GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in PCPG-TP
Pheochromocytoma and Paraganglioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1G44PRF
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 PCPG-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1G44PRF
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 "PCPG-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: 705
Number of samples: 179
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 ] 38
pheno.type: 2 - 4 :[ clus2 ] 70
pheno.type: 3 - 4 :[ clus3 ] 50
pheno.type: 4 - 4 :[ clus4 ] 21

For the expression subtypes of 17994 genes in 180 samples, GSEA found enriched gene sets in each cluster using 179 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG SPHINGOLIPID METABOLISM, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG CARDIAC MUSCLE CONTRACTION, KEGG TIGHT JUNCTION, KEGG LONG TERM POTENTIATION, KEGG TASTE TRANSDUCTION, KEGG VIBRIO CHOLERAE INFECTION, BIOCARTA G1 PATHWAY, BIOCARTA CHREBP2 PATHWAY, PID BARD1PATHWAY

    • And common core enriched genes are PRKCA, PRKCB, PRKCG, CLTA, DNM1, DPYSL2, KIAA1598, KIF4A, KIF4B, MAPK1

  • clus2

    • Top enriched gene sets are KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY, KEGG PRION DISEASES, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA PDGF PATHWAY, BIOCARTA TOLL PATHWAY, ST DIFFERENTIATION PATHWAY IN PC12 CELLS, SIG CD40PATHWAYMAP, PID REELINPATHWAY

    • And common core enriched genes are DDX58, ISG15, MAPK8, HERC5, STAT1, TRIM25, UBA7, UBE2L6, CALM1, CALM2

  • clus3

    • Top enriched gene sets are KEGG NOTCH SIGNALING PATHWAY, KEGG BLADDER CANCER, BIOCARTA NO1 PATHWAY, BIOCARTA VEGF PATHWAY, PID HIF2PATHWAY, PID S1P S1P3 PATHWAY, PID FRA PATHWAY, PID ILK PATHWAY, PID SYNDECAN 1 PATHWAY, PID VEGFR1 PATHWAY

    • And common core enriched genes are SLC2A1, VEGFA, GCK, HK2, ABCG2, EGLN3, EPO, ETS1, FLT1, SERPINE1

  • clus4

    • Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION

    • And common core enriched genes are ACAT1, POMC, SULT2A1, MAT1A, ACAA1, ACADM, ACADS, CGA, CYP11A1, CYP11B1

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 SPHINGOLIPID METABOLISM 36 genes.ES.table 0.52 1.5 0.05 1 0.97 0.17 0.11 0.15 1 0.84
KEGG NUCLEOTIDE EXCISION REPAIR 44 genes.ES.table 0.3 1.4 0.15 1 1 0.59 0.41 0.35 1 0.71
KEGG CARDIAC MUSCLE CONTRACTION 70 genes.ES.table 0.43 1.4 0.056 1 1 0.24 0.1 0.22 1 0.73
KEGG TIGHT JUNCTION 119 genes.ES.table 0.41 1.5 0.026 1 0.97 0.19 0.088 0.18 1 0.78
KEGG LONG TERM POTENTIATION 68 genes.ES.table 0.44 1.5 0.046 1 0.98 0.29 0.19 0.24 1 0.68
KEGG TASTE TRANSDUCTION 39 genes.ES.table 0.56 1.4 0.056 1 0.99 0.49 0.15 0.42 1 0.74
KEGG VIBRIO CHOLERAE INFECTION 51 genes.ES.table 0.38 1.5 0.06 1 0.97 0.14 0.15 0.12 1 0.73
BIOCARTA G1 PATHWAY 28 genes.ES.table 0.51 1.5 0.06 1 0.97 0.36 0.16 0.3 1 0.9
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.34 1.4 0.13 1 1 0.34 0.28 0.25 1 0.72
PID BARD1PATHWAY 29 genes.ES.table 0.49 1.4 0.15 1 1 0.28 0.2 0.22 1 0.72
genes ES table in pathway: KEGG SPHINGOLIPID METABOLISM

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 SH3GL2 SH3GL2 SH3GL2 150 0.5 0.28 YES
2 KIF4A KIF4A KIF4A 842 0.26 0.39 YES
3 DNM1 DNM1 DNM1 2590 0.11 0.36 YES
4 RPS6KA2 RPS6KA2 RPS6KA2 2819 0.1 0.4 YES
5 DPYSL2 DPYSL2 DPYSL2 3046 0.093 0.45 YES
6 RPS6KA6 RPS6KA6 RPS6KA6 3367 0.084 0.48 YES
7 KIAA1598 KIAA1598 KIAA1598 4203 0.064 0.47 YES
8 MAPK1 MAPK1 MAPK1 4579 0.057 0.48 YES
9 RPS6KA4 RPS6KA4 RPS6KA4 4677 0.055 0.5 YES
10 SRC SRC SRC 5216 0.046 0.5 YES
11 KIF4B KIF4B KIF4B 5454 0.042 0.51 YES
12 CLTA CLTA CLTA 5597 0.04 0.53 YES
13 RPS6KA5 RPS6KA5 RPS6KA5 8401 0.0079 0.38 NO
14 DNM2 DNM2 DNM2 8408 0.0078 0.38 NO
15 NUMB NUMB NUMB 8654 0.0049 0.37 NO
16 L1CAM L1CAM L1CAM 8719 0.0043 0.37 NO
17 AP2B1 AP2B1 AP2B1 8892 0.0023 0.36 NO
18 CLTC CLTC CLTC 9142 -0.00034 0.35 NO
19 MSN MSN MSN 9874 -0.0086 0.31 NO
20 AP2A1 AP2A1 AP2A1 10508 -0.015 0.28 NO
21 AP2S1 AP2S1 AP2S1 10660 -0.018 0.29 NO
22 AP2A2 AP2A2 AP2A2 10704 -0.018 0.3 NO
23 RDX RDX RDX 10716 -0.018 0.3 NO
24 RPS6KA1 RPS6KA1 RPS6KA1 10949 -0.021 0.3 NO
25 RPS6KA3 RPS6KA3 RPS6KA3 11602 -0.03 0.28 NO
26 AP2M1 AP2M1 AP2M1 12342 -0.043 0.27 NO
27 EZR EZR EZR 13759 -0.078 0.24 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 SPHINGOLIPID METABOLISM.

Figure S2.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPHINGOLIPID 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 NUCLEOTIDE EXCISION REPAIR

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 CCNA1 CCNA1 CCNA1 322 0.4 0.12 YES
2 CCNE1 CCNE1 CCNE1 359 0.38 0.25 YES
3 CDC25A CDC25A CDC25A 1202 0.21 0.27 YES
4 TGFB2 TGFB2 TGFB2 1381 0.19 0.33 YES
5 E2F1 E2F1 E2F1 1464 0.18 0.38 YES
6 CDK1 CDK1 CDK1 1781 0.16 0.42 YES
7 CDK6 CDK6 CDK6 2465 0.12 0.42 YES
8 HDAC1 HDAC1 HDAC1 2671 0.11 0.44 YES
9 DHFR DHFR DHFR 2760 0.1 0.48 YES
10 CDKN2A CDKN2A CDKN2A 2820 0.1 0.51 YES
11 RB1 RB1 RB1 3879 0.071 0.47 NO
12 TGFB1 TGFB1 TGFB1 5054 0.048 0.42 NO
13 TFDP1 TFDP1 TFDP1 5118 0.048 0.44 NO
14 SMAD4 SMAD4 SMAD4 5705 0.039 0.42 NO
15 CDK4 CDK4 CDK4 5792 0.038 0.42 NO
16 SMAD3 SMAD3 SMAD3 6051 0.034 0.42 NO
17 GSK3B GSK3B GSK3B 6944 0.024 0.38 NO
18 CDKN1B CDKN1B CDKN1B 8306 0.0088 0.31 NO
19 TP53 TP53 TP53 9508 -0.0042 0.24 NO
20 CDK2 CDK2 CDK2 10578 -0.016 0.19 NO
21 ATM ATM ATM 10690 -0.018 0.19 NO
22 CCND1 CCND1 CCND1 10975 -0.021 0.18 NO
23 ABL1 ABL1 ABL1 11316 -0.026 0.17 NO
24 CDKN1A CDKN1A CDKN1A 13158 -0.061 0.086 NO
25 SKP2 SKP2 SKP2 13572 -0.072 0.088 NO
26 ATR ATR ATR 13911 -0.083 0.097 NO
27 CDKN2B CDKN2B CDKN2B 14105 -0.089 0.12 NO
28 TGFB3 TGFB3 TGFB3 16835 -0.29 0.064 NO

Figure S3.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NUCLEOTIDE EXCISION REPAIR.

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

genes ES table in pathway: KEGG CARDIAC MUSCLE CONTRACTION

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 GAL3ST1 GAL3ST1 GAL3ST1 123 0.52 0.16 YES
2 UGT8 UGT8 UGT8 329 0.4 0.28 YES
3 DEGS2 DEGS2 DEGS2 380 0.38 0.4 YES
4 SGPP2 SGPP2 SGPP2 542 0.32 0.5 YES
5 CERK CERK CERK 1371 0.19 0.51 YES
6 ACER3 ACER3 ACER3 2047 0.14 0.52 YES
7 PPAP2C PPAP2C PPAP2C 3379 0.083 0.47 NO
8 ASAH2 ASAH2 ASAH2 3953 0.07 0.46 NO
9 SGPL1 SGPL1 SGPL1 5362 0.044 0.4 NO
10 SMPD4 SMPD4 SMPD4 5536 0.041 0.4 NO
11 PPAP2A PPAP2A PPAP2A 6276 0.031 0.37 NO
12 DEGS1 DEGS1 DEGS1 7049 0.022 0.34 NO
13 SGPP1 SGPP1 SGPP1 7113 0.022 0.34 NO
14 SMPD3 SMPD3 SMPD3 7237 0.02 0.34 NO
15 ASAH1 ASAH1 ASAH1 7421 0.018 0.33 NO
16 NEU4 NEU4 NEU4 7814 0.014 0.32 NO
17 SPHK2 SPHK2 SPHK2 7881 0.013 0.32 NO
18 KDSR KDSR KDSR 8134 0.011 0.31 NO
19 SPHK1 SPHK1 SPHK1 8442 0.0073 0.29 NO
20 PPAP2B PPAP2B PPAP2B 8915 0.0021 0.27 NO
21 UGCG UGCG UGCG 8961 0.0016 0.26 NO
22 SMPD1 SMPD1 SMPD1 9741 -0.0069 0.22 NO
23 SPTLC2 SPTLC2 SPTLC2 9754 -0.0071 0.22 NO
24 GLB1 GLB1 GLB1 10018 -0.01 0.21 NO
25 SPTLC1 SPTLC1 SPTLC1 10445 -0.015 0.19 NO
26 NEU1 NEU1 NEU1 10492 -0.015 0.2 NO
27 ACER2 ACER2 ACER2 10831 -0.019 0.18 NO
28 NEU3 NEU3 NEU3 11019 -0.022 0.18 NO
29 SGMS1 SGMS1 SGMS1 11507 -0.029 0.16 NO
30 SMPD2 SMPD2 SMPD2 11876 -0.035 0.15 NO
31 ARSA ARSA ARSA 12745 -0.051 0.12 NO
32 GBA GBA GBA 13172 -0.061 0.12 NO
33 B4GALT6 B4GALT6 B4GALT6 13258 -0.064 0.13 NO
34 SGMS2 SGMS2 SGMS2 14102 -0.089 0.12 NO
35 GALC GALC GALC 15321 -0.15 0.098 NO
36 GLA GLA GLA 15368 -0.16 0.14 NO

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

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

genes ES table in pathway: KEGG TIGHT JUNCTION

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 TJP3 TJP3 TJP3 32 0.69 0.047 YES
2 PRKCG PRKCG PRKCG 50 0.63 0.09 YES
3 MYH14 MYH14 MYH14 85 0.57 0.13 YES
4 CLDN6 CLDN6 CLDN6 292 0.41 0.15 YES
5 MYH7 MYH7 MYH7 306 0.4 0.17 YES
6 CLDN11 CLDN11 CLDN11 497 0.34 0.19 YES
7 PARD6B PARD6B PARD6B 549 0.32 0.21 YES
8 CTNNA2 CTNNA2 CTNNA2 624 0.3 0.22 YES
9 CTNNA3 CTNNA3 CTNNA3 699 0.29 0.24 YES
10 MYH7B MYH7B MYH7B 822 0.26 0.25 YES
11 CLDN3 CLDN3 CLDN3 843 0.26 0.27 YES
12 CLDN15 CLDN15 CLDN15 883 0.25 0.28 YES
13 LLGL2 LLGL2 LLGL2 946 0.24 0.3 YES
14 MYH3 MYH3 MYH3 948 0.24 0.32 YES
15 OCLN OCLN OCLN 949 0.24 0.33 YES
16 RAB3B RAB3B RAB3B 978 0.24 0.35 YES
17 PRKCQ PRKCQ PRKCQ 1111 0.22 0.36 YES
18 CLDN4 CLDN4 CLDN4 1234 0.21 0.36 YES
19 CRB3 CRB3 CRB3 1338 0.2 0.37 YES
20 PRKCA PRKCA PRKCA 1344 0.2 0.38 YES
21 CLDN10 CLDN10 CLDN10 1556 0.18 0.39 YES
22 MYL5 MYL5 MYL5 1575 0.17 0.4 YES
23 PRKCB PRKCB PRKCB 1582 0.17 0.41 YES
24 CLDN23 CLDN23 CLDN23 1952 0.14 0.4 NO
25 PARD6G PARD6G PARD6G 2276 0.12 0.39 NO
26 PARD3 PARD3 PARD3 2586 0.11 0.38 NO
27 CLDN9 CLDN9 CLDN9 2862 0.099 0.37 NO
28 CGN CGN CGN 2892 0.098 0.38 NO
29 ZAK ZAK ZAK 2899 0.097 0.38 NO
30 PRKCZ PRKCZ PRKCZ 2934 0.096 0.39 NO
31 EPB41 EPB41 EPB41 2955 0.096 0.39 NO
32 PPP2R2C PPP2R2C PPP2R2C 3009 0.094 0.4 NO
33 SYMPK SYMPK SYMPK 3052 0.093 0.4 NO
34 INADL INADL INADL 3348 0.084 0.39 NO
35 PPP2R2A PPP2R2A PPP2R2A 3396 0.083 0.39 NO
36 AKT3 AKT3 AKT3 3550 0.079 0.39 NO
37 LLGL1 LLGL1 LLGL1 3625 0.077 0.39 NO
38 CASK CASK CASK 3864 0.072 0.38 NO
39 PPP2R2D PPP2R2D PPP2R2D 4278 0.062 0.36 NO
40 MPP5 MPP5 MPP5 4649 0.055 0.35 NO
41 ACTN2 ACTN2 ACTN2 4651 0.055 0.35 NO
42 PPP2CB PPP2CB PPP2CB 4815 0.052 0.35 NO
43 ASH1L ASH1L ASH1L 5072 0.048 0.34 NO
44 SRC SRC SRC 5216 0.046 0.33 NO
45 EPB41L3 EPB41L3 EPB41L3 5311 0.044 0.33 NO
46 PRKCI PRKCI PRKCI 5394 0.043 0.33 NO
47 CSNK2A1 CSNK2A1 CSNK2A1 5449 0.043 0.33 NO
48 CLDN18 CLDN18 CLDN18 5516 0.042 0.33 NO
49 GNAI3 GNAI3 GNAI3 5560 0.041 0.33 NO
50 CDK4 CDK4 CDK4 5792 0.038 0.32 NO
51 NRAS NRAS NRAS 5902 0.036 0.31 NO
52 MAGI3 MAGI3 MAGI3 6114 0.033 0.3 NO
53 SPTAN1 SPTAN1 SPTAN1 6243 0.032 0.3 NO
54 EPB41L2 EPB41L2 EPB41L2 6279 0.031 0.3 NO
55 CSNK2A2 CSNK2A2 CSNK2A2 6372 0.03 0.3 NO
56 VAPA VAPA VAPA 6459 0.029 0.29 NO
57 TJAP1 TJAP1 TJAP1 6568 0.028 0.29 NO
58 MAGI2 MAGI2 MAGI2 6569 0.028 0.29 NO
59 CSDA CSDA CSDA 6596 0.027 0.29 NO
60 MLLT4 MLLT4 MLLT4 6693 0.026 0.29 NO
61 EXOC3 EXOC3 EXOC3 6909 0.024 0.28 NO
62 CTNNB1 CTNNB1 CTNNB1 7083 0.022 0.27 NO
63 PRKCH PRKCH PRKCH 7301 0.02 0.26 NO
64 CDC42 CDC42 CDC42 7378 0.019 0.26 NO
65 PPP2R1A PPP2R1A PPP2R1A 7441 0.018 0.25 NO
66 KRAS KRAS KRAS 7518 0.017 0.25 NO
67 GNAI2 GNAI2 GNAI2 7862 0.014 0.23 NO
68 AKT2 AKT2 AKT2 8033 0.012 0.22 NO
69 JAM3 JAM3 JAM3 8056 0.011 0.22 NO
70 TJP2 TJP2 TJP2 8226 0.0097 0.21 NO
71 MPDZ MPDZ MPDZ 8580 0.0057 0.2 NO
72 CSNK2B CSNK2B CSNK2B 8791 0.0034 0.18 NO
73 GNAI1 GNAI1 GNAI1 9502 -0.0042 0.14 NO
74 RHOA RHOA RHOA 9992 -0.0098 0.12 NO
75 PRKCE PRKCE PRKCE 10217 -0.012 0.1 NO
76 PTEN PTEN PTEN 10395 -0.014 0.096 NO
77 EPB41L1 EPB41L1 EPB41L1 10449 -0.015 0.094 NO
78 YES1 YES1 YES1 10552 -0.016 0.09 NO
79 TJP1 TJP1 TJP1 10742 -0.018 0.081 NO
80 CTNNA1 CTNNA1 CTNNA1 10805 -0.019 0.078 NO
81 EXOC4 EXOC4 EXOC4 10936 -0.021 0.073 NO
82 PPP2CA PPP2CA PPP2CA 11104 -0.023 0.065 NO
83 CTTN CTTN CTTN 11160 -0.024 0.064 NO
84 MYH10 MYH10 MYH10 11290 -0.026 0.058 NO
85 PARD6A PARD6A PARD6A 11741 -0.033 0.035 NO
86 MYH9 MYH9 MYH9 12025 -0.037 0.022 NO
87 MAGI1 MAGI1 MAGI1 12165 -0.039 0.017 NO
88 JAM2 JAM2 JAM2 12253 -0.041 0.015 NO
89 MYL12B MYL12B MYL12B 12463 -0.045 0.0065 NO
90 ACTN4 ACTN4 ACTN4 12528 -0.046 0.0062 NO
91 RRAS2 RRAS2 RRAS2 12575 -0.047 0.0069 NO
92 RRAS RRAS RRAS 12605 -0.048 0.0087 NO
93 HRAS HRAS HRAS 12613 -0.048 0.012 NO
94 ACTB ACTB ACTB 12659 -0.049 0.013 NO
95 RAB13 RAB13 RAB13 12944 -0.056 0.00065 NO
96 AKT1 AKT1 AKT1 13122 -0.06 -0.005 NO
97 F11R F11R F11R 13306 -0.065 -0.011 NO
98 CLDN5 CLDN5 CLDN5 13409 -0.068 -0.012 NO
99 ACTG1 ACTG1 ACTG1 13450 -0.068 -0.0091 NO
100 AMOTL1 AMOTL1 AMOTL1 13469 -0.069 -0.0052 NO
101 MYL12A MYL12A MYL12A 13704 -0.076 -0.013 NO
102 ACTN3 ACTN3 ACTN3 14016 -0.087 -0.024 NO
103 ACTN1 ACTN1 ACTN1 14625 -0.11 -0.05 NO
104 PPP2R1B PPP2R1B PPP2R1B 14674 -0.12 -0.045 NO
105 MRAS MRAS MRAS 14733 -0.12 -0.04 NO
106 MYL9 MYL9 MYL9 14855 -0.12 -0.038 NO
107 CLDN7 CLDN7 CLDN7 14951 -0.13 -0.034 NO
108 MYH11 MYH11 MYH11 14979 -0.13 -0.026 NO
109 MYH6 MYH6 MYH6 15164 -0.14 -0.026 NO
110 PPP2R2B PPP2R2B PPP2R2B 15196 -0.14 -0.018 NO
111 CLDN2 CLDN2 CLDN2 15397 -0.16 -0.018 NO
112 HCLS1 HCLS1 HCLS1 15456 -0.16 -0.01 NO
113 CLDN14 CLDN14 CLDN14 15690 -0.18 -0.011 NO
114 CLDN1 CLDN1 CLDN1 16004 -0.21 -0.014 NO
115 MYH15 MYH15 MYH15 16792 -0.29 -0.038 NO
116 PRKCD PRKCD PRKCD 16836 -0.29 -0.02 NO
117 MYLPF MYLPF MYLPF 17100 -0.33 -0.011 NO
118 CLDN20 CLDN20 CLDN20 17136 -0.34 0.011 NO
119 IGSF5 IGSF5 IGSF5 17830 -0.52 0.0082 NO

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

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

genes ES table in pathway: KEGG LONG TERM POTENTIATION

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 PRKCG PRKCG PRKCG 50 0.63 0.16 YES
2 ATP6V0A4 ATP6V0A4 ATP6V0A4 64 0.61 0.32 YES
3 PRKCA PRKCA PRKCA 1344 0.2 0.3 YES
4 PRKCB PRKCB PRKCB 1582 0.17 0.33 YES
5 PRKACG PRKACG PRKACG 1892 0.15 0.36 YES
6 SEC61A2 SEC61A2 SEC61A2 2250 0.13 0.37 YES
7 PRKX PRKX PRKX 2634 0.11 0.38 YES
8 ADCY9 ADCY9 ADCY9 3715 0.075 0.34 NO
9 PLCG1 PLCG1 PLCG1 3801 0.073 0.35 NO
10 ATP6V1B2 ATP6V1B2 ATP6V1B2 3974 0.069 0.36 NO
11 ATP6V1G2 ATP6V1G2 ATP6V1G2 4824 0.052 0.32 NO
12 ATP6V1E2 ATP6V1E2 ATP6V1E2 5091 0.048 0.32 NO
13 SLC12A2 SLC12A2 SLC12A2 5398 0.043 0.32 NO
14 ATP6V1F ATP6V1F ATP6V1F 5817 0.037 0.3 NO
15 ATP6V1C1 ATP6V1C1 ATP6V1C1 6438 0.029 0.28 NO
16 GNAS GNAS GNAS 6794 0.025 0.26 NO
17 ATP6V1H ATP6V1H ATP6V1H 6849 0.025 0.27 NO
18 ATP6V1A ATP6V1A ATP6V1A 6873 0.024 0.27 NO
19 KDELR1 KDELR1 KDELR1 6995 0.023 0.27 NO
20 ADCY3 ADCY3 ADCY3 7102 0.022 0.27 NO
21 KDELR2 KDELR2 KDELR2 7810 0.014 0.24 NO
22 TJP2 TJP2 TJP2 8226 0.0097 0.22 NO
23 ATP6V1E1 ATP6V1E1 ATP6V1E1 8335 0.0085 0.21 NO
24 ERO1L ERO1L ERO1L 8603 0.0054 0.2 NO
25 ATP6V0A1 ATP6V0A1 ATP6V0A1 8714 0.0043 0.19 NO
26 PDIA4 PDIA4 PDIA4 8966 0.0016 0.18 NO
27 ATP6V1D ATP6V1D ATP6V1D 9104 0.000079 0.17 NO
28 ATP6V1G1 ATP6V1G1 ATP6V1G1 9128 -0.00026 0.17 NO
29 ATP6V0D2 ATP6V0D2 ATP6V0D2 9200 -0.00094 0.17 NO
30 ATP6V0E1 ATP6V0E1 ATP6V0E1 9268 -0.0017 0.16 NO
31 ATP6AP1 ATP6AP1 ATP6AP1 10330 -0.014 0.11 NO
32 ATP6V0C ATP6V0C ATP6V0C 10386 -0.014 0.11 NO
33 SEC61A1 SEC61A1 SEC61A1 10589 -0.016 0.1 NO
34 ATP6V1C2 ATP6V1C2 ATP6V1C2 10619 -0.017 0.1 NO
35 TJP1 TJP1 TJP1 10742 -0.018 0.1 NO
36 ATP6V0A2 ATP6V0A2 ATP6V0A2 11102 -0.023 0.088 NO
37 ARF1 ARF1 ARF1 11247 -0.025 0.086 NO
38 SEC61B SEC61B SEC61B 11580 -0.03 0.076 NO
39 ATP6V0B ATP6V0B ATP6V0B 11634 -0.031 0.081 NO
40 ATP6V0D1 ATP6V0D1 ATP6V0D1 11721 -0.032 0.085 NO
41 ATP6V0E2 ATP6V0E2 ATP6V0E2 11767 -0.033 0.091 NO
42 PRKACA PRKACA PRKACA 11943 -0.036 0.09 NO
43 ACTB ACTB ACTB 12659 -0.049 0.064 NO
44 PLCG2 PLCG2 PLCG2 12966 -0.056 0.061 NO
45 SEC61G SEC61G SEC61G 13140 -0.06 0.068 NO
46 ACTG1 ACTG1 ACTG1 13450 -0.068 0.068 NO
47 KDELR3 KDELR3 KDELR3 13970 -0.085 0.062 NO
48 PRKACB PRKACB PRKACB 14045 -0.088 0.081 NO
49 ATP6V1B1 ATP6V1B1 ATP6V1B1 14393 -0.1 0.088 NO
50 TCIRG1 TCIRG1 TCIRG1 14540 -0.11 0.11 NO
51 KCNQ1 KCNQ1 KCNQ1 17018 -0.32 0.053 NO

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

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LONG TERM POTENTIATION, 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 TASTE TRANSDUCTION

