GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in KIRC-TP
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
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 KIRC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1TH8KWD
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 KIRC-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: 194
Number of samples: 533
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 ] 116
pheno.type: 2 - 3 :[ clus2 ] 223
pheno.type: 3 - 3 :[ clus3 ] 194

For the expression subtypes of 18278 genes in 534 samples, GSEA found enriched gene sets in each cluster using 533 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA RHO PATHWAY, BIOCARTA GPCR PATHWAY, BIOCARTA CREB PATHWAY, KEGG OXIDATIVE PHOSPHORYLATION, KEGG O GLYCAN BIOSYNTHESIS, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG CARDIAC MUSCLE CONTRACTION, KEGG WNT SIGNALING PATHWAY

    • And common core enriched genes are PRKCA, CTNNB1, CXXC4, DAAM1, DKK1, FRAT1, FZD2, FZD3, FZD6, FZD7

  • clus2

    • Top enriched gene sets are BIOCARTA AT1R PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA VEGF PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG GALACTOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION

    • And common core enriched genes are EHHADH, ACADM, ALDH3A2, ACSL1, HMGCS2, SLC27A2, ABAT, ACAT1, ALDH6A1, ALDH7A1

  • clus3

    • Top enriched gene sets are BIOCARTA INFLAM PATHWAY, BIOCARTA GSK3 PATHWAY, BIOCARTA WNT PATHWAY, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG DNA REPLICATION, KEGG BASE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG CELL CYCLE, KEGG OOCYTE MEIOSIS

    • And common core enriched genes are CCL5, IL1B, IL6, IL18, PYCARD, CCNB1, CCNB2, CCNE1, CCNE2, CDK1

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 NO1 PATHWAY 28 genes.ES.table 0.57 1.4 0.064 0.68 0.93 0.46 0.18 0.38 0.52 0.22
BIOCARTA AGR PATHWAY 34 genes.ES.table 0.58 1.7 0.0021 0.57 0.49 0.26 0.14 0.23 0 0.19
BIOCARTA RHO PATHWAY 31 genes.ES.table 0.43 1.6 0.024 0.79 0.78 0.19 0.16 0.16 0.5 0.26
BIOCARTA GPCR PATHWAY 32 genes.ES.table 0.48 1.5 0.061 0.56 0.86 0.47 0.26 0.35 0.37 0.18
BIOCARTA CREB PATHWAY 25 genes.ES.table 0.46 1.5 0.069 0.56 0.88 0.44 0.26 0.32 0.38 0.16
KEGG OXIDATIVE PHOSPHORYLATION 113 genes.ES.table 0.5 1.5 0.16 0.63 0.91 0.6 0.32 0.41 0.46 0.2
KEGG O GLYCAN BIOSYNTHESIS 28 genes.ES.table 0.48 1.3 0.086 0.73 0.97 0.46 0.19 0.38 0.61 0.24
KEGG INOSITOL PHOSPHATE METABOLISM 53 genes.ES.table 0.37 1.3 0.15 0.63 0.98 0.36 0.23 0.28 0.53 0.19
KEGG CARDIAC MUSCLE CONTRACTION 66 genes.ES.table 0.45 1.3 0.09 0.6 0.98 0.3 0.14 0.26 0.51 0.17
KEGG WNT SIGNALING PATHWAY 145 genes.ES.table 0.46 1.5 0.037 0.76 0.82 0.37 0.21 0.3 0.49 0.26
genes ES table in pathway: BIOCARTA NO1 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 ATP6V0A4 ATP6V0A4 ATP6V0A4 8 0.69 0.12 YES
2 ATP6V1B1 ATP6V1B1 ATP6V1B1 40 0.59 0.22 YES
3 CFTR CFTR CFTR 54 0.58 0.32 YES
4 ATP6V0D2 ATP6V0D2 ATP6V0D2 139 0.48 0.4 YES
5 PLCG2 PLCG2 PLCG2 1071 0.23 0.38 YES
6 KCNQ1 KCNQ1 KCNQ1 1101 0.22 0.42 YES
7 ATP6V1C2 ATP6V1C2 ATP6V1C2 1102 0.22 0.46 YES
8 ATP6V1G2 ATP6V1G2 ATP6V1G2 1115 0.22 0.5 YES
9 SLC12A2 SLC12A2 SLC12A2 1997 0.14 0.47 YES
10 ATP6V1A ATP6V1A ATP6V1A 2299 0.12 0.48 YES
11 ATP6V1D ATP6V1D ATP6V1D 2454 0.11 0.49 YES
12 ATP6V1H ATP6V1H ATP6V1H 2724 0.1 0.49 YES
13 PRKCA PRKCA PRKCA 2922 0.092 0.5 YES
14 ATP6V0B ATP6V0B ATP6V0B 3032 0.088 0.5 YES
15 ATP6V0A2 ATP6V0A2 ATP6V0A2 3047 0.088 0.52 YES
16 TJP1 TJP1 TJP1 3400 0.076 0.51 NO
17 ATP6V0E2 ATP6V0E2 ATP6V0E2 3670 0.068 0.51 NO
18 ATP6V0D1 ATP6V0D1 ATP6V0D1 4097 0.059 0.5 NO
19 ATP6V0C ATP6V0C ATP6V0C 4127 0.058 0.5 NO
20 ATP6V1G1 ATP6V1G1 ATP6V1G1 4243 0.056 0.51 NO
21 ATP6AP1 ATP6AP1 ATP6AP1 4491 0.051 0.5 NO
22 GNAS GNAS GNAS 4530 0.05 0.51 NO
23 ATP6V1E1 ATP6V1E1 ATP6V1E1 4740 0.046 0.51 NO
24 PRKACB PRKACB PRKACB 4823 0.045 0.51 NO
25 TJP2 TJP2 TJP2 5652 0.032 0.47 NO
26 PRKACA PRKACA PRKACA 5827 0.03 0.46 NO
27 ATP6V1F ATP6V1F ATP6V1F 5830 0.03 0.47 NO
28 ACTG1 ACTG1 ACTG1 6293 0.024 0.45 NO
29 KDELR1 KDELR1 KDELR1 6742 0.019 0.43 NO
30 ATP6V0E1 ATP6V0E1 ATP6V0E1 7328 0.012 0.4 NO
31 ATP6V1C1 ATP6V1C1 ATP6V1C1 7633 0.0092 0.38 NO
32 ACTB ACTB ACTB 7964 0.0061 0.37 NO
33 PRKX PRKX PRKX 8539 0.0004 0.33 NO
34 PLCG1 PLCG1 PLCG1 9144 -0.0056 0.3 NO
35 SEC61B SEC61B SEC61B 9394 -0.0081 0.29 NO
36 ARF1 ARF1 ARF1 9606 -0.01 0.28 NO
37 MUC2 MUC2 MUC2 9991 -0.014 0.26 NO
38 KDELR2 KDELR2 KDELR2 10537 -0.02 0.24 NO
39 SEC61A1 SEC61A1 SEC61A1 10820 -0.024 0.22 NO
40 ERO1L ERO1L ERO1L 11918 -0.038 0.17 NO
41 ADCY9 ADCY9 ADCY9 11963 -0.039 0.17 NO
42 ATP6V1B2 ATP6V1B2 ATP6V1B2 12650 -0.051 0.14 NO
43 PDIA4 PDIA4 PDIA4 13627 -0.072 0.1 NO
44 SEC61G SEC61G SEC61G 13650 -0.073 0.12 NO
45 ATP6V0A1 ATP6V0A1 ATP6V0A1 13734 -0.075 0.12 NO
46 KDELR3 KDELR3 KDELR3 14435 -0.096 0.1 NO
47 SEC61A2 SEC61A2 SEC61A2 14609 -0.1 0.11 NO
48 TCIRG1 TCIRG1 TCIRG1 14615 -0.1 0.13 NO
49 ATP6V1E2 ATP6V1E2 ATP6V1E2 14777 -0.11 0.14 NO
50 PRKCG PRKCG PRKCG 14786 -0.11 0.16 NO
51 PRKCB PRKCB PRKCB 16685 -0.2 0.086 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 NO1 PATHWAY.

Figure S2.  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 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 LAMA2 LAMA2 LAMA2 32 0.6 0.17 YES
2 PAK6 PAK6 PAK6 48 0.58 0.33 YES
3 PAK7 PAK7 PAK7 401 0.36 0.41 YES
4 CHRM1 CHRM1 CHRM1 1076 0.23 0.44 YES
5 ACTA1 ACTA1 ACTA1 1193 0.21 0.49 YES
6 NRG2 NRG2 NRG2 1221 0.21 0.55 YES
7 DMD DMD DMD 1942 0.14 0.55 YES
8 DAG1 DAG1 DAG1 2222 0.12 0.56 YES
9 LAMA3 LAMA3 LAMA3 2552 0.11 0.58 YES
10 MAPK8 MAPK8 MAPK8 4785 0.046 0.47 NO
11 PTK2 PTK2 PTK2 5172 0.039 0.46 NO
12 PAK4 PAK4 PAK4 5807 0.03 0.43 NO
13 CDC42 CDC42 CDC42 6780 0.018 0.38 NO
14 UTRN UTRN UTRN 6948 0.017 0.38 NO
15 ITGB1 ITGB1 ITGB1 7161 0.014 0.37 NO
16 CHRNA1 CHRNA1 CHRNA1 7700 0.0087 0.34 NO
17 RAC1 RAC1 RAC1 7856 0.0071 0.34 NO
18 CTTN CTTN CTTN 8870 -0.003 0.28 NO
19 MAPK3 MAPK3 MAPK3 9071 -0.005 0.27 NO
20 PXN PXN PXN 9426 -0.0084 0.26 NO
21 ITGA1 ITGA1 ITGA1 9512 -0.0093 0.25 NO
22 PAK2 PAK2 PAK2 9603 -0.01 0.25 NO
23 DVL1 DVL1 DVL1 9928 -0.013 0.24 NO
24 LAMA4 LAMA4 LAMA4 10475 -0.019 0.21 NO
25 MAPK1 MAPK1 MAPK1 11822 -0.037 0.15 NO
26 SP1 SP1 SP1 12235 -0.043 0.14 NO
27 SRC SRC SRC 12472 -0.048 0.14 NO
28 PAK1 PAK1 PAK1 12783 -0.054 0.14 NO
29 PAK3 PAK3 PAK3 13640 -0.073 0.11 NO
30 EGFR EGFR EGFR 13768 -0.076 0.12 NO
31 JUN JUN JUN 13855 -0.079 0.14 NO
32 NRG1 NRG1 NRG1 14797 -0.11 0.12 NO
33 RAPSN RAPSN RAPSN 15023 -0.12 0.14 NO
34 GIT2 GIT2 GIT2 15488 -0.14 0.15 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 AGR PATHWAY.

Figure S4.  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 RHO PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SFRP1 SFRP1 SFRP1 82 0.54 0.057 YES
2 PYGO1 PYGO1 PYGO1 205 0.45 0.1 YES
3 NKD1 NKD1 NKD1 294 0.4 0.14 YES
4 WNT4 WNT4 WNT4 374 0.37 0.18 YES
5 WNT7A WNT7A WNT7A 473 0.34 0.22 YES
6 WNT11 WNT11 WNT11 479 0.34 0.25 YES
7 WNT2 WNT2 WNT2 529 0.33 0.29 YES
8 TLE2 TLE2 TLE2 622 0.3 0.32 YES
9 FZD7 FZD7 FZD7 869 0.26 0.33 YES
10 WNT7B WNT7B WNT7B 881 0.26 0.36 YES
11 DAAM1 DAAM1 DAAM1 901 0.25 0.39 YES
12 FZD2 FZD2 FZD2 1235 0.21 0.4 YES
13 WISP1 WISP1 WISP1 1346 0.2 0.41 YES
14 WNT5A WNT5A WNT5A 1750 0.16 0.41 YES
15 CXXC4 CXXC4 CXXC4 1853 0.15 0.42 YES
16 FZD3 FZD3 FZD3 1867 0.15 0.44 YES
17 HPRT1 HPRT1 HPRT1 2067 0.13 0.44 YES
18 PORCN PORCN PORCN 2124 0.13 0.45 YES
19 TCF7L1 TCF7L1 TCF7L1 2223 0.12 0.46 YES
20 TLE1 TLE1 TLE1 2416 0.11 0.46 YES
21 WNT6 WNT6 WNT6 2428 0.11 0.48 YES
22 FRAT1 FRAT1 FRAT1 2550 0.11 0.48 YES
23 LEF1 LEF1 LEF1 2713 0.1 0.48 YES
24 WIF1 WIF1 WIF1 3046 0.088 0.48 YES
25 WNT5B WNT5B WNT5B 3265 0.08 0.47 YES
26 LRP6 LRP6 LRP6 3351 0.078 0.48 YES
27 FZD6 FZD6 FZD6 3366 0.077 0.48 YES
28 BCL9 BCL9 BCL9 3373 0.077 0.49 YES
29 WNT9A WNT9A WNT9A 3451 0.074 0.5 YES
30 DKK1 DKK1 DKK1 3532 0.072 0.5 YES
31 CTNNB1 CTNNB1 CTNNB1 3624 0.069 0.5 YES
32 TCF7 TCF7 TCF7 3722 0.067 0.51 YES
33 GSK3B GSK3B GSK3B 3846 0.065 0.51 YES
34 FBXW2 FBXW2 FBXW2 4267 0.055 0.49 NO
35 FZD8 FZD8 FZD8 4475 0.051 0.49 NO
36 CTNNBIP1 CTNNBIP1 CTNNBIP1 4946 0.043 0.46 NO
37 FOXN1 FOXN1 FOXN1 5052 0.041 0.46 NO
38 AES AES AES 5328 0.037 0.45 NO
39 FBXW11 FBXW11 FBXW11 5534 0.034 0.45 NO
40 CSNK2A1 CSNK2A1 CSNK2A1 6036 0.027 0.42 NO
41 SOX17 SOX17 SOX17 6841 0.018 0.38 NO
42 BTRC BTRC BTRC 7082 0.015 0.37 NO
43 RHOU RHOU RHOU 7219 0.014 0.36 NO
44 KREMEN1 KREMEN1 KREMEN1 7243 0.013 0.36 NO
45 EP300 EP300 EP300 7375 0.012 0.36 NO
46 PPP2R1A PPP2R1A PPP2R1A 7410 0.012 0.36 NO
47 DVL2 DVL2 DVL2 7756 0.008 0.34 NO
48 GSK3A GSK3A GSK3A 7769 0.008 0.34 NO
49 LRP5 LRP5 LRP5 7838 0.0072 0.34 NO
50 PPP2CA PPP2CA PPP2CA 7844 0.0072 0.34 NO
51 ACTB ACTB ACTB 7964 0.0061 0.33 NO
52 CSNK1G1 CSNK1G1 CSNK1G1 7990 0.0059 0.33 NO
53 RPL13A RPL13A RPL13A 8052 0.0054 0.33 NO
54 SENP2 SENP2 SENP2 8266 0.0032 0.32 NO
55 CSNK1D CSNK1D CSNK1D 8383 0.0019 0.31 NO
56 APC APC APC 8501 0.00067 0.3 NO
57 CTBP1 CTBP1 CTBP1 8673 -0.001 0.29 NO
58 AXIN1 AXIN1 AXIN1 9215 -0.0063 0.26 NO
59 CTBP2 CTBP2 CTBP2 9452 -0.0087 0.25 NO
60 CCND3 CCND3 CCND3 9559 -0.0098 0.25 NO
61 CCND2 CCND2 CCND2 9809 -0.012 0.24 NO
62 FRZB FRZB FRZB 9810 -0.012 0.24 NO
63 NLK NLK NLK 9827 -0.012 0.24 NO
64 DVL1 DVL1 DVL1 9928 -0.013 0.23 NO
65 FBXW4 FBXW4 FBXW4 10095 -0.015 0.22 NO
66 CSNK1A1 CSNK1A1 CSNK1A1 10525 -0.02 0.2 NO
67 B2M B2M B2M 11404 -0.031 0.16 NO
68 SFRP4 SFRP4 SFRP4 11774 -0.036 0.14 NO
69 FZD4 FZD4 FZD4 12617 -0.05 0.1 NO
70 FOSL1 FOSL1 FOSL1 13077 -0.059 0.084 NO
71 GAPDH GAPDH GAPDH 13153 -0.061 0.087 NO
72 WNT16 WNT16 WNT16 13175 -0.062 0.093 NO
73 WNT2B WNT2B WNT2B 13310 -0.064 0.093 NO
74 JUN JUN JUN 13855 -0.079 0.072 NO
75 DIXDC1 DIXDC1 DIXDC1 13935 -0.081 0.077 NO
76 WNT10A WNT10A WNT10A 13945 -0.081 0.086 NO
77 CCND1 CCND1 CCND1 14009 -0.083 0.092 NO
78 SLC9A3R1 SLC9A3R1 SLC9A3R1 15432 -0.13 0.029 NO
79 FZD1 FZD1 FZD1 15552 -0.14 0.038 NO
80 PITX2 PITX2 PITX2 15717 -0.14 0.046 NO
81 MYC MYC MYC 15790 -0.15 0.059 NO
82 WNT3 WNT3 WNT3 15824 -0.15 0.074 NO
83 FZD5 FZD5 FZD5 16822 -0.21 0.044 NO
84 WNT1 WNT1 WNT1 17674 -0.31 0.032 NO

