GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in HNSC-TP
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C13J3C5F
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 HNSC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C13J3C5F
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 HNSC-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: 192
Number of samples: 520
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 144
pheno.type: 2 - 3 :[ clus2 ] 214
pheno.type: 3 - 3 :[ clus3 ] 162

For the expression subtypes of 18378 genes in 521 samples, GSEA found enriched gene sets in each cluster using 520 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA CARM ER PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA FMLP PATHWAY

    • And common core enriched genes are PPP1R12B, ACTA1, ARHGAP6, MYL2, MYLK, PIP5K1B, ACTN1, ACTN2, ACTN3, CAV1

  • clus2

    • Top enriched gene sets are BIOCARTA CHREBP2 PATHWAY, BIOCARTA WNT PATHWAY, KEGG FATTY ACID METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION, KEGG SELENOAMINO ACID METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG BUTANOATE METABOLISM

    • And common core enriched genes are UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT2A1, UGT2B15

  • clus3

    • Top enriched gene sets are BIOCARTA ERK PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA IL1R PATHWAY, KEGG PYRIMIDINE METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME, KEGG RNA POLYMERASE

    • And common core enriched genes are IFNG, POMP, PSMA1, PSMA2, PSMA3, PSMA4, PSMA5, PSMA6, PSMA7, PSMB1

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 NO1 PATHWAY 28 genes.ES.table 0.75 1.8 0 0.032 0.29 0.25 0.061 0.24 0 0
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.73 2 0 0.012 0.059 0.26 0.084 0.24 0 0
BIOCARTA ALK PATHWAY 34 genes.ES.table 0.64 1.8 0 0.032 0.29 0.44 0.2 0.35 0 0
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.58 2.1 0.0019 0.014 0.027 0.28 0.22 0.22 0 0.002
BIOCARTA BIOPEPTIDES PATHWAY 40 genes.ES.table 0.63 2.1 0 0.0093 0.028 0.1 0.013 0.099 0 0
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.43 1.5 0.072 0.13 0.89 0.24 0.24 0.18 0.091 0
BIOCARTA HDAC PATHWAY 27 genes.ES.table 0.64 1.8 0 0.033 0.28 0.52 0.27 0.38 0 0
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.57 1.8 0.0082 0.034 0.32 0.4 0.26 0.3 0 0
BIOCARTA ERK PATHWAY 27 genes.ES.table 0.46 1.5 0.069 0.12 0.86 0.26 0.22 0.2 0.08 0
BIOCARTA FMLP PATHWAY 35 genes.ES.table 0.4 1.3 0.18 0.24 0.98 0.29 0.24 0.22 0.2 0.002
genes ES table in pathway: BIOCARTA NO1 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 MYL2 MYL2 MYL2 27 1.5 0.44 YES
2 ARHGAP6 ARHGAP6 ARHGAP6 413 0.43 0.54 YES
3 PPP1R12B PPP1R12B PPP1R12B 1332 0.23 0.55 YES
4 PIP5K1B PIP5K1B PIP5K1B 1692 0.2 0.59 YES
5 MYLK MYLK MYLK 1784 0.19 0.64 YES
6 VCL VCL VCL 3822 0.082 0.55 NO
7 ARPC1B ARPC1B ARPC1B 4005 0.076 0.56 NO
8 ARHGAP1 ARHGAP1 ARHGAP1 4329 0.066 0.56 NO
9 OPHN1 OPHN1 OPHN1 4937 0.052 0.55 NO
10 LIMK1 LIMK1 LIMK1 5215 0.046 0.54 NO
11 GSN GSN GSN 5405 0.042 0.55 NO
12 ROCK1 ROCK1 ROCK1 5448 0.042 0.56 NO
13 SRC SRC SRC 5662 0.038 0.55 NO
14 PFN1 PFN1 PFN1 6036 0.033 0.54 NO
15 CFL1 CFL1 CFL1 6213 0.03 0.54 NO
16 ACTR2 ACTR2 ACTR2 6612 0.024 0.53 NO
17 ARHGAP5 ARHGAP5 ARHGAP5 6772 0.022 0.52 NO
18 DIAPH1 DIAPH1 DIAPH1 7177 0.018 0.51 NO
19 RHOA RHOA RHOA 7290 0.016 0.51 NO
20 ARHGEF1 ARHGEF1 ARHGEF1 7380 0.016 0.51 NO
21 ARPC2 ARPC2 ARPC2 7838 0.011 0.48 NO
22 ACTR3 ACTR3 ACTR3 8431 0.0048 0.45 NO
23 PIP5K1A PIP5K1A PIP5K1A 8745 0.0017 0.44 NO
24 ARHGEF11 ARHGEF11 ARHGEF11 9077 -0.0013 0.42 NO
25 ARPC4 ARPC4 ARPC4 9109 -0.0017 0.42 NO
26 ARPC1A ARPC1A ARPC1A 10262 -0.012 0.36 NO
27 ARPC5 ARPC5 ARPC5 11350 -0.022 0.31 NO
28 ARPC3 ARPC3 ARPC3 11460 -0.024 0.31 NO
29 BAIAP2 BAIAP2 BAIAP2 13640 -0.049 0.2 NO
30 ARHGEF5 ARHGEF5 ARHGEF5 14645 -0.065 0.17 NO
31 ARHGAP4 ARHGAP4 ARHGAP4 16608 -0.13 0.096 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 NO1 PATHWAY.

Figure S2.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 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 AGR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACTN2 ACTN2 ACTN2 21 1.5 0.26 YES
2 ACTA1 ACTA1 ACTA1 23 1.5 0.52 YES
3 ACTN3 ACTN3 ACTN3 433 0.42 0.57 YES
4 TNS1 TNS1 TNS1 883 0.29 0.6 YES
5 ITGA1 ITGA1 ITGA1 1307 0.23 0.61 YES
6 PPP1R12B PPP1R12B PPP1R12B 1332 0.23 0.65 YES
7 CAV1 CAV1 CAV1 1791 0.19 0.66 YES
8 ACTN1 ACTN1 ACTN1 2421 0.14 0.65 YES
9 ITGB1 ITGB1 ITGB1 2836 0.12 0.65 YES
10 RAPGEF1 RAPGEF1 RAPGEF1 3030 0.11 0.65 YES
11 FYN FYN FYN 3039 0.11 0.67 YES
12 PXN PXN PXN 3089 0.11 0.69 YES
13 VCL VCL VCL 3822 0.082 0.66 NO
14 MAPK8 MAPK8 MAPK8 4036 0.075 0.66 NO
15 BCAR1 BCAR1 BCAR1 4296 0.067 0.66 NO
16 ZYX ZYX ZYX 4367 0.065 0.67 NO
17 SHC1 SHC1 SHC1 4745 0.056 0.66 NO
18 PTK2 PTK2 PTK2 5277 0.045 0.64 NO
19 RAP1A RAP1A RAP1A 5378 0.043 0.64 NO
20 ROCK1 ROCK1 ROCK1 5448 0.042 0.64 NO
21 SRC SRC SRC 5662 0.038 0.64 NO
22 JUN JUN JUN 5847 0.035 0.63 NO
23 MAPK1 MAPK1 MAPK1 7096 0.019 0.57 NO
24 RHOA RHOA RHOA 7290 0.016 0.56 NO
25 SOS1 SOS1 SOS1 7663 0.013 0.54 NO
26 CRKL CRKL CRKL 7686 0.012 0.54 NO
27 MAP2K1 MAP2K1 MAP2K1 8211 0.0071 0.51 NO
28 CAPN1 CAPN1 CAPN1 8817 0.001 0.48 NO
29 CAPNS1 CAPNS1 CAPNS1 8972 -0.00034 0.47 NO
30 GRB2 GRB2 GRB2 9523 -0.0055 0.44 NO
31 HRAS HRAS HRAS 10029 -0.0099 0.42 NO
32 RAF1 RAF1 RAF1 10715 -0.016 0.38 NO
33 BCR BCR BCR 11943 -0.029 0.32 NO
34 MAPK3 MAPK3 MAPK3 12238 -0.032 0.31 NO
35 MAP2K2 MAP2K2 MAP2K2 12299 -0.033 0.31 NO
36 CSK CSK CSK 12816 -0.038 0.29 NO
37 CAPNS2 CAPNS2 CAPNS2 14593 -0.064 0.21 NO

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

Figure S4.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AGR 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 ALK PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HSPB2 HSPB2 HSPB2 176 0.79 0.21 YES
2 MEF2C MEF2C MEF2C 207 0.7 0.41 YES
3 TGFB3 TGFB3 TGFB3 743 0.32 0.47 YES
4 TGFB2 TGFB2 TGFB2 1098 0.26 0.52 YES
5 ATF2 ATF2 ATF2 3433 0.095 0.42 NO
6 TGFBR1 TGFBR1 TGFBR1 3516 0.092 0.45 NO
7 MEF2D MEF2D MEF2D 3558 0.091 0.47 NO
8 RAPGEF2 RAPGEF2 RAPGEF2 3679 0.087 0.49 NO
9 MEF2A MEF2A MEF2A 3907 0.079 0.5 NO
10 TGFB1 TGFB1 TGFB1 4308 0.067 0.49 NO
11 STAT1 STAT1 STAT1 4431 0.063 0.5 NO
12 SHC1 SHC1 SHC1 4745 0.056 0.5 NO
13 MAP3K7 MAP3K7 MAP3K7 7673 0.012 0.35 NO
14 ELK1 ELK1 ELK1 7699 0.012 0.35 NO
15 CDC42 CDC42 CDC42 7701 0.012 0.35 NO
16 CREB1 CREB1 CREB1 7720 0.012 0.36 NO
17 MAP2K4 MAP2K4 MAP2K4 7787 0.011 0.36 NO
18 MAPKAPK2 MAPKAPK2 MAPKAPK2 7978 0.0094 0.35 NO
19 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 8169 0.0076 0.34 NO
20 MAP3K1 MAP3K1 MAP3K1 8199 0.0073 0.34 NO
21 MAPK14 MAPK14 MAPK14 8829 0.001 0.31 NO
22 RIPK1 RIPK1 RIPK1 8866 0.00062 0.3 NO
23 MKNK1 MKNK1 MKNK1 9066 -0.0013 0.29 NO
24 DAXX DAXX DAXX 9335 -0.0036 0.28 NO
25 GRB2 GRB2 GRB2 9523 -0.0055 0.27 NO
26 HRAS HRAS HRAS 10029 -0.0099 0.25 NO
27 MAX MAX MAX 10456 -0.014 0.23 NO
28 MYC MYC MYC 10473 -0.014 0.23 NO
29 MAPKAPK5 MAPKAPK5 MAPKAPK5 11631 -0.025 0.17 NO
30 RAC1 RAC1 RAC1 11810 -0.027 0.17 NO
31 TRADD TRADD TRADD 12692 -0.037 0.13 NO
32 DDIT3 DDIT3 DDIT3 12919 -0.04 0.13 NO
33 TRAF2 TRAF2 TRAF2 13831 -0.051 0.098 NO
34 MAP3K9 MAP3K9 MAP3K9 13990 -0.053 0.1 NO
35 MAP3K5 MAP3K5 MAP3K5 14205 -0.057 0.11 NO
36 RPS6KA5 RPS6KA5 RPS6KA5 14280 -0.058 0.12 NO
37 HSPB1 HSPB1 HSPB1 14376 -0.06 0.13 NO
38 MAP2K6 MAP2K6 MAP2K6 16679 -0.13 0.045 NO
39 PLA2G4A PLA2G4A PLA2G4A 17276 -0.17 0.059 NO

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

Figure S6.  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 AT1R PATHWAY

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 ACTA1 ACTA1 ACTA1 23 1.5 0.48 YES
2 PGR PGR PGR 435 0.42 0.59 YES
3 PRKACB PRKACB PRKACB 3285 0.1 0.46 NO
4 PAQR5 PAQR5 PAQR5 3910 0.079 0.45 NO
5 PRKAR2A PRKAR2A PRKAR2A 3922 0.079 0.48 NO
6 ARPC1B ARPC1B ARPC1B 4005 0.076 0.5 NO
7 PRKAR2B PRKAR2B PRKAR2B 4318 0.066 0.5 NO
8 SRC SRC SRC 5662 0.038 0.44 NO
9 GNB1 GNB1 GNB1 5805 0.036 0.44 NO
10 CAP1 CAP1 CAP1 5880 0.035 0.45 NO
11 PRKAR1A PRKAR1A PRKAR1A 5926 0.034 0.46 NO
12 ACTR2 ACTR2 ACTR2 6612 0.024 0.43 NO
13 PAQR7 PAQR7 PAQR7 6814 0.022 0.42 NO
14 GNAS GNAS GNAS 6865 0.021 0.43 NO
15 MAPK1 MAPK1 MAPK1 7096 0.019 0.42 NO
16 RPS6KA1 RPS6KA1 RPS6KA1 7131 0.018 0.42 NO
17 GNAI1 GNAI1 GNAI1 7163 0.018 0.43 NO
18 ARPC2 ARPC2 ARPC2 7838 0.011 0.4 NO
19 ACTR3 ACTR3 ACTR3 8431 0.0048 0.36 NO
20 ARPC4 ARPC4 ARPC4 9109 -0.0017 0.33 NO
21 HRAS HRAS HRAS 10029 -0.0099 0.28 NO
22 ARPC1A ARPC1A ARPC1A 10262 -0.012 0.27 NO
23 ARPC5 ARPC5 ARPC5 11350 -0.022 0.22 NO
24 ARPC3 ARPC3 ARPC3 11460 -0.024 0.22 NO
25 MAPK3 MAPK3 MAPK3 12238 -0.032 0.19 NO
26 PIN1 PIN1 PIN1 12372 -0.033 0.19 NO
27 PRKAR1B PRKAR1B PRKAR1B 12892 -0.039 0.18 NO
28 MYT1 MYT1 MYT1 14377 -0.06 0.11 NO
29 GNGT1 GNGT1 GNGT1 14607 -0.064 0.12 NO
30 CCNB1 CCNB1 CCNB1 14962 -0.072 0.12 NO
31 CDK1 CDK1 CDK1 15682 -0.092 0.12 NO
32 CDC25C CDC25C CDC25C 15913 -0.1 0.13 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: BIOCARTA AT1R PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R 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 BIOPEPTIDES PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AGT AGT AGT 234 0.63 0.26 YES
2 AGTR1 AGTR1 AGTR1 291 0.52 0.48 YES
3 PRKCA PRKCA PRKCA 1761 0.19 0.48 YES
4 PRKCB PRKCB PRKCB 3324 0.098 0.44 YES
5 ATF2 ATF2 ATF2 3433 0.095 0.47 YES
6 MEF2D MEF2D MEF2D 3558 0.091 0.5 YES
7 MEF2A MEF2A MEF2A 3907 0.079 0.52 YES
8 MAPK8 MAPK8 MAPK8 4036 0.075 0.55 YES
9 EGFR EGFR EGFR 4060 0.074 0.58 YES
10 SHC1 SHC1 SHC1 4745 0.056 0.56 NO
11 PTK2 PTK2 PTK2 5277 0.045 0.55 NO
12 SRC SRC SRC 5662 0.038 0.55 NO
13 JUN JUN JUN 5847 0.035 0.55 NO
14 CALM1 CALM1 CALM1 6049 0.032 0.56 NO
15 PTK2B PTK2B PTK2B 6162 0.031 0.56 NO
16 MAPK1 MAPK1 MAPK1 7096 0.019 0.52 NO
17 SOS1 SOS1 SOS1 7663 0.013 0.5 NO
18 ELK1 ELK1 ELK1 7699 0.012 0.5 NO
19 MAP2K4 MAP2K4 MAP2K4 7787 0.011 0.5 NO
20 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 8169 0.0076 0.48 NO
21 MAP3K1 MAP3K1 MAP3K1 8199 0.0073 0.48 NO
22 MAP2K1 MAP2K1 MAP2K1 8211 0.0071 0.48 NO
23 CALM3 CALM3 CALM3 8268 0.0065 0.48 NO
24 CALM2 CALM2 CALM2 8837 0.00092 0.45 NO
25 GRB2 GRB2 GRB2 9523 -0.0055 0.42 NO
26 GNAQ GNAQ GNAQ 9599 -0.0062 0.42 NO
27 HRAS HRAS HRAS 10029 -0.0099 0.4 NO
28 RAF1 RAF1 RAF1 10715 -0.016 0.37 NO
29 PAK1 PAK1 PAK1 11209 -0.021 0.35 NO
30 RAC1 RAC1 RAC1 11810 -0.027 0.33 NO
31 MAPK3 MAPK3 MAPK3 12238 -0.032 0.32 NO
32 MAP2K2 MAP2K2 MAP2K2 12299 -0.033 0.33 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: BIOCARTA BIOPEPTIDES PATHWAY.

