GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in UCEC-TP
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1KS6R13
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in UCEC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1KS6R13
Overview
Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes having more than three samples and the input expression file "UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. 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: 721
Number of samples: 545
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 189
pheno.type: 2 - 4 :[ clus2 ] 124
pheno.type: 3 - 4 :[ clus3 ] 94
pheno.type: 4 - 4 :[ clus4 ] 138

For the expression subtypes of 18545 genes in 546 samples, GSEA found enriched gene sets in each cluster using 545 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG CELL CYCLE, ST MYOCYTE AD PATHWAY, PID FANCONI PATHWAY, PID ATR PATHWAY, PID EPHBFWDPATHWAY, PID MYC ACTIVPATHWAY, PID MYC PATHWAY, PID AURORA A PATHWAY, REACTOME METABOLISM OF NON CODING RNA, REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES

    • And common core enriched genes are NUP107, NUP133, NUP153, NUP155, NUP205, NUP210, NUP35, NUP85, RAE1, SEH1L

  • clus2

    • Top enriched gene sets are KEGG WNT SIGNALING PATHWAY, KEGG GNRH SIGNALING PATHWAY, KEGG MELANOMA, BIOCARTA ALK PATHWAY, BIOCARTA GSK3 PATHWAY, BIOCARTA P38MAPK PATHWAY, BIOCARTA WNT PATHWAY, ST WNT BETA CATENIN PATHWAY, PID PS1PATHWAY, PID BETACATENIN NUC PATHWAY

    • And common core enriched genes are CCND1, WIF1, DKK1, FZD1, LEF1, AXIN2, DKK2, DKK4, NKD1, PPARD

  • clus3

    • Top enriched gene sets are KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, KEGG CYTOSOLIC DNA SENSING PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA PYK2 PATHWAY, ST TUMOR NECROSIS FACTOR PATHWAY, ST INTERLEUKIN 4 PATHWAY, PID TNFPATHWAY, PID P53DOWNSTREAMPATHWAY, PID HIVNEFPATHWAY, PID CASPASE PATHWAY

    • And common core enriched genes are AP1B1, AP1G1, AP1M2, AP1S1, AP3B1, AP4E1, ARF1, ARRB1, BLOC1S1, CLTC

  • clus4

    • Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG FATTY ACID METABOLISM, KEGG TYROSINE METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG BUTANOATE METABOLISM, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM CYTOCHROME P450, KEGG ABC TRANSPORTERS

    • And common core enriched genes are ADH1A, ADH1B, ADH1C, ADH4, ADH6, ADH7, GSTA1, GSTA2, GSTA3, GSTM1

Results
Subtype clus1 enriched pathways

Table 3.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG CELL CYCLE 118 genes.ES.table 0.47 1.6 0.064 0.95 0.9 0.38 0.18 0.31 0.45 0.28
ST MYOCYTE AD PATHWAY 26 genes.ES.table 0.61 1.6 0.01 0.99 0.88 0.19 0.057 0.18 0.47 0.29
PID FANCONI PATHWAY 46 genes.ES.table 0.57 1.6 0.083 0.7 0.94 0.44 0.22 0.34 0.37 0.21
PID ATR PATHWAY 39 genes.ES.table 0.6 1.6 0.062 0.89 0.91 0.49 0.19 0.4 0.44 0.27
PID EPHBFWDPATHWAY 40 genes.ES.table 0.53 1.8 0.014 1 0.65 0.22 0.1 0.2 0.42 0.31
PID MYC ACTIVPATHWAY 79 genes.ES.table 0.41 1.6 0.052 0.73 0.93 0.35 0.26 0.26 0.38 0.22
PID MYC PATHWAY 25 genes.ES.table 0.45 1.8 0.016 1 0.65 0.36 0.31 0.25 0.62 0.38
PID AURORA A PATHWAY 31 genes.ES.table 0.5 1.6 0.08 0.77 0.93 0.32 0.16 0.27 0.4 0.23
REACTOME METABOLISM OF NON CODING RNA 47 genes.ES.table 0.45 1.6 0.1 0.71 0.93 0.6 0.37 0.38 0.38 0.21
REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 65 genes.ES.table 0.52 1.8 0.017 1 0.5 0.45 0.3 0.31 0 0.4
genes ES table in pathway: KEGG CELL CYCLE

Table S1.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HERC5 HERC5 HERC5 97 0.56 0.098 YES
2 MX2 MX2 MX2 176 0.5 0.18 YES
3 IFIT1 IFIT1 IFIT1 421 0.41 0.25 YES
4 MX1 MX1 MX1 1465 0.23 0.23 YES
5 EIF2AK2 EIF2AK2 EIF2AK2 1619 0.22 0.26 YES
6 NUP155 NUP155 NUP155 1829 0.2 0.29 YES
7 RAE1 RAE1 RAE1 1984 0.19 0.32 YES
8 STAT1 STAT1 STAT1 2140 0.18 0.34 YES
9 DDX58 DDX58 DDX58 2149 0.18 0.37 YES
10 ISG15 ISG15 ISG15 2765 0.14 0.36 YES
11 USP18 USP18 USP18 2842 0.14 0.38 YES
12 UBE2L6 UBE2L6 UBE2L6 3046 0.13 0.4 YES
13 NUP153 NUP153 NUP153 3218 0.12 0.41 YES
14 EIF4A3 EIF4A3 EIF4A3 3310 0.12 0.43 YES
15 KPNA2 KPNA2 KPNA2 3476 0.11 0.44 YES
16 NUP107 NUP107 NUP107 3540 0.11 0.46 YES
17 KPNA4 KPNA4 KPNA4 4264 0.088 0.43 YES
18 SEH1L SEH1L SEH1L 4360 0.086 0.44 YES
19 NUP35 NUP35 NUP35 4502 0.083 0.45 YES
20 EIF4G1 EIF4G1 EIF4G1 4667 0.079 0.46 YES
21 NUP85 NUP85 NUP85 4790 0.076 0.46 YES
22 NUP210 NUP210 NUP210 4972 0.072 0.47 YES
23 RPS27A RPS27A RPS27A 5042 0.07 0.48 YES
24 MAPK3 MAPK3 MAPK3 5269 0.065 0.48 YES
25 NUP205 NUP205 NUP205 5279 0.065 0.49 YES
26 UBE2E1 UBE2E1 UBE2E1 5409 0.063 0.49 YES
27 IRF3 IRF3 IRF3 5515 0.061 0.5 YES
28 JAK1 JAK1 JAK1 5517 0.061 0.51 YES
29 NUP133 NUP133 NUP133 5546 0.06 0.52 YES
30 EIF4A2 EIF4A2 EIF4A2 5876 0.054 0.51 NO
31 KPNA1 KPNA1 KPNA1 6071 0.051 0.51 NO
32 NUP54 NUP54 NUP54 6115 0.051 0.52 NO
33 NUP62 NUP62 NUP62 6626 0.042 0.5 NO
34 PPM1B PPM1B PPM1B 6866 0.038 0.49 NO
35 NUP93 NUP93 NUP93 7644 0.027 0.45 NO
36 NUP37 NUP37 NUP37 7706 0.026 0.45 NO
37 AAAS AAAS AAAS 7756 0.025 0.46 NO
38 NUPL1 NUPL1 NUPL1 7778 0.025 0.46 NO
39 NUP43 NUP43 NUP43 8041 0.022 0.45 NO
40 KPNB1 KPNB1 KPNB1 8059 0.021 0.45 NO
41 POM121 POM121 POM121 8215 0.019 0.45 NO
42 UBA52 UBA52 UBA52 8416 0.016 0.44 NO
43 TPR TPR TPR 8545 0.014 0.43 NO
44 TRIM25 TRIM25 TRIM25 8668 0.012 0.43 NO
45 PIN1 PIN1 PIN1 8682 0.012 0.43 NO
46 EIF4G3 EIF4G3 EIF4G3 8921 0.0088 0.42 NO
47 NUP88 NUP88 NUP88 9174 0.0053 0.41 NO
48 KPNA5 KPNA5 KPNA5 9237 0.0043 0.4 NO
49 NUP214 NUP214 NUP214 9321 0.0029 0.4 NO
50 PLCG1 PLCG1 PLCG1 9523 0.00023 0.39 NO
51 UBE2N UBE2N UBE2N 9560 -0.0003 0.39 NO
52 NUPL2 NUPL2 NUPL2 9583 -0.00076 0.39 NO
53 EIF4G2 EIF4G2 EIF4G2 9909 -0.0051 0.37 NO
54 EIF4E3 EIF4E3 EIF4E3 10206 -0.0094 0.36 NO
55 NUP50 NUP50 NUP50 10344 -0.011 0.35 NO
56 ARIH1 ARIH1 ARIH1 10860 -0.02 0.33 NO
57 EIF4E2 EIF4E2 EIF4E2 10914 -0.021 0.33 NO
58 KPNA3 KPNA3 KPNA3 10918 -0.021 0.33 NO
59 EIF4A1 EIF4A1 EIF4A1 11333 -0.028 0.31 NO
60 FLNB FLNB FLNB 11431 -0.029 0.31 NO
61 RANBP2 RANBP2 RANBP2 12783 -0.054 0.25 NO
62 UBA7 UBA7 UBA7 12899 -0.056 0.25 NO
63 NUP188 NUP188 NUP188 13053 -0.059 0.26 NO
64 EIF4E EIF4E EIF4E 14662 -0.1 0.19 NO
65 NEDD4 NEDD4 NEDD4 15040 -0.12 0.19 NO

Figure S1.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CELL CYCLE.

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

genes ES table in pathway: ST MYOCYTE AD 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 CDKN2A CDKN2A CDKN2A 105 0.56 0.31 YES
2 MYC MYC MYC 1954 0.19 0.32 YES
3 ACTL6A ACTL6A ACTL6A 3126 0.13 0.33 YES
4 SKP2 SKP2 SKP2 3411 0.12 0.38 YES
5 RUVBL1 RUVBL1 RUVBL1 4362 0.086 0.38 YES
6 PAK2 PAK2 PAK2 4576 0.081 0.41 YES
7 GSK3B GSK3B GSK3B 5027 0.07 0.43 YES
8 TRRAP TRRAP TRRAP 5707 0.058 0.42 YES
9 SUPT7L SUPT7L SUPT7L 5767 0.056 0.45 YES
10 SUPT3H SUPT3H SUPT3H 7625 0.027 0.37 NO
11 KAT5 KAT5 KAT5 7912 0.024 0.37 NO
12 MAX MAX MAX 8533 0.014 0.34 NO
13 PIN1 PIN1 PIN1 8682 0.012 0.34 NO
14 PPP2CA PPP2CA PPP2CA 8748 0.011 0.34 NO
15 PML PML PML 9047 0.007 0.33 NO
16 HBP1 HBP1 HBP1 9197 0.0049 0.32 NO
17 KAT2A KAT2A KAT2A 9235 0.0044 0.33 NO
18 PPP2R5A PPP2R5A PPP2R5A 10246 -0.0099 0.28 NO
19 AXIN1 AXIN1 AXIN1 10532 -0.014 0.27 NO
20 ZBTB17 ZBTB17 ZBTB17 10861 -0.02 0.26 NO
21 TAF12 TAF12 TAF12 10989 -0.022 0.27 NO
22 RUVBL2 RUVBL2 RUVBL2 11880 -0.037 0.24 NO
23 TAF10 TAF10 TAF10 13005 -0.058 0.21 NO
24 FBXW7 FBXW7 FBXW7 13160 -0.062 0.24 NO
25 TAF9 TAF9 TAF9 14133 -0.085 0.24 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: ST MYOCYTE AD PATHWAY.

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

genes ES table in pathway: PID FANCONI PATHWAY

Table 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 EPHB2 EPHB2 EPHB2 113 0.55 0.11 YES
2 EPHB1 EPHB1 EPHB1 149 0.52 0.21 YES
3 EFNB3 EFNB3 EFNB3 196 0.49 0.31 YES
4 DNM1 DNM1 DNM1 818 0.31 0.34 YES
5 GRB7 GRB7 GRB7 869 0.31 0.4 YES
6 EFNB2 EFNB2 EFNB2 1249 0.26 0.43 YES
7 EFNB1 EFNB1 EFNB1 1361 0.24 0.48 YES
8 PIK3CA PIK3CA PIK3CA 1435 0.24 0.52 YES
9 KALRN KALRN KALRN 1933 0.19 0.53 YES
10 EFNA5 EFNA5 EFNA5 2997 0.13 0.5 NO
11 NRAS NRAS NRAS 3191 0.12 0.52 NO
12 TF TF TF 3938 0.097 0.5 NO
13 GRIA1 GRIA1 GRIA1 4262 0.088 0.5 NO
14 RRAS RRAS RRAS 4541 0.082 0.5 NO
15 ITSN1 ITSN1 ITSN1 4630 0.08 0.51 NO
16 KRAS KRAS KRAS 5100 0.069 0.5 NO
17 MAPK3 MAPK3 MAPK3 5269 0.065 0.5 NO
18 PXN PXN PXN 5609 0.059 0.5 NO
19 GRB2 GRB2 GRB2 5969 0.053 0.49 NO
20 NCK1 NCK1 NCK1 6218 0.049 0.49 NO
21 PTK2 PTK2 PTK2 6397 0.046 0.49 NO
22 ROCK1 ROCK1 ROCK1 6845 0.039 0.47 NO
23 EPHB4 EPHB4 EPHB4 6995 0.037 0.47 NO
24 SRC SRC SRC 7336 0.031 0.46 NO
25 SHC1 SHC1 SHC1 7396 0.03 0.46 NO
26 MAP4K4 MAP4K4 MAP4K4 8042 0.022 0.43 NO
27 RAP1A RAP1A RAP1A 8801 0.01 0.39 NO
28 CDC42 CDC42 CDC42 8843 0.0098 0.39 NO
29 MAPK1 MAPK1 MAPK1 9619 -0.0012 0.35 NO
30 CRK CRK CRK 10087 -0.0076 0.33 NO
31 MAP2K1 MAP2K1 MAP2K1 10372 -0.012 0.31 NO
32 RASA1 RASA1 RASA1 10905 -0.021 0.29 NO
33 EPHB3 EPHB3 EPHB3 11027 -0.022 0.29 NO
34 WASL WASL WASL 11174 -0.025 0.28 NO
35 RAC1 RAC1 RAC1 11214 -0.026 0.29 NO
36 HRAS HRAS HRAS 11571 -0.032 0.27 NO
37 RAP1B RAP1B RAP1B 12317 -0.045 0.24 NO
38 SYNJ1 SYNJ1 SYNJ1 13047 -0.059 0.22 NO
39 PAK1 PAK1 PAK1 13925 -0.08 0.18 NO
40 PIK3R1 PIK3R1 PIK3R1 17830 -0.31 0.038 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: PID FANCONI PATHWAY.

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

genes ES table in pathway: PID ATR 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 GCK GCK GCK 28 0.66 0.21 YES
2 SLC2A4 SLC2A4 SLC2A4 238 0.47 0.36 YES
3 NUP155 NUP155 NUP155 1829 0.2 0.34 YES
4 RAE1 RAE1 RAE1 1984 0.19 0.39 YES
5 SLC2A1 SLC2A1 SLC2A1 3134 0.13 0.37 YES
6 NUP153 NUP153 NUP153 3218 0.12 0.4 YES
7 NUP107 NUP107 NUP107 3540 0.11 0.42 YES
8 SEH1L SEH1L SEH1L 4360 0.086 0.4 YES
9 NUP35 NUP35 NUP35 4502 0.083 0.42 YES
10 NUP85 NUP85 NUP85 4790 0.076 0.43 YES
11 NUP210 NUP210 NUP210 4972 0.072 0.45 YES
12 GCKR GCKR GCKR 5053 0.07 0.46 YES
13 NUP205 NUP205 NUP205 5279 0.065 0.47 YES
14 NUP133 NUP133 NUP133 5546 0.06 0.48 YES
15 NUP54 NUP54 NUP54 6115 0.051 0.46 NO
16 NUP62 NUP62 NUP62 6626 0.042 0.45 NO
17 NUP93 NUP93 NUP93 7644 0.027 0.4 NO
18 NUP37 NUP37 NUP37 7706 0.026 0.41 NO
19 AAAS AAAS AAAS 7756 0.025 0.42 NO
20 NUPL1 NUPL1 NUPL1 7778 0.025 0.42 NO
21 NUP43 NUP43 NUP43 8041 0.022 0.42 NO
22 POM121 POM121 POM121 8215 0.019 0.41 NO
23 TPR TPR TPR 8545 0.014 0.4 NO
24 NUP88 NUP88 NUP88 9174 0.0053 0.37 NO
25 NUP214 NUP214 NUP214 9321 0.0029 0.36 NO
26 NUPL2 NUPL2 NUPL2 9583 -0.00076 0.35 NO
27 NUP50 NUP50 NUP50 10344 -0.011 0.31 NO
28 HK1 HK1 HK1 10374 -0.012 0.31 NO
29 SLC37A4 SLC37A4 SLC37A4 11004 -0.022 0.28 NO
30 SLC2A3 SLC2A3 SLC2A3 11462 -0.03 0.27 NO
31 HK2 HK2 HK2 11866 -0.037 0.26 NO
32 G6PC G6PC G6PC 12147 -0.042 0.26 NO
33 RANBP2 RANBP2 RANBP2 12783 -0.054 0.24 NO
34 NUP188 NUP188 NUP188 13053 -0.059 0.25 NO
35 HK3 HK3 HK3 13664 -0.073 0.24 NO
36 G6PC3 G6PC3 G6PC3 13929 -0.08 0.25 NO

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

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

genes ES table in pathway: PID EPHBFWDPATHWAY

Table 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 CSTF1 CSTF1 CSTF1 3258 0.12 -0.11 YES
2 THOC4 THOC4 THOC4 3332 0.12 -0.043 YES
3 CLP1 CLP1 CLP1 3405 0.12 0.019 YES
4 ZNF473 ZNF473 ZNF473 3519 0.11 0.077 YES
5 NCBP2 NCBP2 NCBP2 3542 0.11 0.14 YES
6 UPF3B UPF3B UPF3B 3693 0.1 0.19 YES
7 MAGOH MAGOH MAGOH 4658 0.079 0.18 YES
8 RBM8A RBM8A RBM8A 4864 0.074 0.22 YES
9 CPSF3 CPSF3 CPSF3 4883 0.074 0.26 YES
10 SNRPB SNRPB SNRPB 5149 0.068 0.28 YES
11 SNRPE SNRPE SNRPE 5206 0.066 0.32 YES
12 SLBP SLBP SLBP 5242 0.066 0.35 YES
13 CDC40 CDC40 CDC40 5424 0.062 0.38 YES
14 CPSF7 CPSF7 CPSF7 5639 0.059 0.4 YES
15 LSM11 LSM11 LSM11 6075 0.051 0.41 YES
16 U2AF1 U2AF1 U2AF1 6151 0.05 0.43 YES
17 RNPS1 RNPS1 RNPS1 6282 0.048 0.45 YES
18 SNRPF SNRPF SNRPF 6841 0.039 0.44 YES
19 CSTF2 CSTF2 CSTF2 6865 0.038 0.46 YES
20 PAPOLA PAPOLA PAPOLA 6884 0.038 0.49 YES
21 SNRPD3 SNRPD3 SNRPD3 6889 0.038 0.51 YES
22 U2AF2 U2AF2 U2AF2 6989 0.037 0.52 YES
23 SNRPG SNRPG SNRPG 7359 0.031 0.52 YES
24 PABPN1 PABPN1 PABPN1 7531 0.028 0.53 YES
25 CPSF1 CPSF1 CPSF1 7958 0.023 0.52 YES
26 CSTF3 CSTF3 CSTF3 8003 0.022 0.53 YES
27 NUDT21 NUDT21 NUDT21 8803 0.01 0.49 NO
28 SRRM1 SRRM1 SRRM1 9108 0.0062 0.48 NO
29 PCF11 PCF11 PCF11 9451 0.00097 0.46 NO
30 LSM10 LSM10 LSM10 9502 0.00051 0.46 NO
31 NFX1 NFX1 NFX1 9744 -0.0029 0.45 NO
32 NCBP1 NCBP1 NCBP1 9861 -0.0043 0.44 NO
33 CPSF2 CPSF2 CPSF2 9944 -0.0056 0.44 NO
34 DHX38 DHX38 DHX38 11970 -0.038 0.35 NO

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

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

genes ES table in pathway: PID MYC ACTIVPATHWAY

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 CLDN6 CLDN6 CLDN6 3 0.87 0.17 YES
2 CLDN19 CLDN19 CLDN19 79 0.58 0.28 YES
3 CLDN9 CLDN9 CLDN9 92 0.57 0.38 YES
4 CLDN16 CLDN16 CLDN16 199 0.49 0.47 YES
5 CLDN1 CLDN1 CLDN1 698 0.34 0.51 YES
6 CLDN11 CLDN11 CLDN11 924 0.3 0.56 YES
7 PARD6B PARD6B PARD6B 1283 0.25 0.59 YES
8 PRKCI PRKCI PRKCI 1295 0.25 0.63 YES
9 PARD6G PARD6G PARD6G 3953 0.097 0.51 NO
10 PARD3 PARD3 PARD3 3965 0.096 0.53 NO
11 CLDN18 CLDN18 CLDN18 5284 0.065 0.47 NO
12 CLDN4 CLDN4 CLDN4 6514 0.045 0.41 NO
13 CLDN15 CLDN15 CLDN15 8658 0.012 0.3 NO
14 CLDN5 CLDN5 CLDN5 8783 0.01 0.29 NO
15 MPP5 MPP5 MPP5 9126 0.0059 0.28 NO
16 CLDN3 CLDN3 CLDN3 9430 0.0013 0.26 NO
17 CLDN8 CLDN8 CLDN8 10014 -0.0065 0.23 NO
18 CLDN7 CLDN7 CLDN7 11166 -0.025 0.17 NO
19 INADL INADL INADL 12616 -0.05 0.1 NO
20 F11R F11R F11R 12673 -0.052 0.11 NO
21 CLDN12 CLDN12 CLDN12 13140 -0.061 0.096 NO
22 CLDN10 CLDN10 CLDN10 13328 -0.065 0.099 NO
23 CLDN20 CLDN20 CLDN20 15518 -0.13 0.0061 NO
24 CRB3 CRB3 CRB3 15570 -0.14 0.03 NO
25 PARD6A PARD6A PARD6A 16436 -0.18 0.018 NO
26 CLDN14 CLDN14 CLDN14 17052 -0.22 0.027 NO
27 CLDN2 CLDN2 CLDN2 17554 -0.27 0.052 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: PID MYC ACTIVPATHWAY.

