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

Colon 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 COAD-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1N015W2

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 "COAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:

For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.
Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).
Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).
Checks if the top core genes are up-regulated or down-regulated.
Checks if the top core genes are high expressed or low expressed.
Checks if the top core genes are significantly differently expressed genes.

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 711
Number of samples: 457
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 ] 129
pheno.type: 2 - 4 :[ clus2 ] 95
pheno.type: 3 - 4 :[ clus3 ] 98
pheno.type: 4 - 4 :[ clus4 ] 135

For the expression subtypes of 18012 genes in 458 samples, GSEA found enriched gene sets in each cluster using 457 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG LYSINE DEGRADATION, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RNA DEGRADATION, KEGG SPLICEOSOME, 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, CPSF1, CPSF3, MAGOH, NCBP1, NCBP2, UPF3B, CLP1, CPSF2, CPSF7

clus2

Top enriched gene sets are KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG BASE EXCISION REPAIR, BIOCARTA FAS PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA TNFR1 PATHWAY, PID TRAIL PATHWAY

And common core enriched genes are MAPK8, CASP8, MDM2, CASP3, CASP7, FAS, LMNA, LMNB1, PARP1, RIPK1

clus3

Top enriched gene sets are KEGG TRYPTOPHAN METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, 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

And common core enriched genes are PIK3CA, AKT3, PIK3CD, PIK3R5, IRS1, MAPK11, PIK3R1, PREX1, RAPGEF1, RPS6KA2

clus4

Top enriched gene sets are KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG PARKINSONS DISEASE, 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 PROTEIN FOLDING, REACTOME METABOLISM OF PROTEINS

And common core enriched genes are HIST1H2AB, HIST1H2AJ, HIST1H2BC, HIST1H2BE, HIST1H2BG, HIST1H2BH, HIST1H2BI, HIST1H2BJ, HIST1H2BL, HIST1H2BN

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	0.48	1.9	0.0085	0.57	0.26	0.46	0.29	0.32	0	0.099
KEGG AMINOACYL TRNA BIOSYNTHESIS	41	genes.ES.table	0.4	1.5	0.12	0.61	0.97	0.66	0.38	0.41	0.39	0.18
KEGG RNA DEGRADATION	56	genes.ES.table	0.37	1.5	0.12	0.61	0.97	0.71	0.41	0.42	0.38	0.18
KEGG SPLICEOSOME	114	genes.ES.table	0.36	1.6	0.084	0.49	0.89	0.57	0.36	0.37	0.22	0.13
PID ATM PATHWAY	34	genes.ES.table	0.5	1.6	0.062	0.49	0.88	0.71	0.35	0.46	0.2	0.12
PID BARD1PATHWAY	29	genes.ES.table	0.52	1.6	0.081	0.53	0.93	0.41	0.21	0.33	0.28	0.15
REACTOME METABOLISM OF NON CODING RNA	47	genes.ES.table	0.45	1.6	0.088	0.5	0.93	0.72	0.36	0.47	0.26	0.13
REACTOME METABOLISM OF VITAMINS AND COFACTORS	50	genes.ES.table	0.41	1.5	0.05	0.5	0.94	0.22	0.11	0.2	0.27	0.14
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA	126	genes.ES.table	0.42	1.7	0.062	0.46	0.78	0.59	0.39	0.36	0.15	0.11
REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM	44	genes.ES.table	0.5	1.7	0.026	0.47	0.67	0.64	0.37	0.4	0.12	0.11

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	100	0.37	0.14	YES
2	OGDHL	OGDHL	OGDHL	238	0.29	0.25	YES
3	SETDB2	SETDB2	SETDB2	993	0.17	0.27	YES
4	SETMAR	SETMAR	SETMAR	1950	0.11	0.26	YES
5	TMLHE	TMLHE	TMLHE	2171	0.1	0.29	YES
6	AASDHPPT	AASDHPPT	AASDHPPT	2416	0.095	0.31	YES
7	AADAT	AADAT	AADAT	2658	0.089	0.33	YES
8	ALDH7A1	ALDH7A1	ALDH7A1	3423	0.071	0.32	YES
9	SETD2	SETD2	SETD2	3480	0.069	0.34	YES
10	SUV39H2	SUV39H2	SUV39H2	3540	0.068	0.36	YES
11	ASH1L	ASH1L	ASH1L	3541	0.068	0.39	YES
12	ALDH1B1	ALDH1B1	ALDH1B1	4112	0.057	0.38	YES
13	AASS	AASS	AASS	4145	0.057	0.4	YES
14	ACAT1	ACAT1	ACAT1	4254	0.055	0.42	YES
15	ACAT2	ACAT2	ACAT2	4373	0.054	0.43	YES
16	WHSC1L1	WHSC1L1	WHSC1L1	4549	0.05	0.44	YES
17	SUV39H1	SUV39H1	SUV39H1	4577	0.05	0.46	YES
18	SUV420H1	SUV420H1	SUV420H1	4703	0.048	0.47	YES
19	PLOD2	PLOD2	PLOD2	5117	0.042	0.46	YES
20	AASDH	AASDH	AASDH	5164	0.041	0.48	YES
21	SETDB1	SETDB1	SETDB1	5661	0.034	0.46	NO
22	SETD1A	SETD1A	SETD1A	6204	0.027	0.44	NO
23	EHMT2	EHMT2	EHMT2	6691	0.021	0.43	NO
24	ALDH2	ALDH2	ALDH2	6738	0.021	0.43	NO
25	PLOD3	PLOD3	PLOD3	6912	0.018	0.43	NO
26	HADHA	HADHA	HADHA	7421	0.012	0.41	NO
27	ALDH9A1	ALDH9A1	ALDH9A1	7529	0.011	0.4	NO
28	WHSC1	WHSC1	WHSC1	7684	0.0092	0.4	NO
29	GCDH	GCDH	GCDH	7698	0.009	0.4	NO
30	HADH	HADH	HADH	7757	0.0082	0.4	NO
31	SUV420H2	SUV420H2	SUV420H2	7953	0.0057	0.39	NO
32	SETD1B	SETD1B	SETD1B	8596	-0.0025	0.36	NO
33	NSD1	NSD1	NSD1	8799	-0.0052	0.35	NO
34	EHHADH	EHHADH	EHHADH	9061	-0.0086	0.34	NO
35	BBOX1	BBOX1	BBOX1	9227	-0.011	0.33	NO
36	OGDH	OGDH	OGDH	9394	-0.014	0.33	NO
37	SETD8	SETD8	SETD8	9509	-0.015	0.33	NO
38	EHMT1	EHMT1	EHMT1	10089	-0.023	0.3	NO
39	SETD7	SETD7	SETD7	10874	-0.037	0.28	NO
40	ECHS1	ECHS1	ECHS1	11028	-0.04	0.28	NO
41	DOT1L	DOT1L	DOT1L	11685	-0.053	0.27	NO
42	ALDH3A2	ALDH3A2	ALDH3A2	11981	-0.06	0.27	NO
43	DLST	DLST	DLST	12569	-0.075	0.27	NO
44	PLOD1	PLOD1	PLOD1	12741	-0.08	0.29	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 AMINOACYL TRNA BIOSYNTHESIS

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	86	0.38	0.27	YES
2	PRKAA2	PRKAA2	PRKAA2	1176	0.15	0.32	YES
3	STRADB	STRADB	STRADB	1729	0.12	0.38	YES
4	RHEB	RHEB	RHEB	2124	0.1	0.43	YES
5	PDE3B	PDE3B	PDE3B	2317	0.098	0.49	YES
6	PRKAB1	PRKAB1	PRKAB1	3671	0.066	0.46	NO
7	RPS6KB1	RPS6KB1	RPS6KB1	4631	0.049	0.44	NO
8	PRKAA1	PRKAA1	PRKAA1	5150	0.041	0.44	NO
9	TSC1	TSC1	TSC1	5213	0.04	0.47	NO
10	RPS6	RPS6	RPS6	5510	0.036	0.48	NO
11	EEF2K	EEF2K	EEF2K	6037	0.03	0.47	NO
12	PRKAB2	PRKAB2	PRKAB2	6462	0.024	0.47	NO
13	CAB39	CAB39	CAB39	6967	0.018	0.45	NO
14	RPTOR	RPTOR	RPTOR	7378	0.013	0.44	NO
15	TSC2	TSC2	TSC2	7461	0.012	0.44	NO
16	EIF4B	EIF4B	EIF4B	7650	0.0096	0.44	NO
17	AKT2	AKT2	AKT2	8144	0.0031	0.41	NO
18	PRKAG2	PRKAG2	PRKAG2	8350	0.00061	0.4	NO
19	EIF4G1	EIF4G1	EIF4G1	8545	-0.002	0.39	NO
20	PRKAG1	PRKAG1	PRKAG1	8710	-0.004	0.38	NO
21	EIF4E	EIF4E	EIF4E	8948	-0.0071	0.38	NO
22	STK11	STK11	STK11	9615	-0.016	0.35	NO
23	MLST8	MLST8	MLST8	10168	-0.024	0.34	NO
24	PPM1A	PPM1A	PPM1A	10314	-0.026	0.35	NO
25	EIF4EBP1	EIF4EBP1	EIF4EBP1	10346	-0.027	0.37	NO
26	MTOR	MTOR	MTOR	10708	-0.034	0.37	NO
27	STRADA	STRADA	STRADA	11366	-0.046	0.37	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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RNA DEGRADATION

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	1365	0.14	0.023	YES
2	NCBP2	NCBP2	NCBP2	2076	0.11	0.059	YES
3	CSTF3	CSTF3	CSTF3	2962	0.081	0.067	YES
4	PCF11	PCF11	PCF11	3149	0.077	0.11	YES
5	SNRPE	SNRPE	SNRPE	3183	0.076	0.16	YES
6	CSTF1	CSTF1	CSTF1	3388	0.071	0.2	YES
7	MAGOH	MAGOH	MAGOH	3950	0.06	0.22	YES
8	ZNF473	ZNF473	ZNF473	3991	0.06	0.26	YES
9	CPSF3	CPSF3	CPSF3	3999	0.059	0.3	YES
10	SNRPG	SNRPG	SNRPG	4015	0.059	0.34	YES
11	NUDT21	NUDT21	NUDT21	4247	0.056	0.36	YES
12	CSTF2	CSTF2	CSTF2	4525	0.051	0.38	YES
13	LSM11	LSM11	LSM11	4653	0.048	0.41	YES
14	CDC40	CDC40	CDC40	4800	0.046	0.44	YES
15	PAPOLA	PAPOLA	PAPOLA	4918	0.044	0.46	YES
16	NCBP1	NCBP1	NCBP1	4932	0.044	0.49	YES
17	CPSF1	CPSF1	CPSF1	5456	0.037	0.49	YES
18	SNRPF	SNRPF	SNRPF	5954	0.031	0.48	YES
19	SNRPD3	SNRPD3	SNRPD3	6100	0.029	0.5	YES
20	SNRPB	SNRPB	SNRPB	6420	0.024	0.5	YES
21	CPSF7	CPSF7	CPSF7	6434	0.024	0.51	YES
22	SLBP	SLBP	SLBP	6561	0.023	0.52	YES
23	NFX1	NFX1	NFX1	6904	0.018	0.52	YES
24	CPSF2	CPSF2	CPSF2	7078	0.016	0.52	YES
25	RNPS1	RNPS1	RNPS1	7259	0.014	0.52	YES
26	PABPN1	PABPN1	PABPN1	7291	0.014	0.52	YES
27	U2AF2	U2AF2	U2AF2	7456	0.012	0.52	YES
28	THOC4	THOC4	THOC4	7488	0.011	0.53	YES
29	CLP1	CLP1	CLP1	7541	0.011	0.54	YES
30	DHX38	DHX38	DHX38	7758	0.0082	0.53	NO
31	U2AF1	U2AF1	U2AF1	7933	0.006	0.52	NO
32	SRRM1	SRRM1	SRRM1	8564	-0.0022	0.49	NO
33	RBM8A	RBM8A	RBM8A	8834	-0.0056	0.48	NO
34	LSM10	LSM10	LSM10	11223	-0.043	0.38	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 RNA DEGRADATION.

Figure S6. 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 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	1365	0.14	0.061	YES
2	NCBP2	NCBP2	NCBP2	2076	0.11	0.13	YES
3	CSTF3	CSTF3	CSTF3	2962	0.081	0.16	YES
4	PCF11	PCF11	PCF11	3149	0.077	0.22	YES
5	CSTF1	CSTF1	CSTF1	3388	0.071	0.28	YES
6	MAGOH	MAGOH	MAGOH	3950	0.06	0.31	YES
7	CPSF3	CPSF3	CPSF3	3999	0.059	0.36	YES
8	NUDT21	NUDT21	NUDT21	4247	0.056	0.4	YES
9	CSTF2	CSTF2	CSTF2	4525	0.051	0.44	YES
10	CDC40	CDC40	CDC40	4800	0.046	0.47	YES
11	PAPOLA	PAPOLA	PAPOLA	4918	0.044	0.51	YES
12	NCBP1	NCBP1	NCBP1	4932	0.044	0.55	YES
13	CPSF1	CPSF1	CPSF1	5456	0.037	0.56	YES
14	CPSF7	CPSF7	CPSF7	6434	0.024	0.53	YES
15	NFX1	NFX1	NFX1	6904	0.018	0.52	YES
16	CPSF2	CPSF2	CPSF2	7078	0.016	0.52	YES
17	RNPS1	RNPS1	RNPS1	7259	0.014	0.53	YES
18	PABPN1	PABPN1	PABPN1	7291	0.014	0.54	YES
19	U2AF2	U2AF2	U2AF2	7456	0.012	0.54	YES
20	THOC4	THOC4	THOC4	7488	0.011	0.55	YES
21	CLP1	CLP1	CLP1	7541	0.011	0.56	YES
22	DHX38	DHX38	DHX38	7758	0.0082	0.56	NO
23	U2AF1	U2AF1	U2AF1	7933	0.006	0.55	NO
24	SRRM1	SRRM1	SRRM1	8564	-0.0022	0.52	NO
25	RBM8A	RBM8A	RBM8A	8834	-0.0056	0.51	NO

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

Figure S8. 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 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	RAE1	RAE1	RAE1	1357	0.14	-0.00012	YES
2	UPF3B	UPF3B	UPF3B	1365	0.14	0.075	YES
3	NUPL2	NUPL2	NUPL2	1542	0.13	0.14	YES
4	NCBP2	NCBP2	NCBP2	2076	0.11	0.16	YES
5	NUP35	NUP35	NUP35	2511	0.093	0.19	YES
6	NUPL1	NUPL1	NUPL1	3230	0.075	0.19	YES
7	NUP107	NUP107	NUP107	3525	0.069	0.21	YES
8	NUP155	NUP155	NUP155	3758	0.064	0.23	YES
9	MAGOH	MAGOH	MAGOH	3950	0.06	0.25	YES
10	CPSF3	CPSF3	CPSF3	3999	0.059	0.28	YES
11	NUP43	NUP43	NUP43	4280	0.055	0.3	YES
12	NUP153	NUP153	NUP153	4501	0.051	0.31	YES
13	NUP205	NUP205	NUP205	4664	0.048	0.33	YES
14	NUP54	NUP54	NUP54	4668	0.048	0.36	YES
15	CDC40	CDC40	CDC40	4800	0.046	0.37	YES
16	NUP133	NUP133	NUP133	4903	0.044	0.39	YES
17	NCBP1	NCBP1	NCBP1	4932	0.044	0.41	YES
18	NUP210	NUP210	NUP210	5057	0.042	0.43	YES
19	TPR	TPR	TPR	5282	0.039	0.44	YES
20	NUP85	NUP85	NUP85	5364	0.038	0.46	YES
21	CPSF1	CPSF1	CPSF1	5456	0.037	0.47	YES
22	RANBP2	RANBP2	RANBP2	5521	0.036	0.49	YES
23	NUP37	NUP37	NUP37	5788	0.033	0.49	YES
24	NUP214	NUP214	NUP214	6043	0.03	0.49	YES
25	POM121	POM121	POM121	6409	0.024	0.48	YES
26	SLBP	SLBP	SLBP	6561	0.023	0.49	YES
27	NXF1	NXF1	NXF1	6614	0.022	0.5	YES
28	NUP93	NUP93	NUP93	6716	0.021	0.5	YES
29	NFX1	NFX1	NFX1	6904	0.018	0.5	NO
30	CPSF2	CPSF2	CPSF2	7078	0.016	0.5	NO
31	RNPS1	RNPS1	RNPS1	7259	0.014	0.5	NO
32	U2AF2	U2AF2	U2AF2	7456	0.012	0.49	NO
33	THOC4	THOC4	THOC4	7488	0.011	0.5	NO
34	DHX38	DHX38	DHX38	7758	0.0082	0.49	NO
35	U2AF1	U2AF1	U2AF1	7933	0.006	0.48	NO
36	NUP88	NUP88	NUP88	8482	-0.0011	0.45	NO
37	SRRM1	SRRM1	SRRM1	8564	-0.0022	0.45	NO
38	NUP50	NUP50	NUP50	8610	-0.0027	0.45	NO
39	RBM8A	RBM8A	RBM8A	8834	-0.0056	0.44	NO
40	EIF4E	EIF4E	EIF4E	8948	-0.0071	0.44	NO
41	AAAS	AAAS	AAAS	9214	-0.011	0.43	NO
42	NUP62	NUP62	NUP62	9934	-0.021	0.4	NO
43	NUP188	NUP188	NUP188	11002	-0.039	0.36	NO
44	SEH1L	SEH1L	SEH1L	11799	-0.056	0.34	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	A1CF	A1CF	A1CF	190	0.31	0.042	YES
2	GTF2F2	GTF2F2	GTF2F2	1053	0.16	0.02	YES
3	RAE1	RAE1	RAE1	1357	0.14	0.027	YES
4	UPF3B	UPF3B	UPF3B	1365	0.14	0.05	YES
5	NUPL2	NUPL2	NUPL2	1542	0.13	0.062	YES
6	POLR2K	POLR2K	POLR2K	1800	0.12	0.067	YES
7	PRPF6	PRPF6	PRPF6	1959	0.11	0.077	YES
8	NCBP2	NCBP2	NCBP2	2076	0.11	0.088	YES
9	CCAR1	CCAR1	CCAR1	2395	0.096	0.087	YES
10	SNRPB2	SNRPB2	SNRPB2	2470	0.094	0.098	YES
11	NUP35	NUP35	NUP35	2511	0.093	0.11	YES
12	CSTF3	CSTF3	CSTF3	2962	0.081	0.1	YES
13	CCNH	CCNH	CCNH	3007	0.08	0.11	YES
14	PCF11	PCF11	PCF11	3149	0.077	0.12	YES
15	SNRPE	SNRPE	SNRPE	3183	0.076	0.13	YES
16	SNRPA1	SNRPA1	SNRPA1	3214	0.075	0.14	YES
17	NUPL1	NUPL1	NUPL1	3230	0.075	0.15	YES
18	CDK7	CDK7	CDK7	3253	0.074	0.16	YES
19	SF3B14	SF3B14	SF3B14	3355	0.072	0.17	YES
20	CSTF1	CSTF1	CSTF1	3388	0.071	0.18	YES
21	NUP107	NUP107	NUP107	3525	0.069	0.18	YES
22	NUP155	NUP155	NUP155	3758	0.064	0.18	YES
23	MAGOH	MAGOH	MAGOH	3950	0.06	0.18	YES
24	ZNF473	ZNF473	ZNF473	3991	0.06	0.19	YES
25	CPSF3	CPSF3	CPSF3	3999	0.059	0.2	YES
26	SNRPG	SNRPG	SNRPG	4015	0.059	0.2	YES
27	GTF2H1	GTF2H1	GTF2H1	4087	0.058	0.21	YES
28	NUDT21	NUDT21	NUDT21	4247	0.056	0.21	YES
29	NUP43	NUP43	NUP43	4280	0.055	0.22	YES
30	NUP153	NUP153	NUP153	4501	0.051	0.22	YES
31	CSTF2	CSTF2	CSTF2	4525	0.051	0.22	YES
32	LSM11	LSM11	LSM11	4653	0.048	0.22	YES
33	POLR2D	POLR2D	POLR2D	4656	0.048	0.23	YES
34	NUP205	NUP205	NUP205	4664	0.048	0.24	YES
35	NUP54	NUP54	NUP54	4668	0.048	0.25	YES
36	POLR2J	POLR2J	POLR2J	4680	0.048	0.25	YES
37	RBMX	RBMX	RBMX	4733	0.047	0.26	YES
38	ERCC3	ERCC3	ERCC3	4792	0.046	0.26	YES
39	CDC40	CDC40	CDC40	4800	0.046	0.27	YES
40	NUP133	NUP133	NUP133	4903	0.044	0.27	YES
41	PAPOLA	PAPOLA	PAPOLA	4918	0.044	0.28	YES
42	NCBP1	NCBP1	NCBP1	4932	0.044	0.29	YES
43	NUP210	NUP210	NUP210	5057	0.042	0.29	YES
44	POLR2F	POLR2F	POLR2F	5244	0.04	0.28	YES
45	HNRNPK	HNRNPK	HNRNPK	5260	0.039	0.29	YES
46	TPR	TPR	TPR	5282	0.039	0.29	YES
47	HNRNPH2	HNRNPH2	HNRNPH2	5325	0.039	0.3	YES
48	SF3B1	SF3B1	SF3B1	5354	0.038	0.3	YES
49	NUP85	NUP85	NUP85	5364	0.038	0.31	YES
50	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	5419	0.037	0.31	YES
51	CPSF1	CPSF1	CPSF1	5456	0.037	0.32	YES
52	HNRNPU	HNRNPU	HNRNPU	5470	0.037	0.32	YES
53	RANBP2	RANBP2	RANBP2	5521	0.036	0.32	YES
54	HNRNPA3	HNRNPA3	HNRNPA3	5581	0.036	0.33	YES
55	SNRNP200	SNRNP200	SNRNP200	5599	0.035	0.33	YES
56	POLR2C	POLR2C	POLR2C	5689	0.034	0.33	YES
57	NUP37	NUP37	NUP37	5788	0.033	0.33	YES
58	SF3B3	SF3B3	SF3B3	5809	0.032	0.34	YES
59	SMC1A	SMC1A	SMC1A	5861	0.032	0.34	YES
60	SNRPF	SNRPF	SNRPF	5954	0.031	0.34	YES
61	NUP214	NUP214	NUP214	6043	0.03	0.34	YES
62	SF3B2	SF3B2	SF3B2	6070	0.029	0.34	YES
63	SNRPD3	SNRPD3	SNRPD3	6100	0.029	0.35	YES
64	HNRNPD	HNRNPD	HNRNPD	6103	0.029	0.35	YES
65	CD2BP2	CD2BP2	CD2BP2	6267	0.026	0.35	YES
66	SNRPD2	SNRPD2	SNRPD2	6320	0.026	0.35	YES
67	MNAT1	MNAT1	MNAT1	6332	0.026	0.35	YES
68	POM121	POM121	POM121	6409	0.024	0.35	YES
69	SNRPB	SNRPB	SNRPB	6420	0.024	0.36	YES
70	SNRPA	SNRPA	SNRPA	6425	0.024	0.36	YES
71	CPSF7	CPSF7	CPSF7	6434	0.024	0.36	YES
72	SLBP	SLBP	SLBP	6561	0.023	0.36	YES
73	NXF1	NXF1	NXF1	6614	0.022	0.36	YES
74	HNRNPUL1	HNRNPUL1	HNRNPUL1	6670	0.022	0.36	YES
75	RBM5	RBM5	RBM5	6698	0.021	0.36	YES
76	HNRNPL	HNRNPL	HNRNPL	6711	0.021	0.36	YES
77	NUP93	NUP93	NUP93	6716	0.021	0.37	YES
78	HNRNPR	HNRNPR	HNRNPR	6737	0.021	0.37	YES
79	EFTUD2	EFTUD2	EFTUD2	6764	0.02	0.37	YES
80	HNRNPH1	HNRNPH1	HNRNPH1	6895	0.018	0.37	NO
81	NFX1	NFX1	NFX1	6904	0.018	0.37	NO
82	DHX9	DHX9	DHX9	6940	0.018	0.37	NO
83	CPSF2	CPSF2	CPSF2	7078	0.016	0.37	NO
84	APOBEC1	APOBEC1	APOBEC1	7142	0.016	0.37	NO
85	FUS	FUS	FUS	7198	0.015	0.37	NO
86	SF3A3	SF3A3	SF3A3	7212	0.015	0.37	NO
87	YBX1	YBX1	YBX1	7248	0.014	0.37	NO
88	RNPS1	RNPS1	RNPS1	7259	0.014	0.37	NO
89	PABPN1	PABPN1	PABPN1	7291	0.014	0.37	NO
90	GTF2H3	GTF2H3	GTF2H3	7411	0.012	0.37	NO
91	U2AF2	U2AF2	U2AF2	7456	0.012	0.37	NO
92	THOC4	THOC4	THOC4	7488	0.011	0.37	NO
93	POLR2H	POLR2H	POLR2H	7501	0.011	0.37	NO
94	CLP1	CLP1	CLP1	7541	0.011	0.37	NO
95	HNRNPF	HNRNPF	HNRNPF	7626	0.0098	0.36	NO
96	PTBP1	PTBP1	PTBP1	7638	0.0097	0.36	NO
97	RNGTT	RNGTT	RNGTT	7652	0.0095	0.37	NO
98	NHP2L1	NHP2L1	NHP2L1	7668	0.0094	0.37	NO
99	SNRNP70	SNRNP70	SNRNP70	7724	0.0086	0.36	NO
100	DHX38	DHX38	DHX38	7758	0.0082	0.36	NO
101	SF3A2	SF3A2	SF3A2	7778	0.0079	0.36	NO
102	POLR2B	POLR2B	POLR2B	7828	0.0073	0.36	NO
103	SF3B4	SF3B4	SF3B4	7850	0.007	0.36	NO
104	U2AF1	U2AF1	U2AF1	7933	0.006	0.36	NO
105	HNRNPC	HNRNPC	HNRNPC	7981	0.0053	0.36	NO
106	HNRNPA0	HNRNPA0	HNRNPA0	7986	0.0052	0.36	NO
107	GTF2F1	GTF2F1	GTF2F1	8007	0.005	0.36	NO
108	DNAJC8	DNAJC8	DNAJC8	8048	0.0045	0.36	NO
109	DDX23	DDX23	DDX23	8107	0.0036	0.35	NO
110	PRPF4	PRPF4	PRPF4	8362	0.00039	0.34	NO
111	PCBP1	PCBP1	PCBP1	8476	-0.001	0.33	NO
112	NUP88	NUP88	NUP88	8482	-0.0011	0.33	NO
113	SRRM1	SRRM1	SRRM1	8564	-0.0022	0.33	NO
114	METTL3	METTL3	METTL3	8580	-0.0024	0.33	NO
115	NUP50	NUP50	NUP50	8610	-0.0027	0.33	NO
116	POLR2G	POLR2G	POLR2G	8691	-0.0037	0.32	NO
117	RBM8A	RBM8A	RBM8A	8834	-0.0056	0.32	NO
118	HNRNPM	HNRNPM	HNRNPM	8851	-0.0058	0.32	NO
119	EIF4E	EIF4E	EIF4E	8948	-0.0071	0.31	NO
120	PCBP2	PCBP2	PCBP2	9165	-0.01	0.3	NO
121	AAAS	AAAS	AAAS	9214	-0.011	0.3	NO
122	LSM2	LSM2	LSM2	9319	-0.012	0.3	NO
123	GTF2H4	GTF2H4	GTF2H4	9395	-0.014	0.3	NO
124	ERCC2	ERCC2	ERCC2	9411	-0.014	0.3	NO
125	SUPT5H	SUPT5H	SUPT5H	9490	-0.015	0.3	NO
126	PHF5A	PHF5A	PHF5A	9784	-0.019	0.28	NO
127	HNRNPA1	HNRNPA1	HNRNPA1	9834	-0.02	0.28	NO
128	POLR2E	POLR2E	POLR2E	9929	-0.021	0.28	NO
129	NUP62	NUP62	NUP62	9934	-0.021	0.28	NO
130	SF3A1	SF3A1	SF3A1	10217	-0.025	0.27	NO
131	SNRPD1	SNRPD1	SNRPD1	10219	-0.025	0.28	NO
132	POLR2I	POLR2I	POLR2I	10256	-0.026	0.28	NO
133	SNRNP40	SNRNP40	SNRNP40	10540	-0.031	0.27	NO
134	SF3B5	SF3B5	SF3B5	10626	-0.032	0.27	NO
135	ADAR	ADAR	ADAR	10750	-0.034	0.27	NO
136	NUP188	NUP188	NUP188	11002	-0.039	0.26	NO
137	LSM10	LSM10	LSM10	11223	-0.043	0.26	NO
138	RNMT	RNMT	RNMT	11512	-0.05	0.25	NO
139	GTF2H2	GTF2H2	GTF2H2	11613	-0.052	0.25	NO
140	PRPF8	PRPF8	PRPF8	11733	-0.054	0.25	NO
141	SEH1L	SEH1L	SEH1L	11799	-0.056	0.26	NO
142	POLR2A	POLR2A	POLR2A	12857	-0.084	0.21	NO
143	TXNL4A	TXNL4A	TXNL4A	12983	-0.087	0.22	NO
144	POLR2L	POLR2L	POLR2L	13158	-0.094	0.23	NO
145	ADARB1	ADARB1	ADARB1	13734	-0.12	0.21	NO
146	GTF2H2B	GTF2H2B	GTF2H2B	14430	-0.14	0.2	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	GTF2F2	GTF2F2	GTF2F2	1053	0.16	-0.025	YES
2	RAE1	RAE1	RAE1	1357	0.14	-0.012	YES
3	UPF3B	UPF3B	UPF3B	1365	0.14	0.017	YES
4	NUPL2	NUPL2	NUPL2	1542	0.13	0.034	YES
5	POLR2K	POLR2K	POLR2K	1800	0.12	0.045	YES
6	PRPF6	PRPF6	PRPF6	1959	0.11	0.059	YES
7	NCBP2	NCBP2	NCBP2	2076	0.11	0.075	YES
8	CCAR1	CCAR1	CCAR1	2395	0.096	0.078	YES
9	SNRPB2	SNRPB2	SNRPB2	2470	0.094	0.094	YES
10	NUP35	NUP35	NUP35	2511	0.093	0.11	YES
11	CSTF3	CSTF3	CSTF3	2962	0.081	0.1	YES
12	PCF11	PCF11	PCF11	3149	0.077	0.11	YES
13	SNRPE	SNRPE	SNRPE	3183	0.076	0.12	YES
14	SNRPA1	SNRPA1	SNRPA1	3214	0.075	0.14	YES
15	NUPL1	NUPL1	NUPL1	3230	0.075	0.15	YES
16	SF3B14	SF3B14	SF3B14	3355	0.072	0.16	YES
17	CSTF1	CSTF1	CSTF1	3388	0.071	0.17	YES
18	NUP107	NUP107	NUP107	3525	0.069	0.18	YES
19	NUP155	NUP155	NUP155	3758	0.064	0.18	YES
20	MAGOH	MAGOH	MAGOH	3950	0.06	0.18	YES
21	CPSF3	CPSF3	CPSF3	3999	0.059	0.19	YES
22	SNRPG	SNRPG	SNRPG	4015	0.059	0.2	YES
23	NUDT21	NUDT21	NUDT21	4247	0.056	0.2	YES
24	NUP43	NUP43	NUP43	4280	0.055	0.21	YES
25	NUP153	NUP153	NUP153	4501	0.051	0.21	YES
26	CSTF2	CSTF2	CSTF2	4525	0.051	0.22	YES
27	POLR2D	POLR2D	POLR2D	4656	0.048	0.22	YES
28	NUP205	NUP205	NUP205	4664	0.048	0.23	YES
29	NUP54	NUP54	NUP54	4668	0.048	0.24	YES
30	POLR2J	POLR2J	POLR2J	4680	0.048	0.25	YES
31	RBMX	RBMX	RBMX	4733	0.047	0.26	YES
32	CDC40	CDC40	CDC40	4800	0.046	0.27	YES
33	NUP133	NUP133	NUP133	4903	0.044	0.27	YES
34	PAPOLA	PAPOLA	PAPOLA	4918	0.044	0.28	YES
35	NCBP1	NCBP1	NCBP1	4932	0.044	0.29	YES
36	NUP210	NUP210	NUP210	5057	0.042	0.29	YES
37	POLR2F	POLR2F	POLR2F	5244	0.04	0.29	YES
38	HNRNPK	HNRNPK	HNRNPK	5260	0.039	0.3	YES
39	TPR	TPR	TPR	5282	0.039	0.3	YES
40	HNRNPH2	HNRNPH2	HNRNPH2	5325	0.039	0.31	YES
41	SF3B1	SF3B1	SF3B1	5354	0.038	0.31	YES
42	NUP85	NUP85	NUP85	5364	0.038	0.32	YES
43	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	5419	0.037	0.33	YES
44	CPSF1	CPSF1	CPSF1	5456	0.037	0.33	YES
45	HNRNPU	HNRNPU	HNRNPU	5470	0.037	0.34	YES
46	RANBP2	RANBP2	RANBP2	5521	0.036	0.34	YES
47	HNRNPA3	HNRNPA3	HNRNPA3	5581	0.036	0.35	YES
48	SNRNP200	SNRNP200	SNRNP200	5599	0.035	0.36	YES
49	POLR2C	POLR2C	POLR2C	5689	0.034	0.36	YES
50	NUP37	NUP37	NUP37	5788	0.033	0.36	YES
51	SF3B3	SF3B3	SF3B3	5809	0.032	0.36	YES
52	SMC1A	SMC1A	SMC1A	5861	0.032	0.37	YES
53	SNRPF	SNRPF	SNRPF	5954	0.031	0.37	YES
54	NUP214	NUP214	NUP214	6043	0.03	0.37	YES
55	SF3B2	SF3B2	SF3B2	6070	0.029	0.38	YES
56	SNRPD3	SNRPD3	SNRPD3	6100	0.029	0.38	YES
57	HNRNPD	HNRNPD	HNRNPD	6103	0.029	0.39	YES
58	CD2BP2	CD2BP2	CD2BP2	6267	0.026	0.38	YES
59	SNRPD2	SNRPD2	SNRPD2	6320	0.026	0.38	YES
60	POM121	POM121	POM121	6409	0.024	0.38	YES
61	SNRPB	SNRPB	SNRPB	6420	0.024	0.39	YES
62	SNRPA	SNRPA	SNRPA	6425	0.024	0.4	YES
63	CPSF7	CPSF7	CPSF7	6434	0.024	0.4	YES
64	SLBP	SLBP	SLBP	6561	0.023	0.4	YES
65	NXF1	NXF1	NXF1	6614	0.022	0.4	YES
66	HNRNPUL1	HNRNPUL1	HNRNPUL1	6670	0.022	0.4	YES
67	RBM5	RBM5	RBM5	6698	0.021	0.4	YES
68	HNRNPL	HNRNPL	HNRNPL	6711	0.021	0.41	YES
69	NUP93	NUP93	NUP93	6716	0.021	0.41	YES
70	HNRNPR	HNRNPR	HNRNPR	6737	0.021	0.41	YES
71	EFTUD2	EFTUD2	EFTUD2	6764	0.02	0.42	YES
72	HNRNPH1	HNRNPH1	HNRNPH1	6895	0.018	0.41	YES
73	NFX1	NFX1	NFX1	6904	0.018	0.42	YES
74	DHX9	DHX9	DHX9	6940	0.018	0.42	YES
75	CPSF2	CPSF2	CPSF2	7078	0.016	0.42	NO
76	FUS	FUS	FUS	7198	0.015	0.41	NO
77	SF3A3	SF3A3	SF3A3	7212	0.015	0.41	NO
78	YBX1	YBX1	YBX1	7248	0.014	0.42	NO
79	RNPS1	RNPS1	RNPS1	7259	0.014	0.42	NO
80	PABPN1	PABPN1	PABPN1	7291	0.014	0.42	NO
81	U2AF2	U2AF2	U2AF2	7456	0.012	0.41	NO
82	THOC4	THOC4	THOC4	7488	0.011	0.41	NO
83	POLR2H	POLR2H	POLR2H	7501	0.011	0.41	NO
84	CLP1	CLP1	CLP1	7541	0.011	0.41	NO
85	HNRNPF	HNRNPF	HNRNPF	7626	0.0098	0.41	NO
86	PTBP1	PTBP1	PTBP1	7638	0.0097	0.41	NO
87	NHP2L1	NHP2L1	NHP2L1	7668	0.0094	0.41	NO
88	SNRNP70	SNRNP70	SNRNP70	7724	0.0086	0.41	NO
89	DHX38	DHX38	DHX38	7758	0.0082	0.41	NO
90	SF3A2	SF3A2	SF3A2	7778	0.0079	0.41	NO
91	POLR2B	POLR2B	POLR2B	7828	0.0073	0.41	NO
92	SF3B4	SF3B4	SF3B4	7850	0.007	0.41	NO
93	U2AF1	U2AF1	U2AF1	7933	0.006	0.41	NO
94	HNRNPC	HNRNPC	HNRNPC	7981	0.0053	0.41	NO
95	HNRNPA0	HNRNPA0	HNRNPA0	7986	0.0052	0.41	NO
96	GTF2F1	GTF2F1	GTF2F1	8007	0.005	0.41	NO
97	DNAJC8	DNAJC8	DNAJC8	8048	0.0045	0.41	NO
98	DDX23	DDX23	DDX23	8107	0.0036	0.4	NO
99	PRPF4	PRPF4	PRPF4	8362	0.00039	0.39	NO
100	PCBP1	PCBP1	PCBP1	8476	-0.001	0.38	NO
101	NUP88	NUP88	NUP88	8482	-0.0011	0.38	NO
102	SRRM1	SRRM1	SRRM1	8564	-0.0022	0.38	NO
103	METTL3	METTL3	METTL3	8580	-0.0024	0.38	NO
104	NUP50	NUP50	NUP50	8610	-0.0027	0.38	NO
105	POLR2G	POLR2G	POLR2G	8691	-0.0037	0.38	NO
106	RBM8A	RBM8A	RBM8A	8834	-0.0056	0.37	NO
107	HNRNPM	HNRNPM	HNRNPM	8851	-0.0058	0.37	NO
108	EIF4E	EIF4E	EIF4E	8948	-0.0071	0.36	NO
109	PCBP2	PCBP2	PCBP2	9165	-0.01	0.35	NO
110	AAAS	AAAS	AAAS	9214	-0.011	0.35	NO
111	LSM2	LSM2	LSM2	9319	-0.012	0.35	NO
112	PHF5A	PHF5A	PHF5A	9784	-0.019	0.33	NO
113	HNRNPA1	HNRNPA1	HNRNPA1	9834	-0.02	0.33	NO
114	POLR2E	POLR2E	POLR2E	9929	-0.021	0.33	NO
115	NUP62	NUP62	NUP62	9934	-0.021	0.33	NO
116	SF3A1	SF3A1	SF3A1	10217	-0.025	0.32	NO
117	SNRPD1	SNRPD1	SNRPD1	10219	-0.025	0.33	NO
118	POLR2I	POLR2I	POLR2I	10256	-0.026	0.33	NO
119	SNRNP40	SNRNP40	SNRNP40	10540	-0.031	0.32	NO
120	SF3B5	SF3B5	SF3B5	10626	-0.032	0.32	NO
121	NUP188	NUP188	NUP188	11002	-0.039	0.31	NO
122	PRPF8	PRPF8	PRPF8	11733	-0.054	0.28	NO
123	SEH1L	SEH1L	SEH1L	11799	-0.056	0.29	NO
124	POLR2A	POLR2A	POLR2A	12857	-0.084	0.25	NO
125	TXNL4A	TXNL4A	TXNL4A	12983	-0.087	0.26	NO
126	POLR2L	POLR2L	POLR2L	13158	-0.094	0.27	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	RAE1	RAE1	RAE1	1357	0.14	0.017	YES
2	NUPL2	NUPL2	NUPL2	1542	0.13	0.092	YES
3	NCBP2	NCBP2	NCBP2	2076	0.11	0.13	YES
4	NUP35	NUP35	NUP35	2511	0.093	0.17	YES
5	NUPL1	NUPL1	NUPL1	3230	0.075	0.18	YES
6	NUP107	NUP107	NUP107	3525	0.069	0.21	YES
7	NUP155	NUP155	NUP155	3758	0.064	0.24	YES
8	CPSF3	CPSF3	CPSF3	3999	0.059	0.26	YES
9	NUP43	NUP43	NUP43	4280	0.055	0.28	YES
10	NUP153	NUP153	NUP153	4501	0.051	0.31	YES
11	NUP205	NUP205	NUP205	4664	0.048	0.33	YES
12	NUP54	NUP54	NUP54	4668	0.048	0.36	YES
13	NUP133	NUP133	NUP133	4903	0.044	0.38	YES
14	NCBP1	NCBP1	NCBP1	4932	0.044	0.4	YES
15	NUP210	NUP210	NUP210	5057	0.042	0.42	YES
16	TPR	TPR	TPR	5282	0.039	0.44	YES
17	NUP85	NUP85	NUP85	5364	0.038	0.46	YES
18	CPSF1	CPSF1	CPSF1	5456	0.037	0.48	YES
19	RANBP2	RANBP2	RANBP2	5521	0.036	0.5	YES
20	NUP37	NUP37	NUP37	5788	0.033	0.51	YES
21	NUP214	NUP214	NUP214	6043	0.03	0.51	YES
22	POM121	POM121	POM121	6409	0.024	0.51	YES
23	NXF1	NXF1	NXF1	6614	0.022	0.51	YES
24	NUP93	NUP93	NUP93	6716	0.021	0.52	YES
25	CPSF2	CPSF2	CPSF2	7078	0.016	0.51	NO
26	THOC4	THOC4	THOC4	7488	0.011	0.49	NO
27	NUP88	NUP88	NUP88	8482	-0.0011	0.44	NO
28	NUP50	NUP50	NUP50	8610	-0.0027	0.43	NO
29	EIF4E	EIF4E	EIF4E	8948	-0.0071	0.42	NO
30	AAAS	AAAS	AAAS	9214	-0.011	0.41	NO
31	NUP62	NUP62	NUP62	9934	-0.021	0.39	NO
32	NUP188	NUP188	NUP188	11002	-0.039	0.35	NO
33	SEH1L	SEH1L	SEH1L	11799	-0.056	0.34	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	RAE1	RAE1	RAE1	1357	0.14	0.02	YES
2	NUPL2	NUPL2	NUPL2	1542	0.13	0.099	YES
3	NUP35	NUP35	NUP35	2511	0.093	0.11	YES
4	PSIP1	PSIP1	PSIP1	2945	0.081	0.14	YES
5	NUPL1	NUPL1	NUPL1	3230	0.075	0.18	YES
6	NUP107	NUP107	NUP107	3525	0.069	0.21	YES
7	NUP155	NUP155	NUP155	3758	0.064	0.24	YES
8	NUP43	NUP43	NUP43	4280	0.055	0.24	YES
9	NUP153	NUP153	NUP153	4501	0.051	0.27	YES
10	NUP205	NUP205	NUP205	4664	0.048	0.29	YES
11	NUP54	NUP54	NUP54	4668	0.048	0.32	YES
12	NUP133	NUP133	NUP133	4903	0.044	0.34	YES
13	NUP210	NUP210	NUP210	5057	0.042	0.36	YES
14	TPR	TPR	TPR	5282	0.039	0.38	YES
15	SLC25A6	SLC25A6	SLC25A6	5319	0.039	0.4	YES
16	NUP85	NUP85	NUP85	5364	0.038	0.42	YES
17	BANF1	BANF1	BANF1	5451	0.037	0.44	YES
18	RANBP2	RANBP2	RANBP2	5521	0.036	0.47	YES
19	NUP37	NUP37	NUP37	5788	0.033	0.47	YES
20	NUP214	NUP214	NUP214	6043	0.03	0.48	YES
21	POM121	POM121	POM121	6409	0.024	0.48	NO
22	NUP93	NUP93	NUP93	6716	0.021	0.47	NO
23	KPNA1	KPNA1	KPNA1	6864	0.019	0.48	NO
24	HMGA1	HMGA1	HMGA1	8086	0.004	0.41	NO
25	NUP88	NUP88	NUP88	8482	-0.0011	0.39	NO
26	NUP50	NUP50	NUP50	8610	-0.0027	0.39	NO
27	AAAS	AAAS	AAAS	9214	-0.011	0.36	NO
28	SLC25A5	SLC25A5	SLC25A5	9724	-0.018	0.34	NO
29	NUP62	NUP62	NUP62	9934	-0.021	0.35	NO
30	NUP188	NUP188	NUP188	11002	-0.039	0.31	NO
31	SLC25A4	SLC25A4	SLC25A4	11706	-0.054	0.31	NO
32	SEH1L	SEH1L	SEH1L	11799	-0.056	0.34	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	MRE11A	MRE11A	MRE11A	918	0.17	0.04	YES
2	RAD50	RAD50	RAD50	2055	0.11	0.033	YES
3	CHEK2	CHEK2	CHEK2	2282	0.1	0.072	YES
4	BRCA1	BRCA1	BRCA1	2498	0.093	0.11	YES
5	CDC25A	CDC25A	CDC25A	2520	0.092	0.16	YES
6	YWHAB	YWHAB	YWHAB	2609	0.09	0.2	YES
7	ATM	ATM	ATM	2749	0.086	0.24	YES
8	BLM	BLM	BLM	3043	0.079	0.26	YES
9	XRCC4	XRCC4	XRCC4	3250	0.074	0.29	YES
10	SMC3	SMC3	SMC3	3524	0.069	0.31	YES
11	MDC1	MDC1	MDC1	3713	0.065	0.33	YES
12	CDC25C	CDC25C	CDC25C	3750	0.064	0.36	YES
13	DCLRE1C	DCLRE1C	DCLRE1C	4061	0.058	0.38	YES
14	RAD17	RAD17	RAD17	4096	0.058	0.41	YES
15	RNF8	RNF8	RNF8	4161	0.057	0.43	YES
16	FAM175A	FAM175A	FAM175A	4237	0.056	0.46	YES
17	RFWD2	RFWD2	RFWD2	4652	0.048	0.46	YES
18	TP53BP1	TP53BP1	TP53BP1	4852	0.045	0.47	YES
19	UIMC1	UIMC1	UIMC1	4980	0.043	0.49	YES
20	NBN	NBN	NBN	5436	0.037	0.48	YES
21	UBE2N	UBE2N	UBE2N	5715	0.034	0.48	YES
22	SMC1A	SMC1A	SMC1A	5861	0.032	0.49	YES
23	FANCD2	FANCD2	FANCD2	6176	0.028	0.49	YES
24	TERF2	TERF2	TERF2	6231	0.027	0.5	YES
25	ABL1	ABL1	ABL1	7270	0.014	0.45	NO
26	BID	BID	BID	7525	0.011	0.44	NO
27	RAD9A	RAD9A	RAD9A	7700	0.009	0.44	NO
28	KAT5	KAT5	KAT5	9123	-0.0095	0.36	NO
29	CTBP1	CTBP1	CTBP1	9168	-0.01	0.37	NO
30	TRIM28	TRIM28	TRIM28	9335	-0.013	0.36	NO
31	H2AFX	H2AFX	H2AFX	10150	-0.024	0.33	NO
32	RBBP8	RBBP8	RBBP8	11019	-0.04	0.3	NO
33	MDM2	MDM2	MDM2	12611	-0.077	0.26	NO
34	TOP3A	TOP3A	TOP3A	12917	-0.086	0.28	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	0.38	1.3	0.19	1	1	0.32	0.12	0.28	1	0.8
KEGG BUTANOATE METABOLISM	30	genes.ES.table	0.43	1.3	0.21	1	1	0.57	0.2	0.45	1	0.8
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM	34	genes.ES.table	0.53	1.4	0.15	1	0.99	0.35	0.1	0.32	1	0.73
KEGG BASE EXCISION REPAIR	33	genes.ES.table	0.38	1.3	0.19	1	1	1	0.62	0.38	1	0.73
BIOCARTA FAS PATHWAY	30	genes.ES.table	0.46	1.6	0.055	1	0.92	0.37	0.22	0.29	1	0.62
BIOCARTA HIVNEF PATHWAY	58	genes.ES.table	0.4	1.7	0.044	1	0.79	0.4	0.26	0.3	0.83	0.45
BIOCARTA DEATH PATHWAY	33	genes.ES.table	0.36	1.5	0.086	1	0.98	0.46	0.21	0.36	1	0.7
BIOCARTA PYK2 PATHWAY	28	genes.ES.table	0.32	1.3	0.15	1	1	0.36	0.21	0.28	1	0.73
BIOCARTA TNFR1 PATHWAY	29	genes.ES.table	0.35	1.4	0.1	1	0.99	0.48	0.3	0.34	1	0.73
PID TRAIL PATHWAY	28	genes.ES.table	0.42	1.5	0.087	1	0.97	0.43	0.21	0.34	1	0.68

