GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in MESO-TP
Mesothelioma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1P849ZT
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in MESO-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1P849ZT
Overview
Introduction

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

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

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

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

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

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

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

Summary

Table 1. Get Full Table basic data info

basic data info
Number of Gene Sets: 191
Number of samples: 86
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 26
pheno.type: 2 - 4 :[ clus2 ] 22
pheno.type: 3 - 4 :[ clus3 ] 17
pheno.type: 4 - 4 :[ clus4 ] 21

For the expression subtypes of 18203 genes in 87 samples, GSEA found enriched gene sets in each cluster using 86 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

- clus1

- Top enriched gene sets are BIOCARTA DEATH PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG FATTY ACID METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG TYROSINE METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG SPHINGOLIPID METABOLISM, KEGG PROPANOATE METABOLISM, KEGG BUTANOATE METABOLISM

- And common core enriched genes are ADH1A, ADH1B, ADH1C, ADH4, ADH6, ALDH2, ALDH3A2, ACADS, ADH5, ALDH3B1

- clus2

- Top enriched gene sets are BIOCARTA CHREBP2 PATHWAY, BIOCARTA RHO PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG CITRATE CYCLE TCA CYCLE, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG ARGININE AND PROLINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG TRYPTOPHAN METABOLISM

- And common core enriched genes are ALDH1B1, ALDH7A1, ALDH1A3, ALDH3A1, MAOA, MAOB, ABAT, ACAT1, AOX1, EHHADH

- clus3

- Top enriched gene sets are BIOCARTA BCR PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA TCR PATHWAY, BIOCARTA VEGF PATHWAY, KEGG PROTEASOME, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG CELL CYCLE

- And common core enriched genes are PIK3CG, TNF, AKT3, CHUK, NFKB1, NFKBIA, PIK3R3, PIK3R5, SHC1, TGFB1

- clus4

- Top enriched gene sets are BIOCARTA ALK PATHWAY, BIOCARTA G1 PATHWAY, BIOCARTA WNT PATHWAY, KEGG PURINE METABOLISM, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG CALCIUM SIGNALING PATHWAY, KEGG OOCYTE MEIOSIS, KEGG VASCULAR SMOOTH MUSCLE CONTRACTION, KEGG WNT SIGNALING PATHWAY, KEGG NOTCH SIGNALING PATHWAY

- And common core enriched genes are FZD1, FZD10, FZD2, FZD3, FZD4, FZD7, FZD8, FZD9, LEF1, TCF7

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BIOCARTA DEATH PATHWAY | 32 | genes.ES.table | 0.33 | 1.2 | 0.27 | 0.94 | 1 | 0.31 | 0.17 | 0.26 | 0.84 | 0.39
KEGG GLYCOLYSIS GLUCONEOGENESIS | 55 | genes.ES.table | 0.46 | 1.5 | 0.037 | 1 | 0.85 | 0.22 | 0.1 | 0.2 | 0.88 | 0.45
KEGG FATTY ACID METABOLISM | 39 | genes.ES.table | 0.61 | 1.9 | 0 | 0.16 | 0.13 | 0.33 | 0.12 | 0.3 | 0 | 0.045
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM | 29 | genes.ES.table | 0.38 | 1.2 | 0.18 | 1 | 1 | 0.24 | 0.087 | 0.22 | 0.9 | 0.43
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION | 42 | genes.ES.table | 0.33 | 1.2 | 0.29 | 0.98 | 1 | 0.52 | 0.28 | 0.38 | 0.89 | 0.42
KEGG TYROSINE METABOLISM | 40 | genes.ES.table | 0.52 | 1.4 | 0.04 | 0.87 | 0.94 | 0.25 | 0.059 | 0.24 | 0.67 | 0.3
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM | 42 | genes.ES.table | 0.42 | 1.5 | 0.098 | 0.91 | 0.92 | 0.24 | 0.11 | 0.21 | 0.67 | 0.32
KEGG SPHINGOLIPID METABOLISM | 37 | genes.ES.table | 0.38 | 1.2 | 0.25 | 0.9 | 1 | 0.27 | 0.14 | 0.23 | 0.83 | 0.35
KEGG PROPANOATE METABOLISM | 31 | genes.ES.table | 0.35 | 1.1 | 0.33 | 0.96 | 1 | 0.39 | 0.23 | 0.3 | 0.9 | 0.4
KEGG BUTANOATE METABOLISM | 28 | genes.ES.table | 0.49 | 1.5 | 0.052 | 1 | 0.88 | 0.29 | 0.1 | 0.26 | 0.74 | 0.36

genes ES table in pathway: BIOCARTA DEATH PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | ADH6 | ADH6 | ADH6 | 1 | 1.3 | 0.17 | YES
2 | ADH1A | ADH1A | ADH1A | 2 | 1.2 | 0.32 | YES
3 | ADH1B | ADH1B | ADH1B | 13 | 0.79 | 0.43 | YES
4 | ACSL6 | ACSL6 | ACSL6 | 341 | 0.4 | 0.47 | YES
5 | ADH1C | ADH1C | ADH1C | 640 | 0.31 | 0.49 | YES
6 | ADH4 | ADH4 | ADH4 | 671 | 0.3 | 0.53 | YES
7 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 1083 | 0.23 | 0.54 | YES
8 | ACSL5 | ACSL5 | ACSL5 | 1103 | 0.22 | 0.56 | YES
9 | ACADS | ACADS | ACADS | 1421 | 0.19 | 0.57 | YES
10 | ADH5 | ADH5 | ADH5 | 1713 | 0.16 | 0.58 | YES
11 | ALDH2 | ALDH2 | ALDH2 | 1818 | 0.15 | 0.59 | YES
12 | ACADM | ACADM | ACADM | 2007 | 0.14 | 0.6 | YES
13 | ACSL1 | ACSL1 | ACSL1 | 2123 | 0.13 | 0.61 | YES
14 | CPT2 | CPT2 | CPT2 | 3144 | 0.086 | 0.57 | NO
15 | DCI | DCI | DCI | 3614 | 0.072 | 0.55 | NO
16 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 4232 | 0.057 | 0.52 | NO
17 | HADHB | HADHB | HADHB | 4613 | 0.048 | 0.51 | NO
18 | ACAA2 | ACAA2 | ACAA2 | 4738 | 0.045 | 0.51 | NO
19 | ACADVL | ACADVL | ACADVL | 4804 | 0.044 | 0.51 | NO
20 | HADH | HADH | HADH | 5060 | 0.039 | 0.5 | NO
21 | ECHS1 | ECHS1 | ECHS1 | 5469 | 0.032 | 0.48 | NO
22 | CPT1B | CPT1B | CPT1B | 5643 | 0.029 | 0.48 | NO
23 | ACAA1 | ACAA1 | ACAA1 | 6207 | 0.021 | 0.45 | NO
24 | HADHA | HADHA | HADHA | 6751 | 0.013 | 0.42 | NO
25 | CPT1A | CPT1A | CPT1A | 6781 | 0.012 | 0.42 | NO
26 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 7531 | 0.0023 | 0.38 | NO
27 | ACAT2 | ACAT2 | ACAT2 | 7596 | 0.0014 | 0.38 | NO
28 | ACAT1 | ACAT1 | ACAT1 | 8804 | -0.016 | 0.32 | NO
29 | ACADSB | ACADSB | ACADSB | 9017 | -0.02 | 0.31 | NO
30 | GCDH | GCDH | GCDH | 9555 | -0.028 | 0.28 | NO
31 | ACSL3 | ACSL3 | ACSL3 | 10411 | -0.042 | 0.24 | NO
32 | ACOX3 | ACOX3 | ACOX3 | 11730 | -0.07 | 0.18 | NO
33 | ACADL | ACADL | ACADL | 12986 | -0.11 | 0.12 | NO
34 | ACSL4 | ACSL4 | ACSL4 | 13053 | -0.11 | 0.13 | NO
35 | PECI | PECI | PECI | 13641 | -0.13 | 0.12 | NO
36 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 14707 | -0.18 | 0.082 | NO
37 | CYP4A11 | CYP4A11 | CYP4A11 | 15329 | -0.22 | 0.076 | NO
38 | EHHADH | EHHADH | EHHADH | 16376 | -0.29 | 0.057 | NO
39 | CPT1C | CPT1C | CPT1C | 16689 | -0.32 | 0.082 | NO

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

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

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 | ADH6 | ADH6 | ADH6 | 1 | 1.3 | 0.13 | YES
2 | ADH1A | ADH1A | ADH1A | 2 | 1.2 | 0.25 | YES
3 | ADH1B | ADH1B | ADH1B | 13 | 0.79 | 0.34 | YES
4 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 520 | 0.33 | 0.34 | YES
5 | ADH1C | ADH1C | ADH1C | 640 | 0.31 | 0.37 | YES
6 | ADH4 | ADH4 | ADH4 | 671 | 0.3 | 0.4 | YES
7 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 849 | 0.26 | 0.42 | YES
8 | PGM1 | PGM1 | PGM1 | 910 | 0.25 | 0.44 | YES
9 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 1083 | 0.23 | 0.45 | YES
10 | PGM2 | PGM2 | PGM2 | 1669 | 0.16 | 0.44 | YES
11 | ADH5 | ADH5 | ADH5 | 1713 | 0.16 | 0.45 | YES
12 | ALDH2 | ALDH2 | ALDH2 | 1818 | 0.15 | 0.46 | YES
13 | PFKM | PFKM | PFKM | 3235 | 0.084 | 0.39 | NO
14 | LDHA | LDHA | LDHA | 3333 | 0.08 | 0.4 | NO
15 | PDHB | PDHB | PDHB | 3497 | 0.075 | 0.39 | NO
16 | PCK2 | PCK2 | PCK2 | 3642 | 0.071 | 0.39 | NO
17 | HK2 | HK2 | HK2 | 3693 | 0.07 | 0.4 | NO
18 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 4232 | 0.057 | 0.38 | NO
19 | DLD | DLD | DLD | 4312 | 0.055 | 0.38 | NO
20 | DLAT | DLAT | DLAT | 4464 | 0.051 | 0.37 | NO
21 | ALDOA | ALDOA | ALDOA | 4999 | 0.04 | 0.35 | NO
22 | ACSS2 | ACSS2 | ACSS2 | 5305 | 0.035 | 0.34 | NO
23 | GPI | GPI | GPI | 5338 | 0.035 | 0.34 | NO
24 | PGAM1 | PGAM1 | PGAM1 | 5522 | 0.032 | 0.33 | NO
25 | AKR1A1 | AKR1A1 | AKR1A1 | 5961 | 0.024 | 0.31 | NO
26 | PGAM4 | PGAM4 | PGAM4 | 6134 | 0.022 | 0.3 | NO
27 | ENO1 | ENO1 | ENO1 | 6254 | 0.02 | 0.3 | NO
28 | TPI1 | TPI1 | TPI1 | 6709 | 0.013 | 0.27 | NO
29 | PFKL | PFKL | PFKL | 6941 | 0.01 | 0.26 | NO
30 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 7531 | 0.0023 | 0.23 | NO
31 | PFKP | PFKP | PFKP | 7562 | 0.0018 | 0.23 | NO
32 | PGK1 | PGK1 | PGK1 | 7797 | -0.0017 | 0.22 | NO
33 | LDHAL6A | LDHAL6A | LDHAL6A | 8524 | -0.012 | 0.18 | NO
34 | HK3 | HK3 | HK3 | 8609 | -0.013 | 0.17 | NO
35 | PDHA1 | PDHA1 | PDHA1 | 9793 | -0.032 | 0.11 | NO
36 | PKM2 | PKM2 | PKM2 | 9965 | -0.035 | 0.1 | NO
37 | GAPDH | GAPDH | GAPDH | 10062 | -0.036 | 0.1 | NO
38 | FBP1 | FBP1 | FBP1 | 10107 | -0.037 | 0.1 | NO
39 | LDHB | LDHB | LDHB | 11151 | -0.058 | 0.054 | NO
40 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 11239 | -0.06 | 0.055 | NO
41 | ENO2 | ENO2 | ENO2 | 12235 | -0.083 | 0.009 | NO
42 | ACSS1 | ACSS1 | ACSS1 | 13114 | -0.11 | -0.028 | NO
43 | ENO3 | ENO3 | ENO3 | 13341 | -0.12 | -0.028 | NO
44 | BPGM | BPGM | BPGM | 13894 | -0.14 | -0.043 | NO
45 | ALDOB | ALDOB | ALDOB | 14515 | -0.17 | -0.06 | NO
46 | PKLR | PKLR | PKLR | 14678 | -0.18 | -0.051 | NO
47 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 14707 | -0.18 | -0.034 | NO
48 | HK1 | HK1 | HK1 | 14745 | -0.18 | -0.017 | NO
49 | GALM | GALM | GALM | 14883 | -0.19 | -0.005 | NO
50 | LDHAL6B | LDHAL6B | LDHAL6B | 15461 | -0.22 | -0.014 | NO
51 | PCK1 | PCK1 | PCK1 | 15695 | -0.24 | -0.0015 | NO
52 | PGAM2 | PGAM2 | PGAM2 | 16218 | -0.28 | -0.0013 | NO
53 | ALDOC | ALDOC | ALDOC | 16399 | -0.29 | 0.019 | NO
54 | GCK | GCK | GCK | 16619 | -0.31 | 0.04 | NO
55 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 17650 | -0.45 | 0.03 | 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 GLYCOLYSIS GLUCONEOGENESIS.

Figure S4. 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 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 | ACSM1 | ACSM1 | ACSM1 | 310 | 0.41 | 0.11 | YES
2 | BDH2 | BDH2 | BDH2 | 817 | 0.27 | 0.17 | YES
3 | ALDH5A1 | ALDH5A1 | ALDH5A1 | 855 | 0.26 | 0.24 | YES
4 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 1083 | 0.23 | 0.3 | YES
5 | AACS | AACS | AACS | 1163 | 0.21 | 0.36 | YES
6 | ACADS | ACADS | ACADS | 1421 | 0.19 | 0.41 | YES
7 | ABAT | ABAT | ABAT | 1582 | 0.17 | 0.45 | YES
8 | ALDH2 | ALDH2 | ALDH2 | 1818 | 0.15 | 0.49 | YES
9 | HMGCL | HMGCL | HMGCL | 3421 | 0.077 | 0.42 | NO
10 | PDHB | PDHB | PDHB | 3497 | 0.075 | 0.44 | NO
11 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 4232 | 0.057 | 0.42 | NO
12 | ACSM5 | ACSM5 | ACSM5 | 4575 | 0.049 | 0.42 | NO
13 | HADH | HADH | HADH | 5060 | 0.039 | 0.4 | NO
14 | ECHS1 | ECHS1 | ECHS1 | 5469 | 0.032 | 0.39 | NO
15 | HADHA | HADHA | HADHA | 6751 | 0.013 | 0.32 | NO
16 | L2HGDH | L2HGDH | L2HGDH | 6842 | 0.012 | 0.32 | NO
17 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 7531 | 0.0023 | 0.28 | NO
18 | ACAT2 | ACAT2 | ACAT2 | 7596 | 0.0014 | 0.28 | NO
19 | ACAT1 | ACAT1 | ACAT1 | 8804 | -0.016 | 0.22 | NO
20 | GAD1 | GAD1 | GAD1 | 8826 | -0.017 | 0.22 | NO
21 | PDHA1 | PDHA1 | PDHA1 | 9793 | -0.032 | 0.18 | NO
22 | OXCT1 | OXCT1 | OXCT1 | 11053 | -0.056 | 0.13 | NO
23 | ACSM3 | ACSM3 | ACSM3 | 11744 | -0.071 | 0.11 | NO
24 | AKR1B10 | AKR1B10 | AKR1B10 | 12346 | -0.087 | 0.1 | NO
25 | BDH1 | BDH1 | BDH1 | 13113 | -0.11 | 0.097 | NO
26 | HMGCS1 | HMGCS1 | HMGCS1 | 13912 | -0.14 | 0.097 | NO
27 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 14707 | -0.18 | 0.11 | NO
28 | OXCT2 | OXCT2 | OXCT2 | 16148 | -0.27 | 0.11 | 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 FATTY ACID METABOLISM.

Figure S6. 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 ALANINE ASPARTATE AND GLUTAMATE 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 | GFPT2 | GFPT2 | GFPT2 | 386 | 0.38 | 0.073 | YES
2 | GALK2 | GALK2 | GALK2 | 907 | 0.25 | 0.11 | YES
3 | PGM1 | PGM1 | PGM1 | 910 | 0.25 | 0.17 | YES
4 | CHIT1 | CHIT1 | CHIT1 | 1044 | 0.23 | 0.22 | YES
5 | UGP2 | UGP2 | UGP2 | 1353 | 0.19 | 0.25 | YES
6 | FPGT | FPGT | FPGT | 1436 | 0.18 | 0.29 | YES
7 | GALE | GALE | GALE | 1442 | 0.18 | 0.34 | YES
8 | FUK | FUK | FUK | 1539 | 0.18 | 0.38 | YES
9 | PGM2 | PGM2 | PGM2 | 1669 | 0.16 | 0.41 | YES
10 | AMDHD2 | AMDHD2 | AMDHD2 | 2071 | 0.13 | 0.42 | YES
11 | PMM2 | PMM2 | PMM2 | 2965 | 0.092 | 0.4 | NO
12 | NANP | NANP | NANP | 3499 | 0.075 | 0.38 | NO
13 | MPI | MPI | MPI | 3621 | 0.072 | 0.4 | NO
14 | HK2 | HK2 | HK2 | 3693 | 0.07 | 0.41 | NO
15 | UGDH | UGDH | UGDH | 4340 | 0.054 | 0.39 | NO
16 | CMAS | CMAS | CMAS | 4470 | 0.051 | 0.39 | NO
17 | GMPPB | GMPPB | GMPPB | 5014 | 0.04 | 0.37 | NO
18 | GNPDA1 | GNPDA1 | GNPDA1 | 5306 | 0.035 | 0.36 | NO
19 | GPI | GPI | GPI | 5338 | 0.035 | 0.37 | NO
20 | HEXA | HEXA | HEXA | 5399 | 0.034 | 0.38 | NO
21 | GFPT1 | GFPT1 | GFPT1 | 5671 | 0.029 | 0.37 | NO
22 | GMPPA | GMPPA | GMPPA | 5768 | 0.027 | 0.37 | NO
23 | GMDS | GMDS | GMDS | 6273 | 0.02 | 0.35 | NO
24 | GALT | GALT | GALT | 6372 | 0.018 | 0.35 | NO
25 | GALK1 | GALK1 | GALK1 | 6418 | 0.018 | 0.35 | NO
26 | RENBP | RENBP | RENBP | 7453 | 0.0034 | 0.29 | NO
27 | TSTA3 | TSTA3 | TSTA3 | 7598 | 0.0013 | 0.28 | NO
28 | NAGK | NAGK | NAGK | 7875 | -0.0026 | 0.27 | NO
29 | PMM1 | PMM1 | PMM1 | 8538 | -0.012 | 0.24 | NO
30 | HK3 | HK3 | HK3 | 8609 | -0.013 | 0.24 | NO
31 | NANS | NANS | NANS | 8638 | -0.014 | 0.24 | NO
32 | CYB5R1 | CYB5R1 | CYB5R1 | 8720 | -0.015 | 0.24 | NO
33 | NPL | NPL | NPL | 8848 | -0.017 | 0.24 | NO
34 | HEXB | HEXB | HEXB | 8970 | -0.019 | 0.23 | NO
35 | UXS1 | UXS1 | UXS1 | 9906 | -0.034 | 0.19 | NO
36 | UAP1 | UAP1 | UAP1 | 10014 | -0.036 | 0.19 | NO
37 | PGM3 | PGM3 | PGM3 | 12099 | -0.08 | 0.098 | NO
38 | GNPDA2 | GNPDA2 | GNPDA2 | 12106 | -0.08 | 0.12 | NO
39 | GNE | GNE | GNE | 14120 | -0.15 | 0.044 | NO
40 | HK1 | HK1 | HK1 | 14745 | -0.18 | 0.055 | NO
41 | GNPNAT1 | GNPNAT1 | GNPNAT1 | 15609 | -0.23 | 0.065 | NO
42 | GCK | GCK | GCK | 16619 | -0.31 | 0.086 | 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

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

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 | ADH6 | ADH6 | ADH6 | 1 | 1.3 | 0.14 | YES
2 | ADH1A | ADH1A | ADH1A | 2 | 1.2 | 0.26 | YES
3 | ADH1B | ADH1B | ADH1B | 13 | 0.79 | 0.35 | YES
4 | TAT | TAT | TAT | 143 | 0.51 | 0.4 | YES
5 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 520 | 0.33 | 0.41 | YES
6 | ADH1C | ADH1C | ADH1C | 640 | 0.31 | 0.44 | YES
7 | ADH4 | ADH4 | ADH4 | 671 | 0.3 | 0.47 | YES
8 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 849 | 0.26 | 0.48 | YES
9 | AOC2 | AOC2 | AOC2 | 935 | 0.25 | 0.51 | YES
10 | DCT | DCT | DCT | 1069 | 0.23 | 0.52 | YES
11 | ADH5 | ADH5 | ADH5 | 1713 | 0.16 | 0.51 | NO
12 | HPD | HPD | HPD | 2896 | 0.094 | 0.45 | NO
13 | GSTZ1 | GSTZ1 | GSTZ1 | 2945 | 0.092 | 0.46 | NO
14 | LCMT2 | LCMT2 | LCMT2 | 3105 | 0.087 | 0.46 | NO
15 | METTL6 | METTL6 | METTL6 | 3422 | 0.077 | 0.45 | NO
16 | MIF | MIF | MIF | 3857 | 0.065 | 0.43 | NO
17 | GOT1 | GOT1 | GOT1 | 4102 | 0.06 | 0.43 | NO
18 | TPO | TPO | TPO | 5344 | 0.034 | 0.36 | NO
19 | METTL2B | METTL2B | METTL2B | 7599 | 0.0013 | 0.24 | NO
20 | MAOB | MAOB | MAOB | 7718 | -0.00055 | 0.23 | NO
21 | DDC | DDC | DDC | 8694 | -0.014 | 0.18 | NO
22 | COMT | COMT | COMT | 8702 | -0.015 | 0.18 | NO
23 | FAH | FAH | FAH | 8771 | -0.016 | 0.18 | NO
24 | IL4I1 | IL4I1 | IL4I1 | 9149 | -0.022 | 0.16 | NO
25 | WBSCR22 | WBSCR22 | WBSCR22 | 9357 | -0.025 | 0.15 | NO
26 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 11239 | -0.06 | 0.054 | NO
27 | LCMT1 | LCMT1 | LCMT1 | 11441 | -0.064 | 0.05 | NO
28 | GOT2 | GOT2 | GOT2 | 11988 | -0.077 | 0.028 | NO
29 | TRMT11 | TRMT11 | TRMT11 | 12908 | -0.1 | -0.012 | NO
30 | TYR | TYR | TYR | 13600 | -0.13 | -0.036 | NO
31 | HEMK1 | HEMK1 | HEMK1 | 13667 | -0.13 | -0.025 | NO
32 | NAT6 | NAT6 | NAT6 | 13840 | -0.14 | -0.02 | NO
33 | AOX1 | AOX1 | AOX1 | 15163 | -0.2 | -0.07 | NO
34 | TH | TH | TH | 15317 | -0.21 | -0.056 | NO
35 | HGD | HGD | HGD | 15536 | -0.23 | -0.043 | NO
36 | AOC3 | AOC3 | AOC3 | 15746 | -0.24 | -0.029 | NO
37 | DBH | DBH | DBH | 16682 | -0.32 | -0.046 | NO
38 | PNMT | PNMT | PNMT | 16709 | -0.32 | -0.014 | NO
39 | MAOA | MAOA | MAOA | 17583 | -0.43 | -0.015 | NO
40 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 17650 | -0.45 | 0.03 | 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S10. 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 TYROSINE METABOLISM

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 | GPR37 | GPR37 | GPR37 | 135 | 0.52 | 0.066 | YES
2 | SNCA | SNCA | SNCA | 393 | 0.38 | 0.1 | YES
3 | PARK2 | PARK2 | PARK2 | 801 | 0.27 | 0.12 | YES
4 | SLC6A3 | SLC6A3 | SLC6A3 | 1192 | 0.21 | 0.13 | YES
5 | SLC25A4 | SLC25A4 | SLC25A4 | 1242 | 0.2 | 0.15 | YES
6 | NDUFC1 | NDUFC1 | NDUFC1 | 1445 | 0.18 | 0.17 | YES
7 | UBE2L6 | UBE2L6 | UBE2L6 | 1824 | 0.15 | 0.17 | YES
8 | NDUFB1 | NDUFB1 | NDUFB1 | 1904 | 0.14 | 0.18 | YES
9 | CASP3 | CASP3 | CASP3 | 2083 | 0.13 | 0.19 | YES
10 | NDUFB5 | NDUFB5 | NDUFB5 | 2511 | 0.11 | 0.19 | YES
11 | COX7A1 | COX7A1 | COX7A1 | 2793 | 0.099 | 0.18 | YES
12 | ATP5G1 | ATP5G1 | ATP5G1 | 3037 | 0.089 | 0.18 | YES
13 | ATP5H | ATP5H | ATP5H | 3065 | 0.088 | 0.2 | YES
14 | NDUFA2 | NDUFA2 | NDUFA2 | 3110 | 0.087 | 0.2 | YES
15 | CASP9 | CASP9 | CASP9 | 3126 | 0.087 | 0.22 | YES
16 | ATP5G3 | ATP5G3 | ATP5G3 | 3195 | 0.085 | 0.22 | YES
17 | NDUFA3 | NDUFA3 | NDUFA3 | 3388 | 0.079 | 0.22 | YES
18 | NDUFB4 | NDUFB4 | NDUFB4 | 3542 | 0.074 | 0.23 | YES
19 | SDHD | SDHD | SDHD | 3648 | 0.071 | 0.23 | YES
20 | COX7C | COX7C | COX7C | 3775 | 0.068 | 0.23 | YES
21 | UQCR10 | UQCR10 | UQCR10 | 3849 | 0.066 | 0.24 | YES
22 | NDUFV3 | NDUFV3 | NDUFV3 | 3858 | 0.065 | 0.25 | YES
23 | COX5B | COX5B | COX5B | 3887 | 0.065 | 0.26 | YES
24 | SLC25A6 | SLC25A6 | SLC25A6 | 3897 | 0.064 | 0.26 | YES
25 | NDUFB6 | NDUFB6 | NDUFB6 | 3928 | 0.064 | 0.27 | YES
26 | ATP5F1 | ATP5F1 | ATP5F1 | 3954 | 0.063 | 0.28 | YES
27 | COX8C | COX8C | COX8C | 3959 | 0.063 | 0.29 | YES
28 | UBE2J2 | UBE2J2 | UBE2J2 | 4030 | 0.061 | 0.29 | YES
29 | NDUFA7 | NDUFA7 | NDUFA7 | 4063 | 0.06 | 0.3 | YES
30 | NDUFS8 | NDUFS8 | NDUFS8 | 4173 | 0.058 | 0.3 | YES
31 | NDUFS4 | NDUFS4 | NDUFS4 | 4238 | 0.057 | 0.3 | YES
32 | ATP5A1 | ATP5A1 | ATP5A1 | 4243 | 0.057 | 0.31 | YES
33 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 4264 | 0.056 | 0.32 | YES
34 | HTRA2 | HTRA2 | HTRA2 | 4356 | 0.053 | 0.32 | YES
35 | ATP5C1 | ATP5C1 | ATP5C1 | 4425 | 0.052 | 0.33 | YES
36 | COX6A1 | COX6A1 | COX6A1 | 4499 | 0.05 | 0.33 | YES
37 | ATP5B | ATP5B | ATP5B | 4525 | 0.05 | 0.33 | YES
38 | PARK7 | PARK7 | PARK7 | 4678 | 0.046 | 0.33 | YES
39 | PINK1 | PINK1 | PINK1 | 4689 | 0.046 | 0.34 | YES
40 | UBA7 | UBA7 | UBA7 | 4698 | 0.046 | 0.34 | YES
41 | UQCRB | UQCRB | UQCRB | 4795 | 0.044 | 0.34 | YES
42 | COX7B | COX7B | COX7B | 4924 | 0.042 | 0.34 | YES
43 | NDUFV1 | NDUFV1 | NDUFV1 | 4942 | 0.042 | 0.35 | YES
44 | ATP5G2 | ATP5G2 | ATP5G2 | 4991 | 0.041 | 0.35 | YES
45 | NDUFA10 | NDUFA10 | NDUFA10 | 5054 | 0.039 | 0.35 | YES
46 | NDUFB3 | NDUFB3 | NDUFB3 | 5069 | 0.039 | 0.36 | YES
47 | UQCRQ | UQCRQ | UQCRQ | 5117 | 0.038 | 0.36 | YES
48 | ATP5O | ATP5O | ATP5O | 5140 | 0.038 | 0.37 | YES
49 | NDUFS5 | NDUFS5 | NDUFS5 | 5153 | 0.038 | 0.37 | YES
50 | NDUFA9 | NDUFA9 | NDUFA9 | 5377 | 0.034 | 0.36 | YES
51 | COX4I1 | COX4I1 | COX4I1 | 5403 | 0.034 | 0.37 | YES
52 | NDUFB10 | NDUFB10 | NDUFB10 | 5417 | 0.033 | 0.37 | YES
53 | NDUFB7 | NDUFB7 | NDUFB7 | 5512 | 0.032 | 0.37 | YES
54 | NDUFA8 | NDUFA8 | NDUFA8 | 5541 | 0.031 | 0.37 | YES
55 | UQCR11 | UQCR11 | UQCR11 | 5567 | 0.031 | 0.38 | YES
56 | VDAC2 | VDAC2 | VDAC2 | 5612 | 0.03 | 0.38 | YES
57 | UQCRC2 | UQCRC2 | UQCRC2 | 5771 | 0.027 | 0.37 | YES
58 | COX8A | COX8A | COX8A | 5813 | 0.026 | 0.37 | YES
59 | NDUFS3 | NDUFS3 | NDUFS3 | 5823 | 0.026 | 0.38 | YES
60 | COX6C | COX6C | COX6C | 5847 | 0.026 | 0.38 | YES
61 | ATP5J | ATP5J | ATP5J | 5874 | 0.025 | 0.38 | YES
62 | COX7A2L | COX7A2L | COX7A2L | 5938 | 0.025 | 0.38 | YES
63 | SDHA | SDHA | SDHA | 6020 | 0.024 | 0.38 | YES
64 | NDUFB2 | NDUFB2 | NDUFB2 | 6048 | 0.023 | 0.38 | YES
65 | UBE2L3 | UBE2L3 | UBE2L3 | 6129 | 0.022 | 0.38 | YES
66 | NDUFB8 | NDUFB8 | NDUFB8 | 6149 | 0.022 | 0.38 | YES
67 | NDUFS1 | NDUFS1 | NDUFS1 | 6173 | 0.021 | 0.38 | YES
68 | SDHB | SDHB | SDHB | 6182 | 0.021 | 0.39 | YES
69 | UBB | UBB | UBB | 6302 | 0.02 | 0.38 | NO
70 | NDUFV2 | NDUFV2 | NDUFV2 | 6475 | 0.017 | 0.38 | NO
71 | NDUFA1 | NDUFA1 | NDUFA1 | 6557 | 0.016 | 0.37 | NO
72 | CYCS | CYCS | CYCS | 6572 | 0.015 | 0.38 | NO
73 | NDUFS2 | NDUFS2 | NDUFS2 | 6601 | 0.015 | 0.38 | NO
74 | UBA1 | UBA1 | UBA1 | 6606 | 0.015 | 0.38 | NO
75 | NDUFC2 | NDUFC2 | NDUFC2 | 6933 | 0.01 | 0.36 | NO
76 | VDAC3 | VDAC3 | VDAC3 | 6982 | 0.0096 | 0.36 | NO
77 | NDUFA4 | NDUFA4 | NDUFA4 | 6988 | 0.0095 | 0.36 | NO
78 | ATP5E | ATP5E | ATP5E | 7044 | 0.0088 | 0.36 | NO
79 | CYC1 | CYC1 | CYC1 | 7207 | 0.0068 | 0.35 | NO
80 | ATP5D | ATP5D | ATP5D | 7433 | 0.0036 | 0.34 | NO
81 | NDUFS7 | NDUFS7 | NDUFS7 | 7585 | 0.0015 | 0.33 | NO
82 | NDUFA5 | NDUFA5 | NDUFA5 | 7606 | 0.0012 | 0.33 | NO
83 | UQCRHL | UQCRHL | UQCRHL | 7725 | -0.00062 | 0.32 | NO
84 | UQCRH | UQCRH | UQCRH | 7834 | -0.0021 | 0.32 | NO
85 | PPID | PPID | PPID | 7843 | -0.0022 | 0.32 | NO
86 | COX7A2 | COX7A2 | COX7A2 | 7866 | -0.0025 | 0.32 | NO
87 | COX5A | COX5A | COX5A | 8017 | -0.0048 | 0.31 | NO
88 | SDHC | SDHC | SDHC | 8170 | -0.0068 | 0.3 | NO
89 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 8329 | -0.0094 | 0.29 | NO
90 | COX6B1 | COX6B1 | COX6B1 | 8469 | -0.011 | 0.29 | NO
91 | NDUFS6 | NDUFS6 | NDUFS6 | 8569 | -0.013 | 0.28 | NO
92 | NDUFB9 | NDUFB9 | NDUFB9 | 8587 | -0.013 | 0.28 | NO
93 | UBE2G2 | UBE2G2 | UBE2G2 | 8896 | -0.018 | 0.27 | NO
94 | UBE2J1 | UBE2J1 | UBE2J1 | 9007 | -0.019 | 0.27 | NO
95 | SLC25A5 | SLC25A5 | SLC25A5 | 9571 | -0.028 | 0.24 | NO
96 | VDAC1 | VDAC1 | VDAC1 | 9658 | -0.03 | 0.24 | NO
97 | NDUFA6 | NDUFA6 | NDUFA6 | 10364 | -0.042 | 0.21 | NO
98 | UQCRC1 | UQCRC1 | UQCRC1 | 10462 | -0.043 | 0.21 | NO
99 | UBE2G1 | UBE2G1 | UBE2G1 | 10514 | -0.044 | 0.21 | NO
100 | SNCAIP | SNCAIP | SNCAIP | 11117 | -0.057 | 0.19 | NO
101 | NDUFA4L2 | NDUFA4L2 | NDUFA4L2 | 11319 | -0.062 | 0.18 | NO
102 | SLC18A1 | SLC18A1 | SLC18A1 | 11425 | -0.064 | 0.19 | NO
103 | LRRK2 | LRRK2 | LRRK2 | 12386 | -0.088 | 0.15 | NO
104 | APAF1 | APAF1 | APAF1 | 13002 | -0.11 | 0.13 | NO
105 | UCHL1 | UCHL1 | UCHL1 | 14023 | -0.14 | 0.091 | NO
106 | SLC18A2 | SLC18A2 | SLC18A2 | 14444 | -0.16 | 0.09 | NO
107 | COX6A2 | COX6A2 | COX6A2 | 14495 | -0.16 | 0.11 | NO
108 | COX6B2 | COX6B2 | COX6B2 | 15122 | -0.2 | 0.1 | NO
109 | TH | TH | TH | 15317 | -0.21 | 0.12 | NO
110 | COX4I2 | COX4I2 | COX4I2 | 15785 | -0.24 | 0.13 | 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 TYROSINE METABOLISM.