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

genes ES table in pathway: BIOCARTA CARM ER PATHWAY

Table 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 CAV3 CAV3 CAV3 13 1.6 0.046 YES
2 MYLPF MYLPF MYLPF 20 1.6 0.091 YES
3 ACTN2 ACTN2 ACTN2 21 1.5 0.14 YES
4 MYL2 MYL2 MYL2 27 1.5 0.18 YES
5 MYLK2 MYLK2 MYLK2 127 0.97 0.2 YES
6 FLNC FLNC FLNC 148 0.87 0.23 YES
7 THBS4 THBS4 THBS4 150 0.86 0.25 YES
8 MYLK3 MYLK3 MYLK3 204 0.71 0.27 YES
9 ITGA7 ITGA7 ITGA7 213 0.69 0.29 YES
10 EGF EGF EGF 350 0.46 0.3 YES
11 LAMA2 LAMA2 LAMA2 355 0.46 0.31 YES
12 IGF1 IGF1 IGF1 393 0.44 0.32 YES
13 ACTN3 ACTN3 ACTN3 433 0.42 0.33 YES
14 TNN TNN TNN 460 0.41 0.34 YES
15 RELN RELN RELN 498 0.4 0.35 YES
16 ITGB3 ITGB3 ITGB3 499 0.39 0.36 YES
17 COL11A1 COL11A1 COL11A1 574 0.37 0.37 YES
18 FN1 FN1 FN1 691 0.33 0.37 YES
19 ITGA10 ITGA10 ITGA10 696 0.33 0.38 YES
20 THBS2 THBS2 THBS2 728 0.32 0.39 YES
21 ITGA9 ITGA9 ITGA9 760 0.32 0.4 YES
22 ITGA11 ITGA11 ITGA11 776 0.31 0.4 YES
23 TNXB TNXB TNXB 788 0.31 0.41 YES
24 COMP COMP COMP 790 0.31 0.42 YES
25 VEGFC VEGFC VEGFC 809 0.3 0.43 YES
26 COL5A1 COL5A1 COL5A1 849 0.3 0.44 YES
27 COL4A6 COL4A6 COL4A6 852 0.3 0.44 YES
28 COL5A2 COL5A2 COL5A2 868 0.3 0.45 YES
29 RASGRF1 RASGRF1 RASGRF1 955 0.28 0.46 YES
30 ITGA8 ITGA8 ITGA8 1080 0.26 0.46 YES
31 COL3A1 COL3A1 COL3A1 1082 0.26 0.46 YES
32 COL6A3 COL6A3 COL6A3 1090 0.26 0.47 YES
33 FLT4 FLT4 FLT4 1120 0.26 0.48 YES
34 COL5A3 COL5A3 COL5A3 1157 0.25 0.48 YES
35 COL1A2 COL1A2 COL1A2 1162 0.25 0.49 YES
36 TNC TNC TNC 1206 0.24 0.49 YES
37 COL1A1 COL1A1 COL1A1 1214 0.24 0.5 YES
38 PDGFC PDGFC PDGFC 1273 0.24 0.5 YES
39 THBS1 THBS1 THBS1 1291 0.24 0.51 YES
40 PDGFRA PDGFRA PDGFRA 1300 0.23 0.52 YES
41 ITGA1 ITGA1 ITGA1 1307 0.23 0.52 YES
42 PDGFRB PDGFRB PDGFRB 1311 0.23 0.53 YES
43 MYL9 MYL9 MYL9 1337 0.23 0.54 YES
44 COL4A4 COL4A4 COL4A4 1391 0.22 0.54 YES
45 IBSP IBSP IBSP 1411 0.22 0.54 YES
46 COL6A1 COL6A1 COL6A1 1412 0.22 0.55 YES
47 VTN VTN VTN 1414 0.22 0.56 YES
48 LAMA4 LAMA4 LAMA4 1415 0.22 0.56 YES
49 COL6A2 COL6A2 COL6A2 1456 0.22 0.57 YES
50 LAMA1 LAMA1 LAMA1 1507 0.21 0.57 YES
51 ITGA5 ITGA5 ITGA5 1523 0.21 0.58 YES
52 LAMA3 LAMA3 LAMA3 1549 0.21 0.58 YES
53 ITGB6 ITGB6 ITGB6 1584 0.21 0.59 YES
54 ITGA4 ITGA4 ITGA4 1679 0.2 0.59 YES
55 PDGFB PDGFB PDGFB 1705 0.19 0.59 YES
56 SHC2 SHC2 SHC2 1722 0.19 0.6 YES
57 LAMC2 LAMC2 LAMC2 1725 0.19 0.6 YES
58 PRKCA PRKCA PRKCA 1761 0.19 0.6 YES
59 MYLK MYLK MYLK 1784 0.19 0.61 YES
60 CAV1 CAV1 CAV1 1791 0.19 0.61 YES
61 TLN2 TLN2 TLN2 1804 0.18 0.62 YES
62 KDR KDR KDR 1913 0.18 0.62 YES
63 HGF HGF HGF 1924 0.18 0.62 YES
64 FIGF FIGF FIGF 2007 0.17 0.62 YES
65 LAMC3 LAMC3 LAMC3 2023 0.17 0.63 YES
66 PIK3CG PIK3CG PIK3CG 2105 0.16 0.63 YES
67 SHC3 SHC3 SHC3 2142 0.16 0.63 YES
68 COL2A1 COL2A1 COL2A1 2157 0.16 0.63 YES
69 AKT3 AKT3 AKT3 2213 0.16 0.64 YES
70 PIK3R1 PIK3R1 PIK3R1 2283 0.15 0.64 YES
71 LAMB2 LAMB2 LAMB2 2380 0.14 0.64 YES
72 ACTN1 ACTN1 ACTN1 2421 0.14 0.64 YES
73 LAMB1 LAMB1 LAMB1 2443 0.14 0.64 YES
74 COL4A2 COL4A2 COL4A2 2459 0.14 0.64 YES
75 PIK3CD PIK3CD PIK3CD 2506 0.14 0.64 YES
76 COL4A1 COL4A1 COL4A1 2515 0.14 0.65 YES
77 ITGAV ITGAV ITGAV 2581 0.13 0.65 YES
78 THBS3 THBS3 THBS3 2610 0.13 0.65 YES
79 PARVA PARVA PARVA 2648 0.13 0.65 YES
80 ITGA3 ITGA3 ITGA3 2672 0.13 0.66 YES
81 PAK3 PAK3 PAK3 2767 0.12 0.65 YES
82 LAMB4 LAMB4 LAMB4 2771 0.12 0.66 YES
83 PARVB PARVB PARVB 2804 0.12 0.66 YES
84 ITGB1 ITGB1 ITGB1 2836 0.12 0.66 YES
85 PDGFD PDGFD PDGFD 2933 0.12 0.66 YES
86 COL6A6 COL6A6 COL6A6 2945 0.12 0.66 YES
87 LAMB3 LAMB3 LAMB3 2948 0.12 0.66 YES
88 TNR TNR TNR 2961 0.12 0.67 YES
89 ROCK2 ROCK2 ROCK2 3027 0.11 0.67 YES
90 ITGA6 ITGA6 ITGA6 3029 0.11 0.67 YES
91 RAPGEF1 RAPGEF1 RAPGEF1 3030 0.11 0.67 YES
92 FYN FYN FYN 3039 0.11 0.68 YES
93 ITGB5 ITGB5 ITGB5 3043 0.11 0.68 YES
94 MYL7 MYL7 MYL7 3048 0.11 0.68 YES
95 LAMC1 LAMC1 LAMC1 3058 0.11 0.68 YES
96 PDGFA PDGFA PDGFA 3072 0.11 0.69 YES
97 PXN PXN PXN 3089 0.11 0.69 YES
98 PIK3R5 PIK3R5 PIK3R5 3156 0.1 0.69 YES
99 MET MET MET 3208 0.1 0.69 YES
100 TLN1 TLN1 TLN1 3272 0.1 0.69 YES
101 PRKCB PRKCB PRKCB 3324 0.098 0.69 YES
102 VAV2 VAV2 VAV2 3329 0.098 0.69 YES
103 CAV2 CAV2 CAV2 3540 0.091 0.68 NO
104 PARVG PARVG PARVG 3584 0.09 0.68 NO
105 CCND1 CCND1 CCND1 3631 0.088 0.68 NO
106 VWF VWF VWF 3747 0.085 0.68 NO
107 FLNA FLNA FLNA 3768 0.084 0.68 NO
108 SPP1 SPP1 SPP1 3808 0.082 0.68 NO
109 VCL VCL VCL 3822 0.082 0.68 NO
110 DOCK1 DOCK1 DOCK1 3825 0.082 0.68 NO
111 SHC4 SHC4 SHC4 3854 0.081 0.69 NO
112 ILK ILK ILK 3889 0.08 0.69 NO
113 IGF1R IGF1R IGF1R 4006 0.075 0.68 NO
114 MAPK8 MAPK8 MAPK8 4036 0.075 0.68 NO
115 EGFR EGFR EGFR 4060 0.074 0.68 NO
116 BIRC2 BIRC2 BIRC2 4193 0.07 0.68 NO
117 FLT1 FLT1 FLT1 4248 0.068 0.68 NO
118 BCAR1 BCAR1 BCAR1 4296 0.067 0.68 NO
119 ZYX ZYX ZYX 4367 0.065 0.68 NO
120 ITGB4 ITGB4 ITGB4 4485 0.061 0.67 NO
121 ITGA2 ITGA2 ITGA2 4709 0.057 0.66 NO
122 SHC1 SHC1 SHC1 4745 0.056 0.66 NO
123 PTEN PTEN PTEN 5081 0.048 0.64 NO
124 SOS2 SOS2 SOS2 5145 0.047 0.64 NO
125 VAV3 VAV3 VAV3 5176 0.047 0.64 NO
126 MYL12A MYL12A MYL12A 5220 0.046 0.64 NO
127 PTK2 PTK2 PTK2 5277 0.045 0.64 NO
128 RAC2 RAC2 RAC2 5281 0.045 0.64 NO
129 CRK CRK CRK 5360 0.043 0.64 NO
130 RAP1A RAP1A RAP1A 5378 0.043 0.64 NO
131 ROCK1 ROCK1 ROCK1 5448 0.042 0.63 NO
132 PIP5K1C PIP5K1C PIP5K1C 5587 0.039 0.63 NO
133 SRC SRC SRC 5662 0.038 0.62 NO
134 VEGFB VEGFB VEGFB 5713 0.037 0.62 NO
135 JUN JUN JUN 5847 0.035 0.62 NO
136 CHAD CHAD CHAD 5876 0.035 0.62 NO
137 PPP1R12A PPP1R12A PPP1R12A 6070 0.032 0.6 NO
138 AKT1 AKT1 AKT1 6455 0.026 0.58 NO
139 PIK3CA PIK3CA PIK3CA 6594 0.025 0.58 NO
140 CTNNB1 CTNNB1 CTNNB1 6626 0.024 0.58 NO
141 GSK3B GSK3B GSK3B 6665 0.024 0.58 NO
142 ACTB ACTB ACTB 6686 0.024 0.57 NO
143 XIAP XIAP XIAP 6705 0.023 0.57 NO
144 ARHGAP5 ARHGAP5 ARHGAP5 6772 0.022 0.57 NO
145 CCND2 CCND2 CCND2 6821 0.022 0.57 NO
146 RAP1B RAP1B RAP1B 6997 0.02 0.56 NO
147 CCND3 CCND3 CCND3 7001 0.02 0.56 NO
148 MAPK1 MAPK1 MAPK1 7096 0.019 0.56 NO
149 DIAPH1 DIAPH1 DIAPH1 7177 0.018 0.55 NO
150 CAPN2 CAPN2 CAPN2 7201 0.017 0.55 NO
151 VASP VASP VASP 7211 0.017 0.55 NO
152 RHOA RHOA RHOA 7290 0.016 0.55 NO
153 PAK2 PAK2 PAK2 7510 0.014 0.54 NO
154 PDPK1 PDPK1 PDPK1 7614 0.013 0.53 NO
155 SOS1 SOS1 SOS1 7663 0.013 0.53 NO
156 CRKL CRKL CRKL 7686 0.012 0.53 NO
157 ELK1 ELK1 ELK1 7699 0.012 0.53 NO
158 CDC42 CDC42 CDC42 7701 0.012 0.53 NO
159 LAMA5 LAMA5 LAMA5 7895 0.01 0.52 NO
160 PPP1CA PPP1CA PPP1CA 7921 0.0099 0.52 NO
161 GRLF1 GRLF1 GRLF1 8099 0.0084 0.51 NO
162 AKT2 AKT2 AKT2 8176 0.0075 0.5 NO
163 FLNB FLNB FLNB 8185 0.0074 0.5 NO
164 MAP2K1 MAP2K1 MAP2K1 8211 0.0071 0.5 NO
165 ACTN4 ACTN4 ACTN4 8225 0.007 0.5 NO
166 VAV1 VAV1 VAV1 8577 0.0032 0.48 NO
167 MAPK9 MAPK9 MAPK9 9328 -0.0036 0.44 NO
168 GRB2 GRB2 GRB2 9523 -0.0055 0.43 NO
169 PPP1CB PPP1CB PPP1CB 9749 -0.0075 0.42 NO
170 MYL12B MYL12B MYL12B 9755 -0.0075 0.42 NO
171 ACTG1 ACTG1 ACTG1 9993 -0.0096 0.4 NO
172 PIK3R2 PIK3R2 PIK3R2 10327 -0.012 0.39 NO
173 RAF1 RAF1 RAF1 10715 -0.016 0.37 NO
174 BAD BAD BAD 10768 -0.017 0.36 NO
175 PPP1CC PPP1CC PPP1CC 10860 -0.018 0.36 NO
176 PAK1 PAK1 PAK1 11209 -0.021 0.34 NO
177 BCL2 BCL2 BCL2 11595 -0.025 0.32 NO
178 RAC1 RAC1 RAC1 11810 -0.027 0.31 NO
179 MAPK3 MAPK3 MAPK3 12238 -0.032 0.29 NO
180 COL11A2 COL11A2 COL11A2 12443 -0.034 0.28 NO
181 ITGB8 ITGB8 ITGB8 12634 -0.036 0.27 NO
182 PIK3CB PIK3CB PIK3CB 12946 -0.04 0.25 NO
183 PAK6 PAK6 PAK6 13455 -0.046 0.22 NO
184 PGF PGF PGF 13942 -0.053 0.2 NO
185 PAK4 PAK4 PAK4 14104 -0.055 0.19 NO
186 ITGB7 ITGB7 ITGB7 14110 -0.055 0.19 NO
187 BIRC3 BIRC3 BIRC3 14392 -0.06 0.18 NO
188 RAC3 RAC3 RAC3 14667 -0.066 0.17 NO
189 BRAF BRAF BRAF 14967 -0.072 0.15 NO
190 ERBB2 ERBB2 ERBB2 15187 -0.078 0.14 NO
191 PIK3R3 PIK3R3 PIK3R3 15707 -0.092 0.12 NO
192 VEGFA VEGFA VEGFA 16216 -0.11 0.092 NO
193 PAK7 PAK7 PAK7 16361 -0.12 0.088 NO
194 MYL5 MYL5 MYL5 17135 -0.16 0.05 NO
195 PRKCG PRKCG PRKCG 17294 -0.17 0.046 NO
196 MAPK10 MAPK10 MAPK10 17701 -0.2 0.029 NO
197 ITGA2B ITGA2B ITGA2B 17971 -0.24 0.022 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: BIOCARTA CARM ER PATHWAY.

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

genes ES table in pathway: BIOCARTA HDAC PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACTN2 ACTN2 ACTN2 21 1.5 0.21 YES
2 CTNNA3 CTNNA3 CTNNA3 147 0.87 0.32 YES
3 SORBS1 SORBS1 SORBS1 272 0.55 0.38 YES
4 ACTN3 ACTN3 ACTN3 433 0.42 0.43 YES
5 SNAI1 SNAI1 SNAI1 1059 0.26 0.43 YES
6 PTPRM PTPRM PTPRM 1226 0.24 0.46 YES
7 PTPRB PTPRB PTPRB 1641 0.2 0.46 YES
8 TGFBR2 TGFBR2 TGFBR2 1838 0.18 0.48 YES
9 ACTN1 ACTN1 ACTN1 2421 0.14 0.46 YES
10 WASF3 WASF3 WASF3 2454 0.14 0.48 YES
11 SNAI2 SNAI2 SNAI2 2510 0.14 0.5 YES
12 FGFR1 FGFR1 FGFR1 2699 0.13 0.5 YES
13 FYN FYN FYN 3039 0.11 0.5 YES
14 CTNNA2 CTNNA2 CTNNA2 3149 0.1 0.51 YES
15 MET MET MET 3208 0.1 0.52 YES
16 TCF7 TCF7 TCF7 3418 0.095 0.52 YES
17 TGFBR1 TGFBR1 TGFBR1 3516 0.092 0.52 YES
18 VCL VCL VCL 3822 0.082 0.52 YES
19 PVRL3 PVRL3 PVRL3 3831 0.082 0.53 YES
20 LEF1 LEF1 LEF1 3954 0.078 0.53 YES
21 IGF1R IGF1R IGF1R 4006 0.075 0.54 YES
22 EGFR EGFR EGFR 4060 0.074 0.55 YES
23 WAS WAS WAS 4432 0.063 0.54 YES
24 PTPRJ PTPRJ PTPRJ 4544 0.06 0.54 YES
25 TCF7L1 TCF7L1 TCF7L1 4626 0.058 0.54 YES
26 INSR INSR INSR 4738 0.056 0.54 YES
27 LMO7 LMO7 LMO7 4778 0.055 0.55 YES
28 TCF7L2 TCF7L2 TCF7L2 5002 0.05 0.54 NO
29 RAC2 RAC2 RAC2 5281 0.045 0.53 NO
30 SRC SRC SRC 5662 0.038 0.52 NO
31 IQGAP1 IQGAP1 IQGAP1 5792 0.036 0.52 NO
32 PTPN1 PTPN1 PTPN1 5846 0.035 0.52 NO
33 CSNK2A2 CSNK2A2 CSNK2A2 5861 0.035 0.52 NO
34 CTNNB1 CTNNB1 CTNNB1 6626 0.024 0.48 NO
35 ACTB ACTB ACTB 6686 0.024 0.48 NO
36 EP300 EP300 EP300 6825 0.022 0.48 NO
37 SMAD4 SMAD4 SMAD4 7043 0.02 0.47 NO
38 MAPK1 MAPK1 MAPK1 7096 0.019 0.47 NO
39 RHOA RHOA RHOA 7290 0.016 0.46 NO
40 CREBBP CREBBP CREBBP 7325 0.016 0.46 NO
41 MAP3K7 MAP3K7 MAP3K7 7673 0.012 0.44 NO
42 CDC42 CDC42 CDC42 7701 0.012 0.44 NO
43 ACTN4 ACTN4 ACTN4 8225 0.007 0.42 NO
44 FER FER FER 8694 0.0022 0.39 NO
45 CSNK2A1 CSNK2A1 CSNK2A1 9020 -0.0008 0.37 NO
46 PTPRF PTPRF PTPRF 9262 -0.003 0.36 NO
47 WASL WASL WASL 9564 -0.0059 0.34 NO
48 SSX2IP SSX2IP SSX2IP 9857 -0.0084 0.33 NO
49 PVRL2 PVRL2 PVRL2 9860 -0.0084 0.33 NO
50 CTNNA1 CTNNA1 CTNNA1 9907 -0.0088 0.33 NO
51 ACTG1 ACTG1 ACTG1 9993 -0.0096 0.33 NO
52 PTPN6 PTPN6 PTPN6 10178 -0.011 0.32 NO
53 YES1 YES1 YES1 10290 -0.012 0.31 NO
54 WASF2 WASF2 WASF2 10360 -0.013 0.31 NO
55 TJP1 TJP1 TJP1 10497 -0.014 0.31 NO
56 CSNK2B CSNK2B CSNK2B 11656 -0.026 0.25 NO
57 RAC1 RAC1 RAC1 11810 -0.027 0.24 NO
58 CTNND1 CTNND1 CTNND1 11973 -0.029 0.24 NO
59 MAPK3 MAPK3 MAPK3 12238 -0.032 0.23 NO
60 SMAD2 SMAD2 SMAD2 12476 -0.035 0.22 NO
61 FARP2 FARP2 FARP2 12539 -0.035 0.22 NO
62 MLLT4 MLLT4 MLLT4 12683 -0.037 0.22 NO
63 CDH1 CDH1 CDH1 13261 -0.044 0.19 NO
64 PVRL1 PVRL1 PVRL1 13298 -0.044 0.2 NO
65 WASF1 WASF1 WASF1 13345 -0.045 0.2 NO
66 ACP1 ACP1 ACP1 13391 -0.045 0.2 NO
67 SMAD3 SMAD3 SMAD3 13421 -0.046 0.21 NO
68 BAIAP2 BAIAP2 BAIAP2 13640 -0.049 0.2 NO
69 NLK NLK NLK 13667 -0.049 0.21 NO
70 PARD3 PARD3 PARD3 13808 -0.051 0.21 NO
71 RAC3 RAC3 RAC3 14667 -0.066 0.17 NO
72 ERBB2 ERBB2 ERBB2 15187 -0.078 0.15 NO
73 PVRL4 PVRL4 PVRL4 17430 -0.18 0.051 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: BIOCARTA HDAC PATHWAY.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA HDAC 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 EGF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CAMK2A CAMK2A CAMK2A 128 0.97 0.2 YES
2 CAMK2B CAMK2B CAMK2B 175 0.79 0.36 YES
3 MAPT MAPT MAPT 222 0.66 0.5 YES
4 AGT AGT AGT 234 0.63 0.63 YES
5 PRKCA PRKCA PRKCA 1761 0.19 0.58 NO
6 MYLK MYLK MYLK 1784 0.19 0.62 NO
7 STAT4 STAT4 STAT4 2865 0.12 0.59 NO
8 FYN FYN FYN 3039 0.11 0.6 NO
9 PRKCB PRKCB PRKCB 3324 0.098 0.61 NO
10 CAMK2D CAMK2D CAMK2D 3828 0.082 0.6 NO
11 MAPK8 MAPK8 MAPK8 4036 0.075 0.6 NO
12 STAT2 STAT2 STAT2 4234 0.069 0.61 NO
13 STAT1 STAT1 STAT1 4431 0.063 0.61 NO
14 STAT5B STAT5B STAT5B 4638 0.058 0.61 NO
15 SHC1 SHC1 SHC1 4745 0.056 0.62 NO
16 GNA11 GNA11 GNA11 5103 0.048 0.61 NO
17 KNG1 KNG1 KNG1 5273 0.045 0.61 NO
18 PLCG1 PLCG1 PLCG1 5399 0.042 0.61 NO
19 GNB1 GNB1 GNB1 5805 0.036 0.59 NO
20 CALM1 CALM1 CALM1 6049 0.032 0.59 NO
21 PTK2B PTK2B PTK2B 6162 0.031 0.59 NO
22 STAT5A STAT5A STAT5A 6715 0.023 0.56 NO
23 CAMK2G CAMK2G CAMK2G 6721 0.023 0.57 NO
24 JAK2 JAK2 JAK2 6768 0.023 0.57 NO
25 MAPK1 MAPK1 MAPK1 7096 0.019 0.56 NO
26 GNAI1 GNAI1 GNAI1 7163 0.018 0.56 NO
27 SOS1 SOS1 SOS1 7663 0.013 0.53 NO
28 MAP2K1 MAP2K1 MAP2K1 8211 0.0071 0.5 NO
29 CALM3 CALM3 CALM3 8268 0.0065 0.5 NO
30 MAPK14 MAPK14 MAPK14 8829 0.001 0.47 NO
31 CALM2 CALM2 CALM2 8837 0.00092 0.47 NO
32 GRB2 GRB2 GRB2 9523 -0.0055 0.43 NO
33 STAT6 STAT6 STAT6 9788 -0.0078 0.42 NO
34 RAF1 RAF1 RAF1 10715 -0.016 0.37 NO
35 CDK5 CDK5 CDK5 10935 -0.018 0.37 NO
36 STAT3 STAT3 STAT3 11471 -0.024 0.34 NO
37 MAPK3 MAPK3 MAPK3 12238 -0.032 0.31 NO
38 MAP2K2 MAP2K2 MAP2K2 12299 -0.033 0.31 NO
39 F2 F2 F2 12461 -0.034 0.31 NO
40 GNGT1 GNGT1 GNGT1 14607 -0.064 0.2 NO

