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

Thymoma (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 THYM-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1J38S2H

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 "THYM-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: 715
Number of samples: 120
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 46
pheno.type: 2 - 4 :[ clus2 ] 30
pheno.type: 3 - 4 :[ clus3 ] 30
pheno.type: 4 - 4 :[ clus4 ] 14

For the expression subtypes of 18301 genes in 121 samples, GSEA found enriched gene sets in each cluster using 120 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 BUTANOATE METABOLISM, KEGG DRUG METABOLISM OTHER ENZYMES, KEGG NUCLEOTIDE EXCISION REPAIR, REACTOME SIGNALING BY WNT, REACTOME MEIOSIS, REACTOME TCR SIGNALING, REACTOME RNA POL I TRANSCRIPTION, REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE, REACTOME TRANSCRIPTION

And common core enriched genes are GTF2H2, CCNH, CDK7, CDK9, GTF2A2, GTF2E2, GTF2H2B, HIST1H2AB, HIST1H2AD, HIST1H2AE

clus2

Top enriched gene sets are KEGG RIBOSOME, KEGG SPLICEOSOME, REACTOME TRANSLATION, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES, REACTOME ORC1 REMOVAL FROM CHROMATIN, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, REACTOME PEPTIDE CHAIN ELONGATION, REACTOME MRNA SPLICING

And common core enriched genes are FAU, RPS10, RPS11, RPS12, RPS13, RPS14, RPS15, RPS15A, RPS16, RPS17

clus3

Top enriched gene sets are KEGG O GLYCAN BIOSYNTHESIS, KEGG FOCAL ADHESION, KEGG ADHERENS JUNCTION, KEGG ARRHYTHMOGENIC RIGHT VENTRICULAR CARDIOMYOPATHY ARVC, ST G ALPHA I PATHWAY, ST INTEGRIN SIGNALING PATHWAY, PID ERBB4 PATHWAY, PID WNT NONCANONICAL PATHWAY, PID EPHBFWDPATHWAY, PID ARF6 TRAFFICKINGPATHWAY

And common core enriched genes are PIK3CA, PTK2, CRK, CTNNA1, CTNNB1, MAPK8, PTPN11, BCAR1, CAMK2A, YES1

clus4

Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG ETHER LIPID METABOLISM, KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, KEGG CYTOSOLIC DNA SENSING PATHWAY, KEGG TYPE I DIABETES MELLITUS, KEGG LEISHMANIA INFECTION, KEGG AUTOIMMUNE THYROID DISEASE, KEGG ALLOGRAFT REJECTION, KEGG GRAFT VERSUS HOST DISEASE

And common core enriched genes are IRF7, CAMK2B, CAMK2D, CD44, CIITA, FCGR1A, FCGR1B, GBP1, GBP2, GBP4

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	0.53	1.7	0.054	1	0.77	0.62	0.31	0.43	1	0.53
KEGG BUTANOATE METABOLISM	31	genes.ES.table	0.53	1.6	0.046	1	0.87	0.42	0.21	0.33	0.63	0.35
KEGG DRUG METABOLISM OTHER ENZYMES	34	genes.ES.table	0.53	1.5	0.038	1	0.96	0.26	0.098	0.24	0.66	0.33
KEGG NUCLEOTIDE EXCISION REPAIR	44	genes.ES.table	0.46	1.6	0.062	1	0.9	0.48	0.32	0.33	0.66	0.37
REACTOME SIGNALING BY WNT	63	genes.ES.table	0.47	1.5	0.087	1	0.95	0.65	0.36	0.42	0.73	0.38
REACTOME MEIOSIS	103	genes.ES.table	0.71	1.6	0.016	1	0.9	0.55	0.16	0.46	0.65	0.35
REACTOME TCR SIGNALING	50	genes.ES.table	0.62	1.5	0.11	0.97	0.96	0.38	0.14	0.33	0.64	0.31
REACTOME RNA POL I TRANSCRIPTION	80	genes.ES.table	0.72	1.5	0.057	1	0.95	0.52	0.13	0.46	0.76	0.39
REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE	53	genes.ES.table	0.51	1.5	0.13	1	0.96	0.74	0.39	0.45	0.77	0.38
REACTOME TRANSCRIPTION	190	genes.ES.table	0.53	1.6	0.039	1	0.8	0.46	0.29	0.33	0.98	0.5

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	DSG3	DSG3	DSG3	30	1.1	0.14	YES
2	HIST1H1D	HIST1H1D	HIST1H1D	246	0.6	0.21	YES
3	DSG1	DSG1	DSG1	323	0.53	0.27	YES
4	HIST1H1B	HIST1H1B	HIST1H1B	509	0.44	0.32	YES
5	HIST1H1E	HIST1H1E	HIST1H1E	661	0.4	0.36	YES
6	MAPT	MAPT	MAPT	897	0.35	0.4	YES
7	MST4	MST4	MST4	1534	0.26	0.4	YES
8	PRKCQ	PRKCQ	PRKCQ	1544	0.26	0.43	YES
9	HMGB2	HMGB2	HMGB2	2107	0.21	0.43	YES
10	CASP6	CASP6	CASP6	2284	0.2	0.44	YES
11	HIST1H1C	HIST1H1C	HIST1H1C	2536	0.18	0.45	YES
12	SATB1	SATB1	SATB1	2557	0.18	0.48	YES
13	LMNB1	LMNB1	LMNB1	2727	0.17	0.49	YES
14	LOC647859	LOC647859	LOC647859	2733	0.17	0.51	YES
15	APC	APC	APC	3647	0.12	0.48	NO
16	SPTAN1	SPTAN1	SPTAN1	3941	0.11	0.48	NO
17	PKP1	PKP1	PKP1	5497	0.07	0.4	NO
18	BCAP31	BCAP31	BCAP31	6224	0.055	0.37	NO
19	HMGB1	HMGB1	HMGB1	6404	0.052	0.36	NO
20	ACIN1	ACIN1	ACIN1	6777	0.045	0.35	NO
21	DBNL	DBNL	DBNL	7650	0.03	0.3	NO
22	PAK2	PAK2	PAK2	7671	0.03	0.31	NO
23	CASP7	CASP7	CASP7	7924	0.026	0.3	NO
24	KPNB1	KPNB1	KPNB1	8245	0.021	0.28	NO
25	KPNA1	KPNA1	KPNA1	8371	0.019	0.28	NO
26	CASP8	CASP8	CASP8	8487	0.017	0.27	NO
27	FNTA	FNTA	FNTA	8827	0.011	0.26	NO
28	DNM1L	DNM1L	DNM1L	9797	-0.0061	0.2	NO
29	ROCK1	ROCK1	ROCK1	10296	-0.015	0.18	NO
30	BIRC2	BIRC2	BIRC2	10414	-0.017	0.18	NO
31	DFFA	DFFA	DFFA	10778	-0.025	0.16	NO
32	CDH1	CDH1	CDH1	11099	-0.032	0.14	NO
33	GAS2	GAS2	GAS2	11151	-0.033	0.15	NO
34	LMNA	LMNA	LMNA	11193	-0.034	0.15	NO
35	ADD1	ADD1	ADD1	11204	-0.034	0.15	NO
36	TJP2	TJP2	TJP2	11368	-0.039	0.15	NO
37	CASP3	CASP3	CASP3	11883	-0.052	0.13	NO
38	VIM	VIM	VIM	11951	-0.054	0.13	NO
39	DSP	DSP	DSP	12121	-0.06	0.13	NO
40	STK24	STK24	STK24	12123	-0.06	0.14	NO
41	PLEC	PLEC	PLEC	12203	-0.062	0.14	NO
42	DFFB	DFFB	DFFB	12260	-0.064	0.15	NO
43	TJP1	TJP1	TJP1	13135	-0.095	0.11	NO
44	H1F0	H1F0	H1F0	13208	-0.098	0.12	NO
45	DSG2	DSG2	DSG2	13387	-0.1	0.12	NO
46	PTK2	PTK2	PTK2	13405	-0.11	0.14	NO
47	CTNNB1	CTNNB1	CTNNB1	14463	-0.16	0.1	NO
48	PRKCD	PRKCD	PRKCD	14599	-0.17	0.12	NO
49	OCLN	OCLN	OCLN	15129	-0.21	0.11	NO
50	BMX	BMX	BMX	15308	-0.22	0.13	NO
51	GSN	GSN	GSN	15435	-0.24	0.16	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 BUTANOATE METABOLISM

Table S2. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	OGDHL	OGDHL	OGDHL	319	0.53	0.14	YES
2	PCK1	PCK1	PCK1	587	0.42	0.24	YES
3	ACO1	ACO1	ACO1	2258	0.2	0.21	YES
4	IDH3A	IDH3A	IDH3A	2327	0.19	0.26	YES
5	IDH2	IDH2	IDH2	2537	0.18	0.3	YES
6	FH	FH	FH	3071	0.15	0.31	YES
7	ACO2	ACO2	ACO2	3251	0.14	0.34	YES
8	DLD	DLD	DLD	3275	0.14	0.38	YES
9	SDHC	SDHC	SDHC	3707	0.12	0.39	YES
10	OGDH	OGDH	OGDH	3724	0.12	0.43	YES
11	SDHA	SDHA	SDHA	3821	0.11	0.46	YES
12	PDHA1	PDHA1	PDHA1	3834	0.11	0.49	YES
13	MDH2	MDH2	MDH2	4339	0.098	0.49	YES
14	SDHD	SDHD	SDHD	4736	0.087	0.49	YES
15	MDH1	MDH1	MDH1	4759	0.087	0.52	YES
16	SDHB	SDHB	SDHB	5077	0.079	0.52	YES
17	DLST	DLST	DLST	5514	0.07	0.52	YES
18	SUCLG1	SUCLG1	SUCLG1	5589	0.068	0.53	YES
19	IDH3G	IDH3G	IDH3G	6317	0.054	0.51	NO
20	PDHB	PDHB	PDHB	6781	0.045	0.5	NO
21	CS	CS	CS	7111	0.04	0.49	NO
22	IDH3B	IDH3B	IDH3B	7161	0.039	0.5	NO
23	DLAT	DLAT	DLAT	7929	0.026	0.46	NO
24	ACLY	ACLY	ACLY	8545	0.016	0.43	NO
25	SUCLG2	SUCLG2	SUCLG2	9983	-0.0098	0.36	NO
26	SUCLA2	SUCLA2	SUCLA2	11224	-0.035	0.3	NO
27	PCK2	PCK2	PCK2	11641	-0.045	0.29	NO
28	IDH1	IDH1	IDH1	11881	-0.052	0.29	NO
29	PC	PC	PC	15032	-0.2	0.18	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 BUTANOATE METABOLISM.

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

genes ES table in pathway: KEGG DRUG METABOLISM OTHER ENZYMES

Table S3. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HIST1H2AE	HIST1H2AE	HIST1H2AE	293	0.56	0.0057	YES
2	HIST1H2BN	HIST1H2BN	HIST1H2BN	333	0.53	0.024	YES
3	HIST1H3H	HIST1H3H	HIST1H3H	344	0.52	0.044	YES
4	HIST1H3J	HIST1H3J	HIST1H3J	372	0.5	0.062	YES
5	HIST1H2BG	HIST1H2BG	HIST1H2BG	381	0.5	0.082	YES
6	HIST1H3G	HIST1H3G	HIST1H3G	382	0.5	0.1	YES
7	HIST1H4E	HIST1H4E	HIST1H4E	391	0.5	0.12	YES
8	HIST1H2BO	HIST1H2BO	HIST1H2BO	395	0.49	0.14	YES
9	HIST1H2AB	HIST1H2AB	HIST1H2AB	455	0.46	0.15	YES
10	HIST1H4C	HIST1H4C	HIST1H4C	477	0.45	0.17	YES
11	HIST1H2BI	HIST1H2BI	HIST1H2BI	480	0.45	0.19	YES
12	HIST1H4H	HIST1H4H	HIST1H4H	492	0.45	0.21	YES
13	HIST1H4L	HIST1H4L	HIST1H4L	515	0.44	0.22	YES
14	HIST1H2BB	HIST1H2BB	HIST1H2BB	519	0.44	0.24	YES
15	HIST1H2BC	HIST1H2BC	HIST1H2BC	522	0.44	0.26	YES
16	HIST1H4B	HIST1H4B	HIST1H4B	552	0.43	0.27	YES
17	HIST2H2AC	HIST2H2AC	HIST2H2AC	596	0.41	0.28	YES
18	HIST2H3D	HIST2H3D	HIST2H3D	643	0.4	0.3	YES
19	HIST1H3I	HIST1H3I	HIST1H3I	651	0.4	0.31	YES
20	HIST1H3C	HIST1H3C	HIST1H3C	663	0.4	0.33	YES
21	HIST1H3A	HIST1H3A	HIST1H3A	673	0.39	0.34	YES
22	HIST1H4J	HIST1H4J	HIST1H4J	689	0.39	0.36	YES
23	HIST1H3E	HIST1H3E	HIST1H3E	751	0.38	0.37	YES
24	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	762	0.37	0.38	YES
25	HIST1H2BL	HIST1H2BL	HIST1H2BL	773	0.37	0.4	YES
26	HIST1H2BH	HIST1H2BH	HIST1H2BH	836	0.36	0.41	YES
27	HIST1H4I	HIST1H4I	HIST1H4I	867	0.36	0.42	YES
28	HIST1H3D	HIST1H3D	HIST1H3D	893	0.35	0.43	YES
29	HIST1H3F	HIST1H3F	HIST1H3F	915	0.35	0.44	YES
30	HIST1H2BM	HIST1H2BM	HIST1H2BM	957	0.34	0.46	YES
31	HIST1H2BF	HIST1H2BF	HIST1H2BF	1144	0.31	0.46	YES
32	HIST1H2AD	HIST1H2AD	HIST1H2AD	1147	0.31	0.47	YES
33	HIST1H3B	HIST1H3B	HIST1H3B	1294	0.29	0.47	YES
34	HIST1H4A	HIST1H4A	HIST1H4A	1322	0.29	0.48	YES
35	HIST2H3C	HIST2H3C	HIST2H3C	1418	0.28	0.49	YES
36	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1485	0.27	0.5	YES
37	GTF2H2	GTF2H2	GTF2H2	1639	0.25	0.5	YES
38	HIST1H4D	HIST1H4D	HIST1H4D	1707	0.25	0.5	YES
39	LZTS1	LZTS1	LZTS1	1782	0.24	0.51	YES
40	HIST1H2BE	HIST1H2BE	HIST1H2BE	1941	0.22	0.51	YES
41	HIST1H2BD	HIST1H2BD	HIST1H2BD	1961	0.22	0.52	YES
42	HIST1H4F	HIST1H4F	HIST1H4F	2245	0.2	0.51	YES
43	HIST2H2BE	HIST2H2BE	HIST2H2BE	2332	0.19	0.51	YES
44	CDK7	CDK7	CDK7	2754	0.16	0.5	YES
45	H2AFX	H2AFX	H2AFX	2759	0.16	0.5	YES
46	H2AFZ	H2AFZ	H2AFZ	2821	0.16	0.5	YES
47	TAF12	TAF12	TAF12	3105	0.14	0.5	YES
48	HIST1H4K	HIST1H4K	HIST1H4K	3200	0.14	0.5	YES
49	SNRPG	SNRPG	SNRPG	3296	0.14	0.5	YES
50	LSM10	LSM10	LSM10	3323	0.14	0.5	YES
51	TAF1A	TAF1A	TAF1A	3327	0.14	0.5	YES
52	TAF5	TAF5	TAF5	3390	0.13	0.51	YES
53	UPF3B	UPF3B	UPF3B	3455	0.13	0.51	YES
54	H3F3A	H3F3A	H3F3A	3674	0.12	0.5	YES
55	POLR2J	POLR2J	POLR2J	3797	0.12	0.5	YES
56	TAF9	TAF9	TAF9	3802	0.12	0.5	YES
57	POLR3GL	POLR3GL	POLR3GL	3850	0.11	0.5	YES
58	GTF2E2	GTF2E2	GTF2E2	3874	0.11	0.51	YES
59	MTERF	MTERF	MTERF	3911	0.11	0.51	YES
60	NCBP1	NCBP1	NCBP1	4024	0.11	0.51	YES
61	SNAPC5	SNAPC5	SNAPC5	4136	0.1	0.51	YES
62	BRF2	BRF2	BRF2	4200	0.1	0.51	YES
63	GTF2H2B	GTF2H2B	GTF2H2B	4211	0.1	0.51	YES
64	POLR2G	POLR2G	POLR2G	4261	0.1	0.51	YES
65	MNAT1	MNAT1	MNAT1	4418	0.096	0.51	YES
66	TAF10	TAF10	TAF10	4477	0.094	0.51	YES
67	SLBP	SLBP	SLBP	4599	0.091	0.5	YES
68	RBM8A	RBM8A	RBM8A	4609	0.09	0.51	YES
69	MAGOH	MAGOH	MAGOH	4619	0.09	0.51	YES
70	CBX3	CBX3	CBX3	4640	0.09	0.51	YES
71	SNRPE	SNRPE	SNRPE	4652	0.09	0.52	YES
72	HIST4H4	HIST4H4	HIST4H4	4707	0.088	0.52	YES
73	TFB2M	TFB2M	TFB2M	4773	0.086	0.52	YES
74	TAF6	TAF6	TAF6	4802	0.085	0.52	YES
75	TAF4	TAF4	TAF4	4851	0.084	0.52	YES
76	CDK9	CDK9	CDK9	4857	0.084	0.52	YES
77	TCEB1	TCEB1	TCEB1	4892	0.083	0.52	YES
78	POLR2I	POLR2I	POLR2I	4917	0.082	0.52	YES
79	HIST2H4A	HIST2H4A	HIST2H4A	4923	0.082	0.53	YES
80	TAF1C	TAF1C	TAF1C	4966	0.081	0.53	YES
81	CCNH	CCNH	CCNH	4988	0.081	0.53	YES
82	GTF2A2	GTF2A2	GTF2A2	5069	0.079	0.53	YES
83	PAPOLA	PAPOLA	PAPOLA	5087	0.079	0.53	YES
84	SNRPF	SNRPF	SNRPF	5176	0.077	0.53	YES
85	SNAPC2	SNAPC2	SNAPC2	5231	0.076	0.53	YES
86	SNRPB	SNRPB	SNRPB	5277	0.075	0.53	YES
87	CPSF1	CPSF1	CPSF1	5294	0.075	0.53	YES
88	CPSF3	CPSF3	CPSF3	5357	0.073	0.53	NO
89	TCEB2	TCEB2	TCEB2	5429	0.072	0.53	NO
90	HIST1H2AC	HIST1H2AC	HIST1H2AC	5549	0.069	0.53	NO
91	THOC4	THOC4	THOC4	5595	0.068	0.53	NO
92	POLR2D	POLR2D	POLR2D	5682	0.066	0.52	NO
93	PABPN1	PABPN1	PABPN1	5746	0.065	0.52	NO
94	NFX1	NFX1	NFX1	5812	0.064	0.52	NO
95	GTF3C5	GTF3C5	GTF3C5	5894	0.062	0.52	NO
96	CSTF3	CSTF3	CSTF3	5901	0.062	0.52	NO
97	POLR3C	POLR3C	POLR3C	5974	0.06	0.52	NO
98	POLR2F	POLR2F	POLR2F	6075	0.058	0.52	NO
99	POLR2H	POLR2H	POLR2H	6157	0.057	0.52	NO
100	POLR3K	POLR3K	POLR3K	6162	0.057	0.52	NO
101	HIST1H2BK	HIST1H2BK	HIST1H2BK	6304	0.054	0.51	NO
102	MBD2	MBD2	MBD2	6327	0.053	0.51	NO
103	TAF1	TAF1	TAF1	6328	0.053	0.51	NO
104	CPSF2	CPSF2	CPSF2	6442	0.051	0.51	NO
105	U2AF2	U2AF2	U2AF2	6507	0.05	0.51	NO
106	ZNF143	ZNF143	ZNF143	6521	0.05	0.51	NO
107	TAF11	TAF11	TAF11	6756	0.046	0.5	NO
108	ZNF473	ZNF473	ZNF473	6758	0.046	0.5	NO
109	SNRPD3	SNRPD3	SNRPD3	6896	0.043	0.49	NO
110	SUPT16H	SUPT16H	SUPT16H	6944	0.042	0.49	NO
111	CSTF2	CSTF2	CSTF2	6979	0.042	0.49	NO
112	BRF1	BRF1	BRF1	7257	0.037	0.48	NO
113	RNPS1	RNPS1	RNPS1	7386	0.035	0.47	NO
114	U2AF1	U2AF1	U2AF1	7387	0.035	0.48	NO
115	POLR2C	POLR2C	POLR2C	7484	0.033	0.47	NO
116	ERCC3	ERCC3	ERCC3	7537	0.032	0.47	NO
117	UBTF	UBTF	UBTF	7541	0.032	0.47	NO
118	GTF2B	GTF2B	GTF2B	7550	0.032	0.47	NO
119	CTDP1	CTDP1	CTDP1	7556	0.032	0.47	NO
120	TH1L	TH1L	TH1L	7582	0.031	0.47	NO
121	RNGTT	RNGTT	RNGTT	7600	0.031	0.47	NO
122	COBRA1	COBRA1	COBRA1	7639	0.03	0.47	NO
123	POLR2K	POLR2K	POLR2K	7714	0.029	0.47	NO
124	GTF3C3	GTF3C3	GTF3C3	7740	0.029	0.47	NO
125	POLRMT	POLRMT	POLRMT	7873	0.026	0.46	NO
126	CPSF7	CPSF7	CPSF7	7915	0.026	0.46	NO
127	PCF11	PCF11	PCF11	7971	0.025	0.46	NO
128	SRRM1	SRRM1	SRRM1	8197	0.021	0.45	NO
129	GTF2F2	GTF2F2	GTF2F2	8297	0.02	0.44	NO
130	GTF2E1	GTF2E1	GTF2E1	8351	0.019	0.44	NO
131	GTF2H4	GTF2H4	GTF2H4	8525	0.016	0.43	NO
132	RRN3	RRN3	RRN3	8539	0.016	0.43	NO
133	CSTF1	CSTF1	CSTF1	8586	0.015	0.43	NO
134	TCEA1	TCEA1	TCEA1	8678	0.014	0.42	NO
135	POLR3F	POLR3F	POLR3F	8697	0.014	0.42	NO
136	POLR3D	POLR3D	POLR3D	8739	0.013	0.42	NO
137	CLP1	CLP1	CLP1	8781	0.012	0.42	NO
138	SUPT5H	SUPT5H	SUPT5H	8801	0.011	0.42	NO
139	NUDT21	NUDT21	NUDT21	8855	0.011	0.42	NO
140	POLR2B	POLR2B	POLR2B	9014	0.0081	0.41	NO
141	DHX38	DHX38	DHX38	9015	0.0081	0.41	NO
142	TCEB3	TCEB3	TCEB3	9083	0.0069	0.41	NO
143	RDBP	RDBP	RDBP	9130	0.0061	0.4	NO
144	SNAPC3	SNAPC3	SNAPC3	9184	0.0049	0.4	NO
145	CDC40	CDC40	CDC40	9237	0.0041	0.4	NO
146	GTF3C2	GTF3C2	GTF3C2	9244	0.004	0.4	NO
147	TBP	TBP	TBP	9257	0.0038	0.4	NO
148	SSB	SSB	SSB	9283	0.0034	0.4	NO
149	ERCC6	ERCC6	ERCC6	9314	0.0029	0.4	NO
150	POLR1D	POLR1D	POLR1D	9496	-0.0002	0.38	NO
151	TFAM	TFAM	TFAM	9544	-0.0014	0.38	NO
152	SUPT4H1	SUPT4H1	SUPT4H1	9675	-0.004	0.38	NO
153	HIST3H2BB	HIST3H2BB	HIST3H2BB	9695	-0.0044	0.37	NO
154	KAT2B	KAT2B	KAT2B	9740	-0.0052	0.37	NO
155	POLR2E	POLR2E	POLR2E	9795	-0.0061	0.37	NO
156	SNAPC4	SNAPC4	SNAPC4	9963	-0.0093	0.36	NO
157	EHMT2	EHMT2	EHMT2	9989	-0.0099	0.36	NO
158	GTF2F1	GTF2F1	GTF2F1	10013	-0.01	0.36	NO
159	ERCC2	ERCC2	ERCC2	10091	-0.012	0.36	NO
160	POLR3H	POLR3H	POLR3H	10144	-0.013	0.35	NO
161	WHSC2	WHSC2	WHSC2	10298	-0.015	0.34	NO
162	SSRP1	SSRP1	SSRP1	10604	-0.021	0.33	NO
163	SNAPC1	SNAPC1	SNAPC1	10762	-0.025	0.32	NO
164	CCNT2	CCNT2	CCNT2	10796	-0.026	0.32	NO
165	POLR3E	POLR3E	POLR3E	11063	-0.031	0.31	NO
166	NFIB	NFIB	NFIB	11069	-0.031	0.31	NO
167	TAF13	TAF13	TAF13	11170	-0.034	0.3	NO
168	POLR3A	POLR3A	POLR3A	11483	-0.042	0.29	NO
169	POLR2L	POLR2L	POLR2L	11675	-0.046	0.28	NO
170	POLR3B	POLR3B	POLR3B	11784	-0.049	0.28	NO
171	ELL	ELL	ELL	11948	-0.054	0.27	NO
172	POLR1A	POLR1A	POLR1A	11975	-0.055	0.27	NO
173	TAF1B	TAF1B	TAF1B	11989	-0.056	0.27	NO
174	POLR2A	POLR2A	POLR2A	12028	-0.057	0.27	NO
175	POLR1B	POLR1B	POLR1B	12073	-0.058	0.27	NO
176	H3F3B	H3F3B	H3F3B	12173	-0.062	0.27	NO
177	NCBP2	NCBP2	NCBP2	12184	-0.062	0.27	NO
178	RNMT	RNMT	RNMT	12498	-0.071	0.26	NO
179	GTF2A1	GTF2A1	GTF2A1	12560	-0.073	0.25	NO
180	GTF2H1	GTF2H1	GTF2H1	12622	-0.075	0.25	NO
181	LSM11	LSM11	LSM11	12773	-0.081	0.25	NO
182	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	12923	-0.086	0.24	NO
183	POLR1C	POLR1C	POLR1C	12969	-0.088	0.24	NO
184	MAPK3	MAPK3	MAPK3	13417	-0.11	0.22	NO
185	POU2F1	POU2F1	POU2F1	13532	-0.11	0.22	NO
186	GTF3C4	GTF3C4	GTF3C4	14287	-0.15	0.19	NO
187	GTF2H3	GTF2H3	GTF2H3	14289	-0.15	0.19	NO
188	TAF4B	TAF4B	TAF4B	14575	-0.17	0.18	NO
189	CCNT1	CCNT1	CCNT1	15211	-0.22	0.16	NO
190	PTRF	PTRF	PTRF	16154	-0.32	0.12	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 DRUG METABOLISM OTHER ENZYMES.

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

genes ES table in pathway: KEGG NUCLEOTIDE EXCISION REPAIR

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HIST1H2AE	HIST1H2AE	HIST1H2AE	293	0.56	0.011	YES
2	HIST1H2BN	HIST1H2BN	HIST1H2BN	333	0.53	0.034	YES
3	HIST1H3H	HIST1H3H	HIST1H3H	344	0.52	0.058	YES
4	HIST1H3J	HIST1H3J	HIST1H3J	372	0.5	0.081	YES
5	HIST1H2BG	HIST1H2BG	HIST1H2BG	381	0.5	0.1	YES
6	HIST1H3G	HIST1H3G	HIST1H3G	382	0.5	0.13	YES
7	HIST1H4E	HIST1H4E	HIST1H4E	391	0.5	0.15	YES
8	HIST1H2BO	HIST1H2BO	HIST1H2BO	395	0.49	0.18	YES
9	HIST1H2AB	HIST1H2AB	HIST1H2AB	455	0.46	0.2	YES
10	HIST1H4C	HIST1H4C	HIST1H4C	477	0.45	0.22	YES
11	HIST1H2BI	HIST1H2BI	HIST1H2BI	480	0.45	0.24	YES
12	HIST1H4H	HIST1H4H	HIST1H4H	492	0.45	0.26	YES
13	HIST1H4L	HIST1H4L	HIST1H4L	515	0.44	0.28	YES
14	HIST1H2BB	HIST1H2BB	HIST1H2BB	519	0.44	0.3	YES
15	HIST1H2BC	HIST1H2BC	HIST1H2BC	522	0.44	0.32	YES
16	HIST1H4B	HIST1H4B	HIST1H4B	552	0.43	0.34	YES
17	HIST2H2AC	HIST2H2AC	HIST2H2AC	596	0.41	0.36	YES
18	HIST2H3D	HIST2H3D	HIST2H3D	643	0.4	0.37	YES
19	HIST1H3I	HIST1H3I	HIST1H3I	651	0.4	0.39	YES
20	HIST1H3C	HIST1H3C	HIST1H3C	663	0.4	0.41	YES
21	HIST1H3A	HIST1H3A	HIST1H3A	673	0.39	0.43	YES
22	HIST1H4J	HIST1H4J	HIST1H4J	689	0.39	0.45	YES
23	HIST1H3E	HIST1H3E	HIST1H3E	751	0.38	0.46	YES
24	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	762	0.37	0.48	YES
25	HIST1H2BL	HIST1H2BL	HIST1H2BL	773	0.37	0.5	YES
26	HIST1H2BH	HIST1H2BH	HIST1H2BH	836	0.36	0.51	YES
27	HIST1H4I	HIST1H4I	HIST1H4I	867	0.36	0.53	YES
28	HIST1H3D	HIST1H3D	HIST1H3D	893	0.35	0.54	YES
29	HIST1H3F	HIST1H3F	HIST1H3F	915	0.35	0.56	YES
30	HIST1H2BM	HIST1H2BM	HIST1H2BM	957	0.34	0.57	YES
31	HIST1H2BF	HIST1H2BF	HIST1H2BF	1144	0.31	0.58	YES
32	HIST1H2AD	HIST1H2AD	HIST1H2AD	1147	0.31	0.59	YES
33	HIST1H3B	HIST1H3B	HIST1H3B	1294	0.29	0.6	YES
34	HIST1H4A	HIST1H4A	HIST1H4A	1322	0.29	0.61	YES
35	HIST2H3C	HIST2H3C	HIST2H3C	1418	0.28	0.62	YES
36	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1485	0.27	0.63	YES
37	GTF2H2	GTF2H2	GTF2H2	1639	0.25	0.63	YES
38	HIST1H4D	HIST1H4D	HIST1H4D	1707	0.25	0.64	YES
39	LZTS1	LZTS1	LZTS1	1782	0.24	0.65	YES
40	HIST1H2BE	HIST1H2BE	HIST1H2BE	1941	0.22	0.65	YES
41	HIST1H2BD	HIST1H2BD	HIST1H2BD	1961	0.22	0.66	YES
42	HIST1H4F	HIST1H4F	HIST1H4F	2245	0.2	0.65	NO
43	HIST2H2BE	HIST2H2BE	HIST2H2BE	2332	0.19	0.66	NO
44	CDK7	CDK7	CDK7	2754	0.16	0.64	NO
45	H2AFX	H2AFX	H2AFX	2759	0.16	0.65	NO
46	H2AFZ	H2AFZ	H2AFZ	2821	0.16	0.65	NO
47	HIST1H4K	HIST1H4K	HIST1H4K	3200	0.14	0.64	NO
48	TAF1A	TAF1A	TAF1A	3327	0.14	0.64	NO
49	H3F3A	H3F3A	H3F3A	3674	0.12	0.63	NO
50	POLR3GL	POLR3GL	POLR3GL	3850	0.11	0.62	NO
51	MTERF	MTERF	MTERF	3911	0.11	0.62	NO
52	SNAPC5	SNAPC5	SNAPC5	4136	0.1	0.62	NO
53	BRF2	BRF2	BRF2	4200	0.1	0.62	NO
54	GTF2H2B	GTF2H2B	GTF2H2B	4211	0.1	0.62	NO
55	MNAT1	MNAT1	MNAT1	4418	0.096	0.62	NO
56	CBX3	CBX3	CBX3	4640	0.09	0.61	NO
57	HIST4H4	HIST4H4	HIST4H4	4707	0.088	0.61	NO
58	TFB2M	TFB2M	TFB2M	4773	0.086	0.61	NO
59	HIST2H4A	HIST2H4A	HIST2H4A	4923	0.082	0.6	NO
60	TAF1C	TAF1C	TAF1C	4966	0.081	0.61	NO
61	CCNH	CCNH	CCNH	4988	0.081	0.61	NO
62	SNAPC2	SNAPC2	SNAPC2	5231	0.076	0.6	NO
63	HIST1H2AC	HIST1H2AC	HIST1H2AC	5549	0.069	0.59	NO
64	GTF3C5	GTF3C5	GTF3C5	5894	0.062	0.57	NO
65	POLR3C	POLR3C	POLR3C	5974	0.06	0.57	NO
66	POLR2F	POLR2F	POLR2F	6075	0.058	0.57	NO
67	POLR2H	POLR2H	POLR2H	6157	0.057	0.56	NO
68	POLR3K	POLR3K	POLR3K	6162	0.057	0.57	NO
69	HIST1H2BK	HIST1H2BK	HIST1H2BK	6304	0.054	0.56	NO
70	MBD2	MBD2	MBD2	6327	0.053	0.56	NO
71	ZNF143	ZNF143	ZNF143	6521	0.05	0.56	NO
72	BRF1	BRF1	BRF1	7257	0.037	0.52	NO
73	ERCC3	ERCC3	ERCC3	7537	0.032	0.5	NO
74	UBTF	UBTF	UBTF	7541	0.032	0.5	NO
75	POLR2K	POLR2K	POLR2K	7714	0.029	0.5	NO
76	GTF3C3	GTF3C3	GTF3C3	7740	0.029	0.5	NO
77	POLRMT	POLRMT	POLRMT	7873	0.026	0.49	NO
78	GTF2H4	GTF2H4	GTF2H4	8525	0.016	0.45	NO
79	RRN3	RRN3	RRN3	8539	0.016	0.45	NO
80	POLR3F	POLR3F	POLR3F	8697	0.014	0.45	NO
81	POLR3D	POLR3D	POLR3D	8739	0.013	0.44	NO
82	SNAPC3	SNAPC3	SNAPC3	9184	0.0049	0.42	NO
83	GTF3C2	GTF3C2	GTF3C2	9244	0.004	0.42	NO
84	TBP	TBP	TBP	9257	0.0038	0.42	NO
85	SSB	SSB	SSB	9283	0.0034	0.42	NO
86	ERCC6	ERCC6	ERCC6	9314	0.0029	0.41	NO
87	POLR1D	POLR1D	POLR1D	9496	-0.0002	0.4	NO
88	TFAM	TFAM	TFAM	9544	-0.0014	0.4	NO
89	HIST3H2BB	HIST3H2BB	HIST3H2BB	9695	-0.0044	0.39	NO
90	KAT2B	KAT2B	KAT2B	9740	-0.0052	0.39	NO
91	POLR2E	POLR2E	POLR2E	9795	-0.0061	0.39	NO
92	SNAPC4	SNAPC4	SNAPC4	9963	-0.0093	0.38	NO
93	EHMT2	EHMT2	EHMT2	9989	-0.0099	0.38	NO
94	ERCC2	ERCC2	ERCC2	10091	-0.012	0.37	NO
95	POLR3H	POLR3H	POLR3H	10144	-0.013	0.37	NO
96	SNAPC1	SNAPC1	SNAPC1	10762	-0.025	0.34	NO
97	POLR3E	POLR3E	POLR3E	11063	-0.031	0.32	NO
98	NFIB	NFIB	NFIB	11069	-0.031	0.33	NO
99	POLR3A	POLR3A	POLR3A	11483	-0.042	0.3	NO
100	POLR2L	POLR2L	POLR2L	11675	-0.046	0.3	NO
101	POLR3B	POLR3B	POLR3B	11784	-0.049	0.29	NO
102	POLR1A	POLR1A	POLR1A	11975	-0.055	0.28	NO
103	TAF1B	TAF1B	TAF1B	11989	-0.056	0.29	NO
104	POLR1B	POLR1B	POLR1B	12073	-0.058	0.28	NO
105	H3F3B	H3F3B	H3F3B	12173	-0.062	0.28	NO
106	GTF2H1	GTF2H1	GTF2H1	12622	-0.075	0.26	NO
107	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	12923	-0.086	0.25	NO
108	POLR1C	POLR1C	POLR1C	12969	-0.088	0.25	NO
109	MAPK3	MAPK3	MAPK3	13417	-0.11	0.23	NO
110	POU2F1	POU2F1	POU2F1	13532	-0.11	0.23	NO
111	GTF3C4	GTF3C4	GTF3C4	14287	-0.15	0.2	NO
112	GTF2H3	GTF2H3	GTF2H3	14289	-0.15	0.2	NO
113	PTRF	PTRF	PTRF	16154	-0.32	0.12	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 NUCLEOTIDE EXCISION REPAIR.

