GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in MESO-TP
Mesothelioma (Primary solid tumor)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1R78DP8
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in MESO-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1R78DP8
Overview
Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes having more than three samples and the input expression file "MESO-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:

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

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

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

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

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

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

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 717
Number of samples: 87
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 26
pheno.type: 2 - 4 :[ clus2 ] 21
pheno.type: 3 - 4 :[ clus3 ] 19
pheno.type: 4 - 4 :[ clus4 ] 21

For the expression subtypes of 18209 genes in 88 samples, GSEA found enriched gene sets in each cluster using 87 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

- clus1

- Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG FATTY ACID METABOLISM, KEGG TYROSINE METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, KEGG PARKINSONS DISEASE, PID CASPASE PATHWAY, PID A6B1 A6B4 INTEGRIN PATHWAY, REACTOME TRANSLATION, REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES

- And common core enriched genes are ISG15, DDX58, HERC5, IFIH1, IFNB1, IRF2, IRF7, NLRC5, NLRX1, RNF125

- clus2

- Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG HISTIDINE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG PYRUVATE METABOLISM, KEGG PROPANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM CYTOCHROME P450, PID NCADHERINPATHWAY

- And common core enriched genes are AP1M2, AP1S1, AP3B1, AP3S1, AP4E1, ARF1, ARRB1, BLOC1S1, CPD, DNAJC6

- clus3

- Top enriched gene sets are KEGG PROTEASOME, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG CELL CYCLE, KEGG APOPTOSIS, KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY, KEGG CYTOSOLIC DNA SENSING PATHWAY, KEGG HEMATOPOIETIC CELL LINEAGE, KEGG T CELL RECEPTOR SIGNALING PATHWAY, KEGG B CELL RECEPTOR SIGNALING PATHWAY, KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS

- And common core enriched genes are PSMA3, PSMA5, PSMA6, PSMA7, PSMA8, PSMB10, PSMB2, PSMB3, PSMB5, PSMB6

- clus4

- Top enriched gene sets are KEGG WNT SIGNALING PATHWAY, KEGG TGF BETA SIGNALING PATHWAY, KEGG LONG TERM POTENTIATION, KEGG MELANOGENESIS, KEGG BASAL CELL CARCINOMA, BIOCARTA ALK PATHWAY, ST WNT BETA CATENIN PATHWAY, PID EPHBFWDPATHWAY, PID P75NTRPATHWAY, PID HEDGEHOG GLIPATHWAY

- And common core enriched genes are B3GAT1, B3GAT2, BCAN, BGN, CSPG4, GPC1, GPC2, GPC3, GPC4, GPC5

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
KEGG GLYCOLYSIS GLUCONEOGENESIS | 56 | genes.ES.table | 0.46 | 1.5 | 0.053 | 1 | 0.99 | 0.21 | 0.098 | 0.19 | 1 | 0.6
KEGG FATTY ACID METABOLISM | 38 | genes.ES.table | 0.63 | 1.9 | 0 | 0.54 | 0.26 | 0.34 | 0.12 | 0.3 | 0 | 0.13
KEGG TYROSINE METABOLISM | 41 | genes.ES.table | 0.5 | 1.4 | 0.066 | 1 | 1 | 0.24 | 0.058 | 0.23 | 1 | 0.6
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM | 43 | genes.ES.table | 0.4 | 1.4 | 0.15 | 1 | 1 | 0.23 | 0.11 | 0.21 | 1 | 0.54
KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS | 25 | genes.ES.table | 0.39 | 1.5 | 0.086 | 1 | 0.98 | 0.4 | 0.21 | 0.32 | 1 | 0.54
KEGG PARKINSONS DISEASE | 111 | genes.ES.table | 0.39 | 1.4 | 0.17 | 1 | 1 | 0.63 | 0.34 | 0.42 | 1 | 0.56
PID CASPASE PATHWAY | 51 | genes.ES.table | 0.39 | 1.5 | 0.064 | 1 | 0.98 | 0.33 | 0.18 | 0.28 | 1 | 0.52
PID A6B1 A6B4 INTEGRIN PATHWAY | 46 | genes.ES.table | 0.5 | 1.5 | 0.081 | 1 | 0.98 | 0.24 | 0.12 | 0.21 | 1 | 0.56
REACTOME TRANSLATION | 146 | genes.ES.table | 0.43 | 1.4 | 0.2 | 1 | 1 | 0.6 | 0.37 | 0.38 | 1 | 0.58
REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES | 65 | genes.ES.table | 0.46 | 1.7 | 0.05 | 0.75 | 0.8 | 0.11 | 0.023 | 0.11 | 0.34 | 0.22

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 | ADH6 | ADH6 | ADH6 | 1 | 1.3 | 0.17 | YES
2 | ADH1A | ADH1A | ADH1A | 2 | 1.2 | 0.33 | YES
3 | ADH1B | ADH1B | ADH1B | 13 | 0.8 | 0.44 | YES
4 | ACSL6 | ACSL6 | ACSL6 | 340 | 0.41 | 0.48 | YES
5 | ADH1C | ADH1C | ADH1C | 595 | 0.32 | 0.51 | YES
6 | ADH4 | ADH4 | ADH4 | 666 | 0.3 | 0.54 | YES
7 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 1053 | 0.23 | 0.55 | YES
8 | ACSL5 | ACSL5 | ACSL5 | 1151 | 0.22 | 0.58 | YES
9 | ACADS | ACADS | ACADS | 1437 | 0.19 | 0.59 | YES
10 | ADH5 | ADH5 | ADH5 | 1724 | 0.16 | 0.6 | YES
11 | ALDH2 | ALDH2 | ALDH2 | 1786 | 0.16 | 0.61 | YES
12 | ACADM | ACADM | ACADM | 2014 | 0.14 | 0.62 | YES
13 | ACSL1 | ACSL1 | ACSL1 | 2178 | 0.13 | 0.63 | YES
14 | CPT2 | CPT2 | CPT2 | 3209 | 0.086 | 0.58 | NO
15 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 4274 | 0.057 | 0.53 | NO
16 | HADHB | HADHB | HADHB | 4667 | 0.048 | 0.52 | NO
17 | ACAA2 | ACAA2 | ACAA2 | 4827 | 0.044 | 0.51 | NO
18 | ACADVL | ACADVL | ACADVL | 4850 | 0.044 | 0.52 | NO
19 | HADH | HADH | HADH | 5109 | 0.04 | 0.51 | NO
20 | CPT1B | CPT1B | CPT1B | 5394 | 0.034 | 0.5 | NO
21 | ECHS1 | ECHS1 | ECHS1 | 5409 | 0.034 | 0.5 | NO
22 | ACAA1 | ACAA1 | ACAA1 | 6274 | 0.02 | 0.46 | NO
23 | HADHA | HADHA | HADHA | 6875 | 0.012 | 0.43 | NO
24 | ACOX1 | ACOX1 | ACOX1 | 7042 | 0.0097 | 0.42 | NO
25 | CPT1A | CPT1A | CPT1A | 7150 | 0.0081 | 0.41 | NO
26 | ACAT2 | ACAT2 | ACAT2 | 7323 | 0.006 | 0.41 | NO
27 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 7455 | 0.0039 | 0.4 | NO
28 | ACAT1 | ACAT1 | ACAT1 | 8728 | -0.014 | 0.33 | NO
29 | ACADSB | ACADSB | ACADSB | 8866 | -0.017 | 0.33 | NO
30 | GCDH | GCDH | GCDH | 9514 | -0.027 | 0.29 | NO
31 | ACSL3 | ACSL3 | ACSL3 | 10383 | -0.042 | 0.25 | NO
32 | ACOX3 | ACOX3 | ACOX3 | 11823 | -0.073 | 0.18 | NO
33 | ACADL | ACADL | ACADL | 12655 | -0.096 | 0.15 | NO
34 | ACSL4 | ACSL4 | ACSL4 | 13053 | -0.11 | 0.14 | NO
35 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 14871 | -0.19 | 0.068 | NO
36 | CYP4A11 | CYP4A11 | CYP4A11 | 15549 | -0.23 | 0.062 | NO
37 | EHHADH | EHHADH | EHHADH | 16392 | -0.29 | 0.055 | NO
38 | CPT1C | CPT1C | CPT1C | 16725 | -0.32 | 0.081 | NO

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

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table 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 | SAA1 | SAA1 | SAA1 | 95 | 0.57 | 0.083 | YES
2 | HERC5 | HERC5 | HERC5 | 158 | 0.5 | 0.16 | YES
3 | ISG15 | ISG15 | ISG15 | 238 | 0.45 | 0.22 | YES
4 | DDX58 | DDX58 | DDX58 | 412 | 0.38 | 0.27 | YES
5 | IFIH1 | IFIH1 | IFIH1 | 500 | 0.34 | 0.32 | YES
6 | IRF7 | IRF7 | IRF7 | 519 | 0.34 | 0.37 | YES
7 | IFNB1 | IFNB1 | IFNB1 | 611 | 0.32 | 0.41 | YES
8 | DHX58 | DHX58 | DHX58 | 816 | 0.27 | 0.44 | YES
9 | S100A12 | S100A12 | S100A12 | 1224 | 0.21 | 0.45 | YES
10 | TRIM25 | TRIM25 | TRIM25 | 1424 | 0.19 | 0.47 | YES
11 | IRF2 | IRF2 | IRF2 | 1671 | 0.16 | 0.48 | YES
12 | DAK | DAK | DAK | 1675 | 0.16 | 0.51 | YES
13 | UBE2L6 | UBE2L6 | UBE2L6 | 1819 | 0.15 | 0.52 | YES
14 | CASP10 | CASP10 | CASP10 | 2426 | 0.12 | 0.51 | YES
15 | CASP8 | CASP8 | CASP8 | 2595 | 0.11 | 0.52 | YES
16 | UBE2D3 | UBE2D3 | UBE2D3 | 2902 | 0.095 | 0.52 | YES
17 | IRF1 | IRF1 | IRF1 | 2964 | 0.093 | 0.53 | YES
18 | RNF125 | RNF125 | RNF125 | 3183 | 0.086 | 0.53 | YES
19 | NFKBIA | NFKBIA | NFKBIA | 3650 | 0.072 | 0.51 | YES
20 | RNF135 | RNF135 | RNF135 | 3653 | 0.072 | 0.52 | YES
21 | NLRX1 | NLRX1 | NLRX1 | 3742 | 0.069 | 0.53 | YES
22 | FADD | FADD | FADD | 3774 | 0.068 | 0.54 | YES
23 | AGER | AGER | AGER | 3875 | 0.066 | 0.54 | YES
24 | NLRC5 | NLRC5 | NLRC5 | 3915 | 0.065 | 0.55 | YES
25 | TANK | TANK | TANK | 4263 | 0.057 | 0.54 | NO
26 | NFKB2 | NFKB2 | NFKB2 | 4424 | 0.053 | 0.54 | NO
27 | RIPK1 | RIPK1 | RIPK1 | 4723 | 0.046 | 0.53 | NO
28 | RPS27A | RPS27A | RPS27A | 4792 | 0.045 | 0.53 | NO
29 | UBA7 | UBA7 | UBA7 | 4834 | 0.044 | 0.54 | NO
30 | SIKE1 | SIKE1 | SIKE1 | 4977 | 0.042 | 0.54 | NO
31 | MAVS | MAVS | MAVS | 5207 | 0.038 | 0.53 | NO
32 | PCBP2 | PCBP2 | PCBP2 | 5397 | 0.034 | 0.52 | NO
33 | CHUK | CHUK | CHUK | 5532 | 0.032 | 0.52 | NO
34 | APP | APP | APP | 5643 | 0.03 | 0.52 | NO
35 | TRAF3 | TRAF3 | TRAF3 | 5752 | 0.028 | 0.52 | NO
36 | UBE2K | UBE2K | UBE2K | 6656 | 0.015 | 0.47 | NO
37 | TBK1 | TBK1 | TBK1 | 6706 | 0.014 | 0.47 | NO
38 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 6858 | 0.012 | 0.46 | NO
39 | OTUD5 | OTUD5 | OTUD5 | 6912 | 0.011 | 0.46 | NO
40 | RELA | RELA | RELA | 6919 | 0.011 | 0.46 | NO
41 | IKBKE | IKBKE | IKBKE | 7298 | 0.0063 | 0.45 | NO
42 | CYLD | CYLD | CYLD | 7603 | 0.0017 | 0.43 | NO
43 | UBA52 | UBA52 | UBA52 | 7844 | -0.0019 | 0.42 | NO
44 | UBE2D2 | UBE2D2 | UBE2D2 | 7879 | -0.0023 | 0.42 | NO
45 | IRF3 | IRF3 | IRF3 | 7933 | -0.0029 | 0.41 | NO
46 | IKBKB | IKBKB | IKBKB | 8605 | -0.013 | 0.38 | NO
47 | HMGB1 | HMGB1 | HMGB1 | 9050 | -0.02 | 0.36 | NO
48 | CREBBP | CREBBP | CREBBP | 9274 | -0.023 | 0.35 | NO
49 | EP300 | EP300 | EP300 | 9451 | -0.026 | 0.34 | NO
50 | ATG5 | ATG5 | ATG5 | 9660 | -0.029 | 0.33 | NO
51 | PIN1 | PIN1 | PIN1 | 10310 | -0.04 | 0.3 | NO
52 | MAP3K1 | MAP3K1 | MAP3K1 | 10410 | -0.042 | 0.31 | NO
53 | ATG12 | ATG12 | ATG12 | 10490 | -0.044 | 0.31 | NO
54 | IKBKG | IKBKG | IKBKG | 11246 | -0.06 | 0.28 | NO
55 | UBE2D1 | UBE2D1 | UBE2D1 | 11608 | -0.068 | 0.27 | NO
56 | TRAF2 | TRAF2 | TRAF2 | 11880 | -0.074 | 0.26 | NO
57 | TRAF6 | TRAF6 | TRAF6 | 12417 | -0.088 | 0.25 | NO
58 | NFKBIB | NFKBIB | NFKBIB | 12614 | -0.095 | 0.25 | NO
59 | S100B | S100B | S100B | 14063 | -0.15 | 0.19 | NO
60 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 15364 | -0.22 | 0.16 | NO

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

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

genes ES table in pathway: KEGG TYROSINE METABOLISM

Table 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 | HERC5 | HERC5 | HERC5 | 158 | 0.5 | 0.15 | YES
2 | ISG15 | ISG15 | ISG15 | 238 | 0.45 | 0.3 | YES
3 | DDX58 | DDX58 | DDX58 | 412 | 0.38 | 0.41 | YES
4 | IFIH1 | IFIH1 | IFIH1 | 500 | 0.34 | 0.52 | YES
5 | TRIM25 | TRIM25 | TRIM25 | 1424 | 0.19 | 0.53 | YES
6 | UBE2L6 | UBE2L6 | UBE2L6 | 1819 | 0.15 | 0.56 | YES
7 | UBE2D3 | UBE2D3 | UBE2D3 | 2902 | 0.095 | 0.53 | YES
8 | RNF125 | RNF125 | RNF125 | 3183 | 0.086 | 0.54 | YES
9 | RNF135 | RNF135 | RNF135 | 3653 | 0.072 | 0.54 | YES
10 | NLRX1 | NLRX1 | NLRX1 | 3742 | 0.069 | 0.56 | YES
11 | NLRC5 | NLRC5 | NLRC5 | 3915 | 0.065 | 0.57 | YES
12 | RPS27A | RPS27A | RPS27A | 4792 | 0.045 | 0.54 | NO
13 | UBA7 | UBA7 | UBA7 | 4834 | 0.044 | 0.55 | NO
14 | MAVS | MAVS | MAVS | 5207 | 0.038 | 0.54 | NO
15 | PCBP2 | PCBP2 | PCBP2 | 5397 | 0.034 | 0.54 | NO
16 | TRAF3 | TRAF3 | TRAF3 | 5752 | 0.028 | 0.53 | NO
17 | UBE2K | UBE2K | UBE2K | 6656 | 0.015 | 0.49 | NO
18 | TBK1 | TBK1 | TBK1 | 6706 | 0.014 | 0.49 | NO
19 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 6858 | 0.012 | 0.48 | NO
20 | OTUD5 | OTUD5 | OTUD5 | 6912 | 0.011 | 0.48 | NO
21 | IKBKE | IKBKE | IKBKE | 7298 | 0.0063 | 0.47 | NO
22 | CYLD | CYLD | CYLD | 7603 | 0.0017 | 0.45 | NO
23 | UBA52 | UBA52 | UBA52 | 7844 | -0.0019 | 0.44 | NO
24 | UBE2D2 | UBE2D2 | UBE2D2 | 7879 | -0.0023 | 0.44 | NO
25 | IRF3 | IRF3 | IRF3 | 7933 | -0.0029 | 0.43 | NO
26 | ATG5 | ATG5 | ATG5 | 9660 | -0.029 | 0.35 | NO
27 | PIN1 | PIN1 | PIN1 | 10310 | -0.04 | 0.33 | NO
28 | ATG12 | ATG12 | ATG12 | 10490 | -0.044 | 0.33 | NO
29 | UBE2D1 | UBE2D1 | UBE2D1 | 11608 | -0.068 | 0.29 | NO
30 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 15364 | -0.22 | 0.16 | NO

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

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

genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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 | OASL | OASL | OASL | 103 | 0.56 | 0.047 | YES
2 | IFIT1 | IFIT1 | IFIT1 | 111 | 0.55 | 0.098 | YES
3 | IFIT2 | IFIT2 | IFIT2 | 155 | 0.5 | 0.14 | YES
4 | IFIT3 | IFIT3 | IFIT3 | 165 | 0.49 | 0.19 | YES
5 | IFI6 | IFI6 | IFI6 | 213 | 0.46 | 0.23 | YES
6 | MX1 | MX1 | MX1 | 224 | 0.46 | 0.27 | YES
7 | ISG15 | ISG15 | ISG15 | 238 | 0.45 | 0.32 | YES
8 | USP18 | USP18 | USP18 | 264 | 0.44 | 0.36 | YES
9 | MX2 | MX2 | MX2 | 311 | 0.42 | 0.39 | YES
10 | OAS1 | OAS1 | OAS1 | 318 | 0.42 | 0.43 | YES
11 | OAS2 | OAS2 | OAS2 | 331 | 0.41 | 0.47 | YES
12 | IFI27 | IFI27 | IFI27 | 367 | 0.4 | 0.5 | YES
13 | ISG20 | ISG20 | ISG20 | 376 | 0.39 | 0.54 | YES
14 | HLA-G | HLA-G | HLA-G | 451 | 0.36 | 0.57 | YES
15 | IRF7 | IRF7 | IRF7 | 519 | 0.34 | 0.6 | YES
16 | IFNB1 | IFNB1 | IFNB1 | 611 | 0.32 | 0.62 | YES
17 | OAS3 | OAS3 | OAS3 | 706 | 0.3 | 0.64 | YES
18 | XAF1 | XAF1 | XAF1 | 726 | 0.29 | 0.67 | YES
19 | HLA-F | HLA-F | HLA-F | 859 | 0.26 | 0.69 | YES
20 | IFI35 | IFI35 | IFI35 | 951 | 0.25 | 0.71 | YES
21 | IFITM1 | IFITM1 | IFITM1 | 1204 | 0.21 | 0.71 | YES
22 | PSMB8 | PSMB8 | PSMB8 | 1504 | 0.18 | 0.71 | YES
23 | IRF9 | IRF9 | IRF9 | 1506 | 0.18 | 0.73 | YES
24 | IRF2 | IRF2 | IRF2 | 1671 | 0.16 | 0.74 | YES
25 | HLA-C | HLA-C | HLA-C | 1962 | 0.14 | 0.73 | YES
26 | HLA-B | HLA-B | HLA-B | 2103 | 0.13 | 0.74 | YES
27 | IFITM2 | IFITM2 | IFITM2 | 2235 | 0.13 | 0.74 | YES
28 | HLA-A | HLA-A | HLA-A | 2327 | 0.12 | 0.75 | YES
29 | STAT1 | STAT1 | STAT1 | 2411 | 0.12 | 0.76 | YES
30 | STAT2 | STAT2 | STAT2 | 2877 | 0.096 | 0.74 | NO
31 | IRF1 | IRF1 | IRF1 | 2964 | 0.093 | 0.74 | NO
32 | IFITM3 | IFITM3 | IFITM3 | 3378 | 0.08 | 0.73 | NO
33 | PTPN6 | PTPN6 | PTPN6 | 3494 | 0.076 | 0.73 | NO
34 | IRF5 | IRF5 | IRF5 | 5136 | 0.039 | 0.64 | NO
35 | JAK1 | JAK1 | JAK1 | 5351 | 0.035 | 0.63 | NO
36 | IFNAR1 | IFNAR1 | IFNAR1 | 5671 | 0.03 | 0.62 | NO
37 | ADAR | ADAR | ADAR | 6198 | 0.022 | 0.59 | NO
38 | EGR1 | EGR1 | EGR1 | 7054 | 0.0095 | 0.55 | NO
39 | RNASEL | RNASEL | RNASEL | 7127 | 0.0085 | 0.54 | NO
40 | IFNAR2 | IFNAR2 | IFNAR2 | 7697 | 0.00024 | 0.51 | NO
41 | IRF3 | IRF3 | IRF3 | 7933 | -0.0029 | 0.5 | NO
42 | IRF4 | IRF4 | IRF4 | 8530 | -0.012 | 0.47 | NO
43 | GBP2 | GBP2 | GBP2 | 8726 | -0.014 | 0.46 | NO
44 | TYK2 | TYK2 | TYK2 | 9069 | -0.02 | 0.44 | NO
45 | SOCS3 | SOCS3 | SOCS3 | 9473 | -0.027 | 0.42 | NO
46 | IP6K2 | IP6K2 | IP6K2 | 9606 | -0.029 | 0.42 | NO
47 | IRF8 | IRF8 | IRF8 | 9859 | -0.033 | 0.4 | NO
48 | PTPN1 | PTPN1 | PTPN1 | 11237 | -0.06 | 0.34 | NO
49 | SOCS1 | SOCS1 | SOCS1 | 15615 | -0.23 | 0.12 | NO
50 | IRF6 | IRF6 | IRF6 | 16252 | -0.28 | 0.11 | NO

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

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

genes ES table in pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS

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 | IFIT1 | IFIT1 | IFIT1 | 111 | 0.55 | 0.077 | YES
2 | HERC5 | HERC5 | HERC5 | 158 | 0.5 | 0.15 | YES
3 | MX1 | MX1 | MX1 | 224 | 0.46 | 0.22 | YES
4 | ISG15 | ISG15 | ISG15 | 238 | 0.45 | 0.28 | YES
5 | USP18 | USP18 | USP18 | 264 | 0.44 | 0.35 | YES
6 | MX2 | MX2 | MX2 | 311 | 0.42 | 0.41 | YES
7 | DDX58 | DDX58 | DDX58 | 412 | 0.38 | 0.46 | YES
8 | TRIM25 | TRIM25 | TRIM25 | 1424 | 0.19 | 0.43 | NO
9 | UBE2L6 | UBE2L6 | UBE2L6 | 1819 | 0.15 | 0.43 | NO
10 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 2307 | 0.12 | 0.43 | NO
11 | STAT1 | STAT1 | STAT1 | 2411 | 0.12 | 0.44 | NO
12 | EIF4E3 | EIF4E3 | EIF4E3 | 3006 | 0.092 | 0.42 | NO
13 | NUP85 | NUP85 | NUP85 | 3943 | 0.064 | 0.38 | NO
14 | AAAS | AAAS | AAAS | 4211 | 0.058 | 0.37 | NO
15 | MAPK3 | MAPK3 | MAPK3 | 4435 | 0.053 | 0.37 | NO
16 | EIF4G3 | EIF4G3 | EIF4G3 | 4464 | 0.052 | 0.37 | NO
17 | RPS27A | RPS27A | RPS27A | 4792 | 0.045 | 0.36 | NO
18 | UBA7 | UBA7 | UBA7 | 4834 | 0.044 | 0.37 | NO
19 | NUP35 | NUP35 | NUP35 | 4886 | 0.043 | 0.37 | NO
20 | PPM1B | PPM1B | PPM1B | 4899 | 0.043 | 0.38 | NO
21 | JAK1 | JAK1 | JAK1 | 5351 | 0.035 | 0.36 | NO
22 | EIF4E | EIF4E | EIF4E | 5590 | 0.031 | 0.35 | NO
23 | NUP37 | NUP37 | NUP37 | 5817 | 0.027 | 0.34 | NO
24 | EIF4A1 | EIF4A1 | EIF4A1 | 6056 | 0.024 | 0.33 | NO
25 | POM121 | POM121 | POM121 | 6272 | 0.02 | 0.32 | NO
26 | NUP88 | NUP88 | NUP88 | 6551 | 0.017 | 0.31 | NO
27 | KPNB1 | KPNB1 | KPNB1 | 6589 | 0.016 | 0.31 | NO
28 | EIF4A3 | EIF4A3 | EIF4A3 | 6820 | 0.013 | 0.3 | NO
29 | TPR | TPR | TPR | 6964 | 0.011 | 0.29 | NO
30 | EIF4G1 | EIF4G1 | EIF4G1 | 7103 | 0.0088 | 0.28 | NO
31 | EIF4A2 | EIF4A2 | EIF4A2 | 7125 | 0.0085 | 0.28 | NO
32 | EIF4G2 | EIF4G2 | EIF4G2 | 7260 | 0.0067 | 0.28 | NO
33 | EIF4E2 | EIF4E2 | EIF4E2 | 7456 | 0.0039 | 0.27 | NO
34 | NUP133 | NUP133 | NUP133 | 7521 | 0.0028 | 0.27 | NO
35 | NUP214 | NUP214 | NUP214 | 7600 | 0.0017 | 0.26 | NO
36 | UBA52 | UBA52 | UBA52 | 7844 | -0.0019 | 0.25 | NO
37 | IRF3 | IRF3 | IRF3 | 7933 | -0.0029 | 0.24 | NO
38 | RANBP2 | RANBP2 | RANBP2 | 8069 | -0.0046 | 0.24 | NO
39 | UBE2E1 | UBE2E1 | UBE2E1 | 8146 | -0.0057 | 0.23 | NO
40 | NUPL2 | NUPL2 | NUPL2 | 8177 | -0.006 | 0.23 | NO
41 | NUP210 | NUP210 | NUP210 | 8539 | -0.012 | 0.22 | NO
42 | NUP54 | NUP54 | NUP54 | 8611 | -0.013 | 0.21 | NO
43 | KPNA1 | KPNA1 | KPNA1 | 8690 | -0.014 | 0.21 | NO
44 | RAE1 | RAE1 | RAE1 | 8758 | -0.015 | 0.21 | NO
45 | ARIH1 | ARIH1 | ARIH1 | 9410 | -0.025 | 0.18 | NO
46 | NUP107 | NUP107 | NUP107 | 9435 | -0.026 | 0.18 | NO
47 | NUP205 | NUP205 | NUP205 | 9938 | -0.034 | 0.16 | NO
48 | KPNA4 | KPNA4 | KPNA4 | 10145 | -0.038 | 0.15 | NO
49 | PIN1 | PIN1 | PIN1 | 10310 | -0.04 | 0.15 | NO
50 | NUP50 | NUP50 | NUP50 | 10355 | -0.041 | 0.15 | NO
51 | NUP153 | NUP153 | NUP153 | 10610 | -0.046 | 0.14 | NO
52 | SEH1L | SEH1L | SEH1L | 10764 | -0.049 | 0.14 | NO
53 | NUP62 | NUP62 | NUP62 | 10885 | -0.052 | 0.15 | NO
54 | UBE2N | UBE2N | UBE2N | 11341 | -0.062 | 0.13 | NO
55 | NUP155 | NUP155 | NUP155 | 11680 | -0.07 | 0.12 | NO
56 | NUPL1 | NUPL1 | NUPL1 | 11816 | -0.073 | 0.12 | NO
57 | PLCG1 | PLCG1 | PLCG1 | 12502 | -0.091 | 0.1 | NO
58 | NUP188 | NUP188 | NUP188 | 12635 | -0.096 | 0.11 | NO
59 | KPNA3 | KPNA3 | KPNA3 | 12841 | -0.1 | 0.11 | NO
60 | NUP43 | NUP43 | NUP43 | 13039 | -0.11 | 0.12 | NO
61 | NUP93 | NUP93 | NUP93 | 13676 | -0.13 | 0.1 | NO
62 | KPNA2 | KPNA2 | KPNA2 | 14581 | -0.17 | 0.079 | NO
63 | NEDD4 | NEDD4 | NEDD4 | 14658 | -0.18 | 0.1 | NO
64 | FLNB | FLNB | FLNB | 14987 | -0.19 | 0.11 | NO
65 | KPNA5 | KPNA5 | KPNA5 | 17556 | -0.43 | 0.035 | NO

