GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in CHOL-TP
Cholangiocarcinoma (Primary solid tumor)
21 August 2015 | analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1BK1BGT
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 CHOL-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1BK1BGT
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 CHOL-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: 192
Number of samples: 36
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 12
pheno.type: 2 - 3 :[ clus2 ] 15
pheno.type: 3 - 3 :[ clus3 ] 9

For the expression subtypes of 18131 genes in 37 samples, GSEA found enriched gene sets in each cluster using 36 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

- clus1

- Top enriched gene sets are BIOCARTA BCR PATHWAY, BIOCARTA G1 PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA GSK3 PATHWAY, BIOCARTA KERATINOCYTE PATHWAY, BIOCARTA MYOSIN PATHWAY

- And common core enriched genes are EGF, BIRC3, BCL2, FAS, MAP3K5, PRKCB, PRKCD, PRKCG, TNF, TNFRSF1B

- clus2

- Top enriched gene sets are BIOCARTA DEATH PATHWAY, KEGG OXIDATIVE PHOSPHORYLATION, KEGG RNA DEGRADATION, KEGG RNA POLYMERASE, KEGG SPLICEOSOME, KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, KEGG NOTCH SIGNALING PATHWAY, KEGG VASOPRESSIN REGULATED WATER REABSORPTION, KEGG HUNTINGTONS DISEASE

- And common core enriched genes are LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, NAA38, ATP5A1, ATP5C1, ATP5D

- clus3

- Top enriched gene sets are BIOCARTA AT1R PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA PPARA PATHWAY, BIOCARTA CHREBP2 PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS

- And common core enriched genes are LDHAL6B, ACAA1, ACOX1, ACSL1, ACSL5, ACSL6, EHHADH, PCK1, PCK2, SCP2

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 BCR PATHWAY | 33 | genes.ES.table | 0.54 | 1.5 | 0.074 | 0.23 | 0.83 | 0.52 | 0.32 | 0.35 | 0.16 | 0.024
BIOCARTA G1 PATHWAY | 27 | genes.ES.table | 0.51 | 1.5 | 0.083 | 0.22 | 0.86 | 0.52 | 0.28 | 0.37 | 0.15 | 0.017
BIOCARTA HDAC PATHWAY | 27 | genes.ES.table | 0.5 | 1.5 | 0.064 | 0.22 | 0.8 | 0.26 | 0.2 | 0.21 | 0.14 | 0.023
BIOCARTA FAS PATHWAY | 29 | genes.ES.table | 0.45 | 1.6 | 0.06 | 0.27 | 0.74 | 0.59 | 0.4 | 0.35 | 0.16 | 0.047
BIOCARTA FCER1 PATHWAY | 37 | genes.ES.table | 0.53 | 1.5 | 0.087 | 0.23 | 0.85 | 0.51 | 0.32 | 0.35 | 0.16 | 0.022
BIOCARTA HIVNEF PATHWAY | 57 | genes.ES.table | 0.43 | 1.8 | 0.018 | 0.23 | 0.23 | 0.53 | 0.4 | 0.32 | 0 | 0.068
BIOCARTA IL2RB PATHWAY | 37 | genes.ES.table | 0.6 | 1.6 | 0.053 | 0.24 | 0.75 | 0.4 | 0.19 | 0.33 | 0.15 | 0.036
BIOCARTA GSK3 PATHWAY | 26 | genes.ES.table | 0.53 | 1.6 | 0.04 | 0.25 | 0.74 | 0.23 | 0.13 | 0.2 | 0.15 | 0.035
BIOCARTA KERATINOCYTE PATHWAY | 45 | genes.ES.table | 0.56 | 1.8 | 0.0041 | 0.34 | 0.23 | 0.31 | 0.19 | 0.25 | 0 | 0.12
BIOCARTA MYOSIN PATHWAY | 28 | genes.ES.table | 0.42 | 1.4 | 0.09 | 0.25 | 0.95 | 0.46 | 0.34 | 0.31 | 0.19 | 0.005

genes ES table in pathway: BIOCARTA BCR 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 | HERC3 | HERC3 | HERC3 | 1080 | 0.39 | -0.017 | YES
2 | SOCS1 | SOCS1 | SOCS1 | 1713 | 0.32 | -0.018 | YES
3 | SOCS3 | SOCS3 | SOCS3 | 1728 | 0.32 | 0.016 | YES
4 | UBE2C | UBE2C | UBE2C | 2034 | 0.28 | 0.03 | YES
5 | CDC20 | CDC20 | CDC20 | 2381 | 0.26 | 0.038 | YES
6 | MID1 | MID1 | MID1 | 2629 | 0.24 | 0.05 | YES
7 | UBE2E2 | UBE2E2 | UBE2E2 | 2854 | 0.22 | 0.062 | YES
8 | AIRE | AIRE | AIRE | 2902 | 0.22 | 0.082 | YES
9 | DET1 | DET1 | DET1 | 2955 | 0.21 | 0.1 | YES
10 | PARK2 | PARK2 | PARK2 | 3209 | 0.2 | 0.11 | YES
11 | BIRC3 | BIRC3 | BIRC3 | 3519 | 0.18 | 0.11 | YES
12 | FBXW7 | FBXW7 | FBXW7 | 3899 | 0.16 | 0.11 | YES
13 | CBLB | CBLB | CBLB | 3978 | 0.16 | 0.12 | YES
14 | TRAF6 | TRAF6 | TRAF6 | 4194 | 0.15 | 0.12 | YES
15 | CDC26 | CDC26 | CDC26 | 4226 | 0.14 | 0.14 | YES
16 | UBE2J1 | UBE2J1 | UBE2J1 | 4274 | 0.14 | 0.15 | YES
17 | BRCA1 | BRCA1 | BRCA1 | 4336 | 0.14 | 0.16 | YES
18 | UBE2S | UBE2S | UBE2S | 4358 | 0.14 | 0.18 | YES
19 | PML | PML | PML | 4407 | 0.14 | 0.19 | YES
20 | SMURF2 | SMURF2 | SMURF2 | 4577 | 0.13 | 0.2 | YES
21 | UBE2O | UBE2O | UBE2O | 5080 | 0.11 | 0.18 | YES
22 | UBE4B | UBE4B | UBE4B | 5094 | 0.11 | 0.19 | YES
23 | SKP2 | SKP2 | SKP2 | 5128 | 0.11 | 0.2 | YES
24 | UBA7 | UBA7 | UBA7 | 5274 | 0.1 | 0.2 | YES
25 | ANAPC10 | ANAPC10 | ANAPC10 | 5310 | 0.1 | 0.21 | YES
26 | VHL | VHL | VHL | 5319 | 0.1 | 0.22 | YES
27 | UBE2U | UBE2U | UBE2U | 5333 | 0.1 | 0.24 | YES
28 | NHLRC1 | NHLRC1 | NHLRC1 | 5719 | 0.092 | 0.22 | YES
29 | UBA3 | UBA3 | UBA3 | 5852 | 0.088 | 0.23 | YES
30 | CUL1 | CUL1 | CUL1 | 6039 | 0.084 | 0.22 | YES
31 | UBE2E1 | UBE2E1 | UBE2E1 | 6094 | 0.082 | 0.23 | YES
32 | CDC16 | CDC16 | CDC16 | 6147 | 0.081 | 0.24 | YES
33 | TRIM32 | TRIM32 | TRIM32 | 6375 | 0.076 | 0.23 | YES
34 | FANCL | FANCL | FANCL | 6386 | 0.075 | 0.24 | YES
35 | UBA6 | UBA6 | UBA6 | 6482 | 0.073 | 0.24 | YES
36 | CBL | CBL | CBL | 6627 | 0.07 | 0.24 | YES
37 | UBE2H | UBE2H | UBE2H | 6631 | 0.07 | 0.25 | YES
38 | RCHY1 | RCHY1 | RCHY1 | 6721 | 0.068 | 0.25 | YES
39 | CDC27 | CDC27 | CDC27 | 6962 | 0.064 | 0.24 | YES
40 | CUL4A | CUL4A | CUL4A | 7012 | 0.063 | 0.25 | YES
41 | PIAS1 | PIAS1 | PIAS1 | 7090 | 0.061 | 0.25 | YES
42 | UBR5 | UBR5 | UBR5 | 7139 | 0.06 | 0.26 | YES
43 | BIRC6 | BIRC6 | BIRC6 | 7240 | 0.058 | 0.26 | YES
44 | TCEB1 | TCEB1 | TCEB1 | 7340 | 0.056 | 0.26 | YES
45 | UBE2J2 | UBE2J2 | UBE2J2 | 7453 | 0.054 | 0.26 | YES
46 | KLHL9 | KLHL9 | KLHL9 | 7502 | 0.054 | 0.26 | YES
47 | UBE2D1 | UBE2D1 | UBE2D1 | 7584 | 0.052 | 0.26 | YES
48 | HERC2 | HERC2 | HERC2 | 7620 | 0.051 | 0.26 | YES
49 | ANAPC1 | ANAPC1 | ANAPC1 | 7691 | 0.05 | 0.27 | YES
50 | UBE3C | UBE3C | UBE3C | 7723 | 0.05 | 0.27 | YES
51 | BIRC2 | BIRC2 | BIRC2 | 7866 | 0.047 | 0.27 | YES
52 | UBE2L6 | UBE2L6 | UBE2L6 | 7877 | 0.046 | 0.27 | YES
53 | UBE2F | UBE2F | UBE2F | 8025 | 0.044 | 0.27 | YES
54 | ITCH | ITCH | ITCH | 8044 | 0.043 | 0.27 | YES
55 | UBE2K | UBE2K | UBE2K | 8085 | 0.042 | 0.27 | YES
56 | UBE2W | UBE2W | UBE2W | 8092 | 0.042 | 0.28 | YES
57 | UBE2D4 | UBE2D4 | UBE2D4 | 8184 | 0.041 | 0.28 | YES
58 | RHOBTB2 | RHOBTB2 | RHOBTB2 | 8226 | 0.04 | 0.28 | YES
59 | ANAPC4 | ANAPC4 | ANAPC4 | 8300 | 0.039 | 0.28 | YES
60 | ANAPC13 | ANAPC13 | ANAPC13 | 8320 | 0.039 | 0.28 | YES
61 | TRIM37 | TRIM37 | TRIM37 | 8329 | 0.039 | 0.29 | YES
62 | ANAPC2 | ANAPC2 | ANAPC2 | 8408 | 0.037 | 0.29 | YES
63 | UBE2D3 | UBE2D3 | UBE2D3 | 8415 | 0.037 | 0.29 | YES
64 | MDM2 | MDM2 | MDM2 | 8417 | 0.037 | 0.29 | YES
65 | UBE2Q2 | UBE2Q2 | UBE2Q2 | 8424 | 0.037 | 0.3 | YES
66 | UBA2 | UBA2 | UBA2 | 8440 | 0.037 | 0.3 | YES
67 | STUB1 | STUB1 | STUB1 | 8650 | 0.034 | 0.29 | NO
68 | PIAS3 | PIAS3 | PIAS3 | 8651 | 0.034 | 0.3 | NO
69 | UBE2N | UBE2N | UBE2N | 8729 | 0.032 | 0.3 | NO
70 | HERC4 | HERC4 | HERC4 | 8776 | 0.031 | 0.3 | NO
71 | CDC23 | CDC23 | CDC23 | 8843 | 0.03 | 0.3 | NO
72 | RNF7 | RNF7 | RNF7 | 8923 | 0.029 | 0.3 | NO
73 | UBOX5 | UBOX5 | UBOX5 | 8975 | 0.028 | 0.3 | NO
74 | KEAP1 | KEAP1 | KEAP1 | 9025 | 0.028 | 0.3 | NO
75 | UBE2I | UBE2I | UBE2I | 9069 | 0.027 | 0.3 | NO
76 | UBE3A | UBE3A | UBE3A | 9118 | 0.026 | 0.3 | NO
77 | UBA1 | UBA1 | UBA1 | 9146 | 0.026 | 0.3 | NO
78 | UBE2Z | UBE2Z | UBE2Z | 9319 | 0.023 | 0.29 | NO
79 | PRPF19 | PRPF19 | PRPF19 | 9551 | 0.019 | 0.28 | NO
80 | ANAPC11 | ANAPC11 | ANAPC11 | 9566 | 0.019 | 0.28 | NO
81 | HERC1 | HERC1 | HERC1 | 9572 | 0.019 | 0.28 | NO
82 | WWP2 | WWP2 | WWP2 | 9640 | 0.018 | 0.28 | NO
83 | CUL2 | CUL2 | CUL2 | 9657 | 0.018 | 0.28 | NO
84 | HUWE1 | HUWE1 | HUWE1 | 9723 | 0.017 | 0.28 | NO
85 | UBE2D2 | UBE2D2 | UBE2D2 | 9746 | 0.016 | 0.28 | NO
86 | UBE2A | UBE2A | UBE2A | 9766 | 0.016 | 0.28 | NO
87 | XIAP | XIAP | XIAP | 9958 | 0.013 | 0.27 | NO
88 | TRIP12 | TRIP12 | TRIP12 | 10029 | 0.012 | 0.27 | NO
89 | UBE2R2 | UBE2R2 | UBE2R2 | 10165 | 0.01 | 0.26 | NO
90 | UBE4A | UBE4A | UBE4A | 10245 | 0.0089 | 0.26 | NO
91 | FBXW8 | FBXW8 | FBXW8 | 10498 | 0.0051 | 0.25 | NO
92 | TCEB2 | TCEB2 | TCEB2 | 10577 | 0.0039 | 0.24 | NO
93 | UBE2B | UBE2B | UBE2B | 10630 | 0.0031 | 0.24 | NO
94 | CUL5 | CUL5 | CUL5 | 10680 | 0.0024 | 0.24 | NO
95 | CUL3 | CUL3 | CUL3 | 10816 | 0.00021 | 0.23 | NO
96 | PIAS2 | PIAS2 | PIAS2 | 10839 | -0.00019 | 0.23 | NO
97 | SMURF1 | SMURF1 | SMURF1 | 10884 | -0.00082 | 0.23 | NO
98 | FBXO4 | FBXO4 | FBXO4 | 10896 | -0.0011 | 0.23 | NO
99 | FZR1 | FZR1 | FZR1 | 11229 | -0.0066 | 0.21 | NO
100 | CUL4B | CUL4B | CUL4B | 11300 | -0.0078 | 0.2 | NO
101 | UBE2G1 | UBE2G1 | UBE2G1 | 11460 | -0.011 | 0.2 | NO
102 | SKP1 | SKP1 | SKP1 | 11461 | -0.011 | 0.2 | NO
103 | UBE2NL | UBE2NL | UBE2NL | 11641 | -0.013 | 0.19 | NO
104 | UBE2L3 | UBE2L3 | UBE2L3 | 11678 | -0.014 | 0.19 | NO
105 | RBX1 | RBX1 | RBX1 | 11916 | -0.018 | 0.18 | NO
106 | FBXO2 | FBXO2 | FBXO2 | 11965 | -0.018 | 0.18 | NO
107 | MGRN1 | MGRN1 | MGRN1 | 12002 | -0.019 | 0.18 | NO
108 | ANAPC7 | ANAPC7 | ANAPC7 | 12126 | -0.021 | 0.17 | NO
109 | UBE2QL1 | UBE2QL1 | UBE2QL1 | 12271 | -0.023 | 0.17 | NO
110 | ANAPC5 | ANAPC5 | ANAPC5 | 12294 | -0.024 | 0.17 | NO
111 | SIAH1 | SIAH1 | SIAH1 | 12413 | -0.026 | 0.16 | NO
112 | WWP1 | WWP1 | WWP1 | 12703 | -0.031 | 0.15 | NO
113 | DDB1 | DDB1 | DDB1 | 12747 | -0.031 | 0.15 | NO
114 | UBE3B | UBE3B | UBE3B | 12913 | -0.035 | 0.15 | NO
115 | UBE2E3 | UBE2E3 | UBE2E3 | 12969 | -0.036 | 0.15 | NO
116 | NEDD4L | NEDD4L | NEDD4L | 13002 | -0.036 | 0.15 | NO
117 | UBE2M | UBE2M | UBE2M | 13041 | -0.037 | 0.15 | NO
118 | UBE2Q1 | UBE2Q1 | UBE2Q1 | 13213 | -0.04 | 0.15 | NO
119 | UBE2G2 | UBE2G2 | UBE2G2 | 13256 | -0.041 | 0.15 | NO
120 | PIAS4 | PIAS4 | PIAS4 | 13331 | -0.042 | 0.15 | NO
121 | PPIL2 | PPIL2 | PPIL2 | 13340 | -0.042 | 0.15 | NO
122 | CUL7 | CUL7 | CUL7 | 13472 | -0.045 | 0.15 | NO
123 | SAE1 | SAE1 | SAE1 | 13586 | -0.047 | 0.15 | NO
124 | MAP3K1 | MAP3K1 | MAP3K1 | 13631 | -0.048 | 0.15 | NO
125 | DDB2 | DDB2 | DDB2 | 13700 | -0.05 | 0.16 | NO
126 | SYVN1 | SYVN1 | SYVN1 | 13838 | -0.054 | 0.15 | NO
127 | ERCC8 | ERCC8 | ERCC8 | 13914 | -0.056 | 0.16 | NO
128 | CDC34 | CDC34 | CDC34 | 14698 | -0.077 | 0.12 | NO
129 | FBXW11 | FBXW11 | FBXW11 | 14963 | -0.087 | 0.12 | NO
130 | RFWD2 | RFWD2 | RFWD2 | 15326 | -0.1 | 0.11 | NO
131 | KLHL13 | KLHL13 | KLHL13 | 15817 | -0.13 | 0.093 | NO
132 | NEDD4 | NEDD4 | NEDD4 | 15975 | -0.14 | 0.099 | NO
133 | CBLC | CBLC | CBLC | 16625 | -0.18 | 0.083 | 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 BCR PATHWAY.

Figure S2. 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 G1 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 | HOXA7 | HOXA7 | HOXA7 | 112 | 0.68 | 0.096 | YES
2 | PRKCB | PRKCB | PRKCB | 329 | 0.56 | 0.17 | YES
3 | EGF | EGF | EGF | 450 | 0.52 | 0.24 | YES
4 | FASLG | FASLG | FASLG | 549 | 0.49 | 0.31 | YES
5 | MAP3K5 | MAP3K5 | MAP3K5 | 1246 | 0.37 | 0.33 | YES
6 | PRKCH | PRKCH | PRKCH | 1314 | 0.36 | 0.38 | YES
7 | TNFRSF1B | TNFRSF1B | TNFRSF1B | 1327 | 0.36 | 0.43 | YES
8 | PRKCQ | PRKCQ | PRKCQ | 2301 | 0.26 | 0.42 | YES
9 | ETS1 | ETS1 | ETS1 | 2521 | 0.25 | 0.44 | YES
10 | TNF | TNF | TNF | 2602 | 0.24 | 0.47 | YES
11 | BCL2 | BCL2 | BCL2 | 2609 | 0.24 | 0.51 | YES
12 | PRKCG | PRKCG | PRKCG | 2832 | 0.22 | 0.53 | YES
13 | PRKCD | PRKCD | PRKCD | 3276 | 0.19 | 0.54 | YES
14 | FAS | FAS | FAS | 3413 | 0.19 | 0.56 | YES
15 | MAPK8 | MAPK8 | MAPK8 | 4907 | 0.12 | 0.49 | NO
16 | FOS | FOS | FOS | 5125 | 0.11 | 0.5 | NO
17 | MAP2K1 | MAP2K1 | MAP2K1 | 5241 | 0.11 | 0.5 | NO
18 | MAPK3 | MAPK3 | MAPK3 | 5820 | 0.09 | 0.49 | NO
19 | IKBKB | IKBKB | IKBKB | 6705 | 0.069 | 0.45 | NO
20 | MAP3K14 | MAP3K14 | MAP3K14 | 7079 | 0.061 | 0.44 | NO
21 | HRAS | HRAS | HRAS | 7390 | 0.055 | 0.43 | NO
22 | RAF1 | RAF1 | RAF1 | 8071 | 0.043 | 0.4 | NO
23 | NFKB1 | NFKB1 | NFKB1 | 8321 | 0.039 | 0.39 | NO
24 | PRKCE | PRKCE | PRKCE | 8633 | 0.034 | 0.38 | NO
25 | MAPK1 | MAPK1 | MAPK1 | 9347 | 0.023 | 0.34 | NO
26 | MAP2K6 | MAP2K6 | MAP2K6 | 9409 | 0.022 | 0.34 | NO
27 | CHUK | CHUK | CHUK | 9445 | 0.021 | 0.34 | NO
28 | NFKBIA | NFKBIA | NFKBIA | 9478 | 0.02 | 0.34 | NO
29 | RELA | RELA | RELA | 10068 | 0.011 | 0.31 | NO
30 | PRKCA | PRKCA | PRKCA | 10189 | 0.0097 | 0.31 | NO
31 | ETS2 | ETS2 | ETS2 | 10656 | 0.0027 | 0.28 | NO
32 | DAXX | DAXX | DAXX | 10909 | -0.0013 | 0.27 | NO
33 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 10911 | -0.0013 | 0.27 | NO
34 | PPP2CA | PPP2CA | PPP2CA | 11118 | -0.0048 | 0.26 | NO
35 | JUN | JUN | JUN | 11328 | -0.0084 | 0.25 | NO
36 | MAPK14 | MAPK14 | MAPK14 | 12581 | -0.029 | 0.18 | NO
37 | MAP2K7 | MAP2K7 | MAP2K7 | 12749 | -0.031 | 0.18 | NO
38 | SP1 | SP1 | SP1 | 13188 | -0.039 | 0.16 | NO
39 | MAP3K1 | MAP3K1 | MAP3K1 | 13631 | -0.048 | 0.14 | NO
40 | MAP2K4 | MAP2K4 | MAP2K4 | 13924 | -0.056 | 0.14 | NO
41 | RIPK1 | RIPK1 | RIPK1 | 14375 | -0.068 | 0.12 | NO
42 | MAP2K3 | MAP2K3 | MAP2K3 | 14962 | -0.087 | 0.1 | NO
43 | EGFR | EGFR | EGFR | 15766 | -0.12 | 0.075 | NO
44 | MAPK13 | MAPK13 | MAPK13 | 16126 | -0.15 | 0.077 | NO
45 | CEBPA | CEBPA | CEBPA | 16898 | -0.22 | 0.067 | 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 G1 PATHWAY.

Figure S4. 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 HDAC 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 | MAP3K5 | MAP3K5 | MAP3K5 | 1246 | 0.37 | -0.00078 | YES
2 | TNFRSF1B | TNFRSF1B | TNFRSF1B | 1327 | 0.36 | 0.061 | YES
3 | ARHGDIB | ARHGDIB | ARHGDIB | 2192 | 0.27 | 0.064 | YES
4 | TNF | TNF | TNF | 2602 | 0.24 | 0.086 | YES
5 | BCL2 | BCL2 | BCL2 | 2609 | 0.24 | 0.13 | YES
6 | CDK11A | CDK11A | CDK11A | 2979 | 0.21 | 0.15 | YES
7 | PRKCD | PRKCD | PRKCD | 3276 | 0.19 | 0.17 | YES
8 | FAS | FAS | FAS | 3413 | 0.19 | 0.2 | YES
9 | TRAF1 | TRAF1 | TRAF1 | 3440 | 0.18 | 0.23 | YES
10 | BIRC3 | BIRC3 | BIRC3 | 3519 | 0.18 | 0.26 | YES
11 | BID | BID | BID | 3604 | 0.18 | 0.28 | YES
12 | DFFB | DFFB | DFFB | 3821 | 0.16 | 0.3 | YES
13 | DFFA | DFFA | DFFA | 4111 | 0.15 | 0.31 | YES
14 | GSN | GSN | GSN | 4275 | 0.14 | 0.33 | YES
15 | LMNB1 | LMNB1 | LMNB1 | 4591 | 0.13 | 0.34 | YES
16 | LMNB2 | LMNB2 | LMNB2 | 4734 | 0.12 | 0.35 | YES
17 | MAPK8 | MAPK8 | MAPK8 | 4907 | 0.12 | 0.37 | YES
18 | RB1 | RB1 | RB1 | 4944 | 0.12 | 0.38 | YES
19 | CASP3 | CASP3 | CASP3 | 5224 | 0.11 | 0.39 | YES
20 | CDK11B | CDK11B | CDK11B | 5613 | 0.096 | 0.39 | YES
21 | TRADD | TRADD | TRADD | 5762 | 0.091 | 0.4 | YES
22 | CFLAR | CFLAR | CFLAR | 5916 | 0.087 | 0.4 | YES
23 | PAK2 | PAK2 | PAK2 | 6231 | 0.079 | 0.4 | YES
24 | PRKDC | PRKDC | PRKDC | 6313 | 0.077 | 0.41 | YES
25 | CASP9 | CASP9 | CASP9 | 6572 | 0.072 | 0.41 | YES
26 | BAG4 | BAG4 | BAG4 | 6739 | 0.068 | 0.41 | YES
27 | FADD | FADD | FADD | 6938 | 0.064 | 0.41 | YES
28 | MAP3K14 | MAP3K14 | MAP3K14 | 7079 | 0.061 | 0.42 | YES
29 | CASP8 | CASP8 | CASP8 | 7108 | 0.061 | 0.43 | YES
30 | CASP7 | CASP7 | CASP7 | 7214 | 0.059 | 0.43 | YES
31 | PTK2 | PTK2 | PTK2 | 7509 | 0.053 | 0.42 | NO
32 | CASP2 | CASP2 | CASP2 | 7593 | 0.052 | 0.43 | NO
33 | BIRC2 | BIRC2 | BIRC2 | 7866 | 0.047 | 0.42 | NO
34 | NUMA1 | NUMA1 | NUMA1 | 7962 | 0.045 | 0.43 | NO
35 | NFKB1 | NFKB1 | NFKB1 | 8321 | 0.039 | 0.41 | NO
36 | MDM2 | MDM2 | MDM2 | 8417 | 0.037 | 0.42 | NO
37 | CASP6 | CASP6 | CASP6 | 8419 | 0.037 | 0.42 | NO
38 | TRAF2 | TRAF2 | TRAF2 | 9424 | 0.022 | 0.37 | NO
39 | CHUK | CHUK | CHUK | 9445 | 0.021 | 0.37 | NO
40 | NFKBIA | NFKBIA | NFKBIA | 9478 | 0.02 | 0.38 | NO
41 | PSEN1 | PSEN1 | PSEN1 | 9677 | 0.017 | 0.37 | NO
42 | PARP1 | PARP1 | PARP1 | 9829 | 0.015 | 0.36 | NO
43 | XIAP | XIAP | XIAP | 9958 | 0.013 | 0.36 | NO
44 | RELA | RELA | RELA | 10068 | 0.011 | 0.35 | NO
45 | CYCS | CYCS | CYCS | 10411 | 0.0064 | 0.34 | NO
46 | DAXX | DAXX | DAXX | 10909 | -0.0013 | 0.31 | NO
47 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 10911 | -0.0013 | 0.31 | NO
48 | ACTG1 | ACTG1 | ACTG1 | 11169 | -0.0055 | 0.3 | NO
49 | APAF1 | APAF1 | APAF1 | 11881 | -0.017 | 0.26 | NO
50 | SPTAN1 | SPTAN1 | SPTAN1 | 11942 | -0.018 | 0.26 | NO
51 | RASA1 | RASA1 | RASA1 | 12732 | -0.031 | 0.22 | NO
52 | MAP2K7 | MAP2K7 | MAP2K7 | 12749 | -0.031 | 0.23 | NO
53 | LMNA | LMNA | LMNA | 13352 | -0.043 | 0.2 | NO
54 | MAP3K1 | MAP3K1 | MAP3K1 | 13631 | -0.048 | 0.19 | NO
55 | RIPK1 | RIPK1 | RIPK1 | 14375 | -0.068 | 0.17 | NO
56 | PSEN2 | PSEN2 | PSEN2 | 14798 | -0.081 | 0.16 | NO
57 | CRADD | CRADD | CRADD | 16035 | -0.14 | 0.12 | 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 HDAC PATHWAY.