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 PRKCG PRKCG PRKCG 50 0.63 0.07 YES
2 ERBB3 ERBB3 ERBB3 57 0.62 0.14 YES
3 BTC BTC BTC 361 0.38 0.17 YES
4 NRG4 NRG4 NRG4 682 0.29 0.18 YES
5 ADCY5 ADCY5 ADCY5 738 0.28 0.21 YES
6 MATK MATK MATK 926 0.25 0.23 YES
7 ADCY1 ADCY1 ADCY1 1042 0.23 0.25 YES
8 NRG1 NRG1 NRG1 1110 0.22 0.27 YES
9 ERBB2 ERBB2 ERBB2 1257 0.2 0.29 YES
10 PHLPP1 PHLPP1 PHLPP1 1296 0.2 0.31 YES
11 GRB7 GRB7 GRB7 1339 0.2 0.33 YES
12 PRKCA PRKCA PRKCA 1344 0.2 0.35 YES
13 TRIB3 TRIB3 TRIB3 1676 0.16 0.35 YES
14 CDK1 CDK1 CDK1 1781 0.16 0.36 YES
15 PRKACG PRKACG PRKACG 1892 0.15 0.37 YES
16 GAB1 GAB1 GAB1 2275 0.13 0.37 YES
17 PRKAR1B PRKAR1B PRKAR1B 2309 0.12 0.38 YES
18 MAP2K1 MAP2K1 MAP2K1 2372 0.12 0.39 YES
19 PDE1B PDE1B PDE1B 2477 0.12 0.4 YES
20 FOXO4 FOXO4 FOXO4 2900 0.097 0.38 NO
21 CAMK4 CAMK4 CAMK4 3455 0.081 0.36 NO
22 AKT3 AKT3 AKT3 3550 0.079 0.37 NO
23 ADCY9 ADCY9 ADCY9 3715 0.075 0.36 NO
24 FOXO3 FOXO3 FOXO3 3757 0.074 0.37 NO
25 ADCY6 ADCY6 ADCY6 3759 0.074 0.38 NO
26 PLCG1 PLCG1 PLCG1 3801 0.073 0.39 NO
27 RICTOR RICTOR RICTOR 4061 0.067 0.38 NO
28 CALM3 CALM3 CALM3 4492 0.058 0.36 NO
29 MAPK1 MAPK1 MAPK1 4579 0.057 0.36 NO
30 RPS27A RPS27A RPS27A 4642 0.056 0.37 NO
31 FYN FYN FYN 5021 0.049 0.35 NO
32 MTOR MTOR MTOR 5047 0.049 0.36 NO
33 RNF41 RNF41 RNF41 5164 0.047 0.35 NO
34 CASP9 CASP9 CASP9 5202 0.046 0.36 NO
35 SRC SRC SRC 5216 0.046 0.36 NO
36 MDM2 MDM2 MDM2 5738 0.038 0.34 NO
37 FOXO1 FOXO1 FOXO1 5815 0.037 0.34 NO
38 NRAS NRAS NRAS 5902 0.036 0.34 NO
39 MLST8 MLST8 MLST8 6106 0.034 0.33 NO
40 CREB1 CREB1 CREB1 6275 0.031 0.32 NO
41 CHUK CHUK CHUK 6583 0.027 0.31 NO
42 ADCY3 ADCY3 ADCY3 7102 0.022 0.28 NO
43 USP8 USP8 USP8 7136 0.021 0.28 NO
44 MAP2K2 MAP2K2 MAP2K2 7196 0.021 0.28 NO
45 PRKAR2A PRKAR2A PRKAR2A 7232 0.02 0.28 NO
46 GSK3A GSK3A GSK3A 7303 0.02 0.28 NO
47 ADCY4 ADCY4 ADCY4 7305 0.019 0.28 NO
48 KRAS KRAS KRAS 7518 0.017 0.27 NO
49 CUL5 CUL5 CUL5 7535 0.017 0.28 NO
50 EGF EGF EGF 7586 0.016 0.27 NO
51 ADCY8 ADCY8 ADCY8 7690 0.015 0.27 NO
52 AKT2 AKT2 AKT2 8033 0.012 0.25 NO
53 MAPK3 MAPK3 MAPK3 8303 0.0088 0.24 NO
54 CDKN1B CDKN1B CDKN1B 8306 0.0088 0.24 NO
55 SOS1 SOS1 SOS1 8659 0.0048 0.22 NO
56 PDPK1 PDPK1 PDPK1 8707 0.0044 0.22 NO
57 UBA52 UBA52 UBA52 8830 0.003 0.21 NO
58 AKT1S1 AKT1S1 AKT1S1 9393 -0.003 0.18 NO
59 CDC37 CDC37 CDC37 9463 -0.0038 0.18 NO
60 STUB1 STUB1 STUB1 9721 -0.0066 0.16 NO
61 GRB2 GRB2 GRB2 9762 -0.0071 0.16 NO
62 RAF1 RAF1 RAF1 9844 -0.008 0.16 NO
63 ITPR3 ITPR3 ITPR3 10110 -0.011 0.14 NO
64 PRKCE PRKCE PRKCE 10217 -0.012 0.14 NO
65 PRKAR1A PRKAR1A PRKAR1A 10292 -0.013 0.14 NO
66 PTEN PTEN PTEN 10395 -0.014 0.13 NO
67 YES1 YES1 YES1 10552 -0.016 0.13 NO
68 BAD BAD BAD 10585 -0.016 0.13 NO
69 ERBB4 ERBB4 ERBB4 10605 -0.017 0.13 NO
70 HSP90AA1 HSP90AA1 HSP90AA1 10771 -0.019 0.12 NO
71 ITPR2 ITPR2 ITPR2 10840 -0.02 0.12 NO
72 PIK3CA PIK3CA PIK3CA 10908 -0.02 0.12 NO
73 ADCY2 ADCY2 ADCY2 11074 -0.023 0.11 NO
74 NRG2 NRG2 NRG2 11153 -0.024 0.11 NO
75 ADRBK1 ADRBK1 ADRBK1 11246 -0.025 0.11 NO
76 YWHAB YWHAB YWHAB 11678 -0.032 0.086 NO
77 MAPKAP1 MAPKAP1 MAPKAP1 11775 -0.033 0.084 NO
78 PRKACA PRKACA PRKACA 11943 -0.036 0.079 NO
79 RPS6KB2 RPS6KB2 RPS6KB2 12147 -0.039 0.072 NO
80 THEM4 THEM4 THEM4 12464 -0.045 0.06 NO
81 HRAS HRAS HRAS 12613 -0.048 0.057 NO
82 AKT1 AKT1 AKT1 13122 -0.06 0.036 NO
83 CDKN1A CDKN1A CDKN1A 13158 -0.061 0.041 NO
84 PDE1A PDE1A PDE1A 13237 -0.063 0.044 NO
85 CALM1 CALM1 CALM1 13369 -0.067 0.044 NO
86 TSC2 TSC2 TSC2 13393 -0.067 0.05 NO
87 PRKACB PRKACB PRKACB 14045 -0.088 0.024 NO
88 CALM2 CALM2 CALM2 14096 -0.089 0.031 NO
89 ADCY7 ADCY7 ADCY7 14115 -0.09 0.041 NO
90 PRKAR2B PRKAR2B PRKAR2B 14234 -0.095 0.045 NO
91 SHC1 SHC1 SHC1 14788 -0.12 0.028 NO
92 HBEGF HBEGF HBEGF 15116 -0.14 0.026 NO
93 PIK3R1 PIK3R1 PIK3R1 15236 -0.15 0.036 NO
94 NR4A1 NR4A1 NR4A1 15633 -0.17 0.034 NO
95 EGFR EGFR EGFR 16036 -0.21 0.035 NO
96 PRKCD PRKCD PRKCD 16836 -0.29 0.024 NO
97 EREG EREG EREG 17196 -0.34 0.044 NO

Figure S11.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TASTE TRANSDUCTION.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TASTE TRANSDUCTION, 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 VIBRIO CHOLERAE INFECTION

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 VPS37D VPS37D VPS37D 261 0.43 0.34 YES
2 CHMP6 CHMP6 CHMP6 2966 0.096 0.27 YES
3 VTA1 VTA1 VTA1 3698 0.075 0.29 YES
4 CHMP2B CHMP2B CHMP2B 3789 0.073 0.34 YES
5 VPS36 VPS36 VPS36 4042 0.067 0.38 YES
6 RPS27A RPS27A RPS27A 4642 0.056 0.4 YES
7 CHMP7 CHMP7 CHMP7 5049 0.049 0.42 YES
8 VPS37C VPS37C VPS37C 6211 0.032 0.38 YES
9 VPS25 VPS25 VPS25 6236 0.032 0.4 YES
10 VPS37A VPS37A VPS37A 6337 0.031 0.42 YES
11 CHMP5 CHMP5 CHMP5 6982 0.023 0.4 NO
12 STAM STAM STAM 7381 0.019 0.4 NO
13 TSG101 TSG101 TSG101 8563 0.0059 0.34 NO
14 SNF8 SNF8 SNF8 8692 0.0045 0.33 NO
15 UBA52 UBA52 UBA52 8830 0.003 0.33 NO
16 STAM2 STAM2 STAM2 9234 -0.0013 0.31 NO
17 CHMP4B CHMP4B CHMP4B 9453 -0.0037 0.3 NO
18 VPS4A VPS4A VPS4A 10143 -0.011 0.27 NO
19 VPS4B VPS4B VPS4B 10298 -0.013 0.27 NO
20 HGS HGS HGS 10534 -0.016 0.27 NO
21 VPS28 VPS28 VPS28 10863 -0.02 0.27 NO
22 CHMP2A CHMP2A CHMP2A 11037 -0.022 0.28 NO
23 CHMP4C CHMP4C CHMP4C 11210 -0.024 0.29 NO
24 CHMP4A CHMP4A CHMP4A 12402 -0.044 0.26 NO
25 VPS37B VPS37B VPS37B 13219 -0.062 0.26 NO

Figure S13.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VIBRIO CHOLERAE INFECTION.

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

genes ES table in pathway: BIOCARTA G1 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 PRKCG PRKCG PRKCG 50 0.63 0.099 YES
2 GRIN1 GRIN1 GRIN1 56 0.62 0.2 YES
3 GRM5 GRM5 GRM5 494 0.34 0.23 YES
4 ADCY1 ADCY1 ADCY1 1042 0.23 0.23 YES
5 PPP1R1A PPP1R1A PPP1R1A 1181 0.21 0.26 YES
6 GRIN2B GRIN2B GRIN2B 1334 0.2 0.28 YES
7 PRKCA PRKCA PRKCA 1344 0.2 0.32 YES
8 PRKCB PRKCB PRKCB 1582 0.17 0.33 YES
9 CHP2 CHP2 CHP2 1794 0.15 0.34 YES
10 CACNA1C CACNA1C CACNA1C 1859 0.15 0.36 YES
11 PRKACG PRKACG PRKACG 1892 0.15 0.38 YES
12 MAP2K1 MAP2K1 MAP2K1 2372 0.12 0.38 YES
13 PRKX PRKX PRKX 2634 0.11 0.38 YES
14 RPS6KA2 RPS6KA2 RPS6KA2 2819 0.1 0.39 YES
15 CAMK2D CAMK2D CAMK2D 3010 0.094 0.39 YES
16 GRM1 GRM1 GRM1 3144 0.09 0.4 YES
17 PPP3R1 PPP3R1 PPP3R1 3159 0.089 0.41 YES
18 GRIN2A GRIN2A GRIN2A 3208 0.088 0.42 YES
19 RPS6KA6 RPS6KA6 RPS6KA6 3367 0.084 0.43 YES
20 CAMK4 CAMK4 CAMK4 3455 0.081 0.44 YES
21 CREBBP CREBBP CREBBP 4143 0.065 0.41 NO
22 PPP1R12A PPP1R12A PPP1R12A 4194 0.064 0.42 NO
23 PLCB1 PLCB1 PLCB1 4410 0.06 0.41 NO
24 CALM3 CALM3 CALM3 4492 0.058 0.42 NO
25 MAPK1 MAPK1 MAPK1 4579 0.057 0.42 NO
26 EP300 EP300 EP300 5026 0.049 0.4 NO
27 GNAQ GNAQ GNAQ 5502 0.042 0.38 NO
28 PPP3CA PPP3CA PPP3CA 5619 0.04 0.38 NO
29 ITPR1 ITPR1 ITPR1 5627 0.04 0.39 NO
30 NRAS NRAS NRAS 5902 0.036 0.38 NO
31 PLCB4 PLCB4 PLCB4 6517 0.028 0.35 NO
32 PPP3CB PPP3CB PPP3CB 6813 0.025 0.34 NO
33 MAP2K2 MAP2K2 MAP2K2 7196 0.021 0.32 NO
34 PPP1CC PPP1CC PPP1CC 7451 0.018 0.31 NO
35 KRAS KRAS KRAS 7518 0.017 0.31 NO
36 ARAF ARAF ARAF 7532 0.017 0.31 NO
37 ADCY8 ADCY8 ADCY8 7690 0.015 0.3 NO
38 PLCB3 PLCB3 PLCB3 8109 0.011 0.28 NO
39 MAPK3 MAPK3 MAPK3 8303 0.0088 0.27 NO
40 BRAF BRAF BRAF 8378 0.008 0.27 NO
41 PPP3CC PPP3CC PPP3CC 8931 0.002 0.24 NO
42 RAF1 RAF1 RAF1 9844 -0.008 0.19 NO
43 ITPR3 ITPR3 ITPR3 10110 -0.011 0.18 NO
44 PPP1CB PPP1CB PPP1CB 10321 -0.013 0.17 NO
45 ATF4 ATF4 ATF4 10836 -0.02 0.14 NO
46 ITPR2 ITPR2 ITPR2 10840 -0.02 0.15 NO
47 RPS6KA1 RPS6KA1 RPS6KA1 10949 -0.021 0.14 NO
48 CHP CHP CHP 11200 -0.024 0.13 NO
49 RAP1A RAP1A RAP1A 11487 -0.028 0.12 NO
50 RPS6KA3 RPS6KA3 RPS6KA3 11602 -0.03 0.12 NO
51 PRKACA PRKACA PRKACA 11943 -0.036 0.11 NO
52 CAMK2G CAMK2G CAMK2G 12359 -0.043 0.09 NO
53 GRIN2C GRIN2C GRIN2C 12362 -0.043 0.097 NO
54 RAP1B RAP1B RAP1B 12364 -0.043 0.1 NO
55 RAPGEF3 RAPGEF3 RAPGEF3 12530 -0.046 0.1 NO
56 GRIN2D GRIN2D GRIN2D 12561 -0.047 0.11 NO
57 HRAS HRAS HRAS 12613 -0.048 0.11 NO
58 GRIA2 GRIA2 GRIA2 12737 -0.051 0.11 NO
59 PPP3R2 PPP3R2 PPP3R2 13250 -0.063 0.096 NO
60 CALM1 CALM1 CALM1 13369 -0.067 0.1 NO
61 GRIA1 GRIA1 GRIA1 13540 -0.071 0.1 NO
62 PPP1CA PPP1CA PPP1CA 13557 -0.071 0.11 NO
63 CALML6 CALML6 CALML6 13837 -0.08 0.11 NO
64 CAMK2B CAMK2B CAMK2B 13967 -0.085 0.12 NO
65 PRKACB PRKACB PRKACB 14045 -0.088 0.13 NO
66 CALM2 CALM2 CALM2 14096 -0.089 0.14 NO
67 CAMK2A CAMK2A CAMK2A 16332 -0.24 0.051 NO
68 PLCB2 PLCB2 PLCB2 16515 -0.25 0.082 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: BIOCARTA G1 PATHWAY.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

Table 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 CCNA1 CCNA1 CCNA1 322 0.4 0.097 YES
2 CCNE1 CCNE1 CCNE1 359 0.38 0.21 YES
3 CDT1 CDT1 CDT1 691 0.29 0.27 YES
4 TYMS TYMS TYMS 1008 0.24 0.32 YES
5 CDC25A CDC25A CDC25A 1202 0.21 0.37 YES
6 CDC45 CDC45 CDC45 1255 0.2 0.43 YES
7 E2F1 E2F1 E2F1 1464 0.18 0.47 YES
8 PRIM1 PRIM1 PRIM1 1673 0.16 0.51 YES
9 CDK1 CDK1 CDK1 1781 0.16 0.55 YES
10 FBXO5 FBXO5 FBXO5 1840 0.15 0.58 YES
11 CDC6 CDC6 CDC6 1993 0.14 0.62 YES
12 PPP2R3B PPP2R3B PPP2R3B 2506 0.11 0.62 YES
13 DHFR DHFR DHFR 2760 0.1 0.64 YES
14 RB1 RB1 RB1 3879 0.071 0.6 NO
15 PPP2CB PPP2CB PPP2CB 4815 0.052 0.56 NO
16 TFDP1 TFDP1 TFDP1 5118 0.048 0.56 NO
17 PCNA PCNA PCNA 6502 0.028 0.49 NO
18 POLA1 POLA1 POLA1 6506 0.028 0.5 NO
19 POLA2 POLA2 POLA2 6735 0.026 0.49 NO
20 PPP2R1A PPP2R1A PPP2R1A 7441 0.018 0.46 NO
21 CCNB1 CCNB1 CCNB1 7497 0.017 0.46 NO
22 PPP2CA PPP2CA PPP2CA 11104 -0.023 0.26 NO
23 PRIM2 PRIM2 PRIM2 11984 -0.036 0.22 NO
24 TK2 TK2 TK2 13428 -0.068 0.16 NO
25 MCM8 MCM8 MCM8 13727 -0.077 0.17 NO
26 RRM2 RRM2 RRM2 14646 -0.11 0.15 NO
27 PPP2R1B PPP2R1B PPP2R1B 14674 -0.12 0.18 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: BIOCARTA CHREBP2 PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID BARD1PATHWAY

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 GNG13 GNG13 GNG13 13 0.79 0.12 YES
2 GNG3 GNG3 GNG3 102 0.56 0.19 YES
3 TAS2R4 TAS2R4 TAS2R4 122 0.52 0.27 YES
4 TAS2R5 TAS2R5 TAS2R5 537 0.32 0.29 YES
5 TAS2R19 TAS2R19 TAS2R19 615 0.31 0.34 YES
6 TAS2R20 TAS2R20 TAS2R20 820 0.26 0.36 YES
7 TAS2R50 TAS2R50 TAS2R50 1142 0.22 0.38 YES
8 TAS2R3 TAS2R3 TAS2R3 1170 0.22 0.41 YES
9 TAS2R14 TAS2R14 TAS2R14 1382 0.19 0.42 YES
10 KCNB1 KCNB1 KCNB1 1398 0.19 0.45 YES
11 TAS2R10 TAS2R10 TAS2R10 1506 0.18 0.47 YES
12 TAS2R31 TAS2R31 TAS2R31 1695 0.16 0.48 YES
13 TAS1R3 TAS1R3 TAS1R3 1703 0.16 0.51 YES
14 PRKACG PRKACG PRKACG 1892 0.15 0.52 YES
15 SCNN1B SCNN1B SCNN1B 2007 0.14 0.53 YES
16 SCNN1G SCNN1G SCNN1G 2256 0.13 0.54 YES
17 TAS2R8 TAS2R8 TAS2R8 2399 0.12 0.55 YES
18 PRKX PRKX PRKX 2634 0.11 0.55 YES
19 TAS2R43 TAS2R43 TAS2R43 2689 0.11 0.56 YES
20 TAS2R42 TAS2R42 TAS2R42 3467 0.081 0.53 NO
21 ADCY6 ADCY6 ADCY6 3759 0.074 0.53 NO
22 TAS2R13 TAS2R13 TAS2R13 4235 0.063 0.51 NO
23 GNAS GNAS GNAS 6794 0.025 0.37 NO
24 GNB1 GNB1 GNB1 6836 0.025 0.37 NO
25 ADCY4 ADCY4 ADCY4 7305 0.019 0.35 NO
26 ADCY8 ADCY8 ADCY8 7690 0.015 0.33 NO
27 ITPR3 ITPR3 ITPR3 10110 -0.011 0.2 NO
28 GRM4 GRM4 GRM4 11619 -0.031 0.12 NO
29 PRKACA PRKACA PRKACA 11943 -0.036 0.1 NO
30 PDE1A PDE1A PDE1A 13237 -0.063 0.042 NO
31 TRPM5 TRPM5 TRPM5 13427 -0.068 0.042 NO
32 PRKACB PRKACB PRKACB 14045 -0.088 0.02 NO
33 CACNA1B CACNA1B CACNA1B 14583 -0.11 0.0069 NO
34 SCNN1A SCNN1A SCNN1A 15458 -0.16 -0.018 NO
35 ACCN1 ACCN1 ACCN1 15880 -0.19 -0.013 NO
36 CACNA1A CACNA1A CACNA1A 15923 -0.2 0.014 NO
37 GNB3 GNB3 GNB3 16002 -0.21 0.04 NO
38 TAS1R1 TAS1R1 TAS1R1 16162 -0.22 0.064 NO
39 PLCB2 PLCB2 PLCB2 16515 -0.25 0.082 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: PID BARD1PATHWAY.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: PID BARD1PATHWAY, 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 GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS 25 genes.ES.table 0.38 1.3 0.19 1 1 0.32 0.3 0.22 1 0.81
KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY 57 genes.ES.table 0.47 1.6 0.038 1 0.9 0.32 0.14 0.27 0.93 0.48
KEGG PRION DISEASES 32 genes.ES.table 0.47 1.3 0.2 1 1 0.31 0.19 0.25 1 0.81
BIOCARTA BIOPEPTIDES PATHWAY 38 genes.ES.table 0.45 1.7 0.027 1 0.77 0.4 0.21 0.31 0.94 0.48
BIOCARTA PYK2 PATHWAY 28 genes.ES.table 0.4 1.6 0.039 1 0.87 0.32 0.18 0.26 1 0.54
BIOCARTA PDGF PATHWAY 32 genes.ES.table 0.45 1.4 0.12 1 0.99 0.34 0.2 0.27 1 0.66
BIOCARTA TOLL PATHWAY 37 genes.ES.table 0.51 1.5 0.086 1 0.98 0.46 0.22 0.36 1 0.62
ST DIFFERENTIATION PATHWAY IN PC12 CELLS 44 genes.ES.table 0.48 1.5 0.049 1 0.96 0.3 0.15 0.25 1 0.5
SIG CD40PATHWAYMAP 33 genes.ES.table 0.38 1.5 0.081 1 0.98 0.46 0.34 0.3 1 0.64
PID REELINPATHWAY 29 genes.ES.table 0.46 1.4 0.13 1 0.99 0.38 0.2 0.3 1 0.67
genes ES table in pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS

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 MX1 MX1 MX1 262 0.42 0.06 YES
2 USP18 USP18 USP18 361 0.38 0.12 YES
3 HERC5 HERC5 HERC5 415 0.36 0.18 YES
4 EIF4E3 EIF4E3 EIF4E3 484 0.34 0.24 YES
5 DDX58 DDX58 DDX58 971 0.24 0.26 YES
6 IFIT1 IFIT1 IFIT1 981 0.24 0.3 YES
7 MX2 MX2 MX2 1024 0.24 0.34 YES
8 EIF2AK2 EIF2AK2 EIF2AK2 1052 0.23 0.38 YES
9 UBA7 UBA7 UBA7 1129 0.22 0.42 YES
10 STAT1 STAT1 STAT1 1487 0.19 0.43 YES
11 ISG15 ISG15 ISG15 2059 0.15 0.43 YES
12 KPNA2 KPNA2 KPNA2 2216 0.14 0.45 YES
13 NUP210 NUP210 NUP210 2964 0.11 0.42 YES
14 NUP155 NUP155 NUP155 3110 0.11 0.44 YES
15 UBE2L6 UBE2L6 UBE2L6 3428 0.097 0.44 YES
16 RANBP2 RANBP2 RANBP2 3576 0.093 0.44 YES
17 NUPL1 NUPL1 NUPL1 3655 0.091 0.46 YES
18 TRIM25 TRIM25 TRIM25 3702 0.089 0.47 YES
19 FLNB FLNB FLNB 3954 0.082 0.47 YES
20 KPNB1 KPNB1 KPNB1 4012 0.081 0.48 YES
21 MAPK3 MAPK3 MAPK3 4575 0.067 0.46 NO
22 TPR TPR TPR 5060 0.058 0.44 NO
23 EIF4E EIF4E EIF4E 5157 0.056 0.45 NO
24 SEH1L SEH1L SEH1L 5203 0.055 0.46 NO
25 EIF4A3 EIF4A3 EIF4A3 5458 0.05 0.45 NO
26 NEDD4 NEDD4 NEDD4 5665 0.047 0.45 NO
27 EIF4G2 EIF4G2 EIF4G2 5725 0.046 0.45 NO
28 NUP107 NUP107 NUP107 5846 0.044 0.46 NO
29 NUP35 NUP35 NUP35 5963 0.042 0.46 NO
30 NUP133 NUP133 NUP133 5966 0.042 0.46 NO
31 PPM1B PPM1B PPM1B 6258 0.038 0.45 NO
32 NUP205 NUP205 NUP205 6280 0.037 0.46 NO
33 NUP93 NUP93 NUP93 6395 0.036 0.46 NO
34 NUP37 NUP37 NUP37 6654 0.032 0.45 NO
35 NUP188 NUP188 NUP188 7028 0.027 0.44 NO
36 ARIH1 ARIH1 ARIH1 7106 0.026 0.44 NO
37 NUP153 NUP153 NUP153 7168 0.025 0.44 NO
38 NUP214 NUP214 NUP214 7660 0.018 0.41 NO
39 KPNA3 KPNA3 KPNA3 7966 0.014 0.4 NO
40 UBE2N UBE2N UBE2N 7995 0.013 0.4 NO
41 NUP43 NUP43 NUP43 8489 0.0069 0.37 NO
42 PIN1 PIN1 PIN1 9046 -0.00048 0.34 NO
43 NUPL2 NUPL2 NUPL2 9862 -0.012 0.3 NO
44 POM121 POM121 POM121 9894 -0.012 0.3 NO
45 RAE1 RAE1 RAE1 10039 -0.014 0.29 NO
46 KPNA5 KPNA5 KPNA5 10281 -0.018 0.28 NO
47 UBE2E1 UBE2E1 UBE2E1 10690 -0.025 0.26 NO
48 EIF4A2 EIF4A2 EIF4A2 10815 -0.027 0.26 NO
49 NUP88 NUP88 NUP88 11147 -0.032 0.25 NO
50 NUP54 NUP54 NUP54 11150 -0.032 0.26 NO
51 KPNA4 KPNA4 KPNA4 11151 -0.032 0.26 NO
52 NUP62 NUP62 NUP62 11182 -0.033 0.26 NO
53 EIF4G1 EIF4G1 EIF4G1 11213 -0.034 0.27 NO
54 NUP50 NUP50 NUP50 11416 -0.037 0.26 NO
55 EIF4G3 EIF4G3 EIF4G3 11603 -0.041 0.26 NO
56 EIF4A1 EIF4A1 EIF4A1 11653 -0.042 0.27 NO
57 UBA52 UBA52 UBA52 11676 -0.042 0.27 NO
58 AAAS AAAS AAAS 11709 -0.043 0.28 NO
59 KPNA1 KPNA1 KPNA1 11813 -0.044 0.28 NO
60 PLCG1 PLCG1 PLCG1 11909 -0.047 0.28 NO
61 EIF4E2 EIF4E2 EIF4E2 11969 -0.048 0.29 NO
62 NUP85 NUP85 NUP85 12142 -0.051 0.29 NO
63 RPS27A RPS27A RPS27A 12290 -0.054 0.29 NO
64 JAK1 JAK1 JAK1 12863 -0.068 0.27 NO
65 IRF3 IRF3 IRF3 13336 -0.08 0.26 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 GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RIG I LIKE RECEPTOR 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 STAT4 STAT4 STAT4 37 0.63 0.16 YES
2 PTK2B PTK2B PTK2B 1265 0.21 0.14 YES
3 STAT5A STAT5A STAT5A 1277 0.21 0.2 YES
4 STAT1 STAT1 STAT1 1487 0.19 0.24 YES
5 SHC1 SHC1 SHC1 1991 0.16 0.25 YES
6 MAPK8 MAPK8 MAPK8 2096 0.15 0.28 YES
7 CAMK2G CAMK2G CAMK2G 2116 0.15 0.32 YES
8 CALM1 CALM1 CALM1 2258 0.14 0.34 YES
9 CALM2 CALM2 CALM2 2349 0.14 0.37 YES
10 MAPT MAPT MAPT 2596 0.12 0.39 YES
11 PRKCB PRKCB PRKCB 3145 0.11 0.39 YES
12 HRAS HRAS HRAS 3320 0.1 0.4 YES
13 CAMK2B CAMK2B CAMK2B 3347 0.099 0.43 YES
14 JAK2 JAK2 JAK2 3635 0.092 0.44 YES
15 GNA11 GNA11 GNA11 3792 0.086 0.45 YES
16 MAPK3 MAPK3 MAPK3 4575 0.067 0.42 NO
17 STAT6 STAT6 STAT6 5132 0.056 0.41 NO
18 STAT5B STAT5B STAT5B 5308 0.053 0.41 NO
19 MAPK14 MAPK14 MAPK14 6053 0.041 0.38 NO
20 SOS1 SOS1 SOS1 6165 0.039 0.38 NO
21 GNAI1 GNAI1 GNAI1 6234 0.038 0.39 NO
22 STAT2 STAT2 STAT2 6440 0.035 0.39 NO
23 GRB2 GRB2 GRB2 6873 0.029 0.37 NO
24 CDK5 CDK5 CDK5 9209 -0.0025 0.24 NO
25 CALM3 CALM3 CALM3 9402 -0.0054 0.23 NO
26 CAMK2D CAMK2D CAMK2D 10024 -0.014 0.2 NO
27 STAT3 STAT3 STAT3 10440 -0.02 0.18 NO
28 MAPK1 MAPK1 MAPK1 10662 -0.024 0.18 NO
29 MAP2K2 MAP2K2 MAP2K2 11804 -0.044 0.12 NO
30 PLCG1 PLCG1 PLCG1 11909 -0.047 0.13 NO
31 MAP2K1 MAP2K1 MAP2K1 12582 -0.062 0.11 NO
32 GNB1 GNB1 GNB1 12774 -0.066 0.11 NO
33 RAF1 RAF1 RAF1 13028 -0.072 0.12 NO
34 FYN FYN FYN 13946 -0.1 0.093 NO
35 CAMK2A CAMK2A CAMK2A 14254 -0.11 0.1 NO
36 AGT AGT AGT 14510 -0.12 0.12 NO
37 PRKCA PRKCA PRKCA 14548 -0.13 0.15 NO
38 MYLK MYLK MYLK 15023 -0.15 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 RIG I LIKE RECEPTOR SIGNALING PATHWAY.

