GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in TGCT-TP
Testicular Germ Cell Tumors (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in TGCT-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1MC8Z4V
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 in TGCT-TP. This pipeline has the following features:

  1. 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.

  2. Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).

  3. Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).

  4. Checks if the top core genes are up-regulated or down-regulated.

  5. Checks if the top core genes are high expressed or low expressed.

  6. 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: 198
Number of samples: 150
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 70
pheno.type: 2 - 3 :[ clus2 ] 40
pheno.type: 3 - 3 :[ clus3 ] 40

For the expression subtypes of 19071 genes in 151 samples, GSEA found enriched gene sets in each cluster using 150 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA NKT PATHWAY, BIOCARTA TCR PATHWAY, KEGG BASE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION, KEGG ANTIGEN PROCESSING AND PRESENTATION, KEGG CYTOSOLIC DNA SENSING PATHWAY, KEGG HEMATOPOIETIC CELL LINEAGE, KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY, KEGG T CELL RECEPTOR SIGNALING PATHWAY, KEGG B CELL RECEPTOR SIGNALING PATHWAY

    • And common core enriched genes are CD40LG, CD28, CD40, HLA-DMB, HLA-DOB, HLA-DQA1, HLA-DQA2, IFNG, IL10, TNF

  • clus2

    • Top enriched gene sets are BIOCARTA MPR PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG LYSINE DEGRADATION, KEGG SELENOAMINO ACID METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME, KEGG RNA DEGRADATION

    • And common core enriched genes are SDHB, SDHD, AP2B1, AP2M1, AP2S1, ATP5B, ATP5C1, ATP5D, ATP5F1, ATP5G1

  • clus3

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA MYOSIN PATHWAY, BIOCARTA CHREBP2 PATHWAY, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG DRUG METABOLISM OTHER ENZYMES, KEGG WNT SIGNALING PATHWAY

    • And common core enriched genes are PRKCA, AGT, EGFR, JUN, BMP2, BMP4, BMP5, BMP7, CHRD, SMAD1

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
BIOCARTA NKT PATHWAY 27 genes.ES.table 0.65 1.3 0.25 1 0.99 0.67 0.17 0.55 1 0.58
BIOCARTA TCR PATHWAY 43 genes.ES.table 0.45 1.1 0.36 1 1 0.26 0.11 0.23 1 0.66
KEGG BASE EXCISION REPAIR 32 genes.ES.table 0.27 1 0.45 1 1 0.22 0.23 0.17 1 0.76
KEGG HOMOLOGOUS RECOMBINATION 27 genes.ES.table 0.44 1.2 0.31 1 0.99 0.44 0.34 0.3 1 0.53
KEGG ANTIGEN PROCESSING AND PRESENTATION 68 genes.ES.table 0.6 1.3 0.22 1 0.97 0.57 0.24 0.44 1 0.6
KEGG CYTOSOLIC DNA SENSING PATHWAY 42 genes.ES.table 0.54 1.3 0.25 1 0.98 0.64 0.33 0.43 1 0.59
KEGG HEMATOPOIETIC CELL LINEAGE 81 genes.ES.table 0.45 1 0.49 1 1 0.4 0.12 0.35 1 0.75
KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY 118 genes.ES.table 0.38 1 0.48 1 1 0.33 0.15 0.28 1 0.72
KEGG T CELL RECEPTOR SIGNALING PATHWAY 107 genes.ES.table 0.49 1.4 0.2 1 0.95 0.4 0.18 0.33 1 0.7
KEGG B CELL RECEPTOR SIGNALING PATHWAY 74 genes.ES.table 0.37 1.1 0.42 1 1 0.36 0.24 0.28 1 0.74
genes ES table in pathway: BIOCARTA NKT PATHWAY

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 HIST1H3C HIST1H3C HIST1H3C 18 1.6 0.03 YES
2 HIST1H2AJ HIST1H2AJ HIST1H2AJ 65 1.3 0.052 YES
3 HIST1H2AL HIST1H2AL HIST1H2AL 66 1.3 0.078 YES
4 HIST1H3A HIST1H3A HIST1H3A 67 1.3 0.1 YES
5 HIST1H2BA HIST1H2BA HIST1H2BA 72 1.2 0.13 YES
6 HIST1H2AB HIST1H2AB HIST1H2AB 112 1.1 0.15 YES
7 HIST1H2AA HIST1H2AA HIST1H2AA 129 1.1 0.17 YES
8 HIST1H2BL HIST1H2BL HIST1H2BL 152 1 0.18 YES
9 HIST1H2BM HIST1H2BM HIST1H2BM 153 1 0.2 YES
10 HIST1H2AE HIST1H2AE HIST1H2AE 158 1 0.22 YES
11 HIST1H3H HIST1H3H HIST1H3H 198 0.92 0.24 YES
12 HIST1H4D HIST1H4D HIST1H4D 203 0.92 0.26 YES
13 HIST1H2BE HIST1H2BE HIST1H2BE 242 0.87 0.27 YES
14 HIST1H2BB HIST1H2BB HIST1H2BB 290 0.83 0.29 YES
15 HIST1H2AM HIST1H2AM HIST1H2AM 347 0.79 0.3 YES
16 HIST1H2BG HIST1H2BG HIST1H2BG 355 0.78 0.32 YES
17 IFNG IFNG IFNG 378 0.77 0.33 YES
18 CD40LG CD40LG CD40LG 424 0.73 0.34 YES
19 HIST1H3D HIST1H3D HIST1H3D 503 0.7 0.35 YES
20 HIST1H2BO HIST1H2BO HIST1H2BO 541 0.67 0.36 YES
21 HIST1H2BF HIST1H2BF HIST1H2BF 542 0.67 0.38 YES
22 HIST1H3E HIST1H3E HIST1H3E 543 0.67 0.39 YES
23 HIST1H2BC HIST1H2BC HIST1H2BC 563 0.67 0.4 YES
24 HIST2H2BF HIST2H2BF HIST2H2BF 576 0.66 0.41 YES
25 HIST1H4H HIST1H4H HIST1H4H 592 0.66 0.43 YES
26 HIST1H4E HIST1H4E HIST1H4E 613 0.64 0.44 YES
27 HIST1H3G HIST1H3G HIST1H3G 712 0.61 0.44 YES
28 HIST1H2BJ HIST1H2BJ HIST1H2BJ 777 0.59 0.45 YES
29 HIST1H2BK HIST1H2BK HIST1H2BK 780 0.59 0.46 YES
30 HIST1H2AC HIST1H2AC HIST1H2AC 794 0.58 0.48 YES
31 HLA-DOB HLA-DOB HLA-DOB 807 0.58 0.48 YES
32 HIST1H4C HIST1H4C HIST1H4C 812 0.58 0.5 YES
33 HIST1H2BD HIST1H2BD HIST1H2BD 817 0.58 0.51 YES
34 CD28 CD28 CD28 841 0.57 0.52 YES
35 HIST1H2AG HIST1H2AG HIST1H2AG 902 0.55 0.52 YES
36 HIST1H2AD HIST1H2AD HIST1H2AD 917 0.55 0.54 YES
37 HIST1H4B HIST1H4B HIST1H4B 920 0.55 0.55 YES
38 TNF TNF TNF 955 0.54 0.56 YES
39 HIST1H3B HIST1H3B HIST1H3B 1013 0.52 0.56 YES
40 HLA-DQA2 HLA-DQA2 HLA-DQA2 1192 0.48 0.56 YES
41 IL10 IL10 IL10 1214 0.48 0.57 YES
42 HIST1H2AK HIST1H2AK HIST1H2AK 1237 0.47 0.58 YES
43 CD80 CD80 CD80 1496 0.42 0.57 YES
44 HIST3H2BB HIST3H2BB HIST3H2BB 1619 0.4 0.57 YES
45 HIST1H2BI HIST1H2BI HIST1H2BI 1793 0.37 0.57 YES
46 HIST3H2A HIST3H2A HIST3H2A 1881 0.36 0.57 YES
47 HIST1H4I HIST1H4I HIST1H4I 1953 0.35 0.58 YES
48 C8G C8G C8G 2054 0.33 0.58 YES
49 HIST1H2BN HIST1H2BN HIST1H2BN 2136 0.32 0.58 YES
50 HLA-DMB HLA-DMB HLA-DMB 2144 0.32 0.59 YES
51 C1QB C1QB C1QB 2233 0.31 0.59 YES
52 CD40 CD40 CD40 2242 0.31 0.59 YES
53 FCGR1A FCGR1A FCGR1A 2277 0.3 0.6 YES
54 HLA-DQA1 HLA-DQA1 HLA-DQA1 2280 0.3 0.6 YES
55 HIST1H4J HIST1H4J HIST1H4J 2304 0.3 0.61 YES
56 CD86 CD86 CD86 2401 0.29 0.61 YES
57 HLA-DQB1 HLA-DQB1 HLA-DQB1 2425 0.29 0.61 YES
58 HIST1H4F HIST1H4F HIST1H4F 2460 0.28 0.62 YES
59 C1QA C1QA C1QA 2573 0.27 0.62 NO
60 C2 C2 C2 2922 0.24 0.6 NO
61 C1QC C1QC C1QC 2988 0.24 0.6 NO
62 HLA-DMA HLA-DMA HLA-DMA 2992 0.24 0.61 NO
63 HLA-DPA1 HLA-DPA1 HLA-DPA1 3117 0.23 0.61 NO
64 HLA-DOA HLA-DOA HLA-DOA 3118 0.23 0.61 NO
65 HLA-DRA HLA-DRA HLA-DRA 3258 0.22 0.61 NO
66 ACTN3 ACTN3 ACTN3 3403 0.21 0.6 NO
67 HIST2H2BE HIST2H2BE HIST2H2BE 3436 0.21 0.61 NO
68 HIST1H4K HIST1H4K HIST1H4K 3482 0.2 0.61 NO
69 HIST1H2AH HIST1H2AH HIST1H2AH 3919 0.18 0.59 NO
70 HIST1H4A HIST1H4A HIST1H4A 3981 0.17 0.59 NO
71 HLA-DRB1 HLA-DRB1 HLA-DRB1 4067 0.17 0.59 NO
72 HIST1H3I HIST1H3I HIST1H3I 4105 0.17 0.59 NO
73 HLA-DPB1 HLA-DPB1 HLA-DPB1 4379 0.15 0.58 NO
74 H2AFY2 H2AFY2 H2AFY2 4487 0.15 0.58 NO
75 HLA-DRB5 HLA-DRB5 HLA-DRB5 4626 0.14 0.57 NO
76 C7 C7 C7 5513 0.1 0.53 NO
77 H2BFWT H2BFWT H2BFWT 6190 0.08 0.49 NO
78 TRIM21 TRIM21 TRIM21 7182 0.049 0.44 NO
79 SNRPB SNRPB SNRPB 7253 0.047 0.44 NO
80 H2AFV H2AFV H2AFV 7273 0.047 0.44 NO
81 C4A C4A C4A 7338 0.045 0.44 NO
82 SNRPD3 SNRPD3 SNRPD3 7970 0.027 0.4 NO
83 H3F3A H3F3A H3F3A 8357 0.015 0.38 NO
84 ACTN1 ACTN1 ACTN1 8818 0.0014 0.36 NO
85 FCGR2C FCGR2C FCGR2C 8956 -0.0021 0.35 NO
86 FCGR2B FCGR2B FCGR2B 9003 -0.0035 0.35 NO
87 HIST1H3J HIST1H3J HIST1H3J 9821 -0.027 0.31 NO
88 SNRPD1 SNRPD1 SNRPD1 10005 -0.032 0.3 NO
89 TROVE2 TROVE2 TROVE2 10102 -0.035 0.29 NO
90 C9 C9 C9 10521 -0.049 0.27 NO
91 FCGR2A FCGR2A FCGR2A 10608 -0.052 0.27 NO
92 HIST1H4L HIST1H4L HIST1H4L 11012 -0.065 0.25 NO
93 HIST1H2BH HIST1H2BH HIST1H2BH 11123 -0.069 0.24 NO
94 FCGR3A FCGR3A FCGR3A 11581 -0.085 0.22 NO
95 H3F3B H3F3B H3F3B 11954 -0.1 0.2 NO
96 H2AFY H2AFY H2AFY 11979 -0.1 0.2 NO
97 SSB SSB SSB 12051 -0.1 0.2 NO
98 HIST2H3D HIST2H3D HIST2H3D 12362 -0.12 0.19 NO
99 H2AFZ H2AFZ H2AFZ 12406 -0.12 0.19 NO
100 H2BFM H2BFM H2BFM 12432 -0.12 0.19 NO
101 C3 C3 C3 12762 -0.13 0.18 NO
102 ACTN4 ACTN4 ACTN4 12963 -0.14 0.17 NO
103 HIST1H3F HIST1H3F HIST1H3F 12979 -0.14 0.17 NO
104 HIST4H4 HIST4H4 HIST4H4 13132 -0.15 0.16 NO
105 C8B C8B C8B 13302 -0.16 0.16 NO
106 HIST2H2AB HIST2H2AB HIST2H2AB 13578 -0.18 0.15 NO
107 GRIN2A GRIN2A GRIN2A 13775 -0.19 0.14 NO
108 ACTN2 ACTN2 ACTN2 13779 -0.19 0.14 NO
109 C5 C5 C5 13897 -0.2 0.14 NO
110 H3F3C H3F3C H3F3C 13948 -0.2 0.14 NO
111 C6 C6 C6 14031 -0.21 0.14 NO
112 H2AFX H2AFX H2AFX 14831 -0.27 0.11 NO
113 C1S C1S C1S 14876 -0.27 0.11 NO
114 FCGR3B FCGR3B FCGR3B 15586 -0.34 0.078 NO
115 H2AFB1 H2AFB1 H2AFB1 15644 -0.35 0.082 NO
116 HIST2H4A HIST2H4A HIST2H4A 15865 -0.38 0.078 NO
117 C1R C1R C1R 15939 -0.38 0.082 NO
118 H2AFJ H2AFJ H2AFJ 16322 -0.43 0.07 NO
119 HIST2H2AC HIST2H2AC HIST2H2AC 16370 -0.44 0.076 NO
120 ELANE ELANE ELANE 17252 -0.58 0.041 NO
121 GRIN2B GRIN2B GRIN2B 17365 -0.6 0.047 NO
122 CTSG CTSG CTSG 17553 -0.64 0.05 NO
123 C8A C8A C8A 17556 -0.64 0.062 NO
124 HIST2H3C HIST2H3C HIST2H3C 18292 -0.84 0.04 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: BIOCARTA NKT PATHWAY.

Figure S2.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NKT 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 TCR 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 IL12B IL12B IL12B 13 1.6 0.14 YES
2 IFNG IFNG IFNG 378 0.77 0.18 YES
3 CD40LG CD40LG CD40LG 424 0.73 0.24 YES
4 FASLG FASLG FASLG 550 0.67 0.3 YES
5 HLA-DOB HLA-DOB HLA-DOB 807 0.58 0.33 YES
6 CD28 CD28 CD28 841 0.57 0.38 YES
7 TNF TNF TNF 955 0.54 0.42 YES
8 HLA-DQA2 HLA-DQA2 HLA-DQA2 1192 0.48 0.45 YES
9 IL10 IL10 IL10 1214 0.48 0.49 YES
10 CD80 CD80 CD80 1496 0.42 0.51 YES
11 IL2 IL2 IL2 1573 0.4 0.54 YES
12 PRF1 PRF1 PRF1 1727 0.38 0.56 YES
13 GZMB GZMB GZMB 1996 0.34 0.58 YES
14 HLA-DMB HLA-DMB HLA-DMB 2144 0.32 0.6 YES
15 CD40 CD40 CD40 2242 0.31 0.62 YES
16 HLA-DQA1 HLA-DQA1 HLA-DQA1 2280 0.3 0.64 YES
17 CD86 CD86 CD86 2401 0.29 0.66 YES
18 HLA-DMA HLA-DMA HLA-DMA 2992 0.24 0.65 YES
19 HLA-F HLA-F HLA-F 3000 0.24 0.67 YES
20 HLA-DPA1 HLA-DPA1 HLA-DPA1 3117 0.23 0.68 YES
21 HLA-DOA HLA-DOA HLA-DOA 3118 0.23 0.7 YES
22 IL4 IL4 IL4 3138 0.23 0.72 YES
23 HLA-DRA HLA-DRA HLA-DRA 3258 0.22 0.73 YES
24 IL5 IL5 IL5 3291 0.22 0.75 YES
25 HLA-DRB1 HLA-DRB1 HLA-DRB1 4067 0.17 0.72 NO
26 HLA-DPB1 HLA-DPB1 HLA-DPB1 4379 0.15 0.72 NO
27 HLA-DRB5 HLA-DRB5 HLA-DRB5 4626 0.14 0.72 NO
28 HLA-B HLA-B HLA-B 6184 0.08 0.64 NO
29 HLA-E HLA-E HLA-E 6838 0.06 0.62 NO
30 HLA-A HLA-A HLA-A 7367 0.044 0.59 NO
31 IL12A IL12A IL12A 7770 0.032 0.57 NO
32 HLA-C HLA-C HLA-C 8317 0.016 0.55 NO
33 HLA-G HLA-G HLA-G 11663 -0.088 0.38 NO
34 FAS FAS FAS 12846 -0.14 0.33 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: BIOCARTA TCR PATHWAY.

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

genes ES table in pathway: KEGG BASE EXCISION REPAIR

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 PIK3CG PIK3CG PIK3CG 318 0.82 0.013 YES
2 IFNG IFNG IFNG 378 0.77 0.037 YES
3 CD40LG CD40LG CD40LG 424 0.73 0.062 YES
4 PDCD1 PDCD1 PDCD1 580 0.66 0.077 YES
5 CD3G CD3G CD3G 605 0.65 0.099 YES
6 ITK ITK ITK 722 0.61 0.12 YES
7 CTLA4 CTLA4 CTLA4 751 0.6 0.14 YES
8 MAP3K8 MAP3K8 MAP3K8 796 0.58 0.15 YES
9 TEC TEC TEC 834 0.57 0.17 YES
10 CD28 CD28 CD28 841 0.57 0.19 YES
11 CD3E CD3E CD3E 845 0.57 0.21 YES
12 CD3D CD3D CD3D 877 0.56 0.23 YES
13 TNF TNF TNF 955 0.54 0.25 YES
14 CD247 CD247 CD247 975 0.54 0.26 YES
15 CD8A CD8A CD8A 988 0.53 0.28 YES
16 ICOS ICOS ICOS 1151 0.49 0.29 YES
17 IL10 IL10 IL10 1214 0.48 0.31 YES
18 PTPRC PTPRC PTPRC 1228 0.48 0.32 YES
19 PIK3CD PIK3CD PIK3CD 1363 0.44 0.33 YES
20 GRAP2 GRAP2 GRAP2 1374 0.44 0.35 YES
21 VAV1 VAV1 VAV1 1379 0.44 0.36 YES
22 CSF2 CSF2 CSF2 1438 0.43 0.38 YES
23 CD8B CD8B CD8B 1455 0.43 0.39 YES
24 LAT LAT LAT 1554 0.41 0.4 YES
25 IL2 IL2 IL2 1573 0.4 0.41 YES
26 ZAP70 ZAP70 ZAP70 1601 0.4 0.43 YES
27 LCP2 LCP2 LCP2 1623 0.4 0.44 YES
28 PIK3R3 PIK3R3 PIK3R3 1713 0.38 0.45 YES
29 PAK7 PAK7 PAK7 1852 0.36 0.46 YES
30 RASGRP1 RASGRP1 RASGRP1 2025 0.34 0.46 YES
31 PPP3CC PPP3CC PPP3CC 2140 0.32 0.46 YES
32 CBLB CBLB CBLB 2416 0.29 0.46 YES
33 CBL CBL CBL 2618 0.27 0.46 YES
34 PRKCQ PRKCQ PRKCQ 2653 0.27 0.47 YES
35 NFKBIB NFKBIB NFKBIB 3070 0.23 0.45 YES
36 NCK2 NCK2 NCK2 3095 0.23 0.46 YES
37 PPP3R2 PPP3R2 PPP3R2 3107 0.23 0.47 YES
38 IL4 IL4 IL4 3138 0.23 0.47 YES
39 CD4 CD4 CD4 3228 0.22 0.48 YES
40 MAPK11 MAPK11 MAPK11 3262 0.22 0.48 YES
41 IL5 IL5 IL5 3291 0.22 0.49 YES
42 NFATC2 NFATC2 NFATC2 3500 0.2 0.49 YES
43 MAPK12 MAPK12 MAPK12 3506 0.2 0.49 YES
44 LCK LCK LCK 3674 0.19 0.49 NO
45 CHP CHP CHP 3948 0.17 0.48 NO
46 MAPK1 MAPK1 MAPK1 4341 0.16 0.47 NO
47 PIK3R2 PIK3R2 PIK3R2 4375 0.15 0.47 NO
48 VAV2 VAV2 VAV2 4435 0.15 0.47 NO
49 MAP3K14 MAP3K14 MAP3K14 4812 0.13 0.46 NO
50 CHUK CHUK CHUK 4966 0.13 0.46 NO
51 PIK3R5 PIK3R5 PIK3R5 5083 0.12 0.45 NO
52 MALT1 MALT1 MALT1 5219 0.12 0.45 NO
53 PTPN6 PTPN6 PTPN6 5295 0.11 0.45 NO
54 NCK1 NCK1 NCK1 5334 0.11 0.45 NO
55 MAP2K7 MAP2K7 MAP2K7 5412 0.11 0.45 NO
56 SOS1 SOS1 SOS1 5783 0.094 0.44 NO
57 NFATC3 NFATC3 NFATC3 6063 0.084 0.42 NO
58 PAK3 PAK3 PAK3 6071 0.084 0.43 NO
59 PDK1 PDK1 PDK1 6342 0.075 0.42 NO
60 NFKBIE NFKBIE NFKBIE 6436 0.072 0.41 NO
61 IKBKB IKBKB IKBKB 6911 0.058 0.39 NO
62 GSK3B GSK3B GSK3B 7041 0.053 0.39 NO
63 AKT3 AKT3 AKT3 7116 0.051 0.38 NO
64 MAP3K7 MAP3K7 MAP3K7 7126 0.051 0.38 NO
65 RAF1 RAF1 RAF1 7500 0.04 0.37 NO
66 FYN FYN FYN 7774 0.032 0.35 NO
67 PLCG1 PLCG1 PLCG1 7952 0.027 0.34 NO
68 PPP3R1 PPP3R1 PPP3R1 8234 0.019 0.33 NO
69 MAP2K2 MAP2K2 MAP2K2 8279 0.017 0.33 NO
70 MAP2K1 MAP2K1 MAP2K1 8300 0.017 0.33 NO
71 PIK3CA PIK3CA PIK3CA 8721 0.0043 0.31 NO
72 PPP3CB PPP3CB PPP3CB 8841 0.00059 0.3 NO
73 RELA RELA RELA 8884 -0.00072 0.3 NO
74 DLG1 DLG1 DLG1 8955 -0.0021 0.3 NO
75 AKT2 AKT2 AKT2 9207 -0.0094 0.28 NO
76 RHOA RHOA RHOA 9748 -0.025 0.25 NO
77 KRAS KRAS KRAS 10065 -0.034 0.24 NO
78 NFKBIA NFKBIA NFKBIA 10156 -0.037 0.24 NO
79 IKBKG IKBKG IKBKG 10595 -0.051 0.21 NO
80 CDK4 CDK4 CDK4 10598 -0.051 0.22 NO
81 PAK4 PAK4 PAK4 10671 -0.054 0.21 NO
82 CDC42 CDC42 CDC42 11087 -0.068 0.19 NO
83 NFAT5 NFAT5 NFAT5 11190 -0.071 0.19 NO
84 BCL10 BCL10 BCL10 11372 -0.077 0.18 NO
85 NFATC1 NFATC1 NFATC1 11441 -0.08 0.18 NO
86 GRB2 GRB2 GRB2 11451 -0.08 0.19 NO
87 AKT1 AKT1 AKT1 11562 -0.084 0.18 NO
88 PAK2 PAK2 PAK2 11907 -0.098 0.17 NO
89 MAPK14 MAPK14 MAPK14 11981 -0.1 0.17 NO
90 PIK3CB PIK3CB PIK3CB 12048 -0.1 0.17 NO
91 PIK3R1 PIK3R1 PIK3R1 12478 -0.12 0.15 NO
92 VAV3 VAV3 VAV3 12709 -0.13 0.14 NO
93 MAPK3 MAPK3 MAPK3 12737 -0.13 0.15 NO
94 NRAS NRAS NRAS 12752 -0.13 0.15 NO
95 NFKB1 NFKB1 NFKB1 12815 -0.14 0.15 NO
96 MAPK9 MAPK9 MAPK9 13633 -0.18 0.12 NO
97 NFATC4 NFATC4 NFATC4 13691 -0.18 0.12 NO
98 PAK1 PAK1 PAK1 14290 -0.22 0.096 NO
99 CBLC CBLC CBLC 15033 -0.28 0.067 NO
100 SOS2 SOS2 SOS2 15400 -0.32 0.06 NO
101 PAK6 PAK6 PAK6 15535 -0.33 0.064 NO
102 CARD11 CARD11 CARD11 15683 -0.35 0.069 NO
103 PPP3CA PPP3CA PPP3CA 15775 -0.36 0.078 NO
104 MAPK13 MAPK13 MAPK13 16287 -0.43 0.066 NO
105 FOS FOS FOS 16871 -0.52 0.054 NO
106 JUN JUN JUN 17379 -0.6 0.049 NO
107 CHP2 CHP2 CHP2 18761 -1.1 0.015 NO

Figure S5.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BASE EXCISION REPAIR.

