GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in DLBC-TP
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C10P0Z10
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 DLBC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C10P0Z10
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 DLBC-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: 188
Number of samples: 28
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 2 :[ clus1 ] 15
pheno.type: 2 - 2 :[ clus2 ] 13

For the expression subtypes of 17576 genes in 29 samples, GSEA found enriched gene sets in each cluster using 28 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

- clus1

- Top enriched gene sets are BIOCARTA INFLAM PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA IL1R PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG PYRIMIDINE METABOLISM, KEGG LYSINE DEGRADATION, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG PYRUVATE METABOLISM

- And common core enriched genes are GMPPB, HK2, HK3, DLST, AMDHD2, CHIA, CHIT1, GALE, GALK1, GFPT2

- clus2

- Top enriched gene sets are BIOCARTA ALK PATHWAY, BIOCARTA CARM ER PATHWAY, BIOCARTA GH PATHWAY, BIOCARTA TCR PATHWAY, KEGG FATTY ACID METABOLISM, KEGG ABC TRANSPORTERS, KEGG CARDIAC MUSCLE CONTRACTION, KEGG WNT SIGNALING PATHWAY, KEGG CELL ADHESION MOLECULES CAMS, KEGG INTESTINAL IMMUNE NETWORK FOR IGA PRODUCTION

- And common core enriched genes are CDH1, LEF1, TCF7, TCF7L1, GH1, HNF1A, IRS1, PLCG1, PRKCA, PRKCB

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 INFLAM PATHWAY | 25 | genes.ES.table | 0.58 | 1.3 | 0.1 | 0.56 | 0.97 | 0.4 | 0.19 | 0.32 | 0.51 | 0.12
BIOCARTA RACCYCD PATHWAY | 25 | genes.ES.table | 0.42 | 1.5 | 0.071 | 0.41 | 0.84 | 0.52 | 0.36 | 0.34 | 0.31 | 0.083
BIOCARTA IL1R PATHWAY | 31 | genes.ES.table | 0.55 | 1.5 | 0.067 | 0.39 | 0.89 | 0.36 | 0.19 | 0.29 | 0.31 | 0.053
KEGG CITRATE CYCLE TCA CYCLE | 29 | genes.ES.table | 0.49 | 1.7 | 0.034 | 0.41 | 0.42 | 0.59 | 0.34 | 0.39 | 0 | 0.14
KEGG PENTOSE PHOSPHATE PATHWAY | 26 | genes.ES.table | 0.52 | 1.4 | 0.15 | 0.54 | 0.96 | 0.58 | 0.25 | 0.43 | 0.48 | 0.11
KEGG FRUCTOSE AND MANNOSE METABOLISM | 32 | genes.ES.table | 0.52 | 1.7 | 0.012 | 0.31 | 0.46 | 0.34 | 0.2 | 0.28 | 0 | 0.082
KEGG PYRIMIDINE METABOLISM | 97 | genes.ES.table | 0.35 | 1.5 | 0.054 | 0.43 | 0.83 | 0.3 | 0.22 | 0.23 | 0.32 | 0.098
KEGG LYSINE DEGRADATION | 43 | genes.ES.table | 0.43 | 1.7 | 0.026 | 0.32 | 0.56 | 0.37 | 0.24 | 0.28 | 0.17 | 0.078
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM | 43 | genes.ES.table | 0.51 | 1.9 | 0.0098 | 0.12 | 0.086 | 0.51 | 0.26 | 0.38 | 0 | 0.046
KEGG PYRUVATE METABOLISM | 37 | genes.ES.table | 0.41 | 1.3 | 0.16 | 0.59 | 0.97 | 0.43 | 0.24 | 0.33 | 0.53 | 0.14

genes ES table in pathway: BIOCARTA INFLAM 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 | HK3 | HK3 | HK3 | 184 | 0.49 | 0.1 | YES
2 | GFPT2 | GFPT2 | GFPT2 | 206 | 0.48 | 0.21 | YES
3 | CHIT1 | CHIT1 | CHIT1 | 491 | 0.36 | 0.28 | YES
4 | NPL | NPL | NPL | 1329 | 0.21 | 0.28 | YES
5 | HEXB | HEXB | HEXB | 1685 | 0.18 | 0.3 | YES
6 | HK2 | HK2 | HK2 | 1761 | 0.17 | 0.33 | YES
7 | PGM3 | PGM3 | PGM3 | 1806 | 0.17 | 0.37 | YES
8 | GMPPB | GMPPB | GMPPB | 2421 | 0.13 | 0.37 | YES
9 | PGM2 | PGM2 | PGM2 | 2525 | 0.12 | 0.39 | YES
10 | PGM1 | PGM1 | PGM1 | 2853 | 0.11 | 0.39 | YES
11 | GALE | GALE | GALE | 3056 | 0.1 | 0.41 | YES
12 | CHIA | CHIA | CHIA | 3152 | 0.096 | 0.42 | YES
13 | GALK1 | GALK1 | GALK1 | 3266 | 0.091 | 0.44 | YES
14 | HEXA | HEXA | HEXA | 3274 | 0.091 | 0.46 | YES
15 | RENBP | RENBP | RENBP | 3292 | 0.09 | 0.48 | YES
16 | GNE | GNE | GNE | 3547 | 0.08 | 0.48 | YES
17 | UGP2 | UGP2 | UGP2 | 3705 | 0.076 | 0.49 | YES
18 | UAP1 | UAP1 | UAP1 | 3822 | 0.072 | 0.5 | YES
19 | HK1 | HK1 | HK1 | 4210 | 0.061 | 0.49 | YES
20 | AMDHD2 | AMDHD2 | AMDHD2 | 4284 | 0.058 | 0.5 | YES
21 | GNPNAT1 | GNPNAT1 | GNPNAT1 | 4525 | 0.052 | 0.5 | YES
22 | PMM2 | PMM2 | PMM2 | 4571 | 0.051 | 0.51 | YES
23 | GPI | GPI | GPI | 5231 | 0.037 | 0.48 | NO
24 | GMPPA | GMPPA | GMPPA | 5563 | 0.031 | 0.47 | NO
25 | UGDH | UGDH | UGDH | 5679 | 0.029 | 0.47 | NO
26 | CMAS | CMAS | CMAS | 5939 | 0.024 | 0.46 | NO
27 | PMM1 | PMM1 | PMM1 | 6015 | 0.023 | 0.46 | NO
28 | CYB5R1 | CYB5R1 | CYB5R1 | 6193 | 0.02 | 0.45 | NO
29 | MPI | MPI | MPI | 6279 | 0.019 | 0.45 | NO
30 | GMDS | GMDS | GMDS | 6590 | 0.014 | 0.44 | NO
31 | GALK2 | GALK2 | GALK2 | 6744 | 0.012 | 0.43 | NO
32 | NANS | NANS | NANS | 6903 | 0.0097 | 0.42 | NO
33 | NANP | NANP | NANP | 6958 | 0.0089 | 0.42 | NO
34 | FPGT | FPGT | FPGT | 8567 | -0.013 | 0.34 | NO
35 | GFPT1 | GFPT1 | GFPT1 | 9707 | -0.029 | 0.28 | NO
36 | TSTA3 | TSTA3 | TSTA3 | 10251 | -0.038 | 0.25 | NO
37 | NAGK | NAGK | NAGK | 10351 | -0.039 | 0.26 | NO
38 | UXS1 | UXS1 | UXS1 | 10551 | -0.043 | 0.26 | NO
39 | GNPDA2 | GNPDA2 | GNPDA2 | 11170 | -0.054 | 0.23 | NO
40 | GALT | GALT | GALT | 11503 | -0.061 | 0.23 | NO
41 | GNPDA1 | GNPDA1 | GNPDA1 | 12057 | -0.074 | 0.21 | NO
42 | FUK | FUK | FUK | 12350 | -0.08 | 0.22 | NO
43 | GCK | GCK | GCK | 16631 | -0.36 | 0.053 | 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 INFLAM PATHWAY.

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

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | PC | PC | PC | 781 | 0.29 | 0.12 | YES
2 | ACO1 | ACO1 | ACO1 | 908 | 0.27 | 0.26 | YES
3 | IDH1 | IDH1 | IDH1 | 1681 | 0.18 | 0.32 | YES
4 | PCK2 | PCK2 | PCK2 | 2970 | 0.1 | 0.3 | YES
5 | DLAT | DLAT | DLAT | 3464 | 0.083 | 0.32 | YES
6 | IDH3A | IDH3A | IDH3A | 3625 | 0.078 | 0.36 | YES
7 | DLST | DLST | DLST | 3955 | 0.068 | 0.38 | YES
8 | PCK1 | PCK1 | PCK1 | 4162 | 0.062 | 0.4 | YES
9 | ACLY | ACLY | ACLY | 4448 | 0.054 | 0.41 | YES
10 | SDHB | SDHB | SDHB | 4818 | 0.045 | 0.42 | YES
11 | SDHA | SDHA | SDHA | 4826 | 0.045 | 0.44 | YES
12 | IDH2 | IDH2 | IDH2 | 4958 | 0.042 | 0.46 | YES
13 | CS | CS | CS | 5280 | 0.036 | 0.46 | YES
14 | SUCLA2 | SUCLA2 | SUCLA2 | 5408 | 0.034 | 0.47 | YES
15 | DLD | DLD | DLD | 5438 | 0.033 | 0.49 | YES
16 | MDH2 | MDH2 | MDH2 | 5858 | 0.025 | 0.48 | YES
17 | SDHD | SDHD | SDHD | 5899 | 0.025 | 0.49 | YES
18 | SDHC | SDHC | SDHC | 6418 | 0.017 | 0.47 | NO
19 | MDH1 | MDH1 | MDH1 | 6746 | 0.012 | 0.46 | NO
20 | OGDH | OGDH | OGDH | 7606 | 0.000046 | 0.41 | NO
21 | SUCLG1 | SUCLG1 | SUCLG1 | 7785 | -0.0025 | 0.4 | NO
22 | SUCLG2 | SUCLG2 | SUCLG2 | 7997 | -0.0057 | 0.39 | NO
23 | IDH3B | IDH3B | IDH3B | 8122 | -0.0073 | 0.39 | NO
24 | PDHA1 | PDHA1 | PDHA1 | 8231 | -0.0087 | 0.39 | NO
25 | ACO2 | ACO2 | ACO2 | 8675 | -0.015 | 0.37 | NO
26 | PDHB | PDHB | PDHB | 8908 | -0.018 | 0.36 | NO
27 | IDH3G | IDH3G | IDH3G | 9764 | -0.03 | 0.33 | NO
28 | FH | FH | FH | 11210 | -0.055 | 0.28 | NO
29 | OGDHL | OGDHL | OGDHL | 14234 | -0.14 | 0.19 | NO

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

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

genes ES table in pathway: BIOCARTA IL1R PATHWAY

Table S3. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | HK3 | HK3 | HK3 | 184 | 0.49 | 0.14 | YES
2 | PFKFB3 | PFKFB3 | PFKFB3 | 341 | 0.41 | 0.26 | YES
3 | PFKFB4 | PFKFB4 | PFKFB4 | 363 | 0.4 | 0.38 | YES
4 | FBP1 | FBP1 | FBP1 | 1135 | 0.24 | 0.4 | YES
5 | HK2 | HK2 | HK2 | 1761 | 0.17 | 0.42 | YES
6 | PFKP | PFKP | PFKP | 2333 | 0.14 | 0.43 | YES
7 | GMPPB | GMPPB | GMPPB | 2421 | 0.13 | 0.46 | YES
8 | SORD | SORD | SORD | 2675 | 0.12 | 0.48 | YES
9 | AKR1B1 | AKR1B1 | AKR1B1 | 3035 | 0.1 | 0.5 | YES
10 | ALDOB | ALDOB | ALDOB | 3165 | 0.095 | 0.52 | YES
11 | TPI1 | TPI1 | TPI1 | 3484 | 0.082 | 0.52 | YES
12 | HK1 | HK1 | HK1 | 4210 | 0.061 | 0.5 | NO
13 | PMM2 | PMM2 | PMM2 | 4571 | 0.051 | 0.5 | NO
14 | MTMR2 | MTMR2 | MTMR2 | 5153 | 0.038 | 0.47 | NO
15 | MTMR6 | MTMR6 | MTMR6 | 5508 | 0.032 | 0.46 | NO
16 | GMPPA | GMPPA | GMPPA | 5563 | 0.031 | 0.47 | NO
17 | PMM1 | PMM1 | PMM1 | 6015 | 0.023 | 0.45 | NO
18 | MPI | MPI | MPI | 6279 | 0.019 | 0.44 | NO
19 | GMDS | GMDS | GMDS | 6590 | 0.014 | 0.43 | NO
20 | PFKL | PFKL | PFKL | 7251 | 0.0048 | 0.39 | NO
21 | PHPT1 | PHPT1 | PHPT1 | 7672 | -0.00097 | 0.37 | NO
22 | ALDOC | ALDOC | ALDOC | 7829 | -0.0029 | 0.36 | NO
23 | PFKM | PFKM | PFKM | 7872 | -0.0035 | 0.36 | NO
24 | FPGT | FPGT | FPGT | 8567 | -0.013 | 0.32 | NO
25 | KHK | KHK | KHK | 9270 | -0.023 | 0.29 | NO
26 | TSTA3 | TSTA3 | TSTA3 | 10251 | -0.038 | 0.24 | NO
27 | PFKFB2 | PFKFB2 | PFKFB2 | 10279 | -0.038 | 0.26 | NO
28 | MTMR1 | MTMR1 | MTMR1 | 11123 | -0.053 | 0.22 | NO
29 | MTMR7 | MTMR7 | MTMR7 | 11216 | -0.055 | 0.24 | NO
30 | FUK | FUK | FUK | 12350 | -0.08 | 0.2 | NO
31 | PFKFB1 | PFKFB1 | PFKFB1 | 14620 | -0.17 | 0.12 | NO
32 | FBP2 | FBP2 | FBP2 | 14687 | -0.17 | 0.16 | NO

Figure S5. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL1R PATHWAY.