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

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

genes ES table in pathway: KEGG PARKINSONS DISEASE

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 | OASL | OASL | OASL | 103 | 0.56 | 0.026 | YES
2 | IFIT1 | IFIT1 | IFIT1 | 111 | 0.55 | 0.057 | YES
3 | IFIT2 | IFIT2 | IFIT2 | 155 | 0.5 | 0.083 | YES
4 | HERC5 | HERC5 | HERC5 | 158 | 0.5 | 0.11 | YES
5 | IFIT3 | IFIT3 | IFIT3 | 165 | 0.49 | 0.14 | YES
6 | IFI6 | IFI6 | IFI6 | 213 | 0.46 | 0.16 | YES
7 | MX1 | MX1 | MX1 | 224 | 0.46 | 0.19 | YES
8 | ISG15 | ISG15 | ISG15 | 238 | 0.45 | 0.21 | YES
9 | USP18 | USP18 | USP18 | 264 | 0.44 | 0.24 | YES
10 | MX2 | MX2 | MX2 | 311 | 0.42 | 0.26 | YES
11 | OAS1 | OAS1 | OAS1 | 318 | 0.42 | 0.28 | YES
12 | OAS2 | OAS2 | OAS2 | 331 | 0.41 | 0.3 | YES
13 | IFI27 | IFI27 | IFI27 | 367 | 0.4 | 0.32 | YES
14 | ISG20 | ISG20 | ISG20 | 376 | 0.39 | 0.35 | YES
15 | DDX58 | DDX58 | DDX58 | 412 | 0.38 | 0.37 | YES
16 | HLA-G | HLA-G | HLA-G | 451 | 0.36 | 0.38 | YES
17 | IRF7 | IRF7 | IRF7 | 519 | 0.34 | 0.4 | YES
18 | IFNB1 | IFNB1 | IFNB1 | 611 | 0.32 | 0.41 | YES
19 | OAS3 | OAS3 | OAS3 | 706 | 0.3 | 0.42 | YES
20 | XAF1 | XAF1 | XAF1 | 726 | 0.29 | 0.44 | YES
21 | HLA-F | HLA-F | HLA-F | 859 | 0.26 | 0.45 | YES
22 | IFI35 | IFI35 | IFI35 | 951 | 0.25 | 0.46 | YES
23 | IFITM1 | IFITM1 | IFITM1 | 1204 | 0.21 | 0.45 | YES
24 | TRIM25 | TRIM25 | TRIM25 | 1424 | 0.19 | 0.45 | YES
25 | PSMB8 | PSMB8 | PSMB8 | 1504 | 0.18 | 0.46 | YES
26 | IRF9 | IRF9 | IRF9 | 1506 | 0.18 | 0.47 | YES
27 | IRF2 | IRF2 | IRF2 | 1671 | 0.16 | 0.47 | YES
28 | UBE2L6 | UBE2L6 | UBE2L6 | 1819 | 0.15 | 0.47 | YES
29 | SP100 | SP100 | SP100 | 1912 | 0.15 | 0.47 | YES
30 | HLA-C | HLA-C | HLA-C | 1962 | 0.14 | 0.48 | YES
31 | HLA-B | HLA-B | HLA-B | 2103 | 0.13 | 0.48 | YES
32 | GBP4 | GBP4 | GBP4 | 2165 | 0.13 | 0.48 | YES
33 | CAMK2D | CAMK2D | CAMK2D | 2214 | 0.13 | 0.49 | YES
34 | IFITM2 | IFITM2 | IFITM2 | 2235 | 0.13 | 0.49 | YES
35 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 2307 | 0.12 | 0.5 | YES
36 | HLA-A | HLA-A | HLA-A | 2327 | 0.12 | 0.5 | YES
37 | STAT1 | STAT1 | STAT1 | 2411 | 0.12 | 0.5 | YES
38 | MT2A | MT2A | MT2A | 2797 | 0.1 | 0.49 | NO
39 | B2M | B2M | B2M | 2836 | 0.098 | 0.49 | NO
40 | STAT2 | STAT2 | STAT2 | 2877 | 0.096 | 0.49 | NO
41 | IRF1 | IRF1 | IRF1 | 2964 | 0.093 | 0.5 | NO
42 | EIF4E3 | EIF4E3 | EIF4E3 | 3006 | 0.092 | 0.5 | NO
43 | IFITM3 | IFITM3 | IFITM3 | 3378 | 0.08 | 0.48 | NO
44 | PTPN6 | PTPN6 | PTPN6 | 3494 | 0.076 | 0.48 | NO
45 | PTPN2 | PTPN2 | PTPN2 | 3833 | 0.067 | 0.46 | NO
46 | NUP85 | NUP85 | NUP85 | 3943 | 0.064 | 0.46 | NO
47 | GBP1 | GBP1 | GBP1 | 4201 | 0.058 | 0.45 | NO
48 | AAAS | AAAS | AAAS | 4211 | 0.058 | 0.45 | NO
49 | GBP7 | GBP7 | GBP7 | 4253 | 0.057 | 0.46 | NO
50 | MAPK3 | MAPK3 | MAPK3 | 4435 | 0.053 | 0.45 | NO
51 | EIF4G3 | EIF4G3 | EIF4G3 | 4464 | 0.052 | 0.45 | NO
52 | GBP6 | GBP6 | GBP6 | 4600 | 0.05 | 0.44 | NO
53 | RPS27A | RPS27A | RPS27A | 4792 | 0.045 | 0.44 | NO
54 | UBA7 | UBA7 | UBA7 | 4834 | 0.044 | 0.44 | NO
55 | NUP35 | NUP35 | NUP35 | 4886 | 0.043 | 0.44 | NO
56 | PPM1B | PPM1B | PPM1B | 4899 | 0.043 | 0.44 | NO
57 | IRF5 | IRF5 | IRF5 | 5136 | 0.039 | 0.43 | NO
58 | JAK1 | JAK1 | JAK1 | 5351 | 0.035 | 0.42 | NO
59 | EIF4E | EIF4E | EIF4E | 5590 | 0.031 | 0.41 | NO
60 | JAK2 | JAK2 | JAK2 | 5601 | 0.031 | 0.41 | NO
61 | IFNAR1 | IFNAR1 | IFNAR1 | 5671 | 0.03 | 0.4 | NO
62 | NUP37 | NUP37 | NUP37 | 5817 | 0.027 | 0.4 | NO
63 | EIF4A1 | EIF4A1 | EIF4A1 | 6056 | 0.024 | 0.39 | NO
64 | ADAR | ADAR | ADAR | 6198 | 0.022 | 0.38 | NO
65 | POM121 | POM121 | POM121 | 6272 | 0.02 | 0.38 | NO
66 | NUP88 | NUP88 | NUP88 | 6551 | 0.017 | 0.36 | NO
67 | KPNB1 | KPNB1 | KPNB1 | 6589 | 0.016 | 0.36 | NO
68 | EIF4A3 | EIF4A3 | EIF4A3 | 6820 | 0.013 | 0.35 | NO
69 | TPR | TPR | TPR | 6964 | 0.011 | 0.34 | NO
70 | FCGR1A | FCGR1A | FCGR1A | 6974 | 0.011 | 0.34 | NO
71 | GBP5 | GBP5 | GBP5 | 6987 | 0.01 | 0.34 | NO
72 | EGR1 | EGR1 | EGR1 | 7054 | 0.0095 | 0.34 | NO
73 | EIF4G1 | EIF4G1 | EIF4G1 | 7103 | 0.0088 | 0.34 | NO
74 | EIF4A2 | EIF4A2 | EIF4A2 | 7125 | 0.0085 | 0.34 | NO
75 | RNASEL | RNASEL | RNASEL | 7127 | 0.0085 | 0.34 | NO
76 | EIF4G2 | EIF4G2 | EIF4G2 | 7260 | 0.0067 | 0.33 | NO
77 | FCGR1B | FCGR1B | FCGR1B | 7290 | 0.0064 | 0.33 | NO
78 | EIF4E2 | EIF4E2 | EIF4E2 | 7456 | 0.0039 | 0.32 | NO
79 | NUP133 | NUP133 | NUP133 | 7521 | 0.0028 | 0.32 | NO
80 | NUP214 | NUP214 | NUP214 | 7600 | 0.0017 | 0.31 | NO
81 | SUMO1 | SUMO1 | SUMO1 | 7650 | 0.001 | 0.31 | NO
82 | IFNAR2 | IFNAR2 | IFNAR2 | 7697 | 0.00024 | 0.31 | NO
83 | UBA52 | UBA52 | UBA52 | 7844 | -0.0019 | 0.3 | NO
84 | IRF3 | IRF3 | IRF3 | 7933 | -0.0029 | 0.3 | NO
85 | RANBP2 | RANBP2 | RANBP2 | 8069 | -0.0046 | 0.29 | NO
86 | UBE2E1 | UBE2E1 | UBE2E1 | 8146 | -0.0057 | 0.28 | NO
87 | NUPL2 | NUPL2 | NUPL2 | 8177 | -0.006 | 0.28 | NO
88 | IRF4 | IRF4 | IRF4 | 8530 | -0.012 | 0.26 | NO
89 | NUP210 | NUP210 | NUP210 | 8539 | -0.012 | 0.26 | NO
90 | NUP54 | NUP54 | NUP54 | 8611 | -0.013 | 0.26 | NO
91 | HLA-DRB1 | HLA-DRB1 | HLA-DRB1 | 8671 | -0.014 | 0.26 | NO
92 | KPNA1 | KPNA1 | KPNA1 | 8690 | -0.014 | 0.26 | NO
93 | GBP2 | GBP2 | GBP2 | 8726 | -0.014 | 0.26 | NO
94 | RAE1 | RAE1 | RAE1 | 8758 | -0.015 | 0.26 | NO
95 | TYK2 | TYK2 | TYK2 | 9069 | -0.02 | 0.24 | NO
96 | PML | PML | PML | 9118 | -0.021 | 0.24 | NO
97 | CAMK2B | CAMK2B | CAMK2B | 9339 | -0.024 | 0.23 | NO
98 | ARIH1 | ARIH1 | ARIH1 | 9410 | -0.025 | 0.22 | NO
99 | NUP107 | NUP107 | NUP107 | 9435 | -0.026 | 0.22 | NO
100 | SOCS3 | SOCS3 | SOCS3 | 9473 | -0.027 | 0.22 | NO
101 | IP6K2 | IP6K2 | IP6K2 | 9606 | -0.029 | 0.22 | NO
102 | IRF8 | IRF8 | IRF8 | 9859 | -0.033 | 0.21 | NO
103 | NUP205 | NUP205 | NUP205 | 9938 | -0.034 | 0.2 | NO
104 | KPNA4 | KPNA4 | KPNA4 | 10145 | -0.038 | 0.2 | NO
105 | PTAFR | PTAFR | PTAFR | 10189 | -0.038 | 0.2 | NO
106 | PIN1 | PIN1 | PIN1 | 10310 | -0.04 | 0.19 | NO
107 | NUP50 | NUP50 | NUP50 | 10355 | -0.041 | 0.19 | NO
108 | NUP153 | NUP153 | NUP153 | 10610 | -0.046 | 0.18 | NO
109 | HLA-DRB5 | HLA-DRB5 | HLA-DRB5 | 10627 | -0.046 | 0.18 | NO
110 | SEH1L | SEH1L | SEH1L | 10764 | -0.049 | 0.18 | NO
111 | HLA-DPA1 | HLA-DPA1 | HLA-DPA1 | 10866 | -0.051 | 0.17 | NO
112 | NUP62 | NUP62 | NUP62 | 10885 | -0.052 | 0.18 | NO
113 | IFNGR1 | IFNGR1 | IFNGR1 | 10984 | -0.054 | 0.17 | NO
114 | PTPN1 | PTPN1 | PTPN1 | 11237 | -0.06 | 0.16 | NO
115 | UBE2N | UBE2N | UBE2N | 11341 | -0.062 | 0.16 | NO
116 | PIAS1 | PIAS1 | PIAS1 | 11348 | -0.062 | 0.16 | NO
117 | ICAM1 | ICAM1 | ICAM1 | 11569 | -0.067 | 0.16 | NO
118 | HLA-DPB1 | HLA-DPB1 | HLA-DPB1 | 11652 | -0.069 | 0.15 | NO
119 | NUP155 | NUP155 | NUP155 | 11680 | -0.07 | 0.16 | NO
120 | NUPL1 | NUPL1 | NUPL1 | 11816 | -0.073 | 0.15 | NO
121 | PRKCD | PRKCD | PRKCD | 12148 | -0.081 | 0.14 | NO
122 | HLA-DQA2 | HLA-DQA2 | HLA-DQA2 | 12156 | -0.082 | 0.14 | NO
123 | CIITA | CIITA | CIITA | 12345 | -0.086 | 0.14 | NO
124 | CD44 | CD44 | CD44 | 12467 | -0.09 | 0.14 | NO
125 | PLCG1 | PLCG1 | PLCG1 | 12502 | -0.091 | 0.14 | NO
126 | IFNGR2 | IFNGR2 | IFNGR2 | 12631 | -0.095 | 0.14 | NO
127 | NUP188 | NUP188 | NUP188 | 12635 | -0.096 | 0.14 | NO
128 | KPNA3 | KPNA3 | KPNA3 | 12841 | -0.1 | 0.14 | NO
129 | NUP43 | NUP43 | NUP43 | 13039 | -0.11 | 0.13 | NO
130 | IFNG | IFNG | IFNG | 13659 | -0.13 | 0.11 | NO
131 | NUP93 | NUP93 | NUP93 | 13676 | -0.13 | 0.11 | NO
132 | HLA-DQA1 | HLA-DQA1 | HLA-DQA1 | 13934 | -0.14 | 0.11 | NO
133 | VCAM1 | VCAM1 | VCAM1 | 14160 | -0.15 | 0.1 | NO
134 | KPNA2 | KPNA2 | KPNA2 | 14581 | -0.17 | 0.09 | NO
135 | NEDD4 | NEDD4 | NEDD4 | 14658 | -0.18 | 0.095 | NO
136 | FLNB | FLNB | FLNB | 14987 | -0.19 | 0.088 | NO
137 | NCAM1 | NCAM1 | NCAM1 | 15355 | -0.22 | 0.08 | NO
138 | SOCS1 | SOCS1 | SOCS1 | 15615 | -0.23 | 0.079 | NO
139 | IRF6 | IRF6 | IRF6 | 16252 | -0.28 | 0.06 | NO
140 | CAMK2A | CAMK2A | CAMK2A | 17457 | -0.41 | 0.016 | NO
141 | KPNA5 | KPNA5 | KPNA5 | 17556 | -0.43 | 0.035 | NO

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

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

genes ES table in pathway: PID CASPASE PATHWAY

Table 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 | NDUFC1 | NDUFC1 | NDUFC1 | 1454 | 0.18 | -0.026 | YES
2 | NDUFB1 | NDUFB1 | NDUFB1 | 1904 | 0.15 | -0.007 | YES
3 | NDUFB5 | NDUFB5 | NDUFB5 | 2498 | 0.11 | -0.0063 | YES
4 | ETFB | ETFB | ETFB | 2722 | 0.1 | 0.012 | YES
5 | ATP5H | ATP5H | ATP5H | 3002 | 0.092 | 0.024 | YES
6 | ATP5G1 | ATP5G1 | ATP5G1 | 3017 | 0.091 | 0.05 | YES
7 | NDUFA2 | NDUFA2 | NDUFA2 | 3039 | 0.09 | 0.075 | YES
8 | NDUFA3 | NDUFA3 | NDUFA3 | 3336 | 0.082 | 0.083 | YES
9 | UCP2 | UCP2 | UCP2 | 3454 | 0.078 | 0.099 | YES
10 | NDUFB4 | NDUFB4 | NDUFB4 | 3485 | 0.077 | 0.12 | YES
11 | SDHD | SDHD | SDHD | 3591 | 0.073 | 0.14 | YES
12 | COX7C | COX7C | COX7C | 3651 | 0.072 | 0.15 | YES
13 | ATP5L | ATP5L | ATP5L | 3701 | 0.07 | 0.17 | YES
14 | ATP5I | ATP5I | ATP5I | 3722 | 0.07 | 0.19 | YES
15 | COX5B | COX5B | COX5B | 3804 | 0.068 | 0.21 | YES
16 | NDUFB6 | NDUFB6 | NDUFB6 | 3854 | 0.066 | 0.22 | YES
17 | NDUFV3 | NDUFV3 | NDUFV3 | 3861 | 0.066 | 0.24 | YES
18 | NDUFA7 | NDUFA7 | NDUFA7 | 3925 | 0.064 | 0.26 | YES
19 | ATP5F1 | ATP5F1 | ATP5F1 | 3947 | 0.064 | 0.28 | YES
20 | NDUFS8 | NDUFS8 | NDUFS8 | 4092 | 0.061 | 0.29 | YES
21 | NDUFS4 | NDUFS4 | NDUFS4 | 4199 | 0.058 | 0.3 | YES
22 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 4218 | 0.058 | 0.31 | YES
23 | ATP5A1 | ATP5A1 | ATP5A1 | 4243 | 0.057 | 0.33 | YES
24 | COX6A1 | COX6A1 | COX6A1 | 4342 | 0.055 | 0.34 | YES
25 | ATP5C1 | ATP5C1 | ATP5C1 | 4427 | 0.053 | 0.35 | YES
26 | ATP5B | ATP5B | ATP5B | 4500 | 0.051 | 0.36 | YES
27 | UCP1 | UCP1 | UCP1 | 4629 | 0.049 | 0.37 | YES
28 | UQCRB | UQCRB | UQCRB | 4702 | 0.047 | 0.38 | YES
29 | NDUFA13 | NDUFA13 | NDUFA13 | 4756 | 0.046 | 0.39 | YES
30 | ETFDH | ETFDH | ETFDH | 4782 | 0.045 | 0.4 | YES
31 | COX7B | COX7B | COX7B | 4793 | 0.045 | 0.42 | YES
32 | NDUFV1 | NDUFV1 | NDUFV1 | 4863 | 0.044 | 0.42 | YES
33 | NDUFB3 | NDUFB3 | NDUFB3 | 5000 | 0.041 | 0.43 | YES
34 | NDUFA10 | NDUFA10 | NDUFA10 | 5044 | 0.041 | 0.44 | YES
35 | ATP5O | ATP5O | ATP5O | 5074 | 0.04 | 0.45 | YES
36 | UQCRQ | UQCRQ | UQCRQ | 5075 | 0.04 | 0.46 | YES
37 | NDUFS5 | NDUFS5 | NDUFS5 | 5134 | 0.039 | 0.47 | YES
38 | NDUFA9 | NDUFA9 | NDUFA9 | 5308 | 0.036 | 0.47 | YES
39 | NDUFB10 | NDUFB10 | NDUFB10 | 5309 | 0.036 | 0.48 | YES
40 | COX4I1 | COX4I1 | COX4I1 | 5320 | 0.036 | 0.49 | YES
41 | NDUFB7 | NDUFB7 | NDUFB7 | 5408 | 0.034 | 0.5 | YES
42 | NDUFA8 | NDUFA8 | NDUFA8 | 5490 | 0.033 | 0.5 | YES
43 | UQCR11 | UQCR11 | UQCR11 | 5502 | 0.032 | 0.51 | YES
44 | ATP5J2 | ATP5J2 | ATP5J2 | 5622 | 0.03 | 0.51 | YES
45 | COX6C | COX6C | COX6C | 5687 | 0.03 | 0.52 | YES
46 | NDUFS3 | NDUFS3 | NDUFS3 | 5730 | 0.029 | 0.52 | YES
47 | UQCRC2 | UQCRC2 | UQCRC2 | 5750 | 0.028 | 0.53 | YES
48 | ATP5J | ATP5J | ATP5J | 5774 | 0.028 | 0.54 | YES
49 | COX8A | COX8A | COX8A | 5779 | 0.028 | 0.55 | YES
50 | COX7A2L | COX7A2L | COX7A2L | 5926 | 0.025 | 0.55 | YES
51 | SDHA | SDHA | SDHA | 5937 | 0.025 | 0.55 | YES
52 | NDUFB2 | NDUFB2 | NDUFB2 | 6053 | 0.024 | 0.55 | YES
53 | NDUFB8 | NDUFB8 | NDUFB8 | 6119 | 0.022 | 0.56 | YES
54 | SDHB | SDHB | SDHB | 6156 | 0.022 | 0.56 | YES
55 | NDUFV2 | NDUFV2 | NDUFV2 | 6233 | 0.021 | 0.56 | YES
56 | NDUFS1 | NDUFS1 | NDUFS1 | 6247 | 0.021 | 0.57 | YES
57 | NDUFA1 | NDUFA1 | NDUFA1 | 6418 | 0.018 | 0.56 | NO
58 | CYCS | CYCS | CYCS | 6577 | 0.016 | 0.56 | NO
59 | NDUFS2 | NDUFS2 | NDUFS2 | 6590 | 0.016 | 0.56 | NO
60 | NDUFC2 | NDUFC2 | NDUFC2 | 6786 | 0.013 | 0.56 | NO
61 | NDUFA4 | NDUFA4 | NDUFA4 | 6905 | 0.011 | 0.55 | NO
62 | ATP5E | ATP5E | ATP5E | 7043 | 0.0097 | 0.55 | NO
63 | CYC1 | CYC1 | CYC1 | 7083 | 0.0092 | 0.55 | NO
64 | NDUFA11 | NDUFA11 | NDUFA11 | 7186 | 0.0076 | 0.55 | NO
65 | ATP5D | ATP5D | ATP5D | 7283 | 0.0064 | 0.54 | NO
66 | NDUFS7 | NDUFS7 | NDUFS7 | 7488 | 0.0034 | 0.53 | NO
67 | NDUFA5 | NDUFA5 | NDUFA5 | 7560 | 0.0024 | 0.53 | NO
68 | UQCRHL | UQCRHL | UQCRHL | 7606 | 0.0017 | 0.53 | NO
69 | UQCRH | UQCRH | UQCRH | 7632 | 0.0014 | 0.53 | NO
70 | ETFA | ETFA | ETFA | 7853 | -0.002 | 0.52 | NO
71 | COX5A | COX5A | COX5A | 7898 | -0.0026 | 0.51 | NO
72 | NDUFA12 | NDUFA12 | NDUFA12 | 7965 | -0.0034 | 0.51 | NO
73 | SDHC | SDHC | SDHC | 8108 | -0.005 | 0.5 | NO
74 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 8288 | -0.0077 | 0.5 | NO
75 | COX6B1 | COX6B1 | COX6B1 | 8349 | -0.0086 | 0.5 | NO
76 | NDUFB9 | NDUFB9 | NDUFB9 | 8378 | -0.0093 | 0.5 | NO
77 | NDUFS6 | NDUFS6 | NDUFS6 | 8416 | -0.0099 | 0.5 | NO
78 | NDUFA6 | NDUFA6 | NDUFA6 | 10418 | -0.042 | 0.4 | NO
79 | UQCRC1 | UQCRC1 | UQCRC1 | 10445 | -0.043 | 0.41 | NO
80 | UCP3 | UCP3 | UCP3 | 11041 | -0.055 | 0.4 | NO

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

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

genes ES table in pathway: PID A6B1 A6B4 INTEGRIN 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 | GAS2 | GAS2 | GAS2 | 120 | 0.54 | 0.094 | YES
2 | CASP6 | CASP6 | CASP6 | 722 | 0.29 | 0.12 | YES
3 | TFAP2A | TFAP2A | TFAP2A | 815 | 0.27 | 0.16 | YES
4 | GZMB | GZMB | GZMB | 837 | 0.26 | 0.21 | YES
5 | CASP1 | CASP1 | CASP1 | 1067 | 0.23 | 0.24 | YES
6 | PRF1 | PRF1 | PRF1 | 1269 | 0.2 | 0.27 | YES
7 | CASP4 | CASP4 | CASP4 | 1851 | 0.15 | 0.26 | YES
8 | KRT18 | KRT18 | KRT18 | 2052 | 0.14 | 0.28 | YES
9 | CASP3 | CASP3 | CASP3 | 2146 | 0.13 | 0.3 | YES
10 | CASP10 | CASP10 | CASP10 | 2426 | 0.12 | 0.3 | YES
11 | CASP8 | CASP8 | CASP8 | 2595 | 0.11 | 0.32 | YES
12 | TRADD | TRADD | TRADD | 2784 | 0.1 | 0.32 | YES
13 | TNF | TNF | TNF | 2803 | 0.1 | 0.34 | YES
14 | SPTAN1 | SPTAN1 | SPTAN1 | 2875 | 0.096 | 0.36 | YES
15 | BIRC3 | BIRC3 | BIRC3 | 2883 | 0.096 | 0.37 | YES
16 | CASP9 | CASP9 | CASP9 | 3165 | 0.087 | 0.38 | YES
17 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 3180 | 0.086 | 0.39 | YES
18 | RIPK1 | RIPK1 | RIPK1 | 4723 | 0.046 | 0.31 | NO
19 | PTK2 | PTK2 | PTK2 | 4783 | 0.045 | 0.32 | NO
20 | APP | APP | APP | 5643 | 0.03 | 0.28 | NO
21 | CRADD | CRADD | CRADD | 6185 | 0.022 | 0.25 | NO
22 | MADD | MADD | MADD | 6391 | 0.019 | 0.24 | NO
23 | NUMA1 | NUMA1 | NUMA1 | 6543 | 0.017 | 0.24 | NO
24 | CYCS | CYCS | CYCS | 6577 | 0.016 | 0.24 | NO
25 | DIABLO | DIABLO | DIABLO | 6615 | 0.016 | 0.24 | NO
26 | BID | BID | BID | 6761 | 0.014 | 0.24 | NO
27 | TOP1 | TOP1 | TOP1 | 6859 | 0.012 | 0.23 | NO
28 | BIRC2 | BIRC2 | BIRC2 | 6949 | 0.011 | 0.23 | NO
29 | CASP7 | CASP7 | CASP7 | 8418 | -0.0099 | 0.15 | NO
30 | CFL2 | CFL2 | CFL2 | 8919 | -0.018 | 0.13 | NO
31 | BAX | BAX | BAX | 9303 | -0.024 | 0.11 | NO
32 | GSN | GSN | GSN | 9764 | -0.031 | 0.09 | NO
33 | SLK | SLK | SLK | 9962 | -0.035 | 0.086 | NO
34 | XIAP | XIAP | XIAP | 10289 | -0.04 | 0.075 | NO
35 | MAP3K1 | MAP3K1 | MAP3K1 | 10410 | -0.042 | 0.076 | NO
36 | PARP1 | PARP1 | PARP1 | 11079 | -0.056 | 0.05 | NO
37 | ARHGDIB | ARHGDIB | ARHGDIB | 11153 | -0.057 | 0.057 | NO
38 | DFFA | DFFA | DFFA | 11361 | -0.062 | 0.057 | NO
39 | SREBF1 | SREBF1 | SREBF1 | 11811 | -0.073 | 0.046 | NO
40 | TRAF2 | TRAF2 | TRAF2 | 11880 | -0.074 | 0.056 | NO
41 | LIMK1 | LIMK1 | LIMK1 | 11913 | -0.075 | 0.069 | NO
42 | LMNB1 | LMNB1 | LMNB1 | 12304 | -0.085 | 0.063 | NO
43 | LMNA | LMNA | LMNA | 12331 | -0.086 | 0.078 | NO
44 | CASP2 | CASP2 | CASP2 | 12562 | -0.093 | 0.083 | NO
45 | DFFB | DFFB | DFFB | 12834 | -0.1 | 0.087 | NO
46 | APAF1 | APAF1 | APAF1 | 13027 | -0.11 | 0.097 | NO
47 | LMNB2 | LMNB2 | LMNB2 | 14745 | -0.18 | 0.036 | NO
48 | ACTA1 | ACTA1 | ACTA1 | 14902 | -0.19 | 0.063 | NO
49 | BCL2 | BCL2 | BCL2 | 15120 | -0.2 | 0.089 | NO
50 | VIM | VIM | VIM | 15268 | -0.21 | 0.12 | NO
51 | SATB1 | SATB1 | SATB1 | 15359 | -0.22 | 0.16 | NO

Figure S15. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID A6B1 A6B4 INTEGRIN PATHWAY.

Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: PID A6B1 A6B4 INTEGRIN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TRANSLATION

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 | LAMB3 | LAMB3 | LAMB3 | 239 | 0.45 | 0.076 | YES
2 | CDH1 | CDH1 | CDH1 | 404 | 0.38 | 0.14 | YES
3 | LAMA3 | LAMA3 | LAMA3 | 435 | 0.37 | 0.21 | YES
4 | MST1R | MST1R | MST1R | 438 | 0.36 | 0.28 | YES
5 | MET | MET | MET | 502 | 0.34 | 0.34 | YES
6 | SFN | SFN | SFN | 585 | 0.32 | 0.4 | YES
7 | ITGB4 | ITGB4 | ITGB4 | 773 | 0.28 | 0.45 | YES
8 | MST1 | MST1 | MST1 | 1160 | 0.22 | 0.47 | YES
9 | LAMA4 | LAMA4 | LAMA4 | 1866 | 0.15 | 0.46 | YES
10 | EGFR | EGFR | EGFR | 1867 | 0.15 | 0.49 | YES
11 | ERBB2 | ERBB2 | ERBB2 | 2090 | 0.13 | 0.5 | YES
12 | CD9 | CD9 | CD9 | 3049 | 0.09 | 0.47 | NO
13 | ERBB3 | ERBB3 | ERBB3 | 3853 | 0.066 | 0.44 | NO
14 | LAMA5 | LAMA5 | LAMA5 | 4401 | 0.053 | 0.42 | NO
15 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 4453 | 0.052 | 0.42 | NO
16 | RXRA | RXRA | RXRA | 5060 | 0.04 | 0.4 | NO
17 | HRAS | HRAS | HRAS | 5174 | 0.038 | 0.4 | NO
18 | PIK3R1 | PIK3R1 | PIK3R1 | 5467 | 0.033 | 0.39 | NO
19 | PIK3CA | PIK3CA | PIK3CA | 5885 | 0.026 | 0.37 | NO
20 | EGF | EGF | EGF | 6108 | 0.023 | 0.36 | NO
21 | GRB2 | GRB2 | GRB2 | 6636 | 0.015 | 0.34 | NO
22 | RXRG | RXRG | RXRG | 6940 | 0.011 | 0.32 | NO
23 | YWHAZ | YWHAZ | YWHAZ | 7261 | 0.0066 | 0.31 | NO
24 | LAMA1 | LAMA1 | LAMA1 | 7424 | 0.0044 | 0.3 | NO
25 | YWHAB | YWHAB | YWHAB | 7929 | -0.0028 | 0.27 | NO
26 | RXRB | RXRB | RXRB | 8112 | -0.0051 | 0.26 | NO
27 | CASP7 | CASP7 | CASP7 | 8418 | -0.0099 | 0.25 | NO
28 | YWHAE | YWHAE | YWHAE | 8897 | -0.017 | 0.22 | NO
29 | YWHAH | YWHAH | YWHAH | 8910 | -0.017 | 0.23 | NO
30 | RAC1 | RAC1 | RAC1 | 9626 | -0.029 | 0.19 | NO
31 | YWHAQ | YWHAQ | YWHAQ | 9733 | -0.031 | 0.19 | NO
32 | SHC1 | SHC1 | SHC1 | 10313 | -0.04 | 0.17 | NO
33 | AKT1 | AKT1 | AKT1 | 10341 | -0.041 | 0.18 | NO
34 | YWHAG | YWHAG | YWHAG | 10556 | -0.045 | 0.17 | NO
35 | ITGA6 | ITGA6 | ITGA6 | 10680 | -0.047 | 0.18 | NO
36 | LAMB2 | LAMB2 | LAMB2 | 10905 | -0.052 | 0.17 | NO
37 | COL17A1 | COL17A1 | COL17A1 | 11742 | -0.071 | 0.14 | NO
38 | LAMA2 | LAMA2 | LAMA2 | 11855 | -0.074 | 0.15 | NO
39 | ITGB1 | ITGB1 | ITGB1 | 11967 | -0.076 | 0.16 | NO
40 | LAMC3 | LAMC3 | LAMC3 | 12129 | -0.081 | 0.16 | NO
41 | PMP22 | PMP22 | PMP22 | 12231 | -0.083 | 0.18 | NO
42 | LAMC1 | LAMC1 | LAMC1 | 13186 | -0.11 | 0.14 | NO
43 | IL1A | IL1A | IL1A | 13920 | -0.14 | 0.13 | NO
44 | LAMC2 | LAMC2 | LAMC2 | 14341 | -0.16 | 0.14 | NO
45 | LAMB1 | LAMB1 | LAMB1 | 14704 | -0.18 | 0.16 | NO
46 | PRKCA | PRKCA | PRKCA | 14943 | -0.19 | 0.18 | NO

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

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

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

Table S10. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GPLD1 | GPLD1 | GPLD1 | 547 | 0.33 | 0.13 | YES
2 | PIGF | PIGF | PIGF | 1656 | 0.17 | 0.14 | YES
3 | PIGZ | PIGZ | PIGZ | 1729 | 0.16 | 0.22 | YES
4 | PIGP | PIGP | PIGP | 2403 | 0.12 | 0.23 | YES
5 | PIGH | PIGH | PIGH | 2507 | 0.11 | 0.28 | YES
6 | PIGY | PIGY | PIGY | 3244 | 0.084 | 0.28 | YES
7 | PIGG | PIGG | PIGG | 3361 | 0.081 | 0.31 | YES
8 | PIGB | PIGB | PIGB | 3394 | 0.08 | 0.35 | YES
9 | PIGV | PIGV | PIGV | 3644 | 0.072 | 0.37 | YES
10 | PIGO | PIGO | PIGO | 3789 | 0.068 | 0.39 | YES
11 | PIGS | PIGS | PIGS | 4305 | 0.056 | 0.39 | NO
12 | PIGL | PIGL | PIGL | 5364 | 0.035 | 0.35 | NO
13 | PIGK | PIGK | PIGK | 7395 | 0.0049 | 0.24 | NO
14 | PIGQ | PIGQ | PIGQ | 7715 | -0.000027 | 0.22 | NO
15 | PIGW | PIGW | PIGW | 8564 | -0.012 | 0.18 | NO
16 | PIGC | PIGC | PIGC | 8781 | -0.015 | 0.17 | NO
17 | PIGU | PIGU | PIGU | 8943 | -0.018 | 0.17 | NO
18 | PIGT | PIGT | PIGT | 9649 | -0.029 | 0.15 | NO
19 | GPAA1 | GPAA1 | GPAA1 | 10365 | -0.041 | 0.13 | NO
20 | DPM2 | DPM2 | DPM2 | 10884 | -0.052 | 0.12 | NO
21 | PIGM | PIGM | PIGM | 11136 | -0.057 | 0.14 | NO
22 | PIGN | PIGN | PIGN | 11719 | -0.071 | 0.14 | NO
23 | PIGX | PIGX | PIGX | 11775 | -0.072 | 0.17 | NO
24 | PIGA | PIGA | PIGA | 12514 | -0.092 | 0.17 | NO
25 | PGAP1 | PGAP1 | PGAP1 | 16494 | -0.3 | 0.094 | NO

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

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

Fold change

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

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

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
KEGG GLYCOLYSIS GLUCONEOGENESIS | 56 | genes.ES.table | 0.45 | 1.5 | 0.052 | 1 | 0.99 | 0.25 | 0.2 | 0.2 | 0.99 | 0.5
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION | 43 | genes.ES.table | 0.46 | 1.6 | 0.081 | 1 | 0.94 | 0.58 | 0.35 | 0.38 | 0.97 | 0.48
KEGG HISTIDINE METABOLISM | 29 | genes.ES.table | 0.6 | 1.6 | 0.014 | 1 | 0.94 | 0.52 | 0.27 | 0.38 | 0.85 | 0.44
KEGG STARCH AND SUCROSE METABOLISM | 35 | genes.ES.table | 0.58 | 1.5 | 0.041 | 1 | 0.97 | 0.31 | 0.11 | 0.28 | 0.85 | 0.44
KEGG PYRUVATE METABOLISM | 38 | genes.ES.table | 0.43 | 1.5 | 0.038 | 1 | 0.97 | 0.47 | 0.33 | 0.32 | 0.8 | 0.4
KEGG PROPANOATE METABOLISM | 32 | genes.ES.table | 0.51 | 1.5 | 0.072 | 1 | 0.97 | 0.53 | 0.34 | 0.35 | 0.83 | 0.41
KEGG AMINOACYL TRNA BIOSYNTHESIS | 41 | genes.ES.table | 0.38 | 1.4 | 0.17 | 1 | 1 | 0.39 | 0.34 | 0.26 | 0.97 | 0.49
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 | 52 | genes.ES.table | 0.62 | 1.6 | 0.0067 | 1 | 0.96 | 0.54 | 0.2 | 0.43 | 0.89 | 0.46
KEGG DRUG METABOLISM CYTOCHROME P450 | 55 | genes.ES.table | 0.65 | 1.6 | 0 | 1 | 0.92 | 0.55 | 0.2 | 0.44 | 1 | 0.55
PID NCADHERINPATHWAY | 33 | genes.ES.table | 0.5 | 1.7 | 0.014 | 1 | 0.81 | 0.46 | 0.28 | 0.33 | 1 | 0.52