Figure S12. 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 S7. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | ZBP1 | ZBP1 | ZBP1 | 193 | 0.47 | 0.095 | YES
2 | DDX58 | DDX58 | DDX58 | 394 | 0.38 | 0.17 | YES
3 | IRF7 | IRF7 | IRF7 | 516 | 0.33 | 0.24 | YES
4 | IFNB1 | IFNB1 | IFNB1 | 614 | 0.31 | 0.3 | YES
5 | IL1B | IL1B | IL1B | 840 | 0.26 | 0.34 | YES
6 | IL18 | IL18 | IL18 | 892 | 0.25 | 0.4 | YES
7 | CASP1 | CASP1 | CASP1 | 1062 | 0.23 | 0.44 | YES
8 | CXCL10 | CXCL10 | CXCL10 | 1216 | 0.21 | 0.48 | YES
9 | NFKB1 | NFKB1 | NFKB1 | 2469 | 0.11 | 0.43 | NO
10 | CCL5 | CCL5 | CCL5 | 2488 | 0.11 | 0.46 | NO
11 | POLR3B | POLR3B | POLR3B | 3245 | 0.083 | 0.43 | NO
12 | NFKBIA | NFKBIA | NFKBIA | 3559 | 0.073 | 0.43 | NO
13 | PYCARD | PYCARD | PYCARD | 4116 | 0.059 | 0.42 | NO
14 | CCL4 | CCL4 | CCL4 | 4272 | 0.056 | 0.42 | NO
15 | RIPK3 | RIPK3 | RIPK3 | 4512 | 0.05 | 0.42 | NO
16 | POLR1C | POLR1C | POLR1C | 4632 | 0.047 | 0.42 | NO
17 | RIPK1 | RIPK1 | RIPK1 | 4653 | 0.047 | 0.43 | NO
18 | CCL4L2 | CCL4L2 | CCL4L2 | 4868 | 0.043 | 0.43 | NO
19 | MAVS | MAVS | MAVS | 5145 | 0.038 | 0.42 | NO
20 | CHUK | CHUK | CHUK | 5494 | 0.032 | 0.41 | NO
21 | ADAR | ADAR | ADAR | 6218 | 0.02 | 0.38 | NO
22 | TREX1 | TREX1 | TREX1 | 6258 | 0.02 | 0.38 | NO
23 | TBK1 | TBK1 | TBK1 | 6773 | 0.012 | 0.35 | NO
24 | RELA | RELA | RELA | 6940 | 0.01 | 0.34 | NO
25 | IKBKE | IKBKE | IKBKE | 7298 | 0.0056 | 0.33 | NO
26 | IRF3 | IRF3 | IRF3 | 7933 | -0.0036 | 0.29 | NO
27 | POLR1D | POLR1D | POLR1D | 8110 | -0.0061 | 0.28 | NO
28 | POLR3K | POLR3K | POLR3K | 8413 | -0.01 | 0.27 | NO
29 | IKBKB | IKBKB | IKBKB | 8682 | -0.014 | 0.26 | NO
30 | POLR3C | POLR3C | POLR3C | 8722 | -0.015 | 0.26 | NO
31 | POLR3A | POLR3A | POLR3A | 9068 | -0.02 | 0.24 | NO
32 | POLR3H | POLR3H | POLR3H | 9670 | -0.03 | 0.22 | NO
33 | AIM2 | AIM2 | AIM2 | 10237 | -0.039 | 0.2 | NO
34 | IL6 | IL6 | IL6 | 11005 | -0.054 | 0.16 | NO
35 | IKBKG | IKBKG | IKBKG | 11219 | -0.06 | 0.17 | NO
36 | POLR3GL | POLR3GL | POLR3GL | 12142 | -0.081 | 0.13 | NO
37 | NFKBIB | NFKBIB | NFKBIB | 12614 | -0.095 | 0.13 | NO
38 | TMEM173 | TMEM173 | TMEM173 | 12644 | -0.096 | 0.15 | NO
39 | POLR3F | POLR3F | POLR3F | 12692 | -0.098 | 0.17 | NO
40 | POLR3D | POLR3D | POLR3D | 13213 | -0.12 | 0.16 | NO
41 | IL33 | IL33 | IL33 | 13804 | -0.14 | 0.16 | NO
42 | POLR3G | POLR3G | POLR3G | 17041 | -0.35 | 0.063 | NO

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

Figure S14. 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 SPHINGOLIPID METABOLISM

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 | DCP1B | DCP1B | DCP1B | 2265 | 0.12 | -0.08 | YES
2 | EXOSC9 | EXOSC9 | EXOSC9 | 2310 | 0.12 | -0.039 | YES
3 | LSM3 | LSM3 | LSM3 | 2610 | 0.11 | -0.018 | YES
4 | EXOSC6 | EXOSC6 | EXOSC6 | 2730 | 0.1 | 0.012 | YES
5 | PNPT1 | PNPT1 | PNPT1 | 3503 | 0.075 | -0.0038 | YES
6 | SKIV2L2 | SKIV2L2 | SKIV2L2 | 3698 | 0.069 | 0.01 | YES
7 | LSM6 | LSM6 | LSM6 | 3715 | 0.069 | 0.034 | YES
8 | XRN1 | XRN1 | XRN1 | 4081 | 0.06 | 0.035 | YES
9 | CNOT4 | CNOT4 | CNOT4 | 4193 | 0.058 | 0.05 | YES
10 | CNOT6L | CNOT6L | CNOT6L | 4580 | 0.049 | 0.046 | YES
11 | CNOT1 | CNOT1 | CNOT1 | 4719 | 0.046 | 0.055 | YES
12 | WDR61 | WDR61 | WDR61 | 4851 | 0.043 | 0.063 | YES
13 | C1D | C1D | C1D | 5080 | 0.039 | 0.064 | YES
14 | NAA38 | NAA38 | NAA38 | 5342 | 0.034 | 0.062 | YES
15 | SKIV2L | SKIV2L | SKIV2L | 5418 | 0.033 | 0.07 | YES
16 | CNOT6 | CNOT6 | CNOT6 | 5714 | 0.028 | 0.064 | YES
17 | EXOSC10 | EXOSC10 | EXOSC10 | 5746 | 0.028 | 0.072 | YES
18 | LSM5 | LSM5 | LSM5 | 5822 | 0.026 | 0.077 | YES
19 | PAPOLA | PAPOLA | PAPOLA | 5843 | 0.026 | 0.086 | YES
20 | DDX6 | DDX6 | DDX6 | 5901 | 0.025 | 0.091 | YES
21 | EDC4 | EDC4 | EDC4 | 6195 | 0.021 | 0.083 | YES
22 | ENO1 | ENO1 | ENO1 | 6254 | 0.02 | 0.087 | YES
23 | LSM4 | LSM4 | LSM4 | 6311 | 0.019 | 0.09 | YES
24 | EXOSC3 | EXOSC3 | EXOSC3 | 6346 | 0.019 | 0.095 | YES
25 | PARN | PARN | PARN | 6351 | 0.019 | 0.1 | YES
26 | CNOT2 | CNOT2 | CNOT2 | 6986 | 0.0095 | 0.07 | YES
27 | CNOT10 | CNOT10 | CNOT10 | 7059 | 0.0086 | 0.069 | YES
28 | CNOT7 | CNOT7 | CNOT7 | 7082 | 0.0084 | 0.071 | YES
29 | HSPD1 | HSPD1 | HSPD1 | 7091 | 0.0082 | 0.074 | YES
30 | DIS3 | DIS3 | DIS3 | 7492 | 0.0029 | 0.053 | YES
31 | EXOSC4 | EXOSC4 | EXOSC4 | 7518 | 0.0025 | 0.052 | YES
32 | LSM1 | LSM1 | LSM1 | 7699 | -0.00035 | 0.042 | YES
33 | EXOSC8 | EXOSC8 | EXOSC8 | 7810 | -0.0018 | 0.037 | YES
34 | HSPA9 | HSPA9 | HSPA9 | 7862 | -0.0024 | 0.035 | YES
35 | PATL1 | PATL1 | PATL1 | 8041 | -0.0052 | 0.027 | YES
36 | EXOSC5 | EXOSC5 | EXOSC5 | 9313 | -0.024 | -0.034 | YES
37 | EXOSC1 | EXOSC1 | EXOSC1 | 9453 | -0.027 | -0.033 | YES
38 | EXOSC2 | EXOSC2 | EXOSC2 | 10077 | -0.037 | -0.054 | YES
39 | XRN2 | XRN2 | XRN2 | 10447 | -0.043 | -0.059 | YES
40 | DCP2 | DCP2 | DCP2 | 10461 | -0.043 | -0.044 | YES
41 | TTC37 | TTC37 | TTC37 | 10657 | -0.047 | -0.038 | YES
42 | MPHOSPH6 | MPHOSPH6 | MPHOSPH6 | 10716 | -0.048 | -0.024 | YES
43 | CNOT3 | CNOT3 | CNOT3 | 10765 | -0.049 | -0.009 | YES
44 | LSM7 | LSM7 | LSM7 | 11197 | -0.059 | -0.012 | YES
45 | ZCCHC7 | ZCCHC7 | ZCCHC7 | 11224 | -0.06 | 0.0083 | YES
46 | LSM2 | LSM2 | LSM2 | 11690 | -0.07 | 0.0076 | YES
47 | DCP1A | DCP1A | DCP1A | 12173 | -0.082 | 0.01 | YES
48 | PAPOLB | PAPOLB | PAPOLB | 12200 | -0.082 | 0.038 | YES
49 | ENO2 | ENO2 | ENO2 | 12235 | -0.083 | 0.066 | YES
50 | PAPOLG | PAPOLG | PAPOLG | 12289 | -0.085 | 0.094 | YES
51 | EDC3 | EDC3 | EDC3 | 12420 | -0.089 | 0.12 | YES
52 | PAPD7 | PAPD7 | PAPD7 | 12576 | -0.094 | 0.14 | YES
53 | DCPS | DCPS | DCPS | 12995 | -0.11 | 0.16 | YES
54 | RQCD1 | RQCD1 | RQCD1 | 13150 | -0.11 | 0.19 | YES
55 | ENO3 | ENO3 | ENO3 | 13341 | -0.12 | 0.22 | YES
56 | EXOSC7 | EXOSC7 | EXOSC7 | 13450 | -0.12 | 0.26 | YES

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

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

genes ES table in pathway: KEGG PROPANOATE METABOLISM

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 | KIR2DL3 | KIR2DL3 | KIR2DL3 | 286 | 0.42 | 0.066 | YES
2 | HLA-G | HLA-G | HLA-G | 420 | 0.37 | 0.13 | YES
3 | KLRC1 | KLRC1 | KLRC1 | 453 | 0.36 | 0.2 | YES
4 | KIR3DL1 | KIR3DL1 | KIR3DL1 | 592 | 0.32 | 0.25 | YES
5 | KLRD1 | KLRD1 | KLRD1 | 613 | 0.31 | 0.31 | YES
6 | KIR2DL1 | KIR2DL1 | KIR2DL1 | 677 | 0.3 | 0.36 | YES
7 | GZMB | GZMB | GZMB | 819 | 0.27 | 0.41 | YES
8 | IL1B | IL1B | IL1B | 840 | 0.26 | 0.46 | YES
9 | HLA-F | HLA-F | HLA-F | 846 | 0.26 | 0.51 | YES
10 | PRF1 | PRF1 | PRF1 | 1185 | 0.21 | 0.53 | YES
11 | KIR3DL2 | KIR3DL2 | KIR3DL2 | 1504 | 0.18 | 0.55 | YES
12 | HLA-C | HLA-C | HLA-C | 1913 | 0.14 | 0.55 | YES
13 | HLA-B | HLA-B | HLA-B | 2059 | 0.14 | 0.57 | YES
14 | HLA-A | HLA-A | HLA-A | 2270 | 0.12 | 0.58 | YES
15 | HLA-E | HLA-E | HLA-E | 2281 | 0.12 | 0.6 | YES
16 | CD28 | CD28 | CD28 | 2299 | 0.12 | 0.63 | YES
17 | FASLG | FASLG | FASLG | 2339 | 0.12 | 0.65 | YES
18 | TNF | TNF | TNF | 3012 | 0.09 | 0.63 | NO
19 | HLA-DOB | HLA-DOB | HLA-DOB | 3478 | 0.076 | 0.62 | NO
20 | CD86 | CD86 | CD86 | 6678 | 0.014 | 0.44 | NO
21 | FAS | FAS | FAS | 6713 | 0.013 | 0.44 | NO
22 | HLA-DMA | HLA-DMA | HLA-DMA | 6811 | 0.012 | 0.44 | NO
23 | HLA-DRB1 | HLA-DRB1 | HLA-DRB1 | 8432 | -0.011 | 0.35 | NO
24 | IL2 | IL2 | IL2 | 8996 | -0.019 | 0.33 | NO
25 | CD80 | CD80 | CD80 | 9363 | -0.025 | 0.31 | NO
26 | HLA-DMB | HLA-DMB | HLA-DMB | 9534 | -0.028 | 0.31 | NO
27 | HLA-DRB5 | HLA-DRB5 | HLA-DRB5 | 10259 | -0.04 | 0.28 | NO
28 | HLA-DRA | HLA-DRA | HLA-DRA | 10522 | -0.044 | 0.27 | NO
29 | HLA-DPA1 | HLA-DPA1 | HLA-DPA1 | 10766 | -0.049 | 0.26 | NO
30 | IL6 | IL6 | IL6 | 11005 | -0.054 | 0.26 | NO
31 | HLA-DPB1 | HLA-DPB1 | HLA-DPB1 | 11547 | -0.066 | 0.24 | NO
32 | HLA-DQA2 | HLA-DQA2 | HLA-DQA2 | 11952 | -0.076 | 0.24 | NO
33 | IFNG | IFNG | IFNG | 13517 | -0.13 | 0.18 | NO
34 | HLA-DOA | HLA-DOA | HLA-DOA | 13704 | -0.13 | 0.19 | NO
35 | HLA-DQA1 | HLA-DQA1 | HLA-DQA1 | 13884 | -0.14 | 0.21 | NO
36 | IL1A | IL1A | IL1A | 14074 | -0.15 | 0.23 | NO

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

Figure S18. 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 BUTANOATE METABOLISM

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 | SNCA | SNCA | SNCA | 393 | 0.38 | 0.01 | YES
2 | PLCB1 | PLCB1 | PLCB1 | 449 | 0.36 | 0.038 | YES
3 | CHP | CHP | CHP | 590 | 0.32 | 0.057 | YES
4 | ERN1 | ERN1 | ERN1 | 652 | 0.3 | 0.079 | YES
5 | CACNA1F | CACNA1F | CACNA1F | 667 | 0.3 | 0.1 | YES
6 | IL1B | IL1B | IL1B | 840 | 0.26 | 0.12 | YES
7 | GRIN2B | GRIN2B | GRIN2B | 1270 | 0.2 | 0.11 | YES
8 | MAPT | MAPT | MAPT | 1284 | 0.2 | 0.13 | YES
9 | NDUFC1 | NDUFC1 | NDUFC1 | 1445 | 0.18 | 0.13 | YES
10 | CALML5 | CALML5 | CALML5 | 1446 | 0.18 | 0.15 | YES
11 | GRIN2A | GRIN2A | GRIN2A | 1773 | 0.16 | 0.14 | YES
12 | NDUFB1 | NDUFB1 | NDUFB1 | 1904 | 0.14 | 0.15 | YES
13 | CASP3 | CASP3 | CASP3 | 2083 | 0.13 | 0.15 | YES
14 | BACE2 | BACE2 | BACE2 | 2446 | 0.11 | 0.14 | YES
15 | NDUFB5 | NDUFB5 | NDUFB5 | 2511 | 0.11 | 0.15 | YES
16 | ITPR3 | ITPR3 | ITPR3 | 2616 | 0.11 | 0.15 | YES
17 | ATP2A1 | ATP2A1 | ATP2A1 | 2623 | 0.1 | 0.16 | YES
18 | CASP8 | CASP8 | CASP8 | 2633 | 0.1 | 0.17 | YES
19 | COX7A1 | COX7A1 | COX7A1 | 2793 | 0.099 | 0.17 | YES
20 | CHP2 | CHP2 | CHP2 | 2833 | 0.097 | 0.17 | YES
21 | TNF | TNF | TNF | 3012 | 0.09 | 0.17 | YES
22 | ATP5G1 | ATP5G1 | ATP5G1 | 3037 | 0.089 | 0.18 | YES
23 | ATP5H | ATP5H | ATP5H | 3065 | 0.088 | 0.18 | YES
24 | NDUFA2 | NDUFA2 | NDUFA2 | 3110 | 0.087 | 0.19 | YES
25 | CASP9 | CASP9 | CASP9 | 3126 | 0.087 | 0.19 | YES
26 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 3155 | 0.086 | 0.2 | YES
27 | ATP5G3 | ATP5G3 | ATP5G3 | 3195 | 0.085 | 0.2 | YES
28 | NDUFA3 | NDUFA3 | NDUFA3 | 3388 | 0.079 | 0.2 | YES
29 | NDUFB4 | NDUFB4 | NDUFB4 | 3542 | 0.074 | 0.2 | YES
30 | SDHD | SDHD | SDHD | 3648 | 0.071 | 0.2 | YES
31 | COX7C | COX7C | COX7C | 3775 | 0.068 | 0.2 | YES
32 | UQCR10 | UQCR10 | UQCR10 | 3849 | 0.066 | 0.2 | YES
33 | NDUFV3 | NDUFV3 | NDUFV3 | 3858 | 0.065 | 0.2 | YES
34 | COX5B | COX5B | COX5B | 3887 | 0.065 | 0.21 | YES
35 | FADD | FADD | FADD | 3888 | 0.065 | 0.21 | YES
36 | NDUFB6 | NDUFB6 | NDUFB6 | 3928 | 0.064 | 0.22 | YES
37 | ATP5F1 | ATP5F1 | ATP5F1 | 3954 | 0.063 | 0.22 | YES
38 | COX8C | COX8C | COX8C | 3959 | 0.063 | 0.23 | YES
39 | NDUFA7 | NDUFA7 | NDUFA7 | 4063 | 0.06 | 0.22 | YES
40 | NDUFS8 | NDUFS8 | NDUFS8 | 4173 | 0.058 | 0.22 | YES
41 | NDUFS4 | NDUFS4 | NDUFS4 | 4238 | 0.057 | 0.22 | YES
42 | ATP5A1 | ATP5A1 | ATP5A1 | 4243 | 0.057 | 0.23 | YES
43 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 4264 | 0.056 | 0.23 | YES
44 | MAPK3 | MAPK3 | MAPK3 | 4374 | 0.053 | 0.23 | YES
45 | ATP5C1 | ATP5C1 | ATP5C1 | 4425 | 0.052 | 0.23 | YES
46 | COX6A1 | COX6A1 | COX6A1 | 4499 | 0.05 | 0.23 | YES
47 | ATP5B | ATP5B | ATP5B | 4525 | 0.05 | 0.24 | YES
48 | PSEN1 | PSEN1 | PSEN1 | 4547 | 0.049 | 0.24 | YES
49 | BAD | BAD | BAD | 4577 | 0.049 | 0.24 | YES
50 | PSEN2 | PSEN2 | PSEN2 | 4673 | 0.046 | 0.24 | YES
51 | NAE1 | NAE1 | NAE1 | 4759 | 0.045 | 0.24 | YES
52 | UQCRB | UQCRB | UQCRB | 4795 | 0.044 | 0.24 | YES
53 | COX7B | COX7B | COX7B | 4924 | 0.042 | 0.24 | YES
54 | NDUFV1 | NDUFV1 | NDUFV1 | 4942 | 0.042 | 0.24 | YES
55 | ATP5G2 | ATP5G2 | ATP5G2 | 4991 | 0.041 | 0.24 | YES
56 | NDUFA10 | NDUFA10 | NDUFA10 | 5054 | 0.039 | 0.24 | YES
57 | NDUFB3 | NDUFB3 | NDUFB3 | 5069 | 0.039 | 0.24 | YES
58 | UQCRQ | UQCRQ | UQCRQ | 5117 | 0.038 | 0.24 | YES
59 | ATP5O | ATP5O | ATP5O | 5140 | 0.038 | 0.25 | YES
60 | NDUFS5 | NDUFS5 | NDUFS5 | 5153 | 0.038 | 0.25 | YES
61 | PPP3CA | PPP3CA | PPP3CA | 5327 | 0.035 | 0.24 | YES
62 | NDUFA9 | NDUFA9 | NDUFA9 | 5377 | 0.034 | 0.24 | YES
63 | CAPN2 | CAPN2 | CAPN2 | 5380 | 0.034 | 0.25 | YES
64 | COX4I1 | COX4I1 | COX4I1 | 5403 | 0.034 | 0.25 | YES
65 | NDUFB10 | NDUFB10 | NDUFB10 | 5417 | 0.033 | 0.25 | YES
66 | CAPN1 | CAPN1 | CAPN1 | 5429 | 0.033 | 0.25 | YES
67 | APH1A | APH1A | APH1A | 5433 | 0.033 | 0.25 | YES
68 | ADAM10 | ADAM10 | ADAM10 | 5478 | 0.032 | 0.26 | YES
69 | APP | APP | APP | 5493 | 0.032 | 0.26 | YES
70 | NDUFB7 | NDUFB7 | NDUFB7 | 5512 | 0.032 | 0.26 | YES
71 | NDUFA8 | NDUFA8 | NDUFA8 | 5541 | 0.031 | 0.26 | YES
72 | UQCR11 | UQCR11 | UQCR11 | 5567 | 0.031 | 0.26 | YES
73 | GSK3B | GSK3B | GSK3B | 5571 | 0.03 | 0.26 | YES
74 | PSENEN | PSENEN | PSENEN | 5592 | 0.03 | 0.26 | YES
75 | CALML3 | CALML3 | CALML3 | 5684 | 0.029 | 0.26 | YES
76 | APOE | APOE | APOE | 5708 | 0.028 | 0.26 | YES
77 | UQCRC2 | UQCRC2 | UQCRC2 | 5771 | 0.027 | 0.26 | YES
78 | COX8A | COX8A | COX8A | 5813 | 0.026 | 0.26 | YES
79 | NDUFS3 | NDUFS3 | NDUFS3 | 5823 | 0.026 | 0.26 | YES
80 | COX6C | COX6C | COX6C | 5847 | 0.026 | 0.26 | YES
81 | ATP5J | ATP5J | ATP5J | 5874 | 0.025 | 0.26 | YES
82 | COX7A2L | COX7A2L | COX7A2L | 5938 | 0.025 | 0.26 | NO
83 | SDHA | SDHA | SDHA | 6020 | 0.024 | 0.26 | NO
84 | NDUFB2 | NDUFB2 | NDUFB2 | 6048 | 0.023 | 0.26 | NO
85 | NDUFB8 | NDUFB8 | NDUFB8 | 6149 | 0.022 | 0.26 | NO
86 | NDUFS1 | NDUFS1 | NDUFS1 | 6173 | 0.021 | 0.26 | NO
87 | SDHB | SDHB | SDHB | 6182 | 0.021 | 0.26 | NO
88 | NDUFV2 | NDUFV2 | NDUFV2 | 6475 | 0.017 | 0.24 | NO
89 | NDUFA1 | NDUFA1 | NDUFA1 | 6557 | 0.016 | 0.24 | NO
90 | CYCS | CYCS | CYCS | 6572 | 0.015 | 0.24 | NO
91 | NDUFS2 | NDUFS2 | NDUFS2 | 6601 | 0.015 | 0.24 | NO
92 | BID | BID | BID | 6660 | 0.014 | 0.24 | NO
93 | FAS | FAS | FAS | 6713 | 0.013 | 0.24 | NO
94 | EIF2AK3 | EIF2AK3 | EIF2AK3 | 6774 | 0.012 | 0.24 | NO
95 | ITPR1 | ITPR1 | ITPR1 | 6900 | 0.011 | 0.23 | NO
96 | LRP1 | LRP1 | LRP1 | 6919 | 0.01 | 0.23 | NO
97 | NDUFC2 | NDUFC2 | NDUFC2 | 6933 | 0.01 | 0.23 | NO
98 | PLCB2 | PLCB2 | PLCB2 | 6968 | 0.0097 | 0.23 | NO
99 | NDUFA4 | NDUFA4 | NDUFA4 | 6988 | 0.0095 | 0.23 | NO
100 | ATP5E | ATP5E | ATP5E | 7044 | 0.0088 | 0.23 | NO
101 | CALM2 | CALM2 | CALM2 | 7182 | 0.007 | 0.22 | NO
102 | CYC1 | CYC1 | CYC1 | 7207 | 0.0068 | 0.22 | NO
103 | PPP3CC | PPP3CC | PPP3CC | 7313 | 0.0054 | 0.21 | NO
104 | ATP5D | ATP5D | ATP5D | 7433 | 0.0036 | 0.21 | NO
105 | NDUFS7 | NDUFS7 | NDUFS7 | 7585 | 0.0015 | 0.2 | NO
106 | NDUFA5 | NDUFA5 | NDUFA5 | 7606 | 0.0012 | 0.2 | NO
107 | UQCRHL | UQCRHL | UQCRHL | 7725 | -0.00062 | 0.19 | NO
108 | UQCRH | UQCRH | UQCRH | 7834 | -0.0021 | 0.19 | NO
109 | COX7A2 | COX7A2 | COX7A2 | 7866 | -0.0025 | 0.18 | NO
110 | CALM3 | CALM3 | CALM3 | 7942 | -0.0038 | 0.18 | NO
111 | COX5A | COX5A | COX5A | 8017 | -0.0048 | 0.18 | NO
112 | HSD17B10 | HSD17B10 | HSD17B10 | 8053 | -0.0054 | 0.18 | NO
113 | CASP7 | CASP7 | CASP7 | 8055 | -0.0054 | 0.18 | NO
114 | NCSTN | NCSTN | NCSTN | 8163 | -0.0067 | 0.17 | NO
115 | SDHC | SDHC | SDHC | 8170 | -0.0068 | 0.17 | NO
116 | NDUFAB1 | NDUFAB1 | NDUFAB1 | 8329 | -0.0094 | 0.16 | NO
117 | COX6B1 | COX6B1 | COX6B1 | 8469 | -0.011 | 0.16 | NO
118 | NDUFS6 | NDUFS6 | NDUFS6 | 8569 | -0.013 | 0.15 | NO
119 | NDUFB9 | NDUFB9 | NDUFB9 | 8587 | -0.013 | 0.15 | NO
120 | GNAQ | GNAQ | GNAQ | 8717 | -0.015 | 0.15 | NO
121 | ITPR2 | ITPR2 | ITPR2 | 8719 | -0.015 | 0.15 | NO
122 | MAPK1 | MAPK1 | MAPK1 | 8903 | -0.018 | 0.14 | NO
123 | CALM1 | CALM1 | CALM1 | 9026 | -0.02 | 0.13 | NO
124 | CDK5 | CDK5 | CDK5 | 9311 | -0.024 | 0.12 | NO
125 | PPP3CB | PPP3CB | PPP3CB | 9558 | -0.028 | 0.11 | NO
126 | PPP3R1 | PPP3R1 | PPP3R1 | 9759 | -0.032 | 0.1 | NO
127 | ATP2A2 | ATP2A2 | ATP2A2 | 9836 | -0.033 | 0.098 | NO
128 | GAPDH | GAPDH | GAPDH | 10062 | -0.036 | 0.089 | NO
129 | GRIN2C | GRIN2C | GRIN2C | 10101 | -0.037 | 0.09 | NO
130 | BACE1 | BACE1 | BACE1 | 10232 | -0.039 | 0.086 | NO
131 | NDUFA6 | NDUFA6 | NDUFA6 | 10364 | -0.042 | 0.082 | NO
132 | UQCRC1 | UQCRC1 | UQCRC1 | 10462 | -0.043 | 0.081 | NO
133 | PLCB3 | PLCB3 | PLCB3 | 10753 | -0.049 | 0.069 | NO
134 | CALML6 | CALML6 | CALML6 | 10930 | -0.052 | 0.064 | NO
135 | ADAM17 | ADAM17 | ADAM17 | 11293 | -0.061 | 0.049 | NO
136 | NDUFA4L2 | NDUFA4L2 | NDUFA4L2 | 11319 | -0.062 | 0.053 | NO
137 | ATF6 | ATF6 | ATF6 | 11339 | -0.062 | 0.057 | NO
138 | ATP2A3 | ATP2A3 | ATP2A3 | 11949 | -0.076 | 0.03 | NO
139 | IDE | IDE | IDE | 12068 | -0.079 | 0.03 | NO
140 | LPL | LPL | LPL | 12988 | -0.11 | -0.012 | NO
141 | APAF1 | APAF1 | APAF1 | 13002 | -0.11 | -0.0038 | NO
142 | CACNA1D | CACNA1D | CACNA1D | 13336 | -0.12 | -0.012 | NO
143 | GRIN1 | GRIN1 | GRIN1 | 13485 | -0.12 | -0.0098 | NO
144 | APBB1 | APBB1 | APBB1 | 13504 | -0.12 | -9e-05 | NO
145 | COX6A2 | COX6A2 | COX6A2 | 14495 | -0.16 | -0.041 | NO
146 | COX6B2 | COX6B2 | COX6B2 | 15122 | -0.2 | -0.058 | NO
147 | CACNA1C | CACNA1C | CACNA1C | 15563 | -0.23 | -0.063 | NO
148 | CDK5R1 | CDK5R1 | CDK5R1 | 15583 | -0.23 | -0.045 | NO
149 | COX4I2 | COX4I2 | COX4I2 | 15785 | -0.24 | -0.035 | NO
150 | CACNA1S | CACNA1S | CACNA1S | 15974 | -0.26 | -0.024 | NO
151 | MME | MME | MME | 17062 | -0.36 | -0.054 | NO
152 | PLCB4 | PLCB4 | PLCB4 | 17326 | -0.39 | -0.035 | NO
153 | GRIN2D | GRIN2D | GRIN2D | 17395 | -0.4 | -0.0044 | NO
154 | RYR3 | RYR3 | RYR3 | 18001 | -0.57 | 0.01 | NO

