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

Ovarian Serous Cystadenocarcinoma (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 OV-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1FN15P2

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 "OV-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: 714
Number of samples: 303
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 79
pheno.type: 2 - 3 :[ clus2 ] 110
pheno.type: 3 - 3 :[ clus3 ] 114

For the expression subtypes of 18585 genes in 304 samples, GSEA found enriched gene sets in each cluster using 303 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG PEROXISOME, KEGG ANTIGEN PROCESSING AND PRESENTATION, KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY, KEGG CYTOSOLIC DNA SENSING PATHWAY, REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT, REACTOME MITOCHONDRIAL PROTEIN IMPORT, REACTOME ACTIVATION OF NF KAPPAB IN B CELLS, REACTOME RESPIRATORY ELECTRON TRANSPORT, REACTOME REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU RICH ELEMENTS

And common core enriched genes are DDX58, IFIH1, IKBKE, ISG15, RNF125, HERC5, NLRC5, NLRX1, UBA7, UBE2L6

clus2

Top enriched gene sets are BIOCARTA MPR PATHWAY, BIOCARTA CHREBP2 PATHWAY, PID FANCONI PATHWAY, PID HEDGEHOG GLIPATHWAY, REACTOME METABOLISM OF NON CODING RNA, REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA, REACTOME GENERIC TRANSCRIPTION PATHWAY, REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM, REACTOME NEUROTRANSMITTER RELEASE CYCLE, REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES

And common core enriched genes are AAAS, NCBP2, NUP107, NUP133, NUP153, NUP155, NUP188, NUP210, NUP35, NUP37

clus3

Top enriched gene sets are KEGG PURINE METABOLISM, KEGG N GLYCAN BIOSYNTHESIS, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG MAPK SIGNALING PATHWAY, KEGG ERBB SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION

And common core enriched genes are GAB1, GRB2, MAPK1, PIK3CD, PRKCA, ACTR3, ARPC1B, BAIAP2, EPS8, FOS

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 CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.47	1.6	0.085	0.67	0.95	0.62	0.32	0.42	0.37	0.18
KEGG PEROXISOME	75	genes.ES.table	0.52	2	0	0.27	0.14	0.49	0.28	0.36	0	0.072
KEGG ANTIGEN PROCESSING AND PRESENTATION	67	genes.ES.table	0.7	1.6	0.051	0.78	0.93	0.58	0.18	0.48	0.41	0.21
KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY	56	genes.ES.table	0.54	1.8	0.015	0.68	0.62	0.5	0.23	0.38	0.23	0.16
KEGG CYTOSOLIC DNA SENSING PATHWAY	42	genes.ES.table	0.67	1.7	0.0084	0.73	0.76	0.4	0.088	0.37	0.29	0.19
REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT	116	genes.ES.table	0.51	1.7	0.078	0.79	0.86	0.72	0.32	0.49	0.37	0.21
REACTOME MITOCHONDRIAL PROTEIN IMPORT	49	genes.ES.table	0.52	1.6	0.086	0.69	0.94	0.69	0.34	0.46	0.36	0.19
REACTOME ACTIVATION OF NF KAPPAB IN B CELLS	61	genes.ES.table	0.42	1.6	0.062	0.65	0.94	0.59	0.36	0.38	0.34	0.18
REACTOME RESPIRATORY ELECTRON TRANSPORT	64	genes.ES.table	0.65	1.6	0.06	0.82	0.93	0.86	0.32	0.58	0.43	0.23
REACTOME REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU RICH ELEMENTS	81	genes.ES.table	0.42	1.8	0.037	0.6	0.64	0.51	0.36	0.32	0.21	0.14

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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	158	0.3	0.067	YES
2	DDO	DDO	DDO	225	0.27	0.13	YES
3	ACSL5	ACSL5	ACSL5	483	0.22	0.18	YES
4	PEX11G	PEX11G	PEX11G	966	0.17	0.19	YES
5	PEX11A	PEX11A	PEX11A	1604	0.13	0.19	YES
6	ACOX2	ACOX2	ACOX2	1725	0.12	0.21	YES
7	MPV17L	MPV17L	MPV17L	1833	0.12	0.24	YES
8	IDH2	IDH2	IDH2	2171	0.1	0.25	YES
9	GSTK1	GSTK1	GSTK1	2471	0.093	0.25	YES
10	MLYCD	MLYCD	MLYCD	2536	0.09	0.27	YES
11	SOD2	SOD2	SOD2	2688	0.085	0.29	YES
12	PAOX	PAOX	PAOX	2843	0.081	0.3	YES
13	PEX6	PEX6	PEX6	2951	0.078	0.31	YES
14	SCP2	SCP2	SCP2	2959	0.078	0.33	YES
15	PEX16	PEX16	PEX16	3093	0.074	0.34	YES
16	ABCD1	ABCD1	ABCD1	3358	0.067	0.34	YES
17	PECR	PECR	PECR	3412	0.066	0.36	YES
18	ACAA1	ACAA1	ACAA1	3589	0.061	0.36	YES
19	IDH1	IDH1	IDH1	3608	0.061	0.38	YES
20	EPHX2	EPHX2	EPHX2	3667	0.06	0.39	YES
21	CAT	CAT	CAT	3692	0.059	0.41	YES
22	PXMP4	PXMP4	PXMP4	3747	0.058	0.42	YES
23	PEX7	PEX7	PEX7	4017	0.054	0.42	YES
24	ACSL6	ACSL6	ACSL6	4266	0.05	0.42	YES
25	PMVK	PMVK	PMVK	4267	0.05	0.43	YES
26	PRDX5	PRDX5	PRDX5	4385	0.048	0.43	YES
27	NUDT12	NUDT12	NUDT12	4418	0.047	0.44	YES
28	SOD1	SOD1	SOD1	4423	0.047	0.46	YES
29	HMGCL	HMGCL	HMGCL	4449	0.047	0.47	YES
30	DHRS4	DHRS4	DHRS4	4455	0.047	0.48	YES
31	CRAT	CRAT	CRAT	4458	0.047	0.49	YES
32	HACL1	HACL1	HACL1	4622	0.044	0.49	YES
33	PRDX1	PRDX1	PRDX1	4655	0.044	0.5	YES
34	PEX11B	PEX11B	PEX11B	4893	0.04	0.5	YES
35	ACOX3	ACOX3	ACOX3	4951	0.04	0.51	YES
36	HAO2	HAO2	HAO2	4952	0.04	0.52	YES
37	ACOT8	ACOT8	ACOT8	5122	0.037	0.52	YES
38	ABCD2	ABCD2	ABCD2	5695	0.029	0.49	NO
39	PEX10	PEX10	PEX10	5768	0.028	0.5	NO
40	PEX2	PEX2	PEX2	5993	0.026	0.49	NO
41	XDH	XDH	XDH	6121	0.024	0.49	NO
42	NUDT19	NUDT19	NUDT19	6181	0.023	0.49	NO
43	PEX12	PEX12	PEX12	6188	0.023	0.5	NO
44	ACOX1	ACOX1	ACOX1	6256	0.022	0.5	NO
45	FAR2	FAR2	FAR2	6313	0.022	0.5	NO
46	AMACR	AMACR	AMACR	6574	0.019	0.49	NO
47	AGPS	AGPS	AGPS	6622	0.018	0.5	NO
48	SLC25A17	SLC25A17	SLC25A17	6819	0.016	0.49	NO
49	MVK	MVK	MVK	6831	0.016	0.49	NO
50	SLC27A2	SLC27A2	SLC27A2	6903	0.015	0.49	NO
51	PEX26	PEX26	PEX26	7019	0.014	0.49	NO
52	PXMP2	PXMP2	PXMP2	8267	0.0014	0.42	NO
53	DECR2	DECR2	DECR2	8292	0.0012	0.42	NO
54	HSD17B4	HSD17B4	HSD17B4	8300	0.0012	0.42	NO
55	ACSL4	ACSL4	ACSL4	8365	0.00048	0.42	NO
56	EHHADH	EHHADH	EHHADH	8399	0.00013	0.42	NO
57	PEX13	PEX13	PEX13	8835	-0.0044	0.39	NO
58	ACSL3	ACSL3	ACSL3	9185	-0.0073	0.38	NO
59	MPV17	MPV17	MPV17	9222	-0.0077	0.38	NO
60	PEX1	PEX1	PEX1	9258	-0.008	0.38	NO
61	GNPAT	GNPAT	GNPAT	9649	-0.012	0.36	NO
62	ABCD3	ABCD3	ABCD3	9809	-0.013	0.35	NO
63	ACSL1	ACSL1	ACSL1	9834	-0.014	0.36	NO
64	BAAT	BAAT	BAAT	10017	-0.015	0.35	NO
65	ECH1	ECH1	ECH1	10018	-0.015	0.35	NO
66	PEX14	PEX14	PEX14	10059	-0.016	0.36	NO
67	FAR1	FAR1	FAR1	10794	-0.023	0.32	NO
68	PEX19	PEX19	PEX19	10937	-0.024	0.32	NO
69	PEX5	PEX5	PEX5	11588	-0.032	0.29	NO
70	PHYH	PHYH	PHYH	12101	-0.038	0.28	NO
71	CROT	CROT	CROT	12292	-0.041	0.28	NO
72	PEX3	PEX3	PEX3	12475	-0.043	0.28	NO
73	ABCD4	ABCD4	ABCD4	12880	-0.049	0.27	NO
74	AGXT	AGXT	AGXT	13177	-0.054	0.26	NO
75	NOS2	NOS2	NOS2	15311	-0.11	0.18	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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG PEROXISOME

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	IFIH1	IFIH1	IFIH1	873	0.18	0.066	YES
2	RNF125	RNF125	RNF125	883	0.18	0.18	YES
3	UBA7	UBA7	UBA7	1231	0.15	0.25	YES
4	ISG15	ISG15	ISG15	1307	0.14	0.34	YES
5	NLRC5	NLRC5	NLRC5	1468	0.14	0.42	YES
6	IKBKE	IKBKE	IKBKE	1626	0.13	0.49	YES
7	UBE2L6	UBE2L6	UBE2L6	1766	0.12	0.56	YES
8	DDX58	DDX58	DDX58	2161	0.1	0.6	YES
9	HERC5	HERC5	HERC5	2414	0.095	0.65	YES
10	NLRX1	NLRX1	NLRX1	3391	0.066	0.64	NO
11	TAX1BP1	TAX1BP1	TAX1BP1	5069	0.037	0.57	NO
12	RNF135	RNF135	RNF135	5639	0.03	0.56	NO
13	CYLD	CYLD	CYLD	5873	0.027	0.56	NO
14	TBK1	TBK1	TBK1	6211	0.023	0.56	NO
15	UBA52	UBA52	UBA52	6569	0.019	0.55	NO
16	TRAF3	TRAF3	TRAF3	6850	0.016	0.55	NO
17	IRF3	IRF3	IRF3	6882	0.016	0.56	NO
18	UBE2D2	UBE2D2	UBE2D2	6923	0.015	0.56	NO
19	RPS27A	RPS27A	RPS27A	6978	0.015	0.57	NO
20	UBE2K	UBE2K	UBE2K	7499	0.0093	0.55	NO
21	PIN1	PIN1	PIN1	7641	0.0079	0.54	NO
22	TNFAIP3	TNFAIP3	TNFAIP3	7798	0.0062	0.54	NO
23	UBE2D3	UBE2D3	UBE2D3	8156	0.0024	0.52	NO
24	MAVS	MAVS	MAVS	8472	-0.00064	0.5	NO
25	UBE2D1	UBE2D1	UBE2D1	8494	-0.00098	0.5	NO
26	OTUD5	OTUD5	OTUD5	9038	-0.0061	0.48	NO
27	ATG12	ATG12	ATG12	9051	-0.0062	0.48	NO
28	TRIM25	TRIM25	TRIM25	9565	-0.011	0.46	NO
29	PCBP2	PCBP2	PCBP2	9951	-0.015	0.45	NO
30	ATG5	ATG5	ATG5	10810	-0.023	0.42	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 PEROXISOME.

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

genes ES table in pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION

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	SAA1	SAA1	SAA1	53	0.37	0.091	YES
2	IRF1	IRF1	IRF1	660	0.2	0.11	YES
3	IFIH1	IFIH1	IFIH1	873	0.18	0.14	YES
4	RNF125	RNF125	RNF125	883	0.18	0.19	YES
5	IRF7	IRF7	IRF7	1168	0.16	0.21	YES
6	IFNB1	IFNB1	IFNB1	1221	0.15	0.25	YES
7	UBA7	UBA7	UBA7	1231	0.15	0.28	YES
8	ISG15	ISG15	ISG15	1307	0.14	0.32	YES
9	NLRC5	NLRC5	NLRC5	1468	0.14	0.34	YES
10	CASP10	CASP10	CASP10	1570	0.13	0.37	YES
11	IKBKE	IKBKE	IKBKE	1626	0.13	0.4	YES
12	DHX58	DHX58	DHX58	1655	0.13	0.43	YES
13	UBE2L6	UBE2L6	UBE2L6	1766	0.12	0.46	YES
14	DDX58	DDX58	DDX58	2161	0.1	0.46	YES
15	HERC5	HERC5	HERC5	2414	0.095	0.47	YES
16	AGER	AGER	AGER	2626	0.087	0.48	YES
17	TANK	TANK	TANK	2846	0.081	0.49	YES
18	CASP8	CASP8	CASP8	3082	0.074	0.5	YES
19	IKBKB	IKBKB	IKBKB	3260	0.07	0.5	YES
20	IKBKG	IKBKG	IKBKG	3315	0.068	0.52	YES
21	S100A12	S100A12	S100A12	3352	0.067	0.53	YES
22	NLRX1	NLRX1	NLRX1	3391	0.066	0.55	YES
23	NFKBIA	NFKBIA	NFKBIA	3629	0.06	0.55	YES
24	DAK	DAK	DAK	3787	0.058	0.56	YES
25	FADD	FADD	FADD	4006	0.054	0.56	YES
26	TRAF2	TRAF2	TRAF2	4935	0.04	0.52	NO
27	IRF2	IRF2	IRF2	5053	0.038	0.52	NO
28	TAX1BP1	TAX1BP1	TAX1BP1	5069	0.037	0.53	NO
29	RELA	RELA	RELA	5126	0.037	0.54	NO
30	RNF135	RNF135	RNF135	5639	0.03	0.52	NO
31	CYLD	CYLD	CYLD	5873	0.027	0.51	NO
32	MAP3K1	MAP3K1	MAP3K1	6037	0.025	0.51	NO
33	TBK1	TBK1	TBK1	6211	0.023	0.5	NO
34	UBA52	UBA52	UBA52	6569	0.019	0.49	NO
35	TRAF3	TRAF3	TRAF3	6850	0.016	0.48	NO
36	IRF3	IRF3	IRF3	6882	0.016	0.48	NO
37	UBE2D2	UBE2D2	UBE2D2	6923	0.015	0.48	NO
38	RPS27A	RPS27A	RPS27A	6978	0.015	0.48	NO
39	NFKB2	NFKB2	NFKB2	7071	0.014	0.48	NO
40	TRAF6	TRAF6	TRAF6	7472	0.0096	0.46	NO
41	UBE2K	UBE2K	UBE2K	7499	0.0093	0.46	NO
42	PIN1	PIN1	PIN1	7641	0.0079	0.46	NO
43	TNFAIP3	TNFAIP3	TNFAIP3	7798	0.0062	0.45	NO
44	UBE2D3	UBE2D3	UBE2D3	8156	0.0024	0.43	NO
45	MAVS	MAVS	MAVS	8472	-0.00064	0.42	NO
46	UBE2D1	UBE2D1	UBE2D1	8494	-0.00098	0.42	NO
47	RIPK1	RIPK1	RIPK1	8935	-0.0053	0.39	NO
48	OTUD5	OTUD5	OTUD5	9038	-0.0061	0.39	NO
49	ATG12	ATG12	ATG12	9051	-0.0062	0.39	NO
50	EP300	EP300	EP300	9336	-0.0087	0.38	NO
51	HMGB1	HMGB1	HMGB1	9550	-0.011	0.37	NO
52	TRIM25	TRIM25	TRIM25	9565	-0.011	0.37	NO
53	PCBP2	PCBP2	PCBP2	9951	-0.015	0.35	NO
54	ATG5	ATG5	ATG5	10810	-0.023	0.31	NO
55	NFKBIB	NFKBIB	NFKBIB	12041	-0.037	0.26	NO
56	SIKE1	SIKE1	SIKE1	12968	-0.05	0.22	NO
57	CHUK	CHUK	CHUK	13368	-0.058	0.21	NO
58	CREBBP	CREBBP	CREBBP	13747	-0.064	0.21	NO
59	APP	APP	APP	14643	-0.086	0.18	NO
60	S100B	S100B	S100B	15697	-0.12	0.16	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 ANTIGEN PROCESSING AND PRESENTATION.

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

genes ES table in pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IL12A	IL12A	IL12A	117	0.32	0.064	YES
2	CXCL10	CXCL10	CXCL10	303	0.25	0.11	YES
3	TMEM173	TMEM173	TMEM173	751	0.19	0.13	YES
4	IFIH1	IFIH1	IFIH1	873	0.18	0.16	YES
5	RNF125	RNF125	RNF125	883	0.18	0.2	YES
6	IRF7	IRF7	IRF7	1168	0.16	0.22	YES
7	IFNB1	IFNB1	IFNB1	1221	0.15	0.25	YES
8	IL8	IL8	IL8	1274	0.15	0.28	YES
9	ISG15	ISG15	ISG15	1307	0.14	0.31	YES
10	IFNE	IFNE	IFNE	1385	0.14	0.34	YES
11	TNF	TNF	TNF	1533	0.13	0.36	YES
12	CASP10	CASP10	CASP10	1570	0.13	0.38	YES
13	MAPK13	MAPK13	MAPK13	1598	0.13	0.41	YES
14	IKBKE	IKBKE	IKBKE	1626	0.13	0.44	YES
15	IL12B	IL12B	IL12B	1632	0.13	0.46	YES
16	DHX58	DHX58	DHX58	1655	0.13	0.49	YES
17	TRADD	TRADD	TRADD	1753	0.12	0.51	YES
18	DDX58	DDX58	DDX58	2161	0.1	0.51	YES
19	TANK	TANK	TANK	2846	0.081	0.5	YES
20	CASP8	CASP8	CASP8	3082	0.074	0.5	YES
21	IKBKB	IKBKB	IKBKB	3260	0.07	0.5	YES
22	IKBKG	IKBKG	IKBKG	3315	0.068	0.52	YES
23	NLRX1	NLRX1	NLRX1	3391	0.066	0.53	YES
24	NFKBIA	NFKBIA	NFKBIA	3629	0.06	0.53	YES
25	DAK	DAK	DAK	3787	0.058	0.53	YES
26	FADD	FADD	FADD	4006	0.054	0.53	YES
27	NFKB1	NFKB1	NFKB1	4174	0.051	0.53	YES
28	IFNW1	IFNW1	IFNW1	4345	0.049	0.54	YES
29	TRAF2	TRAF2	TRAF2	4935	0.04	0.51	NO
30	RELA	RELA	RELA	5126	0.037	0.51	NO
31	CYLD	CYLD	CYLD	5873	0.027	0.48	NO
32	MAP3K1	MAP3K1	MAP3K1	6037	0.025	0.47	NO
33	TBK1	TBK1	TBK1	6211	0.023	0.47	NO
34	TRAF3	TRAF3	TRAF3	6850	0.016	0.44	NO
35	IRF3	IRF3	IRF3	6882	0.016	0.44	NO
36	MAPK11	MAPK11	MAPK11	6963	0.015	0.44	NO
37	TRAF6	TRAF6	TRAF6	7472	0.0096	0.41	NO
38	PIN1	PIN1	PIN1	7641	0.0079	0.41	NO
39	DDX3X	DDX3X	DDX3X	7718	0.0071	0.4	NO
40	MAVS	MAVS	MAVS	8472	-0.00064	0.36	NO
41	MAPK9	MAPK9	MAPK9	8774	-0.0038	0.35	NO
42	RIPK1	RIPK1	RIPK1	8935	-0.0053	0.34	NO
43	MAPK14	MAPK14	MAPK14	8965	-0.0055	0.34	NO
44	OTUD5	OTUD5	OTUD5	9038	-0.0061	0.34	NO
45	ATG12	ATG12	ATG12	9051	-0.0062	0.34	NO
46	TRIM25	TRIM25	TRIM25	9565	-0.011	0.31	NO
47	ATG5	ATG5	ATG5	10810	-0.023	0.25	NO
48	AZI2	AZI2	AZI2	11405	-0.03	0.22	NO
49	NFKBIB	NFKBIB	NFKBIB	12041	-0.037	0.2	NO
50	SIKE1	SIKE1	SIKE1	12968	-0.05	0.16	NO
51	CHUK	CHUK	CHUK	13368	-0.058	0.15	NO
52	MAPK12	MAPK12	MAPK12	13702	-0.064	0.15	NO
53	MAPK8	MAPK8	MAPK8	13886	-0.068	0.15	NO
54	MAP3K7	MAP3K7	MAP3K7	14595	-0.085	0.13	NO
55	TBKBP1	TBKBP1	TBKBP1	16521	-0.16	0.064	NO
56	MAPK10	MAPK10	MAPK10	17161	-0.21	0.076	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 RIG I LIKE RECEPTOR SIGNALING PATHWAY.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIG I LIKE RECEPTOR 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 CYTOSOLIC DNA SENSING 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	PSMB9	PSMB9	PSMB9	231	0.27	0.071	YES
2	PSMB10	PSMB10	PSMB10	384	0.24	0.13	YES
3	PSMB8	PSMB8	PSMB8	563	0.21	0.19	YES
4	PSME2	PSME2	PSME2	1251	0.15	0.2	YES
5	PSME1	PSME1	PSME1	1606	0.13	0.22	YES
6	EXOSC4	EXOSC4	EXOSC4	2057	0.11	0.23	YES
7	PRKCD	PRKCD	PRKCD	2116	0.1	0.26	YES
8	TNFSF13	TNFSF13	TNFSF13	2158	0.1	0.29	YES
9	PSMA5	PSMA5	PSMA5	2727	0.084	0.28	YES
10	HSPB1	HSPB1	HSPB1	2751	0.083	0.3	YES
11	PSMA6	PSMA6	PSMA6	2974	0.077	0.32	YES
12	PSMA4	PSMA4	PSMA4	3505	0.063	0.31	YES
13	PSMD10	PSMD10	PSMD10	3921	0.055	0.3	YES
14	PABPC1	PABPC1	PABPC1	4020	0.054	0.31	YES
15	PSMA3	PSMA3	PSMA3	4264	0.05	0.31	YES
16	AKT1	AKT1	AKT1	4296	0.049	0.33	YES
17	HSPA1B	HSPA1B	HSPA1B	4335	0.049	0.34	YES
18	PSMB2	PSMB2	PSMB2	4377	0.048	0.35	YES
19	PSMA8	PSMA8	PSMA8	4629	0.044	0.35	YES
20	XRN1	XRN1	XRN1	4742	0.043	0.36	YES
21	YWHAZ	YWHAZ	YWHAZ	5027	0.038	0.36	YES
22	PSMA2	PSMA2	PSMA2	5293	0.034	0.35	YES
23	EXOSC3	EXOSC3	EXOSC3	5343	0.034	0.36	YES
24	PSMB4	PSMB4	PSMB4	5556	0.031	0.36	YES
25	EXOSC2	EXOSC2	EXOSC2	5570	0.031	0.37	YES
26	PSMC2	PSMC2	PSMC2	5700	0.029	0.37	YES
27	EXOSC5	EXOSC5	EXOSC5	5786	0.028	0.37	YES
28	PSMD6	PSMD6	PSMD6	5817	0.028	0.38	YES
29	PSMA1	PSMA1	PSMA1	5887	0.027	0.38	YES
30	PSMC3	PSMC3	PSMC3	5906	0.027	0.39	YES
31	ZFP36	ZFP36	ZFP36	6049	0.025	0.39	YES
32	PSMD5	PSMD5	PSMD5	6145	0.024	0.39	YES
33	PSMA7	PSMA7	PSMA7	6154	0.024	0.4	YES
34	PSMC1	PSMC1	PSMC1	6223	0.023	0.4	YES
35	PSMB3	PSMB3	PSMB3	6428	0.02	0.4	YES
36	PSMD7	PSMD7	PSMD7	6568	0.019	0.4	YES
37	UBA52	UBA52	UBA52	6569	0.019	0.4	YES
38	PSMD9	PSMD9	PSMD9	6577	0.019	0.41	YES
39	HSPA8	HSPA8	HSPA8	6637	0.018	0.41	YES
40	PSMB5	PSMB5	PSMB5	6676	0.018	0.41	YES
41	PSMD4	PSMD4	PSMD4	6708	0.018	0.42	YES
42	MAPK11	MAPK11	MAPK11	6963	0.015	0.41	NO
43	RPS27A	RPS27A	RPS27A	6978	0.015	0.41	NO
44	PSMD14	PSMD14	PSMD14	7047	0.014	0.41	NO
45	EXOSC7	EXOSC7	EXOSC7	7168	0.012	0.41	NO
46	ANP32A	ANP32A	ANP32A	7169	0.012	0.41	NO
47	PSMB7	PSMB7	PSMB7	7202	0.012	0.42	NO
48	PSMF1	PSMF1	PSMF1	7238	0.012	0.42	NO
49	PSMC6	PSMC6	PSMC6	7414	0.01	0.41	NO
50	PSMB1	PSMB1	PSMB1	7514	0.0091	0.41	NO
51	EXOSC8	EXOSC8	EXOSC8	7545	0.0089	0.41	NO
52	PSMD8	PSMD8	PSMD8	7858	0.0056	0.4	NO
53	PRKCA	PRKCA	PRKCA	8595	-0.0018	0.36	NO
54	PSMC5	PSMC5	PSMC5	8623	-0.0022	0.36	NO
55	YWHAB	YWHAB	YWHAB	8773	-0.0038	0.35	NO
56	PSMD12	PSMD12	PSMD12	8869	-0.0047	0.34	NO
57	NUP214	NUP214	NUP214	8890	-0.0048	0.34	NO
58	HNRNPD	HNRNPD	HNRNPD	8906	-0.005	0.34	NO
59	EIF4G1	EIF4G1	EIF4G1	8949	-0.0054	0.34	NO
60	MAPK14	MAPK14	MAPK14	8965	-0.0055	0.34	NO
61	PARN	PARN	PARN	9339	-0.0087	0.33	NO
62	ELAVL1	ELAVL1	ELAVL1	9850	-0.014	0.3	NO
63	EXOSC6	EXOSC6	EXOSC6	9893	-0.014	0.31	NO
64	MAPKAPK2	MAPKAPK2	MAPKAPK2	9912	-0.014	0.31	NO
65	PSMB6	PSMB6	PSMB6	9950	-0.015	0.31	NO
66	PSMD2	PSMD2	PSMD2	9968	-0.015	0.32	NO
67	PSMD13	PSMD13	PSMD13	9973	-0.015	0.32	NO
68	XPO1	XPO1	XPO1	10115	-0.016	0.32	NO
69	PSMD11	PSMD11	PSMD11	10399	-0.019	0.31	NO
70	ZFP36L1	ZFP36L1	ZFP36L1	10696	-0.022	0.3	NO
71	EXOSC1	EXOSC1	EXOSC1	10746	-0.023	0.3	NO
72	DCP1A	DCP1A	DCP1A	11300	-0.029	0.28	NO
73	KHSRP	KHSRP	KHSRP	11357	-0.029	0.29	NO
74	PSME4	PSME4	PSME4	11382	-0.03	0.3	NO
75	TNPO1	TNPO1	TNPO1	11395	-0.03	0.3	NO
76	PSMD3	PSMD3	PSMD3	11448	-0.03	0.31	NO
77	PSMD1	PSMD1	PSMD1	11698	-0.033	0.31	NO
78	EXOSC9	EXOSC9	EXOSC9	11780	-0.034	0.31	NO
79	DCP2	DCP2	DCP2	13296	-0.056	0.25	NO
80	PSMC4	PSMC4	PSMC4	13326	-0.057	0.26	NO
81	DIS3	DIS3	DIS3	13641	-0.062	0.27	NO

