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

Liver Hepatocellular Carcinoma (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 LIHC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1DJ5F2G

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 "LIHC-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: 702
Number of samples: 371
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 5 :[ clus1 ] 68
pheno.type: 2 - 5 :[ clus2 ] 88
pheno.type: 3 - 5 :[ clus3 ] 74
pheno.type: 4 - 5 :[ clus4 ] 71
pheno.type: 5 - 5 :[ clus5 ] 70

For the expression subtypes of 17745 genes in 372 samples, GSEA found enriched gene sets in each cluster using 371 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

clus1

Top enriched gene sets are KEGG CELL CYCLE, KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, BIOCARTA FMLP PATHWAY, PID IL2 PI3KPATHWAY, PID CASPASE PATHWAY, REACTOME CELL CYCLE, REACTOME MHC CLASS II ANTIGEN PRESENTATION, REACTOME RNA POL II TRANSCRIPTION, REACTOME CELL CYCLE MITOTIC, REACTOME CELL CYCLE CHECKPOINTS

And common core enriched genes are TCEB1, AAAS, BANF1, CD4, COBRA1, CTDP1, GTF2B, GTF2E1, GTF2E2, GTF2F2

clus2

Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG FATTY ACID METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION, KEGG STARCH AND SUCROSE METABOLISM, KEGG PYRUVATE METABOLISM, KEGG PROPANOATE METABOLISM, KEGG RETINOL METABOLISM

And common core enriched genes are ACAT1, ACAT2, ALDH2, ALDH7A1, ALDH9A1, EHHADH, PIPOX, ACACB, ACSS2, LDHAL6B

clus3

Top enriched gene sets are KEGG RIBOSOME, PID ATM PATHWAY, REACTOME TRANSLATION, REACTOME METABOLISM OF NON CODING RNA, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME SIGNALLING TO RAS, REACTOME SIGNALLING TO ERKS, REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, REACTOME PEPTIDE CHAIN ELONGATION

And common core enriched genes are FAM153A, RPL10, RPL10A, RPL12, RPL13A, RPL14, RPL15, RPL17, RPL18, RPL18A

clus4

Top enriched gene sets are KEGG GALACTOSE METABOLISM, KEGG PURINE METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG N GLYCAN BIOSYNTHESIS, KEGG O GLYCAN BIOSYNTHESIS, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG GLYCEROPHOSPHOLIPID METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG ARACHIDONIC ACID METABOLISM

And common core enriched genes are ADCY2, ADCY3, ADCY4, ADCY5, AKT3, CAMK4, ITPR3, PDE1A, PDE1B, PRKAR2B

clus5

Top enriched gene sets are KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG LYSINE DEGRADATION, KEGG TYROSINE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM CYTOCHROME P450

And common core enriched genes are UGT1A1, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A8, UGT1A9, UGT2B10, UGT2B11, UGT2B28

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 CELL CYCLE	118	genes.ES.table	0.59	1.8	0.0058	0.32	0.57	0.33	0.14	0.29	0.084	0.078
KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY	60	genes.ES.table	0.67	1.8	0.01	0.35	0.51	0.38	0.14	0.33	0.095	0.083
BIOCARTA FMLP PATHWAY	36	genes.ES.table	0.55	1.8	0.01	0.22	0.66	0.28	0.22	0.22	0.076	0.054
PID IL2 PI3KPATHWAY	33	genes.ES.table	0.66	2	0	0.28	0.13	0.24	0.094	0.22	0	0.077
PID CASPASE PATHWAY	51	genes.ES.table	0.46	1.8	0.0042	0.26	0.6	0.51	0.37	0.32	0.07	0.07
REACTOME CELL CYCLE	376	genes.ES.table	0.56	1.8	0.017	0.39	0.47	0.46	0.27	0.34	0	0.09
REACTOME MHC CLASS II ANTIGEN PRESENTATION	89	genes.ES.table	0.52	1.8	0.004	0.25	0.6	0.32	0.2	0.25	0.067	0.063
REACTOME RNA POL II TRANSCRIPTION	93	genes.ES.table	0.4	1.9	0.012	0.37	0.28	0.73	0.52	0.35	0	0.081
REACTOME CELL CYCLE MITOTIC	297	genes.ES.table	0.6	1.8	0.0097	0.31	0.52	0.33	0.15	0.28	0.083	0.072
REACTOME CELL CYCLE CHECKPOINTS	105	genes.ES.table	0.56	1.8	0.027	0.3	0.59	0.4	0.27	0.29	0.081	0.074

genes ES table in pathway: KEGG CELL 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	PSMA8	PSMA8	PSMA8	220	0.47	0.022	YES
2	CCR5	CCR5	CCR5	832	0.33	0.012	YES
3	CD8B	CD8B	CD8B	948	0.32	0.028	YES
4	HCK	HCK	HCK	1253	0.29	0.032	YES
5	AP1M2	AP1M2	AP1M2	1275	0.28	0.052	YES
6	DOCK2	DOCK2	DOCK2	1450	0.27	0.062	YES
7	LCK	LCK	LCK	1530	0.26	0.076	YES
8	APOBEC3G	APOBEC3G	APOBEC3G	1567	0.26	0.093	YES
9	PSMB9	PSMB9	PSMB9	1778	0.24	0.099	YES
10	HMGA1	HMGA1	HMGA1	1784	0.24	0.12	YES
11	CD28	CD28	CD28	1858	0.24	0.13	YES
12	RCC1	RCC1	RCC1	1941	0.23	0.14	YES
13	TAF4B	TAF4B	TAF4B	2370	0.2	0.13	YES
14	FEN1	FEN1	FEN1	2433	0.2	0.14	YES
15	CD247	CD247	CD247	2505	0.19	0.15	YES
16	XRCC4	XRCC4	XRCC4	2622	0.19	0.16	YES
17	CXCR4	CXCR4	CXCR4	3007	0.17	0.15	YES
18	NUP37	NUP37	NUP37	3033	0.17	0.16	YES
19	NUP188	NUP188	NUP188	3118	0.16	0.17	YES
20	NUP93	NUP93	NUP93	3299	0.15	0.17	YES
21	NUP210	NUP210	NUP210	3337	0.15	0.18	YES
22	NUP62	NUP62	NUP62	3421	0.15	0.18	YES
23	NUP107	NUP107	NUP107	3450	0.15	0.19	YES
24	PSMB8	PSMB8	PSMB8	3634	0.14	0.19	YES
25	GTF2H2B	GTF2H2B	GTF2H2B	3651	0.14	0.2	YES
26	NUP43	NUP43	NUP43	3727	0.14	0.21	YES
27	GTF2H2	GTF2H2	GTF2H2	3730	0.14	0.22	YES
28	PSMB10	PSMB10	PSMB10	3811	0.13	0.22	YES
29	RAN	RAN	RAN	3951	0.13	0.23	YES
30	NUP205	NUP205	NUP205	3971	0.13	0.23	YES
31	LIG1	LIG1	LIG1	4146	0.12	0.23	YES
32	PSMD14	PSMD14	PSMD14	4220	0.12	0.24	YES
33	NUP155	NUP155	NUP155	4261	0.12	0.24	YES
34	VPS37C	VPS37C	VPS37C	4280	0.12	0.25	YES
35	TAF12	TAF12	TAF12	4377	0.12	0.26	YES
36	TAF6	TAF6	TAF6	4439	0.11	0.26	YES
37	PSMA5	PSMA5	PSMA5	4626	0.11	0.26	YES
38	AP1S2	AP1S2	AP1S2	4636	0.11	0.26	YES
39	PSMB2	PSMB2	PSMB2	4724	0.1	0.27	YES
40	NUP85	NUP85	NUP85	4786	0.1	0.27	YES
41	TCEB1	TCEB1	TCEB1	4897	0.1	0.27	YES
42	POLR2D	POLR2D	POLR2D	5178	0.092	0.26	YES
43	TBP	TBP	TBP	5225	0.091	0.27	YES
44	NPM1	NPM1	NPM1	5312	0.089	0.27	YES
45	ELMO1	ELMO1	ELMO1	5353	0.088	0.27	YES
46	HLA-A	HLA-A	HLA-A	5381	0.087	0.28	YES
47	RNGTT	RNGTT	RNGTT	5400	0.087	0.28	YES
48	RANBP1	RANBP1	RANBP1	5401	0.087	0.29	YES
49	GTF2E2	GTF2E2	GTF2E2	5434	0.086	0.29	YES
50	SSRP1	SSRP1	SSRP1	5545	0.083	0.29	YES
51	PSMD2	PSMD2	PSMD2	5622	0.081	0.3	YES
52	CD4	CD4	CD4	5637	0.081	0.3	YES
53	PSIP1	PSIP1	PSIP1	5643	0.081	0.31	YES
54	PACS1	PACS1	PACS1	5797	0.077	0.3	YES
55	KPNB1	KPNB1	KPNB1	5866	0.076	0.3	YES
56	RDBP	RDBP	RDBP	5906	0.075	0.31	YES
57	GTF2H1	GTF2H1	GTF2H1	5939	0.074	0.31	YES
58	POLR2H	POLR2H	POLR2H	5946	0.074	0.32	YES
59	POLR2G	POLR2G	POLR2G	5971	0.074	0.32	YES
60	GTF2H3	GTF2H3	GTF2H3	6050	0.072	0.32	YES
61	SEH1L	SEH1L	SEH1L	6075	0.072	0.33	YES
62	PSMD10	PSMD10	PSMD10	6085	0.072	0.33	YES
63	NCBP2	NCBP2	NCBP2	6133	0.071	0.33	YES
64	TCEB3	TCEB3	TCEB3	6253	0.069	0.33	YES
65	PSMD12	PSMD12	PSMD12	6318	0.067	0.33	YES
66	RAC1	RAC1	RAC1	6340	0.067	0.34	YES
67	NUPL1	NUPL1	NUPL1	6360	0.067	0.34	YES
68	VPS37A	VPS37A	VPS37A	6415	0.066	0.34	YES
69	TAF9	TAF9	TAF9	6583	0.063	0.34	YES
70	PPIA	PPIA	PPIA	6587	0.062	0.34	YES
71	BANF1	BANF1	BANF1	6621	0.062	0.34	YES
72	PSMD13	PSMD13	PSMD13	6700	0.061	0.34	YES
73	PSMB3	PSMB3	PSMB3	6741	0.06	0.35	YES
74	PSMA1	PSMA1	PSMA1	6781	0.059	0.35	YES
75	NUP35	NUP35	NUP35	6783	0.059	0.35	YES
76	NCBP1	NCBP1	NCBP1	6825	0.059	0.36	YES
77	PSMC4	PSMC4	PSMC4	6990	0.055	0.35	YES
78	PSMD1	PSMD1	PSMD1	7002	0.055	0.35	YES
79	AP2S1	AP2S1	AP2S1	7020	0.055	0.36	YES
80	TAF13	TAF13	TAF13	7047	0.055	0.36	YES
81	SUPT5H	SUPT5H	SUPT5H	7092	0.054	0.36	YES
82	POLR2K	POLR2K	POLR2K	7315	0.05	0.35	YES
83	CTDP1	CTDP1	CTDP1	7329	0.05	0.35	YES
84	RAE1	RAE1	RAE1	7340	0.05	0.36	YES
85	MNAT1	MNAT1	MNAT1	7354	0.049	0.36	YES
86	PSMD7	PSMD7	PSMD7	7381	0.049	0.36	YES
87	PSMB1	PSMB1	PSMB1	7387	0.049	0.36	YES
88	SLC25A6	SLC25A6	SLC25A6	7439	0.048	0.37	YES
89	PSMD3	PSMD3	PSMD3	7449	0.048	0.37	YES
90	GTF2E1	GTF2E1	GTF2E1	7523	0.047	0.37	YES
91	RNMT	RNMT	RNMT	7527	0.047	0.37	YES
92	GTF2F2	GTF2F2	GTF2F2	7571	0.046	0.37	YES
93	SUPT16H	SUPT16H	SUPT16H	7609	0.046	0.37	YES
94	GTF2B	GTF2B	GTF2B	7628	0.045	0.38	YES
95	PSMD9	PSMD9	PSMD9	7683	0.045	0.38	YES
96	AP1B1	AP1B1	AP1B1	7735	0.044	0.38	YES
97	PSMD11	PSMD11	PSMD11	7789	0.043	0.38	YES
98	COBRA1	COBRA1	COBRA1	7831	0.042	0.38	YES
99	NUPL2	NUPL2	NUPL2	7842	0.042	0.38	YES
100	PSMA4	PSMA4	PSMA4	7875	0.042	0.38	YES
101	TAF10	TAF10	TAF10	7879	0.042	0.38	YES
102	AAAS	AAAS	AAAS	7913	0.041	0.38	YES
103	VPS37B	VPS37B	VPS37B	7927	0.041	0.39	YES
104	POLR2I	POLR2I	POLR2I	7971	0.04	0.39	YES
105	PSMA3	PSMA3	PSMA3	7979	0.04	0.39	YES
106	POLR2B	POLR2B	POLR2B	8051	0.039	0.39	YES
107	POLR2L	POLR2L	POLR2L	8131	0.038	0.39	YES
108	PAK2	PAK2	PAK2	8140	0.038	0.39	YES
109	RBX1	RBX1	RBX1	8167	0.038	0.39	YES
110	WHSC2	WHSC2	WHSC2	8171	0.038	0.39	YES
111	PSMD8	PSMD8	PSMD8	8176	0.037	0.4	YES
112	PSMD5	PSMD5	PSMD5	8290	0.036	0.39	YES
113	ATP6V1H	ATP6V1H	ATP6V1H	8320	0.035	0.39	YES
114	CDK7	CDK7	CDK7	8343	0.035	0.39	YES
115	PSMC5	PSMC5	PSMC5	8363	0.035	0.4	YES
116	PSME2	PSME2	PSME2	8417	0.034	0.4	YES
117	PSMC3	PSMC3	PSMC3	8446	0.034	0.4	YES
118	XRCC6	XRCC6	XRCC6	8459	0.034	0.4	YES
119	XPO1	XPO1	XPO1	8557	0.032	0.4	NO
120	AP2M1	AP2M1	AP2M1	8661	0.03	0.39	NO
121	TCEB2	TCEB2	TCEB2	8675	0.03	0.39	NO
122	RPS27A	RPS27A	RPS27A	8697	0.03	0.39	NO
123	PSMB4	PSMB4	PSMB4	8722	0.03	0.39	NO
124	XRCC5	XRCC5	XRCC5	8783	0.029	0.39	NO
125	RANGAP1	RANGAP1	RANGAP1	8813	0.028	0.39	NO
126	NUP54	NUP54	NUP54	8872	0.027	0.39	NO
127	NUP214	NUP214	NUP214	8905	0.027	0.39	NO
128	PSMB7	PSMB7	PSMB7	8968	0.026	0.39	NO
129	PSMA7	PSMA7	PSMA7	8973	0.026	0.39	NO
130	PSMA6	PSMA6	PSMA6	9021	0.025	0.39	NO
131	TAF11	TAF11	TAF11	9154	0.024	0.39	NO
132	ERCC2	ERCC2	ERCC2	9218	0.023	0.38	NO
133	ERCC3	ERCC3	ERCC3	9288	0.022	0.38	NO
134	POLR2J	POLR2J	POLR2J	9297	0.022	0.38	NO
135	PSMC1	PSMC1	PSMC1	9404	0.02	0.38	NO
136	PSMC2	PSMC2	PSMC2	9407	0.02	0.38	NO
137	SUPT4H1	SUPT4H1	SUPT4H1	9417	0.02	0.38	NO
138	PSMD4	PSMD4	PSMD4	9467	0.019	0.38	NO
139	PSME4	PSME4	PSME4	9480	0.019	0.38	NO
140	TSG101	TSG101	TSG101	9509	0.018	0.38	NO
141	GTF2F1	GTF2F1	GTF2F1	9571	0.017	0.38	NO
142	NUP153	NUP153	NUP153	9575	0.017	0.38	NO
143	PSMD6	PSMD6	PSMD6	9653	0.016	0.38	NO
144	SLC25A5	SLC25A5	SLC25A5	9722	0.015	0.37	NO
145	AP2B1	AP2B1	AP2B1	9752	0.015	0.37	NO
146	TAF4	TAF4	TAF4	9774	0.014	0.37	NO
147	TAF5	TAF5	TAF5	9784	0.014	0.37	NO
148	CDK9	CDK9	CDK9	9806	0.014	0.37	NO
149	TCEA1	TCEA1	TCEA1	9863	0.013	0.37	NO
150	AP1S1	AP1S1	AP1S1	9938	0.012	0.37	NO
151	CCNH	CCNH	CCNH	9975	0.011	0.36	NO
152	GTF2H4	GTF2H4	GTF2H4	9995	0.011	0.36	NO
153	UBA52	UBA52	UBA52	10003	0.011	0.36	NO
154	NUP50	NUP50	NUP50	10014	0.011	0.36	NO
155	POLR2A	POLR2A	POLR2A	10130	0.0091	0.36	NO
156	PSMB6	PSMB6	PSMB6	10219	0.0077	0.36	NO
157	B2M	B2M	B2M	10267	0.0071	0.35	NO
158	AP1M1	AP1M1	AP1M1	10452	0.0045	0.34	NO
159	AP2A2	AP2A2	AP2A2	10576	0.0029	0.34	NO
160	PSMC6	PSMC6	PSMC6	10581	0.0028	0.34	NO
161	GTF2A2	GTF2A2	GTF2A2	10595	0.0026	0.34	NO
162	CCNT2	CCNT2	CCNT2	10601	0.0024	0.34	NO
163	PSMB5	PSMB5	PSMB5	10629	0.0022	0.33	NO
164	AP2A1	AP2A1	AP2A1	10647	0.0018	0.33	NO
165	PSME1	PSME1	PSME1	10693	0.0011	0.33	NO
166	TPR	TPR	TPR	10709	0.00086	0.33	NO
167	SKP1	SKP1	SKP1	10734	0.00053	0.33	NO
168	NMT1	NMT1	NMT1	10786	-0.00027	0.33	NO
169	POLR2C	POLR2C	POLR2C	11031	-0.004	0.31	NO
170	POM121	POM121	POM121	11050	-0.0044	0.31	NO
171	AP1G1	AP1G1	AP1G1	11051	-0.0044	0.31	NO
172	NUP133	NUP133	NUP133	11195	-0.0066	0.3	NO
173	RANBP2	RANBP2	RANBP2	11229	-0.007	0.3	NO
174	VPS28	VPS28	VPS28	11317	-0.0084	0.3	NO
175	ARF1	ARF1	ARF1	11364	-0.009	0.3	NO
176	PSMF1	PSMF1	PSMF1	11406	-0.0096	0.3	NO
177	PSMA2	PSMA2	PSMA2	11435	-0.01	0.29	NO
178	TH1L	TH1L	TH1L	11439	-0.01	0.29	NO
179	POLR2E	POLR2E	POLR2E	11449	-0.01	0.3	NO
180	ELL	ELL	ELL	11557	-0.012	0.29	NO
181	TAF1	TAF1	TAF1	11569	-0.012	0.29	NO
182	CUL5	CUL5	CUL5	12048	-0.02	0.26	NO
183	NUP88	NUP88	NUP88	12072	-0.021	0.26	NO
184	CCNT1	CCNT1	CCNT1	12282	-0.025	0.25	NO
185	POLR2F	POLR2F	POLR2F	12287	-0.025	0.26	NO
186	KPNA1	KPNA1	KPNA1	12769	-0.034	0.23	NO
187	BTRC	BTRC	BTRC	13409	-0.048	0.2	NO
188	GTF2A1	GTF2A1	GTF2A1	13556	-0.052	0.19	NO
189	LIG4	LIG4	LIG4	14291	-0.072	0.16	NO
190	SLC25A4	SLC25A4	SLC25A4	14552	-0.08	0.15	NO
191	NMT2	NMT2	NMT2	14951	-0.097	0.13	NO
192	FYN	FYN	FYN	15313	-0.11	0.12	NO
193	VPS37D	VPS37D	VPS37D	16923	-0.24	0.046	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 CELL CYCLE.

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

genes ES table in pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY

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	MYB	MYB	MYB	203	0.47	0.11	YES
2	IL2RA	IL2RA	IL2RA	247	0.46	0.23	YES
3	IL2RG	IL2RG	IL2RG	253	0.46	0.35	YES
4	JAK3	JAK3	JAK3	543	0.38	0.43	YES
5	IL2RB	IL2RB	IL2RB	861	0.33	0.5	YES
6	E2F1	E2F1	E2F1	1194	0.29	0.56	YES
7	LCK	LCK	LCK	1530	0.26	0.61	YES
8	TERT	TERT	TERT	1671	0.25	0.66	YES
9	RAC1	RAC1	RAC1	6340	0.067	0.42	NO
10	GRB2	GRB2	GRB2	6666	0.061	0.42	NO
11	RPS6KB1	RPS6KB1	RPS6KB1	7090	0.054	0.41	NO
12	HSP90AA1	HSP90AA1	HSP90AA1	7854	0.042	0.37	NO
13	UGCG	UGCG	UGCG	8163	0.038	0.37	NO
14	MTOR	MTOR	MTOR	8379	0.035	0.36	NO
15	SHC1	SHC1	SHC1	8406	0.034	0.37	NO
16	RPS6	RPS6	RPS6	8792	0.028	0.36	NO
17	JAK1	JAK1	JAK1	9654	0.016	0.31	NO
18	RELA	RELA	RELA	9664	0.016	0.32	NO
19	MYC	MYC	MYC	9782	0.014	0.31	NO
20	NFKB1	NFKB1	NFKB1	9885	0.013	0.31	NO
21	PIK3CA	PIK3CA	PIK3CA	10261	0.0072	0.29	NO
22	GAB2	GAB2	GAB2	10350	0.0061	0.29	NO
23	FOXO3	FOXO3	FOXO3	10963	-0.003	0.25	NO
24	EIF3A	EIF3A	EIF3A	11041	-0.0042	0.25	NO
25	AKT1	AKT1	AKT1	11480	-0.011	0.23	NO
26	SOS1	SOS1	SOS1	11761	-0.016	0.22	NO
27	PTPN11	PTPN11	PTPN11	12284	-0.025	0.19	NO
28	PRKCZ	PRKCZ	PRKCZ	12826	-0.036	0.17	NO
29	BCL2	BCL2	BCL2	12850	-0.036	0.18	NO
30	SGMS1	SGMS1	SGMS1	12946	-0.038	0.18	NO
31	BCL2L1	BCL2L1	BCL2L1	14117	-0.067	0.14	NO
32	SMPD1	SMPD1	SMPD1	14192	-0.069	0.15	NO
33	PIK3R1	PIK3R1	PIK3R1	16441	-0.19	0.073	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 NOD LIKE RECEPTOR SIGNALING PATHWAY.

Figure S4. 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: BIOCARTA FMLP PATHWAY

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	CCR5	CCR5	CCR5	832	0.33	-0.0039	YES
2	HMGA1	HMGA1	HMGA1	1784	0.24	-0.027	YES
3	RCC1	RCC1	RCC1	1941	0.23	-0.0058	YES
4	TAF4B	TAF4B	TAF4B	2370	0.2	-0.004	YES
5	FEN1	FEN1	FEN1	2433	0.2	0.018	YES
6	XRCC4	XRCC4	XRCC4	2622	0.19	0.031	YES
7	CXCR4	CXCR4	CXCR4	3007	0.17	0.031	YES
8	NUP37	NUP37	NUP37	3033	0.17	0.051	YES
9	NUP188	NUP188	NUP188	3118	0.16	0.068	YES
10	NUP93	NUP93	NUP93	3299	0.15	0.077	YES
11	NUP210	NUP210	NUP210	3337	0.15	0.095	YES
12	NUP62	NUP62	NUP62	3421	0.15	0.11	YES
13	NUP107	NUP107	NUP107	3450	0.15	0.13	YES
14	GTF2H2B	GTF2H2B	GTF2H2B	3651	0.14	0.13	YES
15	NUP43	NUP43	NUP43	3727	0.14	0.15	YES
16	GTF2H2	GTF2H2	GTF2H2	3730	0.14	0.16	YES
17	RAN	RAN	RAN	3951	0.13	0.17	YES
18	NUP205	NUP205	NUP205	3971	0.13	0.18	YES
19	LIG1	LIG1	LIG1	4146	0.12	0.19	YES
20	NUP155	NUP155	NUP155	4261	0.12	0.2	YES
21	VPS37C	VPS37C	VPS37C	4280	0.12	0.21	YES
22	TAF12	TAF12	TAF12	4377	0.12	0.22	YES
23	TAF6	TAF6	TAF6	4439	0.11	0.24	YES
24	NUP85	NUP85	NUP85	4786	0.1	0.23	YES
25	TCEB1	TCEB1	TCEB1	4897	0.1	0.24	YES
26	POLR2D	POLR2D	POLR2D	5178	0.092	0.23	YES
27	TBP	TBP	TBP	5225	0.091	0.24	YES
28	RNGTT	RNGTT	RNGTT	5400	0.087	0.24	YES
29	RANBP1	RANBP1	RANBP1	5401	0.087	0.25	YES
30	GTF2E2	GTF2E2	GTF2E2	5434	0.086	0.26	YES
31	SSRP1	SSRP1	SSRP1	5545	0.083	0.27	YES
32	CD4	CD4	CD4	5637	0.081	0.27	YES
33	PSIP1	PSIP1	PSIP1	5643	0.081	0.28	YES
34	RDBP	RDBP	RDBP	5906	0.075	0.28	YES
35	GTF2H1	GTF2H1	GTF2H1	5939	0.074	0.28	YES
36	POLR2H	POLR2H	POLR2H	5946	0.074	0.3	YES
37	POLR2G	POLR2G	POLR2G	5971	0.074	0.3	YES
38	GTF2H3	GTF2H3	GTF2H3	6050	0.072	0.31	YES
39	SEH1L	SEH1L	SEH1L	6075	0.072	0.32	YES
40	NCBP2	NCBP2	NCBP2	6133	0.071	0.32	YES
41	TCEB3	TCEB3	TCEB3	6253	0.069	0.32	YES
42	NUPL1	NUPL1	NUPL1	6360	0.067	0.33	YES
43	VPS37A	VPS37A	VPS37A	6415	0.066	0.33	YES
44	TAF9	TAF9	TAF9	6583	0.063	0.33	YES
45	PPIA	PPIA	PPIA	6587	0.062	0.34	YES
46	BANF1	BANF1	BANF1	6621	0.062	0.34	YES
47	NUP35	NUP35	NUP35	6783	0.059	0.34	YES
48	NCBP1	NCBP1	NCBP1	6825	0.059	0.35	YES
49	TAF13	TAF13	TAF13	7047	0.055	0.34	YES
50	SUPT5H	SUPT5H	SUPT5H	7092	0.054	0.35	YES
51	POLR2K	POLR2K	POLR2K	7315	0.05	0.34	YES
52	CTDP1	CTDP1	CTDP1	7329	0.05	0.35	YES
53	RAE1	RAE1	RAE1	7340	0.05	0.35	YES
54	MNAT1	MNAT1	MNAT1	7354	0.049	0.36	YES
55	GTF2E1	GTF2E1	GTF2E1	7523	0.047	0.36	YES
56	RNMT	RNMT	RNMT	7527	0.047	0.36	YES
57	GTF2F2	GTF2F2	GTF2F2	7571	0.046	0.36	YES
58	SUPT16H	SUPT16H	SUPT16H	7609	0.046	0.37	YES
59	GTF2B	GTF2B	GTF2B	7628	0.045	0.37	YES
60	COBRA1	COBRA1	COBRA1	7831	0.042	0.37	YES
61	NUPL2	NUPL2	NUPL2	7842	0.042	0.37	YES
62	TAF10	TAF10	TAF10	7879	0.042	0.38	YES
63	AAAS	AAAS	AAAS	7913	0.041	0.38	YES
64	VPS37B	VPS37B	VPS37B	7927	0.041	0.38	YES
65	POLR2I	POLR2I	POLR2I	7971	0.04	0.39	YES
66	POLR2B	POLR2B	POLR2B	8051	0.039	0.39	YES
67	POLR2L	POLR2L	POLR2L	8131	0.038	0.39	YES
68	WHSC2	WHSC2	WHSC2	8171	0.038	0.39	YES
69	CDK7	CDK7	CDK7	8343	0.035	0.38	NO
70	XRCC6	XRCC6	XRCC6	8459	0.034	0.38	NO
71	XPO1	XPO1	XPO1	8557	0.032	0.38	NO
72	TCEB2	TCEB2	TCEB2	8675	0.03	0.38	NO
73	RPS27A	RPS27A	RPS27A	8697	0.03	0.38	NO
74	XRCC5	XRCC5	XRCC5	8783	0.029	0.38	NO
75	RANGAP1	RANGAP1	RANGAP1	8813	0.028	0.38	NO
76	NUP54	NUP54	NUP54	8872	0.027	0.38	NO
77	NUP214	NUP214	NUP214	8905	0.027	0.38	NO
78	TAF11	TAF11	TAF11	9154	0.024	0.37	NO
79	ERCC2	ERCC2	ERCC2	9218	0.023	0.37	NO
80	ERCC3	ERCC3	ERCC3	9288	0.022	0.37	NO
81	POLR2J	POLR2J	POLR2J	9297	0.022	0.37	NO
82	SUPT4H1	SUPT4H1	SUPT4H1	9417	0.02	0.37	NO
83	TSG101	TSG101	TSG101	9509	0.018	0.37	NO
84	GTF2F1	GTF2F1	GTF2F1	9571	0.017	0.36	NO
85	NUP153	NUP153	NUP153	9575	0.017	0.37	NO
86	TAF4	TAF4	TAF4	9774	0.014	0.36	NO
87	TAF5	TAF5	TAF5	9784	0.014	0.36	NO
88	CDK9	CDK9	CDK9	9806	0.014	0.36	NO
89	TCEA1	TCEA1	TCEA1	9863	0.013	0.36	NO
90	CCNH	CCNH	CCNH	9975	0.011	0.35	NO
91	GTF2H4	GTF2H4	GTF2H4	9995	0.011	0.35	NO
92	UBA52	UBA52	UBA52	10003	0.011	0.36	NO
93	NUP50	NUP50	NUP50	10014	0.011	0.36	NO
94	POLR2A	POLR2A	POLR2A	10130	0.0091	0.35	NO
95	GTF2A2	GTF2A2	GTF2A2	10595	0.0026	0.32	NO
96	CCNT2	CCNT2	CCNT2	10601	0.0024	0.32	NO
97	TPR	TPR	TPR	10709	0.00086	0.32	NO
98	NMT1	NMT1	NMT1	10786	-0.00027	0.31	NO
99	POLR2C	POLR2C	POLR2C	11031	-0.004	0.3	NO
100	POM121	POM121	POM121	11050	-0.0044	0.3	NO
101	NUP133	NUP133	NUP133	11195	-0.0066	0.29	NO
102	RANBP2	RANBP2	RANBP2	11229	-0.007	0.29	NO
103	VPS28	VPS28	VPS28	11317	-0.0084	0.29	NO
104	TH1L	TH1L	TH1L	11439	-0.01	0.28	NO
105	POLR2E	POLR2E	POLR2E	11449	-0.01	0.28	NO
106	ELL	ELL	ELL	11557	-0.012	0.28	NO
107	TAF1	TAF1	TAF1	11569	-0.012	0.28	NO
108	NUP88	NUP88	NUP88	12072	-0.021	0.25	NO
109	CCNT1	CCNT1	CCNT1	12282	-0.025	0.25	NO
110	POLR2F	POLR2F	POLR2F	12287	-0.025	0.25	NO
111	GTF2A1	GTF2A1	GTF2A1	13556	-0.052	0.18	NO
112	LIG4	LIG4	LIG4	14291	-0.072	0.15	NO
113	NMT2	NMT2	NMT2	14951	-0.097	0.13	NO
114	VPS37D	VPS37D	VPS37D	16923	-0.24	0.046	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: BIOCARTA FMLP PATHWAY.

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FMLP 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 IL2 PI3KPATHWAY

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	CSTF2	CSTF2	CSTF2	1782	0.24	-0.054	YES
2	TAF4B	TAF4B	TAF4B	2370	0.2	-0.048	YES
3	UPF3B	UPF3B	UPF3B	2645	0.18	-0.027	YES
4	THOC4	THOC4	THOC4	3349	0.15	-0.037	YES
5	GTF2H2B	GTF2H2B	GTF2H2B	3651	0.14	-0.027	YES
6	GTF2H2	GTF2H2	GTF2H2	3730	0.14	-0.0043	YES
7	SNRPB	SNRPB	SNRPB	4003	0.13	0.0052	YES
8	TAF12	TAF12	TAF12	4377	0.12	0.0067	YES
9	SNRPF	SNRPF	SNRPF	4393	0.12	0.028	YES
10	TAF6	TAF6	TAF6	4439	0.11	0.048	YES
11	TCEB1	TCEB1	TCEB1	4897	0.1	0.042	YES
12	LSM10	LSM10	LSM10	4982	0.098	0.056	YES
13	POLR2D	POLR2D	POLR2D	5178	0.092	0.063	YES
14	TBP	TBP	TBP	5225	0.091	0.078	YES
15	RNPS1	RNPS1	RNPS1	5348	0.088	0.088	YES
16	RNGTT	RNGTT	RNGTT	5400	0.087	0.1	YES
17	GTF2E2	GTF2E2	GTF2E2	5434	0.086	0.12	YES
18	MAGOH	MAGOH	MAGOH	5494	0.084	0.13	YES
19	SSRP1	SSRP1	SSRP1	5545	0.083	0.14	YES
20	CPSF3	CPSF3	CPSF3	5554	0.083	0.16	YES
21	SLBP	SLBP	SLBP	5795	0.077	0.16	YES
22	RDBP	RDBP	RDBP	5906	0.075	0.17	YES
23	GTF2H1	GTF2H1	GTF2H1	5939	0.074	0.18	YES
24	POLR2H	POLR2H	POLR2H	5946	0.074	0.2	YES
25	POLR2G	POLR2G	POLR2G	5971	0.074	0.21	YES
26	ZNF473	ZNF473	ZNF473	5987	0.074	0.22	YES
27	U2AF2	U2AF2	U2AF2	6026	0.073	0.24	YES
28	GTF2H3	GTF2H3	GTF2H3	6050	0.072	0.25	YES
29	SNRPG	SNRPG	SNRPG	6125	0.071	0.26	YES
30	NCBP2	NCBP2	NCBP2	6133	0.071	0.27	YES
31	TCEB3	TCEB3	TCEB3	6253	0.069	0.28	YES
32	TAF9	TAF9	TAF9	6583	0.063	0.27	YES
33	NCBP1	NCBP1	NCBP1	6825	0.059	0.27	YES
34	SNRPE	SNRPE	SNRPE	6925	0.057	0.28	YES
35	TAF13	TAF13	TAF13	7047	0.055	0.28	YES
36	RBM8A	RBM8A	RBM8A	7060	0.054	0.29	YES
37	U2AF1	U2AF1	U2AF1	7076	0.054	0.3	YES
38	SUPT5H	SUPT5H	SUPT5H	7092	0.054	0.31	YES
39	POLR2K	POLR2K	POLR2K	7315	0.05	0.31	YES
40	CTDP1	CTDP1	CTDP1	7329	0.05	0.32	YES
41	MNAT1	MNAT1	MNAT1	7354	0.049	0.32	YES
42	GTF2E1	GTF2E1	GTF2E1	7523	0.047	0.32	YES
43	RNMT	RNMT	RNMT	7527	0.047	0.33	YES
44	GTF2F2	GTF2F2	GTF2F2	7571	0.046	0.34	YES
45	SUPT16H	SUPT16H	SUPT16H	7609	0.046	0.34	YES
46	CSTF3	CSTF3	CSTF3	7614	0.046	0.35	YES
47	GTF2B	GTF2B	GTF2B	7628	0.045	0.36	YES
48	SRRM1	SRRM1	SRRM1	7701	0.044	0.37	YES
49	COBRA1	COBRA1	COBRA1	7831	0.042	0.37	YES
50	TAF10	TAF10	TAF10	7879	0.042	0.37	YES
51	POLR2I	POLR2I	POLR2I	7971	0.04	0.38	YES
52	POLR2B	POLR2B	POLR2B	8051	0.039	0.38	YES
53	POLR2L	POLR2L	POLR2L	8131	0.038	0.38	YES
54	WHSC2	WHSC2	WHSC2	8171	0.038	0.39	YES
55	DHX38	DHX38	DHX38	8288	0.036	0.39	YES
56	CDK7	CDK7	CDK7	8343	0.035	0.39	YES
57	CPSF1	CPSF1	CPSF1	8500	0.033	0.39	YES
58	PAPOLA	PAPOLA	PAPOLA	8562	0.032	0.39	YES
59	TCEB2	TCEB2	TCEB2	8675	0.03	0.39	YES
60	PABPN1	PABPN1	PABPN1	8693	0.03	0.4	YES
61	NUDT21	NUDT21	NUDT21	8825	0.028	0.39	YES
62	CPSF2	CPSF2	CPSF2	9041	0.025	0.39	YES
63	TAF11	TAF11	TAF11	9154	0.024	0.38	YES
64	CDC40	CDC40	CDC40	9196	0.023	0.39	YES
65	ERCC2	ERCC2	ERCC2	9218	0.023	0.39	YES
66	ERCC3	ERCC3	ERCC3	9288	0.022	0.39	YES
67	POLR2J	POLR2J	POLR2J	9297	0.022	0.4	YES
68	CLP1	CLP1	CLP1	9306	0.021	0.4	YES
69	SUPT4H1	SUPT4H1	SUPT4H1	9417	0.02	0.4	NO
70	GTF2F1	GTF2F1	GTF2F1	9571	0.017	0.39	NO
71	TAF4	TAF4	TAF4	9774	0.014	0.38	NO
72	TAF5	TAF5	TAF5	9784	0.014	0.38	NO
73	CDK9	CDK9	CDK9	9806	0.014	0.39	NO
74	TCEA1	TCEA1	TCEA1	9863	0.013	0.38	NO
75	CCNH	CCNH	CCNH	9975	0.011	0.38	NO
76	GTF2H4	GTF2H4	GTF2H4	9995	0.011	0.38	NO
77	CPSF7	CPSF7	CPSF7	10105	0.0096	0.38	NO
78	POLR2A	POLR2A	POLR2A	10130	0.0091	0.38	NO
79	GTF2A2	GTF2A2	GTF2A2	10595	0.0026	0.35	NO
80	CCNT2	CCNT2	CCNT2	10601	0.0024	0.35	NO
81	SNRPD3	SNRPD3	SNRPD3	10702	0.00097	0.35	NO
82	POLR2C	POLR2C	POLR2C	11031	-0.004	0.33	NO
83	TH1L	TH1L	TH1L	11439	-0.01	0.31	NO
84	POLR2E	POLR2E	POLR2E	11449	-0.01	0.31	NO
85	LSM11	LSM11	LSM11	11473	-0.011	0.31	NO
86	ELL	ELL	ELL	11557	-0.012	0.31	NO
87	TAF1	TAF1	TAF1	11569	-0.012	0.31	NO
88	NFX1	NFX1	NFX1	12262	-0.024	0.28	NO
89	CCNT1	CCNT1	CCNT1	12282	-0.025	0.28	NO
90	POLR2F	POLR2F	POLR2F	12287	-0.025	0.28	NO
91	CSTF1	CSTF1	CSTF1	12322	-0.026	0.29	NO
92	PCF11	PCF11	PCF11	13281	-0.046	0.24	NO
93	GTF2A1	GTF2A1	GTF2A1	13556	-0.052	0.24	NO

Figure S7. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID IL2 PI3KPATHWAY.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: PID IL2 PI3KPATHWAY, 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 CASPASE PATHWAY

Table S5. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PSMA8	PSMA8	PSMA8	220	0.47	0.039	YES
2	CD8B	CD8B	CD8B	948	0.32	0.034	YES
3	HCK	HCK	HCK	1253	0.29	0.048	YES
4	AP1M2	AP1M2	AP1M2	1275	0.28	0.078	YES
5	DOCK2	DOCK2	DOCK2	1450	0.27	0.098	YES
6	LCK	LCK	LCK	1530	0.26	0.12	YES
7	APOBEC3G	APOBEC3G	APOBEC3G	1567	0.26	0.15	YES
8	PSMB9	PSMB9	PSMB9	1778	0.24	0.16	YES
9	HMGA1	HMGA1	HMGA1	1784	0.24	0.19	YES
10	CD28	CD28	CD28	1858	0.24	0.21	YES
11	RCC1	RCC1	RCC1	1941	0.23	0.23	YES
12	CD247	CD247	CD247	2505	0.19	0.22	YES
13	NUP37	NUP37	NUP37	3033	0.17	0.21	YES
14	NUP188	NUP188	NUP188	3118	0.16	0.22	YES
15	NUP93	NUP93	NUP93	3299	0.15	0.23	YES
16	NUP210	NUP210	NUP210	3337	0.15	0.25	YES
17	NUP62	NUP62	NUP62	3421	0.15	0.26	YES
18	NUP107	NUP107	NUP107	3450	0.15	0.27	YES
19	PSMB8	PSMB8	PSMB8	3634	0.14	0.28	YES
20	NUP43	NUP43	NUP43	3727	0.14	0.29	YES
21	PSMB10	PSMB10	PSMB10	3811	0.13	0.3	YES
22	RAN	RAN	RAN	3951	0.13	0.3	YES
23	NUP205	NUP205	NUP205	3971	0.13	0.32	YES
24	PSMD14	PSMD14	PSMD14	4220	0.12	0.32	YES
25	NUP155	NUP155	NUP155	4261	0.12	0.33	YES
26	PSMA5	PSMA5	PSMA5	4626	0.11	0.32	YES
27	AP1S2	AP1S2	AP1S2	4636	0.11	0.33	YES
28	PSMB2	PSMB2	PSMB2	4724	0.1	0.34	YES
29	NUP85	NUP85	NUP85	4786	0.1	0.34	YES
30	TCEB1	TCEB1	TCEB1	4897	0.1	0.35	YES
31	NPM1	NPM1	NPM1	5312	0.089	0.34	YES
32	ELMO1	ELMO1	ELMO1	5353	0.088	0.34	YES
33	HLA-A	HLA-A	HLA-A	5381	0.087	0.35	YES
34	RANBP1	RANBP1	RANBP1	5401	0.087	0.36	YES
35	PSMD2	PSMD2	PSMD2	5622	0.081	0.36	YES
36	CD4	CD4	CD4	5637	0.081	0.36	YES
37	PSIP1	PSIP1	PSIP1	5643	0.081	0.37	YES
38	PACS1	PACS1	PACS1	5797	0.077	0.37	YES
39	KPNB1	KPNB1	KPNB1	5866	0.076	0.38	YES
40	SEH1L	SEH1L	SEH1L	6075	0.072	0.37	YES
41	PSMD10	PSMD10	PSMD10	6085	0.072	0.38	YES
42	PSMD12	PSMD12	PSMD12	6318	0.067	0.38	YES
43	RAC1	RAC1	RAC1	6340	0.067	0.38	YES
44	NUPL1	NUPL1	NUPL1	6360	0.067	0.39	YES
45	PPIA	PPIA	PPIA	6587	0.062	0.38	YES
46	BANF1	BANF1	BANF1	6621	0.062	0.39	YES
47	PSMD13	PSMD13	PSMD13	6700	0.061	0.39	YES
48	PSMB3	PSMB3	PSMB3	6741	0.06	0.39	YES
49	PSMA1	PSMA1	PSMA1	6781	0.059	0.4	YES
50	NUP35	NUP35	NUP35	6783	0.059	0.4	YES
51	PSMC4	PSMC4	PSMC4	6990	0.055	0.4	YES
52	PSMD1	PSMD1	PSMD1	7002	0.055	0.4	YES
53	AP2S1	AP2S1	AP2S1	7020	0.055	0.41	YES
54	RAE1	RAE1	RAE1	7340	0.05	0.4	YES
55	PSMD7	PSMD7	PSMD7	7381	0.049	0.4	YES
56	PSMB1	PSMB1	PSMB1	7387	0.049	0.41	YES
57	SLC25A6	SLC25A6	SLC25A6	7439	0.048	0.41	YES
58	PSMD3	PSMD3	PSMD3	7449	0.048	0.41	YES
59	PSMD9	PSMD9	PSMD9	7683	0.045	0.4	YES
60	AP1B1	AP1B1	AP1B1	7735	0.044	0.41	YES
61	PSMD11	PSMD11	PSMD11	7789	0.043	0.41	YES
62	NUPL2	NUPL2	NUPL2	7842	0.042	0.41	YES
63	PSMA4	PSMA4	PSMA4	7875	0.042	0.41	YES
64	AAAS	AAAS	AAAS	7913	0.041	0.42	YES
65	PSMA3	PSMA3	PSMA3	7979	0.04	0.42	YES
66	PAK2	PAK2	PAK2	8140	0.038	0.41	YES
67	RBX1	RBX1	RBX1	8167	0.038	0.41	YES
68	PSMD8	PSMD8	PSMD8	8176	0.037	0.42	YES
69	PSMD5	PSMD5	PSMD5	8290	0.036	0.42	YES
70	ATP6V1H	ATP6V1H	ATP6V1H	8320	0.035	0.42	YES
71	PSMC5	PSMC5	PSMC5	8363	0.035	0.42	YES
72	PSME2	PSME2	PSME2	8417	0.034	0.42	YES
73	PSMC3	PSMC3	PSMC3	8446	0.034	0.42	YES
74	XPO1	XPO1	XPO1	8557	0.032	0.42	YES
75	AP2M1	AP2M1	AP2M1	8661	0.03	0.42	YES
76	TCEB2	TCEB2	TCEB2	8675	0.03	0.42	YES
77	RPS27A	RPS27A	RPS27A	8697	0.03	0.42	YES
78	PSMB4	PSMB4	PSMB4	8722	0.03	0.42	YES
79	RANGAP1	RANGAP1	RANGAP1	8813	0.028	0.42	YES
80	NUP54	NUP54	NUP54	8872	0.027	0.42	YES
81	NUP214	NUP214	NUP214	8905	0.027	0.42	YES
82	PSMB7	PSMB7	PSMB7	8968	0.026	0.42	YES
83	PSMA7	PSMA7	PSMA7	8973	0.026	0.42	YES
84	PSMA6	PSMA6	PSMA6	9021	0.025	0.42	YES
85	PSMC1	PSMC1	PSMC1	9404	0.02	0.4	NO
86	PSMC2	PSMC2	PSMC2	9407	0.02	0.41	NO
87	PSMD4	PSMD4	PSMD4	9467	0.019	0.41	NO
88	PSME4	PSME4	PSME4	9480	0.019	0.41	NO
89	NUP153	NUP153	NUP153	9575	0.017	0.4	NO
90	PSMD6	PSMD6	PSMD6	9653	0.016	0.4	NO
91	SLC25A5	SLC25A5	SLC25A5	9722	0.015	0.4	NO
92	AP2B1	AP2B1	AP2B1	9752	0.015	0.4	NO
93	CDK9	CDK9	CDK9	9806	0.014	0.4	NO
94	AP1S1	AP1S1	AP1S1	9938	0.012	0.39	NO
95	UBA52	UBA52	UBA52	10003	0.011	0.39	NO
96	NUP50	NUP50	NUP50	10014	0.011	0.39	NO
97	PSMB6	PSMB6	PSMB6	10219	0.0077	0.38	NO
98	B2M	B2M	B2M	10267	0.0071	0.38	NO
99	AP1M1	AP1M1	AP1M1	10452	0.0045	0.37	NO
100	AP2A2	AP2A2	AP2A2	10576	0.0029	0.36	NO
101	PSMC6	PSMC6	PSMC6	10581	0.0028	0.36	NO
102	PSMB5	PSMB5	PSMB5	10629	0.0022	0.36	NO
103	AP2A1	AP2A1	AP2A1	10647	0.0018	0.36	NO
104	PSME1	PSME1	PSME1	10693	0.0011	0.36	NO
105	TPR	TPR	TPR	10709	0.00086	0.35	NO
106	SKP1	SKP1	SKP1	10734	0.00053	0.35	NO
107	POM121	POM121	POM121	11050	-0.0044	0.34	NO
108	AP1G1	AP1G1	AP1G1	11051	-0.0044	0.34	NO
109	NUP133	NUP133	NUP133	11195	-0.0066	0.33	NO
110	RANBP2	RANBP2	RANBP2	11229	-0.007	0.33	NO
111	ARF1	ARF1	ARF1	11364	-0.009	0.32	NO
112	PSMF1	PSMF1	PSMF1	11406	-0.0096	0.32	NO
113	PSMA2	PSMA2	PSMA2	11435	-0.01	0.32	NO
114	CUL5	CUL5	CUL5	12048	-0.02	0.29	NO
115	NUP88	NUP88	NUP88	12072	-0.021	0.29	NO
116	CCNT1	CCNT1	CCNT1	12282	-0.025	0.28	NO
117	KPNA1	KPNA1	KPNA1	12769	-0.034	0.26	NO
118	BTRC	BTRC	BTRC	13409	-0.048	0.22	NO
119	SLC25A4	SLC25A4	SLC25A4	14552	-0.08	0.17	NO
120	FYN	FYN	FYN	15313	-0.11	0.14	NO