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

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EGF 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 ERK PATHWAY

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 PPP1R3A PPP1R3A PPP1R3A 43 1.4 0.095 YES
2 PRKAG3 PRKAG3 PRKAG3 48 1.4 0.19 YES
3 PHKG1 PHKG1 PHKG1 141 0.92 0.25 YES
4 PYGM PYGM PYGM 143 0.9 0.31 YES
5 SORBS1 SORBS1 SORBS1 272 0.55 0.34 YES
6 PRKAA2 PRKAA2 PRKAA2 359 0.46 0.37 YES
7 FBP2 FBP2 FBP2 367 0.45 0.4 YES
8 PPARGC1A PPARGC1A PPARGC1A 458 0.41 0.42 YES
9 PPP1R3C PPP1R3C PPP1R3C 546 0.38 0.44 YES
10 SLC2A4 SLC2A4 SLC2A4 613 0.35 0.46 YES
11 PDE3A PDE3A PDE3A 732 0.32 0.48 YES
12 ACACB ACACB ACACB 1176 0.25 0.47 YES
13 IRS1 IRS1 IRS1 1471 0.22 0.47 YES
14 SHC2 SHC2 SHC2 1722 0.19 0.46 YES
15 HK3 HK3 HK3 1898 0.18 0.47 YES
16 PIK3CG PIK3CG PIK3CG 2105 0.16 0.47 YES
17 SHC3 SHC3 SHC3 2142 0.16 0.48 YES
18 AKT3 AKT3 AKT3 2213 0.16 0.48 YES
19 PIK3R1 PIK3R1 PIK3R1 2283 0.15 0.49 YES
20 PRKAB2 PRKAB2 PRKAB2 2376 0.14 0.49 YES
21 PIK3CD PIK3CD PIK3CD 2506 0.14 0.5 YES
22 CBLB CBLB CBLB 2878 0.12 0.48 YES
23 FOXO1 FOXO1 FOXO1 2882 0.12 0.49 YES
24 IRS2 IRS2 IRS2 3005 0.11 0.49 YES
25 RHOQ RHOQ RHOQ 3028 0.11 0.5 YES
26 RAPGEF1 RAPGEF1 RAPGEF1 3030 0.11 0.51 YES
27 PIK3R5 PIK3R5 PIK3R5 3156 0.1 0.51 YES
28 PRKACB PRKACB PRKACB 3285 0.1 0.51 NO
29 SHC4 SHC4 SHC4 3854 0.081 0.48 NO
30 PRKAR2A PRKAR2A PRKAR2A 3922 0.079 0.48 NO
31 MAPK8 MAPK8 MAPK8 4036 0.075 0.48 NO
32 PYGL PYGL PYGL 4126 0.072 0.48 NO
33 SH2B2 SH2B2 SH2B2 4146 0.071 0.49 NO
34 PRKAR2B PRKAR2B PRKAR2B 4318 0.066 0.48 NO
35 INSR INSR INSR 4738 0.056 0.46 NO
36 SHC1 SHC1 SHC1 4745 0.056 0.46 NO
37 CBL CBL CBL 5031 0.05 0.45 NO
38 CALML6 CALML6 CALML6 5048 0.049 0.46 NO
39 SOS2 SOS2 SOS2 5145 0.047 0.45 NO
40 PCK1 PCK1 PCK1 5301 0.044 0.45 NO
41 CRK CRK CRK 5360 0.043 0.45 NO
42 PHKA1 PHKA1 PHKA1 5462 0.042 0.44 NO
43 SOCS4 SOCS4 SOCS4 5509 0.041 0.44 NO
44 PRKACA PRKACA PRKACA 5610 0.039 0.44 NO
45 INPP5K INPP5K INPP5K 5659 0.038 0.44 NO
46 SOCS3 SOCS3 SOCS3 5665 0.038 0.44 NO
47 PRKAA1 PRKAA1 PRKAA1 5674 0.038 0.45 NO
48 MTOR MTOR MTOR 5786 0.036 0.44 NO
49 GYS1 GYS1 GYS1 5804 0.036 0.44 NO
50 PTPN1 PTPN1 PTPN1 5846 0.035 0.44 NO
51 FLOT1 FLOT1 FLOT1 5922 0.034 0.44 NO
52 PRKAR1A PRKAR1A PRKAR1A 5926 0.034 0.44 NO
53 CALM1 CALM1 CALM1 6049 0.032 0.44 NO
54 PYGB PYGB PYGB 6086 0.032 0.44 NO
55 SOCS2 SOCS2 SOCS2 6131 0.031 0.44 NO
56 ARAF ARAF ARAF 6169 0.031 0.44 NO
57 RPTOR RPTOR RPTOR 6406 0.027 0.43 NO
58 AKT1 AKT1 AKT1 6455 0.026 0.43 NO
59 PIK3CA PIK3CA PIK3CA 6594 0.025 0.42 NO
60 GSK3B GSK3B GSK3B 6665 0.024 0.42 NO
61 NRAS NRAS NRAS 6901 0.021 0.41 NO
62 PHKB PHKB PHKB 6948 0.02 0.41 NO
63 MAPK1 MAPK1 MAPK1 7096 0.019 0.4 NO
64 FBP1 FBP1 FBP1 7102 0.019 0.4 NO
65 PPP1R3B PPP1R3B PPP1R3B 7139 0.018 0.4 NO
66 PDPK1 PDPK1 PDPK1 7614 0.013 0.38 NO
67 SOS1 SOS1 SOS1 7663 0.013 0.37 NO
68 CRKL CRKL CRKL 7686 0.012 0.37 NO
69 ELK1 ELK1 ELK1 7699 0.012 0.37 NO
70 PRKAG1 PRKAG1 PRKAG1 7722 0.012 0.37 NO
71 PPP1CA PPP1CA PPP1CA 7921 0.0099 0.36 NO
72 HK1 HK1 HK1 7970 0.0095 0.36 NO
73 EIF4E2 EIF4E2 EIF4E2 8038 0.0089 0.36 NO
74 AKT2 AKT2 AKT2 8176 0.0075 0.35 NO
75 EXOC7 EXOC7 EXOC7 8190 0.0074 0.35 NO
76 MAP2K1 MAP2K1 MAP2K1 8211 0.0071 0.35 NO
77 CALM3 CALM3 CALM3 8268 0.0065 0.35 NO
78 TSC1 TSC1 TSC1 8489 0.0041 0.34 NO
79 CALM2 CALM2 CALM2 8837 0.00092 0.32 NO
80 MKNK1 MKNK1 MKNK1 9066 -0.0013 0.3 NO
81 PTPRF PTPRF PTPRF 9262 -0.003 0.29 NO
82 MAPK9 MAPK9 MAPK9 9328 -0.0036 0.29 NO
83 GRB2 GRB2 GRB2 9523 -0.0055 0.28 NO
84 PKLR PKLR PKLR 9595 -0.0062 0.28 NO
85 PPP1CB PPP1CB PPP1CB 9749 -0.0075 0.27 NO
86 RHEB RHEB RHEB 9938 -0.0091 0.26 NO
87 TSC2 TSC2 TSC2 10157 -0.011 0.25 NO
88 PIK3R2 PIK3R2 PIK3R2 10327 -0.012 0.24 NO
89 RPS6KB2 RPS6KB2 RPS6KB2 10579 -0.015 0.23 NO
90 RAF1 RAF1 RAF1 10715 -0.016 0.22 NO
91 BAD BAD BAD 10768 -0.017 0.22 NO
92 PPP1CC PPP1CC PPP1CC 10860 -0.018 0.22 NO
93 INPP5D INPP5D INPP5D 11478 -0.024 0.18 NO
94 PRKAG2 PRKAG2 PRKAG2 11496 -0.024 0.18 NO
95 KRAS KRAS KRAS 11542 -0.024 0.18 NO
96 PRKCI PRKCI PRKCI 11546 -0.024 0.18 NO
97 PRKAB1 PRKAB1 PRKAB1 11617 -0.025 0.18 NO
98 RPS6KB1 RPS6KB1 RPS6KB1 11685 -0.026 0.18 NO
99 IKBKB IKBKB IKBKB 11926 -0.028 0.17 NO
100 TRIP10 TRIP10 TRIP10 12161 -0.031 0.16 NO
101 MAPK3 MAPK3 MAPK3 12238 -0.032 0.16 NO
102 MAP2K2 MAP2K2 MAP2K2 12299 -0.033 0.16 NO
103 GYS2 GYS2 GYS2 12456 -0.034 0.15 NO
104 EIF4E EIF4E EIF4E 12656 -0.037 0.14 NO
105 PRKAR1B PRKAR1B PRKAR1B 12892 -0.039 0.13 NO
106 ACACA ACACA ACACA 12918 -0.04 0.13 NO
107 PIK3CB PIK3CB PIK3CB 12946 -0.04 0.13 NO
108 FLOT2 FLOT2 FLOT2 13052 -0.041 0.13 NO
109 PHKA2 PHKA2 PHKA2 13081 -0.041 0.13 NO
110 RPS6 RPS6 RPS6 13209 -0.043 0.13 NO
111 CALML3 CALML3 CALML3 13378 -0.045 0.12 NO
112 PRKCZ PRKCZ PRKCZ 13381 -0.045 0.12 NO
113 FASN FASN FASN 13630 -0.049 0.11 NO
114 PCK2 PCK2 PCK2 14018 -0.054 0.096 NO
115 SOCS1 SOCS1 SOCS1 14625 -0.064 0.067 NO
116 HK2 HK2 HK2 14758 -0.067 0.064 NO
117 PHKG2 PHKG2 PHKG2 14764 -0.068 0.069 NO
118 BRAF BRAF BRAF 14967 -0.072 0.062 NO
119 EIF4EBP1 EIF4EBP1 EIF4EBP1 15178 -0.078 0.056 NO
120 PIK3R3 PIK3R3 PIK3R3 15707 -0.092 0.034 NO
121 MKNK2 MKNK2 MKNK2 15823 -0.097 0.034 NO
122 PPP1R3D PPP1R3D PPP1R3D 15831 -0.097 0.04 NO
123 SREBF1 SREBF1 SREBF1 15899 -0.099 0.043 NO
124 PDE3B PDE3B PDE3B 15902 -0.099 0.05 NO
125 LIPE LIPE LIPE 16653 -0.13 0.017 NO
126 CBLC CBLC CBLC 17186 -0.16 -0.00089 NO
127 GCK GCK GCK 17235 -0.16 0.0076 NO
128 PRKX PRKX PRKX 17497 -0.18 0.0057 NO
129 CALML5 CALML5 CALML5 17675 -0.2 0.0094 NO
130 MAPK10 MAPK10 MAPK10 17701 -0.2 0.022 NO
131 IRS4 IRS4 IRS4 17834 -0.21 0.029 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: BIOCARTA ERK PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ERK 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 FMLP PATHWAY