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

genes ES table in pathway: KEGG HOMOLOGOUS RECOMBINATION

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 CD40LG CD40LG CD40LG 424 0.73 0.044 YES
2 CD19 CD19 CD19 452 0.72 0.11 YES
3 AICDA AICDA AICDA 587 0.66 0.16 YES
4 CD3E CD3E CD3E 845 0.57 0.2 YES
5 CD3D CD3D CD3D 877 0.56 0.25 YES
6 CD79A CD79A CD79A 931 0.54 0.3 YES
7 IL7R IL7R IL7R 1006 0.53 0.34 YES
8 TNFRSF13B TNFRSF13B TNFRSF13B 1126 0.5 0.38 YES
9 ICOS ICOS ICOS 1151 0.49 0.42 YES
10 PTPRC PTPRC PTPRC 1228 0.48 0.46 YES
11 IL2RG IL2RG IL2RG 1284 0.46 0.5 YES
12 CD8B CD8B CD8B 1455 0.43 0.53 YES
13 ZAP70 ZAP70 ZAP70 1601 0.4 0.56 YES
14 CIITA CIITA CIITA 1722 0.38 0.59 YES
15 BTK BTK BTK 2035 0.33 0.6 YES
16 CD40 CD40 CD40 2242 0.31 0.62 YES
17 JAK3 JAK3 JAK3 2503 0.28 0.63 YES
18 TNFRSF13C TNFRSF13C TNFRSF13C 2606 0.27 0.65 YES
19 BLNK BLNK BLNK 2813 0.25 0.66 YES
20 CD4 CD4 CD4 3228 0.22 0.66 YES
21 UNG UNG UNG 3235 0.22 0.68 YES
22 RFXAP RFXAP RFXAP 3512 0.2 0.68 YES
23 LCK LCK LCK 3674 0.19 0.69 YES
24 TAP1 TAP1 TAP1 3914 0.18 0.7 YES
25 RFX5 RFX5 RFX5 4256 0.16 0.69 YES
26 TAP2 TAP2 TAP2 4418 0.15 0.7 YES
27 IGLL1 IGLL1 IGLL1 5662 0.099 0.64 NO
28 AIRE AIRE AIRE 9227 -0.01 0.45 NO
29 RFXANK RFXANK RFXANK 9837 -0.027 0.42 NO
30 IKBKG IKBKG IKBKG 10595 -0.051 0.39 NO
31 ADA ADA ADA 10931 -0.062 0.38 NO
32 DCLRE1C DCLRE1C DCLRE1C 11000 -0.065 0.38 NO
33 RAG1 RAG1 RAG1 16672 -0.48 0.12 NO

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

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

genes ES table in pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION

Table 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 HLA-DOB HLA-DOB HLA-DOB 807 0.58 -0.0005 YES
2 LTA LTA LTA 852 0.57 0.038 YES
3 CD8A CD8A CD8A 988 0.53 0.069 YES
4 HLA-DQA2 HLA-DQA2 HLA-DQA2 1192 0.48 0.094 YES
5 KIR2DL3 KIR2DL3 KIR2DL3 1400 0.44 0.11 YES
6 CD8B CD8B CD8B 1455 0.43 0.14 YES
7 KIR3DL2 KIR3DL2 KIR3DL2 1536 0.41 0.17 YES
8 KLRC3 KLRC3 KLRC3 1659 0.39 0.19 YES
9 KIR2DL1 KIR2DL1 KIR2DL1 1668 0.39 0.22 YES
10 CIITA CIITA CIITA 1722 0.38 0.24 YES
11 CTSS CTSS CTSS 1872 0.36 0.26 YES
12 KLRD1 KLRD1 KLRD1 1930 0.35 0.28 YES
13 KIR3DL3 KIR3DL3 KIR3DL3 2076 0.33 0.3 YES
14 KIR2DL4 KIR2DL4 KIR2DL4 2107 0.32 0.32 YES
15 HLA-DMB HLA-DMB HLA-DMB 2144 0.32 0.34 YES
16 KLRC2 KLRC2 KLRC2 2167 0.32 0.36 YES
17 KLRC1 KLRC1 KLRC1 2202 0.31 0.38 YES
18 HSPA1L HSPA1L HSPA1L 2270 0.3 0.4 YES
19 HLA-DQA1 HLA-DQA1 HLA-DQA1 2280 0.3 0.42 YES
20 HLA-DQB1 HLA-DQB1 HLA-DQB1 2425 0.29 0.44 YES
21 KIR2DS4 KIR2DS4 KIR2DS4 2587 0.27 0.45 YES
22 KIR3DL1 KIR3DL1 KIR3DL1 2797 0.25 0.46 YES
23 HLA-DMA HLA-DMA HLA-DMA 2992 0.24 0.46 YES
24 HLA-F HLA-F HLA-F 3000 0.24 0.48 YES
25 IFNA21 IFNA21 IFNA21 3054 0.23 0.49 YES
26 HLA-DPA1 HLA-DPA1 HLA-DPA1 3117 0.23 0.51 YES
27 HLA-DOA HLA-DOA HLA-DOA 3118 0.23 0.52 YES
28 CD4 CD4 CD4 3228 0.22 0.53 YES
29 HLA-DRA HLA-DRA HLA-DRA 3258 0.22 0.55 YES
30 CD74 CD74 CD74 3265 0.22 0.56 YES
31 RFXAP RFXAP RFXAP 3512 0.2 0.56 YES
32 TAP1 TAP1 TAP1 3914 0.18 0.56 YES
33 HLA-DRB1 HLA-DRB1 HLA-DRB1 4067 0.17 0.56 YES
34 KLRC4 KLRC4 KLRC4 4120 0.17 0.57 YES
35 RFX5 RFX5 RFX5 4256 0.16 0.57 YES
36 HLA-DPB1 HLA-DPB1 HLA-DPB1 4379 0.15 0.58 YES
37 TAP2 TAP2 TAP2 4418 0.15 0.59 YES
38 IFI30 IFI30 IFI30 4499 0.15 0.59 YES
39 HLA-DRB5 HLA-DRB5 HLA-DRB5 4626 0.14 0.6 YES
40 B2M B2M B2M 5799 0.094 0.54 NO
41 CREB1 CREB1 CREB1 6181 0.08 0.53 NO
42 HLA-B HLA-B HLA-B 6184 0.08 0.53 NO
43 HSP90AA1 HSP90AA1 HSP90AA1 6191 0.08 0.54 NO
44 CTSL1 CTSL1 CTSL1 6285 0.077 0.54 NO
45 NFYA NFYA NFYA 6628 0.066 0.53 NO
46 PSME2 PSME2 PSME2 6677 0.065 0.53 NO
47 HLA-E HLA-E HLA-E 6838 0.06 0.52 NO
48 HSPA4 HSPA4 HSPA4 7128 0.051 0.51 NO
49 CTSB CTSB CTSB 7325 0.046 0.5 NO
50 HLA-A HLA-A HLA-A 7367 0.044 0.51 NO
51 TAPBP TAPBP TAPBP 7924 0.028 0.48 NO
52 HLA-C HLA-C HLA-C 8317 0.016 0.46 NO
53 PDIA3 PDIA3 PDIA3 8400 0.014 0.46 NO
54 PSME3 PSME3 PSME3 9051 -0.0048 0.42 NO
55 NFYB NFYB NFYB 9347 -0.013 0.41 NO
56 RFXANK RFXANK RFXANK 9837 -0.027 0.38 NO
57 PSME1 PSME1 PSME1 9943 -0.031 0.38 NO
58 LGMN LGMN LGMN 10542 -0.05 0.35 NO
59 HSPA1B HSPA1B HSPA1B 10933 -0.063 0.34 NO
60 HSPA8 HSPA8 HSPA8 11045 -0.066 0.34 NO
61 HSPA1A HSPA1A HSPA1A 11047 -0.066 0.34 NO
62 NFYC NFYC NFYC 11182 -0.071 0.34 NO
63 HSPA5 HSPA5 HSPA5 11632 -0.087 0.32 NO
64 HLA-G HLA-G HLA-G 11663 -0.088 0.33 NO
65 CANX CANX CANX 11758 -0.092 0.33 NO
66 CALR CALR CALR 12685 -0.13 0.29 NO
67 HSPA2 HSPA2 HSPA2 15104 -0.29 0.18 NO
68 HSPA6 HSPA6 HSPA6 15768 -0.36 0.17 NO

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

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

genes ES table in pathway: KEGG CYTOSOLIC DNA SENSING PATHWAY

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 CD40LG CD40LG CD40LG 424 0.73 0.046 YES
2 FASLG FASLG FASLG 550 0.67 0.1 YES
3 CTLA4 CTLA4 CTLA4 751 0.6 0.15 YES
4 HLA-DOB HLA-DOB HLA-DOB 807 0.58 0.2 YES
5 CD28 CD28 CD28 841 0.57 0.25 YES
6 HLA-DQA2 HLA-DQA2 HLA-DQA2 1192 0.48 0.28 YES
7 IL10 IL10 IL10 1214 0.48 0.32 YES
8 CD80 CD80 CD80 1496 0.42 0.34 YES
9 TSHR TSHR TSHR 1551 0.41 0.38 YES
10 IL2 IL2 IL2 1573 0.4 0.42 YES
11 PRF1 PRF1 PRF1 1727 0.38 0.44 YES
12 GZMB GZMB GZMB 1996 0.34 0.46 YES
13 HLA-DMB HLA-DMB HLA-DMB 2144 0.32 0.48 YES
14 CD40 CD40 CD40 2242 0.31 0.51 YES
15 HLA-DQA1 HLA-DQA1 HLA-DQA1 2280 0.3 0.53 YES
16 CD86 CD86 CD86 2401 0.29 0.55 YES
17 HLA-DQB1 HLA-DQB1 HLA-DQB1 2425 0.29 0.58 YES
18 HLA-DMA HLA-DMA HLA-DMA 2992 0.24 0.57 YES
19 HLA-F HLA-F HLA-F 3000 0.24 0.59 YES
20 HLA-DPA1 HLA-DPA1 HLA-DPA1 3117 0.23 0.61 YES
21 HLA-DOA HLA-DOA HLA-DOA 3118 0.23 0.63 YES
22 IL4 IL4 IL4 3138 0.23 0.65 YES
23 HLA-DRA HLA-DRA HLA-DRA 3258 0.22 0.66 YES
24 IL5 IL5 IL5 3291 0.22 0.68 YES
25 HLA-DRB1 HLA-DRB1 HLA-DRB1 4067 0.17 0.66 NO
26 HLA-DPB1 HLA-DPB1 HLA-DPB1 4379 0.15 0.65 NO
27 HLA-DRB5 HLA-DRB5 HLA-DRB5 4626 0.14 0.66 NO
28 TPO TPO TPO 5895 0.09 0.6 NO
29 HLA-B HLA-B HLA-B 6184 0.08 0.59 NO
30 HLA-E HLA-E HLA-E 6838 0.06 0.56 NO
31 HLA-A HLA-A HLA-A 7367 0.044 0.54 NO
32 HLA-C HLA-C HLA-C 8317 0.016 0.49 NO
33 TG TG TG 11102 -0.068 0.35 NO
34 HLA-G HLA-G HLA-G 11663 -0.088 0.33 NO
35 FAS FAS FAS 12846 -0.14 0.28 NO
36 CGA CGA CGA 16942 -0.53 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: KEGG CYTOSOLIC DNA SENSING PATHWAY.

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

genes ES table in pathway: KEGG HEMATOPOIETIC CELL LINEAGE

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 AIM2 AIM2 AIM2 339 0.8 0.086 YES
2 IL18 IL18 IL18 703 0.61 0.15 YES
3 ZBP1 ZBP1 ZBP1 798 0.58 0.22 YES
4 CCL5 CCL5 CCL5 1530 0.41 0.23 YES
5 CCL4 CCL4 CCL4 1741 0.38 0.27 YES
6 CCL4L2 CCL4L2 CCL4L2 1791 0.37 0.32 YES
7 IL6 IL6 IL6 1981 0.34 0.35 YES
8 RIPK3 RIPK3 RIPK3 2075 0.33 0.39 YES
9 POLR1C POLR1C POLR1C 2920 0.24 0.38 YES
10 CXCL10 CXCL10 CXCL10 2960 0.24 0.41 YES
11 PYCARD PYCARD PYCARD 3028 0.23 0.44 YES
12 NFKBIB NFKBIB NFKBIB 3070 0.23 0.46 YES
13 TREX1 TREX1 TREX1 3805 0.18 0.45 YES
14 POLR3C POLR3C POLR3C 3806 0.18 0.47 YES
15 IL1B IL1B IL1B 3901 0.18 0.49 YES
16 CASP1 CASP1 CASP1 4028 0.17 0.5 YES
17 IRF7 IRF7 IRF7 4623 0.14 0.49 YES
18 POLR3A POLR3A POLR3A 4695 0.14 0.51 YES
19 CHUK CHUK CHUK 4966 0.13 0.51 YES
20 IKBKE IKBKE IKBKE 5022 0.12 0.52 YES
21 ADAR ADAR ADAR 5674 0.099 0.5 YES
22 IL33 IL33 IL33 5710 0.097 0.51 YES
23 MAVS MAVS MAVS 5781 0.095 0.52 YES
24 TBK1 TBK1 TBK1 5928 0.089 0.52 YES
25 POLR3F POLR3F POLR3F 6230 0.079 0.52 YES
26 POLR3D POLR3D POLR3D 6250 0.078 0.53 YES
27 POLR3G POLR3G POLR3G 6258 0.078 0.54 YES
28 IKBKB IKBKB IKBKB 6911 0.058 0.51 NO
29 POLR3B POLR3B POLR3B 7107 0.051 0.51 NO
30 RELA RELA RELA 8884 -0.00072 0.41 NO
31 POLR1D POLR1D POLR1D 9017 -0.0038 0.41 NO
32 IFNB1 IFNB1 IFNB1 9555 -0.02 0.38 NO
33 NFKBIA NFKBIA NFKBIA 10156 -0.037 0.36 NO
34 DDX58 DDX58 DDX58 10356 -0.044 0.35 NO
35 IRF3 IRF3 IRF3 10485 -0.048 0.35 NO
36 IKBKG IKBKG IKBKG 10595 -0.051 0.35 NO
37 POLR3GL POLR3GL POLR3GL 10630 -0.052 0.36 NO
38 RIPK1 RIPK1 RIPK1 11456 -0.08 0.32 NO
39 POLR3H POLR3H POLR3H 12105 -0.11 0.3 NO
40 POLR3K POLR3K POLR3K 12166 -0.11 0.31 NO
41 NFKB1 NFKB1 NFKB1 12815 -0.14 0.3 NO
42 TMEM173 TMEM173 TMEM173 14441 -0.23 0.24 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: KEGG HEMATOPOIETIC CELL LINEAGE.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HEMATOPOIETIC CELL LINEAGE, 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 NATURAL KILLER CELL MEDIATED CYTOTOXICITY

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 IL12B IL12B IL12B 13 1.6 0.16 YES
2 IFNG IFNG IFNG 378 0.77 0.21 YES
3 CD40LG CD40LG CD40LG 424 0.73 0.28 YES
4 CXCR3 CXCR3 CXCR3 825 0.57 0.31 YES
5 CD28 CD28 CD28 841 0.57 0.37 YES
6 IL12RB1 IL12RB1 IL12RB1 843 0.57 0.42 YES
7 CCR5 CCR5 CCR5 1342 0.45 0.44 YES
8 IL12RB2 IL12RB2 IL12RB2 1568 0.41 0.47 YES
9 IL2 IL2 IL2 1573 0.4 0.51 YES
10 CCL4 CCL4 CCL4 1741 0.38 0.53 YES
11 CCL3 CCL3 CCL3 1770 0.37 0.57 YES
12 CCR7 CCR7 CCR7 2562 0.27 0.55 YES
13 IL4R IL4R IL4R 2885 0.24 0.56 YES
14 CCR1 CCR1 CCR1 2912 0.24 0.58 YES
15 CCR4 CCR4 CCR4 3007 0.24 0.6 YES
16 IL4 IL4 IL4 3138 0.23 0.62 YES
17 CD4 CD4 CD4 3228 0.22 0.63 YES
18 IL5 IL5 IL5 3291 0.22 0.65 YES
19 IL18R1 IL18R1 IL18R1 4284 0.16 0.61 NO
20 CXCR4 CXCR4 CXCR4 4919 0.13 0.59 NO
21 IFNGR1 IFNGR1 IFNGR1 6432 0.072 0.52 NO
22 IL12A IL12A IL12A 7770 0.032 0.45 NO
23 TGFB1 TGFB1 TGFB1 9280 -0.012 0.37 NO
24 CCR3 CCR3 CCR3 10019 -0.033 0.34 NO
25 IFNGR2 IFNGR2 IFNGR2 11666 -0.088 0.26 NO
26 TGFB3 TGFB3 TGFB3 15855 -0.37 0.076 NO
27 TGFB2 TGFB2 TGFB2 18557 -0.95 0.026 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: KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY, 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 T CELL RECEPTOR SIGNALING PATHWAY

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 IFNG IFNG IFNG 378 0.77 0.048 YES
2 FASLG FASLG FASLG 550 0.67 0.098 YES
3 HLA-DOB HLA-DOB HLA-DOB 807 0.58 0.14 YES
4 CD28 CD28 CD28 841 0.57 0.18 YES
5 TNF TNF TNF 955 0.54 0.23 YES
6 HLA-DQA2 HLA-DQA2 HLA-DQA2 1192 0.48 0.26 YES
7 KIR2DL3 KIR2DL3 KIR2DL3 1400 0.44 0.28 YES
8 CD80 CD80 CD80 1496 0.42 0.32 YES
9 KIR3DL2 KIR3DL2 KIR3DL2 1536 0.41 0.35 YES
10 IL2 IL2 IL2 1573 0.4 0.38 YES
11 KIR2DL1 KIR2DL1 KIR2DL1 1668 0.39 0.41 YES
12 PRF1 PRF1 PRF1 1727 0.38 0.44 YES
13 KLRD1 KLRD1 KLRD1 1930 0.35 0.46 YES
14 IL6 IL6 IL6 1981 0.34 0.49 YES
15 GZMB GZMB GZMB 1996 0.34 0.52 YES
16 HLA-DMB HLA-DMB HLA-DMB 2144 0.32 0.54 YES
17 KLRC1 KLRC1 KLRC1 2202 0.31 0.57 YES
18 HLA-DQA1 HLA-DQA1 HLA-DQA1 2280 0.3 0.59 YES
19 CD86 CD86 CD86 2401 0.29 0.61 YES
20 KIR3DL1 KIR3DL1 KIR3DL1 2797 0.25 0.61 YES
21 HLA-DMA HLA-DMA HLA-DMA 2992 0.24 0.62 YES
22 HLA-F HLA-F HLA-F 3000 0.24 0.64 YES
23 HLA-DPA1 HLA-DPA1 HLA-DPA1 3117 0.23 0.66 YES
24 HLA-DOA HLA-DOA HLA-DOA 3118 0.23 0.68 YES
25 HLA-DRA HLA-DRA HLA-DRA 3258 0.22 0.69 YES
26 IL1B IL1B IL1B 3901 0.18 0.67 NO
27 HLA-DRB1 HLA-DRB1 HLA-DRB1 4067 0.17 0.68 NO
28 HLA-DPB1 HLA-DPB1 HLA-DPB1 4379 0.15 0.67 NO
29 HLA-DRB5 HLA-DRB5 HLA-DRB5 4626 0.14 0.67 NO
30 HLA-B HLA-B HLA-B 6184 0.08 0.6 NO
31 HLA-E HLA-E HLA-E 6838 0.06 0.57 NO
32 HLA-A HLA-A HLA-A 7367 0.044 0.55 NO
33 HLA-C HLA-C HLA-C 8317 0.016 0.5 NO
34 HLA-G HLA-G HLA-G 11663 -0.088 0.33 NO
35 FAS FAS FAS 12846 -0.14 0.28 NO
36 IL1A IL1A IL1A 17052 -0.55 0.1 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: KEGG T CELL RECEPTOR SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG B CELL RECEPTOR SIGNALING PATHWAY