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

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

genes ES table in pathway: REACTOME CELL CYCLE

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	CDC25A	CDC25A	CDC25A	114	0.52	0.034	YES
2	CDC45	CDC45	CDC45	158	0.5	0.071	YES
3	PSMA8	PSMA8	PSMA8	220	0.47	0.1	YES
4	CDC6	CDC6	CDC6	305	0.44	0.13	YES
5	GINS1	GINS1	GINS1	331	0.43	0.17	YES
6	CDT1	CDT1	CDT1	358	0.42	0.2	YES
7	CCNE1	CCNE1	CCNE1	563	0.38	0.22	YES
8	CCNE2	CCNE2	CCNE2	675	0.36	0.24	YES
9	POLE2	POLE2	POLE2	729	0.35	0.26	YES
10	CCNA2	CCNA2	CCNA2	746	0.35	0.29	YES
11	GINS4	GINS4	GINS4	757	0.35	0.32	YES
12	MCM8	MCM8	MCM8	1049	0.31	0.32	YES
13	GINS2	GINS2	GINS2	1164	0.29	0.34	YES
14	MCM2	MCM2	MCM2	1213	0.29	0.36	YES
15	CDC25B	CDC25B	CDC25B	1399	0.27	0.37	YES
16	PRIM1	PRIM1	PRIM1	1641	0.25	0.38	YES
17	RFC4	RFC4	RFC4	1766	0.24	0.39	YES
18	PSMB9	PSMB9	PSMB9	1778	0.24	0.41	YES
19	POLA2	POLA2	POLA2	1986	0.23	0.41	YES
20	DNA2	DNA2	DNA2	2017	0.22	0.43	YES
21	MCM6	MCM6	MCM6	2057	0.22	0.44	YES
22	MCM4	MCM4	MCM4	2098	0.22	0.46	YES
23	FEN1	FEN1	FEN1	2433	0.2	0.46	YES
24	MCM7	MCM7	MCM7	2511	0.19	0.47	YES
25	PRIM2	PRIM2	PRIM2	2547	0.19	0.48	YES
26	POLA1	POLA1	POLA1	2568	0.19	0.49	YES
27	POLD1	POLD1	POLD1	2647	0.18	0.5	YES
28	MCM5	MCM5	MCM5	3333	0.15	0.48	YES
29	MCM3	MCM3	MCM3	3454	0.15	0.48	YES
30	POLD3	POLD3	POLD3	3496	0.15	0.49	YES
31	PSMB8	PSMB8	PSMB8	3634	0.14	0.49	YES
32	CKS1B	CKS1B	CKS1B	3666	0.14	0.5	YES
33	SKP2	SKP2	SKP2	3700	0.14	0.51	YES
34	CDK4	CDK4	CDK4	3779	0.14	0.52	YES
35	PSMB10	PSMB10	PSMB10	3811	0.13	0.53	YES
36	CCNA1	CCNA1	CCNA1	3998	0.13	0.53	YES
37	RFC3	RFC3	RFC3	4037	0.13	0.53	YES
38	LIG1	LIG1	LIG1	4146	0.12	0.54	YES
39	PCNA	PCNA	PCNA	4148	0.12	0.55	YES
40	PSMD14	PSMD14	PSMD14	4220	0.12	0.55	YES
41	RFC2	RFC2	RFC2	4288	0.12	0.56	YES
42	RPA2	RPA2	RPA2	4335	0.12	0.56	YES
43	CDK2	CDK2	CDK2	4374	0.12	0.57	YES
44	RFC5	RFC5	RFC5	4574	0.11	0.57	YES
45	PSMA5	PSMA5	PSMA5	4626	0.11	0.57	YES
46	PSMB2	PSMB2	PSMB2	4724	0.1	0.58	YES
47	RPA3	RPA3	RPA3	5359	0.087	0.55	NO
48	PSMD2	PSMD2	PSMD2	5622	0.081	0.54	NO
49	PSMD10	PSMD10	PSMD10	6085	0.072	0.52	NO
50	POLE	POLE	POLE	6157	0.07	0.52	NO
51	PSMD12	PSMD12	PSMD12	6318	0.067	0.52	NO
52	MAX	MAX	MAX	6397	0.066	0.52	NO
53	PSMD13	PSMD13	PSMD13	6700	0.061	0.5	NO
54	PSMB3	PSMB3	PSMB3	6741	0.06	0.51	NO
55	PSMA1	PSMA1	PSMA1	6781	0.059	0.51	NO
56	PSMC4	PSMC4	PSMC4	6990	0.055	0.5	NO
57	PSMD1	PSMD1	PSMD1	7002	0.055	0.51	NO
58	RPA1	RPA1	RPA1	7222	0.052	0.5	NO
59	MNAT1	MNAT1	MNAT1	7354	0.049	0.5	NO
60	PSMD7	PSMD7	PSMD7	7381	0.049	0.5	NO
61	PSMB1	PSMB1	PSMB1	7387	0.049	0.5	NO
62	PSMD3	PSMD3	PSMD3	7449	0.048	0.5	NO
63	PSMD9	PSMD9	PSMD9	7683	0.045	0.49	NO
64	PSMD11	PSMD11	PSMD11	7789	0.043	0.49	NO
65	PSMA4	PSMA4	PSMA4	7875	0.042	0.49	NO
66	PSMA3	PSMA3	PSMA3	7979	0.04	0.48	NO
67	PSMD8	PSMD8	PSMD8	8176	0.037	0.48	NO
68	PSMD5	PSMD5	PSMD5	8290	0.036	0.47	NO
69	WEE1	WEE1	WEE1	8316	0.036	0.47	NO
70	POLD2	POLD2	POLD2	8327	0.035	0.48	NO
71	CDK7	CDK7	CDK7	8343	0.035	0.48	NO
72	PSMC5	PSMC5	PSMC5	8363	0.035	0.48	NO
73	PSME2	PSME2	PSME2	8417	0.034	0.48	NO
74	PSMC3	PSMC3	PSMC3	8446	0.034	0.48	NO
75	RPS27A	RPS27A	RPS27A	8697	0.03	0.47	NO
76	PSMB4	PSMB4	PSMB4	8722	0.03	0.47	NO
77	PSMB7	PSMB7	PSMB7	8968	0.026	0.46	NO
78	PSMA7	PSMA7	PSMA7	8973	0.026	0.46	NO
79	PSMA6	PSMA6	PSMA6	9021	0.025	0.46	NO
80	PSMC1	PSMC1	PSMC1	9404	0.02	0.44	NO
81	PSMC2	PSMC2	PSMC2	9407	0.02	0.44	NO
82	PSMD4	PSMD4	PSMD4	9467	0.019	0.44	NO
83	PSME4	PSME4	PSME4	9480	0.019	0.44	NO
84	PSMD6	PSMD6	PSMD6	9653	0.016	0.43	NO
85	MYC	MYC	MYC	9782	0.014	0.42	NO
86	CCNH	CCNH	CCNH	9975	0.011	0.41	NO
87	UBA52	UBA52	UBA52	10003	0.011	0.41	NO
88	PSMB6	PSMB6	PSMB6	10219	0.0077	0.4	NO
89	PSMC6	PSMC6	PSMC6	10581	0.0028	0.38	NO
90	PSMB5	PSMB5	PSMB5	10629	0.0022	0.38	NO
91	PSME1	PSME1	PSME1	10693	0.0011	0.38	NO
92	SKP1	SKP1	SKP1	10734	0.00053	0.37	NO
93	CUL1	CUL1	CUL1	11082	-0.0049	0.35	NO
94	PSMF1	PSMF1	PSMF1	11406	-0.0096	0.34	NO
95	PSMA2	PSMA2	PSMA2	11435	-0.01	0.34	NO
96	POLD4	POLD4	POLD4	11922	-0.018	0.31	NO
97	RB1	RB1	RB1	12314	-0.025	0.29	NO
98	CDKN1B	CDKN1B	CDKN1B	12848	-0.036	0.26	NO
99	CDKN1A	CDKN1A	CDKN1A	13155	-0.043	0.25	NO
100	CCND1	CCND1	CCND1	15847	-0.14	0.11	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 CELL CYCLE.

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

genes ES table in pathway: REACTOME MHC CLASS II ANTIGEN PRESENTATION

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	E2F2	E2F2	E2F2	29	0.61	0.033	YES
2	MCM10	MCM10	MCM10	58	0.57	0.063	YES
3	MYBL2	MYBL2	MYBL2	60	0.57	0.095	YES
4	CDC25A	CDC25A	CDC25A	114	0.52	0.12	YES
5	PKMYT1	PKMYT1	PKMYT1	140	0.5	0.15	YES
6	CDC45	CDC45	CDC45	158	0.5	0.17	YES
7	CDC7	CDC7	CDC7	289	0.44	0.19	YES
8	CDC6	CDC6	CDC6	305	0.44	0.22	YES
9	CDT1	CDT1	CDT1	358	0.42	0.24	YES
10	CDKN2A	CDKN2A	CDKN2A	361	0.42	0.26	YES
11	CCNB1	CCNB1	CCNB1	455	0.4	0.28	YES
12	CDK1	CDK1	CDK1	477	0.4	0.3	YES
13	CCNE1	CCNE1	CCNE1	563	0.38	0.31	YES
14	FBXO5	FBXO5	FBXO5	595	0.37	0.33	YES
15	RRM2	RRM2	RRM2	661	0.36	0.35	YES
16	CCNE2	CCNE2	CCNE2	675	0.36	0.37	YES
17	POLE2	POLE2	POLE2	729	0.35	0.38	YES
18	CCNA2	CCNA2	CCNA2	746	0.35	0.4	YES
19	RBL1	RBL1	RBL1	964	0.32	0.41	YES
20	MCM8	MCM8	MCM8	1049	0.31	0.42	YES
21	E2F1	E2F1	E2F1	1194	0.29	0.43	YES
22	MCM2	MCM2	MCM2	1213	0.29	0.44	YES
23	E2F5	E2F5	E2F5	1303	0.28	0.46	YES
24	DBF4	DBF4	DBF4	1389	0.27	0.47	YES
25	PRIM1	PRIM1	PRIM1	1641	0.25	0.47	YES
26	PSMB9	PSMB9	PSMB9	1778	0.24	0.47	YES
27	TYMS	TYMS	TYMS	1841	0.24	0.48	YES
28	CDKN2C	CDKN2C	CDKN2C	1943	0.23	0.49	YES
29	POLA2	POLA2	POLA2	1986	0.23	0.5	YES
30	MCM6	MCM6	MCM6	2057	0.22	0.51	YES
31	MCM4	MCM4	MCM4	2098	0.22	0.52	YES
32	RPA4	RPA4	RPA4	2328	0.2	0.52	YES
33	CDKN2B	CDKN2B	CDKN2B	2343	0.2	0.53	YES
34	CDKN2D	CDKN2D	CDKN2D	2344	0.2	0.54	YES
35	LIN9	LIN9	LIN9	2449	0.2	0.54	YES
36	MCM7	MCM7	MCM7	2511	0.19	0.55	YES
37	PRIM2	PRIM2	PRIM2	2547	0.19	0.56	YES
38	POLA1	POLA1	POLA1	2568	0.19	0.57	YES
39	E2F3	E2F3	E2F3	2690	0.18	0.57	YES
40	MCM5	MCM5	MCM5	3333	0.15	0.54	YES
41	MCM3	MCM3	MCM3	3454	0.15	0.55	YES
42	PSMB8	PSMB8	PSMB8	3634	0.14	0.54	YES
43	CKS1B	CKS1B	CKS1B	3666	0.14	0.55	YES
44	SKP2	SKP2	SKP2	3700	0.14	0.55	YES
45	CDK4	CDK4	CDK4	3779	0.14	0.56	YES
46	PSMB10	PSMB10	PSMB10	3811	0.13	0.56	YES
47	CCNA1	CCNA1	CCNA1	3998	0.13	0.56	YES
48	PCNA	PCNA	PCNA	4148	0.12	0.56	YES
49	HDAC1	HDAC1	HDAC1	4197	0.12	0.56	YES
50	PSMD14	PSMD14	PSMD14	4220	0.12	0.57	YES
51	RPA2	RPA2	RPA2	4335	0.12	0.57	YES
52	CDK2	CDK2	CDK2	4374	0.12	0.57	YES
53	PSMA5	PSMA5	PSMA5	4626	0.11	0.56	NO
54	PSMB2	PSMB2	PSMB2	4724	0.1	0.56	NO
55	CCND2	CCND2	CCND2	5006	0.097	0.55	NO
56	E2F4	E2F4	E2F4	5241	0.09	0.55	NO
57	RPA3	RPA3	RPA3	5359	0.087	0.54	NO
58	PSMD2	PSMD2	PSMD2	5622	0.081	0.53	NO
59	RBBP4	RBBP4	RBBP4	5722	0.079	0.53	NO
60	PSMD10	PSMD10	PSMD10	6085	0.072	0.52	NO
61	POLE	POLE	POLE	6157	0.07	0.52	NO
62	PSMD12	PSMD12	PSMD12	6318	0.067	0.51	NO
63	PPP2R3B	PPP2R3B	PPP2R3B	6322	0.067	0.51	NO
64	MAX	MAX	MAX	6397	0.066	0.51	NO
65	CCND3	CCND3	CCND3	6468	0.065	0.51	NO
66	PSMD13	PSMD13	PSMD13	6700	0.061	0.5	NO
67	PSMB3	PSMB3	PSMB3	6741	0.06	0.5	NO
68	PSMA1	PSMA1	PSMA1	6781	0.059	0.5	NO
69	PSMC4	PSMC4	PSMC4	6990	0.055	0.5	NO
70	PSMD1	PSMD1	PSMD1	7002	0.055	0.5	NO
71	LIN37	LIN37	LIN37	7021	0.055	0.5	NO
72	RPA1	RPA1	RPA1	7222	0.052	0.49	NO
73	MNAT1	MNAT1	MNAT1	7354	0.049	0.49	NO
74	PSMD7	PSMD7	PSMD7	7381	0.049	0.49	NO
75	PSMB1	PSMB1	PSMB1	7387	0.049	0.49	NO
76	PSMD3	PSMD3	PSMD3	7449	0.048	0.49	NO
77	LIN54	LIN54	LIN54	7592	0.046	0.48	NO
78	PSMD9	PSMD9	PSMD9	7683	0.045	0.48	NO
79	PSMD11	PSMD11	PSMD11	7789	0.043	0.48	NO
80	PSMA4	PSMA4	PSMA4	7875	0.042	0.48	NO
81	PPP2R1A	PPP2R1A	PPP2R1A	7883	0.042	0.48	NO
82	PSMA3	PSMA3	PSMA3	7979	0.04	0.48	NO
83	PSMD8	PSMD8	PSMD8	8176	0.037	0.47	NO
84	PSMD5	PSMD5	PSMD5	8290	0.036	0.46	NO
85	WEE1	WEE1	WEE1	8316	0.036	0.46	NO
86	CDK7	CDK7	CDK7	8343	0.035	0.46	NO
87	PSMC5	PSMC5	PSMC5	8363	0.035	0.46	NO
88	PSME2	PSME2	PSME2	8417	0.034	0.46	NO
89	PSMC3	PSMC3	PSMC3	8446	0.034	0.46	NO
90	PPP2CA	PPP2CA	PPP2CA	8533	0.032	0.46	NO
91	RPS27A	RPS27A	RPS27A	8697	0.03	0.45	NO
92	PSMB4	PSMB4	PSMB4	8722	0.03	0.45	NO
93	TFDP1	TFDP1	TFDP1	8914	0.027	0.44	NO
94	PSMB7	PSMB7	PSMB7	8968	0.026	0.44	NO
95	PSMA7	PSMA7	PSMA7	8973	0.026	0.44	NO
96	PSMA6	PSMA6	PSMA6	9021	0.025	0.44	NO
97	PPP2R2A	PPP2R2A	PPP2R2A	9071	0.024	0.44	NO
98	DHFR	DHFR	DHFR	9114	0.024	0.44	NO
99	PSMC1	PSMC1	PSMC1	9404	0.02	0.42	NO
100	PSMC2	PSMC2	PSMC2	9407	0.02	0.42	NO
101	PSMD4	PSMD4	PSMD4	9467	0.019	0.42	NO
102	PSMD6	PSMD6	PSMD6	9653	0.016	0.41	NO
103	MYC	MYC	MYC	9782	0.014	0.41	NO
104	CCNH	CCNH	CCNH	9975	0.011	0.4	NO
105	UBA52	UBA52	UBA52	10003	0.011	0.4	NO
106	PSMB6	PSMB6	PSMB6	10219	0.0077	0.38	NO
107	PSMC6	PSMC6	PSMC6	10581	0.0028	0.36	NO
108	PSMB5	PSMB5	PSMB5	10629	0.0022	0.36	NO
109	PSME1	PSME1	PSME1	10693	0.0011	0.36	NO
110	SKP1	SKP1	SKP1	10734	0.00053	0.36	NO
111	CUL1	CUL1	CUL1	11082	-0.0049	0.34	NO
112	PSMF1	PSMF1	PSMF1	11406	-0.0096	0.32	NO
113	PSMA2	PSMA2	PSMA2	11435	-0.01	0.32	NO
114	PPP2CB	PPP2CB	PPP2CB	11558	-0.012	0.31	NO
115	CDK6	CDK6	CDK6	12086	-0.021	0.28	NO
116	RB1	RB1	RB1	12314	-0.025	0.27	NO
117	CDKN1B	CDKN1B	CDKN1B	12848	-0.036	0.24	NO
118	CDKN1A	CDKN1A	CDKN1A	13155	-0.043	0.23	NO
119	DYRK1A	DYRK1A	DYRK1A	13306	-0.046	0.22	NO
120	TK2	TK2	TK2	14701	-0.086	0.15	NO
121	RBL2	RBL2	RBL2	14964	-0.098	0.14	NO
122	LIN52	LIN52	LIN52	15083	-0.1	0.14	NO
123	PPP2R1B	PPP2R1B	PPP2R1B	15145	-0.1	0.14	NO
124	CCND1	CCND1	CCND1	15847	-0.14	0.11	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 MHC CLASS II ANTIGEN PRESENTATION.

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

genes ES table in pathway: REACTOME RNA POL II 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	KIF2C	KIF2C	KIF2C	19	0.63	0.01	YES
2	E2F2	E2F2	E2F2	29	0.61	0.02	YES
3	CDC20	CDC20	CDC20	49	0.58	0.029	YES
4	CENPA	CENPA	CENPA	51	0.58	0.04	YES
5	ERCC6L	ERCC6L	ERCC6L	53	0.58	0.05	YES
6	MCM10	MCM10	MCM10	58	0.57	0.059	YES
7	MYBL2	MYBL2	MYBL2	60	0.57	0.069	YES
8	SGOL1	SGOL1	SGOL1	74	0.56	0.078	YES
9	KIF18A	KIF18A	KIF18A	78	0.55	0.088	YES
10	SKA1	SKA1	SKA1	86	0.54	0.097	YES
11	BIRC5	BIRC5	BIRC5	99	0.53	0.11	YES
12	CDC25A	CDC25A	CDC25A	114	0.52	0.11	YES
13	PLK1	PLK1	PLK1	128	0.51	0.12	YES
14	BUB1	BUB1	BUB1	131	0.51	0.13	YES
15	KIF23	KIF23	KIF23	133	0.51	0.14	YES
16	PKMYT1	PKMYT1	PKMYT1	140	0.5	0.15	YES
17	CDCA8	CDCA8	CDCA8	146	0.5	0.16	YES
18	BUB1B	BUB1B	BUB1B	147	0.5	0.16	YES
19	PLK4	PLK4	PLK4	149	0.5	0.17	YES
20	CDC45	CDC45	CDC45	158	0.5	0.18	YES
21	PTTG1	PTTG1	PTTG1	165	0.49	0.19	YES
22	CENPM	CENPM	CENPM	168	0.49	0.2	YES
23	NDC80	NDC80	NDC80	171	0.49	0.21	YES
24	SPC25	SPC25	SPC25	173	0.49	0.22	YES
25	CDC25C	CDC25C	CDC25C	186	0.48	0.22	YES
26	NUF2	NUF2	NUF2	197	0.47	0.23	YES
27	CENPI	CENPI	CENPI	218	0.47	0.24	YES
28	PSMA8	PSMA8	PSMA8	220	0.47	0.25	YES
29	CENPK	CENPK	CENPK	229	0.46	0.25	YES
30	HJURP	HJURP	HJURP	250	0.46	0.26	YES
31	AURKB	AURKB	AURKB	256	0.46	0.27	YES
32	KIF20A	KIF20A	KIF20A	264	0.45	0.28	YES
33	SGOL2	SGOL2	SGOL2	279	0.45	0.28	YES
34	OIP5	OIP5	OIP5	288	0.44	0.29	YES
35	CDC7	CDC7	CDC7	289	0.44	0.3	YES
36	CCNB2	CCNB2	CCNB2	293	0.44	0.31	YES
37	CDC6	CDC6	CDC6	305	0.44	0.31	YES
38	NEK2	NEK2	NEK2	321	0.43	0.32	YES
39	GINS1	GINS1	GINS1	331	0.43	0.33	YES
40	CDT1	CDT1	CDT1	358	0.42	0.33	YES
41	CDKN2A	CDKN2A	CDKN2A	361	0.42	0.34	YES
42	MAD2L1	MAD2L1	MAD2L1	398	0.41	0.34	YES
43	CCNB1	CCNB1	CCNB1	455	0.4	0.35	YES
44	CDK1	CDK1	CDK1	477	0.4	0.35	YES
45	CENPO	CENPO	CENPO	485	0.39	0.36	YES
46	CENPH	CENPH	CENPH	510	0.39	0.37	YES
47	CCNE1	CCNE1	CCNE1	563	0.38	0.37	YES
48	UBE2C	UBE2C	UBE2C	589	0.37	0.38	YES
49	FBXO5	FBXO5	FBXO5	595	0.37	0.38	YES
50	RRM2	RRM2	RRM2	661	0.36	0.38	YES
51	CCNE2	CCNE2	CCNE2	675	0.36	0.39	YES
52	POLE2	POLE2	POLE2	729	0.35	0.39	YES
53	CCNA2	CCNA2	CCNA2	746	0.35	0.4	YES
54	GINS4	GINS4	GINS4	757	0.35	0.4	YES
55	SMC1B	SMC1B	SMC1B	819	0.34	0.41	YES
56	RBL1	RBL1	RBL1	964	0.32	0.4	YES
57	MCM8	MCM8	MCM8	1049	0.31	0.4	YES
58	KNTC1	KNTC1	KNTC1	1072	0.31	0.41	YES
59	CHEK1	CHEK1	CHEK1	1102	0.3	0.41	YES
60	MLF1IP	MLF1IP	MLF1IP	1127	0.3	0.42	YES
61	ZWINT	ZWINT	ZWINT	1151	0.3	0.42	YES
62	GINS2	GINS2	GINS2	1164	0.29	0.42	YES
63	E2F1	E2F1	E2F1	1194	0.29	0.43	YES
64	LMNB1	LMNB1	LMNB1	1196	0.29	0.43	YES
65	MCM2	MCM2	MCM2	1213	0.29	0.44	YES
66	BRCA1	BRCA1	BRCA1	1229	0.29	0.44	YES
67	CENPJ	CENPJ	CENPJ	1262	0.28	0.44	YES
68	E2F5	E2F5	E2F5	1303	0.28	0.45	YES
69	CEP135	CEP135	CEP135	1360	0.28	0.45	YES
70	SPC24	SPC24	SPC24	1386	0.27	0.45	YES
71	DBF4	DBF4	DBF4	1389	0.27	0.46	YES
72	CDC25B	CDC25B	CDC25B	1399	0.27	0.46	YES
73	CDC14A	CDC14A	CDC14A	1454	0.27	0.46	YES
74	CCDC99	CCDC99	CCDC99	1469	0.27	0.46	YES
75	CENPL	CENPL	CENPL	1616	0.25	0.46	YES
76	KIF2A	KIF2A	KIF2A	1634	0.25	0.46	YES
77	PRIM1	PRIM1	PRIM1	1641	0.25	0.47	YES
78	PRKAR2B	PRKAR2B	PRKAR2B	1667	0.25	0.47	YES
79	TERT	TERT	TERT	1671	0.25	0.48	YES
80	RFC4	RFC4	RFC4	1766	0.24	0.48	YES
81	PSMB9	PSMB9	PSMB9	1778	0.24	0.48	YES
82	TYMS	TYMS	TYMS	1841	0.24	0.48	YES
83	HIST1H4D	HIST1H4D	HIST1H4D	1882	0.23	0.48	YES
84	TUBA4A	TUBA4A	TUBA4A	1899	0.23	0.48	YES
85	ITGB3BP	ITGB3BP	ITGB3BP	1912	0.23	0.49	YES
86	CENPP	CENPP	CENPP	1935	0.23	0.49	YES
87	CDKN2C	CDKN2C	CDKN2C	1943	0.23	0.49	YES
88	POLA2	POLA2	POLA2	1986	0.23	0.5	YES
89	HIST1H2AB	HIST1H2AB	HIST1H2AB	2010	0.22	0.5	YES
90	AURKA	AURKA	AURKA	2016	0.22	0.5	YES
91	DNA2	DNA2	DNA2	2017	0.22	0.5	YES
92	INCENP	INCENP	INCENP	2027	0.22	0.51	YES
93	MCM6	MCM6	MCM6	2057	0.22	0.51	YES
94	MCM4	MCM4	MCM4	2098	0.22	0.51	YES
95	HIST1H2AD	HIST1H2AD	HIST1H2AD	2140	0.22	0.51	YES
96	AZI1	AZI1	AZI1	2170	0.21	0.52	YES
97	H2AFX	H2AFX	H2AFX	2177	0.21	0.52	YES
98	HIST1H2BL	HIST1H2BL	HIST1H2BL	2268	0.21	0.52	YES
99	HIST1H4E	HIST1H4E	HIST1H4E	2291	0.21	0.52	YES
100	RPA4	RPA4	RPA4	2328	0.2	0.52	YES
101	CDKN2B	CDKN2B	CDKN2B	2343	0.2	0.52	YES
102	CDKN2D	CDKN2D	CDKN2D	2344	0.2	0.53	YES
103	CENPQ	CENPQ	CENPQ	2415	0.2	0.53	YES
104	FEN1	FEN1	FEN1	2433	0.2	0.53	YES
105	RCC2	RCC2	RCC2	2437	0.2	0.53	YES
106	HIST1H2AJ	HIST1H2AJ	HIST1H2AJ	2444	0.2	0.54	YES
107	LIN9	LIN9	LIN9	2449	0.2	0.54	YES
108	MCM7	MCM7	MCM7	2511	0.19	0.54	YES
109	PRIM2	PRIM2	PRIM2	2547	0.19	0.54	YES
110	POLA1	POLA1	POLA1	2568	0.19	0.54	YES
111	H2AFZ	H2AFZ	H2AFZ	2579	0.19	0.55	YES
112	REC8	REC8	REC8	2643	0.18	0.55	YES
113	POLD1	POLD1	POLD1	2647	0.18	0.55	YES
114	E2F3	E2F3	E2F3	2690	0.18	0.55	YES
115	HIST1H4A	HIST1H4A	HIST1H4A	2701	0.18	0.55	YES
116	HIST1H4H	HIST1H4H	HIST1H4H	2741	0.18	0.55	YES
117	ZWILCH	ZWILCH	ZWILCH	2827	0.17	0.55	YES
118	APITD1	APITD1	APITD1	2828	0.17	0.55	YES
119	HIST1H2BG	HIST1H2BG	HIST1H2BG	2942	0.17	0.55	YES
120	NUP37	NUP37	NUP37	3033	0.17	0.55	YES
121	NEDD1	NEDD1	NEDD1	3135	0.16	0.55	YES
122	HIST1H2BN	HIST1H2BN	HIST1H2BN	3177	0.16	0.55	YES
123	HIST1H4C	HIST1H4C	HIST1H4C	3262	0.16	0.54	YES
124	ACD	ACD	ACD	3279	0.16	0.55	YES
125	HIST1H2BO	HIST1H2BO	HIST1H2BO	3283	0.16	0.55	YES
126	MCM5	MCM5	MCM5	3333	0.15	0.55	YES
127	B9D2	B9D2	B9D2	3352	0.15	0.55	YES
128	CEP72	CEP72	CEP72	3400	0.15	0.55	YES
129	HIST4H4	HIST4H4	HIST4H4	3403	0.15	0.55	YES
130	NUP107	NUP107	NUP107	3450	0.15	0.55	YES
131	MCM3	MCM3	MCM3	3454	0.15	0.55	YES
132	TUBG1	TUBG1	TUBG1	3456	0.15	0.56	YES
133	HIST1H2BM	HIST1H2BM	HIST1H2BM	3491	0.15	0.56	YES
134	POLD3	POLD3	POLD3	3496	0.15	0.56	YES
135	SYCP2	SYCP2	SYCP2	3603	0.14	0.56	YES
136	PSMB8	PSMB8	PSMB8	3634	0.14	0.56	YES
137	CKS1B	CKS1B	CKS1B	3666	0.14	0.56	YES
138	SKP2	SKP2	SKP2	3700	0.14	0.56	YES
139	NUP43	NUP43	NUP43	3727	0.14	0.56	YES
140	CDK4	CDK4	CDK4	3779	0.14	0.56	YES
141	DKC1	DKC1	DKC1	3783	0.14	0.56	YES
142	PSMB10	PSMB10	PSMB10	3811	0.13	0.56	YES
143	CENPN	CENPN	CENPN	3852	0.13	0.56	YES
144	CCNA1	CCNA1	CCNA1	3998	0.13	0.56	YES
145	UBE2D1	UBE2D1	UBE2D1	4001	0.13	0.56	YES
146	UBE2I	UBE2I	UBE2I	4007	0.13	0.56	YES
147	RFC3	RFC3	RFC3	4037	0.13	0.56	YES
148	CASC5	CASC5	CASC5	4059	0.13	0.56	YES
149	WRAP53	WRAP53	WRAP53	4093	0.12	0.56	YES
150	MAPRE1	MAPRE1	MAPRE1	4115	0.12	0.56	YES
151	LIG1	LIG1	LIG1	4146	0.12	0.56	YES
152	PCNA	PCNA	PCNA	4148	0.12	0.56	YES
153	HDAC1	HDAC1	HDAC1	4197	0.12	0.56	YES
154	PSMD14	PSMD14	PSMD14	4220	0.12	0.56	YES
155	RFC2	RFC2	RFC2	4288	0.12	0.56	YES
156	RPA2	RPA2	RPA2	4335	0.12	0.56	YES
157	CHEK2	CHEK2	CHEK2	4370	0.12	0.56	YES
158	CDK2	CDK2	CDK2	4374	0.12	0.56	YES
159	RUVBL1	RUVBL1	RUVBL1	4501	0.11	0.56	YES
160	RFC5	RFC5	RFC5	4574	0.11	0.56	YES
161	RAD9A	RAD9A	RAD9A	4621	0.11	0.56	YES
162	PSMA5	PSMA5	PSMA5	4626	0.11	0.56	YES
163	CKAP5	CKAP5	CKAP5	4658	0.11	0.56	YES
164	SMARCA5	SMARCA5	SMARCA5	4661	0.11	0.56	YES
165	PPP1CC	PPP1CC	PPP1CC	4672	0.11	0.56	YES
166	HIST1H2BF	HIST1H2BF	HIST1H2BF	4680	0.11	0.56	YES
167	DSN1	DSN1	DSN1	4714	0.1	0.56	YES
168	RAD1	RAD1	RAD1	4719	0.1	0.56	YES
169	PSMB2	PSMB2	PSMB2	4724	0.1	0.56	YES
170	NUDC	NUDC	NUDC	4777	0.1	0.56	YES
171	NUP85	NUP85	NUP85	4786	0.1	0.56	YES
172	ANAPC7	ANAPC7	ANAPC7	4821	0.1	0.56	NO
173	TUBB	TUBB	TUBB	4868	0.1	0.56	NO
174	TUBG2	TUBG2	TUBG2	4964	0.098	0.56	NO
175	CCND2	CCND2	CCND2	5006	0.097	0.56	NO
176	HIST1H4B	HIST1H4B	HIST1H4B	5017	0.096	0.56	NO
177	CEP164	CEP164	CEP164	5042	0.096	0.56	NO
178	HIST1H2BJ	HIST1H2BJ	HIST1H2BJ	5079	0.095	0.56	NO
179	E2F4	E2F4	E2F4	5241	0.09	0.55	NO
180	NPM1	NPM1	NPM1	5312	0.089	0.55	NO
181	ATRIP	ATRIP	ATRIP	5325	0.088	0.55	NO
182	HSPA2	HSPA2	HSPA2	5346	0.088	0.55	NO
183	RPA3	RPA3	RPA3	5359	0.087	0.55	NO
184	HIST2H2AC	HIST2H2AC	HIST2H2AC	5476	0.085	0.55	NO
185	RPS27	RPS27	RPS27	5510	0.084	0.55	NO
186	UBE2E1	UBE2E1	UBE2E1	5548	0.083	0.55	NO
187	PSMD2	PSMD2	PSMD2	5622	0.081	0.54	NO
188	CEP250	CEP250	CEP250	5697	0.08	0.54	NO
189	RBBP4	RBBP4	RBBP4	5722	0.079	0.54	NO
190	DYNLL1	DYNLL1	DYNLL1	5728	0.079	0.54	NO
191	CSNK1D	CSNK1D	CSNK1D	5729	0.079	0.54	NO
192	TUBA1A	TUBA1A	TUBA1A	5733	0.079	0.54	NO
193	DYNC1H1	DYNC1H1	DYNC1H1	5780	0.078	0.54	NO
194	RUVBL2	RUVBL2	RUVBL2	5876	0.076	0.54	NO
195	TEX12	TEX12	TEX12	5897	0.075	0.54	NO
196	RAD21	RAD21	RAD21	6028	0.073	0.53	NO
197	SEH1L	SEH1L	SEH1L	6075	0.072	0.53	NO
198	PSMD10	PSMD10	PSMD10	6085	0.072	0.53	NO
199	POLE	POLE	POLE	6157	0.07	0.53	NO
200	DCTN2	DCTN2	DCTN2	6174	0.07	0.53	NO
201	SSNA1	SSNA1	SSNA1	6314	0.067	0.52	NO
202	PSMD12	PSMD12	PSMD12	6318	0.067	0.52	NO
203	PPP2R3B	PPP2R3B	PPP2R3B	6322	0.067	0.52	NO
204	CDC27	CDC27	CDC27	6332	0.067	0.52	NO
205	OFD1	OFD1	OFD1	6344	0.067	0.53	NO
206	MAX	MAX	MAX	6397	0.066	0.52	NO
207	HIST1H2BH	HIST1H2BH	HIST1H2BH	6466	0.065	0.52	NO
208	CCND3	CCND3	CCND3	6468	0.065	0.52	NO
209	TAOK1	TAOK1	TAOK1	6694	0.061	0.51	NO
210	PSMD13	PSMD13	PSMD13	6700	0.061	0.51	NO
211	PSMB3	PSMB3	PSMB3	6741	0.06	0.51	NO
212	BUB3	BUB3	BUB3	6749	0.06	0.51	NO
213	RBBP7	RBBP7	RBBP7	6764	0.06	0.51	NO
214	CDK5RAP2	CDK5RAP2	CDK5RAP2	6777	0.059	0.51	NO
215	PSMA1	PSMA1	PSMA1	6781	0.059	0.51	NO
216	HIST1H2BC	HIST1H2BC	HIST1H2BC	6798	0.059	0.51	NO
217	SMC1A	SMC1A	SMC1A	6821	0.059	0.51	NO
218	ANAPC1	ANAPC1	ANAPC1	6840	0.058	0.51	NO
219	ANAPC11	ANAPC11	ANAPC11	6903	0.057	0.51	NO
220	GMNN	GMNN	GMNN	6955	0.056	0.51	NO
221	HIST2H4A	HIST2H4A	HIST2H4A	6978	0.056	0.51	NO
222	PSMC4	PSMC4	PSMC4	6990	0.055	0.51	NO
223	PSMD1	PSMD1	PSMD1	7002	0.055	0.51	NO
224	LIN37	LIN37	LIN37	7021	0.055	0.51	NO
225	SEC13	SEC13	SEC13	7039	0.055	0.51	NO
226	CEP290	CEP290	CEP290	7048	0.055	0.51	NO
227	ATR	ATR	ATR	7117	0.054	0.5	NO
228	ANAPC4	ANAPC4	ANAPC4	7169	0.053	0.5	NO
229	DCTN1	DCTN1	DCTN1	7187	0.052	0.5	NO
230	RPA1	RPA1	RPA1	7222	0.052	0.5	NO
231	ATM	ATM	ATM	7350	0.049	0.5	NO
232	MNAT1	MNAT1	MNAT1	7354	0.049	0.5	NO
233	PSMD7	PSMD7	PSMD7	7381	0.049	0.5	NO
234	PSMB1	PSMB1	PSMB1	7387	0.049	0.5	NO
235	PSMD3	PSMD3	PSMD3	7449	0.048	0.49	NO
236	LIN54	LIN54	LIN54	7592	0.046	0.49	NO
237	NHP2	NHP2	NHP2	7608	0.046	0.49	NO
238	PCNT	PCNT	PCNT	7619	0.046	0.49	NO
239	PSMD9	PSMD9	PSMD9	7683	0.045	0.48	NO
240	CENPT	CENPT	CENPT	7692	0.044	0.48	NO
241	ALMS1	ALMS1	ALMS1	7728	0.044	0.48	NO
242	FGFR1OP	FGFR1OP	FGFR1OP	7772	0.043	0.48	NO
243	PSMD11	PSMD11	PSMD11	7789	0.043	0.48	NO
244	CSNK1E	CSNK1E	CSNK1E	7818	0.042	0.48	NO
245	HSP90AA1	HSP90AA1	HSP90AA1	7854	0.042	0.48	NO
246	ANAPC5	ANAPC5	ANAPC5	7860	0.042	0.48	NO
247	PSMA4	PSMA4	PSMA4	7875	0.042	0.48	NO
248	PPP2R1A	PPP2R1A	PPP2R1A	7883	0.042	0.48	NO
249	PSMA3	PSMA3	PSMA3	7979	0.04	0.47	NO
250	PPP2R5E	PPP2R5E	PPP2R5E	8010	0.04	0.47	NO
251	YWHAG	YWHAG	YWHAG	8059	0.039	0.47	NO
252	CDC26	CDC26	CDC26	8080	0.039	0.47	NO
253	PSMD8	PSMD8	PSMD8	8176	0.037	0.47	NO
254	SKA2	SKA2	SKA2	8191	0.037	0.47	NO
255	LMNA	LMNA	LMNA	8251	0.036	0.46	NO
256	PPP2R5B	PPP2R5B	PPP2R5B	8265	0.036	0.46	NO
257	PSMD5	PSMD5	PSMD5	8290	0.036	0.46	NO
258	WEE1	WEE1	WEE1	8316	0.036	0.46	NO
259	POLD2	POLD2	POLD2	8327	0.035	0.46	NO
260	CDK7	CDK7	CDK7	8343	0.035	0.46	NO
261	PSMC5	PSMC5	PSMC5	8363	0.035	0.46	NO
262	HIST3H2BB	HIST3H2BB	HIST3H2BB	8400	0.034	0.46	NO
263	PSME2	PSME2	PSME2	8417	0.034	0.46	NO
264	PSMC3	PSMC3	PSMC3	8446	0.034	0.46	NO
265	PPP2CA	PPP2CA	PPP2CA	8533	0.032	0.45	NO
266	XPO1	XPO1	XPO1	8557	0.032	0.45	NO
267	RPS27A	RPS27A	RPS27A	8697	0.03	0.44	NO
268	TERF1	TERF1	TERF1	8710	0.03	0.44	NO
269	PSMB4	PSMB4	PSMB4	8722	0.03	0.44	NO
270	RANGAP1	RANGAP1	RANGAP1	8813	0.028	0.44	NO
271	TFDP1	TFDP1	TFDP1	8914	0.027	0.44	NO
272	PSMB7	PSMB7	PSMB7	8968	0.026	0.43	NO
273	PSMA7	PSMA7	PSMA7	8973	0.026	0.43	NO
274	CDC23	CDC23	CDC23	8980	0.026	0.43	NO
275	PSMA6	PSMA6	PSMA6	9021	0.025	0.43	NO
276	PPP2R2A	PPP2R2A	PPP2R2A	9071	0.024	0.43	NO
277	DCTN3	DCTN3	DCTN3	9090	0.024	0.43	NO
278	DHFR	DHFR	DHFR	9114	0.024	0.43	NO
279	DYNC1I2	DYNC1I2	DYNC1I2	9220	0.022	0.42	NO
280	PCM1	PCM1	PCM1	9317	0.021	0.42	NO
281	RSF1	RSF1	RSF1	9396	0.02	0.41	NO
282	PSMC1	PSMC1	PSMC1	9404	0.02	0.41	NO
283	PSMC2	PSMC2	PSMC2	9407	0.02	0.41	NO
284	CEP76	CEP76	CEP76	9421	0.02	0.41	NO
285	HUS1	HUS1	HUS1	9440	0.019	0.41	NO
286	PSMD4	PSMD4	PSMD4	9467	0.019	0.41	NO
287	PSME4	PSME4	PSME4	9480	0.019	0.41	NO
288	CETN2	CETN2	CETN2	9547	0.018	0.41	NO
289	HAUS2	HAUS2	HAUS2	9550	0.018	0.41	NO
290	CEP192	CEP192	CEP192	9574	0.017	0.4	NO
291	PSMD6	PSMD6	PSMD6	9653	0.016	0.4	NO
292	ZW10	ZW10	ZW10	9665	0.016	0.4	NO
293	PPP2R5D	PPP2R5D	PPP2R5D	9750	0.015	0.4	NO
294	MYC	MYC	MYC	9782	0.014	0.39	NO
295	STAG2	STAG2	STAG2	9835	0.013	0.39	NO
296	PMF1	PMF1	PMF1	9856	0.013	0.39	NO
297	CCNH	CCNH	CCNH	9975	0.011	0.38	NO
298	UBA52	UBA52	UBA52	10003	0.011	0.38	NO
299	YWHAE	YWHAE	YWHAE	10008	0.011	0.38	NO
300	GORASP1	GORASP1	GORASP1	10161	0.0086	0.37	NO
301	POT1	POT1	POT1	10213	0.0078	0.37	NO
302	PSMB6	PSMB6	PSMB6	10219	0.0077	0.37	NO
303	MAD1L1	MAD1L1	MAD1L1	10510	0.0038	0.36	NO
304	PSMC6	PSMC6	PSMC6	10581	0.0028	0.35	NO
305	PSMB5	PSMB5	PSMB5	10629	0.0022	0.35	NO
306	PSME1	PSME1	PSME1	10693	0.0011	0.34	NO
307	SKP1	SKP1	SKP1	10734	0.00053	0.34	NO
308	CLIP1	CLIP1	CLIP1	10753	0.00018	0.34	NO
309	NSL1	NSL1	NSL1	10758	0.000067	0.34	NO
310	CDC16	CDC16	CDC16	10778	-0.00015	0.34	NO
311	ACTR1A	ACTR1A	ACTR1A	10901	-0.002	0.33	NO
312	NUMA1	NUMA1	NUMA1	10911	-0.0022	0.33	NO
313	TUBGCP2	TUBGCP2	TUBGCP2	11012	-0.0037	0.33	NO
314	CEP63	CEP63	CEP63	11028	-0.0039	0.33	NO
315	RFWD2	RFWD2	RFWD2	11030	-0.004	0.33	NO
316	CUL1	CUL1	CUL1	11082	-0.0049	0.32	NO
317	ANAPC10	ANAPC10	ANAPC10	11087	-0.005	0.32	NO
318	DIDO1	DIDO1	DIDO1	11131	-0.0056	0.32	NO
319	MDM2	MDM2	MDM2	11147	-0.0058	0.32	NO
320	NUP133	NUP133	NUP133	11195	-0.0066	0.32	NO
321	RANBP2	RANBP2	RANBP2	11229	-0.007	0.32	NO
322	SMC3	SMC3	SMC3	11239	-0.0072	0.32	NO
323	SDCCAG8	SDCCAG8	SDCCAG8	11242	-0.0072	0.32	NO
324	TUBGCP3	TUBGCP3	TUBGCP3	11400	-0.0096	0.31	NO
325	PSMF1	PSMF1	PSMF1	11406	-0.0096	0.31	NO
326	PSMA2	PSMA2	PSMA2	11435	-0.01	0.3	NO
327	PPP2CB	PPP2CB	PPP2CB	11558	-0.012	0.3	NO
328	AHCTF1	AHCTF1	AHCTF1	11598	-0.013	0.3	NO
329	AKAP9	AKAP9	AKAP9	11630	-0.014	0.29	NO
330	RAD17	RAD17	RAD17	11668	-0.014	0.29	NO
331	ANAPC2	ANAPC2	ANAPC2	11787	-0.016	0.29	NO
332	HIST1H2BK	HIST1H2BK	HIST1H2BK	11891	-0.018	0.28	NO
333	POLD4	POLD4	POLD4	11922	-0.018	0.28	NO
334	CDK6	CDK6	CDK6	12086	-0.021	0.27	NO
335	STAG1	STAG1	STAG1	12089	-0.021	0.27	NO
336	RB1	RB1	RB1	12314	-0.025	0.26	NO
337	HIST1H4K	HIST1H4K	HIST1H4K	12391	-0.027	0.25	NO
338	TERF2	TERF2	TERF2	12401	-0.027	0.25	NO
339	HIST1H4I	HIST1H4I	HIST1H4I	12568	-0.03	0.24	NO
340	HIST1H2BE	HIST1H2BE	HIST1H2BE	12669	-0.032	0.24	NO
341	TINF2	TINF2	TINF2	12691	-0.033	0.24	NO
342	MIS12	MIS12	MIS12	12743	-0.034	0.24	NO
343	CLASP1	CLASP1	CLASP1	12808	-0.035	0.23	NO
344	CDKN1B	CDKN1B	CDKN1B	12848	-0.036	0.23	NO
345	PAFAH1B1	PAFAH1B1	PAFAH1B1	12863	-0.036	0.23	NO
346	TERF2IP	TERF2IP	TERF2IP	12970	-0.038	0.23	NO
347	CEP70	CEP70	CEP70	13019	-0.04	0.22	NO
348	CDKN1A	CDKN1A	CDKN1A	13155	-0.043	0.22	NO
349	CEP57	CEP57	CEP57	13178	-0.044	0.22	NO
350	PPP2R5C	PPP2R5C	PPP2R5C	13195	-0.044	0.22	NO
351	DYRK1A	DYRK1A	DYRK1A	13306	-0.046	0.21	NO
352	HIST2H2BE	HIST2H2BE	HIST2H2BE	13336	-0.047	0.21	NO
353	HIST1H2AE	HIST1H2AE	HIST1H2AE	13349	-0.047	0.21	NO
354	BTRC	BTRC	BTRC	13409	-0.048	0.21	NO
355	TUBGCP6	TUBGCP6	TUBGCP6	13415	-0.048	0.21	NO
356	TP53	TP53	TP53	13854	-0.06	0.18	NO
357	HIST1H2BD	HIST1H2BD	HIST1H2BD	13993	-0.063	0.18	NO
358	SYNE1	SYNE1	SYNE1	14060	-0.065	0.17	NO
359	SYNE2	SYNE2	SYNE2	14243	-0.071	0.16	NO
360	PPP2R5A	PPP2R5A	PPP2R5A	14363	-0.075	0.16	NO
361	HIST1H2AC	HIST1H2AC	HIST1H2AC	14383	-0.075	0.16	NO
362	HIST2H2AA3	HIST2H2AA3	HIST2H2AA3	14419	-0.077	0.16	NO
363	PRKACA	PRKACA	PRKACA	14668	-0.085	0.15	NO
364	TK2	TK2	TK2	14701	-0.086	0.15	NO
365	TUBGCP5	TUBGCP5	TUBGCP5	14723	-0.087	0.15	NO
366	CENPC1	CENPC1	CENPC1	14733	-0.088	0.15	NO
367	RBL2	RBL2	RBL2	14964	-0.098	0.14	NO
368	LIN52	LIN52	LIN52	15083	-0.1	0.13	NO
369	PPP2R1B	PPP2R1B	PPP2R1B	15145	-0.1	0.13	NO
370	NDEL1	NDEL1	NDEL1	15228	-0.11	0.13	NO
371	SUN2	SUN2	SUN2	15485	-0.12	0.11	NO
372	CCND1	CCND1	CCND1	15847	-0.14	0.095	NO
373	NINL	NINL	NINL	15861	-0.14	0.097	NO
374	STAG3	STAG3	STAG3	16042	-0.16	0.089	NO
375	HIST1H4J	HIST1H4J	HIST1H4J	16660	-0.21	0.057	NO
376	FKBP6	FKBP6	FKBP6	16918	-0.24	0.047	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 II TRANSCRIPTION.

