GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in THYM-TP
Thymoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in THYM-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1K35SS3
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 THYM-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: 193
Number of samples: 120
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 46
pheno.type: 2 - 4 :[ clus2 ] 31
pheno.type: 3 - 4 :[ clus3 ] 29
pheno.type: 4 - 4 :[ clus4 ] 14

For the expression subtypes of 18301 genes in 121 samples, GSEA found enriched gene sets in each cluster using 120 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA CARM ER PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG PYRIMIDINE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG GLYCEROLIPID METABOLISM, KEGG BUTANOATE METABOLISM, KEGG DRUG METABOLISM OTHER ENZYMES, KEGG DNA REPLICATION

    • And common core enriched genes are PDHA1, RPA3, RPA4, ACAT2, ACSM1, ACSM3, AKR1B10, ALDH5A1, ALDH9A1, BDH1

  • clus2

    • Top enriched gene sets are BIOCARTA TCR PATHWAY, BIOCARTA WNT PATHWAY, KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG RIBOSOME, KEGG RNA DEGRADATION, KEGG RNA POLYMERASE, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG PROTEASOME

    • And common core enriched genes are LSM2, LSM3, LSM4, LSM5, LSM7, NAA38, FAU, MRPL13, RPL10, RPL10A

  • clus3

    • Top enriched gene sets are BIOCARTA AGR PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA EDG1 PATHWAY, KEGG N GLYCAN BIOSYNTHESIS, KEGG O GLYCAN BIOSYNTHESIS, KEGG WNT SIGNALING PATHWAY, KEGG TGF BETA SIGNALING PATHWAY, KEGG AXON GUIDANCE, KEGG FOCAL ADHESION, KEGG ECM RECEPTOR INTERACTION

    • And common core enriched genes are ACTN3, ITGA1, ITGA10, ITGA2, ITGA2B, ITGA3, ITGA6, ITGA8, ITGA9, ITGAV

  • clus4

    • Top enriched gene sets are BIOCARTA FMLP PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA DEATH PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG ARGININE AND PROLINE METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG ARACHIDONIC ACID METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM

    • And common core enriched genes are IL1B, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQA2, HLA-DRA

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 CARM ER PATHWAY 34 genes.ES.table 0.39 1.4 0.14 0.83 0.95 0.41 0.32 0.28 0.69 0.34
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.53 1.7 0.054 0.54 0.5 0.62 0.31 0.43 0.26 0.19
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.4 1.3 0.22 0.86 0.99 0.15 0.11 0.14 0.79 0.35
KEGG STEROID HORMONE BIOSYNTHESIS 36 genes.ES.table 0.51 1.2 0.17 0.84 0.99 0.36 0.13 0.31 0.78 0.35
KEGG PYRIMIDINE METABOLISM 97 genes.ES.table 0.32 1.3 0.22 0.91 0.99 0.44 0.34 0.3 0.84 0.39
KEGG STARCH AND SUCROSE METABOLISM 31 genes.ES.table 0.49 1.5 0.047 1 0.9 0.26 0.11 0.23 0.76 0.41
KEGG GLYCEROLIPID METABOLISM 45 genes.ES.table 0.38 1.3 0.12 1 0.99 0.2 0.13 0.17 0.89 0.44
KEGG BUTANOATE METABOLISM 30 genes.ES.table 0.56 1.7 0.02 1 0.48 0.43 0.21 0.34 0 0.35
KEGG DRUG METABOLISM OTHER ENZYMES 34 genes.ES.table 0.45 1.3 0.15 0.97 0.99 0.24 0.098 0.21 0.88 0.42
KEGG DNA REPLICATION 35 genes.ES.table 0.66 1.4 0.14 0.91 0.91 0.77 0.28 0.56 0.69 0.36
genes ES table in pathway: BIOCARTA CARM ER 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 AKR1B10 AKR1B10 AKR1B10 5 1.5 0.24 YES
2 HMGCS2 HMGCS2 HMGCS2 41 1 0.4 YES
3 ACSM1 ACSM1 ACSM1 447 0.46 0.45 YES
4 ACSM3 ACSM3 ACSM3 1255 0.3 0.45 YES
5 BDH1 BDH1 BDH1 1668 0.25 0.47 YES
6 ALDH5A1 ALDH5A1 ALDH5A1 1844 0.24 0.5 YES
7 OXCT1 OXCT1 OXCT1 1984 0.22 0.53 YES
8 ALDH9A1 ALDH9A1 ALDH9A1 2147 0.21 0.55 YES
9 L2HGDH L2HGDH L2HGDH 2916 0.16 0.53 YES
10 HADH HADH HADH 3284 0.14 0.53 YES
11 OXCT2 OXCT2 OXCT2 3616 0.12 0.54 YES
12 ACAT2 ACAT2 ACAT2 3767 0.12 0.55 YES
13 PDHA1 PDHA1 PDHA1 3834 0.11 0.56 YES
14 ACAT1 ACAT1 ACAT1 4304 0.099 0.55 NO
15 ACADS ACADS ACADS 4909 0.082 0.53 NO
16 HMGCL HMGCL HMGCL 6258 0.055 0.46 NO
17 ALDH1B1 ALDH1B1 ALDH1B1 6656 0.047 0.45 NO
18 PDHB PDHB PDHB 6781 0.045 0.45 NO
19 ECHS1 ECHS1 ECHS1 7364 0.036 0.42 NO
20 HADHA HADHA HADHA 7702 0.029 0.41 NO
21 BDH2 BDH2 BDH2 8872 0.01 0.35 NO
22 AACS AACS AACS 10511 -0.02 0.26 NO
23 ABAT ABAT ABAT 10699 -0.023 0.26 NO
24 HMGCS1 HMGCS1 HMGCS1 11374 -0.039 0.22 NO
25 GAD1 GAD1 GAD1 12393 -0.068 0.18 NO
26 ALDH7A1 ALDH7A1 ALDH7A1 12874 -0.085 0.17 NO
27 ALDH2 ALDH2 ALDH2 14256 -0.15 0.12 NO
28 ACSM5 ACSM5 ACSM5 14867 -0.19 0.11 NO
29 GAD2 GAD2 GAD2 15302 -0.22 0.12 NO
30 ALDH3A2 ALDH3A2 ALDH3A2 15567 -0.25 0.15 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 CARM ER PATHWAY.

Figure S2.  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: KEGG CITRATE CYCLE TCA CYCLE

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 OGDHL OGDHL OGDHL 319 0.53 0.14 YES
2 PCK1 PCK1 PCK1 587 0.42 0.24 YES
3 ACO1 ACO1 ACO1 2258 0.2 0.21 YES
4 IDH3A IDH3A IDH3A 2327 0.19 0.26 YES
5 IDH2 IDH2 IDH2 2537 0.18 0.3 YES
6 FH FH FH 3071 0.15 0.31 YES
7 ACO2 ACO2 ACO2 3251 0.14 0.34 YES
8 DLD DLD DLD 3275 0.14 0.38 YES
9 SDHC SDHC SDHC 3707 0.12 0.39 YES
10 OGDH OGDH OGDH 3724 0.12 0.43 YES
11 SDHA SDHA SDHA 3821 0.11 0.46 YES
12 PDHA1 PDHA1 PDHA1 3834 0.11 0.49 YES
13 MDH2 MDH2 MDH2 4339 0.098 0.49 YES
14 SDHD SDHD SDHD 4736 0.087 0.49 YES
15 MDH1 MDH1 MDH1 4759 0.087 0.52 YES
16 SDHB SDHB SDHB 5077 0.079 0.52 YES
17 DLST DLST DLST 5514 0.07 0.52 YES
18 SUCLG1 SUCLG1 SUCLG1 5589 0.068 0.53 YES
19 IDH3G IDH3G IDH3G 6317 0.054 0.51 NO
20 PDHB PDHB PDHB 6781 0.045 0.5 NO
21 CS CS CS 7111 0.04 0.49 NO
22 IDH3B IDH3B IDH3B 7161 0.039 0.5 NO
23 DLAT DLAT DLAT 7929 0.026 0.46 NO
24 ACLY ACLY ACLY 8545 0.016 0.43 NO
25 SUCLG2 SUCLG2 SUCLG2 9983 -0.0098 0.36 NO
26 SUCLA2 SUCLA2 SUCLA2 11224 -0.035 0.3 NO
27 PCK2 PCK2 PCK2 11641 -0.045 0.29 NO
28 IDH1 IDH1 IDH1 11881 -0.052 0.29 NO
29 PC PC PC 15032 -0.2 0.18 NO