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

genes ES table in pathway: PID MYC PATHWAY

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 CDKN2B CDKN2B CDKN2B 1023 0.28 0.067 YES
2 TGIF2 TGIF2 TGIF2 1191 0.26 0.17 YES
3 E2F5 E2F5 E2F5 1808 0.2 0.22 YES
4 MYC MYC MYC 1954 0.19 0.3 YES
5 SKIL SKIL SKIL 2470 0.16 0.34 YES
6 RBL1 RBL1 RBL1 2676 0.15 0.39 YES
7 SMAD7 SMAD7 SMAD7 2921 0.13 0.43 YES
8 SMAD3 SMAD3 SMAD3 4822 0.075 0.36 YES
9 SKI SKI SKI 5031 0.07 0.38 YES
10 RPS27A RPS27A RPS27A 5042 0.07 0.41 YES
11 PARP1 PARP1 PARP1 5069 0.069 0.44 YES
12 WWTR1 WWTR1 WWTR1 5166 0.068 0.46 YES
13 MEN1 MEN1 MEN1 5340 0.064 0.48 YES
14 CCNT1 CCNT1 CCNT1 5406 0.063 0.5 YES
15 CDK8 CDK8 CDK8 5732 0.057 0.51 YES
16 TRIM33 TRIM33 TRIM33 6864 0.038 0.47 NO
17 USP9X USP9X USP9X 7049 0.036 0.47 NO
18 JUNB JUNB JUNB 7052 0.036 0.49 NO
19 UBE2D1 UBE2D1 UBE2D1 7332 0.032 0.49 NO
20 TFDP1 TFDP1 TFDP1 7509 0.029 0.49 NO
21 HDAC1 HDAC1 HDAC1 7984 0.022 0.47 NO
22 SMAD2 SMAD2 SMAD2 8123 0.02 0.48 NO
23 UBA52 UBA52 UBA52 8416 0.016 0.47 NO
24 SMAD4 SMAD4 SMAD4 8758 0.011 0.45 NO
25 NCOR2 NCOR2 NCOR2 9357 0.0025 0.42 NO
26 CCNT2 CCNT2 CCNT2 9359 0.0025 0.42 NO
27 E2F4 E2F4 E2F4 9376 0.0022 0.42 NO
28 UBE2D3 UBE2D3 UBE2D3 9782 -0.0034 0.4 NO
29 PPM1A PPM1A PPM1A 9831 -0.004 0.4 NO
30 SERPINE1 SERPINE1 SERPINE1 10077 -0.0075 0.39 NO
31 CCNC CCNC CCNC 10299 -0.011 0.38 NO
32 SMURF2 SMURF2 SMURF2 10335 -0.011 0.39 NO
33 CDK9 CDK9 CDK9 10517 -0.014 0.38 NO
34 SP1 SP1 SP1 11023 -0.022 0.36 NO
35 TGIF1 TGIF1 TGIF1 12017 -0.039 0.33 NO
36 NCOR1 NCOR1 NCOR1 12865 -0.056 0.31 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: PID MYC PATHWAY.

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

genes ES table in pathway: PID AURORA A PATHWAY

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 CDKN2B CDKN2B CDKN2B 1023 0.28 0.099 YES
2 TGIF2 TGIF2 TGIF2 1191 0.26 0.23 YES
3 E2F5 E2F5 E2F5 1808 0.2 0.31 YES
4 MYC MYC MYC 1954 0.19 0.4 YES
5 RBL1 RBL1 RBL1 2676 0.15 0.44 YES
6 SMAD7 SMAD7 SMAD7 2921 0.13 0.5 YES
7 SMAD3 SMAD3 SMAD3 4822 0.075 0.44 YES
8 RPS27A RPS27A RPS27A 5042 0.07 0.47 YES
9 WWTR1 WWTR1 WWTR1 5166 0.068 0.5 YES
10 MEN1 MEN1 MEN1 5340 0.064 0.52 YES
11 CCNT1 CCNT1 CCNT1 5406 0.063 0.55 YES
12 CDK8 CDK8 CDK8 5732 0.057 0.56 YES
13 JUNB JUNB JUNB 7052 0.036 0.51 NO
14 TFDP1 TFDP1 TFDP1 7509 0.029 0.5 NO
15 HDAC1 HDAC1 HDAC1 7984 0.022 0.49 NO
16 SMAD2 SMAD2 SMAD2 8123 0.02 0.49 NO
17 UBA52 UBA52 UBA52 8416 0.016 0.49 NO
18 SMAD4 SMAD4 SMAD4 8758 0.011 0.47 NO
19 CCNT2 CCNT2 CCNT2 9359 0.0025 0.44 NO
20 E2F4 E2F4 E2F4 9376 0.0022 0.44 NO
21 SERPINE1 SERPINE1 SERPINE1 10077 -0.0075 0.41 NO
22 CCNC CCNC CCNC 10299 -0.011 0.4 NO
23 CDK9 CDK9 CDK9 10517 -0.014 0.4 NO
24 SP1 SP1 SP1 11023 -0.022 0.38 NO
25 TGIF1 TGIF1 TGIF1 12017 -0.039 0.35 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: PID AURORA A PATHWAY.

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

genes ES table in pathway: REACTOME METABOLISM OF NON CODING RNA

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 GCK GCK GCK 28 0.66 0.3 YES
2 NUP155 NUP155 NUP155 1829 0.2 0.3 YES
3 RAE1 RAE1 RAE1 1984 0.19 0.37 YES
4 NUP153 NUP153 NUP153 3218 0.12 0.36 YES
5 NUP107 NUP107 NUP107 3540 0.11 0.4 YES
6 SEH1L SEH1L SEH1L 4360 0.086 0.39 YES
7 NUP35 NUP35 NUP35 4502 0.083 0.42 YES
8 NUP85 NUP85 NUP85 4790 0.076 0.44 YES
9 NUP210 NUP210 NUP210 4972 0.072 0.46 YES
10 GCKR GCKR GCKR 5053 0.07 0.49 YES
11 NUP205 NUP205 NUP205 5279 0.065 0.51 YES
12 NUP133 NUP133 NUP133 5546 0.06 0.52 YES
13 NUP54 NUP54 NUP54 6115 0.051 0.52 NO
14 NUP62 NUP62 NUP62 6626 0.042 0.51 NO
15 NUP93 NUP93 NUP93 7644 0.027 0.47 NO
16 NUP37 NUP37 NUP37 7706 0.026 0.47 NO
17 AAAS AAAS AAAS 7756 0.025 0.48 NO
18 NUPL1 NUPL1 NUPL1 7778 0.025 0.49 NO
19 NUP43 NUP43 NUP43 8041 0.022 0.49 NO
20 POM121 POM121 POM121 8215 0.019 0.49 NO
21 TPR TPR TPR 8545 0.014 0.48 NO
22 NUP88 NUP88 NUP88 9174 0.0053 0.45 NO
23 NUP214 NUP214 NUP214 9321 0.0029 0.44 NO
24 NUPL2 NUPL2 NUPL2 9583 -0.00076 0.43 NO
25 NUP50 NUP50 NUP50 10344 -0.011 0.39 NO
26 RANBP2 RANBP2 RANBP2 12783 -0.054 0.28 NO
27 NUP188 NUP188 NUP188 13053 -0.059 0.3 NO

Figure S17.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME METABOLISM OF NON CODING RNA.

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

genes ES table in pathway: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES

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 RYR1 RYR1 RYR1 17 0.7 0.19 YES
2 PTX3 PTX3 PTX3 30 0.66 0.36 YES
3 EPHB2 EPHB2 EPHB2 113 0.55 0.51 YES
4 RHO RHO RHO 1021 0.29 0.54 YES
5 KCNJ3 KCNJ3 KCNJ3 1050 0.28 0.61 YES
6 KCNJ5 KCNJ5 KCNJ5 3439 0.11 0.51 NO
7 DLG4 DLG4 DLG4 4836 0.075 0.46 NO
8 DAG1 DAG1 DAG1 5834 0.055 0.42 NO
9 CFB CFB CFB 5835 0.055 0.43 NO
10 KAT5 KAT5 KAT5 7912 0.024 0.33 NO
11 GAST GAST GAST 8304 0.018 0.31 NO
12 GNAI1 GNAI1 GNAI1 8840 0.0098 0.28 NO
13 APC APC APC 8932 0.0086 0.28 NO
14 PITX2 PITX2 PITX2 9280 0.0036 0.26 NO
15 MAPK1 MAPK1 MAPK1 9619 -0.0012 0.25 NO
16 ITPR3 ITPR3 ITPR3 9866 -0.0044 0.24 NO
17 ADRB1 ADRB1 ADRB1 10755 -0.018 0.19 NO
18 RAC1 RAC1 RAC1 11214 -0.026 0.17 NO
19 AKT1 AKT1 AKT1 11950 -0.038 0.14 NO
20 ASAH1 ASAH1 ASAH1 12630 -0.051 0.12 NO
21 KCNJ9 KCNJ9 KCNJ9 13594 -0.072 0.088 NO
22 GNAQ GNAQ GNAQ 14124 -0.085 0.083 NO
23 ITPR2 ITPR2 ITPR2 15050 -0.12 0.064 NO
24 PLN PLN PLN 15426 -0.13 0.079 NO
25 ITPR1 ITPR1 ITPR1 16028 -0.16 0.089 NO
26 CAMP CAMP CAMP 16298 -0.17 0.12 NO

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

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES, 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
KEGG WNT SIGNALING PATHWAY 146 genes.ES.table 0.48 1.7 0.0079 0.63 0.74 0.25 0.15 0.22 0.21 0.16
KEGG GNRH SIGNALING PATHWAY 96 genes.ES.table 0.47 1.7 0.004 0.58 0.76 0.24 0.12 0.21 0.2 0.15
KEGG MELANOMA 67 genes.ES.table 0.52 1.6 0.0061 0.57 0.87 0.34 0.16 0.29 0.25 0.16
BIOCARTA ALK PATHWAY 36 genes.ES.table 0.56 1.6 0.012 0.59 0.87 0.33 0.17 0.28 0.26 0.16
BIOCARTA GSK3 PATHWAY 27 genes.ES.table 0.57 1.8 0.012 0.81 0.69 0.3 0.14 0.26 0.24 0.19
BIOCARTA P38MAPK PATHWAY 39 genes.ES.table 0.45 1.7 0.0039 0.72 0.69 0.23 0.2 0.18 0.22 0.18
BIOCARTA WNT PATHWAY 26 genes.ES.table 0.62 2.1 0 0.23 0.062 0.15 0.09 0.14 0 0.05
ST WNT BETA CATENIN PATHWAY 33 genes.ES.table 0.77 2.1 0 0.29 0.14 0.3 0.085 0.28 0 0.056
PID PS1PATHWAY 46 genes.ES.table 0.51 1.8 0.002 0.71 0.49 0.24 0.17 0.2 0 0.15
PID BETACATENIN NUC PATHWAY 73 genes.ES.table 0.54 1.8 0.0098 1 0.65 0.3 0.14 0.26 0.29 0.23
genes ES table in pathway: KEGG WNT SIGNALING 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 WIF1 WIF1 WIF1 14 0.68 0.3 YES
2 LEF1 LEF1 LEF1 49 0.55 0.54 YES
3 FZD1 FZD1 FZD1 696 0.23 0.61 YES
4 CCND1 CCND1 CCND1 1659 0.15 0.62 YES
5 PPARD PPARD PPARD 3160 0.083 0.58 NO
6 NLK NLK NLK 3493 0.074 0.6 NO
7 CSNK1A1 CSNK1A1 CSNK1A1 5520 0.037 0.5 NO
8 CTNNB1 CTNNB1 CTNNB1 5649 0.035 0.51 NO
9 BTRC BTRC BTRC 5685 0.035 0.52 NO
10 APC APC APC 6047 0.03 0.52 NO
11 AXIN1 AXIN1 AXIN1 6060 0.03 0.53 NO
12 TLE1 TLE1 TLE1 6816 0.022 0.5 NO
13 CTBP1 CTBP1 CTBP1 7167 0.018 0.49 NO
14 SMAD4 SMAD4 SMAD4 7524 0.014 0.48 NO
15 CREBBP CREBBP CREBBP 8389 0.0059 0.43 NO
16 DVL1 DVL1 DVL1 8867 0.0014 0.41 NO
17 TAB1 TAB1 TAB1 9112 -0.00094 0.39 NO
18 FRAT1 FRAT1 FRAT1 9365 -0.0034 0.38 NO
19 PPP2CA PPP2CA PPP2CA 10315 -0.012 0.34 NO
20 GSK3B GSK3B GSK3B 10514 -0.014 0.33 NO
21 CSNK1D CSNK1D CSNK1D 10936 -0.018 0.32 NO
22 MAP3K7 MAP3K7 MAP3K7 11398 -0.023 0.3 NO
23 HDAC1 HDAC1 HDAC1 12052 -0.029 0.28 NO
24 WNT1 WNT1 WNT1 12202 -0.031 0.28 NO
25 CSNK2A1 CSNK2A1 CSNK2A1 13466 -0.048 0.24 NO
26 MYC MYC MYC 15005 -0.079 0.19 NO

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

Figure S22.  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

genes ES table in pathway: KEGG GNRH SIGNALING 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 NKD1 NKD1 NKD1 4 0.79 0.15 YES
2 DKK4 DKK4 DKK4 8 0.73 0.29 YES
3 WIF1 WIF1 WIF1 14 0.68 0.41 YES
4 AXIN2 AXIN2 AXIN2 53 0.55 0.52 YES
5 DACT1 DACT1 DACT1 87 0.5 0.61 YES
6 DKK1 DKK1 DKK1 107 0.46 0.69 YES
7 NKD2 NKD2 NKD2 574 0.25 0.72 YES
8 DKK2 DKK2 DKK2 981 0.2 0.73 YES
9 DKK3 DKK3 DKK3 1096 0.19 0.76 YES
10 CXXC4 CXXC4 CXXC4 1567 0.15 0.76 YES
11 AKT3 AKT3 AKT3 2063 0.13 0.76 NO
12 RPSA RPSA RPSA 4526 0.052 0.64 NO
13 LRP1 LRP1 LRP1 5415 0.039 0.6 NO
14 CSNK1A1 CSNK1A1 CSNK1A1 5520 0.037 0.6 NO
15 CTNNB1 CTNNB1 CTNNB1 5649 0.035 0.6 NO
16 APC APC APC 6047 0.03 0.58 NO
17 AXIN1 AXIN1 AXIN1 6060 0.03 0.59 NO
18 FSTL1 FSTL1 FSTL1 6198 0.028 0.59 NO
19 AKT1 AKT1 AKT1 6217 0.028 0.59 NO
20 SFRP1 SFRP1 SFRP1 7221 0.017 0.54 NO
21 DVL1 DVL1 DVL1 8867 0.0014 0.45 NO
22 ANKRD6 ANKRD6 ANKRD6 9294 -0.0028 0.43 NO
23 FRAT1 FRAT1 FRAT1 9365 -0.0034 0.42 NO
24 PSEN1 PSEN1 PSEN1 9372 -0.0035 0.43 NO
25 CBY1 CBY1 CBY1 9436 -0.0041 0.42 NO
26 GSK3A GSK3A GSK3A 10232 -0.011 0.38 NO
27 GSK3B GSK3B GSK3B 10514 -0.014 0.37 NO
28 PTPRA PTPRA PTPRA 11306 -0.022 0.33 NO
29 PIN1 PIN1 PIN1 11897 -0.028 0.3 NO
30 AKT2 AKT2 AKT2 13214 -0.044 0.24 NO
31 CER1 CER1 CER1 13225 -0.044 0.25 NO
32 SENP2 SENP2 SENP2 15585 -0.098 0.14 NO
33 MVP MVP MVP 15630 -0.1 0.16 NO

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

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GNRH 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 MELANOMA