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

genes ES table in pathway: REACTOME CELL CYCLE MITOTIC

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	RCC1	RCC1	RCC1	1941	0.23	-0.072	YES
2	TAF4B	TAF4B	TAF4B	2370	0.2	-0.063	YES
3	NUP37	NUP37	NUP37	3033	0.17	-0.073	YES
4	NUP188	NUP188	NUP188	3118	0.16	-0.051	YES
5	NUP93	NUP93	NUP93	3299	0.15	-0.036	YES
6	NUP210	NUP210	NUP210	3337	0.15	-0.013	YES
7	NUP62	NUP62	NUP62	3421	0.15	0.0072	YES
8	NUP107	NUP107	NUP107	3450	0.15	0.03	YES
9	GTF2H2B	GTF2H2B	GTF2H2B	3651	0.14	0.042	YES
10	NUP43	NUP43	NUP43	3727	0.14	0.06	YES
11	GTF2H2	GTF2H2	GTF2H2	3730	0.14	0.083	YES
12	RAN	RAN	RAN	3951	0.13	0.092	YES
13	NUP205	NUP205	NUP205	3971	0.13	0.11	YES
14	NUP155	NUP155	NUP155	4261	0.12	0.12	YES
15	VPS37C	VPS37C	VPS37C	4280	0.12	0.13	YES
16	TAF12	TAF12	TAF12	4377	0.12	0.15	YES
17	TAF6	TAF6	TAF6	4439	0.11	0.16	YES
18	NUP85	NUP85	NUP85	4786	0.1	0.16	YES
19	TCEB1	TCEB1	TCEB1	4897	0.1	0.17	YES
20	POLR2D	POLR2D	POLR2D	5178	0.092	0.17	YES
21	TBP	TBP	TBP	5225	0.091	0.18	YES
22	RNGTT	RNGTT	RNGTT	5400	0.087	0.19	YES
23	RANBP1	RANBP1	RANBP1	5401	0.087	0.2	YES
24	GTF2E2	GTF2E2	GTF2E2	5434	0.086	0.21	YES
25	SSRP1	SSRP1	SSRP1	5545	0.083	0.22	YES
26	RDBP	RDBP	RDBP	5906	0.075	0.21	YES
27	GTF2H1	GTF2H1	GTF2H1	5939	0.074	0.22	YES
28	POLR2H	POLR2H	POLR2H	5946	0.074	0.24	YES
29	POLR2G	POLR2G	POLR2G	5971	0.074	0.25	YES
30	GTF2H3	GTF2H3	GTF2H3	6050	0.072	0.25	YES
31	SEH1L	SEH1L	SEH1L	6075	0.072	0.26	YES
32	NCBP2	NCBP2	NCBP2	6133	0.071	0.27	YES
33	TCEB3	TCEB3	TCEB3	6253	0.069	0.28	YES
34	NUPL1	NUPL1	NUPL1	6360	0.067	0.28	YES
35	VPS37A	VPS37A	VPS37A	6415	0.066	0.29	YES
36	TAF9	TAF9	TAF9	6583	0.063	0.29	YES
37	NUP35	NUP35	NUP35	6783	0.059	0.29	YES
38	NCBP1	NCBP1	NCBP1	6825	0.059	0.3	YES
39	TAF13	TAF13	TAF13	7047	0.055	0.29	YES
40	SUPT5H	SUPT5H	SUPT5H	7092	0.054	0.3	YES
41	POLR2K	POLR2K	POLR2K	7315	0.05	0.3	YES
42	CTDP1	CTDP1	CTDP1	7329	0.05	0.3	YES
43	RAE1	RAE1	RAE1	7340	0.05	0.31	YES
44	MNAT1	MNAT1	MNAT1	7354	0.049	0.32	YES
45	GTF2E1	GTF2E1	GTF2E1	7523	0.047	0.32	YES
46	RNMT	RNMT	RNMT	7527	0.047	0.32	YES
47	GTF2F2	GTF2F2	GTF2F2	7571	0.046	0.33	YES
48	SUPT16H	SUPT16H	SUPT16H	7609	0.046	0.33	YES
49	GTF2B	GTF2B	GTF2B	7628	0.045	0.34	YES
50	COBRA1	COBRA1	COBRA1	7831	0.042	0.34	YES
51	NUPL2	NUPL2	NUPL2	7842	0.042	0.34	YES
52	TAF10	TAF10	TAF10	7879	0.042	0.35	YES
53	AAAS	AAAS	AAAS	7913	0.041	0.35	YES
54	VPS37B	VPS37B	VPS37B	7927	0.041	0.36	YES
55	POLR2I	POLR2I	POLR2I	7971	0.04	0.36	YES
56	POLR2B	POLR2B	POLR2B	8051	0.039	0.36	YES
57	POLR2L	POLR2L	POLR2L	8131	0.038	0.37	YES
58	WHSC2	WHSC2	WHSC2	8171	0.038	0.37	YES
59	CDK7	CDK7	CDK7	8343	0.035	0.37	NO
60	XPO1	XPO1	XPO1	8557	0.032	0.36	NO
61	TCEB2	TCEB2	TCEB2	8675	0.03	0.36	NO
62	RPS27A	RPS27A	RPS27A	8697	0.03	0.36	NO
63	RANGAP1	RANGAP1	RANGAP1	8813	0.028	0.36	NO
64	NUP54	NUP54	NUP54	8872	0.027	0.36	NO
65	NUP214	NUP214	NUP214	8905	0.027	0.36	NO
66	TAF11	TAF11	TAF11	9154	0.024	0.35	NO
67	ERCC2	ERCC2	ERCC2	9218	0.023	0.35	NO
68	ERCC3	ERCC3	ERCC3	9288	0.022	0.35	NO
69	POLR2J	POLR2J	POLR2J	9297	0.022	0.36	NO
70	SUPT4H1	SUPT4H1	SUPT4H1	9417	0.02	0.35	NO
71	TSG101	TSG101	TSG101	9509	0.018	0.35	NO
72	GTF2F1	GTF2F1	GTF2F1	9571	0.017	0.35	NO
73	NUP153	NUP153	NUP153	9575	0.017	0.35	NO
74	TAF4	TAF4	TAF4	9774	0.014	0.34	NO
75	TAF5	TAF5	TAF5	9784	0.014	0.35	NO
76	CDK9	CDK9	CDK9	9806	0.014	0.35	NO
77	TCEA1	TCEA1	TCEA1	9863	0.013	0.35	NO
78	CCNH	CCNH	CCNH	9975	0.011	0.34	NO
79	GTF2H4	GTF2H4	GTF2H4	9995	0.011	0.34	NO
80	UBA52	UBA52	UBA52	10003	0.011	0.34	NO
81	NUP50	NUP50	NUP50	10014	0.011	0.34	NO
82	POLR2A	POLR2A	POLR2A	10130	0.0091	0.34	NO
83	GTF2A2	GTF2A2	GTF2A2	10595	0.0026	0.31	NO
84	CCNT2	CCNT2	CCNT2	10601	0.0024	0.31	NO
85	TPR	TPR	TPR	10709	0.00086	0.31	NO
86	NMT1	NMT1	NMT1	10786	-0.00027	0.3	NO
87	POLR2C	POLR2C	POLR2C	11031	-0.004	0.29	NO
88	POM121	POM121	POM121	11050	-0.0044	0.29	NO
89	NUP133	NUP133	NUP133	11195	-0.0066	0.28	NO
90	RANBP2	RANBP2	RANBP2	11229	-0.007	0.28	NO
91	VPS28	VPS28	VPS28	11317	-0.0084	0.28	NO
92	TH1L	TH1L	TH1L	11439	-0.01	0.27	NO
93	POLR2E	POLR2E	POLR2E	11449	-0.01	0.28	NO
94	ELL	ELL	ELL	11557	-0.012	0.27	NO
95	TAF1	TAF1	TAF1	11569	-0.012	0.27	NO
96	NUP88	NUP88	NUP88	12072	-0.021	0.25	NO
97	CCNT1	CCNT1	CCNT1	12282	-0.025	0.24	NO
98	POLR2F	POLR2F	POLR2F	12287	-0.025	0.24	NO
99	GTF2A1	GTF2A1	GTF2A1	13556	-0.052	0.18	NO
100	NMT2	NMT2	NMT2	14951	-0.097	0.12	NO
101	VPS37D	VPS37D	VPS37D	16923	-0.24	0.046	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 CELL CYCLE MITOTIC.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME CELL CYCLE MITOTIC, 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 CELL CYCLE CHECKPOINTS

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	CARD18	CARD18	CARD18	137	0.5	0.048	YES
2	CASP5	CASP5	CASP5	257	0.46	0.091	YES
3	CCL13	CCL13	CCL13	439	0.4	0.12	YES
4	CXCL1	CXCL1	CXCL1	457	0.4	0.17	YES
5	IL18	IL18	IL18	520	0.39	0.21	YES
6	MAPK13	MAPK13	MAPK13	560	0.38	0.25	YES
7	IL1B	IL1B	IL1B	638	0.36	0.28	YES
8	IL8	IL8	IL8	782	0.34	0.31	YES
9	PYCARD	PYCARD	PYCARD	800	0.34	0.35	YES
10	PSTPIP1	PSTPIP1	PSTPIP1	907	0.32	0.38	YES
11	NLRC4	NLRC4	NLRC4	976	0.32	0.41	YES
12	BIRC3	BIRC3	BIRC3	1035	0.31	0.44	YES
13	CARD9	CARD9	CARD9	1036	0.31	0.47	YES
14	TNF	TNF	TNF	1046	0.31	0.51	YES
15	NOD2	NOD2	NOD2	1074	0.31	0.54	YES
16	CARD6	CARD6	CARD6	1221	0.29	0.56	YES
17	CASP1	CASP1	CASP1	1235	0.29	0.59	YES
18	CCL5	CCL5	CCL5	1500	0.26	0.61	YES
19	CCL8	CCL8	CCL8	1862	0.24	0.61	YES
20	NLRP3	NLRP3	NLRP3	1933	0.23	0.64	YES
21	RIPK2	RIPK2	RIPK2	2024	0.22	0.65	YES
22	NAIP	NAIP	NAIP	2382	0.2	0.66	YES
23	MEFV	MEFV	MEFV	2502	0.19	0.67	YES
24	NLRP1	NLRP1	NLRP1	3304	0.15	0.64	NO
25	CASP8	CASP8	CASP8	4134	0.12	0.61	NO
26	IL6	IL6	IL6	4587	0.11	0.6	NO
27	NOD1	NOD1	NOD1	4941	0.099	0.59	NO
28	MAP3K7	MAP3K7	MAP3K7	5063	0.095	0.59	NO
29	MAPK12	MAPK12	MAPK12	5577	0.082	0.57	NO
30	MAPK3	MAPK3	MAPK3	5609	0.082	0.58	NO
31	IKBKG	IKBKG	IKBKG	5771	0.078	0.58	NO
32	NFKBIB	NFKBIB	NFKBIB	6539	0.063	0.54	NO
33	HSP90AB1	HSP90AB1	HSP90AB1	7256	0.051	0.5	NO
34	TNFAIP3	TNFAIP3	TNFAIP3	7548	0.046	0.49	NO
35	HSP90B1	HSP90B1	HSP90B1	7804	0.043	0.48	NO
36	HSP90AA1	HSP90AA1	HSP90AA1	7854	0.042	0.49	NO
37	XIAP	XIAP	XIAP	9455	0.019	0.4	NO
38	SUGT1	SUGT1	SUGT1	9506	0.018	0.4	NO
39	CCL2	CCL2	CCL2	9545	0.018	0.4	NO
40	RELA	RELA	RELA	9664	0.016	0.39	NO
41	NFKB1	NFKB1	NFKB1	9885	0.013	0.38	NO
42	IKBKB	IKBKB	IKBKB	9916	0.012	0.38	NO
43	CXCL2	CXCL2	CXCL2	10615	0.0023	0.34	NO
44	ERBB2IP	ERBB2IP	ERBB2IP	10934	-0.0025	0.32	NO
45	TAB2	TAB2	TAB2	11209	-0.0068	0.31	NO
46	MAPK1	MAPK1	MAPK1	11247	-0.0072	0.31	NO
47	BIRC2	BIRC2	BIRC2	11284	-0.0079	0.31	NO
48	MAPK9	MAPK9	MAPK9	11597	-0.013	0.29	NO
49	MAPK14	MAPK14	MAPK14	11602	-0.013	0.29	NO
50	CARD8	CARD8	CARD8	11620	-0.013	0.29	NO
51	TAB3	TAB3	TAB3	11793	-0.016	0.28	NO
52	TRIP6	TRIP6	TRIP6	12491	-0.028	0.25	NO
53	TAB1	TAB1	TAB1	13035	-0.04	0.22	NO
54	TRAF6	TRAF6	TRAF6	13407	-0.048	0.2	NO
55	CCL11	CCL11	CCL11	13445	-0.049	0.21	NO
56	NFKBIA	NFKBIA	NFKBIA	13481	-0.05	0.21	NO
57	MAPK10	MAPK10	MAPK10	13524	-0.051	0.22	NO
58	CHUK	CHUK	CHUK	13904	-0.061	0.2	NO
59	MAPK11	MAPK11	MAPK11	14030	-0.064	0.2	NO
60	MAPK8	MAPK8	MAPK8	14556	-0.081	0.18	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 CELL CYCLE CHECKPOINTS.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS)	Size(#genes)	genes.ES.table	ES	NES	NOM.p.val	FDR.q.val	FWER.p.val	Tag..	Gene..	Signal	FDR..median.	glob.p.val
KEGG CITRATE CYCLE TCA CYCLE	29	genes.ES.table	0.62	1.7	0.032	0.3	0.77	0.55	0.21	0.44	0.13	0.071
KEGG FATTY ACID METABOLISM	40	genes.ES.table	0.7	1.6	0.038	0.35	0.9	0.72	0.17	0.6	0.18	0.076
KEGG GLYCINE SERINE AND THREONINE METABOLISM	31	genes.ES.table	0.78	1.7	0.0058	0.28	0.82	0.84	0.18	0.69	0.13	0.059
KEGG CYSTEINE AND METHIONINE METABOLISM	34	genes.ES.table	0.57	1.7	0.018	0.29	0.78	0.38	0.11	0.34	0.12	0.067
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION	44	genes.ES.table	0.62	1.7	0.035	0.31	0.82	0.73	0.17	0.61	0.14	0.067
KEGG LYSINE DEGRADATION	44	genes.ES.table	0.59	2	0.0019	0.21	0.17	0.32	0.12	0.28	0	0.057
KEGG STARCH AND SUCROSE METABOLISM	48	genes.ES.table	0.65	1.6	0.032	0.36	0.96	0.52	0.11	0.46	0.21	0.073
KEGG PYRUVATE METABOLISM	39	genes.ES.table	0.59	1.8	0.008	0.28	0.44	0.46	0.11	0.41	0	0.059
KEGG PROPANOATE METABOLISM	32	genes.ES.table	0.72	1.9	0	0.22	0.3	0.75	0.17	0.62	0	0.049
KEGG RETINOL METABOLISM	62	genes.ES.table	0.77	1.6	0.006	0.34	0.91	0.61	0.1	0.55	0.18	0.071

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

Table S11. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	AADAT	AADAT	AADAT	27	0.61	0.11	YES
2	BBOX1	BBOX1	BBOX1	51	0.56	0.21	YES
3	AASS	AASS	AASS	136	0.45	0.29	YES
4	OGDHL	OGDHL	OGDHL	443	0.32	0.33	YES
5	EHHADH	EHHADH	EHHADH	472	0.31	0.39	YES
6	PIPOX	PIPOX	PIPOX	523	0.3	0.44	YES
7	GCDH	GCDH	GCDH	952	0.22	0.46	YES
8	ALDH7A1	ALDH7A1	ALDH7A1	1138	0.19	0.48	YES
9	ALDH2	ALDH2	ALDH2	1329	0.18	0.5	YES
10	ACAT1	ACAT1	ACAT1	1540	0.16	0.52	YES
11	ACAT2	ACAT2	ACAT2	1658	0.15	0.54	YES
12	ALDH9A1	ALDH9A1	ALDH9A1	1827	0.14	0.55	YES
13	SETD7	SETD7	SETD7	1834	0.14	0.58	YES
14	HADH	HADH	HADH	2072	0.12	0.59	YES
15	ALDH1B1	ALDH1B1	ALDH1B1	2519	0.1	0.58	NO
16	ECHS1	ECHS1	ECHS1	2984	0.082	0.57	NO
17	OGDH	OGDH	OGDH	3145	0.077	0.57	NO
18	TMLHE	TMLHE	TMLHE	3714	0.059	0.55	NO
19	HADHA	HADHA	HADHA	4099	0.049	0.54	NO
20	DLST	DLST	DLST	4217	0.047	0.54	NO
21	PLOD1	PLOD1	PLOD1	4516	0.04	0.53	NO
22	SETD2	SETD2	SETD2	4849	0.033	0.52	NO
23	AASDH	AASDH	AASDH	5874	0.014	0.46	NO
24	SUV39H1	SUV39H1	SUV39H1	5928	0.014	0.46	NO
25	AASDHPPT	AASDHPPT	AASDHPPT	6249	0.0082	0.45	NO
26	PLOD3	PLOD3	PLOD3	6909	-0.0016	0.41	NO
27	SUV420H1	SUV420H1	SUV420H1	7096	-0.0044	0.4	NO
28	ALDH3A2	ALDH3A2	ALDH3A2	7358	-0.0084	0.39	NO
29	EHMT1	EHMT1	EHMT1	8100	-0.019	0.35	NO
30	SETD1A	SETD1A	SETD1A	8348	-0.022	0.34	NO
31	DOT1L	DOT1L	DOT1L	8929	-0.031	0.31	NO
32	WHSC1L1	WHSC1L1	WHSC1L1	9053	-0.032	0.31	NO
33	ASH1L	ASH1L	ASH1L	9157	-0.034	0.31	NO
34	NSD1	NSD1	NSD1	9723	-0.043	0.29	NO
35	SETMAR	SETMAR	SETMAR	10680	-0.058	0.24	NO
36	SETD1B	SETD1B	SETD1B	10964	-0.063	0.24	NO
37	SETDB2	SETDB2	SETDB2	11093	-0.065	0.24	NO
38	PLOD2	PLOD2	PLOD2	11783	-0.08	0.22	NO
39	SETD8	SETD8	SETD8	12034	-0.085	0.22	NO
40	WHSC1	WHSC1	WHSC1	12251	-0.09	0.22	NO
41	SUV39H2	SUV39H2	SUV39H2	12970	-0.11	0.2	NO
42	SETDB1	SETDB1	SETDB1	13020	-0.11	0.22	NO
43	SUV420H2	SUV420H2	SUV420H2	13276	-0.12	0.23	NO
44	EHMT2	EHMT2	EHMT2	13591	-0.13	0.23	NO

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

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ALDH6A1	ALDH6A1	ALDH6A1	407	0.33	0.046	YES
2	ABAT	ABAT	ABAT	434	0.32	0.11	YES
3	ACACB	ACACB	ACACB	470	0.31	0.18	YES
4	EHHADH	EHHADH	EHHADH	472	0.31	0.24	YES
5	MUT	MUT	MUT	847	0.23	0.27	YES
6	ACADM	ACADM	ACADM	1048	0.2	0.3	YES
7	ALDH7A1	ALDH7A1	ALDH7A1	1138	0.19	0.33	YES
8	ACSS2	ACSS2	ACSS2	1195	0.19	0.37	YES
9	MLYCD	MLYCD	MLYCD	1299	0.18	0.4	YES
10	ALDH2	ALDH2	ALDH2	1329	0.18	0.44	YES
11	LDHC	LDHC	LDHC	1449	0.16	0.46	YES
12	ACAT1	ACAT1	ACAT1	1540	0.16	0.49	YES
13	MCEE	MCEE	MCEE	1550	0.15	0.52	YES
14	LDHAL6B	LDHAL6B	LDHAL6B	1598	0.15	0.55	YES
15	ACAT2	ACAT2	ACAT2	1658	0.15	0.58	YES
16	SUCLG2	SUCLG2	SUCLG2	1793	0.14	0.6	YES
17	ALDH9A1	ALDH9A1	ALDH9A1	1827	0.14	0.63	YES
18	PCCA	PCCA	PCCA	1855	0.13	0.65	YES
19	PCCB	PCCB	PCCB	2044	0.12	0.67	YES
20	HIBCH	HIBCH	HIBCH	2181	0.12	0.68	YES
21	SUCLG1	SUCLG1	SUCLG1	2286	0.11	0.7	YES
22	ALDH1B1	ALDH1B1	ALDH1B1	2519	0.1	0.71	YES
23	ACSS3	ACSS3	ACSS3	2794	0.089	0.71	YES
24	ECHS1	ECHS1	ECHS1	2984	0.082	0.72	YES
25	HADHA	HADHA	HADHA	4099	0.049	0.67	NO
26	ALDH3A2	ALDH3A2	ALDH3A2	7358	-0.0084	0.48	NO
27	LDHA	LDHA	LDHA	7840	-0.016	0.46	NO
28	SUCLA2	SUCLA2	SUCLA2	7956	-0.017	0.46	NO
29	LDHAL6A	LDHAL6A	LDHAL6A	9038	-0.032	0.4	NO
30	ACACA	ACACA	ACACA	10802	-0.06	0.32	NO
31	LDHB	LDHB	LDHB	13920	-0.14	0.17	NO
32	ACSS1	ACSS1	ACSS1	15739	-0.22	0.11	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 FATTY ACID METABOLISM.

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

genes ES table in pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM

Table S13. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	ACOT12	ACOT12	ACOT12	104	0.48	0.078	YES
2	PCK1	PCK1	PCK1	180	0.43	0.15	YES
3	ACACB	ACACB	ACACB	470	0.31	0.19	YES
4	PCK2	PCK2	PCK2	471	0.31	0.24	YES
5	LDHD	LDHD	LDHD	663	0.26	0.28	YES
6	PKLR	PKLR	PKLR	730	0.25	0.32	YES
7	HAGH	HAGH	HAGH	861	0.23	0.35	YES
8	ALDH7A1	ALDH7A1	ALDH7A1	1138	0.19	0.37	YES
9	ACYP2	ACYP2	ACYP2	1154	0.19	0.4	YES
10	ACSS2	ACSS2	ACSS2	1195	0.19	0.43	YES
11	ALDH2	ALDH2	ALDH2	1329	0.18	0.45	YES
12	LDHC	LDHC	LDHC	1449	0.16	0.47	YES
13	GRHPR	GRHPR	GRHPR	1523	0.16	0.5	YES
14	ACAT1	ACAT1	ACAT1	1540	0.16	0.52	YES
15	LDHAL6B	LDHAL6B	LDHAL6B	1598	0.15	0.55	YES
16	ACAT2	ACAT2	ACAT2	1658	0.15	0.57	YES
17	ALDH9A1	ALDH9A1	ALDH9A1	1827	0.14	0.58	YES
18	PC	PC	PC	2018	0.12	0.59	YES
19	ALDH1B1	ALDH1B1	ALDH1B1	2519	0.1	0.58	NO
20	MDH1	MDH1	MDH1	3259	0.073	0.55	NO
21	DLD	DLD	DLD	3771	0.057	0.54	NO
22	PDHB	PDHB	PDHB	4935	0.031	0.47	NO
23	PDHA1	PDHA1	PDHA1	5542	0.02	0.44	NO
24	GLO1	GLO1	GLO1	5549	0.02	0.45	NO
25	ME3	ME3	ME3	6620	0.0029	0.39	NO
26	ME1	ME1	ME1	6789	0.00032	0.38	NO
27	ALDH3A2	ALDH3A2	ALDH3A2	7358	-0.0084	0.35	NO
28	MDH2	MDH2	MDH2	7820	-0.015	0.32	NO
29	LDHA	LDHA	LDHA	7840	-0.016	0.32	NO
30	DLAT	DLAT	DLAT	8323	-0.022	0.3	NO
31	LDHAL6A	LDHAL6A	LDHAL6A	9038	-0.032	0.27	NO
32	ME2	ME2	ME2	10097	-0.049	0.22	NO
33	ACACA	ACACA	ACACA	10802	-0.06	0.19	NO
34	ACYP1	ACYP1	ACYP1	12175	-0.088	0.12	NO
35	LDHB	LDHB	LDHB	13920	-0.14	0.049	NO
36	AKR1B1	AKR1B1	AKR1B1	14188	-0.15	0.06	NO
37	ACSS1	ACSS1	ACSS1	15739	-0.22	0.011	NO
38	PKM2	PKM2	PKM2	16111	-0.25	0.033	NO
39	HAGHL	HAGHL	HAGHL	17012	-0.33	0.04	NO

Figure S25. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCINE SERINE AND THREONINE METABOLISM.

Figure S26. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCINE SERINE AND THREONINE 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 CYSTEINE AND METHIONINE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	FOXO1	FOXO1	FOXO1	1734	0.14	0.0034	YES
2	CDKN1A	CDKN1A	CDKN1A	1971	0.13	0.082	YES
3	MTOR	MTOR	MTOR	1982	0.13	0.17	YES
4	CASP9	CASP9	CASP9	2594	0.097	0.21	YES
5	FOXO4	FOXO4	FOXO4	3257	0.073	0.22	YES
6	BAD	BAD	BAD	3376	0.069	0.27	YES
7	NR4A1	NR4A1	NR4A1	3454	0.067	0.31	YES
8	AKT1	AKT1	AKT1	3694	0.059	0.34	YES
9	PHLPP1	PHLPP1	PHLPP1	3706	0.059	0.38	YES
10	CDKN1B	CDKN1B	CDKN1B	3744	0.058	0.42	YES
11	AKT2	AKT2	AKT2	3910	0.053	0.45	YES
12	MDM2	MDM2	MDM2	4626	0.038	0.44	NO
13	TSC2	TSC2	TSC2	5515	0.021	0.4	NO
14	AKT3	AKT3	AKT3	5569	0.02	0.41	NO
15	RPS6KB2	RPS6KB2	RPS6KB2	5654	0.018	0.42	NO
16	PDPK1	PDPK1	PDPK1	6166	0.0097	0.4	NO
17	PTEN	PTEN	PTEN	6792	0.00028	0.36	NO
18	MAPKAP1	MAPKAP1	MAPKAP1	7328	-0.008	0.34	NO
19	FOXO3	FOXO3	FOXO3	7455	-0.0098	0.34	NO
20	MLST8	MLST8	MLST8	7575	-0.012	0.34	NO
21	RICTOR	RICTOR	RICTOR	7726	-0.014	0.34	NO
22	CHUK	CHUK	CHUK	7870	-0.016	0.35	NO
23	AKT1S1	AKT1S1	AKT1S1	8853	-0.03	0.31	NO
24	CREB1	CREB1	CREB1	9884	-0.046	0.29	NO
25	GSK3A	GSK3A	GSK3A	10493	-0.055	0.29	NO
26	TRIB3	TRIB3	TRIB3	10936	-0.062	0.31	NO
27	THEM4	THEM4	THEM4	12555	-0.097	0.29	NO

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

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYSTEINE AND METHIONINE 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION

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	HAO2	HAO2	HAO2	9	0.74	0.064	YES
2	XDH	XDH	XDH	37	0.59	0.11	YES
3	DAO	DAO	DAO	90	0.5	0.15	YES
4	SLC27A2	SLC27A2	SLC27A2	266	0.38	0.18	YES
5	AGXT	AGXT	AGXT	272	0.37	0.21	YES
6	PEX11G	PEX11G	PEX11G	337	0.35	0.24	YES
7	HAO1	HAO1	HAO1	438	0.32	0.26	YES
8	EHHADH	EHHADH	EHHADH	472	0.31	0.28	YES
9	EPHX2	EPHX2	EPHX2	477	0.31	0.31	YES
10	ACOX2	ACOX2	ACOX2	511	0.3	0.33	YES
11	PIPOX	PIPOX	PIPOX	523	0.3	0.36	YES
12	PXMP2	PXMP2	PXMP2	588	0.28	0.38	YES
13	ACSL1	ACSL1	ACSL1	673	0.26	0.4	YES
14	SCP2	SCP2	SCP2	706	0.26	0.42	YES
15	BAAT	BAAT	BAAT	793	0.24	0.43	YES
16	NOS2	NOS2	NOS2	829	0.23	0.45	YES
17	CAT	CAT	CAT	938	0.22	0.46	YES
18	NUDT12	NUDT12	NUDT12	961	0.21	0.48	YES
19	PHYH	PHYH	PHYH	1212	0.19	0.48	YES
20	ACOX1	ACOX1	ACOX1	1249	0.18	0.5	YES
21	DHRS4	DHRS4	DHRS4	1282	0.18	0.51	YES
22	MLYCD	MLYCD	MLYCD	1299	0.18	0.53	YES
23	HACL1	HACL1	HACL1	1614	0.15	0.52	YES
24	ACAA1	ACAA1	ACAA1	1723	0.14	0.53	YES
25	PEX1	PEX1	PEX1	1762	0.14	0.54	YES
26	PECR	PECR	PECR	1780	0.14	0.55	YES
27	HMGCL	HMGCL	HMGCL	1881	0.13	0.55	YES
28	GSTK1	GSTK1	GSTK1	1913	0.13	0.56	YES
29	MPV17L	MPV17L	MPV17L	1966	0.13	0.57	YES
30	PAOX	PAOX	PAOX	2077	0.12	0.58	YES
31	PEX7	PEX7	PEX7	2313	0.11	0.57	YES
32	PEX14	PEX14	PEX14	2316	0.11	0.58	YES
33	DDO	DDO	DDO	2504	0.1	0.58	YES
34	HSD17B4	HSD17B4	HSD17B4	2581	0.098	0.58	YES
35	SOD1	SOD1	SOD1	2615	0.096	0.59	YES
36	PXMP4	PXMP4	PXMP4	2679	0.094	0.6	YES
37	SLC25A17	SLC25A17	SLC25A17	2742	0.091	0.6	YES
38	CRAT	CRAT	CRAT	2757	0.09	0.61	YES
39	PEX12	PEX12	PEX12	2816	0.088	0.61	YES
40	PEX19	PEX19	PEX19	2851	0.087	0.62	YES
41	PEX16	PEX16	PEX16	2875	0.086	0.62	YES
42	CROT	CROT	CROT	2887	0.085	0.63	YES
43	ACOX3	ACOX3	ACOX3	2983	0.082	0.63	YES
44	PEX3	PEX3	PEX3	2994	0.082	0.64	YES
45	ACOT8	ACOT8	ACOT8	3566	0.063	0.61	NO
46	IDH1	IDH1	IDH1	3633	0.061	0.61	NO
47	PEX6	PEX6	PEX6	3778	0.057	0.61	NO
48	DECR2	DECR2	DECR2	3797	0.056	0.61	NO
49	ECH1	ECH1	ECH1	3900	0.054	0.61	NO
50	ABCD4	ABCD4	ABCD4	3901	0.054	0.62	NO
51	PEX13	PEX13	PEX13	4143	0.048	0.61	NO
52	ABCD3	ABCD3	ABCD3	4203	0.047	0.61	NO
53	AMACR	AMACR	AMACR	4214	0.047	0.61	NO
54	PEX10	PEX10	PEX10	4496	0.04	0.6	NO
55	PRDX5	PRDX5	PRDX5	4981	0.031	0.57	NO
56	ACSL5	ACSL5	ACSL5	4992	0.03	0.58	NO
57	PEX26	PEX26	PEX26	5173	0.027	0.57	NO
58	PMVK	PMVK	PMVK	5488	0.021	0.55	NO
59	IDH2	IDH2	IDH2	5651	0.019	0.55	NO
60	PRDX1	PRDX1	PRDX1	6115	0.01	0.52	NO
61	MVK	MVK	MVK	6374	0.0063	0.5	NO
62	SOD2	SOD2	SOD2	6554	0.0038	0.5	NO
63	PEX11A	PEX11A	PEX11A	6769	0.0006	0.48	NO
64	PEX5	PEX5	PEX5	6929	-0.0019	0.48	NO
65	PEX11B	PEX11B	PEX11B	8066	-0.019	0.41	NO
66	NUDT19	NUDT19	NUDT19	9018	-0.032	0.36	NO
67	PEX2	PEX2	PEX2	9882	-0.046	0.32	NO
68	AGPS	AGPS	AGPS	11088	-0.065	0.25	NO
69	ACSL6	ACSL6	ACSL6	12659	-0.1	0.17	NO
70	ABCD1	ABCD1	ABCD1	13026	-0.11	0.16	NO
71	GNPAT	GNPAT	GNPAT	13918	-0.14	0.12	NO
72	ACSL3	ACSL3	ACSL3	14202	-0.15	0.12	NO
73	FAR1	FAR1	FAR1	14287	-0.15	0.13	NO
74	MPV17	MPV17	MPV17	14387	-0.16	0.14	NO
75	ABCD2	ABCD2	ABCD2	15162	-0.19	0.11	NO
76	ACSL4	ACSL4	ACSL4	15436	-0.2	0.11	NO
77	FAR2	FAR2	FAR2	15524	-0.21	0.12	NO

Figure S29. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

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	GYS2	GYS2	GYS2	19	0.63	0.066	YES
2	PFKFB1	PFKFB1	PFKFB1	52	0.56	0.12	YES
3	ALDOB	ALDOB	ALDOB	140	0.45	0.16	YES
4	PCK1	PCK1	PCK1	180	0.43	0.21	YES
5	FBP1	FBP1	FBP1	189	0.42	0.25	YES
6	ENO3	ENO3	ENO3	342	0.35	0.28	YES
7	PCK2	PCK2	PCK2	471	0.31	0.3	YES
8	AGL	AGL	AGL	676	0.26	0.32	YES
9	PHKG1	PHKG1	PHKG1	683	0.26	0.35	YES
10	PKLR	PKLR	PKLR	730	0.25	0.37	YES
11	FBP2	FBP2	FBP2	903	0.22	0.38	YES
12	UGP2	UGP2	UGP2	1021	0.21	0.4	YES
13	PGM2	PGM2	PGM2	1113	0.2	0.42	YES
14	ALDOC	ALDOC	ALDOC	1114	0.2	0.44	YES
15	PYGL	PYGL	PYGL	1189	0.19	0.45	YES
16	SLC25A10	SLC25A10	SLC25A10	1469	0.16	0.45	YES
17	PGM1	PGM1	PGM1	1521	0.16	0.47	YES
18	GOT1	GOT1	GOT1	1617	0.15	0.48	YES
19	GOT2	GOT2	GOT2	1896	0.13	0.48	YES
20	GBE1	GBE1	GBE1	1987	0.13	0.48	YES
21	PC	PC	PC	2018	0.12	0.5	YES
22	PPP2R1B	PPP2R1B	PPP2R1B	2890	0.085	0.45	NO
23	PHKA1	PHKA1	PHKA1	3110	0.078	0.45	NO
24	MDH1	MDH1	MDH1	3259	0.073	0.45	NO
25	SLC25A13	SLC25A13	SLC25A13	3540	0.064	0.44	NO
26	PHKG2	PHKG2	PHKG2	3631	0.061	0.44	NO
27	CALM1	CALM1	CALM1	4442	0.042	0.4	NO
28	PPP2CB	PPP2CB	PPP2CB	4616	0.038	0.39	NO
29	PFKL	PFKL	PFKL	5109	0.028	0.37	NO
30	SLC25A11	SLC25A11	SLC25A11	5268	0.025	0.36	NO
31	SLC25A1	SLC25A1	SLC25A1	5472	0.021	0.35	NO
32	PRKACA	PRKACA	PRKACA	5666	0.018	0.34	NO
33	PHKB	PHKB	PHKB	6131	0.01	0.32	NO
34	GPI	GPI	GPI	6307	0.0073	0.31	NO
35	TPI1	TPI1	TPI1	6686	0.002	0.29	NO
36	PGAM1	PGAM1	PGAM1	6727	0.0012	0.29	NO
37	PRKACB	PRKACB	PRKACB	6859	-0.00077	0.28	NO
38	PPP2CA	PPP2CA	PPP2CA	7017	-0.0032	0.27	NO
39	PPP2R5D	PPP2R5D	PPP2R5D	7127	-0.005	0.27	NO
40	PGK1	PGK1	PGK1	7286	-0.0073	0.26	NO
41	MDH2	MDH2	MDH2	7820	-0.015	0.23	NO
42	PHKA2	PHKA2	PHKA2	8107	-0.019	0.22	NO
43	CALM2	CALM2	CALM2	8576	-0.026	0.19	NO
44	PYGB	PYGB	PYGB	10296	-0.052	0.099	NO
45	ENO1	ENO1	ENO1	10555	-0.056	0.09	NO
46	GAPDH	GAPDH	GAPDH	10813	-0.06	0.082	NO
47	GAPDHS	GAPDHS	GAPDHS	11767	-0.079	0.036	NO
48	PYGM	PYGM	PYGM	12075	-0.086	0.028	NO
49	GYS1	GYS1	GYS1	12091	-0.086	0.036	NO
50	PPP2R1A	PPP2R1A	PPP2R1A	12160	-0.088	0.042	NO
51	CALM3	CALM3	CALM3	12203	-0.089	0.049	NO
52	GYG2	GYG2	GYG2	12472	-0.095	0.043	NO
53	PFKFB4	PFKFB4	PFKFB4	13653	-0.13	-0.0099	NO
54	SLC25A12	SLC25A12	SLC25A12	13658	-0.13	0.0034	NO
55	ALDOA	ALDOA	ALDOA	13724	-0.13	0.014	NO
56	PGAM2	PGAM2	PGAM2	14335	-0.15	-0.0049	NO
57	PFKFB2	PFKFB2	PFKFB2	14492	-0.16	0.0032	NO
58	GYG1	GYG1	GYG1	14670	-0.17	0.011	NO
59	PFKFB3	PFKFB3	PFKFB3	14941	-0.18	0.015	NO
60	PFKM	PFKM	PFKM	15212	-0.2	0.02	NO
61	PKM2	PKM2	PKM2	16111	-0.25	-0.0051	NO
62	PFKP	PFKP	PFKP	17509	-0.44	-0.038	NO
63	ENO2	ENO2	ENO2	17602	-0.48	0.0071	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: KEGG LYSINE DEGRADATION.

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

genes ES table in pathway: KEGG STARCH AND SUCROSE METABOLISM

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	PFKFB1	PFKFB1	PFKFB1	52	0.56	0.11	YES
2	ALDOB	ALDOB	ALDOB	140	0.45	0.2	YES
3	PCK1	PCK1	PCK1	180	0.43	0.29	YES
4	FBP1	FBP1	FBP1	189	0.42	0.37	YES
5	ENO3	ENO3	ENO3	342	0.35	0.44	YES
6	PCK2	PCK2	PCK2	471	0.31	0.5	YES
7	FBP2	FBP2	FBP2	903	0.22	0.52	YES
8	ALDOC	ALDOC	ALDOC	1114	0.2	0.55	YES
9	SLC25A10	SLC25A10	SLC25A10	1469	0.16	0.56	YES
10	GOT1	GOT1	GOT1	1617	0.15	0.58	YES
11	GOT2	GOT2	GOT2	1896	0.13	0.59	YES
12	PC	PC	PC	2018	0.12	0.61	YES
13	MDH1	MDH1	MDH1	3259	0.073	0.56	NO
14	SLC25A13	SLC25A13	SLC25A13	3540	0.064	0.55	NO
15	SLC25A11	SLC25A11	SLC25A11	5268	0.025	0.46	NO
16	SLC25A1	SLC25A1	SLC25A1	5472	0.021	0.46	NO
17	PRKACA	PRKACA	PRKACA	5666	0.018	0.45	NO
18	GPI	GPI	GPI	6307	0.0073	0.41	NO
19	TPI1	TPI1	TPI1	6686	0.002	0.39	NO
20	PGAM1	PGAM1	PGAM1	6727	0.0012	0.39	NO
21	PRKACB	PRKACB	PRKACB	6859	-0.00077	0.38	NO
22	PGK1	PGK1	PGK1	7286	-0.0073	0.36	NO
23	MDH2	MDH2	MDH2	7820	-0.015	0.33	NO
24	ENO1	ENO1	ENO1	10555	-0.056	0.19	NO
25	GAPDH	GAPDH	GAPDH	10813	-0.06	0.19	NO
26	GAPDHS	GAPDHS	GAPDHS	11767	-0.079	0.15	NO
27	SLC25A12	SLC25A12	SLC25A12	13658	-0.13	0.071	NO
28	ALDOA	ALDOA	ALDOA	13724	-0.13	0.095	NO
29	PGAM2	PGAM2	PGAM2	14335	-0.15	0.092	NO
30	ENO2	ENO2	ENO2	17602	-0.48	0.0071	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: KEGG STARCH AND SUCROSE METABOLISM.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STARCH AND SUCROSE 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 PYRUVATE METABOLISM

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	GLS2	GLS2	GLS2	10	0.72	0.022	YES
2	TAT	TAT	TAT	21	0.63	0.042	YES
3	AADAT	AADAT	AADAT	27	0.61	0.061	YES
4	BBOX1	BBOX1	BBOX1	51	0.56	0.078	YES
5	IDO2	IDO2	IDO2	71	0.52	0.093	YES
6	IYD	IYD	IYD	81	0.51	0.11	YES
7	DAO	DAO	DAO	90	0.5	0.12	YES
8	BHMT	BHMT	BHMT	105	0.48	0.14	YES
9	TDO2	TDO2	TDO2	123	0.46	0.15	YES
10	AASS	AASS	AASS	136	0.45	0.17	YES
11	ACMSD	ACMSD	ACMSD	146	0.45	0.18	YES
12	HAL	HAL	HAL	154	0.44	0.19	YES
13	PRODH	PRODH	PRODH	163	0.44	0.21	YES
14	UROC1	UROC1	UROC1	167	0.43	0.22	YES
15	ARG1	ARG1	ARG1	188	0.42	0.23	YES
16	KMO	KMO	KMO	250	0.38	0.24	YES
17	CTH	CTH	CTH	255	0.38	0.25	YES
18	AGXT	AGXT	AGXT	272	0.37	0.26	YES
19	INHBC	INHBC	INHBC	307	0.36	0.27	YES
20	AGXT2	AGXT2	AGXT2	336	0.35	0.28	YES
21	HAAO	HAAO	HAAO	382	0.34	0.29	YES
22	DIO1	DIO1	DIO1	386	0.34	0.3	YES
23	OTC	OTC	OTC	388	0.34	0.31	YES
24	CPS1	CPS1	CPS1	394	0.33	0.32	YES
25	ALDH6A1	ALDH6A1	ALDH6A1	407	0.33	0.33	YES
26	DBH	DBH	DBH	413	0.33	0.34	YES
27	SLC25A15	SLC25A15	SLC25A15	421	0.33	0.35	YES
28	GSTZ1	GSTZ1	GSTZ1	431	0.32	0.36	YES
29	HAO1	HAO1	HAO1	438	0.32	0.37	YES
30	HPD	HPD	HPD	467	0.31	0.38	YES
31	AMDHD1	AMDHD1	AMDHD1	483	0.31	0.39	YES
32	CBS	CBS	CBS	506	0.3	0.4	YES
33	HDC	HDC	HDC	508	0.3	0.41	YES
34	CDO1	CDO1	CDO1	554	0.29	0.41	YES
35	SHMT1	SHMT1	SHMT1	594	0.28	0.42	YES
36	PNMT	PNMT	PNMT	625	0.27	0.43	YES
37	GPT	GPT	GPT	738	0.25	0.43	YES
38	BCKDHB	BCKDHB	BCKDHB	770	0.24	0.44	YES
39	FTCD	FTCD	FTCD	785	0.24	0.44	YES
40	GCDH	GCDH	GCDH	952	0.22	0.44	YES
41	MAT1A	MAT1A	MAT1A	986	0.21	0.44	YES
42	HGD	HGD	HGD	1080	0.2	0.45	YES
43	ALDH7A1	ALDH7A1	ALDH7A1	1138	0.19	0.45	YES
44	PAH	PAH	PAH	1206	0.19	0.45	YES
45	GATM	GATM	GATM	1230	0.18	0.46	YES
46	CCBL1	CCBL1	CCBL1	1283	0.18	0.46	YES
47	IVD	IVD	IVD	1303	0.18	0.46	YES
48	GPT2	GPT2	GPT2	1328	0.18	0.47	YES
49	INHBE	INHBE	INHBE	1332	0.17	0.47	YES
50	ASL	ASL	ASL	1359	0.17	0.48	YES
51	DIO2	DIO2	DIO2	1372	0.17	0.48	YES
52	AGMAT	AGMAT	AGMAT	1376	0.17	0.49	YES
53	FAH	FAH	FAH	1440	0.17	0.49	YES
54	SLC25A10	SLC25A10	SLC25A10	1469	0.16	0.49	YES
55	NAGS	NAGS	NAGS	1491	0.16	0.5	YES
56	DBT	DBT	DBT	1497	0.16	0.5	YES
57	ASS1	ASS1	ASS1	1499	0.16	0.5	YES
58	GRHPR	GRHPR	GRHPR	1523	0.16	0.51	YES
59	ACAT1	ACAT1	ACAT1	1540	0.16	0.51	YES
60	ADI1	ADI1	ADI1	1579	0.15	0.52	YES
61	GOT1	GOT1	GOT1	1617	0.15	0.52	YES
62	ACADSB	ACADSB	ACADSB	1621	0.15	0.52	YES
63	QDPR	QDPR	QDPR	1656	0.15	0.52	YES
64	PHGDH	PHGDH	PHGDH	1773	0.14	0.52	YES
65	ALDH9A1	ALDH9A1	ALDH9A1	1827	0.14	0.52	YES
66	SUOX	SUOX	SUOX	1839	0.13	0.53	YES
67	TST	TST	TST	1886	0.13	0.53	YES
68	GOT2	GOT2	GOT2	1896	0.13	0.53	YES
69	PAOX	PAOX	PAOX	2077	0.12	0.53	YES
70	ETHE1	ETHE1	ETHE1	2089	0.12	0.53	YES
71	INHBA	INHBA	INHBA	2114	0.12	0.53	YES
72	HSD17B10	HSD17B10	HSD17B10	2131	0.12	0.54	YES
73	CSAD	CSAD	CSAD	2141	0.12	0.54	YES
74	HIBCH	HIBCH	HIBCH	2181	0.12	0.54	YES
75	ACAD8	ACAD8	ACAD8	2263	0.11	0.54	YES
76	MCCC1	MCCC1	MCCC1	2340	0.11	0.54	YES
77	GAMT	GAMT	GAMT	2362	0.11	0.54	YES
78	DDC	DDC	DDC	2403	0.11	0.54	YES
79	CGA	CGA	CGA	2503	0.1	0.54	NO
80	GCLC	GCLC	GCLC	2712	0.092	0.53	NO
81	BCKDHA	BCKDHA	BCKDHA	2822	0.088	0.53	NO
82	MCCC2	MCCC2	MCCC2	2993	0.082	0.52	NO
83	OGDH	OGDH	OGDH	3145	0.077	0.51	NO
84	OAZ2	OAZ2	OAZ2	3266	0.073	0.51	NO
85	PCBD1	PCBD1	PCBD1	3354	0.07	0.51	NO
86	INHBB	INHBB	INHBB	3464	0.066	0.5	NO
87	ADC	ADC	ADC	3580	0.063	0.5	NO
88	MAT2B	MAT2B	MAT2B	3614	0.062	0.5	NO
89	HIBADH	HIBADH	HIBADH	3646	0.061	0.5	NO
90	TMLHE	TMLHE	TMLHE	3714	0.059	0.5	NO
91	PSMB8	PSMB8	PSMB8	3753	0.058	0.5	NO
92	DLD	DLD	DLD	3771	0.057	0.5	NO
93	PSMA2	PSMA2	PSMA2	3842	0.055	0.49	NO
94	ALDH4A1	ALDH4A1	ALDH4A1	4148	0.048	0.48	NO
95	DLST	DLST	DLST	4217	0.047	0.48	NO
96	BCAT2	BCAT2	BCAT2	4226	0.046	0.48	NO
97	GCLM	GCLM	GCLM	4235	0.046	0.48	NO
98	AHCY	AHCY	AHCY	4299	0.045	0.48	NO
99	PSAT1	PSAT1	PSAT1	4368	0.043	0.47	NO
100	PSMC3	PSMC3	PSMC3	4380	0.043	0.47	NO
101	PSME4	PSME4	PSME4	4591	0.039	0.46	NO
102	CNDP2	CNDP2	CNDP2	4617	0.038	0.46	NO
103	CCBL2	CCBL2	CCBL2	4639	0.037	0.46	NO
104	SAT1	SAT1	SAT1	4641	0.037	0.46	NO
105	AUH	AUH	AUH	4656	0.037	0.46	NO
106	SLC25A2	SLC25A2	SLC25A2	4711	0.036	0.46	NO
107	PSME1	PSME1	PSME1	4800	0.034	0.46	NO
108	AFMID	AFMID	AFMID	4826	0.034	0.46	NO
109	ARG2	ARG2	ARG2	4858	0.033	0.46	NO
110	KYNU	KYNU	KYNU	4887	0.032	0.46	NO
111	PSMA7	PSMA7	PSMA7	5040	0.03	0.45	NO
112	PSMC5	PSMC5	PSMC5	5113	0.028	0.45	NO
113	PSMC2	PSMC2	PSMC2	5156	0.028	0.44	NO
114	MAT2A	MAT2A	MAT2A	5162	0.027	0.44	NO
115	PSMD12	PSMD12	PSMD12	5611	0.019	0.42	NO
116	ODC1	ODC1	ODC1	5684	0.018	0.42	NO
117	PSMD6	PSMD6	PSMD6	5962	0.013	0.4	NO
118	MTAP	MTAP	MTAP	6011	0.012	0.4	NO
119	PSMB2	PSMB2	PSMB2	6092	0.011	0.39	NO
120	PSMD2	PSMD2	PSMD2	6096	0.011	0.4	NO
121	PSMF1	PSMF1	PSMF1	6138	0.01	0.39	NO
122	PSMC1	PSMC1	PSMC1	6359	0.0066	0.38	NO
123	PSMA6	PSMA6	PSMA6	6408	0.0057	0.38	NO
124	PSMC4	PSMC4	PSMC4	6422	0.0055	0.38	NO
125	PSMC6	PSMC6	PSMC6	6456	0.0051	0.38	NO
126	PSMB9	PSMB9	PSMB9	6458	0.0051	0.38	NO
127	PSMD9	PSMD9	PSMD9	6590	0.0033	0.37	NO
128	PSMD8	PSMD8	PSMD8	6640	0.0027	0.36	NO
129	PSMA3	PSMA3	PSMA3	6683	0.002	0.36	NO
130	PSMB7	PSMB7	PSMB7	6702	0.0017	0.36	NO
131	PSMB1	PSMB1	PSMB1	6767	0.00062	0.36	NO
132	PSMD3	PSMD3	PSMD3	6794	0.00023	0.36	NO
133	PSMD7	PSMD7	PSMD7	6832	-0.00016	0.36	NO
134	PSME2	PSME2	PSME2	6850	-0.00053	0.35	NO
135	PSMD13	PSMD13	PSMD13	7048	-0.0037	0.34	NO
136	PSMD11	PSMD11	PSMD11	7091	-0.0043	0.34	NO
137	MRI1	MRI1	MRI1	7285	-0.0073	0.33	NO
138	PSMA4	PSMA4	PSMA4	7374	-0.0086	0.32	NO
139	PSMA1	PSMA1	PSMA1	7839	-0.016	0.3	NO
140	PSMB3	PSMB3	PSMB3	7962	-0.017	0.29	NO
141	OAZ1	OAZ1	OAZ1	8007	-0.018	0.29	NO
142	PSMB6	PSMB6	PSMB6	8096	-0.019	0.29	NO
143	PSMA5	PSMA5	PSMA5	8343	-0.022	0.27	NO
144	PSMB10	PSMB10	PSMB10	8628	-0.027	0.26	NO
145	PSMB5	PSMB5	PSMB5	8744	-0.028	0.25	NO
146	PSMD5	PSMD5	PSMD5	8882	-0.03	0.24	NO
147	PSMD1	PSMD1	PSMD1	9008	-0.032	0.24	NO
148	SQRDL	SQRDL	SQRDL	9786	-0.044	0.2	NO
149	APIP	APIP	APIP	9943	-0.046	0.19	NO
150	PSMD10	PSMD10	PSMD10	9955	-0.047	0.19	NO
151	PSMB4	PSMB4	PSMB4	10041	-0.048	0.19	NO
152	CKMT2	CKMT2	CKMT2	10294	-0.052	0.17	NO
153	PSMD14	PSMD14	PSMD14	10679	-0.058	0.15	NO
154	ENOPH1	ENOPH1	ENOPH1	11034	-0.064	0.14	NO
155	GLUD1	GLUD1	GLUD1	11339	-0.07	0.12	NO
156	SRM	SRM	SRM	11631	-0.076	0.11	NO
157	AMD1	AMD1	AMD1	11720	-0.078	0.1	NO
158	PSMD4	PSMD4	PSMD4	11803	-0.08	0.1	NO
159	TH	TH	TH	12159	-0.088	0.084	NO
160	SMS	SMS	SMS	12252	-0.09	0.082	NO
161	ALDH18A1	ALDH18A1	ALDH18A1	12677	-0.1	0.061	NO
162	GLS	GLS	GLS	13159	-0.11	0.037	NO
163	AZIN1	AZIN1	AZIN1	13274	-0.12	0.034	NO
164	IDO1	IDO1	IDO1	13352	-0.12	0.033	NO
165	MTR	MTR	MTR	13478	-0.12	0.03	NO
166	TPH1	TPH1	TPH1	13787	-0.13	0.017	NO
167	OAZ3	OAZ3	OAZ3	13832	-0.14	0.019	NO
168	PSPH	PSPH	PSPH	13878	-0.14	0.02	NO
169	POMC	POMC	POMC	14310	-0.15	0.00068	NO
170	CKM	CKM	CKM	14463	-0.16	-0.0029	NO
171	SLC25A21	SLC25A21	SLC25A21	14824	-0.18	-0.018	NO
172	PSMA8	PSMA8	PSMA8	15049	-0.19	-0.025	NO
173	GLUL	GLUL	GLUL	15121	-0.19	-0.023	NO
174	LHB	LHB	LHB	15366	-0.2	-0.03	NO
175	PCSK1	PCSK1	PCSK1	15398	-0.2	-0.026	NO
176	AANAT	AANAT	AANAT	15742	-0.22	-0.038	NO
177	CKB	CKB	CKB	15806	-0.23	-0.034	NO
178	CKMT1A	CKMT1A	CKMT1A	15810	-0.23	-0.027	NO
179	BCAT1	BCAT1	BCAT1	16158	-0.25	-0.039	NO
180	DIO3	DIO3	DIO3	16561	-0.28	-0.053	NO
181	CKMT1B	CKMT1B	CKMT1B	16597	-0.29	-0.046	NO
182	NQO1	NQO1	NQO1	16630	-0.29	-0.039	NO
183	SLC5A5	SLC5A5	SLC5A5	17179	-0.36	-0.058	NO
184	OAT	OAT	OAT	17213	-0.37	-0.048	NO
185	INHA	INHA	INHA	17215	-0.37	-0.037	NO
186	ASNS	ASNS	ASNS	17475	-0.42	-0.038	NO
187	PYCR1	PYCR1	PYCR1	17490	-0.43	-0.025	NO
188	SMOX	SMOX	SMOX	17646	-0.52	-0.018	NO
189	SLC6A8	SLC6A8	SLC6A8	17722	-0.7	0.00034	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: KEGG PYRUVATE METABOLISM.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRUVATE 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 PROPANOATE METABOLISM