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

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPA4 RPA4 RPA4 264 0.58 0.14 YES
2 POLE2 POLE2 POLE2 1474 0.27 0.14 YES
3 GTF2H2 GTF2H2 GTF2H2 1639 0.25 0.2 YES
4 CDK7 CDK7 CDK7 2754 0.16 0.19 YES
5 RPA3 RPA3 RPA3 2996 0.15 0.21 YES
6 RFC4 RFC4 RFC4 3076 0.15 0.25 YES
7 PCNA PCNA PCNA 3347 0.13 0.27 YES
8 POLE4 POLE4 POLE4 3505 0.13 0.29 YES
9 GTF2H5 GTF2H5 GTF2H5 3645 0.12 0.32 YES
10 RFC5 RFC5 RFC5 4256 0.1 0.31 YES
11 RBX1 RBX1 RBX1 4310 0.098 0.34 YES
12 MNAT1 MNAT1 MNAT1 4418 0.096 0.36 YES
13 POLE3 POLE3 POLE3 4546 0.092 0.37 YES
14 POLE POLE POLE 4588 0.091 0.39 YES
15 POLD1 POLD1 POLD1 4774 0.086 0.41 YES
16 RFC3 RFC3 RFC3 4825 0.085 0.43 YES
17 CCNH CCNH CCNH 4988 0.081 0.44 YES
18 LIG1 LIG1 LIG1 5010 0.08 0.46 YES
19 ERCC4 ERCC4 ERCC4 5285 0.075 0.46 YES
20 XPA XPA XPA 5621 0.067 0.46 YES
21 RFC2 RFC2 RFC2 5757 0.065 0.47 YES
22 POLD4 POLD4 POLD4 6398 0.052 0.45 NO
23 POLD2 POLD2 POLD2 6625 0.048 0.45 NO
24 CUL4B CUL4B CUL4B 6971 0.042 0.44 NO
25 DDB2 DDB2 DDB2 7193 0.038 0.44 NO
26 ERCC3 ERCC3 ERCC3 7537 0.032 0.43 NO
27 ERCC5 ERCC5 ERCC5 7622 0.031 0.44 NO
28 POLD3 POLD3 POLD3 7667 0.03 0.44 NO
29 ERCC1 ERCC1 ERCC1 8026 0.024 0.43 NO
30 RPA2 RPA2 RPA2 8068 0.023 0.43 NO
31 GTF2H4 GTF2H4 GTF2H4 8525 0.016 0.41 NO
32 ERCC6 ERCC6 ERCC6 9314 0.0029 0.37 NO
33 RFC1 RFC1 RFC1 9463 0.00036 0.36 NO
34 RAD23A RAD23A RAD23A 9622 -0.0028 0.35 NO
35 RPA1 RPA1 RPA1 9892 -0.0079 0.34 NO
36 ERCC2 ERCC2 ERCC2 10091 -0.012 0.33 NO
37 ERCC8 ERCC8 ERCC8 10235 -0.014 0.33 NO
38 CUL4A CUL4A CUL4A 10430 -0.018 0.32 NO
39 CETN2 CETN2 CETN2 11359 -0.038 0.28 NO
40 XPC XPC XPC 12146 -0.061 0.26 NO
41 GTF2H1 GTF2H1 GTF2H1 12622 -0.075 0.25 NO
42 DDB1 DDB1 DDB1 12666 -0.077 0.27 NO
43 GTF2H3 GTF2H3 GTF2H3 14289 -0.15 0.22 NO

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

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

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 RPA4 RPA4 RPA4 264 0.58 0.14 YES
2 RAD54B RAD54B RAD54B 647 0.4 0.23 YES
3 RAD51L1 RAD51L1 RAD51L1 1538 0.26 0.25 YES
4 RAD54L RAD54L RAD54L 1608 0.26 0.31 YES
5 RAD51 RAD51 RAD51 1717 0.25 0.37 YES
6 BLM BLM BLM 1807 0.24 0.43 YES
7 XRCC2 XRCC2 XRCC2 2215 0.2 0.46 YES
8 EME1 EME1 EME1 2217 0.2 0.52 YES
9 RPA3 RPA3 RPA3 2996 0.15 0.52 YES
10 SHFM1 SHFM1 SHFM1 3282 0.14 0.54 YES
11 RAD51L3 RAD51L3 RAD51L3 3420 0.13 0.56 YES
12 SSBP1 SSBP1 SSBP1 3473 0.13 0.59 YES
13 XRCC3 XRCC3 XRCC3 3907 0.11 0.6 YES
14 BRCA2 BRCA2 BRCA2 3998 0.11 0.62 YES
15 TOP3B TOP3B TOP3B 4205 0.1 0.64 YES
16 POLD1 POLD1 POLD1 4774 0.086 0.63 NO
17 MUS81 MUS81 MUS81 5392 0.073 0.62 NO
18 TOP3A TOP3A TOP3A 6040 0.059 0.6 NO
19 POLD4 POLD4 POLD4 6398 0.052 0.59 NO
20 POLD2 POLD2 POLD2 6625 0.048 0.59 NO
21 POLD3 POLD3 POLD3 7667 0.03 0.54 NO
22 RPA2 RPA2 RPA2 8068 0.023 0.53 NO
23 RAD50 RAD50 RAD50 9473 0.00026 0.45 NO
24 MRE11A MRE11A MRE11A 9552 -0.0016 0.45 NO
25 RPA1 RPA1 RPA1 9892 -0.0079 0.43 NO
26 NBN NBN NBN 10307 -0.016 0.41 NO
27 RAD52 RAD52 RAD52 13085 -0.093 0.28 NO

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

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

genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

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 ENPP3 ENPP3 ENPP3 12 1.3 0.18 YES
2 UGT2B7 UGT2B7 UGT2B7 80 0.86 0.3 YES
3 AMY1A AMY1A AMY1A 155 0.72 0.4 YES
4 AMY2A AMY2A AMY2A 573 0.42 0.43 YES
5 PYGM PYGM PYGM 1459 0.27 0.42 YES
6 UGT1A6 UGT1A6 UGT1A6 1786 0.24 0.44 YES
7 GPI GPI GPI 1833 0.24 0.47 YES
8 HK3 HK3 HK3 2015 0.22 0.49 YES
9 GYS1 GYS1 GYS1 3002 0.15 0.46 NO
10 AMY2B AMY2B AMY2B 3003 0.15 0.48 NO
11 UGP2 UGP2 UGP2 3294 0.14 0.48 NO
12 PGM2L1 PGM2L1 PGM2L1 4005 0.11 0.46 NO
13 AGL AGL AGL 5420 0.072 0.39 NO
14 PGM1 PGM1 PGM1 6474 0.051 0.34 NO
15 HK1 HK1 HK1 7538 0.032 0.28 NO
16 PYGB PYGB PYGB 8824 0.011 0.21 NO
17 HK2 HK2 HK2 9632 -0.003 0.17 NO
18 UGT1A9 UGT1A9 UGT1A9 9677 -0.004 0.17 NO
19 GUSB GUSB GUSB 9723 -0.0049 0.17 NO
20 GANC GANC GANC 9831 -0.0069 0.16 NO
21 GCK GCK GCK 10662 -0.022 0.12 NO
22 GAA GAA GAA 11072 -0.031 0.1 NO
23 PGM2 PGM2 PGM2 11657 -0.046 0.076 NO
24 ENPP1 ENPP1 ENPP1 13470 -0.11 -0.008 NO
25 GYS2 GYS2 GYS2 13513 -0.11 0.0052 NO
26 GBE1 GBE1 GBE1 14187 -0.15 -0.011 NO
27 UGDH UGDH UGDH 14603 -0.17 -0.01 NO
28 PYGL PYGL PYGL 15656 -0.26 -0.031 NO
29 UGT2B15 UGT2B15 UGT2B15 16011 -0.3 -0.0084 NO
30 MGAM MGAM MGAM 16837 -0.43 0.0062 NO
31 GBA3 GBA3 GBA3 17259 -0.52 0.056 NO