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

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA RHO 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 GPCR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PIP5K1B PIP5K1B PIP5K1B 153 0.48 0.22 YES
2 PPP1R12B PPP1R12B PPP1R12B 1424 0.19 0.24 YES
3 ARHGAP6 ARHGAP6 ARHGAP6 1448 0.19 0.33 YES
4 OPHN1 OPHN1 OPHN1 1687 0.16 0.39 YES
5 ARHGAP5 ARHGAP5 ARHGAP5 2449 0.11 0.4 YES
6 VCL VCL VCL 2901 0.093 0.42 YES
7 RHOA RHOA RHOA 3584 0.07 0.42 NO
8 GSN GSN GSN 4218 0.056 0.41 NO
9 ARPC4 ARPC4 ARPC4 4736 0.046 0.41 NO
10 ROCK1 ROCK1 ROCK1 5280 0.038 0.4 NO
11 ARHGEF5 ARHGEF5 ARHGEF5 6673 0.02 0.33 NO
12 MYLK MYLK MYLK 7163 0.014 0.31 NO
13 CFL1 CFL1 CFL1 7406 0.012 0.3 NO
14 ARHGAP1 ARHGAP1 ARHGAP1 7956 0.0062 0.27 NO
15 ARHGEF11 ARHGEF11 ARHGEF11 7969 0.0061 0.28 NO
16 ARPC1A ARPC1A ARPC1A 8094 0.0051 0.27 NO
17 PIP5K1A PIP5K1A PIP5K1A 9120 -0.0055 0.22 NO
18 LIMK1 LIMK1 LIMK1 9521 -0.0095 0.2 NO
19 ACTR2 ACTR2 ACTR2 10211 -0.016 0.17 NO
20 BAIAP2 BAIAP2 BAIAP2 10248 -0.017 0.18 NO
21 ACTR3 ACTR3 ACTR3 10509 -0.02 0.17 NO
22 ARPC2 ARPC2 ARPC2 10643 -0.021 0.18 NO
23 ARPC3 ARPC3 ARPC3 10761 -0.023 0.18 NO
24 DIAPH1 DIAPH1 DIAPH1 11468 -0.032 0.16 NO
25 ARPC5 ARPC5 ARPC5 11502 -0.032 0.17 NO
26 PFN1 PFN1 PFN1 11981 -0.04 0.16 NO
27 SRC SRC SRC 12472 -0.048 0.16 NO
28 ARPC1B ARPC1B ARPC1B 13225 -0.063 0.15 NO
29 ARHGAP4 ARHGAP4 ARHGAP4 13538 -0.07 0.16 NO
30 MYL2 MYL2 MYL2 14368 -0.094 0.16 NO
31 ARHGEF1 ARHGEF1 ARHGEF1 14741 -0.11 0.19 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: BIOCARTA GPCR PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GPCR 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 CREB PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SFRP1 SFRP1 SFRP1 82 0.54 0.034 YES
2 NKD1 NKD1 NKD1 294 0.4 0.052 YES
3 WNT4 WNT4 WNT4 374 0.37 0.074 YES
4 AXIN2 AXIN2 AXIN2 434 0.35 0.097 YES
5 WNT7A WNT7A WNT7A 473 0.34 0.12 YES
6 WNT11 WNT11 WNT11 479 0.34 0.14 YES
7 WNT2 WNT2 WNT2 529 0.33 0.16 YES
8 FZD9 FZD9 FZD9 576 0.32 0.18 YES
9 CAMK2A CAMK2A CAMK2A 697 0.29 0.2 YES
10 DKK2 DKK2 DKK2 808 0.27 0.21 YES
11 CAMK2B CAMK2B CAMK2B 847 0.26 0.23 YES
12 FZD7 FZD7 FZD7 869 0.26 0.25 YES
13 WNT7B WNT7B WNT7B 881 0.26 0.26 YES
14 DAAM1 DAAM1 DAAM1 901 0.25 0.28 YES
15 FZD10 FZD10 FZD10 923 0.25 0.3 YES
16 WNT9B WNT9B WNT9B 1213 0.21 0.3 YES
17 FZD2 FZD2 FZD2 1235 0.21 0.31 YES
18 SFRP2 SFRP2 SFRP2 1276 0.2 0.32 YES
19 TBL1Y TBL1Y TBL1Y 1387 0.19 0.33 YES
20 VANGL2 VANGL2 VANGL2 1492 0.18 0.34 YES
21 PRICKLE1 PRICKLE1 PRICKLE1 1548 0.18 0.35 YES
22 MMP7 MMP7 MMP7 1698 0.16 0.35 YES
23 WNT5A WNT5A WNT5A 1750 0.16 0.36 YES
24 CXXC4 CXXC4 CXXC4 1853 0.15 0.37 YES
25 FZD3 FZD3 FZD3 1867 0.15 0.38 YES
26 CHP2 CHP2 CHP2 1970 0.14 0.38 YES
27 RAC3 RAC3 RAC3 2111 0.13 0.38 YES
28 PORCN PORCN PORCN 2124 0.13 0.39 YES
29 FRAT2 FRAT2 FRAT2 2160 0.13 0.4 YES
30 TCF7L1 TCF7L1 TCF7L1 2223 0.12 0.4 YES
31 NFATC4 NFATC4 NFATC4 2354 0.12 0.4 YES
32 WNT6 WNT6 WNT6 2428 0.11 0.41 YES
33 FRAT1 FRAT1 FRAT1 2550 0.11 0.41 YES
34 PPP2R5A PPP2R5A PPP2R5A 2659 0.1 0.41 YES
35 LEF1 LEF1 LEF1 2713 0.1 0.42 YES
36 PRKCA PRKCA PRKCA 2922 0.092 0.41 YES
37 MAPK10 MAPK10 MAPK10 2972 0.09 0.42 YES
38 PPP3CA PPP3CA PPP3CA 3017 0.089 0.42 YES
39 WIF1 WIF1 WIF1 3046 0.088 0.42 YES
40 PPP2R5E PPP2R5E PPP2R5E 3078 0.087 0.43 YES
41 WNT5B WNT5B WNT5B 3265 0.08 0.42 YES
42 LRP6 LRP6 LRP6 3351 0.078 0.42 YES
43 FZD6 FZD6 FZD6 3366 0.077 0.43 YES
44 PSEN1 PSEN1 PSEN1 3392 0.076 0.43 YES
45 WNT9A WNT9A WNT9A 3451 0.074 0.44 YES
46 DKK1 DKK1 DKK1 3532 0.072 0.44 YES
47 PPP2R5C PPP2R5C PPP2R5C 3539 0.072 0.44 YES
48 RHOA RHOA RHOA 3584 0.07 0.44 YES
49 CTNNB1 CTNNB1 CTNNB1 3624 0.069 0.45 YES
50 PPP3CB PPP3CB PPP3CB 3652 0.069 0.45 YES
51 TCF7 TCF7 TCF7 3722 0.067 0.45 YES
52 SMAD4 SMAD4 SMAD4 3739 0.067 0.46 YES
53 WNT3A WNT3A WNT3A 3793 0.066 0.46 YES
54 GSK3B GSK3B GSK3B 3846 0.065 0.46 YES
55 NFAT5 NFAT5 NFAT5 4102 0.059 0.45 NO
56 SMAD2 SMAD2 SMAD2 4140 0.058 0.45 NO
57 CHP CHP CHP 4294 0.055 0.45 NO
58 SFRP5 SFRP5 SFRP5 4448 0.052 0.44 NO
59 FZD8 FZD8 FZD8 4475 0.051 0.44 NO
60 MAPK8 MAPK8 MAPK8 4785 0.046 0.43 NO
61 PRKACB PRKACB PRKACB 4823 0.045 0.43 NO
62 CTNNBIP1 CTNNBIP1 CTNNBIP1 4946 0.043 0.43 NO
63 DAAM2 DAAM2 DAAM2 5227 0.039 0.42 NO
64 SIAH1 SIAH1 SIAH1 5273 0.038 0.42 NO
65 ROCK1 ROCK1 ROCK1 5280 0.038 0.42 NO
66 PPP2R1B PPP2R1B PPP2R1B 5432 0.036 0.41 NO
67 CSNK1A1L CSNK1A1L CSNK1A1L 5484 0.035 0.41 NO
68 CHD8 CHD8 CHD8 5523 0.034 0.41 NO
69 FBXW11 FBXW11 FBXW11 5534 0.034 0.42 NO
70 MAP3K7 MAP3K7 MAP3K7 5657 0.032 0.41 NO
71 ROCK2 ROCK2 ROCK2 5664 0.032 0.41 NO
72 SKP1 SKP1 SKP1 5816 0.03 0.41 NO
73 PRKACA PRKACA PRKACA 5827 0.03 0.41 NO
74 WNT8B WNT8B WNT8B 5931 0.029 0.4 NO
75 CSNK2A1 CSNK2A1 CSNK2A1 6036 0.027 0.4 NO
76 CSNK2A2 CSNK2A2 CSNK2A2 6144 0.026 0.4 NO
77 PPP2R5D PPP2R5D PPP2R5D 6358 0.023 0.39 NO
78 PRICKLE2 PRICKLE2 PRICKLE2 6561 0.021 0.38 NO
79 RUVBL1 RUVBL1 RUVBL1 6686 0.02 0.37 NO
80 PPP3CC PPP3CC PPP3CC 6750 0.019 0.37 NO
81 SOX17 SOX17 SOX17 6841 0.018 0.37 NO
82 BTRC BTRC BTRC 7082 0.015 0.35 NO
83 CAMK2D CAMK2D CAMK2D 7114 0.015 0.35 NO
84 PPP2CB PPP2CB PPP2CB 7143 0.014 0.35 NO
85 CUL1 CUL1 CUL1 7320 0.012 0.34 NO
86 DVL3 DVL3 DVL3 7351 0.012 0.34 NO
87 EP300 EP300 EP300 7375 0.012 0.34 NO
88 PPP2R1A PPP2R1A PPP2R1A 7410 0.012 0.34 NO
89 CREBBP CREBBP CREBBP 7421 0.012 0.34 NO
90 PPARD PPARD PPARD 7532 0.01 0.34 NO
91 DVL2 DVL2 DVL2 7756 0.008 0.32 NO
92 LRP5 LRP5 LRP5 7838 0.0072 0.32 NO
93 PPP2CA PPP2CA PPP2CA 7844 0.0072 0.32 NO
94 RAC1 RAC1 RAC1 7856 0.0071 0.32 NO
95 TCF7L2 TCF7L2 TCF7L2 8131 0.0046 0.31 NO
96 SENP2 SENP2 SENP2 8266 0.0032 0.3 NO
97 APC APC APC 8501 0.00067 0.29 NO
98 PRKX PRKX PRKX 8539 0.0004 0.28 NO
99 SMAD3 SMAD3 SMAD3 8644 -0.00078 0.28 NO
100 CTBP1 CTBP1 CTBP1 8673 -0.001 0.28 NO
101 AXIN1 AXIN1 AXIN1 9215 -0.0063 0.25 NO
102 PPP3R1 PPP3R1 PPP3R1 9272 -0.0068 0.24 NO
103 CAMK2G CAMK2G CAMK2G 9293 -0.007 0.24 NO
104 VANGL1 VANGL1 VANGL1 9352 -0.0077 0.24 NO
105 CTBP2 CTBP2 CTBP2 9452 -0.0087 0.24 NO
106 RBX1 RBX1 RBX1 9516 -0.0094 0.23 NO
107 CCND3 CCND3 CCND3 9559 -0.0098 0.23 NO
108 CSNK1E CSNK1E CSNK1E 9786 -0.012 0.22 NO
109 CCND2 CCND2 CCND2 9809 -0.012 0.22 NO
110 NLK NLK NLK 9827 -0.012 0.22 NO
111 DVL1 DVL1 DVL1 9928 -0.013 0.22 NO
112 CSNK2B CSNK2B CSNK2B 10190 -0.016 0.2 NO
113 NFATC3 NFATC3 NFATC3 10243 -0.017 0.2 NO
114 TBL1X TBL1X TBL1X 10295 -0.017 0.2 NO
115 CSNK1A1 CSNK1A1 CSNK1A1 10525 -0.02 0.19 NO
116 MAPK9 MAPK9 MAPK9 10740 -0.023 0.18 NO
117 TP53 TP53 TP53 10780 -0.023 0.18 NO
118 PLCB3 PLCB3 PLCB3 11190 -0.028 0.16 NO
119 CACYBP CACYBP CACYBP 11742 -0.036 0.13 NO
120 SFRP4 SFRP4 SFRP4 11774 -0.036 0.13 NO
121 NFATC2 NFATC2 NFATC2 11938 -0.039 0.12 NO
122 NFATC1 NFATC1 NFATC1 12103 -0.041 0.12 NO
123 FZD4 FZD4 FZD4 12617 -0.05 0.094 NO
124 APC2 APC2 APC2 12767 -0.054 0.089 NO
125 FOSL1 FOSL1 FOSL1 13077 -0.059 0.076 NO
126 WNT16 WNT16 WNT16 13175 -0.062 0.076 NO
127 TBL1XR1 TBL1XR1 TBL1XR1 13218 -0.062 0.078 NO
128 WNT2B WNT2B WNT2B 13310 -0.064 0.077 NO
129 PLCB4 PLCB4 PLCB4 13605 -0.072 0.066 NO
130 JUN JUN JUN 13855 -0.079 0.058 NO
131 WNT10A WNT10A WNT10A 13945 -0.081 0.059 NO
132 CCND1 CCND1 CCND1 14009 -0.083 0.062 NO
133 NKD2 NKD2 NKD2 14675 -0.1 0.032 NO
134 PRKCG PRKCG PRKCG 14786 -0.11 0.034 NO
135 PPP3R2 PPP3R2 PPP3R2 15055 -0.12 0.028 NO
136 FZD1 FZD1 FZD1 15552 -0.14 0.011 NO
137 MYC MYC MYC 15790 -0.15 0.0083 NO
138 WNT3 WNT3 WNT3 15824 -0.15 0.017 NO
139 WNT10B WNT10B WNT10B 15843 -0.15 0.027 NO
140 PRKCB PRKCB PRKCB 16685 -0.2 -0.0044 NO
141 PLCB1 PLCB1 PLCB1 16818 -0.21 0.0037 NO
142 FZD5 FZD5 FZD5 16822 -0.21 0.019 NO
143 RAC2 RAC2 RAC2 17187 -0.25 0.017 NO
144 PLCB2 PLCB2 PLCB2 17454 -0.28 0.022 NO
145 WNT1 WNT1 WNT1 17674 -0.31 0.032 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: BIOCARTA CREB PATHWAY.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CREB 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 OXIDATIVE PHOSPHORYLATION

