GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in PCPG-TP
Pheochromocytoma and Paraganglioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C14Q7T3G
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in PCPG-TP. Broad Institute of MIT and Harvard. doi:10.7908/C14Q7T3G
Overview
Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes in PCPG-TP. This pipeline has the following features:

  1. For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.

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

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

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

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

  6. Checks if the top core genes are significantly differently expressed genes.

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 187
Number of samples: 179
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 39
pheno.type: 2 - 4 :[ clus2 ] 69
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 BIOCARTA G1 PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA MYOSIN PATHWAY, BIOCARTA CHREBP2 PATHWAY, KEGG SPHINGOLIPID METABOLISM, KEGG RIBOSOME, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION, KEGG ERBB SIGNALING PATHWAY, KEGG OOCYTE MEIOSIS

    • And common core enriched genes are PRKCA, PRKCB, PRKCG, MYH7, PRKACG, CACNA1C, CERK, DEGS2, GAL3ST1, SGPP2

  • clus2

    • Top enriched gene sets are BIOCARTA AT1R PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA PDGF PATHWAY, BIOCARTA TOLL PATHWAY, KEGG ABC TRANSPORTERS, KEGG PEROXISOME, KEGG ANTIGEN PROCESSING AND PRESENTATION, KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY

    • And common core enriched genes are MAPK8, MAP3K1, PRKCB, SHC1, CALM1, CALM2, PTK2B, STAT1, STAT4, STAT5A

  • clus3

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA VEGF PATHWAY, KEGG PURINE METABOLISM, KEGG PYRIMIDINE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG DRUG METABOLISM OTHER ENZYMES, KEGG RIBOSOME, KEGG CALCIUM SIGNALING PATHWAY, KEGG VASCULAR SMOOTH MUSCLE CONTRACTION

    • And common core enriched genes are VEGFA, FLT1, FLT4, KDR, NOS3, DLL1, DLL4, DTX2, DVL1, HDAC1

  • clus4

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA FMLP PATHWAY, BIOCARTA GH PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA MPR PATHWAY, BIOCARTA IL2RB PATHWAY

    • And common core enriched genes are ACAT1, ACAT2, ALDH1B1, ALDH2, ALDH3A2, ALDH7A1, AOX1, IL4I1, GSTZ1, ACAA1

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA G1 PATHWAY 27 genes.ES.table 0.44 1.3 0.15 0.95 0.94 0.3 0.15 0.25 0.72 0.36
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.26 1.1 0.34 1 1 0.04 0.018 0.039 1 0.54
BIOCARTA MYOSIN PATHWAY 27 genes.ES.table 0.4 1.2 0.22 0.82 0.98 0.22 0.12 0.2 0.67 0.29
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.34 1.3 0.14 0.76 0.95 0.34 0.27 0.25 0.58 0.25
KEGG SPHINGOLIPID METABOLISM 36 genes.ES.table 0.49 1.4 0.09 1 0.88 0.14 0.078 0.13 1 0.8
KEGG RIBOSOME 84 genes.ES.table 0.39 1 0.5 1 1 0.57 0.41 0.34 0.95 0.45
KEGG NUCLEOTIDE EXCISION REPAIR 43 genes.ES.table 0.3 1.3 0.15 0.85 0.95 0.58 0.39 0.36 0.65 0.3
KEGG HOMOLOGOUS RECOMBINATION 27 genes.ES.table 0.42 1.1 0.35 1 0.99 0.41 0.24 0.31 0.98 0.49
KEGG ERBB SIGNALING PATHWAY 85 genes.ES.table 0.29 1 0.42 0.98 1 0.11 0.074 0.099 0.91 0.41
KEGG OOCYTE MEIOSIS 106 genes.ES.table 0.31 1.1 0.36 1 1 0.35 0.27 0.26 0.99 0.49
genes ES table in pathway: BIOCARTA G1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GAL3ST1 GAL3ST1 GAL3ST1 146 0.49 0.15 YES
2 UGT8 UGT8 UGT8 341 0.38 0.26 YES
3 DEGS2 DEGS2 DEGS2 418 0.35 0.38 YES
4 SGPP2 SGPP2 SGPP2 467 0.34 0.48 YES
5 CERK CERK CERK 1412 0.18 0.49 YES
6 ACER3 ACER3 ACER3 2170 0.13 0.49 NO
7 ASAH2 ASAH2 ASAH2 3172 0.087 0.46 NO
8 PPAP2C PPAP2C PPAP2C 4402 0.059 0.41 NO
9 SGPL1 SGPL1 SGPL1 4915 0.05 0.4 NO
10 SMPD3 SMPD3 SMPD3 5818 0.037 0.36 NO
11 SMPD4 SMPD4 SMPD4 5888 0.036 0.37 NO
12 SGPP1 SGPP1 SGPP1 7333 0.018 0.29 NO
13 PPAP2A PPAP2A PPAP2A 7391 0.018 0.3 NO
14 ASAH1 ASAH1 ASAH1 7485 0.016 0.3 NO
15 SPHK2 SPHK2 SPHK2 7737 0.014 0.29 NO
16 KDSR KDSR KDSR 8190 0.0089 0.26 NO
17 DEGS1 DEGS1 DEGS1 8204 0.0087 0.27 NO
18 UGCG UGCG UGCG 8302 0.0076 0.26 NO
19 SPTLC2 SPTLC2 SPTLC2 9422 -0.0048 0.2 NO
20 NEU4 NEU4 NEU4 9538 -0.0062 0.2 NO
21 SMPD1 SMPD1 SMPD1 9890 -0.01 0.18 NO
22 GLB1 GLB1 GLB1 10049 -0.012 0.18 NO
23 NEU1 NEU1 NEU1 10225 -0.014 0.17 NO
24 SPTLC1 SPTLC1 SPTLC1 10251 -0.014 0.18 NO
25 NEU3 NEU3 NEU3 10543 -0.018 0.16 NO
26 SGMS1 SGMS1 SGMS1 10975 -0.023 0.15 NO
27 PPAP2B PPAP2B PPAP2B 11038 -0.024 0.15 NO
28 ACER2 ACER2 ACER2 11112 -0.025 0.16 NO
29 SPHK1 SPHK1 SPHK1 11482 -0.031 0.15 NO
30 SMPD2 SMPD2 SMPD2 11547 -0.032 0.15 NO
31 GBA GBA GBA 12725 -0.055 0.11 NO
32 ARSA ARSA ARSA 12925 -0.06 0.11 NO
33 B4GALT6 B4GALT6 B4GALT6 13219 -0.067 0.12 NO
34 SGMS2 SGMS2 SGMS2 15027 -0.14 0.065 NO
35 GALC GALC GALC 15094 -0.15 0.11 NO
36 GLA GLA GLA 15278 -0.16 0.15 NO

Figure S1.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA G1 PATHWAY.

Figure S2.  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 RACCYCD PATHWAY

Table S2.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TJP3 TJP3 TJP3 32 0.68 0.046 YES
2 PRKCG PRKCG PRKCG 48 0.63 0.089 YES
3 MYH14 MYH14 MYH14 66 0.6 0.13 YES
4 CLDN6 CLDN6 CLDN6 243 0.43 0.15 YES
5 MYH7 MYH7 MYH7 447 0.34 0.16 YES
6 PARD6B PARD6B PARD6B 517 0.32 0.18 YES
7 CTNNA3 CTNNA3 CTNNA3 544 0.32 0.2 YES
8 CTNNA2 CTNNA2 CTNNA2 618 0.3 0.22 YES
9 CLDN3 CLDN3 CLDN3 637 0.3 0.24 YES
10 CLDN11 CLDN11 CLDN11 701 0.28 0.25 YES
11 RAB3B RAB3B RAB3B 799 0.26 0.27 YES
12 MYH7B MYH7B MYH7B 870 0.25 0.28 YES
13 OCLN OCLN OCLN 879 0.25 0.3 YES
14 CLDN15 CLDN15 CLDN15 886 0.25 0.31 YES
15 LLGL2 LLGL2 LLGL2 953 0.24 0.33 YES
16 CLDN4 CLDN4 CLDN4 1031 0.23 0.34 YES
17 MYH3 MYH3 MYH3 1093 0.22 0.35 YES
18 PRKCA PRKCA PRKCA 1247 0.2 0.36 YES
19 CRB3 CRB3 CRB3 1306 0.2 0.36 YES
20 PRKCQ PRKCQ PRKCQ 1351 0.19 0.38 YES
21 MYL5 MYL5 MYL5 1619 0.17 0.37 YES
22 CLDN10 CLDN10 CLDN10 1652 0.16 0.38 YES
23 PRKCB PRKCB PRKCB 2078 0.13 0.37 YES
24 PARD6G PARD6G PARD6G 2325 0.12 0.36 YES
25 CGN CGN CGN 2359 0.12 0.37 YES
26 PARD3 PARD3 PARD3 2458 0.11 0.37 YES
27 EPB41 EPB41 EPB41 2545 0.11 0.37 YES
28 CLDN23 CLDN23 CLDN23 2588 0.11 0.38 YES
29 CLDN9 CLDN9 CLDN9 2615 0.11 0.38 YES
30 PRKCZ PRKCZ PRKCZ 2653 0.11 0.39 YES
31 INADL INADL INADL 2773 0.1 0.39 YES
32 SYMPK SYMPK SYMPK 2941 0.095 0.39 NO
33 ZAK ZAK ZAK 3014 0.092 0.39 NO
34 PPP2R2C PPP2R2C PPP2R2C 3150 0.088 0.39 NO
35 PPP2R2A PPP2R2A PPP2R2A 3290 0.084 0.39 NO
36 LLGL1 LLGL1 LLGL1 3598 0.076 0.38 NO
37 CASK CASK CASK 3599 0.076 0.38 NO
38 AKT3 AKT3 AKT3 3745 0.073 0.38 NO
39 MPP5 MPP5 MPP5 3977 0.068 0.37 NO
40 PPP2R2D PPP2R2D PPP2R2D 4052 0.066 0.37 NO
41 PPP2CB PPP2CB PPP2CB 4629 0.055 0.34 NO
42 ASH1L ASH1L ASH1L 4759 0.052 0.34 NO
43 CLDN18 CLDN18 CLDN18 4933 0.049 0.33 NO
44 PRKCI PRKCI PRKCI 5096 0.047 0.32 NO
45 CSNK2A1 CSNK2A1 CSNK2A1 5298 0.044 0.32 NO
46 EPB41L3 EPB41L3 EPB41L3 5411 0.042 0.31 NO
47 CDK4 CDK4 CDK4 5588 0.04 0.31 NO
48 GNAI3 GNAI3 GNAI3 5733 0.038 0.3 NO
49 NRAS NRAS NRAS 5809 0.037 0.3 NO
50 MAGI3 MAGI3 MAGI3 5822 0.037 0.3 NO
51 SRC SRC SRC 5861 0.036 0.3 NO
52 MAGI2 MAGI2 MAGI2 5957 0.035 0.3 NO
53 ACTN2 ACTN2 ACTN2 5977 0.035 0.3 NO
54 VAPA VAPA VAPA 6104 0.033 0.3 NO
55 CSNK2A2 CSNK2A2 CSNK2A2 6316 0.03 0.29 NO
56 TJAP1 TJAP1 TJAP1 6328 0.03 0.29 NO
57 SPTAN1 SPTAN1 SPTAN1 6403 0.029 0.28 NO
58 CDC42 CDC42 CDC42 7014 0.022 0.25 NO
59 EXOC3 EXOC3 EXOC3 7018 0.022 0.25 NO
60 MLLT4 MLLT4 MLLT4 7049 0.021 0.25 NO
61 KRAS KRAS KRAS 7270 0.019 0.24 NO
62 CTNNB1 CTNNB1 CTNNB1 7468 0.017 0.23 NO
63 PPP2R1A PPP2R1A PPP2R1A 7495 0.016 0.23 NO
64 GNAI2 GNAI2 GNAI2 7795 0.013 0.22 NO
65 AKT2 AKT2 AKT2 8138 0.0096 0.2 NO
66 EPB41L2 EPB41L2 EPB41L2 8217 0.0086 0.19 NO
67 TJP2 TJP2 TJP2 8577 0.0049 0.18 NO
68 JAM3 JAM3 JAM3 8905 0.0011 0.16 NO
69 MPDZ MPDZ MPDZ 8929 0.00079 0.16 NO
70 GNAI1 GNAI1 GNAI1 9099 -0.0012 0.15 NO
71 CSNK2B CSNK2B CSNK2B 9177 -0.0021 0.14 NO
72 PTEN PTEN PTEN 9642 -0.0072 0.12 NO
73 RHOA RHOA RHOA 9931 -0.01 0.1 NO
74 PRKCE PRKCE PRKCE 9964 -0.011 0.1 NO
75 EPB41L1 EPB41L1 EPB41L1 10282 -0.015 0.083 NO
76 PRKCH PRKCH PRKCH 10348 -0.016 0.08 NO
77 CSDA CSDA CSDA 10406 -0.016 0.078 NO
78 TJP1 TJP1 TJP1 10526 -0.018 0.073 NO
79 YES1 YES1 YES1 10652 -0.019 0.067 NO
80 EXOC4 EXOC4 EXOC4 10863 -0.022 0.057 NO
81 PPP2CA PPP2CA PPP2CA 10947 -0.023 0.054 NO
82 CTNNA1 CTNNA1 CTNNA1 11214 -0.027 0.041 NO
83 PARD6A PARD6A PARD6A 11335 -0.029 0.036 NO
84 CTTN CTTN CTTN 11594 -0.033 0.024 NO
85 MYH10 MYH10 MYH10 11618 -0.033 0.025 NO
86 MAGI1 MAGI1 MAGI1 12012 -0.04 0.0058 NO
87 MYL12B MYL12B MYL12B 12302 -0.046 -0.0072 NO
88 MYH9 MYH9 MYH9 12456 -0.049 -0.012 NO
89 RRAS RRAS RRAS 12563 -0.052 -0.015 NO
90 ACTB ACTB ACTB 12610 -0.053 -0.014 NO
91 ACTN4 ACTN4 ACTN4 12664 -0.054 -0.013 NO
92 RAB13 RAB13 RAB13 12835 -0.058 -0.018 NO
93 AKT1 AKT1 AKT1 12998 -0.061 -0.023 NO
94 RRAS2 RRAS2 RRAS2 13104 -0.064 -0.025 NO
95 ACTG1 ACTG1 ACTG1 13265 -0.068 -0.029 NO
96 F11R F11R F11R 13309 -0.07 -0.026 NO
97 AMOTL1 AMOTL1 AMOTL1 13343 -0.071 -0.023 NO
98 CLDN5 CLDN5 CLDN5 13430 -0.073 -0.023 NO
99 JAM2 JAM2 JAM2 13640 -0.079 -0.029 NO
100 MYL12A MYL12A MYL12A 13886 -0.088 -0.037 NO
101 ACTN3 ACTN3 ACTN3 14366 -0.11 -0.056 NO
102 PPP2R1B PPP2R1B PPP2R1B 14567 -0.12 -0.059 NO
103 MRAS MRAS MRAS 14579 -0.12 -0.052 NO
104 ACTN1 ACTN1 ACTN1 14688 -0.12 -0.049 NO
105 PPP2R2B PPP2R2B PPP2R2B 14981 -0.14 -0.056 NO
106 MYL9 MYL9 MYL9 15119 -0.15 -0.053 NO
107 MYH11 MYH11 MYH11 15272 -0.16 -0.051 NO
108 MYH6 MYH6 MYH6 15276 -0.16 -0.04 NO
109 CLDN7 CLDN7 CLDN7 15341 -0.16 -0.032 NO
110 CLDN2 CLDN2 CLDN2 15470 -0.17 -0.028 NO
111 CLDN14 CLDN14 CLDN14 15774 -0.19 -0.031 NO
112 HCLS1 HCLS1 HCLS1 15795 -0.2 -0.019 NO
113 CLDN1 CLDN1 CLDN1 16168 -0.23 -0.024 NO
114 MYH15 MYH15 MYH15 16667 -0.28 -0.032 NO
115 PRKCD PRKCD PRKCD 16702 -0.28 -0.014 NO
116 MYLPF MYLPF MYLPF 17016 -0.33 -0.0085 NO
117 CLDN20 CLDN20 CLDN20 17217 -0.36 0.0055 NO
118 IGSF5 IGSF5 IGSF5 17843 -0.53 0.0074 NO

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

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

genes ES table in pathway: BIOCARTA MYOSIN PATHWAY

Table 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 PRKCG PRKCG PRKCG 48 0.63 0.16 YES
2 ATP6V0A4 ATP6V0A4 ATP6V0A4 75 0.58 0.32 YES
3 PRKCA PRKCA PRKCA 1247 0.2 0.31 YES
4 PRKACG PRKACG PRKACG 2059 0.13 0.3 YES
5 PRKCB PRKCB PRKCB 2078 0.13 0.33 YES
6 SEC61A2 SEC61A2 SEC61A2 2233 0.12 0.36 YES
7 ADCY9 ADCY9 ADCY9 3543 0.078 0.3 NO
8 PLCG1 PLCG1 PLCG1 3755 0.073 0.31 NO
9 ATP6V1B2 ATP6V1B2 ATP6V1B2 3921 0.069 0.32 NO
10 PRKX PRKX PRKX 4074 0.066 0.33 NO
11 ATP6V1G2 ATP6V1G2 ATP6V1G2 4804 0.052 0.3 NO
12 ATP6V1E2 ATP6V1E2 ATP6V1E2 5395 0.043 0.28 NO
13 SLC12A2 SLC12A2 SLC12A2 5585 0.04 0.28 NO
14 ATP6V1F ATP6V1F ATP6V1F 5796 0.037 0.28 NO
15 ATP6V1C1 ATP6V1C1 ATP6V1C1 6234 0.031 0.26 NO
16 ATP6V1A ATP6V1A ATP6V1A 6689 0.026 0.25 NO
17 ATP6V1H ATP6V1H ATP6V1H 6774 0.025 0.25 NO
18 GNAS GNAS GNAS 6861 0.024 0.25 NO
19 KDELR1 KDELR1 KDELR1 6921 0.023 0.25 NO
20 KDELR2 KDELR2 KDELR2 7609 0.015 0.22 NO
21 ATP6V1E1 ATP6V1E1 ATP6V1E1 8296 0.0077 0.18 NO
22 ATP6V0A1 ATP6V0A1 ATP6V0A1 8381 0.0069 0.18 NO
23 TJP2 TJP2 TJP2 8577 0.0049 0.17 NO
24 ATP6V1D ATP6V1D ATP6V1D 8693 0.0033 0.16 NO
25 PDIA4 PDIA4 PDIA4 8849 0.0017 0.16 NO
26 ERO1L ERO1L ERO1L 8947 0.00061 0.15 NO
27 ATP6V1G1 ATP6V1G1 ATP6V1G1 9011 -0.00017 0.15 NO
28 ATP6V0E1 ATP6V0E1 ATP6V0E1 9594 -0.0067 0.12 NO
29 ATP6V0C ATP6V0C ATP6V0C 9970 -0.011 0.098 NO
30 ATP6V0D2 ATP6V0D2 ATP6V0D2 9988 -0.011 0.1 NO
31 ATP6AP1 ATP6AP1 ATP6AP1 10081 -0.012 0.098 NO
32 SEC61A1 SEC61A1 SEC61A1 10273 -0.014 0.091 NO
33 TJP1 TJP1 TJP1 10526 -0.018 0.082 NO
34 ATP6V0A2 ATP6V0A2 ATP6V0A2 10653 -0.019 0.08 NO
35 ATP6V0B ATP6V0B ATP6V0B 11097 -0.025 0.062 NO
36 ATP6V0E2 ATP6V0E2 ATP6V0E2 11255 -0.028 0.061 NO
37 ARF1 ARF1 ARF1 11288 -0.028 0.066 NO
38 ATP6V0D1 ATP6V0D1 ATP6V0D1 11311 -0.028 0.073 NO
39 ATP6V1C2 ATP6V1C2 ATP6V1C2 11538 -0.032 0.069 NO
40 SEC61B SEC61B SEC61B 11637 -0.034 0.072 NO
41 PRKACA PRKACA PRKACA 11704 -0.035 0.078 NO
42 ACTB ACTB ACTB 12610 -0.053 0.041 NO
43 SEC61G SEC61G SEC61G 12974 -0.061 0.037 NO
44 ACTG1 ACTG1 ACTG1 13265 -0.068 0.039 NO
45 KDELR3 KDELR3 KDELR3 13703 -0.081 0.036 NO
46 PRKACB PRKACB PRKACB 13807 -0.085 0.053 NO
47 PLCG2 PLCG2 PLCG2 14222 -0.1 0.057 NO
48 ATP6V1B1 ATP6V1B1 ATP6V1B1 14368 -0.11 0.077 NO
49 TCIRG1 TCIRG1 TCIRG1 14535 -0.12 0.099 NO
50 KCNQ1 KCNQ1 KCNQ1 17146 -0.35 0.046 NO