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL1R 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 CITRATE CYCLE TCA CYCLE

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 | PLOD2 | PLOD2 | PLOD2 | 62 | 0.64 | 0.2 | YES
2 | BBOX1 | BBOX1 | BBOX1 | 1809 | 0.17 | 0.15 | YES
3 | PLOD1 | PLOD1 | PLOD1 | 1875 | 0.17 | 0.2 | YES
4 | ACAT2 | ACAT2 | ACAT2 | 2358 | 0.13 | 0.21 | YES
5 | PIPOX | PIPOX | PIPOX | 2453 | 0.13 | 0.25 | YES
6 | TMLHE | TMLHE | TMLHE | 2495 | 0.12 | 0.29 | YES
7 | ACAT1 | ACAT1 | ACAT1 | 3195 | 0.094 | 0.28 | YES
8 | SUV39H2 | SUV39H2 | SUV39H2 | 3254 | 0.092 | 0.3 | YES
9 | PLOD3 | PLOD3 | PLOD3 | 3332 | 0.089 | 0.32 | YES
10 | ALDH2 | ALDH2 | ALDH2 | 3701 | 0.076 | 0.33 | YES
11 | SETD7 | SETD7 | SETD7 | 3770 | 0.074 | 0.35 | YES
12 | DLST | DLST | DLST | 3955 | 0.068 | 0.36 | YES
13 | WHSC1L1 | WHSC1L1 | WHSC1L1 | 4025 | 0.066 | 0.38 | YES
14 | SUV39H1 | SUV39H1 | SUV39H1 | 4029 | 0.066 | 0.4 | YES
15 | SETD8 | SETD8 | SETD8 | 4128 | 0.063 | 0.41 | YES
16 | ALDH1B1 | ALDH1B1 | ALDH1B1 | 4193 | 0.061 | 0.42 | YES
17 | WHSC1 | WHSC1 | WHSC1 | 6056 | 0.022 | 0.33 | NO
18 | HADHA | HADHA | HADHA | 6221 | 0.02 | 0.32 | NO
19 | AASDH | AASDH | AASDH | 6911 | 0.0096 | 0.29 | NO
20 | HADH | HADH | HADH | 7113 | 0.0065 | 0.28 | NO
21 | SETMAR | SETMAR | SETMAR | 7197 | 0.0056 | 0.27 | NO
22 | SETDB2 | SETDB2 | SETDB2 | 7432 | 0.0023 | 0.26 | NO
23 | SUV420H1 | SUV420H1 | SUV420H1 | 7438 | 0.0022 | 0.26 | NO
24 | OGDH | OGDH | OGDH | 7606 | 0.000046 | 0.25 | NO
25 | GCDH | GCDH | GCDH | 8309 | -0.0097 | 0.22 | NO
26 | AASDHPPT | AASDHPPT | AASDHPPT | 8533 | -0.013 | 0.21 | NO
27 | NSD1 | NSD1 | NSD1 | 8629 | -0.014 | 0.21 | NO
28 | SETD2 | SETD2 | SETD2 | 8730 | -0.016 | 0.2 | NO
29 | DOT1L | DOT1L | DOT1L | 8795 | -0.016 | 0.21 | NO
30 | AADAT | AADAT | AADAT | 9739 | -0.03 | 0.16 | NO
31 | SETD1A | SETD1A | SETD1A | 10030 | -0.034 | 0.16 | NO
32 | ECHS1 | ECHS1 | ECHS1 | 10113 | -0.036 | 0.16 | NO
33 | ALDH9A1 | ALDH9A1 | ALDH9A1 | 10370 | -0.04 | 0.16 | NO
34 | ALDH3A2 | ALDH3A2 | ALDH3A2 | 10635 | -0.044 | 0.16 | NO
35 | SETDB1 | SETDB1 | SETDB1 | 10956 | -0.05 | 0.16 | NO
36 | ALDH7A1 | ALDH7A1 | ALDH7A1 | 11372 | -0.058 | 0.15 | NO
37 | AASS | AASS | AASS | 12202 | -0.077 | 0.13 | NO
38 | SUV420H2 | SUV420H2 | SUV420H2 | 12235 | -0.078 | 0.15 | NO
39 | EHMT1 | EHMT1 | EHMT1 | 12265 | -0.079 | 0.17 | NO
40 | SETD1B | SETD1B | SETD1B | 12284 | -0.079 | 0.2 | NO
41 | EHMT2 | EHMT2 | EHMT2 | 12352 | -0.08 | 0.22 | NO
42 | ASH1L | ASH1L | ASH1L | 13147 | -0.1 | 0.21 | NO
43 | OGDHL | OGDHL | OGDHL | 14234 | -0.14 | 0.19 | 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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

Table 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 | DNA2 | DNA2 | DNA2 | 1691 | 0.18 | -0.0058 | YES
2 | POLE2 | POLE2 | POLE2 | 2093 | 0.15 | 0.047 | YES
3 | PRIM1 | PRIM1 | PRIM1 | 2329 | 0.14 | 0.1 | YES
4 | POLD3 | POLD3 | POLD3 | 2594 | 0.12 | 0.15 | YES
5 | MCM4 | MCM4 | MCM4 | 2739 | 0.11 | 0.2 | YES
6 | POLA2 | POLA2 | POLA2 | 2949 | 0.1 | 0.24 | YES
7 | RPA3 | RPA3 | RPA3 | 3143 | 0.096 | 0.28 | YES
8 | POLD1 | POLD1 | POLD1 | 3530 | 0.081 | 0.3 | YES
9 | MCM6 | MCM6 | MCM6 | 3739 | 0.074 | 0.32 | YES
10 | FEN1 | FEN1 | FEN1 | 3859 | 0.071 | 0.35 | YES
11 | PRIM2 | PRIM2 | PRIM2 | 3912 | 0.069 | 0.38 | YES
12 | MCM3 | MCM3 | MCM3 | 3921 | 0.069 | 0.42 | YES
13 | RNASEH1 | RNASEH1 | RNASEH1 | 3925 | 0.069 | 0.45 | YES
14 | RFC4 | RFC4 | RFC4 | 3927 | 0.069 | 0.49 | YES
15 | PCNA | PCNA | PCNA | 4004 | 0.067 | 0.52 | YES
16 | RFC3 | RFC3 | RFC3 | 4251 | 0.059 | 0.53 | YES
17 | RFC5 | RFC5 | RFC5 | 4434 | 0.054 | 0.55 | YES
18 | MCM7 | MCM7 | MCM7 | 4568 | 0.051 | 0.57 | YES
19 | RNASEH2A | RNASEH2A | RNASEH2A | 4685 | 0.048 | 0.58 | YES
20 | MCM2 | MCM2 | MCM2 | 4806 | 0.046 | 0.6 | YES
21 | POLE | POLE | POLE | 5570 | 0.031 | 0.57 | NO
22 | POLD4 | POLD4 | POLD4 | 5594 | 0.03 | 0.59 | NO
23 | LIG1 | LIG1 | LIG1 | 5868 | 0.025 | 0.58 | NO
24 | RFC2 | RFC2 | RFC2 | 6034 | 0.023 | 0.58 | NO
25 | RFC1 | RFC1 | RFC1 | 7152 | 0.006 | 0.52 | NO
26 | POLD2 | POLD2 | POLD2 | 7301 | 0.004 | 0.52 | NO
27 | RNASEH2C | RNASEH2C | RNASEH2C | 7421 | 0.0024 | 0.51 | NO
28 | MCM5 | MCM5 | MCM5 | 7501 | 0.0014 | 0.51 | NO
29 | POLE3 | POLE3 | POLE3 | 7511 | 0.0012 | 0.51 | NO
30 | RPA4 | RPA4 | RPA4 | 7892 | -0.0038 | 0.49 | NO
31 | SSBP1 | SSBP1 | SSBP1 | 7980 | -0.0054 | 0.49 | NO
32 | RPA2 | RPA2 | RPA2 | 8696 | -0.015 | 0.45 | NO
33 | POLE4 | POLE4 | POLE4 | 9381 | -0.025 | 0.43 | NO
34 | RPA1 | RPA1 | RPA1 | 9885 | -0.032 | 0.42 | NO
35 | RNASEH2B | RNASEH2B | RNASEH2B | 10736 | -0.046 | 0.39 | 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 PENTOSE PHOSPHATE PATHWAY.

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

Table 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 | SLC11A1 | SLC11A1 | SLC11A1 | 8 | 0.88 | 0.077 | YES
2 | CTSK | CTSK | CTSK | 430 | 0.38 | 0.087 | YES
3 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 666 | 0.32 | 0.1 | YES
4 | CTSL1 | CTSL1 | CTSL1 | 921 | 0.27 | 0.11 | YES
5 | GLA | GLA | GLA | 1087 | 0.24 | 0.12 | YES
6 | CTSB | CTSB | CTSB | 1337 | 0.21 | 0.13 | YES
7 | HEXB | HEXB | HEXB | 1685 | 0.18 | 0.12 | YES
8 | GALC | GALC | GALC | 1801 | 0.17 | 0.13 | YES
9 | ARSB | ARSB | ARSB | 1837 | 0.17 | 0.14 | YES
10 | CTSW | CTSW | CTSW | 1913 | 0.16 | 0.16 | YES
11 | SCARB2 | SCARB2 | SCARB2 | 1938 | 0.16 | 0.17 | YES
12 | SORT1 | SORT1 | SORT1 | 1951 | 0.16 | 0.18 | YES
13 | ACP5 | ACP5 | ACP5 | 2050 | 0.15 | 0.19 | YES
14 | ACP2 | ACP2 | ACP2 | 2105 | 0.15 | 0.2 | YES
15 | CTSD | CTSD | CTSD | 2110 | 0.15 | 0.21 | YES
16 | CD68 | CD68 | CD68 | 2196 | 0.14 | 0.22 | YES
17 | GLB1 | GLB1 | GLB1 | 2245 | 0.14 | 0.23 | YES
18 | PSAP | PSAP | PSAP | 2385 | 0.13 | 0.23 | YES
19 | SLC17A5 | SLC17A5 | SLC17A5 | 2398 | 0.13 | 0.24 | YES
20 | NPC1 | NPC1 | NPC1 | 2475 | 0.13 | 0.25 | YES
21 | GNS | GNS | GNS | 2481 | 0.13 | 0.26 | YES
22 | LAMP2 | LAMP2 | LAMP2 | 2581 | 0.12 | 0.27 | YES
23 | ASAH1 | ASAH1 | ASAH1 | 2600 | 0.12 | 0.28 | YES
24 | DNASE2B | DNASE2B | DNASE2B | 2711 | 0.12 | 0.28 | YES
25 | ATP6V1H | ATP6V1H | ATP6V1H | 2759 | 0.11 | 0.29 | YES
26 | GALNS | GALNS | GALNS | 2851 | 0.11 | 0.29 | YES
27 | CD63 | CD63 | CD63 | 2863 | 0.11 | 0.3 | YES
28 | GM2A | GM2A | GM2A | 2912 | 0.11 | 0.31 | YES
29 | LGMN | LGMN | LGMN | 3003 | 0.1 | 0.31 | YES
30 | IGF2R | IGF2R | IGF2R | 3023 | 0.1 | 0.32 | YES
31 | LAPTM4B | LAPTM4B | LAPTM4B | 3108 | 0.098 | 0.32 | YES
32 | NAGA | NAGA | NAGA | 3126 | 0.097 | 0.33 | YES
33 | ENTPD4 | ENTPD4 | ENTPD4 | 3130 | 0.097 | 0.34 | YES
34 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 3175 | 0.095 | 0.34 | YES
35 | GBA | GBA | GBA | 3179 | 0.095 | 0.35 | YES
36 | CTSS | CTSS | CTSS | 3183 | 0.094 | 0.36 | YES
37 | CTSL2 | CTSL2 | CTSL2 | 3198 | 0.094 | 0.37 | YES
38 | HEXA | HEXA | HEXA | 3274 | 0.091 | 0.37 | YES
39 | GAA | GAA | GAA | 3275 | 0.091 | 0.38 | YES
40 | CTSZ | CTSZ | CTSZ | 3352 | 0.088 | 0.38 | YES
41 | DNASE2 | DNASE2 | DNASE2 | 3425 | 0.085 | 0.39 | YES
42 | TCIRG1 | TCIRG1 | TCIRG1 | 3685 | 0.076 | 0.38 | YES
43 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 3707 | 0.076 | 0.38 | YES
44 | ATP6V0B | ATP6V0B | ATP6V0B | 3801 | 0.072 | 0.39 | YES
45 | NEU1 | NEU1 | NEU1 | 3886 | 0.07 | 0.39 | YES
46 | ARSA | ARSA | ARSA | 3975 | 0.067 | 0.39 | YES
47 | CTSA | CTSA | CTSA | 4019 | 0.066 | 0.39 | YES
48 | SLC11A2 | SLC11A2 | SLC11A2 | 4044 | 0.065 | 0.4 | YES
49 | NAPSA | NAPSA | NAPSA | 4095 | 0.064 | 0.4 | YES
50 | ATP6V0C | ATP6V0C | ATP6V0C | 4134 | 0.063 | 0.4 | YES
51 | MANBA | MANBA | MANBA | 4140 | 0.063 | 0.41 | YES
52 | AGA | AGA | AGA | 4472 | 0.053 | 0.39 | NO
53 | CTSH | CTSH | CTSH | 4649 | 0.049 | 0.39 | NO
54 | AP4E1 | AP4E1 | AP4E1 | 4693 | 0.048 | 0.39 | NO
55 | PPT1 | PPT1 | PPT1 | 4764 | 0.047 | 0.39 | NO
56 | AP4M1 | AP4M1 | AP4M1 | 4909 | 0.044 | 0.38 | NO
57 | LAPTM4A | LAPTM4A | LAPTM4A | 4995 | 0.042 | 0.38 | NO
58 | LIPA | LIPA | LIPA | 5002 | 0.042 | 0.39 | NO
59 | LAMP1 | LAMP1 | LAMP1 | 5018 | 0.041 | 0.39 | NO
60 | NAGLU | NAGLU | NAGLU | 5102 | 0.039 | 0.39 | NO
61 | MAN2B1 | MAN2B1 | MAN2B1 | 5197 | 0.037 | 0.39 | NO
62 | AP3M2 | AP3M2 | AP3M2 | 5242 | 0.037 | 0.39 | NO
63 | IDS | IDS | IDS | 5620 | 0.03 | 0.37 | NO
64 | M6PR | M6PR | M6PR | 5940 | 0.024 | 0.35 | NO
65 | AP3S1 | AP3S1 | AP3S1 | 5960 | 0.024 | 0.35 | NO
66 | NPC2 | NPC2 | NPC2 | 5967 | 0.024 | 0.36 | NO
67 | CLTA | CLTA | CLTA | 5973 | 0.024 | 0.36 | NO
68 | GNPTAB | GNPTAB | GNPTAB | 5998 | 0.023 | 0.36 | NO
69 | SUMF1 | SUMF1 | SUMF1 | 6092 | 0.022 | 0.35 | NO
70 | PLA2G15 | PLA2G15 | PLA2G15 | 6421 | 0.017 | 0.34 | NO
71 | CLTC | CLTC | CLTC | 6463 | 0.016 | 0.34 | NO
72 | TPP1 | TPP1 | TPP1 | 6551 | 0.015 | 0.33 | NO
73 | AP1S2 | AP1S2 | AP1S2 | 6598 | 0.014 | 0.33 | NO
74 | AP3B1 | AP3B1 | AP3B1 | 7085 | 0.007 | 0.3 | NO
75 | GGA2 | GGA2 | GGA2 | 7318 | 0.0038 | 0.29 | NO
76 | CTNS | CTNS | CTNS | 7400 | 0.0027 | 0.29 | NO
77 | AP3M1 | AP3M1 | AP3M1 | 7424 | 0.0024 | 0.28 | NO
78 | AP3S2 | AP3S2 | AP3S2 | 7490 | 0.0015 | 0.28 | NO
79 | CTSC | CTSC | CTSC | 7613 | -0.000051 | 0.27 | NO
80 | CLN3 | CLN3 | CLN3 | 7739 | -0.002 | 0.27 | NO
81 | SMPD1 | SMPD1 | SMPD1 | 8272 | -0.0092 | 0.24 | NO
82 | NAGPA | NAGPA | NAGPA | 8380 | -0.011 | 0.23 | NO
83 | AP3D1 | AP3D1 | AP3D1 | 8594 | -0.014 | 0.22 | NO
84 | AP4B1 | AP4B1 | AP4B1 | 8639 | -0.014 | 0.22 | NO
85 | PPT2 | PPT2 | PPT2 | 8797 | -0.016 | 0.21 | NO
86 | AP1B1 | AP1B1 | AP1B1 | 8825 | -0.017 | 0.21 | NO
87 | GGA3 | GGA3 | GGA3 | 8830 | -0.017 | 0.21 | NO
88 | CTSO | CTSO | CTSO | 8923 | -0.018 | 0.21 | NO
89 | GNPTG | GNPTG | GNPTG | 9251 | -0.023 | 0.19 | NO
90 | MCOLN1 | MCOLN1 | MCOLN1 | 9710 | -0.03 | 0.17 | NO
91 | GUSB | GUSB | GUSB | 9728 | -0.03 | 0.17 | NO
92 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 10011 | -0.034 | 0.16 | NO
93 | CLTB | CLTB | CLTB | 10082 | -0.035 | 0.16 | NO
94 | SGSH | SGSH | SGSH | 10169 | -0.037 | 0.16 | NO
95 | AP1S1 | AP1S1 | AP1S1 | 10193 | -0.037 | 0.16 | NO
96 | AP1G1 | AP1G1 | AP1G1 | 10194 | -0.037 | 0.16 | NO
97 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 10384 | -0.04 | 0.15 | NO
98 | MFSD8 | MFSD8 | MFSD8 | 10613 | -0.044 | 0.14 | NO
99 | AP1M1 | AP1M1 | AP1M1 | 10619 | -0.044 | 0.15 | NO
100 | LAPTM5 | LAPTM5 | LAPTM5 | 11085 | -0.052 | 0.13 | NO
101 | CD164 | CD164 | CD164 | 11342 | -0.058 | 0.12 | NO
102 | ARSG | ARSG | ARSG | 11575 | -0.062 | 0.11 | NO
103 | HYAL1 | HYAL1 | HYAL1 | 12194 | -0.076 | 0.08 | NO
104 | CTSF | CTSF | CTSF | 12622 | -0.087 | 0.063 | NO
105 | CLN5 | CLN5 | CLN5 | 12815 | -0.092 | 0.06 | NO
106 | GGA1 | GGA1 | GGA1 | 12975 | -0.096 | 0.06 | NO
107 | AP1S3 | AP1S3 | AP1S3 | 13304 | -0.11 | 0.05 | NO
108 | FUCA1 | FUCA1 | FUCA1 | 13644 | -0.12 | 0.041 | NO
109 | AP4S1 | AP4S1 | AP4S1 | 14269 | -0.15 | 0.019 | NO
110 | IDUA | IDUA | IDUA | 14286 | -0.15 | 0.031 | NO
111 | AP1M2 | AP1M2 | AP1M2 | 14569 | -0.16 | 0.029 | NO
112 | ABCA2 | ABCA2 | ABCA2 | 14729 | -0.17 | 0.035 | NO
113 | AP3B2 | AP3B2 | AP3B2 | 14794 | -0.18 | 0.048 | NO
114 | CTSE | CTSE | CTSE | 14883 | -0.18 | 0.059 | NO
115 | LAMP3 | LAMP3 | LAMP3 | 15501 | -0.23 | 0.043 | NO
116 | CLTCL1 | CLTCL1 | CLTCL1 | 15564 | -0.23 | 0.06 | NO
117 | CTSG | CTSG | CTSG | 16167 | -0.29 | 0.052 | NO
118 | ABCB9 | ABCB9 | ABCB9 | 16390 | -0.32 | 0.067 | 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 FRUCTOSE AND MANNOSE METABOLISM.