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

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

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
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BIOCARTA CHREBP2 PATHWAY | 40 | genes.ES.table | 0.32 | 1.2 | 0.24 | 1 | 1 | 0.12 | 0.1 | 0.11 | 0.99 | 0.49
BIOCARTA RHO PATHWAY | 31 | genes.ES.table | 0.4 | 1.5 | 0.055 | 0.51 | 0.88 | 0.097 | 0.079 | 0.089 | 0.37 | 0.14
KEGG GLYCOLYSIS GLUCONEOGENESIS | 55 | genes.ES.table | 0.41 | 1.3 | 0.12 | 0.77 | 0.98 | 0.46 | 0.33 | 0.3 | 0.64 | 0.25
KEGG CITRATE CYCLE TCA CYCLE | 29 | genes.ES.table | 0.39 | 1.3 | 0.17 | 0.83 | 0.98 | 0.69 | 0.42 | 0.4 | 0.69 | 0.29
KEGG STEROID HORMONE BIOSYNTHESIS | 39 | genes.ES.table | 0.5 | 1.2 | 0.17 | 1 | 1 | 0.54 | 0.2 | 0.43 | 0.96 | 0.47
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION | 42 | genes.ES.table | 0.47 | 1.6 | 0.065 | 0.85 | 0.67 | 0.45 | 0.29 | 0.32 | 0.53 | 0.29
KEGG ARGININE AND PROLINE METABOLISM | 51 | genes.ES.table | 0.36 | 1.2 | 0.21 | 1 | 1 | 0.26 | 0.16 | 0.21 | 0.94 | 0.46
KEGG HISTIDINE METABOLISM | 28 | genes.ES.table | 0.62 | 1.6 | 0.012 | 1 | 0.67 | 0.54 | 0.25 | 0.4 | 1 | 0.52
KEGG TYROSINE METABOLISM | 40 | genes.ES.table | 0.44 | 1.2 | 0.2 | 1 | 1 | 0.22 | 0.11 | 0.2 | 0.94 | 0.46
KEGG TRYPTOPHAN METABOLISM | 37 | genes.ES.table | 0.43 | 1.2 | 0.26 | 1 | 1 | 0.14 | 0.052 | 0.13 | 0.93 | 0.44

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | MAOA | MAOA | MAOA | 26 | 0.71 | 0.18 | YES
2 | MAOB | MAOB | MAOB | 159 | 0.53 | 0.3 | YES
3 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 508 | 0.38 | 0.38 | YES
4 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 515 | 0.37 | 0.47 | YES
5 | FTCD | FTCD | FTCD | 902 | 0.3 | 0.52 | YES
6 | HEMK1 | HEMK1 | HEMK1 | 1925 | 0.19 | 0.52 | YES
7 | AMDHD1 | AMDHD1 | AMDHD1 | 2301 | 0.17 | 0.54 | YES
8 | HAL | HAL | HAL | 2814 | 0.14 | 0.54 | YES
9 | HNMT | HNMT | HNMT | 2940 | 0.13 | 0.57 | YES
10 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3282 | 0.12 | 0.58 | YES
11 | LCMT1 | LCMT1 | LCMT1 | 3782 | 0.1 | 0.58 | YES
12 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 4116 | 0.091 | 0.58 | YES
13 | TRMT11 | TRMT11 | TRMT11 | 4186 | 0.09 | 0.6 | YES
14 | WBSCR22 | WBSCR22 | WBSCR22 | 4415 | 0.083 | 0.61 | YES
15 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 4559 | 0.08 | 0.62 | YES
16 | METTL2B | METTL2B | METTL2B | 6152 | 0.048 | 0.55 | NO
17 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6741 | 0.039 | 0.52 | NO
18 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 7049 | 0.034 | 0.52 | NO
19 | ALDH2 | ALDH2 | ALDH2 | 7424 | 0.029 | 0.5 | NO
20 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 8236 | 0.018 | 0.46 | NO
21 | DDC | DDC | DDC | 8777 | 0.011 | 0.44 | NO
22 | UROC1 | UROC1 | UROC1 | 10109 | -0.0062 | 0.36 | NO
23 | HDC | HDC | HDC | 10263 | -0.008 | 0.36 | NO
24 | LCMT2 | LCMT2 | LCMT2 | 11004 | -0.017 | 0.32 | NO
25 | METTL6 | METTL6 | METTL6 | 13187 | -0.052 | 0.22 | NO
26 | ACY3 | ACY3 | ACY3 | 13489 | -0.058 | 0.21 | NO
27 | ABP1 | ABP1 | ABP1 | 14377 | -0.081 | 0.18 | NO
28 | ASPA | ASPA | ASPA | 14986 | -0.1 | 0.18 | NO

Figure S21. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CHREBP2 PATHWAY.

Figure S22. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA RHO PATHWAY

Table S12. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | AOX1 | AOX1 | AOX1 | 73 | 0.62 | 0.14 | YES
2 | EHHADH | EHHADH | EHHADH | 322 | 0.45 | 0.23 | YES
3 | AUH | AUH | AUH | 1123 | 0.27 | 0.25 | YES
4 | ACADSB | ACADSB | ACADSB | 1313 | 0.25 | 0.29 | YES
5 | BCKDHB | BCKDHB | BCKDHB | 1397 | 0.24 | 0.34 | YES
6 | HIBCH | HIBCH | HIBCH | 1815 | 0.2 | 0.37 | YES
7 | ACAT1 | ACAT1 | ACAT1 | 2961 | 0.13 | 0.33 | YES
8 | PCCA | PCCA | PCCA | 3029 | 0.13 | 0.36 | YES
9 | ABAT | ABAT | ABAT | 3270 | 0.12 | 0.37 | YES
10 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3282 | 0.12 | 0.4 | YES
11 | MCEE | MCEE | MCEE | 3407 | 0.11 | 0.42 | YES
12 | HIBADH | HIBADH | HIBADH | 3572 | 0.11 | 0.44 | YES
13 | ACAD8 | ACAD8 | ACAD8 | 3665 | 0.1 | 0.46 | YES
14 | OXCT1 | OXCT1 | OXCT1 | 4173 | 0.09 | 0.45 | YES
15 | MUT | MUT | MUT | 4500 | 0.081 | 0.45 | YES
16 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 4559 | 0.08 | 0.46 | YES
17 | HADH | HADH | HADH | 4898 | 0.072 | 0.46 | YES
18 | MCCC1 | MCCC1 | MCCC1 | 5162 | 0.067 | 0.46 | YES
19 | ACAA2 | ACAA2 | ACAA2 | 5261 | 0.065 | 0.47 | YES
20 | DLD | DLD | DLD | 5720 | 0.056 | 0.46 | NO
21 | HMGCS1 | HMGCS1 | HMGCS1 | 6090 | 0.049 | 0.45 | NO
22 | HSD17B10 | HSD17B10 | HSD17B10 | 6093 | 0.049 | 0.46 | NO
23 | MCCC2 | MCCC2 | MCCC2 | 6223 | 0.047 | 0.47 | NO
24 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6741 | 0.039 | 0.45 | NO
25 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 7049 | 0.034 | 0.44 | NO
26 | DBT | DBT | DBT | 7064 | 0.034 | 0.44 | NO
27 | ALDH2 | ALDH2 | ALDH2 | 7424 | 0.029 | 0.43 | NO
28 | HMGCL | HMGCL | HMGCL | 8346 | 0.017 | 0.38 | NO
29 | BCKDHA | BCKDHA | BCKDHA | 8473 | 0.015 | 0.38 | NO
30 | ACAA1 | ACAA1 | ACAA1 | 9114 | 0.0069 | 0.35 | NO
31 | ACADM | ACADM | ACADM | 9381 | 0.0034 | 0.33 | NO
32 | BCAT2 | BCAT2 | BCAT2 | 10413 | -0.01 | 0.28 | NO
33 | PCCB | PCCB | PCCB | 10627 | -0.013 | 0.27 | NO
34 | HADHB | HADHB | HADHB | 10638 | -0.013 | 0.27 | NO
35 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 10738 | -0.014 | 0.27 | NO
36 | HADHA | HADHA | HADHA | 10838 | -0.015 | 0.27 | NO
37 | ECHS1 | ECHS1 | ECHS1 | 11889 | -0.029 | 0.22 | NO
38 | ACADS | ACADS | ACADS | 12479 | -0.038 | 0.19 | NO
39 | IL4I1 | IL4I1 | IL4I1 | 13313 | -0.054 | 0.16 | NO
40 | IVD | IVD | IVD | 14022 | -0.071 | 0.14 | NO
41 | ACAT2 | ACAT2 | ACAT2 | 16370 | -0.17 | 0.048 | NO
42 | OXCT2 | OXCT2 | OXCT2 | 17055 | -0.23 | 0.062 | NO

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

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

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

Table 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 | UGT1A9 | UGT1A9 | UGT1A9 | 324 | 0.45 | 0.083 | YES
2 | MGAM | MGAM | MGAM | 452 | 0.4 | 0.16 | YES
3 | UGT1A1 | UGT1A1 | UGT1A1 | 948 | 0.29 | 0.2 | YES
4 | GCK | GCK | GCK | 1039 | 0.28 | 0.26 | YES
5 | UGT1A6 | UGT1A6 | UGT1A6 | 1082 | 0.27 | 0.32 | YES
6 | AMY2B | AMY2B | AMY2B | 1409 | 0.24 | 0.36 | YES
7 | UGT1A10 | UGT1A10 | UGT1A10 | 1441 | 0.23 | 0.41 | YES
8 | PYGM | PYGM | PYGM | 1458 | 0.23 | 0.46 | YES
9 | GBA3 | GBA3 | GBA3 | 1467 | 0.23 | 0.51 | YES
10 | UGT2A1 | UGT2A1 | UGT2A1 | 1717 | 0.21 | 0.54 | YES
11 | UGT1A8 | UGT1A8 | UGT1A8 | 1787 | 0.2 | 0.58 | YES
12 | ENPP1 | ENPP1 | ENPP1 | 2132 | 0.18 | 0.6 | YES
13 | AGL | AGL | AGL | 4695 | 0.077 | 0.48 | NO
14 | AMY1A | AMY1A | AMY1A | 5201 | 0.066 | 0.47 | NO
15 | GBE1 | GBE1 | GBE1 | 5629 | 0.058 | 0.46 | NO
16 | PGM2 | PGM2 | PGM2 | 6001 | 0.05 | 0.45 | NO
17 | GPI | GPI | GPI | 6764 | 0.038 | 0.42 | NO
18 | UGP2 | UGP2 | UGP2 | 7611 | 0.026 | 0.37 | NO
19 | GUSB | GUSB | GUSB | 7744 | 0.025 | 0.37 | NO
20 | HK2 | HK2 | HK2 | 8708 | 0.012 | 0.32 | NO
21 | AMY2A | AMY2A | AMY2A | 9306 | 0.0043 | 0.29 | NO
22 | GAA | GAA | GAA | 10438 | -0.01 | 0.23 | NO
23 | UGDH | UGDH | UGDH | 11341 | -0.022 | 0.19 | NO
24 | PYGB | PYGB | PYGB | 11507 | -0.024 | 0.18 | NO
25 | ENPP3 | ENPP3 | ENPP3 | 12329 | -0.036 | 0.14 | NO
26 | GYS2 | GYS2 | GYS2 | 12338 | -0.036 | 0.15 | NO
27 | PGM1 | PGM1 | PGM1 | 13320 | -0.054 | 0.11 | NO
28 | GYS1 | GYS1 | GYS1 | 13365 | -0.055 | 0.12 | NO
29 | HK1 | HK1 | HK1 | 13681 | -0.062 | 0.12 | NO
30 | PYGL | PYGL | PYGL | 13946 | -0.069 | 0.12 | NO
31 | GANC | GANC | GANC | 14660 | -0.091 | 0.099 | NO
32 | PGM2L1 | PGM2L1 | PGM2L1 | 14938 | -0.1 | 0.11 | NO
33 | TREH | TREH | TREH | 16139 | -0.16 | 0.076 | NO
34 | HK3 | HK3 | HK3 | 16274 | -0.17 | 0.1 | 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 GLYCOLYSIS GLUCONEOGENESIS.

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

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

Table 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 | 26 | 0.71 | 0.072 | YES
2 | AOX1 | AOX1 | AOX1 | 73 | 0.62 | 0.13 | YES
3 | MAOB | MAOB | MAOB | 159 | 0.53 | 0.18 | YES
4 | UGT1A9 | UGT1A9 | UGT1A9 | 324 | 0.45 | 0.22 | YES
5 | ADH1C | ADH1C | ADH1C | 426 | 0.41 | 0.26 | YES
6 | CYP2E1 | CYP2E1 | CYP2E1 | 428 | 0.41 | 0.3 | YES
7 | MGST1 | MGST1 | MGST1 | 492 | 0.38 | 0.33 | YES
8 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 508 | 0.38 | 0.37 | YES
9 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 515 | 0.37 | 0.41 | YES
10 | GSTM2 | GSTM2 | GSTM2 | 701 | 0.34 | 0.43 | YES
11 | UGT1A1 | UGT1A1 | UGT1A1 | 948 | 0.29 | 0.45 | YES
12 | FMO4 | FMO4 | FMO4 | 993 | 0.29 | 0.48 | YES
13 | UGT1A6 | UGT1A6 | UGT1A6 | 1082 | 0.27 | 0.5 | YES
14 | GSTO2 | GSTO2 | GSTO2 | 1134 | 0.27 | 0.53 | YES
15 | CYP2C18 | CYP2C18 | CYP2C18 | 1139 | 0.27 | 0.55 | YES
16 | GSTA4 | GSTA4 | GSTA4 | 1374 | 0.24 | 0.56 | YES
17 | UGT1A10 | UGT1A10 | UGT1A10 | 1441 | 0.23 | 0.59 | YES
18 | GSTM3 | GSTM3 | GSTM3 | 1652 | 0.21 | 0.6 | YES
19 | UGT2A1 | UGT2A1 | UGT2A1 | 1717 | 0.21 | 0.61 | YES
20 | UGT1A8 | UGT1A8 | UGT1A8 | 1787 | 0.2 | 0.63 | YES
21 | GSTM4 | GSTM4 | GSTM4 | 1842 | 0.2 | 0.65 | YES
22 | MGST2 | MGST2 | MGST2 | 2651 | 0.15 | 0.62 | NO
23 | GSTM1 | GSTM1 | GSTM1 | 2833 | 0.14 | 0.62 | NO
24 | CYP3A7 | CYP3A7 | CYP3A7 | 2885 | 0.14 | 0.63 | NO
25 | FMO5 | FMO5 | FMO5 | 3123 | 0.12 | 0.63 | NO
26 | CYP2C8 | CYP2C8 | CYP2C8 | 3306 | 0.12 | 0.64 | NO
27 | CYP2C9 | CYP2C9 | CYP2C9 | 3415 | 0.11 | 0.64 | NO
28 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 4116 | 0.091 | 0.61 | NO
29 | CYP2A7 | CYP2A7 | CYP2A7 | 4154 | 0.09 | 0.62 | NO
30 | FMO1 | FMO1 | FMO1 | 4384 | 0.084 | 0.62 | NO
31 | ADH1B | ADH1B | ADH1B | 4591 | 0.079 | 0.61 | NO
32 | CYP2A6 | CYP2A6 | CYP2A6 | 4650 | 0.078 | 0.62 | NO
33 | MGST3 | MGST3 | MGST3 | 4957 | 0.071 | 0.61 | NO
34 | GSTK1 | GSTK1 | GSTK1 | 6186 | 0.048 | 0.55 | NO
35 | CYP3A5 | CYP3A5 | CYP3A5 | 6222 | 0.047 | 0.55 | NO
36 | GSTP1 | GSTP1 | GSTP1 | 6438 | 0.044 | 0.54 | NO
37 | CYP2D6 | CYP2D6 | CYP2D6 | 6969 | 0.035 | 0.52 | NO
38 | GSTA1 | GSTA1 | GSTA1 | 8026 | 0.021 | 0.46 | NO
39 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 8236 | 0.018 | 0.45 | NO
40 | ADH5 | ADH5 | ADH5 | 10310 | -0.0087 | 0.34 | NO
41 | CYP2A13 | CYP2A13 | CYP2A13 | 10380 | -0.0095 | 0.33 | NO
42 | GSTT1 | GSTT1 | GSTT1 | 10709 | -0.014 | 0.32 | NO
43 | GSTO1 | GSTO1 | GSTO1 | 10976 | -0.017 | 0.3 | NO
44 | FMO3 | FMO3 | FMO3 | 12007 | -0.031 | 0.25 | NO
45 | ADH6 | ADH6 | ADH6 | 12575 | -0.04 | 0.22 | NO
46 | GSTT2 | GSTT2 | GSTT2 | 12911 | -0.046 | 0.21 | NO
47 | CYP1A2 | CYP1A2 | CYP1A2 | 13263 | -0.053 | 0.2 | NO
48 | FMO2 | FMO2 | FMO2 | 13850 | -0.067 | 0.17 | NO
49 | CYP3A43 | CYP3A43 | CYP3A43 | 13870 | -0.067 | 0.18 | NO
50 | ADH4 | ADH4 | ADH4 | 14516 | -0.086 | 0.15 | NO
51 | GSTM5 | GSTM5 | GSTM5 | 14559 | -0.087 | 0.16 | NO
52 | GSTA2 | GSTA2 | GSTA2 | 15419 | -0.12 | 0.12 | NO
53 | ADH1A | ADH1A | ADH1A | 15697 | -0.13 | 0.12 | NO
54 | GSTZ1 | GSTZ1 | GSTZ1 | 16497 | -0.18 | 0.093 | 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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

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 | ACSS3 | ACSS3 | ACSS3 | 176 | 0.52 | 0.16 | YES
2 | EHHADH | EHHADH | EHHADH | 322 | 0.45 | 0.3 | YES
3 | LDHAL6A | LDHAL6A | LDHAL6A | 1532 | 0.22 | 0.31 | YES
4 | HIBCH | HIBCH | HIBCH | 1815 | 0.2 | 0.36 | YES
5 | ACAT1 | ACAT1 | ACAT1 | 2961 | 0.13 | 0.34 | YES
6 | PCCA | PCCA | PCCA | 3029 | 0.13 | 0.38 | YES
7 | ABAT | ABAT | ABAT | 3270 | 0.12 | 0.41 | YES
8 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3282 | 0.12 | 0.45 | YES
9 | MCEE | MCEE | MCEE | 3407 | 0.11 | 0.48 | YES
10 | SUCLA2 | SUCLA2 | SUCLA2 | 4235 | 0.088 | 0.46 | YES
11 | MUT | MUT | MUT | 4500 | 0.081 | 0.48 | YES
12 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 4559 | 0.08 | 0.5 | YES
13 | MLYCD | MLYCD | MLYCD | 4675 | 0.077 | 0.52 | YES
14 | ACSS1 | ACSS1 | ACSS1 | 5322 | 0.064 | 0.51 | NO
15 | SUCLG2 | SUCLG2 | SUCLG2 | 5520 | 0.06 | 0.52 | NO
16 | ACSS2 | ACSS2 | ACSS2 | 5900 | 0.052 | 0.51 | NO
17 | ACACA | ACACA | ACACA | 6295 | 0.046 | 0.5 | NO
18 | SUCLG1 | SUCLG1 | SUCLG1 | 6683 | 0.04 | 0.5 | NO
19 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6741 | 0.039 | 0.51 | NO
20 | LDHA | LDHA | LDHA | 6990 | 0.035 | 0.5 | NO
21 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 7049 | 0.034 | 0.51 | NO
22 | ALDH2 | ALDH2 | ALDH2 | 7424 | 0.029 | 0.5 | NO
23 | LDHB | LDHB | LDHB | 9079 | 0.0072 | 0.41 | NO
24 | ACADM | ACADM | ACADM | 9381 | 0.0034 | 0.4 | NO
25 | LDHAL6B | LDHAL6B | LDHAL6B | 10230 | -0.0077 | 0.35 | NO
26 | ACACB | ACACB | ACACB | 10433 | -0.01 | 0.35 | NO
27 | PCCB | PCCB | PCCB | 10627 | -0.013 | 0.34 | NO
28 | ALDH6A1 | ALDH6A1 | ALDH6A1 | 10738 | -0.014 | 0.34 | NO
29 | HADHA | HADHA | HADHA | 10838 | -0.015 | 0.34 | NO
30 | ECHS1 | ECHS1 | ECHS1 | 11889 | -0.029 | 0.29 | NO
31 | ACAT2 | ACAT2 | ACAT2 | 16370 | -0.17 | 0.1 | 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 STEROID HORMONE BIOSYNTHESIS.

Figure S30. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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

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 | UGT1A9 | UGT1A9 | UGT1A9 | 324 | 0.45 | 0.034 | YES
2 | CYP2S1 | CYP2S1 | CYP2S1 | 377 | 0.43 | 0.08 | YES
3 | ADH1C | ADH1C | ADH1C | 426 | 0.41 | 0.12 | YES
4 | CYP2E1 | CYP2E1 | CYP2E1 | 428 | 0.41 | 0.17 | YES
5 | MGST1 | MGST1 | MGST1 | 492 | 0.38 | 0.21 | YES
6 | ALDH1A3 | ALDH1A3 | ALDH1A3 | 508 | 0.38 | 0.25 | YES
7 | ALDH3A1 | ALDH3A1 | ALDH3A1 | 515 | 0.37 | 0.3 | YES
8 | AKR1C2 | AKR1C2 | AKR1C2 | 686 | 0.34 | 0.33 | YES
9 | GSTM2 | GSTM2 | GSTM2 | 701 | 0.34 | 0.36 | YES
10 | UGT1A1 | UGT1A1 | UGT1A1 | 948 | 0.29 | 0.38 | YES
11 | UGT1A6 | UGT1A6 | UGT1A6 | 1082 | 0.27 | 0.41 | YES
12 | GSTO2 | GSTO2 | GSTO2 | 1134 | 0.27 | 0.44 | YES
13 | CYP2C18 | CYP2C18 | CYP2C18 | 1139 | 0.27 | 0.47 | YES
14 | GSTA4 | GSTA4 | GSTA4 | 1374 | 0.24 | 0.48 | YES
15 | UGT1A10 | UGT1A10 | UGT1A10 | 1441 | 0.23 | 0.51 | YES
16 | AKR1C1 | AKR1C1 | AKR1C1 | 1563 | 0.22 | 0.53 | YES
17 | GSTM3 | GSTM3 | GSTM3 | 1652 | 0.21 | 0.55 | YES
18 | UGT2A1 | UGT2A1 | UGT2A1 | 1717 | 0.21 | 0.57 | YES
19 | UGT1A8 | UGT1A8 | UGT1A8 | 1787 | 0.2 | 0.58 | YES
20 | GSTM4 | GSTM4 | GSTM4 | 1842 | 0.2 | 0.6 | YES
21 | CYP2F1 | CYP2F1 | CYP2F1 | 2588 | 0.15 | 0.58 | YES
22 | MGST2 | MGST2 | MGST2 | 2651 | 0.15 | 0.6 | YES
23 | GSTM1 | GSTM1 | GSTM1 | 2833 | 0.14 | 0.6 | YES
24 | CYP3A7 | CYP3A7 | CYP3A7 | 2885 | 0.14 | 0.61 | YES
25 | AKR1C3 | AKR1C3 | AKR1C3 | 3170 | 0.12 | 0.61 | YES
26 | CYP2C8 | CYP2C8 | CYP2C8 | 3306 | 0.12 | 0.62 | YES
27 | CYP2C9 | CYP2C9 | CYP2C9 | 3415 | 0.11 | 0.62 | YES
28 | CYP1B1 | CYP1B1 | CYP1B1 | 3660 | 0.1 | 0.62 | NO
29 | EPHX1 | EPHX1 | EPHX1 | 4012 | 0.095 | 0.62 | NO
30 | ALDH3B1 | ALDH3B1 | ALDH3B1 | 4116 | 0.091 | 0.62 | NO
31 | ADH1B | ADH1B | ADH1B | 4591 | 0.079 | 0.6 | NO
32 | MGST3 | MGST3 | MGST3 | 4957 | 0.071 | 0.59 | NO
33 | GSTK1 | GSTK1 | GSTK1 | 6186 | 0.048 | 0.53 | NO
34 | CYP3A5 | CYP3A5 | CYP3A5 | 6222 | 0.047 | 0.53 | NO
35 | GSTP1 | GSTP1 | GSTP1 | 6438 | 0.044 | 0.53 | NO
36 | GSTA1 | GSTA1 | GSTA1 | 8026 | 0.021 | 0.44 | NO
37 | ALDH3B2 | ALDH3B2 | ALDH3B2 | 8236 | 0.018 | 0.43 | NO
38 | CYP1A1 | CYP1A1 | CYP1A1 | 8695 | 0.012 | 0.41 | NO
39 | ADH5 | ADH5 | ADH5 | 10310 | -0.0087 | 0.32 | NO
40 | GSTT1 | GSTT1 | GSTT1 | 10709 | -0.014 | 0.3 | NO
41 | GSTO1 | GSTO1 | GSTO1 | 10976 | -0.017 | 0.29 | NO
42 | ADH6 | ADH6 | ADH6 | 12575 | -0.04 | 0.2 | NO
43 | GSTT2 | GSTT2 | GSTT2 | 12911 | -0.046 | 0.19 | NO
44 | CYP1A2 | CYP1A2 | CYP1A2 | 13263 | -0.053 | 0.18 | NO
45 | CYP3A43 | CYP3A43 | CYP3A43 | 13870 | -0.067 | 0.15 | NO
46 | ADH4 | ADH4 | ADH4 | 14516 | -0.086 | 0.12 | NO
47 | GSTM5 | GSTM5 | GSTM5 | 14559 | -0.087 | 0.13 | NO
48 | GSTA2 | GSTA2 | GSTA2 | 15419 | -0.12 | 0.099 | NO
49 | ADH1A | ADH1A | ADH1A | 15697 | -0.13 | 0.099 | NO
50 | DHDH | DHDH | DHDH | 16001 | -0.15 | 0.1 | NO
51 | GSTZ1 | GSTZ1 | GSTZ1 | 16497 | -0.18 | 0.093 | 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S32. 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 ARGININE AND PROLINE METABOLISM

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 | ME1 | ME1 | ME1 | 864 | 0.31 | 0.06 | YES
2 | PKLR | PKLR | PKLR | 1521 | 0.22 | 0.1 | YES
3 | LDHAL6A | LDHAL6A | LDHAL6A | 1532 | 0.22 | 0.18 | YES
4 | LDHD | LDHD | LDHD | 2668 | 0.14 | 0.17 | YES
5 | ACAT1 | ACAT1 | ACAT1 | 2961 | 0.13 | 0.2 | YES
6 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 3282 | 0.12 | 0.22 | YES
7 | AKR1B1 | AKR1B1 | AKR1B1 | 3473 | 0.11 | 0.25 | YES
8 | HAGHL | HAGHL | HAGHL | 3662 | 0.1 | 0.28 | YES
9 | PCK1 | PCK1 | PCK1 | 3748 | 0.1 | 0.31 | YES
10 | ME3 | ME3 | ME3 | 3837 | 0.1 | 0.34 | YES
11 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 4559 | 0.08 | 0.33 | YES
12 | PDHB | PDHB | PDHB | 4805 | 0.074 | 0.34 | YES
13 | HAGH | HAGH | HAGH | 4886 | 0.072 | 0.36 | YES
14 | PDHA1 | PDHA1 | PDHA1 | 5094 | 0.068 | 0.38 | YES
15 | ACSS1 | ACSS1 | ACSS1 | 5322 | 0.064 | 0.38 | YES
16 | GLO1 | GLO1 | GLO1 | 5538 | 0.059 | 0.39 | YES
17 | DLD | DLD | DLD | 5720 | 0.056 | 0.4 | YES
18 | ACSS2 | ACSS2 | ACSS2 | 5900 | 0.052 | 0.41 | YES
19 | PC | PC | PC | 5909 | 0.052 | 0.43 | YES
20 | ACACA | ACACA | ACACA | 6295 | 0.046 | 0.42 | NO
21 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 6741 | 0.039 | 0.41 | NO
22 | LDHA | LDHA | LDHA | 6990 | 0.035 | 0.41 | NO
23 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 7049 | 0.034 | 0.42 | NO
24 | ALDH2 | ALDH2 | ALDH2 | 7424 | 0.029 | 0.41 | NO
25 | MDH2 | MDH2 | MDH2 | 7509 | 0.028 | 0.42 | NO
26 | MDH1 | MDH1 | MDH1 | 7685 | 0.025 | 0.42 | NO
27 | PKM2 | PKM2 | PKM2 | 8198 | 0.019 | 0.39 | NO
28 | DLAT | DLAT | DLAT | 8334 | 0.017 | 0.39 | NO
29 | LDHB | LDHB | LDHB | 9079 | 0.0072 | 0.35 | NO
30 | ME2 | ME2 | ME2 | 9146 | 0.0064 | 0.35 | NO
31 | LDHAL6B | LDHAL6B | LDHAL6B | 10230 | -0.0077 | 0.3 | NO
32 | ACACB | ACACB | ACACB | 10433 | -0.01 | 0.29 | NO
33 | GRHPR | GRHPR | GRHPR | 11787 | -0.028 | 0.22 | NO
34 | ACYP2 | ACYP2 | ACYP2 | 12370 | -0.037 | 0.2 | NO
35 | ACYP1 | ACYP1 | ACYP1 | 13010 | -0.048 | 0.19 | NO
36 | PCK2 | PCK2 | PCK2 | 15246 | -0.11 | 0.1 | NO
37 | ACAT2 | ACAT2 | ACAT2 | 16370 | -0.17 | 0.1 | 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 ARGININE AND PROLINE METABOLISM.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ARGININE AND PROLINE 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 HISTIDINE METABOLISM

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 | PPP1R12B | PPP1R12B | PPP1R12B | 623 | 0.35 | 0.15 | YES
2 | ARHGAP6 | ARHGAP6 | ARHGAP6 | 876 | 0.31 | 0.3 | YES
3 | ARHGEF5 | ARHGEF5 | ARHGEF5 | 1430 | 0.24 | 0.4 | YES
4 | MYL2 | MYL2 | MYL2 | 4078 | 0.092 | 0.3 | NO
5 | RHOA | RHOA | RHOA | 6431 | 0.044 | 0.2 | NO
6 | ARPC1A | ARPC1A | ARPC1A | 6786 | 0.038 | 0.2 | NO
7 | PIP5K1A | PIP5K1A | PIP5K1A | 6819 | 0.038 | 0.22 | NO
8 | ARPC5 | ARPC5 | ARPC5 | 6822 | 0.038 | 0.24 | NO
9 | MYLK | MYLK | MYLK | 7341 | 0.03 | 0.22 | NO
10 | ACTR3 | ACTR3 | ACTR3 | 8093 | 0.02 | 0.19 | NO
11 | ARHGEF11 | ARHGEF11 | ARHGEF11 | 8353 | 0.017 | 0.19 | NO
12 | LIMK1 | LIMK1 | LIMK1 | 8445 | 0.016 | 0.19 | NO
13 | ARPC1B | ARPC1B | ARPC1B | 8800 | 0.011 | 0.18 | NO
14 | ARPC3 | ARPC3 | ARPC3 | 9195 | 0.0058 | 0.16 | NO
15 | PIP5K1B | PIP5K1B | PIP5K1B | 9767 | -0.0018 | 0.13 | NO
16 | ARHGAP4 | ARHGAP4 | ARHGAP4 | 9962 | -0.0044 | 0.12 | NO
17 | OPHN1 | OPHN1 | OPHN1 | 10398 | -0.0098 | 0.1 | NO
18 | BAIAP2 | BAIAP2 | BAIAP2 | 10541 | -0.012 | 0.1 | NO
19 | ACTR2 | ACTR2 | ACTR2 | 11116 | -0.019 | 0.08 | NO
20 | ARHGEF1 | ARHGEF1 | ARHGEF1 | 11157 | -0.019 | 0.088 | NO
21 | DIAPH1 | DIAPH1 | DIAPH1 | 11171 | -0.02 | 0.098 | NO
22 | GSN | GSN | GSN | 11473 | -0.024 | 0.094 | NO
23 | CFL1 | CFL1 | CFL1 | 11647 | -0.026 | 0.098 | NO
24 | ARPC2 | ARPC2 | ARPC2 | 11880 | -0.029 | 0.1 | NO
25 | ARHGAP5 | ARHGAP5 | ARHGAP5 | 12596 | -0.041 | 0.083 | NO
26 | ARHGAP1 | ARHGAP1 | ARHGAP1 | 12995 | -0.048 | 0.087 | NO
27 | ARPC4 | ARPC4 | ARPC4 | 13655 | -0.062 | 0.084 | NO
28 | PFN1 | PFN1 | PFN1 | 13808 | -0.066 | 0.11 | NO
29 | ROCK1 | ROCK1 | ROCK1 | 13986 | -0.07 | 0.14 | NO
30 | VCL | VCL | VCL | 14275 | -0.078 | 0.16 | NO
31 | SRC | SRC | SRC | 14758 | -0.094 | 0.19 | 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 HISTIDINE METABOLISM.