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	TP53AIP1	TP53AIP1	TP53AIP1	251	0.26	0.1	YES
2	KAT2B	KAT2B	KAT2B	1221	0.12	0.1	YES
3	MDM2	MDM2	MDM2	1320	0.11	0.15	YES
4	HIPK2	HIPK2	HIPK2	1409	0.1	0.19	YES
5	CSNK1G1	CSNK1G1	CSNK1G1	2298	0.07	0.17	YES
6	CSNK1G3	CSNK1G3	CSNK1G3	2385	0.067	0.2	YES
7	PPP1R13L	PPP1R13L	PPP1R13L	2392	0.067	0.22	YES
8	TP53	TP53	TP53	2574	0.063	0.24	YES
9	DYRK2	DYRK2	DYRK2	2652	0.06	0.27	YES
10	CCNG1	CCNG1	CCNG1	2697	0.059	0.29	YES
11	PPM1D	PPM1D	PPM1D	2940	0.055	0.3	YES
12	SETD7	SETD7	SETD7	2972	0.054	0.32	YES
13	CSNK1A1	CSNK1A1	CSNK1A1	3187	0.05	0.33	YES
14	SETD8	SETD8	SETD8	3375	0.046	0.34	YES
15	CCNA2	CCNA2	CCNA2	3426	0.046	0.36	YES
16	EP300	EP300	EP300	3463	0.045	0.38	YES
17	PPP2R4	PPP2R4	PPP2R4	3709	0.041	0.38	YES
18	MAPK8	MAPK8	MAPK8	3718	0.041	0.4	YES
19	PRMT5	PRMT5	PRMT5	4138	0.035	0.39	YES
20	AKT1	AKT1	AKT1	4289	0.032	0.4	YES
21	RASSF1	RASSF1	RASSF1	4600	0.028	0.4	YES
22	RPL11	RPL11	RPL11	4671	0.027	0.4	YES
23	PPP2CA	PPP2CA	PPP2CA	5791	0.014	0.35	NO
24	MAPK9	MAPK9	MAPK9	6114	0.011	0.34	NO
25	PRKCD	PRKCD	PRKCD	6270	0.0093	0.33	NO
26	RPL5	RPL5	RPL5	6353	0.0084	0.33	NO
27	CSNK1E	CSNK1E	CSNK1E	6380	0.008	0.33	NO
28	CDK2	CDK2	CDK2	6456	0.0071	0.33	NO
29	CHEK2	CHEK2	CHEK2	6489	0.0067	0.33	NO
30	FBXO11	FBXO11	FBXO11	6579	0.0056	0.33	NO
31	DAXX	DAXX	DAXX	6686	0.0044	0.33	NO
32	YY1	YY1	YY1	6735	0.0039	0.32	NO
33	PIN1	PIN1	PIN1	7099	0.00022	0.3	NO
34	KAT5	KAT5	KAT5	7352	-0.0027	0.29	NO
35	RFWD2	RFWD2	RFWD2	7617	-0.0057	0.28	NO
36	GSK3B	GSK3B	GSK3B	7625	-0.0058	0.28	NO
37	UBE2D1	UBE2D1	UBE2D1	7676	-0.0064	0.28	NO
38	SMYD2	SMYD2	SMYD2	7842	-0.0082	0.28	NO
39	RCHY1	RCHY1	RCHY1	7863	-0.0084	0.28	NO
40	CSNK1D	CSNK1D	CSNK1D	7908	-0.0089	0.28	NO
41	NEDD8	NEDD8	NEDD8	7942	-0.0093	0.28	NO
42	CSNK1G2	CSNK1G2	CSNK1G2	7947	-0.0093	0.29	NO
43	CREBBP	CREBBP	CREBBP	8274	-0.013	0.28	NO
44	TTC5	TTC5	TTC5	8317	-0.013	0.28	NO
45	HUWE1	HUWE1	HUWE1	8478	-0.015	0.28	NO
46	CHEK1	CHEK1	CHEK1	8552	-0.016	0.28	NO
47	ABL1	ABL1	ABL1	8625	-0.017	0.28	NO
48	ATM	ATM	ATM	8776	-0.019	0.28	NO
49	TRIM28	TRIM28	TRIM28	8992	-0.022	0.28	NO
50	ATR	ATR	ATR	9210	-0.025	0.28	NO
51	USP7	USP7	USP7	9245	-0.025	0.29	NO
52	RPL23	RPL23	RPL23	9336	-0.026	0.3	NO
53	SKP2	SKP2	SKP2	9758	-0.032	0.29	NO
54	MDM4	MDM4	MDM4	9963	-0.035	0.29	NO
55	E4F1	E4F1	E4F1	10085	-0.037	0.3	NO
56	MAPK14	MAPK14	MAPK14	11295	-0.06	0.26	NO
57	CSE1L	CSE1L	CSE1L	12302	-0.085	0.24	NO
58	CDKN2A	CDKN2A	CDKN2A	14380	-0.17	0.2	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 BUTANOATE 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	MAP3K5	MAP3K5	MAP3K5	525	0.19	0.045	YES
2	CASP7	CASP7	CASP7	703	0.16	0.099	YES
3	FAS	FAS	FAS	820	0.15	0.15	YES
4	BCL2	BCL2	BCL2	888	0.14	0.2	YES
5	BIRC3	BIRC3	BIRC3	1131	0.12	0.24	YES
6	MDM2	MDM2	MDM2	1320	0.11	0.27	YES
7	APAF1	APAF1	APAF1	1598	0.094	0.29	YES
8	LMNA	LMNA	LMNA	2238	0.071	0.28	YES
9	CASP3	CASP3	CASP3	2326	0.069	0.3	YES
10	RIPK1	RIPK1	RIPK1	2398	0.067	0.32	YES
11	GSN	GSN	GSN	2755	0.058	0.33	YES
12	PSEN1	PSEN1	PSEN1	2859	0.056	0.34	YES
13	CASP9	CASP9	CASP9	3274	0.048	0.34	YES
14	CASP8	CASP8	CASP8	3555	0.044	0.34	YES
15	CYCS	CYCS	CYCS	3607	0.043	0.35	YES
16	MAPK8	MAPK8	MAPK8	3718	0.041	0.36	YES
17	BIRC2	BIRC2	BIRC2	3787	0.04	0.38	YES
18	PARP1	PARP1	PARP1	3989	0.037	0.38	YES
19	LMNB1	LMNB1	LMNB1	3998	0.036	0.39	YES
20	BAG4	BAG4	BAG4	4147	0.034	0.4	YES
21	CDK11B	CDK11B	CDK11B	4504	0.03	0.39	YES
22	MAP2K7	MAP2K7	MAP2K7	4658	0.027	0.39	YES
23	SPTAN1	SPTAN1	SPTAN1	4665	0.027	0.4	YES
24	CHUK	CHUK	CHUK	5282	0.02	0.37	NO
25	PAK2	PAK2	PAK2	5373	0.019	0.38	NO
26	NFKB1	NFKB1	NFKB1	5384	0.019	0.38	NO
27	CRADD	CRADD	CRADD	5451	0.018	0.39	NO
28	FASLG	FASLG	FASLG	5595	0.017	0.38	NO
29	ACTG1	ACTG1	ACTG1	5815	0.014	0.38	NO
30	PRKCD	PRKCD	PRKCD	6270	0.0093	0.36	NO
31	NFKBIA	NFKBIA	NFKBIA	6371	0.0081	0.35	NO
32	RB1	RB1	RB1	6417	0.0075	0.36	NO
33	CASP2	CASP2	CASP2	6623	0.0051	0.34	NO
34	DAXX	DAXX	DAXX	6686	0.0044	0.34	NO
35	CASP6	CASP6	CASP6	6753	0.0038	0.34	NO
36	LMNB2	LMNB2	LMNB2	6770	0.0036	0.34	NO
37	RASA1	RASA1	RASA1	6779	0.0035	0.34	NO
38	TRAF2	TRAF2	TRAF2	6999	0.0013	0.33	NO
39	MAP3K1	MAP3K1	MAP3K1	7176	-0.00061	0.32	NO
40	DFFB	DFFB	DFFB	7598	-0.0055	0.3	NO
41	TNFRSF1A	TNFRSF1A	TNFRSF1A	7613	-0.0057	0.3	NO
42	TRADD	TRADD	TRADD	7776	-0.0075	0.3	NO
43	NUMA1	NUMA1	NUMA1	7893	-0.0087	0.29	NO
44	XIAP	XIAP	XIAP	8230	-0.013	0.28	NO
45	RELA	RELA	RELA	8267	-0.013	0.28	NO
46	ARHGDIB	ARHGDIB	ARHGDIB	8494	-0.016	0.28	NO
47	CDK11A	CDK11A	CDK11A	8825	-0.02	0.26	NO
48	DFFA	DFFA	DFFA	9419	-0.027	0.24	NO
49	PTK2	PTK2	PTK2	9477	-0.028	0.25	NO
50	FADD	FADD	FADD	9587	-0.03	0.25	NO
51	MAP3K14	MAP3K14	MAP3K14	10347	-0.041	0.23	NO
52	TNFRSF1B	TNFRSF1B	TNFRSF1B	10475	-0.043	0.24	NO
53	PRKDC	PRKDC	PRKDC	10506	-0.044	0.25	NO
54	PSEN2	PSEN2	PSEN2	10839	-0.05	0.25	NO
55	BID	BID	BID	11041	-0.054	0.26	NO
56	CFLAR	CFLAR	CFLAR	11091	-0.055	0.28	NO
57	TNF	TNF	TNF	12983	-0.11	0.22	NO
58	TRAF1	TRAF1	TRAF1	14144	-0.16	0.22	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 BUTANOATE METABOLISM.

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

genes ES table in pathway: KEGG PORPHYRIN AND CHLOROPHYLL 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	PTPN13	PTPN13	PTPN13	457	0.21	0.12	YES
2	CASP7	CASP7	CASP7	703	0.16	0.22	YES
3	FAS	FAS	FAS	820	0.15	0.31	YES
4	MAP2K4	MAP2K4	MAP2K4	1887	0.083	0.31	YES
5	CASP10	CASP10	CASP10	1955	0.08	0.36	YES
6	LMNA	LMNA	LMNA	2238	0.071	0.4	YES
7	CASP3	CASP3	CASP3	2326	0.069	0.44	YES
8	CASP8	CASP8	CASP8	3555	0.044	0.4	YES
9	MAPK8	MAPK8	MAPK8	3718	0.041	0.42	YES
10	PARP1	PARP1	PARP1	3989	0.037	0.43	YES
11	LMNB1	LMNB1	LMNB1	3998	0.036	0.46	YES
12	SPTAN1	SPTAN1	SPTAN1	4665	0.027	0.44	NO
13	PAK1	PAK1	PAK1	5047	0.022	0.43	NO
14	PAK2	PAK2	PAK2	5373	0.019	0.43	NO
15	FASLG	FASLG	FASLG	5595	0.017	0.42	NO
16	RB1	RB1	RB1	6417	0.0075	0.38	NO
17	DAXX	DAXX	DAXX	6686	0.0044	0.37	NO
18	CASP6	CASP6	CASP6	6753	0.0038	0.37	NO
19	LMNB2	LMNB2	LMNB2	6770	0.0036	0.37	NO
20	MAP3K1	MAP3K1	MAP3K1	7176	-0.00061	0.35	NO
21	DFFB	DFFB	DFFB	7598	-0.0055	0.33	NO
22	ARHGDIB	ARHGDIB	ARHGDIB	8494	-0.016	0.29	NO
23	JUN	JUN	JUN	9085	-0.023	0.28	NO
24	DFFA	DFFA	DFFA	9419	-0.027	0.28	NO
25	FADD	FADD	FADD	9587	-0.03	0.29	NO
26	FAF1	FAF1	FAF1	9648	-0.03	0.3	NO
27	MAP3K7	MAP3K7	MAP3K7	9896	-0.034	0.31	NO
28	PRKDC	PRKDC	PRKDC	10506	-0.044	0.31	NO
29	CFLAR	CFLAR	CFLAR	11091	-0.055	0.32	NO
30	RIPK2	RIPK2	RIPK2	12732	-0.1	0.29	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 PORPHYRIN AND CHLOROPHYLL METABOLISM.

Figure S26. 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 BASE EXCISION REPAIR

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	PLA2G4D	PLA2G4D	PLA2G4D	124	0.33	0.1	YES
2	PLA2G4A	PLA2G4A	PLA2G4A	160	0.32	0.21	YES
3	PLA2G2A	PLA2G2A	PLA2G2A	274	0.26	0.29	YES
4	PLA2G10	PLA2G10	PLA2G10	388	0.22	0.36	YES
5	AGPAT9	AGPAT9	AGPAT9	544	0.19	0.41	YES
6	LPCAT4	LPCAT4	LPCAT4	645	0.17	0.46	YES
7	AGPAT4	AGPAT4	AGPAT4	802	0.15	0.51	YES
8	PLD1	PLD1	PLD1	974	0.14	0.54	YES
9	PLA2G2F	PLA2G2F	PLA2G2F	1200	0.12	0.57	YES
10	LPCAT1	LPCAT1	LPCAT1	2042	0.077	0.55	NO
11	AGPAT5	AGPAT5	AGPAT5	2736	0.058	0.53	NO
12	PLD2	PLD2	PLD2	2851	0.056	0.54	NO
13	PLA2G1B	PLA2G1B	PLA2G1B	3282	0.048	0.54	NO
14	GPD1L	GPD1L	GPD1L	3591	0.043	0.53	NO
15	GNPAT	GNPAT	GNPAT	4407	0.031	0.5	NO
16	AGPAT2	AGPAT2	AGPAT2	4905	0.024	0.48	NO
17	PLA2G12A	PLA2G12A	PLA2G12A	5476	0.018	0.45	NO
18	AGPAT6	AGPAT6	AGPAT6	6602	0.0053	0.39	NO
19	LCLAT1	LCLAT1	LCLAT1	7084	0.00034	0.36	NO
20	GPD1	GPD1	GPD1	7524	-0.0046	0.34	NO
21	AGPAT3	AGPAT3	AGPAT3	8147	-0.012	0.31	NO
22	AGPAT1	AGPAT1	AGPAT1	8679	-0.018	0.29	NO
23	GPAM	GPAM	GPAM	9299	-0.026	0.26	NO
24	PLA2G2D	PLA2G2D	PLA2G2D	13905	-0.15	0.054	NO
25	GPAT2	GPAT2	GPAT2	14035	-0.15	0.098	NO
26	PLA2G5	PLA2G5	PLA2G5	17222	-0.36	0.043	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 BASE EXCISION REPAIR.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BASE EXCISION REPAIR, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA FAS PATHWAY

Table S15. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	TNFRSF10D	TNFRSF10D	TNFRSF10D	1726	0.089	-0.026	YES
2	MAP2K4	MAP2K4	MAP2K4	1887	0.083	0.03	YES
3	TNFRSF10A	TNFRSF10A	TNFRSF10A	1928	0.081	0.092	YES
4	CASP10	CASP10	CASP10	1955	0.08	0.15	YES
5	TNFSF10	TNFSF10	TNFSF10	2104	0.075	0.2	YES
6	PIK3R3	PIK3R3	PIK3R3	2261	0.071	0.25	YES
7	RIPK1	RIPK1	RIPK1	2398	0.067	0.3	YES
8	TNFRSF10B	TNFRSF10B	TNFRSF10B	2472	0.065	0.34	YES
9	PIK3CB	PIK3CB	PIK3CB	2999	0.053	0.36	YES
10	MAPK3	MAPK3	MAPK3	3506	0.044	0.36	YES
11	CASP8	CASP8	CASP8	3555	0.044	0.4	YES
12	MAPK8	MAPK8	MAPK8	3718	0.041	0.42	YES
13	CHUK	CHUK	CHUK	5282	0.02	0.35	NO
14	MAPK1	MAPK1	MAPK1	5571	0.017	0.34	NO
15	TRAF2	TRAF2	TRAF2	6999	0.0013	0.26	NO
16	MAP3K1	MAP3K1	MAP3K1	7176	-0.00061	0.26	NO
17	TNFRSF10C	TNFRSF10C	TNFRSF10C	7264	-0.0017	0.25	NO
18	DAP3	DAP3	DAP3	7369	-0.0029	0.25	NO
19	PIK3CA	PIK3CA	PIK3CA	7612	-0.0056	0.24	NO
20	TRADD	TRADD	TRADD	7776	-0.0075	0.24	NO
21	PIK3R2	PIK3R2	PIK3R2	8607	-0.017	0.2	NO
22	FADD	FADD	FADD	9587	-0.03	0.17	NO
23	IKBKB	IKBKB	IKBKB	9741	-0.032	0.19	NO
24	PIK3R1	PIK3R1	PIK3R1	10005	-0.036	0.2	NO
25	CFLAR	CFLAR	CFLAR	11091	-0.055	0.19	NO
26	PIK3CD	PIK3CD	PIK3CD	11430	-0.063	0.22	NO
27	IKBKG	IKBKG	IKBKG	12531	-0.093	0.23	NO
28	SMPD1	SMPD1	SMPD1	12632	-0.096	0.3	NO

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

Figure S30. 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 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	CASP7	CASP7	CASP7	703	0.16	0.039	YES
2	BCL2	BCL2	BCL2	888	0.14	0.096	YES
3	BIRC3	BIRC3	BIRC3	1131	0.12	0.14	YES
4	APAF1	APAF1	APAF1	1598	0.094	0.16	YES
5	TNFRSF10A	TNFRSF10A	TNFRSF10A	1928	0.081	0.18	YES
6	CASP10	CASP10	CASP10	1955	0.08	0.21	YES
7	TNFSF10	TNFSF10	TNFSF10	2104	0.075	0.24	YES
8	LMNA	LMNA	LMNA	2238	0.071	0.27	YES
9	CASP3	CASP3	CASP3	2326	0.069	0.3	YES
10	RIPK1	RIPK1	RIPK1	2398	0.067	0.32	YES
11	TNFRSF10B	TNFRSF10B	TNFRSF10B	2472	0.065	0.35	YES
12	CASP9	CASP9	CASP9	3274	0.048	0.33	YES
13	CASP8	CASP8	CASP8	3555	0.044	0.33	YES
14	CYCS	CYCS	CYCS	3607	0.043	0.35	YES
15	BIRC2	BIRC2	BIRC2	3787	0.04	0.36	YES
16	SPTAN1	SPTAN1	SPTAN1	4665	0.027	0.32	NO
17	CHUK	CHUK	CHUK	5282	0.02	0.3	NO
18	NFKB1	NFKB1	NFKB1	5384	0.019	0.3	NO
19	NFKBIA	NFKBIA	NFKBIA	6371	0.0081	0.25	NO
20	CASP6	CASP6	CASP6	6753	0.0038	0.23	NO
21	TRAF2	TRAF2	TRAF2	6999	0.0013	0.22	NO
22	DFFB	DFFB	DFFB	7598	-0.0055	0.18	NO
23	TRADD	TRADD	TRADD	7776	-0.0075	0.18	NO
24	XIAP	XIAP	XIAP	8230	-0.013	0.16	NO
25	RELA	RELA	RELA	8267	-0.013	0.16	NO
26	DFFA	DFFA	DFFA	9419	-0.027	0.11	NO
27	FADD	FADD	FADD	9587	-0.03	0.12	NO
28	MAP3K14	MAP3K14	MAP3K14	10347	-0.041	0.094	NO
29	BID	BID	BID	11041	-0.054	0.081	NO
30	CFLAR	CFLAR	CFLAR	11091	-0.055	0.1	NO
31	TNFSF12	TNFSF12	TNFSF12	12375	-0.088	0.074	NO
32	TNFRSF25	TNFRSF25	TNFRSF25	15804	-0.25	-0.0012	NO
33	GAS2	GAS2	GAS2	16037	-0.26	0.11	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 HIVNEF PATHWAY.