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 FGF9 FGF9 FGF9 1 0.72 0.11 YES
2 PDGFRA PDGFRA PDGFRA 131 0.49 0.17 YES
3 FGF7 FGF7 FGF7 189 0.45 0.24 YES
4 FGF1 FGF1 FGF1 320 0.39 0.29 YES
5 FGF13 FGF13 FGF13 389 0.37 0.34 YES
6 FGF12 FGF12 FGF12 482 0.34 0.38 YES
7 FGF14 FGF14 FGF14 775 0.27 0.41 YES
8 IGF1 IGF1 IGF1 907 0.25 0.44 YES
9 FGF18 FGF18 FGF18 987 0.24 0.47 YES
10 EGF EGF EGF 1856 0.15 0.44 NO
11 BRAF BRAF BRAF 3062 0.087 0.39 NO
12 FGFR1 FGFR1 FGFR1 3154 0.084 0.4 NO
13 MITF MITF MITF 3266 0.08 0.4 NO
14 IGF1R IGF1R IGF1R 3519 0.072 0.4 NO
15 RAF1 RAF1 RAF1 3843 0.065 0.39 NO
16 PDGFC PDGFC PDGFC 3908 0.063 0.4 NO
17 AKT1 AKT1 AKT1 4126 0.059 0.39 NO
18 PIK3CA PIK3CA PIK3CA 4213 0.056 0.4 NO
19 PIK3R3 PIK3R3 PIK3R3 4584 0.049 0.38 NO
20 ARAF ARAF ARAF 4791 0.046 0.38 NO
21 CDH1 CDH1 CDH1 4809 0.045 0.39 NO
22 AKT3 AKT3 AKT3 5114 0.04 0.38 NO
23 KRAS KRAS KRAS 5274 0.038 0.37 NO
24 PTEN PTEN PTEN 5552 0.034 0.36 NO
25 AKT2 AKT2 AKT2 6078 0.027 0.34 NO
26 CDK4 CDK4 CDK4 6104 0.026 0.34 NO
27 PDGFRB PDGFRB PDGFRB 6252 0.025 0.34 NO
28 MAP2K1 MAP2K1 MAP2K1 6602 0.02 0.32 NO
29 CDK6 CDK6 CDK6 6926 0.017 0.3 NO
30 FGF23 FGF23 FGF23 7154 0.014 0.29 NO
31 PDGFD PDGFD PDGFD 8065 0.0053 0.24 NO
32 CDKN1A CDKN1A CDKN1A 8102 0.005 0.24 NO
33 PIK3R2 PIK3R2 PIK3R2 8205 0.0037 0.24 NO
34 MAP2K2 MAP2K2 MAP2K2 8354 0.0022 0.23 NO
35 FGF2 FGF2 FGF2 8769 -0.0019 0.21 NO
36 MAPK3 MAPK3 MAPK3 9071 -0.005 0.19 NO
37 HRAS HRAS HRAS 9562 -0.0099 0.17 NO
38 HGF HGF HGF 9895 -0.013 0.15 NO
39 BAD BAD BAD 10023 -0.014 0.14 NO
40 PDGFA PDGFA PDGFA 10103 -0.015 0.14 NO
41 FGF8 FGF8 FGF8 10294 -0.017 0.14 NO
42 TP53 TP53 TP53 10780 -0.023 0.11 NO
43 PDGFB PDGFB PDGFB 11761 -0.036 0.063 NO
44 MAPK1 MAPK1 MAPK1 11822 -0.037 0.065 NO
45 NRAS NRAS NRAS 11870 -0.038 0.068 NO
46 RB1 RB1 RB1 12567 -0.049 0.038 NO
47 PIK3CB PIK3CB PIK3CB 12586 -0.05 0.044 NO
48 E2F3 E2F3 E2F3 12723 -0.052 0.044 NO
49 MET MET MET 12800 -0.054 0.048 NO
50 MDM2 MDM2 MDM2 13396 -0.067 0.025 NO
51 FGF17 FGF17 FGF17 13462 -0.068 0.032 NO
52 PIK3R1 PIK3R1 PIK3R1 13632 -0.073 0.033 NO
53 EGFR EGFR EGFR 13768 -0.076 0.037 NO
54 CCND1 CCND1 CCND1 14009 -0.083 0.036 NO
55 PIK3CD PIK3CD PIK3CD 14676 -0.1 0.015 NO
56 FGF5 FGF5 FGF5 14723 -0.11 0.028 NO
57 FGF20 FGF20 FGF20 15402 -0.13 0.01 NO
58 FGF11 FGF11 FGF11 15892 -0.15 0.0062 NO
59 PIK3CG PIK3CG PIK3CG 16171 -0.17 0.016 NO
60 CDKN2A CDKN2A CDKN2A 16564 -0.19 0.023 NO
61 PIK3R5 PIK3R5 PIK3R5 16760 -0.21 0.043 NO
62 E2F2 E2F2 E2F2 17347 -0.26 0.05 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 OXIDATIVE PHOSPHORYLATION.

Figure S12.  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 O GLYCAN BIOSYNTHESIS

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 KCNJ1 KCNJ1 KCNJ1 86 0.53 0.1 YES
2 FXYD4 FXYD4 FXYD4 158 0.47 0.19 YES
3 SCNN1A SCNN1A SCNN1A 178 0.46 0.28 YES
4 NR3C2 NR3C2 NR3C2 550 0.32 0.32 YES
5 IGF1 IGF1 IGF1 907 0.25 0.35 YES
6 HSD11B2 HSD11B2 HSD11B2 1183 0.21 0.38 YES
7 IRS1 IRS1 IRS1 1223 0.21 0.42 YES
8 HSD11B1 HSD11B1 HSD11B1 1256 0.2 0.46 YES
9 SCNN1G SCNN1G SCNN1G 1337 0.2 0.49 YES
10 ATP1A2 ATP1A2 ATP1A2 1427 0.19 0.52 YES
11 NEDD4L NEDD4L NEDD4L 1887 0.15 0.52 YES
12 IRS2 IRS2 IRS2 1940 0.14 0.55 YES
13 PRKCA PRKCA PRKCA 2922 0.092 0.51 NO
14 ATP1A1 ATP1A1 ATP1A1 2947 0.092 0.53 NO
15 SCNN1B SCNN1B SCNN1B 3012 0.089 0.55 NO
16 PIK3CA PIK3CA PIK3CA 4213 0.056 0.49 NO
17 PIK3R3 PIK3R3 PIK3R3 4584 0.049 0.48 NO
18 ATP1B2 ATP1B2 ATP1B2 4940 0.043 0.47 NO
19 SFN SFN SFN 4995 0.042 0.47 NO
20 KRAS KRAS KRAS 5274 0.038 0.47 NO
21 SLC9A3R2 SLC9A3R2 SLC9A3R2 5705 0.032 0.45 NO
22 ATP1B3 ATP1B3 ATP1B3 5990 0.028 0.44 NO
23 ATP1A4 ATP1A4 ATP1A4 6232 0.025 0.43 NO
24 PDPK1 PDPK1 PDPK1 8176 0.0041 0.32 NO
25 PIK3R2 PIK3R2 PIK3R2 8205 0.0037 0.32 NO
26 MAPK3 MAPK3 MAPK3 9071 -0.005 0.28 NO
27 INSR INSR INSR 11069 -0.026 0.17 NO
28 ATP1B1 ATP1B1 ATP1B1 11626 -0.034 0.15 NO
29 MAPK1 MAPK1 MAPK1 11822 -0.037 0.15 NO
30 PIK3CB PIK3CB PIK3CB 12586 -0.05 0.11 NO
31 ATP1A3 ATP1A3 ATP1A3 13011 -0.058 0.1 NO
32 PIK3R1 PIK3R1 PIK3R1 13632 -0.073 0.082 NO
33 SGK1 SGK1 SGK1 13946 -0.081 0.081 NO
34 PIK3CD PIK3CD PIK3CD 14676 -0.1 0.061 NO
35 PRKCG PRKCG PRKCG 14786 -0.11 0.076 NO
36 PIK3CG PIK3CG PIK3CG 16171 -0.17 0.033 NO
37 PRKCB PRKCB PRKCB 16685 -0.2 0.045 NO
38 PIK3R5 PIK3R5 PIK3R5 16760 -0.21 0.082 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 O GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG INOSITOL PHOSPHATE METABOLISM

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 ADCY1 ADCY1 ADCY1 355 0.38 0.17 YES
2 PRKAR2A PRKAR2A PRKAR2A 1578 0.17 0.18 YES
3 NFATC4 NFATC4 NFATC4 2354 0.12 0.2 YES
4 PRKAR2B PRKAR2B PRKAR2B 2492 0.11 0.24 YES
5 PRKAR1B PRKAR1B PRKAR1B 2794 0.097 0.28 YES
6 PRKCA PRKCA PRKCA 2922 0.092 0.31 YES
7 PPP3CA PPP3CA PPP3CA 3017 0.089 0.35 YES
8 GNAI1 GNAI1 GNAI1 3629 0.069 0.35 YES
9 PPP3CB PPP3CB PPP3CB 3652 0.069 0.39 YES
10 RAF1 RAF1 RAF1 3843 0.065 0.41 YES
11 GNAQ GNAQ GNAQ 4157 0.058 0.42 YES
12 GNAS GNAS GNAS 4530 0.05 0.42 YES
13 CALM2 CALM2 CALM2 4576 0.049 0.44 YES
14 PRKAR1A PRKAR1A PRKAR1A 4691 0.047 0.46 YES
15 PRKACB PRKACB PRKACB 4823 0.045 0.48 YES
16 CALM1 CALM1 CALM1 5702 0.032 0.44 NO
17 MAP2K1 MAP2K1 MAP2K1 6602 0.02 0.4 NO
18 PPP3CC PPP3CC PPP3CC 6750 0.019 0.4 NO
19 CREB1 CREB1 CREB1 7413 0.012 0.37 NO
20 ELK1 ELK1 ELK1 7962 0.0061 0.35 NO
21 GNB1 GNB1 GNB1 8337 0.0025 0.33 NO
22 GNGT1 GNGT1 GNGT1 8583 -0.000015 0.31 NO
23 FOS FOS FOS 9031 -0.0046 0.29 NO
24 MAPK3 MAPK3 MAPK3 9071 -0.005 0.29 NO
25 PLCG1 PLCG1 PLCG1 9144 -0.0056 0.29 NO
26 NFATC3 NFATC3 NFATC3 10243 -0.017 0.24 NO
27 RPS6KA3 RPS6KA3 RPS6KA3 10715 -0.022 0.22 NO
28 CALM3 CALM3 CALM3 11035 -0.026 0.22 NO
29 NFATC2 NFATC2 NFATC2 11938 -0.039 0.19 NO
30 NFATC1 NFATC1 NFATC1 12103 -0.041 0.2 NO
31 JUN JUN JUN 13855 -0.079 0.14 NO
32 PRKCB PRKCB PRKCB 16685 -0.2 0.086 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 INOSITOL PHOSPHATE METABOLISM.

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

genes ES table in pathway: KEGG CARDIAC MUSCLE CONTRACTION

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 CAMK2A CAMK2A CAMK2A 697 0.29 0.13 YES
2 CAMK2B CAMK2B CAMK2B 847 0.26 0.26 YES
3 PRKAR2A PRKAR2A PRKAR2A 1578 0.17 0.32 YES
4 PRKAR2B PRKAR2B PRKAR2B 2492 0.11 0.34 YES
5 PRKAR1B PRKAR1B PRKAR1B 2794 0.097 0.38 YES
6 PRKCA PRKCA PRKCA 2922 0.092 0.42 YES
7 AKT1 AKT1 AKT1 4126 0.059 0.39 YES
8 PIK3CA PIK3CA PIK3CA 4213 0.056 0.42 YES
9 GNAS GNAS GNAS 4530 0.05 0.43 YES
10 PRKAR1A PRKAR1A PRKAR1A 4691 0.047 0.44 YES
11 PRKACB PRKACB PRKACB 4823 0.045 0.46 YES
12 CAMK2D CAMK2D CAMK2D 7114 0.015 0.35 NO
13 CREB1 CREB1 CREB1 7413 0.012 0.34 NO
14 RAC1 RAC1 RAC1 7856 0.0071 0.32 NO
15 MAPK3 MAPK3 MAPK3 9071 -0.005 0.25 NO
16 CAMK2G CAMK2G CAMK2G 9293 -0.007 0.24 NO
17 SOS1 SOS1 SOS1 9555 -0.0098 0.24 NO
18 HRAS HRAS HRAS 9562 -0.0099 0.24 NO
19 MAPK14 MAPK14 MAPK14 10093 -0.015 0.22 NO
20 RPS6KA5 RPS6KA5 RPS6KA5 10268 -0.017 0.22 NO
21 GRB2 GRB2 GRB2 11603 -0.034 0.17 NO
22 RPS6KA1 RPS6KA1 RPS6KA1 11644 -0.034 0.18 NO
23 MAPK1 MAPK1 MAPK1 11822 -0.037 0.2 NO
24 PIK3R1 PIK3R1 PIK3R1 13632 -0.073 0.14 NO
25 PRKCB PRKCB PRKCB 16685 -0.2 0.086 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 CARDIAC MUSCLE CONTRACTION.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CARDIAC MUSCLE CONTRACTION, 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 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 ATP6V0A4 ATP6V0A4 ATP6V0A4 8 0.69 0.08 YES
2 ATP6V1B1 ATP6V1B1 ATP6V1B1 40 0.59 0.15 YES
3 ATP6V0D2 ATP6V0D2 ATP6V0D2 139 0.48 0.2 YES
4 ATP12A ATP12A ATP12A 251 0.42 0.24 YES
5 COX7A1 COX7A1 COX7A1 721 0.28 0.25 YES
6 ATP4B ATP4B ATP4B 838 0.26 0.27 YES
7 ATP6V1C2 ATP6V1C2 ATP6V1C2 1102 0.22 0.28 YES
8 ATP6V1G2 ATP6V1G2 ATP6V1G2 1115 0.22 0.31 YES
9 COX6B2 COX6B2 COX6B2 1785 0.16 0.29 YES
10 UQCRHL UQCRHL UQCRHL 1858 0.15 0.3 YES
11 UQCRH UQCRH UQCRH 2066 0.13 0.31 YES
12 NDUFA4 NDUFA4 NDUFA4 2221 0.12 0.31 YES
13 ATP6V1A ATP6V1A ATP6V1A 2299 0.12 0.32 YES
14 UQCRFS1 UQCRFS1 UQCRFS1 2367 0.12 0.33 YES
15 UQCRC1 UQCRC1 UQCRC1 2391 0.12 0.34 YES
16 ATP6V1D ATP6V1D ATP6V1D 2454 0.11 0.36 YES
17 ATP6V1H ATP6V1H ATP6V1H 2724 0.1 0.35 YES
18 ATP5A1 ATP5A1 ATP5A1 2943 0.092 0.35 YES
19 ATP6V0B ATP6V0B ATP6V0B 3032 0.088 0.36 YES
20 ATP6V0A2 ATP6V0A2 ATP6V0A2 3047 0.088 0.36 YES
21 NDUFA6 NDUFA6 NDUFA6 3055 0.088 0.38 YES
22 COX5A COX5A COX5A 3205 0.082 0.38 YES
23 PPA2 PPA2 PPA2 3211 0.082 0.39 YES
24 NDUFB1 NDUFB1 NDUFB1 3353 0.078 0.39 YES
25 NDUFC2 NDUFC2 NDUFC2 3523 0.072 0.39 YES
26 COX7A2 COX7A2 COX7A2 3603 0.07 0.39 YES
27 ATP5B ATP5B ATP5B 3610 0.07 0.4 YES
28 ATP6V0E2 ATP6V0E2 ATP6V0E2 3670 0.068 0.4 YES
29 ATP5L ATP5L ATP5L 3686 0.068 0.41 YES
30 COX7B COX7B COX7B 3687 0.068 0.42 YES
31 NDUFA8 NDUFA8 NDUFA8 3758 0.067 0.42 YES
32 NDUFS8 NDUFS8 NDUFS8 3769 0.066 0.43 YES
33 UQCRC2 UQCRC2 UQCRC2 3852 0.064 0.43 YES
34 COX10 COX10 COX10 3930 0.063 0.44 YES
35 ATP6V0D1 ATP6V0D1 ATP6V0D1 4097 0.059 0.43 YES
36 ATP6V0C ATP6V0C ATP6V0C 4127 0.058 0.44 YES
37 SDHD SDHD SDHD 4164 0.058 0.44 YES
38 COX6C COX6C COX6C 4235 0.056 0.44 YES
39 ATP6V1G1 ATP6V1G1 ATP6V1G1 4243 0.056 0.45 YES
40 NDUFB5 NDUFB5 NDUFB5 4274 0.055 0.46 YES
41 NDUFA3 NDUFA3 NDUFA3 4413 0.052 0.46 YES
42 NDUFB9 NDUFB9 NDUFB9 4441 0.052 0.46 YES
43 ATP6AP1 ATP6AP1 ATP6AP1 4491 0.051 0.46 YES
44 NDUFB2 NDUFB2 NDUFB2 4521 0.05 0.47 YES
45 NDUFS3 NDUFS3 NDUFS3 4524 0.05 0.47 YES
46 COX8A COX8A COX8A 4590 0.049 0.47 YES
47 ATP6V1E1 ATP6V1E1 ATP6V1E1 4740 0.046 0.47 YES
48 UQCR11 UQCR11 UQCR11 4761 0.046 0.48 YES
49 UQCR10 UQCR10 UQCR10 4926 0.043 0.47 YES
50 NDUFS1 NDUFS1 NDUFS1 4927 0.043 0.48 YES
51 UQCRB UQCRB UQCRB 4937 0.043 0.48 YES
52 NDUFV1 NDUFV1 NDUFV1 4985 0.042 0.48 YES
53 COX4I1 COX4I1 COX4I1 5027 0.042 0.49 YES
54 ATP5E ATP5E ATP5E 5071 0.041 0.49 YES
55 NDUFA9 NDUFA9 NDUFA9 5112 0.04 0.49 YES
56 COX6B1 COX6B1 COX6B1 5135 0.04 0.5 YES
57 COX4I2 COX4I2 COX4I2 5157 0.04 0.5 YES
58 ATP5D ATP5D ATP5D 5346 0.037 0.49 YES
59 COX6A1 COX6A1 COX6A1 5413 0.036 0.49 YES
60 NDUFA5 NDUFA5 NDUFA5 5430 0.036 0.5 YES
61 NDUFB6 NDUFB6 NDUFB6 5498 0.035 0.5 YES
62 ATP5G1 ATP5G1 ATP5G1 5504 0.035 0.5 YES
63 ATP5J ATP5J ATP5J 5536 0.034 0.5 YES
64 NDUFB7 NDUFB7 NDUFB7 5668 0.032 0.5 YES
65 ATP5F1 ATP5F1 ATP5F1 5679 0.032 0.5 YES
66 COX7A2L COX7A2L COX7A2L 5732 0.032 0.5 YES
67 ATP6V1F ATP6V1F ATP6V1F 5830 0.03 0.5 YES
68 ATP5J2 ATP5J2 ATP5J2 5855 0.03 0.5 YES
69 NDUFA11 NDUFA11 NDUFA11 6313 0.024 0.48 NO
70 ATP5I ATP5I ATP5I 6346 0.023 0.48 NO
71 ATP5O ATP5O ATP5O 6414 0.022 0.48 NO
72 COX7C COX7C COX7C 6505 0.021 0.48 NO
73 NDUFB8 NDUFB8 NDUFB8 6532 0.021 0.48 NO
74 ATP5H ATP5H ATP5H 6560 0.021 0.48 NO
75 COX5B COX5B COX5B 6606 0.02 0.48 NO
76 NDUFA1 NDUFA1 NDUFA1 6685 0.02 0.48 NO
77 NDUFS2 NDUFS2 NDUFS2 6717 0.019 0.48 NO
78 NDUFAB1 NDUFAB1 NDUFAB1 6761 0.019 0.48 NO
79 COX17 COX17 COX17 6800 0.018 0.48 NO
80 NDUFS7 NDUFS7 NDUFS7 6813 0.018 0.48 NO
81 NDUFS6 NDUFS6 NDUFS6 6883 0.017 0.48 NO
82 CYC1 CYC1 CYC1 6898 0.017 0.48 NO
83 ATP5C1 ATP5C1 ATP5C1 6920 0.017 0.48 NO
84 NDUFA10 NDUFA10 NDUFA10 7257 0.013 0.46 NO
85 ATP6V0E1 ATP6V0E1 ATP6V0E1 7328 0.012 0.46 NO
86 NDUFB10 NDUFB10 NDUFB10 7453 0.011 0.46 NO
87 NDUFV2 NDUFV2 NDUFV2 7512 0.011 0.45 NO
88 NDUFS4 NDUFS4 NDUFS4 7551 0.01 0.45 NO
89 ATP6V1C1 ATP6V1C1 ATP6V1C1 7633 0.0092 0.45 NO
90 NDUFS5 NDUFS5 NDUFS5 8024 0.0056 0.43 NO
91 SDHA SDHA SDHA 8032 0.0056 0.43 NO
92 COX11 COX11 COX11 8046 0.0055 0.43 NO
93 SDHC SDHC SDHC 8418 0.0016 0.41 NO
94 NDUFA7 NDUFA7 NDUFA7 8438 0.0014 0.41 NO
95 ATP5G3 ATP5G3 ATP5G3 8476 0.00098 0.4 NO
96 SDHB SDHB SDHB 8493 0.00078 0.4 NO
97 NDUFB3 NDUFB3 NDUFB3 8804 -0.0022 0.39 NO
98 NDUFB4 NDUFB4 NDUFB4 9664 -0.011 0.34 NO
99 UQCRQ UQCRQ UQCRQ 9813 -0.012 0.34 NO
100 LHPP LHPP LHPP 10114 -0.015 0.32 NO
101 ATP5G2 ATP5G2 ATP5G2 10512 -0.02 0.3 NO
102 NDUFV3 NDUFV3 NDUFV3 10721 -0.022 0.29 NO
103 COX15 COX15 COX15 10933 -0.025 0.28 NO
104 PPA1 PPA1 PPA1 11679 -0.035 0.25 NO
105 NDUFA2 NDUFA2 NDUFA2 12209 -0.043 0.22 NO
106 ATP6V1B2 ATP6V1B2 ATP6V1B2 12650 -0.051 0.2 NO
107 COX8C COX8C COX8C 12898 -0.056 0.2 NO
108 NDUFC1 NDUFC1 NDUFC1 13031 -0.058 0.2 NO
109 ATP6V0A1 ATP6V0A1 ATP6V0A1 13734 -0.075 0.17 NO
110 TCIRG1 TCIRG1 TCIRG1 14615 -0.1 0.13 NO
111 ATP6V1E2 ATP6V1E2 ATP6V1E2 14777 -0.11 0.13 NO
112 COX6A2 COX6A2 COX6A2 16805 -0.21 0.046 NO
113 NDUFA4L2 NDUFA4L2 NDUFA4L2 17561 -0.29 0.038 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 WNT SIGNALING PATHWAY.