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 MYH1 MYH1 MYH1 16 1.6 0.056 YES
2 MYLPF MYLPF MYLPF 20 1.6 0.11 YES
3 ACTN2 ACTN2 ACTN2 21 1.5 0.17 YES
4 MYH8 MYH8 MYH8 25 1.5 0.22 YES
5 MYL2 MYL2 MYL2 27 1.5 0.28 YES
6 MYH7 MYH7 MYH7 53 1.4 0.33 YES
7 MYH2 MYH2 MYH2 68 1.3 0.37 YES
8 MYH4 MYH4 MYH4 72 1.2 0.42 YES
9 MYH6 MYH6 MYH6 82 1.2 0.46 YES
10 MYH3 MYH3 MYH3 83 1.2 0.5 YES
11 CTNNA3 CTNNA3 CTNNA3 147 0.87 0.53 YES
12 MYH13 MYH13 MYH13 166 0.82 0.56 YES
13 JAM2 JAM2 JAM2 368 0.45 0.57 YES
14 MRAS MRAS MRAS 387 0.44 0.58 YES
15 ACTN3 ACTN3 ACTN3 433 0.42 0.6 YES
16 PRKCQ PRKCQ PRKCQ 582 0.37 0.6 YES
17 MYH7B MYH7B MYH7B 624 0.35 0.61 YES
18 MYH15 MYH15 MYH15 936 0.28 0.6 YES
19 MPDZ MPDZ MPDZ 1050 0.27 0.61 YES
20 JAM3 JAM3 JAM3 1085 0.26 0.62 YES
21 MYL9 MYL9 MYL9 1337 0.23 0.61 YES
22 MYH11 MYH11 MYH11 1344 0.23 0.62 YES
23 CLDN5 CLDN5 CLDN5 1368 0.23 0.62 YES
24 PRKCA PRKCA PRKCA 1761 0.19 0.61 NO
25 ZAK ZAK ZAK 1978 0.17 0.6 NO
26 CLDN14 CLDN14 CLDN14 2062 0.17 0.61 NO
27 CLDN11 CLDN11 CLDN11 2074 0.16 0.61 NO
28 AKT3 AKT3 AKT3 2213 0.16 0.61 NO
29 ACTN1 ACTN1 ACTN1 2421 0.14 0.6 NO
30 MYH10 MYH10 MYH10 2611 0.13 0.6 NO
31 MYL7 MYL7 MYL7 3048 0.11 0.58 NO
32 CTNNA2 CTNNA2 CTNNA2 3149 0.1 0.58 NO
33 CLDN9 CLDN9 CLDN9 3233 0.1 0.57 NO
34 PRKCB PRKCB PRKCB 3324 0.098 0.57 NO
35 RRAS RRAS RRAS 3435 0.095 0.57 NO
36 PPP2R2C PPP2R2C PPP2R2C 3748 0.085 0.56 NO
37 CLDN19 CLDN19 CLDN19 3873 0.08 0.55 NO
38 AMOTL1 AMOTL1 AMOTL1 4350 0.066 0.53 NO
39 EPB41L3 EPB41L3 EPB41L3 4471 0.062 0.52 NO
40 GNAI2 GNAI2 GNAI2 4539 0.06 0.52 NO
41 MYH9 MYH9 MYH9 4601 0.059 0.52 NO
42 EPB41L2 EPB41L2 EPB41L2 4742 0.056 0.52 NO
43 TJAP1 TJAP1 TJAP1 4792 0.055 0.52 NO
44 HCLS1 HCLS1 HCLS1 5005 0.05 0.51 NO
45 PTEN PTEN PTEN 5081 0.048 0.5 NO
46 MYL12A MYL12A MYL12A 5220 0.046 0.5 NO
47 SRC SRC SRC 5662 0.038 0.48 NO
48 CSDA CSDA CSDA 5811 0.036 0.47 NO
49 CSNK2A2 CSNK2A2 CSNK2A2 5861 0.035 0.47 NO
50 LLGL1 LLGL1 LLGL1 5899 0.035 0.47 NO
51 CTTN CTTN CTTN 6435 0.027 0.44 NO
52 AKT1 AKT1 AKT1 6455 0.026 0.44 NO
53 RRAS2 RRAS2 RRAS2 6512 0.026 0.44 NO
54 CTNNB1 CTNNB1 CTNNB1 6626 0.024 0.43 NO
55 ACTB ACTB ACTB 6686 0.024 0.43 NO
56 SPTAN1 SPTAN1 SPTAN1 6811 0.022 0.42 NO
57 NRAS NRAS NRAS 6901 0.021 0.42 NO
58 RAB3B RAB3B RAB3B 7058 0.019 0.41 NO
59 GNAI1 GNAI1 GNAI1 7163 0.018 0.4 NO
60 RHOA RHOA RHOA 7290 0.016 0.4 NO
61 CLDN23 CLDN23 CLDN23 7569 0.014 0.38 NO
62 CDC42 CDC42 CDC42 7701 0.012 0.38 NO
63 MAGI2 MAGI2 MAGI2 7881 0.01 0.37 NO
64 PPP2R1A PPP2R1A PPP2R1A 7944 0.0098 0.36 NO
65 AKT2 AKT2 AKT2 8176 0.0075 0.35 NO
66 ACTN4 ACTN4 ACTN4 8225 0.007 0.35 NO
67 ASH1L ASH1L ASH1L 8289 0.0063 0.35 NO
68 EXOC4 EXOC4 EXOC4 8415 0.005 0.34 NO
69 RAB13 RAB13 RAB13 8775 0.0015 0.32 NO
70 PPP2R2D PPP2R2D PPP2R2D 8915 0.0002 0.31 NO
71 CSNK2A1 CSNK2A1 CSNK2A1 9020 -0.0008 0.31 NO
72 MPP5 MPP5 MPP5 9086 -0.0014 0.3 NO
73 GNAI3 GNAI3 GNAI3 9176 -0.0022 0.3 NO
74 EXOC3 EXOC3 EXOC3 9512 -0.0054 0.28 NO
75 MYL12B MYL12B MYL12B 9755 -0.0075 0.27 NO
76 CASK CASK CASK 9906 -0.0088 0.26 NO
77 CTNNA1 CTNNA1 CTNNA1 9907 -0.0088 0.26 NO
78 ACTG1 ACTG1 ACTG1 9993 -0.0096 0.26 NO
79 PPP2R1B PPP2R1B PPP2R1B 10012 -0.0097 0.26 NO
80 VAPA VAPA VAPA 10027 -0.0098 0.26 NO
81 YES1 YES1 YES1 10290 -0.012 0.24 NO
82 SYMPK SYMPK SYMPK 10326 -0.012 0.24 NO
83 TJP1 TJP1 TJP1 10497 -0.014 0.23 NO
84 PPP2CB PPP2CB PPP2CB 10943 -0.018 0.21 NO
85 PPP2CA PPP2CA PPP2CA 11335 -0.022 0.19 NO
86 KRAS KRAS KRAS 11542 -0.024 0.18 NO
87 PRKCI PRKCI PRKCI 11546 -0.024 0.18 NO
88 CSNK2B CSNK2B CSNK2B 11656 -0.026 0.17 NO
89 CDK4 CDK4 CDK4 11701 -0.026 0.17 NO
90 MAGI1 MAGI1 MAGI1 12027 -0.03 0.15 NO
91 INADL INADL INADL 12082 -0.03 0.15 NO
92 PARD6G PARD6G PARD6G 12637 -0.036 0.12 NO
93 PRKCH PRKCH PRKCH 12672 -0.037 0.12 NO
94 MLLT4 MLLT4 MLLT4 12683 -0.037 0.12 NO
95 F11R F11R F11R 13022 -0.041 0.11 NO
96 PRKCD PRKCD PRKCD 13341 -0.045 0.09 NO
97 PRKCZ PRKCZ PRKCZ 13381 -0.045 0.089 NO
98 PRKCE PRKCE PRKCE 13654 -0.049 0.076 NO
99 PARD3 PARD3 PARD3 13808 -0.051 0.07 NO
100 PPP2R2A PPP2R2A PPP2R2A 14403 -0.06 0.039 NO
101 PPP2R2B PPP2R2B PPP2R2B 14557 -0.063 0.033 NO
102 TJP2 TJP2 TJP2 14615 -0.064 0.032 NO
103 CLDN15 CLDN15 CLDN15 14724 -0.067 0.029 NO
104 CLDN2 CLDN2 CLDN2 14750 -0.067 0.03 NO
105 EPB41 EPB41 EPB41 14818 -0.068 0.029 NO
106 EPB41L1 EPB41L1 EPB41L1 15017 -0.073 0.021 NO
107 CLDN17 CLDN17 CLDN17 15175 -0.078 0.015 NO
108 MAGI3 MAGI3 MAGI3 15179 -0.078 0.017 NO
109 CLDN6 CLDN6 CLDN6 15409 -0.084 0.0079 NO
110 CLDN1 CLDN1 CLDN1 15476 -0.086 0.0074 NO
111 CLDN18 CLDN18 CLDN18 15737 -0.094 -0.0034 NO
112 CLDN20 CLDN20 CLDN20 16347 -0.12 -0.033 NO
113 MYH14 MYH14 MYH14 16416 -0.12 -0.032 NO
114 IGSF5 IGSF5 IGSF5 16939 -0.15 -0.055 NO
115 CLDN8 CLDN8 CLDN8 17124 -0.16 -0.06 NO
116 MYL5 MYL5 MYL5 17135 -0.16 -0.054 NO
117 PRKCG PRKCG PRKCG 17294 -0.17 -0.057 NO
118 PARD6A PARD6A PARD6A 17312 -0.17 -0.052 NO
119 LLGL2 LLGL2 LLGL2 17447 -0.18 -0.053 NO
120 CLDN16 CLDN16 CLDN16 17502 -0.18 -0.049 NO
121 PARD6B PARD6B PARD6B 17874 -0.22 -0.061 NO
122 CLDN10 CLDN10 CLDN10 18041 -0.24 -0.062 NO
123 CRB3 CRB3 CRB3 18067 -0.25 -0.054 NO
124 CLDN4 CLDN4 CLDN4 18101 -0.26 -0.046 NO
125 CLDN7 CLDN7 CLDN7 18178 -0.28 -0.04 NO
126 OCLN OCLN OCLN 18285 -0.32 -0.035 NO
127 CGN CGN CGN 18301 -0.32 -0.024 NO
128 CLDN3 CLDN3 CLDN3 18309 -0.33 -0.012 NO
129 TJP3 TJP3 TJP3 18359 -0.41 0.00011 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: BIOCARTA FMLP PATHWAY.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FMLP 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

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 1.3 0.18 0.84 0.99 0.12 0.12 0.11 0.73 0.3
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.4 1.5 0.088 1 0.92 0.16 0.15 0.14 1 0.69
KEGG FATTY ACID METABOLISM 40 genes.ES.table 0.42 1.3 0.18 0.81 0.99 0.38 0.31 0.26 0.72 0.29
KEGG GLYCINE SERINE AND THREONINE METABOLISM 29 genes.ES.table 0.59 1.5 0.038 1 0.93 0.55 0.25 0.42 1 0.62
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.41 1.4 0.11 1 0.95 0.56 0.41 0.33 1 0.51
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.32 1.3 0.16 0.88 0.98 0.46 0.38 0.29 0.75 0.34
KEGG SELENOAMINO ACID METABOLISM 25 genes.ES.table 0.43 1.3 0.15 0.87 0.99 0.28 0.24 0.21 0.76 0.33
KEGG STARCH AND SUCROSE METABOLISM 39 genes.ES.table 0.57 1.5 0.061 1 0.92 0.41 0.16 0.34 1 0.78
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES 25 genes.ES.table 0.52 1.4 0.093 0.92 0.97 0.28 0.13 0.24 0.78 0.36
KEGG BUTANOATE METABOLISM 29 genes.ES.table 0.46 1.3 0.11 0.83 0.98 0.45 0.33 0.3 0.7 0.3
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 UGT1A9 UGT1A9 UGT1A9 272 0.48 0.079 YES
2 UGT1A6 UGT1A6 UGT1A6 273 0.48 0.17 YES
3 UGT2A1 UGT2A1 UGT2A1 375 0.45 0.26 YES
4 CP CP CP 408 0.45 0.34 YES
5 UGT1A8 UGT1A8 UGT1A8 623 0.4 0.41 YES
6 UGT1A3 UGT1A3 UGT1A3 659 0.39 0.48 YES
7 UGT1A7 UGT1A7 UGT1A7 1113 0.33 0.53 YES
8 UGT1A4 UGT1A4 UGT1A4 1434 0.3 0.57 YES
9 UGT1A10 UGT1A10 UGT1A10 2604 0.22 0.55 YES
10 UGT1A1 UGT1A1 UGT1A1 2934 0.2 0.57 YES
11 UGT2B15 UGT2B15 UGT2B15 2960 0.2 0.6 YES
12 PPOX PPOX PPOX 4022 0.15 0.57 NO
13 UGT2B7 UGT2B7 UGT2B7 4986 0.12 0.55 NO
14 FECH FECH FECH 5219 0.11 0.56 NO
15 MMAB MMAB MMAB 5808 0.097 0.54 NO
16 GUSB GUSB GUSB 5912 0.094 0.55 NO
17 CPOX CPOX CPOX 6173 0.088 0.56 NO
18 EARS2 EARS2 EARS2 8354 0.046 0.45 NO
19 BLVRB BLVRB BLVRB 9010 0.036 0.42 NO
20 EPRS EPRS EPRS 9338 0.032 0.41 NO
21 COX15 COX15 COX15 9733 0.026 0.39 NO
22 FTH1 FTH1 FTH1 9796 0.025 0.39 NO
23 UROS UROS UROS 10198 0.02 0.38 NO
24 ALAD ALAD ALAD 10526 0.016 0.36 NO
25 COX10 COX10 COX10 10711 0.012 0.35 NO
26 BLVRA BLVRA BLVRA 12128 -0.0068 0.28 NO
27 ALAS1 ALAS1 ALAS1 12322 -0.0095 0.27 NO
28 ALAS2 ALAS2 ALAS2 13489 -0.029 0.21 NO
29 HMBS HMBS HMBS 13524 -0.03 0.21 NO
30 UROD UROD UROD 13680 -0.032 0.21 NO
31 HMOX1 HMOX1 HMOX1 15350 -0.072 0.14 NO
32 HMOX2 HMOX2 HMOX2 16857 -0.15 0.082 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 WNT 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 UGT1A9 UGT1A9 UGT1A9 272 0.48 0.049 YES
2 UGT1A6 UGT1A6 UGT1A6 273 0.48 0.11 YES
3 UGT2A1 UGT2A1 UGT2A1 375 0.45 0.17 YES
4 GCK GCK GCK 452 0.44 0.22 YES
5 UGT1A8 UGT1A8 UGT1A8 623 0.4 0.26 YES
6 UGT1A3 UGT1A3 UGT1A3 659 0.39 0.32 YES
7 AMY2B AMY2B AMY2B 757 0.38 0.36 YES
8 UGT1A7 UGT1A7 UGT1A7 1113 0.33 0.39 YES
9 AMY2A AMY2A AMY2A 1175 0.32 0.42 YES
10 UGT1A4 UGT1A4 UGT1A4 1434 0.3 0.45 YES
11 AMY1A AMY1A AMY1A 1456 0.3 0.49 YES
12 ENPP3 ENPP3 ENPP3 1486 0.29 0.53 YES
13 GBA3 GBA3 GBA3 1573 0.29 0.56 YES
14 UGT1A10 UGT1A10 UGT1A10 2604 0.22 0.53 YES
15 UGT1A1 UGT1A1 UGT1A1 2934 0.2 0.54 YES
16 UGT2B15 UGT2B15 UGT2B15 2960 0.2 0.56 YES
17 TREH TREH TREH 4189 0.14 0.52 NO
18 ENPP1 ENPP1 ENPP1 4811 0.12 0.5 NO
19 UGT2B7 UGT2B7 UGT2B7 4986 0.12 0.51 NO
20 UGDH UGDH UGDH 5298 0.11 0.5 NO
21 GUSB GUSB GUSB 5912 0.094 0.48 NO
22 GAA GAA GAA 6333 0.084 0.47 NO
23 AGL AGL AGL 7136 0.068 0.44 NO
24 GPI GPI GPI 7781 0.055 0.41 NO
25 PGM2L1 PGM2L1 PGM2L1 7858 0.054 0.41 NO
26 HK1 HK1 HK1 12363 -0.01 0.17 NO
27 HK3 HK3 HK3 12618 -0.014 0.16 NO
28 GYS2 GYS2 GYS2 12834 -0.017 0.15 NO
29 GBE1 GBE1 GBE1 13337 -0.026 0.12 NO
30 UGP2 UGP2 UGP2 13712 -0.033 0.11 NO
31 PGM1 PGM1 PGM1 14113 -0.041 0.09 NO
32 PYGB PYGB PYGB 14237 -0.044 0.089 NO
33 PGM2 PGM2 PGM2 14629 -0.052 0.075 NO
34 HK2 HK2 HK2 15422 -0.074 0.041 NO
35 GYS1 GYS1 GYS1 15719 -0.085 0.036 NO
36 MGAM MGAM MGAM 15915 -0.092 0.038 NO
37 GANC GANC GANC 16607 -0.13 0.018 NO
38 PYGL PYGL PYGL 17774 -0.29 -0.0072 NO
39 PYGM PYGM PYGM 17782 -0.29 0.032 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 WNT PATHWAY.

Figure S24.  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 FATTY ACID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 WNT1 WNT1 WNT1 811 0.37 0.13 YES
2 WIF1 WIF1 WIF1 1169 0.32 0.26 YES
3 LEF1 LEF1 LEF1 1810 0.27 0.35 YES
4 FRAT1 FRAT1 FRAT1 2763 0.21 0.4 YES
5 SMAD4 SMAD4 SMAD4 5530 0.1 0.3 NO
6 NLK NLK NLK 5827 0.096 0.32 NO
7 APC APC APC 7490 0.061 0.26 NO
8 TAB1 TAB1 TAB1 7535 0.06 0.29 NO
9 FZD1 FZD1 FZD1 7710 0.057 0.3 NO
10 CREBBP CREBBP CREBBP 8581 0.043 0.28 NO
11 CTNNB1 CTNNB1 CTNNB1 10078 0.022 0.21 NO
12 HDAC1 HDAC1 HDAC1 10180 0.02 0.21 NO
13 GSK3B GSK3B GSK3B 10297 0.018 0.21 NO
14 TLE1 TLE1 TLE1 11447 0.0029 0.15 NO
15 CSNK2A1 CSNK2A1 CSNK2A1 12247 -0.0083 0.11 NO
16 CTBP1 CTBP1 CTBP1 12281 -0.0088 0.11 NO
17 AXIN1 AXIN1 AXIN1 12288 -0.0089 0.12 NO
18 MAP3K7 MAP3K7 MAP3K7 12293 -0.009 0.12 NO
19 CSNK1D CSNK1D CSNK1D 12300 -0.0092 0.12 NO
20 PPP2CA PPP2CA PPP2CA 13973 -0.038 0.052 NO
21 CCND1 CCND1 CCND1 14631 -0.052 0.041 NO
22 MYC MYC MYC 14874 -0.058 0.055 NO
23 BTRC BTRC BTRC 15352 -0.072 0.063 NO
24 CSNK1A1 CSNK1A1 CSNK1A1 15869 -0.091 0.077 NO
25 DVL1 DVL1 DVL1 16534 -0.13 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 FATTY ACID METABOLISM.