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

Figure S10. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYTOSOLIC DNA SENSING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT

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	ZBP1	ZBP1	ZBP1	104	0.33	0.069	YES
2	CCL4L2	CCL4L2	CCL4L2	155	0.3	0.14	YES
3	CXCL10	CXCL10	CXCL10	303	0.25	0.18	YES
4	CCL5	CCL5	CCL5	480	0.22	0.23	YES
5	CCL4	CCL4	CCL4	522	0.22	0.27	YES
6	CASP1	CASP1	CASP1	586	0.21	0.32	YES
7	RIPK3	RIPK3	RIPK3	651	0.2	0.36	YES
8	IL1B	IL1B	IL1B	665	0.2	0.4	YES
9	TMEM173	TMEM173	TMEM173	751	0.19	0.44	YES
10	IL33	IL33	IL33	803	0.18	0.48	YES
11	PYCARD	PYCARD	PYCARD	1163	0.16	0.5	YES
12	IRF7	IRF7	IRF7	1168	0.16	0.54	YES
13	IFNB1	IFNB1	IFNB1	1221	0.15	0.57	YES
14	IL18	IL18	IL18	1229	0.15	0.6	YES
15	AIM2	AIM2	AIM2	1336	0.14	0.63	YES
16	TREX1	TREX1	TREX1	1397	0.14	0.66	YES
17	IKBKE	IKBKE	IKBKE	1626	0.13	0.67	YES
18	DDX58	DDX58	DDX58	2161	0.1	0.67	NO
19	IKBKB	IKBKB	IKBKB	3260	0.07	0.63	NO
20	IKBKG	IKBKG	IKBKG	3315	0.068	0.64	NO
21	NFKBIA	NFKBIA	NFKBIA	3629	0.06	0.64	NO
22	POLR1C	POLR1C	POLR1C	3998	0.054	0.63	NO
23	POLR3K	POLR3K	POLR3K	4046	0.053	0.64	NO
24	NFKB1	NFKB1	NFKB1	4174	0.051	0.64	NO
25	RELA	RELA	RELA	5126	0.037	0.6	NO
26	TBK1	TBK1	TBK1	6211	0.023	0.55	NO
27	POLR1D	POLR1D	POLR1D	6473	0.02	0.54	NO
28	POLR3H	POLR3H	POLR3H	6741	0.017	0.53	NO
29	IRF3	IRF3	IRF3	6882	0.016	0.52	NO
30	ADAR	ADAR	ADAR	7834	0.0058	0.47	NO
31	MAVS	MAVS	MAVS	8472	-0.00064	0.44	NO
32	RIPK1	RIPK1	RIPK1	8935	-0.0053	0.41	NO
33	POLR3GL	POLR3GL	POLR3GL	8975	-0.0056	0.41	NO
34	POLR3C	POLR3C	POLR3C	9681	-0.012	0.38	NO
35	NFKBIB	NFKBIB	NFKBIB	12041	-0.037	0.26	NO
36	IL6	IL6	IL6	12836	-0.048	0.23	NO
37	POLR3B	POLR3B	POLR3B	12922	-0.05	0.23	NO
38	POLR3F	POLR3F	POLR3F	13134	-0.053	0.24	NO
39	CHUK	CHUK	CHUK	13368	-0.058	0.24	NO
40	POLR3A	POLR3A	POLR3A	13639	-0.062	0.24	NO
41	POLR3G	POLR3G	POLR3G	13780	-0.065	0.24	NO
42	POLR3D	POLR3D	POLR3D	13910	-0.068	0.25	NO

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

Figure S12. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME MITOCHONDRIAL PROTEIN IMPORT

Table 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	CARD9	CARD9	CARD9	144	0.3	0.11	YES
2	NOD2	NOD2	NOD2	184	0.29	0.22	YES
3	IRAK2	IRAK2	IRAK2	247	0.26	0.32	YES
4	BIRC3	BIRC3	BIRC3	386	0.24	0.41	YES
5	CASP1	CASP1	CASP1	586	0.21	0.48	YES
6	MAPK13	MAPK13	MAPK13	1598	0.13	0.48	YES
7	RIPK2	RIPK2	RIPK2	1999	0.11	0.5	YES
8	IRAK1	IRAK1	IRAK1	2447	0.094	0.51	YES
9	CASP4	CASP4	CASP4	2649	0.087	0.53	YES
10	CASP8	CASP8	CASP8	3082	0.074	0.54	YES
11	IKBKB	IKBKB	IKBKB	3260	0.07	0.56	YES
12	IKBKG	IKBKG	IKBKG	3315	0.068	0.58	YES
13	NOD1	NOD1	NOD1	4509	0.046	0.53	NO
14	CYLD	CYLD	CYLD	5873	0.027	0.47	NO
15	TAB3	TAB3	TAB3	6847	0.016	0.42	NO
16	MAPK11	MAPK11	MAPK11	6963	0.015	0.42	NO
17	TRAF6	TRAF6	TRAF6	7472	0.0096	0.4	NO
18	TNFAIP3	TNFAIP3	TNFAIP3	7798	0.0062	0.39	NO
19	TAB1	TAB1	TAB1	7955	0.0047	0.38	NO
20	UBE2N	UBE2N	UBE2N	8633	-0.0023	0.34	NO
21	MAPK14	MAPK14	MAPK14	8965	-0.0055	0.33	NO
22	CASP2	CASP2	CASP2	9729	-0.012	0.29	NO
23	BIRC2	BIRC2	BIRC2	10353	-0.018	0.27	NO
24	TAB2	TAB2	TAB2	12818	-0.048	0.15	NO
25	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	13137	-0.053	0.16	NO
26	CHUK	CHUK	CHUK	13368	-0.058	0.16	NO
27	CASP9	CASP9	CASP9	13452	-0.059	0.18	NO
28	MAPK12	MAPK12	MAPK12	13702	-0.064	0.2	NO
29	MAP2K6	MAP2K6	MAP2K6	14546	-0.084	0.18	NO
30	MAP3K7	MAP3K7	MAP3K7	14595	-0.085	0.21	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 MITOCHONDRIAL PROTEIN IMPORT.

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

genes ES table in pathway: REACTOME ACTIVATION OF NF KAPPAB IN B CELLS

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	UQCRHL	UQCRHL	UQCRHL	1491	0.14	-0.059	YES
2	IDH3A	IDH3A	IDH3A	1681	0.12	-0.05	YES
3	COX6C	COX6C	COX6C	1785	0.12	-0.036	YES
4	PDP1	PDP1	PDP1	1871	0.12	-0.022	YES
5	COX7B	COX7B	COX7B	1889	0.11	-0.0052	YES
6	COX5A	COX5A	COX5A	1896	0.11	0.013	YES
7	UQCRH	UQCRH	UQCRH	1901	0.11	0.031	YES
8	CYC1	CYC1	CYC1	1935	0.11	0.047	YES
9	NDUFA1	NDUFA1	NDUFA1	1948	0.11	0.064	YES
10	IDH2	IDH2	IDH2	2171	0.1	0.068	YES
11	SLC16A3	SLC16A3	SLC16A3	2418	0.094	0.07	YES
12	SUCLG2	SUCLG2	SUCLG2	2440	0.094	0.084	YES
13	ADHFE1	ADHFE1	ADHFE1	2517	0.09	0.094	YES
14	PDHA1	PDHA1	PDHA1	2638	0.087	0.1	YES
15	NDUFS6	NDUFS6	NDUFS6	2681	0.086	0.11	YES
16	IDH3G	IDH3G	IDH3G	2747	0.083	0.12	YES
17	UQCRQ	UQCRQ	UQCRQ	2807	0.082	0.13	YES
18	ETFA	ETFA	ETFA	2833	0.081	0.14	YES
19	UQCRB	UQCRB	UQCRB	2883	0.08	0.15	YES
20	ETFB	ETFB	ETFB	3010	0.076	0.16	YES
21	NDUFA8	NDUFA8	NDUFA8	3017	0.076	0.17	YES
22	ATP5D	ATP5D	ATP5D	3080	0.074	0.18	YES
23	D2HGDH	D2HGDH	D2HGDH	3206	0.071	0.18	YES
24	NDUFA2	NDUFA2	NDUFA2	3224	0.071	0.2	YES
25	SDHA	SDHA	SDHA	3239	0.07	0.2	YES
26	UQCR11	UQCR11	UQCR11	3245	0.07	0.22	YES
27	NDUFB9	NDUFB9	NDUFB9	3334	0.068	0.22	YES
28	NDUFS7	NDUFS7	NDUFS7	3361	0.067	0.23	YES
29	NDUFV1	NDUFV1	NDUFV1	3372	0.067	0.24	YES
30	NDUFA6	NDUFA6	NDUFA6	3379	0.067	0.25	YES
31	NDUFAB1	NDUFAB1	NDUFAB1	3429	0.065	0.26	YES
32	COX4I1	COX4I1	COX4I1	3431	0.065	0.27	YES
33	NDUFV3	NDUFV3	NDUFV3	3484	0.064	0.28	YES
34	COX8A	COX8A	COX8A	3501	0.064	0.29	YES
35	ATP5H	ATP5H	ATP5H	3568	0.062	0.29	YES
36	NDUFS3	NDUFS3	NDUFS3	3583	0.062	0.3	YES
37	ATP5J2	ATP5J2	ATP5J2	3596	0.061	0.31	YES
38	IDH1	IDH1	IDH1	3608	0.061	0.32	YES
39	NDUFC2	NDUFC2	NDUFC2	3626	0.061	0.33	YES
40	NDUFB2	NDUFB2	NDUFB2	3633	0.06	0.34	YES
41	ACO2	ACO2	ACO2	3645	0.06	0.35	YES
42	SDHD	SDHD	SDHD	3663	0.06	0.36	YES
43	MDH2	MDH2	MDH2	3727	0.059	0.36	YES
44	NDUFB5	NDUFB5	NDUFB5	3790	0.058	0.37	YES
45	NDUFS4	NDUFS4	NDUFS4	3812	0.057	0.38	YES
46	NDUFS8	NDUFS8	NDUFS8	3877	0.056	0.38	YES
47	UQCRC2	UQCRC2	UQCRC2	3970	0.055	0.38	YES
48	COX5B	COX5B	COX5B	3994	0.054	0.39	YES
49	ATP5G1	ATP5G1	ATP5G1	4087	0.053	0.4	YES
50	NDUFB6	NDUFB6	NDUFB6	4113	0.052	0.4	YES
51	ATP5I	ATP5I	ATP5I	4157	0.052	0.41	YES
52	COX6A1	COX6A1	COX6A1	4213	0.05	0.41	YES
53	NDUFA7	NDUFA7	NDUFA7	4255	0.05	0.42	YES
54	UCP2	UCP2	UCP2	4273	0.05	0.43	YES
55	NDUFB3	NDUFB3	NDUFB3	4299	0.049	0.43	YES
56	NDUFB1	NDUFB1	NDUFB1	4383	0.048	0.44	YES
57	NDUFV2	NDUFV2	NDUFV2	4400	0.048	0.44	YES
58	ATP5F1	ATP5F1	ATP5F1	4446	0.047	0.45	YES
59	NDUFA13	NDUFA13	NDUFA13	4658	0.044	0.44	YES
60	ATP5L	ATP5L	ATP5L	4669	0.044	0.45	YES
61	SDHB	SDHB	SDHB	4688	0.044	0.46	YES
62	NDUFS5	NDUFS5	NDUFS5	4728	0.043	0.46	YES
63	NDUFB4	NDUFB4	NDUFB4	4735	0.043	0.47	YES
64	SUCLG1	SUCLG1	SUCLG1	4744	0.043	0.47	YES
65	FH	FH	FH	4962	0.04	0.47	YES
66	NDUFB10	NDUFB10	NDUFB10	4978	0.039	0.47	YES
67	NDUFA12	NDUFA12	NDUFA12	5048	0.038	0.48	YES
68	NDUFA11	NDUFA11	NDUFA11	5057	0.038	0.48	YES
69	UCP3	UCP3	UCP3	5115	0.037	0.48	YES
70	CYCS	CYCS	CYCS	5210	0.036	0.48	YES
71	NDUFB7	NDUFB7	NDUFB7	5239	0.035	0.49	YES
72	ETFDH	ETFDH	ETFDH	5416	0.033	0.48	YES
73	UQCRC1	UQCRC1	UQCRC1	5433	0.033	0.49	YES
74	ATP5C1	ATP5C1	ATP5C1	5455	0.032	0.49	YES
75	NDUFC1	NDUFC1	NDUFC1	5465	0.032	0.5	YES
76	LDHA	LDHA	LDHA	5492	0.032	0.5	YES
77	ATP5O	ATP5O	ATP5O	5528	0.031	0.5	YES
78	DLAT	DLAT	DLAT	5563	0.031	0.51	YES
79	ATP5B	ATP5B	ATP5B	5744	0.029	0.5	YES
80	ATP5A1	ATP5A1	ATP5A1	5783	0.028	0.5	YES
81	NDUFA4	NDUFA4	NDUFA4	5821	0.028	0.51	YES
82	SDHC	SDHC	SDHC	5880	0.027	0.51	YES
83	COX7C	COX7C	COX7C	5931	0.026	0.51	YES
84	NDUFS2	NDUFS2	NDUFS2	6027	0.025	0.51	NO
85	PDHX	PDHX	PDHX	6163	0.024	0.5	NO
86	OGDH	OGDH	OGDH	6409	0.02	0.5	NO
87	ATP5J	ATP5J	ATP5J	6412	0.02	0.5	NO
88	UQCRFS1	UQCRFS1	UQCRFS1	6425	0.02	0.5	NO
89	NDUFA10	NDUFA10	NDUFA10	6433	0.02	0.5	NO
90	BSG	BSG	BSG	6596	0.019	0.5	NO
91	PDHB	PDHB	PDHB	6688	0.018	0.5	NO
92	COX6B1	COX6B1	COX6B1	6871	0.016	0.49	NO
93	CS	CS	CS	7034	0.014	0.48	NO
94	DLD	DLD	DLD	7181	0.012	0.48	NO
95	NDUFA9	NDUFA9	NDUFA9	7242	0.012	0.48	NO
96	NDUFA3	NDUFA3	NDUFA3	7763	0.0065	0.45	NO
97	NDUFB8	NDUFB8	NDUFB8	7766	0.0065	0.45	NO
98	NDUFA5	NDUFA5	NDUFA5	7910	0.0051	0.44	NO
99	L2HGDH	L2HGDH	L2HGDH	7984	0.0044	0.44	NO
100	NDUFS1	NDUFS1	NDUFS1	7993	0.0042	0.44	NO
101	ATP5E	ATP5E	ATP5E	8107	0.0029	0.43	NO
102	DLST	DLST	DLST	8407	0.000034	0.42	NO
103	PDP2	PDP2	PDP2	9010	-0.0058	0.38	NO
104	NNT	NNT	NNT	9031	-0.006	0.38	NO
105	COX7A2L	COX7A2L	COX7A2L	9451	-0.0098	0.36	NO
106	IDH3B	IDH3B	IDH3B	9847	-0.014	0.34	NO
107	SLC16A8	SLC16A8	SLC16A8	12125	-0.038	0.23	NO
108	PDPR	PDPR	PDPR	12416	-0.042	0.22	NO
109	PDK1	PDK1	PDK1	12489	-0.043	0.22	NO
110	SUCLA2	SUCLA2	SUCLA2	13065	-0.052	0.2	NO
111	PDK3	PDK3	PDK3	13857	-0.067	0.17	NO
112	PDK4	PDK4	PDK4	14114	-0.073	0.16	NO
113	LDHB	LDHB	LDHB	14682	-0.088	0.15	NO
114	PDK2	PDK2	PDK2	15278	-0.11	0.13	NO
115	SLC16A1	SLC16A1	SLC16A1	15373	-0.11	0.14	NO
116	UCP1	UCP1	UCP1	16775	-0.18	0.097	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 ACTIVATION OF NF KAPPAB IN B CELLS.

