GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in MESO-TP
Mesothelioma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1R49Q0C
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in MESO-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1R49Q0C
Overview
Introduction

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

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

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

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

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

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

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

Summary

Table 1.  Get Full Table basic data info

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

Table 2.  Get Full Table pheno data info

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

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

  • clus1

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

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

  • clus2

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

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

  • clus3

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

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

  • clus4

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

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

Results
Subtype clus1 enriched pathways

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

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

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

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

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

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

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADH6 ADH6 ADH6 1 1.3 0.13 YES
2 ADH1A ADH1A ADH1A 2 1.2 0.25 YES
3 ADH1B ADH1B ADH1B 13 0.79 0.34 YES
4 ALDH3B2 ALDH3B2 ALDH3B2 520 0.33 0.34 YES
5 ADH1C ADH1C ADH1C 640 0.31 0.37 YES
6 ADH4 ADH4 ADH4 671 0.3 0.4 YES
7 ALDH3B1 ALDH3B1 ALDH3B1 849 0.26 0.42 YES
8 PGM1 PGM1 PGM1 910 0.25 0.44 YES
9 ALDH3A2 ALDH3A2 ALDH3A2 1083 0.23 0.45 YES
10 PGM2 PGM2 PGM2 1669 0.16 0.44 YES
11 ADH5 ADH5 ADH5 1713 0.16 0.45 YES
12 ALDH2 ALDH2 ALDH2 1818 0.15 0.46 YES
13 PFKM PFKM PFKM 3235 0.084 0.39 NO
14 LDHA LDHA LDHA 3333 0.08 0.4 NO
15 PDHB PDHB PDHB 3497 0.075 0.39 NO
16 PCK2 PCK2 PCK2 3642 0.071 0.39 NO
17 HK2 HK2 HK2 3693 0.07 0.4 NO
18 ALDH9A1 ALDH9A1 ALDH9A1 4232 0.057 0.38 NO
19 DLD DLD DLD 4312 0.055 0.38 NO
20 DLAT DLAT DLAT 4464 0.051 0.37 NO
21 ALDOA ALDOA ALDOA 4999 0.04 0.35 NO
22 ACSS2 ACSS2 ACSS2 5305 0.035 0.34 NO
23 GPI GPI GPI 5338 0.035 0.34 NO
24 PGAM1 PGAM1 PGAM1 5522 0.032 0.33 NO
25 AKR1A1 AKR1A1 AKR1A1 5961 0.024 0.31 NO
26 PGAM4 PGAM4 PGAM4 6134 0.022 0.3 NO
27 ENO1 ENO1 ENO1 6254 0.02 0.3 NO
28 TPI1 TPI1 TPI1 6709 0.013 0.27 NO
29 PFKL PFKL PFKL 6941 0.01 0.26 NO
30 ALDH7A1 ALDH7A1 ALDH7A1 7531 0.0023 0.23 NO
31 PFKP PFKP PFKP 7562 0.0018 0.23 NO
32 PGK1 PGK1 PGK1 7797 -0.0017 0.22 NO
33 LDHAL6A LDHAL6A LDHAL6A 8524 -0.012 0.18 NO
34 HK3 HK3 HK3 8609 -0.013 0.17 NO
35 PDHA1 PDHA1 PDHA1 9793 -0.032 0.11 NO
36 PKM2 PKM2 PKM2 9965 -0.035 0.1 NO
37 GAPDH GAPDH GAPDH 10062 -0.036 0.1 NO
38 FBP1 FBP1 FBP1 10107 -0.037 0.1 NO
39 LDHB LDHB LDHB 11151 -0.058 0.054 NO
40 ALDH3A1 ALDH3A1 ALDH3A1 11239 -0.06 0.055 NO
41 ENO2 ENO2 ENO2 12235 -0.083 0.009 NO
42 ACSS1 ACSS1 ACSS1 13114 -0.11 -0.028 NO
43 ENO3 ENO3 ENO3 13341 -0.12 -0.028 NO
44 BPGM BPGM BPGM 13894 -0.14 -0.043 NO
45 ALDOB ALDOB ALDOB 14515 -0.17 -0.06 NO
46 PKLR PKLR PKLR 14678 -0.18 -0.051 NO
47 ALDH1B1 ALDH1B1 ALDH1B1 14707 -0.18 -0.034 NO
48 HK1 HK1 HK1 14745 -0.18 -0.017 NO
49 GALM GALM GALM 14883 -0.19 -0.005 NO
50 LDHAL6B LDHAL6B LDHAL6B 15461 -0.22 -0.014 NO
51 PCK1 PCK1 PCK1 15695 -0.24 -0.0015 NO
52 PGAM2 PGAM2 PGAM2 16218 -0.28 -0.0013 NO
53 ALDOC ALDOC ALDOC 16399 -0.29 0.019 NO
54 GCK GCK GCK 16619 -0.31 0.04 NO
55 ALDH1A3 ALDH1A3 ALDH1A3 17650 -0.45 0.03 NO

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

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACSM1 ACSM1 ACSM1 310 0.41 0.11 YES
2 BDH2 BDH2 BDH2 817 0.27 0.17 YES
3 ALDH5A1 ALDH5A1 ALDH5A1 855 0.26 0.24 YES
4 ALDH3A2 ALDH3A2 ALDH3A2 1083 0.23 0.3 YES
5 AACS AACS AACS 1163 0.21 0.36 YES
6 ACADS ACADS ACADS 1421 0.19 0.41 YES
7 ABAT ABAT ABAT 1582 0.17 0.45 YES
8 ALDH2 ALDH2 ALDH2 1818 0.15 0.49 YES
9 HMGCL HMGCL HMGCL 3421 0.077 0.42 NO
10 PDHB PDHB PDHB 3497 0.075 0.44 NO
11 ALDH9A1 ALDH9A1 ALDH9A1 4232 0.057 0.42 NO
12 ACSM5 ACSM5 ACSM5 4575 0.049 0.42 NO
13 HADH HADH HADH 5060 0.039 0.4 NO
14 ECHS1 ECHS1 ECHS1 5469 0.032 0.39 NO
15 HADHA HADHA HADHA 6751 0.013 0.32 NO
16 L2HGDH L2HGDH L2HGDH 6842 0.012 0.32 NO
17 ALDH7A1 ALDH7A1 ALDH7A1 7531 0.0023 0.28 NO
18 ACAT2 ACAT2 ACAT2 7596 0.0014 0.28 NO
19 ACAT1 ACAT1 ACAT1 8804 -0.016 0.22 NO
20 GAD1 GAD1 GAD1 8826 -0.017 0.22 NO
21 PDHA1 PDHA1 PDHA1 9793 -0.032 0.18 NO
22 OXCT1 OXCT1 OXCT1 11053 -0.056 0.13 NO
23 ACSM3 ACSM3 ACSM3 11744 -0.071 0.11 NO
24 AKR1B10 AKR1B10 AKR1B10 12346 -0.087 0.1 NO
25 BDH1 BDH1 BDH1 13113 -0.11 0.097 NO
26 HMGCS1 HMGCS1 HMGCS1 13912 -0.14 0.097 NO
27 ALDH1B1 ALDH1B1 ALDH1B1 14707 -0.18 0.11 NO
28 OXCT2 OXCT2 OXCT2 16148 -0.27 0.11 NO

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

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

Table S4.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GFPT2 GFPT2 GFPT2 386 0.38 0.073 YES
2 GALK2 GALK2 GALK2 907 0.25 0.11 YES
3 PGM1 PGM1 PGM1 910 0.25 0.17 YES
4 CHIT1 CHIT1 CHIT1 1044 0.23 0.22 YES
5 UGP2 UGP2 UGP2 1353 0.19 0.25 YES
6 FPGT FPGT FPGT 1436 0.18 0.29 YES
7 GALE GALE GALE 1442 0.18 0.34 YES
8 FUK FUK FUK 1539 0.18 0.38 YES
9 PGM2 PGM2 PGM2 1669 0.16 0.41 YES
10 AMDHD2 AMDHD2 AMDHD2 2071 0.13 0.42 YES
11 PMM2 PMM2 PMM2 2965 0.092 0.4 NO
12 NANP NANP NANP 3499 0.075 0.38 NO
13 MPI MPI MPI 3621 0.072 0.4 NO
14 HK2 HK2 HK2 3693 0.07 0.41 NO
15 UGDH UGDH UGDH 4340 0.054 0.39 NO
16 CMAS CMAS CMAS 4470 0.051 0.39 NO
17 GMPPB GMPPB GMPPB 5014 0.04 0.37 NO
18 GNPDA1 GNPDA1 GNPDA1 5306 0.035 0.36 NO
19 GPI GPI GPI 5338 0.035 0.37 NO
20 HEXA HEXA HEXA 5399 0.034 0.38 NO
21 GFPT1 GFPT1 GFPT1 5671 0.029 0.37 NO
22 GMPPA GMPPA GMPPA 5768 0.027 0.37 NO
23 GMDS GMDS GMDS 6273 0.02 0.35 NO
24 GALT GALT GALT 6372 0.018 0.35 NO
25 GALK1 GALK1 GALK1 6418 0.018 0.35 NO
26 RENBP RENBP RENBP 7453 0.0034 0.29 NO
27 TSTA3 TSTA3 TSTA3 7598 0.0013 0.28 NO
28 NAGK NAGK NAGK 7875 -0.0026 0.27 NO
29 PMM1 PMM1 PMM1 8538 -0.012 0.24 NO
30 HK3 HK3 HK3 8609 -0.013 0.24 NO
31 NANS NANS NANS 8638 -0.014 0.24 NO
32 CYB5R1 CYB5R1 CYB5R1 8720 -0.015 0.24 NO
33 NPL NPL NPL 8848 -0.017 0.24 NO
34 HEXB HEXB HEXB 8970 -0.019 0.23 NO
35 UXS1 UXS1 UXS1 9906 -0.034 0.19 NO
36 UAP1 UAP1 UAP1 10014 -0.036 0.19 NO
37 PGM3 PGM3 PGM3 12099 -0.08 0.098 NO
38 GNPDA2 GNPDA2 GNPDA2 12106 -0.08 0.12 NO
39 GNE GNE GNE 14120 -0.15 0.044 NO
40 HK1 HK1 HK1 14745 -0.18 0.055 NO
41 GNPNAT1 GNPNAT1 GNPNAT1 15609 -0.23 0.065 NO
42 GCK GCK GCK 16619 -0.31 0.086 NO

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

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

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

Table S5.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADH6 ADH6 ADH6 1 1.3 0.14 YES
2 ADH1A ADH1A ADH1A 2 1.2 0.26 YES
3 ADH1B ADH1B ADH1B 13 0.79 0.35 YES
4 TAT TAT TAT 143 0.51 0.4 YES
5 ALDH3B2 ALDH3B2 ALDH3B2 520 0.33 0.41 YES
6 ADH1C ADH1C ADH1C 640 0.31 0.44 YES
7 ADH4 ADH4 ADH4 671 0.3 0.47 YES
8 ALDH3B1 ALDH3B1 ALDH3B1 849 0.26 0.48 YES
9 AOC2 AOC2 AOC2 935 0.25 0.51 YES
10 DCT DCT DCT 1069 0.23 0.52 YES
11 ADH5 ADH5 ADH5 1713 0.16 0.51 NO
12 HPD HPD HPD 2896 0.094 0.45 NO
13 GSTZ1 GSTZ1 GSTZ1 2945 0.092 0.46 NO
14 LCMT2 LCMT2 LCMT2 3105 0.087 0.46 NO
15 METTL6 METTL6 METTL6 3422 0.077 0.45 NO
16 MIF MIF MIF 3857 0.065 0.43 NO
17 GOT1 GOT1 GOT1 4102 0.06 0.43 NO
18 TPO TPO TPO 5344 0.034 0.36 NO
19 METTL2B METTL2B METTL2B 7599 0.0013 0.24 NO
20 MAOB MAOB MAOB 7718 -0.00055 0.23 NO
21 DDC DDC DDC 8694 -0.014 0.18 NO
22 COMT COMT COMT 8702 -0.015 0.18 NO
23 FAH FAH FAH 8771 -0.016 0.18 NO
24 IL4I1 IL4I1 IL4I1 9149 -0.022 0.16 NO
25 WBSCR22 WBSCR22 WBSCR22 9357 -0.025 0.15 NO
26 ALDH3A1 ALDH3A1 ALDH3A1 11239 -0.06 0.054 NO
27 LCMT1 LCMT1 LCMT1 11441 -0.064 0.05 NO
28 GOT2 GOT2 GOT2 11988 -0.077 0.028 NO
29 TRMT11 TRMT11 TRMT11 12908 -0.1 -0.012 NO
30 TYR TYR TYR 13600 -0.13 -0.036 NO
31 HEMK1 HEMK1 HEMK1 13667 -0.13 -0.025 NO
32 NAT6 NAT6 NAT6 13840 -0.14 -0.02 NO
33 AOX1 AOX1 AOX1 15163 -0.2 -0.07 NO
34 TH TH TH 15317 -0.21 -0.056 NO
35 HGD HGD HGD 15536 -0.23 -0.043 NO
36 AOC3 AOC3 AOC3 15746 -0.24 -0.029 NO
37 DBH DBH DBH 16682 -0.32 -0.046 NO
38 PNMT PNMT PNMT 16709 -0.32 -0.014 NO
39 MAOA MAOA MAOA 17583 -0.43 -0.015 NO
40 ALDH1A3 ALDH1A3 ALDH1A3 17650 -0.45 0.03 NO