Figure S36. 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 TYROSINE METABOLISM

Table S19. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | SNAP25 | SNAP25 | SNAP25 | 1124 | 0.27 | 0.07 | YES
2 | STX1B | STX1B | STX1B | 1824 | 0.2 | 0.13 | YES
3 | VAMP4 | VAMP4 | VAMP4 | 2975 | 0.13 | 0.13 | YES
4 | BET1 | BET1 | BET1 | 3218 | 0.12 | 0.18 | YES
5 | STX3 | STX3 | STX3 | 3412 | 0.11 | 0.22 | YES
6 | STX2 | STX2 | STX2 | 5349 | 0.064 | 0.15 | YES
7 | VAMP7 | VAMP7 | VAMP7 | 5559 | 0.059 | 0.16 | YES
8 | VAMP1 | VAMP1 | VAMP1 | 5608 | 0.058 | 0.19 | YES
9 | STX7 | STX7 | STX7 | 5622 | 0.058 | 0.22 | YES
10 | STX10 | STX10 | STX10 | 5783 | 0.054 | 0.24 | YES
11 | VAMP8 | VAMP8 | VAMP8 | 6246 | 0.046 | 0.23 | YES
12 | TSNARE1 | TSNARE1 | TSNARE1 | 6260 | 0.046 | 0.26 | YES
13 | STX19 | STX19 | STX19 | 6261 | 0.046 | 0.28 | YES
14 | STX4 | STX4 | STX4 | 6335 | 0.045 | 0.3 | YES
15 | STX8 | STX8 | STX8 | 6530 | 0.042 | 0.31 | YES
16 | STX6 | STX6 | STX6 | 6550 | 0.042 | 0.33 | YES
17 | BET1L | BET1L | BET1L | 6561 | 0.042 | 0.35 | YES
18 | SNAP23 | SNAP23 | SNAP23 | 7084 | 0.034 | 0.33 | YES
19 | GOSR1 | GOSR1 | GOSR1 | 7148 | 0.033 | 0.35 | YES
20 | USE1 | USE1 | USE1 | 7423 | 0.029 | 0.35 | NO
21 | SNAP47 | SNAP47 | SNAP47 | 8309 | 0.017 | 0.3 | NO
22 | YKT6 | YKT6 | YKT6 | 8808 | 0.011 | 0.28 | NO
23 | STX5 | STX5 | STX5 | 9655 | -0.00039 | 0.24 | NO
24 | STX1A | STX1A | STX1A | 9885 | -0.0034 | 0.23 | NO
25 | SEC22B | SEC22B | SEC22B | 9930 | -0.0039 | 0.22 | NO
26 | STX18 | STX18 | STX18 | 10091 | -0.0059 | 0.22 | NO
27 | VAMP3 | VAMP3 | VAMP3 | 10562 | -0.012 | 0.2 | NO
28 | VAMP2 | VAMP2 | VAMP2 | 10571 | -0.012 | 0.2 | NO
29 | STX16 | STX16 | STX16 | 10664 | -0.013 | 0.21 | NO
30 | STX17 | STX17 | STX17 | 10848 | -0.015 | 0.2 | NO
31 | GOSR2 | GOSR2 | GOSR2 | 11005 | -0.017 | 0.2 | NO
32 | STX12 | STX12 | STX12 | 11605 | -0.025 | 0.18 | NO
33 | BNIP1 | BNIP1 | BNIP1 | 13302 | -0.054 | 0.12 | NO
34 | VTI1A | VTI1A | VTI1A | 13525 | -0.059 | 0.13 | NO
35 | STX11 | STX11 | STX11 | 13782 | -0.065 | 0.15 | NO
36 | VAMP5 | VAMP5 | VAMP5 | 14166 | -0.075 | 0.17 | NO
37 | VTI1B | VTI1B | VTI1B | 15259 | -0.11 | 0.16 | NO

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

Figure S38. 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 TRYPTOPHAN METABOLISM

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 | PSTK | PSTK | PSTK | 1600 | 0.22 | -0.0034 | YES
2 | TARSL2 | TARSL2 | TARSL2 | 1742 | 0.2 | 0.068 | YES
3 | CARS2 | CARS2 | CARS2 | 1998 | 0.19 | 0.13 | YES
4 | NARS2 | NARS2 | NARS2 | 2029 | 0.18 | 0.2 | YES
5 | MARS2 | MARS2 | MARS2 | 2427 | 0.16 | 0.24 | YES
6 | EARS2 | EARS2 | EARS2 | 2481 | 0.16 | 0.29 | YES
7 | PARS2 | PARS2 | PARS2 | 2858 | 0.14 | 0.33 | YES
8 | LARS2 | LARS2 | LARS2 | 3101 | 0.12 | 0.36 | YES
9 | IARS2 | IARS2 | IARS2 | 4361 | 0.085 | 0.32 | YES
10 | LARS | LARS | LARS | 4976 | 0.071 | 0.32 | YES
11 | EPRS | EPRS | EPRS | 5434 | 0.062 | 0.32 | YES
12 | RARS2 | RARS2 | RARS2 | 5457 | 0.061 | 0.34 | YES
13 | YARS | YARS | YARS | 5899 | 0.052 | 0.34 | YES
14 | DARS2 | DARS2 | DARS2 | 6146 | 0.048 | 0.34 | YES
15 | QARS | QARS | QARS | 6320 | 0.045 | 0.35 | YES
16 | DARS | DARS | DARS | 6344 | 0.045 | 0.37 | YES
17 | HARS2 | HARS2 | HARS2 | 7003 | 0.035 | 0.34 | NO
18 | FARS2 | FARS2 | FARS2 | 7370 | 0.03 | 0.33 | NO
19 | GARS | GARS | GARS | 7654 | 0.026 | 0.33 | NO
20 | FARSB | FARSB | FARSB | 8053 | 0.021 | 0.32 | NO
21 | WARS2 | WARS2 | WARS2 | 8231 | 0.018 | 0.31 | NO
22 | HARS | HARS | HARS | 8340 | 0.017 | 0.31 | NO
23 | AARS | AARS | AARS | 8369 | 0.017 | 0.32 | NO
24 | MTFMT | MTFMT | MTFMT | 8436 | 0.016 | 0.32 | NO
25 | CARS | CARS | CARS | 8619 | 0.013 | 0.32 | NO
26 | VARS2 | VARS2 | VARS2 | 8645 | 0.013 | 0.32 | NO
27 | NARS | NARS | NARS | 8669 | 0.013 | 0.32 | NO
28 | IARS | IARS | IARS | 9183 | 0.006 | 0.3 | NO
29 | AARS2 | AARS2 | AARS2 | 9319 | 0.0042 | 0.29 | NO
30 | KARS | KARS | KARS | 9333 | 0.004 | 0.29 | NO
31 | VARS | VARS | VARS | 9908 | -0.0036 | 0.26 | NO
32 | SEPSECS | SEPSECS | SEPSECS | 10045 | -0.0054 | 0.26 | NO
33 | RARS | RARS | RARS | 10205 | -0.0074 | 0.25 | NO
34 | FARSA | FARSA | FARSA | 10522 | -0.011 | 0.24 | NO
35 | YARS2 | YARS2 | YARS2 | 11738 | -0.027 | 0.18 | NO
36 | TARS | TARS | TARS | 12053 | -0.032 | 0.18 | NO
37 | SARS | SARS | SARS | 13036 | -0.049 | 0.14 | NO
38 | MARS | MARS | MARS | 13153 | -0.051 | 0.15 | NO
39 | SARS2 | SARS2 | SARS2 | 15476 | -0.12 | 0.073 | NO
40 | WARS | WARS | WARS | 16710 | -0.2 | 0.081 | NO

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

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TRYPTOPHAN METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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

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

Expression level

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

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

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

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

Significant gene list

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

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

Subtype clus3 enriched pathways

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

GeneSet(GS) | Size(#genes) | genes.ES.table | ES | NES | NOM.p.val | FDR.q.val | FWER.p.val | Tag.. | Gene.. | Signal | FDR..median. | glob.p.val
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BIOCARTA BCR PATHWAY | 33 | genes.ES.table | 0.58 | 1.6 | 0.037 | 0.29 | 0.66 | 0.42 | 0.19 | 0.34 | 0.19 | 0.056
BIOCARTA HIVNEF PATHWAY | 57 | genes.ES.table | 0.39 | 1.7 | 0.056 | 0.46 | 0.6 | 0.46 | 0.3 | 0.32 | 0.27 | 0.15
BIOCARTA IL2RB PATHWAY | 37 | genes.ES.table | 0.57 | 1.6 | 0.041 | 0.25 | 0.69 | 0.54 | 0.28 | 0.39 | 0.17 | 0.036
BIOCARTA RACCYCD PATHWAY | 25 | genes.ES.table | 0.39 | 1.5 | 0.054 | 0.28 | 0.83 | 0.44 | 0.3 | 0.31 | 0.2 | 0.031
BIOCARTA INTEGRIN PATHWAY | 37 | genes.ES.table | 0.46 | 1.6 | 0.072 | 0.28 | 0.81 | 0.6 | 0.33 | 0.4 | 0.2 | 0.03
BIOCARTA TCR PATHWAY | 43 | genes.ES.table | 0.64 | 1.6 | 0.031 | 0.34 | 0.64 | 0.3 | 0.086 | 0.28 | 0.22 | 0.078
BIOCARTA VEGF PATHWAY | 28 | genes.ES.table | 0.57 | 1.7 | 0.018 | 0.89 | 0.53 | 0.36 | 0.19 | 0.29 | 0.49 | 0.32
KEGG PROTEASOME | 42 | genes.ES.table | 0.6 | 1.6 | 0.037 | 0.27 | 0.69 | 0.93 | 0.39 | 0.56 | 0.18 | 0.042
KEGG CHEMOKINE SIGNALING PATHWAY | 184 | genes.ES.table | 0.56 | 1.6 | 0.029 | 0.26 | 0.73 | 0.47 | 0.2 | 0.38 | 0.18 | 0.038
KEGG CELL CYCLE | 123 | genes.ES.table | 0.51 | 1.6 | 0.041 | 0.41 | 0.62 | 0.31 | 0.19 | 0.25 | 0.25 | 0.1

genes ES table in pathway: BIOCARTA BCR PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | MECOM | MECOM | MECOM | 178 | 0.53 | 0.066 | YES
2 | PIK3CG | PIK3CG | PIK3CG | 432 | 0.44 | 0.12 | YES
3 | PIK3R5 | PIK3R5 | PIK3R5 | 791 | 0.36 | 0.15 | YES
4 | TGFB1 | TGFB1 | TGFB1 | 1801 | 0.24 | 0.12 | YES
5 | SHC3 | SHC3 | SHC3 | 1901 | 0.23 | 0.15 | YES
6 | AKT3 | AKT3 | AKT3 | 2151 | 0.21 | 0.17 | YES
7 | PIK3R3 | PIK3R3 | PIK3R3 | 2285 | 0.2 | 0.19 | YES
8 | TGFBR1 | TGFBR1 | TGFBR1 | 2700 | 0.17 | 0.19 | YES
9 | E2F3 | E2F3 | E2F3 | 2726 | 0.17 | 0.21 | YES
10 | TGFBR2 | TGFBR2 | TGFBR2 | 2899 | 0.16 | 0.23 | YES
11 | E2F2 | E2F2 | E2F2 | 3056 | 0.15 | 0.24 | YES
12 | NRAS | NRAS | NRAS | 3061 | 0.15 | 0.26 | YES
13 | CDKN1A | CDKN1A | CDKN1A | 3377 | 0.13 | 0.26 | YES
14 | SHC1 | SHC1 | SHC1 | 3482 | 0.12 | 0.27 | YES
15 | MAP2K1 | MAP2K1 | MAP2K1 | 3489 | 0.12 | 0.29 | YES
16 | CCND1 | CCND1 | CCND1 | 3547 | 0.12 | 0.3 | YES
17 | CBL | CBL | CBL | 3760 | 0.11 | 0.31 | YES
18 | GAB2 | GAB2 | GAB2 | 3792 | 0.11 | 0.32 | YES
19 | PIK3CD | PIK3CD | PIK3CD | 3885 | 0.11 | 0.33 | YES
20 | RUNX1 | RUNX1 | RUNX1 | 3987 | 0.1 | 0.34 | YES
21 | CRK | CRK | CRK | 4192 | 0.095 | 0.35 | YES
22 | CDK6 | CDK6 | CDK6 | 4400 | 0.088 | 0.35 | YES
23 | HDAC1 | HDAC1 | HDAC1 | 4514 | 0.084 | 0.35 | YES
24 | CTBP2 | CTBP2 | CTBP2 | 4617 | 0.082 | 0.36 | YES
25 | SHC4 | SHC4 | SHC4 | 4712 | 0.079 | 0.36 | YES
26 | BCL2L1 | BCL2L1 | BCL2L1 | 4783 | 0.077 | 0.37 | YES
27 | NFKBIA | NFKBIA | NFKBIA | 4907 | 0.073 | 0.38 | YES
28 | GRB2 | GRB2 | GRB2 | 5020 | 0.07 | 0.38 | YES
29 | MAPK1 | MAPK1 | MAPK1 | 5081 | 0.068 | 0.39 | YES
30 | BRAF | BRAF | BRAF | 5082 | 0.068 | 0.4 | YES
31 | AKT1 | AKT1 | AKT1 | 5146 | 0.066 | 0.4 | YES
32 | NFKB1 | NFKB1 | NFKB1 | 5152 | 0.066 | 0.41 | YES
33 | PTPN11 | PTPN11 | PTPN11 | 5248 | 0.064 | 0.42 | YES
34 | CHUK | CHUK | CHUK | 5416 | 0.06 | 0.42 | YES
35 | CBLB | CBLB | CBLB | 5615 | 0.055 | 0.41 | YES
36 | KRAS | KRAS | KRAS | 5788 | 0.051 | 0.41 | YES
37 | CDKN2A | CDKN2A | CDKN2A | 5799 | 0.051 | 0.42 | YES
38 | RB1 | RB1 | RB1 | 6667 | 0.034 | 0.37 | NO
39 | IKBKG | IKBKG | IKBKG | 6928 | 0.028 | 0.36 | NO
40 | RAF1 | RAF1 | RAF1 | 7057 | 0.026 | 0.36 | NO
41 | HRAS | HRAS | HRAS | 7235 | 0.023 | 0.35 | NO
42 | CDK4 | CDK4 | CDK4 | 7329 | 0.022 | 0.35 | NO
43 | HDAC2 | HDAC2 | HDAC2 | 7407 | 0.02 | 0.35 | NO
44 | MYC | MYC | MYC | 7482 | 0.019 | 0.35 | NO
45 | CRKL | CRKL | CRKL | 7525 | 0.018 | 0.35 | NO
46 | PIK3CA | PIK3CA | PIK3CA | 7906 | 0.012 | 0.33 | NO
47 | RELA | RELA | RELA | 7927 | 0.011 | 0.33 | NO
48 | MAP2K2 | MAP2K2 | MAP2K2 | 8004 | 0.0098 | 0.33 | NO
49 | STAT5B | STAT5B | STAT5B | 8267 | 0.0056 | 0.31 | NO
50 | MDM2 | MDM2 | MDM2 | 8504 | 0.00086 | 0.3 | NO
51 | SOS2 | SOS2 | SOS2 | 8545 | 5.2e-06 | 0.3 | NO
52 | CDKN1B | CDKN1B | CDKN1B | 8995 | -0.0075 | 0.28 | NO
53 | ARAF | ARAF | ARAF | 9112 | -0.0094 | 0.27 | NO
54 | SMAD3 | SMAD3 | SMAD3 | 9521 | -0.017 | 0.25 | NO
55 | AKT2 | AKT2 | AKT2 | 9654 | -0.02 | 0.24 | NO
56 | CBLC | CBLC | CBLC | 9728 | -0.021 | 0.24 | NO
57 | ABL1 | ABL1 | ABL1 | 9849 | -0.023 | 0.24 | NO
58 | IKBKB | IKBKB | IKBKB | 10274 | -0.031 | 0.22 | NO
59 | CTBP1 | CTBP1 | CTBP1 | 10281 | -0.031 | 0.23 | NO
60 | SMAD4 | SMAD4 | SMAD4 | 10390 | -0.033 | 0.22 | NO
61 | STAT5A | STAT5A | STAT5A | 10621 | -0.037 | 0.22 | NO
62 | TP53 | TP53 | TP53 | 10764 | -0.04 | 0.22 | NO
63 | SOS1 | SOS1 | SOS1 | 11394 | -0.054 | 0.19 | NO
64 | PIK3CB | PIK3CB | PIK3CB | 11615 | -0.059 | 0.18 | NO
65 | PIK3R2 | PIK3R2 | PIK3R2 | 12371 | -0.078 | 0.15 | NO
66 | MAPK3 | MAPK3 | MAPK3 | 13360 | -0.11 | 0.12 | NO
67 | PIK3R1 | PIK3R1 | PIK3R1 | 13476 | -0.11 | 0.12 | NO
68 | TGFB2 | TGFB2 | TGFB2 | 13539 | -0.12 | 0.14 | NO
69 | BAD | BAD | BAD | 13682 | -0.12 | 0.15 | NO
70 | BCR | BCR | BCR | 14164 | -0.14 | 0.14 | NO
71 | TGFB3 | TGFB3 | TGFB3 | 15446 | -0.22 | 0.1 | NO
72 | SHC2 | SHC2 | SHC2 | 16709 | -0.34 | 0.082 | NO

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

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

genes ES table in pathway: BIOCARTA HIVNEF 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 | FLT4 | FLT4 | FLT4 | 216 | 0.51 | 0.12 | YES
2 | PIK3CG | PIK3CG | PIK3CG | 432 | 0.44 | 0.21 | YES
3 | NOS3 | NOS3 | NOS3 | 490 | 0.42 | 0.32 | YES
4 | FLT1 | FLT1 | FLT1 | 655 | 0.39 | 0.4 | YES
5 | PRKCB | PRKCB | PRKCB | 879 | 0.35 | 0.48 | YES
6 | PRKCA | PRKCA | PRKCA | 1560 | 0.26 | 0.51 | YES
7 | HIF1A | HIF1A | HIF1A | 1589 | 0.26 | 0.57 | YES
8 | EIF2S1 | EIF2S1 | EIF2S1 | 2840 | 0.16 | 0.54 | YES
9 | PXN | PXN | PXN | 3064 | 0.15 | 0.56 | YES
10 | SHC1 | SHC1 | SHC1 | 3482 | 0.12 | 0.57 | YES
11 | EIF2S2 | EIF2S2 | EIF2S2 | 4757 | 0.078 | 0.52 | NO
12 | EIF2B2 | EIF2B2 | EIF2B2 | 5373 | 0.061 | 0.5 | NO
13 | EIF2B3 | EIF2B3 | EIF2B3 | 5575 | 0.056 | 0.51 | NO
14 | EIF2B5 | EIF2B5 | EIF2B5 | 6481 | 0.037 | 0.47 | NO
15 | VHL | VHL | VHL | 6727 | 0.032 | 0.46 | NO
16 | EIF2B4 | EIF2B4 | EIF2B4 | 6889 | 0.029 | 0.46 | NO
17 | EIF1 | EIF1 | EIF1 | 7418 | 0.02 | 0.44 | NO
18 | PIK3CA | PIK3CA | PIK3CA | 7906 | 0.012 | 0.41 | NO
19 | VEGFA | VEGFA | VEGFA | 8371 | 0.0032 | 0.39 | NO
20 | ELAVL1 | ELAVL1 | ELAVL1 | 9235 | -0.012 | 0.34 | NO
21 | EIF2S3 | EIF2S3 | EIF2S3 | 9315 | -0.013 | 0.34 | NO
22 | EIF1AX | EIF1AX | EIF1AX | 9534 | -0.017 | 0.33 | NO
23 | PLCG1 | PLCG1 | PLCG1 | 9574 | -0.018 | 0.34 | NO
24 | EIF2B1 | EIF2B1 | EIF2B1 | 10801 | -0.041 | 0.28 | NO
25 | PTK2 | PTK2 | PTK2 | 10935 | -0.043 | 0.28 | NO
26 | ARNT | ARNT | ARNT | 12784 | -0.09 | 0.2 | NO
27 | PIK3R1 | PIK3R1 | PIK3R1 | 13476 | -0.11 | 0.19 | NO
28 | KDR | KDR | KDR | 15985 | -0.26 | 0.12 | NO

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

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

Table 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 | IL12A | IL12A | IL12A | 53 | 0.66 | 0.049 | YES
2 | CR1 | CR1 | CR1 | 63 | 0.64 | 0.099 | YES
3 | IFNG | IFNG | IFNG | 162 | 0.54 | 0.14 | YES
4 | NOS2 | NOS2 | NOS2 | 168 | 0.54 | 0.18 | YES
5 | TLR4 | TLR4 | TLR4 | 610 | 0.39 | 0.19 | YES
6 | ITGA4 | ITGA4 | ITGA4 | 647 | 0.39 | 0.21 | YES
7 | FCGR1A | FCGR1A | FCGR1A | 731 | 0.37 | 0.24 | YES
8 | NCF2 | NCF2 | NCF2 | 760 | 0.37 | 0.27 | YES
9 | IL12B | IL12B | IL12B | 847 | 0.35 | 0.29 | YES
10 | PRKCB | PRKCB | PRKCB | 879 | 0.35 | 0.32 | YES
11 | HLA-DQA2 | HLA-DQA2 | HLA-DQA2 | 1130 | 0.31 | 0.33 | YES
12 | TNF | TNF | TNF | 1134 | 0.31 | 0.35 | YES
13 | HLA-DQA1 | HLA-DQA1 | HLA-DQA1 | 1322 | 0.29 | 0.36 | YES
14 | FCGR3B | FCGR3B | FCGR3B | 1325 | 0.29 | 0.39 | YES
15 | FCGR3A | FCGR3A | FCGR3A | 1326 | 0.29 | 0.41 | YES
16 | NCF1 | NCF1 | NCF1 | 1538 | 0.26 | 0.42 | YES
17 | NCF4 | NCF4 | NCF4 | 1558 | 0.26 | 0.44 | YES
18 | HLA-DOB | HLA-DOB | HLA-DOB | 1653 | 0.25 | 0.45 | YES
19 | HLA-DOA | HLA-DOA | HLA-DOA | 1671 | 0.25 | 0.47 | YES
20 | FCGR2A | FCGR2A | FCGR2A | 1745 | 0.24 | 0.49 | YES
21 | HLA-DMB | HLA-DMB | HLA-DMB | 1769 | 0.24 | 0.51 | YES
22 | TGFB1 | TGFB1 | TGFB1 | 1801 | 0.24 | 0.52 | YES
23 | ITGAM | ITGAM | ITGAM | 1870 | 0.23 | 0.54 | YES
24 | HLA-DRB5 | HLA-DRB5 | HLA-DRB5 | 1942 | 0.22 | 0.55 | YES
25 | ITGB2 | ITGB2 | ITGB2 | 1997 | 0.22 | 0.56 | YES
26 | HLA-DQB1 | HLA-DQB1 | HLA-DQB1 | 2063 | 0.21 | 0.58 | YES
27 | HLA-DPA1 | HLA-DPA1 | HLA-DPA1 | 2242 | 0.2 | 0.58 | YES
28 | HLA-DPB1 | HLA-DPB1 | HLA-DPB1 | 2369 | 0.19 | 0.59 | YES
29 | HLA-DMA | HLA-DMA | HLA-DMA | 2464 | 0.18 | 0.6 | YES
30 | HLA-DRA | HLA-DRA | HLA-DRA | 2585 | 0.17 | 0.61 | YES
31 | HLA-DRB1 | HLA-DRB1 | HLA-DRB1 | 2743 | 0.16 | 0.61 | YES
32 | JAK2 | JAK2 | JAK2 | 2836 | 0.16 | 0.62 | YES
33 | ITGB1 | ITGB1 | ITGB1 | 3078 | 0.14 | 0.62 | YES
34 | NFKBIB | NFKBIB | NFKBIB | 3172 | 0.14 | 0.63 | YES
35 | FCGR2C | FCGR2C | FCGR2C | 3335 | 0.13 | 0.63 | YES
36 | IL10 | IL10 | IL10 | 3497 | 0.12 | 0.63 | YES
37 | CYBA | CYBA | CYBA | 3670 | 0.12 | 0.63 | YES
38 | STAT1 | STAT1 | STAT1 | 3739 | 0.11 | 0.63 | YES
39 | PTPN6 | PTPN6 | PTPN6 | 3947 | 0.1 | 0.63 | YES
40 | MAPK11 | MAPK11 | MAPK11 | 3971 | 0.1 | 0.64 | YES
41 | MAPK13 | MAPK13 | MAPK13 | 4521 | 0.084 | 0.61 | NO
42 | TLR2 | TLR2 | TLR2 | 4579 | 0.083 | 0.62 | NO
43 | TRAF6 | TRAF6 | TRAF6 | 4632 | 0.081 | 0.62 | NO
44 | NFKBIA | NFKBIA | NFKBIA | 4907 | 0.073 | 0.61 | NO
45 | MAPK1 | MAPK1 | MAPK1 | 5081 | 0.068 | 0.61 | NO
46 | NFKB1 | NFKB1 | NFKB1 | 5152 | 0.066 | 0.61 | NO
47 | IFNGR2 | IFNGR2 | IFNGR2 | 5193 | 0.065 | 0.61 | NO
48 | JUN | JUN | JUN | 5321 | 0.062 | 0.61 | NO
49 | JAK1 | JAK1 | JAK1 | 6146 | 0.044 | 0.57 | NO
50 | MAPK14 | MAPK14 | MAPK14 | 6155 | 0.043 | 0.57 | NO
51 | IFNGR1 | IFNGR1 | IFNGR1 | 6184 | 0.043 | 0.57 | NO
52 | MYD88 | MYD88 | MYD88 | 6339 | 0.04 | 0.57 | NO
53 | MAPK12 | MAPK12 | MAPK12 | 7078 | 0.026 | 0.53 | NO
54 | IRAK1 | IRAK1 | IRAK1 | 7129 | 0.025 | 0.53 | NO
55 | IL1A | IL1A | IL1A | 7776 | 0.014 | 0.49 | NO
56 | RELA | RELA | RELA | 7927 | 0.011 | 0.48 | NO
57 | MAP3K7 | MAP3K7 | MAP3K7 | 7958 | 0.011 | 0.48 | NO
58 | TAB2 | TAB2 | TAB2 | 8204 | 0.0066 | 0.47 | NO
59 | ELK1 | ELK1 | ELK1 | 9441 | -0.015 | 0.4 | NO
60 | MARCKSL1 | MARCKSL1 | MARCKSL1 | 9749 | -0.021 | 0.39 | NO
61 | TAB1 | TAB1 | TAB1 | 10012 | -0.026 | 0.38 | NO
62 | IRAK4 | IRAK4 | IRAK4 | 10416 | -0.033 | 0.36 | NO
63 | FOS | FOS | FOS | 10728 | -0.039 | 0.34 | NO
64 | IL1B | IL1B | IL1B | 11062 | -0.046 | 0.33 | NO
65 | MAPK3 | MAPK3 | MAPK3 | 13360 | -0.11 | 0.21 | NO
66 | TGFB2 | TGFB2 | TGFB2 | 13539 | -0.12 | 0.21 | NO
67 | TGFB3 | TGFB3 | TGFB3 | 15446 | -0.22 | 0.12 | NO
68 | C3 | C3 | C3 | 16989 | -0.38 | 0.066 | NO

Figure S45. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL2RB PATHWAY.