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

Figure S10.  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 STARCH AND SUCROSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPA4 RPA4 RPA4 264 0.58 0.12 YES
2 DNA2 DNA2 DNA2 1265 0.3 0.13 YES
3 POLE2 POLE2 POLE2 1474 0.27 0.18 YES
4 RNASEH2B RNASEH2B RNASEH2B 2050 0.21 0.2 YES
5 MCM6 MCM6 MCM6 2347 0.19 0.23 YES
6 RNASEH2A RNASEH2A RNASEH2A 2797 0.16 0.24 YES
7 FEN1 FEN1 FEN1 2948 0.15 0.27 YES
8 RPA3 RPA3 RPA3 2996 0.15 0.3 YES
9 RFC4 RFC4 RFC4 3076 0.15 0.33 YES
10 PRIM1 PRIM1 PRIM1 3241 0.14 0.35 YES
11 RNASEH1 RNASEH1 RNASEH1 3341 0.13 0.38 YES
12 PCNA PCNA PCNA 3347 0.13 0.41 YES
13 SSBP1 SSBP1 SSBP1 3473 0.13 0.43 YES
14 POLE4 POLE4 POLE4 3505 0.13 0.46 YES
15 MCM7 MCM7 MCM7 3630 0.12 0.48 YES
16 RNASEH2C RNASEH2C RNASEH2C 3831 0.11 0.49 YES
17 PRIM2 PRIM2 PRIM2 4010 0.11 0.51 YES
18 MCM2 MCM2 MCM2 4061 0.11 0.53 YES
19 RFC5 RFC5 RFC5 4256 0.1 0.54 YES
20 POLA2 POLA2 POLA2 4302 0.099 0.56 YES
21 POLE3 POLE3 POLE3 4546 0.092 0.57 YES
22 POLE POLE POLE 4588 0.091 0.59 YES
23 MCM5 MCM5 MCM5 4643 0.09 0.6 YES
24 POLD1 POLD1 POLD1 4774 0.086 0.62 YES
25 RFC3 RFC3 RFC3 4825 0.085 0.63 YES
26 LIG1 LIG1 LIG1 5010 0.08 0.64 YES
27 MCM3 MCM3 MCM3 5027 0.08 0.66 YES
28 RFC2 RFC2 RFC2 5757 0.065 0.63 NO
29 MCM4 MCM4 MCM4 5760 0.065 0.65 NO
30 POLD4 POLD4 POLD4 6398 0.052 0.63 NO
31 POLD2 POLD2 POLD2 6625 0.048 0.62 NO
32 POLD3 POLD3 POLD3 7667 0.03 0.57 NO
33 RPA2 RPA2 RPA2 8068 0.023 0.56 NO
34 RFC1 RFC1 RFC1 9463 0.00036 0.48 NO
35 RPA1 RPA1 RPA1 9892 -0.0079 0.46 NO

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

Figure S12.  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 GLYCEROLIPID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 VAV3 VAV3 VAV3 165 0.7 0.038 YES
2 CD40LG CD40LG CD40LG 288 0.56 0.069 YES
3 CD28 CD28 CD28 539 0.43 0.084 YES
4 CHP2 CHP2 CHP2 592 0.41 0.11 YES
5 GRAP2 GRAP2 GRAP2 781 0.37 0.12 YES
6 CD3G CD3G CD3G 834 0.36 0.14 YES
7 ITK ITK ITK 901 0.35 0.16 YES
8 CD3D CD3D CD3D 971 0.34 0.18 YES
9 PAK7 PAK7 PAK7 975 0.34 0.21 YES
10 CD3E CD3E CD3E 1088 0.32 0.22 YES
11 CD247 CD247 CD247 1093 0.32 0.24 YES
12 RASGRP1 RASGRP1 RASGRP1 1262 0.3 0.25 YES
13 CD8A CD8A CD8A 1359 0.28 0.27 YES
14 CD8B CD8B CD8B 1435 0.27 0.28 YES
15 LCK LCK LCK 1468 0.27 0.3 YES
16 LAT LAT LAT 1512 0.27 0.31 YES
17 PIK3R1 PIK3R1 PIK3R1 1516 0.27 0.33 YES
18 PRKCQ PRKCQ PRKCQ 1544 0.26 0.35 YES
19 ICOS ICOS ICOS 1569 0.26 0.36 YES
20 ZAP70 ZAP70 ZAP70 1964 0.22 0.36 YES
21 PTPRC PTPRC PTPRC 2138 0.21 0.36 YES
22 AKT3 AKT3 AKT3 2200 0.2 0.37 YES
23 LCP2 LCP2 LCP2 2338 0.19 0.38 YES
24 PDCD1 PDCD1 PDCD1 2533 0.18 0.38 YES
25 IKBKG IKBKG IKBKG 2550 0.18 0.39 YES
26 CD4 CD4 CD4 2573 0.18 0.4 YES
27 IL4 IL4 IL4 2607 0.17 0.41 YES
28 NFATC3 NFATC3 NFATC3 2611 0.17 0.42 YES
29 VAV1 VAV1 VAV1 2816 0.16 0.42 YES
30 JUN JUN JUN 2875 0.16 0.43 YES
31 PDK1 PDK1 PDK1 2899 0.16 0.44 YES
32 PIK3R3 PIK3R3 PIK3R3 2935 0.16 0.44 YES
33 PIK3R5 PIK3R5 PIK3R5 3072 0.15 0.45 YES
34 FYN FYN FYN 3080 0.15 0.46 YES
35 CTLA4 CTLA4 CTLA4 3360 0.13 0.45 NO
36 PIK3CG PIK3CG PIK3CG 3417 0.13 0.46 NO
37 PTPN6 PTPN6 PTPN6 3579 0.12 0.46 NO
38 CARD11 CARD11 CARD11 3898 0.11 0.44 NO
39 PLCG1 PLCG1 PLCG1 4048 0.11 0.44 NO
40 PIK3CD PIK3CD PIK3CD 4305 0.099 0.44 NO
41 CBL CBL CBL 4751 0.087 0.42 NO
42 NFKBIB NFKBIB NFKBIB 4910 0.082 0.41 NO
43 MAP3K14 MAP3K14 MAP3K14 4933 0.082 0.42 NO
44 CHUK CHUK CHUK 4971 0.081 0.42 NO
45 AKT1 AKT1 AKT1 5281 0.075 0.41 NO
46 MAPK9 MAPK9 MAPK9 5295 0.075 0.41 NO
47 GSK3B GSK3B GSK3B 5604 0.068 0.4 NO
48 PPP3R2 PPP3R2 PPP3R2 5608 0.068 0.41 NO
49 PIK3R2 PIK3R2 PIK3R2 5892 0.062 0.4 NO
50 IL10 IL10 IL10 6344 0.053 0.37 NO
51 IL5 IL5 IL5 6352 0.053 0.38 NO
52 TEC TEC TEC 6460 0.051 0.37 NO
53 PPP3CC PPP3CC PPP3CC 6490 0.05 0.38 NO
54 NCK1 NCK1 NCK1 6534 0.05 0.38 NO
55 MAP2K1 MAP2K1 MAP2K1 6654 0.048 0.37 NO
56 NRAS NRAS NRAS 6801 0.045 0.37 NO
57 FOS FOS FOS 6986 0.042 0.36 NO
58 IKBKB IKBKB IKBKB 7407 0.035 0.34 NO
59 MAPK12 MAPK12 MAPK12 7573 0.032 0.33 NO
60 PAK2 PAK2 PAK2 7671 0.03 0.33 NO
61 PIK3CB PIK3CB PIK3CB 7695 0.03 0.33 NO
62 KRAS KRAS KRAS 7905 0.026 0.32 NO
63 PPP3R1 PPP3R1 PPP3R1 8009 0.024 0.32 NO
64 MAP3K7 MAP3K7 MAP3K7 8116 0.022 0.31 NO
65 PPP3CB PPP3CB PPP3CB 8385 0.018 0.3 NO
66 CDK4 CDK4 CDK4 8442 0.017 0.3 NO
67 RAF1 RAF1 RAF1 8578 0.015 0.29 NO
68 MAPK14 MAPK14 MAPK14 8934 0.0093 0.27 NO
69 SOS2 SOS2 SOS2 9070 0.0071 0.26 NO
70 AKT2 AKT2 AKT2 9213 0.0044 0.26 NO
71 RELA RELA RELA 9317 0.0028 0.25 NO
72 CDC42 CDC42 CDC42 9326 0.0027 0.25 NO
73 PAK1 PAK1 PAK1 9352 0.0023 0.25 NO
74 MAP2K2 MAP2K2 MAP2K2 9429 0.00098 0.25 NO
75 NFKB1 NFKB1 NFKB1 9539 -0.0014 0.24 NO
76 CSF2 CSF2 CSF2 9971 -0.0096 0.22 NO
77 MALT1 MALT1 MALT1 10016 -0.01 0.22 NO
78 GRB2 GRB2 GRB2 10051 -0.011 0.22 NO
79 RHOA RHOA RHOA 10619 -0.022 0.18 NO
80 BCL10 BCL10 BCL10 10744 -0.024 0.18 NO
81 MAP2K7 MAP2K7 MAP2K7 10975 -0.029 0.17 NO
82 MAPK11 MAPK11 MAPK11 11120 -0.032 0.16 NO
83 PPP3CA PPP3CA PPP3CA 11320 -0.038 0.16 NO
84 DLG1 DLG1 DLG1 11655 -0.046 0.14 NO
85 MAPK13 MAPK13 MAPK13 11721 -0.048 0.14 NO
86 MAPK1 MAPK1 MAPK1 11892 -0.052 0.13 NO
87 CBLC CBLC CBLC 12034 -0.057 0.13 NO
88 PIK3CA PIK3CA PIK3CA 12318 -0.065 0.12 NO
89 NFKBIA NFKBIA NFKBIA 12520 -0.072 0.11 NO
90 CHP CHP CHP 12566 -0.074 0.11 NO
91 PAK4 PAK4 PAK4 12775 -0.081 0.11 NO
92 PAK3 PAK3 PAK3 12971 -0.088 0.1 NO
93 TNF TNF TNF 13059 -0.092 0.1 NO
94 SOS1 SOS1 SOS1 13324 -0.1 0.097 NO
95 MAPK3 MAPK3 MAPK3 13417 -0.11 0.099 NO
96 VAV2 VAV2 VAV2 13613 -0.12 0.096 NO
97 NFKBIE NFKBIE NFKBIE 13659 -0.12 0.1 NO
98 IL2 IL2 IL2 14146 -0.14 0.085 NO
99 IFNG IFNG IFNG 14265 -0.15 0.088 NO
100 NCK2 NCK2 NCK2 14332 -0.16 0.095 NO
101 NFATC1 NFATC1 NFATC1 14715 -0.18 0.086 NO
102 NFAT5 NFAT5 NFAT5 15066 -0.2 0.08 NO
103 MAP3K8 MAP3K8 MAP3K8 15155 -0.21 0.09 NO
104 CBLB CBLB CBLB 15454 -0.24 0.089 NO
105 PAK6 PAK6 PAK6 15720 -0.27 0.093 NO
106 NFATC2 NFATC2 NFATC2 16310 -0.34 0.083 NO
107 NFATC4 NFATC4 NFATC4 16550 -0.38 0.095 NO