Figure S9.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG TYROSINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GPR37 GPR37 GPR37 135 0.52 0.066 YES
2 SNCA SNCA SNCA 393 0.38 0.1 YES
3 PARK2 PARK2 PARK2 801 0.27 0.12 YES
4 SLC6A3 SLC6A3 SLC6A3 1192 0.21 0.13 YES
5 SLC25A4 SLC25A4 SLC25A4 1242 0.2 0.15 YES
6 NDUFC1 NDUFC1 NDUFC1 1445 0.18 0.17 YES
7 UBE2L6 UBE2L6 UBE2L6 1824 0.15 0.17 YES
8 NDUFB1 NDUFB1 NDUFB1 1904 0.14 0.18 YES
9 CASP3 CASP3 CASP3 2083 0.13 0.19 YES
10 NDUFB5 NDUFB5 NDUFB5 2511 0.11 0.19 YES
11 COX7A1 COX7A1 COX7A1 2793 0.099 0.18 YES
12 ATP5G1 ATP5G1 ATP5G1 3037 0.089 0.18 YES
13 ATP5H ATP5H ATP5H 3065 0.088 0.2 YES
14 NDUFA2 NDUFA2 NDUFA2 3110 0.087 0.2 YES
15 CASP9 CASP9 CASP9 3126 0.087 0.22 YES
16 ATP5G3 ATP5G3 ATP5G3 3195 0.085 0.22 YES
17 NDUFA3 NDUFA3 NDUFA3 3388 0.079 0.22 YES
18 NDUFB4 NDUFB4 NDUFB4 3542 0.074 0.23 YES
19 SDHD SDHD SDHD 3648 0.071 0.23 YES
20 COX7C COX7C COX7C 3775 0.068 0.23 YES
21 UQCR10 UQCR10 UQCR10 3849 0.066 0.24 YES
22 NDUFV3 NDUFV3 NDUFV3 3858 0.065 0.25 YES
23 COX5B COX5B COX5B 3887 0.065 0.26 YES
24 SLC25A6 SLC25A6 SLC25A6 3897 0.064 0.26 YES
25 NDUFB6 NDUFB6 NDUFB6 3928 0.064 0.27 YES
26 ATP5F1 ATP5F1 ATP5F1 3954 0.063 0.28 YES
27 COX8C COX8C COX8C 3959 0.063 0.29 YES
28 UBE2J2 UBE2J2 UBE2J2 4030 0.061 0.29 YES
29 NDUFA7 NDUFA7 NDUFA7 4063 0.06 0.3 YES
30 NDUFS8 NDUFS8 NDUFS8 4173 0.058 0.3 YES
31 NDUFS4 NDUFS4 NDUFS4 4238 0.057 0.3 YES
32 ATP5A1 ATP5A1 ATP5A1 4243 0.057 0.31 YES
33 UQCRFS1 UQCRFS1 UQCRFS1 4264 0.056 0.32 YES
34 HTRA2 HTRA2 HTRA2 4356 0.053 0.32 YES
35 ATP5C1 ATP5C1 ATP5C1 4425 0.052 0.33 YES
36 COX6A1 COX6A1 COX6A1 4499 0.05 0.33 YES
37 ATP5B ATP5B ATP5B 4525 0.05 0.33 YES
38 PARK7 PARK7 PARK7 4678 0.046 0.33 YES
39 PINK1 PINK1 PINK1 4689 0.046 0.34 YES
40 UBA7 UBA7 UBA7 4698 0.046 0.34 YES
41 UQCRB UQCRB UQCRB 4795 0.044 0.34 YES
42 COX7B COX7B COX7B 4924 0.042 0.34 YES
43 NDUFV1 NDUFV1 NDUFV1 4942 0.042 0.35 YES
44 ATP5G2 ATP5G2 ATP5G2 4991 0.041 0.35 YES
45 NDUFA10 NDUFA10 NDUFA10 5054 0.039 0.35 YES
46 NDUFB3 NDUFB3 NDUFB3 5069 0.039 0.36 YES
47 UQCRQ UQCRQ UQCRQ 5117 0.038 0.36 YES
48 ATP5O ATP5O ATP5O 5140 0.038 0.37 YES
49 NDUFS5 NDUFS5 NDUFS5 5153 0.038 0.37 YES
50 NDUFA9 NDUFA9 NDUFA9 5377 0.034 0.36 YES
51 COX4I1 COX4I1 COX4I1 5403 0.034 0.37 YES
52 NDUFB10 NDUFB10 NDUFB10 5417 0.033 0.37 YES
53 NDUFB7 NDUFB7 NDUFB7 5512 0.032 0.37 YES
54 NDUFA8 NDUFA8 NDUFA8 5541 0.031 0.37 YES
55 UQCR11 UQCR11 UQCR11 5567 0.031 0.38 YES
56 VDAC2 VDAC2 VDAC2 5612 0.03 0.38 YES
57 UQCRC2 UQCRC2 UQCRC2 5771 0.027 0.37 YES
58 COX8A COX8A COX8A 5813 0.026 0.37 YES
59 NDUFS3 NDUFS3 NDUFS3 5823 0.026 0.38 YES
60 COX6C COX6C COX6C 5847 0.026 0.38 YES
61 ATP5J ATP5J ATP5J 5874 0.025 0.38 YES
62 COX7A2L COX7A2L COX7A2L 5938 0.025 0.38 YES
63 SDHA SDHA SDHA 6020 0.024 0.38 YES
64 NDUFB2 NDUFB2 NDUFB2 6048 0.023 0.38 YES
65 UBE2L3 UBE2L3 UBE2L3 6129 0.022 0.38 YES
66 NDUFB8 NDUFB8 NDUFB8 6149 0.022 0.38 YES
67 NDUFS1 NDUFS1 NDUFS1 6173 0.021 0.38 YES
68 SDHB SDHB SDHB 6182 0.021 0.39 YES
69 UBB UBB UBB 6302 0.02 0.38 NO
70 NDUFV2 NDUFV2 NDUFV2 6475 0.017 0.38 NO
71 NDUFA1 NDUFA1 NDUFA1 6557 0.016 0.37 NO
72 CYCS CYCS CYCS 6572 0.015 0.38 NO
73 NDUFS2 NDUFS2 NDUFS2 6601 0.015 0.38 NO
74 UBA1 UBA1 UBA1 6606 0.015 0.38 NO
75 NDUFC2 NDUFC2 NDUFC2 6933 0.01 0.36 NO
76 VDAC3 VDAC3 VDAC3 6982 0.0096 0.36 NO
77 NDUFA4 NDUFA4 NDUFA4 6988 0.0095 0.36 NO
78 ATP5E ATP5E ATP5E 7044 0.0088 0.36 NO
79 CYC1 CYC1 CYC1 7207 0.0068 0.35 NO
80 ATP5D ATP5D ATP5D 7433 0.0036 0.34 NO
81 NDUFS7 NDUFS7 NDUFS7 7585 0.0015 0.33 NO
82 NDUFA5 NDUFA5 NDUFA5 7606 0.0012 0.33 NO
83 UQCRHL UQCRHL UQCRHL 7725 -0.00062 0.32 NO
84 UQCRH UQCRH UQCRH 7834 -0.0021 0.32 NO
85 PPID PPID PPID 7843 -0.0022 0.32 NO
86 COX7A2 COX7A2 COX7A2 7866 -0.0025 0.32 NO
87 COX5A COX5A COX5A 8017 -0.0048 0.31 NO
88 SDHC SDHC SDHC 8170 -0.0068 0.3 NO
89 NDUFAB1 NDUFAB1 NDUFAB1 8329 -0.0094 0.29 NO
90 COX6B1 COX6B1 COX6B1 8469 -0.011 0.29 NO
91 NDUFS6 NDUFS6 NDUFS6 8569 -0.013 0.28 NO
92 NDUFB9 NDUFB9 NDUFB9 8587 -0.013 0.28 NO
93 UBE2G2 UBE2G2 UBE2G2 8896 -0.018 0.27 NO
94 UBE2J1 UBE2J1 UBE2J1 9007 -0.019 0.27 NO
95 SLC25A5 SLC25A5 SLC25A5 9571 -0.028 0.24 NO
96 VDAC1 VDAC1 VDAC1 9658 -0.03 0.24 NO
97 NDUFA6 NDUFA6 NDUFA6 10364 -0.042 0.21 NO
98 UQCRC1 UQCRC1 UQCRC1 10462 -0.043 0.21 NO
99 UBE2G1 UBE2G1 UBE2G1 10514 -0.044 0.21 NO
100 SNCAIP SNCAIP SNCAIP 11117 -0.057 0.19 NO
101 NDUFA4L2 NDUFA4L2 NDUFA4L2 11319 -0.062 0.18 NO
102 SLC18A1 SLC18A1 SLC18A1 11425 -0.064 0.19 NO
103 LRRK2 LRRK2 LRRK2 12386 -0.088 0.15 NO
104 APAF1 APAF1 APAF1 13002 -0.11 0.13 NO
105 UCHL1 UCHL1 UCHL1 14023 -0.14 0.091 NO
106 SLC18A2 SLC18A2 SLC18A2 14444 -0.16 0.09 NO
107 COX6A2 COX6A2 COX6A2 14495 -0.16 0.11 NO
108 COX6B2 COX6B2 COX6B2 15122 -0.2 0.1 NO
109 TH TH TH 15317 -0.21 0.12 NO
110 COX4I2 COX4I2 COX4I2 15785 -0.24 0.13 NO

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

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

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

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

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

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

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

genes ES table in pathway: KEGG SPHINGOLIPID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 DCP1B DCP1B DCP1B 2265 0.12 -0.08 YES
2 EXOSC9 EXOSC9 EXOSC9 2310 0.12 -0.039 YES
3 LSM3 LSM3 LSM3 2610 0.11 -0.018 YES
4 EXOSC6 EXOSC6 EXOSC6 2730 0.1 0.012 YES
5 PNPT1 PNPT1 PNPT1 3503 0.075 -0.0038 YES
6 SKIV2L2 SKIV2L2 SKIV2L2 3698 0.069 0.01 YES
7 LSM6 LSM6 LSM6 3715 0.069 0.034 YES
8 XRN1 XRN1 XRN1 4081 0.06 0.035 YES
9 CNOT4 CNOT4 CNOT4 4193 0.058 0.05 YES
10 CNOT6L CNOT6L CNOT6L 4580 0.049 0.046 YES
11 CNOT1 CNOT1 CNOT1 4719 0.046 0.055 YES
12 WDR61 WDR61 WDR61 4851 0.043 0.063 YES
13 C1D C1D C1D 5080 0.039 0.064 YES
14 NAA38 NAA38 NAA38 5342 0.034 0.062 YES
15 SKIV2L SKIV2L SKIV2L 5418 0.033 0.07 YES
16 CNOT6 CNOT6 CNOT6 5714 0.028 0.064 YES
17 EXOSC10 EXOSC10 EXOSC10 5746 0.028 0.072 YES
18 LSM5 LSM5 LSM5 5822 0.026 0.077 YES
19 PAPOLA PAPOLA PAPOLA 5843 0.026 0.086 YES
20 DDX6 DDX6 DDX6 5901 0.025 0.091 YES
21 EDC4 EDC4 EDC4 6195 0.021 0.083 YES
22 ENO1 ENO1 ENO1 6254 0.02 0.087 YES
23 LSM4 LSM4 LSM4 6311 0.019 0.09 YES
24 EXOSC3 EXOSC3 EXOSC3 6346 0.019 0.095 YES
25 PARN PARN PARN 6351 0.019 0.1 YES
26 CNOT2 CNOT2 CNOT2 6986 0.0095 0.07 YES
27 CNOT10 CNOT10 CNOT10 7059 0.0086 0.069 YES
28 CNOT7 CNOT7 CNOT7 7082 0.0084 0.071 YES
29 HSPD1 HSPD1 HSPD1 7091 0.0082 0.074 YES
30 DIS3 DIS3 DIS3 7492 0.0029 0.053 YES
31 EXOSC4 EXOSC4 EXOSC4 7518 0.0025 0.052 YES
32 LSM1 LSM1 LSM1 7699 -0.00035 0.042 YES
33 EXOSC8 EXOSC8 EXOSC8 7810 -0.0018 0.037 YES
34 HSPA9 HSPA9 HSPA9 7862 -0.0024 0.035 YES
35 PATL1 PATL1 PATL1 8041 -0.0052 0.027 YES
36 EXOSC5 EXOSC5 EXOSC5 9313 -0.024 -0.034 YES
37 EXOSC1 EXOSC1 EXOSC1 9453 -0.027 -0.033 YES
38 EXOSC2 EXOSC2 EXOSC2 10077 -0.037 -0.054 YES
39 XRN2 XRN2 XRN2 10447 -0.043 -0.059 YES
40 DCP2 DCP2 DCP2 10461 -0.043 -0.044 YES
41 TTC37 TTC37 TTC37 10657 -0.047 -0.038 YES
42 MPHOSPH6 MPHOSPH6 MPHOSPH6 10716 -0.048 -0.024 YES
43 CNOT3 CNOT3 CNOT3 10765 -0.049 -0.009 YES
44 LSM7 LSM7 LSM7 11197 -0.059 -0.012 YES
45 ZCCHC7 ZCCHC7 ZCCHC7 11224 -0.06 0.0083 YES
46 LSM2 LSM2 LSM2 11690 -0.07 0.0076 YES
47 DCP1A DCP1A DCP1A 12173 -0.082 0.01 YES
48 PAPOLB PAPOLB PAPOLB 12200 -0.082 0.038 YES
49 ENO2 ENO2 ENO2 12235 -0.083 0.066 YES
50 PAPOLG PAPOLG PAPOLG 12289 -0.085 0.094 YES
51 EDC3 EDC3 EDC3 12420 -0.089 0.12 YES
52 PAPD7 PAPD7 PAPD7 12576 -0.094 0.14 YES
53 DCPS DCPS DCPS 12995 -0.11 0.16 YES
54 RQCD1 RQCD1 RQCD1 13150 -0.11 0.19 YES
55 ENO3 ENO3 ENO3 13341 -0.12 0.22 YES
56 EXOSC7 EXOSC7 EXOSC7 13450 -0.12 0.26 YES

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

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

genes ES table in pathway: KEGG PROPANOATE METABOLISM

Table S9.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 KIR2DL3 KIR2DL3 KIR2DL3 286 0.42 0.066 YES
2 HLA-G HLA-G HLA-G 420 0.37 0.13 YES
3 KLRC1 KLRC1 KLRC1 453 0.36 0.2 YES
4 KIR3DL1 KIR3DL1 KIR3DL1 592 0.32 0.25 YES
5 KLRD1 KLRD1 KLRD1 613 0.31 0.31 YES
6 KIR2DL1 KIR2DL1 KIR2DL1 677 0.3 0.36 YES
7 GZMB GZMB GZMB 819 0.27 0.41 YES
8 IL1B IL1B IL1B 840 0.26 0.46 YES
9 HLA-F HLA-F HLA-F 846 0.26 0.51 YES
10 PRF1 PRF1 PRF1 1185 0.21 0.53 YES
11 KIR3DL2 KIR3DL2 KIR3DL2 1504 0.18 0.55 YES
12 HLA-C HLA-C HLA-C 1913 0.14 0.55 YES
13 HLA-B HLA-B HLA-B 2059 0.14 0.57 YES
14 HLA-A HLA-A HLA-A 2270 0.12 0.58 YES
15 HLA-E HLA-E HLA-E 2281 0.12 0.6 YES
16 CD28 CD28 CD28 2299 0.12 0.63 YES
17 FASLG FASLG FASLG 2339 0.12 0.65 YES
18 TNF TNF TNF 3012 0.09 0.63 NO
19 HLA-DOB HLA-DOB HLA-DOB 3478 0.076 0.62 NO
20 CD86 CD86 CD86 6678 0.014 0.44 NO
21 FAS FAS FAS 6713 0.013 0.44 NO
22 HLA-DMA HLA-DMA HLA-DMA 6811 0.012 0.44 NO
23 HLA-DRB1 HLA-DRB1 HLA-DRB1 8432 -0.011 0.35 NO
24 IL2 IL2 IL2 8996 -0.019 0.33 NO
25 CD80 CD80 CD80 9363 -0.025 0.31 NO
26 HLA-DMB HLA-DMB HLA-DMB 9534 -0.028 0.31 NO
27 HLA-DRB5 HLA-DRB5 HLA-DRB5 10259 -0.04 0.28 NO
28 HLA-DRA HLA-DRA HLA-DRA 10522 -0.044 0.27 NO
29 HLA-DPA1 HLA-DPA1 HLA-DPA1 10766 -0.049 0.26 NO
30 IL6 IL6 IL6 11005 -0.054 0.26 NO
31 HLA-DPB1 HLA-DPB1 HLA-DPB1 11547 -0.066 0.24 NO
32 HLA-DQA2 HLA-DQA2 HLA-DQA2 11952 -0.076 0.24 NO
33 IFNG IFNG IFNG 13517 -0.13 0.18 NO
34 HLA-DOA HLA-DOA HLA-DOA 13704 -0.13 0.19 NO
35 HLA-DQA1 HLA-DQA1 HLA-DQA1 13884 -0.14 0.21 NO
36 IL1A IL1A IL1A 14074 -0.15 0.23 NO