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	PCK1	PCK1	PCK1	180	0.43	0.14	YES
2	OGDHL	OGDHL	OGDHL	443	0.32	0.24	YES
3	PCK2	PCK2	PCK2	471	0.31	0.34	YES
4	ACO1	ACO1	ACO1	1276	0.18	0.36	YES
5	SDHD	SDHD	SDHD	1767	0.14	0.38	YES
6	SUCLG2	SUCLG2	SUCLG2	1793	0.14	0.43	YES
7	PC	PC	PC	2018	0.12	0.46	YES
8	SDHB	SDHB	SDHB	2250	0.11	0.48	YES
9	SUCLG1	SUCLG1	SUCLG1	2286	0.11	0.52	YES
10	FH	FH	FH	2392	0.11	0.55	YES
11	OGDH	OGDH	OGDH	3145	0.077	0.54	YES
12	SDHA	SDHA	SDHA	3177	0.076	0.56	YES
13	MDH1	MDH1	MDH1	3259	0.073	0.58	YES
14	ACO2	ACO2	ACO2	3483	0.066	0.59	YES
15	IDH1	IDH1	IDH1	3633	0.061	0.6	YES
16	DLD	DLD	DLD	3771	0.057	0.62	YES
17	DLST	DLST	DLST	4217	0.047	0.61	NO
18	IDH3A	IDH3A	IDH3A	4530	0.04	0.6	NO
19	SDHC	SDHC	SDHC	4925	0.032	0.59	NO
20	PDHB	PDHB	PDHB	4935	0.031	0.6	NO
21	PDHA1	PDHA1	PDHA1	5542	0.02	0.58	NO
22	IDH2	IDH2	IDH2	5651	0.019	0.58	NO
23	IDH3B	IDH3B	IDH3B	6355	0.0067	0.54	NO
24	MDH2	MDH2	MDH2	7820	-0.015	0.46	NO
25	SUCLA2	SUCLA2	SUCLA2	7956	-0.017	0.46	NO
26	DLAT	DLAT	DLAT	8323	-0.022	0.45	NO
27	IDH3G	IDH3G	IDH3G	9025	-0.032	0.42	NO
28	ACLY	ACLY	ACLY	11279	-0.069	0.32	NO
29	CS	CS	CS	13950	-0.14	0.21	NO

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

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

genes ES table in pathway: KEGG RETINOL METABOLISM

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	TAT	TAT	TAT	21	0.63	0.1	YES
2	SDS	SDS	SDS	22	0.63	0.2	YES
3	DNMT3L	DNMT3L	DNMT3L	66	0.54	0.29	YES
4	BHMT	BHMT	BHMT	105	0.48	0.36	YES
5	CTH	CTH	CTH	255	0.38	0.42	YES
6	CBS	CBS	CBS	506	0.3	0.45	YES
7	CDO1	CDO1	CDO1	554	0.29	0.49	YES
8	MAT1A	MAT1A	MAT1A	986	0.21	0.5	YES
9	LDHC	LDHC	LDHC	1449	0.16	0.5	YES
10	ADI1	ADI1	ADI1	1579	0.15	0.52	YES
11	LDHAL6B	LDHAL6B	LDHAL6B	1598	0.15	0.55	YES
12	GOT1	GOT1	GOT1	1617	0.15	0.57	YES
13	GOT2	GOT2	GOT2	1896	0.13	0.57	YES
14	AHCYL2	AHCYL2	AHCYL2	2253	0.11	0.57	NO
15	MAT2B	MAT2B	MAT2B	3614	0.062	0.5	NO
16	MPST	MPST	MPST	4105	0.049	0.48	NO
17	AHCY	AHCY	AHCY	4299	0.045	0.48	NO
18	MAT2A	MAT2A	MAT2A	5162	0.027	0.44	NO
19	AHCYL1	AHCYL1	AHCYL1	5983	0.012	0.39	NO
20	MTAP	MTAP	MTAP	6011	0.012	0.39	NO
21	LDHA	LDHA	LDHA	7840	-0.016	0.29	NO
22	LDHAL6A	LDHAL6A	LDHAL6A	9038	-0.032	0.23	NO
23	DNMT1	DNMT1	DNMT1	9575	-0.04	0.21	NO
24	APIP	APIP	APIP	9943	-0.046	0.19	NO
25	TRDMT1	TRDMT1	TRDMT1	10963	-0.063	0.14	NO
26	ENOPH1	ENOPH1	ENOPH1	11034	-0.064	0.15	NO
27	SRM	SRM	SRM	11631	-0.076	0.13	NO
28	AMD1	AMD1	AMD1	11720	-0.078	0.14	NO
29	SMS	SMS	SMS	12252	-0.09	0.12	NO
30	MTR	MTR	MTR	13478	-0.12	0.073	NO
31	LDHB	LDHB	LDHB	13920	-0.14	0.07	NO
32	DNMT3B	DNMT3B	DNMT3B	14753	-0.17	0.051	NO
33	DNMT3A	DNMT3A	DNMT3A	16352	-0.27	0.0039	NO
34	IL4I1	IL4I1	IL4I1	17561	-0.46	0.0094	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: KEGG RETINOL METABOLISM.

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

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 RIBOSOME	86	genes.ES.table	0.59	1.5	0.17	1	0.98	0.8	0.29	0.57	0.79	0.4
PID ATM PATHWAY	34	genes.ES.table	0.52	1.5	0.12	1	0.98	0.47	0.27	0.34	0.84	0.43
REACTOME TRANSLATION	146	genes.ES.table	0.53	1.7	0.089	1	0.85	0.7	0.34	0.47	1	0.74
REACTOME METABOLISM OF NON CODING RNA	47	genes.ES.table	0.48	1.7	0.061	1	0.86	0.64	0.4	0.38	1	0.59
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE	109	genes.ES.table	0.58	1.6	0.11	1	0.93	0.8	0.33	0.54	0.8	0.42
REACTOME SIGNALLING TO RAS	27	genes.ES.table	0.46	1.4	0.098	1	0.99	0.11	0.064	0.1	0.85	0.42
REACTOME SIGNALLING TO ERKS	35	genes.ES.table	0.43	1.5	0.063	1	0.97	0.43	0.37	0.27	0.78	0.41
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA	126	genes.ES.table	0.38	1.5	0.096	1	0.98	0.59	0.4	0.35	0.79	0.41
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S	57	genes.ES.table	0.5	1.5	0.14	1	0.98	0.7	0.34	0.47	0.79	0.4
REACTOME PEPTIDE CHAIN ELONGATION	85	genes.ES.table	0.62	1.5	0.13	1	0.97	0.85	0.29	0.6	0.91	0.46

genes ES table in pathway: KEGG RIBOSOME

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	RPL21	RPL21	RPL21	884	0.26	-0.027	YES
2	RPL36A	RPL36A	RPL36A	1468	0.2	-0.043	YES
3	RPL9	RPL9	RPL9	1788	0.17	-0.046	YES
4	GSPT2	GSPT2	GSPT2	1932	0.16	-0.04	YES
5	FAM153A	FAM153A	FAM153A	1939	0.16	-0.026	YES
6	RPS24	RPS24	RPS24	1956	0.16	-0.013	YES
7	RPS19	RPS19	RPS19	2207	0.15	-0.014	YES
8	RPSA	RPSA	RPSA	2217	0.15	-0.0016	YES
9	RPSAP9	RPSAP9	RPSAP9	2231	0.15	0.01	YES
10	RPLP0	RPLP0	RPLP0	2454	0.14	0.0098	YES
11	RPS21	RPS21	RPS21	2515	0.13	0.018	YES
12	SEC11C	SEC11C	SEC11C	2517	0.13	0.03	YES
13	SSR2	SSR2	SSR2	2580	0.13	0.038	YES
14	RPL39	RPL39	RPL39	2600	0.13	0.048	YES
15	RPL27A	RPL27A	RPL27A	2612	0.13	0.058	YES
16	RPS10	RPS10	RPS10	2613	0.13	0.07	YES
17	RPS12	RPS12	RPS12	2677	0.13	0.077	YES
18	RPS27	RPS27	RPS27	2735	0.12	0.085	YES
19	RPS17	RPS17	RPS17	2737	0.12	0.096	YES
20	RPS3	RPS3	RPS3	2761	0.12	0.1	YES
21	RPL23A	RPL23A	RPL23A	2768	0.12	0.12	YES
22	RPS7	RPS7	RPS7	2788	0.12	0.12	YES
23	RPS18	RPS18	RPS18	2794	0.12	0.14	YES
24	RPL26	RPL26	RPL26	2852	0.12	0.14	YES
25	RPS5	RPS5	RPS5	2871	0.12	0.15	YES
26	RPS27A	RPS27A	RPS27A	2884	0.12	0.16	YES
27	RPS15	RPS15	RPS15	2892	0.12	0.17	YES
28	RPL18A	RPL18A	RPL18A	2917	0.12	0.18	YES
29	RPS29	RPS29	RPS29	2934	0.12	0.19	YES
30	RPL28	RPL28	RPL28	2952	0.12	0.2	YES
31	RPL37A	RPL37A	RPL37A	3192	0.11	0.2	YES
32	EEF1B2	EEF1B2	EEF1B2	3243	0.11	0.2	YES
33	RPL36	RPL36	RPL36	3272	0.11	0.21	YES
34	RPS28	RPS28	RPS28	3286	0.1	0.22	YES
35	RPL7	RPL7	RPL7	3288	0.1	0.23	YES
36	RPLP2	RPLP2	RPLP2	3289	0.1	0.24	YES
37	RPS4X	RPS4X	RPS4X	3293	0.1	0.25	YES
38	RPL32	RPL32	RPL32	3331	0.1	0.25	YES
39	RPL18	RPL18	RPL18	3335	0.1	0.26	YES
40	RPL6	RPL6	RPL6	3358	0.1	0.27	YES
41	EEF1G	EEF1G	EEF1G	3365	0.1	0.28	YES
42	RPL31	RPL31	RPL31	3366	0.1	0.29	YES
43	RPL7A	RPL7A	RPL7A	3376	0.1	0.3	YES
44	RPL27	RPL27	RPL27	3384	0.1	0.3	YES
45	RPL38	RPL38	RPL38	3414	0.1	0.31	YES
46	RPL17	RPL17	RPL17	3417	0.1	0.32	YES
47	RPL13A	RPL13A	RPL13A	3488	0.1	0.32	YES
48	RPS16	RPS16	RPS16	3532	0.099	0.33	YES
49	RPL35A	RPL35A	RPL35A	3619	0.097	0.34	YES
50	RPL14	RPL14	RPL14	3627	0.096	0.34	YES
51	SEC61A2	SEC61A2	SEC61A2	3647	0.096	0.35	YES
52	RPL3	RPL3	RPL3	3661	0.095	0.36	YES
53	RPL10A	RPL10A	RPL10A	3670	0.095	0.36	YES
54	RPS11	RPS11	RPS11	3681	0.094	0.37	YES
55	RPL4	RPL4	RPL4	3741	0.093	0.38	YES
56	RPL23	RPL23	RPL23	4022	0.085	0.37	YES
57	RPL35	RPL35	RPL35	4077	0.084	0.37	YES
58	RPS9	RPS9	RPS9	4088	0.084	0.38	YES
59	SSR4	SSR4	SSR4	4105	0.083	0.39	YES
60	RPL8	RPL8	RPL8	4107	0.083	0.39	YES
61	RPL41	RPL41	RPL41	4108	0.083	0.4	YES
62	RPS6	RPS6	RPS6	4116	0.083	0.41	YES
63	RPS2	RPS2	RPS2	4195	0.081	0.41	YES
64	RPL37	RPL37	RPL37	4259	0.08	0.41	YES
65	RPS23	RPS23	RPS23	4261	0.08	0.42	YES
66	RPL24	RPL24	RPL24	4266	0.08	0.43	YES
67	SEC11A	SEC11A	SEC11A	4272	0.08	0.44	YES
68	RPL30	RPL30	RPL30	4292	0.079	0.44	YES
69	RPS13	RPS13	RPS13	4332	0.078	0.44	YES
70	RPS25	RPS25	RPS25	4342	0.078	0.45	YES
71	EIF3D	EIF3D	EIF3D	4456	0.075	0.45	YES
72	EIF2S3	EIF2S3	EIF2S3	4494	0.074	0.46	YES
73	RPLP1	RPLP1	RPLP1	4504	0.074	0.46	YES
74	PABPC1	PABPC1	PABPC1	4626	0.072	0.46	YES
75	RPL29	RPL29	RPL29	4630	0.072	0.47	YES
76	EIF2S2	EIF2S2	EIF2S2	4715	0.07	0.47	YES
77	RPL12	RPL12	RPL12	4729	0.07	0.47	YES
78	SPCS2	SPCS2	SPCS2	4844	0.068	0.47	YES
79	SRP9	SRP9	SRP9	4864	0.067	0.48	YES
80	RPL15	RPL15	RPL15	4885	0.067	0.48	YES
81	RPS20	RPS20	RPS20	4902	0.066	0.49	YES
82	EIF4A1	EIF4A1	EIF4A1	4963	0.065	0.49	YES
83	EIF4A2	EIF4A2	EIF4A2	4972	0.065	0.5	YES
84	EEF1A1	EEF1A1	EEF1A1	4988	0.064	0.5	YES
85	RPS14	RPS14	RPS14	5088	0.062	0.5	YES
86	LOC653566	LOC653566	LOC653566	5174	0.061	0.5	YES
87	RPS3A	RPS3A	RPS3A	5206	0.06	0.5	YES
88	RPL10	RPL10	RPL10	5212	0.06	0.51	YES
89	RPL5	RPL5	RPL5	5219	0.06	0.51	YES
90	SEC61G	SEC61G	SEC61G	5265	0.059	0.52	YES
91	UBA52	UBA52	UBA52	5362	0.057	0.52	YES
92	RPL34	RPL34	RPL34	5551	0.054	0.51	YES
93	RPL19	RPL19	RPL19	5664	0.052	0.51	YES
94	EEF1D	EEF1D	EEF1D	5669	0.052	0.51	YES
95	EIF4B	EIF4B	EIF4B	5738	0.051	0.51	YES
96	RPS8	RPS8	RPS8	5783	0.05	0.52	YES
97	RPN2	RPN2	RPN2	5793	0.05	0.52	YES
98	RPS15A	RPS15A	RPS15A	5804	0.05	0.52	YES
99	SSR1	SSR1	SSR1	5816	0.049	0.53	YES
100	EIF3K	EIF3K	EIF3K	5900	0.048	0.53	YES
101	EIF3F	EIF3F	EIF3F	5948	0.047	0.53	YES
102	RPL13	RPL13	RPL13	5986	0.046	0.53	YES
103	RPS26	RPS26	RPS26	6149	0.044	0.52	NO
104	SRPRB	SRPRB	SRPRB	6241	0.042	0.52	NO
105	EIF3G	EIF3G	EIF3G	6317	0.041	0.52	NO
106	FAU	FAU	FAU	6458	0.039	0.52	NO
107	EIF3E	EIF3E	EIF3E	6583	0.036	0.51	NO
108	EIF3B	EIF3B	EIF3B	6773	0.034	0.5	NO
109	SRP14	SRP14	SRP14	7002	0.03	0.5	NO
110	RPL11	RPL11	RPL11	7214	0.027	0.48	NO
111	RPL22	RPL22	RPL22	7268	0.026	0.48	NO
112	SRP68	SRP68	SRP68	7408	0.024	0.48	NO
113	SSR3	SSR3	SSR3	7590	0.021	0.47	NO
114	SEC61B	SEC61B	SEC61B	7976	0.015	0.45	NO
115	RPN1	RPN1	RPN1	7994	0.014	0.45	NO
116	EEF2	EEF2	EEF2	8073	0.013	0.45	NO
117	EIF1AX	EIF1AX	EIF1AX	8327	0.01	0.43	NO
118	EIF5B	EIF5B	EIF5B	8410	0.0087	0.43	NO
119	SRP72	SRP72	SRP72	8414	0.0086	0.43	NO
120	EIF2B4	EIF2B4	EIF2B4	8535	0.0068	0.42	NO
121	EIF3A	EIF3A	EIF3A	8556	0.0066	0.42	NO
122	SEC61A1	SEC61A1	SEC61A1	8632	0.0052	0.42	NO
123	EIF3J	EIF3J	EIF3J	8723	0.0038	0.41	NO
124	EIF3H	EIF3H	EIF3H	8844	0.0019	0.41	NO
125	TRAM1	TRAM1	TRAM1	9035	-0.00076	0.4	NO
126	EIF2B5	EIF2B5	EIF2B5	9167	-0.0028	0.39	NO
127	EIF2B1	EIF2B1	EIF2B1	9362	-0.0057	0.38	NO
128	SRP19	SRP19	SRP19	9449	-0.0073	0.38	NO
129	EIF5	EIF5	EIF5	9797	-0.013	0.36	NO
130	EIF4E	EIF4E	EIF4E	9994	-0.016	0.35	NO
131	EIF4H	EIF4H	EIF4H	10191	-0.02	0.34	NO
132	EIF2B2	EIF2B2	EIF2B2	10407	-0.023	0.33	NO
133	SPCS1	SPCS1	SPCS1	10513	-0.025	0.32	NO
134	DDOST	DDOST	DDOST	10683	-0.028	0.32	NO
135	EIF2S1	EIF2S1	EIF2S1	10844	-0.03	0.31	NO
136	ETF1	ETF1	ETF1	11080	-0.034	0.3	NO
137	EIF3C	EIF3C	EIF3C	11701	-0.046	0.27	NO
138	SRP54	SRP54	SRP54	11703	-0.046	0.27	NO
139	EIF4EBP1	EIF4EBP1	EIF4EBP1	11826	-0.048	0.27	NO
140	EIF4G1	EIF4G1	EIF4G1	12581	-0.064	0.23	NO
141	EIF3I	EIF3I	EIF3I	12667	-0.066	0.23	NO
142	SRPR	SRPR	SRPR	12687	-0.066	0.24	NO
143	SPCS3	SPCS3	SPCS3	13086	-0.075	0.22	NO
144	RPL26L1	RPL26L1	RPL26L1	13573	-0.087	0.2	NO
145	EIF2B3	EIF2B3	EIF2B3	15494	-0.16	0.11	NO
146	RPS4Y1	RPS4Y1	RPS4Y1	16645	-0.24	0.062	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 RIBOSOME.

Figure S42. 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: PID ATM PATHWAY

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	SMN1	SMN1	SMN1	1945	0.16	-0.048	YES
2	GEMIN7	GEMIN7	GEMIN7	2025	0.16	0.0064	YES
3	SNRPE	SNRPE	SNRPE	2268	0.14	0.047	YES
4	SNRPD1	SNRPD1	SNRPD1	2587	0.13	0.078	YES
5	NUP210	NUP210	NUP210	2790	0.12	0.11	YES
6	SNRPF	SNRPF	SNRPF	2829	0.12	0.16	YES
7	NUP133	NUP133	NUP133	3352	0.1	0.17	YES
8	SNRPB	SNRPB	SNRPB	3425	0.1	0.2	YES
9	NUP50	NUP50	NUP50	3689	0.094	0.22	YES
10	TPR	TPR	TPR	3693	0.094	0.26	YES
11	RAE1	RAE1	RAE1	3982	0.086	0.27	YES
12	SNRPG	SNRPG	SNRPG	4041	0.085	0.3	YES
13	NUP88	NUP88	NUP88	4204	0.081	0.32	YES
14	SMN2	SMN2	SMN2	4271	0.08	0.35	YES
15	NCBP2	NCBP2	NCBP2	4440	0.076	0.37	YES
16	SNRPD3	SNRPD3	SNRPD3	4545	0.073	0.39	YES
17	POM121	POM121	POM121	4614	0.072	0.41	YES
18	SNRPD2	SNRPD2	SNRPD2	4777	0.069	0.43	YES
19	NUP43	NUP43	NUP43	5203	0.06	0.43	YES
20	NUP85	NUP85	NUP85	5425	0.056	0.44	YES
21	GEMIN4	GEMIN4	GEMIN4	5684	0.052	0.44	YES
22	NUP37	NUP37	NUP37	5781	0.05	0.46	YES
23	NUP62	NUP62	NUP62	6439	0.039	0.43	YES
24	NUP205	NUP205	NUP205	6454	0.039	0.45	YES
25	AAAS	AAAS	AAAS	6673	0.035	0.45	YES
26	NUP214	NUP214	NUP214	6834	0.033	0.45	YES
27	SEH1L	SEH1L	SEH1L	6848	0.032	0.46	YES
28	NUP107	NUP107	NUP107	6928	0.031	0.47	YES
29	SNUPN	SNUPN	SNUPN	7047	0.029	0.48	YES
30	NUP35	NUP35	NUP35	7132	0.028	0.48	YES
31	CLNS1A	CLNS1A	CLNS1A	7375	0.025	0.48	NO
32	NUPL2	NUPL2	NUPL2	7769	0.018	0.46	NO
33	NUP155	NUP155	NUP155	7775	0.018	0.47	NO
34	NUP153	NUP153	NUP153	8016	0.014	0.46	NO
35	NUP188	NUP188	NUP188	8129	0.013	0.46	NO
36	RANBP2	RANBP2	RANBP2	8408	0.0088	0.44	NO
37	TGS1	TGS1	TGS1	8764	0.0032	0.43	NO
38	WDR77	WDR77	WDR77	8983	0.000074	0.41	NO
39	GEMIN6	GEMIN6	GEMIN6	8994	-0.00014	0.41	NO
40	NUPL1	NUPL1	NUPL1	9184	-0.003	0.4	NO
41	GEMIN5	GEMIN5	GEMIN5	9812	-0.013	0.37	NO
42	PHAX	PHAX	PHAX	10484	-0.024	0.34	NO
43	NCBP1	NCBP1	NCBP1	10645	-0.027	0.35	NO
44	PRMT5	PRMT5	PRMT5	10737	-0.029	0.35	NO
45	DDX20	DDX20	DDX20	10819	-0.03	0.36	NO
46	NUP54	NUP54	NUP54	11550	-0.043	0.33	NO
47	NUP93	NUP93	NUP93	11578	-0.043	0.35	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: PID ATM PATHWAY.

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

genes ES table in pathway: REACTOME TRANSLATION

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	RPL21	RPL21	RPL21	884	0.26	-0.023	YES
2	RPL36A	RPL36A	RPL36A	1468	0.2	-0.035	YES
3	RPL9	RPL9	RPL9	1788	0.17	-0.035	YES
4	GSPT2	GSPT2	GSPT2	1932	0.16	-0.026	YES
5	FAM153A	FAM153A	FAM153A	1939	0.16	-0.009	YES
6	RPS24	RPS24	RPS24	1956	0.16	0.007	YES
7	RPS19	RPS19	RPS19	2207	0.15	0.0083	YES
8	RPSA	RPSA	RPSA	2217	0.15	0.023	YES
9	RPSAP9	RPSAP9	RPSAP9	2231	0.15	0.038	YES
10	RPLP0	RPLP0	RPLP0	2454	0.14	0.04	YES
11	RPS21	RPS21	RPS21	2515	0.13	0.05	YES
12	RPL39	RPL39	RPL39	2600	0.13	0.059	YES
13	RPL27A	RPL27A	RPL27A	2612	0.13	0.072	YES
14	RPS10	RPS10	RPS10	2613	0.13	0.085	YES
15	RPS12	RPS12	RPS12	2677	0.13	0.095	YES
16	RPS27	RPS27	RPS27	2735	0.12	0.1	YES
17	RPS17	RPS17	RPS17	2737	0.12	0.12	YES
18	RPS3	RPS3	RPS3	2761	0.12	0.13	YES
19	RPL23A	RPL23A	RPL23A	2768	0.12	0.14	YES
20	RPS7	RPS7	RPS7	2788	0.12	0.15	YES
21	RPS18	RPS18	RPS18	2794	0.12	0.17	YES
22	RPL26	RPL26	RPL26	2852	0.12	0.18	YES
23	RPS5	RPS5	RPS5	2871	0.12	0.19	YES
24	RPS27A	RPS27A	RPS27A	2884	0.12	0.2	YES
25	RPS15	RPS15	RPS15	2892	0.12	0.21	YES
26	RPL18A	RPL18A	RPL18A	2917	0.12	0.22	YES
27	RPS29	RPS29	RPS29	2934	0.12	0.23	YES
28	RPL28	RPL28	RPL28	2952	0.12	0.24	YES
29	RPL37A	RPL37A	RPL37A	3192	0.11	0.24	YES
30	RPL36	RPL36	RPL36	3272	0.11	0.25	YES
31	RPS28	RPS28	RPS28	3286	0.1	0.26	YES
32	RPL7	RPL7	RPL7	3288	0.1	0.27	YES
33	RPLP2	RPLP2	RPLP2	3289	0.1	0.28	YES
34	RPS4X	RPS4X	RPS4X	3293	0.1	0.29	YES
35	RPL32	RPL32	RPL32	3331	0.1	0.3	YES
36	RPL18	RPL18	RPL18	3335	0.1	0.31	YES
37	UPF3A	UPF3A	UPF3A	3350	0.1	0.32	YES
38	RPL6	RPL6	RPL6	3358	0.1	0.33	YES
39	RPL31	RPL31	RPL31	3366	0.1	0.34	YES
40	RPL7A	RPL7A	RPL7A	3376	0.1	0.35	YES
41	RPL27	RPL27	RPL27	3384	0.1	0.36	YES
42	RPL38	RPL38	RPL38	3414	0.1	0.37	YES
43	RPL17	RPL17	RPL17	3417	0.1	0.38	YES
44	RPL13A	RPL13A	RPL13A	3488	0.1	0.39	YES
45	RPS16	RPS16	RPS16	3532	0.099	0.4	YES
46	RPL35A	RPL35A	RPL35A	3619	0.097	0.4	YES
47	RPL14	RPL14	RPL14	3627	0.096	0.41	YES
48	RPL3	RPL3	RPL3	3661	0.095	0.42	YES
49	RPL10A	RPL10A	RPL10A	3670	0.095	0.43	YES
50	RPS11	RPS11	RPS11	3681	0.094	0.44	YES
51	RPL4	RPL4	RPL4	3741	0.093	0.44	YES
52	SMG5	SMG5	SMG5	3809	0.091	0.45	YES
53	RPL23	RPL23	RPL23	4022	0.085	0.45	YES
54	RPL35	RPL35	RPL35	4077	0.084	0.45	YES
55	RPS9	RPS9	RPS9	4088	0.084	0.46	YES
56	RPL8	RPL8	RPL8	4107	0.083	0.47	YES
57	RPL41	RPL41	RPL41	4108	0.083	0.48	YES
58	RPS6	RPS6	RPS6	4116	0.083	0.49	YES
59	RPS2	RPS2	RPS2	4195	0.081	0.49	YES
60	RPL37	RPL37	RPL37	4259	0.08	0.5	YES
61	RPS23	RPS23	RPS23	4261	0.08	0.5	YES
62	RPL24	RPL24	RPL24	4266	0.08	0.51	YES
63	RPL30	RPL30	RPL30	4292	0.079	0.52	YES
64	RPS13	RPS13	RPS13	4332	0.078	0.52	YES
65	RPS25	RPS25	RPS25	4342	0.078	0.53	YES
66	NCBP2	NCBP2	NCBP2	4440	0.076	0.54	YES
67	RBM8A	RBM8A	RBM8A	4488	0.074	0.54	YES
68	RPLP1	RPLP1	RPLP1	4504	0.074	0.55	YES
69	PABPC1	PABPC1	PABPC1	4626	0.072	0.55	YES
70	RPL29	RPL29	RPL29	4630	0.072	0.56	YES
71	RPL12	RPL12	RPL12	4729	0.07	0.56	YES
72	RPL15	RPL15	RPL15	4885	0.067	0.55	YES
73	SMG7	SMG7	SMG7	4892	0.067	0.56	YES
74	RPS20	RPS20	RPS20	4902	0.066	0.57	YES
75	RPS14	RPS14	RPS14	5088	0.062	0.56	YES
76	RPS3A	RPS3A	RPS3A	5206	0.06	0.56	YES
77	RPL10	RPL10	RPL10	5212	0.06	0.57	YES
78	RPL5	RPL5	RPL5	5219	0.06	0.57	YES
79	PPP2R1A	PPP2R1A	PPP2R1A	5230	0.06	0.58	YES
80	UBA52	UBA52	UBA52	5362	0.057	0.58	NO
81	RPL34	RPL34	RPL34	5551	0.054	0.57	NO
82	RPL19	RPL19	RPL19	5664	0.052	0.57	NO
83	RPS8	RPS8	RPS8	5783	0.05	0.57	NO
84	RPS15A	RPS15A	RPS15A	5804	0.05	0.58	NO
85	SMG6	SMG6	SMG6	5933	0.047	0.57	NO
86	RPL13	RPL13	RPL13	5986	0.046	0.58	NO
87	UPF2	UPF2	UPF2	6013	0.046	0.58	NO
88	RPS26	RPS26	RPS26	6149	0.044	0.58	NO
89	FAU	FAU	FAU	6458	0.039	0.56	NO
90	RPL11	RPL11	RPL11	7214	0.027	0.52	NO
91	RPL22	RPL22	RPL22	7268	0.026	0.52	NO
92	CASC3	CASC3	CASC3	7763	0.018	0.5	NO
93	EIF4A3	EIF4A3	EIF4A3	8136	0.012	0.48	NO
94	UPF3B	UPF3B	UPF3B	8568	0.0063	0.45	NO
95	PPP2CA	PPP2CA	PPP2CA	8969	0.00031	0.43	NO
96	RNPS1	RNPS1	RNPS1	10306	-0.022	0.36	NO
97	NCBP1	NCBP1	NCBP1	10645	-0.027	0.34	NO
98	ETF1	ETF1	ETF1	11080	-0.034	0.32	NO
99	MAGOH	MAGOH	MAGOH	11661	-0.045	0.29	NO
100	SMG1	SMG1	SMG1	11991	-0.051	0.28	NO
101	EIF4G1	EIF4G1	EIF4G1	12581	-0.064	0.25	NO
102	PPP2R2A	PPP2R2A	PPP2R2A	12599	-0.064	0.26	NO
103	RPL26L1	RPL26L1	RPL26L1	13573	-0.087	0.21	NO
104	RPS4Y1	RPS4Y1	RPS4Y1	16645	-0.24	0.062	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: REACTOME TRANSLATION.

Figure S46. 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 METABOLISM OF NON CODING RNA

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	RPL21	RPL21	RPL21	884	0.26	-0.026	YES
2	RPL36A	RPL36A	RPL36A	1468	0.2	-0.04	YES
3	RPL9	RPL9	RPL9	1788	0.17	-0.042	YES
4	FAM153A	FAM153A	FAM153A	1939	0.16	-0.036	YES
5	RPS24	RPS24	RPS24	1956	0.16	-0.022	YES
6	RPS19	RPS19	RPS19	2207	0.15	-0.022	YES
7	RPSA	RPSA	RPSA	2217	0.15	-0.0091	YES
8	RPSAP9	RPSAP9	RPSAP9	2231	0.15	0.0038	YES
9	RPLP0	RPLP0	RPLP0	2454	0.14	0.0038	YES
10	RPS21	RPS21	RPS21	2515	0.13	0.013	YES
11	RPL39	RPL39	RPL39	2600	0.13	0.02	YES
12	RPL27A	RPL27A	RPL27A	2612	0.13	0.031	YES
13	RPS10	RPS10	RPS10	2613	0.13	0.043	YES
14	RPS12	RPS12	RPS12	2677	0.13	0.052	YES
15	RPS27	RPS27	RPS27	2735	0.12	0.06	YES
16	RPS17	RPS17	RPS17	2737	0.12	0.071	YES
17	RPS3	RPS3	RPS3	2761	0.12	0.082	YES
18	RPL23A	RPL23A	RPL23A	2768	0.12	0.093	YES
19	RPS7	RPS7	RPS7	2788	0.12	0.1	YES
20	NUP210	NUP210	NUP210	2790	0.12	0.11	YES
21	RPS18	RPS18	RPS18	2794	0.12	0.13	YES
22	RPL26	RPL26	RPL26	2852	0.12	0.13	YES
23	RPS5	RPS5	RPS5	2871	0.12	0.14	YES
24	RPS27A	RPS27A	RPS27A	2884	0.12	0.15	YES
25	RPS15	RPS15	RPS15	2892	0.12	0.16	YES
26	RPL18A	RPL18A	RPL18A	2917	0.12	0.17	YES
27	RPS29	RPS29	RPS29	2934	0.12	0.18	YES
28	RPL28	RPL28	RPL28	2952	0.12	0.19	YES
29	IPO5	IPO5	IPO5	3030	0.11	0.2	YES
30	RPL37A	RPL37A	RPL37A	3192	0.11	0.2	YES
31	RPL36	RPL36	RPL36	3272	0.11	0.21	YES
32	RPS28	RPS28	RPS28	3286	0.1	0.22	YES
33	RPL7	RPL7	RPL7	3288	0.1	0.22	YES
34	RPLP2	RPLP2	RPLP2	3289	0.1	0.24	YES
35	RPS4X	RPS4X	RPS4X	3293	0.1	0.24	YES
36	RPL32	RPL32	RPL32	3331	0.1	0.25	YES
37	RPL18	RPL18	RPL18	3335	0.1	0.26	YES
38	NUP133	NUP133	NUP133	3352	0.1	0.27	YES
39	RPL6	RPL6	RPL6	3358	0.1	0.28	YES
40	RPL31	RPL31	RPL31	3366	0.1	0.29	YES
41	RPL7A	RPL7A	RPL7A	3376	0.1	0.3	YES
42	RPL27	RPL27	RPL27	3384	0.1	0.31	YES
43	RPL38	RPL38	RPL38	3414	0.1	0.32	YES
44	RPL17	RPL17	RPL17	3417	0.1	0.32	YES
45	RPL13A	RPL13A	RPL13A	3488	0.1	0.33	YES
46	POLR2H	POLR2H	POLR2H	3505	0.1	0.34	YES
47	RPS16	RPS16	RPS16	3532	0.099	0.35	YES
48	RPL35A	RPL35A	RPL35A	3619	0.097	0.35	YES
49	RPL14	RPL14	RPL14	3627	0.096	0.36	YES
50	RPL3	RPL3	RPL3	3661	0.095	0.36	YES
51	RPL10A	RPL10A	RPL10A	3670	0.095	0.37	YES
52	RPS11	RPS11	RPS11	3681	0.094	0.38	YES
53	NUP50	NUP50	NUP50	3689	0.094	0.39	YES
54	TPR	TPR	TPR	3693	0.094	0.4	YES
55	RPL4	RPL4	RPL4	3741	0.093	0.4	YES
56	RAE1	RAE1	RAE1	3982	0.086	0.4	YES
57	RPL23	RPL23	RPL23	4022	0.085	0.4	YES
58	RPL35	RPL35	RPL35	4077	0.084	0.41	YES
59	RPS9	RPS9	RPS9	4088	0.084	0.42	YES
60	RPL8	RPL8	RPL8	4107	0.083	0.42	YES
61	RPL41	RPL41	RPL41	4108	0.083	0.43	YES
62	RPS6	RPS6	RPS6	4116	0.083	0.44	YES
63	RPS2	RPS2	RPS2	4195	0.081	0.44	YES
64	NUP88	NUP88	NUP88	4204	0.081	0.45	YES
65	RPL37	RPL37	RPL37	4259	0.08	0.45	YES
66	RPS23	RPS23	RPS23	4261	0.08	0.46	YES
67	RPL24	RPL24	RPL24	4266	0.08	0.47	YES
68	RPL30	RPL30	RPL30	4292	0.079	0.47	YES
69	RPS13	RPS13	RPS13	4332	0.078	0.48	YES
70	RPS25	RPS25	RPS25	4342	0.078	0.48	YES
71	RPLP1	RPLP1	RPLP1	4504	0.074	0.48	YES
72	POM121	POM121	POM121	4614	0.072	0.48	YES
73	RPL29	RPL29	RPL29	4630	0.072	0.49	YES
74	RPL12	RPL12	RPL12	4729	0.07	0.49	YES
75	POLR2D	POLR2D	POLR2D	4858	0.067	0.49	YES
76	RPL15	RPL15	RPL15	4885	0.067	0.49	YES
77	RPS20	RPS20	RPS20	4902	0.066	0.5	YES
78	RPS14	RPS14	RPS14	5088	0.062	0.49	YES
79	POLR2F	POLR2F	POLR2F	5124	0.062	0.5	YES
80	NUP43	NUP43	NUP43	5203	0.06	0.5	YES
81	RPS3A	RPS3A	RPS3A	5206	0.06	0.5	YES
82	RPL10	RPL10	RPL10	5212	0.06	0.51	YES
83	RPL5	RPL5	RPL5	5219	0.06	0.52	YES
84	UBA52	UBA52	UBA52	5362	0.057	0.51	YES
85	GTF2F2	GTF2F2	GTF2F2	5412	0.056	0.52	YES
86	NUP85	NUP85	NUP85	5425	0.056	0.52	YES
87	RPL34	RPL34	RPL34	5551	0.054	0.52	YES
88	RPL19	RPL19	RPL19	5664	0.052	0.52	YES
89	NUP37	NUP37	NUP37	5781	0.05	0.51	YES
90	RPS8	RPS8	RPS8	5783	0.05	0.52	YES
91	RPS15A	RPS15A	RPS15A	5804	0.05	0.52	YES
92	RPL13	RPL13	RPL13	5986	0.046	0.52	NO
93	RPS26	RPS26	RPS26	6149	0.044	0.51	NO
94	RAN	RAN	RAN	6180	0.043	0.51	NO
95	GTF2F1	GTF2F1	GTF2F1	6267	0.042	0.51	NO
96	CLTA	CLTA	CLTA	6330	0.041	0.51	NO
97	NUP62	NUP62	NUP62	6439	0.039	0.51	NO
98	NUP205	NUP205	NUP205	6454	0.039	0.51	NO
99	FAU	FAU	FAU	6458	0.039	0.52	NO
100	POLR2I	POLR2I	POLR2I	6615	0.036	0.51	NO
101	HSP90AA1	HSP90AA1	HSP90AA1	6669	0.035	0.51	NO
102	AAAS	AAAS	AAAS	6673	0.035	0.51	NO
103	NUP214	NUP214	NUP214	6834	0.033	0.51	NO
104	SEH1L	SEH1L	SEH1L	6848	0.032	0.51	NO
105	NUP107	NUP107	NUP107	6928	0.031	0.51	NO
106	XPO1	XPO1	XPO1	6991	0.03	0.51	NO
107	NUP35	NUP35	NUP35	7132	0.028	0.5	NO
108	RPL11	RPL11	RPL11	7214	0.027	0.5	NO
109	RPL22	RPL22	RPL22	7268	0.026	0.5	NO
110	POLR2J	POLR2J	POLR2J	7462	0.023	0.49	NO
111	KPNB1	KPNB1	KPNB1	7521	0.022	0.49	NO
112	NUPL2	NUPL2	NUPL2	7769	0.018	0.48	NO
113	NUP155	NUP155	NUP155	7775	0.018	0.48	NO
114	CALR	CALR	CALR	7999	0.014	0.47	NO
115	NUP153	NUP153	NUP153	8016	0.014	0.47	NO
116	NUP188	NUP188	NUP188	8129	0.013	0.46	NO
117	POLR2G	POLR2G	POLR2G	8198	0.012	0.46	NO
118	POLR2B	POLR2B	POLR2B	8200	0.012	0.46	NO
119	RANBP2	RANBP2	RANBP2	8408	0.0088	0.45	NO
120	NUPL1	NUPL1	NUPL1	9184	-0.003	0.41	NO
121	POLR2A	POLR2A	POLR2A	9461	-0.0075	0.39	NO
122	KPNA1	KPNA1	KPNA1	9467	-0.0076	0.39	NO
123	POLR2E	POLR2E	POLR2E	9788	-0.013	0.37	NO
124	DNAJC3	DNAJC3	DNAJC3	9816	-0.013	0.37	NO
125	CANX	CANX	CANX	9887	-0.014	0.37	NO
126	POLR2K	POLR2K	POLR2K	10232	-0.02	0.35	NO
127	CLTC	CLTC	CLTC	10471	-0.024	0.34	NO
128	POLR2L	POLR2L	POLR2L	11359	-0.04	0.3	NO
129	NUP54	NUP54	NUP54	11550	-0.043	0.29	NO
130	NUP93	NUP93	NUP93	11578	-0.043	0.29	NO
131	GRSF1	GRSF1	GRSF1	12923	-0.071	0.22	NO
132	POLR2C	POLR2C	POLR2C	13546	-0.087	0.19	NO
133	RPL26L1	RPL26L1	RPL26L1	13573	-0.087	0.2	NO
134	HSPA1B	HSPA1B	HSPA1B	15062	-0.14	0.13	NO
135	RPS4Y1	RPS4Y1	RPS4Y1	16645	-0.24	0.062	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: REACTOME METABOLISM OF NON CODING RNA.