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HDAC 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 FAS 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 | PIK3CG | PIK3CG | PIK3CG | 75 | 0.72 | 0.12 | YES
2 | EGF | EGF | EGF | 450 | 0.52 | 0.18 | YES
3 | PIK3R5 | PIK3R5 | PIK3R5 | 466 | 0.51 | 0.26 | YES
4 | LEF1 | LEF1 | LEF1 | 638 | 0.47 | 0.34 | YES
5 | AXIN2 | AXIN2 | AXIN2 | 869 | 0.43 | 0.39 | YES
6 | PIK3CD | PIK3CD | PIK3CD | 895 | 0.42 | 0.46 | YES
7 | TCF7 | TCF7 | TCF7 | 1115 | 0.39 | 0.52 | YES
8 | MYC | MYC | MYC | 3158 | 0.2 | 0.44 | NO
9 | PIK3R3 | PIK3R3 | PIK3R3 | 4370 | 0.14 | 0.39 | NO
10 | PIK3CA | PIK3CA | PIK3CA | 4897 | 0.12 | 0.38 | NO
11 | AKT3 | AKT3 | AKT3 | 5193 | 0.11 | 0.38 | NO
12 | MAP2K1 | MAP2K1 | MAP2K1 | 5241 | 0.11 | 0.4 | NO
13 | SOS1 | SOS1 | SOS1 | 5817 | 0.09 | 0.38 | NO
14 | MAPK3 | MAPK3 | MAPK3 | 5820 | 0.09 | 0.4 | NO
15 | KRAS | KRAS | KRAS | 6308 | 0.077 | 0.38 | NO
16 | CASP9 | CASP9 | CASP9 | 6572 | 0.072 | 0.38 | NO
17 | CTNNB1 | CTNNB1 | CTNNB1 | 6591 | 0.071 | 0.39 | NO
18 | PIK3CB | PIK3CB | PIK3CB | 6609 | 0.071 | 0.4 | NO
19 | FOXO3 | FOXO3 | FOXO3 | 7114 | 0.061 | 0.38 | NO
20 | CTNNA2 | CTNNA2 | CTNNA2 | 8021 | 0.044 | 0.34 | NO
21 | GSK3B | GSK3B | GSK3B | 8056 | 0.043 | 0.35 | NO
22 | RAF1 | RAF1 | RAF1 | 8071 | 0.043 | 0.35 | NO
23 | MLH1 | MLH1 | MLH1 | 8634 | 0.034 | 0.33 | NO
24 | GRB2 | GRB2 | GRB2 | 8881 | 0.03 | 0.32 | NO
25 | APC2 | APC2 | APC2 | 9296 | 0.024 | 0.3 | NO
26 | MAPK1 | MAPK1 | MAPK1 | 9347 | 0.023 | 0.3 | NO
27 | PDPK1 | PDPK1 | PDPK1 | 9474 | 0.02 | 0.3 | NO
28 | PTEN | PTEN | PTEN | 9549 | 0.019 | 0.3 | NO
29 | AKT1 | AKT1 | AKT1 | 9715 | 0.017 | 0.29 | NO
30 | AXIN1 | AXIN1 | AXIN1 | 9803 | 0.015 | 0.29 | NO
31 | ERBB2 | ERBB2 | ERBB2 | 10041 | 0.012 | 0.28 | NO
32 | ELK1 | ELK1 | ELK1 | 10062 | 0.012 | 0.28 | NO
33 | TCF7L1 | TCF7L1 | TCF7L1 | 10191 | 0.0097 | 0.27 | NO
34 | BRAF | BRAF | BRAF | 10737 | 0.0016 | 0.24 | NO
35 | MAP2K2 | MAP2K2 | MAP2K2 | 10978 | -0.0024 | 0.23 | NO
36 | ILK | ILK | ILK | 11240 | -0.0067 | 0.22 | NO
37 | ARAF | ARAF | ARAF | 11378 | -0.0092 | 0.21 | NO
38 | TP53 | TP53 | TP53 | 11484 | -0.011 | 0.21 | NO
39 | AKT2 | AKT2 | AKT2 | 11585 | -0.012 | 0.2 | NO
40 | CTNNA1 | CTNNA1 | CTNNA1 | 11948 | -0.018 | 0.19 | NO
41 | SOS2 | SOS2 | SOS2 | 12019 | -0.019 | 0.18 | NO
42 | PIK3R2 | PIK3R2 | PIK3R2 | 12661 | -0.03 | 0.16 | NO
43 | TCF7L2 | TCF7L2 | TCF7L2 | 13289 | -0.041 | 0.13 | NO
44 | APC | APC | APC | 13644 | -0.049 | 0.12 | NO
45 | BAD | BAD | BAD | 13854 | -0.054 | 0.11 | NO
46 | NRAS | NRAS | NRAS | 14613 | -0.074 | 0.084 | NO
47 | PIK3R1 | PIK3R1 | PIK3R1 | 14733 | -0.078 | 0.09 | NO
48 | CDH1 | CDH1 | CDH1 | 15755 | -0.12 | 0.054 | NO
49 | EGFR | EGFR | EGFR | 15766 | -0.12 | 0.074 | NO
50 | CTNNA3 | CTNNA3 | CTNNA3 | 16274 | -0.16 | 0.073 | NO
51 | CCND1 | CCND1 | CCND1 | 16472 | -0.17 | 0.091 | 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 FAS PATHWAY.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FAS 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 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 | PIK3CG | PIK3CG | PIK3CG | 75 | 0.72 | 0.093 | YES
2 | PRKCB | PRKCB | PRKCB | 329 | 0.56 | 0.15 | YES
3 | EGF | EGF | EGF | 450 | 0.52 | 0.22 | YES
4 | PIK3R5 | PIK3R5 | PIK3R5 | 466 | 0.51 | 0.29 | YES
5 | RARB | RARB | RARB | 774 | 0.44 | 0.33 | YES
6 | PIK3CD | PIK3CD | PIK3CD | 895 | 0.42 | 0.38 | YES
7 | CDK6 | CDK6 | CDK6 | 1092 | 0.39 | 0.42 | YES
8 | RXRG | RXRG | RXRG | 1397 | 0.35 | 0.45 | YES
9 | RASSF5 | RASSF5 | RASSF5 | 1962 | 0.29 | 0.46 | YES
10 | PRKCG | PRKCG | PRKCG | 2832 | 0.22 | 0.44 | YES
11 | E2F2 | E2F2 | E2F2 | 3179 | 0.2 | 0.45 | YES
12 | PIK3R3 | PIK3R3 | PIK3R3 | 4370 | 0.14 | 0.4 | YES
13 | STK4 | STK4 | STK4 | 4371 | 0.14 | 0.42 | YES
14 | CDKN2A | CDKN2A | CDKN2A | 4606 | 0.13 | 0.43 | YES
15 | PIK3CA | PIK3CA | PIK3CA | 4897 | 0.12 | 0.43 | YES
16 | RB1 | RB1 | RB1 | 4944 | 0.12 | 0.44 | YES
17 | RASSF1 | RASSF1 | RASSF1 | 5168 | 0.11 | 0.44 | YES
18 | AKT3 | AKT3 | AKT3 | 5193 | 0.11 | 0.46 | YES
19 | PLCG1 | PLCG1 | PLCG1 | 5209 | 0.11 | 0.47 | YES
20 | MAP2K1 | MAP2K1 | MAP2K1 | 5241 | 0.11 | 0.48 | YES
21 | FHIT | FHIT | FHIT | 5598 | 0.096 | 0.48 | YES
22 | SOS1 | SOS1 | SOS1 | 5817 | 0.09 | 0.48 | YES
23 | MAPK3 | MAPK3 | MAPK3 | 5820 | 0.09 | 0.49 | YES
24 | KRAS | KRAS | KRAS | 6308 | 0.077 | 0.47 | NO
25 | CASP9 | CASP9 | CASP9 | 6572 | 0.072 | 0.47 | NO
26 | PIK3CB | PIK3CB | PIK3CB | 6609 | 0.071 | 0.47 | NO
27 | PLCG2 | PLCG2 | PLCG2 | 6768 | 0.067 | 0.48 | NO
28 | FOXO3 | FOXO3 | FOXO3 | 7114 | 0.061 | 0.46 | NO
29 | HRAS | HRAS | HRAS | 7390 | 0.055 | 0.46 | NO
30 | RAF1 | RAF1 | RAF1 | 8071 | 0.043 | 0.42 | NO
31 | CDK4 | CDK4 | CDK4 | 8334 | 0.038 | 0.42 | NO
32 | GRB2 | GRB2 | GRB2 | 8881 | 0.03 | 0.39 | NO
33 | MAPK1 | MAPK1 | MAPK1 | 9347 | 0.023 | 0.37 | NO
34 | PDPK1 | PDPK1 | PDPK1 | 9474 | 0.02 | 0.36 | NO
35 | AKT1 | AKT1 | AKT1 | 9715 | 0.017 | 0.35 | NO
36 | ERBB2 | ERBB2 | ERBB2 | 10041 | 0.012 | 0.33 | NO
37 | PRKCA | PRKCA | PRKCA | 10189 | 0.0097 | 0.33 | NO
38 | BRAF | BRAF | BRAF | 10737 | 0.0016 | 0.3 | NO
39 | MAP2K2 | MAP2K2 | MAP2K2 | 10978 | -0.0024 | 0.28 | NO
40 | ARAF | ARAF | ARAF | 11378 | -0.0092 | 0.26 | NO
41 | TP53 | TP53 | TP53 | 11484 | -0.011 | 0.26 | NO
42 | AKT2 | AKT2 | AKT2 | 11585 | -0.012 | 0.26 | NO
43 | SOS2 | SOS2 | SOS2 | 12019 | -0.019 | 0.23 | NO
44 | RXRA | RXRA | RXRA | 12611 | -0.029 | 0.2 | NO
45 | PIK3R2 | PIK3R2 | PIK3R2 | 12661 | -0.03 | 0.21 | NO
46 | RXRB | RXRB | RXRB | 12792 | -0.032 | 0.2 | NO
47 | BAD | BAD | BAD | 13854 | -0.054 | 0.15 | NO
48 | TGFA | TGFA | TGFA | 14453 | -0.07 | 0.13 | NO
49 | NRAS | NRAS | NRAS | 14613 | -0.074 | 0.13 | NO
50 | PIK3R1 | PIK3R1 | PIK3R1 | 14733 | -0.078 | 0.13 | NO
51 | E2F3 | E2F3 | E2F3 | 15088 | -0.092 | 0.13 | NO
52 | EGFR | EGFR | EGFR | 15766 | -0.12 | 0.11 | NO
53 | CCND1 | CCND1 | CCND1 | 16472 | -0.17 | 0.091 | NO

Figure S9. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.

Figure S10. 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 HIVNEF PATHWAY

Table S6. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PIK3CG | PIK3CG | PIK3CG | 75 | 0.72 | 0.098 | YES
2 | PIK3R5 | PIK3R5 | PIK3R5 | 466 | 0.51 | 0.15 | YES
3 | LEF1 | LEF1 | LEF1 | 638 | 0.47 | 0.21 | YES
4 | AXIN2 | AXIN2 | AXIN2 | 869 | 0.43 | 0.26 | YES
5 | PIK3CD | PIK3CD | PIK3CD | 895 | 0.42 | 0.32 | YES
6 | TCF7 | TCF7 | TCF7 | 1115 | 0.39 | 0.36 | YES
7 | BCL2 | BCL2 | BCL2 | 2609 | 0.24 | 0.31 | YES
8 | BIRC5 | BIRC5 | BIRC5 | 2763 | 0.23 | 0.34 | YES
9 | DCC | DCC | DCC | 2990 | 0.21 | 0.35 | YES
10 | MYC | MYC | MYC | 3158 | 0.2 | 0.37 | YES
11 | MAPK10 | MAPK10 | MAPK10 | 3646 | 0.17 | 0.37 | YES
12 | PIK3R3 | PIK3R3 | PIK3R3 | 4370 | 0.14 | 0.35 | YES
13 | TGFB1 | TGFB1 | TGFB1 | 4599 | 0.13 | 0.36 | YES
14 | RAC2 | RAC2 | RAC2 | 4610 | 0.13 | 0.38 | YES
15 | PIK3CA | PIK3CA | PIK3CA | 4897 | 0.12 | 0.38 | YES
16 | MAPK8 | MAPK8 | MAPK8 | 4907 | 0.12 | 0.39 | YES
17 | RALGDS | RALGDS | RALGDS | 5052 | 0.11 | 0.4 | YES
18 | FOS | FOS | FOS | 5125 | 0.11 | 0.41 | YES
19 | AKT3 | AKT3 | AKT3 | 5193 | 0.11 | 0.42 | YES
20 | TGFBR1 | TGFBR1 | TGFBR1 | 5216 | 0.11 | 0.44 | YES
21 | CASP3 | CASP3 | CASP3 | 5224 | 0.11 | 0.45 | YES
22 | MAP2K1 | MAP2K1 | MAP2K1 | 5241 | 0.11 | 0.47 | YES
23 | MAPK3 | MAPK3 | MAPK3 | 5820 | 0.09 | 0.45 | YES
24 | APPL1 | APPL1 | APPL1 | 5835 | 0.089 | 0.46 | YES
25 | MSH6 | MSH6 | MSH6 | 6149 | 0.081 | 0.46 | YES
26 | KRAS | KRAS | KRAS | 6308 | 0.077 | 0.46 | YES
27 | CASP9 | CASP9 | CASP9 | 6572 | 0.072 | 0.45 | YES
28 | CTNNB1 | CTNNB1 | CTNNB1 | 6591 | 0.071 | 0.46 | YES
29 | PIK3CB | PIK3CB | PIK3CB | 6609 | 0.071 | 0.47 | YES
30 | RHOA | RHOA | RHOA | 6847 | 0.066 | 0.47 | YES
31 | TGFBR2 | TGFBR2 | TGFBR2 | 6868 | 0.065 | 0.48 | YES
32 | MSH2 | MSH2 | MSH2 | 7273 | 0.057 | 0.46 | NO
33 | GSK3B | GSK3B | GSK3B | 8056 | 0.043 | 0.42 | NO
34 | RAF1 | RAF1 | RAF1 | 8071 | 0.043 | 0.43 | NO
35 | RAC3 | RAC3 | RAC3 | 8258 | 0.04 | 0.43 | NO
36 | MLH1 | MLH1 | MLH1 | 8634 | 0.034 | 0.41 | NO
37 | RAC1 | RAC1 | RAC1 | 9013 | 0.028 | 0.39 | NO
38 | APC2 | APC2 | APC2 | 9296 | 0.024 | 0.38 | NO
39 | MAPK1 | MAPK1 | MAPK1 | 9347 | 0.023 | 0.38 | NO
40 | AKT1 | AKT1 | AKT1 | 9715 | 0.017 | 0.36 | NO
41 | AXIN1 | AXIN1 | AXIN1 | 9803 | 0.015 | 0.36 | NO
42 | TCF7L1 | TCF7L1 | TCF7L1 | 10191 | 0.0097 | 0.34 | NO
43 | CYCS | CYCS | CYCS | 10411 | 0.0064 | 0.33 | NO
44 | TGFB2 | TGFB2 | TGFB2 | 10735 | 0.0016 | 0.31 | NO
45 | BRAF | BRAF | BRAF | 10737 | 0.0016 | 0.31 | NO
46 | MAPK9 | MAPK9 | MAPK9 | 10743 | 0.0014 | 0.31 | NO
47 | SMAD3 | SMAD3 | SMAD3 | 11078 | -0.0041 | 0.29 | NO
48 | JUN | JUN | JUN | 11328 | -0.0084 | 0.28 | NO
49 | ARAF | ARAF | ARAF | 11378 | -0.0092 | 0.28 | NO
50 | TP53 | TP53 | TP53 | 11484 | -0.011 | 0.28 | NO
51 | AKT2 | AKT2 | AKT2 | 11585 | -0.012 | 0.27 | NO
52 | SMAD2 | SMAD2 | SMAD2 | 12081 | -0.02 | 0.25 | NO
53 | PIK3R2 | PIK3R2 | PIK3R2 | 12661 | -0.03 | 0.22 | NO
54 | TCF7L2 | TCF7L2 | TCF7L2 | 13289 | -0.041 | 0.19 | NO
55 | APC | APC | APC | 13644 | -0.049 | 0.18 | NO
56 | MSH3 | MSH3 | MSH3 | 13846 | -0.054 | 0.18 | NO
57 | BAD | BAD | BAD | 13854 | -0.054 | 0.18 | NO
58 | SMAD4 | SMAD4 | SMAD4 | 13935 | -0.056 | 0.19 | NO
59 | BAX | BAX | BAX | 14236 | -0.064 | 0.18 | NO
60 | PIK3R1 | PIK3R1 | PIK3R1 | 14733 | -0.078 | 0.16 | NO
61 | CCND1 | CCND1 | CCND1 | 16472 | -0.17 | 0.091 | 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: BIOCARTA HIVNEF PATHWAY.

Figure S12. 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 IL2RB PATHWAY

Table S7. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | ZBP1 | ZBP1 | ZBP1 | 83 | 0.71 | 0.094 | YES
2 | CCL4L2 | CCL4L2 | CCL4L2 | 155 | 0.64 | 0.18 | YES
3 | CCL4 | CCL4 | CCL4 | 287 | 0.57 | 0.25 | YES
4 | AIM2 | AIM2 | AIM2 | 359 | 0.55 | 0.32 | YES
5 | CCL5 | CCL5 | CCL5 | 504 | 0.5 | 0.39 | YES
6 | CASP1 | CASP1 | CASP1 | 607 | 0.48 | 0.45 | YES
7 | IL6 | IL6 | IL6 | 662 | 0.47 | 0.51 | YES
8 | CXCL10 | CXCL10 | CXCL10 | 942 | 0.41 | 0.55 | YES
9 | IFNB1 | IFNB1 | IFNB1 | 1215 | 0.37 | 0.59 | YES
10 | TMEM173 | TMEM173 | TMEM173 | 1366 | 0.35 | 0.63 | YES
11 | RIPK3 | RIPK3 | RIPK3 | 1476 | 0.34 | 0.67 | YES
12 | IL1B | IL1B | IL1B | 2302 | 0.26 | 0.66 | NO
13 | IL33 | IL33 | IL33 | 3464 | 0.18 | 0.62 | NO
14 | POLR3K | POLR3K | POLR3K | 4761 | 0.12 | 0.57 | NO
15 | TREX1 | TREX1 | TREX1 | 5167 | 0.11 | 0.56 | NO
16 | POLR1D | POLR1D | POLR1D | 6426 | 0.074 | 0.5 | NO
17 | TBK1 | TBK1 | TBK1 | 6471 | 0.074 | 0.51 | NO
18 | IKBKE | IKBKE | IKBKE | 6478 | 0.073 | 0.52 | NO
19 | IKBKB | IKBKB | IKBKB | 6705 | 0.069 | 0.52 | NO
20 | POLR3D | POLR3D | POLR3D | 7664 | 0.05 | 0.47 | NO
21 | POLR3GL | POLR3GL | POLR3GL | 7710 | 0.05 | 0.48 | NO
22 | POLR1C | POLR1C | POLR1C | 7727 | 0.049 | 0.48 | NO
23 | NFKB1 | NFKB1 | NFKB1 | 8321 | 0.039 | 0.45 | NO
24 | IKBKG | IKBKG | IKBKG | 8583 | 0.035 | 0.44 | NO
25 | NFKBIB | NFKBIB | NFKBIB | 9379 | 0.022 | 0.4 | NO
26 | CHUK | CHUK | CHUK | 9445 | 0.021 | 0.4 | NO
27 | NFKBIA | NFKBIA | NFKBIA | 9478 | 0.02 | 0.4 | NO
28 | POLR3H | POLR3H | POLR3H | 9776 | 0.016 | 0.39 | NO
29 | POLR3G | POLR3G | POLR3G | 10001 | 0.012 | 0.38 | NO
30 | RELA | RELA | RELA | 10068 | 0.011 | 0.38 | NO
31 | POLR3A | POLR3A | POLR3A | 10491 | 0.0052 | 0.36 | NO
32 | PYCARD | PYCARD | PYCARD | 11119 | -0.0048 | 0.32 | NO
33 | IL18 | IL18 | IL18 | 11824 | -0.016 | 0.28 | NO
34 | POLR3C | POLR3C | POLR3C | 12085 | -0.02 | 0.27 | NO
35 | DDX58 | DDX58 | DDX58 | 12317 | -0.024 | 0.26 | NO
36 | MAVS | MAVS | MAVS | 13170 | -0.039 | 0.22 | NO
37 | ADAR | ADAR | ADAR | 13209 | -0.04 | 0.22 | NO
38 | POLR3F | POLR3F | POLR3F | 13400 | -0.044 | 0.22 | NO
39 | IRF7 | IRF7 | IRF7 | 13907 | -0.055 | 0.2 | NO
40 | IRF3 | IRF3 | IRF3 | 13930 | -0.056 | 0.21 | NO
41 | RIPK1 | RIPK1 | RIPK1 | 14375 | -0.068 | 0.19 | NO
42 | POLR3B | POLR3B | POLR3B | 15511 | -0.11 | 0.14 | 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: BIOCARTA IL2RB PATHWAY.