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIG I 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 PRION DISEASES

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 PTK2B PTK2B PTK2B 1265 0.21 0.027 YES
2 SHC1 SHC1 SHC1 1991 0.16 0.058 YES
3 MAPK8 MAPK8 MAPK8 2096 0.15 0.12 YES
4 CALM1 CALM1 CALM1 2258 0.14 0.18 YES
5 MAP3K1 MAP3K1 MAP3K1 2283 0.14 0.24 YES
6 CALM2 CALM2 CALM2 2349 0.14 0.3 YES
7 PAK1 PAK1 PAK1 2468 0.13 0.35 YES
8 PRKCB PRKCB PRKCB 3145 0.11 0.36 YES
9 HRAS HRAS HRAS 3320 0.1 0.4 YES
10 MAPK3 MAPK3 MAPK3 4575 0.067 0.36 NO
11 GNAQ GNAQ GNAQ 5208 0.055 0.35 NO
12 MAPK14 MAPK14 MAPK14 6053 0.041 0.32 NO
13 SOS1 SOS1 SOS1 6165 0.039 0.33 NO
14 GRB2 GRB2 GRB2 6873 0.029 0.31 NO
15 CALM3 CALM3 CALM3 9402 -0.0054 0.17 NO
16 SRC SRC SRC 9714 -0.0098 0.16 NO
17 CRKL CRKL CRKL 10570 -0.023 0.12 NO
18 MAPK1 MAPK1 MAPK1 10662 -0.024 0.12 NO
19 MAP2K4 MAP2K4 MAP2K4 10792 -0.026 0.13 NO
20 BCAR1 BCAR1 BCAR1 10896 -0.028 0.14 NO
21 RAC1 RAC1 RAC1 11558 -0.04 0.12 NO
22 MAP2K2 MAP2K2 MAP2K2 11804 -0.044 0.12 NO
23 PLCG1 PLCG1 PLCG1 11909 -0.047 0.14 NO
24 MAP2K1 MAP2K1 MAP2K1 12582 -0.062 0.13 NO
25 JUN JUN JUN 12606 -0.062 0.16 NO
26 RAF1 RAF1 RAF1 13028 -0.072 0.17 NO
27 MAP2K3 MAP2K3 MAP2K3 14040 -0.1 0.16 NO
28 PRKCA PRKCA PRKCA 14548 -0.13 0.19 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 PRION DISEASES.

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

genes ES table in pathway: BIOCARTA BIOPEPTIDES PATHWAY

Table 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 HERC5 HERC5 HERC5 415 0.36 0.11 YES
2 IFIH1 IFIH1 IFIH1 696 0.29 0.2 YES
3 IKBKE IKBKE IKBKE 955 0.24 0.27 YES
4 DDX58 DDX58 DDX58 971 0.24 0.36 YES
5 UBA7 UBA7 UBA7 1129 0.22 0.43 YES
6 TRAF3 TRAF3 TRAF3 1684 0.18 0.46 YES
7 ISG15 ISG15 ISG15 2059 0.15 0.5 YES
8 CYLD CYLD CYLD 2548 0.13 0.52 YES
9 UBE2L6 UBE2L6 UBE2L6 3428 0.097 0.5 YES
10 TRIM25 TRIM25 TRIM25 3702 0.089 0.52 YES
11 UBE2D1 UBE2D1 UBE2D1 4486 0.069 0.5 NO
12 NLRC5 NLRC5 NLRC5 4872 0.061 0.5 NO
13 ATG12 ATG12 ATG12 5147 0.056 0.51 NO
14 TBK1 TBK1 TBK1 5581 0.048 0.5 NO
15 UBE2D3 UBE2D3 UBE2D3 5969 0.042 0.49 NO
16 OTUD5 OTUD5 OTUD5 8046 0.013 0.38 NO
17 TAX1BP1 TAX1BP1 TAX1BP1 8271 0.0096 0.37 NO
18 UBE2K UBE2K UBE2K 8539 0.0063 0.36 NO
19 PIN1 PIN1 PIN1 9046 -0.00048 0.33 NO
20 UBE2D2 UBE2D2 UBE2D2 9141 -0.0016 0.33 NO
21 RNF135 RNF135 RNF135 10191 -0.016 0.28 NO
22 MAVS MAVS MAVS 10978 -0.029 0.24 NO
23 PCBP2 PCBP2 PCBP2 11102 -0.032 0.25 NO
24 ATG5 ATG5 ATG5 11361 -0.036 0.25 NO
25 RNF125 RNF125 RNF125 11503 -0.039 0.25 NO
26 UBA52 UBA52 UBA52 11676 -0.042 0.26 NO
27 RPS27A RPS27A RPS27A 12290 -0.054 0.24 NO
28 NLRX1 NLRX1 NLRX1 12296 -0.054 0.26 NO
29 TNFAIP3 TNFAIP3 TNFAIP3 12834 -0.068 0.26 NO
30 IRF3 IRF3 IRF3 13336 -0.08 0.26 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 BIOPEPTIDES PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 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 MAPK13 MAPK13 MAPK13 495 0.34 0.035 YES
2 IFIH1 IFIH1 IFIH1 696 0.29 0.077 YES
3 IKBKE IKBKE IKBKE 955 0.24 0.11 YES
4 DDX58 DDX58 DDX58 971 0.24 0.15 YES
5 CXCL10 CXCL10 CXCL10 1142 0.22 0.18 YES
6 IFNA21 IFNA21 IFNA21 1226 0.22 0.22 YES
7 IFNW1 IFNW1 IFNW1 1331 0.2 0.25 YES
8 IL8 IL8 IL8 1641 0.18 0.27 YES
9 TRAF3 TRAF3 TRAF3 1684 0.18 0.3 YES
10 ISG15 ISG15 ISG15 2059 0.15 0.3 YES
11 MAPK8 MAPK8 MAPK8 2096 0.15 0.33 YES
12 MAP3K1 MAP3K1 MAP3K1 2283 0.14 0.34 YES
13 TNF TNF TNF 2298 0.14 0.37 YES
14 IL12B IL12B IL12B 2440 0.13 0.39 YES
15 TRAF6 TRAF6 TRAF6 2443 0.13 0.41 YES
16 CYLD CYLD CYLD 2548 0.13 0.43 YES
17 IRF7 IRF7 IRF7 2582 0.13 0.45 YES
18 DDX3Y DDX3Y DDX3Y 2603 0.12 0.47 YES
19 MAPK9 MAPK9 MAPK9 3538 0.094 0.44 NO
20 TRIM25 TRIM25 TRIM25 3702 0.089 0.44 NO
21 AZI2 AZI2 AZI2 3739 0.088 0.46 NO
22 CHUK CHUK CHUK 4322 0.073 0.44 NO
23 DHX58 DHX58 DHX58 4681 0.065 0.43 NO
24 MAPK11 MAPK11 MAPK11 4692 0.065 0.44 NO
25 MAPK10 MAPK10 MAPK10 4731 0.064 0.45 NO
26 ATG12 ATG12 ATG12 5147 0.056 0.44 NO
27 MAPK12 MAPK12 MAPK12 5294 0.053 0.44 NO
28 TBK1 TBK1 TBK1 5581 0.048 0.44 NO
29 MAPK14 MAPK14 MAPK14 6053 0.041 0.42 NO
30 RIPK1 RIPK1 RIPK1 6213 0.038 0.42 NO
31 DAK DAK DAK 6632 0.032 0.4 NO
32 TANK TANK TANK 6633 0.032 0.4 NO
33 MAP3K7 MAP3K7 MAP3K7 6726 0.031 0.4 NO
34 OTUD5 OTUD5 OTUD5 8046 0.013 0.33 NO
35 DDX3X DDX3X DDX3X 8239 0.01 0.32 NO
36 NFKB1 NFKB1 NFKB1 8858 0.002 0.29 NO
37 PIN1 PIN1 PIN1 9046 -0.00048 0.28 NO
38 TRADD TRADD TRADD 9620 -0.0084 0.25 NO
39 IKBKG IKBKG IKBKG 9737 -0.01 0.24 NO
40 TRAF2 TRAF2 TRAF2 10080 -0.015 0.23 NO
41 IL12A IL12A IL12A 10353 -0.019 0.22 NO
42 IKBKB IKBKB IKBKB 10634 -0.024 0.2 NO
43 FADD FADD FADD 10767 -0.026 0.2 NO
44 MAVS MAVS MAVS 10978 -0.029 0.2 NO
45 ATG5 ATG5 ATG5 11361 -0.036 0.18 NO
46 IFNA5 IFNA5 IFNA5 11384 -0.036 0.19 NO
47 RNF125 RNF125 RNF125 11503 -0.039 0.19 NO
48 NFKBIA NFKBIA NFKBIA 11858 -0.045 0.18 NO
49 TBKBP1 TBKBP1 TBKBP1 11943 -0.048 0.18 NO
50 CASP8 CASP8 CASP8 12050 -0.049 0.18 NO
51 NLRX1 NLRX1 NLRX1 12296 -0.054 0.18 NO
52 NFKBIB NFKBIB NFKBIB 12807 -0.067 0.16 NO
53 RELA RELA RELA 13039 -0.073 0.16 NO
54 IRF3 IRF3 IRF3 13336 -0.08 0.16 NO
55 SIKE1 SIKE1 SIKE1 13677 -0.092 0.16 NO
56 CASP10 CASP10 CASP10 15857 -0.21 0.078 NO
57 TMEM173 TMEM173 TMEM173 16020 -0.22 0.11 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 PYK2 PATHWAY.

Figure S30.  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: BIOCARTA PDGF 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 SHC3 SHC3 SHC3 21 0.72 0.22 YES
2 NTRK1 NTRK1 NTRK1 179 0.46 0.36 YES
3 MAPK13 MAPK13 MAPK13 495 0.34 0.45 YES
4 MAPKAPK3 MAPKAPK3 MAPKAPK3 1296 0.21 0.47 YES
5 SHC1 SHC1 SHC1 1991 0.16 0.48 YES
6 HRAS HRAS HRAS 3320 0.1 0.44 NO
7 MAPK3 MAPK3 MAPK3 4575 0.067 0.39 NO
8 MAPK11 MAPK11 MAPK11 4692 0.065 0.4 NO
9 RALGDS RALGDS RALGDS 4862 0.061 0.41 NO
10 YWHAB YWHAB YWHAB 5113 0.057 0.42 NO
11 MAPK12 MAPK12 MAPK12 5294 0.053 0.42 NO
12 RALB RALB RALB 5535 0.049 0.42 NO
13 MAPK14 MAPK14 MAPK14 6053 0.041 0.41 NO
14 SOS1 SOS1 SOS1 6165 0.039 0.41 NO
15 GRB2 GRB2 GRB2 6873 0.029 0.38 NO
16 KRAS KRAS KRAS 7628 0.018 0.35 NO
17 MAPKAPK2 MAPKAPK2 MAPKAPK2 7835 0.015 0.34 NO
18 SHC2 SHC2 SHC2 8763 0.0032 0.29 NO
19 RALA RALA RALA 9669 -0.0091 0.24 NO
20 SRC SRC SRC 9714 -0.0098 0.24 NO
21 MAPK1 MAPK1 MAPK1 10662 -0.024 0.2 NO
22 MAP2K2 MAP2K2 MAP2K2 11804 -0.044 0.15 NO
23 MAP2K1 MAP2K1 MAP2K1 12582 -0.062 0.12 NO
24 RAF1 RAF1 RAF1 13028 -0.072 0.12 NO
25 NRAS NRAS NRAS 14925 -0.14 0.062 NO
26 NGF NGF NGF 15275 -0.17 0.094 NO
27 CDK1 CDK1 CDK1 15469 -0.18 0.14 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 PDGF PATHWAY.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PDGF 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 TOLL 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 SHC3 SHC3 SHC3 21 0.72 0.17 YES
2 NTRK1 NTRK1 NTRK1 179 0.46 0.27 YES
3 RIT2 RIT2 RIT2 355 0.38 0.34 YES
4 MAPK13 MAPK13 MAPK13 495 0.34 0.42 YES
5 MAPKAPK3 MAPKAPK3 MAPKAPK3 1296 0.21 0.42 YES
6 SHC1 SHC1 SHC1 1991 0.16 0.42 YES
7 BRAF BRAF BRAF 2290 0.14 0.43 YES
8 HRAS HRAS HRAS 3320 0.1 0.4 NO
9 KIDINS220 KIDINS220 KIDINS220 3808 0.086 0.39 NO
10 FRS2 FRS2 FRS2 4076 0.079 0.4 NO
11 MAPK3 MAPK3 MAPK3 4575 0.067 0.38 NO
12 MAPK11 MAPK11 MAPK11 4692 0.065 0.39 NO
13 RALGDS RALGDS RALGDS 4862 0.061 0.4 NO
14 YWHAB YWHAB YWHAB 5113 0.057 0.4 NO
15 MAPK12 MAPK12 MAPK12 5294 0.053 0.4 NO
16 RALB RALB RALB 5535 0.049 0.4 NO
17 MAPK14 MAPK14 MAPK14 6053 0.041 0.38 NO
18 SOS1 SOS1 SOS1 6165 0.039 0.38 NO
19 GRB2 GRB2 GRB2 6873 0.029 0.35 NO
20 KRAS KRAS KRAS 7628 0.018 0.31 NO
21 MAPKAPK2 MAPKAPK2 MAPKAPK2 7835 0.015 0.3 NO
22 SHC2 SHC2 SHC2 8763 0.0032 0.25 NO
23 RALA RALA RALA 9669 -0.0091 0.2 NO
24 SRC SRC SRC 9714 -0.0098 0.2 NO
25 MAPK1 MAPK1 MAPK1 10662 -0.024 0.16 NO
26 MAP2K2 MAP2K2 MAP2K2 11804 -0.044 0.1 NO
27 PLCG1 PLCG1 PLCG1 11909 -0.047 0.11 NO
28 RIT1 RIT1 RIT1 11928 -0.047 0.12 NO
29 MAP2K1 MAP2K1 MAP2K1 12582 -0.062 0.095 NO
30 RAF1 RAF1 RAF1 13028 -0.072 0.088 NO
31 RAPGEF1 RAPGEF1 RAPGEF1 13287 -0.079 0.092 NO
32 CRK CRK CRK 14317 -0.12 0.061 NO
33 RAP1A RAP1A RAP1A 14463 -0.12 0.082 NO
34 NRAS NRAS NRAS 14925 -0.14 0.09 NO
35 NGF NGF NGF 15275 -0.17 0.11 NO
36 CDK1 CDK1 CDK1 15469 -0.18 0.14 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 TOLL PATHWAY.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TOLL 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 DIFFERENTIATION PATHWAY IN PC12 CELLS

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 CREB5 CREB5 CREB5 105 0.52 0.11 YES
2 NTRK1 NTRK1 NTRK1 179 0.46 0.2 YES
3 EGR4 EGR4 EGR4 571 0.31 0.25 YES
4 CAMP CAMP CAMP 823 0.27 0.29 YES
5 EGR1 EGR1 EGR1 1400 0.2 0.3 YES
6 PIK3R1 PIK3R1 PIK3R1 1774 0.17 0.32 YES
7 EGR2 EGR2 EGR2 1821 0.17 0.35 YES
8 SHC1 SHC1 SHC1 1991 0.16 0.38 YES
9 MAPK8 MAPK8 MAPK8 2096 0.15 0.4 YES
10 BRAF BRAF BRAF 2290 0.14 0.42 YES
11 EGR3 EGR3 EGR3 2350 0.14 0.45 YES
12 MAP1B MAP1B MAP1B 2636 0.12 0.46 YES
13 TH TH TH 2682 0.12 0.48 YES
14 MAPK9 MAPK9 MAPK9 3538 0.094 0.46 NO
15 MAPK8IP1 MAPK8IP1 MAPK8IP1 3585 0.093 0.47 NO
16 FRS2 FRS2 FRS2 4076 0.079 0.46 NO
17 MAPK3 MAPK3 MAPK3 4575 0.067 0.45 NO
18 PTPN11 PTPN11 PTPN11 4614 0.066 0.46 NO
19 MAPK10 MAPK10 MAPK10 4731 0.064 0.47 NO
20 RPS6KA3 RPS6KA3 RPS6KA3 4802 0.063 0.48 NO
21 GNAQ GNAQ GNAQ 5208 0.055 0.47 NO
22 TERF2IP TERF2IP TERF2IP 5905 0.043 0.44 NO
23 MAPK8IP3 MAPK8IP3 MAPK8IP3 6802 0.03 0.4 NO
24 MAPK8IP2 MAPK8IP2 MAPK8IP2 6849 0.029 0.4 NO
25 AKT1 AKT1 AKT1 6853 0.029 0.41 NO
26 ASAH1 ASAH1 ASAH1 6865 0.029 0.41 NO
27 CREB3 CREB3 CREB3 6976 0.027 0.41 NO
28 CREB1 CREB1 CREB1 8603 0.0054 0.32 NO
29 CREBBP CREBBP CREBBP 8731 0.0038 0.32 NO
30 MAP2K7 MAP2K7 MAP2K7 9234 -0.0029 0.29 NO
31 TUBA1A TUBA1A TUBA1A 9403 -0.0054 0.28 NO
32 SRC SRC SRC 9714 -0.0098 0.26 NO
33 CRKL CRKL CRKL 10570 -0.023 0.22 NO
34 MAPK1 MAPK1 MAPK1 10662 -0.024 0.22 NO
35 ELK1 ELK1 ELK1 10790 -0.026 0.22 NO
36 MAP2K4 MAP2K4 MAP2K4 10792 -0.026 0.23 NO
37 ATF1 ATF1 ATF1 10849 -0.027 0.23 NO
38 DAG1 DAG1 DAG1 11450 -0.038 0.2 NO
39 PIK3CA PIK3CA PIK3CA 11459 -0.038 0.21 NO
40 JUN JUN JUN 12606 -0.062 0.16 NO
41 PIK3C2G PIK3C2G PIK3C2G 12837 -0.068 0.16 NO
42 PIK3CD PIK3CD PIK3CD 13083 -0.074 0.17 NO
43 RASGRF2 RASGRF2 RASGRF2 16265 -0.24 0.04 NO
44 GAST GAST GAST 16447 -0.25 0.085 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 DIFFERENTIATION PATHWAY IN PC12 CELLS.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: ST DIFFERENTIATION PATHWAY IN PC12 CELLS, 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: SIG CD40PATHWAYMAP

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 MAPK13 MAPK13 MAPK13 495 0.34 0.12 YES
2 TRAF3 TRAF3 TRAF3 1684 0.18 0.14 YES
3 PIK3R1 PIK3R1 PIK3R1 1774 0.17 0.21 YES
4 MAPK8 MAPK8 MAPK8 2096 0.15 0.26 YES
5 TRAF6 TRAF6 TRAF6 2443 0.13 0.3 YES
6 MAPK9 MAPK9 MAPK9 3538 0.094 0.28 YES
7 MAPK8IP1 MAPK8IP1 MAPK8IP1 3585 0.093 0.32 YES
8 CD40 CD40 CD40 4154 0.077 0.32 YES
9 MAPK3 MAPK3 MAPK3 4575 0.067 0.32 YES
10 MAPK11 MAPK11 MAPK11 4692 0.065 0.35 YES
11 MAPK10 MAPK10 MAPK10 4731 0.064 0.37 YES
12 MAPK12 MAPK12 MAPK12 5294 0.053 0.37 YES
13 TRAF5 TRAF5 TRAF5 5833 0.044 0.36 YES
14 MAPK14 MAPK14 MAPK14 6053 0.041 0.36 YES
15 NFKBIE NFKBIE NFKBIE 6058 0.041 0.38 YES
16 MAPK8IP3 MAPK8IP3 MAPK8IP3 6802 0.03 0.35 NO
17 MAPK8IP2 MAPK8IP2 MAPK8IP2 6849 0.029 0.36 NO
18 DUSP1 DUSP1 DUSP1 6971 0.027 0.37 NO
19 GORASP1 GORASP1 GORASP1 7677 0.017 0.34 NO
20 NFKB1 NFKB1 NFKB1 8858 0.002 0.27 NO
21 MAP2K7 MAP2K7 MAP2K7 9234 -0.0029 0.25 NO
22 IKBKG IKBKG IKBKG 9737 -0.01 0.23 NO
23 TRAF2 TRAF2 TRAF2 10080 -0.015 0.22 NO
24 MAPKAPK5 MAPKAPK5 MAPKAPK5 10114 -0.015 0.22 NO
25 MAPK1 MAPK1 MAPK1 10662 -0.024 0.2 NO
26 MAP2K4 MAP2K4 MAP2K4 10792 -0.026 0.21 NO
27 SYT1 SYT1 SYT1 10885 -0.028 0.21 NO
28 NFKBIL1 NFKBIL1 NFKBIL1 11135 -0.032 0.21 NO
29 PIK3CA PIK3CA PIK3CA 11459 -0.038 0.21 NO
30 NFKBIA NFKBIA NFKBIA 11858 -0.045 0.21 NO
31 NFKBIB NFKBIB NFKBIB 12807 -0.067 0.19 NO
32 PIK3CD PIK3CD PIK3CD 13083 -0.074 0.21 NO
33 NFKB2 NFKB2 NFKB2 14991 -0.15 0.17 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: SIG CD40PATHWAYMAP.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: SIG CD40PATHWAYMAP, 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 REELINPATHWAY

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 TLR9 TLR9 TLR9 749 0.28 0.028 YES
2 MAP2K6 MAP2K6 MAP2K6 966 0.24 0.078 YES
3 EIF2AK2 EIF2AK2 EIF2AK2 1052 0.23 0.13 YES
4 TLR10 TLR10 TLR10 1151 0.22 0.18 YES
5 TLR3 TLR3 TLR3 1181 0.22 0.24 YES
6 PGLYRP1 PGLYRP1 PGLYRP1 1206 0.22 0.29 YES
7 TLR6 TLR6 TLR6 1527 0.19 0.32 YES
8 MYD88 MYD88 MYD88 1690 0.18 0.36 YES
9 TLR7 TLR7 TLR7 1957 0.16 0.38 YES
10 MAPK8 MAPK8 MAPK8 2096 0.15 0.41 YES
11 MAP3K1 MAP3K1 MAP3K1 2283 0.14 0.44 YES
12 TLR4 TLR4 TLR4 2404 0.13 0.46 YES
13 TRAF6 TRAF6 TRAF6 2443 0.13 0.5 YES
14 TLR2 TLR2 TLR2 3132 0.11 0.48 YES
15 TIRAP TIRAP TIRAP 3194 0.1 0.51 YES
16 FOS FOS FOS 3686 0.09 0.5 YES
17 TOLLIP TOLLIP TOLLIP 3860 0.084 0.51 YES
18 CHUK CHUK CHUK 4322 0.073 0.51 NO
19 MAP3K14 MAP3K14 MAP3K14 4870 0.061 0.49 NO
20 MAPK14 MAPK14 MAPK14 6053 0.041 0.44 NO
21 CD14 CD14 CD14 6257 0.038 0.43 NO
22 MAP3K7 MAP3K7 MAP3K7 6726 0.031 0.42 NO
23 NFKB1 NFKB1 NFKB1 8858 0.002 0.3 NO
24 TAB2 TAB2 TAB2 9342 -0.0045 0.27 NO
25 IRAK1 IRAK1 IRAK1 9444 -0.0061 0.27 NO
26 IKBKG IKBKG IKBKG 9737 -0.01 0.25 NO
27 IKBKB IKBKB IKBKB 10634 -0.024 0.21 NO
28 ELK1 ELK1 ELK1 10790 -0.026 0.21 NO
29 MAP2K4 MAP2K4 MAP2K4 10792 -0.026 0.22 NO
30 NFKBIA NFKBIA NFKBIA 11858 -0.045 0.17 NO
31 JUN JUN JUN 12606 -0.062 0.14 NO
32 ECSIT ECSIT ECSIT 12973 -0.071 0.14 NO
33 RELA RELA RELA 13039 -0.073 0.15 NO
34 PPARA PPARA PPARA 13427 -0.084 0.15 NO
35 MAP2K3 MAP2K3 MAP2K3 14040 -0.1 0.14 NO
36 TAB1 TAB1 TAB1 14772 -0.14 0.14 NO
37 LY96 LY96 LY96 15104 -0.16 0.16 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 REELINPATHWAY.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: PID REELINPATHWAY, 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 NOTCH SIGNALING PATHWAY 46 genes.ES.table 0.48 1.5 0.076 1 0.97 0.35 0.18 0.28 1 0.69
KEGG BLADDER CANCER 42 genes.ES.table 0.54 1.5 0.048 1 0.98 0.38 0.17 0.32 1 0.66
BIOCARTA NO1 PATHWAY 29 genes.ES.table 0.61 1.5 0.038 1 0.96 0.48 0.15 0.41 1 0.71
BIOCARTA VEGF PATHWAY 29 genes.ES.table 0.46 1.4 0.096 1 0.98 0.17 0.078 0.16 1 0.59
PID HIF2PATHWAY 34 genes.ES.table 0.77 1.9 0.0021 0.76 0.33 0.44 0.09 0.4 0 0.16
PID S1P S1P3 PATHWAY 29 genes.ES.table 0.6 1.6 0.034 1 0.9 0.31 0.084 0.28 1 0.63
PID FRA PATHWAY 36 genes.ES.table 0.66 1.5 0.057 1 0.98 0.61 0.2 0.49 1 0.62
PID ILK PATHWAY 45 genes.ES.table 0.41 1.5 0.086 1 0.98 0.29 0.2 0.23 1 0.69
PID SYNDECAN 1 PATHWAY 45 genes.ES.table 0.63 1.4 0.064 1 0.98 0.53 0.14 0.46 1 0.62
PID VEGFR1 PATHWAY 26 genes.ES.table 0.47 1.5 0.075 1 0.98 0.19 0.078 0.18 1 0.67
genes ES table in pathway: KEGG NOTCH 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 HK2 HK2 HK2 14 0.64 0.2 YES
2 SLC2A1 SLC2A1 SLC2A1 341 0.36 0.3 YES
3 GCK GCK GCK 420 0.34 0.4 YES
4 SLC2A3 SLC2A3 SLC2A3 1288 0.21 0.42 YES
5 SLC2A4 SLC2A4 SLC2A4 1438 0.19 0.47 YES
6 HK3 HK3 HK3 1506 0.19 0.53 YES
7 G6PC2 G6PC2 G6PC2 1837 0.16 0.56 YES
8 NUP85 NUP85 NUP85 5509 0.035 0.36 NO
9 NUP50 NUP50 NUP50 5629 0.033 0.37 NO
10 NUPL2 NUPL2 NUPL2 5738 0.031 0.37 NO
11 AAAS AAAS AAAS 6452 0.02 0.34 NO
12 NUP214 NUP214 NUP214 6685 0.016 0.33 NO
13 POM121 POM121 POM121 6868 0.014 0.33 NO
14 NUP88 NUP88 NUP88 6873 0.014 0.33 NO
15 HK1 HK1 HK1 7496 0.0063 0.3 NO
16 NUP54 NUP54 NUP54 7663 0.0041 0.29 NO
17 NUP62 NUP62 NUP62 8053 -0.00095 0.27 NO
18 NUP188 NUP188 NUP188 8677 -0.0086 0.24 NO
19 NUP43 NUP43 NUP43 8752 -0.0094 0.24 NO
20 NUP93 NUP93 NUP93 9093 -0.013 0.22 NO
21 NUP205 NUP205 NUP205 9629 -0.02 0.2 NO
22 NUP107 NUP107 NUP107 9817 -0.022 0.19 NO
23 RAE1 RAE1 RAE1 9871 -0.022 0.2 NO
24 G6PC3 G6PC3 G6PC3 9950 -0.023 0.2 NO
25 NUP153 NUP153 NUP153 10220 -0.026 0.19 NO
26 NUP35 NUP35 NUP35 10671 -0.032 0.18 NO
27 NUP37 NUP37 NUP37 10754 -0.034 0.18 NO
28 NUP133 NUP133 NUP133 11204 -0.039 0.17 NO
29 TPR TPR TPR 11416 -0.042 0.17 NO
30 SLC37A4 SLC37A4 SLC37A4 11876 -0.048 0.16 NO
31 SEH1L SEH1L SEH1L 12459 -0.057 0.15 NO
32 NUPL1 NUPL1 NUPL1 13063 -0.067 0.14 NO
33 RANBP2 RANBP2 RANBP2 13736 -0.08 0.12 NO
34 NUP155 NUP155 NUP155 14209 -0.09 0.13 NO
35 NUP210 NUP210 NUP210 15190 -0.12 0.11 NO
36 GCKR GCKR GCKR 15745 -0.14 0.12 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 NOTCH SIGNALING PATHWAY.