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

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

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	LSM11	LSM11	LSM11	1211	0.22	-0.04	YES
2	GTF2H2B	GTF2H2B	GTF2H2B	1713	0.18	-0.045	YES
3	ZNF473	ZNF473	ZNF473	1903	0.16	-0.034	YES
4	SNRPA1	SNRPA1	SNRPA1	2054	0.16	-0.022	YES
5	SNRPE	SNRPE	SNRPE	2268	0.14	-0.016	YES
6	SF3A2	SF3A2	SF3A2	2304	0.14	0.00092	YES
7	SNRPD1	SNRPD1	SNRPD1	2587	0.13	0.0019	YES
8	CDK7	CDK7	CDK7	2609	0.13	0.018	YES
9	NUP210	NUP210	NUP210	2790	0.12	0.023	YES
10	SNRPF	SNRPF	SNRPF	2829	0.12	0.037	YES
11	LSM2	LSM2	LSM2	2950	0.12	0.045	YES
12	THOC4	THOC4	THOC4	3135	0.11	0.049	YES
13	NUP133	NUP133	NUP133	3352	0.1	0.05	YES
14	SNRPB	SNRPB	SNRPB	3425	0.1	0.06	YES
15	POLR2H	POLR2H	POLR2H	3505	0.1	0.068	YES
16	HNRNPA0	HNRNPA0	HNRNPA0	3555	0.098	0.078	YES
17	HNRNPA1	HNRNPA1	HNRNPA1	3571	0.098	0.09	YES
18	NUP50	NUP50	NUP50	3689	0.094	0.096	YES
19	TPR	TPR	TPR	3693	0.094	0.11	YES
20	NHP2L1	NHP2L1	NHP2L1	3823	0.09	0.11	YES
21	RAE1	RAE1	RAE1	3982	0.086	0.11	YES
22	SNRPG	SNRPG	SNRPG	4041	0.085	0.12	YES
23	U2AF1	U2AF1	U2AF1	4153	0.082	0.13	YES
24	NUP88	NUP88	NUP88	4204	0.081	0.13	YES
25	NCBP2	NCBP2	NCBP2	4440	0.076	0.13	YES
26	RBM8A	RBM8A	RBM8A	4488	0.074	0.14	YES
27	SNRPA	SNRPA	SNRPA	4492	0.074	0.15	YES
28	SNRPD3	SNRPD3	SNRPD3	4545	0.073	0.15	YES
29	SNRNP70	SNRNP70	SNRNP70	4590	0.072	0.16	YES
30	POM121	POM121	POM121	4614	0.072	0.17	YES
31	SNRPD2	SNRPD2	SNRPD2	4777	0.069	0.17	YES
32	POLR2D	POLR2D	POLR2D	4858	0.067	0.17	YES
33	RBMX	RBMX	RBMX	4863	0.067	0.18	YES
34	HNRNPUL1	HNRNPUL1	HNRNPUL1	4866	0.067	0.19	YES
35	CCAR1	CCAR1	CCAR1	4920	0.066	0.2	YES
36	FUS	FUS	FUS	4923	0.066	0.2	YES
37	A1CF	A1CF	A1CF	4978	0.065	0.21	YES
38	PRPF6	PRPF6	PRPF6	5004	0.064	0.22	YES
39	PABPN1	PABPN1	PABPN1	5038	0.063	0.22	YES
40	SF3B4	SF3B4	SF3B4	5039	0.063	0.23	YES
41	PHF5A	PHF5A	PHF5A	5040	0.063	0.24	YES
42	HNRNPA3	HNRNPA3	HNRNPA3	5060	0.063	0.25	YES
43	POLR2F	POLR2F	POLR2F	5124	0.062	0.25	YES
44	RBM5	RBM5	RBM5	5195	0.06	0.26	YES
45	NUP43	NUP43	NUP43	5203	0.06	0.26	YES
46	SLBP	SLBP	SLBP	5213	0.06	0.27	YES
47	HNRNPH1	HNRNPH1	HNRNPH1	5261	0.059	0.27	YES
48	SUPT5H	SUPT5H	SUPT5H	5359	0.057	0.28	YES
49	GTF2F2	GTF2F2	GTF2F2	5412	0.056	0.28	YES
50	NUP85	NUP85	NUP85	5425	0.056	0.29	YES
51	HNRNPU	HNRNPU	HNRNPU	5503	0.055	0.29	YES
52	ERCC2	ERCC2	ERCC2	5564	0.054	0.29	YES
53	PTBP1	PTBP1	PTBP1	5611	0.053	0.3	YES
54	SNRPB2	SNRPB2	SNRPB2	5718	0.051	0.3	YES
55	CPSF1	CPSF1	CPSF1	5773	0.05	0.3	YES
56	NUP37	NUP37	NUP37	5781	0.05	0.31	YES
57	PCF11	PCF11	PCF11	5909	0.048	0.31	YES
58	GTF2H4	GTF2H4	GTF2H4	5918	0.048	0.31	YES
59	RNMT	RNMT	RNMT	5954	0.047	0.32	YES
60	U2AF2	U2AF2	U2AF2	6004	0.046	0.32	YES
61	DHX9	DHX9	DHX9	6022	0.046	0.32	YES
62	HNRNPL	HNRNPL	HNRNPL	6030	0.046	0.33	YES
63	TXNL4A	TXNL4A	TXNL4A	6162	0.044	0.33	YES
64	NXF1	NXF1	NXF1	6238	0.042	0.33	YES
65	GTF2F1	GTF2F1	GTF2F1	6267	0.042	0.33	YES
66	CPSF7	CPSF7	CPSF7	6313	0.041	0.34	YES
67	NUP62	NUP62	NUP62	6439	0.039	0.34	YES
68	NUP205	NUP205	NUP205	6454	0.039	0.34	YES
69	GTF2H1	GTF2H1	GTF2H1	6460	0.039	0.34	YES
70	HNRNPC	HNRNPC	HNRNPC	6537	0.037	0.34	YES
71	POLR2I	POLR2I	POLR2I	6615	0.036	0.34	YES
72	HNRNPM	HNRNPM	HNRNPM	6653	0.036	0.35	YES
73	AAAS	AAAS	AAAS	6673	0.035	0.35	YES
74	NUP214	NUP214	NUP214	6834	0.033	0.35	YES
75	PAPOLA	PAPOLA	PAPOLA	6845	0.032	0.35	YES
76	SEH1L	SEH1L	SEH1L	6848	0.032	0.35	YES
77	SF3B14	SF3B14	SF3B14	6878	0.032	0.36	YES
78	NUP107	NUP107	NUP107	6928	0.031	0.36	YES
79	HNRNPF	HNRNPF	HNRNPF	6943	0.031	0.36	YES
80	METTL3	METTL3	METTL3	6981	0.03	0.36	YES
81	CSTF3	CSTF3	CSTF3	6984	0.03	0.37	YES
82	SF3B5	SF3B5	SF3B5	7005	0.03	0.37	YES
83	HNRNPD	HNRNPD	HNRNPD	7096	0.029	0.37	YES
84	NUP35	NUP35	NUP35	7132	0.028	0.37	YES
85	POLR2J	POLR2J	POLR2J	7462	0.023	0.35	NO
86	ERCC3	ERCC3	ERCC3	7684	0.02	0.34	NO
87	EFTUD2	EFTUD2	EFTUD2	7711	0.019	0.34	NO
88	NUPL2	NUPL2	NUPL2	7769	0.018	0.34	NO
89	NUP155	NUP155	NUP155	7775	0.018	0.35	NO
90	ADARB1	ADARB1	ADARB1	7819	0.017	0.35	NO
91	PRPF8	PRPF8	PRPF8	7846	0.017	0.35	NO
92	CPSF3	CPSF3	CPSF3	8002	0.014	0.34	NO
93	NUP153	NUP153	NUP153	8016	0.014	0.34	NO
94	SF3B1	SF3B1	SF3B1	8060	0.014	0.34	NO
95	NUP188	NUP188	NUP188	8129	0.013	0.34	NO
96	DDX23	DDX23	DDX23	8165	0.012	0.34	NO
97	POLR2G	POLR2G	POLR2G	8198	0.012	0.34	NO
98	POLR2B	POLR2B	POLR2B	8200	0.012	0.34	NO
99	PCBP2	PCBP2	PCBP2	8205	0.012	0.34	NO
100	HNRNPA2B1	HNRNPA2B1	HNRNPA2B1	8348	0.0098	0.33	NO
101	CSTF1	CSTF1	CSTF1	8369	0.0095	0.33	NO
102	RANBP2	RANBP2	RANBP2	8408	0.0088	0.33	NO
103	UPF3B	UPF3B	UPF3B	8568	0.0063	0.32	NO
104	ADAR	ADAR	ADAR	8583	0.0061	0.32	NO
105	SF3B2	SF3B2	SF3B2	8767	0.0032	0.31	NO
106	PRPF4	PRPF4	PRPF4	8951	0.00049	0.3	NO
107	NFX1	NFX1	NFX1	9037	-0.00077	0.3	NO
108	NUPL1	NUPL1	NUPL1	9184	-0.003	0.29	NO
109	HNRNPK	HNRNPK	HNRNPK	9265	-0.0042	0.29	NO
110	SNRNP200	SNRNP200	SNRNP200	9301	-0.0047	0.28	NO
111	POLR2A	POLR2A	POLR2A	9461	-0.0075	0.28	NO
112	PCBP1	PCBP1	PCBP1	9474	-0.0078	0.28	NO
113	SNRNP40	SNRNP40	SNRNP40	9574	-0.0092	0.27	NO
114	CLP1	CLP1	CLP1	9643	-0.01	0.27	NO
115	MNAT1	MNAT1	MNAT1	9722	-0.012	0.27	NO
116	POLR2E	POLR2E	POLR2E	9788	-0.013	0.27	NO
117	RNGTT	RNGTT	RNGTT	9938	-0.015	0.26	NO
118	EIF4E	EIF4E	EIF4E	9994	-0.016	0.26	NO
119	SF3A1	SF3A1	SF3A1	10204	-0.02	0.25	NO
120	CPSF2	CPSF2	CPSF2	10206	-0.02	0.25	NO
121	POLR2K	POLR2K	POLR2K	10232	-0.02	0.25	NO
122	RNPS1	RNPS1	RNPS1	10306	-0.022	0.25	NO
123	GTF2H2	GTF2H2	GTF2H2	10477	-0.024	0.24	NO
124	NCBP1	NCBP1	NCBP1	10645	-0.027	0.24	NO
125	SMC1A	SMC1A	SMC1A	10867	-0.031	0.23	NO
126	POLR2L	POLR2L	POLR2L	11359	-0.04	0.21	NO
127	HNRNPR	HNRNPR	HNRNPR	11478	-0.042	0.21	NO
128	NUP54	NUP54	NUP54	11550	-0.043	0.21	NO
129	NUP93	NUP93	NUP93	11578	-0.043	0.21	NO
130	YBX1	YBX1	YBX1	11655	-0.045	0.21	NO
131	MAGOH	MAGOH	MAGOH	11661	-0.045	0.22	NO
132	CDC40	CDC40	CDC40	11761	-0.047	0.22	NO
133	CD2BP2	CD2BP2	CD2BP2	11803	-0.047	0.22	NO
134	SF3A3	SF3A3	SF3A3	11879	-0.049	0.23	NO
135	SF3B3	SF3B3	SF3B3	11927	-0.05	0.23	NO
136	NUDT21	NUDT21	NUDT21	11931	-0.05	0.24	NO
137	HNRNPH2	HNRNPH2	HNRNPH2	11943	-0.05	0.24	NO
138	DNAJC8	DNAJC8	DNAJC8	12013	-0.051	0.24	NO
139	SRRM1	SRRM1	SRRM1	12978	-0.072	0.2	NO
140	DHX38	DHX38	DHX38	13133	-0.076	0.2	NO
141	GTF2H3	GTF2H3	GTF2H3	13272	-0.08	0.2	NO
142	POLR2C	POLR2C	POLR2C	13546	-0.087	0.2	NO
143	CCNH	CCNH	CCNH	13982	-0.098	0.19	NO
144	CSTF2	CSTF2	CSTF2	14018	-0.099	0.2	NO
145	LSM10	LSM10	LSM10	14219	-0.1	0.2	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: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S50. 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 SIGNALLING TO RAS

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	RPL21	RPL21	RPL21	884	0.26	-0.023	YES
2	RPL36A	RPL36A	RPL36A	1468	0.2	-0.036	YES
3	RPL9	RPL9	RPL9	1788	0.17	-0.036	YES
4	FAM153A	FAM153A	FAM153A	1939	0.16	-0.028	YES
5	RPS24	RPS24	RPS24	1956	0.16	-0.012	YES
6	RPS19	RPS19	RPS19	2207	0.15	-0.011	YES
7	RPSA	RPSA	RPSA	2217	0.15	0.0041	YES
8	RPSAP9	RPSAP9	RPSAP9	2231	0.15	0.018	YES
9	RPLP0	RPLP0	RPLP0	2454	0.14	0.02	YES
10	RPS21	RPS21	RPS21	2515	0.13	0.03	YES
11	SEC11C	SEC11C	SEC11C	2517	0.13	0.044	YES
12	SSR2	SSR2	SSR2	2580	0.13	0.054	YES
13	RPL39	RPL39	RPL39	2600	0.13	0.066	YES
14	RPL27A	RPL27A	RPL27A	2612	0.13	0.079	YES
15	RPS10	RPS10	RPS10	2613	0.13	0.092	YES
16	RPS12	RPS12	RPS12	2677	0.13	0.1	YES
17	RPS27	RPS27	RPS27	2735	0.12	0.11	YES
18	RPS17	RPS17	RPS17	2737	0.12	0.12	YES
19	RPS3	RPS3	RPS3	2761	0.12	0.14	YES
20	RPL23A	RPL23A	RPL23A	2768	0.12	0.15	YES
21	RPS7	RPS7	RPS7	2788	0.12	0.16	YES
22	RPS18	RPS18	RPS18	2794	0.12	0.17	YES
23	RPL26	RPL26	RPL26	2852	0.12	0.18	YES
24	RPS5	RPS5	RPS5	2871	0.12	0.19	YES
25	RPS27A	RPS27A	RPS27A	2884	0.12	0.2	YES
26	RPS15	RPS15	RPS15	2892	0.12	0.22	YES
27	RPL18A	RPL18A	RPL18A	2917	0.12	0.23	YES
28	RPS29	RPS29	RPS29	2934	0.12	0.24	YES
29	RPL28	RPL28	RPL28	2952	0.12	0.25	YES
30	RPL37A	RPL37A	RPL37A	3192	0.11	0.25	YES
31	RPL36	RPL36	RPL36	3272	0.11	0.25	YES
32	RPS28	RPS28	RPS28	3286	0.1	0.26	YES
33	RPL7	RPL7	RPL7	3288	0.1	0.27	YES
34	RPLP2	RPLP2	RPLP2	3289	0.1	0.28	YES
35	RPS4X	RPS4X	RPS4X	3293	0.1	0.3	YES
36	RPL32	RPL32	RPL32	3331	0.1	0.3	YES
37	RPL18	RPL18	RPL18	3335	0.1	0.32	YES
38	RPL6	RPL6	RPL6	3358	0.1	0.32	YES
39	RPL31	RPL31	RPL31	3366	0.1	0.33	YES
40	RPL7A	RPL7A	RPL7A	3376	0.1	0.34	YES
41	RPL27	RPL27	RPL27	3384	0.1	0.36	YES
42	RPL38	RPL38	RPL38	3414	0.1	0.36	YES
43	RPL17	RPL17	RPL17	3417	0.1	0.37	YES
44	RPL13A	RPL13A	RPL13A	3488	0.1	0.38	YES
45	RPS16	RPS16	RPS16	3532	0.099	0.39	YES
46	RPL35A	RPL35A	RPL35A	3619	0.097	0.39	YES
47	RPL14	RPL14	RPL14	3627	0.096	0.4	YES
48	SEC61A2	SEC61A2	SEC61A2	3647	0.096	0.41	YES
49	RPL3	RPL3	RPL3	3661	0.095	0.42	YES
50	RPL10A	RPL10A	RPL10A	3670	0.095	0.43	YES
51	RPS11	RPS11	RPS11	3681	0.094	0.44	YES
52	RPL4	RPL4	RPL4	3741	0.093	0.44	YES
53	RPL23	RPL23	RPL23	4022	0.085	0.44	YES
54	RPL35	RPL35	RPL35	4077	0.084	0.44	YES
55	RPS9	RPS9	RPS9	4088	0.084	0.45	YES
56	SSR4	SSR4	SSR4	4105	0.083	0.46	YES
57	RPL8	RPL8	RPL8	4107	0.083	0.47	YES
58	RPL41	RPL41	RPL41	4108	0.083	0.48	YES
59	RPS6	RPS6	RPS6	4116	0.083	0.48	YES
60	RPS2	RPS2	RPS2	4195	0.081	0.49	YES
61	RPL37	RPL37	RPL37	4259	0.08	0.49	YES
62	RPS23	RPS23	RPS23	4261	0.08	0.5	YES
63	RPL24	RPL24	RPL24	4266	0.08	0.51	YES
64	SEC11A	SEC11A	SEC11A	4272	0.08	0.52	YES
65	RPL30	RPL30	RPL30	4292	0.079	0.52	YES
66	RPS13	RPS13	RPS13	4332	0.078	0.53	YES
67	RPS25	RPS25	RPS25	4342	0.078	0.54	YES
68	RPLP1	RPLP1	RPLP1	4504	0.074	0.54	YES
69	RPL29	RPL29	RPL29	4630	0.072	0.54	YES
70	RPL12	RPL12	RPL12	4729	0.07	0.54	YES
71	SPCS2	SPCS2	SPCS2	4844	0.068	0.54	YES
72	SRP9	SRP9	SRP9	4864	0.067	0.55	YES
73	RPL15	RPL15	RPL15	4885	0.067	0.55	YES
74	RPS20	RPS20	RPS20	4902	0.066	0.56	YES
75	RPS14	RPS14	RPS14	5088	0.062	0.55	YES
76	LOC653566	LOC653566	LOC653566	5174	0.061	0.55	YES
77	RPS3A	RPS3A	RPS3A	5206	0.06	0.56	YES
78	RPL10	RPL10	RPL10	5212	0.06	0.56	YES
79	RPL5	RPL5	RPL5	5219	0.06	0.57	YES
80	SEC61G	SEC61G	SEC61G	5265	0.059	0.57	YES
81	UBA52	UBA52	UBA52	5362	0.057	0.57	YES
82	RPL34	RPL34	RPL34	5551	0.054	0.57	YES
83	RPL19	RPL19	RPL19	5664	0.052	0.57	YES
84	RPS8	RPS8	RPS8	5783	0.05	0.57	YES
85	RPN2	RPN2	RPN2	5793	0.05	0.57	YES
86	RPS15A	RPS15A	RPS15A	5804	0.05	0.58	YES
87	SSR1	SSR1	SSR1	5816	0.049	0.58	YES
88	RPL13	RPL13	RPL13	5986	0.046	0.57	NO
89	RPS26	RPS26	RPS26	6149	0.044	0.57	NO
90	SRPRB	SRPRB	SRPRB	6241	0.042	0.57	NO
91	FAU	FAU	FAU	6458	0.039	0.56	NO
92	SRP14	SRP14	SRP14	7002	0.03	0.53	NO
93	RPL11	RPL11	RPL11	7214	0.027	0.52	NO
94	RPL22	RPL22	RPL22	7268	0.026	0.52	NO
95	SRP68	SRP68	SRP68	7408	0.024	0.52	NO
96	SSR3	SSR3	SSR3	7590	0.021	0.51	NO
97	SEC61B	SEC61B	SEC61B	7976	0.015	0.49	NO
98	RPN1	RPN1	RPN1	7994	0.014	0.49	NO
99	SRP72	SRP72	SRP72	8414	0.0086	0.47	NO
100	SEC61A1	SEC61A1	SEC61A1	8632	0.0052	0.46	NO
101	TRAM1	TRAM1	TRAM1	9035	-0.00076	0.43	NO
102	SRP19	SRP19	SRP19	9449	-0.0073	0.41	NO
103	SPCS1	SPCS1	SPCS1	10513	-0.025	0.35	NO
104	DDOST	DDOST	DDOST	10683	-0.028	0.35	NO
105	SRP54	SRP54	SRP54	11703	-0.046	0.29	NO
106	SRPR	SRPR	SRPR	12687	-0.066	0.24	NO
107	SPCS3	SPCS3	SPCS3	13086	-0.075	0.23	NO
108	RPL26L1	RPL26L1	RPL26L1	13573	-0.087	0.21	NO
109	RPS4Y1	RPS4Y1	RPS4Y1	16645	-0.24	0.062	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: REACTOME SIGNALLING TO RAS.

Figure S52. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SIGNALLING TO RAS, 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 SIGNALLING TO ERKS

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	RPL21	RPL21	RPL21	884	0.26	-0.022	YES
2	RPL36A	RPL36A	RPL36A	1468	0.2	-0.034	YES
3	RPL9	RPL9	RPL9	1788	0.17	-0.033	YES
4	FAM153A	FAM153A	FAM153A	1939	0.16	-0.024	YES
5	RPS24	RPS24	RPS24	1956	0.16	-0.008	YES
6	RPS19	RPS19	RPS19	2207	0.15	-0.0064	YES
7	RPSA	RPSA	RPSA	2217	0.15	0.0089	YES
8	RPSAP9	RPSAP9	RPSAP9	2231	0.15	0.024	YES
9	RPLP0	RPLP0	RPLP0	2454	0.14	0.026	YES
10	RPS21	RPS21	RPS21	2515	0.13	0.037	YES
11	RPL39	RPL39	RPL39	2600	0.13	0.046	YES
12	RPL27A	RPL27A	RPL27A	2612	0.13	0.059	YES
13	RPS10	RPS10	RPS10	2613	0.13	0.073	YES
14	RPS12	RPS12	RPS12	2677	0.13	0.083	YES
15	RPS27	RPS27	RPS27	2735	0.12	0.093	YES
16	RPS17	RPS17	RPS17	2737	0.12	0.11	YES
17	RPS3	RPS3	RPS3	2761	0.12	0.12	YES
18	RPL23A	RPL23A	RPL23A	2768	0.12	0.13	YES
19	RPS7	RPS7	RPS7	2788	0.12	0.14	YES
20	RPS18	RPS18	RPS18	2794	0.12	0.16	YES
21	RPL26	RPL26	RPL26	2852	0.12	0.16	YES
22	RPS5	RPS5	RPS5	2871	0.12	0.18	YES
23	RPS27A	RPS27A	RPS27A	2884	0.12	0.19	YES
24	RPS15	RPS15	RPS15	2892	0.12	0.2	YES
25	RPL18A	RPL18A	RPL18A	2917	0.12	0.21	YES
26	RPS29	RPS29	RPS29	2934	0.12	0.22	YES
27	RPL28	RPL28	RPL28	2952	0.12	0.24	YES
28	RPL37A	RPL37A	RPL37A	3192	0.11	0.23	YES
29	RPL36	RPL36	RPL36	3272	0.11	0.24	YES
30	RPS28	RPS28	RPS28	3286	0.1	0.25	YES
31	RPL7	RPL7	RPL7	3288	0.1	0.26	YES
32	RPLP2	RPLP2	RPLP2	3289	0.1	0.27	YES
33	RPS4X	RPS4X	RPS4X	3293	0.1	0.28	YES
34	RPL32	RPL32	RPL32	3331	0.1	0.29	YES
35	RPL18	RPL18	RPL18	3335	0.1	0.3	YES
36	RPL6	RPL6	RPL6	3358	0.1	0.32	YES
37	RPL31	RPL31	RPL31	3366	0.1	0.32	YES
38	RPL7A	RPL7A	RPL7A	3376	0.1	0.34	YES
39	RPL27	RPL27	RPL27	3384	0.1	0.35	YES
40	RPL38	RPL38	RPL38	3414	0.1	0.36	YES
41	RPL17	RPL17	RPL17	3417	0.1	0.37	YES
42	RPL13A	RPL13A	RPL13A	3488	0.1	0.37	YES
43	RPS16	RPS16	RPS16	3532	0.099	0.38	YES
44	RPL35A	RPL35A	RPL35A	3619	0.097	0.39	YES
45	RPL14	RPL14	RPL14	3627	0.096	0.4	YES
46	RPL3	RPL3	RPL3	3661	0.095	0.4	YES
47	RPL10A	RPL10A	RPL10A	3670	0.095	0.42	YES
48	RPS11	RPS11	RPS11	3681	0.094	0.42	YES
49	RPL4	RPL4	RPL4	3741	0.093	0.43	YES
50	RPL23	RPL23	RPL23	4022	0.085	0.42	YES
51	RPL35	RPL35	RPL35	4077	0.084	0.43	YES
52	RPS9	RPS9	RPS9	4088	0.084	0.44	YES
53	RPL8	RPL8	RPL8	4107	0.083	0.45	YES
54	RPL41	RPL41	RPL41	4108	0.083	0.46	YES
55	RPS6	RPS6	RPS6	4116	0.083	0.46	YES
56	RPS2	RPS2	RPS2	4195	0.081	0.47	YES
57	RPL37	RPL37	RPL37	4259	0.08	0.47	YES
58	RPS23	RPS23	RPS23	4261	0.08	0.48	YES
59	RPL24	RPL24	RPL24	4266	0.08	0.49	YES
60	RPL30	RPL30	RPL30	4292	0.079	0.5	YES
61	RPS13	RPS13	RPS13	4332	0.078	0.5	YES
62	RPS25	RPS25	RPS25	4342	0.078	0.51	YES
63	EIF3D	EIF3D	EIF3D	4456	0.075	0.51	YES
64	EIF2S3	EIF2S3	EIF2S3	4494	0.074	0.52	YES
65	RPLP1	RPLP1	RPLP1	4504	0.074	0.52	YES
66	PABPC1	PABPC1	PABPC1	4626	0.072	0.53	YES
67	RPL29	RPL29	RPL29	4630	0.072	0.53	YES
68	EIF2S2	EIF2S2	EIF2S2	4715	0.07	0.54	YES
69	RPL12	RPL12	RPL12	4729	0.07	0.54	YES
70	RPL15	RPL15	RPL15	4885	0.067	0.54	YES
71	RPS20	RPS20	RPS20	4902	0.066	0.55	YES
72	EIF4A1	EIF4A1	EIF4A1	4963	0.065	0.55	YES
73	EIF4A2	EIF4A2	EIF4A2	4972	0.065	0.56	YES
74	RPS14	RPS14	RPS14	5088	0.062	0.56	YES
75	RPS3A	RPS3A	RPS3A	5206	0.06	0.56	YES
76	RPL10	RPL10	RPL10	5212	0.06	0.56	YES
77	RPL5	RPL5	RPL5	5219	0.06	0.57	YES
78	UBA52	UBA52	UBA52	5362	0.057	0.57	YES
79	RPL34	RPL34	RPL34	5551	0.054	0.56	YES
80	RPL19	RPL19	RPL19	5664	0.052	0.56	YES
81	EIF4B	EIF4B	EIF4B	5738	0.051	0.56	YES
82	RPS8	RPS8	RPS8	5783	0.05	0.57	YES
83	RPS15A	RPS15A	RPS15A	5804	0.05	0.57	YES
84	EIF3K	EIF3K	EIF3K	5900	0.048	0.57	YES
85	EIF3F	EIF3F	EIF3F	5948	0.047	0.57	YES
86	RPL13	RPL13	RPL13	5986	0.046	0.57	YES
87	RPS26	RPS26	RPS26	6149	0.044	0.57	NO
88	EIF3G	EIF3G	EIF3G	6317	0.041	0.57	NO
89	FAU	FAU	FAU	6458	0.039	0.56	NO
90	EIF3E	EIF3E	EIF3E	6583	0.036	0.56	NO
91	EIF3B	EIF3B	EIF3B	6773	0.034	0.55	NO
92	RPL11	RPL11	RPL11	7214	0.027	0.53	NO
93	RPL22	RPL22	RPL22	7268	0.026	0.53	NO
94	EIF1AX	EIF1AX	EIF1AX	8327	0.01	0.47	NO
95	EIF3A	EIF3A	EIF3A	8556	0.0066	0.46	NO
96	EIF3J	EIF3J	EIF3J	8723	0.0038	0.45	NO
97	EIF3H	EIF3H	EIF3H	8844	0.0019	0.44	NO
98	EIF4E	EIF4E	EIF4E	9994	-0.016	0.38	NO
99	EIF4H	EIF4H	EIF4H	10191	-0.02	0.37	NO
100	EIF2S1	EIF2S1	EIF2S1	10844	-0.03	0.34	NO
101	EIF3C	EIF3C	EIF3C	11701	-0.046	0.29	NO
102	EIF4G1	EIF4G1	EIF4G1	12581	-0.064	0.25	NO
103	EIF3I	EIF3I	EIF3I	12667	-0.066	0.25	NO
104	RPL26L1	RPL26L1	RPL26L1	13573	-0.087	0.21	NO
105	RPS4Y1	RPS4Y1	RPS4Y1	16645	-0.24	0.062	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: REACTOME SIGNALLING TO ERKS.

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

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

Table 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	RPL21	RPL21	RPL21	884	0.26	-0.036	YES
2	RPL36A	RPL36A	RPL36A	1468	0.2	-0.057	YES
3	RPL9	RPL9	RPL9	1788	0.17	-0.066	YES
4	C2orf29	C2orf29	C2orf29	1857	0.17	-0.06	YES
5	PRKCD	PRKCD	PRKCD	1858	0.17	-0.05	YES
6	GSPT2	GSPT2	GSPT2	1932	0.16	-0.045	YES
7	FAM153A	FAM153A	FAM153A	1939	0.16	-0.036	YES
8	SMN1	SMN1	SMN1	1945	0.16	-0.027	YES
9	RPS24	RPS24	RPS24	1956	0.16	-0.018	YES
10	GEMIN7	GEMIN7	GEMIN7	2025	0.16	-0.013	YES
11	RPS19	RPS19	RPS19	2207	0.15	-0.015	YES
12	RPSA	RPSA	RPSA	2217	0.15	-0.0072	YES
13	RPSAP9	RPSAP9	RPSAP9	2231	0.15	0.00051	YES
14	SNRPE	SNRPE	SNRPE	2268	0.14	0.0068	YES
15	RPLP0	RPLP0	RPLP0	2454	0.14	0.004	YES
16	RPS21	RPS21	RPS21	2515	0.13	0.0082	YES
17	SNRPD1	SNRPD1	SNRPD1	2587	0.13	0.012	YES
18	RPL39	RPL39	RPL39	2600	0.13	0.018	YES
19	RPL27A	RPL27A	RPL27A	2612	0.13	0.025	YES
20	RPS10	RPS10	RPS10	2613	0.13	0.032	YES
21	RPS12	RPS12	RPS12	2677	0.13	0.036	YES
22	RPS27	RPS27	RPS27	2735	0.12	0.04	YES
23	RPS17	RPS17	RPS17	2737	0.12	0.047	YES
24	RPS3	RPS3	RPS3	2761	0.12	0.053	YES
25	RPL23A	RPL23A	RPL23A	2768	0.12	0.06	YES
26	RPS7	RPS7	RPS7	2788	0.12	0.066	YES
27	NUP210	NUP210	NUP210	2790	0.12	0.073	YES
28	RPS18	RPS18	RPS18	2794	0.12	0.079	YES
29	SNRPF	SNRPF	SNRPF	2829	0.12	0.084	YES
30	RPL26	RPL26	RPL26	2852	0.12	0.09	YES
31	RPS5	RPS5	RPS5	2871	0.12	0.096	YES
32	RPS27A	RPS27A	RPS27A	2884	0.12	0.1	YES
33	CNOT6	CNOT6	CNOT6	2885	0.12	0.11	YES
34	RPS15	RPS15	RPS15	2892	0.12	0.12	YES
35	RPL18A	RPL18A	RPL18A	2917	0.12	0.12	YES
36	RPS29	RPS29	RPS29	2934	0.12	0.13	YES
37	LSM2	LSM2	LSM2	2950	0.12	0.13	YES
38	RPL28	RPL28	RPL28	2952	0.12	0.14	YES
39	EXOSC8	EXOSC8	EXOSC8	3160	0.11	0.13	YES
40	RPL37A	RPL37A	RPL37A	3192	0.11	0.14	YES
41	RPL36	RPL36	RPL36	3272	0.11	0.14	YES
42	RPS28	RPS28	RPS28	3286	0.1	0.14	YES
43	RPL7	RPL7	RPL7	3288	0.1	0.15	YES
44	RPLP2	RPLP2	RPLP2	3289	0.1	0.16	YES
45	RPS4X	RPS4X	RPS4X	3293	0.1	0.16	YES
46	RPL32	RPL32	RPL32	3331	0.1	0.17	YES
47	RPL18	RPL18	RPL18	3335	0.1	0.17	YES
48	UPF3A	UPF3A	UPF3A	3350	0.1	0.18	YES
49	NUP133	NUP133	NUP133	3352	0.1	0.18	YES
50	RPL6	RPL6	RPL6	3358	0.1	0.19	YES
51	RPL31	RPL31	RPL31	3366	0.1	0.19	YES
52	RPL7A	RPL7A	RPL7A	3376	0.1	0.2	YES
53	RPL27	RPL27	RPL27	3384	0.1	0.2	YES
54	RPL38	RPL38	RPL38	3414	0.1	0.21	YES
55	RPL17	RPL17	RPL17	3417	0.1	0.22	YES
56	SNRPB	SNRPB	SNRPB	3425	0.1	0.22	YES
57	RPL13A	RPL13A	RPL13A	3488	0.1	0.22	YES
58	RPS16	RPS16	RPS16	3532	0.099	0.23	YES
59	KHSRP	KHSRP	KHSRP	3609	0.097	0.23	YES
60	DCP2	DCP2	DCP2	3610	0.097	0.23	YES
61	RPL35A	RPL35A	RPL35A	3619	0.097	0.24	YES
62	RPL14	RPL14	RPL14	3627	0.096	0.24	YES
63	CNOT3	CNOT3	CNOT3	3645	0.096	0.25	YES
64	RPL3	RPL3	RPL3	3661	0.095	0.25	YES
65	RPL10A	RPL10A	RPL10A	3670	0.095	0.26	YES
66	RPS11	RPS11	RPS11	3681	0.094	0.26	YES
67	NUP50	NUP50	NUP50	3689	0.094	0.27	YES
68	TPR	TPR	TPR	3693	0.094	0.27	YES
69	RPL4	RPL4	RPL4	3741	0.093	0.28	YES
70	SMG5	SMG5	SMG5	3809	0.091	0.28	YES
71	EXOSC1	EXOSC1	EXOSC1	3811	0.091	0.28	YES
72	RAE1	RAE1	RAE1	3982	0.086	0.28	YES
73	RPL23	RPL23	RPL23	4022	0.085	0.28	YES
74	SNRPG	SNRPG	SNRPG	4041	0.085	0.28	YES
75	RPL35	RPL35	RPL35	4077	0.084	0.29	YES
76	RPS9	RPS9	RPS9	4088	0.084	0.29	YES
77	RPL8	RPL8	RPL8	4107	0.083	0.29	YES
78	RPL41	RPL41	RPL41	4108	0.083	0.3	YES
79	RPS6	RPS6	RPS6	4116	0.083	0.3	YES
80	RPS2	RPS2	RPS2	4195	0.081	0.3	YES
81	NUP88	NUP88	NUP88	4204	0.081	0.31	YES
82	RPL37	RPL37	RPL37	4259	0.08	0.31	YES
83	RPS23	RPS23	RPS23	4261	0.08	0.31	YES
84	RPL24	RPL24	RPL24	4266	0.08	0.32	YES
85	SMN2	SMN2	SMN2	4271	0.08	0.32	YES
86	RPL30	RPL30	RPL30	4292	0.079	0.32	YES
87	RPS13	RPS13	RPS13	4332	0.078	0.33	YES
88	RPS25	RPS25	RPS25	4342	0.078	0.33	YES
89	NCBP2	NCBP2	NCBP2	4440	0.076	0.33	YES
90	RBM8A	RBM8A	RBM8A	4488	0.074	0.33	YES
91	RPLP1	RPLP1	RPLP1	4504	0.074	0.34	YES
92	SNRPD3	SNRPD3	SNRPD3	4545	0.073	0.34	YES
93	POM121	POM121	POM121	4614	0.072	0.34	YES
94	PABPC1	PABPC1	PABPC1	4626	0.072	0.34	YES
95	RPL29	RPL29	RPL29	4630	0.072	0.34	YES
96	ANP32A	ANP32A	ANP32A	4633	0.072	0.35	YES
97	CNOT10	CNOT10	CNOT10	4635	0.072	0.35	YES
98	RPL12	RPL12	RPL12	4729	0.07	0.35	YES
99	SNRPD2	SNRPD2	SNRPD2	4777	0.069	0.35	YES
100	RPL15	RPL15	RPL15	4885	0.067	0.35	YES
101	SMG7	SMG7	SMG7	4892	0.067	0.35	YES
102	RPS20	RPS20	RPS20	4902	0.066	0.36	YES
103	EIF4A1	EIF4A1	EIF4A1	4963	0.065	0.36	YES
104	EIF4A2	EIF4A2	EIF4A2	4972	0.065	0.36	YES
105	RPS14	RPS14	RPS14	5088	0.062	0.36	YES
106	NUP43	NUP43	NUP43	5203	0.06	0.36	YES
107	RPS3A	RPS3A	RPS3A	5206	0.06	0.36	YES
108	RPL10	RPL10	RPL10	5212	0.06	0.36	YES
109	RPL5	RPL5	RPL5	5219	0.06	0.36	YES
110	DCPS	DCPS	DCPS	5225	0.06	0.37	YES
111	PPP2R1A	PPP2R1A	PPP2R1A	5230	0.06	0.37	YES
112	HSPB1	HSPB1	HSPB1	5257	0.059	0.37	YES
113	UBA52	UBA52	UBA52	5362	0.057	0.37	YES
114	NUP85	NUP85	NUP85	5425	0.056	0.37	YES
115	DCP1B	DCP1B	DCP1B	5517	0.054	0.37	YES
116	RPL34	RPL34	RPL34	5551	0.054	0.37	YES
117	CNOT2	CNOT2	CNOT2	5560	0.054	0.37	YES
118	EXOSC7	EXOSC7	EXOSC7	5563	0.054	0.37	YES
119	EDC3	EDC3	EDC3	5605	0.053	0.38	YES
120	RPL19	RPL19	RPL19	5664	0.052	0.38	YES
121	GEMIN4	GEMIN4	GEMIN4	5684	0.052	0.38	YES
122	LSM4	LSM4	LSM4	5722	0.051	0.38	YES
123	EIF4B	EIF4B	EIF4B	5738	0.051	0.38	YES
124	NUP37	NUP37	NUP37	5781	0.05	0.38	YES
125	RPS8	RPS8	RPS8	5783	0.05	0.38	YES
126	RPS15A	RPS15A	RPS15A	5804	0.05	0.38	YES
127	YWHAZ	YWHAZ	YWHAZ	5817	0.049	0.39	YES
128	SMG6	SMG6	SMG6	5933	0.047	0.38	NO
129	RPL13	RPL13	RPL13	5986	0.046	0.38	NO
130	UPF2	UPF2	UPF2	6013	0.046	0.38	NO
131	RPS26	RPS26	RPS26	6149	0.044	0.38	NO
132	NUP62	NUP62	NUP62	6439	0.039	0.36	NO
133	NUP205	NUP205	NUP205	6454	0.039	0.36	NO
134	FAU	FAU	FAU	6458	0.039	0.37	NO
135	MAPK14	MAPK14	MAPK14	6480	0.038	0.37	NO
136	ELAVL1	ELAVL1	ELAVL1	6557	0.037	0.37	NO
137	EXOSC3	EXOSC3	EXOSC3	6624	0.036	0.36	NO
138	AAAS	AAAS	AAAS	6673	0.035	0.36	NO
139	LSM3	LSM3	LSM3	6769	0.034	0.36	NO
140	NUP214	NUP214	NUP214	6834	0.033	0.36	NO
141	SEH1L	SEH1L	SEH1L	6848	0.032	0.36	NO
142	NUP107	NUP107	NUP107	6928	0.031	0.36	NO
143	XPO1	XPO1	XPO1	6991	0.03	0.36	NO
144	EXOSC4	EXOSC4	EXOSC4	6995	0.03	0.36	NO
145	SNUPN	SNUPN	SNUPN	7047	0.029	0.36	NO
146	HNRNPD	HNRNPD	HNRNPD	7096	0.029	0.35	NO
147	NUP35	NUP35	NUP35	7132	0.028	0.35	NO
148	PSMD4	PSMD4	PSMD4	7196	0.027	0.35	NO
149	RPL11	RPL11	RPL11	7214	0.027	0.35	NO
150	RPL22	RPL22	RPL22	7268	0.026	0.35	NO
151	PSMB5	PSMB5	PSMB5	7288	0.026	0.35	NO
152	CLNS1A	CLNS1A	CLNS1A	7375	0.025	0.35	NO
153	EXOSC2	EXOSC2	EXOSC2	7573	0.022	0.34	NO
154	CASC3	CASC3	CASC3	7763	0.018	0.33	NO
155	NUPL2	NUPL2	NUPL2	7769	0.018	0.33	NO
156	NUP155	NUP155	NUP155	7775	0.018	0.33	NO
157	PSMB4	PSMB4	PSMB4	7880	0.016	0.32	NO
158	PSMA4	PSMA4	PSMA4	7963	0.015	0.32	NO
159	NUP153	NUP153	NUP153	8016	0.014	0.32	NO
160	NUP188	NUP188	NUP188	8129	0.013	0.31	NO
161	EIF4A3	EIF4A3	EIF4A3	8136	0.012	0.31	NO
162	PSMC4	PSMC4	PSMC4	8152	0.012	0.31	NO
163	PSME4	PSME4	PSME4	8224	0.011	0.31	NO
164	DDX6	DDX6	DDX6	8257	0.011	0.31	NO
165	RANBP2	RANBP2	RANBP2	8408	0.0088	0.3	NO
166	DCP1A	DCP1A	DCP1A	8524	0.0071	0.29	NO
167	PSMC6	PSMC6	PSMC6	8545	0.0067	0.29	NO
168	UPF3B	UPF3B	UPF3B	8568	0.0063	0.29	NO
169	TGS1	TGS1	TGS1	8764	0.0032	0.28	NO
170	PSMF1	PSMF1	PSMF1	8789	0.0028	0.28	NO
171	AKT1	AKT1	AKT1	8877	0.0014	0.28	NO
172	LSM1	LSM1	LSM1	8900	0.0011	0.27	NO
173	PPP2CA	PPP2CA	PPP2CA	8969	0.00031	0.27	NO
174	WDR77	WDR77	WDR77	8983	0.000074	0.27	NO
175	PSMD5	PSMD5	PSMD5	8985	7.5e-06	0.27	NO
176	PSMB6	PSMB6	PSMB6	8992	-0.000072	0.27	NO
177	GEMIN6	GEMIN6	GEMIN6	8994	-0.00014	0.27	NO
178	LSM6	LSM6	LSM6	8996	-0.00015	0.27	NO
179	PSMD13	PSMD13	PSMD13	9126	-0.002	0.26	NO
180	EXOSC5	EXOSC5	EXOSC5	9144	-0.0024	0.26	NO
181	NUPL1	NUPL1	NUPL1	9184	-0.003	0.26	NO
182	PSMB1	PSMB1	PSMB1	9199	-0.0032	0.26	NO
183	PSMB3	PSMB3	PSMB3	9237	-0.0038	0.26	NO
184	PSMD8	PSMD8	PSMD8	9300	-0.0047	0.25	NO
185	PATL1	PATL1	PATL1	9429	-0.007	0.25	NO
186	PSMC1	PSMC1	PSMC1	9456	-0.0075	0.24	NO
187	PSMD6	PSMD6	PSMD6	9628	-0.01	0.24	NO
188	CNOT7	CNOT7	CNOT7	9659	-0.011	0.24	NO
189	GEMIN5	GEMIN5	GEMIN5	9812	-0.013	0.23	NO
190	YWHAB	YWHAB	YWHAB	9824	-0.013	0.23	NO
191	PSMA6	PSMA6	PSMA6	9826	-0.013	0.23	NO
192	PSMC5	PSMC5	PSMC5	9836	-0.014	0.23	NO
193	PSMA1	PSMA1	PSMA1	9874	-0.014	0.23	NO
194	PRKCA	PRKCA	PRKCA	9883	-0.014	0.23	NO
195	EIF4E	EIF4E	EIF4E	9994	-0.016	0.22	NO
196	PAIP1	PAIP1	PAIP1	10095	-0.018	0.22	NO
197	RQCD1	RQCD1	RQCD1	10174	-0.019	0.21	NO
198	PSMC3	PSMC3	PSMC3	10181	-0.019	0.21	NO
199	HSPA8	HSPA8	HSPA8	10198	-0.02	0.21	NO
200	RNPS1	RNPS1	RNPS1	10306	-0.022	0.21	NO
201	PHAX	PHAX	PHAX	10484	-0.024	0.2	NO
202	NCBP1	NCBP1	NCBP1	10645	-0.027	0.19	NO
203	MAPK11	MAPK11	MAPK11	10684	-0.028	0.19	NO
204	PSMD10	PSMD10	PSMD10	10730	-0.029	0.19	NO
205	EXOSC9	EXOSC9	EXOSC9	10736	-0.029	0.19	NO
206	PRMT5	PRMT5	PRMT5	10737	-0.029	0.2	NO
207	TNKS1BP1	TNKS1BP1	TNKS1BP1	10805	-0.03	0.19	NO
208	DDX20	DDX20	DDX20	10819	-0.03	0.19	NO
209	PSMB7	PSMB7	PSMB7	10865	-0.031	0.19	NO
210	PSMA2	PSMA2	PSMA2	10910	-0.032	0.19	NO
211	PSMD1	PSMD1	PSMD1	10985	-0.033	0.19	NO
212	PSMD11	PSMD11	PSMD11	11023	-0.034	0.19	NO
213	PSMD14	PSMD14	PSMD14	11076	-0.034	0.19	NO
214	ETF1	ETF1	ETF1	11080	-0.034	0.19	NO
215	CNOT4	CNOT4	CNOT4	11260	-0.038	0.18	NO
216	XRN1	XRN1	XRN1	11396	-0.04	0.18	NO
217	CNOT8	CNOT8	CNOT8	11449	-0.041	0.18	NO
218	PSME1	PSME1	PSME1	11460	-0.042	0.18	NO
219	PSMA3	PSMA3	PSMA3	11466	-0.042	0.18	NO
220	NUP54	NUP54	NUP54	11550	-0.043	0.18	NO
221	NUP93	NUP93	NUP93	11578	-0.043	0.18	NO
222	LSM5	LSM5	LSM5	11622	-0.044	0.18	NO
223	PSMD9	PSMD9	PSMD9	11641	-0.045	0.18	NO
224	PSMD3	PSMD3	PSMD3	11649	-0.045	0.18	NO
225	MAGOH	MAGOH	MAGOH	11661	-0.045	0.18	NO
226	TNPO1	TNPO1	TNPO1	11705	-0.046	0.18	NO
227	PSME2	PSME2	PSME2	11869	-0.048	0.18	NO
228	EDC4	EDC4	EDC4	11904	-0.049	0.18	NO
229	PSMC2	PSMC2	PSMC2	11946	-0.05	0.18	NO
230	ZFP36L1	ZFP36L1	ZFP36L1	11950	-0.05	0.18	NO
231	SMG1	SMG1	SMG1	11991	-0.051	0.18	NO
232	PSMA7	PSMA7	PSMA7	12022	-0.052	0.18	NO
233	PSMD2	PSMD2	PSMD2	12278	-0.057	0.17	NO
234	DIS3	DIS3	DIS3	12438	-0.06	0.17	NO
235	EIF4G1	EIF4G1	EIF4G1	12581	-0.064	0.16	NO
236	PPP2R2A	PPP2R2A	PPP2R2A	12599	-0.064	0.16	NO
237	PSMD12	PSMD12	PSMD12	13033	-0.074	0.14	NO
238	PSMA5	PSMA5	PSMA5	13093	-0.075	0.15	NO
239	MAPKAPK2	MAPKAPK2	MAPKAPK2	13314	-0.081	0.14	NO
240	RPL26L1	RPL26L1	RPL26L1	13573	-0.087	0.13	NO
241	PSMD7	PSMD7	PSMD7	14039	-0.1	0.11	NO
242	EXOSC6	EXOSC6	EXOSC6	14401	-0.11	0.093	NO
243	ZFP36	ZFP36	ZFP36	14454	-0.11	0.096	NO
244	PSMB2	PSMB2	PSMB2	14598	-0.12	0.095	NO
245	PARN	PARN	PARN	14941	-0.13	0.083	NO
246	PSMA8	PSMA8	PSMA8	15031	-0.14	0.086	NO
247	PSMB10	PSMB10	PSMB10	15061	-0.14	0.092	NO
248	HSPA1B	HSPA1B	HSPA1B	15062	-0.14	0.1	NO
249	TNFSF13	TNFSF13	TNFSF13	15753	-0.17	0.07	NO
250	RPS4Y1	RPS4Y1	RPS4Y1	16645	-0.24	0.033	NO
251	PSMB9	PSMB9	PSMB9	16704	-0.25	0.044	NO
252	PSMB8	PSMB8	PSMB8	16750	-0.25	0.056	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: REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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