Figure S14. 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

genes ES table in pathway: BIOCARTA GSK3 PATHWAY

Table S8. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PIP5K1B | PIP5K1B | PIP5K1B | 43 | 0.77 | 0.034 | YES
2 | ACAP1 | ACAP1 | ACAP1 | 121 | 0.67 | 0.061 | YES
3 | IL2RA | IL2RA | IL2RA | 128 | 0.66 | 0.092 | YES
4 | AGAP2 | AGAP2 | AGAP2 | 168 | 0.63 | 0.12 | YES
5 | IQSEC3 | IQSEC3 | IQSEC3 | 201 | 0.62 | 0.15 | YES
6 | CCR5 | CCR5 | CCR5 | 293 | 0.57 | 0.17 | YES
7 | EGF | EGF | EGF | 450 | 0.52 | 0.18 | YES
8 | NTRK1 | NTRK1 | NTRK1 | 502 | 0.5 | 0.21 | YES
9 | IL2RB | IL2RB | IL2RB | 511 | 0.5 | 0.23 | YES
10 | ADRB2 | ADRB2 | ADRB2 | 770 | 0.44 | 0.24 | YES
11 | KIT | KIT | KIT | 798 | 0.44 | 0.26 | YES
12 | IQSEC2 | IQSEC2 | IQSEC2 | 999 | 0.41 | 0.26 | YES
13 | IL2RG | IL2RG | IL2RG | 1089 | 0.39 | 0.28 | YES
14 | ADRB3 | ADRB3 | ADRB3 | 1253 | 0.37 | 0.28 | YES
15 | CXCR4 | CXCR4 | CXCR4 | 1273 | 0.36 | 0.3 | YES
16 | CXCR2 | CXCR2 | CXCR2 | 1388 | 0.35 | 0.31 | YES
17 | ASAP3 | ASAP3 | ASAP3 | 1584 | 0.33 | 0.32 | YES
18 | DNM3 | DNM3 | DNM3 | 1622 | 0.33 | 0.33 | YES
19 | ADRB1 | ADRB1 | ADRB1 | 1889 | 0.3 | 0.33 | YES
20 | IGF1R | IGF1R | IGF1R | 2202 | 0.27 | 0.32 | YES
21 | SH3GL2 | SH3GL2 | SH3GL2 | 2312 | 0.26 | 0.33 | YES
22 | RAB31 | RAB31 | RAB31 | 2465 | 0.25 | 0.33 | YES
23 | GRK5 | GRK5 | GRK5 | 2575 | 0.24 | 0.34 | YES
24 | HLA-G | HLA-G | HLA-G | 2623 | 0.24 | 0.35 | YES
25 | CSF1R | CSF1R | CSF1R | 2802 | 0.22 | 0.35 | YES
26 | SH3GL3 | SH3GL3 | SH3GL3 | 3184 | 0.2 | 0.34 | YES
27 | SH3KBP1 | SH3KBP1 | SH3KBP1 | 3208 | 0.2 | 0.34 | YES
28 | GRK7 | GRK7 | GRK7 | 3294 | 0.19 | 0.35 | YES
29 | ACAP2 | ACAP2 | ACAP2 | 3380 | 0.19 | 0.35 | YES
30 | ARRB1 | ARRB1 | ARRB1 | 3460 | 0.18 | 0.36 | YES
31 | EHD3 | EHD3 | EHD3 | 3466 | 0.18 | 0.37 | YES
32 | PDGFRA | PDGFRA | PDGFRA | 3520 | 0.18 | 0.37 | YES
33 | CBLB | CBLB | CBLB | 3978 | 0.16 | 0.35 | YES
34 | LDLRAP1 | LDLRAP1 | LDLRAP1 | 3998 | 0.16 | 0.36 | YES
35 | CXCR1 | CXCR1 | CXCR1 | 4016 | 0.15 | 0.37 | YES
36 | KDR | KDR | KDR | 4073 | 0.15 | 0.37 | YES
37 | TRAF6 | TRAF6 | TRAF6 | 4194 | 0.15 | 0.37 | YES
38 | HLA-F | HLA-F | HLA-F | 4199 | 0.15 | 0.38 | YES
39 | ADRBK1 | ADRBK1 | ADRBK1 | 4576 | 0.13 | 0.36 | YES
40 | SMURF2 | SMURF2 | SMURF2 | 4577 | 0.13 | 0.37 | YES
41 | RET | RET | RET | 4640 | 0.13 | 0.37 | YES
42 | EHD2 | EHD2 | EHD2 | 4674 | 0.13 | 0.38 | YES
43 | CHMP2B | CHMP2B | CHMP2B | 4697 | 0.13 | 0.38 | YES
44 | GRK6 | GRK6 | GRK6 | 4822 | 0.12 | 0.38 | YES
45 | ADRBK2 | ADRBK2 | ADRBK2 | 4825 | 0.12 | 0.38 | YES
46 | ASAP1 | ASAP1 | ASAP1 | 4831 | 0.12 | 0.39 | YES
47 | HLA-E | HLA-E | HLA-E | 4843 | 0.12 | 0.4 | YES
48 | PRKCI | PRKCI | PRKCI | 4868 | 0.12 | 0.4 | YES
49 | F2R | F2R | F2R | 5153 | 0.11 | 0.39 | NO
50 | SMAP2 | SMAP2 | SMAP2 | 5215 | 0.11 | 0.39 | NO
51 | RAB11FIP2 | RAB11FIP2 | RAB11FIP2 | 5244 | 0.11 | 0.39 | NO
52 | HSPA6 | HSPA6 | HSPA6 | 5322 | 0.1 | 0.4 | NO
53 | VTA1 | VTA1 | VTA1 | 5553 | 0.097 | 0.39 | NO
54 | DNM2 | DNM2 | DNM2 | 5736 | 0.092 | 0.38 | NO
55 | HLA-B | HLA-B | HLA-B | 5861 | 0.088 | 0.38 | NO
56 | GIT1 | GIT1 | GIT1 | 6079 | 0.083 | 0.37 | NO
57 | HSPA1L | HSPA1L | HSPA1L | 6107 | 0.082 | 0.37 | NO
58 | FLT1 | FLT1 | FLT1 | 6154 | 0.081 | 0.37 | NO
59 | HSPA2 | HSPA2 | HSPA2 | 6177 | 0.081 | 0.38 | NO
60 | VPS4A | VPS4A | VPS4A | 6272 | 0.078 | 0.37 | NO
61 | ARAP3 | ARAP3 | ARAP3 | 6322 | 0.077 | 0.38 | NO
62 | IQSEC1 | IQSEC1 | IQSEC1 | 6371 | 0.076 | 0.38 | NO
63 | FAM125B | FAM125B | FAM125B | 6443 | 0.074 | 0.38 | NO
64 | RAB5A | RAB5A | RAB5A | 6520 | 0.072 | 0.38 | NO
65 | EPS15 | EPS15 | EPS15 | 6532 | 0.072 | 0.38 | NO
66 | RAB11FIP3 | RAB11FIP3 | RAB11FIP3 | 6619 | 0.07 | 0.38 | NO
67 | CBL | CBL | CBL | 6627 | 0.07 | 0.38 | NO
68 | PIKFYVE | PIKFYVE | PIKFYVE | 6637 | 0.07 | 0.38 | NO
69 | EHD1 | EHD1 | EHD1 | 6661 | 0.07 | 0.38 | NO
70 | GRK4 | GRK4 | GRK4 | 6728 | 0.068 | 0.38 | NO
71 | TFRC | TFRC | TFRC | 6737 | 0.068 | 0.39 | NO
72 | ARAP1 | ARAP1 | ARAP1 | 6769 | 0.067 | 0.39 | NO
73 | PSD | PSD | PSD | 6932 | 0.064 | 0.38 | NO
74 | SMAP1 | SMAP1 | SMAP1 | 6995 | 0.063 | 0.38 | NO
75 | ZFYVE20 | ZFYVE20 | ZFYVE20 | 7013 | 0.063 | 0.38 | NO
76 | EHD4 | EHD4 | EHD4 | 7047 | 0.062 | 0.38 | NO
77 | HLA-A | HLA-A | HLA-A | 7084 | 0.061 | 0.38 | NO
78 | PARD6A | PARD6A | PARD6A | 7245 | 0.058 | 0.38 | NO
79 | CHMP5 | CHMP5 | CHMP5 | 7392 | 0.055 | 0.37 | NO
80 | VPS36 | VPS36 | VPS36 | 7533 | 0.053 | 0.37 | NO
81 | PDCD6IP | PDCD6IP | PDCD6IP | 7570 | 0.052 | 0.37 | NO
82 | ERBB4 | ERBB4 | ERBB4 | 7726 | 0.05 | 0.36 | NO
83 | RAB11FIP4 | RAB11FIP4 | RAB11FIP4 | 7804 | 0.048 | 0.36 | NO
84 | PIP5K1C | PIP5K1C | PIP5K1C | 7812 | 0.048 | 0.36 | NO
85 | PIP4K2B | PIP4K2B | PIP4K2B | 8033 | 0.044 | 0.35 | NO
86 | ITCH | ITCH | ITCH | 8044 | 0.043 | 0.35 | NO
87 | CDC42 | CDC42 | CDC42 | 8081 | 0.043 | 0.35 | NO
88 | PRKCZ | PRKCZ | PRKCZ | 8210 | 0.04 | 0.35 | NO
89 | DAB2 | DAB2 | DAB2 | 8263 | 0.04 | 0.35 | NO
90 | GIT2 | GIT2 | GIT2 | 8387 | 0.038 | 0.34 | NO
91 | MDM2 | MDM2 | MDM2 | 8417 | 0.037 | 0.34 | NO
92 | CHMP4B | CHMP4B | CHMP4B | 8512 | 0.036 | 0.34 | NO
93 | ACAP3 | ACAP3 | ACAP3 | 8564 | 0.035 | 0.34 | NO
94 | SH3GL1 | SH3GL1 | SH3GL1 | 8740 | 0.032 | 0.33 | NO
95 | ARRB2 | ARRB2 | ARRB2 | 8848 | 0.03 | 0.32 | NO
96 | RNF41 | RNF41 | RNF41 | 9139 | 0.026 | 0.31 | NO
97 | RAB22A | RAB22A | RAB22A | 9210 | 0.025 | 0.31 | NO
98 | ARFGAP1 | ARFGAP1 | ARFGAP1 | 9215 | 0.025 | 0.31 | NO
99 | HSPA8 | HSPA8 | HSPA8 | 9295 | 0.024 | 0.3 | NO
100 | SH3GLB1 | SH3GLB1 | SH3GLB1 | 9333 | 0.023 | 0.3 | NO
101 | VPS37B | VPS37B | VPS37B | 9547 | 0.019 | 0.29 | NO
102 | EEA1 | EEA1 | EEA1 | 9576 | 0.019 | 0.29 | NO
103 | DNAJC6 | DNAJC6 | DNAJC6 | 9771 | 0.016 | 0.28 | NO
104 | USP8 | USP8 | USP8 | 9789 | 0.016 | 0.28 | NO
105 | MET | MET | MET | 9870 | 0.014 | 0.28 | NO
106 | STAMBP | STAMBP | STAMBP | 10003 | 0.012 | 0.27 | NO
107 | RAB11FIP5 | RAB11FIP5 | RAB11FIP5 | 10051 | 0.012 | 0.27 | NO
108 | AP2M1 | AP2M1 | AP2M1 | 10102 | 0.011 | 0.27 | NO
109 | AP2B1 | AP2B1 | AP2B1 | 10213 | 0.0093 | 0.26 | NO
110 | VPS25 | VPS25 | VPS25 | 10218 | 0.0093 | 0.26 | NO
111 | HGS | HGS | HGS | 10253 | 0.0087 | 0.26 | NO
112 | RABEP1 | RABEP1 | RABEP1 | 10297 | 0.008 | 0.26 | NO
113 | PSD2 | PSD2 | PSD2 | 10346 | 0.0072 | 0.26 | NO
114 | ARFGAP3 | ARFGAP3 | ARFGAP3 | 10361 | 0.0071 | 0.26 | NO
115 | AP2A2 | AP2A2 | AP2A2 | 10394 | 0.0066 | 0.25 | NO
116 | HLA-C | HLA-C | HLA-C | 10436 | 0.006 | 0.25 | NO
117 | HSPA1B | HSPA1B | HSPA1B | 10473 | 0.0055 | 0.25 | NO
118 | CHMP4A | CHMP4A | CHMP4A | 10668 | 0.0026 | 0.24 | NO
119 | TSG101 | TSG101 | TSG101 | 10739 | 0.0015 | 0.24 | NO
120 | CHMP1B | CHMP1B | CHMP1B | 10770 | 0.001 | 0.23 | NO
121 | ARFGAP2 | ARFGAP2 | ARFGAP2 | 10781 | 0.00088 | 0.23 | NO
122 | SH3GLB2 | SH3GLB2 | SH3GLB2 | 10795 | 0.00065 | 0.23 | NO
123 | VPS37A | VPS37A | VPS37A | 10802 | 0.00046 | 0.23 | NO
124 | SMURF1 | SMURF1 | SMURF1 | 10884 | -0.00082 | 0.23 | NO
125 | RAB5C | RAB5C | RAB5C | 10927 | -0.0016 | 0.23 | NO
126 | SRC | SRC | SRC | 10938 | -0.0018 | 0.22 | NO
127 | DNM1 | DNM1 | DNM1 | 11003 | -0.0028 | 0.22 | NO
128 | HSPA1A | HSPA1A | HSPA1A | 11061 | -0.0037 | 0.22 | NO
129 | CHMP6 | CHMP6 | CHMP6 | 11192 | -0.0059 | 0.21 | NO
130 | PSD4 | PSD4 | PSD4 | 11289 | -0.0076 | 0.21 | NO
131 | RUFY1 | RUFY1 | RUFY1 | 11463 | -0.011 | 0.2 | NO
132 | VPS37D | VPS37D | VPS37D | 11571 | -0.012 | 0.19 | NO
133 | VPS4B | VPS4B | VPS4B | 11652 | -0.013 | 0.19 | NO
134 | DNM1L | DNM1L | DNM1L | 11661 | -0.014 | 0.19 | NO
135 | ARF6 | ARF6 | ARF6 | 11784 | -0.015 | 0.18 | NO
136 | VPS37C | VPS37C | VPS37C | 11788 | -0.015 | 0.18 | NO
137 | AP2A1 | AP2A1 | AP2A1 | 11792 | -0.015 | 0.18 | NO
138 | VPS24 | VPS24 | VPS24 | 11845 | -0.016 | 0.18 | NO
139 | RAB5B | RAB5B | RAB5B | 11864 | -0.017 | 0.18 | NO
140 | ASAP2 | ASAP2 | ASAP2 | 11929 | -0.018 | 0.18 | NO
141 | VPS28 | VPS28 | VPS28 | 12021 | -0.019 | 0.18 | NO
142 | CLTC | CLTC | CLTC | 12122 | -0.021 | 0.17 | NO
143 | STAM2 | STAM2 | STAM2 | 12182 | -0.022 | 0.17 | NO
144 | SNF8 | SNF8 | SNF8 | 12217 | -0.022 | 0.17 | NO
145 | STAM | STAM | STAM | 12297 | -0.024 | 0.16 | NO
146 | PLD2 | PLD2 | PLD2 | 12364 | -0.025 | 0.16 | NO
147 | AGAP1 | AGAP1 | AGAP1 | 12379 | -0.025 | 0.16 | NO
148 | PIP5K1A | PIP5K1A | PIP5K1A | 12394 | -0.025 | 0.16 | NO
149 | WWP1 | WWP1 | WWP1 | 12703 | -0.031 | 0.15 | NO
150 | EPN2 | EPN2 | EPN2 | 12728 | -0.031 | 0.15 | NO
151 | AP2S1 | AP2S1 | AP2S1 | 12816 | -0.033 | 0.14 | NO
152 | ARAP2 | ARAP2 | ARAP2 | 12847 | -0.033 | 0.14 | NO
153 | NEDD4L | NEDD4L | NEDD4L | 13002 | -0.036 | 0.14 | NO
154 | CLTB | CLTB | CLTB | 13052 | -0.037 | 0.14 | NO
155 | FAM125A | FAM125A | FAM125A | 13250 | -0.041 | 0.13 | NO
156 | RAB11A | RAB11A | RAB11A | 13270 | -0.041 | 0.13 | NO
157 | EPN3 | EPN3 | EPN3 | 13334 | -0.042 | 0.12 | NO
158 | RAB11B | RAB11B | RAB11B | 13448 | -0.045 | 0.12 | NO
159 | LDLR | LDLR | LDLR | 13693 | -0.05 | 0.11 | NO
160 | PARD6G | PARD6G | PARD6G | 13754 | -0.052 | 0.11 | NO
161 | CLTA | CLTA | CLTA | 13994 | -0.058 | 0.098 | NO
162 | RAB11FIP1 | RAB11FIP1 | RAB11FIP1 | 14182 | -0.063 | 0.091 | NO
163 | CHMP2A | CHMP2A | CHMP2A | 14359 | -0.067 | 0.084 | NO
164 | CLTCL1 | CLTCL1 | CLTCL1 | 14410 | -0.069 | 0.085 | NO
165 | EPN1 | EPN1 | EPN1 | 14669 | -0.076 | 0.074 | NO
166 | PSD3 | PSD3 | PSD3 | 14677 | -0.076 | 0.077 | NO
167 | VPS45 | VPS45 | VPS45 | 14725 | -0.078 | 0.078 | NO
168 | RAB4A | RAB4A | RAB4A | 15217 | -0.097 | 0.056 | NO
169 | CHMP4C | CHMP4C | CHMP4C | 15693 | -0.12 | 0.035 | NO
170 | EGFR | EGFR | EGFR | 15766 | -0.12 | 0.036 | NO
171 | NEDD4 | NEDD4 | NEDD4 | 15975 | -0.14 | 0.031 | NO
172 | PARD6B | PARD6B | PARD6B | 16095 | -0.14 | 0.032 | NO
173 | CBLC | CBLC | CBLC | 16625 | -0.18 | 0.011 | NO
174 | PARD3 | PARD3 | PARD3 | 16626 | -0.18 | 0.02 | NO
175 | PLD1 | PLD1 | PLD1 | 16637 | -0.19 | 0.028 | NO
176 | FGFR2 | FGFR2 | FGFR2 | 17228 | -0.26 | 0.0074 | NO
177 | ERBB3 | ERBB3 | ERBB3 | 17276 | -0.27 | 0.017 | NO
178 | FGFR3 | FGFR3 | FGFR3 | 17405 | -0.3 | 0.024 | NO
179 | FGFR4 | FGFR4 | FGFR4 | 17525 | -0.32 | 0.033 | NO

Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA GSK3 PATHWAY.

Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GSK3 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA KERATINOCYTE 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 | CD8B | CD8B | CD8B | 8 | 0.9 | 0.04 | YES
2 | CTLA4 | CTLA4 | CTLA4 | 28 | 0.81 | 0.075 | YES
3 | CD8A | CD8A | CD8A | 63 | 0.73 | 0.11 | YES
4 | PIK3CG | PIK3CG | PIK3CG | 75 | 0.72 | 0.14 | YES
5 | ICOS | ICOS | ICOS | 111 | 0.68 | 0.17 | YES
6 | IFNG | IFNG | IFNG | 118 | 0.67 | 0.2 | YES
7 | IL10 | IL10 | IL10 | 129 | 0.66 | 0.22 | YES
8 | LCK | LCK | LCK | 140 | 0.66 | 0.25 | YES
9 | ITK | ITK | ITK | 211 | 0.61 | 0.28 | YES
10 | PTPRC | PTPRC | PTPRC | 304 | 0.56 | 0.3 | YES
11 | CD247 | CD247 | CD247 | 321 | 0.56 | 0.32 | YES
12 | CD3E | CD3E | CD3E | 326 | 0.56 | 0.35 | YES
13 | CD28 | CD28 | CD28 | 328 | 0.56 | 0.37 | YES
14 | RASGRP1 | RASGRP1 | RASGRP1 | 366 | 0.54 | 0.4 | YES
15 | PIK3R5 | PIK3R5 | PIK3R5 | 466 | 0.51 | 0.41 | YES
16 | GRAP2 | GRAP2 | GRAP2 | 565 | 0.49 | 0.43 | YES
17 | ZAP70 | ZAP70 | ZAP70 | 647 | 0.47 | 0.44 | YES
18 | CD3D | CD3D | CD3D | 807 | 0.44 | 0.46 | YES
19 | PIK3CD | PIK3CD | PIK3CD | 895 | 0.42 | 0.47 | YES
20 | IL2 | IL2 | IL2 | 926 | 0.42 | 0.49 | YES
21 | CD3G | CD3G | CD3G | 980 | 0.41 | 0.5 | YES
22 | CD40LG | CD40LG | CD40LG | 1073 | 0.4 | 0.52 | YES
23 | FYN | FYN | FYN | 1142 | 0.38 | 0.53 | YES
24 | CARD11 | CARD11 | CARD11 | 1458 | 0.34 | 0.53 | YES
25 | LCP2 | LCP2 | LCP2 | 1525 | 0.34 | 0.54 | YES
26 | PDCD1 | PDCD1 | PDCD1 | 1616 | 0.33 | 0.55 | YES
27 | TEC | TEC | TEC | 1732 | 0.32 | 0.56 | YES
28 | PDK1 | PDK1 | PDK1 | 1770 | 0.31 | 0.57 | YES
29 | VAV1 | VAV1 | VAV1 | 1856 | 0.3 | 0.58 | YES
30 | CSF2 | CSF2 | CSF2 | 1900 | 0.3 | 0.59 | YES
31 | CD4 | CD4 | CD4 | 2066 | 0.28 | 0.59 | YES
32 | PRKCQ | PRKCQ | PRKCQ | 2301 | 0.26 | 0.59 | YES
33 | CHP2 | CHP2 | CHP2 | 2408 | 0.25 | 0.6 | YES
34 | LAT | LAT | LAT | 2562 | 0.24 | 0.6 | YES
35 | TNF | TNF | TNF | 2602 | 0.24 | 0.61 | YES
36 | MAP3K8 | MAP3K8 | MAP3K8 | 2838 | 0.22 | 0.6 | NO
37 | PPP3CA | PPP3CA | PPP3CA | 3201 | 0.2 | 0.59 | NO
38 | NFATC2 | NFATC2 | NFATC2 | 3669 | 0.17 | 0.57 | NO
39 | NFATC4 | NFATC4 | NFATC4 | 3671 | 0.17 | 0.58 | NO
40 | CBLB | CBLB | CBLB | 3978 | 0.16 | 0.57 | NO
41 | NCK1 | NCK1 | NCK1 | 4220 | 0.14 | 0.56 | NO
42 | PIK3R3 | PIK3R3 | PIK3R3 | 4370 | 0.14 | 0.56 | NO
43 | MAP3K7 | MAP3K7 | MAP3K7 | 4605 | 0.13 | 0.56 | NO
44 | PIK3CA | PIK3CA | PIK3CA | 4897 | 0.12 | 0.55 | NO
45 | FOS | FOS | FOS | 5125 | 0.11 | 0.54 | NO
46 | AKT3 | AKT3 | AKT3 | 5193 | 0.11 | 0.54 | NO
47 | PLCG1 | PLCG1 | PLCG1 | 5209 | 0.11 | 0.54 | NO
48 | MAP2K1 | MAP2K1 | MAP2K1 | 5241 | 0.11 | 0.55 | NO
49 | PTPN6 | PTPN6 | PTPN6 | 5429 | 0.1 | 0.54 | NO
50 | BCL10 | BCL10 | BCL10 | 5679 | 0.094 | 0.53 | NO
51 | SOS1 | SOS1 | SOS1 | 5817 | 0.09 | 0.53 | NO
52 | MAPK3 | MAPK3 | MAPK3 | 5820 | 0.09 | 0.53 | NO
53 | PAK2 | PAK2 | PAK2 | 6231 | 0.079 | 0.51 | NO
54 | KRAS | KRAS | KRAS | 6308 | 0.077 | 0.51 | NO
55 | VAV2 | VAV2 | VAV2 | 6458 | 0.074 | 0.5 | NO
56 | PIK3CB | PIK3CB | PIK3CB | 6609 | 0.071 | 0.5 | NO
57 | CBL | CBL | CBL | 6627 | 0.07 | 0.5 | NO
58 | IKBKB | IKBKB | IKBKB | 6705 | 0.069 | 0.5 | NO
59 | RHOA | RHOA | RHOA | 6847 | 0.066 | 0.5 | NO
60 | PPP3CC | PPP3CC | PPP3CC | 6948 | 0.064 | 0.49 | NO
61 | MAP3K14 | MAP3K14 | MAP3K14 | 7079 | 0.061 | 0.49 | NO
62 | NFAT5 | NFAT5 | NFAT5 | 7361 | 0.056 | 0.48 | NO
63 | NFATC3 | NFATC3 | NFATC3 | 7632 | 0.051 | 0.46 | NO
64 | PPP3R1 | PPP3R1 | PPP3R1 | 7745 | 0.049 | 0.46 | NO
65 | NFKBIE | NFKBIE | NFKBIE | 7821 | 0.048 | 0.46 | NO
66 | GSK3B | GSK3B | GSK3B | 8056 | 0.043 | 0.45 | NO
67 | RAF1 | RAF1 | RAF1 | 8071 | 0.043 | 0.45 | NO
68 | CDC42 | CDC42 | CDC42 | 8081 | 0.043 | 0.45 | NO
69 | NFKB1 | NFKB1 | NFKB1 | 8321 | 0.039 | 0.44 | NO
70 | CDK4 | CDK4 | CDK4 | 8334 | 0.038 | 0.44 | NO
71 | DLG1 | DLG1 | DLG1 | 8497 | 0.036 | 0.43 | NO
72 | IKBKG | IKBKG | IKBKG | 8583 | 0.035 | 0.43 | NO
73 | PPP3CB | PPP3CB | PPP3CB | 8804 | 0.031 | 0.42 | NO
74 | GRB2 | GRB2 | GRB2 | 8881 | 0.03 | 0.41 | NO
75 | PAK1 | PAK1 | PAK1 | 8904 | 0.03 | 0.41 | NO
76 | MAPK1 | MAPK1 | MAPK1 | 9347 | 0.023 | 0.39 | NO
77 | NFKBIB | NFKBIB | NFKBIB | 9379 | 0.022 | 0.39 | NO
78 | CHUK | CHUK | CHUK | 9445 | 0.021 | 0.39 | NO
79 | NFKBIA | NFKBIA | NFKBIA | 9478 | 0.02 | 0.39 | NO
80 | NFATC1 | NFATC1 | NFATC1 | 9479 | 0.02 | 0.39 | NO
81 | AKT1 | AKT1 | AKT1 | 9715 | 0.017 | 0.38 | NO
82 | RELA | RELA | RELA | 10068 | 0.011 | 0.36 | NO
83 | MAPK9 | MAPK9 | MAPK9 | 10743 | 0.0014 | 0.32 | NO
84 | MAP2K2 | MAP2K2 | MAP2K2 | 10978 | -0.0024 | 0.31 | NO
85 | MALT1 | MALT1 | MALT1 | 11187 | -0.0058 | 0.3 | NO
86 | JUN | JUN | JUN | 11328 | -0.0084 | 0.29 | NO
87 | PAK3 | PAK3 | PAK3 | 11333 | -0.0084 | 0.29 | NO
88 | AKT2 | AKT2 | AKT2 | 11585 | -0.012 | 0.27 | NO
89 | SOS2 | SOS2 | SOS2 | 12019 | -0.019 | 0.25 | NO
90 | MAPK14 | MAPK14 | MAPK14 | 12581 | -0.029 | 0.22 | NO
91 | PIK3R2 | PIK3R2 | PIK3R2 | 12661 | -0.03 | 0.22 | NO
92 | MAP2K7 | MAP2K7 | MAP2K7 | 12749 | -0.031 | 0.21 | NO
93 | PAK4 | PAK4 | PAK4 | 13787 | -0.052 | 0.16 | NO
94 | CHP | CHP | CHP | 14055 | -0.059 | 0.15 | NO
95 | MAPK11 | MAPK11 | MAPK11 | 14282 | -0.065 | 0.14 | NO
96 | NRAS | NRAS | NRAS | 14613 | -0.074 | 0.12 | NO
97 | PIK3R1 | PIK3R1 | PIK3R1 | 14733 | -0.078 | 0.12 | NO
98 | NCK2 | NCK2 | NCK2 | 15315 | -0.1 | 0.092 | NO
99 | MAPK13 | MAPK13 | MAPK13 | 16126 | -0.15 | 0.053 | NO
100 | VAV3 | VAV3 | VAV3 | 16601 | -0.18 | 0.035 | NO
101 | CBLC | CBLC | CBLC | 16625 | -0.18 | 0.042 | NO
102 | MAPK12 | MAPK12 | MAPK12 | 17332 | -0.28 | 0.016 | NO
103 | PAK6 | PAK6 | PAK6 | 17364 | -0.28 | 0.027 | NO
104 | PAK7 | PAK7 | PAK7 | 17562 | -0.33 | 0.031 | NO