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

genes ES table in pathway: REACTOME RESPIRATORY ELECTRON TRANSPORT

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	CIITA	CIITA	CIITA	149	0.3	0.017	YES
2	HLA-DRB5	HLA-DRB5	HLA-DRB5	167	0.29	0.04	YES
3	GBP5	GBP5	GBP5	187	0.28	0.063	YES
4	GBP4	GBP4	GBP4	381	0.24	0.072	YES
5	OASL	OASL	OASL	396	0.23	0.09	YES
6	HLA-DRB1	HLA-DRB1	HLA-DRB1	448	0.23	0.11	YES
7	FCGR1B	FCGR1B	FCGR1B	538	0.22	0.12	YES
8	FCGR1A	FCGR1A	FCGR1A	553	0.21	0.14	YES
9	PSMB8	PSMB8	PSMB8	563	0.21	0.15	YES
10	IFI27	IFI27	IFI27	604	0.21	0.17	YES
11	OAS1	OAS1	OAS1	606	0.21	0.18	YES
12	HLA-F	HLA-F	HLA-F	633	0.2	0.2	YES
13	IRF1	IRF1	IRF1	660	0.2	0.22	YES
14	PTAFR	PTAFR	PTAFR	746	0.19	0.23	YES
15	HLA-DPA1	HLA-DPA1	HLA-DPA1	756	0.19	0.24	YES
16	HLA-DQA1	HLA-DQA1	HLA-DQA1	759	0.19	0.26	YES
17	HLA-DPB1	HLA-DPB1	HLA-DPB1	778	0.19	0.27	YES
18	EIF4E3	EIF4E3	EIF4E3	808	0.18	0.28	YES
19	GBP2	GBP2	GBP2	816	0.18	0.3	YES
20	IFIT2	IFIT2	IFIT2	916	0.18	0.31	YES
21	IFNG	IFNG	IFNG	970	0.17	0.32	YES
22	ISG20	ISG20	ISG20	1149	0.16	0.32	YES
23	IRF7	IRF7	IRF7	1168	0.16	0.34	YES
24	OAS2	OAS2	OAS2	1194	0.15	0.35	YES
25	IFNB1	IFNB1	IFNB1	1221	0.15	0.36	YES
26	MX1	MX1	MX1	1228	0.15	0.37	YES
27	UBA7	UBA7	UBA7	1231	0.15	0.38	YES
28	ISG15	ISG15	ISG15	1307	0.14	0.39	YES
29	IRF8	IRF8	IRF8	1412	0.14	0.4	YES
30	IFI35	IFI35	IFI35	1488	0.14	0.4	YES
31	MT2A	MT2A	MT2A	1548	0.13	0.41	YES
32	OAS3	OAS3	OAS3	1575	0.13	0.42	YES
33	IFITM1	IFITM1	IFITM1	1685	0.12	0.42	YES
34	GBP6	GBP6	GBP6	1692	0.12	0.43	YES
35	XAF1	XAF1	XAF1	1710	0.12	0.44	YES
36	GBP1	GBP1	GBP1	1717	0.12	0.45	YES
37	IFIT3	IFIT3	IFIT3	1719	0.12	0.46	YES
38	HLA-B	HLA-B	HLA-B	1726	0.12	0.47	YES
39	UBE2L6	UBE2L6	UBE2L6	1766	0.12	0.48	YES
40	B2M	B2M	B2M	1802	0.12	0.49	YES
41	HLA-C	HLA-C	HLA-C	1810	0.12	0.5	YES
42	IFIT1	IFIT1	IFIT1	2000	0.11	0.5	YES
43	PRKCD	PRKCD	PRKCD	2116	0.1	0.5	YES
44	DDX58	DDX58	DDX58	2161	0.1	0.5	YES
45	HLA-DQA2	HLA-DQA2	HLA-DQA2	2297	0.098	0.5	YES
46	PML	PML	PML	2372	0.096	0.51	YES
47	HERC5	HERC5	HERC5	2414	0.095	0.52	YES
48	SP100	SP100	SP100	2516	0.09	0.52	YES
49	HLA-G	HLA-G	HLA-G	2552	0.09	0.52	YES
50	JAK2	JAK2	JAK2	2735	0.084	0.52	YES
51	HLA-A	HLA-A	HLA-A	2744	0.083	0.53	YES
52	IRF9	IRF9	IRF9	2809	0.082	0.53	YES
53	IRF5	IRF5	IRF5	2907	0.079	0.53	YES
54	IFITM2	IFITM2	IFITM2	2938	0.078	0.54	YES
55	USP18	USP18	USP18	2948	0.078	0.54	YES
56	MX2	MX2	MX2	3293	0.069	0.53	NO
57	IRF4	IRF4	IRF4	3339	0.068	0.53	NO
58	CD44	CD44	CD44	3567	0.062	0.52	NO
59	MAPK3	MAPK3	MAPK3	3740	0.059	0.52	NO
60	IFITM3	IFITM3	IFITM3	4066	0.053	0.51	NO
61	IFNAR2	IFNAR2	IFNAR2	4198	0.051	0.5	NO
62	NUP37	NUP37	NUP37	4228	0.05	0.51	NO
63	UBE2E1	UBE2E1	UBE2E1	4362	0.048	0.5	NO
64	IFI6	IFI6	IFI6	4511	0.046	0.5	NO
65	IRF6	IRF6	IRF6	4518	0.046	0.5	NO
66	SOCS1	SOCS1	SOCS1	4535	0.046	0.5	NO
67	EIF2AK2	EIF2AK2	EIF2AK2	4852	0.041	0.49	NO
68	IFNGR1	IFNGR1	IFNGR1	4913	0.04	0.49	NO
69	GBP7	GBP7	GBP7	4997	0.039	0.49	NO
70	IRF2	IRF2	IRF2	5053	0.038	0.49	NO
71	STAT1	STAT1	STAT1	5213	0.036	0.48	NO
72	PTPN6	PTPN6	PTPN6	5333	0.034	0.48	NO
73	ARIH1	ARIH1	ARIH1	5374	0.033	0.48	NO
74	NUP210	NUP210	NUP210	5434	0.033	0.48	NO
75	NUP85	NUP85	NUP85	5513	0.032	0.48	NO
76	ICAM1	ICAM1	ICAM1	5543	0.031	0.48	NO
77	FLNB	FLNB	FLNB	5576	0.031	0.48	NO
78	IFNGR2	IFNGR2	IFNGR2	5619	0.03	0.48	NO
79	IFNAR1	IFNAR1	IFNAR1	5655	0.03	0.48	NO
80	PIAS1	PIAS1	PIAS1	5815	0.028	0.48	NO
81	NUP35	NUP35	NUP35	5830	0.028	0.48	NO
82	STAT2	STAT2	STAT2	6237	0.023	0.46	NO
83	KPNA2	KPNA2	KPNA2	6244	0.023	0.46	NO
84	EIF4A3	EIF4A3	EIF4A3	6402	0.021	0.45	NO
85	NUPL2	NUPL2	NUPL2	6500	0.02	0.45	NO
86	UBA52	UBA52	UBA52	6569	0.019	0.44	NO
87	SOCS3	SOCS3	SOCS3	6722	0.017	0.44	NO
88	EGR1	EGR1	EGR1	6799	0.017	0.44	NO
89	IRF3	IRF3	IRF3	6882	0.016	0.43	NO
90	JAK1	JAK1	JAK1	6966	0.015	0.43	NO
91	RPS27A	RPS27A	RPS27A	6978	0.015	0.43	NO
92	PTPN2	PTPN2	PTPN2	7204	0.012	0.42	NO
93	NUP205	NUP205	NUP205	7612	0.0083	0.4	NO
94	PIN1	PIN1	PIN1	7641	0.0079	0.4	NO
95	ADAR	ADAR	ADAR	7834	0.0058	0.39	NO
96	EIF4A1	EIF4A1	EIF4A1	8544	-0.0014	0.35	NO
97	EIF4A2	EIF4A2	EIF4A2	8576	-0.0016	0.35	NO
98	UBE2N	UBE2N	UBE2N	8633	-0.0023	0.34	NO
99	NUP214	NUP214	NUP214	8890	-0.0048	0.33	NO
100	SUMO1	SUMO1	SUMO1	8943	-0.0053	0.33	NO
101	EIF4G1	EIF4G1	EIF4G1	8949	-0.0054	0.33	NO
102	SEH1L	SEH1L	SEH1L	8958	-0.0054	0.33	NO
103	TYK2	TYK2	TYK2	9275	-0.0081	0.31	NO
104	NUP54	NUP54	NUP54	9358	-0.0088	0.31	NO
105	NUP50	NUP50	NUP50	9411	-0.0094	0.31	NO
106	NUP93	NUP93	NUP93	9436	-0.0096	0.3	NO
107	KPNA1	KPNA1	KPNA1	9546	-0.011	0.3	NO
108	TRIM25	TRIM25	TRIM25	9565	-0.011	0.3	NO
109	AAAS	AAAS	AAAS	9678	-0.012	0.3	NO
110	PTPN1	PTPN1	PTPN1	9981	-0.015	0.28	NO
111	NUP62	NUP62	NUP62	10007	-0.015	0.28	NO
112	RAE1	RAE1	RAE1	10168	-0.016	0.27	NO
113	NUP88	NUP88	NUP88	10248	-0.017	0.27	NO
114	EIF4E	EIF4E	EIF4E	10454	-0.019	0.26	NO
115	IP6K2	IP6K2	IP6K2	10756	-0.023	0.25	NO
116	KPNA4	KPNA4	KPNA4	11319	-0.029	0.22	NO
117	PPM1B	PPM1B	PPM1B	11322	-0.029	0.22	NO
118	NUP153	NUP153	NUP153	11379	-0.03	0.22	NO
119	KPNB1	KPNB1	KPNB1	11704	-0.033	0.2	NO
120	NUPL1	NUPL1	NUPL1	11708	-0.033	0.21	NO
121	EIF4E2	EIF4E2	EIF4E2	11734	-0.034	0.21	NO
122	NUP133	NUP133	NUP133	11845	-0.035	0.2	NO
123	POM121	POM121	POM121	11849	-0.035	0.21	NO
124	RNASEL	RNASEL	RNASEL	11855	-0.035	0.21	NO
125	NUP155	NUP155	NUP155	11946	-0.036	0.21	NO
126	NUP43	NUP43	NUP43	11963	-0.036	0.21	NO
127	TPR	TPR	TPR	12051	-0.037	0.21	NO
128	NUP107	NUP107	NUP107	12055	-0.038	0.21	NO
129	EIF4G2	EIF4G2	EIF4G2	12437	-0.043	0.2	NO
130	NUP188	NUP188	NUP188	12569	-0.044	0.19	NO
131	RANBP2	RANBP2	RANBP2	12972	-0.05	0.17	NO
132	CAMK2B	CAMK2B	CAMK2B	14394	-0.08	0.1	NO
133	EIF4G3	EIF4G3	EIF4G3	14609	-0.086	0.099	NO
134	KPNA3	KPNA3	KPNA3	14676	-0.087	0.1	NO
135	CAMK2D	CAMK2D	CAMK2D	14745	-0.089	0.11	NO
136	NEDD4	NEDD4	NEDD4	16135	-0.14	0.042	NO
137	VCAM1	VCAM1	VCAM1	16347	-0.15	0.043	NO
138	PLCG1	PLCG1	PLCG1	16582	-0.17	0.044	NO
139	NCAM1	NCAM1	NCAM1	17246	-0.21	0.026	NO
140	KPNA5	KPNA5	KPNA5	17541	-0.24	0.03	NO
141	CAMK2A	CAMK2A	CAMK2A	18089	-0.31	0.026	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 RESPIRATORY ELECTRON TRANSPORT.

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

genes ES table in pathway: REACTOME REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU RICH ELEMENTS

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	SAA1	SAA1	SAA1	53	0.37	0.018	YES
2	DEFB1	DEFB1	DEFB1	87	0.34	0.036	YES
3	ZBP1	ZBP1	ZBP1	104	0.33	0.054	YES
4	CARD9	CARD9	CARD9	144	0.3	0.069	YES
5	NOD2	NOD2	NOD2	184	0.29	0.083	YES
6	TLR6	TLR6	TLR6	239	0.27	0.096	YES
7	IRAK2	IRAK2	IRAK2	247	0.26	0.11	YES
8	BIRC3	BIRC3	BIRC3	386	0.24	0.12	YES
9	TLR7	TLR7	TLR7	455	0.23	0.13	YES
10	CD180	CD180	CD180	550	0.21	0.13	YES
11	LY86	LY86	LY86	551	0.21	0.14	YES
12	CASP1	CASP1	CASP1	586	0.21	0.16	YES
13	CFB	CFB	CFB	644	0.2	0.16	YES
14	RIPK3	RIPK3	RIPK3	651	0.2	0.18	YES
15	IRF1	IRF1	IRF1	660	0.2	0.19	YES
16	DEFB4A	DEFB4A	DEFB4A	675	0.2	0.2	YES
17	BTK	BTK	BTK	720	0.19	0.2	YES
18	C4BPA	C4BPA	C4BPA	726	0.19	0.22	YES
19	TLR10	TLR10	TLR10	799	0.19	0.22	YES
20	IFIH1	IFIH1	IFIH1	873	0.18	0.23	YES
21	RNF125	RNF125	RNF125	883	0.18	0.24	YES
22	TLR1	TLR1	TLR1	903	0.18	0.25	YES
23	TLR5	TLR5	TLR5	1068	0.16	0.25	YES
24	C3	C3	C3	1074	0.16	0.26	YES
25	LGALS3	LGALS3	LGALS3	1080	0.16	0.27	YES
26	C2	C2	C2	1129	0.16	0.27	YES
27	TLR3	TLR3	TLR3	1153	0.16	0.28	YES
28	PYCARD	PYCARD	PYCARD	1163	0.16	0.29	YES
29	IRF7	IRF7	IRF7	1168	0.16	0.3	YES
30	UNC93B1	UNC93B1	UNC93B1	1211	0.15	0.3	YES
31	IFNB1	IFNB1	IFNB1	1221	0.15	0.31	YES
32	UBA7	UBA7	UBA7	1231	0.15	0.32	YES
33	ISG15	ISG15	ISG15	1307	0.14	0.32	YES
34	AIM2	AIM2	AIM2	1336	0.14	0.33	YES
35	C4BPB	C4BPB	C4BPB	1362	0.14	0.34	YES
36	CTSS	CTSS	CTSS	1413	0.14	0.34	YES
37	NLRC5	NLRC5	NLRC5	1468	0.14	0.35	YES
38	C1QA	C1QA	C1QA	1480	0.14	0.35	YES
39	TLR8	TLR8	TLR8	1538	0.13	0.36	YES
40	NLRP3	NLRP3	NLRP3	1547	0.13	0.37	YES
41	C1QB	C1QB	C1QB	1554	0.13	0.37	YES
42	CASP10	CASP10	CASP10	1570	0.13	0.38	YES
43	MEFV	MEFV	MEFV	1592	0.13	0.39	YES
44	MAPK13	MAPK13	MAPK13	1598	0.13	0.39	YES
45	LY96	LY96	LY96	1623	0.13	0.4	YES
46	IKBKE	IKBKE	IKBKE	1626	0.13	0.41	YES
47	C4A	C4A	C4A	1631	0.13	0.41	YES
48	C1QC	C1QC	C1QC	1653	0.13	0.42	YES
49	DHX58	DHX58	DHX58	1655	0.13	0.43	YES
50	UBE2L6	UBE2L6	UBE2L6	1766	0.12	0.43	YES
51	C7	C7	C7	1886	0.11	0.43	YES
52	NLRC4	NLRC4	NLRC4	1902	0.11	0.43	YES
53	DUSP4	DUSP4	DUSP4	1970	0.11	0.44	YES
54	P2RX7	P2RX7	P2RX7	1976	0.11	0.44	YES
55	RIPK2	RIPK2	RIPK2	1999	0.11	0.45	YES
56	CCR2	CCR2	CCR2	2049	0.11	0.45	YES
57	TLR4	TLR4	TLR4	2077	0.11	0.46	YES
58	TLR2	TLR2	TLR2	2143	0.1	0.46	YES
59	DDX58	DDX58	DDX58	2161	0.1	0.46	YES
60	TIRAP	TIRAP	TIRAP	2190	0.1	0.47	YES
61	CD14	CD14	CD14	2197	0.1	0.47	YES
62	ART1	ART1	ART1	2207	0.1	0.48	YES
63	PSTPIP1	PSTPIP1	PSTPIP1	2247	0.1	0.48	YES
64	TXN	TXN	TXN	2253	0.1	0.49	YES
65	HERC5	HERC5	HERC5	2414	0.095	0.48	YES
66	IRAK1	IRAK1	IRAK1	2447	0.094	0.49	YES
67	CR1	CR1	CR1	2458	0.093	0.49	YES
68	AGER	AGER	AGER	2626	0.087	0.49	YES
69	CASP4	CASP4	CASP4	2649	0.087	0.49	YES
70	CD55	CD55	CD55	2684	0.085	0.49	YES
71	TICAM1	TICAM1	TICAM1	2789	0.082	0.49	YES
72	TANK	TANK	TANK	2846	0.081	0.5	YES
73	MYD88	MYD88	MYD88	2865	0.08	0.5	YES
74	CD4	CD4	CD4	2925	0.079	0.5	YES
75	CASP8	CASP8	CASP8	3082	0.074	0.5	YES
76	PELI3	PELI3	PELI3	3165	0.072	0.5	YES
77	MEF2C	MEF2C	MEF2C	3219	0.071	0.5	YES
78	IKBKB	IKBKB	IKBKB	3260	0.07	0.5	YES
79	IKBKG	IKBKG	IKBKG	3315	0.068	0.5	YES
80	S100A12	S100A12	S100A12	3352	0.067	0.5	YES
81	NLRX1	NLRX1	NLRX1	3391	0.066	0.5	YES
82	DEFB124	DEFB124	DEFB124	3491	0.064	0.5	YES
83	PELI2	PELI2	PELI2	3591	0.061	0.5	YES
84	NFKBIA	NFKBIA	NFKBIA	3629	0.06	0.5	YES
85	C8G	C8G	C8G	3687	0.06	0.5	YES
86	TICAM2	TICAM2	TICAM2	3730	0.059	0.5	YES
87	MAPK3	MAPK3	MAPK3	3740	0.059	0.5	YES
88	DAK	DAK	DAK	3787	0.058	0.51	YES
89	FADD	FADD	FADD	4006	0.054	0.5	NO
90	CD46	CD46	CD46	4018	0.054	0.5	NO
91	SIGIRR	SIGIRR	SIGIRR	4125	0.052	0.5	NO
92	RPS6KA3	RPS6KA3	RPS6KA3	4337	0.049	0.49	NO
93	NOD1	NOD1	NOD1	4509	0.046	0.48	NO
94	FOS	FOS	FOS	4527	0.046	0.48	NO
95	CTSL1	CTSL1	CTSL1	4654	0.044	0.48	NO
96	MAP2K3	MAP2K3	MAP2K3	4750	0.043	0.48	NO
97	CTSB	CTSB	CTSB	4751	0.043	0.48	NO
98	TRAF2	TRAF2	TRAF2	4935	0.04	0.47	NO
99	C6	C6	C6	5030	0.038	0.47	NO
100	IRF2	IRF2	IRF2	5053	0.038	0.47	NO
101	TAX1BP1	TAX1BP1	TAX1BP1	5069	0.037	0.47	NO
102	RELA	RELA	RELA	5126	0.037	0.47	NO
103	RPS6KA1	RPS6KA1	RPS6KA1	5198	0.036	0.47	NO
104	ELK1	ELK1	ELK1	5224	0.035	0.47	NO
105	IRAK4	IRAK4	IRAK4	5294	0.034	0.47	NO
106	TXNIP	TXNIP	TXNIP	5347	0.034	0.46	NO
107	RNF135	RNF135	RNF135	5639	0.03	0.45	NO
108	EEA1	EEA1	EEA1	5667	0.03	0.45	NO
109	CYLD	CYLD	CYLD	5873	0.027	0.44	NO
110	CFI	CFI	CFI	5918	0.026	0.44	NO
111	CFH	CFH	CFH	6007	0.025	0.44	NO
112	MAP3K1	MAP3K1	MAP3K1	6037	0.025	0.44	NO
113	CAPZA2	CAPZA2	CAPZA2	6097	0.024	0.44	NO
114	TBK1	TBK1	TBK1	6211	0.023	0.43	NO
115	CFD	CFD	CFD	6341	0.021	0.42	NO
116	MAP2K1	MAP2K1	MAP2K1	6437	0.02	0.42	NO
117	UBA52	UBA52	UBA52	6569	0.019	0.42	NO
118	DEFB123	DEFB123	DEFB123	6782	0.017	0.4	NO
119	TAB3	TAB3	TAB3	6847	0.016	0.4	NO
120	TRAF3	TRAF3	TRAF3	6850	0.016	0.4	NO
121	ATF1	ATF1	ATF1	6865	0.016	0.4	NO
122	IRF3	IRF3	IRF3	6882	0.016	0.4	NO
123	MAPKAPK3	MAPKAPK3	MAPKAPK3	6884	0.016	0.4	NO
124	DUSP6	DUSP6	DUSP6	6908	0.015	0.4	NO
125	UBE2D2	UBE2D2	UBE2D2	6923	0.015	0.4	NO
126	MAPK11	MAPK11	MAPK11	6963	0.015	0.4	NO
127	RPS27A	RPS27A	RPS27A	6978	0.015	0.4	NO
128	CAPZA1	CAPZA1	CAPZA1	6986	0.014	0.4	NO
129	NFKB2	NFKB2	NFKB2	7071	0.014	0.4	NO
130	HSP90AB1	HSP90AB1	HSP90AB1	7297	0.011	0.39	NO
131	TRAF6	TRAF6	TRAF6	7472	0.0096	0.38	NO
132	BCL2	BCL2	BCL2	7489	0.0094	0.38	NO
133	UBE2K	UBE2K	UBE2K	7499	0.0093	0.38	NO
134	MAP2K2	MAP2K2	MAP2K2	7566	0.0087	0.38	NO
135	PIN1	PIN1	PIN1	7641	0.0079	0.37	NO
136	MEF2A	MEF2A	MEF2A	7652	0.0077	0.37	NO
137	PPP2CA	PPP2CA	PPP2CA	7719	0.007	0.37	NO
138	PPP2R1B	PPP2R1B	PPP2R1B	7775	0.0064	0.36	NO
139	TNFAIP3	TNFAIP3	TNFAIP3	7798	0.0062	0.36	NO
140	DNM2	DNM2	DNM2	7891	0.0053	0.36	NO
141	TAB1	TAB1	TAB1	7955	0.0047	0.36	NO
142	CDK1	CDK1	CDK1	8075	0.0034	0.35	NO
143	HSP90B1	HSP90B1	HSP90B1	8083	0.0033	0.35	NO
144	ZFYVE20	ZFYVE20	ZFYVE20	8106	0.0029	0.35	NO
145	UBE2D3	UBE2D3	UBE2D3	8156	0.0024	0.35	NO
146	DUSP7	DUSP7	DUSP7	8157	0.0024	0.35	NO
147	MAVS	MAVS	MAVS	8472	-0.00064	0.33	NO
148	UBE2D1	UBE2D1	UBE2D1	8494	-0.00098	0.33	NO
149	UBE2N	UBE2N	UBE2N	8633	-0.0023	0.32	NO
150	CNPY3	CNPY3	CNPY3	8668	-0.0026	0.32	NO
151	MAPK9	MAPK9	MAPK9	8774	-0.0038	0.31	NO
152	RIPK1	RIPK1	RIPK1	8935	-0.0053	0.3	NO
153	MAPK14	MAPK14	MAPK14	8965	-0.0055	0.3	NO
154	OTUD5	OTUD5	OTUD5	9038	-0.0061	0.3	NO
155	ATG12	ATG12	ATG12	9051	-0.0062	0.3	NO
156	ECSIT	ECSIT	ECSIT	9183	-0.0073	0.29	NO
157	RPS6KA2	RPS6KA2	RPS6KA2	9303	-0.0084	0.29	NO
158	EP300	EP300	EP300	9336	-0.0087	0.29	NO
159	HMGB1	HMGB1	HMGB1	9550	-0.011	0.28	NO
160	TRIM25	TRIM25	TRIM25	9565	-0.011	0.28	NO
161	DEFB126	DEFB126	DEFB126	9625	-0.012	0.27	NO
162	CASP2	CASP2	CASP2	9729	-0.012	0.27	NO
163	PELI1	PELI1	PELI1	9773	-0.013	0.27	NO
164	MAPKAPK2	MAPKAPK2	MAPKAPK2	9912	-0.014	0.26	NO
165	PCBP2	PCBP2	PCBP2	9951	-0.015	0.26	NO
166	C5	C5	C5	10014	-0.015	0.26	NO
167	MAPK1	MAPK1	MAPK1	10163	-0.016	0.25	NO
168	PPP2R5D	PPP2R5D	PPP2R5D	10198	-0.017	0.25	NO
169	BIRC2	BIRC2	BIRC2	10353	-0.018	0.24	NO
170	DDOST	DDOST	DDOST	10415	-0.019	0.24	NO
171	LGMN	LGMN	LGMN	10573	-0.021	0.23	NO
172	PPP2CB	PPP2CB	PPP2CB	10592	-0.021	0.23	NO
173	PRKCSH	PRKCSH	PRKCSH	10635	-0.021	0.23	NO
174	ATG5	ATG5	ATG5	10810	-0.023	0.22	NO
175	MAP2K7	MAP2K7	MAP2K7	10934	-0.024	0.22	NO
176	BCL2L1	BCL2L1	BCL2L1	11043	-0.026	0.21	NO
177	RPS6KA5	RPS6KA5	RPS6KA5	11051	-0.026	0.21	NO
178	PIK3C3	PIK3C3	PIK3C3	11323	-0.029	0.2	NO
179	DUSP3	DUSP3	DUSP3	11442	-0.03	0.2	NO
180	TLR9	TLR9	TLR9	11519	-0.031	0.19	NO
181	PIK3R4	PIK3R4	PIK3R4	11532	-0.031	0.19	NO
182	PPP2R1A	PPP2R1A	PPP2R1A	11601	-0.032	0.19	NO
183	NFKBIB	NFKBIB	NFKBIB	12041	-0.037	0.17	NO
184	PLCG2	PLCG2	PLCG2	12241	-0.04	0.16	NO
185	MASP2	MASP2	MASP2	12342	-0.041	0.16	NO
186	JUN	JUN	JUN	12535	-0.044	0.15	NO
187	PANX1	PANX1	PANX1	12567	-0.044	0.15	NO
188	IRAK3	IRAK3	IRAK3	12698	-0.046	0.15	NO
189	C1S	C1S	C1S	12768	-0.047	0.15	NO
190	TAB2	TAB2	TAB2	12818	-0.048	0.15	NO
191	SIKE1	SIKE1	SIKE1	12968	-0.05	0.14	NO
192	TMEM189-UBE2V1	TMEM189-UBE2V1	TMEM189-UBE2V1	13137	-0.053	0.14	NO
193	ATF2	ATF2	ATF2	13231	-0.055	0.13	NO
194	CCR6	CCR6	CCR6	13256	-0.056	0.14	NO
195	CHUK	CHUK	CHUK	13368	-0.058	0.13	NO
196	CASP9	CASP9	CASP9	13452	-0.059	0.13	NO
197	MAPK12	MAPK12	MAPK12	13702	-0.064	0.12	NO
198	CREB1	CREB1	CREB1	13732	-0.064	0.12	NO
199	CREBBP	CREBBP	CREBBP	13747	-0.064	0.13	NO
200	MAPK8	MAPK8	MAPK8	13886	-0.068	0.12	NO
201	MAP2K6	MAP2K6	MAP2K6	14546	-0.084	0.091	NO
202	NLRP1	NLRP1	NLRP1	14574	-0.085	0.094	NO
203	MAP3K7	MAP3K7	MAP3K7	14595	-0.085	0.098	NO
204	MAP2K4	MAP2K4	MAP2K4	14633	-0.086	0.1	NO
205	APP	APP	APP	14643	-0.086	0.11	NO
206	DEFA1B	DEFA1B	DEFA1B	14970	-0.096	0.093	NO
207	DNM1	DNM1	DNM1	15201	-0.1	0.087	NO
208	MAPK7	MAPK7	MAPK7	15523	-0.11	0.076	NO
209	S100B	S100B	S100B	15697	-0.12	0.073	NO
210	PROS1	PROS1	PROS1	16033	-0.14	0.063	NO
211	MAPK10	MAPK10	MAPK10	17161	-0.21	0.013	NO
212	LBP	LBP	LBP	17184	-0.21	0.024	NO
213	CFHR3	CFHR3	CFHR3	17740	-0.26	0.0089	NO
214	CTSK	CTSK	CTSK	17973	-0.3	0.013	NO
215	MASP1	MASP1	MASP1	18215	-0.33	0.019	NO