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

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

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

Table 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 CACNG7 CACNG7 CACNG7 1 1.1 0.12 YES
2 CACNG6 CACNG6 CACNG6 232 0.43 0.15 YES
3 CACNA2D2 CACNA2D2 CACNA2D2 392 0.36 0.18 YES
4 ATP1A2 ATP1A2 ATP1A2 394 0.36 0.21 YES
5 MYH7 MYH7 MYH7 447 0.34 0.24 YES
6 COX6B2 COX6B2 COX6B2 509 0.32 0.27 YES
7 TNNI3 TNNI3 TNNI3 617 0.3 0.3 YES
8 COX4I2 COX4I2 COX4I2 663 0.29 0.32 YES
9 CACNG8 CACNG8 CACNG8 805 0.26 0.34 YES
10 CACNB1 CACNB1 CACNB1 1203 0.21 0.34 YES
11 COX8C COX8C COX8C 1255 0.2 0.36 YES
12 ATP1B2 ATP1B2 ATP1B2 1314 0.2 0.38 YES
13 RYR2 RYR2 RYR2 1585 0.17 0.38 YES
14 CACNG2 CACNG2 CACNG2 1740 0.16 0.39 YES
15 CACNB4 CACNB4 CACNB4 1833 0.15 0.4 YES
16 CACNA1C CACNA1C CACNA1C 1871 0.15 0.41 YES
17 CACNB2 CACNB2 CACNB2 1959 0.14 0.42 YES
18 FXYD2 FXYD2 FXYD2 2060 0.13 0.43 YES
19 CACNB3 CACNB3 CACNB3 2182 0.13 0.43 YES
20 UQCRHL UQCRHL UQCRHL 2455 0.11 0.43 NO
21 UQCRH UQCRH UQCRH 3243 0.085 0.39 NO
22 COX7C COX7C COX7C 4625 0.055 0.32 NO
23 COX7A2L COX7A2L COX7A2L 4626 0.055 0.33 NO
24 CACNG3 CACNG3 CACNG3 5008 0.048 0.31 NO
25 ATP1A3 ATP1A3 ATP1A3 6227 0.031 0.25 NO
26 SLC9A6 SLC9A6 SLC9A6 6229 0.031 0.25 NO
27 UQCRB UQCRB UQCRB 6240 0.031 0.25 NO
28 COX7A2 COX7A2 COX7A2 6371 0.03 0.25 NO
29 UQCRFS1 UQCRFS1 UQCRFS1 6439 0.029 0.25 NO
30 ATP2A2 ATP2A2 ATP2A2 6613 0.026 0.24 NO
31 COX4I1 COX4I1 COX4I1 7558 0.016 0.19 NO
32 ATP1A4 ATP1A4 ATP1A4 7637 0.015 0.19 NO
33 UQCR11 UQCR11 UQCR11 8747 0.0029 0.12 NO
34 COX8A COX8A COX8A 8854 0.0017 0.12 NO
35 COX6B1 COX6B1 COX6B1 9283 -0.0034 0.096 NO
36 ATP1B1 ATP1B1 ATP1B1 9593 -0.0067 0.079 NO
37 CYC1 CYC1 CYC1 9705 -0.008 0.074 NO
38 CACNA2D1 CACNA2D1 CACNA2D1 9919 -0.01 0.063 NO
39 COX6A1 COX6A1 COX6A1 9977 -0.011 0.061 NO
40 COX6C COX6C COX6C 9999 -0.011 0.061 NO
41 UQCR10 UQCR10 UQCR10 10100 -0.013 0.056 NO
42 SLC8A1 SLC8A1 SLC8A1 10397 -0.016 0.042 NO
43 COX5A COX5A COX5A 10522 -0.018 0.036 NO
44 COX7B COX7B COX7B 10735 -0.02 0.027 NO
45 COX5B COX5B COX5B 11051 -0.024 0.012 NO
46 CACNA1D CACNA1D CACNA1D 11201 -0.027 0.006 NO
47 UQCRC1 UQCRC1 UQCRC1 11607 -0.033 -0.013 NO
48 UQCRQ UQCRQ UQCRQ 11980 -0.04 -0.03 NO
49 TPM3 TPM3 TPM3 12063 -0.041 -0.03 NO
50 CACNG4 CACNG4 CACNG4 12619 -0.053 -0.056 NO
51 SLC9A1 SLC9A1 SLC9A1 13114 -0.064 -0.077 NO
52 COX7A1 COX7A1 COX7A1 13304 -0.069 -0.081 NO
53 ATP1A1 ATP1A1 ATP1A1 13324 -0.07 -0.074 NO
54 TPM1 TPM1 TPM1 13649 -0.079 -0.085 NO
55 TNNC1 TNNC1 TNNC1 14064 -0.095 -0.098 NO
56 TPM4 TPM4 TPM4 14083 -0.095 -0.089 NO
57 ATP1B3 ATP1B3 ATP1B3 14605 -0.12 -0.11 NO
58 CACNG1 CACNG1 CACNG1 14674 -0.12 -0.098 NO
59 MYH6 MYH6 MYH6 15276 -0.16 -0.12 NO
60 ACTC1 ACTC1 ACTC1 15289 -0.16 -0.1 NO
61 TPM2 TPM2 TPM2 15473 -0.17 -0.093 NO
62 CACNG5 CACNG5 CACNG5 15784 -0.2 -0.09 NO
63 CACNA1S CACNA1S CACNA1S 15865 -0.2 -0.074 NO
64 MYL3 MYL3 MYL3 15884 -0.2 -0.055 NO
65 CACNA2D4 CACNA2D4 CACNA2D4 16073 -0.22 -0.043 NO
66 TNNT2 TNNT2 TNNT2 16639 -0.28 -0.046 NO
67 COX6A2 COX6A2 COX6A2 17085 -0.34 -0.036 NO
68 CACNA1F CACNA1F CACNA1F 17283 -0.37 -0.0092 NO
69 CACNA2D3 CACNA2D3 CACNA2D3 17710 -0.47 0.015 NO

Figure S7.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CHREBP2 PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG SPHINGOLIPID METABOLISM

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 48 0.63 0.1 YES
2 GRIN1 GRIN1 GRIN1 64 0.6 0.21 YES
3 GRM5 GRM5 GRM5 390 0.36 0.25 YES
4 PRKCA PRKCA PRKCA 1247 0.2 0.24 YES
5 PPP1R1A PPP1R1A PPP1R1A 1253 0.2 0.27 YES
6 GRIN2B GRIN2B GRIN2B 1413 0.18 0.29 YES
7 CACNA1C CACNA1C CACNA1C 1871 0.15 0.29 YES
8 CHP2 CHP2 CHP2 1926 0.14 0.32 YES
9 PRKACG PRKACG PRKACG 2059 0.13 0.33 YES
10 PRKCB PRKCB PRKCB 2078 0.13 0.35 YES
11 MAP2K1 MAP2K1 MAP2K1 2281 0.12 0.36 YES
12 RPS6KA6 RPS6KA6 RPS6KA6 2860 0.097 0.35 YES
13 PPP3R1 PPP3R1 PPP3R1 3038 0.092 0.35 YES
14 CAMK2D CAMK2D CAMK2D 3205 0.086 0.36 YES
15 GRM1 GRM1 GRM1 3382 0.081 0.36 YES
16 GRIN2A GRIN2A GRIN2A 3429 0.08 0.37 YES
17 CAMK4 CAMK4 CAMK4 3828 0.071 0.36 YES
18 CREBBP CREBBP CREBBP 3837 0.071 0.37 YES
19 RPS6KA2 RPS6KA2 RPS6KA2 3946 0.069 0.38 YES
20 PPP1R12A PPP1R12A PPP1R12A 4014 0.067 0.39 YES
21 PRKX PRKX PRKX 4074 0.066 0.4 YES
22 PLCB1 PLCB1 PLCB1 4449 0.058 0.38 YES
23 MAPK1 MAPK1 MAPK1 4549 0.056 0.39 YES
24 CALM3 CALM3 CALM3 4571 0.056 0.4 YES
25 EP300 EP300 EP300 4747 0.053 0.4 NO
26 GNAQ GNAQ GNAQ 5698 0.038 0.35 NO
27 NRAS NRAS NRAS 5809 0.037 0.35 NO
28 PPP3CA PPP3CA PPP3CA 6195 0.031 0.33 NO
29 ITPR1 ITPR1 ITPR1 6210 0.031 0.34 NO
30 PLCB4 PLCB4 PLCB4 6285 0.03 0.34 NO
31 PPP3CB PPP3CB PPP3CB 6583 0.027 0.33 NO
32 PPP1CC PPP1CC PPP1CC 6865 0.024 0.32 NO
33 MAP2K2 MAP2K2 MAP2K2 7019 0.022 0.31 NO
34 ARAF ARAF ARAF 7164 0.02 0.31 NO
35 KRAS KRAS KRAS 7270 0.019 0.3 NO
36 PLCB3 PLCB3 PLCB3 7669 0.014 0.28 NO
37 BRAF BRAF BRAF 7985 0.011 0.27 NO
38 MAPK3 MAPK3 MAPK3 8088 0.01 0.26 NO
39 PPP3CC PPP3CC PPP3CC 8573 0.0049 0.24 NO
40 ADCY8 ADCY8 ADCY8 8879 0.0015 0.22 NO
41 RAF1 RAF1 RAF1 9989 -0.011 0.16 NO
42 PPP1CB PPP1CB PPP1CB 10047 -0.012 0.16 NO
43 RPS6KA1 RPS6KA1 RPS6KA1 10121 -0.013 0.16 NO
44 ATF4 ATF4 ATF4 10413 -0.016 0.14 NO
45 ITPR2 ITPR2 ITPR2 10432 -0.016 0.15 NO
46 ITPR3 ITPR3 ITPR3 10996 -0.024 0.12 NO
47 CHP CHP CHP 11012 -0.024 0.12 NO
48 RPS6KA3 RPS6KA3 RPS6KA3 11056 -0.024 0.12 NO
49 GRIA1 GRIA1 GRIA1 11703 -0.035 0.094 NO
50 PRKACA PRKACA PRKACA 11704 -0.035 0.1 NO
51 RAP1A RAP1A RAP1A 11948 -0.039 0.093 NO
52 CAMK2G CAMK2G CAMK2G 11965 -0.039 0.098 NO
53 GRIA2 GRIA2 GRIA2 12376 -0.048 0.084 NO
54 RAP1B RAP1B RAP1B 12377 -0.048 0.092 NO
55 HRAS HRAS HRAS 12643 -0.053 0.086 NO
56 PPP3R2 PPP3R2 PPP3R2 12648 -0.053 0.095 NO
57 GRIN2D GRIN2D GRIN2D 12812 -0.057 0.096 NO
58 CALM1 CALM1 CALM1 13195 -0.066 0.086 NO
59 PPP1CA PPP1CA PPP1CA 13390 -0.072 0.087 NO
60 GRIN2C GRIN2C GRIN2C 13534 -0.075 0.092 NO
61 CALML6 CALML6 CALML6 13636 -0.079 0.1 NO
62 RAPGEF3 RAPGEF3 RAPGEF3 13687 -0.08 0.11 NO
63 CAMK2B CAMK2B CAMK2B 13692 -0.081 0.12 NO
64 PRKACB PRKACB PRKACB 13807 -0.085 0.13 NO
65 CALM2 CALM2 CALM2 14002 -0.093 0.14 NO
66 CAMK2A CAMK2A CAMK2A 15882 -0.2 0.067 NO
67 PLCB2 PLCB2 PLCB2 16756 -0.29 0.068 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 SPHINGOLIPID METABOLISM.

Figure S10.  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 RIBOSOME

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 CCNE1 CCNE1 CCNE1 333 0.39 0.12 YES
2 CCNA1 CCNA1 CCNA1 342 0.38 0.26 YES
3 CDC25A CDC25A CDC25A 1257 0.2 0.28 YES
4 TGFB2 TGFB2 TGFB2 1376 0.19 0.34 YES
5 CDK1 CDK1 CDK1 1732 0.16 0.38 YES
6 CDK6 CDK6 CDK6 2296 0.12 0.39 YES
7 HDAC1 HDAC1 HDAC1 2415 0.12 0.42 YES
8 DHFR DHFR DHFR 2703 0.1 0.44 YES
9 CDKN2A CDKN2A CDKN2A 3631 0.075 0.42 NO
10 RB1 RB1 RB1 4073 0.066 0.42 NO
11 SMAD3 SMAD3 SMAD3 5128 0.046 0.38 NO
12 SMAD4 SMAD4 SMAD4 5219 0.045 0.39 NO
13 TFDP1 TFDP1 TFDP1 5232 0.045 0.4 NO
14 CDK4 CDK4 CDK4 5588 0.04 0.4 NO
15 GSK3B GSK3B GSK3B 6435 0.029 0.36 NO
16 TGFB1 TGFB1 TGFB1 6818 0.024 0.35 NO
17 CDKN1B CDKN1B CDKN1B 7597 0.015 0.31 NO
18 CDK2 CDK2 CDK2 9664 -0.0075 0.2 NO
19 ATM ATM ATM 10727 -0.02 0.14 NO
20 TP53 TP53 TP53 10886 -0.022 0.14 NO
21 CCND1 CCND1 CCND1 11072 -0.025 0.14 NO
22 ABL1 ABL1 ABL1 11285 -0.028 0.14 NO
23 SKP2 SKP2 SKP2 13046 -0.062 0.065 NO
24 CDKN1A CDKN1A CDKN1A 13278 -0.069 0.077 NO
25 ATR ATR ATR 13691 -0.081 0.083 NO
26 CDKN2B CDKN2B CDKN2B 14565 -0.12 0.076 NO
27 TGFB3 TGFB3 TGFB3 16944 -0.32 0.058 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 RIBOSOME.

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

genes ES table in pathway: KEGG NUCLEOTIDE EXCISION REPAIR

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 POLE POLE POLE 1518 0.17 0.0073 YES
2 POLD1 POLD1 POLD1 2741 0.1 -0.0072 YES
3 POLE2 POLE2 POLE2 3010 0.093 0.027 YES
4 LIG1 LIG1 LIG1 3047 0.091 0.073 YES
5 ERCC2 ERCC2 ERCC2 3318 0.083 0.1 YES
6 RPA1 RPA1 RPA1 3810 0.072 0.11 YES
7 RPA4 RPA4 RPA4 4130 0.065 0.13 YES
8 RPA2 RPA2 RPA2 4801 0.052 0.12 YES
9 RFC1 RFC1 RFC1 5154 0.046 0.12 YES
10 MNAT1 MNAT1 MNAT1 5218 0.045 0.14 YES
11 CUL4A CUL4A CUL4A 5355 0.043 0.16 YES
12 ERCC6 ERCC6 ERCC6 5415 0.042 0.18 YES
13 CUL4B CUL4B CUL4B 5490 0.041 0.2 YES
14 POLD3 POLD3 POLD3 5661 0.039 0.21 YES
15 GTF2H1 GTF2H1 GTF2H1 5749 0.038 0.22 YES
16 RFC4 RFC4 RFC4 5800 0.037 0.24 YES
17 DDB2 DDB2 DDB2 5894 0.036 0.25 YES
18 PCNA PCNA PCNA 6016 0.034 0.26 YES
19 GTF2H4 GTF2H4 GTF2H4 6376 0.029 0.26 YES
20 GTF2H3 GTF2H3 GTF2H3 6482 0.028 0.27 YES
21 ERCC4 ERCC4 ERCC4 6602 0.027 0.28 YES
22 RFC5 RFC5 RFC5 6709 0.025 0.28 YES
23 GTF2H2 GTF2H2 GTF2H2 6822 0.024 0.29 YES
24 XPC XPC XPC 6927 0.023 0.3 YES
25 GTF2H5 GTF2H5 GTF2H5 7041 0.021 0.3 YES
26 XPA XPA XPA 7778 0.013 0.27 NO
27 POLD2 POLD2 POLD2 7897 0.012 0.27 NO
28 RFC2 RFC2 RFC2 8924 0.00082 0.21 NO
29 ERCC1 ERCC1 ERCC1 8966 0.00038 0.21 NO
30 RBX1 RBX1 RBX1 9207 -0.0025 0.2 NO
31 ERCC3 ERCC3 ERCC3 9754 -0.0084 0.17 NO
32 DDB1 DDB1 DDB1 9759 -0.0085 0.17 NO
33 RAD23A RAD23A RAD23A 10697 -0.02 0.13 NO
34 POLE3 POLE3 POLE3 10751 -0.02 0.14 NO
35 ERCC5 ERCC5 ERCC5 10824 -0.021 0.15 NO
36 ERCC8 ERCC8 ERCC8 10986 -0.024 0.15 NO
37 CETN2 CETN2 CETN2 11340 -0.029 0.15 NO
38 RFC3 RFC3 RFC3 11485 -0.031 0.16 NO
39 RPA3 RPA3 RPA3 12300 -0.046 0.13 NO
40 CCNH CCNH CCNH 12580 -0.052 0.15 NO
41 CDK7 CDK7 CDK7 12865 -0.058 0.16 NO
42 POLD4 POLD4 POLD4 13781 -0.084 0.15 NO
43 POLE4 POLE4 POLE4 15155 -0.15 0.16 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 NUCLEOTIDE EXCISION REPAIR.

Figure S14.  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 HOMOLOGOUS RECOMBINATION

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 MLXIPL MLXIPL MLXIPL 199 0.45 0.16 YES
2 PKLR PKLR PKLR 1494 0.18 0.15 YES
3 PRKACG PRKACG PRKACG 2059 0.13 0.17 YES
4 PRKAA2 PRKAA2 PRKAA2 2083 0.13 0.22 YES
5 PRKAR1B PRKAR1B PRKAR1B 2351 0.12 0.24 YES
6 PPP2R3B PPP2R3B PPP2R3B 2578 0.11 0.27 YES
7 PPP2R2C PPP2R2C PPP2R2C 3150 0.088 0.27 YES
8 PPP2R2A PPP2R2A PPP2R2A 3290 0.084 0.3 YES
9 PRKAB1 PRKAB1 PRKAB1 3902 0.069 0.29 YES
10 PPP2R2D PPP2R2D PPP2R2D 4052 0.066 0.3 YES
11 PPP2CB PPP2CB PPP2CB 4629 0.055 0.29 YES
12 PRKAB2 PRKAB2 PRKAB2 4682 0.054 0.31 YES
13 PPP2R5E PPP2R5E PPP2R5E 4797 0.052 0.32 YES
14 PRKAG1 PRKAG1 PRKAG1 4873 0.05 0.34 YES
15 YWHAH YWHAH YWHAH 5920 0.035 0.29 NO
16 PRKAR2A PRKAR2A PRKAR2A 6560 0.027 0.27 NO
17 PPP2R5D PPP2R5D PPP2R5D 6693 0.026 0.27 NO
18 YWHAE YWHAE YWHAE 7361 0.018 0.24 NO
19 PPP2R1A PPP2R1A PPP2R1A 7495 0.016 0.24 NO
20 YWHAQ YWHAQ YWHAQ 7587 0.015 0.24 NO
21 PPP2R5C PPP2R5C PPP2R5C 8652 0.0038 0.18 NO
22 ACACA ACACA ACACA 8809 0.0022 0.17 NO
23 YWHAG YWHAG YWHAG 8971 0.00035 0.16 NO
24 PRKAR1A PRKAR1A PRKAR1A 10058 -0.012 0.11 NO
25 PRKAA1 PRKAA1 PRKAA1 10681 -0.02 0.079 NO
26 PPP2CA PPP2CA PPP2CA 10947 -0.023 0.072 NO
27 PPP2R4 PPP2R4 PPP2R4 11029 -0.024 0.077 NO
28 YWHAZ YWHAZ YWHAZ 11032 -0.024 0.086 NO
29 YWHAB YWHAB YWHAB 11338 -0.029 0.08 NO
30 GCK GCK GCK 11377 -0.03 0.088 NO
31 PPP2R5A PPP2R5A PPP2R5A 11555 -0.032 0.09 NO
32 PRKACA PRKACA PRKACA 11704 -0.035 0.095 NO
33 FASN FASN FASN 11890 -0.038 0.099 NO
34 MLX MLX MLX 12002 -0.04 0.11 NO
35 PPP2R5B PPP2R5B PPP2R5B 12310 -0.046 0.11 NO
36 PPP2R3A PPP2R3A PPP2R3A 12413 -0.048 0.12 NO
37 PRKAG2 PRKAG2 PRKAG2 13487 -0.074 0.087 NO
38 PRKACB PRKACB PRKACB 13807 -0.085 0.1 NO
39 PRKAR2B PRKAR2B PRKAR2B 14182 -0.099 0.12 NO
40 PPP2R1B PPP2R1B PPP2R1B 14567 -0.12 0.14 NO
41 PPP2R2B PPP2R2B PPP2R2B 14981 -0.14 0.17 NO

Figure S15.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HOMOLOGOUS RECOMBINATION.