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

genes ES table in pathway: REACTOME SIGNALING BY WNT

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	CD28	CD28	CD28	539	0.43	0.001	YES
2	CD247	CD247	CD247	1093	0.32	-0.0066	YES
3	CD8B	CD8B	CD8B	1435	0.27	-0.0058	YES
4	LCK	LCK	LCK	1468	0.27	0.012	YES
5	GTF2H2	GTF2H2	GTF2H2	1639	0.25	0.021	YES
6	AP1M2	AP1M2	AP1M2	2131	0.21	0.0083	YES
7	CXCR4	CXCR4	CXCR4	2299	0.2	0.013	YES
8	NUPL2	NUPL2	NUPL2	2305	0.2	0.027	YES
9	SLC25A5	SLC25A5	SLC25A5	2505	0.18	0.029	YES
10	CD4	CD4	CD4	2573	0.18	0.038	YES
11	DOCK2	DOCK2	DOCK2	2712	0.17	0.042	YES
12	CDK7	CDK7	CDK7	2754	0.16	0.052	YES
13	AP1S2	AP1S2	AP1S2	2937	0.16	0.052	YES
14	FEN1	FEN1	FEN1	2948	0.15	0.063	YES
15	FYN	FYN	FYN	3080	0.15	0.066	YES
16	TAF12	TAF12	TAF12	3105	0.14	0.075	YES
17	RCC1	RCC1	RCC1	3278	0.14	0.076	YES
18	PSMC2	PSMC2	PSMC2	3324	0.14	0.083	YES
19	TAF5	TAF5	TAF5	3390	0.13	0.089	YES
20	PSMA6	PSMA6	PSMA6	3427	0.13	0.096	YES
21	LIG4	LIG4	LIG4	3599	0.12	0.095	YES
22	PSMA3	PSMA3	PSMA3	3702	0.12	0.098	YES
23	PSMB10	PSMB10	PSMB10	3765	0.12	0.1	YES
24	POLR2J	POLR2J	POLR2J	3797	0.12	0.11	YES
25	TAF9	TAF9	TAF9	3802	0.12	0.12	YES
26	PSMD10	PSMD10	PSMD10	3813	0.12	0.12	YES
27	NUP210	NUP210	NUP210	3815	0.11	0.13	YES
28	PSMB4	PSMB4	PSMB4	3861	0.11	0.14	YES
29	GTF2E2	GTF2E2	GTF2E2	3874	0.11	0.15	YES
30	PSMA2	PSMA2	PSMA2	3875	0.11	0.15	YES
31	PSMC1	PSMC1	PSMC1	3999	0.11	0.16	YES
32	NUP93	NUP93	NUP93	4020	0.11	0.16	YES
33	NCBP1	NCBP1	NCBP1	4024	0.11	0.17	YES
34	PSMA7	PSMA7	PSMA7	4156	0.1	0.17	YES
35	NUP50	NUP50	NUP50	4172	0.1	0.18	YES
36	GTF2H2B	GTF2H2B	GTF2H2B	4211	0.1	0.18	YES
37	POLR2G	POLR2G	POLR2G	4261	0.1	0.19	YES
38	PSMD7	PSMD7	PSMD7	4272	0.1	0.19	YES
39	RBX1	RBX1	RBX1	4310	0.098	0.2	YES
40	RANBP1	RANBP1	RANBP1	4379	0.097	0.2	YES
41	MNAT1	MNAT1	MNAT1	4418	0.096	0.2	YES
42	TAF10	TAF10	TAF10	4477	0.094	0.21	YES
43	PSMD4	PSMD4	PSMD4	4533	0.093	0.21	YES
44	SLC25A4	SLC25A4	SLC25A4	4535	0.093	0.22	YES
45	PSMB9	PSMB9	PSMB9	4577	0.092	0.22	YES
46	PSMD14	PSMD14	PSMD14	4696	0.088	0.22	YES
47	PSMB2	PSMB2	PSMB2	4745	0.087	0.23	YES
48	PPIA	PPIA	PPIA	4795	0.086	0.23	YES
49	TAF6	TAF6	TAF6	4802	0.085	0.24	YES
50	PSME2	PSME2	PSME2	4829	0.085	0.24	YES
51	TAF4	TAF4	TAF4	4851	0.084	0.24	YES
52	CDK9	CDK9	CDK9	4857	0.084	0.25	YES
53	TCEB1	TCEB1	TCEB1	4892	0.083	0.26	YES
54	ATP6V1H	ATP6V1H	ATP6V1H	4912	0.082	0.26	YES
55	POLR2I	POLR2I	POLR2I	4917	0.082	0.27	YES
56	BANF1	BANF1	BANF1	4938	0.082	0.27	YES
57	PSIP1	PSIP1	PSIP1	4977	0.081	0.27	YES
58	CCNH	CCNH	CCNH	4988	0.081	0.28	YES
59	LIG1	LIG1	LIG1	5010	0.08	0.28	YES
60	PSMD11	PSMD11	PSMD11	5026	0.08	0.29	YES
61	GTF2A2	GTF2A2	GTF2A2	5069	0.079	0.29	YES
62	PSMA5	PSMA5	PSMA5	5138	0.078	0.29	YES
63	PSMB3	PSMB3	PSMB3	5170	0.077	0.3	YES
64	PSMB7	PSMB7	PSMB7	5182	0.077	0.3	YES
65	PSMB8	PSMB8	PSMB8	5314	0.074	0.3	YES
66	NUP205	NUP205	NUP205	5415	0.072	0.3	YES
67	AP1M1	AP1M1	AP1M1	5421	0.072	0.3	YES
68	TCEB2	TCEB2	TCEB2	5429	0.072	0.31	YES
69	PSMB5	PSMB5	PSMB5	5436	0.072	0.32	YES
70	RAE1	RAE1	RAE1	5453	0.071	0.32	YES
71	PSMB6	PSMB6	PSMB6	5523	0.069	0.32	YES
72	PSMA4	PSMA4	PSMA4	5569	0.068	0.32	YES
73	NMT2	NMT2	NMT2	5616	0.067	0.32	YES
74	POLR2D	POLR2D	POLR2D	5682	0.066	0.33	YES
75	NUP85	NUP85	NUP85	5772	0.064	0.33	YES
76	PSMD12	PSMD12	PSMD12	5813	0.064	0.33	YES
77	XRCC6	XRCC6	XRCC6	5854	0.063	0.33	YES
78	PSMC6	PSMC6	PSMC6	5900	0.062	0.33	YES
79	PSMD8	PSMD8	PSMD8	5933	0.061	0.34	YES
80	SLC25A6	SLC25A6	SLC25A6	6001	0.06	0.34	YES
81	SEH1L	SEH1L	SEH1L	6020	0.059	0.34	YES
82	UBA52	UBA52	UBA52	6022	0.059	0.34	YES
83	AP2S1	AP2S1	AP2S1	6035	0.059	0.35	YES
84	NUP37	NUP37	NUP37	6062	0.058	0.35	YES
85	NUP88	NUP88	NUP88	6074	0.058	0.35	YES
86	POLR2F	POLR2F	POLR2F	6075	0.058	0.36	YES
87	POLR2H	POLR2H	POLR2H	6157	0.057	0.36	YES
88	VPS37A	VPS37A	VPS37A	6190	0.056	0.36	YES
89	ELMO1	ELMO1	ELMO1	6303	0.054	0.36	YES
90	TAF1	TAF1	TAF1	6328	0.053	0.36	YES
91	PSMA1	PSMA1	PSMA1	6336	0.053	0.36	YES
92	PSMC4	PSMC4	PSMC4	6403	0.052	0.36	YES
93	NUP214	NUP214	NUP214	6516	0.05	0.36	YES
94	NUP43	NUP43	NUP43	6533	0.05	0.36	YES
95	NUP133	NUP133	NUP133	6566	0.049	0.36	YES
96	PSMD6	PSMD6	PSMD6	6567	0.049	0.37	YES
97	PSMD13	PSMD13	PSMD13	6619	0.048	0.37	YES
98	RAN	RAN	RAN	6673	0.047	0.37	YES
99	TAF11	TAF11	TAF11	6756	0.046	0.37	YES
100	NUP62	NUP62	NUP62	6917	0.043	0.36	YES
101	SUPT16H	SUPT16H	SUPT16H	6944	0.042	0.36	YES
102	XRCC4	XRCC4	XRCC4	6996	0.041	0.36	YES
103	PSME1	PSME1	PSME1	7040	0.041	0.36	YES
104	PSMC3	PSMC3	PSMC3	7059	0.04	0.37	YES
105	ARF1	ARF1	ARF1	7144	0.039	0.36	YES
106	NUP155	NUP155	NUP155	7235	0.038	0.36	YES
107	AP1G1	AP1G1	AP1G1	7255	0.037	0.36	YES
108	XRCC5	XRCC5	XRCC5	7268	0.037	0.36	YES
109	RANGAP1	RANGAP1	RANGAP1	7323	0.036	0.36	YES
110	AP1S1	AP1S1	AP1S1	7354	0.036	0.37	YES
111	PSMF1	PSMF1	PSMF1	7401	0.035	0.37	YES
112	NUP107	NUP107	NUP107	7462	0.034	0.36	YES
113	POLR2C	POLR2C	POLR2C	7484	0.033	0.37	YES
114	AAAS	AAAS	AAAS	7511	0.033	0.37	YES
115	ERCC3	ERCC3	ERCC3	7537	0.032	0.37	YES
116	GTF2B	GTF2B	GTF2B	7550	0.032	0.37	YES
117	CTDP1	CTDP1	CTDP1	7556	0.032	0.37	YES
118	PSMD2	PSMD2	PSMD2	7557	0.032	0.37	YES
119	TH1L	TH1L	TH1L	7582	0.031	0.38	YES
120	RNGTT	RNGTT	RNGTT	7600	0.031	0.38	YES
121	COBRA1	COBRA1	COBRA1	7639	0.03	0.38	YES
122	PAK2	PAK2	PAK2	7671	0.03	0.38	YES
123	NPM1	NPM1	NPM1	7676	0.03	0.38	YES
124	POLR2K	POLR2K	POLR2K	7714	0.029	0.38	YES
125	PSMD1	PSMD1	PSMD1	7734	0.029	0.38	YES
126	NUPL1	NUPL1	NUPL1	7763	0.028	0.38	YES
127	NUP188	NUP188	NUP188	7966	0.025	0.37	NO
128	POM121	POM121	POM121	7967	0.025	0.37	NO
129	TPR	TPR	TPR	8069	0.023	0.37	NO
130	KPNB1	KPNB1	KPNB1	8245	0.021	0.36	NO
131	GTF2F2	GTF2F2	GTF2F2	8297	0.02	0.36	NO
132	GTF2E1	GTF2E1	GTF2E1	8351	0.019	0.36	NO
133	KPNA1	KPNA1	KPNA1	8371	0.019	0.36	NO
134	B2M	B2M	B2M	8409	0.018	0.36	NO
135	RPS27A	RPS27A	RPS27A	8478	0.017	0.35	NO
136	GTF2H4	GTF2H4	GTF2H4	8525	0.016	0.35	NO
137	PSMB1	PSMB1	PSMB1	8530	0.016	0.35	NO
138	AP2B1	AP2B1	AP2B1	8538	0.016	0.35	NO
139	XPO1	XPO1	XPO1	8630	0.014	0.35	NO
140	PSMD3	PSMD3	PSMD3	8663	0.014	0.35	NO
141	TCEA1	TCEA1	TCEA1	8678	0.014	0.35	NO
142	SUPT5H	SUPT5H	SUPT5H	8801	0.011	0.34	NO
143	NUP54	NUP54	NUP54	8921	0.0096	0.34	NO
144	PSMC5	PSMC5	PSMC5	8944	0.0092	0.34	NO
145	VPS28	VPS28	VPS28	8951	0.009	0.34	NO
146	POLR2B	POLR2B	POLR2B	9014	0.0081	0.34	NO
147	TCEB3	TCEB3	TCEB3	9083	0.0069	0.33	NO
148	RDBP	RDBP	RDBP	9130	0.0061	0.33	NO
149	TBP	TBP	TBP	9257	0.0038	0.32	NO
150	AP1B1	AP1B1	AP1B1	9260	0.0038	0.32	NO
151	BTRC	BTRC	BTRC	9279	0.0035	0.32	NO
152	PSMD5	PSMD5	PSMD5	9512	-0.00053	0.31	NO
153	HMGA1	HMGA1	HMGA1	9518	-0.00072	0.31	NO
154	SUPT4H1	SUPT4H1	SUPT4H1	9675	-0.004	0.3	NO
155	PSMD9	PSMD9	PSMD9	9682	-0.0042	0.3	NO
156	PSME4	PSME4	PSME4	9768	-0.0058	0.3	NO
157	POLR2E	POLR2E	POLR2E	9795	-0.0061	0.3	NO
158	GTF2F1	GTF2F1	GTF2F1	10013	-0.01	0.28	NO
159	ERCC2	ERCC2	ERCC2	10091	-0.012	0.28	NO
160	VPS37B	VPS37B	VPS37B	10164	-0.013	0.28	NO
161	NUP35	NUP35	NUP35	10191	-0.014	0.28	NO
162	WHSC2	WHSC2	WHSC2	10298	-0.015	0.27	NO
163	SSRP1	SSRP1	SSRP1	10604	-0.021	0.26	NO
164	AP2M1	AP2M1	AP2M1	10741	-0.024	0.25	NO
165	CCNT2	CCNT2	CCNT2	10796	-0.026	0.25	NO
166	TSG101	TSG101	TSG101	10849	-0.027	0.25	NO
167	HLA-A	HLA-A	HLA-A	10862	-0.027	0.25	NO
168	RANBP2	RANBP2	RANBP2	11005	-0.03	0.24	NO
169	CUL5	CUL5	CUL5	11076	-0.032	0.24	NO
170	AP2A2	AP2A2	AP2A2	11101	-0.032	0.24	NO
171	TAF13	TAF13	TAF13	11170	-0.034	0.24	NO
172	SKP1	SKP1	SKP1	11205	-0.034	0.24	NO
173	NUP153	NUP153	NUP153	11352	-0.038	0.24	NO
174	NMT1	NMT1	NMT1	11367	-0.039	0.24	NO
175	VPS37D	VPS37D	VPS37D	11472	-0.042	0.24	NO
176	AP2A1	AP2A1	AP2A1	11579	-0.044	0.24	NO
177	POLR2L	POLR2L	POLR2L	11675	-0.046	0.23	NO
178	ELL	ELL	ELL	11948	-0.054	0.22	NO
179	POLR2A	POLR2A	POLR2A	12028	-0.057	0.22	NO
180	RAC1	RAC1	RAC1	12183	-0.062	0.22	NO
181	NCBP2	NCBP2	NCBP2	12184	-0.062	0.22	NO
182	PACS1	PACS1	PACS1	12258	-0.064	0.22	NO
183	PSMA8	PSMA8	PSMA8	12304	-0.065	0.22	NO
184	APOBEC3G	APOBEC3G	APOBEC3G	12314	-0.065	0.23	NO
185	RNMT	RNMT	RNMT	12498	-0.071	0.22	NO
186	GTF2A1	GTF2A1	GTF2A1	12560	-0.073	0.22	NO
187	GTF2H1	GTF2H1	GTF2H1	12622	-0.075	0.23	NO
188	HCK	HCK	HCK	14150	-0.14	0.15	NO
189	GTF2H3	GTF2H3	GTF2H3	14289	-0.15	0.16	NO
190	TAF4B	TAF4B	TAF4B	14575	-0.17	0.15	NO
191	VPS37C	VPS37C	VPS37C	14858	-0.19	0.15	NO
192	CCNT1	CCNT1	CCNT1	15211	-0.22	0.15	NO
193	CCR5	CCR5	CCR5	16110	-0.32	0.12	NO

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

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

genes ES table in pathway: REACTOME MEIOSIS

Table 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	CD28	CD28	CD28	539	0.43	0.018	YES
2	CD247	CD247	CD247	1093	0.32	0.023	YES
3	CD8B	CD8B	CD8B	1435	0.27	0.035	YES
4	LCK	LCK	LCK	1468	0.27	0.063	YES
5	AP1M2	AP1M2	AP1M2	2131	0.21	0.05	YES
6	NUPL2	NUPL2	NUPL2	2305	0.2	0.062	YES
7	SLC25A5	SLC25A5	SLC25A5	2505	0.18	0.071	YES
8	CD4	CD4	CD4	2573	0.18	0.087	YES
9	DOCK2	DOCK2	DOCK2	2712	0.17	0.098	YES
10	AP1S2	AP1S2	AP1S2	2937	0.16	0.1	YES
11	FYN	FYN	FYN	3080	0.15	0.11	YES
12	RCC1	RCC1	RCC1	3278	0.14	0.12	YES
13	PSMC2	PSMC2	PSMC2	3324	0.14	0.13	YES
14	PSMA6	PSMA6	PSMA6	3427	0.13	0.14	YES
15	PSMA3	PSMA3	PSMA3	3702	0.12	0.14	YES
16	PSMB10	PSMB10	PSMB10	3765	0.12	0.14	YES
17	PSMD10	PSMD10	PSMD10	3813	0.12	0.16	YES
18	NUP210	NUP210	NUP210	3815	0.11	0.17	YES
19	PSMB4	PSMB4	PSMB4	3861	0.11	0.18	YES
20	PSMA2	PSMA2	PSMA2	3875	0.11	0.19	YES
21	PSMC1	PSMC1	PSMC1	3999	0.11	0.2	YES
22	NUP93	NUP93	NUP93	4020	0.11	0.2	YES
23	PSMA7	PSMA7	PSMA7	4156	0.1	0.21	YES
24	NUP50	NUP50	NUP50	4172	0.1	0.22	YES
25	PSMD7	PSMD7	PSMD7	4272	0.1	0.23	YES
26	RBX1	RBX1	RBX1	4310	0.098	0.24	YES
27	RANBP1	RANBP1	RANBP1	4379	0.097	0.24	YES
28	PSMD4	PSMD4	PSMD4	4533	0.093	0.24	YES
29	SLC25A4	SLC25A4	SLC25A4	4535	0.093	0.25	YES
30	PSMB9	PSMB9	PSMB9	4577	0.092	0.26	YES
31	PSMD14	PSMD14	PSMD14	4696	0.088	0.26	YES
32	PSMB2	PSMB2	PSMB2	4745	0.087	0.27	YES
33	PPIA	PPIA	PPIA	4795	0.086	0.28	YES
34	PSME2	PSME2	PSME2	4829	0.085	0.29	YES
35	CDK9	CDK9	CDK9	4857	0.084	0.29	YES
36	TCEB1	TCEB1	TCEB1	4892	0.083	0.3	YES
37	ATP6V1H	ATP6V1H	ATP6V1H	4912	0.082	0.31	YES
38	BANF1	BANF1	BANF1	4938	0.082	0.32	YES
39	PSIP1	PSIP1	PSIP1	4977	0.081	0.32	YES
40	PSMD11	PSMD11	PSMD11	5026	0.08	0.33	YES
41	PSMA5	PSMA5	PSMA5	5138	0.078	0.33	YES
42	PSMB3	PSMB3	PSMB3	5170	0.077	0.34	YES
43	PSMB7	PSMB7	PSMB7	5182	0.077	0.35	YES
44	PSMB8	PSMB8	PSMB8	5314	0.074	0.35	YES
45	NUP205	NUP205	NUP205	5415	0.072	0.35	YES
46	AP1M1	AP1M1	AP1M1	5421	0.072	0.36	YES
47	TCEB2	TCEB2	TCEB2	5429	0.072	0.37	YES
48	PSMB5	PSMB5	PSMB5	5436	0.072	0.37	YES
49	RAE1	RAE1	RAE1	5453	0.071	0.38	YES
50	PSMB6	PSMB6	PSMB6	5523	0.069	0.38	YES
51	PSMA4	PSMA4	PSMA4	5569	0.068	0.39	YES
52	NUP85	NUP85	NUP85	5772	0.064	0.39	YES
53	PSMD12	PSMD12	PSMD12	5813	0.064	0.39	YES
54	PSMC6	PSMC6	PSMC6	5900	0.062	0.39	YES
55	PSMD8	PSMD8	PSMD8	5933	0.061	0.4	YES
56	SLC25A6	SLC25A6	SLC25A6	6001	0.06	0.4	YES
57	SEH1L	SEH1L	SEH1L	6020	0.059	0.41	YES
58	UBA52	UBA52	UBA52	6022	0.059	0.41	YES
59	AP2S1	AP2S1	AP2S1	6035	0.059	0.42	YES
60	NUP37	NUP37	NUP37	6062	0.058	0.42	YES
61	NUP88	NUP88	NUP88	6074	0.058	0.43	YES
62	ELMO1	ELMO1	ELMO1	6303	0.054	0.42	YES
63	PSMA1	PSMA1	PSMA1	6336	0.053	0.43	YES
64	PSMC4	PSMC4	PSMC4	6403	0.052	0.43	YES
65	NUP214	NUP214	NUP214	6516	0.05	0.43	YES
66	NUP43	NUP43	NUP43	6533	0.05	0.43	YES
67	NUP133	NUP133	NUP133	6566	0.049	0.44	YES
68	PSMD6	PSMD6	PSMD6	6567	0.049	0.44	YES
69	PSMD13	PSMD13	PSMD13	6619	0.048	0.45	YES
70	RAN	RAN	RAN	6673	0.047	0.45	YES
71	NUP62	NUP62	NUP62	6917	0.043	0.44	YES
72	PSME1	PSME1	PSME1	7040	0.041	0.44	YES
73	PSMC3	PSMC3	PSMC3	7059	0.04	0.44	YES
74	ARF1	ARF1	ARF1	7144	0.039	0.44	YES
75	NUP155	NUP155	NUP155	7235	0.038	0.44	YES
76	AP1G1	AP1G1	AP1G1	7255	0.037	0.44	YES
77	RANGAP1	RANGAP1	RANGAP1	7323	0.036	0.44	YES
78	AP1S1	AP1S1	AP1S1	7354	0.036	0.45	YES
79	PSMF1	PSMF1	PSMF1	7401	0.035	0.45	YES
80	NUP107	NUP107	NUP107	7462	0.034	0.45	YES
81	AAAS	AAAS	AAAS	7511	0.033	0.45	YES
82	PSMD2	PSMD2	PSMD2	7557	0.032	0.45	YES
83	PAK2	PAK2	PAK2	7671	0.03	0.45	YES
84	NPM1	NPM1	NPM1	7676	0.03	0.45	YES
85	PSMD1	PSMD1	PSMD1	7734	0.029	0.45	YES
86	NUPL1	NUPL1	NUPL1	7763	0.028	0.45	YES
87	NUP188	NUP188	NUP188	7966	0.025	0.44	NO
88	POM121	POM121	POM121	7967	0.025	0.45	NO
89	TPR	TPR	TPR	8069	0.023	0.44	NO
90	KPNB1	KPNB1	KPNB1	8245	0.021	0.44	NO
91	KPNA1	KPNA1	KPNA1	8371	0.019	0.43	NO
92	B2M	B2M	B2M	8409	0.018	0.43	NO
93	RPS27A	RPS27A	RPS27A	8478	0.017	0.43	NO
94	PSMB1	PSMB1	PSMB1	8530	0.016	0.43	NO
95	AP2B1	AP2B1	AP2B1	8538	0.016	0.43	NO
96	XPO1	XPO1	XPO1	8630	0.014	0.43	NO
97	PSMD3	PSMD3	PSMD3	8663	0.014	0.42	NO
98	NUP54	NUP54	NUP54	8921	0.0096	0.41	NO
99	PSMC5	PSMC5	PSMC5	8944	0.0092	0.41	NO
100	AP1B1	AP1B1	AP1B1	9260	0.0038	0.4	NO
101	BTRC	BTRC	BTRC	9279	0.0035	0.4	NO
102	PSMD5	PSMD5	PSMD5	9512	-0.00053	0.38	NO
103	HMGA1	HMGA1	HMGA1	9518	-0.00072	0.38	NO
104	PSMD9	PSMD9	PSMD9	9682	-0.0042	0.37	NO
105	PSME4	PSME4	PSME4	9768	-0.0058	0.37	NO
106	NUP35	NUP35	NUP35	10191	-0.014	0.35	NO
107	AP2M1	AP2M1	AP2M1	10741	-0.024	0.32	NO
108	HLA-A	HLA-A	HLA-A	10862	-0.027	0.32	NO
109	RANBP2	RANBP2	RANBP2	11005	-0.03	0.31	NO
110	CUL5	CUL5	CUL5	11076	-0.032	0.31	NO
111	AP2A2	AP2A2	AP2A2	11101	-0.032	0.31	NO
112	SKP1	SKP1	SKP1	11205	-0.034	0.31	NO
113	NUP153	NUP153	NUP153	11352	-0.038	0.31	NO
114	AP2A1	AP2A1	AP2A1	11579	-0.044	0.3	NO
115	RAC1	RAC1	RAC1	12183	-0.062	0.27	NO
116	PACS1	PACS1	PACS1	12258	-0.064	0.28	NO
117	PSMA8	PSMA8	PSMA8	12304	-0.065	0.28	NO
118	APOBEC3G	APOBEC3G	APOBEC3G	12314	-0.065	0.29	NO
119	HCK	HCK	HCK	14150	-0.14	0.2	NO
120	CCNT1	CCNT1	CCNT1	15211	-0.22	0.17	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 MEIOSIS.

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

genes ES table in pathway: REACTOME TCR SIGNALING

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	AKR1B10	AKR1B10	AKR1B10	5	1.5	0.23	YES
2	HMGCS2	HMGCS2	HMGCS2	41	1	0.38	YES
3	ACSM1	ACSM1	ACSM1	447	0.46	0.43	YES
4	ACSM3	ACSM3	ACSM3	1255	0.3	0.43	YES
5	BDH1	BDH1	BDH1	1668	0.25	0.45	YES
6	ALDH5A1	ALDH5A1	ALDH5A1	1844	0.24	0.47	YES
7	OXCT1	OXCT1	OXCT1	1984	0.22	0.5	YES
8	ALDH9A1	ALDH9A1	ALDH9A1	2147	0.21	0.52	YES
9	L2HGDH	L2HGDH	L2HGDH	2916	0.16	0.5	YES
10	HADH	HADH	HADH	3284	0.14	0.5	YES
11	OXCT2	OXCT2	OXCT2	3616	0.12	0.5	YES
12	ACAT2	ACAT2	ACAT2	3767	0.12	0.51	YES
13	PDHA1	PDHA1	PDHA1	3834	0.11	0.53	YES
14	ACAT1	ACAT1	ACAT1	4304	0.099	0.52	NO
15	ACADS	ACADS	ACADS	4909	0.082	0.5	NO
16	HMGCL	HMGCL	HMGCL	6258	0.055	0.43	NO
17	ALDH1B1	ALDH1B1	ALDH1B1	6656	0.047	0.41	NO
18	PDHB	PDHB	PDHB	6781	0.045	0.42	NO
19	ECHS1	ECHS1	ECHS1	7364	0.036	0.39	NO
20	HADHA	HADHA	HADHA	7702	0.029	0.37	NO
21	BDH2	BDH2	BDH2	8872	0.01	0.31	NO
22	AACS	AACS	AACS	10511	-0.02	0.22	NO
23	ABAT	ABAT	ABAT	10699	-0.023	0.22	NO
24	HMGCS1	HMGCS1	HMGCS1	11374	-0.039	0.19	NO
25	GAD1	GAD1	GAD1	12393	-0.068	0.14	NO
26	ALDH7A1	ALDH7A1	ALDH7A1	12874	-0.085	0.13	NO
27	ALDH2	ALDH2	ALDH2	14256	-0.15	0.075	NO
28	ACSM5	ACSM5	ACSM5	14867	-0.19	0.071	NO
29	GAD2	GAD2	GAD2	15302	-0.22	0.081	NO
30	ALDH3A2	ALDH3A2	ALDH3A2	15567	-0.25	0.1	NO
31	EHHADH	EHHADH	EHHADH	15905	-0.29	0.13	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 TCR SIGNALING.

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

genes ES table in pathway: REACTOME RNA POL I TRANSCRIPTION

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	RPA4	RPA4	RPA4	264	0.58	0.14	YES
2	POLE2	POLE2	POLE2	1474	0.27	0.14	YES
3	GTF2H2	GTF2H2	GTF2H2	1639	0.25	0.2	YES
4	CDK7	CDK7	CDK7	2754	0.16	0.18	YES
5	RPA3	RPA3	RPA3	2996	0.15	0.21	YES
6	RFC4	RFC4	RFC4	3076	0.15	0.24	YES
7	PCNA	PCNA	PCNA	3347	0.13	0.26	YES
8	POLE4	POLE4	POLE4	3505	0.13	0.29	YES
9	GTF2H5	GTF2H5	GTF2H5	3645	0.12	0.31	YES
10	RFC5	RFC5	RFC5	4256	0.1	0.3	YES
11	RBX1	RBX1	RBX1	4310	0.098	0.33	YES
12	MNAT1	MNAT1	MNAT1	4418	0.096	0.35	YES
13	POLE3	POLE3	POLE3	4546	0.092	0.36	YES
14	POLE	POLE	POLE	4588	0.091	0.39	YES
15	POLD1	POLD1	POLD1	4774	0.086	0.4	YES
16	RFC3	RFC3	RFC3	4825	0.085	0.42	YES
17	CCNH	CCNH	CCNH	4988	0.081	0.43	YES
18	LIG1	LIG1	LIG1	5010	0.08	0.45	YES
19	ERCC4	ERCC4	ERCC4	5285	0.075	0.46	YES
20	XPA	XPA	XPA	5621	0.067	0.45	YES
21	RFC2	RFC2	RFC2	5757	0.065	0.46	YES
22	POLD4	POLD4	POLD4	6398	0.052	0.44	NO
23	POLD2	POLD2	POLD2	6625	0.048	0.44	NO
24	RAD23B	RAD23B	RAD23B	6732	0.046	0.45	NO
25	CUL4B	CUL4B	CUL4B	6971	0.042	0.45	NO
26	DDB2	DDB2	DDB2	7193	0.038	0.44	NO
27	ERCC3	ERCC3	ERCC3	7537	0.032	0.44	NO
28	ERCC5	ERCC5	ERCC5	7622	0.031	0.44	NO
29	POLD3	POLD3	POLD3	7667	0.03	0.44	NO
30	ERCC1	ERCC1	ERCC1	8026	0.024	0.43	NO
31	RPA2	RPA2	RPA2	8068	0.023	0.43	NO
32	GTF2H4	GTF2H4	GTF2H4	8525	0.016	0.41	NO
33	ERCC6	ERCC6	ERCC6	9314	0.0029	0.37	NO
34	RFC1	RFC1	RFC1	9463	0.00036	0.36	NO
35	RAD23A	RAD23A	RAD23A	9622	-0.0028	0.36	NO
36	RPA1	RPA1	RPA1	9892	-0.0079	0.34	NO
37	ERCC2	ERCC2	ERCC2	10091	-0.012	0.33	NO
38	ERCC8	ERCC8	ERCC8	10235	-0.014	0.33	NO
39	CUL4A	CUL4A	CUL4A	10430	-0.018	0.32	NO
40	CETN2	CETN2	CETN2	11359	-0.038	0.28	NO
41	XPC	XPC	XPC	12146	-0.061	0.26	NO
42	GTF2H1	GTF2H1	GTF2H1	12622	-0.075	0.25	NO
43	DDB1	DDB1	DDB1	12666	-0.077	0.27	NO
44	GTF2H3	GTF2H3	GTF2H3	14289	-0.15	0.22	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 RNA POL I TRANSCRIPTION.