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 OR7E24 OR7E24 OR7E24 17 1.6 0.051 YES
2 OR7D4 OR7D4 OR7D4 61 1.3 0.092 YES
3 OR2L2 OR2L2 OR2L2 90 1.2 0.13 YES
4 OR2B6 OR2B6 OR2B6 176 0.96 0.16 YES
5 OR51I1 OR51I1 OR51I1 190 0.94 0.19 YES
6 OR2C3 OR2C3 OR2C3 319 0.82 0.21 YES
7 OR52D1 OR52D1 OR52D1 387 0.77 0.23 YES
8 OR52E6 OR52E6 OR52E6 449 0.72 0.25 YES
9 OR1C1 OR1C1 OR1C1 457 0.72 0.27 YES
10 OR6F1 OR6F1 OR6F1 510 0.69 0.29 YES
11 OR10AD1 OR10AD1 OR10AD1 781 0.59 0.3 YES
12 OR7C1 OR7C1 OR7C1 863 0.56 0.31 YES
13 OR1L8 OR1L8 OR1L8 880 0.56 0.33 YES
14 OR2W3 OR2W3 OR2W3 967 0.54 0.34 YES
15 OR5AU1 OR5AU1 OR5AU1 1075 0.51 0.35 YES
16 OR3A3 OR3A3 OR3A3 1323 0.45 0.36 YES
17 OR51B5 OR51B5 OR51B5 1334 0.45 0.37 YES
18 OR52N4 OR52N4 OR52N4 1349 0.45 0.38 YES
19 OR2B2 OR2B2 OR2B2 1448 0.43 0.39 YES
20 OR8G5 OR8G5 OR8G5 1507 0.42 0.4 YES
21 OR56B1 OR56B1 OR56B1 1680 0.39 0.41 YES
22 OR1J2 OR1J2 OR1J2 1812 0.37 0.41 YES
23 OR4N4 OR4N4 OR4N4 1890 0.36 0.42 YES
24 CAMK2A CAMK2A CAMK2A 1957 0.35 0.43 YES
25 OR13G1 OR13G1 OR13G1 1959 0.35 0.44 YES
26 OR1K1 OR1K1 OR1K1 2134 0.32 0.44 YES
27 OR1E2 OR1E2 OR1E2 2344 0.3 0.44 YES
28 OR6C2 OR6C2 OR6C2 2400 0.29 0.45 YES
29 OR2T8 OR2T8 OR2T8 2412 0.29 0.46 YES
30 OR1J1 OR1J1 OR1J1 2733 0.26 0.45 YES
31 OR3A1 OR3A1 OR3A1 2899 0.24 0.45 YES
32 OR2C1 OR2C1 OR2C1 2904 0.24 0.45 YES
33 OR2L13 OR2L13 OR2L13 2994 0.24 0.46 YES
34 OR51B4 OR51B4 OR51B4 3277 0.22 0.45 NO
35 OR1E1 OR1E1 OR1E1 3614 0.19 0.44 NO
36 OR3A2 OR3A2 OR3A2 3875 0.18 0.43 NO
37 OR5K2 OR5K2 OR5K2 3924 0.18 0.43 NO
38 CAMK2G CAMK2G CAMK2G 3940 0.17 0.44 NO
39 GNAL GNAL GNAL 4381 0.15 0.42 NO
40 OR4C6 OR4C6 OR4C6 4392 0.15 0.42 NO
41 OR6C70 OR6C70 OR6C70 4437 0.15 0.43 NO
42 GUCA1A GUCA1A GUCA1A 5514 0.1 0.37 NO
43 OR2AG2 OR2AG2 OR2AG2 5945 0.089 0.35 NO
44 CALM2 CALM2 CALM2 6124 0.082 0.35 NO
45 OR2A1 OR2A1 OR2A1 6176 0.08 0.35 NO
46 ADRBK2 ADRBK2 ADRBK2 6259 0.078 0.35 NO
47 PRKACG PRKACG PRKACG 6424 0.072 0.34 NO
48 CNGB1 CNGB1 CNGB1 6531 0.069 0.34 NO
49 ARRB2 ARRB2 ARRB2 6572 0.068 0.34 NO
50 PRKX PRKX PRKX 7846 0.03 0.27 NO
51 CAMK2D CAMK2D CAMK2D 8475 0.012 0.24 NO
52 CNGA3 CNGA3 CNGA3 8486 0.011 0.24 NO
53 GUCA1B GUCA1B GUCA1B 8563 0.0092 0.23 NO
54 OR9A4 OR9A4 OR9A4 8611 0.0079 0.23 NO
55 PRKACB PRKACB PRKACB 8669 0.0057 0.23 NO
56 PRKACA PRKACA PRKACA 8995 -0.0032 0.21 NO
57 OR7D2 OR7D2 OR7D2 9165 -0.0085 0.2 NO
58 PDE1C PDE1C PDE1C 10091 -0.035 0.16 NO
59 OR6B2 OR6B2 OR6B2 10385 -0.044 0.14 NO
60 CALM1 CALM1 CALM1 10430 -0.046 0.14 NO
61 CNGA4 CNGA4 CNGA4 10475 -0.048 0.14 NO
62 ADCY3 ADCY3 ADCY3 10557 -0.05 0.14 NO
63 OR2H2 OR2H2 OR2H2 10565 -0.05 0.14 NO
64 CALM3 CALM3 CALM3 10915 -0.062 0.12 NO
65 OR52N2 OR52N2 OR52N2 11241 -0.073 0.11 NO
66 OR2A25 OR2A25 OR2A25 11536 -0.083 0.095 NO
67 OR56B4 OR56B4 OR56B4 11965 -0.1 0.076 NO
68 OR51Q1 OR51Q1 OR51Q1 12579 -0.12 0.047 NO
69 OR2A4 OR2A4 OR2A4 13028 -0.15 0.028 NO
70 PRKG2 PRKG2 PRKG2 13561 -0.18 0.0063 NO
71 CLCA2 CLCA2 CLCA2 13965 -0.2 -0.0083 NO
72 OR13A1 OR13A1 OR13A1 14121 -0.21 -0.0095 NO
73 OR2A7 OR2A7 OR2A7 14155 -0.21 -0.0042 NO
74 CLCA4 CLCA4 CLCA4 14411 -0.23 -0.01 NO
75 CALML6 CALML6 CALML6 14517 -0.24 -0.0076 NO
76 GUCY2D GUCY2D GUCY2D 14787 -0.26 -0.013 NO
77 OR10A3 OR10A3 OR10A3 14937 -0.28 -0.012 NO
78 OR2T4 OR2T4 OR2T4 15686 -0.35 -0.04 NO
79 OR5M11 OR5M11 OR5M11 15833 -0.37 -0.035 NO
80 OR7A5 OR7A5 OR7A5 15955 -0.38 -0.029 NO
81 PRKG1 PRKG1 PRKG1 16021 -0.39 -0.02 NO
82 OR13J1 OR13J1 OR13J1 16713 -0.49 -0.04 NO
83 CALML3 CALML3 CALML3 16989 -0.54 -0.037 NO
84 CAMK2B CAMK2B CAMK2B 17191 -0.57 -0.028 NO
85 CLCA1 CLCA1 CLCA1 17591 -0.65 -0.028 NO
86 OR1F1 OR1F1 OR1F1 17795 -0.7 -0.016 NO
87 OR51E1 OR51E1 OR51E1 18051 -0.77 -0.0038 NO
88 CALML5 CALML5 CALML5 18101 -0.78 0.019 NO
89 OR51E2 OR51E2 OR51E2 18509 -0.93 0.029 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: KEGG B CELL RECEPTOR SIGNALING PATHWAY.

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

Fold change

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

Expression level

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

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA MPR PATHWAY 33 genes.ES.table 0.53 1.7 0.0082 0.34 0.34 0.33 0.16 0.28 0 0.11
KEGG CITRATE CYCLE TCA CYCLE 30 genes.ES.table 0.5 1.7 0.037 0.36 0.5 0.5 0.21 0.39 0 0.11
KEGG OXIDATIVE PHOSPHORYLATION 115 genes.ES.table 0.45 1.6 0.12 0.48 0.68 0.66 0.35 0.43 0.23 0.15
KEGG PYRIMIDINE METABOLISM 96 genes.ES.table 0.32 1.5 0.074 0.51 0.87 0.38 0.29 0.28 0.32 0.15
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.32 1.4 0.12 0.63 0.92 0.19 0.18 0.15 0.46 0.22
KEGG SELENOAMINO ACID METABOLISM 25 genes.ES.table 0.51 1.7 0.01 0.39 0.45 0.56 0.3 0.39 0 0.12
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 43 genes.ES.table 0.4 1.4 0.11 0.6 0.91 0.44 0.22 0.34 0.42 0.2
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.45 1.4 0.17 0.6 0.92 0.68 0.38 0.42 0.43 0.2
KEGG RIBOSOME 86 genes.ES.table 0.5 1.4 0.22 0.61 0.92 0.71 0.42 0.42 0.43 0.2
KEGG RNA DEGRADATION 56 genes.ES.table 0.44 1.6 0.1 0.47 0.69 0.68 0.4 0.41 0.24 0.14
genes ES table in pathway: BIOCARTA MPR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BDNF BDNF BDNF 138 1 0.031 YES
2 COX7A1 COX7A1 COX7A1 274 0.8 0.055 YES
3 GRIN1 GRIN1 GRIN1 411 0.68 0.074 YES
4 HAP1 HAP1 HAP1 512 0.62 0.092 YES
5 CREB3L1 CREB3L1 CREB3L1 530 0.61 0.12 YES
6 CREB5 CREB5 CREB5 863 0.48 0.12 YES
7 UCP1 UCP1 UCP1 963 0.46 0.13 YES
8 BBC3 BBC3 BBC3 1056 0.43 0.14 YES
9 UQCRHL UQCRHL UQCRHL 1153 0.41 0.15 YES
10 AP2B1 AP2B1 AP2B1 1416 0.35 0.15 YES
11 SLC25A4 SLC25A4 SLC25A4 1417 0.35 0.16 YES
12 PLCB4 PLCB4 PLCB4 1601 0.32 0.17 YES
13 NDUFS5 NDUFS5 NDUFS5 1624 0.32 0.18 YES
14 UQCRH UQCRH UQCRH 1626 0.32 0.19 YES
15 COX7B COX7B COX7B 1893 0.29 0.19 YES
16 VDAC1 VDAC1 VDAC1 1984 0.28 0.19 YES
17 ATP5H ATP5H ATP5H 2086 0.26 0.2 YES
18 ATP5G1 ATP5G1 ATP5G1 2151 0.26 0.2 YES
19 NDUFS6 NDUFS6 NDUFS6 2302 0.25 0.2 YES
20 NDUFC2 NDUFC2 NDUFC2 2371 0.24 0.21 YES
21 VDAC2 VDAC2 VDAC2 2372 0.24 0.22 YES
22 HDAC1 HDAC1 HDAC1 2395 0.24 0.23 YES
23 SLC25A5 SLC25A5 SLC25A5 2441 0.23 0.23 YES
24 POLR2H POLR2H POLR2H 2509 0.23 0.24 YES
25 NDUFA9 NDUFA9 NDUFA9 2535 0.23 0.25 YES
26 POLR2G POLR2G POLR2G 2616 0.22 0.25 YES
27 DNAH2 DNAH2 DNAH2 2697 0.22 0.26 YES
28 NDUFA4 NDUFA4 NDUFA4 2705 0.22 0.26 YES
29 NDUFA8 NDUFA8 NDUFA8 2804 0.21 0.27 YES
30 COX5A COX5A COX5A 2880 0.2 0.27 YES
31 NDUFAB1 NDUFAB1 NDUFAB1 2989 0.2 0.27 YES
32 HIP1 HIP1 HIP1 3063 0.19 0.28 YES
33 COX7A2 COX7A2 COX7A2 3075 0.19 0.28 YES
34 BAX BAX BAX 3086 0.19 0.29 YES
35 ATP5G3 ATP5G3 ATP5G3 3130 0.19 0.29 YES
36 NDUFB10 NDUFB10 NDUFB10 3151 0.19 0.3 YES
37 TFAM TFAM TFAM 3279 0.18 0.3 YES
38 CYC1 CYC1 CYC1 3332 0.18 0.3 YES
39 CASP3 CASP3 CASP3 3422 0.17 0.31 YES
40 NDUFA6 NDUFA6 NDUFA6 3434 0.17 0.31 YES
41 ATP5B ATP5B ATP5B 3473 0.17 0.32 YES
42 COX5B COX5B COX5B 3608 0.17 0.32 YES
43 CLTB CLTB CLTB 3620 0.17 0.32 YES
44 AP2M1 AP2M1 AP2M1 3680 0.16 0.32 YES
45 SDHB SDHB SDHB 3771 0.16 0.33 YES
46 NDUFB9 NDUFB9 NDUFB9 3791 0.16 0.33 YES
47 SDHD SDHD SDHD 3841 0.16 0.34 YES
48 COX8A COX8A COX8A 3872 0.15 0.34 YES
49 ATP5C1 ATP5C1 ATP5C1 3929 0.15 0.34 YES
50 COX7C COX7C COX7C 3965 0.15 0.35 YES
51 NDUFS8 NDUFS8 NDUFS8 3968 0.15 0.35 YES
52 ATP5F1 ATP5F1 ATP5F1 3983 0.15 0.36 YES
53 NDUFA3 NDUFA3 NDUFA3 4046 0.15 0.36 YES
54 NDUFA1 NDUFA1 NDUFA1 4078 0.14 0.36 YES
55 ATP5J ATP5J ATP5J 4155 0.14 0.36 YES
56 COX6A1 COX6A1 COX6A1 4168 0.14 0.37 YES
57 ATP5O ATP5O ATP5O 4177 0.14 0.37 YES
58 COX4I1 COX4I1 COX4I1 4284 0.14 0.37 YES
59 AP2S1 AP2S1 AP2S1 4288 0.14 0.38 YES
60 NDUFS7 NDUFS7 NDUFS7 4301 0.14 0.38 YES
61 CYCS CYCS CYCS 4365 0.13 0.38 YES
62 UQCRFS1 UQCRFS1 UQCRFS1 4384 0.13 0.39 YES
63 CLTA CLTA CLTA 4388 0.13 0.39 YES
64 ATP5D ATP5D ATP5D 4769 0.12 0.38 YES
65 NDUFB2 NDUFB2 NDUFB2 4806 0.12 0.38 YES
66 NDUFS4 NDUFS4 NDUFS4 4810 0.12 0.38 YES
67 SLC25A6 SLC25A6 SLC25A6 4817 0.12 0.39 YES
68 NDUFB8 NDUFB8 NDUFB8 4855 0.12 0.39 YES
69 HTT HTT HTT 4906 0.11 0.39 YES
70 NDUFV2 NDUFV2 NDUFV2 4930 0.11 0.4 YES
71 HDAC2 HDAC2 HDAC2 4976 0.11 0.4 YES
72 UQCRC2 UQCRC2 UQCRC2 4982 0.11 0.4 YES
73 COX6C COX6C COX6C 5021 0.11 0.4 YES
74 POLR2E POLR2E POLR2E 5109 0.11 0.4 YES
75 POLR2F POLR2F POLR2F 5132 0.1 0.41 YES
76 RCOR1 RCOR1 RCOR1 5179 0.1 0.41 YES
77 UQCR11 UQCR11 UQCR11 5247 0.1 0.41 YES
78 TAF4 TAF4 TAF4 5256 0.1 0.41 YES
79 NDUFV1 NDUFV1 NDUFV1 5316 0.099 0.41 YES
80 NDUFS2 NDUFS2 NDUFS2 5321 0.099 0.42 YES
81 POLR2A POLR2A POLR2A 5477 0.094 0.41 YES
82 UQCRQ UQCRQ UQCRQ 5499 0.093 0.41 YES
83 TAF4B TAF4B TAF4B 5532 0.092 0.42 YES
84 NDUFA4L2 NDUFA4L2 NDUFA4L2 5537 0.092 0.42 YES
85 CASP9 CASP9 CASP9 5619 0.09 0.42 YES
86 NDUFB1 NDUFB1 NDUFB1 5640 0.089 0.42 YES
87 COX6B1 COX6B1 COX6B1 5657 0.089 0.42 YES
88 NDUFB6 NDUFB6 NDUFB6 5881 0.083 0.42 YES
89 CREB3 CREB3 CREB3 5989 0.079 0.41 YES
90 TBPL1 TBPL1 TBPL1 6018 0.079 0.41 YES
91 PPARGC1A PPARGC1A PPARGC1A 6054 0.078 0.42 YES
92 TP53 TP53 TP53 6112 0.076 0.42 YES
93 POLR2C POLR2C POLR2C 6123 0.075 0.42 YES
94 NDUFA2 NDUFA2 NDUFA2 6337 0.069 0.41 YES
95 GPX1 GPX1 GPX1 6347 0.069 0.41 YES
96 NDUFB7 NDUFB7 NDUFB7 6369 0.068 0.41 YES
97 UQCRB UQCRB UQCRB 6375 0.068 0.41 YES
98 REST REST REST 6382 0.068 0.42 YES
99 TBP TBP TBP 6441 0.066 0.42 YES
100 NDUFB3 NDUFB3 NDUFB3 6457 0.066 0.42 YES
101 SDHC SDHC SDHC 6518 0.064 0.42 YES
102 NDUFV3 NDUFV3 NDUFV3 6556 0.063 0.42 YES
103 NDUFS1 NDUFS1 NDUFS1 6592 0.063 0.42 YES
104 POLR2L POLR2L POLR2L 6600 0.062 0.42 YES
105 NDUFA5 NDUFA5 NDUFA5 6617 0.062 0.42 YES
106 VDAC3 VDAC3 VDAC3 6631 0.062 0.42 YES
107 NDUFA7 NDUFA7 NDUFA7 6690 0.06 0.42 NO
108 UQCRC1 UQCRC1 UQCRC1 6817 0.056 0.42 NO
109 POLR2J POLR2J POLR2J 6824 0.056 0.42 NO
110 APAF1 APAF1 APAF1 6843 0.055 0.42 NO
111 POLR2I POLR2I POLR2I 7033 0.051 0.41 NO
112 DNAI2 DNAI2 DNAI2 7063 0.05 0.41 NO
113 DCTN2 DCTN2 DCTN2 7235 0.045 0.41 NO
114 SP1 SP1 SP1 7259 0.045 0.41 NO
115 AP2A1 AP2A1 AP2A1 7294 0.044 0.41 NO
116 NDUFA10 NDUFA10 NDUFA10 7367 0.042 0.4 NO
117 UQCR10 UQCR10 UQCR10 7411 0.041 0.4 NO
118 NDUFB5 NDUFB5 NDUFB5 7416 0.04 0.4 NO
119 CLTC CLTC CLTC 7431 0.04 0.41 NO
120 NDUFB4 NDUFB4 NDUFB4 7505 0.038 0.4 NO
121 NDUFS3 NDUFS3 NDUFS3 7604 0.036 0.4 NO
122 ATP5A1 ATP5A1 ATP5A1 7613 0.036 0.4 NO
123 NDUFC1 NDUFC1 NDUFC1 7713 0.033 0.4 NO
124 CREB3L4 CREB3L4 CREB3L4 7966 0.026 0.38 NO
125 COX7B2 COX7B2 COX7B2 7986 0.026 0.38 NO
126 PPID PPID PPID 8368 0.016 0.36 NO
127 POLR2D POLR2D POLR2D 8501 0.013 0.36 NO
128 PLCB3 PLCB3 PLCB3 8512 0.013 0.36 NO
129 DNAH3 DNAH3 DNAH3 8851 0.0045 0.34 NO
130 ATP5G2 ATP5G2 ATP5G2 8925 0.0027 0.34 NO
131 POLR2K POLR2K POLR2K 8983 0.00073 0.33 NO
132 ATP5E ATP5E ATP5E 9000 8e-05 0.33 NO
133 POLR2B POLR2B POLR2B 9081 -0.0021 0.33 NO
134 NRF1 NRF1 NRF1 9114 -0.0029 0.33 NO
135 SIN3A SIN3A SIN3A 9143 -0.0036 0.33 NO
136 TBPL2 TBPL2 TBPL2 9189 -0.0051 0.32 NO
137 SDHA SDHA SDHA 9242 -0.0067 0.32 NO
138 AP2A2 AP2A2 AP2A2 9807 -0.022 0.29 NO
139 POLR2J2 POLR2J2 POLR2J2 9855 -0.023 0.29 NO
140 TGM2 TGM2 TGM2 9975 -0.027 0.28 NO
141 CASP8 CASP8 CASP8 10218 -0.033 0.27 NO
142 DCTN1 DCTN1 DCTN1 10254 -0.034 0.27 NO
143 EP300 EP300 EP300 10453 -0.039 0.26 NO
144 SOD1 SOD1 SOD1 10456 -0.039 0.26 NO
145 COX7A2L COX7A2L COX7A2L 10514 -0.041 0.26 NO
146 IFT57 IFT57 IFT57 10582 -0.043 0.26 NO
147 DCTN4 DCTN4 DCTN4 10776 -0.049 0.25 NO
148 GRM5 GRM5 GRM5 11289 -0.064 0.23 NO
149 POLR2J3 POLR2J3 POLR2J3 11618 -0.073 0.21 NO
150 COX8C COX8C COX8C 11890 -0.082 0.2 NO
151 DNAL1 DNAL1 DNAL1 11997 -0.085 0.2 NO
152 CREBBP CREBBP CREBBP 12148 -0.09 0.2 NO
153 GNAQ GNAQ GNAQ 12321 -0.095 0.19 NO
154 CLTCL1 CLTCL1 CLTCL1 13079 -0.12 0.16 NO
155 SOD2 SOD2 SOD2 13129 -0.12 0.16 NO
156 CREB3L2 CREB3L2 CREB3L2 13154 -0.12 0.16 NO
157 CREB1 CREB1 CREB1 13319 -0.13 0.16 NO
158 COX6A2 COX6A2 COX6A2 13418 -0.13 0.16 NO
159 DLG4 DLG4 DLG4 13656 -0.14 0.15 NO
160 PLCB2 PLCB2 PLCB2 13809 -0.14 0.15 NO
161 COX4I2 COX4I2 COX4I2 13858 -0.15 0.15 NO
162 GRIN2B GRIN2B GRIN2B 13924 -0.15 0.15 NO
163 DNALI1 DNALI1 DNALI1 14842 -0.19 0.11 NO
164 PLCB1 PLCB1 PLCB1 14921 -0.19 0.11 NO
165 DNAL4 DNAL4 DNAL4 15489 -0.22 0.093 NO
166 SLC25A31 SLC25A31 SLC25A31 15665 -0.23 0.093 NO
167 COX6B2 COX6B2 COX6B2 16272 -0.27 0.071 NO
168 CREB3L3 CREB3L3 CREB3L3 16527 -0.29 0.068 NO
169 ITPR1 ITPR1 ITPR1 16585 -0.29 0.077 NO
170 DNAI1 DNAI1 DNAI1 17933 -0.44 0.022 NO
171 PPARG PPARG PPARG 18097 -0.47 0.032 NO
172 DNAH1 DNAH1 DNAH1 18163 -0.49 0.047 NO

