GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in DLBC-TP
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
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/C1T152TB
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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA 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

Expression level

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

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

Significant gene list

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

Methods & Data
Input
  • Gene set database = c2.cp.v3.0-2.symbols.gmt

  • Expression data file = 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.

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)