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

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SNCA SNCA SNCA 393 0.38 0.01 YES
2 PLCB1 PLCB1 PLCB1 449 0.36 0.038 YES
3 CHP CHP CHP 590 0.32 0.057 YES
4 ERN1 ERN1 ERN1 652 0.3 0.079 YES
5 CACNA1F CACNA1F CACNA1F 667 0.3 0.1 YES
6 IL1B IL1B IL1B 840 0.26 0.12 YES
7 GRIN2B GRIN2B GRIN2B 1270 0.2 0.11 YES
8 MAPT MAPT MAPT 1284 0.2 0.13 YES
9 NDUFC1 NDUFC1 NDUFC1 1445 0.18 0.13 YES
10 CALML5 CALML5 CALML5 1446 0.18 0.15 YES
11 GRIN2A GRIN2A GRIN2A 1773 0.16 0.14 YES
12 NDUFB1 NDUFB1 NDUFB1 1904 0.14 0.15 YES
13 CASP3 CASP3 CASP3 2083 0.13 0.15 YES
14 BACE2 BACE2 BACE2 2446 0.11 0.14 YES
15 NDUFB5 NDUFB5 NDUFB5 2511 0.11 0.15 YES
16 ITPR3 ITPR3 ITPR3 2616 0.11 0.15 YES
17 ATP2A1 ATP2A1 ATP2A1 2623 0.1 0.16 YES
18 CASP8 CASP8 CASP8 2633 0.1 0.17 YES
19 COX7A1 COX7A1 COX7A1 2793 0.099 0.17 YES
20 CHP2 CHP2 CHP2 2833 0.097 0.17 YES
21 TNF TNF TNF 3012 0.09 0.17 YES
22 ATP5G1 ATP5G1 ATP5G1 3037 0.089 0.18 YES
23 ATP5H ATP5H ATP5H 3065 0.088 0.18 YES
24 NDUFA2 NDUFA2 NDUFA2 3110 0.087 0.19 YES
25 CASP9 CASP9 CASP9 3126 0.087 0.19 YES
26 TNFRSF1A TNFRSF1A TNFRSF1A 3155 0.086 0.2 YES
27 ATP5G3 ATP5G3 ATP5G3 3195 0.085 0.2 YES
28 NDUFA3 NDUFA3 NDUFA3 3388 0.079 0.2 YES
29 NDUFB4 NDUFB4 NDUFB4 3542 0.074 0.2 YES
30 SDHD SDHD SDHD 3648 0.071 0.2 YES
31 COX7C COX7C COX7C 3775 0.068 0.2 YES
32 UQCR10 UQCR10 UQCR10 3849 0.066 0.2 YES
33 NDUFV3 NDUFV3 NDUFV3 3858 0.065 0.2 YES
34 COX5B COX5B COX5B 3887 0.065 0.21 YES
35 FADD FADD FADD 3888 0.065 0.21 YES
36 NDUFB6 NDUFB6 NDUFB6 3928 0.064 0.22 YES
37 ATP5F1 ATP5F1 ATP5F1 3954 0.063 0.22 YES
38 COX8C COX8C COX8C 3959 0.063 0.23 YES
39 NDUFA7 NDUFA7 NDUFA7 4063 0.06 0.22 YES
40 NDUFS8 NDUFS8 NDUFS8 4173 0.058 0.22 YES
41 NDUFS4 NDUFS4 NDUFS4 4238 0.057 0.22 YES
42 ATP5A1 ATP5A1 ATP5A1 4243 0.057 0.23 YES
43 UQCRFS1 UQCRFS1 UQCRFS1 4264 0.056 0.23 YES
44 MAPK3 MAPK3 MAPK3 4374 0.053 0.23 YES
45 ATP5C1 ATP5C1 ATP5C1 4425 0.052 0.23 YES
46 COX6A1 COX6A1 COX6A1 4499 0.05 0.23 YES
47 ATP5B ATP5B ATP5B 4525 0.05 0.24 YES
48 PSEN1 PSEN1 PSEN1 4547 0.049 0.24 YES
49 BAD BAD BAD 4577 0.049 0.24 YES
50 PSEN2 PSEN2 PSEN2 4673 0.046 0.24 YES
51 NAE1 NAE1 NAE1 4759 0.045 0.24 YES
52 UQCRB UQCRB UQCRB 4795 0.044 0.24 YES
53 COX7B COX7B COX7B 4924 0.042 0.24 YES
54 NDUFV1 NDUFV1 NDUFV1 4942 0.042 0.24 YES
55 ATP5G2 ATP5G2 ATP5G2 4991 0.041 0.24 YES
56 NDUFA10 NDUFA10 NDUFA10 5054 0.039 0.24 YES
57 NDUFB3 NDUFB3 NDUFB3 5069 0.039 0.24 YES
58 UQCRQ UQCRQ UQCRQ 5117 0.038 0.24 YES
59 ATP5O ATP5O ATP5O 5140 0.038 0.25 YES
60 NDUFS5 NDUFS5 NDUFS5 5153 0.038 0.25 YES
61 PPP3CA PPP3CA PPP3CA 5327 0.035 0.24 YES
62 NDUFA9 NDUFA9 NDUFA9 5377 0.034 0.24 YES
63 CAPN2 CAPN2 CAPN2 5380 0.034 0.25 YES
64 COX4I1 COX4I1 COX4I1 5403 0.034 0.25 YES
65 NDUFB10 NDUFB10 NDUFB10 5417 0.033 0.25 YES
66 CAPN1 CAPN1 CAPN1 5429 0.033 0.25 YES
67 APH1A APH1A APH1A 5433 0.033 0.25 YES
68 ADAM10 ADAM10 ADAM10 5478 0.032 0.26 YES
69 APP APP APP 5493 0.032 0.26 YES
70 NDUFB7 NDUFB7 NDUFB7 5512 0.032 0.26 YES
71 NDUFA8 NDUFA8 NDUFA8 5541 0.031 0.26 YES
72 UQCR11 UQCR11 UQCR11 5567 0.031 0.26 YES
73 GSK3B GSK3B GSK3B 5571 0.03 0.26 YES
74 PSENEN PSENEN PSENEN 5592 0.03 0.26 YES
75 CALML3 CALML3 CALML3 5684 0.029 0.26 YES
76 APOE APOE APOE 5708 0.028 0.26 YES
77 UQCRC2 UQCRC2 UQCRC2 5771 0.027 0.26 YES
78 COX8A COX8A COX8A 5813 0.026 0.26 YES
79 NDUFS3 NDUFS3 NDUFS3 5823 0.026 0.26 YES
80 COX6C COX6C COX6C 5847 0.026 0.26 YES
81 ATP5J ATP5J ATP5J 5874 0.025 0.26 YES
82 COX7A2L COX7A2L COX7A2L 5938 0.025 0.26 NO
83 SDHA SDHA SDHA 6020 0.024 0.26 NO
84 NDUFB2 NDUFB2 NDUFB2 6048 0.023 0.26 NO
85 NDUFB8 NDUFB8 NDUFB8 6149 0.022 0.26 NO
86 NDUFS1 NDUFS1 NDUFS1 6173 0.021 0.26 NO
87 SDHB SDHB SDHB 6182 0.021 0.26 NO
88 NDUFV2 NDUFV2 NDUFV2 6475 0.017 0.24 NO
89 NDUFA1 NDUFA1 NDUFA1 6557 0.016 0.24 NO
90 CYCS CYCS CYCS 6572 0.015 0.24 NO
91 NDUFS2 NDUFS2 NDUFS2 6601 0.015 0.24 NO
92 BID BID BID 6660 0.014 0.24 NO
93 FAS FAS FAS 6713 0.013 0.24 NO
94 EIF2AK3 EIF2AK3 EIF2AK3 6774 0.012 0.24 NO
95 ITPR1 ITPR1 ITPR1 6900 0.011 0.23 NO
96 LRP1 LRP1 LRP1 6919 0.01 0.23 NO
97 NDUFC2 NDUFC2 NDUFC2 6933 0.01 0.23 NO
98 PLCB2 PLCB2 PLCB2 6968 0.0097 0.23 NO
99 NDUFA4 NDUFA4 NDUFA4 6988 0.0095 0.23 NO
100 ATP5E ATP5E ATP5E 7044 0.0088 0.23 NO
101 CALM2 CALM2 CALM2 7182 0.007 0.22 NO
102 CYC1 CYC1 CYC1 7207 0.0068 0.22 NO
103 PPP3CC PPP3CC PPP3CC 7313 0.0054 0.21 NO
104 ATP5D ATP5D ATP5D 7433 0.0036 0.21 NO
105 NDUFS7 NDUFS7 NDUFS7 7585 0.0015 0.2 NO
106 NDUFA5 NDUFA5 NDUFA5 7606 0.0012 0.2 NO
107 UQCRHL UQCRHL UQCRHL 7725 -0.00062 0.19 NO
108 UQCRH UQCRH UQCRH 7834 -0.0021 0.19 NO
109 COX7A2 COX7A2 COX7A2 7866 -0.0025 0.18 NO
110 CALM3 CALM3 CALM3 7942 -0.0038 0.18 NO
111 COX5A COX5A COX5A 8017 -0.0048 0.18 NO
112 HSD17B10 HSD17B10 HSD17B10 8053 -0.0054 0.18 NO
113 CASP7 CASP7 CASP7 8055 -0.0054 0.18 NO
114 NCSTN NCSTN NCSTN 8163 -0.0067 0.17 NO
115 SDHC SDHC SDHC 8170 -0.0068 0.17 NO
116 NDUFAB1 NDUFAB1 NDUFAB1 8329 -0.0094 0.16 NO
117 COX6B1 COX6B1 COX6B1 8469 -0.011 0.16 NO
118 NDUFS6 NDUFS6 NDUFS6 8569 -0.013 0.15 NO
119 NDUFB9 NDUFB9 NDUFB9 8587 -0.013 0.15 NO
120 GNAQ GNAQ GNAQ 8717 -0.015 0.15 NO
121 ITPR2 ITPR2 ITPR2 8719 -0.015 0.15 NO
122 MAPK1 MAPK1 MAPK1 8903 -0.018 0.14 NO
123 CALM1 CALM1 CALM1 9026 -0.02 0.13 NO
124 CDK5 CDK5 CDK5 9311 -0.024 0.12 NO
125 PPP3CB PPP3CB PPP3CB 9558 -0.028 0.11 NO
126 PPP3R1 PPP3R1 PPP3R1 9759 -0.032 0.1 NO
127 ATP2A2 ATP2A2 ATP2A2 9836 -0.033 0.098 NO
128 GAPDH GAPDH GAPDH 10062 -0.036 0.089 NO
129 GRIN2C GRIN2C GRIN2C 10101 -0.037 0.09 NO
130 BACE1 BACE1 BACE1 10232 -0.039 0.086 NO
131 NDUFA6 NDUFA6 NDUFA6 10364 -0.042 0.082 NO
132 UQCRC1 UQCRC1 UQCRC1 10462 -0.043 0.081 NO
133 PLCB3 PLCB3 PLCB3 10753 -0.049 0.069 NO
134 CALML6 CALML6 CALML6 10930 -0.052 0.064 NO
135 ADAM17 ADAM17 ADAM17 11293 -0.061 0.049 NO
136 NDUFA4L2 NDUFA4L2 NDUFA4L2 11319 -0.062 0.053 NO
137 ATF6 ATF6 ATF6 11339 -0.062 0.057 NO
138 ATP2A3 ATP2A3 ATP2A3 11949 -0.076 0.03 NO
139 IDE IDE IDE 12068 -0.079 0.03 NO
140 LPL LPL LPL 12988 -0.11 -0.012 NO
141 APAF1 APAF1 APAF1 13002 -0.11 -0.0038 NO
142 CACNA1D CACNA1D CACNA1D 13336 -0.12 -0.012 NO
143 GRIN1 GRIN1 GRIN1 13485 -0.12 -0.0098 NO
144 APBB1 APBB1 APBB1 13504 -0.12 -9e-05 NO
145 COX6A2 COX6A2 COX6A2 14495 -0.16 -0.041 NO
146 COX6B2 COX6B2 COX6B2 15122 -0.2 -0.058 NO
147 CACNA1C CACNA1C CACNA1C 15563 -0.23 -0.063 NO
148 CDK5R1 CDK5R1 CDK5R1 15583 -0.23 -0.045 NO
149 COX4I2 COX4I2 COX4I2 15785 -0.24 -0.035 NO
150 CACNA1S CACNA1S CACNA1S 15974 -0.26 -0.024 NO
151 MME MME MME 17062 -0.36 -0.054 NO
152 PLCB4 PLCB4 PLCB4 17326 -0.39 -0.035 NO
153 GRIN2D GRIN2D GRIN2D 17395 -0.4 -0.0044 NO
154 RYR3 RYR3 RYR3 18001 -0.57 0.01 NO

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

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

Fold change

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

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

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

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

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

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

genes ES table in pathway: BIOCARTA RHO PATHWAY

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

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

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

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

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

Table S13.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 UGT1A9 UGT1A9 UGT1A9 324 0.45 0.083 YES
2 MGAM MGAM MGAM 452 0.4 0.16 YES
3 UGT1A1 UGT1A1 UGT1A1 948 0.29 0.2 YES
4 GCK GCK GCK 1039 0.28 0.26 YES
5 UGT1A6 UGT1A6 UGT1A6 1082 0.27 0.32 YES
6 AMY2B AMY2B AMY2B 1409 0.24 0.36 YES
7 UGT1A10 UGT1A10 UGT1A10 1441 0.23 0.41 YES
8 PYGM PYGM PYGM 1458 0.23 0.46 YES
9 GBA3 GBA3 GBA3 1467 0.23 0.51 YES
10 UGT2A1 UGT2A1 UGT2A1 1717 0.21 0.54 YES
11 UGT1A8 UGT1A8 UGT1A8 1787 0.2 0.58 YES
12 ENPP1 ENPP1 ENPP1 2132 0.18 0.6 YES
13 AGL AGL AGL 4695 0.077 0.48 NO
14 AMY1A AMY1A AMY1A 5201 0.066 0.47 NO
15 GBE1 GBE1 GBE1 5629 0.058 0.46 NO
16 PGM2 PGM2 PGM2 6001 0.05 0.45 NO
17 GPI GPI GPI 6764 0.038 0.42 NO
18 UGP2 UGP2 UGP2 7611 0.026 0.37 NO
19 GUSB GUSB GUSB 7744 0.025 0.37 NO
20 HK2 HK2 HK2 8708 0.012 0.32 NO
21 AMY2A AMY2A AMY2A 9306 0.0043 0.29 NO
22 GAA GAA GAA 10438 -0.01 0.23 NO
23 UGDH UGDH UGDH 11341 -0.022 0.19 NO
24 PYGB PYGB PYGB 11507 -0.024 0.18 NO
25 ENPP3 ENPP3 ENPP3 12329 -0.036 0.14 NO
26 GYS2 GYS2 GYS2 12338 -0.036 0.15 NO
27 PGM1 PGM1 PGM1 13320 -0.054 0.11 NO
28 GYS1 GYS1 GYS1 13365 -0.055 0.12 NO
29 HK1 HK1 HK1 13681 -0.062 0.12 NO
30 PYGL PYGL PYGL 13946 -0.069 0.12 NO
31 GANC GANC GANC 14660 -0.091 0.099 NO
32 PGM2L1 PGM2L1 PGM2L1 14938 -0.1 0.11 NO
33 TREH TREH TREH 16139 -0.16 0.076 NO
34 HK3 HK3 HK3 16274 -0.17 0.1 NO

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

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

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MAOA MAOA MAOA 26 0.71 0.072 YES
2 AOX1 AOX1 AOX1 73 0.62 0.13 YES
3 MAOB MAOB MAOB 159 0.53 0.18 YES
4 UGT1A9 UGT1A9 UGT1A9 324 0.45 0.22 YES
5 ADH1C ADH1C ADH1C 426 0.41 0.26 YES
6 CYP2E1 CYP2E1 CYP2E1 428 0.41 0.3 YES
7 MGST1 MGST1 MGST1 492 0.38 0.33 YES
8 ALDH1A3 ALDH1A3 ALDH1A3 508 0.38 0.37 YES
9 ALDH3A1 ALDH3A1 ALDH3A1 515 0.37 0.41 YES
10 GSTM2 GSTM2 GSTM2 701 0.34 0.43 YES
11 UGT1A1 UGT1A1 UGT1A1 948 0.29 0.45 YES
12 FMO4 FMO4 FMO4 993 0.29 0.48 YES
13 UGT1A6 UGT1A6 UGT1A6 1082 0.27 0.5 YES
14 GSTO2 GSTO2 GSTO2 1134 0.27 0.53 YES
15 CYP2C18 CYP2C18 CYP2C18 1139 0.27 0.55 YES
16 GSTA4 GSTA4 GSTA4 1374 0.24 0.56 YES
17 UGT1A10 UGT1A10 UGT1A10 1441 0.23 0.59 YES
18 GSTM3 GSTM3 GSTM3 1652 0.21 0.6 YES
19 UGT2A1 UGT2A1 UGT2A1 1717 0.21 0.61 YES
20 UGT1A8 UGT1A8 UGT1A8 1787 0.2 0.63 YES
21 GSTM4 GSTM4 GSTM4 1842 0.2 0.65 YES
22 MGST2 MGST2 MGST2 2651 0.15 0.62 NO
23 GSTM1 GSTM1 GSTM1 2833 0.14 0.62 NO
24 CYP3A7 CYP3A7 CYP3A7 2885 0.14 0.63 NO
25 FMO5 FMO5 FMO5 3123 0.12 0.63 NO
26 CYP2C8 CYP2C8 CYP2C8 3306 0.12 0.64 NO
27 CYP2C9 CYP2C9 CYP2C9 3415 0.11 0.64 NO
28 ALDH3B1 ALDH3B1 ALDH3B1 4116 0.091 0.61 NO
29 CYP2A7 CYP2A7 CYP2A7 4154 0.09 0.62 NO
30 FMO1 FMO1 FMO1 4384 0.084 0.62 NO
31 ADH1B ADH1B ADH1B 4591 0.079 0.61 NO
32 CYP2A6 CYP2A6 CYP2A6 4650 0.078 0.62 NO
33 MGST3 MGST3 MGST3 4957 0.071 0.61 NO
34 GSTK1 GSTK1 GSTK1 6186 0.048 0.55 NO
35 CYP3A5 CYP3A5 CYP3A5 6222 0.047 0.55 NO
36 GSTP1 GSTP1 GSTP1 6438 0.044 0.54 NO
37 CYP2D6 CYP2D6 CYP2D6 6969 0.035 0.52 NO
38 GSTA1 GSTA1 GSTA1 8026 0.021 0.46 NO
39 ALDH3B2 ALDH3B2 ALDH3B2 8236 0.018 0.45 NO
40 ADH5 ADH5 ADH5 10310 -0.0087 0.34 NO
41 CYP2A13 CYP2A13 CYP2A13 10380 -0.0095 0.33 NO
42 GSTT1 GSTT1 GSTT1 10709 -0.014 0.32 NO
43 GSTO1 GSTO1 GSTO1 10976 -0.017 0.3 NO
44 FMO3 FMO3 FMO3 12007 -0.031 0.25 NO
45 ADH6 ADH6 ADH6 12575 -0.04 0.22 NO
46 GSTT2 GSTT2 GSTT2 12911 -0.046 0.21 NO
47 CYP1A2 CYP1A2 CYP1A2 13263 -0.053 0.2 NO
48 FMO2 FMO2 FMO2 13850 -0.067 0.17 NO
49 CYP3A43 CYP3A43 CYP3A43 13870 -0.067 0.18 NO
50 ADH4 ADH4 ADH4 14516 -0.086 0.15 NO
51 GSTM5 GSTM5 GSTM5 14559 -0.087 0.16 NO
52 GSTA2 GSTA2 GSTA2 15419 -0.12 0.12 NO
53 ADH1A ADH1A ADH1A 15697 -0.13 0.12 NO
54 GSTZ1 GSTZ1 GSTZ1 16497 -0.18 0.093 NO

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

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACSS3 ACSS3 ACSS3 176 0.52 0.16 YES
2 EHHADH EHHADH EHHADH 322 0.45 0.3 YES
3 LDHAL6A LDHAL6A LDHAL6A 1532 0.22 0.31 YES
4 HIBCH HIBCH HIBCH 1815 0.2 0.36 YES
5 ACAT1 ACAT1 ACAT1 2961 0.13 0.34 YES
6 PCCA PCCA PCCA 3029 0.13 0.38 YES
7 ABAT ABAT ABAT 3270 0.12 0.41 YES
8 ALDH1B1 ALDH1B1 ALDH1B1 3282 0.12 0.45 YES
9 MCEE MCEE MCEE 3407 0.11 0.48 YES
10 SUCLA2 SUCLA2 SUCLA2 4235 0.088 0.46 YES
11 MUT MUT MUT 4500 0.081 0.48 YES
12 ALDH7A1 ALDH7A1 ALDH7A1 4559 0.08 0.5 YES
13 MLYCD MLYCD MLYCD 4675 0.077 0.52 YES
14 ACSS1 ACSS1 ACSS1 5322 0.064 0.51 NO
15 SUCLG2 SUCLG2 SUCLG2 5520 0.06 0.52 NO
16 ACSS2 ACSS2 ACSS2 5900 0.052 0.51 NO
17 ACACA ACACA ACACA 6295 0.046 0.5 NO
18 SUCLG1 SUCLG1 SUCLG1 6683 0.04 0.5 NO
19 ALDH3A2 ALDH3A2 ALDH3A2 6741 0.039 0.51 NO
20 LDHA LDHA LDHA 6990 0.035 0.5 NO
21 ALDH9A1 ALDH9A1 ALDH9A1 7049 0.034 0.51 NO
22 ALDH2 ALDH2 ALDH2 7424 0.029 0.5 NO
23 LDHB LDHB LDHB 9079 0.0072 0.41 NO
24 ACADM ACADM ACADM 9381 0.0034 0.4 NO
25 LDHAL6B LDHAL6B LDHAL6B 10230 -0.0077 0.35 NO
26 ACACB ACACB ACACB 10433 -0.01 0.35 NO
27 PCCB PCCB PCCB 10627 -0.013 0.34 NO
28 ALDH6A1 ALDH6A1 ALDH6A1 10738 -0.014 0.34 NO
29 HADHA HADHA HADHA 10838 -0.015 0.34 NO
30 ECHS1 ECHS1 ECHS1 11889 -0.029 0.29 NO
31 ACAT2 ACAT2 ACAT2 16370 -0.17 0.1 NO