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 BMX BMX BMX 99 0.47 0.16 YES
2 PRKCQ PRKCQ PRKCQ 350 0.31 0.26 YES
3 DSG3 DSG3 DSG3 613 0.25 0.33 YES
4 DSG1 DSG1 DSG1 912 0.21 0.38 YES
5 GAS2 GAS2 GAS2 1060 0.19 0.44 YES
6 LOC647859 LOC647859 LOC647859 1564 0.15 0.47 YES
7 PKP1 PKP1 PKP1 1785 0.14 0.51 YES
8 VIM VIM VIM 1879 0.14 0.55 YES
9 SATB1 SATB1 SATB1 2112 0.12 0.58 YES
10 TJP1 TJP1 TJP1 5467 0.038 0.41 NO
11 CTNNB1 CTNNB1 CTNNB1 5649 0.035 0.41 NO
12 APC APC APC 6047 0.03 0.4 NO
13 GSN GSN GSN 6281 0.028 0.4 NO
14 ROCK1 ROCK1 ROCK1 6781 0.022 0.38 NO
15 ACIN1 ACIN1 ACIN1 7298 0.016 0.36 NO
16 CASP7 CASP7 CASP7 7430 0.015 0.36 NO
17 CASP6 CASP6 CASP6 7759 0.012 0.34 NO
18 SPTAN1 SPTAN1 SPTAN1 8077 0.009 0.33 NO
19 ADD1 ADD1 ADD1 8227 0.0076 0.32 NO
20 MAPT MAPT MAPT 8318 0.0067 0.32 NO
21 DSG2 DSG2 DSG2 8419 0.0057 0.32 NO
22 BIRC2 BIRC2 BIRC2 8565 0.0043 0.31 NO
23 FNTA FNTA FNTA 9711 -0.0064 0.25 NO
24 PTK2 PTK2 PTK2 9777 -0.0069 0.25 NO
25 CASP3 CASP3 CASP3 9894 -0.0079 0.25 NO
26 CDH1 CDH1 CDH1 11177 -0.021 0.18 NO
27 LMNB1 LMNB1 LMNB1 11563 -0.024 0.17 NO
28 PLEC PLEC PLEC 11719 -0.026 0.17 NO
29 DBNL DBNL DBNL 12078 -0.03 0.16 NO
30 DSP DSP DSP 12269 -0.032 0.16 NO
31 STK24 STK24 STK24 12357 -0.033 0.17 NO
32 TJP2 TJP2 TJP2 12666 -0.037 0.17 NO
33 BCAP31 BCAP31 BCAP31 12955 -0.04 0.17 NO
34 LMNA LMNA LMNA 13498 -0.048 0.15 NO
35 OCLN OCLN OCLN 14224 -0.061 0.14 NO
36 CASP8 CASP8 CASP8 14249 -0.062 0.16 NO
37 MST4 MST4 MST4 15455 -0.094 0.12 NO
38 PRKCD PRKCD PRKCD 16176 -0.12 0.13 NO

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

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

genes ES table in pathway: BIOCARTA ALK PATHWAY

Table 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 NKD1 NKD1 NKD1 4 0.79 0.18 YES
2 WIF1 WIF1 WIF1 14 0.68 0.33 YES
3 DKK1 DKK1 DKK1 107 0.46 0.43 YES
4 FZD1 FZD1 FZD1 696 0.23 0.45 YES
5 DKK2 DKK2 DKK2 981 0.2 0.48 YES
6 DLL1 DLL1 DLL1 1149 0.18 0.51 YES
7 CCND1 CCND1 CCND1 1659 0.15 0.51 YES
8 RBPJ RBPJ RBPJ 2429 0.11 0.5 YES
9 HNF1A HNF1A HNF1A 2927 0.09 0.49 YES
10 NEDD4 NEDD4 NEDD4 3084 0.085 0.5 YES
11 PPARD PPARD PPARD 3160 0.083 0.51 YES
12 NLK NLK NLK 3493 0.074 0.51 NO
13 JUN JUN JUN 4340 0.055 0.48 NO
14 AES AES AES 4601 0.05 0.48 NO
15 NCSTN NCSTN NCSTN 4968 0.045 0.47 NO
16 CSNK1A1 CSNK1A1 CSNK1A1 5520 0.037 0.44 NO
17 CTNNB1 CTNNB1 CTNNB1 5649 0.035 0.45 NO
18 APC APC APC 6047 0.03 0.43 NO
19 AXIN1 AXIN1 AXIN1 6060 0.03 0.44 NO
20 TLE1 TLE1 TLE1 6816 0.022 0.4 NO
21 CTBP1 CTBP1 CTBP1 7167 0.018 0.39 NO
22 LRP6 LRP6 LRP6 7301 0.016 0.38 NO
23 MAPK1 MAPK1 MAPK1 8156 0.0082 0.34 NO
24 CREBBP CREBBP CREBBP 8389 0.0059 0.33 NO
25 DVL1 DVL1 DVL1 8867 0.0014 0.3 NO
26 TAB1 TAB1 TAB1 9112 -0.00094 0.29 NO
27 FRAT1 FRAT1 FRAT1 9365 -0.0034 0.28 NO
28 PSEN1 PSEN1 PSEN1 9372 -0.0035 0.28 NO
29 PPP2R5D PPP2R5D PPP2R5D 10237 -0.011 0.23 NO
30 FBXW11 FBXW11 FBXW11 10367 -0.012 0.23 NO
31 GSK3B GSK3B GSK3B 10514 -0.014 0.22 NO
32 FOS FOS FOS 10657 -0.015 0.22 NO
33 NOTCH1 NOTCH1 NOTCH1 11102 -0.02 0.2 NO
34 MAP3K7 MAP3K7 MAP3K7 11398 -0.023 0.19 NO
35 APH1B APH1B APH1B 11673 -0.026 0.18 NO
36 SSPO SSPO SSPO 11709 -0.026 0.18 NO
37 ADAM10 ADAM10 ADAM10 11811 -0.027 0.18 NO
38 APH1A APH1A APH1A 12048 -0.029 0.18 NO
39 HDAC1 HDAC1 HDAC1 12052 -0.029 0.18 NO
40 WNT1 WNT1 WNT1 12202 -0.031 0.18 NO
41 CSNK2A1 CSNK2A1 CSNK2A1 13466 -0.048 0.13 NO
42 MYC MYC MYC 15005 -0.079 0.06 NO
43 MAPK3 MAPK3 MAPK3 15069 -0.081 0.075 NO
44 KREMEN2 KREMEN2 KREMEN2 16064 -0.12 0.047 NO
45 PSENEN PSENEN PSENEN 16129 -0.12 0.07 NO
46 DTX1 DTX1 DTX1 17939 -0.27 0.032 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: BIOCARTA ALK PATHWAY.

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

genes ES table in pathway: BIOCARTA GSK3 PATHWAY

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 SP5 SP5 SP5 5 0.76 0.084 YES
2 DKK4 DKK4 DKK4 8 0.73 0.16 YES
3 LEF1 LEF1 LEF1 49 0.55 0.22 YES
4 AXIN2 AXIN2 AXIN2 53 0.55 0.28 YES
5 DKK1 DKK1 DKK1 107 0.46 0.33 YES
6 MMP2 MMP2 MMP2 362 0.31 0.35 YES
7 ZCCHC12 ZCCHC12 ZCCHC12 363 0.31 0.39 YES
8 SNAI2 SNAI2 SNAI2 479 0.27 0.41 YES
9 SFN SFN SFN 637 0.24 0.43 YES
10 TCF7 TCF7 TCF7 690 0.23 0.45 YES
11 TLE2 TLE2 TLE2 972 0.2 0.46 YES
12 TCF4 TCF4 TCF4 1211 0.18 0.46 YES
13 VCAN VCAN VCAN 1416 0.16 0.47 YES
14 CAMK4 CAMK4 CAMK4 1486 0.16 0.49 YES
15 CCND1 CCND1 CCND1 1659 0.15 0.49 YES
16 MDFIC MDFIC MDFIC 1671 0.15 0.51 YES
17 AR AR AR 1857 0.14 0.51 YES
18 CCND2 CCND2 CCND2 1998 0.13 0.52 YES
19 KRT1 KRT1 KRT1 2180 0.12 0.52 YES
20 MITF MITF MITF 2361 0.11 0.53 YES
21 TERT TERT TERT 2456 0.11 0.53 YES
22 KLF4 KLF4 KLF4 2508 0.11 0.54 YES
23 CTNNBIP1 CTNNBIP1 CTNNBIP1 3330 0.078 0.51 NO
24 ID2 ID2 ID2 4133 0.059 0.47 NO
25 JUN JUN JUN 4340 0.055 0.46 NO
26 PITX2 PITX2 PITX2 4443 0.053 0.46 NO
27 AES AES AES 4601 0.05 0.46 NO
28 CYR61 CYR61 CYR61 5071 0.043 0.44 NO
29 TCF7L2 TCF7L2 TCF7L2 5247 0.041 0.44 NO
30 BCL9 BCL9 BCL9 5268 0.04 0.44 NO
31 NCOA2 NCOA2 NCOA2 5595 0.036 0.43 NO
32 CTNNB1 CTNNB1 CTNNB1 5649 0.035 0.43 NO
33 APC APC APC 6047 0.03 0.41 NO
34 CACNA1G CACNA1G CACNA1G 6048 0.03 0.41 NO
35 TLE1 TLE1 TLE1 6816 0.022 0.37 NO
36 SMARCA4 SMARCA4 SMARCA4 6979 0.02 0.37 NO
37 CTBP1 CTBP1 CTBP1 7167 0.018 0.36 NO
38 YWHAE YWHAE YWHAE 7252 0.017 0.36 NO
39 EP300 EP300 EP300 7415 0.015 0.35 NO
40 YWHAG YWHAG YWHAG 7716 0.012 0.33 NO
41 HBP1 HBP1 HBP1 7949 0.01 0.32 NO
42 MED12 MED12 MED12 8507 0.0049 0.29 NO
43 YWHAQ YWHAQ YWHAQ 8826 0.0018 0.28 NO
44 CUL1 CUL1 CUL1 8945 0.00073 0.27 NO
45 CBY1 CBY1 CBY1 9436 -0.0041 0.24 NO
46 HDAC2 HDAC2 HDAC2 9621 -0.0055 0.23 NO
47 CHD8 CHD8 CHD8 9906 -0.008 0.22 NO
48 SKP1 SKP1 SKP1 10469 -0.013 0.19 NO
49 XPO1 XPO1 XPO1 10747 -0.016 0.18 NO
50 DVL3 DVL3 DVL3 10928 -0.018 0.17 NO
51 CDH1 CDH1 CDH1 11177 -0.021 0.16 NO
52 TRRAP TRRAP TRRAP 11620 -0.025 0.14 NO
53 SSPO SSPO SSPO 11709 -0.026 0.14 NO
54 HDAC1 HDAC1 HDAC1 12052 -0.029 0.12 NO
55 CDX1 CDX1 CDX1 12143 -0.031 0.12 NO
56 YWHAH YWHAH YWHAH 12377 -0.034 0.11 NO
57 YWHAZ YWHAZ YWHAZ 12952 -0.04 0.083 NO
58 IL8 IL8 IL8 13068 -0.042 0.081 NO
59 YWHAB YWHAB YWHAB 13335 -0.046 0.072 NO
60 MMP9 MMP9 MMP9 13793 -0.054 0.053 NO
61 TBL1X TBL1X TBL1X 14173 -0.06 0.039 NO
62 INCENP INCENP INCENP 14234 -0.061 0.043 NO
63 RUVBL2 RUVBL2 RUVBL2 14319 -0.063 0.045 NO
64 KCNIP4 KCNIP4 KCNIP4 14386 -0.065 0.049 NO
65 ADCY7 ADCY7 ADCY7 14710 -0.072 0.039 NO
66 TCF7L1 TCF7L1 TCF7L1 14724 -0.072 0.046 NO
67 TBL1XR1 TBL1XR1 TBL1XR1 14880 -0.076 0.046 NO
68 MYC MYC MYC 15005 -0.079 0.048 NO
69 TNIK TNIK TNIK 15326 -0.09 0.041 NO
70 SALL4 SALL4 SALL4 15706 -0.1 0.032 NO
71 TLE4 TLE4 TLE4 17486 -0.21 -0.041 NO
72 IGF2BP1 IGF2BP1 IGF2BP1 18350 -0.36 -0.048 NO
73 CDKN2A CDKN2A CDKN2A 18510 -0.52 0.00081 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: BIOCARTA GSK3 PATHWAY.

Figure S30.  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 P38MAPK PATHWAY

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 ITGA1 ITGA1 ITGA1 300 0.33 0.13 YES
2 FIGF FIGF FIGF 691 0.23 0.21 YES
3 ITGA2 ITGA2 ITGA2 695 0.23 0.31 YES
4 ITGA4 ITGA4 ITGA4 731 0.23 0.4 YES
5 COL1A2 COL1A2 COL1A2 1675 0.15 0.42 YES
6 COL1A1 COL1A1 COL1A1 2120 0.12 0.44 YES
7 FN1 FN1 FN1 2203 0.12 0.49 YES
8 FLT4 FLT4 FLT4 2234 0.12 0.54 YES
9 VEGFC VEGFC VEGFC 2490 0.11 0.57 YES
10 PIK3R1 PIK3R1 PIK3R1 2497 0.11 0.62 YES
11 MAP2K4 MAP2K4 MAP2K4 3639 0.07 0.59 NO
12 ITGB1 ITGB1 ITGB1 4113 0.06 0.59 NO
13 CRK CRK CRK 5927 0.032 0.5 NO
14 AKT1 AKT1 AKT1 6217 0.028 0.5 NO
15 ITGA5 ITGA5 ITGA5 6384 0.026 0.5 NO
16 SHC1 SHC1 SHC1 7783 0.012 0.43 NO
17 MAPK1 MAPK1 MAPK1 8156 0.0082 0.42 NO
18 MAPK11 MAPK11 MAPK11 8836 0.0017 0.38 NO
19 RPS6KA1 RPS6KA1 RPS6KA1 9759 -0.0067 0.33 NO
20 CREB1 CREB1 CREB1 11168 -0.021 0.26 NO
21 MAPK14 MAPK14 MAPK14 11574 -0.024 0.25 NO
22 SOS1 SOS1 SOS1 11629 -0.025 0.26 NO
23 GRB2 GRB2 GRB2 13528 -0.049 0.18 NO
24 MAPK3 MAPK3 MAPK3 15069 -0.081 0.13 NO
25 PIK3CA PIK3CA PIK3CA 16332 -0.13 0.12 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: BIOCARTA P38MAPK PATHWAY.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA P38MAPK 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 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 TLR4 TLR4 TLR4 43 0.57 0.2 YES
2 LEF1 LEF1 LEF1 49 0.55 0.38 YES
3 FZD1 FZD1 FZD1 696 0.23 0.43 YES
4 TIRAP TIRAP TIRAP 1223 0.18 0.46 YES
5 GJA1 GJA1 GJA1 1610 0.15 0.5 YES
6 CCND1 CCND1 CCND1 1659 0.15 0.54 YES
7 GNAI1 GNAI1 GNAI1 2301 0.12 0.55 YES
8 PIK3R1 PIK3R1 PIK3R1 2497 0.11 0.57 YES
9 CTNNB1 CTNNB1 CTNNB1 5649 0.035 0.42 NO
10 APC APC APC 6047 0.03 0.4 NO
11 AXIN1 AXIN1 AXIN1 6060 0.03 0.42 NO
12 AKT1 AKT1 AKT1 6217 0.028 0.42 NO
13 TOLLIP TOLLIP TOLLIP 8841 0.0017 0.28 NO
14 DVL1 DVL1 DVL1 8867 0.0014 0.27 NO
15 MYD88 MYD88 MYD88 8964 0.00056 0.27 NO
16 RELA RELA RELA 8968 0.00051 0.27 NO
17 PDPK1 PDPK1 PDPK1 10244 -0.011 0.2 NO
18 PPP2CA PPP2CA PPP2CA 10315 -0.012 0.2 NO
19 GSK3B GSK3B GSK3B 10514 -0.014 0.2 NO
20 NFKB1 NFKB1 NFKB1 11137 -0.02 0.17 NO
21 LY96 LY96 LY96 12096 -0.03 0.13 NO
22 WNT1 WNT1 WNT1 12202 -0.031 0.14 NO
23 CD14 CD14 CD14 13150 -0.043 0.099 NO
24 IRAK1 IRAK1 IRAK1 14776 -0.073 0.036 NO
25 PIK3CA PIK3CA PIK3CA 16332 -0.13 -0.0034 NO
26 EIF2AK2 EIF2AK2 EIF2AK2 16465 -0.14 0.036 NO
27 LBP LBP LBP 17538 -0.22 0.053 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: BIOCARTA WNT PATHWAY.

Figure S34.  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: ST WNT BETA CATENIN PATHWAY

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 PLA2G4A PLA2G4A PLA2G4A 88 0.49 0.18 YES
2 TGFB2 TGFB2 TGFB2 241 0.36 0.31 YES
3 RPS6KA5 RPS6KA5 RPS6KA5 596 0.25 0.38 YES
4 MAP2K6 MAP2K6 MAP2K6 1234 0.18 0.41 YES
5 TGFB3 TGFB3 TGFB3 1829 0.14 0.43 YES
6 MAP3K9 MAP3K9 MAP3K9 2613 0.1 0.43 YES
7 MEF2C MEF2C MEF2C 2836 0.093 0.45 YES
8 MAP2K4 MAP2K4 MAP2K4 3639 0.07 0.43 YES
9 RAPGEF2 RAPGEF2 RAPGEF2 3725 0.068 0.46 YES
10 TGFBR1 TGFBR1 TGFBR1 4381 0.054 0.44 NO
11 TGFB1 TGFB1 TGFB1 4993 0.044 0.42 NO
12 HRAS HRAS HRAS 6646 0.024 0.34 NO
13 MAPKAPK2 MAPKAPK2 MAPKAPK2 6862 0.021 0.34 NO
14 TRADD TRADD TRADD 7295 0.016 0.32 NO
15 ATF2 ATF2 ATF2 7296 0.016 0.33 NO
16 SHC1 SHC1 SHC1 7783 0.012 0.31 NO
17 HMGN1 HMGN1 HMGN1 8301 0.0069 0.28 NO
18 MEF2D MEF2D MEF2D 8512 0.0048 0.27 NO
19 ELK1 ELK1 ELK1 9196 -0.0017 0.24 NO
20 MAX MAX MAX 9577 -0.0052 0.22 NO
21 HSPB2 HSPB2 HSPB2 10063 -0.0094 0.19 NO
22 RAC1 RAC1 RAC1 10081 -0.0095 0.2 NO
23 RIPK1 RIPK1 RIPK1 10837 -0.017 0.16 NO
24 MKNK1 MKNK1 MKNK1 11057 -0.019 0.16 NO
25 CREB1 CREB1 CREB1 11168 -0.021 0.16 NO
26 HSPB1 HSPB1 HSPB1 11208 -0.021 0.16 NO
27 MAP3K7 MAP3K7 MAP3K7 11398 -0.023 0.16 NO
28 MAP3K1 MAP3K1 MAP3K1 11457 -0.023 0.17 NO
29 MEF2A MEF2A MEF2A 11476 -0.024 0.18 NO
30 MAPK14 MAPK14 MAPK14 11574 -0.024 0.18 NO
31 DAXX DAXX DAXX 11684 -0.026 0.18 NO
32 CDC42 CDC42 CDC42 11869 -0.027 0.18 NO
33 TRAF2 TRAF2 TRAF2 13420 -0.047 0.12 NO
34 GRB2 GRB2 GRB2 13528 -0.049 0.13 NO
35 MAPKAPK5 MAPKAPK5 MAPKAPK5 13831 -0.054 0.14 NO
36 DDIT3 DDIT3 DDIT3 14284 -0.063 0.13 NO
37 MAP3K5 MAP3K5 MAP3K5 14541 -0.068 0.15 NO
38 MYC MYC MYC 15005 -0.079 0.15 NO
39 STAT1 STAT1 STAT1 15829 -0.11 0.15 NO

Figure S35.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST WNT BETA CATENIN PATHWAY.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: ST WNT BETA CATENIN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID PS1PATHWAY