Figure S19. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU RICH ELEMENTS.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU RICH ELEMENTS, 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
BIOCARTA MPR PATHWAY	33	genes.ES.table	0.42	1.4	0.1	1	1	0.18	0.12	0.16	0.91	0.47
BIOCARTA CHREBP2 PATHWAY	41	genes.ES.table	0.39	1.5	0.069	1	0.98	0.098	0.064	0.092	0.67	0.35
PID FANCONI PATHWAY	46	genes.ES.table	0.51	1.5	0.096	1	0.97	0.72	0.42	0.42	0.7	0.37
PID HEDGEHOG GLIPATHWAY	48	genes.ES.table	0.41	1.5	0.079	1	0.98	0.29	0.22	0.23	0.68	0.36
REACTOME METABOLISM OF NON CODING RNA	47	genes.ES.table	0.44	1.7	0.038	1	0.85	0.77	0.5	0.38	1	0.7
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA	126	genes.ES.table	0.37	1.6	0.046	1	0.93	0.66	0.49	0.34	0.96	0.48
REACTOME GENERIC TRANSCRIPTION PATHWAY	339	genes.ES.table	0.4	1.5	0.11	1	0.99	0.47	0.31	0.33	0.89	0.46
REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM	44	genes.ES.table	0.42	1.6	0.051	1	0.92	0.57	0.42	0.33	1	0.55
REACTOME NEUROTRANSMITTER RELEASE CYCLE	33	genes.ES.table	0.56	1.4	0.076	1	1	0.48	0.2	0.39	0.85	0.44
REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES	59	genes.ES.table	0.37	1.5	0.076	1	0.96	0.71	0.49	0.36	0.79	0.41

genes ES table in pathway: BIOCARTA MPR PATHWAY

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	NUP107	NUP107	NUP107	3430	0.13	-0.13	YES
2	SNRPE	SNRPE	SNRPE	3988	0.11	-0.11	YES
3	NUP133	NUP133	NUP133	4381	0.097	-0.088	YES
4	GEMIN4	GEMIN4	GEMIN4	4601	0.092	-0.059	YES
5	NUP43	NUP43	NUP43	4695	0.09	-0.024	YES
6	SNRPF	SNRPF	SNRPF	4723	0.089	0.014	YES
7	WDR77	WDR77	WDR77	4789	0.088	0.05	YES
8	DDX20	DDX20	DDX20	4874	0.086	0.083	YES
9	AAAS	AAAS	AAAS	4972	0.084	0.12	YES
10	NUP155	NUP155	NUP155	4974	0.084	0.15	YES
11	TPR	TPR	TPR	5085	0.081	0.18	YES
12	RANBP2	RANBP2	RANBP2	5518	0.072	0.19	YES
13	NUP153	NUP153	NUP153	5845	0.066	0.2	YES
14	RAE1	RAE1	RAE1	5918	0.065	0.23	YES
15	SNRPG	SNRPG	SNRPG	6311	0.058	0.23	YES
16	TGS1	TGS1	TGS1	6351	0.058	0.26	YES
17	SNRPB	SNRPB	SNRPB	6443	0.057	0.28	YES
18	POM121	POM121	POM121	6455	0.057	0.3	YES
19	NUP35	NUP35	NUP35	6865	0.051	0.3	YES
20	PRMT5	PRMT5	PRMT5	6909	0.05	0.32	YES
21	SNRPD1	SNRPD1	SNRPD1	6921	0.05	0.34	YES
22	NUPL2	NUPL2	NUPL2	7148	0.047	0.35	YES
23	NUP37	NUP37	NUP37	7282	0.045	0.37	YES
24	NUP88	NUP88	NUP88	7381	0.044	0.38	YES
25	NCBP2	NCBP2	NCBP2	7606	0.041	0.39	YES
26	NUP210	NUP210	NUP210	7707	0.039	0.4	YES
27	NUP188	NUP188	NUP188	7771	0.038	0.41	YES
28	NUP93	NUP93	NUP93	8156	0.034	0.41	YES
29	CLNS1A	CLNS1A	CLNS1A	8249	0.033	0.42	YES
30	SMN2	SMN2	SMN2	8487	0.03	0.42	YES
31	SEH1L	SEH1L	SEH1L	8641	0.028	0.42	YES
32	NUPL1	NUPL1	NUPL1	8939	0.025	0.42	YES
33	NUP205	NUP205	NUP205	9104	0.022	0.42	YES
34	SNRPD2	SNRPD2	SNRPD2	9106	0.022	0.43	YES
35	NUP214	NUP214	NUP214	9132	0.022	0.44	YES
36	GEMIN6	GEMIN6	GEMIN6	9267	0.02	0.44	YES
37	GEMIN5	GEMIN5	GEMIN5	9482	0.017	0.43	NO
38	NUP54	NUP54	NUP54	9743	0.014	0.42	NO
39	GEMIN7	GEMIN7	GEMIN7	10006	0.011	0.42	NO
40	NCBP1	NCBP1	NCBP1	10306	0.0071	0.4	NO
41	NUP50	NUP50	NUP50	10809	0.00026	0.38	NO
42	SMN1	SMN1	SMN1	11620	-0.011	0.34	NO
43	PHAX	PHAX	PHAX	11816	-0.014	0.33	NO
44	SNUPN	SNUPN	SNUPN	11849	-0.014	0.34	NO
45	SNRPD3	SNRPD3	SNRPD3	11993	-0.016	0.34	NO
46	NUP62	NUP62	NUP62	12092	-0.018	0.34	NO
47	NUP85	NUP85	NUP85	12468	-0.023	0.33	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: BIOCARTA MPR PATHWAY.

Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MPR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

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	NUP107	NUP107	NUP107	3430	0.13	-0.16	YES
2	SNRPE	SNRPE	SNRPE	3988	0.11	-0.18	YES
3	SNRNP200	SNRNP200	SNRNP200	4332	0.098	-0.18	YES
4	UPF3B	UPF3B	UPF3B	4371	0.098	-0.16	YES
5	NUP133	NUP133	NUP133	4381	0.097	-0.15	YES
6	NUP43	NUP43	NUP43	4695	0.09	-0.15	YES
7	SNRPF	SNRPF	SNRPF	4723	0.089	-0.13	YES
8	AAAS	AAAS	AAAS	4972	0.084	-0.13	YES
9	NUP155	NUP155	NUP155	4974	0.084	-0.12	YES
10	TPR	TPR	TPR	5085	0.081	-0.11	YES
11	CPSF3	CPSF3	CPSF3	5498	0.073	-0.12	YES
12	RANBP2	RANBP2	RANBP2	5518	0.072	-0.11	YES
13	HNRNPA1	HNRNPA1	HNRNPA1	5629	0.07	-0.1	YES
14	POLR2A	POLR2A	POLR2A	5635	0.07	-0.089	YES
15	CDC40	CDC40	CDC40	5672	0.069	-0.079	YES
16	ZNF473	ZNF473	ZNF473	5704	0.069	-0.069	YES
17	ERCC3	ERCC3	ERCC3	5742	0.068	-0.059	YES
18	RBM8A	RBM8A	RBM8A	5743	0.068	-0.047	YES
19	DHX9	DHX9	DHX9	5764	0.068	-0.037	YES
20	RNMT	RNMT	RNMT	5783	0.068	-0.026	YES
21	NUP153	NUP153	NUP153	5845	0.066	-0.018	YES
22	RAE1	RAE1	RAE1	5918	0.065	-0.01	YES
23	POLR2I	POLR2I	POLR2I	5933	0.065	0.00018	YES
24	FUS	FUS	FUS	6006	0.064	0.0073	YES
25	RNPS1	RNPS1	RNPS1	6115	0.061	0.012	YES
26	POLR2D	POLR2D	POLR2D	6214	0.06	0.017	YES
27	SNRPG	SNRPG	SNRPG	6311	0.058	0.022	YES
28	SF3B1	SF3B1	SF3B1	6367	0.058	0.029	YES
29	SNRPB	SNRPB	SNRPB	6443	0.057	0.035	YES
30	POM121	POM121	POM121	6455	0.057	0.044	YES
31	SUPT5H	SUPT5H	SUPT5H	6456	0.057	0.054	YES
32	RBMX	RBMX	RBMX	6501	0.056	0.061	YES
33	SRRM1	SRRM1	SRRM1	6529	0.056	0.07	YES
34	SF3B3	SF3B3	SF3B3	6552	0.055	0.078	YES
35	RNGTT	RNGTT	RNGTT	6559	0.055	0.087	YES
36	PCBP2	PCBP2	PCBP2	6655	0.054	0.092	YES
37	NUP35	NUP35	NUP35	6865	0.051	0.089	YES
38	HNRNPU	HNRNPU	HNRNPU	6899	0.05	0.096	YES
39	PRPF8	PRPF8	PRPF8	6916	0.05	0.1	YES
40	SNRPD1	SNRPD1	SNRPD1	6921	0.05	0.11	YES
41	HNRNPR	HNRNPR	HNRNPR	7013	0.049	0.12	YES
42	RBM5	RBM5	RBM5	7140	0.047	0.12	YES
43	NUPL2	NUPL2	NUPL2	7148	0.047	0.12	YES
44	CCAR1	CCAR1	CCAR1	7183	0.046	0.13	YES
45	CDK7	CDK7	CDK7	7208	0.046	0.14	YES
46	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	7212	0.046	0.15	YES
47	SNRNP40	SNRNP40	SNRNP40	7252	0.046	0.15	YES
48	HNRNPD	HNRNPD	HNRNPD	7270	0.045	0.16	YES
49	NUP37	NUP37	NUP37	7282	0.045	0.17	YES
50	HNRNPA3	HNRNPA3	HNRNPA3	7285	0.045	0.17	YES
51	SNRPB2	SNRPB2	SNRPB2	7291	0.045	0.18	YES
52	GTF2H3	GTF2H3	GTF2H3	7313	0.045	0.19	YES
53	METTL3	METTL3	METTL3	7326	0.044	0.2	YES
54	SF3A3	SF3A3	SF3A3	7367	0.044	0.2	YES
55	SF3B14	SF3B14	SF3B14	7368	0.044	0.21	YES
56	NUP88	NUP88	NUP88	7381	0.044	0.22	YES
57	MAGOH	MAGOH	MAGOH	7414	0.043	0.22	YES
58	PABPN1	PABPN1	PABPN1	7450	0.043	0.23	YES
59	EFTUD2	EFTUD2	EFTUD2	7460	0.042	0.23	YES
60	HNRNPUL1	HNRNPUL1	HNRNPUL1	7467	0.042	0.24	YES
61	NUDT21	NUDT21	NUDT21	7515	0.042	0.24	YES
62	POLR2C	POLR2C	POLR2C	7578	0.041	0.25	YES
63	LSM2	LSM2	LSM2	7584	0.041	0.26	YES
64	HNRNPM	HNRNPM	HNRNPM	7596	0.041	0.26	YES
65	NCBP2	NCBP2	NCBP2	7606	0.041	0.27	YES
66	DDX23	DDX23	DDX23	7620	0.04	0.27	YES
67	HNRNPA0	HNRNPA0	HNRNPA0	7642	0.04	0.28	YES
68	CSTF1	CSTF1	CSTF1	7705	0.039	0.28	YES
69	NUP210	NUP210	NUP210	7707	0.039	0.29	YES
70	MNAT1	MNAT1	MNAT1	7717	0.039	0.3	YES
71	DHX38	DHX38	DHX38	7742	0.039	0.3	YES
72	HNRNPH1	HNRNPH1	HNRNPH1	7758	0.039	0.31	YES
73	NUP188	NUP188	NUP188	7771	0.038	0.31	YES
74	GTF2F2	GTF2F2	GTF2F2	7823	0.038	0.32	YES
75	GTF2H4	GTF2H4	GTF2H4	7843	0.038	0.32	YES
76	SNRPA	SNRPA	SNRPA	7945	0.036	0.32	YES
77	HNRNPL	HNRNPL	HNRNPL	8013	0.035	0.33	YES
78	NUP93	NUP93	NUP93	8156	0.034	0.32	YES
79	HNRNPC	HNRNPC	HNRNPC	8353	0.032	0.32	YES
80	CLP1	CLP1	CLP1	8407	0.031	0.32	YES
81	SMC1A	SMC1A	SMC1A	8537	0.029	0.32	YES
82	PRPF6	PRPF6	PRPF6	8588	0.029	0.32	YES
83	SEH1L	SEH1L	SEH1L	8641	0.028	0.32	YES
84	POLR2J	POLR2J	POLR2J	8722	0.027	0.32	YES
85	SF3B4	SF3B4	SF3B4	8871	0.025	0.32	YES
86	NUPL1	NUPL1	NUPL1	8939	0.025	0.32	YES
87	CPSF7	CPSF7	CPSF7	8950	0.024	0.33	YES
88	DNAJC8	DNAJC8	DNAJC8	9081	0.023	0.32	YES
89	CD2BP2	CD2BP2	CD2BP2	9096	0.022	0.33	YES
90	NUP205	NUP205	NUP205	9104	0.022	0.33	YES
91	SNRPD2	SNRPD2	SNRPD2	9106	0.022	0.33	YES
92	GTF2H2B	GTF2H2B	GTF2H2B	9128	0.022	0.34	YES
93	NUP214	NUP214	NUP214	9132	0.022	0.34	YES
94	SF3B5	SF3B5	SF3B5	9230	0.021	0.34	NO
95	U2AF1	U2AF1	U2AF1	9319	0.02	0.34	NO
96	CSTF3	CSTF3	CSTF3	9417	0.018	0.33	NO
97	SLBP	SLBP	SLBP	9484	0.017	0.33	NO
98	HNRNPK	HNRNPK	HNRNPK	9489	0.017	0.34	NO
99	U2AF2	U2AF2	U2AF2	9568	0.016	0.34	NO
100	SF3B2	SF3B2	SF3B2	9606	0.016	0.34	NO
101	NUP54	NUP54	NUP54	9743	0.014	0.33	NO
102	SF3A2	SF3A2	SF3A2	9943	0.011	0.32	NO
103	NXF1	NXF1	NXF1	9957	0.011	0.32	NO
104	EIF4E	EIF4E	EIF4E	9991	0.011	0.32	NO
105	CSTF2	CSTF2	CSTF2	10040	0.01	0.32	NO
106	PTBP1	PTBP1	PTBP1	10132	0.0092	0.32	NO
107	PRPF4	PRPF4	PRPF4	10186	0.0085	0.32	NO
108	PCBP1	PCBP1	PCBP1	10262	0.0076	0.32	NO
109	NCBP1	NCBP1	NCBP1	10306	0.0071	0.31	NO
110	SF3A1	SF3A1	SF3A1	10314	0.007	0.32	NO
111	THOC4	THOC4	THOC4	10339	0.0066	0.32	NO
112	POLR2H	POLR2H	POLR2H	10357	0.0063	0.32	NO
113	TXNL4A	TXNL4A	TXNL4A	10402	0.0058	0.31	NO
114	PAPOLA	PAPOLA	PAPOLA	10416	0.0057	0.31	NO
115	GTF2F1	GTF2F1	GTF2F1	10488	0.0047	0.31	NO
116	POLR2B	POLR2B	POLR2B	10580	0.0035	0.31	NO
117	YBX1	YBX1	YBX1	10746	0.001	0.3	NO
118	SNRNP70	SNRNP70	SNRNP70	10785	0.00054	0.3	NO
119	ERCC2	ERCC2	ERCC2	10790	0.00048	0.3	NO
120	NUP50	NUP50	NUP50	10809	0.00026	0.29	NO
121	CPSF2	CPSF2	CPSF2	11011	-0.0024	0.28	NO
122	ADAR	ADAR	ADAR	11351	-0.0069	0.27	NO
123	GTF2H1	GTF2H1	GTF2H1	11455	-0.0084	0.26	NO
124	NFX1	NFX1	NFX1	11986	-0.016	0.24	NO
125	SNRPD3	SNRPD3	SNRPD3	11993	-0.016	0.24	NO
126	SNRPA1	SNRPA1	SNRPA1	11994	-0.016	0.24	NO
127	POLR2F	POLR2F	POLR2F	12058	-0.017	0.24	NO
128	NUP62	NUP62	NUP62	12092	-0.018	0.24	NO
129	HNRNPH2	HNRNPH2	HNRNPH2	12202	-0.019	0.24	NO
130	POLR2E	POLR2E	POLR2E	12259	-0.02	0.24	NO
131	POLR2G	POLR2G	POLR2G	12345	-0.021	0.24	NO
132	NUP85	NUP85	NUP85	12468	-0.023	0.24	NO
133	LSM10	LSM10	LSM10	12555	-0.024	0.24	NO
134	HNRNPF	HNRNPF	HNRNPF	12637	-0.026	0.24	NO
135	CCNH	CCNH	CCNH	12688	-0.027	0.24	NO
136	PCF11	PCF11	PCF11	12724	-0.027	0.24	NO
137	NHP2L1	NHP2L1	NHP2L1	12798	-0.029	0.24	NO
138	CPSF1	CPSF1	CPSF1	12987	-0.032	0.24	NO
139	PHF5A	PHF5A	PHF5A	13048	-0.033	0.24	NO
140	LSM11	LSM11	LSM11	13353	-0.039	0.23	NO
141	POLR2L	POLR2L	POLR2L	13413	-0.04	0.24	NO
142	GTF2H2	GTF2H2	GTF2H2	14343	-0.062	0.2	NO
143	ADARB1	ADARB1	ADARB1	15363	-0.095	0.16	NO
144	POLR2K	POLR2K	POLR2K	15496	-0.1	0.17	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: BIOCARTA CHREBP2 PATHWAY.

Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 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 FANCONI PATHWAY

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	NUP107	NUP107	NUP107	3430	0.13	-0.12	YES
2	UPF3B	UPF3B	UPF3B	4371	0.098	-0.12	YES
3	NUP133	NUP133	NUP133	4381	0.097	-0.072	YES
4	NUP43	NUP43	NUP43	4695	0.09	-0.043	YES
5	AAAS	AAAS	AAAS	4972	0.084	-0.015	YES
6	NUP155	NUP155	NUP155	4974	0.084	0.027	YES
7	TPR	TPR	TPR	5085	0.081	0.063	YES
8	CPSF3	CPSF3	CPSF3	5498	0.073	0.078	YES
9	RANBP2	RANBP2	RANBP2	5518	0.072	0.11	YES
10	CDC40	CDC40	CDC40	5672	0.069	0.14	YES
11	RBM8A	RBM8A	RBM8A	5743	0.068	0.17	YES
12	NUP153	NUP153	NUP153	5845	0.066	0.2	YES
13	RAE1	RAE1	RAE1	5918	0.065	0.23	YES
14	RNPS1	RNPS1	RNPS1	6115	0.061	0.25	YES
15	POM121	POM121	POM121	6455	0.057	0.26	YES
16	SRRM1	SRRM1	SRRM1	6529	0.056	0.28	YES
17	NUP35	NUP35	NUP35	6865	0.051	0.29	YES
18	NUPL2	NUPL2	NUPL2	7148	0.047	0.3	YES
19	NUP37	NUP37	NUP37	7282	0.045	0.32	YES
20	NUP88	NUP88	NUP88	7381	0.044	0.33	YES
21	MAGOH	MAGOH	MAGOH	7414	0.043	0.36	YES
22	NCBP2	NCBP2	NCBP2	7606	0.041	0.36	YES
23	NUP210	NUP210	NUP210	7707	0.039	0.38	YES
24	DHX38	DHX38	DHX38	7742	0.039	0.4	YES
25	NUP188	NUP188	NUP188	7771	0.038	0.42	YES
26	NUP93	NUP93	NUP93	8156	0.034	0.41	NO
27	SEH1L	SEH1L	SEH1L	8641	0.028	0.4	NO
28	NUPL1	NUPL1	NUPL1	8939	0.025	0.4	NO
29	NUP205	NUP205	NUP205	9104	0.022	0.4	NO
30	NUP214	NUP214	NUP214	9132	0.022	0.41	NO
31	U2AF1	U2AF1	U2AF1	9319	0.02	0.41	NO
32	SLBP	SLBP	SLBP	9484	0.017	0.41	NO
33	U2AF2	U2AF2	U2AF2	9568	0.016	0.41	NO
34	NUP54	NUP54	NUP54	9743	0.014	0.41	NO
35	NXF1	NXF1	NXF1	9957	0.011	0.4	NO
36	EIF4E	EIF4E	EIF4E	9991	0.011	0.41	NO
37	NCBP1	NCBP1	NCBP1	10306	0.0071	0.4	NO
38	THOC4	THOC4	THOC4	10339	0.0066	0.4	NO
39	NUP50	NUP50	NUP50	10809	0.00026	0.37	NO
40	CPSF2	CPSF2	CPSF2	11011	-0.0024	0.36	NO
41	NFX1	NFX1	NFX1	11986	-0.016	0.32	NO
42	NUP62	NUP62	NUP62	12092	-0.018	0.32	NO
43	NUP85	NUP85	NUP85	12468	-0.023	0.31	NO
44	CPSF1	CPSF1	CPSF1	12987	-0.032	0.3	NO

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

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

genes ES table in pathway: PID HEDGEHOG GLIPATHWAY

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	NUP107	NUP107	NUP107	3430	0.13	-0.16	YES
2	SNRPE	SNRPE	SNRPE	3988	0.11	-0.17	YES
3	SNRNP200	SNRNP200	SNRNP200	4332	0.098	-0.17	YES
4	UPF3B	UPF3B	UPF3B	4371	0.098	-0.15	YES
5	NUP133	NUP133	NUP133	4381	0.097	-0.13	YES
6	NUP43	NUP43	NUP43	4695	0.09	-0.13	YES
7	SNRPF	SNRPF	SNRPF	4723	0.089	-0.11	YES
8	AAAS	AAAS	AAAS	4972	0.084	-0.11	YES
9	NUP155	NUP155	NUP155	4974	0.084	-0.094	YES
10	TPR	TPR	TPR	5085	0.081	-0.084	YES
11	CPSF3	CPSF3	CPSF3	5498	0.073	-0.091	YES
12	RANBP2	RANBP2	RANBP2	5518	0.072	-0.078	YES
13	HNRNPA1	HNRNPA1	HNRNPA1	5629	0.07	-0.07	YES
14	POLR2A	POLR2A	POLR2A	5635	0.07	-0.056	YES
15	CDC40	CDC40	CDC40	5672	0.069	-0.044	YES
16	RBM8A	RBM8A	RBM8A	5743	0.068	-0.034	YES
17	DHX9	DHX9	DHX9	5764	0.068	-0.022	YES
18	NUP153	NUP153	NUP153	5845	0.066	-0.013	YES
19	RAE1	RAE1	RAE1	5918	0.065	-0.0034	YES
20	POLR2I	POLR2I	POLR2I	5933	0.065	0.0088	YES
21	FUS	FUS	FUS	6006	0.064	0.018	YES
22	RNPS1	RNPS1	RNPS1	6115	0.061	0.024	YES
23	POLR2D	POLR2D	POLR2D	6214	0.06	0.031	YES
24	SNRPG	SNRPG	SNRPG	6311	0.058	0.037	YES
25	SF3B1	SF3B1	SF3B1	6367	0.058	0.046	YES
26	SNRPB	SNRPB	SNRPB	6443	0.057	0.053	YES
27	POM121	POM121	POM121	6455	0.057	0.064	YES
28	RBMX	RBMX	RBMX	6501	0.056	0.073	YES
29	SRRM1	SRRM1	SRRM1	6529	0.056	0.082	YES
30	SF3B3	SF3B3	SF3B3	6552	0.055	0.092	YES
31	PCBP2	PCBP2	PCBP2	6655	0.054	0.098	YES
32	NUP35	NUP35	NUP35	6865	0.051	0.096	YES
33	HNRNPU	HNRNPU	HNRNPU	6899	0.05	0.1	YES
34	PRPF8	PRPF8	PRPF8	6916	0.05	0.11	YES
35	SNRPD1	SNRPD1	SNRPD1	6921	0.05	0.12	YES
36	HNRNPR	HNRNPR	HNRNPR	7013	0.049	0.13	YES
37	RBM5	RBM5	RBM5	7140	0.047	0.13	YES
38	NUPL2	NUPL2	NUPL2	7148	0.047	0.14	YES
39	CCAR1	CCAR1	CCAR1	7183	0.046	0.15	YES
40	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	7212	0.046	0.16	YES
41	SNRNP40	SNRNP40	SNRNP40	7252	0.046	0.16	YES
42	HNRNPD	HNRNPD	HNRNPD	7270	0.045	0.17	YES
43	NUP37	NUP37	NUP37	7282	0.045	0.18	YES
44	HNRNPA3	HNRNPA3	HNRNPA3	7285	0.045	0.19	YES
45	SNRPB2	SNRPB2	SNRPB2	7291	0.045	0.2	YES
46	METTL3	METTL3	METTL3	7326	0.044	0.2	YES
47	SF3A3	SF3A3	SF3A3	7367	0.044	0.21	YES
48	SF3B14	SF3B14	SF3B14	7368	0.044	0.22	YES
49	NUP88	NUP88	NUP88	7381	0.044	0.23	YES
50	MAGOH	MAGOH	MAGOH	7414	0.043	0.23	YES
51	PABPN1	PABPN1	PABPN1	7450	0.043	0.24	YES
52	EFTUD2	EFTUD2	EFTUD2	7460	0.042	0.25	YES
53	HNRNPUL1	HNRNPUL1	HNRNPUL1	7467	0.042	0.26	YES
54	NUDT21	NUDT21	NUDT21	7515	0.042	0.26	YES
55	POLR2C	POLR2C	POLR2C	7578	0.041	0.27	YES
56	LSM2	LSM2	LSM2	7584	0.041	0.28	YES
57	HNRNPM	HNRNPM	HNRNPM	7596	0.041	0.28	YES
58	NCBP2	NCBP2	NCBP2	7606	0.041	0.29	YES
59	DDX23	DDX23	DDX23	7620	0.04	0.3	YES
60	HNRNPA0	HNRNPA0	HNRNPA0	7642	0.04	0.3	YES
61	CSTF1	CSTF1	CSTF1	7705	0.039	0.31	YES
62	NUP210	NUP210	NUP210	7707	0.039	0.32	YES
63	DHX38	DHX38	DHX38	7742	0.039	0.32	YES
64	HNRNPH1	HNRNPH1	HNRNPH1	7758	0.039	0.33	YES
65	NUP188	NUP188	NUP188	7771	0.038	0.34	YES
66	GTF2F2	GTF2F2	GTF2F2	7823	0.038	0.34	YES
67	SNRPA	SNRPA	SNRPA	7945	0.036	0.34	YES
68	HNRNPL	HNRNPL	HNRNPL	8013	0.035	0.35	YES
69	NUP93	NUP93	NUP93	8156	0.034	0.35	YES
70	HNRNPC	HNRNPC	HNRNPC	8353	0.032	0.34	YES
71	CLP1	CLP1	CLP1	8407	0.031	0.34	YES
72	SMC1A	SMC1A	SMC1A	8537	0.029	0.34	YES
73	PRPF6	PRPF6	PRPF6	8588	0.029	0.35	YES
74	SEH1L	SEH1L	SEH1L	8641	0.028	0.35	YES
75	POLR2J	POLR2J	POLR2J	8722	0.027	0.35	YES
76	SF3B4	SF3B4	SF3B4	8871	0.025	0.35	YES
77	NUPL1	NUPL1	NUPL1	8939	0.025	0.35	YES
78	CPSF7	CPSF7	CPSF7	8950	0.024	0.35	YES
79	DNAJC8	DNAJC8	DNAJC8	9081	0.023	0.35	YES
80	CD2BP2	CD2BP2	CD2BP2	9096	0.022	0.35	YES
81	NUP205	NUP205	NUP205	9104	0.022	0.36	YES
82	SNRPD2	SNRPD2	SNRPD2	9106	0.022	0.36	YES
83	NUP214	NUP214	NUP214	9132	0.022	0.37	YES
84	SF3B5	SF3B5	SF3B5	9230	0.021	0.36	NO
85	U2AF1	U2AF1	U2AF1	9319	0.02	0.36	NO
86	CSTF3	CSTF3	CSTF3	9417	0.018	0.36	NO
87	SLBP	SLBP	SLBP	9484	0.017	0.36	NO
88	HNRNPK	HNRNPK	HNRNPK	9489	0.017	0.37	NO
89	U2AF2	U2AF2	U2AF2	9568	0.016	0.36	NO
90	SF3B2	SF3B2	SF3B2	9606	0.016	0.37	NO
91	NUP54	NUP54	NUP54	9743	0.014	0.36	NO
92	SF3A2	SF3A2	SF3A2	9943	0.011	0.35	NO
93	NXF1	NXF1	NXF1	9957	0.011	0.35	NO
94	EIF4E	EIF4E	EIF4E	9991	0.011	0.35	NO
95	CSTF2	CSTF2	CSTF2	10040	0.01	0.35	NO
96	PTBP1	PTBP1	PTBP1	10132	0.0092	0.35	NO
97	PRPF4	PRPF4	PRPF4	10186	0.0085	0.35	NO
98	PCBP1	PCBP1	PCBP1	10262	0.0076	0.35	NO
99	NCBP1	NCBP1	NCBP1	10306	0.0071	0.35	NO
100	SF3A1	SF3A1	SF3A1	10314	0.007	0.35	NO
101	THOC4	THOC4	THOC4	10339	0.0066	0.35	NO
102	POLR2H	POLR2H	POLR2H	10357	0.0063	0.35	NO
103	TXNL4A	TXNL4A	TXNL4A	10402	0.0058	0.35	NO
104	PAPOLA	PAPOLA	PAPOLA	10416	0.0057	0.35	NO
105	GTF2F1	GTF2F1	GTF2F1	10488	0.0047	0.34	NO
106	POLR2B	POLR2B	POLR2B	10580	0.0035	0.34	NO
107	YBX1	YBX1	YBX1	10746	0.001	0.33	NO
108	SNRNP70	SNRNP70	SNRNP70	10785	0.00054	0.33	NO
109	NUP50	NUP50	NUP50	10809	0.00026	0.33	NO
110	CPSF2	CPSF2	CPSF2	11011	-0.0024	0.32	NO
111	NFX1	NFX1	NFX1	11986	-0.016	0.27	NO
112	SNRPD3	SNRPD3	SNRPD3	11993	-0.016	0.27	NO
113	SNRPA1	SNRPA1	SNRPA1	11994	-0.016	0.27	NO
114	POLR2F	POLR2F	POLR2F	12058	-0.017	0.27	NO
115	NUP62	NUP62	NUP62	12092	-0.018	0.28	NO
116	HNRNPH2	HNRNPH2	HNRNPH2	12202	-0.019	0.27	NO
117	POLR2E	POLR2E	POLR2E	12259	-0.02	0.28	NO
118	POLR2G	POLR2G	POLR2G	12345	-0.021	0.27	NO
119	NUP85	NUP85	NUP85	12468	-0.023	0.27	NO
120	HNRNPF	HNRNPF	HNRNPF	12637	-0.026	0.27	NO
121	PCF11	PCF11	PCF11	12724	-0.027	0.27	NO
122	NHP2L1	NHP2L1	NHP2L1	12798	-0.029	0.27	NO
123	CPSF1	CPSF1	CPSF1	12987	-0.032	0.27	NO
124	PHF5A	PHF5A	PHF5A	13048	-0.033	0.27	NO
125	POLR2L	POLR2L	POLR2L	13413	-0.04	0.26	NO
126	POLR2K	POLR2K	POLR2K	15496	-0.1	0.17	NO

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

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: PID HEDGEHOG GLIPATHWAY, 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 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	NINL	NINL	NINL	817	0.3	0.055	YES
2	CEP290	CEP290	CEP290	2630	0.16	0.01	YES
3	FGFR1OP	FGFR1OP	FGFR1OP	2732	0.16	0.056	YES
4	ALMS1	ALMS1	ALMS1	2925	0.15	0.095	YES
5	TUBA1A	TUBA1A	TUBA1A	3254	0.13	0.12	YES
6	CEP250	CEP250	CEP250	3404	0.13	0.16	YES
7	NEK2	NEK2	NEK2	3659	0.12	0.18	YES
8	CEP76	CEP76	CEP76	3923	0.11	0.2	YES
9	CENPJ	CENPJ	CENPJ	4508	0.094	0.2	YES
10	CLASP1	CLASP1	CLASP1	4822	0.087	0.22	YES
11	PCM1	PCM1	PCM1	5454	0.074	0.21	YES
12	CDK5RAP2	CDK5RAP2	CDK5RAP2	5460	0.074	0.23	YES
13	DCTN2	DCTN2	DCTN2	5994	0.064	0.22	YES
14	PLK4	PLK4	PLK4	6051	0.063	0.24	YES
15	TUBB	TUBB	TUBB	6128	0.061	0.26	YES
16	PRKAR2B	PRKAR2B	PRKAR2B	6217	0.06	0.27	YES
17	CKAP5	CKAP5	CKAP5	6555	0.055	0.27	YES
18	PCNT	PCNT	PCNT	6637	0.054	0.29	YES
19	YWHAE	YWHAE	YWHAE	6704	0.053	0.3	YES
20	MAPRE1	MAPRE1	MAPRE1	6838	0.051	0.31	YES
21	DCTN1	DCTN1	DCTN1	6966	0.05	0.32	YES
22	OFD1	OFD1	OFD1	7155	0.047	0.32	YES
23	CSNK1E	CSNK1E	CSNK1E	7258	0.046	0.33	YES
24	AZI1	AZI1	AZI1	7295	0.045	0.35	YES
25	PAFAH1B1	PAFAH1B1	PAFAH1B1	7447	0.043	0.35	YES
26	DYNC1I2	DYNC1I2	DYNC1I2	7601	0.041	0.36	YES
27	PRKACA	PRKACA	PRKACA	7650	0.04	0.37	YES
28	TUBG1	TUBG1	TUBG1	7743	0.039	0.38	YES
29	NEDD1	NEDD1	NEDD1	7759	0.039	0.39	YES
30	CEP164	CEP164	CEP164	7856	0.037	0.4	YES
31	CEP192	CEP192	CEP192	8035	0.035	0.4	YES
32	CEP70	CEP70	CEP70	8371	0.031	0.39	YES
33	PLK1	PLK1	PLK1	8382	0.031	0.4	YES
34	PPP2R1A	PPP2R1A	PPP2R1A	8667	0.028	0.39	YES
35	CDK1	CDK1	CDK1	8677	0.028	0.4	YES
36	AKAP9	AKAP9	AKAP9	8849	0.026	0.4	YES
37	CEP57	CEP57	CEP57	9023	0.023	0.4	YES
38	CEP135	CEP135	CEP135	9092	0.023	0.4	YES
39	CETN2	CETN2	CETN2	9467	0.018	0.39	NO
40	DYNLL1	DYNLL1	DYNLL1	9655	0.015	0.38	NO
41	ACTR1A	ACTR1A	ACTR1A	9670	0.015	0.39	NO
42	SDCCAG8	SDCCAG8	SDCCAG8	10263	0.0076	0.36	NO
43	HAUS2	HAUS2	HAUS2	10426	0.0055	0.35	NO
44	CEP63	CEP63	CEP63	10499	0.0046	0.35	NO
45	YWHAG	YWHAG	YWHAG	10605	0.0031	0.34	NO
46	DCTN3	DCTN3	DCTN3	10772	0.00066	0.34	NO
47	DYNC1H1	DYNC1H1	DYNC1H1	10984	-0.002	0.32	NO
48	CSNK1D	CSNK1D	CSNK1D	11214	-0.0052	0.31	NO
49	HSP90AA1	HSP90AA1	HSP90AA1	12101	-0.018	0.27	NO
50	SSNA1	SSNA1	SSNA1	12307	-0.021	0.27	NO
51	CEP72	CEP72	CEP72	12394	-0.022	0.27	NO
52	TUBA4A	TUBA4A	TUBA4A	16807	-0.19	0.095	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: REACTOME METABOLISM OF NON CODING RNA.

Figure S30. 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 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA

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	NUP107	NUP107	NUP107	3430	0.13	-0.09	YES
2	NUP133	NUP133	NUP133	4381	0.097	-0.069	YES
3	NUP43	NUP43	NUP43	4695	0.09	-0.02	YES
4	AAAS	AAAS	AAAS	4972	0.084	0.027	YES
5	NUP155	NUP155	NUP155	4974	0.084	0.089	YES
6	TPR	TPR	TPR	5085	0.081	0.14	YES
7	RANBP2	RANBP2	RANBP2	5518	0.072	0.17	YES
8	NUP153	NUP153	NUP153	5845	0.066	0.21	YES
9	RAE1	RAE1	RAE1	5918	0.065	0.25	YES
10	POM121	POM121	POM121	6455	0.057	0.26	YES
11	NUP35	NUP35	NUP35	6865	0.051	0.28	YES
12	KPNB1	KPNB1	KPNB1	7046	0.048	0.3	YES
13	NUPL2	NUPL2	NUPL2	7148	0.047	0.33	YES
14	NUP37	NUP37	NUP37	7282	0.045	0.36	YES
15	NUP88	NUP88	NUP88	7381	0.044	0.39	YES
16	NUP210	NUP210	NUP210	7707	0.039	0.4	YES
17	NUP188	NUP188	NUP188	7771	0.038	0.42	YES
18	NUP93	NUP93	NUP93	8156	0.034	0.43	YES
19	SEH1L	SEH1L	SEH1L	8641	0.028	0.42	YES
20	KPNA1	KPNA1	KPNA1	8784	0.026	0.44	YES
21	NUPL1	NUPL1	NUPL1	8939	0.025	0.44	YES
22	NUP205	NUP205	NUP205	9104	0.022	0.45	YES
23	NUP214	NUP214	NUP214	9132	0.022	0.47	YES
24	NUP54	NUP54	NUP54	9743	0.014	0.44	NO
25	NUP50	NUP50	NUP50	10809	0.00026	0.39	NO
26	NUP62	NUP62	NUP62	12092	-0.018	0.33	NO
27	NUP85	NUP85	NUP85	12468	-0.023	0.33	NO

Figure S31. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA.

Figure S32. 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 GENERIC TRANSCRIPTION 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	NUP107	NUP107	NUP107	3430	0.13	-0.092	YES
2	NUP133	NUP133	NUP133	4381	0.097	-0.073	YES
3	NUP43	NUP43	NUP43	4695	0.09	-0.025	YES
4	AAAS	AAAS	AAAS	4972	0.084	0.021	YES
5	NUP155	NUP155	NUP155	4974	0.084	0.081	YES
6	TPR	TPR	TPR	5085	0.081	0.13	YES
7	RANBP2	RANBP2	RANBP2	5518	0.072	0.16	YES
8	NUP153	NUP153	NUP153	5845	0.066	0.19	YES
9	RAE1	RAE1	RAE1	5918	0.065	0.24	YES
10	XPO1	XPO1	XPO1	6426	0.057	0.25	YES
11	POM121	POM121	POM121	6455	0.057	0.29	YES
12	NUP35	NUP35	NUP35	6865	0.051	0.3	YES
13	RAN	RAN	RAN	6950	0.05	0.34	YES
14	NUPL2	NUPL2	NUPL2	7148	0.047	0.36	YES
15	NUP37	NUP37	NUP37	7282	0.045	0.38	YES
16	NUP88	NUP88	NUP88	7381	0.044	0.41	YES
17	NUP210	NUP210	NUP210	7707	0.039	0.42	YES
18	NUP188	NUP188	NUP188	7771	0.038	0.45	YES
19	NUP93	NUP93	NUP93	8156	0.034	0.45	YES
20	SEH1L	SEH1L	SEH1L	8641	0.028	0.44	YES
21	NUPL1	NUPL1	NUPL1	8939	0.025	0.45	YES
22	NUP205	NUP205	NUP205	9104	0.022	0.45	YES
23	NUP214	NUP214	NUP214	9132	0.022	0.47	YES
24	NUP54	NUP54	NUP54	9743	0.014	0.45	NO
25	NUP50	NUP50	NUP50	10809	0.00026	0.39	NO
26	NUP62	NUP62	NUP62	12092	-0.018	0.33	NO
27	NUP85	NUP85	NUP85	12468	-0.023	0.33	NO

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

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

genes ES table in pathway: REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NUP107	NUP107	NUP107	3430	0.13	-0.097	YES
2	NUP133	NUP133	NUP133	4381	0.097	-0.082	YES
3	NUP43	NUP43	NUP43	4695	0.09	-0.037	YES
4	AAAS	AAAS	AAAS	4972	0.084	0.0052	YES
5	NUP155	NUP155	NUP155	4974	0.084	0.062	YES
6	TPR	TPR	TPR	5085	0.081	0.11	YES
7	CPSF3	CPSF3	CPSF3	5498	0.073	0.14	YES
8	RANBP2	RANBP2	RANBP2	5518	0.072	0.19	YES
9	NUP153	NUP153	NUP153	5845	0.066	0.22	YES
10	RAE1	RAE1	RAE1	5918	0.065	0.26	YES
11	POM121	POM121	POM121	6455	0.057	0.27	YES
12	NUP35	NUP35	NUP35	6865	0.051	0.28	YES
13	NUPL2	NUPL2	NUPL2	7148	0.047	0.3	YES
14	NUP37	NUP37	NUP37	7282	0.045	0.32	YES
15	NUP88	NUP88	NUP88	7381	0.044	0.35	YES
16	NCBP2	NCBP2	NCBP2	7606	0.041	0.36	YES
17	NUP210	NUP210	NUP210	7707	0.039	0.38	YES
18	NUP188	NUP188	NUP188	7771	0.038	0.41	YES
19	NUP93	NUP93	NUP93	8156	0.034	0.41	YES
20	SEH1L	SEH1L	SEH1L	8641	0.028	0.4	YES
21	NUPL1	NUPL1	NUPL1	8939	0.025	0.4	YES
22	NUP205	NUP205	NUP205	9104	0.022	0.41	YES
23	NUP214	NUP214	NUP214	9132	0.022	0.42	YES
24	NUP54	NUP54	NUP54	9743	0.014	0.4	NO
25	NXF1	NXF1	NXF1	9957	0.011	0.4	NO
26	EIF4E	EIF4E	EIF4E	9991	0.011	0.4	NO
27	NCBP1	NCBP1	NCBP1	10306	0.0071	0.39	NO
28	THOC4	THOC4	THOC4	10339	0.0066	0.39	NO
29	NUP50	NUP50	NUP50	10809	0.00026	0.37	NO
30	CPSF2	CPSF2	CPSF2	11011	-0.0024	0.36	NO
31	NUP62	NUP62	NUP62	12092	-0.018	0.31	NO
32	NUP85	NUP85	NUP85	12468	-0.023	0.31	NO
33	CPSF1	CPSF1	CPSF1	12987	-0.032	0.3	NO