Figure S26.  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 GLYCINE SERINE AND THREONINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CHDH CHDH CHDH 24 0.67 0.12 YES
2 CBS CBS CBS 50 0.61 0.22 YES
3 GNMT GNMT GNMT 412 0.44 0.28 YES
4 GATM GATM GATM 589 0.41 0.34 YES
5 PHGDH PHGDH PHGDH 705 0.39 0.4 YES
6 BHMT BHMT BHMT 1098 0.33 0.44 YES
7 PIPOX PIPOX PIPOX 1219 0.32 0.49 YES
8 MAOB MAOB MAOB 1534 0.29 0.52 YES
9 PSAT1 PSAT1 PSAT1 2911 0.2 0.48 YES
10 MAOA MAOA MAOA 3014 0.19 0.51 YES
11 GAMT GAMT GAMT 3304 0.18 0.52 YES
12 DMGDH DMGDH DMGDH 3534 0.17 0.54 YES
13 GCAT GCAT GCAT 4104 0.15 0.54 YES
14 SARDH SARDH SARDH 4111 0.15 0.56 YES
15 AOC2 AOC2 AOC2 4327 0.14 0.57 YES
16 PSPH PSPH PSPH 4518 0.13 0.59 YES
17 DAO DAO DAO 5272 0.11 0.57 NO
18 SHMT2 SHMT2 SHMT2 6301 0.085 0.52 NO
19 SHMT1 SHMT1 SHMT1 6317 0.084 0.54 NO
20 AGXT AGXT AGXT 6789 0.074 0.53 NO
21 SDS SDS SDS 8397 0.045 0.45 NO
22 DLD DLD DLD 8562 0.043 0.44 NO
23 CTH CTH CTH 8604 0.042 0.45 NO
24 ALAS1 ALAS1 ALAS1 12322 -0.0095 0.25 NO
25 SRR SRR SRR 12940 -0.019 0.22 NO
26 ALAS2 ALAS2 ALAS2 13489 -0.029 0.19 NO
27 GLYCTK GLYCTK GLYCTK 13525 -0.03 0.2 NO
28 AOC3 AOC3 AOC3 16991 -0.16 0.037 NO
29 GLDC GLDC GLDC 17383 -0.22 0.053 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 GLYCINE SERINE AND THREONINE METABOLISM.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCINE SERINE AND THREONINE 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 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 NEIL1 NEIL1 NEIL1 438 0.44 0.13 YES
2 LIG1 LIG1 LIG1 4045 0.15 -0.009 YES
3 MUTYH MUTYH MUTYH 4139 0.14 0.038 YES
4 UNG UNG UNG 4789 0.12 0.048 YES
5 NEIL3 NEIL3 NEIL3 4966 0.12 0.082 YES
6 POLE2 POLE2 POLE2 5004 0.12 0.12 YES
7 OGG1 OGG1 OGG1 5075 0.12 0.16 YES
8 PARP1 PARP1 PARP1 5155 0.12 0.2 YES
9 POLB POLB POLB 5548 0.1 0.21 YES
10 MBD4 MBD4 MBD4 5679 0.1 0.24 YES
11 POLE POLE POLE 5732 0.099 0.28 YES
12 NTHL1 NTHL1 NTHL1 5860 0.095 0.3 YES
13 XRCC1 XRCC1 XRCC1 5944 0.093 0.33 YES
14 PCNA PCNA PCNA 6208 0.087 0.35 YES
15 LIG3 LIG3 LIG3 6461 0.081 0.36 YES
16 FEN1 FEN1 FEN1 6756 0.075 0.38 YES
17 POLD3 POLD3 POLD3 6900 0.072 0.39 YES
18 PARP3 PARP3 PARP3 7000 0.07 0.41 YES
19 PARP2 PARP2 PARP2 7036 0.069 0.44 YES
20 PARP4 PARP4 PARP4 7558 0.059 0.43 YES
21 POLD1 POLD1 POLD1 7625 0.058 0.45 YES
22 NEIL2 NEIL2 NEIL2 8351 0.046 0.42 NO
23 POLE3 POLE3 POLE3 8503 0.044 0.43 NO
24 APEX1 APEX1 APEX1 8986 0.037 0.42 NO
25 POLL POLL POLL 9298 0.032 0.41 NO
26 SMUG1 SMUG1 SMUG1 9880 0.024 0.39 NO
27 APEX2 APEX2 APEX2 11364 0.0038 0.31 NO
28 POLD2 POLD2 POLD2 12781 -0.016 0.24 NO
29 TDG TDG TDG 12983 -0.02 0.24 NO
30 MPG MPG MPG 13701 -0.033 0.21 NO
31 POLE4 POLE4 POLE4 14227 -0.044 0.2 NO
32 POLD4 POLD4 POLD4 15747 -0.085 0.14 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S30.  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 LYSINE 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 GSTA1 GSTA1 GSTA1 133 0.54 0.038 YES
2 UGT1A9 UGT1A9 UGT1A9 272 0.48 0.07 YES
3 UGT1A6 UGT1A6 UGT1A6 273 0.48 0.11 YES
4 GSTA2 GSTA2 GSTA2 359 0.46 0.14 YES
5 UGT2A1 UGT2A1 UGT2A1 375 0.45 0.18 YES
6 ADH1C ADH1C ADH1C 436 0.44 0.22 YES
7 ADH6 ADH6 ADH6 496 0.43 0.25 YES
8 CYP2F1 CYP2F1 CYP2F1 526 0.42 0.28 YES
9 UGT1A8 UGT1A8 UGT1A8 623 0.4 0.31 YES
10 UGT1A3 UGT1A3 UGT1A3 659 0.39 0.34 YES
11 ADH7 ADH7 ADH7 689 0.39 0.37 YES
12 ALDH3A1 ALDH3A1 ALDH3A1 702 0.39 0.4 YES
13 UGT1A7 UGT1A7 UGT1A7 1113 0.33 0.41 YES
14 GSTM4 GSTM4 GSTM4 1386 0.3 0.42 YES
15 UGT1A4 UGT1A4 UGT1A4 1434 0.3 0.44 YES
16 CYP2E1 CYP2E1 CYP2E1 1544 0.29 0.46 YES
17 MGST1 MGST1 MGST1 1604 0.28 0.48 YES
18 CYP2S1 CYP2S1 CYP2S1 1627 0.28 0.5 YES
19 GSTM2 GSTM2 GSTM2 1670 0.28 0.52 YES
20 GSTM3 GSTM3 GSTM3 1959 0.26 0.53 YES
21 EPHX1 EPHX1 EPHX1 2157 0.24 0.54 YES
22 CYP1B1 CYP1B1 CYP1B1 2288 0.24 0.55 YES
23 CYP2C19 CYP2C19 CYP2C19 2389 0.23 0.56 YES
24 UGT1A10 UGT1A10 UGT1A10 2604 0.22 0.57 YES
25 CYP2C9 CYP2C9 CYP2C9 2900 0.2 0.57 YES
26 UGT1A1 UGT1A1 UGT1A1 2934 0.2 0.59 YES
27 UGT2B15 UGT2B15 UGT2B15 2960 0.2 0.6 YES
28 DHDH DHDH DHDH 3112 0.19 0.61 YES
29 CYP3A5 CYP3A5 CYP3A5 3334 0.18 0.61 YES
30 AKR1C1 AKR1C1 AKR1C1 3407 0.17 0.62 YES
31 CYP3A7 CYP3A7 CYP3A7 3790 0.16 0.61 YES
32 ADH1A ADH1A ADH1A 4365 0.14 0.59 YES
33 CYP1A1 CYP1A1 CYP1A1 4512 0.13 0.6 YES
34 GSTA3 GSTA3 GSTA3 4563 0.13 0.6 YES
35 CYP2B6 CYP2B6 CYP2B6 4747 0.13 0.61 YES
36 AKR1C3 AKR1C3 AKR1C3 4804 0.12 0.61 YES
37 GSTA4 GSTA4 GSTA4 4888 0.12 0.62 YES
38 AKR1C2 AKR1C2 AKR1C2 4939 0.12 0.63 YES
39 UGT2B7 UGT2B7 UGT2B7 4986 0.12 0.63 YES
40 ALDH3B1 ALDH3B1 ALDH3B1 6234 0.086 0.57 NO
41 MGST2 MGST2 MGST2 6540 0.08 0.56 NO
42 GSTM1 GSTM1 GSTM1 6752 0.075 0.56 NO
43 GSTT1 GSTT1 GSTT1 6832 0.074 0.56 NO
44 CYP2C8 CYP2C8 CYP2C8 7657 0.058 0.52 NO
45 CYP2C18 CYP2C18 CYP2C18 7769 0.056 0.52 NO
46 GSTT2 GSTT2 GSTT2 7874 0.054 0.52 NO
47 MGST3 MGST3 MGST3 8523 0.043 0.48 NO
48 GSTM5 GSTM5 GSTM5 8648 0.042 0.48 NO
49 ADH5 ADH5 ADH5 8935 0.037 0.47 NO
50 ADH1B ADH1B ADH1B 9668 0.027 0.43 NO
51 ADH4 ADH4 ADH4 9841 0.025 0.42 NO
52 GSTO2 GSTO2 GSTO2 9977 0.023 0.42 NO
53 GSTZ1 GSTZ1 GSTZ1 11299 0.0047 0.35 NO
54 GSTK1 GSTK1 GSTK1 14141 -0.042 0.2 NO
55 GSTO1 GSTO1 GSTO1 14222 -0.044 0.19 NO
56 GSTP1 GSTP1 GSTP1 14499 -0.05 0.18 NO
57 ALDH1A3 ALDH1A3 ALDH1A3 15336 -0.072 0.14 NO
58 ALDH3B2 ALDH3B2 ALDH3B2 17620 -0.26 0.04 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 LYSINE DEGRADATION.

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

genes ES table in pathway: KEGG SELENOAMINO ACID 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 ACADSB ACADSB ACADSB 1480 0.29 -0.014 YES
2 IVD IVD IVD 1560 0.29 0.047 YES
3 ALDH6A1 ALDH6A1 ALDH6A1 1714 0.28 0.1 YES
4 BCKDHB BCKDHB BCKDHB 1761 0.27 0.16 YES
5 ABAT ABAT ABAT 2066 0.25 0.2 YES
6 MCCC1 MCCC1 MCCC1 2230 0.24 0.25 YES
7 PCCA PCCA PCCA 3147 0.19 0.24 YES
8 ACAT2 ACAT2 ACAT2 3579 0.17 0.25 YES
9 BCAT2 BCAT2 BCAT2 3620 0.16 0.29 YES
10 PCCB PCCB PCCB 4371 0.14 0.28 YES
11 IL4I1 IL4I1 IL4I1 4635 0.13 0.29 YES
12 HADH HADH HADH 4726 0.13 0.32 YES
13 ACADS ACADS ACADS 4926 0.12 0.33 YES
14 ALDH3A2 ALDH3A2 ALDH3A2 5247 0.11 0.34 YES
15 EHHADH EHHADH EHHADH 5589 0.1 0.35 YES
16 OXCT2 OXCT2 OXCT2 5606 0.1 0.37 YES
17 HMGCS2 HMGCS2 HMGCS2 5844 0.096 0.38 YES
18 MCCC2 MCCC2 MCCC2 6068 0.09 0.39 YES
19 ACADM ACADM ACADM 6248 0.086 0.4 YES
20 HIBADH HIBADH HIBADH 6399 0.082 0.41 YES
21 AUH AUH AUH 6666 0.077 0.41 YES
22 ALDH1B1 ALDH1B1 ALDH1B1 7044 0.069 0.4 YES
23 HIBCH HIBCH HIBCH 7330 0.064 0.4 YES
24 DBT DBT DBT 7461 0.061 0.41 YES
25 ACAD8 ACAD8 ACAD8 7741 0.056 0.41 NO
26 BCKDHA BCKDHA BCKDHA 7977 0.052 0.41 NO
27 DLD DLD DLD 8562 0.043 0.38 NO
28 OXCT1 OXCT1 OXCT1 8937 0.037 0.37 NO
29 ALDH9A1 ALDH9A1 ALDH9A1 8995 0.036 0.38 NO
30 ALDH2 ALDH2 ALDH2 9500 0.03 0.36 NO
31 MUT MUT MUT 9727 0.026 0.35 NO
32 MCEE MCEE MCEE 9789 0.026 0.35 NO
33 HSD17B10 HSD17B10 HSD17B10 10360 0.017 0.33 NO
34 ECHS1 ECHS1 ECHS1 10431 0.017 0.33 NO
35 ACAT1 ACAT1 ACAT1 11395 0.0035 0.27 NO
36 ACAA2 ACAA2 ACAA2 11529 0.0017 0.27 NO
37 HMGCS1 HMGCS1 HMGCS1 11731 -0.001 0.26 NO
38 HADHB HADHB HADHB 12856 -0.018 0.2 NO
39 HMGCL HMGCL HMGCL 13123 -0.022 0.19 NO
40 HADHA HADHA HADHA 13565 -0.03 0.17 NO
41 ACAA1 ACAA1 ACAA1 15851 -0.09 0.068 NO
42 AOX1 AOX1 AOX1 16187 -0.1 0.074 NO
43 ALDH7A1 ALDH7A1 ALDH7A1 17263 -0.2 0.06 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 SELENOAMINO ACID METABOLISM.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SELENOAMINO 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 STARCH AND SUCROSE 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 GSTA1 GSTA1 GSTA1 133 0.54 0.038 YES
2 UGT1A9 UGT1A9 UGT1A9 272 0.48 0.07 YES
3 UGT1A6 UGT1A6 UGT1A6 273 0.48 0.11 YES
4 GSTA2 GSTA2 GSTA2 359 0.46 0.14 YES
5 UGT2A1 UGT2A1 UGT2A1 375 0.45 0.18 YES
6 ADH1C ADH1C ADH1C 436 0.44 0.22 YES
7 ADH6 ADH6 ADH6 496 0.43 0.25 YES
8 UGT1A8 UGT1A8 UGT1A8 623 0.4 0.27 YES
9 UGT1A3 UGT1A3 UGT1A3 659 0.39 0.31 YES
10 ADH7 ADH7 ADH7 689 0.39 0.34 YES
11 ALDH3A1 ALDH3A1 ALDH3A1 702 0.39 0.37 YES
12 UGT1A7 UGT1A7 UGT1A7 1113 0.33 0.37 YES
13 FMO3 FMO3 FMO3 1137 0.33 0.4 YES
14 CYP2A6 CYP2A6 CYP2A6 1163 0.32 0.43 YES
15 GSTM4 GSTM4 GSTM4 1386 0.3 0.44 YES
16 UGT1A4 UGT1A4 UGT1A4 1434 0.3 0.46 YES
17 CYP2D6 CYP2D6 CYP2D6 1517 0.29 0.48 YES
18 MAOB MAOB MAOB 1534 0.29 0.5 YES
19 CYP2E1 CYP2E1 CYP2E1 1544 0.29 0.53 YES
20 MGST1 MGST1 MGST1 1604 0.28 0.55 YES
21 GSTM2 GSTM2 GSTM2 1670 0.28 0.57 YES
22 GSTM3 GSTM3 GSTM3 1959 0.26 0.57 YES
23 CYP2C19 CYP2C19 CYP2C19 2389 0.23 0.57 YES
24 UGT1A10 UGT1A10 UGT1A10 2604 0.22 0.58 YES
25 CYP2C9 CYP2C9 CYP2C9 2900 0.2 0.58 YES
26 UGT1A1 UGT1A1 UGT1A1 2934 0.2 0.59 YES
27 UGT2B15 UGT2B15 UGT2B15 2960 0.2 0.61 YES
28 MAOA MAOA MAOA 3014 0.19 0.62 YES
29 CYP3A5 CYP3A5 CYP3A5 3334 0.18 0.62 NO
30 CYP3A7 CYP3A7 CYP3A7 3790 0.16 0.61 NO
31 ADH1A ADH1A ADH1A 4365 0.14 0.59 NO
32 GSTA3 GSTA3 GSTA3 4563 0.13 0.59 NO
33 CYP2B6 CYP2B6 CYP2B6 4747 0.13 0.59 NO
34 GSTA4 GSTA4 GSTA4 4888 0.12 0.59 NO
35 UGT2B7 UGT2B7 UGT2B7 4986 0.12 0.59 NO
36 FMO5 FMO5 FMO5 5448 0.11 0.58 NO
37 FMO2 FMO2 FMO2 5643 0.1 0.58 NO
38 ALDH3B1 ALDH3B1 ALDH3B1 6234 0.086 0.55 NO
39 MGST2 MGST2 MGST2 6540 0.08 0.54 NO
40 GSTM1 GSTM1 GSTM1 6752 0.075 0.54 NO
41 GSTT1 GSTT1 GSTT1 6832 0.074 0.54 NO
42 FMO4 FMO4 FMO4 7466 0.061 0.51 NO
43 CYP2C8 CYP2C8 CYP2C8 7657 0.058 0.5 NO
44 CYP2C18 CYP2C18 CYP2C18 7769 0.056 0.5 NO
45 GSTT2 GSTT2 GSTT2 7874 0.054 0.5 NO
46 MGST3 MGST3 MGST3 8523 0.043 0.47 NO
47 GSTM5 GSTM5 GSTM5 8648 0.042 0.46 NO
48 ADH5 ADH5 ADH5 8935 0.037 0.45 NO
49 ADH1B ADH1B ADH1B 9668 0.027 0.42 NO
50 ADH4 ADH4 ADH4 9841 0.025 0.41 NO
51 GSTO2 GSTO2 GSTO2 9977 0.023 0.4 NO
52 GSTZ1 GSTZ1 GSTZ1 11299 0.0047 0.33 NO
53 GSTK1 GSTK1 GSTK1 14141 -0.042 0.18 NO
54 GSTO1 GSTO1 GSTO1 14222 -0.044 0.18 NO
55 GSTP1 GSTP1 GSTP1 14499 -0.05 0.17 NO
56 ALDH1A3 ALDH1A3 ALDH1A3 15336 -0.072 0.13 NO
57 FMO1 FMO1 FMO1 15834 -0.089 0.11 NO
58 AOX1 AOX1 AOX1 16187 -0.1 0.097 NO
59 ALDH3B2 ALDH3B2 ALDH3B2 17620 -0.26 0.04 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 STARCH AND SUCROSE METABOLISM.

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

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

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 CACNA1B CACNA1B CACNA1B 65 0.59 0.095 YES
2 GNB3 GNB3 GNB3 607 0.4 0.13 YES
3 GNG3 GNG3 GNG3 1172 0.32 0.16 YES
4 PRKX PRKX PRKX 1245 0.32 0.2 YES
5 TAS2R19 TAS2R19 TAS2R19 1615 0.28 0.23 YES
6 TAS2R20 TAS2R20 TAS2R20 1640 0.28 0.28 YES
7 TAS2R31 TAS2R31 TAS2R31 1654 0.28 0.32 YES
8 TRPM5 TRPM5 TRPM5 1887 0.26 0.36 YES
9 TAS1R3 TAS1R3 TAS1R3 2005 0.25 0.39 YES
10 SCNN1A SCNN1A SCNN1A 2218 0.24 0.42 YES
11 TAS2R14 TAS2R14 TAS2R14 2223 0.24 0.46 YES
12 ADCY6 ADCY6 ADCY6 2300 0.24 0.49 YES
13 TAS2R43 TAS2R43 TAS2R43 2748 0.21 0.5 YES
14 TAS2R4 TAS2R4 TAS2R4 2802 0.2 0.54 YES
15 SCNN1B SCNN1B SCNN1B 3268 0.18 0.54 YES
16 PLCB2 PLCB2 PLCB2 3703 0.16 0.54 YES
17 TAS1R1 TAS1R1 TAS1R1 3897 0.15 0.56 YES
18 TAS2R10 TAS2R10 TAS2R10 4044 0.15 0.57 YES
19 TAS2R5 TAS2R5 TAS2R5 4335 0.14 0.58 YES
20 ADCY8 ADCY8 ADCY8 4769 0.13 0.58 NO
21 SCNN1G SCNN1G SCNN1G 6077 0.09 0.52 NO
22 TAS2R13 TAS2R13 TAS2R13 6611 0.078 0.51 NO
23 TAS2R38 TAS2R38 TAS2R38 8962 0.037 0.39 NO
24 PDE1A PDE1A PDE1A 9282 0.033 0.37 NO
25 GNAS GNAS GNAS 9615 0.028 0.36 NO
26 PRKACA PRKACA PRKACA 9901 0.024 0.35 NO
27 CACNA1A CACNA1A CACNA1A 10676 0.013 0.31 NO
28 PRKACB PRKACB PRKACB 12398 -0.011 0.22 NO
29 ITPR3 ITPR3 ITPR3 13558 -0.03 0.16 NO
30 GNB1 GNB1 GNB1 13847 -0.036 0.15 NO
31 GRM4 GRM4 GRM4 14111 -0.041 0.14 NO
32 ACCN1 ACCN1 ACCN1 14657 -0.053 0.12 NO
33 ADCY4 ADCY4 ADCY4 14723 -0.055 0.13 NO
34 KCNB1 KCNB1 KCNB1 17035 -0.17 0.028 NO
35 TAS2R60 TAS2R60 TAS2R60 17667 -0.27 0.038 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