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 WFS1 WFS1 WFS1 957 0.2 0.04 YES
2 PDIA5 PDIA5 PDIA5 1116 0.19 0.12 YES
3 FKBP14 FKBP14 FKBP14 1203 0.18 0.19 YES
4 EXTL3 EXTL3 EXTL3 1375 0.17 0.26 YES
5 WIPI1 WIPI1 WIPI1 1930 0.13 0.29 YES
6 TSPYL2 TSPYL2 TSPYL2 2931 0.09 0.28 YES
7 DNAJB9 DNAJB9 DNAJB9 2946 0.09 0.32 YES
8 C19orf10 C19orf10 C19orf10 3091 0.085 0.35 YES
9 PPP2R5B PPP2R5B PPP2R5B 3679 0.07 0.35 YES
10 XBP1 XBP1 XBP1 4176 0.058 0.35 YES
11 DDX11 DDX11 DDX11 4644 0.05 0.34 YES
12 PREB PREB PREB 5130 0.042 0.34 YES
13 SRPR SRPR SRPR 5301 0.04 0.35 YES
14 DNAJC3 DNAJC3 DNAJC3 5483 0.038 0.35 YES
15 HYOU1 HYOU1 HYOU1 5825 0.033 0.35 YES
16 ACADVL ACADVL ACADVL 5838 0.033 0.36 YES
17 SYVN1 SYVN1 SYVN1 5939 0.032 0.37 YES
18 SEC31A SEC31A SEC31A 5976 0.031 0.38 YES
19 SULT1A3 SULT1A3 SULT1A3 6140 0.029 0.39 YES
20 CXXC1 CXXC1 CXXC1 6170 0.029 0.4 YES
21 TPP1 TPP1 TPP1 6278 0.028 0.41 YES
22 EDEM1 EDEM1 EDEM1 6329 0.027 0.42 YES
23 SSR1 SSR1 SSR1 6909 0.021 0.4 NO
24 TLN1 TLN1 TLN1 7391 0.016 0.38 NO
25 SHC1 SHC1 SHC1 7783 0.012 0.36 NO
26 ZBTB17 ZBTB17 ZBTB17 7915 0.011 0.36 NO
27 SRPRB SRPRB SRPRB 8063 0.0091 0.36 NO
28 ADD1 ADD1 ADD1 8227 0.0076 0.35 NO
29 YIF1A YIF1A YIF1A 8739 0.0027 0.32 NO
30 TATDN2 TATDN2 TATDN2 8821 0.0019 0.32 NO
31 SERP1 SERP1 SERP1 9612 -0.0055 0.28 NO
32 GOSR2 GOSR2 GOSR2 9934 -0.0082 0.27 NO
33 GSK3A GSK3A GSK3A 10232 -0.011 0.25 NO
34 CTDSP2 CTDSP2 CTDSP2 10381 -0.012 0.25 NO
35 DCTN1 DCTN1 DCTN1 10397 -0.012 0.26 NO
36 KDELR3 KDELR3 KDELR3 10997 -0.019 0.23 NO
37 ARFGAP1 ARFGAP1 ARFGAP1 11187 -0.021 0.23 NO
38 PDIA6 PDIA6 PDIA6 11519 -0.024 0.22 NO
39 ATP6V0D1 ATP6V0D1 ATP6V0D1 12479 -0.035 0.19 NO
40 KLHDC3 KLHDC3 KLHDC3 12871 -0.04 0.19 NO
41 DNAJB11 DNAJB11 DNAJB11 12999 -0.041 0.2 NO
42 LMNA LMNA LMNA 13498 -0.048 0.19 NO
43 CUL7 CUL7 CUL7 14796 -0.074 0.16 NO
44 HDGF HDGF HDGF 15661 -0.1 0.16 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: PID PS1PATHWAY.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: PID PS1PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID BETACATENIN NUC PATHWAY

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 FGF20 FGF20 FGF20 1 0.84 0.15 YES
2 FGF3 FGF3 FGF3 12 0.69 0.27 YES
3 FGF19 FGF19 FGF19 20 0.64 0.39 YES
4 FGF8 FGF8 FGF8 73 0.52 0.48 YES
5 FGF22 FGF22 FGF22 178 0.4 0.54 YES
6 FGF17 FGF17 FGF17 594 0.25 0.57 YES
7 FGF9 FGF9 FGF9 861 0.21 0.59 YES
8 SPRY2 SPRY2 SPRY2 890 0.21 0.63 YES
9 FGFR1 FGFR1 FGFR1 2705 0.098 0.55 NO
10 FGF7 FGF7 FGF7 2724 0.097 0.56 NO
11 KL KL KL 2729 0.097 0.58 NO
12 FGF2 FGF2 FGF2 3800 0.066 0.53 NO
13 FGF5 FGF5 FGF5 6565 0.025 0.39 NO
14 FGF23 FGF23 FGF23 6617 0.024 0.39 NO
15 CBL CBL CBL 6994 0.02 0.37 NO
16 FRS2 FRS2 FRS2 7468 0.015 0.35 NO
17 MAPK1 MAPK1 MAPK1 8156 0.0082 0.31 NO
18 FGF18 FGF18 FGF18 8571 0.0042 0.29 NO
19 PPP2CB PPP2CB PPP2CB 8625 0.0037 0.29 NO
20 PPP2CA PPP2CA PPP2CA 10315 -0.012 0.2 NO
21 UBA52 UBA52 UBA52 10349 -0.012 0.2 NO
22 PPP2R1A PPP2R1A PPP2R1A 10908 -0.018 0.18 NO
23 MKNK1 MKNK1 MKNK1 11057 -0.019 0.17 NO
24 FGF1 FGF1 FGF1 11373 -0.023 0.16 NO
25 SRC SRC SRC 12886 -0.04 0.082 NO
26 RPS27A RPS27A RPS27A 13416 -0.047 0.062 NO
27 GRB2 GRB2 GRB2 13528 -0.049 0.065 NO
28 BRAF BRAF BRAF 13563 -0.05 0.072 NO
29 MAPK3 MAPK3 MAPK3 15069 -0.081 0.0052 NO
30 FGFR2 FGFR2 FGFR2 15854 -0.11 -0.018 NO
31 FGFR4 FGFR4 FGFR4 16736 -0.15 -0.038 NO
32 KLB KLB KLB 18115 -0.3 -0.059 NO
33 FGFR3 FGFR3 FGFR3 18479 -0.45 0.0025 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: PID BETACATENIN NUC PATHWAY.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: PID BETACATENIN NUC 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 clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY 61 genes.ES.table 0.67 1.8 0.002 0.34 0.5 0.34 0.081 0.32 0.071 0.08
KEGG CYTOSOLIC DNA SENSING PATHWAY 42 genes.ES.table 0.66 1.8 0.0041 0.3 0.56 0.26 0.059 0.25 0.068 0.072
BIOCARTA HIVNEF PATHWAY 58 genes.ES.table 0.49 2 0.0079 0.18 0.19 0.5 0.27 0.37 0 0.037
BIOCARTA PYK2 PATHWAY 28 genes.ES.table 0.45 1.8 0.016 0.3 0.58 0.29 0.14 0.25 0.07 0.077
ST TUMOR NECROSIS FACTOR PATHWAY 28 genes.ES.table 0.55 1.8 0.025 0.34 0.67 0.71 0.27 0.52 0.099 0.086
ST INTERLEUKIN 4 PATHWAY 26 genes.ES.table 0.63 1.9 0.0021 0.3 0.4 0.5 0.22 0.39 0 0.067
PID TNFPATHWAY 46 genes.ES.table 0.48 1.8 0.014 0.32 0.51 0.5 0.27 0.37 0.067 0.077
PID P53DOWNSTREAMPATHWAY 134 genes.ES.table 0.48 1.8 0.011 0.34 0.64 0.3 0.13 0.26 0.09 0.082
PID HIVNEFPATHWAY 35 genes.ES.table 0.58 1.9 0.008 0.28 0.35 0.69 0.27 0.5 0 0.063
PID CASPASE PATHWAY 51 genes.ES.table 0.5 1.9 0.0041 0.26 0.3 0.31 0.14 0.27 0 0.057
genes ES table in pathway: KEGG NOD LIKE RECEPTOR SIGNALING 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 GNPNAT1 GNPNAT1 GNPNAT1 1517 0.12 0.013 YES
2 ALG12 ALG12 ALG12 2040 0.091 0.059 YES
3 GMPPB GMPPB GMPPB 2119 0.088 0.13 YES
4 ALG1 ALG1 ALG1 2225 0.084 0.19 YES
5 MPI MPI MPI 2372 0.079 0.25 YES
6 PMM2 PMM2 PMM2 2403 0.078 0.31 YES
7 GFPT2 GFPT2 GFPT2 2517 0.073 0.36 YES
8 DOLPP1 DOLPP1 DOLPP1 2745 0.067 0.4 YES
9 ALG5 ALG5 ALG5 2788 0.066 0.46 YES
10 GMPPA GMPPA GMPPA 3131 0.057 0.48 YES
11 DPM2 DPM2 DPM2 3348 0.052 0.52 YES
12 PGM3 PGM3 PGM3 3542 0.048 0.54 YES
13 ALG3 ALG3 ALG3 3766 0.044 0.57 YES
14 PMM1 PMM1 PMM1 3783 0.044 0.6 YES
15 ALG2 ALG2 ALG2 4203 0.037 0.61 YES
16 DOLK DOLK DOLK 4671 0.03 0.61 YES
17 DPM3 DPM3 DPM3 4677 0.03 0.64 YES
18 DPAGT1 DPAGT1 DPAGT1 5509 0.02 0.61 NO
19 RFT1 RFT1 RFT1 5802 0.016 0.6 NO
20 ALG13 ALG13 ALG13 6275 0.011 0.59 NO
21 ALG11 ALG11 ALG11 6500 0.0089 0.58 NO
22 ALG6 ALG6 ALG6 7345 0.00021 0.54 NO
23 ALG14 ALG14 ALG14 7542 -0.002 0.53 NO
24 ALG9 ALG9 ALG9 7546 -0.0021 0.53 NO
25 ALG10 ALG10 ALG10 7801 -0.0046 0.52 NO
26 ALG8 ALG8 ALG8 8531 -0.011 0.49 NO
27 DPM1 DPM1 DPM1 8988 -0.016 0.48 NO
28 ALG10B ALG10B ALG10B 11622 -0.047 0.37 NO

Figure S41.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG CYTOSOLIC DNA SENSING PATHWAY

Table 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 CPD CPD CPD 1043 0.15 0.0045 YES
2 TBC1D8B TBC1D8B TBC1D8B 1177 0.14 0.054 YES
3 ARRB1 ARRB1 ARRB1 1706 0.11 0.069 YES
4 FTH1 FTH1 FTH1 1727 0.1 0.11 YES
5 TPD52 TPD52 TPD52 2069 0.09 0.13 YES
6 RAB5C RAB5C RAB5C 2583 0.072 0.13 YES
7 AP1B1 AP1B1 AP1B1 2981 0.061 0.13 YES
8 YIPF6 YIPF6 YIPF6 2983 0.06 0.16 YES
9 AP1M2 AP1M2 AP1M2 3017 0.06 0.18 YES
10 AP1G1 AP1G1 AP1G1 3020 0.06 0.2 YES
11 TFRC TFRC TFRC 3105 0.058 0.22 YES
12 VAMP8 VAMP8 VAMP8 3361 0.052 0.23 YES
13 FTL FTL FTL 3379 0.052 0.25 YES
14 AP1S1 AP1S1 AP1S1 3432 0.051 0.27 YES
15 SNAP23 SNAP23 SNAP23 3473 0.05 0.28 YES
16 NECAP1 NECAP1 NECAP1 3595 0.047 0.3 YES
17 NAPA NAPA NAPA 3755 0.044 0.31 YES
18 DNM2 DNM2 DNM2 3763 0.044 0.32 YES
19 AP4E1 AP4E1 AP4E1 3810 0.043 0.34 YES
20 SNX9 SNX9 SNX9 3815 0.043 0.36 YES
21 SNAPIN SNAPIN SNAPIN 3847 0.043 0.37 YES
22 TGOLN2 TGOLN2 TGOLN2 4064 0.039 0.38 YES
23 SNX2 SNX2 SNX2 4139 0.038 0.39 YES
24 TXNDC5 TXNDC5 TXNDC5 4230 0.036 0.4 YES
25 SNX5 SNX5 SNX5 4247 0.036 0.41 YES
26 HIP1R HIP1R HIP1R 4252 0.036 0.42 YES
27 GAK GAK GAK 4313 0.035 0.44 YES
28 PICALM PICALM PICALM 4819 0.028 0.42 YES
29 ARF1 ARF1 ARF1 4920 0.027 0.43 YES
30 IGF2R IGF2R IGF2R 5024 0.026 0.43 YES
31 BLOC1S1 BLOC1S1 BLOC1S1 5125 0.024 0.44 YES
32 STX4 STX4 STX4 5126 0.024 0.44 YES
33 PLDN PLDN PLDN 5145 0.024 0.45 YES
34 AP3B1 AP3B1 AP3B1 5241 0.023 0.46 YES
35 HSPA8 HSPA8 HSPA8 5459 0.02 0.45 YES
36 CLTC CLTC CLTC 5505 0.02 0.46 YES
37 CLTA CLTA CLTA 5667 0.018 0.46 NO
38 GBF1 GBF1 GBF1 5864 0.015 0.45 NO
39 AP4B1 AP4B1 AP4B1 5992 0.014 0.45 NO
40 AP3S1 AP3S1 AP3S1 6113 0.013 0.45 NO
41 VAMP7 VAMP7 VAMP7 6270 0.011 0.45 NO
42 SH3D19 SH3D19 SH3D19 6409 0.0099 0.44 NO
43 M6PR M6PR M6PR 6690 0.0069 0.43 NO
44 CTSZ CTSZ CTSZ 6743 0.0063 0.43 NO
45 PIK3C2A PIK3C2A PIK3C2A 7267 0.0011 0.4 NO
46 DNASE2 DNASE2 DNASE2 7326 0.00038 0.4 NO
47 BLOC1S3 BLOC1S3 BLOC1S3 7496 -0.0016 0.39 NO
48 GNS GNS GNS 7529 -0.0018 0.39 NO
49 SORT1 SORT1 SORT1 7797 -0.0046 0.38 NO
50 VAMP2 VAMP2 VAMP2 7806 -0.0047 0.38 NO
51 CNO CNO CNO 9084 -0.017 0.32 NO
52 OCRL OCRL OCRL 9857 -0.025 0.29 NO
53 AP1M1 AP1M1 AP1M1 9911 -0.026 0.29 NO
54 PUM1 PUM1 PUM1 10107 -0.028 0.29 NO
55 DTNBP1 DTNBP1 DTNBP1 10703 -0.034 0.28 NO
56 AP1S2 AP1S2 AP1S2 12618 -0.062 0.2 NO
57 TPD52L1 TPD52L1 TPD52L1 13071 -0.071 0.2 NO
58 SH3GL2 SH3GL2 SH3GL2 14242 -0.098 0.18 NO
59 DNAJC6 DNAJC6 DNAJC6 15329 -0.13 0.17 NO

Figure S43.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CYTOSOLIC DNA SENSING PATHWAY.

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

genes ES table in pathway: BIOCARTA HIVNEF 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 CPD CPD CPD 1043 0.15 0.0073 YES
2 TBC1D8B TBC1D8B TBC1D8B 1177 0.14 0.06 YES
3 ARRB1 ARRB1 ARRB1 1706 0.11 0.076 YES
4 FTH1 FTH1 FTH1 1727 0.1 0.12 YES
5 TPD52 TPD52 TPD52 2069 0.09 0.14 YES
6 RAB5C RAB5C RAB5C 2583 0.072 0.14 YES
7 AP1B1 AP1B1 AP1B1 2981 0.061 0.14 YES
8 YIPF6 YIPF6 YIPF6 2983 0.06 0.17 YES
9 AP1M2 AP1M2 AP1M2 3017 0.06 0.19 YES
10 AP1G1 AP1G1 AP1G1 3020 0.06 0.22 YES
11 TFRC TFRC TFRC 3105 0.058 0.24 YES
12 VAMP8 VAMP8 VAMP8 3361 0.052 0.25 YES
13 FTL FTL FTL 3379 0.052 0.27 YES
14 AP1S1 AP1S1 AP1S1 3432 0.051 0.29 YES
15 NECAP1 NECAP1 NECAP1 3595 0.047 0.3 YES
16 NAPA NAPA NAPA 3755 0.044 0.31 YES
17 DNM2 DNM2 DNM2 3763 0.044 0.33 YES
18 AP4E1 AP4E1 AP4E1 3810 0.043 0.34 YES
19 SNX9 SNX9 SNX9 3815 0.043 0.36 YES
20 SNAPIN SNAPIN SNAPIN 3847 0.043 0.38 YES
21 TGOLN2 TGOLN2 TGOLN2 4064 0.039 0.38 YES
22 SNX2 SNX2 SNX2 4139 0.038 0.39 YES
23 TXNDC5 TXNDC5 TXNDC5 4230 0.036 0.4 YES
24 SNX5 SNX5 SNX5 4247 0.036 0.42 YES
25 HIP1R HIP1R HIP1R 4252 0.036 0.43 YES
26 GAK GAK GAK 4313 0.035 0.44 YES
27 PICALM PICALM PICALM 4819 0.028 0.43 YES
28 ARF1 ARF1 ARF1 4920 0.027 0.44 YES
29 IGF2R IGF2R IGF2R 5024 0.026 0.44 YES
30 BLOC1S1 BLOC1S1 BLOC1S1 5125 0.024 0.45 YES
31 PLDN PLDN PLDN 5145 0.024 0.46 YES
32 AP3B1 AP3B1 AP3B1 5241 0.023 0.46 YES
33 HSPA8 HSPA8 HSPA8 5459 0.02 0.46 YES
34 CLTC CLTC CLTC 5505 0.02 0.46 YES
35 CLTA CLTA CLTA 5667 0.018 0.46 NO
36 AP4B1 AP4B1 AP4B1 5992 0.014 0.45 NO
37 AP3S1 AP3S1 AP3S1 6113 0.013 0.45 NO
38 VAMP7 VAMP7 VAMP7 6270 0.011 0.44 NO
39 SH3D19 SH3D19 SH3D19 6409 0.0099 0.44 NO
40 PIK3C2A PIK3C2A PIK3C2A 7267 0.0011 0.4 NO
41 BLOC1S3 BLOC1S3 BLOC1S3 7496 -0.0016 0.38 NO
42 SORT1 SORT1 SORT1 7797 -0.0046 0.37 NO
43 VAMP2 VAMP2 VAMP2 7806 -0.0047 0.37 NO
44 CNO CNO CNO 9084 -0.017 0.31 NO
45 OCRL OCRL OCRL 9857 -0.025 0.28 NO
46 AP1M1 AP1M1 AP1M1 9911 -0.026 0.29 NO
47 PUM1 PUM1 PUM1 10107 -0.028 0.29 NO
48 DTNBP1 DTNBP1 DTNBP1 10703 -0.034 0.27 NO
49 AP1S2 AP1S2 AP1S2 12618 -0.062 0.19 NO
50 TPD52L1 TPD52L1 TPD52L1 13071 -0.071 0.2 NO
51 SH3GL2 SH3GL2 SH3GL2 14242 -0.098 0.18 NO
52 DNAJC6 DNAJC6 DNAJC6 15329 -0.13 0.17 NO