Figure S32. 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 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	TFF1	TFF1	TFF1	13	0.48	0.096	YES
2	C4BPB	C4BPB	C4BPB	17	0.47	0.19	YES
3	KLK3	KLK3	KLK3	93	0.36	0.26	YES
4	CYP2C18	CYP2C18	CYP2C18	128	0.33	0.32	YES
5	FOXA1	FOXA1	FOXA1	211	0.29	0.38	YES
6	SERPINA1	SERPINA1	SERPINA1	261	0.26	0.42	YES
7	FOXA3	FOXA3	FOXA3	587	0.18	0.44	YES
8	FOS	FOS	FOS	767	0.16	0.46	YES
9	SFTPA2	SFTPA2	SFTPA2	877	0.14	0.49	YES
10	NKX3-1	NKX3-1	NKX3-1	1553	0.097	0.47	NO
11	XBP1	XBP1	XBP1	1678	0.091	0.48	NO
12	ATP5J	ATP5J	ATP5J	2874	0.056	0.43	NO
13	SOD1	SOD1	SOD1	3076	0.052	0.42	NO
14	SP1	SP1	SP1	3159	0.05	0.43	NO
15	EP300	EP300	EP300	3463	0.045	0.42	NO
16	NDUFV3	NDUFV3	NDUFV3	3618	0.042	0.42	NO
17	NRIP1	NRIP1	NRIP1	3914	0.038	0.41	NO
18	NFIA	NFIA	NFIA	4019	0.036	0.42	NO
19	BRCA1	BRCA1	BRCA1	4603	0.028	0.39	NO
20	NFIB	NFIB	NFIB	4699	0.027	0.39	NO
21	VTN	VTN	VTN	5103	0.022	0.37	NO
22	FOXA2	FOXA2	FOXA2	5677	0.016	0.34	NO
23	NFIC	NFIC	NFIC	5726	0.015	0.34	NO
24	POU2F1	POU2F1	POU2F1	6257	0.0094	0.32	NO
25	AP1B1	AP1B1	AP1B1	6261	0.0094	0.32	NO
26	NR2F2	NR2F2	NR2F2	7371	-0.0029	0.26	NO
27	CREBBP	CREBBP	CREBBP	8274	-0.013	0.21	NO
28	JUN	JUN	JUN	9085	-0.023	0.17	NO
29	CDKN1B	CDKN1B	CDKN1B	9547	-0.029	0.15	NO
30	PISD	PISD	PISD	9999	-0.036	0.13	NO
31	PRDM15	PRDM15	PRDM15	10049	-0.036	0.13	NO
32	NCOA3	NCOA3	NCOA3	11978	-0.077	0.042	NO
33	DSCAM	DSCAM	DSCAM	11979	-0.077	0.057	NO
34	GCG	GCG	GCG	12082	-0.079	0.067	NO
35	SFTPD	SFTPD	SFTPD	12728	-0.099	0.051	NO
36	SHH	SHH	SHH	12941	-0.11	0.061	NO
37	AR	AR	AR	13387	-0.12	0.061	NO
38	SFTPA1	SFTPA1	SFTPA1	13495	-0.13	0.081	NO
39	COL18A1	COL18A1	COL18A1	14033	-0.15	0.081	NO
40	ESR1	ESR1	ESR1	14876	-0.19	0.073	NO
41	CEBPB	CEBPB	CEBPB	15001	-0.2	0.11	NO
42	APOB	APOB	APOB	16574	-0.3	0.079	NO

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

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

genes ES table in pathway: BIOCARTA PYK2 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	MAP2K4	MAP2K4	MAP2K4	1887	0.083	-0.015	YES
2	LMNA	LMNA	LMNA	2238	0.071	0.044	YES
3	CASP3	CASP3	CASP3	2326	0.069	0.11	YES
4	RIPK1	RIPK1	RIPK1	2398	0.067	0.18	YES
5	CASP8	CASP8	CASP8	3555	0.044	0.17	YES
6	MAPK8	MAPK8	MAPK8	3718	0.041	0.2	YES
7	PARP1	PARP1	PARP1	3989	0.037	0.23	YES
8	LMNB1	LMNB1	LMNB1	3998	0.036	0.27	YES
9	BAG4	BAG4	BAG4	4147	0.034	0.3	YES
10	MADD	MADD	MADD	4629	0.028	0.3	YES
11	SPTAN1	SPTAN1	SPTAN1	4665	0.027	0.33	YES
12	PAK1	PAK1	PAK1	5047	0.022	0.33	YES
13	PAK2	PAK2	PAK2	5373	0.019	0.33	YES
14	CRADD	CRADD	CRADD	5451	0.018	0.35	YES
15	RB1	RB1	RB1	6417	0.0075	0.3	NO
16	CASP2	CASP2	CASP2	6623	0.0051	0.3	NO
17	LMNB2	LMNB2	LMNB2	6770	0.0036	0.29	NO
18	TRAF2	TRAF2	TRAF2	6999	0.0013	0.28	NO
19	MAP3K1	MAP3K1	MAP3K1	7176	-0.00061	0.27	NO
20	DFFB	DFFB	DFFB	7598	-0.0055	0.26	NO
21	TNFRSF1A	TNFRSF1A	TNFRSF1A	7613	-0.0057	0.26	NO
22	TRADD	TRADD	TRADD	7776	-0.0075	0.26	NO
23	ARHGDIB	ARHGDIB	ARHGDIB	8494	-0.016	0.24	NO
24	JUN	JUN	JUN	9085	-0.023	0.23	NO
25	DFFA	DFFA	DFFA	9419	-0.027	0.24	NO
26	FADD	FADD	FADD	9587	-0.03	0.26	NO
27	MAP3K7	MAP3K7	MAP3K7	9896	-0.034	0.28	NO
28	PRKDC	PRKDC	PRKDC	10506	-0.044	0.3	NO
29	TNF	TNF	TNF	12983	-0.11	0.28	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 PYK2 PATHWAY.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA TNFR1 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	SPDEF	SPDEF	SPDEF	4	0.55	0.14	YES
2	KLK3	KLK3	KLK3	93	0.36	0.24	YES
3	PDE9A	PDE9A	PDE9A	972	0.14	0.22	YES
4	HOXB13	HOXB13	HOXB13	1051	0.13	0.25	YES
5	KLK2	KLK2	KLK2	1157	0.12	0.28	YES
6	KAT2B	KAT2B	KAT2B	1221	0.12	0.3	YES
7	MDM2	MDM2	MDM2	1320	0.11	0.33	YES
8	TMPRSS2	TMPRSS2	TMPRSS2	1862	0.084	0.32	YES
9	MAP2K4	MAP2K4	MAP2K4	1887	0.083	0.34	YES
10	GATA2	GATA2	GATA2	2347	0.069	0.33	YES
11	MAP2K6	MAP2K6	MAP2K6	2618	0.061	0.34	YES
12	REL	REL	REL	2967	0.054	0.33	YES
13	HDAC1	HDAC1	HDAC1	3011	0.053	0.34	YES
14	SMARCA2	SMARCA2	SMARCA2	3146	0.05	0.35	YES
15	SIRT1	SIRT1	SIRT1	3349	0.047	0.35	YES
16	EP300	EP300	EP300	3463	0.045	0.36	YES
17	NR2C1	NR2C1	NR2C1	3508	0.044	0.36	YES
18	MAPK8	MAPK8	MAPK8	3718	0.041	0.36	YES
19	NCOA1	NCOA1	NCOA1	3838	0.039	0.37	YES
20	HSP90AA1	HSP90AA1	HSP90AA1	4237	0.033	0.35	NO
21	APPBP2	APPBP2	APPBP2	5039	0.023	0.32	NO
22	RXRA	RXRA	RXRA	5757	0.015	0.28	NO
23	POU2F1	POU2F1	POU2F1	6257	0.0094	0.25	NO
24	GNB2L1	GNB2L1	GNB2L1	7308	-0.0022	0.2	NO
25	KAT5	KAT5	KAT5	7352	-0.0027	0.19	NO
26	GSK3B	GSK3B	GSK3B	7625	-0.0058	0.18	NO
27	SMARCE1	SMARCE1	SMARCE1	7650	-0.006	0.18	NO
28	RCHY1	RCHY1	RCHY1	7863	-0.0084	0.17	NO
29	NR2C2	NR2C2	NR2C2	7925	-0.0091	0.17	NO
30	CREBBP	CREBBP	CREBBP	8274	-0.013	0.16	NO
31	RXRB	RXRB	RXRB	8302	-0.013	0.16	NO
32	DNAJA1	DNAJA1	DNAJA1	8346	-0.014	0.16	NO
33	HDAC7	HDAC7	HDAC7	8452	-0.015	0.16	NO
34	SENP1	SENP1	SENP1	8479	-0.015	0.16	NO
35	SMARCC1	SMARCC1	SMARCC1	8561	-0.016	0.16	NO
36	SRC	SRC	SRC	9083	-0.023	0.14	NO
37	JUN	JUN	JUN	9085	-0.023	0.14	NO
38	NCOA2	NCOA2	NCOA2	9447	-0.028	0.13	NO
39	TRIM24	TRIM24	TRIM24	9939	-0.035	0.11	NO
40	CARM1	CARM1	CARM1	10243	-0.039	0.1	NO
41	EGR1	EGR1	EGR1	10383	-0.042	0.11	NO
42	EHMT2	EHMT2	EHMT2	10717	-0.047	0.1	NO
43	ZMIZ2	ZMIZ2	ZMIZ2	10960	-0.052	0.1	NO
44	MAPK14	MAPK14	MAPK14	11295	-0.06	0.099	NO
45	PKN1	PKN1	PKN1	12028	-0.078	0.079	NO
46	CEBPA	CEBPA	CEBPA	12303	-0.085	0.087	NO
47	FOXO1	FOXO1	FOXO1	12947	-0.11	0.08	NO
48	AR	AR	AR	13387	-0.12	0.088	NO
49	NR3C1	NR3C1	NR3C1	14358	-0.17	0.078	NO
50	NR0B1	NR0B1	NR0B1	14932	-0.19	0.098	NO
51	RXRG	RXRG	RXRG	16219	-0.28	0.099	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 TNFR1 PATHWAY.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID TRAIL PATHWAY

Table 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	XDH	XDH	XDH	375	0.23	0.085	YES
2	GDA	GDA	GDA	505	0.2	0.17	YES
3	NT5E	NT5E	NT5E	637	0.18	0.24	YES
4	GMPR	GMPR	GMPR	682	0.17	0.32	YES
5	ADSSL1	ADSSL1	ADSSL1	696	0.17	0.4	YES
6	PNP	PNP	PNP	2954	0.054	0.3	NO
7	NT5C2	NT5C2	NT5C2	3865	0.039	0.26	NO
8	DCK	DCK	DCK	4009	0.036	0.27	NO
9	PFAS	PFAS	PFAS	4206	0.034	0.28	NO
10	ADSS	ADSS	ADSS	4663	0.027	0.26	NO
11	PAICS	PAICS	PAICS	5239	0.02	0.24	NO
12	PPAT	PPAT	PPAT	5591	0.017	0.23	NO
13	GMPR2	GMPR2	GMPR2	5685	0.016	0.23	NO
14	IMPDH2	IMPDH2	IMPDH2	5734	0.015	0.24	NO
15	HPRT1	HPRT1	HPRT1	5804	0.014	0.24	NO
16	GART	GART	GART	6599	0.0053	0.2	NO
17	NT5C	NT5C	NT5C	7186	-0.00074	0.16	NO
18	GMPS	GMPS	GMPS	7435	-0.0037	0.15	NO
19	APRT	APRT	APRT	7522	-0.0046	0.15	NO
20	AMPD3	AMPD3	AMPD3	8942	-0.021	0.081	NO
21	CAT	CAT	CAT	9158	-0.024	0.081	NO
22	AMPD2	AMPD2	AMPD2	9257	-0.025	0.087	NO
23	DGUOK	DGUOK	DGUOK	9346	-0.026	0.094	NO
24	IMPDH1	IMPDH1	IMPDH1	10935	-0.052	0.03	NO
25	GPX1	GPX1	GPX1	11070	-0.055	0.048	NO
26	ADSL	ADSL	ADSL	11126	-0.056	0.071	NO
27	ATIC	ATIC	ATIC	11216	-0.058	0.093	NO
28	AMPD1	AMPD1	AMPD1	11572	-0.067	0.1	NO
29	ADAL	ADAL	ADAL	12425	-0.089	0.099	NO
30	ADK	ADK	ADK	13869	-0.14	0.086	NO
31	NT5C1B	NT5C1B	NT5C1B	13911	-0.15	0.15	NO
32	ADA	ADA	ADA	14245	-0.16	0.21	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: PID TRAIL PATHWAY.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype 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	0.55	1.6	0.017	0.09	0.91	0.24	0.12	0.22	0.045	0
KEGG O GLYCAN BIOSYNTHESIS	29	genes.ES.table	0.49	1.3	0.13	0.19	0.99	0.28	0.18	0.23	0.14	0
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	43	genes.ES.table	0.39	1.5	0.094	0.12	0.97	0.07	0.038	0.067	0.074	0
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE	25	genes.ES.table	0.57	1.5	0.032	0.1	0.94	0.4	0.23	0.31	0.059	0
KEGG INOSITOL PHOSPHATE METABOLISM	52	genes.ES.table	0.35	1.3	0.13	0.19	0.99	0.33	0.31	0.22	0.14	0
KEGG ABC TRANSPORTERS	43	genes.ES.table	0.49	1.4	0.067	0.16	0.98	0.21	0.12	0.18	0.11	0
KEGG MAPK SIGNALING PATHWAY	250	genes.ES.table	0.5	1.7	0	0.076	0.66	0.37	0.28	0.27	0.021	0.008
KEGG ERBB SIGNALING PATHWAY	86	genes.ES.table	0.46	1.7	0.013	0.077	0.66	0.13	0.076	0.12	0.021	0.009
KEGG CALCIUM SIGNALING PATHWAY	164	genes.ES.table	0.61	1.6	0.0021	0.084	0.85	0.52	0.25	0.4	0.035	0.002
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION	236	genes.ES.table	0.62	1.5	0.026	0.1	0.95	0.49	0.19	0.4	0.059	0

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	0.68	0.018	YES
2	PDE1A	PDE1A	PDE1A	337	0.63	0.042	YES
3	NGFR	NGFR	NGFR	343	0.63	0.07	YES
4	AKT3	AKT3	AKT3	521	0.57	0.087	YES
5	TIAM1	TIAM1	TIAM1	649	0.55	0.1	YES
6	ADCYAP1	ADCYAP1	ADCYAP1	743	0.52	0.12	YES
7	ADCY2	ADCY2	ADCY2	786	0.52	0.14	YES
8	NGF	NGF	NGF	1066	0.46	0.15	YES
9	ARHGEF6	ARHGEF6	ARHGEF6	1106	0.46	0.17	YES
10	NTRK1	NTRK1	NTRK1	1180	0.45	0.19	YES
11	MEF2C	MEF2C	MEF2C	1461	0.41	0.19	YES
12	PCSK5	PCSK5	PCSK5	1466	0.4	0.21	YES
13	MAPK11	MAPK11	MAPK11	1533	0.4	0.22	YES
14	ADCY5	ADCY5	ADCY5	1655	0.38	0.23	YES
15	FGD2	FGD2	FGD2	1767	0.37	0.24	YES
16	RASGRF2	RASGRF2	RASGRF2	1843	0.36	0.26	YES
17	ARHGEF17	ARHGEF17	ARHGEF17	1881	0.35	0.27	YES
18	CAMK4	CAMK4	CAMK4	1898	0.35	0.28	YES
19	SORCS3	SORCS3	SORCS3	1902	0.35	0.3	YES
20	PRKAR2B	PRKAR2B	PRKAR2B	1976	0.34	0.31	YES
21	ADCY1	ADCY1	ADCY1	2094	0.33	0.32	YES
22	VAV1	VAV1	VAV1	2198	0.32	0.33	YES
23	MCF2	MCF2	MCF2	2401	0.29	0.33	YES
24	ADORA2A	ADORA2A	ADORA2A	2524	0.28	0.34	YES
25	PLEKHG2	PLEKHG2	PLEKHG2	2646	0.27	0.34	YES
26	ADCY4	ADCY4	ADCY4	2693	0.26	0.35	YES
27	PREX1	PREX1	PREX1	2787	0.25	0.36	YES
28	TIAM2	TIAM2	TIAM2	2973	0.23	0.36	YES
29	NTRK2	NTRK2	NTRK2	3000	0.23	0.37	YES
30	ARHGEF4	ARHGEF4	ARHGEF4	3052	0.22	0.38	YES
31	DNM1	DNM1	DNM1	3058	0.22	0.39	YES
32	RPS6KA2	RPS6KA2	RPS6KA2	3120	0.22	0.39	YES
33	IRS1	IRS1	IRS1	3240	0.2	0.4	YES
34	ADCY7	ADCY7	ADCY7	3504	0.18	0.39	YES
35	FGD1	FGD1	FGD1	3508	0.18	0.4	YES
36	ITPR2	ITPR2	ITPR2	3553	0.18	0.4	YES
37	PIK3CA	PIK3CA	PIK3CA	3573	0.18	0.41	YES
38	MAPK12	MAPK12	MAPK12	3642	0.17	0.41	YES
39	FOXO1	FOXO1	FOXO1	3696	0.17	0.42	YES
40	MAG	MAG	MAG	3858	0.16	0.42	YES
41	ITSN1	ITSN1	ITSN1	3873	0.16	0.42	YES
42	AKAP13	AKAP13	AKAP13	3962	0.15	0.42	YES
43	DUSP4	DUSP4	DUSP4	4116	0.14	0.42	YES
44	MEF2A	MEF2A	MEF2A	4201	0.14	0.42	YES
45	ADCY9	ADCY9	ADCY9	4351	0.13	0.42	YES
46	BCL2L11	BCL2L11	BCL2L11	4392	0.13	0.43	YES
47	KIDINS220	KIDINS220	KIDINS220	4396	0.13	0.43	YES
48	ARHGEF3	ARHGEF3	ARHGEF3	4564	0.12	0.43	YES
49	LINGO1	LINGO1	LINGO1	4599	0.12	0.43	YES
50	RICTOR	RICTOR	RICTOR	4620	0.12	0.44	YES
51	SHC2	SHC2	SHC2	4712	0.11	0.44	YES
52	APH1B	APH1B	APH1B	4717	0.11	0.44	YES
53	ARHGAP4	ARHGAP4	ARHGAP4	4770	0.11	0.44	YES
54	TRIO	TRIO	TRIO	4785	0.11	0.45	YES
55	NGFRAP1	NGFRAP1	NGFRAP1	5008	0.1	0.44	YES
56	SOS1	SOS1	SOS1	5044	0.099	0.44	YES
57	RAPGEF1	RAPGEF1	RAPGEF1	5055	0.098	0.45	YES
58	FOXO4	FOXO4	FOXO4	5069	0.098	0.45	YES
59	FGD3	FGD3	FGD3	5086	0.097	0.45	YES
60	PRKAR1A	PRKAR1A	PRKAR1A	5136	0.096	0.46	YES
61	DUSP7	DUSP7	DUSP7	5197	0.093	0.46	YES
62	RASGRF1	RASGRF1	RASGRF1	5285	0.09	0.46	YES
63	CREB1	CREB1	CREB1	5330	0.088	0.46	YES
64	ARHGEF12	ARHGEF12	ARHGEF12	5398	0.086	0.46	YES
65	ADAM17	ADAM17	ADAM17	5450	0.085	0.46	YES
66	PIK3R1	PIK3R1	PIK3R1	5759	0.077	0.44	NO
67	PRKCE	PRKCE	PRKCE	5921	0.073	0.44	NO
68	RAP1A	RAP1A	RAP1A	5925	0.072	0.44	NO
69	FRS2	FRS2	FRS2	5939	0.072	0.44	NO
70	ARHGEF2	ARHGEF2	ARHGEF2	6042	0.07	0.44	NO
71	SOS2	SOS2	SOS2	6080	0.069	0.44	NO
72	NFKBIA	NFKBIA	NFKBIA	6124	0.068	0.44	NO
73	SHC1	SHC1	SHC1	6210	0.066	0.44	NO
74	DUSP3	DUSP3	DUSP3	6226	0.066	0.44	NO
75	ARHGEF1	ARHGEF1	ARHGEF1	6251	0.065	0.44	NO
76	MTOR	MTOR	MTOR	6358	0.063	0.44	NO
77	PTEN	PTEN	PTEN	6576	0.058	0.43	NO
78	GRB2	GRB2	GRB2	6785	0.054	0.42	NO
79	PRKACA	PRKACA	PRKACA	6809	0.054	0.42	NO
80	PLCG1	PLCG1	PLCG1	6814	0.053	0.43	NO
81	BRAF	BRAF	BRAF	6874	0.052	0.43	NO
82	TRAF6	TRAF6	TRAF6	6889	0.052	0.43	NO
83	RPS6KA5	RPS6KA5	RPS6KA5	6918	0.051	0.43	NO
84	RIT1	RIT1	RIT1	6967	0.05	0.43	NO
85	MAPKAPK2	MAPKAPK2	MAPKAPK2	7015	0.049	0.43	NO
86	MAPK7	MAPK7	MAPK7	7017	0.049	0.43	NO
87	SH3GL2	SH3GL2	SH3GL2	7024	0.049	0.43	NO
88	NR4A1	NR4A1	NR4A1	7094	0.048	0.43	NO
89	STAT3	STAT3	STAT3	7190	0.046	0.43	NO
90	PRKCA	PRKCA	PRKCA	7209	0.045	0.43	NO
91	ARHGEF18	ARHGEF18	ARHGEF18	7235	0.045	0.43	NO
92	PIK3CB	PIK3CB	PIK3CB	7239	0.045	0.43	NO
93	PRKCG	PRKCG	PRKCG	7292	0.044	0.43	NO
94	CRK	CRK	CRK	7369	0.043	0.43	NO
95	CHUK	CHUK	CHUK	7389	0.043	0.43	NO
96	KRAS	KRAS	KRAS	7479	0.041	0.42	NO
97	FURIN	FURIN	FURIN	7499	0.041	0.43	NO
98	ATF1	ATF1	ATF1	7520	0.04	0.43	NO
99	RIPK2	RIPK2	RIPK2	7533	0.04	0.43	NO
100	ELK1	ELK1	ELK1	7595	0.039	0.43	NO
101	MAP2K1	MAP2K1	MAP2K1	7607	0.039	0.43	NO
102	RALB	RALB	RALB	7608	0.039	0.43	NO
103	PDPK1	PDPK1	PDPK1	7609	0.039	0.43	NO
104	MAPK8	MAPK8	MAPK8	7660	0.038	0.43	NO
105	NET1	NET1	NET1	7690	0.037	0.43	NO
106	FGD4	FGD4	FGD4	7694	0.037	0.43	NO
107	PRKACB	PRKACB	PRKACB	7719	0.037	0.43	NO
108	RPS27A	RPS27A	RPS27A	7772	0.036	0.43	NO
109	CDKN1B	CDKN1B	CDKN1B	7821	0.035	0.43	NO
110	IKBKB	IKBKB	IKBKB	7884	0.034	0.43	NO
111	ARHGEF9	ARHGEF9	ARHGEF9	7911	0.034	0.43	NO
112	IRS2	IRS2	IRS2	8010	0.032	0.42	NO
113	PRKCI	PRKCI	PRKCI	8086	0.031	0.42	NO
114	RALGDS	RALGDS	RALGDS	8087	0.031	0.42	NO
115	ARHGEF11	ARHGEF11	ARHGEF11	8168	0.03	0.42	NO
116	MAGED1	MAGED1	MAGED1	8188	0.029	0.42	NO
117	RELA	RELA	RELA	8255	0.028	0.42	NO
118	ECT2	ECT2	ECT2	8364	0.027	0.41	NO
119	AP2M1	AP2M1	AP2M1	8422	0.026	0.41	NO
120	AP2A1	AP2A1	AP2A1	8508	0.024	0.41	NO
121	MYD88	MYD88	MYD88	8616	0.023	0.4	NO
122	NCSTN	NCSTN	NCSTN	8819	0.02	0.39	NO
123	FOXO3	FOXO3	FOXO3	8826	0.02	0.39	NO
124	MAPK1	MAPK1	MAPK1	8927	0.018	0.39	NO
125	NRAS	NRAS	NRAS	8928	0.018	0.39	NO
126	CLTC	CLTC	CLTC	9003	0.018	0.38	NO
127	MDM2	MDM2	MDM2	9123	0.016	0.38	NO
128	ABR	ABR	ABR	9138	0.016	0.38	NO
129	PSEN1	PSEN1	PSEN1	9153	0.016	0.38	NO
130	RHOA	RHOA	RHOA	9156	0.016	0.38	NO
131	PPP2CB	PPP2CB	PPP2CB	9165	0.015	0.38	NO
132	ADCY3	ADCY3	ADCY3	9240	0.014	0.38	NO
133	RTN4	RTN4	RTN4	9278	0.013	0.37	NO
134	AATF	AATF	AATF	9318	0.013	0.37	NO
135	PHLPP1	PHLPP1	PHLPP1	9513	0.0099	0.36	NO
136	IRAK1	IRAK1	IRAK1	9514	0.0098	0.36	NO
137	MAPKAP1	MAPKAP1	MAPKAP1	9533	0.0095	0.36	NO
138	AP2B1	AP2B1	AP2B1	9647	0.0081	0.36	NO
139	CALM3	CALM3	CALM3	9751	0.0064	0.35	NO
140	CASP2	CASP2	CASP2	9767	0.0062	0.35	NO
141	YWHAB	YWHAB	YWHAB	9789	0.0059	0.35	NO
142	AKT1	AKT1	AKT1	9834	0.0053	0.35	NO
143	GSK3A	GSK3A	GSK3A	9855	0.0051	0.35	NO
144	SQSTM1	SQSTM1	SQSTM1	9871	0.0048	0.34	NO
145	PRDM4	PRDM4	PRDM4	9877	0.0048	0.34	NO
146	CALM1	CALM1	CALM1	9912	0.0044	0.34	NO
147	MAPK14	MAPK14	MAPK14	10276	-0.00059	0.32	NO
148	CALM2	CALM2	CALM2	10364	-0.0018	0.32	NO
149	OMG	OMG	OMG	10368	-0.0018	0.32	NO
150	CASP9	CASP9	CASP9	10375	-0.0019	0.32	NO
151	DUSP6	DUSP6	DUSP6	10401	-0.0024	0.32	NO
152	AP2A2	AP2A2	AP2A2	10409	-0.0025	0.32	NO
153	DNAL4	DNAL4	DNAL4	10480	-0.0035	0.31	NO
154	RALA	RALA	RALA	10515	-0.0041	0.31	NO
155	PRKAR2A	PRKAR2A	PRKAR2A	10560	-0.0047	0.31	NO
156	TSC2	TSC2	TSC2	10581	-0.005	0.31	NO
157	ITPR3	ITPR3	ITPR3	10607	-0.0054	0.31	NO
158	RAF1	RAF1	RAF1	10611	-0.0054	0.31	NO
159	CASP3	CASP3	CASP3	10677	-0.0064	0.3	NO
160	SHC3	SHC3	SHC3	10720	-0.0071	0.3	NO
161	ARHGDIA	ARHGDIA	ARHGDIA	10763	-0.0078	0.3	NO
162	HDAC2	HDAC2	HDAC2	10875	-0.0096	0.29	NO
163	PPP2R1B	PPP2R1B	PPP2R1B	10912	-0.01	0.29	NO
164	AKT2	AKT2	AKT2	11018	-0.012	0.29	NO
165	PPP2R5D	PPP2R5D	PPP2R5D	11060	-0.012	0.28	NO
166	RPS6KA3	RPS6KA3	RPS6KA3	11109	-0.013	0.28	NO
167	HDAC3	HDAC3	HDAC3	11242	-0.015	0.28	NO
168	PSENEN	PSENEN	PSENEN	11247	-0.015	0.28	NO
169	PRKCD	PRKCD	PRKCD	11331	-0.016	0.27	NO
170	CDKN1A	CDKN1A	CDKN1A	11383	-0.017	0.27	NO
171	OBSCN	OBSCN	OBSCN	11397	-0.017	0.27	NO
172	APH1A	APH1A	APH1A	11426	-0.017	0.27	NO
173	YWHAE	YWHAE	YWHAE	11432	-0.018	0.27	NO
174	PSEN2	PSEN2	PSEN2	11497	-0.018	0.27	NO
175	RAC1	RAC1	RAC1	11915	-0.025	0.24	NO
176	PPP2R1A	PPP2R1A	PPP2R1A	11975	-0.026	0.24	NO
177	PPP2CA	PPP2CA	PPP2CA	11986	-0.026	0.24	NO
178	SRC	SRC	SRC	12005	-0.027	0.24	NO
179	HDAC1	HDAC1	HDAC1	12079	-0.028	0.24	NO
180	AKT1S1	AKT1S1	AKT1S1	12220	-0.03	0.24	NO
181	MAP2K5	MAP2K5	MAP2K5	12249	-0.031	0.24	NO
182	ADCY6	ADCY6	ADCY6	12296	-0.031	0.23	NO
183	ADRBK1	ADRBK1	ADRBK1	12321	-0.032	0.23	NO
184	PIK3R2	PIK3R2	PIK3R2	12407	-0.033	0.23	NO
185	THEM4	THEM4	THEM4	12626	-0.036	0.22	NO
186	KALRN	KALRN	KALRN	12729	-0.038	0.22	NO
187	CDK1	CDK1	CDK1	12971	-0.042	0.2	NO
188	DNM2	DNM2	DNM2	13045	-0.044	0.2	NO
189	AP2S1	AP2S1	AP2S1	13096	-0.044	0.2	NO
190	HRAS	HRAS	HRAS	13243	-0.047	0.2	NO
191	MAPKAPK3	MAPKAPK3	MAPKAPK3	13398	-0.05	0.19	NO
192	BAD	BAD	BAD	13679	-0.055	0.18	NO
193	ITGB3BP	ITGB3BP	ITGB3BP	13715	-0.056	0.18	NO
194	MAP2K2	MAP2K2	MAP2K2	13800	-0.058	0.17	NO
195	MAPK3	MAPK3	MAPK3	13966	-0.061	0.17	NO
196	UBA52	UBA52	UBA52	14153	-0.065	0.16	NO
197	RPS6KA1	RPS6KA1	RPS6KA1	14408	-0.071	0.15	NO
198	TRIB3	TRIB3	TRIB3	14604	-0.076	0.14	NO
199	CLTA	CLTA	CLTA	14605	-0.076	0.14	NO
200	MAPK13	MAPK13	MAPK13	14662	-0.077	0.15	NO
201	PCSK6	PCSK6	PCSK6	14831	-0.082	0.14	NO
202	PRKAR1B	PRKAR1B	PRKAR1B	15053	-0.088	0.13	NO
203	MLST8	MLST8	MLST8	15125	-0.09	0.13	NO
204	RPS6KB2	RPS6KB2	RPS6KB2	15463	-0.1	0.12	NO
205	ARHGEF16	ARHGEF16	ARHGEF16	15473	-0.1	0.12	NO
206	NGEF	NGEF	NGEF	15930	-0.12	0.1	NO
207	SMPD2	SMPD2	SMPD2	16522	-0.15	0.075	NO
208	VAV3	VAV3	VAV3	16601	-0.16	0.078	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 O GLYCAN BIOSYNTHESIS

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	TGFB3	TGFB3	TGFB3	115	0.74	0.072	YES
2	VEGFC	VEGFC	VEGFC	211	0.69	0.14	YES
3	AKT3	AKT3	AKT3	521	0.57	0.18	YES
4	PIK3R5	PIK3R5	PIK3R5	562	0.56	0.24	YES
5	HGF	HGF	HGF	597	0.56	0.3	YES
6	PIK3CG	PIK3CG	PIK3CG	611	0.55	0.35	YES
7	TGFB2	TGFB2	TGFB2	937	0.49	0.39	YES
8	PAK3	PAK3	PAK3	1116	0.46	0.42	YES
9	PIK3CD	PIK3CD	PIK3CD	1218	0.44	0.46	YES
10	ARNT2	ARNT2	ARNT2	1392	0.42	0.5	YES
11	ETS1	ETS1	ETS1	2187	0.32	0.49	YES
12	PDGFB	PDGFB	PDGFB	2332	0.3	0.51	YES
13	FIGF	FIGF	FIGF	2494	0.28	0.53	YES
14	TGFB1	TGFB1	TGFB1	2752	0.26	0.55	YES
15	PGF	PGF	PGF	2985	0.23	0.56	YES
16	PIK3CA	PIK3CA	PIK3CA	3573	0.18	0.54	NO
17	HIF1A	HIF1A	HIF1A	3840	0.16	0.54	NO
18	EPAS1	EPAS1	EPAS1	4773	0.11	0.5	NO
19	EP300	EP300	EP300	5040	0.099	0.5	NO
20	SOS1	SOS1	SOS1	5044	0.099	0.51	NO
21	RAPGEF1	RAPGEF1	RAPGEF1	5055	0.098	0.52	NO
22	PIK3R3	PIK3R3	PIK3R3	5205	0.093	0.52	NO
23	CREBBP	CREBBP	CREBBP	5352	0.088	0.52	NO
24	ARNT	ARNT	ARNT	5435	0.085	0.53	NO
25	PIK3R1	PIK3R1	PIK3R1	5759	0.077	0.52	NO
26	RAP1A	RAP1A	RAP1A	5925	0.072	0.52	NO
27	SOS2	SOS2	SOS2	6080	0.069	0.51	NO
28	PTPN11	PTPN11	PTPN11	6089	0.069	0.52	NO
29	GRB2	GRB2	GRB2	6785	0.054	0.49	NO
30	FLCN	FLCN	FLCN	6864	0.052	0.49	NO
31	BRAF	BRAF	BRAF	6874	0.052	0.49	NO
32	PAK2	PAK2	PAK2	7107	0.047	0.48	NO
33	PIK3CB	PIK3CB	PIK3CB	7239	0.045	0.48	NO
34	VEGFB	VEGFB	VEGFB	7348	0.043	0.48	NO
35	CRK	CRK	CRK	7369	0.043	0.48	NO
36	KRAS	KRAS	KRAS	7479	0.041	0.48	NO
37	MAP2K1	MAP2K1	MAP2K1	7607	0.039	0.48	NO
38	CDC42	CDC42	CDC42	8075	0.031	0.46	NO
39	GAB1	GAB1	GAB1	8625	0.023	0.43	NO
40	CRKL	CRKL	CRKL	8665	0.022	0.43	NO
41	TGFA	TGFA	TGFA	8831	0.02	0.42	NO
42	MAPK1	MAPK1	MAPK1	8927	0.018	0.42	NO
43	NRAS	NRAS	NRAS	8928	0.018	0.42	NO
44	MET	MET	MET	9092	0.016	0.41	NO
45	AKT1	AKT1	AKT1	9834	0.0053	0.37	NO
46	CUL2	CUL2	CUL2	9939	0.004	0.37	NO
47	EGLN2	EGLN2	EGLN2	10045	0.0026	0.36	NO
48	JUN	JUN	JUN	10052	0.0025	0.36	NO
49	EGLN3	EGLN3	EGLN3	10255	-0.00018	0.35	NO
50	RAF1	RAF1	RAF1	10611	-0.0054	0.33	NO
51	EGLN1	EGLN1	EGLN1	10712	-0.007	0.33	NO
52	SLC2A1	SLC2A1	SLC2A1	10832	-0.0089	0.32	NO
53	VHL	VHL	VHL	10997	-0.011	0.31	NO
54	AKT2	AKT2	AKT2	11018	-0.012	0.31	NO
55	VEGFA	VEGFA	VEGFA	11198	-0.014	0.3	NO
56	TCEB1	TCEB1	TCEB1	11877	-0.024	0.27	NO
57	ARAF	ARAF	ARAF	11885	-0.025	0.27	NO
58	RAC1	RAC1	RAC1	11915	-0.025	0.27	NO
59	PAK1	PAK1	PAK1	12117	-0.028	0.26	NO
60	PIK3R2	PIK3R2	PIK3R2	12407	-0.033	0.25	NO
61	RAP1B	RAP1B	RAP1B	12423	-0.033	0.25	NO
62	HRAS	HRAS	HRAS	13243	-0.047	0.21	NO
63	RBX1	RBX1	RBX1	13347	-0.049	0.21	NO
64	PAK4	PAK4	PAK4	13574	-0.053	0.21	NO
65	MAP2K2	MAP2K2	MAP2K2	13800	-0.058	0.2	NO
66	MAPK3	MAPK3	MAPK3	13966	-0.061	0.2	NO
67	FH	FH	FH	14970	-0.085	0.15	NO
68	PAK6	PAK6	PAK6	15098	-0.089	0.15	NO
69	TCEB2	TCEB2	TCEB2	15236	-0.093	0.15	NO

Figure S43. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG O GLYCAN BIOSYNTHESIS.