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

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

Table 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 CD40LG CD40LG CD40LG 288 0.56 0.064 YES
2 RAG2 RAG2 RAG2 681 0.39 0.099 YES
3 IL7R IL7R IL7R 844 0.36 0.14 YES
4 CD3D CD3D CD3D 971 0.34 0.18 YES
5 IGLL1 IGLL1 IGLL1 979 0.34 0.23 YES
6 CD79A CD79A CD79A 1012 0.33 0.28 YES
7 CD19 CD19 CD19 1068 0.32 0.32 YES
8 CD3E CD3E CD3E 1088 0.32 0.37 YES
9 TNFRSF13B TNFRSF13B TNFRSF13B 1099 0.32 0.41 YES
10 ADA ADA ADA 1252 0.3 0.44 YES
11 CD8B CD8B CD8B 1435 0.27 0.48 YES
12 LCK LCK LCK 1468 0.27 0.51 YES
13 RAG1 RAG1 RAG1 1522 0.27 0.55 YES
14 ICOS ICOS ICOS 1569 0.26 0.58 YES
15 IL2RG IL2RG IL2RG 1942 0.22 0.59 YES
16 ZAP70 ZAP70 ZAP70 1964 0.22 0.62 YES
17 PTPRC PTPRC PTPRC 2138 0.21 0.64 YES
18 AICDA AICDA AICDA 2431 0.19 0.66 YES
19 IKBKG IKBKG IKBKG 2550 0.18 0.67 YES
20 CD4 CD4 CD4 2573 0.18 0.7 YES
21 AIRE AIRE AIRE 3158 0.14 0.69 NO
22 TNFRSF13C TNFRSF13C TNFRSF13C 3618 0.12 0.68 NO
23 JAK3 JAK3 JAK3 5247 0.076 0.6 NO
24 RFXANK RFXANK RFXANK 6152 0.057 0.56 NO
25 TAP2 TAP2 TAP2 7710 0.029 0.48 NO
26 BTK BTK BTK 8051 0.024 0.46 NO
27 CIITA CIITA CIITA 8111 0.023 0.46 NO
28 RFXAP RFXAP RFXAP 8294 0.02 0.46 NO
29 UNG UNG UNG 8593 0.015 0.44 NO
30 RFX5 RFX5 RFX5 9206 0.0045 0.41 NO
31 TAP1 TAP1 TAP1 9345 0.0024 0.4 NO
32 BLNK BLNK BLNK 11551 -0.043 0.29 NO
33 DCLRE1C DCLRE1C DCLRE1C 13389 -0.1 0.2 NO
34 CD40 CD40 CD40 17033 -0.47 0.068 NO

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

Figure S16.  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

genes ES table in pathway: KEGG DRUG METABOLISM OTHER ENZYMES

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 PPARGC1A PPARGC1A PPARGC1A 102 0.8 0.2 YES
2 HDAC9 HDAC9 HDAC9 461 0.46 0.3 YES
3 HIST2H3C HIST2H3C HIST2H3C 1418 0.28 0.32 YES
4 NR0B1 NR0B1 NR0B1 2631 0.17 0.3 YES
5 HDAC10 HDAC10 HDAC10 2680 0.17 0.34 YES
6 HDAC4 HDAC4 HDAC4 3354 0.13 0.34 YES
7 BRCA1 BRCA1 BRCA1 3430 0.13 0.37 YES
8 GRIP1 GRIP1 GRIP1 4590 0.091 0.33 YES
9 HDAC7 HDAC7 HDAC7 4659 0.089 0.35 YES
10 HDAC8 HDAC8 HDAC8 5132 0.078 0.35 YES
11 HDAC3 HDAC3 HDAC3 5241 0.076 0.36 YES
12 HDAC11 HDAC11 HDAC11 5531 0.069 0.36 YES
13 NRIP1 NRIP1 NRIP1 5636 0.067 0.38 YES
14 HDAC6 HDAC6 HDAC6 5751 0.065 0.39 YES
15 SRA1 SRA1 SRA1 6867 0.044 0.34 NO
16 ESR1 ESR1 ESR1 7154 0.039 0.33 NO
17 PHB2 PHB2 PHB2 7471 0.033 0.32 NO
18 ERCC3 ERCC3 ERCC3 7537 0.032 0.33 NO
19 HDAC1 HDAC1 HDAC1 7610 0.031 0.33 NO
20 HDAC2 HDAC2 HDAC2 7668 0.03 0.34 NO
21 GTF2E1 GTF2E1 GTF2E1 8351 0.019 0.3 NO
22 TBP TBP TBP 9257 0.0038 0.26 NO
23 GTF2F1 GTF2F1 GTF2F1 10013 -0.01 0.22 NO
24 PELP1 PELP1 PELP1 10645 -0.022 0.19 NO
25 NCOR2 NCOR2 NCOR2 11029 -0.03 0.18 NO
26 MED1 MED1 MED1 11228 -0.035 0.17 NO
27 CREBBP CREBBP CREBBP 11580 -0.044 0.17 NO
28 EP300 EP300 EP300 11775 -0.049 0.17 NO
29 POLR2A POLR2A POLR2A 12028 -0.057 0.17 NO
30 SPEN SPEN SPEN 12458 -0.07 0.16 NO
31 GTF2A1 GTF2A1 GTF2A1 12560 -0.073 0.18 NO
32 CARM1 CARM1 CARM1 12708 -0.078 0.19 NO
33 HDAC5 HDAC5 HDAC5 13728 -0.12 0.17 NO
34 CCND1 CCND1 CCND1 16076 -0.31 0.12 NO

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

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM OTHER ENZYMES, 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 DNA REPLICATION