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 | ADHFE1 | ADHFE1 | ADHFE1 | 2056 | 0.18 | -0.033 | YES
2 | PDP2 | PDP2 | PDP2 | 2179 | 0.18 | 0.037 | YES
3 | FH | FH | FH | 2622 | 0.15 | 0.078 | YES
4 | PDK1 | PDK1 | PDK1 | 2788 | 0.14 | 0.13 | YES
5 | SLC16A1 | SLC16A1 | SLC16A1 | 3788 | 0.1 | 0.12 | YES
6 | IDH3A | IDH3A | IDH3A | 4320 | 0.088 | 0.13 | YES
7 | NNT | NNT | NNT | 4555 | 0.082 | 0.15 | YES
8 | BSG | BSG | BSG | 4626 | 0.08 | 0.18 | YES
9 | SUCLA2 | SUCLA2 | SUCLA2 | 4671 | 0.079 | 0.21 | YES
10 | L2HGDH | L2HGDH | L2HGDH | 5196 | 0.068 | 0.21 | YES
11 | SDHC | SDHC | SDHC | 5240 | 0.066 | 0.24 | YES
12 | PDK2 | PDK2 | PDK2 | 5267 | 0.066 | 0.27 | YES
13 | PDHB | PDHB | PDHB | 5455 | 0.062 | 0.28 | YES
14 | PDHA1 | PDHA1 | PDHA1 | 5550 | 0.061 | 0.3 | YES
15 | PDK3 | PDK3 | PDK3 | 5936 | 0.053 | 0.31 | YES
16 | PDHX | PDHX | PDHX | 6003 | 0.052 | 0.33 | YES
17 | SUCLG2 | SUCLG2 | SUCLG2 | 6098 | 0.051 | 0.34 | YES
18 | DLD | DLD | DLD | 6347 | 0.046 | 0.35 | YES
19 | PDP1 | PDP1 | PDP1 | 6562 | 0.043 | 0.36 | YES
20 | ACO2 | ACO2 | ACO2 | 6710 | 0.041 | 0.37 | YES
21 | SUCLG1 | SUCLG1 | SUCLG1 | 6787 | 0.04 | 0.38 | YES
22 | IDH3G | IDH3G | IDH3G | 6809 | 0.04 | 0.4 | YES
23 | SLC16A3 | SLC16A3 | SLC16A3 | 6841 | 0.039 | 0.41 | YES
24 | LDHA | LDHA | LDHA | 6964 | 0.037 | 0.42 | YES
25 | SDHA | SDHA | SDHA | 7070 | 0.035 | 0.43 | YES
26 | PDPR | PDPR | PDPR | 7594 | 0.028 | 0.41 | NO
27 | MDH2 | MDH2 | MDH2 | 7606 | 0.028 | 0.42 | NO
28 | SDHD | SDHD | SDHD | 8290 | 0.019 | 0.4 | NO
29 | SLC16A8 | SLC16A8 | SLC16A8 | 8742 | 0.013 | 0.38 | NO
30 | D2HGDH | D2HGDH | D2HGDH | 9045 | 0.0096 | 0.36 | NO
31 | LDHB | LDHB | LDHB | 9091 | 0.009 | 0.36 | NO
32 | DLAT | DLAT | DLAT | 9243 | 0.0071 | 0.36 | NO
33 | IDH1 | IDH1 | IDH1 | 9443 | 0.0046 | 0.35 | NO
34 | IDH3B | IDH3B | IDH3B | 10243 | -0.0052 | 0.31 | NO
35 | SDHB | SDHB | SDHB | 11263 | -0.019 | 0.26 | NO
36 | CS | CS | CS | 11269 | -0.019 | 0.27 | NO
37 | OGDH | OGDH | OGDH | 12276 | -0.033 | 0.23 | NO
38 | IDH2 | IDH2 | IDH2 | 12342 | -0.034 | 0.24 | NO
39 | DLST | DLST | DLST | 14659 | -0.089 | 0.15 | NO
40 | PDK4 | PDK4 | PDK4 | 15118 | -0.1 | 0.17 | NO

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

Figure S22. 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION

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 | CNR1 | CNR1 | CNR1 | 469 | 0.4 | 0.12 | YES
2 | GAP43 | GAP43 | GAP43 | 1553 | 0.23 | 0.15 | YES
3 | GRIA2 | GRIA2 | GRIA2 | 1949 | 0.19 | 0.2 | YES
4 | CDH2 | CDH2 | CDH2 | 2576 | 0.15 | 0.23 | YES
5 | FER | FER | FER | 2943 | 0.14 | 0.26 | YES
6 | JUP | JUP | JUP | 3249 | 0.12 | 0.29 | YES
7 | GJA1 | GJA1 | GJA1 | 3287 | 0.12 | 0.33 | YES
8 | MAPK8 | MAPK8 | MAPK8 | 3333 | 0.12 | 0.37 | YES
9 | MYL2 | MYL2 | MYL2 | 3594 | 0.11 | 0.4 | YES
10 | AXIN1 | AXIN1 | AXIN1 | 4168 | 0.092 | 0.4 | YES
11 | PTPN11 | PTPN11 | PTPN11 | 4219 | 0.091 | 0.43 | YES
12 | CTTN | CTTN | CTTN | 4558 | 0.082 | 0.45 | YES
13 | LRP5 | LRP5 | LRP5 | 4585 | 0.081 | 0.48 | YES
14 | DAGLB | DAGLB | DAGLB | 4892 | 0.074 | 0.49 | YES
15 | DAGLA | DAGLA | DAGLA | 5092 | 0.07 | 0.5 | YES
16 | RHOA | RHOA | RHOA | 6536 | 0.044 | 0.44 | NO
17 | PTPN1 | PTPN1 | PTPN1 | 6988 | 0.037 | 0.43 | NO
18 | PIK3R1 | PIK3R1 | PIK3R1 | 6996 | 0.037 | 0.44 | NO
19 | RAC1 | RAC1 | RAC1 | 8052 | 0.022 | 0.39 | NO
20 | PIK3CA | PIK3CA | PIK3CA | 8717 | 0.014 | 0.36 | NO
21 | CTNND1 | CTNND1 | CTNND1 | 9534 | 0.0036 | 0.32 | NO
22 | CAMK2G | CAMK2G | CAMK2G | 10063 | -0.0029 | 0.29 | NO
23 | CTNNA1 | CTNNA1 | CTNNA1 | 10505 | -0.0086 | 0.27 | NO
24 | CDC42 | CDC42 | CDC42 | 10724 | -0.012 | 0.26 | NO
25 | PIP5K1C | PIP5K1C | PIP5K1C | 10889 | -0.014 | 0.26 | NO
26 | MAPRE1 | MAPRE1 | MAPRE1 | 11916 | -0.028 | 0.21 | NO
27 | CTNNB1 | CTNNB1 | CTNNB1 | 11948 | -0.028 | 0.22 | NO
28 | GSN | GSN | GSN | 12013 | -0.029 | 0.23 | NO
29 | DCTN1 | DCTN1 | DCTN1 | 12251 | -0.033 | 0.23 | NO
30 | KIF5B | KIF5B | KIF5B | 12923 | -0.044 | 0.21 | NO
31 | ROCK1 | ROCK1 | ROCK1 | 13983 | -0.069 | 0.17 | NO
32 | FGFR1 | FGFR1 | FGFR1 | 13987 | -0.069 | 0.2 | NO
33 | PLCG1 | PLCG1 | PLCG1 | 14462 | -0.082 | 0.2 | NO

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

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

genes ES table in pathway: KEGG HISTIDINE METABOLISM

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 | AP1M2 | AP1M2 | AP1M2 | 525 | 0.38 | 0.098 | YES
2 | TBC1D8B | TBC1D8B | TBC1D8B | 1048 | 0.28 | 0.16 | YES
3 | TPD52 | TPD52 | TPD52 | 1348 | 0.25 | 0.23 | YES
4 | SORT1 | SORT1 | SORT1 | 2910 | 0.14 | 0.19 | YES
5 | TPD52L1 | TPD52L1 | TPD52L1 | 3408 | 0.12 | 0.2 | YES
6 | TFRC | TFRC | TFRC | 3635 | 0.11 | 0.22 | YES
7 | SH3D19 | SH3D19 | SH3D19 | 3719 | 0.1 | 0.25 | YES
8 | AP4E1 | AP4E1 | AP4E1 | 3989 | 0.098 | 0.27 | YES
9 | AP3S1 | AP3S1 | AP3S1 | 4013 | 0.097 | 0.3 | YES
10 | AP3B1 | AP3B1 | AP3B1 | 4391 | 0.086 | 0.31 | YES
11 | CPD | CPD | CPD | 4804 | 0.076 | 0.31 | YES
12 | AP1S1 | AP1S1 | AP1S1 | 5480 | 0.062 | 0.29 | YES
13 | ARF1 | ARF1 | ARF1 | 5500 | 0.062 | 0.31 | YES
14 | ARRB1 | ARRB1 | ARRB1 | 5789 | 0.056 | 0.32 | YES
15 | PIK3C2A | PIK3C2A | PIK3C2A | 5798 | 0.056 | 0.33 | YES
16 | SNX9 | SNX9 | SNX9 | 6124 | 0.05 | 0.33 | YES
17 | VAMP7 | VAMP7 | VAMP7 | 6178 | 0.049 | 0.35 | YES
18 | BLOC1S1 | BLOC1S1 | BLOC1S1 | 6247 | 0.048 | 0.36 | YES
19 | VAMP8 | VAMP8 | VAMP8 | 6458 | 0.045 | 0.36 | YES
20 | DNAJC6 | DNAJC6 | DNAJC6 | 6825 | 0.039 | 0.36 | YES
21 | SNAPIN | SNAPIN | SNAPIN | 6847 | 0.039 | 0.37 | YES
22 | YIPF6 | YIPF6 | YIPF6 | 7013 | 0.036 | 0.37 | YES
23 | SNX2 | SNX2 | SNX2 | 7588 | 0.028 | 0.35 | NO
24 | PUM1 | PUM1 | PUM1 | 7799 | 0.026 | 0.34 | NO
25 | BLOC1S3 | BLOC1S3 | BLOC1S3 | 7939 | 0.024 | 0.34 | NO
26 | AP1M1 | AP1M1 | AP1M1 | 8705 | 0.014 | 0.31 | NO
27 | OCRL | OCRL | OCRL | 8777 | 0.013 | 0.31 | NO
28 | HSPA8 | HSPA8 | HSPA8 | 8827 | 0.012 | 0.31 | NO
29 | AP4B1 | AP4B1 | AP4B1 | 9020 | 0.0099 | 0.3 | NO
30 | NAPA | NAPA | NAPA | 9098 | 0.0088 | 0.3 | NO
31 | FTH1 | FTH1 | FTH1 | 9164 | 0.008 | 0.3 | NO
32 | DNM2 | DNM2 | DNM2 | 9331 | 0.0061 | 0.29 | NO
33 | AP1G1 | AP1G1 | AP1G1 | 9458 | 0.0044 | 0.29 | NO
34 | PLDN | PLDN | PLDN | 9493 | 0.004 | 0.29 | NO
35 | PICALM | PICALM | PICALM | 9530 | 0.0037 | 0.28 | NO
36 | RAB5C | RAB5C | RAB5C | 9583 | 0.0031 | 0.28 | NO
37 | DTNBP1 | DTNBP1 | DTNBP1 | 9684 | 0.0019 | 0.28 | NO
38 | TXNDC5 | TXNDC5 | TXNDC5 | 9693 | 0.0017 | 0.28 | NO
39 | TGOLN2 | TGOLN2 | TGOLN2 | 9983 | -0.0019 | 0.26 | NO
40 | CNO | CNO | CNO | 10402 | -0.0072 | 0.24 | NO
41 | CLTC | CLTC | CLTC | 10423 | -0.0076 | 0.24 | NO
42 | SNX5 | SNX5 | SNX5 | 10612 | -0.01 | 0.24 | NO
43 | VAMP2 | VAMP2 | VAMP2 | 10757 | -0.012 | 0.23 | NO
44 | GAK | GAK | GAK | 10964 | -0.015 | 0.23 | NO
45 | IGF2R | IGF2R | IGF2R | 11092 | -0.016 | 0.22 | NO
46 | NECAP1 | NECAP1 | NECAP1 | 11165 | -0.017 | 0.23 | NO
47 | AP1S2 | AP1S2 | AP1S2 | 12431 | -0.036 | 0.17 | NO
48 | CLTA | CLTA | CLTA | 12802 | -0.042 | 0.16 | NO
49 | AP1B1 | AP1B1 | AP1B1 | 12830 | -0.043 | 0.18 | NO
50 | FTL | FTL | FTL | 13755 | -0.062 | 0.14 | NO
51 | HIP1R | HIP1R | HIP1R | 13979 | -0.069 | 0.16 | NO
52 | SH3GL2 | SH3GL2 | SH3GL2 | 17092 | -0.23 | 0.061 | NO

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

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

genes ES table in pathway: KEGG STARCH AND SUCROSE METABOLISM

Table 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 | MAOA | MAOA | MAOA | 74 | 0.62 | 0.06 | YES
2 | AOX1 | AOX1 | AOX1 | 103 | 0.59 | 0.12 | YES
3 | MAOB | MAOB | MAOB | 271 | 0.47 | 0.16 | YES
4 | UGT1A9 | UGT1A9 | UGT1A9 | 348 | 0.44 | 0.2 | YES
5 | CYP2E1 | CYP2E1 | CYP2E1 | 362 | 0.44 | 0.24 | YES
6 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 460 | 0.4 | 0.28 | YES
7 | ADH1C | ADH1C | ADH1C | 548 | 0.38 | 0.32 | YES
8 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 588 | 0.37 | 0.35 | YES
9 | MGST1 | MGST1 | MGST1 | 684 | 0.35 | 0.38 | YES
10 | GSTM2 | GSTM2 | GSTM2 | 829 | 0.32 | 0.41 | YES
11 | CYP2C18 | CYP2C18 | CYP2C18 | 959 | 0.3 | 0.43 | YES
12 | UGT1A1 | UGT1A1 | UGT1A1 | 1002 | 0.29 | 0.46 | YES
13 | UGT1A6 | UGT1A6 | UGT1A6 | 1070 | 0.28 | 0.48 | YES
14 | UGT1A10 | UGT1A10 | UGT1A10 | 1165 | 0.27 | 0.51 | YES
15 | FMO4 | FMO4 | FMO4 | 1200 | 0.26 | 0.53 | YES
16 | GSTA4 | GSTA4 | GSTA4 | 1548 | 0.23 | 0.54 | YES
17 | UGT1A8 | UGT1A8 | UGT1A8 | 1566 | 0.23 | 0.56 | YES
18 | UGT2A1 | UGT2A1 | UGT2A1 | 1655 | 0.22 | 0.58 | YES
19 | GSTO2 | GSTO2 | GSTO2 | 1721 | 0.21 | 0.59 | YES
20 | GSTM3 | GSTM3 | GSTM3 | 1727 | 0.21 | 0.62 | YES
21 | GSTM4 | GSTM4 | GSTM4 | 2247 | 0.17 | 0.6 | YES
22 | GSTM1 | GSTM1 | GSTM1 | 2307 | 0.17 | 0.62 | YES
23 | CYP2C9 | CYP2C9 | CYP2C9 | 2951 | 0.13 | 0.6 | YES
24 | CYP3A7 | CYP3A7 | CYP3A7 | 3004 | 0.13 | 0.61 | YES
25 | MGST2 | MGST2 | MGST2 | 3084 | 0.13 | 0.62 | YES
26 | FMO5 | FMO5 | FMO5 | 3161 | 0.12 | 0.63 | YES
27 | CYP2C8 | CYP2C8 | CYP2C8 | 3301 | 0.12 | 0.63 | YES
28 | CYP2A7 | CYP2A7 | CYP2A7 | 3435 | 0.11 | 0.64 | YES
29 | CYP2A6 | CYP2A6 | CYP2A6 | 3513 | 0.11 | 0.64 | YES
30 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 3621 | 0.11 | 0.65 | YES
31 | CYP3A5 | CYP3A5 | CYP3A5 | 4271 | 0.089 | 0.62 | NO
32 | ADH1B | ADH1B | ADH1B | 4970 | 0.072 | 0.59 | NO
33 | MGST3 | MGST3 | MGST3 | 5017 | 0.071 | 0.6 | NO
34 | FMO1 | FMO1 | FMO1 | 5435 | 0.063 | 0.58 | NO
35 | CYP2D6 | CYP2D6 | CYP2D6 | 5457 | 0.062 | 0.58 | NO
36 | GSTK1 | GSTK1 | GSTK1 | 6437 | 0.045 | 0.53 | NO
37 | GSTP1 | GSTP1 | GSTP1 | 6496 | 0.044 | 0.54 | NO
38 | GSTT1 | GSTT1 | GSTT1 | 6561 | 0.043 | 0.54 | NO
39 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 7541 | 0.029 | 0.48 | NO
40 | CYP2A13 | CYP2A13 | CYP2A13 | 8524 | 0.016 | 0.43 | NO
41 | GSTA1 | GSTA1 | GSTA1 | 10249 | -0.0054 | 0.34 | NO
42 | CYP3A4 | CYP3A4 | CYP3A4 | 11305 | -0.019 | 0.28 | NO
43 | ADH5 | ADH5 | ADH5 | 11306 | -0.019 | 0.28 | NO
44 | GSTO1 | GSTO1 | GSTO1 | 11413 | -0.021 | 0.28 | NO
45 | FMO3 | FMO3 | FMO3 | 11869 | -0.027 | 0.26 | NO
46 | ADH6 | ADH6 | ADH6 | 12001 | -0.029 | 0.25 | NO
47 | CYP3A43 | CYP3A43 | CYP3A43 | 13347 | -0.053 | 0.18 | NO
48 | GSTM5 | GSTM5 | GSTM5 | 13556 | -0.058 | 0.18 | NO
49 | CYP1A2 | CYP1A2 | CYP1A2 | 13661 | -0.06 | 0.18 | NO
50 | GSTT2 | GSTT2 | GSTT2 | 14021 | -0.07 | 0.17 | NO
51 | FMO2 | FMO2 | FMO2 | 14283 | -0.077 | 0.16 | NO
52 | GSTA2 | GSTA2 | GSTA2 | 14846 | -0.095 | 0.14 | NO
53 | ADH4 | ADH4 | ADH4 | 15310 | -0.11 | 0.13 | NO
54 | ADH1A | ADH1A | ADH1A | 15866 | -0.14 | 0.11 | NO
55 | GSTZ1 | GSTZ1 | GSTZ1 | 16426 | -0.18 | 0.097 | 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 STARCH AND SUCROSE METABOLISM.

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

genes ES table in pathway: KEGG PYRUVATE METABOLISM

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 | AP1M2 | AP1M2 | AP1M2 | 525 | 0.38 | 0.086 | YES
2 | TBC1D8B | TBC1D8B | TBC1D8B | 1048 | 0.28 | 0.14 | YES
3 | TPD52 | TPD52 | TPD52 | 1348 | 0.25 | 0.2 | YES
4 | SORT1 | SORT1 | SORT1 | 2910 | 0.14 | 0.15 | YES
5 | TPD52L1 | TPD52L1 | TPD52L1 | 3408 | 0.12 | 0.16 | YES
6 | TFRC | TFRC | TFRC | 3635 | 0.11 | 0.18 | YES
7 | SH3D19 | SH3D19 | SH3D19 | 3719 | 0.1 | 0.21 | YES
8 | DNASE2 | DNASE2 | DNASE2 | 3726 | 0.1 | 0.24 | YES
9 | AP4E1 | AP4E1 | AP4E1 | 3989 | 0.098 | 0.25 | YES
10 | AP3S1 | AP3S1 | AP3S1 | 4013 | 0.097 | 0.28 | YES
11 | AP3B1 | AP3B1 | AP3B1 | 4391 | 0.086 | 0.29 | YES
12 | CPD | CPD | CPD | 4804 | 0.076 | 0.29 | YES
13 | AP1S1 | AP1S1 | AP1S1 | 5480 | 0.062 | 0.27 | YES
14 | ARF1 | ARF1 | ARF1 | 5500 | 0.062 | 0.28 | YES
15 | ARRB1 | ARRB1 | ARRB1 | 5789 | 0.056 | 0.28 | YES
16 | PIK3C2A | PIK3C2A | PIK3C2A | 5798 | 0.056 | 0.3 | YES
17 | STX4 | STX4 | STX4 | 6018 | 0.052 | 0.3 | YES
18 | SNX9 | SNX9 | SNX9 | 6124 | 0.05 | 0.31 | YES
19 | VAMP7 | VAMP7 | VAMP7 | 6178 | 0.049 | 0.33 | YES
20 | BLOC1S1 | BLOC1S1 | BLOC1S1 | 6247 | 0.048 | 0.34 | YES
21 | VAMP8 | VAMP8 | VAMP8 | 6458 | 0.045 | 0.34 | YES
22 | DNAJC6 | DNAJC6 | DNAJC6 | 6825 | 0.039 | 0.33 | YES
23 | SNAPIN | SNAPIN | SNAPIN | 6847 | 0.039 | 0.34 | YES
24 | YIPF6 | YIPF6 | YIPF6 | 7013 | 0.036 | 0.34 | YES
25 | SNAP23 | SNAP23 | SNAP23 | 7508 | 0.029 | 0.32 | NO
26 | SNX2 | SNX2 | SNX2 | 7588 | 0.028 | 0.33 | NO
27 | PUM1 | PUM1 | PUM1 | 7799 | 0.026 | 0.32 | NO
28 | BLOC1S3 | BLOC1S3 | BLOC1S3 | 7939 | 0.024 | 0.32 | NO
29 | AP1M1 | AP1M1 | AP1M1 | 8705 | 0.014 | 0.28 | NO
30 | OCRL | OCRL | OCRL | 8777 | 0.013 | 0.28 | NO
31 | HSPA8 | HSPA8 | HSPA8 | 8827 | 0.012 | 0.29 | NO
32 | AP4B1 | AP4B1 | AP4B1 | 9020 | 0.0099 | 0.28 | NO
33 | NAPA | NAPA | NAPA | 9098 | 0.0088 | 0.28 | NO
34 | FTH1 | FTH1 | FTH1 | 9164 | 0.008 | 0.28 | NO
35 | DNM2 | DNM2 | DNM2 | 9331 | 0.0061 | 0.27 | NO
36 | AP1G1 | AP1G1 | AP1G1 | 9458 | 0.0044 | 0.26 | NO
37 | PLDN | PLDN | PLDN | 9493 | 0.004 | 0.26 | NO
38 | PICALM | PICALM | PICALM | 9530 | 0.0037 | 0.26 | NO
39 | RAB5C | RAB5C | RAB5C | 9583 | 0.0031 | 0.26 | NO
40 | DTNBP1 | DTNBP1 | DTNBP1 | 9684 | 0.0019 | 0.25 | NO
41 | TXNDC5 | TXNDC5 | TXNDC5 | 9693 | 0.0017 | 0.25 | NO
42 | TGOLN2 | TGOLN2 | TGOLN2 | 9983 | -0.0019 | 0.24 | NO
43 | CNO | CNO | CNO | 10402 | -0.0072 | 0.22 | NO
44 | CLTC | CLTC | CLTC | 10423 | -0.0076 | 0.22 | NO
45 | GNS | GNS | GNS | 10479 | -0.0083 | 0.22 | NO
46 | SNX5 | SNX5 | SNX5 | 10612 | -0.01 | 0.21 | NO
47 | VAMP2 | VAMP2 | VAMP2 | 10757 | -0.012 | 0.21 | NO
48 | GAK | GAK | GAK | 10964 | -0.015 | 0.2 | NO
49 | IGF2R | IGF2R | IGF2R | 11092 | -0.016 | 0.2 | NO
50 | NECAP1 | NECAP1 | NECAP1 | 11165 | -0.017 | 0.2 | NO
51 | CTSZ | CTSZ | CTSZ | 12232 | -0.033 | 0.15 | NO
52 | GBF1 | GBF1 | GBF1 | 12340 | -0.034 | 0.16 | NO
53 | AP1S2 | AP1S2 | AP1S2 | 12431 | -0.036 | 0.16 | NO
54 | CLTA | CLTA | CLTA | 12802 | -0.042 | 0.16 | NO
55 | AP1B1 | AP1B1 | AP1B1 | 12830 | -0.043 | 0.17 | NO
56 | FTL | FTL | FTL | 13755 | -0.062 | 0.13 | NO
57 | M6PR | M6PR | M6PR | 13940 | -0.068 | 0.14 | NO
58 | HIP1R | HIP1R | HIP1R | 13979 | -0.069 | 0.16 | NO
59 | SH3GL2 | SH3GL2 | SH3GL2 | 17092 | -0.23 | 0.061 | 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 PYRUVATE METABOLISM.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRUVATE 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 PROPANOATE METABOLISM

Table S16. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | AOX1 | AOX1 | AOX1 | 103 | 0.59 | 0.14 | YES
2 | EHHADH | EHHADH | EHHADH | 388 | 0.43 | 0.22 | YES
3 | AUH | AUH | AUH | 1313 | 0.25 | 0.23 | YES
4 | ACADSB | ACADSB | ACADSB | 1493 | 0.23 | 0.28 | YES
5 | BCKDHB | BCKDHB | BCKDHB | 1599 | 0.22 | 0.33 | YES
6 | HIBCH | HIBCH | HIBCH | 2063 | 0.18 | 0.35 | YES
7 | BCAT1 | BCAT1 | BCAT1 | 3296 | 0.12 | 0.31 | YES
8 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3331 | 0.12 | 0.34 | YES
9 | PCCA | PCCA | PCCA | 3607 | 0.11 | 0.35 | YES
10 | ACAT1 | ACAT1 | ACAT1 | 3741 | 0.1 | 0.36 | YES
11 | HIBADH | HIBADH | HIBADH | 3903 | 0.1 | 0.38 | YES
12 | ACAD8 | ACAD8 | ACAD8 | 3917 | 0.1 | 0.4 | YES
13 | MCEE | MCEE | MCEE | 3969 | 0.098 | 0.42 | YES
14 | ABAT | ABAT | ABAT | 4406 | 0.086 | 0.42 | YES
15 | OXCT1 | OXCT1 | OXCT1 | 4461 | 0.084 | 0.44 | YES
16 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 4876 | 0.074 | 0.43 | YES
17 | HADH | HADH | HADH | 5258 | 0.066 | 0.43 | YES
18 | MUT | MUT | MUT | 5568 | 0.06 | 0.42 | YES
19 | ACAA2 | ACAA2 | ACAA2 | 5778 | 0.056 | 0.43 | YES
20 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6005 | 0.052 | 0.43 | YES
21 | HMGCS1 | HMGCS1 | HMGCS1 | 6017 | 0.052 | 0.44 | YES
22 | MCCC1 | MCCC1 | MCCC1 | 6273 | 0.048 | 0.44 | YES
23 | HSD17B10 | HSD17B10 | HSD17B10 | 6298 | 0.047 | 0.45 | YES
24 | DLD | DLD | DLD | 6347 | 0.046 | 0.46 | YES
25 | MCCC2 | MCCC2 | MCCC2 | 6373 | 0.046 | 0.46 | YES
26 | BCKDHA | BCKDHA | BCKDHA | 7426 | 0.03 | 0.41 | NO
27 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 7507 | 0.029 | 0.42 | NO
28 | DBT | DBT | DBT | 7630 | 0.028 | 0.42 | NO
29 | ALDH2 | ALDH2 | ALDH2 | 8041 | 0.022 | 0.4 | NO
30 | HMGCL | HMGCL | HMGCL | 9040 | 0.0096 | 0.35 | NO
31 | ACAA1 | ACAA1 | ACAA1 | 9448 | 0.0046 | 0.32 | NO
32 | ACADM | ACADM | ACADM | 9704 | 0.0016 | 0.31 | NO
33 | BCAT2 | BCAT2 | BCAT2 | 10570 | -0.0095 | 0.27 | NO
34 | HADHB | HADHB | HADHB | 10881 | -0.014 | 0.25 | NO
35 | HADHA | HADHA | HADHA | 11168 | -0.017 | 0.24 | NO
36 | PCCB | PCCB | PCCB | 11191 | -0.018 | 0.24 | NO
37 | ACADS | ACADS | ACADS | 11374 | -0.02 | 0.24 | NO
38 | IL4I1 | IL4I1 | IL4I1 | 11749 | -0.025 | 0.22 | NO
39 | ECHS1 | ECHS1 | ECHS1 | 12207 | -0.032 | 0.21 | NO
40 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 13412 | -0.054 | 0.15 | NO
41 | IVD | IVD | IVD | 14260 | -0.076 | 0.12 | NO
42 | ACAT2 | ACAT2 | ACAT2 | 16363 | -0.17 | 0.051 | NO
43 | OXCT2 | OXCT2 | OXCT2 | 16806 | -0.21 | 0.076 | 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 PROPANOATE METABOLISM.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PROPANOATE 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 AMINOACYL TRNA BIOSYNTHESIS

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 | MAOA | MAOA | MAOA | 74 | 0.62 | 0.15 | YES
2 | MAOB | MAOB | MAOB | 271 | 0.47 | 0.26 | YES
3 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 460 | 0.4 | 0.35 | YES
4 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 588 | 0.37 | 0.44 | YES
5 | FTCD | FTCD | FTCD | 827 | 0.32 | 0.51 | YES
6 | HAL | HAL | HAL | 1887 | 0.2 | 0.5 | YES
7 | HEMK1 | HEMK1 | HEMK1 | 2014 | 0.19 | 0.54 | YES
8 | AMDHD1 | AMDHD1 | AMDHD1 | 2538 | 0.16 | 0.55 | YES
9 | HNMT | HNMT | HNMT | 3306 | 0.12 | 0.54 | YES
10 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3331 | 0.12 | 0.57 | YES
11 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 3621 | 0.11 | 0.58 | YES
12 | LCMT1 | LCMT1 | LCMT1 | 4058 | 0.096 | 0.58 | YES
13 | TRMT11 | TRMT11 | TRMT11 | 4291 | 0.089 | 0.59 | YES
14 | WBSCR22 | WBSCR22 | WBSCR22 | 4610 | 0.08 | 0.59 | YES
15 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 4876 | 0.074 | 0.6 | YES
16 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6005 | 0.052 | 0.55 | NO
17 | UROC1 | UROC1 | UROC1 | 6906 | 0.038 | 0.51 | NO
18 | METTL2B | METTL2B | METTL2B | 7081 | 0.035 | 0.51 | NO
19 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 7507 | 0.029 | 0.49 | NO
20 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 7541 | 0.029 | 0.5 | NO
21 | ALDH2 | ALDH2 | ALDH2 | 8041 | 0.022 | 0.47 | NO
22 | DDC | DDC | DDC | 8799 | 0.013 | 0.44 | NO
23 | HDC | HDC | HDC | 9501 | 0.0039 | 0.4 | NO
24 | LCMT2 | LCMT2 | LCMT2 | 10562 | -0.0094 | 0.34 | NO
25 | ACY3 | ACY3 | ACY3 | 11370 | -0.02 | 0.3 | NO
26 | CNDP1 | CNDP1 | CNDP1 | 12425 | -0.036 | 0.25 | NO
27 | METTL6 | METTL6 | METTL6 | 13169 | -0.049 | 0.22 | NO
28 | ABP1 | ABP1 | ABP1 | 14931 | -0.098 | 0.15 | NO
29 | ASPA | ASPA | ASPA | 15138 | -0.11 | 0.17 | 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 AMINOACYL TRNA BIOSYNTHESIS.