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

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

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IGF1	IGF1	IGF1	220	0.68	0.092	YES
2	AKT3	AKT3	AKT3	521	0.57	0.16	YES
3	PIK3R5	PIK3R5	PIK3R5	562	0.56	0.25	YES
4	PAK3	PAK3	PAK3	1116	0.46	0.29	YES
5	PIK3CD	PIK3CD	PIK3CD	1218	0.44	0.35	YES
6	CREB5	CREB5	CREB5	2596	0.27	0.31	YES
7	PREX1	PREX1	PREX1	2787	0.25	0.34	YES
8	RPS6KA2	RPS6KA2	RPS6KA2	3120	0.22	0.36	YES
9	ERBB4	ERBB4	ERBB4	3161	0.21	0.39	YES
10	IRS1	IRS1	IRS1	3240	0.2	0.41	YES
11	F2RL2	F2RL2	F2RL2	3495	0.18	0.43	YES
12	PIK3CA	PIK3CA	PIK3CA	3573	0.18	0.45	YES
13	CYTH3	CYTH3	CYTH3	3584	0.18	0.48	YES
14	SLC2A4	SLC2A4	SLC2A4	4134	0.14	0.47	NO
15	SOS1	SOS1	SOS1	5044	0.099	0.43	NO
16	CREB1	CREB1	CREB1	5330	0.088	0.43	NO
17	RPS6KB1	RPS6KB1	RPS6KB1	5884	0.074	0.41	NO
18	SOS2	SOS2	SOS2	6080	0.069	0.41	NO
19	SHC1	SHC1	SHC1	6210	0.066	0.41	NO
20	MTOR	MTOR	MTOR	6358	0.063	0.41	NO
21	PTEN	PTEN	PTEN	6576	0.058	0.41	NO
22	GRB2	GRB2	GRB2	6785	0.054	0.41	NO
23	GADD45A	GADD45A	GADD45A	6843	0.053	0.41	NO
24	YWHAG	YWHAG	YWHAG	7059	0.048	0.41	NO
25	PAK2	PAK2	PAK2	7107	0.047	0.41	NO
26	YWHAH	YWHAH	YWHAH	7517	0.04	0.4	NO
27	CDKN1B	CDKN1B	CDKN1B	7821	0.035	0.38	NO
28	BCL2L1	BCL2L1	BCL2L1	7975	0.033	0.38	NO
29	IRS2	IRS2	IRS2	8010	0.032	0.38	NO
30	NOLC1	NOLC1	NOLC1	8040	0.032	0.39	NO
31	CDC42	CDC42	CDC42	8075	0.031	0.39	NO
32	PTPN1	PTPN1	PTPN1	8121	0.03	0.39	NO
33	PARD3	PARD3	PARD3	8241	0.028	0.39	NO
34	CDKN2A	CDKN2A	CDKN2A	8362	0.027	0.39	NO
35	PTK2	PTK2	PTK2	8371	0.027	0.39	NO
36	TSC1	TSC1	TSC1	8485	0.025	0.39	NO
37	GAB1	GAB1	GAB1	8625	0.023	0.38	NO
38	INPPL1	INPPL1	INPPL1	8814	0.02	0.38	NO
39	FOXO3	FOXO3	FOXO3	8826	0.02	0.38	NO
40	GSK3B	GSK3B	GSK3B	8853	0.02	0.38	NO
41	MET	MET	MET	9092	0.016	0.37	NO
42	YWHAZ	YWHAZ	YWHAZ	9749	0.0064	0.34	NO
43	YWHAB	YWHAB	YWHAB	9789	0.0059	0.33	NO
44	CDK2	CDK2	CDK2	9809	0.0056	0.33	NO
45	AKT1	AKT1	AKT1	9834	0.0053	0.33	NO
46	GSK3A	GSK3A	GSK3A	9855	0.0051	0.33	NO
47	CREB3	CREB3	CREB3	9862	0.005	0.33	NO
48	TSC2	TSC2	TSC2	10581	-0.005	0.29	NO
49	PPP1R13B	PPP1R13B	PPP1R13B	10690	-0.0066	0.29	NO
50	AKT2	AKT2	AKT2	11018	-0.012	0.27	NO
51	RPS6KA3	RPS6KA3	RPS6KA3	11109	-0.013	0.27	NO
52	YWHAE	YWHAE	YWHAE	11432	-0.018	0.25	NO
53	IFI27	IFI27	IFI27	11603	-0.02	0.25	NO
54	YWHAQ	YWHAQ	YWHAQ	11648	-0.021	0.25	NO
55	PAK1	PAK1	PAK1	12117	-0.028	0.23	NO
56	MYC	MYC	MYC	12212	-0.03	0.23	NO
57	PDK1	PDK1	PDK1	12817	-0.04	0.2	NO
58	IGFBP1	IGFBP1	IGFBP1	12954	-0.042	0.2	NO
59	SFN	SFN	SFN	13083	-0.044	0.2	NO
60	PAK4	PAK4	PAK4	13574	-0.053	0.18	NO
61	BAD	BAD	BAD	13679	-0.055	0.18	NO
62	RPS6KA1	RPS6KA1	RPS6KA1	14408	-0.071	0.15	NO
63	PAK6	PAK6	PAK6	15098	-0.089	0.13	NO
64	PARD6A	PARD6A	PARD6A	15742	-0.11	0.11	NO
65	EBP	EBP	EBP	16031	-0.12	0.11	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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S46. 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 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	PPP2R2B	PPP2R2B	PPP2R2B	127	0.73	0.043	YES
2	PIK3R5	PIK3R5	PIK3R5	562	0.56	0.058	YES
3	PIK3CG	PIK3CG	PIK3CG	611	0.55	0.093	YES
4	FGR	FGR	FGR	616	0.55	0.13	YES
5	PIK3R6	PIK3R6	PIK3R6	664	0.54	0.17	YES
6	SPHK1	SPHK1	SPHK1	913	0.49	0.19	YES
7	SLA	SLA	SLA	939	0.49	0.22	YES
8	ITGB3	ITGB3	ITGB3	1077	0.46	0.24	YES
9	MYOCD	MYOCD	MYOCD	1205	0.44	0.26	YES
10	PIK3CD	PIK3CD	PIK3CD	1218	0.44	0.3	YES
11	DOCK4	DOCK4	DOCK4	1341	0.42	0.32	YES
12	HCK	HCK	HCK	1347	0.42	0.35	YES
13	MAPK10	MAPK10	MAPK10	1365	0.42	0.37	YES
14	S1PR1	S1PR1	S1PR1	1455	0.41	0.4	YES
15	TAGLN	TAGLN	TAGLN	1620	0.38	0.41	YES
16	PDGFRB	PDGFRB	PDGFRB	1827	0.36	0.43	YES
17	FYN	FYN	FYN	2193	0.32	0.43	YES
18	ACTA2	ACTA2	ACTA2	2237	0.31	0.45	YES
19	PDGFB	PDGFB	PDGFB	2332	0.3	0.46	YES
20	JAK2	JAK2	JAK2	3053	0.22	0.44	YES
21	ITGAV	ITGAV	ITGAV	3070	0.22	0.45	YES
22	LCK	LCK	LCK	3127	0.22	0.46	YES
23	BLK	BLK	BLK	3169	0.21	0.48	YES
24	PIK3CA	PIK3CA	PIK3CA	3573	0.18	0.47	YES
25	STAT1	STAT1	STAT1	3797	0.16	0.46	YES
26	LRP1	LRP1	LRP1	3875	0.16	0.47	YES
27	EIF2AK2	EIF2AK2	EIF2AK2	4112	0.14	0.47	YES
28	CBL	CBL	CBL	4160	0.14	0.48	YES
29	PLA2G4A	PLA2G4A	PLA2G4A	4321	0.13	0.48	YES
30	SOS1	SOS1	SOS1	5044	0.099	0.44	YES
31	RAPGEF1	RAPGEF1	RAPGEF1	5055	0.098	0.45	YES
32	PTPRJ	PTPRJ	PTPRJ	5191	0.093	0.45	YES
33	PIK3R3	PIK3R3	PIK3R3	5205	0.093	0.45	YES
34	KSR1	KSR1	KSR1	5253	0.091	0.46	YES
35	PAG1	PAG1	PAG1	5426	0.086	0.45	YES
36	SIPA1	SIPA1	SIPA1	5458	0.084	0.46	YES
37	STAT5A	STAT5A	STAT5A	5529	0.082	0.46	YES
38	GRB10	GRB10	GRB10	5537	0.082	0.46	YES
39	BAIAP2	BAIAP2	BAIAP2	5685	0.079	0.46	YES
40	PIK3R1	PIK3R1	PIK3R1	5759	0.077	0.46	YES
41	VAV2	VAV2	VAV2	5824	0.075	0.46	YES
42	ARAP1	ARAP1	ARAP1	5830	0.075	0.47	YES
43	STAT5B	STAT5B	STAT5B	5892	0.073	0.47	YES
44	PRKCE	PRKCE	PRKCE	5921	0.073	0.47	YES
45	RAP1A	RAP1A	RAP1A	5925	0.072	0.48	YES
46	LYN	LYN	LYN	5970	0.072	0.48	YES
47	NCK1	NCK1	NCK1	6008	0.07	0.48	YES
48	SRF	SRF	SRF	6066	0.069	0.48	YES
49	PTPN11	PTPN11	PTPN11	6089	0.069	0.49	YES
50	RASA1	RASA1	RASA1	6134	0.068	0.49	YES
51	SHC1	SHC1	SHC1	6210	0.066	0.49	YES
52	SLC9A3R2	SLC9A3R2	SLC9A3R2	6326	0.063	0.49	YES
53	ABL1	ABL1	ABL1	6374	0.062	0.49	YES
54	WASF2	WASF2	WASF2	6379	0.062	0.49	YES
55	ACTR2	ACTR2	ACTR2	6408	0.062	0.5	YES
56	PTEN	PTEN	PTEN	6576	0.058	0.49	NO
57	IQGAP1	IQGAP1	IQGAP1	6705	0.056	0.49	NO
58	GRB2	GRB2	GRB2	6785	0.054	0.49	NO
59	PLCG1	PLCG1	PLCG1	6814	0.053	0.49	NO
60	BRAF	BRAF	BRAF	6874	0.052	0.49	NO
61	YWHAG	YWHAG	YWHAG	7059	0.048	0.48	NO
62	MAP2K7	MAP2K7	MAP2K7	7082	0.048	0.48	NO
63	PTPN2	PTPN2	PTPN2	7101	0.048	0.49	NO
64	STAT3	STAT3	STAT3	7190	0.046	0.49	NO
65	FOS	FOS	FOS	7194	0.046	0.49	NO
66	PRKCA	PRKCA	PRKCA	7209	0.045	0.49	NO
67	PIK3CB	PIK3CB	PIK3CB	7239	0.045	0.49	NO
68	CRK	CRK	CRK	7369	0.043	0.49	NO
69	RAB5A	RAB5A	RAB5A	7410	0.042	0.49	NO
70	KRAS	KRAS	KRAS	7479	0.041	0.49	NO
71	YWHAH	YWHAH	YWHAH	7517	0.04	0.49	NO
72	MAP2K4	MAP2K4	MAP2K4	7559	0.04	0.49	NO
73	ELK1	ELK1	ELK1	7595	0.039	0.49	NO
74	MAP2K1	MAP2K1	MAP2K1	7607	0.039	0.49	NO
75	MAPK8	MAPK8	MAPK8	7660	0.038	0.49	NO
76	DOK1	DOK1	DOK1	7876	0.034	0.48	NO
77	NCKAP1	NCKAP1	NCKAP1	7889	0.034	0.48	NO
78	ARPC3	ARPC3	ARPC3	8117	0.03	0.47	NO
79	PTPN1	PTPN1	PTPN1	8121	0.03	0.48	NO
80	GAB1	GAB1	GAB1	8625	0.023	0.45	NO
81	ACTR3	ACTR3	ACTR3	8754	0.021	0.44	NO
82	MLLT4	MLLT4	MLLT4	8894	0.019	0.44	NO
83	MAPK1	MAPK1	MAPK1	8927	0.018	0.44	NO
84	NRAS	NRAS	NRAS	8928	0.018	0.44	NO
85	BCAR1	BCAR1	BCAR1	8976	0.018	0.44	NO
86	ARPC1B	ARPC1B	ARPC1B	9012	0.017	0.44	NO
87	ARPC2	ARPC2	ARPC2	9061	0.017	0.43	NO
88	RHOA	RHOA	RHOA	9156	0.016	0.43	NO
89	ACTN4	ACTN4	ACTN4	9182	0.015	0.43	NO
90	YES1	YES1	YES1	9183	0.015	0.43	NO
91	ABI1	ABI1	ABI1	9298	0.013	0.42	NO
92	EPS8	EPS8	EPS8	9568	0.009	0.41	NO
93	YWHAZ	YWHAZ	YWHAZ	9749	0.0064	0.4	NO
94	WASL	WASL	WASL	9785	0.0059	0.4	NO
95	YWHAB	YWHAB	YWHAB	9789	0.0059	0.4	NO
96	JUN	JUN	JUN	10052	0.0025	0.38	NO
97	NCK2	NCK2	NCK2	10123	0.0015	0.38	NO
98	CSK	CSK	CSK	10196	0.00053	0.38	NO
99	ARPC5	ARPC5	ARPC5	10281	-0.00066	0.37	NO
100	USP6NL	USP6NL	USP6NL	10376	-0.0019	0.37	NO
101	RAF1	RAF1	RAF1	10611	-0.0054	0.35	NO
102	ARHGDIA	ARHGDIA	ARHGDIA	10763	-0.0078	0.35	NO
103	RPS6KA3	RPS6KA3	RPS6KA3	11109	-0.013	0.33	NO
104	PRKCD	PRKCD	PRKCD	11331	-0.016	0.32	NO
105	YWHAE	YWHAE	YWHAE	11432	-0.018	0.31	NO
106	ARPC4	ARPC4	ARPC4	11495	-0.018	0.31	NO
107	CTTN	CTTN	CTTN	11556	-0.019	0.31	NO
108	MAPK9	MAPK9	MAPK9	11622	-0.02	0.3	NO
109	YWHAQ	YWHAQ	YWHAQ	11648	-0.021	0.3	NO
110	CYFIP2	CYFIP2	CYFIP2	11705	-0.022	0.3	NO
111	RAC1	RAC1	RAC1	11915	-0.025	0.29	NO
112	PPP2R1A	PPP2R1A	PPP2R1A	11975	-0.026	0.29	NO
113	PPP2CA	PPP2CA	PPP2CA	11986	-0.026	0.29	NO
114	SRC	SRC	SRC	12005	-0.027	0.29	NO
115	PAK1	PAK1	PAK1	12117	-0.028	0.29	NO
116	MYC	MYC	MYC	12212	-0.03	0.29	NO
117	PIK3R2	PIK3R2	PIK3R2	12407	-0.033	0.28	NO
118	RAP1B	RAP1B	RAP1B	12423	-0.033	0.28	NO
119	PIN1	PIN1	PIN1	12661	-0.037	0.27	NO
120	JUND	JUND	JUND	12919	-0.041	0.26	NO
121	DNM2	DNM2	DNM2	13045	-0.044	0.25	NO
122	SFN	SFN	SFN	13083	-0.044	0.26	NO
123	RAB4A	RAB4A	RAB4A	13211	-0.047	0.25	NO
124	HRAS	HRAS	HRAS	13243	-0.047	0.25	NO
125	MAP2K2	MAP2K2	MAP2K2	13800	-0.058	0.22	NO
126	MAPK3	MAPK3	MAPK3	13966	-0.061	0.22	NO
127	SLC9A3R1	SLC9A3R1	SLC9A3R1	14773	-0.08	0.18	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 GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.

Figure S48. 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 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	PRKCB	PRKCB	PRKCB	683	0.54	0.039	YES
2	ITGB3	ITGB3	ITGB3	1077	0.46	0.084	YES
3	MAPK11	MAPK11	MAPK11	1533	0.4	0.12	YES
4	FYN	FYN	FYN	2193	0.32	0.12	YES
5	CDH5	CDH5	CDH5	2208	0.31	0.17	YES
6	VTN	VTN	VTN	2255	0.31	0.21	YES
7	KDR	KDR	KDR	2287	0.31	0.25	YES
8	CAV1	CAV1	CAV1	2406	0.29	0.29	YES
9	FES	FES	FES	2486	0.28	0.32	YES
10	FLT1	FLT1	FLT1	2523	0.28	0.36	YES
11	PRKAA2	PRKAA2	PRKAA2	2768	0.26	0.39	YES
12	ITGAV	ITGAV	ITGAV	3070	0.22	0.4	YES
13	MYOF	MYOF	MYOF	3518	0.18	0.4	YES
14	PIK3CA	PIK3CA	PIK3CA	3573	0.18	0.42	YES
15	ROCK1	ROCK1	ROCK1	3707	0.17	0.44	YES
16	VCL	VCL	VCL	4110	0.14	0.44	YES
17	CBL	CBL	CBL	4160	0.14	0.46	YES
18	NOS3	NOS3	NOS3	4486	0.12	0.46	YES
19	NEDD4	NEDD4	NEDD4	5178	0.094	0.43	YES
20	PTPRJ	PTPRJ	PTPRJ	5191	0.093	0.44	YES
21	GRB10	GRB10	GRB10	5537	0.082	0.44	YES
22	PIK3R1	PIK3R1	PIK3R1	5759	0.077	0.43	YES
23	NCK1	NCK1	NCK1	6008	0.07	0.43	YES
24	PTPN11	PTPN11	PTPN11	6089	0.069	0.44	YES
25	FBXW11	FBXW11	FBXW11	6198	0.066	0.44	YES
26	IQGAP1	IQGAP1	IQGAP1	6705	0.056	0.42	YES
27	GRB2	GRB2	GRB2	6785	0.054	0.42	YES
28	PRKACA	PRKACA	PRKACA	6809	0.054	0.43	YES
29	PLCG1	PLCG1	PLCG1	6814	0.053	0.44	YES
30	BRAF	BRAF	BRAF	6874	0.052	0.44	YES
31	PTPN6	PTPN6	PTPN6	6962	0.05	0.44	YES
32	MAPKAPK2	MAPKAPK2	MAPKAPK2	7015	0.049	0.45	YES
33	PTPN2	PTPN2	PTPN2	7101	0.048	0.45	YES
34	PAK2	PAK2	PAK2	7107	0.047	0.46	YES
35	HSP90AA1	HSP90AA1	HSP90AA1	7164	0.046	0.46	YES
36	SH2D2A	SH2D2A	SH2D2A	7181	0.046	0.46	YES
37	PRKCA	PRKCA	PRKCA	7209	0.045	0.47	YES
38	MAP2K1	MAP2K1	MAP2K1	7607	0.039	0.45	NO
39	PDPK1	PDPK1	PDPK1	7609	0.039	0.46	NO
40	PRKAA1	PRKAA1	PRKAA1	7894	0.034	0.45	NO
41	PTK2B	PTK2B	PTK2B	7906	0.034	0.45	NO
42	CDC42	CDC42	CDC42	8075	0.031	0.45	NO
43	PTK2	PTK2	PTK2	8371	0.027	0.44	NO
44	CAMKK2	CAMKK2	CAMKK2	8514	0.024	0.43	NO
45	GAB1	GAB1	GAB1	8625	0.023	0.43	NO
46	HSP90AB1	HSP90AB1	HSP90AB1	8713	0.022	0.43	NO
47	MAPK1	MAPK1	MAPK1	8927	0.018	0.42	NO
48	PXN	PXN	PXN	8958	0.018	0.42	NO
49	RHOA	RHOA	RHOA	9156	0.016	0.41	NO
50	AKT1	AKT1	AKT1	9834	0.0053	0.37	NO
51	MAP2K3	MAP2K3	MAP2K3	9933	0.0042	0.37	NO
52	NCK2	NCK2	NCK2	10123	0.0015	0.36	NO
53	MAPK14	MAPK14	MAPK14	10276	-0.00059	0.35	NO
54	CTNNB1	CTNNB1	CTNNB1	10504	-0.004	0.34	NO
55	CTNNA1	CTNNA1	CTNNA1	10529	-0.0044	0.34	NO
56	RAF1	RAF1	RAF1	10611	-0.0054	0.33	NO
57	VEGFA	VEGFA	VEGFA	11198	-0.014	0.3	NO
58	PRKCD	PRKCD	PRKCD	11331	-0.016	0.3	NO
59	HGS	HGS	HGS	11509	-0.019	0.29	NO
60	PRKAG1	PRKAG1	PRKAG1	11694	-0.021	0.28	NO
61	SHB	SHB	SHB	11814	-0.024	0.28	NO
62	SRC	SRC	SRC	12005	-0.027	0.27	NO
63	AKAP1	AKAP1	AKAP1	12129	-0.029	0.27	NO
64	DNM2	DNM2	DNM2	13045	-0.044	0.22	NO
65	ARF1	ARF1	ARF1	13308	-0.048	0.22	NO
66	MAP2K2	MAP2K2	MAP2K2	13800	-0.058	0.2	NO
67	MAPK3	MAPK3	MAPK3	13966	-0.061	0.2	NO
68	PRKAB1	PRKAB1	PRKAB1	15006	-0.086	0.15	NO
69	MAP2K6	MAP2K6	MAP2K6	15551	-0.1	0.14	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 INOSITOL PHOSPHATE METABOLISM.

Figure S50. 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 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	ESR1	ESR1	ESR1	171	0.71	0.065	YES
2	AR	AR	AR	670	0.54	0.094	YES
3	IL10	IL10	IL10	1042	0.47	0.12	YES
4	NR3C1	NR3C1	NR3C1	1069	0.46	0.17	YES
5	GATA3	GATA3	GATA3	1160	0.45	0.21	YES
6	SERPINE1	SERPINE1	SERPINE1	1289	0.43	0.25	YES
7	RUNX2	RUNX2	RUNX2	1376	0.42	0.29	YES
8	MEF2C	MEF2C	MEF2C	1461	0.41	0.33	YES
9	GSC	GSC	GSC	1578	0.39	0.36	YES
10	RUNX3	RUNX3	RUNX3	1952	0.34	0.38	YES
11	COL1A2	COL1A2	COL1A2	2072	0.33	0.4	YES
12	CDKN2B	CDKN2B	CDKN2B	2367	0.3	0.42	YES
13	KAT2B	KAT2B	KAT2B	3056	0.22	0.4	YES
14	LAMC1	LAMC1	LAMC1	3450	0.18	0.4	YES
15	RUNX1	RUNX1	RUNX1	3514	0.18	0.42	YES
16	FOXO1	FOXO1	FOXO1	3696	0.17	0.42	YES
17	PIAS3	PIAS3	PIAS3	3759	0.16	0.44	YES
18	NCOA2	NCOA2	NCOA2	3993	0.15	0.44	YES
19	DLX1	DLX1	DLX1	4135	0.14	0.45	YES
20	SMAD7	SMAD7	SMAD7	4251	0.13	0.46	YES
21	NCOA1	NCOA1	NCOA1	4622	0.12	0.45	YES
22	ATF2	ATF2	ATF2	4753	0.11	0.45	YES
23	ITGB5	ITGB5	ITGB5	4958	0.1	0.45	YES
24	EP300	EP300	EP300	5040	0.099	0.46	YES
25	FOXO4	FOXO4	FOXO4	5069	0.098	0.46	YES
26	IRF7	IRF7	IRF7	5078	0.097	0.47	YES
27	TFE3	TFE3	TFE3	5220	0.092	0.48	YES
28	CREB1	CREB1	CREB1	5330	0.088	0.48	YES
29	SKI	SKI	SKI	5336	0.088	0.49	YES
30	CREBBP	CREBBP	CREBBP	5352	0.088	0.5	YES
31	TGIF2	TGIF2	TGIF2	5355	0.088	0.51	YES
32	SKIL	SKIL	SKIL	5385	0.087	0.51	YES
33	NCOR1	NCOR1	NCOR1	5960	0.072	0.49	NO
34	SAP30	SAP30	SAP30	6068	0.069	0.49	NO
35	SMAD2	SMAD2	SMAD2	6308	0.064	0.48	NO
36	SMAD3	SMAD3	SMAD3	6426	0.061	0.48	NO
37	MAX	MAX	MAX	6546	0.059	0.48	NO
38	SIN3A	SIN3A	SIN3A	6571	0.058	0.49	NO
39	SP3	SP3	SP3	6715	0.055	0.48	NO
40	IL5	IL5	IL5	6775	0.054	0.49	NO
41	SNIP1	SNIP1	SNIP1	6834	0.053	0.49	NO
42	SIN3B	SIN3B	SIN3B	7067	0.048	0.48	NO
43	FOS	FOS	FOS	7194	0.046	0.48	NO
44	SP1	SP1	SP1	7275	0.044	0.48	NO
45	ATF3	ATF3	ATF3	7420	0.042	0.48	NO
46	RBL1	RBL1	RBL1	7536	0.04	0.47	NO
47	MED15	MED15	MED15	7622	0.039	0.47	NO
48	ZBTB17	ZBTB17	ZBTB17	7676	0.038	0.48	NO
49	SMAD4	SMAD4	SMAD4	7951	0.033	0.46	NO
50	CBFB	CBFB	CBFB	8000	0.032	0.46	NO
51	DCP1A	DCP1A	DCP1A	8441	0.025	0.44	NO
52	FOXO3	FOXO3	FOXO3	8826	0.02	0.42	NO
53	CEBPB	CEBPB	CEBPB	9030	0.017	0.41	NO
54	VDR	VDR	VDR	9380	0.012	0.4	NO
55	CDK2	CDK2	CDK2	9809	0.0056	0.37	NO
56	AKT1	AKT1	AKT1	9834	0.0053	0.37	NO
57	RBBP4	RBBP4	RBBP4	9845	0.0052	0.37	NO
58	JUN	JUN	JUN	10052	0.0025	0.36	NO
59	HSPA8	HSPA8	HSPA8	10306	-0.001	0.34	NO
60	PIAS4	PIAS4	PIAS4	10573	-0.0048	0.33	NO
61	TGIF1	TGIF1	TGIF1	10839	-0.009	0.32	NO
62	HDAC2	HDAC2	HDAC2	10875	-0.0096	0.32	NO
63	CDKN1A	CDKN1A	CDKN1A	11383	-0.017	0.29	NO
64	TCF3	TCF3	TCF3	11473	-0.018	0.29	NO
65	E2F5	E2F5	E2F5	11631	-0.02	0.28	NO
66	CTBP1	CTBP1	CTBP1	11871	-0.024	0.27	NO
67	HDAC1	HDAC1	HDAC1	12079	-0.028	0.26	NO
68	MYC	MYC	MYC	12212	-0.03	0.26	NO
69	HNF4A	HNF4A	HNF4A	12223	-0.03	0.26	NO
70	TFDP1	TFDP1	TFDP1	12432	-0.034	0.25	NO
71	E2F4	E2F4	E2F4	12506	-0.035	0.25	NO
72	SAP18	SAP18	SAP18	12959	-0.042	0.23	NO
73	CDK4	CDK4	CDK4	13519	-0.052	0.2	NO
74	RBBP7	RBBP7	RBBP7	13548	-0.053	0.21	NO
75	KAT2A	KAT2A	KAT2A	13603	-0.054	0.21	NO
76	CITED1	CITED1	CITED1	13960	-0.061	0.2	NO
77	FOXG1	FOXG1	FOXG1	14461	-0.072	0.18	NO
78	FOXH1	FOXH1	FOXH1	16954	-0.2	0.058	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 ABC TRANSPORTERS.

Figure S52. 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 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	KLF8	KLF8	KLF8	1137	0.45	0.019	YES
2	ITGA5	ITGA5	ITGA5	1640	0.38	0.061	YES
3	ELMO1	ELMO1	ELMO1	2108	0.33	0.094	YES
4	ETS1	ETS1	ETS1	2187	0.32	0.15	YES
5	FYN	FYN	FYN	2193	0.32	0.2	YES
6	BMX	BMX	BMX	2369	0.3	0.25	YES
7	MMP14	MMP14	MMP14	2528	0.28	0.29	YES
8	ITGAV	ITGAV	ITGAV	3070	0.22	0.3	YES
9	ASAP1	ASAP1	ASAP1	3467	0.18	0.31	YES
10	PIK3CA	PIK3CA	PIK3CA	3573	0.18	0.34	YES
11	TLN1	TLN1	TLN1	3986	0.15	0.34	YES
12	VCL	VCL	VCL	4110	0.14	0.36	YES
13	PTPN21	PTPN21	PTPN21	4204	0.14	0.38	YES
14	ACTN1	ACTN1	ACTN1	4480	0.12	0.39	YES
15	GIT2	GIT2	GIT2	4499	0.12	0.41	YES
16	ACTA1	ACTA1	ACTA1	4856	0.11	0.41	YES
17	DOCK1	DOCK1	DOCK1	4928	0.1	0.42	YES
18	ITGB5	ITGB5	ITGB5	4958	0.1	0.44	YES
19	ITGB1	ITGB1	ITGB1	5005	0.1	0.46	YES
20	SOS1	SOS1	SOS1	5044	0.099	0.47	YES
21	RAPGEF1	RAPGEF1	RAPGEF1	5055	0.098	0.49	YES
22	PIK3R1	PIK3R1	PIK3R1	5759	0.077	0.47	YES
23	RAP1A	RAP1A	RAP1A	5925	0.072	0.47	YES
24	NCK1	NCK1	NCK1	6008	0.07	0.48	YES
25	RASA1	RASA1	RASA1	6134	0.068	0.48	YES
26	CCND1	CCND1	CCND1	6209	0.066	0.49	YES
27	ROCK2	ROCK2	ROCK2	6608	0.058	0.48	YES
28	GRB2	GRB2	GRB2	6785	0.054	0.48	YES
29	PLCG1	PLCG1	PLCG1	6814	0.053	0.49	YES
30	BRAF	BRAF	BRAF	6874	0.052	0.49	YES
31	CAPN2	CAPN2	CAPN2	7272	0.044	0.48	YES
32	CRK	CRK	CRK	7369	0.043	0.48	YES
33	MAP2K4	MAP2K4	MAP2K4	7559	0.04	0.48	YES
34	RGNEF	RGNEF	RGNEF	7566	0.039	0.49	YES
35	MAP2K1	MAP2K1	MAP2K1	7607	0.039	0.49	YES
36	MAPK8	MAPK8	MAPK8	7660	0.038	0.5	YES
37	RRAS	RRAS	RRAS	7999	0.032	0.48	NO
38	ARHGEF11	ARHGEF11	ARHGEF11	8168	0.03	0.48	NO
39	PTK2	PTK2	PTK2	8371	0.027	0.47	NO
40	MAPK1	MAPK1	MAPK1	8927	0.018	0.44	NO
41	PXN	PXN	PXN	8958	0.018	0.45	NO
42	BCAR1	BCAR1	BCAR1	8976	0.018	0.45	NO
43	ARHGEF7	ARHGEF7	ARHGEF7	9054	0.017	0.45	NO
44	RHOA	RHOA	RHOA	9156	0.016	0.44	NO
45	SH3GL1	SH3GL1	SH3GL1	9163	0.015	0.45	NO
46	YES1	YES1	YES1	9183	0.015	0.45	NO
47	ARHGAP26	ARHGAP26	ARHGAP26	9723	0.0068	0.42	NO
48	WASL	WASL	WASL	9785	0.0059	0.42	NO
49	JUN	JUN	JUN	10052	0.0025	0.4	NO
50	NCK2	NCK2	NCK2	10123	0.0015	0.4	NO
51	RAF1	RAF1	RAF1	10611	-0.0054	0.37	NO
52	MAPK9	MAPK9	MAPK9	11622	-0.02	0.32	NO
53	RAC1	RAC1	RAC1	11915	-0.025	0.31	NO
54	SRC	SRC	SRC	12005	-0.027	0.31	NO
55	PAK1	PAK1	PAK1	12117	-0.028	0.31	NO
56	MAPK8IP3	MAPK8IP3	MAPK8IP3	12418	-0.033	0.3	NO
57	RAP1B	RAP1B	RAP1B	12423	-0.033	0.3	NO
58	GRB7	GRB7	GRB7	13041	-0.044	0.28	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 MAPK SIGNALING PATHWAY.