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

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

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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 HSPA6 HSPA6 HSPA6 840 0.49 -0.0075 YES
2 HSPA2 HSPA2 HSPA2 1147 0.41 0.0072 YES
3 MAGOH MAGOH MAGOH 1301 0.38 0.028 YES
4 PPIH PPIH PPIH 1638 0.32 0.034 YES
5 MAGOHB MAGOHB MAGOHB 1988 0.28 0.036 YES
6 SNRPA1 SNRPA1 SNRPA1 2084 0.26 0.051 YES
7 SNRPF SNRPF SNRPF 2400 0.24 0.052 YES
8 THOC3 THOC3 THOC3 2550 0.23 0.062 YES
9 THOC4 THOC4 THOC4 2654 0.22 0.073 YES
10 SNRPC SNRPC SNRPC 2784 0.21 0.082 YES
11 TXNL4A TXNL4A TXNL4A 2813 0.21 0.096 YES
12 SF3A3 SF3A3 SF3A3 2882 0.2 0.11 YES
13 BCAS2 BCAS2 BCAS2 2915 0.2 0.12 YES
14 SNRNP40 SNRNP40 SNRNP40 3037 0.2 0.13 YES
15 WBP11 WBP11 WBP11 3057 0.19 0.14 YES
16 PRPF38A PRPF38A PRPF38A 3068 0.19 0.16 YES
17 PPIL1 PPIL1 PPIL1 3101 0.19 0.17 YES
18 RBM22 RBM22 RBM22 3228 0.18 0.18 YES
19 LSM3 LSM3 LSM3 3236 0.18 0.19 YES
20 SNRPD1 SNRPD1 SNRPD1 3315 0.18 0.2 YES
21 ZMAT2 ZMAT2 ZMAT2 3551 0.17 0.2 YES
22 BUD31 BUD31 BUD31 3579 0.17 0.21 YES
23 SNRNP27 SNRNP27 SNRNP27 3624 0.17 0.22 YES
24 EIF4A3 EIF4A3 EIF4A3 3717 0.16 0.23 YES
25 SNRPG SNRPG SNRPG 3840 0.16 0.24 YES
26 RBM8A RBM8A RBM8A 3877 0.15 0.24 YES
27 LSM7 LSM7 LSM7 3899 0.15 0.26 YES
28 LSM6 LSM6 LSM6 3909 0.15 0.27 YES
29 HSPA1A HSPA1A HSPA1A 3995 0.15 0.27 YES
30 PCBP1 PCBP1 PCBP1 4032 0.15 0.28 YES
31 EFTUD2 EFTUD2 EFTUD2 4264 0.14 0.28 YES
32 PPIE PPIE PPIE 4322 0.14 0.29 YES
33 DHX15 DHX15 DHX15 4402 0.13 0.29 YES
34 DHX8 DHX8 DHX8 4414 0.13 0.3 YES
35 HSPA1B HSPA1B HSPA1B 4434 0.13 0.31 YES
36 SNRPB2 SNRPB2 SNRPB2 4495 0.13 0.32 YES
37 PRPF4 PRPF4 PRPF4 4533 0.13 0.33 YES
38 SNRPD3 SNRPD3 SNRPD3 4550 0.13 0.33 YES
39 SNRPA SNRPA SNRPA 4616 0.12 0.34 YES
40 SFRS4 SFRS4 SFRS4 4715 0.12 0.34 YES
41 RBMX RBMX RBMX 4716 0.12 0.35 YES
42 HSPA8 HSPA8 HSPA8 4735 0.12 0.36 YES
43 CWC15 CWC15 CWC15 4745 0.12 0.37 YES
44 SMNDC1 SMNDC1 SMNDC1 4809 0.12 0.38 YES
45 PRPF40A PRPF40A PRPF40A 4878 0.12 0.38 YES
46 SFRS9 SFRS9 SFRS9 4931 0.11 0.39 YES
47 HNRNPA3 HNRNPA3 HNRNPA3 4940 0.11 0.39 YES
48 HNRNPM HNRNPM HNRNPM 4956 0.11 0.4 YES
49 SNRPB SNRPB SNRPB 4983 0.11 0.41 YES
50 PUF60 PUF60 PUF60 5040 0.11 0.41 YES
51 NAA38 NAA38 NAA38 5141 0.1 0.42 YES
52 DDX46 DDX46 DDX46 5374 0.097 0.41 YES
53 NHP2L1 NHP2L1 NHP2L1 5375 0.097 0.42 YES
54 SR140 SR140 SR140 5388 0.097 0.43 YES
55 PRPF8 PRPF8 PRPF8 5411 0.096 0.43 YES
56 SYF2 SYF2 SYF2 5435 0.095 0.44 YES
57 HNRNPC HNRNPC HNRNPC 5540 0.092 0.44 YES
58 SFRS1 SFRS1 SFRS1 5554 0.092 0.45 YES
59 U2AF1 U2AF1 U2AF1 5586 0.091 0.45 YES
60 PRPF18 PRPF18 PRPF18 5618 0.09 0.46 YES
61 PRPF3 PRPF3 PRPF3 5632 0.089 0.46 YES
62 THOC2 THOC2 THOC2 5633 0.089 0.47 YES
63 SF3B14 SF3B14 SF3B14 5659 0.088 0.47 YES
64 LSM2 LSM2 LSM2 5703 0.088 0.48 YES
65 LSM5 LSM5 LSM5 5792 0.085 0.48 YES
66 PQBP1 PQBP1 PQBP1 5863 0.083 0.48 YES
67 SART1 SART1 SART1 6032 0.078 0.48 YES
68 SFRS3 SFRS3 SFRS3 6100 0.076 0.48 YES
69 USP39 USP39 USP39 6176 0.074 0.48 YES
70 SF3B2 SF3B2 SF3B2 6253 0.072 0.48 YES
71 SFRS7 SFRS7 SFRS7 6275 0.071 0.49 YES
72 HNRNPK HNRNPK HNRNPK 6276 0.071 0.5 YES
73 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 6306 0.07 0.5 YES
74 SNRPE SNRPE SNRPE 6380 0.068 0.5 YES
75 CDC40 CDC40 CDC40 6393 0.068 0.5 YES
76 U2AF2 U2AF2 U2AF2 6401 0.067 0.51 YES
77 PHF5A PHF5A PHF5A 6419 0.067 0.51 YES
78 BAT1 BAT1 BAT1 6449 0.066 0.52 YES
79 HNRNPA1 HNRNPA1 HNRNPA1 6497 0.065 0.52 YES
80 TRA2B TRA2B TRA2B 6513 0.064 0.52 YES
81 CTNNBL1 CTNNBL1 CTNNBL1 6610 0.062 0.52 YES
82 PRPF19 PRPF19 PRPF19 6650 0.061 0.52 YES
83 SNRPD2 SNRPD2 SNRPD2 6656 0.061 0.53 YES
84 TCERG1 TCERG1 TCERG1 6739 0.059 0.53 YES
85 LSM4 LSM4 LSM4 6742 0.059 0.53 YES
86 SF3A2 SF3A2 SF3A2 6769 0.058 0.54 YES
87 RBM17 RBM17 RBM17 6801 0.056 0.54 YES
88 SFRS2 SFRS2 SFRS2 6802 0.056 0.54 YES
89 HNRNPU HNRNPU HNRNPU 7000 0.051 0.54 NO
90 SF3A1 SF3A1 SF3A1 7001 0.051 0.54 NO
91 PRPF31 PRPF31 PRPF31 7110 0.048 0.54 NO
92 ISY1 ISY1 ISY1 7137 0.048 0.54 NO
93 NCBP1 NCBP1 NCBP1 7179 0.047 0.54 NO
94 PRPF6 PRPF6 PRPF6 7329 0.043 0.54 NO
95 CDC5L CDC5L CDC5L 7396 0.041 0.54 NO
96 SF3B4 SF3B4 SF3B4 7424 0.04 0.54 NO
97 SLU7 SLU7 SLU7 7448 0.04 0.54 NO
98 SF3B3 SF3B3 SF3B3 7466 0.039 0.54 NO
99 DDX42 DDX42 DDX42 7525 0.038 0.54 NO
100 SNW1 SNW1 SNW1 7658 0.034 0.54 NO
101 SNRNP70 SNRNP70 SNRNP70 7757 0.032 0.54 NO
102 DDX23 DDX23 DDX23 7984 0.026 0.53 NO
103 SF3B5 SF3B5 SF3B5 8024 0.025 0.53 NO
104 CCDC12 CCDC12 CCDC12 8382 0.016 0.51 NO
105 DHX16 DHX16 DHX16 8400 0.016 0.51 NO
106 CRNKL1 CRNKL1 CRNKL1 8874 0.004 0.48 NO
107 SFRS13A SFRS13A SFRS13A 8887 0.0036 0.48 NO
108 DHX38 DHX38 DHX38 8951 0.0018 0.48 NO
109 AQR AQR AQR 9232 -0.0065 0.47 NO
110 DDX5 DDX5 DDX5 9274 -0.0075 0.46 NO
111 ACIN1 ACIN1 ACIN1 9341 -0.0095 0.46 NO
112 SNRNP200 SNRNP200 SNRNP200 9530 -0.015 0.45 NO
113 CHERP CHERP CHERP 9576 -0.016 0.45 NO
114 PLRG1 PLRG1 PLRG1 9633 -0.018 0.45 NO
115 SFRS2B SFRS2B SFRS2B 9667 -0.018 0.45 NO
116 THOC1 THOC1 THOC1 9757 -0.021 0.45 NO
117 TRA2A TRA2A TRA2A 9912 -0.025 0.44 NO
118 SF3B1 SF3B1 SF3B1 9960 -0.026 0.44 NO
119 XAB2 XAB2 XAB2 9997 -0.027 0.44 NO
120 RBM25 RBM25 RBM25 10268 -0.034 0.43 NO
121 PRPF38B PRPF38B PRPF38B 10357 -0.037 0.43 NO
122 SFRS6 SFRS6 SFRS6 10494 -0.04 0.42 NO
123 SFRS5 SFRS5 SFRS5 10566 -0.042 0.42 NO
124 PRPF40B PRPF40B PRPF40B 13385 -0.13 0.28 NO
125 HSPA1L HSPA1L HSPA1L 15479 -0.22 0.19 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 CITRATE CYCLE TCA CYCLE.

Figure S24.  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 OXIDATIVE PHOSPHORYLATION

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 PRKACG PRKACG PRKACG 432 0.67 0.11 YES
2 ACTA1 ACTA1 ACTA1 580 0.58 0.22 YES
3 PAQR5 PAQR5 PAQR5 1635 0.32 0.23 YES
4 PRKAR1B PRKAR1B PRKAR1B 1897 0.29 0.28 YES
5 CDC25C CDC25C CDC25C 2273 0.25 0.31 YES
6 CCNB1 CCNB1 CCNB1 2468 0.23 0.35 YES
7 GNAI1 GNAI1 GNAI1 2628 0.22 0.38 YES
8 PRKAR2A PRKAR2A PRKAR2A 2638 0.22 0.43 YES
9 CDK1 CDK1 CDK1 2642 0.22 0.47 YES
10 GNGT1 GNGT1 GNGT1 2916 0.2 0.5 YES
11 RPS6KA1 RPS6KA1 RPS6KA1 3061 0.19 0.53 YES
12 HRAS HRAS HRAS 4611 0.12 0.47 NO
13 ARPC1B ARPC1B ARPC1B 4664 0.12 0.5 NO
14 GNAS GNAS GNAS 5579 0.091 0.47 NO
15 ARPC2 ARPC2 ARPC2 5878 0.083 0.47 NO
16 ACTR3 ACTR3 ACTR3 5929 0.082 0.48 NO
17 CAP1 CAP1 CAP1 6115 0.076 0.49 NO
18 ARPC4 ARPC4 ARPC4 6167 0.074 0.5 NO
19 MAPK3 MAPK3 MAPK3 6779 0.057 0.48 NO
20 PRKAR2B PRKAR2B PRKAR2B 7212 0.046 0.46 NO
21 PIN1 PIN1 PIN1 7582 0.036 0.45 NO
22 GNB1 GNB1 GNB1 7924 0.028 0.44 NO
23 ARPC3 ARPC3 ARPC3 8092 0.023 0.44 NO
24 ARPC5 ARPC5 ARPC5 9322 -0.0088 0.37 NO
25 PRKAR1A PRKAR1A PRKAR1A 9518 -0.014 0.37 NO
26 ARPC1A ARPC1A ARPC1A 9577 -0.016 0.37 NO
27 ACTR2 ACTR2 ACTR2 10628 -0.044 0.32 NO
28 MAPK1 MAPK1 MAPK1 11102 -0.058 0.31 NO
29 PGR PGR PGR 11402 -0.067 0.31 NO
30 PAQR7 PAQR7 PAQR7 11546 -0.071 0.31 NO
31 SRC SRC SRC 11612 -0.073 0.32 NO
32 MYT1 MYT1 MYT1 12340 -0.096 0.3 NO
33 PRKACB PRKACB PRKACB 15700 -0.23 0.18 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 OXIDATIVE PHOSPHORYLATION.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, 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 PYRIMIDINE 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 CBS CBS CBS 182 0.93 0.22 YES
2 CTH CTH CTH 766 0.51 0.32 YES
3 SEPHS1 SEPHS1 SEPHS1 1192 0.4 0.4 YES
4 PAPSS2 PAPSS2 PAPSS2 2991 0.2 0.35 YES
5 GGT1 GGT1 GGT1 3312 0.18 0.38 YES
6 AHCYL1 AHCYL1 AHCYL1 3604 0.17 0.41 YES
7 TRMT11 TRMT11 TRMT11 4345 0.13 0.4 YES
8 LCMT1 LCMT1 LCMT1 4377 0.13 0.44 YES
9 MAT2A MAT2A MAT2A 4661 0.12 0.45 YES
10 AHCYL2 AHCYL2 AHCYL2 5239 0.1 0.45 YES
11 MAT2B MAT2B MAT2B 5384 0.097 0.46 YES
12 AHCY AHCY AHCY 5496 0.093 0.48 YES
13 METTL2B METTL2B METTL2B 5530 0.092 0.5 YES
14 MARS MARS MARS 5774 0.086 0.51 YES
15 MARS2 MARS2 MARS2 6219 0.073 0.51 NO
16 SCLY SCLY SCLY 7244 0.045 0.46 NO
17 METTL6 METTL6 METTL6 7733 0.032 0.45 NO
18 WBSCR22 WBSCR22 WBSCR22 7746 0.032 0.45 NO
19 HEMK1 HEMK1 HEMK1 9969 -0.027 0.34 NO
20 MAT1A MAT1A MAT1A 10887 -0.052 0.31 NO
21 GGT6 GGT6 GGT6 11107 -0.058 0.31 NO
22 PAPSS1 PAPSS1 PAPSS1 11395 -0.067 0.31 NO
23 GGT7 GGT7 GGT7 11454 -0.069 0.33 NO
24 GGT5 GGT5 GGT5 11834 -0.08 0.33 NO
25 LCMT2 LCMT2 LCMT2 15134 -0.2 0.21 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 PYRIMIDINE METABOLISM.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRIMIDINE 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 LYSINE 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 PDHA1 PDHA1 PDHA1 1221 0.39 0.024 YES
2 DLAT DLAT DLAT 1602 0.32 0.076 YES
3 PC PC PC 2129 0.26 0.11 YES
4 MDH2 MDH2 MDH2 2217 0.25 0.16 YES
5 IDH1 IDH1 IDH1 2786 0.21 0.18 YES
6 SUCLA2 SUCLA2 SUCLA2 2888 0.2 0.22 YES
7 PDHB PDHB PDHB 2902 0.2 0.26 YES
8 IDH3G IDH3G IDH3G 2943 0.2 0.3 YES
9 OGDHL OGDHL OGDHL 2970 0.2 0.35 YES
10 IDH3B IDH3B IDH3B 3443 0.17 0.36 YES
11 SUCLG1 SUCLG1 SUCLG1 3692 0.16 0.39 YES
12 SDHB SDHB SDHB 3771 0.16 0.42 YES
13 SDHD SDHD SDHD 3841 0.16 0.45 YES
14 IDH3A IDH3A IDH3A 3870 0.15 0.48 YES
15 DLD DLD DLD 4052 0.15 0.5 YES
16 FH FH FH 4643 0.12 0.5 NO
17 PDHA2 PDHA2 PDHA2 5739 0.086 0.46 NO
18 DLST DLST DLST 6247 0.072 0.45 NO
19 CS CS CS 6325 0.069 0.46 NO
20 SDHC SDHC SDHC 6518 0.064 0.47 NO
21 PCK2 PCK2 PCK2 6876 0.054 0.46 NO
22 MDH1 MDH1 MDH1 7052 0.05 0.46 NO
23 ACLY ACLY ACLY 8018 0.025 0.42 NO
24 SDHA SDHA SDHA 9242 -0.0067 0.36 NO
25 ACO2 ACO2 ACO2 9601 -0.017 0.34 NO
26 ACO1 ACO1 ACO1 10168 -0.032 0.32 NO
27 IDH2 IDH2 IDH2 11443 -0.069 0.27 NO
28 OGDH OGDH OGDH 11918 -0.082 0.26 NO
29 PCK1 PCK1 PCK1 15991 -0.25 0.1 NO
30 SUCLG2 SUCLG2 SUCLG2 16081 -0.26 0.16 NO

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

Figure S30.  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 SELENOAMINO ACID METABOLISM

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 PSMB2 PSMB2 PSMB2 1782 0.3 -0.046 YES
2 PSMD11 PSMD11 PSMD11 1905 0.29 -0.0064 YES
3 PSMB6 PSMB6 PSMB6 1935 0.28 0.037 YES
4 PSMA5 PSMA5 PSMA5 2141 0.26 0.068 YES
5 PSMB3 PSMB3 PSMB3 2455 0.23 0.089 YES
6 PSMC4 PSMC4 PSMC4 2574 0.22 0.12 YES
7 PSMA7 PSMA7 PSMA7 2588 0.22 0.15 YES
8 PSMD12 PSMD12 PSMD12 2706 0.22 0.18 YES
9 PSMA2 PSMA2 PSMA2 2885 0.2 0.2 YES
10 PSMD3 PSMD3 PSMD3 3083 0.19 0.22 YES
11 PSMA1 PSMA1 PSMA1 3214 0.18 0.25 YES
12 PSMB5 PSMB5 PSMB5 3308 0.18 0.27 YES
13 PSMD7 PSMD7 PSMD7 3505 0.17 0.29 YES
14 PSMC1 PSMC1 PSMC1 3516 0.17 0.32 YES
15 POMP POMP POMP 3655 0.16 0.33 YES
16 PSMC2 PSMC2 PSMC2 3697 0.16 0.36 YES
17 PSMA6 PSMA6 PSMA6 3971 0.15 0.37 YES
18 PSME4 PSME4 PSME4 3998 0.15 0.39 YES
19 PSMB7 PSMB7 PSMB7 4109 0.14 0.41 YES
20 PSMA3 PSMA3 PSMA3 4219 0.14 0.42 YES
21 PSMC3 PSMC3 PSMC3 4292 0.14 0.44 YES
22 PSMD6 PSMD6 PSMD6 4298 0.14 0.46 YES
23 PSMC5 PSMC5 PSMC5 4366 0.13 0.48 YES
24 PSMB1 PSMB1 PSMB1 4448 0.13 0.5 YES
25 SHFM1 SHFM1 SHFM1 4549 0.13 0.51 YES
26 PSME3 PSME3 PSME3 4641 0.12 0.53 YES
27 PSMD2 PSMD2 PSMD2 4650 0.12 0.55 YES
28 PSMB4 PSMB4 PSMB4 4675 0.12 0.56 YES
29 PSMD14 PSMD14 PSMD14 4777 0.12 0.58 YES
30 PSMA4 PSMA4 PSMA4 5075 0.11 0.58 YES
31 PSMD13 PSMD13 PSMD13 5171 0.1 0.59 YES
32 PSMD4 PSMD4 PSMD4 5565 0.091 0.58 NO
33 PSMC6 PSMC6 PSMC6 5986 0.08 0.57 NO
34 PSMD1 PSMD1 PSMD1 6244 0.072 0.57 NO
35 PSMD8 PSMD8 PSMD8 7284 0.044 0.52 NO
36 PSME2 PSME2 PSME2 8622 0.01 0.46 NO
37 PSME1 PSME1 PSME1 10401 -0.038 0.37 NO
38 PSMF1 PSMF1 PSMF1 11071 -0.057 0.34 NO
39 PSMB8 PSMB8 PSMB8 12244 -0.093 0.3 NO
40 PSMA8 PSMA8 PSMA8 12708 -0.11 0.29 NO
41 PSMB9 PSMB9 PSMB9 13196 -0.12 0.28 NO
42 IFNG IFNG IFNG 14069 -0.16 0.26 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 SELENOAMINO ACID METABOLISM.

Figure S32.  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 AMINO SUGAR AND NUCLEOTIDE SUGAR 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 ATP12A ATP12A ATP12A 229 0.86 0.041 YES
2 COX7A1 COX7A1 COX7A1 274 0.8 0.088 YES
3 UQCRHL UQCRHL UQCRHL 1153 0.41 0.066 YES
4 ATP6V1C2 ATP6V1C2 ATP6V1C2 1452 0.35 0.072 YES
5 NDUFS5 NDUFS5 NDUFS5 1624 0.32 0.082 YES
6 UQCRH UQCRH UQCRH 1626 0.32 0.1 YES
7 COX7B COX7B COX7B 1893 0.29 0.1 YES
8 ATP6V0A4 ATP6V0A4 ATP6V0A4 1934 0.28 0.12 YES
9 ATP5H ATP5H ATP5H 2086 0.26 0.13 YES
10 ATP5G1 ATP5G1 ATP5G1 2151 0.26 0.14 YES
11 NDUFS6 NDUFS6 NDUFS6 2302 0.25 0.15 YES
12 NDUFC2 NDUFC2 NDUFC2 2371 0.24 0.16 YES
13 NDUFA9 NDUFA9 NDUFA9 2535 0.23 0.16 YES
14 NDUFA4 NDUFA4 NDUFA4 2705 0.22 0.17 YES
15 NDUFA8 NDUFA8 NDUFA8 2804 0.21 0.18 YES
16 COX5A COX5A COX5A 2880 0.2 0.18 YES
17 NDUFAB1 NDUFAB1 NDUFAB1 2989 0.2 0.19 YES
18 COX7A2 COX7A2 COX7A2 3075 0.19 0.2 YES
19 ATP5G3 ATP5G3 ATP5G3 3130 0.19 0.21 YES
20 NDUFB10 NDUFB10 NDUFB10 3151 0.19 0.22 YES
21 COX11 COX11 COX11 3188 0.19 0.23 YES
22 CYC1 CYC1 CYC1 3332 0.18 0.23 YES
23 ATP5I ATP5I ATP5I 3367 0.18 0.24 YES
24 ATP5J2 ATP5J2 ATP5J2 3387 0.18 0.25 YES
25 NDUFA6 NDUFA6 NDUFA6 3434 0.17 0.26 YES
26 ATP5B ATP5B ATP5B 3473 0.17 0.27 YES
27 COX5B COX5B COX5B 3608 0.17 0.27 YES
28 ATP6V0B ATP6V0B ATP6V0B 3623 0.17 0.28 YES
29 ATP6V0E1 ATP6V0E1 ATP6V0E1 3752 0.16 0.28 YES
30 SDHB SDHB SDHB 3771 0.16 0.29 YES
31 NDUFB9 NDUFB9 NDUFB9 3791 0.16 0.3 YES
32 SDHD SDHD SDHD 3841 0.16 0.31 YES
33 COX8A COX8A COX8A 3872 0.15 0.32 YES
34 ATP5C1 ATP5C1 ATP5C1 3929 0.15 0.32 YES
35 COX7C COX7C COX7C 3965 0.15 0.33 YES
36 NDUFS8 NDUFS8 NDUFS8 3968 0.15 0.34 YES
37 ATP5F1 ATP5F1 ATP5F1 3983 0.15 0.35 YES
38 NDUFA3 NDUFA3 NDUFA3 4046 0.15 0.35 YES
39 NDUFA1 NDUFA1 NDUFA1 4078 0.14 0.36 YES
40 ATP5J ATP5J ATP5J 4155 0.14 0.36 YES
41 COX6A1 COX6A1 COX6A1 4168 0.14 0.37 YES
42 ATP5O ATP5O ATP5O 4177 0.14 0.38 YES
43 COX4I1 COX4I1 COX4I1 4284 0.14 0.38 YES
44 NDUFS7 NDUFS7 NDUFS7 4301 0.14 0.39 YES
45 UQCRFS1 UQCRFS1 UQCRFS1 4384 0.13 0.39 YES
46 ATP6V1F ATP6V1F ATP6V1F 4749 0.12 0.38 YES
47 ATP5L ATP5L ATP5L 4754 0.12 0.39 YES
48 ATP5D ATP5D ATP5D 4769 0.12 0.4 YES
49 NDUFB2 NDUFB2 NDUFB2 4806 0.12 0.4 YES
50 NDUFS4 NDUFS4 NDUFS4 4810 0.12 0.41 YES
51 COX17 COX17 COX17 4823 0.12 0.41 YES
52 NDUFB8 NDUFB8 NDUFB8 4855 0.12 0.42 YES
53 NDUFV2 NDUFV2 NDUFV2 4930 0.11 0.42 YES
54 UQCRC2 UQCRC2 UQCRC2 4982 0.11 0.43 YES
55 COX6C COX6C COX6C 5021 0.11 0.43 YES
56 UQCR11 UQCR11 UQCR11 5247 0.1 0.42 YES
57 NDUFV1 NDUFV1 NDUFV1 5316 0.099 0.43 YES
58 NDUFS2 NDUFS2 NDUFS2 5321 0.099 0.43 YES
59 ATP6V0E2 ATP6V0E2 ATP6V0E2 5390 0.096 0.44 YES
60 UQCRQ UQCRQ UQCRQ 5499 0.093 0.44 YES
61 NDUFA4L2 NDUFA4L2 NDUFA4L2 5537 0.092 0.44 YES
62 NDUFB1 NDUFB1 NDUFB1 5640 0.089 0.44 YES
63 COX6B1 COX6B1 COX6B1 5657 0.089 0.44 YES
64 NDUFA11 NDUFA11 NDUFA11 5841 0.084 0.44 YES
65 NDUFB6 NDUFB6 NDUFB6 5881 0.083 0.44 YES
66 PPA1 PPA1 PPA1 5982 0.08 0.44 YES
67 ATP6V1G1 ATP6V1G1 ATP6V1G1 6084 0.077 0.44 YES
68 NDUFA2 NDUFA2 NDUFA2 6337 0.069 0.43 YES
69 NDUFB7 NDUFB7 NDUFB7 6369 0.068 0.44 YES
70 UQCRB UQCRB UQCRB 6375 0.068 0.44 YES
71 NDUFB3 NDUFB3 NDUFB3 6457 0.066 0.44 YES
72 ATP6V1A ATP6V1A ATP6V1A 6474 0.066 0.44 YES
73 SDHC SDHC SDHC 6518 0.064 0.44 YES
74 NDUFV3 NDUFV3 NDUFV3 6556 0.063 0.45 YES
75 NDUFS1 NDUFS1 NDUFS1 6592 0.063 0.45 YES
76 NDUFA5 NDUFA5 NDUFA5 6617 0.062 0.45 YES
77 NDUFA7 NDUFA7 NDUFA7 6690 0.06 0.45 NO
78 UQCRC1 UQCRC1 UQCRC1 6817 0.056 0.45 NO
79 ATP6AP1 ATP6AP1 ATP6AP1 6888 0.054 0.45 NO
80 LHPP LHPP LHPP 7237 0.045 0.43 NO
81 ATP6V1D ATP6V1D ATP6V1D 7275 0.044 0.43 NO
82 NDUFA10 NDUFA10 NDUFA10 7367 0.042 0.43 NO
83 ATP6V0D1 ATP6V0D1 ATP6V0D1 7401 0.041 0.43 NO
84 UQCR10 UQCR10 UQCR10 7411 0.041 0.43 NO
85 NDUFB5 NDUFB5 NDUFB5 7416 0.04 0.44 NO
86 NDUFB4 NDUFB4 NDUFB4 7505 0.038 0.43 NO
87 NDUFS3 NDUFS3 NDUFS3 7604 0.036 0.43 NO
88 ATP5A1 ATP5A1 ATP5A1 7613 0.036 0.43 NO
89 ATP6V1E1 ATP6V1E1 ATP6V1E1 7653 0.034 0.43 NO
90 NDUFC1 NDUFC1 NDUFC1 7713 0.033 0.43 NO
91 ATP6V0C ATP6V0C ATP6V0C 7932 0.027 0.42 NO
92 COX7B2 COX7B2 COX7B2 7986 0.026 0.42 NO
93 COX10 COX10 COX10 8178 0.021 0.41 NO
94 ATP6V1H ATP6V1H ATP6V1H 8206 0.02 0.41 NO
95 ATP6V1C1 ATP6V1C1 ATP6V1C1 8562 0.012 0.39 NO
96 ATP6V0D2 ATP6V0D2 ATP6V0D2 8899 0.0034 0.37 NO
97 ATP5G2 ATP5G2 ATP5G2 8925 0.0027 0.37 NO
98 ATP5E ATP5E ATP5E 9000 8e-05 0.37 NO
99 ATP6V1B2 ATP6V1B2 ATP6V1B2 9070 -0.0019 0.37 NO
100 SDHA SDHA SDHA 9242 -0.0067 0.36 NO
101 ATP6V0A1 ATP6V0A1 ATP6V0A1 10027 -0.028 0.32 NO
102 COX7A2L COX7A2L COX7A2L 10514 -0.041 0.29 NO
103 ATP6V0A2 ATP6V0A2 ATP6V0A2 10857 -0.051 0.28 NO
104 COX8C COX8C COX8C 11890 -0.082 0.23 NO
105 COX15 COX15 COX15 12038 -0.086 0.23 NO
106 ATP6V1G2 ATP6V1G2 ATP6V1G2 13052 -0.12 0.18 NO
107 TCIRG1 TCIRG1 TCIRG1 13212 -0.12 0.18 NO
108 COX6A2 COX6A2 COX6A2 13418 -0.13 0.18 NO
109 COX4I2 COX4I2 COX4I2 13858 -0.15 0.16 NO
110 ATP6V1E2 ATP6V1E2 ATP6V1E2 14281 -0.16 0.15 NO
111 PPA2 PPA2 PPA2 14540 -0.18 0.15 NO
112 COX6B2 COX6B2 COX6B2 16272 -0.27 0.074 NO
113 ATP4B ATP4B ATP4B 16708 -0.3 0.069 NO
114 ATP4A ATP4A ATP4A 17924 -0.44 0.032 NO
115 ATP6V1B1 ATP6V1B1 ATP6V1B1 17959 -0.45 0.058 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S34.  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 AMINOACYL TRNA BIOSYNTHESIS