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

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

genes ES table in pathway: REACTOME NEUROTRANSMITTER RELEASE CYCLE

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	NINL	NINL	NINL	817	0.3	0.046	YES
2	CEP290	CEP290	CEP290	2630	0.16	-0.0027	YES
3	FGFR1OP	FGFR1OP	FGFR1OP	2732	0.16	0.039	YES
4	ALMS1	ALMS1	ALMS1	2925	0.15	0.074	YES
5	TUBA1A	TUBA1A	TUBA1A	3254	0.13	0.097	YES
6	CEP250	CEP250	CEP250	3404	0.13	0.13	YES
7	NEK2	NEK2	NEK2	3659	0.12	0.15	YES
8	CEP76	CEP76	CEP76	3923	0.11	0.17	YES
9	CENPJ	CENPJ	CENPJ	4508	0.094	0.17	YES
10	CLASP1	CLASP1	CLASP1	4822	0.087	0.18	YES
11	PCM1	PCM1	PCM1	5454	0.074	0.16	YES
12	CDK5RAP2	CDK5RAP2	CDK5RAP2	5460	0.074	0.19	YES
13	DCTN2	DCTN2	DCTN2	5994	0.064	0.18	YES
14	PLK4	PLK4	PLK4	6051	0.063	0.19	YES
15	TUBB	TUBB	TUBB	6128	0.061	0.21	YES
16	PRKAR2B	PRKAR2B	PRKAR2B	6217	0.06	0.22	YES
17	TUBG2	TUBG2	TUBG2	6280	0.059	0.24	YES
18	CCNB1	CCNB1	CCNB1	6539	0.056	0.24	YES
19	CKAP5	CKAP5	CKAP5	6555	0.055	0.25	YES
20	PCNT	PCNT	PCNT	6637	0.054	0.27	YES
21	YWHAE	YWHAE	YWHAE	6704	0.053	0.28	YES
22	MAPRE1	MAPRE1	MAPRE1	6838	0.051	0.29	YES
23	DCTN1	DCTN1	DCTN1	6966	0.05	0.3	YES
24	OFD1	OFD1	OFD1	7155	0.047	0.3	YES
25	CSNK1E	CSNK1E	CSNK1E	7258	0.046	0.31	YES
26	AZI1	AZI1	AZI1	7295	0.045	0.32	YES
27	PAFAH1B1	PAFAH1B1	PAFAH1B1	7447	0.043	0.32	YES
28	DYNC1I2	DYNC1I2	DYNC1I2	7601	0.041	0.33	YES
29	PRKACA	PRKACA	PRKACA	7650	0.04	0.34	YES
30	TUBG1	TUBG1	TUBG1	7743	0.039	0.34	YES
31	NEDD1	NEDD1	NEDD1	7759	0.039	0.36	YES
32	CEP164	CEP164	CEP164	7856	0.037	0.36	YES
33	CEP192	CEP192	CEP192	8035	0.035	0.36	YES
34	CEP70	CEP70	CEP70	8371	0.031	0.35	YES
35	PLK1	PLK1	PLK1	8382	0.031	0.36	YES
36	NUMA1	NUMA1	NUMA1	8477	0.03	0.37	YES
37	PPP2R1A	PPP2R1A	PPP2R1A	8667	0.028	0.36	YES
38	CDK1	CDK1	CDK1	8677	0.028	0.37	YES
39	AKAP9	AKAP9	AKAP9	8849	0.026	0.37	YES
40	CEP57	CEP57	CEP57	9023	0.023	0.37	YES
41	CEP135	CEP135	CEP135	9092	0.023	0.37	YES
42	TUBGCP3	TUBGCP3	TUBGCP3	9179	0.021	0.37	YES
43	CETN2	CETN2	CETN2	9467	0.018	0.36	NO
44	DYNLL1	DYNLL1	DYNLL1	9655	0.015	0.36	NO
45	ACTR1A	ACTR1A	ACTR1A	9670	0.015	0.36	NO
46	SDCCAG8	SDCCAG8	SDCCAG8	10263	0.0076	0.33	NO
47	TUBGCP2	TUBGCP2	TUBGCP2	10267	0.0076	0.33	NO
48	HAUS2	HAUS2	HAUS2	10426	0.0055	0.33	NO
49	CEP63	CEP63	CEP63	10499	0.0046	0.32	NO
50	YWHAG	YWHAG	YWHAG	10605	0.0031	0.32	NO
51	DCTN3	DCTN3	DCTN3	10772	0.00066	0.31	NO
52	DYNC1H1	DYNC1H1	DYNC1H1	10984	-0.002	0.3	NO
53	CSNK1D	CSNK1D	CSNK1D	11214	-0.0052	0.29	NO
54	TUBGCP5	TUBGCP5	TUBGCP5	11770	-0.013	0.26	NO
55	HSP90AA1	HSP90AA1	HSP90AA1	12101	-0.018	0.25	NO
56	SSNA1	SSNA1	SSNA1	12307	-0.021	0.25	NO
57	CEP72	CEP72	CEP72	12394	-0.022	0.25	NO
58	TUBGCP6	TUBGCP6	TUBGCP6	15250	-0.091	0.12	NO
59	TUBA4A	TUBA4A	TUBA4A	16807	-0.19	0.095	NO

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

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

genes ES table in pathway: REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES

Table S20. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NINL	NINL	NINL	817	0.3	0.031	YES
2	CEP290	CEP290	CEP290	2630	0.16	-0.027	YES
3	FGFR1OP	FGFR1OP	FGFR1OP	2732	0.16	0.0068	YES
4	CDC25A	CDC25A	CDC25A	2836	0.15	0.039	YES
5	ALMS1	ALMS1	ALMS1	2925	0.15	0.072	YES
6	TUBA1A	TUBA1A	TUBA1A	3254	0.13	0.088	YES
7	CEP250	CEP250	CEP250	3404	0.13	0.11	YES
8	NEK2	NEK2	NEK2	3659	0.12	0.13	YES
9	CEP76	CEP76	CEP76	3923	0.11	0.14	YES
10	CENPJ	CENPJ	CENPJ	4508	0.094	0.13	YES
11	CLASP1	CLASP1	CLASP1	4822	0.087	0.14	YES
12	WEE1	WEE1	WEE1	5394	0.075	0.13	YES
13	PCM1	PCM1	PCM1	5454	0.074	0.14	YES
14	CDK5RAP2	CDK5RAP2	CDK5RAP2	5460	0.074	0.16	YES
15	E2F3	E2F3	E2F3	5649	0.07	0.17	YES
16	CDK2	CDK2	CDK2	5989	0.064	0.16	YES
17	DCTN2	DCTN2	DCTN2	5994	0.064	0.18	YES
18	PLK4	PLK4	PLK4	6051	0.063	0.19	YES
19	TUBB	TUBB	TUBB	6128	0.061	0.2	YES
20	PRKAR2B	PRKAR2B	PRKAR2B	6217	0.06	0.22	YES
21	TUBG2	TUBG2	TUBG2	6280	0.059	0.23	YES
22	XPO1	XPO1	XPO1	6426	0.057	0.23	YES
23	CCNB1	CCNB1	CCNB1	6539	0.056	0.24	YES
24	CKAP5	CKAP5	CKAP5	6555	0.055	0.25	YES
25	PCNT	PCNT	PCNT	6637	0.054	0.26	YES
26	YWHAE	YWHAE	YWHAE	6704	0.053	0.27	YES
27	MAPRE1	MAPRE1	MAPRE1	6838	0.051	0.28	YES
28	DCTN1	DCTN1	DCTN1	6966	0.05	0.28	YES
29	E2F1	E2F1	E2F1	7081	0.048	0.29	YES
30	OFD1	OFD1	OFD1	7155	0.047	0.3	YES
31	CDK7	CDK7	CDK7	7208	0.046	0.31	YES
32	CSNK1E	CSNK1E	CSNK1E	7258	0.046	0.32	YES
33	AZI1	AZI1	AZI1	7295	0.045	0.32	YES
34	PAFAH1B1	PAFAH1B1	PAFAH1B1	7447	0.043	0.33	YES
35	DYNC1I2	DYNC1I2	DYNC1I2	7601	0.041	0.33	YES
36	PRKACA	PRKACA	PRKACA	7650	0.04	0.34	YES
37	MNAT1	MNAT1	MNAT1	7717	0.039	0.34	YES
38	TUBG1	TUBG1	TUBG1	7743	0.039	0.35	YES
39	CCNA2	CCNA2	CCNA2	7745	0.039	0.36	YES
40	NEDD1	NEDD1	NEDD1	7759	0.039	0.37	YES
41	CEP164	CEP164	CEP164	7856	0.037	0.37	YES
42	CEP192	CEP192	CEP192	8035	0.035	0.37	YES
43	CEP70	CEP70	CEP70	8371	0.031	0.36	YES
44	PLK1	PLK1	PLK1	8382	0.031	0.37	YES
45	NUMA1	NUMA1	NUMA1	8477	0.03	0.37	YES
46	PPP2R1A	PPP2R1A	PPP2R1A	8667	0.028	0.37	YES
47	CDK1	CDK1	CDK1	8677	0.028	0.38	YES
48	CDC25C	CDC25C	CDC25C	8728	0.027	0.38	YES
49	AKAP9	AKAP9	AKAP9	8849	0.026	0.38	YES
50	CEP57	CEP57	CEP57	9023	0.023	0.38	YES
51	CEP135	CEP135	CEP135	9092	0.023	0.38	YES
52	TUBGCP3	TUBGCP3	TUBGCP3	9179	0.021	0.38	YES
53	CCNB2	CCNB2	CCNB2	9198	0.021	0.38	YES
54	CCNA1	CCNA1	CCNA1	9201	0.021	0.39	YES
55	CETN2	CETN2	CETN2	9467	0.018	0.38	NO
56	DYNLL1	DYNLL1	DYNLL1	9655	0.015	0.37	NO
57	ACTR1A	ACTR1A	ACTR1A	9670	0.015	0.37	NO
58	SDCCAG8	SDCCAG8	SDCCAG8	10263	0.0076	0.34	NO
59	TUBGCP2	TUBGCP2	TUBGCP2	10267	0.0076	0.35	NO
60	CDC25B	CDC25B	CDC25B	10330	0.0067	0.34	NO
61	HAUS2	HAUS2	HAUS2	10426	0.0055	0.34	NO
62	CEP63	CEP63	CEP63	10499	0.0046	0.34	NO
63	YWHAG	YWHAG	YWHAG	10605	0.0031	0.33	NO
64	DCTN3	DCTN3	DCTN3	10772	0.00066	0.32	NO
65	PKMYT1	PKMYT1	PKMYT1	10795	0.00044	0.32	NO
66	DYNC1H1	DYNC1H1	DYNC1H1	10984	-0.002	0.31	NO
67	CSNK1D	CSNK1D	CSNK1D	11214	-0.0052	0.3	NO
68	TUBGCP5	TUBGCP5	TUBGCP5	11770	-0.013	0.28	NO
69	HSP90AA1	HSP90AA1	HSP90AA1	12101	-0.018	0.26	NO
70	SSNA1	SSNA1	SSNA1	12307	-0.021	0.26	NO
71	CEP72	CEP72	CEP72	12394	-0.022	0.26	NO
72	CCNH	CCNH	CCNH	12688	-0.027	0.25	NO
73	TUBGCP6	TUBGCP6	TUBGCP6	15250	-0.091	0.13	NO
74	TUBA4A	TUBA4A	TUBA4A	16807	-0.19	0.095	NO

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

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus3 enriched pathways

Table 5. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus3. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG PURINE METABOLISM	153	genes.ES.table	0.3	1.3	0.026	0.22	1	0.17	0.15	0.14	0.18	0
KEGG N GLYCAN BIOSYNTHESIS	46	genes.ES.table	0.33	1.5	0.092	0.14	0.99	0.24	0.22	0.19	0.098	0
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	43	genes.ES.table	0.45	1.6	0.054	0.079	0.91	0.42	0.28	0.3	0.04	0.001
KEGG MAPK SIGNALING PATHWAY	255	genes.ES.table	0.43	1.6	0.012	0.097	0.96	0.28	0.18	0.23	0.055	0
KEGG ERBB SIGNALING PATHWAY	87	genes.ES.table	0.43	1.7	0.011	0.074	0.88	0.22	0.16	0.18	0.035	0.001
KEGG CALCIUM SIGNALING PATHWAY	170	genes.ES.table	0.52	1.5	0.008	0.12	0.98	0.32	0.13	0.28	0.072	0
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION	236	genes.ES.table	0.68	1.7	0	0.062	0.81	0.57	0.14	0.49	0.025	0.001
KEGG CHEMOKINE SIGNALING PATHWAY	184	genes.ES.table	0.65	1.8	0.0021	0.042	0.59	0.4	0.14	0.35	0.013	0.001
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM	74	genes.ES.table	0.41	1.5	0.056	0.14	0.99	0.24	0.19	0.2	0.096	0
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION	234	genes.ES.table	0.48	1.3	0.057	0.23	1	0.35	0.13	0.3	0.19	0

genes ES table in pathway: KEGG PURINE 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	F2RL2	F2RL2	F2RL2	239	0.49	0.082	YES
2	DUSP1	DUSP1	DUSP1	1487	0.2	0.054	YES
3	MEF2C	MEF2C	MEF2C	1517	0.2	0.091	YES
4	ZFP36	ZFP36	ZFP36	1740	0.18	0.11	YES
5	RIN1	RIN1	RIN1	1799	0.17	0.14	YES
6	CHN2	CHN2	CHN2	1842	0.17	0.17	YES
7	FOS	FOS	FOS	1905	0.16	0.2	YES
8	PIK3CD	PIK3CD	PIK3CD	1922	0.16	0.23	YES
9	EGR1	EGR1	EGR1	2019	0.15	0.26	YES
10	SFN	SFN	SFN	2022	0.15	0.28	YES
11	PRKCA	PRKCA	PRKCA	2381	0.13	0.29	YES
12	DIAPH3	DIAPH3	DIAPH3	2386	0.13	0.31	YES
13	ARPC1B	ARPC1B	ARPC1B	2558	0.11	0.32	YES
14	EGFR	EGFR	EGFR	2804	0.098	0.33	YES
15	YWHAH	YWHAH	YWHAH	3262	0.078	0.32	YES
16	MAPK9	MAPK9	MAPK9	3317	0.076	0.33	YES
17	MAP3K2	MAP3K2	MAP3K2	3727	0.063	0.32	YES
18	VAV2	VAV2	VAV2	3735	0.063	0.34	YES
19	BAIAP2	BAIAP2	BAIAP2	3800	0.06	0.34	YES
20	ACTR3	ACTR3	ACTR3	3824	0.06	0.35	YES
21	GAB1	GAB1	GAB1	3829	0.06	0.36	YES
22	YWHAZ	YWHAZ	YWHAZ	3856	0.059	0.37	YES
23	RPS6KA4	RPS6KA4	RPS6KA4	4011	0.054	0.38	YES
24	GRB2	GRB2	GRB2	4022	0.054	0.39	YES
25	MAPK1	MAPK1	MAPK1	4087	0.052	0.39	YES
26	EPS8	EPS8	EPS8	4317	0.047	0.39	YES
27	STAT3	STAT3	STAT3	4318	0.047	0.4	YES
28	PLD1	PLD1	PLD1	4385	0.046	0.4	YES
29	PPP5C	PPP5C	PPP5C	4523	0.043	0.4	YES
30	SMAD1	SMAD1	SMAD1	4632	0.041	0.41	YES
31	SRF	SRF	SRF	4854	0.037	0.4	YES
32	IQGAP1	IQGAP1	IQGAP1	4866	0.037	0.41	YES
33	RPS6KA3	RPS6KA3	RPS6KA3	4888	0.036	0.41	YES
34	HRAS	HRAS	HRAS	5015	0.034	0.41	YES
35	CAPN2	CAPN2	CAPN2	5135	0.032	0.41	YES
36	ARPC2	ARPC2	ARPC2	5301	0.029	0.41	YES
37	BCL2L1	BCL2L1	BCL2L1	5338	0.028	0.41	YES
38	PDPK1	PDPK1	PDPK1	5407	0.027	0.42	YES
39	ACTR2	ACTR2	ACTR2	5487	0.026	0.42	YES
40	ABI1	ABI1	ABI1	5507	0.026	0.42	YES
41	ARPC5	ARPC5	ARPC5	5602	0.024	0.42	YES
42	YWHAG	YWHAG	YWHAG	5778	0.022	0.41	YES
43	STAT1	STAT1	STAT1	5797	0.022	0.42	YES
44	CDC42	CDC42	CDC42	5991	0.019	0.41	YES
45	SLC9A1	SLC9A1	SLC9A1	6004	0.019	0.41	YES
46	MAPK3	MAPK3	MAPK3	6019	0.019	0.42	YES
47	PPP2CA	PPP2CA	PPP2CA	6024	0.019	0.42	YES
48	JUN	JUN	JUN	6078	0.018	0.42	YES
49	WASF2	WASF2	WASF2	6087	0.018	0.42	YES
50	PIK3CB	PIK3CB	PIK3CB	6124	0.018	0.42	YES
51	ARF4	ARF4	ARF4	6138	0.017	0.43	YES
52	YWHAB	YWHAB	YWHAB	6322	0.015	0.42	NO
53	DUSP6	DUSP6	DUSP6	6351	0.015	0.42	NO
54	ARPC4	ARPC4	ARPC4	6483	0.013	0.42	NO
55	MAPK7	MAPK7	MAPK7	6486	0.013	0.42	NO
56	PIK3CA	PIK3CA	PIK3CA	6568	0.012	0.42	NO
57	MAP2K1	MAP2K1	MAP2K1	6584	0.012	0.42	NO
58	ARPC3	ARPC3	ARPC3	6759	0.0098	0.41	NO
59	MAPKAP1	MAPKAP1	MAPKAP1	6984	0.0072	0.4	NO
60	MAP2K2	MAP2K2	MAP2K2	7089	0.0062	0.4	NO
61	BAD	BAD	BAD	7107	0.006	0.4	NO
62	PPP2R2A	PPP2R2A	PPP2R2A	7197	0.0051	0.39	NO
63	RAC1	RAC1	RAC1	7228	0.0048	0.39	NO
64	RPS6KA5	RPS6KA5	RPS6KA5	7285	0.0041	0.39	NO
65	PIK3R3	PIK3R3	PIK3R3	7309	0.0037	0.39	NO
66	AKT1	AKT1	AKT1	7603	0.00076	0.37	NO
67	PIK3R1	PIK3R1	PIK3R1	7734	-0.00047	0.37	NO
68	PPP2R1A	PPP2R1A	PPP2R1A	7784	-0.0009	0.36	NO
69	NCKAP1	NCKAP1	NCKAP1	7923	-0.0022	0.36	NO
70	WASL	WASL	WASL	7999	-0.0029	0.35	NO
71	YWHAQ	YWHAQ	YWHAQ	8144	-0.0042	0.35	NO
72	RAB5A	RAB5A	RAB5A	8154	-0.0043	0.35	NO
73	MAP2K4	MAP2K4	MAP2K4	8232	-0.005	0.34	NO
74	MLST8	MLST8	MLST8	8894	-0.011	0.31	NO
75	NRAS	NRAS	NRAS	8988	-0.012	0.31	NO
76	ATF2	ATF2	ATF2	9011	-0.012	0.31	NO
77	EGF	EGF	EGF	9062	-0.013	0.31	NO
78	SOS1	SOS1	SOS1	9102	-0.013	0.31	NO
79	RALA	RALA	RALA	9307	-0.015	0.3	NO
80	RALGDS	RALGDS	RALGDS	9434	-0.016	0.3	NO
81	MTOR	MTOR	MTOR	9451	-0.016	0.3	NO
82	RAF1	RAF1	RAF1	9666	-0.018	0.29	NO
83	RICTOR	RICTOR	RICTOR	10190	-0.023	0.27	NO
84	PLD2	PLD2	PLD2	10274	-0.023	0.27	NO
85	BRAF	BRAF	BRAF	10349	-0.024	0.27	NO
86	SRC	SRC	SRC	10399	-0.024	0.27	NO
87	YWHAE	YWHAE	YWHAE	10607	-0.026	0.26	NO
88	PRKCD	PRKCD	PRKCD	10842	-0.029	0.26	NO
89	CREB1	CREB1	CREB1	11138	-0.031	0.25	NO
90	MAPK8	MAPK8	MAPK8	11235	-0.032	0.25	NO
91	ATF1	ATF1	ATF1	11553	-0.035	0.24	NO
92	MAP3K1	MAP3K1	MAP3K1	11717	-0.037	0.24	NO
93	KRAS	KRAS	KRAS	12003	-0.04	0.23	NO
94	MAP2K5	MAP2K5	MAP2K5	12029	-0.04	0.23	NO
95	RPS6	RPS6	RPS6	12363	-0.043	0.22	NO
96	PIK3R2	PIK3R2	PIK3R2	12906	-0.05	0.2	NO
97	PRKCZ	PRKCZ	PRKCZ	13005	-0.051	0.21	NO
98	SH2D2A	SH2D2A	SH2D2A	13356	-0.056	0.2	NO
99	USP6NL	USP6NL	USP6NL	13428	-0.057	0.21	NO
100	PEBP1	PEBP1	PEBP1	13457	-0.057	0.22	NO
101	ELK1	ELK1	ELK1	13844	-0.063	0.21	NO
102	CYFIP2	CYFIP2	CYFIP2	14266	-0.07	0.2	NO
103	KSR1	KSR1	KSR1	14944	-0.085	0.18	NO
104	MYLPF	MYLPF	MYLPF	15206	-0.091	0.18	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 PURINE METABOLISM.