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

genes ES table in pathway: KEGG PYRIMIDINE 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 | SPP1 | SPP1 | SPP1 | 14 | 0.81 | 0.094 | YES
2 | IL8 | IL8 | IL8 | 221 | 0.47 | 0.14 | YES
3 | IL6 | IL6 | IL6 | 334 | 0.42 | 0.18 | YES
4 | CTSK | CTSK | CTSK | 430 | 0.38 | 0.22 | YES
5 | TLR8 | TLR8 | TLR8 | 588 | 0.33 | 0.25 | YES
6 | MAPK8 | MAPK8 | MAPK8 | 725 | 0.3 | 0.28 | YES
7 | TLR2 | TLR2 | TLR2 | 777 | 0.29 | 0.31 | YES
8 | FOS | FOS | FOS | 794 | 0.29 | 0.34 | YES
9 | CD14 | CD14 | CD14 | 1114 | 0.24 | 0.35 | YES
10 | MAPK10 | MAPK10 | MAPK10 | 1226 | 0.22 | 0.37 | YES
11 | IL1B | IL1B | IL1B | 1390 | 0.21 | 0.38 | YES
12 | TLR1 | TLR1 | TLR1 | 1602 | 0.19 | 0.4 | YES
13 | CCL3 | CCL3 | CCL3 | 1800 | 0.17 | 0.4 | YES
14 | CCL4 | CCL4 | CCL4 | 1812 | 0.17 | 0.42 | YES
15 | MAP3K8 | MAP3K8 | MAP3K8 | 1954 | 0.16 | 0.43 | YES
16 | CD80 | CD80 | CD80 | 2144 | 0.15 | 0.44 | YES
17 | JUN | JUN | JUN | 2150 | 0.15 | 0.46 | YES
18 | TLR3 | TLR3 | TLR3 | 2599 | 0.12 | 0.44 | YES
19 | TLR4 | TLR4 | TLR4 | 2749 | 0.11 | 0.45 | YES
20 | IFNB1 | IFNB1 | IFNB1 | 2858 | 0.11 | 0.46 | YES
21 | TICAM2 | TICAM2 | TICAM2 | 2922 | 0.11 | 0.46 | YES
22 | CHUK | CHUK | CHUK | 3001 | 0.1 | 0.47 | YES
23 | CXCL10 | CXCL10 | CXCL10 | 3188 | 0.094 | 0.47 | YES
24 | IFNAR2 | IFNAR2 | IFNAR2 | 3616 | 0.078 | 0.46 | NO
25 | PIK3CG | PIK3CG | PIK3CG | 3754 | 0.074 | 0.46 | NO
26 | CD40 | CD40 | CD40 | 3933 | 0.068 | 0.46 | NO
27 | CCL5 | CCL5 | CCL5 | 4045 | 0.065 | 0.46 | NO
28 | AKT3 | AKT3 | AKT3 | 4274 | 0.059 | 0.45 | NO
29 | IFNA21 | IFNA21 | IFNA21 | 4442 | 0.054 | 0.45 | NO
30 | IFNAR1 | IFNAR1 | IFNAR1 | 4524 | 0.052 | 0.45 | NO
31 | STAT1 | STAT1 | STAT1 | 4616 | 0.05 | 0.45 | NO
32 | IRAK1 | IRAK1 | IRAK1 | 4702 | 0.048 | 0.45 | NO
33 | MAPK11 | MAPK11 | MAPK11 | 5154 | 0.038 | 0.43 | NO
34 | MAPK13 | MAPK13 | MAPK13 | 5275 | 0.036 | 0.43 | NO
35 | NFKB1 | NFKB1 | NFKB1 | 5452 | 0.033 | 0.42 | NO
36 | FADD | FADD | FADD | 5541 | 0.031 | 0.42 | NO
37 | AKT1 | AKT1 | AKT1 | 5625 | 0.03 | 0.42 | NO
38 | MAPK14 | MAPK14 | MAPK14 | 5815 | 0.026 | 0.41 | NO
39 | MYD88 | MYD88 | MYD88 | 5922 | 0.024 | 0.41 | NO
40 | PIK3CA | PIK3CA | PIK3CA | 5953 | 0.024 | 0.41 | NO
41 | RIPK1 | RIPK1 | RIPK1 | 6051 | 0.022 | 0.4 | NO
42 | CXCL11 | CXCL11 | CXCL11 | 6172 | 0.02 | 0.4 | NO
43 | MAP3K7 | MAP3K7 | MAP3K7 | 6456 | 0.016 | 0.39 | NO
44 | TICAM1 | TICAM1 | TICAM1 | 6468 | 0.016 | 0.39 | NO
45 | LY96 | LY96 | LY96 | 6513 | 0.015 | 0.39 | NO
46 | TIRAP | TIRAP | TIRAP | 6525 | 0.015 | 0.39 | NO
47 | PIK3CB | PIK3CB | PIK3CB | 6558 | 0.015 | 0.39 | NO
48 | CD86 | CD86 | CD86 | 6616 | 0.014 | 0.39 | NO
49 | RELA | RELA | RELA | 6691 | 0.012 | 0.38 | NO
50 | MAPK9 | MAPK9 | MAPK9 | 6730 | 0.012 | 0.38 | NO
51 | IKBKG | IKBKG | IKBKG | 7106 | 0.0066 | 0.36 | NO
52 | RAC1 | RAC1 | RAC1 | 7174 | 0.0058 | 0.36 | NO
53 | PIK3R1 | PIK3R1 | PIK3R1 | 7176 | 0.0058 | 0.36 | NO
54 | MAPK3 | MAPK3 | MAPK3 | 7202 | 0.0055 | 0.36 | NO
55 | TNF | TNF | TNF | 7433 | 0.0023 | 0.35 | NO
56 | MAPK1 | MAPK1 | MAPK1 | 7463 | 0.002 | 0.34 | NO
57 | MAP2K1 | MAP2K1 | MAP2K1 | 7506 | 0.0013 | 0.34 | NO
58 | MAP2K3 | MAP2K3 | MAP2K3 | 7616 | -0.00012 | 0.34 | NO
59 | AKT2 | AKT2 | AKT2 | 7663 | -0.0008 | 0.33 | NO
60 | MAPK12 | MAPK12 | MAPK12 | 7946 | -0.0047 | 0.32 | NO
61 | MAP2K6 | MAP2K6 | MAP2K6 | 7993 | -0.0056 | 0.32 | NO
62 | NFKBIA | NFKBIA | NFKBIA | 8172 | -0.0078 | 0.31 | NO
63 | TAB2 | TAB2 | TAB2 | 8282 | -0.0093 | 0.3 | NO
64 | MAP2K4 | MAP2K4 | MAP2K4 | 8889 | -0.018 | 0.27 | NO
65 | TOLLIP | TOLLIP | TOLLIP | 9017 | -0.019 | 0.26 | NO
66 | IL12A | IL12A | IL12A | 9080 | -0.02 | 0.26 | NO
67 | IRAK4 | IRAK4 | IRAK4 | 9199 | -0.022 | 0.26 | NO
68 | CXCL9 | CXCL9 | CXCL9 | 9450 | -0.026 | 0.25 | NO
69 | PIK3R2 | PIK3R2 | PIK3R2 | 9652 | -0.028 | 0.24 | NO
70 | IRF5 | IRF5 | IRF5 | 10235 | -0.038 | 0.21 | NO
71 | MAP2K2 | MAP2K2 | MAP2K2 | 10917 | -0.05 | 0.18 | NO
72 | TRAF3 | TRAF3 | TRAF3 | 10947 | -0.05 | 0.18 | NO
73 | PIK3CD | PIK3CD | PIK3CD | 10951 | -0.05 | 0.19 | NO
74 | IRF3 | IRF3 | IRF3 | 10953 | -0.05 | 0.19 | NO
75 | TAB1 | TAB1 | TAB1 | 11256 | -0.056 | 0.18 | NO
76 | TRAF6 | TRAF6 | TRAF6 | 11431 | -0.059 | 0.18 | NO
77 | IKBKE | IKBKE | IKBKE | 11572 | -0.062 | 0.18 | NO
78 | PIK3R5 | PIK3R5 | PIK3R5 | 11719 | -0.065 | 0.18 | NO
79 | MAP2K7 | MAP2K7 | MAP2K7 | 11806 | -0.067 | 0.18 | NO
80 | CASP8 | CASP8 | CASP8 | 11809 | -0.067 | 0.19 | NO
81 | TLR5 | TLR5 | TLR5 | 12282 | -0.079 | 0.17 | NO
82 | IKBKB | IKBKB | IKBKB | 12515 | -0.085 | 0.17 | NO
83 | IRF7 | IRF7 | IRF7 | 12535 | -0.085 | 0.18 | NO
84 | PIK3R3 | PIK3R3 | PIK3R3 | 12626 | -0.087 | 0.18 | NO
85 | TLR6 | TLR6 | TLR6 | 13200 | -0.1 | 0.16 | NO
86 | LBP | LBP | LBP | 14526 | -0.16 | 0.1 | NO
87 | IL12B | IL12B | IL12B | 14572 | -0.16 | 0.12 | NO
88 | TLR7 | TLR7 | TLR7 | 15249 | -0.21 | 0.11 | NO
89 | TLR9 | TLR9 | TLR9 | 15499 | -0.23 | 0.12 | 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 PYRIMIDINE METABOLISM.