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	RPL21	RPL21	RPL21	884	0.26	-0.022	YES
2	RPL36A	RPL36A	RPL36A	1468	0.2	-0.033	YES
3	RPL9	RPL9	RPL9	1788	0.17	-0.032	YES
4	FAM153A	FAM153A	FAM153A	1939	0.16	-0.023	YES
5	RPS24	RPS24	RPS24	1956	0.16	-0.0065	YES
6	RPS19	RPS19	RPS19	2207	0.15	-0.0047	YES
7	RPSA	RPSA	RPSA	2217	0.15	0.011	YES
8	RPSAP9	RPSAP9	RPSAP9	2231	0.15	0.026	YES
9	RPLP0	RPLP0	RPLP0	2454	0.14	0.028	YES
10	RPS21	RPS21	RPS21	2515	0.13	0.039	YES
11	RPL39	RPL39	RPL39	2600	0.13	0.049	YES
12	RPL27A	RPL27A	RPL27A	2612	0.13	0.062	YES
13	RPS10	RPS10	RPS10	2613	0.13	0.076	YES
14	RPS12	RPS12	RPS12	2677	0.13	0.086	YES
15	RPS27	RPS27	RPS27	2735	0.12	0.096	YES
16	RPS17	RPS17	RPS17	2737	0.12	0.11	YES
17	RPS3	RPS3	RPS3	2761	0.12	0.12	YES
18	RPL23A	RPL23A	RPL23A	2768	0.12	0.14	YES
19	RPS7	RPS7	RPS7	2788	0.12	0.15	YES
20	RPS18	RPS18	RPS18	2794	0.12	0.16	YES
21	RPL26	RPL26	RPL26	2852	0.12	0.17	YES
22	RPS5	RPS5	RPS5	2871	0.12	0.18	YES
23	RPS27A	RPS27A	RPS27A	2884	0.12	0.19	YES
24	RPS15	RPS15	RPS15	2892	0.12	0.21	YES
25	RPL18A	RPL18A	RPL18A	2917	0.12	0.22	YES
26	RPS29	RPS29	RPS29	2934	0.12	0.23	YES
27	RPL28	RPL28	RPL28	2952	0.12	0.24	YES
28	IPO5	IPO5	IPO5	3030	0.11	0.25	YES
29	RPL37A	RPL37A	RPL37A	3192	0.11	0.25	YES
30	RPL36	RPL36	RPL36	3272	0.11	0.26	YES
31	RPS28	RPS28	RPS28	3286	0.1	0.27	YES
32	RPL7	RPL7	RPL7	3288	0.1	0.28	YES
33	RPLP2	RPLP2	RPLP2	3289	0.1	0.29	YES
34	RPS4X	RPS4X	RPS4X	3293	0.1	0.3	YES
35	RPL32	RPL32	RPL32	3331	0.1	0.31	YES
36	RPL18	RPL18	RPL18	3335	0.1	0.32	YES
37	RPL6	RPL6	RPL6	3358	0.1	0.33	YES
38	RPL31	RPL31	RPL31	3366	0.1	0.34	YES
39	RPL7A	RPL7A	RPL7A	3376	0.1	0.36	YES
40	RPL27	RPL27	RPL27	3384	0.1	0.37	YES
41	RPL38	RPL38	RPL38	3414	0.1	0.38	YES
42	RPL17	RPL17	RPL17	3417	0.1	0.39	YES
43	RPL13A	RPL13A	RPL13A	3488	0.1	0.39	YES
44	POLR2H	POLR2H	POLR2H	3505	0.1	0.4	YES
45	RPS16	RPS16	RPS16	3532	0.099	0.41	YES
46	RPL35A	RPL35A	RPL35A	3619	0.097	0.42	YES
47	RPL14	RPL14	RPL14	3627	0.096	0.43	YES
48	RPL3	RPL3	RPL3	3661	0.095	0.44	YES
49	RPL10A	RPL10A	RPL10A	3670	0.095	0.45	YES
50	RPS11	RPS11	RPS11	3681	0.094	0.46	YES
51	RPL4	RPL4	RPL4	3741	0.093	0.46	YES
52	RPL23	RPL23	RPL23	4022	0.085	0.46	YES
53	RPL35	RPL35	RPL35	4077	0.084	0.46	YES
54	RPS9	RPS9	RPS9	4088	0.084	0.47	YES
55	RPL8	RPL8	RPL8	4107	0.083	0.48	YES
56	RPL41	RPL41	RPL41	4108	0.083	0.49	YES
57	RPS6	RPS6	RPS6	4116	0.083	0.5	YES
58	RPS2	RPS2	RPS2	4195	0.081	0.5	YES
59	RPL37	RPL37	RPL37	4259	0.08	0.51	YES
60	RPS23	RPS23	RPS23	4261	0.08	0.52	YES
61	RPL24	RPL24	RPL24	4266	0.08	0.52	YES
62	RPL30	RPL30	RPL30	4292	0.079	0.53	YES
63	RPS13	RPS13	RPS13	4332	0.078	0.54	YES
64	RPS25	RPS25	RPS25	4342	0.078	0.55	YES
65	RPLP1	RPLP1	RPLP1	4504	0.074	0.54	YES
66	RPL29	RPL29	RPL29	4630	0.072	0.54	YES
67	RPL12	RPL12	RPL12	4729	0.07	0.55	YES
68	POLR2D	POLR2D	POLR2D	4858	0.067	0.55	YES
69	RPL15	RPL15	RPL15	4885	0.067	0.55	YES
70	RPS20	RPS20	RPS20	4902	0.066	0.56	YES
71	RPS14	RPS14	RPS14	5088	0.062	0.56	YES
72	POLR2F	POLR2F	POLR2F	5124	0.062	0.56	YES
73	RPS3A	RPS3A	RPS3A	5206	0.06	0.56	YES
74	RPL10	RPL10	RPL10	5212	0.06	0.57	YES
75	RPL5	RPL5	RPL5	5219	0.06	0.57	YES
76	UBA52	UBA52	UBA52	5362	0.057	0.57	YES
77	GTF2F2	GTF2F2	GTF2F2	5412	0.056	0.57	YES
78	RPL34	RPL34	RPL34	5551	0.054	0.57	YES
79	RPL19	RPL19	RPL19	5664	0.052	0.57	YES
80	RPS8	RPS8	RPS8	5783	0.05	0.57	YES
81	RPS15A	RPS15A	RPS15A	5804	0.05	0.57	YES
82	RPL13	RPL13	RPL13	5986	0.046	0.57	NO
83	RPS26	RPS26	RPS26	6149	0.044	0.57	NO
84	GTF2F1	GTF2F1	GTF2F1	6267	0.042	0.56	NO
85	FAU	FAU	FAU	6458	0.039	0.56	NO
86	POLR2I	POLR2I	POLR2I	6615	0.036	0.55	NO
87	HSP90AA1	HSP90AA1	HSP90AA1	6669	0.035	0.55	NO
88	RPL11	RPL11	RPL11	7214	0.027	0.52	NO
89	RPL22	RPL22	RPL22	7268	0.026	0.52	NO
90	POLR2J	POLR2J	POLR2J	7462	0.023	0.52	NO
91	POLR2G	POLR2G	POLR2G	8198	0.012	0.48	NO
92	POLR2B	POLR2B	POLR2B	8200	0.012	0.48	NO
93	POLR2A	POLR2A	POLR2A	9461	-0.0075	0.41	NO
94	POLR2E	POLR2E	POLR2E	9788	-0.013	0.39	NO
95	DNAJC3	DNAJC3	DNAJC3	9816	-0.013	0.39	NO
96	POLR2K	POLR2K	POLR2K	10232	-0.02	0.37	NO
97	POLR2L	POLR2L	POLR2L	11359	-0.04	0.31	NO
98	GRSF1	GRSF1	GRSF1	12923	-0.071	0.23	NO
99	POLR2C	POLR2C	POLR2C	13546	-0.087	0.2	NO
100	RPL26L1	RPL26L1	RPL26L1	13573	-0.087	0.21	NO
101	RPS4Y1	RPS4Y1	RPS4Y1	16645	-0.24	0.061	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: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S58. 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 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	RPL21	RPL21	RPL21	884	0.26	-0.019	YES
2	RPL36A	RPL36A	RPL36A	1468	0.2	-0.029	YES
3	RPL9	RPL9	RPL9	1788	0.17	-0.026	YES
4	FAM153A	FAM153A	FAM153A	1939	0.16	-0.016	YES
5	RPS24	RPS24	RPS24	1956	0.16	0.0026	YES
6	RPS19	RPS19	RPS19	2207	0.15	0.0058	YES
7	RPSA	RPSA	RPSA	2217	0.15	0.023	YES
8	RPSAP9	RPSAP9	RPSAP9	2231	0.15	0.039	YES
9	RPLP0	RPLP0	RPLP0	2454	0.14	0.043	YES
10	RPS21	RPS21	RPS21	2515	0.13	0.055	YES
11	RPL39	RPL39	RPL39	2600	0.13	0.066	YES
12	RPL27A	RPL27A	RPL27A	2612	0.13	0.08	YES
13	RPS10	RPS10	RPS10	2613	0.13	0.095	YES
14	RPS12	RPS12	RPS12	2677	0.13	0.11	YES
15	RPS27	RPS27	RPS27	2735	0.12	0.12	YES
16	RPS17	RPS17	RPS17	2737	0.12	0.13	YES
17	RPS3	RPS3	RPS3	2761	0.12	0.15	YES
18	RPL23A	RPL23A	RPL23A	2768	0.12	0.16	YES
19	RPS7	RPS7	RPS7	2788	0.12	0.17	YES
20	RPS18	RPS18	RPS18	2794	0.12	0.19	YES
21	RPL26	RPL26	RPL26	2852	0.12	0.2	YES
22	RPS5	RPS5	RPS5	2871	0.12	0.21	YES
23	RPS27A	RPS27A	RPS27A	2884	0.12	0.22	YES
24	RPS15	RPS15	RPS15	2892	0.12	0.24	YES
25	RPL18A	RPL18A	RPL18A	2917	0.12	0.25	YES
26	RPS29	RPS29	RPS29	2934	0.12	0.26	YES
27	RPL28	RPL28	RPL28	2952	0.12	0.28	YES
28	RPL37A	RPL37A	RPL37A	3192	0.11	0.28	YES
29	RPL36	RPL36	RPL36	3272	0.11	0.28	YES
30	RPS28	RPS28	RPS28	3286	0.1	0.3	YES
31	RPL7	RPL7	RPL7	3288	0.1	0.31	YES
32	RPLP2	RPLP2	RPLP2	3289	0.1	0.32	YES
33	RPS4X	RPS4X	RPS4X	3293	0.1	0.33	YES
34	RPL32	RPL32	RPL32	3331	0.1	0.34	YES
35	RPL18	RPL18	RPL18	3335	0.1	0.36	YES
36	RPL6	RPL6	RPL6	3358	0.1	0.37	YES
37	RPL31	RPL31	RPL31	3366	0.1	0.38	YES
38	RPL7A	RPL7A	RPL7A	3376	0.1	0.39	YES
39	RPL27	RPL27	RPL27	3384	0.1	0.4	YES
40	RPL38	RPL38	RPL38	3414	0.1	0.41	YES
41	RPL17	RPL17	RPL17	3417	0.1	0.42	YES
42	RPL13A	RPL13A	RPL13A	3488	0.1	0.43	YES
43	RPS16	RPS16	RPS16	3532	0.099	0.44	YES
44	RPL35A	RPL35A	RPL35A	3619	0.097	0.45	YES
45	RPL14	RPL14	RPL14	3627	0.096	0.46	YES
46	RPL3	RPL3	RPL3	3661	0.095	0.47	YES
47	RPL10A	RPL10A	RPL10A	3670	0.095	0.48	YES
48	RPS11	RPS11	RPS11	3681	0.094	0.49	YES
49	RPL4	RPL4	RPL4	3741	0.093	0.5	YES
50	RPL23	RPL23	RPL23	4022	0.085	0.49	YES
51	RPL35	RPL35	RPL35	4077	0.084	0.5	YES
52	RPS9	RPS9	RPS9	4088	0.084	0.51	YES
53	RPL8	RPL8	RPL8	4107	0.083	0.52	YES
54	RPL41	RPL41	RPL41	4108	0.083	0.52	YES
55	RPS6	RPS6	RPS6	4116	0.083	0.53	YES
56	RPS2	RPS2	RPS2	4195	0.081	0.54	YES
57	RPL37	RPL37	RPL37	4259	0.08	0.55	YES
58	RPS23	RPS23	RPS23	4261	0.08	0.56	YES
59	RPL24	RPL24	RPL24	4266	0.08	0.56	YES
60	RPL30	RPL30	RPL30	4292	0.079	0.57	YES
61	RPS13	RPS13	RPS13	4332	0.078	0.58	YES
62	RPS25	RPS25	RPS25	4342	0.078	0.59	YES
63	RPLP1	RPLP1	RPLP1	4504	0.074	0.59	YES
64	RPL29	RPL29	RPL29	4630	0.072	0.59	YES
65	RPL12	RPL12	RPL12	4729	0.07	0.59	YES
66	RPL15	RPL15	RPL15	4885	0.067	0.59	YES
67	RPS20	RPS20	RPS20	4902	0.066	0.6	YES
68	EEF1A1	EEF1A1	EEF1A1	4988	0.064	0.6	YES
69	RPS14	RPS14	RPS14	5088	0.062	0.6	YES
70	RPS3A	RPS3A	RPS3A	5206	0.06	0.6	YES
71	RPL10	RPL10	RPL10	5212	0.06	0.61	YES
72	RPL5	RPL5	RPL5	5219	0.06	0.62	YES
73	UBA52	UBA52	UBA52	5362	0.057	0.61	NO
74	RPL34	RPL34	RPL34	5551	0.054	0.61	NO
75	RPL19	RPL19	RPL19	5664	0.052	0.61	NO
76	RPS8	RPS8	RPS8	5783	0.05	0.61	NO
77	RPS15A	RPS15A	RPS15A	5804	0.05	0.61	NO
78	RPL13	RPL13	RPL13	5986	0.046	0.61	NO
79	RPS26	RPS26	RPS26	6149	0.044	0.6	NO
80	FAU	FAU	FAU	6458	0.039	0.59	NO
81	RPL11	RPL11	RPL11	7214	0.027	0.55	NO
82	RPL22	RPL22	RPL22	7268	0.026	0.55	NO
83	EEF2	EEF2	EEF2	8073	0.013	0.51	NO
84	RPL26L1	RPL26L1	RPL26L1	13573	-0.087	0.21	NO
85	RPS4Y1	RPS4Y1	RPS4Y1	16645	-0.24	0.061	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: REACTOME PEPTIDE CHAIN ELONGATION.

Figure S60. 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

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 GALACTOSE METABOLISM	25	genes.ES.table	0.47	1.4	0.093	0.18	0.99	0.28	0.2	0.22	0.14	0
KEGG PURINE METABOLISM	154	genes.ES.table	0.4	1.7	0.002	0.074	0.72	0.21	0.19	0.17	0.025	0.004
KEGG SELENOAMINO ACID METABOLISM	26	genes.ES.table	0.49	1.7	0.026	0.071	0.82	0.12	0.092	0.1	0.029	0.001
KEGG N GLYCAN BIOSYNTHESIS	46	genes.ES.table	0.35	1.4	0.15	0.18	0.99	0.15	0.23	0.12	0.14	0
KEGG O GLYCAN BIOSYNTHESIS	27	genes.ES.table	0.66	1.7	0.0084	0.076	0.85	0.67	0.27	0.49	0.034	0.001
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	43	genes.ES.table	0.36	1.3	0.18	0.21	1	0.4	0.38	0.25	0.18	0
KEGG INOSITOL PHOSPHATE METABOLISM	53	genes.ES.table	0.51	1.7	0.0042	0.071	0.74	0.4	0.33	0.26	0.024	0.002
KEGG GLYCEROPHOSPHOLIPID METABOLISM	70	genes.ES.table	0.46	1.7	0.002	0.075	0.86	0.36	0.28	0.26	0.034	0.001
KEGG ETHER LIPID METABOLISM	27	genes.ES.table	0.5	1.4	0.064	0.16	0.99	0.52	0.3	0.36	0.12	0
KEGG ARACHIDONIC ACID METABOLISM	49	genes.ES.table	0.63	1.6	0.012	0.081	0.91	0.31	0.1	0.28	0.04	0

genes ES table in pathway: KEGG GALACTOSE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PDE1A	PDE1A	PDE1A	18	0.85	0.074	YES
2	FGF1	FGF1	FGF1	107	0.7	0.13	YES
3	ADCY5	ADCY5	ADCY5	290	0.58	0.17	YES
4	FGFR1	FGFR1	FGFR1	422	0.53	0.21	YES
5	FGF7	FGF7	FGF7	451	0.52	0.26	YES
6	FGF18	FGF18	FGF18	489	0.5	0.3	YES
7	PRKAR2B	PRKAR2B	PRKAR2B	509	0.5	0.34	YES
8	AKT3	AKT3	AKT3	693	0.45	0.37	YES
9	ADCY2	ADCY2	ADCY2	781	0.43	0.41	YES
10	ADCY4	ADCY4	ADCY4	988	0.4	0.43	YES
11	CAMK4	CAMK4	CAMK4	1018	0.39	0.46	YES
12	ITPR3	ITPR3	ITPR3	1059	0.39	0.49	YES
13	ADCY3	ADCY3	ADCY3	1078	0.38	0.53	YES
14	FGFR2	FGFR2	FGFR2	1471	0.34	0.54	YES
15	PDE1B	PDE1B	PDE1B	1715	0.31	0.55	YES
16	ADCY7	ADCY7	ADCY7	2157	0.27	0.55	NO
17	PRKAR1B	PRKAR1B	PRKAR1B	2663	0.23	0.54	NO
18	NR4A1	NR4A1	NR4A1	3130	0.2	0.53	NO
19	CDKN1A	CDKN1A	CDKN1A	4361	0.13	0.47	NO
20	FGF19	FGF19	FGF19	4478	0.12	0.48	NO
21	PRKCE	PRKCE	PRKCE	4698	0.11	0.48	NO
22	FGF9	FGF9	FGF9	4870	0.1	0.48	NO
23	ADCY1	ADCY1	ADCY1	5684	0.075	0.44	NO
24	MAPK3	MAPK3	MAPK3	6203	0.061	0.41	NO
25	FGF2	FGF2	FGF2	6332	0.058	0.41	NO
26	FOXO1	FOXO1	FOXO1	6344	0.058	0.41	NO
27	MAP2K1	MAP2K1	MAP2K1	6532	0.054	0.41	NO
28	KL	KL	KL	6620	0.051	0.41	NO
29	SHC1	SHC1	SHC1	6672	0.05	0.41	NO
30	CALM2	CALM2	CALM2	6772	0.048	0.41	NO
31	YWHAB	YWHAB	YWHAB	6957	0.045	0.4	NO
32	GAB1	GAB1	GAB1	7034	0.043	0.4	NO
33	CALM1	CALM1	CALM1	7105	0.042	0.4	NO
34	KRAS	KRAS	KRAS	7315	0.038	0.39	NO
35	ADCY9	ADCY9	ADCY9	7427	0.036	0.39	NO
36	PRKACA	PRKACA	PRKACA	7454	0.036	0.39	NO
37	AKT1	AKT1	AKT1	7500	0.035	0.39	NO
38	BAD	BAD	BAD	7526	0.034	0.39	NO
39	CREB1	CREB1	CREB1	8078	0.026	0.36	NO
40	FOXO3	FOXO3	FOXO3	8135	0.025	0.36	NO
41	PIK3CA	PIK3CA	PIK3CA	8146	0.024	0.36	NO
42	FGFR3	FGFR3	FGFR3	8179	0.024	0.36	NO
43	ADRBK1	ADRBK1	ADRBK1	8439	0.02	0.35	NO
44	RICTOR	RICTOR	RICTOR	8684	0.017	0.34	NO
45	TRIB3	TRIB3	TRIB3	8719	0.016	0.34	NO
46	GSK3A	GSK3A	GSK3A	8736	0.016	0.34	NO
47	TSC2	TSC2	TSC2	8966	0.013	0.33	NO
48	PTEN	PTEN	PTEN	9336	0.0085	0.31	NO
49	MLST8	MLST8	MLST8	9614	0.0054	0.29	NO
50	PDPK1	PDPK1	PDPK1	9655	0.0049	0.29	NO
51	ADCY6	ADCY6	ADCY6	9659	0.0049	0.29	NO
52	MAP2K2	MAP2K2	MAP2K2	9980	0.0005	0.27	NO
53	PRKCD	PRKCD	PRKCD	10070	-0.0005	0.27	NO
54	HRAS	HRAS	HRAS	10357	-0.0038	0.25	NO
55	MDM2	MDM2	MDM2	10436	-0.0048	0.25	NO
56	CHUK	CHUK	CHUK	10594	-0.0064	0.24	NO
57	PRKAR1A	PRKAR1A	PRKAR1A	10944	-0.01	0.22	NO
58	PRKACB	PRKACB	PRKACB	11062	-0.012	0.22	NO
59	CALM3	CALM3	CALM3	11068	-0.012	0.22	NO
60	AKT1S1	AKT1S1	AKT1S1	11225	-0.014	0.21	NO
61	ADCY8	ADCY8	ADCY8	11454	-0.016	0.2	NO
62	MAPK1	MAPK1	MAPK1	11516	-0.017	0.2	NO
63	PLCG1	PLCG1	PLCG1	11609	-0.018	0.19	NO
64	SOS1	SOS1	SOS1	11693	-0.019	0.19	NO
65	FRS2	FRS2	FRS2	11702	-0.019	0.19	NO
66	THEM4	THEM4	THEM4	12090	-0.024	0.17	NO
67	AKT2	AKT2	AKT2	12138	-0.025	0.17	NO
68	CDKN1B	CDKN1B	CDKN1B	12303	-0.027	0.16	NO
69	RPS6KB2	RPS6KB2	RPS6KB2	12462	-0.029	0.16	NO
70	MAPKAP1	MAPKAP1	MAPKAP1	12478	-0.029	0.16	NO
71	GRB2	GRB2	GRB2	12627	-0.031	0.15	NO
72	PRKCG	PRKCG	PRKCG	12791	-0.033	0.15	NO
73	MTOR	MTOR	MTOR	12792	-0.033	0.15	NO
74	NRAS	NRAS	NRAS	13024	-0.036	0.14	NO
75	CASP9	CASP9	CASP9	13317	-0.04	0.13	NO
76	FGF22	FGF22	FGF22	13588	-0.044	0.11	NO
77	FRS3	FRS3	FRS3	14394	-0.059	0.074	NO
78	FOXO4	FOXO4	FOXO4	14432	-0.06	0.077	NO
79	FGFR4	FGFR4	FGFR4	14458	-0.061	0.081	NO
80	PIK3R1	PIK3R1	PIK3R1	14604	-0.063	0.078	NO
81	RAF1	RAF1	RAF1	14721	-0.066	0.078	NO
82	PRKAR2A	PRKAR2A	PRKAR2A	15298	-0.081	0.052	NO
83	PRKCA	PRKCA	PRKCA	16077	-0.11	0.018	NO
84	PHLPP1	PHLPP1	PHLPP1	16197	-0.12	0.022	NO
85	ITPR2	ITPR2	ITPR2	16227	-0.12	0.032	NO
86	FGF17	FGF17	FGF17	16767	-0.16	0.015	NO
87	KLB	KLB	KLB	17188	-0.2	0.0098	NO
88	CDK1	CDK1	CDK1	17369	-0.23	0.02	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 GALACTOSE METABOLISM.

Figure S62. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GALACTOSE 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 PURINE 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	PDE1A	PDE1A	PDE1A	18	0.85	0.067	YES
2	FGF1	FGF1	FGF1	107	0.7	0.12	YES
3	IL17RD	IL17RD	IL17RD	245	0.6	0.16	YES
4	ADCY5	ADCY5	ADCY5	290	0.58	0.2	YES
5	FGFR1	FGFR1	FGFR1	422	0.53	0.24	YES
6	FGF7	FGF7	FGF7	451	0.52	0.28	YES
7	FGF18	FGF18	FGF18	489	0.5	0.32	YES
8	PRKAR2B	PRKAR2B	PRKAR2B	509	0.5	0.36	YES
9	AKT3	AKT3	AKT3	693	0.45	0.38	YES
10	ADCY2	ADCY2	ADCY2	781	0.43	0.41	YES
11	ADCY4	ADCY4	ADCY4	988	0.4	0.43	YES
12	CAMK4	CAMK4	CAMK4	1018	0.39	0.46	YES
13	ITPR3	ITPR3	ITPR3	1059	0.39	0.49	YES
14	ADCY3	ADCY3	ADCY3	1078	0.38	0.52	YES
15	FGFR2	FGFR2	FGFR2	1471	0.34	0.52	YES
16	PDE1B	PDE1B	PDE1B	1715	0.31	0.53	YES
17	ADCY7	ADCY7	ADCY7	2157	0.27	0.53	NO
18	PRKAR1B	PRKAR1B	PRKAR1B	2663	0.23	0.52	NO
19	NR4A1	NR4A1	NR4A1	3130	0.2	0.51	NO
20	CBL	CBL	CBL	4136	0.14	0.46	NO
21	SPRY2	SPRY2	SPRY2	4356	0.13	0.46	NO
22	CDKN1A	CDKN1A	CDKN1A	4361	0.13	0.47	NO
23	FGF19	FGF19	FGF19	4478	0.12	0.48	NO
24	PRKCE	PRKCE	PRKCE	4698	0.11	0.47	NO
25	FGF9	FGF9	FGF9	4870	0.1	0.47	NO
26	SRC	SRC	SRC	5246	0.091	0.46	NO
27	PPP2CB	PPP2CB	PPP2CB	5670	0.076	0.44	NO
28	ADCY1	ADCY1	ADCY1	5684	0.075	0.44	NO
29	MAPK3	MAPK3	MAPK3	6203	0.061	0.42	NO
30	FGF2	FGF2	FGF2	6332	0.058	0.42	NO
31	FOXO1	FOXO1	FOXO1	6344	0.058	0.42	NO
32	MAP2K1	MAP2K1	MAP2K1	6532	0.054	0.42	NO
33	KL	KL	KL	6620	0.051	0.42	NO
34	SHC1	SHC1	SHC1	6672	0.05	0.42	NO
35	PPP2R1A	PPP2R1A	PPP2R1A	6706	0.05	0.42	NO
36	CALM2	CALM2	CALM2	6772	0.048	0.42	NO
37	YWHAB	YWHAB	YWHAB	6957	0.045	0.41	NO
38	GAB1	GAB1	GAB1	7034	0.043	0.41	NO
39	CALM1	CALM1	CALM1	7105	0.042	0.41	NO
40	KRAS	KRAS	KRAS	7315	0.038	0.4	NO
41	ADCY9	ADCY9	ADCY9	7427	0.036	0.4	NO
42	PRKACA	PRKACA	PRKACA	7454	0.036	0.4	NO
43	AKT1	AKT1	AKT1	7500	0.035	0.4	NO
44	BAD	BAD	BAD	7526	0.034	0.4	NO
45	CREB1	CREB1	CREB1	8078	0.026	0.37	NO
46	FOXO3	FOXO3	FOXO3	8135	0.025	0.37	NO
47	PIK3CA	PIK3CA	PIK3CA	8146	0.024	0.37	NO
48	FGFR3	FGFR3	FGFR3	8179	0.024	0.37	NO
49	ADRBK1	ADRBK1	ADRBK1	8439	0.02	0.36	NO
50	RICTOR	RICTOR	RICTOR	8684	0.017	0.35	NO
51	TRIB3	TRIB3	TRIB3	8719	0.016	0.34	NO
52	GSK3A	GSK3A	GSK3A	8736	0.016	0.35	NO
53	TSC2	TSC2	TSC2	8966	0.013	0.33	NO
54	PTEN	PTEN	PTEN	9336	0.0085	0.31	NO
55	MKNK1	MKNK1	MKNK1	9448	0.0073	0.31	NO
56	MLST8	MLST8	MLST8	9614	0.0054	0.3	NO
57	PDPK1	PDPK1	PDPK1	9655	0.0049	0.3	NO
58	ADCY6	ADCY6	ADCY6	9659	0.0049	0.3	NO
59	MAP2K2	MAP2K2	MAP2K2	9980	0.0005	0.28	NO
60	PRKCD	PRKCD	PRKCD	10070	-0.0005	0.27	NO
61	HRAS	HRAS	HRAS	10357	-0.0038	0.26	NO
62	PPP2CA	PPP2CA	PPP2CA	10385	-0.0042	0.26	NO
63	MDM2	MDM2	MDM2	10436	-0.0048	0.26	NO
64	CHUK	CHUK	CHUK	10594	-0.0064	0.25	NO
65	PRKAR1A	PRKAR1A	PRKAR1A	10944	-0.01	0.23	NO
66	PRKACB	PRKACB	PRKACB	11062	-0.012	0.22	NO
67	CALM3	CALM3	CALM3	11068	-0.012	0.22	NO
68	AKT1S1	AKT1S1	AKT1S1	11225	-0.014	0.22	NO
69	ADCY8	ADCY8	ADCY8	11454	-0.016	0.2	NO
70	MAPK1	MAPK1	MAPK1	11516	-0.017	0.2	NO
71	UBA52	UBA52	UBA52	11591	-0.018	0.2	NO
72	PLCG1	PLCG1	PLCG1	11609	-0.018	0.2	NO
73	SOS1	SOS1	SOS1	11693	-0.019	0.2	NO
74	FRS2	FRS2	FRS2	11702	-0.019	0.2	NO
75	RPS27A	RPS27A	RPS27A	11897	-0.022	0.19	NO
76	THEM4	THEM4	THEM4	12090	-0.024	0.18	NO
77	AKT2	AKT2	AKT2	12138	-0.025	0.18	NO
78	CDKN1B	CDKN1B	CDKN1B	12303	-0.027	0.17	NO
79	RPS6KB2	RPS6KB2	RPS6KB2	12462	-0.029	0.16	NO
80	MAPKAP1	MAPKAP1	MAPKAP1	12478	-0.029	0.16	NO
81	GRB2	GRB2	GRB2	12627	-0.031	0.16	NO
82	PRKCG	PRKCG	PRKCG	12791	-0.033	0.15	NO
83	MTOR	MTOR	MTOR	12792	-0.033	0.16	NO
84	NRAS	NRAS	NRAS	13024	-0.036	0.14	NO
85	CASP9	CASP9	CASP9	13317	-0.04	0.13	NO
86	FGF22	FGF22	FGF22	13588	-0.044	0.12	NO
87	FRS3	FRS3	FRS3	14394	-0.059	0.079	NO
88	FOXO4	FOXO4	FOXO4	14432	-0.06	0.082	NO
89	FGFR4	FGFR4	FGFR4	14458	-0.061	0.085	NO
90	PIK3R1	PIK3R1	PIK3R1	14604	-0.063	0.082	NO
91	RAF1	RAF1	RAF1	14721	-0.066	0.081	NO
92	BRAF	BRAF	BRAF	15109	-0.075	0.065	NO
93	PRKAR2A	PRKAR2A	PRKAR2A	15298	-0.081	0.061	NO
94	PRKCA	PRKCA	PRKCA	16077	-0.11	0.026	NO
95	PHLPP1	PHLPP1	PHLPP1	16197	-0.12	0.029	NO
96	ITPR2	ITPR2	ITPR2	16227	-0.12	0.037	NO
97	FGF17	FGF17	FGF17	16767	-0.16	0.019	NO
98	KLB	KLB	KLB	17188	-0.2	0.012	NO
99	CDK1	CDK1	CDK1	17369	-0.23	0.02	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 PURINE METABOLISM.

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

genes ES table in pathway: KEGG SELENOAMINO ACID METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PDE1A	PDE1A	PDE1A	18	0.85	0.082	YES
2	PDGFRA	PDGFRA	PDGFRA	142	0.67	0.14	YES
3	ADCY5	ADCY5	ADCY5	290	0.58	0.19	YES
4	PRKAR2B	PRKAR2B	PRKAR2B	509	0.5	0.22	YES
5	AKT3	AKT3	AKT3	693	0.45	0.26	YES
6	ADCY2	ADCY2	ADCY2	781	0.43	0.3	YES
7	ADCY4	ADCY4	ADCY4	988	0.4	0.32	YES
8	CAMK4	CAMK4	CAMK4	1018	0.39	0.36	YES
9	ITPR3	ITPR3	ITPR3	1059	0.39	0.4	YES
10	ADCY3	ADCY3	ADCY3	1078	0.38	0.43	YES
11	PDE1B	PDE1B	PDE1B	1715	0.31	0.42	YES
12	PDGFA	PDGFA	PDGFA	1897	0.29	0.44	YES
13	ADCY7	ADCY7	ADCY7	2157	0.27	0.46	YES
14	NCK2	NCK2	NCK2	2175	0.27	0.48	YES
15	PDGFRB	PDGFRB	PDGFRB	2202	0.27	0.5	YES
16	PRKAR1B	PRKAR1B	PRKAR1B	2663	0.23	0.5	NO
17	NR4A1	NR4A1	NR4A1	3130	0.2	0.5	NO
18	PDGFB	PDGFB	PDGFB	3314	0.19	0.5	NO
19	CDKN1A	CDKN1A	CDKN1A	4361	0.13	0.46	NO
20	BCAR1	BCAR1	BCAR1	4488	0.12	0.46	NO
21	PRKCE	PRKCE	PRKCE	4698	0.11	0.46	NO
22	STAT5A	STAT5A	STAT5A	4974	0.1	0.46	NO
23	SRC	SRC	SRC	5246	0.091	0.45	NO
24	STAT3	STAT3	STAT3	5331	0.088	0.45	NO
25	CRK	CRK	CRK	5648	0.076	0.44	NO
26	ADCY1	ADCY1	ADCY1	5684	0.075	0.45	NO
27	STAT1	STAT1	STAT1	5965	0.068	0.44	NO
28	MAPK3	MAPK3	MAPK3	6203	0.061	0.43	NO
29	FOXO1	FOXO1	FOXO1	6344	0.058	0.43	NO
30	MAP2K1	MAP2K1	MAP2K1	6532	0.054	0.42	NO
31	NCK1	NCK1	NCK1	6647	0.051	0.42	NO
32	CALM2	CALM2	CALM2	6772	0.048	0.42	NO
33	YWHAB	YWHAB	YWHAB	6957	0.045	0.41	NO
34	CALM1	CALM1	CALM1	7105	0.042	0.41	NO
35	STAT6	STAT6	STAT6	7228	0.04	0.4	NO
36	KRAS	KRAS	KRAS	7315	0.038	0.4	NO
37	ADCY9	ADCY9	ADCY9	7427	0.036	0.4	NO
38	PRKACA	PRKACA	PRKACA	7454	0.036	0.4	NO
39	AKT1	AKT1	AKT1	7500	0.035	0.4	NO
40	BAD	BAD	BAD	7526	0.034	0.41	NO
41	RAPGEF1	RAPGEF1	RAPGEF1	7573	0.033	0.41	NO
42	RASA1	RASA1	RASA1	7789	0.03	0.4	NO
43	CREB1	CREB1	CREB1	8078	0.026	0.38	NO
44	FOXO3	FOXO3	FOXO3	8135	0.025	0.38	NO
45	PIK3CA	PIK3CA	PIK3CA	8146	0.024	0.38	NO
46	ADRBK1	ADRBK1	ADRBK1	8439	0.02	0.37	NO
47	RICTOR	RICTOR	RICTOR	8684	0.017	0.36	NO
48	TRIB3	TRIB3	TRIB3	8719	0.016	0.36	NO
49	GSK3A	GSK3A	GSK3A	8736	0.016	0.36	NO
50	TSC2	TSC2	TSC2	8966	0.013	0.35	NO
51	PIK3CB	PIK3CB	PIK3CB	9266	0.0094	0.33	NO
52	PTEN	PTEN	PTEN	9336	0.0085	0.33	NO
53	MLST8	MLST8	MLST8	9614	0.0054	0.31	NO
54	PDPK1	PDPK1	PDPK1	9655	0.0049	0.31	NO
55	ADCY6	ADCY6	ADCY6	9659	0.0049	0.31	NO
56	MAP2K2	MAP2K2	MAP2K2	9980	0.0005	0.29	NO
57	PRKCD	PRKCD	PRKCD	10070	-0.0005	0.29	NO
58	HRAS	HRAS	HRAS	10357	-0.0038	0.27	NO
59	MDM2	MDM2	MDM2	10436	-0.0048	0.27	NO
60	CHUK	CHUK	CHUK	10594	-0.0064	0.26	NO
61	PRKAR1A	PRKAR1A	PRKAR1A	10944	-0.01	0.24	NO
62	PRKACB	PRKACB	PRKACB	11062	-0.012	0.24	NO
63	CALM3	CALM3	CALM3	11068	-0.012	0.24	NO
64	AKT1S1	AKT1S1	AKT1S1	11225	-0.014	0.23	NO
65	ADCY8	ADCY8	ADCY8	11454	-0.016	0.22	NO
66	MAPK1	MAPK1	MAPK1	11516	-0.017	0.22	NO
67	PLCG1	PLCG1	PLCG1	11609	-0.018	0.21	NO
68	SOS1	SOS1	SOS1	11693	-0.019	0.21	NO
69	THEM4	THEM4	THEM4	12090	-0.024	0.19	NO
70	AKT2	AKT2	AKT2	12138	-0.025	0.19	NO
71	CDKN1B	CDKN1B	CDKN1B	12303	-0.027	0.18	NO
72	PIK3R2	PIK3R2	PIK3R2	12460	-0.029	0.18	NO
73	RPS6KB2	RPS6KB2	RPS6KB2	12462	-0.029	0.18	NO
74	MAPKAP1	MAPKAP1	MAPKAP1	12478	-0.029	0.18	NO
75	GRB2	GRB2	GRB2	12627	-0.031	0.18	NO
76	PRKCG	PRKCG	PRKCG	12791	-0.033	0.17	NO
77	MTOR	MTOR	MTOR	12792	-0.033	0.17	NO
78	STAT5B	STAT5B	STAT5B	12851	-0.034	0.17	NO
79	NRAS	NRAS	NRAS	13024	-0.036	0.17	NO
80	CASP9	CASP9	CASP9	13317	-0.04	0.15	NO
81	GRB7	GRB7	GRB7	14375	-0.059	0.1	NO
82	FOXO4	FOXO4	FOXO4	14432	-0.06	0.1	NO
83	CRKL	CRKL	CRKL	14581	-0.063	0.1	NO
84	PIK3R1	PIK3R1	PIK3R1	14604	-0.063	0.1	NO
85	RAF1	RAF1	RAF1	14721	-0.066	0.1	NO
86	PRKAR2A	PRKAR2A	PRKAR2A	15298	-0.081	0.08	NO
87	PRKCA	PRKCA	PRKCA	16077	-0.11	0.047	NO
88	PHLPP1	PHLPP1	PHLPP1	16197	-0.12	0.052	NO
89	ITPR2	ITPR2	ITPR2	16227	-0.12	0.062	NO
90	CDK1	CDK1	CDK1	17369	-0.23	0.02	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 SELENOAMINO ACID METABOLISM.

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

genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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	PDE1A	PDE1A	PDE1A	18	0.85	0.064	YES
2	FGF1	FGF1	FGF1	107	0.7	0.11	YES
3	IL17RD	IL17RD	IL17RD	245	0.6	0.15	YES
4	ADCY5	ADCY5	ADCY5	290	0.58	0.19	YES
5	FGFR1	FGFR1	FGFR1	422	0.53	0.22	YES
6	FGF7	FGF7	FGF7	451	0.52	0.26	YES
7	FGF18	FGF18	FGF18	489	0.5	0.3	YES
8	PRKAR2B	PRKAR2B	PRKAR2B	509	0.5	0.34	YES
9	AKT3	AKT3	AKT3	693	0.45	0.36	YES
10	ADCY2	ADCY2	ADCY2	781	0.43	0.39	YES
11	ADCY4	ADCY4	ADCY4	988	0.4	0.4	YES
12	CAMK4	CAMK4	CAMK4	1018	0.39	0.43	YES
13	ITPR3	ITPR3	ITPR3	1059	0.39	0.46	YES
14	ADCY3	ADCY3	ADCY3	1078	0.38	0.49	YES
15	FGFR2	FGFR2	FGFR2	1471	0.34	0.49	YES
16	PDE1B	PDE1B	PDE1B	1715	0.31	0.5	YES
17	ADCY7	ADCY7	ADCY7	2157	0.27	0.5	NO
18	PRKAR1B	PRKAR1B	PRKAR1B	2663	0.23	0.49	NO
19	NR4A1	NR4A1	NR4A1	3130	0.2	0.48	NO
20	CBL	CBL	CBL	4136	0.14	0.43	NO
21	SPRY2	SPRY2	SPRY2	4356	0.13	0.43	NO
22	CDKN1A	CDKN1A	CDKN1A	4361	0.13	0.44	NO
23	FGF19	FGF19	FGF19	4478	0.12	0.44	NO
24	PRKCE	PRKCE	PRKCE	4698	0.11	0.44	NO
25	FGF9	FGF9	FGF9	4870	0.1	0.43	NO
26	STAT5A	STAT5A	STAT5A	4974	0.1	0.44	NO
27	SRC	SRC	SRC	5246	0.091	0.43	NO
28	STAT3	STAT3	STAT3	5331	0.088	0.43	NO
29	PPP2CB	PPP2CB	PPP2CB	5670	0.076	0.42	NO
30	ADCY1	ADCY1	ADCY1	5684	0.075	0.42	NO
31	STAT1	STAT1	STAT1	5965	0.068	0.41	NO
32	MAPK3	MAPK3	MAPK3	6203	0.061	0.4	NO
33	FGF2	FGF2	FGF2	6332	0.058	0.4	NO
34	FOXO1	FOXO1	FOXO1	6344	0.058	0.4	NO
35	CUX1	CUX1	CUX1	6385	0.057	0.4	NO
36	MAP2K1	MAP2K1	MAP2K1	6532	0.054	0.4	NO
37	KL	KL	KL	6620	0.051	0.4	NO
38	SHC1	SHC1	SHC1	6672	0.05	0.4	NO
39	PPP2R1A	PPP2R1A	PPP2R1A	6706	0.05	0.4	NO
40	CALM2	CALM2	CALM2	6772	0.048	0.4	NO
41	BCR	BCR	BCR	6814	0.048	0.4	NO
42	GAB2	GAB2	GAB2	6936	0.045	0.4	NO
43	YWHAB	YWHAB	YWHAB	6957	0.045	0.4	NO
44	GAB1	GAB1	GAB1	7034	0.043	0.4	NO
45	CALM1	CALM1	CALM1	7105	0.042	0.4	NO
46	KRAS	KRAS	KRAS	7315	0.038	0.39	NO
47	ADCY9	ADCY9	ADCY9	7427	0.036	0.39	NO
48	PRKACA	PRKACA	PRKACA	7454	0.036	0.39	NO
49	AKT1	AKT1	AKT1	7500	0.035	0.39	NO
50	BAD	BAD	BAD	7526	0.034	0.39	NO
51	CREB1	CREB1	CREB1	8078	0.026	0.36	NO
52	FOXO3	FOXO3	FOXO3	8135	0.025	0.36	NO
53	PIK3CA	PIK3CA	PIK3CA	8146	0.024	0.36	NO
54	FGFR3	FGFR3	FGFR3	8179	0.024	0.36	NO
55	ADRBK1	ADRBK1	ADRBK1	8439	0.02	0.35	NO
56	RICTOR	RICTOR	RICTOR	8684	0.017	0.33	NO
57	TRIB3	TRIB3	TRIB3	8719	0.016	0.33	NO
58	GSK3A	GSK3A	GSK3A	8736	0.016	0.33	NO
59	FGFR1OP2	FGFR1OP2	FGFR1OP2	8858	0.014	0.33	NO
60	TSC2	TSC2	TSC2	8966	0.013	0.32	NO
61	PTEN	PTEN	PTEN	9336	0.0085	0.3	NO
62	MKNK1	MKNK1	MKNK1	9448	0.0073	0.3	NO
63	MLST8	MLST8	MLST8	9614	0.0054	0.29	NO
64	PDPK1	PDPK1	PDPK1	9655	0.0049	0.29	NO
65	ADCY6	ADCY6	ADCY6	9659	0.0049	0.29	NO
66	ZMYM2	ZMYM2	ZMYM2	9663	0.0048	0.29	NO
67	CPSF6	CPSF6	CPSF6	9939	0.001	0.27	NO
68	MAP2K2	MAP2K2	MAP2K2	9980	0.0005	0.27	NO
69	PRKCD	PRKCD	PRKCD	10070	-0.0005	0.26	NO
70	HRAS	HRAS	HRAS	10357	-0.0038	0.25	NO
71	PPP2CA	PPP2CA	PPP2CA	10385	-0.0042	0.25	NO
72	MDM2	MDM2	MDM2	10436	-0.0048	0.24	NO
73	MYO18A	MYO18A	MYO18A	10443	-0.0049	0.24	NO
74	CHUK	CHUK	CHUK	10594	-0.0064	0.24	NO
75	PRKAR1A	PRKAR1A	PRKAR1A	10944	-0.01	0.22	NO
76	PRKACB	PRKACB	PRKACB	11062	-0.012	0.21	NO
77	CALM3	CALM3	CALM3	11068	-0.012	0.21	NO
78	AKT1S1	AKT1S1	AKT1S1	11225	-0.014	0.2	NO
79	ADCY8	ADCY8	ADCY8	11454	-0.016	0.19	NO
80	MAPK1	MAPK1	MAPK1	11516	-0.017	0.19	NO
81	UBA52	UBA52	UBA52	11591	-0.018	0.19	NO
82	PLCG1	PLCG1	PLCG1	11609	-0.018	0.19	NO
83	SOS1	SOS1	SOS1	11693	-0.019	0.18	NO
84	FRS2	FRS2	FRS2	11702	-0.019	0.19	NO
85	FGFR1OP	FGFR1OP	FGFR1OP	11805	-0.021	0.18	NO
86	RPS27A	RPS27A	RPS27A	11897	-0.022	0.18	NO
87	THEM4	THEM4	THEM4	12090	-0.024	0.17	NO
88	AKT2	AKT2	AKT2	12138	-0.025	0.17	NO
89	CDKN1B	CDKN1B	CDKN1B	12303	-0.027	0.16	NO
90	RPS6KB2	RPS6KB2	RPS6KB2	12462	-0.029	0.15	NO
91	MAPKAP1	MAPKAP1	MAPKAP1	12478	-0.029	0.16	NO
92	GRB2	GRB2	GRB2	12627	-0.031	0.15	NO
93	PRKCG	PRKCG	PRKCG	12791	-0.033	0.14	NO
94	MTOR	MTOR	MTOR	12792	-0.033	0.14	NO
95	STAT5B	STAT5B	STAT5B	12851	-0.034	0.14	NO
96	NRAS	NRAS	NRAS	13024	-0.036	0.14	NO
97	CASP9	CASP9	CASP9	13317	-0.04	0.12	NO
98	FGF22	FGF22	FGF22	13588	-0.044	0.11	NO
99	FRS3	FRS3	FRS3	14394	-0.059	0.071	NO
100	FOXO4	FOXO4	FOXO4	14432	-0.06	0.073	NO
101	FGFR4	FGFR4	FGFR4	14458	-0.061	0.076	NO
102	PIK3R1	PIK3R1	PIK3R1	14604	-0.063	0.073	NO
103	RAF1	RAF1	RAF1	14721	-0.066	0.071	NO
104	BRAF	BRAF	BRAF	15109	-0.075	0.055	NO
105	PRKAR2A	PRKAR2A	PRKAR2A	15298	-0.081	0.051	NO
106	PRKCA	PRKCA	PRKCA	16077	-0.11	0.015	NO
107	PHLPP1	PHLPP1	PHLPP1	16197	-0.12	0.018	NO
108	ITPR2	ITPR2	ITPR2	16227	-0.12	0.025	NO
109	FGF17	FGF17	FGF17	16767	-0.16	0.007	NO
110	TRIM24	TRIM24	TRIM24	17010	-0.18	0.0073	NO
111	KLB	KLB	KLB	17188	-0.2	0.013	NO
112	CDK1	CDK1	CDK1	17369	-0.23	0.02	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 N GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