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

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 UGT1A9 UGT1A9 UGT1A9 324 0.45 0.034 YES
2 CYP2S1 CYP2S1 CYP2S1 377 0.43 0.08 YES
3 ADH1C ADH1C ADH1C 426 0.41 0.12 YES
4 CYP2E1 CYP2E1 CYP2E1 428 0.41 0.17 YES
5 MGST1 MGST1 MGST1 492 0.38 0.21 YES
6 ALDH1A3 ALDH1A3 ALDH1A3 508 0.38 0.25 YES
7 ALDH3A1 ALDH3A1 ALDH3A1 515 0.37 0.3 YES
8 AKR1C2 AKR1C2 AKR1C2 686 0.34 0.33 YES
9 GSTM2 GSTM2 GSTM2 701 0.34 0.36 YES
10 UGT1A1 UGT1A1 UGT1A1 948 0.29 0.38 YES
11 UGT1A6 UGT1A6 UGT1A6 1082 0.27 0.41 YES
12 GSTO2 GSTO2 GSTO2 1134 0.27 0.44 YES
13 CYP2C18 CYP2C18 CYP2C18 1139 0.27 0.47 YES
14 GSTA4 GSTA4 GSTA4 1374 0.24 0.48 YES
15 UGT1A10 UGT1A10 UGT1A10 1441 0.23 0.51 YES
16 AKR1C1 AKR1C1 AKR1C1 1563 0.22 0.53 YES
17 GSTM3 GSTM3 GSTM3 1652 0.21 0.55 YES
18 UGT2A1 UGT2A1 UGT2A1 1717 0.21 0.57 YES
19 UGT1A8 UGT1A8 UGT1A8 1787 0.2 0.58 YES
20 GSTM4 GSTM4 GSTM4 1842 0.2 0.6 YES
21 CYP2F1 CYP2F1 CYP2F1 2588 0.15 0.58 YES
22 MGST2 MGST2 MGST2 2651 0.15 0.6 YES
23 GSTM1 GSTM1 GSTM1 2833 0.14 0.6 YES
24 CYP3A7 CYP3A7 CYP3A7 2885 0.14 0.61 YES
25 AKR1C3 AKR1C3 AKR1C3 3170 0.12 0.61 YES
26 CYP2C8 CYP2C8 CYP2C8 3306 0.12 0.62 YES
27 CYP2C9 CYP2C9 CYP2C9 3415 0.11 0.62 YES
28 CYP1B1 CYP1B1 CYP1B1 3660 0.1 0.62 NO
29 EPHX1 EPHX1 EPHX1 4012 0.095 0.62 NO
30 ALDH3B1 ALDH3B1 ALDH3B1 4116 0.091 0.62 NO
31 ADH1B ADH1B ADH1B 4591 0.079 0.6 NO
32 MGST3 MGST3 MGST3 4957 0.071 0.59 NO
33 GSTK1 GSTK1 GSTK1 6186 0.048 0.53 NO
34 CYP3A5 CYP3A5 CYP3A5 6222 0.047 0.53 NO
35 GSTP1 GSTP1 GSTP1 6438 0.044 0.53 NO
36 GSTA1 GSTA1 GSTA1 8026 0.021 0.44 NO
37 ALDH3B2 ALDH3B2 ALDH3B2 8236 0.018 0.43 NO
38 CYP1A1 CYP1A1 CYP1A1 8695 0.012 0.41 NO
39 ADH5 ADH5 ADH5 10310 -0.0087 0.32 NO
40 GSTT1 GSTT1 GSTT1 10709 -0.014 0.3 NO
41 GSTO1 GSTO1 GSTO1 10976 -0.017 0.29 NO
42 ADH6 ADH6 ADH6 12575 -0.04 0.2 NO
43 GSTT2 GSTT2 GSTT2 12911 -0.046 0.19 NO
44 CYP1A2 CYP1A2 CYP1A2 13263 -0.053 0.18 NO
45 CYP3A43 CYP3A43 CYP3A43 13870 -0.067 0.15 NO
46 ADH4 ADH4 ADH4 14516 -0.086 0.12 NO
47 GSTM5 GSTM5 GSTM5 14559 -0.087 0.13 NO
48 GSTA2 GSTA2 GSTA2 15419 -0.12 0.099 NO
49 ADH1A ADH1A ADH1A 15697 -0.13 0.099 NO
50 DHDH DHDH DHDH 16001 -0.15 0.1 NO
51 GSTZ1 GSTZ1 GSTZ1 16497 -0.18 0.093 NO

Figure S31.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG ARGININE AND PROLINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ME1 ME1 ME1 864 0.31 0.06 YES
2 PKLR PKLR PKLR 1521 0.22 0.1 YES
3 LDHAL6A LDHAL6A LDHAL6A 1532 0.22 0.18 YES
4 LDHD LDHD LDHD 2668 0.14 0.17 YES
5 ACAT1 ACAT1 ACAT1 2961 0.13 0.2 YES
6 ALDH1B1 ALDH1B1 ALDH1B1 3282 0.12 0.22 YES
7 AKR1B1 AKR1B1 AKR1B1 3473 0.11 0.25 YES
8 HAGHL HAGHL HAGHL 3662 0.1 0.28 YES
9 PCK1 PCK1 PCK1 3748 0.1 0.31 YES
10 ME3 ME3 ME3 3837 0.1 0.34 YES
11 ALDH7A1 ALDH7A1 ALDH7A1 4559 0.08 0.33 YES
12 PDHB PDHB PDHB 4805 0.074 0.34 YES
13 HAGH HAGH HAGH 4886 0.072 0.36 YES
14 PDHA1 PDHA1 PDHA1 5094 0.068 0.38 YES
15 ACSS1 ACSS1 ACSS1 5322 0.064 0.38 YES
16 GLO1 GLO1 GLO1 5538 0.059 0.39 YES
17 DLD DLD DLD 5720 0.056 0.4 YES
18 ACSS2 ACSS2 ACSS2 5900 0.052 0.41 YES
19 PC PC PC 5909 0.052 0.43 YES
20 ACACA ACACA ACACA 6295 0.046 0.42 NO
21 ALDH3A2 ALDH3A2 ALDH3A2 6741 0.039 0.41 NO
22 LDHA LDHA LDHA 6990 0.035 0.41 NO
23 ALDH9A1 ALDH9A1 ALDH9A1 7049 0.034 0.42 NO
24 ALDH2 ALDH2 ALDH2 7424 0.029 0.41 NO
25 MDH2 MDH2 MDH2 7509 0.028 0.42 NO
26 MDH1 MDH1 MDH1 7685 0.025 0.42 NO
27 PKM2 PKM2 PKM2 8198 0.019 0.39 NO
28 DLAT DLAT DLAT 8334 0.017 0.39 NO
29 LDHB LDHB LDHB 9079 0.0072 0.35 NO
30 ME2 ME2 ME2 9146 0.0064 0.35 NO
31 LDHAL6B LDHAL6B LDHAL6B 10230 -0.0077 0.3 NO
32 ACACB ACACB ACACB 10433 -0.01 0.29 NO
33 GRHPR GRHPR GRHPR 11787 -0.028 0.22 NO
34 ACYP2 ACYP2 ACYP2 12370 -0.037 0.2 NO
35 ACYP1 ACYP1 ACYP1 13010 -0.048 0.19 NO
36 PCK2 PCK2 PCK2 15246 -0.11 0.1 NO
37 ACAT2 ACAT2 ACAT2 16370 -0.17 0.1 NO

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

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

genes ES table in pathway: KEGG HISTIDINE METABOLISM

Table S18.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PPP1R12B PPP1R12B PPP1R12B 623 0.35 0.15 YES
2 ARHGAP6 ARHGAP6 ARHGAP6 876 0.31 0.3 YES
3 ARHGEF5 ARHGEF5 ARHGEF5 1430 0.24 0.4 YES
4 MYL2 MYL2 MYL2 4078 0.092 0.3 NO
5 RHOA RHOA RHOA 6431 0.044 0.2 NO
6 ARPC1A ARPC1A ARPC1A 6786 0.038 0.2 NO
7 PIP5K1A PIP5K1A PIP5K1A 6819 0.038 0.22 NO
8 ARPC5 ARPC5 ARPC5 6822 0.038 0.24 NO
9 MYLK MYLK MYLK 7341 0.03 0.22 NO
10 ACTR3 ACTR3 ACTR3 8093 0.02 0.19 NO
11 ARHGEF11 ARHGEF11 ARHGEF11 8353 0.017 0.19 NO
12 LIMK1 LIMK1 LIMK1 8445 0.016 0.19 NO
13 ARPC1B ARPC1B ARPC1B 8800 0.011 0.18 NO
14 ARPC3 ARPC3 ARPC3 9195 0.0058 0.16 NO
15 PIP5K1B PIP5K1B PIP5K1B 9767 -0.0018 0.13 NO
16 ARHGAP4 ARHGAP4 ARHGAP4 9962 -0.0044 0.12 NO
17 OPHN1 OPHN1 OPHN1 10398 -0.0098 0.1 NO
18 BAIAP2 BAIAP2 BAIAP2 10541 -0.012 0.1 NO
19 ACTR2 ACTR2 ACTR2 11116 -0.019 0.08 NO
20 ARHGEF1 ARHGEF1 ARHGEF1 11157 -0.019 0.088 NO
21 DIAPH1 DIAPH1 DIAPH1 11171 -0.02 0.098 NO
22 GSN GSN GSN 11473 -0.024 0.094 NO
23 CFL1 CFL1 CFL1 11647 -0.026 0.098 NO
24 ARPC2 ARPC2 ARPC2 11880 -0.029 0.1 NO
25 ARHGAP5 ARHGAP5 ARHGAP5 12596 -0.041 0.083 NO
26 ARHGAP1 ARHGAP1 ARHGAP1 12995 -0.048 0.087 NO
27 ARPC4 ARPC4 ARPC4 13655 -0.062 0.084 NO
28 PFN1 PFN1 PFN1 13808 -0.066 0.11 NO
29 ROCK1 ROCK1 ROCK1 13986 -0.07 0.14 NO
30 VCL VCL VCL 14275 -0.078 0.16 NO
31 SRC SRC SRC 14758 -0.094 0.19 NO

Figure S35.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HISTIDINE METABOLISM.

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

genes ES table in pathway: KEGG TYROSINE METABOLISM

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

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

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

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

genes ES table in pathway: KEGG TRYPTOPHAN METABOLISM

Table S20.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PSTK PSTK PSTK 1600 0.22 -0.0034 YES
2 TARSL2 TARSL2 TARSL2 1742 0.2 0.068 YES
3 CARS2 CARS2 CARS2 1998 0.19 0.13 YES
4 NARS2 NARS2 NARS2 2029 0.18 0.2 YES
5 MARS2 MARS2 MARS2 2427 0.16 0.24 YES
6 EARS2 EARS2 EARS2 2481 0.16 0.29 YES
7 PARS2 PARS2 PARS2 2858 0.14 0.33 YES
8 LARS2 LARS2 LARS2 3101 0.12 0.36 YES
9 IARS2 IARS2 IARS2 4361 0.085 0.32 YES
10 LARS LARS LARS 4976 0.071 0.32 YES
11 EPRS EPRS EPRS 5434 0.062 0.32 YES
12 RARS2 RARS2 RARS2 5457 0.061 0.34 YES
13 YARS YARS YARS 5899 0.052 0.34 YES
14 DARS2 DARS2 DARS2 6146 0.048 0.34 YES
15 QARS QARS QARS 6320 0.045 0.35 YES
16 DARS DARS DARS 6344 0.045 0.37 YES
17 HARS2 HARS2 HARS2 7003 0.035 0.34 NO
18 FARS2 FARS2 FARS2 7370 0.03 0.33 NO
19 GARS GARS GARS 7654 0.026 0.33 NO
20 FARSB FARSB FARSB 8053 0.021 0.32 NO
21 WARS2 WARS2 WARS2 8231 0.018 0.31 NO
22 HARS HARS HARS 8340 0.017 0.31 NO
23 AARS AARS AARS 8369 0.017 0.32 NO
24 MTFMT MTFMT MTFMT 8436 0.016 0.32 NO
25 CARS CARS CARS 8619 0.013 0.32 NO
26 VARS2 VARS2 VARS2 8645 0.013 0.32 NO
27 NARS NARS NARS 8669 0.013 0.32 NO
28 IARS IARS IARS 9183 0.006 0.3 NO
29 AARS2 AARS2 AARS2 9319 0.0042 0.29 NO
30 KARS KARS KARS 9333 0.004 0.29 NO
31 VARS VARS VARS 9908 -0.0036 0.26 NO
32 SEPSECS SEPSECS SEPSECS 10045 -0.0054 0.26 NO
33 RARS RARS RARS 10205 -0.0074 0.25 NO
34 FARSA FARSA FARSA 10522 -0.011 0.24 NO
35 YARS2 YARS2 YARS2 11738 -0.027 0.18 NO
36 TARS TARS TARS 12053 -0.032 0.18 NO
37 SARS SARS SARS 13036 -0.049 0.14 NO
38 MARS MARS MARS 13153 -0.051 0.15 NO
39 SARS2 SARS2 SARS2 15476 -0.12 0.073 NO
40 WARS WARS WARS 16710 -0.2 0.081 NO

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

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

Fold change

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

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 clus3 enriched pathways

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

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

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

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

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

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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

Table S22.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FLT4 FLT4 FLT4 216 0.51 0.12 YES
2 PIK3CG PIK3CG PIK3CG 432 0.44 0.21 YES
3 NOS3 NOS3 NOS3 490 0.42 0.32 YES
4 FLT1 FLT1 FLT1 655 0.39 0.4 YES
5 PRKCB PRKCB PRKCB 879 0.35 0.48 YES
6 PRKCA PRKCA PRKCA 1560 0.26 0.51 YES
7 HIF1A HIF1A HIF1A 1589 0.26 0.57 YES
8 EIF2S1 EIF2S1 EIF2S1 2840 0.16 0.54 YES
9 PXN PXN PXN 3064 0.15 0.56 YES
10 SHC1 SHC1 SHC1 3482 0.12 0.57 YES
11 EIF2S2 EIF2S2 EIF2S2 4757 0.078 0.52 NO
12 EIF2B2 EIF2B2 EIF2B2 5373 0.061 0.5 NO
13 EIF2B3 EIF2B3 EIF2B3 5575 0.056 0.51 NO
14 EIF2B5 EIF2B5 EIF2B5 6481 0.037 0.47 NO
15 VHL VHL VHL 6727 0.032 0.46 NO
16 EIF2B4 EIF2B4 EIF2B4 6889 0.029 0.46 NO
17 EIF1 EIF1 EIF1 7418 0.02 0.44 NO
18 PIK3CA PIK3CA PIK3CA 7906 0.012 0.41 NO
19 VEGFA VEGFA VEGFA 8371 0.0032 0.39 NO
20 ELAVL1 ELAVL1 ELAVL1 9235 -0.012 0.34 NO
21 EIF2S3 EIF2S3 EIF2S3 9315 -0.013 0.34 NO
22 EIF1AX EIF1AX EIF1AX 9534 -0.017 0.33 NO
23 PLCG1 PLCG1 PLCG1 9574 -0.018 0.34 NO
24 EIF2B1 EIF2B1 EIF2B1 10801 -0.041 0.28 NO
25 PTK2 PTK2 PTK2 10935 -0.043 0.28 NO
26 ARNT ARNT ARNT 12784 -0.09 0.2 NO
27 PIK3R1 PIK3R1 PIK3R1 13476 -0.11 0.19 NO
28 KDR KDR KDR 15985 -0.26 0.12 NO

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

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

Table S23.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IL12A IL12A IL12A 53 0.66 0.049 YES
2 CR1 CR1 CR1 63 0.64 0.099 YES
3 IFNG IFNG IFNG 162 0.54 0.14 YES
4 NOS2 NOS2 NOS2 168 0.54 0.18 YES
5 TLR4 TLR4 TLR4 610 0.39 0.19 YES
6 ITGA4 ITGA4 ITGA4 647 0.39 0.21 YES
7 FCGR1A FCGR1A FCGR1A 731 0.37 0.24 YES
8 NCF2 NCF2 NCF2 760 0.37 0.27 YES
9 IL12B IL12B IL12B 847 0.35 0.29 YES
10 PRKCB PRKCB PRKCB 879 0.35 0.32 YES
11 HLA-DQA2 HLA-DQA2 HLA-DQA2 1130 0.31 0.33 YES
12 TNF TNF TNF 1134 0.31 0.35 YES
13 HLA-DQA1 HLA-DQA1 HLA-DQA1 1322 0.29 0.36 YES
14 FCGR3B FCGR3B FCGR3B 1325 0.29 0.39 YES
15 FCGR3A FCGR3A FCGR3A 1326 0.29 0.41 YES
16 NCF1 NCF1 NCF1 1538 0.26 0.42 YES
17 NCF4 NCF4 NCF4 1558 0.26 0.44 YES
18 HLA-DOB HLA-DOB HLA-DOB 1653 0.25 0.45 YES
19 HLA-DOA HLA-DOA HLA-DOA 1671 0.25 0.47 YES
20 FCGR2A FCGR2A FCGR2A 1745 0.24 0.49 YES
21 HLA-DMB HLA-DMB HLA-DMB 1769 0.24 0.51 YES
22 TGFB1 TGFB1 TGFB1 1801 0.24 0.52 YES
23 ITGAM ITGAM ITGAM 1870 0.23 0.54 YES
24 HLA-DRB5 HLA-DRB5 HLA-DRB5 1942 0.22 0.55 YES
25 ITGB2 ITGB2 ITGB2 1997 0.22 0.56 YES
26 HLA-DQB1 HLA-DQB1 HLA-DQB1 2063 0.21 0.58 YES
27 HLA-DPA1 HLA-DPA1 HLA-DPA1 2242 0.2 0.58 YES
28 HLA-DPB1 HLA-DPB1 HLA-DPB1 2369 0.19 0.59 YES
29 HLA-DMA HLA-DMA HLA-DMA 2464 0.18 0.6 YES
30 HLA-DRA HLA-DRA HLA-DRA 2585 0.17 0.61 YES
31 HLA-DRB1 HLA-DRB1 HLA-DRB1 2743 0.16 0.61 YES
32 JAK2 JAK2 JAK2 2836 0.16 0.62 YES
33 ITGB1 ITGB1 ITGB1 3078 0.14 0.62 YES
34 NFKBIB NFKBIB NFKBIB 3172 0.14 0.63 YES
35 FCGR2C FCGR2C FCGR2C 3335 0.13 0.63 YES
36 IL10 IL10 IL10 3497 0.12 0.63 YES
37 CYBA CYBA CYBA 3670 0.12 0.63 YES
38 STAT1 STAT1 STAT1 3739 0.11 0.63 YES
39 PTPN6 PTPN6 PTPN6 3947 0.1 0.63 YES
40 MAPK11 MAPK11 MAPK11 3971 0.1 0.64 YES
41 MAPK13 MAPK13 MAPK13 4521 0.084 0.61 NO
42 TLR2 TLR2 TLR2 4579 0.083 0.62 NO
43 TRAF6 TRAF6 TRAF6 4632 0.081 0.62 NO
44 NFKBIA NFKBIA NFKBIA 4907 0.073 0.61 NO
45 MAPK1 MAPK1 MAPK1 5081 0.068 0.61 NO
46 NFKB1 NFKB1 NFKB1 5152 0.066 0.61 NO
47 IFNGR2 IFNGR2 IFNGR2 5193 0.065 0.61 NO
48 JUN JUN JUN 5321 0.062 0.61 NO
49 JAK1 JAK1 JAK1 6146 0.044 0.57 NO
50 MAPK14 MAPK14 MAPK14 6155 0.043 0.57 NO
51 IFNGR1 IFNGR1 IFNGR1 6184 0.043 0.57 NO
52 MYD88 MYD88 MYD88 6339 0.04 0.57 NO
53 MAPK12 MAPK12 MAPK12 7078 0.026 0.53 NO
54 IRAK1 IRAK1 IRAK1 7129 0.025 0.53 NO
55 IL1A IL1A IL1A 7776 0.014 0.49 NO
56 RELA RELA RELA 7927 0.011 0.48 NO
57 MAP3K7 MAP3K7 MAP3K7 7958 0.011 0.48 NO
58 TAB2 TAB2 TAB2 8204 0.0066 0.47 NO
59 ELK1 ELK1 ELK1 9441 -0.015 0.4 NO
60 MARCKSL1 MARCKSL1 MARCKSL1 9749 -0.021 0.39 NO
61 TAB1 TAB1 TAB1 10012 -0.026 0.38 NO
62 IRAK4 IRAK4 IRAK4 10416 -0.033 0.36 NO
63 FOS FOS FOS 10728 -0.039 0.34 NO
64 IL1B IL1B IL1B 11062 -0.046 0.33 NO
65 MAPK3 MAPK3 MAPK3 13360 -0.11 0.21 NO
66 TGFB2 TGFB2 TGFB2 13539 -0.12 0.21 NO
67 TGFB3 TGFB3 TGFB3 15446 -0.22 0.12 NO
68 C3 C3 C3 16989 -0.38 0.066 NO