Figure S54. 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 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	WAS	WAS	WAS	950	0.48	0.011	YES
2	SNAI2	SNAI2	SNAI2	1048	0.47	0.068	YES
3	FGFR1	FGFR1	FGFR1	1381	0.42	0.1	YES
4	PTPRM	PTPRM	PTPRM	1656	0.38	0.14	YES
5	WASF3	WASF3	WASF3	2007	0.34	0.16	YES
6	FYN	FYN	FYN	2193	0.32	0.2	YES
7	SORBS1	SORBS1	SORBS1	2253	0.31	0.23	YES
8	WASF1	WASF1	WASF1	2436	0.29	0.26	YES
9	TCF7L1	TCF7L1	TCF7L1	2437	0.29	0.3	YES
10	ACTN3	ACTN3	ACTN3	2609	0.27	0.33	YES
11	SNAI1	SNAI1	SNAI1	2636	0.27	0.36	YES
12	ACTN2	ACTN2	ACTN2	2649	0.27	0.4	YES
13	LEF1	LEF1	LEF1	2672	0.26	0.43	YES
14	CTNNA3	CTNNA3	CTNNA3	2793	0.25	0.46	YES
15	FER	FER	FER	3171	0.21	0.46	YES
16	TGFBR1	TGFBR1	TGFBR1	4060	0.14	0.43	YES
17	VCL	VCL	VCL	4110	0.14	0.45	YES
18	RAC2	RAC2	RAC2	4406	0.13	0.45	YES
19	ACTN1	ACTN1	ACTN1	4480	0.12	0.46	YES
20	EGFR	EGFR	EGFR	4745	0.11	0.46	YES
21	TGFBR2	TGFBR2	TGFBR2	4879	0.11	0.47	YES
22	EP300	EP300	EP300	5040	0.099	0.47	YES
23	PTPRJ	PTPRJ	PTPRJ	5191	0.093	0.48	YES
24	IGF1R	IGF1R	IGF1R	5232	0.092	0.49	YES
25	CREBBP	CREBBP	CREBBP	5352	0.088	0.49	YES
26	TJP1	TJP1	TJP1	5673	0.079	0.48	YES
27	BAIAP2	BAIAP2	BAIAP2	5685	0.079	0.49	YES
28	CTNNA2	CTNNA2	CTNNA2	6297	0.064	0.47	YES
29	PTPRB	PTPRB	PTPRB	6299	0.064	0.48	YES
30	SMAD2	SMAD2	SMAD2	6308	0.064	0.48	YES
31	WASF2	WASF2	WASF2	6379	0.062	0.49	YES
32	SMAD3	SMAD3	SMAD3	6426	0.061	0.49	YES
33	LMO7	LMO7	LMO7	6569	0.058	0.49	NO
34	IQGAP1	IQGAP1	IQGAP1	6705	0.056	0.49	NO
35	MAP3K7	MAP3K7	MAP3K7	6852	0.053	0.49	NO
36	PTPN6	PTPN6	PTPN6	6962	0.05	0.49	NO
37	INSR	INSR	INSR	7433	0.042	0.47	NO
38	SMAD4	SMAD4	SMAD4	7951	0.033	0.45	NO
39	CDC42	CDC42	CDC42	8075	0.031	0.44	NO
40	PTPN1	PTPN1	PTPN1	8121	0.03	0.45	NO
41	SSX2IP	SSX2IP	SSX2IP	8156	0.03	0.45	NO
42	CTNND1	CTNND1	CTNND1	8191	0.029	0.45	NO
43	PARD3	PARD3	PARD3	8241	0.028	0.45	NO
44	MLLT4	MLLT4	MLLT4	8894	0.019	0.42	NO
45	MAPK1	MAPK1	MAPK1	8927	0.018	0.42	NO
46	MET	MET	MET	9092	0.016	0.41	NO
47	PVRL2	PVRL2	PVRL2	9136	0.016	0.41	NO
48	RHOA	RHOA	RHOA	9156	0.016	0.41	NO
49	ACTN4	ACTN4	ACTN4	9182	0.015	0.41	NO
50	YES1	YES1	YES1	9183	0.015	0.42	NO
51	CSNK2A1	CSNK2A1	CSNK2A1	9208	0.015	0.42	NO
52	ACTB	ACTB	ACTB	9644	0.0081	0.39	NO
53	WASL	WASL	WASL	9785	0.0059	0.38	NO
54	RAC3	RAC3	RAC3	10214	0.00033	0.36	NO
55	CTNNB1	CTNNB1	CTNNB1	10504	-0.004	0.34	NO
56	CTNNA1	CTNNA1	CTNNA1	10529	-0.0044	0.34	NO
57	PTPRF	PTPRF	PTPRF	10824	-0.0088	0.33	NO
58	PVRL1	PVRL1	PVRL1	11067	-0.012	0.32	NO
59	TCF7L2	TCF7L2	TCF7L2	11310	-0.016	0.31	NO
60	PVRL3	PVRL3	PVRL3	11342	-0.016	0.31	NO
61	CDH1	CDH1	CDH1	11586	-0.02	0.3	NO
62	NLK	NLK	NLK	11593	-0.02	0.3	NO
63	TCF7	TCF7	TCF7	11709	-0.022	0.29	NO
64	ACTG1	ACTG1	ACTG1	11875	-0.024	0.29	NO
65	ERBB2	ERBB2	ERBB2	11894	-0.025	0.29	NO
66	RAC1	RAC1	RAC1	11915	-0.025	0.29	NO
67	SRC	SRC	SRC	12005	-0.027	0.29	NO
68	FARP2	FARP2	FARP2	12262	-0.031	0.28	NO
69	ACP1	ACP1	ACP1	13047	-0.044	0.24	NO
70	PVRL4	PVRL4	PVRL4	13745	-0.057	0.21	NO
71	CSNK2B	CSNK2B	CSNK2B	13889	-0.059	0.21	NO
72	MAPK3	MAPK3	MAPK3	13966	-0.061	0.22	NO
73	CSNK2A2	CSNK2A2	CSNK2A2	14335	-0.069	0.2	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 ERBB SIGNALING PATHWAY.

Figure S56. 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 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	PDE1B	PDE1B	PDE1B	237	0.68	0.039	YES
2	PDE1A	PDE1A	PDE1A	337	0.63	0.082	YES
3	AKT3	AKT3	AKT3	521	0.57	0.12	YES
4	ADCYAP1	ADCYAP1	ADCYAP1	743	0.52	0.14	YES
5	ADCY2	ADCY2	ADCY2	786	0.52	0.18	YES
6	NGF	NGF	NGF	1066	0.46	0.2	YES
7	NTRK1	NTRK1	NTRK1	1180	0.45	0.23	YES
8	MEF2C	MEF2C	MEF2C	1461	0.41	0.25	YES
9	MAPK11	MAPK11	MAPK11	1533	0.4	0.27	YES
10	ADCY5	ADCY5	ADCY5	1655	0.38	0.3	YES
11	CAMK4	CAMK4	CAMK4	1898	0.35	0.31	YES
12	PRKAR2B	PRKAR2B	PRKAR2B	1976	0.34	0.33	YES
13	ADCY1	ADCY1	ADCY1	2094	0.33	0.35	YES
14	ADORA2A	ADORA2A	ADORA2A	2524	0.28	0.35	YES
15	ADCY4	ADCY4	ADCY4	2693	0.26	0.36	YES
16	NTRK2	NTRK2	NTRK2	3000	0.23	0.36	YES
17	DNM1	DNM1	DNM1	3058	0.22	0.37	YES
18	RPS6KA2	RPS6KA2	RPS6KA2	3120	0.22	0.38	YES
19	IRS1	IRS1	IRS1	3240	0.2	0.39	YES
20	ADCY7	ADCY7	ADCY7	3504	0.18	0.39	YES
21	ITPR2	ITPR2	ITPR2	3553	0.18	0.4	YES
22	PIK3CA	PIK3CA	PIK3CA	3573	0.18	0.42	YES
23	MAPK12	MAPK12	MAPK12	3642	0.17	0.43	YES
24	FOXO1	FOXO1	FOXO1	3696	0.17	0.44	YES
25	DUSP4	DUSP4	DUSP4	4116	0.14	0.42	YES
26	MEF2A	MEF2A	MEF2A	4201	0.14	0.43	YES
27	ADCY9	ADCY9	ADCY9	4351	0.13	0.43	YES
28	KIDINS220	KIDINS220	KIDINS220	4396	0.13	0.44	YES
29	RICTOR	RICTOR	RICTOR	4620	0.12	0.44	YES
30	SHC2	SHC2	SHC2	4712	0.11	0.44	YES
31	SOS1	SOS1	SOS1	5044	0.099	0.43	YES
32	RAPGEF1	RAPGEF1	RAPGEF1	5055	0.098	0.44	YES
33	FOXO4	FOXO4	FOXO4	5069	0.098	0.44	YES
34	PRKAR1A	PRKAR1A	PRKAR1A	5136	0.096	0.44	YES
35	DUSP7	DUSP7	DUSP7	5197	0.093	0.45	YES
36	CREB1	CREB1	CREB1	5330	0.088	0.45	NO
37	PIK3R1	PIK3R1	PIK3R1	5759	0.077	0.43	NO
38	PRKCE	PRKCE	PRKCE	5921	0.073	0.43	NO
39	RAP1A	RAP1A	RAP1A	5925	0.072	0.43	NO
40	FRS2	FRS2	FRS2	5939	0.072	0.44	NO
41	SHC1	SHC1	SHC1	6210	0.066	0.43	NO
42	DUSP3	DUSP3	DUSP3	6226	0.066	0.43	NO
43	MTOR	MTOR	MTOR	6358	0.063	0.43	NO
44	PTEN	PTEN	PTEN	6576	0.058	0.42	NO
45	GRB2	GRB2	GRB2	6785	0.054	0.41	NO
46	PRKACA	PRKACA	PRKACA	6809	0.054	0.42	NO
47	PLCG1	PLCG1	PLCG1	6814	0.053	0.42	NO
48	BRAF	BRAF	BRAF	6874	0.052	0.42	NO
49	RPS6KA5	RPS6KA5	RPS6KA5	6918	0.051	0.42	NO
50	RIT1	RIT1	RIT1	6967	0.05	0.42	NO
51	MAPKAPK2	MAPKAPK2	MAPKAPK2	7015	0.049	0.42	NO
52	MAPK7	MAPK7	MAPK7	7017	0.049	0.43	NO
53	SH3GL2	SH3GL2	SH3GL2	7024	0.049	0.43	NO
54	NR4A1	NR4A1	NR4A1	7094	0.048	0.43	NO
55	STAT3	STAT3	STAT3	7190	0.046	0.43	NO
56	PRKCA	PRKCA	PRKCA	7209	0.045	0.43	NO
57	PIK3CB	PIK3CB	PIK3CB	7239	0.045	0.44	NO
58	PRKCG	PRKCG	PRKCG	7292	0.044	0.44	NO
59	CRK	CRK	CRK	7369	0.043	0.43	NO
60	CHUK	CHUK	CHUK	7389	0.043	0.44	NO
61	KRAS	KRAS	KRAS	7479	0.041	0.44	NO
62	ATF1	ATF1	ATF1	7520	0.04	0.44	NO
63	ELK1	ELK1	ELK1	7595	0.039	0.43	NO
64	MAP2K1	MAP2K1	MAP2K1	7607	0.039	0.44	NO
65	RALB	RALB	RALB	7608	0.039	0.44	NO
66	PDPK1	PDPK1	PDPK1	7609	0.039	0.44	NO
67	PRKACB	PRKACB	PRKACB	7719	0.037	0.44	NO
68	CDKN1B	CDKN1B	CDKN1B	7821	0.035	0.44	NO
69	IRS2	IRS2	IRS2	8010	0.032	0.43	NO
70	RALGDS	RALGDS	RALGDS	8087	0.031	0.43	NO
71	AP2M1	AP2M1	AP2M1	8422	0.026	0.41	NO
72	AP2A1	AP2A1	AP2A1	8508	0.024	0.41	NO
73	FOXO3	FOXO3	FOXO3	8826	0.02	0.39	NO
74	MAPK1	MAPK1	MAPK1	8927	0.018	0.39	NO
75	NRAS	NRAS	NRAS	8928	0.018	0.39	NO
76	CLTC	CLTC	CLTC	9003	0.018	0.38	NO
77	MDM2	MDM2	MDM2	9123	0.016	0.38	NO
78	RHOA	RHOA	RHOA	9156	0.016	0.38	NO
79	PPP2CB	PPP2CB	PPP2CB	9165	0.015	0.38	NO
80	ADCY3	ADCY3	ADCY3	9240	0.014	0.38	NO
81	PHLPP1	PHLPP1	PHLPP1	9513	0.0099	0.36	NO
82	MAPKAP1	MAPKAP1	MAPKAP1	9533	0.0095	0.36	NO
83	AP2B1	AP2B1	AP2B1	9647	0.0081	0.36	NO
84	CALM3	CALM3	CALM3	9751	0.0064	0.35	NO
85	YWHAB	YWHAB	YWHAB	9789	0.0059	0.35	NO
86	AKT1	AKT1	AKT1	9834	0.0053	0.35	NO
87	GSK3A	GSK3A	GSK3A	9855	0.0051	0.35	NO
88	CALM1	CALM1	CALM1	9912	0.0044	0.34	NO
89	MAPK14	MAPK14	MAPK14	10276	-0.00059	0.32	NO
90	CALM2	CALM2	CALM2	10364	-0.0018	0.32	NO
91	CASP9	CASP9	CASP9	10375	-0.0019	0.32	NO
92	DUSP6	DUSP6	DUSP6	10401	-0.0024	0.32	NO
93	AP2A2	AP2A2	AP2A2	10409	-0.0025	0.32	NO
94	DNAL4	DNAL4	DNAL4	10480	-0.0035	0.31	NO
95	RALA	RALA	RALA	10515	-0.0041	0.31	NO
96	PRKAR2A	PRKAR2A	PRKAR2A	10560	-0.0047	0.31	NO
97	TSC2	TSC2	TSC2	10581	-0.005	0.31	NO
98	ITPR3	ITPR3	ITPR3	10607	-0.0054	0.31	NO
99	RAF1	RAF1	RAF1	10611	-0.0054	0.31	NO
100	SHC3	SHC3	SHC3	10720	-0.0071	0.3	NO
101	PPP2R1B	PPP2R1B	PPP2R1B	10912	-0.01	0.29	NO
102	AKT2	AKT2	AKT2	11018	-0.012	0.29	NO
103	PPP2R5D	PPP2R5D	PPP2R5D	11060	-0.012	0.29	NO
104	RPS6KA3	RPS6KA3	RPS6KA3	11109	-0.013	0.28	NO
105	PRKCD	PRKCD	PRKCD	11331	-0.016	0.27	NO
106	CDKN1A	CDKN1A	CDKN1A	11383	-0.017	0.27	NO
107	PPP2R1A	PPP2R1A	PPP2R1A	11975	-0.026	0.24	NO
108	PPP2CA	PPP2CA	PPP2CA	11986	-0.026	0.24	NO
109	SRC	SRC	SRC	12005	-0.027	0.24	NO
110	AKT1S1	AKT1S1	AKT1S1	12220	-0.03	0.23	NO
111	MAP2K5	MAP2K5	MAP2K5	12249	-0.031	0.24	NO
112	ADCY6	ADCY6	ADCY6	12296	-0.031	0.24	NO
113	ADRBK1	ADRBK1	ADRBK1	12321	-0.032	0.24	NO
114	PIK3R2	PIK3R2	PIK3R2	12407	-0.033	0.23	NO
115	THEM4	THEM4	THEM4	12626	-0.036	0.22	NO
116	CDK1	CDK1	CDK1	12971	-0.042	0.21	NO
117	DNM2	DNM2	DNM2	13045	-0.044	0.21	NO
118	AP2S1	AP2S1	AP2S1	13096	-0.044	0.21	NO
119	HRAS	HRAS	HRAS	13243	-0.047	0.2	NO
120	MAPKAPK3	MAPKAPK3	MAPKAPK3	13398	-0.05	0.2	NO
121	BAD	BAD	BAD	13679	-0.055	0.19	NO
122	MAP2K2	MAP2K2	MAP2K2	13800	-0.058	0.18	NO
123	MAPK3	MAPK3	MAPK3	13966	-0.061	0.18	NO
124	RPS6KA1	RPS6KA1	RPS6KA1	14408	-0.071	0.16	NO
125	TRIB3	TRIB3	TRIB3	14604	-0.076	0.16	NO
126	CLTA	CLTA	CLTA	14605	-0.076	0.16	NO
127	MAPK13	MAPK13	MAPK13	14662	-0.077	0.16	NO
128	PRKAR1B	PRKAR1B	PRKAR1B	15053	-0.088	0.15	NO
129	MLST8	MLST8	MLST8	15125	-0.09	0.15	NO
130	RPS6KB2	RPS6KB2	RPS6KB2	15463	-0.1	0.14	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 CALCIUM SIGNALING PATHWAY.

Figure S58. 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 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	THBS4	THBS4	THBS4	72	0.78	0.042	YES
2	PDE1B	PDE1B	PDE1B	237	0.68	0.072	YES
3	PDE1A	PDE1A	PDE1A	337	0.63	0.1	YES
4	THBS2	THBS2	THBS2	464	0.59	0.13	YES
5	AKT3	AKT3	AKT3	521	0.57	0.16	YES
6	SPP1	SPP1	SPP1	783	0.52	0.18	YES
7	ADCY2	ADCY2	ADCY2	786	0.52	0.21	YES
8	PDGFC	PDGFC	PDGFC	1027	0.47	0.22	YES
9	COL5A2	COL5A2	COL5A2	1515	0.4	0.22	YES
10	COL6A3	COL6A3	COL6A3	1610	0.39	0.24	YES
11	ADCY5	ADCY5	ADCY5	1655	0.38	0.25	YES
12	PDGFRB	PDGFRB	PDGFRB	1827	0.36	0.27	YES
13	COL5A1	COL5A1	COL5A1	1869	0.36	0.28	YES
14	CAMK4	CAMK4	CAMK4	1898	0.35	0.3	YES
15	COL4A4	COL4A4	COL4A4	1915	0.35	0.32	YES
16	PRKAR2B	PRKAR2B	PRKAR2B	1976	0.34	0.34	YES
17	COL1A1	COL1A1	COL1A1	2056	0.33	0.36	YES
18	COL1A2	COL1A2	COL1A2	2072	0.33	0.37	YES
19	ADCY1	ADCY1	ADCY1	2094	0.33	0.39	YES
20	COL3A1	COL3A1	COL3A1	2096	0.33	0.41	YES
21	PDGFB	PDGFB	PDGFB	2332	0.3	0.42	YES
22	COL6A2	COL6A2	COL6A2	2351	0.3	0.43	YES
23	COL6A1	COL6A1	COL6A1	2445	0.29	0.44	YES
24	PDGFRA	PDGFRA	PDGFRA	2467	0.29	0.46	YES
25	ADCY4	ADCY4	ADCY4	2693	0.26	0.46	YES
26	PDGFD	PDGFD	PDGFD	2747	0.26	0.47	YES
27	THBS1	THBS1	THBS1	2820	0.25	0.48	YES
28	COL4A2	COL4A2	COL4A2	2950	0.23	0.49	YES
29	COL4A3	COL4A3	COL4A3	3036	0.22	0.5	YES
30	COL4A1	COL4A1	COL4A1	3083	0.22	0.51	YES
31	THBS3	THBS3	THBS3	3135	0.22	0.52	YES
32	PLAT	PLAT	PLAT	3258	0.2	0.52	YES
33	ADCY7	ADCY7	ADCY7	3504	0.18	0.52	YES
34	ITPR2	ITPR2	ITPR2	3553	0.18	0.53	YES
35	PIK3CA	PIK3CA	PIK3CA	3573	0.18	0.54	YES
36	FOXO1	FOXO1	FOXO1	3696	0.17	0.54	YES
37	STAT1	STAT1	STAT1	3797	0.16	0.54	YES
38	ADCY9	ADCY9	ADCY9	4351	0.13	0.52	NO
39	RICTOR	RICTOR	RICTOR	4620	0.12	0.51	NO
40	SOS1	SOS1	SOS1	5044	0.099	0.49	NO
41	RAPGEF1	RAPGEF1	RAPGEF1	5055	0.098	0.5	NO
42	FOXO4	FOXO4	FOXO4	5069	0.098	0.5	NO
43	PRKAR1A	PRKAR1A	PRKAR1A	5136	0.096	0.51	NO
44	CREB1	CREB1	CREB1	5330	0.088	0.5	NO
45	STAT5A	STAT5A	STAT5A	5529	0.082	0.49	NO
46	PIK3R1	PIK3R1	PIK3R1	5759	0.077	0.49	NO
47	STAT5B	STAT5B	STAT5B	5892	0.073	0.48	NO
48	PRKCE	PRKCE	PRKCE	5921	0.073	0.49	NO
49	NCK1	NCK1	NCK1	6008	0.07	0.48	NO
50	PDGFA	PDGFA	PDGFA	6122	0.068	0.48	NO
51	RASA1	RASA1	RASA1	6134	0.068	0.49	NO
52	MTOR	MTOR	MTOR	6358	0.063	0.48	NO
53	PTEN	PTEN	PTEN	6576	0.058	0.47	NO
54	GRB2	GRB2	GRB2	6785	0.054	0.46	NO
55	PRKACA	PRKACA	PRKACA	6809	0.054	0.46	NO
56	PLCG1	PLCG1	PLCG1	6814	0.053	0.46	NO
57	NR4A1	NR4A1	NR4A1	7094	0.048	0.45	NO
58	STAT3	STAT3	STAT3	7190	0.046	0.45	NO
59	PRKCA	PRKCA	PRKCA	7209	0.045	0.45	NO
60	PIK3CB	PIK3CB	PIK3CB	7239	0.045	0.45	NO
61	PRKCG	PRKCG	PRKCG	7292	0.044	0.45	NO
62	CRK	CRK	CRK	7369	0.043	0.45	NO
63	CHUK	CHUK	CHUK	7389	0.043	0.45	NO
64	KRAS	KRAS	KRAS	7479	0.041	0.45	NO
65	FURIN	FURIN	FURIN	7499	0.041	0.45	NO
66	MAP2K1	MAP2K1	MAP2K1	7607	0.039	0.45	NO
67	PDPK1	PDPK1	PDPK1	7609	0.039	0.45	NO
68	PRKACB	PRKACB	PRKACB	7719	0.037	0.44	NO
69	CDKN1B	CDKN1B	CDKN1B	7821	0.035	0.44	NO
70	CRKL	CRKL	CRKL	8665	0.022	0.4	NO
71	FOXO3	FOXO3	FOXO3	8826	0.02	0.39	NO
72	MAPK1	MAPK1	MAPK1	8927	0.018	0.38	NO
73	NRAS	NRAS	NRAS	8928	0.018	0.38	NO
74	BCAR1	BCAR1	BCAR1	8976	0.018	0.38	NO
75	MDM2	MDM2	MDM2	9123	0.016	0.38	NO
76	ADCY3	ADCY3	ADCY3	9240	0.014	0.37	NO
77	COL9A3	COL9A3	COL9A3	9365	0.012	0.36	NO
78	PHLPP1	PHLPP1	PHLPP1	9513	0.0099	0.36	NO
79	MAPKAP1	MAPKAP1	MAPKAP1	9533	0.0095	0.36	NO
80	CALM3	CALM3	CALM3	9751	0.0064	0.34	NO
81	YWHAB	YWHAB	YWHAB	9789	0.0059	0.34	NO
82	AKT1	AKT1	AKT1	9834	0.0053	0.34	NO
83	GSK3A	GSK3A	GSK3A	9855	0.0051	0.34	NO
84	CALM1	CALM1	CALM1	9912	0.0044	0.34	NO
85	NCK2	NCK2	NCK2	10123	0.0015	0.32	NO
86	CALM2	CALM2	CALM2	10364	-0.0018	0.31	NO
87	CASP9	CASP9	CASP9	10375	-0.0019	0.31	NO
88	STAT6	STAT6	STAT6	10446	-0.0031	0.31	NO
89	PRKAR2A	PRKAR2A	PRKAR2A	10560	-0.0047	0.3	NO
90	TSC2	TSC2	TSC2	10581	-0.005	0.3	NO
91	ITPR3	ITPR3	ITPR3	10607	-0.0054	0.3	NO
92	RAF1	RAF1	RAF1	10611	-0.0054	0.3	NO
93	AKT2	AKT2	AKT2	11018	-0.012	0.28	NO
94	PRKCD	PRKCD	PRKCD	11331	-0.016	0.26	NO
95	CDKN1A	CDKN1A	CDKN1A	11383	-0.017	0.26	NO
96	COL4A5	COL4A5	COL4A5	11699	-0.021	0.24	NO
97	SRC	SRC	SRC	12005	-0.027	0.23	NO
98	AKT1S1	AKT1S1	AKT1S1	12220	-0.03	0.22	NO
99	ADCY6	ADCY6	ADCY6	12296	-0.031	0.21	NO
100	ADRBK1	ADRBK1	ADRBK1	12321	-0.032	0.22	NO
101	PIK3R2	PIK3R2	PIK3R2	12407	-0.033	0.21	NO
102	THEM4	THEM4	THEM4	12626	-0.036	0.2	NO
103	CDK1	CDK1	CDK1	12971	-0.042	0.18	NO
104	GRB7	GRB7	GRB7	13041	-0.044	0.18	NO
105	HRAS	HRAS	HRAS	13243	-0.047	0.18	NO
106	COL2A1	COL2A1	COL2A1	13315	-0.048	0.17	NO
107	BAD	BAD	BAD	13679	-0.055	0.16	NO
108	MAP2K2	MAP2K2	MAP2K2	13800	-0.058	0.15	NO
109	MAPK3	MAPK3	MAPK3	13966	-0.061	0.15	NO
110	TRIB3	TRIB3	TRIB3	14604	-0.076	0.12	NO
111	PRKAR1B	PRKAR1B	PRKAR1B	15053	-0.088	0.097	NO
112	MLST8	MLST8	MLST8	15125	-0.09	0.098	NO
113	RPS6KB2	RPS6KB2	RPS6KB2	15463	-0.1	0.085	NO
114	COL9A1	COL9A1	COL9A1	17094	-0.21	0.0063	NO
115	COL9A2	COL9A2	COL9A2	17242	-0.24	0.012	NO
116	PLG	PLG	PLG	17921	-0.52	0.0042	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 CYTOKINE CYTOKINE RECEPTOR INTERACTION.

Figure S60. 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

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 FRUCTOSE AND MANNOSE METABOLISM	34	genes.ES.table	0.5	1.7	0.016	0.94	0.82	0.62	0.3	0.44	0.32	0.23
KEGG PARKINSONS DISEASE	109	genes.ES.table	0.42	1.6	0.064	0.76	0.86	0.55	0.34	0.36	0.29	0.2
KEGG PATHOGENIC ESCHERICHIA COLI INFECTION	52	genes.ES.table	0.49	1.8	0.0021	1	0.53	0.19	0.12	0.17	0.8	0.44
KEGG SYSTEMIC LUPUS ERYTHEMATOSUS	116	genes.ES.table	0.76	1.7	0.0022	1	0.78	0.65	0.15	0.55	0.34	0.24
REACTOME TRANSLATION	146	genes.ES.table	0.49	1.6	0.1	0.76	0.89	0.13	0.12	0.12	0.34	0.21
REACTOME MEIOSIS	97	genes.ES.table	0.67	1.7	0.012	1	0.78	0.41	0.12	0.37	0.38	0.26
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE	109	genes.ES.table	0.55	1.6	0.083	0.72	0.86	0.16	0.12	0.14	0.27	0.19
REACTOME RNA POL I TRANSCRIPTION	77	genes.ES.table	0.73	1.7	0.016	0.75	0.82	0.51	0.12	0.45	0.25	0.19
REACTOME PROTEIN FOLDING	48	genes.ES.table	0.38	1.7	0.027	0.86	0.82	0.21	0.18	0.17	0.29	0.22
REACTOME METABOLISM OF PROTEINS	415	genes.ES.table	0.31	1.7	0.027	1	0.75	0.26	0.28	0.19	0.43	0.29

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	TUBB8	TUBB8	TUBB8	54	1.2	0.19	YES
2	TUBA1A	TUBA1A	TUBA1A	439	0.5	0.24	YES
3	TUBB2A	TUBB2A	TUBB2A	489	0.46	0.31	YES
4	TUBA3D	TUBA3D	TUBA3D	640	0.38	0.37	YES
5	TUBB3	TUBB3	TUBB3	699	0.36	0.42	YES
6	TUBA3E	TUBA3E	TUBA3E	1258	0.25	0.43	YES
7	TUBAL3	TUBAL3	TUBAL3	1544	0.22	0.44	YES
8	TUBB2B	TUBB2B	TUBB2B	1858	0.19	0.46	YES
9	CD14	CD14	CD14	2067	0.17	0.47	YES
10	TUBA1C	TUBA1C	TUBA1C	2168	0.16	0.49	YES
11	WAS	WAS	WAS	2740	0.13	0.48	NO
12	TUBB6	TUBB6	TUBB6	3286	0.11	0.47	NO
13	TUBA8	TUBA8	TUBA8	3754	0.095	0.46	NO
14	ARPC5L	ARPC5L	ARPC5L	4395	0.078	0.43	NO
15	TUBA4A	TUBA4A	TUBA4A	4833	0.068	0.42	NO
16	TUBA1B	TUBA1B	TUBA1B	4843	0.068	0.43	NO
17	OCLN	OCLN	OCLN	5496	0.054	0.4	NO
18	ARPC1B	ARPC1B	ARPC1B	5625	0.052	0.4	NO
19	ACTB	ACTB	ACTB	5716	0.05	0.41	NO
20	ACTG1	ACTG1	ACTG1	6495	0.037	0.37	NO
21	HCLS1	HCLS1	HCLS1	6693	0.033	0.36	NO
22	ARPC1A	ARPC1A	ARPC1A	6950	0.029	0.35	NO
23	KRT18	KRT18	KRT18	7120	0.026	0.35	NO
24	YWHAQ	YWHAQ	YWHAQ	7278	0.024	0.34	NO
25	TUBB	TUBB	TUBB	7490	0.02	0.33	NO
26	LY96	LY96	LY96	7648	0.018	0.33	NO
27	CTNNB1	CTNNB1	CTNNB1	7721	0.017	0.33	NO
28	ARPC2	ARPC2	ARPC2	7767	0.016	0.33	NO
29	CTTN	CTTN	CTTN	7800	0.016	0.33	NO
30	ARPC4	ARPC4	ARPC4	8177	0.01	0.31	NO
31	RHOA	RHOA	RHOA	8429	0.0065	0.3	NO
32	ARPC5	ARPC5	ARPC5	9063	-0.0026	0.26	NO
33	EZR	EZR	EZR	9246	-0.0052	0.25	NO
34	NCK2	NCK2	NCK2	9291	-0.0057	0.25	NO
35	FYN	FYN	FYN	11312	-0.034	0.14	NO
36	ITGB1	ITGB1	ITGB1	11612	-0.039	0.13	NO
37	TLR4	TLR4	TLR4	11816	-0.042	0.13	NO
38	YWHAZ	YWHAZ	YWHAZ	11934	-0.043	0.13	NO
39	ABL1	ABL1	ABL1	12430	-0.051	0.11	NO
40	CLDN1	CLDN1	CLDN1	12947	-0.059	0.088	NO
41	NCK1	NCK1	NCK1	12961	-0.059	0.096	NO
42	CDC42	CDC42	CDC42	13006	-0.06	0.1	NO
43	CDH1	CDH1	CDH1	13044	-0.061	0.11	NO
44	ARHGEF2	ARHGEF2	ARHGEF2	13476	-0.068	0.098	NO
45	WASL	WASL	WASL	13602	-0.07	0.1	NO
46	TUBB1	TUBB1	TUBB1	13785	-0.073	0.1	NO
47	PRKCA	PRKCA	PRKCA	15178	-0.1	0.041	NO
48	NCL	NCL	NCL	15559	-0.11	0.037	NO
49	ROCK1	ROCK1	ROCK1	16396	-0.13	0.011	NO
50	ARPC3	ARPC3	ARPC3	16440	-0.14	0.03	NO
51	TLR5	TLR5	TLR5	17321	-0.18	0.0093	NO
52	ROCK2	ROCK2	ROCK2	17334	-0.18	0.037	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 FRUCTOSE AND MANNOSE METABOLISM.