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

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA KERATINOCYTE 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 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 | PIK3CG | PIK3CG | PIK3CG | 75 | 0.72 | 0.088 | YES
2 | EGF | EGF | EGF | 450 | 0.52 | 0.13 | YES
3 | PIK3R5 | PIK3R5 | PIK3R5 | 466 | 0.51 | 0.2 | YES
4 | PIK3CD | PIK3CD | PIK3CD | 895 | 0.42 | 0.23 | YES
5 | CDK6 | CDK6 | CDK6 | 1092 | 0.39 | 0.27 | YES
6 | BRCA2 | BRCA2 | BRCA2 | 1376 | 0.35 | 0.3 | YES
7 | VEGFC | VEGFC | VEGFC | 1453 | 0.35 | 0.34 | YES
8 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 1553 | 0.33 | 0.38 | YES
9 | E2F2 | E2F2 | E2F2 | 3179 | 0.2 | 0.31 | YES
10 | MAPK10 | MAPK10 | MAPK10 | 3646 | 0.17 | 0.31 | YES
11 | FIGF | FIGF | FIGF | 3843 | 0.16 | 0.32 | YES
12 | PIK3R3 | PIK3R3 | PIK3R3 | 4370 | 0.14 | 0.31 | YES
13 | RAD51 | RAD51 | RAD51 | 4559 | 0.13 | 0.31 | YES
14 | TGFB1 | TGFB1 | TGFB1 | 4599 | 0.13 | 0.33 | YES
15 | CDKN2A | CDKN2A | CDKN2A | 4606 | 0.13 | 0.34 | YES
16 | RAC2 | RAC2 | RAC2 | 4610 | 0.13 | 0.36 | YES
17 | PIK3CA | PIK3CA | PIK3CA | 4897 | 0.12 | 0.36 | YES
18 | MAPK8 | MAPK8 | MAPK8 | 4907 | 0.12 | 0.38 | YES
19 | RB1 | RB1 | RB1 | 4944 | 0.12 | 0.39 | YES
20 | RALGDS | RALGDS | RALGDS | 5052 | 0.11 | 0.4 | YES
21 | AKT3 | AKT3 | AKT3 | 5193 | 0.11 | 0.4 | YES
22 | TGFBR1 | TGFBR1 | TGFBR1 | 5216 | 0.11 | 0.42 | YES
23 | MAP2K1 | MAP2K1 | MAP2K1 | 5241 | 0.11 | 0.43 | YES
24 | MAPK3 | MAPK3 | MAPK3 | 5820 | 0.09 | 0.41 | NO
25 | KRAS | KRAS | KRAS | 6308 | 0.077 | 0.39 | NO
26 | CASP9 | CASP9 | CASP9 | 6572 | 0.072 | 0.38 | NO
27 | PIK3CB | PIK3CB | PIK3CB | 6609 | 0.071 | 0.39 | NO
28 | IKBKB | IKBKB | IKBKB | 6705 | 0.069 | 0.4 | NO
29 | RALBP1 | RALBP1 | RALBP1 | 6724 | 0.068 | 0.4 | NO
30 | STAT3 | STAT3 | STAT3 | 6821 | 0.066 | 0.41 | NO
31 | TGFBR2 | TGFBR2 | TGFBR2 | 6868 | 0.065 | 0.41 | NO
32 | RALA | RALA | RALA | 7695 | 0.05 | 0.37 | NO
33 | RAF1 | RAF1 | RAF1 | 8071 | 0.043 | 0.36 | NO
34 | CDC42 | CDC42 | CDC42 | 8081 | 0.043 | 0.36 | NO
35 | RAC3 | RAC3 | RAC3 | 8258 | 0.04 | 0.36 | NO
36 | NFKB1 | NFKB1 | NFKB1 | 8321 | 0.039 | 0.36 | NO
37 | CDK4 | CDK4 | CDK4 | 8334 | 0.038 | 0.36 | NO
38 | IKBKG | IKBKG | IKBKG | 8583 | 0.035 | 0.35 | NO
39 | RAC1 | RAC1 | RAC1 | 9013 | 0.028 | 0.33 | NO
40 | MAPK1 | MAPK1 | MAPK1 | 9347 | 0.023 | 0.32 | NO
41 | CHUK | CHUK | CHUK | 9445 | 0.021 | 0.32 | NO
42 | TGFB3 | TGFB3 | TGFB3 | 9525 | 0.02 | 0.31 | NO
43 | AKT1 | AKT1 | AKT1 | 9715 | 0.017 | 0.31 | NO
44 | PGF | PGF | PGF | 10033 | 0.012 | 0.29 | NO
45 | ERBB2 | ERBB2 | ERBB2 | 10041 | 0.012 | 0.29 | NO
46 | RELA | RELA | RELA | 10068 | 0.011 | 0.29 | NO
47 | TGFB2 | TGFB2 | TGFB2 | 10735 | 0.0016 | 0.25 | NO
48 | BRAF | BRAF | BRAF | 10737 | 0.0016 | 0.25 | NO
49 | MAPK9 | MAPK9 | MAPK9 | 10743 | 0.0014 | 0.25 | NO
50 | JAK1 | JAK1 | JAK1 | 10784 | 0.00084 | 0.25 | NO
51 | SMAD3 | SMAD3 | SMAD3 | 11078 | -0.0041 | 0.24 | NO
52 | ARAF | ARAF | ARAF | 11378 | -0.0092 | 0.22 | NO
53 | TP53 | TP53 | TP53 | 11484 | -0.011 | 0.22 | NO
54 | AKT2 | AKT2 | AKT2 | 11585 | -0.012 | 0.21 | NO
55 | RALB | RALB | RALB | 12044 | -0.02 | 0.19 | NO
56 | SMAD2 | SMAD2 | SMAD2 | 12081 | -0.02 | 0.19 | NO
57 | VEGFB | VEGFB | VEGFB | 12100 | -0.02 | 0.19 | NO
58 | PIK3R2 | PIK3R2 | PIK3R2 | 12661 | -0.03 | 0.16 | NO
59 | STAT1 | STAT1 | STAT1 | 12770 | -0.032 | 0.16 | NO
60 | BAD | BAD | BAD | 13854 | -0.054 | 0.11 | NO
61 | SMAD4 | SMAD4 | SMAD4 | 13935 | -0.056 | 0.11 | NO
62 | TGFA | TGFA | TGFA | 14453 | -0.07 | 0.093 | NO
63 | PIK3R1 | PIK3R1 | PIK3R1 | 14733 | -0.078 | 0.088 | NO
64 | VEGFA | VEGFA | VEGFA | 14801 | -0.081 | 0.094 | NO
65 | E2F3 | E2F3 | E2F3 | 15088 | -0.092 | 0.09 | NO
66 | BCL2L1 | BCL2L1 | BCL2L1 | 15606 | -0.12 | 0.076 | NO
67 | EGFR | EGFR | EGFR | 15766 | -0.12 | 0.084 | NO
68 | CCND1 | CCND1 | CCND1 | 16472 | -0.17 | 0.067 | NO
69 | PLD1 | PLD1 | PLD1 | 16637 | -0.19 | 0.082 | NO

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

Figure S20. 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

Fold change

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

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

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

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

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

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Subtype clus2 enriched pathways

Table 4. Get Full Table This table shows top 9 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 DEATH PATHWAY | 32 | genes.ES.table | 0.24 | 0.92 | 0.54 | 1 | 1 | 1 | 0.76 | 0.24 | 1 | 0.86
KEGG OXIDATIVE PHOSPHORYLATION | 111 | genes.ES.table | 0.24 | 0.73 | 0.65 | 1 | 1 | 0.37 | 0.3 | 0.26 | 1 | 0.96
KEGG RNA DEGRADATION | 55 | genes.ES.table | 0.23 | 1.1 | 0.38 | 1 | 1 | 1 | 0.77 | 0.23 | 1 | 0.79
KEGG RNA POLYMERASE | 28 | genes.ES.table | 0.17 | 0.65 | 0.88 | 1 | 1 | 0.29 | 0.23 | 0.22 | 1 | 0.89
KEGG SPLICEOSOME | 125 | genes.ES.table | 0.24 | 1.1 | 0.37 | 1 | 1 | 0.98 | 0.67 | 0.33 | 1 | 0.98
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT | 37 | genes.ES.table | 0.13 | 0.57 | 0.96 | 0.94 | 1 | 0.4 | 0.29 | 0.29 | 0.95 | 0.037
KEGG NOTCH SIGNALING PATHWAY | 46 | genes.ES.table | 0.15 | 0.57 | 0.96 | 1 | 1 | 0.17 | 0.16 | 0.15 | 1 | 0.87
KEGG VASOPRESSIN REGULATED WATER REABSORPTION | 41 | genes.ES.table | 0.19 | 0.68 | 0.86 | 1 | 1 | 0.15 | 0.1 | 0.13 | 1 | 0.96
KEGG HUNTINGTONS DISEASE | 166 | genes.ES.table | 0.17 | 0.77 | 0.69 | 1 | 1 | 0.24 | 0.23 | 0.19 | 1 | 0.98

genes ES table in pathway: BIOCARTA DEATH 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 | PRPF40B | PRPF40B | PRPF40B | 963 | 0.19 | -0.012 | YES
2 | SNRPE | SNRPE | SNRPE | 2480 | 0.096 | -0.075 | YES
3 | LSM2 | LSM2 | LSM2 | 2887 | 0.082 | -0.079 | YES
4 | SF3B4 | SF3B4 | SF3B4 | 3122 | 0.075 | -0.076 | YES
5 | PRPF3 | PRPF3 | PRPF3 | 3229 | 0.072 | -0.065 | YES
6 | PRPF18 | PRPF18 | PRPF18 | 3561 | 0.064 | -0.07 | YES
7 | TXNL4A | TXNL4A | TXNL4A | 3612 | 0.062 | -0.059 | YES
8 | BCAS2 | BCAS2 | BCAS2 | 3847 | 0.057 | -0.059 | YES
9 | HSPA1L | HSPA1L | HSPA1L | 4169 | 0.05 | -0.066 | YES
10 | SNRPB | SNRPB | SNRPB | 4202 | 0.049 | -0.057 | YES
11 | PQBP1 | PQBP1 | PQBP1 | 4292 | 0.048 | -0.051 | YES
12 | SNRPB2 | SNRPB2 | SNRPB2 | 4337 | 0.047 | -0.043 | YES
13 | SFRS2B | SFRS2B | SFRS2B | 4362 | 0.046 | -0.034 | YES
14 | PPIH | PPIH | PPIH | 4444 | 0.044 | -0.029 | YES
15 | CRNKL1 | CRNKL1 | CRNKL1 | 4540 | 0.043 | -0.025 | YES
16 | SFRS9 | SFRS9 | SFRS9 | 4561 | 0.042 | -0.017 | YES
17 | SNRPC | SNRPC | SNRPC | 4565 | 0.042 | -0.0074 | YES
18 | PLRG1 | PLRG1 | PLRG1 | 4755 | 0.039 | -0.0093 | YES
19 | XAB2 | XAB2 | XAB2 | 4782 | 0.038 | -0.0023 | YES
20 | PRPF31 | PRPF31 | PRPF31 | 4880 | 0.036 | 0.00042 | YES
21 | HNRNPA1 | HNRNPA1 | HNRNPA1 | 4885 | 0.036 | 0.0083 | YES
22 | CWC15 | CWC15 | CWC15 | 4943 | 0.035 | 0.013 | YES
23 | RBM8A | RBM8A | RBM8A | 5020 | 0.034 | 0.016 | YES
24 | BAT1 | BAT1 | BAT1 | 5038 | 0.034 | 0.023 | YES
25 | SF3A2 | SF3A2 | SF3A2 | 5122 | 0.032 | 0.025 | YES
26 | SNRNP70 | SNRNP70 | SNRNP70 | 5137 | 0.032 | 0.032 | YES
27 | HSPA6 | HSPA6 | HSPA6 | 5307 | 0.029 | 0.029 | YES
28 | THOC1 | THOC1 | THOC1 | 5349 | 0.028 | 0.033 | YES
29 | LSM7 | LSM7 | LSM7 | 5393 | 0.028 | 0.036 | YES
30 | SFRS3 | SFRS3 | SFRS3 | 5437 | 0.027 | 0.04 | YES
31 | RBM17 | RBM17 | RBM17 | 5441 | 0.027 | 0.046 | YES
32 | LSM3 | LSM3 | LSM3 | 5461 | 0.026 | 0.05 | YES
33 | U2AF1 | U2AF1 | U2AF1 | 5465 | 0.026 | 0.056 | YES
34 | RBM22 | RBM22 | RBM22 | 5657 | 0.023 | 0.05 | YES
35 | SNRPD1 | SNRPD1 | SNRPD1 | 5702 | 0.022 | 0.053 | YES
36 | HNRNPU | HNRNPU | HNRNPU | 5817 | 0.021 | 0.051 | YES
37 | DHX16 | DHX16 | DHX16 | 5869 | 0.02 | 0.053 | YES
38 | PRPF6 | PRPF6 | PRPF6 | 5999 | 0.018 | 0.05 | YES
39 | CCDC12 | CCDC12 | CCDC12 | 6011 | 0.018 | 0.053 | YES
40 | HNRNPA1L2 | HNRNPA1L2 | HNRNPA1L2 | 6038 | 0.017 | 0.056 | YES
41 | LSM4 | LSM4 | LSM4 | 6044 | 0.017 | 0.059 | YES
42 | DDX23 | DDX23 | DDX23 | 6217 | 0.015 | 0.053 | YES
43 | PPIE | PPIE | PPIE | 6314 | 0.013 | 0.05 | YES
44 | PRPF38A | PRPF38A | PRPF38A | 6352 | 0.013 | 0.051 | YES
45 | SNRPD2 | SNRPD2 | SNRPD2 | 6355 | 0.013 | 0.054 | YES
46 | SNRPF | SNRPF | SNRPF | 6542 | 0.01 | 0.046 | YES
47 | SART1 | SART1 | SART1 | 6605 | 0.0092 | 0.044 | YES
48 | HNRNPC | HNRNPC | HNRNPC | 6661 | 0.0085 | 0.043 | YES
49 | CDC5L | CDC5L | CDC5L | 6684 | 0.0081 | 0.044 | YES
50 | CTNNBL1 | CTNNBL1 | CTNNBL1 | 6726 | 0.0076 | 0.043 | YES
51 | HNRNPM | HNRNPM | HNRNPM | 6830 | 0.0062 | 0.039 | YES
52 | ACIN1 | ACIN1 | ACIN1 | 6920 | 0.0048 | 0.035 | YES
53 | SNRPD3 | SNRPD3 | SNRPD3 | 6924 | 0.0047 | 0.036 | YES
54 | NAA38 | NAA38 | NAA38 | 6971 | 0.0041 | 0.034 | YES
55 | TRA2A | TRA2A | TRA2A | 6993 | 0.0038 | 0.034 | YES
56 | SF3B2 | SF3B2 | SF3B2 | 7140 | 0.0018 | 0.026 | YES
57 | PRPF19 | PRPF19 | PRPF19 | 7203 | 0.00073 | 0.023 | YES
58 | MAGOHB | MAGOHB | MAGOHB | 7302 | -0.0005 | 0.018 | YES
59 | RBMX | RBMX | RBMX | 7463 | -0.003 | 0.0092 | YES
60 | PUF60 | PUF60 | PUF60 | 7464 | -0.003 | 0.0099 | YES
61 | SFRS6 | SFRS6 | SFRS6 | 7477 | -0.0031 | 0.0099 | YES
62 | PRPF8 | PRPF8 | PRPF8 | 7478 | -0.0031 | 0.011 | YES
63 | ZMAT2 | ZMAT2 | ZMAT2 | 7588 | -0.0045 | 0.0055 | YES
64 | NHP2L1 | NHP2L1 | NHP2L1 | 7707 | -0.0066 | 0.00043 | YES
65 | WBP11 | WBP11 | WBP11 | 7795 | -0.0078 | -0.0027 | YES
66 | HNRNPA3 | HNRNPA3 | HNRNPA3 | 7804 | -0.008 | -0.0014 | YES
67 | U2AF2 | U2AF2 | U2AF2 | 7891 | -0.009 | -0.0042 | YES
68 | SMNDC1 | SMNDC1 | SMNDC1 | 7998 | -0.011 | -0.0077 | YES
69 | DHX8 | DHX8 | DHX8 | 8158 | -0.013 | -0.014 | YES
70 | SNW1 | SNW1 | SNW1 | 8164 | -0.013 | -0.011 | YES
71 | SFRS1 | SFRS1 | SFRS1 | 8311 | -0.015 | -0.016 | YES
72 | SNRPA | SNRPA | SNRPA | 8367 | -0.016 | -0.015 | YES
73 | DDX42 | DDX42 | DDX42 | 8415 | -0.016 | -0.014 | YES
74 | SNRNP200 | SNRNP200 | SNRNP200 | 8441 | -0.017 | -0.012 | YES
75 | SFRS4 | SFRS4 | SFRS4 | 8446 | -0.017 | -0.0085 | YES
76 | SF3A3 | SF3A3 | SF3A3 | 8458 | -0.017 | -0.0053 | YES
77 | DHX15 | DHX15 | DHX15 | 8463 | -0.017 | -0.0017 | YES
78 | DDX46 | DDX46 | DDX46 | 8549 | -0.019 | -0.0023 | YES
79 | SLU7 | SLU7 | SLU7 | 8567 | -0.019 | 0.00096 | YES
80 | SNRPG | SNRPG | SNRPG | 8596 | -0.02 | 0.0037 | YES
81 | PRPF4 | PRPF4 | PRPF4 | 8675 | -0.021 | 0.0039 | YES
82 | PCBP1 | PCBP1 | PCBP1 | 8765 | -0.022 | 0.0038 | YES
83 | SF3B3 | SF3B3 | SF3B3 | 8810 | -0.022 | 0.0063 | YES
84 | CHERP | CHERP | CHERP | 8886 | -0.024 | 0.0074 | YES
85 | SF3B14 | SF3B14 | SF3B14 | 8927 | -0.024 | 0.01 | YES
86 | HNRNPK | HNRNPK | HNRNPK | 8988 | -0.025 | 0.013 | YES
87 | SF3A1 | SF3A1 | SF3A1 | 9165 | -0.028 | 0.0091 | YES
88 | PPIL1 | PPIL1 | PPIL1 | 9282 | -0.03 | 0.0092 | YES
89 | SYF2 | SYF2 | SYF2 | 9326 | -0.03 | 0.014 | YES
90 | DDX5 | DDX5 | DDX5 | 9457 | -0.032 | 0.013 | YES
91 | SFRS2 | SFRS2 | SFRS2 | 9514 | -0.033 | 0.018 | YES
92 | MAGOH | MAGOH | MAGOH | 9563 | -0.034 | 0.022 | YES
93 | SNRNP27 | SNRNP27 | SNRNP27 | 9639 | -0.035 | 0.026 | YES
94 | PRPF38B | PRPF38B | PRPF38B | 9648 | -0.035 | 0.033 | YES
95 | AQR | AQR | AQR | 9704 | -0.036 | 0.038 | YES
96 | BUD31 | BUD31 | BUD31 | 9824 | -0.038 | 0.04 | YES
97 | PRPF40A | PRPF40A | PRPF40A | 9826 | -0.038 | 0.048 | YES
98 | EIF4A3 | EIF4A3 | EIF4A3 | 9845 | -0.038 | 0.055 | YES
99 | DHX38 | DHX38 | DHX38 | 9886 | -0.038 | 0.062 | YES
100 | TRA2B | TRA2B | TRA2B | 9998 | -0.04 | 0.064 | YES
101 | THOC3 | THOC3 | THOC3 | 10131 | -0.042 | 0.066 | YES
102 | THOC4 | THOC4 | THOC4 | 10181 | -0.043 | 0.073 | YES
103 | SF3B5 | SF3B5 | SF3B5 | 10308 | -0.045 | 0.076 | YES
104 | LSM6 | LSM6 | LSM6 | 10351 | -0.046 | 0.084 | YES
105 | SNRPA1 | SNRPA1 | SNRPA1 | 10398 | -0.047 | 0.092 | YES
106 | RBM25 | RBM25 | RBM25 | 10409 | -0.047 | 0.1 | YES
107 | SFRS7 | SFRS7 | SFRS7 | 10564 | -0.049 | 0.1 | YES
108 | EFTUD2 | EFTUD2 | EFTUD2 | 10578 | -0.05 | 0.11 | YES
109 | TCERG1 | TCERG1 | TCERG1 | 10658 | -0.051 | 0.12 | YES
110 | SF3B1 | SF3B1 | SF3B1 | 10699 | -0.052 | 0.13 | YES
111 | HSPA1B | HSPA1B | HSPA1B | 10786 | -0.054 | 0.14 | YES
112 | SFRS5 | SFRS5 | SFRS5 | 10845 | -0.055 | 0.15 | YES
113 | USP39 | USP39 | USP39 | 11006 | -0.058 | 0.15 | YES
114 | LSM5 | LSM5 | LSM5 | 11021 | -0.058 | 0.16 | YES
115 | SNRNP40 | SNRNP40 | SNRNP40 | 11042 | -0.059 | 0.17 | YES
116 | HSPA8 | HSPA8 | HSPA8 | 11100 | -0.06 | 0.18 | YES
117 | SFRS13A | SFRS13A | SFRS13A | 11165 | -0.062 | 0.19 | YES
118 | THOC2 | THOC2 | THOC2 | 11222 | -0.063 | 0.2 | YES
119 | PHF5A | PHF5A | PHF5A | 11684 | -0.073 | 0.2 | YES
120 | HSPA1A | HSPA1A | HSPA1A | 11697 | -0.074 | 0.21 | YES
121 | ISY1 | ISY1 | ISY1 | 11885 | -0.078 | 0.22 | YES
122 | SR140 | SR140 | SR140 | 12013 | -0.081 | 0.23 | YES
123 | NCBP1 | NCBP1 | NCBP1 | 12110 | -0.083 | 0.24 | YES
124 | CDC40 | CDC40 | CDC40 | 13844 | -0.14 | 0.18 | NO
125 | HSPA2 | HSPA2 | HSPA2 | 15798 | -0.27 | 0.13 | 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 DEATH PATHWAY.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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 | ENO3 | ENO3 | ENO3 | 223 | 0.32 | 0.11 | YES
2 | LSM2 | LSM2 | LSM2 | 2887 | 0.082 | -0.012 | YES
3 | EXOSC4 | EXOSC4 | EXOSC4 | 4302 | 0.048 | -0.073 | YES
4 | EDC3 | EDC3 | EDC3 | 4387 | 0.046 | -0.06 | YES
5 | CNOT6L | CNOT6L | CNOT6L | 4419 | 0.045 | -0.046 | YES
6 | SKIV2L2 | SKIV2L2 | SKIV2L2 | 4608 | 0.041 | -0.041 | YES
7 | LSM1 | LSM1 | LSM1 | 4643 | 0.041 | -0.028 | YES
8 | SKIV2L | SKIV2L | SKIV2L | 4917 | 0.036 | -0.03 | YES
9 | CNOT7 | CNOT7 | CNOT7 | 5021 | 0.034 | -0.023 | YES
10 | CNOT2 | CNOT2 | CNOT2 | 5331 | 0.029 | -0.03 | YES
11 | LSM7 | LSM7 | LSM7 | 5393 | 0.028 | -0.023 | YES
12 | LSM3 | LSM3 | LSM3 | 5461 | 0.026 | -0.017 | YES
13 | EXOSC9 | EXOSC9 | EXOSC9 | 5564 | 0.025 | -0.014 | YES
14 | EXOSC3 | EXOSC3 | EXOSC3 | 5651 | 0.023 | -0.0097 | YES
15 | DDX6 | DDX6 | DDX6 | 5753 | 0.022 | -0.0073 | YES
16 | LSM4 | LSM4 | LSM4 | 6044 | 0.017 | -0.017 | YES
17 | WDR61 | WDR61 | WDR61 | 6361 | 0.013 | -0.03 | YES
18 | XRN2 | XRN2 | XRN2 | 6522 | 0.01 | -0.035 | YES
19 | CNOT10 | CNOT10 | CNOT10 | 6635 | 0.0088 | -0.038 | YES
20 | CNOT3 | CNOT3 | CNOT3 | 6785 | 0.0068 | -0.044 | YES
21 | NAA38 | NAA38 | NAA38 | 6971 | 0.0041 | -0.052 | YES
22 | EXOSC7 | EXOSC7 | EXOSC7 | 7046 | 0.003 | -0.055 | YES
23 | EXOSC8 | EXOSC8 | EXOSC8 | 7375 | -0.0015 | -0.073 | YES
24 | DCP1B | DCP1B | DCP1B | 7440 | -0.0026 | -0.076 | YES
25 | CNOT4 | CNOT4 | CNOT4 | 7927 | -0.0095 | -0.099 | YES
26 | EXOSC2 | EXOSC2 | EXOSC2 | 8630 | -0.02 | -0.13 | YES
27 | PAPD7 | PAPD7 | PAPD7 | 8725 | -0.021 | -0.13 | YES
28 | ENO2 | ENO2 | ENO2 | 8815 | -0.022 | -0.12 | YES
29 | EDC4 | EDC4 | EDC4 | 8890 | -0.024 | -0.12 | YES
30 | EXOSC6 | EXOSC6 | EXOSC6 | 8922 | -0.024 | -0.11 | YES
31 | PATL1 | PATL1 | PATL1 | 8939 | -0.024 | -0.1 | YES
32 | EXOSC10 | EXOSC10 | EXOSC10 | 9006 | -0.025 | -0.099 | YES
33 | C1D | C1D | C1D | 9010 | -0.026 | -0.09 | YES
34 | PARN | PARN | PARN | 9039 | -0.026 | -0.082 | YES
35 | EXOSC1 | EXOSC1 | EXOSC1 | 9147 | -0.028 | -0.078 | YES
36 | ZCCHC7 | ZCCHC7 | ZCCHC7 | 9262 | -0.029 | -0.073 | YES
37 | CNOT6 | CNOT6 | CNOT6 | 9646 | -0.035 | -0.082 | YES
38 | EXOSC5 | EXOSC5 | EXOSC5 | 9682 | -0.035 | -0.071 | YES
39 | DCPS | DCPS | DCPS | 9724 | -0.036 | -0.06 | YES
40 | DCP1A | DCP1A | DCP1A | 10344 | -0.046 | -0.077 | YES
41 | LSM6 | LSM6 | LSM6 | 10351 | -0.046 | -0.06 | YES
42 | PAPOLA | PAPOLA | PAPOLA | 10583 | -0.05 | -0.055 | YES
43 | HSPA9 | HSPA9 | HSPA9 | 10901 | -0.056 | -0.052 | YES
44 | LSM5 | LSM5 | LSM5 | 11021 | -0.058 | -0.037 | YES
45 | CNOT1 | CNOT1 | CNOT1 | 11320 | -0.065 | -0.03 | YES
46 | XRN1 | XRN1 | XRN1 | 11463 | -0.068 | -0.013 | YES
47 | PNPT1 | PNPT1 | PNPT1 | 11486 | -0.069 | 0.011 | YES
48 | HSPD1 | HSPD1 | HSPD1 | 12431 | -0.092 | -0.0072 | YES
49 | ENO1 | ENO1 | ENO1 | 12845 | -0.11 | 0.0088 | YES
50 | TTC37 | TTC37 | TTC37 | 13124 | -0.12 | 0.036 | YES
51 | RQCD1 | RQCD1 | RQCD1 | 13191 | -0.12 | 0.075 | YES
52 | DCP2 | DCP2 | DCP2 | 13353 | -0.12 | 0.11 | YES
53 | PAPOLG | PAPOLG | PAPOLG | 13494 | -0.13 | 0.15 | YES
54 | DIS3 | DIS3 | DIS3 | 13580 | -0.13 | 0.2 | YES
55 | MPHOSPH6 | MPHOSPH6 | MPHOSPH6 | 14015 | -0.15 | 0.23 | YES