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

genes ES table in pathway: KEGG ERBB SIGNALING PATHWAY

Table S9.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GNG13 GNG13 GNG13 16 0.76 0.11 YES
2 GNG3 GNG3 GNG3 87 0.56 0.19 YES
3 TAS2R4 TAS2R4 TAS2R4 105 0.54 0.28 YES
4 TAS2R5 TAS2R5 TAS2R5 493 0.33 0.3 YES
5 TAS2R19 TAS2R19 TAS2R19 683 0.28 0.34 YES
6 TAS2R20 TAS2R20 TAS2R20 835 0.26 0.36 YES
7 TAS2R3 TAS2R3 TAS2R3 1086 0.22 0.38 YES
8 TAS2R50 TAS2R50 TAS2R50 1128 0.22 0.42 YES
9 TAS1R3 TAS1R3 TAS1R3 1310 0.2 0.43 YES
10 KCNB1 KCNB1 KCNB1 1502 0.18 0.45 YES
11 TAS2R14 TAS2R14 TAS2R14 1683 0.16 0.46 YES
12 TAS2R10 TAS2R10 TAS2R10 1979 0.14 0.47 YES
13 PRKACG PRKACG PRKACG 2059 0.13 0.48 YES
14 TAS2R31 TAS2R31 TAS2R31 2181 0.13 0.5 YES
15 SCNN1B SCNN1B SCNN1B 2280 0.12 0.51 YES
16 TAS2R8 TAS2R8 TAS2R8 2283 0.12 0.53 YES
17 SCNN1G SCNN1G SCNN1G 2770 0.1 0.52 NO
18 TAS2R43 TAS2R43 TAS2R43 2952 0.094 0.52 NO
19 TAS2R13 TAS2R13 TAS2R13 3140 0.088 0.52 NO
20 ADCY6 ADCY6 ADCY6 3642 0.075 0.51 NO
21 TAS2R42 TAS2R42 TAS2R42 3976 0.068 0.5 NO
22 PRKX PRKX PRKX 4074 0.066 0.5 NO
23 GNB1 GNB1 GNB1 6300 0.03 0.38 NO
24 GNAS GNAS GNAS 6861 0.024 0.36 NO
25 ADCY8 ADCY8 ADCY8 8879 0.0015 0.24 NO
26 ADCY4 ADCY4 ADCY4 10995 -0.024 0.13 NO
27 ITPR3 ITPR3 ITPR3 10996 -0.024 0.13 NO
28 PRKACA PRKACA PRKACA 11704 -0.035 0.098 NO
29 GRM4 GRM4 GRM4 12240 -0.045 0.075 NO
30 TRPM5 TRPM5 TRPM5 13727 -0.082 0.0047 NO
31 PRKACB PRKACB PRKACB 13807 -0.085 0.013 NO
32 CACNA1B CACNA1B CACNA1B 14305 -0.1 0.0011 NO
33 PDE1A PDE1A PDE1A 14342 -0.11 0.015 NO
34 SCNN1A SCNN1A SCNN1A 15411 -0.17 -0.02 NO
35 GNB3 GNB3 GNB3 15637 -0.18 -0.0047 NO
36 CACNA1A CACNA1A CACNA1A 15660 -0.18 0.022 NO
37 ACCN1 ACCN1 ACCN1 15791 -0.2 0.044 NO
38 TAS1R1 TAS1R1 TAS1R1 16093 -0.22 0.061 NO
39 PLCB2 PLCB2 PLCB2 16756 -0.29 0.068 NO

Figure S17.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ERBB SIGNALING PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ERBB 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 OOCYTE MEIOSIS

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 GRIN1 GRIN1 GRIN1 64 0.6 0.051 YES
2 GRM5 GRM5 GRM5 390 0.36 0.066 YES
3 NDUFA4L2 NDUFA4L2 NDUFA4L2 480 0.33 0.091 YES
4 DNAI1 DNAI1 DNAI1 481 0.33 0.12 YES
5 COX6B2 COX6B2 COX6B2 509 0.32 0.15 YES
6 DNAH2 DNAH2 DNAH2 528 0.32 0.18 YES
7 HAP1 HAP1 HAP1 570 0.31 0.2 YES
8 COX4I2 COX4I2 COX4I2 663 0.29 0.22 YES
9 COX8C COX8C COX8C 1255 0.2 0.21 YES
10 GRIN2B GRIN2B GRIN2B 1413 0.18 0.22 YES
11 BBC3 BBC3 BBC3 1645 0.16 0.22 YES
12 CREB3L4 CREB3L4 CREB3L4 2241 0.12 0.2 YES
13 RCOR1 RCOR1 RCOR1 2259 0.12 0.21 YES
14 POLR2J3 POLR2J3 POLR2J3 2327 0.12 0.21 YES
15 PPARGC1A PPARGC1A PPARGC1A 2370 0.12 0.22 YES
16 HDAC1 HDAC1 HDAC1 2415 0.12 0.23 YES
17 DLG4 DLG4 DLG4 2423 0.12 0.24 YES
18 UQCRHL UQCRHL UQCRHL 2455 0.11 0.25 YES
19 DNAH3 DNAH3 DNAH3 3185 0.087 0.22 NO
20 UQCRH UQCRH UQCRH 3243 0.085 0.22 NO
21 TBPL1 TBPL1 TBPL1 3813 0.072 0.19 NO
22 CREBBP CREBBP CREBBP 3837 0.071 0.2 NO
23 SLC25A31 SLC25A31 SLC25A31 3856 0.07 0.2 NO
24 HDAC2 HDAC2 HDAC2 3881 0.07 0.21 NO
25 BAX BAX BAX 4314 0.061 0.19 NO
26 TBP TBP TBP 4351 0.06 0.2 NO
27 PLCB1 PLCB1 PLCB1 4449 0.058 0.19 NO
28 COX7C COX7C COX7C 4625 0.055 0.19 NO
29 COX7A2L COX7A2L COX7A2L 4626 0.055 0.2 NO
30 NDUFS4 NDUFS4 NDUFS4 4695 0.054 0.2 NO
31 NRF1 NRF1 NRF1 4698 0.054 0.2 NO
32 POLR2J2 POLR2J2 POLR2J2 4725 0.053 0.2 NO
33 EP300 EP300 EP300 4747 0.053 0.21 NO
34 VDAC2 VDAC2 VDAC2 4756 0.052 0.21 NO
35 CASP9 CASP9 CASP9 4878 0.05 0.21 NO
36 DCTN4 DCTN4 DCTN4 5192 0.046 0.2 NO
37 DNAL4 DNAL4 DNAL4 5304 0.044 0.19 NO
38 CLTA CLTA CLTA 5680 0.038 0.18 NO
39 GNAQ GNAQ GNAQ 5698 0.038 0.18 NO
40 ATP5F1 ATP5F1 ATP5F1 5795 0.037 0.18 NO
41 CREB1 CREB1 CREB1 5918 0.035 0.17 NO
42 TAF4 TAF4 TAF4 5940 0.035 0.18 NO
43 UQCRC2 UQCRC2 UQCRC2 5991 0.034 0.18 NO
44 SIN3A SIN3A SIN3A 6079 0.033 0.17 NO
45 NDUFV3 NDUFV3 NDUFV3 6131 0.032 0.17 NO
46 TFAM TFAM TFAM 6172 0.032 0.17 NO
47 ITPR1 ITPR1 ITPR1 6210 0.031 0.18 NO
48 SP1 SP1 SP1 6218 0.031 0.18 NO
49 UQCRB UQCRB UQCRB 6240 0.031 0.18 NO
50 HTT HTT HTT 6265 0.031 0.18 NO
51 PLCB4 PLCB4 PLCB4 6285 0.03 0.18 NO
52 COX7A2 COX7A2 COX7A2 6371 0.03 0.18 NO
53 UQCRFS1 UQCRFS1 UQCRFS1 6439 0.029 0.18 NO
54 DCTN2 DCTN2 DCTN2 6449 0.029 0.18 NO
55 DCTN1 DCTN1 DCTN1 6488 0.028 0.18 NO
56 POLR2G POLR2G POLR2G 6507 0.028 0.18 NO
57 VDAC3 VDAC3 VDAC3 6534 0.027 0.18 NO
58 POLR2H POLR2H POLR2H 6683 0.026 0.18 NO
59 NDUFS7 NDUFS7 NDUFS7 6684 0.026 0.18 NO
60 NDUFA9 NDUFA9 NDUFA9 6685 0.026 0.18 NO
61 ATP5G3 ATP5G3 ATP5G3 6828 0.024 0.18 NO
62 HIP1 HIP1 HIP1 6915 0.023 0.17 NO
63 ATP5B ATP5B ATP5B 6934 0.023 0.18 NO
64 SLC25A5 SLC25A5 SLC25A5 6951 0.022 0.18 NO
65 ATP5O ATP5O ATP5O 7150 0.02 0.17 NO
66 CLTCL1 CLTCL1 CLTCL1 7183 0.02 0.17 NO
67 NDUFC2 NDUFC2 NDUFC2 7197 0.02 0.17 NO
68 ATP5A1 ATP5A1 ATP5A1 7218 0.02 0.17 NO
69 CREB3L2 CREB3L2 CREB3L2 7520 0.016 0.15 NO
70 COX4I1 COX4I1 COX4I1 7558 0.016 0.15 NO
71 NDUFV1 NDUFV1 NDUFV1 7629 0.015 0.15 NO
72 PLCB3 PLCB3 PLCB3 7669 0.014 0.15 NO
73 POLR2B POLR2B POLR2B 7743 0.014 0.15 NO
74 ATP5G2 ATP5G2 ATP5G2 7914 0.012 0.14 NO
75 NDUFB9 NDUFB9 NDUFB9 7956 0.011 0.14 NO
76 POLR2E POLR2E POLR2E 7997 0.011 0.14 NO
77 CYCS CYCS CYCS 8083 0.01 0.13 NO
78 ATP5J ATP5J ATP5J 8113 0.0098 0.13 NO
79 AP2B1 AP2B1 AP2B1 8584 0.0048 0.1 NO
80 NDUFS6 NDUFS6 NDUFS6 8700 0.0032 0.098 NO
81 NDUFS5 NDUFS5 NDUFS5 8703 0.0032 0.099 NO
82 UQCR11 UQCR11 UQCR11 8747 0.0029 0.096 NO
83 SLC25A4 SLC25A4 SLC25A4 8812 0.0021 0.093 NO
84 ATP5C1 ATP5C1 ATP5C1 8819 0.002 0.093 NO
85 COX8A COX8A COX8A 8854 0.0017 0.091 NO
86 DNAL1 DNAL1 DNAL1 8866 0.0015 0.091 NO
87 CLTC CLTC CLTC 8872 0.0015 0.09 NO
88 NDUFB10 NDUFB10 NDUFB10 8880 0.0014 0.09 NO
89 SOD2 SOD2 SOD2 8948 0.00059 0.086 NO
90 NDUFA8 NDUFA8 NDUFA8 8962 0.00041 0.086 NO
91 NDUFA6 NDUFA6 NDUFA6 8969 0.00035 0.086 NO
92 PPID PPID PPID 9071 -0.00086 0.08 NO
93 NDUFB6 NDUFB6 NDUFB6 9260 -0.0031 0.07 NO
94 COX6B1 COX6B1 COX6B1 9283 -0.0034 0.069 NO
95 POLR2C POLR2C POLR2C 9333 -0.004 0.066 NO
96 POLR2D POLR2D POLR2D 9415 -0.0047 0.062 NO
97 SDHD SDHD SDHD 9499 -0.0057 0.058 NO
98 NDUFA10 NDUFA10 NDUFA10 9557 -0.0064 0.055 NO
99 POLR2A POLR2A POLR2A 9645 -0.0073 0.051 NO
100 POLR2I POLR2I POLR2I 9700 -0.0079 0.049 NO
101 CYC1 CYC1 CYC1 9705 -0.008 0.049 NO
102 SOD1 SOD1 SOD1 9727 -0.0081 0.049 NO
103 ATP5G1 ATP5G1 ATP5G1 9794 -0.0089 0.046 NO
104 NDUFAB1 NDUFAB1 NDUFAB1 9850 -0.0094 0.044 NO
105 NDUFA7 NDUFA7 NDUFA7 9969 -0.011 0.038 NO
106 COX6A1 COX6A1 COX6A1 9977 -0.011 0.039 NO
107 COX6C COX6C COX6C 9999 -0.011 0.039 NO
108 UQCR10 UQCR10 UQCR10 10100 -0.013 0.034 NO
109 NDUFB8 NDUFB8 NDUFB8 10197 -0.014 0.03 NO
110 NDUFB2 NDUFB2 NDUFB2 10240 -0.014 0.029 NO
111 APAF1 APAF1 APAF1 10277 -0.014 0.028 NO
112 SDHA SDHA SDHA 10329 -0.015 0.027 NO
113 NDUFS8 NDUFS8 NDUFS8 10330 -0.015 0.028 NO
114 AP2A1 AP2A1 AP2A1 10363 -0.016 0.028 NO
115 IFT57 IFT57 IFT57 10429 -0.016 0.026 NO
116 COX5A COX5A COX5A 10522 -0.018 0.022 NO
117 NDUFB7 NDUFB7 NDUFB7 10597 -0.018 0.02 NO
118 NDUFB5 NDUFB5 NDUFB5 10619 -0.019 0.02 NO
119 AP2S1 AP2S1 AP2S1 10663 -0.019 0.019 NO
120 NDUFS2 NDUFS2 NDUFS2 10674 -0.02 0.021 NO
121 CLTB CLTB CLTB 10684 -0.02 0.022 NO
122 COX7B COX7B COX7B 10735 -0.02 0.021 NO
123 NDUFA5 NDUFA5 NDUFA5 10797 -0.021 0.019 NO
124 NDUFA1 NDUFA1 NDUFA1 10798 -0.021 0.021 NO
125 AP2A2 AP2A2 AP2A2 10855 -0.022 0.02 NO
126 TP53 TP53 TP53 10886 -0.022 0.02 NO
127 COX5B COX5B COX5B 11051 -0.024 0.014 NO
128 POLR2F POLR2F POLR2F 11331 -0.029 0.0004 NO
129 NDUFS3 NDUFS3 NDUFS3 11356 -0.029 0.0017 NO
130 NDUFA2 NDUFA2 NDUFA2 11395 -0.03 0.0023 NO
131 ATP5E ATP5E ATP5E 11451 -0.031 0.002 NO
132 UQCRC1 UQCRC1 UQCRC1 11607 -0.033 -0.0038 NO
133 UQCRQ UQCRQ UQCRQ 11980 -0.04 -0.021 NO
134 AP2M1 AP2M1 AP2M1 12021 -0.04 -0.02 NO
135 ATP5D ATP5D ATP5D 12025 -0.04 -0.016 NO
136 POLR2J POLR2J POLR2J 12093 -0.042 -0.016 NO
137 ATP5H ATP5H ATP5H 12138 -0.042 -0.015 NO
138 SDHB SDHB SDHB 12281 -0.046 -0.019 NO
139 SLC25A6 SLC25A6 SLC25A6 12322 -0.046 -0.017 NO
140 NDUFV2 NDUFV2 NDUFV2 12365 -0.047 -0.015 NO
141 NDUFB1 NDUFB1 NDUFB1 12369 -0.047 -0.011 NO
142 POLR2K POLR2K POLR2K 12587 -0.052 -0.018 NO
143 NDUFS1 NDUFS1 NDUFS1 12606 -0.053 -0.014 NO
144 CREB3L3 CREB3L3 CREB3L3 12649 -0.053 -0.012 NO
145 SDHC SDHC SDHC 12730 -0.055 -0.011 NO
146 VDAC1 VDAC1 VDAC1 12915 -0.06 -0.016 NO
147 CREB3 CREB3 CREB3 12989 -0.061 -0.015 NO
148 NDUFA3 NDUFA3 NDUFA3 13068 -0.063 -0.014 NO
149 DNAH1 DNAH1 DNAH1 13158 -0.065 -0.013 NO
150 NDUFB3 NDUFB3 NDUFB3 13181 -0.066 -0.0079 NO
151 COX7A1 COX7A1 COX7A1 13304 -0.069 -0.0085 NO
152 NDUFB4 NDUFB4 NDUFB4 13327 -0.07 -0.0034 NO
153 REST REST REST 13349 -0.071 0.0019 NO
154 DNALI1 DNALI1 DNALI1 13367 -0.071 0.0074 NO
155 NDUFC1 NDUFC1 NDUFC1 13409 -0.072 0.012 NO
156 PPARG PPARG PPARG 13549 -0.076 0.011 NO
157 NDUFA4 NDUFA4 NDUFA4 13878 -0.088 0.00023 NO
158 CASP3 CASP3 CASP3 14058 -0.094 -0.0013 NO
159 POLR2L POLR2L POLR2L 14114 -0.096 0.0044 NO
160 TAF4B TAF4B TAF4B 14458 -0.11 -0.0048 NO
161 GPX1 GPX1 GPX1 14651 -0.12 -0.0046 NO
162 CASP8 CASP8 CASP8 15079 -0.14 -0.015 NO
163 BDNF BDNF BDNF 15832 -0.2 -0.04 NO
164 TGM2 TGM2 TGM2 16015 -0.22 -0.03 NO
165 PLCB2 PLCB2 PLCB2 16756 -0.29 -0.045 NO
166 COX6A2 COX6A2 COX6A2 17085 -0.34 -0.033 NO
167 CREB5 CREB5 CREB5 17408 -0.4 -0.015 NO
168 CREB3L1 CREB3L1 CREB3L1 17826 -0.52 0.0084 NO

Figure S19.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OOCYTE MEIOSIS.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.3 1.1 0.37 1 1 0.28 0.14 0.24 1 0.56
BIOCARTA BIOPEPTIDES PATHWAY 37 genes.ES.table 0.43 1.6 0.04 1 0.72 0.35 0.2 0.28 0.61 0.34
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.39 1.2 0.25 1 0.99 0.3 0.17 0.25 1 0.54
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.44 1.7 0.036 0.9 0.49 0.3 0.14 0.26 0 0.31
BIOCARTA PDGF PATHWAY 31 genes.ES.table 0.49 1.5 0.089 0.7 0.84 0.32 0.17 0.27 0.48 0.24
BIOCARTA TOLL PATHWAY 36 genes.ES.table 0.57 1.5 0.057 0.78 0.75 0.44 0.17 0.37 0.5 0.26
KEGG ABC TRANSPORTERS 39 genes.ES.table 0.39 1.1 0.32 1 1 0.13 0.062 0.12 1 0.63
KEGG PEROXISOME 75 genes.ES.table 0.3 1.1 0.3 1 0.99 0.29 0.23 0.23 1 0.58
KEGG ANTIGEN PROCESSING AND PRESENTATION 68 genes.ES.table 0.48 1.2 0.29 1 0.99 0.53 0.29 0.38 1 0.5
KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY 88 genes.ES.table 0.5 1.3 0.19 1 0.96 0.38 0.17 0.31 1 0.58
genes ES table in pathway: BIOCARTA AT1R PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PTK2B PTK2B PTK2B 1246 0.22 0.033 YES
2 SHC1 SHC1 SHC1 2007 0.16 0.065 YES
3 MAPK8 MAPK8 MAPK8 2241 0.14 0.12 YES
4 MAP3K1 MAP3K1 MAP3K1 2259 0.14 0.19 YES
5 CALM1 CALM1 CALM1 2289 0.14 0.25 YES
6 PAK1 PAK1 PAK1 2324 0.14 0.32 YES
7 CALM2 CALM2 CALM2 2330 0.14 0.38 YES
8 PRKCB PRKCB PRKCB 2465 0.13 0.44 YES
9 MAPK3 MAPK3 MAPK3 4685 0.067 0.34 NO
10 GNAQ GNAQ GNAQ 5168 0.057 0.34 NO
11 MAPK14 MAPK14 MAPK14 6173 0.04 0.31 NO
12 SOS1 SOS1 SOS1 6339 0.038 0.32 NO
13 GRB2 GRB2 GRB2 7081 0.027 0.29 NO
14 SRC SRC SRC 9312 -0.0031 0.16 NO
15 CALM3 CALM3 CALM3 9409 -0.0043 0.16 NO
16 MAP2K4 MAP2K4 MAP2K4 10746 -0.025 0.098 NO
17 CRKL CRKL CRKL 10748 -0.025 0.11 NO
18 MAPK1 MAPK1 MAPK1 10750 -0.025 0.12 NO
19 BCAR1 BCAR1 BCAR1 11110 -0.031 0.12 NO
20 RAC1 RAC1 RAC1 11563 -0.039 0.11 NO
21 MAP2K2 MAP2K2 MAP2K2 11890 -0.046 0.11 NO
22 PLCG1 PLCG1 PLCG1 11996 -0.048 0.13 NO
23 JUN JUN JUN 12397 -0.056 0.13 NO
24 MAP2K1 MAP2K1 MAP2K1 12783 -0.064 0.14 NO
25 RAF1 RAF1 RAF1 13027 -0.07 0.16 NO
26 MAP2K3 MAP2K3 MAP2K3 14186 -0.11 0.15 NO
27 PRKCA PRKCA PRKCA 14826 -0.14 0.18 NO

Figure S21.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA AT1R PATHWAY.