Figure S38.  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 BUTANOATE 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 SMC1B SMC1B SMC1B 219 0.5 0.029 YES
2 E2F5 E2F5 E2F5 238 0.49 0.068 YES
3 CDKN2C CDKN2C CDKN2C 1029 0.34 0.053 YES
4 WEE2 WEE2 WEE2 1518 0.29 0.05 YES
5 CDC14A CDC14A CDC14A 1595 0.28 0.069 YES
6 TFDP2 TFDP2 TFDP2 1865 0.26 0.076 YES
7 CCNB3 CCNB3 CCNB3 1879 0.26 0.097 YES
8 CDKN2A CDKN2A CDKN2A 2313 0.23 0.092 YES
9 CDC7 CDC7 CDC7 2720 0.21 0.087 YES
10 E2F1 E2F1 E2F1 2800 0.2 0.099 YES
11 CDC25C CDC25C CDC25C 2816 0.2 0.12 YES
12 TP53 TP53 TP53 2938 0.2 0.12 YES
13 E2F2 E2F2 E2F2 2982 0.19 0.14 YES
14 MCM2 MCM2 MCM2 3126 0.19 0.14 YES
15 CHEK2 CHEK2 CHEK2 3153 0.19 0.16 YES
16 ESPL1 ESPL1 ESPL1 3323 0.18 0.16 YES
17 CCNE2 CCNE2 CCNE2 3474 0.17 0.17 YES
18 CDC14B CDC14B CDC14B 3512 0.17 0.18 YES
19 PTTG2 PTTG2 PTTG2 3610 0.16 0.19 YES
20 ORC1L ORC1L ORC1L 3765 0.16 0.2 YES
21 CDC45 CDC45 CDC45 3819 0.16 0.2 YES
22 CDC25A CDC25A CDC25A 3906 0.15 0.21 YES
23 CDK1 CDK1 CDK1 4272 0.14 0.2 YES
24 MCM6 MCM6 MCM6 4298 0.14 0.21 YES
25 BUB1B BUB1B BUB1B 4333 0.14 0.22 YES
26 CDC6 CDC6 CDC6 4390 0.14 0.23 YES
27 MCM5 MCM5 MCM5 4576 0.13 0.23 YES
28 MAD2L1 MAD2L1 MAD2L1 4677 0.13 0.24 YES
29 MCM7 MCM7 MCM7 4758 0.13 0.24 YES
30 MCM3 MCM3 MCM3 5009 0.12 0.24 YES
31 ATR ATR ATR 5114 0.12 0.24 YES
32 CDKN1B CDKN1B CDKN1B 5142 0.12 0.25 YES
33 TTK TTK TTK 5189 0.11 0.26 YES
34 STAG1 STAG1 STAG1 5198 0.11 0.27 YES
35 ORC6L ORC6L ORC6L 5264 0.11 0.27 YES
36 RBL1 RBL1 RBL1 5280 0.11 0.28 YES
37 MDM2 MDM2 MDM2 5379 0.11 0.28 YES
38 CDK2 CDK2 CDK2 5512 0.1 0.28 YES
39 SMAD4 SMAD4 SMAD4 5530 0.1 0.29 YES
40 WEE1 WEE1 WEE1 5555 0.1 0.3 YES
41 SMAD2 SMAD2 SMAD2 5785 0.098 0.3 YES
42 GADD45G GADD45G GADD45G 5882 0.095 0.3 YES
43 ORC2L ORC2L ORC2L 5914 0.094 0.3 YES
44 ATM ATM ATM 6023 0.091 0.3 YES
45 CCNB2 CCNB2 CCNB2 6069 0.09 0.31 YES
46 CDK4 CDK4 CDK4 6105 0.089 0.32 YES
47 PCNA PCNA PCNA 6208 0.087 0.32 YES
48 BUB1 BUB1 BUB1 6221 0.087 0.32 YES
49 CDKN1C CDKN1C CDKN1C 6408 0.082 0.32 YES
50 CCNA2 CCNA2 CCNA2 6507 0.08 0.32 YES
51 CDKN2D CDKN2D CDKN2D 6603 0.078 0.32 YES
52 ORC4L ORC4L ORC4L 6699 0.076 0.32 YES
53 HDAC2 HDAC2 HDAC2 6706 0.076 0.33 YES
54 SMAD3 SMAD3 SMAD3 6743 0.075 0.33 YES
55 ORC3L ORC3L ORC3L 6759 0.075 0.34 YES
56 ANAPC7 ANAPC7 ANAPC7 6760 0.075 0.34 YES
57 SMC3 SMC3 SMC3 7233 0.066 0.32 NO
58 ANAPC10 ANAPC10 ANAPC10 7570 0.059 0.31 NO
59 SMC1A SMC1A SMC1A 7614 0.058 0.31 NO
60 MCM4 MCM4 MCM4 7643 0.058 0.32 NO
61 SKP2 SKP2 SKP2 7678 0.057 0.32 NO
62 PTTG1 PTTG1 PTTG1 7762 0.056 0.32 NO
63 CHEK1 CHEK1 CHEK1 7812 0.055 0.32 NO
64 CDC26 CDC26 CDC26 7903 0.053 0.32 NO
65 ANAPC1 ANAPC1 ANAPC1 7963 0.052 0.32 NO
66 ORC5L ORC5L ORC5L 8248 0.047 0.31 NO
67 E2F3 E2F3 E2F3 8378 0.046 0.31 NO
68 EP300 EP300 EP300 8457 0.044 0.31 NO
69 STAG2 STAG2 STAG2 8501 0.044 0.31 NO
70 CREBBP CREBBP CREBBP 8581 0.043 0.31 NO
71 RAD21 RAD21 RAD21 8991 0.037 0.29 NO
72 PLK1 PLK1 PLK1 9036 0.036 0.29 NO
73 CCNB1 CCNB1 CCNB1 9168 0.034 0.28 NO
74 CDC23 CDC23 CDC23 9278 0.033 0.28 NO
75 CCNE1 CCNE1 CCNE1 9669 0.027 0.26 NO
76 ANAPC5 ANAPC5 ANAPC5 9747 0.026 0.26 NO
77 CCNH CCNH CCNH 9826 0.025 0.26 NO
78 RBL2 RBL2 RBL2 9873 0.024 0.26 NO
79 HDAC1 HDAC1 HDAC1 10180 0.02 0.24 NO
80 GSK3B GSK3B GSK3B 10297 0.018 0.24 NO
81 FZR1 FZR1 FZR1 10370 0.017 0.23 NO
82 PRKDC PRKDC PRKDC 10417 0.017 0.23 NO
83 ANAPC13 ANAPC13 ANAPC13 10459 0.016 0.23 NO
84 CCND3 CCND3 CCND3 10476 0.016 0.23 NO
85 ANAPC11 ANAPC11 ANAPC11 10601 0.014 0.23 NO
86 BUB3 BUB3 BUB3 10638 0.014 0.22 NO
87 ABL1 ABL1 ABL1 11281 0.005 0.19 NO
88 YWHAH YWHAH YWHAH 11375 0.0037 0.18 NO
89 ANAPC2 ANAPC2 ANAPC2 11577 0.0011 0.17 NO
90 CUL1 CUL1 CUL1 11611 0.0006 0.17 NO
91 PKMYT1 PKMYT1 PKMYT1 11627 0.00031 0.17 NO
92 SKP1 SKP1 SKP1 11726 -0.00091 0.17 NO
93 ANAPC4 ANAPC4 ANAPC4 12107 -0.0066 0.15 NO
94 YWHAE YWHAE YWHAE 12294 -0.0091 0.14 NO
95 TFDP1 TFDP1 TFDP1 12352 -0.01 0.14 NO
96 MAD2L2 MAD2L2 MAD2L2 12442 -0.011 0.13 NO
97 CDC20 CDC20 CDC20 12639 -0.014 0.12 NO
98 RBX1 RBX1 RBX1 13095 -0.022 0.098 NO
99 YWHAG YWHAG YWHAG 13564 -0.03 0.075 NO
100 CDKN2B CDKN2B CDKN2B 13773 -0.034 0.066 NO
101 CDC27 CDC27 CDC27 14156 -0.042 0.048 NO
102 GADD45A GADD45A GADD45A 14208 -0.043 0.049 NO
103 E2F4 E2F4 E2F4 14217 -0.044 0.052 NO
104 YWHAQ YWHAQ YWHAQ 14344 -0.046 0.049 NO
105 CCND2 CCND2 CCND2 14468 -0.049 0.046 NO
106 CDC16 CDC16 CDC16 14606 -0.052 0.043 NO
107 RB1 RB1 RB1 14607 -0.052 0.048 NO
108 CCND1 CCND1 CCND1 14631 -0.052 0.05 NO
109 YWHAB YWHAB YWHAB 14736 -0.055 0.049 NO
110 ZBTB17 ZBTB17 ZBTB17 14764 -0.056 0.052 NO
111 MYC MYC MYC 14874 -0.058 0.051 NO
112 MAD1L1 MAD1L1 MAD1L1 14943 -0.06 0.052 NO
113 CDK7 CDK7 CDK7 15570 -0.079 0.024 NO
114 GADD45B GADD45B GADD45B 15927 -0.093 0.013 NO
115 YWHAZ YWHAZ YWHAZ 16009 -0.096 0.016 NO
116 CDC25B CDC25B CDC25B 16117 -0.1 0.018 NO
117 TGFB3 TGFB3 TGFB3 16310 -0.11 0.017 NO
118 TGFB1 TGFB1 TGFB1 16576 -0.13 0.013 NO
119 CDKN1A CDKN1A CDKN1A 16627 -0.13 0.021 NO
120 TGFB2 TGFB2 TGFB2 16937 -0.16 0.017 NO
121 CDK6 CDK6 CDK6 17185 -0.19 0.019 NO
122 SFN SFN SFN 17381 -0.21 0.026 NO
123 CCNA1 CCNA1 CCNA1 17935 -0.34 0.023 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 BUTANOATE METABOLISM.

Figure S40.  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 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 ERK PATHWAY 27 genes.ES.table 0.24 0.78 0.72 1 1 0.22 0.13 0.19 1 0.63
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.28 1.2 0.27 0.9 1 0.2 0.1 0.18 0.82 0.35
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.23 0.89 0.58 0.98 1 0.3 0.16 0.25 0.97 0.45
BIOCARTA IL1R PATHWAY 32 genes.ES.table 0.34 0.97 0.51 0.97 1 0.34 0.16 0.29 0.93 0.42
KEGG PYRIMIDINE METABOLISM 96 genes.ES.table 0.21 0.94 0.5 0.98 1 0.083 0.056 0.079 0.95 0.44
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 42 genes.ES.table 0.21 0.83 0.68 1 1 0.21 0.1 0.19 1 0.59
KEGG ETHER LIPID METABOLISM 28 genes.ES.table 0.32 0.94 0.54 0.93 1 0.18 0.044 0.17 0.9 0.36
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.35 1.4 0.13 0.74 0.97 1 0.65 0.35 0.57 0.26
KEGG RIBOSOME 85 genes.ES.table 0.61 1.5 0.12 0.53 0.87 0.88 0.26 0.65 0.35 0.15
KEGG RNA POLYMERASE 28 genes.ES.table 0.28 0.99 0.42 1 1 0.93 0.49 0.48 0.97 0.46
genes ES table in pathway: BIOCARTA ERK 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 PSMB8 PSMB8 PSMB8 2091 0.076 -0.068 YES
2 PSMD6 PSMD6 PSMD6 2137 0.074 -0.025 YES
3 PSME2 PSME2 PSME2 2249 0.07 0.011 YES
4 PSMA5 PSMA5 PSMA5 2268 0.069 0.053 YES
5 PSMB7 PSMB7 PSMB7 2306 0.068 0.092 YES
6 POMP POMP POMP 2338 0.067 0.13 YES
7 PSMD13 PSMD13 PSMD13 2351 0.067 0.17 YES
8 PSMA6 PSMA6 PSMA6 2698 0.056 0.19 YES
9 PSMB5 PSMB5 PSMB5 2859 0.051 0.21 YES
10 PSMC1 PSMC1 PSMC1 2867 0.051 0.24 YES
11 PSMB2 PSMB2 PSMB2 3058 0.047 0.26 YES
12 PSMB6 PSMB6 PSMB6 3119 0.045 0.28 YES
13 PSME1 PSME1 PSME1 3153 0.044 0.31 YES
14 PSMD12 PSMD12 PSMD12 3309 0.042 0.32 YES
15 PSMA4 PSMA4 PSMA4 3381 0.04 0.34 YES
16 PSMA3 PSMA3 PSMA3 3420 0.039 0.37 YES
17 PSMB9 PSMB9 PSMB9 3422 0.039 0.39 YES
18 PSMC3 PSMC3 PSMC3 3447 0.039 0.41 YES
19 PSMA2 PSMA2 PSMA2 3506 0.037 0.43 YES
20 PSMD7 PSMD7 PSMD7 3556 0.037 0.45 YES
21 PSMC6 PSMC6 PSMC6 3690 0.034 0.47 YES
22 PSMA7 PSMA7 PSMA7 3708 0.034 0.48 YES
23 PSMB1 PSMB1 PSMB1 3744 0.033 0.5 YES
24 PSMD8 PSMD8 PSMD8 3803 0.032 0.52 YES
25 PSME3 PSME3 PSME3 3808 0.032 0.54 YES
26 PSMD1 PSMD1 PSMD1 3936 0.03 0.55 YES
27 PSMB3 PSMB3 PSMB3 3967 0.029 0.57 YES
28 PSMF1 PSMF1 PSMF1 4007 0.029 0.58 YES
29 PSMA1 PSMA1 PSMA1 4123 0.027 0.59 YES
30 PSMC5 PSMC5 PSMC5 4556 0.019 0.58 YES
31 SHFM1 SHFM1 SHFM1 4790 0.016 0.58 YES
32 PSMD3 PSMD3 PSMD3 4845 0.015 0.58 YES
33 PSMD14 PSMD14 PSMD14 4877 0.014 0.59 YES
34 IFNG IFNG IFNG 4938 0.013 0.6 YES
35 PSMD4 PSMD4 PSMD4 5211 0.0085 0.58 NO
36 PSMC4 PSMC4 PSMC4 5296 0.0071 0.58 NO
37 PSMD11 PSMD11 PSMD11 5850 -0.0014 0.56 NO
38 PSMB4 PSMB4 PSMB4 6201 -0.0067 0.54 NO
39 PSMC2 PSMC2 PSMC2 6286 -0.0078 0.54 NO
40 PSMD2 PSMD2 PSMD2 6862 -0.016 0.52 NO
41 PSME4 PSME4 PSME4 7400 -0.025 0.5 NO
42 PSMA8 PSMA8 PSMA8 13189 -0.15 0.28 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 ERK PATHWAY.

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA ERK 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 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 IL1B IL1B IL1B 320 0.31 0.074 YES
2 IL18 IL18 IL18 334 0.31 0.16 YES
3 POLR3G POLR3G POLR3G 394 0.28 0.24 YES
4 AIM2 AIM2 AIM2 604 0.22 0.29 YES
5 CASP1 CASP1 CASP1 698 0.19 0.35 YES
6 IRF7 IRF7 IRF7 711 0.19 0.4 YES
7 PYCARD PYCARD PYCARD 720 0.19 0.46 YES
8 IFNA13 IFNA13 IFNA13 806 0.18 0.5 YES
9 DDX58 DDX58 DDX58 890 0.16 0.55 YES
10 IFNA1 IFNA1 IFNA1 975 0.15 0.59 YES
11 CXCL10 CXCL10 CXCL10 1283 0.12 0.61 YES
12 ZBP1 ZBP1 ZBP1 1680 0.094 0.61 YES
13 RIPK3 RIPK3 RIPK3 2846 0.052 0.56 NO
14 CCL5 CCL5 CCL5 2944 0.05 0.57 NO
15 POLR1D POLR1D POLR1D 3240 0.043 0.57 NO
16 POLR3B POLR3B POLR3B 3363 0.04 0.57 NO
17 POLR3H POLR3H POLR3H 3557 0.036 0.57 NO
18 RELA RELA RELA 4106 0.027 0.55 NO
19 IRF3 IRF3 IRF3 4414 0.022 0.54 NO
20 NFKBIB NFKBIB NFKBIB 4421 0.021 0.55 NO
21 POLR3A POLR3A POLR3A 4660 0.018 0.54 NO
22 RIPK1 RIPK1 RIPK1 5029 0.012 0.52 NO
23 POLR1C POLR1C POLR1C 5148 0.0095 0.52 NO
24 IFNB1 IFNB1 IFNB1 5165 0.0092 0.52 NO
25 NFKBIA NFKBIA NFKBIA 5419 0.0052 0.51 NO
26 NFKB1 NFKB1 NFKB1 5544 0.0032 0.5 NO
27 IL33 IL33 IL33 5889 -0.0019 0.49 NO
28 IKBKG IKBKG IKBKG 5923 -0.0025 0.48 NO
29 CHUK CHUK CHUK 6098 -0.0053 0.48 NO
30 TMEM173 TMEM173 TMEM173 6311 -0.0082 0.47 NO
31 ADAR ADAR ADAR 6661 -0.013 0.45 NO
32 POLR3F POLR3F POLR3F 6687 -0.014 0.46 NO
33 CCL4 CCL4 CCL4 7340 -0.024 0.43 NO
34 TREX1 TREX1 TREX1 7833 -0.031 0.41 NO
35 IL6 IL6 IL6 7998 -0.034 0.41 NO
36 POLR3K POLR3K POLR3K 8109 -0.036 0.41 NO
37 MAVS MAVS MAVS 8501 -0.042 0.4 NO
38 TBK1 TBK1 TBK1 8519 -0.042 0.42 NO
39 IKBKE IKBKE IKBKE 8737 -0.046 0.42 NO
40 POLR3C POLR3C POLR3C 8821 -0.047 0.43 NO
41 POLR3D POLR3D POLR3D 8956 -0.05 0.43 NO
42 IKBKB IKBKB IKBKB 9933 -0.068 0.4 NO
43 CCL4L2 CCL4L2 CCL4L2 10514 -0.08 0.39 NO
44 POLR3GL POLR3GL POLR3GL 12195 -0.12 0.34 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 RACCYCD PATHWAY.