Figure S20.  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

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 AT1R PATHWAY 32 genes.ES.table 0.34 1.3 0.18 0.72 0.98 0.094 0.1 0.084 0.6 0.23
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.32 1.2 0.29 0.82 1 0.56 0.37 0.36 0.74 0.28
BIOCARTA VEGF PATHWAY 28 genes.ES.table 0.41 1.3 0.23 0.71 0.99 0.18 0.14 0.15 0.62 0.22
KEGG GLYCOLYSIS GLUCONEOGENESIS 57 genes.ES.table 0.39 1.2 0.21 0.78 1 0.14 0.047 0.13 0.69 0.26
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS 26 genes.ES.table 0.67 1.4 0.11 0.99 0.96 0.42 0.1 0.38 0.8 0.38
KEGG GALACTOSE METABOLISM 25 genes.ES.table 0.41 1.3 0.18 0.72 0.99 0.12 0.025 0.12 0.63 0.22
KEGG FATTY ACID METABOLISM 40 genes.ES.table 0.52 1.4 0.14 0.87 0.96 0.32 0.12 0.29 0.7 0.32
KEGG GLYCINE SERINE AND THREONINE METABOLISM 30 genes.ES.table 0.52 1.2 0.23 0.79 1 0.4 0.12 0.35 0.7 0.26
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.59 1.6 0.074 1 0.75 0.7 0.28 0.5 0.68 0.38
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.34 1.3 0.16 0.67 0.98 0.33 0.26 0.24 0.57 0.2
genes ES table in pathway: BIOCARTA AT1R 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 CYP4A11 CYP4A11 CYP4A11 2 0.83 0.082 YES
2 CYP4A22 CYP4A22 CYP4A22 40 0.59 0.14 YES
3 SLC27A2 SLC27A2 SLC27A2 48 0.57 0.2 YES
4 PCK1 PCK1 PCK1 60 0.55 0.25 YES
5 AQP7 AQP7 AQP7 104 0.48 0.29 YES
6 FABP4 FABP4 FABP4 140 0.45 0.34 YES
7 ACADL ACADL ACADL 192 0.42 0.38 YES
8 HMGCS2 HMGCS2 HMGCS2 208 0.41 0.42 YES
9 CD36 CD36 CD36 416 0.32 0.44 YES
10 EHHADH EHHADH EHHADH 589 0.28 0.45 YES
11 RXRG RXRG RXRG 850 0.22 0.46 YES
12 CYP27A1 CYP27A1 CYP27A1 930 0.21 0.48 YES
13 PLIN1 PLIN1 PLIN1 1158 0.18 0.48 YES
14 LPL LPL LPL 1170 0.18 0.5 YES
15 GK GK GK 1189 0.18 0.52 YES
16 FABP1 FABP1 FABP1 1290 0.17 0.53 YES
17 ANGPTL4 ANGPTL4 ANGPTL4 1521 0.15 0.53 YES
18 ACADM ACADM ACADM 1565 0.15 0.55 YES
19 CPT2 CPT2 CPT2 1600 0.15 0.56 YES
20 PCK2 PCK2 PCK2 1805 0.14 0.56 YES
21 ACSL1 ACSL1 ACSL1 1830 0.13 0.57 YES
22 FABP7 FABP7 FABP7 1967 0.13 0.58 YES
23 PPARG PPARG PPARG 2095 0.12 0.58 YES
24 CPT1A CPT1A CPT1A 2171 0.12 0.59 YES
25 PPARA PPARA PPARA 2804 0.092 0.56 NO
26 FABP3 FABP3 FABP3 3888 0.062 0.51 NO
27 ACOX1 ACOX1 ACOX1 4519 0.05 0.48 NO
28 FABP2 FABP2 FABP2 4549 0.049 0.48 NO
29 PDPK1 PDPK1 PDPK1 4977 0.042 0.46 NO
30 SCP2 SCP2 SCP2 5236 0.038 0.45 NO
31 SCD5 SCD5 SCD5 5326 0.037 0.45 NO
32 CPT1B CPT1B CPT1B 5677 0.032 0.44 NO
33 RXRB RXRB RXRB 5814 0.03 0.43 NO
34 SCD SCD SCD 6237 0.024 0.41 NO
35 ILK ILK ILK 6403 0.023 0.4 NO
36 ACAA1 ACAA1 ACAA1 6952 0.016 0.38 NO
37 SORBS1 SORBS1 SORBS1 7859 0.0057 0.33 NO
38 PPARD PPARD PPARD 8237 0.0011 0.31 NO
39 NR1H3 NR1H3 NR1H3 8541 -0.0023 0.29 NO
40 UBC UBC UBC 8864 -0.006 0.27 NO
41 FADS2 FADS2 FADS2 8886 -0.0064 0.27 NO
42 RXRA RXRA RXRA 9230 -0.01 0.25 NO
43 ACSL3 ACSL3 ACSL3 9963 -0.019 0.22 NO
44 ACSL6 ACSL6 ACSL6 10111 -0.021 0.21 NO
45 SLC27A1 SLC27A1 SLC27A1 10185 -0.022 0.21 NO
46 CYP7A1 CYP7A1 CYP7A1 10407 -0.024 0.2 NO
47 CPT1C CPT1C CPT1C 11021 -0.032 0.17 NO
48 OLR1 OLR1 OLR1 11762 -0.043 0.13 NO
49 FABP6 FABP6 FABP6 12675 -0.058 0.087 NO
50 FABP5 FABP5 FABP5 12948 -0.063 0.078 NO
51 ACSL5 ACSL5 ACSL5 13195 -0.069 0.072 NO
52 APOA2 APOA2 APOA2 13380 -0.074 0.069 NO
53 CYP8B1 CYP8B1 CYP8B1 13455 -0.076 0.072 NO
54 SLC27A4 SLC27A4 SLC27A4 13578 -0.079 0.073 NO
55 DBI DBI DBI 13651 -0.081 0.077 NO
56 ADIPOQ ADIPOQ ADIPOQ 13792 -0.084 0.078 NO
57 ACSL4 ACSL4 ACSL4 14134 -0.095 0.069 NO
58 MMP1 MMP1 MMP1 14280 -0.1 0.07 NO
59 ACOX3 ACOX3 ACOX3 14632 -0.11 0.062 NO
60 SLC27A5 SLC27A5 SLC27A5 15757 -0.18 0.018 NO
61 APOA1 APOA1 APOA1 15978 -0.19 0.025 NO
62 APOC3 APOC3 APOC3 16695 -0.25 0.011 NO
63 ME1 ME1 ME1 17052 -0.29 0.02 NO
64 PLTP PLTP PLTP 17916 -0.46 0.019 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 AT1R PATHWAY.

Figure S22.  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 DEATH PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HMGCS2 HMGCS2 HMGCS2 208 0.41 0.08 YES
2 ALDH6A1 ALDH6A1 ALDH6A1 346 0.34 0.15 YES
3 AOX1 AOX1 AOX1 456 0.31 0.21 YES
4 EHHADH EHHADH EHHADH 589 0.28 0.26 YES
5 ALDH3A2 ALDH3A2 ALDH3A2 862 0.22 0.3 YES
6 ACAA2 ACAA2 ACAA2 906 0.22 0.35 YES
7 HIBCH HIBCH HIBCH 982 0.2 0.39 YES
8 ABAT ABAT ABAT 1040 0.2 0.43 YES
9 ACAT1 ACAT1 ACAT1 1266 0.18 0.46 YES
10 ACADM ACADM ACADM 1565 0.15 0.47 YES
11 PCCA PCCA PCCA 1576 0.15 0.51 YES
12 AUH AUH AUH 1675 0.14 0.53 YES
13 ACADSB ACADSB ACADSB 1806 0.14 0.56 YES
14 MUT MUT MUT 2315 0.11 0.55 YES
15 ALDH9A1 ALDH9A1 ALDH9A1 2638 0.097 0.56 YES
16 ALDH7A1 ALDH7A1 ALDH7A1 3122 0.082 0.55 YES
17 IVD IVD IVD 3749 0.065 0.53 YES
18 ALDH2 ALDH2 ALDH2 3788 0.064 0.54 YES
19 ACADS ACADS ACADS 3860 0.063 0.55 YES
20 MCEE MCEE MCEE 4359 0.052 0.54 YES
21 BCKDHB BCKDHB BCKDHB 4392 0.052 0.55 YES
22 MCCC1 MCCC1 MCCC1 4544 0.049 0.55 YES
23 DBT DBT DBT 4632 0.048 0.56 YES
24 HMGCL HMGCL HMGCL 4708 0.047 0.56 YES
25 HADHB HADHB HADHB 4720 0.047 0.57 YES
26 HADHA HADHA HADHA 4730 0.047 0.58 YES
27 HIBADH HIBADH HIBADH 4886 0.044 0.58 YES
28 HMGCS1 HMGCS1 HMGCS1 4899 0.044 0.59 YES
29 ACAD8 ACAD8 ACAD8 5148 0.04 0.59 YES
30 BCKDHA BCKDHA BCKDHA 5197 0.039 0.59 YES
31 ALDH1B1 ALDH1B1 ALDH1B1 5616 0.032 0.58 NO
32 OXCT1 OXCT1 OXCT1 6260 0.024 0.55 NO
33 ECHS1 ECHS1 ECHS1 6506 0.022 0.54 NO
34 ACAA1 ACAA1 ACAA1 6952 0.016 0.52 NO
35 MCCC2 MCCC2 MCCC2 7312 0.012 0.5 NO
36 DLD DLD DLD 8567 -0.0026 0.43 NO
37 HADH HADH HADH 8673 -0.0038 0.43 NO
38 IL4I1 IL4I1 IL4I1 9171 -0.0095 0.4 NO
39 BCAT2 BCAT2 BCAT2 10122 -0.021 0.36 NO
40 HSD17B10 HSD17B10 HSD17B10 12118 -0.049 0.26 NO
41 ACAT2 ACAT2 ACAT2 12516 -0.055 0.25 NO
42 PCCB PCCB PCCB 13086 -0.067 0.23 NO
43 OXCT2 OXCT2 OXCT2 16486 -0.24 0.097 NO

Figure S23.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA DEATH PATHWAY.

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

genes ES table in pathway: BIOCARTA VEGF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AMDHD1 AMDHD1 AMDHD1 28 0.62 0.13 YES
2 DDC DDC DDC 82 0.51 0.24 YES
3 ASPA ASPA ASPA 168 0.43 0.32 YES
4 FTCD FTCD FTCD 170 0.43 0.42 YES
5 ACY3 ACY3 ACY3 567 0.28 0.45 YES
6 ABP1 ABP1 ABP1 689 0.26 0.5 YES
7 HDC HDC HDC 726 0.25 0.55 YES
8 ALDH3A2 ALDH3A2 ALDH3A2 862 0.22 0.59 YES
9 MAOB MAOB MAOB 1080 0.19 0.62 YES
10 HNMT HNMT HNMT 1716 0.14 0.62 NO
11 ALDH9A1 ALDH9A1 ALDH9A1 2638 0.097 0.59 NO
12 ALDH7A1 ALDH7A1 ALDH7A1 3122 0.082 0.58 NO
13 LCMT2 LCMT2 LCMT2 3714 0.066 0.56 NO
14 ALDH2 ALDH2 ALDH2 3788 0.064 0.57 NO
15 HAL HAL HAL 4303 0.054 0.55 NO
16 ALDH1B1 ALDH1B1 ALDH1B1 5616 0.032 0.49 NO
17 ALDH3A1 ALDH3A1 ALDH3A1 5855 0.029 0.48 NO
18 TRMT11 TRMT11 TRMT11 6152 0.025 0.47 NO
19 HEMK1 HEMK1 HEMK1 7412 0.011 0.4 NO
20 ALDH3B1 ALDH3B1 ALDH3B1 7707 0.0076 0.39 NO
21 METTL2B METTL2B METTL2B 8232 0.0012 0.36 NO
22 UROC1 UROC1 UROC1 10124 -0.021 0.26 NO
23 MAOA MAOA MAOA 10573 -0.026 0.24 NO
24 LCMT1 LCMT1 LCMT1 11018 -0.032 0.22 NO
25 WBSCR22 WBSCR22 WBSCR22 13246 -0.07 0.12 NO
26 METTL6 METTL6 METTL6 13876 -0.087 0.1 NO
27 ALDH3B2 ALDH3B2 ALDH3B2 15603 -0.17 0.041 NO
28 ALDH1A3 ALDH1A3 ALDH1A3 17979 -0.49 0.015 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: BIOCARTA VEGF PATHWAY.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA VEGF 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 GLYCOLYSIS GLUCONEOGENESIS

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 ALDH6A1 ALDH6A1 ALDH6A1 346 0.34 0.085 YES
2 EHHADH EHHADH EHHADH 589 0.28 0.16 YES
3 ALDH3A2 ALDH3A2 ALDH3A2 862 0.22 0.21 YES
4 HIBCH HIBCH HIBCH 982 0.2 0.27 YES
5 ABAT ABAT ABAT 1040 0.2 0.33 YES
6 ACAT1 ACAT1 ACAT1 1266 0.18 0.37 YES
7 ACADM ACADM ACADM 1565 0.15 0.4 YES
8 PCCA PCCA PCCA 1576 0.15 0.44 YES
9 MLYCD MLYCD MLYCD 2254 0.11 0.44 YES
10 MUT MUT MUT 2315 0.11 0.47 YES
11 ALDH9A1 ALDH9A1 ALDH9A1 2638 0.097 0.48 YES
12 LDHAL6A LDHAL6A LDHAL6A 2745 0.094 0.51 YES
13 ALDH7A1 ALDH7A1 ALDH7A1 3122 0.082 0.51 YES
14 ACSS3 ACSS3 ACSS3 3136 0.081 0.54 YES
15 ACSS1 ACSS1 ACSS1 3287 0.077 0.55 YES
16 SUCLA2 SUCLA2 SUCLA2 3371 0.074 0.57 YES
17 ALDH2 ALDH2 ALDH2 3788 0.064 0.57 NO
18 MCEE MCEE MCEE 4359 0.052 0.55 NO
19 HADHA HADHA HADHA 4730 0.047 0.55 NO
20 ACACB ACACB ACACB 5401 0.035 0.52 NO
21 ALDH1B1 ALDH1B1 ALDH1B1 5616 0.032 0.52 NO
22 LDHA LDHA LDHA 5933 0.028 0.51 NO
23 ECHS1 ECHS1 ECHS1 6506 0.022 0.49 NO
24 SUCLG1 SUCLG1 SUCLG1 8368 -0.00036 0.38 NO
25 ACSS2 ACSS2 ACSS2 9894 -0.018 0.31 NO
26 SUCLG2 SUCLG2 SUCLG2 11049 -0.033 0.25 NO
27 LDHB LDHB LDHB 12499 -0.055 0.19 NO
28 ACAT2 ACAT2 ACAT2 12516 -0.055 0.21 NO
29 PCCB PCCB PCCB 13086 -0.067 0.2 NO
30 ACACA ACACA ACACA 14505 -0.11 0.15 NO
31 LDHAL6B LDHAL6B LDHAL6B 15780 -0.18 0.14 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 GLYCOLYSIS GLUCONEOGENESIS.