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

genes ES table in pathway: REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE

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	HSPA2	HSPA2	HSPA2	87	0.83	0.031	YES
2	FKBP6	FKBP6	FKBP6	148	0.73	0.059	YES
3	HIST1H2AE	HIST1H2AE	HIST1H2AE	293	0.56	0.074	YES
4	HIST1H2BN	HIST1H2BN	HIST1H2BN	333	0.53	0.095	YES
5	HIST1H3H	HIST1H3H	HIST1H3H	344	0.52	0.12	YES
6	HIST1H3J	HIST1H3J	HIST1H3J	372	0.5	0.14	YES
7	HIST1H2BG	HIST1H2BG	HIST1H2BG	381	0.5	0.16	YES
8	HIST1H3G	HIST1H3G	HIST1H3G	382	0.5	0.18	YES
9	HIST1H4E	HIST1H4E	HIST1H4E	391	0.5	0.2	YES
10	HIST1H2BO	HIST1H2BO	HIST1H2BO	395	0.49	0.22	YES
11	HIST1H2AB	HIST1H2AB	HIST1H2AB	455	0.46	0.24	YES
12	HIST1H4C	HIST1H4C	HIST1H4C	477	0.45	0.26	YES
13	HIST1H2BI	HIST1H2BI	HIST1H2BI	480	0.45	0.28	YES
14	HIST1H4H	HIST1H4H	HIST1H4H	492	0.45	0.29	YES
15	HIST1H4L	HIST1H4L	HIST1H4L	515	0.44	0.31	YES
16	HIST1H2BB	HIST1H2BB	HIST1H2BB	519	0.44	0.33	YES
17	HIST1H2BC	HIST1H2BC	HIST1H2BC	522	0.44	0.35	YES
18	HIST1H4B	HIST1H4B	HIST1H4B	552	0.43	0.36	YES
19	HIST2H2AC	HIST2H2AC	HIST2H2AC	596	0.41	0.38	YES
20	HIST2H3D	HIST2H3D	HIST2H3D	643	0.4	0.39	YES
21	HIST1H3I	HIST1H3I	HIST1H3I	651	0.4	0.41	YES
22	HIST1H3C	HIST1H3C	HIST1H3C	663	0.4	0.43	YES
23	HIST1H3A	HIST1H3A	HIST1H3A	673	0.39	0.44	YES
24	HIST1H4J	HIST1H4J	HIST1H4J	689	0.39	0.46	YES
25	HIST1H3E	HIST1H3E	HIST1H3E	751	0.38	0.47	YES
26	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	762	0.37	0.49	YES
27	HIST1H2BL	HIST1H2BL	HIST1H2BL	773	0.37	0.5	YES
28	HIST1H2BH	HIST1H2BH	HIST1H2BH	836	0.36	0.52	YES
29	HIST1H4I	HIST1H4I	HIST1H4I	867	0.36	0.53	YES
30	MND1	MND1	MND1	875	0.35	0.54	YES
31	HIST1H3D	HIST1H3D	HIST1H3D	893	0.35	0.56	YES
32	HIST1H3F	HIST1H3F	HIST1H3F	915	0.35	0.57	YES
33	HIST1H2BM	HIST1H2BM	HIST1H2BM	957	0.34	0.58	YES
34	HIST1H2BF	HIST1H2BF	HIST1H2BF	1144	0.31	0.59	YES
35	HIST1H2AD	HIST1H2AD	HIST1H2AD	1147	0.31	0.6	YES
36	DMC1	DMC1	DMC1	1175	0.31	0.61	YES
37	HIST1H3B	HIST1H3B	HIST1H3B	1294	0.29	0.62	YES
38	HIST1H4A	HIST1H4A	HIST1H4A	1322	0.29	0.63	YES
39	HIST2H3C	HIST2H3C	HIST2H3C	1418	0.28	0.64	YES
40	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1485	0.27	0.64	YES
41	SYNE1	SYNE1	SYNE1	1509	0.27	0.65	YES
42	HIST1H4D	HIST1H4D	HIST1H4D	1707	0.25	0.65	YES
43	RAD51	RAD51	RAD51	1717	0.25	0.66	YES
44	BLM	BLM	BLM	1807	0.24	0.67	YES
45	HIST1H2BE	HIST1H2BE	HIST1H2BE	1941	0.22	0.67	YES
46	HIST1H2BD	HIST1H2BD	HIST1H2BD	1961	0.22	0.68	YES
47	REC8	REC8	REC8	2025	0.22	0.68	YES
48	SYCP3	SYCP3	SYCP3	2032	0.22	0.69	YES
49	HIST1H4F	HIST1H4F	HIST1H4F	2245	0.2	0.69	YES
50	HIST2H2BE	HIST2H2BE	HIST2H2BE	2332	0.19	0.69	YES
51	LMNB1	LMNB1	LMNB1	2727	0.17	0.68	YES
52	H2AFX	H2AFX	H2AFX	2759	0.16	0.68	YES
53	RAD51C	RAD51C	RAD51C	2794	0.16	0.69	YES
54	H2AFZ	H2AFZ	H2AFZ	2821	0.16	0.7	YES
55	RBBP8	RBBP8	RBBP8	2946	0.15	0.7	YES
56	STAG3	STAG3	STAG3	2961	0.15	0.7	YES
57	RPA3	RPA3	RPA3	2996	0.15	0.71	YES
58	HIST1H4K	HIST1H4K	HIST1H4K	3200	0.14	0.7	NO
59	BRCA1	BRCA1	BRCA1	3430	0.13	0.69	NO
60	H3F3A	H3F3A	H3F3A	3674	0.12	0.68	NO
61	BRCA2	BRCA2	BRCA2	3998	0.11	0.67	NO
62	TERF2IP	TERF2IP	TERF2IP	4287	0.099	0.66	NO
63	TINF2	TINF2	TINF2	4342	0.098	0.66	NO
64	CDK2	CDK2	CDK2	4362	0.097	0.66	NO
65	SUN2	SUN2	SUN2	4550	0.092	0.66	NO
66	MSH5	MSH5	MSH5	4604	0.09	0.66	NO
67	HIST4H4	HIST4H4	HIST4H4	4707	0.088	0.66	NO
68	TEX12	TEX12	TEX12	4775	0.086	0.66	NO
69	HIST2H4A	HIST2H4A	HIST2H4A	4923	0.082	0.65	NO
70	MLH1	MLH1	MLH1	5213	0.076	0.64	NO
71	MSH4	MSH4	MSH4	5447	0.071	0.63	NO
72	HIST1H2AC	HIST1H2AC	HIST1H2AC	5549	0.069	0.63	NO
73	ACD	ACD	ACD	5729	0.065	0.62	NO
74	TEX15	TEX15	TEX15	5922	0.061	0.61	NO
75	TOP3A	TOP3A	TOP3A	6040	0.059	0.61	NO
76	SMC1B	SMC1B	SMC1B	6080	0.058	0.61	NO
77	POT1	POT1	POT1	6195	0.056	0.61	NO
78	HIST1H2BK	HIST1H2BK	HIST1H2BK	6304	0.054	0.6	NO
79	STAG2	STAG2	STAG2	6586	0.049	0.59	NO
80	SYNE2	SYNE2	SYNE2	7027	0.041	0.57	NO
81	TERF2	TERF2	TERF2	7067	0.04	0.57	NO
82	SMC3	SMC3	SMC3	7103	0.04	0.57	NO
83	ATM	ATM	ATM	7176	0.039	0.56	NO
84	ATR	ATR	ATR	7569	0.032	0.54	NO
85	SMC1A	SMC1A	SMC1A	7586	0.031	0.54	NO
86	RPA2	RPA2	RPA2	8068	0.023	0.52	NO
87	CDK4	CDK4	CDK4	8442	0.017	0.5	NO
88	UBE2I	UBE2I	UBE2I	8809	0.011	0.48	NO
89	RAD21	RAD21	RAD21	8991	0.0084	0.47	NO
90	MLH3	MLH3	MLH3	9238	0.0041	0.46	NO
91	RAD50	RAD50	RAD50	9473	0.00026	0.44	NO
92	MRE11A	MRE11A	MRE11A	9552	-0.0016	0.44	NO
93	HIST3H2BB	HIST3H2BB	HIST3H2BB	9695	-0.0044	0.43	NO
94	RPA1	RPA1	RPA1	9892	-0.0079	0.42	NO
95	DIDO1	DIDO1	DIDO1	10306	-0.016	0.4	NO
96	NBN	NBN	NBN	10307	-0.016	0.4	NO
97	LMNA	LMNA	LMNA	11193	-0.034	0.35	NO
98	H3F3B	H3F3B	H3F3B	12173	-0.062	0.3	NO
99	STAG1	STAG1	STAG1	12461	-0.07	0.29	NO
100	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	12923	-0.086	0.27	NO
101	PRDM9	PRDM9	PRDM9	13258	-0.1	0.25	NO
102	TERF1	TERF1	TERF1	14105	-0.14	0.21	NO
103	SYCP2	SYCP2	SYCP2	16771	-0.42	0.083	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 P53 DEPENDENT G1 DNA DAMAGE RESPONSE.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME P53 DEPENDENT G1 DNA DAMAGE RESPONSE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TRANSCRIPTION

Table S10. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	HSPA2	HSPA2	HSPA2	87	0.83	0.047	YES
2	FKBP6	FKBP6	FKBP6	148	0.73	0.089	YES
3	HIST1H2AE	HIST1H2AE	HIST1H2AE	293	0.56	0.12	YES
4	HIST1H2BN	HIST1H2BN	HIST1H2BN	333	0.53	0.15	YES
5	HIST1H2BG	HIST1H2BG	HIST1H2BG	381	0.5	0.18	YES
6	HIST1H4E	HIST1H4E	HIST1H4E	391	0.5	0.21	YES
7	HIST1H2BO	HIST1H2BO	HIST1H2BO	395	0.49	0.24	YES
8	HIST1H2AB	HIST1H2AB	HIST1H2AB	455	0.46	0.26	YES
9	HIST1H4C	HIST1H4C	HIST1H4C	477	0.45	0.29	YES
10	HIST1H2BI	HIST1H2BI	HIST1H2BI	480	0.45	0.32	YES
11	HIST1H4H	HIST1H4H	HIST1H4H	492	0.45	0.34	YES
12	HIST1H4L	HIST1H4L	HIST1H4L	515	0.44	0.37	YES
13	HIST1H2BB	HIST1H2BB	HIST1H2BB	519	0.44	0.4	YES
14	HIST1H2BC	HIST1H2BC	HIST1H2BC	522	0.44	0.42	YES
15	HIST1H4B	HIST1H4B	HIST1H4B	552	0.43	0.45	YES
16	HIST2H2AC	HIST2H2AC	HIST2H2AC	596	0.41	0.47	YES
17	HIST1H4J	HIST1H4J	HIST1H4J	689	0.39	0.49	YES
18	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	762	0.37	0.51	YES
19	HIST1H2BL	HIST1H2BL	HIST1H2BL	773	0.37	0.53	YES
20	HIST1H2BH	HIST1H2BH	HIST1H2BH	836	0.36	0.55	YES
21	HIST1H4I	HIST1H4I	HIST1H4I	867	0.36	0.57	YES
22	HIST1H2BM	HIST1H2BM	HIST1H2BM	957	0.34	0.59	YES
23	HIST1H2BF	HIST1H2BF	HIST1H2BF	1144	0.31	0.6	YES
24	HIST1H2AD	HIST1H2AD	HIST1H2AD	1147	0.31	0.62	YES
25	HIST1H4A	HIST1H4A	HIST1H4A	1322	0.29	0.63	YES
26	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	1485	0.27	0.64	YES
27	SYNE1	SYNE1	SYNE1	1509	0.27	0.65	YES
28	HIST1H4D	HIST1H4D	HIST1H4D	1707	0.25	0.66	YES
29	HIST1H2BE	HIST1H2BE	HIST1H2BE	1941	0.22	0.66	YES
30	HIST1H2BD	HIST1H2BD	HIST1H2BD	1961	0.22	0.67	YES
31	REC8	REC8	REC8	2025	0.22	0.68	YES
32	SYCP3	SYCP3	SYCP3	2032	0.22	0.69	YES
33	HIST1H4F	HIST1H4F	HIST1H4F	2245	0.2	0.69	YES
34	HIST2H2BE	HIST2H2BE	HIST2H2BE	2332	0.19	0.7	YES
35	LMNB1	LMNB1	LMNB1	2727	0.17	0.69	YES
36	H2AFX	H2AFX	H2AFX	2759	0.16	0.7	YES
37	H2AFZ	H2AFZ	H2AFZ	2821	0.16	0.7	YES
38	STAG3	STAG3	STAG3	2961	0.15	0.71	YES
39	HIST1H4K	HIST1H4K	HIST1H4K	3200	0.14	0.7	NO
40	BRCA1	BRCA1	BRCA1	3430	0.13	0.7	NO
41	TERF2IP	TERF2IP	TERF2IP	4287	0.099	0.66	NO
42	TINF2	TINF2	TINF2	4342	0.098	0.66	NO
43	SUN2	SUN2	SUN2	4550	0.092	0.65	NO
44	HIST4H4	HIST4H4	HIST4H4	4707	0.088	0.65	NO
45	TEX12	TEX12	TEX12	4775	0.086	0.65	NO
46	HIST2H4A	HIST2H4A	HIST2H4A	4923	0.082	0.65	NO
47	HIST1H2AC	HIST1H2AC	HIST1H2AC	5549	0.069	0.62	NO
48	ACD	ACD	ACD	5729	0.065	0.61	NO
49	SMC1B	SMC1B	SMC1B	6080	0.058	0.6	NO
50	POT1	POT1	POT1	6195	0.056	0.6	NO
51	HIST1H2BK	HIST1H2BK	HIST1H2BK	6304	0.054	0.59	NO
52	STAG2	STAG2	STAG2	6586	0.049	0.58	NO
53	SYNE2	SYNE2	SYNE2	7027	0.041	0.56	NO
54	TERF2	TERF2	TERF2	7067	0.04	0.56	NO
55	SMC3	SMC3	SMC3	7103	0.04	0.56	NO
56	ATR	ATR	ATR	7569	0.032	0.54	NO
57	SMC1A	SMC1A	SMC1A	7586	0.031	0.54	NO
58	UBE2I	UBE2I	UBE2I	8809	0.011	0.47	NO
59	RAD21	RAD21	RAD21	8991	0.0084	0.46	NO
60	HIST3H2BB	HIST3H2BB	HIST3H2BB	9695	-0.0044	0.42	NO
61	DIDO1	DIDO1	DIDO1	10306	-0.016	0.39	NO
62	LMNA	LMNA	LMNA	11193	-0.034	0.34	NO
63	STAG1	STAG1	STAG1	12461	-0.07	0.28	NO
64	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	12923	-0.086	0.26	NO
65	TERF1	TERF1	TERF1	14105	-0.14	0.2	NO
66	SYCP2	SYCP2	SYCP2	16771	-0.42	0.083	NO

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

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSCRIPTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus2 enriched pathways

Table 4. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus2. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG RIBOSOME	86	genes.ES.table	0.66	1.5	0.062	0.88	0.94	0.95	0.33	0.64	0.54	0.26
KEGG SPLICEOSOME	114	genes.ES.table	0.39	1.4	0.19	1	1	0.59	0.36	0.38	1	0.57
REACTOME TRANSLATION	147	genes.ES.table	0.53	1.6	0.046	1	0.82	0.71	0.33	0.48	1	0.67
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX	49	genes.ES.table	0.59	1.6	0.045	0.96	0.94	0.84	0.33	0.56	0.58	0.28
REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES	47	genes.ES.table	0.46	1.4	0.12	1	0.99	0.66	0.38	0.41	0.9	0.45
REACTOME ORC1 REMOVAL FROM CHROMATIN	59	genes.ES.table	0.49	1.4	0.22	1	1	0.59	0.32	0.41	1	0.6
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE	110	genes.ES.table	0.59	1.6	0.058	0.9	0.91	0.8	0.33	0.54	0.51	0.27
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S	57	genes.ES.table	0.55	1.6	0.049	1	0.88	0.75	0.33	0.51	0.56	0.3
REACTOME PEPTIDE CHAIN ELONGATION	86	genes.ES.table	0.62	1.5	0.095	0.96	0.97	0.92	0.33	0.62	0.64	0.3
REACTOME MRNA SPLICING	97	genes.ES.table	0.5	1.4	0.14	1	0.99	0.67	0.38	0.42	0.87	0.44

genes ES table in pathway: KEGG RIBOSOME

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	RPL21	RPL21	RPL21	510	0.38	0.0058	YES
2	RPL3L	RPL3L	RPL3L	713	0.34	0.025	YES
3	RPS28	RPS28	RPS28	1969	0.19	-0.028	YES
4	RPSAP9	RPSAP9	RPSAP9	2593	0.15	-0.049	YES
5	RPL18A	RPL18A	RPL18A	2740	0.14	-0.045	YES
6	RPSA	RPSA	RPSA	2761	0.14	-0.034	YES
7	RPL39	RPL39	RPL39	3005	0.13	-0.035	YES
8	RPLP2	RPLP2	RPLP2	3057	0.13	-0.027	YES
9	SEC61B	SEC61B	SEC61B	3109	0.13	-0.019	YES
10	RPL14	RPL14	RPL14	3291	0.12	-0.018	YES
11	RPL24	RPL24	RPL24	3293	0.12	-0.0075	YES
12	RPS7	RPS7	RPS7	3362	0.12	-0.00087	YES
13	SEC61G	SEC61G	SEC61G	3386	0.12	0.0081	YES
14	RPL28	RPL28	RPL28	3441	0.12	0.015	YES
15	RPL13	RPL13	RPL13	3474	0.11	0.024	YES
16	RPL29	RPL29	RPL29	3483	0.11	0.033	YES
17	RPS8	RPS8	RPS8	3513	0.11	0.041	YES
18	RPL34	RPL34	RPL34	3516	0.11	0.051	YES
19	RPL32	RPL32	RPL32	3527	0.11	0.06	YES
20	RPS10	RPS10	RPS10	3547	0.11	0.069	YES
21	RPL27A	RPL27A	RPL27A	3560	0.11	0.078	YES
22	RPS9	RPS9	RPS9	3576	0.11	0.087	YES
23	EIF4EBP1	EIF4EBP1	EIF4EBP1	3584	0.11	0.096	YES
24	EIF3F	EIF3F	EIF3F	3587	0.11	0.11	YES
25	RPL18	RPL18	RPL18	3636	0.11	0.11	YES
26	RPS24	RPS24	RPS24	3647	0.11	0.12	YES
27	FAU	FAU	FAU	3658	0.11	0.13	YES
28	RPL23A	RPL23A	RPL23A	3703	0.11	0.14	YES
29	UBA52	UBA52	UBA52	3734	0.1	0.14	YES
30	RPL35A	RPL35A	RPL35A	3789	0.1	0.15	YES
31	RPL35	RPL35	RPL35	3798	0.1	0.16	YES
32	RPS21	RPS21	RPS21	3807	0.1	0.17	YES
33	RPS13	RPS13	RPS13	3815	0.1	0.18	YES
34	RPS16	RPS16	RPS16	3830	0.1	0.18	YES
35	RPS11	RPS11	RPS11	3833	0.1	0.19	YES
36	RPS19	RPS19	RPS19	3834	0.1	0.2	YES
37	RPS23	RPS23	RPS23	3868	0.1	0.21	YES
38	EEF1B2	EEF1B2	EEF1B2	3891	0.1	0.22	YES
39	RPL26	RPL26	RPL26	3981	0.097	0.22	YES
40	RPS29	RPS29	RPS29	3983	0.097	0.23	YES
41	EEF1D	EEF1D	EEF1D	4006	0.096	0.24	YES
42	EIF3K	EIF3K	EIF3K	4018	0.096	0.24	YES
43	RPL22	RPL22	RPL22	4036	0.096	0.25	YES
44	RPS6	RPS6	RPS6	4046	0.095	0.26	YES
45	RPL37A	RPL37A	RPL37A	4072	0.094	0.27	YES
46	RPL37	RPL37	RPL37	4079	0.094	0.28	YES
47	RPL27	RPL27	RPL27	4121	0.093	0.28	YES
48	EIF2B3	EIF2B3	EIF2B3	4122	0.093	0.29	YES
49	RPL31	RPL31	RPL31	4172	0.092	0.3	YES
50	EIF4A1	EIF4A1	EIF4A1	4205	0.091	0.3	YES
51	RPS20	RPS20	RPS20	4207	0.091	0.31	YES
52	RPS12	RPS12	RPS12	4230	0.091	0.32	YES
53	RPS15	RPS15	RPS15	4233	0.091	0.32	YES
54	RPS3A	RPS3A	RPS3A	4238	0.091	0.33	YES
55	RPL11	RPL11	RPL11	4278	0.09	0.34	YES
56	RPS3	RPS3	RPS3	4284	0.089	0.34	YES
57	RPL5	RPL5	RPL5	4307	0.089	0.35	YES
58	RPS17	RPS17	RPS17	4330	0.088	0.36	YES
59	RPLP1	RPLP1	RPLP1	4354	0.088	0.36	YES
60	RPS2	RPS2	RPS2	4372	0.088	0.37	YES
61	RPL26L1	RPL26L1	RPL26L1	4390	0.087	0.38	YES
62	RPL38	RPL38	RPL38	4417	0.086	0.38	YES
63	RPL19	RPL19	RPL19	4454	0.085	0.39	YES
64	RPL36	RPL36	RPL36	4503	0.084	0.39	YES
65	RPL23	RPL23	RPL23	4531	0.083	0.4	YES
66	RPS5	RPS5	RPS5	4599	0.081	0.4	YES
67	RPS14	RPS14	RPS14	4645	0.08	0.41	YES
68	RPL15	RPL15	RPL15	4724	0.078	0.41	YES
69	RPLP0	RPLP0	RPLP0	4740	0.078	0.42	YES
70	RPL36A	RPL36A	RPL36A	4835	0.075	0.42	YES
71	RPL10A	RPL10A	RPL10A	4854	0.075	0.42	YES
72	RPS27A	RPS27A	RPS27A	4877	0.074	0.43	YES
73	EIF3G	EIF3G	EIF3G	4931	0.073	0.43	YES
74	RPL4	RPL4	RPL4	4972	0.072	0.44	YES
75	RPL30	RPL30	RPL30	5001	0.072	0.44	YES
76	SRP14	SRP14	SRP14	5026	0.071	0.45	YES
77	RPL6	RPL6	RPL6	5045	0.071	0.45	YES
78	RPL12	RPL12	RPL12	5075	0.07	0.46	YES
79	RPL13A	RPL13A	RPL13A	5082	0.07	0.46	YES
80	RPS25	RPS25	RPS25	5089	0.07	0.47	YES
81	RPS26	RPS26	RPS26	5153	0.068	0.47	YES
82	EIF2B5	EIF2B5	EIF2B5	5185	0.068	0.47	YES
83	EIF3B	EIF3B	EIF3B	5204	0.067	0.48	YES
84	RPL41	RPL41	RPL41	5234	0.066	0.48	YES
85	EIF3I	EIF3I	EIF3I	5290	0.065	0.49	YES
86	RPL7A	RPL7A	RPL7A	5404	0.062	0.48	YES
87	SPCS2	SPCS2	SPCS2	5412	0.062	0.49	YES
88	EIF3D	EIF3D	EIF3D	5455	0.061	0.49	YES
89	RPS18	RPS18	RPS18	5514	0.059	0.5	YES
90	SSR2	SSR2	SSR2	5547	0.058	0.5	YES
91	RPS15A	RPS15A	RPS15A	5670	0.055	0.5	YES
92	RPL10	RPL10	RPL10	5767	0.053	0.5	YES
93	EIF2S2	EIF2S2	EIF2S2	5780	0.053	0.5	YES
94	EEF1G	EEF1G	EEF1G	5788	0.053	0.5	YES
95	RPS4Y1	RPS4Y1	RPS4Y1	5796	0.053	0.51	YES
96	EIF3H	EIF3H	EIF3H	5845	0.051	0.51	YES
97	SEC61A2	SEC61A2	SEC61A2	5913	0.05	0.51	YES
98	RPL7	RPL7	RPL7	5978	0.048	0.51	YES
99	RPN1	RPN1	RPN1	6009	0.048	0.52	YES
100	RPS4X	RPS4X	RPS4X	6032	0.047	0.52	YES
101	SRP19	SRP19	SRP19	6037	0.047	0.52	YES
102	RPL8	RPL8	RPL8	6043	0.047	0.52	YES
103	SPCS1	SPCS1	SPCS1	6083	0.046	0.53	YES
104	EIF2B4	EIF2B4	EIF2B4	6087	0.046	0.53	YES
105	RPL17	RPL17	RPL17	6360	0.041	0.52	NO
106	EEF1A1	EEF1A1	EEF1A1	6393	0.04	0.52	NO
107	SSR4	SSR4	SSR4	6397	0.04	0.52	NO
108	EIF2B1	EIF2B1	EIF2B1	6457	0.039	0.52	NO
109	SEC11C	SEC11C	SEC11C	6473	0.038	0.53	NO
110	RPL3	RPL3	RPL3	6546	0.037	0.53	NO
111	RPL9	RPL9	RPL9	6567	0.036	0.53	NO
112	DDOST	DDOST	DDOST	6759	0.032	0.52	NO
113	EIF4E	EIF4E	EIF4E	6779	0.032	0.52	NO
114	LOC653566	LOC653566	LOC653566	6882	0.03	0.52	NO
115	TRAM1	TRAM1	TRAM1	7398	0.02	0.49	NO
116	SEC61A1	SEC61A1	SEC61A1	7539	0.016	0.49	NO
117	SRP68	SRP68	SRP68	7791	0.011	0.47	NO
118	EIF3E	EIF3E	EIF3E	7836	0.0098	0.47	NO
119	SRPRB	SRPRB	SRPRB	8105	0.0042	0.46	NO
120	EIF2B2	EIF2B2	EIF2B2	8154	0.0032	0.46	NO
121	SRP9	SRP9	SRP9	8280	0.00065	0.45	NO
122	SRP72	SRP72	SRP72	8405	-0.0022	0.44	NO
123	EIF3J	EIF3J	EIF3J	8521	-0.0045	0.44	NO
124	EIF4B	EIF4B	EIF4B	8559	-0.0052	0.44	NO
125	SPCS3	SPCS3	SPCS3	8613	-0.0067	0.43	NO
126	RPS27	RPS27	RPS27	8639	-0.0073	0.43	NO
127	EIF2S3	EIF2S3	EIF2S3	8808	-0.011	0.42	NO
128	RPN2	RPN2	RPN2	8817	-0.011	0.42	NO
129	EEF2	EEF2	EEF2	8842	-0.012	0.42	NO
130	SSR1	SSR1	SSR1	9091	-0.016	0.41	NO
131	GSPT2	GSPT2	GSPT2	9158	-0.017	0.41	NO
132	PABPC1	PABPC1	PABPC1	9194	-0.018	0.41	NO
133	EIF2S1	EIF2S1	EIF2S1	9321	-0.021	0.4	NO
134	SSR3	SSR3	SSR3	9423	-0.023	0.4	NO
135	EIF4H	EIF4H	EIF4H	9440	-0.024	0.4	NO
136	SEC11A	SEC11A	SEC11A	9489	-0.025	0.4	NO
137	EIF5B	EIF5B	EIF5B	9624	-0.027	0.4	NO
138	EIF1AX	EIF1AX	EIF1AX	10012	-0.035	0.38	NO
139	EIF5	EIF5	EIF5	10059	-0.036	0.38	NO
140	EIF4A2	EIF4A2	EIF4A2	10831	-0.055	0.34	NO
141	SRP54	SRP54	SRP54	11021	-0.059	0.34	NO
142	SRPR	SRPR	SRPR	11057	-0.06	0.34	NO
143	EIF4G1	EIF4G1	EIF4G1	11387	-0.068	0.33	NO
144	EIF3A	EIF3A	EIF3A	11974	-0.084	0.3	NO
145	ETF1	ETF1	ETF1	13160	-0.12	0.25	NO
146	EIF3C	EIF3C	EIF3C	14164	-0.17	0.21	NO
147	FAM153A	FAM153A	FAM153A	15146	-0.23	0.17	NO

Figure S21. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RIBOSOME.

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

genes ES table in pathway: KEGG SPLICEOSOME

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	RPL21	RPL21	RPL21	510	0.38	0.0048	YES
2	RPL3L	RPL3L	RPL3L	713	0.34	0.023	YES
3	RPS28	RPS28	RPS28	1969	0.19	-0.03	YES
4	RPSAP9	RPSAP9	RPSAP9	2593	0.15	-0.052	YES
5	POLR2I	POLR2I	POLR2I	2661	0.14	-0.043	YES
6	RPL18A	RPL18A	RPL18A	2740	0.14	-0.035	YES
7	RPSA	RPSA	RPSA	2761	0.14	-0.025	YES
8	POLR2F	POLR2F	POLR2F	2771	0.14	-0.013	YES
9	RPL39	RPL39	RPL39	3005	0.13	-0.015	YES
10	RPLP2	RPLP2	RPLP2	3057	0.13	-0.0068	YES
11	POLR2L	POLR2L	POLR2L	3062	0.13	0.004	YES
12	RPL14	RPL14	RPL14	3291	0.12	0.0016	YES
13	RPL24	RPL24	RPL24	3293	0.12	0.012	YES
14	RPS7	RPS7	RPS7	3362	0.12	0.018	YES
15	RPL28	RPL28	RPL28	3441	0.12	0.024	YES
16	RPL13	RPL13	RPL13	3474	0.11	0.032	YES
17	RPL29	RPL29	RPL29	3483	0.11	0.041	YES
18	POLR2J	POLR2J	POLR2J	3485	0.11	0.05	YES
19	RPS8	RPS8	RPS8	3513	0.11	0.058	YES
20	RPL34	RPL34	RPL34	3516	0.11	0.068	YES
21	RPL32	RPL32	RPL32	3527	0.11	0.077	YES
22	RPS10	RPS10	RPS10	3547	0.11	0.085	YES
23	RPL27A	RPL27A	RPL27A	3560	0.11	0.094	YES
24	RPS9	RPS9	RPS9	3576	0.11	0.1	YES
25	RPL18	RPL18	RPL18	3636	0.11	0.11	YES
26	RPS24	RPS24	RPS24	3647	0.11	0.12	YES
27	FAU	FAU	FAU	3658	0.11	0.13	YES
28	RPL23A	RPL23A	RPL23A	3703	0.11	0.13	YES
29	POLR2G	POLR2G	POLR2G	3728	0.1	0.14	YES
30	UBA52	UBA52	UBA52	3734	0.1	0.15	YES
31	RPL35A	RPL35A	RPL35A	3789	0.1	0.16	YES
32	RPL35	RPL35	RPL35	3798	0.1	0.16	YES
33	RPS21	RPS21	RPS21	3807	0.1	0.17	YES
34	RPS13	RPS13	RPS13	3815	0.1	0.18	YES
35	RPS16	RPS16	RPS16	3830	0.1	0.19	YES
36	RPS11	RPS11	RPS11	3833	0.1	0.2	YES
37	RPS19	RPS19	RPS19	3834	0.1	0.2	YES
38	POLR2H	POLR2H	POLR2H	3850	0.1	0.21	YES
39	RPS23	RPS23	RPS23	3868	0.1	0.22	YES
40	POLR2D	POLR2D	POLR2D	3934	0.099	0.22	YES
41	RPL26	RPL26	RPL26	3981	0.097	0.23	YES
42	RPS29	RPS29	RPS29	3983	0.097	0.24	YES
43	RPL22	RPL22	RPL22	4036	0.096	0.24	YES
44	RPS6	RPS6	RPS6	4046	0.095	0.25	YES
45	RPL37A	RPL37A	RPL37A	4072	0.094	0.26	YES
46	RPL37	RPL37	RPL37	4079	0.094	0.27	YES
47	RPL27	RPL27	RPL27	4121	0.093	0.27	YES
48	RPL31	RPL31	RPL31	4172	0.092	0.28	YES
49	RPS20	RPS20	RPS20	4207	0.091	0.28	YES
50	RPS12	RPS12	RPS12	4230	0.091	0.29	YES
51	RPS15	RPS15	RPS15	4233	0.091	0.3	YES
52	RPS3A	RPS3A	RPS3A	4238	0.091	0.3	YES
53	RPL11	RPL11	RPL11	4278	0.09	0.31	YES
54	RPS3	RPS3	RPS3	4284	0.089	0.32	YES
55	RPL5	RPL5	RPL5	4307	0.089	0.32	YES
56	GRSF1	GRSF1	GRSF1	4311	0.089	0.33	YES
57	RPS17	RPS17	RPS17	4330	0.088	0.34	YES
58	RPLP1	RPLP1	RPLP1	4354	0.088	0.34	YES
59	RPS2	RPS2	RPS2	4372	0.088	0.35	YES
60	RPL26L1	RPL26L1	RPL26L1	4390	0.087	0.36	YES
61	RPL38	RPL38	RPL38	4417	0.086	0.36	YES
62	RPL19	RPL19	RPL19	4454	0.085	0.37	YES
63	NUP210	NUP210	NUP210	4492	0.084	0.37	YES
64	RPL36	RPL36	RPL36	4503	0.084	0.38	YES
65	RPL23	RPL23	RPL23	4531	0.083	0.39	YES
66	POLR2E	POLR2E	POLR2E	4574	0.082	0.39	YES
67	AAAS	AAAS	AAAS	4588	0.081	0.4	YES
68	RPS5	RPS5	RPS5	4599	0.081	0.4	YES
69	NUP88	NUP88	NUP88	4632	0.08	0.41	YES
70	RPS14	RPS14	RPS14	4645	0.08	0.41	YES
71	RPL15	RPL15	RPL15	4724	0.078	0.42	YES
72	RPLP0	RPLP0	RPLP0	4740	0.078	0.42	YES
73	SEH1L	SEH1L	SEH1L	4829	0.076	0.42	YES
74	RPL36A	RPL36A	RPL36A	4835	0.075	0.43	YES
75	RPL10A	RPL10A	RPL10A	4854	0.075	0.44	YES
76	RPS27A	RPS27A	RPS27A	4877	0.074	0.44	YES
77	RAN	RAN	RAN	4940	0.073	0.44	YES
78	RPL4	RPL4	RPL4	4972	0.072	0.45	YES
79	RPL30	RPL30	RPL30	5001	0.072	0.45	YES
80	RPL6	RPL6	RPL6	5045	0.071	0.46	YES
81	GTF2F2	GTF2F2	GTF2F2	5046	0.071	0.46	YES
82	RPL12	RPL12	RPL12	5075	0.07	0.47	YES
83	RPL13A	RPL13A	RPL13A	5082	0.07	0.47	YES
84	RPS25	RPS25	RPS25	5089	0.07	0.48	YES
85	NUP93	NUP93	NUP93	5109	0.069	0.48	YES
86	NUP85	NUP85	NUP85	5119	0.069	0.49	YES
87	RPS26	RPS26	RPS26	5153	0.068	0.49	YES
88	RPL41	RPL41	RPL41	5234	0.066	0.49	YES
89	NUP214	NUP214	NUP214	5351	0.064	0.49	YES
90	RPL7A	RPL7A	RPL7A	5404	0.062	0.5	YES
91	RPS18	RPS18	RPS18	5514	0.059	0.49	YES
92	RAE1	RAE1	RAE1	5557	0.058	0.5	YES
93	GTF2F1	GTF2F1	GTF2F1	5652	0.056	0.5	YES
94	RPS15A	RPS15A	RPS15A	5670	0.055	0.5	YES
95	CALR	CALR	CALR	5716	0.054	0.5	YES
96	RPL10	RPL10	RPL10	5767	0.053	0.5	YES
97	RPS4Y1	RPS4Y1	RPS4Y1	5796	0.053	0.51	YES
98	NUP37	NUP37	NUP37	5839	0.051	0.51	YES
99	CLTA	CLTA	CLTA	5937	0.049	0.51	YES
100	RPL7	RPL7	RPL7	5978	0.048	0.51	YES
101	RPS4X	RPS4X	RPS4X	6032	0.047	0.51	YES
102	RPL8	RPL8	RPL8	6043	0.047	0.51	YES
103	POLR2K	POLR2K	POLR2K	6315	0.042	0.5	NO
104	NUP43	NUP43	NUP43	6358	0.041	0.5	NO
105	RPL17	RPL17	RPL17	6360	0.041	0.51	NO
106	NUP50	NUP50	NUP50	6398	0.04	0.51	NO
107	POLR2C	POLR2C	POLR2C	6516	0.037	0.5	NO
108	RPL3	RPL3	RPL3	6546	0.037	0.51	NO
109	RPL9	RPL9	RPL9	6567	0.036	0.51	NO
110	IPO5	IPO5	IPO5	7290	0.021	0.47	NO
111	NUP35	NUP35	NUP35	7294	0.021	0.47	NO
112	NUP188	NUP188	NUP188	7525	0.017	0.46	NO
113	NUP62	NUP62	NUP62	7584	0.015	0.46	NO
114	NUP54	NUP54	NUP54	7928	0.0081	0.44	NO
115	RPS27	RPS27	RPS27	8639	-0.0073	0.4	NO
116	POLR2A	POLR2A	POLR2A	8796	-0.011	0.4	NO
117	XPO1	XPO1	XPO1	8838	-0.012	0.39	NO
118	NUP107	NUP107	NUP107	9294	-0.021	0.37	NO
119	HSP90AA1	HSP90AA1	HSP90AA1	9904	-0.033	0.34	NO
120	DNAJC3	DNAJC3	DNAJC3	9998	-0.035	0.34	NO
121	CANX	CANX	CANX	10107	-0.038	0.34	NO
122	KPNA1	KPNA1	KPNA1	10508	-0.047	0.32	NO
123	NUPL1	NUPL1	NUPL1	10593	-0.048	0.32	NO
124	POLR2B	POLR2B	POLR2B	10607	-0.049	0.32	NO
125	KPNB1	KPNB1	KPNB1	10691	-0.051	0.32	NO
126	RANBP2	RANBP2	RANBP2	10924	-0.057	0.31	NO
127	POM121	POM121	POM121	10942	-0.057	0.32	NO
128	NUP133	NUP133	NUP133	11010	-0.059	0.32	NO
129	NUP205	NUP205	NUP205	11340	-0.067	0.3	NO
130	CLTC	CLTC	CLTC	11398	-0.069	0.31	NO
131	NUPL2	NUPL2	NUPL2	11785	-0.079	0.29	NO
132	TPR	TPR	TPR	12615	-0.1	0.26	NO
133	NUP153	NUP153	NUP153	12628	-0.1	0.26	NO
134	NUP155	NUP155	NUP155	13887	-0.15	0.21	NO
135	HSPA1B	HSPA1B	HSPA1B	14224	-0.17	0.2	NO
136	FAM153A	FAM153A	FAM153A	15146	-0.23	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: KEGG SPLICEOSOME.