Figure S44.  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 PYK2 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 RPL36A RPL36A RPL36A 1134 0.13 -0.024 YES
2 RPL39 RPL39 RPL39 1913 0.082 -0.044 YES
3 RPL36AL RPL36AL RPL36AL 1932 0.082 -0.022 YES
4 RPL9 RPL9 RPL9 2039 0.078 -0.0057 YES
5 RPLP2 RPLP2 RPLP2 2290 0.069 0.000021 YES
6 RPL22L1 RPL22L1 RPL22L1 2305 0.068 0.018 YES
7 RPS13 RPS13 RPS13 2372 0.066 0.034 YES
8 RPL35 RPL35 RPL35 2380 0.066 0.052 YES
9 RPL29 RPL29 RPL29 2397 0.065 0.069 YES
10 RPL27A RPL27A RPL27A 2447 0.064 0.084 YES
11 RPL11 RPL11 RPL11 2579 0.059 0.094 YES
12 RPL18A RPL18A RPL18A 2585 0.059 0.11 YES
13 RPS3 RPS3 RPS3 2621 0.058 0.12 YES
14 RPL36 RPL36 RPL36 2653 0.057 0.14 YES
15 RPL38 RPL38 RPL38 2684 0.056 0.15 YES
16 RPL26L1 RPL26L1 RPL26L1 2807 0.053 0.16 YES
17 RPS10 RPS10 RPS10 2812 0.052 0.18 YES
18 RPS12 RPS12 RPS12 2833 0.052 0.19 YES
19 RPS29 RPS29 RPS29 2848 0.052 0.2 YES
20 RPS2 RPS2 RPS2 2902 0.05 0.21 YES
21 MRPL13 MRPL13 MRPL13 2930 0.05 0.23 YES
22 RPS15 RPS15 RPS15 2938 0.05 0.24 YES
23 RPL34 RPL34 RPL34 2949 0.049 0.25 YES
24 RPL27 RPL27 RPL27 2964 0.049 0.27 YES
25 RPS16 RPS16 RPS16 2976 0.049 0.28 YES
26 RPL14 RPL14 RPL14 3068 0.047 0.29 YES
27 RPS25 RPS25 RPS25 3127 0.045 0.3 YES
28 FAU FAU FAU 3152 0.044 0.31 YES
29 RPSA RPSA RPSA 3205 0.044 0.32 YES
30 RPL8 RPL8 RPL8 3241 0.043 0.33 YES
31 UBA52 UBA52 UBA52 3275 0.042 0.34 YES
32 RPS24 RPS24 RPS24 3290 0.042 0.35 YES
33 RPL13 RPL13 RPL13 3305 0.042 0.36 YES
34 RPS21 RPS21 RPS21 3336 0.041 0.37 YES
35 RPL28 RPL28 RPL28 3408 0.04 0.38 YES
36 RPL4 RPL4 RPL4 3483 0.038 0.38 YES
37 RPS26 RPS26 RPS26 3600 0.036 0.39 YES
38 RPS18 RPS18 RPS18 3602 0.036 0.4 YES
39 RPL26 RPL26 RPL26 3615 0.036 0.41 YES
40 RPS5 RPS5 RPS5 3719 0.034 0.41 YES
41 RPL7A RPL7A RPL7A 3729 0.034 0.42 YES
42 RPS15A RPS15A RPS15A 3741 0.033 0.43 YES
43 RPS17 RPS17 RPS17 3759 0.033 0.44 YES
44 RPL37A RPL37A RPL37A 3787 0.033 0.44 YES
45 RPL32 RPL32 RPL32 3823 0.032 0.45 YES
46 RPL3L RPL3L RPL3L 3839 0.032 0.46 YES
47 RPS9 RPS9 RPS9 3843 0.032 0.47 YES
48 RPL12 RPL12 RPL12 3851 0.032 0.48 YES
49 RPL23A RPL23A RPL23A 3867 0.031 0.48 YES
50 RPS8 RPS8 RPS8 3894 0.031 0.49 YES
51 RPL6 RPL6 RPL6 3895 0.031 0.5 YES
52 RPS6 RPS6 RPS6 3916 0.03 0.51 YES
53 RPL5 RPL5 RPL5 3929 0.03 0.52 YES
54 RPL7 RPL7 RPL7 3937 0.03 0.52 YES
55 RPL37 RPL37 RPL37 3948 0.03 0.53 YES
56 RPL24 RPL24 RPL24 4023 0.028 0.54 YES
57 RPS7 RPS7 RPS7 4087 0.027 0.54 YES
58 RPS23 RPS23 RPS23 4103 0.027 0.55 YES
59 RPL17 RPL17 RPL17 4122 0.027 0.55 YES
60 RPL30 RPL30 RPL30 4198 0.026 0.56 YES
61 RPS20 RPS20 RPS20 4242 0.025 0.56 YES
62 RPS27A RPS27A RPS27A 4244 0.025 0.57 YES
63 RPL19 RPL19 RPL19 4285 0.024 0.57 YES
64 RPL13A RPL13A RPL13A 4302 0.024 0.58 YES
65 RPS4X RPS4X RPS4X 4303 0.024 0.58 YES
66 RPL10A RPL10A RPL10A 4340 0.023 0.59 YES
67 RPS3A RPS3A RPS3A 4366 0.022 0.59 YES
68 RPL31 RPL31 RPL31 4430 0.021 0.6 YES
69 RPS19 RPS19 RPS19 4468 0.021 0.6 YES
70 RPL22 RPL22 RPL22 4519 0.02 0.6 YES
71 RPL10 RPL10 RPL10 4531 0.02 0.61 YES
72 RPL23 RPL23 RPL23 4607 0.018 0.61 YES
73 RPS11 RPS11 RPS11 4759 0.016 0.6 YES
74 RSL24D1 RSL24D1 RSL24D1 4796 0.016 0.61 YES
75 RPLP0 RPLP0 RPLP0 4835 0.015 0.61 YES
76 RPLP1 RPLP1 RPLP1 5277 0.0074 0.59 NO
77 RPL3 RPL3 RPL3 5375 0.0059 0.58 NO
78 RPS28 RPS28 RPS28 5537 0.0034 0.58 NO
79 RPL41 RPL41 RPL41 5808 -0.00081 0.56 NO
80 RPL15 RPL15 RPL15 6554 -0.012 0.52 NO
81 RPS27L RPS27L RPS27L 6664 -0.013 0.52 NO
82 RPL35A RPL35A RPL35A 6830 -0.016 0.52 NO
83 RPS27 RPS27 RPS27 8072 -0.035 0.46 NO
84 RPS4Y1 RPS4Y1 RPS4Y1 12636 -0.14 0.25 NO
85 RPL21 RPL21 RPL21 15213 -0.23 0.17 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 PYK2 PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA IL1R PATHWAY

Table 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 WARS WARS WARS 1138 0.13 0.017 YES
2 RARS RARS RARS 1598 0.098 0.05 YES
3 GARS GARS GARS 2141 0.074 0.064 YES
4 FARS2 FARS2 FARS2 2267 0.069 0.098 YES
5 SARS SARS SARS 2272 0.069 0.14 YES
6 HARS HARS HARS 2471 0.063 0.16 YES
7 CARS2 CARS2 CARS2 2568 0.06 0.19 YES
8 VARS VARS VARS 2642 0.057 0.22 YES
9 KARS KARS KARS 2710 0.056 0.25 YES
10 YARS YARS YARS 2721 0.055 0.28 YES
11 FARSB FARSB FARSB 3095 0.046 0.29 YES
12 CARS CARS CARS 3861 0.031 0.27 YES
13 TARS TARS TARS 4128 0.027 0.27 YES
14 YARS2 YARS2 YARS2 4532 0.02 0.26 YES
15 FARSA FARSA FARSA 4795 0.016 0.25 YES
16 QARS QARS QARS 4918 0.014 0.26 YES
17 HARS2 HARS2 HARS2 5275 0.0074 0.24 YES
18 TARSL2 TARSL2 TARSL2 5346 0.0064 0.24 YES
19 SARS2 SARS2 SARS2 5638 0.0019 0.22 YES
20 DARS DARS DARS 6345 -0.0086 0.19 YES
21 LARS2 LARS2 LARS2 6473 -0.01 0.19 YES
22 NARS2 NARS2 NARS2 6550 -0.012 0.19 YES
23 MARS MARS MARS 6821 -0.016 0.19 YES
24 EARS2 EARS2 EARS2 6851 -0.016 0.2 YES
25 IARS2 IARS2 IARS2 6904 -0.017 0.2 YES
26 NARS NARS NARS 6928 -0.017 0.21 YES
27 EPRS EPRS EPRS 7039 -0.019 0.22 YES
28 RARS2 RARS2 RARS2 7073 -0.02 0.23 YES
29 IARS IARS IARS 7219 -0.022 0.23 YES
30 MTFMT MTFMT MTFMT 7302 -0.023 0.24 YES
31 LARS LARS LARS 7523 -0.026 0.24 YES
32 WARS2 WARS2 WARS2 7756 -0.03 0.25 YES
33 AARS2 AARS2 AARS2 8380 -0.04 0.24 YES
34 VARS2 VARS2 VARS2 8470 -0.041 0.26 YES
35 AARS AARS AARS 8787 -0.047 0.27 YES
36 DARS2 DARS2 DARS2 9110 -0.053 0.28 YES
37 PSTK PSTK PSTK 10217 -0.074 0.26 YES
38 SEPSECS SEPSECS SEPSECS 10868 -0.087 0.28 YES
39 PARS2 PARS2 PARS2 11445 -0.1 0.31 YES
40 MARS2 MARS2 MARS2 11996 -0.12 0.35 YES

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 IL1R PATHWAY.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

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 HSPA2 HSPA2 HSPA2 2097 0.076 -0.092 YES
2 EIF4A3 EIF4A3 EIF4A3 2244 0.07 -0.078 YES
3 CWC15 CWC15 CWC15 3077 0.047 -0.11 YES
4 CCDC12 CCDC12 CCDC12 3134 0.045 -0.098 YES
5 HSPA8 HSPA8 HSPA8 3166 0.044 -0.086 YES
6 SNRPB2 SNRPB2 SNRPB2 3183 0.044 -0.074 YES
7 CTNNBL1 CTNNBL1 CTNNBL1 3203 0.044 -0.061 YES
8 DHX38 DHX38 DHX38 3328 0.041 -0.055 YES
9 SF3B5 SF3B5 SF3B5 3329 0.041 -0.042 YES
10 PLRG1 PLRG1 PLRG1 3541 0.037 -0.043 YES
11 PPIL1 PPIL1 PPIL1 3618 0.036 -0.036 YES
12 SNRPA1 SNRPA1 SNRPA1 3665 0.034 -0.028 YES
13 SFRS5 SFRS5 SFRS5 3745 0.033 -0.022 YES
14 SNRPD1 SNRPD1 SNRPD1 3819 0.032 -0.016 YES
15 PUF60 PUF60 PUF60 4003 0.029 -0.017 YES
16 SNRPC SNRPC SNRPC 4097 0.027 -0.014 YES
17 PRPF31 PRPF31 PRPF31 4134 0.026 -0.0077 YES
18 SNRPF SNRPF SNRPF 4300 0.024 -0.0094 YES
19 TRA2A TRA2A TRA2A 4395 0.022 -0.0078 YES
20 PPIE PPIE PPIE 4416 0.022 -0.0023 YES
21 SF3B14 SF3B14 SF3B14 4527 0.02 -0.0022 YES
22 SNRPD2 SNRPD2 SNRPD2 4536 0.02 0.0034 YES
23 ZMAT2 ZMAT2 ZMAT2 4610 0.018 0.0051 YES
24 AQR AQR AQR 4630 0.018 0.0097 YES
25 SNRPB SNRPB SNRPB 4678 0.018 0.013 YES
26 PCBP1 PCBP1 PCBP1 4680 0.018 0.018 YES
27 DHX15 DHX15 DHX15 4682 0.018 0.023 YES
28 LSM7 LSM7 LSM7 4733 0.017 0.026 YES
29 SNRPD3 SNRPD3 SNRPD3 4737 0.017 0.031 YES
30 LSM5 LSM5 LSM5 4911 0.014 0.025 YES
31 BUD31 BUD31 BUD31 4939 0.013 0.028 YES
32 PPIH PPIH PPIH 4994 0.012 0.029 YES
33 HNRNPC HNRNPC HNRNPC 5068 0.011 0.028 YES
34 SFRS2B SFRS2B SFRS2B 5093 0.01 0.03 YES
35 SNW1 SNW1 SNW1 5121 0.0099 0.032 YES
36 SNRNP70 SNRNP70 SNRNP70 5137 0.0097 0.034 YES
37 EFTUD2 EFTUD2 EFTUD2 5158 0.0093 0.036 YES
38 MAGOH MAGOH MAGOH 5170 0.0091 0.038 YES
39 SMNDC1 SMNDC1 SMNDC1 5251 0.0078 0.036 YES
40 SNRPG SNRPG SNRPG 5271 0.0075 0.037 YES
41 SART1 SART1 SART1 5361 0.0061 0.034 YES
42 PRPF6 PRPF6 PRPF6 5379 0.0058 0.035 YES
43 PRPF38A PRPF38A PRPF38A 5423 0.0052 0.034 YES
44 SF3A2 SF3A2 SF3A2 5452 0.0048 0.034 YES
45 RBM22 RBM22 RBM22 5507 0.0038 0.032 YES
46 TXNL4A TXNL4A TXNL4A 5510 0.0038 0.033 YES
47 LSM3 LSM3 LSM3 5568 0.0029 0.031 YES
48 PQBP1 PQBP1 PQBP1 5592 0.0027 0.031 YES
49 PRPF19 PRPF19 PRPF19 5657 0.0017 0.028 YES
50 BAT1 BAT1 BAT1 5783 -0.00032 0.021 YES
51 XAB2 XAB2 XAB2 5805 -0.00074 0.02 YES
52 SNRPA SNRPA SNRPA 5811 -0.00083 0.02 YES
53 SFRS1 SFRS1 SFRS1 5916 -0.0024 0.015 YES
54 RBM25 RBM25 RBM25 6006 -0.004 0.011 YES
55 HNRNPM HNRNPM HNRNPM 6063 -0.0047 0.0097 YES
56 PRPF40B PRPF40B PRPF40B 6091 -0.0052 0.0098 YES
57 HNRNPK HNRNPK HNRNPK 6102 -0.0054 0.011 YES
58 SYF2 SYF2 SYF2 6144 -0.006 0.011 YES
59 U2AF2 U2AF2 U2AF2 6171 -0.0064 0.011 YES
60 THOC4 THOC4 THOC4 6186 -0.0065 0.012 YES
61 SF3B2 SF3B2 SF3B2 6192 -0.0066 0.014 YES
62 NHP2L1 NHP2L1 NHP2L1 6250 -0.0073 0.013 YES
63 SF3B3 SF3B3 SF3B3 6258 -0.0075 0.015 YES
64 NCBP1 NCBP1 NCBP1 6277 -0.0077 0.017 YES
65 SFRS3 SFRS3 SFRS3 6339 -0.0085 0.016 YES
66 HNRNPA1 HNRNPA1 HNRNPA1 6347 -0.0086 0.018 YES
67 RBM17 RBM17 RBM17 6378 -0.009 0.019 YES
68 SFRS9 SFRS9 SFRS9 6386 -0.0091 0.022 YES
69 U2AF1 U2AF1 U2AF1 6400 -0.0093 0.024 YES
70 SF3A3 SF3A3 SF3A3 6496 -0.011 0.022 YES
71 DHX16 DHX16 DHX16 6516 -0.011 0.024 YES
72 TCERG1 TCERG1 TCERG1 6520 -0.011 0.027 YES
73 SLU7 SLU7 SLU7 6540 -0.011 0.03 YES
74 SFRS4 SFRS4 SFRS4 6544 -0.011 0.033 YES
75 DDX23 DDX23 DDX23 6645 -0.013 0.032 YES
76 SFRS2 SFRS2 SFRS2 6653 -0.013 0.035 YES
77 RBM8A RBM8A RBM8A 6716 -0.014 0.036 YES
78 PRPF40A PRPF40A PRPF40A 6765 -0.015 0.038 YES
79 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 6841 -0.016 0.039 YES
80 SFRS6 SFRS6 SFRS6 6873 -0.016 0.042 YES
81 ACIN1 ACIN1 ACIN1 6878 -0.016 0.047 YES
82 DHX8 DHX8 DHX8 6986 -0.018 0.047 YES
83 CRNKL1 CRNKL1 CRNKL1 7011 -0.019 0.051 YES
84 DDX5 DDX5 DDX5 7071 -0.02 0.054 YES
85 SNRNP40 SNRNP40 SNRNP40 7161 -0.021 0.056 YES
86 SF3B4 SF3B4 SF3B4 7205 -0.022 0.06 YES
87 SNRPE SNRPE SNRPE 7231 -0.022 0.065 YES
88 LSM4 LSM4 LSM4 7258 -0.022 0.071 YES
89 LSM2 LSM2 LSM2 7329 -0.024 0.074 YES
90 PHF5A PHF5A PHF5A 7436 -0.025 0.076 YES
91 PRPF18 PRPF18 PRPF18 7470 -0.026 0.082 YES
92 LSM6 LSM6 LSM6 7491 -0.026 0.089 YES
93 PRPF4 PRPF4 PRPF4 7529 -0.026 0.095 YES
94 HNRNPU HNRNPU HNRNPU 7691 -0.029 0.096 YES
95 BCAS2 BCAS2 BCAS2 7702 -0.029 0.1 YES
96 THOC1 THOC1 THOC1 7789 -0.03 0.11 YES
97 DDX46 DDX46 DDX46 7817 -0.031 0.12 YES
98 SFRS7 SFRS7 SFRS7 7928 -0.033 0.12 YES
99 PRPF38B PRPF38B PRPF38B 7967 -0.034 0.13 YES
100 CDC5L CDC5L CDC5L 7989 -0.034 0.14 YES
101 SFRS13A SFRS13A SFRS13A 8164 -0.037 0.14 YES
102 DDX42 DDX42 DDX42 8176 -0.037 0.15 YES
103 HNRNPA3 HNRNPA3 HNRNPA3 8257 -0.038 0.16 YES
104 HSPA6 HSPA6 HSPA6 8337 -0.039 0.17 YES
105 MAGOHB MAGOHB MAGOHB 8349 -0.039 0.18 YES
106 PRPF8 PRPF8 PRPF8 8432 -0.04 0.19 YES
107 SF3B1 SF3B1 SF3B1 8477 -0.041 0.2 YES
108 PRPF3 PRPF3 PRPF3 8482 -0.041 0.21 YES
109 CDC40 CDC40 CDC40 8551 -0.042 0.22 YES
110 ISY1 ISY1 ISY1 8560 -0.043 0.23 YES
111 SNRNP27 SNRNP27 SNRNP27 8621 -0.044 0.24 YES
112 SR140 SR140 SR140 8626 -0.044 0.25 YES
113 HSPA1B HSPA1B HSPA1B 8738 -0.046 0.26 YES
114 CHERP CHERP CHERP 8742 -0.046 0.28 YES
115 TRA2B TRA2B TRA2B 8743 -0.046 0.29 YES
116 THOC2 THOC2 THOC2 8769 -0.046 0.3 YES
117 SF3A1 SF3A1 SF3A1 8773 -0.047 0.32 YES
118 NAA38 NAA38 NAA38 9038 -0.051 0.32 YES
119 RBMX RBMX RBMX 9062 -0.052 0.33 YES
120 SNRNP200 SNRNP200 SNRNP200 9180 -0.054 0.34 YES
121 THOC3 THOC3 THOC3 9405 -0.058 0.35 YES
122 WBP11 WBP11 WBP11 9915 -0.067 0.34 YES
123 HSPA1A HSPA1A HSPA1A 10033 -0.07 0.36 YES
124 USP39 USP39 USP39 10601 -0.082 0.35 NO
125 HSPA1L HSPA1L HSPA1L 15344 -0.24 0.16 NO