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

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HAO2 HAO2 HAO2 15 0.74 0.095 YES
2 SLC27A2 SLC27A2 SLC27A2 48 0.57 0.17 YES
3 DAO DAO DAO 297 0.36 0.2 YES
4 EHHADH EHHADH EHHADH 589 0.28 0.22 YES
5 PXMP2 PXMP2 PXMP2 723 0.25 0.25 YES
6 AGXT AGXT AGXT 738 0.24 0.28 YES
7 EPHX2 EPHX2 EPHX2 878 0.22 0.3 YES
8 NOS2 NOS2 NOS2 1031 0.2 0.32 YES
9 DDO DDO DDO 1131 0.19 0.34 YES
10 FAR2 FAR2 FAR2 1293 0.17 0.35 YES
11 PECR PECR PECR 1299 0.17 0.37 YES
12 PEX11A PEX11A PEX11A 1327 0.17 0.39 YES
13 ACSL1 ACSL1 ACSL1 1830 0.13 0.38 YES
14 DECR2 DECR2 DECR2 2015 0.12 0.39 YES
15 NUDT12 NUDT12 NUDT12 2131 0.12 0.4 YES
16 MLYCD MLYCD MLYCD 2254 0.11 0.4 YES
17 PEX11G PEX11G PEX11G 2329 0.11 0.42 YES
18 PAOX PAOX PAOX 2420 0.1 0.42 YES
19 PHYH PHYH PHYH 2555 0.1 0.43 YES
20 DHRS4 DHRS4 DHRS4 2654 0.097 0.44 YES
21 CRAT CRAT CRAT 2665 0.096 0.45 YES
22 AGPS AGPS AGPS 2714 0.095 0.46 YES
23 CAT CAT CAT 2786 0.092 0.47 YES
24 ECH1 ECH1 ECH1 2840 0.091 0.48 YES
25 PEX1 PEX1 PEX1 2970 0.086 0.48 YES
26 ABCD3 ABCD3 ABCD3 3084 0.083 0.48 YES
27 PECI PECI PECI 3432 0.073 0.47 NO
28 MPV17L MPV17L MPV17L 3601 0.069 0.47 NO
29 ABCD4 ABCD4 ABCD4 3751 0.065 0.47 NO
30 AMACR AMACR AMACR 3844 0.063 0.48 NO
31 PEX3 PEX3 PEX3 3949 0.061 0.48 NO
32 PEX7 PEX7 PEX7 4410 0.052 0.46 NO
33 PEX10 PEX10 PEX10 4467 0.051 0.46 NO
34 ACOX1 ACOX1 ACOX1 4519 0.05 0.47 NO
35 PMVK PMVK PMVK 4567 0.049 0.47 NO
36 HMGCL HMGCL HMGCL 4708 0.047 0.47 NO
37 ABCD2 ABCD2 ABCD2 5027 0.042 0.46 NO
38 PEX5 PEX5 PEX5 5052 0.041 0.46 NO
39 SCP2 SCP2 SCP2 5236 0.038 0.46 NO
40 PEX11B PEX11B PEX11B 5460 0.035 0.45 NO
41 PEX19 PEX19 PEX19 6569 0.021 0.39 NO
42 PEX26 PEX26 PEX26 6590 0.021 0.39 NO
43 PEX12 PEX12 PEX12 6891 0.017 0.38 NO
44 ACAA1 ACAA1 ACAA1 6952 0.016 0.38 NO
45 PIPOX PIPOX PIPOX 7085 0.015 0.37 NO
46 PEX13 PEX13 PEX13 7090 0.015 0.37 NO
47 SLC25A17 SLC25A17 SLC25A17 7477 0.01 0.35 NO
48 SOD1 SOD1 SOD1 8555 -0.0025 0.3 NO
49 CROT CROT CROT 8832 -0.0056 0.28 NO
50 GNPAT GNPAT GNPAT 9056 -0.0082 0.27 NO
51 HSD17B4 HSD17B4 HSD17B4 9175 -0.0096 0.26 NO
52 PEX14 PEX14 PEX14 9435 -0.013 0.25 NO
53 PEX6 PEX6 PEX6 9912 -0.018 0.23 NO
54 ACSL3 ACSL3 ACSL3 9963 -0.019 0.23 NO
55 ACSL6 ACSL6 ACSL6 10111 -0.021 0.22 NO
56 GSTK1 GSTK1 GSTK1 10609 -0.027 0.2 NO
57 IDH2 IDH2 IDH2 10659 -0.027 0.2 NO
58 ABCD1 ABCD1 ABCD1 10747 -0.029 0.2 NO
59 PEX2 PEX2 PEX2 11255 -0.036 0.18 NO
60 FAR1 FAR1 FAR1 11319 -0.036 0.18 NO
61 MPV17 MPV17 MPV17 11841 -0.044 0.15 NO
62 PRDX5 PRDX5 PRDX5 12146 -0.049 0.14 NO
63 PRDX1 PRDX1 PRDX1 12312 -0.052 0.14 NO
64 PEX16 PEX16 PEX16 12334 -0.052 0.15 NO
65 HACL1 HACL1 HACL1 12355 -0.053 0.15 NO
66 ACSL5 ACSL5 ACSL5 13195 -0.069 0.12 NO
67 NUDT19 NUDT19 NUDT19 13396 -0.074 0.11 NO
68 SOD2 SOD2 SOD2 13549 -0.078 0.12 NO
69 MVK MVK MVK 13559 -0.078 0.12 NO
70 ACOT8 ACOT8 ACOT8 13789 -0.084 0.12 NO
71 PXMP4 PXMP4 PXMP4 13805 -0.085 0.13 NO
72 ACSL4 ACSL4 ACSL4 14134 -0.095 0.13 NO
73 ACOX3 ACOX3 ACOX3 14632 -0.11 0.12 NO
74 IDH1 IDH1 IDH1 14782 -0.12 0.12 NO
75 BAAT BAAT BAAT 14874 -0.12 0.13 NO
76 XDH XDH XDH 17674 -0.4 0.032 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS.

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

genes ES table in pathway: KEGG GALACTOSE 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 G6PC G6PC G6PC 27 0.64 0.1 YES
2 PCK1 PCK1 PCK1 60 0.55 0.19 YES
3 CD36 CD36 CD36 416 0.32 0.22 YES
4 G6PC2 G6PC2 G6PC2 458 0.31 0.26 YES
5 RXRG RXRG RXRG 850 0.22 0.28 YES
6 PRKAA2 PRKAA2 PRKAA2 1485 0.16 0.27 YES
7 SLC2A4 SLC2A4 SLC2A4 1712 0.14 0.28 YES
8 PCK2 PCK2 PCK2 1805 0.14 0.3 YES
9 ACSL1 ACSL1 ACSL1 1830 0.13 0.32 YES
10 MAPK8 MAPK8 MAPK8 1836 0.13 0.34 YES
11 PPARGC1A PPARGC1A PPARGC1A 1847 0.13 0.36 YES
12 AKT3 AKT3 AKT3 2165 0.12 0.36 YES
13 CPT1A CPT1A CPT1A 2171 0.12 0.38 YES
14 MAPK10 MAPK10 MAPK10 2413 0.1 0.38 YES
15 NFKBIA NFKBIA NFKBIA 2614 0.098 0.39 YES
16 PPARA PPARA PPARA 2804 0.092 0.39 YES
17 PRKAB1 PRKAB1 PRKAB1 3576 0.07 0.36 NO
18 LEPR LEPR LEPR 4069 0.058 0.34 NO
19 CAMKK1 CAMKK1 CAMKK1 4122 0.057 0.35 NO
20 NFKB1 NFKB1 NFKB1 4513 0.05 0.34 NO
21 NFKBIE NFKBIE NFKBIE 4780 0.046 0.33 NO
22 TRADD TRADD TRADD 4848 0.045 0.33 NO
23 PRKAA1 PRKAA1 PRKAA1 5315 0.037 0.31 NO
24 JAK2 JAK2 JAK2 5316 0.037 0.32 NO
25 ACACB ACACB ACACB 5401 0.035 0.32 NO
26 CPT1B CPT1B CPT1B 5677 0.032 0.31 NO
27 RXRB RXRB RXRB 5814 0.03 0.31 NO
28 CHUK CHUK CHUK 5920 0.028 0.3 NO
29 TRAF2 TRAF2 TRAF2 6275 0.024 0.29 NO
30 PRKAB2 PRKAB2 PRKAB2 7185 0.014 0.24 NO
31 IKBKB IKBKB IKBKB 7991 0.0042 0.2 NO
32 NFKBIB NFKBIB NFKBIB 8133 0.0023 0.19 NO
33 MAPK9 MAPK9 MAPK9 8630 -0.0034 0.16 NO
34 ADIPOR1 ADIPOR1 ADIPOR1 8663 -0.0037 0.16 NO
35 RELA RELA RELA 8793 -0.0052 0.16 NO
36 STAT3 STAT3 STAT3 8849 -0.0058 0.16 NO
37 RXRA RXRA RXRA 9230 -0.01 0.14 NO
38 ADIPOR2 ADIPOR2 ADIPOR2 9590 -0.015 0.12 NO
39 AKT2 AKT2 AKT2 9906 -0.018 0.1 NO
40 ACSL3 ACSL3 ACSL3 9963 -0.019 0.1 NO
41 STK11 STK11 STK11 10042 -0.02 0.1 NO
42 ACSL6 ACSL6 ACSL6 10111 -0.021 0.1 NO
43 PRKAG1 PRKAG1 PRKAG1 10133 -0.021 0.1 NO
44 TNFRSF1B TNFRSF1B TNFRSF1B 10148 -0.021 0.11 NO
45 MTOR MTOR MTOR 10232 -0.022 0.11 NO
46 CAMKK2 CAMKK2 CAMKK2 10283 -0.023 0.11 NO
47 AKT1 AKT1 AKT1 10352 -0.024 0.11 NO
48 CPT1C CPT1C CPT1C 11021 -0.032 0.076 NO
49 PTPN11 PTPN11 PTPN11 11033 -0.032 0.08 NO
50 TNFRSF1A TNFRSF1A TNFRSF1A 11406 -0.038 0.066 NO
51 PRKAG2 PRKAG2 PRKAG2 11691 -0.042 0.057 NO
52 PRKCQ PRKCQ PRKCQ 12116 -0.049 0.042 NO
53 SLC2A1 SLC2A1 SLC2A1 12418 -0.054 0.034 NO
54 TNF TNF TNF 13078 -0.066 0.0081 NO
55 IKBKG IKBKG IKBKG 13157 -0.068 0.015 NO
56 ACSL5 ACSL5 ACSL5 13195 -0.069 0.024 NO
57 ADIPOQ ADIPOQ ADIPOQ 13792 -0.084 0.0047 NO
58 ACSL4 ACSL4 ACSL4 14134 -0.095 0.0012 NO
59 SOCS3 SOCS3 SOCS3 14708 -0.12 -0.012 NO
60 IRS1 IRS1 IRS1 15689 -0.17 -0.038 NO
61 POMC POMC POMC 15694 -0.17 -0.01 NO
62 AGRP AGRP AGRP 16498 -0.24 -0.017 NO
63 IRS2 IRS2 IRS2 17433 -0.35 -0.012 NO
64 LEP LEP LEP 17496 -0.36 0.042 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 GALACTOSE METABOLISM.

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

genes ES table in pathway: KEGG FATTY ACID 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 DHDH DHDH DHDH 67 0.53 0.14 YES
2 UGT2A3 UGT2A3 UGT2A3 327 0.35 0.22 YES
3 UGT1A9 UGT1A9 UGT1A9 331 0.34 0.32 YES
4 XYLB XYLB XYLB 436 0.31 0.4 YES
5 UGT2B7 UGT2B7 UGT2B7 636 0.27 0.46 YES
6 UGT2B11 UGT2B11 UGT2B11 640 0.27 0.53 YES
7 UGT1A6 UGT1A6 UGT1A6 1406 0.16 0.54 YES
8 UGT1A8 UGT1A8 UGT1A8 1479 0.16 0.57 YES
9 UGT2B10 UGT2B10 UGT2B10 1599 0.15 0.61 YES
10 CRYL1 CRYL1 CRYL1 1649 0.15 0.65 YES
11 UGT1A1 UGT1A1 UGT1A1 1899 0.13 0.67 YES
12 UGT1A3 UGT1A3 UGT1A3 5066 0.041 0.51 NO
13 UGT2A1 UGT2A1 UGT2A1 5231 0.038 0.51 NO
14 UGT1A4 UGT1A4 UGT1A4 5609 0.032 0.5 NO
15 UGT1A7 UGT1A7 UGT1A7 6219 0.024 0.47 NO
16 LOC729020 LOC729020 LOC729020 6398 0.023 0.47 NO
17 UGT1A5 UGT1A5 UGT1A5 8729 -0.0045 0.34 NO
18 UGT2B15 UGT2B15 UGT2B15 10169 -0.022 0.27 NO
19 RPE RPE RPE 10333 -0.024 0.26 NO
20 UGT2B28 UGT2B28 UGT2B28 11882 -0.045 0.19 NO
21 GUSB GUSB GUSB 12691 -0.058 0.16 NO
22 UGT2B4 UGT2B4 UGT2B4 12854 -0.062 0.17 NO
23 UGP2 UGP2 UGP2 13169 -0.068 0.17 NO
24 DCXR DCXR DCXR 13226 -0.07 0.19 NO
25 AKR1B1 AKR1B1 AKR1B1 13641 -0.08 0.19 NO
26 UGT1A10 UGT1A10 UGT1A10 16475 -0.23 0.098 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 FATTY ACID METABOLISM.

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

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

Table 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 CYP4A11 CYP4A11 CYP4A11 2 0.83 0.14 YES
2 CYP4A22 CYP4A22 CYP4A22 40 0.59 0.23 YES
3 ADH6 ADH6 ADH6 121 0.47 0.3 YES
4 ACADL ACADL ACADL 192 0.42 0.37 YES
5 EHHADH EHHADH EHHADH 589 0.28 0.39 YES
6 ALDH3A2 ALDH3A2 ALDH3A2 862 0.22 0.41 YES
7 ACAA2 ACAA2 ACAA2 906 0.22 0.44 YES
8 ACAT1 ACAT1 ACAT1 1266 0.18 0.45 YES
9 ACADM ACADM ACADM 1565 0.15 0.46 YES
10 CPT2 CPT2 CPT2 1600 0.15 0.48 YES
11 ACADSB ACADSB ACADSB 1806 0.14 0.5 YES
12 ACSL1 ACSL1 ACSL1 1830 0.13 0.52 YES
13 CPT1A CPT1A CPT1A 2171 0.12 0.52 YES
14 ALDH9A1 ALDH9A1 ALDH9A1 2638 0.097 0.51 NO
15 ALDH7A1 ALDH7A1 ALDH7A1 3122 0.082 0.49 NO
16 PECI PECI PECI 3432 0.073 0.49 NO
17 ADH5 ADH5 ADH5 3512 0.071 0.5 NO
18 ALDH2 ALDH2 ALDH2 3788 0.064 0.49 NO
19 ACADS ACADS ACADS 3860 0.063 0.5 NO
20 ACADVL ACADVL ACADVL 4284 0.054 0.48 NO
21 HADHB HADHB HADHB 4720 0.047 0.47 NO
22 HADHA HADHA HADHA 4730 0.047 0.48 NO
23 DCI DCI DCI 5194 0.039 0.46 NO
24 ALDH1B1 ALDH1B1 ALDH1B1 5616 0.032 0.44 NO
25 CPT1B CPT1B CPT1B 5677 0.032 0.44 NO
26 ECHS1 ECHS1 ECHS1 6506 0.022 0.4 NO
27 ACAA1 ACAA1 ACAA1 6952 0.016 0.38 NO
28 HADH HADH HADH 8673 -0.0038 0.28 NO
29 ACSL3 ACSL3 ACSL3 9963 -0.019 0.22 NO
30 ACSL6 ACSL6 ACSL6 10111 -0.021 0.21 NO
31 CPT1C CPT1C CPT1C 11021 -0.032 0.16 NO
32 GCDH GCDH GCDH 12035 -0.047 0.12 NO
33 ACAT2 ACAT2 ACAT2 12516 -0.055 0.1 NO
34 ACSL5 ACSL5 ACSL5 13195 -0.069 0.074 NO
35 ACSL4 ACSL4 ACSL4 14134 -0.095 0.038 NO
36 ACOX3 ACOX3 ACOX3 14632 -0.11 0.03 NO
37 ADH1B ADH1B ADH1B 15704 -0.17 -0.0011 NO
38 ADH1A ADH1A ADH1A 16469 -0.23 -0.005 NO
39 ADH4 ADH4 ADH4 16779 -0.26 0.021 NO
40 ADH1C ADH1C ADH1C 17552 -0.37 0.039 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 GLYCINE SERINE AND THREONINE METABOLISM.