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

genes ES table in pathway: REACTOME TRANSLATION

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	RPL21	RPL21	RPL21	510	0.38	-0.0052	YES
2	RPL3L	RPL3L	RPL3L	713	0.34	0.0042	YES
3	PSMA8	PSMA8	PSMA8	898	0.31	0.012	YES
4	RPS28	RPS28	RPS28	1969	0.19	-0.036	YES
5	LSM2	LSM2	LSM2	1978	0.19	-0.025	YES
6	EXOSC8	EXOSC8	EXOSC8	2065	0.18	-0.019	YES
7	PSMB10	PSMB10	PSMB10	2433	0.16	-0.03	YES
8	EXOSC5	EXOSC5	EXOSC5	2500	0.15	-0.024	YES
9	LSM4	LSM4	LSM4	2522	0.15	-0.016	YES
10	LSM5	LSM5	LSM5	2533	0.15	-0.0078	YES
11	RPSAP9	RPSAP9	RPSAP9	2593	0.15	-0.0022	YES
12	RPL18A	RPL18A	RPL18A	2740	0.14	-0.0018	YES
13	LSM3	LSM3	LSM3	2747	0.14	0.0062	YES
14	RPSA	RPSA	RPSA	2761	0.14	0.014	YES
15	EXOSC4	EXOSC4	EXOSC4	2762	0.14	0.022	YES
16	EXOSC9	EXOSC9	EXOSC9	2770	0.14	0.03	YES
17	MAGOH	MAGOH	MAGOH	2881	0.14	0.032	YES
18	PSMD9	PSMD9	PSMD9	2920	0.13	0.038	YES
19	PSMD13	PSMD13	PSMD13	2988	0.13	0.042	YES
20	PSMB3	PSMB3	PSMB3	2996	0.13	0.05	YES
21	PSMB6	PSMB6	PSMB6	2997	0.13	0.057	YES
22	RPL39	RPL39	RPL39	3005	0.13	0.065	YES
23	PSMA6	PSMA6	PSMA6	3016	0.13	0.072	YES
24	RPLP2	RPLP2	RPLP2	3057	0.13	0.078	YES
25	PSMC3	PSMC3	PSMC3	3112	0.13	0.082	YES
26	EXOSC7	EXOSC7	EXOSC7	3207	0.12	0.084	YES
27	RPL14	RPL14	RPL14	3291	0.12	0.087	YES
28	RPL24	RPL24	RPL24	3293	0.12	0.094	YES
29	RPS7	RPS7	RPS7	3362	0.12	0.097	YES
30	PSMB7	PSMB7	PSMB7	3440	0.12	0.1	YES
31	RPL28	RPL28	RPL28	3441	0.12	0.11	YES
32	PSMA4	PSMA4	PSMA4	3448	0.12	0.11	YES
33	PSMB1	PSMB1	PSMB1	3463	0.11	0.12	YES
34	RPL13	RPL13	RPL13	3474	0.11	0.13	YES
35	RPL29	RPL29	RPL29	3483	0.11	0.13	YES
36	RPS8	RPS8	RPS8	3513	0.11	0.14	YES
37	RPL34	RPL34	RPL34	3516	0.11	0.14	YES
38	RPL32	RPL32	RPL32	3527	0.11	0.15	YES
39	RPS10	RPS10	RPS10	3547	0.11	0.16	YES
40	RPL27A	RPL27A	RPL27A	3560	0.11	0.16	YES
41	RPS9	RPS9	RPS9	3576	0.11	0.17	YES
42	CNOT10	CNOT10	CNOT10	3622	0.11	0.17	YES
43	RPL18	RPL18	RPL18	3636	0.11	0.18	YES
44	RPS24	RPS24	RPS24	3647	0.11	0.18	YES
45	FAU	FAU	FAU	3658	0.11	0.19	YES
46	EXOSC1	EXOSC1	EXOSC1	3685	0.11	0.19	YES
47	RPL23A	RPL23A	RPL23A	3703	0.11	0.2	YES
48	UBA52	UBA52	UBA52	3734	0.1	0.2	YES
49	PSMC1	PSMC1	PSMC1	3776	0.1	0.21	YES
50	RPL35A	RPL35A	RPL35A	3789	0.1	0.21	YES
51	RPL35	RPL35	RPL35	3798	0.1	0.22	YES
52	RPS21	RPS21	RPS21	3807	0.1	0.22	YES
53	RPS13	RPS13	RPS13	3815	0.1	0.23	YES
54	RPS16	RPS16	RPS16	3830	0.1	0.24	YES
55	RPS11	RPS11	RPS11	3833	0.1	0.24	YES
56	RPS19	RPS19	RPS19	3834	0.1	0.25	YES
57	RPS23	RPS23	RPS23	3868	0.1	0.25	YES
58	PSMA5	PSMA5	PSMA5	3907	0.1	0.26	YES
59	DCP2	DCP2	DCP2	3976	0.098	0.26	YES
60	RPL26	RPL26	RPL26	3981	0.097	0.26	YES
61	RPS29	RPS29	RPS29	3983	0.097	0.27	YES
62	RPL22	RPL22	RPL22	4036	0.096	0.27	YES
63	RPS6	RPS6	RPS6	4046	0.095	0.28	YES
64	RPL37A	RPL37A	RPL37A	4072	0.094	0.28	YES
65	RPL37	RPL37	RPL37	4079	0.094	0.29	YES
66	RPL27	RPL27	RPL27	4121	0.093	0.29	YES
67	HNRNPD	HNRNPD	HNRNPD	4123	0.093	0.3	YES
68	RPL31	RPL31	RPL31	4172	0.092	0.3	YES
69	PSME1	PSME1	PSME1	4185	0.092	0.3	YES
70	EIF4A1	EIF4A1	EIF4A1	4205	0.091	0.31	YES
71	RPS20	RPS20	RPS20	4207	0.091	0.31	YES
72	RPS12	RPS12	RPS12	4230	0.091	0.32	YES
73	RPS15	RPS15	RPS15	4233	0.091	0.32	YES
74	RPS3A	RPS3A	RPS3A	4238	0.091	0.33	YES
75	RPL11	RPL11	RPL11	4278	0.09	0.33	YES
76	RPS3	RPS3	RPS3	4284	0.089	0.34	YES
77	RPL5	RPL5	RPL5	4307	0.089	0.34	YES
78	RPS17	RPS17	RPS17	4330	0.088	0.34	YES
79	RPLP1	RPLP1	RPLP1	4354	0.088	0.35	YES
80	RPS2	RPS2	RPS2	4372	0.088	0.35	YES
81	RPL26L1	RPL26L1	RPL26L1	4390	0.087	0.36	YES
82	RPL38	RPL38	RPL38	4417	0.086	0.36	YES
83	RPL19	RPL19	RPL19	4454	0.085	0.36	YES
84	PSMB8	PSMB8	PSMB8	4488	0.084	0.37	YES
85	RPL36	RPL36	RPL36	4503	0.084	0.37	YES
86	UPF3A	UPF3A	UPF3A	4527	0.083	0.37	YES
87	RPL23	RPL23	RPL23	4531	0.083	0.38	YES
88	DCP1B	DCP1B	DCP1B	4554	0.082	0.38	YES
89	RPS5	RPS5	RPS5	4599	0.081	0.38	YES
90	RPS14	RPS14	RPS14	4645	0.08	0.39	YES
91	RPL15	RPL15	RPL15	4724	0.078	0.39	YES
92	DCPS	DCPS	DCPS	4727	0.078	0.39	YES
93	RPLP0	RPLP0	RPLP0	4740	0.078	0.4	YES
94	ANP32A	ANP32A	ANP32A	4755	0.077	0.4	YES
95	RPL36A	RPL36A	RPL36A	4835	0.075	0.4	YES
96	RPL10A	RPL10A	RPL10A	4854	0.075	0.4	YES
97	RPS27A	RPS27A	RPS27A	4877	0.074	0.41	YES
98	RPL4	RPL4	RPL4	4972	0.072	0.41	YES
99	RPL30	RPL30	RPL30	5001	0.072	0.41	YES
100	RPL6	RPL6	RPL6	5045	0.071	0.41	YES
101	EDC4	EDC4	EDC4	5059	0.07	0.41	YES
102	RPL12	RPL12	RPL12	5075	0.07	0.42	YES
103	RPL13A	RPL13A	RPL13A	5082	0.07	0.42	YES
104	RPS25	RPS25	RPS25	5089	0.07	0.42	YES
105	PSMC5	PSMC5	PSMC5	5135	0.069	0.43	YES
106	PSMD8	PSMD8	PSMD8	5140	0.068	0.43	YES
107	RPS26	RPS26	RPS26	5153	0.068	0.43	YES
108	RPL41	RPL41	RPL41	5234	0.066	0.43	YES
109	PSMB9	PSMB9	PSMB9	5307	0.065	0.43	YES
110	NUP214	NUP214	NUP214	5351	0.064	0.44	YES
111	RPL7A	RPL7A	RPL7A	5404	0.062	0.44	YES
112	PSMD6	PSMD6	PSMD6	5424	0.062	0.44	YES
113	LSM6	LSM6	LSM6	5491	0.06	0.44	YES
114	RPS18	RPS18	RPS18	5514	0.059	0.44	YES
115	PSMD4	PSMD4	PSMD4	5587	0.057	0.44	YES
116	PSME2	PSME2	PSME2	5595	0.057	0.44	YES
117	RNPS1	RNPS1	RNPS1	5631	0.056	0.44	YES
118	RPS15A	RPS15A	RPS15A	5670	0.055	0.45	YES
119	PSMD7	PSMD7	PSMD7	5727	0.054	0.45	YES
120	RPL10	RPL10	RPL10	5767	0.053	0.45	YES
121	PSMB2	PSMB2	PSMB2	5789	0.053	0.45	YES
122	RPS4Y1	RPS4Y1	RPS4Y1	5796	0.053	0.45	YES
123	RPL7	RPL7	RPL7	5978	0.048	0.44	YES
124	RPS4X	RPS4X	RPS4X	6032	0.047	0.44	YES
125	RPL8	RPL8	RPL8	6043	0.047	0.45	YES
126	PPP2CA	PPP2CA	PPP2CA	6064	0.046	0.45	YES
127	PPP2R1A	PPP2R1A	PPP2R1A	6216	0.044	0.44	YES
128	EXOSC2	EXOSC2	EXOSC2	6221	0.043	0.44	YES
129	C2orf29	C2orf29	C2orf29	6244	0.043	0.45	YES
130	PSMC4	PSMC4	PSMC4	6292	0.042	0.45	YES
131	EIF4A3	EIF4A3	EIF4A3	6317	0.042	0.45	YES
132	PSMA7	PSMA7	PSMA7	6333	0.041	0.45	YES
133	RPL17	RPL17	RPL17	6360	0.041	0.45	YES
134	CNOT2	CNOT2	CNOT2	6389	0.04	0.45	YES
135	PSMA1	PSMA1	PSMA1	6436	0.039	0.45	YES
136	PSMA2	PSMA2	PSMA2	6484	0.038	0.45	YES
137	LSM1	LSM1	LSM1	6511	0.038	0.45	YES
138	RPL3	RPL3	RPL3	6546	0.037	0.45	YES
139	EXOSC3	EXOSC3	EXOSC3	6557	0.037	0.45	YES
140	RPL9	RPL9	RPL9	6567	0.036	0.46	YES
141	CNOT3	CNOT3	CNOT3	6758	0.032	0.45	NO
142	PSMB4	PSMB4	PSMB4	6777	0.032	0.45	NO
143	EIF4E	EIF4E	EIF4E	6779	0.032	0.45	NO
144	CNOT8	CNOT8	CNOT8	6781	0.032	0.45	NO
145	PSMD3	PSMD3	PSMD3	6791	0.032	0.45	NO
146	PSMA3	PSMA3	PSMA3	6934	0.029	0.45	NO
147	KHSRP	KHSRP	KHSRP	7126	0.025	0.44	NO
148	ELAVL1	ELAVL1	ELAVL1	7154	0.024	0.44	NO
149	EXOSC6	EXOSC6	EXOSC6	7161	0.024	0.44	NO
150	NCBP2	NCBP2	NCBP2	7213	0.023	0.44	NO
151	PSMF1	PSMF1	PSMF1	7436	0.019	0.43	NO
152	EDC3	EDC3	EDC3	7647	0.014	0.42	NO
153	CNOT6	CNOT6	CNOT6	7729	0.012	0.41	NO
154	PARN	PARN	PARN	8011	0.0062	0.4	NO
155	YWHAB	YWHAB	YWHAB	8036	0.0055	0.4	NO
156	PSMC6	PSMC6	PSMC6	8049	0.0053	0.39	NO
157	SMG6	SMG6	SMG6	8130	0.0036	0.39	NO
158	AKT1	AKT1	AKT1	8206	0.0022	0.39	NO
159	HSPA8	HSPA8	HSPA8	8216	0.002	0.39	NO
160	MAPK14	MAPK14	MAPK14	8309	-3e-05	0.38	NO
161	CASC3	CASC3	CASC3	8353	-0.0011	0.38	NO
162	PSMD14	PSMD14	PSMD14	8360	-0.0013	0.38	NO
163	PSMD2	PSMD2	PSMD2	8389	-0.0018	0.38	NO
164	EIF4B	EIF4B	EIF4B	8559	-0.0052	0.37	NO
165	YWHAZ	YWHAZ	YWHAZ	8628	-0.007	0.36	NO
166	RPS27	RPS27	RPS27	8639	-0.0073	0.36	NO
167	CNOT7	CNOT7	CNOT7	8700	-0.0088	0.36	NO
168	PRKCA	PRKCA	PRKCA	8750	-0.01	0.36	NO
169	PAIP1	PAIP1	PAIP1	8756	-0.01	0.36	NO
170	RBM8A	RBM8A	RBM8A	8759	-0.01	0.36	NO
171	XPO1	XPO1	XPO1	8838	-0.012	0.36	NO
172	MAPK11	MAPK11	MAPK11	8921	-0.013	0.35	NO
173	DDX6	DDX6	DDX6	8975	-0.014	0.35	NO
174	DCP1A	DCP1A	DCP1A	9084	-0.016	0.35	NO
175	GSPT2	GSPT2	GSPT2	9158	-0.017	0.34	NO
176	PABPC1	PABPC1	PABPC1	9194	-0.018	0.34	NO
177	PSMB5	PSMB5	PSMB5	9415	-0.023	0.33	NO
178	PSMC2	PSMC2	PSMC2	9432	-0.023	0.33	NO
179	SMG5	SMG5	SMG5	9751	-0.03	0.32	NO
180	HSPB1	HSPB1	HSPB1	9873	-0.032	0.31	NO
181	PSMD1	PSMD1	PSMD1	9876	-0.032	0.31	NO
182	TNFSF13	TNFSF13	TNFSF13	9915	-0.033	0.31	NO
183	NCBP1	NCBP1	NCBP1	10071	-0.037	0.31	NO
184	UPF3B	UPF3B	UPF3B	10157	-0.039	0.3	NO
185	PSME4	PSME4	PSME4	10382	-0.044	0.29	NO
186	SMG7	SMG7	SMG7	10535	-0.047	0.29	NO
187	EIF4A2	EIF4A2	EIF4A2	10831	-0.055	0.28	NO
188	UPF2	UPF2	UPF2	10892	-0.056	0.28	NO
189	PSMD10	PSMD10	PSMD10	10943	-0.058	0.28	NO
190	DIS3	DIS3	DIS3	11277	-0.066	0.26	NO
191	EIF4G1	EIF4G1	EIF4G1	11387	-0.068	0.26	NO
192	PSMD12	PSMD12	PSMD12	11573	-0.073	0.25	NO
193	PPP2R2A	PPP2R2A	PPP2R2A	11644	-0.075	0.25	NO
194	XRN1	XRN1	XRN1	11957	-0.084	0.24	NO
195	MAPKAPK2	MAPKAPK2	MAPKAPK2	11969	-0.084	0.25	NO
196	PSMD11	PSMD11	PSMD11	11978	-0.084	0.25	NO
197	SMG1	SMG1	SMG1	12054	-0.086	0.25	NO
198	TNKS1BP1	TNKS1BP1	TNKS1BP1	12096	-0.088	0.26	NO
199	CNOT4	CNOT4	CNOT4	12204	-0.091	0.26	NO
200	PATL1	PATL1	PATL1	12219	-0.091	0.26	NO
201	TNPO1	TNPO1	TNPO1	12266	-0.092	0.26	NO
202	PRKCD	PRKCD	PRKCD	12333	-0.094	0.26	NO
203	PSMD5	PSMD5	PSMD5	12678	-0.11	0.25	NO
204	ZFP36L1	ZFP36L1	ZFP36L1	12951	-0.12	0.24	NO
205	ETF1	ETF1	ETF1	13160	-0.12	0.24	NO
206	RQCD1	RQCD1	RQCD1	13809	-0.15	0.21	NO
207	HSPA1B	HSPA1B	HSPA1B	14224	-0.17	0.2	NO
208	ZFP36	ZFP36	ZFP36	14412	-0.18	0.2	NO
209	FAM153A	FAM153A	FAM153A	15146	-0.23	0.17	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: REACTOME TRANSLATION.

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

genes ES table in pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX

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	RPL21	RPL21	RPL21	510	0.38	0.013	YES
2	RPL3L	RPL3L	RPL3L	713	0.34	0.038	YES
3	RPS28	RPS28	RPS28	1969	0.19	-0.012	YES
4	RPSAP9	RPSAP9	RPSAP9	2593	0.15	-0.03	YES
5	RPL18A	RPL18A	RPL18A	2740	0.14	-0.023	YES
6	RPSA	RPSA	RPSA	2761	0.14	-0.0096	YES
7	RPL39	RPL39	RPL39	3005	0.13	-0.0092	YES
8	RPLP2	RPLP2	RPLP2	3057	0.13	0.0015	YES
9	RPL14	RPL14	RPL14	3291	0.12	0.0014	YES
10	RPL24	RPL24	RPL24	3293	0.12	0.014	YES
11	RPS7	RPS7	RPS7	3362	0.12	0.023	YES
12	RPL28	RPL28	RPL28	3441	0.12	0.03	YES
13	RPL13	RPL13	RPL13	3474	0.11	0.041	YES
14	RPL29	RPL29	RPL29	3483	0.11	0.052	YES
15	RPS8	RPS8	RPS8	3513	0.11	0.062	YES
16	RPL34	RPL34	RPL34	3516	0.11	0.074	YES
17	RPL32	RPL32	RPL32	3527	0.11	0.086	YES
18	RPS10	RPS10	RPS10	3547	0.11	0.096	YES
19	RPL27A	RPL27A	RPL27A	3560	0.11	0.11	YES
20	RPS9	RPS9	RPS9	3576	0.11	0.12	YES
21	EIF3F	EIF3F	EIF3F	3587	0.11	0.13	YES
22	RPL18	RPL18	RPL18	3636	0.11	0.14	YES
23	RPS24	RPS24	RPS24	3647	0.11	0.15	YES
24	FAU	FAU	FAU	3658	0.11	0.16	YES
25	RPL23A	RPL23A	RPL23A	3703	0.11	0.17	YES
26	UBA52	UBA52	UBA52	3734	0.1	0.18	YES
27	RPL35A	RPL35A	RPL35A	3789	0.1	0.18	YES
28	RPL35	RPL35	RPL35	3798	0.1	0.2	YES
29	RPS21	RPS21	RPS21	3807	0.1	0.21	YES
30	RPS13	RPS13	RPS13	3815	0.1	0.22	YES
31	RPS16	RPS16	RPS16	3830	0.1	0.23	YES
32	RPS11	RPS11	RPS11	3833	0.1	0.24	YES
33	RPS19	RPS19	RPS19	3834	0.1	0.25	YES
34	RPS23	RPS23	RPS23	3868	0.1	0.26	YES
35	RPL26	RPL26	RPL26	3981	0.097	0.26	YES
36	RPS29	RPS29	RPS29	3983	0.097	0.27	YES
37	EIF3K	EIF3K	EIF3K	4018	0.096	0.28	YES
38	RPL22	RPL22	RPL22	4036	0.096	0.29	YES
39	RPS6	RPS6	RPS6	4046	0.095	0.3	YES
40	RPL37A	RPL37A	RPL37A	4072	0.094	0.31	YES
41	RPL37	RPL37	RPL37	4079	0.094	0.32	YES
42	RPL27	RPL27	RPL27	4121	0.093	0.32	YES
43	RPL31	RPL31	RPL31	4172	0.092	0.33	YES
44	EIF4A1	EIF4A1	EIF4A1	4205	0.091	0.34	YES
45	RPS20	RPS20	RPS20	4207	0.091	0.35	YES
46	RPS12	RPS12	RPS12	4230	0.091	0.36	YES
47	RPS15	RPS15	RPS15	4233	0.091	0.37	YES
48	RPS3A	RPS3A	RPS3A	4238	0.091	0.38	YES
49	RPL11	RPL11	RPL11	4278	0.09	0.38	YES
50	RPS3	RPS3	RPS3	4284	0.089	0.39	YES
51	RPL5	RPL5	RPL5	4307	0.089	0.4	YES
52	RPS17	RPS17	RPS17	4330	0.088	0.41	YES
53	RPLP1	RPLP1	RPLP1	4354	0.088	0.42	YES
54	RPS2	RPS2	RPS2	4372	0.088	0.42	YES
55	RPL26L1	RPL26L1	RPL26L1	4390	0.087	0.43	YES
56	RPL38	RPL38	RPL38	4417	0.086	0.44	YES
57	RPL19	RPL19	RPL19	4454	0.085	0.45	YES
58	RPL36	RPL36	RPL36	4503	0.084	0.45	YES
59	RPL23	RPL23	RPL23	4531	0.083	0.46	YES
60	RPS5	RPS5	RPS5	4599	0.081	0.47	YES
61	RPS14	RPS14	RPS14	4645	0.08	0.47	YES
62	RPL15	RPL15	RPL15	4724	0.078	0.48	YES
63	RPLP0	RPLP0	RPLP0	4740	0.078	0.48	YES
64	RPL36A	RPL36A	RPL36A	4835	0.075	0.49	YES
65	RPL10A	RPL10A	RPL10A	4854	0.075	0.49	YES
66	RPS27A	RPS27A	RPS27A	4877	0.074	0.5	YES
67	EIF3G	EIF3G	EIF3G	4931	0.073	0.5	YES
68	RPL4	RPL4	RPL4	4972	0.072	0.51	YES
69	RPL30	RPL30	RPL30	5001	0.072	0.52	YES
70	RPL6	RPL6	RPL6	5045	0.071	0.52	YES
71	RPL12	RPL12	RPL12	5075	0.07	0.53	YES
72	RPL13A	RPL13A	RPL13A	5082	0.07	0.53	YES
73	RPS25	RPS25	RPS25	5089	0.07	0.54	YES
74	RPS26	RPS26	RPS26	5153	0.068	0.54	YES
75	EIF3B	EIF3B	EIF3B	5204	0.067	0.55	YES
76	RPL41	RPL41	RPL41	5234	0.066	0.55	YES
77	EIF3I	EIF3I	EIF3I	5290	0.065	0.56	YES
78	RPL7A	RPL7A	RPL7A	5404	0.062	0.56	YES
79	EIF3D	EIF3D	EIF3D	5455	0.061	0.56	YES
80	RPS18	RPS18	RPS18	5514	0.059	0.56	YES
81	RPS15A	RPS15A	RPS15A	5670	0.055	0.56	YES
82	RPL10	RPL10	RPL10	5767	0.053	0.56	YES
83	EIF2S2	EIF2S2	EIF2S2	5780	0.053	0.57	YES
84	RPS4Y1	RPS4Y1	RPS4Y1	5796	0.053	0.57	YES
85	EIF3H	EIF3H	EIF3H	5845	0.051	0.57	YES
86	RPL7	RPL7	RPL7	5978	0.048	0.57	YES
87	RPS4X	RPS4X	RPS4X	6032	0.047	0.57	YES
88	RPL8	RPL8	RPL8	6043	0.047	0.58	YES
89	RPL17	RPL17	RPL17	6360	0.041	0.57	NO
90	RPL3	RPL3	RPL3	6546	0.037	0.56	NO
91	RPL9	RPL9	RPL9	6567	0.036	0.56	NO
92	EIF4E	EIF4E	EIF4E	6779	0.032	0.55	NO
93	EIF3E	EIF3E	EIF3E	7836	0.0098	0.5	NO
94	EIF3J	EIF3J	EIF3J	8521	-0.0045	0.46	NO
95	EIF4B	EIF4B	EIF4B	8559	-0.0052	0.46	NO
96	RPS27	RPS27	RPS27	8639	-0.0073	0.46	NO
97	EIF2S3	EIF2S3	EIF2S3	8808	-0.011	0.45	NO
98	PABPC1	PABPC1	PABPC1	9194	-0.018	0.43	NO
99	EIF2S1	EIF2S1	EIF2S1	9321	-0.021	0.42	NO
100	EIF4H	EIF4H	EIF4H	9440	-0.024	0.42	NO
101	EIF1AX	EIF1AX	EIF1AX	10012	-0.035	0.39	NO
102	EIF4A2	EIF4A2	EIF4A2	10831	-0.055	0.35	NO
103	EIF4G1	EIF4G1	EIF4G1	11387	-0.068	0.33	NO
104	EIF3A	EIF3A	EIF3A	11974	-0.084	0.3	NO
105	EIF3C	EIF3C	EIF3C	14164	-0.17	0.2	NO
106	FAM153A	FAM153A	FAM153A	15146	-0.23	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: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, 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 CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES

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	RPS28	RPS28	RPS28	1969	0.19	-0.066	YES
2	RPSAP9	RPSAP9	RPSAP9	2593	0.15	-0.067	YES
3	RPSA	RPSA	RPSA	2761	0.14	-0.045	YES
4	RPS7	RPS7	RPS7	3362	0.12	-0.052	YES
5	RPS8	RPS8	RPS8	3513	0.11	-0.035	YES
6	RPS10	RPS10	RPS10	3547	0.11	-0.012	YES
7	RPS9	RPS9	RPS9	3576	0.11	0.011	YES
8	EIF4EBP1	EIF4EBP1	EIF4EBP1	3584	0.11	0.035	YES
9	EIF3F	EIF3F	EIF3F	3587	0.11	0.059	YES
10	RPS24	RPS24	RPS24	3647	0.11	0.08	YES
11	FAU	FAU	FAU	3658	0.11	0.1	YES
12	RPS21	RPS21	RPS21	3807	0.1	0.12	YES
13	RPS13	RPS13	RPS13	3815	0.1	0.14	YES
14	RPS16	RPS16	RPS16	3830	0.1	0.16	YES
15	RPS11	RPS11	RPS11	3833	0.1	0.18	YES
16	RPS19	RPS19	RPS19	3834	0.1	0.21	YES
17	RPS23	RPS23	RPS23	3868	0.1	0.23	YES
18	RPS29	RPS29	RPS29	3983	0.097	0.24	YES
19	EIF3K	EIF3K	EIF3K	4018	0.096	0.26	YES
20	RPS6	RPS6	RPS6	4046	0.095	0.28	YES
21	EIF4A1	EIF4A1	EIF4A1	4205	0.091	0.3	YES
22	RPS20	RPS20	RPS20	4207	0.091	0.32	YES
23	RPS12	RPS12	RPS12	4230	0.091	0.34	YES
24	RPS15	RPS15	RPS15	4233	0.091	0.36	YES
25	RPS3A	RPS3A	RPS3A	4238	0.091	0.38	YES
26	RPS3	RPS3	RPS3	4284	0.089	0.39	YES
27	RPS17	RPS17	RPS17	4330	0.088	0.41	YES
28	RPS2	RPS2	RPS2	4372	0.088	0.43	YES
29	RPS5	RPS5	RPS5	4599	0.081	0.43	YES
30	RPS14	RPS14	RPS14	4645	0.08	0.45	YES
31	RPS27A	RPS27A	RPS27A	4877	0.074	0.45	YES
32	EIF3G	EIF3G	EIF3G	4931	0.073	0.46	YES
33	RPS25	RPS25	RPS25	5089	0.07	0.47	YES
34	RPS26	RPS26	RPS26	5153	0.068	0.48	YES
35	EIF3B	EIF3B	EIF3B	5204	0.067	0.5	YES
36	EIF3I	EIF3I	EIF3I	5290	0.065	0.51	YES
37	EIF3D	EIF3D	EIF3D	5455	0.061	0.51	YES
38	RPS18	RPS18	RPS18	5514	0.059	0.52	YES
39	RPS15A	RPS15A	RPS15A	5670	0.055	0.52	YES
40	EIF2S2	EIF2S2	EIF2S2	5780	0.053	0.53	YES
41	RPS4Y1	RPS4Y1	RPS4Y1	5796	0.053	0.54	YES
42	EIF3H	EIF3H	EIF3H	5845	0.051	0.55	YES
43	RPS4X	RPS4X	RPS4X	6032	0.047	0.55	YES
44	EIF4E	EIF4E	EIF4E	6779	0.032	0.52	NO
45	EIF3E	EIF3E	EIF3E	7836	0.0098	0.46	NO
46	EIF3J	EIF3J	EIF3J	8521	-0.0045	0.42	NO
47	EIF4B	EIF4B	EIF4B	8559	-0.0052	0.42	NO
48	RPS27	RPS27	RPS27	8639	-0.0073	0.42	NO
49	EIF2S3	EIF2S3	EIF2S3	8808	-0.011	0.41	NO
50	PABPC1	PABPC1	PABPC1	9194	-0.018	0.4	NO
51	EIF2S1	EIF2S1	EIF2S1	9321	-0.021	0.4	NO
52	EIF4H	EIF4H	EIF4H	9440	-0.024	0.39	NO
53	EIF1AX	EIF1AX	EIF1AX	10012	-0.035	0.37	NO
54	EIF4A2	EIF4A2	EIF4A2	10831	-0.055	0.34	NO
55	EIF4G1	EIF4G1	EIF4G1	11387	-0.068	0.32	NO
56	EIF3A	EIF3A	EIF3A	11974	-0.084	0.31	NO
57	EIF3C	EIF3C	EIF3C	14164	-0.17	0.23	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 CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES.