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

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

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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

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

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

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

genes ES table in pathway: BIOCARTA INTEGRIN PATHWAY

Table S25.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TNF TNF TNF 1134 0.31 -0.00046 YES
2 LMNB1 LMNB1 LMNB1 2227 0.2 -0.021 YES
3 TRAF1 TRAF1 TRAF1 2277 0.2 0.016 YES
4 ARHGDIB ARHGDIB ARHGDIB 2316 0.2 0.052 YES
5 CFLAR CFLAR CFLAR 2363 0.19 0.088 YES
6 TNFRSF1B TNFRSF1B TNFRSF1B 2384 0.19 0.12 YES
7 MAP3K5 MAP3K5 MAP3K5 2487 0.18 0.15 YES
8 MAPK8 MAPK8 MAPK8 2498 0.18 0.19 YES
9 PRKCD PRKCD PRKCD 2608 0.17 0.22 YES
10 MAP3K14 MAP3K14 MAP3K14 2877 0.16 0.23 YES
11 LMNB2 LMNB2 LMNB2 2977 0.15 0.26 YES
12 TRAF2 TRAF2 TRAF2 3102 0.14 0.28 YES
13 CASP7 CASP7 CASP7 3202 0.14 0.3 YES
14 PAK2 PAK2 PAK2 3512 0.12 0.31 YES
15 BID BID BID 3524 0.12 0.33 YES
16 BAG4 BAG4 BAG4 3758 0.11 0.34 YES
17 RASA1 RASA1 RASA1 4416 0.088 0.32 YES
18 BCL2 BCL2 BCL2 4509 0.085 0.34 YES
19 CASP3 CASP3 CASP3 4662 0.08 0.34 YES
20 NFKBIA NFKBIA NFKBIA 4907 0.073 0.34 YES
21 FAS FAS FAS 5116 0.067 0.35 YES
22 PSEN1 PSEN1 PSEN1 5147 0.066 0.36 YES
23 NFKB1 NFKB1 NFKB1 5152 0.066 0.37 YES
24 BIRC3 BIRC3 BIRC3 5206 0.065 0.38 YES
25 LMNA LMNA LMNA 5367 0.061 0.38 YES
26 CHUK CHUK CHUK 5416 0.06 0.39 YES
27 CYCS CYCS CYCS 5660 0.054 0.39 NO
28 APAF1 APAF1 APAF1 6244 0.042 0.37 NO
29 PRKDC PRKDC PRKDC 6391 0.039 0.37 NO
30 RB1 RB1 RB1 6667 0.034 0.36 NO
31 ACTG1 ACTG1 ACTG1 7414 0.02 0.32 NO
32 DFFA DFFA DFFA 7432 0.02 0.32 NO
33 PARP1 PARP1 PARP1 7887 0.012 0.3 NO
34 BIRC2 BIRC2 BIRC2 7896 0.012 0.3 NO
35 RELA RELA RELA 7927 0.011 0.3 NO
36 CDK11A CDK11A CDK11A 8142 0.0077 0.29 NO
37 MDM2 MDM2 MDM2 8504 0.00086 0.27 NO
38 DAXX DAXX DAXX 8702 -0.0026 0.26 NO
39 CASP8 CASP8 CASP8 8848 -0.0054 0.26 NO
40 RIPK1 RIPK1 RIPK1 9173 -0.01 0.24 NO
41 GSN GSN GSN 9185 -0.011 0.24 NO
42 CDK11B CDK11B CDK11B 9197 -0.011 0.24 NO
43 TRADD TRADD TRADD 9419 -0.015 0.23 NO
44 FADD FADD FADD 10022 -0.026 0.2 NO
45 XIAP XIAP XIAP 10057 -0.027 0.21 NO
46 CASP2 CASP2 CASP2 10377 -0.032 0.2 NO
47 PTK2 PTK2 PTK2 10935 -0.043 0.18 NO
48 TNFRSF1A TNFRSF1A TNFRSF1A 11080 -0.046 0.18 NO
49 DFFB DFFB DFFB 11536 -0.057 0.16 NO
50 MAP3K1 MAP3K1 MAP3K1 11861 -0.064 0.16 NO
51 MAP2K7 MAP2K7 MAP2K7 12245 -0.075 0.15 NO
52 SPTAN1 SPTAN1 SPTAN1 12348 -0.078 0.16 NO
53 CRADD CRADD CRADD 13692 -0.12 0.11 NO
54 CASP9 CASP9 CASP9 13740 -0.12 0.13 NO
55 PSEN2 PSEN2 PSEN2 14264 -0.14 0.13 NO
56 NUMA1 NUMA1 NUMA1 14423 -0.15 0.15 NO
57 CASP6 CASP6 CASP6 16035 -0.27 0.12 NO

Figure S49.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA INTEGRIN PATHWAY.

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

genes ES table in pathway: BIOCARTA TCR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CDC25A CDC25A CDC25A 396 0.45 0.0081 YES
2 ORC1L ORC1L ORC1L 437 0.44 0.035 YES
3 TTK TTK TTK 472 0.43 0.062 YES
4 CDC45 CDC45 CDC45 475 0.43 0.09 YES
5 CDC20 CDC20 CDC20 568 0.4 0.11 YES
6 BUB1 BUB1 BUB1 594 0.4 0.14 YES
7 CCNE2 CCNE2 CCNE2 758 0.37 0.15 YES
8 ESPL1 ESPL1 ESPL1 759 0.37 0.18 YES
9 PKMYT1 PKMYT1 PKMYT1 779 0.36 0.2 YES
10 CCNA2 CCNA2 CCNA2 898 0.34 0.22 YES
11 CDC25C CDC25C CDC25C 902 0.34 0.24 YES
12 CCNE1 CCNE1 CCNE1 931 0.34 0.26 YES
13 PLK1 PLK1 PLK1 941 0.34 0.28 YES
14 RBL1 RBL1 RBL1 1165 0.31 0.29 YES
15 PTTG1 PTTG1 PTTG1 1213 0.3 0.31 YES
16 GADD45A GADD45A GADD45A 1226 0.3 0.33 YES
17 BUB1B BUB1B BUB1B 1335 0.29 0.34 YES
18 CDC7 CDC7 CDC7 1428 0.28 0.36 YES
19 CCNB1 CCNB1 CCNB1 1488 0.27 0.37 YES
20 CDC6 CDC6 CDC6 1537 0.26 0.39 YES
21 CDK1 CDK1 CDK1 1581 0.26 0.4 YES
22 ORC6L ORC6L ORC6L 1681 0.25 0.41 YES
23 TGFB1 TGFB1 TGFB1 1801 0.24 0.42 YES
24 PTTG2 PTTG2 PTTG2 1876 0.23 0.44 YES
25 CDC14A CDC14A CDC14A 1928 0.22 0.45 YES
26 MAD2L1 MAD2L1 MAD2L1 2032 0.22 0.46 YES
27 CHEK1 CHEK1 CHEK1 2069 0.21 0.47 YES
28 CCNB2 CCNB2 CCNB2 2466 0.18 0.46 YES
29 MCM5 MCM5 MCM5 2673 0.17 0.46 YES
30 E2F3 E2F3 E2F3 2726 0.17 0.47 YES
31 GADD45G GADD45G GADD45G 2806 0.16 0.47 YES
32 PCNA PCNA PCNA 2862 0.16 0.48 YES
33 E2F2 E2F2 E2F2 3056 0.15 0.48 YES
34 CDKN2D CDKN2D CDKN2D 3085 0.14 0.49 YES
35 MCM4 MCM4 MCM4 3194 0.14 0.49 YES
36 BUB3 BUB3 BUB3 3228 0.14 0.5 YES
37 WEE1 WEE1 WEE1 3332 0.13 0.5 YES
38 CDKN1A CDKN1A CDKN1A 3377 0.13 0.51 YES
39 CCND1 CCND1 CCND1 3547 0.12 0.51 NO
40 YWHAH YWHAH YWHAH 3785 0.11 0.5 NO
41 E2F1 E2F1 E2F1 3942 0.1 0.5 NO
42 GADD45B GADD45B GADD45B 4005 0.1 0.5 NO
43 CDK2 CDK2 CDK2 4145 0.096 0.5 NO
44 CHEK2 CHEK2 CHEK2 4308 0.091 0.5 NO
45 MAD2L2 MAD2L2 MAD2L2 4330 0.09 0.5 NO
46 CDK6 CDK6 CDK6 4400 0.088 0.51 NO
47 HDAC1 HDAC1 HDAC1 4514 0.084 0.51 NO
48 CDC27 CDC27 CDC27 4642 0.081 0.5 NO
49 MCM7 MCM7 MCM7 5090 0.068 0.48 NO
50 SMC1A SMC1A SMC1A 5150 0.066 0.48 NO
51 SMC3 SMC3 SMC3 5178 0.065 0.49 NO
52 CDC23 CDC23 CDC23 5203 0.065 0.49 NO
53 YWHAQ YWHAQ YWHAQ 5253 0.064 0.49 NO
54 CDC25B CDC25B CDC25B 5425 0.06 0.49 NO
55 RBX1 RBX1 RBX1 5485 0.058 0.49 NO
56 MCM2 MCM2 MCM2 5489 0.058 0.49 NO
57 YWHAG YWHAG YWHAG 5597 0.056 0.49 NO
58 CDK7 CDK7 CDK7 5649 0.055 0.49 NO
59 CDKN2A CDKN2A CDKN2A 5799 0.051 0.49 NO
60 YWHAB YWHAB YWHAB 5922 0.048 0.48 NO
61 YWHAZ YWHAZ YWHAZ 6106 0.044 0.48 NO
62 MCM6 MCM6 MCM6 6255 0.042 0.47 NO
63 MCM3 MCM3 MCM3 6353 0.04 0.47 NO
64 PRKDC PRKDC PRKDC 6391 0.039 0.47 NO
65 FZR1 FZR1 FZR1 6534 0.036 0.46 NO
66 ANAPC7 ANAPC7 ANAPC7 6579 0.035 0.46 NO
67 E2F4 E2F4 E2F4 6598 0.035 0.46 NO
68 RB1 RB1 RB1 6667 0.034 0.46 NO
69 TFDP1 TFDP1 TFDP1 6784 0.031 0.46 NO
70 ANAPC10 ANAPC10 ANAPC10 6959 0.028 0.45 NO
71 CCND3 CCND3 CCND3 6969 0.028 0.45 NO
72 SKP2 SKP2 SKP2 7008 0.027 0.45 NO
73 ANAPC1 ANAPC1 ANAPC1 7149 0.024 0.44 NO
74 CCNA1 CCNA1 CCNA1 7284 0.022 0.44 NO
75 CDK4 CDK4 CDK4 7329 0.022 0.44 NO
76 HDAC2 HDAC2 HDAC2 7407 0.02 0.44 NO
77 MYC MYC MYC 7482 0.019 0.43 NO
78 CDC26 CDC26 CDC26 7555 0.017 0.43 NO
79 MAD1L1 MAD1L1 MAD1L1 7748 0.014 0.42 NO
80 CDC14B CDC14B CDC14B 7751 0.014 0.42 NO
81 SMAD2 SMAD2 SMAD2 7798 0.013 0.42 NO
82 CCNH CCNH CCNH 7851 0.012 0.42 NO
83 CUL1 CUL1 CUL1 7972 0.01 0.41 NO
84 ZBTB17 ZBTB17 ZBTB17 8084 0.0086 0.4 NO
85 EP300 EP300 EP300 8100 0.0084 0.4 NO
86 YWHAE YWHAE YWHAE 8279 0.0052 0.4 NO
87 ORC3L ORC3L ORC3L 8407 0.0028 0.39 NO
88 GSK3B GSK3B GSK3B 8476 0.0014 0.38 NO
89 MDM2 MDM2 MDM2 8504 0.00086 0.38 NO
90 ORC5L ORC5L ORC5L 8591 -0.00071 0.38 NO
91 CDKN1B CDKN1B CDKN1B 8995 -0.0075 0.36 NO
92 STAG1 STAG1 STAG1 9150 -0.01 0.35 NO
93 ANAPC11 ANAPC11 ANAPC11 9155 -0.01 0.35 NO
94 RAD21 RAD21 RAD21 9220 -0.012 0.35 NO
95 SMAD3 SMAD3 SMAD3 9521 -0.017 0.33 NO
96 SFN SFN SFN 9836 -0.023 0.32 NO
97 ABL1 ABL1 ABL1 9849 -0.023 0.32 NO
98 CDKN2C CDKN2C CDKN2C 10011 -0.026 0.31 NO
99 ANAPC2 ANAPC2 ANAPC2 10302 -0.031 0.3 NO
100 SMAD4 SMAD4 SMAD4 10390 -0.033 0.29 NO
101 ANAPC5 ANAPC5 ANAPC5 10514 -0.035 0.29 NO
102 CDKN1C CDKN1C CDKN1C 10549 -0.036 0.29 NO
103 ATR ATR ATR 10650 -0.038 0.29 NO
104 TP53 TP53 TP53 10764 -0.04 0.28 NO
105 ORC2L ORC2L ORC2L 10879 -0.042 0.28 NO
106 SKP1 SKP1 SKP1 10893 -0.042 0.28 NO
107 ANAPC13 ANAPC13 ANAPC13 11199 -0.049 0.27 NO
108 STAG2 STAG2 STAG2 11255 -0.05 0.27 NO
109 ANAPC4 ANAPC4 ANAPC4 11458 -0.055 0.26 NO
110 CREBBP CREBBP CREBBP 11686 -0.06 0.25 NO
111 WEE2 WEE2 WEE2 11813 -0.064 0.25 NO
112 RBL2 RBL2 RBL2 11828 -0.064 0.25 NO
113 CDKN2B CDKN2B CDKN2B 12416 -0.08 0.22 NO
114 CDC16 CDC16 CDC16 12473 -0.081 0.23 NO
115 ATM ATM ATM 12959 -0.095 0.21 NO
116 E2F5 E2F5 E2F5 13056 -0.099 0.21 NO
117 SMC1B SMC1B SMC1B 13092 -0.1 0.21 NO
118 ORC4L ORC4L ORC4L 13351 -0.11 0.21 NO
119 TGFB2 TGFB2 TGFB2 13539 -0.12 0.2 NO
120 TFDP2 TFDP2 TFDP2 14292 -0.15 0.17 NO
121 CCNB3 CCNB3 CCNB3 15346 -0.21 0.13 NO
122 TGFB3 TGFB3 TGFB3 15446 -0.22 0.14 NO
123 CCND2 CCND2 CCND2 15513 -0.22 0.15 NO