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOTCH 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 BLADDER CANCER

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 ADORA2A ADORA2A ADORA2A 111 0.46 0.09 YES
2 EPO EPO EPO 114 0.45 0.19 YES
3 SLC2A1 SLC2A1 SLC2A1 341 0.36 0.25 YES
4 EGLN3 EGLN3 EGLN3 383 0.35 0.32 YES
5 EFNA1 EFNA1 EFNA1 559 0.3 0.37 YES
6 SERPINE1 SERPINE1 SERPINE1 804 0.26 0.42 YES
7 FLT1 FLT1 FLT1 844 0.26 0.47 YES
8 KDR KDR KDR 980 0.24 0.51 YES
9 MMP14 MMP14 MMP14 1095 0.23 0.55 YES
10 ETS1 ETS1 ETS1 1272 0.21 0.59 YES
11 EPAS1 EPAS1 EPAS1 1319 0.2 0.63 YES
12 VEGFA VEGFA VEGFA 1339 0.2 0.67 YES
13 ABCG2 ABCG2 ABCG2 1522 0.19 0.7 YES
14 POU5F1 POU5F1 POU5F1 1543 0.18 0.73 YES
15 TWIST1 TWIST1 TWIST1 1613 0.18 0.77 YES
16 SP1 SP1 SP1 2902 0.1 0.72 NO
17 PGK1 PGK1 PGK1 5298 0.038 0.59 NO
18 EGLN2 EGLN2 EGLN2 5741 0.031 0.57 NO
19 EP300 EP300 EP300 6568 0.018 0.53 NO
20 BHLHE40 BHLHE40 BHLHE40 6746 0.016 0.52 NO
21 TCEB2 TCEB2 TCEB2 7094 0.011 0.51 NO
22 ARNT ARNT ARNT 7201 0.01 0.5 NO
23 EIF3E EIF3E EIF3E 7261 0.0093 0.5 NO
24 ELK1 ELK1 ELK1 7860 0.0015 0.47 NO
25 TCEB1 TCEB1 TCEB1 8134 -0.0019 0.46 NO
26 EGLN1 EGLN1 EGLN1 8644 -0.0079 0.43 NO
27 CREBBP CREBBP CREBBP 9542 -0.018 0.38 NO
28 SLC11A2 SLC11A2 SLC11A2 9971 -0.024 0.36 NO
29 APEX1 APEX1 APEX1 10314 -0.028 0.35 NO
30 CITED2 CITED2 CITED2 10609 -0.032 0.34 NO
31 HIF1AN HIF1AN HIF1AN 11830 -0.048 0.28 NO
32 SIRT1 SIRT1 SIRT1 13265 -0.07 0.22 NO
33 FXN FXN FXN 14515 -0.098 0.17 NO
34 VHL VHL VHL 15027 -0.11 0.16 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 BLADDER CANCER.

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BLADDER CANCER, 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 NO1 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 HK2 HK2 HK2 14 0.64 0.083 YES
2 EPO EPO EPO 114 0.45 0.14 YES
3 CA9 CA9 CA9 168 0.42 0.19 YES
4 IGFBP1 IGFBP1 IGFBP1 317 0.37 0.23 YES
5 SLC2A1 SLC2A1 SLC2A1 341 0.36 0.28 YES
6 EGLN3 EGLN3 EGLN3 383 0.35 0.32 YES
7 GCK GCK GCK 420 0.34 0.36 YES
8 NDRG1 NDRG1 NDRG1 696 0.28 0.38 YES
9 SERPINE1 SERPINE1 SERPINE1 804 0.26 0.41 YES
10 ETS1 ETS1 ETS1 1272 0.21 0.42 YES
11 VEGFA VEGFA VEGFA 1339 0.2 0.44 YES
12 ENG ENG ENG 1385 0.2 0.46 YES
13 ABCG2 ABCG2 ABCG2 1522 0.19 0.48 YES
14 ENO1 ENO1 ENO1 1638 0.18 0.5 YES
15 TFF3 TFF3 TFF3 2004 0.15 0.5 YES
16 HMOX1 HMOX1 HMOX1 2023 0.15 0.51 YES
17 CXCL12 CXCL12 CXCL12 2221 0.14 0.52 YES
18 TF TF TF 2235 0.14 0.54 YES
19 PLIN2 PLIN2 PLIN2 2343 0.13 0.55 YES
20 HDAC7 HDAC7 HDAC7 2512 0.12 0.56 YES
21 ID2 ID2 ID2 2772 0.11 0.56 YES
22 PFKL PFKL PFKL 2791 0.11 0.57 YES
23 SP1 SP1 SP1 2902 0.1 0.58 YES
24 BNIP3 BNIP3 BNIP3 2955 0.1 0.59 YES
25 CXCR4 CXCR4 CXCR4 3160 0.093 0.59 YES
26 PFKFB3 PFKFB3 PFKFB3 3708 0.075 0.57 NO
27 LDHA LDHA LDHA 3886 0.071 0.57 NO
28 GATA2 GATA2 GATA2 3975 0.068 0.57 NO
29 FURIN FURIN FURIN 4969 0.045 0.52 NO
30 PGK1 PGK1 PGK1 5298 0.038 0.51 NO
31 JUN JUN JUN 5461 0.036 0.5 NO
32 TFRC TFRC TFRC 5801 0.03 0.49 NO
33 PGM1 PGM1 PGM1 6152 0.024 0.47 NO
34 PKM2 PKM2 PKM2 6177 0.024 0.47 NO
35 ALDOA ALDOA ALDOA 6516 0.018 0.46 NO
36 EP300 EP300 EP300 6568 0.018 0.46 NO
37 BHLHE40 BHLHE40 BHLHE40 6746 0.016 0.45 NO
38 ARNT ARNT ARNT 7201 0.01 0.43 NO
39 MCL1 MCL1 MCL1 7340 0.0084 0.42 NO
40 HK1 HK1 HK1 7496 0.0063 0.41 NO
41 EDN1 EDN1 EDN1 7591 0.005 0.41 NO
42 CREB1 CREB1 CREB1 7919 0.00072 0.39 NO
43 AKT1 AKT1 AKT1 8168 -0.0023 0.38 NO
44 CP CP CP 8377 -0.0048 0.36 NO
45 LEP LEP LEP 8395 -0.005 0.36 NO
46 HIF1A HIF1A HIF1A 8428 -0.0054 0.36 NO
47 EGLN1 EGLN1 EGLN1 8644 -0.0079 0.35 NO
48 NPM1 NPM1 NPM1 9086 -0.013 0.33 NO
49 CREBBP CREBBP CREBBP 9542 -0.018 0.31 NO
50 SMAD4 SMAD4 SMAD4 9634 -0.02 0.3 NO
51 ITGB2 ITGB2 ITGB2 10366 -0.028 0.27 NO
52 COPS5 COPS5 COPS5 10485 -0.03 0.26 NO
53 CITED2 CITED2 CITED2 10609 -0.032 0.26 NO
54 FOS FOS FOS 12499 -0.057 0.16 NO
55 NT5E NT5E NT5E 12677 -0.06 0.16 NO
56 FECH FECH FECH 12823 -0.063 0.16 NO
57 ADM ADM ADM 12993 -0.065 0.16 NO
58 NCOA1 NCOA1 NCOA1 13224 -0.07 0.16 NO
59 BHLHE41 BHLHE41 BHLHE41 14366 -0.094 0.11 NO
60 SMAD3 SMAD3 SMAD3 14641 -0.1 0.1 NO
61 ABCB1 ABCB1 ABCB1 15226 -0.12 0.087 NO
62 RORA RORA RORA 15717 -0.14 0.078 NO
63 NOS2 NOS2 NOS2 16019 -0.16 0.082 NO
64 NCOA2 NCOA2 NCOA2 16697 -0.2 0.071 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 NO1 PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA VEGF 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 LFNG LFNG LFNG 170 0.42 0.044 YES
2 HEY2 HEY2 HEY2 183 0.41 0.095 YES
3 DLL4 DLL4 DLL4 378 0.35 0.13 YES
4 DLL1 DLL1 DLL1 567 0.3 0.16 YES
5 NOTCH3 NOTCH3 NOTCH3 652 0.29 0.19 YES
6 MFNG MFNG MFNG 686 0.28 0.22 YES
7 HEYL HEYL HEYL 695 0.28 0.26 YES
8 JAG2 JAG2 JAG2 876 0.25 0.28 YES
9 NOTCH4 NOTCH4 NOTCH4 1103 0.23 0.29 YES
10 JAG1 JAG1 JAG1 1206 0.22 0.32 YES
11 MYC MYC MYC 1680 0.17 0.31 YES
12 HES1 HES1 HES1 2176 0.14 0.3 YES
13 MAML3 MAML3 MAML3 2229 0.14 0.31 YES
14 ATP2A3 ATP2A3 ATP2A3 2255 0.14 0.33 YES
15 HDAC7 HDAC7 HDAC7 2512 0.12 0.33 YES
16 TBL1X TBL1X TBL1X 2530 0.12 0.34 YES
17 HDAC1 HDAC1 HDAC1 2682 0.11 0.35 YES
18 DTX2 DTX2 DTX2 2753 0.11 0.36 YES
19 ST3GAL6 ST3GAL6 ST3GAL6 2839 0.11 0.37 YES
20 MIB2 MIB2 MIB2 2945 0.1 0.38 YES
21 TP53 TP53 TP53 3054 0.096 0.38 YES
22 HES5 HES5 HES5 3061 0.096 0.39 YES
23 MOV10 MOV10 MOV10 3149 0.093 0.4 YES
24 CDK8 CDK8 CDK8 3167 0.092 0.41 YES
25 B4GALT1 B4GALT1 B4GALT1 3293 0.088 0.42 YES
26 DLK1 DLK1 DLK1 3952 0.069 0.39 NO
27 RBPJ RBPJ RBPJ 4002 0.067 0.39 NO
28 PSENEN PSENEN PSENEN 4286 0.06 0.38 NO
29 EIF2C1 EIF2C1 EIF2C1 4316 0.059 0.39 NO
30 NOTCH2 NOTCH2 NOTCH2 4366 0.058 0.4 NO
31 ARRB2 ARRB2 ARRB2 4462 0.056 0.4 NO
32 RBX1 RBX1 RBX1 4528 0.054 0.4 NO
33 ARRB1 ARRB1 ARRB1 4586 0.053 0.4 NO
34 FURIN FURIN FURIN 4969 0.045 0.39 NO
35 ST3GAL3 ST3GAL3 ST3GAL3 5001 0.044 0.39 NO
36 TFDP1 TFDP1 TFDP1 5038 0.044 0.4 NO
37 HDAC3 HDAC3 HDAC3 5156 0.041 0.39 NO
38 JUN JUN JUN 5461 0.036 0.38 NO
39 HDAC9 HDAC9 HDAC9 5477 0.036 0.38 NO
40 EIF2C4 EIF2C4 EIF2C4 5520 0.035 0.39 NO
41 UBA52 UBA52 UBA52 5813 0.029 0.38 NO
42 EIF2C2 EIF2C2 EIF2C2 5866 0.029 0.38 NO
43 HEY1 HEY1 HEY1 5938 0.027 0.38 NO
44 HDAC2 HDAC2 HDAC2 6096 0.025 0.37 NO
45 CCNC CCNC CCNC 6169 0.024 0.37 NO
46 MAML1 MAML1 MAML1 6323 0.022 0.36 NO
47 HDAC5 HDAC5 HDAC5 6445 0.02 0.36 NO
48 CUL1 CUL1 CUL1 6482 0.019 0.36 NO
49 EP300 EP300 EP300 6568 0.018 0.36 NO
50 NCSTN NCSTN NCSTN 6646 0.017 0.35 NO
51 EIF2C3 EIF2C3 EIF2C3 6684 0.016 0.35 NO
52 RPS27A RPS27A RPS27A 6768 0.015 0.35 NO
53 HDAC10 HDAC10 HDAC10 6889 0.014 0.35 NO
54 DNER DNER DNER 6935 0.014 0.34 NO
55 ATP2A2 ATP2A2 ATP2A2 7411 0.0073 0.32 NO
56 HDAC6 HDAC6 HDAC6 7743 0.0031 0.3 NO
57 HDAC8 HDAC8 HDAC8 7933 0.00055 0.29 NO
58 TBL1XR1 TBL1XR1 TBL1XR1 7986 -0.00012 0.29 NO
59 E2F1 E2F1 E2F1 8045 -0.00085 0.28 NO
60 TMED2 TMED2 TMED2 8236 -0.0032 0.28 NO
61 TLE2 TLE2 TLE2 8266 -0.0034 0.27 NO
62 HIF1A HIF1A HIF1A 8428 -0.0054 0.26 NO
63 MAMLD1 MAMLD1 MAMLD1 8458 -0.0056 0.26 NO
64 TLE3 TLE3 TLE3 8733 -0.0091 0.25 NO
65 PSEN1 PSEN1 PSEN1 8757 -0.0094 0.25 NO
66 TNRC6B TNRC6B TNRC6B 8854 -0.01 0.25 NO
67 NCOR1 NCOR1 NCOR1 9423 -0.017 0.22 NO
68 PSEN2 PSEN2 PSEN2 9459 -0.018 0.22 NO
69 CREBBP CREBBP CREBBP 9542 -0.018 0.21 NO
70 TLE1 TLE1 TLE1 9591 -0.019 0.21 NO
71 HDAC4 HDAC4 HDAC4 9662 -0.02 0.21 NO
72 APH1A APH1A APH1A 9763 -0.021 0.21 NO
73 RFNG RFNG RFNG 9864 -0.022 0.21 NO
74 SEL1L SEL1L SEL1L 9967 -0.024 0.2 NO
75 TNRC6A TNRC6A TNRC6A 10126 -0.026 0.2 NO
76 SNW1 SNW1 SNW1 10176 -0.026 0.2 NO
77 POFUT1 POFUT1 POFUT1 10186 -0.026 0.2 NO
78 CCND1 CCND1 CCND1 10291 -0.027 0.2 NO
79 NCOR2 NCOR2 NCOR2 10426 -0.029 0.2 NO
80 ADAM17 ADAM17 ADAM17 10586 -0.031 0.19 NO
81 DTX4 DTX4 DTX4 10882 -0.035 0.18 NO
82 SKP1 SKP1 SKP1 10982 -0.036 0.18 NO
83 NUMB NUMB NUMB 11039 -0.037 0.18 NO
84 ATP2A1 ATP2A1 ATP2A1 11058 -0.038 0.18 NO
85 TNRC6C TNRC6C TNRC6C 11234 -0.04 0.18 NO
86 MIB1 MIB1 MIB1 11638 -0.045 0.16 NO
87 KAT2A KAT2A KAT2A 11808 -0.048 0.16 NO
88 RAB6A RAB6A RAB6A 11848 -0.048 0.16 NO
89 TLE4 TLE4 TLE4 13032 -0.066 0.1 NO
90 FBXW7 FBXW7 FBXW7 13085 -0.067 0.11 NO
91 HDAC11 HDAC11 HDAC11 13325 -0.072 0.1 NO
92 ADAM10 ADAM10 ADAM10 14216 -0.09 0.067 NO
93 NEURL NEURL NEURL 14738 -0.1 0.051 NO
94 KAT2B KAT2B KAT2B 14822 -0.11 0.06 NO
95 APH1B APH1B APH1B 15283 -0.12 0.05 NO
96 CNTN1 CNTN1 CNTN1 15919 -0.15 0.033 NO
97 E2F3 E2F3 E2F3 16284 -0.17 0.034 NO
98 MAML2 MAML2 MAML2 16541 -0.19 0.044 NO
99 DTX1 DTX1 DTX1 17395 -0.29 0.032 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 VEGF PATHWAY.

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

genes ES table in pathway: PID HIF2PATHWAY

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 GNA14 GNA14 GNA14 238 0.4 0.1 YES
2 ITGB3 ITGB3 ITGB3 416 0.34 0.19 YES
3 S1PR3 S1PR3 S1PR3 743 0.27 0.25 YES
4 PDGFRB PDGFRB PDGFRB 814 0.26 0.32 YES
5 FLT1 FLT1 FLT1 844 0.26 0.39 YES
6 PDGFB PDGFB PDGFB 866 0.25 0.46 YES
7 S1PR1 S1PR1 S1PR1 1189 0.22 0.51 YES
8 VEGFA VEGFA VEGFA 1339 0.2 0.56 YES
9 GNA15 GNA15 GNA15 1514 0.19 0.6 YES
10 CXCR4 CXCR4 CXCR4 3160 0.093 0.54 NO
11 GNAI3 GNAI3 GNAI3 3467 0.082 0.55 NO
12 ITGAV ITGAV ITGAV 3706 0.075 0.55 NO
13 GNAI2 GNAI2 GNAI2 4853 0.047 0.5 NO
14 GNAZ GNAZ GNAZ 5610 0.033 0.47 NO
15 RAC1 RAC1 RAC1 5635 0.033 0.48 NO
16 RHOA RHOA RHOA 6209 0.023 0.45 NO
17 AKT1 AKT1 AKT1 8168 -0.0023 0.34 NO
18 GNAO1 GNAO1 GNAO1 8259 -0.0034 0.34 NO
19 MAPK1 MAPK1 MAPK1 8606 -0.0075 0.32 NO
20 GNA12 GNA12 GNA12 8902 -0.011 0.31 NO
21 JAK2 JAK2 JAK2 11228 -0.04 0.19 NO
22 GNA11 GNA11 GNA11 12759 -0.061 0.12 NO
23 GNA13 GNA13 GNA13 12809 -0.062 0.14 NO
24 AKT3 AKT3 AKT3 13025 -0.066 0.15 NO
25 MAPK3 MAPK3 MAPK3 13077 -0.067 0.16 NO
26 GNAI1 GNAI1 GNAI1 13384 -0.073 0.17 NO
27 SRC SRC SRC 13394 -0.073 0.19 NO
28 GNAQ GNAQ GNAQ 13417 -0.074 0.21 NO
29 S1PR2 S1PR2 S1PR2 16064 -0.16 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: PID HIF2PATHWAY.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: PID HIF2PATHWAY, 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 S1P S1P3 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 HEY2 HEY2 HEY2 183 0.41 0.14 YES
2 HEYL HEYL HEYL 695 0.28 0.2 YES
3 MYC MYC MYC 1680 0.17 0.21 YES
4 HES1 HES1 HES1 2176 0.14 0.23 YES
5 MAML3 MAML3 MAML3 2229 0.14 0.28 YES
6 HDAC7 HDAC7 HDAC7 2512 0.12 0.3 YES
7 TBL1X TBL1X TBL1X 2530 0.12 0.35 YES
8 HDAC1 HDAC1 HDAC1 2682 0.11 0.38 YES
9 HES5 HES5 HES5 3061 0.096 0.39 YES
10 CDK8 CDK8 CDK8 3167 0.092 0.42 YES
11 RBPJ RBPJ RBPJ 4002 0.067 0.39 NO
12 RBX1 RBX1 RBX1 4528 0.054 0.38 NO
13 HDAC3 HDAC3 HDAC3 5156 0.041 0.36 NO
14 HDAC9 HDAC9 HDAC9 5477 0.036 0.36 NO
15 UBA52 UBA52 UBA52 5813 0.029 0.35 NO
16 HEY1 HEY1 HEY1 5938 0.027 0.35 NO
17 HDAC2 HDAC2 HDAC2 6096 0.025 0.35 NO
18 CCNC CCNC CCNC 6169 0.024 0.36 NO
19 MAML1 MAML1 MAML1 6323 0.022 0.36 NO
20 HDAC5 HDAC5 HDAC5 6445 0.02 0.36 NO
21 CUL1 CUL1 CUL1 6482 0.019 0.36 NO
22 EP300 EP300 EP300 6568 0.018 0.36 NO
23 RPS27A RPS27A RPS27A 6768 0.015 0.36 NO
24 HDAC10 HDAC10 HDAC10 6889 0.014 0.36 NO
25 HDAC6 HDAC6 HDAC6 7743 0.0031 0.31 NO
26 HDAC8 HDAC8 HDAC8 7933 0.00055 0.3 NO
27 TBL1XR1 TBL1XR1 TBL1XR1 7986 -0.00012 0.3 NO
28 TLE2 TLE2 TLE2 8266 -0.0034 0.28 NO
29 HIF1A HIF1A HIF1A 8428 -0.0054 0.27 NO
30 MAMLD1 MAMLD1 MAMLD1 8458 -0.0056 0.27 NO
31 TLE3 TLE3 TLE3 8733 -0.0091 0.26 NO
32 NCOR1 NCOR1 NCOR1 9423 -0.017 0.23 NO
33 CREBBP CREBBP CREBBP 9542 -0.018 0.23 NO
34 TLE1 TLE1 TLE1 9591 -0.019 0.23 NO
35 HDAC4 HDAC4 HDAC4 9662 -0.02 0.24 NO
36 SNW1 SNW1 SNW1 10176 -0.026 0.22 NO
37 NCOR2 NCOR2 NCOR2 10426 -0.029 0.21 NO
38 SKP1 SKP1 SKP1 10982 -0.036 0.2 NO
39 KAT2A KAT2A KAT2A 11808 -0.048 0.17 NO
40 TLE4 TLE4 TLE4 13032 -0.066 0.12 NO
41 FBXW7 FBXW7 FBXW7 13085 -0.067 0.14 NO
42 HDAC11 HDAC11 HDAC11 13325 -0.072 0.15 NO
43 KAT2B KAT2B KAT2B 14822 -0.11 0.11 NO
44 MAML2 MAML2 MAML2 16541 -0.19 0.08 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: PID S1P S1P3 PATHWAY.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: PID S1P S1P3 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 FRA PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RYR2 RYR2 RYR2 128 0.44 0.094 YES
2 BDKRB2 BDKRB2 BDKRB2 202 0.41 0.18 YES
3 FLT4 FLT4 FLT4 593 0.3 0.23 YES
4 CAV1 CAV1 CAV1 700 0.28 0.29 YES
5 FLT1 FLT1 FLT1 844 0.26 0.34 YES
6 PDE2A PDE2A PDE2A 852 0.26 0.4 YES
7 KDR KDR KDR 980 0.24 0.44 YES
8 PDE3A PDE3A PDE3A 1128 0.22 0.49 YES
9 VEGFA VEGFA VEGFA 1339 0.2 0.52 YES
10 NOS3 NOS3 NOS3 1394 0.2 0.56 YES
11 PRKG1 PRKG1 PRKG1 1975 0.15 0.57 YES
12 CHRNA1 CHRNA1 CHRNA1 2072 0.15 0.6 YES
13 ACTA1 ACTA1 ACTA1 2398 0.13 0.61 YES
14 TNNI1 TNNI1 TNNI1 2749 0.11 0.61 YES
15 CHRM1 CHRM1 CHRM1 6904 0.014 0.38 NO
16 AKT1 AKT1 AKT1 8168 -0.0023 0.32 NO
17 PRKACB PRKACB PRKACB 9582 -0.019 0.24 NO
18 CALM3 CALM3 CALM3 10350 -0.028 0.2 NO
19 PDE3B PDE3B PDE3B 10736 -0.033 0.19 NO
20 PRKAR1A PRKAR1A PRKAR1A 10887 -0.035 0.19 NO
21 HSP90AA1 HSP90AA1 HSP90AA1 11302 -0.04 0.18 NO
22 CALM2 CALM2 CALM2 12676 -0.06 0.11 NO
23 PRKG2 PRKG2 PRKG2 12998 -0.066 0.11 NO
24 CALM1 CALM1 CALM1 13871 -0.083 0.081 NO
25 SLC7A1 SLC7A1 SLC7A1 13878 -0.083 0.1 NO
26 PRKAR1B PRKAR1B PRKAR1B 14570 -0.1 0.084 NO
27 PRKACG PRKACG PRKACG 14594 -0.1 0.11 NO
28 PRKAR2A PRKAR2A PRKAR2A 16189 -0.17 0.055 NO
29 PRKAR2B PRKAR2B PRKAR2B 16555 -0.19 0.079 NO