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

genes ES table in pathway: REACTOME ORC1 REMOVAL FROM CHROMATIN

Table 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	RPL21	RPL21	RPL21	510	0.38	-0.009	YES
2	RPL3L	RPL3L	RPL3L	713	0.34	-0.003	YES
3	PSMA8	PSMA8	PSMA8	898	0.31	0.0023	YES
4	RPS28	RPS28	RPS28	1969	0.19	-0.048	YES
5	LSM2	LSM2	LSM2	1978	0.19	-0.039	YES
6	EXOSC8	EXOSC8	EXOSC8	2065	0.18	-0.035	YES
7	SNRPF	SNRPF	SNRPF	2204	0.17	-0.034	YES
8	PSMB10	PSMB10	PSMB10	2433	0.16	-0.039	YES
9	EXOSC5	EXOSC5	EXOSC5	2500	0.15	-0.035	YES
10	LSM4	LSM4	LSM4	2522	0.15	-0.028	YES
11	LSM5	LSM5	LSM5	2533	0.15	-0.021	YES
12	RPSAP9	RPSAP9	RPSAP9	2593	0.15	-0.017	YES
13	SNRPD1	SNRPD1	SNRPD1	2615	0.15	-0.011	YES
14	SNRPD2	SNRPD2	SNRPD2	2648	0.14	-0.0052	YES
15	RPL18A	RPL18A	RPL18A	2740	0.14	-0.0032	YES
16	LSM3	LSM3	LSM3	2747	0.14	0.0035	YES
17	RPSA	RPSA	RPSA	2761	0.14	0.0098	YES
18	EXOSC4	EXOSC4	EXOSC4	2762	0.14	0.017	YES
19	EXOSC9	EXOSC9	EXOSC9	2770	0.14	0.023	YES
20	SNRPG	SNRPG	SNRPG	2801	0.14	0.029	YES
21	MAGOH	MAGOH	MAGOH	2881	0.14	0.031	YES
22	PSMD9	PSMD9	PSMD9	2920	0.13	0.036	YES
23	PSMD13	PSMD13	PSMD13	2988	0.13	0.038	YES
24	PSMB3	PSMB3	PSMB3	2996	0.13	0.044	YES
25	PSMB6	PSMB6	PSMB6	2997	0.13	0.051	YES
26	RPL39	RPL39	RPL39	3005	0.13	0.057	YES
27	PSMA6	PSMA6	PSMA6	3016	0.13	0.063	YES
28	RPLP2	RPLP2	RPLP2	3057	0.13	0.067	YES
29	PSMC3	PSMC3	PSMC3	3112	0.13	0.071	YES
30	EXOSC7	EXOSC7	EXOSC7	3207	0.12	0.072	YES
31	SNRPB	SNRPB	SNRPB	3247	0.12	0.076	YES
32	RPL14	RPL14	RPL14	3291	0.12	0.079	YES
33	RPL24	RPL24	RPL24	3293	0.12	0.085	YES
34	RPS7	RPS7	RPS7	3362	0.12	0.087	YES
35	PSMB7	PSMB7	PSMB7	3440	0.12	0.089	YES
36	RPL28	RPL28	RPL28	3441	0.12	0.094	YES
37	PSMA4	PSMA4	PSMA4	3448	0.12	0.1	YES
38	PSMB1	PSMB1	PSMB1	3463	0.11	0.1	YES
39	RPL13	RPL13	RPL13	3474	0.11	0.11	YES
40	RPL29	RPL29	RPL29	3483	0.11	0.12	YES
41	RPS8	RPS8	RPS8	3513	0.11	0.12	YES
42	RPL34	RPL34	RPL34	3516	0.11	0.12	YES
43	RPL32	RPL32	RPL32	3527	0.11	0.13	YES
44	RPS10	RPS10	RPS10	3547	0.11	0.13	YES
45	RPL27A	RPL27A	RPL27A	3560	0.11	0.14	YES
46	SNRPE	SNRPE	SNRPE	3562	0.11	0.14	YES
47	RPS9	RPS9	RPS9	3576	0.11	0.15	YES
48	CNOT10	CNOT10	CNOT10	3622	0.11	0.15	YES
49	RPL18	RPL18	RPL18	3636	0.11	0.16	YES
50	RPS24	RPS24	RPS24	3647	0.11	0.16	YES
51	FAU	FAU	FAU	3658	0.11	0.17	YES
52	EXOSC1	EXOSC1	EXOSC1	3685	0.11	0.17	YES
53	RPL23A	RPL23A	RPL23A	3703	0.11	0.18	YES
54	UBA52	UBA52	UBA52	3734	0.1	0.18	YES
55	PSMC1	PSMC1	PSMC1	3776	0.1	0.18	YES
56	RPL35A	RPL35A	RPL35A	3789	0.1	0.19	YES
57	RPL35	RPL35	RPL35	3798	0.1	0.19	YES
58	RPS21	RPS21	RPS21	3807	0.1	0.2	YES
59	RPS13	RPS13	RPS13	3815	0.1	0.2	YES
60	RPS16	RPS16	RPS16	3830	0.1	0.2	YES
61	RPS11	RPS11	RPS11	3833	0.1	0.21	YES
62	RPS19	RPS19	RPS19	3834	0.1	0.21	YES
63	RPS23	RPS23	RPS23	3868	0.1	0.22	YES
64	GEMIN6	GEMIN6	GEMIN6	3878	0.1	0.22	YES
65	PSMA5	PSMA5	PSMA5	3907	0.1	0.23	YES
66	DCP2	DCP2	DCP2	3976	0.098	0.23	YES
67	RPL26	RPL26	RPL26	3981	0.097	0.23	YES
68	RPS29	RPS29	RPS29	3983	0.097	0.24	YES
69	RPL22	RPL22	RPL22	4036	0.096	0.24	YES
70	SNRPD3	SNRPD3	SNRPD3	4045	0.095	0.24	YES
71	RPS6	RPS6	RPS6	4046	0.095	0.25	YES
72	RPL37A	RPL37A	RPL37A	4072	0.094	0.25	YES
73	RPL37	RPL37	RPL37	4079	0.094	0.26	YES
74	RPL27	RPL27	RPL27	4121	0.093	0.26	YES
75	HNRNPD	HNRNPD	HNRNPD	4123	0.093	0.26	YES
76	RPL31	RPL31	RPL31	4172	0.092	0.26	YES
77	PSME1	PSME1	PSME1	4185	0.092	0.27	YES
78	EIF4A1	EIF4A1	EIF4A1	4205	0.091	0.27	YES
79	RPS20	RPS20	RPS20	4207	0.091	0.28	YES
80	RPS12	RPS12	RPS12	4230	0.091	0.28	YES
81	RPS15	RPS15	RPS15	4233	0.091	0.28	YES
82	RPS3A	RPS3A	RPS3A	4238	0.091	0.29	YES
83	RPL11	RPL11	RPL11	4278	0.09	0.29	YES
84	RPS3	RPS3	RPS3	4284	0.089	0.29	YES
85	RPL5	RPL5	RPL5	4307	0.089	0.3	YES
86	RPS17	RPS17	RPS17	4330	0.088	0.3	YES
87	RPLP1	RPLP1	RPLP1	4354	0.088	0.3	YES
88	RPS2	RPS2	RPS2	4372	0.088	0.31	YES
89	RPL26L1	RPL26L1	RPL26L1	4390	0.087	0.31	YES
90	RPL38	RPL38	RPL38	4417	0.086	0.31	YES
91	RPL19	RPL19	RPL19	4454	0.085	0.32	YES
92	GEMIN7	GEMIN7	GEMIN7	4483	0.084	0.32	YES
93	PSMB8	PSMB8	PSMB8	4488	0.084	0.32	YES
94	NUP210	NUP210	NUP210	4492	0.084	0.33	YES
95	RPL36	RPL36	RPL36	4503	0.084	0.33	YES
96	UPF3A	UPF3A	UPF3A	4527	0.083	0.33	YES
97	RPL23	RPL23	RPL23	4531	0.083	0.34	YES
98	DCP1B	DCP1B	DCP1B	4554	0.082	0.34	YES
99	AAAS	AAAS	AAAS	4588	0.081	0.34	YES
100	RPS5	RPS5	RPS5	4599	0.081	0.35	YES
101	NUP88	NUP88	NUP88	4632	0.08	0.35	YES
102	RPS14	RPS14	RPS14	4645	0.08	0.35	YES
103	RPL15	RPL15	RPL15	4724	0.078	0.35	YES
104	DCPS	DCPS	DCPS	4727	0.078	0.36	YES
105	RPLP0	RPLP0	RPLP0	4740	0.078	0.36	YES
106	ANP32A	ANP32A	ANP32A	4755	0.077	0.36	YES
107	SEH1L	SEH1L	SEH1L	4829	0.076	0.36	YES
108	RPL36A	RPL36A	RPL36A	4835	0.075	0.36	YES
109	RPL10A	RPL10A	RPL10A	4854	0.075	0.37	YES
110	RPS27A	RPS27A	RPS27A	4877	0.074	0.37	YES
111	RPL4	RPL4	RPL4	4972	0.072	0.37	YES
112	RPL30	RPL30	RPL30	5001	0.072	0.37	YES
113	RPL6	RPL6	RPL6	5045	0.071	0.37	YES
114	EDC4	EDC4	EDC4	5059	0.07	0.37	YES
115	RPL12	RPL12	RPL12	5075	0.07	0.38	YES
116	RPL13A	RPL13A	RPL13A	5082	0.07	0.38	YES
117	RPS25	RPS25	RPS25	5089	0.07	0.38	YES
118	NUP93	NUP93	NUP93	5109	0.069	0.38	YES
119	NUP85	NUP85	NUP85	5119	0.069	0.39	YES
120	PSMC5	PSMC5	PSMC5	5135	0.069	0.39	YES
121	PSMD8	PSMD8	PSMD8	5140	0.068	0.39	YES
122	RPS26	RPS26	RPS26	5153	0.068	0.4	YES
123	RPL41	RPL41	RPL41	5234	0.066	0.4	YES
124	SNUPN	SNUPN	SNUPN	5244	0.066	0.4	YES
125	PSMB9	PSMB9	PSMB9	5307	0.065	0.4	YES
126	NUP214	NUP214	NUP214	5351	0.064	0.4	YES
127	RPL7A	RPL7A	RPL7A	5404	0.062	0.4	YES
128	PSMD6	PSMD6	PSMD6	5424	0.062	0.4	YES
129	LSM6	LSM6	LSM6	5491	0.06	0.4	YES
130	RPS18	RPS18	RPS18	5514	0.059	0.4	YES
131	CLNS1A	CLNS1A	CLNS1A	5522	0.059	0.4	YES
132	RAE1	RAE1	RAE1	5557	0.058	0.41	YES
133	PSMD4	PSMD4	PSMD4	5587	0.057	0.41	YES
134	WDR77	WDR77	WDR77	5589	0.057	0.41	YES
135	PSME2	PSME2	PSME2	5595	0.057	0.41	YES
136	RNPS1	RNPS1	RNPS1	5631	0.056	0.41	YES
137	RPS15A	RPS15A	RPS15A	5670	0.055	0.41	YES
138	PSMD7	PSMD7	PSMD7	5727	0.054	0.41	YES
139	RPL10	RPL10	RPL10	5767	0.053	0.41	YES
140	PSMB2	PSMB2	PSMB2	5789	0.053	0.42	YES
141	RPS4Y1	RPS4Y1	RPS4Y1	5796	0.053	0.42	YES
142	NUP37	NUP37	NUP37	5839	0.051	0.42	YES
143	RPL7	RPL7	RPL7	5978	0.048	0.41	YES
144	RPS4X	RPS4X	RPS4X	6032	0.047	0.41	YES
145	RPL8	RPL8	RPL8	6043	0.047	0.41	YES
146	PPP2CA	PPP2CA	PPP2CA	6064	0.046	0.42	YES
147	PPP2R1A	PPP2R1A	PPP2R1A	6216	0.044	0.41	YES
148	EXOSC2	EXOSC2	EXOSC2	6221	0.043	0.41	YES
149	C2orf29	C2orf29	C2orf29	6244	0.043	0.41	YES
150	PSMC4	PSMC4	PSMC4	6292	0.042	0.41	YES
151	EIF4A3	EIF4A3	EIF4A3	6317	0.042	0.41	YES
152	PSMA7	PSMA7	PSMA7	6333	0.041	0.41	YES
153	NUP43	NUP43	NUP43	6358	0.041	0.41	YES
154	RPL17	RPL17	RPL17	6360	0.041	0.42	YES
155	CNOT2	CNOT2	CNOT2	6389	0.04	0.42	YES
156	NUP50	NUP50	NUP50	6398	0.04	0.42	YES
157	PSMA1	PSMA1	PSMA1	6436	0.039	0.42	YES
158	PSMA2	PSMA2	PSMA2	6484	0.038	0.42	YES
159	GEMIN4	GEMIN4	GEMIN4	6510	0.038	0.42	YES
160	LSM1	LSM1	LSM1	6511	0.038	0.42	YES
161	RPL3	RPL3	RPL3	6546	0.037	0.42	YES
162	EXOSC3	EXOSC3	EXOSC3	6557	0.037	0.42	YES
163	RPL9	RPL9	RPL9	6567	0.036	0.42	YES
164	CNOT3	CNOT3	CNOT3	6758	0.032	0.41	NO
165	PSMB4	PSMB4	PSMB4	6777	0.032	0.41	NO
166	EIF4E	EIF4E	EIF4E	6779	0.032	0.42	NO
167	CNOT8	CNOT8	CNOT8	6781	0.032	0.42	NO
168	PSMD3	PSMD3	PSMD3	6791	0.032	0.42	NO
169	PSMA3	PSMA3	PSMA3	6934	0.029	0.41	NO
170	KHSRP	KHSRP	KHSRP	7126	0.025	0.4	NO
171	ELAVL1	ELAVL1	ELAVL1	7154	0.024	0.4	NO
172	EXOSC6	EXOSC6	EXOSC6	7161	0.024	0.4	NO
173	NCBP2	NCBP2	NCBP2	7213	0.023	0.4	NO
174	SMN2	SMN2	SMN2	7222	0.023	0.4	NO
175	NUP35	NUP35	NUP35	7294	0.021	0.4	NO
176	PSMF1	PSMF1	PSMF1	7436	0.019	0.39	NO
177	NUP188	NUP188	NUP188	7525	0.017	0.39	NO
178	NUP62	NUP62	NUP62	7584	0.015	0.39	NO
179	EDC3	EDC3	EDC3	7647	0.014	0.38	NO
180	CNOT6	CNOT6	CNOT6	7729	0.012	0.38	NO
181	NUP54	NUP54	NUP54	7928	0.0081	0.37	NO
182	DDX20	DDX20	DDX20	7974	0.0071	0.37	NO
183	PARN	PARN	PARN	8011	0.0062	0.36	NO
184	YWHAB	YWHAB	YWHAB	8036	0.0055	0.36	NO
185	PSMC6	PSMC6	PSMC6	8049	0.0053	0.36	NO
186	SMG6	SMG6	SMG6	8130	0.0036	0.36	NO
187	AKT1	AKT1	AKT1	8206	0.0022	0.36	NO
188	HSPA8	HSPA8	HSPA8	8216	0.002	0.35	NO
189	MAPK14	MAPK14	MAPK14	8309	-3e-05	0.35	NO
190	CASC3	CASC3	CASC3	8353	-0.0011	0.35	NO
191	PSMD14	PSMD14	PSMD14	8360	-0.0013	0.35	NO
192	PSMD2	PSMD2	PSMD2	8389	-0.0018	0.34	NO
193	EIF4B	EIF4B	EIF4B	8559	-0.0052	0.34	NO
194	YWHAZ	YWHAZ	YWHAZ	8628	-0.007	0.33	NO
195	RPS27	RPS27	RPS27	8639	-0.0073	0.33	NO
196	CNOT7	CNOT7	CNOT7	8700	-0.0088	0.33	NO
197	PRKCA	PRKCA	PRKCA	8750	-0.01	0.33	NO
198	PAIP1	PAIP1	PAIP1	8756	-0.01	0.33	NO
199	RBM8A	RBM8A	RBM8A	8759	-0.01	0.33	NO
200	PRMT5	PRMT5	PRMT5	8826	-0.011	0.32	NO
201	XPO1	XPO1	XPO1	8838	-0.012	0.32	NO
202	MAPK11	MAPK11	MAPK11	8921	-0.013	0.32	NO
203	DDX6	DDX6	DDX6	8975	-0.014	0.32	NO
204	DCP1A	DCP1A	DCP1A	9084	-0.016	0.31	NO
205	GSPT2	GSPT2	GSPT2	9158	-0.017	0.31	NO
206	PABPC1	PABPC1	PABPC1	9194	-0.018	0.31	NO
207	NUP107	NUP107	NUP107	9294	-0.021	0.3	NO
208	PSMB5	PSMB5	PSMB5	9415	-0.023	0.3	NO
209	PSMC2	PSMC2	PSMC2	9432	-0.023	0.3	NO
210	SMG5	SMG5	SMG5	9751	-0.03	0.28	NO
211	HSPB1	HSPB1	HSPB1	9873	-0.032	0.28	NO
212	PSMD1	PSMD1	PSMD1	9876	-0.032	0.28	NO
213	TNFSF13	TNFSF13	TNFSF13	9915	-0.033	0.28	NO
214	NCBP1	NCBP1	NCBP1	10071	-0.037	0.27	NO
215	UPF3B	UPF3B	UPF3B	10157	-0.039	0.27	NO
216	PSME4	PSME4	PSME4	10382	-0.044	0.26	NO
217	SMG7	SMG7	SMG7	10535	-0.047	0.25	NO
218	NUPL1	NUPL1	NUPL1	10593	-0.048	0.25	NO
219	TGS1	TGS1	TGS1	10672	-0.051	0.25	NO
220	EIF4A2	EIF4A2	EIF4A2	10831	-0.055	0.24	NO
221	UPF2	UPF2	UPF2	10892	-0.056	0.24	NO
222	RANBP2	RANBP2	RANBP2	10924	-0.057	0.25	NO
223	POM121	POM121	POM121	10942	-0.057	0.25	NO
224	PSMD10	PSMD10	PSMD10	10943	-0.058	0.25	NO
225	NUP133	NUP133	NUP133	11010	-0.059	0.25	NO
226	DIS3	DIS3	DIS3	11277	-0.066	0.24	NO
227	NUP205	NUP205	NUP205	11340	-0.067	0.24	NO
228	EIF4G1	EIF4G1	EIF4G1	11387	-0.068	0.24	NO
229	PSMD12	PSMD12	PSMD12	11573	-0.073	0.23	NO
230	PPP2R2A	PPP2R2A	PPP2R2A	11644	-0.075	0.23	NO
231	NUPL2	NUPL2	NUPL2	11785	-0.079	0.23	NO
232	XRN1	XRN1	XRN1	11957	-0.084	0.22	NO
233	MAPKAPK2	MAPKAPK2	MAPKAPK2	11969	-0.084	0.23	NO
234	PSMD11	PSMD11	PSMD11	11978	-0.084	0.23	NO
235	SMG1	SMG1	SMG1	12054	-0.086	0.23	NO
236	PHAX	PHAX	PHAX	12094	-0.088	0.23	NO
237	TNKS1BP1	TNKS1BP1	TNKS1BP1	12096	-0.088	0.24	NO
238	GEMIN5	GEMIN5	GEMIN5	12199	-0.091	0.24	NO
239	CNOT4	CNOT4	CNOT4	12204	-0.091	0.24	NO
240	PATL1	PATL1	PATL1	12219	-0.091	0.24	NO
241	TNPO1	TNPO1	TNPO1	12266	-0.092	0.25	NO
242	PRKCD	PRKCD	PRKCD	12333	-0.094	0.25	NO
243	TPR	TPR	TPR	12615	-0.1	0.24	NO
244	NUP153	NUP153	NUP153	12628	-0.1	0.24	NO
245	PSMD5	PSMD5	PSMD5	12678	-0.11	0.24	NO
246	ZFP36L1	ZFP36L1	ZFP36L1	12951	-0.12	0.24	NO
247	ETF1	ETF1	ETF1	13160	-0.12	0.23	NO
248	RQCD1	RQCD1	RQCD1	13809	-0.15	0.2	NO
249	NUP155	NUP155	NUP155	13887	-0.15	0.2	NO
250	HSPA1B	HSPA1B	HSPA1B	14224	-0.17	0.2	NO
251	ZFP36	ZFP36	ZFP36	14412	-0.18	0.19	NO
252	SMN1	SMN1	SMN1	14676	-0.2	0.19	NO
253	FAM153A	FAM153A	FAM153A	15146	-0.23	0.17	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 ORC1 REMOVAL FROM CHROMATIN.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ORC1 REMOVAL FROM CHROMATIN, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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

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	RPL21	RPL21	RPL21	510	0.38	0.013	YES
2	RPL3L	RPL3L	RPL3L	713	0.34	0.039	YES
3	RPS28	RPS28	RPS28	1969	0.19	-0.0097	YES
4	RPSAP9	RPSAP9	RPSAP9	2593	0.15	-0.028	YES
5	RPL18A	RPL18A	RPL18A	2740	0.14	-0.021	YES
6	RPSA	RPSA	RPSA	2761	0.14	-0.0069	YES
7	RPL39	RPL39	RPL39	3005	0.13	-0.0062	YES
8	RPLP2	RPLP2	RPLP2	3057	0.13	0.0048	YES
9	SEC61B	SEC61B	SEC61B	3109	0.13	0.016	YES
10	RPL14	RPL14	RPL14	3291	0.12	0.019	YES
11	RPL24	RPL24	RPL24	3293	0.12	0.032	YES
12	RPS7	RPS7	RPS7	3362	0.12	0.04	YES
13	SEC61G	SEC61G	SEC61G	3386	0.12	0.052	YES
14	RPL28	RPL28	RPL28	3441	0.12	0.061	YES
15	RPL13	RPL13	RPL13	3474	0.11	0.072	YES
16	RPL29	RPL29	RPL29	3483	0.11	0.083	YES
17	RPS8	RPS8	RPS8	3513	0.11	0.094	YES
18	RPL34	RPL34	RPL34	3516	0.11	0.11	YES
19	RPL32	RPL32	RPL32	3527	0.11	0.12	YES
20	RPS10	RPS10	RPS10	3547	0.11	0.13	YES
21	RPL27A	RPL27A	RPL27A	3560	0.11	0.14	YES
22	RPS9	RPS9	RPS9	3576	0.11	0.15	YES
23	RPL18	RPL18	RPL18	3636	0.11	0.16	YES
24	RPS24	RPS24	RPS24	3647	0.11	0.17	YES
25	FAU	FAU	FAU	3658	0.11	0.18	YES
26	RPL23A	RPL23A	RPL23A	3703	0.11	0.19	YES
27	UBA52	UBA52	UBA52	3734	0.1	0.2	YES
28	RPL35A	RPL35A	RPL35A	3789	0.1	0.21	YES
29	RPL35	RPL35	RPL35	3798	0.1	0.22	YES
30	RPS21	RPS21	RPS21	3807	0.1	0.23	YES
31	RPS13	RPS13	RPS13	3815	0.1	0.24	YES
32	RPS16	RPS16	RPS16	3830	0.1	0.25	YES
33	RPS11	RPS11	RPS11	3833	0.1	0.26	YES
34	RPS19	RPS19	RPS19	3834	0.1	0.27	YES
35	RPS23	RPS23	RPS23	3868	0.1	0.28	YES
36	RPL26	RPL26	RPL26	3981	0.097	0.28	YES
37	RPS29	RPS29	RPS29	3983	0.097	0.3	YES
38	RPL22	RPL22	RPL22	4036	0.096	0.3	YES
39	RPS6	RPS6	RPS6	4046	0.095	0.31	YES
40	RPL37A	RPL37A	RPL37A	4072	0.094	0.32	YES
41	RPL37	RPL37	RPL37	4079	0.094	0.33	YES
42	RPL27	RPL27	RPL27	4121	0.093	0.34	YES
43	RPL31	RPL31	RPL31	4172	0.092	0.35	YES
44	RPS20	RPS20	RPS20	4207	0.091	0.35	YES
45	RPS12	RPS12	RPS12	4230	0.091	0.36	YES
46	RPS15	RPS15	RPS15	4233	0.091	0.37	YES
47	RPS3A	RPS3A	RPS3A	4238	0.091	0.38	YES
48	RPL11	RPL11	RPL11	4278	0.09	0.39	YES
49	RPS3	RPS3	RPS3	4284	0.089	0.4	YES
50	RPL5	RPL5	RPL5	4307	0.089	0.41	YES
51	RPS17	RPS17	RPS17	4330	0.088	0.42	YES
52	RPLP1	RPLP1	RPLP1	4354	0.088	0.42	YES
53	RPS2	RPS2	RPS2	4372	0.088	0.43	YES
54	RPL26L1	RPL26L1	RPL26L1	4390	0.087	0.44	YES
55	RPL38	RPL38	RPL38	4417	0.086	0.45	YES
56	RPL19	RPL19	RPL19	4454	0.085	0.46	YES
57	RPL36	RPL36	RPL36	4503	0.084	0.46	YES
58	RPL23	RPL23	RPL23	4531	0.083	0.47	YES
59	RPS5	RPS5	RPS5	4599	0.081	0.47	YES
60	RPS14	RPS14	RPS14	4645	0.08	0.48	YES
61	RPL15	RPL15	RPL15	4724	0.078	0.48	YES
62	RPLP0	RPLP0	RPLP0	4740	0.078	0.49	YES
63	RPL36A	RPL36A	RPL36A	4835	0.075	0.49	YES
64	RPL10A	RPL10A	RPL10A	4854	0.075	0.5	YES
65	RPS27A	RPS27A	RPS27A	4877	0.074	0.51	YES
66	RPL4	RPL4	RPL4	4972	0.072	0.51	YES
67	RPL30	RPL30	RPL30	5001	0.072	0.52	YES
68	SRP14	SRP14	SRP14	5026	0.071	0.52	YES
69	RPL6	RPL6	RPL6	5045	0.071	0.53	YES
70	RPL12	RPL12	RPL12	5075	0.07	0.54	YES
71	RPL13A	RPL13A	RPL13A	5082	0.07	0.54	YES
72	RPS25	RPS25	RPS25	5089	0.07	0.55	YES
73	RPS26	RPS26	RPS26	5153	0.068	0.55	YES
74	RPL41	RPL41	RPL41	5234	0.066	0.56	YES
75	RPL7A	RPL7A	RPL7A	5404	0.062	0.55	YES
76	SPCS2	SPCS2	SPCS2	5412	0.062	0.56	YES
77	RPS18	RPS18	RPS18	5514	0.059	0.56	YES
78	SSR2	SSR2	SSR2	5547	0.058	0.57	YES
79	RPS15A	RPS15A	RPS15A	5670	0.055	0.56	YES
80	RPL10	RPL10	RPL10	5767	0.053	0.56	YES
81	RPS4Y1	RPS4Y1	RPS4Y1	5796	0.053	0.57	YES
82	SEC61A2	SEC61A2	SEC61A2	5913	0.05	0.57	YES
83	RPL7	RPL7	RPL7	5978	0.048	0.57	YES
84	RPN1	RPN1	RPN1	6009	0.048	0.57	YES
85	RPS4X	RPS4X	RPS4X	6032	0.047	0.58	YES
86	SRP19	SRP19	SRP19	6037	0.047	0.58	YES
87	RPL8	RPL8	RPL8	6043	0.047	0.59	YES
88	SPCS1	SPCS1	SPCS1	6083	0.046	0.59	YES
89	RPL17	RPL17	RPL17	6360	0.041	0.58	NO
90	SSR4	SSR4	SSR4	6397	0.04	0.58	NO
91	SEC11C	SEC11C	SEC11C	6473	0.038	0.58	NO
92	RPL3	RPL3	RPL3	6546	0.037	0.58	NO
93	RPL9	RPL9	RPL9	6567	0.036	0.58	NO
94	DDOST	DDOST	DDOST	6759	0.032	0.58	NO
95	LOC653566	LOC653566	LOC653566	6882	0.03	0.57	NO
96	TRAM1	TRAM1	TRAM1	7398	0.02	0.55	NO
97	SEC61A1	SEC61A1	SEC61A1	7539	0.016	0.54	NO
98	SRP68	SRP68	SRP68	7791	0.011	0.53	NO
99	SRPRB	SRPRB	SRPRB	8105	0.0042	0.51	NO
100	SRP9	SRP9	SRP9	8280	0.00065	0.5	NO
101	SRP72	SRP72	SRP72	8405	-0.0022	0.5	NO
102	SPCS3	SPCS3	SPCS3	8613	-0.0067	0.48	NO
103	RPS27	RPS27	RPS27	8639	-0.0073	0.48	NO
104	RPN2	RPN2	RPN2	8817	-0.011	0.48	NO
105	SSR1	SSR1	SSR1	9091	-0.016	0.46	NO
106	SSR3	SSR3	SSR3	9423	-0.023	0.45	NO
107	SEC11A	SEC11A	SEC11A	9489	-0.025	0.45	NO
108	SRP54	SRP54	SRP54	11021	-0.059	0.37	NO
109	SRPR	SRPR	SRPR	11057	-0.06	0.37	NO
110	FAM153A	FAM153A	FAM153A	15146	-0.23	0.17	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 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

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

genes ES table in pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

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	RPS28	RPS28	RPS28	1969	0.19	-0.062	YES
2	RPSAP9	RPSAP9	RPSAP9	2593	0.15	-0.06	YES
3	RPSA	RPSA	RPSA	2761	0.14	-0.035	YES
4	RPS7	RPS7	RPS7	3362	0.12	-0.039	YES
5	RPS8	RPS8	RPS8	3513	0.11	-0.019	YES
6	RPS10	RPS10	RPS10	3547	0.11	0.006	YES
7	RPS9	RPS9	RPS9	3576	0.11	0.032	YES
8	EIF3F	EIF3F	EIF3F	3587	0.11	0.058	YES
9	RPS24	RPS24	RPS24	3647	0.11	0.081	YES
10	FAU	FAU	FAU	3658	0.11	0.11	YES
11	RPS21	RPS21	RPS21	3807	0.1	0.12	YES
12	RPS13	RPS13	RPS13	3815	0.1	0.15	YES
13	RPS16	RPS16	RPS16	3830	0.1	0.17	YES
14	RPS11	RPS11	RPS11	3833	0.1	0.2	YES
15	RPS19	RPS19	RPS19	3834	0.1	0.22	YES
16	RPS23	RPS23	RPS23	3868	0.1	0.24	YES
17	RPS29	RPS29	RPS29	3983	0.097	0.26	YES
18	EIF3K	EIF3K	EIF3K	4018	0.096	0.28	YES
19	RPS6	RPS6	RPS6	4046	0.095	0.31	YES
20	RPS20	RPS20	RPS20	4207	0.091	0.32	YES
21	RPS12	RPS12	RPS12	4230	0.091	0.34	YES
22	RPS15	RPS15	RPS15	4233	0.091	0.36	YES
23	RPS3A	RPS3A	RPS3A	4238	0.091	0.38	YES
24	RPS3	RPS3	RPS3	4284	0.089	0.4	YES
25	RPS17	RPS17	RPS17	4330	0.088	0.42	YES
26	RPS2	RPS2	RPS2	4372	0.088	0.44	YES
27	RPS5	RPS5	RPS5	4599	0.081	0.45	YES
28	RPS14	RPS14	RPS14	4645	0.08	0.47	YES
29	RPS27A	RPS27A	RPS27A	4877	0.074	0.47	YES
30	EIF3G	EIF3G	EIF3G	4931	0.073	0.49	YES
31	RPS25	RPS25	RPS25	5089	0.07	0.5	YES
32	RPS26	RPS26	RPS26	5153	0.068	0.51	YES
33	EIF3B	EIF3B	EIF3B	5204	0.067	0.52	YES
34	EIF3I	EIF3I	EIF3I	5290	0.065	0.54	YES
35	EIF3D	EIF3D	EIF3D	5455	0.061	0.54	YES
36	RPS18	RPS18	RPS18	5514	0.059	0.55	YES
37	RPS15A	RPS15A	RPS15A	5670	0.055	0.56	YES
38	EIF2S2	EIF2S2	EIF2S2	5780	0.053	0.56	YES
39	RPS4Y1	RPS4Y1	RPS4Y1	5796	0.053	0.58	YES
40	EIF3H	EIF3H	EIF3H	5845	0.051	0.59	YES
41	RPS4X	RPS4X	RPS4X	6032	0.047	0.59	YES
42	EIF3E	EIF3E	EIF3E	7836	0.0098	0.49	NO
43	EIF3J	EIF3J	EIF3J	8521	-0.0045	0.46	NO
44	RPS27	RPS27	RPS27	8639	-0.0073	0.45	NO
45	EIF2S3	EIF2S3	EIF2S3	8808	-0.011	0.44	NO
46	EIF2S1	EIF2S1	EIF2S1	9321	-0.021	0.42	NO
47	EIF1AX	EIF1AX	EIF1AX	10012	-0.035	0.39	NO
48	EIF3A	EIF3A	EIF3A	11974	-0.084	0.3	NO
49	EIF3C	EIF3C	EIF3C	14164	-0.17	0.23	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 ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME PEPTIDE CHAIN ELONGATION

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	RPL21	RPL21	RPL21	510	0.38	0.018	YES
2	RPL3L	RPL3L	RPL3L	713	0.34	0.049	YES
3	RPS28	RPS28	RPS28	1969	0.19	0.0023	YES
4	RPL18A	RPL18A	RPL18A	2740	0.14	-0.023	YES
5	RPSA	RPSA	RPSA	2761	0.14	-0.0073	YES
6	RPL39	RPL39	RPL39	3005	0.13	-0.0049	YES
7	RPLP2	RPLP2	RPLP2	3057	0.13	0.0078	YES
8	RPL14	RPL14	RPL14	3291	0.12	0.0095	YES
9	RPL24	RPL24	RPL24	3293	0.12	0.024	YES
10	RPL22L1	RPL22L1	RPL22L1	3310	0.12	0.037	YES
11	RPS7	RPS7	RPS7	3362	0.12	0.049	YES
12	RPL28	RPL28	RPL28	3441	0.12	0.058	YES
13	RPL13	RPL13	RPL13	3474	0.11	0.07	YES
14	RPL29	RPL29	RPL29	3483	0.11	0.084	YES
15	RPS27L	RPS27L	RPS27L	3510	0.11	0.096	YES
16	RPS8	RPS8	RPS8	3513	0.11	0.11	YES
17	RPL34	RPL34	RPL34	3516	0.11	0.12	YES
18	RPL32	RPL32	RPL32	3527	0.11	0.14	YES
19	RPS10	RPS10	RPS10	3547	0.11	0.15	YES
20	RPL27A	RPL27A	RPL27A	3560	0.11	0.16	YES
21	RPS9	RPS9	RPS9	3576	0.11	0.17	YES
22	RPL18	RPL18	RPL18	3636	0.11	0.18	YES
23	RPS24	RPS24	RPS24	3647	0.11	0.2	YES
24	FAU	FAU	FAU	3658	0.11	0.21	YES
25	RPL36AL	RPL36AL	RPL36AL	3672	0.11	0.22	YES
26	RPL23A	RPL23A	RPL23A	3703	0.11	0.23	YES
27	UBA52	UBA52	UBA52	3734	0.1	0.24	YES
28	RPL35A	RPL35A	RPL35A	3789	0.1	0.25	YES
29	RPL35	RPL35	RPL35	3798	0.1	0.26	YES
30	RPS21	RPS21	RPS21	3807	0.1	0.28	YES
31	RPS13	RPS13	RPS13	3815	0.1	0.29	YES
32	RPS16	RPS16	RPS16	3830	0.1	0.3	YES
33	RPS11	RPS11	RPS11	3833	0.1	0.31	YES
34	RPS19	RPS19	RPS19	3834	0.1	0.32	YES
35	RPS23	RPS23	RPS23	3868	0.1	0.33	YES
36	RPL26	RPL26	RPL26	3981	0.097	0.34	YES
37	RPS29	RPS29	RPS29	3983	0.097	0.35	YES
38	RPL22	RPL22	RPL22	4036	0.096	0.36	YES
39	RPS6	RPS6	RPS6	4046	0.095	0.37	YES
40	RPL37A	RPL37A	RPL37A	4072	0.094	0.38	YES
41	RPL37	RPL37	RPL37	4079	0.094	0.39	YES
42	RPL27	RPL27	RPL27	4121	0.093	0.4	YES
43	RPL31	RPL31	RPL31	4172	0.092	0.41	YES
44	RPS20	RPS20	RPS20	4207	0.091	0.42	YES
45	RPS12	RPS12	RPS12	4230	0.091	0.43	YES
46	RPS15	RPS15	RPS15	4233	0.091	0.44	YES
47	RPS3A	RPS3A	RPS3A	4238	0.091	0.45	YES
48	RPL11	RPL11	RPL11	4278	0.09	0.46	YES
49	RPS3	RPS3	RPS3	4284	0.089	0.47	YES
50	RPL5	RPL5	RPL5	4307	0.089	0.48	YES
51	RPS17	RPS17	RPS17	4330	0.088	0.49	YES
52	RPLP1	RPLP1	RPLP1	4354	0.088	0.5	YES
53	RPS2	RPS2	RPS2	4372	0.088	0.51	YES
54	RPL26L1	RPL26L1	RPL26L1	4390	0.087	0.52	YES
55	RPL38	RPL38	RPL38	4417	0.086	0.52	YES
56	RPL19	RPL19	RPL19	4454	0.085	0.53	YES
57	RSL24D1	RSL24D1	RSL24D1	4494	0.084	0.54	YES
58	RPL36	RPL36	RPL36	4503	0.084	0.55	YES
59	RPL23	RPL23	RPL23	4531	0.083	0.56	YES
60	RPS5	RPS5	RPS5	4599	0.081	0.56	YES
61	RPL15	RPL15	RPL15	4724	0.078	0.57	YES
62	RPLP0	RPLP0	RPLP0	4740	0.078	0.58	YES
63	RPL36A	RPL36A	RPL36A	4835	0.075	0.58	YES
64	RPL10A	RPL10A	RPL10A	4854	0.075	0.59	YES
65	RPS27A	RPS27A	RPS27A	4877	0.074	0.6	YES
66	RPL4	RPL4	RPL4	4972	0.072	0.6	YES
67	RPL30	RPL30	RPL30	5001	0.072	0.61	YES
68	RPL6	RPL6	RPL6	5045	0.071	0.61	YES
69	RPL12	RPL12	RPL12	5075	0.07	0.62	YES
70	RPL13A	RPL13A	RPL13A	5082	0.07	0.63	YES
71	RPS25	RPS25	RPS25	5089	0.07	0.64	YES
72	RPS26	RPS26	RPS26	5153	0.068	0.64	YES
73	RPL41	RPL41	RPL41	5234	0.066	0.64	YES
74	RPL7A	RPL7A	RPL7A	5404	0.062	0.64	YES
75	RPS18	RPS18	RPS18	5514	0.059	0.64	YES
76	MRPL13	MRPL13	MRPL13	5582	0.057	0.65	YES
77	RPS15A	RPS15A	RPS15A	5670	0.055	0.65	YES
78	RPL10	RPL10	RPL10	5767	0.053	0.65	YES
79	RPS4Y1	RPS4Y1	RPS4Y1	5796	0.053	0.65	YES
80	RPL7	RPL7	RPL7	5978	0.048	0.65	YES
81	RPS4X	RPS4X	RPS4X	6032	0.047	0.65	YES
82	RPL8	RPL8	RPL8	6043	0.047	0.66	YES
83	RPL17	RPL17	RPL17	6360	0.041	0.64	NO
84	RPL3	RPL3	RPL3	6546	0.037	0.64	NO
85	RPL9	RPL9	RPL9	6567	0.036	0.64	NO
86	RPS27	RPS27	RPS27	8639	-0.0073	0.53	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 PEPTIDE CHAIN ELONGATION.

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

genes ES table in pathway: REACTOME MRNA SPLICING

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	RPL21	RPL21	RPL21	510	0.38	0.013	YES
2	RPL3L	RPL3L	RPL3L	713	0.34	0.039	YES
3	RPS28	RPS28	RPS28	1969	0.19	-0.0099	YES
4	RPSAP9	RPSAP9	RPSAP9	2593	0.15	-0.028	YES
5	RPL18A	RPL18A	RPL18A	2740	0.14	-0.021	YES
6	RPSA	RPSA	RPSA	2761	0.14	-0.0072	YES
7	MAGOH	MAGOH	MAGOH	2881	0.14	0.00081	YES
8	RPL39	RPL39	RPL39	3005	0.13	0.0081	YES
9	RPLP2	RPLP2	RPLP2	3057	0.13	0.019	YES
10	RPL14	RPL14	RPL14	3291	0.12	0.019	YES
11	RPL24	RPL24	RPL24	3293	0.12	0.032	YES
12	RPS7	RPS7	RPS7	3362	0.12	0.041	YES
13	RPL28	RPL28	RPL28	3441	0.12	0.049	YES
14	RPL13	RPL13	RPL13	3474	0.11	0.059	YES
15	RPL29	RPL29	RPL29	3483	0.11	0.071	YES
16	RPS8	RPS8	RPS8	3513	0.11	0.082	YES
17	RPL34	RPL34	RPL34	3516	0.11	0.094	YES
18	RPL32	RPL32	RPL32	3527	0.11	0.1	YES
19	RPS10	RPS10	RPS10	3547	0.11	0.12	YES
20	RPL27A	RPL27A	RPL27A	3560	0.11	0.13	YES
21	RPS9	RPS9	RPS9	3576	0.11	0.14	YES
22	RPL18	RPL18	RPL18	3636	0.11	0.15	YES
23	RPS24	RPS24	RPS24	3647	0.11	0.16	YES
24	FAU	FAU	FAU	3658	0.11	0.17	YES
25	RPL23A	RPL23A	RPL23A	3703	0.11	0.18	YES
26	UBA52	UBA52	UBA52	3734	0.1	0.19	YES
27	RPL35A	RPL35A	RPL35A	3789	0.1	0.2	YES
28	RPL35	RPL35	RPL35	3798	0.1	0.21	YES
29	RPS21	RPS21	RPS21	3807	0.1	0.22	YES
30	RPS13	RPS13	RPS13	3815	0.1	0.23	YES
31	RPS16	RPS16	RPS16	3830	0.1	0.24	YES
32	RPS11	RPS11	RPS11	3833	0.1	0.25	YES
33	RPS19	RPS19	RPS19	3834	0.1	0.26	YES
34	RPS23	RPS23	RPS23	3868	0.1	0.27	YES
35	RPL26	RPL26	RPL26	3981	0.097	0.27	YES
36	RPS29	RPS29	RPS29	3983	0.097	0.28	YES
37	RPL22	RPL22	RPL22	4036	0.096	0.29	YES
38	RPS6	RPS6	RPS6	4046	0.095	0.3	YES
39	RPL37A	RPL37A	RPL37A	4072	0.094	0.31	YES
40	RPL37	RPL37	RPL37	4079	0.094	0.32	YES
41	RPL27	RPL27	RPL27	4121	0.093	0.33	YES
42	RPL31	RPL31	RPL31	4172	0.092	0.33	YES
43	RPS20	RPS20	RPS20	4207	0.091	0.34	YES
44	RPS12	RPS12	RPS12	4230	0.091	0.35	YES
45	RPS15	RPS15	RPS15	4233	0.091	0.36	YES
46	RPS3A	RPS3A	RPS3A	4238	0.091	0.37	YES
47	RPL11	RPL11	RPL11	4278	0.09	0.38	YES
48	RPS3	RPS3	RPS3	4284	0.089	0.38	YES
49	RPL5	RPL5	RPL5	4307	0.089	0.39	YES
50	RPS17	RPS17	RPS17	4330	0.088	0.4	YES
51	RPLP1	RPLP1	RPLP1	4354	0.088	0.41	YES
52	RPS2	RPS2	RPS2	4372	0.088	0.42	YES
53	RPL26L1	RPL26L1	RPL26L1	4390	0.087	0.43	YES
54	RPL38	RPL38	RPL38	4417	0.086	0.44	YES
55	RPL19	RPL19	RPL19	4454	0.085	0.44	YES
56	RPL36	RPL36	RPL36	4503	0.084	0.45	YES
57	UPF3A	UPF3A	UPF3A	4527	0.083	0.46	YES
58	RPL23	RPL23	RPL23	4531	0.083	0.46	YES
59	RPS5	RPS5	RPS5	4599	0.081	0.47	YES
60	RPS14	RPS14	RPS14	4645	0.08	0.48	YES
61	RPL15	RPL15	RPL15	4724	0.078	0.48	YES
62	RPLP0	RPLP0	RPLP0	4740	0.078	0.49	YES
63	RPL36A	RPL36A	RPL36A	4835	0.075	0.49	YES
64	RPL10A	RPL10A	RPL10A	4854	0.075	0.5	YES
65	RPS27A	RPS27A	RPS27A	4877	0.074	0.5	YES
66	RPL4	RPL4	RPL4	4972	0.072	0.51	YES
67	RPL30	RPL30	RPL30	5001	0.072	0.51	YES
68	RPL6	RPL6	RPL6	5045	0.071	0.52	YES
69	RPL12	RPL12	RPL12	5075	0.07	0.52	YES
70	RPL13A	RPL13A	RPL13A	5082	0.07	0.53	YES
71	RPS25	RPS25	RPS25	5089	0.07	0.54	YES
72	RPS26	RPS26	RPS26	5153	0.068	0.54	YES
73	RPL41	RPL41	RPL41	5234	0.066	0.55	YES
74	RPL7A	RPL7A	RPL7A	5404	0.062	0.54	YES
75	RPS18	RPS18	RPS18	5514	0.059	0.54	YES
76	RNPS1	RNPS1	RNPS1	5631	0.056	0.54	YES
77	RPS15A	RPS15A	RPS15A	5670	0.055	0.55	YES
78	RPL10	RPL10	RPL10	5767	0.053	0.55	YES
79	RPS4Y1	RPS4Y1	RPS4Y1	5796	0.053	0.55	YES
80	RPL7	RPL7	RPL7	5978	0.048	0.55	YES
81	RPS4X	RPS4X	RPS4X	6032	0.047	0.55	YES
82	RPL8	RPL8	RPL8	6043	0.047	0.55	YES
83	PPP2CA	PPP2CA	PPP2CA	6064	0.046	0.56	YES
84	PPP2R1A	PPP2R1A	PPP2R1A	6216	0.044	0.55	NO
85	EIF4A3	EIF4A3	EIF4A3	6317	0.042	0.55	NO
86	RPL17	RPL17	RPL17	6360	0.041	0.55	NO
87	RPL3	RPL3	RPL3	6546	0.037	0.55	NO
88	RPL9	RPL9	RPL9	6567	0.036	0.55	NO
89	NCBP2	NCBP2	NCBP2	7213	0.023	0.52	NO
90	SMG6	SMG6	SMG6	8130	0.0036	0.47	NO
91	CASC3	CASC3	CASC3	8353	-0.0011	0.46	NO
92	RPS27	RPS27	RPS27	8639	-0.0073	0.44	NO
93	RBM8A	RBM8A	RBM8A	8759	-0.01	0.44	NO
94	GSPT2	GSPT2	GSPT2	9158	-0.017	0.42	NO
95	PABPC1	PABPC1	PABPC1	9194	-0.018	0.42	NO
96	SMG5	SMG5	SMG5	9751	-0.03	0.39	NO
97	NCBP1	NCBP1	NCBP1	10071	-0.037	0.37	NO
98	UPF3B	UPF3B	UPF3B	10157	-0.039	0.37	NO
99	SMG7	SMG7	SMG7	10535	-0.047	0.36	NO
100	UPF2	UPF2	UPF2	10892	-0.056	0.34	NO
101	EIF4G1	EIF4G1	EIF4G1	11387	-0.068	0.32	NO
102	PPP2R2A	PPP2R2A	PPP2R2A	11644	-0.075	0.32	NO
103	SMG1	SMG1	SMG1	12054	-0.086	0.3	NO
104	ETF1	ETF1	ETF1	13160	-0.12	0.26	NO
105	FAM153A	FAM153A	FAM153A	15146	-0.23	0.17	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 MRNA SPLICING.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MRNA SPLICING, 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 O GLYCAN BIOSYNTHESIS	28	genes.ES.table	0.61	1.5	0.016	1	0.96	0.46	0.25	0.35	0.83	0.43
KEGG FOCAL ADHESION	195	genes.ES.table	0.52	1.5	0.016	1	0.96	0.45	0.22	0.35	0.94	0.47
KEGG ADHERENS JUNCTION	73	genes.ES.table	0.47	1.5	0.008	1	0.96	0.47	0.23	0.36	0.99	0.5
KEGG ARRHYTHMOGENIC RIGHT VENTRICULAR CARDIOMYOPATHY ARVC	70	genes.ES.table	0.55	1.5	0.015	1	0.97	0.49	0.18	0.4	0.74	0.38
ST G ALPHA I PATHWAY	34	genes.ES.table	0.53	1.5	0.017	1	0.94	0.41	0.28	0.3	1	0.64
ST INTEGRIN SIGNALING PATHWAY	81	genes.ES.table	0.45	1.5	0.028	1	0.97	0.32	0.24	0.24	0.77	0.39
PID ERBB4 PATHWAY	37	genes.ES.table	0.5	1.5	0.01	1	0.96	0.27	0.16	0.23	0.75	0.4
PID WNT NONCANONICAL PATHWAY	32	genes.ES.table	0.59	1.5	0.0078	1	0.94	0.47	0.26	0.35	1	0.7
PID EPHBFWDPATHWAY	40	genes.ES.table	0.53	1.5	0.021	1	0.96	0.45	0.3	0.32	0.87	0.45
PID ARF6 TRAFFICKINGPATHWAY	48	genes.ES.table	0.51	1.5	0.032	1	0.95	0.4	0.23	0.3	1	0.51