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

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

genes ES table in pathway: KEGG RNA DEGRADATION

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 | CASP6 | CASP6 | CASP6 | 2710 | 0.087 | -0.1 | YES
2 | TNFRSF10B | TNFRSF10B | TNFRSF10B | 3243 | 0.072 | -0.092 | YES
3 | LMNA | LMNA | LMNA | 3487 | 0.066 | -0.07 | YES
4 | TNFSF12 | TNFSF12 | TNFSF12 | 3765 | 0.059 | -0.053 | YES
5 | GAS2 | GAS2 | GAS2 | 3974 | 0.054 | -0.035 | YES
6 | RIPK1 | RIPK1 | RIPK1 | 4475 | 0.044 | -0.038 | YES
7 | TRAF2 | TRAF2 | TRAF2 | 4578 | 0.042 | -0.021 | YES
8 | NFKB1 | NFKB1 | NFKB1 | 4989 | 0.035 | -0.025 | YES
9 | RELA | RELA | RELA | 5069 | 0.033 | -0.011 | YES
10 | SPTAN1 | SPTAN1 | SPTAN1 | 5201 | 0.031 | -0.0014 | YES
11 | XIAP | XIAP | XIAP | 7206 | 0.00068 | -0.11 | YES
12 | CASP10 | CASP10 | CASP10 | 8002 | -0.011 | -0.15 | YES
13 | CASP3 | CASP3 | CASP3 | 8081 | -0.012 | -0.15 | YES
14 | APAF1 | APAF1 | APAF1 | 8194 | -0.014 | -0.15 | YES
15 | TNFSF10 | TNFSF10 | TNFSF10 | 8366 | -0.016 | -0.15 | YES
16 | BIRC2 | BIRC2 | BIRC2 | 8492 | -0.018 | -0.14 | YES
17 | NFKBIA | NFKBIA | NFKBIA | 9572 | -0.034 | -0.19 | YES
18 | CASP8 | CASP8 | CASP8 | 9769 | -0.037 | -0.18 | YES
19 | CASP9 | CASP9 | CASP9 | 9910 | -0.039 | -0.16 | YES
20 | MAP3K14 | MAP3K14 | MAP3K14 | 10264 | -0.044 | -0.16 | YES
21 | TRADD | TRADD | TRADD | 10484 | -0.048 | -0.14 | YES
22 | CASP7 | CASP7 | CASP7 | 10871 | -0.055 | -0.14 | YES
23 | CHUK | CHUK | CHUK | 11278 | -0.064 | -0.12 | YES
24 | FADD | FADD | FADD | 11526 | -0.069 | -0.099 | YES
25 | TNFRSF25 | TNFRSF25 | TNFRSF25 | 11872 | -0.078 | -0.076 | YES
26 | CYCS | CYCS | CYCS | 12000 | -0.081 | -0.039 | YES
27 | DFFA | DFFA | DFFA | 12384 | -0.091 | -0.011 | YES
28 | DFFB | DFFB | DFFB | 12658 | -0.099 | 0.028 | YES
29 | TNFRSF10A | TNFRSF10A | TNFRSF10A | 12815 | -0.1 | 0.077 | YES
30 | CFLAR | CFLAR | CFLAR | 13320 | -0.12 | 0.12 | YES
31 | BCL2 | BCL2 | BCL2 | 13522 | -0.13 | 0.18 | YES
32 | BIRC3 | BIRC3 | BIRC3 | 13827 | -0.14 | 0.24 | YES

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

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

genes ES table in pathway: KEGG RNA POLYMERASE

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 | GRM5 | GRM5 | GRM5 | 322 | 0.29 | 0.012 | YES
2 | CREB5 | CREB5 | CREB5 | 481 | 0.25 | 0.029 | YES
3 | CLTCL1 | CLTCL1 | CLTCL1 | 796 | 0.21 | 0.032 | YES
4 | DNAI1 | DNAI1 | DNAI1 | 933 | 0.19 | 0.044 | YES
5 | ATP5C1 | ATP5C1 | ATP5C1 | 1640 | 0.13 | 0.019 | YES
6 | NDUFC1 | NDUFC1 | NDUFC1 | 1680 | 0.13 | 0.03 | YES
7 | DNALI1 | DNALI1 | DNALI1 | 1686 | 0.13 | 0.043 | YES
8 | BBC3 | BBC3 | BBC3 | 1698 | 0.13 | 0.055 | YES
9 | NDUFS4 | NDUFS4 | NDUFS4 | 1708 | 0.13 | 0.068 | YES
10 | HAP1 | HAP1 | HAP1 | 1771 | 0.13 | 0.077 | YES
11 | CREB3L4 | CREB3L4 | CREB3L4 | 1804 | 0.12 | 0.088 | YES
12 | TP53 | TP53 | TP53 | 1879 | 0.12 | 0.096 | YES
13 | PPARGC1A | PPARGC1A | PPARGC1A | 2151 | 0.11 | 0.092 | YES
14 | NDUFS2 | NDUFS2 | NDUFS2 | 2181 | 0.11 | 0.1 | YES
15 | COX6B2 | COX6B2 | COX6B2 | 2195 | 0.11 | 0.11 | YES
16 | ATP5G2 | ATP5G2 | ATP5G2 | 2352 | 0.1 | 0.11 | YES
17 | DNAL4 | DNAL4 | DNAL4 | 2726 | 0.087 | 0.1 | YES
18 | CLTB | CLTB | CLTB | 2801 | 0.085 | 0.1 | YES
19 | GRIN1 | GRIN1 | GRIN1 | 2888 | 0.082 | 0.11 | YES
20 | NDUFA4L2 | NDUFA4L2 | NDUFA4L2 | 2932 | 0.081 | 0.11 | YES
21 | POLR2J3 | POLR2J3 | POLR2J3 | 3028 | 0.078 | 0.12 | YES
22 | DNAH2 | DNAH2 | DNAH2 | 3065 | 0.077 | 0.12 | YES
23 | ATP5D | ATP5D | ATP5D | 3068 | 0.077 | 0.13 | YES
24 | CREB3 | CREB3 | CREB3 | 3225 | 0.072 | 0.13 | YES
25 | NDUFS3 | NDUFS3 | NDUFS3 | 3255 | 0.072 | 0.14 | YES
26 | SDHC | SDHC | SDHC | 3327 | 0.07 | 0.14 | YES
27 | ATP5A1 | ATP5A1 | ATP5A1 | 3381 | 0.068 | 0.14 | YES
28 | POLR2I | POLR2I | POLR2I | 3589 | 0.063 | 0.14 | YES
29 | CLTA | CLTA | CLTA | 3591 | 0.063 | 0.14 | YES
30 | NDUFS5 | NDUFS5 | NDUFS5 | 3658 | 0.062 | 0.15 | YES
31 | POLR2A | POLR2A | POLR2A | 3744 | 0.059 | 0.15 | YES
32 | NDUFC2 | NDUFC2 | NDUFC2 | 3802 | 0.058 | 0.15 | YES
33 | ATP5O | ATP5O | ATP5O | 3820 | 0.058 | 0.15 | YES
34 | NDUFA7 | NDUFA7 | NDUFA7 | 4018 | 0.053 | 0.15 | YES
35 | SP1 | SP1 | SP1 | 4048 | 0.053 | 0.15 | YES
36 | NDUFB7 | NDUFB7 | NDUFB7 | 4069 | 0.052 | 0.16 | YES
37 | BAX | BAX | BAX | 4086 | 0.052 | 0.16 | YES
38 | POLR2J2 | POLR2J2 | POLR2J2 | 4134 | 0.051 | 0.16 | YES
39 | AP2A2 | AP2A2 | AP2A2 | 4187 | 0.05 | 0.17 | YES
40 | COX7A1 | COX7A1 | COX7A1 | 4204 | 0.049 | 0.17 | YES
41 | ATP5J | ATP5J | ATP5J | 4447 | 0.044 | 0.16 | NO
42 | NDUFS6 | NDUFS6 | NDUFS6 | 4468 | 0.044 | 0.16 | NO
43 | NDUFV2 | NDUFV2 | NDUFV2 | 4795 | 0.038 | 0.15 | NO
44 | NDUFA3 | NDUFA3 | NDUFA3 | 4818 | 0.038 | 0.15 | NO
45 | COX7C | COX7C | COX7C | 4846 | 0.037 | 0.16 | NO
46 | NDUFB1 | NDUFB1 | NDUFB1 | 4993 | 0.034 | 0.15 | NO
47 | DCTN2 | DCTN2 | DCTN2 | 5036 | 0.034 | 0.15 | NO
48 | DCTN1 | DCTN1 | DCTN1 | 5049 | 0.034 | 0.15 | NO
49 | UQCRB | UQCRB | UQCRB | 5095 | 0.033 | 0.16 | NO
50 | NDUFB2 | NDUFB2 | NDUFB2 | 5132 | 0.032 | 0.16 | NO
51 | NDUFA9 | NDUFA9 | NDUFA9 | 5141 | 0.032 | 0.16 | NO
52 | NDUFV3 | NDUFV3 | NDUFV3 | 5204 | 0.031 | 0.16 | NO
53 | POLR2F | POLR2F | POLR2F | 5285 | 0.029 | 0.16 | NO
54 | NDUFB9 | NDUFB9 | NDUFB9 | 5290 | 0.029 | 0.16 | NO
55 | SLC25A4 | SLC25A4 | SLC25A4 | 5319 | 0.029 | 0.16 | NO
56 | NDUFA6 | NDUFA6 | NDUFA6 | 5328 | 0.029 | 0.16 | NO
57 | UQCRQ | UQCRQ | UQCRQ | 5384 | 0.028 | 0.16 | NO
58 | NDUFS7 | NDUFS7 | NDUFS7 | 5432 | 0.027 | 0.16 | NO
59 | COX6A1 | COX6A1 | COX6A1 | 5453 | 0.026 | 0.16 | NO
60 | PLCB3 | PLCB3 | PLCB3 | 5468 | 0.026 | 0.17 | NO
61 | HIP1 | HIP1 | HIP1 | 5575 | 0.024 | 0.16 | NO
62 | POLR2G | POLR2G | POLR2G | 5738 | 0.022 | 0.16 | NO
63 | TAF4 | TAF4 | TAF4 | 5739 | 0.022 | 0.16 | NO
64 | COX8A | COX8A | COX8A | 5743 | 0.022 | 0.16 | NO
65 | NDUFB6 | NDUFB6 | NDUFB6 | 5922 | 0.019 | 0.15 | NO
66 | UQCR11 | UQCR11 | UQCR11 | 6005 | 0.018 | 0.15 | NO
67 | POLR2K | POLR2K | POLR2K | 6077 | 0.017 | 0.15 | NO
68 | SIN3A | SIN3A | SIN3A | 6111 | 0.016 | 0.15 | NO
69 | NDUFB3 | NDUFB3 | NDUFB3 | 6116 | 0.016 | 0.15 | NO
70 | COX6B1 | COX6B1 | COX6B1 | 6290 | 0.014 | 0.14 | NO
71 | PPID | PPID | PPID | 6303 | 0.014 | 0.14 | NO
72 | ATP5B | ATP5B | ATP5B | 6328 | 0.013 | 0.14 | NO
73 | NDUFA1 | NDUFA1 | NDUFA1 | 6347 | 0.013 | 0.14 | NO
74 | HDAC1 | HDAC1 | HDAC1 | 6382 | 0.013 | 0.14 | NO
75 | POLR2L | POLR2L | POLR2L | 6410 | 0.012 | 0.14 | NO
76 | VDAC3 | VDAC3 | VDAC3 | 6433 | 0.012 | 0.14 | NO
77 | NDUFA10 | NDUFA10 | NDUFA10 | 6475 | 0.011 | 0.14 | NO
78 | NRF1 | NRF1 | NRF1 | 6509 | 0.011 | 0.14 | NO
79 | UQCRHL | UQCRHL | UQCRHL | 6520 | 0.01 | 0.14 | NO
80 | UQCRH | UQCRH | UQCRH | 6608 | 0.0092 | 0.14 | NO
81 | NDUFV1 | NDUFV1 | NDUFV1 | 6632 | 0.0088 | 0.14 | NO
82 | CREBBP | CREBBP | CREBBP | 6681 | 0.0082 | 0.13 | NO
83 | AP2S1 | AP2S1 | AP2S1 | 6778 | 0.007 | 0.13 | NO
84 | NDUFB10 | NDUFB10 | NDUFB10 | 6795 | 0.0067 | 0.13 | NO
85 | COX7A2L | COX7A2L | COX7A2L | 6801 | 0.0066 | 0.13 | NO
86 | CYC1 | CYC1 | CYC1 | 6834 | 0.0062 | 0.13 | NO
87 | VDAC1 | VDAC1 | VDAC1 | 6838 | 0.006 | 0.13 | NO
88 | UQCRC1 | UQCRC1 | UQCRC1 | 6960 | 0.0042 | 0.12 | NO
89 | POLR2H | POLR2H | POLR2H | 6962 | 0.0042 | 0.12 | NO
90 | SDHA | SDHA | SDHA | 7091 | 0.0024 | 0.12 | NO
91 | NDUFB8 | NDUFB8 | NDUFB8 | 7216 | 0.00056 | 0.11 | NO
92 | ATP5H | ATP5H | ATP5H | 7229 | 0.00042 | 0.11 | NO
93 | DNAL1 | DNAL1 | DNAL1 | 7239 | 0.00026 | 0.11 | NO
94 | COX5B | COX5B | COX5B | 7273 | -0.00016 | 0.11 | NO
95 | ATP5G3 | ATP5G3 | ATP5G3 | 7329 | -0.00087 | 0.1 | NO
96 | IFT57 | IFT57 | IFT57 | 7462 | -0.003 | 0.096 | NO
97 | SLC25A6 | SLC25A6 | SLC25A6 | 7488 | -0.0032 | 0.095 | NO
98 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 7506 | -0.0035 | 0.094 | NO
99 | NDUFA2 | NDUFA2 | NDUFA2 | 7572 | -0.0043 | 0.091 | NO
100 | NDUFA4 | NDUFA4 | NDUFA4 | 7705 | -0.0065 | 0.084 | NO
101 | NDUFA8 | NDUFA8 | NDUFA8 | 7786 | -0.0078 | 0.081 | NO
102 | UQCRC2 | UQCRC2 | UQCRC2 | 7817 | -0.0081 | 0.08 | NO
103 | POLR2E | POLR2E | POLR2E | 7824 | -0.0082 | 0.08 | NO
104 | ATP5E | ATP5E | ATP5E | 7883 | -0.0088 | 0.078 | NO
105 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 7892 | -0.009 | 0.078 | NO
106 | NDUFS8 | NDUFS8 | NDUFS8 | 8028 | -0.011 | 0.072 | NO
107 | CASP3 | CASP3 | CASP3 | 8081 | -0.012 | 0.07 | NO
108 | AP2M1 | AP2M1 | AP2M1 | 8151 | -0.013 | 0.068 | NO
109 | POLR2J | POLR2J | POLR2J | 8152 | -0.013 | 0.069 | NO
110 | DCTN4 | DCTN4 | DCTN4 | 8163 | -0.013 | 0.07 | NO
111 | APAF1 | APAF1 | APAF1 | 8194 | -0.014 | 0.07 | NO
112 | NDUFB4 | NDUFB4 | NDUFB4 | 8198 | -0.014 | 0.071 | NO
113 | AP2B1 | AP2B1 | AP2B1 | 8330 | -0.015 | 0.065 | NO
114 | VDAC2 | VDAC2 | VDAC2 | 8337 | -0.015 | 0.066 | NO
115 | POLR2B | POLR2B | POLR2B | 8363 | -0.016 | 0.066 | NO
116 | ATP5F1 | ATP5F1 | ATP5F1 | 8444 | -0.017 | 0.064 | NO
117 | EP300 | EP300 | EP300 | 8547 | -0.019 | 0.06 | NO
118 | COX4I1 | COX4I1 | COX4I1 | 8559 | -0.019 | 0.061 | NO
119 | COX5A | COX5A | COX5A | 8566 | -0.019 | 0.063 | NO
120 | COX7B | COX7B | COX7B | 8634 | -0.02 | 0.061 | NO
121 | COX6C | COX6C | COX6C | 8698 | -0.021 | 0.06 | NO
122 | SDHD | SDHD | SDHD | 8729 | -0.021 | 0.06 | NO
123 | NDUFS1 | NDUFS1 | NDUFS1 | 8805 | -0.022 | 0.058 | NO
124 | UQCR10 | UQCR10 | UQCR10 | 9167 | -0.028 | 0.041 | NO
125 | POLR2D | POLR2D | POLR2D | 9361 | -0.031 | 0.033 | NO
126 | ATP5G1 | ATP5G1 | ATP5G1 | 9507 | -0.033 | 0.029 | NO
127 | NDUFB5 | NDUFB5 | NDUFB5 | 9585 | -0.034 | 0.028 | NO
128 | CASP8 | CASP8 | CASP8 | 9769 | -0.037 | 0.021 | NO
129 | CREB1 | CREB1 | CREB1 | 9788 | -0.037 | 0.024 | NO
130 | RCOR1 | RCOR1 | RCOR1 | 9839 | -0.038 | 0.025 | NO
131 | CASP9 | CASP9 | CASP9 | 9910 | -0.039 | 0.025 | NO
132 | COX7A2 | COX7A2 | COX7A2 | 9914 | -0.039 | 0.029 | NO
133 | CLTC | CLTC | CLTC | 9962 | -0.04 | 0.03 | NO
134 | HDAC2 | HDAC2 | HDAC2 | 10018 | -0.041 | 0.031 | NO
135 | SLC25A5 | SLC25A5 | SLC25A5 | 10127 | -0.042 | 0.03 | NO
136 | SOD1 | SOD1 | SOD1 | 10141 | -0.042 | 0.033 | NO
137 | PLCB1 | PLCB1 | PLCB1 | 10147 | -0.042 | 0.037 | NO
138 | AP2A1 | AP2A1 | AP2A1 | 10365 | -0.046 | 0.03 | NO
139 | HTT | HTT | HTT | 10412 | -0.047 | 0.032 | NO
140 | GPX1 | GPX1 | GPX1 | 10429 | -0.047 | 0.036 | NO
141 | DNAH1 | DNAH1 | DNAH1 | 10499 | -0.048 | 0.037 | NO
142 | COX4I2 | COX4I2 | COX4I2 | 10721 | -0.052 | 0.03 | NO
143 | POLR2C | POLR2C | POLR2C | 10763 | -0.053 | 0.033 | NO
144 | NDUFA5 | NDUFA5 | NDUFA5 | 10790 | -0.054 | 0.037 | NO
145 | TBPL1 | TBPL1 | TBPL1 | 11096 | -0.06 | 0.026 | NO
146 | DLG4 | DLG4 | DLG4 | 11256 | -0.063 | 0.024 | NO
147 | TFAM | TFAM | TFAM | 11381 | -0.066 | 0.024 | NO
148 | DNAI2 | DNAI2 | DNAI2 | 11537 | -0.07 | 0.022 | NO
149 | SDHB | SDHB | SDHB | 11859 | -0.077 | 0.012 | NO
150 | CYCS | CYCS | CYCS | 12000 | -0.081 | 0.012 | NO
151 | SOD2 | SOD2 | SOD2 | 12184 | -0.085 | 0.011 | NO
152 | GNAQ | GNAQ | GNAQ | 12350 | -0.09 | 0.011 | NO
153 | DNAH3 | DNAH3 | DNAH3 | 12479 | -0.093 | 0.013 | NO
154 | COX6A2 | COX6A2 | COX6A2 | 12676 | -0.1 | 0.012 | NO
155 | ITPR1 | ITPR1 | ITPR1 | 12688 | -0.1 | 0.022 | NO
156 | TBP | TBP | TBP | 12766 | -0.1 | 0.028 | NO
157 | CREB3L2 | CREB3L2 | CREB3L2 | 13321 | -0.12 | 0.0094 | NO
158 | PPARG | PPARG | PPARG | 13746 | -0.14 | -0.000025 | NO
159 | REST | REST | REST | 14469 | -0.18 | -0.022 | NO
160 | TGM2 | TGM2 | TGM2 | 14583 | -0.18 | -0.0097 | NO
161 | PLCB4 | PLCB4 | PLCB4 | 14848 | -0.2 | -0.004 | NO
162 | BDNF | BDNF | BDNF | 15966 | -0.29 | -0.037 | NO
163 | CREB3L3 | CREB3L3 | CREB3L3 | 16062 | -0.3 | -0.012 | NO
164 | CREB3L1 | CREB3L1 | CREB3L1 | 16471 | -0.34 | -0.00054 | NO
165 | PLCB2 | PLCB2 | PLCB2 | 17139 | -0.45 | 0.0077 | NO
166 | TAF4B | TAF4B | TAF4B | 17198 | -0.46 | 0.051 | NO

Figure S27. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RNA POLYMERASE.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA POLYMERASE, 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 SPLICEOSOME