Figure S45.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA HIVNEF PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HIVNEF 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 PYK2 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BIRC3 BIRC3 BIRC3 44 0.41 0.16 YES
2 IRAK2 IRAK2 IRAK2 208 0.29 0.27 YES
3 CASP1 CASP1 CASP1 368 0.24 0.36 YES
4 MAPK11 MAPK11 MAPK11 457 0.22 0.44 YES
5 MAPK12 MAPK12 MAPK12 702 0.19 0.5 YES
6 CARD9 CARD9 CARD9 889 0.16 0.56 YES
7 MAPK13 MAPK13 MAPK13 940 0.16 0.62 YES
8 CASP4 CASP4 CASP4 943 0.16 0.68 YES
9 IRAK1 IRAK1 IRAK1 2605 0.071 0.62 NO
10 RIPK2 RIPK2 RIPK2 2895 0.063 0.63 NO
11 CASP8 CASP8 CASP8 3194 0.056 0.63 NO
12 TMEM189-UBE2V1 TMEM189-UBE2V1 TMEM189-UBE2V1 3807 0.043 0.62 NO
13 CYLD CYLD CYLD 4223 0.036 0.61 NO
14 NOD2 NOD2 NOD2 4605 0.031 0.6 NO
15 IKBKG IKBKG IKBKG 4752 0.029 0.6 NO
16 CHUK CHUK CHUK 4784 0.029 0.61 NO
17 TNFAIP3 TNFAIP3 TNFAIP3 6658 0.0073 0.52 NO
18 CASP2 CASP2 CASP2 7463 -0.0011 0.47 NO
19 NOD1 NOD1 NOD1 7501 -0.0016 0.47 NO
20 MAPK14 MAPK14 MAPK14 7668 -0.0034 0.46 NO
21 UBE2N UBE2N UBE2N 8053 -0.007 0.45 NO
22 BIRC2 BIRC2 BIRC2 8085 -0.0072 0.45 NO
23 TAB1 TAB1 TAB1 8338 -0.0095 0.44 NO
24 TAB2 TAB2 TAB2 8835 -0.015 0.42 NO
25 IKBKB IKBKB IKBKB 8911 -0.015 0.42 NO
26 TAB3 TAB3 TAB3 8954 -0.016 0.42 NO
27 TRAF6 TRAF6 TRAF6 10940 -0.037 0.33 NO
28 CASP9 CASP9 CASP9 12218 -0.056 0.28 NO
29 MAP3K7 MAP3K7 MAP3K7 12394 -0.059 0.3 NO
30 MAP2K6 MAP2K6 MAP2K6 13853 -0.088 0.25 NO

Figure S47.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PYK2 PATHWAY.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: ST TUMOR NECROSIS FACTOR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 XDH XDH XDH 2 0.6 0.1 YES
2 GDA GDA GDA 6 0.54 0.19 YES
3 CDA CDA CDA 71 0.37 0.25 YES
4 UPP1 UPP1 UPP1 254 0.28 0.29 YES
5 DPYD DPYD DPYD 576 0.2 0.31 YES
6 TYMP TYMP TYMP 642 0.2 0.34 YES
7 GSR GSR GSR 793 0.18 0.36 YES
8 GLRX GLRX GLRX 846 0.17 0.38 YES
9 RRM2 RRM2 RRM2 874 0.17 0.41 YES
10 AMPD1 AMPD1 AMPD1 1096 0.15 0.42 YES
11 NT5E NT5E NT5E 1363 0.13 0.43 YES
12 CMPK1 CMPK1 CMPK1 1367 0.13 0.45 YES
13 UPB1 UPB1 UPB1 1878 0.098 0.44 YES
14 TK1 TK1 TK1 2208 0.085 0.44 YES
15 AK1 AK1 AK1 2265 0.082 0.45 YES
16 PNP PNP PNP 2282 0.082 0.46 YES
17 TK2 TK2 TK2 2393 0.078 0.47 YES
18 TXNRD1 TXNRD1 TXNRD1 2457 0.076 0.48 YES
19 CAT CAT CAT 2477 0.075 0.49 YES
20 APRT APRT APRT 2607 0.071 0.5 YES
21 IMPDH1 IMPDH1 IMPDH1 2653 0.07 0.51 YES
22 NT5C3 NT5C3 NT5C3 2729 0.067 0.51 YES
23 DCK DCK DCK 3018 0.06 0.51 NO
24 GPX1 GPX1 GPX1 3409 0.051 0.5 NO
25 ATIC ATIC ATIC 3587 0.047 0.49 NO
26 HPRT1 HPRT1 HPRT1 3784 0.044 0.49 NO
27 PPAT PPAT PPAT 3868 0.042 0.49 NO
28 GUK1 GUK1 GUK1 3967 0.04 0.5 NO
29 UCK2 UCK2 UCK2 4167 0.037 0.49 NO
30 DHODH DHODH DHODH 4185 0.037 0.5 NO
31 DTYMK DTYMK DTYMK 4259 0.036 0.5 NO
32 DCTD DCTD DCTD 4308 0.035 0.5 NO
33 RRM1 RRM1 RRM1 4370 0.034 0.5 NO
34 TYMS TYMS TYMS 4598 0.031 0.5 NO
35 ADSS ADSS ADSS 4684 0.03 0.5 NO
36 TXN TXN TXN 4805 0.028 0.5 NO
37 NT5C2 NT5C2 NT5C2 4938 0.027 0.49 NO
38 ADK ADK ADK 5183 0.024 0.48 NO
39 NME1 NME1 NME1 5565 0.019 0.47 NO
40 UCK1 UCK1 UCK1 5570 0.019 0.47 NO
41 AK2 AK2 AK2 5702 0.017 0.46 NO
42 DUT DUT DUT 5719 0.017 0.47 NO
43 NME1-NME2 NME1-NME2 NME1-NME2 5798 0.016 0.47 NO
44 GART GART GART 5804 0.016 0.47 NO
45 NT5C NT5C NT5C 5875 0.015 0.47 NO
46 UMPS UMPS UMPS 5884 0.015 0.47 NO
47 GMPS GMPS GMPS 6793 0.0058 0.42 NO
48 NME2 NME2 NME2 6922 0.0046 0.42 NO
49 ADSL ADSL ADSL 7230 0.0015 0.4 NO
50 CTPS CTPS CTPS 7364 0.000012 0.39 NO
51 ADA ADA ADA 7433 -0.00075 0.39 NO
52 RRM2B RRM2B RRM2B 7465 -0.0011 0.39 NO
53 GMPR2 GMPR2 GMPR2 7699 -0.0036 0.37 NO
54 PAICS PAICS PAICS 7844 -0.005 0.37 NO
55 IMPDH2 IMPDH2 IMPDH2 8641 -0.012 0.33 NO
56 DGUOK DGUOK DGUOK 9031 -0.017 0.31 NO
57 NME4 NME4 NME4 9525 -0.021 0.28 NO
58 PFAS PFAS PFAS 9988 -0.026 0.26 NO
59 CAD CAD CAD 10582 -0.033 0.24 NO
60 AMPD2 AMPD2 AMPD2 11554 -0.046 0.19 NO
61 DPYS DPYS DPYS 11666 -0.047 0.2 NO
62 CTPS2 CTPS2 CTPS2 12562 -0.062 0.16 NO
63 AMPD3 AMPD3 AMPD3 13138 -0.073 0.14 NO
64 UPP2 UPP2 UPP2 13890 -0.089 0.11 NO
65 NT5M NT5M NT5M 14302 -0.1 0.11 NO
66 GMPR GMPR GMPR 14531 -0.11 0.11 NO
67 ADAL ADAL ADAL 14949 -0.12 0.11 NO
68 AK5 AK5 AK5 15457 -0.14 0.11 NO
69 ADSSL1 ADSSL1 ADSSL1 15991 -0.16 0.1 NO
70 NT5C1B NT5C1B NT5C1B 16536 -0.19 0.11 NO

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

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: ST TUMOR NECROSIS FACTOR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: ST INTERLEUKIN 4 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BIRC3 BIRC3 BIRC3 44 0.41 0.12 YES
2 MAP3K5 MAP3K5 MAP3K5 367 0.24 0.18 YES
3 FASLG FASLG FASLG 571 0.21 0.23 YES
4 FAS FAS FAS 778 0.18 0.27 YES
5 TNF TNF TNF 1226 0.14 0.29 YES
6 TRADD TRADD TRADD 1673 0.11 0.3 YES
7 LMNA LMNA LMNA 1745 0.1 0.33 YES
8 MAP3K14 MAP3K14 MAP3K14 2141 0.087 0.33 YES
9 ARHGDIB ARHGDIB ARHGDIB 2214 0.084 0.36 YES
10 BID BID BID 2468 0.075 0.36 YES
11 CRADD CRADD CRADD 2504 0.074 0.38 YES
12 CFLAR CFLAR CFLAR 2704 0.068 0.4 YES
13 BAG4 BAG4 BAG4 2851 0.064 0.41 YES
14 NFKB1 NFKB1 NFKB1 3171 0.056 0.41 YES
15 CASP8 CASP8 CASP8 3194 0.056 0.42 YES
16 TRAF1 TRAF1 TRAF1 3282 0.054 0.43 YES
17 RB1 RB1 RB1 3438 0.05 0.44 YES
18 CASP3 CASP3 CASP3 3527 0.049 0.45 YES
19 TNFRSF1B TNFRSF1B TNFRSF1B 4049 0.039 0.44 YES
20 ACTG1 ACTG1 ACTG1 4066 0.039 0.45 YES
21 TNFRSF1A TNFRSF1A TNFRSF1A 4115 0.038 0.46 YES
22 APAF1 APAF1 APAF1 4283 0.036 0.46 YES
23 FADD FADD FADD 4408 0.034 0.46 YES
24 CASP7 CASP7 CASP7 4474 0.033 0.47 YES
25 TRAF2 TRAF2 TRAF2 4582 0.032 0.47 YES
26 NFKBIA NFKBIA NFKBIA 4601 0.031 0.48 YES
27 XIAP XIAP XIAP 4711 0.03 0.48 YES
28 CHUK CHUK CHUK 4784 0.029 0.49 YES
29 RIPK1 RIPK1 RIPK1 4924 0.027 0.49 YES
30 DFFB DFFB DFFB 5550 0.019 0.46 NO
31 CYCS CYCS CYCS 5567 0.019 0.46 NO
32 LMNB2 LMNB2 LMNB2 6028 0.014 0.44 NO
33 MDM2 MDM2 MDM2 6314 0.011 0.43 NO
34 CASP6 CASP6 CASP6 6374 0.01 0.43 NO
35 DAXX DAXX DAXX 6482 0.0091 0.43 NO
36 PSEN1 PSEN1 PSEN1 6687 0.007 0.42 NO
37 PRKCD PRKCD PRKCD 7428 -0.00068 0.38 NO
38 CASP2 CASP2 CASP2 7463 -0.0011 0.38 NO
39 MAP2K7 MAP2K7 MAP2K7 7630 -0.0029 0.37 NO
40 SPTAN1 SPTAN1 SPTAN1 7665 -0.0033 0.37 NO
41 DFFA DFFA DFFA 7727 -0.0039 0.37 NO
42 PAK2 PAK2 PAK2 7802 -0.0046 0.36 NO
43 RELA RELA RELA 7946 -0.006 0.36 NO
44 CDK11B CDK11B CDK11B 7948 -0.006 0.36 NO
45 LMNB1 LMNB1 LMNB1 7983 -0.0063 0.36 NO
46 BIRC2 BIRC2 BIRC2 8085 -0.0072 0.36 NO
47 PARP1 PARP1 PARP1 8601 -0.012 0.33 NO
48 RASA1 RASA1 RASA1 8604 -0.012 0.34 NO
49 CDK11A CDK11A CDK11A 8673 -0.013 0.34 NO
50 GSN GSN GSN 9746 -0.024 0.29 NO
51 NUMA1 NUMA1 NUMA1 10909 -0.037 0.24 NO
52 PTK2 PTK2 PTK2 10944 -0.037 0.24 NO
53 MAP3K1 MAP3K1 MAP3K1 11272 -0.042 0.24 NO
54 CASP9 CASP9 CASP9 12218 -0.056 0.2 NO
55 MAPK8 MAPK8 MAPK8 12245 -0.056 0.22 NO
56 PRKDC PRKDC PRKDC 12978 -0.069 0.2 NO
57 PSEN2 PSEN2 PSEN2 13198 -0.074 0.21 NO
58 BCL2 BCL2 BCL2 17315 -0.25 0.066 NO

Figure S51.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST INTERLEUKIN 4 PATHWAY.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: ST INTERLEUKIN 4 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID TNFPATHWAY

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 BIRC3 BIRC3 BIRC3 44 0.41 0.1 YES
2 GZMB GZMB GZMB 274 0.27 0.16 YES
3 PRF1 PRF1 PRF1 276 0.27 0.23 YES
4 CASP1 CASP1 CASP1 368 0.24 0.29 YES
5 CASP4 CASP4 CASP4 943 0.16 0.3 YES
6 CASP10 CASP10 CASP10 1079 0.15 0.33 YES
7 TNF TNF TNF 1226 0.14 0.36 YES
8 TRADD TRADD TRADD 1673 0.11 0.36 YES
9 LMNA LMNA LMNA 1745 0.1 0.39 YES
10 KRT18 KRT18 KRT18 1775 0.1 0.41 YES
11 SREBF1 SREBF1 SREBF1 1961 0.094 0.43 YES
12 TFAP2A TFAP2A TFAP2A 2154 0.086 0.44 YES
13 SLK SLK SLK 2199 0.085 0.46 YES
14 ARHGDIB ARHGDIB ARHGDIB 2214 0.084 0.48 YES
15 BID BID BID 2468 0.075 0.49 YES
16 CRADD CRADD CRADD 2504 0.074 0.5 YES
17 CASP8 CASP8 CASP8 3194 0.056 0.48 NO
18 CASP3 CASP3 CASP3 3527 0.049 0.48 NO
19 TNFRSF1A TNFRSF1A TNFRSF1A 4115 0.038 0.45 NO
20 APAF1 APAF1 APAF1 4283 0.036 0.45 NO
21 LIMK1 LIMK1 LIMK1 4414 0.034 0.46 NO
22 CASP7 CASP7 CASP7 4474 0.033 0.46 NO
23 TRAF2 TRAF2 TRAF2 4582 0.032 0.46 NO
24 XIAP XIAP XIAP 4711 0.03 0.46 NO
25 BAX BAX BAX 4852 0.028 0.46 NO
26 RIPK1 RIPK1 RIPK1 4924 0.027 0.47 NO
27 MADD MADD MADD 5348 0.022 0.45 NO
28 DFFB DFFB DFFB 5550 0.019 0.44 NO
29 CYCS CYCS CYCS 5567 0.019 0.45 NO
30 LMNB2 LMNB2 LMNB2 6028 0.014 0.43 NO
31 TOP1 TOP1 TOP1 6052 0.014 0.43 NO
32 CASP6 CASP6 CASP6 6374 0.01 0.41 NO
33 APP APP APP 6979 0.004 0.38 NO
34 CASP2 CASP2 CASP2 7463 -0.0011 0.36 NO
35 SPTAN1 SPTAN1 SPTAN1 7665 -0.0033 0.35 NO
36 DFFA DFFA DFFA 7727 -0.0039 0.34 NO
37 LMNB1 LMNB1 LMNB1 7983 -0.0063 0.33 NO
38 DIABLO DIABLO DIABLO 7999 -0.0065 0.33 NO
39 BIRC2 BIRC2 BIRC2 8085 -0.0072 0.33 NO
40 PARP1 PARP1 PARP1 8601 -0.012 0.3 NO
41 GSN GSN GSN 9746 -0.024 0.25 NO
42 NUMA1 NUMA1 NUMA1 10909 -0.037 0.2 NO
43 PTK2 PTK2 PTK2 10944 -0.037 0.2 NO
44 MAP3K1 MAP3K1 MAP3K1 11272 -0.042 0.2 NO
45 ACTA1 ACTA1 ACTA1 11528 -0.045 0.2 NO
46 CASP9 CASP9 CASP9 12218 -0.056 0.17 NO
47 CFL2 CFL2 CFL2 12594 -0.062 0.17 NO
48 SATB1 SATB1 SATB1 13400 -0.078 0.14 NO
49 VIM VIM VIM 14694 -0.11 0.1 NO
50 GAS2 GAS2 GAS2 15740 -0.15 0.086 NO
51 BCL2 BCL2 BCL2 17315 -0.25 0.066 NO

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

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

genes ES table in pathway: PID P53DOWNSTREAMPATHWAY

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 BIRC3 BIRC3 BIRC3 44 0.41 0.15 YES
2 MAP3K5 MAP3K5 MAP3K5 367 0.24 0.22 YES
3 FASLG FASLG FASLG 571 0.21 0.28 YES
4 CD247 CD247 CD247 584 0.2 0.35 YES
5 FAS FAS FAS 778 0.18 0.41 YES
6 TNF TNF TNF 1226 0.14 0.43 YES
7 TRADD TRADD TRADD 1673 0.11 0.45 YES
8 MAP3K14 MAP3K14 MAP3K14 2141 0.087 0.46 YES
9 BID BID BID 2468 0.075 0.46 YES
10 CRADD CRADD CRADD 2504 0.074 0.49 YES
11 CFLAR CFLAR CFLAR 2704 0.068 0.5 YES
12 BAG4 BAG4 BAG4 2851 0.064 0.52 YES
13 NFKB1 NFKB1 NFKB1 3171 0.056 0.52 YES
14 CASP8 CASP8 CASP8 3194 0.056 0.54 YES
15 TRAF1 TRAF1 TRAF1 3282 0.054 0.56 YES
16 CASP3 CASP3 CASP3 3527 0.049 0.56 YES
17 TNFRSF1A TNFRSF1A TNFRSF1A 4115 0.038 0.54 YES
18 APAF1 APAF1 APAF1 4283 0.036 0.55 YES
19 FADD FADD FADD 4408 0.034 0.55 YES
20 CASP7 CASP7 CASP7 4474 0.033 0.56 YES
21 TRAF2 TRAF2 TRAF2 4582 0.032 0.56 YES
22 NFKBIA NFKBIA NFKBIA 4601 0.031 0.58 YES
23 CHUK CHUK CHUK 4784 0.029 0.58 YES
24 RIPK1 RIPK1 RIPK1 4924 0.027 0.58 YES
25 DFFB DFFB DFFB 5550 0.019 0.55 NO
26 CYCS CYCS CYCS 5567 0.019 0.56 NO
27 CASP6 CASP6 CASP6 6374 0.01 0.52 NO
28 DAXX DAXX DAXX 6482 0.0091 0.52 NO
29 CASP2 CASP2 CASP2 7463 -0.0011 0.46 NO
30 MAP2K7 MAP2K7 MAP2K7 7630 -0.0029 0.46 NO
31 DFFA DFFA DFFA 7727 -0.0039 0.45 NO
32 RELA RELA RELA 7946 -0.006 0.44 NO
33 CASP9 CASP9 CASP9 12218 -0.056 0.23 NO
34 MAPK8 MAPK8 MAPK8 12245 -0.056 0.25 NO
35 BCL2 BCL2 BCL2 17315 -0.25 0.065 NO

Figure S55.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID P53DOWNSTREAMPATHWAY.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: PID P53DOWNSTREAMPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID HIVNEFPATHWAY

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 PI3 PI3 PI3 32 0.42 0.21 YES
2 SERPINA4 SERPINA4 SERPINA4 271 0.27 0.33 YES
3 IL2RG IL2RG IL2RG 456 0.22 0.43 YES
4 IL4R IL4R IL4R 926 0.16 0.48 YES
5 NR0B2 NR0B2 NR0B2 1335 0.13 0.53 YES
6 INPP5D INPP5D INPP5D 1812 0.1 0.55 YES
7 CISH CISH CISH 2467 0.075 0.55 YES
8 SRC SRC SRC 2571 0.072 0.58 YES
9 JAK3 JAK3 JAK3 2608 0.071 0.62 YES
10 JAK2 JAK2 JAK2 3139 0.057 0.62 YES
11 STAT6 STAT6 STAT6 3772 0.044 0.6 YES
12 GRB2 GRB2 GRB2 3837 0.043 0.62 YES
13 IARS IARS IARS 4069 0.039 0.63 YES
14 JAK1 JAK1 JAK1 5961 0.014 0.53 NO
15 SHC1 SHC1 SHC1 6663 0.0072 0.5 NO
16 TYK2 TYK2 TYK2 7102 0.0028 0.48 NO
17 SOS2 SOS2 SOS2 7431 -0.00072 0.46 NO
18 RPS6KB1 RPS6KB1 RPS6KB1 7689 -0.0036 0.45 NO
19 AKT1 AKT1 AKT1 7968 -0.0062 0.43 NO
20 AKT3 AKT3 AKT3 8549 -0.011 0.41 NO
21 PIK3CA PIK3CA PIK3CA 8847 -0.015 0.4 NO
22 IL13RA1 IL13RA1 IL13RA1 9375 -0.02 0.38 NO
23 AKT2 AKT2 AKT2 11115 -0.039 0.31 NO
24 PPP1R13B PPP1R13B PPP1R13B 11740 -0.048 0.3 NO
25 SOS1 SOS1 SOS1 12289 -0.057 0.3 NO
26 IL4 IL4 IL4 13698 -0.085 0.26 NO