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

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	PVRL3	PVRL3	PVRL3	61	1.1	0.14	YES
2	ITGB3	ITGB3	ITGB3	395	0.78	0.22	YES
3	CLDN1	CLDN1	CLDN1	1800	0.48	0.21	YES
4	PDGFB	PDGFB	PDGFB	2227	0.42	0.24	YES
5	MLLT4	MLLT4	MLLT4	2437	0.39	0.28	YES
6	ITGAV	ITGAV	ITGAV	2552	0.38	0.32	YES
7	PDGFRB	PDGFRB	PDGFRB	2701	0.37	0.36	YES
8	PVRL2	PVRL2	PVRL2	2714	0.37	0.41	YES
9	PIK3CA	PIK3CA	PIK3CA	2735	0.36	0.46	YES
10	FARP2	FARP2	FARP2	3128	0.33	0.48	YES
11	PTPRM	PTPRM	PTPRM	3669	0.28	0.49	YES
12	CRK	CRK	CRK	3745	0.28	0.52	YES
13	PTK2	PTK2	PTK2	3868	0.27	0.55	YES
14	CTNNB1	CTNNB1	CTNNB1	4031	0.26	0.58	YES
15	PVRL1	PVRL1	PVRL1	4092	0.26	0.61	YES
16	CDH1	CDH1	CDH1	4105	0.26	0.64	YES
17	CTNNA1	CTNNA1	CTNNA1	4251	0.25	0.66	YES
18	VAV2	VAV2	VAV2	6157	0.15	0.58	NO
19	TLN1	TLN1	TLN1	6977	0.11	0.55	NO
20	RAPGEF1	RAPGEF1	RAPGEF1	7252	0.1	0.55	NO
21	IQGAP1	IQGAP1	IQGAP1	7316	0.098	0.56	NO
22	F11R	F11R	F11R	7612	0.086	0.55	NO
23	PIK3R1	PIK3R1	PIK3R1	8836	0.042	0.49	NO
24	PIP5K1C	PIP5K1C	PIP5K1C	8981	0.036	0.49	NO
25	SRC	SRC	SRC	9127	0.032	0.48	NO
26	PVR	PVR	PVR	9154	0.031	0.49	NO
27	RAC1	RAC1	RAC1	9409	0.023	0.48	NO
28	RAP1A	RAP1A	RAP1A	9624	0.015	0.47	NO
29	CDC42	CDC42	CDC42	9995	0.0024	0.45	NO
30	RAP1B	RAP1B	RAP1B	11868	-0.062	0.35	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 O GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG FOCAL ADHESION

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	GAP43	GAP43	GAP43	719	0.68	0.073	YES
2	FER	FER	FER	1384	0.54	0.13	YES
3	GRIA2	GRIA2	GRIA2	1599	0.5	0.2	YES
4	MAPK8	MAPK8	MAPK8	2100	0.44	0.24	YES
5	PIK3CA	PIK3CA	PIK3CA	2735	0.36	0.27	YES
6	LRP5	LRP5	LRP5	2972	0.34	0.32	YES
7	FGFR1	FGFR1	FGFR1	3574	0.29	0.33	YES
8	CTNND1	CTNND1	CTNND1	3618	0.29	0.38	YES
9	GJA1	GJA1	GJA1	3824	0.27	0.41	YES
10	CTNNB1	CTNNB1	CTNNB1	4031	0.26	0.44	YES
11	CTNNA1	CTNNA1	CTNNA1	4251	0.25	0.47	YES
12	JUP	JUP	JUP	4599	0.22	0.49	YES
13	CDH2	CDH2	CDH2	5333	0.18	0.48	YES
14	PTPN11	PTPN11	PTPN11	5349	0.18	0.51	YES
15	ROCK1	ROCK1	ROCK1	5388	0.18	0.54	YES
16	DAGLA	DAGLA	DAGLA	5883	0.16	0.54	YES
17	GSN	GSN	GSN	6108	0.15	0.55	YES
18	CTTN	CTTN	CTTN	6435	0.14	0.56	YES
19	KIF5B	KIF5B	KIF5B	8197	0.064	0.47	NO
20	PIK3R1	PIK3R1	PIK3R1	8836	0.042	0.44	NO
21	PIP5K1C	PIP5K1C	PIP5K1C	8981	0.036	0.44	NO
22	RAC1	RAC1	RAC1	9409	0.023	0.42	NO
23	PTPN1	PTPN1	PTPN1	9935	0.0043	0.39	NO
24	DCTN1	DCTN1	DCTN1	9972	0.0032	0.39	NO
25	CDC42	CDC42	CDC42	9995	0.0024	0.39	NO
26	RHOA	RHOA	RHOA	10086	-0.00067	0.38	NO
27	CAMK2G	CAMK2G	CAMK2G	10476	-0.014	0.37	NO
28	AXIN1	AXIN1	AXIN1	10992	-0.032	0.34	NO
29	MAPRE1	MAPRE1	MAPRE1	11507	-0.049	0.32	NO
30	MYL2	MYL2	MYL2	11596	-0.052	0.33	NO
31	PLCG1	PLCG1	PLCG1	11732	-0.057	0.33	NO
32	CNR1	CNR1	CNR1	12540	-0.089	0.3	NO
33	DAGLB	DAGLB	DAGLB	12573	-0.09	0.31	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 FOCAL ADHESION.

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

genes ES table in pathway: KEGG ADHERENS JUNCTION

Table 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	IRS2	IRS2	IRS2	1356	0.55	0.024	YES
2	PRKD1	PRKD1	PRKD1	2239	0.42	0.051	YES
3	PIK3CA	PIK3CA	PIK3CA	2735	0.36	0.09	YES
4	IGF1R	IGF1R	IGF1R	3074	0.33	0.13	YES
5	PDPK1	PDPK1	PDPK1	3336	0.31	0.17	YES
6	GRB10	GRB10	GRB10	3338	0.31	0.23	YES
7	IRS1	IRS1	IRS1	3622	0.29	0.27	YES
8	CRK	CRK	CRK	3745	0.28	0.31	YES
9	BCAR1	BCAR1	BCAR1	3777	0.28	0.36	YES
10	PTK2	PTK2	PTK2	3868	0.27	0.4	YES
11	NCK2	NCK2	NCK2	4842	0.21	0.39	YES
12	IGF1	IGF1	IGF1	5072	0.2	0.41	YES
13	PTPN11	PTPN11	PTPN11	5349	0.18	0.43	YES
14	PXN	PXN	PXN	5431	0.18	0.46	YES
15	PRKCD	PRKCD	PRKCD	5466	0.18	0.48	YES
16	SOS1	SOS1	SOS1	5841	0.16	0.49	YES
17	CRKL	CRKL	CRKL	5962	0.16	0.52	YES
18	RPS6KB1	RPS6KB1	RPS6KB1	6826	0.12	0.49	NO
19	SHC1	SHC1	SHC1	7239	0.1	0.48	NO
20	PIK3R1	PIK3R1	PIK3R1	8836	0.042	0.4	NO
21	RAF1	RAF1	RAF1	9465	0.02	0.37	NO
22	PTPN1	PTPN1	PTPN1	9935	0.0043	0.35	NO
23	PRKCZ	PRKCZ	PRKCZ	10237	-0.0063	0.33	NO
24	GRB2	GRB2	GRB2	10411	-0.012	0.33	NO
25	YWHAE	YWHAE	YWHAE	10675	-0.021	0.32	NO
26	YWHAZ	YWHAZ	YWHAZ	10684	-0.022	0.32	NO
27	AKT1	AKT1	AKT1	12632	-0.092	0.23	NO
28	HRAS	HRAS	HRAS	13199	-0.12	0.22	NO
29	GNB2L1	GNB2L1	GNB2L1	13307	-0.12	0.24	NO
30	BAD	BAD	BAD	15128	-0.21	0.17	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 ADHERENS JUNCTION.

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

genes ES table in pathway: KEGG ARRHYTHMOGENIC RIGHT VENTRICULAR CARDIOMYOPATHY ARVC

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	UNC5C	UNC5C	UNC5C	1039	0.61	0.034	YES
2	NTN1	NTN1	NTN1	1068	0.6	0.12	YES
3	MAP1B	MAP1B	MAP1B	1652	0.5	0.16	YES
4	DOCK1	DOCK1	DOCK1	1883	0.46	0.22	YES
5	UNC5B	UNC5B	UNC5B	2132	0.43	0.27	YES
6	TRIO	TRIO	TRIO	2235	0.42	0.33	YES
7	PIK3CA	PIK3CA	PIK3CA	2735	0.36	0.36	YES
8	MYO10	MYO10	MYO10	2831	0.35	0.4	YES
9	YES1	YES1	YES1	3162	0.33	0.43	YES
10	WASL	WASL	WASL	3694	0.28	0.45	YES
11	BCAR1	BCAR1	BCAR1	3777	0.28	0.48	YES
12	CAMK2A	CAMK2A	CAMK2A	3832	0.27	0.52	YES
13	PTK2	PTK2	PTK2	3868	0.27	0.56	YES
14	MAPK1	MAPK1	MAPK1	5070	0.2	0.52	NO
15	MAP2K1	MAP2K1	MAP2K1	7569	0.087	0.4	NO
16	MAPK3	MAPK3	MAPK3	7893	0.075	0.39	NO
17	PAK1	PAK1	PAK1	8161	0.065	0.39	NO
18	DAPK1	DAPK1	DAPK1	8447	0.056	0.38	NO
19	PIK3R1	PIK3R1	PIK3R1	8836	0.042	0.36	NO
20	NCK1	NCK1	NCK1	9122	0.033	0.36	NO
21	SRC	SRC	SRC	9127	0.032	0.36	NO
22	PITPNA	PITPNA	PITPNA	9368	0.024	0.35	NO
23	RAC1	RAC1	RAC1	9409	0.023	0.35	NO
24	CDC42	CDC42	CDC42	9995	0.0024	0.32	NO
25	RHOA	RHOA	RHOA	10086	-0.00067	0.31	NO
26	DCC	DCC	DCC	10851	-0.027	0.28	NO
27	ELMO1	ELMO1	ELMO1	11023	-0.033	0.27	NO
28	PLCG1	PLCG1	PLCG1	11732	-0.057	0.24	NO
29	UNC5A	UNC5A	UNC5A	11831	-0.061	0.25	NO
30	MAP2K2	MAP2K2	MAP2K2	13403	-0.12	0.18	NO
31	FYN	FYN	FYN	14831	-0.19	0.13	NO
32	AGAP2	AGAP2	AGAP2	17164	-0.41	0.061	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 ARRHYTHMOGENIC RIGHT VENTRICULAR CARDIOMYOPATHY ARVC.

Figure S48. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ARRHYTHMOGENIC RIGHT VENTRICULAR CARDIOMYOPATHY ARVC, 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: ST G ALPHA I 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	NFATC2	NFATC2	NFATC2	71	1	0.13	YES
2	FZD7	FZD7	FZD7	259	0.85	0.22	YES
3	WNT5A	WNT5A	WNT5A	807	0.66	0.27	YES
4	DAAM1	DAAM1	DAAM1	989	0.62	0.34	YES
5	ROR2	ROR2	ROR2	1007	0.62	0.42	YES
6	MAPK8	MAPK8	MAPK8	2100	0.44	0.41	YES
7	FZD5	FZD5	FZD5	2226	0.42	0.46	YES
8	FZD2	FZD2	FZD2	2633	0.38	0.48	YES
9	YES1	YES1	YES1	3162	0.33	0.49	YES
10	FZD6	FZD6	FZD6	3521	0.3	0.51	YES
11	CHD7	CHD7	CHD7	3545	0.29	0.54	YES
12	CAMK2A	CAMK2A	CAMK2A	3832	0.27	0.56	YES
13	MAPK10	MAPK10	MAPK10	4299	0.24	0.57	YES
14	DVL3	DVL3	DVL3	4725	0.22	0.57	YES
15	CTHRC1	CTHRC1	CTHRC1	4790	0.21	0.59	YES
16	ROCK1	ROCK1	ROCK1	5388	0.18	0.58	NO
17	MAP3K7	MAP3K7	MAP3K7	5618	0.17	0.59	NO
18	TAB2	TAB2	TAB2	6335	0.14	0.57	NO
19	FLNA	FLNA	FLNA	6430	0.14	0.58	NO
20	NLK	NLK	NLK	9050	0.035	0.44	NO
21	RAC1	RAC1	RAC1	9409	0.023	0.42	NO
22	TAB1	TAB1	TAB1	9640	0.014	0.41	NO
23	DVL1	DVL1	DVL1	9914	0.0052	0.4	NO
24	MAPK9	MAPK9	MAPK9	9957	0.0038	0.4	NO
25	CDC42	CDC42	CDC42	9995	0.0024	0.4	NO
26	CSNK1A1	CSNK1A1	CSNK1A1	10075	-0.00027	0.39	NO
27	RHOA	RHOA	RHOA	10086	-0.00067	0.39	NO
28	PRKCZ	PRKCZ	PRKCZ	10237	-0.0063	0.38	NO
29	DVL2	DVL2	DVL2	10457	-0.014	0.37	NO
30	SETDB1	SETDB1	SETDB1	11200	-0.039	0.34	NO
31	PPARG	PPARG	PPARG	14713	-0.19	0.17	NO
32	ARRB2	ARRB2	ARRB2	15276	-0.22	0.16	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: ST G ALPHA I PATHWAY.

Figure S50. Get High-res Image For the top 5 core enriched genes in the pathway: ST G ALPHA I 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: ST INTEGRIN 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	RGS20	RGS20	RGS20	355	0.8	0.091	YES
2	KCNJ5	KCNJ5	KCNJ5	555	0.72	0.18	YES
3	EGFR	EGFR	EGFR	702	0.68	0.26	YES
4	DRD2	DRD2	DRD2	1540	0.51	0.29	YES
5	PLCB1	PLCB1	PLCB1	1641	0.5	0.35	YES
6	ITPR1	ITPR1	ITPR1	2331	0.41	0.37	YES
7	CFB	CFB	CFB	2352	0.4	0.43	YES
8	DAG1	DAG1	DAG1	2778	0.36	0.45	YES
9	ASAH1	ASAH1	ASAH1	2932	0.34	0.49	YES
10	ITPR3	ITPR3	ITPR3	3716	0.28	0.49	YES
11	BRAF	BRAF	BRAF	4425	0.24	0.48	YES
12	ITPKA	ITPKA	ITPKA	4464	0.23	0.51	YES
13	SOS2	SOS2	SOS2	4919	0.21	0.51	YES
14	MAPK1	MAPK1	MAPK1	5070	0.2	0.53	YES
15	SOS1	SOS1	SOS1	5841	0.16	0.51	NO
16	STAT3	STAT3	STAT3	5939	0.16	0.53	NO
17	EPHB2	EPHB2	EPHB2	6624	0.13	0.51	NO
18	SHC1	SHC1	SHC1	7239	0.1	0.49	NO
19	KCNJ9	KCNJ9	KCNJ9	7389	0.095	0.5	NO
20	AKT2	AKT2	AKT2	8521	0.053	0.44	NO
21	AKT3	AKT3	AKT3	8692	0.047	0.44	NO
22	PIK3CB	PIK3CB	PIK3CB	8986	0.036	0.43	NO
23	SRC	SRC	SRC	9127	0.032	0.42	NO
24	RAF1	RAF1	RAF1	9465	0.02	0.41	NO
25	ITPR2	ITPR2	ITPR2	9981	0.0028	0.38	NO
26	PLCB3	PLCB3	PLCB3	10006	0.002	0.38	NO
27	GRB2	GRB2	GRB2	10411	-0.012	0.36	NO
28	ITPKB	ITPKB	ITPKB	11226	-0.04	0.32	NO
29	PLCB2	PLCB2	PLCB2	11632	-0.053	0.3	NO
30	PI3	PI3	PI3	11753	-0.058	0.3	NO
31	PLCB4	PLCB4	PLCB4	12404	-0.082	0.28	NO
32	AKT1	AKT1	AKT1	12632	-0.092	0.28	NO
33	PITX2	PITX2	PITX2	12825	-0.1	0.28	NO
34	TERF2IP	TERF2IP	TERF2IP	12997	-0.11	0.29	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: ST INTEGRIN SIGNALING PATHWAY.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: ST INTEGRIN 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: PID ERBB4 PATHWAY

Table S27. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PTPN21	PTPN21	PTPN21	246	0.86	0.059	YES
2	ROCK2	ROCK2	ROCK2	290	0.84	0.13	YES
3	DOCK1	DOCK1	DOCK1	1883	0.46	0.078	YES
4	GRB7	GRB7	GRB7	2013	0.45	0.11	YES
5	MAPK8	MAPK8	MAPK8	2100	0.44	0.14	YES
6	MMP14	MMP14	MMP14	2217	0.42	0.17	YES
7	RGNEF	RGNEF	RGNEF	2344	0.41	0.2	YES
8	ITGAV	ITGAV	ITGAV	2552	0.38	0.22	YES
9	PIK3CA	PIK3CA	PIK3CA	2735	0.36	0.24	YES
10	ITGB5	ITGB5	ITGB5	2781	0.36	0.26	YES
11	VCL	VCL	VCL	2924	0.35	0.29	YES
12	KLF8	KLF8	KLF8	2927	0.35	0.32	YES
13	YES1	YES1	YES1	3162	0.33	0.33	YES
14	ASAP1	ASAP1	ASAP1	3282	0.32	0.35	YES
15	CCND1	CCND1	CCND1	3398	0.31	0.37	YES
16	ARHGEF11	ARHGEF11	ARHGEF11	3512	0.3	0.39	YES
17	ITGB1	ITGB1	ITGB1	3620	0.29	0.41	YES
18	WASL	WASL	WASL	3694	0.28	0.42	YES
19	CRK	CRK	CRK	3745	0.28	0.45	YES
20	BCAR1	BCAR1	BCAR1	3777	0.28	0.47	YES
21	PTK2	PTK2	PTK2	3868	0.27	0.48	YES
22	CAPN2	CAPN2	CAPN2	3981	0.26	0.5	YES
23	RASA1	RASA1	RASA1	4340	0.24	0.5	YES
24	BRAF	BRAF	BRAF	4425	0.24	0.52	YES
25	NCK2	NCK2	NCK2	4842	0.21	0.51	NO
26	MAPK1	MAPK1	MAPK1	5070	0.2	0.52	NO
27	PXN	PXN	PXN	5431	0.18	0.51	NO
28	SOS1	SOS1	SOS1	5841	0.16	0.5	NO
29	RRAS	RRAS	RRAS	6066	0.15	0.5	NO
30	MAP2K4	MAP2K4	MAP2K4	6236	0.14	0.5	NO
31	ACTN1	ACTN1	ACTN1	6936	0.11	0.48	NO
32	TLN1	TLN1	TLN1	6977	0.11	0.48	NO
33	RAPGEF1	RAPGEF1	RAPGEF1	7252	0.1	0.48	NO
34	BMX	BMX	BMX	7344	0.097	0.48	NO
35	MAP2K1	MAP2K1	MAP2K1	7569	0.087	0.48	NO
36	JUN	JUN	JUN	7738	0.081	0.47	NO
37	PAK1	PAK1	PAK1	8161	0.065	0.46	NO
38	PIK3R1	PIK3R1	PIK3R1	8836	0.042	0.42	NO
39	NCK1	NCK1	NCK1	9122	0.033	0.41	NO
40	SRC	SRC	SRC	9127	0.032	0.41	NO
41	MAPK8IP3	MAPK8IP3	MAPK8IP3	9355	0.024	0.4	NO
42	RAC1	RAC1	RAC1	9409	0.023	0.4	NO
43	RAF1	RAF1	RAF1	9465	0.02	0.4	NO
44	ITGA5	ITGA5	ITGA5	9567	0.017	0.39	NO
45	RAP1A	RAP1A	RAP1A	9624	0.015	0.39	NO
46	MAPK9	MAPK9	MAPK9	9957	0.0038	0.37	NO
47	RHOA	RHOA	RHOA	10086	-0.00067	0.37	NO
48	SH3GL1	SH3GL1	SH3GL1	10159	-0.003	0.36	NO
49	GIT2	GIT2	GIT2	10242	-0.0064	0.36	NO
50	GRB2	GRB2	GRB2	10411	-0.012	0.35	NO
51	ELMO1	ELMO1	ELMO1	11023	-0.033	0.32	NO
52	ETS1	ETS1	ETS1	11135	-0.037	0.32	NO
53	PLCG1	PLCG1	PLCG1	11732	-0.057	0.29	NO
54	RAP1B	RAP1B	RAP1B	11868	-0.062	0.29	NO
55	ARHGEF7	ARHGEF7	ARHGEF7	12814	-0.099	0.24	NO
56	ARHGAP26	ARHGAP26	ARHGAP26	13350	-0.12	0.22	NO
57	FYN	FYN	FYN	14831	-0.19	0.16	NO
58	ACTA1	ACTA1	ACTA1	16840	-0.36	0.079	NO

Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ERBB4 PATHWAY.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: PID ERBB4 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID WNT NONCANONICAL PATHWAY

Table 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	ITGA9	ITGA9	ITGA9	92	1	0.11	YES
2	ITGB3	ITGB3	ITGB3	395	0.78	0.19	YES
3	RPS6KA6	RPS6KA6	RPS6KA6	551	0.72	0.26	YES
4	EGFR	EGFR	EGFR	702	0.68	0.33	YES
5	NRP1	NRP1	NRP1	778	0.66	0.4	YES
6	ITGA2B	ITGA2B	ITGA2B	939	0.63	0.47	YES
7	RPS6KA5	RPS6KA5	RPS6KA5	2361	0.4	0.44	YES
8	ITGAV	ITGAV	ITGAV	2552	0.38	0.47	YES
9	RPS6KA2	RPS6KA2	RPS6KA2	3260	0.32	0.47	YES
10	FGFR1	FGFR1	FGFR1	3574	0.29	0.48	YES
11	ITGB1	ITGB1	ITGB1	3620	0.29	0.51	YES
12	MAPK1	MAPK1	MAPK1	5070	0.2	0.46	NO
13	NCAM1	NCAM1	NCAM1	5344	0.18	0.46	NO
14	CLTC	CLTC	CLTC	6850	0.12	0.4	NO
15	MAP2K1	MAP2K1	MAP2K1	7569	0.087	0.37	NO
16	RPS6KA3	RPS6KA3	RPS6KA3	7737	0.081	0.37	NO
17	MAPK3	MAPK3	MAPK3	7893	0.075	0.37	NO
18	PAK1	PAK1	PAK1	8161	0.065	0.36	NO
19	AP2A1	AP2A1	AP2A1	8240	0.062	0.36	NO
20	CSNK2A2	CSNK2A2	CSNK2A2	8486	0.054	0.36	NO
21	CSNK2A1	CSNK2A1	CSNK2A1	8545	0.052	0.36	NO
22	AP2B1	AP2B1	AP2B1	8860	0.041	0.34	NO
23	RAC1	RAC1	RAC1	9409	0.023	0.32	NO
24	ITGA5	ITGA5	ITGA5	9567	0.017	0.31	NO
25	AP2M1	AP2M1	AP2M1	10549	-0.017	0.26	NO
26	AP2A2	AP2A2	AP2A2	11032	-0.033	0.24	NO
27	RPS6KA4	RPS6KA4	RPS6KA4	11509	-0.049	0.22	NO
28	CLTA	CLTA	CLTA	12727	-0.096	0.16	NO
29	MAP2K2	MAP2K2	MAP2K2	13403	-0.12	0.14	NO
30	L1CAM	L1CAM	L1CAM	13557	-0.13	0.14	NO
31	CSNK2B	CSNK2B	CSNK2B	13707	-0.14	0.15	NO
32	RPS6KA1	RPS6KA1	RPS6KA1	14045	-0.15	0.15	NO
33	AP2S1	AP2S1	AP2S1	15885	-0.26	0.08	NO
34	SH3GL2	SH3GL2	SH3GL2	17393	-0.44	0.049	NO

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

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

genes ES table in pathway: PID EPHBFWDPATHWAY

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	GALNT3	GALNT3	GALNT3	117	0.98	0.021	YES
2	B3GNT7	B3GNT7	B3GNT7	470	0.75	0.022	YES
3	GALNT13	GALNT13	GALNT13	527	0.73	0.039	YES
4	MUC5B	MUC5B	MUC5B	538	0.73	0.059	YES
5	MGAT5	MGAT5	MGAT5	566	0.72	0.077	YES
6	GCNT1	GCNT1	GCNT1	683	0.68	0.09	YES
7	PROS1	PROS1	PROS1	753	0.67	0.1	YES
8	GALNT5	GALNT5	GALNT5	811	0.66	0.12	YES
9	SEMA6D	SEMA6D	SEMA6D	869	0.64	0.13	YES
10	MUC2	MUC2	MUC2	871	0.64	0.15	YES
11	UGGT2	UGGT2	UGGT2	906	0.64	0.17	YES
12	GALNTL6	GALNTL6	GALNTL6	1017	0.61	0.18	YES
13	ARSJ	ARSJ	ARSJ	1106	0.59	0.19	YES
14	MGAT3	MGAT3	MGAT3	1118	0.59	0.21	YES
15	ARSI	ARSI	ARSI	1306	0.56	0.21	YES
16	TUSC3	TUSC3	TUSC3	1336	0.55	0.22	YES
17	WBSCR17	WBSCR17	WBSCR17	1561	0.51	0.23	YES
18	ST6GALNAC3	ST6GALNAC3	ST6GALNAC3	1566	0.51	0.24	YES
19	GFPT2	GFPT2	GFPT2	1714	0.49	0.24	YES
20	PGM3	PGM3	PGM3	1770	0.48	0.26	YES
21	B3GNT5	B3GNT5	B3GNT5	1845	0.47	0.26	YES
22	PGAP1	PGAP1	PGAP1	2006	0.45	0.27	YES
23	GALNT8	GALNT8	GALNT8	2053	0.44	0.28	YES
24	GALNTL2	GALNTL2	GALNTL2	2111	0.44	0.29	YES
25	MAN2A1	MAN2A1	MAN2A1	2147	0.43	0.3	YES
26	SEC24D	SEC24D	SEC24D	2160	0.43	0.31	YES
27	MAN1A2	MAN1A2	MAN1A2	2269	0.41	0.31	YES
28	MANEA	MANEA	MANEA	2341	0.41	0.32	YES
29	ARSE	ARSE	ARSE	2408	0.4	0.33	YES
30	B4GALT4	B4GALT4	B4GALT4	2645	0.38	0.32	YES
31	B3GNT9	B3GNT9	B3GNT9	2760	0.36	0.33	YES
32	MAN1A1	MAN1A1	MAN1A1	2789	0.36	0.34	YES
33	F7	F7	F7	2860	0.35	0.34	YES
34	ST6GALNAC2	ST6GALNAC2	ST6GALNAC2	2918	0.35	0.35	YES
35	ALG10B	ALG10B	ALG10B	3005	0.34	0.35	YES
36	ARSB	ARSB	ARSB	3094	0.33	0.36	YES
37	MUC15	MUC15	MUC15	3125	0.33	0.37	YES
38	MUC4	MUC4	MUC4	3236	0.32	0.37	YES
39	MAN1C1	MAN1C1	MAN1C1	3329	0.31	0.37	YES
40	ST8SIA6	ST8SIA6	ST8SIA6	3371	0.31	0.38	YES
41	MCFD2	MCFD2	MCFD2	3391	0.31	0.39	YES
42	B4GALT5	B4GALT5	B4GALT5	3430	0.3	0.39	YES
43	GALNT9	GALNT9	GALNT9	3583	0.29	0.39	YES
44	GGCX	GGCX	GGCX	3815	0.27	0.39	YES
45	B3GNT3	B3GNT3	B3GNT3	3963	0.26	0.39	YES
46	SUMF1	SUMF1	SUMF1	4033	0.26	0.39	YES
47	LMAN1	LMAN1	LMAN1	4158	0.25	0.39	YES
48	ALG10	ALG10	ALG10	4212	0.25	0.39	YES
49	GALNT10	GALNT10	GALNT10	4293	0.24	0.4	YES
50	PIGK	PIGK	PIGK	4442	0.23	0.39	NO
51	GALNTL4	GALNTL4	GALNTL4	4627	0.22	0.39	NO
52	ARSK	ARSK	ARSK	4930	0.21	0.38	NO
53	EIF5A2	EIF5A2	EIF5A2	5197	0.19	0.37	NO
54	GALNT11	GALNT11	GALNT11	5332	0.18	0.37	NO
55	ARSG	ARSG	ARSG	5571	0.17	0.36	NO
56	EDEM3	EDEM3	EDEM3	5641	0.17	0.36	NO
57	SEC31A	SEC31A	SEC31A	5689	0.17	0.36	NO
58	SEC23A	SEC23A	SEC23A	5696	0.17	0.37	NO
59	CANX	CANX	CANX	5736	0.17	0.37	NO
60	MUC6	MUC6	MUC6	5779	0.16	0.37	NO
61	PIGN	PIGN	PIGN	5830	0.16	0.37	NO
62	GALNTL1	GALNTL1	GALNTL1	5902	0.16	0.37	NO
63	MUC13	MUC13	MUC13	6052	0.15	0.37	NO
64	SEC24B	SEC24B	SEC24B	6379	0.14	0.36	NO
65	ALG2	ALG2	ALG2	6385	0.14	0.36	NO
66	B4GALT1	B4GALT1	B4GALT1	6612	0.13	0.35	NO
67	STT3A	STT3A	STT3A	6651	0.13	0.35	NO
68	FURIN	FURIN	FURIN	6681	0.12	0.35	NO
69	GANAB	GANAB	GANAB	6914	0.11	0.34	NO
70	MLEC	MLEC	MLEC	7298	0.099	0.32	NO
71	PIGV	PIGV	PIGV	7330	0.097	0.33	NO
72	PIGT	PIGT	PIGT	7335	0.097	0.33	NO
73	PIGO	PIGO	PIGO	7354	0.097	0.33	NO
74	GALNT14	GALNT14	GALNT14	7608	0.086	0.32	NO
75	PDIA3	PDIA3	PDIA3	7744	0.081	0.31	NO
76	ALG13	ALG13	ALG13	7946	0.073	0.3	NO
77	ST3GAL3	ST3GAL3	ST3GAL3	7955	0.072	0.31	NO
78	ALG11	ALG11	ALG11	8024	0.07	0.3	NO
79	RPN2	RPN2	RPN2	8051	0.069	0.3	NO
80	B3GNT2	B3GNT2	B3GNT2	8169	0.065	0.3	NO
81	GALNT1	GALNT1	GALNT1	8212	0.063	0.3	NO
82	GNPNAT1	GNPNAT1	GNPNAT1	8242	0.062	0.3	NO
83	PIGL	PIGL	PIGL	8310	0.06	0.3	NO
84	PIGG	PIGG	PIGG	8394	0.058	0.29	NO
85	UGGT1	UGGT1	UGGT1	8473	0.055	0.29	NO
86	DDOST	DDOST	DDOST	8718	0.046	0.28	NO
87	MGAT4A	MGAT4A	MGAT4A	8820	0.042	0.28	NO
88	GCNT3	GCNT3	GCNT3	8874	0.04	0.27	NO
89	MGAT4B	MGAT4B	MGAT4B	8961	0.037	0.27	NO
90	F2	F2	F2	9093	0.033	0.26	NO
91	PIGF	PIGF	PIGF	9115	0.033	0.26	NO
92	ALG14	ALG14	ALG14	9177	0.03	0.26	NO
93	C1GALT1	C1GALT1	C1GALT1	9201	0.03	0.26	NO
94	PRKCSH	PRKCSH	PRKCSH	9233	0.029	0.26	NO
95	CALR	CALR	CALR	9252	0.028	0.26	NO
96	C1GALT1C1	C1GALT1C1	C1GALT1C1	9297	0.026	0.26	NO
97	STS	STS	STS	9353	0.024	0.26	NO
98	DOLK	DOLK	DOLK	9417	0.022	0.25	NO
99	MAN1B1	MAN1B1	MAN1B1	9429	0.022	0.25	NO
100	PIGM	PIGM	PIGM	9536	0.018	0.25	NO
101	SEC24C	SEC24C	SEC24C	9667	0.013	0.24	NO
102	ST3GAL2	ST3GAL2	ST3GAL2	9678	0.013	0.24	NO
103	DPAGT1	DPAGT1	DPAGT1	9685	0.012	0.24	NO
104	MGAT2	MGAT2	MGAT2	9730	0.011	0.24	NO
105	ALG1	ALG1	ALG1	9813	0.0079	0.23	NO
106	PIGS	PIGS	PIGS	9844	0.0068	0.23	NO
107	ALG9	ALG9	ALG9	9852	0.0067	0.23	NO
108	ST6GALNAC4	ST6GALNAC4	ST6GALNAC4	9885	0.006	0.23	NO
109	ST8SIA2	ST8SIA2	ST8SIA2	9933	0.0043	0.23	NO
110	PIGA	PIGA	PIGA	9949	0.0039	0.23	NO
111	DPM1	DPM1	DPM1	9975	0.003	0.22	NO
112	MGAT1	MGAT1	MGAT1	9993	0.0025	0.22	NO
113	GCNT4	GCNT4	GCNT4	10004	0.0021	0.22	NO
114	RPN1	RPN1	RPN1	10155	-0.0028	0.22	NO
115	ALG8	ALG8	ALG8	10281	-0.008	0.21	NO
116	GALNT2	GALNT2	GALNT2	10405	-0.012	0.2	NO
117	GALNT7	GALNT7	GALNT7	10444	-0.013	0.2	NO
118	B4GALT2	B4GALT2	B4GALT2	10497	-0.015	0.2	NO
119	FUT8	FUT8	FUT8	10600	-0.019	0.19	NO
120	PLAUR	PLAUR	PLAUR	10770	-0.024	0.18	NO
121	PIGW	PIGW	PIGW	10788	-0.025	0.18	NO
122	PIGB	PIGB	PIGB	10825	-0.026	0.18	NO
123	RFT1	RFT1	RFT1	10899	-0.029	0.18	NO
124	B4GALT6	B4GALT6	B4GALT6	10989	-0.032	0.18	NO
125	ALG12	ALG12	ALG12	11050	-0.034	0.17	NO
126	ALG6	ALG6	ALG6	11110	-0.036	0.17	NO
127	GALNT12	GALNT12	GALNT12	11260	-0.041	0.16	NO
128	SUMF2	SUMF2	SUMF2	11398	-0.045	0.16	NO
129	SAR1B	SAR1B	SAR1B	11543	-0.05	0.15	NO
130	MOGS	MOGS	MOGS	11563	-0.051	0.15	NO
131	PIGH	PIGH	PIGH	11564	-0.051	0.15	NO
132	PIGP	PIGP	PIGP	12047	-0.069	0.13	NO
133	PIGQ	PIGQ	PIGQ	12089	-0.071	0.13	NO
134	GPAA1	GPAA1	GPAA1	12241	-0.076	0.12	NO
135	SEC13	SEC13	SEC13	12323	-0.079	0.12	NO
136	ARSA	ARSA	ARSA	12347	-0.08	0.12	NO
137	MPI	MPI	MPI	12551	-0.089	0.11	NO
138	B4GALT3	B4GALT3	B4GALT3	12606	-0.091	0.11	NO
139	PIGC	PIGC	PIGC	12649	-0.093	0.11	NO
140	DOLPP1	DOLPP1	DOLPP1	12676	-0.094	0.11	NO
141	ALG5	ALG5	ALG5	12688	-0.094	0.12	NO
142	PIGU	PIGU	PIGU	12732	-0.096	0.12	NO
143	ST6GAL1	ST6GAL1	ST6GAL1	12958	-0.1	0.1	NO
144	VKORC1	VKORC1	VKORC1	12990	-0.11	0.11	NO
145	B3GNT4	B3GNT4	B3GNT4	13353	-0.12	0.09	NO
146	EDEM2	EDEM2	EDEM2	13589	-0.13	0.081	NO
147	PMM1	PMM1	PMM1	13835	-0.14	0.071	NO
148	DAD1	DAD1	DAD1	13847	-0.14	0.074	NO
149	PIGX	PIGX	PIGX	13883	-0.14	0.076	NO
150	EDEM1	EDEM1	EDEM1	13936	-0.15	0.078	NO
151	PREB	PREB	PREB	14148	-0.16	0.07	NO
152	MUC16	MUC16	MUC16	14269	-0.16	0.068	NO
153	ST3GAL1	ST3GAL1	ST3GAL1	14392	-0.17	0.066	NO
154	B3GNTL1	B3GNTL1	B3GNTL1	14781	-0.19	0.05	NO
155	DPM2	DPM2	DPM2	14811	-0.19	0.054	NO
156	ALG3	ALG3	ALG3	14934	-0.2	0.052	NO
157	DHPS	DHPS	DHPS	14941	-0.2	0.058	NO
158	GMPPB	GMPPB	GMPPB	15012	-0.2	0.059	NO
159	PMM2	PMM2	PMM2	15110	-0.21	0.06	NO
160	GMPPA	GMPPA	GMPPA	15156	-0.21	0.063	NO
161	GALNT6	GALNT6	GALNT6	15299	-0.22	0.061	NO
162	EIF5A	EIF5A	EIF5A	15533	-0.23	0.055	NO
163	DOHH	DOHH	DOHH	15804	-0.25	0.047	NO
164	PROZ	PROZ	PROZ	15812	-0.25	0.054	NO
165	B3GNT8	B3GNT8	B3GNT8	15978	-0.27	0.052	NO
166	MUC12	MUC12	MUC12	16762	-0.34	0.018	NO
167	DPM3	DPM3	DPM3	16947	-0.37	0.018	NO
168	MGAT4C	MGAT4C	MGAT4C	17340	-0.44	0.0086	NO
169	F10	F10	F10	17581	-0.49	0.0089	NO
170	ARSF	ARSF	ARSF	17700	-0.52	0.017	NO
171	PROC	PROC	PROC	17825	-0.56	0.025	NO