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

Figure S54.  Get High-res Image For the top 5 core enriched genes in the pathway: PID FRA 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 ILK PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 KDELR3 KDELR3 KDELR3 1721 0.17 -0.019 YES
2 DNAJB11 DNAJB11 DNAJB11 2168 0.14 0.021 YES
3 PDIA5 PDIA5 PDIA5 2325 0.13 0.072 YES
4 WIPI1 WIPI1 WIPI1 2660 0.11 0.11 YES
5 ZBTB17 ZBTB17 ZBTB17 3037 0.097 0.13 YES
6 DDX11 DDX11 DDX11 3157 0.093 0.17 YES
7 LMNA LMNA LMNA 3185 0.092 0.21 YES
8 WFS1 WFS1 WFS1 3310 0.088 0.24 YES
9 CTDSP2 CTDSP2 CTDSP2 3850 0.072 0.24 YES
10 FKBP14 FKBP14 FKBP14 4128 0.064 0.26 YES
11 CXXC1 CXXC1 CXXC1 4731 0.05 0.24 YES
12 PPP2R5B PPP2R5B PPP2R5B 4750 0.049 0.27 YES
13 SRPRB SRPRB SRPRB 4915 0.046 0.28 YES
14 EXTL3 EXTL3 EXTL3 4922 0.046 0.3 YES
15 GSK3A GSK3A GSK3A 5203 0.04 0.3 YES
16 ARFGAP1 ARFGAP1 ARFGAP1 5365 0.037 0.31 YES
17 XBP1 XBP1 XBP1 5371 0.037 0.33 YES
18 SERP1 SERP1 SERP1 5425 0.036 0.34 YES
19 HDGF HDGF HDGF 5451 0.036 0.36 YES
20 ACADVL ACADVL ACADVL 5884 0.028 0.34 NO
21 SULT1A3 SULT1A3 SULT1A3 6389 0.02 0.33 NO
22 PDIA6 PDIA6 PDIA6 6544 0.018 0.33 NO
23 C19orf10 C19orf10 C19orf10 6654 0.017 0.33 NO
24 DNAJB9 DNAJB9 DNAJB9 6775 0.015 0.33 NO
25 ATP6V0D1 ATP6V0D1 ATP6V0D1 7400 0.0074 0.3 NO
26 SYVN1 SYVN1 SYVN1 7592 0.005 0.29 NO
27 GOSR2 GOSR2 GOSR2 7764 0.0028 0.28 NO
28 YIF1A YIF1A YIF1A 7929 0.00056 0.27 NO
29 KLHDC3 KLHDC3 KLHDC3 7951 0.0003 0.27 NO
30 SSR1 SSR1 SSR1 8261 -0.0034 0.26 NO
31 TLN1 TLN1 TLN1 8299 -0.0038 0.25 NO
32 SRPR SRPR SRPR 9036 -0.013 0.22 NO
33 CUL7 CUL7 CUL7 9089 -0.013 0.22 NO
34 DCTN1 DCTN1 DCTN1 9269 -0.015 0.22 NO
35 SEC31A SEC31A SEC31A 9642 -0.02 0.21 NO
36 DNAJC3 DNAJC3 DNAJC3 9925 -0.023 0.2 NO
37 ADD1 ADD1 ADD1 10170 -0.026 0.2 NO
38 PREB PREB PREB 10777 -0.034 0.18 NO
39 SHC1 SHC1 SHC1 11576 -0.044 0.16 NO
40 HYOU1 HYOU1 HYOU1 11912 -0.049 0.16 NO
41 EDEM1 EDEM1 EDEM1 12609 -0.059 0.15 NO
42 TATDN2 TATDN2 TATDN2 12643 -0.06 0.18 NO
43 TSPYL2 TSPYL2 TSPYL2 14962 -0.11 0.097 NO
44 TPP1 TPP1 TPP1 15980 -0.15 0.11 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 ILK PATHWAY.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ILK 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 SYNDECAN 1 PATHWAY

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 LFNG LFNG LFNG 170 0.42 0.072 YES
2 DLL4 DLL4 DLL4 378 0.35 0.13 YES
3 DLL1 DLL1 DLL1 567 0.3 0.18 YES
4 NOTCH3 NOTCH3 NOTCH3 652 0.29 0.23 YES
5 MFNG MFNG MFNG 686 0.28 0.28 YES
6 JAG2 JAG2 JAG2 876 0.25 0.32 YES
7 NOTCH4 NOTCH4 NOTCH4 1103 0.23 0.35 YES
8 NOTCH1 NOTCH1 NOTCH1 1106 0.22 0.39 YES
9 JAG1 JAG1 JAG1 1206 0.22 0.43 YES
10 PTCRA PTCRA PTCRA 1712 0.17 0.43 YES
11 HES1 HES1 HES1 2176 0.14 0.44 YES
12 MAML3 MAML3 MAML3 2229 0.14 0.46 YES
13 HDAC1 HDAC1 HDAC1 2682 0.11 0.46 YES
14 DTX2 DTX2 DTX2 2753 0.11 0.47 YES
15 HES5 HES5 HES5 3061 0.096 0.48 YES
16 DVL1 DVL1 DVL1 3312 0.088 0.48 YES
17 RBPJ RBPJ RBPJ 4002 0.067 0.45 NO
18 PSENEN PSENEN PSENEN 4286 0.06 0.45 NO
19 NOTCH2 NOTCH2 NOTCH2 4366 0.058 0.46 NO
20 DVL3 DVL3 DVL3 4573 0.053 0.45 NO
21 CTBP2 CTBP2 CTBP2 5952 0.027 0.38 NO
22 HDAC2 HDAC2 HDAC2 6096 0.025 0.38 NO
23 MAML1 MAML1 MAML1 6323 0.022 0.37 NO
24 EP300 EP300 EP300 6568 0.018 0.36 NO
25 NCSTN NCSTN NCSTN 6646 0.017 0.36 NO
26 DVL2 DVL2 DVL2 7061 0.012 0.34 NO
27 DTX3 DTX3 DTX3 7556 0.0055 0.31 NO
28 PSEN1 PSEN1 PSEN1 8757 -0.0094 0.25 NO
29 CTBP1 CTBP1 CTBP1 8899 -0.011 0.24 NO
30 PSEN2 PSEN2 PSEN2 9459 -0.018 0.21 NO
31 CREBBP CREBBP CREBBP 9542 -0.018 0.21 NO
32 APH1A APH1A APH1A 9763 -0.021 0.2 NO
33 RFNG RFNG RFNG 9864 -0.022 0.2 NO
34 SNW1 SNW1 SNW1 10176 -0.026 0.19 NO
35 NCOR2 NCOR2 NCOR2 10426 -0.029 0.18 NO
36 ADAM17 ADAM17 ADAM17 10586 -0.031 0.18 NO
37 DTX4 DTX4 DTX4 10882 -0.035 0.17 NO
38 DTX3L DTX3L DTX3L 11008 -0.037 0.17 NO
39 NUMB NUMB NUMB 11039 -0.037 0.18 NO
40 CIR1 CIR1 CIR1 11184 -0.039 0.18 NO
41 KAT2A KAT2A KAT2A 11808 -0.048 0.15 NO
42 NUMBL NUMBL NUMBL 12622 -0.059 0.12 NO
43 KAT2B KAT2B KAT2B 14822 -0.11 0.014 NO
44 MAML2 MAML2 MAML2 16541 -0.19 -0.044 NO
45 DTX1 DTX1 DTX1 17395 -0.29 -0.036 NO
46 DLL3 DLL3 DLL3 17671 -0.35 0.017 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 SYNDECAN 1 PATHWAY.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: PID SYNDECAN 1 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 VEGFR1 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 COL23A1 COL23A1 COL23A1 123 0.45 0.026 YES
2 COL17A1 COL17A1 COL17A1 130 0.44 0.058 YES
3 COL13A1 COL13A1 COL13A1 137 0.44 0.089 YES
4 ADAMTS2 ADAMTS2 ADAMTS2 145 0.43 0.12 YES
5 TPSAB1 TPSAB1 TPSAB1 247 0.39 0.14 YES
6 COL4A6 COL4A6 COL4A6 314 0.37 0.17 YES
7 ADAMTS14 ADAMTS14 ADAMTS14 407 0.34 0.19 YES
8 COL5A3 COL5A3 COL5A3 418 0.34 0.21 YES
9 MMP11 MMP11 MMP11 556 0.31 0.22 YES
10 BMP1 BMP1 BMP1 561 0.3 0.25 YES
11 CTSG CTSG CTSG 626 0.29 0.26 YES
12 COL4A5 COL4A5 COL4A5 682 0.28 0.28 YES
13 COL27A1 COL27A1 COL27A1 694 0.28 0.3 YES
14 COL25A1 COL25A1 COL25A1 722 0.28 0.32 YES
15 COL21A1 COL21A1 COL21A1 918 0.25 0.33 YES
16 MMP9 MMP9 MMP9 937 0.24 0.34 YES
17 COL24A1 COL24A1 COL24A1 977 0.24 0.36 YES
18 TLL1 TLL1 TLL1 998 0.24 0.38 YES
19 COL6A2 COL6A2 COL6A2 1047 0.23 0.39 YES
20 MMP2 MMP2 MMP2 1078 0.23 0.4 YES
21 MMP1 MMP1 MMP1 1088 0.23 0.42 YES
22 COL11A2 COL11A2 COL11A2 1093 0.23 0.44 YES
23 MMP14 MMP14 MMP14 1095 0.23 0.45 YES
24 COL4A1 COL4A1 COL4A1 1100 0.23 0.47 YES
25 COL4A2 COL4A2 COL4A2 1119 0.22 0.48 YES
26 COL9A1 COL9A1 COL9A1 1191 0.22 0.5 YES
27 PCOLCE PCOLCE PCOLCE 1404 0.2 0.5 YES
28 COL5A2 COL5A2 COL5A2 1439 0.19 0.51 YES
29 SERPINH1 SERPINH1 SERPINH1 1463 0.19 0.52 YES
30 COL15A1 COL15A1 COL15A1 1598 0.18 0.53 YES
31 COL16A1 COL16A1 COL16A1 1665 0.17 0.54 YES
32 COL5A1 COL5A1 COL5A1 1728 0.17 0.55 YES
33 COL6A3 COL6A3 COL6A3 1735 0.17 0.56 YES
34 COL2A1 COL2A1 COL2A1 1795 0.16 0.57 YES
35 MMP10 MMP10 MMP10 1893 0.16 0.57 YES
36 PLOD1 PLOD1 PLOD1 2092 0.14 0.57 YES
37 COL14A1 COL14A1 COL14A1 2301 0.13 0.57 YES
38 PLOD2 PLOD2 PLOD2 2323 0.13 0.58 YES
39 COL1A2 COL1A2 COL1A2 2399 0.13 0.58 YES
40 COL3A1 COL3A1 COL3A1 2401 0.13 0.59 YES
41 COL1A1 COL1A1 COL1A1 2469 0.12 0.6 YES
42 COL6A1 COL6A1 COL6A1 2485 0.12 0.61 YES
43 LEPREL1 LEPREL1 LEPREL1 2545 0.12 0.61 YES
44 ADAMTS3 ADAMTS3 ADAMTS3 2619 0.12 0.62 YES
45 PCOLCE2 PCOLCE2 PCOLCE2 2748 0.11 0.62 YES
46 GLT25D1 GLT25D1 GLT25D1 3380 0.086 0.59 NO
47 PPIB PPIB PPIB 3530 0.08 0.59 NO
48 COL12A1 COL12A1 COL12A1 3897 0.07 0.57 NO
49 PLOD3 PLOD3 PLOD3 4072 0.065 0.57 NO
50 COL19A1 COL19A1 COL19A1 4481 0.055 0.55 NO
51 TIMP1 TIMP1 TIMP1 4539 0.054 0.55 NO
52 LEPREL2 LEPREL2 LEPREL2 4680 0.051 0.54 NO
53 FURIN FURIN FURIN 4969 0.045 0.53 NO
54 P4HB P4HB P4HB 5080 0.043 0.53 NO
55 TIMP2 TIMP2 TIMP2 6022 0.026 0.48 NO
56 MMP25 MMP25 MMP25 6590 0.017 0.45 NO
57 COL4A4 COL4A4 COL4A4 6915 0.014 0.43 NO
58 KLKB1 KLKB1 KLKB1 6970 0.013 0.43 NO
59 COL9A3 COL9A3 COL9A3 8871 -0.011 0.32 NO
60 MMP15 MMP15 MMP15 9028 -0.013 0.31 NO
61 COL8A1 COL8A1 COL8A1 9358 -0.016 0.3 NO
62 ELANE ELANE ELANE 9909 -0.023 0.27 NO
63 CRTAP CRTAP CRTAP 10169 -0.026 0.26 NO
64 MMP24 MMP24 MMP24 11559 -0.044 0.18 NO
65 COL11A1 COL11A1 COL11A1 13905 -0.083 0.056 NO
66 COL7A1 COL7A1 COL7A1 14059 -0.087 0.054 NO
67 MMP17 MMP17 MMP17 14100 -0.088 0.058 NO
68 CTRB2 CTRB2 CTRB2 14587 -0.1 0.038 NO
69 COL8A2 COL8A2 COL8A2 15009 -0.11 0.023 NO
70 COL4A3 COL4A3 COL4A3 15538 -0.13 0.0029 NO
71 COL28A1 COL28A1 COL28A1 16030 -0.16 -0.013 NO
72 COL9A2 COL9A2 COL9A2 16308 -0.17 -0.016 NO
73 TLL2 TLL2 TLL2 16741 -0.21 -0.025 NO
74 COL10A1 COL10A1 COL10A1 16925 -0.23 -0.019 NO
75 MMP16 MMP16 MMP16 17014 -0.24 -0.0063 NO
76 COL22A1 COL22A1 COL22A1 17210 -0.26 0.0016 NO
77 GLT25D2 GLT25D2 GLT25D2 17954 -0.57 0.0012 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 VEGFR1 PATHWAY.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: PID VEGFR1 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 55 genes.ES.table 0.65 1.9 0 0.22 0.34 0.31 0.13 0.27 0 0.05
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.49 1.6 0.08 0.15 0.9 0.48 0.34 0.32 0.083 0.004
KEGG PENTOSE PHOSPHATE PATHWAY 25 genes.ES.table 0.53 1.6 0.04 0.14 0.9 0.28 0.17 0.23 0.081 0.003
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.45 1.4 0.09 0.21 0.99 0.15 0.074 0.14 0.16 0.004
KEGG FATTY ACID METABOLISM 36 genes.ES.table 0.63 1.8 0.0047 0.14 0.45 0.56 0.22 0.43 0 0.029
KEGG STEROID HORMONE BIOSYNTHESIS 35 genes.ES.table 0.83 1.8 0 0.13 0.47 0.43 0.056 0.4 0 0.026
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 29 genes.ES.table 0.49 1.4 0.061 0.21 0.99 0.34 0.2 0.28 0.15 0.003
KEGG GLYCINE SERINE AND THREONINE METABOLISM 29 genes.ES.table 0.68 1.7 0 0.14 0.68 0.41 0.16 0.35 0.061 0.012
KEGG CYSTEINE AND METHIONINE METABOLISM 33 genes.ES.table 0.48 1.5 0.052 0.18 0.97 0.42 0.24 0.32 0.13 0.002
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.68 2.1 0.0043 0.15 0.091 0.6 0.22 0.47 0 0.045
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 HSD3B2 HSD3B2 HSD3B2 9 2 0.024 YES
2 CYP17A1 CYP17A1 CYP17A1 13 1.9 0.046 YES
3 CYP21A2 CYP21A2 CYP21A2 14 1.9 0.069 YES
4 SULT2A1 SULT2A1 SULT2A1 15 1.9 0.092 YES
5 CYP11B1 CYP11B1 CYP11B1 17 1.8 0.11 YES
6 STAR STAR STAR 22 1.7 0.13 YES
7 CYP11A1 CYP11A1 CYP11A1 28 1.6 0.15 YES
8 CYP11B2 CYP11B2 CYP11B2 35 1.5 0.17 YES
9 ABCC3 ABCC3 ABCC3 56 1.3 0.19 YES
10 PLA2G1B PLA2G1B PLA2G1B 70 1.3 0.2 YES
11 CYP19A1 CYP19A1 CYP19A1 85 1.2 0.22 YES
12 DHCR24 DHCR24 DHCR24 141 1 0.22 YES
13 SLC44A4 SLC44A4 SLC44A4 143 1 0.24 YES
14 HSD11B1 HSD11B1 HSD11B1 145 1 0.25 YES
15 ELOVL3 ELOVL3 ELOVL3 288 0.76 0.25 YES
16 PIK3C2G PIK3C2G PIK3C2G 293 0.76 0.26 YES
17 G0S2 G0S2 G0S2 295 0.76 0.27 YES
18 APOE APOE APOE 313 0.74 0.28 YES
19 ABCB4 ABCB4 ABCB4 337 0.72 0.28 YES
20 ALAS1 ALAS1 ALAS1 353 0.7 0.29 YES
21 LDLR LDLR LDLR 403 0.66 0.3 YES
22 FHL2 FHL2 FHL2 451 0.63 0.3 YES
23 PNPLA3 PNPLA3 PNPLA3 457 0.63 0.31 YES
24 ARSJ ARSJ ARSJ 513 0.58 0.31 YES
25 POMC POMC POMC 578 0.56 0.32 YES
26 ACADL ACADL ACADL 582 0.55 0.32 YES
27 PLIN2 PLIN2 PLIN2 616 0.54 0.33 YES
28 PLA2G2A PLA2G2A PLA2G2A 655 0.53 0.33 YES
29 SCARB1 SCARB1 SCARB1 679 0.52 0.34 YES
30 PLD1 PLD1 PLD1 685 0.52 0.34 YES
31 CYP7B1 CYP7B1 CYP7B1 738 0.5 0.34 YES
32 PLTP PLTP PLTP 746 0.49 0.35 YES
33 LRAT LRAT LRAT 783 0.48 0.35 YES
34 PIK3R5 PIK3R5 PIK3R5 785 0.48 0.36 YES
35 LDLRAP1 LDLRAP1 LDLRAP1 797 0.47 0.36 YES
36 CYP39A1 CYP39A1 CYP39A1 890 0.45 0.36 YES
37 PLA2G4A PLA2G4A PLA2G4A 912 0.45 0.37 YES
38 TM7SF2 TM7SF2 TM7SF2 928 0.45 0.37 YES
39 AKR1B1 AKR1B1 AKR1B1 933 0.44 0.38 YES
40 APOC2 APOC2 APOC2 968 0.44 0.38 YES
41 GLIPR1 GLIPR1 GLIPR1 977 0.44 0.39 YES
42 PLA2G2D PLA2G2D PLA2G2D 987 0.43 0.39 YES
43 LIPE LIPE LIPE 1024 0.43 0.4 YES
44 PIP5K1B PIP5K1B PIP5K1B 1026 0.42 0.4 YES
45 SDC1 SDC1 SDC1 1034 0.42 0.4 YES
46 MBOAT1 MBOAT1 MBOAT1 1069 0.42 0.41 YES
47 ACADS ACADS ACADS 1101 0.41 0.41 YES
48 HSD3B7 HSD3B7 HSD3B7 1168 0.4 0.41 YES
49 ABCA1 ABCA1 ABCA1 1172 0.4 0.42 YES
50 PLD4 PLD4 PLD4 1187 0.39 0.42 YES
51 EBP EBP EBP 1201 0.39 0.42 YES
52 IDH1 IDH1 IDH1 1247 0.38 0.43 YES
53 LHB LHB LHB 1260 0.38 0.43 YES
54 CH25H CH25H CH25H 1261 0.38 0.44 YES
55 DHCR7 DHCR7 DHCR7 1294 0.38 0.44 YES
56 SGMS2 SGMS2 SGMS2 1306 0.37 0.44 YES
57 PLIN1 PLIN1 PLIN1 1319 0.37 0.45 YES
58 PLA2G4D PLA2G4D PLA2G4D 1369 0.36 0.45 YES
59 YAP1 YAP1 YAP1 1393 0.36 0.45 YES
60 RBP2 RBP2 RBP2 1449 0.34 0.45 YES
61 FADS2 FADS2 FADS2 1471 0.34 0.45 YES
62 PLA2G5 PLA2G5 PLA2G5 1530 0.33 0.46 YES
63 MED11 MED11 MED11 1558 0.33 0.46 YES
64 FABP4 FABP4 FABP4 1568 0.33 0.46 YES
65 ANKRD1 ANKRD1 ANKRD1 1598 0.32 0.46 YES
66 LPIN3 LPIN3 LPIN3 1715 0.31 0.46 YES
67 MVD MVD MVD 1731 0.31 0.46 YES
68 PLBD1 PLBD1 PLBD1 1757 0.3 0.46 YES
69 HMGCS1 HMGCS1 HMGCS1 1806 0.3 0.47 YES
70 CGA CGA CGA 1807 0.3 0.47 YES
71 NPAS2 NPAS2 NPAS2 1839 0.29 0.47 YES
72 CTGF CTGF CTGF 1896 0.29 0.47 YES
73 BMP1 BMP1 BMP1 1934 0.28 0.47 YES
74 SRD5A2 SRD5A2 SRD5A2 1935 0.28 0.48 YES
75 FDPS FDPS FDPS 1940 0.28 0.48 YES
76 NSDHL NSDHL NSDHL 2026 0.27 0.48 YES
77 HMGCR HMGCR HMGCR 2048 0.26 0.48 YES
78 PRKD1 PRKD1 PRKD1 2054 0.26 0.48 YES
79 FABP6 FABP6 FABP6 2072 0.26 0.48 YES
80 GPD1 GPD1 GPD1 2085 0.26 0.49 YES
81 SQLE SQLE SQLE 2138 0.25 0.49 YES
82 PCCA PCCA PCCA 2146 0.25 0.49 YES
83 IDI2 IDI2 IDI2 2187 0.25 0.49 YES
84 SLC27A2 SLC27A2 SLC27A2 2241 0.24 0.49 YES
85 CYP27B1 CYP27B1 CYP27B1 2258 0.24 0.49 YES
86 ELOVL6 ELOVL6 ELOVL6 2260 0.24 0.5 YES
87 CDS1 CDS1 CDS1 2284 0.24 0.5 YES
88 STARD5 STARD5 STARD5 2323 0.23 0.5 YES
89 ARSK ARSK ARSK 2325 0.23 0.5 YES
90 CYP8B1 CYP8B1 CYP8B1 2329 0.23 0.5 YES
91 FADS1 FADS1 FADS1 2372 0.23 0.5 YES
92 ARSI ARSI ARSI 2395 0.22 0.5 YES
93 PIK3CD PIK3CD PIK3CD 2410 0.22 0.51 YES
94 IDI1 IDI1 IDI1 2430 0.22 0.51 YES
95 AMN AMN AMN 2435 0.22 0.51 YES
96 PCYT1B PCYT1B PCYT1B 2440 0.22 0.51 YES
97 ACADVL ACADVL ACADVL 2445 0.22 0.52 YES
98 GK GK GK 2472 0.22 0.52 YES
99 GPAM GPAM GPAM 2479 0.22 0.52 YES
100 FDFT1 FDFT1 FDFT1 2487 0.22 0.52 YES
101 AGT AGT AGT 2491 0.22 0.52 YES
102 ACSL5 ACSL5 ACSL5 2568 0.21 0.52 YES
103 ACAA1 ACAA1 ACAA1 2594 0.21 0.52 YES
104 DECR1 DECR1 DECR1 2624 0.2 0.52 YES
105 SREBF1 SREBF1 SREBF1 2640 0.2 0.53 YES
106 SLC44A5 SLC44A5 SLC44A5 2642 0.2 0.53 YES
107 CPT2 CPT2 CPT2 2649 0.2 0.53 YES
108 UGCG UGCG UGCG 2656 0.2 0.53 YES
109 PPAP2C PPAP2C PPAP2C 2689 0.2 0.53 YES
110 PCCB PCCB PCCB 2717 0.2 0.53 YES
111 ACADM ACADM ACADM 2745 0.19 0.54 YES
112 SYNJ2 SYNJ2 SYNJ2 2773 0.19 0.54 YES
113 LPL LPL LPL 2805 0.19 0.54 YES
114 TEAD2 TEAD2 TEAD2 2811 0.19 0.54 YES
115 ANGPTL4 ANGPTL4 ANGPTL4 2837 0.19 0.54 YES
116 PEX11A PEX11A PEX11A 2886 0.18 0.54 YES
117 CYP51A1 CYP51A1 CYP51A1 2901 0.18 0.54 YES
118 CHPT1 CHPT1 CHPT1 2933 0.18 0.54 YES
119 CYP27A1 CYP27A1 CYP27A1 2936 0.18 0.54 YES
120 INPP4B INPP4B INPP4B 2973 0.17 0.54 YES
121 MVK MVK MVK 2985 0.17 0.54 YES
122 CTSA CTSA CTSA 3076 0.17 0.54 YES
123 HMGCL HMGCL HMGCL 3078 0.17 0.54 YES
124 RORA RORA RORA 3108 0.16 0.54 YES
125 TPTE2 TPTE2 TPTE2 3126 0.16 0.54 YES
126 ACAT1 ACAT1 ACAT1 3139 0.16 0.55 YES
127 ARNTL ARNTL ARNTL 3154 0.16 0.55 YES
128 HADHB HADHB HADHB 3169 0.16 0.55 YES
129 CHKA CHKA CHKA 3200 0.16 0.55 YES
130 MCEE MCEE MCEE 3245 0.16 0.55 YES
131 ARSG ARSG ARSG 3256 0.16 0.55 YES
132 SLC25A20 SLC25A20 SLC25A20 3275 0.15 0.55 YES
133 ABCD1 ABCD1 ABCD1 3289 0.15 0.55 YES
134 MTM1 MTM1 MTM1 3296 0.15 0.55 YES
135 ME1 ME1 ME1 3299 0.15 0.55 YES
136 LCAT LCAT LCAT 3331 0.15 0.55 YES
137 APOA1 APOA1 APOA1 3337 0.15 0.56 YES
138 GPD1L GPD1L GPD1L 3393 0.15 0.55 NO
139 DGAT1 DGAT1 DGAT1 3414 0.14 0.55 NO
140 PIK3CG PIK3CG PIK3CG 3478 0.14 0.55 NO
141 MGLL MGLL MGLL 3480 0.14 0.55 NO
142 PHYH PHYH PHYH 3531 0.14 0.55 NO
143 DGAT2 DGAT2 DGAT2 3618 0.13 0.55 NO
144 AGPAT2 AGPAT2 AGPAT2 3627 0.13 0.55 NO
145 ELOVL1 ELOVL1 ELOVL1 3629 0.13 0.55 NO
146 APOB APOB APOB 3636 0.13 0.55 NO
147 LGMN LGMN LGMN 3679 0.13 0.55 NO
148 SMARCD3 SMARCD3 SMARCD3 3690 0.13 0.55 NO
149 CPT1B CPT1B CPT1B 3788 0.12 0.55 NO
150 CPT1A CPT1A CPT1A 3792 0.12 0.55 NO
151 LSS LSS LSS 3811 0.12 0.55 NO
152 ALB ALB ALB 3833 0.12 0.55 NO
153 SAR1B SAR1B SAR1B 3855 0.12 0.55 NO
154 ELOVL5 ELOVL5 ELOVL5 3925 0.12 0.55 NO
155 PCYT2 PCYT2 PCYT2 3936 0.12 0.55 NO
156 HSD17B7 HSD17B7 HSD17B7 3956 0.12 0.55 NO
157 PIK3CA PIK3CA PIK3CA 4090 0.11 0.54 NO
158 HSD17B3 HSD17B3 HSD17B3 4107 0.11 0.55 NO
159 PTDSS2 PTDSS2 PTDSS2 4184 0.11 0.54 NO
160 PHOSPHO1 PHOSPHO1 PHOSPHO1 4217 0.11 0.54 NO
161 ACACB ACACB ACACB 4224 0.11 0.54 NO
162 PPARA PPARA PPARA 4244 0.1 0.54 NO
163 CRLS1 CRLS1 CRLS1 4252 0.1 0.54 NO
164 MBOAT7 MBOAT7 MBOAT7 4253 0.1 0.55 NO
165 AGPAT3 AGPAT3 AGPAT3 4315 0.1 0.54 NO
166 PNPLA2 PNPLA2 PNPLA2 4321 0.1 0.54 NO
167 SUMF2 SUMF2 SUMF2 4330 0.1 0.54 NO
168 SMPD2 SMPD2 SMPD2 4357 0.1 0.54 NO
169 MTTP MTTP MTTP 4394 0.1 0.54 NO
170 PPARGC1A PPARGC1A PPARGC1A 4406 0.099 0.54 NO
171 ACSL1 ACSL1 ACSL1 4427 0.099 0.54 NO
172 PIK3CB PIK3CB PIK3CB 4512 0.096 0.54 NO
173 SCP2 SCP2 SCP2 4527 0.095 0.54 NO
174 MTMR14 MTMR14 MTMR14 4547 0.095 0.54 NO
175 GM2A GM2A GM2A 4613 0.093 0.54 NO
176 SC5DL SC5DL SC5DL 4634 0.092 0.54 NO
177 TECR TECR TECR 4662 0.091 0.54 NO
178 LPCAT3 LPCAT3 LPCAT3 4742 0.089 0.53 NO
179 ACOX3 ACOX3 ACOX3 4797 0.087 0.53 NO
180 HSD17B4 HSD17B4 HSD17B4 4857 0.085 0.53 NO
181 FASN FASN FASN 4905 0.084 0.53 NO
182 CRAT CRAT CRAT 4958 0.082 0.53 NO
183 CYP7A1 CYP7A1 CYP7A1 4959 0.082 0.53 NO
184 HEXB HEXB HEXB 4960 0.082 0.53 NO
185 PCYT1A PCYT1A PCYT1A 5079 0.079 0.52 NO
186 MED8 MED8 MED8 5154 0.077 0.52 NO
187 CETP CETP CETP 5190 0.077 0.52 NO
188 CHKB CHKB CHKB 5228 0.076 0.52 NO
189 ECHS1 ECHS1 ECHS1 5231 0.076 0.52 NO
190 MED18 MED18 MED18 5250 0.075 0.52 NO
191 SLC27A5 SLC27A5 SLC27A5 5267 0.075 0.52 NO
192 MED30 MED30 MED30 5288 0.074 0.52 NO
193 AGPAT6 AGPAT6 AGPAT6 5304 0.074 0.52 NO
194 PLA2G16 PLA2G16 PLA2G16 5336 0.073 0.52 NO
195 VAPA VAPA VAPA 5367 0.072 0.52 NO
196 ABHD5 ABHD5 ABHD5 5420 0.07 0.51 NO
197 SLC25A1 SLC25A1 SLC25A1 5445 0.069 0.51 NO
198 PIP4K2A PIP4K2A PIP4K2A 5485 0.068 0.51 NO
199 P4HB P4HB P4HB 5498 0.068 0.51 NO
200 ACOT8 ACOT8 ACOT8 5506 0.068 0.51 NO
201 MED31 MED31 MED31 5522 0.067 0.51 NO
202 AMACR AMACR AMACR 5538 0.067 0.51 NO
203 GLA GLA GLA 5544 0.067 0.51 NO
204 GPAT2 GPAT2 GPAT2 5553 0.066 0.51 NO
205 CEPT1 CEPT1 CEPT1 5562 0.066 0.51 NO
206 SLC44A1 SLC44A1 SLC44A1 5604 0.065 0.51 NO
207 PPARG PPARG PPARG 5635 0.064 0.51 NO
208 SLC27A1 SLC27A1 SLC27A1 5643 0.064 0.51 NO
209 ACSL4 ACSL4 ACSL4 5655 0.064 0.51 NO
210 SGMS1 SGMS1 SGMS1 5723 0.062 0.51 NO
211 RXRA RXRA RXRA 5735 0.062 0.51 NO
212 GPCPD1 GPCPD1 GPCPD1 5762 0.061 0.51 NO
213 TEAD4 TEAD4 TEAD4 5783 0.06 0.51 NO
214 BDH1 BDH1 BDH1 5805 0.06 0.51 NO
215 GLB1 GLB1 GLB1 5831 0.059 0.51 NO
216 HSD17B1 HSD17B1 HSD17B1 5914 0.057 0.5 NO
217 MED7 MED7 MED7 5978 0.056 0.5 NO
218 LPGAT1 LPGAT1 LPGAT1 6000 0.056 0.5 NO
219 PPAP2B PPAP2B PPAP2B 6034 0.055 0.5 NO
220 PI4K2B PI4K2B PI4K2B 6051 0.054 0.5 NO
221 MED12 MED12 MED12 6070 0.054 0.5 NO
222 PLA2G4C PLA2G4C PLA2G4C 6180 0.052 0.49 NO
223 PNPLA8 PNPLA8 PNPLA8 6193 0.051 0.49 NO
224 TXNRD1 TXNRD1 TXNRD1 6239 0.051 0.49 NO
225 ACACA ACACA ACACA 6305 0.049 0.49 NO
226 ACOX1 ACOX1 ACOX1 6309 0.049 0.49 NO
227 LIPC LIPC LIPC 6319 0.049 0.49 NO
228 CCNC CCNC CCNC 6373 0.048 0.48 NO
229 ARSB ARSB ARSB 6445 0.046 0.48 NO
230 OSBP OSBP OSBP 6533 0.045 0.48 NO
231 SREBF2 SREBF2 SREBF2 6622 0.043 0.47 NO
232 SLC10A1 SLC10A1 SLC10A1 6684 0.042 0.47 NO
233 ESRRA ESRRA ESRRA 6712 0.042 0.47 NO
234 NFYB NFYB NFYB 6751 0.041 0.47 NO
235 PEMT PEMT PEMT 6839 0.039 0.46 NO
236 ARSA ARSA ARSA 6840 0.039 0.46 NO
237 PPP1CA PPP1CA PPP1CA 6858 0.039 0.46 NO
238 PPAP2A PPAP2A PPAP2A 6883 0.038 0.46 NO
239 MED9 MED9 MED9 6924 0.038 0.46 NO
240 HDAC3 HDAC3 HDAC3 6933 0.037 0.46 NO
241 CROT CROT CROT 6935 0.037 0.46 NO
242 A2M A2M A2M 6967 0.037 0.46 NO
243 HEXA HEXA HEXA 6998 0.036 0.46 NO
244 PPP1CC PPP1CC PPP1CC 7016 0.036 0.46 NO
245 NEU1 NEU1 NEU1 7040 0.035 0.46 NO
246 HACL1 HACL1 HACL1 7047 0.035 0.46 NO
247 HSD17B12 HSD17B12 HSD17B12 7056 0.035 0.46 NO
248 MED25 MED25 MED25 7078 0.035 0.45 NO
249 TEAD3 TEAD3 TEAD3 7232 0.032 0.45 NO
250 PIK3R6 PIK3R6 PIK3R6 7264 0.031 0.44 NO
251 CD36 CD36 CD36 7273 0.031 0.44 NO
252 SPTLC2 SPTLC2 SPTLC2 7274 0.031 0.44 NO
253 HADHA HADHA HADHA 7303 0.03 0.44 NO
254 NCOA3 NCOA3 NCOA3 7304 0.03 0.44 NO
255 PMVK PMVK PMVK 7333 0.03 0.44 NO
256 SUMF1 SUMF1 SUMF1 7394 0.029 0.44 NO
257 SLC44A3 SLC44A3 SLC44A3 7399 0.029 0.44 NO
258 PRKACG PRKACG PRKACG 7458 0.028 0.44 NO
259 PPP1CB PPP1CB PPP1CB 7633 0.024 0.43 NO
260 HADH HADH HADH 7660 0.024 0.43 NO
261 PTDSS1 PTDSS1 PTDSS1 7702 0.023 0.42 NO
262 INPP5K INPP5K INPP5K 7732 0.023 0.42 NO
263 PI4K2A PI4K2A PI4K2A 7742 0.022 0.42 NO
264 ACSL3 ACSL3 ACSL3 7820 0.021 0.42 NO
265 SPHK1 SPHK1 SPHK1 7835 0.021 0.42 NO
266 WWTR1 WWTR1 WWTR1 7890 0.02 0.42 NO
267 AGPAT5 AGPAT5 AGPAT5 7930 0.019 0.41 NO
268 SGPP1 SGPP1 SGPP1 8015 0.018 0.41 NO
269 SRD5A3 SRD5A3 SRD5A3 8057 0.018 0.41 NO
270 RDH11 RDH11 RDH11 8059 0.018 0.41 NO
271 PRKACA PRKACA PRKACA 8061 0.018 0.41 NO
272 TAZ TAZ TAZ 8111 0.017 0.4 NO
273 TBL1XR1 TBL1XR1 TBL1XR1 8146 0.016 0.4 NO
274 PIK3R4 PIK3R4 PIK3R4 8166 0.016 0.4 NO
275 AGPAT9 AGPAT9 AGPAT9 8184 0.016 0.4 NO
276 ETNK2 ETNK2 ETNK2 8267 0.014 0.4 NO
277 LPCAT2 LPCAT2 LPCAT2 8282 0.014 0.4 NO
278 ACOX2 ACOX2 ACOX2 8293 0.014 0.4 NO
279 ABCG5 ABCG5 ABCG5 8327 0.013 0.39 NO
280 ASAH1 ASAH1 ASAH1 8355 0.013 0.39 NO
281 PLD6 PLD6 PLD6 8375 0.012 0.39 NO
282 AGPS AGPS AGPS 8414 0.012 0.39 NO
283 CSNK1G2 CSNK1G2 CSNK1G2 8432 0.011 0.39 NO
284 GNPAT GNPAT GNPAT 8573 0.0092 0.38 NO
285 GALC GALC GALC 8692 0.0077 0.37 NO
286 COL4A3BP COL4A3BP COL4A3BP 8696 0.0076 0.37 NO
287 MED15 MED15 MED15 8748 0.0068 0.37 NO
288 PRKAG2 PRKAG2 PRKAG2 8775 0.0064 0.37 NO
289 MED24 MED24 MED24 8813 0.0059 0.37 NO
290 INPPL1 INPPL1 INPPL1 8946 0.0038 0.36 NO
291 PRKAA2 PRKAA2 PRKAA2 9065 0.0021 0.35 NO
292 PIK3C2A PIK3C2A PIK3C2A 9073 0.002 0.35 NO
293 HSPG2 HSPG2 HSPG2 9103 0.0016 0.35 NO
294 MED23 MED23 MED23 9224 -0.00028 0.34 NO
295 ACLY ACLY ACLY 9263 -0.00087 0.34 NO
296 ABCG1 ABCG1 ABCG1 9345 -0.0021 0.34 NO
297 ETNK1 ETNK1 ETNK1 9375 -0.0025 0.34 NO
298 OXCT1 OXCT1 OXCT1 9407 -0.0029 0.33 NO
299 PSAP PSAP PSAP 9439 -0.0035 0.33 NO
300 MED4 MED4 MED4 9593 -0.0055 0.32 NO
301 MUT MUT MUT 9629 -0.006 0.32 NO
302 SLC25A17 SLC25A17 SLC25A17 9755 -0.0078 0.31 NO
303 FIG4 FIG4 FIG4 9766 -0.0079 0.31 NO
304 SLC44A2 SLC44A2 SLC44A2 9848 -0.0093 0.31 NO
305 VAPB VAPB VAPB 9863 -0.0095 0.31 NO
306 MED21 MED21 MED21 9898 -0.01 0.31 NO
307 CERK CERK CERK 10066 -0.012 0.3 NO
308 CDIPT CDIPT CDIPT 10070 -0.012 0.3 NO
309 SACM1L SACM1L SACM1L 10088 -0.013 0.3 NO
310 MED26 MED26 MED26 10175 -0.014 0.29 NO
311 ARF1 ARF1 ARF1 10185 -0.014 0.29 NO
312 LPCAT1 LPCAT1 LPCAT1 10192 -0.014 0.29 NO
313 SPHK2 SPHK2 SPHK2 10204 -0.014 0.29 NO
314 SPTLC1 SPTLC1 SPTLC1 10212 -0.014 0.29 NO
315 MED19 MED19 MED19 10224 -0.015 0.29 NO
316 GGPS1 GGPS1 GGPS1 10268 -0.016 0.29 NO
317 AKR1C4 AKR1C4 AKR1C4 10353 -0.017 0.28 NO
318 TIAM2 TIAM2 TIAM2 10522 -0.019 0.27 NO
319 SIN3B SIN3B SIN3B 10584 -0.02 0.27 NO
320 VAC14 VAC14 VAC14 10625 -0.021 0.27 NO
321 MED29 MED29 MED29 10646 -0.021 0.27 NO
322 FAR1 FAR1 FAR1 10682 -0.021 0.27 NO
323 GPD2 GPD2 GPD2 10687 -0.022 0.27 NO
324 TGS1 TGS1 TGS1 10690 -0.022 0.27 NO
325 MTMR6 MTMR6 MTMR6 10779 -0.023 0.26 NO
326 PIK3R1 PIK3R1 PIK3R1 10823 -0.024 0.26 NO
327 MTMR3 MTMR3 MTMR3 10832 -0.024 0.26 NO
328 MED16 MED16 MED16 11035 -0.027 0.25 NO
329 PLD3 PLD3 PLD3 11075 -0.028 0.25 NO
330 PLA2G12A PLA2G12A PLA2G12A 11110 -0.028 0.24 NO
331 SMPD1 SMPD1 SMPD1 11260 -0.03 0.24 NO
332 MED17 MED17 MED17 11306 -0.031 0.23 NO
333 MTMR1 MTMR1 MTMR1 11334 -0.031 0.23 NO
334 INPP5E INPP5E INPP5E 11340 -0.031 0.23 NO
335 NRF1 NRF1 NRF1 11362 -0.031 0.23 NO
336 PRKAB2 PRKAB2 PRKAB2 11537 -0.034 0.22 NO
337 MED22 MED22 MED22 11542 -0.034 0.22 NO
338 CHAT CHAT CHAT 11544 -0.034 0.22 NO
339 GBA GBA GBA 11606 -0.035 0.22 NO
340 PTEN PTEN PTEN 11616 -0.035 0.22 NO
341 PIK3C3 PIK3C3 PIK3C3 11712 -0.037 0.22 NO
342 OCRL OCRL OCRL 11765 -0.037 0.21 NO
343 PIK3R2 PIK3R2 PIK3R2 11782 -0.038 0.21 NO
344 CAV1 CAV1 CAV1 11853 -0.039 0.21 NO
345 LRP2 LRP2 LRP2 11905 -0.04 0.21 NO
346 CDK19 CDK19 CDK19 11935 -0.04 0.2 NO
347 PGS1 PGS1 PGS1 11940 -0.04 0.21 NO
348 PI4KB PI4KB PI4KB 12083 -0.042 0.2 NO
349 LBR LBR LBR 12110 -0.043 0.2 NO
350 PLA2G6 PLA2G6 PLA2G6 12234 -0.045 0.19 NO
351 NCOR2 NCOR2 NCOR2 12253 -0.045 0.19 NO
352 PIP4K2B PIP4K2B PIP4K2B 12273 -0.046 0.19 NO
353 MED1 MED1 MED1 12401 -0.048 0.18 NO
354 MED10 MED10 MED10 12431 -0.048 0.18 NO
355 MED27 MED27 MED27 12475 -0.049 0.18 NO
356 ELOVL7 ELOVL7 ELOVL7 12498 -0.049 0.18 NO
357 ARF3 ARF3 ARF3 12521 -0.05 0.18 NO
358 MTMR4 MTMR4 MTMR4 12530 -0.05 0.18 NO
359 MED14 MED14 MED14 12556 -0.05 0.18 NO
360 KDSR KDSR KDSR 12799 -0.054 0.16 NO
361 PLD2 PLD2 PLD2 12811 -0.054 0.16 NO
362 GBA2 GBA2 GBA2 12888 -0.056 0.16 NO
363 MED20 MED20 MED20 12947 -0.057 0.16 NO
364 CYP2R1 CYP2R1 CYP2R1 12971 -0.057 0.16 NO
365 STARD4 STARD4 STARD4 13007 -0.058 0.16 NO
366 DEGS1 DEGS1 DEGS1 13043 -0.058 0.16 NO
367 LPIN1 LPIN1 LPIN1 13048 -0.058 0.16 NO
368 PITPNB PITPNB PITPNB 13058 -0.058 0.16 NO
369 NCOR1 NCOR1 NCOR1 13071 -0.059 0.16 NO
370 MED13L MED13L MED13L 13094 -0.059 0.16 NO
371 MTMR2 MTMR2 MTMR2 13105 -0.059 0.16 NO
372 LPIN2 LPIN2 LPIN2 13115 -0.059 0.16 NO
373 NCOA1 NCOA1 NCOA1 13125 -0.06 0.16 NO
374 PIK3R3 PIK3R3 PIK3R3 13256 -0.062 0.15 NO
375 DEGS2 DEGS2 DEGS2 13259 -0.062 0.15 NO
376 SMPD4 SMPD4 SMPD4 13366 -0.064 0.14 NO
377 AGPAT1 AGPAT1 AGPAT1 13372 -0.064 0.14 NO
378 MED6 MED6 MED6 13476 -0.066 0.14 NO
379 ACER2 ACER2 ACER2 13645 -0.07 0.13 NO
380 EP300 EP300 EP300 13657 -0.07 0.13 NO
381 NR1D1 NR1D1 NR1D1 13668 -0.071 0.13 NO
382 SIN3A SIN3A SIN3A 13696 -0.071 0.13 NO
383 PIP5K1C PIP5K1C PIP5K1C 13722 -0.072 0.13 NO
384 PRKACB PRKACB PRKACB 13913 -0.076 0.12 NO
385 CDK8 CDK8 CDK8 13959 -0.077 0.12 NO
386 EPT1 EPT1 EPT1 13981 -0.078 0.12 NO
387 CYP46A1 CYP46A1 CYP46A1 14018 -0.079 0.12 NO
388 CREBBP CREBBP CREBBP 14064 -0.08 0.12 NO
389 SGPL1 SGPL1 SGPL1 14072 -0.08 0.12 NO
390 TBL1X TBL1X TBL1X 14243 -0.084 0.11 NO
391 NFYA NFYA NFYA 14336 -0.086 0.1 NO
392 ACER3 ACER3 ACER3 14347 -0.086 0.1 NO
393 TRIB3 TRIB3 TRIB3 14367 -0.087 0.1 NO
394 CDS2 CDS2 CDS2 14451 -0.089 0.1 NO
395 STS STS STS 14462 -0.09 0.1 NO
396 PIKFYVE PIKFYVE PIKFYVE 14477 -0.09 0.1 NO
397 PI4KA PI4KA PI4KA 14512 -0.091 0.1 NO
398 NCOA6 NCOA6 NCOA6 14712 -0.096 0.09 NO
399 TEAD1 TEAD1 TEAD1 14713 -0.096 0.092 NO
400 TNFRSF21 TNFRSF21 TNFRSF21 14863 -0.1 0.084 NO
401 NEU4 NEU4 NEU4 14954 -0.1 0.08 NO
402 AGPAT4 AGPAT4 AGPAT4 14967 -0.1 0.081 NO
403 MTMR7 MTMR7 MTMR7 15029 -0.1 0.079 NO
404 LCLAT1 LCLAT1 LCLAT1 15045 -0.11 0.079 NO
405 PPM1L PPM1L PPM1L 15055 -0.11 0.08 NO
406 ARSF ARSF ARSF 15199 -0.11 0.073 NO
407 PRIC285 PRIC285 PRIC285 15232 -0.11 0.073 NO
408 ABCG8 ABCG8 ABCG8 15593 -0.13 0.054 NO
409 ACHE ACHE ACHE 15637 -0.13 0.053 NO
410 PIK3C2B PIK3C2B PIK3C2B 15669 -0.13 0.053 NO
411 CLOCK CLOCK CLOCK 16007 -0.14 0.035 NO
412 SRD5A1 SRD5A1 SRD5A1 16023 -0.14 0.036 NO
413 BAAT BAAT BAAT 16029 -0.15 0.038 NO
414 SYNJ1 SYNJ1 SYNJ1 16087 -0.15 0.036 NO
415 ACSL6 ACSL6 ACSL6 16119 -0.15 0.036 NO
416 NEU3 NEU3 NEU3 16136 -0.15 0.037 NO
417 NCOA2 NCOA2 NCOA2 16185 -0.15 0.036 NO
418 GRHL1 GRHL1 GRHL1 16307 -0.16 0.031 NO
419 CYP1A1 CYP1A1 CYP1A1 16482 -0.17 0.023 NO
420 STARD6 STARD6 STARD6 16598 -0.18 0.019 NO
421 LPCAT4 LPCAT4 LPCAT4 16670 -0.18 0.017 NO
422 CYP4A11 CYP4A11 CYP4A11 16704 -0.18 0.018 NO
423 BCMO1 BCMO1 BCMO1 16715 -0.18 0.019 NO
424 ASAH2 ASAH2 ASAH2 16801 -0.19 0.017 NO
425 CUBN CUBN CUBN 16812 -0.19 0.018 NO
426 SGPP2 SGPP2 SGPP2 16956 -0.2 0.013 NO
427 APOA2 APOA2 APOA2 16985 -0.21 0.014 NO
428 GAL3ST1 GAL3ST1 GAL3ST1 17007 -0.21 0.015 NO
429 FAR2 FAR2 FAR2 17011 -0.21 0.017 NO
430 MBOAT2 MBOAT2 MBOAT2 17262 -0.24 0.0059 NO
431 SMPD3 SMPD3 SMPD3 17298 -0.24 0.0068 NO
432 INPP5J INPP5J INPP5J 17441 -0.26 0.0019 NO
433 ARSE ARSE ARSE 17606 -0.29 -0.004 NO
434 ELOVL4 ELOVL4 ELOVL4 17612 -0.29 -0.00081 NO
435 ELOVL2 ELOVL2 ELOVL2 17667 -0.3 -0.00025 NO
436 PLA2G10 PLA2G10 PLA2G10 17792 -0.34 -0.0033 NO
437 PPARGC1B PPARGC1B PPARGC1B 17822 -0.34 -0.00074 NO
438 PLA2G4F PLA2G4F PLA2G4F 17873 -0.37 0.0009 NO
439 APOA5 APOA5 APOA5 17923 -0.41 0.003 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 CITRATE CYCLE TCA CYCLE