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 PAPOLB PAPOLB PAPOLB 450 0.66 0.082 YES
2 ENO1 ENO1 ENO1 1671 0.31 0.067 YES
3 EXOSC3 EXOSC3 EXOSC3 2693 0.22 0.048 YES
4 ENO3 ENO3 ENO3 2738 0.21 0.08 YES
5 C1D C1D C1D 2747 0.21 0.11 YES
6 EXOSC4 EXOSC4 EXOSC4 2904 0.2 0.14 YES
7 HSPA9 HSPA9 HSPA9 3139 0.19 0.16 YES
8 EXOSC7 EXOSC7 EXOSC7 3163 0.19 0.18 YES
9 ENO2 ENO2 ENO2 3225 0.18 0.21 YES
10 LSM3 LSM3 LSM3 3236 0.18 0.24 YES
11 EXOSC2 EXOSC2 EXOSC2 3275 0.18 0.27 YES
12 EXOSC8 EXOSC8 EXOSC8 3541 0.17 0.28 YES
13 EXOSC9 EXOSC9 EXOSC9 3577 0.17 0.3 YES
14 LSM7 LSM7 LSM7 3899 0.15 0.31 YES
15 LSM6 LSM6 LSM6 3909 0.15 0.34 YES
16 PATL1 PATL1 PATL1 4447 0.13 0.33 YES
17 EDC4 EDC4 EDC4 4548 0.13 0.34 YES
18 EXOSC1 EXOSC1 EXOSC1 4658 0.12 0.36 YES
19 HSPD1 HSPD1 HSPD1 4761 0.12 0.37 YES
20 PARN PARN PARN 4840 0.12 0.39 YES
21 DCPS DCPS DCPS 5028 0.11 0.39 YES
22 PAPOLG PAPOLG PAPOLG 5083 0.11 0.41 YES
23 NAA38 NAA38 NAA38 5141 0.1 0.42 YES
24 EXOSC10 EXOSC10 EXOSC10 5417 0.096 0.42 YES
25 LSM2 LSM2 LSM2 5703 0.088 0.42 YES
26 LSM5 LSM5 LSM5 5792 0.085 0.43 YES
27 MPHOSPH6 MPHOSPH6 MPHOSPH6 6187 0.073 0.42 YES
28 DCP1A DCP1A DCP1A 6197 0.073 0.43 YES
29 RQCD1 RQCD1 RQCD1 6693 0.06 0.42 YES
30 CNOT6 CNOT6 CNOT6 6699 0.06 0.42 YES
31 LSM4 LSM4 LSM4 6742 0.059 0.43 YES
32 SKIV2L2 SKIV2L2 SKIV2L2 6832 0.056 0.44 YES
33 PAPD7 PAPD7 PAPD7 7193 0.046 0.42 YES
34 SKIV2L SKIV2L SKIV2L 7341 0.042 0.42 YES
35 CNOT3 CNOT3 CNOT3 7417 0.04 0.43 YES
36 DCP1B DCP1B DCP1B 7470 0.039 0.43 YES
37 XRN2 XRN2 XRN2 7497 0.039 0.44 YES
38 LSM1 LSM1 LSM1 7562 0.037 0.44 YES
39 CNOT1 CNOT1 CNOT1 7866 0.029 0.43 NO
40 CNOT10 CNOT10 CNOT10 8219 0.02 0.41 NO
41 EXOSC5 EXOSC5 EXOSC5 8334 0.017 0.41 NO
42 EXOSC6 EXOSC6 EXOSC6 8722 0.0076 0.39 NO
43 PNPT1 PNPT1 PNPT1 8864 0.0043 0.38 NO
44 DIS3 DIS3 DIS3 8940 0.0022 0.38 NO
45 PAPOLA PAPOLA PAPOLA 9267 -0.0073 0.36 NO
46 TTC37 TTC37 TTC37 9756 -0.021 0.34 NO
47 WDR61 WDR61 WDR61 10148 -0.031 0.32 NO
48 ZCCHC7 ZCCHC7 ZCCHC7 10234 -0.033 0.32 NO
49 EDC3 EDC3 EDC3 10476 -0.04 0.32 NO
50 CNOT7 CNOT7 CNOT7 10772 -0.049 0.31 NO
51 CNOT2 CNOT2 CNOT2 10893 -0.052 0.31 NO
52 DCP2 DCP2 DCP2 11273 -0.063 0.3 NO
53 CNOT4 CNOT4 CNOT4 12053 -0.087 0.28 NO
54 DDX6 DDX6 DDX6 13961 -0.15 0.2 NO
55 CNOT6L CNOT6L CNOT6L 14191 -0.16 0.21 NO
56 XRN1 XRN1 XRN1 16188 -0.26 0.15 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 AMINOACYL TRNA BIOSYNTHESIS.

Figure S36.  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 RIBOSOME

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 RNASEH2B RNASEH2B RNASEH2B 2101 0.26 -0.049 YES
2 RPA3 RPA3 RPA3 2357 0.24 -0.0068 YES
3 RFC2 RFC2 RFC2 2516 0.23 0.038 YES
4 RFC5 RFC5 RFC5 2597 0.22 0.085 YES
5 PRIM1 PRIM1 PRIM1 2825 0.21 0.12 YES
6 MCM4 MCM4 MCM4 2858 0.21 0.17 YES
7 RNASEH1 RNASEH1 RNASEH1 3159 0.19 0.2 YES
8 RFC3 RFC3 RFC3 3377 0.18 0.22 YES
9 RFC4 RFC4 RFC4 3467 0.17 0.26 YES
10 POLE4 POLE4 POLE4 3470 0.17 0.3 YES
11 SSBP1 SSBP1 SSBP1 3499 0.17 0.34 YES
12 MCM2 MCM2 MCM2 3699 0.16 0.36 YES
13 POLA2 POLA2 POLA2 3815 0.16 0.4 YES
14 RNASEH2A RNASEH2A RNASEH2A 4572 0.13 0.38 YES
15 PRIM2 PRIM2 PRIM2 4712 0.12 0.4 YES
16 DNA2 DNA2 DNA2 4763 0.12 0.43 YES
17 RPA2 RPA2 RPA2 4829 0.12 0.45 YES
18 PCNA PCNA PCNA 4978 0.11 0.47 YES
19 RNASEH2C RNASEH2C RNASEH2C 5229 0.1 0.48 YES
20 MCM7 MCM7 MCM7 5319 0.099 0.5 YES
21 MCM6 MCM6 MCM6 5365 0.097 0.52 YES
22 FEN1 FEN1 FEN1 5572 0.091 0.53 YES
23 POLD1 POLD1 POLD1 5855 0.084 0.54 YES
24 POLD2 POLD2 POLD2 6036 0.078 0.54 YES
25 MCM3 MCM3 MCM3 6351 0.069 0.54 YES
26 MCM5 MCM5 MCM5 6494 0.065 0.55 YES
27 POLE2 POLE2 POLE2 9365 -0.01 0.4 NO
28 RFC1 RFC1 RFC1 9649 -0.018 0.39 NO
29 POLE POLE POLE 9836 -0.023 0.39 NO
30 POLD3 POLD3 POLD3 10085 -0.03 0.38 NO
31 POLE3 POLE3 POLE3 10110 -0.03 0.39 NO
32 POLD4 POLD4 POLD4 11674 -0.075 0.32 NO
33 RPA4 RPA4 RPA4 11676 -0.075 0.34 NO
34 LIG1 LIG1 LIG1 12310 -0.095 0.33 NO
35 RPA1 RPA1 RPA1 12955 -0.12 0.32 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 RIBOSOME.

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

genes ES table in pathway: KEGG RNA DEGRADATION

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 CCNA1 CCNA1 CCNA1 70 1.2 0.054 YES
2 GADD45A GADD45A GADD45A 543 0.6 0.058 YES
3 MAD2L2 MAD2L2 MAD2L2 651 0.56 0.08 YES
4 ORC1L ORC1L ORC1L 772 0.51 0.098 YES
5 CDC20 CDC20 CDC20 1178 0.4 0.096 YES
6 CCNE1 CCNE1 CCNE1 1230 0.39 0.11 YES
7 SFN SFN SFN 1263 0.38 0.13 YES
8 CDC6 CDC6 CDC6 1354 0.36 0.14 YES
9 MAD2L1 MAD2L1 MAD2L1 1385 0.36 0.16 YES
10 CDKN1C CDKN1C CDKN1C 1394 0.36 0.18 YES
11 PLK1 PLK1 PLK1 1513 0.34 0.19 YES
12 CDK6 CDK6 CDK6 1584 0.32 0.2 YES
13 MYC MYC MYC 1721 0.31 0.21 YES
14 CCNA2 CCNA2 CCNA2 1769 0.3 0.22 YES
15 CDKN1A CDKN1A CDKN1A 2051 0.27 0.22 YES
16 GADD45B GADD45B GADD45B 2061 0.27 0.23 YES
17 CCND1 CCND1 CCND1 2095 0.26 0.24 YES
18 CCND3 CCND3 CCND3 2109 0.26 0.25 YES
19 CDC25C CDC25C CDC25C 2273 0.25 0.26 YES
20 E2F5 E2F5 E2F5 2300 0.25 0.27 YES
21 PTTG1 PTTG1 PTTG1 2321 0.24 0.28 YES
22 HDAC1 HDAC1 HDAC1 2395 0.24 0.28 YES
23 CCNB1 CCNB1 CCNB1 2468 0.23 0.29 YES
24 CDK7 CDK7 CDK7 2619 0.22 0.3 YES
25 CDC25A CDC25A CDC25A 2620 0.22 0.3 YES
26 CDK1 CDK1 CDK1 2642 0.22 0.32 YES
27 TFDP2 TFDP2 TFDP2 2744 0.21 0.32 YES
28 MCM4 MCM4 MCM4 2858 0.21 0.32 YES
29 CDC26 CDC26 CDC26 3105 0.19 0.32 YES
30 CDC16 CDC16 CDC16 3457 0.17 0.31 YES
31 ANAPC11 ANAPC11 ANAPC11 3576 0.17 0.31 YES
32 ORC6L ORC6L ORC6L 3643 0.16 0.32 YES
33 ORC4L ORC4L ORC4L 3694 0.16 0.32 YES
34 MCM2 MCM2 MCM2 3699 0.16 0.33 YES
35 PKMYT1 PKMYT1 PKMYT1 3748 0.16 0.34 YES
36 YWHAH YWHAH YWHAH 3882 0.15 0.34 YES
37 CHEK2 CHEK2 CHEK2 4058 0.15 0.33 YES
38 CCNB2 CCNB2 CCNB2 4190 0.14 0.33 YES
39 SKP2 SKP2 SKP2 4232 0.14 0.34 YES
40 E2F4 E2F4 E2F4 4318 0.14 0.34 YES
41 CHEK1 CHEK1 CHEK1 4393 0.13 0.34 YES
42 MDM2 MDM2 MDM2 4565 0.13 0.34 YES
43 TFDP1 TFDP1 TFDP1 4614 0.12 0.34 YES
44 BUB1 BUB1 BUB1 4694 0.12 0.34 YES
45 CDC45 CDC45 CDC45 4965 0.11 0.34 YES
46 HDAC2 HDAC2 HDAC2 4976 0.11 0.34 YES
47 PCNA PCNA PCNA 4978 0.11 0.35 YES
48 E2F3 E2F3 E2F3 5106 0.11 0.34 YES
49 SMAD4 SMAD4 SMAD4 5210 0.1 0.34 YES
50 YWHAE YWHAE YWHAE 5214 0.1 0.35 YES
51 MCM7 MCM7 MCM7 5319 0.099 0.35 YES
52 MCM6 MCM6 MCM6 5365 0.097 0.35 YES
53 ANAPC5 ANAPC5 ANAPC5 5525 0.092 0.35 YES
54 CUL1 CUL1 CUL1 5548 0.092 0.35 YES
55 SKP1 SKP1 SKP1 5584 0.091 0.35 YES
56 ANAPC10 ANAPC10 ANAPC10 5643 0.089 0.35 YES
57 STAG2 STAG2 STAG2 5838 0.084 0.35 NO
58 CCNH CCNH CCNH 6016 0.079 0.34 NO
59 PRKDC PRKDC PRKDC 6017 0.079 0.35 NO
60 YWHAZ YWHAZ YWHAZ 6048 0.078 0.35 NO
61 TP53 TP53 TP53 6112 0.076 0.35 NO
62 MCM3 MCM3 MCM3 6351 0.069 0.34 NO
63 MCM5 MCM5 MCM5 6494 0.065 0.34 NO
64 E2F1 E2F1 E2F1 6586 0.063 0.33 NO
65 MAD1L1 MAD1L1 MAD1L1 6815 0.056 0.32 NO
66 ANAPC1 ANAPC1 ANAPC1 6826 0.056 0.33 NO
67 CDKN1B CDKN1B CDKN1B 7161 0.047 0.31 NO
68 CDK4 CDK4 CDK4 7242 0.045 0.31 NO
69 BUB3 BUB3 BUB3 7269 0.044 0.31 NO
70 TTK TTK TTK 7451 0.04 0.3 NO
71 ORC2L ORC2L ORC2L 7484 0.039 0.3 NO
72 ESPL1 ESPL1 ESPL1 7549 0.037 0.3 NO
73 SMC1A SMC1A SMC1A 7572 0.037 0.3 NO
74 YWHAQ YWHAQ YWHAQ 7574 0.037 0.3 NO
75 CDKN2D CDKN2D CDKN2D 7715 0.033 0.3 NO
76 CDC23 CDC23 CDC23 8034 0.025 0.28 NO
77 CDC7 CDC7 CDC7 8233 0.02 0.27 NO
78 CDC27 CDC27 CDC27 8252 0.019 0.27 NO
79 GADD45G GADD45G GADD45G 8595 0.011 0.25 NO
80 FZR1 FZR1 FZR1 9132 -0.0033 0.23 NO
81 SMC3 SMC3 SMC3 9231 -0.0064 0.22 NO
82 YWHAB YWHAB YWHAB 9302 -0.0082 0.22 NO
83 YWHAG YWHAG YWHAG 9325 -0.0089 0.22 NO
84 ZBTB17 ZBTB17 ZBTB17 9337 -0.0093 0.22 NO
85 RBX1 RBX1 RBX1 9741 -0.02 0.2 NO
86 ORC5L ORC5L ORC5L 9990 -0.027 0.18 NO
87 RAD21 RAD21 RAD21 9996 -0.027 0.19 NO
88 EP300 EP300 EP300 10453 -0.039 0.16 NO
89 CDC14B CDC14B CDC14B 10833 -0.05 0.15 NO
90 CCNB3 CCNB3 CCNB3 10849 -0.051 0.15 NO
91 ANAPC2 ANAPC2 ANAPC2 11090 -0.058 0.14 NO
92 SMAD2 SMAD2 SMAD2 11119 -0.058 0.14 NO
93 TGFB3 TGFB3 TGFB3 11122 -0.058 0.14 NO
94 TGFB2 TGFB2 TGFB2 11134 -0.059 0.14 NO
95 STAG1 STAG1 STAG1 11161 -0.06 0.15 NO
96 PTTG2 PTTG2 PTTG2 11252 -0.062 0.14 NO
97 BUB1B BUB1B BUB1B 11316 -0.065 0.14 NO
98 ORC3L ORC3L ORC3L 11470 -0.069 0.14 NO
99 CDC25B CDC25B CDC25B 11626 -0.074 0.14 NO
100 ANAPC13 ANAPC13 ANAPC13 12084 -0.088 0.12 NO
101 TGFB1 TGFB1 TGFB1 12113 -0.088 0.12 NO
102 CREBBP CREBBP CREBBP 12148 -0.09 0.12 NO
103 WEE1 WEE1 WEE1 12481 -0.1 0.11 NO
104 GSK3B GSK3B GSK3B 12628 -0.1 0.1 NO
105 RBL1 RBL1 RBL1 12788 -0.11 0.1 NO
106 E2F2 E2F2 E2F2 12948 -0.12 0.1 NO
107 ANAPC7 ANAPC7 ANAPC7 13017 -0.12 0.1 NO
108 CDK2 CDK2 CDK2 13789 -0.14 0.068 NO
109 ABL1 ABL1 ABL1 14305 -0.17 0.049 NO
110 ANAPC4 ANAPC4 ANAPC4 14408 -0.17 0.052 NO
111 CCND2 CCND2 CCND2 14850 -0.19 0.038 NO
112 ATM ATM ATM 15073 -0.2 0.036 NO
113 SMAD3 SMAD3 SMAD3 15632 -0.23 0.017 NO
114 RB1 RB1 RB1 15675 -0.23 0.026 NO
115 WEE2 WEE2 WEE2 16308 -0.27 0.0064 NO
116 ATR ATR ATR 16388 -0.28 0.016 NO
117 CDC14A CDC14A CDC14A 16550 -0.29 0.022 NO
118 CDKN2A CDKN2A CDKN2A 16643 -0.3 0.031 NO
119 RBL2 RBL2 RBL2 17154 -0.34 0.021 NO
120 CCNE2 CCNE2 CCNE2 17204 -0.34 0.035 NO
121 SMC1B SMC1B SMC1B 17306 -0.36 0.047 NO
122 CDKN2C CDKN2C CDKN2C 17493 -0.38 0.056 NO
123 CDKN2B CDKN2B CDKN2B 18388 -0.55 0.035 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 RNA DEGRADATION.

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

Fold change

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

Expression level

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

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

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
BIOCARTA NO1 PATHWAY 29 genes.ES.table 0.58 1.5 0.046 0.67 0.89 0.41 0.16 0.35 0.45 0.23
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.51 1.4 0.066 0.61 0.89 0.4 0.27 0.29 0.42 0.19
BIOCARTA ALK PATHWAY 36 genes.ES.table 0.65 1.6 0 1 0.54 0.39 0.2 0.31 0.51 0.36
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.55 1.8 0.002 0.78 0.28 0.19 0.15 0.16 0 0.22
BIOCARTA BIOPEPTIDES PATHWAY 41 genes.ES.table 0.48 1.6 0.019 1 0.68 0.29 0.23 0.22 0.78 0.42
BIOCARTA MYOSIN PATHWAY 30 genes.ES.table 0.5 1.5 0.039 0.87 0.8 0.37 0.24 0.28 0.53 0.3
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.38 1.4 0.091 0.54 0.9 0.12 0.09 0.11 0.38 0.16
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 31 genes.ES.table 0.53 1.5 0.084 0.64 0.89 0.36 0.23 0.27 0.43 0.22
KEGG DRUG METABOLISM OTHER ENZYMES 40 genes.ES.table 0.58 1.5 0.042 0.9 0.87 0.42 0.21 0.34 0.6 0.33
KEGG WNT SIGNALING PATHWAY 149 genes.ES.table 0.44 1.4 0.042 0.55 0.89 0.29 0.21 0.23 0.39 0.17
genes ES table in pathway: BIOCARTA NO1 PATHWAY

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 AGT AGT AGT 27 1.5 0.23 YES
2 AGTR1 AGTR1 AGTR1 1112 0.78 0.29 YES
3 EGFR EGFR EGFR 1637 0.65 0.36 YES
4 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 1892 0.6 0.44 YES
5 JUN JUN JUN 1991 0.59 0.52 YES
6 PRKCA PRKCA PRKCA 2877 0.45 0.55 YES
7 SRC SRC SRC 4643 0.26 0.49 NO
8 SHC1 SHC1 SHC1 6405 0.14 0.42 NO
9 MAPK3 MAPK3 MAPK3 7027 0.11 0.41 NO
10 MAPK8 MAPK8 MAPK8 7093 0.11 0.42 NO
11 MAP2K4 MAP2K4 MAP2K4 7177 0.1 0.43 NO
12 MEF2A MEF2A MEF2A 7283 0.098 0.44 NO
13 SOS1 SOS1 SOS1 7574 0.086 0.44 NO
14 CALM3 CALM3 CALM3 7597 0.085 0.45 NO
15 HRAS HRAS HRAS 8209 0.061 0.43 NO
16 PTK2B PTK2B PTK2B 8650 0.044 0.41 NO
17 ATF2 ATF2 ATF2 9345 0.02 0.38 NO
18 CALM1 CALM1 CALM1 9354 0.019 0.38 NO
19 ELK1 ELK1 ELK1 9533 0.014 0.37 NO
20 PAK1 PAK1 PAK1 9702 0.0083 0.36 NO
21 GNAQ GNAQ GNAQ 10375 -0.013 0.33 NO
22 GRB2 GRB2 GRB2 10416 -0.014 0.33 NO
23 MAP3K1 MAP3K1 MAP3K1 10885 -0.028 0.31 NO
24 RAC1 RAC1 RAC1 10891 -0.028 0.32 NO
25 CALM2 CALM2 CALM2 10948 -0.03 0.32 NO
26 RAF1 RAF1 RAF1 11249 -0.039 0.31 NO
27 MEF2D MEF2D MEF2D 11280 -0.04 0.31 NO
28 PTK2 PTK2 PTK2 11282 -0.04 0.32 NO
29 MAP2K2 MAP2K2 MAP2K2 11743 -0.053 0.3 NO
30 MAP2K1 MAP2K1 MAP2K1 12422 -0.073 0.28 NO
31 MAPK1 MAPK1 MAPK1 14349 -0.14 0.2 NO
32 PRKCB PRKCB PRKCB 17060 -0.33 0.1 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: BIOCARTA NO1 PATHWAY.

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 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 AGR 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 BMP5 BMP5 BMP5 3 1.8 0.14 YES
2 HNF1A HNF1A HNF1A 58 1.4 0.24 YES
3 TGFB2 TGFB2 TGFB2 85 1.3 0.34 YES
4 BMP2 BMP2 BMP2 358 1 0.4 YES
5 NOG NOG NOG 882 0.84 0.44 YES
6 BMP4 BMP4 BMP4 1144 0.76 0.48 YES
7 FZD1 FZD1 FZD1 1537 0.67 0.51 YES
8 NKX2-5 NKX2-5 NKX2-5 1769 0.62 0.55 YES
9 BMP7 BMP7 BMP7 2087 0.57 0.57 YES
10 TGFB3 TGFB3 TGFB3 2501 0.51 0.59 YES
11 CHRD CHRD CHRD 2828 0.46 0.61 YES
12 SMAD6 SMAD6 SMAD6 2966 0.44 0.63 YES
13 SMAD1 SMAD1 SMAD1 3428 0.38 0.64 YES
14 TGFBR2 TGFBR2 TGFBR2 3722 0.35 0.65 YES
15 CTNNB1 CTNNB1 CTNNB1 4402 0.29 0.63 NO
16 SMAD4 SMAD4 SMAD4 5033 0.23 0.62 NO
17 NPPB NPPB NPPB 5135 0.22 0.63 NO
18 MYL2 MYL2 MYL2 5994 0.16 0.6 NO
19 TGFBR3 TGFBR3 TGFBR3 6084 0.16 0.6 NO
20 BMPR2 BMPR2 BMPR2 6417 0.14 0.6 NO
21 TGFB1 TGFB1 TGFB1 7215 0.1 0.56 NO
22 SMAD5 SMAD5 SMAD5 7920 0.071 0.53 NO
23 WNT1 WNT1 WNT1 8107 0.065 0.52 NO
24 BMPR1A BMPR1A BMPR1A 8198 0.061 0.52 NO
25 APC APC APC 8495 0.05 0.51 NO
26 GSK3B GSK3B GSK3B 8891 0.036 0.5 NO
27 ATF2 ATF2 ATF2 9345 0.02 0.47 NO
28 TGFBR1 TGFBR1 TGFBR1 9586 0.012 0.46 NO
29 AXIN1 AXIN1 AXIN1 10367 -0.013 0.42 NO
30 RFC1 RFC1 RFC1 10517 -0.017 0.42 NO
31 NPPA NPPA NPPA 10867 -0.027 0.4 NO
32 GATA4 GATA4 GATA4 11517 -0.047 0.37 NO
33 ACVR1 ACVR1 ACVR1 12155 -0.065 0.34 NO
34 DVL1 DVL1 DVL1 13235 -0.099 0.29 NO
35 BMP10 BMP10 BMP10 13282 -0.1 0.3 NO
36 MAP3K7 MAP3K7 MAP3K7 13555 -0.11 0.29 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: BIOCARTA AGR PATHWAY.