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

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: PID EPHBFWDPATHWAY, 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 ARF6 TRAFFICKINGPATHWAY

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	SLIT2	SLIT2	SLIT2	99	1	0.094	YES
2	NTN4	NTN4	NTN4	459	0.76	0.15	YES
3	RGMB	RGMB	RGMB	998	0.62	0.18	YES
4	UNC5C	UNC5C	UNC5C	1039	0.61	0.24	YES
5	NTN1	NTN1	NTN1	1068	0.6	0.3	YES
6	UNC5D	UNC5D	UNC5D	1644	0.5	0.31	YES
7	ROBO1	ROBO1	ROBO1	1857	0.47	0.35	YES
8	DOCK1	DOCK1	DOCK1	1883	0.46	0.39	YES
9	NEO1	NEO1	NEO1	2092	0.44	0.42	YES
10	UNC5B	UNC5B	UNC5B	2132	0.43	0.47	YES
11	TRIO	TRIO	TRIO	2235	0.42	0.5	YES
12	MYO10	MYO10	MYO10	2831	0.35	0.5	YES
13	TRPC6	TRPC6	TRPC6	3052	0.34	0.52	YES
14	TRPC3	TRPC3	TRPC3	3578	0.29	0.52	YES
15	WASL	WASL	WASL	3694	0.28	0.55	YES
16	PTK2	PTK2	PTK2	3868	0.27	0.56	YES
17	ABLIM1	ABLIM1	ABLIM1	3950	0.26	0.59	YES
18	SLIT3	SLIT3	SLIT3	5444	0.18	0.52	NO
19	SIAH1	SIAH1	SIAH1	5795	0.16	0.52	NO
20	RGMA	RGMA	RGMA	8127	0.066	0.4	NO
21	TRPC4	TRPC4	TRPC4	8322	0.06	0.39	NO
22	NCK1	NCK1	NCK1	9122	0.033	0.35	NO
23	SRC	SRC	SRC	9127	0.032	0.36	NO
24	PITPNA	PITPNA	PITPNA	9368	0.024	0.34	NO
25	RAC1	RAC1	RAC1	9409	0.023	0.34	NO
26	CDC42	CDC42	CDC42	9995	0.0024	0.31	NO
27	DCC	DCC	DCC	10851	-0.027	0.27	NO
28	EZR	EZR	EZR	11196	-0.039	0.25	NO
29	PLCG1	PLCG1	PLCG1	11732	-0.057	0.23	NO
30	UNC5A	UNC5A	UNC5A	11831	-0.061	0.23	NO
31	SIAH2	SIAH2	SIAH2	11939	-0.065	0.23	NO
32	HFE2	HFE2	HFE2	12418	-0.083	0.21	NO
33	TRPC5	TRPC5	TRPC5	12469	-0.086	0.22	NO
34	SLIT1	SLIT1	SLIT1	12763	-0.098	0.21	NO
35	FYN	FYN	FYN	14831	-0.19	0.12	NO
36	ABLIM3	ABLIM3	ABLIM3	16640	-0.33	0.052	NO
37	PRKCQ	PRKCQ	PRKCQ	17068	-0.39	0.067	NO

Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ARF6 TRAFFICKINGPATHWAY.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: PID ARF6 TRAFFICKINGPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus4 enriched pathways

Table 6. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus4. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG GLYCOLYSIS GLUCONEOGENESIS	57	genes.ES.table	0.52	1.8	0	0.53	0.54	0.42	0.23	0.32	0.2	0.15
KEGG ETHER LIPID METABOLISM	27	genes.ES.table	0.63	1.7	0.0044	0.57	0.67	0.3	0.066	0.28	0.24	0.14
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT	38	genes.ES.table	0.37	1.6	0.037	0.45	0.82	0.24	0.24	0.18	0.24	0.12
KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY	61	genes.ES.table	0.6	1.7	0.027	0.51	0.73	0.39	0.16	0.33	0.25	0.13
KEGG CYTOSOLIC DNA SENSING PATHWAY	43	genes.ES.table	0.65	1.8	0.0042	0.34	0.33	0.49	0.21	0.38	0	0.1
KEGG TYPE I DIABETES MELLITUS	40	genes.ES.table	0.75	1.7	0.014	0.6	0.71	0.88	0.2	0.7	0.27	0.16
KEGG LEISHMANIA INFECTION	70	genes.ES.table	0.64	1.7	0.022	0.58	0.61	0.66	0.21	0.52	0.23	0.15
KEGG AUTOIMMUNE THYROID DISEASE	37	genes.ES.table	0.68	1.7	0.016	0.49	0.74	0.78	0.2	0.63	0.24	0.13
KEGG ALLOGRAFT REJECTION	35	genes.ES.table	0.75	1.7	0.013	0.46	0.74	0.86	0.2	0.69	0.23	0.12
KEGG GRAFT VERSUS HOST DISEASE	37	genes.ES.table	0.76	1.7	0.016	0.44	0.75	0.92	0.2	0.73	0.21	0.12

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	NOS2	NOS2	NOS2	687	0.57	0.05	YES
2	ATP6V1B1	ATP6V1B1	ATP6V1B1	872	0.52	0.12	YES
3	NOS3	NOS3	NOS3	889	0.52	0.2	YES
4	ATP6V1C2	ATP6V1C2	ATP6V1C2	942	0.5	0.27	YES
5	LTF	LTF	LTF	978	0.5	0.35	YES
6	CAMP	CAMP	CAMP	1057	0.48	0.42	YES
7	NCF2	NCF2	NCF2	1355	0.42	0.46	YES
8	ATP6V1E2	ATP6V1E2	ATP6V1E2	1478	0.4	0.52	YES
9	CYBB	CYBB	CYBB	1867	0.34	0.55	YES
10	SLC11A1	SLC11A1	SLC11A1	2561	0.26	0.55	YES
11	NCF4	NCF4	NCF4	2600	0.25	0.59	YES
12	ATP6V0D2	ATP6V0D2	ATP6V0D2	2839	0.23	0.61	YES
13	TCIRG1	TCIRG1	TCIRG1	2974	0.22	0.64	YES
14	CYBA	CYBA	CYBA	3365	0.19	0.65	YES
15	NOS1	NOS1	NOS1	3404	0.19	0.67	YES
16	ATP6V0B	ATP6V0B	ATP6V0B	3701	0.16	0.68	YES
17	ATP6V0C	ATP6V0C	ATP6V0C	3871	0.15	0.7	YES
18	ATP6V0E1	ATP6V0E1	ATP6V0E1	3980	0.15	0.71	YES
19	ATP6V0A4	ATP6V0A4	ATP6V0A4	4456	0.12	0.71	NO
20	ATP6V1B2	ATP6V1B2	ATP6V1B2	6679	0.043	0.59	NO
21	ATP6V1A	ATP6V1A	ATP6V1A	7246	0.028	0.56	NO
22	ATP6V1F	ATP6V1F	ATP6V1F	7461	0.022	0.56	NO
23	ATP6V1G1	ATP6V1G1	ATP6V1G1	8466	-0.0011	0.5	NO
24	ATP6V1G2	ATP6V1G2	ATP6V1G2	8654	-0.006	0.49	NO
25	ATP6V1C1	ATP6V1C1	ATP6V1C1	8812	-0.0095	0.48	NO
26	ATP6V0D1	ATP6V0D1	ATP6V0D1	9559	-0.028	0.45	NO
27	ATP6V1E1	ATP6V1E1	ATP6V1E1	10118	-0.04	0.42	NO
28	ATP6V0A2	ATP6V0A2	ATP6V0A2	10265	-0.043	0.42	NO
29	ATP6V1D	ATP6V1D	ATP6V1D	10545	-0.05	0.41	NO
30	ATP6V1H	ATP6V1H	ATP6V1H	11089	-0.062	0.39	NO

Figure S61. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS.

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

genes ES table in pathway: KEGG ETHER LIPID METABOLISM

Table S32. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IFNG	IFNG	IFNG	76	0.98	0.032	YES
2	OASL	OASL	OASL	110	0.93	0.064	YES
3	IRF4	IRF4	IRF4	275	0.76	0.083	YES
4	GBP5	GBP5	GBP5	344	0.72	0.1	YES
5	FCGR1B	FCGR1B	FCGR1B	398	0.68	0.13	YES
6	FCGR1A	FCGR1A	FCGR1A	470	0.65	0.15	YES
7	CIITA	CIITA	CIITA	592	0.6	0.16	YES
8	PTAFR	PTAFR	PTAFR	839	0.53	0.17	YES
9	HLA-G	HLA-G	HLA-G	854	0.53	0.19	YES
10	IRF5	IRF5	IRF5	918	0.51	0.2	YES
11	OAS1	OAS1	OAS1	927	0.51	0.22	YES
12	GBP4	GBP4	GBP4	1014	0.49	0.23	YES
13	GBP2	GBP2	GBP2	1054	0.48	0.25	YES
14	IRF7	IRF7	IRF7	1284	0.43	0.25	YES
15	HLA-DQA2	HLA-DQA2	HLA-DQA2	1306	0.43	0.27	YES
16	IFI27	IFI27	IFI27	1337	0.42	0.28	YES
17	HLA-F	HLA-F	HLA-F	1437	0.4	0.29	YES
18	GBP7	GBP7	GBP7	1516	0.39	0.3	YES
19	OAS2	OAS2	OAS2	1521	0.39	0.31	YES
20	ICAM1	ICAM1	ICAM1	1680	0.37	0.32	YES
21	HLA-DQA1	HLA-DQA1	HLA-DQA1	1837	0.34	0.32	YES
22	HLA-DRB5	HLA-DRB5	HLA-DRB5	1856	0.34	0.33	YES
23	GBP1	GBP1	GBP1	1889	0.33	0.34	YES
24	MT2A	MT2A	MT2A	2073	0.31	0.35	YES
25	USP18	USP18	USP18	2109	0.31	0.36	YES
26	ISG20	ISG20	ISG20	2193	0.3	0.36	YES
27	XAF1	XAF1	XAF1	2310	0.28	0.36	YES
28	IFI35	IFI35	IFI35	2314	0.28	0.38	YES
29	SOCS3	SOCS3	SOCS3	2325	0.28	0.38	YES
30	CAMK2D	CAMK2D	CAMK2D	2343	0.28	0.4	YES
31	ISG15	ISG15	ISG15	2403	0.28	0.4	YES
32	CD44	CD44	CD44	2440	0.27	0.41	YES
33	HLA-DRB1	HLA-DRB1	HLA-DRB1	2470	0.27	0.42	YES
34	HLA-B	HLA-B	HLA-B	2475	0.27	0.43	YES
35	OAS3	OAS3	OAS3	2543	0.26	0.43	YES
36	IFI6	IFI6	IFI6	2639	0.25	0.44	YES
37	MX1	MX1	MX1	2710	0.24	0.44	YES
38	EIF2AK2	EIF2AK2	EIF2AK2	2712	0.24	0.45	YES
39	IFNB1	IFNB1	IFNB1	2743	0.24	0.46	YES
40	VCAM1	VCAM1	VCAM1	2764	0.24	0.47	YES
41	IRF1	IRF1	IRF1	2838	0.23	0.47	YES
42	PRKCD	PRKCD	PRKCD	2958	0.22	0.47	YES
43	HLA-C	HLA-C	HLA-C	2972	0.22	0.48	YES
44	HLA-A	HLA-A	HLA-A	3013	0.22	0.48	YES
45	MX2	MX2	MX2	3021	0.22	0.49	YES
46	HLA-DPA1	HLA-DPA1	HLA-DPA1	3060	0.21	0.5	YES
47	CAMK2B	CAMK2B	CAMK2B	3131	0.21	0.5	YES
48	IFNGR2	IFNGR2	IFNGR2	3176	0.2	0.51	YES
49	HLA-DPB1	HLA-DPB1	HLA-DPB1	3191	0.2	0.51	YES
50	STAT1	STAT1	STAT1	3217	0.2	0.52	YES
51	JAK2	JAK2	JAK2	3236	0.2	0.53	YES
52	NCAM1	NCAM1	NCAM1	3368	0.19	0.52	YES
53	IFITM1	IFITM1	IFITM1	3434	0.18	0.53	YES
54	IFIT3	IFIT3	IFIT3	3530	0.18	0.53	YES
55	SOCS1	SOCS1	SOCS1	3587	0.17	0.53	YES
56	IFIT2	IFIT2	IFIT2	3900	0.15	0.52	NO
57	PML	PML	PML	4019	0.15	0.52	NO
58	SP100	SP100	SP100	4410	0.13	0.5	NO
59	IRF9	IRF9	IRF9	4442	0.12	0.51	NO
60	IFITM3	IFITM3	IFITM3	4448	0.12	0.51	NO
61	IFIT1	IFIT1	IFIT1	4525	0.12	0.51	NO
62	B2M	B2M	B2M	4666	0.11	0.51	NO
63	IRF6	IRF6	IRF6	4728	0.11	0.51	NO
64	IRF3	IRF3	IRF3	4971	0.1	0.5	NO
65	STAT2	STAT2	STAT2	5059	0.098	0.5	NO
66	EIF4E2	EIF4E2	EIF4E2	5141	0.094	0.5	NO
67	PSMB8	PSMB8	PSMB8	5235	0.091	0.49	NO
68	EIF4G1	EIF4G1	EIF4G1	5409	0.084	0.49	NO
69	UBA7	UBA7	UBA7	5423	0.083	0.49	NO
70	IFITM2	IFITM2	IFITM2	5636	0.076	0.48	NO
71	PTPN6	PTPN6	PTPN6	5670	0.075	0.48	NO
72	UBE2L6	UBE2L6	UBE2L6	5724	0.073	0.48	NO
73	EIF4A1	EIF4A1	EIF4A1	5800	0.07	0.48	NO
74	IRF2	IRF2	IRF2	5925	0.067	0.48	NO
75	ADAR	ADAR	ADAR	5947	0.066	0.48	NO
76	RPS27A	RPS27A	RPS27A	6074	0.062	0.47	NO
77	EGR1	EGR1	EGR1	6133	0.06	0.47	NO
78	IRF8	IRF8	IRF8	6169	0.059	0.47	NO
79	TRIM25	TRIM25	TRIM25	6440	0.05	0.46	NO
80	HERC5	HERC5	HERC5	6558	0.047	0.45	NO
81	IFNA21	IFNA21	IFNA21	6754	0.041	0.44	NO
82	UBA52	UBA52	UBA52	6781	0.04	0.44	NO
83	TYK2	TYK2	TYK2	6942	0.036	0.44	NO
84	KPNB1	KPNB1	KPNB1	7055	0.033	0.43	NO
85	NUP88	NUP88	NUP88	7518	0.021	0.41	NO
86	CAMK2A	CAMK2A	CAMK2A	7933	0.011	0.38	NO
87	IFNAR1	IFNAR1	IFNAR1	8435	-0.00032	0.36	NO
88	RNASEL	RNASEL	RNASEL	8551	-0.0035	0.35	NO
89	GBP6	GBP6	GBP6	8580	-0.0043	0.35	NO
90	KPNA1	KPNA1	KPNA1	8582	-0.0044	0.35	NO
91	UBE2E1	UBE2E1	UBE2E1	8631	-0.0056	0.35	NO
92	NUP85	NUP85	NUP85	8651	-0.0059	0.35	NO
93	NUP37	NUP37	NUP37	8857	-0.011	0.34	NO
94	NUP155	NUP155	NUP155	8954	-0.013	0.33	NO
95	MAPK3	MAPK3	MAPK3	8962	-0.013	0.33	NO
96	AAAS	AAAS	AAAS	9035	-0.015	0.33	NO
97	NUP133	NUP133	NUP133	9223	-0.02	0.32	NO
98	RAE1	RAE1	RAE1	9230	-0.02	0.32	NO
99	EIF4A3	EIF4A3	EIF4A3	9342	-0.022	0.31	NO
100	NUP210	NUP210	NUP210	9492	-0.026	0.31	NO
101	EIF4E	EIF4E	EIF4E	9515	-0.027	0.31	NO
102	TPR	TPR	TPR	9527	-0.027	0.31	NO
103	KPNA3	KPNA3	KPNA3	9902	-0.035	0.29	NO
104	UBE2N	UBE2N	UBE2N	10040	-0.038	0.28	NO
105	NUPL2	NUPL2	NUPL2	10065	-0.039	0.28	NO
106	KPNA2	KPNA2	KPNA2	10135	-0.04	0.28	NO
107	PTPN1	PTPN1	PTPN1	10315	-0.044	0.27	NO
108	PIAS1	PIAS1	PIAS1	10427	-0.047	0.27	NO
109	PIN1	PIN1	PIN1	10491	-0.049	0.26	NO
110	EIF4A2	EIF4A2	EIF4A2	10710	-0.054	0.25	NO
111	NUP107	NUP107	NUP107	10768	-0.055	0.25	NO
112	NUP62	NUP62	NUP62	10945	-0.059	0.24	NO
113	JAK1	JAK1	JAK1	11112	-0.063	0.24	NO
114	EIF4G2	EIF4G2	EIF4G2	11155	-0.064	0.24	NO
115	SUMO1	SUMO1	SUMO1	11220	-0.066	0.24	NO
116	ARIH1	ARIH1	ARIH1	11228	-0.066	0.24	NO
117	KPNA4	KPNA4	KPNA4	11365	-0.069	0.23	NO
118	NUP35	NUP35	NUP35	11430	-0.071	0.23	NO
119	DDX58	DDX58	DDX58	11490	-0.072	0.23	NO
120	IP6K2	IP6K2	IP6K2	11599	-0.075	0.23	NO
121	EIF4G3	EIF4G3	EIF4G3	11723	-0.079	0.23	NO
122	RANBP2	RANBP2	RANBP2	11736	-0.079	0.23	NO
123	POM121	POM121	POM121	11897	-0.083	0.22	NO
124	NUPL1	NUPL1	NUPL1	12171	-0.091	0.21	NO
125	SEH1L	SEH1L	SEH1L	12270	-0.094	0.21	NO
126	NUP205	NUP205	NUP205	12283	-0.094	0.21	NO
127	PPM1B	PPM1B	PPM1B	12626	-0.1	0.2	NO
128	NUP43	NUP43	NUP43	12758	-0.11	0.19	NO
129	NUP214	NUP214	NUP214	12863	-0.11	0.19	NO
130	NUP50	NUP50	NUP50	12934	-0.11	0.19	NO
131	NUP188	NUP188	NUP188	13077	-0.12	0.19	NO
132	IFNAR2	IFNAR2	IFNAR2	13420	-0.13	0.17	NO
133	NUP54	NUP54	NUP54	13507	-0.13	0.17	NO
134	NUP153	NUP153	NUP153	13589	-0.13	0.17	NO
135	IFNGR1	IFNGR1	IFNGR1	13741	-0.14	0.17	NO
136	FLNB	FLNB	FLNB	14146	-0.16	0.16	NO
137	NUP93	NUP93	NUP93	14835	-0.19	0.12	NO
138	PLCG1	PLCG1	PLCG1	15201	-0.21	0.11	NO
139	PTPN2	PTPN2	PTPN2	15586	-0.24	0.099	NO
140	EIF4E3	EIF4E3	EIF4E3	16253	-0.29	0.073	NO
141	KPNA5	KPNA5	KPNA5	17338	-0.43	0.029	NO
142	NEDD4	NEDD4	NEDD4	17979	-0.63	0.017	NO

Figure S63. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ETHER LIPID METABOLISM.

Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ETHER LIPID 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 SNARE INTERACTIONS IN VESICULAR TRANSPORT

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	CCL4	CCL4	CCL4	54	1	0.095	YES
2	ZBP1	ZBP1	ZBP1	60	1	0.19	YES
3	AIM2	AIM2	AIM2	130	0.89	0.27	YES
4	CXCL10	CXCL10	CXCL10	286	0.76	0.34	YES
5	CCL5	CCL5	CCL5	496	0.64	0.39	YES
6	IL6	IL6	IL6	837	0.53	0.42	YES
7	CCL4L2	CCL4L2	CCL4L2	953	0.5	0.46	YES
8	IL1B	IL1B	IL1B	1127	0.46	0.5	YES
9	IRF7	IRF7	IRF7	1284	0.43	0.53	YES
10	IL33	IL33	IL33	2011	0.32	0.52	YES
11	POLR3D	POLR3D	POLR3D	2179	0.3	0.54	YES
12	PYCARD	PYCARD	PYCARD	2494	0.27	0.55	YES
13	IL18	IL18	IL18	2566	0.26	0.57	YES
14	TBK1	TBK1	TBK1	2680	0.25	0.59	YES
15	IFNB1	IFNB1	IFNB1	2743	0.24	0.61	YES
16	CASP1	CASP1	CASP1	3190	0.2	0.6	YES
17	POLR3G	POLR3G	POLR3G	3240	0.2	0.62	YES
18	NFKBIA	NFKBIA	NFKBIA	3366	0.19	0.63	YES
19	RIPK3	RIPK3	RIPK3	3708	0.16	0.63	YES
20	NFKBIB	NFKBIB	NFKBIB	3777	0.16	0.64	YES
21	IKBKE	IKBKE	IKBKE	3915	0.15	0.65	YES
22	POLR1C	POLR1C	POLR1C	4825	0.11	0.61	NO
23	IRF3	IRF3	IRF3	4971	0.1	0.61	NO
24	TREX1	TREX1	TREX1	5447	0.083	0.59	NO
25	RELA	RELA	RELA	5511	0.08	0.6	NO
26	POLR3B	POLR3B	POLR3B	5517	0.08	0.6	NO
27	POLR3C	POLR3C	POLR3C	5693	0.074	0.6	NO
28	POLR3K	POLR3K	POLR3K	5736	0.073	0.61	NO
29	ADAR	ADAR	ADAR	5947	0.066	0.6	NO
30	POLR1D	POLR1D	POLR1D	6121	0.06	0.6	NO
31	TMEM173	TMEM173	TMEM173	6237	0.057	0.6	NO
32	IKBKB	IKBKB	IKBKB	6261	0.056	0.6	NO
33	IFNA21	IFNA21	IFNA21	6754	0.041	0.58	NO
34	POLR3H	POLR3H	POLR3H	7215	0.029	0.56	NO
35	IKBKG	IKBKG	IKBKG	7676	0.017	0.53	NO
36	POLR3F	POLR3F	POLR3F	7760	0.015	0.53	NO
37	POLR3A	POLR3A	POLR3A	8169	0.0053	0.51	NO
38	MAVS	MAVS	MAVS	8945	-0.013	0.47	NO
39	CHUK	CHUK	CHUK	10686	-0.053	0.38	NO
40	DDX58	DDX58	DDX58	11490	-0.072	0.34	NO
41	RIPK1	RIPK1	RIPK1	11918	-0.084	0.32	NO
42	POLR3GL	POLR3GL	POLR3GL	13534	-0.13	0.25	NO
43	NFKB1	NFKB1	NFKB1	13614	-0.14	0.26	NO

Figure S65. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT.

Figure S66. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SNARE INTERACTIONS IN VESICULAR 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: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY

Table S34. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IFNG	IFNG	IFNG	76	0.98	0.05	YES
2	OASL	OASL	OASL	110	0.93	0.1	YES
3	IRF4	IRF4	IRF4	275	0.76	0.13	YES
4	GBP5	GBP5	GBP5	344	0.72	0.17	YES
5	FCGR1B	FCGR1B	FCGR1B	398	0.68	0.2	YES
6	FCGR1A	FCGR1A	FCGR1A	470	0.65	0.24	YES
7	CIITA	CIITA	CIITA	592	0.6	0.26	YES
8	PTAFR	PTAFR	PTAFR	839	0.53	0.28	YES
9	HLA-G	HLA-G	HLA-G	854	0.53	0.31	YES
10	IRF5	IRF5	IRF5	918	0.51	0.33	YES
11	OAS1	OAS1	OAS1	927	0.51	0.36	YES
12	GBP4	GBP4	GBP4	1014	0.49	0.38	YES
13	GBP2	GBP2	GBP2	1054	0.48	0.41	YES
14	IRF7	IRF7	IRF7	1284	0.43	0.42	YES
15	HLA-DQA2	HLA-DQA2	HLA-DQA2	1306	0.43	0.44	YES
16	HLA-F	HLA-F	HLA-F	1437	0.4	0.46	YES
17	GBP7	GBP7	GBP7	1516	0.39	0.48	YES
18	OAS2	OAS2	OAS2	1521	0.39	0.5	YES
19	ICAM1	ICAM1	ICAM1	1680	0.37	0.51	YES
20	HLA-DQA1	HLA-DQA1	HLA-DQA1	1837	0.34	0.52	YES
21	HLA-DRB5	HLA-DRB5	HLA-DRB5	1856	0.34	0.54	YES
22	GBP1	GBP1	GBP1	1889	0.33	0.55	YES
23	MT2A	MT2A	MT2A	2073	0.31	0.56	YES
24	SOCS3	SOCS3	SOCS3	2325	0.28	0.56	YES
25	CAMK2D	CAMK2D	CAMK2D	2343	0.28	0.58	YES
26	CD44	CD44	CD44	2440	0.27	0.59	YES
27	HLA-DRB1	HLA-DRB1	HLA-DRB1	2470	0.27	0.6	YES
28	HLA-B	HLA-B	HLA-B	2475	0.27	0.62	YES
29	OAS3	OAS3	OAS3	2543	0.26	0.63	YES
30	VCAM1	VCAM1	VCAM1	2764	0.24	0.63	YES
31	IRF1	IRF1	IRF1	2838	0.23	0.64	YES
32	PRKCD	PRKCD	PRKCD	2958	0.22	0.64	YES
33	HLA-C	HLA-C	HLA-C	2972	0.22	0.65	YES
34	HLA-A	HLA-A	HLA-A	3013	0.22	0.66	YES
35	HLA-DPA1	HLA-DPA1	HLA-DPA1	3060	0.21	0.67	YES
36	CAMK2B	CAMK2B	CAMK2B	3131	0.21	0.68	YES
37	IFNGR2	IFNGR2	IFNGR2	3176	0.2	0.69	YES
38	HLA-DPB1	HLA-DPB1	HLA-DPB1	3191	0.2	0.7	YES
39	STAT1	STAT1	STAT1	3217	0.2	0.71	YES
40	JAK2	JAK2	JAK2	3236	0.2	0.72	YES
41	NCAM1	NCAM1	NCAM1	3368	0.19	0.72	YES
42	SOCS1	SOCS1	SOCS1	3587	0.17	0.72	NO
43	PML	PML	PML	4019	0.15	0.7	NO
44	SP100	SP100	SP100	4410	0.13	0.69	NO
45	IRF9	IRF9	IRF9	4442	0.12	0.7	NO
46	B2M	B2M	B2M	4666	0.11	0.69	NO
47	IRF6	IRF6	IRF6	4728	0.11	0.69	NO
48	IRF3	IRF3	IRF3	4971	0.1	0.68	NO
49	PTPN6	PTPN6	PTPN6	5670	0.075	0.65	NO
50	IRF2	IRF2	IRF2	5925	0.067	0.64	NO
51	IRF8	IRF8	IRF8	6169	0.059	0.63	NO
52	CAMK2A	CAMK2A	CAMK2A	7933	0.011	0.53	NO
53	GBP6	GBP6	GBP6	8580	-0.0043	0.5	NO
54	PTPN1	PTPN1	PTPN1	10315	-0.044	0.41	NO
55	PIAS1	PIAS1	PIAS1	10427	-0.047	0.4	NO
56	JAK1	JAK1	JAK1	11112	-0.063	0.37	NO
57	SUMO1	SUMO1	SUMO1	11220	-0.066	0.37	NO
58	IFNGR1	IFNGR1	IFNGR1	13741	-0.14	0.24	NO
59	PTPN2	PTPN2	PTPN2	15586	-0.24	0.15	NO

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

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOD 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 S35. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FBP1	FBP1	FBP1	208	0.82	0.075	YES
2	ALDH3B1	ALDH3B1	ALDH3B1	735	0.56	0.1	YES
3	ALDOC	ALDOC	ALDOC	857	0.53	0.15	YES
4	HK3	HK3	HK3	957	0.5	0.2	YES
5	ALDH3A1	ALDH3A1	ALDH3A1	988	0.49	0.25	YES
6	ALDOB	ALDOB	ALDOB	1672	0.37	0.25	YES
7	ADH6	ADH6	ADH6	2047	0.32	0.26	YES
8	PCK2	PCK2	PCK2	2106	0.31	0.29	YES
9	ADH1A	ADH1A	ADH1A	2233	0.29	0.32	YES
10	FBP2	FBP2	FBP2	2234	0.29	0.35	YES
11	ALDH1B1	ALDH1B1	ALDH1B1	2258	0.29	0.38	YES
12	ADH7	ADH7	ADH7	2335	0.28	0.4	YES
13	PKLR	PKLR	PKLR	2422	0.27	0.42	YES
14	PFKL	PFKL	PFKL	2853	0.23	0.42	YES
15	GALM	GALM	GALM	3117	0.21	0.43	YES
16	ENO2	ENO2	ENO2	3428	0.18	0.43	YES
17	HK2	HK2	HK2	3568	0.17	0.44	YES
18	TPI1	TPI1	TPI1	3613	0.17	0.46	YES
19	PFKP	PFKP	PFKP	3636	0.17	0.48	YES
20	ADH1C	ADH1C	ADH1C	3664	0.17	0.49	YES
21	PKM2	PKM2	PKM2	3721	0.16	0.51	YES
22	ACSS2	ACSS2	ACSS2	3811	0.16	0.52	YES
23	ACSS1	ACSS1	ACSS1	4179	0.14	0.51	YES
24	PCK1	PCK1	PCK1	4222	0.14	0.52	YES
25	HK1	HK1	HK1	4660	0.11	0.51	NO
26	ENO1	ENO1	ENO1	4788	0.11	0.52	NO
27	ALDOA	ALDOA	ALDOA	5607	0.077	0.48	NO
28	PGM2	PGM2	PGM2	5613	0.076	0.49	NO
29	ALDH3B2	ALDH3B2	ALDH3B2	5905	0.067	0.48	NO
30	GPI	GPI	GPI	6266	0.056	0.46	NO
31	GAPDH	GAPDH	GAPDH	6299	0.055	0.47	NO
32	PGAM1	PGAM1	PGAM1	6509	0.048	0.46	NO
33	LDHA	LDHA	LDHA	6943	0.036	0.44	NO
34	PGAM4	PGAM4	PGAM4	7667	0.017	0.4	NO
35	ADH1B	ADH1B	ADH1B	7730	0.016	0.4	NO
36	LDHAL6B	LDHAL6B	LDHAL6B	7943	0.01	0.39	NO
37	DLD	DLD	DLD	8553	-0.0035	0.36	NO
38	ALDH3A2	ALDH3A2	ALDH3A2	8682	-0.0067	0.35	NO
39	PGK1	PGK1	PGK1	8691	-0.0069	0.35	NO
40	AKR1A1	AKR1A1	AKR1A1	8971	-0.014	0.34	NO
41	LDHC	LDHC	LDHC	9129	-0.017	0.33	NO
42	ENO3	ENO3	ENO3	9194	-0.019	0.33	NO
43	ALDH2	ALDH2	ALDH2	9949	-0.036	0.29	NO
44	PFKM	PFKM	PFKM	10005	-0.037	0.29	NO
45	DLAT	DLAT	DLAT	10125	-0.04	0.29	NO
46	PDHA1	PDHA1	PDHA1	10291	-0.044	0.29	NO
47	PGAM2	PGAM2	PGAM2	10366	-0.046	0.29	NO
48	ALDH1A3	ALDH1A3	ALDH1A3	11145	-0.064	0.25	NO
49	ALDH9A1	ALDH9A1	ALDH9A1	11517	-0.073	0.24	NO
50	GCK	GCK	GCK	12298	-0.094	0.21	NO
51	PDHB	PDHB	PDHB	12311	-0.095	0.22	NO
52	LDHB	LDHB	LDHB	12513	-0.1	0.22	NO
53	BPGM	BPGM	BPGM	13288	-0.12	0.18	NO
54	ADH5	ADH5	ADH5	13320	-0.13	0.2	NO
55	PGM1	PGM1	PGM1	14158	-0.16	0.17	NO
56	ALDH7A1	ALDH7A1	ALDH7A1	15746	-0.25	0.11	NO
57	LDHAL6A	LDHAL6A	LDHAL6A	16511	-0.32	0.097	NO