Figure S46. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | CSF2RB | CSF2RB | CSF2RB | 204 | 0.52 | 0.04 | YES
2 | IRAK2 | IRAK2 | IRAK2 | 226 | 0.5 | 0.088 | YES
3 | TNFRSF10C | TNFRSF10C | TNFRSF10C | 242 | 0.5 | 0.14 | YES
4 | PIK3CG | PIK3CG | PIK3CG | 432 | 0.44 | 0.17 | YES
5 | TNFRSF10A | TNFRSF10A | TNFRSF10A | 447 | 0.43 | 0.21 | YES
6 | IL3RA | IL3RA | IL3RA | 631 | 0.39 | 0.24 | YES
7 | PIK3R5 | PIK3R5 | PIK3R5 | 791 | 0.36 | 0.26 | YES
8 | TNFSF10 | TNFSF10 | TNFSF10 | 814 | 0.36 | 0.3 | YES
9 | TNF | TNF | TNF | 1134 | 0.31 | 0.31 | YES
10 | TNFRSF10D | TNFRSF10D | TNFRSF10D | 1159 | 0.31 | 0.34 | YES
11 | NGF | NGF | NGF | 1963 | 0.22 | 0.32 | YES
12 | PRKACB | PRKACB | PRKACB | 1970 | 0.22 | 0.34 | YES
13 | PRKAR2A | PRKAR2A | PRKAR2A | 2059 | 0.21 | 0.36 | YES
14 | AKT3 | AKT3 | AKT3 | 2151 | 0.21 | 0.37 | YES
15 | PIK3R3 | PIK3R3 | PIK3R3 | 2285 | 0.2 | 0.38 | YES
16 | NTRK1 | NTRK1 | NTRK1 | 2339 | 0.19 | 0.4 | YES
17 | CFLAR | CFLAR | CFLAR | 2363 | 0.19 | 0.42 | YES
18 | TNFRSF10B | TNFRSF10B | TNFRSF10B | 2649 | 0.17 | 0.42 | YES
19 | MAP3K14 | MAP3K14 | MAP3K14 | 2877 | 0.16 | 0.42 | YES
20 | PPP3CC | PPP3CC | PPP3CC | 3052 | 0.15 | 0.43 | YES
21 | TRAF2 | TRAF2 | TRAF2 | 3102 | 0.14 | 0.44 | YES
22 | CASP7 | CASP7 | CASP7 | 3202 | 0.14 | 0.45 | YES
23 | EXOG | EXOG | EXOG | 3379 | 0.13 | 0.45 | YES
24 | BID | BID | BID | 3524 | 0.12 | 0.45 | YES
25 | PIK3CD | PIK3CD | PIK3CD | 3885 | 0.11 | 0.44 | NO
26 | BAX | BAX | BAX | 3925 | 0.1 | 0.45 | NO
27 | BCL2 | BCL2 | BCL2 | 4509 | 0.085 | 0.43 | NO
28 | CASP3 | CASP3 | CASP3 | 4662 | 0.08 | 0.43 | NO
29 | BCL2L1 | BCL2L1 | BCL2L1 | 4783 | 0.077 | 0.43 | NO
30 | NFKBIA | NFKBIA | NFKBIA | 4907 | 0.073 | 0.43 | NO
31 | FAS | FAS | FAS | 5116 | 0.067 | 0.42 | NO
32 | AKT1 | AKT1 | AKT1 | 5146 | 0.066 | 0.43 | NO
33 | NFKB1 | NFKB1 | NFKB1 | 5152 | 0.066 | 0.44 | NO
34 | BIRC3 | BIRC3 | BIRC3 | 5206 | 0.065 | 0.44 | NO
35 | CHUK | CHUK | CHUK | 5416 | 0.06 | 0.43 | NO
36 | CYCS | CYCS | CYCS | 5660 | 0.054 | 0.42 | NO
37 | PPP3R1 | PPP3R1 | PPP3R1 | 5824 | 0.05 | 0.42 | NO
38 | APAF1 | APAF1 | APAF1 | 6244 | 0.042 | 0.4 | NO
39 | MYD88 | MYD88 | MYD88 | 6339 | 0.04 | 0.4 | NO
40 | IKBKG | IKBKG | IKBKG | 6928 | 0.028 | 0.37 | NO
41 | IRAK1 | IRAK1 | IRAK1 | 7129 | 0.025 | 0.36 | NO
42 | DFFA | DFFA | DFFA | 7432 | 0.02 | 0.35 | NO
43 | PRKAR1A | PRKAR1A | PRKAR1A | 7467 | 0.019 | 0.35 | NO
44 | IL1A | IL1A | IL1A | 7776 | 0.014 | 0.33 | NO
45 | PRKACA | PRKACA | PRKACA | 7846 | 0.012 | 0.33 | NO
46 | BIRC2 | BIRC2 | BIRC2 | 7896 | 0.012 | 0.33 | NO
47 | PIK3CA | PIK3CA | PIK3CA | 7906 | 0.012 | 0.33 | NO
48 | RELA | RELA | RELA | 7927 | 0.011 | 0.33 | NO
49 | PRKX | PRKX | PRKX | 8319 | 0.0045 | 0.31 | NO
50 | ENDOG | ENDOG | ENDOG | 8726 | -0.0031 | 0.28 | NO
51 | CASP8 | CASP8 | CASP8 | 8848 | -0.0054 | 0.28 | NO
52 | RIPK1 | RIPK1 | RIPK1 | 9173 | -0.01 | 0.26 | NO
53 | TRADD | TRADD | TRADD | 9419 | -0.015 | 0.25 | NO
54 | AKT2 | AKT2 | AKT2 | 9654 | -0.02 | 0.24 | NO
55 | AIFM1 | AIFM1 | AIFM1 | 9778 | -0.022 | 0.23 | NO
56 | IL1R1 | IL1R1 | IL1R1 | 9863 | -0.023 | 0.23 | NO
57 | FADD | FADD | FADD | 10022 | -0.026 | 0.23 | NO
58 | XIAP | XIAP | XIAP | 10057 | -0.027 | 0.23 | NO
59 | IKBKB | IKBKB | IKBKB | 10274 | -0.031 | 0.22 | NO
60 | IRAK4 | IRAK4 | IRAK4 | 10416 | -0.033 | 0.21 | NO
61 | TP53 | TP53 | TP53 | 10764 | -0.04 | 0.2 | NO
62 | PPP3CA | PPP3CA | PPP3CA | 10887 | -0.042 | 0.2 | NO
63 | IL1B | IL1B | IL1B | 11062 | -0.046 | 0.19 | NO
64 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 11080 | -0.046 | 0.19 | NO
65 | IRAK3 | IRAK3 | IRAK3 | 11429 | -0.055 | 0.18 | NO
66 | PPP3CB | PPP3CB | PPP3CB | 11518 | -0.056 | 0.18 | NO
67 | DFFB | DFFB | DFFB | 11536 | -0.057 | 0.18 | NO
68 | CAPN2 | CAPN2 | CAPN2 | 11548 | -0.057 | 0.19 | NO
69 | PIK3CB | PIK3CB | PIK3CB | 11615 | -0.059 | 0.19 | NO
70 | PRKAR2B | PRKAR2B | PRKAR2B | 11630 | -0.059 | 0.2 | NO
71 | CAPN1 | CAPN1 | CAPN1 | 11794 | -0.063 | 0.2 | NO
72 | CASP10 | CASP10 | CASP10 | 12257 | -0.075 | 0.18 | NO
73 | IL1RAP | IL1RAP | IL1RAP | 12312 | -0.077 | 0.18 | NO
74 | PIK3R2 | PIK3R2 | PIK3R2 | 12371 | -0.078 | 0.19 | NO
75 | ATM | ATM | ATM | 12959 | -0.095 | 0.16 | NO
76 | PIK3R1 | PIK3R1 | PIK3R1 | 13476 | -0.11 | 0.14 | NO
77 | BAD | BAD | BAD | 13682 | -0.12 | 0.15 | NO
78 | CASP9 | CASP9 | CASP9 | 13740 | -0.12 | 0.16 | NO
79 | ENDOD1 | ENDOD1 | ENDOD1 | 13745 | -0.12 | 0.17 | NO
80 | CHP | CHP | CHP | 14285 | -0.15 | 0.15 | NO
81 | CHP2 | CHP2 | CHP2 | 14696 | -0.17 | 0.14 | NO
82 | PRKAR1B | PRKAR1B | PRKAR1B | 15399 | -0.21 | 0.13 | NO
83 | CASP6 | CASP6 | CASP6 | 16035 | -0.27 | 0.12 | NO

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

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

genes ES table in pathway: BIOCARTA INTEGRIN 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 | TNF | TNF | TNF | 1134 | 0.31 | -0.00046 | YES
2 | LMNB1 | LMNB1 | LMNB1 | 2227 | 0.2 | -0.021 | YES
3 | TRAF1 | TRAF1 | TRAF1 | 2277 | 0.2 | 0.016 | YES
4 | ARHGDIB | ARHGDIB | ARHGDIB | 2316 | 0.2 | 0.052 | YES
5 | CFLAR | CFLAR | CFLAR | 2363 | 0.19 | 0.088 | YES
6 | TNFRSF1B | TNFRSF1B | TNFRSF1B | 2384 | 0.19 | 0.12 | YES
7 | MAP3K5 | MAP3K5 | MAP3K5 | 2487 | 0.18 | 0.15 | YES
8 | MAPK8 | MAPK8 | MAPK8 | 2498 | 0.18 | 0.19 | YES
9 | PRKCD | PRKCD | PRKCD | 2608 | 0.17 | 0.22 | YES
10 | MAP3K14 | MAP3K14 | MAP3K14 | 2877 | 0.16 | 0.23 | YES
11 | LMNB2 | LMNB2 | LMNB2 | 2977 | 0.15 | 0.26 | YES
12 | TRAF2 | TRAF2 | TRAF2 | 3102 | 0.14 | 0.28 | YES
13 | CASP7 | CASP7 | CASP7 | 3202 | 0.14 | 0.3 | YES
14 | PAK2 | PAK2 | PAK2 | 3512 | 0.12 | 0.31 | YES
15 | BID | BID | BID | 3524 | 0.12 | 0.33 | YES
16 | BAG4 | BAG4 | BAG4 | 3758 | 0.11 | 0.34 | YES
17 | RASA1 | RASA1 | RASA1 | 4416 | 0.088 | 0.32 | YES
18 | BCL2 | BCL2 | BCL2 | 4509 | 0.085 | 0.34 | YES
19 | CASP3 | CASP3 | CASP3 | 4662 | 0.08 | 0.34 | YES
20 | NFKBIA | NFKBIA | NFKBIA | 4907 | 0.073 | 0.34 | YES
21 | FAS | FAS | FAS | 5116 | 0.067 | 0.35 | YES
22 | PSEN1 | PSEN1 | PSEN1 | 5147 | 0.066 | 0.36 | YES
23 | NFKB1 | NFKB1 | NFKB1 | 5152 | 0.066 | 0.37 | YES
24 | BIRC3 | BIRC3 | BIRC3 | 5206 | 0.065 | 0.38 | YES
25 | LMNA | LMNA | LMNA | 5367 | 0.061 | 0.38 | YES
26 | CHUK | CHUK | CHUK | 5416 | 0.06 | 0.39 | YES
27 | CYCS | CYCS | CYCS | 5660 | 0.054 | 0.39 | NO
28 | APAF1 | APAF1 | APAF1 | 6244 | 0.042 | 0.37 | NO
29 | PRKDC | PRKDC | PRKDC | 6391 | 0.039 | 0.37 | NO
30 | RB1 | RB1 | RB1 | 6667 | 0.034 | 0.36 | NO
31 | ACTG1 | ACTG1 | ACTG1 | 7414 | 0.02 | 0.32 | NO
32 | DFFA | DFFA | DFFA | 7432 | 0.02 | 0.32 | NO
33 | PARP1 | PARP1 | PARP1 | 7887 | 0.012 | 0.3 | NO
34 | BIRC2 | BIRC2 | BIRC2 | 7896 | 0.012 | 0.3 | NO
35 | RELA | RELA | RELA | 7927 | 0.011 | 0.3 | NO
36 | CDK11A | CDK11A | CDK11A | 8142 | 0.0077 | 0.29 | NO
37 | MDM2 | MDM2 | MDM2 | 8504 | 0.00086 | 0.27 | NO
38 | DAXX | DAXX | DAXX | 8702 | -0.0026 | 0.26 | NO
39 | CASP8 | CASP8 | CASP8 | 8848 | -0.0054 | 0.26 | NO
40 | RIPK1 | RIPK1 | RIPK1 | 9173 | -0.01 | 0.24 | NO
41 | GSN | GSN | GSN | 9185 | -0.011 | 0.24 | NO
42 | CDK11B | CDK11B | CDK11B | 9197 | -0.011 | 0.24 | NO
43 | TRADD | TRADD | TRADD | 9419 | -0.015 | 0.23 | NO
44 | FADD | FADD | FADD | 10022 | -0.026 | 0.2 | NO
45 | XIAP | XIAP | XIAP | 10057 | -0.027 | 0.21 | NO
46 | CASP2 | CASP2 | CASP2 | 10377 | -0.032 | 0.2 | NO
47 | PTK2 | PTK2 | PTK2 | 10935 | -0.043 | 0.18 | NO
48 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 11080 | -0.046 | 0.18 | NO
49 | DFFB | DFFB | DFFB | 11536 | -0.057 | 0.16 | NO
50 | MAP3K1 | MAP3K1 | MAP3K1 | 11861 | -0.064 | 0.16 | NO
51 | MAP2K7 | MAP2K7 | MAP2K7 | 12245 | -0.075 | 0.15 | NO
52 | SPTAN1 | SPTAN1 | SPTAN1 | 12348 | -0.078 | 0.16 | NO
53 | CRADD | CRADD | CRADD | 13692 | -0.12 | 0.11 | NO
54 | CASP9 | CASP9 | CASP9 | 13740 | -0.12 | 0.13 | NO
55 | PSEN2 | PSEN2 | PSEN2 | 14264 | -0.14 | 0.13 | NO
56 | NUMA1 | NUMA1 | NUMA1 | 14423 | -0.15 | 0.15 | NO
57 | CASP6 | CASP6 | CASP6 | 16035 | -0.27 | 0.12 | 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: BIOCARTA INTEGRIN PATHWAY.

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

genes ES table in pathway: BIOCARTA TCR 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 | CDC25A | CDC25A | CDC25A | 396 | 0.45 | 0.0081 | YES
2 | ORC1L | ORC1L | ORC1L | 437 | 0.44 | 0.035 | YES
3 | TTK | TTK | TTK | 472 | 0.43 | 0.062 | YES
4 | CDC45 | CDC45 | CDC45 | 475 | 0.43 | 0.09 | YES
5 | CDC20 | CDC20 | CDC20 | 568 | 0.4 | 0.11 | YES
6 | BUB1 | BUB1 | BUB1 | 594 | 0.4 | 0.14 | YES
7 | CCNE2 | CCNE2 | CCNE2 | 758 | 0.37 | 0.15 | YES
8 | ESPL1 | ESPL1 | ESPL1 | 759 | 0.37 | 0.18 | YES
9 | PKMYT1 | PKMYT1 | PKMYT1 | 779 | 0.36 | 0.2 | YES
10 | CCNA2 | CCNA2 | CCNA2 | 898 | 0.34 | 0.22 | YES
11 | CDC25C | CDC25C | CDC25C | 902 | 0.34 | 0.24 | YES
12 | CCNE1 | CCNE1 | CCNE1 | 931 | 0.34 | 0.26 | YES
13 | PLK1 | PLK1 | PLK1 | 941 | 0.34 | 0.28 | YES
14 | RBL1 | RBL1 | RBL1 | 1165 | 0.31 | 0.29 | YES
15 | PTTG1 | PTTG1 | PTTG1 | 1213 | 0.3 | 0.31 | YES
16 | GADD45A | GADD45A | GADD45A | 1226 | 0.3 | 0.33 | YES
17 | BUB1B | BUB1B | BUB1B | 1335 | 0.29 | 0.34 | YES
18 | CDC7 | CDC7 | CDC7 | 1428 | 0.28 | 0.36 | YES
19 | CCNB1 | CCNB1 | CCNB1 | 1488 | 0.27 | 0.37 | YES
20 | CDC6 | CDC6 | CDC6 | 1537 | 0.26 | 0.39 | YES
21 | CDK1 | CDK1 | CDK1 | 1581 | 0.26 | 0.4 | YES
22 | ORC6L | ORC6L | ORC6L | 1681 | 0.25 | 0.41 | YES
23 | TGFB1 | TGFB1 | TGFB1 | 1801 | 0.24 | 0.42 | YES
24 | PTTG2 | PTTG2 | PTTG2 | 1876 | 0.23 | 0.44 | YES
25 | CDC14A | CDC14A | CDC14A | 1928 | 0.22 | 0.45 | YES
26 | MAD2L1 | MAD2L1 | MAD2L1 | 2032 | 0.22 | 0.46 | YES
27 | CHEK1 | CHEK1 | CHEK1 | 2069 | 0.21 | 0.47 | YES
28 | CCNB2 | CCNB2 | CCNB2 | 2466 | 0.18 | 0.46 | YES
29 | MCM5 | MCM5 | MCM5 | 2673 | 0.17 | 0.46 | YES
30 | E2F3 | E2F3 | E2F3 | 2726 | 0.17 | 0.47 | YES
31 | GADD45G | GADD45G | GADD45G | 2806 | 0.16 | 0.47 | YES
32 | PCNA | PCNA | PCNA | 2862 | 0.16 | 0.48 | YES
33 | E2F2 | E2F2 | E2F2 | 3056 | 0.15 | 0.48 | YES
34 | CDKN2D | CDKN2D | CDKN2D | 3085 | 0.14 | 0.49 | YES
35 | MCM4 | MCM4 | MCM4 | 3194 | 0.14 | 0.49 | YES
36 | BUB3 | BUB3 | BUB3 | 3228 | 0.14 | 0.5 | YES
37 | WEE1 | WEE1 | WEE1 | 3332 | 0.13 | 0.5 | YES
38 | CDKN1A | CDKN1A | CDKN1A | 3377 | 0.13 | 0.51 | YES
39 | CCND1 | CCND1 | CCND1 | 3547 | 0.12 | 0.51 | NO
40 | YWHAH | YWHAH | YWHAH | 3785 | 0.11 | 0.5 | NO
41 | E2F1 | E2F1 | E2F1 | 3942 | 0.1 | 0.5 | NO
42 | GADD45B | GADD45B | GADD45B | 4005 | 0.1 | 0.5 | NO
43 | CDK2 | CDK2 | CDK2 | 4145 | 0.096 | 0.5 | NO
44 | CHEK2 | CHEK2 | CHEK2 | 4308 | 0.091 | 0.5 | NO
45 | MAD2L2 | MAD2L2 | MAD2L2 | 4330 | 0.09 | 0.5 | NO
46 | CDK6 | CDK6 | CDK6 | 4400 | 0.088 | 0.51 | NO
47 | HDAC1 | HDAC1 | HDAC1 | 4514 | 0.084 | 0.51 | NO
48 | CDC27 | CDC27 | CDC27 | 4642 | 0.081 | 0.5 | NO
49 | MCM7 | MCM7 | MCM7 | 5090 | 0.068 | 0.48 | NO
50 | SMC1A | SMC1A | SMC1A | 5150 | 0.066 | 0.48 | NO
51 | SMC3 | SMC3 | SMC3 | 5178 | 0.065 | 0.49 | NO
52 | CDC23 | CDC23 | CDC23 | 5203 | 0.065 | 0.49 | NO
53 | YWHAQ | YWHAQ | YWHAQ | 5253 | 0.064 | 0.49 | NO
54 | CDC25B | CDC25B | CDC25B | 5425 | 0.06 | 0.49 | NO
55 | RBX1 | RBX1 | RBX1 | 5485 | 0.058 | 0.49 | NO
56 | MCM2 | MCM2 | MCM2 | 5489 | 0.058 | 0.49 | NO
57 | YWHAG | YWHAG | YWHAG | 5597 | 0.056 | 0.49 | NO
58 | CDK7 | CDK7 | CDK7 | 5649 | 0.055 | 0.49 | NO
59 | CDKN2A | CDKN2A | CDKN2A | 5799 | 0.051 | 0.49 | NO
60 | YWHAB | YWHAB | YWHAB | 5922 | 0.048 | 0.48 | NO
61 | YWHAZ | YWHAZ | YWHAZ | 6106 | 0.044 | 0.48 | NO
62 | MCM6 | MCM6 | MCM6 | 6255 | 0.042 | 0.47 | NO
63 | MCM3 | MCM3 | MCM3 | 6353 | 0.04 | 0.47 | NO
64 | PRKDC | PRKDC | PRKDC | 6391 | 0.039 | 0.47 | NO
65 | FZR1 | FZR1 | FZR1 | 6534 | 0.036 | 0.46 | NO
66 | ANAPC7 | ANAPC7 | ANAPC7 | 6579 | 0.035 | 0.46 | NO
67 | E2F4 | E2F4 | E2F4 | 6598 | 0.035 | 0.46 | NO
68 | RB1 | RB1 | RB1 | 6667 | 0.034 | 0.46 | NO
69 | TFDP1 | TFDP1 | TFDP1 | 6784 | 0.031 | 0.46 | NO
70 | ANAPC10 | ANAPC10 | ANAPC10 | 6959 | 0.028 | 0.45 | NO
71 | CCND3 | CCND3 | CCND3 | 6969 | 0.028 | 0.45 | NO
72 | SKP2 | SKP2 | SKP2 | 7008 | 0.027 | 0.45 | NO
73 | ANAPC1 | ANAPC1 | ANAPC1 | 7149 | 0.024 | 0.44 | NO
74 | CCNA1 | CCNA1 | CCNA1 | 7284 | 0.022 | 0.44 | NO
75 | CDK4 | CDK4 | CDK4 | 7329 | 0.022 | 0.44 | NO
76 | HDAC2 | HDAC2 | HDAC2 | 7407 | 0.02 | 0.44 | NO
77 | MYC | MYC | MYC | 7482 | 0.019 | 0.43 | NO
78 | CDC26 | CDC26 | CDC26 | 7555 | 0.017 | 0.43 | NO
79 | MAD1L1 | MAD1L1 | MAD1L1 | 7748 | 0.014 | 0.42 | NO
80 | CDC14B | CDC14B | CDC14B | 7751 | 0.014 | 0.42 | NO
81 | SMAD2 | SMAD2 | SMAD2 | 7798 | 0.013 | 0.42 | NO
82 | CCNH | CCNH | CCNH | 7851 | 0.012 | 0.42 | NO
83 | CUL1 | CUL1 | CUL1 | 7972 | 0.01 | 0.41 | NO
84 | ZBTB17 | ZBTB17 | ZBTB17 | 8084 | 0.0086 | 0.4 | NO
85 | EP300 | EP300 | EP300 | 8100 | 0.0084 | 0.4 | NO
86 | YWHAE | YWHAE | YWHAE | 8279 | 0.0052 | 0.4 | NO
87 | ORC3L | ORC3L | ORC3L | 8407 | 0.0028 | 0.39 | NO
88 | GSK3B | GSK3B | GSK3B | 8476 | 0.0014 | 0.38 | NO
89 | MDM2 | MDM2 | MDM2 | 8504 | 0.00086 | 0.38 | NO
90 | ORC5L | ORC5L | ORC5L | 8591 | -0.00071 | 0.38 | NO
91 | CDKN1B | CDKN1B | CDKN1B | 8995 | -0.0075 | 0.36 | NO
92 | STAG1 | STAG1 | STAG1 | 9150 | -0.01 | 0.35 | NO
93 | ANAPC11 | ANAPC11 | ANAPC11 | 9155 | -0.01 | 0.35 | NO
94 | RAD21 | RAD21 | RAD21 | 9220 | -0.012 | 0.35 | NO
95 | SMAD3 | SMAD3 | SMAD3 | 9521 | -0.017 | 0.33 | NO
96 | SFN | SFN | SFN | 9836 | -0.023 | 0.32 | NO
97 | ABL1 | ABL1 | ABL1 | 9849 | -0.023 | 0.32 | NO
98 | CDKN2C | CDKN2C | CDKN2C | 10011 | -0.026 | 0.31 | NO
99 | ANAPC2 | ANAPC2 | ANAPC2 | 10302 | -0.031 | 0.3 | NO
100 | SMAD4 | SMAD4 | SMAD4 | 10390 | -0.033 | 0.29 | NO
101 | ANAPC5 | ANAPC5 | ANAPC5 | 10514 | -0.035 | 0.29 | NO
102 | CDKN1C | CDKN1C | CDKN1C | 10549 | -0.036 | 0.29 | NO
103 | ATR | ATR | ATR | 10650 | -0.038 | 0.29 | NO
104 | TP53 | TP53 | TP53 | 10764 | -0.04 | 0.28 | NO
105 | ORC2L | ORC2L | ORC2L | 10879 | -0.042 | 0.28 | NO
106 | SKP1 | SKP1 | SKP1 | 10893 | -0.042 | 0.28 | NO
107 | ANAPC13 | ANAPC13 | ANAPC13 | 11199 | -0.049 | 0.27 | NO
108 | STAG2 | STAG2 | STAG2 | 11255 | -0.05 | 0.27 | NO
109 | ANAPC4 | ANAPC4 | ANAPC4 | 11458 | -0.055 | 0.26 | NO
110 | CREBBP | CREBBP | CREBBP | 11686 | -0.06 | 0.25 | NO
111 | WEE2 | WEE2 | WEE2 | 11813 | -0.064 | 0.25 | NO
112 | RBL2 | RBL2 | RBL2 | 11828 | -0.064 | 0.25 | NO
113 | CDKN2B | CDKN2B | CDKN2B | 12416 | -0.08 | 0.22 | NO
114 | CDC16 | CDC16 | CDC16 | 12473 | -0.081 | 0.23 | NO
115 | ATM | ATM | ATM | 12959 | -0.095 | 0.21 | NO
116 | E2F5 | E2F5 | E2F5 | 13056 | -0.099 | 0.21 | NO
117 | SMC1B | SMC1B | SMC1B | 13092 | -0.1 | 0.21 | NO
118 | ORC4L | ORC4L | ORC4L | 13351 | -0.11 | 0.21 | NO
119 | TGFB2 | TGFB2 | TGFB2 | 13539 | -0.12 | 0.2 | NO
120 | TFDP2 | TFDP2 | TFDP2 | 14292 | -0.15 | 0.17 | NO
121 | CCNB3 | CCNB3 | CCNB3 | 15346 | -0.21 | 0.13 | NO
122 | TGFB3 | TGFB3 | TGFB3 | 15446 | -0.22 | 0.14 | NO
123 | CCND2 | CCND2 | CCND2 | 15513 | -0.22 | 0.15 | NO

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

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

genes ES table in pathway: BIOCARTA VEGF PATHWAY

Table 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 | IL12A | IL12A | IL12A | 53 | 0.66 | 0.048 | YES
2 | CD80 | CD80 | CD80 | 64 | 0.64 | 0.096 | YES
3 | TLR8 | TLR8 | TLR8 | 118 | 0.57 | 0.14 | YES
4 | CXCL9 | CXCL9 | CXCL9 | 344 | 0.46 | 0.16 | YES
5 | CCL4 | CCL4 | CCL4 | 395 | 0.45 | 0.19 | YES
6 | PIK3CG | PIK3CG | PIK3CG | 432 | 0.44 | 0.22 | YES
7 | CXCL10 | CXCL10 | CXCL10 | 441 | 0.44 | 0.26 | YES
8 | TLR4 | TLR4 | TLR4 | 610 | 0.39 | 0.28 | YES
9 | CCL5 | CCL5 | CCL5 | 719 | 0.37 | 0.3 | YES
10 | PIK3R5 | PIK3R5 | PIK3R5 | 791 | 0.36 | 0.32 | YES
11 | IL6 | IL6 | IL6 | 834 | 0.36 | 0.35 | YES
12 | IL12B | IL12B | IL12B | 847 | 0.35 | 0.38 | YES
13 | CCL3 | CCL3 | CCL3 | 921 | 0.34 | 0.4 | YES
14 | TLR6 | TLR6 | TLR6 | 924 | 0.34 | 0.42 | YES
15 | CXCL11 | CXCL11 | CXCL11 | 930 | 0.34 | 0.45 | YES
16 | TNF | TNF | TNF | 1134 | 0.31 | 0.46 | YES
17 | CD86 | CD86 | CD86 | 1273 | 0.3 | 0.48 | YES
18 | TLR1 | TLR1 | TLR1 | 1443 | 0.27 | 0.49 | YES
19 | CD40 | CD40 | CD40 | 1761 | 0.24 | 0.49 | YES
20 | TICAM2 | TICAM2 | TICAM2 | 1985 | 0.22 | 0.49 | YES
21 | TLR7 | TLR7 | TLR7 | 2079 | 0.21 | 0.51 | YES
22 | AKT3 | AKT3 | AKT3 | 2151 | 0.21 | 0.52 | YES
23 | IL8 | IL8 | IL8 | 2185 | 0.2 | 0.53 | YES
24 | TRAF3 | TRAF3 | TRAF3 | 2192 | 0.2 | 0.55 | YES
25 | PIK3R3 | PIK3R3 | PIK3R3 | 2285 | 0.2 | 0.56 | YES
26 | MAPK8 | MAPK8 | MAPK8 | 2498 | 0.18 | 0.56 | YES
27 | MAP2K1 | MAP2K1 | MAP2K1 | 3489 | 0.12 | 0.51 | NO
28 | CD14 | CD14 | CD14 | 3496 | 0.12 | 0.52 | NO
29 | STAT1 | STAT1 | STAT1 | 3739 | 0.11 | 0.52 | NO
30 | PIK3CD | PIK3CD | PIK3CD | 3885 | 0.11 | 0.52 | NO
31 | SPP1 | SPP1 | SPP1 | 3967 | 0.1 | 0.52 | NO
32 | MAPK11 | MAPK11 | MAPK11 | 3971 | 0.1 | 0.53 | NO
33 | IFNB1 | IFNB1 | IFNB1 | 4385 | 0.089 | 0.51 | NO
34 | MAPK13 | MAPK13 | MAPK13 | 4521 | 0.084 | 0.51 | NO
35 | TLR2 | TLR2 | TLR2 | 4579 | 0.083 | 0.52 | NO
36 | TRAF6 | TRAF6 | TRAF6 | 4632 | 0.081 | 0.52 | NO
37 | LY96 | LY96 | LY96 | 4732 | 0.078 | 0.52 | NO
38 | NFKBIA | NFKBIA | NFKBIA | 4907 | 0.073 | 0.52 | NO
39 | IRF5 | IRF5 | IRF5 | 4963 | 0.072 | 0.52 | NO
40 | MAP2K3 | MAP2K3 | MAP2K3 | 4976 | 0.071 | 0.52 | NO
41 | MAPK1 | MAPK1 | MAPK1 | 5081 | 0.068 | 0.52 | NO
42 | AKT1 | AKT1 | AKT1 | 5146 | 0.066 | 0.52 | NO
43 | NFKB1 | NFKB1 | NFKB1 | 5152 | 0.066 | 0.53 | NO
44 | IKBKE | IKBKE | IKBKE | 5272 | 0.063 | 0.53 | NO
45 | JUN | JUN | JUN | 5321 | 0.062 | 0.53 | NO
46 | CHUK | CHUK | CHUK | 5416 | 0.06 | 0.53 | NO
47 | IFNAR2 | IFNAR2 | IFNAR2 | 5472 | 0.059 | 0.53 | NO
48 | MAPK9 | MAPK9 | MAPK9 | 6030 | 0.046 | 0.5 | NO
49 | MAPK14 | MAPK14 | MAPK14 | 6155 | 0.043 | 0.5 | NO
50 | MYD88 | MYD88 | MYD88 | 6339 | 0.04 | 0.49 | NO
51 | TICAM1 | TICAM1 | TICAM1 | 6364 | 0.039 | 0.49 | NO
52 | IRF3 | IRF3 | IRF3 | 6668 | 0.034 | 0.48 | NO
53 | IKBKG | IKBKG | IKBKG | 6928 | 0.028 | 0.47 | NO
54 | IRF7 | IRF7 | IRF7 | 7039 | 0.026 | 0.46 | NO
55 | MAPK12 | MAPK12 | MAPK12 | 7078 | 0.026 | 0.46 | NO
56 | IRAK1 | IRAK1 | IRAK1 | 7129 | 0.025 | 0.46 | NO
57 | RAC1 | RAC1 | RAC1 | 7823 | 0.013 | 0.42 | NO
58 | PIK3CA | PIK3CA | PIK3CA | 7906 | 0.012 | 0.42 | NO
59 | RELA | RELA | RELA | 7927 | 0.011 | 0.42 | NO
60 | MAP3K7 | MAP3K7 | MAP3K7 | 7958 | 0.011 | 0.42 | NO
61 | MAP2K2 | MAP2K2 | MAP2K2 | 8004 | 0.0098 | 0.42 | NO
62 | TAB2 | TAB2 | TAB2 | 8204 | 0.0066 | 0.41 | NO
63 | LBP | LBP | LBP | 8339 | 0.004 | 0.4 | NO
64 | TOLLIP | TOLLIP | TOLLIP | 8344 | 0.0039 | 0.4 | NO
65 | CASP8 | CASP8 | CASP8 | 8848 | -0.0054 | 0.37 | NO
66 | RIPK1 | RIPK1 | RIPK1 | 9173 | -0.01 | 0.36 | NO
67 | AKT2 | AKT2 | AKT2 | 9654 | -0.02 | 0.33 | NO
68 | TAB1 | TAB1 | TAB1 | 10012 | -0.026 | 0.31 | NO
69 | IFNAR1 | IFNAR1 | IFNAR1 | 10015 | -0.026 | 0.32 | NO
70 | FADD | FADD | FADD | 10022 | -0.026 | 0.32 | NO
71 | IKBKB | IKBKB | IKBKB | 10274 | -0.031 | 0.31 | NO
72 | IRAK4 | IRAK4 | IRAK4 | 10416 | -0.033 | 0.3 | NO
73 | FOS | FOS | FOS | 10728 | -0.039 | 0.29 | NO
74 | IL1B | IL1B | IL1B | 11062 | -0.046 | 0.27 | NO
75 | TLR9 | TLR9 | TLR9 | 11214 | -0.049 | 0.27 | NO
76 | MAP2K4 | MAP2K4 | MAP2K4 | 11219 | -0.05 | 0.27 | NO
77 | PIK3CB | PIK3CB | PIK3CB | 11615 | -0.059 | 0.25 | NO
78 | MAP2K6 | MAP2K6 | MAP2K6 | 11905 | -0.065 | 0.24 | NO
79 | TLR5 | TLR5 | TLR5 | 11955 | -0.067 | 0.24 | NO
80 | MAP2K7 | MAP2K7 | MAP2K7 | 12245 | -0.075 | 0.24 | NO
81 | MAP3K8 | MAP3K8 | MAP3K8 | 12267 | -0.075 | 0.24 | NO
82 | PIK3R2 | PIK3R2 | PIK3R2 | 12371 | -0.078 | 0.24 | NO
83 | TLR3 | TLR3 | TLR3 | 13195 | -0.1 | 0.2 | NO
84 | MAPK3 | MAPK3 | MAPK3 | 13360 | -0.11 | 0.2 | NO
85 | PIK3R1 | PIK3R1 | PIK3R1 | 13476 | -0.11 | 0.2 | NO
86 | CTSK | CTSK | CTSK | 13822 | -0.13 | 0.2 | NO
87 | TIRAP | TIRAP | TIRAP | 14512 | -0.16 | 0.17 | NO
88 | MAPK10 | MAPK10 | MAPK10 | 17321 | -0.44 | 0.048 | 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: BIOCARTA VEGF PATHWAY.