Figure S62. 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 PARKINSONS DISEASE

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	3	1.7	0.063	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	47	1.2	0.11	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	80	1.1	0.14	YES
4	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	150	0.88	0.17	YES
5	HIST2H3C	HIST2H3C	HIST2H3C	195	0.78	0.2	YES
6	HIST2H3D	HIST2H3D	HIST2H3D	250	0.71	0.22	YES
7	GTF2H2B	GTF2H2B	GTF2H2B	299	0.64	0.24	YES
8	HIST1H2BN	HIST1H2BN	HIST1H2BN	344	0.6	0.26	YES
9	HIST1H4J	HIST1H4J	HIST1H4J	408	0.53	0.28	YES
10	HIST1H4I	HIST1H4I	HIST1H4I	503	0.46	0.29	YES
11	GTF2H2	GTF2H2	GTF2H2	511	0.45	0.31	YES
12	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	529	0.44	0.32	YES
13	HIST1H2BE	HIST1H2BE	HIST1H2BE	566	0.42	0.34	YES
14	HIST1H4A	HIST1H4A	HIST1H4A	569	0.42	0.35	YES
15	HIST1H2BL	HIST1H2BL	HIST1H2BL	583	0.41	0.37	YES
16	HIST2H4A	HIST2H4A	HIST2H4A	586	0.41	0.38	YES
17	HIST1H3H	HIST1H3H	HIST1H3H	828	0.32	0.38	YES
18	HIST3H2BB	HIST3H2BB	HIST3H2BB	845	0.32	0.39	YES
19	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	858	0.32	0.4	YES
20	HIST1H4B	HIST1H4B	HIST1H4B	873	0.31	0.41	YES
21	HIST1H4D	HIST1H4D	HIST1H4D	925	0.3	0.42	YES
22	HIST1H3D	HIST1H3D	HIST1H3D	927	0.3	0.43	YES
23	HIST1H4E	HIST1H4E	HIST1H4E	949	0.29	0.44	YES
24	HIST1H3B	HIST1H3B	HIST1H3B	960	0.29	0.45	YES
25	HIST1H4C	HIST1H4C	HIST1H4C	966	0.29	0.46	YES
26	HIST1H3F	HIST1H3F	HIST1H3F	1080	0.27	0.47	YES
27	HIST1H3J	HIST1H3J	HIST1H3J	1221	0.25	0.47	YES
28	HIST1H2BI	HIST1H2BI	HIST1H2BI	1359	0.23	0.47	YES
29	HIST1H3I	HIST1H3I	HIST1H3I	1413	0.23	0.48	YES
30	HIST1H4H	HIST1H4H	HIST1H4H	1474	0.22	0.48	YES
31	HIST1H2BC	HIST1H2BC	HIST1H2BC	1634	0.21	0.48	YES
32	POLR2I	POLR2I	POLR2I	1638	0.21	0.49	YES
33	HIST1H2AB	HIST1H2AB	HIST1H2AB	1699	0.2	0.49	YES
34	HIST1H2BG	HIST1H2BG	HIST1H2BG	1706	0.2	0.5	YES
35	HIST1H2BH	HIST1H2BH	HIST1H2BH	1738	0.2	0.5	YES
36	HIST1H3C	HIST1H3C	HIST1H3C	1745	0.2	0.51	YES
37	HIST1H3G	HIST1H3G	HIST1H3G	1950	0.18	0.51	YES
38	HIST1H3A	HIST1H3A	HIST1H3A	2045	0.17	0.51	YES
39	HIST1H2BM	HIST1H2BM	HIST1H2BM	2066	0.17	0.51	YES
40	HIST1H2BF	HIST1H2BF	HIST1H2BF	2121	0.17	0.52	YES
41	POLR2L	POLR2L	POLR2L	2179	0.16	0.52	YES
42	TAF10	TAF10	TAF10	2450	0.15	0.51	NO
43	H3F3A	H3F3A	H3F3A	2480	0.14	0.51	NO
44	POLR2G	POLR2G	POLR2G	2585	0.14	0.51	NO
45	H2AFX	H2AFX	H2AFX	2653	0.14	0.51	NO
46	POLR3K	POLR3K	POLR3K	3258	0.11	0.48	NO
47	TCEB2	TCEB2	TCEB2	3368	0.11	0.48	NO
48	HIST1H2BK	HIST1H2BK	HIST1H2BK	3383	0.11	0.48	NO
49	LSM10	LSM10	LSM10	3445	0.1	0.48	NO
50	HIST1H2AE	HIST1H2AE	HIST1H2AE	3638	0.098	0.48	NO
51	SNAPC5	SNAPC5	SNAPC5	4039	0.087	0.46	NO
52	POLR2H	POLR2H	POLR2H	4058	0.086	0.46	NO
53	COBRA1	COBRA1	COBRA1	4475	0.076	0.44	NO
54	POLR1C	POLR1C	POLR1C	4567	0.074	0.44	NO
55	SUPT4H1	SUPT4H1	SUPT4H1	4874	0.067	0.42	NO
56	MAPK3	MAPK3	MAPK3	5061	0.063	0.41	NO
57	CSTF1	CSTF1	CSTF1	5154	0.061	0.41	NO
58	POLR2F	POLR2F	POLR2F	5192	0.06	0.41	NO
59	HIST1H2BD	HIST1H2BD	HIST1H2BD	5411	0.056	0.4	NO
60	POLR3H	POLR3H	POLR3H	5423	0.056	0.4	NO
61	THOC4	THOC4	THOC4	5453	0.055	0.4	NO
62	POLR2C	POLR2C	POLR2C	5632	0.052	0.4	NO
63	POLR2J	POLR2J	POLR2J	5656	0.052	0.4	NO
64	SNRPB	SNRPB	SNRPB	5838	0.049	0.39	NO
65	POLR2D	POLR2D	POLR2D	6098	0.044	0.38	NO
66	SNRPF	SNRPF	SNRPF	6124	0.043	0.38	NO
67	CTDP1	CTDP1	CTDP1	6159	0.042	0.37	NO
68	U2AF1	U2AF1	U2AF1	6433	0.038	0.36	NO
69	ERCC2	ERCC2	ERCC2	6471	0.037	0.36	NO
70	BRF2	BRF2	BRF2	6489	0.037	0.36	NO
71	CDK9	CDK9	CDK9	6514	0.036	0.36	NO
72	POLR2E	POLR2E	POLR2E	6525	0.036	0.36	NO
73	CLP1	CLP1	CLP1	6575	0.035	0.36	NO
74	POLRMT	POLRMT	POLRMT	6651	0.034	0.36	NO
75	GTF3C5	GTF3C5	GTF3C5	6759	0.032	0.35	NO
76	RNPS1	RNPS1	RNPS1	6825	0.031	0.35	NO
77	POLR3E	POLR3E	POLR3E	6853	0.031	0.35	NO
78	RDBP	RDBP	RDBP	6867	0.03	0.35	NO
79	POLR3D	POLR3D	POLR3D	6925	0.03	0.35	NO
80	ZNF143	ZNF143	ZNF143	6969	0.029	0.35	NO
81	POLR3C	POLR3C	POLR3C	7034	0.028	0.34	NO
82	TH1L	TH1L	TH1L	7351	0.023	0.33	NO
83	CPSF1	CPSF1	CPSF1	7392	0.022	0.32	NO
84	H2AFZ	H2AFZ	H2AFZ	7459	0.021	0.32	NO
85	POLR3B	POLR3B	POLR3B	7745	0.016	0.31	NO
86	TBP	TBP	TBP	7825	0.015	0.3	NO
87	EHMT2	EHMT2	EHMT2	7964	0.014	0.3	NO
88	GTF2H4	GTF2H4	GTF2H4	8021	0.013	0.29	NO
89	WHSC2	WHSC2	WHSC2	8068	0.012	0.29	NO
90	SLBP	SLBP	SLBP	8321	0.0084	0.28	NO
91	TAF6	TAF6	TAF6	8522	0.005	0.27	NO
92	TAF9	TAF9	TAF9	8588	0.0039	0.26	NO
93	GTF2E2	GTF2E2	GTF2E2	8600	0.0037	0.26	NO
94	SNRPG	SNRPG	SNRPG	8646	0.0032	0.26	NO
95	BRF1	BRF1	BRF1	8790	0.00098	0.25	NO
96	CPSF3	CPSF3	CPSF3	8854	0.00011	0.25	NO
97	HIST1H2AC	HIST1H2AC	HIST1H2AC	9002	-0.0019	0.24	NO
98	SNAPC2	SNAPC2	SNAPC2	9015	-0.002	0.24	NO
99	ELL	ELL	ELL	9157	-0.0038	0.23	NO
100	MNAT1	MNAT1	MNAT1	9325	-0.0062	0.22	NO
101	TCEA1	TCEA1	TCEA1	9356	-0.0068	0.22	NO
102	DHX38	DHX38	DHX38	9407	-0.0075	0.22	NO
103	TAF1C	TAF1C	TAF1C	9415	-0.0076	0.22	NO
104	U2AF2	U2AF2	U2AF2	9637	-0.011	0.21	NO
105	ERCC3	ERCC3	ERCC3	9895	-0.014	0.19	NO
106	POLR1B	POLR1B	POLR1B	10021	-0.016	0.19	NO
107	GTF2E1	GTF2E1	GTF2E1	10060	-0.016	0.18	NO
108	MAGOH	MAGOH	MAGOH	10154	-0.018	0.18	NO
109	GTF2F1	GTF2F1	GTF2F1	10547	-0.023	0.16	NO
110	TCEB1	TCEB1	TCEB1	10581	-0.024	0.16	NO
111	POLR1D	POLR1D	POLR1D	10597	-0.024	0.16	NO
112	POLR2B	POLR2B	POLR2B	10850	-0.028	0.14	NO
113	SNAPC4	SNAPC4	SNAPC4	10912	-0.028	0.14	NO
114	SUPT5H	SUPT5H	SUPT5H	10998	-0.03	0.14	NO
115	POLR3A	POLR3A	POLR3A	11016	-0.03	0.14	NO
116	GTF2H3	GTF2H3	GTF2H3	11145	-0.032	0.13	NO
117	CCNH	CCNH	CCNH	11147	-0.032	0.13	NO
118	GTF3C2	GTF3C2	GTF3C2	11183	-0.032	0.13	NO
119	NCBP1	NCBP1	NCBP1	11309	-0.034	0.13	NO
120	GTF3C3	GTF3C3	GTF3C3	11324	-0.034	0.13	NO
121	TAF5	TAF5	TAF5	11406	-0.036	0.12	NO
122	NFX1	NFX1	NFX1	11587	-0.038	0.12	NO
123	SNRPE	SNRPE	SNRPE	11591	-0.038	0.12	NO
124	SNRPD3	SNRPD3	SNRPD3	11718	-0.04	0.11	NO
125	PABPN1	PABPN1	PABPN1	11785	-0.041	0.11	NO
126	CSTF2	CSTF2	CSTF2	11825	-0.042	0.11	NO
127	TAF4	TAF4	TAF4	11922	-0.043	0.1	NO
128	RBM8A	RBM8A	RBM8A	11931	-0.043	0.11	NO
129	POLR3F	POLR3F	POLR3F	12224	-0.048	0.091	NO
130	CPSF7	CPSF7	CPSF7	12261	-0.048	0.091	NO
131	NUDT21	NUDT21	NUDT21	12310	-0.049	0.09	NO
132	SSRP1	SSRP1	SSRP1	12359	-0.05	0.089	NO
133	GTF2A2	GTF2A2	GTF2A2	12493	-0.052	0.084	NO
134	GTF2H1	GTF2H1	GTF2H1	12545	-0.053	0.083	NO
135	ZNF473	ZNF473	ZNF473	12813	-0.057	0.07	NO
136	RNMT	RNMT	RNMT	12883	-0.058	0.068	NO
137	GTF3C4	GTF3C4	GTF3C4	12897	-0.058	0.07	NO
138	GTF2B	GTF2B	GTF2B	12905	-0.058	0.072	NO
139	NFIB	NFIB	NFIB	12928	-0.059	0.072	NO
140	H3F3B	H3F3B	H3F3B	13149	-0.062	0.062	NO
141	TAF11	TAF11	TAF11	13188	-0.063	0.063	NO
142	TAF12	TAF12	TAF12	13367	-0.066	0.055	NO
143	PTRF	PTRF	PTRF	13646	-0.071	0.042	NO
144	HIST2H2BE	HIST2H2BE	HIST2H2BE	13878	-0.075	0.032	NO
145	SUPT16H	SUPT16H	SUPT16H	13888	-0.075	0.034	NO
146	HIST1H2AD	HIST1H2AD	HIST1H2AD	13897	-0.075	0.036	NO
147	SNAPC3	SNAPC3	SNAPC3	13925	-0.075	0.038	NO
148	NCBP2	NCBP2	NCBP2	13939	-0.076	0.04	NO
149	MBD2	MBD2	MBD2	14074	-0.078	0.035	NO
150	POLR2A	POLR2A	POLR2A	14271	-0.082	0.027	NO
151	TCEB3	TCEB3	TCEB3	14412	-0.084	0.023	NO
152	POLR1A	POLR1A	POLR1A	14554	-0.087	0.018	NO
153	LSM11	LSM11	LSM11	14627	-0.089	0.017	NO
154	CPSF2	CPSF2	CPSF2	14733	-0.091	0.015	NO
155	SRRM1	SRRM1	SRRM1	14749	-0.091	0.017	NO
156	UBTF	UBTF	UBTF	14756	-0.092	0.02	NO
157	RNGTT	RNGTT	RNGTT	14824	-0.093	0.02	NO
158	CDC40	CDC40	CDC40	15070	-0.098	0.0098	NO
159	GTF2F2	GTF2F2	GTF2F2	15083	-0.099	0.013	NO
160	HIST4H4	HIST4H4	HIST4H4	15165	-0.1	0.012	NO
161	POLR2K	POLR2K	POLR2K	15179	-0.1	0.015	NO
162	CCNT2	CCNT2	CCNT2	15265	-0.1	0.014	NO
163	LZTS1	LZTS1	LZTS1	15299	-0.1	0.016	NO
164	PAPOLA	PAPOLA	PAPOLA	15332	-0.1	0.018	NO
165	TFB2M	TFB2M	TFB2M	15336	-0.1	0.022	NO
166	TFAM	TFAM	TFAM	15541	-0.11	0.014	NO
167	RRN3	RRN3	RRN3	15588	-0.11	0.016	NO
168	CCNT1	CCNT1	CCNT1	15695	-0.11	0.014	NO
169	CDK7	CDK7	CDK7	15725	-0.11	0.016	NO
170	HIST1H3E	HIST1H3E	HIST1H3E	15748	-0.11	0.02	NO
171	CSTF3	CSTF3	CSTF3	15812	-0.12	0.02	NO
172	GTF2A1	GTF2A1	GTF2A1	16021	-0.12	0.013	NO
173	PCF11	PCF11	PCF11	16520	-0.14	-0.0098	NO
174	ERCC6	ERCC6	ERCC6	16548	-0.14	-0.0062	NO
175	TAF4B	TAF4B	TAF4B	16864	-0.15	-0.018	NO
176	TAF13	TAF13	TAF13	16901	-0.16	-0.014	NO
177	CBX3	CBX3	CBX3	16917	-0.16	-0.0095	NO
178	MTERF	MTERF	MTERF	17009	-0.16	-0.0086	NO
179	POU2F1	POU2F1	POU2F1	17060	-0.16	-0.0054	NO
180	KAT2B	KAT2B	KAT2B	17096	-0.16	-0.0013	NO
181	POLR3GL	POLR3GL	POLR3GL	17103	-0.16	0.0045	NO
182	UPF3B	UPF3B	UPF3B	17332	-0.18	-0.0016	NO
183	TAF1B	TAF1B	TAF1B	17394	-0.18	0.0018	NO
184	TAF1	TAF1	TAF1	17417	-0.19	0.0076	NO
185	TAF1A	TAF1A	TAF1A	17489	-0.2	0.011	NO
186	SNAPC1	SNAPC1	SNAPC1	17656	-0.22	0.0095	NO
187	SSB	SSB	SSB	17847	-0.26	0.0084	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 PARKINSONS DISEASE.

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

genes ES table in pathway: KEGG PATHOGENIC ESCHERICHIA COLI INFECTION

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	3	1.7	0.076	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	47	1.2	0.13	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	80	1.1	0.18	YES
4	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	150	0.88	0.21	YES
5	HIST2H3C	HIST2H3C	HIST2H3C	195	0.78	0.25	YES
6	HIST2H3D	HIST2H3D	HIST2H3D	250	0.71	0.28	YES
7	GTF2H2B	GTF2H2B	GTF2H2B	299	0.64	0.3	YES
8	HIST1H2BN	HIST1H2BN	HIST1H2BN	344	0.6	0.33	YES
9	HIST1H4J	HIST1H4J	HIST1H4J	408	0.53	0.35	YES
10	HIST1H4I	HIST1H4I	HIST1H4I	503	0.46	0.36	YES
11	GTF2H2	GTF2H2	GTF2H2	511	0.45	0.38	YES
12	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	529	0.44	0.4	YES
13	HIST1H2BE	HIST1H2BE	HIST1H2BE	566	0.42	0.42	YES
14	HIST1H4A	HIST1H4A	HIST1H4A	569	0.42	0.44	YES
15	HIST1H2BL	HIST1H2BL	HIST1H2BL	583	0.41	0.45	YES
16	HIST2H4A	HIST2H4A	HIST2H4A	586	0.41	0.47	YES
17	HIST1H3H	HIST1H3H	HIST1H3H	828	0.32	0.47	YES
18	HIST3H2BB	HIST3H2BB	HIST3H2BB	845	0.32	0.49	YES
19	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	858	0.32	0.5	YES
20	HIST1H4B	HIST1H4B	HIST1H4B	873	0.31	0.51	YES
21	HIST1H4D	HIST1H4D	HIST1H4D	925	0.3	0.52	YES
22	HIST1H3D	HIST1H3D	HIST1H3D	927	0.3	0.54	YES
23	HIST1H4E	HIST1H4E	HIST1H4E	949	0.29	0.55	YES
24	HIST1H3B	HIST1H3B	HIST1H3B	960	0.29	0.56	YES
25	HIST1H4C	HIST1H4C	HIST1H4C	966	0.29	0.57	YES
26	HIST1H3F	HIST1H3F	HIST1H3F	1080	0.27	0.58	YES
27	HIST1H3J	HIST1H3J	HIST1H3J	1221	0.25	0.58	YES
28	HIST1H2BI	HIST1H2BI	HIST1H2BI	1359	0.23	0.59	YES
29	HIST1H3I	HIST1H3I	HIST1H3I	1413	0.23	0.6	YES
30	HIST1H4H	HIST1H4H	HIST1H4H	1474	0.22	0.6	YES
31	HIST1H2BC	HIST1H2BC	HIST1H2BC	1634	0.21	0.6	YES
32	HIST1H2AB	HIST1H2AB	HIST1H2AB	1699	0.2	0.61	YES
33	HIST1H2BG	HIST1H2BG	HIST1H2BG	1706	0.2	0.62	YES
34	HIST1H2BH	HIST1H2BH	HIST1H2BH	1738	0.2	0.62	YES
35	HIST1H3C	HIST1H3C	HIST1H3C	1745	0.2	0.63	YES
36	HIST1H3G	HIST1H3G	HIST1H3G	1950	0.18	0.63	YES
37	HIST1H3A	HIST1H3A	HIST1H3A	2045	0.17	0.63	YES
38	HIST1H2BM	HIST1H2BM	HIST1H2BM	2066	0.17	0.64	YES
39	HIST1H2BF	HIST1H2BF	HIST1H2BF	2121	0.17	0.64	YES
40	POLR2L	POLR2L	POLR2L	2179	0.16	0.65	YES
41	H3F3A	H3F3A	H3F3A	2480	0.14	0.64	NO
42	H2AFX	H2AFX	H2AFX	2653	0.14	0.63	NO
43	POLR3K	POLR3K	POLR3K	3258	0.11	0.6	NO
44	HIST1H2BK	HIST1H2BK	HIST1H2BK	3383	0.11	0.6	NO
45	HIST1H2AE	HIST1H2AE	HIST1H2AE	3638	0.098	0.59	NO
46	SNAPC5	SNAPC5	SNAPC5	4039	0.087	0.57	NO
47	POLR2H	POLR2H	POLR2H	4058	0.086	0.58	NO
48	POLR1C	POLR1C	POLR1C	4567	0.074	0.55	NO
49	MAPK3	MAPK3	MAPK3	5061	0.063	0.53	NO
50	POLR2F	POLR2F	POLR2F	5192	0.06	0.52	NO
51	HIST1H2BD	HIST1H2BD	HIST1H2BD	5411	0.056	0.51	NO
52	POLR3H	POLR3H	POLR3H	5423	0.056	0.51	NO
53	ERCC2	ERCC2	ERCC2	6471	0.037	0.46	NO
54	BRF2	BRF2	BRF2	6489	0.037	0.46	NO
55	POLR2E	POLR2E	POLR2E	6525	0.036	0.46	NO
56	POLRMT	POLRMT	POLRMT	6651	0.034	0.45	NO
57	GTF3C5	GTF3C5	GTF3C5	6759	0.032	0.45	NO
58	POLR3E	POLR3E	POLR3E	6853	0.031	0.44	NO
59	POLR3D	POLR3D	POLR3D	6925	0.03	0.44	NO
60	ZNF143	ZNF143	ZNF143	6969	0.029	0.44	NO
61	POLR3C	POLR3C	POLR3C	7034	0.028	0.44	NO
62	H2AFZ	H2AFZ	H2AFZ	7459	0.021	0.42	NO
63	POLR3B	POLR3B	POLR3B	7745	0.016	0.4	NO
64	TBP	TBP	TBP	7825	0.015	0.4	NO
65	EHMT2	EHMT2	EHMT2	7964	0.014	0.39	NO
66	GTF2H4	GTF2H4	GTF2H4	8021	0.013	0.39	NO
67	BRF1	BRF1	BRF1	8790	0.00098	0.34	NO
68	HIST1H2AC	HIST1H2AC	HIST1H2AC	9002	-0.0019	0.33	NO
69	SNAPC2	SNAPC2	SNAPC2	9015	-0.002	0.33	NO
70	MNAT1	MNAT1	MNAT1	9325	-0.0062	0.31	NO
71	TAF1C	TAF1C	TAF1C	9415	-0.0076	0.31	NO
72	ERCC3	ERCC3	ERCC3	9895	-0.014	0.28	NO
73	POLR1B	POLR1B	POLR1B	10021	-0.016	0.28	NO
74	POLR1D	POLR1D	POLR1D	10597	-0.024	0.25	NO
75	SNAPC4	SNAPC4	SNAPC4	10912	-0.028	0.23	NO
76	POLR3A	POLR3A	POLR3A	11016	-0.03	0.22	NO
77	GTF2H3	GTF2H3	GTF2H3	11145	-0.032	0.22	NO
78	CCNH	CCNH	CCNH	11147	-0.032	0.22	NO
79	GTF3C2	GTF3C2	GTF3C2	11183	-0.032	0.22	NO
80	GTF3C3	GTF3C3	GTF3C3	11324	-0.034	0.21	NO
81	POLR3F	POLR3F	POLR3F	12224	-0.048	0.17	NO
82	GTF2H1	GTF2H1	GTF2H1	12545	-0.053	0.15	NO
83	GTF3C4	GTF3C4	GTF3C4	12897	-0.058	0.13	NO
84	NFIB	NFIB	NFIB	12928	-0.059	0.14	NO
85	H3F3B	H3F3B	H3F3B	13149	-0.062	0.12	NO
86	PTRF	PTRF	PTRF	13646	-0.071	0.1	NO
87	HIST2H2BE	HIST2H2BE	HIST2H2BE	13878	-0.075	0.091	NO
88	HIST1H2AD	HIST1H2AD	HIST1H2AD	13897	-0.075	0.093	NO
89	SNAPC3	SNAPC3	SNAPC3	13925	-0.075	0.095	NO
90	MBD2	MBD2	MBD2	14074	-0.078	0.09	NO
91	POLR1A	POLR1A	POLR1A	14554	-0.087	0.068	NO
92	UBTF	UBTF	UBTF	14756	-0.092	0.06	NO
93	HIST4H4	HIST4H4	HIST4H4	15165	-0.1	0.042	NO
94	POLR2K	POLR2K	POLR2K	15179	-0.1	0.046	NO
95	LZTS1	LZTS1	LZTS1	15299	-0.1	0.044	NO
96	TFB2M	TFB2M	TFB2M	15336	-0.1	0.047	NO
97	TFAM	TFAM	TFAM	15541	-0.11	0.04	NO
98	RRN3	RRN3	RRN3	15588	-0.11	0.043	NO
99	CDK7	CDK7	CDK7	15725	-0.11	0.04	NO
100	HIST1H3E	HIST1H3E	HIST1H3E	15748	-0.11	0.044	NO
101	ERCC6	ERCC6	ERCC6	16548	-0.14	0.0055	NO
102	CBX3	CBX3	CBX3	16917	-0.16	-0.008	NO
103	MTERF	MTERF	MTERF	17009	-0.16	-0.0059	NO
104	POU2F1	POU2F1	POU2F1	17060	-0.16	-0.0013	NO
105	KAT2B	KAT2B	KAT2B	17096	-0.16	0.0042	NO
106	POLR3GL	POLR3GL	POLR3GL	17103	-0.16	0.011	NO
107	TAF1B	TAF1B	TAF1B	17394	-0.18	0.0034	NO
108	TAF1A	TAF1A	TAF1A	17489	-0.2	0.0069	NO
109	SNAPC1	SNAPC1	SNAPC1	17656	-0.22	0.0074	NO
110	SSB	SSB	SSB	17847	-0.26	0.0083	NO

Figure S65. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PATHOGENIC ESCHERICHIA COLI INFECTION.

Figure S66. 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 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	HIST1H4K	HIST1H4K	HIST1H4K	3	1.7	0.089	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	47	1.2	0.15	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	80	1.1	0.21	YES
4	FKBP6	FKBP6	FKBP6	134	0.93	0.25	YES
5	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	150	0.88	0.3	YES
6	HIST1H2BN	HIST1H2BN	HIST1H2BN	344	0.6	0.32	YES
7	HIST1H4J	HIST1H4J	HIST1H4J	408	0.53	0.34	YES
8	STAG3	STAG3	STAG3	448	0.49	0.37	YES
9	HIST1H4I	HIST1H4I	HIST1H4I	503	0.46	0.39	YES
10	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	529	0.44	0.41	YES
11	HIST1H2BE	HIST1H2BE	HIST1H2BE	566	0.42	0.43	YES
12	HIST1H4A	HIST1H4A	HIST1H4A	569	0.42	0.45	YES
13	HIST1H2BL	HIST1H2BL	HIST1H2BL	583	0.41	0.47	YES
14	HIST2H4A	HIST2H4A	HIST2H4A	586	0.41	0.49	YES
15	HIST3H2BB	HIST3H2BB	HIST3H2BB	845	0.32	0.5	YES
16	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	858	0.32	0.51	YES
17	HIST1H4B	HIST1H4B	HIST1H4B	873	0.31	0.53	YES
18	HIST1H4D	HIST1H4D	HIST1H4D	925	0.3	0.54	YES
19	HIST1H4E	HIST1H4E	HIST1H4E	949	0.29	0.56	YES
20	HIST1H4C	HIST1H4C	HIST1H4C	966	0.29	0.57	YES
21	TERT	TERT	TERT	1177	0.26	0.57	YES
22	HIST1H2BI	HIST1H2BI	HIST1H2BI	1359	0.23	0.57	YES
23	HIST1H4H	HIST1H4H	HIST1H4H	1474	0.22	0.58	YES
24	HIST1H2BC	HIST1H2BC	HIST1H2BC	1634	0.21	0.58	YES
25	HIST1H2AB	HIST1H2AB	HIST1H2AB	1699	0.2	0.59	YES
26	HIST1H2BG	HIST1H2BG	HIST1H2BG	1706	0.2	0.6	YES
27	REC8	REC8	REC8	1710	0.2	0.61	YES
28	HIST1H2BH	HIST1H2BH	HIST1H2BH	1738	0.2	0.62	YES
29	HIST1H2BM	HIST1H2BM	HIST1H2BM	2066	0.17	0.61	NO
30	HIST1H2BF	HIST1H2BF	HIST1H2BF	2121	0.17	0.61	NO
31	H2AFX	H2AFX	H2AFX	2653	0.14	0.59	NO
32	HIST1H2BK	HIST1H2BK	HIST1H2BK	3383	0.11	0.56	NO
33	HIST1H2AE	HIST1H2AE	HIST1H2AE	3638	0.098	0.55	NO
34	POLD1	POLD1	POLD1	3930	0.09	0.54	NO
35	RUVBL2	RUVBL2	RUVBL2	4079	0.086	0.53	NO
36	PCNA	PCNA	PCNA	4483	0.076	0.51	NO
37	ACD	ACD	ACD	4657	0.071	0.51	NO
38	SMC1B	SMC1B	SMC1B	4679	0.071	0.51	NO
39	OIP5	OIP5	OIP5	5130	0.062	0.49	NO
40	POLA2	POLA2	POLA2	5204	0.06	0.49	NO
41	NHP2	NHP2	NHP2	5248	0.059	0.49	NO
42	WRAP53	WRAP53	WRAP53	5332	0.057	0.49	NO
43	HIST1H2BD	HIST1H2BD	HIST1H2BD	5411	0.056	0.48	NO
44	PRIM2	PRIM2	PRIM2	5437	0.055	0.49	NO
45	POLE2	POLE2	POLE2	5903	0.047	0.46	NO
46	RFC2	RFC2	RFC2	5972	0.046	0.46	NO
47	POLD2	POLD2	POLD2	6370	0.039	0.44	NO
48	POLD4	POLD4	POLD4	6429	0.038	0.44	NO
49	CENPN	CENPN	CENPN	6430	0.038	0.44	NO
50	UBE2I	UBE2I	UBE2I	6715	0.033	0.43	NO
51	RFC5	RFC5	RFC5	6728	0.033	0.43	NO
52	H2AFZ	H2AFZ	H2AFZ	7459	0.021	0.39	NO
53	RPA2	RPA2	RPA2	7520	0.02	0.39	NO
54	RPA3	RPA3	RPA3	7935	0.014	0.36	NO
55	CENPP	CENPP	CENPP	7944	0.014	0.36	NO
56	RPA1	RPA1	RPA1	8220	0.0097	0.35	NO
57	PRIM1	PRIM1	PRIM1	8281	0.0088	0.35	NO
58	RUVBL1	RUVBL1	RUVBL1	8432	0.0064	0.34	NO
59	LMNA	LMNA	LMNA	8487	0.0056	0.34	NO
60	HIST1H2AC	HIST1H2AC	HIST1H2AC	9002	-0.0019	0.31	NO
61	FEN1	FEN1	FEN1	9084	-0.0028	0.3	NO
62	CENPO	CENPO	CENPO	9267	-0.0054	0.29	NO
63	TINF2	TINF2	TINF2	9273	-0.0055	0.29	NO
64	RBBP7	RBBP7	RBBP7	9448	-0.0081	0.28	NO
65	RFC3	RFC3	RFC3	9450	-0.0081	0.28	NO
66	CENPH	CENPH	CENPH	9487	-0.0087	0.28	NO
67	LMNB1	LMNB1	LMNB1	9673	-0.011	0.27	NO
68	CENPA	CENPA	CENPA	9736	-0.012	0.27	NO
69	LIG1	LIG1	LIG1	10123	-0.017	0.25	NO
70	POLE	POLE	POLE	10147	-0.018	0.25	NO
71	TERF2	TERF2	TERF2	10274	-0.019	0.24	NO
72	RBBP4	RBBP4	RBBP4	10298	-0.02	0.24	NO
73	HJURP	HJURP	HJURP	10988	-0.03	0.2	NO
74	RFC4	RFC4	RFC4	11007	-0.03	0.21	NO
75	HSPA2	HSPA2	HSPA2	11291	-0.034	0.19	NO
76	DIDO1	DIDO1	DIDO1	13072	-0.061	0.096	NO
77	SUN2	SUN2	SUN2	13151	-0.062	0.094	NO
78	POLD3	POLD3	POLD3	13194	-0.063	0.095	NO
79	MLF1IP	MLF1IP	MLF1IP	13366	-0.066	0.089	NO
80	DKC1	DKC1	DKC1	13480	-0.068	0.087	NO
81	POT1	POT1	POT1	13585	-0.07	0.084	NO
82	ATR	ATR	ATR	13592	-0.07	0.088	NO
83	RAD21	RAD21	RAD21	13733	-0.072	0.084	NO
84	HIST2H2BE	HIST2H2BE	HIST2H2BE	13878	-0.075	0.08	NO
85	HIST1H2AD	HIST1H2AD	HIST1H2AD	13897	-0.075	0.082	NO
86	SMC1A	SMC1A	SMC1A	13898	-0.075	0.086	NO
87	CENPI	CENPI	CENPI	14004	-0.076	0.085	NO
88	TERF2IP	TERF2IP	TERF2IP	14105	-0.078	0.083	NO
89	POLA1	POLA1	POLA1	14257	-0.081	0.079	NO
90	BRCA1	BRCA1	BRCA1	15061	-0.098	0.039	NO
91	HIST4H4	HIST4H4	HIST4H4	15165	-0.1	0.039	NO
92	ITGB3BP	ITGB3BP	ITGB3BP	15170	-0.1	0.044	NO
93	SYCP2	SYCP2	SYCP2	15473	-0.11	0.032	NO
94	DNA2	DNA2	DNA2	15653	-0.11	0.028	NO
95	STAG2	STAG2	STAG2	15692	-0.11	0.032	NO
96	SMARCA5	SMARCA5	SMARCA5	15966	-0.12	0.023	NO
97	STAG1	STAG1	STAG1	16010	-0.12	0.027	NO
98	CASC5	CASC5	CASC5	16120	-0.12	0.027	NO
99	TERF1	TERF1	TERF1	16180	-0.13	0.031	NO
100	TEX12	TEX12	TEX12	16561	-0.14	0.017	NO
101	SYNE2	SYNE2	SYNE2	16759	-0.15	0.013	NO
102	SMC3	SMC3	SMC3	16787	-0.15	0.02	NO
103	CENPK	CENPK	CENPK	16801	-0.15	0.027	NO
104	NPM1	NPM1	NPM1	16809	-0.15	0.034	NO
105	SYNE1	SYNE1	SYNE1	17355	-0.18	0.013	NO
106	CENPQ	CENPQ	CENPQ	17377	-0.18	0.022	NO
107	RSF1	RSF1	RSF1	17795	-0.24	0.011	NO

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

Figure S68. 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 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	3	1.7	0.12	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	47	1.2	0.2	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	80	1.1	0.28	YES
4	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	150	0.88	0.33	YES
5	HIST1H2BN	HIST1H2BN	HIST1H2BN	344	0.6	0.36	YES
6	HIST1H4J	HIST1H4J	HIST1H4J	408	0.53	0.4	YES
7	HIST1H4I	HIST1H4I	HIST1H4I	503	0.46	0.42	YES
8	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	529	0.44	0.45	YES
9	HIST1H2BE	HIST1H2BE	HIST1H2BE	566	0.42	0.48	YES
10	HIST1H4A	HIST1H4A	HIST1H4A	569	0.42	0.51	YES
11	HIST1H2BL	HIST1H2BL	HIST1H2BL	583	0.41	0.53	YES
12	HIST2H4A	HIST2H4A	HIST2H4A	586	0.41	0.56	YES
13	HIST3H2BB	HIST3H2BB	HIST3H2BB	845	0.32	0.57	YES
14	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	858	0.32	0.59	YES
15	HIST1H4B	HIST1H4B	HIST1H4B	873	0.31	0.61	YES
16	HIST1H4D	HIST1H4D	HIST1H4D	925	0.3	0.63	YES
17	HIST1H4E	HIST1H4E	HIST1H4E	949	0.29	0.65	YES
18	HIST1H4C	HIST1H4C	HIST1H4C	966	0.29	0.67	YES
19	TERT	TERT	TERT	1177	0.26	0.67	YES
20	HIST1H2BI	HIST1H2BI	HIST1H2BI	1359	0.23	0.68	YES
21	HIST1H4H	HIST1H4H	HIST1H4H	1474	0.22	0.69	YES
22	HIST1H2BC	HIST1H2BC	HIST1H2BC	1634	0.21	0.7	YES
23	HIST1H2AB	HIST1H2AB	HIST1H2AB	1699	0.2	0.7	YES
24	HIST1H2BG	HIST1H2BG	HIST1H2BG	1706	0.2	0.72	YES
25	HIST1H2BH	HIST1H2BH	HIST1H2BH	1738	0.2	0.73	YES
26	HIST1H2BM	HIST1H2BM	HIST1H2BM	2066	0.17	0.72	YES
27	HIST1H2BF	HIST1H2BF	HIST1H2BF	2121	0.17	0.73	YES
28	H2AFX	H2AFX	H2AFX	2653	0.14	0.71	NO
29	HIST1H2BK	HIST1H2BK	HIST1H2BK	3383	0.11	0.68	NO
30	HIST1H2AE	HIST1H2AE	HIST1H2AE	3638	0.098	0.67	NO
31	POLD1	POLD1	POLD1	3930	0.09	0.66	NO
32	RUVBL2	RUVBL2	RUVBL2	4079	0.086	0.66	NO
33	PCNA	PCNA	PCNA	4483	0.076	0.64	NO
34	ACD	ACD	ACD	4657	0.071	0.64	NO
35	POLA2	POLA2	POLA2	5204	0.06	0.61	NO
36	NHP2	NHP2	NHP2	5248	0.059	0.61	NO
37	WRAP53	WRAP53	WRAP53	5332	0.057	0.61	NO
38	HIST1H2BD	HIST1H2BD	HIST1H2BD	5411	0.056	0.61	NO
39	PRIM2	PRIM2	PRIM2	5437	0.055	0.61	NO
40	POLE2	POLE2	POLE2	5903	0.047	0.59	NO
41	RFC2	RFC2	RFC2	5972	0.046	0.59	NO
42	POLD2	POLD2	POLD2	6370	0.039	0.57	NO
43	POLD4	POLD4	POLD4	6429	0.038	0.57	NO
44	RFC5	RFC5	RFC5	6728	0.033	0.56	NO
45	H2AFZ	H2AFZ	H2AFZ	7459	0.021	0.52	NO
46	RPA2	RPA2	RPA2	7520	0.02	0.52	NO
47	RPA3	RPA3	RPA3	7935	0.014	0.49	NO
48	RPA1	RPA1	RPA1	8220	0.0097	0.48	NO
49	PRIM1	PRIM1	PRIM1	8281	0.0088	0.48	NO
50	RUVBL1	RUVBL1	RUVBL1	8432	0.0064	0.47	NO
51	HIST1H2AC	HIST1H2AC	HIST1H2AC	9002	-0.0019	0.44	NO
52	FEN1	FEN1	FEN1	9084	-0.0028	0.43	NO
53	TINF2	TINF2	TINF2	9273	-0.0055	0.42	NO
54	RFC3	RFC3	RFC3	9450	-0.0081	0.41	NO
55	LIG1	LIG1	LIG1	10123	-0.017	0.38	NO
56	POLE	POLE	POLE	10147	-0.018	0.38	NO
57	TERF2	TERF2	TERF2	10274	-0.019	0.37	NO
58	RFC4	RFC4	RFC4	11007	-0.03	0.33	NO
59	POLD3	POLD3	POLD3	13194	-0.063	0.21	NO
60	DKC1	DKC1	DKC1	13480	-0.068	0.2	NO
61	POT1	POT1	POT1	13585	-0.07	0.2	NO
62	HIST2H2BE	HIST2H2BE	HIST2H2BE	13878	-0.075	0.19	NO
63	HIST1H2AD	HIST1H2AD	HIST1H2AD	13897	-0.075	0.19	NO
64	TERF2IP	TERF2IP	TERF2IP	14105	-0.078	0.19	NO
65	POLA1	POLA1	POLA1	14257	-0.081	0.18	NO
66	HIST4H4	HIST4H4	HIST4H4	15165	-0.1	0.14	NO
67	DNA2	DNA2	DNA2	15653	-0.11	0.12	NO
68	TERF1	TERF1	TERF1	16180	-0.13	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 TRANSLATION.