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

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

genes ES table in pathway: BIOCARTA VEGF PATHWAY

Table S27.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IL12A IL12A IL12A 53 0.66 0.048 YES
2 CD80 CD80 CD80 64 0.64 0.096 YES
3 TLR8 TLR8 TLR8 118 0.57 0.14 YES
4 CXCL9 CXCL9 CXCL9 344 0.46 0.16 YES
5 CCL4 CCL4 CCL4 395 0.45 0.19 YES
6 PIK3CG PIK3CG PIK3CG 432 0.44 0.22 YES
7 CXCL10 CXCL10 CXCL10 441 0.44 0.26 YES
8 TLR4 TLR4 TLR4 610 0.39 0.28 YES
9 CCL5 CCL5 CCL5 719 0.37 0.3 YES
10 PIK3R5 PIK3R5 PIK3R5 791 0.36 0.32 YES
11 IL6 IL6 IL6 834 0.36 0.35 YES
12 IL12B IL12B IL12B 847 0.35 0.38 YES
13 CCL3 CCL3 CCL3 921 0.34 0.4 YES
14 TLR6 TLR6 TLR6 924 0.34 0.42 YES
15 CXCL11 CXCL11 CXCL11 930 0.34 0.45 YES
16 TNF TNF TNF 1134 0.31 0.46 YES
17 CD86 CD86 CD86 1273 0.3 0.48 YES
18 TLR1 TLR1 TLR1 1443 0.27 0.49 YES
19 CD40 CD40 CD40 1761 0.24 0.49 YES
20 TICAM2 TICAM2 TICAM2 1985 0.22 0.49 YES
21 TLR7 TLR7 TLR7 2079 0.21 0.51 YES
22 AKT3 AKT3 AKT3 2151 0.21 0.52 YES
23 IL8 IL8 IL8 2185 0.2 0.53 YES
24 TRAF3 TRAF3 TRAF3 2192 0.2 0.55 YES
25 PIK3R3 PIK3R3 PIK3R3 2285 0.2 0.56 YES
26 MAPK8 MAPK8 MAPK8 2498 0.18 0.56 YES
27 MAP2K1 MAP2K1 MAP2K1 3489 0.12 0.51 NO
28 CD14 CD14 CD14 3496 0.12 0.52 NO
29 STAT1 STAT1 STAT1 3739 0.11 0.52 NO
30 PIK3CD PIK3CD PIK3CD 3885 0.11 0.52 NO
31 SPP1 SPP1 SPP1 3967 0.1 0.52 NO
32 MAPK11 MAPK11 MAPK11 3971 0.1 0.53 NO
33 IFNB1 IFNB1 IFNB1 4385 0.089 0.51 NO
34 MAPK13 MAPK13 MAPK13 4521 0.084 0.51 NO
35 TLR2 TLR2 TLR2 4579 0.083 0.52 NO
36 TRAF6 TRAF6 TRAF6 4632 0.081 0.52 NO
37 LY96 LY96 LY96 4732 0.078 0.52 NO
38 NFKBIA NFKBIA NFKBIA 4907 0.073 0.52 NO
39 IRF5 IRF5 IRF5 4963 0.072 0.52 NO
40 MAP2K3 MAP2K3 MAP2K3 4976 0.071 0.52 NO
41 MAPK1 MAPK1 MAPK1 5081 0.068 0.52 NO
42 AKT1 AKT1 AKT1 5146 0.066 0.52 NO
43 NFKB1 NFKB1 NFKB1 5152 0.066 0.53 NO
44 IKBKE IKBKE IKBKE 5272 0.063 0.53 NO
45 JUN JUN JUN 5321 0.062 0.53 NO
46 CHUK CHUK CHUK 5416 0.06 0.53 NO
47 IFNAR2 IFNAR2 IFNAR2 5472 0.059 0.53 NO
48 MAPK9 MAPK9 MAPK9 6030 0.046 0.5 NO
49 MAPK14 MAPK14 MAPK14 6155 0.043 0.5 NO
50 MYD88 MYD88 MYD88 6339 0.04 0.49 NO
51 TICAM1 TICAM1 TICAM1 6364 0.039 0.49 NO
52 IRF3 IRF3 IRF3 6668 0.034 0.48 NO
53 IKBKG IKBKG IKBKG 6928 0.028 0.47 NO
54 IRF7 IRF7 IRF7 7039 0.026 0.46 NO
55 MAPK12 MAPK12 MAPK12 7078 0.026 0.46 NO
56 IRAK1 IRAK1 IRAK1 7129 0.025 0.46 NO
57 RAC1 RAC1 RAC1 7823 0.013 0.42 NO
58 PIK3CA PIK3CA PIK3CA 7906 0.012 0.42 NO
59 RELA RELA RELA 7927 0.011 0.42 NO
60 MAP3K7 MAP3K7 MAP3K7 7958 0.011 0.42 NO
61 MAP2K2 MAP2K2 MAP2K2 8004 0.0098 0.42 NO
62 TAB2 TAB2 TAB2 8204 0.0066 0.41 NO
63 LBP LBP LBP 8339 0.004 0.4 NO
64 TOLLIP TOLLIP TOLLIP 8344 0.0039 0.4 NO
65 CASP8 CASP8 CASP8 8848 -0.0054 0.37 NO
66 RIPK1 RIPK1 RIPK1 9173 -0.01 0.36 NO
67 AKT2 AKT2 AKT2 9654 -0.02 0.33 NO
68 TAB1 TAB1 TAB1 10012 -0.026 0.31 NO
69 IFNAR1 IFNAR1 IFNAR1 10015 -0.026 0.32 NO
70 FADD FADD FADD 10022 -0.026 0.32 NO
71 IKBKB IKBKB IKBKB 10274 -0.031 0.31 NO
72 IRAK4 IRAK4 IRAK4 10416 -0.033 0.3 NO
73 FOS FOS FOS 10728 -0.039 0.29 NO
74 IL1B IL1B IL1B 11062 -0.046 0.27 NO
75 TLR9 TLR9 TLR9 11214 -0.049 0.27 NO
76 MAP2K4 MAP2K4 MAP2K4 11219 -0.05 0.27 NO
77 PIK3CB PIK3CB PIK3CB 11615 -0.059 0.25 NO
78 MAP2K6 MAP2K6 MAP2K6 11905 -0.065 0.24 NO
79 TLR5 TLR5 TLR5 11955 -0.067 0.24 NO
80 MAP2K7 MAP2K7 MAP2K7 12245 -0.075 0.24 NO
81 MAP3K8 MAP3K8 MAP3K8 12267 -0.075 0.24 NO
82 PIK3R2 PIK3R2 PIK3R2 12371 -0.078 0.24 NO
83 TLR3 TLR3 TLR3 13195 -0.1 0.2 NO
84 MAPK3 MAPK3 MAPK3 13360 -0.11 0.2 NO
85 PIK3R1 PIK3R1 PIK3R1 13476 -0.11 0.2 NO
86 CTSK CTSK CTSK 13822 -0.13 0.2 NO
87 TIRAP TIRAP TIRAP 14512 -0.16 0.17 NO
88 MAPK10 MAPK10 MAPK10 17321 -0.44 0.048 NO

Figure S53.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA VEGF PATHWAY.

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

genes ES table in pathway: KEGG PROTEASOME

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CD3G CD3G CD3G 193 0.52 0.066 YES
2 LCK LCK LCK 284 0.48 0.13 YES
3 PIK3CG PIK3CG PIK3CG 432 0.44 0.19 YES
4 CD3D CD3D CD3D 449 0.43 0.25 YES
5 CD3E CD3E CD3E 530 0.41 0.31 YES
6 CD247 CD247 CD247 606 0.4 0.36 YES
7 LAT LAT LAT 636 0.39 0.42 YES
8 ZAP70 ZAP70 ZAP70 813 0.36 0.46 YES
9 PRKCB PRKCB PRKCB 879 0.35 0.51 YES
10 PTPN7 PTPN7 PTPN7 1015 0.33 0.55 YES
11 NFATC2 NFATC2 NFATC2 1458 0.27 0.56 YES
12 VAV1 VAV1 VAV1 1471 0.27 0.6 YES
13 PRKCA PRKCA PRKCA 1560 0.26 0.64 YES
14 MAPK8 MAPK8 MAPK8 2498 0.18 0.61 NO
15 PPP3CC PPP3CC PPP3CC 3052 0.15 0.6 NO
16 SHC1 SHC1 SHC1 3482 0.12 0.6 NO
17 MAP2K1 MAP2K1 MAP2K1 3489 0.12 0.62 NO
18 RASA1 RASA1 RASA1 4416 0.088 0.58 NO
19 NFKBIA NFKBIA NFKBIA 4907 0.073 0.56 NO
20 GRB2 GRB2 GRB2 5020 0.07 0.57 NO
21 NFKB1 NFKB1 NFKB1 5152 0.066 0.57 NO
22 JUN JUN JUN 5321 0.062 0.57 NO
23 CALM1 CALM1 CALM1 5540 0.057 0.57 NO
24 CALM3 CALM3 CALM3 6554 0.036 0.52 NO
25 CALM2 CALM2 CALM2 6654 0.034 0.52 NO
26 RAF1 RAF1 RAF1 7057 0.026 0.5 NO
27 RAC1 RAC1 RAC1 7823 0.013 0.46 NO
28 PIK3CA PIK3CA PIK3CA 7906 0.012 0.45 NO
29 RELA RELA RELA 7927 0.011 0.45 NO
30 ELK1 ELK1 ELK1 9441 -0.015 0.37 NO
31 PLCG1 PLCG1 PLCG1 9574 -0.018 0.37 NO
32 NFATC1 NFATC1 NFATC1 9706 -0.02 0.36 NO
33 FYN FYN FYN 10144 -0.028 0.34 NO
34 FOS FOS FOS 10728 -0.039 0.32 NO
35 PPP3CA PPP3CA PPP3CA 10887 -0.042 0.32 NO
36 MAP2K4 MAP2K4 MAP2K4 11219 -0.05 0.3 NO
37 SOS1 SOS1 SOS1 11394 -0.054 0.3 NO
38 PPP3CB PPP3CB PPP3CB 11518 -0.056 0.3 NO
39 NFATC3 NFATC3 NFATC3 11806 -0.063 0.3 NO
40 MAP3K1 MAP3K1 MAP3K1 11861 -0.064 0.3 NO
41 NFATC4 NFATC4 NFATC4 12288 -0.076 0.29 NO
42 MAPK3 MAPK3 MAPK3 13360 -0.11 0.25 NO
43 PIK3R1 PIK3R1 PIK3R1 13476 -0.11 0.26 NO

Figure S55.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PROTEASOME.

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

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 DAPP1 DAPP1 DAPP1 325 0.47 0.029 YES
2 PIK3CG PIK3CG PIK3CG 432 0.44 0.067 YES
3 CD72 CD72 CD72 448 0.43 0.11 YES
4 LILRB3 LILRB3 LILRB3 635 0.39 0.14 YES
5 PIK3R5 PIK3R5 PIK3R5 791 0.36 0.17 YES
6 PRKCB PRKCB PRKCB 879 0.35 0.2 YES
7 PIK3AP1 PIK3AP1 PIK3AP1 960 0.34 0.22 YES
8 RASGRP3 RASGRP3 RASGRP3 990 0.33 0.26 YES
9 BTK BTK BTK 1384 0.28 0.26 YES
10 NFATC2 NFATC2 NFATC2 1458 0.27 0.29 YES
11 VAV1 VAV1 VAV1 1471 0.27 0.31 YES
12 RAC2 RAC2 RAC2 1481 0.27 0.34 YES
13 CD79B CD79B CD79B 1755 0.24 0.35 YES
14 CD19 CD19 CD19 1830 0.23 0.37 YES
15 BCL10 BCL10 BCL10 1914 0.23 0.38 YES
16 AKT3 AKT3 AKT3 2151 0.21 0.39 YES
17 LYN LYN LYN 2272 0.2 0.41 YES
18 PIK3R3 PIK3R3 PIK3R3 2285 0.2 0.43 YES
19 SYK SYK SYK 2497 0.18 0.43 YES
20 VAV3 VAV3 VAV3 2505 0.18 0.45 YES
21 BLNK BLNK BLNK 2539 0.18 0.46 YES
22 NFKBIE NFKBIE NFKBIE 2557 0.18 0.48 YES
23 CD79A CD79A CD79A 2748 0.16 0.49 YES
24 PPP3CC PPP3CC PPP3CC 3052 0.15 0.49 YES
25 NRAS NRAS NRAS 3061 0.15 0.5 YES
26 PLCG2 PLCG2 PLCG2 3161 0.14 0.51 YES
27 NFKBIB NFKBIB NFKBIB 3172 0.14 0.52 YES
28 CR2 CR2 CR2 3298 0.14 0.53 YES
29 MALT1 MALT1 MALT1 3369 0.13 0.54 YES
30 MAP2K1 MAP2K1 MAP2K1 3489 0.12 0.54 YES
31 FCGR2B FCGR2B FCGR2B 3667 0.12 0.55 YES
32 PIK3CD PIK3CD PIK3CD 3885 0.11 0.55 YES
33 PTPN6 PTPN6 PTPN6 3947 0.1 0.55 YES
34 RAC3 RAC3 RAC3 4513 0.084 0.53 NO
35 NFKBIA NFKBIA NFKBIA 4907 0.073 0.52 NO
36 GRB2 GRB2 GRB2 5020 0.07 0.52 NO
37 MAPK1 MAPK1 MAPK1 5081 0.068 0.52 NO
38 AKT1 AKT1 AKT1 5146 0.066 0.52 NO
39 NFKB1 NFKB1 NFKB1 5152 0.066 0.53 NO
40 JUN JUN JUN 5321 0.062 0.53 NO
41 INPP5D INPP5D INPP5D 5332 0.062 0.53 NO
42 CHUK CHUK CHUK 5416 0.06 0.53 NO
43 KRAS KRAS KRAS 5788 0.051 0.52 NO
44 PPP3R1 PPP3R1 PPP3R1 5824 0.05 0.52 NO
45 IKBKG IKBKG IKBKG 6928 0.028 0.46 NO
46 RAF1 RAF1 RAF1 7057 0.026 0.46 NO
47 RAC1 RAC1 RAC1 7823 0.013 0.42 NO
48 PIK3CA PIK3CA PIK3CA 7906 0.012 0.41 NO
49 RELA RELA RELA 7927 0.011 0.41 NO
50 MAP2K2 MAP2K2 MAP2K2 8004 0.0098 0.41 NO
51 GSK3B GSK3B GSK3B 8476 0.0014 0.38 NO
52 SOS2 SOS2 SOS2 8545 5.2e-06 0.38 NO
53 VAV2 VAV2 VAV2 8600 -0.00084 0.38 NO
54 AKT2 AKT2 AKT2 9654 -0.02 0.32 NO
55 NFATC1 NFATC1 NFATC1 9706 -0.02 0.32 NO
56 CD81 CD81 CD81 10108 -0.028 0.3 NO
57 IKBKB IKBKB IKBKB 10274 -0.031 0.3 NO
58 FOS FOS FOS 10728 -0.039 0.27 NO
59 PPP3CA PPP3CA PPP3CA 10887 -0.042 0.27 NO
60 NFAT5 NFAT5 NFAT5 10979 -0.044 0.27 NO
61 SOS1 SOS1 SOS1 11394 -0.054 0.25 NO
62 PPP3CB PPP3CB PPP3CB 11518 -0.056 0.25 NO
63 PIK3CB PIK3CB PIK3CB 11615 -0.059 0.25 NO
64 NFATC3 NFATC3 NFATC3 11806 -0.063 0.25 NO
65 IFITM1 IFITM1 IFITM1 12199 -0.074 0.23 NO
66 NFATC4 NFATC4 NFATC4 12288 -0.076 0.24 NO
67 PIK3R2 PIK3R2 PIK3R2 12371 -0.078 0.24 NO
68 MAPK3 MAPK3 MAPK3 13360 -0.11 0.2 NO
69 PIK3R1 PIK3R1 PIK3R1 13476 -0.11 0.2 NO
70 CARD11 CARD11 CARD11 13932 -0.13 0.19 NO
71 CHP CHP CHP 14285 -0.15 0.18 NO
72 CD22 CD22 CD22 14298 -0.15 0.2 NO
73 CHP2 CHP2 CHP2 14696 -0.17 0.19 NO

Figure S57.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CHEMOKINE SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG CELL CYCLE

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 879 0.35 0.042 YES
2 BTK BTK BTK 1384 0.28 0.086 YES
3 NFATC2 NFATC2 NFATC2 1458 0.27 0.15 YES
4 VAV1 VAV1 VAV1 1471 0.27 0.22 YES
5 PRKCA PRKCA PRKCA 1560 0.26 0.28 YES
6 CD79B CD79B CD79B 1755 0.24 0.34 YES
7 LYN LYN LYN 2272 0.2 0.36 YES
8 SYK SYK SYK 2497 0.18 0.39 YES
9 MAPK8 MAPK8 MAPK8 2498 0.18 0.44 YES
10 BLNK BLNK BLNK 2539 0.18 0.48 YES
11 CD79A CD79A CD79A 2748 0.16 0.51 YES
12 PPP3CC PPP3CC PPP3CC 3052 0.15 0.54 YES
13 SHC1 SHC1 SHC1 3482 0.12 0.54 YES
14 MAP2K1 MAP2K1 MAP2K1 3489 0.12 0.58 YES
15 GRB2 GRB2 GRB2 5020 0.07 0.51 NO
16 JUN JUN JUN 5321 0.062 0.51 NO
17 CALM1 CALM1 CALM1 5540 0.057 0.51 NO
18 MAPK14 MAPK14 MAPK14 6155 0.043 0.49 NO
19 CALM3 CALM3 CALM3 6554 0.036 0.48 NO
20 CALM2 CALM2 CALM2 6654 0.034 0.48 NO
21 RAF1 RAF1 RAF1 7057 0.026 0.46 NO
22 RAC1 RAC1 RAC1 7823 0.013 0.43 NO
23 ELK1 ELK1 ELK1 9441 -0.015 0.34 NO
24 PLCG1 PLCG1 PLCG1 9574 -0.018 0.34 NO
25 NFATC1 NFATC1 NFATC1 9706 -0.02 0.34 NO
26 FOS FOS FOS 10728 -0.039 0.29 NO
27 PPP3CA PPP3CA PPP3CA 10887 -0.042 0.29 NO
28 SOS1 SOS1 SOS1 11394 -0.054 0.28 NO
29 PPP3CB PPP3CB PPP3CB 11518 -0.056 0.29 NO
30 NFATC3 NFATC3 NFATC3 11806 -0.063 0.29 NO
31 MAP3K1 MAP3K1 MAP3K1 11861 -0.064 0.3 NO
32 NFATC4 NFATC4 NFATC4 12288 -0.076 0.3 NO
33 MAPK3 MAPK3 MAPK3 13360 -0.11 0.27 NO