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AGR 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 ALK PATHWAY

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 AGT AGT AGT 27 1.5 0.15 YES
2 AGTR2 AGTR2 AGTR2 321 1.1 0.25 YES
3 CAMK2B CAMK2B CAMK2B 1465 0.68 0.26 YES
4 F2 F2 F2 2387 0.52 0.26 YES
5 MYLK MYLK MYLK 2587 0.49 0.3 YES
6 GNAI1 GNAI1 GNAI1 2830 0.46 0.34 YES
7 PRKCA PRKCA PRKCA 2877 0.45 0.38 YES
8 MAPT MAPT MAPT 3184 0.41 0.41 YES
9 GNGT1 GNGT1 GNGT1 3658 0.36 0.42 YES
10 CAMK2D CAMK2D CAMK2D 3803 0.34 0.45 YES
11 CAMK2A CAMK2A CAMK2A 3860 0.34 0.48 YES
12 STAT6 STAT6 STAT6 4412 0.29 0.48 YES
13 GNA11 GNA11 GNA11 4903 0.24 0.48 NO
14 MAPK14 MAPK14 MAPK14 6050 0.16 0.44 NO
15 SHC1 SHC1 SHC1 6405 0.14 0.44 NO
16 MAPK3 MAPK3 MAPK3 7027 0.11 0.41 NO
17 MAPK8 MAPK8 MAPK8 7093 0.11 0.42 NO
18 SOS1 SOS1 SOS1 7574 0.086 0.4 NO
19 CALM3 CALM3 CALM3 7597 0.085 0.41 NO
20 PTK2B PTK2B PTK2B 8650 0.044 0.36 NO
21 PLCG1 PLCG1 PLCG1 8791 0.04 0.36 NO
22 GNB1 GNB1 GNB1 9029 0.031 0.35 NO
23 STAT3 STAT3 STAT3 9056 0.03 0.35 NO
24 FYN FYN FYN 9215 0.025 0.35 NO
25 CALM1 CALM1 CALM1 9354 0.019 0.34 NO
26 STAT2 STAT2 STAT2 10186 -0.0078 0.3 NO
27 STAT5B STAT5B STAT5B 10303 -0.011 0.29 NO
28 GRB2 GRB2 GRB2 10416 -0.014 0.29 NO
29 CAMK2G CAMK2G CAMK2G 10642 -0.021 0.28 NO
30 CALM2 CALM2 CALM2 10948 -0.03 0.27 NO
31 RAF1 RAF1 RAF1 11249 -0.039 0.25 NO
32 JAK2 JAK2 JAK2 11735 -0.053 0.23 NO
33 MAP2K2 MAP2K2 MAP2K2 11743 -0.053 0.24 NO
34 STAT5A STAT5A STAT5A 12206 -0.067 0.22 NO
35 MAP2K1 MAP2K1 MAP2K1 12422 -0.073 0.22 NO
36 STAT1 STAT1 STAT1 13413 -0.11 0.18 NO
37 MAPK1 MAPK1 MAPK1 14349 -0.14 0.14 NO
38 CDK5 CDK5 CDK5 15342 -0.19 0.11 NO
39 STAT4 STAT4 STAT4 15601 -0.2 0.12 NO
40 KNG1 KNG1 KNG1 16699 -0.29 0.089 NO
41 PRKCB PRKCB PRKCB 17060 -0.33 0.1 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: BIOCARTA ALK PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ALK 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 AT1R PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BMP5 BMP5 BMP5 3 1.8 0.064 YES
2 PITX2 PITX2 PITX2 73 1.4 0.11 YES
3 TGFB2 TGFB2 TGFB2 85 1.3 0.15 YES
4 BMP2 BMP2 BMP2 358 1 0.18 YES
5 GDF6 GDF6 GDF6 423 1 0.21 YES
6 FST FST FST 516 0.98 0.24 YES
7 GDF7 GDF7 GDF7 743 0.88 0.26 YES
8 GDF5 GDF5 GDF5 1115 0.78 0.26 YES
9 BMP4 BMP4 BMP4 1144 0.76 0.29 YES
10 INHBA INHBA INHBA 1335 0.71 0.3 YES
11 DCN DCN DCN 1416 0.7 0.32 YES
12 ID2 ID2 ID2 1868 0.61 0.32 YES
13 LTBP1 LTBP1 LTBP1 1886 0.6 0.34 YES
14 INHBB INHBB INHBB 1919 0.6 0.36 YES
15 ID3 ID3 ID3 1920 0.6 0.38 YES
16 BMP7 BMP7 BMP7 2087 0.57 0.39 YES
17 AMH AMH AMH 2209 0.55 0.41 YES
18 BMP8B BMP8B BMP8B 2224 0.55 0.42 YES
19 THBS1 THBS1 THBS1 2313 0.53 0.44 YES
20 TGFB3 TGFB3 TGFB3 2501 0.51 0.45 YES
21 CDKN2B CDKN2B CDKN2B 2579 0.49 0.46 YES
22 THBS3 THBS3 THBS3 2600 0.49 0.48 YES
23 INHBC INHBC INHBC 2717 0.47 0.49 YES
24 ID1 ID1 ID1 2735 0.47 0.5 YES
25 CHRD CHRD CHRD 2828 0.46 0.51 YES
26 AMHR2 AMHR2 AMHR2 2945 0.44 0.52 YES
27 SMAD6 SMAD6 SMAD6 2966 0.44 0.54 YES
28 SMAD1 SMAD1 SMAD1 3428 0.38 0.53 YES
29 BMPR1B BMPR1B BMPR1B 3577 0.37 0.53 YES
30 TGFBR2 TGFBR2 TGFBR2 3722 0.35 0.54 YES
31 LEFTY2 LEFTY2 LEFTY2 3779 0.34 0.55 YES
32 INHBE INHBE INHBE 3933 0.33 0.55 YES
33 ACVR2A ACVR2A ACVR2A 4030 0.32 0.55 YES
34 ACVRL1 ACVRL1 ACVRL1 4226 0.3 0.56 YES
35 THBS4 THBS4 THBS4 4351 0.29 0.56 YES
36 THBS2 THBS2 THBS2 4462 0.28 0.56 YES
37 SMAD9 SMAD9 SMAD9 4514 0.28 0.57 YES
38 BMP6 BMP6 BMP6 4543 0.27 0.58 YES
39 SMAD4 SMAD4 SMAD4 5033 0.23 0.56 NO
40 SMAD7 SMAD7 SMAD7 5308 0.21 0.55 NO
41 COMP COMP COMP 5369 0.2 0.56 NO
42 ROCK2 ROCK2 ROCK2 5538 0.2 0.56 NO
43 LEFTY1 LEFTY1 LEFTY1 5944 0.17 0.54 NO
44 BMPR2 BMPR2 BMPR2 6417 0.14 0.52 NO
45 E2F5 E2F5 E2F5 6563 0.13 0.52 NO
46 MAPK3 MAPK3 MAPK3 7027 0.11 0.5 NO
47 ZFYVE16 ZFYVE16 ZFYVE16 7194 0.1 0.49 NO
48 TGFB1 TGFB1 TGFB1 7215 0.1 0.49 NO
49 SMAD3 SMAD3 SMAD3 7385 0.094 0.49 NO
50 TFDP1 TFDP1 TFDP1 7565 0.086 0.48 NO
51 MYC MYC MYC 7829 0.075 0.47 NO
52 SMAD5 SMAD5 SMAD5 7920 0.071 0.47 NO
53 RBL2 RBL2 RBL2 8048 0.067 0.46 NO
54 BMPR1A BMPR1A BMPR1A 8198 0.061 0.46 NO
55 SMURF1 SMURF1 SMURF1 8471 0.051 0.44 NO
56 CREBBP CREBBP CREBBP 8684 0.043 0.44 NO
57 ACVR1C ACVR1C ACVR1C 8859 0.037 0.43 NO
58 RHOA RHOA RHOA 9233 0.024 0.41 NO
59 ROCK1 ROCK1 ROCK1 9425 0.018 0.4 NO
60 TGFBR1 TGFBR1 TGFBR1 9586 0.012 0.39 NO
61 SMAD2 SMAD2 SMAD2 9597 0.012 0.39 NO
62 RPS6KB2 RPS6KB2 RPS6KB2 9598 0.012 0.39 NO
63 PPP2CB PPP2CB PPP2CB 9612 0.011 0.39 NO
64 SMURF2 SMURF2 SMURF2 10097 -0.0045 0.37 NO
65 SKP1 SKP1 SKP1 10219 -0.0088 0.36 NO
66 SP1 SP1 SP1 10338 -0.012 0.35 NO
67 BMP8A BMP8A BMP8A 10469 -0.016 0.35 NO
68 RPS6KB1 RPS6KB1 RPS6KB1 10584 -0.019 0.34 NO
69 PPP2R1A PPP2R1A PPP2R1A 10929 -0.029 0.32 NO
70 PPP2CA PPP2CA PPP2CA 11607 -0.049 0.29 NO
71 E2F4 E2F4 E2F4 11841 -0.056 0.28 NO
72 ACVR1 ACVR1 ACVR1 12155 -0.065 0.27 NO
73 ID4 ID4 ID4 13167 -0.097 0.22 NO
74 RBL1 RBL1 RBL1 13928 -0.12 0.18 NO
75 EP300 EP300 EP300 13964 -0.13 0.18 NO
76 PPP2R1B PPP2R1B PPP2R1B 13992 -0.13 0.19 NO
77 MAPK1 MAPK1 MAPK1 14349 -0.14 0.17 NO
78 RBX1 RBX1 RBX1 14408 -0.14 0.18 NO
79 CUL1 CUL1 CUL1 14457 -0.15 0.18 NO
80 ACVR2B ACVR2B ACVR2B 14633 -0.15 0.17 NO
81 ZFYVE9 ZFYVE9 ZFYVE9 15054 -0.17 0.16 NO
82 NODAL NODAL NODAL 16233 -0.25 0.1 NO
83 TNF TNF TNF 18113 -0.53 0.023 NO
84 IFNG IFNG IFNG 18662 -0.75 0.02 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: BIOCARTA AT1R PATHWAY.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R 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 BIOPEPTIDES PATHWAY

Table S25.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ITGB6 ITGB6 ITGB6 10 1.6 0.025 YES
2 TNN TNN TNN 164 1.2 0.036 YES
3 COL2A1 COL2A1 COL2A1 197 1.2 0.052 YES
4 MAPK10 MAPK10 MAPK10 239 1.1 0.067 YES
5 ITGB8 ITGB8 ITGB8 387 1 0.075 YES
6 MYL7 MYL7 MYL7 444 1 0.088 YES
7 RELN RELN RELN 595 0.94 0.095 YES
8 ITGA8 ITGA8 ITGA8 619 0.93 0.11 YES
9 HGF HGF HGF 640 0.92 0.12 YES
10 LAMB3 LAMB3 LAMB3 669 0.91 0.13 YES
11 COL4A6 COL4A6 COL4A6 711 0.89 0.14 YES
12 LAMB4 LAMB4 LAMB4 946 0.82 0.15 YES
13 ITGA10 ITGA10 ITGA10 962 0.82 0.16 YES
14 VTN VTN VTN 1016 0.8 0.17 YES
15 PDGFC PDGFC PDGFC 1031 0.8 0.18 YES
16 PDGFRA PDGFRA PDGFRA 1183 0.76 0.18 YES
17 CCND1 CCND1 CCND1 1448 0.69 0.18 YES
18 COL5A2 COL5A2 COL5A2 1464 0.68 0.19 YES
19 COL11A2 COL11A2 COL11A2 1467 0.68 0.2 YES
20 CAV3 CAV3 CAV3 1473 0.68 0.21 YES
21 COL3A1 COL3A1 COL3A1 1483 0.68 0.22 YES
22 FIGF FIGF FIGF 1548 0.67 0.23 YES
23 PDGFD PDGFD PDGFD 1562 0.66 0.24 YES
24 EGFR EGFR EGFR 1637 0.65 0.24 YES
25 COL1A1 COL1A1 COL1A1 1705 0.64 0.25 YES
26 COL11A1 COL11A1 COL11A1 1751 0.63 0.26 YES
27 MYLK2 MYLK2 MYLK2 1765 0.62 0.26 YES
28 IBSP IBSP IBSP 1799 0.62 0.27 YES
29 JUN JUN JUN 1991 0.59 0.27 YES
30 FN1 FN1 FN1 1999 0.58 0.28 YES
31 ITGA2 ITGA2 ITGA2 2005 0.58 0.29 YES
32 MET MET MET 2061 0.58 0.3 YES
33 COL5A1 COL5A1 COL5A1 2064 0.57 0.3 YES
34 EGF EGF EGF 2117 0.56 0.31 YES
35 ITGA3 ITGA3 ITGA3 2136 0.56 0.32 YES
36 CAV2 CAV2 CAV2 2157 0.56 0.32 YES
37 PARVA PARVA PARVA 2169 0.56 0.33 YES
38 FLNC FLNC FLNC 2192 0.55 0.34 YES
39 KDR KDR KDR 2289 0.54 0.34 YES
40 THBS1 THBS1 THBS1 2313 0.53 0.35 YES
41 VEGFA VEGFA VEGFA 2451 0.51 0.35 YES
42 TNC TNC TNC 2523 0.5 0.36 YES
43 ITGA11 ITGA11 ITGA11 2542 0.5 0.36 YES
44 ITGA1 ITGA1 ITGA1 2564 0.5 0.37 YES
45 MYLK MYLK MYLK 2587 0.49 0.38 YES
46 THBS3 THBS3 THBS3 2600 0.49 0.38 YES
47 MYL10 MYL10 MYL10 2623 0.48 0.39 YES
48 LAMB2 LAMB2 LAMB2 2647 0.48 0.39 YES
49 COL6A3 COL6A3 COL6A3 2658 0.48 0.4 YES
50 SHC2 SHC2 SHC2 2686 0.48 0.41 YES
51 MYLPF MYLPF MYLPF 2741 0.47 0.41 YES
52 COL1A2 COL1A2 COL1A2 2793 0.46 0.42 YES
53 VEGFC VEGFC VEGFC 2848 0.46 0.42 YES
54 MYLK3 MYLK3 MYLK3 2872 0.45 0.43 YES
55 PRKCA PRKCA PRKCA 2877 0.45 0.43 YES
56 PDGFRB PDGFRB PDGFRB 2879 0.45 0.44 YES
57 PGF PGF PGF 2961 0.44 0.44 YES
58 FLT1 FLT1 FLT1 3008 0.43 0.45 YES
59 LAMB1 LAMB1 LAMB1 3037 0.43 0.45 YES
60 MYL9 MYL9 MYL9 3230 0.41 0.45 YES
61 COL6A2 COL6A2 COL6A2 3231 0.41 0.45 YES
62 PIK3R1 PIK3R1 PIK3R1 3252 0.4 0.46 YES
63 COL6A1 COL6A1 COL6A1 3298 0.4 0.46 YES
64 COL5A3 COL5A3 COL5A3 3363 0.39 0.47 YES
65 ITGA5 ITGA5 ITGA5 3399 0.38 0.47 YES
66 ITGAV ITGAV ITGAV 3414 0.38 0.48 YES
67 ERBB2 ERBB2 ERBB2 3499 0.37 0.48 YES
68 BCL2 BCL2 BCL2 3542 0.37 0.48 YES
69 LAMA2 LAMA2 LAMA2 3685 0.36 0.48 YES
70 CAPN2 CAPN2 CAPN2 3689 0.35 0.48 YES
71 CAV1 CAV1 CAV1 3723 0.35 0.49 YES
72 VWF VWF VWF 3727 0.35 0.49 YES
73 ITGA7 ITGA7 ITGA7 3804 0.34 0.49 YES
74 SOS2 SOS2 SOS2 3838 0.34 0.5 YES
75 LAMC3 LAMC3 LAMC3 3924 0.33 0.5 YES
76 LAMA4 LAMA4 LAMA4 3932 0.33 0.5 YES
77 LAMA3 LAMA3 LAMA3 3978 0.33 0.5 YES
78 LAMC2 LAMC2 LAMC2 3997 0.32 0.51 YES
79 BAD BAD BAD 4007 0.32 0.51 YES
80 VAV3 VAV3 VAV3 4163 0.31 0.51 YES
81 SHC4 SHC4 SHC4 4184 0.31 0.51 YES
82 COL4A1 COL4A1 COL4A1 4330 0.29 0.51 YES
83 THBS4 THBS4 THBS4 4351 0.29 0.51 YES
84 TNXB TNXB TNXB 4369 0.29 0.52 YES
85 CTNNB1 CTNNB1 CTNNB1 4402 0.29 0.52 YES
86 THBS2 THBS2 THBS2 4462 0.28 0.52 YES
87 VEGFB VEGFB VEGFB 4489 0.28 0.52 YES
88 COL4A2 COL4A2 COL4A2 4495 0.28 0.53 YES
89 SRC SRC SRC 4643 0.26 0.52 YES
90 ITGB4 ITGB4 ITGB4 4744 0.26 0.52 YES
91 PAK3 PAK3 PAK3 4746 0.26 0.53 YES
92 FLT4 FLT4 FLT4 4787 0.25 0.53 YES
93 PDGFB PDGFB PDGFB 4842 0.25 0.53 YES
94 DOCK1 DOCK1 DOCK1 4906 0.24 0.53 YES
95 BCAR1 BCAR1 BCAR1 4918 0.24 0.53 YES
96 ITGB3 ITGB3 ITGB3 5007 0.23 0.53 YES
97 CHAD CHAD CHAD 5008 0.23 0.54 YES
98 PAK7 PAK7 PAK7 5208 0.22 0.53 NO
99 TNR TNR TNR 5356 0.21 0.52 NO
100 COMP COMP COMP 5369 0.2 0.53 NO
101 ROCK2 ROCK2 ROCK2 5538 0.2 0.52 NO
102 AKT3 AKT3 AKT3 5541 0.2 0.52 NO
103 GRLF1 GRLF1 GRLF1 5605 0.19 0.52 NO
104 ITGB5 ITGB5 ITGB5 5886 0.17 0.51 NO
105 SPP1 SPP1 SPP1 5888 0.17 0.51 NO
106 MYL5 MYL5 MYL5 5908 0.17 0.52 NO
107 VCL VCL VCL 5943 0.17 0.52 NO
108 MYL2 MYL2 MYL2 5994 0.16 0.52 NO
109 AKT1 AKT1 AKT1 6171 0.15 0.51 NO
110 LAMA1 LAMA1 LAMA1 6274 0.15 0.51 NO
111 IGF1 IGF1 IGF1 6294 0.15 0.51 NO
112 ILK ILK ILK 6305 0.15 0.51 NO
113 SHC1 SHC1 SHC1 6405 0.14 0.51 NO
114 PDPK1 PDPK1 PDPK1 6451 0.14 0.51 NO
115 COL4A4 COL4A4 COL4A4 6487 0.14 0.51 NO
116 PDGFA PDGFA PDGFA 6510 0.14 0.51 NO
117 LAMA5 LAMA5 LAMA5 6536 0.13 0.51 NO
118 FLNA FLNA FLNA 6614 0.13 0.51 NO
119 ITGA9 ITGA9 ITGA9 6730 0.12 0.5 NO
120 BIRC2 BIRC2 BIRC2 6740 0.12 0.5 NO
121 ARHGAP5 ARHGAP5 ARHGAP5 6926 0.11 0.5 NO
122 MAPK3 MAPK3 MAPK3 7027 0.11 0.49 NO
123 PAK6 PAK6 PAK6 7046 0.11 0.49 NO
124 MAPK8 MAPK8 MAPK8 7093 0.11 0.49 NO
125 CCND2 CCND2 CCND2 7372 0.094 0.48 NO
126 SOS1 SOS1 SOS1 7574 0.086 0.47 NO
127 MYL12B MYL12B MYL12B 7600 0.085 0.47 NO
128 TLN1 TLN1 TLN1 7760 0.078 0.46 NO
129 PARVB PARVB PARVB 7771 0.077 0.46 NO
130 PPP1R12A PPP1R12A PPP1R12A 7801 0.076 0.46 NO
131 ITGA4 ITGA4 ITGA4 7911 0.072 0.46 NO
132 MAPK9 MAPK9 MAPK9 8238 0.06 0.44 NO
133 ITGB1 ITGB1 ITGB1 8271 0.058 0.44 NO
134 PIK3CA PIK3CA PIK3CA 8393 0.054 0.43 NO
135 PPP1CB PPP1CB PPP1CB 8397 0.054 0.44 NO
136 AKT2 AKT2 AKT2 8444 0.052 0.43 NO
137 PIP5K1C PIP5K1C PIP5K1C 8535 0.049 0.43 NO
138 ACTG1 ACTG1 ACTG1 8889 0.036 0.41 NO
139 GSK3B GSK3B GSK3B 8891 0.036 0.41 NO
140 PAK4 PAK4 PAK4 9043 0.031 0.4 NO
141 PTEN PTEN PTEN 9141 0.027 0.4 NO
142 FYN FYN FYN 9215 0.025 0.4 NO
143 RHOA RHOA RHOA 9233 0.024 0.4 NO
144 SHC3 SHC3 SHC3 9369 0.019 0.39 NO
145 ACTN1 ACTN1 ACTN1 9375 0.019 0.39 NO
146 ROCK1 ROCK1 ROCK1 9425 0.018 0.39 NO
147 ELK1 ELK1 ELK1 9533 0.014 0.38 NO
148 RAP1A RAP1A RAP1A 9680 0.009 0.37 NO
149 PAK1 PAK1 PAK1 9702 0.0083 0.37 NO
150 LAMC1 LAMC1 LAMC1 9708 0.0082 0.37 NO
151 CDC42 CDC42 CDC42 9744 0.007 0.37 NO
152 PAK2 PAK2 PAK2 9820 0.0045 0.37 NO
153 ACTN4 ACTN4 ACTN4 10030 -0.0021 0.36 NO
154 PIK3R2 PIK3R2 PIK3R2 10039 -0.0024 0.36 NO
155 ACTB ACTB ACTB 10142 -0.006 0.35 NO
156 MYL12A MYL12A MYL12A 10212 -0.0085 0.35 NO
157 ACTN2 ACTN2 ACTN2 10261 -0.0098 0.34 NO
158 GRB2 GRB2 GRB2 10416 -0.014 0.34 NO
159 XIAP XIAP XIAP 10831 -0.026 0.31 NO
160 RAC1 RAC1 RAC1 10891 -0.028 0.31 NO
161 PPP1CC PPP1CC PPP1CC 11076 -0.034 0.3 NO
162 FLNB FLNB FLNB 11110 -0.034 0.3 NO
163 IGF1R IGF1R IGF1R 11150 -0.036 0.3 NO
164 RAF1 RAF1 RAF1 11249 -0.039 0.3 NO
165 CCND3 CCND3 CCND3 11267 -0.039 0.3 NO
166 PTK2 PTK2 PTK2 11282 -0.04 0.29 NO
167 CRK CRK CRK 11290 -0.04 0.3 NO
168 CRKL CRKL CRKL 11528 -0.047 0.28 NO
169 PPP1CA PPP1CA PPP1CA 11900 -0.058 0.26 NO
170 RAP1B RAP1B RAP1B 12027 -0.062 0.26 NO
171 PXN PXN PXN 12268 -0.068 0.25 NO
172 TLN2 TLN2 TLN2 12361 -0.071 0.24 NO
173 MAP2K1 MAP2K1 MAP2K1 12422 -0.073 0.24 NO
174 PIK3R5 PIK3R5 PIK3R5 12457 -0.074 0.24 NO
175 DIAPH1 DIAPH1 DIAPH1 12706 -0.082 0.23 NO
176 PIK3R3 PIK3R3 PIK3R3 13421 -0.11 0.19 NO
177 ZYX ZYX ZYX 13821 -0.12 0.17 NO
178 VASP VASP VASP 13929 -0.12 0.17 NO
179 PIK3CB PIK3CB PIK3CB 14057 -0.13 0.16 NO
180 MAPK1 MAPK1 MAPK1 14349 -0.14 0.15 NO
181 RAPGEF1 RAPGEF1 RAPGEF1 14738 -0.16 0.13 NO
182 COL6A6 COL6A6 COL6A6 14784 -0.16 0.13 NO
183 ITGA6 ITGA6 ITGA6 15333 -0.19 0.11 NO
184 RAC3 RAC3 RAC3 15794 -0.22 0.086 NO
185 ACTN3 ACTN3 ACTN3 15926 -0.22 0.082 NO
186 BRAF BRAF BRAF 16079 -0.23 0.078 NO
187 VAV2 VAV2 VAV2 16156 -0.24 0.078 NO
188 PARVG PARVG PARVG 16811 -0.3 0.048 NO
189 PRKCB PRKCB PRKCB 17060 -0.33 0.04 NO
190 RAC2 RAC2 RAC2 17111 -0.34 0.042 NO
191 BIRC3 BIRC3 BIRC3 17322 -0.37 0.036 NO
192 ITGB7 ITGB7 ITGB7 17388 -0.38 0.039 NO
193 RASGRF1 RASGRF1 RASGRF1 17398 -0.38 0.044 NO
194 PIK3CG PIK3CG PIK3CG 17452 -0.38 0.047 NO
195 PIK3CD PIK3CD PIK3CD 17796 -0.45 0.036 NO
196 VAV1 VAV1 VAV1 17982 -0.49 0.034 NO
197 ITGA2B ITGA2B ITGA2B 18389 -0.62 0.022 NO
198 PRKCG PRKCG PRKCG 18778 -0.84 0.014 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: BIOCARTA BIOPEPTIDES PATHWAY.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA BIOPEPTIDES 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 MYOSIN PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SEMA3E SEMA3E SEMA3E 136 1.2 0.02 YES
2 SEMA3C SEMA3C SEMA3C 181 1.2 0.045 YES
3 EPHA3 EPHA3 EPHA3 187 1.2 0.07 YES
4 EFNA5 EFNA5 EFNA5 196 1.2 0.096 YES
5 SEMA3D SEMA3D SEMA3D 201 1.2 0.12 YES
6 NTN1 NTN1 NTN1 370 1 0.14 YES
7 SEMA5B SEMA5B SEMA5B 427 1 0.16 YES
8 UNC5C UNC5C UNC5C 536 0.97 0.17 YES
9 LRRC4C LRRC4C LRRC4C 746 0.88 0.18 YES
10 SEMA6D SEMA6D SEMA6D 754 0.88 0.2 YES
11 RHOD RHOD RHOD 799 0.86 0.22 YES
12 NTN3 NTN3 NTN3 801 0.86 0.24 YES
13 SLIT3 SLIT3 SLIT3 804 0.86 0.26 YES
14 SEMA5A SEMA5A SEMA5A 853 0.85 0.27 YES
15 SEMA3B SEMA3B SEMA3B 859 0.85 0.29 YES
16 SRGAP3 SRGAP3 SRGAP3 883 0.84 0.31 YES
17 SLIT2 SLIT2 SLIT2 1027 0.8 0.32 YES
18 EPHA4 EPHA4 EPHA4 1320 0.72 0.32 YES
19 EPHA2 EPHA2 EPHA2 1331 0.71 0.33 YES
20 EFNA1 EFNA1 EFNA1 1394 0.7 0.35 YES
21 PLXNB3 PLXNB3 PLXNB3 1456 0.69 0.36 YES
22 ROBO2 ROBO2 ROBO2 1655 0.65 0.36 YES
23 EFNA2 EFNA2 EFNA2 1714 0.64 0.37 YES
24 EFNB1 EFNB1 EFNB1 1755 0.63 0.38 YES
25 EPHB1 EPHB1 EPHB1 1875 0.61 0.39 YES
26 MET MET MET 2061 0.58 0.4 YES
27 ROBO3 ROBO3 ROBO3 2114 0.56 0.4 YES
28 EPHA5 EPHA5 EPHA5 2188 0.55 0.41 YES
29 SEMA3F SEMA3F SEMA3F 2230 0.55 0.42 YES
30 EFNB2 EFNB2 EFNB2 2259 0.54 0.43 YES
31 PPP3CA PPP3CA PPP3CA 2267 0.54 0.45 YES
32 EPHB2 EPHB2 EPHB2 2293 0.53 0.46 YES
33 CHP2 CHP2 CHP2 2434 0.52 0.46 YES
34 SEMA3G SEMA3G SEMA3G 2555 0.5 0.46 YES
35 UNC5A UNC5A UNC5A 2589 0.49 0.47 YES
36 NTN4 NTN4 NTN4 2643 0.48 0.48 YES
37 CFL2 CFL2 CFL2 2694 0.48 0.49 YES
38 ROBO1 ROBO1 ROBO1 2786 0.46 0.5 YES
39 GNAI1 GNAI1 GNAI1 2830 0.46 0.5 YES
40 UNC5B UNC5B UNC5B 2867 0.45 0.51 YES
41 EPHB3 EPHB3 EPHB3 2898 0.45 0.52 YES
42 PLXNA3 PLXNA3 PLXNA3 2977 0.44 0.53 YES
43 NFATC4 NFATC4 NFATC4 3028 0.43 0.53 YES
44 SEMA4G SEMA4G SEMA4G 3110 0.42 0.54 YES
45 PLXNB1 PLXNB1 PLXNB1 3139 0.42 0.55 YES
46 NRP1 NRP1 NRP1 3611 0.36 0.53 YES
47 DCC DCC DCC 3694 0.35 0.53 YES
48 RND1 RND1 RND1 3791 0.34 0.54 YES
49 EFNB3 EFNB3 EFNB3 3822 0.34 0.54 YES
50 EPHB6 EPHB6 EPHB6 4017 0.32 0.54 YES
51 EPHA7 EPHA7 EPHA7 4058 0.32 0.54 YES
52 PLXNA2 PLXNA2 PLXNA2 4081 0.32 0.55 YES
53 ABLIM1 ABLIM1 ABLIM1 4197 0.3 0.55 YES
54 SEMA3A SEMA3A SEMA3A 4277 0.3 0.55 YES
55 SLIT1 SLIT1 SLIT1 4477 0.28 0.55 NO
56 RGS3 RGS3 RGS3 4578 0.27 0.55 NO
57 UNC5D UNC5D UNC5D 4741 0.26 0.55 NO
58 PAK3 PAK3 PAK3 4746 0.26 0.55 NO
59 PLXNB2 PLXNB2 PLXNB2 4875 0.24 0.55 NO
60 SEMA6C SEMA6C SEMA6C 5018 0.23 0.55 NO
61 ARHGEF12 ARHGEF12 ARHGEF12 5196 0.22 0.54 NO
62 PAK7 PAK7 PAK7 5208 0.22 0.55 NO
63 NFATC2 NFATC2 NFATC2 5512 0.2 0.54 NO
64 ROCK2 ROCK2 ROCK2 5538 0.2 0.54 NO
65 NFAT5 NFAT5 NFAT5 5777 0.18 0.53 NO
66 EPHA6 EPHA6 EPHA6 5789 0.18 0.53 NO
67 PLXNA1 PLXNA1 PLXNA1 5851 0.18 0.53 NO
68 SEMA4F SEMA4F SEMA4F 5906 0.17 0.54 NO
69 CXCL12 CXCL12 CXCL12 6462 0.14 0.51 NO
70 SEMA4B SEMA4B SEMA4B 6936 0.11 0.49 NO
71 ABL1 ABL1 ABL1 7024 0.11 0.48 NO
72 MAPK3 MAPK3 MAPK3 7027 0.11 0.49 NO
73 PAK6 PAK6 PAK6 7046 0.11 0.49 NO
74 PLXNC1 PLXNC1 PLXNC1 7135 0.1 0.49 NO
75 ABLIM3 ABLIM3 ABLIM3 7193 0.1 0.48 NO
76 NFATC1 NFATC1 NFATC1 7365 0.094 0.48 NO
77 CXCR4 CXCR4 CXCR4 7544 0.087 0.47 NO
78 GNAI2 GNAI2 GNAI2 7926 0.071 0.45 NO
79 NRAS NRAS NRAS 7987 0.069 0.45 NO
80 SRGAP2 SRGAP2 SRGAP2 8237 0.06 0.44 NO
81 ITGB1 ITGB1 ITGB1 8271 0.058 0.44 NO
82 RASA1 RASA1 RASA1 8318 0.057 0.44 NO
83 PPP3CB PPP3CB PPP3CB 8733 0.042 0.42 NO
84 CFL1 CFL1 CFL1 8792 0.04 0.41 NO
85 GSK3B GSK3B GSK3B 8891 0.036 0.41 NO
86 EPHA1 EPHA1 EPHA1 8977 0.033 0.41 NO
87 PAK4 PAK4 PAK4 9043 0.031 0.4 NO
88 GNAI3 GNAI3 GNAI3 9127 0.027 0.4 NO
89 FYN FYN FYN 9215 0.025 0.4 NO
90 RHOA RHOA RHOA 9233 0.024 0.4 NO
91 ROCK1 ROCK1 ROCK1 9425 0.018 0.38 NO
92 DPYSL2 DPYSL2 DPYSL2 9508 0.015 0.38 NO
93 NFATC3 NFATC3 NFATC3 9602 0.012 0.38 NO
94 PAK1 PAK1 PAK1 9702 0.0083 0.37 NO
95 CDC42 CDC42 CDC42 9744 0.007 0.37 NO
96 PAK2 PAK2 PAK2 9820 0.0045 0.37 NO
97 SEMA6B SEMA6B SEMA6B 9940 0.00063 0.36 NO
98 NCK2 NCK2 NCK2 10357 -0.012 0.34 NO
99 SEMA7A SEMA7A SEMA7A 10591 -0.019 0.33 NO
100 NCK1 NCK1 NCK1 10851 -0.027 0.31 NO
101 RAC1 RAC1 RAC1 10891 -0.028 0.31 NO
102 KRAS KRAS KRAS 11036 -0.032 0.3 NO
103 L1CAM L1CAM L1CAM 11270 -0.039 0.29 NO
104 PTK2 PTK2 PTK2 11282 -0.04 0.29 NO
105 EFNA4 EFNA4 EFNA4 11526 -0.047 0.28 NO
106 PPP3R1 PPP3R1 PPP3R1 11682 -0.051 0.27 NO
107 FES FES FES 11696 -0.052 0.28 NO
108 ABLIM2 ABLIM2 ABLIM2 11844 -0.056 0.27 NO
109 NTNG1 NTNG1 NTNG1 12309 -0.069 0.24 NO
110 SEMA4C SEMA4C SEMA4C 12470 -0.075 0.24 NO
111 PPP3CC PPP3CC PPP3CC 13504 -0.11 0.19 NO
112 LIMK1 LIMK1 LIMK1 13857 -0.12 0.17 NO
113 EFNA3 EFNA3 EFNA3 13923 -0.12 0.17 NO
114 SEMA6A SEMA6A SEMA6A 14070 -0.13 0.16 NO
115 MAPK1 MAPK1 MAPK1 14349 -0.14 0.15 NO
116 DPYSL5 DPYSL5 DPYSL5 14588 -0.15 0.14 NO
117 LIMK2 LIMK2 LIMK2 15303 -0.19 0.11 NO
118 CDK5 CDK5 CDK5 15342 -0.19 0.11 NO
119 EPHB4 EPHB4 EPHB4 15662 -0.21 0.1 NO
120 RAC3 RAC3 RAC3 15794 -0.22 0.099 NO
121 SEMA4D SEMA4D SEMA4D 16400 -0.26 0.072 NO
122 CHP CHP CHP 16545 -0.27 0.071 NO
123 SEMA4A SEMA4A SEMA4A 16609 -0.28 0.074 NO
124 SRGAP1 SRGAP1 SRGAP1 16765 -0.3 0.072 NO
125 RAC2 RAC2 RAC2 17111 -0.34 0.062 NO
126 PPP3R2 PPP3R2 PPP3R2 17217 -0.35 0.064 NO
127 EPHA8 EPHA8 EPHA8 18391 -0.62 0.016 NO
128 NGEF NGEF NGEF 18793 -0.85 0.014 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: BIOCARTA MYOSIN PATHWAY.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MYOSIN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

