	1547	0.12	0.18	YES
3	CSTF3	CSTF3	CSTF3	2817	0.083	0.18	YES
4	PCF11	PCF11	PCF11	3013	0.078	0.25	YES
5	CSTF1	CSTF1	CSTF1	3667	0.065	0.27	YES
6	CPSF3	CPSF3	CPSF3	3739	0.063	0.33	YES
7	NUDT21	NUDT21	NUDT21	3793	0.063	0.39	YES
8	CDC40	CDC40	CDC40	3851	0.062	0.44	YES
9	MAGOH	MAGOH	MAGOH	3903	0.061	0.5	YES
10	PAPOLA	PAPOLA	PAPOLA	4579	0.049	0.51	YES
11	CSTF2	CSTF2	CSTF2	4581	0.049	0.55	YES
12	NCBP1	NCBP1	NCBP1	5165	0.041	0.56	YES
13	CPSF7	CPSF7	CPSF7	6104	0.028	0.53	NO
14	CPSF2	CPSF2	CPSF2	6566	0.022	0.53	NO
15	CPSF1	CPSF1	CPSF1	6866	0.019	0.53	NO
16	CLP1	CLP1	CLP1	6901	0.018	0.55	NO
17	PABPN1	PABPN1	PABPN1	7372	0.012	0.53	NO
18	THOC4	THOC4	THOC4	7476	0.011	0.54	NO
19	NFX1	NFX1	NFX1	7538	0.01	0.54	NO
20	U2AF2	U2AF2	U2AF2	7667	0.0088	0.55	NO
21	DHX38	DHX38	DHX38	7668	0.0088	0.55	NO
22	U2AF1	U2AF1	U2AF1	7789	0.0075	0.55	NO
23	SRRM1	SRRM1	SRRM1	7889	0.0063	0.55	NO
24	RNPS1	RNPS1	RNPS1	7921	0.0058	0.56	NO
25	RBM8A	RBM8A	RBM8A	8142	0.0032	0.55	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: PID FANCONI PATHWAY.

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

genes ES table in pathway: PID ATM PATHWAY

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	UPF3B	UPF3B	UPF3B	1031	0.15	0.025	YES
2	RAE1	RAE1	RAE1	1346	0.13	0.078	YES
3	NCBP2	NCBP2	NCBP2	1547	0.12	0.13	YES
4	NUPL2	NUPL2	NUPL2	1578	0.12	0.2	YES
5	NUP35	NUP35	NUP35	2503	0.09	0.19	YES
6	NUPL1	NUPL1	NUPL1	2597	0.088	0.24	YES
7	NUP107	NUP107	NUP107	3433	0.069	0.23	YES
8	CPSF3	CPSF3	CPSF3	3739	0.063	0.24	YES
9	CDC40	CDC40	CDC40	3851	0.062	0.27	YES
10	MAGOH	MAGOH	MAGOH	3903	0.061	0.3	YES
11	NUP210	NUP210	NUP210	4457	0.051	0.3	YES
12	NUP153	NUP153	NUP153	4461	0.051	0.33	YES
13	TPR	TPR	TPR	4478	0.051	0.35	YES
14	NUP155	NUP155	NUP155	4559	0.05	0.38	YES
15	NUP43	NUP43	NUP43	4659	0.048	0.4	YES
16	NUP54	NUP54	NUP54	4748	0.047	0.42	YES
17	RANBP2	RANBP2	RANBP2	4828	0.046	0.44	YES
18	NUP133	NUP133	NUP133	4858	0.045	0.46	YES
19	NUP205	NUP205	NUP205	4875	0.045	0.48	YES
20	NCBP1	NCBP1	NCBP1	5165	0.041	0.49	YES
21	SLBP	SLBP	SLBP	5956	0.03	0.46	YES
22	NUP37	NUP37	NUP37	5987	0.029	0.48	YES
23	NUP85	NUP85	NUP85	6267	0.026	0.47	YES
24	NUP214	NUP214	NUP214	6488	0.023	0.47	YES
25	CPSF2	CPSF2	CPSF2	6566	0.022	0.48	YES
26	NXF1	NXF1	NXF1	6720	0.02	0.48	YES
27	CPSF1	CPSF1	CPSF1	6866	0.019	0.49	YES
28	NUP93	NUP93	NUP93	6933	0.018	0.49	YES
29	POM121	POM121	POM121	7291	0.013	0.48	NO
30	THOC4	THOC4	THOC4	7476	0.011	0.48	NO
31	NFX1	NFX1	NFX1	7538	0.01	0.48	NO
32	U2AF2	U2AF2	U2AF2	7667	0.0088	0.48	NO
33	DHX38	DHX38	DHX38	7668	0.0088	0.48	NO
34	U2AF1	U2AF1	U2AF1	7789	0.0075	0.48	NO
35	NUP50	NUP50	NUP50	7874	0.0064	0.48	NO
36	SRRM1	SRRM1	SRRM1	7889	0.0063	0.48	NO
37	RNPS1	RNPS1	RNPS1	7921	0.0058	0.48	NO
38	NUP88	NUP88	NUP88	8053	0.0042	0.48	NO
39	RBM8A	RBM8A	RBM8A	8142	0.0032	0.47	NO
40	EIF4E	EIF4E	EIF4E	9319	-0.012	0.41	NO
41	AAAS	AAAS	AAAS	9520	-0.015	0.41	NO
42	NUP62	NUP62	NUP62	10136	-0.024	0.39	NO
43	NUP188	NUP188	NUP188	11386	-0.043	0.34	NO
44	SEH1L	SEH1L	SEH1L	11644	-0.048	0.36	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: PID ATM PATHWAY.

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: PID ATM 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 BARD1PATHWAY

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	GTF2F2	GTF2F2	GTF2F2	1020	0.15	-0.026	YES
2	UPF3B	UPF3B	UPF3B	1031	0.15	0.004	YES
3	RAE1	RAE1	RAE1	1346	0.13	0.013	YES
4	NCBP2	NCBP2	NCBP2	1547	0.12	0.026	YES
5	NUPL2	NUPL2	NUPL2	1578	0.12	0.049	YES
6	POLR2K	POLR2K	POLR2K	1629	0.12	0.07	YES
7	PRPF6	PRPF6	PRPF6	1692	0.12	0.09	YES
8	CCAR1	CCAR1	CCAR1	1914	0.11	0.1	YES
9	SNRPB2	SNRPB2	SNRPB2	1998	0.11	0.12	YES
10	SNRPE	SNRPE	SNRPE	2454	0.091	0.11	YES
11	NUP35	NUP35	NUP35	2503	0.09	0.12	YES
12	NUPL1	NUPL1	NUPL1	2597	0.088	0.14	YES
13	SNRPA1	SNRPA1	SNRPA1	2683	0.086	0.15	YES
14	CSTF3	CSTF3	CSTF3	2817	0.083	0.16	YES
15	SF3B14	SF3B14	SF3B14	2894	0.081	0.17	YES
16	PCF11	PCF11	PCF11	3013	0.078	0.18	YES
17	NUP107	NUP107	NUP107	3433	0.069	0.17	YES
18	SNRPG	SNRPG	SNRPG	3615	0.066	0.18	YES
19	CSTF1	CSTF1	CSTF1	3667	0.065	0.18	YES
20	CPSF3	CPSF3	CPSF3	3739	0.063	0.19	YES
21	NUDT21	NUDT21	NUDT21	3793	0.063	0.2	YES
22	CDC40	CDC40	CDC40	3851	0.062	0.21	YES
23	MAGOH	MAGOH	MAGOH	3903	0.061	0.22	YES
24	SMC1A	SMC1A	SMC1A	4335	0.053	0.21	YES
25	NUP210	NUP210	NUP210	4457	0.051	0.21	YES
26	NUP153	NUP153	NUP153	4461	0.051	0.22	YES
27	TPR	TPR	TPR	4478	0.051	0.23	YES
28	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	4538	0.05	0.24	YES
29	NUP155	NUP155	NUP155	4559	0.05	0.25	YES
30	PAPOLA	PAPOLA	PAPOLA	4579	0.049	0.26	YES
31	CSTF2	CSTF2	CSTF2	4581	0.049	0.27	YES
32	HNRNPK	HNRNPK	HNRNPK	4597	0.049	0.28	YES
33	NUP43	NUP43	NUP43	4659	0.048	0.28	YES
34	NUP54	NUP54	NUP54	4748	0.047	0.29	YES
35	RANBP2	RANBP2	RANBP2	4828	0.046	0.29	YES
36	NUP133	NUP133	NUP133	4858	0.045	0.3	YES
37	HNRNPH2	HNRNPH2	HNRNPH2	4860	0.045	0.31	YES
38	NUP205	NUP205	NUP205	4875	0.045	0.32	YES
39	HNRNPU	HNRNPU	HNRNPU	4909	0.044	0.32	YES
40	RBMX	RBMX	RBMX	4977	0.044	0.33	YES
41	HNRNPR	HNRNPR	HNRNPR	5005	0.043	0.34	YES
42	HNRNPA3	HNRNPA3	HNRNPA3	5035	0.042	0.34	YES
43	SNRNP200	SNRNP200	SNRNP200	5130	0.041	0.35	YES
44	NCBP1	NCBP1	NCBP1	5165	0.041	0.35	YES
45	SNRPF	SNRPF	SNRPF	5206	0.04	0.36	YES
46	POLR2D	POLR2D	POLR2D	5260	0.039	0.36	YES
47	SF3B1	SF3B1	SF3B1	5265	0.039	0.37	YES
48	POLR2J	POLR2J	POLR2J	5306	0.039	0.38	YES
49	HNRNPD	HNRNPD	HNRNPD	5343	0.038	0.38	YES
50	SNRPD3	SNRPD3	SNRPD3	5360	0.038	0.39	YES
51	SF3B2	SF3B2	SF3B2	5390	0.037	0.4	YES
52	CD2BP2	CD2BP2	CD2BP2	5472	0.036	0.4	YES
53	SF3B3	SF3B3	SF3B3	5662	0.034	0.4	YES
54	POLR2F	POLR2F	POLR2F	5738	0.033	0.4	YES
55	SLBP	SLBP	SLBP	5956	0.03	0.39	YES
56	NUP37	NUP37	NUP37	5987	0.029	0.4	YES
57	FUS	FUS	FUS	6052	0.028	0.4	YES
58	CPSF7	CPSF7	CPSF7	6104	0.028	0.4	YES
59	HNRNPUL1	HNRNPUL1	HNRNPUL1	6174	0.027	0.4	YES
60	SNRPD2	SNRPD2	SNRPD2	6213	0.026	0.4	YES
61	POLR2C	POLR2C	POLR2C	6254	0.026	0.41	YES
62	NUP85	NUP85	NUP85	6267	0.026	0.41	YES
63	NUP214	NUP214	NUP214	6488	0.023	0.4	YES
64	HNRNPH1	HNRNPH1	HNRNPH1	6546	0.022	0.41	YES
65	CPSF2	CPSF2	CPSF2	6566	0.022	0.41	YES
66	DHX9	DHX9	DHX9	6645	0.021	0.41	YES
67	SF3A3	SF3A3	SF3A3	6692	0.021	0.41	YES
68	NXF1	NXF1	NXF1	6720	0.02	0.41	YES
69	HNRNPL	HNRNPL	HNRNPL	6844	0.019	0.41	YES
70	SNRPA	SNRPA	SNRPA	6854	0.019	0.41	YES
71	CPSF1	CPSF1	CPSF1	6866	0.019	0.42	YES
72	CLP1	CLP1	CLP1	6901	0.018	0.42	YES
73	NUP93	NUP93	NUP93	6933	0.018	0.42	YES
74	DNAJC8	DNAJC8	DNAJC8	6970	0.017	0.42	YES
75	EFTUD2	EFTUD2	EFTUD2	7060	0.016	0.42	NO
76	POM121	POM121	POM121	7291	0.013	0.41	NO
77	HNRNPF	HNRNPF	HNRNPF	7350	0.013	0.41	NO
78	PABPN1	PABPN1	PABPN1	7372	0.012	0.41	NO
79	GTF2F1	GTF2F1	GTF2F1	7438	0.012	0.41	NO
80	NHP2L1	NHP2L1	NHP2L1	7458	0.011	0.41	NO
81	THOC4	THOC4	THOC4	7476	0.011	0.41	NO
82	HNRNPA0	HNRNPA0	HNRNPA0	7510	0.011	0.41	NO
83	POLR2B	POLR2B	POLR2B	7531	0.01	0.41	NO
84	NFX1	NFX1	NFX1	7538	0.01	0.42	NO
85	DDX23	DDX23	DDX23	7589	0.0098	0.42	NO
86	SNRNP70	SNRNP70	SNRNP70	7646	0.0091	0.41	NO
87	U2AF2	U2AF2	U2AF2	7667	0.0088	0.41	NO
88	DHX38	DHX38	DHX38	7668	0.0088	0.42	NO
89	POLR2H	POLR2H	POLR2H	7758	0.0078	0.41	NO
90	U2AF1	U2AF1	U2AF1	7789	0.0075	0.41	NO
91	SF3A2	SF3A2	SF3A2	7865	0.0066	0.41	NO
92	NUP50	NUP50	NUP50	7874	0.0064	0.41	NO
93	SRRM1	SRRM1	SRRM1	7889	0.0063	0.41	NO
94	RBM5	RBM5	RBM5	7915	0.0058	0.41	NO
95	RNPS1	RNPS1	RNPS1	7921	0.0058	0.41	NO
96	PTBP1	PTBP1	PTBP1	7948	0.0055	0.41	NO
97	NUP88	NUP88	NUP88	8053	0.0042	0.41	NO
98	HNRNPC	HNRNPC	HNRNPC	8088	0.0037	0.4	NO
99	SNRPB	SNRPB	SNRPB	8126	0.0034	0.4	NO
100	RBM8A	RBM8A	RBM8A	8142	0.0032	0.4	NO
101	YBX1	YBX1	YBX1	8313	0.001	0.39	NO
102	PCBP1	PCBP1	PCBP1	8336	0.00072	0.39	NO
103	HNRNPM	HNRNPM	HNRNPM	8542	-0.0017	0.38	NO
104	PRPF4	PRPF4	PRPF4	8643	-0.003	0.38	NO
105	SF3B4	SF3B4	SF3B4	9019	-0.0078	0.36	NO
106	SNRPD1	SNRPD1	SNRPD1	9300	-0.012	0.34	NO
107	EIF4E	EIF4E	EIF4E	9319	-0.012	0.35	NO
108	POLR2E	POLR2E	POLR2E	9462	-0.014	0.34	NO
109	AAAS	AAAS	AAAS	9520	-0.015	0.34	NO
110	POLR2G	POLR2G	POLR2G	9548	-0.015	0.34	NO
111	PCBP2	PCBP2	PCBP2	9933	-0.021	0.32	NO
112	HNRNPA1	HNRNPA1	HNRNPA1	9959	-0.021	0.33	NO
113	METTL3	METTL3	METTL3	9974	-0.021	0.33	NO
114	SF3A1	SF3A1	SF3A1	9996	-0.022	0.33	NO
115	NUP62	NUP62	NUP62	10136	-0.024	0.33	NO
116	LSM2	LSM2	LSM2	10371	-0.027	0.32	NO
117	PRPF8	PRPF8	PRPF8	10621	-0.031	0.32	NO
118	PHF5A	PHF5A	PHF5A	10669	-0.032	0.32	NO
119	SNRNP40	SNRNP40	SNRNP40	11154	-0.039	0.3	NO
120	SF3B5	SF3B5	SF3B5	11329	-0.042	0.3	NO
121	NUP188	NUP188	NUP188	11386	-0.043	0.3	NO
122	POLR2I	POLR2I	POLR2I	11437	-0.044	0.31	NO
123	SEH1L	SEH1L	SEH1L	11644	-0.048	0.31	NO
124	POLR2A	POLR2A	POLR2A	12386	-0.065	0.28	NO
125	TXNL4A	TXNL4A	TXNL4A	12926	-0.079	0.27	NO
126	POLR2L	POLR2L	POLR2L	13200	-0.086	0.27	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: PID BARD1PATHWAY.

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: PID BARD1PATHWAY, 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 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	CTNNBL1	CTNNBL1	CTNNBL1	1036	0.15	-0.032	YES
2	NAA38	NAA38	NAA38	1042	0.15	-0.0061	YES
3	THOC2	THOC2	THOC2	1160	0.14	0.012	YES
4	CWC15	CWC15	CWC15	1467	0.12	0.016	YES
5	NCBP2	NCBP2	NCBP2	1547	0.12	0.033	YES
6	PRPF6	PRPF6	PRPF6	1692	0.12	0.045	YES
7	PRPF40B	PRPF40B	PRPF40B	1711	0.12	0.064	YES
8	SNRNP27	SNRNP27	SNRNP27	1918	0.11	0.071	YES
9	LSM5	LSM5	LSM5	1945	0.11	0.088	YES
10	SNRPB2	SNRPB2	SNRPB2	1998	0.11	0.1	YES
11	SYF2	SYF2	SYF2	2103	0.1	0.12	YES
12	PRPF38B	PRPF38B	PRPF38B	2313	0.095	0.12	YES
13	CRNKL1	CRNKL1	CRNKL1	2415	0.092	0.13	YES
14	SNRPE	SNRPE	SNRPE	2454	0.091	0.14	YES
15	ISY1	ISY1	ISY1	2483	0.09	0.16	YES
16	PRPF40A	PRPF40A	PRPF40A	2497	0.09	0.17	YES
17	SNRPA1	SNRPA1	SNRPA1	2683	0.086	0.18	YES
18	LSM6	LSM6	LSM6	2878	0.081	0.18	YES
19	SF3B14	SF3B14	SF3B14	2894	0.081	0.19	YES
20	PRPF3	PRPF3	PRPF3	2955	0.079	0.2	YES
21	LSM3	LSM3	LSM3	3063	0.077	0.21	YES
22	TCERG1	TCERG1	TCERG1	3106	0.076	0.22	YES
23	SLU7	SLU7	SLU7	3227	0.074	0.23	YES
24	DDX46	DDX46	DDX46	3588	0.066	0.22	YES
25	PRPF18	PRPF18	PRPF18	3597	0.066	0.23	YES
26	SNRPG	SNRPG	SNRPG	3615	0.066	0.24	YES
27	BCAS2	BCAS2	BCAS2	3778	0.063	0.24	YES
28	CDC40	CDC40	CDC40	3851	0.062	0.25	YES
29	CDC5L	CDC5L	CDC5L	3880	0.061	0.26	YES
30	ZMAT2	ZMAT2	ZMAT2	3884	0.061	0.27	YES
31	MAGOH	MAGOH	MAGOH	3903	0.061	0.28	YES
32	PQBP1	PQBP1	PQBP1	3914	0.06	0.29	YES
33	SMNDC1	SMNDC1	SMNDC1	4192	0.055	0.28	YES
34	PPIH	PPIH	PPIH	4312	0.054	0.28	YES
35	RBM25	RBM25	RBM25	4397	0.052	0.29	YES
36	PRPF38A	PRPF38A	PRPF38A	4406	0.052	0.3	YES
37	TRA2A	TRA2A	TRA2A	4460	0.051	0.3	YES
38	MAGOHB	MAGOHB	MAGOHB	4492	0.051	0.31	YES
39	HNRNPK	HNRNPK	HNRNPK	4597	0.049	0.31	YES
40	HNRNPU	HNRNPU	HNRNPU	4909	0.044	0.3	YES
41	RBMX	RBMX	RBMX	4977	0.044	0.31	YES
42	HNRNPA3	HNRNPA3	HNRNPA3	5035	0.042	0.31	YES
43	THOC1	THOC1	THOC1	5115	0.041	0.31	YES
44	SNRNP200	SNRNP200	SNRNP200	5130	0.041	0.32	YES
45	NCBP1	NCBP1	NCBP1	5165	0.041	0.32	YES
46	DDX42	DDX42	DDX42	5171	0.041	0.33	YES
47	SNRPF	SNRPF	SNRPF	5206	0.04	0.34	YES
48	SF3B1	SF3B1	SF3B1	5265	0.039	0.34	YES
49	SNRPD3	SNRPD3	SNRPD3	5360	0.038	0.34	YES
50	SART1	SART1	SART1	5367	0.038	0.35	YES
51	RBM17	RBM17	RBM17	5376	0.038	0.35	YES
52	SF3B2	SF3B2	SF3B2	5390	0.037	0.36	YES
53	SNW1	SNW1	SNW1	5520	0.036	0.36	YES
54	DHX8	DHX8	DHX8	5560	0.035	0.36	YES
55	USP39	USP39	USP39	5654	0.034	0.36	YES
56	SF3B3	SF3B3	SF3B3	5662	0.034	0.37	YES
57	BUD31	BUD31	BUD31	5791	0.032	0.37	YES
58	SNRPC	SNRPC	SNRPC	5796	0.032	0.37	YES
59	CHERP	CHERP	CHERP	6041	0.028	0.36	NO
60	PRPF19	PRPF19	PRPF19	6111	0.027	0.36	NO
61	SNRPD2	SNRPD2	SNRPD2	6213	0.026	0.36	NO
62	AQR	AQR	AQR	6300	0.025	0.36	NO
63	PLRG1	PLRG1	PLRG1	6307	0.025	0.37	NO
64	RBM22	RBM22	RBM22	6689	0.021	0.35	NO
65	SF3A3	SF3A3	SF3A3	6692	0.021	0.35	NO
66	DHX15	DHX15	DHX15	6747	0.02	0.35	NO
67	SNRPA	SNRPA	SNRPA	6854	0.019	0.35	NO
68	DDX5	DDX5	DDX5	6946	0.018	0.35	NO
69	PPIE	PPIE	PPIE	7010	0.017	0.35	NO
70	EFTUD2	EFTUD2	EFTUD2	7060	0.016	0.35	NO
71	PPIL1	PPIL1	PPIL1	7175	0.015	0.34	NO
72	NHP2L1	NHP2L1	NHP2L1	7458	0.011	0.33	NO
73	ACIN1	ACIN1	ACIN1	7466	0.011	0.33	NO
74	THOC4	THOC4	THOC4	7476	0.011	0.33	NO
75	CCDC12	CCDC12	CCDC12	7552	0.01	0.33	NO
76	DDX23	DDX23	DDX23	7589	0.0098	0.33	NO
77	SNRNP70	SNRNP70	SNRNP70	7646	0.0091	0.33	NO
78	U2AF2	U2AF2	U2AF2	7667	0.0088	0.33	NO
79	DHX38	DHX38	DHX38	7668	0.0088	0.33	NO
80	U2AF1	U2AF1	U2AF1	7789	0.0075	0.32	NO
81	WBP11	WBP11	WBP11	7812	0.0072	0.32	NO
82	SF3A2	SF3A2	SF3A2	7865	0.0066	0.32	NO
83	TRA2B	TRA2B	TRA2B	7949	0.0055	0.32	NO
84	HNRNPC	HNRNPC	HNRNPC	8088	0.0037	0.31	NO
85	SNRPB	SNRPB	SNRPB	8126	0.0034	0.31	NO
86	RBM8A	RBM8A	RBM8A	8142	0.0032	0.31	NO
87	PCBP1	PCBP1	PCBP1	8336	0.00072	0.3	NO
88	LSM4	LSM4	LSM4	8503	-0.0014	0.29	NO
89	HNRNPM	HNRNPM	HNRNPM	8542	-0.0017	0.29	NO
90	PRPF4	PRPF4	PRPF4	8643	-0.003	0.28	NO
91	HSPA1A	HSPA1A	HSPA1A	8872	-0.0059	0.27	NO
92	XAB2	XAB2	XAB2	8949	-0.007	0.27	NO
93	DHX16	DHX16	DHX16	8986	-0.0074	0.27	NO
94	SF3B4	SF3B4	SF3B4	9019	-0.0078	0.27	NO
95	SNRPD1	SNRPD1	SNRPD1	9300	-0.012	0.25	NO
96	PUF60	PUF60	PUF60	9426	-0.014	0.25	NO
97	PRPF31	PRPF31	PRPF31	9616	-0.016	0.24	NO
98	HNRNPA1	HNRNPA1	HNRNPA1	9959	-0.021	0.23	NO
99	SF3A1	SF3A1	SF3A1	9996	-0.022	0.23	NO
100	THOC3	THOC3	THOC3	10084	-0.023	0.23	NO
101	LSM7	LSM7	LSM7	10333	-0.026	0.22	NO
102	LSM2	LSM2	LSM2	10371	-0.027	0.22	NO
103	EIF4A3	EIF4A3	EIF4A3	10592	-0.03	0.21	NO
104	HSPA8	HSPA8	HSPA8	10603	-0.03	0.22	NO
105	PRPF8	PRPF8	PRPF8	10621	-0.031	0.22	NO
106	PHF5A	PHF5A	PHF5A	10669	-0.032	0.22	NO
107	SNRNP40	SNRNP40	SNRNP40	11154	-0.039	0.2	NO
108	SF3B5	SF3B5	SF3B5	11329	-0.042	0.2	NO
109	TXNL4A	TXNL4A	TXNL4A	12926	-0.079	0.13	NO
110	HNRNPA1L2	HNRNPA1L2	HNRNPA1L2	13230	-0.088	0.12	NO
111	HSPA1B	HSPA1B	HSPA1B	14548	-0.14	0.076	NO
112	HSPA6	HSPA6	HSPA6	15008	-0.16	0.078	NO
113	HSPA2	HSPA2	HSPA2	15492	-0.19	0.084	NO
114	HSPA1L	HSPA1L	HSPA1L	17087	-0.34	0.052	NO

Figure S13. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME METABOLISM OF NON CODING RNA.

Figure S14. 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 METABOLISM OF VITAMINS AND COFACTORS

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	NAA38	NAA38	NAA38	1042	0.15	-0.0053	YES
2	C1D	C1D	C1D	1078	0.15	0.044	YES
3	PNPT1	PNPT1	PNPT1	1519	0.12	0.063	YES
4	MPHOSPH6	MPHOSPH6	MPHOSPH6	1597	0.12	0.1	YES
5	LSM5	LSM5	LSM5	1945	0.11	0.12	YES
6	HSPD1	HSPD1	HSPD1	2153	0.1	0.14	YES
7	DIS3	DIS3	DIS3	2390	0.093	0.16	YES
8	LSM6	LSM6	LSM6	2878	0.081	0.16	YES
9	LSM3	LSM3	LSM3	3063	0.077	0.18	YES
10	EXOSC8	EXOSC8	EXOSC8	3077	0.077	0.2	YES
11	ZCCHC7	ZCCHC7	ZCCHC7	3470	0.068	0.21	YES
12	TTC37	TTC37	TTC37	3569	0.066	0.22	YES
13	CNOT4	CNOT4	CNOT4	3634	0.065	0.24	YES
14	SKIV2L2	SKIV2L2	SKIV2L2	3666	0.065	0.26	YES
15	PAPOLG	PAPOLG	PAPOLG	3733	0.064	0.28	YES
16	EXOSC5	EXOSC5	EXOSC5	3797	0.063	0.3	YES
17	EXOSC9	EXOSC9	EXOSC9	3987	0.059	0.31	YES
18	XRN2	XRN2	XRN2	4182	0.056	0.32	YES
19	PAPOLA	PAPOLA	PAPOLA	4579	0.049	0.32	YES
20	DCP2	DCP2	DCP2	4752	0.047	0.32	YES
21	HSPA9	HSPA9	HSPA9	4868	0.045	0.33	YES
22	PARN	PARN	PARN	4941	0.044	0.34	YES
23	LSM1	LSM1	LSM1	5200	0.04	0.34	YES
24	CNOT1	CNOT1	CNOT1	5253	0.039	0.35	YES
25	XRN1	XRN1	XRN1	5435	0.037	0.36	YES
26	CNOT10	CNOT10	CNOT10	5464	0.036	0.37	YES
27	PATL1	PATL1	PATL1	5632	0.034	0.37	YES
28	DDX6	DDX6	DDX6	5799	0.032	0.37	YES
29	CNOT6L	CNOT6L	CNOT6L	5810	0.032	0.38	YES
30	DCP1A	DCP1A	DCP1A	5824	0.032	0.39	YES
31	EXOSC3	EXOSC3	EXOSC3	5886	0.031	0.4	YES
32	EXOSC7	EXOSC7	EXOSC7	6148	0.027	0.4	YES
33	EXOSC1	EXOSC1	EXOSC1	6219	0.026	0.4	YES
34	CNOT6	CNOT6	CNOT6	6275	0.026	0.41	YES
35	DCP1B	DCP1B	DCP1B	6341	0.025	0.41	YES
36	PAPD7	PAPD7	PAPD7	6699	0.021	0.4	NO
37	CNOT2	CNOT2	CNOT2	7047	0.016	0.39	NO
38	EXOSC10	EXOSC10	EXOSC10	7501	0.011	0.36	NO
39	EXOSC2	EXOSC2	EXOSC2	7642	0.0091	0.36	NO
40	EDC4	EDC4	EDC4	7829	0.007	0.35	NO
41	SKIV2L	SKIV2L	SKIV2L	8004	0.0048	0.34	NO
42	EDC3	EDC3	EDC3	8228	0.0021	0.33	NO
43	CNOT8	CNOT8	CNOT8	8259	0.0017	0.33	NO
44	CNOT7	CNOT7	CNOT7	8419	-0.00023	0.32	NO
45	LSM4	LSM4	LSM4	8503	-0.0014	0.32	NO
46	ENO3	ENO3	ENO3	9157	-0.0099	0.28	NO
47	CNOT3	CNOT3	CNOT3	9957	-0.021	0.25	NO
48	WDR61	WDR61	WDR61	10121	-0.023	0.25	NO
49	LSM7	LSM7	LSM7	10333	-0.026	0.24	NO
50	LSM2	LSM2	LSM2	10371	-0.027	0.25	NO
51	PAPOLB	PAPOLB	PAPOLB	10905	-0.035	0.23	NO
52	ENO1	ENO1	ENO1	11170	-0.04	0.23	NO
53	EXOSC4	EXOSC4	EXOSC4	11234	-0.041	0.24	NO
54	DCPS	DCPS	DCPS	11976	-0.056	0.22	NO
55	EXOSC6	EXOSC6	EXOSC6	12425	-0.066	0.22	NO
56	RQCD1	RQCD1	RQCD1	12838	-0.077	0.22	NO
57	ENO2	ENO2	ENO2	15396	-0.18	0.15	NO

Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME METABOLISM OF VITAMINS AND COFACTORS.

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

genes ES table in pathway: REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA

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	MRE11A	MRE11A	MRE11A	781	0.17	0.043	YES
2	RAD50	RAD50	RAD50	1761	0.11	0.045	YES
3	XRCC4	XRCC4	XRCC4	2060	0.1	0.08	YES
4	BRCA1	BRCA1	BRCA1	2076	0.1	0.13	YES
5	CHEK2	CHEK2	CHEK2	2277	0.096	0.17	YES
6	YWHAB	YWHAB	YWHAB	2310	0.095	0.21	YES
7	ATM	ATM	ATM	2365	0.094	0.26	YES
8	SMC3	SMC3	SMC3	2522	0.09	0.29	YES
9	CDC25A	CDC25A	CDC25A	2564	0.089	0.33	YES
10	RAD17	RAD17	RAD17	2881	0.081	0.36	YES
11	BLM	BLM	BLM	3010	0.078	0.39	YES
12	FAM175A	FAM175A	FAM175A	3324	0.072	0.41	YES
13	MDC1	MDC1	MDC1	3446	0.069	0.43	YES
14	DCLRE1C	DCLRE1C	DCLRE1C	3483	0.068	0.46	YES
15	CDC25C	CDC25C	CDC25C	3501	0.068	0.5	YES
16	RNF8	RNF8	RNF8	3724	0.064	0.52	YES
17	SMC1A	SMC1A	SMC1A	4335	0.053	0.51	YES
18	NBN	NBN	NBN	4550	0.05	0.52	YES
19	UIMC1	UIMC1	UIMC1	4855	0.045	0.53	YES
20	RFWD2	RFWD2	RFWD2	5284	0.039	0.52	NO
21	TP53BP1	TP53BP1	TP53BP1	5626	0.034	0.52	NO
22	UBE2N	UBE2N	UBE2N	5908	0.03	0.52	NO
23	TERF2	TERF2	TERF2	6524	0.023	0.5	NO
24	FANCD2	FANCD2	FANCD2	6657	0.021	0.5	NO
25	RAD9A	RAD9A	RAD9A	6976	0.017	0.49	NO
26	ABL1	ABL1	ABL1	7828	0.007	0.45	NO
27	CTBP1	CTBP1	CTBP1	9056	-0.0083	0.38	NO
28	BID	BID	BID	9120	-0.0094	0.38	NO
29	KAT5	KAT5	KAT5	9645	-0.017	0.36	NO
30	TRIM28	TRIM28	TRIM28	9986	-0.021	0.36	NO
31	RBBP8	RBBP8	RBBP8	10481	-0.028	0.34	NO
32	H2AFX	H2AFX	H2AFX	11095	-0.038	0.33	NO
33	MDM2	MDM2	MDM2	11775	-0.052	0.32	NO
34	TOP3A	TOP3A	TOP3A	12361	-0.064	0.32	NO

Figure S17. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA, 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 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	RAE1	RAE1	RAE1	1346	0.13	0.013	YES
2	NCBP2	NCBP2	NCBP2	1547	0.12	0.083	YES
3	NUPL2	NUPL2	NUPL2	1578	0.12	0.16	YES
4	NUP35	NUP35	NUP35	2503	0.09	0.17	YES
5	NUPL1	NUPL1	NUPL1	2597	0.088	0.22	YES
6	NUP107	NUP107	NUP107	3433	0.069	0.22	YES
7	CPSF3	CPSF3	CPSF3	3739	0.063	0.25	YES
8	NUP210	NUP210	NUP210	4457	0.051	0.24	YES
9	NUP153	NUP153	NUP153	4461	0.051	0.28	YES
10	TPR	TPR	TPR	4478	0.051	0.31	YES
11	NUP155	NUP155	NUP155	4559	0.05	0.34	YES
12	NUP43	NUP43	NUP43	4659	0.048	0.37	YES
13	NUP54	NUP54	NUP54	4748	0.047	0.4	YES
14	RANBP2	RANBP2	RANBP2	4828	0.046	0.42	YES
15	NUP133	NUP133	NUP133	4858	0.045	0.45	YES
16	NUP205	NUP205	NUP205	4875	0.045	0.48	YES
17	NCBP1	NCBP1	NCBP1	5165	0.041	0.49	YES
18	NUP37	NUP37	NUP37	5987	0.029	0.46	YES
19	NUP85	NUP85	NUP85	6267	0.026	0.47	YES
20	NUP214	NUP214	NUP214	6488	0.023	0.47	YES
21	CPSF2	CPSF2	CPSF2	6566	0.022	0.48	YES
22	NXF1	NXF1	NXF1	6720	0.02	0.48	YES
23	CPSF1	CPSF1	CPSF1	6866	0.019	0.49	YES
24	NUP93	NUP93	NUP93	6933	0.018	0.5	YES
25	POM121	POM121	POM121	7291	0.013	0.49	NO
26	THOC4	THOC4	THOC4	7476	0.011	0.48	NO
27	NUP50	NUP50	NUP50	7874	0.0064	0.47	NO
28	NUP88	NUP88	NUP88	8053	0.0042	0.46	NO
29	EIF4E	EIF4E	EIF4E	9319	-0.012	0.4	NO
30	AAAS	AAAS	AAAS	9520	-0.015	0.4	NO
31	NUP62	NUP62	NUP62	10136	-0.024	0.38	NO
32	NUP188	NUP188	NUP188	11386	-0.043	0.34	NO
33	SEH1L	SEH1L	SEH1L	11644	-0.048	0.36	NO

Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM.