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

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

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 | UGT1A9 | UGT1A9 | UGT1A9 | 348 | 0.44 | 0.032 | YES
2 | CYP2S1 | CYP2S1 | CYP2S1 | 354 | 0.44 | 0.082 | YES
3 | CYP2E1 | CYP2E1 | CYP2E1 | 362 | 0.44 | 0.13 | YES
4 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 460 | 0.4 | 0.17 | YES
5 | ADH1C | ADH1C | ADH1C | 548 | 0.38 | 0.21 | YES
6 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 588 | 0.37 | 0.25 | YES
7 | MGST1 | MGST1 | MGST1 | 684 | 0.35 | 0.28 | YES
8 | GSTM2 | GSTM2 | GSTM2 | 829 | 0.32 | 0.31 | YES
9 | AKR1C2 | AKR1C2 | AKR1C2 | 905 | 0.3 | 0.34 | YES
10 | CYP2C18 | CYP2C18 | CYP2C18 | 959 | 0.3 | 0.38 | YES
11 | UGT1A1 | UGT1A1 | UGT1A1 | 1002 | 0.29 | 0.41 | YES
12 | UGT1A6 | UGT1A6 | UGT1A6 | 1070 | 0.28 | 0.44 | YES
13 | UGT1A10 | UGT1A10 | UGT1A10 | 1165 | 0.27 | 0.46 | YES
14 | GSTA4 | GSTA4 | GSTA4 | 1548 | 0.23 | 0.47 | YES
15 | UGT1A8 | UGT1A8 | UGT1A8 | 1566 | 0.23 | 0.49 | YES
16 | UGT2A1 | UGT2A1 | UGT2A1 | 1655 | 0.22 | 0.51 | YES
17 | GSTO2 | GSTO2 | GSTO2 | 1721 | 0.21 | 0.53 | YES
18 | GSTM3 | GSTM3 | GSTM3 | 1727 | 0.21 | 0.56 | YES
19 | AKR1C1 | AKR1C1 | AKR1C1 | 1955 | 0.19 | 0.57 | YES
20 | GSTM4 | GSTM4 | GSTM4 | 2247 | 0.17 | 0.57 | YES
21 | GSTM1 | GSTM1 | GSTM1 | 2307 | 0.17 | 0.59 | YES
22 | CYP2F1 | CYP2F1 | CYP2F1 | 2646 | 0.15 | 0.58 | YES
23 | CYP2C9 | CYP2C9 | CYP2C9 | 2951 | 0.13 | 0.58 | YES
24 | CYP3A7 | CYP3A7 | CYP3A7 | 3004 | 0.13 | 0.6 | YES
25 | MGST2 | MGST2 | MGST2 | 3084 | 0.13 | 0.61 | YES
26 | CYP2C8 | CYP2C8 | CYP2C8 | 3301 | 0.12 | 0.61 | YES
27 | AKR1C3 | AKR1C3 | AKR1C3 | 3550 | 0.11 | 0.61 | YES
28 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 3621 | 0.11 | 0.62 | YES
29 | CYP3A5 | CYP3A5 | CYP3A5 | 4271 | 0.089 | 0.59 | NO
30 | CYP1B1 | CYP1B1 | CYP1B1 | 4339 | 0.087 | 0.6 | NO
31 | EPHX1 | EPHX1 | EPHX1 | 4457 | 0.084 | 0.6 | NO
32 | ADH1B | ADH1B | ADH1B | 4970 | 0.072 | 0.58 | NO
33 | MGST3 | MGST3 | MGST3 | 5017 | 0.071 | 0.59 | NO
34 | GSTK1 | GSTK1 | GSTK1 | 6437 | 0.045 | 0.51 | NO
35 | GSTP1 | GSTP1 | GSTP1 | 6496 | 0.044 | 0.52 | NO
36 | GSTT1 | GSTT1 | GSTT1 | 6561 | 0.043 | 0.52 | NO
37 | CYP1A1 | CYP1A1 | CYP1A1 | 6777 | 0.04 | 0.51 | NO
38 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 7541 | 0.029 | 0.47 | NO
39 | GSTA1 | GSTA1 | GSTA1 | 10249 | -0.0054 | 0.32 | NO
40 | CYP3A4 | CYP3A4 | CYP3A4 | 11305 | -0.019 | 0.27 | NO
41 | ADH5 | ADH5 | ADH5 | 11306 | -0.019 | 0.27 | NO
42 | GSTO1 | GSTO1 | GSTO1 | 11413 | -0.021 | 0.26 | NO
43 | ADH6 | ADH6 | ADH6 | 12001 | -0.029 | 0.24 | NO
44 | CYP3A43 | CYP3A43 | CYP3A43 | 13347 | -0.053 | 0.17 | NO
45 | GSTM5 | GSTM5 | GSTM5 | 13556 | -0.058 | 0.16 | NO
46 | CYP1A2 | CYP1A2 | CYP1A2 | 13661 | -0.06 | 0.16 | NO
47 | GSTT2 | GSTT2 | GSTT2 | 14021 | -0.07 | 0.15 | NO
48 | GSTA2 | GSTA2 | GSTA2 | 14846 | -0.095 | 0.12 | NO
49 | ADH4 | ADH4 | ADH4 | 15310 | -0.11 | 0.1 | NO
50 | ADH1A | ADH1A | ADH1A | 15866 | -0.14 | 0.09 | NO
51 | DHDH | DHDH | DHDH | 16142 | -0.16 | 0.093 | NO
52 | GSTZ1 | GSTZ1 | GSTZ1 | 16426 | -0.18 | 0.097 | 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 METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG DRUG METABOLISM CYTOCHROME P450

Table 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 | UGT1A9 | UGT1A9 | UGT1A9 | 348 | 0.44 | 0.077 | YES
2 | MGAM | MGAM | MGAM | 445 | 0.41 | 0.16 | YES
3 | GCK | GCK | GCK | 877 | 0.31 | 0.2 | YES
4 | UGT1A1 | UGT1A1 | UGT1A1 | 1002 | 0.29 | 0.26 | YES
5 | PYGM | PYGM | PYGM | 1036 | 0.29 | 0.32 | YES
6 | UGT1A6 | UGT1A6 | UGT1A6 | 1070 | 0.28 | 0.38 | YES
7 | UGT1A10 | UGT1A10 | UGT1A10 | 1165 | 0.27 | 0.44 | YES
8 | AMY2B | AMY2B | AMY2B | 1272 | 0.26 | 0.48 | YES
9 | UGT1A8 | UGT1A8 | UGT1A8 | 1566 | 0.23 | 0.52 | YES
10 | UGT2A1 | UGT2A1 | UGT2A1 | 1655 | 0.22 | 0.56 | YES
11 | GBA3 | GBA3 | GBA3 | 2083 | 0.18 | 0.58 | YES
12 | ENPP1 | ENPP1 | ENPP1 | 2684 | 0.15 | 0.58 | NO
13 | AGL | AGL | AGL | 5027 | 0.071 | 0.46 | NO
14 | AMY1A | AMY1A | AMY1A | 5586 | 0.06 | 0.45 | NO
15 | GPI | GPI | GPI | 6248 | 0.048 | 0.42 | NO
16 | GBE1 | GBE1 | GBE1 | 6733 | 0.041 | 0.4 | NO
17 | UGP2 | UGP2 | UGP2 | 7545 | 0.029 | 0.36 | NO
18 | PGM2 | PGM2 | PGM2 | 7757 | 0.026 | 0.36 | NO
19 | UXS1 | UXS1 | UXS1 | 7760 | 0.026 | 0.36 | NO
20 | GUSB | GUSB | GUSB | 7811 | 0.026 | 0.37 | NO
21 | AMY2A | AMY2A | AMY2A | 7882 | 0.025 | 0.37 | NO
22 | HK2 | HK2 | HK2 | 8075 | 0.022 | 0.36 | NO
23 | GYS2 | GYS2 | GYS2 | 8765 | 0.013 | 0.33 | NO
24 | GAA | GAA | GAA | 10412 | -0.0074 | 0.24 | NO
25 | PYGB | PYGB | PYGB | 12294 | -0.034 | 0.14 | NO
26 | ENPP3 | ENPP3 | ENPP3 | 12591 | -0.038 | 0.13 | NO
27 | UGDH | UGDH | UGDH | 12708 | -0.04 | 0.14 | NO
28 | GYS1 | GYS1 | GYS1 | 13140 | -0.049 | 0.12 | NO
29 | PGM1 | PGM1 | PGM1 | 13562 | -0.058 | 0.11 | NO
30 | HK1 | HK1 | HK1 | 14246 | -0.076 | 0.091 | NO
31 | PYGL | PYGL | PYGL | 14349 | -0.08 | 0.1 | NO
32 | GANC | GANC | GANC | 14789 | -0.093 | 0.099 | NO
33 | TREH | TREH | TREH | 15320 | -0.11 | 0.094 | NO
34 | PGM2L1 | PGM2L1 | PGM2L1 | 15353 | -0.12 | 0.12 | NO
35 | HK3 | HK3 | HK3 | 16456 | -0.18 | 0.096 | 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 DRUG METABOLISM CYTOCHROME P450.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID NCADHERINPATHWAY

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 | LDHC | LDHC | LDHC | 48 | 0.66 | 0.19 | YES
2 | ACSS3 | ACSS3 | ACSS3 | 184 | 0.51 | 0.33 | YES
3 | EHHADH | EHHADH | EHHADH | 388 | 0.43 | 0.44 | YES
4 | LDHAL6A | LDHAL6A | LDHAL6A | 1647 | 0.22 | 0.43 | YES
5 | HIBCH | HIBCH | HIBCH | 2063 | 0.18 | 0.46 | YES
6 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3331 | 0.12 | 0.42 | YES
7 | PCCA | PCCA | PCCA | 3607 | 0.11 | 0.44 | YES
8 | ACAT1 | ACAT1 | ACAT1 | 3741 | 0.1 | 0.46 | YES
9 | MCEE | MCEE | MCEE | 3969 | 0.098 | 0.48 | YES
10 | ABAT | ABAT | ABAT | 4406 | 0.086 | 0.48 | YES
11 | SUCLA2 | SUCLA2 | SUCLA2 | 4671 | 0.079 | 0.49 | YES
12 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 4876 | 0.074 | 0.5 | YES
13 | MUT | MUT | MUT | 5568 | 0.06 | 0.48 | YES
14 | ACACA | ACACA | ACACA | 5966 | 0.053 | 0.47 | YES
15 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6005 | 0.052 | 0.48 | YES
16 | MLYCD | MLYCD | MLYCD | 6052 | 0.052 | 0.5 | YES
17 | SUCLG2 | SUCLG2 | SUCLG2 | 6098 | 0.051 | 0.51 | YES
18 | SUCLG1 | SUCLG1 | SUCLG1 | 6787 | 0.04 | 0.48 | NO
19 | ACSS2 | ACSS2 | ACSS2 | 6917 | 0.038 | 0.48 | NO
20 | LDHA | LDHA | LDHA | 6964 | 0.037 | 0.49 | NO
21 | ACSS1 | ACSS1 | ACSS1 | 7036 | 0.036 | 0.5 | NO
22 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 7507 | 0.029 | 0.48 | NO
23 | ALDH2 | ALDH2 | ALDH2 | 8041 | 0.022 | 0.46 | NO
24 | LDHB | LDHB | LDHB | 9091 | 0.009 | 0.4 | NO
25 | ACADM | ACADM | ACADM | 9704 | 0.0016 | 0.37 | NO
26 | ACACB | ACACB | ACACB | 10596 | -0.0099 | 0.32 | NO
27 | HADHA | HADHA | HADHA | 11168 | -0.017 | 0.3 | NO
28 | PCCB | PCCB | PCCB | 11191 | -0.018 | 0.3 | NO
29 | LDHAL6B | LDHAL6B | LDHAL6B | 12189 | -0.032 | 0.26 | NO
30 | ECHS1 | ECHS1 | ECHS1 | 12207 | -0.032 | 0.26 | NO
31 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 13412 | -0.054 | 0.21 | NO
32 | ACAT2 | ACAT2 | ACAT2 | 16363 | -0.17 | 0.1 | NO

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

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: PID NCADHERINPATHWAY, 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
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
KEGG PROTEASOME | 43 | genes.ES.table | 0.58 | 1.6 | 0.074 | 0.18 | 0.9 | 0.79 | 0.37 | 0.5 | 0.1 | 0.021
KEGG CHEMOKINE SIGNALING PATHWAY | 186 | genes.ES.table | 0.57 | 1.6 | 0.029 | 0.19 | 0.85 | 0.48 | 0.2 | 0.39 | 0.092 | 0.03
KEGG CELL CYCLE | 118 | genes.ES.table | 0.48 | 1.7 | 0.049 | 0.2 | 0.76 | 0.4 | 0.27 | 0.29 | 0.082 | 0.043
KEGG APOPTOSIS | 84 | genes.ES.table | 0.47 | 1.7 | 0.021 | 0.2 | 0.8 | 0.32 | 0.23 | 0.25 | 0.086 | 0.04
KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY | 89 | genes.ES.table | 0.56 | 1.7 | 0.037 | 0.19 | 0.84 | 0.29 | 0.14 | 0.25 | 0.095 | 0.035
KEGG CYTOSOLIC DNA SENSING PATHWAY | 42 | genes.ES.table | 0.6 | 1.7 | 0.046 | 0.19 | 0.84 | 0.19 | 0.053 | 0.18 | 0.095 | 0.035
KEGG HEMATOPOIETIC CELL LINEAGE | 79 | genes.ES.table | 0.67 | 1.6 | 0.023 | 0.2 | 0.95 | 0.65 | 0.15 | 0.55 | 0.12 | 0.016
KEGG T CELL RECEPTOR SIGNALING PATHWAY | 105 | genes.ES.table | 0.59 | 1.6 | 0.036 | 0.19 | 0.88 | 0.42 | 0.2 | 0.34 | 0.097 | 0.023
KEGG B CELL RECEPTOR SIGNALING PATHWAY | 74 | genes.ES.table | 0.57 | 1.7 | 0.025 | 0.22 | 0.75 | 0.42 | 0.2 | 0.34 | 0.089 | 0.047
KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS | 94 | genes.ES.table | 0.45 | 1.7 | 0.026 | 0.2 | 0.83 | 0.42 | 0.21 | 0.33 | 0.093 | 0.037

genes ES table in pathway: KEGG PROTEASOME

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 | CD28 | CD28 | CD28 | 272 | 0.48 | 0.018 | YES
2 | LCK | LCK | LCK | 274 | 0.48 | 0.052 | YES
3 | CD8B | CD8B | CD8B | 313 | 0.46 | 0.082 | YES
4 | CD247 | CD247 | CD247 | 594 | 0.39 | 0.094 | YES
5 | HMGA1 | HMGA1 | HMGA1 | 689 | 0.37 | 0.12 | YES
6 | CCR5 | CCR5 | CCR5 | 976 | 0.33 | 0.12 | YES
7 | HCK | HCK | HCK | 1102 | 0.31 | 0.14 | YES
8 | TAF13 | TAF13 | TAF13 | 1137 | 0.31 | 0.16 | YES
9 | AP1S2 | AP1S2 | AP1S2 | 1339 | 0.28 | 0.17 | YES
10 | DOCK2 | DOCK2 | DOCK2 | 1348 | 0.28 | 0.18 | YES
11 | GTF2A1 | GTF2A1 | GTF2A1 | 1824 | 0.23 | 0.18 | YES
12 | CD4 | CD4 | CD4 | 1859 | 0.23 | 0.19 | YES
13 | ELMO1 | ELMO1 | ELMO1 | 1860 | 0.23 | 0.21 | YES
14 | APOBEC3G | APOBEC3G | APOBEC3G | 1861 | 0.23 | 0.22 | YES
15 | NMT2 | NMT2 | NMT2 | 1908 | 0.23 | 0.24 | YES
16 | RCC1 | RCC1 | RCC1 | 2314 | 0.19 | 0.23 | YES
17 | PSME4 | PSME4 | PSME4 | 2414 | 0.18 | 0.23 | YES
18 | GTF2H2 | GTF2H2 | GTF2H2 | 2661 | 0.17 | 0.23 | YES
19 | CXCR4 | CXCR4 | CXCR4 | 2816 | 0.16 | 0.23 | YES
20 | PAK2 | PAK2 | PAK2 | 3574 | 0.12 | 0.2 | YES
21 | NUP93 | NUP93 | NUP93 | 3627 | 0.11 | 0.21 | YES
22 | AP1B1 | AP1B1 | AP1B1 | 3780 | 0.11 | 0.2 | YES
23 | AP2S1 | AP2S1 | AP2S1 | 3841 | 0.11 | 0.21 | YES
24 | RANGAP1 | RANGAP1 | RANGAP1 | 3873 | 0.1 | 0.22 | YES
25 | VPS37A | VPS37A | VPS37A | 3908 | 0.1 | 0.22 | YES
26 | PSMA5 | PSMA5 | PSMA5 | 3922 | 0.1 | 0.23 | YES
27 | PSMA6 | PSMA6 | PSMA6 | 3951 | 0.1 | 0.23 | YES
28 | PSME2 | PSME2 | PSME2 | 3958 | 0.1 | 0.24 | YES
29 | FEN1 | FEN1 | FEN1 | 3985 | 0.1 | 0.24 | YES
30 | NUP188 | NUP188 | NUP188 | 3998 | 0.1 | 0.25 | YES
31 | RANBP1 | RANBP1 | RANBP1 | 4051 | 0.098 | 0.26 | YES
32 | PSMA8 | PSMA8 | PSMA8 | 4074 | 0.097 | 0.26 | YES
33 | PSMA3 | PSMA3 | PSMA3 | 4102 | 0.096 | 0.27 | YES
34 | NUP155 | NUP155 | NUP155 | 4155 | 0.093 | 0.27 | YES
35 | TAF5 | TAF5 | TAF5 | 4211 | 0.092 | 0.27 | YES
36 | NUP50 | NUP50 | NUP50 | 4222 | 0.092 | 0.28 | YES
37 | PSMD11 | PSMD11 | PSMD11 | 4237 | 0.091 | 0.28 | YES
38 | KPNB1 | KPNB1 | KPNB1 | 4249 | 0.091 | 0.29 | YES
39 | RNGTT | RNGTT | RNGTT | 4333 | 0.088 | 0.29 | YES
40 | ERCC2 | ERCC2 | ERCC2 | 4390 | 0.087 | 0.3 | YES
41 | NUP205 | NUP205 | NUP205 | 4488 | 0.083 | 0.3 | YES
42 | LIG4 | LIG4 | LIG4 | 4489 | 0.083 | 0.3 | YES
43 | PSMD12 | PSMD12 | PSMD12 | 4502 | 0.083 | 0.31 | YES
44 | PSMB10 | PSMB10 | PSMB10 | 4534 | 0.082 | 0.31 | YES
45 | B2M | B2M | B2M | 4536 | 0.082 | 0.32 | YES
46 | PSMC4 | PSMC4 | PSMC4 | 4681 | 0.077 | 0.31 | YES
47 | SLC25A5 | SLC25A5 | SLC25A5 | 4731 | 0.076 | 0.32 | YES
48 | TAF9 | TAF9 | TAF9 | 4761 | 0.075 | 0.32 | YES
49 | PSMC6 | PSMC6 | PSMC6 | 4795 | 0.074 | 0.32 | YES
50 | GTF2E1 | GTF2E1 | GTF2E1 | 4824 | 0.073 | 0.33 | YES
51 | PSMD2 | PSMD2 | PSMD2 | 4832 | 0.073 | 0.33 | YES
52 | PSMD13 | PSMD13 | PSMD13 | 4905 | 0.071 | 0.33 | YES
53 | PSMB5 | PSMB5 | PSMB5 | 5000 | 0.068 | 0.33 | YES
54 | NUPL1 | NUPL1 | NUPL1 | 5012 | 0.068 | 0.34 | YES
55 | PSMA7 | PSMA7 | PSMA7 | 5032 | 0.067 | 0.34 | YES
56 | CCNT1 | CCNT1 | CCNT1 | 5067 | 0.066 | 0.34 | YES
57 | NUP153 | NUP153 | NUP153 | 5081 | 0.066 | 0.35 | YES
58 | TAF12 | TAF12 | TAF12 | 5134 | 0.064 | 0.35 | YES
59 | POLR2D | POLR2D | POLR2D | 5146 | 0.064 | 0.35 | YES
60 | PSMD14 | PSMD14 | PSMD14 | 5185 | 0.063 | 0.35 | YES
61 | PSMC1 | PSMC1 | PSMC1 | 5192 | 0.063 | 0.36 | YES
62 | GTF2H3 | GTF2H3 | GTF2H3 | 5321 | 0.06 | 0.36 | YES
63 | PSMB9 | PSMB9 | PSMB9 | 5349 | 0.059 | 0.36 | YES
64 | GTF2E2 | GTF2E2 | GTF2E2 | 5387 | 0.058 | 0.36 | YES
65 | TCEB3 | TCEB3 | TCEB3 | 5495 | 0.056 | 0.36 | YES
66 | CTDP1 | CTDP1 | CTDP1 | 5540 | 0.055 | 0.36 | YES
67 | PSMF1 | PSMF1 | PSMF1 | 5544 | 0.054 | 0.36 | YES
68 | RBX1 | RBX1 | RBX1 | 5551 | 0.054 | 0.37 | YES
69 | SUPT16H | SUPT16H | SUPT16H | 5557 | 0.054 | 0.37 | YES
70 | PSMB6 | PSMB6 | PSMB6 | 5588 | 0.054 | 0.37 | YES
71 | NUP62 | NUP62 | NUP62 | 5617 | 0.053 | 0.38 | YES
72 | HLA-A | HLA-A | HLA-A | 5675 | 0.052 | 0.38 | YES
73 | PSMD7 | PSMD7 | PSMD7 | 5687 | 0.052 | 0.38 | YES
74 | PSMD6 | PSMD6 | PSMD6 | 5692 | 0.052 | 0.38 | YES
75 | RAN | RAN | RAN | 5716 | 0.051 | 0.38 | YES
76 | NCBP1 | NCBP1 | NCBP1 | 5733 | 0.051 | 0.39 | YES
77 | XRCC6 | XRCC6 | XRCC6 | 5741 | 0.051 | 0.39 | YES
78 | TCEB1 | TCEB1 | TCEB1 | 5758 | 0.051 | 0.39 | YES
79 | KPNA1 | KPNA1 | KPNA1 | 5792 | 0.05 | 0.39 | YES
80 | NUP54 | NUP54 | NUP54 | 5826 | 0.049 | 0.4 | YES
81 | PSMD1 | PSMD1 | PSMD1 | 5884 | 0.048 | 0.4 | YES
82 | LIG1 | LIG1 | LIG1 | 5896 | 0.048 | 0.4 | YES
83 | RANBP2 | RANBP2 | RANBP2 | 5906 | 0.047 | 0.4 | YES
84 | AP2A2 | AP2A2 | AP2A2 | 5937 | 0.046 | 0.4 | YES
85 | PSMB3 | PSMB3 | PSMB3 | 5953 | 0.046 | 0.41 | YES
86 | PSMB2 | PSMB2 | PSMB2 | 6010 | 0.045 | 0.41 | YES
87 | POLR2F | POLR2F | POLR2F | 6074 | 0.043 | 0.4 | YES
88 | PSMD8 | PSMD8 | PSMD8 | 6101 | 0.043 | 0.41 | YES
89 | PSMD3 | PSMD3 | PSMD3 | 6211 | 0.04 | 0.4 | NO
90 | CDK7 | CDK7 | CDK7 | 6324 | 0.038 | 0.4 | NO
91 | GTF2H2B | GTF2H2B | GTF2H2B | 6391 | 0.037 | 0.4 | NO
92 | GTF2B | GTF2B | GTF2B | 6421 | 0.036 | 0.4 | NO
93 | NUP37 | NUP37 | NUP37 | 6437 | 0.036 | 0.4 | NO
94 | PACS1 | PACS1 | PACS1 | 6449 | 0.036 | 0.4 | NO
95 | PSME1 | PSME1 | PSME1 | 6462 | 0.036 | 0.4 | NO
96 | AP2A1 | AP2A1 | AP2A1 | 6544 | 0.034 | 0.4 | NO
97 | PSMD5 | PSMD5 | PSMD5 | 6566 | 0.033 | 0.4 | NO
98 | RAE1 | RAE1 | RAE1 | 6579 | 0.033 | 0.41 | NO
99 | PSMC3 | PSMC3 | PSMC3 | 6656 | 0.032 | 0.4 | NO
100 | SSRP1 | SSRP1 | SSRP1 | 6720 | 0.03 | 0.4 | NO
101 | PSMC2 | PSMC2 | PSMC2 | 6762 | 0.03 | 0.4 | NO
102 | PSMA1 | PSMA1 | PSMA1 | 6806 | 0.029 | 0.4 | NO
103 | GTF2H4 | GTF2H4 | GTF2H4 | 6940 | 0.026 | 0.4 | NO
104 | PSMD9 | PSMD9 | PSMD9 | 6960 | 0.026 | 0.4 | NO
105 | PSMA2 | PSMA2 | PSMA2 | 6996 | 0.025 | 0.4 | NO
106 | AP2M1 | AP2M1 | AP2M1 | 7009 | 0.025 | 0.4 | NO
107 | PPIA | PPIA | PPIA | 7071 | 0.023 | 0.4 | NO
108 | POLR2B | POLR2B | POLR2B | 7102 | 0.023 | 0.4 | NO
109 | NUP107 | NUP107 | NUP107 | 7171 | 0.022 | 0.39 | NO
110 | PSMA4 | PSMA4 | PSMA4 | 7225 | 0.021 | 0.39 | NO
111 | TBP | TBP | TBP | 7246 | 0.02 | 0.39 | NO
112 | NUP88 | NUP88 | NUP88 | 7396 | 0.018 | 0.39 | NO
113 | NUP43 | NUP43 | NUP43 | 7437 | 0.018 | 0.38 | NO
114 | POLR2G | POLR2G | POLR2G | 7452 | 0.017 | 0.39 | NO
115 | VPS37B | VPS37B | VPS37B | 7487 | 0.017 | 0.38 | NO
116 | COBRA1 | COBRA1 | COBRA1 | 7525 | 0.016 | 0.38 | NO
117 | RDBP | RDBP | RDBP | 7578 | 0.015 | 0.38 | NO
118 | POLR2A | POLR2A | POLR2A | 7588 | 0.015 | 0.38 | NO
119 | TAF4B | TAF4B | TAF4B | 7650 | 0.014 | 0.38 | NO
120 | XRCC4 | XRCC4 | XRCC4 | 7691 | 0.013 | 0.38 | NO
121 | PSMB4 | PSMB4 | PSMB4 | 7726 | 0.012 | 0.38 | NO
122 | MNAT1 | MNAT1 | MNAT1 | 7769 | 0.012 | 0.38 | NO
123 | PSMC5 | PSMC5 | PSMC5 | 7862 | 0.0099 | 0.37 | NO
124 | RAC1 | RAC1 | RAC1 | 7867 | 0.0098 | 0.37 | NO
125 | SUPT4H1 | SUPT4H1 | SUPT4H1 | 7903 | 0.0094 | 0.37 | NO
126 | AP1S1 | AP1S1 | AP1S1 | 7940 | 0.0087 | 0.37 | NO
127 | AP2B1 | AP2B1 | AP2B1 | 7986 | 0.0079 | 0.37 | NO
128 | CCNH | CCNH | CCNH | 8008 | 0.0075 | 0.37 | NO
129 | PSMD4 | PSMD4 | PSMD4 | 8010 | 0.0075 | 0.37 | NO
130 | PSMB7 | PSMB7 | PSMB7 | 8065 | 0.0066 | 0.36 | NO
131 | POLR2K | POLR2K | POLR2K | 8142 | 0.0051 | 0.36 | NO
132 | XRCC5 | XRCC5 | XRCC5 | 8195 | 0.0042 | 0.36 | NO
133 | PSMB1 | PSMB1 | PSMB1 | 8237 | 0.0036 | 0.36 | NO
134 | GTF2H1 | GTF2H1 | GTF2H1 | 8310 | 0.0025 | 0.35 | NO
135 | ELL | ELL | ELL | 8383 | 0.001 | 0.35 | NO
136 | NUP85 | NUP85 | NUP85 | 8388 | 0.00095 | 0.35 | NO
137 | ARF1 | ARF1 | ARF1 | 8448 | -0.000096 | 0.34 | NO
138 | GTF2F2 | GTF2F2 | GTF2F2 | 8504 | -0.0011 | 0.34 | NO
139 | AP1G1 | AP1G1 | AP1G1 | 8523 | -0.0013 | 0.34 | NO
140 | TAF1 | TAF1 | TAF1 | 8591 | -0.0025 | 0.34 | NO
141 | BTRC | BTRC | BTRC | 8603 | -0.0027 | 0.34 | NO
142 | NPM1 | NPM1 | NPM1 | 8658 | -0.0035 | 0.34 | NO
143 | TAF11 | TAF11 | TAF11 | 8813 | -0.0061 | 0.33 | NO
144 | POLR2H | POLR2H | POLR2H | 8862 | -0.007 | 0.32 | NO
145 | PSIP1 | PSIP1 | PSIP1 | 9077 | -0.011 | 0.31 | NO
146 | FYN | FYN | FYN | 9108 | -0.011 | 0.31 | NO
147 | TSG101 | TSG101 | TSG101 | 9262 | -0.014 | 0.3 | NO
148 | XPO1 | XPO1 | XPO1 | 9287 | -0.014 | 0.3 | NO
149 | TAF6 | TAF6 | TAF6 | 9312 | -0.014 | 0.3 | NO
150 | SEH1L | SEH1L | SEH1L | 9323 | -0.015 | 0.3 | NO
151 | TCEA1 | TCEA1 | TCEA1 | 9352 | -0.015 | 0.3 | NO
152 | POLR2C | POLR2C | POLR2C | 9367 | -0.016 | 0.3 | NO
153 | SUPT5H | SUPT5H | SUPT5H | 9420 | -0.016 | 0.3 | NO
154 | NMT1 | NMT1 | NMT1 | 9438 | -0.017 | 0.3 | NO
155 | PSMB8 | PSMB8 | PSMB8 | 9607 | -0.019 | 0.3 | NO
156 | PSMD10 | PSMD10 | PSMD10 | 9808 | -0.023 | 0.29 | NO
157 | VPS37C | VPS37C | VPS37C | 9919 | -0.024 | 0.28 | NO
158 | BANF1 | BANF1 | BANF1 | 10009 | -0.026 | 0.28 | NO
159 | NUP214 | NUP214 | NUP214 | 10106 | -0.028 | 0.28 | NO
160 | AP1M1 | AP1M1 | AP1M1 | 10336 | -0.032 | 0.26 | NO
161 | NUP210 | NUP210 | NUP210 | 10432 | -0.033 | 0.26 | NO
162 | NCBP2 | NCBP2 | NCBP2 | 10433 | -0.033 | 0.26 | NO
163 | TH1L | TH1L | TH1L | 10533 | -0.035 | 0.26 | NO
164 | NUPL2 | NUPL2 | NUPL2 | 10576 | -0.036 | 0.26 | NO
165 | UBA52 | UBA52 | UBA52 | 10630 | -0.037 | 0.26 | NO
166 | SKP1 | SKP1 | SKP1 | 10847 | -0.041 | 0.25 | NO
167 | GTF2A2 | GTF2A2 | GTF2A2 | 10888 | -0.042 | 0.25 | NO
168 | TAF4 | TAF4 | TAF4 | 11204 | -0.049 | 0.24 | NO
169 | RPS27A | RPS27A | RPS27A | 11209 | -0.049 | 0.24 | NO
170 | POLR2L | POLR2L | POLR2L | 11223 | -0.049 | 0.24 | NO
171 | POLR2E | POLR2E | POLR2E | 11360 | -0.052 | 0.24 | NO
172 | AP1M2 | AP1M2 | AP1M2 | 11396 | -0.052 | 0.24 | NO
173 | CDK9 | CDK9 | CDK9 | 11499 | -0.055 | 0.24 | NO
174 | WHSC2 | WHSC2 | WHSC2 | 11556 | -0.056 | 0.24 | NO
175 | CCNT2 | CCNT2 | CCNT2 | 11589 | -0.057 | 0.24 | NO
176 | NUP133 | NUP133 | NUP133 | 11640 | -0.058 | 0.24 | NO
177 | POLR2J | POLR2J | POLR2J | 11714 | -0.06 | 0.24 | NO
178 | ERCC3 | ERCC3 | ERCC3 | 11728 | -0.06 | 0.25 | NO
179 | TAF10 | TAF10 | TAF10 | 11737 | -0.06 | 0.25 | NO
180 | TCEB2 | TCEB2 | TCEB2 | 11905 | -0.064 | 0.25 | NO
181 | CUL5 | CUL5 | CUL5 | 11947 | -0.065 | 0.25 | NO
182 | RNMT | RNMT | RNMT | 11976 | -0.066 | 0.25 | NO
183 | TPR | TPR | TPR | 12004 | -0.067 | 0.26 | NO
184 | POM121 | POM121 | POM121 | 12182 | -0.071 | 0.25 | NO
185 | VPS28 | VPS28 | VPS28 | 12323 | -0.075 | 0.25 | NO
186 | ATP6V1H | ATP6V1H | ATP6V1H | 12368 | -0.076 | 0.25 | NO
187 | NUP35 | NUP35 | NUP35 | 12461 | -0.079 | 0.25 | NO
188 | AAAS | AAAS | AAAS | 12969 | -0.093 | 0.23 | NO
189 | GTF2F1 | GTF2F1 | GTF2F1 | 13123 | -0.097 | 0.23 | NO
190 | POLR2I | POLR2I | POLR2I | 13263 | -0.1 | 0.23 | NO
191 | SLC25A6 | SLC25A6 | SLC25A6 | 13760 | -0.12 | 0.21 | NO
192 | SLC25A4 | SLC25A4 | SLC25A4 | 15264 | -0.2 | 0.14 | NO
193 | VPS37D | VPS37D | VPS37D | 16677 | -0.33 | 0.084 | NO