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 VAV3 VAV3 VAV3 165 0.7 0.077 YES
2 PLA2G2D PLA2G2D PLA2G2D 816 0.36 0.086 YES
3 MAP2K6 MAP2K6 MAP2K6 843 0.36 0.13 YES
4 IL13 IL13 IL13 1052 0.33 0.16 YES
5 PRKCB PRKCB PRKCB 1157 0.31 0.19 YES
6 LAT LAT LAT 1512 0.27 0.2 YES
7 PIK3R1 PIK3R1 PIK3R1 1516 0.27 0.24 YES
8 RAC2 RAC2 RAC2 1931 0.22 0.24 YES
9 AKT3 AKT3 AKT3 2200 0.2 0.25 YES
10 LCP2 LCP2 LCP2 2338 0.19 0.26 YES
11 IL4 IL4 IL4 2607 0.17 0.27 YES
12 PLA2G5 PLA2G5 PLA2G5 2615 0.17 0.29 YES
13 PLA2G1B PLA2G1B PLA2G1B 2689 0.17 0.31 YES
14 VAV1 VAV1 VAV1 2816 0.16 0.32 YES
15 PDK1 PDK1 PDK1 2899 0.16 0.34 YES
16 PIK3R3 PIK3R3 PIK3R3 2935 0.16 0.35 YES
17 PIK3R5 PIK3R5 PIK3R5 3072 0.15 0.36 YES
18 FYN FYN FYN 3080 0.15 0.38 YES
19 GAB2 GAB2 GAB2 3279 0.14 0.39 YES
20 PIK3CG PIK3CG PIK3CG 3417 0.13 0.4 YES
21 PLCG1 PLCG1 PLCG1 4048 0.11 0.38 NO
22 PIK3CD PIK3CD PIK3CD 4305 0.099 0.37 NO
23 AKT1 AKT1 AKT1 5281 0.075 0.33 NO
24 MAPK9 MAPK9 MAPK9 5295 0.075 0.34 NO
25 PLA2G6 PLA2G6 PLA2G6 5417 0.072 0.34 NO
26 PIK3R2 PIK3R2 PIK3R2 5892 0.062 0.32 NO
27 PLA2G2A PLA2G2A PLA2G2A 6189 0.056 0.31 NO
28 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 6218 0.056 0.32 NO
29 IL5 IL5 IL5 6352 0.053 0.32 NO
30 SYK SYK SYK 6561 0.049 0.31 NO
31 MAP2K1 MAP2K1 MAP2K1 6654 0.048 0.31 NO
32 NRAS NRAS NRAS 6801 0.045 0.31 NO
33 MAP2K3 MAP2K3 MAP2K3 7075 0.04 0.3 NO
34 MAPK12 MAPK12 MAPK12 7573 0.032 0.28 NO
35 PIK3CB PIK3CB PIK3CB 7695 0.03 0.27 NO
36 KRAS KRAS KRAS 7905 0.026 0.26 NO
37 MAPK10 MAPK10 MAPK10 7980 0.025 0.26 NO
38 BTK BTK BTK 8051 0.024 0.26 NO
39 INPP5D INPP5D INPP5D 8292 0.02 0.25 NO
40 RAF1 RAF1 RAF1 8578 0.015 0.24 NO
41 MS4A2 MS4A2 MS4A2 8917 0.0097 0.22 NO
42 MAPK14 MAPK14 MAPK14 8934 0.0093 0.22 NO
43 SOS2 SOS2 SOS2 9070 0.0071 0.21 NO
44 AKT2 AKT2 AKT2 9213 0.0044 0.21 NO
45 MAP2K2 MAP2K2 MAP2K2 9429 0.00098 0.2 NO
46 MAP2K4 MAP2K4 MAP2K4 9590 -0.0024 0.19 NO
47 CSF2 CSF2 CSF2 9971 -0.0096 0.17 NO
48 GRB2 GRB2 GRB2 10051 -0.011 0.16 NO
49 PRKCA PRKCA PRKCA 10559 -0.021 0.14 NO
50 PLCG2 PLCG2 PLCG2 10613 -0.022 0.14 NO
51 MAPK8 MAPK8 MAPK8 10668 -0.023 0.14 NO
52 MAP2K7 MAP2K7 MAP2K7 10975 -0.029 0.12 NO
53 MAPK11 MAPK11 MAPK11 11120 -0.032 0.12 NO
54 MAPK13 MAPK13 MAPK13 11721 -0.048 0.093 NO
55 MAPK1 MAPK1 MAPK1 11892 -0.052 0.09 NO
56 RAC1 RAC1 RAC1 12183 -0.062 0.082 NO
57 RAC3 RAC3 RAC3 12241 -0.063 0.087 NO
58 PIK3CA PIK3CA PIK3CA 12318 -0.065 0.091 NO
59 PLA2G12A PLA2G12A PLA2G12A 12689 -0.078 0.08 NO
60 TNF TNF TNF 13059 -0.092 0.071 NO
61 SOS1 SOS1 SOS1 13324 -0.1 0.069 NO
62 MAPK3 MAPK3 MAPK3 13417 -0.11 0.077 NO
63 VAV2 VAV2 VAV2 13613 -0.12 0.08 NO
64 FCER1G FCER1G FCER1G 13707 -0.12 0.09 NO
65 FCER1A FCER1A FCER1A 13999 -0.14 0.091 NO
66 LYN LYN LYN 14056 -0.14 0.1 NO
67 PLA2G10 PLA2G10 PLA2G10 14338 -0.16 0.11 NO
68 PLA2G4A PLA2G4A PLA2G4A 14465 -0.16 0.12 NO
69 PRKCD PRKCD PRKCD 14599 -0.17 0.14 NO
70 PRKCE PRKCE PRKCE 15457 -0.24 0.12 NO
71 PLA2G3 PLA2G3 PLA2G3 16062 -0.31 0.12 NO