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 AOX1 AOX1 AOX1 55 1.4 0.17 YES
2 ACADS ACADS ACADS 1101 0.41 0.16 YES
3 ALDH3A2 ALDH3A2 ALDH3A2 1115 0.41 0.22 YES
4 ACAT2 ACAT2 ACAT2 1167 0.4 0.26 YES
5 HIBCH HIBCH HIBCH 1414 0.35 0.3 YES
6 HMGCS1 HMGCS1 HMGCS1 1806 0.3 0.31 YES
7 MCCC1 MCCC1 MCCC1 2038 0.27 0.33 YES
8 PCCA PCCA PCCA 2146 0.25 0.36 YES
9 ALDH2 ALDH2 ALDH2 2210 0.25 0.39 YES
10 ALDH1B1 ALDH1B1 ALDH1B1 2356 0.23 0.41 YES
11 BCAT2 BCAT2 BCAT2 2525 0.21 0.43 YES
12 OXCT2 OXCT2 OXCT2 2537 0.21 0.45 YES
13 ACAA1 ACAA1 ACAA1 2594 0.21 0.48 YES
14 IL4I1 IL4I1 IL4I1 2670 0.2 0.5 YES
15 HIBADH HIBADH HIBADH 2690 0.2 0.52 YES
16 PCCB PCCB PCCB 2717 0.2 0.55 YES
17 ACADM ACADM ACADM 2745 0.19 0.57 YES
18 DBT DBT DBT 2786 0.19 0.59 YES
19 ALDH6A1 ALDH6A1 ALDH6A1 2809 0.19 0.62 YES
20 HMGCL HMGCL HMGCL 3078 0.17 0.62 YES
21 ACAT1 ACAT1 ACAT1 3139 0.16 0.64 YES
22 HADHB HADHB HADHB 3169 0.16 0.66 YES
23 MCEE MCEE MCEE 3245 0.16 0.68 YES
24 MCCC2 MCCC2 MCCC2 3553 0.14 0.68 YES
25 AUH AUH AUH 3736 0.13 0.68 YES
26 ALDH7A1 ALDH7A1 ALDH7A1 3982 0.12 0.68 YES
27 DLD DLD DLD 4839 0.086 0.65 NO
28 ECHS1 ECHS1 ECHS1 5231 0.076 0.63 NO
29 ALDH9A1 ALDH9A1 ALDH9A1 5310 0.074 0.64 NO
30 HSD17B10 HSD17B10 HSD17B10 5374 0.072 0.64 NO
31 BCKDHA BCKDHA BCKDHA 5513 0.068 0.65 NO
32 ACAA2 ACAA2 ACAA2 5674 0.063 0.64 NO
33 ACAD8 ACAD8 ACAD8 6183 0.052 0.62 NO
34 IVD IVD IVD 6625 0.043 0.6 NO
35 EHHADH EHHADH EHHADH 6798 0.04 0.6 NO
36 HADHA HADHA HADHA 7303 0.03 0.57 NO
37 BCAT1 BCAT1 BCAT1 7530 0.026 0.57 NO
38 HADH HADH HADH 7660 0.024 0.56 NO
39 BCKDHB BCKDHB BCKDHB 9066 0.0021 0.48 NO
40 ACADSB ACADSB ACADSB 9178 0.00045 0.48 NO
41 OXCT1 OXCT1 OXCT1 9407 -0.0029 0.47 NO
42 MUT MUT MUT 9629 -0.006 0.45 NO
43 ABAT ABAT ABAT 14428 -0.088 0.2 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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

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 GSTA1 GSTA1 GSTA1 7 2 0.13 YES
2 MGST1 MGST1 MGST1 11 1.9 0.25 YES
3 SULT2A1 SULT2A1 SULT2A1 15 1.9 0.38 YES
4 SULT1E1 SULT1E1 SULT1E1 18 1.8 0.49 YES
5 PAPSS2 PAPSS2 PAPSS2 284 0.77 0.53 YES
6 OPLAH OPLAH OPLAH 328 0.73 0.57 YES
7 GSTM5 GSTM5 GSTM5 401 0.66 0.61 YES
8 ACSM1 ACSM1 ACSM1 512 0.58 0.64 YES
9 GGT5 GGT5 GGT5 1022 0.43 0.64 YES
10 SULT1A2 SULT1A2 SULT1A2 1027 0.42 0.67 YES
11 NNMT NNMT NNMT 1130 0.4 0.69 YES
12 MAT1A MAT1A MAT1A 1517 0.34 0.69 YES
13 GSTA4 GSTA4 GSTA4 1749 0.3 0.7 YES
14 SULT1A1 SULT1A1 SULT1A1 1898 0.28 0.71 YES
15 SLC35D1 SLC35D1 SLC35D1 2068 0.26 0.71 YES
16 GSTM1 GSTM1 GSTM1 2450 0.22 0.71 YES
17 GCLM GCLM GCLM 3052 0.17 0.68 YES
18 SULT2B1 SULT2B1 SULT2B1 3067 0.17 0.69 YES
19 UGDH UGDH UGDH 3129 0.16 0.7 YES
20 COMT COMT COMT 3142 0.16 0.71 YES
21 NAT2 NAT2 NAT2 3146 0.16 0.72 YES
22 UGP2 UGP2 UGP2 4495 0.096 0.65 NO
23 GSS GSS GSS 4771 0.088 0.64 NO
24 MGST2 MGST2 MGST2 4884 0.084 0.64 NO
25 SULT1C2 SULT1C2 SULT1C2 5012 0.081 0.64 NO
26 GGT1 GGT1 GGT1 5044 0.08 0.64 NO
27 NAT1 NAT1 NAT1 5063 0.08 0.65 NO
28 TPMT TPMT TPMT 5128 0.078 0.65 NO
29 GSTO1 GSTO1 GSTO1 5235 0.076 0.65 NO
30 GSTP1 GSTP1 GSTP1 5335 0.073 0.65 NO
31 MGST3 MGST3 MGST3 5533 0.067 0.64 NO
32 GSTM4 GSTM4 GSTM4 6236 0.051 0.6 NO
33 MAT2B MAT2B MAT2B 6285 0.05 0.61 NO
34 AHCY AHCY AHCY 7908 0.02 0.52 NO
35 SULT1A3 SULT1A3 SULT1A3 8774 0.0064 0.47 NO
36 SULT1B1 SULT1B1 SULT1B1 9838 -0.0091 0.41 NO
37 GCLC GCLC GCLC 9957 -0.011 0.4 NO
38 GGCT GGCT GGCT 10474 -0.018 0.38 NO
39 BPNT1 BPNT1 BPNT1 10590 -0.02 0.37 NO
40 SULT1C4 SULT1C4 SULT1C4 11137 -0.028 0.34 NO
41 MAT2A MAT2A MAT2A 11183 -0.029 0.34 NO
42 CNDP2 CNDP2 CNDP2 11350 -0.031 0.34 NO
43 MTR MTR MTR 13263 -0.062 0.23 NO
44 GGT7 GGT7 GGT7 14142 -0.082 0.19 NO
45 GSTO2 GSTO2 GSTO2 14369 -0.087 0.18 NO
46 PAPSS1 PAPSS1 PAPSS1 14678 -0.095 0.17 NO
47 SULT4A1 SULT4A1 SULT4A1 16936 -0.2 0.058 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 PENTOSE PHOSPHATE PATHWAY.