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

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

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

Table 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 | AURKA | AURKA | AURKA | 623 | 0.39 | 0.055 | YES
2 | SNAI1 | SNAI1 | SNAI1 | 773 | 0.36 | 0.13 | YES
3 | PPP1R14A | PPP1R14A | PPP1R14A | 967 | 0.33 | 0.2 | YES
4 | ACTN1 | ACTN1 | ACTN1 | 1519 | 0.26 | 0.22 | YES
5 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 1723 | 0.24 | 0.27 | YES
6 | PARVG | PARVG | PARVG | 2080 | 0.21 | 0.3 | YES
7 | LIMS1 | LIMS1 | LIMS1 | 2117 | 0.21 | 0.34 | YES
8 | PARVB | PARVB | PARVB | 2924 | 0.15 | 0.33 | YES
9 | TACC3 | TACC3 | TACC3 | 2953 | 0.15 | 0.37 | YES
10 | LIMS2 | LIMS2 | LIMS2 | 3094 | 0.14 | 0.39 | YES
11 | PXN | PXN | PXN | 3200 | 0.14 | 0.42 | YES
12 | MYL9 | MYL9 | MYL9 | 3433 | 0.12 | 0.43 | YES
13 | RHOG | RHOG | RHOG | 3476 | 0.12 | 0.46 | YES
14 | ZEB1 | ZEB1 | ZEB1 | 3847 | 0.11 | 0.46 | YES
15 | CCND1 | CCND1 | CCND1 | 3857 | 0.1 | 0.49 | YES
16 | ELMO2 | ELMO2 | ELMO2 | 4359 | 0.087 | 0.48 | YES
17 | CTNNB1 | CTNNB1 | CTNNB1 | 4528 | 0.082 | 0.49 | YES
18 | ILK | ILK | ILK | 4586 | 0.08 | 0.5 | YES
19 | ZYX | ZYX | ZYX | 5019 | 0.067 | 0.5 | YES
20 | TNS1 | TNS1 | TNS1 | 5029 | 0.067 | 0.51 | YES
21 | AKT1 | AKT1 | AKT1 | 5196 | 0.063 | 0.52 | YES
22 | CDC42 | CDC42 | CDC42 | 5592 | 0.054 | 0.51 | YES
23 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 5684 | 0.052 | 0.51 | YES
24 | JUN | JUN | JUN | 5693 | 0.052 | 0.52 | YES
25 | DIAPH1 | DIAPH1 | DIAPH1 | 5820 | 0.049 | 0.53 | YES
26 | CKAP5 | CKAP5 | CKAP5 | 5901 | 0.047 | 0.54 | YES
27 | CDC37 | CDC37 | CDC37 | 6110 | 0.043 | 0.53 | NO
28 | RUVBL2 | RUVBL2 | RUVBL2 | 6392 | 0.037 | 0.53 | NO
29 | PPP1R14B | PPP1R14B | PPP1R14B | 6973 | 0.025 | 0.5 | NO
30 | PPP1R12A | PPP1R12A | PPP1R12A | 7022 | 0.024 | 0.5 | NO
31 | GIT2 | GIT2 | GIT2 | 7191 | 0.021 | 0.5 | NO
32 | PARVA | PARVA | PARVA | 7332 | 0.019 | 0.5 | NO
33 | IQGAP1 | IQGAP1 | IQGAP1 | 7366 | 0.019 | 0.5 | NO
34 | ILKAP | ILKAP | ILKAP | 7444 | 0.017 | 0.5 | NO
35 | RUVBL1 | RUVBL1 | RUVBL1 | 7837 | 0.01 | 0.48 | NO
36 | RAC1 | RAC1 | RAC1 | 7867 | 0.0098 | 0.48 | NO
37 | GSK3B | GSK3B | GSK3B | 8255 | 0.0034 | 0.46 | NO
38 | PARP1 | PARP1 | PARP1 | 8457 | -0.00025 | 0.45 | NO
39 | CREB1 | CREB1 | CREB1 | 8492 | -0.00088 | 0.45 | NO
40 | XPO1 | XPO1 | XPO1 | 9287 | -0.014 | 0.41 | NO
41 | NCK2 | NCK2 | NCK2 | 9362 | -0.015 | 0.41 | NO
42 | PPP1R14C | PPP1R14C | PPP1R14C | 10918 | -0.042 | 0.33 | NO
43 | ARHGEF7 | ARHGEF7 | ARHGEF7 | 11766 | -0.061 | 0.3 | NO
44 | NACA | NACA | NACA | 12143 | -0.07 | 0.29 | NO
45 | RICTOR | RICTOR | RICTOR | 14898 | -0.18 | 0.18 | NO

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

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

genes ES table in pathway: KEGG CELL CYCLE

Table 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 | CD28 | CD28 | CD28 | 272 | 0.48 | 0.034 | YES
2 | LCK | LCK | LCK | 274 | 0.48 | 0.082 | YES
3 | CD8B | CD8B | CD8B | 313 | 0.46 | 0.13 | YES
4 | CD247 | CD247 | CD247 | 594 | 0.39 | 0.15 | YES
5 | HMGA1 | HMGA1 | HMGA1 | 689 | 0.37 | 0.18 | YES
6 | HCK | HCK | HCK | 1102 | 0.31 | 0.19 | YES
7 | AP1S2 | AP1S2 | AP1S2 | 1339 | 0.28 | 0.21 | YES
8 | DOCK2 | DOCK2 | DOCK2 | 1348 | 0.28 | 0.24 | YES
9 | CD4 | CD4 | CD4 | 1859 | 0.23 | 0.23 | YES
10 | ELMO1 | ELMO1 | ELMO1 | 1860 | 0.23 | 0.26 | YES
11 | APOBEC3G | APOBEC3G | APOBEC3G | 1861 | 0.23 | 0.28 | YES
12 | RCC1 | RCC1 | RCC1 | 2314 | 0.19 | 0.28 | YES
13 | PSME4 | PSME4 | PSME4 | 2414 | 0.18 | 0.29 | YES
14 | PAK2 | PAK2 | PAK2 | 3574 | 0.12 | 0.24 | YES
15 | NUP93 | NUP93 | NUP93 | 3627 | 0.11 | 0.25 | YES
16 | AP1B1 | AP1B1 | AP1B1 | 3780 | 0.11 | 0.25 | YES
17 | AP2S1 | AP2S1 | AP2S1 | 3841 | 0.11 | 0.26 | YES
18 | RANGAP1 | RANGAP1 | RANGAP1 | 3873 | 0.1 | 0.26 | YES
19 | PSMA5 | PSMA5 | PSMA5 | 3922 | 0.1 | 0.27 | YES
20 | PSMA6 | PSMA6 | PSMA6 | 3951 | 0.1 | 0.28 | YES
21 | PSME2 | PSME2 | PSME2 | 3958 | 0.1 | 0.29 | YES
22 | NUP188 | NUP188 | NUP188 | 3998 | 0.1 | 0.3 | YES
23 | RANBP1 | RANBP1 | RANBP1 | 4051 | 0.098 | 0.31 | YES
24 | PSMA8 | PSMA8 | PSMA8 | 4074 | 0.097 | 0.32 | YES
25 | PSMA3 | PSMA3 | PSMA3 | 4102 | 0.096 | 0.32 | YES
26 | NUP155 | NUP155 | NUP155 | 4155 | 0.093 | 0.33 | YES
27 | NUP50 | NUP50 | NUP50 | 4222 | 0.092 | 0.34 | YES
28 | PSMD11 | PSMD11 | PSMD11 | 4237 | 0.091 | 0.34 | YES
29 | KPNB1 | KPNB1 | KPNB1 | 4249 | 0.091 | 0.35 | YES
30 | NUP205 | NUP205 | NUP205 | 4488 | 0.083 | 0.35 | YES
31 | PSMD12 | PSMD12 | PSMD12 | 4502 | 0.083 | 0.36 | YES
32 | PSMB10 | PSMB10 | PSMB10 | 4534 | 0.082 | 0.36 | YES
33 | B2M | B2M | B2M | 4536 | 0.082 | 0.37 | YES
34 | PSMC4 | PSMC4 | PSMC4 | 4681 | 0.077 | 0.37 | YES
35 | SLC25A5 | SLC25A5 | SLC25A5 | 4731 | 0.076 | 0.38 | YES
36 | PSMC6 | PSMC6 | PSMC6 | 4795 | 0.074 | 0.38 | YES
37 | PSMD2 | PSMD2 | PSMD2 | 4832 | 0.073 | 0.39 | YES
38 | PSMD13 | PSMD13 | PSMD13 | 4905 | 0.071 | 0.39 | YES
39 | PSMB5 | PSMB5 | PSMB5 | 5000 | 0.068 | 0.39 | YES
40 | NUPL1 | NUPL1 | NUPL1 | 5012 | 0.068 | 0.4 | YES
41 | PSMA7 | PSMA7 | PSMA7 | 5032 | 0.067 | 0.4 | YES
42 | CCNT1 | CCNT1 | CCNT1 | 5067 | 0.066 | 0.41 | YES
43 | NUP153 | NUP153 | NUP153 | 5081 | 0.066 | 0.41 | YES
44 | PSMD14 | PSMD14 | PSMD14 | 5185 | 0.063 | 0.42 | YES
45 | PSMC1 | PSMC1 | PSMC1 | 5192 | 0.063 | 0.42 | YES
46 | PSMB9 | PSMB9 | PSMB9 | 5349 | 0.059 | 0.42 | YES
47 | PSMF1 | PSMF1 | PSMF1 | 5544 | 0.054 | 0.41 | YES
48 | RBX1 | RBX1 | RBX1 | 5551 | 0.054 | 0.42 | YES
49 | PSMB6 | PSMB6 | PSMB6 | 5588 | 0.054 | 0.42 | YES
50 | NUP62 | NUP62 | NUP62 | 5617 | 0.053 | 0.43 | YES
51 | HLA-A | HLA-A | HLA-A | 5675 | 0.052 | 0.43 | YES
52 | PSMD7 | PSMD7 | PSMD7 | 5687 | 0.052 | 0.43 | YES
53 | PSMD6 | PSMD6 | PSMD6 | 5692 | 0.052 | 0.44 | YES
54 | RAN | RAN | RAN | 5716 | 0.051 | 0.44 | YES
55 | TCEB1 | TCEB1 | TCEB1 | 5758 | 0.051 | 0.44 | YES
56 | KPNA1 | KPNA1 | KPNA1 | 5792 | 0.05 | 0.45 | YES
57 | NUP54 | NUP54 | NUP54 | 5826 | 0.049 | 0.45 | YES
58 | PSMD1 | PSMD1 | PSMD1 | 5884 | 0.048 | 0.45 | YES
59 | RANBP2 | RANBP2 | RANBP2 | 5906 | 0.047 | 0.46 | YES
60 | AP2A2 | AP2A2 | AP2A2 | 5937 | 0.046 | 0.46 | YES
61 | PSMB3 | PSMB3 | PSMB3 | 5953 | 0.046 | 0.46 | YES
62 | PSMB2 | PSMB2 | PSMB2 | 6010 | 0.045 | 0.46 | YES
63 | PSMD8 | PSMD8 | PSMD8 | 6101 | 0.043 | 0.46 | NO
64 | PSMD3 | PSMD3 | PSMD3 | 6211 | 0.04 | 0.46 | NO
65 | NUP37 | NUP37 | NUP37 | 6437 | 0.036 | 0.45 | NO
66 | PACS1 | PACS1 | PACS1 | 6449 | 0.036 | 0.46 | NO
67 | PSME1 | PSME1 | PSME1 | 6462 | 0.036 | 0.46 | NO
68 | AP2A1 | AP2A1 | AP2A1 | 6544 | 0.034 | 0.46 | NO
69 | PSMD5 | PSMD5 | PSMD5 | 6566 | 0.033 | 0.46 | NO
70 | RAE1 | RAE1 | RAE1 | 6579 | 0.033 | 0.46 | NO
71 | PSMC3 | PSMC3 | PSMC3 | 6656 | 0.032 | 0.46 | NO
72 | PSMC2 | PSMC2 | PSMC2 | 6762 | 0.03 | 0.46 | NO
73 | PSMA1 | PSMA1 | PSMA1 | 6806 | 0.029 | 0.46 | NO
74 | PSMD9 | PSMD9 | PSMD9 | 6960 | 0.026 | 0.46 | NO
75 | PSMA2 | PSMA2 | PSMA2 | 6996 | 0.025 | 0.46 | NO
76 | AP2M1 | AP2M1 | AP2M1 | 7009 | 0.025 | 0.46 | NO
77 | PPIA | PPIA | PPIA | 7071 | 0.023 | 0.46 | NO
78 | NUP107 | NUP107 | NUP107 | 7171 | 0.022 | 0.45 | NO
79 | PSMA4 | PSMA4 | PSMA4 | 7225 | 0.021 | 0.45 | NO
80 | NUP88 | NUP88 | NUP88 | 7396 | 0.018 | 0.44 | NO
81 | NUP43 | NUP43 | NUP43 | 7437 | 0.018 | 0.44 | NO
82 | PSMB4 | PSMB4 | PSMB4 | 7726 | 0.012 | 0.43 | NO
83 | PSMC5 | PSMC5 | PSMC5 | 7862 | 0.0099 | 0.42 | NO
84 | RAC1 | RAC1 | RAC1 | 7867 | 0.0098 | 0.42 | NO
85 | AP1S1 | AP1S1 | AP1S1 | 7940 | 0.0087 | 0.42 | NO
86 | AP2B1 | AP2B1 | AP2B1 | 7986 | 0.0079 | 0.42 | NO
87 | PSMD4 | PSMD4 | PSMD4 | 8010 | 0.0075 | 0.42 | NO
88 | PSMB7 | PSMB7 | PSMB7 | 8065 | 0.0066 | 0.42 | NO
89 | PSMB1 | PSMB1 | PSMB1 | 8237 | 0.0036 | 0.41 | NO
90 | NUP85 | NUP85 | NUP85 | 8388 | 0.00095 | 0.4 | NO
91 | ARF1 | ARF1 | ARF1 | 8448 | -0.000096 | 0.4 | NO
92 | AP1G1 | AP1G1 | AP1G1 | 8523 | -0.0013 | 0.39 | NO
93 | BTRC | BTRC | BTRC | 8603 | -0.0027 | 0.39 | NO
94 | NPM1 | NPM1 | NPM1 | 8658 | -0.0035 | 0.38 | NO
95 | PSIP1 | PSIP1 | PSIP1 | 9077 | -0.011 | 0.36 | NO
96 | FYN | FYN | FYN | 9108 | -0.011 | 0.36 | NO
97 | XPO1 | XPO1 | XPO1 | 9287 | -0.014 | 0.36 | NO
98 | SEH1L | SEH1L | SEH1L | 9323 | -0.015 | 0.35 | NO
99 | PSMB8 | PSMB8 | PSMB8 | 9607 | -0.019 | 0.34 | NO
100 | PSMD10 | PSMD10 | PSMD10 | 9808 | -0.023 | 0.33 | NO
101 | BANF1 | BANF1 | BANF1 | 10009 | -0.026 | 0.32 | NO
102 | NUP214 | NUP214 | NUP214 | 10106 | -0.028 | 0.32 | NO
103 | AP1M1 | AP1M1 | AP1M1 | 10336 | -0.032 | 0.31 | NO
104 | NUP210 | NUP210 | NUP210 | 10432 | -0.033 | 0.31 | NO
105 | NUPL2 | NUPL2 | NUPL2 | 10576 | -0.036 | 0.3 | NO
106 | UBA52 | UBA52 | UBA52 | 10630 | -0.037 | 0.31 | NO
107 | SKP1 | SKP1 | SKP1 | 10847 | -0.041 | 0.3 | NO
108 | RPS27A | RPS27A | RPS27A | 11209 | -0.049 | 0.28 | NO
109 | AP1M2 | AP1M2 | AP1M2 | 11396 | -0.052 | 0.28 | NO
110 | CDK9 | CDK9 | CDK9 | 11499 | -0.055 | 0.28 | NO
111 | NUP133 | NUP133 | NUP133 | 11640 | -0.058 | 0.28 | NO
112 | TCEB2 | TCEB2 | TCEB2 | 11905 | -0.064 | 0.27 | NO
113 | CUL5 | CUL5 | CUL5 | 11947 | -0.065 | 0.27 | NO
114 | TPR | TPR | TPR | 12004 | -0.067 | 0.28 | NO
115 | POM121 | POM121 | POM121 | 12182 | -0.071 | 0.27 | NO
116 | ATP6V1H | ATP6V1H | ATP6V1H | 12368 | -0.076 | 0.27 | NO
117 | NUP35 | NUP35 | NUP35 | 12461 | -0.079 | 0.28 | NO
118 | AAAS | AAAS | AAAS | 12969 | -0.093 | 0.26 | NO
119 | SLC25A6 | SLC25A6 | SLC25A6 | 13760 | -0.12 | 0.22 | NO
120 | SLC25A4 | SLC25A4 | SLC25A4 | 15264 | -0.2 | 0.16 | 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: KEGG CELL CYCLE.

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

genes ES table in pathway: KEGG APOPTOSIS

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 | RASGRP3 | RASGRP3 | RASGRP3 | 764 | 0.36 | -0.0058 | YES
2 | PRKCB | PRKCB | PRKCB | 937 | 0.34 | 0.018 | YES
3 | PIK3AP1 | PIK3AP1 | PIK3AP1 | 1009 | 0.32 | 0.047 | YES
4 | CD79B | CD79B | CD79B | 1311 | 0.28 | 0.059 | YES
5 | ORAI1 | ORAI1 | ORAI1 | 1428 | 0.27 | 0.08 | YES
6 | CD19 | CD19 | CD19 | 1461 | 0.27 | 0.1 | YES
7 | BTK | BTK | BTK | 1475 | 0.26 | 0.13 | YES
8 | VAV1 | VAV1 | VAV1 | 1548 | 0.26 | 0.15 | YES
9 | BCL10 | BCL10 | BCL10 | 1914 | 0.22 | 0.16 | YES
10 | AKT3 | AKT3 | AKT3 | 2102 | 0.21 | 0.17 | YES
11 | REL | REL | REL | 2147 | 0.2 | 0.18 | YES
12 | LYN | LYN | LYN | 2185 | 0.2 | 0.2 | YES
13 | TRIB3 | TRIB3 | TRIB3 | 2392 | 0.18 | 0.21 | YES
14 | PSME4 | PSME4 | PSME4 | 2414 | 0.18 | 0.23 | YES
15 | CD79A | CD79A | CD79A | 2451 | 0.18 | 0.24 | YES
16 | SYK | SYK | SYK | 2617 | 0.17 | 0.25 | YES
17 | BLK | BLK | BLK | 2793 | 0.16 | 0.26 | YES
18 | BLNK | BLNK | BLNK | 2903 | 0.15 | 0.27 | YES
19 | NFKBIE | NFKBIE | NFKBIE | 3014 | 0.15 | 0.28 | YES
20 | PLCG2 | PLCG2 | PLCG2 | 3148 | 0.14 | 0.28 | YES
21 | NRAS | NRAS | NRAS | 3244 | 0.13 | 0.29 | YES
22 | CDKN1A | CDKN1A | CDKN1A | 3324 | 0.13 | 0.3 | YES
23 | MALT1 | MALT1 | MALT1 | 3359 | 0.13 | 0.31 | YES
24 | NFKBIB | NFKBIB | NFKBIB | 3408 | 0.12 | 0.32 | YES
25 | CBL | CBL | CBL | 3547 | 0.12 | 0.32 | YES
26 | SHC1 | SHC1 | SHC1 | 3580 | 0.12 | 0.34 | YES
27 | PSMA5 | PSMA5 | PSMA5 | 3922 | 0.1 | 0.33 | YES
28 | PSMA6 | PSMA6 | PSMA6 | 3951 | 0.1 | 0.34 | YES
29 | PSME2 | PSME2 | PSME2 | 3958 | 0.1 | 0.34 | YES
30 | PIK3CD | PIK3CD | PIK3CD | 4067 | 0.097 | 0.35 | YES
31 | PSMA8 | PSMA8 | PSMA8 | 4074 | 0.097 | 0.36 | YES
32 | PSMA3 | PSMA3 | PSMA3 | 4102 | 0.096 | 0.37 | YES
33 | PSMD11 | PSMD11 | PSMD11 | 4237 | 0.091 | 0.37 | YES
34 | PSMD12 | PSMD12 | PSMD12 | 4502 | 0.083 | 0.36 | YES
35 | PSMB10 | PSMB10 | PSMB10 | 4534 | 0.082 | 0.37 | YES
36 | STIM1 | STIM1 | STIM1 | 4547 | 0.082 | 0.38 | YES
37 | PSMC4 | PSMC4 | PSMC4 | 4681 | 0.077 | 0.38 | YES
38 | PSMC6 | PSMC6 | PSMC6 | 4795 | 0.074 | 0.38 | YES
39 | CBLB | CBLB | CBLB | 4827 | 0.073 | 0.38 | YES
40 | PSMD2 | PSMD2 | PSMD2 | 4832 | 0.073 | 0.39 | YES
41 | PSMD13 | PSMD13 | PSMD13 | 4905 | 0.071 | 0.39 | YES
42 | PSMB5 | PSMB5 | PSMB5 | 5000 | 0.068 | 0.4 | YES
43 | PSMA7 | PSMA7 | PSMA7 | 5032 | 0.067 | 0.4 | YES
44 | RASGRP1 | RASGRP1 | RASGRP1 | 5083 | 0.066 | 0.4 | YES
45 | PSMD14 | PSMD14 | PSMD14 | 5185 | 0.063 | 0.4 | YES
46 | PSMC1 | PSMC1 | PSMC1 | 5192 | 0.063 | 0.41 | YES
47 | AKT1 | AKT1 | AKT1 | 5196 | 0.063 | 0.42 | YES
48 | CHUK | CHUK | CHUK | 5216 | 0.062 | 0.42 | YES
49 | CALM1 | CALM1 | CALM1 | 5304 | 0.06 | 0.42 | YES
50 | MTOR | MTOR | MTOR | 5310 | 0.06 | 0.43 | YES
51 | GRB2 | GRB2 | GRB2 | 5323 | 0.06 | 0.44 | YES
52 | PSMB9 | PSMB9 | PSMB9 | 5349 | 0.059 | 0.44 | YES
53 | PSMF1 | PSMF1 | PSMF1 | 5544 | 0.054 | 0.44 | YES
54 | PSMB6 | PSMB6 | PSMB6 | 5588 | 0.054 | 0.44 | YES
55 | PSMD7 | PSMD7 | PSMD7 | 5687 | 0.052 | 0.44 | YES
56 | PSMD6 | PSMD6 | PSMD6 | 5692 | 0.052 | 0.44 | YES
57 | NFKBIA | NFKBIA | NFKBIA | 5831 | 0.049 | 0.44 | YES
58 | PSMD1 | PSMD1 | PSMD1 | 5884 | 0.048 | 0.44 | YES
59 | FOXO1 | FOXO1 | FOXO1 | 5936 | 0.047 | 0.44 | YES
60 | PSMB3 | PSMB3 | PSMB3 | 5953 | 0.046 | 0.45 | YES
61 | PSMB2 | PSMB2 | PSMB2 | 6010 | 0.045 | 0.45 | YES
62 | KRAS | KRAS | KRAS | 6089 | 0.043 | 0.45 | YES
63 | PSMD8 | PSMD8 | PSMD8 | 6101 | 0.043 | 0.45 | YES
64 | PSMD3 | PSMD3 | PSMD3 | 6211 | 0.04 | 0.45 | NO
65 | PSME1 | PSME1 | PSME1 | 6462 | 0.036 | 0.44 | NO
66 | PSMD5 | PSMD5 | PSMD5 | 6566 | 0.033 | 0.44 | NO
67 | PSMC3 | PSMC3 | PSMC3 | 6656 | 0.032 | 0.44 | NO
68 | SH3KBP1 | SH3KBP1 | SH3KBP1 | 6725 | 0.03 | 0.44 | NO
69 | PSMC2 | PSMC2 | PSMC2 | 6762 | 0.03 | 0.44 | NO
70 | PSMA1 | PSMA1 | PSMA1 | 6806 | 0.029 | 0.44 | NO
71 | CALM2 | CALM2 | CALM2 | 6902 | 0.027 | 0.43 | NO
72 | IKBKG | IKBKG | IKBKG | 6912 | 0.026 | 0.44 | NO
73 | CALM3 | CALM3 | CALM3 | 6936 | 0.026 | 0.44 | NO
74 | PSMD9 | PSMD9 | PSMD9 | 6960 | 0.026 | 0.44 | NO
75 | PSMA2 | PSMA2 | PSMA2 | 6996 | 0.025 | 0.44 | NO
76 | PSMA4 | PSMA4 | PSMA4 | 7225 | 0.021 | 0.43 | NO
77 | NCK1 | NCK1 | NCK1 | 7228 | 0.021 | 0.43 | NO
78 | MAP3K7 | MAP3K7 | MAP3K7 | 7309 | 0.019 | 0.43 | NO
79 | PSMB4 | PSMB4 | PSMB4 | 7726 | 0.012 | 0.41 | NO
80 | CUL1 | CUL1 | CUL1 | 7741 | 0.012 | 0.41 | NO
81 | PSMC5 | PSMC5 | PSMC5 | 7862 | 0.0099 | 0.4 | NO
82 | PSMD4 | PSMD4 | PSMD4 | 8010 | 0.0075 | 0.4 | NO
83 | HRAS | HRAS | HRAS | 8032 | 0.0071 | 0.39 | NO
84 | PSMB7 | PSMB7 | PSMB7 | 8065 | 0.0066 | 0.39 | NO
85 | GSK3A | GSK3A | GSK3A | 8108 | 0.0058 | 0.39 | NO
86 | PHLPP1 | PHLPP1 | PHLPP1 | 8179 | 0.0045 | 0.39 | NO
87 | PSMB1 | PSMB1 | PSMB1 | 8237 | 0.0036 | 0.38 | NO
88 | PDPK1 | PDPK1 | PDPK1 | 8252 | 0.0034 | 0.38 | NO
89 | AKT1S1 | AKT1S1 | AKT1S1 | 8333 | 0.002 | 0.38 | NO
90 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 8426 | 0.00023 | 0.38 | NO
91 | RELA | RELA | RELA | 8468 | -0.00039 | 0.37 | NO
92 | CREB1 | CREB1 | CREB1 | 8492 | -0.00088 | 0.37 | NO
93 | BTRC | BTRC | BTRC | 8603 | -0.0027 | 0.37 | NO
94 | NR4A1 | NR4A1 | NR4A1 | 8713 | -0.0045 | 0.36 | NO
95 | PLCG1 | PLCG1 | PLCG1 | 8947 | -0.0085 | 0.35 | NO
96 | CDKN1B | CDKN1B | CDKN1B | 9078 | -0.011 | 0.34 | NO
97 | FYN | FYN | FYN | 9108 | -0.011 | 0.34 | NO
98 | MDM2 | MDM2 | MDM2 | 9172 | -0.012 | 0.34 | NO
99 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 9249 | -0.014 | 0.34 | NO
100 | PSMB8 | PSMB8 | PSMB8 | 9607 | -0.019 | 0.32 | NO
101 | PSMD10 | PSMD10 | PSMD10 | 9808 | -0.023 | 0.31 | NO
102 | PTEN | PTEN | PTEN | 9923 | -0.025 | 0.31 | NO
103 | IKBKB | IKBKB | IKBKB | 10285 | -0.031 | 0.29 | NO
104 | TSC2 | TSC2 | TSC2 | 10290 | -0.031 | 0.29 | NO
105 | AKT2 | AKT2 | AKT2 | 10369 | -0.032 | 0.29 | NO
106 | UBA52 | UBA52 | UBA52 | 10630 | -0.037 | 0.28 | NO
107 | SKP1 | SKP1 | SKP1 | 10847 | -0.041 | 0.27 | NO
108 | FOXO3 | FOXO3 | FOXO3 | 11064 | -0.045 | 0.27 | NO
109 | SOS1 | SOS1 | SOS1 | 11126 | -0.047 | 0.27 | NO
110 | RPS27A | RPS27A | RPS27A | 11209 | -0.049 | 0.27 | NO
111 | ITPR2 | ITPR2 | ITPR2 | 11711 | -0.06 | 0.25 | NO
112 | MLST8 | MLST8 | MLST8 | 11819 | -0.062 | 0.25 | NO
113 | FBXW11 | FBXW11 | FBXW11 | 12087 | -0.069 | 0.24 | NO
114 | ITPR3 | ITPR3 | ITPR3 | 12197 | -0.072 | 0.24 | NO
115 | PIK3R1 | PIK3R1 | PIK3R1 | 12438 | -0.078 | 0.23 | NO
116 | THEM4 | THEM4 | THEM4 | 13274 | -0.1 | 0.2 | NO
117 | BAD | BAD | BAD | 13782 | -0.12 | 0.18 | NO
118 | CASP9 | CASP9 | CASP9 | 13795 | -0.12 | 0.19 | NO
119 | FOXO4 | FOXO4 | FOXO4 | 13891 | -0.13 | 0.2 | NO
120 | RICTOR | RICTOR | RICTOR | 14898 | -0.18 | 0.16 | NO
121 | CARD11 | CARD11 | CARD11 | 15051 | -0.18 | 0.17 | 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 APOPTOSIS.