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

genes ES table in pathway: KEGG PROTEASOME

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 | CD3G | CD3G | CD3G | 193 | 0.52 | 0.066 | YES
2 | LCK | LCK | LCK | 284 | 0.48 | 0.13 | YES
3 | PIK3CG | PIK3CG | PIK3CG | 432 | 0.44 | 0.19 | YES
4 | CD3D | CD3D | CD3D | 449 | 0.43 | 0.25 | YES
5 | CD3E | CD3E | CD3E | 530 | 0.41 | 0.31 | YES
6 | CD247 | CD247 | CD247 | 606 | 0.4 | 0.36 | YES
7 | LAT | LAT | LAT | 636 | 0.39 | 0.42 | YES
8 | ZAP70 | ZAP70 | ZAP70 | 813 | 0.36 | 0.46 | YES
9 | PRKCB | PRKCB | PRKCB | 879 | 0.35 | 0.51 | YES
10 | PTPN7 | PTPN7 | PTPN7 | 1015 | 0.33 | 0.55 | YES
11 | NFATC2 | NFATC2 | NFATC2 | 1458 | 0.27 | 0.56 | YES
12 | VAV1 | VAV1 | VAV1 | 1471 | 0.27 | 0.6 | YES
13 | PRKCA | PRKCA | PRKCA | 1560 | 0.26 | 0.64 | YES
14 | MAPK8 | MAPK8 | MAPK8 | 2498 | 0.18 | 0.61 | NO
15 | PPP3CC | PPP3CC | PPP3CC | 3052 | 0.15 | 0.6 | NO
16 | SHC1 | SHC1 | SHC1 | 3482 | 0.12 | 0.6 | NO
17 | MAP2K1 | MAP2K1 | MAP2K1 | 3489 | 0.12 | 0.62 | NO
18 | RASA1 | RASA1 | RASA1 | 4416 | 0.088 | 0.58 | NO
19 | NFKBIA | NFKBIA | NFKBIA | 4907 | 0.073 | 0.56 | NO
20 | GRB2 | GRB2 | GRB2 | 5020 | 0.07 | 0.57 | NO
21 | NFKB1 | NFKB1 | NFKB1 | 5152 | 0.066 | 0.57 | NO
22 | JUN | JUN | JUN | 5321 | 0.062 | 0.57 | NO
23 | CALM1 | CALM1 | CALM1 | 5540 | 0.057 | 0.57 | NO
24 | CALM3 | CALM3 | CALM3 | 6554 | 0.036 | 0.52 | NO
25 | CALM2 | CALM2 | CALM2 | 6654 | 0.034 | 0.52 | NO
26 | RAF1 | RAF1 | RAF1 | 7057 | 0.026 | 0.5 | NO
27 | RAC1 | RAC1 | RAC1 | 7823 | 0.013 | 0.46 | NO
28 | PIK3CA | PIK3CA | PIK3CA | 7906 | 0.012 | 0.45 | NO
29 | RELA | RELA | RELA | 7927 | 0.011 | 0.45 | NO
30 | ELK1 | ELK1 | ELK1 | 9441 | -0.015 | 0.37 | NO
31 | PLCG1 | PLCG1 | PLCG1 | 9574 | -0.018 | 0.37 | NO
32 | NFATC1 | NFATC1 | NFATC1 | 9706 | -0.02 | 0.36 | NO
33 | FYN | FYN | FYN | 10144 | -0.028 | 0.34 | NO
34 | FOS | FOS | FOS | 10728 | -0.039 | 0.32 | NO
35 | PPP3CA | PPP3CA | PPP3CA | 10887 | -0.042 | 0.32 | NO
36 | MAP2K4 | MAP2K4 | MAP2K4 | 11219 | -0.05 | 0.3 | NO
37 | SOS1 | SOS1 | SOS1 | 11394 | -0.054 | 0.3 | NO
38 | PPP3CB | PPP3CB | PPP3CB | 11518 | -0.056 | 0.3 | NO
39 | NFATC3 | NFATC3 | NFATC3 | 11806 | -0.063 | 0.3 | NO
40 | MAP3K1 | MAP3K1 | MAP3K1 | 11861 | -0.064 | 0.3 | NO
41 | NFATC4 | NFATC4 | NFATC4 | 12288 | -0.076 | 0.29 | NO
42 | MAPK3 | MAPK3 | MAPK3 | 13360 | -0.11 | 0.25 | NO
43 | PIK3R1 | PIK3R1 | PIK3R1 | 13476 | -0.11 | 0.26 | 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 PROTEASOME.

Figure S56. 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 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 | DAPP1 | DAPP1 | DAPP1 | 325 | 0.47 | 0.029 | YES
2 | PIK3CG | PIK3CG | PIK3CG | 432 | 0.44 | 0.067 | YES
3 | CD72 | CD72 | CD72 | 448 | 0.43 | 0.11 | YES
4 | LILRB3 | LILRB3 | LILRB3 | 635 | 0.39 | 0.14 | YES
5 | PIK3R5 | PIK3R5 | PIK3R5 | 791 | 0.36 | 0.17 | YES
6 | PRKCB | PRKCB | PRKCB | 879 | 0.35 | 0.2 | YES
7 | PIK3AP1 | PIK3AP1 | PIK3AP1 | 960 | 0.34 | 0.22 | YES
8 | RASGRP3 | RASGRP3 | RASGRP3 | 990 | 0.33 | 0.26 | YES
9 | BTK | BTK | BTK | 1384 | 0.28 | 0.26 | YES
10 | NFATC2 | NFATC2 | NFATC2 | 1458 | 0.27 | 0.29 | YES
11 | VAV1 | VAV1 | VAV1 | 1471 | 0.27 | 0.31 | YES
12 | RAC2 | RAC2 | RAC2 | 1481 | 0.27 | 0.34 | YES
13 | CD79B | CD79B | CD79B | 1755 | 0.24 | 0.35 | YES
14 | CD19 | CD19 | CD19 | 1830 | 0.23 | 0.37 | YES
15 | BCL10 | BCL10 | BCL10 | 1914 | 0.23 | 0.38 | YES
16 | AKT3 | AKT3 | AKT3 | 2151 | 0.21 | 0.39 | YES
17 | LYN | LYN | LYN | 2272 | 0.2 | 0.41 | YES
18 | PIK3R3 | PIK3R3 | PIK3R3 | 2285 | 0.2 | 0.43 | YES
19 | SYK | SYK | SYK | 2497 | 0.18 | 0.43 | YES
20 | VAV3 | VAV3 | VAV3 | 2505 | 0.18 | 0.45 | YES
21 | BLNK | BLNK | BLNK | 2539 | 0.18 | 0.46 | YES
22 | NFKBIE | NFKBIE | NFKBIE | 2557 | 0.18 | 0.48 | YES
23 | CD79A | CD79A | CD79A | 2748 | 0.16 | 0.49 | YES
24 | PPP3CC | PPP3CC | PPP3CC | 3052 | 0.15 | 0.49 | YES
25 | NRAS | NRAS | NRAS | 3061 | 0.15 | 0.5 | YES
26 | PLCG2 | PLCG2 | PLCG2 | 3161 | 0.14 | 0.51 | YES
27 | NFKBIB | NFKBIB | NFKBIB | 3172 | 0.14 | 0.52 | YES
28 | CR2 | CR2 | CR2 | 3298 | 0.14 | 0.53 | YES
29 | MALT1 | MALT1 | MALT1 | 3369 | 0.13 | 0.54 | YES
30 | MAP2K1 | MAP2K1 | MAP2K1 | 3489 | 0.12 | 0.54 | YES
31 | FCGR2B | FCGR2B | FCGR2B | 3667 | 0.12 | 0.55 | YES
32 | PIK3CD | PIK3CD | PIK3CD | 3885 | 0.11 | 0.55 | YES
33 | PTPN6 | PTPN6 | PTPN6 | 3947 | 0.1 | 0.55 | YES
34 | RAC3 | RAC3 | RAC3 | 4513 | 0.084 | 0.53 | NO
35 | NFKBIA | NFKBIA | NFKBIA | 4907 | 0.073 | 0.52 | NO
36 | GRB2 | GRB2 | GRB2 | 5020 | 0.07 | 0.52 | NO
37 | MAPK1 | MAPK1 | MAPK1 | 5081 | 0.068 | 0.52 | NO
38 | AKT1 | AKT1 | AKT1 | 5146 | 0.066 | 0.52 | NO
39 | NFKB1 | NFKB1 | NFKB1 | 5152 | 0.066 | 0.53 | NO
40 | JUN | JUN | JUN | 5321 | 0.062 | 0.53 | NO
41 | INPP5D | INPP5D | INPP5D | 5332 | 0.062 | 0.53 | NO
42 | CHUK | CHUK | CHUK | 5416 | 0.06 | 0.53 | NO
43 | KRAS | KRAS | KRAS | 5788 | 0.051 | 0.52 | NO
44 | PPP3R1 | PPP3R1 | PPP3R1 | 5824 | 0.05 | 0.52 | NO
45 | IKBKG | IKBKG | IKBKG | 6928 | 0.028 | 0.46 | NO
46 | RAF1 | RAF1 | RAF1 | 7057 | 0.026 | 0.46 | NO
47 | RAC1 | RAC1 | RAC1 | 7823 | 0.013 | 0.42 | NO
48 | PIK3CA | PIK3CA | PIK3CA | 7906 | 0.012 | 0.41 | NO
49 | RELA | RELA | RELA | 7927 | 0.011 | 0.41 | NO
50 | MAP2K2 | MAP2K2 | MAP2K2 | 8004 | 0.0098 | 0.41 | NO
51 | GSK3B | GSK3B | GSK3B | 8476 | 0.0014 | 0.38 | NO
52 | SOS2 | SOS2 | SOS2 | 8545 | 5.2e-06 | 0.38 | NO
53 | VAV2 | VAV2 | VAV2 | 8600 | -0.00084 | 0.38 | NO
54 | AKT2 | AKT2 | AKT2 | 9654 | -0.02 | 0.32 | NO
55 | NFATC1 | NFATC1 | NFATC1 | 9706 | -0.02 | 0.32 | NO
56 | CD81 | CD81 | CD81 | 10108 | -0.028 | 0.3 | NO
57 | IKBKB | IKBKB | IKBKB | 10274 | -0.031 | 0.3 | NO
58 | FOS | FOS | FOS | 10728 | -0.039 | 0.27 | NO
59 | PPP3CA | PPP3CA | PPP3CA | 10887 | -0.042 | 0.27 | NO
60 | NFAT5 | NFAT5 | NFAT5 | 10979 | -0.044 | 0.27 | NO
61 | SOS1 | SOS1 | SOS1 | 11394 | -0.054 | 0.25 | NO
62 | PPP3CB | PPP3CB | PPP3CB | 11518 | -0.056 | 0.25 | NO
63 | PIK3CB | PIK3CB | PIK3CB | 11615 | -0.059 | 0.25 | NO
64 | NFATC3 | NFATC3 | NFATC3 | 11806 | -0.063 | 0.25 | NO
65 | IFITM1 | IFITM1 | IFITM1 | 12199 | -0.074 | 0.23 | NO
66 | NFATC4 | NFATC4 | NFATC4 | 12288 | -0.076 | 0.24 | NO
67 | PIK3R2 | PIK3R2 | PIK3R2 | 12371 | -0.078 | 0.24 | NO
68 | MAPK3 | MAPK3 | MAPK3 | 13360 | -0.11 | 0.2 | NO
69 | PIK3R1 | PIK3R1 | PIK3R1 | 13476 | -0.11 | 0.2 | NO
70 | CARD11 | CARD11 | CARD11 | 13932 | -0.13 | 0.19 | NO
71 | CHP | CHP | CHP | 14285 | -0.15 | 0.18 | NO
72 | CD22 | CD22 | CD22 | 14298 | -0.15 | 0.2 | NO
73 | CHP2 | CHP2 | CHP2 | 14696 | -0.17 | 0.19 | 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 CHEMOKINE SIGNALING PATHWAY.

Figure S58. 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 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 | PRKCB | PRKCB | PRKCB | 879 | 0.35 | 0.042 | YES
2 | BTK | BTK | BTK | 1384 | 0.28 | 0.086 | YES
3 | NFATC2 | NFATC2 | NFATC2 | 1458 | 0.27 | 0.15 | YES
4 | VAV1 | VAV1 | VAV1 | 1471 | 0.27 | 0.22 | YES
5 | PRKCA | PRKCA | PRKCA | 1560 | 0.26 | 0.28 | YES
6 | CD79B | CD79B | CD79B | 1755 | 0.24 | 0.34 | YES
7 | LYN | LYN | LYN | 2272 | 0.2 | 0.36 | YES
8 | SYK | SYK | SYK | 2497 | 0.18 | 0.39 | YES
9 | MAPK8 | MAPK8 | MAPK8 | 2498 | 0.18 | 0.44 | YES
10 | BLNK | BLNK | BLNK | 2539 | 0.18 | 0.48 | YES
11 | CD79A | CD79A | CD79A | 2748 | 0.16 | 0.51 | YES
12 | PPP3CC | PPP3CC | PPP3CC | 3052 | 0.15 | 0.54 | YES
13 | SHC1 | SHC1 | SHC1 | 3482 | 0.12 | 0.54 | YES
14 | MAP2K1 | MAP2K1 | MAP2K1 | 3489 | 0.12 | 0.58 | YES
15 | GRB2 | GRB2 | GRB2 | 5020 | 0.07 | 0.51 | NO
16 | JUN | JUN | JUN | 5321 | 0.062 | 0.51 | NO
17 | CALM1 | CALM1 | CALM1 | 5540 | 0.057 | 0.51 | NO
18 | MAPK14 | MAPK14 | MAPK14 | 6155 | 0.043 | 0.49 | NO
19 | CALM3 | CALM3 | CALM3 | 6554 | 0.036 | 0.48 | NO
20 | CALM2 | CALM2 | CALM2 | 6654 | 0.034 | 0.48 | NO
21 | RAF1 | RAF1 | RAF1 | 7057 | 0.026 | 0.46 | NO
22 | RAC1 | RAC1 | RAC1 | 7823 | 0.013 | 0.43 | NO
23 | ELK1 | ELK1 | ELK1 | 9441 | -0.015 | 0.34 | NO
24 | PLCG1 | PLCG1 | PLCG1 | 9574 | -0.018 | 0.34 | NO
25 | NFATC1 | NFATC1 | NFATC1 | 9706 | -0.02 | 0.34 | NO
26 | FOS | FOS | FOS | 10728 | -0.039 | 0.29 | NO
27 | PPP3CA | PPP3CA | PPP3CA | 10887 | -0.042 | 0.29 | NO
28 | SOS1 | SOS1 | SOS1 | 11394 | -0.054 | 0.28 | NO
29 | PPP3CB | PPP3CB | PPP3CB | 11518 | -0.056 | 0.29 | NO
30 | NFATC3 | NFATC3 | NFATC3 | 11806 | -0.063 | 0.29 | NO
31 | MAP3K1 | MAP3K1 | MAP3K1 | 11861 | -0.064 | 0.3 | NO
32 | NFATC4 | NFATC4 | NFATC4 | 12288 | -0.076 | 0.3 | NO
33 | MAPK3 | MAPK3 | MAPK3 | 13360 | -0.11 | 0.27 | 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 CELL CYCLE.

Figure S60. 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

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
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BIOCARTA ALK PATHWAY | 35 | genes.ES.table | 0.6 | 1.7 | 0.0041 | 0.54 | 0.5 | 0.23 | 0.078 | 0.21 | 0.13 | 0.18
BIOCARTA G1 PATHWAY | 27 | genes.ES.table | 0.5 | 1.4 | 0.13 | 0.48 | 0.96 | 0.44 | 0.26 | 0.33 | 0.38 | 0.092
BIOCARTA WNT PATHWAY | 25 | genes.ES.table | 0.4 | 1.4 | 0.11 | 0.44 | 0.94 | 0.44 | 0.35 | 0.29 | 0.34 | 0.082
KEGG PURINE METABOLISM | 154 | genes.ES.table | 0.35 | 1.4 | 0.046 | 0.49 | 0.96 | 0.18 | 0.18 | 0.15 | 0.39 | 0.1
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES | 25 | genes.ES.table | 0.52 | 1.4 | 0.066 | 0.49 | 0.97 | 0.4 | 0.17 | 0.33 | 0.4 | 0.096
KEGG CALCIUM SIGNALING PATHWAY | 163 | genes.ES.table | 0.46 | 1.4 | 0.057 | 0.47 | 0.97 | 0.36 | 0.19 | 0.29 | 0.38 | 0.085
KEGG OOCYTE MEIOSIS | 105 | genes.ES.table | 0.45 | 1.5 | 0.072 | 0.37 | 0.86 | 0.3 | 0.25 | 0.22 | 0.27 | 0.074
KEGG VASCULAR SMOOTH MUSCLE CONTRACTION | 106 | genes.ES.table | 0.49 | 1.4 | 0.069 | 0.45 | 0.93 | 0.29 | 0.16 | 0.25 | 0.35 | 0.092
KEGG WNT SIGNALING PATHWAY | 144 | genes.ES.table | 0.49 | 1.6 | 0.012 | 0.43 | 0.62 | 0.29 | 0.19 | 0.24 | 0.23 | 0.13
KEGG NOTCH SIGNALING PATHWAY | 46 | genes.ES.table | 0.46 | 1.6 | 0.016 | 0.3 | 0.72 | 0.52 | 0.34 | 0.34 | 0.18 | 0.061

genes ES table in pathway: BIOCARTA ALK 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 | TGFB2 | TGFB2 | TGFB2 | 61 | 0.67 | 0.042 | YES
2 | INHBC | INHBC | INHBC | 109 | 0.61 | 0.08 | YES
3 | LEFTY1 | LEFTY1 | LEFTY1 | 181 | 0.56 | 0.11 | YES
4 | LEFTY2 | LEFTY2 | LEFTY2 | 197 | 0.55 | 0.15 | YES
5 | CHRD | CHRD | CHRD | 218 | 0.54 | 0.19 | YES
6 | INHBE | INHBE | INHBE | 250 | 0.53 | 0.22 | YES
7 | BMP7 | BMP7 | BMP7 | 262 | 0.52 | 0.25 | YES
8 | BMP6 | BMP6 | BMP6 | 342 | 0.49 | 0.28 | YES
9 | AMH | AMH | AMH | 496 | 0.45 | 0.3 | YES
10 | NODAL | NODAL | NODAL | 533 | 0.44 | 0.33 | YES
11 | SMAD6 | SMAD6 | SMAD6 | 594 | 0.42 | 0.36 | YES
12 | LTBP1 | LTBP1 | LTBP1 | 668 | 0.41 | 0.38 | YES
13 | GDF7 | GDF7 | GDF7 | 725 | 0.4 | 0.4 | YES
14 | AMHR2 | AMHR2 | AMHR2 | 891 | 0.37 | 0.42 | YES
15 | BMP5 | BMP5 | BMP5 | 934 | 0.36 | 0.44 | YES
16 | COMP | COMP | COMP | 1111 | 0.34 | 0.46 | YES
17 | BMPR1B | BMPR1B | BMPR1B | 1247 | 0.32 | 0.47 | YES
18 | FST | FST | FST | 1267 | 0.31 | 0.49 | YES
19 | TGFB3 | TGFB3 | TGFB3 | 1428 | 0.29 | 0.5 | YES
20 | BMP8A | BMP8A | BMP8A | 1505 | 0.28 | 0.52 | YES
21 | ID3 | ID3 | ID3 | 1583 | 0.28 | 0.53 | YES
22 | THBS4 | THBS4 | THBS4 | 1741 | 0.26 | 0.54 | YES
23 | ID1 | ID1 | ID1 | 1775 | 0.26 | 0.55 | YES
24 | INHBA | INHBA | INHBA | 1922 | 0.25 | 0.56 | YES
25 | SMAD7 | SMAD7 | SMAD7 | 1942 | 0.24 | 0.58 | YES
26 | PITX2 | PITX2 | PITX2 | 2236 | 0.22 | 0.58 | YES
27 | SMAD9 | SMAD9 | SMAD9 | 2309 | 0.22 | 0.59 | YES
28 | BMP8B | BMP8B | BMP8B | 2342 | 0.22 | 0.6 | YES
29 | GDF6 | GDF6 | GDF6 | 2546 | 0.2 | 0.6 | YES
30 | THBS1 | THBS1 | THBS1 | 2854 | 0.18 | 0.6 | NO
31 | BMPR2 | BMPR2 | BMPR2 | 3455 | 0.16 | 0.57 | NO
32 | ACVRL1 | ACVRL1 | ACVRL1 | 3582 | 0.15 | 0.58 | NO
33 | ZFYVE9 | ZFYVE9 | ZFYVE9 | 4271 | 0.12 | 0.55 | NO
34 | SMAD3 | SMAD3 | SMAD3 | 4307 | 0.12 | 0.55 | NO
35 | RBL1 | RBL1 | RBL1 | 4446 | 0.11 | 0.55 | NO
36 | DCN | DCN | DCN | 4555 | 0.11 | 0.56 | NO
37 | BMPR1A | BMPR1A | BMPR1A | 4624 | 0.11 | 0.56 | NO
38 | CREBBP | CREBBP | CREBBP | 4938 | 0.096 | 0.55 | NO
39 | SMAD4 | SMAD4 | SMAD4 | 6038 | 0.069 | 0.49 | NO
40 | ACVR2B | ACVR2B | ACVR2B | 6193 | 0.066 | 0.49 | NO
41 | TGFB1 | TGFB1 | TGFB1 | 6457 | 0.06 | 0.48 | NO
42 | ACVR2A | ACVR2A | ACVR2A | 6536 | 0.058 | 0.48 | NO
43 | SMAD5 | SMAD5 | SMAD5 | 6651 | 0.056 | 0.47 | NO
44 | ROCK1 | ROCK1 | ROCK1 | 6659 | 0.056 | 0.48 | NO
45 | THBS2 | THBS2 | THBS2 | 6684 | 0.055 | 0.48 | NO
46 | PPP2R1A | PPP2R1A | PPP2R1A | 6744 | 0.054 | 0.48 | NO
47 | TFDP1 | TFDP1 | TFDP1 | 6997 | 0.05 | 0.47 | NO
48 | SP1 | SP1 | SP1 | 7251 | 0.045 | 0.46 | NO
49 | SMAD2 | SMAD2 | SMAD2 | 7317 | 0.044 | 0.46 | NO
50 | BMP4 | BMP4 | BMP4 | 7608 | 0.039 | 0.44 | NO
51 | EP300 | EP300 | EP300 | 7923 | 0.034 | 0.43 | NO
52 | PPP2CB | PPP2CB | PPP2CB | 8467 | 0.026 | 0.4 | NO
53 | ACVR1 | ACVR1 | ACVR1 | 8483 | 0.025 | 0.4 | NO
54 | THBS3 | THBS3 | THBS3 | 8703 | 0.022 | 0.39 | NO
55 | SMURF1 | SMURF1 | SMURF1 | 8920 | 0.019 | 0.38 | NO
56 | CUL1 | CUL1 | CUL1 | 9575 | 0.01 | 0.34 | NO
57 | TGFBR1 | TGFBR1 | TGFBR1 | 9984 | 0.0045 | 0.32 | NO
58 | MAPK1 | MAPK1 | MAPK1 | 10177 | 0.0018 | 0.31 | NO
59 | E2F4 | E2F4 | E2F4 | 10345 | -0.00034 | 0.3 | NO
60 | SMAD1 | SMAD1 | SMAD1 | 10672 | -0.0048 | 0.29 | NO
61 | ZFYVE16 | ZFYVE16 | ZFYVE16 | 10851 | -0.0073 | 0.28 | NO
62 | SMURF2 | SMURF2 | SMURF2 | 11342 | -0.014 | 0.25 | NO
63 | ACVR1C | ACVR1C | ACVR1C | 11449 | -0.016 | 0.25 | NO
64 | SKP1 | SKP1 | SKP1 | 12006 | -0.024 | 0.22 | NO
65 | RBX1 | RBX1 | RBX1 | 12016 | -0.024 | 0.22 | NO
66 | ROCK2 | ROCK2 | ROCK2 | 12211 | -0.027 | 0.21 | NO
67 | ID4 | ID4 | ID4 | 12277 | -0.028 | 0.21 | NO
68 | PPP2R1B | PPP2R1B | PPP2R1B | 12936 | -0.039 | 0.17 | NO
69 | TGFBR2 | TGFBR2 | TGFBR2 | 12989 | -0.04 | 0.17 | NO
70 | RHOA | RHOA | RHOA | 13234 | -0.044 | 0.16 | NO
71 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 13342 | -0.046 | 0.16 | NO
72 | PPP2CA | PPP2CA | PPP2CA | 13349 | -0.046 | 0.16 | NO
73 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 13650 | -0.052 | 0.15 | NO
74 | MAPK3 | MAPK3 | MAPK3 | 13791 | -0.055 | 0.15 | NO
75 | E2F5 | E2F5 | E2F5 | 13837 | -0.056 | 0.15 | NO
76 | RBL2 | RBL2 | RBL2 | 14070 | -0.06 | 0.14 | NO
77 | BMP2 | BMP2 | BMP2 | 15717 | -0.11 | 0.054 | NO
78 | INHBB | INHBB | INHBB | 15798 | -0.11 | 0.057 | NO
79 | CDKN2B | CDKN2B | CDKN2B | 16533 | -0.15 | 0.027 | NO
80 | ID2 | ID2 | ID2 | 16742 | -0.16 | 0.026 | NO
81 | MYC | MYC | MYC | 16802 | -0.17 | 0.034 | NO
82 | GDF5 | GDF5 | GDF5 | 16979 | -0.18 | 0.036 | NO
83 | IFNG | IFNG | IFNG | 17184 | -0.2 | 0.039 | NO
84 | TNF | TNF | TNF | 17509 | -0.25 | 0.038 | NO

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

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

genes ES table in pathway: BIOCARTA G1 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 | TGFB2 | TGFB2 | TGFB2 | 61 | 0.67 | 0.13 | YES
2 | CHRD | CHRD | CHRD | 218 | 0.54 | 0.22 | YES
3 | BMP7 | BMP7 | BMP7 | 262 | 0.52 | 0.32 | YES
4 | SMAD6 | SMAD6 | SMAD6 | 594 | 0.42 | 0.39 | YES
5 | NKX2-5 | NKX2-5 | NKX2-5 | 800 | 0.38 | 0.45 | YES
6 | BMP5 | BMP5 | BMP5 | 934 | 0.36 | 0.52 | YES
7 | GATA4 | GATA4 | GATA4 | 1388 | 0.3 | 0.55 | YES
8 | TGFB3 | TGFB3 | TGFB3 | 1428 | 0.29 | 0.6 | YES
9 | FZD1 | FZD1 | FZD1 | 3249 | 0.16 | 0.53 | NO
10 | BMPR2 | BMPR2 | BMPR2 | 3455 | 0.16 | 0.55 | NO
11 | NPPB | NPPB | NPPB | 4004 | 0.13 | 0.55 | NO
12 | BMPR1A | BMPR1A | BMPR1A | 4624 | 0.11 | 0.54 | NO
13 | MAP3K7 | MAP3K7 | MAP3K7 | 4925 | 0.097 | 0.54 | NO
14 | NOG | NOG | NOG | 5106 | 0.092 | 0.55 | NO
15 | TGFBR3 | TGFBR3 | TGFBR3 | 5298 | 0.086 | 0.55 | NO
16 | NPPA | NPPA | NPPA | 5647 | 0.078 | 0.55 | NO
17 | SMAD4 | SMAD4 | SMAD4 | 6038 | 0.069 | 0.54 | NO
18 | CTNNB1 | CTNNB1 | CTNNB1 | 6392 | 0.061 | 0.53 | NO
19 | TGFB1 | TGFB1 | TGFB1 | 6457 | 0.06 | 0.54 | NO
20 | SMAD5 | SMAD5 | SMAD5 | 6651 | 0.056 | 0.54 | NO
21 | HNF1A | HNF1A | HNF1A | 6964 | 0.05 | 0.53 | NO
22 | WNT1 | WNT1 | WNT1 | 7372 | 0.043 | 0.52 | NO
23 | BMP4 | BMP4 | BMP4 | 7608 | 0.039 | 0.51 | NO
24 | ACVR1 | ACVR1 | ACVR1 | 8483 | 0.025 | 0.47 | NO
25 | DVL1 | DVL1 | DVL1 | 8890 | 0.02 | 0.45 | NO
26 | MYL2 | MYL2 | MYL2 | 9014 | 0.018 | 0.45 | NO
27 | TGFBR1 | TGFBR1 | TGFBR1 | 9984 | 0.0045 | 0.4 | NO
28 | GSK3B | GSK3B | GSK3B | 10261 | 0.00077 | 0.38 | NO
29 | SMAD1 | SMAD1 | SMAD1 | 10672 | -0.0048 | 0.36 | NO
30 | RFC1 | RFC1 | RFC1 | 11897 | -0.022 | 0.3 | NO
31 | AXIN1 | AXIN1 | AXIN1 | 12068 | -0.025 | 0.29 | NO
32 | APC | APC | APC | 12801 | -0.037 | 0.26 | NO
33 | TGFBR2 | TGFBR2 | TGFBR2 | 12989 | -0.04 | 0.26 | NO
34 | ATF2 | ATF2 | ATF2 | 13601 | -0.051 | 0.23 | NO
35 | BMP2 | BMP2 | BMP2 | 15717 | -0.11 | 0.14 | NO

Figure S63. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA G1 PATHWAY.