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

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DNA REPLICATION, 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 TCR PATHWAY 43 genes.ES.table 0.35 0.9 0.6 1 1 0.28 0.12 0.25 1 0.78
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.27 0.95 0.51 1 1 0.12 0.075 0.11 1 0.73
KEGG OXIDATIVE PHOSPHORYLATION 114 genes.ES.table 0.38 1.1 0.44 1 1 0.69 0.38 0.43 1 0.55
KEGG PYRIMIDINE METABOLISM 97 genes.ES.table 0.26 0.98 0.5 1 1 0.39 0.26 0.29 1 0.78
KEGG RIBOSOME 85 genes.ES.table 0.65 1.6 0.064 1 0.76 0.94 0.33 0.63 0.72 0.42
KEGG RNA DEGRADATION 56 genes.ES.table 0.35 1.4 0.18 1 0.96 0.38 0.27 0.27 1 0.67
KEGG RNA POLYMERASE 28 genes.ES.table 0.38 1.3 0.21 1 0.98 0.43 0.26 0.32 1 0.61
KEGG DNA REPLICATION 35 genes.ES.table 0.55 1.2 0.38 1 1 0.66 0.2 0.52 0.98 0.49
KEGG SPLICEOSOME 125 genes.ES.table 0.39 1.4 0.19 1 0.96 0.59 0.36 0.38 1 0.55
KEGG PROTEASOME 43 genes.ES.table 0.41 1.1 0.43 1 1 0.65 0.36 0.42 1 0.57
genes ES table in pathway: BIOCARTA TCR 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 RPL21 RPL21 RPL21 505 0.38 0.021 YES
2 RPL3L RPL3L RPL3L 792 0.33 0.047 YES
3 RPS28 RPS28 RPS28 2503 0.15 -0.027 YES
4 RPSA RPSA RPSA 2810 0.14 -0.026 YES
5 RPL18A RPL18A RPL18A 2835 0.14 -0.01 YES
6 RPLP2 RPLP2 RPLP2 3188 0.12 -0.014 YES
7 RPL39 RPL39 RPL39 3270 0.12 -0.0033 YES
8 RPL14 RPL14 RPL14 3390 0.12 0.0049 YES
9 RPL22L1 RPL22L1 RPL22L1 3413 0.12 0.018 YES
10 RPL24 RPL24 RPL24 3417 0.12 0.033 YES
11 RPS7 RPS7 RPS7 3490 0.11 0.043 YES
12 RPL28 RPL28 RPL28 3531 0.11 0.055 YES
13 RPL34 RPL34 RPL34 3594 0.11 0.066 YES
14 RPL13 RPL13 RPL13 3611 0.11 0.078 YES
15 RPL29 RPL29 RPL29 3615 0.11 0.092 YES
16 RPS8 RPS8 RPS8 3626 0.11 0.1 YES
17 RPS27L RPS27L RPS27L 3628 0.11 0.12 YES
18 RPS9 RPS9 RPS9 3633 0.11 0.13 YES
19 RPL32 RPL32 RPL32 3634 0.11 0.15 YES
20 RPS10 RPS10 RPS10 3639 0.11 0.16 YES
21 RPL27A RPL27A RPL27A 3739 0.1 0.17 YES
22 RPS24 RPS24 RPS24 3768 0.1 0.18 YES
23 FAU FAU FAU 3806 0.1 0.19 YES
24 UBA52 UBA52 UBA52 3827 0.1 0.2 YES
25 RPL36AL RPL36AL RPL36AL 3844 0.1 0.21 YES
26 RPL23A RPL23A RPL23A 3893 0.1 0.22 YES
27 RPL35A RPL35A RPL35A 3894 0.1 0.24 YES
28 RPS21 RPS21 RPS21 3902 0.1 0.25 YES
29 RPS13 RPS13 RPS13 3909 0.1 0.26 YES
30 RPS16 RPS16 RPS16 3931 0.099 0.27 YES
31 RPS23 RPS23 RPS23 3960 0.098 0.28 YES
32 RPL35 RPL35 RPL35 3971 0.098 0.3 YES
33 RPS11 RPS11 RPS11 3986 0.097 0.31 YES
34 RPS19 RPS19 RPS19 4038 0.096 0.32 YES
35 RPS29 RPS29 RPS29 4094 0.094 0.33 YES
36 RPL22 RPL22 RPL22 4182 0.092 0.33 YES
37 RPL26 RPL26 RPL26 4206 0.092 0.34 YES
38 RPS6 RPS6 RPS6 4226 0.091 0.35 YES
39 RPL27 RPL27 RPL27 4239 0.091 0.36 YES
40 RPL37A RPL37A RPL37A 4269 0.09 0.38 YES
41 RPL37 RPL37 RPL37 4281 0.09 0.38 YES
42 RPS12 RPS12 RPS12 4304 0.09 0.4 YES
43 RPL31 RPL31 RPL31 4310 0.09 0.41 YES
44 RPS20 RPS20 RPS20 4340 0.088 0.42 YES
45 RPS3A RPS3A RPS3A 4344 0.088 0.43 YES
46 RPS3 RPS3 RPS3 4411 0.087 0.44 YES
47 RPS17 RPS17 RPS17 4417 0.086 0.45 YES
48 RPS15 RPS15 RPS15 4433 0.086 0.46 YES
49 RPL11 RPL11 RPL11 4437 0.086 0.47 YES
50 RPL5 RPL5 RPL5 4445 0.086 0.48 YES
51 RPLP1 RPLP1 RPLP1 4507 0.084 0.48 YES
52 RPL26L1 RPL26L1 RPL26L1 4539 0.083 0.49 YES
53 RPS2 RPS2 RPS2 4592 0.082 0.5 YES
54 RPL19 RPL19 RPL19 4593 0.082 0.51 YES
55 RSL24D1 RSL24D1 RSL24D1 4600 0.082 0.52 YES
56 RPL38 RPL38 RPL38 4660 0.08 0.53 YES
57 RPL23 RPL23 RPL23 4687 0.08 0.54 YES
58 RPS5 RPS5 RPS5 4710 0.079 0.55 YES
59 RPL36 RPL36 RPL36 4745 0.078 0.55 YES
60 RPL36A RPL36A RPL36A 4757 0.078 0.56 YES
61 RPL15 RPL15 RPL15 4861 0.075 0.57 YES
62 RPL10A RPL10A RPL10A 4886 0.074 0.57 YES
63 RPLP0 RPLP0 RPLP0 4908 0.074 0.58 YES
64 RPS27A RPS27A RPS27A 5014 0.072 0.59 YES
65 RPS26 RPS26 RPS26 5042 0.071 0.59 YES
66 RPL4 RPL4 RPL4 5117 0.069 0.6 YES
67 RPL6 RPL6 RPL6 5165 0.068 0.6 YES
68 RPL13A RPL13A RPL13A 5179 0.068 0.61 YES
69 RPL30 RPL30 RPL30 5190 0.068 0.62 YES
70 RPS25 RPS25 RPS25 5223 0.067 0.63 YES
71 RPL12 RPL12 RPL12 5299 0.065 0.63 YES
72 RPL41 RPL41 RPL41 5400 0.062 0.63 YES
73 RPL7A RPL7A RPL7A 5526 0.059 0.64 YES
74 RPS18 RPS18 RPS18 5642 0.056 0.64 YES
75 MRPL13 MRPL13 MRPL13 5691 0.056 0.64 YES
76 RPS15A RPS15A RPS15A 5749 0.054 0.64 YES
77 RPL10 RPL10 RPL10 5885 0.051 0.64 YES
78 RPL9 RPL9 RPL9 5921 0.05 0.65 YES
79 RPL7 RPL7 RPL7 6008 0.048 0.65 YES
80 RPS4X RPS4X RPS4X 6091 0.047 0.65 YES
81 RPL8 RPL8 RPL8 6287 0.042 0.64 NO
82 RPL17 RPL17 RPL17 6491 0.039 0.64 NO
83 RPL3 RPL3 RPL3 6637 0.036 0.64 NO
84 RPS4Y1 RPS4Y1 RPS4Y1 6986 0.029 0.62 NO
85 RPS27 RPS27 RPS27 8079 0.0064 0.56 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 TCR PATHWAY.

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

genes ES table in pathway: BIOCARTA 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 ENO3 ENO3 ENO3 226 0.48 0.091 YES
2 LSM2 LSM2 LSM2 2036 0.18 0.03 YES
3 EXOSC8 EXOSC8 EXOSC8 2080 0.18 0.066 YES
4 LSM7 LSM7 LSM7 2141 0.17 0.099 YES
5 LSM4 LSM4 LSM4 2581 0.15 0.11 YES
6 LSM5 LSM5 LSM5 2603 0.15 0.14 YES
7 EXOSC5 EXOSC5 EXOSC5 2606 0.15 0.17 YES
8 EXOSC9 EXOSC9 EXOSC9 2824 0.14 0.19 YES
9 LSM3 LSM3 LSM3 2841 0.14 0.22 YES
10 ENO2 ENO2 ENO2 2890 0.14 0.24 YES
11 EXOSC4 EXOSC4 EXOSC4 2908 0.13 0.27 YES
12 EXOSC7 EXOSC7 EXOSC7 3294 0.12 0.27 YES
13 PAPOLB PAPOLB PAPOLB 3503 0.11 0.28 YES
14 CNOT10 CNOT10 CNOT10 3616 0.11 0.3 YES
15 EXOSC1 EXOSC1 EXOSC1 3848 0.1 0.31 YES
16 DCP2 DCP2 DCP2 3905 0.1 0.33 YES
17 DCP1B DCP1B DCP1B 4579 0.082 0.31 YES
18 NAA38 NAA38 NAA38 4672 0.08 0.32 YES
19 DCPS DCPS DCPS 4901 0.074 0.32 YES
20 MPHOSPH6 MPHOSPH6 MPHOSPH6 4913 0.074 0.34 YES
21 EDC4 EDC4 EDC4 4953 0.073 0.35 YES
22 LSM6 LSM6 LSM6 5490 0.06 0.34 NO
23 EXOSC10 EXOSC10 EXOSC10 5995 0.049 0.32 NO
24 EXOSC2 EXOSC2 EXOSC2 6276 0.043 0.31 NO
25 C1D C1D C1D 6355 0.041 0.32 NO
26 CNOT2 CNOT2 CNOT2 6372 0.041 0.33 NO
27 LSM1 LSM1 LSM1 6654 0.036 0.32 NO
28 EXOSC3 EXOSC3 EXOSC3 6693 0.035 0.32 NO
29 CNOT3 CNOT3 CNOT3 6741 0.034 0.33 NO
30 WDR61 WDR61 WDR61 6776 0.033 0.33 NO
31 ENO1 ENO1 ENO1 7162 0.025 0.32 NO
32 EXOSC6 EXOSC6 EXOSC6 7271 0.023 0.32 NO
33 EDC3 EDC3 EDC3 7649 0.015 0.3 NO
34 CNOT6 CNOT6 CNOT6 7666 0.015 0.3 NO
35 SKIV2L SKIV2L SKIV2L 7907 0.01 0.29 NO
36 PARN PARN PARN 8090 0.0061 0.28 NO
37 ZCCHC7 ZCCHC7 ZCCHC7 8484 -0.0021 0.26 NO
38 CNOT6L CNOT6L CNOT6L 8527 -0.0029 0.26 NO
39 CNOT7 CNOT7 CNOT7 8682 -0.0063 0.25 NO
40 DDX6 DDX6 DDX6 9027 -0.013 0.24 NO
41 DCP1A DCP1A DCP1A 9046 -0.014 0.24 NO
42 PAPD7 PAPD7 PAPD7 9459 -0.022 0.22 NO
43 CNOT1 CNOT1 CNOT1 9666 -0.026 0.21 NO
44 HSPD1 HSPD1 HSPD1 9996 -0.033 0.2 NO
45 PAPOLA PAPOLA PAPOLA 10373 -0.041 0.19 NO
46 SKIV2L2 SKIV2L2 SKIV2L2 10526 -0.045 0.19 NO
47 DIS3 DIS3 DIS3 11342 -0.065 0.16 NO
48 XRN2 XRN2 XRN2 11636 -0.072 0.16 NO
49 XRN1 XRN1 XRN1 11963 -0.081 0.16 NO
50 PATL1 PATL1 PATL1 12224 -0.088 0.16 NO
51 CNOT4 CNOT4 CNOT4 12343 -0.092 0.18 NO
52 HSPA9 HSPA9 HSPA9 12370 -0.093 0.2 NO
53 PNPT1 PNPT1 PNPT1 12409 -0.094 0.21 NO
54 PAPOLG PAPOLG PAPOLG 13094 -0.12 0.2 NO
55 RQCD1 RQCD1 RQCD1 13594 -0.14 0.2 NO
56 TTC37 TTC37 TTC37 15570 -0.26 0.15 NO