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE PHOSPHATE 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 FRUCTOSE AND MANNOSE 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 GSTA1 GSTA1 GSTA1 7 2 0.044 YES
2 MGST1 MGST1 MGST1 11 1.9 0.087 YES
3 CYP17A1 CYP17A1 CYP17A1 13 1.9 0.13 YES
4 CYP21A2 CYP21A2 CYP21A2 14 1.9 0.17 YES
5 SULT2A1 SULT2A1 SULT2A1 15 1.9 0.21 YES
6 CYP11B1 CYP11B1 CYP11B1 17 1.8 0.25 YES
7 SULT1E1 SULT1E1 SULT1E1 18 1.8 0.29 YES
8 CYP2W1 CYP2W1 CYP2W1 21 1.8 0.33 YES
9 CYP11A1 CYP11A1 CYP11A1 28 1.6 0.37 YES
10 CYP11B2 CYP11B2 CYP11B2 35 1.5 0.4 YES
11 ADH1A ADH1A ADH1A 61 1.3 0.43 YES
12 CYP19A1 CYP19A1 CYP19A1 85 1.2 0.46 YES
13 FMO1 FMO1 FMO1 88 1.2 0.48 YES
14 ADH1B ADH1B ADH1B 116 1.1 0.5 YES
15 FMO2 FMO2 FMO2 164 0.96 0.52 YES
16 CYP4B1 CYP4B1 CYP4B1 270 0.78 0.54 YES
17 PAPSS2 PAPSS2 PAPSS2 284 0.77 0.55 YES
18 OPLAH OPLAH OPLAH 328 0.73 0.57 YES
19 CYP3A5 CYP3A5 CYP3A5 345 0.71 0.58 YES
20 CYP3A4 CYP3A4 CYP3A4 373 0.69 0.6 YES
21 PTGIS PTGIS PTGIS 375 0.69 0.61 YES
22 GSTM5 GSTM5 GSTM5 401 0.66 0.62 YES
23 ADH1C ADH1C ADH1C 476 0.61 0.63 YES
24 ACSM1 ACSM1 ACSM1 512 0.58 0.64 YES
25 ALDH1A1 ALDH1A1 ALDH1A1 567 0.56 0.65 YES
26 FMO3 FMO3 FMO3 573 0.56 0.67 YES
27 POMC POMC POMC 578 0.56 0.68 YES
28 CYP4F11 CYP4F11 CYP4F11 603 0.55 0.69 YES
29 CYP4F12 CYP4F12 CYP4F12 629 0.54 0.7 YES
30 CYP7B1 CYP7B1 CYP7B1 738 0.5 0.7 YES
31 CYP3A7 CYP3A7 CYP3A7 819 0.47 0.71 YES
32 CYP39A1 CYP39A1 CYP39A1 890 0.45 0.72 YES
33 MAOB MAOB MAOB 964 0.44 0.72 YES
34 CYP1B1 CYP1B1 CYP1B1 1004 0.43 0.73 YES
35 GGT5 GGT5 GGT5 1022 0.43 0.74 YES
36 SULT1A2 SULT1A2 SULT1A2 1027 0.42 0.75 YES
37 NNMT NNMT NNMT 1130 0.4 0.75 YES
38 TBXAS1 TBXAS1 TBXAS1 1186 0.39 0.76 YES
39 CYP2S1 CYP2S1 CYP2S1 1346 0.36 0.76 YES
40 PTGS2 PTGS2 PTGS2 1498 0.34 0.76 YES
41 MAT1A MAT1A MAT1A 1517 0.34 0.76 YES
42 ACSS2 ACSS2 ACSS2 1632 0.32 0.76 YES
43 ACSS1 ACSS1 ACSS1 1691 0.31 0.77 YES
44 GSTA4 GSTA4 GSTA4 1749 0.3 0.77 YES
45 SULT1A1 SULT1A1 SULT1A1 1898 0.28 0.77 NO
46 SLC35D1 SLC35D1 SLC35D1 2068 0.26 0.76 NO
47 ALDH2 ALDH2 ALDH2 2210 0.25 0.76 NO
48 CYP27B1 CYP27B1 CYP27B1 2258 0.24 0.76 NO
49 CYP8B1 CYP8B1 CYP8B1 2329 0.23 0.77 NO
50 GSTM1 GSTM1 GSTM1 2450 0.22 0.76 NO
51 MAOA MAOA MAOA 2754 0.19 0.75 NO
52 CYP51A1 CYP51A1 CYP51A1 2901 0.18 0.75 NO
53 CYP27A1 CYP27A1 CYP27A1 2936 0.18 0.75 NO
54 GCLM GCLM GCLM 3052 0.17 0.75 NO
55 SULT2B1 SULT2B1 SULT2B1 3067 0.17 0.75 NO
56 UGDH UGDH UGDH 3129 0.16 0.75 NO
57 COMT COMT COMT 3142 0.16 0.75 NO
58 NAT2 NAT2 NAT2 3146 0.16 0.76 NO
59 CYP2A6 CYP2A6 CYP2A6 3350 0.15 0.75 NO
60 CYP2C8 CYP2C8 CYP2C8 3598 0.14 0.74 NO
61 UGP2 UGP2 UGP2 4495 0.096 0.69 NO
62 GSS GSS GSS 4771 0.088 0.68 NO
63 MGST2 MGST2 MGST2 4884 0.084 0.67 NO
64 CYP7A1 CYP7A1 CYP7A1 4959 0.082 0.67 NO
65 SULT1C2 SULT1C2 SULT1C2 5012 0.081 0.67 NO
66 GGT1 GGT1 GGT1 5044 0.08 0.67 NO
67 NAT1 NAT1 NAT1 5063 0.08 0.67 NO
68 TPMT TPMT TPMT 5128 0.078 0.67 NO
69 GSTO1 GSTO1 GSTO1 5235 0.076 0.66 NO
70 GSTP1 GSTP1 GSTP1 5335 0.073 0.66 NO
71 CYP2E1 CYP2E1 CYP2E1 5466 0.069 0.65 NO
72 MGST3 MGST3 MGST3 5533 0.067 0.65 NO
73 CYP26A1 CYP26A1 CYP26A1 5709 0.062 0.64 NO
74 CYP26C1 CYP26C1 CYP26C1 5784 0.06 0.64 NO
75 GSTM4 GSTM4 GSTM4 6236 0.051 0.62 NO
76 MAT2B MAT2B MAT2B 6285 0.05 0.61 NO
77 PAOX PAOX PAOX 7032 0.036 0.57 NO
78 CYP3A43 CYP3A43 CYP3A43 7409 0.029 0.55 NO
79 AHCY AHCY AHCY 7908 0.02 0.53 NO
80 PTGS1 PTGS1 PTGS1 7928 0.019 0.52 NO
81 SMOX SMOX SMOX 8099 0.017 0.52 NO
82 SULT1A3 SULT1A3 SULT1A3 8774 0.0064 0.48 NO
83 SULT1B1 SULT1B1 SULT1B1 9838 -0.0091 0.42 NO
84 GCLC GCLC GCLC 9957 -0.011 0.41 NO
85 GGCT GGCT GGCT 10474 -0.018 0.38 NO
86 BPNT1 BPNT1 BPNT1 10590 -0.02 0.38 NO
87 CYP4F3 CYP4F3 CYP4F3 10892 -0.025 0.36 NO
88 SULT1C4 SULT1C4 SULT1C4 11137 -0.028 0.35 NO
89 MAT2A MAT2A MAT2A 11183 -0.029 0.35 NO
90 CNDP2 CNDP2 CNDP2 11350 -0.031 0.34 NO
91 CYP2C18 CYP2C18 CYP2C18 11459 -0.033 0.33 NO
92 CYP26B1 CYP26B1 CYP26B1 11468 -0.033 0.33 NO
93 CYP2R1 CYP2R1 CYP2R1 12971 -0.057 0.25 NO
94 MTR MTR MTR 13263 -0.062 0.24 NO
95 CYP46A1 CYP46A1 CYP46A1 14018 -0.079 0.2 NO
96 GGT7 GGT7 GGT7 14142 -0.082 0.19 NO
97 GSTO2 GSTO2 GSTO2 14369 -0.087 0.18 NO
98 CYP2U1 CYP2U1 CYP2U1 14385 -0.087 0.18 NO
99 PAPSS1 PAPSS1 PAPSS1 14678 -0.095 0.17 NO
100 CYP2J2 CYP2J2 CYP2J2 15261 -0.11 0.14 NO
101 CYP2D6 CYP2D6 CYP2D6 15515 -0.12 0.12 NO
102 CYP1A1 CYP1A1 CYP1A1 16482 -0.17 0.075 NO
103 CYP4A11 CYP4A11 CYP4A11 16704 -0.18 0.067 NO
104 SULT4A1 SULT4A1 SULT4A1 16936 -0.2 0.058 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 FRUCTOSE AND MANNOSE METABOLISM.

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table 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 HPD HPD HPD 87 1.2 0.04 YES
2 CKMT2 CKMT2 CKMT2 101 1.1 0.081 YES
3 TST TST TST 151 0.98 0.11 YES
4 CTH CTH CTH 179 0.92 0.15 YES
5 AGMAT AGMAT AGMAT 180 0.92 0.18 YES
6 KYNU KYNU KYNU 413 0.66 0.19 YES
7 ASS1 ASS1 ASS1 414 0.65 0.22 YES
8 AMDHD1 AMDHD1 AMDHD1 468 0.62 0.24 YES
9 INHA INHA INHA 482 0.61 0.26 YES
10 POMC POMC POMC 578 0.56 0.27 YES
11 KMO KMO KMO 714 0.5 0.28 YES
12 FAH FAH FAH 757 0.49 0.3 YES
13 DIO3 DIO3 DIO3 801 0.47 0.31 YES
14 DIO2 DIO2 DIO2 1102 0.41 0.31 YES
15 LHB LHB LHB 1260 0.38 0.32 YES
16 HIBCH HIBCH HIBCH 1414 0.35 0.32 YES
17 SQRDL SQRDL SQRDL 1494 0.34 0.33 YES
18 HGD HGD HGD 1504 0.34 0.34 YES
19 MAT1A MAT1A MAT1A 1517 0.34 0.35 YES
20 GPT GPT GPT 1520 0.34 0.37 YES
21 HAAO HAAO HAAO 1576 0.33 0.38 YES
22 SHMT1 SHMT1 SHMT1 1663 0.32 0.38 YES
23 CGA CGA CGA 1807 0.3 0.38 YES
24 SAT1 SAT1 SAT1 1912 0.28 0.39 YES
25 IDO2 IDO2 IDO2 2021 0.27 0.39 YES
26 MCCC1 MCCC1 MCCC1 2038 0.27 0.4 YES
27 ALDH4A1 ALDH4A1 ALDH4A1 2181 0.25 0.4 YES
28 CDO1 CDO1 CDO1 2324 0.23 0.4 YES
29 NQO1 NQO1 NQO1 2444 0.22 0.41 YES
30 PNMT PNMT PNMT 2468 0.22 0.41 YES
31 BCAT2 BCAT2 BCAT2 2525 0.21 0.42 YES
32 INHBA INHBA INHBA 2543 0.21 0.42 YES
33 ARG1 ARG1 ARG1 2599 0.21 0.43 YES
34 GSTZ1 GSTZ1 GSTZ1 2617 0.2 0.44 YES
35 HIBADH HIBADH HIBADH 2690 0.2 0.44 YES
36 TAT TAT TAT 2695 0.2 0.44 YES
37 GATM GATM GATM 2739 0.19 0.45 YES
38 DBT DBT DBT 2786 0.19 0.45 YES
39 ALDH6A1 ALDH6A1 ALDH6A1 2809 0.19 0.46 YES
40 AASS AASS AASS 2820 0.19 0.47 YES
41 GCLM GCLM GCLM 3052 0.17 0.46 YES
42 GRHPR GRHPR GRHPR 3070 0.17 0.46 YES
43 SMS SMS SMS 3132 0.16 0.47 YES
44 ACAT1 ACAT1 ACAT1 3139 0.16 0.47 YES
45 SLC6A8 SLC6A8 SLC6A8 3421 0.14 0.46 YES
46 PSMB9 PSMB9 PSMB9 3462 0.14 0.47 YES
47 GCDH GCDH GCDH 3504 0.14 0.47 YES
48 ADI1 ADI1 ADI1 3516 0.14 0.47 YES
49 PSME2 PSME2 PSME2 3541 0.14 0.48 YES
50 MCCC2 MCCC2 MCCC2 3553 0.14 0.48 YES
51 GLUL GLUL GLUL 3578 0.14 0.48 YES
52 MTAP MTAP MTAP 3624 0.13 0.49 YES
53 PSMB10 PSMB10 PSMB10 3681 0.13 0.49 YES
54 CKM CKM CKM 3692 0.13 0.49 YES
55 AUH AUH AUH 3736 0.13 0.5 YES
56 APIP APIP APIP 3879 0.12 0.49 YES
57 PSMA5 PSMA5 PSMA5 3931 0.12 0.49 YES
58 ALDH7A1 ALDH7A1 ALDH7A1 3982 0.12 0.5 YES
59 TDO2 TDO2 TDO2 4062 0.11 0.5 YES
60 CCBL2 CCBL2 CCBL2 4124 0.11 0.5 YES
61 OAZ3 OAZ3 OAZ3 4129 0.11 0.5 YES
62 SUOX SUOX SUOX 4140 0.11 0.5 YES
63 CKB CKB CKB 4313 0.1 0.5 NO
64 SLC25A10 SLC25A10 SLC25A10 4383 0.1 0.5 NO
65 PSME1 PSME1 PSME1 4494 0.097 0.49 NO
66 PSMD6 PSMD6 PSMD6 4516 0.096 0.5 NO
67 PSMB3 PSMB3 PSMB3 4646 0.092 0.49 NO
68 PSAT1 PSAT1 PSAT1 4724 0.089 0.49 NO
69 GLUD1 GLUD1 GLUD1 4744 0.089 0.49 NO
70 SLC25A21 SLC25A21 SLC25A21 4772 0.088 0.5 NO
71 DLD DLD DLD 4839 0.086 0.5 NO
72 ETHE1 ETHE1 ETHE1 4898 0.084 0.49 NO
73 PSMB7 PSMB7 PSMB7 5105 0.078 0.49 NO
74 SRM SRM SRM 5238 0.075 0.48 NO
75 ALDH9A1 ALDH9A1 ALDH9A1 5310 0.074 0.48 NO
76 HSD17B10 HSD17B10 HSD17B10 5374 0.072 0.48 NO
77 BHMT BHMT BHMT 5399 0.071 0.48 NO
78 PSMB6 PSMB6 PSMB6 5400 0.071 0.48 NO
79 PSMB8 PSMB8 PSMB8 5452 0.069 0.48 NO
80 GPT2 GPT2 GPT2 5461 0.069 0.48 NO
81 BCKDHA BCKDHA BCKDHA 5513 0.068 0.48 NO
82 DIO1 DIO1 DIO1 5664 0.064 0.48 NO
83 GOT1 GOT1 GOT1 5706 0.062 0.48 NO
84 PSMD12 PSMD12 PSMD12 5733 0.062 0.48 NO
85 PSMD13 PSMD13 PSMD13 5753 0.061 0.48 NO
86 GLS GLS GLS 5822 0.06 0.48 NO
87 PSMA3 PSMA3 PSMA3 5907 0.057 0.48 NO
88 PSMD2 PSMD2 PSMD2 6065 0.054 0.47 NO
89 PSMB4 PSMB4 PSMB4 6072 0.054 0.47 NO
90 DLST DLST DLST 6096 0.053 0.47 NO
91 PSMC3 PSMC3 PSMC3 6112 0.053 0.47 NO
92 ACAD8 ACAD8 ACAD8 6183 0.052 0.47 NO
93 MAT2B MAT2B MAT2B 6285 0.05 0.47 NO
94 SLC25A2 SLC25A2 SLC25A2 6379 0.048 0.46 NO
95 PSMD9 PSMD9 PSMD9 6384 0.048 0.46 NO
96 PSMB1 PSMB1 PSMB1 6395 0.048 0.47 NO
97 ADC ADC ADC 6397 0.048 0.47 NO
98 PSMA6 PSMA6 PSMA6 6452 0.046 0.47 NO
99 IVD IVD IVD 6625 0.043 0.46 NO
100 PSMD4 PSMD4 PSMD4 6810 0.04 0.45 NO
101 PSME4 PSME4 PSME4 6835 0.039 0.45 NO
102 SLC25A15 SLC25A15 SLC25A15 6896 0.038 0.45 NO
103 PSMA4 PSMA4 PSMA4 6927 0.037 0.45 NO
104 PSMC5 PSMC5 PSMC5 6973 0.036 0.45 NO
105 PAOX PAOX PAOX 7032 0.036 0.44 NO
106 PSMA7 PSMA7 PSMA7 7103 0.034 0.44 NO
107 PSMC1 PSMC1 PSMC1 7153 0.033 0.44 NO
108 FTCD FTCD FTCD 7193 0.033 0.44 NO
109 PSMB2 PSMB2 PSMB2 7253 0.031 0.44 NO
110 PSMA2 PSMA2 PSMA2 7291 0.031 0.44 NO
111 HAL HAL HAL 7324 0.03 0.44 NO
112 OAZ1 OAZ1 OAZ1 7336 0.03 0.44 NO
113 PHGDH PHGDH PHGDH 7476 0.027 0.43 NO
114 OAT OAT OAT 7516 0.027 0.43 NO
115 BCAT1 BCAT1 BCAT1 7530 0.026 0.43 NO
116 PSMD7 PSMD7 PSMD7 7590 0.025 0.42 NO
117 PSMC2 PSMC2 PSMC2 7797 0.022 0.42 NO
118 PSPH PSPH PSPH 7856 0.021 0.41 NO
119 TMLHE TMLHE TMLHE 7877 0.02 0.41 NO
120 AHCY AHCY AHCY 7908 0.02 0.41 NO
121 GAMT GAMT GAMT 8045 0.018 0.4 NO
122 MRI1 MRI1 MRI1 8083 0.017 0.4 NO
123 OGDH OGDH OGDH 8093 0.017 0.4 NO
124 SMOX SMOX SMOX 8099 0.017 0.4 NO
125 AMD1 AMD1 AMD1 8318 0.013 0.39 NO
126 PSMC4 PSMC4 PSMC4 8351 0.013 0.39 NO
127 DAO DAO DAO 8578 0.0092 0.38 NO
128 TPH1 TPH1 TPH1 8685 0.0077 0.37 NO
129 PSMD11 PSMD11 PSMD11 8699 0.0076 0.37 NO
130 PSMD8 PSMD8 PSMD8 8760 0.0066 0.37 NO
131 NAGS NAGS NAGS 8773 0.0064 0.37 NO
132 PSMD14 PSMD14 PSMD14 8903 0.0044 0.36 NO
133 BCKDHB BCKDHB BCKDHB 9066 0.0021 0.35 NO
134 PSMD5 PSMD5 PSMD5 9117 0.0014 0.35 NO
135 ACADSB ACADSB ACADSB 9178 0.00045 0.34 NO
136 PSMD3 PSMD3 PSMD3 9181 0.00043 0.34 NO
137 PSMA1 PSMA1 PSMA1 9260 -0.00083 0.34 NO
138 PAH PAH PAH 9295 -0.0013 0.34 NO
139 PSMC6 PSMC6 PSMC6 9364 -0.0023 0.34 NO
140 SLC5A5 SLC5A5 SLC5A5 9426 -0.0032 0.33 NO
141 GOT2 GOT2 GOT2 9455 -0.0037 0.33 NO
142 PSMB5 PSMB5 PSMB5 9681 -0.0067 0.32 NO
143 GCLC GCLC GCLC 9957 -0.011 0.3 NO
144 CSAD CSAD CSAD 10231 -0.015 0.29 NO
145 ALDH18A1 ALDH18A1 ALDH18A1 10313 -0.016 0.28 NO
146 PSMF1 PSMF1 PSMF1 10369 -0.017 0.28 NO
147 DBH DBH DBH 10515 -0.019 0.28 NO
148 ODC1 ODC1 ODC1 10573 -0.02 0.27 NO
149 IDO1 IDO1 IDO1 10645 -0.021 0.27 NO
150 PCBD1 PCBD1 PCBD1 10650 -0.021 0.27 NO
151 MAT2A MAT2A MAT2A 11183 -0.029 0.24 NO
152 CNDP2 CNDP2 CNDP2 11350 -0.031 0.23 NO
153 PSMD1 PSMD1 PSMD1 11629 -0.035 0.22 NO
154 OAZ2 OAZ2 OAZ2 11749 -0.037 0.21 NO
155 PSMD10 PSMD10 PSMD10 11859 -0.039 0.21 NO
156 ARG2 ARG2 ARG2 11994 -0.041 0.2 NO
157 AANAT AANAT AANAT 12494 -0.049 0.18 NO
158 ASL ASL ASL 12597 -0.051 0.17 NO
159 AZIN1 AZIN1 AZIN1 12622 -0.051 0.17 NO
160 CCBL1 CCBL1 CCBL1 12755 -0.054 0.17 NO
161 UROC1 UROC1 UROC1 12955 -0.057 0.16 NO
162 ENOPH1 ENOPH1 ENOPH1 13097 -0.059 0.15 NO
163 MTR MTR MTR 13263 -0.062 0.14 NO
164 ASNS ASNS ASNS 14121 -0.081 0.1 NO
165 QDPR QDPR QDPR 14478 -0.09 0.083 NO
166 INHBB INHBB INHBB 14517 -0.091 0.085 NO
167 TH TH TH 14621 -0.094 0.082 NO
168 INHBE INHBE INHBE 15222 -0.11 0.053 NO
169 PRODH PRODH PRODH 15317 -0.12 0.052 NO
170 AFMID AFMID AFMID 15355 -0.12 0.054 NO
171 HDC HDC HDC 15546 -0.12 0.048 NO
172 OTC OTC OTC 15790 -0.13 0.039 NO
173 TPH2 TPH2 TPH2 15814 -0.14 0.043 NO
174 CBS CBS CBS 15842 -0.14 0.046 NO
175 PCSK1 PCSK1 PCSK1 15922 -0.14 0.047 NO
176 GLS2 GLS2 GLS2 16403 -0.16 0.026 NO
177 CKMT1A CKMT1A CKMT1A 16648 -0.18 0.019 NO
178 CPS1 CPS1 CPS1 16698 -0.18 0.023 NO
179 CKMT1B CKMT1B CKMT1B 16880 -0.2 0.02 NO
180 PYCR1 PYCR1 PYCR1 16898 -0.2 0.027 NO
181 DDC DDC DDC 16945 -0.2 0.032 NO
182 AADAT AADAT AADAT 17164 -0.22 0.028 NO
183 TPO TPO TPO 17208 -0.23 0.034 NO
184 INHBC INHBC INHBC 17448 -0.26 0.03 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 FATTY ACID METABOLISM.

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

Table 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 AKR1B1 AKR1B1 AKR1B1 933 0.44 0.027 YES
2 ALDH3A2 ALDH3A2 ALDH3A2 1115 0.41 0.088 YES
3 ACAT2 ACAT2 ACAT2 1167 0.4 0.16 YES
4 PCK1 PCK1 PCK1 1400 0.35 0.2 YES
5 ACSS2 ACSS2 ACSS2 1632 0.32 0.25 YES
6 ACSS1 ACSS1 ACSS1 1691 0.31 0.3 YES
7 ALDH2 ALDH2 ALDH2 2210 0.25 0.32 YES
8 LDHC LDHC LDHC 2222 0.24 0.36 YES
9 ALDH1B1 ALDH1B1 ALDH1B1 2356 0.23 0.39 YES
10 ACOT12 ACOT12 ACOT12 2357 0.23 0.43 YES
11 ACYP1 ACYP1 ACYP1 2510 0.21 0.46 YES
12 LDHD LDHD LDHD 2792 0.19 0.48 YES
13 GRHPR GRHPR GRHPR 3070 0.17 0.49 YES
14 ACAT1 ACAT1 ACAT1 3139 0.16 0.52 YES
15 ME1 ME1 ME1 3299 0.15 0.53 YES
16 PC PC PC 3640 0.13 0.54 YES
17 ALDH7A1 ALDH7A1 ALDH7A1 3982 0.12 0.54 YES
18 LDHB LDHB LDHB 4088 0.11 0.55 YES
19 ACACB ACACB ACACB 4224 0.11 0.56 YES
20 PDHB PDHB PDHB 4295 0.1 0.58 YES
21 DLD DLD DLD 4839 0.086 0.56 NO
22 ALDH9A1 ALDH9A1 ALDH9A1 5310 0.074 0.55 NO
23 ACYP2 ACYP2 ACYP2 6185 0.052 0.51 NO
24 PDHA1 PDHA1 PDHA1 6186 0.052 0.52 NO
25 MDH2 MDH2 MDH2 6204 0.051 0.53 NO
26 ACACA ACACA ACACA 6305 0.049 0.53 NO
27 HAGH HAGH HAGH 7140 0.034 0.49 NO
28 MDH1 MDH1 MDH1 7561 0.026 0.47 NO
29 LDHA LDHA LDHA 7658 0.024 0.47 NO
30 LDHAL6A LDHAL6A LDHAL6A 8445 0.011 0.43 NO
31 GLO1 GLO1 GLO1 8720 0.0072 0.42 NO
32 ME3 ME3 ME3 8947 0.0038 0.4 NO
33 DLAT DLAT DLAT 10714 -0.022 0.31 NO
34 PKM2 PKM2 PKM2 11420 -0.032 0.28 NO
35 PCK2 PCK2 PCK2 11910 -0.04 0.26 NO
36 ME2 ME2 ME2 12031 -0.042 0.26 NO
37 PKLR PKLR PKLR 14572 -0.093 0.13 NO
38 HAGHL HAGHL HAGHL 15797 -0.13 0.086 NO
39 LDHAL6B LDHAL6B LDHAL6B 16963 -0.2 0.056 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 STEROID HORMONE BIOSYNTHESIS.