Table 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 TGFB2 TGFB2 TGFB2 85 1.3 0.086 YES
2 ARNT2 ARNT2 ARNT2 305 1.1 0.15 YES
3 HGF HGF HGF 640 0.92 0.2 YES
4 FIGF FIGF FIGF 1548 0.67 0.19 YES
5 JUN JUN JUN 1991 0.59 0.21 YES
6 MET MET MET 2061 0.58 0.24 YES
7 VEGFA VEGFA VEGFA 2451 0.51 0.26 YES
8 TGFB3 TGFB3 TGFB3 2501 0.51 0.29 YES
9 TGFA TGFA TGFA 2660 0.48 0.32 YES
10 VEGFC VEGFC VEGFC 2848 0.46 0.34 YES
11 PGF PGF PGF 2961 0.44 0.36 YES
12 PIK3R1 PIK3R1 PIK3R1 3252 0.4 0.38 YES
13 EPAS1 EPAS1 EPAS1 3307 0.4 0.4 YES
14 SOS2 SOS2 SOS2 3838 0.34 0.39 YES
15 VEGFB VEGFB VEGFB 4489 0.28 0.38 YES
16 PAK3 PAK3 PAK3 4746 0.26 0.38 YES
17 PDGFB PDGFB PDGFB 4842 0.25 0.4 YES
18 PAK7 PAK7 PAK7 5208 0.22 0.39 YES
19 GAB1 GAB1 GAB1 5219 0.21 0.4 YES
20 AKT3 AKT3 AKT3 5541 0.2 0.4 NO
21 AKT1 AKT1 AKT1 6171 0.15 0.38 NO
22 EGLN3 EGLN3 EGLN3 6380 0.14 0.38 NO
23 ARAF ARAF ARAF 6872 0.12 0.36 NO
24 MAPK3 MAPK3 MAPK3 7027 0.11 0.36 NO
25 PAK6 PAK6 PAK6 7046 0.11 0.37 NO
26 VHL VHL VHL 7073 0.11 0.37 NO
27 ARNT ARNT ARNT 7078 0.11 0.38 NO
28 TGFB1 TGFB1 TGFB1 7215 0.1 0.38 NO
29 SOS1 SOS1 SOS1 7574 0.086 0.37 NO
30 EGLN1 EGLN1 EGLN1 7589 0.085 0.37 NO
31 NRAS NRAS NRAS 7987 0.069 0.36 NO
32 FLCN FLCN FLCN 8023 0.068 0.36 NO
33 SLC2A1 SLC2A1 SLC2A1 8310 0.057 0.35 NO
34 PIK3CA PIK3CA PIK3CA 8393 0.054 0.35 NO
35 ETS1 ETS1 ETS1 8443 0.052 0.35 NO
36 AKT2 AKT2 AKT2 8444 0.052 0.35 NO
37 CREBBP CREBBP CREBBP 8684 0.043 0.34 NO
38 HIF1A HIF1A HIF1A 9017 0.032 0.33 NO
39 PAK4 PAK4 PAK4 9043 0.031 0.33 NO
40 FH FH FH 9422 0.018 0.31 NO
41 RAP1A RAP1A RAP1A 9680 0.009 0.3 NO
42 PAK1 PAK1 PAK1 9702 0.0083 0.29 NO
43 CDC42 CDC42 CDC42 9744 0.007 0.29 NO
44 PAK2 PAK2 PAK2 9820 0.0045 0.29 NO
45 PIK3R2 PIK3R2 PIK3R2 10039 -0.0024 0.28 NO
46 GRB2 GRB2 GRB2 10416 -0.014 0.26 NO
47 PTPN11 PTPN11 PTPN11 10590 -0.019 0.25 NO
48 RAC1 RAC1 RAC1 10891 -0.028 0.24 NO
49 KRAS KRAS KRAS 11036 -0.032 0.23 NO
50 RAF1 RAF1 RAF1 11249 -0.039 0.22 NO
51 CRK CRK CRK 11290 -0.04 0.22 NO
52 EGLN2 EGLN2 EGLN2 11373 -0.042 0.22 NO
53 CRKL CRKL CRKL 11528 -0.047 0.22 NO
54 MAP2K2 MAP2K2 MAP2K2 11743 -0.053 0.21 NO
55 TCEB2 TCEB2 TCEB2 11990 -0.06 0.2 NO
56 RAP1B RAP1B RAP1B 12027 -0.062 0.2 NO
57 MAP2K1 MAP2K1 MAP2K1 12422 -0.073 0.19 NO
58 PIK3R5 PIK3R5 PIK3R5 12457 -0.074 0.19 NO
59 PIK3R3 PIK3R3 PIK3R3 13421 -0.11 0.15 NO
60 CUL2 CUL2 CUL2 13925 -0.12 0.13 NO
61 EP300 EP300 EP300 13964 -0.13 0.14 NO
62 PIK3CB PIK3CB PIK3CB 14057 -0.13 0.14 NO
63 MAPK1 MAPK1 MAPK1 14349 -0.14 0.14 NO
64 RBX1 RBX1 RBX1 14408 -0.14 0.14 NO
65 RAPGEF1 RAPGEF1 RAPGEF1 14738 -0.16 0.14 NO
66 BRAF BRAF BRAF 16079 -0.23 0.081 NO
67 TCEB1 TCEB1 TCEB1 16466 -0.27 0.079 NO
68 PIK3CG PIK3CG PIK3CG 17452 -0.38 0.053 NO
69 PIK3CD PIK3CD PIK3CD 17796 -0.45 0.066 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: BIOCARTA CHREBP2 PATHWAY.

Figure S54.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM

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 MYL7 MYL7 MYL7 444 1 0.12 YES
2 ARHGEF17 ARHGEF17 ARHGEF17 2006 0.58 0.13 YES
3 MYLK MYLK MYLK 2587 0.49 0.17 YES
4 PLCB1 PLCB1 PLCB1 2770 0.46 0.23 YES
5 ARHGEF19 ARHGEF19 ARHGEF19 2825 0.46 0.29 YES
6 PRKCA PRKCA PRKCA 2877 0.45 0.36 YES
7 GNGT1 GNGT1 GNGT1 3658 0.36 0.37 YES
8 PPP1R12B PPP1R12B PPP1R12B 3664 0.36 0.42 YES
9 ARHGEF4 ARHGEF4 ARHGEF4 3850 0.34 0.46 YES
10 ARHGEF9 ARHGEF9 ARHGEF9 4398 0.29 0.47 YES
11 ARHGEF15 ARHGEF15 ARHGEF15 4536 0.28 0.5 YES
12 ARHGEF12 ARHGEF12 ARHGEF12 5196 0.22 0.5 NO
13 MYL2 MYL2 MYL2 5994 0.16 0.48 NO
14 ARHGAP5 ARHGAP5 ARHGAP5 6926 0.11 0.45 NO
15 ARHGEF6 ARHGEF6 ARHGEF6 6969 0.11 0.47 NO
16 ARHGEF2 ARHGEF2 ARHGEF2 7464 0.091 0.45 NO
17 ARHGEF3 ARHGEF3 ARHGEF3 8068 0.066 0.43 NO
18 PKN1 PKN1 PKN1 8191 0.062 0.43 NO
19 GNA12 GNA12 GNA12 8552 0.048 0.42 NO
20 GNB1 GNB1 GNB1 9029 0.031 0.4 NO
21 ARHGEF18 ARHGEF18 ARHGEF18 9365 0.019 0.39 NO
22 ROCK1 ROCK1 ROCK1 9425 0.018 0.39 NO
23 ARHGEF5 ARHGEF5 ARHGEF5 9554 0.013 0.38 NO
24 ARHGEF7 ARHGEF7 ARHGEF7 10092 -0.0043 0.35 NO
25 GNAQ GNAQ GNAQ 10375 -0.013 0.34 NO
26 ARHGEF11 ARHGEF11 ARHGEF11 11704 -0.052 0.28 NO
27 ARHGEF1 ARHGEF1 ARHGEF1 12174 -0.066 0.26 NO
28 ARHGEF16 ARHGEF16 ARHGEF16 13449 -0.11 0.21 NO
29 ARHGEF10 ARHGEF10 ARHGEF10 16049 -0.23 0.11 NO
30 PRKCB PRKCB PRKCB 17060 -0.33 0.1 NO

Figure S55.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM.