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

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CELL CYCLE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

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 clus4 enriched pathways

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TGFB2 TGFB2 TGFB2 61 0.67 0.042 YES
2 INHBC INHBC INHBC 109 0.61 0.08 YES
3 LEFTY1 LEFTY1 LEFTY1 181 0.56 0.11 YES
4 LEFTY2 LEFTY2 LEFTY2 197 0.55 0.15 YES
5 CHRD CHRD CHRD 218 0.54 0.19 YES
6 INHBE INHBE INHBE 250 0.53 0.22 YES
7 BMP7 BMP7 BMP7 262 0.52 0.25 YES
8 BMP6 BMP6 BMP6 342 0.49 0.28 YES
9 AMH AMH AMH 496 0.45 0.3 YES
10 NODAL NODAL NODAL 533 0.44 0.33 YES
11 SMAD6 SMAD6 SMAD6 594 0.42 0.36 YES
12 LTBP1 LTBP1 LTBP1 668 0.41 0.38 YES
13 GDF7 GDF7 GDF7 725 0.4 0.4 YES
14 AMHR2 AMHR2 AMHR2 891 0.37 0.42 YES
15 BMP5 BMP5 BMP5 934 0.36 0.44 YES
16 COMP COMP COMP 1111 0.34 0.46 YES
17 BMPR1B BMPR1B BMPR1B 1247 0.32 0.47 YES
18 FST FST FST 1267 0.31 0.49 YES
19 TGFB3 TGFB3 TGFB3 1428 0.29 0.5 YES
20 BMP8A BMP8A BMP8A 1505 0.28 0.52 YES
21 ID3 ID3 ID3 1583 0.28 0.53 YES
22 THBS4 THBS4 THBS4 1741 0.26 0.54 YES
23 ID1 ID1 ID1 1775 0.26 0.55 YES
24 INHBA INHBA INHBA 1922 0.25 0.56 YES
25 SMAD7 SMAD7 SMAD7 1942 0.24 0.58 YES
26 PITX2 PITX2 PITX2 2236 0.22 0.58 YES
27 SMAD9 SMAD9 SMAD9 2309 0.22 0.59 YES
28 BMP8B BMP8B BMP8B 2342 0.22 0.6 YES
29 GDF6 GDF6 GDF6 2546 0.2 0.6 YES
30 THBS1 THBS1 THBS1 2854 0.18 0.6 NO
31 BMPR2 BMPR2 BMPR2 3455 0.16 0.57 NO
32 ACVRL1 ACVRL1 ACVRL1 3582 0.15 0.58 NO
33 ZFYVE9 ZFYVE9 ZFYVE9 4271 0.12 0.55 NO
34 SMAD3 SMAD3 SMAD3 4307 0.12 0.55 NO
35 RBL1 RBL1 RBL1 4446 0.11 0.55 NO
36 DCN DCN DCN 4555 0.11 0.56 NO
37 BMPR1A BMPR1A BMPR1A 4624 0.11 0.56 NO
38 CREBBP CREBBP CREBBP 4938 0.096 0.55 NO
39 SMAD4 SMAD4 SMAD4 6038 0.069 0.49 NO
40 ACVR2B ACVR2B ACVR2B 6193 0.066 0.49 NO
41 TGFB1 TGFB1 TGFB1 6457 0.06 0.48 NO
42 ACVR2A ACVR2A ACVR2A 6536 0.058 0.48 NO
43 SMAD5 SMAD5 SMAD5 6651 0.056 0.47 NO
44 ROCK1 ROCK1 ROCK1 6659 0.056 0.48 NO
45 THBS2 THBS2 THBS2 6684 0.055 0.48 NO
46 PPP2R1A PPP2R1A PPP2R1A 6744 0.054 0.48 NO
47 TFDP1 TFDP1 TFDP1 6997 0.05 0.47 NO
48 SP1 SP1 SP1 7251 0.045 0.46 NO
49 SMAD2 SMAD2 SMAD2 7317 0.044 0.46 NO
50 BMP4 BMP4 BMP4 7608 0.039 0.44 NO
51 EP300 EP300 EP300 7923 0.034 0.43 NO
52 PPP2CB PPP2CB PPP2CB 8467 0.026 0.4 NO
53 ACVR1 ACVR1 ACVR1 8483 0.025 0.4 NO
54 THBS3 THBS3 THBS3 8703 0.022 0.39 NO
55 SMURF1 SMURF1 SMURF1 8920 0.019 0.38 NO
56 CUL1 CUL1 CUL1 9575 0.01 0.34 NO
57 TGFBR1 TGFBR1 TGFBR1 9984 0.0045 0.32 NO
58 MAPK1 MAPK1 MAPK1 10177 0.0018 0.31 NO
59 E2F4 E2F4 E2F4 10345 -0.00034 0.3 NO
60 SMAD1 SMAD1 SMAD1 10672 -0.0048 0.29 NO
61 ZFYVE16 ZFYVE16 ZFYVE16 10851 -0.0073 0.28 NO
62 SMURF2 SMURF2 SMURF2 11342 -0.014 0.25 NO
63 ACVR1C ACVR1C ACVR1C 11449 -0.016 0.25 NO
64 SKP1 SKP1 SKP1 12006 -0.024 0.22 NO
65 RBX1 RBX1 RBX1 12016 -0.024 0.22 NO
66 ROCK2 ROCK2 ROCK2 12211 -0.027 0.21 NO
67 ID4 ID4 ID4 12277 -0.028 0.21 NO
68 PPP2R1B PPP2R1B PPP2R1B 12936 -0.039 0.17 NO
69 TGFBR2 TGFBR2 TGFBR2 12989 -0.04 0.17 NO
70 RHOA RHOA RHOA 13234 -0.044 0.16 NO
71 RPS6KB2 RPS6KB2 RPS6KB2 13342 -0.046 0.16 NO
72 PPP2CA PPP2CA PPP2CA 13349 -0.046 0.16 NO
73 RPS6KB1 RPS6KB1 RPS6KB1 13650 -0.052 0.15 NO
74 MAPK3 MAPK3 MAPK3 13791 -0.055 0.15 NO
75 E2F5 E2F5 E2F5 13837 -0.056 0.15 NO
76 RBL2 RBL2 RBL2 14070 -0.06 0.14 NO
77 BMP2 BMP2 BMP2 15717 -0.11 0.054 NO
78 INHBB INHBB INHBB 15798 -0.11 0.057 NO
79 CDKN2B CDKN2B CDKN2B 16533 -0.15 0.027 NO
80 ID2 ID2 ID2 16742 -0.16 0.026 NO
81 MYC MYC MYC 16802 -0.17 0.034 NO
82 GDF5 GDF5 GDF5 16979 -0.18 0.036 NO
83 IFNG IFNG IFNG 17184 -0.2 0.039 NO
84 TNF TNF TNF 17509 -0.25 0.038 NO

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

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

genes ES table in pathway: BIOCARTA G1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TGFB2 TGFB2 TGFB2 61 0.67 0.13 YES
2 CHRD CHRD CHRD 218 0.54 0.22 YES
3 BMP7 BMP7 BMP7 262 0.52 0.32 YES
4 SMAD6 SMAD6 SMAD6 594 0.42 0.39 YES
5 NKX2-5 NKX2-5 NKX2-5 800 0.38 0.45 YES
6 BMP5 BMP5 BMP5 934 0.36 0.52 YES
7 GATA4 GATA4 GATA4 1388 0.3 0.55 YES
8 TGFB3 TGFB3 TGFB3 1428 0.29 0.6 YES
9 FZD1 FZD1 FZD1 3249 0.16 0.53 NO
10 BMPR2 BMPR2 BMPR2 3455 0.16 0.55 NO
11 NPPB NPPB NPPB 4004 0.13 0.55 NO
12 BMPR1A BMPR1A BMPR1A 4624 0.11 0.54 NO
13 MAP3K7 MAP3K7 MAP3K7 4925 0.097 0.54 NO
14 NOG NOG NOG 5106 0.092 0.55 NO
15 TGFBR3 TGFBR3 TGFBR3 5298 0.086 0.55 NO
16 NPPA NPPA NPPA 5647 0.078 0.55 NO
17 SMAD4 SMAD4 SMAD4 6038 0.069 0.54 NO
18 CTNNB1 CTNNB1 CTNNB1 6392 0.061 0.53 NO
19 TGFB1 TGFB1 TGFB1 6457 0.06 0.54 NO
20 SMAD5 SMAD5 SMAD5 6651 0.056 0.54 NO
21 HNF1A HNF1A HNF1A 6964 0.05 0.53 NO
22 WNT1 WNT1 WNT1 7372 0.043 0.52 NO
23 BMP4 BMP4 BMP4 7608 0.039 0.51 NO
24 ACVR1 ACVR1 ACVR1 8483 0.025 0.47 NO
25 DVL1 DVL1 DVL1 8890 0.02 0.45 NO
26 MYL2 MYL2 MYL2 9014 0.018 0.45 NO
27 TGFBR1 TGFBR1 TGFBR1 9984 0.0045 0.4 NO
28 GSK3B GSK3B GSK3B 10261 0.00077 0.38 NO
29 SMAD1 SMAD1 SMAD1 10672 -0.0048 0.36 NO
30 RFC1 RFC1 RFC1 11897 -0.022 0.3 NO
31 AXIN1 AXIN1 AXIN1 12068 -0.025 0.29 NO
32 APC APC APC 12801 -0.037 0.26 NO
33 TGFBR2 TGFBR2 TGFBR2 12989 -0.04 0.26 NO
34 ATF2 ATF2 ATF2 13601 -0.051 0.23 NO
35 BMP2 BMP2 BMP2 15717 -0.11 0.14 NO

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

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

genes ES table in pathway: BIOCARTA WNT PATHWAY

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

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

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

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

genes ES table in pathway: KEGG PURINE METABOLISM

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

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

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

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CAMK2B CAMK2B CAMK2B 117 0.6 0.034 YES
2 ADCY5 ADCY5 ADCY5 167 0.57 0.069 YES
3 WNT11 WNT11 WNT11 182 0.56 0.1 YES
4 GNAO1 GNAO1 GNAO1 385 0.48 0.13 YES
5 WNT6 WNT6 WNT6 442 0.47 0.15 YES
6 CALML3 CALML3 CALML3 455 0.46 0.18 YES
7 ADCY2 ADCY2 ADCY2 502 0.45 0.21 YES
8 WNT5B WNT5B WNT5B 568 0.43 0.24 YES
9 ADCY1 ADCY1 ADCY1 818 0.38 0.25 YES
10 WNT10B WNT10B WNT10B 826 0.38 0.27 YES
11 CALML5 CALML5 CALML5 948 0.36 0.29 YES
12 FZD10 FZD10 FZD10 956 0.36 0.31 YES
13 LEF1 LEF1 LEF1 1080 0.34 0.33 YES
14 FZD8 FZD8 FZD8 1113 0.34 0.35 YES
15 FZD3 FZD3 FZD3 1163 0.33 0.37 YES
16 FZD2 FZD2 FZD2 1403 0.3 0.38 YES
17 PRKCG PRKCG PRKCG 1565 0.28 0.38 YES
18 TCF7L1 TCF7L1 TCF7L1 1669 0.27 0.4 YES
19 TCF7 TCF7 TCF7 2225 0.22 0.38 YES
20 FZD7 FZD7 FZD7 2323 0.22 0.39 YES
21 CREB3L1 CREB3L1 CREB3L1 2359 0.22 0.4 YES
22 WNT9A WNT9A WNT9A 2517 0.2 0.41 YES
23 EDNRB EDNRB EDNRB 2566 0.2 0.42 YES
24 PLCB4 PLCB4 PLCB4 2581 0.2 0.43 YES
25 CREB3L3 CREB3L3 CREB3L3 2711 0.19 0.44 YES
26 TYR TYR TYR 2732 0.19 0.45 YES
27 CAMK2A CAMK2A CAMK2A 2773 0.19 0.46 YES
28 WNT7B WNT7B WNT7B 2808 0.19 0.47 YES
29 WNT8B WNT8B WNT8B 2867 0.18 0.48 YES
30 ADCY8 ADCY8 ADCY8 2880 0.18 0.49 YES
31 FZD9 FZD9 FZD9 2999 0.18 0.5 YES
32 WNT7A WNT7A WNT7A 3062 0.17 0.5 YES
33 FZD1 FZD1 FZD1 3249 0.16 0.5 YES
34 KIT KIT KIT 3308 0.16 0.51 YES
35 TYRP1 TYRP1 TYRP1 3336 0.16 0.52 YES
36 FZD4 FZD4 FZD4 3390 0.16 0.53 YES
37 EDN1 EDN1 EDN1 3624 0.15 0.52 YES
38 WNT3A WNT3A WNT3A 3698 0.14 0.53 YES
39 CAMK2G CAMK2G CAMK2G 4325 0.12 0.5 NO
40 ADCY4 ADCY4 ADCY4 4353 0.12 0.51 NO
41 ADCY6 ADCY6 ADCY6 4620 0.11 0.5 NO
42 MC1R MC1R MC1R 4654 0.1 0.51 NO
43 DVL2 DVL2 DVL2 4862 0.098 0.5 NO
44 CREBBP CREBBP CREBBP 4938 0.096 0.5 NO
45 CALM1 CALM1 CALM1 5734 0.076 0.46 NO
46 WNT2B WNT2B WNT2B 5759 0.075 0.47 NO
47 ASIP ASIP ASIP 5816 0.074 0.47 NO
48 KITLG KITLG KITLG 5955 0.071 0.47 NO
49 PRKACA PRKACA PRKACA 5993 0.07 0.47 NO
50 PRKX PRKX PRKX 6173 0.066 0.46 NO
51 CTNNB1 CTNNB1 CTNNB1 6392 0.061 0.46 NO
52 WNT10A WNT10A WNT10A 6453 0.06 0.46 NO
53 KRAS KRAS KRAS 6619 0.056 0.45 NO
54 CAMK2D CAMK2D CAMK2D 7324 0.044 0.42 NO
55 WNT1 WNT1 WNT1 7372 0.043 0.42 NO
56 CREB1 CREB1 CREB1 7612 0.039 0.41 NO
57 GNAS GNAS GNAS 7824 0.036 0.4 NO
58 MAP2K2 MAP2K2 MAP2K2 7827 0.035 0.4 NO
59 CALM3 CALM3 CALM3 7916 0.034 0.4 NO
60 EP300 EP300 EP300 7923 0.034 0.4 NO
61 FZD6 FZD6 FZD6 7981 0.033 0.4 NO
62 CREB3L4 CREB3L4 CREB3L4 8506 0.025 0.37 NO
63 WNT16 WNT16 WNT16 8595 0.024 0.37 NO
64 DVL1 DVL1 DVL1 8890 0.02 0.35 NO
65 PRKACB PRKACB PRKACB 9119 0.016 0.34 NO
66 CREB3L2 CREB3L2 CREB3L2 9269 0.014 0.33 NO
67 GNAQ GNAQ GNAQ 9307 0.014 0.33 NO
68 MAPK1 MAPK1 MAPK1 10177 0.0018 0.28 NO
69 GSK3B GSK3B GSK3B 10261 0.00077 0.28 NO
70 RAF1 RAF1 RAF1 10279 0.00052 0.28 NO
71 CALML6 CALML6 CALML6 10900 -0.0081 0.24 NO
72 WNT5A WNT5A WNT5A 11060 -0.01 0.24 NO
73 ADCY7 ADCY7 ADCY7 11493 -0.017 0.21 NO
74 POMC POMC POMC 11695 -0.02 0.2 NO
75 CALM2 CALM2 CALM2 11968 -0.024 0.19 NO
76 NRAS NRAS NRAS 11996 -0.024 0.19 NO
77 HRAS HRAS HRAS 12025 -0.024 0.19 NO
78 GNAI2 GNAI2 GNAI2 12159 -0.027 0.18 NO
79 PLCB3 PLCB3 PLCB3 12765 -0.036 0.15 NO
80 ADCY9 ADCY9 ADCY9 13365 -0.047 0.12 NO
81 FZD5 FZD5 FZD5 13376 -0.047 0.13 NO
82 GNAI3 GNAI3 GNAI3 13466 -0.048 0.12 NO
83 MAPK3 MAPK3 MAPK3 13791 -0.055 0.11 NO
84 WNT4 WNT4 WNT4 13847 -0.056 0.11 NO
85 TCF7L2 TCF7L2 TCF7L2 14187 -0.063 0.097 NO
86 MAP2K1 MAP2K1 MAP2K1 14261 -0.065 0.097 NO
87 PRKCA PRKCA PRKCA 14691 -0.075 0.078 NO
88 DVL3 DVL3 DVL3 14782 -0.077 0.078 NO
89 CREB3 CREB3 CREB3 14924 -0.081 0.076 NO
90 PLCB1 PLCB1 PLCB1 15180 -0.088 0.068 NO
91 PLCB2 PLCB2 PLCB2 15250 -0.089 0.07 NO
92 DCT DCT DCT 15474 -0.097 0.064 NO
93 MITF MITF MITF 16437 -0.14 0.02 NO
94 WNT9B WNT9B WNT9B 16726 -0.16 0.015 NO
95 GNAI1 GNAI1 GNAI1 16762 -0.16 0.024 NO
96 WNT3 WNT3 WNT3 16971 -0.18 0.024 NO
97 PRKCB PRKCB PRKCB 17708 -0.28 0.0022 NO
98 WNT2 WNT2 WNT2 17956 -0.36 0.013 NO