Figure S70. 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 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	RPL21	RPL21	RPL21	21	1.4	0.038	YES
2	RPSAP9	RPSAP9	RPSAP9	30	1.3	0.074	YES
3	RPL36A	RPL36A	RPL36A	143	0.91	0.092	YES
4	RPL39	RPL39	RPL39	212	0.76	0.11	YES
5	RPS28	RPS28	RPS28	251	0.71	0.13	YES
6	RPS27	RPS27	RPS27	345	0.59	0.14	YES
7	RPL9	RPL9	RPL9	392	0.54	0.15	YES
8	RPS26	RPS26	RPS26	426	0.51	0.16	YES
9	TUBA1A	TUBA1A	TUBA1A	439	0.5	0.17	YES
10	RPL7	RPL7	RPL7	455	0.49	0.19	YES
11	TUBB2A	TUBB2A	TUBB2A	489	0.46	0.2	YES
12	RPL18A	RPL18A	RPL18A	550	0.43	0.2	YES
13	TUBA3D	TUBA3D	TUBA3D	640	0.38	0.21	YES
14	EIF3C	EIF3C	EIF3C	693	0.37	0.22	YES
15	TUBB3	TUBB3	TUBB3	699	0.36	0.23	YES
16	MUC4	MUC4	MUC4	833	0.32	0.23	YES
17	RPS3A	RPS3A	RPS3A	855	0.32	0.24	YES
18	MUC2	MUC2	MUC2	872	0.31	0.24	YES
19	FAM153A	FAM153A	FAM153A	886	0.31	0.25	YES
20	MUC16	MUC16	MUC16	1092	0.27	0.25	YES
21	B3GNT7	B3GNT7	B3GNT7	1226	0.25	0.25	YES
22	DPM3	DPM3	DPM3	1285	0.24	0.25	YES
23	MUC6	MUC6	MUC6	1331	0.24	0.25	YES
24	RPSA	RPSA	RPSA	1395	0.23	0.26	YES
25	B3GNT4	B3GNT4	B3GNT4	1430	0.22	0.26	YES
26	GALNT9	GALNT9	GALNT9	1442	0.22	0.27	YES
27	RPL23A	RPL23A	RPL23A	1453	0.22	0.27	YES
28	LDHD	LDHD	LDHD	1508	0.22	0.27	YES
29	MUC5B	MUC5B	MUC5B	1742	0.2	0.27	YES
30	TUBB2B	TUBB2B	TUBB2B	1858	0.19	0.26	YES
31	TIMM8B	TIMM8B	TIMM8B	1978	0.18	0.26	YES
32	B3GNT6	B3GNT6	B3GNT6	1979	0.18	0.27	YES
33	GMPPB	GMPPB	GMPPB	2004	0.17	0.27	YES
34	RPS15	RPS15	RPS15	2018	0.17	0.28	YES
35	RPS2	RPS2	RPS2	2060	0.17	0.28	YES
36	EEF1A1	EEF1A1	EEF1A1	2072	0.17	0.28	YES
37	SPCS2	SPCS2	SPCS2	2073	0.17	0.29	YES
38	FBXO6	FBXO6	FBXO6	2105	0.17	0.29	YES
39	CYC1	CYC1	CYC1	2120	0.17	0.29	YES
40	PIGL	PIGL	PIGL	2138	0.16	0.3	YES
41	TUBA1C	TUBA1C	TUBA1C	2168	0.16	0.3	YES
42	GCNT3	GCNT3	GCNT3	2330	0.15	0.29	YES
43	ARSE	ARSE	ARSE	2371	0.15	0.3	YES
44	F2	F2	F2	2390	0.15	0.3	YES
45	SPHK1	SPHK1	SPHK1	2454	0.15	0.3	YES
46	ARSG	ARSG	ARSG	2659	0.14	0.29	YES
47	RPL41	RPL41	RPL41	2713	0.13	0.29	YES
48	RPL13	RPL13	RPL13	2858	0.13	0.29	YES
49	ST6GALNAC4	ST6GALNAC4	ST6GALNAC4	2909	0.12	0.29	YES
50	FBXW5	FBXW5	FBXW5	2985	0.12	0.29	YES
51	GALNT14	GALNT14	GALNT14	3067	0.12	0.28	YES
52	RPLP0	RPLP0	RPLP0	3082	0.12	0.29	YES
53	MTX1	MTX1	MTX1	3111	0.12	0.29	YES
54	RPS5	RPS5	RPS5	3123	0.12	0.29	YES
55	GALNTL6	GALNTL6	GALNTL6	3186	0.11	0.29	YES
56	IDH3G	IDH3G	IDH3G	3227	0.11	0.29	YES
57	EIF4E	EIF4E	EIF4E	3277	0.11	0.29	YES
58	TUBB6	TUBB6	TUBB6	3286	0.11	0.3	YES
59	TUSC3	TUSC3	TUSC3	3310	0.11	0.3	YES
60	GPAA1	GPAA1	GPAA1	3331	0.11	0.3	YES
61	TIMM13	TIMM13	TIMM13	3394	0.11	0.3	YES
62	B3GNTL1	B3GNTL1	B3GNTL1	3451	0.1	0.3	YES
63	EIF4EBP1	EIF4EBP1	EIF4EBP1	3503	0.1	0.3	YES
64	RPL29	RPL29	RPL29	3523	0.1	0.3	YES
65	RPL28	RPL28	RPL28	3529	0.1	0.3	YES
66	TIMM50	TIMM50	TIMM50	3544	0.1	0.3	YES
67	WBSCR17	WBSCR17	WBSCR17	3563	0.1	0.3	YES
68	SSR4	SSR4	SSR4	3600	0.1	0.31	YES
69	GALNT8	GALNT8	GALNT8	3609	0.099	0.31	YES
70	TIMM10	TIMM10	TIMM10	3652	0.098	0.31	YES
71	ST3GAL3	ST3GAL3	ST3GAL3	3799	0.093	0.3	YES
72	UBA52	UBA52	UBA52	3845	0.092	0.3	YES
73	VKORC1	VKORC1	VKORC1	3868	0.091	0.3	YES
74	RPL10	RPL10	RPL10	3877	0.091	0.31	YES
75	RPS14	RPS14	RPS14	3923	0.09	0.31	YES
76	ALG3	ALG3	ALG3	3973	0.088	0.3	YES
77	RPL15	RPL15	RPL15	3997	0.088	0.31	YES
78	BCS1L	BCS1L	BCS1L	4003	0.088	0.31	YES
79	TBCB	TBCB	TBCB	4035	0.087	0.31	YES
80	DOHH	DOHH	DOHH	4062	0.086	0.31	YES
81	RPLP2	RPLP2	RPLP2	4167	0.083	0.31	YES
82	TIMM17B	TIMM17B	TIMM17B	4178	0.083	0.31	YES
83	TIMM44	TIMM44	TIMM44	4197	0.082	0.31	YES
84	GFER	GFER	GFER	4234	0.081	0.31	YES
85	B3GNT8	B3GNT8	B3GNT8	4271	0.081	0.31	YES
86	MGAT4B	MGAT4B	MGAT4B	4283	0.08	0.31	YES
87	PMM1	PMM1	PMM1	4303	0.08	0.31	YES
88	EEF1G	EEF1G	EEF1G	4392	0.078	0.31	YES
89	GFPT2	GFPT2	GFPT2	4447	0.076	0.31	YES
90	ARSH	ARSH	ARSH	4453	0.076	0.31	YES
91	SLC25A4	SLC25A4	SLC25A4	4564	0.074	0.31	YES
92	SEC13	SEC13	SEC13	4581	0.073	0.31	YES
93	DHPS	DHPS	DHPS	4612	0.073	0.31	YES
94	RPS21	RPS21	RPS21	4617	0.073	0.31	YES
95	MUC17	MUC17	MUC17	4647	0.072	0.31	YES
96	ARSI	ARSI	ARSI	4669	0.071	0.31	YES
97	RPS10	RPS10	RPS10	4756	0.069	0.31	YES
98	EIF4H	EIF4H	EIF4H	4763	0.069	0.31	YES
99	ST8SIA6	ST8SIA6	ST8SIA6	4788	0.069	0.31	YES
100	RPL18	RPL18	RPL18	4815	0.068	0.31	YES
101	TUBA4A	TUBA4A	TUBA4A	4833	0.068	0.31	YES
102	TUBA1B	TUBA1B	TUBA1B	4843	0.068	0.31	YES
103	PROZ	PROZ	PROZ	4876	0.067	0.31	YES
104	PMPCA	PMPCA	PMPCA	4882	0.067	0.31	YES
105	RPS3	RPS3	RPS3	4904	0.066	0.31	YES
106	EIF3K	EIF3K	EIF3K	4953	0.065	0.31	YES
107	ATP5B	ATP5B	ATP5B	4988	0.064	0.31	YES
108	MGAT1	MGAT1	MGAT1	5008	0.064	0.31	YES
109	RPL8	RPL8	RPL8	5027	0.064	0.31	YES
110	EDEM2	EDEM2	EDEM2	5079	0.063	0.31	NO
111	RPS9	RPS9	RPS9	5108	0.062	0.31	NO
112	RPL27	RPL27	RPL27	5149	0.061	0.31	NO
113	PFDN5	PFDN5	PFDN5	5198	0.06	0.31	NO
114	RPS4Y1	RPS4Y1	RPS4Y1	5244	0.059	0.31	NO
115	PIGQ	PIGQ	PIGQ	5249	0.059	0.31	NO
116	DOLPP1	DOLPP1	DOLPP1	5256	0.059	0.31	NO
117	PLAUR	PLAUR	PLAUR	5284	0.058	0.31	NO
118	ST6GALNAC3	ST6GALNAC3	ST6GALNAC3	5336	0.057	0.31	NO
119	ALG12	ALG12	ALG12	5385	0.056	0.31	NO
120	EIF5A	EIF5A	EIF5A	5446	0.055	0.31	NO
121	EIF3F	EIF3F	EIF3F	5471	0.055	0.31	NO
122	RPL36	RPL36	RPL36	5485	0.055	0.31	NO
123	RPL26L1	RPL26L1	RPL26L1	5539	0.054	0.31	NO
124	TBCD	TBCD	TBCD	5682	0.051	0.3	NO
125	ACTB	ACTB	ACTB	5716	0.05	0.3	NO
126	RPS16	RPS16	RPS16	5831	0.049	0.3	NO
127	TOMM5	TOMM5	TOMM5	5857	0.048	0.3	NO
128	GMPPA	GMPPA	GMPPA	5949	0.046	0.29	NO
129	ATP5A1	ATP5A1	ATP5A1	5962	0.046	0.29	NO
130	SAMM50	SAMM50	SAMM50	5984	0.046	0.29	NO
131	RPN1	RPN1	RPN1	6039	0.045	0.29	NO
132	ARSA	ARSA	ARSA	6050	0.044	0.29	NO
133	RPL35	RPL35	RPL35	6078	0.044	0.29	NO
134	DDOST	DDOST	DDOST	6127	0.043	0.29	NO
135	TIMM22	TIMM22	TIMM22	6146	0.043	0.29	NO
136	F7	F7	F7	6191	0.042	0.29	NO
137	TOMM7	TOMM7	TOMM7	6195	0.042	0.29	NO
138	CCT2	CCT2	CCT2	6233	0.041	0.29	NO
139	DOLK	DOLK	DOLK	6343	0.039	0.28	NO
140	B4GALT3	B4GALT3	B4GALT3	6362	0.039	0.28	NO
141	TAZ	TAZ	TAZ	6382	0.039	0.28	NO
142	FAU	FAU	FAU	6404	0.038	0.28	NO
143	RPS6	RPS6	RPS6	6427	0.038	0.28	NO
144	MAN1B1	MAN1B1	MAN1B1	6469	0.037	0.28	NO
145	ALG14	ALG14	ALG14	6517	0.036	0.28	NO
146	EIF2B3	EIF2B3	EIF2B3	6552	0.036	0.28	NO
147	RPLP1	RPLP1	RPLP1	6581	0.035	0.28	NO
148	ALG1	ALG1	ALG1	6587	0.035	0.28	NO
149	CCT7	CCT7	CCT7	6618	0.034	0.28	NO
150	EEF2	EEF2	EEF2	6660	0.034	0.28	NO
151	PREB	PREB	PREB	6663	0.034	0.28	NO
152	SPCS1	SPCS1	SPCS1	6697	0.033	0.28	NO
153	RPL17	RPL17	RPL17	6706	0.033	0.28	NO
154	DPM2	DPM2	DPM2	6748	0.032	0.28	NO
155	RPS13	RPS13	RPS13	6751	0.032	0.28	NO
156	PIGH	PIGH	PIGH	6797	0.032	0.27	NO
157	RPS8	RPS8	RPS8	6828	0.031	0.27	NO
158	SAR1B	SAR1B	SAR1B	6830	0.031	0.27	NO
159	SEMA6D	SEMA6D	SEMA6D	6836	0.031	0.28	NO
160	COQ2	COQ2	COQ2	6848	0.031	0.28	NO
161	MPI	MPI	MPI	6870	0.03	0.28	NO
162	EIF4A1	EIF4A1	EIF4A1	6876	0.03	0.28	NO
163	SLC25A6	SLC25A6	SLC25A6	6877	0.03	0.28	NO
164	EEF1D	EEF1D	EEF1D	6900	0.03	0.28	NO
165	CS	CS	CS	6901	0.03	0.28	NO
166	ATP5G1	ATP5G1	ATP5G1	6968	0.029	0.27	NO
167	EIF1AX	EIF1AX	EIF1AX	7021	0.028	0.27	NO
168	C18orf55	C18orf55	C18orf55	7022	0.028	0.27	NO
169	LOC653566	LOC653566	LOC653566	7064	0.027	0.27	NO
170	EIF2B1	EIF2B1	EIF2B1	7070	0.027	0.27	NO
171	SSR2	SSR2	SSR2	7151	0.026	0.27	NO
172	ALG2	ALG2	ALG2	7165	0.026	0.27	NO
173	FBXW4	FBXW4	FBXW4	7200	0.025	0.27	NO
174	TBCC	TBCC	TBCC	7212	0.025	0.27	NO
175	SEC61B	SEC61B	SEC61B	7213	0.025	0.27	NO
176	KIFC3	KIFC3	KIFC3	7242	0.024	0.26	NO
177	EIF3G	EIF3G	EIF3G	7284	0.024	0.26	NO
178	FXN	FXN	FXN	7303	0.024	0.26	NO
179	PMPCB	PMPCB	PMPCB	7333	0.023	0.26	NO
180	F10	F10	F10	7344	0.023	0.26	NO
181	B4GALT2	B4GALT2	B4GALT2	7358	0.023	0.26	NO
182	RFT1	RFT1	RFT1	7380	0.022	0.26	NO
183	ACO2	ACO2	ACO2	7415	0.022	0.26	NO
184	ARSB	ARSB	ARSB	7500	0.02	0.26	NO
185	PIGF	PIGF	PIGF	7580	0.019	0.25	NO
186	B3GNT9	B3GNT9	B3GNT9	7584	0.019	0.25	NO
187	RPS11	RPS11	RPS11	7637	0.018	0.25	NO
188	EIF3I	EIF3I	EIF3I	7672	0.018	0.25	NO
189	MUCL1	MUCL1	MUCL1	7679	0.018	0.25	NO
190	MGAT3	MGAT3	MGAT3	7738	0.016	0.25	NO
191	RPL35A	RPL35A	RPL35A	7755	0.016	0.24	NO
192	B3GNT3	B3GNT3	B3GNT3	7777	0.016	0.24	NO
193	CHCHD4	CHCHD4	CHCHD4	7810	0.016	0.24	NO
194	CCT4	CCT4	CCT4	7813	0.016	0.24	NO
195	SUMF2	SUMF2	SUMF2	7816	0.016	0.24	NO
196	CALR	CALR	CALR	7850	0.015	0.24	NO
197	RPS29	RPS29	RPS29	7857	0.015	0.24	NO
198	RPL6	RPL6	RPL6	7861	0.015	0.24	NO
199	EIF2B2	EIF2B2	EIF2B2	7910	0.014	0.24	NO
200	PIGT	PIGT	PIGT	7967	0.014	0.24	NO
201	CCT5	CCT5	CCT5	8024	0.013	0.24	NO
202	RPS19	RPS19	RPS19	8061	0.012	0.23	NO
203	RPL3	RPL3	RPL3	8099	0.012	0.23	NO
204	EIF2B4	EIF2B4	EIF2B4	8100	0.012	0.23	NO
205	DPAGT1	DPAGT1	DPAGT1	8116	0.011	0.23	NO
206	FKBP9	FKBP9	FKBP9	8120	0.011	0.23	NO
207	RPS15A	RPS15A	RPS15A	8121	0.011	0.23	NO
208	EEF1B2	EEF1B2	EEF1B2	8175	0.01	0.23	NO
209	SUMF1	SUMF1	SUMF1	8197	0.01	0.23	NO
210	ALG5	ALG5	ALG5	8221	0.0097	0.23	NO
211	PMM2	PMM2	PMM2	8246	0.0094	0.22	NO
212	PIGO	PIGO	PIGO	8262	0.0092	0.22	NO
213	SEC61A2	SEC61A2	SEC61A2	8326	0.0083	0.22	NO
214	EIF2B5	EIF2B5	EIF2B5	8332	0.0081	0.22	NO
215	FXC1	FXC1	FXC1	8363	0.0076	0.22	NO
216	RPL10A	RPL10A	RPL10A	8389	0.0071	0.22	NO
217	TCP1	TCP1	TCP1	8407	0.0068	0.22	NO
218	SRP9	SRP9	SRP9	8444	0.0062	0.22	NO
219	PIGG	PIGG	PIGG	8516	0.0051	0.21	NO
220	RPL7A	RPL7A	RPL7A	8566	0.0043	0.21	NO
221	DAD1	DAD1	DAD1	8569	0.0042	0.21	NO
222	ST6GAL1	ST6GAL1	ST6GAL1	8597	0.0038	0.21	NO
223	GALNTL4	GALNTL4	GALNTL4	8661	0.0029	0.2	NO
224	RPS4X	RPS4X	RPS4X	8775	0.0012	0.2	NO
225	SEC61A1	SEC61A1	SEC61A1	8794	0.00092	0.2	NO
226	PIGS	PIGS	PIGS	8798	0.00087	0.2	NO
227	RPL38	RPL38	RPL38	8824	0.00045	0.2	NO
228	FUT8	FUT8	FUT8	8836	0.0003	0.2	NO
229	GGCX	GGCX	GGCX	8864	-3e-05	0.19	NO
230	MOGS	MOGS	MOGS	8865	-0.000044	0.19	NO
231	EIF3B	EIF3B	EIF3B	8868	-0.000096	0.19	NO
232	PIGV	PIGV	PIGV	8916	-0.00074	0.19	NO
233	ALG13	ALG13	ALG13	8930	-0.00088	0.19	NO
234	RPS17	RPS17	RPS17	8937	-0.00099	0.19	NO
235	TOMM22	TOMM22	TOMM22	8948	-0.0012	0.19	NO
236	RPL37A	RPL37A	RPL37A	8999	-0.0018	0.19	NO
237	ST6GALNAC2	ST6GALNAC2	ST6GALNAC2	9014	-0.002	0.19	NO
238	EIF3D	EIF3D	EIF3D	9067	-0.0027	0.18	NO
239	MUC12	MUC12	MUC12	9260	-0.0053	0.17	NO
240	CCT3	CCT3	CCT3	9464	-0.0083	0.16	NO
241	SSR3	SSR3	SSR3	9467	-0.0084	0.16	NO
242	FBXO4	FBXO4	FBXO4	9554	-0.0096	0.16	NO
243	GALNT12	GALNT12	GALNT12	9565	-0.0098	0.16	NO
244	GNPNAT1	GNPNAT1	GNPNAT1	9608	-0.01	0.15	NO
245	EIF4A2	EIF4A2	EIF4A2	9617	-0.01	0.15	NO
246	NOP56	NOP56	NOP56	9627	-0.011	0.15	NO
247	SEC24D	SEC24D	SEC24D	9638	-0.011	0.15	NO
248	PIGU	PIGU	PIGU	9640	-0.011	0.15	NO
249	SRPRB	SRPRB	SRPRB	9651	-0.011	0.15	NO
250	FBXL5	FBXL5	FBXL5	9657	-0.011	0.15	NO
251	RPL31	RPL31	RPL31	9733	-0.012	0.15	NO
252	MUC15	MUC15	MUC15	9745	-0.012	0.15	NO
253	MLEC	MLEC	MLEC	9759	-0.012	0.15	NO
254	FURIN	FURIN	FURIN	9798	-0.013	0.15	NO
255	EIF3H	EIF3H	EIF3H	9805	-0.013	0.15	NO
256	PIGC	PIGC	PIGC	9806	-0.013	0.15	NO
257	ST3GAL2	ST3GAL2	ST3GAL2	9822	-0.013	0.15	NO
258	RPN2	RPN2	RPN2	9877	-0.014	0.14	NO
259	SEC24C	SEC24C	SEC24C	9904	-0.014	0.14	NO
260	EIF2S2	EIF2S2	EIF2S2	9913	-0.014	0.14	NO
261	RPL32	RPL32	RPL32	9941	-0.015	0.14	NO
262	SLC25A13	SLC25A13	SLC25A13	9963	-0.015	0.14	NO
263	VDAC1	VDAC1	VDAC1	9981	-0.015	0.14	NO
264	LONP2	LONP2	LONP2	9997	-0.016	0.14	NO
265	MGAT2	MGAT2	MGAT2	10050	-0.016	0.14	NO
266	RPS23	RPS23	RPS23	10057	-0.016	0.14	NO
267	USP11	USP11	USP11	10089	-0.017	0.14	NO
268	RPL27A	RPL27A	RPL27A	10095	-0.017	0.14	NO
269	STT3A	STT3A	STT3A	10134	-0.018	0.13	NO
270	RPL34	RPL34	RPL34	10156	-0.018	0.13	NO
271	GRPEL1	GRPEL1	GRPEL1	10235	-0.019	0.13	NO
272	RPL37	RPL37	RPL37	10245	-0.019	0.13	NO
273	SRPR	SRPR	SRPR	10284	-0.02	0.13	NO
274	GALNT2	GALNT2	GALNT2	10285	-0.02	0.13	NO
275	RPL22	RPL22	RPL22	10340	-0.02	0.13	NO
276	TOMM20	TOMM20	TOMM20	10343	-0.02	0.13	NO
277	B4GALT1	B4GALT1	B4GALT1	10433	-0.022	0.12	NO
278	GANAB	GANAB	GANAB	10443	-0.022	0.12	NO
279	GALNT11	GALNT11	GALNT11	10498	-0.023	0.12	NO
280	EIF4B	EIF4B	EIF4B	10523	-0.023	0.12	NO
281	ALG9	ALG9	ALG9	10563	-0.023	0.12	NO
282	RPL5	RPL5	RPL5	10583	-0.024	0.12	NO
283	SSR1	SSR1	SSR1	10677	-0.025	0.11	NO
284	EIF5	EIF5	EIF5	10756	-0.026	0.11	NO
285	EDEM1	EDEM1	EDEM1	10763	-0.026	0.11	NO
286	SRP14	SRP14	SRP14	10767	-0.026	0.11	NO
287	PFDN2	PFDN2	PFDN2	10907	-0.028	0.1	NO
288	PGM3	PGM3	PGM3	10981	-0.029	0.099	NO
289	ETF1	ETF1	ETF1	11015	-0.03	0.098	NO
290	SPCS3	SPCS3	SPCS3	11050	-0.03	0.097	NO
291	RPL11	RPL11	RPL11	11053	-0.031	0.098	NO
292	TOMM40	TOMM40	TOMM40	11148	-0.032	0.093	NO
293	RPL30	RPL30	RPL30	11196	-0.033	0.091	NO
294	RPL19	RPL19	RPL19	11282	-0.034	0.088	NO
295	SEC11A	SEC11A	SEC11A	11387	-0.036	0.083	NO
296	PRKCSH	PRKCSH	PRKCSH	11418	-0.036	0.082	NO
297	RPL23	RPL23	RPL23	11447	-0.036	0.081	NO
298	SLC25A12	SLC25A12	SLC25A12	11486	-0.037	0.08	NO
299	EIF4G1	EIF4G1	EIF4G1	11554	-0.038	0.077	NO
300	MTX2	MTX2	MTX2	11600	-0.039	0.076	NO
301	GALNT13	GALNT13	GALNT13	11605	-0.039	0.077	NO
302	HSPA9	HSPA9	HSPA9	11606	-0.039	0.078	NO
303	PABPC1	PABPC1	PABPC1	11650	-0.039	0.076	NO
304	TBCA	TBCA	TBCA	11653	-0.039	0.077	NO
305	SRP68	SRP68	SRP68	11725	-0.04	0.074	NO
306	STS	STS	STS	11737	-0.04	0.075	NO
307	CCT6A	CCT6A	CCT6A	11741	-0.04	0.076	NO
308	MAN1C1	MAN1C1	MAN1C1	11779	-0.041	0.075	NO
309	MUC13	MUC13	MUC13	11801	-0.042	0.075	NO
310	EIF2S1	EIF2S1	EIF2S1	11876	-0.043	0.072	NO
311	HSCB	HSCB	HSCB	11960	-0.044	0.068	NO
312	RPL4	RPL4	RPL4	11962	-0.044	0.069	NO
313	PIGN	PIGN	PIGN	11964	-0.044	0.07	NO
314	FBXW2	FBXW2	FBXW2	11972	-0.044	0.071	NO
315	SEC11C	SEC11C	SEC11C	12013	-0.045	0.07	NO
316	RPL13A	RPL13A	RPL13A	12014	-0.045	0.071	NO
317	SEC24B	SEC24B	SEC24B	12027	-0.045	0.072	NO
318	PFDN1	PFDN1	PFDN1	12055	-0.045	0.072	NO
319	B4GALT4	B4GALT4	B4GALT4	12217	-0.048	0.064	NO
320	RPL14	RPL14	RPL14	12247	-0.048	0.063	NO
321	GRPEL2	GRPEL2	GRPEL2	12253	-0.048	0.064	NO
322	GALNTL1	GALNTL1	GALNTL1	12360	-0.05	0.06	NO
323	XRN2	XRN2	XRN2	12361	-0.05	0.061	NO
324	TOMM70A	TOMM70A	TOMM70A	12385	-0.05	0.061	NO
325	CANX	CANX	CANX	12496	-0.052	0.056	NO
326	TIMM17A	TIMM17A	TIMM17A	12497	-0.052	0.058	NO
327	B4GALT5	B4GALT5	B4GALT5	12522	-0.052	0.058	NO
328	GALNTL2	GALNTL2	GALNTL2	12523	-0.052	0.059	NO
329	PDIA3	PDIA3	PDIA3	12583	-0.053	0.057	NO
330	C1GALT1C1	C1GALT1C1	C1GALT1C1	12659	-0.055	0.054	NO
331	MAN2A1	MAN2A1	MAN2A1	12728	-0.056	0.052	NO
332	GALNT10	GALNT10	GALNT10	12779	-0.057	0.051	NO
333	UGGT1	UGGT1	UGGT1	12791	-0.057	0.052	NO
334	EIF2S3	EIF2S3	EIF2S3	12824	-0.057	0.052	NO
335	SEC31A	SEC31A	SEC31A	12835	-0.057	0.052	NO
336	RPS20	RPS20	RPS20	12944	-0.059	0.048	NO
337	SEC23A	SEC23A	SEC23A	13121	-0.062	0.04	NO
338	MUC21	MUC21	MUC21	13138	-0.062	0.04	NO
339	PIGP	PIGP	PIGP	13166	-0.062	0.041	NO
340	HSPD1	HSPD1	HSPD1	13216	-0.063	0.04	NO
341	RPL26	RPL26	RPL26	13273	-0.064	0.038	NO
342	SRP54	SRP54	SRP54	13311	-0.065	0.038	NO
343	DPM1	DPM1	DPM1	13352	-0.066	0.037	NO
344	AP3M1	AP3M1	AP3M1	13407	-0.067	0.036	NO
345	TIMM9	TIMM9	TIMM9	13415	-0.067	0.037	NO
346	SRP72	SRP72	SRP72	13498	-0.068	0.035	NO
347	PROC	PROC	PROC	13567	-0.069	0.033	NO
348	SEC61G	SEC61G	SEC61G	13594	-0.07	0.033	NO
349	MCFD2	MCFD2	MCFD2	13604	-0.07	0.034	NO
350	ALG8	ALG8	ALG8	13633	-0.07	0.035	NO
351	ST3GAL1	ST3GAL1	ST3GAL1	13688	-0.072	0.034	NO
352	TIMM8A	TIMM8A	TIMM8A	13706	-0.072	0.035	NO
353	ARFGEF2	ARFGEF2	ARFGEF2	13731	-0.072	0.035	NO
354	CCT8	CCT8	CCT8	13732	-0.072	0.037	NO
355	TUBB1	TUBB1	TUBB1	13785	-0.073	0.036	NO
356	RPS7	RPS7	RPS7	13819	-0.074	0.036	NO
357	ARSJ	ARSJ	ARSJ	13825	-0.074	0.038	NO
358	FBXL3	FBXL3	FBXL3	13922	-0.075	0.035	NO
359	LMAN1	LMAN1	LMAN1	14172	-0.08	0.023	NO
360	MAN1A1	MAN1A1	MAN1A1	14224	-0.08	0.022	NO
361	GALNT3	GALNT3	GALNT3	14251	-0.081	0.023	NO
362	TRAM1	TRAM1	TRAM1	14272	-0.082	0.024	NO
363	EIF5A2	EIF5A2	EIF5A2	14287	-0.082	0.025	NO
364	PFDN6	PFDN6	PFDN6	14382	-0.084	0.022	NO
365	TBCE	TBCE	TBCE	14414	-0.084	0.023	NO
366	MGAT4A	MGAT4A	MGAT4A	14421	-0.084	0.025	NO
367	PIGX	PIGX	PIGX	14478	-0.086	0.024	NO
368	FBXW7	FBXW7	FBXW7	14724	-0.091	0.012	NO
369	GCNT4	GCNT4	GCNT4	14765	-0.092	0.013	NO
370	GCNT1	GCNT1	GCNT1	14801	-0.092	0.013	NO
371	VBP1	VBP1	VBP1	14821	-0.093	0.015	NO
372	PIGW	PIGW	PIGW	14851	-0.094	0.016	NO
373	PIGB	PIGB	PIGB	14890	-0.094	0.016	NO
374	B3GNT2	B3GNT2	B3GNT2	15097	-0.099	0.0068	NO
375	PROS1	PROS1	PROS1	15276	-0.1	-0.00048	NO
376	PIGK	PIGK	PIGK	15293	-0.1	0.0014	NO
377	GALNT6	GALNT6	GALNT6	15370	-0.1	-7e-05	NO
378	ALG10B	ALG10B	ALG10B	15390	-0.1	0.0017	NO
379	PIGM	PIGM	PIGM	15452	-0.11	0.0011	NO
380	GALNT1	GALNT1	GALNT1	15537	-0.11	-0.0007	NO
381	SRP19	SRP19	SRP19	15563	-0.11	0.00084	NO
382	ALG11	ALG11	ALG11	15738	-0.11	-0.006	NO
383	KIF13A	KIF13A	KIF13A	15744	-0.11	-0.0032	NO
384	EIF3E	EIF3E	EIF3E	15796	-0.12	-0.0029	NO
385	GALNT7	GALNT7	GALNT7	15830	-0.12	-0.0017	NO
386	EIF3J	EIF3J	EIF3J	15858	-0.12	-3e-05	NO
387	RPS12	RPS12	RPS12	15909	-0.12	0.00033	NO
388	RPS24	RPS24	RPS24	15920	-0.12	0.003	NO
389	GALNT5	GALNT5	GALNT5	15967	-0.12	0.0036	NO
390	RPS25	RPS25	RPS25	16000	-0.12	0.005	NO
391	RPL24	RPL24	RPL24	16028	-0.12	0.0068	NO
392	RPL12	RPL12	RPL12	16147	-0.12	0.0035	NO
393	RPS18	RPS18	RPS18	16152	-0.12	0.0067	NO
394	DNAJC19	DNAJC19	DNAJC19	16250	-0.13	0.0046	NO
395	ALG6	ALG6	ALG6	16252	-0.13	0.0081	NO
396	PIGA	PIGA	PIGA	16357	-0.13	0.0058	NO
397	EIF3A	EIF3A	EIF3A	16385	-0.13	0.0078	NO
398	ARSK	ARSK	ARSK	16444	-0.14	0.0082	NO
399	ST8SIA3	ST8SIA3	ST8SIA3	16470	-0.14	0.01	NO
400	GSPT2	GSPT2	GSPT2	16474	-0.14	0.014	NO
401	UGGT2	UGGT2	UGGT2	16559	-0.14	0.013	NO
402	B3GNT5	B3GNT5	B3GNT5	16741	-0.15	0.0068	NO
403	COX17	COX17	COX17	16816	-0.15	0.0067	NO
404	ALG10	ALG10	ALG10	16876	-0.15	0.0075	NO
405	EDEM3	EDEM3	EDEM3	16966	-0.16	0.0068	NO
406	RPS27A	RPS27A	RPS27A	16977	-0.16	0.01	NO
407	ST8SIA2	ST8SIA2	ST8SIA2	17002	-0.16	0.014	NO
408	C1GALT1	C1GALT1	C1GALT1	17158	-0.17	0.0093	NO
409	MAN1A2	MAN1A2	MAN1A2	17192	-0.17	0.012	NO
410	MGAT5	MGAT5	MGAT5	17267	-0.18	0.013	NO
411	EIF5B	EIF5B	EIF5B	17384	-0.18	0.011	NO
412	PGAP1	PGAP1	PGAP1	17420	-0.19	0.014	NO
413	MANEA	MANEA	MANEA	17559	-0.2	0.012	NO
414	B4GALT6	B4GALT6	B4GALT6	17606	-0.21	0.015	NO
415	PFDN4	PFDN4	PFDN4	17880	-0.27	0.0066	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 MEIOSIS.