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

genes ES table in pathway: KEGG DRUG METABOLISM OTHER ENZYMES

Table 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 TGFB2 TGFB2 TGFB2 85 1.3 0.011 YES
2 HHIP HHIP HHIP 124 1.2 0.023 YES
3 WNT4 WNT4 WNT4 132 1.2 0.037 YES
4 MAPK10 MAPK10 MAPK10 239 1.1 0.045 YES
5 MECOM MECOM MECOM 293 1.1 0.055 YES
6 ARNT2 ARNT2 ARNT2 305 1.1 0.066 YES
7 KITLG KITLG KITLG 307 1.1 0.079 YES
8 FZD2 FZD2 FZD2 308 1.1 0.092 YES
9 BMP2 BMP2 BMP2 358 1 0.1 YES
10 WNT11 WNT11 WNT11 443 1 0.11 YES
11 GLI3 GLI3 GLI3 574 0.95 0.11 YES
12 FZD7 FZD7 FZD7 580 0.95 0.12 YES
13 HGF HGF HGF 640 0.92 0.13 YES
14 FGF5 FGF5 FGF5 641 0.92 0.14 YES
15 WNT5A WNT5A WNT5A 652 0.92 0.15 YES
16 LAMB3 LAMB3 LAMB3 669 0.91 0.16 YES
17 COL4A6 COL4A6 COL4A6 711 0.89 0.17 YES
18 MMP1 MMP1 MMP1 814 0.86 0.17 YES
19 LAMB4 LAMB4 LAMB4 946 0.82 0.18 YES
20 FGF10 FGF10 FGF10 1009 0.8 0.18 YES
21 FGF20 FGF20 FGF20 1045 0.8 0.19 YES
22 BMP4 BMP4 BMP4 1144 0.76 0.19 YES
23 PDGFRA PDGFRA PDGFRA 1183 0.76 0.2 YES
24 RUNX1T1 RUNX1T1 RUNX1T1 1222 0.74 0.21 YES
25 WNT7B WNT7B WNT7B 1333 0.71 0.21 YES
26 FGF1 FGF1 FGF1 1443 0.69 0.21 YES
27 CCND1 CCND1 CCND1 1448 0.69 0.22 YES
28 SHH SHH SHH 1505 0.68 0.22 YES
29 FZD1 FZD1 FZD1 1537 0.67 0.23 YES
30 ZBTB16 ZBTB16 ZBTB16 1539 0.67 0.24 YES
31 FIGF FIGF FIGF 1548 0.67 0.24 YES
32 EGFR EGFR EGFR 1637 0.65 0.25 YES
33 FZD4 FZD4 FZD4 1693 0.64 0.25 YES
34 TCF7L1 TCF7L1 TCF7L1 1785 0.62 0.26 YES
35 TCF7L2 TCF7L2 TCF7L2 1865 0.61 0.26 YES
36 NOS2 NOS2 NOS2 1890 0.6 0.26 YES
37 JUN JUN JUN 1991 0.59 0.26 YES
38 FN1 FN1 FN1 1999 0.58 0.27 YES
39 ITGA2 ITGA2 ITGA2 2005 0.58 0.28 YES
40 MET MET MET 2061 0.58 0.28 YES
41 EGF EGF EGF 2117 0.56 0.28 YES
42 ITGA3 ITGA3 ITGA3 2136 0.56 0.29 YES
43 NTRK1 NTRK1 NTRK1 2262 0.54 0.29 YES
44 FGF23 FGF23 FGF23 2345 0.53 0.29 YES
45 VEGFA VEGFA VEGFA 2451 0.51 0.29 YES
46 FGF12 FGF12 FGF12 2474 0.51 0.3 YES
47 TGFB3 TGFB3 TGFB3 2501 0.51 0.3 YES
48 WNT16 WNT16 WNT16 2571 0.49 0.3 YES
49 CDKN2B CDKN2B CDKN2B 2579 0.49 0.31 YES
50 LAMB2 LAMB2 LAMB2 2647 0.48 0.31 YES
51 TGFA TGFA TGFA 2660 0.48 0.32 YES
52 IL8 IL8 IL8 2827 0.46 0.31 YES
53 PTGS2 PTGS2 PTGS2 2835 0.46 0.32 YES
54 VEGFC VEGFC VEGFC 2848 0.46 0.32 YES
55 FGF17 FGF17 FGF17 2862 0.45 0.33 YES
56 PRKCA PRKCA PRKCA 2877 0.45 0.33 YES
57 PDGFRB PDGFRB PDGFRB 2879 0.45 0.34 YES
58 FGF14 FGF14 FGF14 2901 0.45 0.34 YES
59 PGF PGF PGF 2961 0.44 0.34 YES
60 FGF7 FGF7 FGF7 2978 0.44 0.35 YES
61 LAMB1 LAMB1 LAMB1 3037 0.43 0.35 YES
62 RARB RARB RARB 3088 0.42 0.35 YES
63 CDK6 CDK6 CDK6 3245 0.4 0.35 YES
64 PIK3R1 PIK3R1 PIK3R1 3252 0.4 0.35 YES
65 RXRA RXRA RXRA 3265 0.4 0.36 YES
66 EPAS1 EPAS1 EPAS1 3307 0.4 0.36 YES
67 FZD6 FZD6 FZD6 3362 0.39 0.36 YES
68 ITGAV ITGAV ITGAV 3414 0.38 0.36 YES
69 RARA RARA RARA 3458 0.38 0.36 YES
70 ERBB2 ERBB2 ERBB2 3499 0.37 0.36 YES
71 LEF1 LEF1 LEF1 3529 0.37 0.37 YES
72 BCL2 BCL2 BCL2 3542 0.37 0.37 YES
73 WNT6 WNT6 WNT6 3587 0.37 0.37 YES
74 NKX3-1 NKX3-1 NKX3-1 3625 0.36 0.38 YES
75 CDKN2A CDKN2A CDKN2A 3679 0.36 0.38 YES
76 LAMA2 LAMA2 LAMA2 3685 0.36 0.38 YES
77 DCC DCC DCC 3694 0.35 0.38 YES
78 TGFBR2 TGFBR2 TGFBR2 3722 0.35 0.39 YES
79 CDKN1A CDKN1A CDKN1A 3745 0.35 0.39 YES
80 SOS2 SOS2 SOS2 3838 0.34 0.39 YES
81 LAMC3 LAMC3 LAMC3 3924 0.33 0.39 YES
82 LAMA4 LAMA4 LAMA4 3932 0.33 0.39 YES
83 LAMA3 LAMA3 LAMA3 3978 0.33 0.39 YES
84 WNT10A WNT10A WNT10A 3989 0.32 0.4 YES
85 LAMC2 LAMC2 LAMC2 3997 0.32 0.4 YES
86 FOS FOS FOS 4004 0.32 0.4 YES
87 BAD BAD BAD 4007 0.32 0.41 YES
88 PLD1 PLD1 PLD1 4119 0.31 0.4 YES
89 APC2 APC2 APC2 4281 0.3 0.4 YES
90 COL4A1 COL4A1 COL4A1 4330 0.29 0.4 YES
91 SMO SMO SMO 4342 0.29 0.4 YES
92 CTNNB1 CTNNB1 CTNNB1 4402 0.29 0.4 YES
93 FAS FAS FAS 4461 0.28 0.4 YES
94 VEGFB VEGFB VEGFB 4489 0.28 0.4 YES
95 COL4A2 COL4A2 COL4A2 4495 0.28 0.41 YES
96 WNT2 WNT2 WNT2 4531 0.28 0.41 YES
97 FGF3 FGF3 FGF3 4613 0.27 0.41 NO
98 RB1 RB1 RB1 4790 0.25 0.4 NO
99 PDGFB PDGFB PDGFB 4842 0.25 0.4 NO
100 CDH1 CDH1 CDH1 4876 0.24 0.4 NO
101 WNT5B WNT5B WNT5B 4882 0.24 0.4 NO
102 FGF8 FGF8 FGF8 4892 0.24 0.41 NO
103 SMAD4 SMAD4 SMAD4 5033 0.23 0.4 NO
104 RUNX1 RUNX1 RUNX1 5206 0.22 0.4 NO
105 SUFU SUFU SUFU 5294 0.21 0.39 NO
106 CTNNA1 CTNNA1 CTNNA1 5319 0.21 0.4 NO
107 APPL1 APPL1 APPL1 5326 0.21 0.4 NO
108 CBLC CBLC CBLC 5396 0.2 0.4 NO
109 FGF9 FGF9 FGF9 5417 0.2 0.4 NO
110 NFKB1 NFKB1 NFKB1 5439 0.2 0.4 NO
111 MITF MITF MITF 5451 0.2 0.4 NO
112 AKT3 AKT3 AKT3 5541 0.2 0.4 NO
113 WNT9B WNT9B WNT9B 5578 0.19 0.4 NO
114 TRAF5 TRAF5 TRAF5 5619 0.19 0.4 NO
115 WNT8B WNT8B WNT8B 5646 0.19 0.4 NO
116 CCNE2 CCNE2 CCNE2 5650 0.19 0.4 NO
117 RXRB RXRB RXRB 5840 0.18 0.39 NO
118 DAPK2 DAPK2 DAPK2 6005 0.16 0.38 NO
119 FZD9 FZD9 FZD9 6095 0.16 0.38 NO
120 AKT1 AKT1 AKT1 6171 0.15 0.38 NO
121 FGF2 FGF2 FGF2 6212 0.15 0.38 NO
122 CTBP1 CTBP1 CTBP1 6271 0.15 0.38 NO
123 LAMA1 LAMA1 LAMA1 6274 0.15 0.38 NO
124 IGF1 IGF1 IGF1 6294 0.15 0.38 NO
125 FGFR2 FGFR2 FGFR2 6334 0.14 0.38 NO
126 FOXO1 FOXO1 FOXO1 6369 0.14 0.38 NO
127 EGLN3 EGLN3 EGLN3 6380 0.14 0.38 NO
128 CDKN1B CDKN1B CDKN1B 6476 0.14 0.38 NO
129 AR AR AR 6482 0.14 0.38 NO
130 COL4A4 COL4A4 COL4A4 6487 0.14 0.38 NO
131 PDGFA PDGFA PDGFA 6510 0.14 0.38 NO
132 LAMA5 LAMA5 LAMA5 6536 0.13 0.38 NO
133 MMP2 MMP2 MMP2 6651 0.13 0.38 NO
134 BIRC2 BIRC2 BIRC2 6740 0.12 0.37 NO
135 FGFR1 FGFR1 FGFR1 6781 0.12 0.37 NO
136 TFG TFG TFG 6815 0.12 0.37 NO
137 RXRG RXRG RXRG 6862 0.12 0.37 NO
138 ARAF ARAF ARAF 6872 0.12 0.37 NO
139 FGF11 FGF11 FGF11 7013 0.11 0.37 NO
140 ABL1 ABL1 ABL1 7024 0.11 0.37 NO
141 MAPK3 MAPK3 MAPK3 7027 0.11 0.37 NO
142 RALGDS RALGDS RALGDS 7061 0.11 0.37 NO
143 VHL VHL VHL 7073 0.11 0.37 NO
144 ARNT ARNT ARNT 7078 0.11 0.37 NO
145 MAPK8 MAPK8 MAPK8 7093 0.11 0.37 NO
146 WNT7A WNT7A WNT7A 7175 0.1 0.37 NO
147 BID BID BID 7200 0.1 0.37 NO
148 BCL2L1 BCL2L1 BCL2L1 7213 0.1 0.37 NO
149 TGFB1 TGFB1 TGFB1 7215 0.1 0.37 NO
150 PTCH1 PTCH1 PTCH1 7304 0.097 0.36 NO
151 KLK3 KLK3 KLK3 7308 0.097 0.36 NO
152 RELA RELA RELA 7358 0.095 0.36 NO
153 SMAD3 SMAD3 SMAD3 7385 0.094 0.36 NO
154 MLH1 MLH1 MLH1 7414 0.093 0.36 NO
155 RALB RALB RALB 7500 0.089 0.36 NO
156 SOS1 SOS1 SOS1 7574 0.086 0.36 NO
157 GLI2 GLI2 GLI2 7577 0.086 0.36 NO
158 EGLN1 EGLN1 EGLN1 7589 0.085 0.36 NO
159 FADD FADD FADD 7716 0.08 0.35 NO
160 CDK2 CDK2 CDK2 7799 0.076 0.35 NO
161 MYC MYC MYC 7829 0.075 0.35 NO
162 JAK1 JAK1 JAK1 7954 0.07 0.34 NO
163 NRAS NRAS NRAS 7987 0.069 0.34 NO
164 WNT1 WNT1 WNT1 8107 0.065 0.34 NO
165 MAPK9 MAPK9 MAPK9 8238 0.06 0.33 NO
166 ITGB1 ITGB1 ITGB1 8271 0.058 0.33 NO
167 SLC2A1 SLC2A1 SLC2A1 8310 0.057 0.33 NO
168 CTNNA3 CTNNA3 CTNNA3 8361 0.056 0.32 NO
169 PIK3CA PIK3CA PIK3CA 8393 0.054 0.32 NO
170 ETS1 ETS1 ETS1 8443 0.052 0.32 NO
171 AKT2 AKT2 AKT2 8444 0.052 0.32 NO
172 APC APC APC 8495 0.05 0.32 NO
173 TP53 TP53 TP53 8515 0.049 0.32 NO
174 CREBBP CREBBP CREBBP 8684 0.043 0.31 NO
175 DVL3 DVL3 DVL3 8706 0.042 0.31 NO
176 DAPK3 DAPK3 DAPK3 8739 0.041 0.31 NO
177 PLCG1 PLCG1 PLCG1 8791 0.04 0.31 NO
178 GSK3B GSK3B GSK3B 8891 0.036 0.3 NO
179 HIF1A HIF1A HIF1A 9017 0.032 0.3 NO
180 MAX MAX MAX 9019 0.032 0.3 NO
181 STAT3 STAT3 STAT3 9056 0.03 0.3 NO
182 TRAF3 TRAF3 TRAF3 9073 0.029 0.29 NO
183 RASSF1 RASSF1 RASSF1 9096 0.029 0.29 NO
184 PTEN PTEN PTEN 9141 0.027 0.29 NO
185 IKBKB IKBKB IKBKB 9204 0.025 0.29 NO
186 RHOA RHOA RHOA 9233 0.024 0.29 NO
187 FZD8 FZD8 FZD8 9338 0.02 0.28 NO
188 CDK4 CDK4 CDK4 9343 0.02 0.28 NO
189 CSF1R CSF1R CSF1R 9357 0.019 0.28 NO
190 SKP2 SKP2 SKP2 9370 0.019 0.28 NO
191 FZD3 FZD3 FZD3 9376 0.019 0.28 NO
192 FH FH FH 9422 0.018 0.28 NO
193 DVL2 DVL2 DVL2 9434 0.017 0.28 NO
194 FGF13 FGF13 FGF13 9483 0.016 0.28 NO
195 RALBP1 RALBP1 RALBP1 9534 0.014 0.27 NO
196 NFKBIA NFKBIA NFKBIA 9547 0.013 0.27 NO
197 TGFBR1 TGFBR1 TGFBR1 9586 0.012 0.27 NO
198 CTNNA2 CTNNA2 CTNNA2 9588 0.012 0.27 NO
199 SMAD2 SMAD2 SMAD2 9597 0.012 0.27 NO
200 LAMC1 LAMC1 LAMC1 9708 0.0082 0.26 NO
201 CDC42 CDC42 CDC42 9744 0.007 0.26 NO
202 PML PML PML 9786 0.0055 0.26 NO
203 IKBKG IKBKG IKBKG 9819 0.0045 0.26 NO
204 HDAC1 HDAC1 HDAC1 9877 0.0025 0.26 NO
205 HSP90B1 HSP90B1 HSP90B1 9886 0.0022 0.26 NO
206 WNT3A WNT3A WNT3A 9897 0.0018 0.26 NO
207 JUP JUP JUP 9933 0.00086 0.25 NO
208 GSTP1 GSTP1 GSTP1 9994 -0.0008 0.25 NO
209 PIK3R2 PIK3R2 PIK3R2 10039 -0.0024 0.25 NO
210 CCDC6 CCDC6 CCDC6 10106 -0.0048 0.24 NO
211 STAT5B STAT5B STAT5B 10303 -0.011 0.24 NO
212 AXIN1 AXIN1 AXIN1 10367 -0.013 0.23 NO
213 GRB2 GRB2 GRB2 10416 -0.014 0.23 NO
214 AXIN2 AXIN2 AXIN2 10486 -0.016 0.23 NO
215 BRCA2 BRCA2 BRCA2 10623 -0.02 0.22 NO
216 NCOA4 NCOA4 NCOA4 10705 -0.023 0.21 NO
217 CEBPA CEBPA CEBPA 10726 -0.023 0.21 NO
218 XIAP XIAP XIAP 10831 -0.026 0.21 NO
219 RAC1 RAC1 RAC1 10891 -0.028 0.21 NO
220 KRAS KRAS KRAS 11036 -0.032 0.2 NO
221 IGF1R IGF1R IGF1R 11150 -0.036 0.19 NO
222 GLI1 GLI1 GLI1 11187 -0.036 0.19 NO
223 HDAC2 HDAC2 HDAC2 11245 -0.039 0.19 NO
224 RAF1 RAF1 RAF1 11249 -0.039 0.19 NO
225 PTK2 PTK2 PTK2 11282 -0.04 0.19 NO
226 CRK CRK CRK 11290 -0.04 0.19 NO
227 EGLN2 EGLN2 EGLN2 11373 -0.042 0.18 NO
228 CBLB CBLB CBLB 11485 -0.046 0.18 NO
229 CRKL CRKL CRKL 11528 -0.047 0.18 NO
230 MSH3 MSH3 MSH3 11539 -0.047 0.18 NO
231 CASP9 CASP9 CASP9 11589 -0.049 0.18 NO
232 TRAF6 TRAF6 TRAF6 11692 -0.052 0.17 NO
233 MAP2K2 MAP2K2 MAP2K2 11743 -0.053 0.17 NO
234 TRAF4 TRAF4 TRAF4 11773 -0.054 0.17 NO
235 MMP9 MMP9 MMP9 11784 -0.054 0.17 NO
236 TPR TPR TPR 11919 -0.058 0.16 NO
237 TCEB2 TCEB2 TCEB2 11990 -0.06 0.16 NO
238 PLCG2 PLCG2 PLCG2 12098 -0.064 0.15 NO
239 BCR BCR BCR 12099 -0.064 0.15 NO
240 STK4 STK4 STK4 12124 -0.064 0.15 NO
241 CASP3 CASP3 CASP3 12139 -0.065 0.15 NO
242 FGF22 FGF22 FGF22 12184 -0.066 0.15 NO
243 STK36 STK36 STK36 12195 -0.066 0.15 NO
244 STAT5A STAT5A STAT5A 12206 -0.067 0.15 NO
245 CSF3R CSF3R CSF3R 12249 -0.068 0.15 NO
246 MAP2K1 MAP2K1 MAP2K1 12422 -0.073 0.14 NO
247 PIK3R5 PIK3R5 PIK3R5 12457 -0.074 0.14 NO
248 FGF16 FGF16 FGF16 12618 -0.079 0.13 NO
249 FZD5 FZD5 FZD5 12625 -0.079 0.13 NO
250 FGF18 FGF18 FGF18 12664 -0.08 0.13 NO
251 DAPK1 DAPK1 DAPK1 12666 -0.08 0.13 NO
252 TRAF1 TRAF1 TRAF1 12788 -0.085 0.13 NO
253 TRAF2 TRAF2 TRAF2 12789 -0.085 0.13 NO
254 TPM3 TPM3 TPM3 12820 -0.086 0.13 NO
255 BIRC5 BIRC5 BIRC5 12944 -0.09 0.12 NO
256 CTBP2 CTBP2 CTBP2 13092 -0.095 0.12 NO
257 RALA RALA RALA 13107 -0.095 0.12 NO
258 FLT3LG FLT3LG FLT3LG 13214 -0.098 0.11 NO
259 DVL1 DVL1 DVL1 13235 -0.099 0.11 NO
260 CHUK CHUK CHUK 13281 -0.1 0.11 NO
261 WNT2B WNT2B WNT2B 13342 -0.1 0.11 NO
262 STAT1 STAT1 STAT1 13413 -0.11 0.11 NO
263 PIK3R3 PIK3R3 PIK3R3 13421 -0.11 0.11 NO
264 FGF21 FGF21 FGF21 13559 -0.11 0.1 NO
265 PIAS3 PIAS3 PIAS3 13607 -0.11 0.1 NO
266 RASSF5 RASSF5 RASSF5 13645 -0.12 0.099 NO
267 CKS1B CKS1B CKS1B 13888 -0.12 0.088 NO
268 CUL2 CUL2 CUL2 13925 -0.12 0.087 NO
269 WNT10B WNT10B WNT10B 13944 -0.13 0.088 NO
270 EP300 EP300 EP300 13964 -0.13 0.088 NO
271 E2F3 E2F3 E2F3 14052 -0.13 0.085 NO
272 PIK3CB PIK3CB PIK3CB 14057 -0.13 0.086 NO
273 PPARG PPARG PPARG 14230 -0.14 0.079 NO
274 PIAS1 PIAS1 PIAS1 14249 -0.14 0.08 NO
275 HSP90AB1 HSP90AB1 HSP90AB1 14263 -0.14 0.08 NO
276 MAPK1 MAPK1 MAPK1 14349 -0.14 0.078 NO
277 BAX BAX BAX 14370 -0.14 0.078 NO
278 PAX8 PAX8 PAX8 14401 -0.14 0.078 NO
279 PPARD PPARD PPARD 14407 -0.14 0.08 NO
280 RBX1 RBX1 RBX1 14408 -0.14 0.081 NO
281 MDM2 MDM2 MDM2 14433 -0.14 0.082 NO
282 E2F1 E2F1 E2F1 14511 -0.15 0.079 NO
283 HSP90AA1 HSP90AA1 HSP90AA1 14724 -0.16 0.07 NO
284 CBL CBL CBL 15094 -0.18 0.052 NO
285 CCNA1 CCNA1 CCNA1 15150 -0.18 0.051 NO
286 MSH6 MSH6 MSH6 15195 -0.18 0.051 NO
287 ITGA6 ITGA6 ITGA6 15333 -0.19 0.046 NO
288 FGFR3 FGFR3 FGFR3 15406 -0.19 0.044 NO
289 FZD10 FZD10 FZD10 15605 -0.2 0.036 NO
290 CCNE1 CCNE1 CCNE1 15698 -0.21 0.034 NO
291 RAC3 RAC3 RAC3 15794 -0.22 0.031 NO
292 CSF2RA CSF2RA CSF2RA 15838 -0.22 0.031 NO
293 FGF4 FGF4 FGF4 15869 -0.22 0.032 NO
294 WNT9A WNT9A WNT9A 15981 -0.23 0.029 NO
295 SPI1 SPI1 SPI1 16012 -0.23 0.03 NO
296 BRAF BRAF BRAF 16079 -0.23 0.029 NO
297 PIAS4 PIAS4 PIAS4 16080 -0.23 0.032 NO
298 TCF7 TCF7 TCF7 16237 -0.25 0.026 NO
299 PIAS2 PIAS2 PIAS2 16274 -0.25 0.027 NO
300 FGF19 FGF19 FGF19 16303 -0.25 0.029 NO
301 TCEB1 TCEB1 TCEB1 16466 -0.27 0.023 NO
302 E2F2 E2F2 E2F2 16647 -0.28 0.017 NO
303 CYCS CYCS CYCS 16737 -0.29 0.015 NO
304 CASP8 CASP8 CASP8 16825 -0.3 0.014 NO
305 MSH2 MSH2 MSH2 16942 -0.32 0.012 NO
306 MTOR MTOR MTOR 17015 -0.32 0.012 NO
307 PRKCB PRKCB PRKCB 17060 -0.33 0.013 NO
308 RAC2 RAC2 RAC2 17111 -0.34 0.014 NO
309 KIT KIT KIT 17191 -0.35 0.014 NO
310 PTCH2 PTCH2 PTCH2 17224 -0.35 0.017 NO
311 FLT3 FLT3 FLT3 17248 -0.36 0.019 NO
312 BIRC3 BIRC3 BIRC3 17322 -0.37 0.02 NO
313 PIK3CG PIK3CG PIK3CG 17452 -0.38 0.017 NO
314 NFKB2 NFKB2 NFKB2 17671 -0.42 0.011 NO
315 PIK3CD PIK3CD PIK3CD 17796 -0.45 0.0092 NO
316 WNT3 WNT3 WNT3 17802 -0.45 0.014 NO
317 RAD51 RAD51 RAD51 17911 -0.48 0.014 NO
318 RET RET RET 17948 -0.49 0.018 NO
319 ITGA2B ITGA2B ITGA2B 18389 -0.62 0.0014 NO
320 FASLG FASLG FASLG 18488 -0.66 0.0038 NO
321 WNT8A WNT8A WNT8A 18561 -0.7 0.008 NO
322 IL6 IL6 IL6 18617 -0.72 0.013 NO
323 PRKCG PRKCG PRKCG 18778 -0.84 0.015 NO

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

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

genes ES table in pathway: KEGG WNT SIGNALING PATHWAY

Table S30.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 UGT2B7 UGT2B7 UGT2B7 39 1.4 0.089 YES
2 UGT2A3 UGT2A3 UGT2A3 134 1.2 0.16 YES
3 NAT2 NAT2 NAT2 198 1.2 0.23 YES
4 CYP3A7 CYP3A7 CYP3A7 315 1.1 0.29 YES
5 CYP3A5 CYP3A5 CYP3A5 365 1 0.36 YES
6 UGT2B4 UGT2B4 UGT2B4 722 0.89 0.39 YES
7 UGT2B11 UGT2B11 UGT2B11 802 0.86 0.44 YES
8 CYP2A6 CYP2A6 CYP2A6 927 0.83 0.49 YES
9 UGT2A1 UGT2A1 UGT2A1 1728 0.63 0.49 YES
10 UGT1A6 UGT1A6 UGT1A6 1997 0.58 0.51 YES
11 CES1 CES1 CES1 2288 0.54 0.53 YES
12 UPP2 UPP2 UPP2 2723 0.47 0.54 YES
13 CYP2A13 CYP2A13 CYP2A13 3394 0.39 0.52 YES
14 XDH XDH XDH 3396 0.39 0.55 YES
15 CES2 CES2 CES2 3593 0.36 0.56 YES
16 UGT1A9 UGT1A9 UGT1A9 3824 0.34 0.57 YES
17 UPB1 UPB1 UPB1 4003 0.32 0.58 YES
18 UGT2B15 UGT2B15 UGT2B15 4355 0.29 0.58 NO
19 UGT1A10 UGT1A10 UGT1A10 6225 0.15 0.49 NO
20 TK2 TK2 TK2 6386 0.14 0.49 NO
21 DPYD DPYD DPYD 6734 0.12 0.48 NO
22 TK1 TK1 TK1 6897 0.12 0.48 NO
23 ITPA ITPA ITPA 6916 0.12 0.49 NO
24 IMPDH2 IMPDH2 IMPDH2 7709 0.08 0.45 NO
25 CES7 CES7 CES7 7866 0.074 0.45 NO
26 UCK2 UCK2 UCK2 8080 0.066 0.44 NO
27 TPMT TPMT TPMT 8398 0.054 0.43 NO
28 GUSB GUSB GUSB 8695 0.043 0.41 NO
29 GMPS GMPS GMPS 8929 0.035 0.4 NO
30 HPRT1 HPRT1 HPRT1 9524 0.014 0.37 NO
31 UCK1 UCK1 UCK1 9697 0.0084 0.36 NO
32 UCKL1 UCKL1 UCKL1 11537 -0.047 0.27 NO
33 IMPDH1 IMPDH1 IMPDH1 11934 -0.059 0.25 NO
34 UMPS UMPS UMPS 12157 -0.065 0.25 NO
35 NAT1 NAT1 NAT1 12914 -0.089 0.21 NO
36 CYP3A43 CYP3A43 CYP3A43 13522 -0.11 0.19 NO
37 TYMP TYMP TYMP 15607 -0.2 0.091 NO
38 CDA CDA CDA 16473 -0.27 0.062 NO
39 DPYS DPYS DPYS 17177 -0.34 0.047 NO
40 UPP1 UPP1 UPP1 18764 -0.83 0.015 NO

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

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

Fold change

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

Expression level

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

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

Methods & Data
Input
  • Gene set database = c2.cp.v3.0-2.symbols.gmt

  • Expression data file = TGCT-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = TGCT-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)