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

genes ES table in pathway: KEGG N 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	CTSK	CTSK	CTSK	53	0.73	0.088	YES
2	CTSW	CTSW	CTSW	622	0.35	0.1	YES
3	CLTCL1	CLTCL1	CLTCL1	1059	0.27	0.11	YES
4	CTSG	CTSG	CTSG	1117	0.26	0.14	YES
5	CTSE	CTSE	CTSE	1269	0.24	0.16	YES
6	ATP6V0D2	ATP6V0D2	ATP6V0D2	1282	0.23	0.19	YES
7	LAPTM5	LAPTM5	LAPTM5	1304	0.23	0.22	YES
8	CD68	CD68	CD68	1485	0.2	0.23	YES
9	CTSS	CTSS	CTSS	1497	0.2	0.26	YES
10	ARSB	ARSB	ARSB	1531	0.2	0.28	YES
11	SLC11A1	SLC11A1	SLC11A1	1865	0.17	0.28	YES
12	CTSO	CTSO	CTSO	2132	0.14	0.29	YES
13	SMPD1	SMPD1	SMPD1	2440	0.12	0.28	YES
14	ARSA	ARSA	ARSA	2588	0.11	0.29	YES
15	ACP5	ACP5	ACP5	2815	0.098	0.29	YES
16	NPC1	NPC1	NPC1	2834	0.097	0.3	YES
17	CLTB	CLTB	CLTB	2880	0.095	0.31	YES
18	CTSL1	CTSL1	CTSL1	2931	0.092	0.32	YES
19	TPP1	TPP1	TPP1	3013	0.089	0.33	YES
20	CTSZ	CTSZ	CTSZ	3160	0.082	0.33	YES
21	GALNS	GALNS	GALNS	3259	0.078	0.33	YES
22	NAGA	NAGA	NAGA	3260	0.078	0.34	YES
23	AP1B1	AP1B1	AP1B1	3271	0.078	0.35	YES
24	MCOLN1	MCOLN1	MCOLN1	3297	0.076	0.36	YES
25	AP4E1	AP4E1	AP4E1	3303	0.076	0.37	YES
26	PSAPL1	PSAPL1	PSAPL1	3337	0.075	0.38	YES
27	GM2A	GM2A	GM2A	3338	0.075	0.39	YES
28	LGMN	LGMN	LGMN	3364	0.074	0.4	YES
29	CTSA	CTSA	CTSA	3423	0.072	0.4	YES
30	GAA	GAA	GAA	3464	0.071	0.41	YES
31	AP1S2	AP1S2	AP1S2	3517	0.069	0.41	YES
32	TCIRG1	TCIRG1	TCIRG1	3544	0.068	0.42	YES
33	CTSD	CTSD	CTSD	3579	0.067	0.43	YES
34	GNPTAB	GNPTAB	GNPTAB	3580	0.067	0.44	YES
35	CTSB	CTSB	CTSB	3595	0.067	0.44	YES
36	LAPTM4B	LAPTM4B	LAPTM4B	3681	0.064	0.45	YES
37	LIPA	LIPA	LIPA	3698	0.064	0.45	YES
38	ENTPD4	ENTPD4	ENTPD4	3720	0.063	0.46	YES
39	HEXB	HEXB	HEXB	3738	0.063	0.47	YES
40	ASAH1	ASAH1	ASAH1	3767	0.062	0.47	YES
41	ATP6AP1	ATP6AP1	ATP6AP1	3782	0.061	0.48	YES
42	DNASE2B	DNASE2B	DNASE2B	3789	0.061	0.49	YES
43	AP3S1	AP3S1	AP3S1	3912	0.057	0.49	YES
44	PLA2G15	PLA2G15	PLA2G15	4177	0.05	0.48	YES
45	MANBA	MANBA	MANBA	4234	0.049	0.48	YES
46	CTSC	CTSC	CTSC	4235	0.049	0.49	YES
47	ACP2	ACP2	ACP2	4309	0.048	0.49	YES
48	CTSH	CTSH	CTSH	4408	0.045	0.49	YES
49	IGF2R	IGF2R	IGF2R	4498	0.043	0.49	YES
50	SLC17A5	SLC17A5	SLC17A5	4529	0.043	0.5	YES
51	PSAP	PSAP	PSAP	4558	0.042	0.5	YES
52	GNPTG	GNPTG	GNPTG	4560	0.042	0.5	YES
53	NPC2	NPC2	NPC2	4625	0.041	0.51	YES
54	GGA3	GGA3	GGA3	4627	0.041	0.51	YES
55	CLTC	CLTC	CLTC	4828	0.037	0.5	YES
56	HEXA	HEXA	HEXA	4846	0.037	0.51	YES
57	NAGLU	NAGLU	NAGLU	4883	0.036	0.51	YES
58	LAMP1	LAMP1	LAMP1	5034	0.034	0.51	YES
59	SCARB2	SCARB2	SCARB2	5107	0.032	0.51	YES
60	IDS	IDS	IDS	5113	0.032	0.51	YES
61	CTNS	CTNS	CTNS	5116	0.032	0.52	YES
62	FUCA1	FUCA1	FUCA1	5196	0.031	0.52	NO
63	GBA	GBA	GBA	5327	0.028	0.51	NO
64	CLN3	CLN3	CLN3	5478	0.026	0.51	NO
65	NEU1	NEU1	NEU1	5663	0.024	0.5	NO
66	LAMP3	LAMP3	LAMP3	5705	0.023	0.5	NO
67	ATP6V0C	ATP6V0C	ATP6V0C	5706	0.023	0.5	NO
68	AGA	AGA	AGA	5716	0.023	0.5	NO
69	ATP6V0D1	ATP6V0D1	ATP6V0D1	5882	0.021	0.5	NO
70	ATP6V0A1	ATP6V0A1	ATP6V0A1	5894	0.02	0.5	NO
71	GALC	GALC	GALC	5994	0.019	0.5	NO
72	SGSH	SGSH	SGSH	5999	0.019	0.5	NO
73	GNS	GNS	GNS	6065	0.018	0.5	NO
74	NAGPA	NAGPA	NAGPA	6119	0.018	0.5	NO
75	CLN5	CLN5	CLN5	6234	0.016	0.49	NO
76	ATP6V0B	ATP6V0B	ATP6V0B	6266	0.016	0.49	NO
77	GLA	GLA	GLA	6376	0.014	0.49	NO
78	CD63	CD63	CD63	6381	0.014	0.49	NO
79	AP3D1	AP3D1	AP3D1	6588	0.012	0.48	NO
80	MFSD8	MFSD8	MFSD8	6710	0.01	0.48	NO
81	GGA1	GGA1	GGA1	6719	0.01	0.48	NO
82	AP3B1	AP3B1	AP3B1	6764	0.0097	0.48	NO
83	ABCA2	ABCA2	ABCA2	7087	0.0062	0.46	NO
84	MAN2B1	MAN2B1	MAN2B1	7095	0.0062	0.46	NO
85	LAPTM4A	LAPTM4A	LAPTM4A	7230	0.0048	0.45	NO
86	SORT1	SORT1	SORT1	7381	0.0029	0.45	NO
87	GGA2	GGA2	GGA2	7473	0.0021	0.44	NO
88	AP1M1	AP1M1	AP1M1	7774	-0.00079	0.42	NO
89	ATP6V0A2	ATP6V0A2	ATP6V0A2	7799	-0.001	0.42	NO
90	IDUA	IDUA	IDUA	8067	-0.0035	0.41	NO
91	LAMP2	LAMP2	LAMP2	8150	-0.0043	0.41	NO
92	GUSB	GUSB	GUSB	8503	-0.0077	0.39	NO
93	ABCB9	ABCB9	ABCB9	8558	-0.0082	0.39	NO
94	GLB1	GLB1	GLB1	8628	-0.0088	0.38	NO
95	AP3M1	AP3M1	AP3M1	8706	-0.0095	0.38	NO
96	PPT1	PPT1	PPT1	8756	-0.0099	0.38	NO
97	CTSF	CTSF	CTSF	8987	-0.012	0.37	NO
98	HGSNAT	HGSNAT	HGSNAT	9101	-0.013	0.36	NO
99	AP1G1	AP1G1	AP1G1	9343	-0.015	0.35	NO
100	NAPSA	NAPSA	NAPSA	9654	-0.018	0.34	NO
101	ATP6V0A4	ATP6V0A4	ATP6V0A4	9877	-0.02	0.33	NO
102	CD164	CD164	CD164	9948	-0.021	0.33	NO
103	DNASE2	DNASE2	DNASE2	10139	-0.022	0.32	NO
104	AP4M1	AP4M1	AP4M1	10775	-0.028	0.29	NO
105	AP1M2	AP1M2	AP1M2	10802	-0.028	0.29	NO
106	M6PR	M6PR	M6PR	11469	-0.034	0.26	NO
107	CLTA	CLTA	CLTA	11555	-0.035	0.26	NO
108	ATP6V1H	ATP6V1H	ATP6V1H	11568	-0.035	0.26	NO
109	AP4B1	AP4B1	AP4B1	11633	-0.036	0.26	NO
110	SLC11A2	SLC11A2	SLC11A2	11700	-0.037	0.26	NO
111	AP1S1	AP1S1	AP1S1	11718	-0.037	0.27	NO
112	AP4S1	AP4S1	AP4S1	11744	-0.037	0.27	NO
113	SUMF1	SUMF1	SUMF1	12025	-0.04	0.26	NO
114	AP3S2	AP3S2	AP3S2	12047	-0.04	0.26	NO
115	PPT2	PPT2	PPT2	13386	-0.056	0.2	NO
116	ARSG	ARSG	ARSG	14040	-0.066	0.17	NO
117	HYAL1	HYAL1	HYAL1	14558	-0.076	0.15	NO
118	CTSL2	CTSL2	CTSL2	14715	-0.08	0.16	NO
119	AP3M2	AP3M2	AP3M2	14761	-0.08	0.16	NO
120	AP1S3	AP1S3	AP1S3	15581	-0.1	0.13	NO
121	AP3B2	AP3B2	AP3B2	17848	-0.25	0.039	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 N GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG 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	SPHK1	SPHK1	SPHK1	120	0.6	0.054	YES
2	ACTA2	ACTA2	ACTA2	457	0.39	0.075	YES
3	PIK3CG	PIK3CG	PIK3CG	574	0.36	0.11	YES
4	PDGFRB	PDGFRB	PDGFRB	644	0.34	0.14	YES
5	TAGLN	TAGLN	TAGLN	664	0.34	0.17	YES
6	SLA	SLA	SLA	670	0.34	0.2	YES
7	PIK3R6	PIK3R6	PIK3R6	694	0.33	0.24	YES
8	PIK3R5	PIK3R5	PIK3R5	775	0.32	0.26	YES
9	HCK	HCK	HCK	792	0.32	0.3	YES
10	FGR	FGR	FGR	863	0.3	0.32	YES
11	LCK	LCK	LCK	975	0.28	0.34	YES
12	ITGB3	ITGB3	ITGB3	1097	0.26	0.36	YES
13	DOCK4	DOCK4	DOCK4	1421	0.21	0.37	YES
14	PAG1	PAG1	PAG1	1562	0.2	0.38	YES
15	BLK	BLK	BLK	1668	0.18	0.39	YES
16	PDGFB	PDGFB	PDGFB	1891	0.16	0.4	YES
17	FOS	FOS	FOS	1905	0.16	0.41	YES
18	PIK3CD	PIK3CD	PIK3CD	1922	0.16	0.43	YES
19	S1PR1	S1PR1	S1PR1	1952	0.16	0.44	YES
20	SFN	SFN	SFN	2022	0.15	0.45	YES
21	LRP1	LRP1	LRP1	2162	0.14	0.46	YES
22	PRKCA	PRKCA	PRKCA	2381	0.13	0.46	YES
23	ARPC1B	ARPC1B	ARPC1B	2558	0.11	0.46	YES
24	PPP2R2B	PPP2R2B	PPP2R2B	2772	0.1	0.46	YES
25	LYN	LYN	LYN	3006	0.089	0.46	YES
26	ITGAV	ITGAV	ITGAV	3025	0.088	0.47	YES
27	JAK2	JAK2	JAK2	3210	0.08	0.46	YES
28	YWHAH	YWHAH	YWHAH	3262	0.078	0.47	YES
29	PTPRJ	PTPRJ	PTPRJ	3304	0.076	0.48	YES
30	MAPK9	MAPK9	MAPK9	3317	0.076	0.48	YES
31	BCAR1	BCAR1	BCAR1	3332	0.075	0.49	YES
32	SIPA1	SIPA1	SIPA1	3452	0.071	0.49	YES
33	SHC1	SHC1	SHC1	3631	0.066	0.49	YES
34	VAV2	VAV2	VAV2	3735	0.063	0.49	YES
35	BAIAP2	BAIAP2	BAIAP2	3800	0.06	0.49	YES
36	ACTR3	ACTR3	ACTR3	3824	0.06	0.5	YES
37	GAB1	GAB1	GAB1	3829	0.06	0.5	YES
38	YWHAZ	YWHAZ	YWHAZ	3856	0.059	0.51	YES
39	PTPN1	PTPN1	PTPN1	3861	0.059	0.51	YES
40	GRB2	GRB2	GRB2	4022	0.054	0.51	YES
41	MAPK1	MAPK1	MAPK1	4087	0.052	0.51	YES
42	ACTN4	ACTN4	ACTN4	4225	0.05	0.51	YES
43	PTEN	PTEN	PTEN	4247	0.049	0.51	YES
44	EPS8	EPS8	EPS8	4317	0.047	0.51	YES
45	STAT3	STAT3	STAT3	4318	0.047	0.52	YES
46	RAPGEF1	RAPGEF1	RAPGEF1	4485	0.044	0.51	NO
47	ARHGDIA	ARHGDIA	ARHGDIA	4673	0.04	0.51	NO
48	NCK1	NCK1	NCK1	4836	0.037	0.5	NO
49	SRF	SRF	SRF	4854	0.037	0.5	NO
50	IQGAP1	IQGAP1	IQGAP1	4866	0.037	0.51	NO
51	RPS6KA3	RPS6KA3	RPS6KA3	4888	0.036	0.51	NO
52	RAP1A	RAP1A	RAP1A	4971	0.035	0.51	NO
53	HRAS	HRAS	HRAS	5015	0.034	0.51	NO
54	STAT5A	STAT5A	STAT5A	5036	0.034	0.51	NO
55	ARAP1	ARAP1	ARAP1	5144	0.032	0.51	NO
56	ARPC2	ARPC2	ARPC2	5301	0.029	0.5	NO
57	CRK	CRK	CRK	5416	0.027	0.5	NO
58	SLC9A3R2	SLC9A3R2	SLC9A3R2	5454	0.026	0.5	NO
59	ACTR2	ACTR2	ACTR2	5487	0.026	0.5	NO
60	ABI1	ABI1	ABI1	5507	0.026	0.5	NO
61	ARPC5	ARPC5	ARPC5	5602	0.024	0.5	NO
62	YWHAG	YWHAG	YWHAG	5778	0.022	0.49	NO
63	STAT1	STAT1	STAT1	5797	0.022	0.5	NO
64	RHOA	RHOA	RHOA	5857	0.021	0.49	NO
65	CTTN	CTTN	CTTN	5877	0.021	0.5	NO
66	STAT5B	STAT5B	STAT5B	6018	0.019	0.49	NO
67	MAPK3	MAPK3	MAPK3	6019	0.019	0.49	NO
68	PPP2CA	PPP2CA	PPP2CA	6024	0.019	0.49	NO
69	JUN	JUN	JUN	6078	0.018	0.49	NO
70	WASF2	WASF2	WASF2	6087	0.018	0.49	NO
71	PIK3CB	PIK3CB	PIK3CB	6124	0.018	0.49	NO
72	ABL1	ABL1	ABL1	6159	0.017	0.49	NO
73	YWHAB	YWHAB	YWHAB	6322	0.015	0.49	NO
74	RASA1	RASA1	RASA1	6428	0.014	0.48	NO
75	ARPC4	ARPC4	ARPC4	6483	0.013	0.48	NO
76	PIK3CA	PIK3CA	PIK3CA	6568	0.012	0.48	NO
77	MAP2K1	MAP2K1	MAP2K1	6584	0.012	0.48	NO
78	MAP2K7	MAP2K7	MAP2K7	6678	0.011	0.47	NO
79	ARPC3	ARPC3	ARPC3	6759	0.0098	0.47	NO
80	MAP2K2	MAP2K2	MAP2K2	7089	0.0062	0.45	NO
81	JUND	JUND	JUND	7121	0.0059	0.45	NO
82	GRB10	GRB10	GRB10	7181	0.0052	0.45	NO
83	RAC1	RAC1	RAC1	7228	0.0048	0.45	NO
84	PIK3R3	PIK3R3	PIK3R3	7309	0.0037	0.44	NO
85	RAP1B	RAP1B	RAP1B	7384	0.0029	0.44	NO
86	NCK2	NCK2	NCK2	7630	0.00054	0.43	NO
87	PIK3R1	PIK3R1	PIK3R1	7734	-0.00047	0.42	NO
88	PPP2R1A	PPP2R1A	PPP2R1A	7784	-0.0009	0.42	NO
89	NCKAP1	NCKAP1	NCKAP1	7923	-0.0022	0.41	NO
90	WASL	WASL	WASL	7999	-0.0029	0.41	NO
91	YWHAQ	YWHAQ	YWHAQ	8144	-0.0042	0.4	NO
92	RAB5A	RAB5A	RAB5A	8154	-0.0043	0.4	NO
93	MAP2K4	MAP2K4	MAP2K4	8232	-0.005	0.4	NO
94	CBL	CBL	CBL	8471	-0.0074	0.38	NO
95	EIF2AK2	EIF2AK2	EIF2AK2	8689	-0.0093	0.37	NO
96	NRAS	NRAS	NRAS	8988	-0.012	0.36	NO
97	SOS1	SOS1	SOS1	9102	-0.013	0.35	NO
98	PLCG1	PLCG1	PLCG1	9448	-0.016	0.34	NO
99	CSK	CSK	CSK	9510	-0.017	0.33	NO
100	PTPN11	PTPN11	PTPN11	9556	-0.017	0.33	NO
101	DNM2	DNM2	DNM2	9644	-0.018	0.33	NO
102	RAF1	RAF1	RAF1	9666	-0.018	0.33	NO
103	PTPN2	PTPN2	PTPN2	9796	-0.02	0.33	NO
104	DOK1	DOK1	DOK1	9861	-0.02	0.32	NO
105	BRAF	BRAF	BRAF	10349	-0.024	0.3	NO
106	SRC	SRC	SRC	10399	-0.024	0.3	NO
107	YWHAE	YWHAE	YWHAE	10607	-0.026	0.29	NO
108	MYC	MYC	MYC	10644	-0.027	0.29	NO
109	PRKCD	PRKCD	PRKCD	10842	-0.029	0.28	NO
110	MAPK8	MAPK8	MAPK8	11235	-0.032	0.27	NO
111	RAB4A	RAB4A	RAB4A	11508	-0.035	0.26	NO
112	MAPK10	MAPK10	MAPK10	11932	-0.039	0.24	NO
113	KRAS	KRAS	KRAS	12003	-0.04	0.24	NO
114	PIN1	PIN1	PIN1	12140	-0.041	0.23	NO
115	PRKCE	PRKCE	PRKCE	12307	-0.043	0.23	NO
116	MLLT4	MLLT4	MLLT4	12412	-0.044	0.23	NO
117	YES1	YES1	YES1	12503	-0.045	0.23	NO
118	PIK3R2	PIK3R2	PIK3R2	12906	-0.05	0.21	NO
119	USP6NL	USP6NL	USP6NL	13428	-0.057	0.19	NO
120	ELK1	ELK1	ELK1	13844	-0.063	0.17	NO
121	FYN	FYN	FYN	14056	-0.066	0.17	NO
122	SLC9A3R1	SLC9A3R1	SLC9A3R1	14247	-0.07	0.16	NO
123	CYFIP2	CYFIP2	CYFIP2	14266	-0.07	0.17	NO
124	PAK1	PAK1	PAK1	14551	-0.076	0.16	NO
125	KSR1	KSR1	KSR1	14944	-0.085	0.15	NO
126	PLA2G4A	PLA2G4A	PLA2G4A	15526	-0.1	0.13	NO
127	MYOCD	MYOCD	MYOCD	18325	-0.36	0.013	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 MAPK SIGNALING PATHWAY

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HGF	HGF	HGF	446	0.4	0.056	YES
2	TGFB3	TGFB3	TGFB3	535	0.37	0.13	YES
3	PIK3CG	PIK3CG	PIK3CG	574	0.36	0.2	YES
4	PIK3R5	PIK3R5	PIK3R5	775	0.32	0.25	YES
5	AKT3	AKT3	AKT3	1033	0.27	0.29	YES
6	VEGFC	VEGFC	VEGFC	1415	0.21	0.31	YES
7	ETS1	ETS1	ETS1	1429	0.21	0.36	YES
8	TGFB1	TGFB1	TGFB1	1438	0.21	0.4	YES
9	PGF	PGF	PGF	1448	0.21	0.44	YES
10	PDGFB	PDGFB	PDGFB	1891	0.16	0.45	YES
11	PIK3CD	PIK3CD	PIK3CD	1922	0.16	0.48	YES
12	EPAS1	EPAS1	EPAS1	2110	0.14	0.5	YES
13	EGLN3	EGLN3	EGLN3	2378	0.13	0.51	YES
14	PAK3	PAK3	PAK3	2394	0.13	0.53	YES
15	VEGFB	VEGFB	VEGFB	3802	0.06	0.47	NO
16	GAB1	GAB1	GAB1	3829	0.06	0.48	NO
17	GRB2	GRB2	GRB2	4022	0.054	0.48	NO
18	MAPK1	MAPK1	MAPK1	4087	0.052	0.49	NO
19	RAPGEF1	RAPGEF1	RAPGEF1	4485	0.044	0.48	NO
20	HIF1A	HIF1A	HIF1A	4856	0.037	0.46	NO
21	RAP1A	RAP1A	RAP1A	4971	0.035	0.46	NO
22	HRAS	HRAS	HRAS	5015	0.034	0.47	NO
23	TGFA	TGFA	TGFA	5291	0.029	0.46	NO
24	MET	MET	MET	5323	0.028	0.46	NO
25	VEGFA	VEGFA	VEGFA	5340	0.028	0.47	NO
26	CRK	CRK	CRK	5416	0.027	0.47	NO
27	FLCN	FLCN	FLCN	5618	0.024	0.46	NO
28	EGLN2	EGLN2	EGLN2	5829	0.021	0.46	NO
29	CDC42	CDC42	CDC42	5991	0.019	0.45	NO
30	MAPK3	MAPK3	MAPK3	6019	0.019	0.46	NO
31	CUL2	CUL2	CUL2	6038	0.019	0.46	NO
32	JUN	JUN	JUN	6078	0.018	0.46	NO
33	PIK3CB	PIK3CB	PIK3CB	6124	0.018	0.46	NO
34	ARNT	ARNT	ARNT	6140	0.017	0.46	NO
35	SOS2	SOS2	SOS2	6173	0.017	0.46	NO
36	ARAF	ARAF	ARAF	6484	0.013	0.45	NO
37	PIK3CA	PIK3CA	PIK3CA	6568	0.012	0.45	NO
38	MAP2K1	MAP2K1	MAP2K1	6584	0.012	0.45	NO
39	SLC2A1	SLC2A1	SLC2A1	6797	0.0093	0.44	NO
40	PAK2	PAK2	PAK2	6867	0.0085	0.44	NO
41	MAP2K2	MAP2K2	MAP2K2	7089	0.0062	0.43	NO
42	RAC1	RAC1	RAC1	7228	0.0048	0.42	NO
43	PIK3R3	PIK3R3	PIK3R3	7309	0.0037	0.42	NO
44	CRKL	CRKL	CRKL	7357	0.0032	0.42	NO
45	RAP1B	RAP1B	RAP1B	7384	0.0029	0.42	NO
46	TCEB1	TCEB1	TCEB1	7432	0.0025	0.41	NO
47	AKT1	AKT1	AKT1	7603	0.00076	0.4	NO
48	PIK3R1	PIK3R1	PIK3R1	7734	-0.00047	0.4	NO
49	RBX1	RBX1	RBX1	8264	-0.0054	0.37	NO
50	AKT2	AKT2	AKT2	8273	-0.0054	0.37	NO
51	CREBBP	CREBBP	CREBBP	8625	-0.0088	0.35	NO
52	FIGF	FIGF	FIGF	8669	-0.0092	0.35	NO
53	NRAS	NRAS	NRAS	8988	-0.012	0.34	NO
54	SOS1	SOS1	SOS1	9102	-0.013	0.33	NO
55	PTPN11	PTPN11	PTPN11	9556	-0.017	0.31	NO
56	EGLN1	EGLN1	EGLN1	9587	-0.018	0.32	NO
57	EP300	EP300	EP300	9614	-0.018	0.32	NO
58	RAF1	RAF1	RAF1	9666	-0.018	0.32	NO
59	BRAF	BRAF	BRAF	10349	-0.024	0.29	NO
60	TCEB2	TCEB2	TCEB2	10738	-0.028	0.27	NO
61	FH	FH	FH	11205	-0.032	0.25	NO
62	PAK4	PAK4	PAK4	11432	-0.034	0.25	NO
63	TGFB2	TGFB2	TGFB2	11786	-0.038	0.24	NO
64	KRAS	KRAS	KRAS	12003	-0.04	0.23	NO
65	VHL	VHL	VHL	12272	-0.042	0.22	NO
66	PIK3R2	PIK3R2	PIK3R2	12906	-0.05	0.2	NO
67	PAK6	PAK6	PAK6	13569	-0.059	0.18	NO
68	PAK1	PAK1	PAK1	14551	-0.076	0.14	NO
69	ARNT2	ARNT2	ARNT2	15565	-0.1	0.1	NO
70	PAK7	PAK7	PAK7	18066	-0.28	0.027	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 MAPK SIGNALING PATHWAY.