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

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

genes ES table in pathway: PID CASPASE PATHWAY

Table 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 SAA1 SAA1 SAA1 66 0.37 0.071 YES
2 S100A12 S100A12 S100A12 147 0.32 0.13 YES
3 IRAK2 IRAK2 IRAK2 208 0.29 0.18 YES
4 DUSP4 DUSP4 DUSP4 280 0.27 0.23 YES
5 MAPK11 MAPK11 MAPK11 457 0.22 0.27 YES
6 ZBP1 ZBP1 ZBP1 693 0.19 0.29 YES
7 TLR3 TLR3 TLR3 817 0.17 0.32 YES
8 RIPK3 RIPK3 RIPK3 845 0.17 0.36 YES
9 TICAM1 TICAM1 TICAM1 1084 0.15 0.37 YES
10 FOS FOS FOS 1565 0.11 0.37 YES
11 DUSP3 DUSP3 DUSP3 1694 0.11 0.38 YES
12 RPS6KA1 RPS6KA1 RPS6KA1 1957 0.094 0.39 YES
13 IKBKE IKBKE IKBKE 2049 0.091 0.4 YES
14 MAP2K3 MAP2K3 MAP2K3 2132 0.087 0.41 YES
15 MAP2K1 MAP2K1 MAP2K1 2510 0.074 0.41 YES
16 IRAK1 IRAK1 IRAK1 2605 0.071 0.42 YES
17 MAPKAPK3 MAPKAPK3 MAPKAPK3 2619 0.071 0.43 YES
18 RIPK2 RIPK2 RIPK2 2895 0.063 0.43 YES
19 NFKB2 NFKB2 NFKB2 2927 0.062 0.44 YES
20 RPS6KA3 RPS6KA3 RPS6KA3 2982 0.06 0.45 YES
21 DUSP6 DUSP6 DUSP6 3202 0.055 0.45 NO
22 NFKBIB NFKBIB NFKBIB 3668 0.046 0.43 NO
23 S100B S100B S100B 4202 0.037 0.41 NO
24 TBK1 TBK1 TBK1 4371 0.034 0.41 NO
25 PPP2CB PPP2CB PPP2CB 4403 0.034 0.41 NO
26 NFKBIA NFKBIA NFKBIA 4601 0.031 0.41 NO
27 NOD2 NOD2 NOD2 4605 0.031 0.41 NO
28 MEF2C MEF2C MEF2C 4708 0.03 0.41 NO
29 IKBKG IKBKG IKBKG 4752 0.029 0.42 NO
30 CHUK CHUK CHUK 4784 0.029 0.42 NO
31 RIPK1 RIPK1 RIPK1 4924 0.027 0.42 NO
32 ATF1 ATF1 ATF1 5124 0.024 0.41 NO
33 MAPK1 MAPK1 MAPK1 5251 0.023 0.41 NO
34 IRF7 IRF7 IRF7 5416 0.021 0.41 NO
35 MAP2K4 MAP2K4 MAP2K4 5501 0.02 0.41 NO
36 MAP2K2 MAP2K2 MAP2K2 5777 0.016 0.39 NO
37 PPP2CA PPP2CA PPP2CA 5831 0.016 0.39 NO
38 DUSP7 DUSP7 DUSP7 5847 0.016 0.4 NO
39 MEF2A MEF2A MEF2A 5931 0.015 0.4 NO
40 MAPK9 MAPK9 MAPK9 6068 0.013 0.39 NO
41 MAPKAPK2 MAPKAPK2 MAPKAPK2 6129 0.013 0.39 NO
42 PPP2R1B PPP2R1B PPP2R1B 6332 0.01 0.38 NO
43 IRF3 IRF3 IRF3 6576 0.0081 0.37 NO
44 MAPK3 MAPK3 MAPK3 6829 0.0055 0.36 NO
45 APP APP APP 6979 0.004 0.35 NO
46 NOD1 NOD1 NOD1 7501 -0.0016 0.32 NO
47 MAP2K7 MAP2K7 MAP2K7 7630 -0.0029 0.32 NO
48 PPP2R1A PPP2R1A PPP2R1A 7648 -0.0031 0.32 NO
49 MAPK14 MAPK14 MAPK14 7668 -0.0034 0.32 NO
50 RELA RELA RELA 7946 -0.006 0.3 NO
51 TAB1 TAB1 TAB1 8338 -0.0095 0.28 NO
52 CDK1 CDK1 CDK1 8613 -0.012 0.27 NO
53 HMGB1 HMGB1 HMGB1 8671 -0.013 0.27 NO
54 TAB2 TAB2 TAB2 8835 -0.015 0.26 NO
55 IKBKB IKBKB IKBKB 8911 -0.015 0.26 NO
56 TAB3 TAB3 TAB3 8954 -0.016 0.26 NO
57 ATF2 ATF2 ATF2 8996 -0.016 0.26 NO
58 MAPK7 MAPK7 MAPK7 9341 -0.019 0.25 NO
59 PPP2R5D PPP2R5D PPP2R5D 9390 -0.02 0.25 NO
60 UBA52 UBA52 UBA52 9632 -0.023 0.24 NO
61 ELK1 ELK1 ELK1 9648 -0.023 0.24 NO
62 RPS27A RPS27A RPS27A 10882 -0.036 0.19 NO
63 TRAF6 TRAF6 TRAF6 10940 -0.037 0.19 NO
64 CREB1 CREB1 CREB1 11162 -0.04 0.19 NO
65 RPS6KA2 RPS6KA2 RPS6KA2 11392 -0.043 0.18 NO
66 MAPK8 MAPK8 MAPK8 12245 -0.056 0.15 NO
67 MAP3K7 MAP3K7 MAP3K7 12394 -0.059 0.15 NO
68 JUN JUN JUN 13540 -0.082 0.1 NO
69 MAP2K6 MAP2K6 MAP2K6 13853 -0.088 0.11 NO
70 AGER AGER AGER 15850 -0.15 0.028 NO
71 RPS6KA5 RPS6KA5 RPS6KA5 16904 -0.22 0.014 NO
72 MAPK10 MAPK10 MAPK10 18183 -0.37 0.018 NO

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

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

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 clus4 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG GLYCOLYSIS GLUCONEOGENESIS 60 genes.ES.table 0.51 1.7 0.012 1 0.83 0.25 0.14 0.22 1 0.52
KEGG FATTY ACID METABOLISM 40 genes.ES.table 0.52 1.6 0.027 1 0.89 0.32 0.19 0.26 1 0.5
KEGG TYROSINE METABOLISM 41 genes.ES.table 0.57 1.5 0.034 1 0.96 0.34 0.11 0.3 1 0.52
KEGG GLUTATHIONE METABOLISM 47 genes.ES.table 0.55 1.7 0.014 1 0.75 0.4 0.19 0.33 1 0.53
KEGG STARCH AND SUCROSE METABOLISM 36 genes.ES.table 0.55 1.5 0.029 1 0.96 0.31 0.14 0.26 1 0.56
KEGG ETHER LIPID METABOLISM 31 genes.ES.table 0.52 1.5 0.028 1 0.98 0.48 0.22 0.38 1 0.57
KEGG BUTANOATE METABOLISM 31 genes.ES.table 0.46 1.5 0.093 1 1 0.48 0.27 0.35 1 0.53
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 57 genes.ES.table 0.61 1.5 0.035 1 0.96 0.56 0.18 0.46 1 0.57
KEGG DRUG METABOLISM CYTOCHROME P450 59 genes.ES.table 0.66 1.7 0.0062 1 0.85 0.58 0.16 0.49 0.93 0.48
KEGG ABC TRANSPORTERS 44 genes.ES.table 0.56 1.5 0.018 1 0.98 0.43 0.16 0.36 1 0.56
genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 DNAI1 DNAI1 DNAI1 28 1.2 0.089 YES
2 DNAH3 DNAH3 DNAH3 66 1.1 0.17 YES
3 DNAI2 DNAI2 DNAI2 157 0.87 0.23 YES
4 DNAH2 DNAH2 DNAH2 258 0.69 0.27 YES
5 GRM5 GRM5 GRM5 285 0.65 0.32 YES
6 DNALI1 DNALI1 DNALI1 530 0.45 0.34 YES
7 GRIN1 GRIN1 GRIN1 843 0.33 0.35 YES
8 PLCB1 PLCB1 PLCB1 1086 0.28 0.36 YES
9 CREB3L1 CREB3L1 CREB3L1 1333 0.24 0.36 YES
10 DNAL1 DNAL1 DNAL1 1426 0.23 0.37 YES
11 PLCB4 PLCB4 PLCB4 1546 0.22 0.38 YES
12 DNAH1 DNAH1 DNAH1 1663 0.2 0.39 YES
13 CREB3L4 CREB3L4 CREB3L4 1715 0.2 0.4 YES
14 DNAL4 DNAL4 DNAL4 2075 0.17 0.4 NO
15 PLCB2 PLCB2 PLCB2 2302 0.16 0.39 NO
16 IFT57 IFT57 IFT57 3030 0.12 0.36 NO
17 BDNF BDNF BDNF 3040 0.12 0.37 NO
18 COX6B2 COX6B2 COX6B2 3083 0.12 0.38 NO
19 CREB5 CREB5 CREB5 3093 0.12 0.39 NO
20 ITPR1 ITPR1 ITPR1 3194 0.11 0.39 NO
21 COX8C COX8C COX8C 3517 0.098 0.38 NO
22 UQCR11 UQCR11 UQCR11 3798 0.089 0.37 NO
23 PPARG PPARG PPARG 3819 0.088 0.38 NO
24 UQCRHL UQCRHL UQCRHL 3837 0.088 0.38 NO
25 POLR2I POLR2I POLR2I 3863 0.087 0.39 NO
26 CREB3L2 CREB3L2 CREB3L2 4003 0.083 0.38 NO
27 UQCRH UQCRH UQCRH 4126 0.08 0.38 NO
28 POLR2J2 POLR2J2 POLR2J2 4277 0.075 0.38 NO
29 NDUFA7 NDUFA7 NDUFA7 4482 0.07 0.38 NO
30 NDUFS7 NDUFS7 NDUFS7 4532 0.069 0.38 NO
31 COX4I1 COX4I1 COX4I1 4592 0.067 0.38 NO
32 NDUFA3 NDUFA3 NDUFA3 4627 0.067 0.38 NO
33 ATP5D ATP5D ATP5D 4972 0.059 0.37 NO
34 COX7C COX7C COX7C 5100 0.056 0.36 NO
35 COX7A1 COX7A1 COX7A1 5148 0.055 0.37 NO
36 NDUFC1 NDUFC1 NDUFC1 5257 0.053 0.36 NO
37 PPID PPID PPID 5276 0.052 0.37 NO
38 SLC25A6 SLC25A6 SLC25A6 5302 0.052 0.37 NO
39 SLC25A4 SLC25A4 SLC25A4 5454 0.049 0.36 NO
40 COX6A1 COX6A1 COX6A1 5502 0.048 0.37 NO
41 ATP5G2 ATP5G2 ATP5G2 5541 0.047 0.37 NO
42 NDUFA2 NDUFA2 NDUFA2 5635 0.045 0.37 NO
43 NDUFS5 NDUFS5 NDUFS5 5802 0.042 0.36 NO
44 UQCRQ UQCRQ UQCRQ 5910 0.04 0.36 NO
45 NDUFB1 NDUFB1 NDUFB1 5929 0.04 0.36 NO
46 GPX1 GPX1 GPX1 6026 0.038 0.36 NO
47 AP2B1 AP2B1 AP2B1 6037 0.038 0.36 NO
48 COX5A COX5A COX5A 6065 0.038 0.36 NO
49 SDHA SDHA SDHA 6126 0.037 0.36 NO
50 UQCR10 UQCR10 UQCR10 6230 0.035 0.36 NO
51 NRF1 NRF1 NRF1 6231 0.035 0.36 NO
52 AP2A2 AP2A2 AP2A2 6259 0.035 0.36 NO
53 POLR2E POLR2E POLR2E 6273 0.035 0.36 NO
54 COX7B COX7B COX7B 6284 0.035 0.36 NO
55 ATP5F1 ATP5F1 ATP5F1 6292 0.034 0.37 NO
56 NDUFA8 NDUFA8 NDUFA8 6443 0.032 0.36 NO
57 NDUFB8 NDUFB8 NDUFB8 6502 0.032 0.36 NO
58 AP2S1 AP2S1 AP2S1 6519 0.031 0.36 NO
59 NDUFA1 NDUFA1 NDUFA1 6526 0.031 0.36 NO
60 POLR2G POLR2G POLR2G 6590 0.03 0.36 NO
61 BBC3 BBC3 BBC3 6836 0.027 0.35 NO
62 TP53 TP53 TP53 6841 0.027 0.35 NO
63 CLTB CLTB CLTB 6859 0.026 0.35 NO
64 NDUFV3 NDUFV3 NDUFV3 7193 0.022 0.34 NO
65 UQCRC1 UQCRC1 UQCRC1 7204 0.022 0.34 NO
66 UQCRC2 UQCRC2 UQCRC2 7213 0.022 0.34 NO
67 VDAC3 VDAC3 VDAC3 7354 0.02 0.33 NO
68 CLTA CLTA CLTA 7356 0.02 0.33 NO
69 POLR2J POLR2J POLR2J 7438 0.019 0.33 NO
70 NDUFS8 NDUFS8 NDUFS8 7445 0.018 0.33 NO
71 GNAQ GNAQ GNAQ 7491 0.018 0.33 NO
72 ATP5C1 ATP5C1 ATP5C1 7537 0.017 0.33 NO
73 NDUFS3 NDUFS3 NDUFS3 7626 0.016 0.33 NO
74 CASP9 CASP9 CASP9 7710 0.015 0.32 NO
75 ATP5A1 ATP5A1 ATP5A1 7746 0.015 0.32 NO
76 DCTN1 DCTN1 DCTN1 7764 0.014 0.32 NO
77 SOD1 SOD1 SOD1 7784 0.014 0.32 NO
78 NDUFB10 NDUFB10 NDUFB10 7822 0.014 0.32 NO
79 UQCRB UQCRB UQCRB 7855 0.013 0.32 NO
80 POLR2J3 POLR2J3 POLR2J3 7868 0.013 0.32 NO
81 CASP8 CASP8 CASP8 7950 0.012 0.32 NO
82 NDUFA10 NDUFA10 NDUFA10 8042 0.011 0.31 NO
83 NDUFC2 NDUFC2 NDUFC2 8060 0.011 0.31 NO
84 SIN3A SIN3A SIN3A 8077 0.011 0.31 NO
85 COX6C COX6C COX6C 8235 0.0086 0.3 NO
86 COX7A2 COX7A2 COX7A2 8303 0.0078 0.3 NO
87 NDUFA6 NDUFA6 NDUFA6 8318 0.0077 0.3 NO
88 ATP5E ATP5E ATP5E 8328 0.0076 0.3 NO
89 COX8A COX8A COX8A 8476 0.0059 0.29 NO
90 NDUFS2 NDUFS2 NDUFS2 8487 0.0057 0.29 NO
91 NDUFA9 NDUFA9 NDUFA9 8554 0.0051 0.29 NO
92 NDUFA5 NDUFA5 NDUFA5 8561 0.005 0.29 NO
93 COX6B1 COX6B1 COX6B1 8614 0.0044 0.29 NO
94 DCTN4 DCTN4 DCTN4 8621 0.0044 0.29 NO
95 AP2A1 AP2A1 AP2A1 8633 0.0043 0.29 NO
96 NDUFS4 NDUFS4 NDUFS4 8768 0.0029 0.28 NO
97 NDUFB2 NDUFB2 NDUFB2 8867 0.0016 0.28 NO
98 CASP3 CASP3 CASP3 8871 0.0016 0.28 NO
99 POLR2L POLR2L POLR2L 8899 0.0013 0.28 NO
100 SOD2 SOD2 SOD2 8914 0.0011 0.27 NO
101 EP300 EP300 EP300 9171 -0.0019 0.26 NO
102 BAX BAX BAX 9215 -0.0024 0.26 NO
103 NDUFA4 NDUFA4 NDUFA4 9282 -0.0032 0.26 NO
104 CREB3 CREB3 CREB3 9382 -0.0043 0.25 NO
105 CREBBP CREBBP CREBBP 9479 -0.0055 0.24 NO
106 VDAC2 VDAC2 VDAC2 9541 -0.0061 0.24 NO
107 SP1 SP1 SP1 9612 -0.0068 0.24 NO
108 HIP1 HIP1 HIP1 9657 -0.0073 0.24 NO
109 ATP5G1 ATP5G1 ATP5G1 9829 -0.0089 0.23 NO
110 NDUFV1 NDUFV1 NDUFV1 10023 -0.011 0.22 NO
111 COX7A2L COX7A2L COX7A2L 10060 -0.011 0.22 NO
112 CYC1 CYC1 CYC1 10104 -0.012 0.22 NO
113 HDAC1 HDAC1 HDAC1 10147 -0.012 0.21 NO
114 NDUFB4 NDUFB4 NDUFB4 10189 -0.012 0.21 NO
115 VDAC1 VDAC1 VDAC1 10202 -0.013 0.21 NO
116 CREB3L3 CREB3L3 CREB3L3 10340 -0.014 0.21 NO
117 COX5B COX5B COX5B 10381 -0.014 0.21 NO
118 ATP5O ATP5O ATP5O 10421 -0.015 0.2 NO
119 CLTC CLTC CLTC 10470 -0.015 0.2 NO
120 DCTN2 DCTN2 DCTN2 10473 -0.015 0.2 NO
121 SDHC SDHC SDHC 10485 -0.015 0.2 NO
122 NDUFB7 NDUFB7 NDUFB7 10609 -0.017 0.2 NO
123 NDUFB5 NDUFB5 NDUFB5 10685 -0.018 0.2 NO
124 POLR2H POLR2H POLR2H 10730 -0.018 0.2 NO
125 NDUFAB1 NDUFAB1 NDUFAB1 10750 -0.019 0.2 NO
126 NDUFS6 NDUFS6 NDUFS6 10830 -0.019 0.19 NO
127 POLR2A POLR2A POLR2A 10840 -0.019 0.19 NO
128 NDUFV2 NDUFV2 NDUFV2 10865 -0.02 0.19 NO
129 SDHB SDHB SDHB 10868 -0.02 0.2 NO
130 POLR2C POLR2C POLR2C 10936 -0.02 0.19 NO
131 AP2M1 AP2M1 AP2M1 11008 -0.021 0.19 NO
132 POLR2B POLR2B POLR2B 11204 -0.024 0.18 NO
133 TGM2 TGM2 TGM2 11335 -0.025 0.18 NO
134 ATP5B ATP5B ATP5B 11406 -0.026 0.18 NO
135 SLC25A5 SLC25A5 SLC25A5 11801 -0.03 0.16 NO
136 POLR2F POLR2F POLR2F 11832 -0.03 0.16 NO
137 TBPL1 TBPL1 TBPL1 11846 -0.031 0.16 NO
138 HTT HTT HTT 11859 -0.031 0.16 NO
139 ATP5H ATP5H ATP5H 11887 -0.031 0.16 NO
140 NDUFS1 NDUFS1 NDUFS1 12139 -0.034 0.15 NO
141 ATP5G3 ATP5G3 ATP5G3 12238 -0.035 0.15 NO
142 SDHD SDHD SDHD 12363 -0.037 0.14 NO
143 NDUFB3 NDUFB3 NDUFB3 12423 -0.038 0.14 NO
144 ATP5J ATP5J ATP5J 12623 -0.04 0.13 NO
145 RCOR1 RCOR1 RCOR1 12693 -0.041 0.13 NO
146 TBP TBP TBP 12699 -0.041 0.14 NO
147 POLR2K POLR2K POLR2K 12752 -0.042 0.14 NO
148 CREB1 CREB1 CREB1 12784 -0.043 0.14 NO
149 HDAC2 HDAC2 HDAC2 13118 -0.047 0.12 NO
150 UQCRFS1 UQCRFS1 UQCRFS1 13137 -0.048 0.13 NO
151 CYCS CYCS CYCS 13211 -0.049 0.12 NO
152 NDUFB6 NDUFB6 NDUFB6 13308 -0.05 0.12 NO
153 NDUFB9 NDUFB9 NDUFB9 13321 -0.05 0.13 NO
154 DLG4 DLG4 DLG4 13376 -0.051 0.13 NO
155 REST REST REST 13480 -0.053 0.13 NO
156 APAF1 APAF1 APAF1 13602 -0.055 0.12 NO
157 TAF4 TAF4 TAF4 13936 -0.061 0.11 NO
158 SLC25A31 SLC25A31 SLC25A31 14215 -0.066 0.1 NO
159 PLCB3 PLCB3 PLCB3 14895 -0.08 0.068 NO
160 POLR2D POLR2D POLR2D 15197 -0.088 0.059 NO
161 TFAM TFAM TFAM 15347 -0.092 0.057 NO
162 CLTCL1 CLTCL1 CLTCL1 16000 -0.12 0.03 NO
163 GRIN2B GRIN2B GRIN2B 16393 -0.13 0.019 NO
164 COX6A2 COX6A2 COX6A2 16419 -0.13 0.027 NO
165 PPARGC1A PPARGC1A PPARGC1A 16652 -0.15 0.026 NO
166 TAF4B TAF4B TAF4B 16809 -0.16 0.028 NO
167 UCP1 UCP1 UCP1 17150 -0.18 0.023 NO
168 HAP1 HAP1 HAP1 17261 -0.19 0.031 NO
169 NDUFA4L2 NDUFA4L2 NDUFA4L2 17614 -0.22 0.028 NO
170 COX4I2 COX4I2 COX4I2 18115 -0.29 0.022 NO