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 | ATP12A | ATP12A | ATP12A | 132 | 0.36 | 0.062 | YES
2 | ATP5C1 | ATP5C1 | ATP5C1 | 1640 | 0.13 | 0.0042 | YES
3 | NDUFC1 | NDUFC1 | NDUFC1 | 1680 | 0.13 | 0.027 | YES
4 | NDUFS4 | NDUFS4 | NDUFS4 | 1708 | 0.13 | 0.051 | YES
5 | ATP6V0E2 | ATP6V0E2 | ATP6V0E2 | 2017 | 0.11 | 0.055 | YES
6 | NDUFS2 | NDUFS2 | NDUFS2 | 2181 | 0.11 | 0.067 | YES
7 | COX6B2 | COX6B2 | COX6B2 | 2195 | 0.11 | 0.087 | YES
8 | COX10 | COX10 | COX10 | 2226 | 0.1 | 0.1 | YES
9 | ATP5G2 | ATP5G2 | ATP5G2 | 2352 | 0.1 | 0.12 | YES
10 | NDUFA4L2 | NDUFA4L2 | NDUFA4L2 | 2932 | 0.081 | 0.1 | YES
11 | ATP5D | ATP5D | ATP5D | 3068 | 0.077 | 0.11 | YES
12 | NDUFS3 | NDUFS3 | NDUFS3 | 3255 | 0.072 | 0.11 | YES
13 | PPA2 | PPA2 | PPA2 | 3274 | 0.071 | 0.12 | YES
14 | SDHC | SDHC | SDHC | 3327 | 0.07 | 0.14 | YES
15 | ATP5A1 | ATP5A1 | ATP5A1 | 3381 | 0.068 | 0.14 | YES
16 | NDUFS5 | NDUFS5 | NDUFS5 | 3658 | 0.062 | 0.14 | YES
17 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 3768 | 0.059 | 0.15 | YES
18 | NDUFC2 | NDUFC2 | NDUFC2 | 3802 | 0.058 | 0.16 | YES
19 | ATP5O | ATP5O | ATP5O | 3820 | 0.058 | 0.17 | YES
20 | ATP6V1E2 | ATP6V1E2 | ATP6V1E2 | 3874 | 0.056 | 0.18 | YES
21 | NDUFA7 | NDUFA7 | NDUFA7 | 4018 | 0.053 | 0.18 | YES
22 | NDUFB7 | NDUFB7 | NDUFB7 | 4069 | 0.052 | 0.18 | YES
23 | COX7A1 | COX7A1 | COX7A1 | 4204 | 0.049 | 0.19 | YES
24 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 4266 | 0.048 | 0.19 | YES
25 | ATP5J | ATP5J | ATP5J | 4447 | 0.044 | 0.19 | YES
26 | NDUFS6 | NDUFS6 | NDUFS6 | 4468 | 0.044 | 0.2 | YES
27 | NDUFA11 | NDUFA11 | NDUFA11 | 4779 | 0.038 | 0.19 | YES
28 | NDUFV2 | NDUFV2 | NDUFV2 | 4795 | 0.038 | 0.2 | YES
29 | NDUFA3 | NDUFA3 | NDUFA3 | 4818 | 0.038 | 0.2 | YES
30 | COX7C | COX7C | COX7C | 4846 | 0.037 | 0.21 | YES
31 | NDUFB1 | NDUFB1 | NDUFB1 | 4993 | 0.034 | 0.2 | YES
32 | UQCRB | UQCRB | UQCRB | 5095 | 0.033 | 0.21 | YES
33 | NDUFB2 | NDUFB2 | NDUFB2 | 5132 | 0.032 | 0.21 | YES
34 | NDUFA9 | NDUFA9 | NDUFA9 | 5141 | 0.032 | 0.22 | YES
35 | NDUFV3 | NDUFV3 | NDUFV3 | 5204 | 0.031 | 0.22 | YES
36 | NDUFB9 | NDUFB9 | NDUFB9 | 5290 | 0.029 | 0.22 | YES
37 | NDUFA6 | NDUFA6 | NDUFA6 | 5328 | 0.029 | 0.22 | YES
38 | UQCRQ | UQCRQ | UQCRQ | 5384 | 0.028 | 0.22 | YES
39 | NDUFS7 | NDUFS7 | NDUFS7 | 5432 | 0.027 | 0.23 | YES
40 | COX6A1 | COX6A1 | COX6A1 | 5453 | 0.026 | 0.23 | YES
41 | ATP6V1E1 | ATP6V1E1 | ATP6V1E1 | 5482 | 0.026 | 0.24 | YES
42 | ATP6V1H | ATP6V1H | ATP6V1H | 5570 | 0.024 | 0.24 | NO
43 | COX8A | COX8A | COX8A | 5743 | 0.022 | 0.23 | NO
44 | ATP6V1C2 | ATP6V1C2 | ATP6V1C2 | 5807 | 0.021 | 0.23 | NO
45 | NDUFB6 | NDUFB6 | NDUFB6 | 5922 | 0.019 | 0.23 | NO
46 | ATP6V0C | ATP6V0C | ATP6V0C | 5942 | 0.019 | 0.23 | NO
47 | ATP5I | ATP5I | ATP5I | 5988 | 0.018 | 0.23 | NO
48 | UQCR11 | UQCR11 | UQCR11 | 6005 | 0.018 | 0.23 | NO
49 | NDUFB3 | NDUFB3 | NDUFB3 | 6116 | 0.016 | 0.23 | NO
50 | COX6B1 | COX6B1 | COX6B1 | 6290 | 0.014 | 0.22 | NO
51 | ATP5B | ATP5B | ATP5B | 6328 | 0.013 | 0.22 | NO
52 | NDUFA1 | NDUFA1 | NDUFA1 | 6347 | 0.013 | 0.23 | NO
53 | NDUFA10 | NDUFA10 | NDUFA10 | 6475 | 0.011 | 0.22 | NO
54 | ATP5L | ATP5L | ATP5L | 6513 | 0.01 | 0.22 | NO
55 | UQCRHL | UQCRHL | UQCRHL | 6520 | 0.01 | 0.22 | NO
56 | UQCRH | UQCRH | UQCRH | 6608 | 0.0092 | 0.22 | NO
57 | NDUFV1 | NDUFV1 | NDUFV1 | 6632 | 0.0088 | 0.22 | NO
58 | ATP6V0E1 | ATP6V0E1 | ATP6V0E1 | 6642 | 0.0087 | 0.22 | NO
59 | ATP6V1C1 | ATP6V1C1 | ATP6V1C1 | 6750 | 0.0073 | 0.22 | NO
60 | ATP6V1B1 | ATP6V1B1 | ATP6V1B1 | 6780 | 0.0069 | 0.22 | NO
61 | NDUFB10 | NDUFB10 | NDUFB10 | 6795 | 0.0067 | 0.22 | NO
62 | COX7A2L | COX7A2L | COX7A2L | 6801 | 0.0066 | 0.22 | NO
63 | CYC1 | CYC1 | CYC1 | 6834 | 0.0062 | 0.22 | NO
64 | ATP6V0B | ATP6V0B | ATP6V0B | 6890 | 0.0052 | 0.22 | NO
65 | UQCRC1 | UQCRC1 | UQCRC1 | 6960 | 0.0042 | 0.21 | NO
66 | SDHA | SDHA | SDHA | 7091 | 0.0024 | 0.2 | NO
67 | COX11 | COX11 | COX11 | 7185 | 0.001 | 0.2 | NO
68 | NDUFB8 | NDUFB8 | NDUFB8 | 7216 | 0.00056 | 0.2 | NO
69 | ATP5H | ATP5H | ATP5H | 7229 | 0.00042 | 0.2 | NO
70 | COX5B | COX5B | COX5B | 7273 | -0.00016 | 0.2 | NO
71 | ATP5G3 | ATP5G3 | ATP5G3 | 7329 | -0.00087 | 0.19 | NO
72 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 7506 | -0.0035 | 0.18 | NO
73 | NDUFA2 | NDUFA2 | NDUFA2 | 7572 | -0.0043 | 0.18 | NO
74 | ATP6V1D | ATP6V1D | ATP6V1D | 7692 | -0.0063 | 0.18 | NO
75 | ATP6V1B2 | ATP6V1B2 | ATP6V1B2 | 7695 | -0.0064 | 0.18 | NO
76 | NDUFA4 | NDUFA4 | NDUFA4 | 7705 | -0.0065 | 0.18 | NO
77 | NDUFA8 | NDUFA8 | NDUFA8 | 7786 | -0.0078 | 0.18 | NO
78 | UQCRC2 | UQCRC2 | UQCRC2 | 7817 | -0.0081 | 0.18 | NO
79 | ATP5E | ATP5E | ATP5E | 7883 | -0.0088 | 0.17 | NO
80 | PPA1 | PPA1 | PPA1 | 7885 | -0.0089 | 0.17 | NO
81 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 7892 | -0.009 | 0.18 | NO
82 | NDUFS8 | NDUFS8 | NDUFS8 | 8028 | -0.011 | 0.17 | NO
83 | NDUFB4 | NDUFB4 | NDUFB4 | 8198 | -0.014 | 0.16 | NO
84 | ATP5F1 | ATP5F1 | ATP5F1 | 8444 | -0.017 | 0.15 | NO
85 | COX4I1 | COX4I1 | COX4I1 | 8559 | -0.019 | 0.15 | NO
86 | COX5A | COX5A | COX5A | 8566 | -0.019 | 0.15 | NO
87 | COX7B | COX7B | COX7B | 8634 | -0.02 | 0.15 | NO
88 | COX6C | COX6C | COX6C | 8698 | -0.021 | 0.16 | NO
89 | SDHD | SDHD | SDHD | 8729 | -0.021 | 0.16 | NO
90 | NDUFS1 | NDUFS1 | NDUFS1 | 8805 | -0.022 | 0.16 | NO
91 | UQCR10 | UQCR10 | UQCR10 | 9167 | -0.028 | 0.14 | NO
92 | ATP6V1G2 | ATP6V1G2 | ATP6V1G2 | 9329 | -0.03 | 0.14 | NO
93 | COX15 | COX15 | COX15 | 9382 | -0.031 | 0.14 | NO
94 | ATP6V1G1 | ATP6V1G1 | ATP6V1G1 | 9432 | -0.032 | 0.15 | NO
95 | ATP5G1 | ATP5G1 | ATP5G1 | 9507 | -0.033 | 0.15 | NO
96 | NDUFB5 | NDUFB5 | NDUFB5 | 9585 | -0.034 | 0.15 | NO
97 | ATP6V1F | ATP6V1F | ATP6V1F | 9846 | -0.038 | 0.14 | NO
98 | COX7A2 | COX7A2 | COX7A2 | 9914 | -0.039 | 0.15 | NO
99 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 10083 | -0.042 | 0.15 | NO
100 | COX4I2 | COX4I2 | COX4I2 | 10721 | -0.052 | 0.12 | NO
101 | NDUFA5 | NDUFA5 | NDUFA5 | 10790 | -0.054 | 0.13 | NO
102 | COX17 | COX17 | COX17 | 10908 | -0.056 | 0.13 | NO
103 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 11114 | -0.06 | 0.13 | NO
104 | ATP5J2 | ATP5J2 | ATP5J2 | 11204 | -0.062 | 0.14 | NO
105 | TCIRG1 | TCIRG1 | TCIRG1 | 11563 | -0.07 | 0.13 | NO
106 | SDHB | SDHB | SDHB | 11859 | -0.077 | 0.13 | NO
107 | COX6A2 | COX6A2 | COX6A2 | 12676 | -0.1 | 0.1 | NO
108 | ATP6V1A | ATP6V1A | ATP6V1A | 12937 | -0.11 | 0.11 | NO
109 | LHPP | LHPP | LHPP | 14243 | -0.16 | 0.071 | NO
110 | ATP6V0A4 | ATP6V0A4 | ATP6V0A4 | 16248 | -0.32 | 0.021 | NO
111 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 17056 | -0.43 | 0.059 | NO

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

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPLICEOSOME, 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 SNARE INTERACTIONS IN VESICULAR TRANSPORT

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 | CREB5 | CREB5 | CREB5 | 481 | 0.25 | 0.039 | YES
2 | AQP4 | AQP4 | AQP4 | 534 | 0.24 | 0.099 | YES
3 | AQP3 | AQP3 | AQP3 | 1137 | 0.17 | 0.11 | YES
4 | DCTN6 | DCTN6 | DCTN6 | 1266 | 0.16 | 0.14 | YES
5 | ADCY6 | ADCY6 | ADCY6 | 1391 | 0.15 | 0.18 | YES
6 | CREB3L4 | CREB3L4 | CREB3L4 | 1804 | 0.12 | 0.18 | YES
7 | PRKX | PRKX | PRKX | 3083 | 0.076 | 0.13 | NO
8 | DYNC2LI1 | DYNC2LI1 | DYNC2LI1 | 3215 | 0.072 | 0.14 | NO
9 | CREB3 | CREB3 | CREB3 | 3225 | 0.072 | 0.16 | NO
10 | VAMP2 | VAMP2 | VAMP2 | 3556 | 0.064 | 0.16 | NO
11 | ADCY9 | ADCY9 | ADCY9 | 3584 | 0.063 | 0.18 | NO
12 | RAB11B | RAB11B | RAB11B | 3807 | 0.058 | 0.18 | NO
13 | RAB11A | RAB11A | RAB11A | 4109 | 0.051 | 0.18 | NO
14 | DYNC1I2 | DYNC1I2 | DYNC1I2 | 4635 | 0.041 | 0.16 | NO
15 | PRKACA | PRKACA | PRKACA | 4657 | 0.04 | 0.17 | NO
16 | RAB5B | RAB5B | RAB5B | 4697 | 0.04 | 0.17 | NO
17 | DCTN2 | DCTN2 | DCTN2 | 5036 | 0.034 | 0.16 | NO
18 | DCTN1 | DCTN1 | DCTN1 | 5049 | 0.034 | 0.17 | NO
19 | STX4 | STX4 | STX4 | 5124 | 0.032 | 0.18 | NO
20 | DCTN5 | DCTN5 | DCTN5 | 5130 | 0.032 | 0.18 | NO
21 | DYNC1H1 | DYNC1H1 | DYNC1H1 | 5606 | 0.024 | 0.16 | NO
22 | DYNLL1 | DYNLL1 | DYNLL1 | 5826 | 0.021 | 0.16 | NO
23 | ARHGDIA | ARHGDIA | ARHGDIA | 7946 | -0.0097 | 0.043 | NO
24 | DCTN4 | DCTN4 | DCTN4 | 8163 | -0.013 | 0.034 | NO
25 | DYNC1LI2 | DYNC1LI2 | DYNC1LI2 | 9003 | -0.025 | -0.0057 | NO
26 | RAB5C | RAB5C | RAB5C | 9034 | -0.026 | -0.00073 | NO
27 | DYNC2H1 | DYNC2H1 | DYNC2H1 | 9451 | -0.032 | -0.016 | NO
28 | NSF | NSF | NSF | 9782 | -0.037 | -0.024 | NO
29 | CREB1 | CREB1 | CREB1 | 9788 | -0.037 | -0.015 | NO
30 | DYNC1LI1 | DYNC1LI1 | DYNC1LI1 | 9957 | -0.04 | -0.014 | NO
31 | AVPR2 | AVPR2 | AVPR2 | 11387 | -0.066 | -0.076 | NO
32 | RAB5A | RAB5A | RAB5A | 11758 | -0.075 | -0.077 | NO
33 | DYNLL2 | DYNLL2 | DYNLL2 | 12651 | -0.099 | -0.1 | NO
34 | GNAS | GNAS | GNAS | 12907 | -0.11 | -0.088 | NO
35 | DYNC1I1 | DYNC1I1 | DYNC1I1 | 13093 | -0.11 | -0.069 | NO
36 | CREB3L2 | CREB3L2 | CREB3L2 | 13321 | -0.12 | -0.05 | NO
37 | AQP2 | AQP2 | AQP2 | 14254 | -0.16 | -0.059 | NO
38 | PRKACB | PRKACB | PRKACB | 14771 | -0.2 | -0.037 | NO
39 | ARHGDIB | ARHGDIB | ARHGDIB | 15233 | -0.23 | -0.0044 | NO
40 | CREB3L3 | CREB3L3 | CREB3L3 | 16062 | -0.3 | 0.026 | NO
41 | CREB3L1 | CREB3L1 | CREB3L1 | 16471 | -0.34 | 0.091 | NO

Figure S31. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, 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 NOTCH SIGNALING PATHWAY

Table S17. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | POLR3B | POLR3B | POLR3B | 2408 | 0.098 | -0.059 | YES
2 | POLR2J3 | POLR2J3 | POLR2J3 | 3028 | 0.078 | -0.035 | YES
3 | POLR3C | POLR3C | POLR3C | 3385 | 0.068 | -0.0026 | YES
4 | POLR2I | POLR2I | POLR2I | 3589 | 0.063 | 0.034 | YES
5 | POLR2A | POLR2A | POLR2A | 3744 | 0.059 | 0.07 | YES
6 | POLR3F | POLR3F | POLR3F | 3924 | 0.056 | 0.1 | YES
7 | ZNRD1 | ZNRD1 | ZNRD1 | 4042 | 0.053 | 0.14 | YES
8 | POLR2J2 | POLR2J2 | POLR2J2 | 4134 | 0.051 | 0.17 | YES
9 | POLR3D | POLR3D | POLR3D | 5100 | 0.033 | 0.14 | NO
10 | POLR2F | POLR2F | POLR2F | 5285 | 0.029 | 0.15 | NO
11 | POLR2G | POLR2G | POLR2G | 5738 | 0.022 | 0.14 | NO
12 | POLR1C | POLR1C | POLR1C | 5797 | 0.021 | 0.16 | NO
13 | POLR2K | POLR2K | POLR2K | 6077 | 0.017 | 0.15 | NO
14 | POLR2L | POLR2L | POLR2L | 6410 | 0.012 | 0.14 | NO
15 | POLR1D | POLR1D | POLR1D | 6648 | 0.0086 | 0.14 | NO
16 | POLR1E | POLR1E | POLR1E | 6706 | 0.0079 | 0.14 | NO
17 | POLR2E | POLR2E | POLR2E | 7824 | -0.0082 | 0.086 | NO
18 | POLR2J | POLR2J | POLR2J | 8152 | -0.013 | 0.078 | NO
19 | POLR2B | POLR2B | POLR2B | 8363 | -0.016 | 0.078 | NO
20 | POLR3H | POLR3H | POLR3H | 8782 | -0.022 | 0.071 | NO
21 | POLR3GL | POLR3GL | POLR3GL | 9343 | -0.031 | 0.064 | NO
22 | POLR1B | POLR1B | POLR1B | 9355 | -0.031 | 0.086 | NO
23 | POLR2D | POLR2D | POLR2D | 9361 | -0.031 | 0.11 | NO
24 | POLR3A | POLR3A | POLR3A | 10408 | -0.047 | 0.087 | NO
25 | POLR2C | POLR2C | POLR2C | 10763 | -0.053 | 0.11 | NO
26 | POLR1A | POLR1A | POLR1A | 11022 | -0.058 | 0.14 | NO
27 | POLR3K | POLR3K | POLR3K | 12094 | -0.083 | 0.14 | NO
28 | POLR3G | POLR3G | POLR3G | 15594 | -0.25 | 0.14 | NO

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

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

genes ES table in pathway: KEGG VASOPRESSIN REGULATED WATER REABSORPTION

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 | DTX3 | DTX3 | DTX3 | 200 | 0.33 | 0.086 | YES
2 | HES1 | HES1 | HES1 | 1395 | 0.15 | 0.065 | YES
3 | JAG1 | JAG1 | JAG1 | 1660 | 0.13 | 0.089 | YES
4 | DLL3 | DLL3 | DLL3 | 2002 | 0.11 | 0.1 | YES
5 | PSEN2 | PSEN2 | PSEN2 | 2490 | 0.095 | 0.1 | YES
6 | MAML3 | MAML3 | MAML3 | 2638 | 0.09 | 0.12 | YES
7 | NCSTN | NCSTN | NCSTN | 2852 | 0.083 | 0.14 | YES
8 | CTBP2 | CTBP2 | CTBP2 | 2989 | 0.079 | 0.15 | YES
9 | APH1A | APH1A | APH1A | 3370 | 0.069 | 0.15 | NO
10 | PSENEN | PSENEN | PSENEN | 4154 | 0.05 | 0.12 | NO
11 | NCOR2 | NCOR2 | NCOR2 | 4948 | 0.035 | 0.09 | NO
12 | KAT2A | KAT2A | KAT2A | 5311 | 0.029 | 0.079 | NO
13 | CTBP1 | CTBP1 | CTBP1 | 5330 | 0.029 | 0.086 | NO
14 | DVL2 | DVL2 | DVL2 | 5347 | 0.028 | 0.094 | NO
15 | NOTCH3 | NOTCH3 | NOTCH3 | 6025 | 0.018 | 0.061 | NO
16 | HDAC1 | HDAC1 | HDAC1 | 6382 | 0.013 | 0.045 | NO
17 | CREBBP | CREBBP | CREBBP | 6681 | 0.0082 | 0.031 | NO
18 | DLL4 | DLL4 | DLL4 | 6690 | 0.0081 | 0.033 | NO
19 | JAG2 | JAG2 | JAG2 | 6692 | 0.0081 | 0.036 | NO
20 | HES5 | HES5 | HES5 | 6868 | 0.0056 | 0.028 | NO
21 | NOTCH2 | NOTCH2 | NOTCH2 | 7105 | 0.0022 | 0.015 | NO
22 | CIR1 | CIR1 | CIR1 | 7226 | 0.00043 | 0.0086 | NO
23 | RBPJ | RBPJ | RBPJ | 7660 | -0.0058 | -0.014 | NO
24 | RFNG | RFNG | RFNG | 7721 | -0.0068 | -0.015 | NO
25 | PSEN1 | PSEN1 | PSEN1 | 7756 | -0.0073 | -0.015 | NO
26 | DTX1 | DTX1 | DTX1 | 7788 | -0.0078 | -0.014 | NO
27 | SNW1 | SNW1 | SNW1 | 8164 | -0.013 | -0.031 | NO
28 | EP300 | EP300 | EP300 | 8547 | -0.019 | -0.047 | NO
29 | NOTCH4 | NOTCH4 | NOTCH4 | 8655 | -0.02 | -0.046 | NO
30 | MAML1 | MAML1 | MAML1 | 8733 | -0.021 | -0.044 | NO
31 | HDAC2 | HDAC2 | HDAC2 | 10018 | -0.041 | -0.1 | NO
32 | DVL3 | DVL3 | DVL3 | 10803 | -0.054 | -0.13 | NO
33 | MAML2 | MAML2 | MAML2 | 10919 | -0.056 | -0.12 | NO
34 | NOTCH1 | NOTCH1 | NOTCH1 | 10922 | -0.056 | -0.1 | NO
35 | NUMB | NUMB | NUMB | 10957 | -0.057 | -0.089 | NO
36 | DTX4 | DTX4 | DTX4 | 11125 | -0.061 | -0.08 | NO
37 | NUMBL | NUMBL | NUMBL | 11499 | -0.069 | -0.081 | NO
38 | DVL1 | DVL1 | DVL1 | 11501 | -0.069 | -0.06 | NO
39 | RBPJL | RBPJL | RBPJL | 11753 | -0.075 | -0.052 | NO
40 | DTX3L | DTX3L | DTX3L | 12202 | -0.086 | -0.051 | NO
41 | DTX2 | DTX2 | DTX2 | 12605 | -0.098 | -0.045 | NO
42 | KAT2B | KAT2B | KAT2B | 13429 | -0.13 | -0.053 | NO
43 | ADAM17 | ADAM17 | ADAM17 | 14444 | -0.18 | -0.056 | NO
44 | LFNG | LFNG | LFNG | 15039 | -0.21 | -0.026 | NO
45 | DLL1 | DLL1 | DLL1 | 15964 | -0.29 | 0.0075 | NO
46 | PTCRA | PTCRA | PTCRA | 16754 | -0.38 | 0.075 | 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 VASOPRESSIN REGULATED WATER REABSORPTION.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VASOPRESSIN REGULATED WATER REABSORPTION, 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 HUNTINGTONS DISEASE

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 | SNAP25 | SNAP25 | SNAP25 | 421 | 0.27 | 0.082 | YES
2 | STX3 | STX3 | STX3 | 2197 | 0.11 | 0.025 | YES
3 | STX8 | STX8 | STX8 | 2630 | 0.09 | 0.037 | YES
4 | STX18 | STX18 | STX18 | 2635 | 0.09 | 0.072 | YES
5 | STX1B | STX1B | STX1B | 3455 | 0.067 | 0.052 | YES
6 | USE1 | USE1 | USE1 | 3519 | 0.065 | 0.074 | YES
7 | VAMP2 | VAMP2 | VAMP2 | 3556 | 0.064 | 0.097 | YES
8 | STX19 | STX19 | STX19 | 3940 | 0.055 | 0.098 | YES
9 | VAMP4 | VAMP4 | VAMP4 | 4286 | 0.048 | 0.097 | YES
10 | VAMP8 | VAMP8 | VAMP8 | 4378 | 0.046 | 0.11 | YES
11 | SNAP47 | SNAP47 | SNAP47 | 4881 | 0.036 | 0.097 | YES
12 | STX10 | STX10 | STX10 | 4882 | 0.036 | 0.11 | YES
13 | BNIP1 | BNIP1 | BNIP1 | 4901 | 0.036 | 0.12 | YES
14 | STX4 | STX4 | STX4 | 5124 | 0.032 | 0.12 | YES
15 | STX6 | STX6 | STX6 | 5200 | 0.031 | 0.13 | YES
16 | TSNARE1 | TSNARE1 | TSNARE1 | 6902 | 0.005 | 0.04 | NO
17 | STX5 | STX5 | STX5 | 7037 | 0.0031 | 0.034 | NO
18 | STX1A | STX1A | STX1A | 7295 | -0.00042 | 0.02 | NO
19 | STX16 | STX16 | STX16 | 8859 | -0.023 | -0.057 | NO
20 | STX17 | STX17 | STX17 | 8872 | -0.023 | -0.049 | NO
21 | BET1L | BET1L | BET1L | 8920 | -0.024 | -0.042 | NO
22 | SEC22B | SEC22B | SEC22B | 9356 | -0.031 | -0.054 | NO
23 | VTI1B | VTI1B | VTI1B | 9399 | -0.031 | -0.044 | NO
24 | VAMP7 | VAMP7 | VAMP7 | 9785 | -0.037 | -0.051 | NO
25 | VAMP5 | VAMP5 | VAMP5 | 9805 | -0.037 | -0.037 | NO
26 | STX2 | STX2 | STX2 | 10028 | -0.041 | -0.034 | NO
27 | SNAP23 | SNAP23 | SNAP23 | 10159 | -0.043 | -0.024 | NO
28 | VTI1A | VTI1A | VTI1A | 10438 | -0.047 | -0.021 | NO
29 | GOSR1 | GOSR1 | GOSR1 | 10475 | -0.048 | -0.0044 | NO
30 | GOSR2 | GOSR2 | GOSR2 | 10652 | -0.051 | 0.0058 | NO
31 | YKT6 | YKT6 | YKT6 | 10720 | -0.052 | 0.023 | NO
32 | STX7 | STX7 | STX7 | 10983 | -0.058 | 0.031 | NO
33 | STX12 | STX12 | STX12 | 11724 | -0.074 | 0.019 | NO
34 | VAMP3 | VAMP3 | VAMP3 | 13036 | -0.11 | -0.01 | NO
35 | VAMP1 | VAMP1 | VAMP1 | 14101 | -0.16 | -0.0077 | NO
36 | BET1 | BET1 | BET1 | 14271 | -0.17 | 0.048 | NO
37 | STX11 | STX11 | STX11 | 17012 | -0.42 | 0.061 | 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 HUNTINGTONS DISEASE.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HUNTINGTONS DISEASE, 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

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

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

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

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

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

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 AT1R PATHWAY | 32 | genes.ES.table | 0.38 | 1.5 | 0.081 | 0.18 | 0.88 | 0.16 | 0.15 | 0.13 | 0.13 | 0.004
BIOCARTA BIOPEPTIDES PATHWAY | 39 | genes.ES.table | 0.57 | 2 | 0 | 0.0094 | 0.076 | 0.23 | 0.17 | 0.19 | 0 | 0
BIOCARTA PPARA PATHWAY | 54 | genes.ES.table | 0.62 | 2.1 | 0 | 0.0043 | 0.015 | 0.32 | 0.19 | 0.26 | 0 | 0
BIOCARTA CHREBP2 PATHWAY | 40 | genes.ES.table | 0.38 | 1.4 | 0.094 | 0.24 | 0.94 | 0.22 | 0.18 | 0.18 | 0.18 | 0.012
KEGG GLYCOLYSIS GLUCONEOGENESIS | 57 | genes.ES.table | 0.7 | 2.1 | 0 | 0.0053 | 0.011 | 0.3 | 0.094 | 0.27 | 0 | 0
KEGG CITRATE CYCLE TCA CYCLE | 29 | genes.ES.table | 0.6 | 1.6 | 0.12 | 0.12 | 0.77 | 0.48 | 0.28 | 0.35 | 0.073 | 0.002
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS | 26 | genes.ES.table | 0.79 | 1.5 | 0.04 | 0.14 | 0.81 | 0.54 | 0.061 | 0.51 | 0.089 | 0.001
KEGG FRUCTOSE AND MANNOSE METABOLISM | 32 | genes.ES.table | 0.69 | 2.1 | 0 | 0.0044 | 0.011 | 0.16 | 0.034 | 0.15 | 0 | 0
KEGG FATTY ACID METABOLISM | 40 | genes.ES.table | 0.8 | 1.9 | 0 | 0.01 | 0.086 | 0.6 | 0.14 | 0.52 | 0 | 0
KEGG STEROID HORMONE BIOSYNTHESIS | 50 | genes.ES.table | 0.8 | 1.8 | 0 | 0.03 | 0.35 | 0.48 | 0.061 | 0.45 | 0 | 0

genes ES table in pathway: BIOCARTA AT1R 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 | TAT | TAT | TAT | 27 | 1.9 | 0.17 | YES
2 | BHMT | BHMT | BHMT | 60 | 1.7 | 0.32 | YES
3 | CDO1 | CDO1 | CDO1 | 67 | 1.6 | 0.46 | YES
4 | DNMT3L | DNMT3L | DNMT3L | 131 | 1.2 | 0.57 | YES
5 | MAT1A | MAT1A | MAT1A | 190 | 1 | 0.65 | YES
6 | SDS | SDS | SDS | 284 | 0.73 | 0.71 | YES
7 | CTH | CTH | CTH | 318 | 0.67 | 0.77 | YES
8 | CBS | CBS | CBS | 739 | 0.34 | 0.78 | YES
9 | LDHAL6B | LDHAL6B | LDHAL6B | 795 | 0.33 | 0.8 | YES
10 | GOT1 | GOT1 | GOT1 | 1532 | 0.2 | 0.78 | NO
11 | GOT2 | GOT2 | GOT2 | 1968 | 0.16 | 0.77 | NO
12 | LDHAL6A | LDHAL6A | LDHAL6A | 2287 | 0.14 | 0.77 | NO
13 | MPST | MPST | MPST | 3093 | 0.1 | 0.73 | NO
14 | ADI1 | ADI1 | ADI1 | 3269 | 0.098 | 0.73 | NO
15 | AHCY | AHCY | AHCY | 4629 | 0.062 | 0.66 | NO
16 | MAT2A | MAT2A | MAT2A | 5257 | 0.049 | 0.63 | NO
17 | MTAP | MTAP | MTAP | 5801 | 0.038 | 0.6 | NO
18 | AHCYL1 | AHCYL1 | AHCYL1 | 5893 | 0.037 | 0.6 | NO
19 | MTR | MTR | MTR | 7532 | 0.015 | 0.51 | NO
20 | MAT2B | MAT2B | MAT2B | 7683 | 0.013 | 0.51 | NO
21 | DNMT1 | DNMT1 | DNMT1 | 8359 | 0.005 | 0.47 | NO
22 | AHCYL2 | AHCYL2 | AHCYL2 | 8476 | 0.0037 | 0.46 | NO
23 | SRM | SRM | SRM | 8631 | 0.0018 | 0.46 | NO
24 | LDHA | LDHA | LDHA | 9002 | -0.0022 | 0.44 | NO
25 | AMD1 | AMD1 | AMD1 | 9570 | -0.0085 | 0.4 | NO
26 | SMS | SMS | SMS | 11054 | -0.026 | 0.32 | NO
27 | LDHB | LDHB | LDHB | 13454 | -0.062 | 0.2 | NO
28 | ENOPH1 | ENOPH1 | ENOPH1 | 13723 | -0.067 | 0.19 | NO
29 | DNMT3B | DNMT3B | DNMT3B | 14566 | -0.086 | 0.15 | NO
30 | APIP | APIP | APIP | 14703 | -0.089 | 0.15 | NO
31 | TRDMT1 | TRDMT1 | TRDMT1 | 14721 | -0.09 | 0.16 | NO
32 | DNMT3A | DNMT3A | DNMT3A | 14886 | -0.094 | 0.16 | NO
33 | IL4I1 | IL4I1 | IL4I1 | 17380 | -0.25 | 0.04 | 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: BIOCARTA AT1R PATHWAY.