Figure S48. 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 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	NEDD4	NEDD4	NEDD4	662	0.34	0.046	YES
2	PRKCB	PRKCB	PRKCB	710	0.33	0.12	YES
3	MAPK11	MAPK11	MAPK11	952	0.29	0.18	YES
4	ITGB3	ITGB3	ITGB3	1097	0.26	0.23	YES
5	KDR	KDR	KDR	1567	0.2	0.25	YES
6	FLT1	FLT1	FLT1	1672	0.18	0.29	YES
7	CAV1	CAV1	CAV1	1743	0.18	0.33	YES
8	VTN	VTN	VTN	1881	0.16	0.36	YES
9	CDH5	CDH5	CDH5	1980	0.16	0.4	YES
10	PRKCA	PRKCA	PRKCA	2381	0.13	0.4	YES
11	MYOF	MYOF	MYOF	2404	0.12	0.43	YES
12	PTK2B	PTK2B	PTK2B	2712	0.1	0.44	YES
13	ITGAV	ITGAV	ITGAV	3025	0.088	0.44	YES
14	PTPRJ	PTPRJ	PTPRJ	3304	0.076	0.45	YES
15	VCL	VCL	VCL	3608	0.066	0.45	YES
16	GAB1	GAB1	GAB1	3829	0.06	0.45	YES
17	NOS3	NOS3	NOS3	3857	0.059	0.46	YES
18	GRB2	GRB2	GRB2	4022	0.054	0.47	YES
19	MAPK1	MAPK1	MAPK1	4087	0.052	0.48	YES
20	SHB	SHB	SHB	4770	0.038	0.45	NO
21	PTK2	PTK2	PTK2	4792	0.038	0.46	NO
22	NCK1	NCK1	NCK1	4836	0.037	0.46	NO
23	IQGAP1	IQGAP1	IQGAP1	4866	0.037	0.47	NO
24	ROCK1	ROCK1	ROCK1	5250	0.03	0.46	NO
25	VEGFA	VEGFA	VEGFA	5340	0.028	0.46	NO
26	PDPK1	PDPK1	PDPK1	5407	0.027	0.46	NO
27	PXN	PXN	PXN	5470	0.026	0.46	NO
28	CTNNA1	CTNNA1	CTNNA1	5744	0.023	0.46	NO
29	RHOA	RHOA	RHOA	5857	0.021	0.45	NO
30	CDC42	CDC42	CDC42	5991	0.019	0.45	NO
31	MAPK3	MAPK3	MAPK3	6019	0.019	0.45	NO
32	PRKAA1	PRKAA1	PRKAA1	6132	0.017	0.45	NO
33	PIK3CA	PIK3CA	PIK3CA	6568	0.012	0.43	NO
34	MAP2K1	MAP2K1	MAP2K1	6584	0.012	0.43	NO
35	MAPK14	MAPK14	MAPK14	6593	0.012	0.44	NO
36	PAK2	PAK2	PAK2	6867	0.0085	0.42	NO
37	FBXW11	FBXW11	FBXW11	7003	0.007	0.42	NO
38	HGS	HGS	HGS	7045	0.0066	0.42	NO
39	MAP2K2	MAP2K2	MAP2K2	7089	0.0062	0.42	NO
40	ARF1	ARF1	ARF1	7157	0.0055	0.41	NO
41	GRB10	GRB10	GRB10	7181	0.0052	0.41	NO
42	MAP2K3	MAP2K3	MAP2K3	7510	0.0018	0.4	NO
43	AKT1	AKT1	AKT1	7603	0.00076	0.39	NO
44	NCK2	NCK2	NCK2	7630	0.00054	0.39	NO
45	PIK3R1	PIK3R1	PIK3R1	7734	-0.00047	0.38	NO
46	PTPN6	PTPN6	PTPN6	8060	-0.0034	0.37	NO
47	MAPKAPK2	MAPKAPK2	MAPKAPK2	8134	-0.0041	0.36	NO
48	CBL	CBL	CBL	8471	-0.0074	0.35	NO
49	HSP90AA1	HSP90AA1	HSP90AA1	8844	-0.011	0.33	NO
50	AKAP1	AKAP1	AKAP1	8854	-0.011	0.33	NO
51	CTNNB1	CTNNB1	CTNNB1	8973	-0.012	0.33	NO
52	PLCG1	PLCG1	PLCG1	9448	-0.016	0.31	NO
53	PTPN11	PTPN11	PTPN11	9556	-0.017	0.31	NO
54	DNM2	DNM2	DNM2	9644	-0.018	0.31	NO
55	RAF1	RAF1	RAF1	9666	-0.018	0.31	NO
56	CAMKK2	CAMKK2	CAMKK2	9790	-0.019	0.31	NO
57	PTPN2	PTPN2	PTPN2	9796	-0.02	0.31	NO
58	PRKACA	PRKACA	PRKACA	10336	-0.024	0.29	NO
59	BRAF	BRAF	BRAF	10349	-0.024	0.29	NO
60	SRC	SRC	SRC	10399	-0.024	0.3	NO
61	PRKCD	PRKCD	PRKCD	10842	-0.029	0.28	NO
62	PRKAG1	PRKAG1	PRKAG1	11818	-0.038	0.24	NO
63	HSP90AB1	HSP90AB1	HSP90AB1	11937	-0.039	0.24	NO
64	PRKAB1	PRKAB1	PRKAB1	12895	-0.049	0.2	NO
65	FES	FES	FES	12967	-0.05	0.21	NO
66	SH2D2A	SH2D2A	SH2D2A	13356	-0.056	0.2	NO
67	FYN	FYN	FYN	14056	-0.066	0.18	NO
68	MAP2K6	MAP2K6	MAP2K6	15591	-0.1	0.12	NO
69	PRKAA2	PRKAA2	PRKAA2	17044	-0.17	0.082	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 ERBB SIGNALING PATHWAY.

Figure S50. 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 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	CCL11	CCL11	CCL11	19	0.86	0.17	YES
2	CXCL13	CXCL13	CXCL13	307	0.45	0.24	YES
3	CXCR3	CXCR3	CXCR3	361	0.42	0.32	YES
4	CXCL9	CXCL9	CXCL9	380	0.42	0.4	YES
5	ITGAL	ITGAL	ITGAL	663	0.34	0.45	YES
6	MAPK11	MAPK11	MAPK11	952	0.29	0.49	YES
7	GNG2	GNG2	GNG2	959	0.29	0.54	YES
8	ITGB2	ITGB2	ITGB2	1109	0.26	0.59	YES
9	CXCL11	CXCL11	CXCL11	1154	0.25	0.63	YES
10	CXCL10	CXCL10	CXCL10	1439	0.21	0.66	YES
11	PF4	PF4	PF4	1692	0.18	0.68	YES
12	PIK3CD	PIK3CD	PIK3CD	1922	0.16	0.7	YES
13	DNM1	DNM1	DNM1	2074	0.15	0.72	YES
14	ARRB1	ARRB1	ARRB1	2460	0.12	0.72	YES
15	MAPK1	MAPK1	MAPK1	4087	0.052	0.65	NO
16	GNAI2	GNAI2	GNAI2	5001	0.034	0.6	NO
17	HRAS	HRAS	HRAS	5015	0.034	0.61	NO
18	PDPK1	PDPK1	PDPK1	5407	0.027	0.59	NO
19	MAPK3	MAPK3	MAPK3	6019	0.019	0.56	NO
20	PIK3CB	PIK3CB	PIK3CB	6124	0.018	0.56	NO
21	GNAI3	GNAI3	GNAI3	6410	0.014	0.55	NO
22	PIK3CA	PIK3CA	PIK3CA	6568	0.012	0.54	NO
23	MAP2K1	MAP2K1	MAP2K1	6584	0.012	0.54	NO
24	MAPK14	MAPK14	MAPK14	6593	0.012	0.55	NO
25	GNB1	GNB1	GNB1	6599	0.012	0.55	NO
26	MAPKAP1	MAPKAP1	MAPKAP1	6984	0.0072	0.53	NO
27	MAP2K2	MAP2K2	MAP2K2	7089	0.0062	0.52	NO
28	PIK3R3	PIK3R3	PIK3R3	7309	0.0037	0.51	NO
29	MAP2K3	MAP2K3	MAP2K3	7510	0.0018	0.5	NO
30	AKT1	AKT1	AKT1	7603	0.00076	0.5	NO
31	PIK3R1	PIK3R1	PIK3R1	7734	-0.00047	0.49	NO
32	MLST8	MLST8	MLST8	8894	-0.011	0.43	NO
33	NRAS	NRAS	NRAS	8988	-0.012	0.43	NO
34	GNAI1	GNAI1	GNAI1	9385	-0.016	0.41	NO
35	MTOR	MTOR	MTOR	9451	-0.016	0.41	NO
36	RAF1	RAF1	RAF1	9666	-0.018	0.4	NO
37	RICTOR	RICTOR	RICTOR	10190	-0.023	0.38	NO
38	SRC	SRC	SRC	10399	-0.024	0.37	NO
39	KRAS	KRAS	KRAS	12003	-0.04	0.29	NO
40	PIK3R2	PIK3R2	PIK3R2	12906	-0.05	0.25	NO
41	GNAZ	GNAZ	GNAZ	13335	-0.055	0.24	NO
42	MAP2K6	MAP2K6	MAP2K6	15591	-0.1	0.14	NO
43	GNAO1	GNAO1	GNAO1	15733	-0.11	0.15	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 CALCIUM SIGNALING PATHWAY.

Figure S52. 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 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	SPHK1	SPHK1	SPHK1	120	0.6	0.076	YES
2	ITK	ITK	ITK	163	0.55	0.15	YES
3	MS4A2	MS4A2	MS4A2	173	0.54	0.22	YES
4	BTK	BTK	BTK	499	0.38	0.26	YES
5	FCGR2B	FCGR2B	FCGR2B	626	0.35	0.3	YES
6	PRKCB	PRKCB	PRKCB	710	0.33	0.34	YES
7	LCP2	LCP2	LCP2	778	0.32	0.38	YES
8	FCER1A	FCER1A	FCER1A	850	0.3	0.42	YES
9	LAT2	LAT2	LAT2	868	0.3	0.46	YES
10	VAV1	VAV1	VAV1	1128	0.26	0.48	YES
11	FCER1G	FCER1G	FCER1G	1280	0.23	0.5	YES
12	HCLS1	HCLS1	HCLS1	1311	0.23	0.53	YES
13	WIPF1	WIPF1	WIPF1	1324	0.23	0.56	YES
14	INPP5D	INPP5D	INPP5D	1434	0.21	0.58	YES
15	DUSP1	DUSP1	DUSP1	1487	0.2	0.61	YES
16	PTPN13	PTPN13	PTPN13	1608	0.19	0.63	YES
17	PPAP2A	PPAP2A	PPAP2A	1691	0.18	0.65	YES
18	FOS	FOS	FOS	1905	0.16	0.66	YES
19	S1PR1	S1PR1	S1PR1	1952	0.16	0.68	YES
20	FER	FER	FER	2166	0.14	0.69	YES
21	LAT	LAT	LAT	2211	0.14	0.7	YES
22	LYN	LYN	LYN	3006	0.089	0.67	NO
23	NFKB1	NFKB1	NFKB1	3220	0.079	0.67	NO
24	SHC1	SHC1	SHC1	3631	0.066	0.66	NO
25	GRB2	GRB2	GRB2	4022	0.054	0.65	NO
26	MAPK1	MAPK1	MAPK1	4087	0.052	0.65	NO
27	NFATC2	NFATC2	NFATC2	4170	0.051	0.65	NO
28	PTK2	PTK2	PTK2	4792	0.038	0.62	NO
29	GAB2	GAB2	GAB2	4975	0.035	0.62	NO
30	HRAS	HRAS	HRAS	5015	0.034	0.62	NO
31	IKBKG	IKBKG	IKBKG	5039	0.034	0.62	NO
32	PXN	PXN	PXN	5470	0.026	0.6	NO
33	MAPK3	MAPK3	MAPK3	6019	0.019	0.58	NO
34	JUN	JUN	JUN	6078	0.018	0.58	NO
35	RASA1	RASA1	RASA1	6428	0.014	0.56	NO
36	PIK3CA	PIK3CA	PIK3CA	6568	0.012	0.56	NO
37	MAP2K1	MAP2K1	MAP2K1	6584	0.012	0.56	NO
38	MAP2K7	MAP2K7	MAP2K7	6678	0.011	0.55	NO
39	PAK2	PAK2	PAK2	6867	0.0085	0.54	NO
40	RELA	RELA	RELA	6974	0.0074	0.54	NO
41	MAP2K2	MAP2K2	MAP2K2	7089	0.0062	0.53	NO
42	CHUK	CHUK	CHUK	7180	0.0052	0.53	NO
43	CBLB	CBLB	CBLB	7402	0.0027	0.52	NO
44	AKT1	AKT1	AKT1	7603	0.00076	0.51	NO
45	PIK3R1	PIK3R1	PIK3R1	7734	-0.00047	0.5	NO
46	MAP2K4	MAP2K4	MAP2K4	8232	-0.005	0.47	NO
47	KLRG1	KLRG1	KLRG1	8373	-0.0065	0.47	NO
48	CBL	CBL	CBL	8471	-0.0074	0.46	NO
49	SOS1	SOS1	SOS1	9102	-0.013	0.43	NO
50	PLCG1	PLCG1	PLCG1	9448	-0.016	0.41	NO
51	PTPN11	PTPN11	PTPN11	9556	-0.017	0.41	NO
52	RAF1	RAF1	RAF1	9666	-0.018	0.41	NO
53	DOK1	DOK1	DOK1	9861	-0.02	0.4	NO
54	PLD2	PLD2	PLD2	10274	-0.023	0.38	NO
55	MAPK8	MAPK8	MAPK8	11235	-0.032	0.33	NO
56	IKBKB	IKBKB	IKBKB	11378	-0.033	0.33	NO
57	MAP3K1	MAP3K1	MAP3K1	11717	-0.037	0.32	NO
58	SYK	SYK	SYK	13541	-0.058	0.23	NO
59	FYN	FYN	FYN	14056	-0.066	0.21	NO
60	PLA2G4A	PLA2G4A	PLA2G4A	15526	-0.1	0.14	NO
61	PLA2G1B	PLA2G1B	PLA2G1B	16961	-0.17	0.087	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 CYTOKINE CYTOKINE RECEPTOR INTERACTION.

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

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

Table 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	PTPRC	PTPRC	PTPRC	524	0.38	0.17	YES
2	RAC2	RAC2	RAC2	1321	0.23	0.24	YES
3	MYH11	MYH11	MYH11	1482	0.2	0.34	YES
4	CD72	CD72	CD72	1935	0.16	0.4	YES
5	LIMK2	LIMK2	LIMK2	2528	0.12	0.43	YES
6	MYL9	MYL9	MYL9	2617	0.11	0.48	YES
7	MYH14	MYH14	MYH14	2728	0.1	0.53	YES
8	RRAS	RRAS	RRAS	2803	0.098	0.58	YES
9	MYH9	MYH9	MYH9	2987	0.09	0.62	YES
10	RHOG	RHOG	RHOG	3143	0.083	0.65	YES
11	RHOB	RHOB	RHOB	4295	0.048	0.62	NO
12	MYH10	MYH10	MYH10	5182	0.031	0.58	NO
13	ROCK1	ROCK1	ROCK1	5250	0.03	0.6	NO
14	MET	MET	MET	5323	0.028	0.61	NO
15	RHOC	RHOC	RHOC	5600	0.024	0.61	NO
16	RHOA	RHOA	RHOA	5857	0.021	0.6	NO
17	CDC42	CDC42	CDC42	5991	0.019	0.61	NO
18	SEMA4D	SEMA4D	SEMA4D	6187	0.017	0.6	NO
19	ARHGEF12	ARHGEF12	ARHGEF12	6671	0.011	0.58	NO
20	RAC1	RAC1	RAC1	7228	0.0048	0.56	NO
21	MYL6	MYL6	MYL6	7277	0.0042	0.56	NO
22	MYL12B	MYL12B	MYL12B	7288	0.0041	0.56	NO
23	LIMK1	LIMK1	LIMK1	7366	0.0031	0.56	NO
24	ROCK2	ROCK2	ROCK2	7857	-0.0016	0.53	NO
25	RND1	RND1	RND1	9363	-0.016	0.46	NO
26	ERBB2	ERBB2	ERBB2	10018	-0.021	0.43	NO
27	PLXNB1	PLXNB1	PLXNB1	10284	-0.024	0.43	NO
28	ARHGEF11	ARHGEF11	ARHGEF11	11197	-0.032	0.4	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 CHEMOKINE SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

Table 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	SERPINE1	SERPINE1	SERPINE1	133	0.57	0.18	YES
2	MEF2C	MEF2C	MEF2C	1517	0.2	0.17	YES
3	BHLHE40	BHLHE40	BHLHE40	1786	0.17	0.21	YES
4	CCRN4L	CCRN4L	CCRN4L	1960	0.16	0.25	YES
5	SREBF1	SREBF1	SREBF1	2083	0.15	0.29	YES
6	ARNTL	ARNTL	ARNTL	2191	0.14	0.33	YES
7	PPARGC1A	PPARGC1A	PPARGC1A	2316	0.13	0.37	YES
8	NR3C1	NR3C1	NR3C1	2424	0.12	0.4	YES
9	RORA	RORA	RORA	2502	0.12	0.43	YES
10	PER1	PER1	PER1	2720	0.1	0.46	YES
11	NPAS2	NPAS2	NPAS2	2748	0.1	0.49	YES
12	NR1D1	NR1D1	NR1D1	2837	0.097	0.51	YES
13	SMARCD3	SMARCD3	SMARCD3	3107	0.085	0.53	YES
14	F7	F7	F7	3827	0.06	0.51	YES
15	RXRA	RXRA	RXRA	3950	0.056	0.52	YES
16	CLOCK	CLOCK	CLOCK	3973	0.056	0.53	YES
17	PPARA	PPARA	PPARA	4414	0.045	0.52	YES
18	PRIC285	PRIC285	PRIC285	4472	0.044	0.54	YES
19	NAMPT	NAMPT	NAMPT	4525	0.043	0.55	YES
20	MEF2D	MEF2D	MEF2D	4740	0.039	0.55	YES
21	HIF1A	HIF1A	HIF1A	4856	0.037	0.55	YES
22	ARNTL2	ARNTL2	ARNTL2	4970	0.035	0.56	YES
23	DBP	DBP	DBP	5413	0.027	0.54	NO
24	NCOA3	NCOA3	NCOA3	5648	0.024	0.54	NO
25	FBXL3	FBXL3	FBXL3	6044	0.019	0.52	NO
26	BHLHE41	BHLHE41	BHLHE41	6172	0.017	0.52	NO
27	NCOA1	NCOA1	NCOA1	6887	0.0083	0.49	NO
28	MED1	MED1	MED1	7013	0.0069	0.48	NO
29	CRY2	CRY2	CRY2	7356	0.0032	0.46	NO
30	NCOA2	NCOA2	NCOA2	7491	0.0019	0.46	NO
31	CSNK1E	CSNK1E	CSNK1E	7512	0.0017	0.46	NO
32	TBL1XR1	TBL1XR1	TBL1XR1	7802	-0.0011	0.44	NO
33	NCOR1	NCOR1	NCOR1	7885	-0.0019	0.44	NO
34	CUL1	CUL1	CUL1	7925	-0.0022	0.44	NO
35	CSNK1D	CSNK1D	CSNK1D	8038	-0.0032	0.43	NO
36	SKP1	SKP1	SKP1	8080	-0.0036	0.43	NO
37	CREBBP	CREBBP	CREBBP	8625	-0.0088	0.4	NO
38	PER2	PER2	PER2	8795	-0.01	0.4	NO
39	ATF2	ATF2	ATF2	9011	-0.012	0.39	NO
40	HDAC3	HDAC3	HDAC3	9190	-0.014	0.39	NO
41	ELOVL3	ELOVL3	ELOVL3	9596	-0.018	0.37	NO
42	EP300	EP300	EP300	9614	-0.018	0.37	NO
43	TBL1X	TBL1X	TBL1X	10138	-0.022	0.35	NO
44	UBA52	UBA52	UBA52	10227	-0.023	0.36	NO
45	NCOA6	NCOA6	NCOA6	10818	-0.028	0.33	NO
46	CREB1	CREB1	CREB1	11138	-0.031	0.33	NO
47	BTRC	BTRC	BTRC	11578	-0.035	0.31	NO
48	CPT1A	CPT1A	CPT1A	12071	-0.04	0.3	NO
49	RPS27A	RPS27A	RPS27A	12429	-0.044	0.3	NO
50	TGS1	TGS1	TGS1	12570	-0.045	0.3	NO
51	CRY1	CRY1	CRY1	14158	-0.068	0.24	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 PHOSPHATIDYLINOSITOL SIGNALING SYSTEM.

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

genes ES table in pathway: KEGG NEUROACTIVE LIGAND 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	GRAP2	GRAP2	GRAP2	231	0.5	0.15	YES
2	CD86	CD86	CD86	677	0.34	0.24	YES
3	CD80	CD80	CD80	680	0.34	0.35	YES
4	CD28	CD28	CD28	818	0.31	0.45	YES
5	LCK	LCK	LCK	975	0.28	0.53	YES
6	AKT3	AKT3	AKT3	1033	0.27	0.62	YES
7	VAV1	VAV1	VAV1	1128	0.26	0.7	YES
8	LYN	LYN	LYN	3006	0.089	0.63	NO
9	GRB2	GRB2	GRB2	4022	0.054	0.59	NO
10	PDPK1	PDPK1	PDPK1	5407	0.027	0.53	NO
11	MAP3K8	MAP3K8	MAP3K8	5430	0.027	0.54	NO
12	MAP3K14	MAP3K14	MAP3K14	5971	0.02	0.51	NO
13	CDC42	CDC42	CDC42	5991	0.019	0.52	NO
14	PIK3CA	PIK3CA	PIK3CA	6568	0.012	0.49	NO
15	PAK2	PAK2	PAK2	6867	0.0085	0.48	NO
16	MAPKAP1	MAPKAP1	MAPKAP1	6984	0.0072	0.47	NO
17	RAC1	RAC1	RAC1	7228	0.0048	0.46	NO
18	PIK3R3	PIK3R3	PIK3R3	7309	0.0037	0.46	NO
19	AKT1	AKT1	AKT1	7603	0.00076	0.44	NO
20	PIK3R1	PIK3R1	PIK3R1	7734	-0.00047	0.44	NO
21	AKT2	AKT2	AKT2	8273	-0.0054	0.41	NO
22	MLST8	MLST8	MLST8	8894	-0.011	0.38	NO
23	MTOR	MTOR	MTOR	9451	-0.016	0.35	NO
24	RICTOR	RICTOR	RICTOR	10190	-0.023	0.32	NO
25	SRC	SRC	SRC	10399	-0.024	0.32	NO
26	TRIB3	TRIB3	TRIB3	12204	-0.042	0.24	NO
27	YES1	YES1	YES1	12503	-0.045	0.23	NO
28	PIK3R2	PIK3R2	PIK3R2	12906	-0.05	0.23	NO
29	FYN	FYN	FYN	14056	-0.066	0.19	NO
30	PAK1	PAK1	PAK1	14551	-0.076	0.19	NO
31	THEM4	THEM4	THEM4	15044	-0.087	0.19	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 NEUROACTIVE LIGAND RECEPTOR INTERACTION.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NEUROACTIVE LIGAND 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

Methods & Data

Input

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