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE 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 PDK4 PDK4 PDK4 765 0.49 0.018 YES
2 IDH1 IDH1 IDH1 1247 0.38 0.039 YES
3 ADHFE1 ADHFE1 ADHFE1 2008 0.27 0.031 YES
4 SUCLG2 SUCLG2 SUCLG2 2359 0.23 0.04 YES
5 ETFDH ETFDH ETFDH 2511 0.21 0.058 YES
6 PDK1 PDK1 PDK1 2591 0.21 0.08 YES
7 UCP2 UCP2 UCP2 2965 0.18 0.081 YES
8 NDUFA4 NDUFA4 NDUFA4 3378 0.15 0.076 YES
9 NDUFB4 NDUFB4 NDUFB4 3477 0.14 0.088 YES
10 D2HGDH D2HGDH D2HGDH 3540 0.14 0.1 YES
11 SDHB SDHB SDHB 3573 0.14 0.12 YES
12 ETFA ETFA ETFA 3587 0.14 0.13 YES
13 NDUFS8 NDUFS8 NDUFS8 3654 0.13 0.15 YES
14 PDP1 PDP1 PDP1 4034 0.11 0.14 YES
15 LDHB LDHB LDHB 4088 0.11 0.15 YES
16 FH FH FH 4089 0.11 0.16 YES
17 ATP5C1 ATP5C1 ATP5C1 4283 0.1 0.17 YES
18 CYC1 CYC1 CYC1 4290 0.1 0.18 YES
19 PDHB PDHB PDHB 4295 0.1 0.19 YES
20 NDUFC1 NDUFC1 NDUFC1 4338 0.1 0.2 YES
21 UQCRFS1 UQCRFS1 UQCRFS1 4346 0.1 0.22 YES
22 UQCRQ UQCRQ UQCRQ 4464 0.098 0.22 YES
23 ATP5J2 ATP5J2 ATP5J2 4504 0.096 0.23 YES
24 UQCRC1 UQCRC1 UQCRC1 4563 0.094 0.24 YES
25 NDUFA11 NDUFA11 NDUFA11 4614 0.093 0.25 YES
26 NDUFB5 NDUFB5 NDUFB5 4624 0.092 0.26 YES
27 NDUFA2 NDUFA2 NDUFA2 4664 0.091 0.27 YES
28 SDHA SDHA SDHA 4669 0.091 0.28 YES
29 NDUFS5 NDUFS5 NDUFS5 4759 0.088 0.29 YES
30 NDUFA3 NDUFA3 NDUFA3 4786 0.087 0.3 YES
31 NDUFB1 NDUFB1 NDUFB1 4832 0.086 0.3 YES
32 DLD DLD DLD 4839 0.086 0.31 YES
33 ATP5D ATP5D ATP5D 4851 0.085 0.32 YES
34 ATP5I ATP5I ATP5I 4868 0.084 0.33 YES
35 NDUFV2 NDUFV2 NDUFV2 4912 0.084 0.34 YES
36 ATP5J ATP5J ATP5J 4972 0.082 0.35 YES
37 PDK2 PDK2 PDK2 5408 0.071 0.33 YES
38 COX5B COX5B COX5B 5463 0.069 0.34 YES
39 ETFB ETFB ETFB 5509 0.068 0.34 YES
40 NDUFA6 NDUFA6 NDUFA6 5530 0.067 0.35 YES
41 NDUFS1 NDUFS1 NDUFS1 5649 0.064 0.35 YES
42 ATP5G1 ATP5G1 ATP5G1 5707 0.062 0.36 YES
43 PDHX PDHX PDHX 5715 0.062 0.37 YES
44 NDUFC2 NDUFC2 NDUFC2 5717 0.062 0.37 YES
45 NDUFS3 NDUFS3 NDUFS3 5772 0.061 0.38 YES
46 NDUFA10 NDUFA10 NDUFA10 5898 0.058 0.38 YES
47 NDUFV1 NDUFV1 NDUFV1 5918 0.057 0.38 YES
48 ATP5F1 ATP5F1 ATP5F1 5968 0.056 0.39 YES
49 NDUFB3 NDUFB3 NDUFB3 5997 0.056 0.4 YES
50 DLST DLST DLST 6096 0.053 0.4 YES
51 NDUFS2 NDUFS2 NDUFS2 6106 0.053 0.4 YES
52 SDHC SDHC SDHC 6142 0.052 0.41 YES
53 NDUFA7 NDUFA7 NDUFA7 6150 0.052 0.41 YES
54 PDHA1 PDHA1 PDHA1 6186 0.052 0.42 YES
55 MDH2 MDH2 MDH2 6204 0.051 0.42 YES
56 ATP5H ATP5H ATP5H 6249 0.05 0.43 YES
57 NDUFB2 NDUFB2 NDUFB2 6252 0.05 0.43 YES
58 COX6B1 COX6B1 COX6B1 6284 0.05 0.44 YES
59 NDUFB10 NDUFB10 NDUFB10 6363 0.048 0.44 YES
60 NDUFS4 NDUFS4 NDUFS4 6389 0.048 0.44 YES
61 UQCR11 UQCR11 UQCR11 6464 0.046 0.44 YES
62 COX5A COX5A COX5A 6491 0.046 0.45 YES
63 NDUFB9 NDUFB9 NDUFB9 6565 0.044 0.45 YES
64 NDUFB7 NDUFB7 NDUFB7 6734 0.041 0.45 YES
65 ATP5L ATP5L ATP5L 6754 0.041 0.45 YES
66 ATP5O ATP5O ATP5O 6808 0.04 0.45 YES
67 IDH3G IDH3G IDH3G 7063 0.035 0.44 YES
68 NDUFS6 NDUFS6 NDUFS6 7182 0.033 0.44 YES
69 IDH3B IDH3B IDH3B 7222 0.032 0.44 YES
70 NDUFAB1 NDUFAB1 NDUFAB1 7233 0.032 0.45 YES
71 NDUFA1 NDUFA1 NDUFA1 7269 0.031 0.45 YES
72 BSG BSG BSG 7289 0.031 0.45 YES
73 NDUFA13 NDUFA13 NDUFA13 7311 0.03 0.45 YES
74 NDUFA5 NDUFA5 NDUFA5 7376 0.029 0.45 YES
75 NDUFA8 NDUFA8 NDUFA8 7468 0.027 0.45 YES
76 COX7C COX7C COX7C 7482 0.027 0.45 YES
77 NDUFV3 NDUFV3 NDUFV3 7488 0.027 0.46 YES
78 COX6C COX6C COX6C 7528 0.026 0.46 YES
79 UQCRH UQCRH UQCRH 7529 0.026 0.46 YES
80 COX6A1 COX6A1 COX6A1 7591 0.025 0.46 YES
81 LDHA LDHA LDHA 7658 0.024 0.46 YES
82 IDH3A IDH3A IDH3A 7682 0.023 0.46 YES
83 UQCRHL UQCRHL UQCRHL 7691 0.023 0.46 YES
84 CS CS CS 7719 0.023 0.47 YES
85 NDUFB6 NDUFB6 NDUFB6 7891 0.02 0.46 NO
86 NDUFB8 NDUFB8 NDUFB8 8042 0.018 0.45 NO
87 OGDH OGDH OGDH 8093 0.017 0.45 NO
88 COX7B COX7B COX7B 8097 0.017 0.46 NO
89 NDUFA9 NDUFA9 NDUFA9 8108 0.017 0.46 NO
90 NDUFS7 NDUFS7 NDUFS7 8114 0.017 0.46 NO
91 NDUFA12 NDUFA12 NDUFA12 8204 0.015 0.46 NO
92 ACO2 ACO2 ACO2 8209 0.015 0.46 NO
93 SUCLG1 SUCLG1 SUCLG1 8324 0.013 0.45 NO
94 COX4I1 COX4I1 COX4I1 8401 0.012 0.45 NO
95 UQCRB UQCRB UQCRB 8581 0.0091 0.44 NO
96 ATP5A1 ATP5A1 ATP5A1 8595 0.009 0.44 NO
97 COX7A2L COX7A2L COX7A2L 8599 0.0089 0.44 NO
98 UQCRC2 UQCRC2 UQCRC2 8612 0.0088 0.44 NO
99 ATP5B ATP5B ATP5B 8758 0.0067 0.44 NO
100 SDHD SDHD SDHD 8802 0.006 0.43 NO
101 CYCS CYCS CYCS 8858 0.0054 0.43 NO
102 NNT NNT NNT 8917 0.0042 0.43 NO
103 ATP5E ATP5E ATP5E 9366 -0.0023 0.4 NO
104 SLC16A8 SLC16A8 SLC16A8 9483 -0.004 0.4 NO
105 SUCLA2 SUCLA2 SUCLA2 9493 -0.0041 0.4 NO
106 PDK3 PDK3 PDK3 9521 -0.0045 0.4 NO
107 COX8A COX8A COX8A 10242 -0.015 0.36 NO
108 UCP3 UCP3 UCP3 10270 -0.016 0.36 NO
109 DLAT DLAT DLAT 10714 -0.022 0.34 NO
110 SLC16A1 SLC16A1 SLC16A1 11073 -0.028 0.32 NO
111 IDH2 IDH2 IDH2 11092 -0.028 0.32 NO
112 SLC16A3 SLC16A3 SLC16A3 14060 -0.08 0.17 NO
113 PDPR PDPR PDPR 14910 -0.1 0.13 NO
114 L2HGDH L2HGDH L2HGDH 15983 -0.14 0.089 NO
115 PDP2 PDP2 PDP2 16613 -0.18 0.076 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

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

Table 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 ADH1A ADH1A ADH1A 61 1.3 0.099 YES
2 GALM GALM GALM 97 1.1 0.19 YES
3 ADH1B ADH1B ADH1B 116 1.1 0.27 YES
4 ALDH3B1 ALDH3B1 ALDH3B1 227 0.85 0.33 YES
5 FBP1 FBP1 FBP1 297 0.76 0.39 YES
6 ALDH3B2 ALDH3B2 ALDH3B2 415 0.65 0.43 YES
7 ALDOB ALDOB ALDOB 428 0.65 0.48 YES
8 ADH1C ADH1C ADH1C 476 0.61 0.53 YES
9 ALDH3A2 ALDH3A2 ALDH3A2 1115 0.41 0.52 YES
10 ALDH3A1 ALDH3A1 ALDH3A1 1119 0.41 0.56 YES
11 HK3 HK3 HK3 1335 0.37 0.57 YES
12 PCK1 PCK1 PCK1 1400 0.35 0.6 YES
13 ACSS2 ACSS2 ACSS2 1632 0.32 0.61 YES
14 ACSS1 ACSS1 ACSS1 1691 0.31 0.63 YES
15 ALDH2 ALDH2 ALDH2 2210 0.25 0.62 YES
16 LDHC LDHC LDHC 2222 0.24 0.64 YES
17 ALDH1B1 ALDH1B1 ALDH1B1 2356 0.23 0.65 YES
18 PGM1 PGM1 PGM1 2897 0.18 0.63 NO
19 PGM2 PGM2 PGM2 3122 0.16 0.64 NO
20 ALDH1A3 ALDH1A3 ALDH1A3 3234 0.16 0.64 NO
21 ALDH7A1 ALDH7A1 ALDH7A1 3982 0.12 0.61 NO
22 LDHB LDHB LDHB 4088 0.11 0.61 NO
23 AKR1A1 AKR1A1 AKR1A1 4219 0.11 0.61 NO
24 ENO3 ENO3 ENO3 4263 0.1 0.62 NO
25 PDHB PDHB PDHB 4295 0.1 0.62 NO
26 DLD DLD DLD 4839 0.086 0.6 NO
27 ALDH9A1 ALDH9A1 ALDH9A1 5310 0.074 0.58 NO
28 PDHA1 PDHA1 PDHA1 6186 0.052 0.54 NO
29 ADH5 ADH5 ADH5 6424 0.047 0.53 NO
30 PGAM2 PGAM2 PGAM2 7316 0.03 0.48 NO
31 GCK GCK GCK 7542 0.026 0.47 NO
32 LDHA LDHA LDHA 7658 0.024 0.46 NO
33 LDHAL6A LDHAL6A LDHAL6A 8445 0.011 0.42 NO
34 ENO1 ENO1 ENO1 8686 0.0077 0.41 NO
35 HK2 HK2 HK2 8875 0.005 0.4 NO
36 PGAM1 PGAM1 PGAM1 9165 0.00068 0.38 NO
37 G6PC2 G6PC2 G6PC2 10178 -0.014 0.33 NO
38 PFKM PFKM PFKM 10564 -0.02 0.31 NO
39 BPGM BPGM BPGM 10596 -0.02 0.31 NO
40 GPI GPI GPI 10613 -0.02 0.31 NO
41 DLAT DLAT DLAT 10714 -0.022 0.3 NO
42 PKM2 PKM2 PKM2 11420 -0.032 0.27 NO
43 TPI1 TPI1 TPI1 11746 -0.037 0.25 NO
44 GAPDH GAPDH GAPDH 11829 -0.038 0.25 NO
45 PCK2 PCK2 PCK2 11910 -0.04 0.25 NO
46 ALDOA ALDOA ALDOA 12298 -0.046 0.23 NO
47 PGK1 PGK1 PGK1 12358 -0.047 0.23 NO
48 ALDOC ALDOC ALDOC 12491 -0.049 0.23 NO
49 PGAM4 PGAM4 PGAM4 12849 -0.055 0.21 NO
50 PFKL PFKL PFKL 12917 -0.056 0.21 NO
51 PKLR PKLR PKLR 14572 -0.093 0.13 NO
52 HK1 HK1 HK1 15231 -0.11 0.099 NO
53 ENO2 ENO2 ENO2 16799 -0.19 0.027 NO
54 LDHAL6B LDHAL6B LDHAL6B 16963 -0.2 0.034 NO
55 PFKP PFKP PFKP 17600 -0.29 0.021 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 GLYCINE SERINE AND THREONINE METABOLISM.

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

genes ES table in pathway: KEGG CYSTEINE AND METHIONINE METABOLISM

Table 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 IRS1 IRS1 IRS1 285 0.77 0.21 YES
2 IGF1 IGF1 IGF1 434 0.64 0.39 YES
3 PRKCD PRKCD PRKCD 887 0.45 0.5 YES
4 PRKD1 PRKD1 PRKD1 2054 0.26 0.51 YES
5 PIK3CA PIK3CA PIK3CA 4090 0.11 0.43 NO
6 RAF1 RAF1 RAF1 4917 0.083 0.41 NO
7 IRS2 IRS2 IRS2 5121 0.078 0.42 NO
8 GNB2L1 GNB2L1 GNB2L1 5976 0.056 0.39 NO
9 RPS6KB1 RPS6KB1 RPS6KB1 6250 0.05 0.39 NO
10 PXN PXN PXN 6637 0.043 0.38 NO
11 CRK CRK CRK 6706 0.042 0.39 NO
12 AKT1 AKT1 AKT1 7146 0.033 0.37 NO
13 BAD BAD BAD 7318 0.03 0.37 NO
14 PTPN1 PTPN1 PTPN1 8460 0.011 0.31 NO
15 YWHAE YWHAE YWHAE 8615 0.0088 0.3 NO
16 GRB2 GRB2 GRB2 8956 0.0037 0.29 NO
17 PTK2 PTK2 PTK2 9202 0.0001 0.27 NO
18 PIK3R1 PIK3R1 PIK3R1 10823 -0.024 0.19 NO
19 PTPN11 PTPN11 PTPN11 10845 -0.024 0.2 NO
20 PRKCZ PRKCZ PRKCZ 10847 -0.024 0.2 NO
21 HRAS HRAS HRAS 11443 -0.032 0.18 NO
22 NCK2 NCK2 NCK2 11843 -0.039 0.17 NO
23 YWHAZ YWHAZ YWHAZ 11849 -0.039 0.18 NO
24 IGF1R IGF1R IGF1R 11931 -0.04 0.19 NO
25 SOS1 SOS1 SOS1 13218 -0.061 0.13 NO
26 PDPK1 PDPK1 PDPK1 13361 -0.064 0.14 NO
27 BCAR1 BCAR1 BCAR1 13810 -0.074 0.14 NO
28 CRKL CRKL CRKL 14068 -0.08 0.15 NO
29 SHC1 SHC1 SHC1 14169 -0.082 0.17 NO
30 GRB10 GRB10 GRB10 16149 -0.15 0.1 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 CYSTEINE AND METHIONINE METABOLISM.

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

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

Table 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 SULT2A1 SULT2A1 SULT2A1 15 1.9 0.076 YES
2 ELOVL3 ELOVL3 ELOVL3 288 0.76 0.093 YES
3 G0S2 G0S2 G0S2 295 0.76 0.12 YES
4 ABCB4 ABCB4 ABCB4 337 0.72 0.15 YES
5 ALAS1 ALAS1 ALAS1 353 0.7 0.18 YES
6 FHL2 FHL2 FHL2 451 0.63 0.2 YES
7 ACADL ACADL ACADL 582 0.55 0.22 YES
8 PLIN2 PLIN2 PLIN2 616 0.54 0.24 YES
9 GLIPR1 GLIPR1 GLIPR1 977 0.44 0.23 YES
10 ACADS ACADS ACADS 1101 0.41 0.24 YES
11 ABCA1 ABCA1 ABCA1 1172 0.4 0.26 YES
12 YAP1 YAP1 YAP1 1393 0.36 0.26 YES
13 MED11 MED11 MED11 1558 0.33 0.26 YES
14 ANKRD1 ANKRD1 ANKRD1 1598 0.32 0.27 YES
15 LPIN3 LPIN3 LPIN3 1715 0.31 0.28 YES
16 HMGCS1 HMGCS1 HMGCS1 1806 0.3 0.29 YES
17 NPAS2 NPAS2 NPAS2 1839 0.29 0.3 YES
18 CTGF CTGF CTGF 1896 0.29 0.3 YES
19 HMGCR HMGCR HMGCR 2048 0.26 0.31 YES
20 GPD1 GPD1 GPD1 2085 0.26 0.32 YES
21 PCCA PCCA PCCA 2146 0.25 0.32 YES
22 ELOVL6 ELOVL6 ELOVL6 2260 0.24 0.33 YES
23 FADS1 FADS1 FADS1 2372 0.23 0.33 YES
24 ACADVL ACADVL ACADVL 2445 0.22 0.34 YES
25 GK GK GK 2472 0.22 0.34 YES
26 GPAM GPAM GPAM 2479 0.22 0.35 YES
27 FDFT1 FDFT1 FDFT1 2487 0.22 0.36 YES
28 AGT AGT AGT 2491 0.22 0.37 YES
29 ACSL5 ACSL5 ACSL5 2568 0.21 0.37 YES
30 DECR1 DECR1 DECR1 2624 0.2 0.38 YES
31 SREBF1 SREBF1 SREBF1 2640 0.2 0.38 YES
32 CPT2 CPT2 CPT2 2649 0.2 0.39 YES
33 PCCB PCCB PCCB 2717 0.2 0.4 YES
34 ACADM ACADM ACADM 2745 0.19 0.4 YES
35 TEAD2 TEAD2 TEAD2 2811 0.19 0.41 YES
36 ANGPTL4 ANGPTL4 ANGPTL4 2837 0.19 0.41 YES
37 PEX11A PEX11A PEX11A 2886 0.18 0.42 YES
38 HMGCL HMGCL HMGCL 3078 0.17 0.42 YES
39 RORA RORA RORA 3108 0.16 0.42 YES
40 ACAT1 ACAT1 ACAT1 3139 0.16 0.42 YES
41 ARNTL ARNTL ARNTL 3154 0.16 0.43 YES
42 HADHB HADHB HADHB 3169 0.16 0.44 YES
43 MCEE MCEE MCEE 3245 0.16 0.44 YES
44 SLC25A20 SLC25A20 SLC25A20 3275 0.15 0.44 YES
45 ME1 ME1 ME1 3299 0.15 0.45 YES
46 APOA1 APOA1 APOA1 3337 0.15 0.45 YES
47 GPD1L GPD1L GPD1L 3393 0.15 0.46 YES
48 DGAT1 DGAT1 DGAT1 3414 0.14 0.46 YES
49 DGAT2 DGAT2 DGAT2 3618 0.13 0.45 YES
50 AGPAT2 AGPAT2 AGPAT2 3627 0.13 0.46 YES
51 ELOVL1 ELOVL1 ELOVL1 3629 0.13 0.46 YES
52 SMARCD3 SMARCD3 SMARCD3 3690 0.13 0.47 YES
53 CPT1B CPT1B CPT1B 3788 0.12 0.47 YES
54 CPT1A CPT1A CPT1A 3792 0.12 0.47 YES
55 ELOVL5 ELOVL5 ELOVL5 3925 0.12 0.47 NO
56 ACACB ACACB ACACB 4224 0.11 0.46 NO
57 PPARA PPARA PPARA 4244 0.1 0.46 NO
58 AGPAT3 AGPAT3 AGPAT3 4315 0.1 0.46 NO
59 PPARGC1A PPARGC1A PPARGC1A 4406 0.099 0.46 NO
60 ACSL1 ACSL1 ACSL1 4427 0.099 0.46 NO
61 TECR TECR TECR 4662 0.091 0.45 NO
62 FASN FASN FASN 4905 0.084 0.44 NO
63 CYP7A1 CYP7A1 CYP7A1 4959 0.082 0.44 NO
64 MED8 MED8 MED8 5154 0.077 0.44 NO
65 ECHS1 ECHS1 ECHS1 5231 0.076 0.43 NO
66 MED18 MED18 MED18 5250 0.075 0.44 NO
67 MED30 MED30 MED30 5288 0.074 0.44 NO
68 AGPAT6 AGPAT6 AGPAT6 5304 0.074 0.44 NO
69 SLC25A1 SLC25A1 SLC25A1 5445 0.069 0.43 NO
70 MED31 MED31 MED31 5522 0.067 0.43 NO
71 GPAT2 GPAT2 GPAT2 5553 0.066 0.43 NO
72 PPARG PPARG PPARG 5635 0.064 0.43 NO
73 SLC27A1 SLC27A1 SLC27A1 5643 0.064 0.43 NO
74 ACSL4 ACSL4 ACSL4 5655 0.064 0.44 NO
75 RXRA RXRA RXRA 5735 0.062 0.43 NO
76 TEAD4 TEAD4 TEAD4 5783 0.06 0.43 NO
77 BDH1 BDH1 BDH1 5805 0.06 0.44 NO
78 MED7 MED7 MED7 5978 0.056 0.43 NO
79 MED12 MED12 MED12 6070 0.054 0.42 NO
80 TXNRD1 TXNRD1 TXNRD1 6239 0.051 0.42 NO
81 ACACA ACACA ACACA 6305 0.049 0.42 NO
82 ACOX1 ACOX1 ACOX1 6309 0.049 0.42 NO
83 CCNC CCNC CCNC 6373 0.048 0.42 NO
84 SREBF2 SREBF2 SREBF2 6622 0.043 0.4 NO
85 ESRRA ESRRA ESRRA 6712 0.042 0.4 NO
86 NFYB NFYB NFYB 6751 0.041 0.4 NO
87 MED9 MED9 MED9 6924 0.038 0.39 NO
88 HDAC3 HDAC3 HDAC3 6933 0.037 0.39 NO
89 HSD17B12 HSD17B12 HSD17B12 7056 0.035 0.39 NO
90 MED25 MED25 MED25 7078 0.035 0.39 NO
91 TEAD3 TEAD3 TEAD3 7232 0.032 0.38 NO
92 CD36 CD36 CD36 7273 0.031 0.38 NO
93 HADHA HADHA HADHA 7303 0.03 0.38 NO
94 NCOA3 NCOA3 NCOA3 7304 0.03 0.38 NO
95 HADH HADH HADH 7660 0.024 0.36 NO
96 ACSL3 ACSL3 ACSL3 7820 0.021 0.35 NO
97 WWTR1 WWTR1 WWTR1 7890 0.02 0.35 NO
98 AGPAT5 AGPAT5 AGPAT5 7930 0.019 0.35 NO
99 TBL1XR1 TBL1XR1 TBL1XR1 8146 0.016 0.34 NO
100 AGPAT9 AGPAT9 AGPAT9 8184 0.016 0.34 NO
101 MED15 MED15 MED15 8748 0.0068 0.3 NO
102 PRKAG2 PRKAG2 PRKAG2 8775 0.0064 0.3 NO
103 MED24 MED24 MED24 8813 0.0059 0.3 NO
104 PRKAA2 PRKAA2 PRKAA2 9065 0.0021 0.29 NO
105 MED23 MED23 MED23 9224 -0.00028 0.28 NO
106 ACLY ACLY ACLY 9263 -0.00087 0.28 NO
107 OXCT1 OXCT1 OXCT1 9407 -0.0029 0.27 NO
108 MED4 MED4 MED4 9593 -0.0055 0.26 NO
109 MUT MUT MUT 9629 -0.006 0.26 NO
110 MED21 MED21 MED21 9898 -0.01 0.24 NO
111 MED26 MED26 MED26 10175 -0.014 0.23 NO
112 LPCAT1 LPCAT1 LPCAT1 10192 -0.014 0.23 NO
113 MED19 MED19 MED19 10224 -0.015 0.23 NO
114 TIAM2 TIAM2 TIAM2 10522 -0.019 0.21 NO
115 SIN3B SIN3B SIN3B 10584 -0.02 0.21 NO
116 MED29 MED29 MED29 10646 -0.021 0.2 NO
117 GPD2 GPD2 GPD2 10687 -0.022 0.2 NO
118 TGS1 TGS1 TGS1 10690 -0.022 0.2 NO
119 MED16 MED16 MED16 11035 -0.027 0.19 NO
120 MED17 MED17 MED17 11306 -0.031 0.17 NO
121 NRF1 NRF1 NRF1 11362 -0.031 0.17 NO
122 PRKAB2 PRKAB2 PRKAB2 11537 -0.034 0.16 NO
123 MED22 MED22 MED22 11542 -0.034 0.16 NO
124 CDK19 CDK19 CDK19 11935 -0.04 0.14 NO
125 NCOR2 NCOR2 NCOR2 12253 -0.045 0.13 NO
126 MED1 MED1 MED1 12401 -0.048 0.12 NO
127 MED10 MED10 MED10 12431 -0.048 0.12 NO
128 MED27 MED27 MED27 12475 -0.049 0.12 NO
129 ELOVL7 ELOVL7 ELOVL7 12498 -0.049 0.12 NO
130 MED14 MED14 MED14 12556 -0.05 0.12 NO
131 MED20 MED20 MED20 12947 -0.057 0.1 NO
132 LPIN1 LPIN1 LPIN1 13048 -0.058 0.098 NO
133 NCOR1 NCOR1 NCOR1 13071 -0.059 0.099 NO
134 MED13L MED13L MED13L 13094 -0.059 0.1 NO
135 LPIN2 LPIN2 LPIN2 13115 -0.059 0.1 NO
136 NCOA1 NCOA1 NCOA1 13125 -0.06 0.1 NO
137 AGPAT1 AGPAT1 AGPAT1 13372 -0.064 0.092 NO
138 MED6 MED6 MED6 13476 -0.066 0.09 NO
139 EP300 EP300 EP300 13657 -0.07 0.082 NO
140 NR1D1 NR1D1 NR1D1 13668 -0.071 0.085 NO
141 SIN3A SIN3A SIN3A 13696 -0.071 0.086 NO
142 CDK8 CDK8 CDK8 13959 -0.077 0.074 NO
143 CREBBP CREBBP CREBBP 14064 -0.08 0.072 NO
144 TBL1X TBL1X TBL1X 14243 -0.084 0.065 NO
145 NFYA NFYA NFYA 14336 -0.086 0.064 NO
146 TRIB3 TRIB3 TRIB3 14367 -0.087 0.066 NO
147 NCOA6 NCOA6 NCOA6 14712 -0.096 0.05 NO
148 TEAD1 TEAD1 TEAD1 14713 -0.096 0.054 NO
149 TNFRSF21 TNFRSF21 TNFRSF21 14863 -0.1 0.05 NO
150 AGPAT4 AGPAT4 AGPAT4 14967 -0.1 0.048 NO
151 LCLAT1 LCLAT1 LCLAT1 15045 -0.11 0.048 NO
152 PRIC285 PRIC285 PRIC285 15232 -0.11 0.043 NO
153 CLOCK CLOCK CLOCK 16007 -0.14 0.0052 NO
154 ACSL6 ACSL6 ACSL6 16119 -0.15 0.0052 NO
155 NCOA2 NCOA2 NCOA2 16185 -0.15 0.0078 NO
156 GRHL1 GRHL1 GRHL1 16307 -0.16 0.0076 NO
157 CYP1A1 CYP1A1 CYP1A1 16482 -0.17 0.0048 NO
158 LPCAT4 LPCAT4 LPCAT4 16670 -0.18 0.0018 NO
159 CYP4A11 CYP4A11 CYP4A11 16704 -0.18 0.0075 NO
160 APOA2 APOA2 APOA2 16985 -0.21 0.0003 NO
161 ELOVL4 ELOVL4 ELOVL4 17612 -0.29 -0.023 NO
162 ELOVL2 ELOVL2 ELOVL2 17667 -0.3 -0.014 NO
163 PPARGC1B PPARGC1B PPARGC1B 17822 -0.34 -0.0081 NO
164 APOA5 APOA5 APOA5 17923 -0.41 0.003 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

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 = PCPG-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = PCPG-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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