Figure S64. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA WNT PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PTCH2 | PTCH2 | PTCH2 | 59 | 0.68 | 0.059 | YES
2 | GLI1 | GLI1 | GLI1 | 99 | 0.62 | 0.11 | YES
3 | WNT11 | WNT11 | WNT11 | 182 | 0.56 | 0.16 | YES
4 | PTCH1 | PTCH1 | PTCH1 | 220 | 0.54 | 0.21 | YES
5 | HHIP | HHIP | HHIP | 434 | 0.47 | 0.24 | YES
6 | WNT6 | WNT6 | WNT6 | 442 | 0.47 | 0.28 | YES
7 | WNT5B | WNT5B | WNT5B | 568 | 0.43 | 0.32 | YES
8 | WNT10B | WNT10B | WNT10B | 826 | 0.38 | 0.34 | YES
9 | APC2 | APC2 | APC2 | 839 | 0.38 | 0.37 | YES
10 | FZD10 | FZD10 | FZD10 | 956 | 0.36 | 0.4 | YES
11 | LEF1 | LEF1 | LEF1 | 1080 | 0.34 | 0.42 | YES
12 | FZD8 | FZD8 | FZD8 | 1113 | 0.34 | 0.45 | YES
13 | FZD3 | FZD3 | FZD3 | 1163 | 0.33 | 0.48 | YES
14 | SMO | SMO | SMO | 1285 | 0.31 | 0.5 | YES
15 | FZD2 | FZD2 | FZD2 | 1403 | 0.3 | 0.52 | YES
16 | TCF7L1 | TCF7L1 | TCF7L1 | 1669 | 0.27 | 0.53 | YES
17 | GLI2 | GLI2 | GLI2 | 1960 | 0.24 | 0.54 | YES
18 | TCF7 | TCF7 | TCF7 | 2225 | 0.22 | 0.54 | YES
19 | FZD7 | FZD7 | FZD7 | 2323 | 0.22 | 0.56 | YES
20 | WNT9A | WNT9A | WNT9A | 2517 | 0.2 | 0.56 | YES
21 | WNT7B | WNT7B | WNT7B | 2808 | 0.19 | 0.57 | YES
22 | WNT8B | WNT8B | WNT8B | 2867 | 0.18 | 0.58 | YES
23 | FZD9 | FZD9 | FZD9 | 2999 | 0.18 | 0.59 | YES
24 | WNT7A | WNT7A | WNT7A | 3062 | 0.17 | 0.6 | YES
25 | SHH | SHH | SHH | 3229 | 0.16 | 0.61 | YES
26 | FZD1 | FZD1 | FZD1 | 3249 | 0.16 | 0.62 | YES
27 | FZD4 | FZD4 | FZD4 | 3390 | 0.16 | 0.63 | YES
28 | AXIN2 | AXIN2 | AXIN2 | 4205 | 0.12 | 0.59 | NO
29 | GLI3 | GLI3 | GLI3 | 4216 | 0.12 | 0.6 | NO
30 | TP53 | TP53 | TP53 | 4646 | 0.1 | 0.59 | NO
31 | DVL2 | DVL2 | DVL2 | 4862 | 0.098 | 0.59 | NO
32 | STK36 | STK36 | STK36 | 5190 | 0.089 | 0.58 | NO
33 | WNT2B | WNT2B | WNT2B | 5759 | 0.075 | 0.55 | NO
34 | CTNNB1 | CTNNB1 | CTNNB1 | 6392 | 0.061 | 0.52 | NO
35 | WNT10A | WNT10A | WNT10A | 6453 | 0.06 | 0.53 | NO
36 | WNT1 | WNT1 | WNT1 | 7372 | 0.043 | 0.48 | NO
37 | BMP4 | BMP4 | BMP4 | 7608 | 0.039 | 0.47 | NO
38 | FZD6 | FZD6 | FZD6 | 7981 | 0.033 | 0.45 | NO
39 | WNT16 | WNT16 | WNT16 | 8595 | 0.024 | 0.42 | NO
40 | DVL1 | DVL1 | DVL1 | 8890 | 0.02 | 0.41 | NO
41 | SUFU | SUFU | SUFU | 9006 | 0.018 | 0.4 | NO
42 | GSK3B | GSK3B | GSK3B | 10261 | 0.00077 | 0.33 | NO
43 | WNT5A | WNT5A | WNT5A | 11060 | -0.01 | 0.29 | NO
44 | AXIN1 | AXIN1 | AXIN1 | 12068 | -0.025 | 0.24 | NO
45 | APC | APC | APC | 12801 | -0.037 | 0.2 | NO
46 | FZD5 | FZD5 | FZD5 | 13376 | -0.047 | 0.17 | NO
47 | WNT4 | WNT4 | WNT4 | 13847 | -0.056 | 0.15 | NO
48 | TCF7L2 | TCF7L2 | TCF7L2 | 14187 | -0.063 | 0.14 | NO
49 | DVL3 | DVL3 | DVL3 | 14782 | -0.077 | 0.11 | NO
50 | BMP2 | BMP2 | BMP2 | 15717 | -0.11 | 0.071 | NO
51 | WNT9B | WNT9B | WNT9B | 16726 | -0.16 | 0.03 | NO
52 | WNT3 | WNT3 | WNT3 | 16971 | -0.18 | 0.034 | NO
53 | WNT2 | WNT2 | WNT2 | 17956 | -0.36 | 0.013 | NO

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

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

genes ES table in pathway: KEGG PURINE METABOLISM

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | SFRP5 | SFRP5 | SFRP5 | 107 | 0.61 | 0.026 | YES
2 | CAMK2B | CAMK2B | CAMK2B | 117 | 0.6 | 0.056 | YES
3 | NKD1 | NKD1 | NKD1 | 175 | 0.57 | 0.082 | YES
4 | WNT11 | WNT11 | WNT11 | 182 | 0.56 | 0.11 | YES
5 | NKD2 | NKD2 | NKD2 | 321 | 0.5 | 0.13 | YES
6 | NFATC4 | NFATC4 | NFATC4 | 343 | 0.49 | 0.15 | YES
7 | WNT6 | WNT6 | WNT6 | 442 | 0.47 | 0.17 | YES
8 | CXXC4 | CXXC4 | CXXC4 | 559 | 0.44 | 0.19 | YES
9 | WNT5B | WNT5B | WNT5B | 568 | 0.43 | 0.21 | YES
10 | WNT10B | WNT10B | WNT10B | 826 | 0.38 | 0.21 | YES
11 | APC2 | APC2 | APC2 | 839 | 0.38 | 0.23 | YES
12 | SFRP1 | SFRP1 | SFRP1 | 944 | 0.36 | 0.25 | YES
13 | FZD10 | FZD10 | FZD10 | 956 | 0.36 | 0.26 | YES
14 | PRICKLE1 | PRICKLE1 | PRICKLE1 | 1001 | 0.35 | 0.28 | YES
15 | LEF1 | LEF1 | LEF1 | 1080 | 0.34 | 0.29 | YES
16 | FZD8 | FZD8 | FZD8 | 1113 | 0.34 | 0.31 | YES
17 | FZD3 | FZD3 | FZD3 | 1163 | 0.33 | 0.32 | YES
18 | MAPK10 | MAPK10 | MAPK10 | 1189 | 0.32 | 0.34 | YES
19 | WIF1 | WIF1 | WIF1 | 1258 | 0.31 | 0.35 | YES
20 | DAAM2 | DAAM2 | DAAM2 | 1375 | 0.3 | 0.36 | YES
21 | FZD2 | FZD2 | FZD2 | 1403 | 0.3 | 0.37 | YES
22 | PRKCG | PRKCG | PRKCG | 1565 | 0.28 | 0.38 | YES
23 | TCF7L1 | TCF7L1 | TCF7L1 | 1669 | 0.27 | 0.39 | YES
24 | LRP6 | LRP6 | LRP6 | 1674 | 0.27 | 0.4 | YES
25 | SFRP2 | SFRP2 | SFRP2 | 1933 | 0.25 | 0.4 | YES
26 | RAC3 | RAC3 | RAC3 | 2042 | 0.24 | 0.4 | YES
27 | VANGL2 | VANGL2 | VANGL2 | 2052 | 0.24 | 0.42 | YES
28 | TBL1Y | TBL1Y | TBL1Y | 2207 | 0.23 | 0.42 | YES
29 | TCF7 | TCF7 | TCF7 | 2225 | 0.22 | 0.43 | YES
30 | FZD7 | FZD7 | FZD7 | 2323 | 0.22 | 0.44 | YES
31 | DKK2 | DKK2 | DKK2 | 2384 | 0.21 | 0.44 | YES
32 | SOX17 | SOX17 | SOX17 | 2492 | 0.21 | 0.45 | YES
33 | WNT9A | WNT9A | WNT9A | 2517 | 0.2 | 0.46 | YES
34 | PLCB4 | PLCB4 | PLCB4 | 2581 | 0.2 | 0.46 | YES
35 | CAMK2A | CAMK2A | CAMK2A | 2773 | 0.19 | 0.46 | YES
36 | WNT7B | WNT7B | WNT7B | 2808 | 0.19 | 0.47 | YES
37 | WNT8B | WNT8B | WNT8B | 2867 | 0.18 | 0.48 | YES
38 | FZD9 | FZD9 | FZD9 | 2999 | 0.18 | 0.48 | YES
39 | WNT7A | WNT7A | WNT7A | 3062 | 0.17 | 0.48 | YES
40 | FZD1 | FZD1 | FZD1 | 3249 | 0.16 | 0.48 | YES
41 | FZD4 | FZD4 | FZD4 | 3390 | 0.16 | 0.48 | YES
42 | CTNNBIP1 | CTNNBIP1 | CTNNBIP1 | 3456 | 0.16 | 0.49 | YES
43 | WNT3A | WNT3A | WNT3A | 3698 | 0.14 | 0.48 | NO
44 | TBL1X | TBL1X | TBL1X | 3863 | 0.14 | 0.48 | NO
45 | NFATC1 | NFATC1 | NFATC1 | 3950 | 0.13 | 0.48 | NO
46 | AXIN2 | AXIN2 | AXIN2 | 4205 | 0.12 | 0.47 | NO
47 | SMAD3 | SMAD3 | SMAD3 | 4307 | 0.12 | 0.47 | NO
48 | CAMK2G | CAMK2G | CAMK2G | 4325 | 0.12 | 0.48 | NO
49 | CCND1 | CCND1 | CCND1 | 4475 | 0.11 | 0.48 | NO
50 | TP53 | TP53 | TP53 | 4646 | 0.1 | 0.47 | NO
51 | CSNK1E | CSNK1E | CSNK1E | 4763 | 0.1 | 0.47 | NO
52 | DVL2 | DVL2 | DVL2 | 4862 | 0.098 | 0.47 | NO
53 | MAP3K7 | MAP3K7 | MAP3K7 | 4925 | 0.097 | 0.47 | NO
54 | CREBBP | CREBBP | CREBBP | 4938 | 0.096 | 0.48 | NO
55 | PPP3CA | PPP3CA | PPP3CA | 5165 | 0.09 | 0.47 | NO
56 | FRAT1 | FRAT1 | FRAT1 | 5340 | 0.086 | 0.46 | NO
57 | MMP7 | MMP7 | MMP7 | 5514 | 0.081 | 0.46 | NO
58 | WNT2B | WNT2B | WNT2B | 5759 | 0.075 | 0.45 | NO
59 | PRKACA | PRKACA | PRKACA | 5993 | 0.07 | 0.44 | NO
60 | SMAD4 | SMAD4 | SMAD4 | 6038 | 0.069 | 0.44 | NO
61 | SFRP4 | SFRP4 | SFRP4 | 6080 | 0.068 | 0.44 | NO
62 | PRKX | PRKX | PRKX | 6173 | 0.066 | 0.44 | NO
63 | CTNNB1 | CTNNB1 | CTNNB1 | 6392 | 0.061 | 0.43 | NO
64 | WNT10A | WNT10A | WNT10A | 6453 | 0.06 | 0.43 | NO
65 | ROCK1 | ROCK1 | ROCK1 | 6659 | 0.056 | 0.42 | NO
66 | PPP2R1A | PPP2R1A | PPP2R1A | 6744 | 0.054 | 0.42 | NO
67 | PPARD | PPARD | PPARD | 6827 | 0.053 | 0.42 | NO
68 | PPP2R5D | PPP2R5D | PPP2R5D | 6935 | 0.051 | 0.41 | NO
69 | CHD8 | CHD8 | CHD8 | 7027 | 0.049 | 0.41 | NO
70 | SIAH1 | SIAH1 | SIAH1 | 7232 | 0.045 | 0.4 | NO
71 | SMAD2 | SMAD2 | SMAD2 | 7317 | 0.044 | 0.4 | NO
72 | CAMK2D | CAMK2D | CAMK2D | 7324 | 0.044 | 0.4 | NO
73 | WNT1 | WNT1 | WNT1 | 7372 | 0.043 | 0.4 | NO
74 | PPP3CB | PPP3CB | PPP3CB | 7754 | 0.037 | 0.38 | NO
75 | EP300 | EP300 | EP300 | 7923 | 0.034 | 0.38 | NO
76 | FZD6 | FZD6 | FZD6 | 7981 | 0.033 | 0.37 | NO
77 | NFATC2 | NFATC2 | NFATC2 | 8128 | 0.03 | 0.37 | NO
78 | PPP3R1 | PPP3R1 | PPP3R1 | 8236 | 0.029 | 0.36 | NO
79 | CTBP1 | CTBP1 | CTBP1 | 8433 | 0.026 | 0.35 | NO
80 | PPP2CB | PPP2CB | PPP2CB | 8467 | 0.026 | 0.35 | NO
81 | WNT16 | WNT16 | WNT16 | 8595 | 0.024 | 0.35 | NO
82 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 8603 | 0.024 | 0.35 | NO
83 | NFATC3 | NFATC3 | NFATC3 | 8689 | 0.023 | 0.34 | NO
84 | NFAT5 | NFAT5 | NFAT5 | 8711 | 0.022 | 0.34 | NO
85 | DVL1 | DVL1 | DVL1 | 8890 | 0.02 | 0.34 | NO
86 | PPP2R5C | PPP2R5C | PPP2R5C | 8928 | 0.019 | 0.33 | NO
87 | PRKACB | PRKACB | PRKACB | 9119 | 0.016 | 0.32 | NO
88 | CSNK2A2 | CSNK2A2 | CSNK2A2 | 9310 | 0.014 | 0.31 | NO
89 | CUL1 | CUL1 | CUL1 | 9575 | 0.01 | 0.3 | NO
90 | NLK | NLK | NLK | 9608 | 0.0097 | 0.3 | NO
91 | LRP5 | LRP5 | LRP5 | 9780 | 0.0075 | 0.29 | NO
92 | CACYBP | CACYBP | CACYBP | 9790 | 0.0074 | 0.29 | NO
93 | GSK3B | GSK3B | GSK3B | 10261 | 0.00077 | 0.26 | NO
94 | RAC1 | RAC1 | RAC1 | 10283 | 0.00049 | 0.26 | NO
95 | MAPK8 | MAPK8 | MAPK8 | 10294 | 0.00034 | 0.26 | NO
96 | PPP2R5E | PPP2R5E | PPP2R5E | 10296 | 0.00029 | 0.26 | NO
97 | VANGL1 | VANGL1 | VANGL1 | 10416 | -0.0013 | 0.26 | NO
98 | JUN | JUN | JUN | 10806 | -0.0068 | 0.23 | NO
99 | CTBP2 | CTBP2 | CTBP2 | 10854 | -0.0074 | 0.23 | NO
100 | RUVBL1 | RUVBL1 | RUVBL1 | 10910 | -0.0083 | 0.23 | NO
101 | PRICKLE2 | PRICKLE2 | PRICKLE2 | 11042 | -0.01 | 0.22 | NO
102 | WNT5A | WNT5A | WNT5A | 11060 | -0.01 | 0.22 | NO
103 | FBXW11 | FBXW11 | FBXW11 | 11125 | -0.011 | 0.22 | NO
104 | CSNK2B | CSNK2B | CSNK2B | 11272 | -0.013 | 0.21 | NO
105 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 11306 | -0.014 | 0.21 | NO
106 | FOSL1 | FOSL1 | FOSL1 | 11310 | -0.014 | 0.21 | NO
107 | PSEN1 | PSEN1 | PSEN1 | 11745 | -0.02 | 0.19 | NO
108 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 11777 | -0.021 | 0.19 | NO
109 | PPP2R5A | PPP2R5A | PPP2R5A | 11851 | -0.022 | 0.18 | NO
110 | SKP1 | SKP1 | SKP1 | 12006 | -0.024 | 0.18 | NO
111 | RBX1 | RBX1 | RBX1 | 12016 | -0.024 | 0.18 | NO
112 | BTRC | BTRC | BTRC | 12040 | -0.025 | 0.18 | NO
113 | AXIN1 | AXIN1 | AXIN1 | 12068 | -0.025 | 0.18 | NO
114 | ROCK2 | ROCK2 | ROCK2 | 12211 | -0.027 | 0.17 | NO
115 | CHP2 | CHP2 | CHP2 | 12459 | -0.031 | 0.16 | NO
116 | PLCB3 | PLCB3 | PLCB3 | 12765 | -0.036 | 0.14 | NO
117 | APC | APC | APC | 12801 | -0.037 | 0.14 | NO
118 | PPP2R1B | PPP2R1B | PPP2R1B | 12936 | -0.039 | 0.14 | NO
119 | RHOA | RHOA | RHOA | 13234 | -0.044 | 0.12 | NO
120 | PORCN | PORCN | PORCN | 13235 | -0.044 | 0.13 | NO
121 | DKK1 | DKK1 | DKK1 | 13269 | -0.045 | 0.13 | NO
122 | PPP2CA | PPP2CA | PPP2CA | 13349 | -0.046 | 0.13 | NO
123 | FZD5 | FZD5 | FZD5 | 13376 | -0.047 | 0.13 | NO
124 | CCND3 | CCND3 | CCND3 | 13540 | -0.05 | 0.12 | NO
125 | PPP3CC | PPP3CC | PPP3CC | 13594 | -0.051 | 0.12 | NO
126 | MAPK9 | MAPK9 | MAPK9 | 13598 | -0.051 | 0.12 | NO
127 | WNT4 | WNT4 | WNT4 | 13847 | -0.056 | 0.11 | NO
128 | TCF7L2 | TCF7L2 | TCF7L2 | 14187 | -0.063 | 0.096 | NO
129 | FRAT2 | FRAT2 | FRAT2 | 14622 | -0.073 | 0.076 | NO
130 | PRKCA | PRKCA | PRKCA | 14691 | -0.075 | 0.076 | NO
131 | DVL3 | DVL3 | DVL3 | 14782 | -0.077 | 0.074 | NO
132 | SENP2 | SENP2 | SENP2 | 14833 | -0.078 | 0.076 | NO
133 | PLCB1 | PLCB1 | PLCB1 | 15180 | -0.088 | 0.061 | NO
134 | PLCB2 | PLCB2 | PLCB2 | 15250 | -0.089 | 0.062 | NO
135 | CCND2 | CCND2 | CCND2 | 15615 | -0.1 | 0.047 | NO
136 | RAC2 | RAC2 | RAC2 | 16173 | -0.13 | 0.023 | NO
137 | CSNK1A1L | CSNK1A1L | CSNK1A1L | 16253 | -0.13 | 0.025 | NO
138 | WNT9B | WNT9B | WNT9B | 16726 | -0.16 | 0.0071 | NO
139 | MYC | MYC | MYC | 16802 | -0.17 | 0.012 | NO
140 | WNT3 | WNT3 | WNT3 | 16971 | -0.18 | 0.012 | NO
141 | CHP | CHP | CHP | 17054 | -0.19 | 0.017 | NO
142 | DAAM1 | DAAM1 | DAAM1 | 17525 | -0.25 | 0.0033 | NO
143 | PRKCB | PRKCB | PRKCB | 17708 | -0.28 | 0.0078 | NO
144 | WNT2 | WNT2 | WNT2 | 17956 | -0.36 | 0.013 | 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 PURINE METABOLISM.

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

genes ES table in pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

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 | CAMK2B | CAMK2B | CAMK2B | 117 | 0.6 | 0.034 | YES
2 | ADCY5 | ADCY5 | ADCY5 | 167 | 0.57 | 0.069 | YES
3 | WNT11 | WNT11 | WNT11 | 182 | 0.56 | 0.1 | YES
4 | GNAO1 | GNAO1 | GNAO1 | 385 | 0.48 | 0.13 | YES
5 | WNT6 | WNT6 | WNT6 | 442 | 0.47 | 0.15 | YES
6 | CALML3 | CALML3 | CALML3 | 455 | 0.46 | 0.18 | YES
7 | ADCY2 | ADCY2 | ADCY2 | 502 | 0.45 | 0.21 | YES
8 | WNT5B | WNT5B | WNT5B | 568 | 0.43 | 0.24 | YES
9 | ADCY1 | ADCY1 | ADCY1 | 818 | 0.38 | 0.25 | YES
10 | WNT10B | WNT10B | WNT10B | 826 | 0.38 | 0.27 | YES
11 | CALML5 | CALML5 | CALML5 | 948 | 0.36 | 0.29 | YES
12 | FZD10 | FZD10 | FZD10 | 956 | 0.36 | 0.31 | YES
13 | LEF1 | LEF1 | LEF1 | 1080 | 0.34 | 0.33 | YES
14 | FZD8 | FZD8 | FZD8 | 1113 | 0.34 | 0.35 | YES
15 | FZD3 | FZD3 | FZD3 | 1163 | 0.33 | 0.37 | YES
16 | FZD2 | FZD2 | FZD2 | 1403 | 0.3 | 0.38 | YES
17 | PRKCG | PRKCG | PRKCG | 1565 | 0.28 | 0.38 | YES
18 | TCF7L1 | TCF7L1 | TCF7L1 | 1669 | 0.27 | 0.4 | YES
19 | TCF7 | TCF7 | TCF7 | 2225 | 0.22 | 0.38 | YES
20 | FZD7 | FZD7 | FZD7 | 2323 | 0.22 | 0.39 | YES
21 | CREB3L1 | CREB3L1 | CREB3L1 | 2359 | 0.22 | 0.4 | YES
22 | WNT9A | WNT9A | WNT9A | 2517 | 0.2 | 0.41 | YES
23 | EDNRB | EDNRB | EDNRB | 2566 | 0.2 | 0.42 | YES
24 | PLCB4 | PLCB4 | PLCB4 | 2581 | 0.2 | 0.43 | YES
25 | CREB3L3 | CREB3L3 | CREB3L3 | 2711 | 0.19 | 0.44 | YES
26 | TYR | TYR | TYR | 2732 | 0.19 | 0.45 | YES
27 | CAMK2A | CAMK2A | CAMK2A | 2773 | 0.19 | 0.46 | YES
28 | WNT7B | WNT7B | WNT7B | 2808 | 0.19 | 0.47 | YES
29 | WNT8B | WNT8B | WNT8B | 2867 | 0.18 | 0.48 | YES
30 | ADCY8 | ADCY8 | ADCY8 | 2880 | 0.18 | 0.49 | YES
31 | FZD9 | FZD9 | FZD9 | 2999 | 0.18 | 0.5 | YES
32 | WNT7A | WNT7A | WNT7A | 3062 | 0.17 | 0.5 | YES
33 | FZD1 | FZD1 | FZD1 | 3249 | 0.16 | 0.5 | YES
34 | KIT | KIT | KIT | 3308 | 0.16 | 0.51 | YES
35 | TYRP1 | TYRP1 | TYRP1 | 3336 | 0.16 | 0.52 | YES
36 | FZD4 | FZD4 | FZD4 | 3390 | 0.16 | 0.53 | YES
37 | EDN1 | EDN1 | EDN1 | 3624 | 0.15 | 0.52 | YES
38 | WNT3A | WNT3A | WNT3A | 3698 | 0.14 | 0.53 | YES
39 | CAMK2G | CAMK2G | CAMK2G | 4325 | 0.12 | 0.5 | NO
40 | ADCY4 | ADCY4 | ADCY4 | 4353 | 0.12 | 0.51 | NO
41 | ADCY6 | ADCY6 | ADCY6 | 4620 | 0.11 | 0.5 | NO
42 | MC1R | MC1R | MC1R | 4654 | 0.1 | 0.51 | NO
43 | DVL2 | DVL2 | DVL2 | 4862 | 0.098 | 0.5 | NO
44 | CREBBP | CREBBP | CREBBP | 4938 | 0.096 | 0.5 | NO
45 | CALM1 | CALM1 | CALM1 | 5734 | 0.076 | 0.46 | NO
46 | WNT2B | WNT2B | WNT2B | 5759 | 0.075 | 0.47 | NO
47 | ASIP | ASIP | ASIP | 5816 | 0.074 | 0.47 | NO
48 | KITLG | KITLG | KITLG | 5955 | 0.071 | 0.47 | NO
49 | PRKACA | PRKACA | PRKACA | 5993 | 0.07 | 0.47 | NO
50 | PRKX | PRKX | PRKX | 6173 | 0.066 | 0.46 | NO
51 | CTNNB1 | CTNNB1 | CTNNB1 | 6392 | 0.061 | 0.46 | NO
52 | WNT10A | WNT10A | WNT10A | 6453 | 0.06 | 0.46 | NO
53 | KRAS | KRAS | KRAS | 6619 | 0.056 | 0.45 | NO
54 | CAMK2D | CAMK2D | CAMK2D | 7324 | 0.044 | 0.42 | NO
55 | WNT1 | WNT1 | WNT1 | 7372 | 0.043 | 0.42 | NO
56 | CREB1 | CREB1 | CREB1 | 7612 | 0.039 | 0.41 | NO
57 | GNAS | GNAS | GNAS | 7824 | 0.036 | 0.4 | NO
58 | MAP2K2 | MAP2K2 | MAP2K2 | 7827 | 0.035 | 0.4 | NO
59 | CALM3 | CALM3 | CALM3 | 7916 | 0.034 | 0.4 | NO
60 | EP300 | EP300 | EP300 | 7923 | 0.034 | 0.4 | NO
61 | FZD6 | FZD6 | FZD6 | 7981 | 0.033 | 0.4 | NO
62 | CREB3L4 | CREB3L4 | CREB3L4 | 8506 | 0.025 | 0.37 | NO
63 | WNT16 | WNT16 | WNT16 | 8595 | 0.024 | 0.37 | NO
64 | DVL1 | DVL1 | DVL1 | 8890 | 0.02 | 0.35 | NO
65 | PRKACB | PRKACB | PRKACB | 9119 | 0.016 | 0.34 | NO
66 | CREB3L2 | CREB3L2 | CREB3L2 | 9269 | 0.014 | 0.33 | NO
67 | GNAQ | GNAQ | GNAQ | 9307 | 0.014 | 0.33 | NO
68 | MAPK1 | MAPK1 | MAPK1 | 10177 | 0.0018 | 0.28 | NO
69 | GSK3B | GSK3B | GSK3B | 10261 | 0.00077 | 0.28 | NO
70 | RAF1 | RAF1 | RAF1 | 10279 | 0.00052 | 0.28 | NO
71 | CALML6 | CALML6 | CALML6 | 10900 | -0.0081 | 0.24 | NO
72 | WNT5A | WNT5A | WNT5A | 11060 | -0.01 | 0.24 | NO
73 | ADCY7 | ADCY7 | ADCY7 | 11493 | -0.017 | 0.21 | NO
74 | POMC | POMC | POMC | 11695 | -0.02 | 0.2 | NO
75 | CALM2 | CALM2 | CALM2 | 11968 | -0.024 | 0.19 | NO
76 | NRAS | NRAS | NRAS | 11996 | -0.024 | 0.19 | NO
77 | HRAS | HRAS | HRAS | 12025 | -0.024 | 0.19 | NO
78 | GNAI2 | GNAI2 | GNAI2 | 12159 | -0.027 | 0.18 | NO
79 | PLCB3 | PLCB3 | PLCB3 | 12765 | -0.036 | 0.15 | NO
80 | ADCY9 | ADCY9 | ADCY9 | 13365 | -0.047 | 0.12 | NO
81 | FZD5 | FZD5 | FZD5 | 13376 | -0.047 | 0.13 | NO
82 | GNAI3 | GNAI3 | GNAI3 | 13466 | -0.048 | 0.12 | NO
83 | MAPK3 | MAPK3 | MAPK3 | 13791 | -0.055 | 0.11 | NO
84 | WNT4 | WNT4 | WNT4 | 13847 | -0.056 | 0.11 | NO
85 | TCF7L2 | TCF7L2 | TCF7L2 | 14187 | -0.063 | 0.097 | NO
86 | MAP2K1 | MAP2K1 | MAP2K1 | 14261 | -0.065 | 0.097 | NO
87 | PRKCA | PRKCA | PRKCA | 14691 | -0.075 | 0.078 | NO
88 | DVL3 | DVL3 | DVL3 | 14782 | -0.077 | 0.078 | NO
89 | CREB3 | CREB3 | CREB3 | 14924 | -0.081 | 0.076 | NO
90 | PLCB1 | PLCB1 | PLCB1 | 15180 | -0.088 | 0.068 | NO
91 | PLCB2 | PLCB2 | PLCB2 | 15250 | -0.089 | 0.07 | NO
92 | DCT | DCT | DCT | 15474 | -0.097 | 0.064 | NO
93 | MITF | MITF | MITF | 16437 | -0.14 | 0.02 | NO
94 | WNT9B | WNT9B | WNT9B | 16726 | -0.16 | 0.015 | NO
95 | GNAI1 | GNAI1 | GNAI1 | 16762 | -0.16 | 0.024 | NO
96 | WNT3 | WNT3 | WNT3 | 16971 | -0.18 | 0.024 | NO
97 | PRKCB | PRKCB | PRKCB | 17708 | -0.28 | 0.0022 | NO
98 | WNT2 | WNT2 | WNT2 | 17956 | -0.36 | 0.013 | 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