Figure S40. 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 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 | DPYS | DPYS | DPYS | 44 | 1.8 | 0.17 | YES
2 | UPB1 | UPB1 | UPB1 | 72 | 1.6 | 0.32 | YES
3 | UPP2 | UPP2 | UPP2 | 270 | 0.78 | 0.38 | YES
4 | DPYD | DPYD | DPYD | 844 | 0.32 | 0.38 | YES
5 | DHODH | DHODH | DHODH | 866 | 0.31 | 0.41 | YES
6 | POLR3G | POLR3G | POLR3G | 900 | 0.3 | 0.44 | YES
7 | CDA | CDA | CDA | 918 | 0.3 | 0.46 | YES
8 | ENTPD5 | ENTPD5 | ENTPD5 | 968 | 0.29 | 0.49 | YES
9 | POLE2 | POLE2 | POLE2 | 1239 | 0.24 | 0.5 | YES
10 | RRM2 | RRM2 | RRM2 | 1650 | 0.19 | 0.49 | NO
11 | NT5C1B | NT5C1B | NT5C1B | 2090 | 0.16 | 0.48 | NO
12 | ENTPD8 | ENTPD8 | ENTPD8 | 2433 | 0.14 | 0.48 | NO
13 | NT5E | NT5E | NT5E | 2540 | 0.13 | 0.48 | NO
14 | TK1 | TK1 | TK1 | 3001 | 0.11 | 0.47 | NO
15 | NME1-NME2 | NME1-NME2 | NME1-NME2 | 3845 | 0.081 | 0.43 | NO
16 | TYMS | TYMS | TYMS | 4068 | 0.075 | 0.42 | NO
17 | CMPK1 | CMPK1 | CMPK1 | 4399 | 0.067 | 0.41 | NO
18 | PNP | PNP | PNP | 4901 | 0.055 | 0.39 | NO
19 | POLR3A | POLR3A | POLR3A | 4978 | 0.054 | 0.39 | NO
20 | POLR2C | POLR2C | POLR2C | 5361 | 0.047 | 0.37 | NO
21 | NME1 | NME1 | NME1 | 5373 | 0.046 | 0.38 | NO
22 | NT5M | NT5M | NT5M | 5380 | 0.046 | 0.38 | NO
23 | TXNRD2 | TXNRD2 | TXNRD2 | 5436 | 0.045 | 0.38 | NO
24 | AK3 | AK3 | AK3 | 5598 | 0.042 | 0.38 | NO
25 | POLD4 | POLD4 | POLD4 | 5683 | 0.04 | 0.38 | NO
26 | UPRT | UPRT | UPRT | 5916 | 0.037 | 0.37 | NO
27 | POLR2F | POLR2F | POLR2F | 5941 | 0.036 | 0.37 | NO
28 | POLD2 | POLD2 | POLD2 | 5954 | 0.036 | 0.37 | NO
29 | NME4 | NME4 | NME4 | 6064 | 0.035 | 0.37 | NO
30 | NUDT2 | NUDT2 | NUDT2 | 6556 | 0.028 | 0.34 | NO
31 | POLR1B | POLR1B | POLR1B | 6709 | 0.026 | 0.34 | NO
32 | NT5C2 | NT5C2 | NT5C2 | 6956 | 0.023 | 0.33 | NO
33 | CAD | CAD | CAD | 7404 | 0.017 | 0.3 | NO
34 | PNPT1 | PNPT1 | PNPT1 | 7547 | 0.015 | 0.3 | NO
35 | POLE | POLE | POLE | 7602 | 0.014 | 0.3 | NO
36 | POLR1A | POLR1A | POLR1A | 7830 | 0.011 | 0.28 | NO
37 | NME2 | NME2 | NME2 | 7935 | 0.01 | 0.28 | NO
38 | POLR3H | POLR3H | POLR3H | 7955 | 0.01 | 0.28 | NO
39 | POLR2E | POLR2E | POLR2E | 8034 | 0.009 | 0.28 | NO
40 | TYMP | TYMP | TYMP | 8112 | 0.0082 | 0.27 | NO
41 | POLE4 | POLE4 | POLE4 | 8495 | 0.0035 | 0.25 | NO
42 | POLR3B | POLR3B | POLR3B | 8543 | 0.0029 | 0.25 | NO
43 | CANT1 | CANT1 | CANT1 | 8554 | 0.0028 | 0.25 | NO
44 | UPP1 | UPP1 | UPP1 | 8705 | 0.0011 | 0.24 | NO
45 | RRM2B | RRM2B | RRM2B | 8994 | -0.0021 | 0.22 | NO
46 | POLR2G | POLR2G | POLR2G | 9127 | -0.0035 | 0.22 | NO
47 | TK2 | TK2 | TK2 | 9179 | -0.0042 | 0.22 | NO
48 | POLR2D | POLR2D | POLR2D | 9584 | -0.0087 | 0.19 | NO
49 | POLR1E | POLR1E | POLR1E | 9690 | -0.01 | 0.19 | NO
50 | POLD1 | POLD1 | POLD1 | 9777 | -0.011 | 0.18 | NO
51 | POLE3 | POLE3 | POLE3 | 9811 | -0.011 | 0.18 | NO
52 | UCK1 | UCK1 | UCK1 | 10073 | -0.014 | 0.17 | NO
53 | UMPS | UMPS | UMPS | 10236 | -0.016 | 0.16 | NO
54 | POLR2J | POLR2J | POLR2J | 10264 | -0.017 | 0.16 | NO
55 | POLR3GL | POLR3GL | POLR3GL | 10516 | -0.02 | 0.15 | NO
56 | POLR2H | POLR2H | POLR2H | 10531 | -0.02 | 0.15 | NO
57 | POLR3F | POLR3F | POLR3F | 10582 | -0.02 | 0.15 | NO
58 | DTYMK | DTYMK | DTYMK | 10618 | -0.021 | 0.15 | NO
59 | POLR2I | POLR2I | POLR2I | 10880 | -0.024 | 0.14 | NO
60 | POLR2K | POLR2K | POLR2K | 11010 | -0.026 | 0.14 | NO
61 | NME5 | NME5 | NME5 | 11013 | -0.026 | 0.14 | NO
62 | TXNRD1 | TXNRD1 | TXNRD1 | 11066 | -0.026 | 0.14 | NO
63 | ENTPD6 | ENTPD6 | ENTPD6 | 11513 | -0.032 | 0.12 | NO
64 | RRM1 | RRM1 | RRM1 | 11628 | -0.034 | 0.11 | NO
65 | CMPK2 | CMPK2 | CMPK2 | 11748 | -0.036 | 0.11 | NO
66 | POLR3K | POLR3K | POLR3K | 12141 | -0.041 | 0.092 | NO
67 | POLD3 | POLD3 | POLD3 | 12143 | -0.041 | 0.096 | NO
68 | POLA2 | POLA2 | POLA2 | 12452 | -0.046 | 0.083 | NO
69 | NT5C3 | NT5C3 | NT5C3 | 12592 | -0.048 | 0.08 | NO
70 | ENTPD3 | ENTPD3 | ENTPD3 | 12887 | -0.053 | 0.068 | NO
71 | PRIM1 | PRIM1 | PRIM1 | 13176 | -0.057 | 0.058 | NO
72 | POLR2A | POLR2A | POLR2A | 13308 | -0.059 | 0.056 | NO
73 | NME6 | NME6 | NME6 | 13412 | -0.061 | 0.056 | NO
74 | POLR3C | POLR3C | POLR3C | 13655 | -0.065 | 0.049 | NO
75 | DUT | DUT | DUT | 13700 | -0.066 | 0.053 | NO
76 | POLR2J3 | POLR2J3 | POLR2J3 | 13780 | -0.068 | 0.055 | NO
77 | POLR2L | POLR2L | POLR2L | 14034 | -0.073 | 0.048 | NO
78 | ENTPD1 | ENTPD1 | ENTPD1 | 14134 | -0.075 | 0.05 | NO
79 | ITPA | ITPA | ITPA | 14266 | -0.078 | 0.05 | NO
80 | POLR2B | POLR2B | POLR2B | 14339 | -0.08 | 0.054 | NO
81 | ENTPD4 | ENTPD4 | ENTPD4 | 14385 | -0.081 | 0.059 | NO
82 | DCTD | DCTD | DCTD | 14520 | -0.084 | 0.06 | NO
83 | PRIM2 | PRIM2 | PRIM2 | 14579 | -0.086 | 0.065 | NO
84 | POLA1 | POLA1 | POLA1 | 14582 | -0.086 | 0.073 | NO
85 | POLR1C | POLR1C | POLR1C | 14605 | -0.087 | 0.08 | NO
86 | CTPS2 | CTPS2 | CTPS2 | 14695 | -0.089 | 0.084 | NO
87 | NT5C | NT5C | NT5C | 14741 | -0.09 | 0.09 | NO
88 | NME3 | NME3 | NME3 | 14925 | -0.096 | 0.089 | NO
89 | UCK2 | UCK2 | UCK2 | 15022 | -0.098 | 0.093 | NO
90 | NME7 | NME7 | NME7 | 15079 | -0.1 | 0.1 | NO
91 | POLR1D | POLR1D | POLR1D | 15115 | -0.1 | 0.11 | NO
92 | POLR3D | POLR3D | POLR3D | 15209 | -0.1 | 0.11 | NO
93 | ZNRD1 | ZNRD1 | ZNRD1 | 15264 | -0.11 | 0.12 | NO
94 | DCK | DCK | DCK | 15419 | -0.11 | 0.12 | NO
95 | UCKL1 | UCKL1 | UCKL1 | 15746 | -0.12 | 0.12 | NO
96 | POLR2J2 | POLR2J2 | POLR2J2 | 16583 | -0.17 | 0.085 | 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 BIOPEPTIDES PATHWAY.

Figure S42. 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 PPARA 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 | CYP8B1 | CYP8B1 | CYP8B1 | 28 | 1.9 | 0.074 | YES
2 | APOA5 | APOA5 | APOA5 | 29 | 1.9 | 0.15 | YES
3 | CYP4A22 | CYP4A22 | CYP4A22 | 31 | 1.9 | 0.22 | YES
4 | APOC3 | APOC3 | APOC3 | 61 | 1.7 | 0.29 | YES
5 | APOA1 | APOA1 | APOA1 | 83 | 1.5 | 0.34 | YES
6 | FABP1 | FABP1 | FABP1 | 121 | 1.3 | 0.39 | YES
7 | PCK1 | PCK1 | PCK1 | 140 | 1.2 | 0.44 | YES
8 | CYP7A1 | CYP7A1 | CYP7A1 | 144 | 1.2 | 0.48 | YES
9 | APOA2 | APOA2 | APOA2 | 155 | 1.1 | 0.53 | YES
10 | SLC27A5 | SLC27A5 | SLC27A5 | 156 | 1.1 | 0.57 | YES
11 | HMGCS2 | HMGCS2 | HMGCS2 | 175 | 1 | 0.61 | YES
12 | CYP4A11 | CYP4A11 | CYP4A11 | 239 | 0.83 | 0.64 | YES
13 | PLIN1 | PLIN1 | PLIN1 | 242 | 0.83 | 0.67 | YES
14 | ACADL | ACADL | ACADL | 288 | 0.72 | 0.7 | YES
15 | EHHADH | EHHADH | EHHADH | 333 | 0.65 | 0.72 | YES
16 | ACSL1 | ACSL1 | ACSL1 | 473 | 0.49 | 0.73 | YES
17 | SLC27A2 | SLC27A2 | SLC27A2 | 507 | 0.46 | 0.75 | YES
18 | CYP27A1 | CYP27A1 | CYP27A1 | 581 | 0.42 | 0.76 | YES
19 | CD36 | CD36 | CD36 | 651 | 0.38 | 0.77 | YES
20 | PCK2 | PCK2 | PCK2 | 791 | 0.33 | 0.78 | YES
21 | ANGPTL4 | ANGPTL4 | ANGPTL4 | 805 | 0.33 | 0.79 | YES
22 | ACSL6 | ACSL6 | ACSL6 | 864 | 0.31 | 0.8 | YES
23 | FABP3 | FABP3 | FABP3 | 1179 | 0.25 | 0.79 | YES
24 | ACSL5 | ACSL5 | ACSL5 | 1246 | 0.24 | 0.8 | YES
25 | SCD | SCD | SCD | 1387 | 0.22 | 0.8 | YES
26 | FABP4 | FABP4 | FABP4 | 1465 | 0.21 | 0.8 | YES
27 | ACAA1 | ACAA1 | ACAA1 | 1754 | 0.18 | 0.79 | YES
28 | SCP2 | SCP2 | SCP2 | 1818 | 0.18 | 0.79 | YES
29 | ACADM | ACADM | ACADM | 1865 | 0.17 | 0.8 | YES
30 | RXRG | RXRG | RXRG | 1917 | 0.17 | 0.8 | YES
31 | CPT2 | CPT2 | CPT2 | 1964 | 0.16 | 0.81 | YES
32 | PPARA | PPARA | PPARA | 1990 | 0.16 | 0.81 | YES
33 | ACOX1 | ACOX1 | ACOX1 | 2024 | 0.16 | 0.82 | YES
34 | SORBS1 | SORBS1 | SORBS1 | 2470 | 0.13 | 0.8 | NO
35 | CPT1C | CPT1C | CPT1C | 2480 | 0.13 | 0.8 | NO
36 | AQP7 | AQP7 | AQP7 | 3697 | 0.085 | 0.74 | NO
37 | ACSL3 | ACSL3 | ACSL3 | 4014 | 0.076 | 0.72 | NO
38 | GK | GK | GK | 5111 | 0.052 | 0.66 | NO
39 | CPT1A | CPT1A | CPT1A | 5540 | 0.043 | 0.64 | NO
40 | ME1 | ME1 | ME1 | 6698 | 0.026 | 0.58 | NO
41 | RXRA | RXRA | RXRA | 7058 | 0.021 | 0.56 | NO
42 | FABP5 | FABP5 | FABP5 | 7106 | 0.021 | 0.56 | NO
43 | PDPK1 | PDPK1 | PDPK1 | 7420 | 0.016 | 0.54 | NO
44 | PLTP | PLTP | PLTP | 7779 | 0.012 | 0.52 | NO
45 | ACOX3 | ACOX3 | ACOX3 | 7887 | 0.011 | 0.52 | NO
46 | PPARG | PPARG | PPARG | 8013 | 0.0092 | 0.51 | NO
47 | CPT1B | CPT1B | CPT1B | 8122 | 0.0081 | 0.5 | NO
48 | SLC27A4 | SLC27A4 | SLC27A4 | 9019 | -0.0025 | 0.45 | NO
49 | PPARD | PPARD | PPARD | 9334 | -0.0059 | 0.44 | NO
50 | UBC | UBC | UBC | 9593 | -0.0088 | 0.42 | NO
51 | DBI | DBI | DBI | 10492 | -0.019 | 0.37 | NO
52 | RXRB | RXRB | RXRB | 10934 | -0.025 | 0.35 | NO
53 | FADS2 | FADS2 | FADS2 | 10935 | -0.025 | 0.35 | NO
54 | FABP6 | FABP6 | FABP6 | 11291 | -0.03 | 0.33 | NO
55 | SLC27A1 | SLC27A1 | SLC27A1 | 12327 | -0.044 | 0.28 | NO
56 | ILK | ILK | ILK | 12767 | -0.051 | 0.25 | NO
57 | NR1H3 | NR1H3 | NR1H3 | 13296 | -0.059 | 0.23 | NO
58 | ACSL4 | ACSL4 | ACSL4 | 13367 | -0.06 | 0.23 | NO
59 | SCD5 | SCD5 | SCD5 | 14093 | -0.074 | 0.19 | NO
60 | OLR1 | OLR1 | OLR1 | 15569 | -0.12 | 0.11 | NO
61 | LPL | LPL | LPL | 15982 | -0.13 | 0.094 | NO
62 | MMP1 | MMP1 | MMP1 | 17642 | -0.3 | 0.014 | NO
63 | SLC27A6 | SLC27A6 | SLC27A6 | 17735 | -0.32 | 0.021 | 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 PPARA PATHWAY.

Figure S44. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PPARA 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 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 | HAO1 | HAO1 | HAO1 | 5 | 2.3 | 0.13 | YES
2 | HAO2 | HAO2 | HAO2 | 55 | 1.7 | 0.23 | YES
3 | DAO | DAO | DAO | 58 | 1.7 | 0.33 | YES
4 | AGXT | AGXT | AGXT | 59 | 1.7 | 0.42 | YES
5 | PIPOX | PIPOX | PIPOX | 158 | 1.1 | 0.48 | YES
6 | EHHADH | EHHADH | EHHADH | 333 | 0.65 | 0.51 | YES
7 | ACSL1 | ACSL1 | ACSL1 | 473 | 0.49 | 0.53 | YES
8 | SLC27A2 | SLC27A2 | SLC27A2 | 507 | 0.46 | 0.56 | YES
9 | BAAT | BAAT | BAAT | 568 | 0.42 | 0.58 | YES
10 | XDH | XDH | XDH | 630 | 0.39 | 0.6 | YES
11 | PXMP2 | PXMP2 | PXMP2 | 717 | 0.35 | 0.62 | YES
12 | EPHX2 | EPHX2 | EPHX2 | 853 | 0.32 | 0.63 | YES
13 | ACSL6 | ACSL6 | ACSL6 | 864 | 0.31 | 0.64 | YES
14 | PHYH | PHYH | PHYH | 1233 | 0.24 | 0.64 | YES
15 | ACSL5 | ACSL5 | ACSL5 | 1246 | 0.24 | 0.65 | YES
16 | PECR | PECR | PECR | 1358 | 0.22 | 0.66 | YES
17 | DDO | DDO | DDO | 1422 | 0.21 | 0.67 | YES
18 | ACAA1 | ACAA1 | ACAA1 | 1754 | 0.18 | 0.66 | YES
19 | HMGCL | HMGCL | HMGCL | 1756 | 0.18 | 0.67 | YES
20 | MLYCD | MLYCD | MLYCD | 1769 | 0.18 | 0.68 | YES
21 | CAT | CAT | CAT | 1814 | 0.18 | 0.69 | YES
22 | SCP2 | SCP2 | SCP2 | 1818 | 0.18 | 0.7 | YES
23 | NUDT12 | NUDT12 | NUDT12 | 1867 | 0.17 | 0.7 | YES
24 | PEX11G | PEX11G | PEX11G | 1953 | 0.16 | 0.71 | YES
25 | ACOX1 | ACOX1 | ACOX1 | 2024 | 0.16 | 0.71 | YES
26 | PECI | PECI | PECI | 2341 | 0.14 | 0.7 | YES
27 | ABCD3 | ABCD3 | ABCD3 | 2410 | 0.14 | 0.71 | YES
28 | HSD17B4 | HSD17B4 | HSD17B4 | 2509 | 0.13 | 0.71 | YES
29 | MPV17L | MPV17L | MPV17L | 2547 | 0.13 | 0.72 | YES
30 | AMACR | AMACR | AMACR | 2687 | 0.12 | 0.72 | YES
31 | PEX3 | PEX3 | PEX3 | 2722 | 0.12 | 0.72 | YES
32 | PAOX | PAOX | PAOX | 3189 | 0.1 | 0.7 | NO
33 | IDH1 | IDH1 | IDH1 | 3226 | 0.099 | 0.7 | NO
34 | SOD1 | SOD1 | SOD1 | 3239 | 0.099 | 0.71 | NO
35 | DECR2 | DECR2 | DECR2 | 3360 | 0.095 | 0.71 | NO
36 | DHRS4 | DHRS4 | DHRS4 | 3497 | 0.091 | 0.71 | NO
37 | CROT | CROT | CROT | 3645 | 0.087 | 0.7 | NO
38 | ABCD2 | ABCD2 | ABCD2 | 3830 | 0.082 | 0.7 | NO
39 | ECH1 | ECH1 | ECH1 | 3860 | 0.08 | 0.7 | NO
40 | PEX26 | PEX26 | PEX26 | 3907 | 0.079 | 0.7 | NO
41 | ACSL3 | ACSL3 | ACSL3 | 4014 | 0.076 | 0.7 | NO
42 | FAR2 | FAR2 | FAR2 | 4025 | 0.076 | 0.7 | NO
43 | SLC25A17 | SLC25A17 | SLC25A17 | 4076 | 0.075 | 0.71 | NO
44 | PEX13 | PEX13 | PEX13 | 4095 | 0.074 | 0.71 | NO
45 | NUDT19 | NUDT19 | NUDT19 | 4120 | 0.074 | 0.71 | NO
46 | GSTK1 | GSTK1 | GSTK1 | 4273 | 0.07 | 0.71 | NO
47 | CRAT | CRAT | CRAT | 4335 | 0.068 | 0.71 | NO
48 | MVK | MVK | MVK | 4379 | 0.067 | 0.71 | NO
49 | AGPS | AGPS | AGPS | 4524 | 0.064 | 0.71 | NO
50 | PEX1 | PEX1 | PEX1 | 4824 | 0.057 | 0.69 | NO
51 | PEX11A | PEX11A | PEX11A | 4914 | 0.055 | 0.69 | NO
52 | SOD2 | SOD2 | SOD2 | 5679 | 0.041 | 0.65 | NO
53 | PXMP4 | PXMP4 | PXMP4 | 5841 | 0.038 | 0.64 | NO
54 | HACL1 | HACL1 | HACL1 | 6076 | 0.035 | 0.63 | NO
55 | PEX12 | PEX12 | PEX12 | 6314 | 0.031 | 0.62 | NO
56 | PEX10 | PEX10 | PEX10 | 6612 | 0.027 | 0.61 | NO
57 | PEX19 | PEX19 | PEX19 | 6846 | 0.024 | 0.6 | NO
58 | ABCD4 | ABCD4 | ABCD4 | 7452 | 0.016 | 0.56 | NO
59 | PRDX1 | PRDX1 | PRDX1 | 7805 | 0.012 | 0.55 | NO
60 | ACOX3 | ACOX3 | ACOX3 | 7887 | 0.011 | 0.54 | NO
61 | NOS2 | NOS2 | NOS2 | 7890 | 0.011 | 0.54 | NO
62 | PEX6 | PEX6 | PEX6 | 8172 | 0.0075 | 0.53 | NO
63 | GNPAT | GNPAT | GNPAT | 8305 | 0.0058 | 0.52 | NO
64 | FAR1 | FAR1 | FAR1 | 8459 | 0.0039 | 0.51 | NO
65 | PMVK | PMVK | PMVK | 8755 | 0.00058 | 0.5 | NO
66 | PEX11B | PEX11B | PEX11B | 8783 | 0.00026 | 0.49 | NO
67 | MPV17 | MPV17 | MPV17 | 8998 | -0.0022 | 0.48 | NO
68 | PEX7 | PEX7 | PEX7 | 9164 | -0.004 | 0.47 | NO
69 | IDH2 | IDH2 | IDH2 | 9320 | -0.0058 | 0.46 | NO
70 | PEX5 | PEX5 | PEX5 | 9356 | -0.0062 | 0.46 | NO
71 | PRDX5 | PRDX5 | PRDX5 | 10705 | -0.022 | 0.39 | NO
72 | ABCD1 | ABCD1 | ABCD1 | 11742 | -0.035 | 0.33 | NO
73 | ACOT8 | ACOT8 | ACOT8 | 11979 | -0.039 | 0.32 | NO
74 | PEX16 | PEX16 | PEX16 | 12922 | -0.053 | 0.27 | NO
75 | ACSL4 | ACSL4 | ACSL4 | 13367 | -0.06 | 0.25 | NO
76 | PEX14 | PEX14 | PEX14 | 14218 | -0.077 | 0.21 | NO
77 | PEX2 | PEX2 | PEX2 | 14911 | -0.095 | 0.18 | 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 CHREBP2 PATHWAY.