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

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

Table 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 | MECOM | MECOM | MECOM | 156 | 0.54 | 0.069 | YES
2 | PIK3CG | PIK3CG | PIK3CG | 407 | 0.44 | 0.12 | YES
3 | PIK3R5 | PIK3R5 | PIK3R5 | 835 | 0.35 | 0.14 | YES
4 | SHC3 | SHC3 | SHC3 | 1901 | 0.23 | 0.12 | YES
5 | TGFB1 | TGFB1 | TGFB1 | 1950 | 0.22 | 0.15 | YES
6 | AKT3 | AKT3 | AKT3 | 2102 | 0.21 | 0.17 | YES
7 | PIK3R3 | PIK3R3 | PIK3R3 | 2366 | 0.19 | 0.18 | YES
8 | TGFBR1 | TGFBR1 | TGFBR1 | 2488 | 0.18 | 0.2 | YES
9 | TGFBR2 | TGFBR2 | TGFBR2 | 2549 | 0.18 | 0.22 | YES
10 | E2F3 | E2F3 | E2F3 | 2799 | 0.16 | 0.23 | YES
11 | NRAS | NRAS | NRAS | 3244 | 0.13 | 0.23 | YES
12 | SHC4 | SHC4 | SHC4 | 3263 | 0.13 | 0.24 | YES
13 | CDKN1A | CDKN1A | CDKN1A | 3324 | 0.13 | 0.26 | YES
14 | CBL | CBL | CBL | 3547 | 0.12 | 0.26 | YES
15 | MAP2K1 | MAP2K1 | MAP2K1 | 3548 | 0.12 | 0.28 | YES
16 | SHC1 | SHC1 | SHC1 | 3580 | 0.12 | 0.3 | YES
17 | GAB2 | GAB2 | GAB2 | 3746 | 0.11 | 0.3 | YES
18 | RUNX1 | RUNX1 | RUNX1 | 3795 | 0.11 | 0.32 | YES
19 | CCND1 | CCND1 | CCND1 | 3857 | 0.1 | 0.33 | YES
20 | PIK3CD | PIK3CD | PIK3CD | 4067 | 0.097 | 0.33 | YES
21 | CRK | CRK | CRK | 4274 | 0.09 | 0.33 | YES
22 | HDAC1 | HDAC1 | HDAC1 | 4452 | 0.085 | 0.34 | YES
23 | CDKN2A | CDKN2A | CDKN2A | 4456 | 0.084 | 0.35 | YES
24 | E2F2 | E2F2 | E2F2 | 4462 | 0.084 | 0.36 | YES
25 | BRAF | BRAF | BRAF | 4510 | 0.082 | 0.37 | YES
26 | CTBP2 | CTBP2 | CTBP2 | 4688 | 0.077 | 0.37 | YES
27 | E2F1 | E2F1 | E2F1 | 4750 | 0.075 | 0.38 | YES
28 | MAPK1 | MAPK1 | MAPK1 | 4758 | 0.075 | 0.39 | YES
29 | CBLB | CBLB | CBLB | 4827 | 0.073 | 0.39 | YES
30 | CDK6 | CDK6 | CDK6 | 5071 | 0.066 | 0.39 | YES
31 | AKT1 | AKT1 | AKT1 | 5196 | 0.063 | 0.39 | YES
32 | BCL2L1 | BCL2L1 | BCL2L1 | 5214 | 0.062 | 0.4 | YES
33 | CHUK | CHUK | CHUK | 5216 | 0.062 | 0.41 | YES
34 | GRB2 | GRB2 | GRB2 | 5323 | 0.06 | 0.41 | YES
35 | PTPN11 | PTPN11 | PTPN11 | 5342 | 0.06 | 0.42 | YES
36 | NFKB1 | NFKB1 | NFKB1 | 5404 | 0.058 | 0.42 | YES
37 | NFKBIA | NFKBIA | NFKBIA | 5831 | 0.049 | 0.41 | NO
38 | KRAS | KRAS | KRAS | 6089 | 0.043 | 0.4 | NO
39 | PIK3CA | PIK3CA | PIK3CA | 6489 | 0.035 | 0.38 | NO
40 | RB1 | RB1 | RB1 | 6564 | 0.033 | 0.38 | NO
41 | IKBKG | IKBKG | IKBKG | 6912 | 0.026 | 0.37 | NO
42 | HDAC2 | HDAC2 | HDAC2 | 7028 | 0.024 | 0.37 | NO
43 | SOS2 | SOS2 | SOS2 | 7492 | 0.016 | 0.34 | NO
44 | CRKL | CRKL | CRKL | 7543 | 0.016 | 0.34 | NO
45 | RAF1 | RAF1 | RAF1 | 7585 | 0.015 | 0.34 | NO
46 | CBLC | CBLC | CBLC | 8027 | 0.0072 | 0.32 | NO
47 | HRAS | HRAS | HRAS | 8032 | 0.0071 | 0.32 | NO
48 | STAT5B | STAT5B | STAT5B | 8067 | 0.0065 | 0.32 | NO
49 | CDK4 | CDK4 | CDK4 | 8254 | 0.0034 | 0.31 | NO
50 | ARAF | ARAF | ARAF | 8262 | 0.0032 | 0.31 | NO
51 | MYC | MYC | MYC | 8452 | -0.00018 | 0.3 | NO
52 | RELA | RELA | RELA | 8468 | -0.00039 | 0.3 | NO
53 | MAP2K2 | MAP2K2 | MAP2K2 | 8724 | -0.0046 | 0.28 | NO
54 | CDKN1B | CDKN1B | CDKN1B | 9078 | -0.011 | 0.27 | NO
55 | MDM2 | MDM2 | MDM2 | 9172 | -0.012 | 0.26 | NO
56 | ABL1 | ABL1 | ABL1 | 9901 | -0.024 | 0.23 | NO
57 | IKBKB | IKBKB | IKBKB | 10285 | -0.031 | 0.21 | NO
58 | CTBP1 | CTBP1 | CTBP1 | 10353 | -0.032 | 0.21 | NO
59 | AKT2 | AKT2 | AKT2 | 10369 | -0.032 | 0.22 | NO
60 | SMAD4 | SMAD4 | SMAD4 | 10599 | -0.036 | 0.21 | NO
61 | SOS1 | SOS1 | SOS1 | 11126 | -0.047 | 0.18 | NO
62 | PIK3CB | PIK3CB | PIK3CB | 11271 | -0.05 | 0.18 | NO
63 | STAT5A | STAT5A | STAT5A | 11292 | -0.05 | 0.19 | NO
64 | TP53 | TP53 | TP53 | 11310 | -0.051 | 0.2 | NO
65 | SMAD3 | SMAD3 | SMAD3 | 11400 | -0.053 | 0.2 | NO
66 | PIK3R1 | PIK3R1 | PIK3R1 | 12438 | -0.078 | 0.15 | NO
67 | PIK3R2 | PIK3R2 | PIK3R2 | 12516 | -0.08 | 0.16 | NO
68 | MAPK3 | MAPK3 | MAPK3 | 12813 | -0.088 | 0.16 | NO
69 | TGFB2 | TGFB2 | TGFB2 | 13362 | -0.1 | 0.14 | NO
70 | BCR | BCR | BCR | 13714 | -0.12 | 0.14 | NO
71 | BAD | BAD | BAD | 13782 | -0.12 | 0.15 | NO
72 | TGFB3 | TGFB3 | TGFB3 | 15241 | -0.2 | 0.1 | NO
73 | SHC2 | SHC2 | SHC2 | 17270 | -0.42 | 0.051 | 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 TOLL LIKE RECEPTOR SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG CYTOSOLIC DNA SENSING PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PRKCA | PRKCA | PRKCA | 1659 | 0.25 | -0.034 | YES
2 | PSME4 | PSME4 | PSME4 | 2414 | 0.18 | -0.032 | YES
3 | PRKCD | PRKCD | PRKCD | 2883 | 0.15 | -0.022 | YES
4 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 3484 | 0.12 | -0.027 | YES
5 | MAPK11 | MAPK11 | MAPK11 | 3702 | 0.11 | -0.013 | YES
6 | PSMA5 | PSMA5 | PSMA5 | 3922 | 0.1 | -0.0011 | YES
7 | PSMA6 | PSMA6 | PSMA6 | 3951 | 0.1 | 0.021 | YES
8 | PSME2 | PSME2 | PSME2 | 3958 | 0.1 | 0.044 | YES
9 | PSMA8 | PSMA8 | PSMA8 | 4074 | 0.097 | 0.061 | YES
10 | PSMA3 | PSMA3 | PSMA3 | 4102 | 0.096 | 0.082 | YES
11 | PSMD11 | PSMD11 | PSMD11 | 4237 | 0.091 | 0.096 | YES
12 | EXOSC7 | EXOSC7 | EXOSC7 | 4449 | 0.085 | 0.1 | YES
13 | PSMD12 | PSMD12 | PSMD12 | 4502 | 0.083 | 0.12 | YES
14 | PSMB10 | PSMB10 | PSMB10 | 4534 | 0.082 | 0.14 | YES
15 | PSMC4 | PSMC4 | PSMC4 | 4681 | 0.077 | 0.15 | YES
16 | PSMC6 | PSMC6 | PSMC6 | 4795 | 0.074 | 0.16 | YES
17 | PSMD2 | PSMD2 | PSMD2 | 4832 | 0.073 | 0.17 | YES
18 | PSMD13 | PSMD13 | PSMD13 | 4905 | 0.071 | 0.19 | YES
19 | PSMB5 | PSMB5 | PSMB5 | 5000 | 0.068 | 0.2 | YES
20 | HSPA8 | HSPA8 | HSPA8 | 5020 | 0.067 | 0.21 | YES
21 | PSMA7 | PSMA7 | PSMA7 | 5032 | 0.067 | 0.23 | YES
22 | EIF4G1 | EIF4G1 | EIF4G1 | 5172 | 0.064 | 0.23 | YES
23 | PSMD14 | PSMD14 | PSMD14 | 5185 | 0.063 | 0.25 | YES
24 | PSMC1 | PSMC1 | PSMC1 | 5192 | 0.063 | 0.26 | YES
25 | AKT1 | AKT1 | AKT1 | 5196 | 0.063 | 0.28 | YES
26 | TNPO1 | TNPO1 | TNPO1 | 5299 | 0.06 | 0.29 | YES
27 | PSMB9 | PSMB9 | PSMB9 | 5349 | 0.059 | 0.3 | YES
28 | PSMF1 | PSMF1 | PSMF1 | 5544 | 0.054 | 0.3 | YES
29 | PSMB6 | PSMB6 | PSMB6 | 5588 | 0.054 | 0.31 | YES
30 | PSMD7 | PSMD7 | PSMD7 | 5687 | 0.052 | 0.32 | YES
31 | PSMD6 | PSMD6 | PSMD6 | 5692 | 0.052 | 0.33 | YES
32 | YWHAB | YWHAB | YWHAB | 5760 | 0.051 | 0.34 | YES
33 | PSMD1 | PSMD1 | PSMD1 | 5884 | 0.048 | 0.34 | YES
34 | PSMB3 | PSMB3 | PSMB3 | 5953 | 0.046 | 0.35 | YES
35 | EXOSC3 | EXOSC3 | EXOSC3 | 5961 | 0.046 | 0.36 | YES
36 | MAPK14 | MAPK14 | MAPK14 | 5972 | 0.046 | 0.37 | YES
37 | PSMB2 | PSMB2 | PSMB2 | 6010 | 0.045 | 0.38 | YES
38 | PSMD8 | PSMD8 | PSMD8 | 6101 | 0.043 | 0.38 | YES
39 | HSPB1 | HSPB1 | HSPB1 | 6164 | 0.042 | 0.39 | YES
40 | PSMD3 | PSMD3 | PSMD3 | 6211 | 0.04 | 0.39 | YES
41 | PABPC1 | PABPC1 | PABPC1 | 6221 | 0.04 | 0.4 | YES
42 | ZFP36 | ZFP36 | ZFP36 | 6252 | 0.04 | 0.41 | YES
43 | XRN1 | XRN1 | XRN1 | 6376 | 0.037 | 0.41 | YES
44 | YWHAZ | YWHAZ | YWHAZ | 6400 | 0.036 | 0.42 | YES
45 | EXOSC1 | EXOSC1 | EXOSC1 | 6448 | 0.036 | 0.43 | YES
46 | PSME1 | PSME1 | PSME1 | 6462 | 0.036 | 0.43 | YES
47 | HSPA1B | HSPA1B | HSPA1B | 6537 | 0.034 | 0.44 | YES
48 | PSMD5 | PSMD5 | PSMD5 | 6566 | 0.033 | 0.44 | YES
49 | DCP2 | DCP2 | DCP2 | 6638 | 0.032 | 0.45 | YES
50 | PSMC3 | PSMC3 | PSMC3 | 6656 | 0.032 | 0.45 | YES
51 | PSMC2 | PSMC2 | PSMC2 | 6762 | 0.03 | 0.45 | YES
52 | PSMA1 | PSMA1 | PSMA1 | 6806 | 0.029 | 0.46 | YES
53 | PSMD9 | PSMD9 | PSMD9 | 6960 | 0.026 | 0.46 | YES
54 | PSMA2 | PSMA2 | PSMA2 | 6996 | 0.025 | 0.46 | YES
55 | EXOSC6 | EXOSC6 | EXOSC6 | 7175 | 0.022 | 0.46 | NO
56 | PSMA4 | PSMA4 | PSMA4 | 7225 | 0.021 | 0.46 | NO
57 | HNRNPD | HNRNPD | HNRNPD | 7559 | 0.015 | 0.44 | NO
58 | PSMB4 | PSMB4 | PSMB4 | 7726 | 0.012 | 0.44 | NO
59 | PSMC5 | PSMC5 | PSMC5 | 7862 | 0.0099 | 0.43 | NO
60 | ZFP36L1 | ZFP36L1 | ZFP36L1 | 7947 | 0.0086 | 0.43 | NO
61 | PSMD4 | PSMD4 | PSMD4 | 8010 | 0.0075 | 0.43 | NO
62 | PSMB7 | PSMB7 | PSMB7 | 8065 | 0.0066 | 0.43 | NO
63 | EXOSC4 | EXOSC4 | EXOSC4 | 8132 | 0.0052 | 0.42 | NO
64 | EXOSC9 | EXOSC9 | EXOSC9 | 8170 | 0.0047 | 0.42 | NO
65 | PSMB1 | PSMB1 | PSMB1 | 8237 | 0.0036 | 0.42 | NO
66 | ANP32A | ANP32A | ANP32A | 8432 | 0.00013 | 0.41 | NO
67 | XPO1 | XPO1 | XPO1 | 9287 | -0.014 | 0.36 | NO
68 | EXOSC2 | EXOSC2 | EXOSC2 | 9447 | -0.017 | 0.36 | NO
69 | DCP1A | DCP1A | DCP1A | 9463 | -0.017 | 0.36 | NO
70 | KHSRP | KHSRP | KHSRP | 9547 | -0.018 | 0.36 | NO
71 | PSMB8 | PSMB8 | PSMB8 | 9607 | -0.019 | 0.36 | NO
72 | PSMD10 | PSMD10 | PSMD10 | 9808 | -0.023 | 0.36 | NO
73 | ELAVL1 | ELAVL1 | ELAVL1 | 9858 | -0.023 | 0.36 | NO
74 | TNFSF13 | TNFSF13 | TNFSF13 | 9971 | -0.025 | 0.36 | NO
75 | NUP214 | NUP214 | NUP214 | 10106 | -0.028 | 0.36 | NO
76 | EXOSC8 | EXOSC8 | EXOSC8 | 10561 | -0.036 | 0.34 | NO
77 | UBA52 | UBA52 | UBA52 | 10630 | -0.037 | 0.35 | NO
78 | RPS27A | RPS27A | RPS27A | 11209 | -0.049 | 0.33 | NO
79 | DIS3 | DIS3 | DIS3 | 11530 | -0.056 | 0.32 | NO
80 | EXOSC5 | EXOSC5 | EXOSC5 | 12629 | -0.083 | 0.28 | NO
81 | PARN | PARN | PARN | 13453 | -0.11 | 0.26 | 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 CYTOSOLIC DNA SENSING PATHWAY.

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

genes ES table in pathway: KEGG HEMATOPOIETIC CELL LINEAGE

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 | FOSL1 | FOSL1 | FOSL1 | 18 | 0.74 | 0.082 | YES
2 | MYCT1 | MYCT1 | MYCT1 | 116 | 0.56 | 0.14 | YES
3 | MMP9 | MMP9 | MMP9 | 239 | 0.49 | 0.19 | YES
4 | CDC25A | CDC25A | CDC25A | 574 | 0.4 | 0.21 | YES
5 | CDCA7 | CDCA7 | CDCA7 | 613 | 0.39 | 0.25 | YES
6 | HMGA1 | HMGA1 | HMGA1 | 689 | 0.37 | 0.29 | YES
7 | SNAI1 | SNAI1 | SNAI1 | 773 | 0.36 | 0.33 | YES
8 | PMAIP1 | PMAIP1 | PMAIP1 | 1078 | 0.31 | 0.34 | YES
9 | BIRC5 | BIRC5 | BIRC5 | 1770 | 0.24 | 0.33 | YES
10 | CCNB1 | CCNB1 | CCNB1 | 1856 | 0.23 | 0.36 | YES
11 | TK1 | TK1 | TK1 | 2247 | 0.2 | 0.36 | YES
12 | RCC1 | RCC1 | RCC1 | 2314 | 0.19 | 0.37 | YES
13 | NDUFAF2 | NDUFAF2 | NDUFAF2 | 2388 | 0.19 | 0.39 | YES
14 | SUPT3H | SUPT3H | SUPT3H | 2505 | 0.18 | 0.4 | YES
15 | TFRC | TFRC | TFRC | 2734 | 0.16 | 0.41 | YES
16 | POLR3D | POLR3D | POLR3D | 2789 | 0.16 | 0.42 | YES
17 | E2F3 | E2F3 | E2F3 | 2799 | 0.16 | 0.44 | YES
18 | EIF4E | EIF4E | EIF4E | 3025 | 0.14 | 0.44 | YES
19 | EIF2S1 | EIF2S1 | EIF2S1 | 3039 | 0.14 | 0.46 | YES
20 | SLC2A1 | SLC2A1 | SLC2A1 | 3044 | 0.14 | 0.48 | YES
21 | BCAT1 | BCAT1 | BCAT1 | 3153 | 0.14 | 0.48 | YES
22 | NBN | NBN | NBN | 3679 | 0.11 | 0.47 | NO
23 | PDCD10 | PDCD10 | PDCD10 | 3947 | 0.1 | 0.46 | NO
24 | BAX | BAX | BAX | 4107 | 0.096 | 0.47 | NO
25 | HSPA4 | HSPA4 | HSPA4 | 4742 | 0.076 | 0.44 | NO
26 | TAF9 | TAF9 | TAF9 | 4761 | 0.075 | 0.45 | NO
27 | TERT | TERT | TERT | 4891 | 0.071 | 0.45 | NO
28 | TAF12 | TAF12 | TAF12 | 5134 | 0.064 | 0.44 | NO
29 | EIF4G1 | EIF4G1 | EIF4G1 | 5172 | 0.064 | 0.45 | NO
30 | NME1 | NME1 | NME1 | 5448 | 0.057 | 0.44 | NO
31 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 5684 | 0.052 | 0.43 | NO
32 | GAPDH | GAPDH | GAPDH | 5793 | 0.05 | 0.43 | NO
33 | MINA | MINA | MINA | 5888 | 0.048 | 0.43 | NO
34 | EIF4A1 | EIF4A1 | EIF4A1 | 6206 | 0.041 | 0.42 | NO
35 | LDHA | LDHA | LDHA | 6249 | 0.04 | 0.42 | NO
36 | PIM1 | PIM1 | PIM1 | 6356 | 0.038 | 0.42 | NO
37 | RUVBL2 | RUVBL2 | RUVBL2 | 6392 | 0.037 | 0.42 | NO
38 | ENO1 | ENO1 | ENO1 | 6906 | 0.027 | 0.4 | NO
39 | DDX18 | DDX18 | DDX18 | 6944 | 0.026 | 0.4 | NO
40 | MAX | MAX | MAX | 6961 | 0.026 | 0.4 | NO
41 | SUPT7L | SUPT7L | SUPT7L | 7207 | 0.021 | 0.39 | NO
42 | CAD | CAD | CAD | 7232 | 0.021 | 0.39 | NO
43 | MTDH | MTDH | MTDH | 7282 | 0.02 | 0.39 | NO
44 | ACTL6A | ACTL6A | ACTL6A | 7296 | 0.02 | 0.39 | NO
45 | EP300 | EP300 | EP300 | 7564 | 0.015 | 0.38 | NO
46 | TAF4B | TAF4B | TAF4B | 7650 | 0.014 | 0.37 | NO
47 | RUVBL1 | RUVBL1 | RUVBL1 | 7837 | 0.01 | 0.36 | NO
48 | HUWE1 | HUWE1 | HUWE1 | 8058 | 0.0067 | 0.35 | NO
49 | CDK4 | CDK4 | CDK4 | 8254 | 0.0034 | 0.34 | NO
50 | GPAM | GPAM | GPAM | 8364 | 0.0014 | 0.34 | NO
51 | MYC | MYC | MYC | 8452 | -0.00018 | 0.33 | NO
52 | NCL | NCL | NCL | 8508 | -0.0012 | 0.33 | NO
53 | NPM1 | NPM1 | NPM1 | 8658 | -0.0035 | 0.32 | NO
54 | HSPD1 | HSPD1 | HSPD1 | 9302 | -0.014 | 0.29 | NO
55 | MTA1 | MTA1 | MTA1 | 9752 | -0.022 | 0.26 | NO
56 | BMI1 | BMI1 | BMI1 | 9855 | -0.023 | 0.26 | NO
57 | TRRAP | TRRAP | TRRAP | 9857 | -0.023 | 0.26 | NO
58 | PRDX3 | PRDX3 | PRDX3 | 9895 | -0.024 | 0.26 | NO
59 | NME2 | NME2 | NME2 | 10192 | -0.029 | 0.25 | NO
60 | KAT5 | KAT5 | KAT5 | 10347 | -0.032 | 0.25 | NO
61 | SMAD4 | SMAD4 | SMAD4 | 10599 | -0.036 | 0.24 | NO
62 | IREB2 | IREB2 | IREB2 | 11077 | -0.046 | 0.22 | NO
63 | KIR3DL1 | KIR3DL1 | KIR3DL1 | 11092 | -0.046 | 0.22 | NO
64 | ODC1 | ODC1 | ODC1 | 11290 | -0.05 | 0.21 | NO
65 | TP53 | TP53 | TP53 | 11310 | -0.051 | 0.22 | NO
66 | SMAD3 | SMAD3 | SMAD3 | 11400 | -0.053 | 0.22 | NO
67 | UBTF | UBTF | UBTF | 11537 | -0.056 | 0.22 | NO
68 | TAF10 | TAF10 | TAF10 | 11737 | -0.06 | 0.21 | NO
69 | CREBBP | CREBBP | CREBBP | 11796 | -0.062 | 0.22 | NO
70 | PTMA | PTMA | PTMA | 11854 | -0.063 | 0.22 | NO
71 | RPL11 | RPL11 | RPL11 | 12296 | -0.074 | 0.21 | NO
72 | PEG10 | PEG10 | PEG10 | 12544 | -0.081 | 0.2 | NO
73 | ID2 | ID2 | ID2 | 12766 | -0.086 | 0.2 | NO
74 | KAT2A | KAT2A | KAT2A | 13993 | -0.13 | 0.14 | NO
75 | SHMT1 | SHMT1 | SHMT1 | 14303 | -0.14 | 0.14 | NO
76 | PFKM | PFKM | PFKM | 14823 | -0.17 | 0.14 | NO
77 | CCND2 | CCND2 | CCND2 | 15078 | -0.19 | 0.14 | NO
78 | SERPINI1 | SERPINI1 | SERPINI1 | 16135 | -0.27 | 0.11 | 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 HEMATOPOIETIC CELL LINEAGE.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HEMATOPOIETIC CELL LINEAGE, 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 T CELL RECEPTOR SIGNALING PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | RASGRP3 | RASGRP3 | RASGRP3 | 764 | 0.36 | 0.016 | YES
2 | PRKCB | PRKCB | PRKCB | 937 | 0.34 | 0.06 | YES
3 | BCL10 | BCL10 | BCL10 | 1914 | 0.22 | 0.042 | YES
4 | AKT3 | AKT3 | AKT3 | 2102 | 0.21 | 0.064 | YES
5 | REL | REL | REL | 2147 | 0.2 | 0.095 | YES
6 | TRIB3 | TRIB3 | TRIB3 | 2392 | 0.18 | 0.11 | YES
7 | PSME4 | PSME4 | PSME4 | 2414 | 0.18 | 0.14 | YES
8 | NFKBIE | NFKBIE | NFKBIE | 3014 | 0.15 | 0.13 | YES
9 | NRAS | NRAS | NRAS | 3244 | 0.13 | 0.14 | YES
10 | CDKN1A | CDKN1A | CDKN1A | 3324 | 0.13 | 0.15 | YES
11 | MALT1 | MALT1 | MALT1 | 3359 | 0.13 | 0.17 | YES
12 | NFKBIB | NFKBIB | NFKBIB | 3408 | 0.12 | 0.19 | YES
13 | PSMA5 | PSMA5 | PSMA5 | 3922 | 0.1 | 0.18 | YES
14 | PSMA6 | PSMA6 | PSMA6 | 3951 | 0.1 | 0.19 | YES
15 | PSME2 | PSME2 | PSME2 | 3958 | 0.1 | 0.21 | YES
16 | PSMA8 | PSMA8 | PSMA8 | 4074 | 0.097 | 0.22 | YES
17 | PSMA3 | PSMA3 | PSMA3 | 4102 | 0.096 | 0.23 | YES
18 | PSMD11 | PSMD11 | PSMD11 | 4237 | 0.091 | 0.24 | YES
19 | PSMD12 | PSMD12 | PSMD12 | 4502 | 0.083 | 0.24 | YES
20 | PSMB10 | PSMB10 | PSMB10 | 4534 | 0.082 | 0.25 | YES
21 | PSMC4 | PSMC4 | PSMC4 | 4681 | 0.077 | 0.25 | YES
22 | PSMC6 | PSMC6 | PSMC6 | 4795 | 0.074 | 0.26 | YES
23 | PSMD2 | PSMD2 | PSMD2 | 4832 | 0.073 | 0.27 | YES
24 | PSMD13 | PSMD13 | PSMD13 | 4905 | 0.071 | 0.28 | YES
25 | PSMB5 | PSMB5 | PSMB5 | 5000 | 0.068 | 0.28 | YES
26 | PSMA7 | PSMA7 | PSMA7 | 5032 | 0.067 | 0.29 | YES
27 | RASGRP1 | RASGRP1 | RASGRP1 | 5083 | 0.066 | 0.3 | YES
28 | PSMD14 | PSMD14 | PSMD14 | 5185 | 0.063 | 0.3 | YES
29 | PSMC1 | PSMC1 | PSMC1 | 5192 | 0.063 | 0.31 | YES
30 | AKT1 | AKT1 | AKT1 | 5196 | 0.063 | 0.32 | YES
31 | CHUK | CHUK | CHUK | 5216 | 0.062 | 0.33 | YES
32 | MTOR | MTOR | MTOR | 5310 | 0.06 | 0.34 | YES
33 | PSMB9 | PSMB9 | PSMB9 | 5349 | 0.059 | 0.34 | YES
34 | PSMF1 | PSMF1 | PSMF1 | 5544 | 0.054 | 0.34 | YES
35 | PSMB6 | PSMB6 | PSMB6 | 5588 | 0.054 | 0.35 | YES
36 | PSMD7 | PSMD7 | PSMD7 | 5687 | 0.052 | 0.35 | YES
37 | PSMD6 | PSMD6 | PSMD6 | 5692 | 0.052 | 0.36 | YES
38 | NFKBIA | NFKBIA | NFKBIA | 5831 | 0.049 | 0.36 | YES
39 | PSMD1 | PSMD1 | PSMD1 | 5884 | 0.048 | 0.36 | YES
40 | FOXO1 | FOXO1 | FOXO1 | 5936 | 0.047 | 0.37 | YES
41 | PSMB3 | PSMB3 | PSMB3 | 5953 | 0.046 | 0.38 | YES
42 | PSMB2 | PSMB2 | PSMB2 | 6010 | 0.045 | 0.38 | YES
43 | KRAS | KRAS | KRAS | 6089 | 0.043 | 0.38 | YES
44 | PSMD8 | PSMD8 | PSMD8 | 6101 | 0.043 | 0.39 | YES
45 | PSMD3 | PSMD3 | PSMD3 | 6211 | 0.04 | 0.39 | YES
46 | PSME1 | PSME1 | PSME1 | 6462 | 0.036 | 0.38 | NO
47 | PSMD5 | PSMD5 | PSMD5 | 6566 | 0.033 | 0.38 | NO
48 | PSMC3 | PSMC3 | PSMC3 | 6656 | 0.032 | 0.38 | NO
49 | PSMC2 | PSMC2 | PSMC2 | 6762 | 0.03 | 0.38 | NO
50 | PSMA1 | PSMA1 | PSMA1 | 6806 | 0.029 | 0.38 | NO
51 | IKBKG | IKBKG | IKBKG | 6912 | 0.026 | 0.38 | NO
52 | PSMD9 | PSMD9 | PSMD9 | 6960 | 0.026 | 0.38 | NO
53 | PSMA2 | PSMA2 | PSMA2 | 6996 | 0.025 | 0.38 | NO
54 | PSMA4 | PSMA4 | PSMA4 | 7225 | 0.021 | 0.37 | NO
55 | MAP3K7 | MAP3K7 | MAP3K7 | 7309 | 0.019 | 0.37 | NO
56 | PSMB4 | PSMB4 | PSMB4 | 7726 | 0.012 | 0.35 | NO
57 | CUL1 | CUL1 | CUL1 | 7741 | 0.012 | 0.35 | NO
58 | PSMC5 | PSMC5 | PSMC5 | 7862 | 0.0099 | 0.35 | NO
59 | PSMD4 | PSMD4 | PSMD4 | 8010 | 0.0075 | 0.34 | NO
60 | HRAS | HRAS | HRAS | 8032 | 0.0071 | 0.34 | NO
61 | PSMB7 | PSMB7 | PSMB7 | 8065 | 0.0066 | 0.34 | NO
62 | GSK3A | GSK3A | GSK3A | 8108 | 0.0058 | 0.34 | NO
63 | PHLPP1 | PHLPP1 | PHLPP1 | 8179 | 0.0045 | 0.34 | NO
64 | PSMB1 | PSMB1 | PSMB1 | 8237 | 0.0036 | 0.33 | NO
65 | PDPK1 | PDPK1 | PDPK1 | 8252 | 0.0034 | 0.33 | NO
66 | AKT1S1 | AKT1S1 | AKT1S1 | 8333 | 0.002 | 0.33 | NO
67 | MAPKAP1 | MAPKAP1 | MAPKAP1 | 8426 | 0.00023 | 0.32 | NO
68 | RELA | RELA | RELA | 8468 | -0.00039 | 0.32 | NO
69 | CREB1 | CREB1 | CREB1 | 8492 | -0.00088 | 0.32 | NO
70 | BTRC | BTRC | BTRC | 8603 | -0.0027 | 0.31 | NO
71 | NR4A1 | NR4A1 | NR4A1 | 8713 | -0.0045 | 0.31 | NO
72 | CDKN1B | CDKN1B | CDKN1B | 9078 | -0.011 | 0.29 | NO
73 | MDM2 | MDM2 | MDM2 | 9172 | -0.012 | 0.29 | NO
74 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 9249 | -0.014 | 0.29 | NO
75 | PSMB8 | PSMB8 | PSMB8 | 9607 | -0.019 | 0.27 | NO
76 | PSMD10 | PSMD10 | PSMD10 | 9808 | -0.023 | 0.26 | NO
77 | PTEN | PTEN | PTEN | 9923 | -0.025 | 0.26 | NO
78 | IKBKB | IKBKB | IKBKB | 10285 | -0.031 | 0.24 | NO
79 | TSC2 | TSC2 | TSC2 | 10290 | -0.031 | 0.25 | NO
80 | AKT2 | AKT2 | AKT2 | 10369 | -0.032 | 0.25 | NO
81 | UBA52 | UBA52 | UBA52 | 10630 | -0.037 | 0.24 | NO
82 | SKP1 | SKP1 | SKP1 | 10847 | -0.041 | 0.24 | NO
83 | FOXO3 | FOXO3 | FOXO3 | 11064 | -0.045 | 0.23 | NO
84 | RPS27A | RPS27A | RPS27A | 11209 | -0.049 | 0.23 | NO
85 | MLST8 | MLST8 | MLST8 | 11819 | -0.062 | 0.21 | NO
86 | FBXW11 | FBXW11 | FBXW11 | 12087 | -0.069 | 0.2 | NO
87 | THEM4 | THEM4 | THEM4 | 13274 | -0.1 | 0.16 | NO
88 | BAD | BAD | BAD | 13782 | -0.12 | 0.15 | NO
89 | CASP9 | CASP9 | CASP9 | 13795 | -0.12 | 0.16 | NO
90 | FOXO4 | FOXO4 | FOXO4 | 13891 | -0.13 | 0.18 | NO
91 | RICTOR | RICTOR | RICTOR | 14898 | -0.18 | 0.15 | NO
92 | CARD11 | CARD11 | CARD11 | 15051 | -0.18 | 0.17 | 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 T CELL RECEPTOR SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG B CELL RECEPTOR SIGNALING PATHWAY

Table S29. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | MMP9 | MMP9 | MMP9 | 239 | 0.49 | 0.074 | YES
2 | THBS1 | THBS1 | THBS1 | 375 | 0.44 | 0.15 | YES
3 | ADAM12 | ADAM12 | ADAM12 | 377 | 0.44 | 0.22 | YES
4 | TFPI | TFPI | TFPI | 639 | 0.38 | 0.28 | YES
5 | CCL5 | CCL5 | CCL5 | 848 | 0.35 | 0.33 | YES
6 | TNC | TNC | TNC | 896 | 0.34 | 0.39 | YES
7 | ITGA5 | ITGA5 | ITGA5 | 932 | 0.34 | 0.44 | YES
8 | FGF2 | FGF2 | FGF2 | 1069 | 0.32 | 0.49 | YES
9 | ACTN1 | ACTN1 | ACTN1 | 1519 | 0.26 | 0.52 | YES
10 | FN1 | FN1 | FN1 | 1553 | 0.26 | 0.56 | YES
11 | PRKCA | PRKCA | PRKCA | 1659 | 0.25 | 0.6 | YES
12 | F2 | F2 | F2 | 2126 | 0.2 | 0.61 | YES
13 | TNFRSF13B | TNFRSF13B | TNFRSF13B | 2556 | 0.17 | 0.62 | YES
14 | ITGB1 | ITGB1 | ITGB1 | 2726 | 0.16 | 0.64 | YES
15 | CXCR4 | CXCR4 | CXCR4 | 2816 | 0.16 | 0.66 | YES
16 | PRKCD | PRKCD | PRKCD | 2883 | 0.15 | 0.68 | YES
17 | LAMA1 | LAMA1 | LAMA1 | 3137 | 0.14 | 0.69 | YES
18 | RHOA | RHOA | RHOA | 5381 | 0.058 | 0.58 | NO
19 | SDCBP | SDCBP | SDCBP | 5988 | 0.045 | 0.56 | NO
20 | CXCL12 | CXCL12 | CXCL12 | 6007 | 0.045 | 0.56 | NO
21 | RAC1 | RAC1 | RAC1 | 7867 | 0.0098 | 0.46 | NO
22 | DNM2 | DNM2 | DNM2 | 8093 | 0.0061 | 0.45 | NO
23 | FGFR1 | FGFR1 | FGFR1 | 8845 | -0.0067 | 0.41 | NO
24 | GIPC1 | GIPC1 | GIPC1 | 10019 | -0.026 | 0.35 | NO
25 | SDC4 | SDC4 | SDC4 | 10125 | -0.028 | 0.35 | NO
26 | PTK2 | PTK2 | PTK2 | 10817 | -0.04 | 0.32 | NO
27 | MDK | MDK | MDK | 11429 | -0.053 | 0.29 | NO
28 | FZD7 | FZD7 | FZD7 | 11953 | -0.065 | 0.28 | NO
29 | NUDT16L1 | NUDT16L1 | NUDT16L1 | 12964 | -0.092 | 0.24 | NO
30 | LAMA3 | LAMA3 | LAMA3 | 16246 | -0.28 | 0.11 | 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 B CELL RECEPTOR SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS

Table S30. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | ITK | ITK | ITK | 203 | 0.51 | 0.059 | YES
2 | LCK | LCK | LCK | 274 | 0.48 | 0.12 | YES
3 | DAPP1 | DAPP1 | DAPP1 | 346 | 0.45 | 0.18 | YES
4 | PIK3CG | PIK3CG | PIK3CG | 407 | 0.44 | 0.24 | YES
5 | ARAP3 | ARAP3 | ARAP3 | 478 | 0.42 | 0.29 | YES
6 | LAT | LAT | LAT | 751 | 0.36 | 0.32 | YES
7 | ZAP70 | ZAP70 | ZAP70 | 770 | 0.36 | 0.37 | YES
8 | PIK3R5 | PIK3R5 | PIK3R5 | 835 | 0.35 | 0.42 | YES
9 | HCK | HCK | HCK | 1102 | 0.31 | 0.44 | YES
10 | PIK3R6 | PIK3R6 | PIK3R6 | 1283 | 0.29 | 0.47 | YES
11 | FGR | FGR | FGR | 1325 | 0.28 | 0.51 | YES
12 | BTK | BTK | BTK | 1475 | 0.26 | 0.54 | YES
13 | LYN | LYN | LYN | 2185 | 0.2 | 0.53 | YES
14 | PIK3R3 | PIK3R3 | PIK3R3 | 2366 | 0.19 | 0.54 | YES
15 | SYK | SYK | SYK | 2617 | 0.17 | 0.55 | YES
16 | BLK | BLK | BLK | 2793 | 0.16 | 0.56 | YES
17 | ARF6 | ARF6 | ARF6 | 2866 | 0.16 | 0.58 | YES
18 | ADAP1 | ADAP1 | ADAP1 | 2890 | 0.15 | 0.6 | YES
19 | BLNK | BLNK | BLNK | 2903 | 0.15 | 0.62 | YES
20 | PLCG2 | PLCG2 | PLCG2 | 3148 | 0.14 | 0.63 | YES
21 | NRAS | NRAS | NRAS | 3244 | 0.13 | 0.64 | YES
22 | RAP1A | RAP1A | RAP1A | 3308 | 0.13 | 0.65 | YES
23 | PIK3CD | PIK3CD | PIK3CD | 4067 | 0.097 | 0.63 | NO
24 | SGK1 | SGK1 | SGK1 | 4268 | 0.09 | 0.63 | NO
25 | CYTH1 | CYTH1 | CYTH1 | 4740 | 0.076 | 0.61 | NO
26 | RHOA | RHOA | RHOA | 5381 | 0.058 | 0.58 | NO
27 | INPP5D | INPP5D | INPP5D | 5542 | 0.055 | 0.58 | NO
28 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 5684 | 0.052 | 0.58 | NO
29 | KRAS | KRAS | KRAS | 6089 | 0.043 | 0.57 | NO
30 | PIK3CA | PIK3CA | PIK3CA | 6489 | 0.035 | 0.55 | NO
31 | CYTH2 | CYTH2 | CYTH2 | 6886 | 0.027 | 0.53 | NO
32 | YES1 | YES1 | YES1 | 6969 | 0.025 | 0.53 | NO
33 | INPPL1 | INPPL1 | INPPL1 | 7792 | 0.011 | 0.49 | NO
34 | RAC1 | RAC1 | RAC1 | 7867 | 0.0098 | 0.48 | NO
35 | HRAS | HRAS | HRAS | 8032 | 0.0071 | 0.48 | NO
36 | PDPK1 | PDPK1 | PDPK1 | 8252 | 0.0034 | 0.46 | NO
37 | ARF1 | ARF1 | ARF1 | 8448 | -0.000096 | 0.45 | NO
38 | PLCG1 | PLCG1 | PLCG1 | 8947 | -0.0085 | 0.43 | NO
39 | FYN | FYN | FYN | 9108 | -0.011 | 0.42 | NO
40 | SRC | SRC | SRC | 9350 | -0.015 | 0.41 | NO
41 | PLEKHA2 | PLEKHA2 | PLEKHA2 | 9423 | -0.016 | 0.41 | NO
42 | PTEN | PTEN | PTEN | 9923 | -0.025 | 0.38 | NO
43 | ARF5 | ARF5 | ARF5 | 10473 | -0.034 | 0.36 | NO
44 | FOXO3 | FOXO3 | FOXO3 | 11064 | -0.045 | 0.33 | NO
45 | PIK3CB | PIK3CB | PIK3CB | 11271 | -0.05 | 0.33 | NO
46 | PIK3R1 | PIK3R1 | PIK3R1 | 12438 | -0.078 | 0.27 | NO
47 | PIK3R2 | PIK3R2 | PIK3R2 | 12516 | -0.08 | 0.28 | NO
48 | CYTH3 | CYTH3 | CYTH3 | 12818 | -0.088 | 0.28 | NO
49 | PLEKHA1 | PLEKHA1 | PLEKHA1 | 14570 | -0.16 | 0.2 | NO

Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS, 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 clus4 enriched pathways

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

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
KEGG WNT SIGNALING PATHWAY | 145 | genes.ES.table | 0.48 | 1.7 | 0.0058 | 1 | 0.85 | 0.29 | 0.19 | 0.24 | 0.55 | 0.29
KEGG TGF BETA SIGNALING PATHWAY | 85 | genes.ES.table | 0.59 | 1.7 | 0.0021 | 0.98 | 0.86 | 0.33 | 0.13 | 0.29 | 0.53 | 0.28
KEGG LONG TERM POTENTIATION | 68 | genes.ES.table | 0.49 | 1.6 | 0.0061 | 0.73 | 0.9 | 0.25 | 0.15 | 0.21 | 0.41 | 0.2
KEGG MELANOGENESIS | 99 | genes.ES.table | 0.51 | 1.6 | 0.006 | 0.64 | 0.9 | 0.35 | 0.19 | 0.29 | 0.36 | 0.17
KEGG BASAL CELL CARCINOMA | 54 | genes.ES.table | 0.61 | 1.7 | 0.01 | 0.69 | 0.87 | 0.5 | 0.19 | 0.41 | 0.38 | 0.19
BIOCARTA ALK PATHWAY | 36 | genes.ES.table | 0.6 | 1.7 | 0.0063 | 1 | 0.83 | 0.22 | 0.078 | 0.2 | 0.57 | 0.32
ST WNT BETA CATENIN PATHWAY | 31 | genes.ES.table | 0.58 | 1.6 | 0.012 | 0.53 | 0.91 | 0.23 | 0.07 | 0.21 | 0.3 | 0.14
PID EPHBFWDPATHWAY | 40 | genes.ES.table | 0.45 | 1.6 | 0.0093 | 0.61 | 0.9 | 0.28 | 0.23 | 0.21 | 0.35 | 0.17
PID P75NTRPATHWAY | 68 | genes.ES.table | 0.44 | 1.8 | 0 | 1 | 0.61 | 0.18 | 0.12 | 0.16 | 1 | 0.51
PID HEDGEHOG GLIPATHWAY | 48 | genes.ES.table | 0.45 | 1.7 | 0.0083 | 0.89 | 0.87 | 0.33 | 0.28 | 0.24 | 0.49 | 0.25

genes ES table in pathway: KEGG WNT SIGNALING PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | MAG | MAG | MAG | 125 | 0.6 | 0.075 | YES
2 | NGFR | NGFR | NGFR | 227 | 0.53 | 0.14 | YES
3 | RTN4R | RTN4R | RTN4R | 635 | 0.41 | 0.18 | YES
4 | BEX1 | BEX1 | BEX1 | 854 | 0.37 | 0.22 | YES
5 | MAPK10 | MAPK10 | MAPK10 | 1145 | 0.33 | 0.24 | YES
6 | NTF4 | NTF4 | NTF4 | 1306 | 0.3 | 0.28 | YES
7 | BDNF | BDNF | BDNF | 1309 | 0.3 | 0.32 | YES
8 | NGF | NGF | NGF | 1310 | 0.3 | 0.36 | YES
9 | NTRK1 | NTRK1 | NTRK1 | 1904 | 0.24 | 0.36 | YES
10 | NTF3 | NTF3 | NTF3 | 2038 | 0.24 | 0.39 | YES
11 | LINGO1 | LINGO1 | LINGO1 | 2222 | 0.22 | 0.41 | YES
12 | E2F1 | E2F1 | E2F1 | 2241 | 0.22 | 0.44 | YES
13 | MMP3 | MMP3 | MMP3 | 3893 | 0.13 | 0.36 | NO
14 | NGFRAP1 | NGFRAP1 | NGFRAP1 | 4459 | 0.11 | 0.35 | NO
15 | TP53 | TP53 | TP53 | 4609 | 0.11 | 0.35 | NO
16 | APAF1 | APAF1 | APAF1 | 4676 | 0.1 | 0.36 | NO
17 | BCL2L11 | BCL2L11 | BCL2L11 | 4888 | 0.097 | 0.36 | NO
18 | MMP7 | MMP7 | MMP7 | 5584 | 0.079 | 0.34 | NO
19 | OMG | OMG | OMG | 6942 | 0.051 | 0.27 | NO
20 | APP | APP | APP | 6970 | 0.05 | 0.28 | NO
21 | AKT1 | AKT1 | AKT1 | 7187 | 0.046 | 0.27 | NO
22 | FURIN | FURIN | FURIN | 8045 | 0.032 | 0.23 | NO
23 | DIABLO | DIABLO | DIABLO | 8064 | 0.032 | 0.23 | NO
24 | YWHAE | YWHAE | YWHAE | 8149 | 0.03 | 0.23 | NO
25 | MAGED1 | MAGED1 | MAGED1 | 8469 | 0.025 | 0.22 | NO
26 | XIAP | XIAP | XIAP | 8577 | 0.024 | 0.21 | NO
27 | IKBKG | IKBKG | IKBKG | 9006 | 0.018 | 0.19 | NO
28 | CASP9 | CASP9 | CASP9 | 9318 | 0.014 | 0.18 | NO
29 | PRKACB | PRKACB | PRKACB | 9537 | 0.011 | 0.17 | NO
30 | SHC1 | SHC1 | SHC1 | 9592 | 0.01 | 0.16 | NO
31 | IKBKB | IKBKB | IKBKB | 9799 | 0.0074 | 0.15 | NO
32 | RAC1 | RAC1 | RAC1 | 10220 | 0.0013 | 0.13 | NO
33 | PIK3R1 | PIK3R1 | PIK3R1 | 10547 | -0.0028 | 0.11 | NO
34 | MAPK8 | MAPK8 | MAPK8 | 10610 | -0.0038 | 0.11 | NO
35 | PRKCI | PRKCI | PRKCI | 10804 | -0.0064 | 0.1 | NO
36 | PRDM4 | PRDM4 | PRDM4 | 10932 | -0.0082 | 0.094 | NO
37 | NCSTN | NCSTN | NCSTN | 11042 | -0.0097 | 0.09 | NO
38 | NDN | NDN | NDN | 11689 | -0.019 | 0.057 | NO
39 | SMPD2 | SMPD2 | SMPD2 | 11720 | -0.019 | 0.058 | NO
40 | APH1A | APH1A | APH1A | 11722 | -0.019 | 0.06 | NO
41 | PSEN1 | PSEN1 | PSEN1 | 11754 | -0.02 | 0.061 | NO
42 | ADAM17 | ADAM17 | ADAM17 | 12341 | -0.029 | 0.033 | NO
43 | ARHGDIA | ARHGDIA | ARHGDIA | 12454 | -0.03 | 0.031 | NO
44 | RHOC | RHOC | RHOC | 12492 | -0.031 | 0.033 | NO
45 | BIRC2 | BIRC2 | BIRC2 | 12967 | -0.038 | 0.012 | NO
46 | BAD | BAD | BAD | 13187 | -0.042 | 0.006 | NO
47 | RTN4 | RTN4 | RTN4 | 13199 | -0.043 | 0.011 | NO
48 | RHOA | RHOA | RHOA | 13360 | -0.046 | 0.0087 | NO
49 | SORT1 | SORT1 | SORT1 | 13510 | -0.048 | 0.007 | NO
50 | RHOB | RHOB | RHOB | 13521 | -0.048 | 0.013 | NO
51 | NDNL2 | NDNL2 | NDNL2 | 13597 | -0.05 | 0.016 | NO
52 | MAPK9 | MAPK9 | MAPK9 | 13611 | -0.05 | 0.022 | NO
53 | CHUK | CHUK | CHUK | 13670 | -0.051 | 0.026 | NO
54 | MAGEH1 | MAGEH1 | MAGEH1 | 13758 | -0.053 | 0.028 | NO
55 | IRAK1 | IRAK1 | IRAK1 | 13781 | -0.053 | 0.034 | NO
56 | TRAF6 | TRAF6 | TRAF6 | 14029 | -0.059 | 0.029 | NO
57 | PSENEN | PSENEN | PSENEN | 14623 | -0.072 | 0.0059 | NO
58 | SQSTM1 | SQSTM1 | SQSTM1 | 14784 | -0.076 | 0.0075 | NO
59 | PIK3CA | PIK3CA | PIK3CA | 14831 | -0.077 | 0.016 | NO
60 | APH1B | APH1B | APH1B | 15078 | -0.083 | 0.013 | NO
61 | MYD88 | MYD88 | MYD88 | 15177 | -0.086 | 0.02 | NO
62 | ZNF274 | ZNF274 | ZNF274 | 15640 | -0.1 | 0.0082 | NO
63 | CYCS | CYCS | CYCS | 15743 | -0.11 | 0.017 | NO
64 | PRKCZ | PRKCZ | PRKCZ | 15856 | -0.11 | 0.026 | NO
65 | CASP3 | CASP3 | CASP3 | 15928 | -0.11 | 0.038 | NO
66 | CASP6 | CASP6 | CASP6 | 16188 | -0.13 | 0.041 | NO
67 | RIPK2 | RIPK2 | RIPK2 | 16283 | -0.13 | 0.054 | NO
68 | BIRC3 | BIRC3 | BIRC3 | 18004 | -0.38 | 0.01 | NO

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

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

genes ES table in pathway: KEGG TGF BETA SIGNALING PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GPC2 | GPC2 | GPC2 | 194 | 0.55 | 0.1 | YES
2 | B3GAT1 | B3GAT1 | B3GAT1 | 583 | 0.42 | 0.17 | YES
3 | GPC4 | GPC4 | GPC4 | 596 | 0.42 | 0.25 | YES
4 | GPC5 | GPC5 | GPC5 | 729 | 0.39 | 0.32 | YES
5 | CSPG4 | CSPG4 | CSPG4 | 848 | 0.37 | 0.4 | YES
6 | BCAN | BCAN | BCAN | 1031 | 0.34 | 0.46 | YES
7 | GPC6 | GPC6 | GPC6 | 1253 | 0.31 | 0.51 | YES
8 | B3GAT2 | B3GAT2 | B3GAT2 | 1302 | 0.3 | 0.57 | YES
9 | SDC2 | SDC2 | SDC2 | 1324 | 0.3 | 0.63 | YES
10 | BGN | BGN | BGN | 1920 | 0.24 | 0.64 | YES
11 | VCAN | VCAN | VCAN | 2350 | 0.21 | 0.66 | YES
12 | SDC1 | SDC1 | SDC1 | 3260 | 0.16 | 0.65 | YES
13 | GPC1 | GPC1 | GPC1 | 3427 | 0.16 | 0.67 | YES
14 | GPC3 | GPC3 | GPC3 | 3521 | 0.15 | 0.69 | YES
15 | NCAN | NCAN | NCAN | 4205 | 0.12 | 0.68 | NO
16 | DCN | DCN | DCN | 4617 | 0.11 | 0.68 | NO
17 | HSPG2 | HSPG2 | HSPG2 | 4907 | 0.096 | 0.68 | NO
18 | B3GALT6 | B3GALT6 | B3GALT6 | 5256 | 0.087 | 0.68 | NO
19 | GXYLT1 | GXYLT1 | GXYLT1 | 6980 | 0.05 | 0.6 | NO
20 | SDC3 | SDC3 | SDC3 | 7986 | 0.033 | 0.55 | NO
21 | SDC4 | SDC4 | SDC4 | 9276 | 0.015 | 0.48 | NO
22 | B3GAT3 | B3GAT3 | B3GAT3 | 9916 | 0.0059 | 0.45 | NO
23 | AGRN | AGRN | AGRN | 10246 | 0.00098 | 0.43 | NO
24 | B4GALT7 | B4GALT7 | B4GALT7 | 10282 | 0.00051 | 0.43 | NO
25 | GXYLT2 | GXYLT2 | GXYLT2 | 12868 | -0.037 | 0.29 | NO

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

Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TGF BETA 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 LONG TERM POTENTIATION

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | COL2A1 | COL2A1 | COL2A1 | 44 | 0.7 | 0.061 | YES
2 | COL9A1 | COL9A1 | COL9A1 | 75 | 0.64 | 0.12 | YES
3 | ST8SIA2 | ST8SIA2 | ST8SIA2 | 76 | 0.64 | 0.18 | YES
4 | CACNA1G | CACNA1G | CACNA1G | 170 | 0.57 | 0.22 | YES
5 | CNTN2 | CNTN2 | CNTN2 | 221 | 0.54 | 0.27 | YES
6 | NCAM1 | NCAM1 | NCAM1 | 276 | 0.52 | 0.31 | YES
7 | GFRA2 | GFRA2 | GFRA2 | 316 | 0.5 | 0.36 | YES
8 | NRTN | NRTN | NRTN | 369 | 0.48 | 0.4 | YES
9 | COL9A2 | COL9A2 | COL9A2 | 556 | 0.43 | 0.43 | YES
10 | CACNA1H | CACNA1H | CACNA1H | 628 | 0.41 | 0.46 | YES
11 | COL9A3 | COL9A3 | COL9A3 | 688 | 0.4 | 0.49 | YES
12 | COL4A2 | COL4A2 | COL4A2 | 1351 | 0.3 | 0.48 | YES
13 | COL4A1 | COL4A1 | COL4A1 | 1386 | 0.29 | 0.51 | YES
14 | SPTBN5 | SPTBN5 | SPTBN5 | 1693 | 0.26 | 0.52 | YES
15 | GDNF | GDNF | GDNF | 1724 | 0.26 | 0.54 | YES
16 | CACNA1I | CACNA1I | CACNA1I | 1841 | 0.25 | 0.55 | YES
17 | GFRA1 | GFRA1 | GFRA1 | 2136 | 0.23 | 0.56 | YES
18 | CACNB1 | CACNB1 | CACNB1 | 2286 | 0.22 | 0.57 | YES
19 | COL6A3 | COL6A3 | COL6A3 | 2461 | 0.21 | 0.58 | YES
20 | SPTB | SPTB | SPTB | 2481 | 0.2 | 0.6 | YES
21 | CACNB3 | CACNB3 | CACNB3 | 2496 | 0.2 | 0.61 | YES
22 | CDK1 | CDK1 | CDK1 | 3256 | 0.16 | 0.59 | NO
23 | COL5A1 | COL5A1 | COL5A1 | 3397 | 0.16 | 0.59 | NO
24 | COL3A1 | COL3A1 | COL3A1 | 3751 | 0.14 | 0.59 | NO
25 | COL1A2 | COL1A2 | COL1A2 | 3907 | 0.13 | 0.59 | NO
26 | SRC | SRC | SRC | 4195 | 0.12 | 0.58 | NO
27 | NCAN | NCAN | NCAN | 4205 | 0.12 | 0.6 | NO
28 | CACNA1S | CACNA1S | CACNA1S | 4424 | 0.11 | 0.59 | NO
29 | COL6A1 | COL6A1 | COL6A1 | 4464 | 0.11 | 0.6 | NO
30 | CACNB4 | CACNB4 | CACNB4 | 4674 | 0.1 | 0.6 | NO
31 | COL5A2 | COL5A2 | COL5A2 | 4685 | 0.1 | 0.61 | NO
32 | COL6A2 | COL6A2 | COL6A2 | 5003 | 0.094 | 0.6 | NO
33 | FGFR1 | FGFR1 | FGFR1 | 5272 | 0.086 | 0.59 | NO
34 | COL1A1 | COL1A1 | COL1A1 | 5526 | 0.08 | 0.59 | NO
35 | COL4A5 | COL4A5 | COL4A5 | 5850 | 0.073 | 0.57 | NO
36 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 6567 | 0.057 | 0.54 | NO
37 | KRAS | KRAS | KRAS | 6691 | 0.055 | 0.54 | NO
38 | ARTN | ARTN | ARTN | 6717 | 0.054 | 0.54 | NO
39 | SPTBN1 | SPTBN1 | SPTBN1 | 6862 | 0.052 | 0.54 | NO
40 | PSPN | PSPN | PSPN | 7307 | 0.044 | 0.52 | NO
41 | CREB1 | CREB1 | CREB1 | 7706 | 0.038 | 0.5 | NO
42 | MAP2K2 | MAP2K2 | MAP2K2 | 7770 | 0.037 | 0.5 | NO
43 | SPTBN2 | SPTBN2 | SPTBN2 | 8696 | 0.022 | 0.45 | NO
44 | PTK2 | PTK2 | PTK2 | 8710 | 0.022 | 0.45 | NO
45 | AGRN | AGRN | AGRN | 10246 | 0.00098 | 0.37 | NO
46 | RAF1 | RAF1 | RAF1 | 10267 | 0.00061 | 0.37 | NO
47 | MAPK1 | MAPK1 | MAPK1 | 10386 | -0.00086 | 0.36 | NO
48 | SOS1 | SOS1 | SOS1 | 10627 | -0.004 | 0.35 | NO
49 | COL4A4 | COL4A4 | COL4A4 | 11063 | -0.01 | 0.32 | NO
50 | SPTAN1 | SPTAN1 | SPTAN1 | 11096 | -0.01 | 0.32 | NO
51 | HRAS | HRAS | HRAS | 11904 | -0.022 | 0.28 | NO
52 | YWHAB | YWHAB | YWHAB | 12066 | -0.024 | 0.27 | NO
53 | NRAS | NRAS | NRAS | 12115 | -0.025 | 0.27 | NO
54 | ST8SIA4 | ST8SIA4 | ST8SIA4 | 12746 | -0.035 | 0.24 | NO
55 | GRB2 | GRB2 | GRB2 | 13033 | -0.04 | 0.23 | NO
56 | SPTBN4 | SPTBN4 | SPTBN4 | 13532 | -0.048 | 0.21 | NO
57 | CACNB2 | CACNB2 | CACNB2 | 13727 | -0.052 | 0.2 | NO
58 | MAPK3 | MAPK3 | MAPK3 | 13836 | -0.055 | 0.2 | NO
59 | SPTA1 | SPTA1 | SPTA1 | 14280 | -0.064 | 0.18 | NO
60 | MAP2K1 | MAP2K1 | MAP2K1 | 14342 | -0.066 | 0.18 | NO
61 | PRNP | PRNP | PRNP | 14432 | -0.068 | 0.18 | NO
62 | COL4A3 | COL4A3 | COL4A3 | 14962 | -0.08 | 0.16 | NO
63 | FYN | FYN | FYN | 16837 | -0.17 | 0.075 | NO

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

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

genes ES table in pathway: KEGG MELANOGENESIS

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GPC2 | GPC2 | GPC2 | 194 | 0.55 | 0.061 | YES
2 | UST | UST | UST | 253 | 0.53 | 0.13 | YES
3 | CHST9 | CHST9 | CHST9 | 286 | 0.51 | 0.19 | YES
4 | B3GAT1 | B3GAT1 | B3GAT1 | 583 | 0.42 | 0.23 | YES
5 | GPC4 | GPC4 | GPC4 | 596 | 0.42 | 0.28 | YES
6 | CHSY3 | CHSY3 | CHSY3 | 709 | 0.4 | 0.33 | YES
7 | GPC5 | GPC5 | GPC5 | 729 | 0.39 | 0.38 | YES
8 | CSPG4 | CSPG4 | CSPG4 | 848 | 0.37 | 0.42 | YES
9 | BCAN | BCAN | BCAN | 1031 | 0.34 | 0.46 | YES
10 | GPC6 | GPC6 | GPC6 | 1253 | 0.31 | 0.49 | YES
11 | B3GAT2 | B3GAT2 | B3GAT2 | 1302 | 0.3 | 0.52 | YES
12 | SDC2 | SDC2 | SDC2 | 1324 | 0.3 | 0.56 | YES
13 | BGN | BGN | BGN | 1920 | 0.24 | 0.56 | YES
14 | VCAN | VCAN | VCAN | 2350 | 0.21 | 0.56 | YES
15 | CHST13 | CHST13 | CHST13 | 2917 | 0.18 | 0.56 | YES
16 | SDC1 | SDC1 | SDC1 | 3260 | 0.16 | 0.56 | YES
17 | GPC1 | GPC1 | GPC1 | 3427 | 0.16 | 0.57 | YES
18 | GPC3 | GPC3 | GPC3 | 3521 | 0.15 | 0.58 | YES
19 | CHSY1 | CHSY1 | CHSY1 | 3713 | 0.14 | 0.59 | YES
20 | CHST14 | CHST14 | CHST14 | 4183 | 0.12 | 0.58 | YES
21 | NCAN | NCAN | NCAN | 4205 | 0.12 | 0.6 | YES
22 | DCN | DCN | DCN | 4617 | 0.11 | 0.59 | NO
23 | HSPG2 | HSPG2 | HSPG2 | 4907 | 0.096 | 0.59 | NO
24 | B3GALT6 | B3GALT6 | B3GALT6 | 5256 | 0.087 | 0.58 | NO
25 | CHST11 | CHST11 | CHST11 | 6251 | 0.064 | 0.53 | NO
26 | CSGALNACT2 | CSGALNACT2 | CSGALNACT2 | 6611 | 0.056 | 0.52 | NO
27 | ARSB | ARSB | ARSB | 6634 | 0.056 | 0.52 | NO
28 | GXYLT1 | GXYLT1 | GXYLT1 | 6980 | 0.05 | 0.51 | NO
29 | CHST3 | CHST3 | CHST3 | 7022 | 0.049 | 0.52 | NO
30 | SDC3 | SDC3 | SDC3 | 7986 | 0.033 | 0.47 | NO
31 | CHST12 | CHST12 | CHST12 | 8637 | 0.023 | 0.44 | NO
32 | CHST15 | CHST15 | CHST15 | 8909 | 0.02 | 0.42 | NO
33 | IDS | IDS | IDS | 9049 | 0.018 | 0.42 | NO
34 | SDC4 | SDC4 | SDC4 | 9276 | 0.015 | 0.41 | NO
35 | B3GAT3 | B3GAT3 | B3GAT3 | 9916 | 0.0059 | 0.37 | NO
36 | IDUA | IDUA | IDUA | 9987 | 0.0048 | 0.37 | NO
37 | CHPF2 | CHPF2 | CHPF2 | 10034 | 0.0043 | 0.37 | NO
38 | AGRN | AGRN | AGRN | 10246 | 0.00098 | 0.36 | NO
39 | B4GALT7 | B4GALT7 | B4GALT7 | 10282 | 0.00051 | 0.35 | NO
40 | DSE | DSE | DSE | 11082 | -0.01 | 0.31 | NO
41 | CHPF | CHPF | CHPF | 12621 | -0.033 | 0.23 | NO
42 | GXYLT2 | GXYLT2 | GXYLT2 | 12868 | -0.037 | 0.22 | NO
43 | HEXA | HEXA | HEXA | 13981 | -0.058 | 0.17 | NO
44 | CHST7 | CHST7 | CHST7 | 14707 | -0.074 | 0.14 | NO
45 | HEXB | HEXB | HEXB | 15555 | -0.098 | 0.1 | NO
46 | HYAL1 | HYAL1 | HYAL1 | 15639 | -0.1 | 0.11 | NO
47 | CSGALNACT1 | CSGALNACT1 | CSGALNACT1 | 17298 | -0.21 | 0.049 | NO

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

Figure S68. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MELANOGENESIS, 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 BASAL CELL CARCINOMA

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PRKAR2B | PRKAR2B | PRKAR2B | 1418 | 0.29 | -0.0062 | YES
2 | AZI1 | AZI1 | AZI1 | 2251 | 0.22 | 0.0025 | YES
3 | CENPJ | CENPJ | CENPJ | 2615 | 0.2 | 0.031 | YES
4 | PLK4 | PLK4 | PLK4 | 2860 | 0.18 | 0.063 | YES
5 | TUBA1A | TUBA1A | TUBA1A | 2978 | 0.18 | 0.1 | YES
6 | CDK1 | CDK1 | CDK1 | 3256 | 0.16 | 0.13 | YES
7 | PLK1 | PLK1 | PLK1 | 3266 | 0.16 | 0.16 | YES
8 | NEK2 | NEK2 | NEK2 | 3337 | 0.16 | 0.2 | YES
9 | ALMS1 | ALMS1 | ALMS1 | 3681 | 0.14 | 0.22 | YES
10 | CEP192 | CEP192 | CEP192 | 4133 | 0.12 | 0.22 | YES
11 | CSNK1E | CSNK1E | CSNK1E | 4902 | 0.097 | 0.2 | YES
12 | CEP76 | CEP76 | CEP76 | 4962 | 0.095 | 0.22 | YES
13 | PCNT | PCNT | PCNT | 5034 | 0.093 | 0.24 | YES
14 | CLASP1 | CLASP1 | CLASP1 | 5234 | 0.088 | 0.26 | YES
15 | CEP70 | CEP70 | CEP70 | 5907 | 0.072 | 0.24 | YES
16 | CCNB1 | CCNB1 | CCNB1 | 5929 | 0.071 | 0.25 | YES
17 | CEP135 | CEP135 | CEP135 | 5974 | 0.07 | 0.27 | YES
18 | CEP72 | CEP72 | CEP72 | 6010 | 0.069 | 0.28 | YES
19 | PRKACA | PRKACA | PRKACA | 6057 | 0.068 | 0.3 | YES
20 | OFD1 | OFD1 | OFD1 | 6230 | 0.064 | 0.3 | YES
21 | TUBGCP3 | TUBGCP3 | TUBGCP3 | 6270 | 0.064 | 0.32 | YES
22 | NUMA1 | NUMA1 | NUMA1 | 6309 | 0.063 | 0.33 | YES
23 | CEP57 | CEP57 | CEP57 | 6431 | 0.06 | 0.34 | YES
24 | TUBGCP5 | TUBGCP5 | TUBGCP5 | 6452 | 0.06 | 0.35 | YES
25 | CKAP5 | CKAP5 | CKAP5 | 6453 | 0.06 | 0.37 | YES
26 | CEP250 | CEP250 | CEP250 | 6457 | 0.059 | 0.38 | YES
27 | SSNA1 | SSNA1 | SSNA1 | 6624 | 0.056 | 0.39 | YES
28 | CDK5RAP2 | CDK5RAP2 | CDK5RAP2 | 6683 | 0.055 | 0.4 | YES
29 | PPP2R1A | PPP2R1A | PPP2R1A | 6739 | 0.054 | 0.41 | YES
30 | TUBGCP6 | TUBGCP6 | TUBGCP6 | 6826 | 0.053 | 0.42 | YES
31 | TUBG2 | TUBG2 | TUBG2 | 7088 | 0.048 | 0.41 | NO
32 | PAFAH1B1 | PAFAH1B1 | PAFAH1B1 | 7455 | 0.042 | 0.4 | NO
33 | CEP164 | CEP164 | CEP164 | 7615 | 0.039 | 0.4 | NO
34 | TUBB | TUBB | TUBB | 7988 | 0.033 | 0.39 | NO
35 | YWHAE | YWHAE | YWHAE | 8149 | 0.03 | 0.39 | NO
36 | NINL | NINL | NINL | 8325 | 0.028 | 0.39 | NO
37 | DCTN2 | DCTN2 | DCTN2 | 8544 | 0.024 | 0.38 | NO
38 | PCM1 | PCM1 | PCM1 | 8695 | 0.022 | 0.38 | NO
39 | TUBGCP2 | TUBGCP2 | TUBGCP2 | 9078 | 0.017 | 0.36 | NO
40 | DCTN1 | DCTN1 | DCTN1 | 9226 | 0.015 | 0.36 | NO
41 | NEDD1 | NEDD1 | NEDD1 | 9504 | 0.011 | 0.35 | NO
42 | MAPRE1 | MAPRE1 | MAPRE1 | 9656 | 0.0094 | 0.34 | NO
43 | DYNC1I2 | DYNC1I2 | DYNC1I2 | 10183 | 0.0018 | 0.31 | NO
44 | DYNLL1 | DYNLL1 | DYNLL1 | 10362 | -0.00054 | 0.3 | NO
45 | CEP290 | CEP290 | CEP290 | 10428 | -0.0013 | 0.3 | NO
46 | SDCCAG8 | SDCCAG8 | SDCCAG8 | 10540 | -0.0027 | 0.29 | NO
47 | AKAP9 | AKAP9 | AKAP9 | 10715 | -0.0053 | 0.28 | NO
48 | CSNK1D | CSNK1D | CSNK1D | 11391 | -0.015 | 0.25 | NO
49 | CEP63 | CEP63 | CEP63 | 12321 | -0.028 | 0.21 | NO
50 | HAUS2 | HAUS2 | HAUS2 | 12466 | -0.031 | 0.21 | NO
51 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 12486 | -0.031 | 0.21 | NO
52 | DYNC1H1 | DYNC1H1 | DYNC1H1 | 12575 | -0.032 | 0.22 | NO
53 | DCTN3 | DCTN3 | DCTN3 | 12831 | -0.036 | 0.21 | NO
54 | TUBG1 | TUBG1 | TUBG1 | 12976 | -0.038 | 0.21 | NO
55 | YWHAG | YWHAG | YWHAG | 13261 | -0.044 | 0.21 | NO
56 | ACTR1A | ACTR1A | ACTR1A | 13285 | -0.044 | 0.22 | NO
57 | FGFR1OP | FGFR1OP | FGFR1OP | 13831 | -0.054 | 0.2 | NO
58 | CETN2 | CETN2 | CETN2 | 14532 | -0.07 | 0.18 | NO
59 | TUBA4A | TUBA4A | TUBA4A | 15147 | -0.085 | 0.17 | NO

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

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

genes ES table in pathway: BIOCARTA ALK PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | TGFB2 | TGFB2 | TGFB2 | 61 | 0.67 | 0.13 | YES
2 | CHRD | CHRD | CHRD | 211 | 0.54 | 0.22 | YES
3 | BMP7 | BMP7 | BMP7 | 241 | 0.53 | 0.32 | YES
4 | SMAD6 | SMAD6 | SMAD6 | 582 | 0.42 | 0.38 | YES
5 | NKX2-5 | NKX2-5 | NKX2-5 | 749 | 0.39 | 0.45 | YES
6 | BMP5 | BMP5 | BMP5 | 885 | 0.37 | 0.51 | YES
7 | GATA4 | GATA4 | GATA4 | 1318 | 0.3 | 0.55 | YES
8 | TGFB3 | TGFB3 | TGFB3 | 1429 | 0.29 | 0.6 | YES
9 | FZD1 | FZD1 | FZD1 | 3261 | 0.16 | 0.53 | NO
10 | BMPR2 | BMPR2 | BMPR2 | 3465 | 0.15 | 0.55 | NO
11 | NPPB | NPPB | NPPB | 3905 | 0.13 | 0.55 | NO
12 | BMPR1A | BMPR1A | BMPR1A | 4570 | 0.11 | 0.53 | NO
13 | MAP3K7 | MAP3K7 | MAP3K7 | 4965 | 0.095 | 0.53 | NO
14 | NOG | NOG | NOG | 5399 | 0.083 | 0.52 | NO
15 | TGFBR3 | TGFBR3 | TGFBR3 | 5571 | 0.079 | 0.52 | NO
16 | NPPA | NPPA | NPPA | 5654 | 0.078 | 0.54 | NO
17 | SMAD4 | SMAD4 | SMAD4 | 6012 | 0.069 | 0.53 | NO
18 | CTNNB1 | CTNNB1 | CTNNB1 | 6448 | 0.06 | 0.52 | NO
19 | TGFB1 | TGFB1 | TGFB1 | 6618 | 0.056 | 0.52 | NO
20 | SMAD5 | SMAD5 | SMAD5 | 6687 | 0.055 | 0.52 | NO
21 | HNF1A | HNF1A | HNF1A | 6703 | 0.055 | 0.53 | NO
22 | WNT1 | WNT1 | WNT1 | 7002 | 0.049 | 0.53 | NO
23 | BMP4 | BMP4 | BMP4 | 7173 | 0.046 | 0.53 | NO
24 | MEF2C | MEF2C | MEF2C | 7697 | 0.038 | 0.5 | NO
25 | ACVR1 | ACVR1 | ACVR1 | 8591 | 0.023 | 0.46 | NO
26 | DVL1 | DVL1 | DVL1 | 8800 | 0.021 | 0.45 | NO
27 | MYL2 | MYL2 | MYL2 | 8953 | 0.019 | 0.45 | NO
28 | GSK3B | GSK3B | GSK3B | 10205 | 0.0015 | 0.38 | NO
29 | TGFBR1 | TGFBR1 | TGFBR1 | 10411 | -0.0012 | 0.37 | NO
30 | SMAD1 | SMAD1 | SMAD1 | 11308 | -0.013 | 0.32 | NO
31 | AXIN1 | AXIN1 | AXIN1 | 11831 | -0.021 | 0.3 | NO
32 | RFC1 | RFC1 | RFC1 | 11926 | -0.022 | 0.3 | NO
33 | APC | APC | APC | 13105 | -0.041 | 0.24 | NO
34 | TGFBR2 | TGFBR2 | TGFBR2 | 13298 | -0.044 | 0.24 | NO
35 | ATF2 | ATF2 | ATF2 | 13770 | -0.053 | 0.22 | NO
36 | BMP2 | BMP2 | BMP2 | 15918 | -0.11 | 0.12 | NO