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

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 | SMC1B | SMC1B | SMC1B | 1232 | 0.22 | -0.046 | YES
2 | GADD45G | GADD45G | GADD45G | 1249 | 0.22 | -0.022 | YES
3 | SFN | SFN | SFN | 1281 | 0.22 | 0.00018 | YES
4 | TGFB3 | TGFB3 | TGFB3 | 1477 | 0.2 | 0.011 | YES
5 | E2F2 | E2F2 | E2F2 | 1492 | 0.2 | 0.032 | YES
6 | MAD2L1 | MAD2L1 | MAD2L1 | 1660 | 0.18 | 0.042 | YES
7 | ESPL1 | ESPL1 | ESPL1 | 1678 | 0.18 | 0.062 | YES
8 | CCNA2 | CCNA2 | CCNA2 | 1736 | 0.18 | 0.078 | YES
9 | CDKN1A | CDKN1A | CDKN1A | 1748 | 0.18 | 0.096 | YES
10 | CCNE2 | CCNE2 | CCNE2 | 1787 | 0.17 | 0.11 | YES
11 | BUB1B | BUB1B | BUB1B | 1907 | 0.16 | 0.12 | YES
12 | CDK2 | CDK2 | CDK2 | 1960 | 0.16 | 0.14 | YES
13 | PLK1 | PLK1 | PLK1 | 2022 | 0.16 | 0.15 | YES
14 | PKMYT1 | PKMYT1 | PKMYT1 | 2124 | 0.15 | 0.16 | YES
15 | CDC45 | CDC45 | CDC45 | 2198 | 0.14 | 0.18 | YES
16 | CHEK1 | CHEK1 | CHEK1 | 2200 | 0.14 | 0.19 | YES
17 | CDK1 | CDK1 | CDK1 | 2207 | 0.14 | 0.21 | YES
18 | ORC1L | ORC1L | ORC1L | 2208 | 0.14 | 0.22 | YES
19 | E2F1 | E2F1 | E2F1 | 2213 | 0.14 | 0.24 | YES
20 | RBL1 | RBL1 | RBL1 | 2218 | 0.14 | 0.25 | YES
21 | CDC25C | CDC25C | CDC25C | 2244 | 0.14 | 0.27 | YES
22 | CCNB2 | CCNB2 | CCNB2 | 2443 | 0.13 | 0.27 | YES
23 | CDC14B | CDC14B | CDC14B | 2728 | 0.12 | 0.26 | YES
24 | MCM4 | MCM4 | MCM4 | 2739 | 0.11 | 0.28 | YES
25 | CCNE1 | CCNE1 | CCNE1 | 2764 | 0.11 | 0.29 | YES
26 | PTTG2 | PTTG2 | PTTG2 | 2886 | 0.11 | 0.29 | YES
27 | SKP2 | SKP2 | SKP2 | 2977 | 0.1 | 0.3 | YES
28 | CCNB1 | CCNB1 | CCNB1 | 2983 | 0.1 | 0.31 | YES
29 | CDC6 | CDC6 | CDC6 | 3018 | 0.1 | 0.32 | YES
30 | BUB1 | BUB1 | BUB1 | 3021 | 0.1 | 0.33 | YES
31 | CDKN2D | CDKN2D | CDKN2D | 3093 | 0.098 | 0.34 | YES
32 | CDK6 | CDK6 | CDK6 | 3150 | 0.096 | 0.34 | YES
33 | STAG1 | STAG1 | STAG1 | 3212 | 0.093 | 0.35 | YES
34 | CDC25A | CDC25A | CDC25A | 3277 | 0.091 | 0.36 | YES
35 | TGFB2 | TGFB2 | TGFB2 | 3294 | 0.09 | 0.37 | YES
36 | YWHAH | YWHAH | YWHAH | 3691 | 0.076 | 0.35 | YES
37 | MCM6 | MCM6 | MCM6 | 3739 | 0.074 | 0.36 | YES
38 | TTK | TTK | TTK | 3794 | 0.073 | 0.36 | YES
39 | MCM3 | MCM3 | MCM3 | 3921 | 0.069 | 0.36 | YES
40 | PTTG1 | PTTG1 | PTTG1 | 3973 | 0.068 | 0.37 | YES
41 | CDC20 | CDC20 | CDC20 | 3999 | 0.067 | 0.38 | YES
42 | PCNA | PCNA | PCNA | 4004 | 0.067 | 0.38 | YES
43 | ANAPC10 | ANAPC10 | ANAPC10 | 4038 | 0.066 | 0.39 | YES
44 | CCNA1 | CCNA1 | CCNA1 | 4046 | 0.065 | 0.39 | YES
45 | GADD45A | GADD45A | GADD45A | 4054 | 0.065 | 0.4 | YES
46 | CCND1 | CCND1 | CCND1 | 4113 | 0.064 | 0.4 | YES
47 | CDC14A | CDC14A | CDC14A | 4184 | 0.062 | 0.41 | YES
48 | CDK4 | CDK4 | CDK4 | 4324 | 0.057 | 0.41 | YES
49 | YWHAQ | YWHAQ | YWHAQ | 4423 | 0.054 | 0.41 | YES
50 | TFDP2 | TFDP2 | TFDP2 | 4455 | 0.054 | 0.41 | YES
51 | MCM7 | MCM7 | MCM7 | 4568 | 0.051 | 0.41 | YES
52 | SMC3 | SMC3 | SMC3 | 4738 | 0.047 | 0.4 | YES
53 | YWHAG | YWHAG | YWHAG | 4796 | 0.046 | 0.41 | YES
54 | MCM2 | MCM2 | MCM2 | 4806 | 0.046 | 0.41 | YES
55 | GSK3B | GSK3B | GSK3B | 4858 | 0.045 | 0.41 | YES
56 | RAD21 | RAD21 | RAD21 | 5033 | 0.041 | 0.41 | YES
57 | ORC6L | ORC6L | ORC6L | 5065 | 0.04 | 0.41 | YES
58 | HDAC1 | HDAC1 | HDAC1 | 5151 | 0.038 | 0.41 | YES
59 | PRKDC | PRKDC | PRKDC | 5203 | 0.037 | 0.41 | YES
60 | MAD2L2 | MAD2L2 | MAD2L2 | 5204 | 0.037 | 0.42 | YES
61 | SMC1A | SMC1A | SMC1A | 5262 | 0.036 | 0.42 | YES
62 | CDKN2C | CDKN2C | CDKN2C | 5306 | 0.035 | 0.42 | YES
63 | CDC26 | CDC26 | CDC26 | 5449 | 0.033 | 0.41 | NO
64 | ABL1 | ABL1 | ABL1 | 5506 | 0.032 | 0.41 | NO
65 | CDC25B | CDC25B | CDC25B | 5584 | 0.03 | 0.41 | NO
66 | CDC27 | CDC27 | CDC27 | 5769 | 0.027 | 0.4 | NO
67 | CDK7 | CDK7 | CDK7 | 6038 | 0.022 | 0.39 | NO
68 | SKP1 | SKP1 | SKP1 | 6045 | 0.022 | 0.39 | NO
69 | ANAPC1 | ANAPC1 | ANAPC1 | 6098 | 0.022 | 0.39 | NO
70 | ORC4L | ORC4L | ORC4L | 6121 | 0.021 | 0.39 | NO
71 | ORC2L | ORC2L | ORC2L | 6203 | 0.02 | 0.39 | NO
72 | CUL1 | CUL1 | CUL1 | 6267 | 0.019 | 0.39 | NO
73 | ANAPC5 | ANAPC5 | ANAPC5 | 6311 | 0.018 | 0.39 | NO
74 | CDC23 | CDC23 | CDC23 | 6523 | 0.015 | 0.38 | NO
75 | HDAC2 | HDAC2 | HDAC2 | 6686 | 0.013 | 0.37 | NO
76 | YWHAB | YWHAB | YWHAB | 6915 | 0.0095 | 0.36 | NO
77 | ATR | ATR | ATR | 7209 | 0.0054 | 0.34 | NO
78 | YWHAE | YWHAE | YWHAE | 7212 | 0.0053 | 0.34 | NO
79 | BUB3 | BUB3 | BUB3 | 7451 | 0.0021 | 0.33 | NO
80 | TGFB1 | TGFB1 | TGFB1 | 7493 | 0.0015 | 0.33 | NO
81 | MCM5 | MCM5 | MCM5 | 7501 | 0.0014 | 0.33 | NO
82 | E2F4 | E2F4 | E2F4 | 7530 | 0.00093 | 0.33 | NO
83 | SMAD2 | SMAD2 | SMAD2 | 7556 | 0.00065 | 0.32 | NO
84 | E2F3 | E2F3 | E2F3 | 7849 | -0.0032 | 0.31 | NO
85 | WEE2 | WEE2 | WEE2 | 7874 | -0.0036 | 0.31 | NO
86 | WEE1 | WEE1 | WEE1 | 7999 | -0.0057 | 0.3 | NO
87 | RBX1 | RBX1 | RBX1 | 8066 | -0.0064 | 0.3 | NO
88 | ANAPC7 | ANAPC7 | ANAPC7 | 8071 | -0.0065 | 0.3 | NO
89 | ORC5L | ORC5L | ORC5L | 8174 | -0.0079 | 0.29 | NO
90 | YWHAZ | YWHAZ | YWHAZ | 8292 | -0.0094 | 0.29 | NO
91 | ANAPC2 | ANAPC2 | ANAPC2 | 8635 | -0.014 | 0.27 | NO
92 | FZR1 | FZR1 | FZR1 | 8710 | -0.015 | 0.27 | NO
93 | GADD45B | GADD45B | GADD45B | 8712 | -0.015 | 0.27 | NO
94 | RB1 | RB1 | RB1 | 8866 | -0.017 | 0.26 | NO
95 | CDKN2A | CDKN2A | CDKN2A | 8899 | -0.018 | 0.26 | NO
96 | ANAPC13 | ANAPC13 | ANAPC13 | 9022 | -0.02 | 0.26 | NO
97 | EP300 | EP300 | EP300 | 9095 | -0.021 | 0.26 | NO
98 | STAG2 | STAG2 | STAG2 | 9253 | -0.023 | 0.25 | NO
99 | CCNH | CCNH | CCNH | 9380 | -0.025 | 0.24 | NO
100 | ANAPC4 | ANAPC4 | ANAPC4 | 9566 | -0.027 | 0.24 | NO
101 | CCND3 | CCND3 | CCND3 | 9658 | -0.028 | 0.24 | NO
102 | TFDP1 | TFDP1 | TFDP1 | 9772 | -0.03 | 0.23 | NO
103 | MYC | MYC | MYC | 9799 | -0.031 | 0.23 | NO
104 | ANAPC11 | ANAPC11 | ANAPC11 | 10115 | -0.036 | 0.22 | NO
105 | TP53 | TP53 | TP53 | 10271 | -0.038 | 0.22 | NO
106 | CDKN2B | CDKN2B | CDKN2B | 10315 | -0.039 | 0.22 | NO
107 | MDM2 | MDM2 | MDM2 | 10472 | -0.041 | 0.21 | NO
108 | CHEK2 | CHEK2 | CHEK2 | 10695 | -0.045 | 0.2 | NO
109 | ZBTB17 | ZBTB17 | ZBTB17 | 10709 | -0.046 | 0.21 | NO
110 | SMAD4 | SMAD4 | SMAD4 | 10784 | -0.047 | 0.21 | NO
111 | MAD1L1 | MAD1L1 | MAD1L1 | 10889 | -0.049 | 0.21 | NO
112 | CDC7 | CDC7 | CDC7 | 11060 | -0.052 | 0.2 | NO
113 | CDKN1B | CDKN1B | CDKN1B | 12090 | -0.074 | 0.16 | NO
114 | CCNB3 | CCNB3 | CCNB3 | 12384 | -0.081 | 0.15 | NO
115 | RBL2 | RBL2 | RBL2 | 12520 | -0.085 | 0.15 | NO
116 | E2F5 | E2F5 | E2F5 | 12526 | -0.085 | 0.16 | NO
117 | ATM | ATM | ATM | 12612 | -0.087 | 0.16 | NO
118 | CREBBP | CREBBP | CREBBP | 12832 | -0.092 | 0.16 | NO
119 | ORC3L | ORC3L | ORC3L | 13028 | -0.098 | 0.16 | NO
120 | CDC16 | CDC16 | CDC16 | 13341 | -0.11 | 0.15 | NO
121 | SMAD3 | SMAD3 | SMAD3 | 14908 | -0.18 | 0.084 | NO
122 | CDKN1C | CDKN1C | CDKN1C | 16234 | -0.3 | 0.041 | NO
123 | CCND2 | CCND2 | CCND2 | 16362 | -0.32 | 0.069 | NO