Figure S22.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA BIOPEPTIDES 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 39 0.63 0.16 YES
2 PTK2B PTK2B PTK2B 1246 0.22 0.15 YES
3 STAT5A STAT5A STAT5A 1254 0.22 0.21 YES
4 STAT1 STAT1 STAT1 1500 0.19 0.24 YES
5 SHC1 SHC1 SHC1 2007 0.16 0.26 YES
6 CAMK2G CAMK2G CAMK2G 2192 0.15 0.29 YES
7 MAPK8 MAPK8 MAPK8 2241 0.14 0.32 YES
8 CALM1 CALM1 CALM1 2289 0.14 0.36 YES
9 CALM2 CALM2 CALM2 2330 0.14 0.39 YES
10 PRKCB PRKCB PRKCB 2465 0.13 0.42 YES
11 MAPT MAPT MAPT 2768 0.12 0.43 YES
12 CAMK2B CAMK2B CAMK2B 3472 0.098 0.42 YES
13 JAK2 JAK2 JAK2 3611 0.094 0.44 YES
14 GNA11 GNA11 GNA11 4142 0.079 0.43 NO
15 STAT6 STAT6 STAT6 4682 0.067 0.41 NO
16 MAPK3 MAPK3 MAPK3 4685 0.067 0.43 NO
17 STAT5B STAT5B STAT5B 5482 0.052 0.4 NO
18 MAPK14 MAPK14 MAPK14 6173 0.04 0.37 NO
19 SOS1 SOS1 SOS1 6339 0.038 0.37 NO
20 GNAI1 GNAI1 GNAI1 6480 0.036 0.37 NO
21 STAT2 STAT2 STAT2 6570 0.034 0.38 NO
22 GRB2 GRB2 GRB2 7081 0.027 0.36 NO
23 CALM3 CALM3 CALM3 9409 -0.0043 0.23 NO
24 CDK5 CDK5 CDK5 9470 -0.0052 0.23 NO
25 CAMK2D CAMK2D CAMK2D 9824 -0.0097 0.21 NO
26 STAT3 STAT3 STAT3 10477 -0.02 0.18 NO
27 MAPK1 MAPK1 MAPK1 10750 -0.025 0.17 NO
28 MAP2K2 MAP2K2 MAP2K2 11890 -0.046 0.12 NO
29 PLCG1 PLCG1 PLCG1 11996 -0.048 0.12 NO
30 MAP2K1 MAP2K1 MAP2K1 12783 -0.064 0.097 NO
31 RAF1 RAF1 RAF1 13027 -0.07 0.1 NO
32 GNB1 GNB1 GNB1 13058 -0.071 0.12 NO
33 AGT AGT AGT 13805 -0.094 0.1 NO
34 FYN FYN FYN 13989 -0.1 0.12 NO
35 MYLK MYLK MYLK 14772 -0.13 0.11 NO
36 CAMK2A CAMK2A CAMK2A 14809 -0.14 0.14 NO
37 PRKCA PRKCA PRKCA 14826 -0.14 0.18 NO

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

Figure S24.  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 EGF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TLR9 TLR9 TLR9 679 0.3 0.036 YES
2 TLR3 TLR3 TLR3 934 0.26 0.084 YES
3 MAP2K6 MAP2K6 MAP2K6 980 0.25 0.14 YES
4 TLR10 TLR10 TLR10 1009 0.25 0.2 YES
5 EIF2AK2 EIF2AK2 EIF2AK2 1021 0.24 0.26 YES
6 PGLYRP1 PGLYRP1 PGLYRP1 1159 0.23 0.31 YES
7 TLR6 TLR6 TLR6 1399 0.2 0.35 YES
8 TLR7 TLR7 TLR7 1479 0.19 0.39 YES
9 MYD88 MYD88 MYD88 1737 0.18 0.42 YES
10 MAPK8 MAPK8 MAPK8 2241 0.14 0.43 YES
11 MAP3K1 MAP3K1 MAP3K1 2259 0.14 0.46 YES
12 TLR4 TLR4 TLR4 2420 0.14 0.49 YES
13 TRAF6 TRAF6 TRAF6 2492 0.13 0.52 YES
14 TLR2 TLR2 TLR2 2514 0.13 0.55 YES
15 FOS FOS FOS 3012 0.11 0.55 YES
16 TIRAP TIRAP TIRAP 3067 0.11 0.57 YES
17 TOLLIP TOLLIP TOLLIP 3806 0.088 0.55 NO
18 CHUK CHUK CHUK 4466 0.071 0.53 NO
19 MAP3K14 MAP3K14 MAP3K14 5242 0.056 0.5 NO
20 CD14 CD14 CD14 5885 0.045 0.48 NO
21 MAPK14 MAPK14 MAPK14 6173 0.04 0.47 NO
22 MAP3K7 MAP3K7 MAP3K7 6886 0.03 0.44 NO
23 NFKB1 NFKB1 NFKB1 8668 0.0054 0.34 NO
24 TAB2 TAB2 TAB2 9528 -0.0059 0.3 NO
25 IRAK1 IRAK1 IRAK1 9777 -0.0091 0.28 NO
26 IKBKG IKBKG IKBKG 9993 -0.012 0.27 NO
27 IKBKB IKBKB IKBKB 10587 -0.022 0.25 NO
28 MAP2K4 MAP2K4 MAP2K4 10746 -0.025 0.24 NO
29 ELK1 ELK1 ELK1 11151 -0.032 0.23 NO
30 NFKBIA NFKBIA NFKBIA 11993 -0.048 0.19 NO
31 JUN JUN JUN 12397 -0.056 0.19 NO
32 RELA RELA RELA 12894 -0.067 0.17 NO
33 ECSIT ECSIT ECSIT 13080 -0.072 0.18 NO
34 MAP2K3 MAP2K3 MAP2K3 14186 -0.11 0.15 NO
35 LY96 LY96 LY96 14600 -0.12 0.15 NO
36 TAB1 TAB1 TAB1 14860 -0.14 0.17 NO

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

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EGF 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 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 MAPK13 MAPK13 MAPK13 517 0.34 0.035 YES
2 IFIH1 IFIH1 IFIH1 741 0.28 0.076 YES
3 IKBKE IKBKE IKBKE 808 0.27 0.12 YES
4 CXCL10 CXCL10 CXCL10 920 0.26 0.17 YES
5 DDX58 DDX58 DDX58 925 0.26 0.22 YES
6 IFNW1 IFNW1 IFNW1 1312 0.21 0.23 YES
7 IL8 IL8 IL8 1387 0.2 0.27 YES
8 TRAF3 TRAF3 TRAF3 1608 0.18 0.29 YES
9 TNF TNF TNF 1909 0.16 0.3 YES
10 ISG15 ISG15 ISG15 1926 0.16 0.33 YES
11 MAPK8 MAPK8 MAPK8 2241 0.14 0.34 YES
12 MAP3K1 MAP3K1 MAP3K1 2259 0.14 0.37 YES
13 IRF7 IRF7 IRF7 2315 0.14 0.39 YES
14 IL12B IL12B IL12B 2432 0.14 0.41 YES
15 TRAF6 TRAF6 TRAF6 2492 0.13 0.44 YES
16 CYLD CYLD CYLD 2627 0.13 0.45 YES
17 DDX3Y DDX3Y DDX3Y 3039 0.11 0.45 YES
18 MAPK9 MAPK9 MAPK9 3612 0.094 0.44 YES
19 AZI2 AZI2 AZI2 3737 0.09 0.44 YES
20 TRIM25 TRIM25 TRIM25 3880 0.086 0.45 YES
21 CHUK CHUK CHUK 4466 0.071 0.43 NO
22 MAPK11 MAPK11 MAPK11 4751 0.066 0.43 NO
23 MAPK10 MAPK10 MAPK10 4808 0.064 0.44 NO
24 DHX58 DHX58 DHX58 4863 0.063 0.45 NO
25 ATG12 ATG12 ATG12 5048 0.059 0.45 NO
26 MAPK12 MAPK12 MAPK12 5458 0.052 0.44 NO
27 TBK1 TBK1 TBK1 5651 0.048 0.44 NO
28 RIPK1 RIPK1 RIPK1 6136 0.041 0.42 NO
29 MAPK14 MAPK14 MAPK14 6173 0.04 0.42 NO
30 DAK DAK DAK 6284 0.039 0.42 NO
31 TANK TANK TANK 6711 0.032 0.4 NO
32 MAP3K7 MAP3K7 MAP3K7 6886 0.03 0.4 NO
33 DDX3X DDX3X DDX3X 8113 0.013 0.34 NO
34 OTUD5 OTUD5 OTUD5 8222 0.011 0.33 NO
35 NFKB1 NFKB1 NFKB1 8668 0.0054 0.31 NO
36 PIN1 PIN1 PIN1 9276 -0.0024 0.27 NO
37 TRADD TRADD TRADD 9352 -0.0037 0.27 NO
38 RNF125 RNF125 RNF125 9892 -0.011 0.24 NO
39 IKBKG IKBKG IKBKG 9993 -0.012 0.24 NO
40 TRAF2 TRAF2 TRAF2 10307 -0.018 0.22 NO
41 IKBKB IKBKB IKBKB 10587 -0.022 0.21 NO
42 FADD FADD FADD 10593 -0.022 0.22 NO
43 IFNA5 IFNA5 IFNA5 10932 -0.028 0.2 NO
44 MAVS MAVS MAVS 11062 -0.03 0.2 NO
45 ATG5 ATG5 ATG5 11347 -0.035 0.19 NO
46 CASP8 CASP8 CASP8 11386 -0.036 0.2 NO
47 NFKBIA NFKBIA NFKBIA 11993 -0.048 0.17 NO
48 TBKBP1 TBKBP1 TBKBP1 12014 -0.048 0.18 NO
49 NLRX1 NLRX1 NLRX1 12089 -0.05 0.19 NO
50 NFKBIB NFKBIB NFKBIB 12708 -0.063 0.16 NO
51 IL12A IL12A IL12A 12876 -0.066 0.17 NO
52 RELA RELA RELA 12894 -0.067 0.18 NO
53 IRF3 IRF3 IRF3 13480 -0.083 0.16 NO
54 SIKE1 SIKE1 SIKE1 13907 -0.098 0.16 NO
55 CASP10 CASP10 CASP10 15495 -0.18 0.1 NO
56 TMEM173 TMEM173 TMEM173 15805 -0.2 0.12 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 PYK2 PATHWAY.

Figure S28.  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 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 STAT4 STAT4 STAT4 39 0.63 0.2 YES
2 STAT5A STAT5A STAT5A 1254 0.22 0.2 YES
3 STAT1 STAT1 STAT1 1500 0.19 0.25 YES
4 PIK3R1 PIK3R1 PIK3R1 1846 0.17 0.28 YES
5 SHC1 SHC1 SHC1 2007 0.16 0.33 YES
6 PIK3CG PIK3CG PIK3CG 2134 0.15 0.37 YES
7 MAPK8 MAPK8 MAPK8 2241 0.14 0.41 YES
8 MAP3K1 MAP3K1 MAP3K1 2259 0.14 0.45 YES
9 PRKCB PRKCB PRKCB 2465 0.13 0.48 YES
10 FOS FOS FOS 3012 0.11 0.49 YES
11 STAT6 STAT6 STAT6 4682 0.067 0.42 NO
12 MAPK3 MAPK3 MAPK3 4685 0.067 0.44 NO
13 STAT5B STAT5B STAT5B 5482 0.052 0.41 NO
14 RASA1 RASA1 RASA1 6308 0.038 0.38 NO
15 SOS1 SOS1 SOS1 6339 0.038 0.39 NO
16 STAT2 STAT2 STAT2 6570 0.034 0.39 NO
17 CSNK2A1 CSNK2A1 CSNK2A1 7064 0.027 0.37 NO
18 GRB2 GRB2 GRB2 7081 0.027 0.38 NO
19 PDGFRA PDGFRA PDGFRA 7974 0.014 0.33 NO
20 SRF SRF SRF 9347 -0.0037 0.26 NO
21 STAT3 STAT3 STAT3 10477 -0.02 0.2 NO
22 MAP2K4 MAP2K4 MAP2K4 10746 -0.025 0.19 NO
23 ELK1 ELK1 ELK1 11151 -0.032 0.18 NO
24 PIK3CA PIK3CA PIK3CA 11547 -0.039 0.17 NO
25 PLCG1 PLCG1 PLCG1 11996 -0.048 0.16 NO
26 JUN JUN JUN 12397 -0.056 0.16 NO
27 JAK1 JAK1 JAK1 12745 -0.063 0.16 NO
28 MAP2K1 MAP2K1 MAP2K1 12783 -0.064 0.18 NO
29 RAF1 RAF1 RAF1 13027 -0.07 0.18 NO
30 PRKCA PRKCA PRKCA 14826 -0.14 0.13 NO
31 PDGFA PDGFA PDGFA 15046 -0.15 0.16 NO

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

Figure S30.  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 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 MAPK13 MAPK13 MAPK13 517 0.34 0.008 YES
2 TLR9 TLR9 TLR9 679 0.3 0.032 YES
3 TLR1 TLR1 TLR1 690 0.3 0.064 YES
4 IKBKE IKBKE IKBKE 808 0.27 0.087 YES
5 CXCL10 CXCL10 CXCL10 920 0.26 0.11 YES
6 TLR3 TLR3 TLR3 934 0.26 0.14 YES
7 MAP2K6 MAP2K6 MAP2K6 980 0.25 0.16 YES
8 IFNA21 IFNA21 IFNA21 1355 0.2 0.16 YES
9 IL8 IL8 IL8 1387 0.2 0.18 YES
10 TLR6 TLR6 TLR6 1399 0.2 0.2 YES
11 TLR7 TLR7 TLR7 1479 0.19 0.22 YES
12 STAT1 STAT1 STAT1 1500 0.19 0.24 YES
13 TRAF3 TRAF3 TRAF3 1608 0.18 0.26 YES
14 CD80 CD80 CD80 1631 0.18 0.28 YES
15 CXCL11 CXCL11 CXCL11 1703 0.18 0.29 YES
16 MYD88 MYD88 MYD88 1737 0.18 0.31 YES
17 PIK3R1 PIK3R1 PIK3R1 1846 0.17 0.32 YES
18 TNF TNF TNF 1909 0.16 0.34 YES
19 CXCL9 CXCL9 CXCL9 1946 0.16 0.35 YES
20 PIK3CG PIK3CG PIK3CG 2134 0.15 0.36 YES
21 CD86 CD86 CD86 2209 0.15 0.37 YES
22 MAPK8 MAPK8 MAPK8 2241 0.14 0.38 YES
23 CCL3 CCL3 CCL3 2284 0.14 0.4 YES
24 IRF7 IRF7 IRF7 2315 0.14 0.41 YES
25 CCL4 CCL4 CCL4 2351 0.14 0.42 YES
26 TLR4 TLR4 TLR4 2420 0.14 0.44 YES
27 IL12B IL12B IL12B 2432 0.14 0.45 YES
28 CCL5 CCL5 CCL5 2475 0.13 0.46 YES
29 TRAF6 TRAF6 TRAF6 2492 0.13 0.48 YES
30 TLR2 TLR2 TLR2 2514 0.13 0.49 YES
31 TLR8 TLR8 TLR8 2797 0.12 0.49 YES
32 FOS FOS FOS 3012 0.11 0.49 YES
33 TIRAP TIRAP TIRAP 3067 0.11 0.5 YES
34 MAPK9 MAPK9 MAPK9 3612 0.094 0.48 NO
35 TOLLIP TOLLIP TOLLIP 3806 0.088 0.48 NO
36 IL1B IL1B IL1B 3913 0.085 0.48 NO
37 CHUK CHUK CHUK 4466 0.071 0.46 NO
38 TLR5 TLR5 TLR5 4663 0.067 0.45 NO
39 AKT3 AKT3 AKT3 4679 0.067 0.46 NO
40 MAPK3 MAPK3 MAPK3 4685 0.067 0.46 NO
41 MAPK11 MAPK11 MAPK11 4751 0.066 0.47 NO
42 MAPK10 MAPK10 MAPK10 4808 0.064 0.47 NO
43 CD40 CD40 CD40 4928 0.062 0.47 NO
44 MAPK12 MAPK12 MAPK12 5458 0.052 0.45 NO
45 CD14 CD14 CD14 5885 0.045 0.43 NO
46 PIK3R5 PIK3R5 PIK3R5 6011 0.043 0.43 NO
47 RIPK1 RIPK1 RIPK1 6136 0.041 0.42 NO
48 MAPK14 MAPK14 MAPK14 6173 0.04 0.43 NO
49 AKT1 AKT1 AKT1 6793 0.031 0.4 NO
50 MAP3K7 MAP3K7 MAP3K7 6886 0.03 0.39 NO
51 TICAM1 TICAM1 TICAM1 7922 0.015 0.34 NO
52 SPP1 SPP1 SPP1 8095 0.013 0.33 NO
53 IFNAR2 IFNAR2 IFNAR2 8168 0.012 0.33 NO
54 NFKB1 NFKB1 NFKB1 8668 0.0054 0.3 NO
55 IRAK4 IRAK4 IRAK4 9396 -0.0042 0.26 NO
56 TAB2 TAB2 TAB2 9528 -0.0059 0.25 NO
57 MAP2K7 MAP2K7 MAP2K7 9618 -0.007 0.25 NO
58 IRAK1 IRAK1 IRAK1 9777 -0.0091 0.24 NO
59 IKBKG IKBKG IKBKG 9993 -0.012 0.23 NO
60 PIK3CB PIK3CB PIK3CB 10564 -0.022 0.2 NO
61 IKBKB IKBKB IKBKB 10587 -0.022 0.2 NO
62 FADD FADD FADD 10593 -0.022 0.2 NO
63 IFNAR1 IFNAR1 IFNAR1 10735 -0.025 0.2 NO
64 MAP2K4 MAP2K4 MAP2K4 10746 -0.025 0.2 NO
65 MAPK1 MAPK1 MAPK1 10750 -0.025 0.2 NO
66 IFNA5 IFNA5 IFNA5 10932 -0.028 0.2 NO
67 PIK3R2 PIK3R2 PIK3R2 10950 -0.028 0.2 NO
68 CASP8 CASP8 CASP8 11386 -0.036 0.18 NO
69 PIK3CA PIK3CA PIK3CA 11547 -0.039 0.17 NO
70 RAC1 RAC1 RAC1 11563 -0.039 0.18 NO
71 MAP2K2 MAP2K2 MAP2K2 11890 -0.046 0.16 NO
72 NFKBIA NFKBIA NFKBIA 11993 -0.048 0.16 NO
73 AKT2 AKT2 AKT2 12378 -0.056 0.15 NO
74 JUN JUN JUN 12397 -0.056 0.15 NO
75 MAP2K1 MAP2K1 MAP2K1 12783 -0.064 0.14 NO
76 IL12A IL12A IL12A 12876 -0.066 0.14 NO
77 RELA RELA RELA 12894 -0.067 0.15 NO
78 PIK3CD PIK3CD PIK3CD 12942 -0.068 0.15 NO
79 IL6 IL6 IL6 13015 -0.07 0.16 NO
80 IRF5 IRF5 IRF5 13469 -0.083 0.14 NO
81 IRF3 IRF3 IRF3 13480 -0.083 0.15 NO
82 TICAM2 TICAM2 TICAM2 13718 -0.091 0.14 NO
83 MAP2K3 MAP2K3 MAP2K3 14186 -0.11 0.13 NO
84 PIK3R3 PIK3R3 PIK3R3 14539 -0.12 0.12 NO
85 LY96 LY96 LY96 14600 -0.12 0.14 NO
86 TAB1 TAB1 TAB1 14860 -0.14 0.14 NO
87 MAP3K8 MAP3K8 MAP3K8 15100 -0.15 0.14 NO
88 CTSK CTSK CTSK 15845 -0.2 0.12 NO

Figure S31.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TOLL PATHWAY.

Figure S32.  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: KEGG ABC TRANSPORTERS

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 NCAM2 NCAM2 NCAM2 238 0.43 0.12 YES
2 IL1A IL1A IL1A 341 0.39 0.24 YES
3 C6 C6 C6 608 0.31 0.33 YES
4 EGR1 EGR1 EGR1 1172 0.23 0.37 YES
5 C5 C5 C5 1453 0.2 0.41 YES
6 CCL5 CCL5 CCL5 2475 0.13 0.4 YES
7 PRNP PRNP PRNP 2533 0.13 0.44 YES
8 NCAM1 NCAM1 NCAM1 3056 0.11 0.44 YES
9 PRKACB PRKACB PRKACB 3116 0.11 0.47 YES
10 IL1B IL1B IL1B 3913 0.085 0.46 NO
11 MAPK3 MAPK3 MAPK3 4685 0.067 0.44 NO
12 STIP1 STIP1 STIP1 6019 0.043 0.37 NO
13 HSPA5 HSPA5 HSPA5 6406 0.037 0.36 NO
14 PRKACA PRKACA PRKACA 7007 0.028 0.34 NO
15 HSPA1A HSPA1A HSPA1A 7616 0.019 0.31 NO
16 C1QC C1QC C1QC 8179 0.012 0.28 NO
17 C1QB C1QB C1QB 8256 0.01 0.28 NO
18 SOD1 SOD1 SOD1 8579 0.0066 0.27 NO
19 PRKX PRKX PRKX 10105 -0.014 0.19 NO
20 MAPK1 MAPK1 MAPK1 10750 -0.025 0.16 NO
21 ELK1 ELK1 ELK1 11151 -0.032 0.15 NO
22 PRKACG PRKACG PRKACG 11313 -0.034 0.15 NO
23 C1QA C1QA C1QA 11573 -0.039 0.15 NO
24 C8G C8G C8G 11635 -0.04 0.16 NO
25 MAP2K2 MAP2K2 MAP2K2 11890 -0.046 0.16 NO
26 MAP2K1 MAP2K1 MAP2K1 12783 -0.064 0.13 NO
27 IL6 IL6 IL6 13015 -0.07 0.14 NO
28 LAMC1 LAMC1 LAMC1 13018 -0.07 0.16 NO
29 FYN FYN FYN 13989 -0.1 0.14 NO
30 BAX BAX BAX 14169 -0.11 0.16 NO
31 NOTCH1 NOTCH1 NOTCH1 15342 -0.16 0.15 NO

Figure S33.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ABC TRANSPORTERS.