Figure S69.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

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

genes ES table in pathway: KEGG CALCIUM SIGNALING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADCY5 ADCY5 ADCY5 167 0.57 0.041 YES
2 DRD1 DRD1 DRD1 170 0.57 0.091 YES
3 ADCY2 ADCY2 ADCY2 502 0.45 0.11 YES
4 TUBB8 TUBB8 TUBB8 557 0.44 0.15 YES
5 DRD2 DRD2 DRD2 634 0.42 0.18 YES
6 GUCY1B3 GUCY1B3 GUCY1B3 694 0.4 0.21 YES
7 PRKG1 PRKG1 PRKG1 748 0.39 0.24 YES
8 ADCY1 ADCY1 ADCY1 818 0.38 0.28 YES
9 GUCY1A2 GUCY1A2 GUCY1A2 945 0.36 0.3 YES
10 GUCY1A3 GUCY1A3 GUCY1A3 1087 0.34 0.32 YES
11 TUBA8 TUBA8 TUBA8 1182 0.32 0.35 YES
12 GRM1 GRM1 GRM1 1519 0.28 0.35 YES
13 PDGFRB PDGFRB PDGFRB 1553 0.28 0.38 YES
14 PRKCG PRKCG PRKCG 1565 0.28 0.4 YES
15 TUBB4Q TUBB4Q TUBB4Q 1595 0.28 0.42 YES
16 TUBB1 TUBB1 TUBB1 1751 0.26 0.44 YES
17 TUBA3D TUBA3D TUBA3D 2136 0.23 0.44 YES
18 PDGFC PDGFC PDGFC 2282 0.22 0.45 YES
19 GRM5 GRM5 GRM5 2393 0.21 0.46 YES
20 PLCB4 PLCB4 PLCB4 2581 0.2 0.47 YES
21 PDGFA PDGFA PDGFA 2658 0.2 0.48 YES
22 ADCY8 ADCY8 ADCY8 2880 0.18 0.48 YES
23 TUBA1A TUBA1A TUBA1A 2901 0.18 0.5 YES
24 TUBB2B TUBB2B TUBB2B 3296 0.16 0.49 YES
25 CDK1 CDK1 CDK1 3341 0.16 0.5 YES
26 HTR2B HTR2B HTR2B 3407 0.16 0.51 YES
27 TUBA3E TUBA3E TUBA3E 3448 0.16 0.53 YES
28 SRC SRC SRC 4228 0.12 0.49 NO
29 ADCY4 ADCY4 ADCY4 4353 0.12 0.5 NO
30 ADCY6 ADCY6 ADCY6 4620 0.11 0.49 NO
31 TUBB4 TUBB4 TUBB4 4845 0.099 0.49 NO
32 TUBAL3 TUBAL3 TUBAL3 5005 0.094 0.49 NO
33 MAPK7 MAPK7 MAPK7 5144 0.09 0.49 NO
34 TUBB3 TUBB3 TUBB3 5324 0.086 0.49 NO
35 PRKACA PRKACA PRKACA 5993 0.07 0.46 NO
36 PRKX PRKX PRKX 6173 0.066 0.45 NO
37 EGF EGF EGF 6437 0.06 0.44 NO
38 KRAS KRAS KRAS 6619 0.056 0.44 NO
39 PRKG2 PRKG2 PRKG2 6780 0.053 0.43 NO
40 PDGFRA PDGFRA PDGFRA 7256 0.045 0.41 NO
41 PDGFD PDGFD PDGFD 7802 0.036 0.38 NO
42 GNAS GNAS GNAS 7824 0.036 0.39 NO
43 MAP2K2 MAP2K2 MAP2K2 7827 0.035 0.39 NO
44 TUBA1B TUBA1B TUBA1B 7874 0.035 0.39 NO
45 GNA11 GNA11 GNA11 7888 0.034 0.39 NO
46 TUBB TUBB TUBB 8021 0.032 0.39 NO
47 ADRB1 ADRB1 ADRB1 8504 0.025 0.36 NO
48 TJP1 TJP1 TJP1 8602 0.024 0.36 NO
49 HTR2A HTR2A HTR2A 8662 0.023 0.36 NO
50 PRKACB PRKACB PRKACB 9119 0.016 0.33 NO
51 GNAQ GNAQ GNAQ 9307 0.014 0.32 NO
52 ITPR2 ITPR2 ITPR2 9402 0.012 0.32 NO
53 PDGFB PDGFB PDGFB 9762 0.0078 0.3 NO
54 ITPR3 ITPR3 ITPR3 9776 0.0076 0.3 NO
55 TUBB2C TUBB2C TUBB2C 9989 0.0045 0.29 NO
56 GJA1 GJA1 GJA1 10030 0.0038 0.29 NO
57 MAPK1 MAPK1 MAPK1 10177 0.0018 0.28 NO
58 LPAR1 LPAR1 LPAR1 10206 0.0015 0.28 NO
59 RAF1 RAF1 RAF1 10279 0.00052 0.28 NO
60 SOS1 SOS1 SOS1 10615 -0.004 0.26 NO
61 CSNK1D CSNK1D CSNK1D 11434 -0.016 0.21 NO
62 ADCY7 ADCY7 ADCY7 11493 -0.017 0.21 NO
63 SOS2 SOS2 SOS2 11543 -0.017 0.21 NO
64 MAP2K5 MAP2K5 MAP2K5 11820 -0.021 0.2 NO
65 NRAS NRAS NRAS 11996 -0.024 0.19 NO
66 TUBB6 TUBB6 TUBB6 12010 -0.024 0.19 NO
67 HRAS HRAS HRAS 12025 -0.024 0.19 NO
68 GNAI2 GNAI2 GNAI2 12159 -0.027 0.19 NO
69 PLCB3 PLCB3 PLCB3 12765 -0.036 0.16 NO
70 GRB2 GRB2 GRB2 12984 -0.04 0.15 NO
71 ADCY9 ADCY9 ADCY9 13365 -0.047 0.13 NO
72 GNAI3 GNAI3 GNAI3 13466 -0.048 0.13 NO
73 ITPR1 ITPR1 ITPR1 13553 -0.05 0.13 NO
74 MAPK3 MAPK3 MAPK3 13791 -0.055 0.12 NO
75 TUBB2A TUBB2A TUBB2A 13963 -0.058 0.12 NO
76 MAP2K1 MAP2K1 MAP2K1 14261 -0.065 0.11 NO
77 TUBA1C TUBA1C TUBA1C 14575 -0.072 0.096 NO
78 MAP3K2 MAP3K2 MAP3K2 14600 -0.072 0.1 NO
79 PRKCA PRKCA PRKCA 14691 -0.075 0.1 NO
80 TUBA4A TUBA4A TUBA4A 15065 -0.084 0.09 NO
81 PLCB1 PLCB1 PLCB1 15180 -0.088 0.091 NO
82 PLCB2 PLCB2 PLCB2 15250 -0.089 0.095 NO
83 TUBA3C TUBA3C TUBA3C 15879 -0.11 0.071 NO
84 GNAI1 GNAI1 GNAI1 16762 -0.16 0.036 NO
85 EGFR EGFR EGFR 17086 -0.19 0.036 NO
86 PRKCB PRKCB PRKCB 17708 -0.28 0.026 NO

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

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

genes ES table in pathway: KEGG OOCYTE MEIOSIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NKD1 NKD1 NKD1 175 0.57 0.04 YES
2 WNT11 WNT11 WNT11 182 0.56 0.09 YES
3 WNT6 WNT6 WNT6 442 0.47 0.12 YES
4 CXXC4 CXXC4 CXXC4 559 0.44 0.15 YES
5 WNT5B WNT5B WNT5B 568 0.43 0.19 YES
6 FRZB FRZB FRZB 771 0.39 0.21 YES
7 SFRP1 SFRP1 SFRP1 944 0.36 0.23 YES
8 LEF1 LEF1 LEF1 1080 0.34 0.26 YES
9 FZD8 FZD8 FZD8 1113 0.34 0.28 YES
10 FZD3 FZD3 FZD3 1163 0.33 0.31 YES
11 WIF1 WIF1 WIF1 1258 0.31 0.33 YES
12 FZD2 FZD2 FZD2 1403 0.3 0.35 YES
13 PYGO1 PYGO1 PYGO1 1621 0.27 0.36 YES
14 TCF7L1 TCF7L1 TCF7L1 1669 0.27 0.38 YES
15 LRP6 LRP6 LRP6 1674 0.27 0.41 YES
16 TCF7 TCF7 TCF7 2225 0.22 0.4 YES
17 PITX2 PITX2 PITX2 2236 0.22 0.42 YES
18 TLE2 TLE2 TLE2 2321 0.22 0.43 YES
19 FZD7 FZD7 FZD7 2323 0.22 0.45 YES
20 SOX17 SOX17 SOX17 2492 0.21 0.46 YES
21 WNT9A WNT9A WNT9A 2517 0.2 0.48 YES
22 WNT7B WNT7B WNT7B 2808 0.19 0.48 YES
23 WNT7A WNT7A WNT7A 3062 0.17 0.48 YES
24 FZD1 FZD1 FZD1 3249 0.16 0.48 YES
25 FZD4 FZD4 FZD4 3390 0.16 0.49 YES
26 CTNNBIP1 CTNNBIP1 CTNNBIP1 3456 0.16 0.5 YES
27 DIXDC1 DIXDC1 DIXDC1 3577 0.15 0.5 YES
28 BCL9 BCL9 BCL9 3928 0.13 0.5 NO
29 FOXN1 FOXN1 FOXN1 4459 0.11 0.48 NO
30 CCND1 CCND1 CCND1 4475 0.11 0.49 NO
31 TLE1 TLE1 TLE1 4747 0.1 0.48 NO
32 DVL2 DVL2 DVL2 4862 0.098 0.48 NO
33 FRAT1 FRAT1 FRAT1 5340 0.086 0.46 NO
34 WNT2B WNT2B WNT2B 5759 0.075 0.45 NO
35 SFRP4 SFRP4 SFRP4 6080 0.068 0.44 NO
36 CTNNB1 CTNNB1 CTNNB1 6392 0.061 0.42 NO
37 WNT10A WNT10A WNT10A 6453 0.06 0.43 NO
38 PPP2R1A PPP2R1A PPP2R1A 6744 0.054 0.42 NO
39 AES AES AES 7127 0.047 0.4 NO
40 GSK3A GSK3A GSK3A 7218 0.046 0.4 NO
41 FBXW2 FBXW2 FBXW2 7257 0.045 0.4 NO
42 WNT1 WNT1 WNT1 7372 0.043 0.4 NO
43 FBXW4 FBXW4 FBXW4 7541 0.04 0.39 NO
44 EP300 EP300 EP300 7923 0.034 0.37 NO
45 FZD6 FZD6 FZD6 7981 0.033 0.37 NO
46 RPL13A RPL13A RPL13A 7984 0.033 0.38 NO
47 CTBP1 CTBP1 CTBP1 8433 0.026 0.35 NO
48 WNT16 WNT16 WNT16 8595 0.024 0.35 NO
49 CSNK2A1 CSNK2A1 CSNK2A1 8603 0.024 0.35 NO
50 DVL1 DVL1 DVL1 8890 0.02 0.33 NO
51 NLK NLK NLK 9608 0.0097 0.3 NO
52 LRP5 LRP5 LRP5 9780 0.0075 0.29 NO
53 GSK3B GSK3B GSK3B 10261 0.00077 0.26 NO
54 JUN JUN JUN 10806 -0.0068 0.23 NO
55 CTBP2 CTBP2 CTBP2 10854 -0.0074 0.23 NO
56 WISP1 WISP1 WISP1 10927 -0.0085 0.23 NO
57 WNT5A WNT5A WNT5A 11060 -0.01 0.22 NO
58 FBXW11 FBXW11 FBXW11 11125 -0.011 0.22 NO
59 HPRT1 HPRT1 HPRT1 11189 -0.012 0.21 NO
60 CSNK1A1 CSNK1A1 CSNK1A1 11306 -0.014 0.21 NO
61 FOSL1 FOSL1 FOSL1 11310 -0.014 0.21 NO
62 CSNK1D CSNK1D CSNK1D 11434 -0.016 0.2 NO
63 GAPDH GAPDH GAPDH 11467 -0.016 0.2 NO
64 ACTB ACTB ACTB 11675 -0.019 0.2 NO
65 BTRC BTRC BTRC 12040 -0.025 0.18 NO
66 AXIN1 AXIN1 AXIN1 12068 -0.025 0.18 NO
67 KREMEN1 KREMEN1 KREMEN1 12224 -0.028 0.17 NO
68 APC APC APC 12801 -0.037 0.14 NO
69 CSNK1G1 CSNK1G1 CSNK1G1 13097 -0.042 0.13 NO
70 PORCN PORCN PORCN 13235 -0.044 0.13 NO
71 DKK1 DKK1 DKK1 13269 -0.045 0.13 NO
72 PPP2CA PPP2CA PPP2CA 13349 -0.046 0.13 NO
73 FZD5 FZD5 FZD5 13376 -0.047 0.13 NO
74 CCND3 CCND3 CCND3 13540 -0.05 0.13 NO
75 RHOU RHOU RHOU 13819 -0.055 0.12 NO
76 WNT4 WNT4 WNT4 13847 -0.056 0.12 NO
77 SENP2 SENP2 SENP2 14833 -0.078 0.072 NO
78 SLC9A3R1 SLC9A3R1 SLC9A3R1 15076 -0.084 0.066 NO
79 CCND2 CCND2 CCND2 15615 -0.1 0.045 NO
80 B2M B2M B2M 16198 -0.13 0.025 NO
81 MYC MYC MYC 16802 -0.17 0.0062 NO
82 WNT3 WNT3 WNT3 16971 -0.18 0.013 NO
83 DAAM1 DAAM1 DAAM1 17525 -0.25 0.0042 NO
84 WNT2 WNT2 WNT2 17956 -0.36 0.013 NO

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

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

genes ES table in pathway: KEGG VASCULAR SMOOTH MUSCLE CONTRACTION

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HES5 HES5 HES5 180 0.56 0.09 YES
2 NOTCH3 NOTCH3 NOTCH3 658 0.41 0.14 YES
3 DTX1 DTX1 DTX1 803 0.38 0.2 YES
4 DLL1 DLL1 DLL1 1326 0.3 0.22 YES
5 LFNG LFNG LFNG 1798 0.26 0.24 YES
6 NOTCH4 NOTCH4 NOTCH4 1965 0.24 0.27 YES
7 JAG1 JAG1 JAG1 2190 0.23 0.3 YES
8 HES1 HES1 HES1 2211 0.23 0.34 YES
9 NOTCH1 NOTCH1 NOTCH1 2473 0.21 0.36 YES
10 NOTCH2 NOTCH2 NOTCH2 2750 0.19 0.38 YES
11 JAG2 JAG2 JAG2 2990 0.18 0.4 YES
12 DTX3 DTX3 DTX3 3000 0.18 0.43 YES
13 MAML3 MAML3 MAML3 3481 0.15 0.43 YES
14 HDAC2 HDAC2 HDAC2 3744 0.14 0.44 YES
15 DLL4 DLL4 DLL4 3990 0.13 0.45 YES
16 DLL3 DLL3 DLL3 4520 0.11 0.44 YES
17 DVL2 DVL2 DVL2 4862 0.098 0.44 YES
18 CREBBP CREBBP CREBBP 4938 0.096 0.45 YES
19 NUMBL NUMBL NUMBL 5113 0.091 0.46 YES
20 RBPJ RBPJ RBPJ 5470 0.082 0.45 YES
21 MAML1 MAML1 MAML1 5722 0.076 0.45 YES
22 NCOR2 NCOR2 NCOR2 5846 0.073 0.46 YES
23 HDAC1 HDAC1 HDAC1 6125 0.067 0.46 YES
24 RBPJL RBPJL RBPJL 6184 0.066 0.46 YES
25 KAT2A KAT2A KAT2A 7850 0.035 0.38 NO
26 EP300 EP300 EP300 7923 0.034 0.38 NO
27 MAML2 MAML2 MAML2 7967 0.033 0.38 NO
28 CTBP1 CTBP1 CTBP1 8433 0.026 0.36 NO
29 DVL1 DVL1 DVL1 8890 0.02 0.34 NO
30 NUMB NUMB NUMB 9189 0.015 0.33 NO
31 SNW1 SNW1 SNW1 9574 0.01 0.31 NO
32 CTBP2 CTBP2 CTBP2 10854 -0.0074 0.24 NO
33 NCSTN NCSTN NCSTN 10947 -0.0087 0.23 NO
34 RFNG RFNG RFNG 11340 -0.014 0.22 NO
35 PSEN1 PSEN1 PSEN1 11745 -0.02 0.2 NO
36 CIR1 CIR1 CIR1 11769 -0.021 0.2 NO
37 APH1A APH1A APH1A 11809 -0.021 0.2 NO
38 ADAM17 ADAM17 ADAM17 12345 -0.029 0.18 NO
39 DTX4 DTX4 DTX4 14395 -0.068 0.075 NO
40 PSEN2 PSEN2 PSEN2 14578 -0.072 0.078 NO
41 PSENEN PSENEN PSENEN 14645 -0.073 0.087 NO
42 DVL3 DVL3 DVL3 14782 -0.077 0.093 NO
43 DTX2 DTX2 DTX2 15408 -0.095 0.076 NO
44 DTX3L DTX3L DTX3L 16048 -0.12 0.062 NO
45 KAT2B KAT2B KAT2B 16515 -0.15 0.062 NO
46 PTCRA PTCRA PTCRA 16855 -0.17 0.073 NO

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

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

genes ES table in pathway: KEGG WNT SIGNALING PATHWAY

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

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

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

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

genes ES table in pathway: KEGG NOTCH SIGNALING PATHWAY

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

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

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

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

Fold change

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

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 = MESO-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = MESO-TP.mergedcluster.txt

GSEA analysis

For the Gene Set Enrichment Analysis (GSEA), Broad GSEA-P-R.1.0 version is used with class2: canonical pathways geneses from MSigDB. Further details about statistics are available inThe Broad GSEA website.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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