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

Figure S16. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSINE 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 AMINO SUGAR AND NUCLEOTIDE SUGAR 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 | ENTPD3 | ENTPD3 | ENTPD3 | 90 | 0.58 | 0.067 | YES
2 | CDA | CDA | CDA | 210 | 0.48 | 0.12 | YES
3 | CMPK2 | CMPK2 | CMPK2 | 911 | 0.27 | 0.11 | YES
4 | NT5E | NT5E | NT5E | 1086 | 0.24 | 0.13 | YES
5 | DPYD | DPYD | DPYD | 1242 | 0.22 | 0.15 | YES
6 | TYMP | TYMP | TYMP | 1530 | 0.19 | 0.16 | YES
7 | NT5C1A | NT5C1A | NT5C1A | 1535 | 0.19 | 0.18 | YES
8 | UCK2 | UCK2 | UCK2 | 1778 | 0.17 | 0.19 | YES
9 | NME5 | NME5 | NME5 | 1859 | 0.17 | 0.2 | YES
10 | UPP1 | UPP1 | UPP1 | 2066 | 0.15 | 0.21 | YES
11 | POLE2 | POLE2 | POLE2 | 2093 | 0.15 | 0.23 | YES
12 | TYMS | TYMS | TYMS | 2311 | 0.14 | 0.23 | YES
13 | PRIM1 | PRIM1 | PRIM1 | 2329 | 0.14 | 0.25 | YES
14 | NME6 | NME6 | NME6 | 2534 | 0.12 | 0.25 | YES
15 | POLA1 | POLA1 | POLA1 | 2568 | 0.12 | 0.26 | YES
16 | POLD3 | POLD3 | POLD3 | 2594 | 0.12 | 0.28 | YES
17 | TXNRD1 | TXNRD1 | TXNRD1 | 2666 | 0.12 | 0.29 | YES
18 | PNP | PNP | PNP | 2705 | 0.12 | 0.3 | YES
19 | POLR3D | POLR3D | POLR3D | 2861 | 0.11 | 0.3 | YES
20 | RRM2 | RRM2 | RRM2 | 2893 | 0.11 | 0.32 | YES
21 | POLA2 | POLA2 | POLA2 | 2949 | 0.1 | 0.32 | YES
22 | ENTPD4 | ENTPD4 | ENTPD4 | 3130 | 0.097 | 0.33 | YES
23 | DPYS | DPYS | DPYS | 3235 | 0.092 | 0.33 | YES
24 | NT5C1B | NT5C1B | NT5C1B | 3433 | 0.084 | 0.33 | YES
25 | RRM1 | RRM1 | RRM1 | 3478 | 0.083 | 0.34 | YES
26 | POLD1 | POLD1 | POLD1 | 3530 | 0.081 | 0.34 | YES
27 | NME7 | NME7 | NME7 | 3750 | 0.074 | 0.34 | YES
28 | TK1 | TK1 | TK1 | 3776 | 0.073 | 0.35 | YES
29 | PRIM2 | PRIM2 | PRIM2 | 3912 | 0.069 | 0.35 | YES
30 | NME1-NME2 | NME1-NME2 | NME1-NME2 | 4221 | 0.06 | 0.34 | NO
31 | POLR3A | POLR3A | POLR3A | 4272 | 0.059 | 0.34 | NO
32 | PNPT1 | PNPT1 | PNPT1 | 4385 | 0.055 | 0.34 | NO
33 | DTYMK | DTYMK | DTYMK | 4660 | 0.049 | 0.33 | NO
34 | DCK | DCK | DCK | 4692 | 0.048 | 0.34 | NO
35 | POLR2B | POLR2B | POLR2B | 4741 | 0.047 | 0.34 | NO
36 | POLR3K | POLR3K | POLR3K | 4903 | 0.044 | 0.34 | NO
37 | TK2 | TK2 | TK2 | 4984 | 0.042 | 0.34 | NO
38 | CTPS2 | CTPS2 | CTPS2 | 5075 | 0.04 | 0.34 | NO
39 | RRM2B | RRM2B | RRM2B | 5410 | 0.034 | 0.32 | NO
40 | DUT | DUT | DUT | 5486 | 0.032 | 0.32 | NO
41 | POLE | POLE | POLE | 5570 | 0.031 | 0.32 | NO
42 | POLR1A | POLR1A | POLR1A | 5592 | 0.03 | 0.32 | NO
43 | POLD4 | POLD4 | POLD4 | 5594 | 0.03 | 0.33 | NO
44 | CANT1 | CANT1 | CANT1 | 5644 | 0.029 | 0.33 | NO
45 | POLR2G | POLR2G | POLR2G | 5832 | 0.026 | 0.32 | NO
46 | POLR3F | POLR3F | POLR3F | 5861 | 0.025 | 0.32 | NO
47 | UPRT | UPRT | UPRT | 5880 | 0.025 | 0.32 | NO
48 | ENTPD5 | ENTPD5 | ENTPD5 | 6039 | 0.022 | 0.32 | NO
49 | NME1 | NME1 | NME1 | 6048 | 0.022 | 0.32 | NO
50 | POLR2D | POLR2D | POLR2D | 6271 | 0.019 | 0.31 | NO
51 | POLR2L | POLR2L | POLR2L | 6695 | 0.012 | 0.29 | NO
52 | ENTPD1 | ENTPD1 | ENTPD1 | 6696 | 0.012 | 0.29 | NO
53 | POLR3H | POLR3H | POLR3H | 7184 | 0.0058 | 0.26 | NO
54 | POLR2K | POLR2K | POLR2K | 7213 | 0.0053 | 0.26 | NO
55 | POLR3B | POLR3B | POLR3B | 7220 | 0.0052 | 0.26 | NO
56 | POLD2 | POLD2 | POLD2 | 7301 | 0.004 | 0.26 | NO
57 | POLR2H | POLR2H | POLR2H | 7373 | 0.0031 | 0.25 | NO
58 | POLE3 | POLE3 | POLE3 | 7511 | 0.0012 | 0.25 | NO
59 | UCKL1 | UCKL1 | UCKL1 | 7546 | 0.00078 | 0.24 | NO
60 | ITPA | ITPA | ITPA | 7581 | 0.00034 | 0.24 | NO
61 | UMPS | UMPS | UMPS | 7686 | -0.0012 | 0.24 | NO
62 | CAD | CAD | CAD | 8300 | -0.0096 | 0.2 | NO
63 | POLR1E | POLR1E | POLR1E | 8317 | -0.0098 | 0.2 | NO
64 | DHODH | DHODH | DHODH | 8429 | -0.011 | 0.2 | NO
65 | ENTPD6 | ENTPD6 | ENTPD6 | 8518 | -0.012 | 0.19 | NO
66 | POLR3C | POLR3C | POLR3C | 8539 | -0.013 | 0.19 | NO
67 | POLR1C | POLR1C | POLR1C | 8560 | -0.013 | 0.2 | NO
68 | CMPK1 | CMPK1 | CMPK1 | 8652 | -0.014 | 0.19 | NO
69 | NUDT2 | NUDT2 | NUDT2 | 8805 | -0.016 | 0.18 | NO
70 | AK3 | AK3 | AK3 | 8868 | -0.017 | 0.18 | NO
71 | POLR2F | POLR2F | POLR2F | 9144 | -0.022 | 0.17 | NO
72 | NME2 | NME2 | NME2 | 9254 | -0.023 | 0.17 | NO
73 | TXNRD2 | TXNRD2 | TXNRD2 | 9273 | -0.023 | 0.17 | NO
74 | POLE4 | POLE4 | POLE4 | 9381 | -0.025 | 0.16 | NO
75 | POLR2E | POLR2E | POLR2E | 9499 | -0.026 | 0.16 | NO
76 | DCTD | DCTD | DCTD | 9542 | -0.027 | 0.16 | NO
77 | POLR2C | POLR2C | POLR2C | 9565 | -0.027 | 0.16 | NO
78 | UPB1 | UPB1 | UPB1 | 9918 | -0.033 | 0.15 | NO
79 | NT5C2 | NT5C2 | NT5C2 | 9957 | -0.033 | 0.15 | NO
80 | POLR3G | POLR3G | POLR3G | 10002 | -0.034 | 0.15 | NO
81 | ZNRD1 | ZNRD1 | ZNRD1 | 10043 | -0.034 | 0.15 | NO
82 | POLR2J | POLR2J | POLR2J | 10153 | -0.036 | 0.15 | NO
83 | UCK1 | UCK1 | UCK1 | 10166 | -0.036 | 0.16 | NO
84 | POLR2A | POLR2A | POLR2A | 10375 | -0.04 | 0.15 | NO
85 | POLR2I | POLR2I | POLR2I | 10892 | -0.049 | 0.13 | NO
86 | NT5C3 | NT5C3 | NT5C3 | 10908 | -0.049 | 0.13 | NO
87 | NT5C | NT5C | NT5C | 11196 | -0.054 | 0.12 | NO
88 | POLR1D | POLR1D | POLR1D | 11265 | -0.056 | 0.12 | NO
89 | POLR1B | POLR1B | POLR1B | 12103 | -0.075 | 0.085 | NO
90 | POLR3GL | POLR3GL | POLR3GL | 12119 | -0.075 | 0.094 | NO
91 | NME3 | NME3 | NME3 | 14028 | -0.14 | 0.00086 | NO
92 | ENTPD8 | ENTPD8 | ENTPD8 | 14405 | -0.15 | -0.0018 | NO
93 | NME4 | NME4 | NME4 | 14614 | -0.17 | 0.0066 | NO
94 | POLR2J3 | POLR2J3 | POLR2J3 | 15314 | -0.21 | -0.0074 | NO
95 | UPP2 | UPP2 | UPP2 | 16120 | -0.29 | -0.018 | NO
96 | POLR2J2 | POLR2J2 | POLR2J2 | 16794 | -0.39 | -0.0095 | NO
97 | NT5M | NT5M | NT5M | 17006 | -0.44 | 0.032 | 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S18. 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 PYRUVATE 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 | CDKN1A | CDKN1A | CDKN1A | 1748 | 0.18 | 0.049 | YES
2 | CDK2 | CDK2 | CDK2 | 1960 | 0.16 | 0.17 | YES
3 | CCNE1 | CCNE1 | CCNE1 | 2764 | 0.11 | 0.22 | YES
4 | CHUK | CHUK | CHUK | 3001 | 0.1 | 0.3 | YES
5 | CDK6 | CDK6 | CDK6 | 3150 | 0.096 | 0.37 | YES
6 | CCND1 | CCND1 | CCND1 | 4113 | 0.064 | 0.37 | YES
7 | CDK4 | CDK4 | CDK4 | 4324 | 0.057 | 0.4 | YES
8 | NFKB1 | NFKB1 | NFKB1 | 5452 | 0.033 | 0.37 | YES
9 | AKT1 | AKT1 | AKT1 | 5625 | 0.03 | 0.38 | YES
10 | PAK1 | PAK1 | PAK1 | 5777 | 0.027 | 0.4 | YES
11 | PIK3CA | PIK3CA | PIK3CA | 5953 | 0.024 | 0.41 | YES
12 | RAF1 | RAF1 | RAF1 | 6027 | 0.023 | 0.42 | YES
13 | RHOA | RHOA | RHOA | 6276 | 0.019 | 0.42 | YES
14 | RELA | RELA | RELA | 6691 | 0.012 | 0.41 | NO
15 | IKBKG | IKBKG | IKBKG | 7106 | 0.0066 | 0.39 | NO
16 | RAC1 | RAC1 | RAC1 | 7174 | 0.0058 | 0.4 | NO
17 | PIK3R1 | PIK3R1 | PIK3R1 | 7176 | 0.0058 | 0.4 | NO
18 | MAPK3 | MAPK3 | MAPK3 | 7202 | 0.0055 | 0.4 | NO
19 | MAPK1 | MAPK1 | MAPK1 | 7463 | 0.002 | 0.39 | NO
20 | HRAS | HRAS | HRAS | 7916 | -0.0042 | 0.37 | NO
21 | NFKBIA | NFKBIA | NFKBIA | 8172 | -0.0078 | 0.36 | NO
22 | RB1 | RB1 | RB1 | 8866 | -0.017 | 0.34 | NO
23 | TFDP1 | TFDP1 | TFDP1 | 9772 | -0.03 | 0.31 | NO
24 | CDKN1B | CDKN1B | CDKN1B | 12090 | -0.074 | 0.24 | NO
25 | IKBKB | IKBKB | IKBKB | 12515 | -0.085 | 0.29 | 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 PYRUVATE METABOLISM.

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

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 ALK PATHWAY | 34 | genes.ES.table | 0.46 | 1.3 | 0.1 | 1 | 0.98 | 0.26 | 0.13 | 0.23 | 0.97 | 0.49
BIOCARTA CARM ER PATHWAY | 33 | genes.ES.table | 0.35 | 1.3 | 0.18 | 1 | 0.99 | 0.27 | 0.28 | 0.2 | 0.97 | 0.48
BIOCARTA GH PATHWAY | 26 | genes.ES.table | 0.55 | 1.7 | 0.006 | 0.98 | 0.43 | 0.38 | 0.29 | 0.27 | 0 | 0.3
BIOCARTA TCR PATHWAY | 43 | genes.ES.table | 0.37 | 1.2 | 0.22 | 0.95 | 1 | 0.35 | 0.26 | 0.26 | 0.88 | 0.41
KEGG FATTY ACID METABOLISM | 35 | genes.ES.table | 0.37 | 1.3 | 0.21 | 0.95 | 0.99 | 0.086 | 0.086 | 0.078 | 0.88 | 0.41
KEGG ABC TRANSPORTERS | 41 | genes.ES.table | 0.56 | 1.5 | 0.011 | 1 | 0.78 | 0.46 | 0.24 | 0.35 | 1 | 0.55
KEGG CARDIAC MUSCLE CONTRACTION | 63 | genes.ES.table | 0.43 | 1.4 | 0.051 | 1 | 0.96 | 0.22 | 0.13 | 0.19 | 0.99 | 0.49
KEGG WNT SIGNALING PATHWAY | 140 | genes.ES.table | 0.39 | 1.3 | 0.098 | 1 | 0.98 | 0.21 | 0.15 | 0.18 | 1 | 0.51
KEGG CELL ADHESION MOLECULES CAMS | 126 | genes.ES.table | 0.43 | 1.3 | 0.17 | 0.99 | 0.99 | 0.33 | 0.18 | 0.28 | 0.91 | 0.42
KEGG INTESTINAL IMMUNE NETWORK FOR IGA PRODUCTION | 44 | genes.ES.table | 0.45 | 1.3 | 0.16 | 1 | 0.99 | 0.3 | 0.15 | 0.25 | 1 | 0.5

genes ES table in pathway: BIOCARTA ALK 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 | HNF1A | HNF1A | HNF1A | 1660 | 0.26 | 0.036 | YES
2 | PRKCA | PRKCA | PRKCA | 1756 | 0.25 | 0.16 | YES
3 | PRKCB | PRKCB | PRKCB | 1791 | 0.25 | 0.28 | YES
4 | GH1 | GH1 | GH1 | 1977 | 0.23 | 0.38 | YES
5 | IRS1 | IRS1 | IRS1 | 2476 | 0.2 | 0.45 | YES
6 | PLCG1 | PLCG1 | PLCG1 | 4157 | 0.11 | 0.41 | YES
7 | SLC2A4 | SLC2A4 | SLC2A4 | 4292 | 0.1 | 0.45 | YES
8 | PTPN6 | PTPN6 | PTPN6 | 4321 | 0.1 | 0.5 | YES
9 | SOCS1 | SOCS1 | SOCS1 | 4399 | 0.1 | 0.55 | YES
10 | SOS1 | SOS1 | SOS1 | 5097 | 0.083 | 0.55 | YES
11 | SRF | SRF | SRF | 7990 | 0.028 | 0.4 | NO
12 | STAT5B | STAT5B | STAT5B | 8460 | 0.021 | 0.38 | NO
13 | GHR | GHR | GHR | 9021 | 0.013 | 0.36 | NO
14 | STAT5A | STAT5A | STAT5A | 9532 | 0.0061 | 0.33 | NO
15 | MAP2K1 | MAP2K1 | MAP2K1 | 10055 | -0.0013 | 0.3 | NO
16 | MAPK1 | MAPK1 | MAPK1 | 10098 | -0.002 | 0.3 | NO
17 | MAPK3 | MAPK3 | MAPK3 | 10359 | -0.0055 | 0.29 | NO
18 | PIK3R1 | PIK3R1 | PIK3R1 | 10385 | -0.0058 | 0.29 | NO
19 | JAK2 | JAK2 | JAK2 | 10896 | -0.013 | 0.27 | NO
20 | SHC1 | SHC1 | SHC1 | 11438 | -0.021 | 0.25 | NO
21 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 11466 | -0.022 | 0.26 | NO
22 | RAF1 | RAF1 | RAF1 | 11534 | -0.023 | 0.26 | NO
23 | PIK3CA | PIK3CA | PIK3CA | 11608 | -0.024 | 0.27 | NO
24 | GRB2 | GRB2 | GRB2 | 11623 | -0.024 | 0.28 | NO
25 | INSR | INSR | INSR | 12451 | -0.039 | 0.26 | NO
26 | PIK3CG | PIK3CG | PIK3CG | 13807 | -0.074 | 0.21 | 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 ALK PATHWAY.

Figure S22. 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 CARM ER 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 | ABCA3 | ABCA3 | ABCA3 | 185 | 0.61 | 0.1 | YES
2 | ABCC6 | ABCC6 | ABCC6 | 666 | 0.41 | 0.15 | YES
3 | ABCG2 | ABCG2 | ABCG2 | 997 | 0.35 | 0.2 | YES
4 | ABCB9 | ABCB9 | ABCB9 | 1171 | 0.32 | 0.25 | YES
5 | ABCA10 | ABCA10 | ABCA10 | 1181 | 0.32 | 0.31 | YES
6 | ABCA9 | ABCA9 | ABCA9 | 1436 | 0.29 | 0.35 | YES
7 | ABCB11 | ABCB11 | ABCB11 | 2185 | 0.22 | 0.35 | YES
8 | ABCA6 | ABCA6 | ABCA6 | 2242 | 0.21 | 0.38 | YES
9 | ABCA2 | ABCA2 | ABCA2 | 2832 | 0.17 | 0.38 | YES
10 | ABCC11 | ABCC11 | ABCC11 | 2960 | 0.17 | 0.4 | YES
11 | ABCA4 | ABCA4 | ABCA4 | 2987 | 0.16 | 0.44 | YES
12 | ABCG5 | ABCG5 | ABCG5 | 3274 | 0.15 | 0.45 | YES
13 | ABCG1 | ABCG1 | ABCG1 | 3284 | 0.15 | 0.47 | YES
14 | ABCB4 | ABCB4 | ABCB4 | 3304 | 0.15 | 0.5 | YES
15 | ABCB1 | ABCB1 | ABCB1 | 3341 | 0.14 | 0.52 | YES
16 | ABCC5 | ABCC5 | ABCC5 | 3500 | 0.14 | 0.54 | YES
17 | ABCA7 | ABCA7 | ABCA7 | 3589 | 0.13 | 0.56 | YES
18 | ABCC8 | ABCC8 | ABCC8 | 4048 | 0.11 | 0.56 | YES
19 | ABCA5 | ABCA5 | ABCA5 | 4270 | 0.1 | 0.56 | YES
20 | ABCC2 | ABCC2 | ABCC2 | 5162 | 0.081 | 0.53 | NO
21 | ABCC3 | ABCC3 | ABCC3 | 5416 | 0.075 | 0.53 | NO
22 | ABCB5 | ABCB5 | ABCB5 | 6165 | 0.059 | 0.5 | NO
23 | ABCD1 | ABCD1 | ABCD1 | 6377 | 0.054 | 0.49 | NO
24 | ABCC9 | ABCC9 | ABCC9 | 6683 | 0.049 | 0.49 | NO
25 | ABCD4 | ABCD4 | ABCD4 | 7686 | 0.032 | 0.43 | NO
26 | ABCC1 | ABCC1 | ABCC1 | 7956 | 0.028 | 0.42 | NO
27 | ABCB10 | ABCB10 | ABCB10 | 8809 | 0.016 | 0.38 | NO
28 | ABCA12 | ABCA12 | ABCA12 | 9508 | 0.0063 | 0.34 | NO
29 | ABCC10 | ABCC10 | ABCC10 | 10972 | -0.014 | 0.26 | NO
30 | ABCA1 | ABCA1 | ABCA1 | 11525 | -0.022 | 0.23 | NO
31 | ABCB8 | ABCB8 | ABCB8 | 11694 | -0.025 | 0.23 | NO
32 | ABCG4 | ABCG4 | ABCG4 | 11699 | -0.025 | 0.23 | NO
33 | ABCB7 | ABCB7 | ABCB7 | 12074 | -0.032 | 0.22 | NO
34 | TAP2 | TAP2 | TAP2 | 12142 | -0.033 | 0.22 | NO
35 | ABCB6 | ABCB6 | ABCB6 | 12535 | -0.041 | 0.2 | NO
36 | TAP1 | TAP1 | TAP1 | 13007 | -0.051 | 0.19 | NO
37 | CFTR | CFTR | CFTR | 13290 | -0.059 | 0.18 | NO
38 | ABCD2 | ABCD2 | ABCD2 | 13348 | -0.061 | 0.19 | NO
39 | ABCD3 | ABCD3 | ABCD3 | 13777 | -0.073 | 0.18 | NO
40 | ABCA13 | ABCA13 | ABCA13 | 13992 | -0.08 | 0.18 | NO
41 | ABCC4 | ABCC4 | ABCC4 | 14882 | -0.12 | 0.15 | 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 CARM ER PATHWAY.