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

genes ES table in pathway: KEGG PEROXISOME

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 IL1A IL1A IL1A 341 0.39 0.1 YES
2 KLRC1 KLRC1 KLRC1 971 0.25 0.14 YES
3 FASLG FASLG FASLG 1253 0.22 0.19 YES
4 CD80 CD80 CD80 1631 0.18 0.22 YES
5 TNF TNF TNF 1909 0.16 0.26 YES
6 CD86 CD86 CD86 2209 0.15 0.29 YES
7 KIR2DL1 KIR2DL1 KIR2DL1 2429 0.14 0.32 YES
8 HLA-DOA HLA-DOA HLA-DOA 2680 0.12 0.34 YES
9 HLA-DQA2 HLA-DQA2 HLA-DQA2 2802 0.12 0.37 YES
10 HLA-DOB HLA-DOB HLA-DOB 3332 0.1 0.37 YES
11 HLA-DPA1 HLA-DPA1 HLA-DPA1 3381 0.1 0.4 YES
12 PRF1 PRF1 PRF1 3478 0.098 0.42 YES
13 HLA-G HLA-G HLA-G 3814 0.088 0.43 YES
14 HLA-DQA1 HLA-DQA1 HLA-DQA1 3820 0.088 0.46 YES
15 IL1B IL1B IL1B 3913 0.085 0.48 YES
16 KIR3DL1 KIR3DL1 KIR3DL1 4054 0.081 0.5 YES
17 KIR2DL3 KIR2DL3 KIR2DL3 4055 0.081 0.52 YES
18 HLA-DRB5 HLA-DRB5 HLA-DRB5 4320 0.074 0.53 YES
19 IFNG IFNG IFNG 4866 0.063 0.52 YES
20 KLRD1 KLRD1 KLRD1 4907 0.062 0.53 YES
21 HLA-DMB HLA-DMB HLA-DMB 4977 0.061 0.55 YES
22 HLA-B HLA-B HLA-B 5034 0.06 0.56 YES
23 CD28 CD28 CD28 5084 0.059 0.58 YES
24 HLA-C HLA-C HLA-C 5114 0.058 0.59 YES
25 HLA-DPB1 HLA-DPB1 HLA-DPB1 5136 0.058 0.61 YES
26 HLA-A HLA-A HLA-A 5231 0.056 0.62 YES
27 HLA-DRA HLA-DRA HLA-DRA 6718 0.032 0.55 NO
28 GZMB GZMB GZMB 6748 0.032 0.56 NO
29 FAS FAS FAS 7018 0.028 0.55 NO
30 KIR3DL2 KIR3DL2 KIR3DL2 8629 0.0059 0.46 NO
31 HLA-DRB1 HLA-DRB1 HLA-DRB1 9077 0.00012 0.44 NO
32 HLA-DMA HLA-DMA HLA-DMA 10002 -0.012 0.39 NO
33 HLA-F HLA-F HLA-F 10628 -0.023 0.36 NO
34 IL6 IL6 IL6 13015 -0.07 0.25 NO
35 HLA-E HLA-E HLA-E 13566 -0.086 0.25 NO

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

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

genes ES table in pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION

Table 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 HIST1H3H HIST1H3H HIST1H3H 232 0.44 0.02 YES
2 HIST3H2BB HIST3H2BB HIST3H2BB 309 0.4 0.046 YES
3 C7 C7 C7 450 0.36 0.065 YES
4 HIST1H4I HIST1H4I HIST1H4I 530 0.33 0.086 YES
5 HIST2H2BF HIST2H2BF HIST2H2BF 551 0.33 0.11 YES
6 HIST1H2BG HIST1H2BG HIST1H2BG 589 0.32 0.13 YES
7 HIST1H2AG HIST1H2AG HIST1H2AG 593 0.32 0.16 YES
8 HIST1H4H HIST1H4H HIST1H4H 597 0.31 0.18 YES
9 C6 C6 C6 608 0.31 0.2 YES
10 HIST1H2BN HIST1H2BN HIST1H2BN 642 0.3 0.22 YES
11 HIST1H2BL HIST1H2BL HIST1H2BL 940 0.26 0.22 YES
12 HIST1H2AM HIST1H2AM HIST1H2AM 1041 0.24 0.24 YES
13 TRIM21 TRIM21 TRIM21 1165 0.23 0.25 YES
14 HIST1H3E HIST1H3E HIST1H3E 1185 0.22 0.26 YES
15 FCGR3B FCGR3B FCGR3B 1294 0.21 0.27 YES
16 CD40LG CD40LG CD40LG 1386 0.2 0.28 YES
17 C5 C5 C5 1453 0.2 0.3 YES
18 HIST1H2BC HIST1H2BC HIST1H2BC 1563 0.19 0.3 YES
19 CD80 CD80 CD80 1631 0.18 0.31 YES
20 HIST1H2BO HIST1H2BO HIST1H2BO 1648 0.18 0.33 YES
21 HIST1H2AL HIST1H2AL HIST1H2AL 1663 0.18 0.34 YES
22 HIST1H2AK HIST1H2AK HIST1H2AK 1740 0.18 0.35 YES
23 HIST1H2AD HIST1H2AD HIST1H2AD 1827 0.17 0.36 YES
24 HIST1H3A HIST1H3A HIST1H3A 1850 0.17 0.37 YES
25 FCGR2B FCGR2B FCGR2B 1861 0.17 0.38 YES
26 HIST2H3D HIST2H3D HIST2H3D 1902 0.16 0.39 YES
27 TNF TNF TNF 1909 0.16 0.4 YES
28 HIST1H2AB HIST1H2AB HIST1H2AB 1933 0.16 0.41 YES
29 FCGR2C FCGR2C FCGR2C 1939 0.16 0.42 YES
30 HIST1H2AE HIST1H2AE HIST1H2AE 2095 0.15 0.43 YES
31 CD86 CD86 CD86 2209 0.15 0.43 YES
32 HIST1H2BJ HIST1H2BJ HIST1H2BJ 2273 0.14 0.44 YES
33 ACTN1 ACTN1 ACTN1 2345 0.14 0.45 YES
34 HIST1H3J HIST1H3J HIST1H3J 2385 0.14 0.45 YES
35 H2AFY2 H2AFY2 H2AFY2 2529 0.13 0.46 YES
36 FCGR3A FCGR3A FCGR3A 2600 0.13 0.46 YES
37 IL10 IL10 IL10 2622 0.13 0.47 YES
38 HIST1H2AH HIST1H2AH HIST1H2AH 2673 0.12 0.48 YES
39 HLA-DOA HLA-DOA HLA-DOA 2680 0.12 0.49 YES
40 HIST1H3G HIST1H3G HIST1H3G 2687 0.12 0.5 YES
41 HIST2H2BE HIST2H2BE HIST2H2BE 2717 0.12 0.5 YES
42 HIST1H2BM HIST1H2BM HIST1H2BM 2771 0.12 0.51 YES
43 HLA-DQA2 HLA-DQA2 HLA-DQA2 2802 0.12 0.52 YES
44 HIST1H2BF HIST1H2BF HIST1H2BF 2838 0.12 0.52 YES
45 HIST1H2BE HIST1H2BE HIST1H2BE 3138 0.11 0.52 NO
46 HLA-DOB HLA-DOB HLA-DOB 3332 0.1 0.51 NO
47 HLA-DPA1 HLA-DPA1 HLA-DPA1 3381 0.1 0.52 NO
48 HLA-DQA1 HLA-DQA1 HLA-DQA1 3820 0.088 0.5 NO
49 HIST1H2AC HIST1H2AC HIST1H2AC 3947 0.084 0.5 NO
50 HIST1H3D HIST1H3D HIST1H3D 3979 0.083 0.5 NO
51 HLA-DRB5 HLA-DRB5 HLA-DRB5 4320 0.074 0.49 NO
52 HIST1H2BK HIST1H2BK HIST1H2BK 4662 0.067 0.48 NO
53 HIST1H4E HIST1H4E HIST1H4E 4708 0.066 0.48 NO
54 HIST3H2A HIST3H2A HIST3H2A 4849 0.063 0.48 NO
55 IFNG IFNG IFNG 4866 0.063 0.48 NO
56 CD40 CD40 CD40 4928 0.062 0.48 NO
57 HLA-DMB HLA-DMB HLA-DMB 4977 0.061 0.48 NO
58 CD28 CD28 CD28 5084 0.059 0.48 NO
59 HLA-DPB1 HLA-DPB1 HLA-DPB1 5136 0.058 0.48 NO
60 HIST2H4A HIST2H4A HIST2H4A 5994 0.043 0.44 NO
61 HIST1H4K HIST1H4K HIST1H4K 6197 0.04 0.43 NO
62 HIST1H4D HIST1H4D HIST1H4D 6527 0.035 0.41 NO
63 SNRPD1 SNRPD1 SNRPD1 6565 0.034 0.41 NO
64 C3 C3 C3 6652 0.033 0.41 NO
65 HLA-DRA HLA-DRA HLA-DRA 6718 0.032 0.41 NO
66 TROVE2 TROVE2 TROVE2 6760 0.032 0.41 NO
67 H2AFZ H2AFZ H2AFZ 6866 0.03 0.41 NO
68 SSB SSB SSB 7587 0.02 0.37 NO
69 FCGR1A FCGR1A FCGR1A 7916 0.015 0.35 NO
70 C1QC C1QC C1QC 8179 0.012 0.34 NO
71 ACTN3 ACTN3 ACTN3 8203 0.011 0.34 NO
72 C1QB C1QB C1QB 8256 0.01 0.33 NO
73 HIST1H2AJ HIST1H2AJ HIST1H2AJ 8446 0.008 0.32 NO
74 C1S C1S C1S 8558 0.0068 0.32 NO
75 GRIN2A GRIN2A GRIN2A 8692 0.0053 0.31 NO
76 FCGR2A FCGR2A FCGR2A 9003 0.00096 0.29 NO
77 HLA-DRB1 HLA-DRB1 HLA-DRB1 9077 0.00012 0.29 NO
78 C2 C2 C2 9202 -0.0014 0.28 NO
79 HIST1H2BD HIST1H2BD HIST1H2BD 9360 -0.0038 0.28 NO
80 HIST1H4A HIST1H4A HIST1H4A 9433 -0.0045 0.27 NO
81 H2AFX H2AFX H2AFX 9449 -0.0048 0.27 NO
82 H3F3C H3F3C H3F3C 9853 -0.01 0.25 NO
83 HLA-DMA HLA-DMA HLA-DMA 10002 -0.012 0.24 NO
84 H2AFY H2AFY H2AFY 10256 -0.017 0.23 NO
85 ELANE ELANE ELANE 10330 -0.018 0.23 NO
86 H3F3B H3F3B H3F3B 10705 -0.024 0.21 NO
87 HLA-DQB1 HLA-DQB1 HLA-DQB1 10804 -0.026 0.2 NO
88 H2AFV H2AFV H2AFV 11393 -0.036 0.17 NO
89 C1QA C1QA C1QA 11573 -0.039 0.17 NO
90 C8G C8G C8G 11635 -0.04 0.17 NO
91 SNRPB SNRPB SNRPB 11652 -0.041 0.17 NO
92 SNRPD3 SNRPD3 SNRPD3 12353 -0.055 0.13 NO
93 ACTN4 ACTN4 ACTN4 12476 -0.058 0.13 NO
94 HIST1H3B HIST1H3B HIST1H3B 12583 -0.06 0.13 NO
95 H2AFB1 H2AFB1 H2AFB1 12669 -0.062 0.13 NO
96 H3F3A H3F3A H3F3A 12767 -0.064 0.13 NO
97 C1R C1R C1R 13079 -0.072 0.12 NO
98 H2AFJ H2AFJ H2AFJ 13082 -0.072 0.12 NO
99 GRIN2B GRIN2B GRIN2B 13125 -0.073 0.12 NO
100 HIST2H3C HIST2H3C HIST2H3C 13440 -0.082 0.11 NO
101 ACTN2 ACTN2 ACTN2 13574 -0.086 0.11 NO
102 HIST2H2AB HIST2H2AB HIST2H2AB 14037 -0.1 0.094 NO
103 HIST1H4B HIST1H4B HIST1H4B 14327 -0.11 0.087 NO
104 C4A C4A C4A 14480 -0.12 0.087 NO
105 HIST1H2BH HIST1H2BH HIST1H2BH 14837 -0.14 0.077 NO
106 HIST4H4 HIST4H4 HIST4H4 14865 -0.14 0.086 NO
107 HIST1H4C HIST1H4C HIST1H4C 15443 -0.17 0.067 NO
108 HIST1H3C HIST1H3C HIST1H3C 15998 -0.21 0.052 NO
109 CTSG CTSG CTSG 16321 -0.24 0.052 NO
110 HIST1H4J HIST1H4J HIST1H4J 16585 -0.26 0.056 NO
111 HIST2H2AC HIST2H2AC HIST2H2AC 16833 -0.28 0.064 NO

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

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

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

Table S20.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 STAT4 STAT4 STAT4 39 0.63 0.18 YES
2 STAT5A STAT5A STAT5A 1254 0.22 0.18 YES
3 STAT1 STAT1 STAT1 1500 0.19 0.22 YES
4 PIK3R1 PIK3R1 PIK3R1 1846 0.17 0.26 YES
5 SHC1 SHC1 SHC1 2007 0.16 0.29 YES
6 MAPK8 MAPK8 MAPK8 2241 0.14 0.32 YES
7 MAP3K1 MAP3K1 MAP3K1 2259 0.14 0.36 YES
8 PRKCB PRKCB PRKCB 2465 0.13 0.39 YES
9 FOS FOS FOS 3012 0.11 0.39 YES
10 STAT6 STAT6 STAT6 4682 0.067 0.32 NO
11 MAPK3 MAPK3 MAPK3 4685 0.067 0.34 NO
12 STAT5B STAT5B STAT5B 5482 0.052 0.31 NO
13 RASA1 RASA1 RASA1 6308 0.038 0.28 NO
14 SOS1 SOS1 SOS1 6339 0.038 0.29 NO
15 STAT2 STAT2 STAT2 6570 0.034 0.28 NO
16 CSNK2A1 CSNK2A1 CSNK2A1 7064 0.027 0.26 NO
17 GRB2 GRB2 GRB2 7081 0.027 0.27 NO
18 SRF SRF SRF 9347 -0.0037 0.15 NO
19 STAT3 STAT3 STAT3 10477 -0.02 0.089 NO
20 MAP2K4 MAP2K4 MAP2K4 10746 -0.025 0.082 NO
21 ELK1 ELK1 ELK1 11151 -0.032 0.068 NO
22 PIK3CA PIK3CA PIK3CA 11547 -0.039 0.058 NO
23 PLCG1 PLCG1 PLCG1 11996 -0.048 0.047 NO
24 JUN JUN JUN 12397 -0.056 0.041 NO
25 JAK1 JAK1 JAK1 12745 -0.063 0.04 NO
26 MAP2K1 MAP2K1 MAP2K1 12783 -0.064 0.057 NO
27 RAF1 RAF1 RAF1 13027 -0.07 0.065 NO
28 PRKCA PRKCA PRKCA 14826 -0.14 0.0043 NO
29 EGF EGF EGF 15045 -0.15 0.036 NO
30 EGFR EGFR EGFR 17658 -0.43 0.018 NO

Figure S39.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TOLL 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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA NO1 PATHWAY 28 genes.ES.table 0.6 1.5 0.044 1 0.82 0.46 0.15 0.39 1 0.71
BIOCARTA INTEGRIN PATHWAY 37 genes.ES.table 0.39 1.4 0.12 1 0.89 0.6 0.35 0.39 0.99 0.5
BIOCARTA VEGF PATHWAY 28 genes.ES.table 0.47 1.5 0.11 1 0.86 0.18 0.078 0.16 1 0.59
KEGG PURINE METABOLISM 154 genes.ES.table 0.32 1.3 0.11 1 0.97 0.18 0.14 0.16 1 0.6
KEGG PYRIMIDINE METABOLISM 97 genes.ES.table 0.25 1.2 0.21 1 0.99 0.18 0.18 0.14 1 0.56
KEGG STARCH AND SUCROSE METABOLISM 27 genes.ES.table 0.53 1.4 0.12 1 0.94 0.41 0.18 0.33 1 0.55
KEGG DRUG METABOLISM OTHER ENZYMES 31 genes.ES.table 0.52 1.4 0.1 1 0.94 0.32 0.18 0.26 1 0.52
KEGG RIBOSOME 84 genes.ES.table 0.52 1.4 0.21 1 0.88 0.74 0.37 0.47 1 0.55
KEGG CALCIUM SIGNALING PATHWAY 168 genes.ES.table 0.42 1.2 0.14 1 0.98 0.29 0.13 0.26 1 0.57
KEGG VASCULAR SMOOTH MUSCLE CONTRACTION 103 genes.ES.table 0.48 1.4 0.054 1 0.89 0.29 0.14 0.25 0.88 0.44
genes ES table in pathway: BIOCARTA NO1 PATHWAY

Table S21.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 LFNG LFNG LFNG 170 0.42 0.077 YES
2 DLL4 DLL4 DLL4 378 0.35 0.14 YES
3 DLL1 DLL1 DLL1 567 0.3 0.19 YES
4 NOTCH3 NOTCH3 NOTCH3 652 0.29 0.24 YES
5 JAG2 JAG2 JAG2 876 0.25 0.28 YES
6 NOTCH4 NOTCH4 NOTCH4 1103 0.23 0.32 YES
7 NOTCH1 NOTCH1 NOTCH1 1106 0.22 0.36 YES
8 JAG1 JAG1 JAG1 1206 0.22 0.4 YES
9 PTCRA PTCRA PTCRA 1712 0.17 0.41 YES
10 HES1 HES1 HES1 2176 0.14 0.41 YES
11 MAML3 MAML3 MAML3 2229 0.14 0.44 YES
12 HDAC1 HDAC1 HDAC1 2682 0.11 0.43 YES
13 DTX2 DTX2 DTX2 2753 0.11 0.45 YES
14 HES5 HES5 HES5 3061 0.096 0.45 YES
15 DVL1 DVL1 DVL1 3312 0.088 0.46 YES
16 RBPJ RBPJ RBPJ 4002 0.067 0.43 NO
17 PSENEN PSENEN PSENEN 4286 0.06 0.43 NO
18 NOTCH2 NOTCH2 NOTCH2 4366 0.058 0.44 NO
19 DVL3 DVL3 DVL3 4573 0.053 0.44 NO
20 CTBP2 CTBP2 CTBP2 5952 0.027 0.37 NO
21 HDAC2 HDAC2 HDAC2 6096 0.025 0.36 NO
22 MAML1 MAML1 MAML1 6323 0.022 0.36 NO
23 EP300 EP300 EP300 6568 0.018 0.34 NO
24 NCSTN NCSTN NCSTN 6646 0.017 0.34 NO
25 DVL2 DVL2 DVL2 7061 0.012 0.32 NO
26 DTX3 DTX3 DTX3 7556 0.0055 0.3 NO
27 PSEN1 PSEN1 PSEN1 8757 -0.0094 0.23 NO
28 CTBP1 CTBP1 CTBP1 8899 -0.011 0.23 NO
29 PSEN2 PSEN2 PSEN2 9459 -0.018 0.2 NO
30 CREBBP CREBBP CREBBP 9542 -0.018 0.2 NO
31 APH1A APH1A APH1A 9763 -0.021 0.19 NO
32 RFNG RFNG RFNG 9864 -0.022 0.19 NO
33 SNW1 SNW1 SNW1 10176 -0.026 0.18 NO
34 NCOR2 NCOR2 NCOR2 10426 -0.029 0.17 NO
35 ADAM17 ADAM17 ADAM17 10586 -0.031 0.17 NO
36 DTX4 DTX4 DTX4 10882 -0.035 0.16 NO
37 DTX3L DTX3L DTX3L 11008 -0.037 0.16 NO
38 NUMB NUMB NUMB 11039 -0.037 0.16 NO
39 CIR1 CIR1 CIR1 11184 -0.039 0.16 NO
40 KAT2A KAT2A KAT2A 11808 -0.048 0.14 NO
41 NUMBL NUMBL NUMBL 12622 -0.059 0.11 NO
42 KAT2B KAT2B KAT2B 14822 -0.11 0.0052 NO
43 MAML2 MAML2 MAML2 16541 -0.19 -0.051 NO
44 DTX1 DTX1 DTX1 17395 -0.29 -0.04 NO
45 DLL3 DLL3 DLL3 17671 -0.35 0.017 NO

Figure S41.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA INTEGRIN PATHWAY

Table S22.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RYR2 RYR2 RYR2 128 0.44 0.1 YES
2 BDKRB2 BDKRB2 BDKRB2 202 0.41 0.2 YES
3 FLT4 FLT4 FLT4 593 0.3 0.25 YES
4 FLT1 FLT1 FLT1 844 0.26 0.3 YES
5 PDE2A PDE2A PDE2A 852 0.26 0.36 YES
6 KDR KDR KDR 980 0.24 0.41 YES
7 PDE3A PDE3A PDE3A 1128 0.22 0.46 YES
8 VEGFA VEGFA VEGFA 1339 0.2 0.5 YES
9 NOS3 NOS3 NOS3 1394 0.2 0.54 YES
10 PRKG1 PRKG1 PRKG1 1975 0.15 0.55 YES
11 CHRNA1 CHRNA1 CHRNA1 2072 0.15 0.58 YES
12 ACTA1 ACTA1 ACTA1 2398 0.13 0.59 YES
13 TNNI1 TNNI1 TNNI1 2749 0.11 0.6 YES
14 CHRM1 CHRM1 CHRM1 6904 0.014 0.37 NO
15 AKT1 AKT1 AKT1 8168 -0.0023 0.3 NO
16 PRKACB PRKACB PRKACB 9582 -0.019 0.22 NO
17 CALM3 CALM3 CALM3 10350 -0.028 0.19 NO
18 PDE3B PDE3B PDE3B 10736 -0.033 0.18 NO
19 PRKAR1A PRKAR1A PRKAR1A 10887 -0.035 0.18 NO
20 HSP90AA1 HSP90AA1 HSP90AA1 11302 -0.04 0.16 NO
21 CALM2 CALM2 CALM2 12676 -0.06 0.1 NO
22 PRKG2 PRKG2 PRKG2 12998 -0.066 0.099 NO
23 CALM1 CALM1 CALM1 13871 -0.083 0.071 NO
24 SLC7A1 SLC7A1 SLC7A1 13878 -0.083 0.091 NO
25 PRKAR1B PRKAR1B PRKAR1B 14570 -0.1 0.077 NO
26 PRKACG PRKACG PRKACG 14594 -0.1 0.1 NO
27 PRKAR2A PRKAR2A PRKAR2A 16189 -0.17 0.052 NO
28 PRKAR2B PRKAR2B PRKAR2B 16555 -0.19 0.079 NO

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

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA INTEGRIN 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 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 PGF PGF PGF 76 0.49 0.1 YES
2 EGFR EGFR EGFR 167 0.42 0.18 YES
3 MMP9 MMP9 MMP9 937 0.24 0.19 YES
4 MMP2 MMP2 MMP2 1078 0.23 0.23 YES
5 E2F2 E2F2 E2F2 1086 0.23 0.28 YES
6 MMP1 MMP1 MMP1 1088 0.23 0.33 YES
7 DAPK2 DAPK2 DAPK2 1219 0.21 0.37 YES
8 VEGFA VEGFA VEGFA 1339 0.2 0.4 YES
9 VEGFC VEGFC VEGFC 1576 0.18 0.43 YES
10 MYC MYC MYC 1680 0.17 0.46 YES
11 THBS1 THBS1 THBS1 1849 0.16 0.48 YES
12 NRAS NRAS NRAS 2307 0.13 0.49 YES
13 DAPK1 DAPK1 DAPK1 2465 0.12 0.5 YES
14 TYMP TYMP TYMP 2735 0.11 0.51 YES
15 FGFR3 FGFR3 FGFR3 2969 0.1 0.52 YES
16 TP53 TP53 TP53 3054 0.096 0.54 YES
17 DAPK3 DAPK3 DAPK3 3980 0.068 0.5 NO
18 RASSF1 RASSF1 RASSF1 4261 0.061 0.5 NO
19 ARAF ARAF ARAF 4329 0.059 0.5 NO
20 RAF1 RAF1 RAF1 4794 0.048 0.49 NO
21 ERBB2 ERBB2 ERBB2 5090 0.042 0.48 NO
22 MAP2K2 MAP2K2 MAP2K2 5991 0.027 0.44 NO
23 CDKN1A CDKN1A CDKN1A 6229 0.023 0.43 NO
24 RB1 RB1 RB1 6880 0.014 0.4 NO
25 EGF EGF EGF 7030 0.012 0.39 NO
26 MAP2K1 MAP2K1 MAP2K1 7073 0.012 0.39 NO
27 MDM2 MDM2 MDM2 7442 0.0069 0.37 NO
28 CDK4 CDK4 CDK4 8437 -0.0054 0.32 NO
29 MAPK1 MAPK1 MAPK1 8606 -0.0075 0.31 NO
30 KRAS KRAS KRAS 9144 -0.014 0.28 NO
31 CDH1 CDH1 CDH1 9433 -0.017 0.27 NO
32 CCND1 CCND1 CCND1 10291 -0.027 0.23 NO
33 CDKN2A CDKN2A CDKN2A 10592 -0.032 0.22 NO
34 IL8 IL8 IL8 10639 -0.032 0.22 NO
35 VEGFB VEGFB VEGFB 11708 -0.046 0.17 NO
36 HRAS HRAS HRAS 12816 -0.062 0.12 NO
37 MAPK3 MAPK3 MAPK3 13077 -0.067 0.12 NO
38 RPS6KA5 RPS6KA5 RPS6KA5 14326 -0.093 0.073 NO
39 BRAF BRAF BRAF 14987 -0.11 0.06 NO
40 E2F3 E2F3 E2F3 16284 -0.17 0.024 NO
41 FIGF FIGF FIGF 17608 -0.33 0.02 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 VEGF PATHWAY.