Figure S20. 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

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 FRUCTOSE AND MANNOSE METABOLISM	34	genes.ES.table	0.41	1.4	0.11	1	0.99	0.26	0.099	0.24	1	0.57
KEGG SPHINGOLIPID METABOLISM	37	genes.ES.table	0.4	1.4	0.12	1	1	0.27	0.086	0.25	1	0.57
KEGG RETINOL METABOLISM	52	genes.ES.table	0.61	1.5	0.033	1	0.98	0.38	0.06	0.36	0.83	0.44
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM	34	genes.ES.table	0.56	1.5	0.085	1	0.98	0.24	0.041	0.23	0.8	0.42
KEGG DRUG METABOLISM OTHER ENZYMES	42	genes.ES.table	0.53	1.4	0.094	1	0.99	0.29	0.041	0.28	1	0.6
BIOCARTA FAS PATHWAY	30	genes.ES.table	0.52	1.8	0.021	1	0.59	0.6	0.3	0.42	0.36	0.28
BIOCARTA HIVNEF PATHWAY	58	genes.ES.table	0.45	2	0.0084	0.86	0.25	0.52	0.3	0.36	0	0.15
BIOCARTA DEATH PATHWAY	33	genes.ES.table	0.39	1.6	0.053	1	0.92	0.42	0.18	0.35	0.63	0.36
BIOCARTA KERATINOCYTE PATHWAY	46	genes.ES.table	0.42	1.6	0.056	1	0.93	0.35	0.22	0.27	0.57	0.33
BIOCARTA PYK2 PATHWAY	28	genes.ES.table	0.38	1.6	0.05	1	0.9	0.46	0.28	0.33	0.72	0.39

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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	MAP3K5	MAP3K5	MAP3K5	593	0.18	0.034	YES
2	CASP7	CASP7	CASP7	634	0.17	0.096	YES
3	FAS	FAS	FAS	650	0.17	0.16	YES
4	BCL2	BCL2	BCL2	719	0.16	0.22	YES
5	BIRC3	BIRC3	BIRC3	842	0.15	0.26	YES
6	APAF1	APAF1	APAF1	1339	0.11	0.28	YES
7	MDM2	MDM2	MDM2	1490	0.1	0.31	YES
8	CASP3	CASP3	CASP3	1968	0.08	0.31	YES
9	RIPK1	RIPK1	RIPK1	2497	0.065	0.31	YES
10	CYCS	CYCS	CYCS	2807	0.059	0.31	YES
11	PSEN1	PSEN1	PSEN1	2859	0.058	0.33	YES
12	BIRC2	BIRC2	BIRC2	3180	0.052	0.33	YES
13	MAPK8	MAPK8	MAPK8	3213	0.051	0.35	YES
14	CASP8	CASP8	CASP8	3222	0.051	0.37	YES
15	LMNA	LMNA	LMNA	3308	0.05	0.38	YES
16	GSN	GSN	GSN	3323	0.05	0.4	YES
17	RB1	RB1	RB1	3575	0.045	0.4	YES
18	FASLG	FASLG	FASLG	3672	0.044	0.42	YES
19	BAG4	BAG4	BAG4	3798	0.042	0.42	YES
20	CASP9	CASP9	CASP9	3971	0.039	0.43	YES
21	CHUK	CHUK	CHUK	4162	0.036	0.43	YES
22	PARP1	PARP1	PARP1	4519	0.032	0.43	YES
23	PAK2	PAK2	PAK2	4799	0.028	0.42	YES
24	MAP3K1	MAP3K1	MAP3K1	5061	0.025	0.42	YES
25	LMNB1	LMNB1	LMNB1	5089	0.025	0.42	YES
26	NFKB1	NFKB1	NFKB1	5120	0.024	0.43	YES
27	CASP6	CASP6	CASP6	5142	0.024	0.44	YES
28	RASA1	RASA1	RASA1	5196	0.024	0.45	YES
29	MAP2K7	MAP2K7	MAP2K7	5274	0.023	0.45	YES
30	SPTAN1	SPTAN1	SPTAN1	5351	0.022	0.45	YES
31	PRKCD	PRKCD	PRKCD	6110	0.014	0.42	NO
32	CDK11B	CDK11B	CDK11B	6218	0.013	0.42	NO
33	CRADD	CRADD	CRADD	6549	0.0091	0.4	NO
34	CASP2	CASP2	CASP2	6711	0.0074	0.4	NO
35	XIAP	XIAP	XIAP	6897	0.0054	0.39	NO
36	NFKBIA	NFKBIA	NFKBIA	7073	0.0037	0.38	NO
37	ACTG1	ACTG1	ACTG1	7342	0.00066	0.36	NO
38	DAXX	DAXX	DAXX	7400	-0.000038	0.36	NO
39	DFFB	DFFB	DFFB	7466	-0.00087	0.36	NO
40	LMNB2	LMNB2	LMNB2	7748	-0.0042	0.34	NO
41	ARHGDIB	ARHGDIB	ARHGDIB	8116	-0.0084	0.33	NO
42	PTK2	PTK2	PTK2	8178	-0.0091	0.33	NO
43	TNFRSF1A	TNFRSF1A	TNFRSF1A	8181	-0.0091	0.33	NO
44	NUMA1	NUMA1	NUMA1	8626	-0.014	0.31	NO
45	TRAF2	TRAF2	TRAF2	8690	-0.015	0.31	NO
46	RELA	RELA	RELA	9236	-0.021	0.29	NO
47	PRKDC	PRKDC	PRKDC	9518	-0.024	0.28	NO
48	TRADD	TRADD	TRADD	9564	-0.025	0.29	NO
49	CDK11A	CDK11A	CDK11A	9649	-0.026	0.3	NO
50	DFFA	DFFA	DFFA	9752	-0.028	0.3	NO
51	TNFRSF1B	TNFRSF1B	TNFRSF1B	10356	-0.036	0.28	NO
52	PSEN2	PSEN2	PSEN2	10425	-0.036	0.29	NO
53	FADD	FADD	FADD	10439	-0.037	0.3	NO
54	MAP3K14	MAP3K14	MAP3K14	10440	-0.037	0.32	NO
55	CFLAR	CFLAR	CFLAR	10786	-0.042	0.31	NO
56	BID	BID	BID	11446	-0.054	0.3	NO
57	TNF	TNF	TNF	11841	-0.063	0.3	NO
58	TRAF1	TRAF1	TRAF1	13682	-0.12	0.24	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 FRUCTOSE AND MANNOSE METABOLISM.

Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FRUCTOSE AND MANNOSE 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 SPHINGOLIPID METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PTPN13	PTPN13	PTPN13	473	0.2	0.11	YES
2	CASP7	CASP7	CASP7	634	0.17	0.21	YES
3	FAS	FAS	FAS	650	0.17	0.32	YES
4	CASP10	CASP10	CASP10	1368	0.11	0.35	YES
5	MAP2K4	MAP2K4	MAP2K4	1923	0.082	0.38	YES
6	CASP3	CASP3	CASP3	1968	0.08	0.43	YES
7	MAPK8	MAPK8	MAPK8	3213	0.051	0.39	YES
8	CASP8	CASP8	CASP8	3222	0.051	0.42	YES
9	LMNA	LMNA	LMNA	3308	0.05	0.45	YES
10	RB1	RB1	RB1	3575	0.045	0.47	YES
11	FASLG	FASLG	FASLG	3672	0.044	0.49	YES
12	PARP1	PARP1	PARP1	4519	0.032	0.47	YES
13	PAK1	PAK1	PAK1	4757	0.029	0.47	YES
14	PAK2	PAK2	PAK2	4799	0.028	0.49	YES
15	MAP3K1	MAP3K1	MAP3K1	5061	0.025	0.49	YES
16	LMNB1	LMNB1	LMNB1	5089	0.025	0.51	YES
17	CASP6	CASP6	CASP6	5142	0.024	0.52	YES
18	SPTAN1	SPTAN1	SPTAN1	5351	0.022	0.52	YES
19	DAXX	DAXX	DAXX	7400	-0.000038	0.41	NO
20	DFFB	DFFB	DFFB	7466	-0.00087	0.41	NO
21	LMNB2	LMNB2	LMNB2	7748	-0.0042	0.39	NO
22	ARHGDIB	ARHGDIB	ARHGDIB	8116	-0.0084	0.38	NO
23	MAP3K7	MAP3K7	MAP3K7	8960	-0.018	0.34	NO
24	JUN	JUN	JUN	9008	-0.018	0.35	NO
25	FAF1	FAF1	FAF1	9442	-0.023	0.34	NO
26	PRKDC	PRKDC	PRKDC	9518	-0.024	0.36	NO
27	DFFA	DFFA	DFFA	9752	-0.028	0.36	NO
28	FADD	FADD	FADD	10439	-0.037	0.35	NO
29	CFLAR	CFLAR	CFLAR	10786	-0.042	0.36	NO
30	RIPK2	RIPK2	RIPK2	12146	-0.07	0.33	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 SPHINGOLIPID METABOLISM.

Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPHINGOLIPID 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 RETINOL METABOLISM

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	TP53AIP1	TP53AIP1	TP53AIP1	565	0.18	0.057	YES
2	KAT2B	KAT2B	KAT2B	804	0.15	0.12	YES
3	MDM2	MDM2	MDM2	1490	0.1	0.13	YES
4	HIPK2	HIPK2	HIPK2	1674	0.092	0.16	YES
5	CSNK1G3	CSNK1G3	CSNK1G3	2070	0.077	0.18	YES
6	CCNG1	CCNG1	CCNG1	2119	0.076	0.22	YES
7	DYRK2	DYRK2	DYRK2	2274	0.071	0.24	YES
8	CSNK1G1	CSNK1G1	CSNK1G1	2468	0.066	0.26	YES
9	PPM1D	PPM1D	PPM1D	2952	0.056	0.26	YES
10	MAPK8	MAPK8	MAPK8	3213	0.051	0.28	YES
11	SETD7	SETD7	SETD7	3363	0.049	0.29	YES
12	CSNK1A1	CSNK1A1	CSNK1A1	3371	0.049	0.31	YES
13	CCNA2	CCNA2	CCNA2	3863	0.041	0.31	YES
14	SETD8	SETD8	SETD8	3990	0.039	0.32	YES
15	EP300	EP300	EP300	4065	0.038	0.33	YES
16	TP53	TP53	TP53	4326	0.034	0.34	YES
17	PPP2R4	PPP2R4	PPP2R4	4583	0.031	0.34	YES
18	UBE2D1	UBE2D1	UBE2D1	4784	0.029	0.34	YES
19	PPP1R13L	PPP1R13L	PPP1R13L	5002	0.026	0.34	YES
20	MAPK9	MAPK9	MAPK9	5242	0.023	0.34	YES
21	FBXO11	FBXO11	FBXO11	5383	0.021	0.34	YES
22	PRMT5	PRMT5	PRMT5	5639	0.019	0.34	YES
23	AKT1	AKT1	AKT1	5646	0.019	0.35	YES
24	RPL11	RPL11	RPL11	5675	0.018	0.35	YES
25	PPP2CA	PPP2CA	PPP2CA	5827	0.017	0.35	NO
26	PRKCD	PRKCD	PRKCD	6110	0.014	0.34	NO
27	RPL5	RPL5	RPL5	6228	0.013	0.34	NO
28	CDK2	CDK2	CDK2	6243	0.012	0.35	NO
29	RCHY1	RCHY1	RCHY1	6337	0.012	0.35	NO
30	SMYD2	SMYD2	SMYD2	6519	0.0094	0.34	NO
31	RFWD2	RFWD2	RFWD2	6538	0.0092	0.35	NO
32	CHEK2	CHEK2	CHEK2	6763	0.0069	0.34	NO
33	ATM	ATM	ATM	7159	0.0027	0.32	NO
34	RASSF1	RASSF1	RASSF1	7160	0.0027	0.32	NO
35	YY1	YY1	YY1	7227	0.0019	0.32	NO
36	GSK3B	GSK3B	GSK3B	7277	0.0014	0.32	NO
37	DAXX	DAXX	DAXX	7400	-0.000038	0.31	NO
38	PIN1	PIN1	PIN1	8183	-0.0092	0.27	NO
39	CSNK1D	CSNK1D	CSNK1D	8193	-0.0092	0.27	NO
40	CREBBP	CREBBP	CREBBP	8207	-0.0094	0.28	NO
41	ATR	ATR	ATR	8242	-0.0098	0.28	NO
42	CSNK1E	CSNK1E	CSNK1E	8317	-0.011	0.28	NO
43	USP7	USP7	USP7	8403	-0.012	0.28	NO
44	CSNK1G2	CSNK1G2	CSNK1G2	8501	-0.012	0.28	NO
45	KAT5	KAT5	KAT5	8514	-0.013	0.29	NO
46	ABL1	ABL1	ABL1	8638	-0.014	0.29	NO
47	CHEK1	CHEK1	CHEK1	8769	-0.016	0.29	NO
48	HUWE1	HUWE1	HUWE1	8847	-0.016	0.29	NO
49	NEDD8	NEDD8	NEDD8	8900	-0.017	0.3	NO
50	MDM4	MDM4	MDM4	8920	-0.017	0.31	NO
51	TTC5	TTC5	TTC5	9378	-0.022	0.29	NO
52	RPL23	RPL23	RPL23	9394	-0.023	0.3	NO
53	SKP2	SKP2	SKP2	9828	-0.029	0.29	NO
54	MAPK14	MAPK14	MAPK14	10203	-0.034	0.29	NO
55	TRIM28	TRIM28	TRIM28	10288	-0.035	0.3	NO
56	E4F1	E4F1	E4F1	11440	-0.054	0.26	NO
57	CSE1L	CSE1L	CSE1L	11895	-0.064	0.27	NO
58	CDKN2A	CDKN2A	CDKN2A	14423	-0.15	0.2	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 RETINOL METABOLISM.

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RETINOL 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 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	MAP2K4	MAP2K4	MAP2K4	1923	0.082	-0.017	YES
2	CASP3	CASP3	CASP3	1968	0.08	0.068	YES
3	RIPK1	RIPK1	RIPK1	2497	0.065	0.11	YES
4	MAPK8	MAPK8	MAPK8	3213	0.051	0.13	YES
5	CASP8	CASP8	CASP8	3222	0.051	0.18	YES
6	LMNA	LMNA	LMNA	3308	0.05	0.23	YES
7	RB1	RB1	RB1	3575	0.045	0.27	YES
8	BAG4	BAG4	BAG4	3798	0.042	0.3	YES
9	PARP1	PARP1	PARP1	4519	0.032	0.3	YES
10	PAK1	PAK1	PAK1	4757	0.029	0.31	YES
11	PAK2	PAK2	PAK2	4799	0.028	0.34	YES
12	MAP3K1	MAP3K1	MAP3K1	5061	0.025	0.36	YES
13	LMNB1	LMNB1	LMNB1	5089	0.025	0.38	YES
14	SPTAN1	SPTAN1	SPTAN1	5351	0.022	0.39	YES
15	MADD	MADD	MADD	5452	0.02	0.41	YES
16	CRADD	CRADD	CRADD	6549	0.0091	0.36	NO
17	CASP2	CASP2	CASP2	6711	0.0074	0.36	NO
18	DFFB	DFFB	DFFB	7466	-0.00087	0.31	NO
19	LMNB2	LMNB2	LMNB2	7748	-0.0042	0.3	NO
20	ARHGDIB	ARHGDIB	ARHGDIB	8116	-0.0084	0.29	NO
21	TNFRSF1A	TNFRSF1A	TNFRSF1A	8181	-0.0091	0.3	NO
22	TRAF2	TRAF2	TRAF2	8690	-0.015	0.29	NO
23	MAP3K7	MAP3K7	MAP3K7	8960	-0.018	0.29	NO
24	JUN	JUN	JUN	9008	-0.018	0.31	NO
25	PRKDC	PRKDC	PRKDC	9518	-0.024	0.31	NO
26	TRADD	TRADD	TRADD	9564	-0.025	0.33	NO
27	DFFA	DFFA	DFFA	9752	-0.028	0.35	NO
28	FADD	FADD	FADD	10439	-0.037	0.35	NO
29	TNF	TNF	TNF	11841	-0.063	0.34	NO

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

Figure S28. 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 DRUG METABOLISM OTHER ENZYMES

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	SPDEF	SPDEF	SPDEF	9	0.51	0.14	YES
2	KLK3	KLK3	KLK3	107	0.35	0.23	YES
3	PDE9A	PDE9A	PDE9A	562	0.18	0.26	YES
4	KAT2B	KAT2B	KAT2B	804	0.15	0.28	YES
5	HOXB13	HOXB13	HOXB13	983	0.13	0.31	YES
6	MAP2K6	MAP2K6	MAP2K6	1145	0.12	0.34	YES
7	REL	REL	REL	1341	0.11	0.36	YES
8	MDM2	MDM2	MDM2	1490	0.1	0.38	YES
9	KLK2	KLK2	KLK2	1519	0.099	0.4	YES
10	TMPRSS2	TMPRSS2	TMPRSS2	1738	0.089	0.42	YES
11	MAP2K4	MAP2K4	MAP2K4	1923	0.082	0.43	YES
12	GATA2	GATA2	GATA2	2466	0.066	0.42	YES
13	SMARCA2	SMARCA2	SMARCA2	2879	0.057	0.41	YES
14	SIRT1	SIRT1	SIRT1	2924	0.056	0.42	YES
15	NR2C1	NR2C1	NR2C1	3059	0.054	0.43	YES
16	MAPK8	MAPK8	MAPK8	3213	0.051	0.44	YES
17	HDAC1	HDAC1	HDAC1	3304	0.05	0.44	YES
18	NCOA1	NCOA1	NCOA1	3671	0.044	0.44	NO
19	EP300	EP300	EP300	4065	0.038	0.42	NO
20	APPBP2	APPBP2	APPBP2	4229	0.036	0.42	NO
21	HSP90AA1	HSP90AA1	HSP90AA1	4634	0.03	0.41	NO
22	NCOA2	NCOA2	NCOA2	5399	0.021	0.38	NO
23	RXRA	RXRA	RXRA	6170	0.013	0.34	NO
24	RCHY1	RCHY1	RCHY1	6337	0.012	0.33	NO
25	SENP1	SENP1	SENP1	6535	0.0092	0.32	NO
26	NR2C2	NR2C2	NR2C2	6576	0.0088	0.32	NO
27	GSK3B	GSK3B	GSK3B	7277	0.0014	0.28	NO
28	SMARCE1	SMARCE1	SMARCE1	7606	-0.0026	0.26	NO
29	SMARCC1	SMARCC1	SMARCC1	7993	-0.007	0.25	NO
30	GNB2L1	GNB2L1	GNB2L1	8133	-0.0086	0.24	NO
31	CREBBP	CREBBP	CREBBP	8207	-0.0094	0.24	NO
32	RXRB	RXRB	RXRB	8470	-0.012	0.23	NO
33	KAT5	KAT5	KAT5	8514	-0.013	0.23	NO
34	DNAJA1	DNAJA1	DNAJA1	8545	-0.013	0.23	NO
35	EGR1	EGR1	EGR1	8806	-0.016	0.22	NO
36	TRIM24	TRIM24	TRIM24	8820	-0.016	0.22	NO
37	POU2F1	POU2F1	POU2F1	8991	-0.018	0.22	NO
38	JUN	JUN	JUN	9008	-0.018	0.22	NO
39	SRC	SRC	SRC	9194	-0.021	0.22	NO
40	HDAC7	HDAC7	HDAC7	9197	-0.021	0.22	NO
41	MAPK14	MAPK14	MAPK14	10203	-0.034	0.18	NO
42	CARM1	CARM1	CARM1	11100	-0.047	0.14	NO
43	EHMT2	EHMT2	EHMT2	11424	-0.054	0.14	NO
44	ZMIZ2	ZMIZ2	ZMIZ2	11453	-0.054	0.15	NO
45	CEBPA	CEBPA	CEBPA	11523	-0.056	0.16	NO
46	FOXO1	FOXO1	FOXO1	12600	-0.082	0.13	NO
47	AR	AR	AR	12641	-0.083	0.15	NO
48	PKN1	PKN1	PKN1	12800	-0.088	0.16	NO
49	NR3C1	NR3C1	NR3C1	13422	-0.11	0.16	NO
50	NR0B1	NR0B1	NR0B1	14733	-0.16	0.13	NO
51	RXRG	RXRG	RXRG	15167	-0.19	0.16	NO

Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG DRUG METABOLISM OTHER ENZYMES.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM OTHER ENZYMES, 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 FAS PATHWAY

Table S16. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	MAP3K5	MAP3K5	MAP3K5	593	0.18	0.058	YES
2	CASP7	CASP7	CASP7	634	0.17	0.14	YES
3	FAS	FAS	FAS	650	0.17	0.23	YES
4	BCL2	BCL2	BCL2	719	0.16	0.31	YES
5	BIRC3	BIRC3	BIRC3	842	0.15	0.38	YES
6	APAF1	APAF1	APAF1	1339	0.11	0.4	YES
7	CASP3	CASP3	CASP3	1968	0.08	0.41	YES
8	RIPK1	RIPK1	RIPK1	2497	0.065	0.42	YES
9	CYCS	CYCS	CYCS	2807	0.059	0.43	YES
10	MAPK8	MAPK8	MAPK8	3213	0.051	0.43	YES
11	CASP8	CASP8	CASP8	3222	0.051	0.46	YES
12	FASLG	FASLG	FASLG	3672	0.044	0.46	YES
13	BAG4	BAG4	BAG4	3798	0.042	0.47	YES
14	CASP9	CASP9	CASP9	3971	0.039	0.48	YES
15	CHUK	CHUK	CHUK	4162	0.036	0.49	YES
16	NFKB1	NFKB1	NFKB1	5120	0.024	0.45	NO
17	CASP6	CASP6	CASP6	5142	0.024	0.46	NO
18	MAP2K7	MAP2K7	MAP2K7	5274	0.023	0.47	NO
19	CRADD	CRADD	CRADD	6549	0.0091	0.4	NO
20	CASP2	CASP2	CASP2	6711	0.0074	0.4	NO
21	NFKBIA	NFKBIA	NFKBIA	7073	0.0037	0.38	NO
22	CD247	CD247	CD247	7366	0.00035	0.36	NO
23	DAXX	DAXX	DAXX	7400	-0.000038	0.36	NO
24	DFFB	DFFB	DFFB	7466	-0.00087	0.36	NO
25	TNFRSF1A	TNFRSF1A	TNFRSF1A	8181	-0.0091	0.32	NO
26	TRAF2	TRAF2	TRAF2	8690	-0.015	0.3	NO
27	RELA	RELA	RELA	9236	-0.021	0.28	NO
28	TRADD	TRADD	TRADD	9564	-0.025	0.28	NO
29	DFFA	DFFA	DFFA	9752	-0.028	0.28	NO
30	FADD	FADD	FADD	10439	-0.037	0.26	NO
31	MAP3K14	MAP3K14	MAP3K14	10440	-0.037	0.28	NO
32	CFLAR	CFLAR	CFLAR	10786	-0.042	0.28	NO
33	BID	BID	BID	11446	-0.054	0.27	NO
34	TNF	TNF	TNF	11841	-0.063	0.28	NO
35	TRAF1	TRAF1	TRAF1	13682	-0.12	0.24	NO

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

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FAS 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 HIVNEF PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GNAQ	GNAQ	GNAQ	1144	0.12	0.048	YES
2	PRKCA	PRKCA	PRKCA	1411	0.1	0.13	YES
3	MAP2K4	MAP2K4	MAP2K4	1923	0.082	0.18	YES
4	PTK2B	PTK2B	PTK2B	2191	0.073	0.23	YES
5	CALM2	CALM2	CALM2	3159	0.052	0.22	YES
6	MAP2K1	MAP2K1	MAP2K1	3169	0.052	0.27	YES
7	MAPK8	MAPK8	MAPK8	3213	0.051	0.32	YES
8	MAPK3	MAPK3	MAPK3	3869	0.041	0.32	YES
9	CALM3	CALM3	CALM3	4230	0.036	0.33	YES
10	SOS1	SOS1	SOS1	4619	0.031	0.34	YES
11	PAK1	PAK1	PAK1	4757	0.029	0.35	YES
12	MAP2K3	MAP2K3	MAP2K3	5038	0.025	0.36	YES
13	MAP3K1	MAP3K1	MAP3K1	5061	0.025	0.38	YES
14	MAPK1	MAPK1	MAPK1	5677	0.018	0.37	NO
15	RAC1	RAC1	RAC1	5917	0.016	0.37	NO
16	RAF1	RAF1	RAF1	6585	0.0087	0.34	NO
17	CALM1	CALM1	CALM1	6689	0.0076	0.34	NO
18	GRB2	GRB2	GRB2	7101	0.0034	0.32	NO
19	BCAR1	BCAR1	BCAR1	7207	0.0021	0.32	NO
20	CRKL	CRKL	CRKL	7288	0.0012	0.31	NO
21	MAP2K2	MAP2K2	MAP2K2	7983	-0.0069	0.28	NO
22	JUN	JUN	JUN	9008	-0.018	0.24	NO
23	SHC1	SHC1	SHC1	9015	-0.018	0.26	NO
24	SRC	SRC	SRC	9194	-0.021	0.26	NO
25	MAPK14	MAPK14	MAPK14	10203	-0.034	0.24	NO
26	PRKCB	PRKCB	PRKCB	10831	-0.043	0.24	NO
27	HRAS	HRAS	HRAS	11649	-0.059	0.25	NO
28	PLCG1	PLCG1	PLCG1	13525	-0.11	0.25	NO

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

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

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PLA2G4A	PLA2G4A	PLA2G4A	136	0.33	0.1	YES
2	PLA2G4D	PLA2G4D	PLA2G4D	139	0.33	0.21	YES
3	PLA2G2A	PLA2G2A	PLA2G2A	187	0.3	0.31	YES
4	PLA2G10	PLA2G10	PLA2G10	233	0.27	0.4	YES
5	AGPAT9	AGPAT9	AGPAT9	298	0.24	0.47	YES
6	LPCAT4	LPCAT4	LPCAT4	875	0.14	0.49	YES
7	PLD1	PLD1	PLD1	900	0.14	0.53	YES
8	AGPAT4	AGPAT4	AGPAT4	979	0.13	0.57	YES
9	PLA2G2F	PLA2G2F	PLA2G2F	1343	0.11	0.59	YES
10	GPD1L	GPD1L	GPD1L	2548	0.064	0.54	NO
11	LPCAT1	LPCAT1	LPCAT1	2693	0.061	0.56	NO
12	AGPAT5	AGPAT5	AGPAT5	2738	0.06	0.57	NO
13	PLA2G1B	PLA2G1B	PLA2G1B	2978	0.056	0.58	NO
14	GNPAT	GNPAT	GNPAT	3681	0.044	0.55	NO
15	PLD2	PLD2	PLD2	4066	0.038	0.55	NO
16	GPD1	GPD1	GPD1	4807	0.028	0.51	NO
17	PLA2G12A	PLA2G12A	PLA2G12A	6002	0.015	0.45	NO
18	AGPAT2	AGPAT2	AGPAT2	6723	0.0073	0.41	NO
19	AGPAT6	AGPAT6	AGPAT6	7059	0.0039	0.4	NO
20	GPAM	GPAM	GPAM	7385	0.00016	0.38	NO
21	LCLAT1	LCLAT1	LCLAT1	7399	-0.000034	0.38	NO
22	AGPAT3	AGPAT3	AGPAT3	8108	-0.0084	0.34	NO
23	AGPAT1	AGPAT1	AGPAT1	9528	-0.025	0.27	NO
24	PLA2G2D	PLA2G2D	PLA2G2D	12316	-0.074	0.14	NO
25	GPAT2	GPAT2	GPAT2	14269	-0.14	0.079	NO
26	PLA2G5	PLA2G5	PLA2G5	17641	-0.39	0.021	NO

Figure S35. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA DEATH PATHWAY.

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

genes ES table in pathway: BIOCARTA KERATINOCYTE PATHWAY

Table 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	CASP7	CASP7	CASP7	634	0.17	0.042	YES
2	BCL2	BCL2	BCL2	719	0.16	0.11	YES
3	BIRC3	BIRC3	BIRC3	842	0.15	0.17	YES
4	APAF1	APAF1	APAF1	1339	0.11	0.19	YES
5	CASP10	CASP10	CASP10	1368	0.11	0.24	YES
6	TNFSF10	TNFSF10	TNFSF10	1522	0.098	0.27	YES
7	CASP3	CASP3	CASP3	1968	0.08	0.28	YES
8	RIPK1	RIPK1	RIPK1	2497	0.065	0.29	YES
9	TNFRSF10A	TNFRSF10A	TNFRSF10A	2578	0.063	0.31	YES
10	CYCS	CYCS	CYCS	2807	0.059	0.32	YES
11	BIRC2	BIRC2	BIRC2	3180	0.052	0.33	YES
12	CASP8	CASP8	CASP8	3222	0.051	0.35	YES
13	TNFRSF10B	TNFRSF10B	TNFRSF10B	3292	0.05	0.37	YES
14	LMNA	LMNA	LMNA	3308	0.05	0.39	YES
15	CASP9	CASP9	CASP9	3971	0.039	0.37	NO
16	CHUK	CHUK	CHUK	4162	0.036	0.38	NO
17	NFKB1	NFKB1	NFKB1	5120	0.024	0.33	NO
18	CASP6	CASP6	CASP6	5142	0.024	0.34	NO
19	SPTAN1	SPTAN1	SPTAN1	5351	0.022	0.34	NO
20	XIAP	XIAP	XIAP	6897	0.0054	0.26	NO
21	NFKBIA	NFKBIA	NFKBIA	7073	0.0037	0.25	NO
22	DFFB	DFFB	DFFB	7466	-0.00087	0.23	NO
23	TRAF2	TRAF2	TRAF2	8690	-0.015	0.17	NO
24	RELA	RELA	RELA	9236	-0.021	0.15	NO
25	TRADD	TRADD	TRADD	9564	-0.025	0.14	NO
26	DFFA	DFFA	DFFA	9752	-0.028	0.14	NO
27	FADD	FADD	FADD	10439	-0.037	0.12	NO
28	MAP3K14	MAP3K14	MAP3K14	10440	-0.037	0.14	NO
29	CFLAR	CFLAR	CFLAR	10786	-0.042	0.14	NO
30	BID	BID	BID	11446	-0.054	0.12	NO
31	TNFSF12	TNFSF12	TNFSF12	13303	-0.1	0.068	NO
32	TNFRSF25	TNFRSF25	TNFRSF25	15513	-0.2	0.037	NO
33	GAS2	GAS2	GAS2	15927	-0.22	0.12	NO

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

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

genes ES table in pathway: BIOCARTA PYK2 PATHWAY

Table 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	C4BPB	C4BPB	C4BPB	19	0.46	0.096	YES
2	TFF1	TFF1	TFF1	38	0.43	0.19	YES
3	CYP2C18	CYP2C18	CYP2C18	78	0.37	0.26	YES
4	KLK3	KLK3	KLK3	107	0.35	0.33	YES
5	FOXA1	FOXA1	FOXA1	175	0.3	0.39	YES
6	SERPINA1	SERPINA1	SERPINA1	261	0.26	0.44	YES
7	SFTPA2	SFTPA2	SFTPA2	552	0.18	0.46	YES
8	FOXA3	FOXA3	FOXA3	564	0.18	0.5	YES
9	FOS	FOS	FOS	760	0.16	0.52	YES
10	GCG	GCG	GCG	1034	0.13	0.54	YES
11	XBP1	XBP1	XBP1	1689	0.091	0.52	NO
12	NKX3-1	NKX3-1	NKX3-1	1939	0.082	0.52	NO
13	NRIP1	NRIP1	NRIP1	2388	0.068	0.51	NO
14	ATP5J	ATP5J	ATP5J	2961	0.056	0.49	NO
15	SP1	SP1	SP1	3255	0.051	0.48	NO
16	NFIB	NFIB	NFIB	3583	0.045	0.48	NO
17	NFIA	NFIA	NFIA	3723	0.043	0.48	NO
18	SOD1	SOD1	SOD1	3953	0.04	0.47	NO
19	EP300	EP300	EP300	4065	0.038	0.48	NO
20	NDUFV3	NDUFV3	NDUFV3	4490	0.032	0.46	NO
21	BRCA1	BRCA1	BRCA1	4795	0.029	0.45	NO
22	AP1B1	AP1B1	AP1B1	7371	0.00032	0.3	NO
23	VTN	VTN	VTN	7648	-0.0031	0.29	NO
24	CDKN1B	CDKN1B	CDKN1B	7705	-0.0038	0.29	NO
25	NFIC	NFIC	NFIC	7989	-0.007	0.27	NO
26	FOXA2	FOXA2	FOXA2	8110	-0.0084	0.27	NO
27	CREBBP	CREBBP	CREBBP	8207	-0.0094	0.26	NO
28	POU2F1	POU2F1	POU2F1	8991	-0.018	0.22	NO
29	JUN	JUN	JUN	9008	-0.018	0.23	NO
30	NR2F2	NR2F2	NR2F2	9111	-0.02	0.23	NO
31	PRDM15	PRDM15	PRDM15	9985	-0.031	0.18	NO
32	NCOA3	NCOA3	NCOA3	10776	-0.042	0.15	NO
33	PISD	PISD	PISD	10971	-0.045	0.15	NO
34	DSCAM	DSCAM	DSCAM	11181	-0.049	0.15	NO
35	AR	AR	AR	12641	-0.083	0.083	NO
36	SHH	SHH	SHH	12864	-0.09	0.09	NO
37	SFTPA1	SFTPA1	SFTPA1	14029	-0.13	0.052	NO
38	ESR1	ESR1	ESR1	14104	-0.13	0.076	NO
39	COL18A1	COL18A1	COL18A1	14663	-0.16	0.078	NO
40	SFTPD	SFTPD	SFTPD	14670	-0.16	0.11	NO
41	APOB	APOB	APOB	14974	-0.18	0.13	NO
42	CEBPB	CEBPB	CEBPB	15140	-0.18	0.16	NO

Figure S39. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PYK2 PATHWAY.