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

genes ES table in pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION

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 AGPAT9 AGPAT9 AGPAT9 469 0.3 0.031 YES
2 DGKB DGKB DGKB 662 0.26 0.069 YES
3 DGKI DGKI DGKI 692 0.25 0.11 YES
4 DGKH DGKH DGKH 755 0.24 0.16 YES
5 ALDH3A2 ALDH3A2 ALDH3A2 862 0.22 0.19 YES
6 LIPC LIPC LIPC 904 0.22 0.23 YES
7 LPL LPL LPL 1170 0.18 0.25 YES
8 GK GK GK 1189 0.18 0.28 YES
9 PPAP2B PPAP2B PPAP2B 1206 0.18 0.31 YES
10 DGKE DGKE DGKE 1267 0.18 0.34 YES
11 PPAP2A PPAP2A PPAP2A 1313 0.17 0.37 YES
12 PNPLA3 PNPLA3 PNPLA3 1461 0.16 0.39 YES
13 ALDH9A1 ALDH9A1 ALDH9A1 2638 0.097 0.35 NO
14 ALDH7A1 ALDH7A1 ALDH7A1 3122 0.082 0.34 NO
15 DGKD DGKD DGKD 3207 0.079 0.35 NO
16 DAK DAK DAK 3399 0.074 0.35 NO
17 AGPAT3 AGPAT3 AGPAT3 3579 0.07 0.35 NO
18 ALDH2 ALDH2 ALDH2 3788 0.064 0.35 NO
19 LCLAT1 LCLAT1 LCLAT1 4147 0.056 0.34 NO
20 AKR1A1 AKR1A1 AKR1A1 4798 0.046 0.32 NO
21 ALDH1B1 ALDH1B1 ALDH1B1 5616 0.032 0.28 NO
22 DGKZ DGKZ DGKZ 6086 0.026 0.26 NO
23 AGPAT1 AGPAT1 AGPAT1 6452 0.022 0.24 NO
24 GLYCTK GLYCTK GLYCTK 7373 0.011 0.19 NO
25 MGLL MGLL MGLL 7583 0.0091 0.18 NO
26 AGPAT4 AGPAT4 AGPAT4 9319 -0.012 0.09 NO
27 AGPAT6 AGPAT6 AGPAT6 9404 -0.012 0.088 NO
28 MBOAT2 MBOAT2 MBOAT2 10902 -0.031 0.011 NO
29 GPAM GPAM GPAM 11594 -0.04 -0.019 NO
30 DGKQ DGKQ DGKQ 12113 -0.048 -0.038 NO
31 LIPG LIPG LIPG 12190 -0.05 -0.033 NO
32 AGK AGK AGK 12543 -0.056 -0.042 NO
33 MBOAT1 MBOAT1 MBOAT1 12586 -0.057 -0.034 NO
34 DGAT1 DGAT1 DGAT1 13040 -0.066 -0.047 NO
35 AGPAT2 AGPAT2 AGPAT2 13453 -0.076 -0.055 NO
36 AKR1B1 AKR1B1 AKR1B1 13641 -0.08 -0.051 NO
37 LIPF LIPF LIPF 13645 -0.08 -0.036 NO
38 GPAT2 GPAT2 GPAT2 13679 -0.081 -0.022 NO
39 DGKA DGKA DGKA 14218 -0.098 -0.034 NO
40 AWAT2 AWAT2 AWAT2 14612 -0.11 -0.034 NO
41 GLA GLA GLA 15256 -0.14 -0.043 NO
42 PPAP2C PPAP2C PPAP2C 16140 -0.2 -0.054 NO
43 CEL CEL CEL 16371 -0.22 -0.025 NO
44 DGAT2 DGAT2 DGAT2 16902 -0.28 -0.0031 NO
45 DGKG DGKG DGKG 17764 -0.42 0.027 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

Table 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 CREB3L3 CREB3L3 CREB3L3 258 0.38 0.1 YES
2 AQP4 AQP4 AQP4 417 0.32 0.19 YES
3 AVPR2 AVPR2 AVPR2 1028 0.2 0.21 YES
4 DYNC2H1 DYNC2H1 DYNC2H1 1309 0.17 0.25 YES
5 ADCY9 ADCY9 ADCY9 1441 0.16 0.29 YES
6 CREB5 CREB5 CREB5 1941 0.13 0.3 YES
7 DCTN6 DCTN6 DCTN6 2627 0.097 0.29 YES
8 DYNC2LI1 DYNC2LI1 DYNC2LI1 2712 0.095 0.32 YES
9 AQP3 AQP3 AQP3 2964 0.086 0.33 YES
10 CREB3L4 CREB3L4 CREB3L4 3166 0.08 0.34 YES
11 VAMP2 VAMP2 VAMP2 3196 0.079 0.36 YES
12 DYNLL2 DYNLL2 DYNLL2 3722 0.066 0.35 NO
13 DCTN1 DCTN1 DCTN1 4380 0.052 0.33 NO
14 CREB3 CREB3 CREB3 5007 0.042 0.31 NO
15 DYNC1I2 DYNC1I2 DYNC1I2 5256 0.038 0.31 NO
16 CREB1 CREB1 CREB1 5992 0.027 0.28 NO
17 PRKACB PRKACB PRKACB 7170 0.014 0.22 NO
18 DYNC1LI2 DYNC1LI2 DYNC1LI2 7906 0.0051 0.18 NO
19 ADCY6 ADCY6 ADCY6 8034 0.0035 0.17 NO
20 ARHGDIB ARHGDIB ARHGDIB 8045 0.0034 0.17 NO
21 DYNC1H1 DYNC1H1 DYNC1H1 8266 0.00072 0.16 NO
22 RAB5C RAB5C RAB5C 8527 -0.0021 0.15 NO
23 DCTN4 DCTN4 DCTN4 8569 -0.0026 0.14 NO
24 ARHGDIA ARHGDIA ARHGDIA 8808 -0.0054 0.13 NO
25 RAB5B RAB5B RAB5B 8983 -0.0074 0.12 NO
26 RAB11A RAB11A RAB11A 9140 -0.0092 0.12 NO
27 STX4 STX4 STX4 9267 -0.011 0.12 NO
28 CREB3L2 CREB3L2 CREB3L2 9469 -0.013 0.11 NO
29 DCTN5 DCTN5 DCTN5 10096 -0.021 0.081 NO
30 RAB11B RAB11B RAB11B 10453 -0.025 0.068 NO
31 PRKACA PRKACA PRKACA 10539 -0.026 0.072 NO
32 DYNC1LI1 DYNC1LI1 DYNC1LI1 10756 -0.029 0.068 NO
33 NSF NSF NSF 10888 -0.03 0.07 NO
34 DCTN2 DCTN2 DCTN2 11600 -0.04 0.043 NO
35 RAB5A RAB5A RAB5A 11834 -0.044 0.044 NO
36 PRKX PRKX PRKX 11958 -0.046 0.05 NO
37 DYNLL1 DYNLL1 DYNLL1 12254 -0.051 0.05 NO
38 DYNC1I1 DYNC1I1 DYNC1I1 13525 -0.078 0.0031 NO
39 GNAS GNAS GNAS 14553 -0.11 -0.021 NO
40 AQP2 AQP2 AQP2 15604 -0.17 -0.028 NO
41 CREB3L1 CREB3L1 CREB3L1 18136 -0.58 0.0067 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 LYSINE DEGRADATION.

Figure S40.  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

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 INFLAM PATHWAY 25 genes.ES.table 0.66 1.5 0.063 0.6 0.92 0.76 0.28 0.55 0.47 0.18
BIOCARTA GSK3 PATHWAY 26 genes.ES.table 0.53 1.6 0.028 0.56 0.7 0.15 0.054 0.15 0.34 0.18
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.41 1.4 0.084 0.58 0.93 0.08 0.054 0.076 0.46 0.17
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 43 genes.ES.table 0.47 1.6 0.076 0.54 0.73 0.51 0.35 0.33 0.33 0.17
KEGG DNA REPLICATION 35 genes.ES.table 0.53 1.6 0.075 0.51 0.74 0.66 0.38 0.41 0.33 0.15
KEGG BASE EXCISION REPAIR 32 genes.ES.table 0.44 1.4 0.14 0.59 0.93 0.47 0.36 0.3 0.46 0.17
KEGG HOMOLOGOUS RECOMBINATION 27 genes.ES.table 0.62 1.6 0.061 0.55 0.82 0.41 0.23 0.31 0.38 0.18
KEGG CHEMOKINE SIGNALING PATHWAY 181 genes.ES.table 0.51 1.5 0.089 0.68 0.9 0.44 0.25 0.34 0.52 0.23
KEGG CELL CYCLE 123 genes.ES.table 0.53 1.7 0.043 0.67 0.56 0.23 0.12 0.2 0.34 0.23
KEGG OOCYTE MEIOSIS 106 genes.ES.table 0.42 1.5 0.094 0.68 0.91 0.21 0.14 0.18 0.52 0.23
genes ES table in pathway: BIOCARTA INFLAM 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 IL6 IL6 IL6 260 0.45 0.094 YES
2 C8G C8G C8G 557 0.38 0.17 YES
3 NCAM1 NCAM1 NCAM1 824 0.33 0.23 YES
4 NCAM2 NCAM2 NCAM2 949 0.32 0.3 YES
5 C9 C9 C9 1062 0.3 0.37 YES
6 IL1A IL1A IL1A 1186 0.28 0.43 YES
7 CCL5 CCL5 CCL5 1522 0.25 0.47 YES
8 C1QB C1QB C1QB 1894 0.22 0.5 YES
9 C1QC C1QC C1QC 2119 0.2 0.54 YES
10 IL1B IL1B IL1B 2148 0.2 0.58 YES
11 C1QA C1QA C1QA 2164 0.2 0.63 YES
12 BAX BAX BAX 4091 0.11 0.55 NO
13 ELK1 ELK1 ELK1 4856 0.084 0.53 NO
14 MAP2K2 MAP2K2 MAP2K2 6021 0.059 0.48 NO
15 PRKX PRKX PRKX 6689 0.047 0.46 NO
16 PRNP PRNP PRNP 7173 0.04 0.44 NO
17 C5 C5 C5 7278 0.038 0.44 NO
18 HSPA5 HSPA5 HSPA5 7317 0.038 0.45 NO
19 SOD1 SOD1 SOD1 7875 0.029 0.42 NO
20 STIP1 STIP1 STIP1 8061 0.027 0.42 NO
21 MAP2K1 MAP2K1 MAP2K1 8955 0.015 0.38 NO
22 HSPA1A HSPA1A HSPA1A 9585 0.0069 0.34 NO
23 PRKACA PRKACA PRKACA 9732 0.0048 0.34 NO
24 LAMC1 LAMC1 LAMC1 10575 -0.0057 0.29 NO
25 MAPK3 MAPK3 MAPK3 13069 -0.039 0.16 NO
26 PRKACB PRKACB PRKACB 13598 -0.048 0.15 NO
27 NOTCH1 NOTCH1 NOTCH1 13625 -0.048 0.16 NO
28 MAPK1 MAPK1 MAPK1 13695 -0.05 0.16 NO
29 FYN FYN FYN 15334 -0.087 0.096 NO
30 EGR1 EGR1 EGR1 15866 -0.1 0.093 NO
31 C6 C6 C6 16822 -0.16 0.079 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 INFLAM PATHWAY.

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA INFLAM 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 GSK3 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 AIM2 AIM2 AIM2 96 0.55 0.099 YES
2 IL6 IL6 IL6 260 0.45 0.18 YES
3 ZBP1 ZBP1 ZBP1 370 0.42 0.25 YES
4 IKBKE IKBKE IKBKE 390 0.41 0.32 YES
5 PYCARD PYCARD PYCARD 762 0.34 0.37 YES
6 IFNB1 IFNB1 IFNB1 892 0.32 0.42 YES
7 CCL5 CCL5 CCL5 1522 0.25 0.43 YES
8 CCL4 CCL4 CCL4 1702 0.23 0.47 YES
9 IRF7 IRF7 IRF7 2050 0.2 0.49 YES
10 IL1B IL1B IL1B 2148 0.2 0.52 YES
11 POLR3G POLR3G POLR3G 2152 0.2 0.56 YES
12 CCL4L2 CCL4L2 CCL4L2 2187 0.2 0.59 YES
13 IL18 IL18 IL18 2297 0.19 0.62 YES
14 CASP1 CASP1 CASP1 3214 0.14 0.6 NO
15 RIPK3 RIPK3 RIPK3 3573 0.12 0.6 NO
16 TMEM173 TMEM173 TMEM173 4181 0.1 0.59 NO
17 CXCL10 CXCL10 CXCL10 5000 0.08 0.56 NO
18 IKBKG IKBKG IKBKG 5016 0.08 0.57 NO
19 IRF3 IRF3 IRF3 5240 0.074 0.57 NO
20 POLR3K POLR3K POLR3K 5243 0.074 0.59 NO
21 TBK1 TBK1 TBK1 6725 0.047 0.51 NO
22 POLR3D POLR3D POLR3D 8349 0.023 0.43 NO
23 TREX1 TREX1 TREX1 8395 0.022 0.43 NO
24 NFKBIB NFKBIB NFKBIB 8541 0.021 0.43 NO
25 POLR3H POLR3H POLR3H 8832 0.016 0.41 NO
26 POLR3C POLR3C POLR3C 9033 0.014 0.41 NO
27 IKBKB IKBKB IKBKB 9331 0.01 0.39 NO
28 ADAR ADAR ADAR 9448 0.0086 0.39 NO
29 POLR1C POLR1C POLR1C 9589 0.0069 0.38 NO
30 RELA RELA RELA 9833 0.0034 0.37 NO
31 POLR3A POLR3A POLR3A 9898 0.0025 0.36 NO
32 DDX58 DDX58 DDX58 9989 0.0015 0.36 NO
33 RIPK1 RIPK1 RIPK1 10704 -0.0071 0.32 NO
34 POLR3GL POLR3GL POLR3GL 10808 -0.0084 0.32 NO
35 POLR3F POLR3F POLR3F 11188 -0.013 0.3 NO
36 MAVS MAVS MAVS 11263 -0.014 0.3 NO
37 POLR1D POLR1D POLR1D 11268 -0.014 0.3 NO
38 NFKB1 NFKB1 NFKB1 12805 -0.035 0.22 NO
39 IL33 IL33 IL33 13032 -0.039 0.22 NO
40 POLR3B POLR3B POLR3B 13137 -0.041 0.22 NO
41 CHUK CHUK CHUK 13895 -0.053 0.19 NO
42 NFKBIA NFKBIA NFKBIA 14643 -0.069 0.16 NO
43 IFNA13 IFNA13 IFNA13 15751 -0.1 0.12 NO
44 IFNA5 IFNA5 IFNA5 15835 -0.1 0.13 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 GSK3 PATHWAY.