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

genes ES table in pathway: BIOCARTA GH PATHWAY

Table 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 | CD40LG | CD40LG | CD40LG | 66 | 0.78 | 0.18 | YES
2 | AIRE | AIRE | AIRE | 107 | 0.7 | 0.34 | YES
3 | IGLL1 | IGLL1 | IGLL1 | 1497 | 0.28 | 0.33 | YES
4 | ICOS | ICOS | ICOS | 1509 | 0.28 | 0.39 | YES
5 | ZAP70 | ZAP70 | ZAP70 | 2098 | 0.22 | 0.41 | YES
6 | CD3E | CD3E | CD3E | 2749 | 0.18 | 0.42 | YES
7 | CD3D | CD3D | CD3D | 3001 | 0.16 | 0.44 | YES
8 | LCK | LCK | LCK | 3078 | 0.16 | 0.48 | YES
9 | RAG1 | RAG1 | RAG1 | 3347 | 0.14 | 0.49 | YES
10 | CD79A | CD79A | CD79A | 3494 | 0.14 | 0.52 | YES
11 | RFXAP | RFXAP | RFXAP | 3665 | 0.13 | 0.54 | YES
12 | TNFRSF13C | TNFRSF13C | TNFRSF13C | 5240 | 0.08 | 0.47 | NO
13 | CD19 | CD19 | CD19 | 5268 | 0.079 | 0.48 | NO
14 | BTK | BTK | BTK | 6244 | 0.057 | 0.44 | NO
15 | IL2RG | IL2RG | IL2RG | 6470 | 0.052 | 0.44 | NO
16 | DCLRE1C | DCLRE1C | DCLRE1C | 6703 | 0.048 | 0.44 | NO
17 | RFX5 | RFX5 | RFX5 | 7285 | 0.038 | 0.42 | NO
18 | AICDA | AICDA | AICDA | 7498 | 0.035 | 0.41 | NO
19 | BLNK | BLNK | BLNK | 8078 | 0.026 | 0.38 | NO
20 | JAK3 | JAK3 | JAK3 | 8211 | 0.024 | 0.38 | NO
21 | RFXANK | RFXANK | RFXANK | 8284 | 0.023 | 0.38 | NO
22 | PTPRC | PTPRC | PTPRC | 9229 | 0.01 | 0.33 | NO
23 | IKBKG | IKBKG | IKBKG | 10455 | -0.0066 | 0.26 | NO
24 | CD4 | CD4 | CD4 | 10829 | -0.012 | 0.25 | NO
25 | UNG | UNG | UNG | 11236 | -0.018 | 0.23 | NO
26 | TNFRSF13B | TNFRSF13B | TNFRSF13B | 11652 | -0.024 | 0.21 | NO
27 | TAP2 | TAP2 | TAP2 | 12142 | -0.033 | 0.19 | NO
28 | CIITA | CIITA | CIITA | 12279 | -0.036 | 0.19 | NO
29 | TAP1 | TAP1 | TAP1 | 13007 | -0.051 | 0.16 | NO
30 | CD40 | CD40 | CD40 | 13628 | -0.068 | 0.14 | NO
31 | CD8B | CD8B | CD8B | 14054 | -0.082 | 0.14 | NO
32 | ADA | ADA | ADA | 14772 | -0.11 | 0.12 | NO
33 | IL7R | IL7R | IL7R | 15616 | -0.16 | 0.11 | NO

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

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

genes ES table in pathway: BIOCARTA TCR PATHWAY

Table S14. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | CDH1 | CDH1 | CDH1 | 183 | 0.61 | 0.16 | YES
2 | TCF7 | TCF7 | TCF7 | 389 | 0.49 | 0.3 | YES
3 | RXRG | RXRG | RXRG | 740 | 0.39 | 0.39 | YES
4 | RET | RET | RET | 782 | 0.38 | 0.5 | YES
5 | TCF7L1 | TCF7L1 | TCF7L1 | 1795 | 0.25 | 0.51 | YES
6 | LEF1 | LEF1 | LEF1 | 2274 | 0.21 | 0.55 | YES
7 | TCF7L2 | TCF7L2 | TCF7L2 | 5527 | 0.073 | 0.38 | NO
8 | NTRK1 | NTRK1 | NTRK1 | 5630 | 0.07 | 0.4 | NO
9 | RXRB | RXRB | RXRB | 5702 | 0.069 | 0.41 | NO
10 | MAP2K2 | MAP2K2 | MAP2K2 | 6644 | 0.05 | 0.37 | NO
11 | TP53 | TP53 | TP53 | 7290 | 0.038 | 0.34 | NO
12 | CCDC6 | CCDC6 | CCDC6 | 7388 | 0.037 | 0.35 | NO
13 | MYC | MYC | MYC | 7762 | 0.031 | 0.34 | NO
14 | RXRA | RXRA | RXRA | 9146 | 0.011 | 0.26 | NO
15 | TPR | TPR | TPR | 9547 | 0.0059 | 0.24 | NO
16 | TFG | TFG | TFG | 9728 | 0.003 | 0.23 | NO
17 | MAP2K1 | MAP2K1 | MAP2K1 | 10055 | -0.0013 | 0.21 | NO
18 | MAPK1 | MAPK1 | MAPK1 | 10098 | -0.002 | 0.21 | NO
19 | MAPK3 | MAPK3 | MAPK3 | 10359 | -0.0055 | 0.2 | NO
20 | TPM3 | TPM3 | TPM3 | 10925 | -0.014 | 0.17 | NO
21 | KRAS | KRAS | KRAS | 11611 | -0.024 | 0.14 | NO
22 | CTNNB1 | CTNNB1 | CTNNB1 | 12534 | -0.041 | 0.097 | NO
23 | NCOA4 | NCOA4 | NCOA4 | 12594 | -0.042 | 0.11 | NO
24 | CCND1 | CCND1 | CCND1 | 13448 | -0.064 | 0.076 | NO
25 | NRAS | NRAS | NRAS | 13630 | -0.068 | 0.085 | NO
26 | BRAF | BRAF | BRAF | 14910 | -0.12 | 0.046 | NO
27 | PAX8 | PAX8 | PAX8 | 14987 | -0.12 | 0.077 | NO
28 | PPARG | PPARG | PPARG | 16456 | -0.24 | 0.063 | NO

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

Figure S28. 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: KEGG FATTY ACID METABOLISM

Table S15. Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | CDH1 | CDH1 | CDH1 | 183 | 0.61 | 0.12 | YES
2 | TCF7 | TCF7 | TCF7 | 389 | 0.49 | 0.22 | YES
3 | CTNNA3 | CTNNA3 | CTNNA3 | 1569 | 0.27 | 0.21 | YES
4 | EGFR | EGFR | EGFR | 1574 | 0.27 | 0.27 | YES
5 | AXIN2 | AXIN2 | AXIN2 | 1775 | 0.25 | 0.32 | YES
6 | TCF7L1 | TCF7L1 | TCF7L1 | 1795 | 0.25 | 0.37 | YES
7 | LEF1 | LEF1 | LEF1 | 2274 | 0.21 | 0.39 | YES
8 | ERBB2 | ERBB2 | ERBB2 | 3111 | 0.16 | 0.38 | YES
9 | FOXO3 | FOXO3 | FOXO3 | 3358 | 0.14 | 0.4 | YES
10 | EGF | EGF | EGF | 3676 | 0.13 | 0.41 | YES
11 | CTNNA2 | CTNNA2 | CTNNA2 | 3815 | 0.12 | 0.43 | YES
12 | APC2 | APC2 | APC2 | 3829 | 0.12 | 0.45 | YES
13 | PIK3R3 | PIK3R3 | PIK3R3 | 4935 | 0.087 | 0.41 | NO
14 | SOS1 | SOS1 | SOS1 | 5097 | 0.083 | 0.42 | NO
15 | TCF7L2 | TCF7L2 | TCF7L2 | 5527 | 0.073 | 0.41 | NO
16 | PIK3R5 | PIK3R5 | PIK3R5 | 5842 | 0.065 | 0.4 | NO
17 | PIK3CD | PIK3CD | PIK3CD | 6610 | 0.05 | 0.37 | NO
18 | MAP2K2 | MAP2K2 | MAP2K2 | 6644 | 0.05 | 0.38 | NO
19 | TP53 | TP53 | TP53 | 7290 | 0.038 | 0.35 | NO
20 | MYC | MYC | MYC | 7762 | 0.031 | 0.33 | NO
21 | PIK3R2 | PIK3R2 | PIK3R2 | 7909 | 0.028 | 0.33 | NO
22 | SOS2 | SOS2 | SOS2 | 8082 | 0.026 | 0.33 | NO
23 | AXIN1 | AXIN1 | AXIN1 | 8529 | 0.02 | 0.31 | NO
24 | BAD | BAD | BAD | 9492 | 0.0065 | 0.25 | NO
25 | AKT2 | AKT2 | AKT2 | 9898 | 0.0008 | 0.23 | NO
26 | MAP2K1 | MAP2K1 | MAP2K1 | 10055 | -0.0013 | 0.22 | NO
27 | PDPK1 | PDPK1 | PDPK1 | 10075 | -0.0015 | 0.22 | NO
28 | MAPK1 | MAPK1 | MAPK1 | 10098 | -0.002 | 0.22 | NO
29 | MAPK3 | MAPK3 | MAPK3 | 10359 | -0.0055 | 0.2 | NO
30 | PIK3R1 | PIK3R1 | PIK3R1 | 10385 | -0.0058 | 0.2 | NO
31 | CASP9 | CASP9 | CASP9 | 10548 | -0.008 | 0.2 | NO
32 | PIK3CB | PIK3CB | PIK3CB | 11003 | -0.015 | 0.18 | NO
33 | PTEN | PTEN | PTEN | 11207 | -0.018 | 0.17 | NO
34 | RAF1 | RAF1 | RAF1 | 11534 | -0.023 | 0.15 | NO
35 | PIK3CA | PIK3CA | PIK3CA | 11608 | -0.024 | 0.16 | NO
36 | KRAS | KRAS | KRAS | 11611 | -0.024 | 0.16 | NO
37 | GRB2 | GRB2 | GRB2 | 11623 | -0.024 | 0.16 | NO
38 | APC | APC | APC | 11761 | -0.026 | 0.16 | NO
39 | ARAF | ARAF | ARAF | 11932 | -0.03 | 0.16 | NO
40 | AKT1 | AKT1 | AKT1 | 11936 | -0.03 | 0.17 | NO
41 | CTNNB1 | CTNNB1 | CTNNB1 | 12534 | -0.041 | 0.14 | NO
42 | ILK | ILK | ILK | 12558 | -0.042 | 0.15 | NO
43 | ELK1 | ELK1 | ELK1 | 12609 | -0.043 | 0.16 | NO
44 | GSK3B | GSK3B | GSK3B | 12703 | -0.045 | 0.16 | NO
45 | AKT3 | AKT3 | AKT3 | 13287 | -0.059 | 0.14 | NO
46 | MLH1 | MLH1 | MLH1 | 13350 | -0.061 | 0.15 | NO
47 | CCND1 | CCND1 | CCND1 | 13448 | -0.064 | 0.16 | NO
48 | NRAS | NRAS | NRAS | 13630 | -0.068 | 0.16 | NO
49 | PIK3CG | PIK3CG | PIK3CG | 13807 | -0.074 | 0.17 | NO
50 | CTNNA1 | CTNNA1 | CTNNA1 | 14155 | -0.086 | 0.17 | NO
51 | BRAF | BRAF | BRAF | 14910 | -0.12 | 0.15 | 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 FATTY ACID METABOLISM.