Figure S40. 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

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 TRYPTOPHAN METABOLISM	37	genes.ES.table	0.5	1.5	0.048	0.14	0.98	0.24	0.13	0.21	0.092	0
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	43	genes.ES.table	0.39	1.5	0.086	0.14	0.98	0.07	0.041	0.067	0.092	0
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE	25	genes.ES.table	0.52	1.5	0.048	0.14	0.98	0.6	0.36	0.39	0.091	0
KEGG INOSITOL PHOSPHATE METABOLISM	52	genes.ES.table	0.35	1.3	0.16	0.2	1	0.27	0.25	0.2	0.16	0
KEGG ABC TRANSPORTERS	43	genes.ES.table	0.47	1.3	0.13	0.22	1	0.21	0.14	0.18	0.18	0
KEGG MAPK SIGNALING PATHWAY	250	genes.ES.table	0.48	1.7	0.002	0.11	0.78	0.32	0.24	0.25	0.04	0.012
KEGG ERBB SIGNALING PATHWAY	86	genes.ES.table	0.4	1.5	0.043	0.13	0.97	0.13	0.11	0.12	0.074	0
KEGG CALCIUM SIGNALING PATHWAY	164	genes.ES.table	0.59	1.6	0.0039	0.11	0.88	0.44	0.21	0.36	0.047	0.004
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION	236	genes.ES.table	0.59	1.5	0.053	0.14	0.98	0.51	0.21	0.41	0.089	0
KEGG CHEMOKINE SIGNALING PATHWAY	182	genes.ES.table	0.57	1.6	0.031	0.12	0.94	0.41	0.2	0.33	0.061	0.001

genes ES table in pathway: KEGG TRYPTOPHAN METABOLISM

Table S21. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PDE1B	PDE1B	PDE1B	237	0.62	0.017	YES
2	NGFR	NGFR	NGFR	371	0.57	0.038	YES
3	AKT3	AKT3	AKT3	484	0.54	0.058	YES
4	TIAM1	TIAM1	TIAM1	502	0.53	0.083	YES
5	PDE1A	PDE1A	PDE1A	540	0.53	0.11	YES
6	ADCY2	ADCY2	ADCY2	718	0.49	0.12	YES
7	ADCYAP1	ADCYAP1	ADCYAP1	802	0.47	0.14	YES
8	MAPK11	MAPK11	MAPK11	1156	0.41	0.14	YES
9	PCSK5	PCSK5	PCSK5	1187	0.41	0.16	YES
10	ARHGEF6	ARHGEF6	ARHGEF6	1205	0.41	0.18	YES
11	NGF	NGF	NGF	1279	0.4	0.19	YES
12	MEF2C	MEF2C	MEF2C	1397	0.38	0.2	YES
13	NTRK1	NTRK1	NTRK1	1431	0.38	0.22	YES
14	RASGRF2	RASGRF2	RASGRF2	1518	0.36	0.23	YES
15	PRKAR2B	PRKAR2B	PRKAR2B	1688	0.34	0.24	YES
16	ARHGEF17	ARHGEF17	ARHGEF17	1879	0.32	0.25	YES
17	SORCS3	SORCS3	SORCS3	1883	0.32	0.26	YES
18	FGD2	FGD2	FGD2	1927	0.32	0.28	YES
19	CAMK4	CAMK4	CAMK4	2215	0.28	0.27	YES
20	ADCY5	ADCY5	ADCY5	2294	0.28	0.28	YES
21	VAV1	VAV1	VAV1	2478	0.26	0.28	YES
22	ARHGEF4	ARHGEF4	ARHGEF4	2498	0.26	0.3	YES
23	NTRK2	NTRK2	NTRK2	2610	0.24	0.3	YES
24	ADORA2A	ADORA2A	ADORA2A	2629	0.24	0.31	YES
25	ADCY1	ADCY1	ADCY1	2677	0.24	0.32	YES
26	MCF2	MCF2	MCF2	2682	0.24	0.33	YES
27	DNM1	DNM1	DNM1	2723	0.24	0.34	YES
28	PLEKHG2	PLEKHG2	PLEKHG2	2732	0.24	0.35	YES
29	TIAM2	TIAM2	TIAM2	2738	0.23	0.36	YES
30	ADCY4	ADCY4	ADCY4	2745	0.23	0.38	YES
31	MAPK12	MAPK12	MAPK12	2962	0.21	0.37	YES
32	RPS6KA2	RPS6KA2	RPS6KA2	3130	0.2	0.37	YES
33	PREX1	PREX1	PREX1	3186	0.19	0.38	YES
34	IRS1	IRS1	IRS1	3264	0.19	0.38	YES
35	ADCY7	ADCY7	ADCY7	3412	0.18	0.39	YES
36	DUSP4	DUSP4	DUSP4	3517	0.17	0.39	YES
37	PIK3CA	PIK3CA	PIK3CA	3525	0.17	0.4	YES
38	FOXO1	FOXO1	FOXO1	3578	0.16	0.4	YES
39	ITSN1	ITSN1	ITSN1	3601	0.16	0.41	YES
40	ITPR2	ITPR2	ITPR2	3728	0.15	0.41	YES
41	MEF2A	MEF2A	MEF2A	3872	0.14	0.41	YES
42	AKAP13	AKAP13	AKAP13	3931	0.14	0.41	YES
43	RICTOR	RICTOR	RICTOR	4066	0.13	0.41	YES
44	SHC2	SHC2	SHC2	4194	0.13	0.41	YES
45	LINGO1	LINGO1	LINGO1	4284	0.12	0.41	YES
46	KIDINS220	KIDINS220	KIDINS220	4340	0.12	0.41	YES
47	BCL2L11	BCL2L11	BCL2L11	4344	0.12	0.42	YES
48	ARHGAP4	ARHGAP4	ARHGAP4	4458	0.12	0.42	YES
49	FGD1	FGD1	FGD1	4625	0.11	0.42	YES
50	ADCY9	ADCY9	ADCY9	4694	0.11	0.42	YES
51	ARHGEF3	ARHGEF3	ARHGEF3	4763	0.1	0.42	YES
52	SOS1	SOS1	SOS1	4910	0.1	0.41	YES
53	APH1B	APH1B	APH1B	4929	0.099	0.42	YES
54	PRKAR1A	PRKAR1A	PRKAR1A	4962	0.098	0.42	YES
55	CREB1	CREB1	CREB1	5063	0.094	0.42	YES
56	DUSP7	DUSP7	DUSP7	5087	0.093	0.42	YES
57	NGFRAP1	NGFRAP1	NGFRAP1	5101	0.093	0.43	YES
58	TRIO	TRIO	TRIO	5170	0.091	0.43	YES
59	MAG	MAG	MAG	5200	0.09	0.43	YES
60	RAPGEF1	RAPGEF1	RAPGEF1	5233	0.089	0.43	YES
61	ARHGEF12	ARHGEF12	ARHGEF12	5365	0.086	0.43	NO
62	FRS2	FRS2	FRS2	5411	0.084	0.43	NO
63	FOXO4	FOXO4	FOXO4	5521	0.081	0.43	NO
64	ADAM17	ADAM17	ADAM17	5608	0.079	0.43	NO
65	SOS2	SOS2	SOS2	5721	0.077	0.43	NO
66	RAP1A	RAP1A	RAP1A	5730	0.076	0.43	NO
67	PIK3R1	PIK3R1	PIK3R1	5888	0.072	0.42	NO
68	ARHGEF2	ARHGEF2	ARHGEF2	6092	0.068	0.42	NO
69	NFKBIA	NFKBIA	NFKBIA	6140	0.067	0.42	NO
70	RIT1	RIT1	RIT1	6188	0.066	0.42	NO
71	ARHGEF1	ARHGEF1	ARHGEF1	6266	0.064	0.42	NO
72	PRKCG	PRKCG	PRKCG	6283	0.064	0.42	NO
73	SHC1	SHC1	SHC1	6316	0.063	0.42	NO
74	PTEN	PTEN	PTEN	6334	0.063	0.42	NO
75	KRAS	KRAS	KRAS	6494	0.059	0.42	NO
76	FGD3	FGD3	FGD3	6530	0.058	0.42	NO
77	DUSP3	DUSP3	DUSP3	6674	0.056	0.41	NO
78	MTOR	MTOR	MTOR	6708	0.055	0.41	NO
79	BRAF	BRAF	BRAF	6758	0.054	0.41	NO
80	PRKACA	PRKACA	PRKACA	6931	0.05	0.4	NO
81	SH3GL2	SH3GL2	SH3GL2	6960	0.05	0.4	NO
82	MAPKAPK2	MAPKAPK2	MAPKAPK2	7018	0.049	0.4	NO
83	NET1	NET1	NET1	7062	0.048	0.4	NO
84	MAP2K1	MAP2K1	MAP2K1	7113	0.047	0.4	NO
85	ATF1	ATF1	ATF1	7144	0.046	0.4	NO
86	GRB2	GRB2	GRB2	7156	0.046	0.41	NO
87	ECT2	ECT2	ECT2	7191	0.046	0.41	NO
88	RPS27A	RPS27A	RPS27A	7218	0.045	0.41	NO
89	FGD4	FGD4	FGD4	7290	0.044	0.4	NO
90	FURIN	FURIN	FURIN	7320	0.043	0.41	NO
91	PRKCI	PRKCI	PRKCI	7363	0.043	0.41	NO
92	RIPK2	RIPK2	RIPK2	7422	0.042	0.4	NO
93	TRAF6	TRAF6	TRAF6	7505	0.04	0.4	NO
94	MAPK7	MAPK7	MAPK7	7534	0.04	0.4	NO
95	PRKCE	PRKCE	PRKCE	7546	0.04	0.4	NO
96	CHUK	CHUK	CHUK	7576	0.039	0.4	NO
97	RALB	RALB	RALB	7596	0.039	0.4	NO
98	PIK3CB	PIK3CB	PIK3CB	7625	0.038	0.4	NO
99	STAT3	STAT3	STAT3	7644	0.038	0.41	NO
100	PLCG1	PLCG1	PLCG1	7777	0.036	0.4	NO
101	CDKN1B	CDKN1B	CDKN1B	8045	0.032	0.39	NO
102	ARHGEF18	ARHGEF18	ARHGEF18	8064	0.032	0.39	NO
103	OMG	OMG	OMG	8117	0.031	0.39	NO
104	MAPK8	MAPK8	MAPK8	8118	0.031	0.39	NO
105	RALGDS	RALGDS	RALGDS	8169	0.03	0.39	NO
106	CRK	CRK	CRK	8214	0.03	0.38	NO
107	ARHGEF11	ARHGEF11	ARHGEF11	8314	0.028	0.38	NO
108	PPP2CB	PPP2CB	PPP2CB	8319	0.028	0.38	NO
109	MAGED1	MAGED1	MAGED1	8410	0.027	0.38	NO
110	MDM2	MDM2	MDM2	8491	0.026	0.38	NO
111	RPS6KA5	RPS6KA5	RPS6KA5	8535	0.025	0.37	NO
112	IKBKB	IKBKB	IKBKB	8555	0.025	0.37	NO
113	ELK1	ELK1	ELK1	8603	0.024	0.37	NO
114	NCSTN	NCSTN	NCSTN	8627	0.024	0.37	NO
115	MAPK1	MAPK1	MAPK1	8628	0.024	0.37	NO
116	RELA	RELA	RELA	8676	0.023	0.37	NO
117	AP2M1	AP2M1	AP2M1	8684	0.023	0.37	NO
118	PRKACB	PRKACB	PRKACB	8686	0.023	0.37	NO
119	NR4A1	NR4A1	NR4A1	8793	0.021	0.37	NO
120	PRKCA	PRKCA	PRKCA	8808	0.021	0.37	NO
121	DUSP6	DUSP6	DUSP6	8835	0.02	0.37	NO
122	RHOA	RHOA	RHOA	8846	0.02	0.37	NO
123	MYD88	MYD88	MYD88	8876	0.02	0.37	NO
124	PSEN1	PSEN1	PSEN1	8907	0.02	0.37	NO
125	SHC3	SHC3	SHC3	9009	0.018	0.36	NO
126	IRS2	IRS2	IRS2	9109	0.016	0.36	NO
127	PHLPP1	PHLPP1	PHLPP1	9128	0.016	0.36	NO
128	CASP2	CASP2	CASP2	9144	0.016	0.36	NO
129	RTN4	RTN4	RTN4	9146	0.016	0.36	NO
130	CLTC	CLTC	CLTC	9160	0.016	0.36	NO
131	ARHGEF9	ARHGEF9	ARHGEF9	9182	0.015	0.36	NO
132	CALM1	CALM1	CALM1	9224	0.015	0.36	NO
133	FOXO3	FOXO3	FOXO3	9278	0.014	0.35	NO
134	PDPK1	PDPK1	PDPK1	9294	0.014	0.35	NO
135	NRAS	NRAS	NRAS	9420	0.012	0.35	NO
136	AATF	AATF	AATF	9430	0.012	0.35	NO
137	RALA	RALA	RALA	9437	0.012	0.35	NO
138	ABR	ABR	ABR	9626	0.0093	0.34	NO
139	RASGRF1	RASGRF1	RASGRF1	9650	0.0091	0.34	NO
140	MAPKAP1	MAPKAP1	MAPKAP1	9667	0.0088	0.34	NO
141	AP2A1	AP2A1	AP2A1	9681	0.0087	0.34	NO
142	CALM2	CALM2	CALM2	9757	0.0075	0.33	NO
143	AKT1	AKT1	AKT1	9836	0.0065	0.33	NO
144	SQSTM1	SQSTM1	SQSTM1	9942	0.0047	0.32	NO
145	HDAC2	HDAC2	HDAC2	10070	0.0027	0.32	NO
146	CALM3	CALM3	CALM3	10150	0.0016	0.31	NO
147	PRDM4	PRDM4	PRDM4	10190	0.0012	0.31	NO
148	DNAL4	DNAL4	DNAL4	10254	0.00036	0.31	NO
149	AP2B1	AP2B1	AP2B1	10269	0.00018	0.3	NO
150	GSK3A	GSK3A	GSK3A	10492	-0.0027	0.29	NO
151	CASP3	CASP3	CASP3	10520	-0.003	0.29	NO
152	RAF1	RAF1	RAF1	10537	-0.0033	0.29	NO
153	PPP2R1B	PPP2R1B	PPP2R1B	10570	-0.0039	0.29	NO
154	ADCY3	ADCY3	ADCY3	10591	-0.0042	0.29	NO
155	CASP9	CASP9	CASP9	10637	-0.0048	0.29	NO
156	YWHAB	YWHAB	YWHAB	10681	-0.0055	0.28	NO
157	AP2A2	AP2A2	AP2A2	10858	-0.008	0.27	NO
158	MAPK14	MAPK14	MAPK14	10995	-0.01	0.27	NO
159	YWHAE	YWHAE	YWHAE	11053	-0.011	0.26	NO
160	RPS6KA3	RPS6KA3	RPS6KA3	11062	-0.011	0.26	NO
161	RAC1	RAC1	RAC1	11140	-0.012	0.26	NO
162	ITPR3	ITPR3	ITPR3	11263	-0.014	0.26	NO
163	AKT2	AKT2	AKT2	11374	-0.016	0.25	NO
164	APH1A	APH1A	APH1A	11422	-0.017	0.25	NO
165	ARHGDIA	ARHGDIA	ARHGDIA	11428	-0.017	0.25	NO
166	HDAC3	HDAC3	HDAC3	11443	-0.017	0.25	NO
167	PSENEN	PSENEN	PSENEN	11456	-0.017	0.25	NO
168	IRAK1	IRAK1	IRAK1	11457	-0.017	0.25	NO
169	PPP2R5D	PPP2R5D	PPP2R5D	11481	-0.018	0.25	NO
170	PPP2CA	PPP2CA	PPP2CA	11498	-0.018	0.25	NO
171	TSC2	TSC2	TSC2	11599	-0.02	0.24	NO
172	CDK1	CDK1	CDK1	11737	-0.022	0.24	NO
173	PSEN2	PSEN2	PSEN2	11773	-0.022	0.24	NO
174	PRKCD	PRKCD	PRKCD	11879	-0.024	0.23	NO
175	THEM4	THEM4	THEM4	12041	-0.026	0.22	NO
176	HDAC1	HDAC1	HDAC1	12055	-0.027	0.22	NO
177	OBSCN	OBSCN	OBSCN	12085	-0.027	0.22	NO
178	ADCY6	ADCY6	ADCY6	12151	-0.028	0.22	NO
179	AKT1S1	AKT1S1	AKT1S1	12559	-0.035	0.2	NO
180	PPP2R1A	PPP2R1A	PPP2R1A	12569	-0.035	0.2	NO
181	ITGB3BP	ITGB3BP	ITGB3BP	12683	-0.037	0.2	NO
182	CDKN1A	CDKN1A	CDKN1A	12713	-0.037	0.2	NO
183	MAP2K5	MAP2K5	MAP2K5	12746	-0.038	0.2	NO
184	SRC	SRC	SRC	12823	-0.039	0.2	NO
185	ADRBK1	ADRBK1	ADRBK1	12837	-0.039	0.2	NO
186	PIK3R2	PIK3R2	PIK3R2	13011	-0.042	0.19	NO
187	HRAS	HRAS	HRAS	13053	-0.043	0.19	NO
188	AP2S1	AP2S1	AP2S1	13140	-0.045	0.19	NO
189	DNM2	DNM2	DNM2	13254	-0.047	0.18	NO
190	PRKAR2A	PRKAR2A	PRKAR2A	13362	-0.049	0.18	NO
191	MAPKAPK3	MAPKAPK3	MAPKAPK3	13676	-0.055	0.16	NO
192	KALRN	KALRN	KALRN	13960	-0.061	0.15	NO
193	CLTA	CLTA	CLTA	14188	-0.065	0.14	NO
194	MAPK3	MAPK3	MAPK3	14205	-0.066	0.14	NO
195	UBA52	UBA52	UBA52	14215	-0.066	0.15	NO
196	MAP2K2	MAP2K2	MAP2K2	14316	-0.068	0.14	NO
197	BAD	BAD	BAD	14436	-0.071	0.14	NO
198	RPS6KA1	RPS6KA1	RPS6KA1	14726	-0.079	0.13	NO
199	TRIB3	TRIB3	TRIB3	14804	-0.081	0.13	NO
200	PCSK6	PCSK6	PCSK6	14843	-0.082	0.13	NO
201	MAPK13	MAPK13	MAPK13	15149	-0.091	0.12	NO
202	ARHGEF16	ARHGEF16	ARHGEF16	15471	-0.1	0.1	NO
203	MLST8	MLST8	MLST8	15486	-0.1	0.11	NO
204	PRKAR1B	PRKAR1B	PRKAR1B	15615	-0.11	0.11	NO
205	NGEF	NGEF	NGEF	15781	-0.11	0.1	NO
206	RPS6KB2	RPS6KB2	RPS6KB2	15794	-0.12	0.11	NO
207	SMPD2	SMPD2	SMPD2	16404	-0.15	0.081	NO
208	VAV3	VAV3	VAV3	17005	-0.21	0.057	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 TRYPTOPHAN METABOLISM.

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

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

Table 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	PPP2R2B	PPP2R2B	PPP2R2B	145	0.67	0.041	YES
2	FGR	FGR	FGR	527	0.53	0.059	YES
3	PIK3R5	PIK3R5	PIK3R5	551	0.52	0.096	YES
4	SPHK1	SPHK1	SPHK1	590	0.52	0.13	YES
5	PIK3R6	PIK3R6	PIK3R6	672	0.5	0.16	YES
6	PIK3CG	PIK3CG	PIK3CG	865	0.46	0.19	YES
7	SLA	SLA	SLA	942	0.45	0.22	YES
8	PIK3CD	PIK3CD	PIK3CD	1132	0.41	0.24	YES
9	DOCK4	DOCK4	DOCK4	1143	0.41	0.27	YES
10	ITGB3	ITGB3	ITGB3	1254	0.4	0.29	YES
11	HCK	HCK	HCK	1370	0.38	0.31	YES
12	MYOCD	MYOCD	MYOCD	1464	0.37	0.33	YES
13	TAGLN	TAGLN	TAGLN	1560	0.36	0.35	YES
14	S1PR1	S1PR1	S1PR1	1660	0.35	0.37	YES
15	PDGFRB	PDGFRB	PDGFRB	1829	0.33	0.39	YES
16	MAPK10	MAPK10	MAPK10	1909	0.32	0.41	YES
17	FYN	FYN	FYN	1924	0.32	0.43	YES
18	ACTA2	ACTA2	ACTA2	2150	0.29	0.44	YES
19	PDGFB	PDGFB	PDGFB	2245	0.28	0.45	YES
20	JAK2	JAK2	JAK2	2722	0.24	0.44	YES
21	ITGAV	ITGAV	ITGAV	2832	0.22	0.46	YES
22	LCK	LCK	LCK	2899	0.22	0.47	YES
23	PIK3CA	PIK3CA	PIK3CA	3525	0.17	0.44	YES
24	STAT1	STAT1	STAT1	3532	0.17	0.46	YES
25	PLA2G4A	PLA2G4A	PLA2G4A	3667	0.16	0.46	YES
26	EIF2AK2	EIF2AK2	EIF2AK2	3786	0.15	0.47	YES
27	CBL	CBL	CBL	4013	0.14	0.46	YES
28	BLK	BLK	BLK	4200	0.13	0.46	YES
29	LRP1	LRP1	LRP1	4334	0.12	0.46	YES
30	SOS1	SOS1	SOS1	4910	0.1	0.44	YES
31	PTPRJ	PTPRJ	PTPRJ	5022	0.096	0.44	YES
32	RAPGEF1	RAPGEF1	RAPGEF1	5233	0.089	0.44	YES
33	PIK3R3	PIK3R3	PIK3R3	5260	0.088	0.44	YES
34	RAP1A	RAP1A	RAP1A	5730	0.076	0.42	YES
35	GRB10	GRB10	GRB10	5864	0.073	0.42	YES
36	PTPN11	PTPN11	PTPN11	5877	0.073	0.42	YES
37	PIK3R1	PIK3R1	PIK3R1	5888	0.072	0.43	YES
38	NCK1	NCK1	NCK1	5970	0.071	0.43	YES
39	PAG1	PAG1	PAG1	6046	0.069	0.43	YES
40	LYN	LYN	LYN	6077	0.068	0.43	YES
41	SIPA1	SIPA1	SIPA1	6084	0.068	0.44	YES
42	ACTR2	ACTR2	ACTR2	6149	0.067	0.44	YES
43	BAIAP2	BAIAP2	BAIAP2	6166	0.066	0.44	YES
44	RASA1	RASA1	RASA1	6206	0.065	0.44	YES
45	IQGAP1	IQGAP1	IQGAP1	6298	0.064	0.44	YES
46	SHC1	SHC1	SHC1	6316	0.063	0.45	YES
47	PTEN	PTEN	PTEN	6334	0.063	0.45	YES
48	SLC9A3R2	SLC9A3R2	SLC9A3R2	6365	0.062	0.45	YES
49	VAV2	VAV2	VAV2	6400	0.061	0.46	YES
50	WASF2	WASF2	WASF2	6415	0.061	0.46	YES
51	STAT5A	STAT5A	STAT5A	6418	0.061	0.46	YES
52	STAT5B	STAT5B	STAT5B	6424	0.061	0.47	YES
53	PTPN2	PTPN2	PTPN2	6449	0.06	0.47	YES
54	ARAP1	ARAP1	ARAP1	6486	0.059	0.48	YES
55	KRAS	KRAS	KRAS	6494	0.059	0.48	YES
56	BRAF	BRAF	BRAF	6758	0.054	0.47	YES
57	ABL1	ABL1	ABL1	6761	0.054	0.47	YES
58	YWHAG	YWHAG	YWHAG	6827	0.053	0.47	YES
59	KSR1	KSR1	KSR1	6837	0.052	0.48	YES
60	SRF	SRF	SRF	6845	0.052	0.48	YES
61	RAB5A	RAB5A	RAB5A	6850	0.052	0.48	YES
62	FOS	FOS	FOS	7042	0.048	0.48	NO
63	MAP2K1	MAP2K1	MAP2K1	7113	0.047	0.48	NO
64	GRB2	GRB2	GRB2	7156	0.046	0.48	NO
65	YWHAH	YWHAH	YWHAH	7387	0.042	0.47	NO
66	ARPC3	ARPC3	ARPC3	7537	0.04	0.46	NO
67	PRKCE	PRKCE	PRKCE	7546	0.04	0.46	NO
68	MAP2K7	MAP2K7	MAP2K7	7561	0.04	0.46	NO
69	PIK3CB	PIK3CB	PIK3CB	7625	0.038	0.46	NO
70	NCKAP1	NCKAP1	NCKAP1	7632	0.038	0.47	NO
71	STAT3	STAT3	STAT3	7644	0.038	0.47	NO
72	MAP2K4	MAP2K4	MAP2K4	7675	0.038	0.47	NO
73	PLCG1	PLCG1	PLCG1	7777	0.036	0.47	NO
74	YES1	YES1	YES1	7896	0.035	0.46	NO
75	MAPK8	MAPK8	MAPK8	8118	0.031	0.45	NO
76	CRK	CRK	CRK	8214	0.03	0.45	NO
77	MLLT4	MLLT4	MLLT4	8511	0.025	0.44	NO
78	DOK1	DOK1	DOK1	8556	0.025	0.44	NO
79	ELK1	ELK1	ELK1	8603	0.024	0.43	NO
80	MAPK1	MAPK1	MAPK1	8628	0.024	0.43	NO
81	ACTR3	ACTR3	ACTR3	8642	0.024	0.44	NO
82	ABI1	ABI1	ABI1	8747	0.022	0.43	NO
83	PRKCA	PRKCA	PRKCA	8808	0.021	0.43	NO
84	RHOA	RHOA	RHOA	8846	0.02	0.43	NO
85	WASL	WASL	WASL	8853	0.02	0.43	NO
86	ARPC2	ARPC2	ARPC2	9187	0.015	0.41	NO
87	YWHAZ	YWHAZ	YWHAZ	9208	0.015	0.41	NO
88	ARPC5	ARPC5	ARPC5	9313	0.014	0.41	NO
89	NRAS	NRAS	NRAS	9420	0.012	0.4	NO
90	BCAR1	BCAR1	BCAR1	9423	0.012	0.4	NO
91	ACTN4	ACTN4	ACTN4	9452	0.012	0.4	NO
92	GAB1	GAB1	GAB1	9478	0.012	0.4	NO
93	PTPN1	PTPN1	PTPN1	9598	0.0098	0.4	NO
94	ARPC1B	ARPC1B	ARPC1B	9640	0.0092	0.4	NO
95	JUN	JUN	JUN	10340	-0.00075	0.36	NO
96	EPS8	EPS8	EPS8	10377	-0.0013	0.35	NO
97	RAF1	RAF1	RAF1	10537	-0.0033	0.34	NO
98	YWHAB	YWHAB	YWHAB	10681	-0.0055	0.34	NO
99	USP6NL	USP6NL	USP6NL	10807	-0.0073	0.33	NO
100	CTTN	CTTN	CTTN	10812	-0.0073	0.33	NO
101	CSK	CSK	CSK	10970	-0.0097	0.32	NO
102	YWHAE	YWHAE	YWHAE	11053	-0.011	0.32	NO
103	RPS6KA3	RPS6KA3	RPS6KA3	11062	-0.011	0.32	NO
104	MAPK9	MAPK9	MAPK9	11088	-0.011	0.32	NO
105	RAC1	RAC1	RAC1	11140	-0.012	0.32	NO
106	NCK2	NCK2	NCK2	11352	-0.015	0.31	NO
107	ARHGDIA	ARHGDIA	ARHGDIA	11428	-0.017	0.3	NO
108	PPP2CA	PPP2CA	PPP2CA	11498	-0.018	0.3	NO
109	ARPC4	ARPC4	ARPC4	11509	-0.018	0.3	NO
110	YWHAQ	YWHAQ	YWHAQ	11530	-0.018	0.3	NO
111	RAP1B	RAP1B	RAP1B	11840	-0.023	0.29	NO
112	PRKCD	PRKCD	PRKCD	11879	-0.024	0.29	NO
113	PAK1	PAK1	PAK1	12113	-0.028	0.28	NO
114	PPP2R1A	PPP2R1A	PPP2R1A	12569	-0.035	0.25	NO
115	RAB4A	RAB4A	RAB4A	12790	-0.039	0.24	NO
116	SRC	SRC	SRC	12823	-0.039	0.24	NO
117	PIK3R2	PIK3R2	PIK3R2	13011	-0.042	0.24	NO
118	HRAS	HRAS	HRAS	13053	-0.043	0.24	NO
119	SFN	SFN	SFN	13055	-0.043	0.24	NO
120	PIN1	PIN1	PIN1	13068	-0.044	0.24	NO
121	DNM2	DNM2	DNM2	13254	-0.047	0.24	NO
122	CYFIP2	CYFIP2	CYFIP2	13279	-0.048	0.24	NO
123	JUND	JUND	JUND	13709	-0.056	0.22	NO
124	MYC	MYC	MYC	13899	-0.059	0.21	NO
125	MAPK3	MAPK3	MAPK3	14205	-0.066	0.2	NO
126	MAP2K2	MAP2K2	MAP2K2	14316	-0.068	0.2	NO
127	SLC9A3R1	SLC9A3R1	SLC9A3R1	15630	-0.11	0.13	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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

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

genes ES table in pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

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	KLF8	KLF8	KLF8	1210	0.41	0.011	YES
2	ITGA5	ITGA5	ITGA5	1492	0.37	0.067	YES
3	FYN	FYN	FYN	1924	0.32	0.1	YES
4	ETS1	ETS1	ETS1	2152	0.29	0.15	YES
5	MMP14	MMP14	MMP14	2290	0.28	0.19	YES
6	ELMO1	ELMO1	ELMO1	2296	0.28	0.25	YES
7	BMX	BMX	BMX	2544	0.25	0.28	YES
8	ITGAV	ITGAV	ITGAV	2832	0.22	0.31	YES
9	PIK3CA	PIK3CA	PIK3CA	3525	0.17	0.3	YES
10	ASAP1	ASAP1	ASAP1	3689	0.16	0.32	YES
11	VCL	VCL	VCL	3909	0.14	0.34	YES
12	PTPN21	PTPN21	PTPN21	4008	0.14	0.36	YES
13	TLN1	TLN1	TLN1	4017	0.14	0.39	YES
14	GIT2	GIT2	GIT2	4377	0.12	0.39	YES
15	ACTN1	ACTN1	ACTN1	4426	0.12	0.41	YES
16	ITGB1	ITGB1	ITGB1	4755	0.1	0.41	YES
17	SOS1	SOS1	SOS1	4910	0.1	0.42	YES
18	ITGB5	ITGB5	ITGB5	4922	0.1	0.44	YES
19	DOCK1	DOCK1	DOCK1	5093	0.093	0.45	YES
20	RAPGEF1	RAPGEF1	RAPGEF1	5233	0.089	0.46	YES
21	ACTA1	ACTA1	ACTA1	5246	0.089	0.48	YES
22	CCND1	CCND1	CCND1	5693	0.077	0.47	YES
23	RAP1A	RAP1A	RAP1A	5730	0.076	0.48	YES
24	PIK3R1	PIK3R1	PIK3R1	5888	0.072	0.49	YES
25	NCK1	NCK1	NCK1	5970	0.071	0.5	YES
26	RASA1	RASA1	RASA1	6206	0.065	0.5	NO
27	BRAF	BRAF	BRAF	6758	0.054	0.48	NO
28	MAP2K1	MAP2K1	MAP2K1	7113	0.047	0.46	NO
29	ROCK2	ROCK2	ROCK2	7148	0.046	0.47	NO
30	GRB2	GRB2	GRB2	7156	0.046	0.48	NO
31	CAPN2	CAPN2	CAPN2	7282	0.044	0.48	NO
32	MAP2K4	MAP2K4	MAP2K4	7675	0.038	0.47	NO
33	PLCG1	PLCG1	PLCG1	7777	0.036	0.47	NO
34	YES1	YES1	YES1	7896	0.035	0.47	NO
35	MAPK8	MAPK8	MAPK8	8118	0.031	0.46	NO
36	CRK	CRK	CRK	8214	0.03	0.46	NO
37	ARHGEF11	ARHGEF11	ARHGEF11	8314	0.028	0.46	NO
38	RRAS	RRAS	RRAS	8348	0.028	0.47	NO
39	MAPK1	MAPK1	MAPK1	8628	0.024	0.46	NO
40	PTK2	PTK2	PTK2	8713	0.022	0.46	NO
41	PXN	PXN	PXN	8733	0.022	0.46	NO
42	RHOA	RHOA	RHOA	8846	0.02	0.46	NO
43	WASL	WASL	WASL	8853	0.02	0.46	NO
44	RGNEF	RGNEF	RGNEF	8919	0.019	0.46	NO
45	ARHGEF7	ARHGEF7	ARHGEF7	9113	0.016	0.45	NO
46	BCAR1	BCAR1	BCAR1	9423	0.012	0.44	NO
47	ARHGAP26	ARHGAP26	ARHGAP26	9914	0.0052	0.41	NO
48	SH3GL1	SH3GL1	SH3GL1	10015	0.0034	0.41	NO
49	JUN	JUN	JUN	10340	-0.00075	0.39	NO
50	RAF1	RAF1	RAF1	10537	-0.0033	0.38	NO
51	MAPK9	MAPK9	MAPK9	11088	-0.011	0.35	NO
52	RAC1	RAC1	RAC1	11140	-0.012	0.35	NO
53	NCK2	NCK2	NCK2	11352	-0.015	0.34	NO
54	RAP1B	RAP1B	RAP1B	11840	-0.023	0.32	NO
55	PAK1	PAK1	PAK1	12113	-0.028	0.31	NO
56	MAPK8IP3	MAPK8IP3	MAPK8IP3	12189	-0.029	0.31	NO
57	GRB7	GRB7	GRB7	12736	-0.038	0.29	NO
58	SRC	SRC	SRC	12823	-0.039	0.29	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 GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.