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	PDE1A	PDE1A	PDE1A	18	0.85	0.062	YES
2	NTRK2	NTRK2	NTRK2	34	0.81	0.12	YES
3	ADCY5	ADCY5	ADCY5	290	0.58	0.15	YES
4	PRKAR2B	PRKAR2B	PRKAR2B	509	0.5	0.17	YES
5	AKT3	AKT3	AKT3	693	0.45	0.2	YES
6	ADCY2	ADCY2	ADCY2	781	0.43	0.22	YES
7	ADCY4	ADCY4	ADCY4	988	0.4	0.24	YES
8	DUSP4	DUSP4	DUSP4	1002	0.39	0.27	YES
9	CAMK4	CAMK4	CAMK4	1018	0.39	0.3	YES
10	ITPR3	ITPR3	ITPR3	1059	0.39	0.32	YES
11	ADCY3	ADCY3	ADCY3	1078	0.38	0.35	YES
12	NGF	NGF	NGF	1254	0.36	0.37	YES
13	PDE1B	PDE1B	PDE1B	1715	0.31	0.36	YES
14	MAPK11	MAPK11	MAPK11	2027	0.28	0.37	YES
15	ADCY7	ADCY7	ADCY7	2157	0.27	0.38	YES
16	RPS6KA2	RPS6KA2	RPS6KA2	2317	0.26	0.39	YES
17	MAPK12	MAPK12	MAPK12	2323	0.26	0.41	YES
18	DNM1	DNM1	DNM1	2536	0.24	0.42	YES
19	NTRK1	NTRK1	NTRK1	2617	0.24	0.43	YES
20	PRKAR1B	PRKAR1B	PRKAR1B	2663	0.23	0.44	YES
21	MEF2C	MEF2C	MEF2C	2748	0.23	0.46	YES
22	NR4A1	NR4A1	NR4A1	3130	0.2	0.45	YES
23	MAPK13	MAPK13	MAPK13	3233	0.19	0.46	YES
24	RALGDS	RALGDS	RALGDS	3927	0.15	0.43	NO
25	CDKN1A	CDKN1A	CDKN1A	4361	0.13	0.41	NO
26	ADCYAP1	ADCYAP1	ADCYAP1	4440	0.12	0.42	NO
27	SH3GL2	SH3GL2	SH3GL2	4663	0.11	0.41	NO
28	RALB	RALB	RALB	4687	0.11	0.42	NO
29	PRKCE	PRKCE	PRKCE	4698	0.11	0.43	NO
30	SHC3	SHC3	SHC3	5236	0.091	0.4	NO
31	SRC	SRC	SRC	5246	0.091	0.41	NO
32	STAT3	STAT3	STAT3	5331	0.088	0.41	NO
33	RPS6KA5	RPS6KA5	RPS6KA5	5390	0.085	0.42	NO
34	MAPK7	MAPK7	MAPK7	5445	0.083	0.42	NO
35	MEF2A	MEF2A	MEF2A	5574	0.078	0.42	NO
36	MAPKAPK2	MAPKAPK2	MAPKAPK2	5645	0.076	0.42	NO
37	CRK	CRK	CRK	5648	0.076	0.42	NO
38	DUSP7	DUSP7	DUSP7	5650	0.076	0.43	NO
39	PPP2CB	PPP2CB	PPP2CB	5670	0.076	0.44	NO
40	ADCY1	ADCY1	ADCY1	5684	0.075	0.44	NO
41	MAPK3	MAPK3	MAPK3	6203	0.061	0.41	NO
42	SHC2	SHC2	SHC2	6228	0.061	0.42	NO
43	ADORA2A	ADORA2A	ADORA2A	6249	0.06	0.42	NO
44	DNAL4	DNAL4	DNAL4	6257	0.06	0.42	NO
45	RPS6KA1	RPS6KA1	RPS6KA1	6293	0.059	0.43	NO
46	DUSP6	DUSP6	DUSP6	6296	0.059	0.43	NO
47	FOXO1	FOXO1	FOXO1	6344	0.058	0.43	NO
48	MAP2K1	MAP2K1	MAP2K1	6532	0.054	0.43	NO
49	SHC1	SHC1	SHC1	6672	0.05	0.42	NO
50	PPP2R1A	PPP2R1A	PPP2R1A	6706	0.05	0.42	NO
51	CALM2	CALM2	CALM2	6772	0.048	0.42	NO
52	RIT1	RIT1	RIT1	6809	0.048	0.42	NO
53	YWHAB	YWHAB	YWHAB	6957	0.045	0.42	NO
54	CALM1	CALM1	CALM1	7105	0.042	0.42	NO
55	KRAS	KRAS	KRAS	7315	0.038	0.41	NO
56	KIDINS220	KIDINS220	KIDINS220	7331	0.038	0.41	NO
57	ADCY9	ADCY9	ADCY9	7427	0.036	0.4	NO
58	PRKACA	PRKACA	PRKACA	7454	0.036	0.41	NO
59	AKT1	AKT1	AKT1	7500	0.035	0.41	NO
60	BAD	BAD	BAD	7526	0.034	0.41	NO
61	RAPGEF1	RAPGEF1	RAPGEF1	7573	0.033	0.41	NO
62	DNM2	DNM2	DNM2	7942	0.028	0.39	NO
63	CREB1	CREB1	CREB1	8078	0.026	0.38	NO
64	FOXO3	FOXO3	FOXO3	8135	0.025	0.38	NO
65	PIK3CA	PIK3CA	PIK3CA	8146	0.024	0.38	NO
66	RAP1A	RAP1A	RAP1A	8233	0.023	0.38	NO
67	ADRBK1	ADRBK1	ADRBK1	8439	0.02	0.37	NO
68	AP2A2	AP2A2	AP2A2	8617	0.018	0.36	NO
69	RICTOR	RICTOR	RICTOR	8684	0.017	0.36	NO
70	TRIB3	TRIB3	TRIB3	8719	0.016	0.36	NO
71	GSK3A	GSK3A	GSK3A	8736	0.016	0.36	NO
72	MAP2K5	MAP2K5	MAP2K5	8828	0.015	0.35	NO
73	AP2M1	AP2M1	AP2M1	8874	0.014	0.35	NO
74	AP2B1	AP2B1	AP2B1	8886	0.014	0.35	NO
75	TSC2	TSC2	TSC2	8966	0.013	0.35	NO
76	RHOA	RHOA	RHOA	9181	0.01	0.34	NO
77	PIK3CB	PIK3CB	PIK3CB	9266	0.0094	0.33	NO
78	RALA	RALA	RALA	9329	0.0086	0.33	NO
79	PTEN	PTEN	PTEN	9336	0.0085	0.33	NO
80	MLST8	MLST8	MLST8	9614	0.0054	0.32	NO
81	PDPK1	PDPK1	PDPK1	9655	0.0049	0.31	NO
82	ADCY6	ADCY6	ADCY6	9659	0.0049	0.31	NO
83	MAP2K2	MAP2K2	MAP2K2	9980	0.0005	0.3	NO
84	PRKCD	PRKCD	PRKCD	10070	-0.0005	0.29	NO
85	HRAS	HRAS	HRAS	10357	-0.0038	0.27	NO
86	MAPKAPK3	MAPKAPK3	MAPKAPK3	10382	-0.0041	0.27	NO
87	PPP2CA	PPP2CA	PPP2CA	10385	-0.0042	0.27	NO
88	MDM2	MDM2	MDM2	10436	-0.0048	0.27	NO
89	CHUK	CHUK	CHUK	10594	-0.0064	0.26	NO
90	DUSP3	DUSP3	DUSP3	10606	-0.0066	0.26	NO
91	CLTC	CLTC	CLTC	10832	-0.0092	0.25	NO
92	PRKAR1A	PRKAR1A	PRKAR1A	10944	-0.01	0.24	NO
93	AP2S1	AP2S1	AP2S1	10969	-0.011	0.24	NO
94	CLTA	CLTA	CLTA	11042	-0.012	0.24	NO
95	PRKACB	PRKACB	PRKACB	11062	-0.012	0.24	NO
96	CALM3	CALM3	CALM3	11068	-0.012	0.24	NO
97	IRS2	IRS2	IRS2	11070	-0.012	0.24	NO
98	AKT1S1	AKT1S1	AKT1S1	11225	-0.014	0.24	NO
99	AP2A1	AP2A1	AP2A1	11277	-0.014	0.23	NO
100	ADCY8	ADCY8	ADCY8	11454	-0.016	0.22	NO
101	MAPK1	MAPK1	MAPK1	11516	-0.017	0.22	NO
102	PLCG1	PLCG1	PLCG1	11609	-0.018	0.22	NO
103	SOS1	SOS1	SOS1	11693	-0.019	0.22	NO
104	FRS2	FRS2	FRS2	11702	-0.019	0.22	NO
105	ELK1	ELK1	ELK1	11926	-0.022	0.2	NO
106	PPP2R1B	PPP2R1B	PPP2R1B	12000	-0.023	0.2	NO
107	THEM4	THEM4	THEM4	12090	-0.024	0.2	NO
108	AKT2	AKT2	AKT2	12138	-0.025	0.2	NO
109	CDKN1B	CDKN1B	CDKN1B	12303	-0.027	0.19	NO
110	PIK3R2	PIK3R2	PIK3R2	12460	-0.029	0.18	NO
111	RPS6KB2	RPS6KB2	RPS6KB2	12462	-0.029	0.19	NO
112	MAPKAP1	MAPKAP1	MAPKAP1	12478	-0.029	0.19	NO
113	GRB2	GRB2	GRB2	12627	-0.031	0.18	NO
114	PRKCG	PRKCG	PRKCG	12791	-0.033	0.17	NO
115	MTOR	MTOR	MTOR	12792	-0.033	0.18	NO
116	MAPK14	MAPK14	MAPK14	12970	-0.035	0.17	NO
117	NRAS	NRAS	NRAS	13024	-0.036	0.17	NO
118	CASP9	CASP9	CASP9	13317	-0.04	0.16	NO
119	RPS6KA3	RPS6KA3	RPS6KA3	13891	-0.049	0.13	NO
120	ATF1	ATF1	ATF1	13988	-0.051	0.12	NO
121	FOXO4	FOXO4	FOXO4	14432	-0.06	0.1	NO
122	PIK3R1	PIK3R1	PIK3R1	14604	-0.063	0.099	NO
123	RAF1	RAF1	RAF1	14721	-0.066	0.097	NO
124	BRAF	BRAF	BRAF	15109	-0.075	0.081	NO
125	PRKAR2A	PRKAR2A	PRKAR2A	15298	-0.081	0.076	NO
126	PPP2R5D	PPP2R5D	PPP2R5D	15351	-0.083	0.079	NO
127	PRKCA	PRKCA	PRKCA	16077	-0.11	0.046	NO
128	PHLPP1	PHLPP1	PHLPP1	16197	-0.12	0.048	NO
129	ITPR2	ITPR2	ITPR2	16227	-0.12	0.056	NO
130	IRS1	IRS1	IRS1	16780	-0.16	0.037	NO
131	CDK1	CDK1	CDK1	17369	-0.23	0.02	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 O GLYCAN BIOSYNTHESIS.

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

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

Table 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	PDE1A	PDE1A	PDE1A	18	0.85	0.043	YES
2	THBS2	THBS2	THBS2	121	0.69	0.072	YES
3	PDGFRA	PDGFRA	PDGFRA	142	0.67	0.11	YES
4	COL5A1	COL5A1	COL5A1	187	0.64	0.14	YES
5	ADCY5	ADCY5	ADCY5	290	0.58	0.16	YES
6	COL4A4	COL4A4	COL4A4	313	0.57	0.19	YES
7	PLAT	PLAT	PLAT	344	0.55	0.22	YES
8	COL1A1	COL1A1	COL1A1	402	0.53	0.24	YES
9	COL3A1	COL3A1	COL3A1	433	0.52	0.26	YES
10	PRKAR2B	PRKAR2B	PRKAR2B	509	0.5	0.28	YES
11	COL1A2	COL1A2	COL1A2	548	0.49	0.31	YES
12	SPP1	SPP1	SPP1	670	0.46	0.32	YES
13	AKT3	AKT3	AKT3	693	0.45	0.35	YES
14	ADCY2	ADCY2	ADCY2	781	0.43	0.36	YES
15	COL6A3	COL6A3	COL6A3	830	0.42	0.38	YES
16	PDGFD	PDGFD	PDGFD	904	0.41	0.4	YES
17	COL6A2	COL6A2	COL6A2	956	0.4	0.42	YES
18	ADCY4	ADCY4	ADCY4	988	0.4	0.44	YES
19	CAMK4	CAMK4	CAMK4	1018	0.39	0.45	YES
20	ITPR3	ITPR3	ITPR3	1059	0.39	0.47	YES
21	ADCY3	ADCY3	ADCY3	1078	0.38	0.49	YES
22	COL4A3	COL4A3	COL4A3	1086	0.38	0.51	YES
23	COL6A1	COL6A1	COL6A1	1491	0.33	0.5	YES
24	THBS1	THBS1	THBS1	1657	0.32	0.51	YES
25	PDE1B	PDE1B	PDE1B	1715	0.31	0.52	YES
26	PDGFA	PDGFA	PDGFA	1897	0.29	0.53	YES
27	COL4A2	COL4A2	COL4A2	2141	0.27	0.53	YES
28	ADCY7	ADCY7	ADCY7	2157	0.27	0.54	YES
29	NCK2	NCK2	NCK2	2175	0.27	0.56	YES
30	PDGFRB	PDGFRB	PDGFRB	2202	0.27	0.57	YES
31	COL5A2	COL5A2	COL5A2	2429	0.25	0.57	YES
32	COL4A1	COL4A1	COL4A1	2622	0.24	0.57	YES
33	PRKAR1B	PRKAR1B	PRKAR1B	2663	0.23	0.58	YES
34	COL9A2	COL9A2	COL9A2	2867	0.22	0.58	YES
35	COL9A1	COL9A1	COL9A1	3088	0.2	0.58	YES
36	NR4A1	NR4A1	NR4A1	3130	0.2	0.58	YES
37	PDGFB	PDGFB	PDGFB	3314	0.19	0.58	YES
38	COL4A5	COL4A5	COL4A5	3429	0.18	0.59	YES
39	PDGFC	PDGFC	PDGFC	4173	0.14	0.55	NO
40	CDKN1A	CDKN1A	CDKN1A	4361	0.13	0.55	NO
41	FURIN	FURIN	FURIN	4408	0.13	0.55	NO
42	BCAR1	BCAR1	BCAR1	4488	0.12	0.55	NO
43	PRKCE	PRKCE	PRKCE	4698	0.11	0.55	NO
44	STAT5A	STAT5A	STAT5A	4974	0.1	0.54	NO
45	SRC	SRC	SRC	5246	0.091	0.52	NO
46	STAT3	STAT3	STAT3	5331	0.088	0.52	NO
47	CRK	CRK	CRK	5648	0.076	0.51	NO
48	ADCY1	ADCY1	ADCY1	5684	0.075	0.51	NO
49	THBS3	THBS3	THBS3	5913	0.069	0.5	NO
50	STAT1	STAT1	STAT1	5965	0.068	0.5	NO
51	MAPK3	MAPK3	MAPK3	6203	0.061	0.49	NO
52	FOXO1	FOXO1	FOXO1	6344	0.058	0.49	NO
53	MAP2K1	MAP2K1	MAP2K1	6532	0.054	0.48	NO
54	NCK1	NCK1	NCK1	6647	0.051	0.48	NO
55	CALM2	CALM2	CALM2	6772	0.048	0.47	NO
56	YWHAB	YWHAB	YWHAB	6957	0.045	0.46	NO
57	CALM1	CALM1	CALM1	7105	0.042	0.46	NO
58	STAT6	STAT6	STAT6	7228	0.04	0.45	NO
59	KRAS	KRAS	KRAS	7315	0.038	0.45	NO
60	ADCY9	ADCY9	ADCY9	7427	0.036	0.45	NO
61	PRKACA	PRKACA	PRKACA	7454	0.036	0.45	NO
62	AKT1	AKT1	AKT1	7500	0.035	0.44	NO
63	BAD	BAD	BAD	7526	0.034	0.45	NO
64	RAPGEF1	RAPGEF1	RAPGEF1	7573	0.033	0.44	NO
65	RASA1	RASA1	RASA1	7789	0.03	0.43	NO
66	CREB1	CREB1	CREB1	8078	0.026	0.42	NO
67	FOXO3	FOXO3	FOXO3	8135	0.025	0.42	NO
68	PIK3CA	PIK3CA	PIK3CA	8146	0.024	0.42	NO
69	ADRBK1	ADRBK1	ADRBK1	8439	0.02	0.4	NO
70	RICTOR	RICTOR	RICTOR	8684	0.017	0.39	NO
71	TRIB3	TRIB3	TRIB3	8719	0.016	0.39	NO
72	GSK3A	GSK3A	GSK3A	8736	0.016	0.39	NO
73	TSC2	TSC2	TSC2	8966	0.013	0.38	NO
74	PIK3CB	PIK3CB	PIK3CB	9266	0.0094	0.36	NO
75	PTEN	PTEN	PTEN	9336	0.0085	0.36	NO
76	MLST8	MLST8	MLST8	9614	0.0054	0.34	NO
77	PDPK1	PDPK1	PDPK1	9655	0.0049	0.34	NO
78	ADCY6	ADCY6	ADCY6	9659	0.0049	0.34	NO
79	MAP2K2	MAP2K2	MAP2K2	9980	0.0005	0.32	NO
80	PRKCD	PRKCD	PRKCD	10070	-0.0005	0.32	NO
81	HRAS	HRAS	HRAS	10357	-0.0038	0.3	NO
82	MDM2	MDM2	MDM2	10436	-0.0048	0.3	NO
83	CHUK	CHUK	CHUK	10594	-0.0064	0.29	NO
84	PRKAR1A	PRKAR1A	PRKAR1A	10944	-0.01	0.27	NO
85	PRKACB	PRKACB	PRKACB	11062	-0.012	0.26	NO
86	CALM3	CALM3	CALM3	11068	-0.012	0.26	NO
87	AKT1S1	AKT1S1	AKT1S1	11225	-0.014	0.25	NO
88	ADCY8	ADCY8	ADCY8	11454	-0.016	0.24	NO
89	MAPK1	MAPK1	MAPK1	11516	-0.017	0.24	NO
90	PLCG1	PLCG1	PLCG1	11609	-0.018	0.23	NO
91	SOS1	SOS1	SOS1	11693	-0.019	0.23	NO
92	THEM4	THEM4	THEM4	12090	-0.024	0.21	NO
93	AKT2	AKT2	AKT2	12138	-0.025	0.21	NO
94	CDKN1B	CDKN1B	CDKN1B	12303	-0.027	0.2	NO
95	PIK3R2	PIK3R2	PIK3R2	12460	-0.029	0.19	NO
96	RPS6KB2	RPS6KB2	RPS6KB2	12462	-0.029	0.19	NO
97	MAPKAP1	MAPKAP1	MAPKAP1	12478	-0.029	0.2	NO
98	GRB2	GRB2	GRB2	12627	-0.031	0.19	NO
99	PRKCG	PRKCG	PRKCG	12791	-0.033	0.18	NO
100	MTOR	MTOR	MTOR	12792	-0.033	0.18	NO
101	STAT5B	STAT5B	STAT5B	12851	-0.034	0.18	NO
102	NRAS	NRAS	NRAS	13024	-0.036	0.17	NO
103	CASP9	CASP9	CASP9	13317	-0.04	0.16	NO
104	GRB7	GRB7	GRB7	14375	-0.059	0.1	NO
105	FOXO4	FOXO4	FOXO4	14432	-0.06	0.1	NO
106	CRKL	CRKL	CRKL	14581	-0.063	0.096	NO
107	PIK3R1	PIK3R1	PIK3R1	14604	-0.063	0.098	NO
108	RAF1	RAF1	RAF1	14721	-0.066	0.095	NO
109	COL9A3	COL9A3	COL9A3	15186	-0.078	0.072	NO
110	PRKAR2A	PRKAR2A	PRKAR2A	15298	-0.081	0.07	NO
111	PRKCA	PRKCA	PRKCA	16077	-0.11	0.032	NO
112	PHLPP1	PHLPP1	PHLPP1	16197	-0.12	0.031	NO
113	ITPR2	ITPR2	ITPR2	16227	-0.12	0.036	NO
114	PLG	PLG	PLG	16433	-0.14	0.031	NO
115	COL2A1	COL2A1	COL2A1	17336	-0.23	-0.0083	NO
116	CDK1	CDK1	CDK1	17369	-0.23	0.0019	NO
117	THBS4	THBS4	THBS4	17693	-0.36	0.002	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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S72. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG INOSITOL PHOSPHATE METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PDE1A	PDE1A	PDE1A	18	0.85	0.037	YES
2	NTRK2	NTRK2	NTRK2	34	0.81	0.072	YES
3	NGFR	NGFR	NGFR	65	0.74	0.1	YES
4	ADCY5	ADCY5	ADCY5	290	0.58	0.12	YES
5	PRKAR2B	PRKAR2B	PRKAR2B	509	0.5	0.13	YES
6	ARHGEF4	ARHGEF4	ARHGEF4	589	0.48	0.14	YES
7	ABR	ABR	ABR	686	0.45	0.16	YES
8	AKT3	AKT3	AKT3	693	0.45	0.18	YES
9	ADCY2	ADCY2	ADCY2	781	0.43	0.19	YES
10	ADCY4	ADCY4	ADCY4	988	0.4	0.2	YES
11	DUSP4	DUSP4	DUSP4	1002	0.39	0.21	YES
12	CAMK4	CAMK4	CAMK4	1018	0.39	0.23	YES
13	ITPR3	ITPR3	ITPR3	1059	0.39	0.24	YES
14	ADCY3	ADCY3	ADCY3	1078	0.38	0.26	YES
15	ARHGEF17	ARHGEF17	ARHGEF17	1182	0.37	0.27	YES
16	PCSK5	PCSK5	PCSK5	1195	0.37	0.29	YES
17	OBSCN	OBSCN	OBSCN	1200	0.37	0.3	YES
18	NGF	NGF	NGF	1254	0.36	0.32	YES
19	FGD3	FGD3	FGD3	1312	0.35	0.33	YES
20	LINGO1	LINGO1	LINGO1	1384	0.34	0.34	YES
21	ARHGEF16	ARHGEF16	ARHGEF16	1438	0.34	0.35	YES
22	VAV1	VAV1	VAV1	1689	0.31	0.35	YES
23	PDE1B	PDE1B	PDE1B	1715	0.31	0.36	YES
24	VAV3	VAV3	VAV3	1894	0.29	0.36	YES
25	MAPK11	MAPK11	MAPK11	2027	0.28	0.37	YES
26	ADCY7	ADCY7	ADCY7	2157	0.27	0.38	YES
27	ARHGEF3	ARHGEF3	ARHGEF3	2311	0.26	0.38	YES
28	TIAM2	TIAM2	TIAM2	2314	0.26	0.39	YES
29	RPS6KA2	RPS6KA2	RPS6KA2	2317	0.26	0.4	YES
30	MAPK12	MAPK12	MAPK12	2323	0.26	0.41	YES
31	FGD2	FGD2	FGD2	2431	0.25	0.42	YES
32	PREX1	PREX1	PREX1	2518	0.24	0.42	YES
33	DNM1	DNM1	DNM1	2536	0.24	0.43	YES
34	NTRK1	NTRK1	NTRK1	2617	0.24	0.44	YES
35	PRKAR1B	PRKAR1B	PRKAR1B	2663	0.23	0.45	YES
36	ARHGEF6	ARHGEF6	ARHGEF6	2731	0.23	0.45	YES
37	MEF2C	MEF2C	MEF2C	2748	0.23	0.46	YES
38	NR4A1	NR4A1	NR4A1	3130	0.2	0.45	YES
39	MAPK13	MAPK13	MAPK13	3233	0.19	0.45	YES
40	ARHGAP4	ARHGAP4	ARHGAP4	3292	0.19	0.46	YES
41	RASGRF2	RASGRF2	RASGRF2	3355	0.19	0.46	YES
42	TIAM1	TIAM1	TIAM1	3420	0.18	0.46	YES
43	RALGDS	RALGDS	RALGDS	3927	0.15	0.44	YES
44	FGD4	FGD4	FGD4	4142	0.14	0.44	YES
45	APH1B	APH1B	APH1B	4150	0.14	0.44	YES
46	FGD1	FGD1	FGD1	4335	0.13	0.44	YES
47	CDKN1A	CDKN1A	CDKN1A	4361	0.13	0.44	YES
48	PLEKHG2	PLEKHG2	PLEKHG2	4367	0.13	0.45	YES
49	FURIN	FURIN	FURIN	4408	0.13	0.45	YES
50	ADCYAP1	ADCYAP1	ADCYAP1	4440	0.12	0.46	YES
51	ADAM17	ADAM17	ADAM17	4466	0.12	0.46	YES
52	MCF2	MCF2	MCF2	4585	0.12	0.46	YES
53	SH3GL2	SH3GL2	SH3GL2	4663	0.11	0.46	YES
54	RALB	RALB	RALB	4687	0.11	0.46	YES
55	PRKCE	PRKCE	PRKCE	4698	0.11	0.47	YES
56	PSEN2	PSEN2	PSEN2	5131	0.094	0.44	YES
57	SHC3	SHC3	SHC3	5236	0.091	0.44	YES
58	BCL2L11	BCL2L11	BCL2L11	5241	0.091	0.45	YES
59	SRC	SRC	SRC	5246	0.091	0.45	YES
60	STAT3	STAT3	STAT3	5331	0.088	0.45	YES
61	AKAP13	AKAP13	AKAP13	5368	0.086	0.45	YES
62	RPS6KA5	RPS6KA5	RPS6KA5	5390	0.085	0.46	YES
63	RIPK2	RIPK2	RIPK2	5405	0.084	0.46	YES
64	MAPK7	MAPK7	MAPK7	5445	0.083	0.46	YES
65	ARHGEF2	ARHGEF2	ARHGEF2	5554	0.079	0.46	YES
66	MEF2A	MEF2A	MEF2A	5574	0.078	0.46	YES
67	MAPKAPK2	MAPKAPK2	MAPKAPK2	5645	0.076	0.46	YES
68	CRK	CRK	CRK	5648	0.076	0.46	YES
69	DUSP7	DUSP7	DUSP7	5650	0.076	0.46	YES
70	PPP2CB	PPP2CB	PPP2CB	5670	0.076	0.47	YES
71	ADCY1	ADCY1	ADCY1	5684	0.075	0.47	YES
72	TRIO	TRIO	TRIO	6044	0.065	0.45	NO
73	ARHGEF12	ARHGEF12	ARHGEF12	6081	0.064	0.45	NO
74	IKBKB	IKBKB	IKBKB	6160	0.062	0.45	NO
75	MAPK3	MAPK3	MAPK3	6203	0.061	0.45	NO
76	SHC2	SHC2	SHC2	6228	0.061	0.45	NO
77	ADORA2A	ADORA2A	ADORA2A	6249	0.06	0.45	NO
78	DNAL4	DNAL4	DNAL4	6257	0.06	0.46	NO
79	KALRN	KALRN	KALRN	6284	0.059	0.46	NO
80	RPS6KA1	RPS6KA1	RPS6KA1	6293	0.059	0.46	NO
81	DUSP6	DUSP6	DUSP6	6296	0.059	0.46	NO
82	FOXO1	FOXO1	FOXO1	6344	0.058	0.46	NO
83	MAP2K1	MAP2K1	MAP2K1	6532	0.054	0.45	NO
84	NFKBIA	NFKBIA	NFKBIA	6618	0.052	0.45	NO
85	SHC1	SHC1	SHC1	6672	0.05	0.45	NO
86	PPP2R1A	PPP2R1A	PPP2R1A	6706	0.05	0.45	NO
87	CALM2	CALM2	CALM2	6772	0.048	0.45	NO
88	RIT1	RIT1	RIT1	6809	0.048	0.45	NO
89	YWHAB	YWHAB	YWHAB	6957	0.045	0.44	NO
90	PRDM4	PRDM4	PRDM4	7060	0.043	0.44	NO
91	MAG	MAG	MAG	7086	0.042	0.44	NO
92	CALM1	CALM1	CALM1	7105	0.042	0.44	NO
93	RAC1	RAC1	RAC1	7184	0.041	0.44	NO
94	TRAF6	TRAF6	TRAF6	7208	0.04	0.44	NO
95	NGFRAP1	NGFRAP1	NGFRAP1	7254	0.039	0.44	NO
96	KRAS	KRAS	KRAS	7315	0.038	0.44	NO
97	RTN4	RTN4	RTN4	7317	0.038	0.44	NO
98	KIDINS220	KIDINS220	KIDINS220	7331	0.038	0.44	NO
99	OMG	OMG	OMG	7366	0.037	0.44	NO
100	ADCY9	ADCY9	ADCY9	7427	0.036	0.44	NO
101	PRKACA	PRKACA	PRKACA	7454	0.036	0.44	NO
102	SOS2	SOS2	SOS2	7494	0.035	0.44	NO
103	AKT1	AKT1	AKT1	7500	0.035	0.44	NO
104	BAD	BAD	BAD	7526	0.034	0.44	NO
105	RAPGEF1	RAPGEF1	RAPGEF1	7573	0.033	0.44	NO
106	RASGRF1	RASGRF1	RASGRF1	7669	0.032	0.43	NO
107	DNM2	DNM2	DNM2	7942	0.028	0.42	NO
108	CREB1	CREB1	CREB1	8078	0.026	0.41	NO
109	FOXO3	FOXO3	FOXO3	8135	0.025	0.41	NO
110	PIK3CA	PIK3CA	PIK3CA	8146	0.024	0.41	NO
111	RAP1A	RAP1A	RAP1A	8233	0.023	0.4	NO
112	ITSN1	ITSN1	ITSN1	8256	0.023	0.4	NO
113	ARHGEF18	ARHGEF18	ARHGEF18	8296	0.022	0.4	NO
114	SMPD2	SMPD2	SMPD2	8299	0.022	0.4	NO
115	IRAK1	IRAK1	IRAK1	8340	0.022	0.4	NO
116	ADRBK1	ADRBK1	ADRBK1	8439	0.02	0.4	NO
117	ARHGEF1	ARHGEF1	ARHGEF1	8546	0.018	0.39	NO
118	AP2A2	AP2A2	AP2A2	8617	0.018	0.39	NO
119	CASP2	CASP2	CASP2	8658	0.017	0.39	NO
120	RICTOR	RICTOR	RICTOR	8684	0.017	0.39	NO
121	TRIB3	TRIB3	TRIB3	8719	0.016	0.39	NO
122	GSK3A	GSK3A	GSK3A	8736	0.016	0.39	NO
123	MAP2K5	MAP2K5	MAP2K5	8828	0.015	0.38	NO
124	YWHAE	YWHAE	YWHAE	8847	0.014	0.38	NO
125	AP2M1	AP2M1	AP2M1	8874	0.014	0.38	NO
126	AP2B1	AP2B1	AP2B1	8886	0.014	0.38	NO
127	TSC2	TSC2	TSC2	8966	0.013	0.38	NO
128	PSENEN	PSENEN	PSENEN	8983	0.013	0.38	NO
129	PSEN1	PSEN1	PSEN1	9100	0.011	0.37	NO
130	RHOA	RHOA	RHOA	9181	0.01	0.37	NO
131	PIK3CB	PIK3CB	PIK3CB	9266	0.0094	0.36	NO
132	MAPK8	MAPK8	MAPK8	9314	0.0088	0.36	NO
133	RALA	RALA	RALA	9329	0.0086	0.36	NO
134	PTEN	PTEN	PTEN	9336	0.0085	0.36	NO
135	MLST8	MLST8	MLST8	9614	0.0054	0.34	NO
136	PDPK1	PDPK1	PDPK1	9655	0.0049	0.34	NO
137	ADCY6	ADCY6	ADCY6	9659	0.0049	0.34	NO
138	SQSTM1	SQSTM1	SQSTM1	9861	0.0022	0.33	NO
139	ARHGEF9	ARHGEF9	ARHGEF9	9960	0.0008	0.32	NO
140	MAP2K2	MAP2K2	MAP2K2	9980	0.0005	0.32	NO
141	MAGED1	MAGED1	MAGED1	10006	0.00015	0.32	NO
142	PRKCD	PRKCD	PRKCD	10070	-0.0005	0.32	NO
143	NCSTN	NCSTN	NCSTN	10138	-0.0013	0.31	NO
144	PRKCI	PRKCI	PRKCI	10219	-0.0022	0.31	NO
145	CASP3	CASP3	CASP3	10238	-0.0024	0.31	NO
146	HRAS	HRAS	HRAS	10357	-0.0038	0.3	NO
147	MAPKAPK3	MAPKAPK3	MAPKAPK3	10382	-0.0041	0.3	NO
148	PPP2CA	PPP2CA	PPP2CA	10385	-0.0042	0.3	NO
149	MDM2	MDM2	MDM2	10436	-0.0048	0.3	NO
150	CHUK	CHUK	CHUK	10594	-0.0064	0.29	NO
151	DUSP3	DUSP3	DUSP3	10606	-0.0066	0.29	NO
152	HDAC1	HDAC1	HDAC1	10758	-0.0084	0.28	NO
153	CLTC	CLTC	CLTC	10832	-0.0092	0.28	NO
154	HDAC2	HDAC2	HDAC2	10850	-0.0094	0.28	NO
155	PRKAR1A	PRKAR1A	PRKAR1A	10944	-0.01	0.27	NO
156	HDAC3	HDAC3	HDAC3	10964	-0.011	0.27	NO
157	AP2S1	AP2S1	AP2S1	10969	-0.011	0.27	NO
158	CLTA	CLTA	CLTA	11042	-0.012	0.27	NO
159	PRKACB	PRKACB	PRKACB	11062	-0.012	0.27	NO
160	CALM3	CALM3	CALM3	11068	-0.012	0.27	NO
161	ARHGDIA	ARHGDIA	ARHGDIA	11069	-0.012	0.27	NO
162	IRS2	IRS2	IRS2	11070	-0.012	0.27	NO
163	RELA	RELA	RELA	11135	-0.013	0.27	NO
164	AKT1S1	AKT1S1	AKT1S1	11225	-0.014	0.26	NO
165	AP2A1	AP2A1	AP2A1	11277	-0.014	0.26	NO
166	ADCY8	ADCY8	ADCY8	11454	-0.016	0.25	NO
167	MAPK1	MAPK1	MAPK1	11516	-0.017	0.25	NO
168	UBA52	UBA52	UBA52	11591	-0.018	0.24	NO
169	PLCG1	PLCG1	PLCG1	11609	-0.018	0.24	NO
170	SOS1	SOS1	SOS1	11693	-0.019	0.24	NO
171	FRS2	FRS2	FRS2	11702	-0.019	0.24	NO
172	ARHGEF11	ARHGEF11	ARHGEF11	11816	-0.021	0.24	NO
173	RPS27A	RPS27A	RPS27A	11897	-0.022	0.23	NO
174	ELK1	ELK1	ELK1	11926	-0.022	0.23	NO
175	PPP2R1B	PPP2R1B	PPP2R1B	12000	-0.023	0.23	NO
176	THEM4	THEM4	THEM4	12090	-0.024	0.22	NO
177	AKT2	AKT2	AKT2	12138	-0.025	0.22	NO
178	APH1A	APH1A	APH1A	12139	-0.025	0.22	NO
179	CDKN1B	CDKN1B	CDKN1B	12303	-0.027	0.22	NO
180	PIK3R2	PIK3R2	PIK3R2	12460	-0.029	0.21	NO
181	RPS6KB2	RPS6KB2	RPS6KB2	12462	-0.029	0.21	NO
182	MAPKAP1	MAPKAP1	MAPKAP1	12478	-0.029	0.21	NO
183	GRB2	GRB2	GRB2	12627	-0.031	0.2	NO
184	PRKCG	PRKCG	PRKCG	12791	-0.033	0.19	NO
185	MTOR	MTOR	MTOR	12792	-0.033	0.2	NO
186	MYD88	MYD88	MYD88	12859	-0.034	0.19	NO
187	MAPK14	MAPK14	MAPK14	12970	-0.035	0.19	NO
188	NRAS	NRAS	NRAS	13024	-0.036	0.19	NO
189	CASP9	CASP9	CASP9	13317	-0.04	0.17	NO
190	RPS6KA3	RPS6KA3	RPS6KA3	13891	-0.049	0.14	NO
191	ATF1	ATF1	ATF1	13988	-0.051	0.14	NO
192	AATF	AATF	AATF	14016	-0.052	0.14	NO
193	FOXO4	FOXO4	FOXO4	14432	-0.06	0.12	NO
194	PIK3R1	PIK3R1	PIK3R1	14604	-0.063	0.11	NO
195	NGEF	NGEF	NGEF	14660	-0.064	0.11	NO
196	RAF1	RAF1	RAF1	14721	-0.066	0.11	NO
197	ECT2	ECT2	ECT2	14806	-0.068	0.11	NO
198	BRAF	BRAF	BRAF	15109	-0.075	0.094	NO
199	PRKAR2A	PRKAR2A	PRKAR2A	15298	-0.081	0.087	NO
200	PPP2R5D	PPP2R5D	PPP2R5D	15351	-0.083	0.088	NO
201	NET1	NET1	NET1	15463	-0.087	0.085	NO
202	PCSK6	PCSK6	PCSK6	15792	-0.099	0.071	NO
203	PRKCA	PRKCA	PRKCA	16077	-0.11	0.06	NO
204	PHLPP1	PHLPP1	PHLPP1	16197	-0.12	0.058	NO
205	ITPR2	ITPR2	ITPR2	16227	-0.12	0.062	NO
206	ITGB3BP	ITGB3BP	ITGB3BP	16351	-0.13	0.061	NO
207	IRS1	IRS1	IRS1	16780	-0.16	0.044	NO
208	CDK1	CDK1	CDK1	17369	-0.23	0.02	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 INOSITOL PHOSPHATE METABOLISM.

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

genes ES table in pathway: KEGG GLYCEROPHOSPHOLIPID METABOLISM

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	PDE1A	PDE1A	PDE1A	18	0.85	0.15	YES
2	ADCY5	ADCY5	ADCY5	290	0.58	0.24	YES
3	PLA2G4A	PLA2G4A	PLA2G4A	325	0.56	0.34	YES
4	PRKAR2B	PRKAR2B	PRKAR2B	509	0.5	0.42	YES
5	ADCY2	ADCY2	ADCY2	781	0.43	0.49	YES
6	ADCY4	ADCY4	ADCY4	988	0.4	0.55	YES
7	CAMK4	CAMK4	CAMK4	1018	0.39	0.62	YES
8	ADCY3	ADCY3	ADCY3	1078	0.38	0.68	YES
9	PDE1B	PDE1B	PDE1B	1715	0.31	0.7	YES
10	ADCY7	ADCY7	ADCY7	2157	0.27	0.73	YES
11	PRKAR1B	PRKAR1B	PRKAR1B	2663	0.23	0.74	YES
12	ADCY1	ADCY1	ADCY1	5684	0.075	0.59	NO
13	CALM2	CALM2	CALM2	6772	0.048	0.53	NO
14	CALM1	CALM1	CALM1	7105	0.042	0.52	NO
15	ADCY9	ADCY9	ADCY9	7427	0.036	0.51	NO
16	PRKACA	PRKACA	PRKACA	7454	0.036	0.52	NO
17	CREB1	CREB1	CREB1	8078	0.026	0.49	NO
18	ADRBK1	ADRBK1	ADRBK1	8439	0.02	0.47	NO
19	ADCY6	ADCY6	ADCY6	9659	0.0049	0.4	NO
20	PRKCD	PRKCD	PRKCD	10070	-0.0005	0.38	NO
21	PRKAR1A	PRKAR1A	PRKAR1A	10944	-0.01	0.33	NO
22	PRKACB	PRKACB	PRKACB	11062	-0.012	0.33	NO
23	CALM3	CALM3	CALM3	11068	-0.012	0.33	NO
24	ADCY8	ADCY8	ADCY8	11454	-0.016	0.31	NO
25	MAPK1	MAPK1	MAPK1	11516	-0.017	0.31	NO
26	PRKCG	PRKCG	PRKCG	12791	-0.033	0.24	NO
27	PRKAR2A	PRKAR2A	PRKAR2A	15298	-0.081	0.12	NO
28	PRKCA	PRKCA	PRKCA	16077	-0.11	0.093	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 GLYCEROPHOSPHOLIPID METABOLISM.

Figure S76. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCEROPHOSPHOLIPID 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 ETHER LIPID METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	GATA2	GATA2	GATA2	788	0.43	0.11	YES
2	HDAC9	HDAC9	HDAC9	868	0.42	0.25	YES
3	CAMK4	CAMK4	CAMK4	1018	0.39	0.38	YES
4	GNG2	GNG2	GNG2	2289	0.26	0.4	YES
5	HDAC7	HDAC7	HDAC7	2718	0.23	0.46	YES
6	MEF2C	MEF2C	MEF2C	2748	0.23	0.54	YES
7	ESR1	ESR1	ESR1	4058	0.14	0.51	NO
8	YWHAB	YWHAB	YWHAB	6957	0.045	0.36	NO
9	NCOR2	NCOR2	NCOR2	7033	0.043	0.38	NO
10	UBE2I	UBE2I	UBE2I	7365	0.037	0.37	NO
11	GATA1	GATA1	GATA1	7828	0.029	0.35	NO
12	GNB1	GNB1	GNB1	8072	0.026	0.35	NO
13	HDAC10	HDAC10	HDAC10	8098	0.025	0.36	NO
14	RANBP2	RANBP2	RANBP2	8437	0.02	0.34	NO
15	ADRBK1	ADRBK1	ADRBK1	8439	0.02	0.35	NO
16	YWHAE	YWHAE	YWHAE	8847	0.014	0.33	NO
17	RANGAP1	RANGAP1	RANGAP1	9340	0.0085	0.31	NO
18	SRF	SRF	SRF	9690	0.0044	0.29	NO
19	HSP90AA1	HSP90AA1	HSP90AA1	10040	-0.00018	0.27	NO
20	RAN	RAN	RAN	10156	-0.0015	0.27	NO
21	HDAC3	HDAC3	HDAC3	10964	-0.011	0.22	NO
22	NR3C1	NR3C1	NR3C1	11192	-0.014	0.22	NO
23	SUMO1	SUMO1	SUMO1	11308	-0.015	0.22	NO
24	HDAC11	HDAC11	HDAC11	11348	-0.015	0.22	NO
25	TUBA1B	TUBA1B	TUBA1B	11613	-0.018	0.21	NO
26	BCOR	BCOR	BCOR	12006	-0.023	0.2	NO
27	TUBB2A	TUBB2A	TUBB2A	12334	-0.027	0.19	NO
28	HDAC5	HDAC5	HDAC5	12590	-0.03	0.18	NO
29	XPO1	XPO1	XPO1	12868	-0.034	0.18	NO
30	HDAC4	HDAC4	HDAC4	12872	-0.034	0.19	NO
31	RFXANK	RFXANK	RFXANK	13078	-0.037	0.19	NO
32	ANKRA2	ANKRA2	ANKRA2	14306	-0.057	0.14	NO
33	BCL6	BCL6	BCL6	14324	-0.058	0.16	NO
34	HDAC6	HDAC6	HDAC6	15399	-0.084	0.13	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 ETHER LIPID METABOLISM.

Figure S78. 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 ARACHIDONIC ACID METABOLISM

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

Rank	GENE	SYMBOL	DESC	LIST.LOC	S2N	RES	CORE_ENRICHMENT
1	PRICKLE1	PRICKLE1	PRICKLE1	23	0.84	0.032	YES
2	SFRP4	SFRP4	SFRP4	44	0.77	0.062	YES
3	SFRP1	SFRP1	SFRP1	92	0.72	0.088	YES
4	MAPK10	MAPK10	MAPK10	129	0.68	0.11	YES
5	WNT2	WNT2	WNT2	163	0.66	0.14	YES
6	DKK2	DKK2	DKK2	167	0.66	0.16	YES
7	FZD2	FZD2	FZD2	217	0.62	0.19	YES
8	WNT4	WNT4	WNT4	227	0.61	0.21	YES
9	MMP7	MMP7	MMP7	246	0.6	0.23	YES
10	WNT2B	WNT2B	WNT2B	278	0.59	0.26	YES
11	NKD2	NKD2	NKD2	286	0.58	0.28	YES
12	PLCB4	PLCB4	PLCB4	346	0.55	0.3	YES
13	SFRP5	SFRP5	SFRP5	423	0.53	0.31	YES
14	FZD10	FZD10	FZD10	454	0.52	0.33	YES
15	VANGL2	VANGL2	VANGL2	555	0.49	0.35	YES
16	NFATC1	NFATC1	NFATC1	577	0.48	0.36	YES
17	WNT10A	WNT10A	WNT10A	592	0.48	0.38	YES
18	FZD8	FZD8	FZD8	722	0.44	0.39	YES
19	WNT9A	WNT9A	WNT9A	737	0.44	0.41	YES
20	FZD7	FZD7	FZD7	762	0.44	0.43	YES
21	FZD1	FZD1	FZD1	768	0.44	0.44	YES
22	SOX17	SOX17	SOX17	880	0.41	0.45	YES
23	PRKX	PRKX	PRKX	881	0.41	0.47	YES
24	WNT10B	WNT10B	WNT10B	912	0.41	0.48	YES
25	CTBP2	CTBP2	CTBP2	1010	0.39	0.5	YES
26	PRICKLE2	PRICKLE2	PRICKLE2	1043	0.39	0.51	YES
27	WNT7B	WNT7B	WNT7B	1053	0.39	0.52	YES
28	SFRP2	SFRP2	SFRP2	1069	0.39	0.54	YES
29	CCND2	CCND2	CCND2	1302	0.36	0.54	YES
30	NFATC4	NFATC4	NFATC4	1333	0.35	0.55	YES
31	FOSL1	FOSL1	FOSL1	1466	0.34	0.56	YES
32	PRKCB	PRKCB	PRKCB	1573	0.32	0.56	YES
33	WNT7A	WNT7A	WNT7A	1651	0.32	0.57	YES
34	WNT11	WNT11	WNT11	1706	0.31	0.58	YES
35	PLCB2	PLCB2	PLCB2	1713	0.31	0.59	YES
36	RAC2	RAC2	RAC2	1994	0.28	0.59	NO
37	WNT1	WNT1	WNT1	2204	0.27	0.59	NO
38	LEF1	LEF1	LEF1	2368	0.26	0.59	NO
39	WNT3A	WNT3A	WNT3A	2950	0.21	0.56	NO
40	FZD6	FZD6	FZD6	3333	0.19	0.55	NO
41	WNT9B	WNT9B	WNT9B	3524	0.18	0.55	NO
42	WNT6	WNT6	WNT6	3527	0.18	0.55	NO
43	CAMK2B	CAMK2B	CAMK2B	3529	0.18	0.56	NO
44	MYC	MYC	MYC	3924	0.15	0.55	NO
45	CAMK2A	CAMK2A	CAMK2A	4097	0.14	0.54	NO
46	TP53	TP53	TP53	4293	0.13	0.54	NO
47	FZD3	FZD3	FZD3	4381	0.13	0.54	NO
48	CCND3	CCND3	CCND3	4736	0.11	0.52	NO
49	APC2	APC2	APC2	4843	0.11	0.52	NO
50	WNT16	WNT16	WNT16	5066	0.097	0.51	NO
51	AXIN1	AXIN1	AXIN1	5208	0.092	0.5	NO
52	VANGL1	VANGL1	VANGL1	5260	0.09	0.5	NO
53	NFATC2	NFATC2	NFATC2	5290	0.09	0.51	NO
54	CCND1	CCND1	CCND1	5318	0.088	0.51	NO
55	PPARD	PPARD	PPARD	5335	0.088	0.51	NO
56	PORCN	PORCN	PORCN	5357	0.086	0.51	NO
57	PPP3CC	PPP3CC	PPP3CC	5660	0.076	0.5	NO
58	PPP3CA	PPP3CA	PPP3CA	5663	0.076	0.5	NO
59	PPP2CB	PPP2CB	PPP2CB	5670	0.076	0.5	NO
60	PLCB3	PLCB3	PLCB3	5700	0.075	0.51	NO
61	DAAM2	DAAM2	DAAM2	6004	0.067	0.49	NO
62	PPP2R5E	PPP2R5E	PPP2R5E	6053	0.065	0.49	NO
63	WNT5B	WNT5B	WNT5B	6054	0.065	0.5	NO
64	FBXW11	FBXW11	FBXW11	6330	0.058	0.48	NO
65	CSNK1E	CSNK1E	CSNK1E	6365	0.057	0.48	NO
66	WNT5A	WNT5A	WNT5A	6508	0.054	0.48	NO
67	FZD4	FZD4	FZD4	6565	0.053	0.48	NO
68	PPP2R1A	PPP2R1A	PPP2R1A	6706	0.05	0.47	NO
69	NFAT5	NFAT5	NFAT5	6844	0.047	0.46	NO
70	DAAM1	DAAM1	DAAM1	7004	0.044	0.46	NO
71	SMAD2	SMAD2	SMAD2	7165	0.041	0.45	NO
72	CAMK2D	CAMK2D	CAMK2D	7180	0.041	0.45	NO
73	RAC1	RAC1	RAC1	7184	0.041	0.45	NO
74	PRKACA	PRKACA	PRKACA	7454	0.036	0.44	NO
75	JUN	JUN	JUN	7666	0.032	0.43	NO
76	ROCK1	ROCK1	ROCK1	7688	0.032	0.43	NO
77	SKP1	SKP1	SKP1	7746	0.031	0.42	NO
78	PPP3CB	PPP3CB	PPP3CB	7852	0.029	0.42	NO
79	CHP2	CHP2	CHP2	8040	0.026	0.41	NO
80	CSNK1A1	CSNK1A1	CSNK1A1	8054	0.026	0.41	NO
81	CHP	CHP	CHP	8083	0.026	0.41	NO
82	APC	APC	APC	8139	0.025	0.41	NO
83	PPP2R5B	PPP2R5B	PPP2R5B	8310	0.022	0.4	NO
84	SIAH1	SIAH1	SIAH1	8398	0.021	0.39	NO
85	TCF7L1	TCF7L1	TCF7L1	8490	0.019	0.39	NO
86	MAPK9	MAPK9	MAPK9	8612	0.018	0.38	NO
87	TBL1XR1	TBL1XR1	TBL1XR1	9038	0.012	0.36	NO
88	PSEN1	PSEN1	PSEN1	9100	0.011	0.36	NO
89	CSNK2A1	CSNK2A1	CSNK2A1	9148	0.011	0.36	NO
90	RHOA	RHOA	RHOA	9181	0.01	0.35	NO
91	MAPK8	MAPK8	MAPK8	9314	0.0088	0.35	NO
92	CAMK2G	CAMK2G	CAMK2G	9412	0.0076	0.34	NO
93	RBX1	RBX1	RBX1	9603	0.0055	0.33	NO
94	CREBBP	CREBBP	CREBBP	9745	0.0037	0.32	NO
95	TCF7L2	TCF7L2	TCF7L2	9834	0.0026	0.32	NO
96	CSNK2A2	CSNK2A2	CSNK2A2	9904	0.0016	0.31	NO
97	WNT3	WNT3	WNT3	9961	0.00079	0.31	NO
98	RUVBL1	RUVBL1	RUVBL1	10292	-0.003	0.29	NO
99	PPP2CA	PPP2CA	PPP2CA	10385	-0.0042	0.29	NO
100	SMAD4	SMAD4	SMAD4	10554	-0.006	0.28	NO
101	SMAD3	SMAD3	SMAD3	10611	-0.0066	0.28	NO
102	PPP2R5C	PPP2R5C	PPP2R5C	10660	-0.0073	0.27	NO
103	CTBP1	CTBP1	CTBP1	10801	-0.0088	0.26	NO
104	LRP5	LRP5	LRP5	10873	-0.0096	0.26	NO
105	PRKACB	PRKACB	PRKACB	11062	-0.012	0.25	NO
106	CUL1	CUL1	CUL1	11290	-0.014	0.24	NO
107	GSK3B	GSK3B	GSK3B	11371	-0.016	0.23	NO
108	BTRC	BTRC	BTRC	11415	-0.016	0.23	NO
109	CHD8	CHD8	CHD8	11575	-0.018	0.22	NO
110	DVL3	DVL3	DVL3	11676	-0.019	0.22	NO
111	AXIN2	AXIN2	AXIN2	11886	-0.022	0.21	NO
112	PPP2R1B	PPP2R1B	PPP2R1B	12000	-0.023	0.2	NO
113	PPP3R1	PPP3R1	PPP3R1	12222	-0.026	0.19	NO
114	EP300	EP300	EP300	12280	-0.026	0.19	NO
115	DVL1	DVL1	DVL1	12691	-0.032	0.17	NO
116	LRP6	LRP6	LRP6	12744	-0.032	0.16	NO
117	MAP3K7	MAP3K7	MAP3K7	12788	-0.033	0.16	NO
118	PRKCG	PRKCG	PRKCG	12791	-0.033	0.16	NO
119	CTNNB1	CTNNB1	CTNNB1	12794	-0.033	0.17	NO
120	PPP2R5A	PPP2R5A	PPP2R5A	12850	-0.034	0.16	NO
121	FRAT2	FRAT2	FRAT2	12882	-0.034	0.16	NO
122	FZD9	FZD9	FZD9	12965	-0.035	0.16	NO
123	NLK	NLK	NLK	13325	-0.04	0.14	NO
124	DVL2	DVL2	DVL2	13504	-0.043	0.13	NO
125	NFATC3	NFATC3	NFATC3	13724	-0.046	0.12	NO
126	ROCK2	ROCK2	ROCK2	13989	-0.051	0.11	NO
127	CSNK1A1L	CSNK1A1L	CSNK1A1L	14097	-0.053	0.11	NO
128	CACYBP	CACYBP	CACYBP	14381	-0.059	0.093	NO
129	CSNK2B	CSNK2B	CSNK2B	14724	-0.066	0.076	NO
130	DKK1	DKK1	DKK1	14775	-0.067	0.076	NO
131	FRAT1	FRAT1	FRAT1	14920	-0.071	0.07	NO
132	SENP2	SENP2	SENP2	14951	-0.072	0.072	NO
133	FZD5	FZD5	FZD5	15058	-0.074	0.069	NO
134	TBL1X	TBL1X	TBL1X	15342	-0.083	0.056	NO
135	PPP2R5D	PPP2R5D	PPP2R5D	15351	-0.083	0.059	NO
136	CXXC4	CXXC4	CXXC4	15572	-0.091	0.05	NO
137	CTNNBIP1	CTNNBIP1	CTNNBIP1	15750	-0.097	0.044	NO
138	TBL1Y	TBL1Y	TBL1Y	15976	-0.11	0.035	NO
139	PLCB1	PLCB1	PLCB1	16060	-0.11	0.035	NO
140	PRKCA	PRKCA	PRKCA	16077	-0.11	0.039	NO
141	DKK4	DKK4	DKK4	16819	-0.16	0.0031	NO
142	NKD1	NKD1	NKD1	16854	-0.17	0.008	NO
143	WNT8B	WNT8B	WNT8B	17365	-0.23	-0.012	NO
144	TCF7	TCF7	TCF7	17390	-0.24	-0.0036	NO
145	RAC3	RAC3	RAC3	17526	-0.27	-0.0004	NO
146	WIF1	WIF1	WIF1	17588	-0.3	0.008	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 ARACHIDONIC ACID METABOLISM.