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

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GSTA3 GSTA3 GSTA3 45 1.2 0.23 YES
2 GSTA1 GSTA1 GSTA1 1380 0.24 0.2 YES
3 GSTA2 GSTA2 GSTA2 1517 0.22 0.24 YES
4 GGT6 GGT6 GGT6 1590 0.21 0.28 YES
5 ANPEP ANPEP ANPEP 1844 0.19 0.3 YES
6 GSTM5 GSTM5 GSTM5 1913 0.18 0.33 YES
7 GSTM1 GSTM1 GSTM1 2002 0.18 0.36 YES
8 MGST2 MGST2 MGST2 2470 0.15 0.37 YES
9 GSTM2 GSTM2 GSTM2 2714 0.13 0.38 YES
10 GSR GSR GSR 2772 0.13 0.4 YES
11 GSTO2 GSTO2 GSTO2 2920 0.12 0.42 YES
12 GPX2 GPX2 GPX2 2934 0.12 0.44 YES
13 IDH2 IDH2 IDH2 3070 0.12 0.46 YES
14 GSTZ1 GSTZ1 GSTZ1 3112 0.11 0.48 YES
15 GCLC GCLC GCLC 3171 0.11 0.5 YES
16 GCLM GCLM GCLM 3182 0.11 0.52 YES
17 MGST1 MGST1 MGST1 3295 0.11 0.53 YES
18 GSTK1 GSTK1 GSTK1 3543 0.097 0.54 YES
19 GGT1 GGT1 GGT1 3588 0.096 0.56 YES
20 GPX4 GPX4 GPX4 4702 0.065 0.51 NO
21 GSTT1 GSTT1 GSTT1 5063 0.057 0.5 NO
22 GSTM3 GSTM3 GSTM3 5135 0.055 0.51 NO
23 GPX1 GPX1 GPX1 6026 0.038 0.46 NO
24 SMS SMS SMS 6375 0.033 0.45 NO
25 GSTP1 GSTP1 GSTP1 6845 0.027 0.43 NO
26 IDH1 IDH1 IDH1 6951 0.025 0.43 NO
27 G6PD G6PD G6PD 7031 0.024 0.43 NO
28 GSTA4 GSTA4 GSTA4 7142 0.022 0.43 NO
29 PGD PGD PGD 7199 0.022 0.43 NO
30 GSTM4 GSTM4 GSTM4 7368 0.02 0.43 NO
31 LAP3 LAP3 LAP3 7396 0.019 0.43 NO
32 GSTO1 GSTO1 GSTO1 7530 0.017 0.43 NO
33 GSS GSS GSS 7941 0.012 0.41 NO
34 OPLAH OPLAH OPLAH 8185 0.0092 0.39 NO
35 GGCT GGCT GGCT 8258 0.0083 0.39 NO
36 GGT5 GGT5 GGT5 8277 0.0081 0.39 NO
37 TXNDC12 TXNDC12 TXNDC12 8560 0.005 0.38 NO
38 GPX7 GPX7 GPX7 9194 -0.0022 0.34 NO
39 RRM2B RRM2B RRM2B 9462 -0.0052 0.33 NO
40 MGST3 MGST3 MGST3 11128 -0.023 0.25 NO
41 SRM SRM SRM 12750 -0.042 0.17 NO
42 GSTT2 GSTT2 GSTT2 14405 -0.069 0.09 NO
43 RRM1 RRM1 RRM1 14885 -0.08 0.08 NO
44 ODC1 ODC1 ODC1 15208 -0.088 0.08 NO
45 GGT7 GGT7 GGT7 16575 -0.14 0.034 NO
46 GPX3 GPX3 GPX3 17042 -0.17 0.043 NO
47 RRM2 RRM2 RRM2 17299 -0.19 0.066 NO

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

Figure S64.  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 TYROSINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADH6 ADH6 ADH6 164 0.86 0.12 YES
2 FBP1 FBP1 FBP1 690 0.38 0.14 YES
3 ADH1B ADH1B ADH1B 774 0.35 0.19 YES
4 ALDH3A1 ALDH3A1 ALDH3A1 829 0.34 0.24 YES
5 ADH1C ADH1C ADH1C 831 0.34 0.29 YES
6 ADH1A ADH1A ADH1A 884 0.32 0.33 YES
7 ADH7 ADH7 ADH7 896 0.32 0.38 YES
8 ALDH1A3 ALDH1A3 ALDH1A3 1267 0.25 0.39 YES
9 ALDH3B1 ALDH3B1 ALDH3B1 1400 0.23 0.42 YES
10 ADH4 ADH4 ADH4 1704 0.2 0.43 YES
11 ALDH3B2 ALDH3B2 ALDH3B2 1734 0.2 0.46 YES
12 GALM GALM GALM 2282 0.16 0.45 YES
13 ALDOB ALDOB ALDOB 2299 0.16 0.48 YES
14 PGK2 PGK2 PGK2 2471 0.15 0.49 YES
15 G6PC G6PC G6PC 2511 0.14 0.51 YES
16 ACSS1 ACSS1 ACSS1 2932 0.12 0.5 NO
17 ALDH2 ALDH2 ALDH2 3411 0.1 0.49 NO
18 FBP2 FBP2 FBP2 3455 0.1 0.5 NO
19 PGAM4 PGAM4 PGAM4 3750 0.091 0.5 NO
20 ADH5 ADH5 ADH5 5071 0.056 0.44 NO
21 PFKP PFKP PFKP 6240 0.035 0.38 NO
22 AKR1A1 AKR1A1 AKR1A1 6323 0.034 0.38 NO
23 TPI1 TPI1 TPI1 6488 0.032 0.38 NO
24 PFKL PFKL PFKL 6542 0.031 0.38 NO
25 ALDH3A2 ALDH3A2 ALDH3A2 6685 0.029 0.37 NO
26 HK1 HK1 HK1 6785 0.028 0.37 NO
27 ALDH7A1 ALDH7A1 ALDH7A1 7376 0.019 0.34 NO
28 PDHB PDHB PDHB 7611 0.016 0.33 NO
29 ALDH9A1 ALDH9A1 ALDH9A1 7641 0.016 0.33 NO
30 LDHAL6B LDHAL6B LDHAL6B 7714 0.015 0.33 NO
31 PGM2 PGM2 PGM2 8297 0.0078 0.3 NO
32 PGAM1 PGAM1 PGAM1 8619 0.0044 0.28 NO
33 PKM2 PKM2 PKM2 9104 -0.0012 0.26 NO
34 HK3 HK3 HK3 9176 -0.002 0.26 NO
35 DLAT DLAT DLAT 9691 -0.0077 0.23 NO
36 ENO1 ENO1 ENO1 9714 -0.0079 0.23 NO
37 PKLR PKLR PKLR 10217 -0.013 0.2 NO
38 LDHB LDHB LDHB 10250 -0.013 0.2 NO
39 PCK1 PCK1 PCK1 10433 -0.015 0.2 NO
40 DLD DLD DLD 10672 -0.018 0.19 NO
41 BPGM BPGM BPGM 10715 -0.018 0.19 NO
42 GAPDH GAPDH GAPDH 10737 -0.018 0.19 NO
43 PDHA1 PDHA1 PDHA1 10951 -0.021 0.18 NO
44 PGM1 PGM1 PGM1 11330 -0.025 0.16 NO
45 LDHC LDHC LDHC 11375 -0.025 0.16 NO
46 ALDOA ALDOA ALDOA 11452 -0.026 0.16 NO
47 PGK1 PGK1 PGK1 11475 -0.026 0.17 NO
48 LDHA LDHA LDHA 11957 -0.032 0.14 NO
49 HK2 HK2 HK2 12014 -0.032 0.15 NO
50 GPI GPI GPI 13130 -0.048 0.093 NO
51 ENO2 ENO2 ENO2 13704 -0.056 0.07 NO
52 LDHAL6A LDHAL6A LDHAL6A 14048 -0.063 0.061 NO
53 ACSS2 ACSS2 ACSS2 14372 -0.069 0.053 NO
54 ALDH1B1 ALDH1B1 ALDH1B1 14582 -0.073 0.053 NO
55 PFKM PFKM PFKM 15374 -0.093 0.024 NO
56 ENO3 ENO3 ENO3 15857 -0.11 0.013 NO
57 PCK2 PCK2 PCK2 16334 -0.13 0.0064 NO
58 PGAM2 PGAM2 PGAM2 16432 -0.14 0.021 NO
59 ALDOC ALDOC ALDOC 18217 -0.31 -0.03 NO
60 GCK GCK GCK 18236 -0.32 0.016 NO

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

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

genes ES table in pathway: KEGG GLUTATHIONE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GSTA3 GSTA3 GSTA3 45 1.2 0.094 YES
2 ADH6 ADH6 ADH6 164 0.86 0.16 YES
3 FMO2 FMO2 FMO2 298 0.64 0.2 YES
4 FMO3 FMO3 FMO3 698 0.37 0.21 YES
5 FMO4 FMO4 FMO4 706 0.37 0.24 YES
6 ADH1B ADH1B ADH1B 774 0.35 0.27 YES
7 ALDH3A1 ALDH3A1 ALDH3A1 829 0.34 0.29 YES
8 ADH1C ADH1C ADH1C 831 0.34 0.32 YES
9 CYP2D6 CYP2D6 CYP2D6 851 0.33 0.34 YES
10 ADH1A ADH1A ADH1A 884 0.32 0.37 YES
11 ADH7 ADH7 ADH7 896 0.32 0.4 YES
12 FMO5 FMO5 FMO5 998 0.3 0.41 YES
13 MAOB MAOB MAOB 1048 0.29 0.44 YES
14 UGT2B10 UGT2B10 UGT2B10 1172 0.26 0.45 YES
15 ALDH1A3 ALDH1A3 ALDH1A3 1267 0.25 0.47 YES
16 CYP2C8 CYP2C8 CYP2C8 1355 0.24 0.48 YES
17 GSTA1 GSTA1 GSTA1 1380 0.24 0.5 YES
18 ALDH3B1 ALDH3B1 ALDH3B1 1400 0.23 0.52 YES
19 UGT2B7 UGT2B7 UGT2B7 1435 0.23 0.53 YES
20 GSTA2 GSTA2 GSTA2 1517 0.22 0.55 YES
21 CYP2A6 CYP2A6 CYP2A6 1638 0.21 0.56 YES
22 ADH4 ADH4 ADH4 1704 0.2 0.57 YES
23 ALDH3B2 ALDH3B2 ALDH3B2 1734 0.2 0.58 YES
24 UGT2B15 UGT2B15 UGT2B15 1789 0.19 0.6 YES
25 GSTM5 GSTM5 GSTM5 1913 0.18 0.61 YES
26 GSTM1 GSTM1 GSTM1 2002 0.18 0.62 YES
27 MAOA MAOA MAOA 2005 0.18 0.63 YES
28 UGT2B11 UGT2B11 UGT2B11 2094 0.17 0.64 YES
29 CYP2E1 CYP2E1 CYP2E1 2252 0.16 0.64 YES
30 FMO1 FMO1 FMO1 2300 0.16 0.65 YES
31 MGST2 MGST2 MGST2 2470 0.15 0.66 YES
32 GSTM2 GSTM2 GSTM2 2714 0.13 0.65 YES
33 CYP2A7 CYP2A7 CYP2A7 2844 0.13 0.66 YES
34 GSTO2 GSTO2 GSTO2 2920 0.12 0.66 YES
35 GSTZ1 GSTZ1 GSTZ1 3112 0.11 0.66 NO
36 MGST1 MGST1 MGST1 3295 0.11 0.66 NO
37 GSTK1 GSTK1 GSTK1 3543 0.097 0.66 NO
38 GSTT1 GSTT1 GSTT1 5063 0.057 0.58 NO
39 ADH5 ADH5 ADH5 5071 0.056 0.58 NO
40 GSTM3 GSTM3 GSTM3 5135 0.055 0.58 NO
41 CYP2A13 CYP2A13 CYP2A13 5291 0.052 0.58 NO
42 GSTP1 GSTP1 GSTP1 6845 0.027 0.5 NO
43 GSTA4 GSTA4 GSTA4 7142 0.022 0.48 NO
44 GSTM4 GSTM4 GSTM4 7368 0.02 0.47 NO
45 GSTO1 GSTO1 GSTO1 7530 0.017 0.46 NO
46 MGST3 MGST3 MGST3 11128 -0.023 0.27 NO
47 AOX1 AOX1 AOX1 13062 -0.047 0.17 NO
48 CYP2C18 CYP2C18 CYP2C18 13148 -0.048 0.17 NO
49 CYP2C9 CYP2C9 CYP2C9 13967 -0.062 0.13 NO
50 GSTT2 GSTT2 GSTT2 14405 -0.069 0.11 NO
51 UGT1A6 UGT1A6 UGT1A6 14431 -0.07 0.12 NO
52 CYP3A5 CYP3A5 CYP3A5 15572 -0.099 0.064 NO
53 CYP2C19 CYP2C19 CYP2C19 15957 -0.11 0.052 NO
54 CYP3A43 CYP3A43 CYP3A43 16532 -0.14 0.032 NO
55 CYP3A4 CYP3A4 CYP3A4 16798 -0.16 0.031 NO
56 CYP2B6 CYP2B6 CYP2B6 16819 -0.16 0.042 NO
57 UGT2B4 UGT2B4 UGT2B4 16957 -0.16 0.048 NO
58 CYP3A7 CYP3A7 CYP3A7 17611 -0.22 0.031 NO
59 CYP1A2 CYP1A2 CYP1A2 17658 -0.22 0.047 NO

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

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLUTATHIONE 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 STARCH AND SUCROSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADH6 ADH6 ADH6 164 0.86 0.17 YES
2 ADH1B ADH1B ADH1B 774 0.35 0.21 YES
3 ADH1C ADH1C ADH1C 831 0.34 0.27 YES
4 ADH1A ADH1A ADH1A 884 0.32 0.34 YES
5 ADH7 ADH7 ADH7 896 0.32 0.4 YES
6 ACADL ACADL ACADL 1115 0.28 0.45 YES
7 ADH4 ADH4 ADH4 1704 0.2 0.46 YES
8 ACSL5 ACSL5 ACSL5 1992 0.18 0.48 YES
9 HADH HADH HADH 2467 0.15 0.48 YES
10 ACADS ACADS ACADS 2605 0.14 0.5 YES
11 CPT1B CPT1B CPT1B 2959 0.12 0.51 YES
12 ALDH2 ALDH2 ALDH2 3411 0.1 0.5 YES
13 ACSL6 ACSL6 ACSL6 3456 0.1 0.52 YES
14 ACOX3 ACOX3 ACOX3 3824 0.088 0.52 NO
15 ECHS1 ECHS1 ECHS1 4292 0.075 0.51 NO
16 ACAT1 ACAT1 ACAT1 4588 0.067 0.51 NO
17 ADH5 ADH5 ADH5 5071 0.056 0.49 NO
18 ACADVL ACADVL ACADVL 5072 0.056 0.5 NO
19 ACAA1 ACAA1 ACAA1 5273 0.052 0.5 NO
20 CPT1A CPT1A CPT1A 6544 0.031 0.44 NO
21 ACOX1 ACOX1 ACOX1 6587 0.03 0.45 NO
22 CYP4A11 CYP4A11 CYP4A11 6644 0.03 0.45 NO
23 ALDH3A2 ALDH3A2 ALDH3A2 6685 0.029 0.45 NO
24 CYP4A22 CYP4A22 CYP4A22 6725 0.028 0.46 NO
25 ACSL4 ACSL4 ACSL4 6740 0.028 0.46 NO
26 ACSL3 ACSL3 ACSL3 6918 0.026 0.46 NO
27 ACADSB ACADSB ACADSB 6991 0.024 0.46 NO
28 ALDH7A1 ALDH7A1 ALDH7A1 7376 0.019 0.44 NO
29 ALDH9A1 ALDH9A1 ALDH9A1 7641 0.016 0.43 NO
30 HADHB HADHB HADHB 7838 0.014 0.42 NO
31 HADHA HADHA HADHA 8723 0.0034 0.38 NO
32 CPT2 CPT2 CPT2 8772 0.0028 0.37 NO
33 ACADM ACADM ACADM 11514 -0.027 0.23 NO
34 GCDH GCDH GCDH 12256 -0.035 0.2 NO
35 EHHADH EHHADH EHHADH 12505 -0.039 0.19 NO
36 ALDH1B1 ALDH1B1 ALDH1B1 14582 -0.073 0.095 NO
37 ACAT2 ACAT2 ACAT2 15442 -0.095 0.068 NO
38 ACSL1 ACSL1 ACSL1 16037 -0.12 0.06 NO
39 CPT1C CPT1C CPT1C 17120 -0.18 0.038 NO
40 ACAA2 ACAA2 ACAA2 17241 -0.19 0.07 NO