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

genes ES table in pathway: KEGG PURINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FLT4 FLT4 FLT4 593 0.3 0.1 YES
2 FLT1 FLT1 FLT1 844 0.26 0.21 YES
3 KDR KDR KDR 980 0.24 0.31 YES
4 VEGFA VEGFA VEGFA 1339 0.2 0.38 YES
5 NOS3 NOS3 NOS3 1394 0.2 0.47 YES
6 PTK2 PTK2 PTK2 3996 0.067 0.36 NO
7 EIF2B5 EIF2B5 EIF2B5 5657 0.032 0.28 NO
8 EIF1 EIF1 EIF1 6111 0.025 0.27 NO
9 PXN PXN PXN 6181 0.024 0.27 NO
10 PLCG1 PLCG1 PLCG1 6730 0.016 0.25 NO
11 ARNT ARNT ARNT 7201 0.01 0.23 NO
12 EIF2B3 EIF2B3 EIF2B3 7511 0.0061 0.22 NO
13 PIK3CG PIK3CG PIK3CG 7568 0.0054 0.21 NO
14 PIK3CA PIK3CA PIK3CA 7683 0.0038 0.21 NO
15 ELAVL1 ELAVL1 ELAVL1 7727 0.0032 0.21 NO
16 HIF1A HIF1A HIF1A 8428 -0.0054 0.17 NO
17 EIF2S3 EIF2S3 EIF2S3 8665 -0.0083 0.16 NO
18 EIF2B1 EIF2B1 EIF2B1 8788 -0.0098 0.16 NO
19 EIF2S2 EIF2S2 EIF2S2 9101 -0.013 0.15 NO
20 EIF1AX EIF1AX EIF1AX 9627 -0.02 0.13 NO
21 EIF2S1 EIF2S1 EIF2S1 9800 -0.022 0.13 NO
22 EIF2B4 EIF2B4 EIF2B4 9890 -0.022 0.13 NO
23 SHC1 SHC1 SHC1 11576 -0.044 0.061 NO
24 EIF2B2 EIF2B2 EIF2B2 12126 -0.052 0.054 NO
25 PRKCA PRKCA PRKCA 12730 -0.061 0.049 NO
26 PIK3R1 PIK3R1 PIK3R1 13332 -0.072 0.048 NO
27 VHL VHL VHL 15027 -0.11 0.0066 NO
28 PRKCB PRKCB PRKCB 17634 -0.34 0.019 NO

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

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

genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

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 RPLP0 RPLP0 RPLP0 2939 0.1 -0.13 YES
2 RPS8 RPS8 RPS8 3270 0.089 -0.12 YES
3 RPL21 RPL21 RPL21 3289 0.089 -0.09 YES
4 RPS19 RPS19 RPS19 3340 0.087 -0.063 YES
5 RPL11 RPL11 RPL11 3359 0.086 -0.035 YES
6 RPL39 RPL39 RPL39 3415 0.084 -0.0097 YES
7 RPL5 RPL5 RPL5 3420 0.084 0.018 YES
8 RPS2 RPS2 RPS2 3651 0.077 0.032 YES
9 RPL35A RPL35A RPL35A 3872 0.071 0.043 YES
10 RPL12 RPL12 RPL12 3989 0.068 0.06 YES
11 RPL22L1 RPL22L1 RPL22L1 4067 0.065 0.077 YES
12 RPL24 RPL24 RPL24 4136 0.064 0.095 YES
13 RPS9 RPS9 RPS9 4220 0.062 0.11 YES
14 RPL10 RPL10 RPL10 4446 0.056 0.12 YES
15 RPL22 RPL22 RPL22 4603 0.052 0.13 YES
16 RPS5 RPS5 RPS5 4633 0.052 0.14 YES
17 RPL8 RPL8 RPL8 4651 0.051 0.16 YES
18 RPL3 RPL3 RPL3 4652 0.051 0.18 YES
19 RPL17 RPL17 RPL17 4728 0.05 0.19 YES
20 RPL9 RPL9 RPL9 4815 0.048 0.2 YES
21 RPLP1 RPLP1 RPLP1 4909 0.046 0.21 YES
22 RPL18A RPL18A RPL18A 4924 0.046 0.22 YES
23 RPL23A RPL23A RPL23A 5187 0.04 0.22 YES
24 RPS16 RPS16 RPS16 5189 0.04 0.24 YES
25 RPL19 RPL19 RPL19 5201 0.04 0.25 YES
26 RPL26 RPL26 RPL26 5228 0.04 0.26 YES
27 RPS4Y1 RPS4Y1 RPS4Y1 5259 0.039 0.27 YES
28 RPL13A RPL13A RPL13A 5315 0.038 0.28 YES
29 RPL4 RPL4 RPL4 5349 0.038 0.3 YES
30 RPL30 RPL30 RPL30 5353 0.038 0.31 YES
31 RPL28 RPL28 RPL28 5356 0.038 0.32 YES
32 RPS20 RPS20 RPS20 5402 0.037 0.33 YES
33 RPS7 RPS7 RPS7 5418 0.036 0.34 YES
34 RPS6 RPS6 RPS6 5489 0.035 0.35 YES
35 RPL13 RPL13 RPL13 5502 0.035 0.36 YES
36 RPS12 RPS12 RPS12 5518 0.035 0.37 YES
37 RPS27 RPS27 RPS27 5527 0.035 0.38 YES
38 RPS11 RPS11 RPS11 5634 0.033 0.39 YES
39 RPL7A RPL7A RPL7A 5663 0.032 0.4 YES
40 RPL6 RPL6 RPL6 5691 0.032 0.41 YES
41 RPL37A RPL37A RPL37A 5724 0.031 0.42 YES
42 RPL23 RPL23 RPL23 5743 0.03 0.42 YES
43 RPL37 RPL37 RPL37 5746 0.03 0.43 YES
44 RPS17 RPS17 RPS17 5771 0.03 0.44 YES
45 UBA52 UBA52 UBA52 5813 0.029 0.45 YES
46 RPL35 RPL35 RPL35 5867 0.029 0.46 YES
47 RPL31 RPL31 RPL31 6091 0.025 0.45 YES
48 RPS10 RPS10 RPS10 6123 0.025 0.46 YES
49 RPS15 RPS15 RPS15 6218 0.023 0.46 YES
50 RPS15A RPS15A RPS15A 6286 0.022 0.47 YES
51 RPL27 RPL27 RPL27 6317 0.022 0.47 YES
52 RPL36 RPL36 RPL36 6326 0.022 0.48 YES
53 FAU FAU FAU 6352 0.021 0.48 YES
54 RPS21 RPS21 RPS21 6474 0.019 0.48 YES
55 RPL27A RPL27A RPL27A 6503 0.019 0.49 YES
56 RPL10A RPL10A RPL10A 6520 0.018 0.49 YES
57 RPS18 RPS18 RPS18 6522 0.018 0.5 YES
58 RPL38 RPL38 RPL38 6551 0.018 0.5 YES
59 RPL41 RPL41 RPL41 6563 0.018 0.51 YES
60 RPS4X RPS4X RPS4X 6570 0.018 0.52 YES
61 RPS27L RPS27L RPS27L 6609 0.017 0.52 YES
62 RPL29 RPL29 RPL29 6657 0.017 0.52 YES
63 RPS27A RPS27A RPS27A 6768 0.015 0.52 NO
64 RPL14 RPL14 RPL14 7022 0.012 0.51 NO
65 RPS23 RPS23 RPS23 7116 0.011 0.51 NO
66 RPL34 RPL34 RPL34 7130 0.011 0.51 NO
67 RPS3 RPS3 RPS3 7288 0.009 0.51 NO
68 RPLP2 RPLP2 RPLP2 7328 0.0085 0.51 NO
69 RPS3A RPS3A RPS3A 7366 0.0079 0.51 NO
70 RPS24 RPS24 RPS24 7424 0.0071 0.51 NO
71 RPS28 RPS28 RPS28 7654 0.0042 0.5 NO
72 RPL32 RPL32 RPL32 8051 -0.00091 0.48 NO
73 RPL7 RPL7 RPL7 8104 -0.0016 0.47 NO
74 MRPL13 MRPL13 MRPL13 8283 -0.0037 0.46 NO
75 RPL15 RPL15 RPL15 8303 -0.0039 0.46 NO
76 RPS29 RPS29 RPS29 8432 -0.0054 0.46 NO
77 RPSA RPSA RPSA 8924 -0.011 0.44 NO
78 RSL24D1 RSL24D1 RSL24D1 9127 -0.014 0.43 NO
79 RPS26 RPS26 RPS26 9590 -0.019 0.41 NO
80 RPS25 RPS25 RPS25 9624 -0.019 0.41 NO
81 RPL36AL RPL36AL RPL36AL 11019 -0.037 0.35 NO
82 RPS13 RPS13 RPS13 11203 -0.039 0.35 NO
83 RPL36A RPL36A RPL36A 11259 -0.04 0.36 NO
84 RPL26L1 RPL26L1 RPL26L1 11366 -0.041 0.37 NO

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

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

genes ES table in pathway: KEGG STARCH AND SUCROSE METABOLISM

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 CAV1 CAV1 CAV1 700 0.28 0.087 YES
2 ZYX ZYX ZYX 1761 0.16 0.1 YES
3 FYN FYN FYN 1906 0.16 0.16 YES
4 ACTA1 ACTA1 ACTA1 2398 0.13 0.2 YES
5 TNS1 TNS1 TNS1 2991 0.099 0.21 YES
6 ACTN2 ACTN2 ACTN2 3159 0.093 0.24 YES
7 RAP1A RAP1A RAP1A 3206 0.091 0.28 YES
8 ACTN3 ACTN3 ACTN3 3579 0.079 0.29 YES
9 PTK2 PTK2 PTK2 3996 0.067 0.3 YES
10 RAPGEF1 RAPGEF1 RAPGEF1 4069 0.065 0.33 YES
11 ITGA1 ITGA1 ITGA1 4581 0.053 0.32 YES
12 RAF1 RAF1 RAF1 4794 0.048 0.33 YES
13 BCAR1 BCAR1 BCAR1 5198 0.04 0.33 YES
14 VCL VCL VCL 5267 0.039 0.34 YES
15 CSK CSK CSK 5304 0.038 0.36 YES
16 JUN JUN JUN 5461 0.036 0.36 YES
17 ITGB1 ITGB1 ITGB1 5879 0.028 0.35 YES
18 MAP2K2 MAP2K2 MAP2K2 5991 0.027 0.36 YES
19 CRKL CRKL CRKL 6018 0.026 0.37 YES
20 PXN PXN PXN 6181 0.024 0.37 YES
21 RHOA RHOA RHOA 6209 0.023 0.38 YES
22 BCR BCR BCR 6292 0.022 0.39 YES
23 CAPNS1 CAPNS1 CAPNS1 6788 0.015 0.37 NO
24 MAP2K1 MAP2K1 MAP2K1 7073 0.012 0.36 NO
25 PPP1R12B PPP1R12B PPP1R12B 7763 0.0028 0.32 NO
26 CAPN1 CAPN1 CAPN1 8159 -0.0022 0.3 NO
27 MAPK1 MAPK1 MAPK1 8606 -0.0075 0.28 NO
28 ROCK1 ROCK1 ROCK1 8923 -0.011 0.26 NO
29 SOS1 SOS1 SOS1 9606 -0.019 0.23 NO
30 GRB2 GRB2 GRB2 10496 -0.03 0.2 NO
31 ACTN1 ACTN1 ACTN1 10809 -0.034 0.2 NO
32 SHC1 SHC1 SHC1 11576 -0.044 0.17 NO
33 HRAS HRAS HRAS 12816 -0.062 0.13 NO
34 MAPK3 MAPK3 MAPK3 13077 -0.067 0.15 NO
35 SRC SRC SRC 13394 -0.073 0.16 NO
36 CAPNS2 CAPNS2 CAPNS2 13840 -0.082 0.18 NO
37 MAPK8 MAPK8 MAPK8 15250 -0.12 0.15 NO

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

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

genes ES table in pathway: KEGG DRUG METABOLISM OTHER ENZYMES

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 MYLK3 MYLK3 MYLK3 2 0.71 0.054 YES
2 ADRA1B ADRA1B ADRA1B 38 0.55 0.093 YES
3 ADORA2A ADORA2A ADORA2A 111 0.46 0.12 YES
4 KCNMB1 KCNMB1 KCNMB1 162 0.42 0.15 YES
5 NPR1 NPR1 NPR1 344 0.36 0.17 YES
6 MYLK2 MYLK2 MYLK2 400 0.34 0.19 YES
7 EDNRA EDNRA EDNRA 415 0.34 0.22 YES
8 PRKCH PRKCH PRKCH 473 0.32 0.24 YES
9 MRVI1 MRVI1 MRVI1 481 0.32 0.26 YES
10 GUCY1A2 GUCY1A2 GUCY1A2 496 0.32 0.29 YES
11 CYP4A11 CYP4A11 CYP4A11 560 0.3 0.31 YES
12 RAMP2 RAMP2 RAMP2 568 0.3 0.33 YES
13 ADCY4 ADCY4 ADCY4 651 0.29 0.34 YES
14 PPP1R14A PPP1R14A PPP1R14A 705 0.28 0.36 YES
15 CALCRL CALCRL CALCRL 711 0.28 0.38 YES
16 RAMP3 RAMP3 RAMP3 858 0.25 0.4 YES
17 ADORA2B ADORA2B ADORA2B 1085 0.23 0.4 YES
18 ACTG2 ACTG2 ACTG2 1134 0.22 0.41 YES
19 ADCY1 ADCY1 ADCY1 1179 0.22 0.43 YES
20 MYH11 MYH11 MYH11 1265 0.21 0.44 YES
21 ACTA2 ACTA2 ACTA2 1582 0.18 0.43 YES
22 MYL9 MYL9 MYL9 1611 0.18 0.45 YES
23 MYLK MYLK MYLK 1791 0.16 0.45 YES
24 CALML6 CALML6 CALML6 1829 0.16 0.46 YES
25 PRKG1 PRKG1 PRKG1 1975 0.15 0.46 YES
26 CACNA1C CACNA1C CACNA1C 2050 0.15 0.47 YES
27 ADCY5 ADCY5 ADCY5 2097 0.14 0.48 YES
28 GNAS GNAS GNAS 2279 0.13 0.48 YES
29 KCNMB3 KCNMB3 KCNMB3 2520 0.12 0.47 YES
30 PLA2G4A PLA2G4A PLA2G4A 2527 0.12 0.48 YES
31 PLA2G6 PLA2G6 PLA2G6 3155 0.093 0.45 NO
32 MYL6 MYL6 MYL6 3800 0.073 0.42 NO
33 PLA2G5 PLA2G5 PLA2G5 3858 0.071 0.42 NO
34 ADRA1D ADRA1D ADRA1D 3947 0.069 0.43 NO
35 AVPR1A AVPR1A AVPR1A 3990 0.068 0.43 NO
36 ADCY2 ADCY2 ADCY2 4011 0.067 0.43 NO
37 GUCY1A3 GUCY1A3 GUCY1A3 4065 0.065 0.43 NO
38 ARAF ARAF ARAF 4329 0.059 0.42 NO
39 ARHGEF1 ARHGEF1 ARHGEF1 4359 0.058 0.43 NO
40 PLA2G10 PLA2G10 PLA2G10 4667 0.051 0.41 NO
41 RAF1 RAF1 RAF1 4794 0.048 0.41 NO
42 CALD1 CALD1 CALD1 4877 0.047 0.41 NO
43 CACNA1F CACNA1F CACNA1F 4903 0.046 0.41 NO
44 PLCB2 PLCB2 PLCB2 5185 0.04 0.4 NO
45 ADCY8 ADCY8 ADCY8 5681 0.032 0.37 NO
46 ADCY7 ADCY7 ADCY7 5721 0.031 0.37 NO
47 MAP2K2 MAP2K2 MAP2K2 5991 0.027 0.36 NO
48 PPP1CA PPP1CA PPP1CA 6088 0.025 0.36 NO
49 ADRA1A ADRA1A ADRA1A 6179 0.024 0.35 NO
50 RHOA RHOA RHOA 6209 0.023 0.35 NO
51 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 6211 0.023 0.36 NO
52 KCNMA1 KCNMA1 KCNMA1 6347 0.022 0.35 NO
53 GUCY1B3 GUCY1B3 GUCY1B3 6744 0.016 0.33 NO
54 RAMP1 RAMP1 RAMP1 6886 0.014 0.32 NO
55 MAP2K1 MAP2K1 MAP2K1 7073 0.012 0.31 NO
56 PPP1R12B PPP1R12B PPP1R12B 7763 0.0028 0.27 NO
57 AGTR1 AGTR1 AGTR1 7865 0.0014 0.27 NO
58 ARHGEF12 ARHGEF12 ARHGEF12 8152 -0.0021 0.25 NO
59 PPP1CC PPP1CC PPP1CC 8231 -0.0031 0.25 NO
60 PPP1R12A PPP1R12A PPP1R12A 8450 -0.0055 0.24 NO
61 MAPK1 MAPK1 MAPK1 8606 -0.0075 0.23 NO
62 PLA2G2A PLA2G2A PLA2G2A 8624 -0.0078 0.23 NO
63 GNA12 GNA12 GNA12 8902 -0.011 0.21 NO
64 ROCK1 ROCK1 ROCK1 8923 -0.011 0.21 NO
65 PRKACA PRKACA PRKACA 9045 -0.013 0.21 NO
66 PPP1CB PPP1CB PPP1CB 9084 -0.013 0.21 NO
67 PRKACB PRKACB PRKACB 9582 -0.019 0.18 NO
68 ITPR1 ITPR1 ITPR1 9621 -0.019 0.18 NO
69 CALM3 CALM3 CALM3 10350 -0.028 0.14 NO
70 ADCY6 ADCY6 ADCY6 10728 -0.033 0.12 NO
71 MYL6B MYL6B MYL6B 11153 -0.039 0.1 NO
72 ROCK2 ROCK2 ROCK2 11660 -0.045 0.076 NO
73 ARHGEF11 ARHGEF11 ARHGEF11 12027 -0.05 0.06 NO
74 PLCB4 PLCB4 PLCB4 12031 -0.05 0.063 NO
75 PLCB3 PLCB3 PLCB3 12165 -0.053 0.06 NO
76 CALM2 CALM2 CALM2 12676 -0.06 0.036 NO
77 PRKCA PRKCA PRKCA 12730 -0.061 0.037 NO
78 NPR2 NPR2 NPR2 12747 -0.061 0.041 NO
79 GNA11 GNA11 GNA11 12759 -0.061 0.045 NO
80 GNA13 GNA13 GNA13 12809 -0.062 0.047 NO
81 PRKX PRKX PRKX 12994 -0.065 0.042 NO
82 MAPK3 MAPK3 MAPK3 13077 -0.067 0.042 NO
83 GNAQ GNAQ GNAQ 13417 -0.074 0.029 NO
84 CACNA1D CACNA1D CACNA1D 13727 -0.08 0.018 NO
85 CALM1 CALM1 CALM1 13871 -0.083 0.016 NO
86 CACNA1S CACNA1S CACNA1S 14197 -0.09 0.0044 NO
87 PTGIR PTGIR PTGIR 14465 -0.097 -0.0033 NO
88 PLA2G12A PLA2G12A PLA2G12A 14487 -0.097 0.0029 NO
89 PRKACG PRKACG PRKACG 14594 -0.1 0.0045 NO
90 ADCY9 ADCY9 ADCY9 14620 -0.1 0.011 NO
91 PRKCD PRKCD PRKCD 14756 -0.1 0.011 NO
92 ITPR3 ITPR3 ITPR3 14769 -0.11 0.018 NO
93 BRAF BRAF BRAF 14987 -0.11 0.015 NO
94 KCNMB2 KCNMB2 KCNMB2 15557 -0.13 -0.007 NO
95 PRKCG PRKCG PRKCG 15632 -0.14 -0.00085 NO
96 ITPR2 ITPR2 ITPR2 15833 -0.15 -0.00097 NO
97 KCNMB4 KCNMB4 KCNMB4 15930 -0.15 0.0051 NO
98 PLA2G1B PLA2G1B PLA2G1B 16445 -0.18 -0.0097 NO
99 PRKCE PRKCE PRKCE 16575 -0.19 -0.0023 NO
100 PLCB1 PLCB1 PLCB1 16768 -0.21 0.0029 NO
101 PLA2G2D PLA2G2D PLA2G2D 16845 -0.22 0.015 NO
102 PRKCQ PRKCQ PRKCQ 17448 -0.3 0.0037 NO
103 PRKCB PRKCB PRKCB 17634 -0.34 0.019 NO