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

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 CCDC12 CCDC12 CCDC12 1785 0.2 -0.077 YES
2 SF3B5 SF3B5 SF3B5 1996 0.18 -0.068 YES
3 LSM2 LSM2 LSM2 2036 0.18 -0.051 YES
4 LSM7 LSM7 LSM7 2141 0.17 -0.038 YES
5 THOC4 THOC4 THOC4 2148 0.17 -0.02 YES
6 TXNL4A TXNL4A TXNL4A 2211 0.17 -0.0056 YES
7 SNRPF SNRPF SNRPF 2285 0.16 0.008 YES
8 SNRPC SNRPC SNRPC 2287 0.16 0.026 YES
9 SNRPA SNRPA SNRPA 2297 0.16 0.043 YES
10 LSM4 LSM4 LSM4 2581 0.15 0.043 YES
11 LSM5 LSM5 LSM5 2603 0.15 0.058 YES
12 SNRPD1 SNRPD1 SNRPD1 2684 0.14 0.069 YES
13 MAGOHB MAGOHB MAGOHB 2700 0.14 0.083 YES
14 PPIH PPIH PPIH 2708 0.14 0.098 YES
15 SNRPD2 SNRPD2 SNRPD2 2767 0.14 0.11 YES
16 U2AF1 U2AF1 U2AF1 2783 0.14 0.12 YES
17 LSM3 LSM3 LSM3 2841 0.14 0.14 YES
18 SF3A2 SF3A2 SF3A2 2859 0.14 0.15 YES
19 SNRPG SNRPG SNRPG 2898 0.14 0.16 YES
20 MAGOH MAGOH MAGOH 2938 0.13 0.17 YES
21 SNRPA1 SNRPA1 SNRPA1 3017 0.13 0.18 YES
22 SNRPB2 SNRPB2 SNRPB2 3194 0.12 0.19 YES
23 SART1 SART1 SART1 3249 0.12 0.2 YES
24 SNRPB SNRPB SNRPB 3290 0.12 0.21 YES
25 XAB2 XAB2 XAB2 3341 0.12 0.22 YES
26 HNRNPA1 HNRNPA1 HNRNPA1 3419 0.12 0.22 YES
27 SNRPE SNRPE SNRPE 3614 0.11 0.23 YES
28 PHF5A PHF5A PHF5A 3789 0.1 0.23 YES
29 THOC3 THOC3 THOC3 4030 0.096 0.22 YES
30 CWC15 CWC15 CWC15 4110 0.094 0.23 YES
31 SNRPD3 SNRPD3 SNRPD3 4170 0.093 0.24 YES
32 SFRS3 SFRS3 SFRS3 4184 0.092 0.25 YES
33 SF3B14 SF3B14 SF3B14 4240 0.091 0.25 YES
34 PRPF31 PRPF31 PRPF31 4295 0.09 0.26 YES
35 PRPF38A PRPF38A PRPF38A 4302 0.09 0.27 YES
36 PRPF19 PRPF19 PRPF19 4376 0.088 0.27 YES
37 PPIE PPIE PPIE 4457 0.086 0.28 YES
38 CTNNBL1 CTNNBL1 CTNNBL1 4460 0.086 0.29 YES
39 PQBP1 PQBP1 PQBP1 4509 0.084 0.29 YES
40 SYF2 SYF2 SYF2 4649 0.08 0.3 YES
41 NAA38 NAA38 NAA38 4672 0.08 0.3 YES
42 BUD31 BUD31 BUD31 4679 0.08 0.31 YES
43 SFRS9 SFRS9 SFRS9 4774 0.077 0.31 YES
44 NHP2L1 NHP2L1 NHP2L1 4785 0.077 0.32 YES
45 ISY1 ISY1 ISY1 4799 0.077 0.33 YES
46 SNRNP70 SNRNP70 SNRNP70 4838 0.076 0.34 YES
47 RBM17 RBM17 RBM17 4877 0.075 0.34 YES
48 RBM22 RBM22 RBM22 5113 0.069 0.34 YES
49 PRPF6 PRPF6 PRPF6 5169 0.068 0.34 YES
50 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 5276 0.065 0.34 YES
51 TRA2B TRA2B TRA2B 5348 0.064 0.34 YES
52 SF3A3 SF3A3 SF3A3 5432 0.061 0.34 YES
53 LSM6 LSM6 LSM6 5490 0.06 0.35 YES
54 SF3B2 SF3B2 SF3B2 5600 0.057 0.35 YES
55 HNRNPM HNRNPM HNRNPM 5624 0.057 0.35 YES
56 PRPF18 PRPF18 PRPF18 5673 0.056 0.36 YES
57 PUF60 PUF60 PUF60 5738 0.054 0.36 YES
58 BAT1 BAT1 BAT1 5827 0.052 0.36 YES
59 PCBP1 PCBP1 PCBP1 5880 0.051 0.36 YES
60 USP39 USP39 USP39 6097 0.046 0.36 YES
61 DHX38 DHX38 DHX38 6125 0.046 0.36 YES
62 SFRS7 SFRS7 SFRS7 6127 0.046 0.36 YES
63 PPIL1 PPIL1 PPIL1 6183 0.045 0.37 YES
64 RBMX RBMX RBMX 6191 0.044 0.37 YES
65 SNRNP40 SNRNP40 SNRNP40 6231 0.044 0.37 YES
66 HNRNPA3 HNRNPA3 HNRNPA3 6237 0.044 0.38 YES
67 EIF4A3 EIF4A3 EIF4A3 6247 0.043 0.38 YES
68 HNRNPC HNRNPC HNRNPC 6383 0.041 0.38 YES
69 DDX23 DDX23 DDX23 6440 0.04 0.38 YES
70 SFRS4 SFRS4 SFRS4 6481 0.039 0.38 YES
71 ZMAT2 ZMAT2 ZMAT2 6501 0.038 0.38 YES
72 SFRS2 SFRS2 SFRS2 6582 0.037 0.38 YES
73 SF3B4 SF3B4 SF3B4 6644 0.036 0.38 YES
74 THOC1 THOC1 THOC1 6666 0.035 0.39 YES
75 U2AF2 U2AF2 U2AF2 6804 0.032 0.38 NO
76 SFRS1 SFRS1 SFRS1 6996 0.029 0.38 NO
77 SLU7 SLU7 SLU7 7222 0.024 0.36 NO
78 SFRS6 SFRS6 SFRS6 7275 0.023 0.36 NO
79 EFTUD2 EFTUD2 EFTUD2 7276 0.023 0.37 NO
80 HNRNPK HNRNPK HNRNPK 7286 0.023 0.37 NO
81 DHX16 DHX16 DHX16 7332 0.022 0.37 NO
82 SFRS13A SFRS13A SFRS13A 7526 0.018 0.36 NO
83 SNRNP27 SNRNP27 SNRNP27 7704 0.014 0.35 NO
84 PRPF8 PRPF8 PRPF8 7836 0.011 0.35 NO
85 PRPF3 PRPF3 PRPF3 7944 0.0093 0.34 NO
86 SF3B3 SF3B3 SF3B3 7951 0.0092 0.34 NO
87 DHX8 DHX8 DHX8 8019 0.0077 0.34 NO
88 HNRNPU HNRNPU HNRNPU 8081 0.0063 0.34 NO
89 SMNDC1 SMNDC1 SMNDC1 8091 0.0061 0.34 NO
90 SNRNP200 SNRNP200 SNRNP200 8120 0.0055 0.34 NO
91 HSPA8 HSPA8 HSPA8 8158 0.0046 0.33 NO
92 CDC5L CDC5L CDC5L 8296 0.002 0.33 NO
93 SFRS5 SFRS5 SFRS5 8390 -6.1e-07 0.32 NO
94 ACIN1 ACIN1 ACIN1 8556 -0.0034 0.31 NO
95 WBP11 WBP11 WBP11 8572 -0.004 0.31 NO
96 CRNKL1 CRNKL1 CRNKL1 8602 -0.0045 0.31 NO
97 BCAS2 BCAS2 BCAS2 8714 -0.0069 0.31 NO
98 TRA2A TRA2A TRA2A 8903 -0.01 0.3 NO
99 RBM8A RBM8A RBM8A 9016 -0.013 0.29 NO
100 PRPF4 PRPF4 PRPF4 9053 -0.014 0.29 NO
101 SNW1 SNW1 SNW1 9200 -0.017 0.28 NO
102 DDX5 DDX5 DDX5 9260 -0.018 0.28 NO
103 CHERP CHERP CHERP 9293 -0.019 0.28 NO
104 PLRG1 PLRG1 PLRG1 9426 -0.022 0.28 NO
105 DHX15 DHX15 DHX15 9450 -0.022 0.28 NO
106 CDC40 CDC40 CDC40 9476 -0.023 0.28 NO
107 DDX42 DDX42 DDX42 9560 -0.024 0.28 NO
108 DDX46 DDX46 DDX46 9819 -0.029 0.27 NO
109 SF3A1 SF3A1 SF3A1 9835 -0.029 0.27 NO
110 PRPF38B PRPF38B PRPF38B 9879 -0.03 0.27 NO
111 SFRS2B SFRS2B SFRS2B 9884 -0.03 0.27 NO
112 TCERG1 TCERG1 TCERG1 9917 -0.031 0.28 NO
113 NCBP1 NCBP1 NCBP1 10116 -0.036 0.27 NO
114 SF3B1 SF3B1 SF3B1 10319 -0.04 0.26 NO
115 PRPF40A PRPF40A PRPF40A 10800 -0.051 0.24 NO
116 SR140 SR140 SR140 11245 -0.062 0.22 NO
117 HSPA1L HSPA1L HSPA1L 11503 -0.069 0.22 NO
118 THOC2 THOC2 THOC2 12021 -0.083 0.2 NO
119 PRPF40B PRPF40B PRPF40B 12105 -0.085 0.2 NO
120 AQR AQR AQR 12405 -0.094 0.2 NO
121 RBM25 RBM25 RBM25 12419 -0.094 0.2 NO
122 HSPA1A HSPA1A HSPA1A 13138 -0.12 0.18 NO
123 HSPA6 HSPA6 HSPA6 13236 -0.12 0.18 NO
124 HSPA1B HSPA1B HSPA1B 14226 -0.17 0.15 NO
125 HSPA2 HSPA2 HSPA2 18120 -0.7 0.009 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 OXIDATIVE PHOSPHORYLATION.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, 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 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 ZNRD1 ZNRD1 ZNRD1 1782 0.2 -0.0049 YES
2 POLR2I POLR2I POLR2I 2798 0.14 0.0033 YES
3 POLR2F POLR2F POLR2F 2911 0.13 0.059 YES
4 POLR2L POLR2L POLR2L 3159 0.12 0.1 YES
5 POLR3K POLR3K POLR3K 3477 0.11 0.14 YES
6 POLR2J2 POLR2J2 POLR2J2 3547 0.11 0.18 YES
7 POLR2J POLR2J POLR2J 3643 0.11 0.23 YES
8 POLR2G POLR2G POLR2G 3767 0.1 0.27 YES
9 POLR2D POLR2D POLR2D 3872 0.1 0.31 YES
10 POLR1C POLR1C POLR1C 3963 0.098 0.35 YES
11 POLR2E POLR2E POLR2E 4688 0.08 0.35 YES
12 POLR1D POLR1D POLR1D 4747 0.078 0.38 YES
13 POLR3GL POLR3GL POLR3GL 5781 0.054 0.35 NO
14 POLR1E POLR1E POLR1E 6280 0.043 0.34 NO
15 POLR2K POLR2K POLR2K 6398 0.04 0.35 NO
16 POLR2C POLR2C POLR2C 6487 0.039 0.36 NO
17 POLR3H POLR3H POLR3H 7061 0.027 0.34 NO
18 POLR3F POLR3F POLR3F 7678 0.015 0.32 NO
19 POLR3C POLR3C POLR3C 8008 0.0078 0.3 NO
20 POLR2A POLR2A POLR2A 8745 -0.0077 0.27 NO
21 POLR2J3 POLR2J3 POLR2J3 9264 -0.018 0.25 NO
22 POLR2B POLR2B POLR2B 10560 -0.045 0.2 NO
23 POLR3B POLR3B POLR3B 10950 -0.055 0.2 NO
24 POLR3D POLR3D POLR3D 11781 -0.076 0.19 NO
25 POLR1B POLR1B POLR1B 11850 -0.078 0.22 NO
26 POLR3G POLR3G POLR3G 11980 -0.082 0.25 NO
27 POLR1A POLR1A POLR1A 12305 -0.091 0.28 NO
28 POLR3A POLR3A POLR3A 12966 -0.11 0.29 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 PYRIMIDINE METABOLISM.