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GSK3 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 WNT 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 CDC25C CDC25C CDC25C 156 0.51 0.028 YES
2 BUB1 BUB1 BUB1 190 0.49 0.06 YES
3 CCNE1 CCNE1 CCNE1 265 0.45 0.088 YES
4 PTTG1 PTTG1 PTTG1 277 0.44 0.12 YES
5 PLK1 PLK1 PLK1 300 0.44 0.15 YES
6 CCNB2 CCNB2 CCNB2 377 0.42 0.17 YES
7 CDC20 CDC20 CDC20 407 0.41 0.2 YES
8 PKMYT1 PKMYT1 PKMYT1 459 0.4 0.23 YES
9 ORC6L ORC6L ORC6L 536 0.38 0.25 YES
10 BUB1B BUB1B BUB1B 566 0.37 0.27 YES
11 TTK TTK TTK 603 0.37 0.3 YES
12 SFN SFN SFN 769 0.34 0.31 YES
13 CDC45 CDC45 CDC45 771 0.34 0.34 YES
14 E2F2 E2F2 E2F2 831 0.33 0.36 YES
15 ORC1L ORC1L ORC1L 1000 0.31 0.37 YES
16 CCNA1 CCNA1 CCNA1 1011 0.3 0.39 YES
17 CHEK2 CHEK2 CHEK2 1145 0.29 0.4 YES
18 CCNA2 CCNA2 CCNA2 1149 0.29 0.42 YES
19 ESPL1 ESPL1 ESPL1 1228 0.28 0.44 YES
20 CDKN2A CDKN2A CDKN2A 1278 0.27 0.46 YES
21 CCNB1 CCNB1 CCNB1 1380 0.26 0.47 YES
22 CDK1 CDK1 CDK1 1429 0.26 0.48 YES
23 CDC6 CDC6 CDC6 1595 0.24 0.49 YES
24 SMC1B SMC1B SMC1B 2010 0.21 0.48 YES
25 CCNE2 CCNE2 CCNE2 2026 0.21 0.5 YES
26 CDC25A CDC25A CDC25A 2053 0.2 0.51 YES
27 CDC7 CDC7 CDC7 2185 0.2 0.52 YES
28 MAD2L1 MAD2L1 MAD2L1 2284 0.19 0.53 YES
29 E2F1 E2F1 E2F1 2905 0.16 0.5 NO
30 CDC25B CDC25B CDC25B 2988 0.15 0.51 NO
31 MAD2L2 MAD2L2 MAD2L2 3709 0.12 0.48 NO
32 E2F3 E2F3 E2F3 4130 0.1 0.46 NO
33 CHEK1 CHEK1 CHEK1 4160 0.1 0.47 NO
34 MCM6 MCM6 MCM6 4264 0.1 0.47 NO
35 TGFB1 TGFB1 TGFB1 4266 0.1 0.48 NO
36 MCM2 MCM2 MCM2 4479 0.094 0.47 NO
37 CDK7 CDK7 CDK7 4744 0.086 0.46 NO
38 MAD1L1 MAD1L1 MAD1L1 4864 0.084 0.46 NO
39 PTTG2 PTTG2 PTTG2 4873 0.083 0.47 NO
40 ANAPC11 ANAPC11 ANAPC11 5130 0.077 0.46 NO
41 MCM4 MCM4 MCM4 5162 0.076 0.46 NO
42 ANAPC5 ANAPC5 ANAPC5 5238 0.074 0.46 NO
43 YWHAG YWHAG YWHAG 5383 0.071 0.46 NO
44 RBX1 RBX1 RBX1 5560 0.068 0.46 NO
45 PCNA PCNA PCNA 5756 0.064 0.45 NO
46 CDK4 CDK4 CDK4 5814 0.063 0.45 NO
47 TGFB3 TGFB3 TGFB3 5839 0.062 0.45 NO
48 ORC5L ORC5L ORC5L 5900 0.061 0.46 NO
49 MDM2 MDM2 MDM2 5987 0.059 0.45 NO
50 TP53 TP53 TP53 6107 0.057 0.45 NO
51 MCM5 MCM5 MCM5 6226 0.055 0.45 NO
52 ATR ATR ATR 6267 0.055 0.45 NO
53 CDK2 CDK2 CDK2 6339 0.054 0.45 NO
54 CCNH CCNH CCNH 6559 0.05 0.44 NO
55 MYC MYC MYC 6757 0.046 0.44 NO
56 GADD45G GADD45G GADD45G 6915 0.044 0.43 NO
57 CUL1 CUL1 CUL1 7041 0.042 0.42 NO
58 YWHAZ YWHAZ YWHAZ 7119 0.04 0.42 NO
59 ANAPC7 ANAPC7 ANAPC7 7298 0.038 0.42 NO
60 CDKN2D CDKN2D CDKN2D 7395 0.036 0.41 NO
61 CDK6 CDK6 CDK6 7442 0.036 0.41 NO
62 CCNB3 CCNB3 CCNB3 7579 0.034 0.41 NO
63 E2F4 E2F4 E2F4 7651 0.032 0.41 NO
64 CCND2 CCND2 CCND2 7685 0.032 0.41 NO
65 BUB3 BUB3 BUB3 7688 0.032 0.41 NO
66 ANAPC4 ANAPC4 ANAPC4 7798 0.03 0.41 NO
67 GADD45B GADD45B GADD45B 7840 0.03 0.41 NO
68 YWHAQ YWHAQ YWHAQ 8196 0.025 0.39 NO
69 E2F5 E2F5 E2F5 8213 0.025 0.39 NO
70 CCND3 CCND3 CCND3 8237 0.024 0.39 NO
71 SKP2 SKP2 SKP2 8303 0.024 0.39 NO
72 PRKDC PRKDC PRKDC 8462 0.022 0.38 NO
73 CDKN2C CDKN2C CDKN2C 8572 0.02 0.38 NO
74 RBL1 RBL1 RBL1 8592 0.02 0.38 NO
75 TFDP2 TFDP2 TFDP2 8599 0.02 0.38 NO
76 ZBTB17 ZBTB17 ZBTB17 8614 0.02 0.38 NO
77 CDC16 CDC16 CDC16 8631 0.019 0.38 NO
78 MCM7 MCM7 MCM7 9239 0.011 0.34 NO
79 FZR1 FZR1 FZR1 9531 0.0075 0.33 NO
80 ANAPC1 ANAPC1 ANAPC1 10004 0.0014 0.3 NO
81 HDAC1 HDAC1 HDAC1 10082 0.00028 0.3 NO
82 ANAPC10 ANAPC10 ANAPC10 10482 -0.0046 0.28 NO
83 GADD45A GADD45A GADD45A 10559 -0.0056 0.27 NO
84 YWHAB YWHAB YWHAB 10613 -0.0062 0.27 NO
85 MCM3 MCM3 MCM3 10624 -0.0063 0.27 NO
86 RB1 RB1 RB1 10739 -0.0076 0.27 NO
87 CDKN1A CDKN1A CDKN1A 11031 -0.011 0.25 NO
88 CDC27 CDC27 CDC27 11202 -0.013 0.24 NO
89 YWHAH YWHAH YWHAH 11315 -0.015 0.24 NO
90 ATM ATM ATM 11407 -0.016 0.23 NO
91 RAD21 RAD21 RAD21 11652 -0.019 0.22 NO
92 SKP1 SKP1 SKP1 11804 -0.021 0.21 NO
93 GSK3B GSK3B GSK3B 11889 -0.022 0.21 NO
94 ORC3L ORC3L ORC3L 12250 -0.027 0.19 NO
95 YWHAE YWHAE YWHAE 12383 -0.029 0.19 NO
96 SMC1A SMC1A SMC1A 12430 -0.03 0.19 NO
97 CDKN1B CDKN1B CDKN1B 12524 -0.031 0.18 NO
98 ORC2L ORC2L ORC2L 12553 -0.031 0.18 NO
99 ABL1 ABL1 ABL1 12580 -0.032 0.19 NO
100 SMAD2 SMAD2 SMAD2 12777 -0.035 0.18 NO
101 SMAD3 SMAD3 SMAD3 12834 -0.036 0.18 NO
102 CDC23 CDC23 CDC23 12903 -0.037 0.18 NO
103 HDAC2 HDAC2 HDAC2 12909 -0.037 0.18 NO
104 CREBBP CREBBP CREBBP 13220 -0.042 0.16 NO
105 RBL2 RBL2 RBL2 13384 -0.044 0.16 NO
106 TFDP1 TFDP1 TFDP1 13675 -0.049 0.15 NO
107 ANAPC13 ANAPC13 ANAPC13 13907 -0.053 0.14 NO
108 SMC3 SMC3 SMC3 13973 -0.054 0.14 NO
109 ORC4L ORC4L ORC4L 13997 -0.055 0.14 NO
110 EP300 EP300 EP300 14084 -0.056 0.14 NO
111 TGFB2 TGFB2 TGFB2 14162 -0.058 0.14 NO
112 STAG1 STAG1 STAG1 14331 -0.062 0.13 NO
113 STAG2 STAG2 STAG2 14392 -0.063 0.14 NO
114 WEE1 WEE1 WEE1 14886 -0.075 0.11 NO
115 ANAPC2 ANAPC2 ANAPC2 14900 -0.075 0.12 NO
116 WEE2 WEE2 WEE2 15232 -0.084 0.11 NO
117 CDKN2B CDKN2B CDKN2B 15336 -0.087 0.11 NO
118 SMAD4 SMAD4 SMAD4 15618 -0.096 0.097 NO
119 CDC26 CDC26 CDC26 15759 -0.1 0.097 NO
120 CDKN1C CDKN1C CDKN1C 15977 -0.11 0.093 NO
121 CCND1 CCND1 CCND1 16145 -0.12 0.092 NO
122 CDC14A CDC14A CDC14A 16669 -0.15 0.073 NO
123 CDC14B CDC14B CDC14B 17287 -0.2 0.054 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 WNT PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA WNT 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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 CCNE1 CCNE1 CCNE1 265 0.45 0.043 YES
2 GTSE1 GTSE1 GTSE1 350 0.42 0.092 YES
3 CCNB2 CCNB2 CCNB2 377 0.42 0.14 YES
4 BAI1 BAI1 BAI1 462 0.4 0.19 YES
5 RRM2 RRM2 RRM2 575 0.37 0.23 YES
6 SFN SFN SFN 769 0.34 0.26 YES
7 TP73 TP73 TP73 987 0.31 0.29 YES
8 CHEK2 CHEK2 CHEK2 1145 0.29 0.32 YES
9 SERPINE1 SERPINE1 SERPINE1 1183 0.28 0.35 YES
10 CD82 CD82 CD82 1231 0.28 0.39 YES
11 PMAIP1 PMAIP1 PMAIP1 1262 0.27 0.42 YES
12 CDKN2A CDKN2A CDKN2A 1278 0.27 0.45 YES
13 CCNB1 CCNB1 CCNB1 1380 0.26 0.48 YES
14 CDK1 CDK1 CDK1 1429 0.26 0.51 YES
15 CCNE2 CCNE2 CCNE2 2026 0.21 0.51 YES
16 BID BID BID 2506 0.18 0.5 YES
17 BBC3 BBC3 BBC3 3565 0.12 0.46 YES
18 LRDD LRDD LRDD 3619 0.12 0.47 YES
19 CASP3 CASP3 CASP3 3639 0.12 0.49 YES
20 CASP8 CASP8 CASP8 4019 0.11 0.48 YES
21 BAX BAX BAX 4091 0.11 0.49 YES
22 IGFBP3 IGFBP3 IGFBP3 4112 0.11 0.5 YES
23 CHEK1 CHEK1 CHEK1 4160 0.1 0.51 YES
24 TP53I3 TP53I3 TP53I3 5458 0.07 0.45 NO
25 TNFRSF10B TNFRSF10B TNFRSF10B 5476 0.069 0.46 NO
26 IGF1 IGF1 IGF1 5598 0.067 0.46 NO
27 FAS FAS FAS 5615 0.067 0.47 NO
28 PERP PERP PERP 5721 0.065 0.47 NO
29 CDK4 CDK4 CDK4 5814 0.063 0.47 NO
30 MDM2 MDM2 MDM2 5987 0.059 0.47 NO
31 APAF1 APAF1 APAF1 5991 0.059 0.48 NO
32 TP53 TP53 TP53 6107 0.057 0.48 NO
33 SHISA5 SHISA5 SHISA5 6197 0.056 0.48 NO
34 DDB2 DDB2 DDB2 6263 0.055 0.49 NO
35 ATR ATR ATR 6267 0.055 0.49 NO
36 CDK2 CDK2 CDK2 6339 0.054 0.5 NO
37 RPRM RPRM RPRM 6420 0.052 0.5 NO
38 ZMAT3 ZMAT3 ZMAT3 6595 0.049 0.49 NO
39 SESN3 SESN3 SESN3 6721 0.047 0.49 NO
40 CASP9 CASP9 CASP9 6841 0.045 0.49 NO
41 GADD45G GADD45G GADD45G 6915 0.044 0.49 NO
42 RFWD2 RFWD2 RFWD2 6960 0.043 0.5 NO
43 SESN2 SESN2 SESN2 7141 0.04 0.49 NO
44 CDK6 CDK6 CDK6 7442 0.036 0.48 NO
45 CCNB3 CCNB3 CCNB3 7579 0.034 0.48 NO
46 CCND2 CCND2 CCND2 7685 0.032 0.48 NO
47 GADD45B GADD45B GADD45B 7840 0.03 0.47 NO
48 CCND3 CCND3 CCND3 8237 0.024 0.45 NO
49 RRM2B RRM2B RRM2B 8318 0.023 0.45 NO
50 CYCS CYCS CYCS 8517 0.021 0.44 NO
51 EI24 EI24 EI24 9586 0.0069 0.38 NO
52 SERPINB5 SERPINB5 SERPINB5 9793 0.0039 0.37 NO
53 MDM4 MDM4 MDM4 10234 -0.0015 0.35 NO
54 GADD45A GADD45A GADD45A 10559 -0.0056 0.33 NO
55 TSC2 TSC2 TSC2 11004 -0.011 0.31 NO
56 CDKN1A CDKN1A CDKN1A 11031 -0.011 0.31 NO
57 ATM ATM ATM 11407 -0.016 0.29 NO
58 SIAH1 SIAH1 SIAH1 12035 -0.024 0.26 NO
59 SESN1 SESN1 SESN1 12461 -0.03 0.24 NO
60 PTEN PTEN PTEN 12629 -0.032 0.24 NO
61 THBS1 THBS1 THBS1 13841 -0.052 0.18 NO
62 CCNG2 CCNG2 CCNG2 14301 -0.061 0.16 NO
63 CCNG1 CCNG1 CCNG1 14816 -0.073 0.14 NO
64 TP53AIP1 TP53AIP1 TP53AIP1 14974 -0.077 0.14 NO
65 PPM1D PPM1D PPM1D 15479 -0.091 0.12 NO
66 RCHY1 RCHY1 RCHY1 15787 -0.1 0.12 NO
67 CCND1 CCND1 CCND1 16145 -0.12 0.12 NO

Figure S47.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S48.  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 DNA REPLICATION

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 IL6 IL6 IL6 260 0.45 0.04 YES
2 CASP5 CASP5 CASP5 293 0.44 0.09 YES
3 NOD2 NOD2 NOD2 402 0.41 0.13 YES
4 MEFV MEFV MEFV 591 0.37 0.17 YES
5 CARD9 CARD9 CARD9 672 0.36 0.2 YES
6 PYCARD PYCARD PYCARD 762 0.34 0.24 YES
7 PSTPIP1 PSTPIP1 PSTPIP1 956 0.31 0.27 YES
8 CCL11 CCL11 CCL11 1057 0.3 0.3 YES
9 IL8 IL8 IL8 1086 0.3 0.33 YES
10 PYDC1 PYDC1 PYDC1 1230 0.28 0.36 YES
11 CCL13 CCL13 CCL13 1268 0.27 0.39 YES
12 NLRC4 NLRC4 NLRC4 1342 0.27 0.41 YES
13 CCL7 CCL7 CCL7 1366 0.26 0.44 YES
14 CXCL1 CXCL1 CXCL1 1427 0.26 0.47 YES
15 BIRC3 BIRC3 BIRC3 1435 0.26 0.5 YES
16 CXCL2 CXCL2 CXCL2 1503 0.25 0.53 YES
17 CCL5 CCL5 CCL5 1522 0.25 0.56 YES
18 NAIP NAIP NAIP 1880 0.22 0.56 YES
19 IL1B IL1B IL1B 2148 0.2 0.57 YES
20 IL18 IL18 IL18 2297 0.19 0.58 YES
21 CCL8 CCL8 CCL8 2434 0.18 0.6 YES
22 RIPK2 RIPK2 RIPK2 2488 0.18 0.62 YES
23 NLRP3 NLRP3 NLRP3 2928 0.15 0.61 NO
24 CASP1 CASP1 CASP1 3214 0.14 0.61 NO
25 TNF TNF TNF 3603 0.12 0.61 NO
26 CASP8 CASP8 CASP8 4019 0.11 0.6 NO
27 HSP90B1 HSP90B1 HSP90B1 4638 0.09 0.57 NO
28 IKBKG IKBKG IKBKG 5016 0.08 0.56 NO
29 TRIP6 TRIP6 TRIP6 5290 0.073 0.56 NO
30 MAPK11 MAPK11 MAPK11 5548 0.068 0.55 NO
31 TNFAIP3 TNFAIP3 TNFAIP3 6285 0.055 0.52 NO
32 MAPK13 MAPK13 MAPK13 6640 0.048 0.5 NO
33 NLRP1 NLRP1 NLRP1 7749 0.031 0.44 NO
34 NFKBIB NFKBIB NFKBIB 8541 0.021 0.4 NO
35 MAPK9 MAPK9 MAPK9 8589 0.02 0.4 NO
36 NOD1 NOD1 NOD1 8680 0.019 0.4 NO
37 BIRC2 BIRC2 BIRC2 9091 0.013 0.38 NO
38 MAPK14 MAPK14 MAPK14 9234 0.011 0.37 NO
39 IKBKB IKBKB IKBKB 9331 0.01 0.37 NO
40 ERBB2IP ERBB2IP ERBB2IP 9405 0.0092 0.37 NO
41 CARD8 CARD8 CARD8 9574 0.0071 0.36 NO
42 RELA RELA RELA 9833 0.0034 0.34 NO
43 SUGT1 SUGT1 SUGT1 10073 0.0004 0.33 NO
44 TAB1 TAB1 TAB1 10118 -0.000062 0.33 NO
45 XIAP XIAP XIAP 10159 -0.00064 0.33 NO
46 MAP3K7 MAP3K7 MAP3K7 10980 -0.01 0.28 NO
47 TAB3 TAB3 TAB3 10983 -0.011 0.28 NO
48 TAB2 TAB2 TAB2 11362 -0.016 0.26 NO
49 HSP90AA1 HSP90AA1 HSP90AA1 12550 -0.031 0.2 NO
50 NFKB1 NFKB1 NFKB1 12805 -0.035 0.19 NO
51 MAPK3 MAPK3 MAPK3 13069 -0.039 0.18 NO
52 CARD6 CARD6 CARD6 13331 -0.043 0.18 NO
53 MAPK1 MAPK1 MAPK1 13695 -0.05 0.16 NO
54 CHUK CHUK CHUK 13895 -0.053 0.16 NO
55 CCL2 CCL2 CCL2 14285 -0.061 0.14 NO
56 MAPK12 MAPK12 MAPK12 14300 -0.061 0.15 NO
57 NFKBIA NFKBIA NFKBIA 14643 -0.069 0.14 NO
58 TRAF6 TRAF6 TRAF6 16737 -0.15 0.041 NO
59 MAPK8 MAPK8 MAPK8 17022 -0.18 0.046 NO
60 MAPK10 MAPK10 MAPK10 17066 -0.18 0.066 NO