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

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

genes ES table in pathway: KEGG RIBOSOME

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 HK2 HK2 HK2 14 0.64 0.21 YES
2 GCK GCK GCK 420 0.34 0.3 YES
3 PYGM PYGM PYGM 1386 0.2 0.31 YES
4 HK3 HK3 HK3 1506 0.19 0.36 YES
5 G6PC2 G6PC2 G6PC2 1837 0.16 0.4 YES
6 AMY2B AMY2B AMY2B 2409 0.13 0.41 YES
7 AMY1A AMY1A AMY1A 2423 0.13 0.45 YES
8 PGM2L1 PGM2L1 PGM2L1 2558 0.12 0.48 YES
9 GYS1 GYS1 GYS1 2926 0.1 0.49 YES
10 PGM2 PGM2 PGM2 3202 0.091 0.51 YES
11 GUSB GUSB GUSB 3298 0.088 0.53 YES
12 MGAM MGAM MGAM 4498 0.055 0.48 NO
13 AGL AGL AGL 4895 0.046 0.47 NO
14 UGDH UGDH UGDH 5590 0.034 0.45 NO
15 PGM1 PGM1 PGM1 6152 0.024 0.42 NO
16 GPI GPI GPI 6207 0.023 0.43 NO
17 GAA GAA GAA 7315 0.0087 0.37 NO
18 HK1 HK1 HK1 7496 0.0063 0.36 NO
19 PYGL PYGL PYGL 7846 0.0016 0.34 NO
20 PYGB PYGB PYGB 8912 -0.011 0.29 NO
21 AMY2A AMY2A AMY2A 8972 -0.012 0.29 NO
22 GBE1 GBE1 GBE1 10800 -0.034 0.2 NO
23 UGP2 UGP2 UGP2 10825 -0.034 0.21 NO
24 GYS2 GYS2 GYS2 14705 -0.1 0.024 NO
25 ENPP1 ENPP1 ENPP1 14757 -0.1 0.056 NO
26 GANC GANC GANC 15301 -0.12 0.066 NO
27 ENPP3 ENPP3 ENPP3 17176 -0.25 0.045 NO

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

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

genes ES table in pathway: KEGG CALCIUM SIGNALING 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 CDA CDA CDA 52 0.52 0.15 YES
2 UPB1 UPB1 UPB1 61 0.51 0.3 YES
3 UPP2 UPP2 UPP2 549 0.31 0.36 YES
4 TK1 TK1 TK1 569 0.3 0.44 YES
5 NAT1 NAT1 NAT1 1204 0.22 0.47 YES
6 NAT2 NAT2 NAT2 1707 0.17 0.49 YES
7 TYMP TYMP TYMP 2735 0.11 0.47 YES
8 IMPDH1 IMPDH1 IMPDH1 2827 0.11 0.49 YES
9 DPYD DPYD DPYD 3283 0.089 0.49 YES
10 GUSB GUSB GUSB 3298 0.088 0.52 YES
11 CYP3A43 CYP3A43 CYP3A43 4386 0.058 0.47 NO
12 UCK2 UCK2 UCK2 4631 0.052 0.48 NO
13 UMPS UMPS UMPS 5759 0.03 0.42 NO
14 CYP2A7 CYP2A7 CYP2A7 6001 0.026 0.42 NO
15 CYP3A5 CYP3A5 CYP3A5 6159 0.024 0.41 NO
16 ITPA ITPA ITPA 6840 0.014 0.38 NO
17 CYP3A7 CYP3A7 CYP3A7 7117 0.011 0.37 NO
18 UCK1 UCK1 UCK1 7448 0.0068 0.35 NO
19 UCKL1 UCKL1 UCKL1 7798 0.0024 0.33 NO
20 CYP2A6 CYP2A6 CYP2A6 8759 -0.0094 0.28 NO
21 IMPDH2 IMPDH2 IMPDH2 8876 -0.011 0.28 NO
22 GMPS GMPS GMPS 9476 -0.018 0.25 NO
23 UPP1 UPP1 UPP1 9587 -0.019 0.25 NO
24 HPRT1 HPRT1 HPRT1 10587 -0.031 0.2 NO
25 CES7 CES7 CES7 11900 -0.049 0.14 NO
26 CES2 CES2 CES2 12803 -0.062 0.11 NO
27 TK2 TK2 TK2 12895 -0.064 0.13 NO
28 DPYS DPYS DPYS 12926 -0.064 0.14 NO
29 TPMT TPMT TPMT 14825 -0.11 0.068 NO
30 CES1 CES1 CES1 15535 -0.13 0.067 NO
31 XDH XDH XDH 17040 -0.24 0.052 NO

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

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CALCIUM 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 VASCULAR SMOOTH MUSCLE CONTRACTION

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 PGF PGF PGF 76 0.49 0.073 YES
2 SLC2A1 SLC2A1 SLC2A1 341 0.36 0.12 YES
3 EGLN3 EGLN3 EGLN3 383 0.35 0.17 YES
4 PDGFB PDGFB PDGFB 866 0.25 0.18 YES
5 TGFB2 TGFB2 TGFB2 1015 0.23 0.21 YES
6 ETS1 ETS1 ETS1 1272 0.21 0.23 YES
7 EPAS1 EPAS1 EPAS1 1319 0.2 0.26 YES
8 VEGFA VEGFA VEGFA 1339 0.2 0.29 YES
9 VEGFC VEGFC VEGFC 1576 0.18 0.3 YES
10 MET MET MET 2040 0.15 0.3 YES
11 PIK3R3 PIK3R3 PIK3R3 2210 0.14 0.31 YES
12 NRAS NRAS NRAS 2307 0.13 0.33 YES
13 HGF HGF HGF 2348 0.13 0.35 YES
14 CRK CRK CRK 2402 0.13 0.36 YES
15 CDC42 CDC42 CDC42 3142 0.093 0.34 NO
16 RAP1A RAP1A RAP1A 3206 0.091 0.35 NO
17 TGFB3 TGFB3 TGFB3 3250 0.09 0.36 NO
18 PIK3CD PIK3CD PIK3CD 3657 0.076 0.35 NO
19 TGFB1 TGFB1 TGFB1 3823 0.072 0.35 NO
20 RAPGEF1 RAPGEF1 RAPGEF1 4069 0.065 0.35 NO
21 ARAF ARAF ARAF 4329 0.059 0.34 NO
22 RBX1 RBX1 RBX1 4528 0.054 0.34 NO
23 RAF1 RAF1 RAF1 4794 0.048 0.34 NO
24 PIK3R5 PIK3R5 PIK3R5 5034 0.044 0.33 NO
25 RAP1B RAP1B RAP1B 5227 0.04 0.32 NO
26 JUN JUN JUN 5461 0.036 0.32 NO
27 PAK2 PAK2 PAK2 5545 0.034 0.32 NO
28 RAC1 RAC1 RAC1 5635 0.033 0.32 NO
29 EGLN2 EGLN2 EGLN2 5741 0.031 0.32 NO
30 MAP2K2 MAP2K2 MAP2K2 5991 0.027 0.31 NO
31 CRKL CRKL CRKL 6018 0.026 0.31 NO
32 EP300 EP300 EP300 6568 0.018 0.28 NO
33 TGFA TGFA TGFA 6794 0.015 0.27 NO
34 AKT2 AKT2 AKT2 6822 0.015 0.27 NO
35 MAP2K1 MAP2K1 MAP2K1 7073 0.012 0.26 NO
36 TCEB2 TCEB2 TCEB2 7094 0.011 0.26 NO
37 ARNT ARNT ARNT 7201 0.01 0.26 NO
38 PIK3CG PIK3CG PIK3CG 7568 0.0054 0.24 NO
39 GAB1 GAB1 GAB1 7602 0.0048 0.24 NO
40 PIK3CA PIK3CA PIK3CA 7683 0.0038 0.23 NO
41 PAK4 PAK4 PAK4 7934 0.00052 0.22 NO
42 TCEB1 TCEB1 TCEB1 8134 -0.0019 0.21 NO
43 AKT1 AKT1 AKT1 8168 -0.0023 0.21 NO
44 HIF1A HIF1A HIF1A 8428 -0.0054 0.19 NO
45 PIK3R2 PIK3R2 PIK3R2 8511 -0.0062 0.19 NO
46 MAPK1 MAPK1 MAPK1 8606 -0.0075 0.18 NO
47 EGLN1 EGLN1 EGLN1 8644 -0.0079 0.18 NO
48 KRAS KRAS KRAS 9144 -0.014 0.16 NO
49 CREBBP CREBBP CREBBP 9542 -0.018 0.14 NO
50 SOS1 SOS1 SOS1 9606 -0.019 0.14 NO
51 GRB2 GRB2 GRB2 10496 -0.03 0.093 NO
52 PIK3CB PIK3CB PIK3CB 10570 -0.031 0.094 NO
53 FLCN FLCN FLCN 10842 -0.035 0.084 NO
54 SOS2 SOS2 SOS2 11591 -0.044 0.05 NO
55 VEGFB VEGFB VEGFB 11708 -0.046 0.05 NO
56 PTPN11 PTPN11 PTPN11 12818 -0.062 -0.0017 NO
57 FH FH FH 12930 -0.064 0.0023 NO
58 CUL2 CUL2 CUL2 12982 -0.065 0.0097 NO
59 AKT3 AKT3 AKT3 13025 -0.066 0.018 NO
60 MAPK3 MAPK3 MAPK3 13077 -0.067 0.026 NO
61 PIK3R1 PIK3R1 PIK3R1 13332 -0.072 0.023 NO
62 PAK6 PAK6 PAK6 13891 -0.083 0.0047 NO
63 PAK1 PAK1 PAK1 14573 -0.1 -0.018 NO
64 BRAF BRAF BRAF 14987 -0.11 -0.023 NO
65 VHL VHL VHL 15027 -0.11 -0.007 NO
66 PAK3 PAK3 PAK3 15870 -0.15 -0.031 NO
67 ARNT2 ARNT2 ARNT2 16616 -0.2 -0.041 NO
68 FIGF FIGF FIGF 17608 -0.33 -0.044 NO
69 PAK7 PAK7 PAK7 17806 -0.41 0.0095 NO

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

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VASCULAR SMOOTH MUSCLE CONTRACTION, 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
BIOCARTA NO1 PATHWAY 28 genes.ES.table 0.21 0.52 1 0.98 1 0.11 0.13 0.093 0.98 0.25
BIOCARTA ALK PATHWAY 34 genes.ES.table 0.51 1.3 0.13 0.21 0.95 0.35 0.19 0.28 0.16 0.006
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.5 1.3 0.18 0.22 0.95 0.36 0.28 0.26 0.17 0.005
BIOCARTA ERK PATHWAY 26 genes.ES.table 0.59 1.7 0.016 0.091 0.42 0.23 0.12 0.2 0 0.003
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.49 1.3 0.2 0.22 0.96 0.32 0.24 0.24 0.17 0.003
BIOCARTA FMLP PATHWAY 34 genes.ES.table 0.52 1.5 0.049 0.13 0.77 0.24 0.16 0.2 0.08 0.002
BIOCARTA GH PATHWAY 26 genes.ES.table 0.54 1.5 0.025 0.13 0.79 0.19 0.081 0.18 0.086 0.003
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.34 1.3 0.18 0.21 0.94 0.28 0.26 0.21 0.15 0.006
BIOCARTA MPR PATHWAY 32 genes.ES.table 0.58 1.9 0.002 0.096 0.083 0.16 0.097 0.14 0 0.031
BIOCARTA IL2RB PATHWAY 37 genes.ES.table 0.61 1.5 0.083 0.13 0.8 0.49 0.23 0.38 0.082 0.003
genes ES table in pathway: BIOCARTA NO1 PATHWAY

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 AOX1 AOX1 AOX1 55 1.4 0.17 YES
2 ACADS ACADS ACADS 1101 0.41 0.17 YES
3 ALDH3A2 ALDH3A2 ALDH3A2 1115 0.41 0.22 YES
4 ACAT2 ACAT2 ACAT2 1167 0.4 0.27 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 0.34 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 0.46 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 0.53 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 0.6 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 0.69 YES
27 DLD DLD DLD 4839 0.086 0.65 NO
28 ECHS1 ECHS1 ECHS1 5231 0.076 0.64 NO
29 ALDH9A1 ALDH9A1 ALDH9A1 5310 0.074 0.64 NO
30 HSD17B10 HSD17B10 HSD17B10 5374 0.072 0.65 NO
31 BCKDHA BCKDHA BCKDHA 5513 0.068 0.65 NO
32 ACAA2 ACAA2 ACAA2 5674 0.063 0.65 NO
33 ACAD8 ACAD8 ACAD8 6183 0.052 0.63 NO
34 IVD IVD IVD 6625 0.043 0.61 NO
35 EHHADH EHHADH EHHADH 6798 0.04 0.6 NO
36 HADHA HADHA HADHA 7303 0.03 0.58 NO
37 HADH HADH HADH 7660 0.024 0.56 NO
38 BCKDHB BCKDHB BCKDHB 9066 0.0021 0.48 NO
39 ACADSB ACADSB ACADSB 9178 0.00045 0.48 NO
40 OXCT1 OXCT1 OXCT1 9407 -0.0029 0.46 NO
41 MUT MUT MUT 9629 -0.006 0.45 NO
42 ABAT ABAT ABAT 14428 -0.088 0.2 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: BIOCARTA NO1 PATHWAY.

Figure S62.  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 ALK PATHWAY

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 AKR1B1 AKR1B1 AKR1B1 933 0.44 0.03 YES
2 ALDH3A2 ALDH3A2 ALDH3A2 1115 0.41 0.095 YES
3 ACAT2 ACAT2 ACAT2 1167 0.4 0.17 YES
4 PCK1 PCK1 PCK1 1400 0.35 0.22 YES
5 ACSS2 ACSS2 ACSS2 1632 0.32 0.26 YES
6 ACSS1 ACSS1 ACSS1 1691 0.31 0.32 YES
7 ALDH2 ALDH2 ALDH2 2210 0.25 0.34 YES
8 ALDH1B1 ALDH1B1 ALDH1B1 2356 0.23 0.37 YES
9 ACOT12 ACOT12 ACOT12 2357 0.23 0.41 YES
10 ACYP1 ACYP1 ACYP1 2510 0.21 0.44 YES
11 LDHD LDHD LDHD 2792 0.19 0.46 YES
12 GRHPR GRHPR GRHPR 3070 0.17 0.48 YES
13 ACAT1 ACAT1 ACAT1 3139 0.16 0.5 YES
14 ME1 ME1 ME1 3299 0.15 0.52 YES
15 PC PC PC 3640 0.13 0.53 YES
16 ALDH7A1 ALDH7A1 ALDH7A1 3982 0.12 0.53 YES
17 LDHB LDHB LDHB 4088 0.11 0.54 YES
18 ACACB ACACB ACACB 4224 0.11 0.56 YES
19 PDHB PDHB PDHB 4295 0.1 0.57 YES
20 DLD DLD DLD 4839 0.086 0.56 NO
21 ALDH9A1 ALDH9A1 ALDH9A1 5310 0.074 0.54 NO
22 ACYP2 ACYP2 ACYP2 6185 0.052 0.5 NO
23 PDHA1 PDHA1 PDHA1 6186 0.052 0.51 NO
24 MDH2 MDH2 MDH2 6204 0.051 0.52 NO
25 ACACA ACACA ACACA 6305 0.049 0.53 NO
26 HAGH HAGH HAGH 7140 0.034 0.49 NO
27 MDH1 MDH1 MDH1 7561 0.026 0.47 NO
28 LDHA LDHA LDHA 7658 0.024 0.47 NO
29 LDHAL6A LDHAL6A LDHAL6A 8445 0.011 0.42 NO
30 GLO1 GLO1 GLO1 8720 0.0072 0.41 NO
31 ME3 ME3 ME3 8947 0.0038 0.4 NO
32 DLAT DLAT DLAT 10714 -0.022 0.3 NO
33 PKM2 PKM2 PKM2 11420 -0.032 0.27 NO
34 PCK2 PCK2 PCK2 11910 -0.04 0.25 NO
35 ME2 ME2 ME2 12031 -0.042 0.25 NO
36 PKLR PKLR PKLR 14572 -0.093 0.13 NO
37 HAGHL HAGHL HAGHL 15797 -0.13 0.084 NO
38 LDHAL6B LDHAL6B LDHAL6B 16963 -0.2 0.056 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: BIOCARTA ALK PATHWAY.

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

genes ES table in pathway: BIOCARTA BCR 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 PAQR5 PAQR5 PAQR5 27 1.6 0.31 YES
2 PGR PGR PGR 273 0.78 0.45 YES
3 RPS6KA1 RPS6KA1 RPS6KA1 1093 0.41 0.49 YES
4 PRKAR2B PRKAR2B PRKAR2B 1255 0.38 0.55 YES
5 PAQR7 PAQR7 PAQR7 1741 0.3 0.58 YES
6 SRC SRC SRC 4778 0.088 0.43 NO
7 ARPC4 ARPC4 ARPC4 4861 0.085 0.44 NO
8 ARPC1B ARPC1B ARPC1B 4994 0.081 0.45 NO
9 ACTR3 ACTR3 ACTR3 5442 0.07 0.44 NO
10 GNAI1 GNAI1 GNAI1 5821 0.06 0.43 NO
11 ARPC3 ARPC3 ARPC3 6679 0.042 0.39 NO
12 ARPC1A ARPC1A ARPC1A 7266 0.031 0.37 NO
13 PRKACG PRKACG PRKACG 7458 0.028 0.36 NO
14 CAP1 CAP1 CAP1 8749 0.0068 0.29 NO
15 ARPC2 ARPC2 ARPC2 8912 0.0042 0.28 NO
16 PRKAR1A PRKAR1A PRKAR1A 10274 -0.016 0.21 NO
17 ARPC5 ARPC5 ARPC5 10275 -0.016 0.21 NO
18 MAPK1 MAPK1 MAPK1 10732 -0.022 0.19 NO
19 CCNB1 CCNB1 CCNB1 10951 -0.026 0.18 NO
20 ACTA1 ACTA1 ACTA1 11338 -0.031 0.17 NO
21 HRAS HRAS HRAS 11443 -0.032 0.17 NO
22 PIN1 PIN1 PIN1 11444 -0.032 0.18 NO
23 ACTR2 ACTR2 ACTR2 11556 -0.034 0.18 NO
24 GNB1 GNB1 GNB1 11781 -0.038 0.17 NO
25 MAPK3 MAPK3 MAPK3 11917 -0.04 0.17 NO
26 PRKAR2A PRKAR2A PRKAR2A 13029 -0.058 0.12 NO
27 GNAS GNAS GNAS 13546 -0.068 0.1 NO
28 PRKACB PRKACB PRKACB 13913 -0.076 0.099 NO
29 CDC25C CDC25C CDC25C 15756 -0.13 0.022 NO
30 MYT1 MYT1 MYT1 16012 -0.14 0.036 NO
31 PRKAR1B PRKAR1B PRKAR1B 16610 -0.18 0.037 NO
32 CDK1 CDK1 CDK1 16939 -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: BIOCARTA BCR PATHWAY.