Figure S46. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, 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 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	TGFB3	TGFB3	TGFB3	79	0.72	0.077	YES
2	VEGFC	VEGFC	VEGFC	171	0.66	0.15	YES
3	AKT3	AKT3	AKT3	484	0.54	0.19	YES
4	PIK3R5	PIK3R5	PIK3R5	551	0.52	0.25	YES
5	TGFB2	TGFB2	TGFB2	689	0.5	0.3	YES
6	PIK3CG	PIK3CG	PIK3CG	865	0.46	0.34	YES
7	PIK3CD	PIK3CD	PIK3CD	1132	0.41	0.37	YES
8	HGF	HGF	HGF	1215	0.4	0.41	YES
9	ARNT2	ARNT2	ARNT2	1231	0.4	0.46	YES
10	PAK3	PAK3	PAK3	1353	0.38	0.49	YES
11	ETS1	ETS1	ETS1	2152	0.29	0.48	YES
12	PDGFB	PDGFB	PDGFB	2245	0.28	0.51	YES
13	FIGF	FIGF	FIGF	2476	0.26	0.52	YES
14	TGFB1	TGFB1	TGFB1	2703	0.24	0.54	YES
15	PGF	PGF	PGF	3014	0.21	0.55	YES
16	PIK3CA	PIK3CA	PIK3CA	3525	0.17	0.54	NO
17	HIF1A	HIF1A	HIF1A	3721	0.16	0.54	NO
18	SOS1	SOS1	SOS1	4910	0.1	0.49	NO
19	RAPGEF1	RAPGEF1	RAPGEF1	5233	0.089	0.48	NO
20	EP300	EP300	EP300	5244	0.089	0.49	NO
21	PIK3R3	PIK3R3	PIK3R3	5260	0.088	0.5	NO
22	EPAS1	EPAS1	EPAS1	5305	0.087	0.5	NO
23	ARNT	ARNT	ARNT	5407	0.084	0.51	NO
24	SOS2	SOS2	SOS2	5721	0.077	0.5	NO
25	RAP1A	RAP1A	RAP1A	5730	0.076	0.51	NO
26	PTPN11	PTPN11	PTPN11	5877	0.073	0.51	NO
27	PIK3R1	PIK3R1	PIK3R1	5888	0.072	0.52	NO
28	CREBBP	CREBBP	CREBBP	5977	0.071	0.52	NO
29	KRAS	KRAS	KRAS	6494	0.059	0.5	NO
30	PAK2	PAK2	PAK2	6582	0.057	0.5	NO
31	BRAF	BRAF	BRAF	6758	0.054	0.5	NO
32	FLCN	FLCN	FLCN	6993	0.049	0.49	NO
33	MAP2K1	MAP2K1	MAP2K1	7113	0.047	0.49	NO
34	GRB2	GRB2	GRB2	7156	0.046	0.49	NO
35	TGFA	TGFA	TGFA	7261	0.045	0.49	NO
36	PIK3CB	PIK3CB	PIK3CB	7625	0.038	0.47	NO
37	VEGFB	VEGFB	VEGFB	7693	0.038	0.47	NO
38	CDC42	CDC42	CDC42	7895	0.035	0.47	NO
39	CRK	CRK	CRK	8214	0.03	0.45	NO
40	MAPK1	MAPK1	MAPK1	8628	0.024	0.43	NO
41	MET	MET	MET	8832	0.021	0.42	NO
42	CRKL	CRKL	CRKL	8842	0.02	0.42	NO
43	NRAS	NRAS	NRAS	9420	0.012	0.39	NO
44	GAB1	GAB1	GAB1	9478	0.012	0.39	NO
45	EGLN3	EGLN3	EGLN3	9554	0.01	0.39	NO
46	CUL2	CUL2	CUL2	9768	0.0073	0.38	NO
47	AKT1	AKT1	AKT1	9836	0.0065	0.38	NO
48	EGLN1	EGLN1	EGLN1	9983	0.0039	0.37	NO
49	SLC2A1	SLC2A1	SLC2A1	10231	0.00063	0.35	NO
50	JUN	JUN	JUN	10340	-0.00075	0.35	NO
51	EGLN2	EGLN2	EGLN2	10371	-0.0012	0.35	NO
52	RAF1	RAF1	RAF1	10537	-0.0033	0.34	NO
53	VEGFA	VEGFA	VEGFA	10811	-0.0073	0.32	NO
54	TCEB1	TCEB1	TCEB1	10905	-0.0088	0.32	NO
55	RAC1	RAC1	RAC1	11140	-0.012	0.31	NO
56	VHL	VHL	VHL	11363	-0.016	0.3	NO
57	AKT2	AKT2	AKT2	11374	-0.016	0.3	NO
58	RAP1B	RAP1B	RAP1B	11840	-0.023	0.27	NO
59	PAK1	PAK1	PAK1	12113	-0.028	0.26	NO
60	RBX1	RBX1	RBX1	12631	-0.036	0.24	NO
61	PIK3R2	PIK3R2	PIK3R2	13011	-0.042	0.22	NO
62	HRAS	HRAS	HRAS	13053	-0.043	0.22	NO
63	ARAF	ARAF	ARAF	13395	-0.05	0.21	NO
64	PAK4	PAK4	PAK4	13463	-0.051	0.21	NO
65	PAK6	PAK6	PAK6	14194	-0.065	0.18	NO
66	MAPK3	MAPK3	MAPK3	14205	-0.066	0.19	NO
67	MAP2K2	MAP2K2	MAP2K2	14316	-0.068	0.19	NO
68	FH	FH	FH	14554	-0.075	0.18	NO
69	TCEB2	TCEB2	TCEB2	15089	-0.09	0.16	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 INOSITOL PHOSPHATE METABOLISM.

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

genes ES table in pathway: KEGG ABC TRANSPORTERS

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	PDE1B	PDE1B	PDE1B	237	0.62	0.038	YES
2	AKT3	AKT3	AKT3	484	0.54	0.068	YES
3	PDE1A	PDE1A	PDE1A	540	0.53	0.11	YES
4	ADCY2	ADCY2	ADCY2	718	0.49	0.14	YES
5	ADCYAP1	ADCYAP1	ADCYAP1	802	0.47	0.17	YES
6	MAPK11	MAPK11	MAPK11	1156	0.41	0.18	YES
7	NGF	NGF	NGF	1279	0.4	0.21	YES
8	MEF2C	MEF2C	MEF2C	1397	0.38	0.23	YES
9	NTRK1	NTRK1	NTRK1	1431	0.38	0.26	YES
10	PRKAR2B	PRKAR2B	PRKAR2B	1688	0.34	0.28	YES
11	CAMK4	CAMK4	CAMK4	2215	0.28	0.27	YES
12	ADCY5	ADCY5	ADCY5	2294	0.28	0.29	YES
13	NTRK2	NTRK2	NTRK2	2610	0.24	0.29	YES
14	ADORA2A	ADORA2A	ADORA2A	2629	0.24	0.31	YES
15	ADCY1	ADCY1	ADCY1	2677	0.24	0.33	YES
16	DNM1	DNM1	DNM1	2723	0.24	0.34	YES
17	ADCY4	ADCY4	ADCY4	2745	0.23	0.36	YES
18	MAPK12	MAPK12	MAPK12	2962	0.21	0.37	YES
19	RPS6KA2	RPS6KA2	RPS6KA2	3130	0.2	0.37	YES
20	IRS1	IRS1	IRS1	3264	0.19	0.38	YES
21	ADCY7	ADCY7	ADCY7	3412	0.18	0.39	YES
22	DUSP4	DUSP4	DUSP4	3517	0.17	0.39	YES
23	PIK3CA	PIK3CA	PIK3CA	3525	0.17	0.41	YES
24	FOXO1	FOXO1	FOXO1	3578	0.16	0.42	YES
25	ITPR2	ITPR2	ITPR2	3728	0.15	0.42	YES
26	MEF2A	MEF2A	MEF2A	3872	0.14	0.43	YES
27	RICTOR	RICTOR	RICTOR	4066	0.13	0.43	YES
28	SHC2	SHC2	SHC2	4194	0.13	0.43	YES
29	KIDINS220	KIDINS220	KIDINS220	4340	0.12	0.43	YES
30	ADCY9	ADCY9	ADCY9	4694	0.11	0.42	NO
31	SOS1	SOS1	SOS1	4910	0.1	0.42	NO
32	PRKAR1A	PRKAR1A	PRKAR1A	4962	0.098	0.42	NO
33	CREB1	CREB1	CREB1	5063	0.094	0.42	NO
34	DUSP7	DUSP7	DUSP7	5087	0.093	0.43	NO
35	RAPGEF1	RAPGEF1	RAPGEF1	5233	0.089	0.43	NO
36	FRS2	FRS2	FRS2	5411	0.084	0.43	NO
37	FOXO4	FOXO4	FOXO4	5521	0.081	0.43	NO
38	RAP1A	RAP1A	RAP1A	5730	0.076	0.42	NO
39	PIK3R1	PIK3R1	PIK3R1	5888	0.072	0.42	NO
40	RIT1	RIT1	RIT1	6188	0.066	0.41	NO
41	PRKCG	PRKCG	PRKCG	6283	0.064	0.41	NO
42	SHC1	SHC1	SHC1	6316	0.063	0.41	NO
43	PTEN	PTEN	PTEN	6334	0.063	0.41	NO
44	KRAS	KRAS	KRAS	6494	0.059	0.41	NO
45	DUSP3	DUSP3	DUSP3	6674	0.056	0.4	NO
46	MTOR	MTOR	MTOR	6708	0.055	0.41	NO
47	BRAF	BRAF	BRAF	6758	0.054	0.41	NO
48	PRKACA	PRKACA	PRKACA	6931	0.05	0.4	NO
49	SH3GL2	SH3GL2	SH3GL2	6960	0.05	0.41	NO
50	MAPKAPK2	MAPKAPK2	MAPKAPK2	7018	0.049	0.41	NO
51	MAP2K1	MAP2K1	MAP2K1	7113	0.047	0.4	NO
52	ATF1	ATF1	ATF1	7144	0.046	0.41	NO
53	GRB2	GRB2	GRB2	7156	0.046	0.41	NO
54	MAPK7	MAPK7	MAPK7	7534	0.04	0.39	NO
55	PRKCE	PRKCE	PRKCE	7546	0.04	0.4	NO
56	CHUK	CHUK	CHUK	7576	0.039	0.4	NO
57	RALB	RALB	RALB	7596	0.039	0.4	NO
58	PIK3CB	PIK3CB	PIK3CB	7625	0.038	0.4	NO
59	STAT3	STAT3	STAT3	7644	0.038	0.4	NO
60	PLCG1	PLCG1	PLCG1	7777	0.036	0.4	NO
61	CDKN1B	CDKN1B	CDKN1B	8045	0.032	0.39	NO
62	RALGDS	RALGDS	RALGDS	8169	0.03	0.38	NO
63	CRK	CRK	CRK	8214	0.03	0.38	NO
64	PPP2CB	PPP2CB	PPP2CB	8319	0.028	0.38	NO
65	MDM2	MDM2	MDM2	8491	0.026	0.37	NO
66	RPS6KA5	RPS6KA5	RPS6KA5	8535	0.025	0.37	NO
67	ELK1	ELK1	ELK1	8603	0.024	0.37	NO
68	MAPK1	MAPK1	MAPK1	8628	0.024	0.37	NO
69	AP2M1	AP2M1	AP2M1	8684	0.023	0.37	NO
70	PRKACB	PRKACB	PRKACB	8686	0.023	0.37	NO
71	NR4A1	NR4A1	NR4A1	8793	0.021	0.36	NO
72	PRKCA	PRKCA	PRKCA	8808	0.021	0.37	NO
73	DUSP6	DUSP6	DUSP6	8835	0.02	0.37	NO
74	RHOA	RHOA	RHOA	8846	0.02	0.37	NO
75	SHC3	SHC3	SHC3	9009	0.018	0.36	NO
76	IRS2	IRS2	IRS2	9109	0.016	0.36	NO
77	PHLPP1	PHLPP1	PHLPP1	9128	0.016	0.36	NO
78	CLTC	CLTC	CLTC	9160	0.016	0.36	NO
79	CALM1	CALM1	CALM1	9224	0.015	0.35	NO
80	FOXO3	FOXO3	FOXO3	9278	0.014	0.35	NO
81	PDPK1	PDPK1	PDPK1	9294	0.014	0.35	NO
82	NRAS	NRAS	NRAS	9420	0.012	0.34	NO
83	RALA	RALA	RALA	9437	0.012	0.34	NO
84	MAPKAP1	MAPKAP1	MAPKAP1	9667	0.0088	0.33	NO
85	AP2A1	AP2A1	AP2A1	9681	0.0087	0.33	NO
86	CALM2	CALM2	CALM2	9757	0.0075	0.33	NO
87	AKT1	AKT1	AKT1	9836	0.0065	0.33	NO
88	CALM3	CALM3	CALM3	10150	0.0016	0.31	NO
89	DNAL4	DNAL4	DNAL4	10254	0.00036	0.3	NO
90	AP2B1	AP2B1	AP2B1	10269	0.00018	0.3	NO
91	GSK3A	GSK3A	GSK3A	10492	-0.0027	0.29	NO
92	RAF1	RAF1	RAF1	10537	-0.0033	0.29	NO
93	PPP2R1B	PPP2R1B	PPP2R1B	10570	-0.0039	0.29	NO
94	ADCY3	ADCY3	ADCY3	10591	-0.0042	0.28	NO
95	CASP9	CASP9	CASP9	10637	-0.0048	0.28	NO
96	YWHAB	YWHAB	YWHAB	10681	-0.0055	0.28	NO
97	AP2A2	AP2A2	AP2A2	10858	-0.008	0.27	NO
98	MAPK14	MAPK14	MAPK14	10995	-0.01	0.26	NO
99	RPS6KA3	RPS6KA3	RPS6KA3	11062	-0.011	0.26	NO
100	ITPR3	ITPR3	ITPR3	11263	-0.014	0.25	NO
101	AKT2	AKT2	AKT2	11374	-0.016	0.25	NO
102	PPP2R5D	PPP2R5D	PPP2R5D	11481	-0.018	0.24	NO
103	PPP2CA	PPP2CA	PPP2CA	11498	-0.018	0.24	NO
104	TSC2	TSC2	TSC2	11599	-0.02	0.24	NO
105	CDK1	CDK1	CDK1	11737	-0.022	0.23	NO
106	PRKCD	PRKCD	PRKCD	11879	-0.024	0.23	NO
107	THEM4	THEM4	THEM4	12041	-0.026	0.22	NO
108	ADCY6	ADCY6	ADCY6	12151	-0.028	0.22	NO
109	AKT1S1	AKT1S1	AKT1S1	12559	-0.035	0.2	NO
110	PPP2R1A	PPP2R1A	PPP2R1A	12569	-0.035	0.2	NO
111	CDKN1A	CDKN1A	CDKN1A	12713	-0.037	0.2	NO
112	MAP2K5	MAP2K5	MAP2K5	12746	-0.038	0.2	NO
113	SRC	SRC	SRC	12823	-0.039	0.2	NO
114	ADRBK1	ADRBK1	ADRBK1	12837	-0.039	0.2	NO
115	PIK3R2	PIK3R2	PIK3R2	13011	-0.042	0.19	NO
116	HRAS	HRAS	HRAS	13053	-0.043	0.19	NO
117	AP2S1	AP2S1	AP2S1	13140	-0.045	0.19	NO
118	DNM2	DNM2	DNM2	13254	-0.047	0.19	NO
119	PRKAR2A	PRKAR2A	PRKAR2A	13362	-0.049	0.19	NO
120	MAPKAPK3	MAPKAPK3	MAPKAPK3	13676	-0.055	0.17	NO
121	CLTA	CLTA	CLTA	14188	-0.065	0.15	NO
122	MAPK3	MAPK3	MAPK3	14205	-0.066	0.16	NO
123	MAP2K2	MAP2K2	MAP2K2	14316	-0.068	0.15	NO
124	BAD	BAD	BAD	14436	-0.071	0.15	NO
125	RPS6KA1	RPS6KA1	RPS6KA1	14726	-0.079	0.14	NO
126	TRIB3	TRIB3	TRIB3	14804	-0.081	0.15	NO
127	MAPK13	MAPK13	MAPK13	15149	-0.091	0.13	NO
128	MLST8	MLST8	MLST8	15486	-0.1	0.12	NO
129	PRKAR1B	PRKAR1B	PRKAR1B	15615	-0.11	0.12	NO
130	RPS6KB2	RPS6KB2	RPS6KB2	15794	-0.12	0.12	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 ABC TRANSPORTERS.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ABC TRANSPORTERS, 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 MAPK SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	THBS4	THBS4	THBS4	87	0.71	0.039	YES
2	PDE1B	PDE1B	PDE1B	237	0.62	0.069	YES
3	THBS2	THBS2	THBS2	374	0.57	0.097	YES
4	SPP1	SPP1	SPP1	450	0.55	0.13	YES
5	AKT3	AKT3	AKT3	484	0.54	0.16	YES
6	PDE1A	PDE1A	PDE1A	540	0.53	0.19	YES
7	ADCY2	ADCY2	ADCY2	718	0.49	0.21	YES
8	PDGFC	PDGFC	PDGFC	968	0.44	0.22	YES
9	COL5A2	COL5A2	COL5A2	1392	0.38	0.22	YES
10	COL4A4	COL4A4	COL4A4	1467	0.37	0.24	YES
11	COL6A3	COL6A3	COL6A3	1563	0.36	0.26	YES
12	PRKAR2B	PRKAR2B	PRKAR2B	1688	0.34	0.27	YES
13	COL5A1	COL5A1	COL5A1	1758	0.34	0.29	YES
14	PDGFRB	PDGFRB	PDGFRB	1829	0.33	0.3	YES
15	COL1A1	COL1A1	COL1A1	1912	0.32	0.32	YES
16	COL1A2	COL1A2	COL1A2	1949	0.32	0.34	YES
17	COL3A1	COL3A1	COL3A1	1995	0.31	0.35	YES
18	CAMK4	CAMK4	CAMK4	2215	0.28	0.36	YES
19	PDGFB	PDGFB	PDGFB	2245	0.28	0.37	YES
20	ADCY5	ADCY5	ADCY5	2294	0.28	0.39	YES
21	COL6A2	COL6A2	COL6A2	2341	0.27	0.4	YES
22	COL6A1	COL6A1	COL6A1	2343	0.27	0.42	YES
23	ADCY1	ADCY1	ADCY1	2677	0.24	0.42	YES
24	ADCY4	ADCY4	ADCY4	2745	0.23	0.43	YES
25	THBS1	THBS1	THBS1	2806	0.23	0.44	YES
26	THBS3	THBS3	THBS3	2951	0.21	0.44	YES
27	PDGFRA	PDGFRA	PDGFRA	2958	0.21	0.45	YES
28	COL4A2	COL4A2	COL4A2	2975	0.21	0.47	YES
29	COL4A3	COL4A3	COL4A3	2998	0.21	0.48	YES
30	COL4A1	COL4A1	COL4A1	3032	0.21	0.49	YES
31	PDGFD	PDGFD	PDGFD	3245	0.19	0.49	YES
32	ADCY7	ADCY7	ADCY7	3412	0.18	0.49	YES
33	PIK3CA	PIK3CA	PIK3CA	3525	0.17	0.49	YES
34	STAT1	STAT1	STAT1	3532	0.17	0.5	YES
35	FOXO1	FOXO1	FOXO1	3578	0.16	0.51	YES
36	PLAT	PLAT	PLAT	3622	0.16	0.52	YES
37	ITPR2	ITPR2	ITPR2	3728	0.15	0.52	YES
38	RICTOR	RICTOR	RICTOR	4066	0.13	0.51	NO
39	ADCY9	ADCY9	ADCY9	4694	0.11	0.48	NO
40	SOS1	SOS1	SOS1	4910	0.1	0.48	NO
41	PRKAR1A	PRKAR1A	PRKAR1A	4962	0.098	0.48	NO
42	CREB1	CREB1	CREB1	5063	0.094	0.48	NO
43	RAPGEF1	RAPGEF1	RAPGEF1	5233	0.089	0.48	NO
44	FOXO4	FOXO4	FOXO4	5521	0.081	0.47	NO
45	PIK3R1	PIK3R1	PIK3R1	5888	0.072	0.45	NO
46	PDGFA	PDGFA	PDGFA	5936	0.072	0.45	NO
47	NCK1	NCK1	NCK1	5970	0.071	0.46	NO
48	RASA1	RASA1	RASA1	6206	0.065	0.45	NO
49	PRKCG	PRKCG	PRKCG	6283	0.064	0.45	NO
50	PTEN	PTEN	PTEN	6334	0.063	0.45	NO
51	STAT5A	STAT5A	STAT5A	6418	0.061	0.45	NO
52	STAT5B	STAT5B	STAT5B	6424	0.061	0.45	NO
53	KRAS	KRAS	KRAS	6494	0.059	0.45	NO
54	MTOR	MTOR	MTOR	6708	0.055	0.44	NO
55	PRKACA	PRKACA	PRKACA	6931	0.05	0.43	NO
56	MAP2K1	MAP2K1	MAP2K1	7113	0.047	0.42	NO
57	GRB2	GRB2	GRB2	7156	0.046	0.42	NO
58	FURIN	FURIN	FURIN	7320	0.043	0.42	NO
59	PRKCE	PRKCE	PRKCE	7546	0.04	0.41	NO
60	CHUK	CHUK	CHUK	7576	0.039	0.41	NO
61	PIK3CB	PIK3CB	PIK3CB	7625	0.038	0.41	NO
62	STAT3	STAT3	STAT3	7644	0.038	0.41	NO
63	PLCG1	PLCG1	PLCG1	7777	0.036	0.4	NO
64	CDKN1B	CDKN1B	CDKN1B	8045	0.032	0.39	NO
65	CRK	CRK	CRK	8214	0.03	0.38	NO
66	MDM2	MDM2	MDM2	8491	0.026	0.37	NO
67	MAPK1	MAPK1	MAPK1	8628	0.024	0.36	NO
68	PRKACB	PRKACB	PRKACB	8686	0.023	0.36	NO
69	NR4A1	NR4A1	NR4A1	8793	0.021	0.36	NO
70	PRKCA	PRKCA	PRKCA	8808	0.021	0.36	NO
71	CRKL	CRKL	CRKL	8842	0.02	0.36	NO
72	PHLPP1	PHLPP1	PHLPP1	9128	0.016	0.34	NO
73	CALM1	CALM1	CALM1	9224	0.015	0.34	NO
74	FOXO3	FOXO3	FOXO3	9278	0.014	0.34	NO
75	PDPK1	PDPK1	PDPK1	9294	0.014	0.34	NO
76	NRAS	NRAS	NRAS	9420	0.012	0.33	NO
77	BCAR1	BCAR1	BCAR1	9423	0.012	0.33	NO
78	MAPKAP1	MAPKAP1	MAPKAP1	9667	0.0088	0.32	NO
79	CALM2	CALM2	CALM2	9757	0.0075	0.31	NO
80	AKT1	AKT1	AKT1	9836	0.0065	0.31	NO
81	CALM3	CALM3	CALM3	10150	0.0016	0.29	NO
82	GSK3A	GSK3A	GSK3A	10492	-0.0027	0.27	NO
83	RAF1	RAF1	RAF1	10537	-0.0033	0.27	NO
84	ADCY3	ADCY3	ADCY3	10591	-0.0042	0.27	NO
85	CASP9	CASP9	CASP9	10637	-0.0048	0.27	NO
86	YWHAB	YWHAB	YWHAB	10681	-0.0055	0.26	NO
87	STAT6	STAT6	STAT6	10838	-0.0076	0.26	NO
88	ITPR3	ITPR3	ITPR3	11263	-0.014	0.23	NO
89	NCK2	NCK2	NCK2	11352	-0.015	0.23	NO
90	AKT2	AKT2	AKT2	11374	-0.016	0.23	NO
91	TSC2	TSC2	TSC2	11599	-0.02	0.22	NO
92	CDK1	CDK1	CDK1	11737	-0.022	0.21	NO
93	PRKCD	PRKCD	PRKCD	11879	-0.024	0.2	NO
94	COL9A3	COL9A3	COL9A3	11990	-0.026	0.2	NO
95	THEM4	THEM4	THEM4	12041	-0.026	0.2	NO
96	ADCY6	ADCY6	ADCY6	12151	-0.028	0.2	NO
97	AKT1S1	AKT1S1	AKT1S1	12559	-0.035	0.17	NO
98	CDKN1A	CDKN1A	CDKN1A	12713	-0.037	0.17	NO
99	GRB7	GRB7	GRB7	12736	-0.038	0.17	NO
100	SRC	SRC	SRC	12823	-0.039	0.17	NO
101	ADRBK1	ADRBK1	ADRBK1	12837	-0.039	0.17	NO
102	PIK3R2	PIK3R2	PIK3R2	13011	-0.042	0.16	NO
103	HRAS	HRAS	HRAS	13053	-0.043	0.16	NO
104	PRKAR2A	PRKAR2A	PRKAR2A	13362	-0.049	0.15	NO
105	COL2A1	COL2A1	COL2A1	14099	-0.064	0.11	NO
106	MAPK3	MAPK3	MAPK3	14205	-0.066	0.11	NO
107	MAP2K2	MAP2K2	MAP2K2	14316	-0.068	0.11	NO
108	BAD	BAD	BAD	14436	-0.071	0.1	NO
109	TRIB3	TRIB3	TRIB3	14804	-0.081	0.089	NO
110	MLST8	MLST8	MLST8	15486	-0.1	0.057	NO
111	PRKAR1B	PRKAR1B	PRKAR1B	15615	-0.11	0.057	NO
112	COL4A5	COL4A5	COL4A5	15775	-0.11	0.055	NO
113	RPS6KB2	RPS6KB2	RPS6KB2	15794	-0.12	0.061	NO
114	COL9A1	COL9A1	COL9A1	17252	-0.24	-0.0056	NO
115	COL9A2	COL9A2	COL9A2	17264	-0.25	0.009	NO
116	PLG	PLG	PLG	17969	-0.54	0.0031	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 MAPK SIGNALING PATHWAY.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MAPK 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 ERBB SIGNALING PATHWAY