Figure S72. 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 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	3	1.7	0.1	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	47	1.2	0.18	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	80	1.1	0.24	YES
4	FKBP6	FKBP6	FKBP6	134	0.93	0.3	YES
5	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	150	0.88	0.35	YES
6	HIST1H2BN	HIST1H2BN	HIST1H2BN	344	0.6	0.38	YES
7	HIST1H4J	HIST1H4J	HIST1H4J	408	0.53	0.41	YES
8	STAG3	STAG3	STAG3	448	0.49	0.44	YES
9	HIST1H4I	HIST1H4I	HIST1H4I	503	0.46	0.46	YES
10	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	529	0.44	0.49	YES
11	HIST1H2BE	HIST1H2BE	HIST1H2BE	566	0.42	0.51	YES
12	HIST1H4A	HIST1H4A	HIST1H4A	569	0.42	0.54	YES
13	HIST1H2BL	HIST1H2BL	HIST1H2BL	583	0.41	0.56	YES
14	HIST2H4A	HIST2H4A	HIST2H4A	586	0.41	0.58	YES
15	HIST3H2BB	HIST3H2BB	HIST3H2BB	845	0.32	0.59	YES
16	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	858	0.32	0.61	YES
17	HIST1H4B	HIST1H4B	HIST1H4B	873	0.31	0.63	YES
18	HIST1H4D	HIST1H4D	HIST1H4D	925	0.3	0.64	YES
19	HIST1H4E	HIST1H4E	HIST1H4E	949	0.29	0.66	YES
20	HIST1H4C	HIST1H4C	HIST1H4C	966	0.29	0.68	YES
21	HIST1H2BI	HIST1H2BI	HIST1H2BI	1359	0.23	0.67	YES
22	HIST1H4H	HIST1H4H	HIST1H4H	1474	0.22	0.68	YES
23	HIST1H2BC	HIST1H2BC	HIST1H2BC	1634	0.21	0.68	YES
24	HIST1H2AB	HIST1H2AB	HIST1H2AB	1699	0.2	0.69	YES
25	HIST1H2BG	HIST1H2BG	HIST1H2BG	1706	0.2	0.7	YES
26	REC8	REC8	REC8	1710	0.2	0.71	YES
27	HIST1H2BH	HIST1H2BH	HIST1H2BH	1738	0.2	0.72	YES
28	HIST1H2BM	HIST1H2BM	HIST1H2BM	2066	0.17	0.72	NO
29	HIST1H2BF	HIST1H2BF	HIST1H2BF	2121	0.17	0.72	NO
30	H2AFX	H2AFX	H2AFX	2653	0.14	0.7	NO
31	HIST1H2BK	HIST1H2BK	HIST1H2BK	3383	0.11	0.67	NO
32	HIST1H2AE	HIST1H2AE	HIST1H2AE	3638	0.098	0.66	NO
33	ACD	ACD	ACD	4657	0.071	0.61	NO
34	SMC1B	SMC1B	SMC1B	4679	0.071	0.61	NO
35	HIST1H2BD	HIST1H2BD	HIST1H2BD	5411	0.056	0.57	NO
36	UBE2I	UBE2I	UBE2I	6715	0.033	0.5	NO
37	H2AFZ	H2AFZ	H2AFZ	7459	0.021	0.46	NO
38	LMNA	LMNA	LMNA	8487	0.0056	0.41	NO
39	HIST1H2AC	HIST1H2AC	HIST1H2AC	9002	-0.0019	0.38	NO
40	TINF2	TINF2	TINF2	9273	-0.0055	0.36	NO
41	LMNB1	LMNB1	LMNB1	9673	-0.011	0.34	NO
42	TERF2	TERF2	TERF2	10274	-0.019	0.31	NO
43	HSPA2	HSPA2	HSPA2	11291	-0.034	0.26	NO
44	DIDO1	DIDO1	DIDO1	13072	-0.061	0.16	NO
45	SUN2	SUN2	SUN2	13151	-0.062	0.16	NO
46	POT1	POT1	POT1	13585	-0.07	0.14	NO
47	ATR	ATR	ATR	13592	-0.07	0.14	NO
48	RAD21	RAD21	RAD21	13733	-0.072	0.14	NO
49	HIST2H2BE	HIST2H2BE	HIST2H2BE	13878	-0.075	0.14	NO
50	HIST1H2AD	HIST1H2AD	HIST1H2AD	13897	-0.075	0.14	NO
51	SMC1A	SMC1A	SMC1A	13898	-0.075	0.14	NO
52	TERF2IP	TERF2IP	TERF2IP	14105	-0.078	0.14	NO
53	BRCA1	BRCA1	BRCA1	15061	-0.098	0.09	NO
54	HIST4H4	HIST4H4	HIST4H4	15165	-0.1	0.091	NO
55	SYCP2	SYCP2	SYCP2	15473	-0.11	0.08	NO
56	STAG2	STAG2	STAG2	15692	-0.11	0.075	NO
57	STAG1	STAG1	STAG1	16010	-0.12	0.065	NO
58	TERF1	TERF1	TERF1	16180	-0.13	0.063	NO
59	TEX12	TEX12	TEX12	16561	-0.14	0.05	NO
60	SYNE2	SYNE2	SYNE2	16759	-0.15	0.048	NO
61	SMC3	SMC3	SMC3	16787	-0.15	0.056	NO
62	SYNE1	SYNE1	SYNE1	17355	-0.18	0.036	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 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S74. 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 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	HIST1H4K	HIST1H4K	HIST1H4K	3	1.7	0.077	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	47	1.2	0.13	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	80	1.1	0.18	YES
4	FKBP6	FKBP6	FKBP6	134	0.93	0.22	YES
5	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	150	0.88	0.26	YES
6	HIST2H3C	HIST2H3C	HIST2H3C	195	0.78	0.29	YES
7	HIST2H3D	HIST2H3D	HIST2H3D	250	0.71	0.32	YES
8	HIST1H2BN	HIST1H2BN	HIST1H2BN	344	0.6	0.34	YES
9	HIST1H4J	HIST1H4J	HIST1H4J	408	0.53	0.36	YES
10	STAG3	STAG3	STAG3	448	0.49	0.38	YES
11	HIST1H4I	HIST1H4I	HIST1H4I	503	0.46	0.4	YES
12	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	529	0.44	0.42	YES
13	HIST1H2BE	HIST1H2BE	HIST1H2BE	566	0.42	0.44	YES
14	HIST1H4A	HIST1H4A	HIST1H4A	569	0.42	0.45	YES
15	HIST1H2BL	HIST1H2BL	HIST1H2BL	583	0.41	0.47	YES
16	HIST2H4A	HIST2H4A	HIST2H4A	586	0.41	0.49	YES
17	HIST1H3H	HIST1H3H	HIST1H3H	828	0.32	0.49	YES
18	HIST3H2BB	HIST3H2BB	HIST3H2BB	845	0.32	0.5	YES
19	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	858	0.32	0.52	YES
20	HIST1H4B	HIST1H4B	HIST1H4B	873	0.31	0.53	YES
21	HIST1H4D	HIST1H4D	HIST1H4D	925	0.3	0.54	YES
22	HIST1H3D	HIST1H3D	HIST1H3D	927	0.3	0.56	YES
23	HIST1H4E	HIST1H4E	HIST1H4E	949	0.29	0.57	YES
24	HIST1H3B	HIST1H3B	HIST1H3B	960	0.29	0.58	YES
25	HIST1H4C	HIST1H4C	HIST1H4C	966	0.29	0.6	YES
26	HIST1H3F	HIST1H3F	HIST1H3F	1080	0.27	0.6	YES
27	HIST1H3J	HIST1H3J	HIST1H3J	1221	0.25	0.6	YES
28	HIST1H2BI	HIST1H2BI	HIST1H2BI	1359	0.23	0.61	YES
29	HIST1H3I	HIST1H3I	HIST1H3I	1413	0.23	0.61	YES
30	HIST1H4H	HIST1H4H	HIST1H4H	1474	0.22	0.62	YES
31	HIST1H2BC	HIST1H2BC	HIST1H2BC	1634	0.21	0.62	YES
32	HIST1H2AB	HIST1H2AB	HIST1H2AB	1699	0.2	0.63	YES
33	HIST1H2BG	HIST1H2BG	HIST1H2BG	1706	0.2	0.64	YES
34	REC8	REC8	REC8	1710	0.2	0.64	YES
35	HIST1H2BH	HIST1H2BH	HIST1H2BH	1738	0.2	0.65	YES
36	HIST1H3C	HIST1H3C	HIST1H3C	1745	0.2	0.66	YES
37	HIST1H3G	HIST1H3G	HIST1H3G	1950	0.18	0.66	YES
38	HIST1H3A	HIST1H3A	HIST1H3A	2045	0.17	0.66	YES
39	HIST1H2BM	HIST1H2BM	HIST1H2BM	2066	0.17	0.67	YES
40	HIST1H2BF	HIST1H2BF	HIST1H2BF	2121	0.17	0.67	YES
41	H3F3A	H3F3A	H3F3A	2480	0.14	0.66	NO
42	MSH4	MSH4	MSH4	2487	0.14	0.66	NO
43	H2AFX	H2AFX	H2AFX	2653	0.14	0.66	NO
44	HIST1H2BK	HIST1H2BK	HIST1H2BK	3383	0.11	0.62	NO
45	HIST1H2AE	HIST1H2AE	HIST1H2AE	3638	0.098	0.62	NO
46	ACD	ACD	ACD	4657	0.071	0.56	NO
47	SMC1B	SMC1B	SMC1B	4679	0.071	0.56	NO
48	MSH5	MSH5	MSH5	5259	0.059	0.53	NO
49	HIST1H2BD	HIST1H2BD	HIST1H2BD	5411	0.056	0.53	NO
50	RAD51	RAD51	RAD51	5431	0.056	0.53	NO
51	CDK4	CDK4	CDK4	6474	0.037	0.47	NO
52	UBE2I	UBE2I	UBE2I	6715	0.033	0.46	NO
53	DMC1	DMC1	DMC1	7407	0.022	0.42	NO
54	H2AFZ	H2AFZ	H2AFZ	7459	0.021	0.42	NO
55	RPA2	RPA2	RPA2	7520	0.02	0.42	NO
56	RPA3	RPA3	RPA3	7935	0.014	0.4	NO
57	RPA1	RPA1	RPA1	8220	0.0097	0.38	NO
58	LMNA	LMNA	LMNA	8487	0.0056	0.37	NO
59	HIST1H2AC	HIST1H2AC	HIST1H2AC	9002	-0.0019	0.34	NO
60	TINF2	TINF2	TINF2	9273	-0.0055	0.32	NO
61	LMNB1	LMNB1	LMNB1	9673	-0.011	0.3	NO
62	TERF2	TERF2	TERF2	10274	-0.019	0.27	NO
63	TOP3A	TOP3A	TOP3A	10348	-0.02	0.26	NO
64	RAD51C	RAD51C	RAD51C	11004	-0.03	0.23	NO
65	HSPA2	HSPA2	HSPA2	11291	-0.034	0.22	NO
66	CDK2	CDK2	CDK2	11580	-0.038	0.2	NO
67	MLH1	MLH1	MLH1	12345	-0.05	0.16	NO
68	DIDO1	DIDO1	DIDO1	13072	-0.061	0.12	NO
69	H3F3B	H3F3B	H3F3B	13149	-0.062	0.12	NO
70	SUN2	SUN2	SUN2	13151	-0.062	0.12	NO
71	POT1	POT1	POT1	13585	-0.07	0.1	NO
72	ATR	ATR	ATR	13592	-0.07	0.11	NO
73	RAD21	RAD21	RAD21	13733	-0.072	0.1	NO
74	HIST2H2BE	HIST2H2BE	HIST2H2BE	13878	-0.075	0.097	NO
75	HIST1H2AD	HIST1H2AD	HIST1H2AD	13897	-0.075	0.099	NO
76	SMC1A	SMC1A	SMC1A	13898	-0.075	0.1	NO
77	TERF2IP	TERF2IP	TERF2IP	14105	-0.078	0.095	NO
78	BRCA1	BRCA1	BRCA1	15061	-0.098	0.046	NO
79	HIST4H4	HIST4H4	HIST4H4	15165	-0.1	0.045	NO
80	SYCP2	SYCP2	SYCP2	15473	-0.11	0.032	NO
81	NBN	NBN	NBN	15656	-0.11	0.027	NO
82	STAG2	STAG2	STAG2	15692	-0.11	0.03	NO
83	BLM	BLM	BLM	15706	-0.11	0.035	NO
84	HIST1H3E	HIST1H3E	HIST1H3E	15748	-0.11	0.038	NO
85	MLH3	MLH3	MLH3	15785	-0.12	0.041	NO
86	STAG1	STAG1	STAG1	16010	-0.12	0.034	NO
87	RAD50	RAD50	RAD50	16151	-0.12	0.032	NO
88	TERF1	TERF1	TERF1	16180	-0.13	0.036	NO
89	TEX12	TEX12	TEX12	16561	-0.14	0.021	NO
90	SYNE2	SYNE2	SYNE2	16759	-0.15	0.016	NO
91	RBBP8	RBBP8	RBBP8	16780	-0.15	0.022	NO
92	SMC3	SMC3	SMC3	16787	-0.15	0.028	NO
93	BRCA2	BRCA2	BRCA2	16792	-0.15	0.035	NO
94	MRE11A	MRE11A	MRE11A	17130	-0.17	0.024	NO
95	MND1	MND1	MND1	17183	-0.17	0.029	NO
96	SYNE1	SYNE1	SYNE1	17355	-0.18	0.027	NO
97	ATM	ATM	ATM	17403	-0.19	0.033	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 RNA POL I TRANSCRIPTION.

Figure S76. 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 PROTEIN FOLDING

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	3	1.7	0.057	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	47	1.2	0.097	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	80	1.1	0.13	YES
4	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	150	0.88	0.16	YES
5	FCGR2C	FCGR2C	FCGR2C	188	0.8	0.18	YES
6	HIST2H3C	HIST2H3C	HIST2H3C	195	0.78	0.21	YES
7	HIST2H3D	HIST2H3D	HIST2H3D	250	0.71	0.23	YES
8	FCGR3B	FCGR3B	FCGR3B	272	0.68	0.25	YES
9	HIST1H2BN	HIST1H2BN	HIST1H2BN	344	0.6	0.27	YES
10	FCGR1A	FCGR1A	FCGR1A	367	0.57	0.29	YES
11	HIST2H2BF	HIST2H2BF	HIST2H2BF	381	0.55	0.3	YES
12	HIST1H4J	HIST1H4J	HIST1H4J	408	0.53	0.32	YES
13	HLA-DQA2	HLA-DQA2	HLA-DQA2	414	0.52	0.34	YES
14	HIST3H2A	HIST3H2A	HIST3H2A	422	0.52	0.36	YES
15	HIST1H4I	HIST1H4I	HIST1H4I	503	0.46	0.37	YES
16	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	529	0.44	0.38	YES
17	H3F3C	H3F3C	H3F3C	552	0.43	0.39	YES
18	HIST1H2BE	HIST1H2BE	HIST1H2BE	566	0.42	0.41	YES
19	HIST1H4A	HIST1H4A	HIST1H4A	569	0.42	0.42	YES
20	HLA-DRB5	HLA-DRB5	HLA-DRB5	572	0.42	0.44	YES
21	FCGR2B	FCGR2B	FCGR2B	577	0.42	0.45	YES
22	HIST1H2BL	HIST1H2BL	HIST1H2BL	583	0.41	0.46	YES
23	HIST2H4A	HIST2H4A	HIST2H4A	586	0.41	0.48	YES
24	C8G	C8G	C8G	766	0.34	0.48	YES
25	HIST1H3H	HIST1H3H	HIST1H3H	828	0.32	0.48	YES
26	HIST3H2BB	HIST3H2BB	HIST3H2BB	845	0.32	0.5	YES
27	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	858	0.32	0.5	YES
28	HIST1H4B	HIST1H4B	HIST1H4B	873	0.31	0.52	YES
29	HIST1H2AG	HIST1H2AG	HIST1H2AG	887	0.31	0.52	YES
30	H2AFB1	H2AFB1	H2AFB1	889	0.31	0.54	YES
31	HIST1H2AL	HIST1H2AL	HIST1H2AL	901	0.31	0.55	YES
32	HIST1H4D	HIST1H4D	HIST1H4D	925	0.3	0.55	YES
33	HIST1H3D	HIST1H3D	HIST1H3D	927	0.3	0.56	YES
34	HIST1H4E	HIST1H4E	HIST1H4E	949	0.29	0.57	YES
35	HIST1H3B	HIST1H3B	HIST1H3B	960	0.29	0.58	YES
36	HIST1H4C	HIST1H4C	HIST1H4C	966	0.29	0.59	YES
37	HLA-DQA1	HLA-DQA1	HLA-DQA1	1005	0.28	0.6	YES
38	IL10	IL10	IL10	1027	0.28	0.61	YES
39	HIST1H3F	HIST1H3F	HIST1H3F	1080	0.27	0.61	YES
40	HLA-DRB1	HLA-DRB1	HLA-DRB1	1123	0.26	0.62	YES
41	HIST1H3J	HIST1H3J	HIST1H3J	1221	0.25	0.62	YES
42	HIST1H2AH	HIST1H2AH	HIST1H2AH	1265	0.24	0.63	YES
43	HIST1H2BI	HIST1H2BI	HIST1H2BI	1359	0.23	0.63	YES
44	HIST2H2AB	HIST2H2AB	HIST2H2AB	1370	0.23	0.64	YES
45	HLA-DQB1	HLA-DQB1	HLA-DQB1	1376	0.23	0.65	YES
46	C1QB	C1QB	C1QB	1409	0.23	0.65	YES
47	HIST1H3I	HIST1H3I	HIST1H3I	1413	0.23	0.66	YES
48	HIST1H4H	HIST1H4H	HIST1H4H	1474	0.22	0.66	YES
49	C1QC	C1QC	C1QC	1542	0.22	0.67	YES
50	HLA-DPB1	HLA-DPB1	HLA-DPB1	1554	0.21	0.68	YES
51	HIST1H2AK	HIST1H2AK	HIST1H2AK	1576	0.21	0.68	YES
52	HIST1H2BC	HIST1H2BC	HIST1H2BC	1634	0.21	0.68	YES
53	HLA-DMB	HLA-DMB	HLA-DMB	1686	0.2	0.69	YES
54	HIST1H2AB	HIST1H2AB	HIST1H2AB	1699	0.2	0.7	YES
55	HIST1H2BG	HIST1H2BG	HIST1H2BG	1706	0.2	0.7	YES
56	TNF	TNF	TNF	1711	0.2	0.71	YES
57	HIST1H2AM	HIST1H2AM	HIST1H2AM	1715	0.2	0.71	YES
58	HIST1H2BH	HIST1H2BH	HIST1H2BH	1738	0.2	0.72	YES
59	HIST1H3C	HIST1H3C	HIST1H3C	1745	0.2	0.73	YES
60	CD80	CD80	CD80	1761	0.2	0.73	YES
61	HIST1H3G	HIST1H3G	HIST1H3G	1950	0.18	0.73	YES
62	HIST1H3A	HIST1H3A	HIST1H3A	2045	0.17	0.73	YES
63	HIST1H2BM	HIST1H2BM	HIST1H2BM	2066	0.17	0.73	YES
64	HIST1H2BF	HIST1H2BF	HIST1H2BF	2121	0.17	0.74	YES
65	IFNG	IFNG	IFNG	2142	0.16	0.74	YES
66	HLA-DPA1	HLA-DPA1	HLA-DPA1	2235	0.16	0.74	YES
67	ELANE	ELANE	ELANE	2341	0.15	0.74	YES
68	HLA-DOA	HLA-DOA	HLA-DOA	2471	0.14	0.74	YES
69	H3F3A	H3F3A	H3F3A	2480	0.14	0.74	YES
70	C1QA	C1QA	C1QA	2509	0.14	0.74	YES
71	CD86	CD86	CD86	2515	0.14	0.75	YES
72	CTSG	CTSG	CTSG	2600	0.14	0.75	YES
73	H2AFX	H2AFX	H2AFX	2653	0.14	0.75	YES
74	HLA-DRA	HLA-DRA	HLA-DRA	2662	0.14	0.76	YES
75	FCGR2A	FCGR2A	FCGR2A	2665	0.14	0.76	YES
76	CD40	CD40	CD40	2800	0.13	0.76	NO
77	FCGR3A	FCGR3A	FCGR3A	2887	0.13	0.76	NO
78	HLA-DMA	HLA-DMA	HLA-DMA	3036	0.12	0.75	NO
79	C4A	C4A	C4A	3114	0.12	0.75	NO
80	HLA-DOB	HLA-DOB	HLA-DOB	3361	0.11	0.74	NO
81	HIST1H2BK	HIST1H2BK	HIST1H2BK	3383	0.11	0.74	NO
82	HIST1H2AE	HIST1H2AE	HIST1H2AE	3638	0.098	0.73	NO
83	CD40LG	CD40LG	CD40LG	3712	0.096	0.73	NO
84	CD28	CD28	CD28	4476	0.076	0.69	NO
85	HIST1H2BD	HIST1H2BD	HIST1H2BD	5411	0.056	0.64	NO
86	H2AFJ	H2AFJ	H2AFJ	5760	0.05	0.62	NO
87	C2	C2	C2	5808	0.049	0.62	NO
88	SNRPB	SNRPB	SNRPB	5838	0.049	0.62	NO
89	ACTN2	ACTN2	ACTN2	6309	0.04	0.6	NO
90	C3	C3	C3	6698	0.033	0.58	NO
91	H2AFZ	H2AFZ	H2AFZ	7459	0.021	0.54	NO
92	TRIM21	TRIM21	TRIM21	7676	0.018	0.52	NO
93	C1R	C1R	C1R	7720	0.017	0.52	NO
94	H2AFY	H2AFY	H2AFY	8323	0.0083	0.49	NO
95	H2AFV	H2AFV	H2AFV	8376	0.0073	0.49	NO
96	HIST1H2AC	HIST1H2AC	HIST1H2AC	9002	-0.0019	0.45	NO
97	C9	C9	C9	9849	-0.014	0.4	NO
98	C1S	C1S	C1S	10114	-0.017	0.39	NO
99	C6	C6	C6	10702	-0.025	0.36	NO
100	ACTN1	ACTN1	ACTN1	10914	-0.028	0.35	NO
101	SNRPD1	SNRPD1	SNRPD1	11073	-0.031	0.34	NO
102	ACTN4	ACTN4	ACTN4	11248	-0.034	0.33	NO
103	SNRPD3	SNRPD3	SNRPD3	11718	-0.04	0.31	NO
104	H3F3B	H3F3B	H3F3B	13149	-0.062	0.23	NO
105	H2AFY2	H2AFY2	H2AFY2	13344	-0.065	0.22	NO
106	GRIN2A	GRIN2A	GRIN2A	13698	-0.072	0.2	NO
107	HIST2H2BE	HIST2H2BE	HIST2H2BE	13878	-0.075	0.19	NO
108	HIST1H2AD	HIST1H2AD	HIST1H2AD	13897	-0.075	0.2	NO
109	GRIN2B	GRIN2B	GRIN2B	14111	-0.079	0.19	NO
110	C5	C5	C5	14852	-0.094	0.15	NO
111	ACTN3	ACTN3	ACTN3	15029	-0.097	0.14	NO
112	HIST4H4	HIST4H4	HIST4H4	15165	-0.1	0.14	NO
113	TROVE2	TROVE2	TROVE2	15475	-0.11	0.12	NO
114	HIST1H3E	HIST1H3E	HIST1H3E	15748	-0.11	0.11	NO
115	C7	C7	C7	16089	-0.12	0.098	NO
116	SSB	SSB	SSB	17847	-0.26	0.0083	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 PROTEIN FOLDING.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PROTEIN FOLDING, 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 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	HIST1H4K	HIST1H4K	HIST1H4K	3	1.7	0.09	YES
2	HIST2H2AC	HIST2H2AC	HIST2H2AC	47	1.2	0.15	YES
3	HIST1H2BO	HIST1H2BO	HIST1H2BO	80	1.1	0.21	YES
4	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	150	0.88	0.25	YES
5	HIST2H3C	HIST2H3C	HIST2H3C	195	0.78	0.29	YES
6	HIST2H3D	HIST2H3D	HIST2H3D	250	0.71	0.33	YES
7	HIST1H2BN	HIST1H2BN	HIST1H2BN	344	0.6	0.35	YES
8	HIST1H4J	HIST1H4J	HIST1H4J	408	0.53	0.38	YES
9	NPPA	NPPA	NPPA	445	0.5	0.4	YES
10	HIST1H4I	HIST1H4I	HIST1H4I	503	0.46	0.42	YES
11	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	529	0.44	0.45	YES
12	HIST1H2BE	HIST1H2BE	HIST1H2BE	566	0.42	0.47	YES
13	HIST1H4A	HIST1H4A	HIST1H4A	569	0.42	0.49	YES
14	HIST1H2BL	HIST1H2BL	HIST1H2BL	583	0.41	0.51	YES
15	HIST2H4A	HIST2H4A	HIST2H4A	586	0.41	0.53	YES
16	HIST1H3H	HIST1H3H	HIST1H3H	828	0.32	0.54	YES
17	HIST3H2BB	HIST3H2BB	HIST3H2BB	845	0.32	0.55	YES
18	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	858	0.32	0.57	YES
19	HIST1H4B	HIST1H4B	HIST1H4B	873	0.31	0.58	YES
20	APOA1	APOA1	APOA1	910	0.3	0.6	YES
21	HIST1H4D	HIST1H4D	HIST1H4D	925	0.3	0.61	YES
22	HIST1H3D	HIST1H3D	HIST1H3D	927	0.3	0.63	YES
23	HIST1H4E	HIST1H4E	HIST1H4E	949	0.29	0.64	YES
24	HIST1H3B	HIST1H3B	HIST1H3B	960	0.29	0.66	YES
25	HIST1H4C	HIST1H4C	HIST1H4C	966	0.29	0.67	YES
26	HIST1H3F	HIST1H3F	HIST1H3F	1080	0.27	0.68	YES
27	SAA1	SAA1	SAA1	1214	0.25	0.69	YES
28	HIST1H3J	HIST1H3J	HIST1H3J	1221	0.25	0.7	YES
29	HIST1H2BI	HIST1H2BI	HIST1H2BI	1359	0.23	0.7	YES
30	HIST1H3I	HIST1H3I	HIST1H3I	1413	0.23	0.71	YES
31	HIST1H4H	HIST1H4H	HIST1H4H	1474	0.22	0.72	YES
32	HIST1H2BC	HIST1H2BC	HIST1H2BC	1634	0.21	0.72	YES
33	HIST1H2AB	HIST1H2AB	HIST1H2AB	1699	0.2	0.73	YES
34	HIST1H2BG	HIST1H2BG	HIST1H2BG	1706	0.2	0.74	YES
35	HIST1H2BH	HIST1H2BH	HIST1H2BH	1738	0.2	0.75	YES
36	HIST1H3C	HIST1H3C	HIST1H3C	1745	0.2	0.76	YES
37	HIST1H3G	HIST1H3G	HIST1H3G	1950	0.18	0.76	YES
38	HIST1H3A	HIST1H3A	HIST1H3A	2045	0.17	0.76	YES
39	HIST1H2BM	HIST1H2BM	HIST1H2BM	2066	0.17	0.77	YES
40	HIST1H2BF	HIST1H2BF	HIST1H2BF	2121	0.17	0.78	YES
41	H3F3A	H3F3A	H3F3A	2480	0.14	0.76	NO
42	CST3	CST3	CST3	2615	0.14	0.76	NO
43	H2AFX	H2AFX	H2AFX	2653	0.14	0.77	NO
44	SNCA	SNCA	SNCA	2722	0.13	0.77	NO
45	TTR	TTR	TTR	3062	0.12	0.76	NO
46	HIST1H2BK	HIST1H2BK	HIST1H2BK	3383	0.11	0.75	NO
47	HIST1H2AE	HIST1H2AE	HIST1H2AE	3638	0.098	0.74	NO
48	SEMG1	SEMG1	SEMG1	5114	0.062	0.66	NO
49	HIST1H2BD	HIST1H2BD	HIST1H2BD	5411	0.056	0.65	NO
50	FGA	FGA	FGA	5507	0.054	0.64	NO
51	CALCA	CALCA	CALCA	5601	0.052	0.64	NO
52	LYZ	LYZ	LYZ	5707	0.051	0.64	NO
53	B2M	B2M	B2M	6745	0.032	0.58	NO
54	MFGE8	MFGE8	MFGE8	7121	0.026	0.56	NO
55	H2AFZ	H2AFZ	H2AFZ	7459	0.021	0.55	NO
56	GSN	GSN	GSN	7725	0.017	0.53	NO
57	TGFBI	TGFBI	TGFBI	7751	0.016	0.53	NO
58	HIST1H2AC	HIST1H2AC	HIST1H2AC	9002	-0.0019	0.46	NO
59	LTF	LTF	LTF	10573	-0.024	0.38	NO
60	ITM2B	ITM2B	ITM2B	10871	-0.028	0.36	NO
61	APP	APP	APP	11192	-0.032	0.34	NO
62	ODAM	ODAM	ODAM	11522	-0.037	0.33	NO
63	H3F3B	H3F3B	H3F3B	13149	-0.062	0.24	NO
64	HIST2H2BE	HIST2H2BE	HIST2H2BE	13878	-0.075	0.2	NO
65	HIST1H2AD	HIST1H2AD	HIST1H2AD	13897	-0.075	0.21	NO
66	PRL	PRL	PRL	15021	-0.097	0.15	NO
67	HIST4H4	HIST4H4	HIST4H4	15165	-0.1	0.15	NO
68	HSPG2	HSPG2	HSPG2	15349	-0.1	0.14	NO
69	HIST1H3E	HIST1H3E	HIST1H3E	15748	-0.11	0.12	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 METABOLISM OF PROTEINS.

Figure S80. 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

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 = COAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = COAD-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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