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA BCR 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 ERK PATHWAY

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 AOX1 AOX1 AOX1 55 1.4 0.11 YES
2 ADH1A ADH1A ADH1A 61 1.3 0.23 YES
3 HPD HPD HPD 87 1.2 0.33 YES
4 ADH1B ADH1B ADH1B 116 1.1 0.42 YES
5 ALDH3B1 ALDH3B1 ALDH3B1 227 0.85 0.49 YES
6 ALDH3B2 ALDH3B2 ALDH3B2 415 0.65 0.54 YES
7 ADH1C ADH1C ADH1C 476 0.61 0.59 YES
8 FAH FAH FAH 757 0.49 0.61 YES
9 MAOB MAOB MAOB 964 0.44 0.64 YES
10 AOC3 AOC3 AOC3 1006 0.43 0.67 YES
11 ALDH3A1 ALDH3A1 ALDH3A1 1119 0.41 0.7 YES
12 HGD HGD HGD 1504 0.34 0.71 YES
13 PNMT PNMT PNMT 2468 0.22 0.68 YES
14 GSTZ1 GSTZ1 GSTZ1 2617 0.2 0.69 YES
15 IL4I1 IL4I1 IL4I1 2670 0.2 0.7 YES
16 TAT TAT TAT 2695 0.2 0.72 YES
17 MAOA MAOA MAOA 2754 0.19 0.73 YES
18 COMT COMT COMT 3142 0.16 0.72 YES
19 ALDH1A3 ALDH1A3 ALDH1A3 3234 0.16 0.73 YES
20 HEMK1 HEMK1 HEMK1 4448 0.098 0.67 NO
21 GOT1 GOT1 GOT1 5706 0.062 0.61 NO
22 ADH5 ADH5 ADH5 6424 0.047 0.57 NO
23 WBSCR22 WBSCR22 WBSCR22 6530 0.045 0.57 NO
24 NAT6 NAT6 NAT6 7227 0.032 0.53 NO
25 MIF MIF MIF 8091 0.017 0.49 NO
26 LCMT1 LCMT1 LCMT1 8530 0.0099 0.46 NO
27 METTL6 METTL6 METTL6 9398 -0.0028 0.42 NO
28 GOT2 GOT2 GOT2 9455 -0.0037 0.41 NO
29 AOC2 AOC2 AOC2 9791 -0.0084 0.39 NO
30 TRMT11 TRMT11 TRMT11 10179 -0.014 0.37 NO
31 DBH DBH DBH 10515 -0.019 0.36 NO
32 DCT DCT DCT 12566 -0.05 0.25 NO
33 LCMT2 LCMT2 LCMT2 12585 -0.051 0.25 NO
34 METTL2B METTL2B METTL2B 12916 -0.056 0.24 NO
35 TH TH TH 14621 -0.094 0.15 NO
36 DDC DDC DDC 16945 -0.2 0.038 NO
37 TPO TPO TPO 17208 -0.23 0.043 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: BIOCARTA ERK PATHWAY.

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ERK 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 FCER1 PATHWAY

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 GSTA1 GSTA1 GSTA1 7 2 0.19 YES
2 MGST1 MGST1 MGST1 11 1.9 0.38 YES
3 OPLAH OPLAH OPLAH 328 0.73 0.44 YES
4 GSTM5 GSTM5 GSTM5 401 0.66 0.5 YES
5 GGT5 GGT5 GGT5 1022 0.43 0.5 YES
6 IDH1 IDH1 IDH1 1247 0.38 0.53 YES
7 GSTA4 GSTA4 GSTA4 1749 0.3 0.53 YES
8 ANPEP ANPEP ANPEP 1803 0.3 0.56 YES
9 GSTT2 GSTT2 GSTT2 1855 0.29 0.58 YES
10 GSTM1 GSTM1 GSTM1 2450 0.22 0.57 YES
11 GSTZ1 GSTZ1 GSTZ1 2617 0.2 0.58 YES
12 GPX1 GPX1 GPX1 2978 0.17 0.58 YES
13 GCLM GCLM GCLM 3052 0.17 0.59 YES
14 SMS SMS SMS 3132 0.16 0.6 YES
15 GPX3 GPX3 GPX3 3151 0.16 0.62 YES
16 GSTT1 GSTT1 GSTT1 3335 0.15 0.62 YES
17 GSTK1 GSTK1 GSTK1 3804 0.12 0.61 NO
18 GSTM2 GSTM2 GSTM2 3949 0.12 0.61 NO
19 LAP3 LAP3 LAP3 4692 0.09 0.58 NO
20 GSS GSS GSS 4771 0.088 0.58 NO
21 MGST2 MGST2 MGST2 4884 0.084 0.58 NO
22 GGT1 GGT1 GGT1 5044 0.08 0.58 NO
23 G6PD G6PD G6PD 5187 0.077 0.58 NO
24 GSTO1 GSTO1 GSTO1 5235 0.076 0.59 NO
25 SRM SRM SRM 5238 0.075 0.59 NO
26 GSTP1 GSTP1 GSTP1 5335 0.073 0.6 NO
27 MGST3 MGST3 MGST3 5533 0.067 0.59 NO
28 GPX4 GPX4 GPX4 5661 0.064 0.59 NO
29 GPX7 GPX7 GPX7 6046 0.054 0.57 NO
30 GSTM4 GSTM4 GSTM4 6236 0.051 0.57 NO
31 TXNDC12 TXNDC12 TXNDC12 6407 0.047 0.56 NO
32 RRM1 RRM1 RRM1 6708 0.042 0.55 NO
33 GSTM3 GSTM3 GSTM3 7136 0.034 0.53 NO
34 RRM2B RRM2B RRM2B 8527 0.01 0.45 NO
35 GCLC GCLC GCLC 9957 -0.011 0.38 NO
36 GGCT GGCT GGCT 10474 -0.018 0.35 NO
37 ODC1 ODC1 ODC1 10573 -0.02 0.34 NO
38 GSR GSR GSR 10699 -0.022 0.34 NO
39 IDH2 IDH2 IDH2 11092 -0.028 0.32 NO
40 GGT7 GGT7 GGT7 14142 -0.082 0.16 NO
41 GSTO2 GSTO2 GSTO2 14369 -0.087 0.16 NO
42 RRM2 RRM2 RRM2 14447 -0.089 0.16 NO
43 GPX2 GPX2 GPX2 17894 -0.38 0.0046 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: BIOCARTA FCER1 PATHWAY.

Figure S70.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA FMLP PATHWAY

Table 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 ADH1A ADH1A ADH1A 61 1.3 0.15 YES
2 ADH1B ADH1B ADH1B 116 1.1 0.28 YES
3 ADH1C ADH1C ADH1C 476 0.61 0.33 YES
4 ACADL ACADL ACADL 582 0.55 0.39 YES
5 ACADS ACADS ACADS 1101 0.41 0.41 YES
6 ALDH3A2 ALDH3A2 ALDH3A2 1115 0.41 0.46 YES
7 ACAT2 ACAT2 ACAT2 1167 0.4 0.5 YES
8 ALDH2 ALDH2 ALDH2 2210 0.25 0.47 YES
9 ALDH1B1 ALDH1B1 ALDH1B1 2356 0.23 0.49 YES
10 ACADVL ACADVL ACADVL 2445 0.22 0.51 YES
11 ACSL5 ACSL5 ACSL5 2568 0.21 0.53 YES
12 ACAA1 ACAA1 ACAA1 2594 0.21 0.55 YES
13 CPT2 CPT2 CPT2 2649 0.2 0.57 YES
14 ACADM ACADM ACADM 2745 0.19 0.59 YES
15 ACAT1 ACAT1 ACAT1 3139 0.16 0.59 YES
16 HADHB HADHB HADHB 3169 0.16 0.6 YES
17 GCDH GCDH GCDH 3504 0.14 0.6 YES
18 CPT1B CPT1B CPT1B 3788 0.12 0.6 YES
19 CPT1A CPT1A CPT1A 3792 0.12 0.62 YES
20 ALDH7A1 ALDH7A1 ALDH7A1 3982 0.12 0.62 YES
21 PECI PECI PECI 4068 0.11 0.63 YES
22 ACSL1 ACSL1 ACSL1 4427 0.099 0.62 NO
23 ACOX3 ACOX3 ACOX3 4797 0.087 0.61 NO
24 ECHS1 ECHS1 ECHS1 5231 0.076 0.59 NO
25 ALDH9A1 ALDH9A1 ALDH9A1 5310 0.074 0.6 NO
26 DCI DCI DCI 5383 0.072 0.6 NO
27 ACSL4 ACSL4 ACSL4 5655 0.064 0.6 NO
28 ACAA2 ACAA2 ACAA2 5674 0.063 0.6 NO
29 ADH5 ADH5 ADH5 6424 0.047 0.57 NO
30 EHHADH EHHADH EHHADH 6798 0.04 0.55 NO
31 HADHA HADHA HADHA 7303 0.03 0.52 NO
32 HADH HADH HADH 7660 0.024 0.51 NO
33 ACSL3 ACSL3 ACSL3 7820 0.021 0.5 NO
34 ACADSB ACADSB ACADSB 9178 0.00045 0.43 NO
35 ACSL6 ACSL6 ACSL6 16119 -0.15 0.057 NO
36 CYP4A11 CYP4A11 CYP4A11 16704 -0.18 0.046 NO
37 CPT1C CPT1C CPT1C 16981 -0.21 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: BIOCARTA FMLP PATHWAY.

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

genes ES table in pathway: BIOCARTA GH PATHWAY

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 ADH1A ADH1A ADH1A 61 1.3 0.1 YES
2 GALM GALM GALM 97 1.1 0.19 YES
3 ADH1B ADH1B ADH1B 116 1.1 0.28 YES
4 ALDH3B1 ALDH3B1 ALDH3B1 227 0.85 0.34 YES
5 FBP1 FBP1 FBP1 297 0.76 0.4 YES
6 ALDH3B2 ALDH3B2 ALDH3B2 415 0.65 0.44 YES
7 ALDOB ALDOB ALDOB 428 0.65 0.49 YES
8 ADH1C ADH1C ADH1C 476 0.61 0.54 YES
9 ALDH3A2 ALDH3A2 ALDH3A2 1115 0.41 0.54 YES
10 ALDH3A1 ALDH3A1 ALDH3A1 1119 0.41 0.57 YES
11 HK3 HK3 HK3 1335 0.37 0.59 YES
12 PCK1 PCK1 PCK1 1400 0.35 0.61 YES
13 ACSS2 ACSS2 ACSS2 1632 0.32 0.62 YES
14 ACSS1 ACSS1 ACSS1 1691 0.31 0.64 YES
15 ALDH2 ALDH2 ALDH2 2210 0.25 0.64 YES
16 ALDH1B1 ALDH1B1 ALDH1B1 2356 0.23 0.65 YES
17 PGM1 PGM1 PGM1 2897 0.18 0.63 NO
18 PGM2 PGM2 PGM2 3122 0.16 0.63 NO
19 ALDH1A3 ALDH1A3 ALDH1A3 3234 0.16 0.64 NO
20 ALDH7A1 ALDH7A1 ALDH7A1 3982 0.12 0.6 NO
21 LDHB LDHB LDHB 4088 0.11 0.61 NO
22 AKR1A1 AKR1A1 AKR1A1 4219 0.11 0.61 NO
23 ENO3 ENO3 ENO3 4263 0.1 0.62 NO
24 PDHB PDHB PDHB 4295 0.1 0.62 NO
25 DLD DLD DLD 4839 0.086 0.6 NO
26 ALDH9A1 ALDH9A1 ALDH9A1 5310 0.074 0.58 NO
27 PDHA1 PDHA1 PDHA1 6186 0.052 0.53 NO
28 ADH5 ADH5 ADH5 6424 0.047 0.52 NO
29 PGAM2 PGAM2 PGAM2 7316 0.03 0.48 NO
30 GCK GCK GCK 7542 0.026 0.47 NO
31 LDHA LDHA LDHA 7658 0.024 0.46 NO
32 LDHAL6A LDHAL6A LDHAL6A 8445 0.011 0.42 NO
33 ENO1 ENO1 ENO1 8686 0.0077 0.41 NO
34 HK2 HK2 HK2 8875 0.005 0.4 NO
35 PGAM1 PGAM1 PGAM1 9165 0.00068 0.38 NO
36 G6PC2 G6PC2 G6PC2 10178 -0.014 0.32 NO
37 PFKM PFKM PFKM 10564 -0.02 0.3 NO
38 BPGM BPGM BPGM 10596 -0.02 0.3 NO
39 GPI GPI GPI 10613 -0.02 0.3 NO
40 DLAT DLAT DLAT 10714 -0.022 0.3 NO
41 PKM2 PKM2 PKM2 11420 -0.032 0.26 NO
42 TPI1 TPI1 TPI1 11746 -0.037 0.25 NO
43 GAPDH GAPDH GAPDH 11829 -0.038 0.25 NO
44 PCK2 PCK2 PCK2 11910 -0.04 0.25 NO
45 ALDOA ALDOA ALDOA 12298 -0.046 0.23 NO
46 PGK1 PGK1 PGK1 12358 -0.047 0.23 NO
47 ALDOC ALDOC ALDOC 12491 -0.049 0.23 NO
48 PGAM4 PGAM4 PGAM4 12849 -0.055 0.21 NO
49 PFKL PFKL PFKL 12917 -0.056 0.21 NO
50 PKLR PKLR PKLR 14572 -0.093 0.13 NO
51 HK1 HK1 HK1 15231 -0.11 0.098 NO
52 ENO2 ENO2 ENO2 16799 -0.19 0.026 NO
53 LDHAL6B LDHAL6B LDHAL6B 16963 -0.2 0.034 NO
54 PFKP PFKP PFKP 17600 -0.29 0.021 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: BIOCARTA GH PATHWAY.

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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

Table 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 GSTA1 GSTA1 GSTA1 7 2 0.1 YES
2 MGST1 MGST1 MGST1 11 1.9 0.2 YES
3 AOX1 AOX1 AOX1 55 1.4 0.27 YES
4 ADH1A ADH1A ADH1A 61 1.3 0.34 YES
5 FMO1 FMO1 FMO1 88 1.2 0.4 YES
6 ADH1B ADH1B ADH1B 116 1.1 0.45 YES
7 FMO2 FMO2 FMO2 164 0.96 0.5 YES
8 ALDH3B1 ALDH3B1 ALDH3B1 227 0.85 0.54 YES
9 FMO5 FMO5 FMO5 306 0.75 0.57 YES
10 CYP3A5 CYP3A5 CYP3A5 345 0.71 0.6 YES
11 GSTM5 GSTM5 GSTM5 401 0.66 0.64 YES
12 FMO4 FMO4 FMO4 402 0.66 0.67 YES
13 ALDH3B2 ALDH3B2 ALDH3B2 415 0.65 0.7 YES
14 ADH1C ADH1C ADH1C 476 0.61 0.73 YES
15 FMO3 FMO3 FMO3 573 0.56 0.75 YES
16 CYP3A7 CYP3A7 CYP3A7 819 0.47 0.76 YES
17 MAOB MAOB MAOB 964 0.44 0.78 YES
18 ALDH3A1 ALDH3A1 ALDH3A1 1119 0.41 0.79 YES
19 GSTA4 GSTA4 GSTA4 1749 0.3 0.77 NO
20 GSTT2 GSTT2 GSTT2 1855 0.29 0.78 NO
21 GSTM1 GSTM1 GSTM1 2450 0.22 0.76 NO
22 GSTZ1 GSTZ1 GSTZ1 2617 0.2 0.76 NO
23 MAOA MAOA MAOA 2754 0.19 0.76 NO
24 ALDH1A3 ALDH1A3 ALDH1A3 3234 0.16 0.74 NO
25 GSTT1 GSTT1 GSTT1 3335 0.15 0.75 NO
26 CYP2A6 CYP2A6 CYP2A6 3350 0.15 0.75 NO
27 CYP2C8 CYP2C8 CYP2C8 3598 0.14 0.75 NO
28 GSTK1 GSTK1 GSTK1 3804 0.12 0.74 NO
29 GSTM2 GSTM2 GSTM2 3949 0.12 0.74 NO
30 MGST2 MGST2 MGST2 4884 0.084 0.69 NO
31 GSTO1 GSTO1 GSTO1 5235 0.076 0.68 NO
32 GSTP1 GSTP1 GSTP1 5335 0.073 0.68 NO
33 CYP2E1 CYP2E1 CYP2E1 5466 0.069 0.67 NO
34 MGST3 MGST3 MGST3 5533 0.067 0.67 NO
35 GSTM4 GSTM4 GSTM4 6236 0.051 0.63 NO
36 ADH5 ADH5 ADH5 6424 0.047 0.63 NO
37 GSTM3 GSTM3 GSTM3 7136 0.034 0.59 NO
38 CYP3A43 CYP3A43 CYP3A43 7409 0.029 0.57 NO
39 CYP2C18 CYP2C18 CYP2C18 11459 -0.033 0.35 NO
40 CYP2A7 CYP2A7 CYP2A7 11866 -0.039 0.33 NO
41 GSTO2 GSTO2 GSTO2 14369 -0.087 0.2 NO
42 CYP2D6 CYP2D6 CYP2D6 15515 -0.12 0.14 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: BIOCARTA HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA MPR PATHWAY

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 ACSM3 ACSM3 ACSM3 129 1 0.16 YES
2 ACSM1 ACSM1 ACSM1 512 0.58 0.23 YES
3 ACSM5 ACSM5 ACSM5 985 0.43 0.27 YES
4 ACADS ACADS ACADS 1101 0.41 0.33 YES
5 ALDH3A2 ALDH3A2 ALDH3A2 1115 0.41 0.4 YES
6 ACAT2 ACAT2 ACAT2 1167 0.4 0.46 YES
7 AKR1B10 AKR1B10 AKR1B10 1197 0.39 0.52 YES
8 BDH2 BDH2 BDH2 1711 0.31 0.54 YES
9 HMGCS1 HMGCS1 HMGCS1 1806 0.3 0.58 YES
10 ALDH2 ALDH2 ALDH2 2210 0.25 0.6 YES
11 ALDH1B1 ALDH1B1 ALDH1B1 2356 0.23 0.63 YES
12 OXCT2 OXCT2 OXCT2 2537 0.21 0.65 YES
13 HMGCL HMGCL HMGCL 3078 0.17 0.65 YES
14 ACAT1 ACAT1 ACAT1 3139 0.16 0.67 YES
15 ALDH7A1 ALDH7A1 ALDH7A1 3982 0.12 0.64 NO
16 GAD1 GAD1 GAD1 4110 0.11 0.65 NO
17 PDHB PDHB PDHB 4295 0.1 0.66 NO
18 ECHS1 ECHS1 ECHS1 5231 0.076 0.62 NO
19 ALDH9A1 ALDH9A1 ALDH9A1 5310 0.074 0.63 NO
20 AACS AACS AACS 5685 0.063 0.62 NO
21 BDH1 BDH1 BDH1 5805 0.06 0.62 NO
22 PDHA1 PDHA1 PDHA1 6186 0.052 0.61 NO
23 HADHA HADHA HADHA 7303 0.03 0.55 NO
24 ALDH5A1 ALDH5A1 ALDH5A1 7536 0.026 0.54 NO
25 HADH HADH HADH 7660 0.024 0.54 NO
26 OXCT1 OXCT1 OXCT1 9407 -0.0029 0.44 NO
27 ABAT ABAT ABAT 14428 -0.088 0.18 NO
28 L2HGDH L2HGDH L2HGDH 15983 -0.14 0.11 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: BIOCARTA MPR PATHWAY.

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

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 ALDH3A2 ALDH3A2 ALDH3A2 1115 0.41 0.018 YES
2 ACSS3 ACSS3 ACSS3 1143 0.4 0.095 YES
3 ACAT2 ACAT2 ACAT2 1167 0.4 0.17 YES
4 HIBCH HIBCH HIBCH 1414 0.35 0.23 YES
5 ACSS2 ACSS2 ACSS2 1632 0.32 0.28 YES
6 ACSS1 ACSS1 ACSS1 1691 0.31 0.33 YES
7 PCCA PCCA PCCA 2146 0.25 0.36 YES
8 ALDH2 ALDH2 ALDH2 2210 0.25 0.4 YES
9 ALDH1B1 ALDH1B1 ALDH1B1 2356 0.23 0.44 YES
10 SUCLG2 SUCLG2 SUCLG2 2359 0.23 0.48 YES
11 PCCB PCCB PCCB 2717 0.2 0.5 YES
12 ACADM ACADM ACADM 2745 0.19 0.54 YES
13 ALDH6A1 ALDH6A1 ALDH6A1 2809 0.19 0.57 YES
14 ACAT1 ACAT1 ACAT1 3139 0.16 0.58 YES
15 MCEE MCEE MCEE 3245 0.16 0.61 YES
16 MLYCD MLYCD MLYCD 3625 0.13 0.61 YES
17 ALDH7A1 ALDH7A1 ALDH7A1 3982 0.12 0.62 YES
18 LDHB LDHB LDHB 4088 0.11 0.63 YES
19 ACACB ACACB ACACB 4224 0.11 0.64 YES
20 ECHS1 ECHS1 ECHS1 5231 0.076 0.6 NO
21 ALDH9A1 ALDH9A1 ALDH9A1 5310 0.074 0.61 NO
22 ACACA ACACA ACACA 6305 0.049 0.57 NO
23 EHHADH EHHADH EHHADH 6798 0.04 0.55 NO
24 HADHA HADHA HADHA 7303 0.03 0.53 NO
25 LDHA LDHA LDHA 7658 0.024 0.51 NO
26 SUCLG1 SUCLG1 SUCLG1 8324 0.013 0.48 NO
27 LDHAL6A LDHAL6A LDHAL6A 8445 0.011 0.47 NO
28 SUCLA2 SUCLA2 SUCLA2 9493 -0.0041 0.41 NO
29 MUT MUT MUT 9629 -0.006 0.41 NO
30 ABAT ABAT ABAT 14428 -0.088 0.16 NO
31 LDHAL6B LDHAL6B LDHAL6B 16963 -0.2 0.056 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: BIOCARTA IL2RB PATHWAY.

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input

  • Gene set database = c2.cp.v3.0-2.symbols.gmt

  • Expression data file = 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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