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

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

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

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 IFNE IFNE IFNE 261 0.35 0.055 YES
2 IFNK IFNK IFNK 371 0.29 0.11 YES
3 ISG15 ISG15 ISG15 488 0.25 0.15 YES
4 NLRX1 NLRX1 NLRX1 599 0.22 0.19 YES
5 IRF7 IRF7 IRF7 711 0.19 0.22 YES
6 IFNA13 IFNA13 IFNA13 806 0.18 0.25 YES
7 DDX58 DDX58 DDX58 890 0.16 0.28 YES
8 IL8 IL8 IL8 971 0.15 0.3 YES
9 IFNA1 IFNA1 IFNA1 975 0.15 0.33 YES
10 IFIH1 IFIH1 IFIH1 1024 0.15 0.36 YES
11 MAPK13 MAPK13 MAPK13 1233 0.13 0.37 YES
12 CXCL10 CXCL10 CXCL10 1283 0.12 0.39 YES
13 TRADD TRADD TRADD 1625 0.097 0.39 YES
14 CASP10 CASP10 CASP10 1802 0.087 0.4 YES
15 DHX58 DHX58 DHX58 2646 0.057 0.37 NO
16 MAPK14 MAPK14 MAPK14 2929 0.05 0.36 NO
17 TNF TNF TNF 2951 0.049 0.37 NO
18 DDX3X DDX3X DDX3X 3206 0.044 0.36 NO
19 ATG12 ATG12 ATG12 3392 0.04 0.36 NO
20 CYLD CYLD CYLD 3558 0.036 0.36 NO
21 FADD FADD FADD 3795 0.032 0.35 NO
22 RELA RELA RELA 4106 0.027 0.34 NO
23 CASP8 CASP8 CASP8 4141 0.026 0.34 NO
24 TRIM25 TRIM25 TRIM25 4322 0.023 0.34 NO
25 IRF3 IRF3 IRF3 4414 0.022 0.34 NO
26 NFKBIB NFKBIB NFKBIB 4421 0.021 0.34 NO
27 AZI2 AZI2 AZI2 4469 0.021 0.34 NO
28 RIPK1 RIPK1 RIPK1 5029 0.012 0.32 NO
29 IFNB1 IFNB1 IFNB1 5165 0.0092 0.31 NO
30 MAPK11 MAPK11 MAPK11 5322 0.0068 0.3 NO
31 NFKBIA NFKBIA NFKBIA 5419 0.0052 0.3 NO
32 NFKB1 NFKB1 NFKB1 5544 0.0032 0.29 NO
33 MAP3K7 MAP3K7 MAP3K7 5861 -0.0015 0.28 NO
34 IKBKG IKBKG IKBKG 5923 -0.0025 0.27 NO
35 CHUK CHUK CHUK 6098 -0.0053 0.26 NO
36 PIN1 PIN1 PIN1 6172 -0.0064 0.26 NO
37 TMEM173 TMEM173 TMEM173 6311 -0.0082 0.26 NO
38 TANK TANK TANK 6314 -0.0083 0.26 NO
39 SIKE1 SIKE1 SIKE1 6374 -0.0089 0.26 NO
40 TRAF3 TRAF3 TRAF3 6810 -0.015 0.24 NO
41 MAP3K1 MAP3K1 MAP3K1 6843 -0.016 0.24 NO
42 OTUD5 OTUD5 OTUD5 6947 -0.018 0.24 NO
43 ATG5 ATG5 ATG5 7296 -0.023 0.22 NO
44 DAK DAK DAK 7677 -0.029 0.2 NO
45 MAPK9 MAPK9 MAPK9 7940 -0.033 0.2 NO
46 TRAF6 TRAF6 TRAF6 8104 -0.036 0.2 NO
47 MAVS MAVS MAVS 8501 -0.042 0.18 NO
48 TBK1 TBK1 TBK1 8519 -0.042 0.19 NO
49 IKBKE IKBKE IKBKE 8737 -0.046 0.19 NO
50 TRAF2 TRAF2 TRAF2 9324 -0.056 0.17 NO
51 IKBKB IKBKB IKBKB 9933 -0.068 0.15 NO
52 IL12B IL12B IL12B 10880 -0.087 0.11 NO
53 TBKBP1 TBKBP1 TBKBP1 11247 -0.096 0.11 NO
54 MAPK8 MAPK8 MAPK8 13037 -0.15 0.042 NO
55 MAPK12 MAPK12 MAPK12 13833 -0.18 0.033 NO
56 DDX3Y DDX3Y DDX3Y 13869 -0.18 0.066 NO
57 MAPK10 MAPK10 MAPK10 15010 -0.22 0.048 NO
58 RNF125 RNF125 RNF125 15876 -0.27 0.054 NO
59 IL12A IL12A IL12A 17596 -0.41 0.042 NO

Figure S51.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S52.  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 ETHER LIPID METABOLISM

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 CARD18 CARD18 CARD18 47 0.57 0.084 YES
2 MEFV MEFV MEFV 95 0.49 0.16 YES
3 NOD2 NOD2 NOD2 248 0.36 0.2 YES
4 IL1B IL1B IL1B 320 0.31 0.25 YES
5 IL18 IL18 IL18 334 0.31 0.29 YES
6 CARD6 CARD6 CARD6 518 0.24 0.32 YES
7 CASP1 CASP1 CASP1 698 0.19 0.34 YES
8 PYCARD PYCARD PYCARD 720 0.19 0.37 YES
9 CASP5 CASP5 CASP5 730 0.19 0.4 YES
10 CXCL1 CXCL1 CXCL1 744 0.19 0.42 YES
11 IL8 IL8 IL8 971 0.15 0.44 YES
12 MAPK13 MAPK13 MAPK13 1233 0.13 0.44 YES
13 SUGT1 SUGT1 SUGT1 1305 0.12 0.46 YES
14 MAPK3 MAPK3 MAPK3 1411 0.11 0.47 YES
15 CXCL2 CXCL2 CXCL2 2131 0.074 0.44 NO
16 CCL7 CCL7 CCL7 2686 0.056 0.42 NO
17 NLRP1 NLRP1 NLRP1 2839 0.052 0.42 NO
18 MAPK14 MAPK14 MAPK14 2929 0.05 0.42 NO
19 CCL5 CCL5 CCL5 2944 0.05 0.43 NO
20 TNF TNF TNF 2951 0.049 0.43 NO
21 TRIP6 TRIP6 TRIP6 3115 0.046 0.43 NO
22 RIPK2 RIPK2 RIPK2 3417 0.039 0.42 NO
23 CCL8 CCL8 CCL8 3699 0.034 0.41 NO
24 RELA RELA RELA 4106 0.027 0.39 NO
25 TAB2 TAB2 TAB2 4107 0.027 0.4 NO
26 CASP8 CASP8 CASP8 4141 0.026 0.4 NO
27 NLRP3 NLRP3 NLRP3 4299 0.024 0.39 NO
28 NOD1 NOD1 NOD1 4362 0.022 0.39 NO
29 NFKBIB NFKBIB NFKBIB 4421 0.021 0.4 NO
30 MAPK11 MAPK11 MAPK11 5322 0.0068 0.35 NO
31 NFKBIA NFKBIA NFKBIA 5419 0.0052 0.34 NO
32 NFKB1 NFKB1 NFKB1 5544 0.0032 0.34 NO
33 MAP3K7 MAP3K7 MAP3K7 5861 -0.0015 0.32 NO
34 TNFAIP3 TNFAIP3 TNFAIP3 5887 -0.0019 0.32 NO
35 IKBKG IKBKG IKBKG 5923 -0.0025 0.32 NO
36 HSP90AA1 HSP90AA1 HSP90AA1 6046 -0.0046 0.31 NO
37 BIRC2 BIRC2 BIRC2 6080 -0.005 0.31 NO
38 CHUK CHUK CHUK 6098 -0.0053 0.31 NO
39 TAB3 TAB3 TAB3 6315 -0.0083 0.3 NO
40 MAPK1 MAPK1 MAPK1 6457 -0.01 0.29 NO
41 CCL13 CCL13 CCL13 6614 -0.012 0.29 NO
42 HSP90B1 HSP90B1 HSP90B1 7363 -0.024 0.25 NO
43 XIAP XIAP XIAP 7743 -0.03 0.23 NO
44 MAPK9 MAPK9 MAPK9 7940 -0.033 0.23 NO
45 IL6 IL6 IL6 7998 -0.034 0.23 NO
46 TRAF6 TRAF6 TRAF6 8104 -0.036 0.23 NO
47 CCL11 CCL11 CCL11 9597 -0.061 0.16 NO
48 ERBB2IP ERBB2IP ERBB2IP 9830 -0.066 0.15 NO
49 IKBKB IKBKB IKBKB 9933 -0.068 0.16 NO
50 TAB1 TAB1 TAB1 9935 -0.068 0.17 NO
51 PSTPIP1 PSTPIP1 PSTPIP1 10323 -0.076 0.16 NO
52 PYDC1 PYDC1 PYDC1 12956 -0.15 0.038 NO
53 CCL2 CCL2 CCL2 13025 -0.15 0.056 NO
54 MAPK8 MAPK8 MAPK8 13037 -0.15 0.079 NO
55 CARD8 CARD8 CARD8 13333 -0.16 0.087 NO
56 BIRC3 BIRC3 BIRC3 13459 -0.16 0.1 NO
57 MAPK12 MAPK12 MAPK12 13833 -0.18 0.11 NO
58 CARD9 CARD9 CARD9 14318 -0.19 0.11 NO
59 NLRC4 NLRC4 NLRC4 14422 -0.2 0.14 NO
60 MAPK10 MAPK10 MAPK10 15010 -0.22 0.14 NO
61 NAIP NAIP NAIP 15935 -0.27 0.13 NO

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

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

Table 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 VEGFC VEGFC VEGFC 274 0.34 0.067 YES
2 MMP1 MMP1 MMP1 580 0.22 0.11 YES
3 TYMP TYMP TYMP 708 0.19 0.15 YES
4 PGF PGF PGF 771 0.18 0.19 YES
5 IL8 IL8 IL8 971 0.15 0.21 YES
6 CDKN1A CDKN1A CDKN1A 987 0.15 0.25 YES
7 HRAS HRAS HRAS 1050 0.14 0.28 YES
8 MAPK3 MAPK3 MAPK3 1411 0.11 0.29 YES
9 CDH1 CDH1 CDH1 1799 0.087 0.29 YES
10 FGFR3 FGFR3 FGFR3 1852 0.085 0.31 YES
11 MYC MYC MYC 2028 0.078 0.32 YES
12 DAPK3 DAPK3 DAPK3 2664 0.057 0.3 NO
13 NRAS NRAS NRAS 3390 0.04 0.27 NO
14 RB1 RB1 RB1 3534 0.037 0.27 NO
15 MAP2K2 MAP2K2 MAP2K2 4008 0.029 0.25 NO
16 VEGFA VEGFA VEGFA 4355 0.023 0.24 NO
17 EGFR EGFR EGFR 4701 0.017 0.22 NO
18 MAP2K1 MAP2K1 MAP2K1 5031 0.012 0.21 NO
19 ERBB2 ERBB2 ERBB2 5291 0.0073 0.2 NO
20 THBS1 THBS1 THBS1 5679 0.0014 0.18 NO
21 RASSF1 RASSF1 RASSF1 5735 0.00049 0.17 NO
22 MAPK1 MAPK1 MAPK1 6457 -0.01 0.14 NO
23 VEGFB VEGFB VEGFB 6522 -0.011 0.13 NO
24 CCND1 CCND1 CCND1 7375 -0.024 0.093 NO
25 RAF1 RAF1 RAF1 7446 -0.025 0.096 NO
26 ARAF ARAF ARAF 7927 -0.033 0.078 NO
27 MMP9 MMP9 MMP9 8616 -0.043 0.051 NO
28 BRAF BRAF BRAF 8631 -0.044 0.061 NO
29 KRAS KRAS KRAS 8651 -0.044 0.07 NO
30 E2F2 E2F2 E2F2 9564 -0.06 0.036 NO
31 E2F3 E2F3 E2F3 9790 -0.065 0.039 NO
32 MDM2 MDM2 MDM2 9798 -0.065 0.055 NO
33 DAPK1 DAPK1 DAPK1 10195 -0.073 0.051 NO
34 CDK4 CDK4 CDK4 10389 -0.077 0.06 NO
35 MMP2 MMP2 MMP2 10530 -0.08 0.072 NO
36 DAPK2 DAPK2 DAPK2 11750 -0.11 0.032 NO
37 RPS6KA5 RPS6KA5 RPS6KA5 12198 -0.12 0.037 NO
38 TP53 TP53 TP53 13719 -0.17 -0.0033 NO
39 CDKN2A CDKN2A CDKN2A 13977 -0.18 0.027 NO
40 EGF EGF EGF 17392 -0.39 -0.064 NO
41 FIGF FIGF FIGF 17999 -0.47 0.02 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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RIBOSOME

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 CDKN1A CDKN1A CDKN1A 987 0.15 0.042 YES
2 HRAS HRAS HRAS 1050 0.14 0.13 YES
3 CCNE1 CCNE1 CCNE1 1219 0.13 0.2 YES
4 MAPK3 MAPK3 MAPK3 1411 0.11 0.26 YES
5 CDK6 CDK6 CDK6 1884 0.084 0.28 YES
6 RAC1 RAC1 RAC1 2855 0.052 0.26 NO
7 RB1 RB1 RB1 3534 0.037 0.25 NO
8 TFDP1 TFDP1 TFDP1 3646 0.035 0.27 NO
9 RELA RELA RELA 4106 0.027 0.26 NO
10 RHOA RHOA RHOA 4687 0.017 0.24 NO
11 NFKBIA NFKBIA NFKBIA 5419 0.0052 0.2 NO
12 NFKB1 NFKB1 NFKB1 5544 0.0032 0.2 NO
13 PAK1 PAK1 PAK1 5584 0.0028 0.2 NO
14 IKBKG IKBKG IKBKG 5923 -0.0025 0.18 NO
15 CHUK CHUK CHUK 6098 -0.0053 0.17 NO
16 MAPK1 MAPK1 MAPK1 6457 -0.01 0.16 NO
17 AKT1 AKT1 AKT1 7134 -0.02 0.14 NO
18 CCND1 CCND1 CCND1 7375 -0.024 0.14 NO
19 RAF1 RAF1 RAF1 7446 -0.025 0.15 NO
20 IKBKB IKBKB IKBKB 9933 -0.068 0.056 NO
21 CDK4 CDK4 CDK4 10389 -0.077 0.08 NO
22 CDK2 CDK2 CDK2 11468 -0.1 0.085 NO
23 PIK3CA PIK3CA PIK3CA 12036 -0.12 0.13 NO
24 CDKN1B CDKN1B CDKN1B 12302 -0.12 0.19 NO
25 PIK3R1 PIK3R1 PIK3R1 14952 -0.22 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 RIBOSOME.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIBOSOME, 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 RNA POLYMERASE

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 STX11 STX11 STX11 799 0.18 0.032 YES
2 STX19 STX19 STX19 1357 0.12 0.051 YES
3 VAMP8 VAMP8 VAMP8 1786 0.088 0.065 YES
4 STX3 STX3 STX3 1935 0.082 0.091 YES
5 VAMP3 VAMP3 VAMP3 2084 0.076 0.12 YES
6 VTI1B VTI1B VTI1B 2109 0.075 0.15 YES
7 YKT6 YKT6 YKT6 2176 0.073 0.17 YES
8 STX4 STX4 STX4 2516 0.061 0.18 YES
9 STX10 STX10 STX10 2559 0.06 0.2 YES
10 STX8 STX8 STX8 2874 0.051 0.21 YES
11 STX6 STX6 STX6 3187 0.044 0.21 YES
12 BNIP1 BNIP1 BNIP1 3359 0.041 0.22 YES
13 STX17 STX17 STX17 3386 0.04 0.23 YES
14 VTI1A VTI1A VTI1A 3405 0.04 0.25 YES
15 STX7 STX7 STX7 3528 0.037 0.26 YES
16 STX12 STX12 STX12 3587 0.036 0.27 YES
17 GOSR2 GOSR2 GOSR2 4102 0.027 0.25 NO
18 STX5 STX5 STX5 4269 0.024 0.26 NO
19 STX1A STX1A STX1A 5359 0.0062 0.2 NO
20 BET1L BET1L BET1L 5493 0.004 0.19 NO
21 STX16 STX16 STX16 5936 -0.0028 0.17 NO
22 STX18 STX18 STX18 6018 -0.0042 0.17 NO
23 VAMP7 VAMP7 VAMP7 6857 -0.016 0.13 NO
24 VAMP2 VAMP2 VAMP2 7309 -0.023 0.11 NO
25 GOSR1 GOSR1 GOSR1 7331 -0.024 0.12 NO
26 VAMP4 VAMP4 VAMP4 7345 -0.024 0.13 NO
27 USE1 USE1 USE1 7988 -0.034 0.11 NO
28 SEC22B SEC22B SEC22B 8019 -0.034 0.12 NO
29 SNAP23 SNAP23 SNAP23 8277 -0.038 0.13 NO
30 BET1 BET1 BET1 8514 -0.042 0.13 NO
31 STX2 STX2 STX2 8764 -0.046 0.14 NO
32 STX1B STX1B STX1B 10203 -0.073 0.09 NO
33 SNAP47 SNAP47 SNAP47 10865 -0.087 0.091 NO
34 VAMP5 VAMP5 VAMP5 10938 -0.089 0.12 NO
35 SNAP25 SNAP25 SNAP25 13765 -0.17 0.044 NO
36 TSNARE1 TSNARE1 TSNARE1 13909 -0.18 0.11 NO
37 VAMP1 VAMP1 VAMP1 16436 -0.31 0.1 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 RNA POLYMERASE.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA POLYMERASE, 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 = HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = HNSC-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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