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

Fold change

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

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

Expression level

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

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

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

Significant gene list

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

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

Subtype clus5 enriched pathways

Table 7. Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS	27	genes.ES.table	0.7	1.4	0.1	1	0.99	0.52	0.089	0.47	0.85	0.43
KEGG FATTY ACID METABOLISM	40	genes.ES.table	0.67	1.5	0.047	1	0.97	0.7	0.2	0.56	1	0.57
KEGG STEROID HORMONE BIOSYNTHESIS	52	genes.ES.table	0.67	1.4	0.077	1	0.99	0.6	0.12	0.52	0.9	0.46
KEGG LYSINE DEGRADATION	44	genes.ES.table	0.42	1.4	0.17	1	1	0.39	0.2	0.31	0.84	0.42
KEGG TYROSINE METABOLISM	40	genes.ES.table	0.56	1.5	0.037	1	0.98	0.4	0.11	0.36	1	0.51
KEGG BUTANOATE METABOLISM	31	genes.ES.table	0.56	1.4	0.14	1	0.99	0.52	0.14	0.44	0.8	0.4
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM	39	genes.ES.table	0.66	1.5	0.047	1	0.96	0.49	0.14	0.42	1	0.66
KEGG AMINOACYL TRNA BIOSYNTHESIS	41	genes.ES.table	0.38	1.4	0.15	1	0.99	1	0.62	0.38	0.92	0.46
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450	66	genes.ES.table	0.65	1.5	0.048	1	0.99	0.61	0.13	0.53	0.92	0.46
KEGG DRUG METABOLISM CYTOCHROME P450	69	genes.ES.table	0.62	1.4	0.12	0.98	1	0.61	0.13	0.53	0.79	0.39

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

Table S41. 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	AR	AR	AR	145	0.54	0.1	YES
2	CDK6	CDK6	CDK6	173	0.49	0.2	YES
3	KLK2	KLK2	KLK2	742	0.24	0.22	YES
4	NCOA2	NCOA2	NCOA2	869	0.22	0.25	YES
5	TGIF1	TGIF1	TGIF1	1130	0.19	0.28	YES
6	LATS2	LATS2	LATS2	1348	0.16	0.3	YES
7	CCND1	CCND1	CCND1	1500	0.15	0.32	YES
8	PIAS1	PIAS1	PIAS1	1771	0.13	0.33	YES
9	NRIP1	NRIP1	NRIP1	1778	0.13	0.35	YES
10	NCOA4	NCOA4	NCOA4	1973	0.11	0.36	YES
11	RPS6KA3	RPS6KA3	RPS6KA3	1989	0.11	0.38	YES
12	CTNNB1	CTNNB1	CTNNB1	2081	0.11	0.4	YES
13	KDM4C	KDM4C	KDM4C	2083	0.11	0.42	YES
14	NKX3-1	NKX3-1	NKX3-1	2254	0.099	0.43	YES
15	SVIL	SVIL	SVIL	3807	0.047	0.35	NO
16	KDM3A	KDM3A	KDM3A	4452	0.034	0.32	NO
17	CTDSP1	CTDSP1	CTDSP1	4599	0.031	0.32	NO
18	RANBP9	RANBP9	RANBP9	4601	0.031	0.33	NO
19	HIP1	HIP1	HIP1	4801	0.027	0.32	NO
20	PRDX1	PRDX1	PRDX1	4906	0.025	0.32	NO
21	ZNF318	ZNF318	ZNF318	5023	0.023	0.32	NO
22	MED1	MED1	MED1	5082	0.022	0.32	NO
23	UBE3A	UBE3A	UBE3A	5472	0.015	0.3	NO
24	UBA3	UBA3	UBA3	5778	0.0097	0.29	NO
25	TMF1	TMF1	TMF1	5988	0.0064	0.28	NO
26	PATZ1	PATZ1	PATZ1	6118	0.0044	0.27	NO
27	HNRNPA1	HNRNPA1	HNRNPA1	6262	0.0023	0.26	NO
28	KDM1A	KDM1A	KDM1A	6338	0.0012	0.26	NO
29	FKBP4	FKBP4	FKBP4	6469	-0.00085	0.25	NO
30	CDK11B	CDK11B	CDK11B	6476	-0.001	0.25	NO
31	XRCC6	XRCC6	XRCC6	6530	-0.0018	0.25	NO
32	CCND3	CCND3	CCND3	6831	-0.0065	0.23	NO
33	CTDSP2	CTDSP2	CTDSP2	7213	-0.012	0.21	NO
34	PELP1	PELP1	PELP1	7251	-0.013	0.21	NO
35	NCOA6	NCOA6	NCOA6	7335	-0.014	0.21	NO
36	SRF	SRF	SRF	7545	-0.017	0.2	NO
37	CDKN2A	CDKN2A	CDKN2A	8073	-0.025	0.18	NO
38	GSN	GSN	GSN	8123	-0.026	0.18	NO
39	CASP8	CASP8	CASP8	8375	-0.03	0.17	NO
40	PRKDC	PRKDC	PRKDC	8514	-0.032	0.17	NO
41	XRCC5	XRCC5	XRCC5	8521	-0.032	0.18	NO
42	PIAS4	PIAS4	PIAS4	8594	-0.034	0.18	NO
43	UBE2I	UBE2I	UBE2I	8731	-0.036	0.18	NO
44	CARM1	CARM1	CARM1	8741	-0.036	0.19	NO
45	FHL2	FHL2	FHL2	8883	-0.039	0.19	NO
46	PA2G4	PA2G4	PA2G4	9222	-0.044	0.18	NO
47	APPL1	APPL1	APPL1	9424	-0.048	0.18	NO
48	PIAS3	PIAS3	PIAS3	9495	-0.049	0.18	NO
49	PTK2B	PTK2B	PTK2B	9596	-0.051	0.19	NO
50	SNURF	SNURF	SNURF	9837	-0.056	0.18	NO
51	BRCA1	BRCA1	BRCA1	10001	-0.06	0.19	NO
52	TMPRSS2	TMPRSS2	TMPRSS2	10158	-0.063	0.19	NO
53	MAK	MAK	MAK	11178	-0.091	0.15	NO
54	AKT1	AKT1	AKT1	11395	-0.098	0.16	NO
55	PAWR	PAWR	PAWR	11737	-0.11	0.16	NO
56	TCF4	TCF4	TCF4	11994	-0.12	0.17	NO
57	CMTM2	CMTM2	CMTM2	12964	-0.16	0.15	NO
58	ZMIZ1	ZMIZ1	ZMIZ1	13221	-0.17	0.17	NO
59	TGFB1I1	TGFB1I1	TGFB1I1	13987	-0.21	0.17	NO
60	VAV3	VAV3	VAV3	14205	-0.22	0.2	NO

Figure S81. 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS.

Figure S82. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, 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 FATTY ACID METABOLISM

Table S42. 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	RDBP	RDBP	RDBP	3630	0.051	-0.14	YES
2	POLR2C	POLR2C	POLR2C	3748	0.048	-0.079	YES
3	TCEA1	TCEA1	TCEA1	4650	0.03	-0.09	YES
4	TCEB1	TCEB1	TCEB1	4847	0.026	-0.067	YES
5	POLR2F	POLR2F	POLR2F	5109	0.021	-0.054	YES
6	WHSC2	WHSC2	WHSC2	5158	0.02	-0.03	YES
7	TH1L	TH1L	TH1L	5257	0.018	-0.011	YES
8	SUPT4H1	SUPT4H1	SUPT4H1	5287	0.018	0.011	YES
9	POLR2J	POLR2J	POLR2J	5384	0.016	0.027	YES
10	TCEB2	TCEB2	TCEB2	5438	0.015	0.044	YES
11	POLR2L	POLR2L	POLR2L	5869	0.0084	0.031	YES
12	CDK9	CDK9	CDK9	5876	0.0082	0.042	YES
13	TCEB3	TCEB3	TCEB3	5902	0.0078	0.051	YES
14	CCNT1	CCNT1	CCNT1	6023	0.0058	0.052	YES
15	POLR2A	POLR2A	POLR2A	6049	0.0054	0.058	YES
16	POLR2K	POLR2K	POLR2K	6111	0.0045	0.06	YES
17	GTF2F2	GTF2F2	GTF2F2	6745	-0.0053	0.031	YES
18	POLR2B	POLR2B	POLR2B	6859	-0.0073	0.035	YES
19	POLR2E	POLR2E	POLR2E	6916	-0.008	0.042	YES
20	SUPT16H	SUPT16H	SUPT16H	7509	-0.017	0.031	YES
21	CTDP1	CTDP1	CTDP1	7652	-0.019	0.048	YES
22	CCNT2	CCNT2	CCNT2	7759	-0.02	0.069	YES
23	GTF2F1	GTF2F1	GTF2F1	7784	-0.021	0.096	YES
24	COBRA1	COBRA1	COBRA1	7892	-0.022	0.12	YES
25	POLR2G	POLR2G	POLR2G	8873	-0.038	0.12	YES
26	POLR2D	POLR2D	POLR2D	8992	-0.04	0.16	YES
27	POLR2H	POLR2H	POLR2H	9066	-0.042	0.21	YES
28	SUPT5H	SUPT5H	SUPT5H	9078	-0.042	0.27	YES
29	SSRP1	SSRP1	SSRP1	9303	-0.046	0.32	YES
30	POLR2I	POLR2I	POLR2I	9351	-0.047	0.38	YES
31	ELL	ELL	ELL	10554	-0.072	0.4	YES

Figure S83. 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 FATTY ACID METABOLISM.

Figure S84. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FATTY ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

Table S43. 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	UGT1A3	UGT1A3	UGT1A3	57	0.77	0.1	YES
2	UGT1A5	UGT1A5	UGT1A5	63	0.76	0.21	YES
3	UGT1A4	UGT1A4	UGT1A4	76	0.69	0.3	YES
4	UGT1A1	UGT1A1	UGT1A1	178	0.49	0.36	YES
5	UGT1A9	UGT1A9	UGT1A9	318	0.38	0.41	YES
6	UGT2B28	UGT2B28	UGT2B28	485	0.31	0.44	YES
7	UGT1A6	UGT1A6	UGT1A6	492	0.31	0.49	YES
8	ALAS1	ALAS1	ALAS1	530	0.3	0.52	YES
9	UGT2B10	UGT2B10	UGT2B10	576	0.28	0.56	YES
10	UGT2B7	UGT2B7	UGT2B7	880	0.22	0.57	YES
11	ALAD	ALAD	ALAD	1075	0.19	0.59	YES
12	UGT2B11	UGT2B11	UGT2B11	1116	0.19	0.61	YES
13	UGT1A8	UGT1A8	UGT1A8	1251	0.17	0.63	YES
14	MMAB	MMAB	MMAB	1455	0.15	0.64	YES
15	UGT2B4	UGT2B4	UGT2B4	1580	0.14	0.65	YES
16	BLVRB	BLVRB	BLVRB	1867	0.12	0.65	YES
17	UGT2B15	UGT2B15	UGT2B15	2182	0.1	0.65	YES
18	HMOX2	HMOX2	HMOX2	2290	0.097	0.66	YES
19	EARS2	EARS2	EARS2	2411	0.091	0.66	YES
20	PPOX	PPOX	PPOX	2733	0.079	0.66	NO
21	FECH	FECH	FECH	2869	0.074	0.66	NO
22	COX15	COX15	COX15	3390	0.058	0.64	NO
23	UROS	UROS	UROS	3482	0.056	0.64	NO
24	UROD	UROD	UROD	5590	0.013	0.52	NO
25	CPOX	CPOX	CPOX	5875	0.0082	0.51	NO
26	EPRS	EPRS	EPRS	6012	0.0061	0.5	NO
27	HCCS	HCCS	HCCS	6213	0.003	0.49	NO
28	COX10	COX10	COX10	6252	0.0024	0.49	NO
29	UGT1A7	UGT1A7	UGT1A7	6794	-0.0059	0.46	NO
30	HMBS	HMBS	HMBS	7254	-0.013	0.43	NO
31	ALAS2	ALAS2	ALAS2	7491	-0.016	0.42	NO
32	FTH1	FTH1	FTH1	8711	-0.036	0.36	NO
33	GUSB	GUSB	GUSB	9784	-0.055	0.3	NO
34	HMOX1	HMOX1	HMOX1	11149	-0.09	0.24	NO
35	CP	CP	CP	12185	-0.13	0.2	NO
36	UGT2A1	UGT2A1	UGT2A1	12752	-0.15	0.19	NO
37	UGT1A10	UGT1A10	UGT1A10	12989	-0.16	0.2	NO
38	UGT2A3	UGT2A3	UGT2A3	13750	-0.2	0.18	NO
39	BLVRA	BLVRA	BLVRA	15725	-0.32	0.11	NO

Figure S85. 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 STEROID HORMONE BIOSYNTHESIS.

Figure S86. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STEROID HORMONE 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 LYSINE DEGRADATION

Table S44. 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	ACSL6	ACSL6	ACSL6	55	0.78	0.12	YES
2	ACSL5	ACSL5	ACSL5	176	0.49	0.18	YES
3	ADH1B	ADH1B	ADH1B	197	0.47	0.26	YES
4	ADH4	ADH4	ADH4	235	0.44	0.32	YES
5	ADH6	ADH6	ADH6	255	0.43	0.39	YES
6	EHHADH	EHHADH	EHHADH	644	0.26	0.4	YES
7	ADH1C	ADH1C	ADH1C	718	0.25	0.44	YES
8	ADH7	ADH7	ADH7	879	0.22	0.46	YES
9	ALDH3A2	ALDH3A2	ALDH3A2	886	0.22	0.5	YES
10	ACADL	ACADL	ACADL	1082	0.19	0.52	YES
11	HADH	HADH	HADH	1290	0.17	0.53	YES
12	ALDH1B1	ALDH1B1	ALDH1B1	1406	0.16	0.55	YES
13	ALDH2	ALDH2	ALDH2	1410	0.16	0.57	YES
14	GCDH	GCDH	GCDH	1450	0.15	0.59	YES
15	ACADSB	ACADSB	ACADSB	1566	0.14	0.61	YES
16	ACAA1	ACAA1	ACAA1	1682	0.13	0.62	YES
17	ADH5	ADH5	ADH5	1946	0.12	0.62	YES
18	ADH1A	ADH1A	ADH1A	1961	0.12	0.64	YES
19	CPT2	CPT2	CPT2	2074	0.11	0.65	YES
20	ACADM	ACADM	ACADM	2420	0.09	0.64	YES
21	ECHS1	ECHS1	ECHS1	2427	0.09	0.66	YES
22	CYP4A11	CYP4A11	CYP4A11	2874	0.074	0.64	YES
23	ACOX1	ACOX1	ACOX1	2962	0.071	0.65	YES
24	ALDH7A1	ALDH7A1	ALDH7A1	2998	0.07	0.66	YES
25	CPT1C	CPT1C	CPT1C	3085	0.067	0.66	YES
26	ALDH9A1	ALDH9A1	ALDH9A1	3220	0.062	0.66	YES
27	ACAA2	ACAA2	ACAA2	3471	0.056	0.66	YES
28	CYP4A22	CYP4A22	CYP4A22	3516	0.054	0.67	YES
29	ACSL1	ACSL1	ACSL1	4237	0.038	0.63	NO
30	ACADVL	ACADVL	ACADVL	4427	0.034	0.63	NO
31	ACAT1	ACAT1	ACAT1	4838	0.026	0.61	NO
32	ACSL3	ACSL3	ACSL3	5268	0.018	0.58	NO
33	HADHB	HADHB	HADHB	5635	0.012	0.57	NO
34	HADHA	HADHA	HADHA	5913	0.0076	0.55	NO
35	ACADS	ACADS	ACADS	8631	-0.034	0.4	NO
36	ACAT2	ACAT2	ACAT2	8904	-0.039	0.39	NO
37	ACOX3	ACOX3	ACOX3	9106	-0.042	0.39	NO
38	CPT1A	CPT1A	CPT1A	9209	-0.044	0.39	NO
39	CPT1B	CPT1B	CPT1B	12191	-0.13	0.24	NO
40	ACSL4	ACSL4	ACSL4	17151	-0.47	0.033	NO

Figure S87. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG LYSINE DEGRADATION.

Figure S88. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSINE DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG TYROSINE METABOLISM

Table S45. 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	SULT4A1	SULT4A1	SULT4A1	14	1	0.071	YES
2	UGT1A3	UGT1A3	UGT1A3	57	0.77	0.12	YES
3	UGT1A5	UGT1A5	UGT1A5	63	0.76	0.17	YES
4	CYP1A2	CYP1A2	CYP1A2	68	0.74	0.22	YES
5	UGT1A4	UGT1A4	UGT1A4	76	0.69	0.27	YES
6	SULT1B1	SULT1B1	SULT1B1	85	0.67	0.32	YES
7	UGT1A1	UGT1A1	UGT1A1	178	0.49	0.34	YES
8	GLYAT	GLYAT	GLYAT	184	0.48	0.38	YES
9	SULT2B1	SULT2B1	SULT2B1	285	0.41	0.4	YES
10	UGT1A9	UGT1A9	UGT1A9	318	0.38	0.42	YES
11	NAT2	NAT2	NAT2	382	0.35	0.45	YES
12	UGT2B28	UGT2B28	UGT2B28	485	0.31	0.46	YES
13	UGT1A6	UGT1A6	UGT1A6	492	0.31	0.48	YES
14	SULT2A1	SULT2A1	SULT2A1	533	0.3	0.5	YES
15	UGT2B10	UGT2B10	UGT2B10	576	0.28	0.52	YES
16	ACSM2B	ACSM2B	ACSM2B	591	0.28	0.54	YES
17	UGT2B7	UGT2B7	UGT2B7	880	0.22	0.54	YES
18	GCLC	GCLC	GCLC	1028	0.2	0.54	YES
19	MAT1A	MAT1A	MAT1A	1079	0.19	0.55	YES
20	UGT2B11	UGT2B11	UGT2B11	1116	0.19	0.56	YES
21	GSTM4	GSTM4	GSTM4	1216	0.18	0.57	YES
22	MGST1	MGST1	MGST1	1224	0.18	0.58	YES
23	UGT1A8	UGT1A8	UGT1A8	1251	0.17	0.59	YES
24	MTR	MTR	MTR	1299	0.17	0.6	YES
25	UGT2B4	UGT2B4	UGT2B4	1580	0.14	0.59	YES
26	MGST2	MGST2	MGST2	1626	0.14	0.6	YES
27	GCLM	GCLM	GCLM	1904	0.12	0.59	YES
28	SULT1E1	SULT1E1	SULT1E1	2132	0.1	0.59	YES
29	OPLAH	OPLAH	OPLAH	2143	0.1	0.59	YES
30	TPMT	TPMT	TPMT	2212	0.1	0.6	YES
31	GSTA4	GSTA4	GSTA4	2258	0.098	0.6	YES
32	MAT2B	MAT2B	MAT2B	2273	0.098	0.61	YES
33	ACSM1	ACSM1	ACSM1	2392	0.092	0.6	NO
34	GSTO1	GSTO1	GSTO1	2721	0.079	0.59	NO
35	CNDP2	CNDP2	CNDP2	2841	0.074	0.59	NO
36	GSTM1	GSTM1	GSTM1	2991	0.07	0.59	NO
37	SLC35D1	SLC35D1	SLC35D1	3747	0.048	0.55	NO
38	GSTA1	GSTA1	GSTA1	3918	0.044	0.54	NO
39	GSTA2	GSTA2	GSTA2	3940	0.044	0.54	NO
40	MGST3	MGST3	MGST3	4391	0.035	0.52	NO
41	COMT	COMT	COMT	4942	0.024	0.49	NO
42	GSS	GSS	GSS	5144	0.02	0.48	NO
43	PAPSS2	PAPSS2	PAPSS2	5482	0.015	0.46	NO
44	UGDH	UGDH	UGDH	6212	0.003	0.42	NO
45	UGT1A7	UGT1A7	UGT1A7	6794	-0.0059	0.39	NO
46	GGT7	GGT7	GGT7	6858	-0.0072	0.39	NO
47	GSTO2	GSTO2	GSTO2	7909	-0.022	0.33	NO
48	SULT1A3	SULT1A3	SULT1A3	7960	-0.024	0.33	NO
49	BPNT1	BPNT1	BPNT1	8189	-0.027	0.32	NO
50	AHCY	AHCY	AHCY	9095	-0.042	0.27	NO
51	UGP2	UGP2	UGP2	9256	-0.045	0.26	NO
52	PAPSS1	PAPSS1	PAPSS1	9542	-0.05	0.25	NO
53	NAT1	NAT1	NAT1	9629	-0.052	0.25	NO
54	GGCT	GGCT	GGCT	12216	-0.13	0.11	NO
55	SULT1A1	SULT1A1	SULT1A1	12297	-0.13	0.11	NO
56	MAT2A	MAT2A	MAT2A	12623	-0.14	0.11	NO
57	UGT2A1	UGT2A1	UGT2A1	12752	-0.15	0.11	NO
58	NNMT	NNMT	NNMT	14447	-0.24	0.029	NO
59	GSTM5	GSTM5	GSTM5	14772	-0.26	0.028	NO
60	SULT1A2	SULT1A2	SULT1A2	14875	-0.26	0.041	NO
61	SULT1C2	SULT1C2	SULT1C2	15647	-0.31	0.019	NO
62	SULT1C4	SULT1C4	SULT1C4	15728	-0.32	0.036	NO
63	GSTP1	GSTP1	GSTP1	16091	-0.35	0.04	NO
64	GGT1	GGT1	GGT1	16162	-0.35	0.06	NO
65	GGT5	GGT5	GGT5	16755	-0.41	0.055	NO

Figure S89. 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 TYROSINE METABOLISM.

Figure S90. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TYROSINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG BUTANOATE METABOLISM

Table S46. 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	ALDH3A1	ALDH3A1	ALDH3A1	5	1.2	0.15	YES
2	AOX1	AOX1	AOX1	191	0.48	0.2	YES
3	ADH1B	ADH1B	ADH1B	197	0.47	0.27	YES
4	HPD	HPD	HPD	230	0.44	0.32	YES
5	ADH4	ADH4	ADH4	235	0.44	0.38	YES
6	ADH6	ADH6	ADH6	255	0.43	0.44	YES
7	ADH1C	ADH1C	ADH1C	718	0.25	0.44	YES
8	HGD	HGD	HGD	791	0.23	0.47	YES
9	ADH7	ADH7	ADH7	879	0.22	0.49	YES
10	NAT6	NAT6	NAT6	934	0.21	0.52	YES
11	DDC	DDC	DDC	1226	0.17	0.52	YES
12	MAOA	MAOA	MAOA	1549	0.14	0.52	YES
13	MAOB	MAOB	MAOB	1551	0.14	0.54	YES
14	AOC2	AOC2	AOC2	1847	0.12	0.54	YES
15	ADH5	ADH5	ADH5	1946	0.12	0.55	YES
16	ADH1A	ADH1A	ADH1A	1961	0.12	0.56	YES
17	GSTZ1	GSTZ1	GSTZ1	2218	0.1	0.56	NO
18	TAT	TAT	TAT	2534	0.086	0.56	NO
19	LCMT2	LCMT2	LCMT2	2710	0.079	0.56	NO
20	DCT	DCT	DCT	2911	0.072	0.56	NO
21	HEMK1	HEMK1	HEMK1	3396	0.058	0.54	NO
22	PNMT	PNMT	PNMT	3451	0.056	0.54	NO
23	WBSCR22	WBSCR22	WBSCR22	4350	0.036	0.49	NO
24	GOT2	GOT2	GOT2	4529	0.033	0.49	NO
25	COMT	COMT	COMT	4942	0.024	0.47	NO
26	FAH	FAH	FAH	5838	0.009	0.42	NO
27	METTL6	METTL6	METTL6	6266	0.0022	0.39	NO
28	MIF	MIF	MIF	6495	-0.0014	0.38	NO
29	METTL2B	METTL2B	METTL2B	6783	-0.0058	0.37	NO
30	TRMT11	TRMT11	TRMT11	7047	-0.0099	0.35	NO
31	LCMT1	LCMT1	LCMT1	10264	-0.066	0.18	NO
32	AOC3	AOC3	AOC3	10790	-0.079	0.16	NO
33	TYRP1	TYRP1	TYRP1	10852	-0.08	0.17	NO
34	DBH	DBH	DBH	12740	-0.15	0.08	NO
35	GOT1	GOT1	GOT1	13352	-0.18	0.069	NO
36	TH	TH	TH	13511	-0.19	0.084	NO
37	ALDH1A3	ALDH1A3	ALDH1A3	14394	-0.24	0.065	NO
38	ALDH3B1	ALDH3B1	ALDH3B1	14629	-0.25	0.084	NO
39	ALDH3B2	ALDH3B2	ALDH3B2	15991	-0.34	0.052	NO
40	IL4I1	IL4I1	IL4I1	16181	-0.35	0.088	NO

Figure S91. 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 S92. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BUTANOATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM

Table S47. 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	SLC5A6	SLC5A6	SLC5A6	335	0.37	0.048	YES
2	SLC23A2	SLC23A2	SLC23A2	420	0.34	0.1	YES
3	GPHN	GPHN	GPHN	468	0.32	0.16	YES
4	MTHFD1	MTHFD1	MTHFD1	539	0.29	0.2	YES
5	MOCS2	MOCS2	MOCS2	1268	0.17	0.19	YES
6	PNPO	PNPO	PNPO	1311	0.16	0.22	YES
7	PANK1	PANK1	PANK1	1527	0.14	0.23	YES
8	SLC19A2	SLC19A2	SLC19A2	1623	0.14	0.25	YES
9	QPRT	QPRT	QPRT	1719	0.13	0.27	YES
10	MOCS1	MOCS1	MOCS1	1721	0.13	0.29	YES
11	CYB5A	CYB5A	CYB5A	1807	0.12	0.31	YES
12	SLC23A1	SLC23A1	SLC23A1	2123	0.11	0.31	YES
13	MOCS3	MOCS3	MOCS3	2170	0.1	0.33	YES
14	MOCOS	MOCOS	MOCOS	2175	0.1	0.35	YES
15	THTPA	THTPA	THTPA	2226	0.1	0.36	YES
16	NMNAT3	NMNAT3	NMNAT3	2487	0.088	0.36	YES
17	NFS1	NFS1	NFS1	2510	0.087	0.38	YES
18	ENPP1	ENPP1	ENPP1	2565	0.085	0.39	YES
19	GSTO1	GSTO1	GSTO1	2721	0.079	0.39	YES
20	COASY	COASY	COASY	2812	0.076	0.4	YES
21	SLC25A32	SLC25A32	SLC25A32	2919	0.072	0.41	YES
22	NMNAT1	NMNAT1	NMNAT1	3137	0.065	0.41	NO
23	SHMT1	SHMT1	SHMT1	3659	0.051	0.39	NO
24	AASDHPPT	AASDHPPT	AASDHPPT	3778	0.048	0.39	NO
25	FASN	FASN	FASN	4464	0.034	0.36	NO
26	NADK	NADK	NADK	4513	0.033	0.36	NO
27	SLC19A1	SLC19A1	SLC19A1	4800	0.027	0.35	NO
28	FLAD1	FLAD1	FLAD1	4846	0.026	0.35	NO
29	PANK2	PANK2	PANK2	4861	0.026	0.36	NO
30	FPGS	FPGS	FPGS	4899	0.025	0.36	NO
31	CYB5R3	CYB5R3	CYB5R3	5460	0.015	0.33	NO
32	PPCS	PPCS	PPCS	5476	0.015	0.33	NO
33	SLC46A1	SLC46A1	SLC46A1	5600	0.013	0.33	NO
34	PDXK	PDXK	PDXK	6264	0.0022	0.29	NO
35	SLC2A1	SLC2A1	SLC2A1	7346	-0.014	0.23	NO
36	PANK3	PANK3	PANK3	7891	-0.022	0.2	NO
37	GSTO2	GSTO2	GSTO2	7909	-0.022	0.21	NO
38	PANK4	PANK4	PANK4	9252	-0.045	0.14	NO
39	DHFR	DHFR	DHFR	9598	-0.051	0.13	NO
40	NADSYN1	NADSYN1	NADSYN1	10302	-0.066	0.1	NO
41	MTHFR	MTHFR	MTHFR	10321	-0.067	0.11	NO
42	SLC25A16	SLC25A16	SLC25A16	10754	-0.078	0.1	NO
43	RFK	RFK	RFK	10961	-0.084	0.1	NO
44	TPK1	TPK1	TPK1	11483	-0.1	0.092	NO
45	NAMPT	NAMPT	NAMPT	12503	-0.14	0.059	NO
46	SLC2A3	SLC2A3	SLC2A3	12633	-0.14	0.077	NO
47	PPCDC	PPCDC	PPCDC	12662	-0.14	0.1	NO
48	SLC19A3	SLC19A3	SLC19A3	14954	-0.27	0.02	NO
49	NMNAT2	NMNAT2	NMNAT2	15905	-0.33	0.025	NO
50	ACP5	ACP5	ACP5	16941	-0.44	0.044	NO

Figure S93. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM.

Figure S94. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

Table S48. 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	SLCO1B3	SLCO1B3	SLCO1B3	131	0.57	0.098	YES
2	AMACR	AMACR	AMACR	132	0.56	0.2	YES
3	CYP8B1	CYP8B1	CYP8B1	209	0.46	0.28	YES
4	SLC27A5	SLC27A5	SLC27A5	398	0.34	0.33	YES
5	CYP7B1	CYP7B1	CYP7B1	440	0.33	0.39	YES
6	ABCB11	ABCB11	ABCB11	453	0.32	0.45	YES
7	CH25H	CH25H	CH25H	553	0.29	0.5	YES
8	AKR1C4	AKR1C4	AKR1C4	723	0.25	0.53	YES
9	BAAT	BAAT	BAAT	884	0.22	0.56	YES
10	HSD17B4	HSD17B4	HSD17B4	918	0.21	0.6	YES
11	CYP27A1	CYP27A1	CYP27A1	926	0.21	0.64	YES
12	ACOX2	ACOX2	ACOX2	1163	0.18	0.66	YES
13	SLCO1B1	SLCO1B1	SLCO1B1	1334	0.16	0.68	YES
14	SLC10A1	SLC10A1	SLC10A1	1411	0.16	0.7	YES
15	CYP7A1	CYP7A1	CYP7A1	1920	0.12	0.69	YES
16	SCP2	SCP2	SCP2	2156	0.1	0.7	YES
17	CYP39A1	CYP39A1	CYP39A1	2312	0.096	0.71	YES
18	SLCO1A2	SLCO1A2	SLCO1A2	2326	0.095	0.72	YES
19	CYP46A1	CYP46A1	CYP46A1	3292	0.06	0.68	NO
20	SLC27A2	SLC27A2	SLC27A2	4782	0.027	0.6	NO
21	HSD3B7	HSD3B7	HSD3B7	5761	0.01	0.55	NO
22	ACOT8	ACOT8	ACOT8	8117	-0.026	0.42	NO
23	ALB	ALB	ALB	9661	-0.052	0.34	NO
24	ABCC3	ABCC3	ABCC3	12082	-0.12	0.23	NO
25	AKR1D1	AKR1D1	AKR1D1	12591	-0.14	0.22	NO
26	FABP6	FABP6	FABP6	16229	-0.36	0.085	NO

Figure S95. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS.

Figure S96. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450

Table S49. 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	ALDH3A1	ALDH3A1	ALDH3A1	5	1.2	0.064	YES
2	CYP1A1	CYP1A1	CYP1A1	18	1	0.12	YES
3	UGT1A3	UGT1A3	UGT1A3	57	0.77	0.16	YES
4	UGT1A5	UGT1A5	UGT1A5	63	0.76	0.2	YES
5	CYP1A2	CYP1A2	CYP1A2	68	0.74	0.24	YES
6	UGT1A4	UGT1A4	UGT1A4	76	0.69	0.28	YES
7	CYP3A4	CYP3A4	CYP3A4	87	0.66	0.32	YES
8	CYP2E1	CYP2E1	CYP2E1	92	0.65	0.35	YES
9	UGT1A1	UGT1A1	UGT1A1	178	0.49	0.37	YES
10	ADH1B	ADH1B	ADH1B	197	0.47	0.4	YES
11	ADH4	ADH4	ADH4	235	0.44	0.42	YES
12	ADH6	ADH6	ADH6	255	0.43	0.44	YES
13	UGT1A9	UGT1A9	UGT1A9	318	0.38	0.46	YES
14	CYP2C9	CYP2C9	CYP2C9	418	0.34	0.47	YES
15	CYP3A43	CYP3A43	CYP3A43	444	0.33	0.49	YES
16	UGT2B28	UGT2B28	UGT2B28	485	0.31	0.5	YES
17	UGT1A6	UGT1A6	UGT1A6	492	0.31	0.52	YES
18	AKR1C2	AKR1C2	AKR1C2	501	0.31	0.54	YES
19	UGT2B10	UGT2B10	UGT2B10	576	0.28	0.55	YES
20	AKR1C1	AKR1C1	AKR1C1	666	0.26	0.56	YES
21	ADH1C	ADH1C	ADH1C	718	0.25	0.57	YES
22	AKR1C4	AKR1C4	AKR1C4	723	0.25	0.58	YES
23	CYP2C19	CYP2C19	CYP2C19	758	0.24	0.59	YES
24	ADH7	ADH7	ADH7	879	0.22	0.6	YES
25	UGT2B7	UGT2B7	UGT2B7	880	0.22	0.61	YES
26	UGT2B11	UGT2B11	UGT2B11	1116	0.19	0.61	YES
27	GSTM4	GSTM4	GSTM4	1216	0.18	0.61	YES
28	MGST1	MGST1	MGST1	1224	0.18	0.62	YES
29	EPHX1	EPHX1	EPHX1	1229	0.17	0.63	YES
30	UGT1A8	UGT1A8	UGT1A8	1251	0.17	0.64	YES
31	GSTM3	GSTM3	GSTM3	1254	0.17	0.65	YES
32	UGT2B4	UGT2B4	UGT2B4	1580	0.14	0.64	YES
33	MGST2	MGST2	MGST2	1626	0.14	0.64	YES
34	CYP2C8	CYP2C8	CYP2C8	1912	0.12	0.63	YES
35	ADH5	ADH5	ADH5	1946	0.12	0.64	YES
36	ADH1A	ADH1A	ADH1A	1961	0.12	0.64	YES
37	GSTM2	GSTM2	GSTM2	1995	0.11	0.65	YES
38	UGT2B15	UGT2B15	UGT2B15	2182	0.1	0.64	YES
39	GSTZ1	GSTZ1	GSTZ1	2218	0.1	0.65	YES
40	GSTA4	GSTA4	GSTA4	2258	0.098	0.65	YES
41	GSTO1	GSTO1	GSTO1	2721	0.079	0.63	NO
42	CYP1B1	CYP1B1	CYP1B1	2766	0.077	0.63	NO
43	GSTM1	GSTM1	GSTM1	2991	0.07	0.62	NO
44	GSTK1	GSTK1	GSTK1	3147	0.065	0.62	NO
45	GSTT1	GSTT1	GSTT1	3915	0.044	0.57	NO
46	GSTA1	GSTA1	GSTA1	3918	0.044	0.58	NO
47	GSTA2	GSTA2	GSTA2	3940	0.044	0.58	NO
48	CYP3A5	CYP3A5	CYP3A5	4068	0.042	0.57	NO
49	MGST3	MGST3	MGST3	4391	0.035	0.56	NO
50	CYP2B6	CYP2B6	CYP2B6	5306	0.018	0.51	NO
51	AKR1C3	AKR1C3	AKR1C3	5355	0.017	0.5	NO
52	UGT1A7	UGT1A7	UGT1A7	6794	-0.0059	0.42	NO
53	GSTO2	GSTO2	GSTO2	7909	-0.022	0.36	NO
54	UGT2A1	UGT2A1	UGT2A1	12752	-0.15	0.096	NO
55	UGT1A10	UGT1A10	UGT1A10	12989	-0.16	0.091	NO
56	UGT2A3	UGT2A3	UGT2A3	13750	-0.2	0.059	NO
57	ALDH1A3	ALDH1A3	ALDH1A3	14394	-0.24	0.036	NO
58	ALDH3B1	ALDH3B1	ALDH3B1	14629	-0.25	0.036	NO
59	CYP2C18	CYP2C18	CYP2C18	14766	-0.26	0.043	NO
60	GSTM5	GSTM5	GSTM5	14772	-0.26	0.057	NO
61	GSTT2	GSTT2	GSTT2	15066	-0.28	0.055	NO
62	CYP2S1	CYP2S1	CYP2S1	15460	-0.3	0.05	NO
63	ALDH3B2	ALDH3B2	ALDH3B2	15991	-0.34	0.038	NO
64	GSTP1	GSTP1	GSTP1	16091	-0.35	0.052	NO
65	DHDH	DHDH	DHDH	16156	-0.35	0.068	NO
66	CYP3A7	CYP3A7	CYP3A7	16514	-0.38	0.069	NO

Figure S97. 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 METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S98. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, 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 CYTOCHROME P450

Table S50. 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	ACSL6	ACSL6	ACSL6	55	0.78	0.077	YES
2	AMACR	AMACR	AMACR	132	0.56	0.13	YES
3	ACSL5	ACSL5	ACSL5	176	0.49	0.18	YES
4	HAO1	HAO1	HAO1	602	0.27	0.18	YES
5	EHHADH	EHHADH	EHHADH	644	0.26	0.21	YES
6	PEX11G	PEX11G	PEX11G	715	0.25	0.23	YES
7	PEX12	PEX12	PEX12	810	0.23	0.25	YES
8	BAAT	BAAT	BAAT	884	0.22	0.27	YES
9	HSD17B4	HSD17B4	HSD17B4	918	0.21	0.29	YES
10	PEX11A	PEX11A	PEX11A	981	0.21	0.3	YES
11	DAO	DAO	DAO	1152	0.18	0.31	YES
12	ACOX2	ACOX2	ACOX2	1163	0.18	0.33	YES
13	PECR	PECR	PECR	1237	0.17	0.34	YES
14	MLYCD	MLYCD	MLYCD	1380	0.16	0.35	YES
15	GNPAT	GNPAT	GNPAT	1558	0.14	0.36	YES
16	DECR2	DECR2	DECR2	1591	0.14	0.37	YES
17	PIPOX	PIPOX	PIPOX	1632	0.14	0.38	YES
18	SOD1	SOD1	SOD1	1644	0.14	0.4	YES
19	ACAA1	ACAA1	ACAA1	1682	0.13	0.41	YES
20	PEX5	PEX5	PEX5	1780	0.13	0.41	YES
21	MVK	MVK	MVK	1864	0.12	0.42	YES
22	PAOX	PAOX	PAOX	1949	0.12	0.43	YES
23	PEX6	PEX6	PEX6	2013	0.11	0.44	YES
24	CAT	CAT	CAT	2045	0.11	0.45	YES
25	HMGCL	HMGCL	HMGCL	2082	0.11	0.46	YES
26	SCP2	SCP2	SCP2	2156	0.1	0.46	YES
27	EPHX2	EPHX2	EPHX2	2253	0.099	0.47	YES
28	PEX14	PEX14	PEX14	2315	0.096	0.47	YES
29	CRAT	CRAT	CRAT	2349	0.094	0.48	YES
30	IDH1	IDH1	IDH1	2387	0.092	0.49	YES
31	ABCD3	ABCD3	ABCD3	2780	0.076	0.47	YES
32	PEX2	PEX2	PEX2	2823	0.075	0.48	YES
33	PEX19	PEX19	PEX19	2855	0.074	0.48	YES
34	DHRS4	DHRS4	DHRS4	2904	0.073	0.49	YES
35	ACOX1	ACOX1	ACOX1	2962	0.071	0.49	YES
36	PMVK	PMVK	PMVK	2974	0.07	0.5	YES
37	PEX10	PEX10	PEX10	3048	0.068	0.5	YES
38	GSTK1	GSTK1	GSTK1	3147	0.065	0.5	YES
39	HACL1	HACL1	HACL1	3165	0.064	0.51	YES
40	ABCD2	ABCD2	ABCD2	3176	0.064	0.52	YES
41	PEX1	PEX1	PEX1	3505	0.055	0.5	NO
42	PXMP2	PXMP2	PXMP2	3937	0.044	0.48	NO
43	PEX11B	PEX11B	PEX11B	4040	0.042	0.48	NO
44	ACSL1	ACSL1	ACSL1	4237	0.038	0.48	NO
45	ECH1	ECH1	ECH1	4286	0.037	0.48	NO
46	SLC27A2	SLC27A2	SLC27A2	4782	0.027	0.45	NO
47	PRDX1	PRDX1	PRDX1	4906	0.025	0.45	NO
48	PEX13	PEX13	PEX13	5025	0.023	0.44	NO
49	NUDT12	NUDT12	NUDT12	5040	0.023	0.44	NO
50	ACSL3	ACSL3	ACSL3	5268	0.018	0.43	NO
51	DDO	DDO	DDO	5781	0.0096	0.4	NO
52	AGPS	AGPS	AGPS	5784	0.0096	0.41	NO
53	PEX26	PEX26	PEX26	6003	0.0062	0.39	NO
54	NUDT19	NUDT19	NUDT19	6588	-0.0028	0.36	NO
55	PEX16	PEX16	PEX16	6975	-0.009	0.34	NO
56	PEX3	PEX3	PEX3	7070	-0.01	0.34	NO
57	ABCD1	ABCD1	ABCD1	7242	-0.013	0.33	NO
58	ABCD4	ABCD4	ABCD4	7578	-0.018	0.31	NO
59	IDH2	IDH2	IDH2	7720	-0.02	0.3	NO
60	PEX7	PEX7	PEX7	7798	-0.021	0.3	NO
61	NOS2	NOS2	NOS2	8027	-0.025	0.29	NO
62	ACOT8	ACOT8	ACOT8	8117	-0.026	0.29	NO
63	PXMP4	PXMP4	PXMP4	8494	-0.032	0.27	NO
64	SLC25A17	SLC25A17	SLC25A17	8922	-0.039	0.25	NO
65	ACOX3	ACOX3	ACOX3	9106	-0.042	0.24	NO
66	SOD2	SOD2	SOD2	9777	-0.055	0.21	NO
67	AGXT	AGXT	AGXT	9844	-0.056	0.22	NO
68	PRDX5	PRDX5	PRDX5	10021	-0.06	0.21	NO
69	PHYH	PHYH	PHYH	10228	-0.065	0.21	NO
70	MPV17	MPV17	MPV17	10533	-0.072	0.2	NO
71	MPV17L	MPV17L	MPV17L	12209	-0.13	0.12	NO
72	CROT	CROT	CROT	14170	-0.22	0.026	NO
73	HAO2	HAO2	HAO2	14867	-0.26	0.014	NO
74	XDH	XDH	XDH	15083	-0.28	0.031	NO
75	FAR1	FAR1	FAR1	15459	-0.3	0.041	NO
76	FAR2	FAR2	FAR2	16490	-0.38	0.022	NO
77	ACSL4	ACSL4	ACSL4	17151	-0.47	0.033	NO

Figure S99. 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 CYTOCHROME P450.

Figure S100. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450, 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 = LIHC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt
Phenotype data file = LIHC-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)

Made with Nozzle