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	TGFB3	TGFB3	TGFB3	79	0.72	0.098	YES
2	AKT3	AKT3	AKT3	484	0.54	0.15	YES
3	PIK3R5	PIK3R5	PIK3R5	551	0.52	0.22	YES
4	TGFB2	TGFB2	TGFB2	689	0.5	0.28	YES
5	PIK3CG	PIK3CG	PIK3CG	865	0.46	0.34	YES
6	PIK3CD	PIK3CD	PIK3CD	1132	0.41	0.38	YES
7	MAPK10	MAPK10	MAPK10	1909	0.32	0.38	YES
8	TCF7L1	TCF7L1	TCF7L1	2588	0.25	0.38	YES
9	TGFB1	TGFB1	TGFB1	2703	0.24	0.41	YES
10	LEF1	LEF1	LEF1	2773	0.23	0.44	YES
11	BCL2	BCL2	BCL2	2861	0.22	0.46	YES
12	DCC	DCC	DCC	3180	0.19	0.48	YES
13	APC	APC	APC	3356	0.18	0.49	YES
14	PIK3CA	PIK3CA	PIK3CA	3525	0.17	0.5	YES
15	TGFBR1	TGFBR1	TGFBR1	3767	0.15	0.51	YES
16	RAC2	RAC2	RAC2	4900	0.1	0.46	NO
17	TGFBR2	TGFBR2	TGFBR2	5019	0.096	0.47	NO
18	PIK3R3	PIK3R3	PIK3R3	5260	0.088	0.47	NO
19	CCND1	CCND1	CCND1	5693	0.077	0.46	NO
20	APPL1	APPL1	APPL1	5736	0.076	0.47	NO
21	SMAD2	SMAD2	SMAD2	5779	0.075	0.47	NO
22	PIK3R1	PIK3R1	PIK3R1	5888	0.072	0.48	NO
23	KRAS	KRAS	KRAS	6494	0.059	0.45	NO
24	BRAF	BRAF	BRAF	6758	0.054	0.45	NO
25	SMAD3	SMAD3	SMAD3	6922	0.051	0.44	NO
26	FOS	FOS	FOS	7042	0.048	0.44	NO
27	MAP2K1	MAP2K1	MAP2K1	7113	0.047	0.45	NO
28	SMAD4	SMAD4	SMAD4	7330	0.043	0.44	NO
29	PIK3CB	PIK3CB	PIK3CB	7625	0.038	0.43	NO
30	MAPK8	MAPK8	MAPK8	8118	0.031	0.41	NO
31	RALGDS	RALGDS	RALGDS	8169	0.03	0.41	NO
32	MSH6	MSH6	MSH6	8563	0.024	0.39	NO
33	MAPK1	MAPK1	MAPK1	8628	0.024	0.39	NO
34	RAC3	RAC3	RAC3	8765	0.022	0.38	NO
35	RHOA	RHOA	RHOA	8846	0.02	0.38	NO
36	GSK3B	GSK3B	GSK3B	8880	0.02	0.38	NO
37	MSH3	MSH3	MSH3	8966	0.018	0.38	NO
38	AKT1	AKT1	AKT1	9836	0.0065	0.34	NO
39	MSH2	MSH2	MSH2	10075	0.0026	0.32	NO
40	JUN	JUN	JUN	10340	-0.00075	0.31	NO
41	CASP3	CASP3	CASP3	10520	-0.003	0.3	NO
42	RAF1	RAF1	RAF1	10537	-0.0033	0.3	NO
43	CASP9	CASP9	CASP9	10637	-0.0048	0.29	NO
44	MLH1	MLH1	MLH1	10793	-0.0071	0.28	NO
45	TCF7L2	TCF7L2	TCF7L2	10852	-0.0079	0.28	NO
46	CTNNB1	CTNNB1	CTNNB1	10860	-0.008	0.28	NO
47	MAPK9	MAPK9	MAPK9	11088	-0.011	0.27	NO
48	RAC1	RAC1	RAC1	11140	-0.012	0.27	NO
49	AKT2	AKT2	AKT2	11374	-0.016	0.26	NO
50	CYCS	CYCS	CYCS	12517	-0.034	0.2	NO
51	AXIN1	AXIN1	AXIN1	12557	-0.035	0.2	NO
52	BAX	BAX	BAX	12783	-0.038	0.2	NO
53	APC2	APC2	APC2	12845	-0.04	0.2	NO
54	TCF7	TCF7	TCF7	13002	-0.042	0.2	NO
55	PIK3R2	PIK3R2	PIK3R2	13011	-0.042	0.2	NO
56	ARAF	ARAF	ARAF	13395	-0.05	0.19	NO
57	TP53	TP53	TP53	13611	-0.054	0.18	NO
58	MYC	MYC	MYC	13899	-0.059	0.18	NO
59	MAPK3	MAPK3	MAPK3	14205	-0.066	0.17	NO
60	BIRC5	BIRC5	BIRC5	14258	-0.067	0.18	NO
61	BAD	BAD	BAD	14436	-0.071	0.18	NO
62	AXIN2	AXIN2	AXIN2	16669	-0.17	0.076	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 ERBB SIGNALING PATHWAY.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ERBB 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 CALCIUM SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FGF1	FGF1	FGF1	45	0.75	0.022	YES
2	ITGAM	ITGAM	ITGAM	162	0.67	0.037	YES
3	FGF7	FGF7	FGF7	170	0.66	0.058	YES
4	FGF5	FGF5	FGF5	188	0.65	0.077	YES
5	FGF14	FGF14	FGF14	264	0.62	0.093	YES
6	FGF2	FGF2	FGF2	365	0.58	0.11	YES
7	MRAS	MRAS	MRAS	459	0.55	0.12	YES
8	TIAM1	TIAM1	TIAM1	502	0.53	0.13	YES
9	CHRM2	CHRM2	CHRM2	513	0.53	0.15	YES
10	PIK3R5	PIK3R5	PIK3R5	551	0.52	0.16	YES
11	ITGA10	ITGA10	ITGA10	554	0.52	0.18	YES
12	ITGAX	ITGAX	ITGAX	598	0.51	0.2	YES
13	ITGA11	ITGA11	ITGA11	704	0.49	0.2	YES
14	PIK3CG	PIK3CG	PIK3CG	865	0.46	0.21	YES
15	FGF10	FGF10	FGF10	918	0.45	0.22	YES
16	PDGFC	PDGFC	PDGFC	968	0.44	0.23	YES
17	WAS	WAS	WAS	992	0.44	0.25	YES
18	ITGAL	ITGAL	ITGAL	993	0.44	0.26	YES
19	NCKAP1L	NCKAP1L	NCKAP1L	1039	0.43	0.27	YES
20	MYH10	MYH10	MYH10	1065	0.42	0.28	YES
21	PIK3CD	PIK3CD	PIK3CD	1132	0.41	0.29	YES
22	FN1	FN1	FN1	1141	0.41	0.31	YES
23	ARHGEF6	ARHGEF6	ARHGEF6	1205	0.41	0.32	YES
24	ITGB3	ITGB3	ITGB3	1254	0.4	0.33	YES
25	ITGB2	ITGB2	ITGB2	1303	0.39	0.34	YES
26	FGFR1	FGFR1	FGFR1	1311	0.39	0.35	YES
27	PAK3	PAK3	PAK3	1353	0.38	0.36	YES
28	ITGA7	ITGA7	ITGA7	1402	0.38	0.37	YES
29	MYLK	MYLK	MYLK	1414	0.38	0.38	YES
30	ITGA5	ITGA5	ITGA5	1492	0.37	0.39	YES
31	CFL2	CFL2	CFL2	1566	0.36	0.4	YES
32	FGF12	FGF12	FGF12	1585	0.36	0.41	YES
33	ITGA4	ITGA4	ITGA4	1723	0.34	0.41	YES
34	RDX	RDX	RDX	1752	0.34	0.42	YES
35	FGF11	FGF11	FGF11	1800	0.33	0.43	YES
36	PDGFRB	PDGFRB	PDGFRB	1829	0.33	0.44	YES
37	MYL9	MYL9	MYL9	1838	0.33	0.44	YES
38	WASF1	WASF1	WASF1	1940	0.32	0.45	YES
39	PDGFB	PDGFB	PDGFB	2245	0.28	0.44	YES
40	CD14	CD14	CD14	2249	0.28	0.45	YES
41	MSN	MSN	MSN	2315	0.28	0.46	YES
42	ACTN3	ACTN3	ACTN3	2361	0.27	0.46	YES
43	ACTN2	ACTN2	ACTN2	2434	0.26	0.47	YES
44	VAV1	VAV1	VAV1	2478	0.26	0.47	YES
45	ARHGEF4	ARHGEF4	ARHGEF4	2498	0.26	0.48	YES
46	F2R	F2R	F2R	2531	0.25	0.49	YES
47	CHRM4	CHRM4	CHRM4	2570	0.25	0.49	YES
48	TIAM2	TIAM2	TIAM2	2738	0.23	0.49	YES
49	ITGAV	ITGAV	ITGAV	2832	0.22	0.49	YES
50	ITGA1	ITGA1	ITGA1	2911	0.22	0.5	YES
51	PDGFRA	PDGFRA	PDGFRA	2958	0.21	0.5	YES
52	PIP4K2A	PIP4K2A	PIP4K2A	3045	0.2	0.5	YES
53	ITGB7	ITGB7	ITGB7	3067	0.2	0.51	YES
54	FGF13	FGF13	FGF13	3220	0.19	0.5	YES
55	PDGFD	PDGFD	PDGFD	3245	0.19	0.51	YES
56	FGF9	FGF9	FGF9	3348	0.18	0.51	YES
57	APC	APC	APC	3356	0.18	0.51	YES
58	ITGB8	ITGB8	ITGB8	3376	0.18	0.52	YES
59	FGFR2	FGFR2	FGFR2	3409	0.18	0.52	YES
60	ITGA9	ITGA9	ITGA9	3462	0.17	0.52	YES
61	SSH1	SSH1	SSH1	3469	0.17	0.53	YES
62	ROCK1	ROCK1	ROCK1	3513	0.17	0.53	YES
63	PIK3CA	PIK3CA	PIK3CA	3525	0.17	0.54	YES
64	INSRR	INSRR	INSRR	3559	0.17	0.54	YES
65	ITGAD	ITGAD	ITGAD	3696	0.16	0.54	YES
66	BDKRB1	BDKRB1	BDKRB1	3700	0.16	0.54	YES
67	CHRM5	CHRM5	CHRM5	3731	0.15	0.55	YES
68	VCL	VCL	VCL	3909	0.14	0.54	NO
69	PIKFYVE	PIKFYVE	PIKFYVE	3977	0.14	0.54	NO
70	MYLK3	MYLK3	MYLK3	4090	0.13	0.54	NO
71	MYLK2	MYLK2	MYLK2	4222	0.13	0.54	NO
72	PPP1R12A	PPP1R12A	PPP1R12A	4229	0.13	0.54	NO
73	ACTN1	ACTN1	ACTN1	4426	0.12	0.53	NO
74	ENAH	ENAH	ENAH	4556	0.11	0.53	NO
75	ABI2	ABI2	ABI2	4593	0.11	0.53	NO
76	FGD1	FGD1	FGD1	4625	0.11	0.53	NO
77	FGF18	FGF18	FGF18	4649	0.11	0.54	NO
78	ITGB1	ITGB1	ITGB1	4755	0.1	0.53	NO
79	GSN	GSN	GSN	4756	0.1	0.54	NO
80	RAC2	RAC2	RAC2	4900	0.1	0.53	NO
81	SOS1	SOS1	SOS1	4910	0.1	0.54	NO
82	ITGB5	ITGB5	ITGB5	4922	0.1	0.54	NO
83	PIP5K1C	PIP5K1C	PIP5K1C	4942	0.099	0.54	NO
84	EGFR	EGFR	EGFR	4960	0.098	0.54	NO
85	GNA12	GNA12	GNA12	5048	0.095	0.54	NO
86	DOCK1	DOCK1	DOCK1	5093	0.093	0.54	NO
87	PIK3R3	PIK3R3	PIK3R3	5260	0.088	0.53	NO
88	MYH9	MYH9	MYH9	5314	0.087	0.53	NO
89	ARHGEF12	ARHGEF12	ARHGEF12	5365	0.086	0.53	NO
90	LIMK1	LIMK1	LIMK1	5513	0.081	0.53	NO
91	PIP4K2B	PIP4K2B	PIP4K2B	5531	0.081	0.53	NO
92	SOS2	SOS2	SOS2	5721	0.077	0.52	NO
93	SSH2	SSH2	SSH2	5851	0.073	0.52	NO
94	PIK3R1	PIK3R1	PIK3R1	5888	0.072	0.52	NO
95	PDGFA	PDGFA	PDGFA	5936	0.072	0.52	NO
96	BAIAP2	BAIAP2	BAIAP2	6166	0.066	0.51	NO
97	ARHGEF1	ARHGEF1	ARHGEF1	6266	0.064	0.5	NO
98	GNA13	GNA13	GNA13	6279	0.064	0.5	NO
99	IQGAP1	IQGAP1	IQGAP1	6298	0.064	0.5	NO
100	ITGA2	ITGA2	ITGA2	6329	0.063	0.5	NO
101	VAV2	VAV2	VAV2	6400	0.061	0.5	NO
102	WASF2	WASF2	WASF2	6415	0.061	0.5	NO
103	KRAS	KRAS	KRAS	6494	0.059	0.5	NO
104	FGD3	FGD3	FGD3	6530	0.058	0.5	NO
105	PAK2	PAK2	PAK2	6582	0.057	0.5	NO
106	BRAF	BRAF	BRAF	6758	0.054	0.49	NO
107	FGF3	FGF3	FGF3	6928	0.051	0.48	NO
108	MAP2K1	MAP2K1	MAP2K1	7113	0.047	0.48	NO
109	ROCK2	ROCK2	ROCK2	7148	0.046	0.48	NO
110	PIP5K1A	PIP5K1A	PIP5K1A	7184	0.046	0.48	NO
111	FGF19	FGF19	FGF19	7317	0.044	0.47	NO
112	ARPC3	ARPC3	ARPC3	7537	0.04	0.46	NO
113	PIK3CB	PIK3CB	PIK3CB	7625	0.038	0.46	NO
114	NCKAP1	NCKAP1	NCKAP1	7632	0.038	0.46	NO
115	BDKRB2	BDKRB2	BDKRB2	7663	0.038	0.46	NO
116	PFN2	PFN2	PFN2	7747	0.037	0.45	NO
117	CDC42	CDC42	CDC42	7895	0.035	0.44	NO
118	PIP4K2C	PIP4K2C	PIP4K2C	8030	0.032	0.44	NO
119	SLC9A1	SLC9A1	SLC9A1	8100	0.032	0.44	NO
120	MYL12A	MYL12A	MYL12A	8115	0.031	0.44	NO
121	CRK	CRK	CRK	8214	0.03	0.43	NO
122	RRAS	RRAS	RRAS	8348	0.028	0.42	NO
123	ITGAE	ITGAE	ITGAE	8368	0.027	0.42	NO
124	ITGA8	ITGA8	ITGA8	8389	0.027	0.42	NO
125	EZR	EZR	EZR	8423	0.026	0.42	NO
126	PPP1CB	PPP1CB	PPP1CB	8605	0.024	0.41	NO
127	MAPK1	MAPK1	MAPK1	8628	0.024	0.41	NO
128	PTK2	PTK2	PTK2	8713	0.022	0.41	NO
129	PXN	PXN	PXN	8733	0.022	0.41	NO
130	RAC3	RAC3	RAC3	8765	0.022	0.41	NO
131	CRKL	CRKL	CRKL	8842	0.02	0.4	NO
132	RHOA	RHOA	RHOA	8846	0.02	0.4	NO
133	WASL	WASL	WASL	8853	0.02	0.4	NO
134	FGF23	FGF23	FGF23	8869	0.02	0.4	NO
135	DIAPH1	DIAPH1	DIAPH1	8953	0.019	0.4	NO
136	ARHGEF7	ARHGEF7	ARHGEF7	9113	0.016	0.39	NO
137	ARPC2	ARPC2	ARPC2	9187	0.015	0.39	NO
138	DIAPH2	DIAPH2	DIAPH2	9261	0.014	0.38	NO
139	ARPC5	ARPC5	ARPC5	9313	0.014	0.38	NO
140	FGF20	FGF20	FGF20	9365	0.013	0.38	NO
141	RRAS2	RRAS2	RRAS2	9385	0.013	0.38	NO
142	NRAS	NRAS	NRAS	9420	0.012	0.38	NO
143	BCAR1	BCAR1	BCAR1	9423	0.012	0.38	NO
144	ACTN4	ACTN4	ACTN4	9452	0.012	0.38	NO
145	LIMK2	LIMK2	LIMK2	9506	0.011	0.38	NO
146	ARPC1B	ARPC1B	ARPC1B	9640	0.0092	0.37	NO
147	GNG12	GNG12	GNG12	9645	0.0091	0.37	NO
148	IQGAP2	IQGAP2	IQGAP2	9723	0.008	0.36	NO
149	ACTB	ACTB	ACTB	9737	0.0078	0.36	NO
150	CYFIP1	CYFIP1	CYFIP1	9781	0.0071	0.36	NO
151	ITGA3	ITGA3	ITGA3	9939	0.0048	0.35	NO
152	ITGB4	ITGB4	ITGB4	10110	0.0022	0.34	NO
153	FGF8	FGF8	FGF8	10500	-0.0028	0.32	NO
154	RAF1	RAF1	RAF1	10537	-0.0033	0.32	NO
155	CSK	CSK	CSK	10970	-0.0097	0.3	NO
156	RAC1	RAC1	RAC1	11140	-0.012	0.29	NO
157	PPP1CC	PPP1CC	PPP1CC	11160	-0.012	0.28	NO
158	SCIN	SCIN	SCIN	11351	-0.015	0.28	NO
159	CFL1	CFL1	CFL1	11433	-0.017	0.27	NO
160	ARPC4	ARPC4	ARPC4	11509	-0.018	0.27	NO
161	ITGA6	ITGA6	ITGA6	11515	-0.018	0.27	NO
162	GIT1	GIT1	GIT1	11522	-0.018	0.27	NO
163	MYL12B	MYL12B	MYL12B	11563	-0.019	0.27	NO
164	CHRM3	CHRM3	CHRM3	11593	-0.02	0.26	NO
165	MYH14	MYH14	MYH14	11628	-0.02	0.26	NO
166	TMSB4Y	TMSB4Y	TMSB4Y	11787	-0.022	0.26	NO
167	DIAPH3	DIAPH3	DIAPH3	12013	-0.026	0.24	NO
168	PFN1	PFN1	PFN1	12062	-0.027	0.24	NO
169	ACTG1	ACTG1	ACTG1	12101	-0.028	0.24	NO
170	PAK1	PAK1	PAK1	12113	-0.028	0.24	NO
171	PFN4	PFN4	PFN4	12386	-0.032	0.23	NO
172	IQGAP3	IQGAP3	IQGAP3	12656	-0.036	0.21	NO
173	CHRM1	CHRM1	CHRM1	12734	-0.038	0.21	NO
174	APC2	APC2	APC2	12845	-0.04	0.2	NO
175	ITGB6	ITGB6	ITGB6	12866	-0.04	0.2	NO
176	PIK3R2	PIK3R2	PIK3R2	13011	-0.042	0.2	NO
177	HRAS	HRAS	HRAS	13053	-0.043	0.2	NO
178	SSH3	SSH3	SSH3	13056	-0.044	0.2	NO
179	CYFIP2	CYFIP2	CYFIP2	13279	-0.048	0.19	NO
180	ARAF	ARAF	ARAF	13395	-0.05	0.18	NO
181	PAK4	PAK4	PAK4	13463	-0.051	0.18	NO
182	ARPC1A	ARPC1A	ARPC1A	13558	-0.053	0.18	NO
183	ITGA2B	ITGA2B	ITGA2B	13954	-0.06	0.16	NO
184	PPP1CA	PPP1CA	PPP1CA	14114	-0.064	0.15	NO
185	ARPC5L	ARPC5L	ARPC5L	14175	-0.065	0.15	NO
186	TMSL3	TMSL3	TMSL3	14180	-0.065	0.15	NO
187	PAK6	PAK6	PAK6	14194	-0.065	0.15	NO
188	MAPK3	MAPK3	MAPK3	14205	-0.066	0.15	NO
189	MAP2K2	MAP2K2	MAP2K2	14316	-0.068	0.15	NO
190	FGF17	FGF17	FGF17	14876	-0.083	0.12	NO
191	PIP5K1B	PIP5K1B	PIP5K1B	16038	-0.13	0.06	NO
192	EGF	EGF	EGF	16280	-0.14	0.051	NO
193	FGFR4	FGFR4	FGFR4	16294	-0.14	0.055	NO
194	MYL5	MYL5	MYL5	16726	-0.17	0.036	NO
195	VAV3	VAV3	VAV3	17005	-0.21	0.028	NO
196	F2	F2	F2	17358	-0.26	0.016	NO
197	FGFR3	FGFR3	FGFR3	17372	-0.26	0.024	NO
198	MYLPF	MYLPF	MYLPF	17769	-0.38	0.014	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 CALCIUM SIGNALING PATHWAY.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CALCIUM 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 CYTOKINE CYTOKINE RECEPTOR INTERACTION

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	ESR1	ESR1	ESR1	260	0.62	0.054	YES
2	AR	AR	AR	675	0.5	0.087	YES
3	IL10	IL10	IL10	956	0.44	0.12	YES
4	NR3C1	NR3C1	NR3C1	1052	0.43	0.16	YES
5	RUNX2	RUNX2	RUNX2	1097	0.42	0.21	YES
6	SERPINE1	SERPINE1	SERPINE1	1134	0.41	0.25	YES
7	GATA3	GATA3	GATA3	1202	0.41	0.29	YES
8	MEF2C	MEF2C	MEF2C	1397	0.38	0.32	YES
9	GSC	GSC	GSC	1668	0.35	0.35	YES
10	RUNX3	RUNX3	RUNX3	1866	0.32	0.37	YES
11	COL1A2	COL1A2	COL1A2	1949	0.32	0.4	YES
12	CDKN2B	CDKN2B	CDKN2B	2143	0.29	0.43	YES
13	KAT2B	KAT2B	KAT2B	2947	0.21	0.41	YES
14	DLX1	DLX1	DLX1	3401	0.18	0.4	YES
15	LAMC1	LAMC1	LAMC1	3417	0.18	0.42	YES
16	RUNX1	RUNX1	RUNX1	3430	0.17	0.44	YES
17	PIAS3	PIAS3	PIAS3	3565	0.17	0.45	YES
18	FOXO1	FOXO1	FOXO1	3578	0.16	0.47	YES
19	SMAD7	SMAD7	SMAD7	4489	0.12	0.43	YES
20	NCOA1	NCOA1	NCOA1	4789	0.1	0.42	YES
21	IRF7	IRF7	IRF7	4856	0.1	0.43	YES
22	ITGB5	ITGB5	ITGB5	4922	0.1	0.44	YES
23	NCOA2	NCOA2	NCOA2	4959	0.098	0.45	YES
24	CREB1	CREB1	CREB1	5063	0.094	0.45	YES
25	ATF2	ATF2	ATF2	5122	0.092	0.46	YES
26	EP300	EP300	EP300	5244	0.089	0.46	YES
27	TFE3	TFE3	TFE3	5516	0.081	0.46	YES
28	FOXO4	FOXO4	FOXO4	5521	0.081	0.47	YES
29	SKI	SKI	SKI	5669	0.078	0.47	YES
30	SMAD2	SMAD2	SMAD2	5779	0.075	0.47	YES
31	SKIL	SKIL	SKIL	5909	0.072	0.47	YES
32	SAP30	SAP30	SAP30	5914	0.072	0.48	YES
33	CREBBP	CREBBP	CREBBP	5977	0.071	0.48	YES
34	MAX	MAX	MAX	6098	0.068	0.48	YES
35	IL5	IL5	IL5	6190	0.066	0.49	YES
36	SP3	SP3	SP3	6410	0.061	0.48	YES
37	SIN3A	SIN3A	SIN3A	6650	0.056	0.47	YES
38	NCOR1	NCOR1	NCOR1	6803	0.053	0.47	YES
39	CBFB	CBFB	CBFB	6844	0.052	0.47	YES
40	SMAD3	SMAD3	SMAD3	6922	0.051	0.48	YES
41	SNIP1	SNIP1	SNIP1	6929	0.051	0.48	YES
42	TGIF2	TGIF2	TGIF2	6983	0.05	0.48	YES
43	SP1	SP1	SP1	7016	0.049	0.49	YES
44	FOS	FOS	FOS	7042	0.048	0.49	YES
45	SMAD4	SMAD4	SMAD4	7330	0.043	0.48	NO
46	ATF3	ATF3	ATF3	7449	0.041	0.48	NO
47	SIN3B	SIN3B	SIN3B	7452	0.041	0.48	NO
48	ZBTB17	ZBTB17	ZBTB17	7573	0.039	0.48	NO
49	MED15	MED15	MED15	7959	0.034	0.46	NO
50	DCP1A	DCP1A	DCP1A	8985	0.018	0.41	NO
51	FOXO3	FOXO3	FOXO3	9278	0.014	0.39	NO
52	RBBP4	RBBP4	RBBP4	9391	0.013	0.39	NO
53	RBL1	RBL1	RBL1	9559	0.01	0.38	NO
54	CDK2	CDK2	CDK2	9819	0.0067	0.37	NO
55	AKT1	AKT1	AKT1	9836	0.0065	0.37	NO
56	TGIF1	TGIF1	TGIF1	9941	0.0047	0.36	NO
57	HDAC2	HDAC2	HDAC2	10070	0.0027	0.35	NO
58	VDR	VDR	VDR	10230	0.00063	0.34	NO
59	JUN	JUN	JUN	10340	-0.00075	0.34	NO
60	HSPA8	HSPA8	HSPA8	10604	-0.0043	0.32	NO
61	FOXG1	FOXG1	FOXG1	10758	-0.0066	0.32	NO
62	CEBPB	CEBPB	CEBPB	11135	-0.012	0.3	NO
63	CTBP1	CTBP1	CTBP1	11869	-0.024	0.26	NO
64	E2F5	E2F5	E2F5	12016	-0.026	0.25	NO
65	HDAC1	HDAC1	HDAC1	12055	-0.027	0.26	NO
66	TCF3	TCF3	TCF3	12084	-0.027	0.26	NO
67	PIAS4	PIAS4	PIAS4	12300	-0.03	0.25	NO
68	TFDP1	TFDP1	TFDP1	12506	-0.034	0.24	NO
69	SAP18	SAP18	SAP18	12533	-0.034	0.24	NO
70	CDKN1A	CDKN1A	CDKN1A	12713	-0.037	0.24	NO
71	E2F4	E2F4	E2F4	12748	-0.038	0.24	NO
72	CITED1	CITED1	CITED1	12774	-0.038	0.24	NO
73	RBBP7	RBBP7	RBBP7	13351	-0.049	0.22	NO
74	KAT2A	KAT2A	KAT2A	13746	-0.056	0.2	NO
75	CDK4	CDK4	CDK4	13763	-0.057	0.21	NO
76	MYC	MYC	MYC	13899	-0.059	0.2	NO
77	HNF4A	HNF4A	HNF4A	14034	-0.062	0.2	NO
78	FOXH1	FOXH1	FOXH1	16611	-0.16	0.079	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 CYTOKINE CYTOKINE RECEPTOR INTERACTION.

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

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

Table 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	LY96	LY96	LY96	226	0.63	0.19	YES
2	GJA1	GJA1	GJA1	2021	0.31	0.19	YES
3	CD14	CD14	CD14	2249	0.28	0.27	YES
4	LEF1	LEF1	LEF1	2773	0.23	0.31	YES
5	FZD1	FZD1	FZD1	2850	0.22	0.38	YES
6	APC	APC	APC	3356	0.18	0.41	YES
7	GNAI1	GNAI1	GNAI1	3408	0.18	0.46	YES
8	TLR4	TLR4	TLR4	3491	0.17	0.51	YES
9	PIK3CA	PIK3CA	PIK3CA	3525	0.17	0.56	YES
10	EIF2AK2	EIF2AK2	EIF2AK2	3786	0.15	0.6	YES
11	WNT1	WNT1	WNT1	4282	0.13	0.61	YES
12	CCND1	CCND1	CCND1	5693	0.077	0.56	NO
13	PIK3R1	PIK3R1	PIK3R1	5888	0.072	0.57	NO
14	LBP	LBP	LBP	6951	0.05	0.53	NO
15	NFKB1	NFKB1	NFKB1	7937	0.034	0.48	NO
16	RELA	RELA	RELA	8676	0.023	0.45	NO
17	MYD88	MYD88	MYD88	8876	0.02	0.44	NO
18	GSK3B	GSK3B	GSK3B	8880	0.02	0.45	NO
19	PDPK1	PDPK1	PDPK1	9294	0.014	0.43	NO
20	AKT1	AKT1	AKT1	9836	0.0065	0.4	NO
21	TIRAP	TIRAP	TIRAP	9899	0.0054	0.4	NO
22	CTNNB1	CTNNB1	CTNNB1	10860	-0.008	0.35	NO
23	IRAK1	IRAK1	IRAK1	11457	-0.017	0.32	NO
24	PPP2CA	PPP2CA	PPP2CA	11498	-0.018	0.33	NO
25	TOLLIP	TOLLIP	TOLLIP	12174	-0.029	0.3	NO
26	AXIN1	AXIN1	AXIN1	12557	-0.035	0.29	NO
27	DVL1	DVL1	DVL1	13245	-0.047	0.27	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 CHEMOKINE SIGNALING PATHWAY.

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

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 PATHOGENIC ESCHERICHIA COLI INFECTION	53	genes.ES.table	0.44	1.7	0.021	0.66	0.84	0.21	0.16	0.18	0.25	0.18
KEGG SYSTEMIC LUPUS ERYTHEMATOSUS	117	genes.ES.table	0.74	1.7	0.0039	0.81	0.78	0.52	0.11	0.46	0.28	0.2
REACTOME TRANSLATION	146	genes.ES.table	0.48	1.7	0.088	0.59	0.85	0.1	0.075	0.096	0.22	0.16
REACTOME MEIOSIS	98	genes.ES.table	0.67	1.7	0.014	0.72	0.81	0.4	0.11	0.36	0.25	0.18
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE	109	genes.ES.table	0.55	1.7	0.064	0.69	0.82	0.13	0.075	0.12	0.24	0.18
REACTOME RNA POL I TRANSCRIPTION	77	genes.ES.table	0.72	1.7	0.02	0.63	0.85	0.49	0.11	0.44	0.23	0.17
REACTOME PEPTIDE CHAIN ELONGATION	85	genes.ES.table	0.6	1.6	0.064	0.61	0.88	0.2	0.11	0.18	0.26	0.17
REACTOME METABOLISM OF PROTEINS	416	genes.ES.table	0.31	1.7	0.015	1	0.69	0.2	0.21	0.16	0.39	0.29
REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION	105	genes.ES.table	0.57	1.7	0.06	0.68	0.83	0.14	0.075	0.13	0.25	0.18
REACTOME TRANSCRIPTION	187	genes.ES.table	0.5	1.8	0.021	1	0.64	0.22	0.12	0.2	0.6	0.4

genes ES table in pathway: KEGG PATHOGENIC ESCHERICHIA COLI INFECTION

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	HIST1H4K	HIST1H4K	HIST1H4K	4	1.8	0.09	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	58	1.3	0.15	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	81	1.2	0.21	YES
4	FKBP6	FKBP6	FKBP6	106	1	0.26	YES
5	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	158	0.9	0.3	YES
6	HIST1H2BN	HIST1H2BN	HIST1H2BN	331	0.62	0.33	YES
7	HIST1H4J	HIST1H4J	HIST1H4J	423	0.54	0.35	YES
8	STAG3	STAG3	STAG3	460	0.51	0.37	YES
9	HIST1H2BE	HIST1H2BE	HIST1H2BE	484	0.5	0.4	YES
10	HIST1H2BL	HIST1H2BL	HIST1H2BL	537	0.46	0.42	YES
11	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	553	0.45	0.44	YES
12	HIST1H4I	HIST1H4I	HIST1H4I	556	0.45	0.46	YES
13	HIST2H4A	HIST2H4A	HIST2H4A	580	0.43	0.48	YES
14	HIST1H4A	HIST1H4A	HIST1H4A	623	0.4	0.5	YES
15	HIST1H4B	HIST1H4B	HIST1H4B	761	0.35	0.51	YES
16	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	844	0.32	0.52	YES
17	HIST1H4E	HIST1H4E	HIST1H4E	931	0.3	0.53	YES
18	HIST3H2BB	HIST3H2BB	HIST3H2BB	985	0.28	0.54	YES
19	TERT	TERT	TERT	1009	0.28	0.56	YES
20	HIST1H4C	HIST1H4C	HIST1H4C	1115	0.26	0.56	YES
21	HIST1H4D	HIST1H4D	HIST1H4D	1150	0.25	0.57	YES
22	HIST1H2BH	HIST1H2BH	HIST1H2BH	1439	0.22	0.57	YES
23	HIST1H2BI	HIST1H2BI	HIST1H2BI	1554	0.21	0.57	YES
24	REC8	REC8	REC8	1606	0.2	0.58	YES
25	HIST1H2BC	HIST1H2BC	HIST1H2BC	1766	0.19	0.58	YES
26	HIST1H2AB	HIST1H2AB	HIST1H2AB	1767	0.19	0.59	YES
27	HIST1H4H	HIST1H4H	HIST1H4H	1781	0.19	0.6	YES
28	HIST1H2BG	HIST1H2BG	HIST1H2BG	1887	0.18	0.6	YES
29	HIST1H2BF	HIST1H2BF	HIST1H2BF	1953	0.18	0.61	YES
30	H2AFX	H2AFX	H2AFX	2055	0.17	0.61	YES
31	HIST3H3	HIST3H3	HIST3H3	2394	0.15	0.6	NO
32	HIST1H2BM	HIST1H2BM	HIST1H2BM	3071	0.12	0.57	NO
33	POLD1	POLD1	POLD1	3119	0.12	0.57	NO
34	RUVBL2	RUVBL2	RUVBL2	3370	0.11	0.56	NO
35	HIST1H2BK	HIST1H2BK	HIST1H2BK	3517	0.1	0.56	NO
36	HIST1H2AE	HIST1H2AE	HIST1H2AE	3686	0.099	0.56	NO
37	ACD	ACD	ACD	4688	0.072	0.5	NO
38	OIP5	OIP5	OIP5	4858	0.068	0.5	NO
39	PCNA	PCNA	PCNA	5000	0.065	0.49	NO
40	POLA2	POLA2	POLA2	5203	0.061	0.49	NO
41	WRAP53	WRAP53	WRAP53	5292	0.06	0.48	NO
42	NHP2	NHP2	NHP2	5310	0.059	0.49	NO
43	POLD2	POLD2	POLD2	5515	0.055	0.48	NO
44	HIST1H2BD	HIST1H2BD	HIST1H2BD	5701	0.052	0.47	NO
45	POLE2	POLE2	POLE2	5843	0.049	0.46	NO
46	RFC2	RFC2	RFC2	5996	0.046	0.46	NO
47	PRIM2	PRIM2	PRIM2	6125	0.043	0.45	NO
48	POLD4	POLD4	POLD4	6773	0.032	0.42	NO
49	UBE2I	UBE2I	UBE2I	7232	0.024	0.39	NO
50	CENPN	CENPN	CENPN	7445	0.021	0.38	NO
51	RUVBL1	RUVBL1	RUVBL1	7525	0.019	0.38	NO
52	CENPP	CENPP	CENPP	7583	0.018	0.38	NO
53	H2AFZ	H2AFZ	H2AFZ	7879	0.013	0.36	NO
54	RFC5	RFC5	RFC5	8181	0.0093	0.35	NO
55	SMC1B	SMC1B	SMC1B	8321	0.0068	0.34	NO
56	HIST1H2AC	HIST1H2AC	HIST1H2AC	8453	0.0047	0.33	NO
57	LMNA	LMNA	LMNA	8546	0.0032	0.33	NO
58	LIG1	LIG1	LIG1	8722	0.00076	0.32	NO
59	RPA2	RPA2	RPA2	8730	0.00058	0.32	NO
60	TINF2	TINF2	TINF2	8816	-0.00081	0.31	NO
61	CENPO	CENPO	CENPO	8820	-0.00084	0.31	NO
62	RPA1	RPA1	RPA1	8867	-0.0015	0.31	NO
63	RBBP7	RBBP7	RBBP7	9042	-0.0041	0.3	NO
64	FEN1	FEN1	FEN1	9184	-0.0065	0.29	NO
65	POLE	POLE	POLE	9310	-0.0086	0.28	NO
66	RPA3	RPA3	RPA3	9467	-0.011	0.28	NO
67	CENPA	CENPA	CENPA	9838	-0.016	0.26	NO
68	LMNB1	LMNB1	LMNB1	10246	-0.023	0.24	NO
69	HSPA2	HSPA2	HSPA2	10310	-0.024	0.23	NO
70	TERF2	TERF2	TERF2	10423	-0.025	0.23	NO
71	PRIM1	PRIM1	PRIM1	10452	-0.026	0.23	NO
72	RFC3	RFC3	RFC3	10869	-0.032	0.21	NO
73	RFC4	RFC4	RFC4	10877	-0.032	0.21	NO
74	RBBP4	RBBP4	RBBP4	11088	-0.035	0.2	NO
75	HJURP	HJURP	HJURP	11199	-0.037	0.19	NO
76	CENPH	CENPH	CENPH	11603	-0.043	0.17	NO
77	DKC1	DKC1	DKC1	12370	-0.057	0.13	NO
78	SUN2	SUN2	SUN2	12444	-0.058	0.13	NO
79	DIDO1	DIDO1	DIDO1	12480	-0.058	0.13	NO
80	CENPI	CENPI	CENPI	12913	-0.066	0.11	NO
81	HIST1H2AD	HIST1H2AD	HIST1H2AD	13139	-0.07	0.1	NO
82	ATR	ATR	ATR	13198	-0.071	0.1	NO
83	POLD3	POLD3	POLD3	13315	-0.073	0.1	NO
84	POLA1	POLA1	POLA1	13321	-0.074	0.1	NO
85	SMC1A	SMC1A	SMC1A	13381	-0.075	0.1	NO
86	HIST2H2BE	HIST2H2BE	HIST2H2BE	13479	-0.076	0.1	NO
87	POT1	POT1	POT1	13668	-0.08	0.097	NO
88	TERF2IP	TERF2IP	TERF2IP	13721	-0.081	0.098	NO
89	MLF1IP	MLF1IP	MLF1IP	13744	-0.082	0.1	NO
90	RAD21	RAD21	RAD21	13910	-0.085	0.096	NO
91	BRCA1	BRCA1	BRCA1	14449	-0.096	0.071	NO
92	DNA2	DNA2	DNA2	14562	-0.099	0.07	NO
93	ITGB3BP	ITGB3BP	ITGB3BP	14937	-0.11	0.055	NO
94	SYCP2	SYCP2	SYCP2	15019	-0.11	0.056	NO
95	STAG2	STAG2	STAG2	15046	-0.11	0.06	NO
96	HIST4H4	HIST4H4	HIST4H4	15078	-0.11	0.064	NO
97	CASC5	CASC5	CASC5	15339	-0.12	0.055	NO
98	STAG1	STAG1	STAG1	15479	-0.12	0.054	NO
99	SMARCA5	SMARCA5	SMARCA5	15569	-0.12	0.055	NO
100	SYNE2	SYNE2	SYNE2	15868	-0.13	0.045	NO
101	TERF1	TERF1	TERF1	16455	-0.15	0.02	NO
102	NPM1	NPM1	NPM1	16823	-0.17	0.0078	NO
103	SMC3	SMC3	SMC3	16845	-0.17	0.015	NO
104	TEX12	TEX12	TEX12	16854	-0.17	0.023	NO
105	CENPK	CENPK	CENPK	16886	-0.17	0.03	NO
106	CENPQ	CENPQ	CENPQ	17307	-0.2	0.017	NO
107	SYNE1	SYNE1	SYNE1	17442	-0.21	0.02	NO
108	RSF1	RSF1	RSF1	17785	-0.25	0.013	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 PATHOGENIC ESCHERICHIA COLI INFECTION.