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

Figure S70. 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: KEGG TYPE I DIABETES MELLITUS

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IFNG	IFNG	IFNG	76	0.98	0.046	YES
2	IL1A	IL1A	IL1A	345	0.72	0.069	YES
3	NCF1	NCF1	NCF1	414	0.67	0.1	YES
4	TNF	TNF	TNF	427	0.67	0.13	YES
5	FCGR1A	FCGR1A	FCGR1A	470	0.65	0.17	YES
6	PTGS2	PTGS2	PTGS2	499	0.64	0.2	YES
7	IL10	IL10	IL10	612	0.6	0.22	YES
8	NOS2	NOS2	NOS2	687	0.57	0.25	YES
9	HLA-DOB	HLA-DOB	HLA-DOB	779	0.54	0.27	YES
10	IL1B	IL1B	IL1B	1127	0.46	0.28	YES
11	ITGAM	ITGAM	ITGAM	1169	0.46	0.3	YES
12	HLA-DOA	HLA-DOA	HLA-DOA	1300	0.43	0.31	YES
13	HLA-DQA2	HLA-DQA2	HLA-DQA2	1306	0.43	0.33	YES
14	NCF2	NCF2	NCF2	1355	0.42	0.35	YES
15	IL12A	IL12A	IL12A	1363	0.42	0.38	YES
16	FCGR3A	FCGR3A	FCGR3A	1368	0.42	0.4	YES
17	FCGR2C	FCGR2C	FCGR2C	1522	0.39	0.41	YES
18	TLR2	TLR2	TLR2	1585	0.38	0.42	YES
19	HLA-DQA1	HLA-DQA1	HLA-DQA1	1837	0.34	0.43	YES
20	MAPK12	MAPK12	MAPK12	1840	0.34	0.44	YES
21	HLA-DRB5	HLA-DRB5	HLA-DRB5	1856	0.34	0.46	YES
22	HLA-DMA	HLA-DMA	HLA-DMA	2031	0.32	0.47	YES
23	CR1	CR1	CR1	2197	0.3	0.48	YES
24	FCGR3B	FCGR3B	FCGR3B	2214	0.3	0.49	YES
25	HLA-DRB1	HLA-DRB1	HLA-DRB1	2470	0.27	0.49	YES
26	NCF4	NCF4	NCF4	2600	0.25	0.5	YES
27	C3	C3	C3	2653	0.25	0.51	YES
28	MAPK13	MAPK13	MAPK13	2715	0.24	0.52	YES
29	HLA-DRA	HLA-DRA	HLA-DRA	2740	0.24	0.53	YES
30	FCGR2A	FCGR2A	FCGR2A	2753	0.24	0.54	YES
31	HLA-DMB	HLA-DMB	HLA-DMB	2795	0.24	0.55	YES
32	FOS	FOS	FOS	2827	0.23	0.56	YES
33	MAPK11	MAPK11	MAPK11	2851	0.23	0.57	YES
34	HLA-DPA1	HLA-DPA1	HLA-DPA1	3060	0.21	0.57	YES
35	TLR4	TLR4	TLR4	3096	0.21	0.58	YES
36	IFNGR2	IFNGR2	IFNGR2	3176	0.2	0.58	YES
37	HLA-DPB1	HLA-DPB1	HLA-DPB1	3191	0.2	0.59	YES
38	STAT1	STAT1	STAT1	3217	0.2	0.6	YES
39	JAK2	JAK2	JAK2	3236	0.2	0.61	YES
40	CYBA	CYBA	CYBA	3365	0.19	0.61	YES
41	NFKBIA	NFKBIA	NFKBIA	3366	0.19	0.62	YES
42	HLA-DQB1	HLA-DQB1	HLA-DQB1	3589	0.17	0.62	YES
43	TGFB2	TGFB2	TGFB2	3648	0.17	0.63	YES
44	JUN	JUN	JUN	3699	0.16	0.63	YES
45	NFKBIB	NFKBIB	NFKBIB	3777	0.16	0.64	YES
46	IRAK1	IRAK1	IRAK1	3865	0.15	0.64	YES
47	IL12B	IL12B	IL12B	4810	0.11	0.59	NO
48	TGFB1	TGFB1	TGFB1	5149	0.094	0.58	NO
49	RELA	RELA	RELA	5511	0.08	0.56	NO
50	PTPN6	PTPN6	PTPN6	5670	0.075	0.56	NO
51	MYD88	MYD88	MYD88	6304	0.054	0.53	NO
52	ITGB1	ITGB1	ITGB1	6866	0.038	0.5	NO
53	ELK1	ELK1	ELK1	8125	0.0062	0.43	NO
54	TAB1	TAB1	TAB1	8911	-0.012	0.39	NO
55	MAPK3	MAPK3	MAPK3	8962	-0.013	0.38	NO
56	ITGB2	ITGB2	ITGB2	10004	-0.037	0.33	NO
57	JAK1	JAK1	JAK1	11112	-0.063	0.27	NO
58	IRAK4	IRAK4	IRAK4	11212	-0.065	0.27	NO
59	MARCKSL1	MARCKSL1	MARCKSL1	11568	-0.074	0.26	NO
60	TGFB3	TGFB3	TGFB3	12523	-0.1	0.21	NO
61	MAPK1	MAPK1	MAPK1	12925	-0.11	0.19	NO
62	NFKB1	NFKB1	NFKB1	13614	-0.14	0.16	NO
63	IFNGR1	IFNGR1	IFNGR1	13741	-0.14	0.16	NO
64	TAB2	TAB2	TAB2	13769	-0.14	0.17	NO
65	MAPK14	MAPK14	MAPK14	14222	-0.16	0.15	NO
66	TRAF6	TRAF6	TRAF6	14631	-0.18	0.14	NO
67	MAP3K7	MAP3K7	MAP3K7	15010	-0.2	0.13	NO
68	IL4	IL4	IL4	15305	-0.22	0.12	NO
69	PRKCB	PRKCB	PRKCB	16738	-0.34	0.061	NO
70	ITGA4	ITGA4	ITGA4	17440	-0.46	0.046	NO

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

Figure S72. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TYPE I DIABETES MELLITUS, 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 LEISHMANIA INFECTION

Table S37. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IL2RA	IL2RA	IL2RA	22	1.1	0.02	YES
2	IL1RN	IL1RN	IL1RN	24	1.1	0.042	YES
3	IFNG	IFNG	IFNG	76	0.98	0.058	YES
4	OASL	OASL	OASL	110	0.93	0.074	YES
5	CSF2RB	CSF2RB	CSF2RB	222	0.81	0.083	YES
6	IRF4	IRF4	IRF4	275	0.76	0.095	YES
7	HCK	HCK	HCK	305	0.74	0.11	YES
8	NOD2	NOD2	NOD2	324	0.73	0.12	YES
9	GBP5	GBP5	GBP5	344	0.72	0.13	YES
10	IL1A	IL1A	IL1A	345	0.72	0.15	YES
11	FCGR1B	FCGR1B	FCGR1B	398	0.68	0.16	YES
12	FCGR1A	FCGR1A	FCGR1A	470	0.65	0.16	YES
13	CIITA	CIITA	CIITA	592	0.6	0.17	YES
14	IL5RA	IL5RA	IL5RA	653	0.58	0.18	YES
15	IL7	IL7	IL7	794	0.54	0.18	YES
16	IL6	IL6	IL6	837	0.53	0.19	YES
17	PTAFR	PTAFR	PTAFR	839	0.53	0.2	YES
18	HLA-G	HLA-G	HLA-G	854	0.53	0.21	YES
19	CSF2	CSF2	CSF2	876	0.52	0.22	YES
20	IRF5	IRF5	IRF5	918	0.51	0.22	YES
21	OAS1	OAS1	OAS1	927	0.51	0.23	YES
22	LYN	LYN	LYN	996	0.49	0.24	YES
23	GBP4	GBP4	GBP4	1014	0.49	0.25	YES
24	GBP2	GBP2	GBP2	1054	0.48	0.26	YES
25	PRLR	PRLR	PRLR	1091	0.47	0.26	YES
26	IL1B	IL1B	IL1B	1127	0.46	0.27	YES
27	BLNK	BLNK	BLNK	1264	0.44	0.27	YES
28	IRF7	IRF7	IRF7	1284	0.43	0.28	YES
29	IRAK3	IRAK3	IRAK3	1305	0.43	0.28	YES
30	HLA-DQA2	HLA-DQA2	HLA-DQA2	1306	0.43	0.29	YES
31	IFI27	IFI27	IFI27	1337	0.42	0.3	YES
32	HLA-F	HLA-F	HLA-F	1437	0.4	0.3	YES
33	IL2	IL2	IL2	1474	0.4	0.31	YES
34	GH1	GH1	GH1	1480	0.4	0.31	YES
35	NFKB2	NFKB2	NFKB2	1512	0.39	0.32	YES
36	GBP7	GBP7	GBP7	1516	0.39	0.33	YES
37	OAS2	OAS2	OAS2	1521	0.39	0.33	YES
38	ICAM1	ICAM1	ICAM1	1680	0.37	0.33	YES
39	HLA-DQA1	HLA-DQA1	HLA-DQA1	1837	0.34	0.33	YES
40	HLA-DRB5	HLA-DRB5	HLA-DRB5	1856	0.34	0.34	YES
41	GBP1	GBP1	GBP1	1889	0.33	0.34	YES
42	IL2RB	IL2RB	IL2RB	1928	0.33	0.34	YES
43	MT2A	MT2A	MT2A	2073	0.31	0.34	YES
44	USP18	USP18	USP18	2109	0.31	0.35	YES
45	JAK3	JAK3	JAK3	2144	0.3	0.35	YES
46	ISG20	ISG20	ISG20	2193	0.3	0.35	YES
47	HGF	HGF	HGF	2205	0.3	0.36	YES
48	IL3RA	IL3RA	IL3RA	2224	0.3	0.36	YES
49	XAF1	XAF1	XAF1	2310	0.28	0.36	YES
50	IFI35	IFI35	IFI35	2314	0.28	0.37	YES
51	SOCS3	SOCS3	SOCS3	2325	0.28	0.37	YES
52	CAMK2D	CAMK2D	CAMK2D	2343	0.28	0.38	YES
53	ISG15	ISG15	ISG15	2403	0.28	0.38	YES
54	CD44	CD44	CD44	2440	0.27	0.38	YES
55	RIPK2	RIPK2	RIPK2	2454	0.27	0.39	YES
56	HLA-DRB1	HLA-DRB1	HLA-DRB1	2470	0.27	0.39	YES
57	HLA-B	HLA-B	HLA-B	2475	0.27	0.4	YES
58	OAS3	OAS3	OAS3	2543	0.26	0.4	YES
59	IL18	IL18	IL18	2566	0.26	0.4	YES
60	IFI6	IFI6	IFI6	2639	0.25	0.4	YES
61	MX1	MX1	MX1	2710	0.24	0.4	YES
62	EIF2AK2	EIF2AK2	EIF2AK2	2712	0.24	0.41	YES
63	IFNB1	IFNB1	IFNB1	2743	0.24	0.41	YES
64	VCAM1	VCAM1	VCAM1	2764	0.24	0.42	YES
65	IRF1	IRF1	IRF1	2838	0.23	0.42	YES
66	MAP3K8	MAP3K8	MAP3K8	2911	0.22	0.42	YES
67	PRKCD	PRKCD	PRKCD	2958	0.22	0.42	YES
68	HLA-C	HLA-C	HLA-C	2972	0.22	0.42	YES
69	HLA-A	HLA-A	HLA-A	3013	0.22	0.42	YES
70	MX2	MX2	MX2	3021	0.22	0.43	YES
71	HLA-DPA1	HLA-DPA1	HLA-DPA1	3060	0.21	0.43	YES
72	PELI3	PELI3	PELI3	3063	0.21	0.43	YES
73	STAT5A	STAT5A	STAT5A	3109	0.21	0.43	YES
74	CSF2RA	CSF2RA	CSF2RA	3128	0.21	0.44	YES
75	CAMK2B	CAMK2B	CAMK2B	3131	0.21	0.44	YES
76	IFNGR2	IFNGR2	IFNGR2	3176	0.2	0.44	YES
77	CASP1	CASP1	CASP1	3190	0.2	0.44	YES
78	HLA-DPB1	HLA-DPB1	HLA-DPB1	3191	0.2	0.45	YES
79	STAT1	STAT1	STAT1	3217	0.2	0.45	YES
80	JAK2	JAK2	JAK2	3236	0.2	0.45	YES
81	TNIP2	TNIP2	TNIP2	3334	0.19	0.45	YES
82	NCAM1	NCAM1	NCAM1	3368	0.19	0.45	YES
83	HRAS	HRAS	HRAS	3403	0.19	0.46	YES
84	IFITM1	IFITM1	IFITM1	3434	0.18	0.46	YES
85	IFIT3	IFIT3	IFIT3	3530	0.18	0.46	NO
86	SOCS1	SOCS1	SOCS1	3587	0.17	0.46	NO
87	IL1R2	IL1R2	IL1R2	3669	0.17	0.46	NO
88	IRAK1	IRAK1	IRAK1	3865	0.15	0.45	NO
89	IFIT2	IFIT2	IFIT2	3900	0.15	0.45	NO
90	PML	PML	PML	4019	0.15	0.44	NO
91	SP100	SP100	SP100	4410	0.13	0.42	NO
92	IRF9	IRF9	IRF9	4442	0.12	0.43	NO
93	IFITM3	IFITM3	IFITM3	4448	0.12	0.43	NO
94	STAT3	STAT3	STAT3	4503	0.12	0.43	NO
95	IFIT1	IFIT1	IFIT1	4525	0.12	0.43	NO
96	B2M	B2M	B2M	4666	0.11	0.42	NO
97	IRF6	IRF6	IRF6	4728	0.11	0.42	NO
98	SOS1	SOS1	SOS1	4827	0.11	0.42	NO
99	CRK	CRK	CRK	4891	0.1	0.42	NO
100	IRF3	IRF3	IRF3	4971	0.1	0.41	NO
101	STAT2	STAT2	STAT2	5059	0.098	0.41	NO
102	EIF4E2	EIF4E2	EIF4E2	5141	0.094	0.41	NO
103	SYK	SYK	SYK	5195	0.092	0.41	NO
104	SQSTM1	SQSTM1	SQSTM1	5230	0.091	0.41	NO
105	PSMB8	PSMB8	PSMB8	5235	0.091	0.41	NO
106	EIF4G1	EIF4G1	EIF4G1	5409	0.084	0.4	NO
107	UBA7	UBA7	UBA7	5423	0.083	0.4	NO
108	TOLLIP	TOLLIP	TOLLIP	5480	0.082	0.4	NO
109	RELA	RELA	RELA	5511	0.08	0.4	NO
110	IL6R	IL6R	IL6R	5519	0.08	0.4	NO
111	PIK3CB	PIK3CB	PIK3CB	5568	0.078	0.4	NO
112	IFITM2	IFITM2	IFITM2	5636	0.076	0.4	NO
113	PTPN6	PTPN6	PTPN6	5670	0.075	0.4	NO
114	UBE2L6	UBE2L6	UBE2L6	5724	0.073	0.4	NO
115	EIF4A1	EIF4A1	EIF4A1	5800	0.07	0.39	NO
116	IRF2	IRF2	IRF2	5925	0.067	0.39	NO
117	ADAR	ADAR	ADAR	5947	0.066	0.39	NO
118	RPS27A	RPS27A	RPS27A	6074	0.062	0.38	NO
119	EGR1	EGR1	EGR1	6133	0.06	0.38	NO
120	IRS2	IRS2	IRS2	6160	0.059	0.38	NO
121	IRF8	IRF8	IRF8	6169	0.059	0.38	NO
122	IKBKB	IKBKB	IKBKB	6261	0.056	0.38	NO
123	MYD88	MYD88	MYD88	6304	0.054	0.38	NO
124	TRIM25	TRIM25	TRIM25	6440	0.05	0.37	NO
125	HERC5	HERC5	HERC5	6558	0.047	0.36	NO
126	IFNA21	IFNA21	IFNA21	6754	0.041	0.35	NO
127	UBA52	UBA52	UBA52	6781	0.04	0.35	NO
128	CUL1	CUL1	CUL1	6931	0.036	0.34	NO
129	TYK2	TYK2	TYK2	6942	0.036	0.34	NO
130	YES1	YES1	YES1	6945	0.036	0.34	NO
131	KPNB1	KPNB1	KPNB1	7055	0.033	0.34	NO
132	YWHAZ	YWHAZ	YWHAZ	7279	0.028	0.33	NO
133	IRAK2	IRAK2	IRAK2	7329	0.026	0.33	NO
134	SHC1	SHC1	SHC1	7335	0.026	0.33	NO
135	NUP88	NUP88	NUP88	7518	0.021	0.32	NO
136	IKBKG	IKBKG	IKBKG	7676	0.017	0.31	NO
137	INPPL1	INPPL1	INPPL1	7908	0.011	0.3	NO
138	CAMK2A	CAMK2A	CAMK2A	7933	0.011	0.29	NO
139	KRAS	KRAS	KRAS	8256	0.0034	0.28	NO
140	GHR	GHR	GHR	8426	-0.00018	0.27	NO
141	IFNAR1	IFNAR1	IFNAR1	8435	-0.00032	0.27	NO
142	RNASEL	RNASEL	RNASEL	8551	-0.0035	0.26	NO
143	GBP6	GBP6	GBP6	8580	-0.0043	0.26	NO
144	KPNA1	KPNA1	KPNA1	8582	-0.0044	0.26	NO
145	UBE2E1	UBE2E1	UBE2E1	8631	-0.0056	0.26	NO
146	NUP85	NUP85	NUP85	8651	-0.0059	0.26	NO
147	NUP37	NUP37	NUP37	8857	-0.011	0.24	NO
148	YWHAB	YWHAB	YWHAB	8867	-0.011	0.24	NO
149	PIK3R2	PIK3R2	PIK3R2	8871	-0.011	0.24	NO
150	TAB1	TAB1	TAB1	8911	-0.012	0.24	NO
151	NUP155	NUP155	NUP155	8954	-0.013	0.24	NO
152	GRB2	GRB2	GRB2	8959	-0.013	0.24	NO
153	MAPK3	MAPK3	MAPK3	8962	-0.013	0.24	NO
154	MAP2K2	MAP2K2	MAP2K2	9033	-0.015	0.24	NO
155	AAAS	AAAS	AAAS	9035	-0.015	0.24	NO
156	NUP133	NUP133	NUP133	9223	-0.02	0.23	NO
157	RAE1	RAE1	RAE1	9230	-0.02	0.23	NO
158	NOD1	NOD1	NOD1	9318	-0.022	0.22	NO
159	EIF4A3	EIF4A3	EIF4A3	9342	-0.022	0.22	NO
160	RAPGEF1	RAPGEF1	RAPGEF1	9466	-0.025	0.22	NO
161	NUP210	NUP210	NUP210	9492	-0.026	0.21	NO
162	EIF4E	EIF4E	EIF4E	9515	-0.027	0.21	NO
163	TPR	TPR	TPR	9527	-0.027	0.21	NO
164	VAV1	VAV1	VAV1	9631	-0.029	0.21	NO
165	KPNA3	KPNA3	KPNA3	9902	-0.035	0.19	NO
166	ADAM17	ADAM17	ADAM17	9920	-0.036	0.19	NO
167	UBE2N	UBE2N	UBE2N	10040	-0.038	0.19	NO
168	NUPL2	NUPL2	NUPL2	10065	-0.039	0.19	NO
169	KPNA2	KPNA2	KPNA2	10135	-0.04	0.18	NO
170	TAB3	TAB3	TAB3	10198	-0.042	0.18	NO
171	MAP2K1	MAP2K1	MAP2K1	10226	-0.042	0.18	NO
172	PTPN1	PTPN1	PTPN1	10315	-0.044	0.18	NO
173	IL2RG	IL2RG	IL2RG	10365	-0.046	0.18	NO
174	PIAS1	PIAS1	PIAS1	10427	-0.047	0.17	NO
175	PIN1	PIN1	PIN1	10491	-0.049	0.17	NO
176	CHUK	CHUK	CHUK	10686	-0.053	0.16	NO
177	EIF4A2	EIF4A2	EIF4A2	10710	-0.054	0.16	NO
178	NUP107	NUP107	NUP107	10768	-0.055	0.16	NO
179	NUP62	NUP62	NUP62	10945	-0.059	0.15	NO
180	SH2B1	SH2B1	SH2B1	11103	-0.063	0.14	NO
181	JAK1	JAK1	JAK1	11112	-0.063	0.14	NO
182	EIF4G2	EIF4G2	EIF4G2	11155	-0.064	0.14	NO
183	IRAK4	IRAK4	IRAK4	11212	-0.065	0.14	NO
184	SKP1	SKP1	SKP1	11214	-0.066	0.14	NO
185	SUMO1	SUMO1	SUMO1	11220	-0.066	0.14	NO
186	ARIH1	ARIH1	ARIH1	11228	-0.066	0.14	NO
187	KPNA4	KPNA4	KPNA4	11365	-0.069	0.14	NO
188	NUP35	NUP35	NUP35	11430	-0.071	0.13	NO
189	STAT5B	STAT5B	STAT5B	11436	-0.071	0.14	NO
190	RBX1	RBX1	RBX1	11449	-0.072	0.14	NO
191	DDX58	DDX58	DDX58	11490	-0.072	0.14	NO
192	IP6K2	IP6K2	IP6K2	11599	-0.075	0.13	NO
193	PELI1	PELI1	PELI1	11651	-0.077	0.13	NO
194	EIF4G3	EIF4G3	EIF4G3	11723	-0.079	0.13	NO
195	RANBP2	RANBP2	RANBP2	11736	-0.079	0.13	NO
196	POM121	POM121	POM121	11897	-0.083	0.12	NO
197	BTRC	BTRC	BTRC	11927	-0.084	0.12	NO
198	NUPL1	NUPL1	NUPL1	12171	-0.091	0.11	NO
199	MAP3K3	MAP3K3	MAP3K3	12250	-0.093	0.11	NO
200	SEH1L	SEH1L	SEH1L	12270	-0.094	0.11	NO
201	NUP205	NUP205	NUP205	12283	-0.094	0.11	NO
202	PPM1B	PPM1B	PPM1B	12626	-0.1	0.091	NO
203	NRAS	NRAS	NRAS	12660	-0.1	0.091	NO
204	NUP43	NUP43	NUP43	12758	-0.11	0.088	NO
205	PTK2B	PTK2B	PTK2B	12856	-0.11	0.084	NO
206	NUP214	NUP214	NUP214	12863	-0.11	0.086	NO
207	RAF1	RAF1	RAF1	12916	-0.11	0.086	NO
208	MAPK1	MAPK1	MAPK1	12925	-0.11	0.087	NO
209	NUP50	NUP50	NUP50	12934	-0.11	0.089	NO
210	IL6ST	IL6ST	IL6ST	13067	-0.12	0.084	NO
211	NUP188	NUP188	NUP188	13077	-0.12	0.086	NO
212	IFNAR2	IFNAR2	IFNAR2	13420	-0.13	0.069	NO
213	NUP54	NUP54	NUP54	13507	-0.13	0.067	NO
214	CDK1	CDK1	CDK1	13529	-0.13	0.068	NO
215	NUP153	NUP153	NUP153	13589	-0.13	0.068	NO
216	IFNGR1	IFNGR1	IFNGR1	13741	-0.14	0.062	NO
217	TAB2	TAB2	TAB2	13769	-0.14	0.063	NO
218	FLNB	FLNB	FLNB	14146	-0.16	0.045	NO
219	IL1R1	IL1R1	IL1R1	14160	-0.16	0.048	NO
220	CRKL	CRKL	CRKL	14192	-0.16	0.049	NO
221	MAP2K6	MAP2K6	MAP2K6	14202	-0.16	0.052	NO
222	PIK3CD	PIK3CD	PIK3CD	14252	-0.16	0.052	NO
223	FYN	FYN	FYN	14299	-0.16	0.053	NO
224	IL5	IL5	IL5	14475	-0.17	0.046	NO
225	TRAF6	TRAF6	TRAF6	14631	-0.18	0.041	NO
226	MAP2K4	MAP2K4	MAP2K4	14687	-0.18	0.042	NO
227	PIK3CA	PIK3CA	PIK3CA	14769	-0.19	0.041	NO
228	NUP93	NUP93	NUP93	14835	-0.19	0.041	NO
229	MAP3K7	MAP3K7	MAP3K7	15010	-0.2	0.035	NO
230	PLCG1	PLCG1	PLCG1	15201	-0.21	0.028	NO
231	GAB2	GAB2	GAB2	15349	-0.22	0.024	NO
232	IL1RAP	IL1RAP	IL1RAP	15361	-0.22	0.028	NO
233	PTPN2	PTPN2	PTPN2	15586	-0.24	0.02	NO
234	CISH	CISH	CISH	15769	-0.25	0.015	NO
235	TEC	TEC	TEC	15887	-0.26	0.013	NO
236	PIK3R3	PIK3R3	PIK3R3	15891	-0.26	0.018	NO
237	EIF4E3	EIF4E3	EIF4E3	16253	-0.29	0.0037	NO
238	PIK3R1	PIK3R1	PIK3R1	16317	-0.3	0.0059	NO
239	IL7R	IL7R	IL7R	16810	-0.35	-0.015	NO
240	CBL	CBL	CBL	16933	-0.36	-0.014	NO
241	PRKACB	PRKACB	PRKACB	17119	-0.39	-0.017	NO
242	KPNA5	KPNA5	KPNA5	17338	-0.43	-0.021	NO
243	LCK	LCK	LCK	17540	-0.48	-0.023	NO
244	SOCS2	SOCS2	SOCS2	17697	-0.52	-0.022	NO
245	NEDD4	NEDD4	NEDD4	17979	-0.63	-0.025	NO
246	PELI2	PELI2	PELI2	18044	-0.68	-0.016	NO
247	IRS1	IRS1	IRS1	18138	-0.75	-0.0067	NO
248	PRL	PRL	PRL	18154	-0.76	0.0072	NO

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

Figure S74. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LEISHMANIA INFECTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AUTOIMMUNE THYROID DISEASE

Table S38. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PLA2G3	PLA2G3	PLA2G3	11	1.2	0.17	YES
2	ENPP6	ENPP6	ENPP6	374	0.7	0.24	YES
3	PLA2G2D	PLA2G2D	PLA2G2D	548	0.62	0.32	YES
4	PLA2G5	PLA2G5	PLA2G5	676	0.57	0.39	YES
5	PLA2G7	PLA2G7	PLA2G7	869	0.52	0.45	YES
6	PPAP2C	PPAP2C	PPAP2C	1008	0.49	0.52	YES
7	PLA2G2A	PLA2G2A	PLA2G2A	1037	0.48	0.58	YES
8	PLA2G10	PLA2G10	PLA2G10	1215	0.45	0.63	YES
9	CHPT1	CHPT1	CHPT1	3192	0.2	0.55	NO
10	PLA2G4A	PLA2G4A	PLA2G4A	3211	0.2	0.58	NO
11	ENPP2	ENPP2	ENPP2	3867	0.15	0.56	NO
12	PAFAH1B2	PAFAH1B2	PAFAH1B2	6049	0.062	0.45	NO
13	LPCAT1	LPCAT1	LPCAT1	7324	0.026	0.39	NO
14	PLA2G6	PLA2G6	PLA2G6	7393	0.024	0.39	NO
15	PPAP2A	PPAP2A	PPAP2A	8195	0.0048	0.34	NO
16	PAFAH1B3	PAFAH1B3	PAFAH1B3	8818	-0.0097	0.31	NO
17	PLD2	PLD2	PLD2	8860	-0.011	0.31	NO
18	JMJD7-PLA2G4B	JMJD7-PLA2G4B	JMJD7-PLA2G4B	9235	-0.02	0.29	NO
19	LPCAT4	LPCAT4	LPCAT4	10381	-0.046	0.24	NO
20	PLA2G12A	PLA2G12A	PLA2G12A	10895	-0.058	0.22	NO
21	PAFAH1B1	PAFAH1B1	PAFAH1B1	12240	-0.093	0.16	NO
22	LPCAT2	LPCAT2	LPCAT2	12806	-0.11	0.14	NO
23	PLD1	PLD1	PLD1	13497	-0.13	0.12	NO
24	AGPS	AGPS	AGPS	13815	-0.14	0.12	NO
25	PPAP2B	PPAP2B	PPAP2B	14640	-0.18	0.1	NO
26	PLA2G1B	PLA2G1B	PLA2G1B	15393	-0.22	0.092	NO
27	PAFAH2	PAFAH2	PAFAH2	17507	-0.47	0.042	NO

Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AUTOIMMUNE THYROID DISEASE.

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

genes ES table in pathway: KEGG ALLOGRAFT REJECTION

Table S39. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	IFNG	IFNG	IFNG	76	0.98	0.059	YES
2	CD80	CD80	CD80	115	0.92	0.12	YES
3	GZMB	GZMB	GZMB	209	0.82	0.16	YES
4	IL1A	IL1A	IL1A	345	0.72	0.2	YES
5	TNF	TNF	TNF	427	0.67	0.24	YES
6	FASLG	FASLG	FASLG	673	0.58	0.27	YES
7	HLA-DOB	HLA-DOB	HLA-DOB	779	0.54	0.3	YES
8	HLA-G	HLA-G	HLA-G	854	0.53	0.33	YES
9	IL1B	IL1B	IL1B	1127	0.46	0.34	YES
10	CD86	CD86	CD86	1141	0.46	0.37	YES
11	GAD1	GAD1	GAD1	1147	0.46	0.4	YES
12	LTA	LTA	LTA	1162	0.46	0.43	YES
13	HLA-DOA	HLA-DOA	HLA-DOA	1300	0.43	0.45	YES
14	HLA-DQA2	HLA-DQA2	HLA-DQA2	1306	0.43	0.48	YES
15	IL12A	IL12A	IL12A	1363	0.42	0.5	YES
16	PTPRN	PTPRN	PTPRN	1398	0.41	0.53	YES
17	HLA-F	HLA-F	HLA-F	1437	0.4	0.55	YES
18	IL2	IL2	IL2	1474	0.4	0.57	YES
19	GAD2	GAD2	GAD2	1821	0.34	0.58	YES
20	HLA-DQA1	HLA-DQA1	HLA-DQA1	1837	0.34	0.6	YES
21	HLA-DRB5	HLA-DRB5	HLA-DRB5	1856	0.34	0.62	YES
22	PRF1	PRF1	PRF1	1980	0.32	0.63	YES
23	ICA1	ICA1	ICA1	1981	0.32	0.66	YES
24	HLA-DMA	HLA-DMA	HLA-DMA	2031	0.32	0.67	YES
25	HLA-DRB1	HLA-DRB1	HLA-DRB1	2470	0.27	0.67	YES
26	HLA-B	HLA-B	HLA-B	2475	0.27	0.68	YES
27	HLA-DRA	HLA-DRA	HLA-DRA	2740	0.24	0.68	YES
28	HLA-DMB	HLA-DMB	HLA-DMB	2795	0.24	0.7	YES
29	HLA-C	HLA-C	HLA-C	2972	0.22	0.7	YES
30	HLA-A	HLA-A	HLA-A	3013	0.22	0.71	YES
31	HLA-DPA1	HLA-DPA1	HLA-DPA1	3060	0.21	0.72	YES
32	HLA-DPB1	HLA-DPB1	HLA-DPB1	3191	0.2	0.73	YES
33	FAS	FAS	FAS	3262	0.2	0.74	YES
34	HLA-E	HLA-E	HLA-E	3421	0.18	0.74	YES
35	HLA-DQB1	HLA-DQB1	HLA-DQB1	3589	0.17	0.74	YES
36	HSPD1	HSPD1	HSPD1	4133	0.14	0.72	NO
37	IL12B	IL12B	IL12B	4810	0.11	0.69	NO
38	CD28	CD28	CD28	14800	-0.19	0.16	NO
39	PTPRN2	PTPRN2	PTPRN2	15242	-0.22	0.15	NO
40	CPE	CPE	CPE	16046	-0.27	0.12	NO

Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ALLOGRAFT REJECTION.

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

genes ES table in pathway: KEGG GRAFT VERSUS HOST DISEASE

Table S40. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	OASL	OASL	OASL	110	0.93	0.073	YES
2	IRF4	IRF4	IRF4	275	0.76	0.13	YES
3	HLA-G	HLA-G	HLA-G	854	0.53	0.14	YES
4	IRF5	IRF5	IRF5	918	0.51	0.18	YES
5	OAS1	OAS1	OAS1	927	0.51	0.23	YES
6	GBP2	GBP2	GBP2	1054	0.48	0.26	YES
7	IRF7	IRF7	IRF7	1284	0.43	0.28	YES
8	IFI27	IFI27	IFI27	1337	0.42	0.32	YES
9	HLA-F	HLA-F	HLA-F	1437	0.4	0.35	YES
10	OAS2	OAS2	OAS2	1521	0.39	0.38	YES
11	USP18	USP18	USP18	2109	0.31	0.37	YES
12	ISG20	ISG20	ISG20	2193	0.3	0.39	YES
13	XAF1	XAF1	XAF1	2310	0.28	0.41	YES
14	IFI35	IFI35	IFI35	2314	0.28	0.43	YES
15	SOCS3	SOCS3	SOCS3	2325	0.28	0.46	YES
16	ISG15	ISG15	ISG15	2403	0.28	0.48	YES
17	HLA-B	HLA-B	HLA-B	2475	0.27	0.5	YES
18	OAS3	OAS3	OAS3	2543	0.26	0.51	YES
19	IFI6	IFI6	IFI6	2639	0.25	0.53	YES
20	MX1	MX1	MX1	2710	0.24	0.55	YES
21	IFNB1	IFNB1	IFNB1	2743	0.24	0.57	YES
22	IRF1	IRF1	IRF1	2838	0.23	0.58	YES
23	HLA-C	HLA-C	HLA-C	2972	0.22	0.59	YES
24	HLA-A	HLA-A	HLA-A	3013	0.22	0.61	YES
25	MX2	MX2	MX2	3021	0.22	0.63	YES
26	STAT1	STAT1	STAT1	3217	0.2	0.63	YES
27	IFITM1	IFITM1	IFITM1	3434	0.18	0.64	YES
28	IFIT3	IFIT3	IFIT3	3530	0.18	0.65	YES
29	SOCS1	SOCS1	SOCS1	3587	0.17	0.66	YES
30	IFIT2	IFIT2	IFIT2	3900	0.15	0.65	NO
31	IRF9	IRF9	IRF9	4442	0.12	0.64	NO
32	IFITM3	IFITM3	IFITM3	4448	0.12	0.64	NO
33	IFIT1	IFIT1	IFIT1	4525	0.12	0.65	NO
34	IRF6	IRF6	IRF6	4728	0.11	0.65	NO
35	IRF3	IRF3	IRF3	4971	0.1	0.64	NO
36	STAT2	STAT2	STAT2	5059	0.098	0.65	NO
37	PSMB8	PSMB8	PSMB8	5235	0.091	0.65	NO
38	IFITM2	IFITM2	IFITM2	5636	0.076	0.63	NO
39	PTPN6	PTPN6	PTPN6	5670	0.075	0.64	NO
40	IRF2	IRF2	IRF2	5925	0.067	0.63	NO
41	ADAR	ADAR	ADAR	5947	0.066	0.63	NO
42	EGR1	EGR1	EGR1	6133	0.06	0.63	NO
43	IRF8	IRF8	IRF8	6169	0.059	0.63	NO
44	IFNA21	IFNA21	IFNA21	6754	0.041	0.6	NO
45	TYK2	TYK2	TYK2	6942	0.036	0.6	NO
46	IFNAR1	IFNAR1	IFNAR1	8435	-0.00032	0.51	NO
47	RNASEL	RNASEL	RNASEL	8551	-0.0035	0.51	NO
48	PTPN1	PTPN1	PTPN1	10315	-0.044	0.41	NO
49	JAK1	JAK1	JAK1	11112	-0.063	0.38	NO
50	IP6K2	IP6K2	IP6K2	11599	-0.075	0.36	NO
51	IFNAR2	IFNAR2	IFNAR2	13420	-0.13	0.27	NO

Figure S79. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GRAFT VERSUS HOST DISEASE.

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

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