Figure S49.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG DNA REPLICATION.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DNA REPLICATION, 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 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 LBP LBP LBP 18 0.75 0.22 YES
2 LEF1 LEF1 LEF1 237 0.47 0.35 YES
3 LY96 LY96 LY96 339 0.42 0.47 YES
4 WNT1 WNT1 WNT1 980 0.31 0.53 YES
5 CD14 CD14 CD14 2220 0.19 0.52 NO
6 IRAK1 IRAK1 IRAK1 4288 0.1 0.44 NO
7 MYD88 MYD88 MYD88 5007 0.08 0.42 NO
8 PIK3R1 PIK3R1 PIK3R1 6554 0.05 0.35 NO
9 AXIN1 AXIN1 AXIN1 7714 0.032 0.3 NO
10 EIF2AK2 EIF2AK2 EIF2AK2 9192 0.012 0.22 NO
11 RELA RELA RELA 9833 0.0034 0.19 NO
12 PPP2CA PPP2CA PPP2CA 10526 -0.0052 0.15 NO
13 DVL1 DVL1 DVL1 10599 -0.006 0.15 NO
14 AKT1 AKT1 AKT1 11589 -0.018 0.098 NO
15 GSK3B GSK3B GSK3B 11889 -0.022 0.089 NO
16 NFKB1 NFKB1 NFKB1 12805 -0.035 0.049 NO
17 PDPK1 PDPK1 PDPK1 13588 -0.048 0.021 NO
18 TLR4 TLR4 TLR4 14645 -0.069 -0.017 NO
19 APC APC APC 14740 -0.071 -0.00076 NO
20 PIK3CA PIK3CA PIK3CA 14835 -0.073 0.016 NO
21 FZD1 FZD1 FZD1 14873 -0.074 0.036 NO
22 TIRAP TIRAP TIRAP 14904 -0.075 0.057 NO
23 CTNNB1 CTNNB1 CTNNB1 15277 -0.086 0.062 NO
24 GNAI1 GNAI1 GNAI1 15742 -0.1 0.067 NO
25 CCND1 CCND1 CCND1 16145 -0.12 0.08 NO
26 GJA1 GJA1 GJA1 16201 -0.12 0.11 NO

Figure S51.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BASE EXCISION REPAIR.

Figure S52.  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 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 GFPT2 GFPT2 GFPT2 4 0.89 0.2 YES
2 HK3 HK3 HK3 683 0.35 0.24 YES
3 NPL NPL NPL 1096 0.29 0.28 YES
4 CHIT1 CHIT1 CHIT1 1324 0.27 0.32 YES
5 GCK GCK GCK 1912 0.22 0.34 YES
6 GALK1 GALK1 GALK1 2272 0.19 0.36 YES
7 HK2 HK2 HK2 2323 0.19 0.4 YES
8 PMM2 PMM2 PMM2 3026 0.15 0.39 YES
9 TSTA3 TSTA3 TSTA3 3269 0.14 0.41 YES
10 GALE GALE GALE 3295 0.14 0.44 YES
11 GMPPB GMPPB GMPPB 3779 0.12 0.44 YES
12 UGDH UGDH UGDH 4077 0.11 0.45 YES
13 GMPPA GMPPA GMPPA 4216 0.1 0.46 YES
14 CMAS CMAS CMAS 4780 0.086 0.45 YES
15 NAGK NAGK NAGK 4920 0.082 0.46 YES
16 GMDS GMDS GMDS 5354 0.072 0.45 YES
17 HEXA HEXA HEXA 5660 0.066 0.45 YES
18 UGP2 UGP2 UGP2 5812 0.063 0.46 YES
19 HK1 HK1 HK1 5967 0.06 0.46 YES
20 NANS NANS NANS 6072 0.058 0.47 YES
21 GNPDA1 GNPDA1 GNPDA1 6347 0.053 0.46 YES
22 PGM1 PGM1 PGM1 6385 0.052 0.47 YES
23 HEXB HEXB HEXB 7160 0.04 0.44 NO
24 PGM3 PGM3 PGM3 7346 0.037 0.44 NO
25 AMDHD2 AMDHD2 AMDHD2 7570 0.034 0.43 NO
26 UAP1 UAP1 UAP1 7697 0.032 0.43 NO
27 GPI GPI GPI 8560 0.02 0.39 NO
28 FUK FUK FUK 9758 0.0045 0.32 NO
29 GFPT1 GFPT1 GFPT1 9922 0.0022 0.32 NO
30 RENBP RENBP RENBP 10493 -0.0047 0.29 NO
31 CYB5R1 CYB5R1 CYB5R1 11387 -0.016 0.24 NO
32 NANP NANP NANP 11458 -0.017 0.24 NO
33 UXS1 UXS1 UXS1 11562 -0.018 0.24 NO
34 PGM2 PGM2 PGM2 11756 -0.021 0.23 NO
35 MPI MPI MPI 12483 -0.03 0.2 NO
36 GNPDA2 GNPDA2 GNPDA2 13244 -0.042 0.17 NO
37 FPGT FPGT FPGT 13319 -0.043 0.17 NO
38 GALK2 GALK2 GALK2 13500 -0.046 0.17 NO
39 GNPNAT1 GNPNAT1 GNPNAT1 13530 -0.047 0.18 NO
40 CHIA CHIA CHIA 13872 -0.053 0.17 NO
41 GALT GALT GALT 15035 -0.078 0.13 NO
42 PMM1 PMM1 PMM1 15535 -0.093 0.12 NO
43 GNE GNE GNE 16424 -0.13 0.1 NO

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

Figure S54.  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 CHEMOKINE SIGNALING PATHWAY

Table S28.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 DNA2 DNA2 DNA2 1881 0.22 -0.0081 YES
2 POLD4 POLD4 POLD4 2763 0.16 0.015 YES
3 RPA4 RPA4 RPA4 3298 0.14 0.045 YES
4 RFC4 RFC4 RFC4 3586 0.12 0.084 YES
5 RNASEH2A RNASEH2A RNASEH2A 3752 0.12 0.13 YES
6 POLD1 POLD1 POLD1 3882 0.11 0.17 YES
7 MCM6 MCM6 MCM6 4264 0.1 0.19 YES
8 POLA2 POLA2 POLA2 4295 0.1 0.24 YES
9 MCM2 MCM2 MCM2 4479 0.094 0.27 YES
10 RFC2 RFC2 RFC2 4524 0.093 0.31 YES
11 RNASEH2B RNASEH2B RNASEH2B 4634 0.09 0.34 YES
12 POLE POLE POLE 4934 0.082 0.36 YES
13 LIG1 LIG1 LIG1 5030 0.08 0.39 YES
14 MCM4 MCM4 MCM4 5162 0.076 0.42 YES
15 RFC5 RFC5 RFC5 5384 0.071 0.43 YES
16 PCNA PCNA PCNA 5756 0.064 0.44 YES
17 POLD3 POLD3 POLD3 5948 0.06 0.46 YES
18 SSBP1 SSBP1 SSBP1 6110 0.057 0.47 YES
19 MCM5 MCM5 MCM5 6226 0.055 0.49 YES
20 RNASEH1 RNASEH1 RNASEH1 6522 0.05 0.5 YES
21 RPA3 RPA3 RPA3 6804 0.046 0.5 YES
22 PRIM2 PRIM2 PRIM2 6958 0.043 0.51 YES
23 POLD2 POLD2 POLD2 6979 0.043 0.53 YES
24 FEN1 FEN1 FEN1 7482 0.035 0.52 NO
25 RNASEH2C RNASEH2C RNASEH2C 8472 0.021 0.47 NO
26 MCM7 MCM7 MCM7 9239 0.011 0.44 NO
27 POLE2 POLE2 POLE2 9550 0.0073 0.42 NO
28 RPA2 RPA2 RPA2 9564 0.0072 0.42 NO
29 POLE4 POLE4 POLE4 9729 0.0049 0.42 NO
30 PRIM1 PRIM1 PRIM1 10450 -0.0042 0.38 NO
31 MCM3 MCM3 MCM3 10624 -0.0063 0.37 NO
32 RPA1 RPA1 RPA1 10779 -0.0081 0.37 NO
33 RFC1 RFC1 RFC1 12456 -0.03 0.29 NO
34 POLE3 POLE3 POLE3 12508 -0.031 0.3 NO
35 RFC3 RFC3 RFC3 12655 -0.033 0.31 NO

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

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

genes ES table in pathway: KEGG CELL CYCLE

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 F2 F2 F2 6 0.87 0.063 YES
2 FGA FGA FGA 200 0.48 0.088 YES
3 C1S C1S C1S 251 0.46 0.12 YES
4 C1R C1R C1R 276 0.44 0.15 YES
5 C2 C2 C2 384 0.41 0.17 YES
6 FGG FGG FGG 453 0.4 0.2 YES
7 C8G C8G C8G 557 0.38 0.22 YES
8 FGB FGB FGB 571 0.37 0.25 YES
9 MBL2 MBL2 MBL2 674 0.36 0.27 YES
10 PLAUR PLAUR PLAUR 710 0.35 0.29 YES
11 C4BPA C4BPA C4BPA 852 0.33 0.31 YES
12 CR1 CR1 CR1 858 0.33 0.33 YES
13 CFH CFH CFH 917 0.32 0.35 YES
14 BDKRB1 BDKRB1 BDKRB1 990 0.31 0.37 YES
15 CFB CFB CFB 1001 0.31 0.39 YES
16 C9 C9 C9 1062 0.3 0.41 YES
17 CFD CFD CFD 1067 0.3 0.43 YES
18 C3 C3 C3 1118 0.29 0.45 YES
19 SERPINE1 SERPINE1 SERPINE1 1183 0.28 0.47 YES
20 F3 F3 F3 1218 0.28 0.48 YES
21 PLAU PLAU PLAU 1321 0.27 0.5 YES
22 CR2 CR2 CR2 1714 0.23 0.49 YES
23 F12 F12 F12 1782 0.23 0.51 YES
24 SERPINA5 SERPINA5 SERPINA5 1817 0.22 0.52 YES
25 C1QB C1QB C1QB 1894 0.22 0.53 YES
26 BDKRB2 BDKRB2 BDKRB2 1968 0.21 0.54 YES
27 C1QC C1QC C1QC 2119 0.2 0.55 YES
28 C1QA C1QA C1QA 2164 0.2 0.56 YES
29 SERPINF2 SERPINF2 SERPINF2 2215 0.19 0.57 YES
30 C5AR1 C5AR1 C5AR1 2240 0.19 0.59 YES
31 SERPINA1 SERPINA1 SERPINA1 2288 0.19 0.6 YES
32 SERPING1 SERPING1 SERPING1 2365 0.18 0.61 YES
33 CPB2 CPB2 CPB2 2414 0.18 0.62 YES
34 C3AR1 C3AR1 C3AR1 2694 0.16 0.61 YES
35 F13A1 F13A1 F13A1 2752 0.16 0.62 YES
36 F5 F5 F5 2782 0.16 0.63 YES
37 CFI CFI CFI 3178 0.14 0.62 NO
38 PROS1 PROS1 PROS1 4411 0.096 0.56 NO
39 SERPINC1 SERPINC1 SERPINC1 4879 0.083 0.54 NO
40 C4A C4A C4A 5042 0.079 0.54 NO
41 F10 F10 F10 6029 0.059 0.49 NO
42 SERPIND1 SERPIND1 SERPIND1 6447 0.051 0.47 NO
43 CD55 CD55 CD55 6949 0.044 0.44 NO
44 THBD THBD THBD 7272 0.038 0.43 NO
45 C5 C5 C5 7278 0.038 0.43 NO
46 F2R F2R F2R 9771 0.0043 0.3 NO
47 TFPI TFPI TFPI 10658 -0.0067 0.25 NO
48 KNG1 KNG1 KNG1 12147 -0.026 0.17 NO
49 C7 C7 C7 12739 -0.034 0.14 NO
50 F8 F8 F8 13945 -0.054 0.075 NO
51 CD46 CD46 CD46 14015 -0.055 0.075 NO
52 CD59 CD59 CD59 14089 -0.056 0.076 NO
53 C4BPB C4BPB C4BPB 14533 -0.066 0.056 NO
54 PROC PROC PROC 16111 -0.12 -0.022 NO
55 VWF VWF VWF 16181 -0.12 -0.017 NO
56 F7 F7 F7 16320 -0.13 -0.016 NO
57 KLKB1 KLKB1 KLKB1 16420 -0.13 -0.012 NO
58 C6 C6 C6 16822 -0.16 -0.022 NO
59 PLAT PLAT PLAT 16936 -0.17 -0.016 NO
60 MASP2 MASP2 MASP2 17564 -0.24 -0.033 NO
61 MASP1 MASP1 MASP1 17783 -0.28 -0.025 NO
62 F11 F11 F11 17821 -0.28 -0.0064 NO
63 PLG PLG PLG 18121 -0.42 0.0075 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 CELL CYCLE.

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

genes ES table in pathway: KEGG OOCYTE MEIOSIS

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 EME1 EME1 EME1 299 0.44 0.12 YES
2 RAD54B RAD54B RAD54B 312 0.44 0.25 YES
3 RAD54L RAD54L RAD54L 423 0.4 0.36 YES
4 BLM BLM BLM 708 0.35 0.45 YES
5 RAD51 RAD51 RAD51 1115 0.29 0.52 YES
6 XRCC2 XRCC2 XRCC2 1430 0.26 0.58 YES
7 POLD4 POLD4 POLD4 2763 0.16 0.56 YES
8 RPA4 RPA4 RPA4 3298 0.14 0.57 YES
9 SHFM1 SHFM1 SHFM1 3690 0.12 0.58 YES
10 POLD1 POLD1 POLD1 3882 0.11 0.61 YES
11 BRCA2 BRCA2 BRCA2 4277 0.1 0.62 YES
12 POLD3 POLD3 POLD3 5948 0.06 0.54 NO
13 NBN NBN NBN 6094 0.058 0.55 NO
14 SSBP1 SSBP1 SSBP1 6110 0.057 0.57 NO
15 RPA3 RPA3 RPA3 6804 0.046 0.54 NO
16 RAD51L3 RAD51L3 RAD51L3 6918 0.044 0.55 NO
17 RAD52 RAD52 RAD52 6953 0.044 0.56 NO
18 POLD2 POLD2 POLD2 6979 0.043 0.57 NO
19 XRCC3 XRCC3 XRCC3 7543 0.034 0.55 NO
20 RAD51L1 RAD51L1 RAD51L1 7800 0.03 0.55 NO
21 TOP3B TOP3B TOP3B 8936 0.015 0.49 NO
22 RPA2 RPA2 RPA2 9564 0.0072 0.46 NO
23 MUS81 MUS81 MUS81 10101 0.00014 0.43 NO
24 RPA1 RPA1 RPA1 10779 -0.0081 0.39 NO
25 TOP3A TOP3A TOP3A 11096 -0.012 0.38 NO
26 RAD50 RAD50 RAD50 11583 -0.018 0.36 NO
27 MRE11A MRE11A MRE11A 11908 -0.023 0.35 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 OOCYTE MEIOSIS.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OOCYTE MEIOSIS, 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 = KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = KIRC-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)