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

genes ES table in pathway: KEGG SYSTEMIC LUPUS ERYTHEMATOSUS

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	HIST1H4K	HIST1H4K	HIST1H4K	4	1.8	0.064	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	58	1.3	0.11	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	81	1.2	0.15	YES
4	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	158	0.9	0.18	YES
5	HIST2H3C	HIST2H3C	HIST2H3C	192	0.82	0.2	YES
6	HIST2H3D	HIST2H3D	HIST2H3D	232	0.76	0.23	YES
7	HIST1H2BN	HIST1H2BN	HIST1H2BN	331	0.62	0.24	YES
8	GTF2H2B	GTF2H2B	GTF2H2B	332	0.62	0.27	YES
9	HIST1H4J	HIST1H4J	HIST1H4J	423	0.54	0.28	YES
10	HIST1H2BE	HIST1H2BE	HIST1H2BE	484	0.5	0.3	YES
11	HIST1H2BL	HIST1H2BL	HIST1H2BL	537	0.46	0.31	YES
12	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	553	0.45	0.33	YES
13	HIST1H4I	HIST1H4I	HIST1H4I	556	0.45	0.34	YES
14	GTF2H2	GTF2H2	GTF2H2	570	0.44	0.36	YES
15	HIST2H4A	HIST2H4A	HIST2H4A	580	0.43	0.37	YES
16	HIST1H4A	HIST1H4A	HIST1H4A	623	0.4	0.38	YES
17	HIST1H4B	HIST1H4B	HIST1H4B	761	0.35	0.39	YES
18	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	844	0.32	0.4	YES
19	HIST1H3H	HIST1H3H	HIST1H3H	878	0.31	0.4	YES
20	HIST1H4E	HIST1H4E	HIST1H4E	931	0.3	0.41	YES
21	HIST3H2BB	HIST3H2BB	HIST3H2BB	985	0.28	0.42	YES
22	HIST1H3D	HIST1H3D	HIST1H3D	1034	0.27	0.43	YES
23	HIST1H4C	HIST1H4C	HIST1H4C	1115	0.26	0.43	YES
24	HIST1H3B	HIST1H3B	HIST1H3B	1126	0.26	0.44	YES
25	HIST1H4D	HIST1H4D	HIST1H4D	1150	0.25	0.45	YES
26	HIST1H3F	HIST1H3F	HIST1H3F	1404	0.22	0.44	YES
27	POLR2I	POLR2I	POLR2I	1412	0.22	0.45	YES
28	HIST1H2BH	HIST1H2BH	HIST1H2BH	1439	0.22	0.46	YES
29	HIST1H3J	HIST1H3J	HIST1H3J	1451	0.22	0.46	YES
30	HIST1H2BI	HIST1H2BI	HIST1H2BI	1554	0.21	0.47	YES
31	HIST1H3G	HIST1H3G	HIST1H3G	1668	0.2	0.47	YES
32	HIST1H3A	HIST1H3A	HIST1H3A	1676	0.2	0.47	YES
33	HIST1H2BC	HIST1H2BC	HIST1H2BC	1766	0.19	0.48	YES
34	HIST1H2AB	HIST1H2AB	HIST1H2AB	1767	0.19	0.48	YES
35	HIST1H4H	HIST1H4H	HIST1H4H	1781	0.19	0.49	YES
36	HIST1H2BG	HIST1H2BG	HIST1H2BG	1887	0.18	0.49	YES
37	HIST1H2BF	HIST1H2BF	HIST1H2BF	1953	0.18	0.49	YES
38	HIST1H3I	HIST1H3I	HIST1H3I	1967	0.17	0.5	YES
39	H2AFX	H2AFX	H2AFX	2055	0.17	0.5	YES
40	POLR2L	POLR2L	POLR2L	2127	0.16	0.5	YES
41	TAF10	TAF10	TAF10	2187	0.16	0.5	YES
42	POLR2G	POLR2G	POLR2G	2387	0.15	0.5	NO
43	LSM10	LSM10	LSM10	2749	0.13	0.48	NO
44	H3F3A	H3F3A	H3F3A	2899	0.12	0.48	NO
45	HIST1H2BM	HIST1H2BM	HIST1H2BM	3071	0.12	0.47	NO
46	TCEB2	TCEB2	TCEB2	3273	0.11	0.46	NO
47	HIST1H3C	HIST1H3C	HIST1H3C	3383	0.11	0.46	NO
48	POLR3K	POLR3K	POLR3K	3506	0.1	0.46	NO
49	HIST1H2BK	HIST1H2BK	HIST1H2BK	3517	0.1	0.46	NO
50	HIST1H2AE	HIST1H2AE	HIST1H2AE	3686	0.099	0.46	NO
51	POLR2H	POLR2H	POLR2H	4013	0.089	0.44	NO
52	SNAPC5	SNAPC5	SNAPC5	4107	0.087	0.44	NO
53	COBRA1	COBRA1	COBRA1	4183	0.085	0.44	NO
54	POLR1C	POLR1C	POLR1C	4203	0.084	0.44	NO
55	MAPK3	MAPK3	MAPK3	4640	0.073	0.42	NO
56	POLR2F	POLR2F	POLR2F	4800	0.07	0.41	NO
57	ERCC2	ERCC2	ERCC2	4818	0.069	0.41	NO
58	POLR3H	POLR3H	POLR3H	4837	0.068	0.42	NO
59	SNRPB	SNRPB	SNRPB	4928	0.067	0.41	NO
60	POLRMT	POLRMT	POLRMT	4957	0.066	0.41	NO
61	SUPT4H1	SUPT4H1	SUPT4H1	4967	0.066	0.42	NO
62	POLR2J	POLR2J	POLR2J	5284	0.06	0.4	NO
63	THOC4	THOC4	THOC4	5312	0.059	0.4	NO
64	CSTF1	CSTF1	CSTF1	5410	0.057	0.4	NO
65	HIST1H2BD	HIST1H2BD	HIST1H2BD	5701	0.052	0.38	NO
66	POLR3E	POLR3E	POLR3E	5808	0.05	0.38	NO
67	POLR2C	POLR2C	POLR2C	5889	0.048	0.38	NO
68	POLR2E	POLR2E	POLR2E	5942	0.047	0.38	NO
69	POLR2D	POLR2D	POLR2D	5954	0.047	0.38	NO
70	CPSF1	CPSF1	CPSF1	6113	0.044	0.37	NO
71	RNPS1	RNPS1	RNPS1	6227	0.042	0.36	NO
72	CTDP1	CTDP1	CTDP1	6240	0.041	0.36	NO
73	GTF3C5	GTF3C5	GTF3C5	6378	0.039	0.36	NO
74	CDK9	CDK9	CDK9	6511	0.036	0.35	NO
75	RDBP	RDBP	RDBP	6556	0.036	0.35	NO
76	BRF2	BRF2	BRF2	6731	0.033	0.34	NO
77	POLR3D	POLR3D	POLR3D	6739	0.033	0.34	NO
78	GTF2H4	GTF2H4	GTF2H4	6918	0.029	0.33	NO
79	POLR3C	POLR3C	POLR3C	6932	0.029	0.33	NO
80	CLP1	CLP1	CLP1	6959	0.029	0.33	NO
81	WHSC2	WHSC2	WHSC2	7036	0.028	0.33	NO
82	EHMT2	EHMT2	EHMT2	7097	0.026	0.33	NO
83	BRF1	BRF1	BRF1	7244	0.024	0.32	NO
84	TH1L	TH1L	TH1L	7273	0.023	0.32	NO
85	U2AF1	U2AF1	U2AF1	7307	0.023	0.32	NO
86	POLR3B	POLR3B	POLR3B	7460	0.02	0.31	NO
87	SNRPF	SNRPF	SNRPF	7691	0.016	0.3	NO
88	TAF6	TAF6	TAF6	7701	0.016	0.3	NO
89	H2AFZ	H2AFZ	H2AFZ	7879	0.013	0.29	NO
90	ZNF143	ZNF143	ZNF143	7904	0.013	0.29	NO
91	TAF1C	TAF1C	TAF1C	7912	0.013	0.29	NO
92	TBP	TBP	TBP	8166	0.0094	0.28	NO
93	U2AF2	U2AF2	U2AF2	8403	0.0054	0.26	NO
94	HIST1H2AC	HIST1H2AC	HIST1H2AC	8453	0.0047	0.26	NO
95	SLBP	SLBP	SLBP	8565	0.003	0.25	NO
96	SNAPC4	SNAPC4	SNAPC4	8831	-0.00099	0.24	NO
97	SNAPC2	SNAPC2	SNAPC2	8891	-0.0018	0.24	NO
98	ELL	ELL	ELL	8917	-0.0022	0.23	NO
99	DHX38	DHX38	DHX38	8932	-0.0023	0.23	NO
100	ERCC3	ERCC3	ERCC3	8961	-0.0028	0.23	NO
101	CPSF3	CPSF3	CPSF3	9248	-0.0075	0.22	NO
102	TAF9	TAF9	TAF9	9369	-0.0096	0.21	NO
103	POLR1B	POLR1B	POLR1B	9405	-0.01	0.21	NO
104	GTF2E2	GTF2E2	GTF2E2	9518	-0.012	0.2	NO
105	GTF2F1	GTF2F1	GTF2F1	9729	-0.015	0.19	NO
106	MNAT1	MNAT1	MNAT1	9760	-0.015	0.19	NO
107	POLR3A	POLR3A	POLR3A	9809	-0.016	0.19	NO
108	GTF2E1	GTF2E1	GTF2E1	9969	-0.018	0.18	NO
109	SNRPG	SNRPG	SNRPG	10187	-0.022	0.17	NO
110	GTF3C2	GTF3C2	GTF3C2	10346	-0.024	0.16	NO
111	SUPT5H	SUPT5H	SUPT5H	10368	-0.024	0.16	NO
112	TCEA1	TCEA1	TCEA1	10437	-0.026	0.16	NO
113	CSTF2	CSTF2	CSTF2	10467	-0.026	0.16	NO
114	NFX1	NFX1	NFX1	10643	-0.029	0.15	NO
115	GTF3C3	GTF3C3	GTF3C3	10657	-0.029	0.15	NO
116	POLR2B	POLR2B	POLR2B	10786	-0.031	0.14	NO
117	GTF2H3	GTF2H3	GTF2H3	10792	-0.031	0.14	NO
118	MAGOH	MAGOH	MAGOH	10799	-0.031	0.14	NO
119	POLR1D	POLR1D	POLR1D	11049	-0.034	0.13	NO
120	TAF5	TAF5	TAF5	11234	-0.038	0.12	NO
121	ZNF473	ZNF473	ZNF473	11270	-0.038	0.12	NO
122	SNRPD3	SNRPD3	SNRPD3	11363	-0.04	0.12	NO
123	NCBP1	NCBP1	NCBP1	11393	-0.04	0.12	NO
124	TAF4	TAF4	TAF4	11457	-0.041	0.12	NO
125	CCNH	CCNH	CCNH	11475	-0.041	0.12	NO
126	TCEB1	TCEB1	TCEB1	11640	-0.044	0.11	NO
127	CPSF7	CPSF7	CPSF7	11686	-0.045	0.11	NO
128	SSRP1	SSRP1	SSRP1	11756	-0.046	0.1	NO
129	PABPN1	PABPN1	PABPN1	11786	-0.046	0.1	NO
130	GTF3C4	GTF3C4	GTF3C4	12321	-0.056	0.077	NO
131	RBM8A	RBM8A	RBM8A	12358	-0.056	0.077	NO
132	GTF2H1	GTF2H1	GTF2H1	12399	-0.057	0.077	NO
133	POLR3F	POLR3F	POLR3F	12597	-0.06	0.068	NO
134	NUDT21	NUDT21	NUDT21	12877	-0.065	0.055	NO
135	GTF2A2	GTF2A2	GTF2A2	13005	-0.067	0.05	NO
136	TAF11	TAF11	TAF11	13035	-0.068	0.051	NO
137	GTF2B	GTF2B	GTF2B	13117	-0.07	0.049	NO
138	SNAPC3	SNAPC3	SNAPC3	13126	-0.07	0.051	NO
139	HIST1H2AD	HIST1H2AD	HIST1H2AD	13139	-0.07	0.053	NO
140	RNMT	RNMT	RNMT	13288	-0.073	0.047	NO
141	CCNT1	CCNT1	CCNT1	13302	-0.073	0.049	NO
142	NFIB	NFIB	NFIB	13316	-0.073	0.051	NO
143	H3F3B	H3F3B	H3F3B	13346	-0.074	0.052	NO
144	HIST1H3E	HIST1H3E	HIST1H3E	13354	-0.074	0.054	NO
145	SUPT16H	SUPT16H	SUPT16H	13368	-0.075	0.056	NO
146	POLR1A	POLR1A	POLR1A	13397	-0.075	0.057	NO
147	POLR2A	POLR2A	POLR2A	13398	-0.075	0.06	NO
148	HIST2H2BE	HIST2H2BE	HIST2H2BE	13479	-0.076	0.058	NO
149	SNRPE	SNRPE	SNRPE	13567	-0.078	0.056	NO
150	UBTF	UBTF	UBTF	13909	-0.085	0.04	NO
151	TAF12	TAF12	TAF12	14139	-0.09	0.031	NO
152	TCEB3	TCEB3	TCEB3	14160	-0.09	0.033	NO
153	NCBP2	NCBP2	NCBP2	14253	-0.092	0.031	NO
154	LSM11	LSM11	LSM11	14324	-0.094	0.03	NO
155	SRRM1	SRRM1	SRRM1	14354	-0.094	0.032	NO
156	CPSF2	CPSF2	CPSF2	14570	-0.1	0.024	NO
157	PTRF	PTRF	PTRF	14576	-0.1	0.027	NO
158	GTF2A1	GTF2A1	GTF2A1	14581	-0.1	0.03	NO
159	TFB2M	TFB2M	TFB2M	14751	-0.1	0.025	NO
160	MBD2	MBD2	MBD2	14765	-0.1	0.028	NO
161	CCNT2	CCNT2	CCNT2	14862	-0.11	0.026	NO
162	GTF2F2	GTF2F2	GTF2F2	14887	-0.11	0.029	NO
163	HIST4H4	HIST4H4	HIST4H4	15078	-0.11	0.022	NO
164	PAPOLA	PAPOLA	PAPOLA	15322	-0.12	0.012	NO
165	RRN3	RRN3	RRN3	15376	-0.12	0.014	NO
166	RNGTT	RNGTT	RNGTT	15441	-0.12	0.014	NO
167	CSTF3	CSTF3	CSTF3	15454	-0.12	0.018	NO
168	POLR2K	POLR2K	POLR2K	15639	-0.12	0.012	NO
169	TFAM	TFAM	TFAM	15726	-0.13	0.012	NO
170	LZTS1	LZTS1	LZTS1	15826	-0.13	0.011	NO
171	CDC40	CDC40	CDC40	15918	-0.13	0.011	NO
172	CDK7	CDK7	CDK7	15953	-0.13	0.014	NO
173	ERCC6	ERCC6	ERCC6	16273	-0.14	0.0012	NO
174	PCF11	PCF11	PCF11	16422	-0.15	-0.0018	NO
175	TAF4B	TAF4B	TAF4B	16427	-0.15	0.0033	NO
176	POU2F1	POU2F1	POU2F1	16577	-0.16	0.00056	NO
177	TAF1	TAF1	TAF1	16914	-0.17	-0.012	NO
178	TAF13	TAF13	TAF13	17069	-0.18	-0.014	NO
179	TAF1B	TAF1B	TAF1B	17113	-0.18	-0.01	NO
180	CBX3	CBX3	CBX3	17125	-0.18	-0.0041	NO
181	UPF3B	UPF3B	UPF3B	17163	-0.19	0.00054	NO
182	POLR3GL	POLR3GL	POLR3GL	17199	-0.19	0.0054	NO
183	MTERF	MTERF	MTERF	17276	-0.19	0.0081	NO
184	TAF1A	TAF1A	TAF1A	17480	-0.21	0.0043	NO
185	KAT2B	KAT2B	KAT2B	17579	-0.22	0.0068	NO
186	SNAPC1	SNAPC1	SNAPC1	17677	-0.24	0.0098	NO
187	SSB	SSB	SSB	17850	-0.27	0.0098	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 SYSTEMIC LUPUS ERYTHEMATOSUS.

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

genes ES table in pathway: REACTOME TRANSLATION

Table 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	HIST1H4K	HIST1H4K	HIST1H4K	4	1.8	0.12	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	58	1.3	0.2	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	81	1.2	0.28	YES
4	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	158	0.9	0.34	YES
5	HIST1H2BN	HIST1H2BN	HIST1H2BN	331	0.62	0.37	YES
6	HIST1H4J	HIST1H4J	HIST1H4J	423	0.54	0.4	YES
7	HIST1H2BE	HIST1H2BE	HIST1H2BE	484	0.5	0.43	YES
8	HIST1H2BL	HIST1H2BL	HIST1H2BL	537	0.46	0.46	YES
9	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	553	0.45	0.49	YES
10	HIST1H4I	HIST1H4I	HIST1H4I	556	0.45	0.52	YES
11	HIST2H4A	HIST2H4A	HIST2H4A	580	0.43	0.54	YES
12	HIST1H4A	HIST1H4A	HIST1H4A	623	0.4	0.57	YES
13	HIST1H4B	HIST1H4B	HIST1H4B	761	0.35	0.58	YES
14	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	844	0.32	0.6	YES
15	HIST1H4E	HIST1H4E	HIST1H4E	931	0.3	0.62	YES
16	HIST3H2BB	HIST3H2BB	HIST3H2BB	985	0.28	0.63	YES
17	TERT	TERT	TERT	1009	0.28	0.65	YES
18	HIST1H4C	HIST1H4C	HIST1H4C	1115	0.26	0.66	YES
19	HIST1H4D	HIST1H4D	HIST1H4D	1150	0.25	0.68	YES
20	HIST1H2BH	HIST1H2BH	HIST1H2BH	1439	0.22	0.68	YES
21	HIST1H2BI	HIST1H2BI	HIST1H2BI	1554	0.21	0.68	YES
22	HIST1H2BC	HIST1H2BC	HIST1H2BC	1766	0.19	0.68	YES
23	HIST1H2AB	HIST1H2AB	HIST1H2AB	1767	0.19	0.7	YES
24	HIST1H4H	HIST1H4H	HIST1H4H	1781	0.19	0.71	YES
25	HIST1H2BG	HIST1H2BG	HIST1H2BG	1887	0.18	0.72	YES
26	HIST1H2BF	HIST1H2BF	HIST1H2BF	1953	0.18	0.72	YES
27	H2AFX	H2AFX	H2AFX	2055	0.17	0.73	YES
28	HIST3H3	HIST3H3	HIST3H3	2394	0.15	0.72	NO
29	HIST1H2BM	HIST1H2BM	HIST1H2BM	3071	0.12	0.69	NO
30	POLD1	POLD1	POLD1	3119	0.12	0.7	NO
31	RUVBL2	RUVBL2	RUVBL2	3370	0.11	0.69	NO
32	HIST1H2BK	HIST1H2BK	HIST1H2BK	3517	0.1	0.69	NO
33	HIST1H2AE	HIST1H2AE	HIST1H2AE	3686	0.099	0.68	NO
34	ACD	ACD	ACD	4688	0.072	0.63	NO
35	PCNA	PCNA	PCNA	5000	0.065	0.62	NO
36	POLA2	POLA2	POLA2	5203	0.061	0.61	NO
37	WRAP53	WRAP53	WRAP53	5292	0.06	0.61	NO
38	NHP2	NHP2	NHP2	5310	0.059	0.62	NO
39	POLD2	POLD2	POLD2	5515	0.055	0.61	NO
40	HIST1H2BD	HIST1H2BD	HIST1H2BD	5701	0.052	0.6	NO
41	POLE2	POLE2	POLE2	5843	0.049	0.6	NO
42	RFC2	RFC2	RFC2	5996	0.046	0.59	NO
43	PRIM2	PRIM2	PRIM2	6125	0.043	0.59	NO
44	POLD4	POLD4	POLD4	6773	0.032	0.55	NO
45	RUVBL1	RUVBL1	RUVBL1	7525	0.019	0.51	NO
46	H2AFZ	H2AFZ	H2AFZ	7879	0.013	0.5	NO
47	RFC5	RFC5	RFC5	8181	0.0093	0.48	NO
48	HIST1H2AC	HIST1H2AC	HIST1H2AC	8453	0.0047	0.46	NO
49	LIG1	LIG1	LIG1	8722	0.00076	0.45	NO
50	RPA2	RPA2	RPA2	8730	0.00058	0.45	NO
51	TINF2	TINF2	TINF2	8816	-0.00081	0.44	NO
52	RPA1	RPA1	RPA1	8867	-0.0015	0.44	NO
53	FEN1	FEN1	FEN1	9184	-0.0065	0.42	NO
54	POLE	POLE	POLE	9310	-0.0086	0.42	NO
55	RPA3	RPA3	RPA3	9467	-0.011	0.41	NO
56	TERF2	TERF2	TERF2	10423	-0.025	0.36	NO
57	PRIM1	PRIM1	PRIM1	10452	-0.026	0.36	NO
58	RFC3	RFC3	RFC3	10869	-0.032	0.34	NO
59	RFC4	RFC4	RFC4	10877	-0.032	0.34	NO
60	DKC1	DKC1	DKC1	12370	-0.057	0.26	NO
61	HIST1H2AD	HIST1H2AD	HIST1H2AD	13139	-0.07	0.22	NO
62	POLD3	POLD3	POLD3	13315	-0.073	0.22	NO
63	POLA1	POLA1	POLA1	13321	-0.074	0.22	NO
64	HIST2H2BE	HIST2H2BE	HIST2H2BE	13479	-0.076	0.22	NO
65	POT1	POT1	POT1	13668	-0.08	0.21	NO
66	TERF2IP	TERF2IP	TERF2IP	13721	-0.081	0.22	NO
67	DNA2	DNA2	DNA2	14562	-0.099	0.18	NO
68	HIST4H4	HIST4H4	HIST4H4	15078	-0.11	0.15	NO
69	TERF1	TERF1	TERF1	16455	-0.15	0.087	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: REACTOME TRANSLATION.