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

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

genes ES table in pathway: ST WNT BETA CATENIN PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | SFRP5 | SFRP5 | SFRP5 | 92 | 0.62 | 0.027 | YES
2 | CAMK2B | CAMK2B | CAMK2B | 105 | 0.61 | 0.058 | YES
3 | WNT11 | WNT11 | WNT11 | 158 | 0.57 | 0.084 | YES
4 | NKD1 | NKD1 | NKD1 | 167 | 0.57 | 0.11 | YES
5 | NKD2 | NKD2 | NKD2 | 295 | 0.51 | 0.13 | YES
6 | NFATC4 | NFATC4 | NFATC4 | 368 | 0.48 | 0.15 | YES
7 | WNT6 | WNT6 | WNT6 | 403 | 0.47 | 0.18 | YES
8 | WNT5B | WNT5B | WNT5B | 581 | 0.42 | 0.19 | YES
9 | CXXC4 | CXXC4 | CXXC4 | 587 | 0.42 | 0.21 | YES
10 | WNT10B | WNT10B | WNT10B | 815 | 0.38 | 0.22 | YES
11 | SFRP1 | SFRP1 | SFRP1 | 909 | 0.36 | 0.23 | YES
12 | FZD10 | FZD10 | FZD10 | 927 | 0.36 | 0.25 | YES
13 | APC2 | APC2 | APC2 | 976 | 0.35 | 0.26 | YES
14 | PRICKLE1 | PRICKLE1 | PRICKLE1 | 1032 | 0.34 | 0.28 | YES
15 | LEF1 | LEF1 | LEF1 | 1105 | 0.33 | 0.29 | YES
16 | FZD8 | FZD8 | FZD8 | 1110 | 0.33 | 0.31 | YES
17 | FZD3 | FZD3 | FZD3 | 1114 | 0.33 | 0.32 | YES
18 | MAPK10 | MAPK10 | MAPK10 | 1145 | 0.33 | 0.34 | YES
19 | WIF1 | WIF1 | WIF1 | 1215 | 0.32 | 0.35 | YES
20 | FZD2 | FZD2 | FZD2 | 1363 | 0.3 | 0.36 | YES
21 | PRKCG | PRKCG | PRKCG | 1467 | 0.28 | 0.37 | YES
22 | DAAM2 | DAAM2 | DAAM2 | 1480 | 0.28 | 0.38 | YES
23 | TCF7L1 | TCF7L1 | TCF7L1 | 1703 | 0.26 | 0.38 | YES
24 | LRP6 | LRP6 | LRP6 | 1707 | 0.26 | 0.4 | YES
25 | VANGL2 | VANGL2 | VANGL2 | 1965 | 0.24 | 0.4 | YES
26 | RAC3 | RAC3 | RAC3 | 2021 | 0.24 | 0.4 | YES
27 | SFRP2 | SFRP2 | SFRP2 | 2073 | 0.23 | 0.41 | YES
28 | TBL1Y | TBL1Y | TBL1Y | 2098 | 0.23 | 0.42 | YES
29 | TCF7 | TCF7 | TCF7 | 2209 | 0.22 | 0.43 | YES
30 | WNT9A | WNT9A | WNT9A | 2335 | 0.22 | 0.43 | YES
31 | FZD7 | FZD7 | FZD7 | 2345 | 0.21 | 0.44 | YES
32 | DKK2 | DKK2 | DKK2 | 2442 | 0.21 | 0.45 | YES
33 | WNT7B | WNT7B | WNT7B | 2619 | 0.2 | 0.45 | YES
34 | PLCB4 | PLCB4 | PLCB4 | 2644 | 0.2 | 0.46 | YES
35 | SOX17 | SOX17 | SOX17 | 2683 | 0.19 | 0.47 | YES
36 | CAMK2A | CAMK2A | CAMK2A | 2712 | 0.19 | 0.48 | YES
37 | WNT8B | WNT8B | WNT8B | 2953 | 0.18 | 0.47 | YES
38 | WNT7A | WNT7A | WNT7A | 3021 | 0.17 | 0.48 | YES
39 | FZD9 | FZD9 | FZD9 | 3184 | 0.17 | 0.48 | YES
40 | FZD1 | FZD1 | FZD1 | 3261 | 0.16 | 0.48 | YES
41 | FZD4 | FZD4 | FZD4 | 3444 | 0.15 | 0.48 | YES
42 | CTNNBIP1 | CTNNBIP1 | CTNNBIP1 | 3480 | 0.15 | 0.48 | YES
43 | TBL1X | TBL1X | TBL1X | 3829 | 0.14 | 0.47 | NO
44 | NFATC1 | NFATC1 | NFATC1 | 3938 | 0.13 | 0.47 | NO
45 | WNT3A | WNT3A | WNT3A | 3991 | 0.13 | 0.48 | NO
46 | AXIN2 | AXIN2 | AXIN2 | 4107 | 0.12 | 0.48 | NO
47 | SMAD3 | SMAD3 | SMAD3 | 4173 | 0.12 | 0.48 | NO
48 | CAMK2G | CAMK2G | CAMK2G | 4362 | 0.11 | 0.47 | NO
49 | CCND1 | CCND1 | CCND1 | 4492 | 0.11 | 0.47 | NO
50 | TP53 | TP53 | TP53 | 4609 | 0.11 | 0.47 | NO
51 | DVL2 | DVL2 | DVL2 | 4811 | 0.1 | 0.47 | NO
52 | CSNK1E | CSNK1E | CSNK1E | 4902 | 0.097 | 0.47 | NO
53 | CREBBP | CREBBP | CREBBP | 4912 | 0.096 | 0.47 | NO
54 | MAP3K7 | MAP3K7 | MAP3K7 | 4965 | 0.095 | 0.47 | NO
55 | PPP3CA | PPP3CA | PPP3CA | 5231 | 0.088 | 0.46 | NO
56 | FRAT1 | FRAT1 | FRAT1 | 5312 | 0.086 | 0.46 | NO
57 | WNT2B | WNT2B | WNT2B | 5518 | 0.081 | 0.46 | NO
58 | MMP7 | MMP7 | MMP7 | 5584 | 0.079 | 0.46 | NO
59 | WNT10A | WNT10A | WNT10A | 5748 | 0.075 | 0.45 | NO
60 | SMAD4 | SMAD4 | SMAD4 | 6012 | 0.069 | 0.44 | NO
61 | PRKX | PRKX | PRKX | 6045 | 0.069 | 0.44 | NO
62 | PRKACA | PRKACA | PRKACA | 6057 | 0.068 | 0.44 | NO
63 | SFRP4 | SFRP4 | SFRP4 | 6260 | 0.064 | 0.44 | NO
64 | CTNNB1 | CTNNB1 | CTNNB1 | 6448 | 0.06 | 0.43 | NO
65 | PPP2R1A | PPP2R1A | PPP2R1A | 6739 | 0.054 | 0.42 | NO
66 | ROCK1 | ROCK1 | ROCK1 | 6765 | 0.054 | 0.42 | NO
67 | PPARD | PPARD | PPARD | 6856 | 0.052 | 0.41 | NO
68 | PPP2R5D | PPP2R5D | PPP2R5D | 6993 | 0.05 | 0.41 | NO
69 | WNT1 | WNT1 | WNT1 | 7002 | 0.049 | 0.41 | NO
70 | CHD8 | CHD8 | CHD8 | 7066 | 0.048 | 0.41 | NO
71 | SIAH1 | SIAH1 | SIAH1 | 7162 | 0.047 | 0.41 | NO
72 | SMAD2 | SMAD2 | SMAD2 | 7337 | 0.044 | 0.4 | NO
73 | CAMK2D | CAMK2D | CAMK2D | 7449 | 0.042 | 0.4 | NO
74 | PPP3CB | PPP3CB | PPP3CB | 7887 | 0.034 | 0.37 | NO
75 | FZD6 | FZD6 | FZD6 | 7931 | 0.034 | 0.37 | NO
76 | EP300 | EP300 | EP300 | 8090 | 0.031 | 0.37 | NO
77 | PPP3R1 | PPP3R1 | PPP3R1 | 8286 | 0.028 | 0.36 | NO
78 | CTBP1 | CTBP1 | CTBP1 | 8422 | 0.026 | 0.35 | NO
79 | PPP2CB | PPP2CB | PPP2CB | 8465 | 0.025 | 0.35 | NO
80 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 8504 | 0.025 | 0.35 | NO
81 | NFATC2 | NFATC2 | NFATC2 | 8607 | 0.023 | 0.34 | NO
82 | PPP2R5B | PPP2R5B | PPP2R5B | 8625 | 0.023 | 0.34 | NO
83 | WNT16 | WNT16 | WNT16 | 8633 | 0.023 | 0.34 | NO
84 | NFATC3 | NFATC3 | NFATC3 | 8666 | 0.022 | 0.34 | NO
85 | NFAT5 | NFAT5 | NFAT5 | 8789 | 0.021 | 0.34 | NO
86 | DVL1 | DVL1 | DVL1 | 8800 | 0.021 | 0.34 | NO
87 | PPP2R5C | PPP2R5C | PPP2R5C | 9014 | 0.018 | 0.33 | NO
88 | CSNK2A2 | CSNK2A2 | CSNK2A2 | 9232 | 0.015 | 0.32 | NO
89 | CACYBP | CACYBP | CACYBP | 9485 | 0.012 | 0.3 | NO
90 | PRKACB | PRKACB | PRKACB | 9537 | 0.011 | 0.3 | NO
91 | CUL1 | CUL1 | CUL1 | 9542 | 0.011 | 0.3 | NO
92 | NLK | NLK | NLK | 9710 | 0.0087 | 0.29 | NO
93 | LRP5 | LRP5 | LRP5 | 9911 | 0.0059 | 0.28 | NO
94 | GSK3B | GSK3B | GSK3B | 10205 | 0.0015 | 0.27 | NO
95 | RAC1 | RAC1 | RAC1 | 10220 | 0.0013 | 0.27 | NO
96 | VANGL1 | VANGL1 | VANGL1 | 10412 | -0.0012 | 0.26 | NO
97 | PPP2R5E | PPP2R5E | PPP2R5E | 10461 | -0.0017 | 0.25 | NO
98 | MAPK8 | MAPK8 | MAPK8 | 10610 | -0.0038 | 0.24 | NO
99 | RUVBL1 | RUVBL1 | RUVBL1 | 10762 | -0.0059 | 0.24 | NO
100 | CTBP2 | CTBP2 | CTBP2 | 10877 | -0.0076 | 0.23 | NO
101 | FBXW11 | FBXW11 | FBXW11 | 11065 | -0.01 | 0.22 | NO
102 | CSNK2B | CSNK2B | CSNK2B | 11217 | -0.012 | 0.21 | NO
103 | WNT5A | WNT5A | WNT5A | 11268 | -0.013 | 0.21 | NO
104 | JUN | JUN | JUN | 11364 | -0.014 | 0.21 | NO
105 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 11368 | -0.014 | 0.21 | NO
106 | PRICKLE2 | PRICKLE2 | PRICKLE2 | 11581 | -0.017 | 0.2 | NO
107 | FOSL1 | FOSL1 | FOSL1 | 11743 | -0.02 | 0.19 | NO
108 | PSEN1 | PSEN1 | PSEN1 | 11754 | -0.02 | 0.19 | NO
109 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 11759 | -0.02 | 0.19 | NO
110 | AXIN1 | AXIN1 | AXIN1 | 11831 | -0.021 | 0.19 | NO
111 | SKP1 | SKP1 | SKP1 | 11886 | -0.022 | 0.18 | NO
112 | PPP2R5A | PPP2R5A | PPP2R5A | 11928 | -0.022 | 0.18 | NO
113 | RBX1 | RBX1 | RBX1 | 12075 | -0.024 | 0.18 | NO
114 | BTRC | BTRC | BTRC | 12124 | -0.025 | 0.18 | NO
115 | ROCK2 | ROCK2 | ROCK2 | 12510 | -0.031 | 0.16 | NO
116 | CHP2 | CHP2 | CHP2 | 12524 | -0.032 | 0.16 | NO
117 | PPP2R1B | PPP2R1B | PPP2R1B | 12906 | -0.038 | 0.14 | NO
118 | WNT4 | WNT4 | WNT4 | 12921 | -0.038 | 0.14 | NO
119 | PLCB3 | PLCB3 | PLCB3 | 12923 | -0.038 | 0.14 | NO
120 | APC | APC | APC | 13105 | -0.041 | 0.13 | NO
121 | FZD5 | FZD5 | FZD5 | 13177 | -0.042 | 0.13 | NO
122 | DKK1 | DKK1 | DKK1 | 13265 | -0.044 | 0.13 | NO
123 | PPP2CA | PPP2CA | PPP2CA | 13346 | -0.045 | 0.13 | NO
124 | RHOA | RHOA | RHOA | 13360 | -0.046 | 0.13 | NO
125 | PORCN | PORCN | PORCN | 13481 | -0.048 | 0.12 | NO
126 | CCND3 | CCND3 | CCND3 | 13522 | -0.048 | 0.12 | NO
127 | MAPK9 | MAPK9 | MAPK9 | 13611 | -0.05 | 0.12 | NO
128 | PPP3CC | PPP3CC | PPP3CC | 13753 | -0.053 | 0.12 | NO
129 | TCF7L2 | TCF7L2 | TCF7L2 | 14097 | -0.06 | 0.1 | NO
130 | FRAT2 | FRAT2 | FRAT2 | 14551 | -0.07 | 0.079 | NO
131 | PRKCA | PRKCA | PRKCA | 14773 | -0.075 | 0.071 | NO
132 | SENP2 | SENP2 | SENP2 | 14801 | -0.076 | 0.073 | NO
133 | DVL3 | DVL3 | DVL3 | 14829 | -0.077 | 0.076 | NO
134 | PLCB1 | PLCB1 | PLCB1 | 15271 | -0.089 | 0.056 | NO
135 | PLCB2 | PLCB2 | PLCB2 | 15291 | -0.09 | 0.059 | NO
136 | CCND2 | CCND2 | CCND2 | 15578 | -0.099 | 0.049 | NO
137 | RAC2 | RAC2 | RAC2 | 16241 | -0.13 | 0.019 | NO
138 | CSNK1A1L | CSNK1A1L | CSNK1A1L | 16587 | -0.15 | 0.0073 | NO
139 | MYC | MYC | MYC | 16802 | -0.17 | 0.004 | NO
140 | WNT3 | WNT3 | WNT3 | 16816 | -0.17 | 0.012 | NO
141 | WNT9B | WNT9B | WNT9B | 16829 | -0.17 | 0.02 | NO
142 | CHP | CHP | CHP | 17043 | -0.18 | 0.018 | NO
143 | DAAM1 | DAAM1 | DAAM1 | 17531 | -0.25 | 0.0033 | NO
144 | PRKCB | PRKCB | PRKCB | 17729 | -0.29 | 0.0071 | NO
145 | WNT2 | WNT2 | WNT2 | 17958 | -0.36 | 0.013 | NO

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

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

genes ES table in pathway: PID EPHBFWDPATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | TGFB2 | TGFB2 | TGFB2 | 61 | 0.67 | 0.042 | YES
2 | INHBC | INHBC | INHBC | 107 | 0.61 | 0.081 | YES
3 | LEFTY1 | LEFTY1 | LEFTY1 | 162 | 0.57 | 0.12 | YES
4 | CHRD | CHRD | CHRD | 211 | 0.54 | 0.15 | YES
5 | BMP7 | BMP7 | BMP7 | 241 | 0.53 | 0.18 | YES
6 | INHBE | INHBE | INHBE | 247 | 0.53 | 0.22 | YES
7 | LEFTY2 | LEFTY2 | LEFTY2 | 249 | 0.53 | 0.26 | YES
8 | BMP6 | BMP6 | BMP6 | 378 | 0.48 | 0.28 | YES
9 | AMH | AMH | AMH | 463 | 0.46 | 0.31 | YES
10 | NODAL | NODAL | NODAL | 488 | 0.45 | 0.34 | YES
11 | SMAD6 | SMAD6 | SMAD6 | 582 | 0.42 | 0.36 | YES
12 | GDF7 | GDF7 | GDF7 | 700 | 0.4 | 0.38 | YES
13 | LTBP1 | LTBP1 | LTBP1 | 718 | 0.4 | 0.4 | YES
14 | AMHR2 | AMHR2 | AMHR2 | 827 | 0.38 | 0.42 | YES
15 | BMP5 | BMP5 | BMP5 | 885 | 0.37 | 0.45 | YES
16 | COMP | COMP | COMP | 1135 | 0.33 | 0.45 | YES
17 | BMPR1B | BMPR1B | BMPR1B | 1217 | 0.32 | 0.47 | YES
18 | FST | FST | FST | 1360 | 0.3 | 0.48 | YES
19 | TGFB3 | TGFB3 | TGFB3 | 1429 | 0.29 | 0.5 | YES
20 | THBS4 | THBS4 | THBS4 | 1612 | 0.27 | 0.51 | YES
21 | ID3 | ID3 | ID3 | 1619 | 0.27 | 0.52 | YES
22 | BMP8A | BMP8A | BMP8A | 1663 | 0.27 | 0.54 | YES
23 | ID1 | ID1 | ID1 | 1696 | 0.26 | 0.56 | YES
24 | SMAD7 | SMAD7 | SMAD7 | 1967 | 0.24 | 0.56 | YES
25 | INHBA | INHBA | INHBA | 2141 | 0.23 | 0.56 | YES
26 | PITX2 | PITX2 | PITX2 | 2255 | 0.22 | 0.57 | YES
27 | BMP8B | BMP8B | BMP8B | 2317 | 0.22 | 0.58 | YES
28 | SMAD9 | SMAD9 | SMAD9 | 2369 | 0.21 | 0.6 | YES
29 | GDF6 | GDF6 | GDF6 | 2618 | 0.2 | 0.59 | NO
30 | THBS1 | THBS1 | THBS1 | 3157 | 0.17 | 0.58 | NO
31 | BMPR2 | BMPR2 | BMPR2 | 3465 | 0.15 | 0.57 | NO
32 | ACVRL1 | ACVRL1 | ACVRL1 | 3832 | 0.14 | 0.56 | NO
33 | SMAD3 | SMAD3 | SMAD3 | 4173 | 0.12 | 0.55 | NO
34 | ZFYVE9 | ZFYVE9 | ZFYVE9 | 4276 | 0.12 | 0.55 | NO
35 | RBL1 | RBL1 | RBL1 | 4522 | 0.11 | 0.54 | NO
36 | BMPR1A | BMPR1A | BMPR1A | 4570 | 0.11 | 0.55 | NO
37 | DCN | DCN | DCN | 4617 | 0.11 | 0.55 | NO
38 | CREBBP | CREBBP | CREBBP | 4912 | 0.096 | 0.54 | NO
39 | NOG | NOG | NOG | 5399 | 0.083 | 0.52 | NO
40 | ACVR2B | ACVR2B | ACVR2B | 6001 | 0.07 | 0.49 | NO
41 | SMAD4 | SMAD4 | SMAD4 | 6012 | 0.069 | 0.5 | NO
42 | TGFB1 | TGFB1 | TGFB1 | 6618 | 0.056 | 0.47 | NO
43 | ACVR2A | ACVR2A | ACVR2A | 6636 | 0.056 | 0.47 | NO
44 | SMAD5 | SMAD5 | SMAD5 | 6687 | 0.055 | 0.47 | NO
45 | PPP2R1A | PPP2R1A | PPP2R1A | 6739 | 0.054 | 0.47 | NO
46 | ROCK1 | ROCK1 | ROCK1 | 6765 | 0.054 | 0.48 | NO
47 | TFDP1 | TFDP1 | TFDP1 | 7006 | 0.049 | 0.46 | NO
48 | BMP4 | BMP4 | BMP4 | 7173 | 0.046 | 0.46 | NO
49 | SP1 | SP1 | SP1 | 7220 | 0.046 | 0.46 | NO
50 | THBS2 | THBS2 | THBS2 | 7225 | 0.046 | 0.46 | NO
51 | SMAD2 | SMAD2 | SMAD2 | 7337 | 0.044 | 0.46 | NO
52 | EP300 | EP300 | EP300 | 8090 | 0.031 | 0.42 | NO
53 | PPP2CB | PPP2CB | PPP2CB | 8465 | 0.025 | 0.4 | NO
54 | ACVR1 | ACVR1 | ACVR1 | 8591 | 0.023 | 0.4 | NO
55 | SMURF1 | SMURF1 | SMURF1 | 8910 | 0.02 | 0.38 | NO
56 | THBS3 | THBS3 | THBS3 | 8944 | 0.019 | 0.38 | NO
57 | CUL1 | CUL1 | CUL1 | 9542 | 0.011 | 0.35 | NO
58 | E2F4 | E2F4 | E2F4 | 10349 | -0.00036 | 0.3 | NO
59 | MAPK1 | MAPK1 | MAPK1 | 10386 | -0.00086 | 0.3 | NO
60 | TGFBR1 | TGFBR1 | TGFBR1 | 10411 | -0.0012 | 0.3 | NO
61 | ZFYVE16 | ZFYVE16 | ZFYVE16 | 11035 | -0.0096 | 0.26 | NO
62 | SMURF2 | SMURF2 | SMURF2 | 11277 | -0.013 | 0.25 | NO
63 | SMAD1 | SMAD1 | SMAD1 | 11308 | -0.013 | 0.25 | NO
64 | ACVR1C | ACVR1C | ACVR1C | 11710 | -0.019 | 0.23 | NO
65 | SKP1 | SKP1 | SKP1 | 11886 | -0.022 | 0.22 | NO
66 | RBX1 | RBX1 | RBX1 | 12075 | -0.024 | 0.21 | NO
67 | ID4 | ID4 | ID4 | 12282 | -0.028 | 0.2 | NO
68 | ROCK2 | ROCK2 | ROCK2 | 12510 | -0.031 | 0.19 | NO
69 | PPP2R1B | PPP2R1B | PPP2R1B | 12906 | -0.038 | 0.18 | NO
70 | TGFBR2 | TGFBR2 | TGFBR2 | 13298 | -0.044 | 0.16 | NO
71 | E2F5 | E2F5 | E2F5 | 13330 | -0.045 | 0.16 | NO
72 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 13333 | -0.045 | 0.16 | NO
73 | PPP2CA | PPP2CA | PPP2CA | 13346 | -0.045 | 0.16 | NO
74 | RHOA | RHOA | RHOA | 13360 | -0.046 | 0.16 | NO
75 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 13621 | -0.05 | 0.15 | NO
76 | MAPK3 | MAPK3 | MAPK3 | 13836 | -0.055 | 0.15 | NO
77 | RBL2 | RBL2 | RBL2 | 14122 | -0.061 | 0.13 | NO
78 | BMP2 | BMP2 | BMP2 | 15918 | -0.11 | 0.043 | NO
79 | INHBB | INHBB | INHBB | 16014 | -0.12 | 0.046 | NO
80 | ID2 | ID2 | ID2 | 16703 | -0.16 | 0.018 | NO
81 | CDKN2B | CDKN2B | CDKN2B | 16704 | -0.16 | 0.029 | NO
82 | MYC | MYC | MYC | 16802 | -0.17 | 0.035 | NO
83 | GDF5 | GDF5 | GDF5 | 16929 | -0.18 | 0.04 | NO
84 | IFNG | IFNG | IFNG | 17268 | -0.21 | 0.035 | NO
85 | TNF | TNF | TNF | 17461 | -0.24 | 0.04 | NO

Figure S75. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID EPHBFWDPATHWAY.

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

genes ES table in pathway: PID P75NTRPATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GLI1 | GLI1 | GLI1 | 91 | 0.62 | 0.12 | YES
2 | PTCH1 | PTCH1 | PTCH1 | 202 | 0.55 | 0.22 | YES
3 | GNAO1 | GNAO1 | GNAO1 | 365 | 0.48 | 0.3 | YES
4 | SMO | SMO | SMO | 1272 | 0.31 | 0.32 | YES
5 | GLI2 | GLI2 | GLI2 | 1883 | 0.25 | 0.33 | YES
6 | GNAZ | GNAZ | GNAZ | 2254 | 0.22 | 0.35 | YES
7 | RAB23 | RAB23 | RAB23 | 2548 | 0.2 | 0.38 | YES
8 | SSPO | SSPO | SSPO | 2839 | 0.18 | 0.4 | YES
9 | SHH | SHH | SHH | 3141 | 0.17 | 0.41 | YES
10 | HDAC2 | HDAC2 | HDAC2 | 3743 | 0.14 | 0.41 | YES
11 | GLI3 | GLI3 | GLI3 | 4289 | 0.12 | 0.4 | YES
12 | IFT88 | IFT88 | IFT88 | 4487 | 0.11 | 0.41 | YES
13 | CSNK1E | CSNK1E | CSNK1E | 4902 | 0.097 | 0.41 | YES
14 | CREBBP | CREBBP | CREBBP | 4912 | 0.096 | 0.43 | YES
15 | SIN3B | SIN3B | SIN3B | 5085 | 0.091 | 0.43 | YES
16 | STK36 | STK36 | STK36 | 5116 | 0.09 | 0.45 | YES
17 | KIF3A | KIF3A | KIF3A | 5958 | 0.071 | 0.42 | NO
18 | PRKACA | PRKACA | PRKACA | 6057 | 0.068 | 0.43 | NO
19 | HDAC1 | HDAC1 | HDAC1 | 6188 | 0.066 | 0.43 | NO
20 | CSNK1G2 | CSNK1G2 | CSNK1G2 | 6798 | 0.053 | 0.41 | NO
21 | MTSS1 | MTSS1 | MTSS1 | 6903 | 0.051 | 0.41 | NO
22 | SIN3A | SIN3A | SIN3A | 7031 | 0.049 | 0.42 | NO
23 | AKT1 | AKT1 | AKT1 | 7187 | 0.046 | 0.42 | NO
24 | GNB1 | GNB1 | GNB1 | 8228 | 0.029 | 0.36 | NO
25 | GNG2 | GNG2 | GNG2 | 8356 | 0.027 | 0.36 | NO
26 | XPO1 | XPO1 | XPO1 | 8413 | 0.026 | 0.36 | NO
27 | SUFU | SUFU | SUFU | 9172 | 0.016 | 0.33 | NO
28 | SPOP | SPOP | SPOP | 9387 | 0.013 | 0.32 | NO
29 | CSNK1G3 | CSNK1G3 | CSNK1G3 | 9739 | 0.0082 | 0.3 | NO
30 | SAP18 | SAP18 | SAP18 | 9797 | 0.0074 | 0.3 | NO
31 | RBBP4 | RBBP4 | RBBP4 | 10002 | 0.0046 | 0.29 | NO
32 | GSK3B | GSK3B | GSK3B | 10205 | 0.0015 | 0.28 | NO
33 | RBBP7 | RBBP7 | RBBP7 | 10871 | -0.0076 | 0.24 | NO
34 | FBXW11 | FBXW11 | FBXW11 | 11065 | -0.01 | 0.23 | NO
35 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 11368 | -0.014 | 0.22 | NO
36 | CSNK1D | CSNK1D | CSNK1D | 11391 | -0.015 | 0.22 | NO
37 | PRKCD | PRKCD | PRKCD | 11701 | -0.019 | 0.21 | NO
38 | GNAI2 | GNAI2 | GNAI2 | 12412 | -0.03 | 0.17 | NO
39 | IFT172 | IFT172 | IFT172 | 12987 | -0.039 | 0.15 | NO
40 | CSNK1G1 | CSNK1G1 | CSNK1G1 | 13148 | -0.042 | 0.15 | NO
41 | SAP30 | SAP30 | SAP30 | 13372 | -0.046 | 0.15 | NO
42 | PIAS1 | PIAS1 | PIAS1 | 13458 | -0.047 | 0.15 | NO
43 | GNAI3 | GNAI3 | GNAI3 | 13617 | -0.05 | 0.15 | NO
44 | MAP2K1 | MAP2K1 | MAP2K1 | 14342 | -0.066 | 0.12 | NO
45 | ARRB2 | ARRB2 | ARRB2 | 15069 | -0.083 | 0.1 | NO
46 | FOXA2 | FOXA2 | FOXA2 | 15206 | -0.087 | 0.11 | NO
47 | LGALS3 | LGALS3 | LGALS3 | 15910 | -0.11 | 0.094 | NO
48 | GNAI1 | GNAI1 | GNAI1 | 16753 | -0.16 | 0.079 | NO

Figure S77. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID P75NTRPATHWAY.

Figure S78. Get High-res Image For the top 5 core enriched genes in the pathway: PID P75NTRPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID HEDGEHOG GLIPATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | GRIK4 | GRIK4 | GRIK4 | 119 | 0.6 | 0.11 | YES
2 | GRIK3 | GRIK3 | GRIK3 | 579 | 0.43 | 0.16 | YES
3 | GNGT1 | GNGT1 | GNGT1 | 601 | 0.42 | 0.24 | YES
4 | NCALD | NCALD | NCALD | 665 | 0.4 | 0.31 | YES
5 | GNG13 | GNG13 | GNG13 | 894 | 0.36 | 0.37 | YES
6 | GNB3 | GNB3 | GNB3 | 1068 | 0.34 | 0.42 | YES
7 | GRIK1 | GRIK1 | GRIK1 | 1124 | 0.33 | 0.48 | YES
8 | GRIK5 | GRIK5 | GRIK5 | 1276 | 0.31 | 0.53 | YES
9 | GNG8 | GNG8 | GNG8 | 1333 | 0.3 | 0.59 | YES
10 | GNG4 | GNG4 | GNG4 | 1702 | 0.26 | 0.62 | YES
11 | GNG3 | GNG3 | GNG3 | 2985 | 0.18 | 0.58 | NO
12 | DLG3 | DLG3 | DLG3 | 3570 | 0.15 | 0.57 | NO
13 | GNB5 | GNB5 | GNB5 | 3934 | 0.13 | 0.58 | NO
14 | GRIK2 | GRIK2 | GRIK2 | 4859 | 0.098 | 0.55 | NO
15 | CALM1 | CALM1 | CALM1 | 5854 | 0.073 | 0.51 | NO
16 | GNG11 | GNG11 | GNG11 | 6882 | 0.052 | 0.46 | NO
17 | CALM3 | CALM3 | CALM3 | 7960 | 0.033 | 0.41 | NO
18 | GNB1 | GNB1 | GNB1 | 8228 | 0.029 | 0.4 | NO
19 | GNG2 | GNG2 | GNG2 | 8356 | 0.027 | 0.4 | NO
20 | GNB4 | GNB4 | GNB4 | 8900 | 0.02 | 0.37 | NO
21 | GNG10 | GNG10 | GNG10 | 10178 | 0.0019 | 0.3 | NO
22 | GNB2 | GNB2 | GNB2 | 10884 | -0.0077 | 0.26 | NO
23 | GNG12 | GNG12 | GNG12 | 11897 | -0.022 | 0.21 | NO
24 | CALM2 | CALM2 | CALM2 | 11969 | -0.023 | 0.21 | NO
25 | PLCB3 | PLCB3 | PLCB3 | 12923 | -0.038 | 0.17 | NO
26 | GNG7 | GNG7 | GNG7 | 14120 | -0.061 | 0.11 | NO
27 | DLG1 | DLG1 | DLG1 | 14440 | -0.068 | 0.11 | NO
28 | PLCB1 | PLCB1 | PLCB1 | 15271 | -0.089 | 0.078 | NO
29 | PLCB2 | PLCB2 | PLCB2 | 15291 | -0.09 | 0.094 | NO
30 | GNG5 | GNG5 | GNG5 | 15867 | -0.11 | 0.083 | NO
31 | GNGT2 | GNGT2 | GNGT2 | 17472 | -0.24 | 0.04 | NO

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

Figure S80. Get High-res Image For the top 5 core enriched genes in the pathway: PID HEDGEHOG GLIPATHWAY, 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.v4.0.symbols.gmt

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

- Phenotype data file = MESO-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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