Figure S30. 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 ABC TRANSPORTERS

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 | TGFA | TGFA | TGFA | 428 | 0.48 | 0.081 | YES
2 | RXRG | RXRG | RXRG | 740 | 0.39 | 0.15 | YES
3 | FHIT | FHIT | FHIT | 811 | 0.38 | 0.23 | YES
4 | EGFR | EGFR | EGFR | 1574 | 0.27 | 0.24 | YES
5 | PRKCA | PRKCA | PRKCA | 1756 | 0.25 | 0.29 | YES
6 | PRKCB | PRKCB | PRKCB | 1791 | 0.25 | 0.34 | YES
7 | PRKCG | PRKCG | PRKCG | 1881 | 0.24 | 0.39 | YES
8 | ERBB2 | ERBB2 | ERBB2 | 3111 | 0.16 | 0.36 | YES
9 | FOXO3 | FOXO3 | FOXO3 | 3358 | 0.14 | 0.37 | YES
10 | EGF | EGF | EGF | 3676 | 0.13 | 0.38 | YES
11 | RASSF5 | RASSF5 | RASSF5 | 3881 | 0.12 | 0.4 | YES
12 | PLCG1 | PLCG1 | PLCG1 | 4157 | 0.11 | 0.4 | YES
13 | RARB | RARB | RARB | 4859 | 0.089 | 0.38 | YES
14 | PIK3R3 | PIK3R3 | PIK3R3 | 4935 | 0.087 | 0.4 | YES
15 | SOS1 | SOS1 | SOS1 | 5097 | 0.083 | 0.41 | YES
16 | RXRB | RXRB | RXRB | 5702 | 0.069 | 0.39 | NO
17 | PIK3R5 | PIK3R5 | PIK3R5 | 5842 | 0.065 | 0.4 | NO
18 | PIK3CD | PIK3CD | PIK3CD | 6610 | 0.05 | 0.36 | NO
19 | MAP2K2 | MAP2K2 | MAP2K2 | 6644 | 0.05 | 0.37 | NO
20 | TP53 | TP53 | TP53 | 7290 | 0.038 | 0.34 | NO
21 | PIK3R2 | PIK3R2 | PIK3R2 | 7909 | 0.028 | 0.31 | NO
22 | STK4 | STK4 | STK4 | 8029 | 0.027 | 0.31 | NO
23 | SOS2 | SOS2 | SOS2 | 8082 | 0.026 | 0.32 | NO
24 | PLCG2 | PLCG2 | PLCG2 | 8538 | 0.02 | 0.29 | NO
25 | CDKN2A | CDKN2A | CDKN2A | 8662 | 0.018 | 0.29 | NO
26 | RB1 | RB1 | RB1 | 8695 | 0.017 | 0.29 | NO
27 | RASSF1 | RASSF1 | RASSF1 | 8705 | 0.017 | 0.3 | NO
28 | RXRA | RXRA | RXRA | 9146 | 0.011 | 0.27 | NO
29 | BAD | BAD | BAD | 9492 | 0.0065 | 0.26 | NO
30 | HRAS | HRAS | HRAS | 9645 | 0.0042 | 0.25 | NO
31 | E2F3 | E2F3 | E2F3 | 9712 | 0.0032 | 0.24 | NO
32 | AKT2 | AKT2 | AKT2 | 9898 | 0.0008 | 0.23 | NO
33 | MAP2K1 | MAP2K1 | MAP2K1 | 10055 | -0.0013 | 0.22 | NO
34 | PDPK1 | PDPK1 | PDPK1 | 10075 | -0.0015 | 0.22 | NO
35 | MAPK1 | MAPK1 | MAPK1 | 10098 | -0.002 | 0.22 | NO
36 | MAPK3 | MAPK3 | MAPK3 | 10359 | -0.0055 | 0.21 | NO
37 | PIK3R1 | PIK3R1 | PIK3R1 | 10385 | -0.0058 | 0.21 | NO
38 | CASP9 | CASP9 | CASP9 | 10548 | -0.008 | 0.2 | NO
39 | PIK3CB | PIK3CB | PIK3CB | 11003 | -0.015 | 0.18 | NO
40 | RAF1 | RAF1 | RAF1 | 11534 | -0.023 | 0.15 | NO
41 | PIK3CA | PIK3CA | PIK3CA | 11608 | -0.024 | 0.16 | NO
42 | KRAS | KRAS | KRAS | 11611 | -0.024 | 0.16 | NO
43 | GRB2 | GRB2 | GRB2 | 11623 | -0.024 | 0.16 | NO
44 | ARAF | ARAF | ARAF | 11932 | -0.03 | 0.15 | NO
45 | AKT1 | AKT1 | AKT1 | 11936 | -0.03 | 0.16 | NO
46 | CDK4 | CDK4 | CDK4 | 13237 | -0.057 | 0.098 | NO
47 | AKT3 | AKT3 | AKT3 | 13287 | -0.059 | 0.11 | NO
48 | CCND1 | CCND1 | CCND1 | 13448 | -0.064 | 0.11 | NO
49 | NRAS | NRAS | NRAS | 13630 | -0.068 | 0.12 | NO
50 | PIK3CG | PIK3CG | PIK3CG | 13807 | -0.074 | 0.12 | NO
51 | CDK6 | CDK6 | CDK6 | 14411 | -0.096 | 0.11 | NO
52 | BRAF | BRAF | BRAF | 14910 | -0.12 | 0.11 | NO
53 | E2F2 | E2F2 | E2F2 | 16069 | -0.2 | 0.085 | 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 ABC TRANSPORTERS.

Figure S32. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ABC TRANSPORTERS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CARDIAC MUSCLE CONTRACTION

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 | KCNB1 | KCNB1 | KCNB1 | 189 | 0.6 | 0.11 | YES
2 | CACNA1A | CACNA1A | CACNA1A | 360 | 0.51 | 0.2 | YES
3 | GRM4 | GRM4 | GRM4 | 440 | 0.48 | 0.29 | YES
4 | TAS2R10 | TAS2R10 | TAS2R10 | 1276 | 0.3 | 0.3 | YES
5 | TAS1R3 | TAS1R3 | TAS1R3 | 1689 | 0.26 | 0.33 | YES
6 | TAS2R43 | TAS2R43 | TAS2R43 | 2015 | 0.23 | 0.36 | YES
7 | SCNN1A | SCNN1A | SCNN1A | 2116 | 0.22 | 0.4 | YES
8 | TAS2R20 | TAS2R20 | TAS2R20 | 2170 | 0.22 | 0.44 | YES
9 | SCNN1B | SCNN1B | SCNN1B | 2426 | 0.2 | 0.46 | YES
10 | GNB3 | GNB3 | GNB3 | 2490 | 0.2 | 0.5 | YES
11 | TRPM5 | TRPM5 | TRPM5 | 2736 | 0.18 | 0.52 | YES
12 | TAS2R5 | TAS2R5 | TAS2R5 | 2757 | 0.18 | 0.55 | YES
13 | CACNA1B | CACNA1B | CACNA1B | 3089 | 0.16 | 0.56 | YES
14 | GNG13 | GNG13 | GNG13 | 3698 | 0.13 | 0.56 | YES
15 | TAS1R1 | TAS1R1 | TAS1R1 | 3794 | 0.12 | 0.57 | YES
16 | TAS2R4 | TAS2R4 | TAS2R4 | 4253 | 0.11 | 0.57 | YES
17 | GNG3 | GNG3 | GNG3 | 4332 | 0.1 | 0.58 | YES
18 | SCNN1G | SCNN1G | SCNN1G | 5120 | 0.083 | 0.56 | NO
19 | ADCY6 | ADCY6 | ADCY6 | 5273 | 0.079 | 0.56 | NO
20 | ADCY4 | ADCY4 | ADCY4 | 5559 | 0.072 | 0.56 | NO
21 | TAS2R19 | TAS2R19 | TAS2R19 | 6096 | 0.06 | 0.54 | NO
22 | TAS2R31 | TAS2R31 | TAS2R31 | 6957 | 0.044 | 0.5 | NO
23 | TAS2R46 | TAS2R46 | TAS2R46 | 7024 | 0.042 | 0.51 | NO
24 | GNAS | GNAS | GNAS | 7508 | 0.035 | 0.49 | NO
25 | PRKACA | PRKACA | PRKACA | 8450 | 0.021 | 0.44 | NO
26 | TAS2R14 | TAS2R14 | TAS2R14 | 8751 | 0.017 | 0.42 | NO
27 | ITPR3 | ITPR3 | ITPR3 | 8960 | 0.014 | 0.41 | NO
28 | PLCB2 | PLCB2 | PLCB2 | 9826 | 0.0019 | 0.36 | NO
29 | PRKACB | PRKACB | PRKACB | 10030 | -0.00093 | 0.35 | NO
30 | PRKX | PRKX | PRKX | 12290 | -0.036 | 0.23 | NO
31 | GNB1 | GNB1 | GNB1 | 12453 | -0.039 | 0.23 | NO
32 | TAS2R13 | TAS2R13 | TAS2R13 | 12931 | -0.05 | 0.21 | NO
33 | ACCN1 | ACCN1 | ACCN1 | 14871 | -0.12 | 0.12 | NO
34 | PDE1A | PDE1A | PDE1A | 15400 | -0.14 | 0.12 | 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 CARDIAC MUSCLE CONTRACTION.

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

genes ES table in pathway: KEGG WNT SIGNALING PATHWAY

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 | CACNA2D2 | CACNA2D2 | CACNA2D2 | 435 | 0.48 | 0.037 | YES
2 | ATP1B2 | ATP1B2 | ATP1B2 | 534 | 0.44 | 0.089 | YES
3 | COX4I2 | COX4I2 | COX4I2 | 619 | 0.42 | 0.14 | YES
4 | TNNT2 | TNNT2 | TNNT2 | 947 | 0.36 | 0.17 | YES
5 | CACNA2D3 | CACNA2D3 | CACNA2D3 | 1163 | 0.32 | 0.2 | YES
6 | CACNG2 | CACNG2 | CACNG2 | 1238 | 0.31 | 0.23 | YES
7 | MYL3 | MYL3 | MYL3 | 1258 | 0.31 | 0.27 | YES
8 | CACNG3 | CACNG3 | CACNG3 | 1332 | 0.3 | 0.3 | YES
9 | TNNC1 | TNNC1 | TNNC1 | 1687 | 0.26 | 0.32 | YES
10 | CACNA1F | CACNA1F | CACNA1F | 1744 | 0.26 | 0.35 | YES
11 | CACNA1D | CACNA1D | CACNA1D | 2019 | 0.23 | 0.36 | YES
12 | COX6B2 | COX6B2 | COX6B2 | 2105 | 0.22 | 0.39 | YES
13 | CACNG5 | CACNG5 | CACNG5 | 2146 | 0.22 | 0.41 | YES
14 | MYL2 | MYL2 | MYL2 | 2253 | 0.21 | 0.43 | YES
15 | CACNB1 | CACNB1 | CACNB1 | 2910 | 0.17 | 0.42 | NO
16 | ATP1A3 | ATP1A3 | ATP1A3 | 3657 | 0.13 | 0.39 | NO
17 | CACNB2 | CACNB2 | CACNB2 | 4065 | 0.11 | 0.38 | NO
18 | CACNA2D4 | CACNA2D4 | CACNA2D4 | 4568 | 0.096 | 0.37 | NO
19 | UQCRB | UQCRB | UQCRB | 5266 | 0.079 | 0.34 | NO
20 | CACNA1C | CACNA1C | CACNA1C | 5662 | 0.07 | 0.32 | NO
21 | COX7C | COX7C | COX7C | 6439 | 0.053 | 0.29 | NO
22 | ATP1A2 | ATP1A2 | ATP1A2 | 6527 | 0.052 | 0.29 | NO
23 | COX6B1 | COX6B1 | COX6B1 | 7319 | 0.038 | 0.25 | NO
24 | UQCR10 | UQCR10 | UQCR10 | 7533 | 0.034 | 0.24 | NO
25 | COX4I1 | COX4I1 | COX4I1 | 7547 | 0.034 | 0.24 | NO
26 | UQCR11 | UQCR11 | UQCR11 | 8065 | 0.026 | 0.22 | NO
27 | UQCRH | UQCRH | UQCRH | 8081 | 0.026 | 0.22 | NO
28 | SLC9A1 | SLC9A1 | SLC9A1 | 8290 | 0.023 | 0.21 | NO
29 | UQCRHL | UQCRHL | UQCRHL | 8828 | 0.016 | 0.18 | NO
30 | COX7A2L | COX7A2L | COX7A2L | 8841 | 0.015 | 0.18 | NO
31 | COX6A1 | COX6A1 | COX6A1 | 9427 | 0.0074 | 0.15 | NO
32 | UQCRQ | UQCRQ | UQCRQ | 9573 | 0.0056 | 0.14 | NO
33 | ATP1B1 | ATP1B1 | ATP1B1 | 9649 | 0.0041 | 0.14 | NO
34 | COX6C | COX6C | COX6C | 9676 | 0.0038 | 0.14 | NO
35 | MYH7 | MYH7 | MYH7 | 10255 | -0.0039 | 0.11 | NO
36 | UQCRFS1 | UQCRFS1 | UQCRFS1 | 10700 | -0.01 | 0.082 | NO
37 | TPM3 | TPM3 | TPM3 | 10925 | -0.014 | 0.072 | NO
38 | UQCRC1 | UQCRC1 | UQCRC1 | 11045 | -0.015 | 0.067 | NO
39 | CYC1 | CYC1 | CYC1 | 11421 | -0.021 | 0.048 | NO
40 | COX5B | COX5B | COX5B | 11614 | -0.024 | 0.04 | NO
41 | COX7B | COX7B | COX7B | 11783 | -0.027 | 0.034 | NO
42 | COX5A | COX5A | COX5A | 12072 | -0.032 | 0.022 | NO
43 | FXYD2 | FXYD2 | FXYD2 | 12272 | -0.036 | 0.015 | NO
44 | CACNB4 | CACNB4 | CACNB4 | 12546 | -0.041 | 0.0047 | NO
45 | COX8A | COX8A | COX8A | 12693 | -0.044 | 0.0021 | NO
46 | ATP2A2 | ATP2A2 | ATP2A2 | 12853 | -0.048 | -0.0008 | NO
47 | COX7A1 | COX7A1 | COX7A1 | 12896 | -0.049 | 0.0031 | NO
48 | RYR2 | RYR2 | RYR2 | 13060 | -0.052 | 0.00059 | NO
49 | ATP1B3 | ATP1B3 | ATP1B3 | 13103 | -0.054 | 0.0051 | NO
50 | SLC9A6 | SLC9A6 | SLC9A6 | 13136 | -0.054 | 0.01 | NO
51 | CACNB3 | CACNB3 | CACNB3 | 13400 | -0.062 | 0.0033 | NO
52 | COX7A2 | COX7A2 | COX7A2 | 13609 | -0.068 | 0.00025 | NO
53 | TPM4 | TPM4 | TPM4 | 13617 | -0.068 | 0.0087 | NO
54 | ATP1A1 | ATP1A1 | ATP1A1 | 13789 | -0.073 | 0.0084 | NO
55 | COX8C | COX8C | COX8C | 15105 | -0.13 | -0.05 | NO
56 | TPM2 | TPM2 | TPM2 | 15273 | -0.14 | -0.042 | NO
57 | ATP1A4 | ATP1A4 | ATP1A4 | 15291 | -0.14 | -0.025 | NO
58 | CACNA2D1 | CACNA2D1 | CACNA2D1 | 15547 | -0.16 | -0.02 | NO
59 | TPM1 | TPM1 | TPM1 | 15589 | -0.16 | -0.0014 | NO
60 | MYH6 | MYH6 | MYH6 | 15815 | -0.18 | 0.0085 | NO
61 | SLC8A1 | SLC8A1 | SLC8A1 | 15867 | -0.18 | 0.029 | NO
62 | ACTC1 | ACTC1 | ACTC1 | 16494 | -0.25 | 0.025 | NO
63 | CACNG4 | CACNG4 | CACNG4 | 16694 | -0.28 | 0.05 | 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 WNT SIGNALING PATHWAY.