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

genes ES table in pathway: REACTOME MEIOSIS

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	RPL21	RPL21	RPL21	22	1.5	0.037	YES
2	RPSAP9	RPSAP9	RPSAP9	29	1.4	0.072	YES
3	RPL36A	RPL36A	RPL36A	132	0.97	0.091	YES
4	RPL39	RPL39	RPL39	233	0.76	0.1	YES
5	RPS28	RPS28	RPS28	262	0.72	0.12	YES
6	RPS27	RPS27	RPS27	378	0.58	0.13	YES
7	RPL9	RPL9	RPL9	394	0.57	0.14	YES
8	RPS26	RPS26	RPS26	443	0.52	0.15	YES
9	TUBA1A	TUBA1A	TUBA1A	472	0.5	0.16	YES
10	RPL7	RPL7	RPL7	479	0.5	0.18	YES
11	TUBA3D	TUBA3D	TUBA3D	508	0.48	0.19	YES
12	TUBB2A	TUBB2A	TUBB2A	517	0.47	0.2	YES
13	RPL18A	RPL18A	RPL18A	560	0.44	0.21	YES
14	EIF3C	EIF3C	EIF3C	635	0.4	0.21	YES
15	TUBB3	TUBB3	TUBB3	780	0.34	0.21	YES
16	MUC2	MUC2	MUC2	811	0.33	0.22	YES
17	RPS3A	RPS3A	RPS3A	839	0.32	0.23	YES
18	MUC4	MUC4	MUC4	869	0.31	0.23	YES
19	FAM153A	FAM153A	FAM153A	982	0.29	0.23	YES
20	DPM3	DPM3	DPM3	1058	0.27	0.24	YES
21	MUC6	MUC6	MUC6	1124	0.26	0.24	YES
22	RPSA	RPSA	RPSA	1270	0.24	0.24	YES
23	MUC5B	MUC5B	MUC5B	1305	0.24	0.24	YES
24	RPL23A	RPL23A	RPL23A	1348	0.23	0.24	YES
25	MUC16	MUC16	MUC16	1362	0.23	0.25	YES
26	B3GNT7	B3GNT7	B3GNT7	1373	0.23	0.26	YES
27	B3GNT4	B3GNT4	B3GNT4	1530	0.21	0.25	YES
28	LDHD	LDHD	LDHD	1543	0.21	0.26	YES
29	PIGL	PIGL	PIGL	1574	0.21	0.26	YES
30	B3GNT6	B3GNT6	B3GNT6	1615	0.2	0.26	YES
31	RPS15	RPS15	RPS15	1774	0.19	0.26	YES
32	CYC1	CYC1	CYC1	1844	0.18	0.26	YES
33	TIMM8B	TIMM8B	TIMM8B	1861	0.18	0.26	YES
34	RPS2	RPS2	RPS2	1911	0.18	0.26	YES
35	EEF1A1	EEF1A1	EEF1A1	1970	0.17	0.27	YES
36	GMPPB	GMPPB	GMPPB	1974	0.17	0.27	YES
37	ARSE	ARSE	ARSE	2027	0.17	0.27	YES
38	TUBA1C	TUBA1C	TUBA1C	2117	0.16	0.27	YES
39	FBXO6	FBXO6	FBXO6	2142	0.16	0.27	YES
40	GALNT9	GALNT9	GALNT9	2146	0.16	0.28	YES
41	B3GNTL1	B3GNTL1	B3GNTL1	2218	0.16	0.28	YES
42	F2	F2	F2	2385	0.15	0.27	YES
43	FBXW5	FBXW5	FBXW5	2441	0.14	0.27	YES
44	ST6GALNAC4	ST6GALNAC4	ST6GALNAC4	2456	0.14	0.28	YES
45	IDH3G	IDH3G	IDH3G	2479	0.14	0.28	YES
46	ARSG	ARSG	ARSG	2514	0.14	0.28	YES
47	RPL13	RPL13	RPL13	2550	0.14	0.28	YES
48	TUBB2B	TUBB2B	TUBB2B	2666	0.13	0.28	YES
49	RPS5	RPS5	RPS5	2671	0.13	0.28	YES
50	EIF4EBP1	EIF4EBP1	EIF4EBP1	2679	0.13	0.28	YES
51	GCNT3	GCNT3	GCNT3	2697	0.13	0.29	YES
52	RPL41	RPL41	RPL41	2763	0.13	0.28	YES
53	SPCS2	SPCS2	SPCS2	2765	0.13	0.29	YES
54	RPLP0	RPLP0	RPLP0	2806	0.13	0.29	YES
55	GPAA1	GPAA1	GPAA1	2915	0.12	0.29	YES
56	ARSH	ARSH	ARSH	2918	0.12	0.29	YES
57	TIMM13	TIMM13	TIMM13	2944	0.12	0.29	YES
58	MTX1	MTX1	MTX1	2995	0.12	0.29	YES
59	TIMM17B	TIMM17B	TIMM17B	3092	0.12	0.29	YES
60	RPL29	RPL29	RPL29	3115	0.12	0.29	YES
61	DOHH	DOHH	DOHH	3117	0.12	0.29	YES
62	TIMM50	TIMM50	TIMM50	3141	0.12	0.3	YES
63	SSR4	SSR4	SSR4	3189	0.12	0.3	YES
64	SPHK1	SPHK1	SPHK1	3203	0.11	0.3	YES
65	RPL10	RPL10	RPL10	3261	0.11	0.3	YES
66	RPL28	RPL28	RPL28	3271	0.11	0.3	YES
67	ALG3	ALG3	ALG3	3314	0.11	0.3	YES
68	GALNT8	GALNT8	GALNT8	3332	0.11	0.3	YES
69	VKORC1	VKORC1	VKORC1	3372	0.11	0.3	YES
70	TBCB	TBCB	TBCB	3435	0.11	0.3	YES
71	B3GNT8	B3GNT8	B3GNT8	3473	0.1	0.3	YES
72	BCS1L	BCS1L	BCS1L	3542	0.1	0.3	YES
73	EIF4E	EIF4E	EIF4E	3547	0.1	0.3	YES
74	TUBA3C	TUBA3C	TUBA3C	3569	0.1	0.3	YES
75	PROZ	PROZ	PROZ	3596	0.1	0.31	YES
76	TUBB6	TUBB6	TUBB6	3615	0.1	0.31	YES
77	TIMM44	TIMM44	TIMM44	3689	0.098	0.31	YES
78	UBA52	UBA52	UBA52	3732	0.097	0.31	YES
79	ST3GAL3	ST3GAL3	ST3GAL3	3767	0.096	0.31	YES
80	GFER	GFER	GFER	3784	0.096	0.31	YES
81	RPS14	RPS14	RPS14	3790	0.096	0.31	YES
82	WBSCR17	WBSCR17	WBSCR17	3809	0.095	0.31	YES
83	MGAT4B	MGAT4B	MGAT4B	3880	0.093	0.31	NO
84	TIMM10	TIMM10	TIMM10	3948	0.091	0.31	NO
85	RPL15	RPL15	RPL15	4014	0.089	0.31	NO
86	DHPS	DHPS	DHPS	4078	0.088	0.3	NO
87	PMM1	PMM1	PMM1	4088	0.087	0.31	NO
88	GALNTL6	GALNTL6	GALNTL6	4133	0.086	0.31	NO
89	EEF1G	EEF1G	EEF1G	4185	0.085	0.31	NO
90	RPL18	RPL18	RPL18	4220	0.084	0.31	NO
91	TUBA4A	TUBA4A	TUBA4A	4254	0.083	0.31	NO
92	RPLP2	RPLP2	RPLP2	4320	0.081	0.3	NO
93	PIGQ	PIGQ	PIGQ	4349	0.08	0.3	NO
94	SEC13	SEC13	SEC13	4419	0.079	0.3	NO
95	PMPCA	PMPCA	PMPCA	4471	0.077	0.3	NO
96	SLC25A4	SLC25A4	SLC25A4	4562	0.075	0.3	NO
97	RPS10	RPS10	RPS10	4576	0.074	0.3	NO
98	EIF3K	EIF3K	EIF3K	4621	0.074	0.3	NO
99	DOLPP1	DOLPP1	DOLPP1	4697	0.072	0.3	NO
100	TBCD	TBCD	TBCD	4698	0.072	0.3	NO
101	TAZ	TAZ	TAZ	4728	0.071	0.3	NO
102	ALG12	ALG12	ALG12	4743	0.071	0.3	NO
103	RPS3	RPS3	RPS3	4762	0.07	0.3	NO
104	GALNT14	GALNT14	GALNT14	4854	0.068	0.3	NO
105	RPL8	RPL8	RPL8	4865	0.068	0.3	NO
106	RPS9	RPS9	RPS9	4889	0.068	0.3	NO
107	EIF3F	EIF3F	EIF3F	4945	0.066	0.3	NO
108	MGAT1	MGAT1	MGAT1	5067	0.064	0.29	NO
109	EDEM2	EDEM2	EDEM2	5098	0.064	0.29	NO
110	ST8SIA6	ST8SIA6	ST8SIA6	5118	0.063	0.29	NO
111	ATP5B	ATP5B	ATP5B	5182	0.062	0.29	NO
112	EIF4H	EIF4H	EIF4H	5228	0.061	0.29	NO
113	TUBA1B	TUBA1B	TUBA1B	5262	0.06	0.29	NO
114	RPL36	RPL36	RPL36	5371	0.058	0.28	NO
115	B4GALT3	B4GALT3	B4GALT3	5431	0.057	0.28	NO
116	F7	F7	F7	5521	0.055	0.28	NO
117	RPS21	RPS21	RPS21	5538	0.055	0.28	NO
118	RPS4Y1	RPS4Y1	RPS4Y1	5546	0.055	0.28	NO
119	RPL27	RPL27	RPL27	5552	0.054	0.28	NO
120	SAMM50	SAMM50	SAMM50	5558	0.054	0.28	NO
121	EIF5A	EIF5A	EIF5A	5608	0.053	0.28	NO
122	GMPPA	GMPPA	GMPPA	5629	0.053	0.28	NO
123	MUC17	MUC17	MUC17	5674	0.052	0.28	NO
124	ACTB	ACTB	ACTB	5699	0.052	0.28	NO
125	PFDN5	PFDN5	PFDN5	5747	0.051	0.28	NO
126	RPS16	RPS16	RPS16	5763	0.05	0.28	NO
127	EIF2B3	EIF2B3	EIF2B3	5851	0.049	0.28	NO
128	EEF2	EEF2	EEF2	5872	0.048	0.28	NO
129	ALG1	ALG1	ALG1	5887	0.048	0.28	NO
130	DOLK	DOLK	DOLK	5908	0.048	0.28	NO
131	TOMM5	TOMM5	TOMM5	5910	0.048	0.28	NO
132	SLC25A6	SLC25A6	SLC25A6	5932	0.047	0.28	NO
133	DPM2	DPM2	DPM2	5949	0.047	0.28	NO
134	TUSC3	TUSC3	TUSC3	5987	0.046	0.28	NO
135	ARSA	ARSA	ARSA	5994	0.046	0.28	NO
136	DDOST	DDOST	DDOST	6021	0.045	0.28	NO
137	RPL26L1	RPL26L1	RPL26L1	6051	0.045	0.28	NO
138	RPS6	RPS6	RPS6	6056	0.045	0.28	NO
139	PREB	PREB	PREB	6086	0.044	0.28	NO
140	PIGH	PIGH	PIGH	6094	0.044	0.28	NO
141	EIF3G	EIF3G	EIF3G	6099	0.044	0.28	NO
142	ATP5G1	ATP5G1	ATP5G1	6107	0.044	0.28	NO
143	RPN1	RPN1	RPN1	6127	0.043	0.28	NO
144	ARSI	ARSI	ARSI	6133	0.043	0.28	NO
145	B3GNT9	B3GNT9	B3GNT9	6139	0.043	0.28	NO
146	MPI	MPI	MPI	6175	0.042	0.28	NO
147	B4GALT2	B4GALT2	B4GALT2	6184	0.042	0.28	NO
148	RPL35	RPL35	RPL35	6220	0.042	0.28	NO
149	MAN1B1	MAN1B1	MAN1B1	6241	0.041	0.28	NO
150	ST6GALNAC3	ST6GALNAC3	ST6GALNAC3	6281	0.04	0.28	NO
151	EEF1D	EEF1D	EEF1D	6300	0.04	0.28	NO
152	ALG14	ALG14	ALG14	6321	0.04	0.28	NO
153	RFT1	RFT1	RFT1	6328	0.04	0.28	NO
154	COQ2	COQ2	COQ2	6345	0.039	0.28	NO
155	PLAUR	PLAUR	PLAUR	6372	0.039	0.28	NO
156	B3GNT3	B3GNT3	B3GNT3	6436	0.038	0.28	NO
157	FXN	FXN	FXN	6440	0.037	0.28	NO
158	CCT7	CCT7	CCT7	6503	0.036	0.27	NO
159	RPLP1	RPLP1	RPLP1	6545	0.036	0.27	NO
160	PIGO	PIGO	PIGO	6562	0.035	0.27	NO
161	FAU	FAU	FAU	6579	0.035	0.27	NO
162	TBCC	TBCC	TBCC	6632	0.034	0.27	NO
163	ATP5A1	ATP5A1	ATP5A1	6637	0.034	0.27	NO
164	ACO2	ACO2	ACO2	6653	0.034	0.27	NO
165	RPS8	RPS8	RPS8	6786	0.032	0.26	NO
166	CCT2	CCT2	CCT2	6788	0.032	0.26	NO
167	PIGT	PIGT	PIGT	6917	0.029	0.26	NO
168	SSR2	SSR2	SSR2	6949	0.029	0.26	NO
169	FBXW4	FBXW4	FBXW4	7022	0.028	0.26	NO
170	CS	CS	CS	7106	0.026	0.25	NO
171	RPS13	RPS13	RPS13	7127	0.026	0.25	NO
172	EIF2B1	EIF2B1	EIF2B1	7134	0.026	0.25	NO
173	EIF4A1	EIF4A1	EIF4A1	7186	0.025	0.25	NO
174	EIF2B2	EIF2B2	EIF2B2	7197	0.025	0.25	NO
175	SAR1B	SAR1B	SAR1B	7295	0.023	0.24	NO
176	TIMM22	TIMM22	TIMM22	7317	0.023	0.24	NO
177	ALG2	ALG2	ALG2	7364	0.022	0.24	NO
178	RPL17	RPL17	RPL17	7366	0.022	0.24	NO
179	TOMM7	TOMM7	TOMM7	7415	0.021	0.24	NO
180	RPS11	RPS11	RPS11	7421	0.021	0.24	NO
181	KIFC3	KIFC3	KIFC3	7429	0.021	0.24	NO
182	EIF2B4	EIF2B4	EIF2B4	7438	0.021	0.24	NO
183	EIF3I	EIF3I	EIF3I	7468	0.02	0.24	NO
184	PIGS	PIGS	PIGS	7492	0.02	0.24	NO
185	MUC12	MUC12	MUC12	7511	0.019	0.24	NO
186	DPAGT1	DPAGT1	DPAGT1	7540	0.019	0.24	NO
187	F10	F10	F10	7545	0.019	0.24	NO
188	PIGG	PIGG	PIGG	7587	0.018	0.23	NO
189	RPL3	RPL3	RPL3	7605	0.018	0.23	NO
190	SUMF2	SUMF2	SUMF2	7733	0.016	0.23	NO
191	PMM2	PMM2	PMM2	7758	0.016	0.23	NO
192	SPCS1	SPCS1	SPCS1	7815	0.014	0.22	NO
193	PMPCB	PMPCB	PMPCB	7830	0.014	0.22	NO
194	RPL10A	RPL10A	RPL10A	7864	0.014	0.22	NO
195	RPL6	RPL6	RPL6	7874	0.013	0.22	NO
196	GALNTL4	GALNTL4	GALNTL4	7942	0.012	0.22	NO
197	EIF2B5	EIF2B5	EIF2B5	7950	0.012	0.22	NO
198	SEC61B	SEC61B	SEC61B	7955	0.012	0.22	NO
199	RPS19	RPS19	RPS19	7956	0.012	0.22	NO
200	MUCL1	MUCL1	MUCL1	7973	0.012	0.22	NO
201	SUMF1	SUMF1	SUMF1	7985	0.012	0.22	NO
202	ST6GAL1	ST6GAL1	ST6GAL1	8009	0.011	0.22	NO
203	CCT5	CCT5	CCT5	8048	0.011	0.21	NO
204	EEF1B2	EEF1B2	EEF1B2	8095	0.01	0.21	NO
205	RPL7A	RPL7A	RPL7A	8096	0.01	0.21	NO
206	CHCHD4	CHCHD4	CHCHD4	8150	0.0096	0.21	NO
207	ARSB	ARSB	ARSB	8154	0.0095	0.21	NO
208	RPS4X	RPS4X	RPS4X	8197	0.0089	0.21	NO
209	CCT4	CCT4	CCT4	8229	0.0082	0.2	NO
210	MOGS	MOGS	MOGS	8239	0.008	0.2	NO
211	RPS15A	RPS15A	RPS15A	8272	0.0074	0.2	NO
212	CALR	CALR	CALR	8310	0.007	0.2	NO
213	EIF3D	EIF3D	EIF3D	8387	0.0058	0.2	NO
214	RPL38	RPL38	RPL38	8400	0.0054	0.2	NO
215	USP11	USP11	USP11	8411	0.0053	0.2	NO
216	FXC1	FXC1	FXC1	8417	0.0052	0.2	NO
217	EIF3B	EIF3B	EIF3B	8424	0.0051	0.2	NO
218	FKBP9	FKBP9	FKBP9	8463	0.0046	0.19	NO
219	C18orf55	C18orf55	C18orf55	8474	0.0044	0.19	NO
220	PIGF	PIGF	PIGF	8483	0.0043	0.19	NO
221	EIF1AX	EIF1AX	EIF1AX	8489	0.0041	0.19	NO
222	SEC61A1	SEC61A1	SEC61A1	8582	0.0028	0.19	NO
223	DAD1	DAD1	DAD1	8610	0.0024	0.19	NO
224	RPL35A	RPL35A	RPL35A	8706	0.00098	0.18	NO
225	PIGV	PIGV	PIGV	8829	-0.00098	0.17	NO
226	ALG13	ALG13	ALG13	8842	-0.0011	0.17	NO
227	SEC61A2	SEC61A2	SEC61A2	8880	-0.0016	0.17	NO
228	FURIN	FURIN	FURIN	8904	-0.002	0.17	NO
229	RPL37A	RPL37A	RPL37A	8926	-0.0023	0.17	NO
230	GGCX	GGCX	GGCX	8943	-0.0024	0.17	NO
231	LOC653566	LOC653566	LOC653566	9020	-0.0036	0.16	NO
232	RPS17	RPS17	RPS17	9160	-0.0061	0.16	NO
233	GFPT2	GFPT2	GFPT2	9222	-0.007	0.15	NO
234	CCT3	CCT3	CCT3	9235	-0.0073	0.15	NO
235	NOP56	NOP56	NOP56	9287	-0.0083	0.15	NO
236	EIF3H	EIF3H	EIF3H	9291	-0.0083	0.15	NO
237	RPL32	RPL32	RPL32	9293	-0.0083	0.15	NO
238	RPS29	RPS29	RPS29	9298	-0.0084	0.15	NO
239	ST6GALNAC2	ST6GALNAC2	ST6GALNAC2	9311	-0.0087	0.15	NO
240	FUT8	FUT8	FUT8	9328	-0.009	0.15	NO
241	ST3GAL2	ST3GAL2	ST3GAL2	9331	-0.009	0.15	NO
242	TOMM22	TOMM22	TOMM22	9344	-0.0092	0.15	NO
243	SRPR	SRPR	SRPR	9358	-0.0094	0.15	NO
244	PIGU	PIGU	PIGU	9404	-0.01	0.15	NO
245	SEC24C	SEC24C	SEC24C	9408	-0.01	0.15	NO
246	RPN2	RPN2	RPN2	9423	-0.01	0.14	NO
247	RPL27A	RPL27A	RPL27A	9430	-0.01	0.14	NO
248	TOMM40	TOMM40	TOMM40	9433	-0.01	0.14	NO
249	TCP1	TCP1	TCP1	9469	-0.011	0.14	NO
250	EIF4A2	EIF4A2	EIF4A2	9489	-0.011	0.14	NO
251	SRPRB	SRPRB	SRPRB	9521	-0.012	0.14	NO
252	ALG5	ALG5	ALG5	9563	-0.013	0.14	NO
253	SRP9	SRP9	SRP9	9575	-0.013	0.14	NO
254	LONP2	LONP2	LONP2	9727	-0.015	0.13	NO
255	MUC15	MUC15	MUC15	9773	-0.016	0.13	NO
256	GALNTL1	GALNTL1	GALNTL1	9913	-0.018	0.12	NO
257	GALNT2	GALNT2	GALNT2	9928	-0.018	0.12	NO
258	SEC24D	SEC24D	SEC24D	9951	-0.018	0.12	NO
259	RPL37	RPL37	RPL37	9976	-0.018	0.12	NO
260	GNPNAT1	GNPNAT1	GNPNAT1	10008	-0.019	0.12	NO
261	PIGC	PIGC	PIGC	10060	-0.02	0.12	NO
262	MGAT2	MGAT2	MGAT2	10094	-0.02	0.11	NO
263	FBXO4	FBXO4	FBXO4	10105	-0.02	0.11	NO
264	B4GALT1	B4GALT1	B4GALT1	10147	-0.021	0.11	NO
265	GRPEL1	GRPEL1	GRPEL1	10168	-0.021	0.11	NO
266	STT3A	STT3A	STT3A	10216	-0.022	0.11	NO
267	GANAB	GANAB	GANAB	10232	-0.022	0.11	NO
268	EIF2S2	EIF2S2	EIF2S2	10254	-0.023	0.11	NO
269	VDAC1	VDAC1	VDAC1	10266	-0.023	0.11	NO
270	MLEC	MLEC	MLEC	10283	-0.023	0.11	NO
271	MGAT3	MGAT3	MGAT3	10289	-0.023	0.11	NO
272	RPL31	RPL31	RPL31	10398	-0.025	0.1	NO
273	GALNT11	GALNT11	GALNT11	10418	-0.025	0.1	NO
274	SEMA6D	SEMA6D	SEMA6D	10434	-0.026	0.1	NO
275	RPL5	RPL5	RPL5	10465	-0.026	0.1	NO
276	EIF4B	EIF4B	EIF4B	10496	-0.026	0.1	NO
277	SLC25A13	SLC25A13	SLC25A13	10561	-0.028	0.097	NO
278	TOMM20	TOMM20	TOMM20	10576	-0.028	0.097	NO
279	PRKCSH	PRKCSH	PRKCSH	10587	-0.028	0.097	NO
280	RPL19	RPL19	RPL19	10648	-0.029	0.095	NO
281	FBXL5	FBXL5	FBXL5	10675	-0.029	0.094	NO
282	RPS23	RPS23	RPS23	10710	-0.03	0.093	NO
283	SSR3	SSR3	SSR3	10754	-0.03	0.091	NO
284	SRP14	SRP14	SRP14	10813	-0.031	0.089	NO
285	EIF4G1	EIF4G1	EIF4G1	10822	-0.031	0.089	NO
286	SRP68	SRP68	SRP68	10842	-0.031	0.089	NO
287	EIF5	EIF5	EIF5	10924	-0.032	0.085	NO
288	RPL23	RPL23	RPL23	10957	-0.033	0.084	NO
289	SLC25A12	SLC25A12	SLC25A12	10965	-0.033	0.084	NO
290	RPL30	RPL30	RPL30	10977	-0.033	0.084	NO
291	RPL34	RPL34	RPL34	11009	-0.034	0.084	NO
292	PABPC1	PABPC1	PABPC1	11041	-0.034	0.083	NO
293	RPL22	RPL22	RPL22	11147	-0.036	0.078	NO
294	ALG9	ALG9	ALG9	11160	-0.036	0.078	NO
295	RPL11	RPL11	RPL11	11221	-0.037	0.076	NO
296	PFDN2	PFDN2	PFDN2	11257	-0.038	0.074	NO
297	RPL13A	RPL13A	RPL13A	11261	-0.038	0.075	NO
298	ETF1	ETF1	ETF1	11389	-0.04	0.069	NO
299	EDEM1	EDEM1	EDEM1	11396	-0.04	0.07	NO
300	MUC21	MUC21	MUC21	11439	-0.041	0.068	NO
301	SSR1	SSR1	SSR1	11450	-0.041	0.069	NO
302	RPL4	RPL4	RPL4	11473	-0.041	0.069	NO
303	SEC11A	SEC11A	SEC11A	11505	-0.042	0.068	NO
304	MTX2	MTX2	MTX2	11608	-0.044	0.063	NO
305	PFDN1	PFDN1	PFDN1	11622	-0.044	0.064	NO
306	HSPA9	HSPA9	HSPA9	11673	-0.044	0.062	NO
307	PGM3	PGM3	PGM3	11688	-0.045	0.062	NO
308	SEC24B	SEC24B	SEC24B	11745	-0.046	0.06	NO
309	GALNT13	GALNT13	GALNT13	11923	-0.049	0.051	NO
310	FBXW2	FBXW2	FBXW2	11991	-0.05	0.049	NO
311	RPL14	RPL14	RPL14	11992	-0.05	0.05	NO
312	CCT6A	CCT6A	CCT6A	12050	-0.051	0.048	NO
313	STS	STS	STS	12053	-0.051	0.049	NO
314	GALNT12	GALNT12	GALNT12	12068	-0.052	0.05	NO
315	PROC	PROC	PROC	12092	-0.052	0.05	NO
316	HSCB	HSCB	HSCB	12107	-0.052	0.05	NO
317	MUC13	MUC13	MUC13	12182	-0.053	0.048	NO
318	TOMM70A	TOMM70A	TOMM70A	12191	-0.054	0.048	NO
319	PIGN	PIGN	PIGN	12267	-0.055	0.046	NO
320	XRN2	XRN2	XRN2	12327	-0.056	0.044	NO
321	EIF2S1	EIF2S1	EIF2S1	12336	-0.056	0.045	NO
322	GALNT10	GALNT10	GALNT10	12354	-0.056	0.045	NO
323	UGGT1	UGGT1	UGGT1	12422	-0.058	0.043	NO
324	C1GALT1C1	C1GALT1C1	C1GALT1C1	12524	-0.059	0.038	NO
325	EIF2S3	EIF2S3	EIF2S3	12582	-0.06	0.037	NO
326	GRPEL2	GRPEL2	GRPEL2	12632	-0.061	0.036	NO
327	MAN2A1	MAN2A1	MAN2A1	12691	-0.062	0.034	NO
328	SEC31A	SEC31A	SEC31A	12702	-0.062	0.035	NO
329	SPCS3	SPCS3	SPCS3	12704	-0.062	0.036	NO
330	B4GALT5	B4GALT5	B4GALT5	12737	-0.063	0.036	NO
331	TIMM8A	TIMM8A	TIMM8A	12799	-0.064	0.034	NO
332	B4GALT4	B4GALT4	B4GALT4	12889	-0.065	0.031	NO
333	TBCA	TBCA	TBCA	12894	-0.065	0.032	NO
334	PDIA3	PDIA3	PDIA3	13114	-0.07	0.022	NO
335	RPL26	RPL26	RPL26	13165	-0.07	0.021	NO
336	TIMM9	TIMM9	TIMM9	13167	-0.071	0.022	NO
337	CANX	CANX	CANX	13174	-0.071	0.024	NO
338	HSPD1	HSPD1	HSPD1	13186	-0.071	0.025	NO
339	AP3M1	AP3M1	AP3M1	13201	-0.071	0.026	NO
340	TIMM17A	TIMM17A	TIMM17A	13253	-0.072	0.025	NO
341	SRP72	SRP72	SRP72	13305	-0.073	0.024	NO
342	RPS20	RPS20	RPS20	13347	-0.074	0.023	NO
343	ARFGEF2	ARFGEF2	ARFGEF2	13366	-0.074	0.024	NO
344	SEC23A	SEC23A	SEC23A	13421	-0.075	0.023	NO
345	SEC11C	SEC11C	SEC11C	13483	-0.077	0.022	NO
346	TBCE	TBCE	TBCE	13549	-0.078	0.02	NO
347	SRP54	SRP54	SRP54	13622	-0.079	0.018	NO
348	ALG8	ALG8	ALG8	13637	-0.08	0.019	NO
349	GALNTL2	GALNTL2	GALNTL2	13708	-0.081	0.017	NO
350	PIGP	PIGP	PIGP	13715	-0.081	0.019	NO
351	RPS7	RPS7	RPS7	13785	-0.082	0.017	NO
352	MCFD2	MCFD2	MCFD2	13808	-0.083	0.018	NO
353	DPM1	DPM1	DPM1	13956	-0.086	0.012	NO
354	CCT8	CCT8	CCT8	13957	-0.086	0.014	NO
355	GALNT3	GALNT3	GALNT3	14074	-0.088	0.0094	NO
356	MAN1C1	MAN1C1	MAN1C1	14094	-0.089	0.011	NO
357	GALNT6	GALNT6	GALNT6	14126	-0.089	0.011	NO
358	ST3GAL1	ST3GAL1	ST3GAL1	14150	-0.09	0.012	NO
359	PIGB	PIGB	PIGB	14280	-0.093	0.0071	NO
360	TUBB1	TUBB1	TUBB1	14364	-0.094	0.0048	NO
361	PFDN6	PFDN6	PFDN6	14387	-0.095	0.0059	NO
362	ARSJ	ARSJ	ARSJ	14610	-0.1	-0.0041	NO
363	GALNT5	GALNT5	GALNT5	14625	-0.1	-0.0024	NO
364	VBP1	VBP1	VBP1	14774	-0.1	-0.0081	NO
365	GCNT4	GCNT4	GCNT4	14795	-0.1	-0.0066	NO
366	FBXL3	FBXL3	FBXL3	14807	-0.1	-0.0046	NO
367	LMAN1	LMAN1	LMAN1	14896	-0.11	-0.0069	NO
368	TRAM1	TRAM1	TRAM1	14897	-0.11	-0.0042	NO
369	KIF13A	KIF13A	KIF13A	14923	-0.11	-0.0029	NO
370	PIGW	PIGW	PIGW	14938	-0.11	-0.00097	NO
371	EIF5A2	EIF5A2	EIF5A2	14944	-0.11	0.0015	NO
372	MAN1A1	MAN1A1	MAN1A1	14961	-0.11	0.0033	NO
373	FBXW7	FBXW7	FBXW7	15071	-0.11	-0.000066	NO
374	MGAT4A	MGAT4A	MGAT4A	15077	-0.11	0.0025	NO
375	PIGK	PIGK	PIGK	15207	-0.11	-0.002	NO
376	SEC61G	SEC61G	SEC61G	15256	-0.12	-0.0018	NO
377	PIGX	PIGX	PIGX	15338	-0.12	-0.0034	NO
378	GCNT1	GCNT1	GCNT1	15398	-0.12	-0.0038	NO
379	ALG11	ALG11	ALG11	15437	-0.12	-0.0029	NO
380	EIF3J	EIF3J	EIF3J	15451	-0.12	-0.00057	NO
381	ST8SIA2	ST8SIA2	ST8SIA2	15465	-0.12	0.0017	NO
382	EIF3E	EIF3E	EIF3E	15524	-0.12	0.0015	NO
383	GSPT2	GSPT2	GSPT2	15548	-0.12	0.0033	NO
384	PIGM	PIGM	PIGM	15570	-0.12	0.0053	NO
385	B3GNT2	B3GNT2	B3GNT2	15618	-0.12	0.0058	NO
386	RPS24	RPS24	RPS24	15626	-0.12	0.0085	NO
387	ALG10B	ALG10B	ALG10B	15646	-0.12	0.011	NO
388	RPS18	RPS18	RPS18	15707	-0.13	0.01	NO
389	GALNT1	GALNT1	GALNT1	15728	-0.13	0.012	NO
390	RPL12	RPL12	RPL12	15794	-0.13	0.012	NO
391	RPL24	RPL24	RPL24	15819	-0.13	0.014	NO
392	RPS25	RPS25	RPS25	15952	-0.13	0.0099	NO
393	ALG6	ALG6	ALG6	15965	-0.13	0.013	NO
394	SRP19	SRP19	SRP19	15990	-0.14	0.015	NO
395	EIF3A	EIF3A	EIF3A	16008	-0.14	0.017	NO
396	GALNT7	GALNT7	GALNT7	16016	-0.14	0.02	NO
397	RPS12	RPS12	RPS12	16033	-0.14	0.023	NO
398	PROS1	PROS1	PROS1	16280	-0.14	0.012	NO
399	ALG10	ALG10	ALG10	16295	-0.14	0.015	NO
400	PIGA	PIGA	PIGA	16314	-0.14	0.018	NO
401	MGAT5	MGAT5	MGAT5	16392	-0.15	0.017	NO
402	DNAJC19	DNAJC19	DNAJC19	16464	-0.15	0.017	NO
403	UGGT2	UGGT2	UGGT2	16560	-0.15	0.016	NO
404	ARSK	ARSK	ARSK	16775	-0.16	0.0075	NO
405	EDEM3	EDEM3	EDEM3	16964	-0.17	0.0012	NO
406	RPS27A	RPS27A	RPS27A	16968	-0.17	0.0054	NO
407	COX17	COX17	COX17	17002	-0.18	0.008	NO
408	B3GNT5	B3GNT5	B3GNT5	17042	-0.18	0.01	NO
409	ST8SIA3	ST8SIA3	ST8SIA3	17109	-0.18	0.011	NO
410	MAN1A2	MAN1A2	MAN1A2	17126	-0.18	0.015	NO
411	EIF5B	EIF5B	EIF5B	17230	-0.19	0.014	NO
412	C1GALT1	C1GALT1	C1GALT1	17256	-0.19	0.017	NO
413	PGAP1	PGAP1	PGAP1	17619	-0.23	0.0026	NO
414	MANEA	MANEA	MANEA	17739	-0.24	0.002	NO
415	B4GALT6	B4GALT6	B4GALT6	17803	-0.26	0.005	NO
416	PFDN4	PFDN4	PFDN4	17939	-0.3	0.0049	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: REACTOME MEIOSIS.

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

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

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	HIST1H4K	HIST1H4K	HIST1H4K	4	1.8	0.096	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	58	1.3	0.16	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	81	1.2	0.22	YES
4	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	158	0.9	0.27	YES
5	HIST2H3C	HIST2H3C	HIST2H3C	192	0.82	0.31	YES
6	HIST2H3D	HIST2H3D	HIST2H3D	232	0.76	0.35	YES
7	HIST1H2BN	HIST1H2BN	HIST1H2BN	331	0.62	0.38	YES
8	HIST1H4J	HIST1H4J	HIST1H4J	423	0.54	0.4	YES
9	NPPA	NPPA	NPPA	447	0.52	0.43	YES
10	HIST1H2BE	HIST1H2BE	HIST1H2BE	484	0.5	0.45	YES
11	HIST1H2BL	HIST1H2BL	HIST1H2BL	537	0.46	0.48	YES
12	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	553	0.45	0.5	YES
13	HIST1H4I	HIST1H4I	HIST1H4I	556	0.45	0.52	YES
14	HIST2H4A	HIST2H4A	HIST2H4A	580	0.43	0.55	YES
15	HIST1H4A	HIST1H4A	HIST1H4A	623	0.4	0.56	YES
16	HIST1H4B	HIST1H4B	HIST1H4B	761	0.35	0.58	YES
17	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	844	0.32	0.59	YES
18	HIST1H3H	HIST1H3H	HIST1H3H	878	0.31	0.6	YES
19	HIST1H4E	HIST1H4E	HIST1H4E	931	0.3	0.62	YES
20	HIST3H2BB	HIST3H2BB	HIST3H2BB	985	0.28	0.63	YES
21	HIST1H3D	HIST1H3D	HIST1H3D	1034	0.27	0.64	YES
22	HIST1H4C	HIST1H4C	HIST1H4C	1115	0.26	0.65	YES
23	HIST1H3B	HIST1H3B	HIST1H3B	1126	0.26	0.66	YES
24	HIST1H4D	HIST1H4D	HIST1H4D	1150	0.25	0.68	YES
25	HIST1H3F	HIST1H3F	HIST1H3F	1404	0.22	0.68	YES
26	HIST1H2BH	HIST1H2BH	HIST1H2BH	1439	0.22	0.68	YES
27	HIST1H3J	HIST1H3J	HIST1H3J	1451	0.22	0.7	YES
28	APOA1	APOA1	APOA1	1516	0.21	0.7	YES
29	HIST1H2BI	HIST1H2BI	HIST1H2BI	1554	0.21	0.71	YES
30	HIST1H3G	HIST1H3G	HIST1H3G	1668	0.2	0.72	YES
31	HIST1H3A	HIST1H3A	HIST1H3A	1676	0.2	0.73	YES
32	HIST1H2BC	HIST1H2BC	HIST1H2BC	1766	0.19	0.73	YES
33	HIST1H2AB	HIST1H2AB	HIST1H2AB	1767	0.19	0.74	YES
34	HIST1H4H	HIST1H4H	HIST1H4H	1781	0.19	0.75	YES
35	SAA1	SAA1	SAA1	1869	0.18	0.76	YES
36	HIST1H2BG	HIST1H2BG	HIST1H2BG	1887	0.18	0.77	YES
37	HIST1H2BF	HIST1H2BF	HIST1H2BF	1953	0.18	0.77	YES
38	HIST1H3I	HIST1H3I	HIST1H3I	1967	0.17	0.78	YES
39	H2AFX	H2AFX	H2AFX	2055	0.17	0.79	YES
40	CST3	CST3	CST3	2402	0.15	0.77	NO
41	H3F3A	H3F3A	H3F3A	2899	0.12	0.75	NO
42	HIST1H2BM	HIST1H2BM	HIST1H2BM	3071	0.12	0.75	NO
43	HIST1H3C	HIST1H3C	HIST1H3C	3383	0.11	0.74	NO
44	HIST1H2BK	HIST1H2BK	HIST1H2BK	3517	0.1	0.74	NO
45	HIST1H2AE	HIST1H2AE	HIST1H2AE	3686	0.099	0.73	NO
46	CALCA	CALCA	CALCA	4380	0.08	0.7	NO
47	TTR	TTR	TTR	4719	0.071	0.68	NO
48	SNCA	SNCA	SNCA	5648	0.053	0.64	NO
49	HIST1H2BD	HIST1H2BD	HIST1H2BD	5701	0.052	0.64	NO
50	SEMG1	SEMG1	SEMG1	6569	0.035	0.59	NO
51	MFGE8	MFGE8	MFGE8	7451	0.02	0.54	NO
52	TGFBI	TGFBI	TGFBI	7847	0.014	0.52	NO
53	H2AFZ	H2AFZ	H2AFZ	7879	0.013	0.52	NO
54	B2M	B2M	B2M	7992	0.012	0.51	NO
55	GSN	GSN	GSN	8338	0.0065	0.49	NO
56	HIST1H2AC	HIST1H2AC	HIST1H2AC	8453	0.0047	0.49	NO
57	LYZ	LYZ	LYZ	8980	-0.0031	0.46	NO
58	LTF	LTF	LTF	9272	-0.0079	0.44	NO
59	FGA	FGA	FGA	10750	-0.03	0.36	NO
60	APP	APP	APP	11322	-0.039	0.33	NO
61	ITM2B	ITM2B	ITM2B	11837	-0.048	0.31	NO
62	ODAM	ODAM	ODAM	12249	-0.055	0.29	NO
63	HIST1H2AD	HIST1H2AD	HIST1H2AD	13139	-0.07	0.24	NO
64	H3F3B	H3F3B	H3F3B	13346	-0.074	0.23	NO
65	HIST1H3E	HIST1H3E	HIST1H3E	13354	-0.074	0.24	NO
66	HIST2H2BE	HIST2H2BE	HIST2H2BE	13479	-0.076	0.23	NO
67	HSPG2	HSPG2	HSPG2	14388	-0.095	0.19	NO
68	HIST4H4	HIST4H4	HIST4H4	15078	-0.11	0.16	NO
69	PRL	PRL	PRL	16228	-0.14	0.1	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: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S70. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME RNA POL I TRANSCRIPTION

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	HIST1H4K	HIST1H4K	HIST1H4K	4	1.8	0.11	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	58	1.3	0.18	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	81	1.2	0.25	YES
4	FKBP6	FKBP6	FKBP6	106	1	0.31	YES
5	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	158	0.9	0.36	YES
6	HIST1H2BN	HIST1H2BN	HIST1H2BN	331	0.62	0.39	YES
7	HIST1H4J	HIST1H4J	HIST1H4J	423	0.54	0.41	YES
8	STAG3	STAG3	STAG3	460	0.51	0.44	YES
9	HIST1H2BE	HIST1H2BE	HIST1H2BE	484	0.5	0.47	YES
10	HIST1H2BL	HIST1H2BL	HIST1H2BL	537	0.46	0.5	YES
11	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	553	0.45	0.52	YES
12	HIST1H4I	HIST1H4I	HIST1H4I	556	0.45	0.55	YES
13	HIST2H4A	HIST2H4A	HIST2H4A	580	0.43	0.57	YES
14	HIST1H4A	HIST1H4A	HIST1H4A	623	0.4	0.59	YES
15	HIST1H4B	HIST1H4B	HIST1H4B	761	0.35	0.61	YES
16	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	844	0.32	0.62	YES
17	HIST1H4E	HIST1H4E	HIST1H4E	931	0.3	0.64	YES
18	HIST3H2BB	HIST3H2BB	HIST3H2BB	985	0.28	0.65	YES
19	HIST1H4C	HIST1H4C	HIST1H4C	1115	0.26	0.66	YES
20	HIST1H4D	HIST1H4D	HIST1H4D	1150	0.25	0.67	YES
21	HIST1H2BH	HIST1H2BH	HIST1H2BH	1439	0.22	0.67	YES
22	HIST1H2BI	HIST1H2BI	HIST1H2BI	1554	0.21	0.67	YES
23	REC8	REC8	REC8	1606	0.2	0.68	YES
24	HIST1H2BC	HIST1H2BC	HIST1H2BC	1766	0.19	0.69	YES
25	HIST1H2AB	HIST1H2AB	HIST1H2AB	1767	0.19	0.7	YES
26	HIST1H4H	HIST1H4H	HIST1H4H	1781	0.19	0.71	YES
27	HIST1H2BG	HIST1H2BG	HIST1H2BG	1887	0.18	0.71	YES
28	HIST1H2BF	HIST1H2BF	HIST1H2BF	1953	0.18	0.72	YES
29	H2AFX	H2AFX	H2AFX	2055	0.17	0.72	YES
30	HIST3H3	HIST3H3	HIST3H3	2394	0.15	0.71	NO
31	HIST1H2BM	HIST1H2BM	HIST1H2BM	3071	0.12	0.68	NO
32	HIST1H2BK	HIST1H2BK	HIST1H2BK	3517	0.1	0.66	NO
33	HIST1H2AE	HIST1H2AE	HIST1H2AE	3686	0.099	0.66	NO
34	ACD	ACD	ACD	4688	0.072	0.61	NO
35	HIST1H2BD	HIST1H2BD	HIST1H2BD	5701	0.052	0.56	NO
36	UBE2I	UBE2I	UBE2I	7232	0.024	0.47	NO
37	H2AFZ	H2AFZ	H2AFZ	7879	0.013	0.44	NO
38	SMC1B	SMC1B	SMC1B	8321	0.0068	0.41	NO
39	HIST1H2AC	HIST1H2AC	HIST1H2AC	8453	0.0047	0.41	NO
40	LMNA	LMNA	LMNA	8546	0.0032	0.4	NO
41	TINF2	TINF2	TINF2	8816	-0.00081	0.39	NO
42	LMNB1	LMNB1	LMNB1	10246	-0.023	0.31	NO
43	HSPA2	HSPA2	HSPA2	10310	-0.024	0.31	NO
44	TERF2	TERF2	TERF2	10423	-0.025	0.3	NO
45	SUN2	SUN2	SUN2	12444	-0.058	0.19	NO
46	DIDO1	DIDO1	DIDO1	12480	-0.058	0.19	NO
47	HIST1H2AD	HIST1H2AD	HIST1H2AD	13139	-0.07	0.16	NO
48	ATR	ATR	ATR	13198	-0.071	0.16	NO
49	SMC1A	SMC1A	SMC1A	13381	-0.075	0.16	NO
50	HIST2H2BE	HIST2H2BE	HIST2H2BE	13479	-0.076	0.16	NO
51	POT1	POT1	POT1	13668	-0.08	0.15	NO
52	TERF2IP	TERF2IP	TERF2IP	13721	-0.081	0.15	NO
53	RAD21	RAD21	RAD21	13910	-0.085	0.15	NO
54	BRCA1	BRCA1	BRCA1	14449	-0.096	0.12	NO
55	SYCP2	SYCP2	SYCP2	15019	-0.11	0.097	NO
56	STAG2	STAG2	STAG2	15046	-0.11	0.1	NO
57	HIST4H4	HIST4H4	HIST4H4	15078	-0.11	0.11	NO
58	STAG1	STAG1	STAG1	15479	-0.12	0.092	NO
59	SYNE2	SYNE2	SYNE2	15868	-0.13	0.078	NO
60	TERF1	TERF1	TERF1	16455	-0.15	0.055	NO
61	SMC3	SMC3	SMC3	16845	-0.17	0.043	NO
62	TEX12	TEX12	TEX12	16854	-0.17	0.053	NO
63	SYNE1	SYNE1	SYNE1	17442	-0.21	0.032	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: REACTOME RNA POL I TRANSCRIPTION.