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

genes ES table in pathway: KEGG CALCIUM SIGNALING PATHWAY

Table 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 | ADCY5 | ADCY5 | ADCY5 | 167 | 0.57 | 0.041 | YES
2 | DRD1 | DRD1 | DRD1 | 170 | 0.57 | 0.091 | YES
3 | ADCY2 | ADCY2 | ADCY2 | 502 | 0.45 | 0.11 | YES
4 | TUBB8 | TUBB8 | TUBB8 | 557 | 0.44 | 0.15 | YES
5 | DRD2 | DRD2 | DRD2 | 634 | 0.42 | 0.18 | YES
6 | GUCY1B3 | GUCY1B3 | GUCY1B3 | 694 | 0.4 | 0.21 | YES
7 | PRKG1 | PRKG1 | PRKG1 | 748 | 0.39 | 0.24 | YES
8 | ADCY1 | ADCY1 | ADCY1 | 818 | 0.38 | 0.28 | YES
9 | GUCY1A2 | GUCY1A2 | GUCY1A2 | 945 | 0.36 | 0.3 | YES
10 | GUCY1A3 | GUCY1A3 | GUCY1A3 | 1087 | 0.34 | 0.32 | YES
11 | TUBA8 | TUBA8 | TUBA8 | 1182 | 0.32 | 0.35 | YES
12 | GRM1 | GRM1 | GRM1 | 1519 | 0.28 | 0.35 | YES
13 | PDGFRB | PDGFRB | PDGFRB | 1553 | 0.28 | 0.38 | YES
14 | PRKCG | PRKCG | PRKCG | 1565 | 0.28 | 0.4 | YES
15 | TUBB4Q | TUBB4Q | TUBB4Q | 1595 | 0.28 | 0.42 | YES
16 | TUBB1 | TUBB1 | TUBB1 | 1751 | 0.26 | 0.44 | YES
17 | TUBA3D | TUBA3D | TUBA3D | 2136 | 0.23 | 0.44 | YES
18 | PDGFC | PDGFC | PDGFC | 2282 | 0.22 | 0.45 | YES
19 | GRM5 | GRM5 | GRM5 | 2393 | 0.21 | 0.46 | YES
20 | PLCB4 | PLCB4 | PLCB4 | 2581 | 0.2 | 0.47 | YES
21 | PDGFA | PDGFA | PDGFA | 2658 | 0.2 | 0.48 | YES
22 | ADCY8 | ADCY8 | ADCY8 | 2880 | 0.18 | 0.48 | YES
23 | TUBA1A | TUBA1A | TUBA1A | 2901 | 0.18 | 0.5 | YES
24 | TUBB2B | TUBB2B | TUBB2B | 3296 | 0.16 | 0.49 | YES
25 | CDK1 | CDK1 | CDK1 | 3341 | 0.16 | 0.5 | YES
26 | HTR2B | HTR2B | HTR2B | 3407 | 0.16 | 0.51 | YES
27 | TUBA3E | TUBA3E | TUBA3E | 3448 | 0.16 | 0.53 | YES
28 | SRC | SRC | SRC | 4228 | 0.12 | 0.49 | NO
29 | ADCY4 | ADCY4 | ADCY4 | 4353 | 0.12 | 0.5 | NO
30 | ADCY6 | ADCY6 | ADCY6 | 4620 | 0.11 | 0.49 | NO
31 | TUBB4 | TUBB4 | TUBB4 | 4845 | 0.099 | 0.49 | NO
32 | TUBAL3 | TUBAL3 | TUBAL3 | 5005 | 0.094 | 0.49 | NO
33 | MAPK7 | MAPK7 | MAPK7 | 5144 | 0.09 | 0.49 | NO
34 | TUBB3 | TUBB3 | TUBB3 | 5324 | 0.086 | 0.49 | NO
35 | PRKACA | PRKACA | PRKACA | 5993 | 0.07 | 0.46 | NO
36 | PRKX | PRKX | PRKX | 6173 | 0.066 | 0.45 | NO
37 | EGF | EGF | EGF | 6437 | 0.06 | 0.44 | NO
38 | KRAS | KRAS | KRAS | 6619 | 0.056 | 0.44 | NO
39 | PRKG2 | PRKG2 | PRKG2 | 6780 | 0.053 | 0.43 | NO
40 | PDGFRA | PDGFRA | PDGFRA | 7256 | 0.045 | 0.41 | NO
41 | PDGFD | PDGFD | PDGFD | 7802 | 0.036 | 0.38 | NO
42 | GNAS | GNAS | GNAS | 7824 | 0.036 | 0.39 | NO
43 | MAP2K2 | MAP2K2 | MAP2K2 | 7827 | 0.035 | 0.39 | NO
44 | TUBA1B | TUBA1B | TUBA1B | 7874 | 0.035 | 0.39 | NO
45 | GNA11 | GNA11 | GNA11 | 7888 | 0.034 | 0.39 | NO
46 | TUBB | TUBB | TUBB | 8021 | 0.032 | 0.39 | NO
47 | ADRB1 | ADRB1 | ADRB1 | 8504 | 0.025 | 0.36 | NO
48 | TJP1 | TJP1 | TJP1 | 8602 | 0.024 | 0.36 | NO
49 | HTR2A | HTR2A | HTR2A | 8662 | 0.023 | 0.36 | NO
50 | PRKACB | PRKACB | PRKACB | 9119 | 0.016 | 0.33 | NO
51 | GNAQ | GNAQ | GNAQ | 9307 | 0.014 | 0.32 | NO
52 | ITPR2 | ITPR2 | ITPR2 | 9402 | 0.012 | 0.32 | NO
53 | PDGFB | PDGFB | PDGFB | 9762 | 0.0078 | 0.3 | NO
54 | ITPR3 | ITPR3 | ITPR3 | 9776 | 0.0076 | 0.3 | NO
55 | TUBB2C | TUBB2C | TUBB2C | 9989 | 0.0045 | 0.29 | NO
56 | GJA1 | GJA1 | GJA1 | 10030 | 0.0038 | 0.29 | NO
57 | MAPK1 | MAPK1 | MAPK1 | 10177 | 0.0018 | 0.28 | NO
58 | LPAR1 | LPAR1 | LPAR1 | 10206 | 0.0015 | 0.28 | NO
59 | RAF1 | RAF1 | RAF1 | 10279 | 0.00052 | 0.28 | NO
60 | SOS1 | SOS1 | SOS1 | 10615 | -0.004 | 0.26 | NO
61 | CSNK1D | CSNK1D | CSNK1D | 11434 | -0.016 | 0.21 | NO
62 | ADCY7 | ADCY7 | ADCY7 | 11493 | -0.017 | 0.21 | NO
63 | SOS2 | SOS2 | SOS2 | 11543 | -0.017 | 0.21 | NO
64 | MAP2K5 | MAP2K5 | MAP2K5 | 11820 | -0.021 | 0.2 | NO
65 | NRAS | NRAS | NRAS | 11996 | -0.024 | 0.19 | NO
66 | TUBB6 | TUBB6 | TUBB6 | 12010 | -0.024 | 0.19 | NO
67 | HRAS | HRAS | HRAS | 12025 | -0.024 | 0.19 | NO
68 | GNAI2 | GNAI2 | GNAI2 | 12159 | -0.027 | 0.19 | NO
69 | PLCB3 | PLCB3 | PLCB3 | 12765 | -0.036 | 0.16 | NO
70 | GRB2 | GRB2 | GRB2 | 12984 | -0.04 | 0.15 | NO
71 | ADCY9 | ADCY9 | ADCY9 | 13365 | -0.047 | 0.13 | NO
72 | GNAI3 | GNAI3 | GNAI3 | 13466 | -0.048 | 0.13 | NO
73 | ITPR1 | ITPR1 | ITPR1 | 13553 | -0.05 | 0.13 | NO
74 | MAPK3 | MAPK3 | MAPK3 | 13791 | -0.055 | 0.12 | NO
75 | TUBB2A | TUBB2A | TUBB2A | 13963 | -0.058 | 0.12 | NO
76 | MAP2K1 | MAP2K1 | MAP2K1 | 14261 | -0.065 | 0.11 | NO
77 | TUBA1C | TUBA1C | TUBA1C | 14575 | -0.072 | 0.096 | NO
78 | MAP3K2 | MAP3K2 | MAP3K2 | 14600 | -0.072 | 0.1 | NO
79 | PRKCA | PRKCA | PRKCA | 14691 | -0.075 | 0.1 | NO
80 | TUBA4A | TUBA4A | TUBA4A | 15065 | -0.084 | 0.09 | NO
81 | PLCB1 | PLCB1 | PLCB1 | 15180 | -0.088 | 0.091 | NO
82 | PLCB2 | PLCB2 | PLCB2 | 15250 | -0.089 | 0.095 | NO
83 | TUBA3C | TUBA3C | TUBA3C | 15879 | -0.11 | 0.071 | NO
84 | GNAI1 | GNAI1 | GNAI1 | 16762 | -0.16 | 0.036 | NO
85 | EGFR | EGFR | EGFR | 17086 | -0.19 | 0.036 | NO
86 | PRKCB | PRKCB | PRKCB | 17708 | -0.28 | 0.026 | NO

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

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

genes ES table in pathway: KEGG OOCYTE MEIOSIS

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 | NKD1 | NKD1 | NKD1 | 175 | 0.57 | 0.04 | YES
2 | WNT11 | WNT11 | WNT11 | 182 | 0.56 | 0.09 | YES
3 | WNT6 | WNT6 | WNT6 | 442 | 0.47 | 0.12 | YES
4 | CXXC4 | CXXC4 | CXXC4 | 559 | 0.44 | 0.15 | YES
5 | WNT5B | WNT5B | WNT5B | 568 | 0.43 | 0.19 | YES
6 | FRZB | FRZB | FRZB | 771 | 0.39 | 0.21 | YES
7 | SFRP1 | SFRP1 | SFRP1 | 944 | 0.36 | 0.23 | YES
8 | LEF1 | LEF1 | LEF1 | 1080 | 0.34 | 0.26 | YES
9 | FZD8 | FZD8 | FZD8 | 1113 | 0.34 | 0.28 | YES
10 | FZD3 | FZD3 | FZD3 | 1163 | 0.33 | 0.31 | YES
11 | WIF1 | WIF1 | WIF1 | 1258 | 0.31 | 0.33 | YES
12 | FZD2 | FZD2 | FZD2 | 1403 | 0.3 | 0.35 | YES
13 | PYGO1 | PYGO1 | PYGO1 | 1621 | 0.27 | 0.36 | YES
14 | TCF7L1 | TCF7L1 | TCF7L1 | 1669 | 0.27 | 0.38 | YES
15 | LRP6 | LRP6 | LRP6 | 1674 | 0.27 | 0.41 | YES
16 | TCF7 | TCF7 | TCF7 | 2225 | 0.22 | 0.4 | YES
17 | PITX2 | PITX2 | PITX2 | 2236 | 0.22 | 0.42 | YES
18 | TLE2 | TLE2 | TLE2 | 2321 | 0.22 | 0.43 | YES
19 | FZD7 | FZD7 | FZD7 | 2323 | 0.22 | 0.45 | YES
20 | SOX17 | SOX17 | SOX17 | 2492 | 0.21 | 0.46 | YES
21 | WNT9A | WNT9A | WNT9A | 2517 | 0.2 | 0.48 | YES
22 | WNT7B | WNT7B | WNT7B | 2808 | 0.19 | 0.48 | YES
23 | WNT7A | WNT7A | WNT7A | 3062 | 0.17 | 0.48 | YES
24 | FZD1 | FZD1 | FZD1 | 3249 | 0.16 | 0.48 | YES
25 | FZD4 | FZD4 | FZD4 | 3390 | 0.16 | 0.49 | YES
26 | CTNNBIP1 | CTNNBIP1 | CTNNBIP1 | 3456 | 0.16 | 0.5 | YES
27 | DIXDC1 | DIXDC1 | DIXDC1 | 3577 | 0.15 | 0.5 | YES
28 | BCL9 | BCL9 | BCL9 | 3928 | 0.13 | 0.5 | NO
29 | FOXN1 | FOXN1 | FOXN1 | 4459 | 0.11 | 0.48 | NO
30 | CCND1 | CCND1 | CCND1 | 4475 | 0.11 | 0.49 | NO
31 | TLE1 | TLE1 | TLE1 | 4747 | 0.1 | 0.48 | NO
32 | DVL2 | DVL2 | DVL2 | 4862 | 0.098 | 0.48 | NO
33 | FRAT1 | FRAT1 | FRAT1 | 5340 | 0.086 | 0.46 | NO
34 | WNT2B | WNT2B | WNT2B | 5759 | 0.075 | 0.45 | NO
35 | SFRP4 | SFRP4 | SFRP4 | 6080 | 0.068 | 0.44 | NO
36 | CTNNB1 | CTNNB1 | CTNNB1 | 6392 | 0.061 | 0.42 | NO
37 | WNT10A | WNT10A | WNT10A | 6453 | 0.06 | 0.43 | NO
38 | PPP2R1A | PPP2R1A | PPP2R1A | 6744 | 0.054 | 0.42 | NO
39 | AES | AES | AES | 7127 | 0.047 | 0.4 | NO
40 | GSK3A | GSK3A | GSK3A | 7218 | 0.046 | 0.4 | NO
41 | FBXW2 | FBXW2 | FBXW2 | 7257 | 0.045 | 0.4 | NO
42 | WNT1 | WNT1 | WNT1 | 7372 | 0.043 | 0.4 | NO
43 | FBXW4 | FBXW4 | FBXW4 | 7541 | 0.04 | 0.39 | NO
44 | EP300 | EP300 | EP300 | 7923 | 0.034 | 0.37 | NO
45 | FZD6 | FZD6 | FZD6 | 7981 | 0.033 | 0.37 | NO
46 | RPL13A | RPL13A | RPL13A | 7984 | 0.033 | 0.38 | NO
47 | CTBP1 | CTBP1 | CTBP1 | 8433 | 0.026 | 0.35 | NO
48 | WNT16 | WNT16 | WNT16 | 8595 | 0.024 | 0.35 | NO
49 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 8603 | 0.024 | 0.35 | NO
50 | DVL1 | DVL1 | DVL1 | 8890 | 0.02 | 0.33 | NO
51 | NLK | NLK | NLK | 9608 | 0.0097 | 0.3 | NO
52 | LRP5 | LRP5 | LRP5 | 9780 | 0.0075 | 0.29 | NO
53 | GSK3B | GSK3B | GSK3B | 10261 | 0.00077 | 0.26 | NO
54 | JUN | JUN | JUN | 10806 | -0.0068 | 0.23 | NO
55 | CTBP2 | CTBP2 | CTBP2 | 10854 | -0.0074 | 0.23 | NO
56 | WISP1 | WISP1 | WISP1 | 10927 | -0.0085 | 0.23 | NO
57 | WNT5A | WNT5A | WNT5A | 11060 | -0.01 | 0.22 | NO
58 | FBXW11 | FBXW11 | FBXW11 | 11125 | -0.011 | 0.22 | NO
59 | HPRT1 | HPRT1 | HPRT1 | 11189 | -0.012 | 0.21 | NO
60 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 11306 | -0.014 | 0.21 | NO
61 | FOSL1 | FOSL1 | FOSL1 | 11310 | -0.014 | 0.21 | NO
62 | CSNK1D | CSNK1D | CSNK1D | 11434 | -0.016 | 0.2 | NO
63 | GAPDH | GAPDH | GAPDH | 11467 | -0.016 | 0.2 | NO
64 | ACTB | ACTB | ACTB | 11675 | -0.019 | 0.2 | NO
65 | BTRC | BTRC | BTRC | 12040 | -0.025 | 0.18 | NO
66 | AXIN1 | AXIN1 | AXIN1 | 12068 | -0.025 | 0.18 | NO
67 | KREMEN1 | KREMEN1 | KREMEN1 | 12224 | -0.028 | 0.17 | NO
68 | APC | APC | APC | 12801 | -0.037 | 0.14 | NO
69 | CSNK1G1 | CSNK1G1 | CSNK1G1 | 13097 | -0.042 | 0.13 | NO
70 | PORCN | PORCN | PORCN | 13235 | -0.044 | 0.13 | NO
71 | DKK1 | DKK1 | DKK1 | 13269 | -0.045 | 0.13 | NO
72 | PPP2CA | PPP2CA | PPP2CA | 13349 | -0.046 | 0.13 | NO
73 | FZD5 | FZD5 | FZD5 | 13376 | -0.047 | 0.13 | NO
74 | CCND3 | CCND3 | CCND3 | 13540 | -0.05 | 0.13 | NO
75 | RHOU | RHOU | RHOU | 13819 | -0.055 | 0.12 | NO
76 | WNT4 | WNT4 | WNT4 | 13847 | -0.056 | 0.12 | NO
77 | SENP2 | SENP2 | SENP2 | 14833 | -0.078 | 0.072 | NO
78 | SLC9A3R1 | SLC9A3R1 | SLC9A3R1 | 15076 | -0.084 | 0.066 | NO
79 | CCND2 | CCND2 | CCND2 | 15615 | -0.1 | 0.045 | NO
80 | B2M | B2M | B2M | 16198 | -0.13 | 0.025 | NO
81 | MYC | MYC | MYC | 16802 | -0.17 | 0.0062 | NO
82 | WNT3 | WNT3 | WNT3 | 16971 | -0.18 | 0.013 | NO
83 | DAAM1 | DAAM1 | DAAM1 | 17525 | -0.25 | 0.0042 | NO
84 | WNT2 | WNT2 | WNT2 | 17956 | -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: KEGG OOCYTE MEIOSIS.

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

genes ES table in pathway: KEGG VASCULAR SMOOTH MUSCLE CONTRACTION

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 | HES5 | HES5 | HES5 | 180 | 0.56 | 0.09 | YES
2 | NOTCH3 | NOTCH3 | NOTCH3 | 658 | 0.41 | 0.14 | YES
3 | DTX1 | DTX1 | DTX1 | 803 | 0.38 | 0.2 | YES
4 | DLL1 | DLL1 | DLL1 | 1326 | 0.3 | 0.22 | YES
5 | LFNG | LFNG | LFNG | 1798 | 0.26 | 0.24 | YES
6 | NOTCH4 | NOTCH4 | NOTCH4 | 1965 | 0.24 | 0.27 | YES
7 | JAG1 | JAG1 | JAG1 | 2190 | 0.23 | 0.3 | YES
8 | HES1 | HES1 | HES1 | 2211 | 0.23 | 0.34 | YES
9 | NOTCH1 | NOTCH1 | NOTCH1 | 2473 | 0.21 | 0.36 | YES
10 | NOTCH2 | NOTCH2 | NOTCH2 | 2750 | 0.19 | 0.38 | YES
11 | JAG2 | JAG2 | JAG2 | 2990 | 0.18 | 0.4 | YES
12 | DTX3 | DTX3 | DTX3 | 3000 | 0.18 | 0.43 | YES
13 | MAML3 | MAML3 | MAML3 | 3481 | 0.15 | 0.43 | YES
14 | HDAC2 | HDAC2 | HDAC2 | 3744 | 0.14 | 0.44 | YES
15 | DLL4 | DLL4 | DLL4 | 3990 | 0.13 | 0.45 | YES
16 | DLL3 | DLL3 | DLL3 | 4520 | 0.11 | 0.44 | YES
17 | DVL2 | DVL2 | DVL2 | 4862 | 0.098 | 0.44 | YES
18 | CREBBP | CREBBP | CREBBP | 4938 | 0.096 | 0.45 | YES
19 | NUMBL | NUMBL | NUMBL | 5113 | 0.091 | 0.46 | YES
20 | RBPJ | RBPJ | RBPJ | 5470 | 0.082 | 0.45 | YES
21 | MAML1 | MAML1 | MAML1 | 5722 | 0.076 | 0.45 | YES
22 | NCOR2 | NCOR2 | NCOR2 | 5846 | 0.073 | 0.46 | YES
23 | HDAC1 | HDAC1 | HDAC1 | 6125 | 0.067 | 0.46 | YES
24 | RBPJL | RBPJL | RBPJL | 6184 | 0.066 | 0.46 | YES
25 | KAT2A | KAT2A | KAT2A | 7850 | 0.035 | 0.38 | NO
26 | EP300 | EP300 | EP300 | 7923 | 0.034 | 0.38 | NO
27 | MAML2 | MAML2 | MAML2 | 7967 | 0.033 | 0.38 | NO
28 | CTBP1 | CTBP1 | CTBP1 | 8433 | 0.026 | 0.36 | NO
29 | DVL1 | DVL1 | DVL1 | 8890 | 0.02 | 0.34 | NO
30 | NUMB | NUMB | NUMB | 9189 | 0.015 | 0.33 | NO
31 | SNW1 | SNW1 | SNW1 | 9574 | 0.01 | 0.31 | NO
32 | CTBP2 | CTBP2 | CTBP2 | 10854 | -0.0074 | 0.24 | NO
33 | NCSTN | NCSTN | NCSTN | 10947 | -0.0087 | 0.23 | NO
34 | RFNG | RFNG | RFNG | 11340 | -0.014 | 0.22 | NO
35 | PSEN1 | PSEN1 | PSEN1 | 11745 | -0.02 | 0.2 | NO
36 | CIR1 | CIR1 | CIR1 | 11769 | -0.021 | 0.2 | NO
37 | APH1A | APH1A | APH1A | 11809 | -0.021 | 0.2 | NO
38 | ADAM17 | ADAM17 | ADAM17 | 12345 | -0.029 | 0.18 | NO
39 | DTX4 | DTX4 | DTX4 | 14395 | -0.068 | 0.075 | NO
40 | PSEN2 | PSEN2 | PSEN2 | 14578 | -0.072 | 0.078 | NO
41 | PSENEN | PSENEN | PSENEN | 14645 | -0.073 | 0.087 | NO
42 | DVL3 | DVL3 | DVL3 | 14782 | -0.077 | 0.093 | NO
43 | DTX2 | DTX2 | DTX2 | 15408 | -0.095 | 0.076 | NO
44 | DTX3L | DTX3L | DTX3L | 16048 | -0.12 | 0.062 | NO
45 | KAT2B | KAT2B | KAT2B | 16515 | -0.15 | 0.062 | NO
46 | PTCRA | PTCRA | PTCRA | 16855 | -0.17 | 0.073 | NO

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

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

genes ES table in pathway: KEGG WNT SIGNALING PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | ZIC2 | ZIC2 | ZIC2 | 58 | 0.68 | 0.06 | YES
2 | PTCH2 | PTCH2 | PTCH2 | 59 | 0.68 | 0.12 | YES
3 | GLI1 | GLI1 | GLI1 | 99 | 0.62 | 0.18 | YES
4 | WNT11 | WNT11 | WNT11 | 182 | 0.56 | 0.22 | YES
5 | PTCH1 | PTCH1 | PTCH1 | 220 | 0.54 | 0.27 | YES
6 | BMP7 | BMP7 | BMP7 | 262 | 0.52 | 0.32 | YES
7 | BMP6 | BMP6 | BMP6 | 342 | 0.49 | 0.36 | YES
8 | HHIP | HHIP | HHIP | 434 | 0.47 | 0.4 | YES
9 | WNT6 | WNT6 | WNT6 | 442 | 0.47 | 0.44 | YES
10 | WNT5B | WNT5B | WNT5B | 568 | 0.43 | 0.47 | YES
11 | WNT10B | WNT10B | WNT10B | 826 | 0.38 | 0.5 | YES
12 | BMP5 | BMP5 | BMP5 | 934 | 0.36 | 0.52 | YES
13 | SMO | SMO | SMO | 1285 | 0.31 | 0.53 | YES
14 | BMP8A | BMP8A | BMP8A | 1505 | 0.28 | 0.55 | YES
15 | GLI2 | GLI2 | GLI2 | 1960 | 0.24 | 0.54 | YES
16 | BMP8B | BMP8B | BMP8B | 2342 | 0.22 | 0.54 | YES
17 | RAB23 | RAB23 | RAB23 | 2439 | 0.21 | 0.56 | YES
18 | WNT9A | WNT9A | WNT9A | 2517 | 0.2 | 0.57 | YES
19 | WNT7B | WNT7B | WNT7B | 2808 | 0.19 | 0.57 | YES
20 | WNT8B | WNT8B | WNT8B | 2867 | 0.18 | 0.59 | YES
21 | DHH | DHH | DHH | 3036 | 0.17 | 0.59 | YES
22 | WNT7A | WNT7A | WNT7A | 3062 | 0.17 | 0.61 | YES
23 | SHH | SHH | SHH | 3229 | 0.16 | 0.61 | YES
24 | IHH | IHH | IHH | 3656 | 0.15 | 0.6 | NO
25 | GLI3 | GLI3 | GLI3 | 4216 | 0.12 | 0.58 | NO
26 | CSNK1E | CSNK1E | CSNK1E | 4763 | 0.1 | 0.56 | NO
27 | STK36 | STK36 | STK36 | 5190 | 0.089 | 0.55 | NO
28 | WNT2B | WNT2B | WNT2B | 5759 | 0.075 | 0.52 | NO
29 | PRKACA | PRKACA | PRKACA | 5993 | 0.07 | 0.52 | NO
30 | PRKX | PRKX | PRKX | 6173 | 0.066 | 0.51 | NO
31 | WNT10A | WNT10A | WNT10A | 6453 | 0.06 | 0.5 | NO
32 | CSNK1G2 | CSNK1G2 | CSNK1G2 | 6787 | 0.053 | 0.49 | NO
33 | WNT1 | WNT1 | WNT1 | 7372 | 0.043 | 0.46 | NO
34 | BMP4 | BMP4 | BMP4 | 7608 | 0.039 | 0.45 | NO
35 | WNT16 | WNT16 | WNT16 | 8595 | 0.024 | 0.4 | NO
36 | SUFU | SUFU | SUFU | 9006 | 0.018 | 0.38 | NO
37 | PRKACB | PRKACB | PRKACB | 9119 | 0.016 | 0.38 | NO
38 | CSNK1G3 | CSNK1G3 | CSNK1G3 | 9649 | 0.0092 | 0.35 | NO
39 | GSK3B | GSK3B | GSK3B | 10261 | 0.00077 | 0.31 | NO
40 | WNT5A | WNT5A | WNT5A | 11060 | -0.01 | 0.27 | NO
41 | FBXW11 | FBXW11 | FBXW11 | 11125 | -0.011 | 0.27 | NO
42 | CSNK1A1 | CSNK1A1 | CSNK1A1 | 11306 | -0.014 | 0.26 | NO
43 | CSNK1D | CSNK1D | CSNK1D | 11434 | -0.016 | 0.25 | NO
44 | LRP2 | LRP2 | LRP2 | 11879 | -0.022 | 0.23 | NO
45 | BTRC | BTRC | BTRC | 12040 | -0.025 | 0.22 | NO
46 | CSNK1G1 | CSNK1G1 | CSNK1G1 | 13097 | -0.042 | 0.17 | NO
47 | WNT4 | WNT4 | WNT4 | 13847 | -0.056 | 0.13 | NO
48 | BMP2 | BMP2 | BMP2 | 15717 | -0.11 | 0.04 | NO
49 | CSNK1A1L | CSNK1A1L | CSNK1A1L | 16253 | -0.13 | 0.023 | NO
50 | WNT9B | WNT9B | WNT9B | 16726 | -0.16 | 0.012 | NO
51 | WNT3 | WNT3 | WNT3 | 16971 | -0.18 | 0.015 | NO
52 | GAS1 | GAS1 | GAS1 | 17133 | -0.2 | 0.024 | NO
53 | WNT2 | WNT2 | WNT2 | 17956 | -0.36 | 0.013 | NO

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

Figure S78. 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 NOTCH SIGNALING PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | CAMK2B | CAMK2B | CAMK2B | 117 | 0.6 | 0.076 | YES
2 | CALML3 | CALML3 | CALML3 | 455 | 0.46 | 0.12 | YES
3 | PPP1R1A | PPP1R1A | PPP1R1A | 707 | 0.4 | 0.16 | YES
4 | CALML5 | CALML5 | CALML5 | 948 | 0.36 | 0.2 | YES
5 | RPS6KA6 | RPS6KA6 | RPS6KA6 | 1079 | 0.34 | 0.24 | YES
6 | GRM1 | GRM1 | GRM1 | 1519 | 0.28 | 0.25 | YES
7 | PRKCG | PRKCG | PRKCG | 1565 | 0.28 | 0.29 | YES
8 | RAPGEF3 | RAPGEF3 | RAPGEF3 | 2288 | 0.22 | 0.28 | YES
9 | GRM5 | GRM5 | GRM5 | 2393 | 0.21 | 0.3 | YES
10 | GRIN2A | GRIN2A | GRIN2A | 2435 | 0.21 | 0.33 | YES
11 | GRIA1 | GRIA1 | GRIA1 | 2442 | 0.21 | 0.36 | YES
12 | CACNA1C | CACNA1C | CACNA1C | 2548 | 0.2 | 0.38 | YES
13 | PLCB4 | PLCB4 | PLCB4 | 2581 | 0.2 | 0.4 | YES
14 | GRIN2C | GRIN2C | GRIN2C | 2701 | 0.19 | 0.42 | YES
15 | CAMK2A | CAMK2A | CAMK2A | 2773 | 0.19 | 0.44 | YES
16 | ADCY8 | ADCY8 | ADCY8 | 2880 | 0.18 | 0.46 | YES
17 | CAMK4 | CAMK4 | CAMK4 | 4201 | 0.12 | 0.41 | NO
18 | CAMK2G | CAMK2G | CAMK2G | 4325 | 0.12 | 0.42 | NO
19 | CREBBP | CREBBP | CREBBP | 4938 | 0.096 | 0.4 | NO
20 | PPP3CA | PPP3CA | PPP3CA | 5165 | 0.09 | 0.4 | NO
21 | CALM1 | CALM1 | CALM1 | 5734 | 0.076 | 0.38 | NO
22 | GRIN2D | GRIN2D | GRIN2D | 5884 | 0.073 | 0.38 | NO
23 | PRKACA | PRKACA | PRKACA | 5993 | 0.07 | 0.38 | NO
24 | PRKX | PRKX | PRKX | 6173 | 0.066 | 0.38 | NO
25 | KRAS | KRAS | KRAS | 6619 | 0.056 | 0.36 | NO
26 | CAMK2D | CAMK2D | CAMK2D | 7324 | 0.044 | 0.33 | NO
27 | PPP3CB | PPP3CB | PPP3CB | 7754 | 0.037 | 0.31 | NO
28 | GRIN1 | GRIN1 | GRIN1 | 7776 | 0.036 | 0.32 | NO
29 | MAP2K2 | MAP2K2 | MAP2K2 | 7827 | 0.035 | 0.32 | NO
30 | CALM3 | CALM3 | CALM3 | 7916 | 0.034 | 0.32 | NO
31 | EP300 | EP300 | EP300 | 7923 | 0.034 | 0.32 | NO
32 | PPP3R1 | PPP3R1 | PPP3R1 | 8236 | 0.029 | 0.31 | NO
33 | PPP1R12A | PPP1R12A | PPP1R12A | 8927 | 0.019 | 0.27 | NO
34 | GRIA2 | GRIA2 | GRIA2 | 9016 | 0.018 | 0.27 | NO
35 | PRKACB | PRKACB | PRKACB | 9119 | 0.016 | 0.27 | NO
36 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 9215 | 0.015 | 0.26 | NO
37 | GNAQ | GNAQ | GNAQ | 9307 | 0.014 | 0.26 | NO
38 | ITPR2 | ITPR2 | ITPR2 | 9402 | 0.012 | 0.26 | NO
39 | ITPR3 | ITPR3 | ITPR3 | 9776 | 0.0076 | 0.24 | NO
40 | PPP1CC | PPP1CC | PPP1CC | 9852 | 0.0064 | 0.24 | NO
41 | ATF4 | ATF4 | ATF4 | 9860 | 0.0063 | 0.24 | NO
42 | MAPK1 | MAPK1 | MAPK1 | 10177 | 0.0018 | 0.22 | NO
43 | RAF1 | RAF1 | RAF1 | 10279 | 0.00052 | 0.21 | NO
44 | CALML6 | CALML6 | CALML6 | 10900 | -0.0081 | 0.18 | NO
45 | PPP1CB | PPP1CB | PPP1CB | 11761 | -0.021 | 0.14 | NO
46 | BRAF | BRAF | BRAF | 11891 | -0.022 | 0.13 | NO
47 | ARAF | ARAF | ARAF | 11967 | -0.024 | 0.13 | NO
48 | CALM2 | CALM2 | CALM2 | 11968 | -0.024 | 0.13 | NO
49 | NRAS | NRAS | NRAS | 11996 | -0.024 | 0.14 | NO
50 | HRAS | HRAS | HRAS | 12025 | -0.024 | 0.14 | NO
51 | RAP1B | RAP1B | RAP1B | 12402 | -0.03 | 0.12 | NO
52 | CHP2 | CHP2 | CHP2 | 12459 | -0.031 | 0.12 | NO
53 | PLCB3 | PLCB3 | PLCB3 | 12765 | -0.036 | 0.11 | NO
54 | PPP1CA | PPP1CA | PPP1CA | 12820 | -0.037 | 0.11 | NO
55 | ITPR1 | ITPR1 | ITPR1 | 13553 | -0.05 | 0.077 | NO
56 | PPP3CC | PPP3CC | PPP3CC | 13594 | -0.051 | 0.082 | NO
57 | MAPK3 | MAPK3 | MAPK3 | 13791 | -0.055 | 0.079 | NO
58 | MAP2K1 | MAP2K1 | MAP2K1 | 14261 | -0.065 | 0.062 | NO
59 | PRKCA | PRKCA | PRKCA | 14691 | -0.075 | 0.048 | NO
60 | GRIN2B | GRIN2B | GRIN2B | 15067 | -0.084 | 0.039 | NO
61 | PLCB1 | PLCB1 | PLCB1 | 15180 | -0.088 | 0.045 | NO
62 | PLCB2 | PLCB2 | PLCB2 | 15250 | -0.089 | 0.053 | NO
63 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 15433 | -0.096 | 0.056 | NO
64 | RAP1A | RAP1A | RAP1A | 15449 | -0.096 | 0.069 | NO
65 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 16244 | -0.13 | 0.043 | NO
66 | CHP | CHP | CHP | 17054 | -0.19 | 0.024 | NO
67 | PRKCB | PRKCB | PRKCB | 17708 | -0.28 | 0.026 | NO

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

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

Fold change

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

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

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

Expression level

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

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

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

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

Significant gene list

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

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

Methods & Data
Input

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

- Expression data file = 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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