Figure S36. 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 CELL ADHESION MOLECULES CAMS

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 | FLT3 | FLT3 | FLT3 | 67 | 0.77 | 0.16 | YES
2 | TCF7 | TCF7 | TCF7 | 389 | 0.49 | 0.24 | YES
3 | ZBTB16 | ZBTB16 | ZBTB16 | 988 | 0.35 | 0.28 | YES
4 | KIT | KIT | KIT | 1291 | 0.3 | 0.32 | YES
5 | TCF7L1 | TCF7L1 | TCF7L1 | 1795 | 0.25 | 0.34 | YES
6 | LEF1 | LEF1 | LEF1 | 2274 | 0.21 | 0.36 | YES
7 | PIK3R3 | PIK3R3 | PIK3R3 | 4935 | 0.087 | 0.23 | NO
8 | IKBKB | IKBKB | IKBKB | 5046 | 0.085 | 0.24 | NO
9 | SOS1 | SOS1 | SOS1 | 5097 | 0.083 | 0.25 | NO
10 | RARA | RARA | RARA | 5450 | 0.075 | 0.25 | NO
11 | TCF7L2 | TCF7L2 | TCF7L2 | 5527 | 0.073 | 0.26 | NO
12 | PIK3R5 | PIK3R5 | PIK3R5 | 5842 | 0.065 | 0.25 | NO
13 | PIK3CD | PIK3CD | PIK3CD | 6610 | 0.05 | 0.22 | NO
14 | MAP2K2 | MAP2K2 | MAP2K2 | 6644 | 0.05 | 0.23 | NO
15 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 7296 | 0.038 | 0.2 | NO
16 | MYC | MYC | MYC | 7762 | 0.031 | 0.18 | NO
17 | PIK3R2 | PIK3R2 | PIK3R2 | 7909 | 0.028 | 0.18 | NO
18 | SOS2 | SOS2 | SOS2 | 8082 | 0.026 | 0.17 | NO
19 | STAT5B | STAT5B | STAT5B | 8460 | 0.021 | 0.15 | NO
20 | MTOR | MTOR | MTOR | 9106 | 0.012 | 0.12 | NO
21 | BAD | BAD | BAD | 9492 | 0.0065 | 0.098 | NO
22 | STAT5A | STAT5A | STAT5A | 9532 | 0.0061 | 0.098 | NO
23 | HRAS | HRAS | HRAS | 9645 | 0.0042 | 0.092 | NO
24 | RUNX1T1 | RUNX1T1 | RUNX1T1 | 9870 | 0.0012 | 0.079 | NO
25 | AKT2 | AKT2 | AKT2 | 9898 | 0.0008 | 0.078 | NO
26 | MAP2K1 | MAP2K1 | MAP2K1 | 10055 | -0.0013 | 0.069 | NO
27 | MAPK1 | MAPK1 | MAPK1 | 10098 | -0.002 | 0.067 | NO
28 | MAPK3 | MAPK3 | MAPK3 | 10359 | -0.0055 | 0.054 | NO
29 | PIK3R1 | PIK3R1 | PIK3R1 | 10385 | -0.0058 | 0.053 | NO
30 | IKBKG | IKBKG | IKBKG | 10455 | -0.0066 | 0.051 | NO
31 | PML | PML | PML | 10563 | -0.0081 | 0.046 | NO
32 | RPS6KB2 | RPS6KB2 | RPS6KB2 | 10833 | -0.012 | 0.034 | NO
33 | RELA | RELA | RELA | 10870 | -0.012 | 0.034 | NO
34 | PIK3CB | PIK3CB | PIK3CB | 11003 | -0.015 | 0.03 | NO
35 | RAF1 | RAF1 | RAF1 | 11534 | -0.023 | 0.0039 | NO
36 | PIK3CA | PIK3CA | PIK3CA | 11608 | -0.024 | 0.0046 | NO
37 | KRAS | KRAS | KRAS | 11611 | -0.024 | 0.0094 | NO
38 | GRB2 | GRB2 | GRB2 | 11623 | -0.024 | 0.014 | NO
39 | ARAF | ARAF | ARAF | 11932 | -0.03 | 0.0023 | NO
40 | AKT1 | AKT1 | AKT1 | 11936 | -0.03 | 0.0082 | NO
41 | NFKB1 | NFKB1 | NFKB1 | 12109 | -0.033 | 0.0052 | NO
42 | JUP | JUP | JUP | 12874 | -0.048 | -0.028 | NO
43 | SPI1 | SPI1 | SPI1 | 13214 | -0.057 | -0.036 | NO
44 | AKT3 | AKT3 | AKT3 | 13287 | -0.059 | -0.028 | NO
45 | CCND1 | CCND1 | CCND1 | 13448 | -0.064 | -0.024 | NO
46 | CCNA1 | CCNA1 | CCNA1 | 13515 | -0.065 | -0.015 | NO
47 | NRAS | NRAS | NRAS | 13630 | -0.068 | -0.0071 | NO
48 | PIK3CG | PIK3CG | PIK3CG | 13807 | -0.074 | -0.002 | NO
49 | RUNX1 | RUNX1 | RUNX1 | 14013 | -0.08 | 0.0028 | NO
50 | CHUK | CHUK | CHUK | 14560 | -0.1 | -0.0074 | NO
51 | CEBPA | CEBPA | CEBPA | 14565 | -0.1 | 0.014 | NO
52 | STAT3 | STAT3 | STAT3 | 14838 | -0.12 | 0.022 | NO
53 | BRAF | BRAF | BRAF | 14910 | -0.12 | 0.042 | NO
54 | PIM1 | PIM1 | PIM1 | 15312 | -0.14 | 0.048 | NO
55 | PIM2 | PIM2 | PIM2 | 15605 | -0.16 | 0.064 | NO
56 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 16394 | -0.23 | 0.067 | 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 CELL ADHESION MOLECULES CAMS.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CELL ADHESION MOLECULES CAMS, 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 INTESTINAL IMMUNE NETWORK FOR IGA PRODUCTION

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 | ADCY5 | ADCY5 | ADCY5 | 43 | 0.83 | 0.056 | YES
2 | GNAO1 | GNAO1 | GNAO1 | 169 | 0.62 | 0.093 | YES
3 | TCF7 | TCF7 | TCF7 | 389 | 0.49 | 0.12 | YES
4 | CAMK2B | CAMK2B | CAMK2B | 426 | 0.48 | 0.15 | YES
5 | EDNRB | EDNRB | EDNRB | 484 | 0.46 | 0.18 | YES
6 | WNT10B | WNT10B | WNT10B | 572 | 0.43 | 0.2 | YES
7 | CREB3L3 | CREB3L3 | CREB3L3 | 733 | 0.4 | 0.22 | YES
8 | CALML6 | CALML6 | CALML6 | 790 | 0.38 | 0.24 | YES
9 | WNT6 | WNT6 | WNT6 | 927 | 0.36 | 0.26 | YES
10 | WNT7A | WNT7A | WNT7A | 1136 | 0.32 | 0.27 | YES
11 | WNT16 | WNT16 | WNT16 | 1168 | 0.32 | 0.29 | YES
12 | KIT | KIT | KIT | 1291 | 0.3 | 0.31 | YES
13 | FZD8 | FZD8 | FZD8 | 1324 | 0.3 | 0.33 | YES
14 | ADCY1 | ADCY1 | ADCY1 | 1446 | 0.29 | 0.34 | YES
15 | PLCB4 | PLCB4 | PLCB4 | 1556 | 0.27 | 0.35 | YES
16 | FZD7 | FZD7 | FZD7 | 1614 | 0.27 | 0.37 | YES
17 | WNT1 | WNT1 | WNT1 | 1627 | 0.27 | 0.39 | YES
18 | PRKCA | PRKCA | PRKCA | 1756 | 0.25 | 0.4 | YES
19 | PRKCB | PRKCB | PRKCB | 1791 | 0.25 | 0.41 | YES
20 | TCF7L1 | TCF7L1 | TCF7L1 | 1795 | 0.25 | 0.43 | YES
21 | PRKCG | PRKCG | PRKCG | 1881 | 0.24 | 0.44 | YES
22 | FZD10 | FZD10 | FZD10 | 1958 | 0.24 | 0.46 | YES
23 | LEF1 | LEF1 | LEF1 | 2274 | 0.21 | 0.45 | NO
24 | WNT5B | WNT5B | WNT5B | 2643 | 0.18 | 0.44 | NO
25 | CREB3L2 | CREB3L2 | CREB3L2 | 2929 | 0.17 | 0.44 | NO
26 | EDN1 | EDN1 | EDN1 | 2976 | 0.16 | 0.45 | NO
27 | KITLG | KITLG | KITLG | 3107 | 0.16 | 0.45 | NO
28 | ADCY9 | ADCY9 | ADCY9 | 3994 | 0.12 | 0.41 | NO
29 | CREB3L4 | CREB3L4 | CREB3L4 | 4209 | 0.11 | 0.4 | NO
30 | WNT4 | WNT4 | WNT4 | 4278 | 0.1 | 0.41 | NO
31 | MC1R | MC1R | MC1R | 4343 | 0.1 | 0.41 | NO
32 | CALML5 | CALML5 | CALML5 | 4345 | 0.1 | 0.42 | NO
33 | CAMK2D | CAMK2D | CAMK2D | 4515 | 0.098 | 0.42 | NO
34 | WNT8B | WNT8B | WNT8B | 4587 | 0.096 | 0.42 | NO
35 | CREBBP | CREBBP | CREBBP | 4729 | 0.092 | 0.42 | NO
36 | CAMK2G | CAMK2G | CAMK2G | 4970 | 0.087 | 0.41 | NO
37 | DVL1 | DVL1 | DVL1 | 5125 | 0.083 | 0.41 | NO
38 | ADCY6 | ADCY6 | ADCY6 | 5273 | 0.079 | 0.4 | NO
39 | PLCB1 | PLCB1 | PLCB1 | 5417 | 0.075 | 0.4 | NO
40 | TCF7L2 | TCF7L2 | TCF7L2 | 5527 | 0.073 | 0.4 | NO
41 | ADCY4 | ADCY4 | ADCY4 | 5559 | 0.072 | 0.4 | NO
42 | GNAI1 | GNAI1 | GNAI1 | 5773 | 0.067 | 0.4 | NO
43 | DVL2 | DVL2 | DVL2 | 6435 | 0.053 | 0.36 | NO
44 | MAP2K2 | MAP2K2 | MAP2K2 | 6644 | 0.05 | 0.35 | NO
45 | FZD4 | FZD4 | FZD4 | 6818 | 0.046 | 0.35 | NO
46 | WNT9A | WNT9A | WNT9A | 6842 | 0.046 | 0.35 | NO
47 | ADCY7 | ADCY7 | ADCY7 | 7462 | 0.036 | 0.32 | NO
48 | GNAS | GNAS | GNAS | 7508 | 0.035 | 0.32 | NO
49 | PRKACA | PRKACA | PRKACA | 8450 | 0.021 | 0.26 | NO
50 | EP300 | EP300 | EP300 | 8466 | 0.021 | 0.26 | NO
51 | CREB1 | CREB1 | CREB1 | 8961 | 0.014 | 0.24 | NO
52 | CALML3 | CALML3 | CALML3 | 9268 | 0.0095 | 0.22 | NO
53 | HRAS | HRAS | HRAS | 9645 | 0.0042 | 0.2 | NO
54 | PLCB2 | PLCB2 | PLCB2 | 9826 | 0.0019 | 0.19 | NO
55 | PRKACB | PRKACB | PRKACB | 10030 | -0.00093 | 0.18 | NO
56 | MAP2K1 | MAP2K1 | MAP2K1 | 10055 | -0.0013 | 0.18 | NO
57 | MAPK1 | MAPK1 | MAPK1 | 10098 | -0.002 | 0.17 | NO
58 | WNT3 | WNT3 | WNT3 | 10155 | -0.0026 | 0.17 | NO
59 | CALM3 | CALM3 | CALM3 | 10189 | -0.0031 | 0.17 | NO
60 | WNT2B | WNT2B | WNT2B | 10225 | -0.0036 | 0.17 | NO
61 | MAPK3 | MAPK3 | MAPK3 | 10359 | -0.0055 | 0.16 | NO
62 | POMC | POMC | POMC | 10361 | -0.0055 | 0.16 | NO
63 | DVL3 | DVL3 | DVL3 | 10539 | -0.0078 | 0.15 | NO
64 | CALM1 | CALM1 | CALM1 | 10694 | -0.01 | 0.14 | NO
65 | CREB3 | CREB3 | CREB3 | 10849 | -0.012 | 0.14 | NO
66 | ADCY2 | ADCY2 | ADCY2 | 10901 | -0.013 | 0.13 | NO
67 | FZD3 | FZD3 | FZD3 | 10968 | -0.014 | 0.13 | NO
68 | WNT11 | WNT11 | WNT11 | 11159 | -0.017 | 0.12 | NO
69 | GNAI2 | GNAI2 | GNAI2 | 11508 | -0.022 | 0.1 | NO
70 | RAF1 | RAF1 | RAF1 | 11534 | -0.023 | 0.1 | NO
71 | KRAS | KRAS | KRAS | 11611 | -0.024 | 0.1 | NO
72 | FZD6 | FZD6 | FZD6 | 11618 | -0.024 | 0.1 | NO
73 | PRKX | PRKX | PRKX | 12290 | -0.036 | 0.065 | NO
74 | CTNNB1 | CTNNB1 | CTNNB1 | 12534 | -0.041 | 0.054 | NO
75 | CALM2 | CALM2 | CALM2 | 12587 | -0.042 | 0.054 | NO
76 | GSK3B | GSK3B | GSK3B | 12703 | -0.045 | 0.051 | NO
77 | WNT10A | WNT10A | WNT10A | 13038 | -0.052 | 0.035 | NO
78 | NRAS | NRAS | NRAS | 13630 | -0.068 | 0.0062 | NO
79 | PLCB3 | PLCB3 | PLCB3 | 13754 | -0.072 | 0.0042 | NO
80 | GNAQ | GNAQ | GNAQ | 14066 | -0.082 | -0.0078 | NO
81 | FZD9 | FZD9 | FZD9 | 14185 | -0.087 | -0.0084 | NO
82 | GNAI3 | GNAI3 | GNAI3 | 14273 | -0.091 | -0.007 | NO
83 | FZD2 | FZD2 | FZD2 | 14507 | -0.1 | -0.013 | NO
84 | TYRP1 | TYRP1 | TYRP1 | 14600 | -0.1 | -0.011 | NO
85 | ASIP | ASIP | ASIP | 14907 | -0.12 | -0.02 | NO
86 | WNT7B | WNT7B | WNT7B | 15509 | -0.15 | -0.044 | NO
87 | WNT5A | WNT5A | WNT5A | 15692 | -0.17 | -0.043 | NO
88 | MITF | MITF | MITF | 16364 | -0.23 | -0.065 | NO
89 | FZD5 | FZD5 | FZD5 | 16411 | -0.24 | -0.051 | NO
90 | FZD1 | FZD1 | FZD1 | 16707 | -0.28 | -0.048 | NO
91 | CAMK2A | CAMK2A | CAMK2A | 17098 | -0.37 | -0.045 | NO
92 | CREB3L1 | CREB3L1 | CREB3L1 | 17327 | -0.47 | -0.025 | NO
93 | WNT2 | WNT2 | WNT2 | 17432 | -0.54 | 0.0073 | 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 INTESTINAL IMMUNE NETWORK FOR IGA PRODUCTION.

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG INTESTINAL IMMUNE NETWORK FOR IGA PRODUCTION, 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 = DLBC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

- Phenotype data file = DLBC-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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