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

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

genes ES table in pathway: KEGG ETHER LIPID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SCGB1A1 SCGB1A1 SCGB1A1 281 0.66 0.095 YES
2 C4BPB C4BPB C4BPB 320 0.6 0.19 YES
3 FOXA1 FOXA1 FOXA1 509 0.46 0.26 YES
4 ESR1 ESR1 ESR1 681 0.38 0.32 YES
5 AR AR AR 725 0.36 0.37 YES
6 TFF1 TFF1 TFF1 882 0.32 0.42 YES
7 FOXA2 FOXA2 FOXA2 891 0.32 0.47 YES
8 SHH SHH SHH 1073 0.28 0.51 YES
9 SERPINA1 SERPINA1 SERPINA1 1259 0.25 0.54 YES
10 XBP1 XBP1 XBP1 2117 0.17 0.52 YES
11 NFIA NFIA NFIA 2423 0.15 0.53 YES
12 NFIC NFIC NFIC 2542 0.14 0.55 YES
13 SFTPA2 SFTPA2 SFTPA2 3202 0.11 0.53 NO
14 NKX3-1 NKX3-1 NKX3-1 3314 0.11 0.55 NO
15 NRIP1 NRIP1 NRIP1 3607 0.095 0.55 NO
16 NR2F2 NR2F2 NR2F2 3911 0.086 0.54 NO
17 APOB APOB APOB 4300 0.074 0.53 NO
18 SFTPA1 SFTPA1 SFTPA1 6688 0.029 0.41 NO
19 AP1B1 AP1B1 AP1B1 6797 0.027 0.41 NO
20 NDUFV3 NDUFV3 NDUFV3 7193 0.022 0.39 NO
21 SOD1 SOD1 SOD1 7784 0.014 0.36 NO
22 FOS FOS FOS 8414 0.0066 0.33 NO
23 JUN JUN JUN 8613 0.0044 0.32 NO
24 EP300 EP300 EP300 9171 -0.0019 0.29 NO
25 CREBBP CREBBP CREBBP 9479 -0.0055 0.27 NO
26 SP1 SP1 SP1 9612 -0.0068 0.27 NO
27 POU2F1 POU2F1 POU2F1 10251 -0.013 0.24 NO
28 COL18A1 COL18A1 COL18A1 11482 -0.026 0.17 NO
29 PRDM15 PRDM15 PRDM15 11654 -0.029 0.17 NO
30 ATP5J ATP5J ATP5J 12623 -0.04 0.12 NO
31 CYP2C18 CYP2C18 CYP2C18 13148 -0.048 0.1 NO
32 PISD PISD PISD 13789 -0.058 0.078 NO
33 NFIB NFIB NFIB 14034 -0.063 0.075 NO
34 KLK3 KLK3 KLK3 14447 -0.07 0.064 NO
35 SFTPD SFTPD SFTPD 14539 -0.072 0.071 NO
36 NCOA3 NCOA3 NCOA3 14639 -0.074 0.078 NO
37 DSCAM DSCAM DSCAM 14909 -0.08 0.077 NO
38 CEBPB CEBPB CEBPB 14980 -0.082 0.087 NO
39 VTN VTN VTN 15248 -0.09 0.088 NO
40 BRCA1 BRCA1 BRCA1 15593 -0.099 0.086 NO
41 CDKN1B CDKN1B CDKN1B 17428 -0.2 0.021 NO
42 FOXA3 FOXA3 FOXA3 17709 -0.23 0.044 NO

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

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GSTA3 GSTA3 GSTA3 45 1.2 0.18 YES
2 ACSM1 ACSM1 ACSM1 603 0.41 0.21 YES
3 UGT2B10 UGT2B10 UGT2B10 1172 0.26 0.22 YES
4 NAT1 NAT1 NAT1 1257 0.25 0.25 YES
5 GSTA1 GSTA1 GSTA1 1380 0.24 0.28 YES
6 UGT2B7 UGT2B7 UGT2B7 1435 0.23 0.32 YES
7 GSTA2 GSTA2 GSTA2 1517 0.22 0.34 YES
8 SULT2B1 SULT2B1 SULT2B1 1764 0.2 0.36 YES
9 GSTM5 GSTM5 GSTM5 1913 0.18 0.38 YES
10 GSTM1 GSTM1 GSTM1 2002 0.18 0.4 YES
11 UGT2B11 UGT2B11 UGT2B11 2094 0.17 0.42 YES
12 PAPSS1 PAPSS1 PAPSS1 2096 0.17 0.45 YES
13 SULT1A1 SULT1A1 SULT1A1 2287 0.16 0.46 YES
14 MGST2 MGST2 MGST2 2470 0.15 0.48 YES
15 SULT1A2 SULT1A2 SULT1A2 2549 0.14 0.49 YES
16 GSTO2 GSTO2 GSTO2 2920 0.12 0.49 YES
17 GCLC GCLC GCLC 3171 0.11 0.5 YES
18 GCLM GCLM GCLM 3182 0.11 0.51 YES
19 CNDP2 CNDP2 CNDP2 3266 0.11 0.52 YES
20 MGST1 MGST1 MGST1 3295 0.11 0.54 YES
21 GGT1 GGT1 GGT1 3588 0.096 0.54 NO
22 UGDH UGDH UGDH 4153 0.079 0.52 NO
23 SULT1B1 SULT1B1 SULT1B1 4520 0.069 0.51 NO
24 COMT COMT COMT 5368 0.05 0.47 NO
25 MAT1A MAT1A MAT1A 5549 0.047 0.47 NO
26 PAPSS2 PAPSS2 PAPSS2 5794 0.042 0.46 NO
27 SULT1A3 SULT1A3 SULT1A3 6404 0.033 0.44 NO
28 GSTP1 GSTP1 GSTP1 6845 0.027 0.42 NO
29 GSTA4 GSTA4 GSTA4 7142 0.022 0.4 NO
30 SULT1C4 SULT1C4 SULT1C4 7282 0.021 0.4 NO
31 GSTM4 GSTM4 GSTM4 7368 0.02 0.4 NO
32 GSTO1 GSTO1 GSTO1 7530 0.017 0.39 NO
33 SULT1C2 SULT1C2 SULT1C2 7685 0.016 0.38 NO
34 GSS GSS GSS 7941 0.012 0.37 NO
35 OPLAH OPLAH OPLAH 8185 0.0092 0.36 NO
36 GGCT GGCT GGCT 8258 0.0083 0.36 NO
37 GGT5 GGT5 GGT5 8277 0.0081 0.36 NO
38 BPNT1 BPNT1 BPNT1 9106 -0.0012 0.31 NO
39 MAT2B MAT2B MAT2B 9349 -0.004 0.3 NO
40 AHCY AHCY AHCY 9729 -0.008 0.28 NO
41 MGST3 MGST3 MGST3 11128 -0.023 0.21 NO
42 MTR MTR MTR 11219 -0.024 0.21 NO
43 UGP2 UGP2 UGP2 11449 -0.026 0.2 NO
44 SULT4A1 SULT4A1 SULT4A1 12642 -0.041 0.14 NO
45 TPMT TPMT TPMT 12985 -0.046 0.13 NO
46 MAT2A MAT2A MAT2A 13309 -0.05 0.12 NO
47 UGT1A6 UGT1A6 UGT1A6 14431 -0.07 0.071 NO
48 SLC35D1 SLC35D1 SLC35D1 15214 -0.089 0.042 NO
49 NAT2 NAT2 NAT2 15433 -0.095 0.045 NO
50 SULT1E1 SULT1E1 SULT1E1 16049 -0.12 0.03 NO
51 GGT7 GGT7 GGT7 16575 -0.14 0.023 NO
52 NNMT NNMT NNMT 16700 -0.15 0.039 NO
53 UGT2B4 UGT2B4 UGT2B4 16957 -0.16 0.05 NO
54 CYP1A2 CYP1A2 CYP1A2 17658 -0.22 0.047 NO

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

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FOXA2 FOXA2 FOXA2 891 0.32 0.044 YES
2 SHH SHH SHH 1073 0.28 0.12 YES
3 GLI1 GLI1 GLI1 1152 0.27 0.19 YES
4 IFT172 IFT172 IFT172 1428 0.23 0.24 YES
5 IFT88 IFT88 IFT88 1514 0.22 0.3 YES
6 KIF3A KIF3A KIF3A 2691 0.13 0.27 YES
7 STK36 STK36 STK36 2702 0.13 0.31 YES
8 PRKCD PRKCD PRKCD 2813 0.13 0.34 YES
9 PTCH1 PTCH1 PTCH1 2915 0.12 0.37 YES
10 RBBP7 RBBP7 RBBP7 3208 0.11 0.38 YES
11 CSNK1G1 CSNK1G1 CSNK1G1 3257 0.11 0.41 YES
12 GNAZ GNAZ GNAZ 6450 0.032 0.25 NO
13 SAP30 SAP30 SAP30 6778 0.028 0.24 NO
14 CSNK1G2 CSNK1G2 CSNK1G2 6864 0.026 0.24 NO
15 LGALS3 LGALS3 LGALS3 6885 0.026 0.25 NO
16 SAP18 SAP18 SAP18 7043 0.024 0.25 NO
17 AKT1 AKT1 AKT1 7057 0.024 0.25 NO
18 CSNK1A1 CSNK1A1 CSNK1A1 7147 0.022 0.25 NO
19 CSNK1E CSNK1E CSNK1E 7987 0.012 0.21 NO
20 SPOP SPOP SPOP 8022 0.011 0.21 NO
21 SIN3A SIN3A SIN3A 8077 0.011 0.21 NO
22 GNAI2 GNAI2 GNAI2 8300 0.0078 0.2 NO
23 CSNK1D CSNK1D CSNK1D 8995 0.000044 0.17 NO
24 SSPO SSPO SSPO 9168 -0.0019 0.16 NO
25 SUFU SUFU SUFU 9273 -0.0031 0.15 NO
26 CREBBP CREBBP CREBBP 9479 -0.0055 0.14 NO
27 HDAC1 HDAC1 HDAC1 10147 -0.012 0.11 NO
28 GNB1 GNB1 GNB1 10233 -0.013 0.11 NO
29 CSNK1G3 CSNK1G3 CSNK1G3 10692 -0.018 0.09 NO
30 FBXW11 FBXW11 FBXW11 10731 -0.018 0.093 NO
31 ARRB2 ARRB2 ARRB2 11737 -0.03 0.047 NO
32 PRKACA PRKACA PRKACA 11751 -0.03 0.055 NO
33 PIAS1 PIAS1 PIAS1 12112 -0.034 0.045 NO
34 GNAO1 GNAO1 GNAO1 12243 -0.035 0.048 NO
35 RAB23 RAB23 RAB23 12353 -0.037 0.053 NO
36 RBBP4 RBBP4 RBBP4 12379 -0.037 0.062 NO
37 GNAI3 GNAI3 GNAI3 12756 -0.042 0.054 NO
38 HDAC2 HDAC2 HDAC2 13118 -0.047 0.048 NO
39 SIN3B SIN3B SIN3B 13325 -0.05 0.051 NO
40 MAP2K1 MAP2K1 MAP2K1 14003 -0.062 0.032 NO
41 GSK3B GSK3B GSK3B 14556 -0.072 0.023 NO
42 XPO1 XPO1 XPO1 14756 -0.077 0.034 NO
43 GLI3 GLI3 GLI3 14774 -0.077 0.055 NO
44 SMO SMO SMO 14862 -0.079 0.073 NO
45 GNAI1 GNAI1 GNAI1 15202 -0.088 0.08 NO
46 MTSS1 MTSS1 MTSS1 15474 -0.096 0.093 NO
47 GLI2 GLI2 GLI2 15856 -0.11 0.1 NO
48 GNG2 GNG2 GNG2 16596 -0.14 0.1 NO

Figure S75.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S76.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG DRUG METABOLISM CYTOCHROME P450

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GSTA3 GSTA3 GSTA3 45 1.2 0.1 YES
2 ADH6 ADH6 ADH6 164 0.86 0.18 YES
3 AKR1C4 AKR1C4 AKR1C4 736 0.36 0.18 YES
4 ADH1B ADH1B ADH1B 774 0.35 0.21 YES
5 ALDH3A1 ALDH3A1 ALDH3A1 829 0.34 0.24 YES
6 ADH1C ADH1C ADH1C 831 0.34 0.27 YES
7 ADH1A ADH1A ADH1A 884 0.32 0.3 YES
8 ADH7 ADH7 ADH7 896 0.32 0.32 YES
9 AKR1C3 AKR1C3 AKR1C3 901 0.32 0.35 YES
10 UGT2B10 UGT2B10 UGT2B10 1172 0.26 0.36 YES
11 AKR1C2 AKR1C2 AKR1C2 1263 0.25 0.38 YES
12 ALDH1A3 ALDH1A3 ALDH1A3 1267 0.25 0.4 YES
13 CYP2C8 CYP2C8 CYP2C8 1355 0.24 0.42 YES
14 GSTA1 GSTA1 GSTA1 1380 0.24 0.44 YES
15 ALDH3B1 ALDH3B1 ALDH3B1 1400 0.23 0.46 YES
16 UGT2B7 UGT2B7 UGT2B7 1435 0.23 0.48 YES
17 GSTA2 GSTA2 GSTA2 1517 0.22 0.49 YES
18 ADH4 ADH4 ADH4 1704 0.2 0.5 YES
19 ALDH3B2 ALDH3B2 ALDH3B2 1734 0.2 0.52 YES
20 UGT2B15 UGT2B15 UGT2B15 1789 0.19 0.53 YES
21 AKR1C1 AKR1C1 AKR1C1 1883 0.18 0.55 YES
22 GSTM5 GSTM5 GSTM5 1913 0.18 0.56 YES
23 GSTM1 GSTM1 GSTM1 2002 0.18 0.57 YES
24 UGT2B11 UGT2B11 UGT2B11 2094 0.17 0.58 YES
25 CYP2S1 CYP2S1 CYP2S1 2119 0.17 0.6 YES
26 CYP2E1 CYP2E1 CYP2E1 2252 0.16 0.6 YES
27 MGST2 MGST2 MGST2 2470 0.15 0.6 YES
28 GSTM2 GSTM2 GSTM2 2714 0.13 0.6 YES
29 GSTO2 GSTO2 GSTO2 2920 0.12 0.6 YES
30 GSTZ1 GSTZ1 GSTZ1 3112 0.11 0.6 YES
31 EPHX1 EPHX1 EPHX1 3258 0.11 0.61 YES
32 MGST1 MGST1 MGST1 3295 0.11 0.61 YES
33 GSTK1 GSTK1 GSTK1 3543 0.097 0.61 NO
34 CYP1B1 CYP1B1 CYP1B1 4547 0.068 0.56 NO
35 GSTT1 GSTT1 GSTT1 5063 0.057 0.54 NO
36 ADH5 ADH5 ADH5 5071 0.056 0.54 NO
37 GSTM3 GSTM3 GSTM3 5135 0.055 0.55 NO
38 GSTP1 GSTP1 GSTP1 6845 0.027 0.46 NO
39 GSTA4 GSTA4 GSTA4 7142 0.022 0.44 NO
40 GSTM4 GSTM4 GSTM4 7368 0.02 0.43 NO
41 GSTO1 GSTO1 GSTO1 7530 0.017 0.42 NO
42 CYP2F1 CYP2F1 CYP2F1 9069 -0.00084 0.34 NO
43 MGST3 MGST3 MGST3 11128 -0.023 0.23 NO
44 CYP2C18 CYP2C18 CYP2C18 13148 -0.048 0.13 NO
45 CYP2C9 CYP2C9 CYP2C9 13967 -0.062 0.088 NO
46 CYP1A1 CYP1A1 CYP1A1 14058 -0.063 0.088 NO
47 GSTT2 GSTT2 GSTT2 14405 -0.069 0.076 NO
48 UGT1A6 UGT1A6 UGT1A6 14431 -0.07 0.081 NO
49 CYP3A5 CYP3A5 CYP3A5 15572 -0.099 0.028 NO
50 CYP2C19 CYP2C19 CYP2C19 15957 -0.11 0.018 NO
51 CYP3A43 CYP3A43 CYP3A43 16532 -0.14 -0.00021 NO
52 CYP3A4 CYP3A4 CYP3A4 16798 -0.16 -0.0004 NO
53 CYP2B6 CYP2B6 CYP2B6 16819 -0.16 0.013 NO
54 UGT2B4 UGT2B4 UGT2B4 16957 -0.16 0.02 NO
55 CYP3A7 CYP3A7 CYP3A7 17611 -0.22 0.005 NO
56 CYP1A2 CYP1A2 CYP1A2 17658 -0.22 0.023 NO
57 DHDH DHDH DHDH 17934 -0.26 0.032 NO

Figure S77.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450.

Figure S78.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ABC TRANSPORTERS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TREH TREH TREH 302 0.64 0.13 YES
2 GBA3 GBA3 GBA3 697 0.38 0.19 YES
3 AMY1A AMY1A AMY1A 827 0.34 0.26 YES
4 ENPP3 ENPP3 ENPP3 933 0.31 0.32 YES
5 UGT2B10 UGT2B10 UGT2B10 1172 0.26 0.37 YES
6 UGT2B7 UGT2B7 UGT2B7 1435 0.23 0.41 YES
7 AMY2A AMY2A AMY2A 1448 0.23 0.46 YES
8 UGT2B15 UGT2B15 UGT2B15 1789 0.19 0.48 YES
9 UGT2B11 UGT2B11 UGT2B11 2094 0.17 0.5 YES
10 AMY2B AMY2B AMY2B 2459 0.15 0.52 YES
11 G6PC G6PC G6PC 2511 0.14 0.55 YES
12 UGDH UGDH UGDH 4153 0.079 0.48 NO
13 PGM2L1 PGM2L1 PGM2L1 4558 0.068 0.47 NO
14 GANC GANC GANC 5424 0.049 0.44 NO
15 GBE1 GBE1 GBE1 5733 0.044 0.43 NO
16 PYGL PYGL PYGL 6135 0.037 0.42 NO
17 HK1 HK1 HK1 6785 0.028 0.39 NO
18 PGM2 PGM2 PGM2 8297 0.0078 0.31 NO
19 AGL AGL AGL 8404 0.0067 0.3 NO
20 GYS1 GYS1 GYS1 8534 0.0052 0.3 NO
21 HK3 HK3 HK3 9176 -0.002 0.26 NO
22 UXS1 UXS1 UXS1 10238 -0.013 0.21 NO
23 GUSB GUSB GUSB 10394 -0.014 0.2 NO
24 PGM1 PGM1 PGM1 11330 -0.025 0.16 NO
25 UGP2 UGP2 UGP2 11449 -0.026 0.16 NO
26 HK2 HK2 HK2 12014 -0.032 0.13 NO
27 GYS2 GYS2 GYS2 12066 -0.033 0.14 NO
28 MGAM MGAM MGAM 12293 -0.036 0.13 NO
29 PYGB PYGB PYGB 13039 -0.046 0.1 NO
30 GAA GAA GAA 13040 -0.046 0.12 NO
31 GPI GPI GPI 13130 -0.048 0.12 NO
32 UGT1A6 UGT1A6 UGT1A6 14431 -0.07 0.066 NO
33 ENPP1 ENPP1 ENPP1 14797 -0.078 0.064 NO
34 PYGM PYGM PYGM 16314 -0.13 0.011 NO
35 UGT2B4 UGT2B4 UGT2B4 16957 -0.16 0.013 NO
36 GCK GCK GCK 18236 -0.32 0.016 NO

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

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ABC TRANSPORTERS, 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.v4.0.symbols.gmt

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

  • Phenotype data file = UCEC-TP.mergedcluster.txt

GSEA analysis

For the Gene Set Enrichment Analysis (GSEA), Broad GSEA-P-R.1.0 version is used with class2: canonical pathways geneses from MSigDB. Further details about statistics are available inThe Broad GSEA website.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Subramanian, A. et al, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles., Proc. Natl. Acad. Sci. USA 102(43) (2005)
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