Figure S46. 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 GLYCOLYSIS GLUCONEOGENESIS

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 | ADH4 | ADH4 | ADH4 | 43 | 1.8 | 0.12 | YES
2 | ALDOB | ALDOB | ALDOB | 129 | 1.2 | 0.2 | YES
3 | PCK1 | PCK1 | PCK1 | 140 | 1.2 | 0.28 | YES
4 | ADH1A | ADH1A | ADH1A | 147 | 1.2 | 0.37 | YES
5 | ADH1B | ADH1B | ADH1B | 196 | 0.99 | 0.43 | YES
6 | PKLR | PKLR | PKLR | 279 | 0.74 | 0.48 | YES
7 | G6PC | G6PC | G6PC | 297 | 0.69 | 0.53 | YES
8 | ADH1C | ADH1C | ADH1C | 302 | 0.69 | 0.57 | YES
9 | ADH6 | ADH6 | ADH6 | 329 | 0.66 | 0.62 | YES
10 | FBP1 | FBP1 | FBP1 | 490 | 0.48 | 0.64 | YES
11 | PCK2 | PCK2 | PCK2 | 791 | 0.33 | 0.65 | YES
12 | LDHAL6B | LDHAL6B | LDHAL6B | 795 | 0.33 | 0.67 | YES
13 | ALDH2 | ALDH2 | ALDH2 | 1082 | 0.26 | 0.67 | YES
14 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 1370 | 0.22 | 0.67 | YES
15 | PGAM2 | PGAM2 | PGAM2 | 1378 | 0.22 | 0.69 | YES
16 | HK3 | HK3 | HK3 | 1599 | 0.19 | 0.69 | YES
17 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 1708 | 0.18 | 0.7 | YES
18 | PGM1 | PGM1 | PGM1 | 2116 | 0.15 | 0.68 | NO
19 | ENO3 | ENO3 | ENO3 | 2164 | 0.15 | 0.69 | NO
20 | LDHAL6A | LDHAL6A | LDHAL6A | 2287 | 0.14 | 0.7 | NO
21 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 2555 | 0.13 | 0.69 | NO
22 | PGAM4 | PGAM4 | PGAM4 | 2702 | 0.12 | 0.69 | NO
23 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 2979 | 0.11 | 0.68 | NO
24 | GALM | GALM | GALM | 3147 | 0.1 | 0.68 | NO
25 | ALDOC | ALDOC | ALDOC | 3400 | 0.094 | 0.67 | NO
26 | PDHB | PDHB | PDHB | 4464 | 0.065 | 0.62 | NO
27 | AKR1A1 | AKR1A1 | AKR1A1 | 4495 | 0.064 | 0.62 | NO
28 | DLD | DLD | DLD | 4899 | 0.056 | 0.6 | NO
29 | PGM2 | PGM2 | PGM2 | 6058 | 0.035 | 0.54 | NO
30 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6217 | 0.033 | 0.54 | NO
31 | PGAM1 | PGAM1 | PGAM1 | 6294 | 0.032 | 0.53 | NO
32 | PDHA1 | PDHA1 | PDHA1 | 6509 | 0.029 | 0.52 | NO
33 | ACSS2 | ACSS2 | ACSS2 | 7075 | 0.021 | 0.49 | NO
34 | PFKM | PFKM | PFKM | 7898 | 0.011 | 0.45 | NO
35 | GPI | GPI | GPI | 8060 | 0.0088 | 0.44 | NO
36 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 8254 | 0.0064 | 0.43 | NO
37 | LDHA | LDHA | LDHA | 9002 | -0.0022 | 0.39 | NO
38 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 9412 | -0.0067 | 0.37 | NO
39 | PGK1 | PGK1 | PGK1 | 9470 | -0.0074 | 0.36 | NO
40 | ENO1 | ENO1 | ENO1 | 9872 | -0.012 | 0.34 | NO
41 | PFKL | PFKL | PFKL | 9990 | -0.013 | 0.34 | NO
42 | ADH5 | ADH5 | ADH5 | 10368 | -0.018 | 0.32 | NO
43 | BPGM | BPGM | BPGM | 10665 | -0.021 | 0.3 | NO
44 | GAPDH | GAPDH | GAPDH | 10701 | -0.022 | 0.3 | NO
45 | ACSS1 | ACSS1 | ACSS1 | 11074 | -0.027 | 0.28 | NO
46 | TPI1 | TPI1 | TPI1 | 11099 | -0.027 | 0.28 | NO
47 | DLAT | DLAT | DLAT | 12129 | -0.041 | 0.23 | NO
48 | HK2 | HK2 | HK2 | 12234 | -0.042 | 0.23 | NO
49 | HK1 | HK1 | HK1 | 13126 | -0.056 | 0.18 | NO
50 | LDHB | LDHB | LDHB | 13454 | -0.062 | 0.17 | NO
51 | ALDOA | ALDOA | ALDOA | 13590 | -0.064 | 0.16 | NO
52 | PKM2 | PKM2 | PKM2 | 15166 | -0.1 | 0.085 | NO
53 | PFKP | PFKP | PFKP | 15414 | -0.11 | 0.079 | NO
54 | GCK | GCK | GCK | 16688 | -0.18 | 0.021 | NO
55 | ENO2 | ENO2 | ENO2 | 16948 | -0.2 | 0.02 | NO
56 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 17479 | -0.27 | 0.0098 | NO
57 | G6PC2 | G6PC2 | G6PC2 | 17869 | -0.36 | 0.014 | 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 GLYCOLYSIS GLUCONEOGENESIS.

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

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

Table 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 | PFKFB1 | PFKFB1 | PFKFB1 | 89 | 1.5 | 0.25 | YES
2 | ALDOB | ALDOB | ALDOB | 129 | 1.2 | 0.47 | YES
3 | KHK | KHK | KHK | 416 | 0.54 | 0.55 | YES
4 | FBP1 | FBP1 | FBP1 | 490 | 0.48 | 0.63 | YES
5 | SORD | SORD | SORD | 622 | 0.39 | 0.69 | YES
6 | HK3 | HK3 | HK3 | 1599 | 0.19 | 0.67 | NO
7 | AKR1B10 | AKR1B10 | AKR1B10 | 2122 | 0.15 | 0.67 | NO
8 | ALDOC | ALDOC | ALDOC | 3400 | 0.094 | 0.61 | NO
9 | GMPPA | GMPPA | GMPPA | 4305 | 0.069 | 0.57 | NO
10 | PFKFB3 | PFKFB3 | PFKFB3 | 4816 | 0.057 | 0.56 | NO
11 | PMM2 | PMM2 | PMM2 | 5234 | 0.049 | 0.54 | NO
12 | MPI | MPI | MPI | 5293 | 0.048 | 0.55 | NO
13 | GMPPB | GMPPB | GMPPB | 6062 | 0.035 | 0.51 | NO
14 | FPGT | FPGT | FPGT | 6873 | 0.024 | 0.47 | NO
15 | MTMR7 | MTMR7 | MTMR7 | 7005 | 0.022 | 0.47 | NO
16 | AKR1B1 | AKR1B1 | AKR1B1 | 7026 | 0.022 | 0.47 | NO
17 | PFKM | PFKM | PFKM | 7898 | 0.011 | 0.42 | NO
18 | PFKFB2 | PFKFB2 | PFKFB2 | 8089 | 0.0084 | 0.41 | NO
19 | MTMR6 | MTMR6 | MTMR6 | 8202 | 0.007 | 0.41 | NO
20 | FUK | FUK | FUK | 8528 | 0.0031 | 0.39 | NO
21 | TSTA3 | TSTA3 | TSTA3 | 8712 | 0.001 | 0.38 | NO
22 | MTMR1 | MTMR1 | MTMR1 | 9600 | -0.009 | 0.33 | NO
23 | PFKL | PFKL | PFKL | 9990 | -0.013 | 0.32 | NO
24 | PMM1 | PMM1 | PMM1 | 10481 | -0.019 | 0.29 | NO
25 | TPI1 | TPI1 | TPI1 | 11099 | -0.027 | 0.26 | NO
26 | HK2 | HK2 | HK2 | 12234 | -0.042 | 0.21 | NO
27 | HK1 | HK1 | HK1 | 13126 | -0.056 | 0.17 | NO
28 | GMDS | GMDS | GMDS | 13241 | -0.058 | 0.17 | NO
29 | PHPT1 | PHPT1 | PHPT1 | 14115 | -0.075 | 0.14 | NO
30 | PFKP | PFKP | PFKP | 15414 | -0.11 | 0.084 | NO
31 | MTMR2 | MTMR2 | MTMR2 | 16253 | -0.15 | 0.064 | NO
32 | PFKFB4 | PFKFB4 | PFKFB4 | 17143 | -0.22 | 0.054 | 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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

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 | ARG1 | ARG1 | ARG1 | 12 | 2.1 | 0.13 | YES
2 | CPS1 | CPS1 | CPS1 | 38 | 1.8 | 0.25 | YES
3 | OTC | OTC | OTC | 46 | 1.8 | 0.36 | YES
4 | DAO | DAO | DAO | 58 | 1.7 | 0.47 | YES
5 | PRODH2 | PRODH2 | PRODH2 | 166 | 1.1 | 0.53 | YES
6 | GLS2 | GLS2 | GLS2 | 263 | 0.8 | 0.57 | YES
7 | AGMAT | AGMAT | AGMAT | 516 | 0.46 | 0.59 | YES
8 | NAGS | NAGS | NAGS | 531 | 0.45 | 0.62 | YES
9 | GAMT | GAMT | GAMT | 720 | 0.35 | 0.63 | YES
10 | GATM | GATM | GATM | 731 | 0.35 | 0.65 | YES
11 | ALDH4A1 | ALDH4A1 | ALDH4A1 | 902 | 0.3 | 0.66 | YES
12 | ALDH2 | ALDH2 | ALDH2 | 1082 | 0.26 | 0.67 | YES
13 | PRODH | PRODH | PRODH | 1258 | 0.24 | 0.67 | YES
14 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 1370 | 0.22 | 0.68 | YES
15 | NOS3 | NOS3 | NOS3 | 1412 | 0.22 | 0.69 | YES
16 | PYCR1 | PYCR1 | PYCR1 | 1510 | 0.2 | 0.7 | YES
17 | GOT1 | GOT1 | GOT1 | 1532 | 0.2 | 0.71 | YES
18 | ACY1 | ACY1 | ACY1 | 1681 | 0.19 | 0.72 | YES
19 | GLUD2 | GLUD2 | GLUD2 | 1783 | 0.18 | 0.72 | YES
20 | CKMT2 | CKMT2 | CKMT2 | 1798 | 0.18 | 0.73 | YES
21 | GOT2 | GOT2 | GOT2 | 1968 | 0.16 | 0.73 | YES
22 | ASL | ASL | ASL | 2040 | 0.16 | 0.74 | YES
23 | MAOA | MAOA | MAOA | 2079 | 0.16 | 0.75 | YES
24 | MAOB | MAOB | MAOB | 2413 | 0.14 | 0.74 | NO
25 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 2555 | 0.13 | 0.74 | NO
26 | CKB | CKB | CKB | 3022 | 0.11 | 0.72 | NO
27 | ABP1 | ABP1 | ABP1 | 3043 | 0.11 | 0.72 | NO
28 | ASS1 | ASS1 | ASS1 | 3145 | 0.1 | 0.73 | NO
29 | GLUD1 | GLUD1 | GLUD1 | 3722 | 0.085 | 0.7 | NO
30 | OAT | OAT | OAT | 3863 | 0.08 | 0.7 | NO
31 | CKM | CKM | CKM | 4130 | 0.074 | 0.69 | NO
32 | P4HA2 | P4HA2 | P4HA2 | 4298 | 0.069 | 0.68 | NO
33 | ODC1 | ODC1 | ODC1 | 4655 | 0.061 | 0.67 | NO
34 | ALDH18A1 | ALDH18A1 | ALDH18A1 | 4798 | 0.058 | 0.66 | NO
35 | SAT2 | SAT2 | SAT2 | 5465 | 0.044 | 0.63 | NO
36 | ARG2 | ARG2 | ARG2 | 5534 | 0.043 | 0.63 | NO
37 | LAP3 | LAP3 | LAP3 | 6142 | 0.034 | 0.6 | NO
38 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6217 | 0.033 | 0.59 | NO
39 | NOS2 | NOS2 | NOS2 | 7890 | 0.011 | 0.5 | NO
40 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 8254 | 0.0064 | 0.48 | NO
41 | SRM | SRM | SRM | 8631 | 0.0018 | 0.46 | NO
42 | PYCRL | PYCRL | PYCRL | 9201 | -0.0044 | 0.43 | NO
43 | AMD1 | AMD1 | AMD1 | 9570 | -0.0085 | 0.41 | NO
44 | GLS | GLS | GLS | 9778 | -0.011 | 0.4 | NO
45 | GLUL | GLUL | GLUL | 9813 | -0.011 | 0.4 | NO
46 | P4HA1 | P4HA1 | P4HA1 | 10941 | -0.025 | 0.34 | NO
47 | PYCR2 | PYCR2 | PYCR2 | 11029 | -0.026 | 0.33 | NO
48 | SMS | SMS | SMS | 11054 | -0.026 | 0.34 | NO
49 | P4HA3 | P4HA3 | P4HA3 | 15104 | -0.1 | 0.12 | NO
50 | NOS1 | NOS1 | NOS1 | 16556 | -0.17 | 0.048 | NO
51 | CKMT1A | CKMT1A | CKMT1A | 16620 | -0.17 | 0.055 | NO
52 | CKMT1B | CKMT1B | CKMT1B | 16739 | -0.18 | 0.06 | NO
53 | ADC | ADC | ADC | 17351 | -0.25 | 0.042 | 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS.

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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 | APOA1 | APOA1 | APOA1 | 83 | 1.5 | 0.18 | YES
2 | FABP1 | FABP1 | FABP1 | 121 | 1.3 | 0.33 | YES
3 | APOA2 | APOA2 | APOA2 | 155 | 1.1 | 0.46 | YES
4 | EHHADH | EHHADH | EHHADH | 333 | 0.65 | 0.53 | YES
5 | CD36 | CD36 | CD36 | 651 | 0.38 | 0.56 | YES
6 | NR0B2 | NR0B2 | NR0B2 | 799 | 0.33 | 0.59 | YES
7 | PIK3R1 | PIK3R1 | PIK3R1 | 1936 | 0.17 | 0.55 | YES
8 | PPARA | PPARA | PPARA | 1990 | 0.16 | 0.56 | YES
9 | PTGS2 | PTGS2 | PTGS2 | 2163 | 0.15 | 0.57 | YES
10 | DUSP1 | DUSP1 | DUSP1 | 2318 | 0.14 | 0.58 | YES
11 | HSD17B4 | HSD17B4 | HSD17B4 | 2509 | 0.13 | 0.59 | YES
12 | PRKAR2A | PRKAR2A | PRKAR2A | 2604 | 0.13 | 0.6 | YES
13 | PRKCB | PRKCB | PRKCB | 2728 | 0.12 | 0.6 | YES
14 | PRKAR1B | PRKAR1B | PRKAR1B | 2940 | 0.11 | 0.61 | YES
15 | HSPA1A | HSPA1A | HSPA1A | 3244 | 0.098 | 0.6 | YES
16 | PRKACB | PRKACB | PRKACB | 3272 | 0.097 | 0.61 | YES
17 | NRIP1 | NRIP1 | NRIP1 | 3393 | 0.094 | 0.62 | YES
18 | PRKAR1A | PRKAR1A | PRKAR1A | 4229 | 0.071 | 0.58 | NO
19 | MAPK1 | MAPK1 | MAPK1 | 4358 | 0.068 | 0.58 | NO
20 | PPARGC1A | PPARGC1A | PPARGC1A | 4518 | 0.064 | 0.58 | NO
21 | EP300 | EP300 | EP300 | 4615 | 0.062 | 0.58 | NO
22 | SRA1 | SRA1 | SRA1 | 5137 | 0.051 | 0.56 | NO
23 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 5943 | 0.036 | 0.52 | NO
24 | MYC | MYC | MYC | 5947 | 0.036 | 0.52 | NO
25 | JUN | JUN | JUN | 5981 | 0.036 | 0.52 | NO
26 | NR2F1 | NR2F1 | NR2F1 | 6025 | 0.035 | 0.53 | NO
27 | PIK3CA | PIK3CA | PIK3CA | 6229 | 0.033 | 0.52 | NO
28 | PRKCA | PRKCA | PRKCA | 6691 | 0.026 | 0.5 | NO
29 | ME1 | ME1 | ME1 | 6698 | 0.026 | 0.5 | NO
30 | PRKAR2B | PRKAR2B | PRKAR2B | 6799 | 0.025 | 0.5 | NO
31 | RB1 | RB1 | RB1 | 7017 | 0.022 | 0.49 | NO
32 | RXRA | RXRA | RXRA | 7058 | 0.021 | 0.49 | NO
33 | NFKBIA | NFKBIA | NFKBIA | 7171 | 0.02 | 0.48 | NO
34 | PIK3CG | PIK3CG | PIK3CG | 7376 | 0.017 | 0.47 | NO
35 | NOS2 | NOS2 | NOS2 | 7890 | 0.011 | 0.45 | NO
36 | CPT1B | CPT1B | CPT1B | 8122 | 0.0081 | 0.44 | NO
37 | NCOR2 | NCOR2 | NCOR2 | 8825 | -0.00015 | 0.4 | NO
38 | CITED2 | CITED2 | CITED2 | 8892 | -0.00091 | 0.39 | NO
39 | STAT5B | STAT5B | STAT5B | 9597 | -0.0089 | 0.36 | NO
40 | FAT1 | FAT1 | FAT1 | 9683 | -0.0099 | 0.35 | NO
41 | MED1 | MED1 | MED1 | 9875 | -0.012 | 0.34 | NO
42 | NCOR1 | NCOR1 | NCOR1 | 10218 | -0.016 | 0.32 | NO
43 | PDGFA | PDGFA | PDGFA | 10400 | -0.018 | 0.32 | NO
44 | SP1 | SP1 | SP1 | 10718 | -0.022 | 0.3 | NO
45 | CREBBP | CREBBP | CREBBP | 11359 | -0.03 | 0.27 | NO
46 | MRPL11 | MRPL11 | MRPL11 | 11530 | -0.033 | 0.26 | NO
47 | NCOA1 | NCOA1 | NCOA1 | 13130 | -0.056 | 0.18 | NO
48 | RELA | RELA | RELA | 13172 | -0.057 | 0.19 | NO
49 | NR1H3 | NR1H3 | NR1H3 | 13296 | -0.059 | 0.19 | NO
50 | DUT | DUT | DUT | 13700 | -0.066 | 0.17 | NO
51 | MAPK3 | MAPK3 | MAPK3 | 14189 | -0.076 | 0.16 | NO
52 | LPL | LPL | LPL | 15982 | -0.13 | 0.073 | NO
53 | STAT5A | STAT5A | STAT5A | 16109 | -0.14 | 0.083 | NO
54 | TNF | TNF | TNF | 17258 | -0.24 | 0.047 | 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 FRUCTOSE AND MANNOSE METABOLISM.

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table 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 | ABCB11 | ABCB11 | ABCB11 | 48 | 1.8 | 0.14 | YES
2 | ABCG8 | ABCG8 | ABCG8 | 134 | 1.2 | 0.24 | YES
3 | ABCB4 | ABCB4 | ABCB4 | 142 | 1.2 | 0.34 | YES
4 | ABCG5 | ABCG5 | ABCG5 | 146 | 1.2 | 0.44 | YES
5 | ABCA6 | ABCA6 | ABCA6 | 221 | 0.9 | 0.5 | YES
6 | ABCA9 | ABCA9 | ABCA9 | 381 | 0.58 | 0.54 | YES
7 | ABCC11 | ABCC11 | ABCC11 | 395 | 0.56 | 0.59 | YES
8 | ABCC9 | ABCC9 | ABCC9 | 463 | 0.5 | 0.63 | YES
9 | ABCG2 | ABCG2 | ABCG2 | 476 | 0.49 | 0.67 | YES
10 | ABCA10 | ABCA10 | ABCA10 | 488 | 0.48 | 0.71 | YES
11 | ABCC2 | ABCC2 | ABCC2 | 522 | 0.46 | 0.74 | YES
12 | ABCC6 | ABCC6 | ABCC6 | 775 | 0.33 | 0.76 | YES
13 | ABCA12 | ABCA12 | ABCA12 | 1185 | 0.25 | 0.75 | YES
14 | ABCG4 | ABCG4 | ABCG4 | 1340 | 0.22 | 0.76 | YES
15 | ABCA1 | ABCA1 | ABCA1 | 1641 | 0.19 | 0.76 | NO
16 | ABCA5 | ABCA5 | ABCA5 | 2407 | 0.14 | 0.73 | NO
17 | ABCD3 | ABCD3 | ABCD3 | 2410 | 0.14 | 0.74 | NO
18 | ABCB1 | ABCB1 | ABCB1 | 2682 | 0.12 | 0.74 | NO
19 | ABCB8 | ABCB8 | ABCB8 | 3091 | 0.1 | 0.72 | NO
20 | ABCB10 | ABCB10 | ABCB10 | 3417 | 0.094 | 0.71 | NO
21 | ABCC4 | ABCC4 | ABCC4 | 3662 | 0.086 | 0.71 | NO
22 | ABCD2 | ABCD2 | ABCD2 | 3830 | 0.082 | 0.7 | NO
23 | CFTR | CFTR | CFTR | 4113 | 0.074 | 0.7 | NO
24 | ABCA13 | ABCA13 | ABCA13 | 4507 | 0.064 | 0.68 | NO
25 | ABCB6 | ABCB6 | ABCB6 | 5321 | 0.047 | 0.64 | NO
26 | ABCB9 | ABCB9 | ABCB9 | 7023 | 0.022 | 0.55 | NO
27 | ABCA3 | ABCA3 | ABCA3 | 7046 | 0.022 | 0.55 | NO
28 | ABCC3 | ABCC3 | ABCC3 | 7426 | 0.016 | 0.53 | NO
29 | ABCD4 | ABCD4 | ABCD4 | 7452 | 0.016 | 0.53 | NO
30 | ABCA2 | ABCA2 | ABCA2 | 9576 | -0.0086 | 0.41 | NO
31 | ABCB5 | ABCB5 | ABCB5 | 9592 | -0.0088 | 0.41 | NO
32 | ABCA4 | ABCA4 | ABCA4 | 11440 | -0.032 | 0.31 | NO
33 | ABCC5 | ABCC5 | ABCC5 | 11598 | -0.034 | 0.3 | NO
34 | ABCD1 | ABCD1 | ABCD1 | 11742 | -0.035 | 0.3 | NO
35 | ABCC8 | ABCC8 | ABCC8 | 11872 | -0.037 | 0.3 | NO
36 | TAP1 | TAP1 | TAP1 | 12355 | -0.044 | 0.27 | NO
37 | TAP2 | TAP2 | TAP2 | 12737 | -0.05 | 0.26 | NO
38 | ABCB7 | ABCB7 | ABCB7 | 12788 | -0.051 | 0.26 | NO
39 | ABCC10 | ABCC10 | ABCC10 | 14206 | -0.077 | 0.18 | NO
40 | ABCC1 | ABCC1 | ABCC1 | 14825 | -0.093 | 0.16 | NO
41 | ABCA7 | ABCA7 | ABCA7 | 15165 | -0.1 | 0.15 | NO
42 | ABCG1 | ABCG1 | ABCG1 | 16790 | -0.19 | 0.073 | 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 FATTY ACID METABOLISM.

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

Table 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 | ACOT12 | ACOT12 | ACOT12 | 2 | 2.8 | 0.31 | YES
2 | PCK1 | PCK1 | PCK1 | 140 | 1.2 | 0.43 | YES
3 | PKLR | PKLR | PKLR | 279 | 0.74 | 0.51 | YES
4 | LDHD | LDHD | LDHD | 307 | 0.68 | 0.58 | YES
5 | PC | PC | PC | 465 | 0.5 | 0.63 | YES
6 | PCK2 | PCK2 | PCK2 | 791 | 0.33 | 0.64 | YES
7 | LDHAL6B | LDHAL6B | LDHAL6B | 795 | 0.33 | 0.68 | YES
8 | ALDH2 | ALDH2 | ALDH2 | 1082 | 0.26 | 0.69 | YES
9 | ACAT1 | ACAT1 | ACAT1 | 1163 | 0.25 | 0.72 | YES
10 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 1370 | 0.22 | 0.73 | YES
11 | ACACB | ACACB | ACACB | 1791 | 0.18 | 0.73 | NO
12 | LDHAL6A | LDHAL6A | LDHAL6A | 2287 | 0.14 | 0.72 | NO
13 | GRHPR | GRHPR | GRHPR | 2469 | 0.13 | 0.72 | NO
14 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 2555 | 0.13 | 0.73 | NO
15 | ACAT2 | ACAT2 | ACAT2 | 2902 | 0.11 | 0.72 | NO
16 | HAGH | HAGH | HAGH | 3299 | 0.096 | 0.71 | NO
17 | MDH1 | MDH1 | MDH1 | 3617 | 0.088 | 0.7 | NO
18 | PDHB | PDHB | PDHB | 4464 | 0.065 | 0.66 | NO
19 | DLD | DLD | DLD | 4899 | 0.056 | 0.65 | NO
20 | HAGHL | HAGHL | HAGHL | 5714 | 0.04 | 0.61 | NO
21 | MDH2 | MDH2 | MDH2 | 5897 | 0.037 | 0.6 | NO
22 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6217 | 0.033 | 0.59 | NO
23 | PDHA1 | PDHA1 | PDHA1 | 6509 | 0.029 | 0.57 | NO
24 | ME1 | ME1 | ME1 | 6698 | 0.026 | 0.57 | NO
25 | ME2 | ME2 | ME2 | 6904 | 0.023 | 0.56 | NO
26 | AKR1B1 | AKR1B1 | AKR1B1 | 7026 | 0.022 | 0.55 | NO
27 | ACSS2 | ACSS2 | ACSS2 | 7075 | 0.021 | 0.55 | NO
28 | ACACA | ACACA | ACACA | 7181 | 0.02 | 0.55 | NO
29 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 8254 | 0.0064 | 0.49 | NO
30 | LDHA | LDHA | LDHA | 9002 | -0.0022 | 0.45 | NO
31 | GLO1 | GLO1 | GLO1 | 9121 | -0.0035 | 0.44 | NO
32 | ACYP2 | ACYP2 | ACYP2 | 9525 | -0.008 | 0.42 | NO
33 | ACSS1 | ACSS1 | ACSS1 | 11074 | -0.027 | 0.34 | NO
34 | DLAT | DLAT | DLAT | 12129 | -0.041 | 0.28 | NO
35 | LDHB | LDHB | LDHB | 13454 | -0.062 | 0.22 | NO
36 | ACYP1 | ACYP1 | ACYP1 | 13595 | -0.064 | 0.22 | NO
37 | PKM2 | PKM2 | PKM2 | 15166 | -0.1 | 0.14 | NO
38 | ME3 | ME3 | ME3 | 16734 | -0.18 | 0.076 | 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 STEROID HORMONE BIOSYNTHESIS.

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

Fold change

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

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

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

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

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

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Methods & Data
Input

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

- Expression data file = CHOL-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

- Phenotype data file = CHOL-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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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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