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

genes ES table in pathway: REACTOME PEPTIDE CHAIN ELONGATION

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	HIST1H4K	HIST1H4K	HIST1H4K	4	1.8	0.078	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	58	1.3	0.13	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	81	1.2	0.18	YES
4	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	158	0.9	0.22	YES
5	HIST2H3C	HIST2H3C	HIST2H3C	192	0.82	0.25	YES
6	HIST2H3D	HIST2H3D	HIST2H3D	232	0.76	0.28	YES
7	HIST1H2BN	HIST1H2BN	HIST1H2BN	331	0.62	0.3	YES
8	GTF2H2B	GTF2H2B	GTF2H2B	332	0.62	0.33	YES
9	HIST1H4J	HIST1H4J	HIST1H4J	423	0.54	0.35	YES
10	HIST1H2BE	HIST1H2BE	HIST1H2BE	484	0.5	0.37	YES
11	HIST1H2BL	HIST1H2BL	HIST1H2BL	537	0.46	0.39	YES
12	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	553	0.45	0.41	YES
13	HIST1H4I	HIST1H4I	HIST1H4I	556	0.45	0.43	YES
14	GTF2H2	GTF2H2	GTF2H2	570	0.44	0.44	YES
15	HIST2H4A	HIST2H4A	HIST2H4A	580	0.43	0.46	YES
16	HIST1H4A	HIST1H4A	HIST1H4A	623	0.4	0.48	YES
17	HIST1H4B	HIST1H4B	HIST1H4B	761	0.35	0.49	YES
18	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	844	0.32	0.5	YES
19	HIST1H3H	HIST1H3H	HIST1H3H	878	0.31	0.51	YES
20	HIST1H4E	HIST1H4E	HIST1H4E	931	0.3	0.52	YES
21	HIST3H2BB	HIST3H2BB	HIST3H2BB	985	0.28	0.53	YES
22	HIST1H3D	HIST1H3D	HIST1H3D	1034	0.27	0.54	YES
23	HIST1H4C	HIST1H4C	HIST1H4C	1115	0.26	0.55	YES
24	HIST1H3B	HIST1H3B	HIST1H3B	1126	0.26	0.56	YES
25	HIST1H4D	HIST1H4D	HIST1H4D	1150	0.25	0.57	YES
26	HIST1H3F	HIST1H3F	HIST1H3F	1404	0.22	0.56	YES
27	HIST1H2BH	HIST1H2BH	HIST1H2BH	1439	0.22	0.57	YES
28	HIST1H3J	HIST1H3J	HIST1H3J	1451	0.22	0.58	YES
29	HIST1H2BI	HIST1H2BI	HIST1H2BI	1554	0.21	0.58	YES
30	HIST1H3G	HIST1H3G	HIST1H3G	1668	0.2	0.58	YES
31	HIST1H3A	HIST1H3A	HIST1H3A	1676	0.2	0.59	YES
32	HIST1H2BC	HIST1H2BC	HIST1H2BC	1766	0.19	0.6	YES
33	HIST1H2AB	HIST1H2AB	HIST1H2AB	1767	0.19	0.6	YES
34	HIST1H4H	HIST1H4H	HIST1H4H	1781	0.19	0.61	YES
35	HIST1H2BG	HIST1H2BG	HIST1H2BG	1887	0.18	0.61	YES
36	HIST1H2BF	HIST1H2BF	HIST1H2BF	1953	0.18	0.62	YES
37	HIST1H3I	HIST1H3I	HIST1H3I	1967	0.17	0.62	YES
38	H2AFX	H2AFX	H2AFX	2055	0.17	0.63	YES
39	POLR2L	POLR2L	POLR2L	2127	0.16	0.63	YES
40	H3F3A	H3F3A	H3F3A	2899	0.12	0.59	NO
41	HIST1H2BM	HIST1H2BM	HIST1H2BM	3071	0.12	0.59	NO
42	HIST1H3C	HIST1H3C	HIST1H3C	3383	0.11	0.58	NO
43	POLR3K	POLR3K	POLR3K	3506	0.1	0.57	NO
44	HIST1H2BK	HIST1H2BK	HIST1H2BK	3517	0.1	0.58	NO
45	HIST1H2AE	HIST1H2AE	HIST1H2AE	3686	0.099	0.57	NO
46	POLR2H	POLR2H	POLR2H	4013	0.089	0.56	NO
47	SNAPC5	SNAPC5	SNAPC5	4107	0.087	0.56	NO
48	POLR1C	POLR1C	POLR1C	4203	0.084	0.56	NO
49	MAPK3	MAPK3	MAPK3	4640	0.073	0.54	NO
50	POLR2F	POLR2F	POLR2F	4800	0.07	0.53	NO
51	ERCC2	ERCC2	ERCC2	4818	0.069	0.53	NO
52	POLR3H	POLR3H	POLR3H	4837	0.068	0.53	NO
53	POLRMT	POLRMT	POLRMT	4957	0.066	0.53	NO
54	HIST1H2BD	HIST1H2BD	HIST1H2BD	5701	0.052	0.49	NO
55	POLR3E	POLR3E	POLR3E	5808	0.05	0.49	NO
56	POLR2E	POLR2E	POLR2E	5942	0.047	0.48	NO
57	GTF3C5	GTF3C5	GTF3C5	6378	0.039	0.46	NO
58	BRF2	BRF2	BRF2	6731	0.033	0.44	NO
59	POLR3D	POLR3D	POLR3D	6739	0.033	0.44	NO
60	GTF2H4	GTF2H4	GTF2H4	6918	0.029	0.43	NO
61	POLR3C	POLR3C	POLR3C	6932	0.029	0.43	NO
62	EHMT2	EHMT2	EHMT2	7097	0.026	0.43	NO
63	BRF1	BRF1	BRF1	7244	0.024	0.42	NO
64	POLR3B	POLR3B	POLR3B	7460	0.02	0.41	NO
65	H2AFZ	H2AFZ	H2AFZ	7879	0.013	0.38	NO
66	ZNF143	ZNF143	ZNF143	7904	0.013	0.38	NO
67	TAF1C	TAF1C	TAF1C	7912	0.013	0.38	NO
68	TBP	TBP	TBP	8166	0.0094	0.37	NO
69	HIST1H2AC	HIST1H2AC	HIST1H2AC	8453	0.0047	0.36	NO
70	SNAPC4	SNAPC4	SNAPC4	8831	-0.00099	0.33	NO
71	SNAPC2	SNAPC2	SNAPC2	8891	-0.0018	0.33	NO
72	ERCC3	ERCC3	ERCC3	8961	-0.0028	0.33	NO
73	POLR1B	POLR1B	POLR1B	9405	-0.01	0.3	NO
74	MNAT1	MNAT1	MNAT1	9760	-0.015	0.28	NO
75	POLR3A	POLR3A	POLR3A	9809	-0.016	0.28	NO
76	GTF3C2	GTF3C2	GTF3C2	10346	-0.024	0.25	NO
77	GTF3C3	GTF3C3	GTF3C3	10657	-0.029	0.24	NO
78	GTF2H3	GTF2H3	GTF2H3	10792	-0.031	0.23	NO
79	POLR1D	POLR1D	POLR1D	11049	-0.034	0.22	NO
80	CCNH	CCNH	CCNH	11475	-0.041	0.2	NO
81	GTF3C4	GTF3C4	GTF3C4	12321	-0.056	0.15	NO
82	GTF2H1	GTF2H1	GTF2H1	12399	-0.057	0.15	NO
83	POLR3F	POLR3F	POLR3F	12597	-0.06	0.14	NO
84	SNAPC3	SNAPC3	SNAPC3	13126	-0.07	0.12	NO
85	HIST1H2AD	HIST1H2AD	HIST1H2AD	13139	-0.07	0.12	NO
86	NFIB	NFIB	NFIB	13316	-0.073	0.11	NO
87	H3F3B	H3F3B	H3F3B	13346	-0.074	0.11	NO
88	HIST1H3E	HIST1H3E	HIST1H3E	13354	-0.074	0.12	NO
89	POLR1A	POLR1A	POLR1A	13397	-0.075	0.12	NO
90	HIST2H2BE	HIST2H2BE	HIST2H2BE	13479	-0.076	0.12	NO
91	UBTF	UBTF	UBTF	13909	-0.085	0.095	NO
92	PTRF	PTRF	PTRF	14576	-0.1	0.062	NO
93	TFB2M	TFB2M	TFB2M	14751	-0.1	0.057	NO
94	MBD2	MBD2	MBD2	14765	-0.1	0.06	NO
95	HIST4H4	HIST4H4	HIST4H4	15078	-0.11	0.048	NO
96	RRN3	RRN3	RRN3	15376	-0.12	0.037	NO
97	POLR2K	POLR2K	POLR2K	15639	-0.12	0.028	NO
98	TFAM	TFAM	TFAM	15726	-0.13	0.028	NO
99	LZTS1	LZTS1	LZTS1	15826	-0.13	0.029	NO
100	CDK7	CDK7	CDK7	15953	-0.13	0.028	NO
101	ERCC6	ERCC6	ERCC6	16273	-0.14	0.016	NO
102	POU2F1	POU2F1	POU2F1	16577	-0.16	0.006	NO
103	TAF1B	TAF1B	TAF1B	17113	-0.18	-0.016	NO
104	CBX3	CBX3	CBX3	17125	-0.18	-0.0083	NO
105	POLR3GL	POLR3GL	POLR3GL	17199	-0.19	-0.0041	NO
106	MTERF	MTERF	MTERF	17276	-0.19	0.00027	NO
107	TAF1A	TAF1A	TAF1A	17480	-0.21	-0.0018	NO
108	KAT2B	KAT2B	KAT2B	17579	-0.22	0.0026	NO
109	SNAPC1	SNAPC1	SNAPC1	17677	-0.24	0.0075	NO
110	SSB	SSB	SSB	17850	-0.27	0.0098	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: REACTOME PEPTIDE CHAIN ELONGATION.

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PEPTIDE CHAIN ELONGATION, 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 PROTEINS

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	RPL21	RPL21	RPL21	22	1.5	0.1	YES
2	RPSAP9	RPSAP9	RPSAP9	29	1.4	0.2	YES
3	RPL36A	RPL36A	RPL36A	132	0.97	0.26	YES
4	RPL39	RPL39	RPL39	233	0.76	0.3	YES
5	RPS28	RPS28	RPS28	262	0.72	0.35	YES
6	RPS27	RPS27	RPS27	378	0.58	0.38	YES
7	RPL9	RPL9	RPL9	394	0.57	0.42	YES
8	RPS26	RPS26	RPS26	443	0.52	0.45	YES
9	RPL7	RPL7	RPL7	479	0.5	0.48	YES
10	RPL18A	RPL18A	RPL18A	560	0.44	0.51	YES
11	RPS3A	RPS3A	RPS3A	839	0.32	0.52	YES
12	FAM153A	FAM153A	FAM153A	982	0.29	0.53	YES
13	RPSA	RPSA	RPSA	1270	0.24	0.53	YES
14	RPL23A	RPL23A	RPL23A	1348	0.23	0.54	YES
15	RPS15	RPS15	RPS15	1774	0.19	0.53	NO
16	RPS2	RPS2	RPS2	1911	0.18	0.53	NO
17	RPL13	RPL13	RPL13	2550	0.14	0.5	NO
18	RPS5	RPS5	RPS5	2671	0.13	0.51	NO
19	RPL41	RPL41	RPL41	2763	0.13	0.51	NO
20	RPLP0	RPLP0	RPLP0	2806	0.13	0.52	NO
21	RPL29	RPL29	RPL29	3115	0.12	0.51	NO
22	RPL10	RPL10	RPL10	3261	0.11	0.51	NO
23	RPL28	RPL28	RPL28	3271	0.11	0.52	NO
24	UBA52	UBA52	UBA52	3732	0.097	0.5	NO
25	RPS14	RPS14	RPS14	3790	0.096	0.5	NO
26	RPL15	RPL15	RPL15	4014	0.089	0.49	NO
27	RPL18	RPL18	RPL18	4220	0.084	0.49	NO
28	RPLP2	RPLP2	RPLP2	4320	0.081	0.49	NO
29	EIF4A3	EIF4A3	EIF4A3	4331	0.081	0.49	NO
30	RPS10	RPS10	RPS10	4576	0.074	0.48	NO
31	RPS3	RPS3	RPS3	4762	0.07	0.48	NO
32	RPL8	RPL8	RPL8	4865	0.068	0.48	NO
33	RPS9	RPS9	RPS9	4889	0.068	0.48	NO
34	RPL36	RPL36	RPL36	5371	0.058	0.46	NO
35	RPS21	RPS21	RPS21	5538	0.055	0.45	NO
36	RPS4Y1	RPS4Y1	RPS4Y1	5546	0.055	0.46	NO
37	RPL27	RPL27	RPL27	5552	0.054	0.46	NO
38	RPS16	RPS16	RPS16	5763	0.05	0.45	NO
39	PPP2R1A	PPP2R1A	PPP2R1A	5895	0.048	0.45	NO
40	RPL26L1	RPL26L1	RPL26L1	6051	0.045	0.44	NO
41	RPS6	RPS6	RPS6	6056	0.045	0.44	NO
42	RPL35	RPL35	RPL35	6220	0.042	0.44	NO
43	RNPS1	RNPS1	RNPS1	6227	0.042	0.44	NO
44	RPLP1	RPLP1	RPLP1	6545	0.036	0.42	NO
45	FAU	FAU	FAU	6579	0.035	0.42	NO
46	RPS8	RPS8	RPS8	6786	0.032	0.42	NO
47	RPS13	RPS13	RPS13	7127	0.026	0.4	NO
48	RPL17	RPL17	RPL17	7366	0.022	0.39	NO
49	RPS11	RPS11	RPS11	7421	0.021	0.38	NO
50	RPL3	RPL3	RPL3	7605	0.018	0.38	NO
51	PPP2CA	PPP2CA	PPP2CA	7745	0.016	0.37	NO
52	RPL10A	RPL10A	RPL10A	7864	0.014	0.36	NO
53	RPL6	RPL6	RPL6	7874	0.013	0.36	NO
54	RPS19	RPS19	RPS19	7956	0.012	0.36	NO
55	RPL7A	RPL7A	RPL7A	8096	0.01	0.35	NO
56	PPP2R2A	PPP2R2A	PPP2R2A	8126	0.01	0.35	NO
57	RPS4X	RPS4X	RPS4X	8197	0.0089	0.35	NO
58	RPS15A	RPS15A	RPS15A	8272	0.0074	0.34	NO
59	RPL38	RPL38	RPL38	8400	0.0054	0.34	NO
60	RPL35A	RPL35A	RPL35A	8706	0.00098	0.32	NO
61	RPL37A	RPL37A	RPL37A	8926	-0.0023	0.31	NO
62	RPS17	RPS17	RPS17	9160	-0.0061	0.3	NO
63	RPL32	RPL32	RPL32	9293	-0.0083	0.29	NO
64	RPS29	RPS29	RPS29	9298	-0.0084	0.29	NO
65	RPL27A	RPL27A	RPL27A	9430	-0.01	0.28	NO
66	CASC3	CASC3	CASC3	9635	-0.013	0.27	NO
67	RPL37	RPL37	RPL37	9976	-0.018	0.26	NO
68	SMG5	SMG5	SMG5	10058	-0.02	0.25	NO
69	RPL31	RPL31	RPL31	10398	-0.025	0.24	NO
70	RPL5	RPL5	RPL5	10465	-0.026	0.23	NO
71	RPL19	RPL19	RPL19	10648	-0.029	0.22	NO
72	RPS23	RPS23	RPS23	10710	-0.03	0.22	NO
73	MAGOH	MAGOH	MAGOH	10799	-0.031	0.22	NO
74	EIF4G1	EIF4G1	EIF4G1	10822	-0.031	0.22	NO
75	RPL23	RPL23	RPL23	10957	-0.033	0.22	NO
76	RPL30	RPL30	RPL30	10977	-0.033	0.22	NO
77	RPL34	RPL34	RPL34	11009	-0.034	0.22	NO
78	PABPC1	PABPC1	PABPC1	11041	-0.034	0.22	NO
79	RPL22	RPL22	RPL22	11147	-0.036	0.22	NO
80	RPL11	RPL11	RPL11	11221	-0.037	0.21	NO
81	RPL13A	RPL13A	RPL13A	11261	-0.038	0.22	NO
82	ETF1	ETF1	ETF1	11389	-0.04	0.21	NO
83	NCBP1	NCBP1	NCBP1	11393	-0.04	0.21	NO
84	RPL4	RPL4	RPL4	11473	-0.041	0.21	NO
85	UPF3A	UPF3A	UPF3A	11506	-0.042	0.21	NO
86	RPL14	RPL14	RPL14	11992	-0.05	0.19	NO
87	RBM8A	RBM8A	RBM8A	12358	-0.056	0.17	NO
88	RPL26	RPL26	RPL26	13165	-0.07	0.13	NO
89	RPS20	RPS20	RPS20	13347	-0.074	0.13	NO
90	RPS7	RPS7	RPS7	13785	-0.082	0.11	NO
91	NCBP2	NCBP2	NCBP2	14253	-0.092	0.088	NO
92	SMG6	SMG6	SMG6	14524	-0.098	0.08	NO
93	SMG7	SMG7	SMG7	15081	-0.11	0.056	NO
94	GSPT2	GSPT2	GSPT2	15548	-0.12	0.038	NO
95	RPS24	RPS24	RPS24	15626	-0.12	0.043	NO
96	SMG1	SMG1	SMG1	15690	-0.13	0.048	NO
97	RPS18	RPS18	RPS18	15707	-0.13	0.056	NO
98	RPL12	RPL12	RPL12	15794	-0.13	0.059	NO
99	RPL24	RPL24	RPL24	15819	-0.13	0.067	NO
100	RPS25	RPS25	RPS25	15952	-0.13	0.069	NO
101	RPS12	RPS12	RPS12	16033	-0.14	0.073	NO
102	RPS27A	RPS27A	RPS27A	16968	-0.17	0.033	NO
103	UPF3B	UPF3B	UPF3B	17163	-0.19	0.035	NO
104	UPF2	UPF2	UPF2	17321	-0.2	0.039	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: REACTOME METABOLISM OF PROTEINS.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME METABOLISM OF PROTEINS, 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 3 UTR MEDIATED TRANSLATIONAL REGULATION

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	HIST1H4K	HIST1H4K	HIST1H4K	4	1.8	0.063	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	58	1.3	0.1	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	81	1.2	0.15	YES
4	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	158	0.9	0.17	YES
5	HIST2H3C	HIST2H3C	HIST2H3C	192	0.82	0.2	YES
6	HIST2H3D	HIST2H3D	HIST2H3D	232	0.76	0.23	YES
7	FCGR2C	FCGR2C	FCGR2C	244	0.75	0.25	YES
8	HIST1H2BN	HIST1H2BN	HIST1H2BN	331	0.62	0.27	YES
9	HIST3H2A	HIST3H2A	HIST3H2A	339	0.62	0.29	YES
10	FCGR3B	FCGR3B	FCGR3B	374	0.58	0.31	YES
11	HIST1H4J	HIST1H4J	HIST1H4J	423	0.54	0.33	YES
12	HIST1H2BE	HIST1H2BE	HIST1H2BE	484	0.5	0.34	YES
13	FCGR1A	FCGR1A	FCGR1A	485	0.5	0.36	YES
14	HIST2H2BF	HIST2H2BF	HIST2H2BF	486	0.5	0.38	YES
15	HLA-DQA2	HLA-DQA2	HLA-DQA2	536	0.46	0.39	YES
16	HIST1H2BL	HIST1H2BL	HIST1H2BL	537	0.46	0.41	YES
17	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	553	0.45	0.42	YES
18	HIST1H4I	HIST1H4I	HIST1H4I	556	0.45	0.44	YES
19	H3F3C	H3F3C	H3F3C	569	0.44	0.45	YES
20	HIST2H4A	HIST2H4A	HIST2H4A	580	0.43	0.47	YES
21	HIST1H4A	HIST1H4A	HIST1H4A	623	0.4	0.48	YES
22	HLA-DRB5	HLA-DRB5	HLA-DRB5	624	0.4	0.49	YES
23	HIST1H4B	HIST1H4B	HIST1H4B	761	0.35	0.5	YES
24	FCGR2B	FCGR2B	FCGR2B	782	0.34	0.51	YES
25	H2AFB1	H2AFB1	H2AFB1	793	0.34	0.52	YES
26	C8G	C8G	C8G	837	0.32	0.53	YES
27	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	844	0.32	0.54	YES
28	HIST1H3H	HIST1H3H	HIST1H3H	878	0.31	0.55	YES
29	HIST1H4E	HIST1H4E	HIST1H4E	931	0.3	0.56	YES
30	HIST3H2BB	HIST3H2BB	HIST3H2BB	985	0.28	0.57	YES
31	HIST1H2AG	HIST1H2AG	HIST1H2AG	986	0.28	0.58	YES
32	HIST1H3D	HIST1H3D	HIST1H3D	1034	0.27	0.58	YES
33	HIST1H4C	HIST1H4C	HIST1H4C	1115	0.26	0.59	YES
34	HIST1H2AL	HIST1H2AL	HIST1H2AL	1123	0.26	0.6	YES
35	HIST1H3B	HIST1H3B	HIST1H3B	1126	0.26	0.61	YES
36	HIST1H4D	HIST1H4D	HIST1H4D	1150	0.25	0.61	YES
37	HLA-DRB1	HLA-DRB1	HLA-DRB1	1341	0.23	0.61	YES
38	HLA-DQA1	HLA-DQA1	HLA-DQA1	1395	0.22	0.62	YES
39	HIST1H3F	HIST1H3F	HIST1H3F	1404	0.22	0.62	YES
40	HIST1H2AM	HIST1H2AM	HIST1H2AM	1430	0.22	0.63	YES
41	HIST1H2BH	HIST1H2BH	HIST1H2BH	1439	0.22	0.64	YES
42	HIST1H3J	HIST1H3J	HIST1H3J	1451	0.22	0.64	YES
43	HIST1H2AH	HIST1H2AH	HIST1H2AH	1479	0.21	0.65	YES
44	HIST1H2BI	HIST1H2BI	HIST1H2BI	1554	0.21	0.65	YES
45	HIST1H2AK	HIST1H2AK	HIST1H2AK	1580	0.2	0.66	YES
46	HLA-DQB1	HLA-DQB1	HLA-DQB1	1621	0.2	0.66	YES
47	HIST1H3G	HIST1H3G	HIST1H3G	1668	0.2	0.67	YES
48	HIST1H3A	HIST1H3A	HIST1H3A	1676	0.2	0.68	YES
49	C1QB	C1QB	C1QB	1742	0.19	0.68	YES
50	HIST1H2BC	HIST1H2BC	HIST1H2BC	1766	0.19	0.68	YES
51	HIST1H2AB	HIST1H2AB	HIST1H2AB	1767	0.19	0.69	YES
52	HIST1H4H	HIST1H4H	HIST1H4H	1781	0.19	0.7	YES
53	HIST2H2AB	HIST2H2AB	HIST2H2AB	1802	0.19	0.7	YES
54	C1QC	C1QC	C1QC	1805	0.19	0.71	YES
55	IL10	IL10	IL10	1806	0.19	0.72	YES
56	HIST1H2BG	HIST1H2BG	HIST1H2BG	1887	0.18	0.72	YES
57	HIST1H2BF	HIST1H2BF	HIST1H2BF	1953	0.18	0.72	YES
58	HIST1H3I	HIST1H3I	HIST1H3I	1967	0.17	0.73	YES
59	ELANE	ELANE	ELANE	1977	0.17	0.73	YES
60	HLA-DPB1	HLA-DPB1	HLA-DPB1	2035	0.17	0.74	YES
61	H2AFX	H2AFX	H2AFX	2055	0.17	0.74	YES
62	HLA-DMB	HLA-DMB	HLA-DMB	2209	0.16	0.74	NO
63	HIST3H3	HIST3H3	HIST3H3	2394	0.15	0.73	NO
64	TNF	TNF	TNF	2866	0.13	0.71	NO
65	CD80	CD80	CD80	2897	0.12	0.71	NO
66	H3F3A	H3F3A	H3F3A	2899	0.12	0.72	NO
67	HLA-DPA1	HLA-DPA1	HLA-DPA1	3014	0.12	0.72	NO
68	HIST1H2BM	HIST1H2BM	HIST1H2BM	3071	0.12	0.72	NO
69	HIST1H3C	HIST1H3C	HIST1H3C	3383	0.11	0.7	NO
70	HIST1H2BK	HIST1H2BK	HIST1H2BK	3517	0.1	0.7	NO
71	C1QA	C1QA	C1QA	3673	0.099	0.69	NO
72	HIST1H2AE	HIST1H2AE	HIST1H2AE	3686	0.099	0.7	NO
73	HLA-DRA	HLA-DRA	HLA-DRA	3753	0.097	0.7	NO
74	C4A	C4A	C4A	3867	0.094	0.69	NO
75	HLA-DMA	HLA-DMA	HLA-DMA	4306	0.081	0.67	NO
76	H2AFJ	H2AFJ	H2AFJ	4325	0.081	0.67	NO
77	HLA-DOA	HLA-DOA	HLA-DOA	4526	0.076	0.66	NO
78	FCGR2A	FCGR2A	FCGR2A	4537	0.075	0.67	NO
79	SNRPB	SNRPB	SNRPB	4928	0.067	0.65	NO
80	CTSG	CTSG	CTSG	5200	0.061	0.64	NO
81	CD40	CD40	CD40	5407	0.057	0.63	NO
82	CD86	CD86	CD86	5510	0.055	0.62	NO
83	HIST1H2BD	HIST1H2BD	HIST1H2BD	5701	0.052	0.61	NO
84	IFNG	IFNG	IFNG	5826	0.049	0.61	NO
85	FCGR3A	FCGR3A	FCGR3A	6080	0.044	0.6	NO
86	HLA-DOB	HLA-DOB	HLA-DOB	6654	0.034	0.56	NO
87	CD40LG	CD40LG	CD40LG	6670	0.034	0.56	NO
88	C2	C2	C2	6924	0.029	0.55	NO
89	C9	C9	C9	7513	0.019	0.52	NO
90	H2AFZ	H2AFZ	H2AFZ	7879	0.013	0.5	NO
91	HIST1H2AC	HIST1H2AC	HIST1H2AC	8453	0.0047	0.47	NO
92	H2AFY	H2AFY	H2AFY	8604	0.0024	0.46	NO
93	TRIM21	TRIM21	TRIM21	8887	-0.0017	0.44	NO
94	H2AFV	H2AFV	H2AFV	9350	-0.0093	0.42	NO
95	C1R	C1R	C1R	9694	-0.014	0.4	NO
96	CD28	CD28	CD28	9826	-0.016	0.39	NO
97	C3	C3	C3	9977	-0.018	0.38	NO
98	ACTN4	ACTN4	ACTN4	10380	-0.025	0.36	NO
99	ACTN1	ACTN1	ACTN1	10475	-0.026	0.36	NO
100	H2AFY2	H2AFY2	H2AFY2	10672	-0.029	0.35	NO
101	ACTN2	ACTN2	ACTN2	11316	-0.039	0.32	NO
102	SNRPD3	SNRPD3	SNRPD3	11363	-0.04	0.31	NO
103	GRIN2B	GRIN2B	GRIN2B	11660	-0.044	0.3	NO
104	C1S	C1S	C1S	11885	-0.048	0.29	NO
105	SNRPD1	SNRPD1	SNRPD1	12005	-0.05	0.28	NO
106	HIST1H2AD	HIST1H2AD	HIST1H2AD	13139	-0.07	0.22	NO
107	H3F3B	H3F3B	H3F3B	13346	-0.074	0.21	NO
108	HIST1H3E	HIST1H3E	HIST1H3E	13354	-0.074	0.22	NO
109	HIST2H2BE	HIST2H2BE	HIST2H2BE	13479	-0.076	0.21	NO
110	C6	C6	C6	14722	-0.1	0.15	NO
111	C5	C5	C5	14808	-0.1	0.14	NO
112	HIST4H4	HIST4H4	HIST4H4	15078	-0.11	0.13	NO
113	ACTN3	ACTN3	ACTN3	15486	-0.12	0.12	NO
114	TROVE2	TROVE2	TROVE2	16304	-0.14	0.075	NO
115	GRIN2A	GRIN2A	GRIN2A	16393	-0.15	0.076	NO
116	C7	C7	C7	16757	-0.16	0.061	NO
117	SSB	SSB	SSB	17850	-0.27	0.0098	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: REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME 3 UTR MEDIATED TRANSLATIONAL REGULATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TRANSCRIPTION

Table 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	RPL21	RPL21	RPL21	22	1.5	0.087	YES
2	RPSAP9	RPSAP9	RPSAP9	29	1.4	0.17	YES
3	RPL36A	RPL36A	RPL36A	132	0.97	0.22	YES
4	RPL39	RPL39	RPL39	233	0.76	0.26	YES
5	RPS28	RPS28	RPS28	262	0.72	0.3	YES
6	RPS27	RPS27	RPS27	378	0.58	0.33	YES
7	RPL9	RPL9	RPL9	394	0.57	0.36	YES
8	RPS26	RPS26	RPS26	443	0.52	0.39	YES
9	RPL7	RPL7	RPL7	479	0.5	0.42	YES
10	RPL18A	RPL18A	RPL18A	560	0.44	0.44	YES
11	HSPA1B	HSPA1B	HSPA1B	693	0.38	0.45	YES
12	RPS3A	RPS3A	RPS3A	839	0.32	0.46	YES
13	FAM153A	FAM153A	FAM153A	982	0.29	0.47	YES
14	RPSA	RPSA	RPSA	1270	0.24	0.47	YES
15	RPL23A	RPL23A	RPL23A	1348	0.23	0.48	YES
16	POLR2I	POLR2I	POLR2I	1412	0.22	0.49	YES
17	RPS15	RPS15	RPS15	1774	0.19	0.48	NO
18	RPS2	RPS2	RPS2	1911	0.18	0.48	NO
19	POLR2L	POLR2L	POLR2L	2127	0.16	0.48	NO
20	POLR2G	POLR2G	POLR2G	2387	0.15	0.47	NO
21	RPL13	RPL13	RPL13	2550	0.14	0.47	NO
22	RPS5	RPS5	RPS5	2671	0.13	0.48	NO
23	RPL41	RPL41	RPL41	2763	0.13	0.48	NO
24	RPLP0	RPLP0	RPLP0	2806	0.13	0.48	NO
25	RPL29	RPL29	RPL29	3115	0.12	0.47	NO
26	RPL10	RPL10	RPL10	3261	0.11	0.47	NO
27	RPL28	RPL28	RPL28	3271	0.11	0.48	NO
28	UBA52	UBA52	UBA52	3732	0.097	0.46	NO
29	RPS14	RPS14	RPS14	3790	0.096	0.46	NO
30	POLR2H	POLR2H	POLR2H	4013	0.089	0.45	NO
31	RPL15	RPL15	RPL15	4014	0.089	0.46	NO
32	RPL18	RPL18	RPL18	4220	0.084	0.45	NO
33	RPLP2	RPLP2	RPLP2	4320	0.081	0.45	NO
34	CLTA	CLTA	CLTA	4337	0.081	0.45	NO
35	RAN	RAN	RAN	4511	0.076	0.45	NO
36	RPS10	RPS10	RPS10	4576	0.074	0.45	NO
37	RPS3	RPS3	RPS3	4762	0.07	0.44	NO
38	POLR2F	POLR2F	POLR2F	4800	0.07	0.44	NO
39	RPL8	RPL8	RPL8	4865	0.068	0.45	NO
40	RPS9	RPS9	RPS9	4889	0.068	0.45	NO
41	AAAS	AAAS	AAAS	5186	0.062	0.44	NO
42	POLR2J	POLR2J	POLR2J	5284	0.06	0.43	NO
43	RPL36	RPL36	RPL36	5371	0.058	0.43	NO
44	RPS21	RPS21	RPS21	5538	0.055	0.43	NO
45	RPS4Y1	RPS4Y1	RPS4Y1	5546	0.055	0.43	NO
46	RPL27	RPL27	RPL27	5552	0.054	0.43	NO
47	RPS16	RPS16	RPS16	5763	0.05	0.42	NO
48	POLR2C	POLR2C	POLR2C	5889	0.048	0.42	NO
49	POLR2E	POLR2E	POLR2E	5942	0.047	0.42	NO
50	POLR2D	POLR2D	POLR2D	5954	0.047	0.42	NO
51	RPL26L1	RPL26L1	RPL26L1	6051	0.045	0.42	NO
52	RPS6	RPS6	RPS6	6056	0.045	0.42	NO
53	RPL35	RPL35	RPL35	6220	0.042	0.41	NO
54	RPLP1	RPLP1	RPLP1	6545	0.036	0.4	NO
55	FAU	FAU	FAU	6579	0.035	0.4	NO
56	NUP85	NUP85	NUP85	6744	0.032	0.39	NO
57	POM121	POM121	POM121	6763	0.032	0.39	NO
58	RPS8	RPS8	RPS8	6786	0.032	0.39	NO
59	NUP88	NUP88	NUP88	7009	0.028	0.38	NO
60	NUP93	NUP93	NUP93	7123	0.026	0.38	NO
61	RPS13	RPS13	RPS13	7127	0.026	0.38	NO
62	RPL17	RPL17	RPL17	7366	0.022	0.37	NO
63	RPS11	RPS11	RPS11	7421	0.021	0.36	NO
64	RPL3	RPL3	RPL3	7605	0.018	0.36	NO
65	NUP210	NUP210	NUP210	7615	0.018	0.36	NO
66	NUP188	NUP188	NUP188	7766	0.015	0.35	NO
67	NUP43	NUP43	NUP43	7852	0.014	0.34	NO
68	RPL10A	RPL10A	RPL10A	7864	0.014	0.34	NO
69	RPL6	RPL6	RPL6	7874	0.013	0.34	NO
70	NUP37	NUP37	NUP37	7951	0.012	0.34	NO
71	RPS19	RPS19	RPS19	7956	0.012	0.34	NO
72	RPL7A	RPL7A	RPL7A	8096	0.01	0.33	NO
73	RPS4X	RPS4X	RPS4X	8197	0.0089	0.33	NO
74	RPS15A	RPS15A	RPS15A	8272	0.0074	0.33	NO
75	CALR	CALR	CALR	8310	0.007	0.32	NO
76	RPL38	RPL38	RPL38	8400	0.0054	0.32	NO
77	RPL35A	RPL35A	RPL35A	8706	0.00098	0.3	NO
78	IPO5	IPO5	IPO5	8791	-0.00034	0.3	NO
79	RPL37A	RPL37A	RPL37A	8926	-0.0023	0.29	NO
80	RPS17	RPS17	RPS17	9160	-0.0061	0.28	NO
81	RAE1	RAE1	RAE1	9187	-0.0065	0.28	NO
82	RPL32	RPL32	RPL32	9293	-0.0083	0.27	NO
83	RPS29	RPS29	RPS29	9298	-0.0084	0.27	NO
84	RPL27A	RPL27A	RPL27A	9430	-0.01	0.26	NO
85	NUP62	NUP62	NUP62	9454	-0.011	0.26	NO
86	SEH1L	SEH1L	SEH1L	9588	-0.013	0.26	NO
87	GTF2F1	GTF2F1	GTF2F1	9729	-0.015	0.25	NO
88	RPL37	RPL37	RPL37	9976	-0.018	0.24	NO
89	RPL31	RPL31	RPL31	10398	-0.025	0.22	NO
90	NUP155	NUP155	NUP155	10441	-0.026	0.22	NO
91	RPL5	RPL5	RPL5	10465	-0.026	0.22	NO
92	RPL19	RPL19	RPL19	10648	-0.029	0.21	NO
93	RPS23	RPS23	RPS23	10710	-0.03	0.2	NO
94	POLR2B	POLR2B	POLR2B	10786	-0.031	0.2	NO
95	RPL23	RPL23	RPL23	10957	-0.033	0.2	NO
96	RPL30	RPL30	RPL30	10977	-0.033	0.2	NO
97	RPL34	RPL34	RPL34	11009	-0.034	0.2	NO
98	RPL22	RPL22	RPL22	11147	-0.036	0.19	NO
99	RPL11	RPL11	RPL11	11221	-0.037	0.19	NO
100	RPL13A	RPL13A	RPL13A	11261	-0.038	0.19	NO
101	RPL4	RPL4	RPL4	11473	-0.041	0.18	NO
102	CLTC	CLTC	CLTC	11545	-0.042	0.18	NO
103	GRSF1	GRSF1	GRSF1	11573	-0.043	0.18	NO
104	NUP205	NUP205	NUP205	11815	-0.047	0.17	NO
105	RPL14	RPL14	RPL14	11992	-0.05	0.16	NO
106	NUP214	NUP214	NUP214	12523	-0.059	0.14	NO
107	NUP50	NUP50	NUP50	12600	-0.06	0.14	NO
108	NUP107	NUP107	NUP107	12646	-0.061	0.14	NO
109	DNAJC3	DNAJC3	DNAJC3	12832	-0.064	0.13	NO
110	KPNA1	KPNA1	KPNA1	13014	-0.068	0.12	NO
111	RPL26	RPL26	RPL26	13165	-0.07	0.12	NO
112	CANX	CANX	CANX	13174	-0.071	0.12	NO
113	NUP35	NUP35	NUP35	13277	-0.073	0.12	NO
114	NUP133	NUP133	NUP133	13323	-0.074	0.12	NO
115	RPS20	RPS20	RPS20	13347	-0.074	0.13	NO
116	POLR2A	POLR2A	POLR2A	13398	-0.075	0.13	NO
117	KPNB1	KPNB1	KPNB1	13414	-0.075	0.13	NO
118	NUP54	NUP54	NUP54	13505	-0.077	0.13	NO
119	HSP90AA1	HSP90AA1	HSP90AA1	13703	-0.081	0.12	NO
120	RPS7	RPS7	RPS7	13785	-0.082	0.12	NO
121	NUPL2	NUPL2	NUPL2	14264	-0.092	0.1	NO
122	NUP153	NUP153	NUP153	14300	-0.093	0.11	NO
123	GTF2F2	GTF2F2	GTF2F2	14887	-0.11	0.08	NO
124	NUPL1	NUPL1	NUPL1	15204	-0.11	0.07	NO
125	XPO1	XPO1	XPO1	15540	-0.12	0.058	NO
126	RPS24	RPS24	RPS24	15626	-0.12	0.06	NO
127	POLR2K	POLR2K	POLR2K	15639	-0.12	0.067	NO
128	RPS18	RPS18	RPS18	15707	-0.13	0.071	NO
129	RPL12	RPL12	RPL12	15794	-0.13	0.074	NO
130	RPL24	RPL24	RPL24	15819	-0.13	0.08	NO
131	RPS25	RPS25	RPS25	15952	-0.13	0.08	NO
132	RPS12	RPS12	RPS12	16033	-0.14	0.084	NO
133	TPR	TPR	TPR	16130	-0.14	0.087	NO
134	RANBP2	RANBP2	RANBP2	16443	-0.15	0.078	NO
135	RPS27A	RPS27A	RPS27A	16968	-0.17	0.059	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: REACTOME TRANSCRIPTION.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Methods & Data

Input

Gene set database = c2.cp.v4.0.symbols.gmt
Expression data file = COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = COADREAD-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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