Figure S28.  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 RIBOSOME

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 NEIL3 NEIL3 NEIL3 550 0.37 0.076 YES
2 POLE2 POLE2 POLE2 942 0.3 0.14 YES
3 NEIL1 NEIL1 NEIL1 1079 0.28 0.21 YES
4 FEN1 FEN1 FEN1 1668 0.21 0.24 YES
5 POLD1 POLD1 POLD1 2481 0.15 0.24 YES
6 PCNA PCNA PCNA 2549 0.15 0.28 YES
7 MUTYH MUTYH MUTYH 2712 0.14 0.31 YES
8 POLD2 POLD2 POLD2 2720 0.14 0.35 YES
9 POLE POLE POLE 2733 0.14 0.39 YES
10 NTHL1 NTHL1 NTHL1 2935 0.13 0.42 YES
11 LIG1 LIG1 LIG1 2962 0.13 0.46 YES
12 MPG MPG MPG 3217 0.12 0.48 YES
13 OGG1 OGG1 OGG1 3818 0.1 0.47 NO
14 XRCC1 XRCC1 XRCC1 4604 0.082 0.45 NO
15 POLD4 POLD4 POLD4 5170 0.068 0.44 NO
16 POLD3 POLD3 POLD3 5722 0.055 0.43 NO
17 POLE4 POLE4 POLE4 5743 0.054 0.44 NO
18 POLB POLB POLB 5947 0.05 0.44 NO
19 POLE3 POLE3 POLE3 5991 0.049 0.46 NO
20 NEIL2 NEIL2 NEIL2 6147 0.045 0.46 NO
21 SMUG1 SMUG1 SMUG1 6427 0.04 0.46 NO
22 MBD4 MBD4 MBD4 6697 0.034 0.45 NO
23 UNG UNG UNG 6719 0.034 0.46 NO
24 TDG TDG TDG 6984 0.029 0.45 NO
25 APEX1 APEX1 APEX1 7876 0.011 0.41 NO
26 POLL POLL POLL 8732 -0.0073 0.36 NO
27 PARP2 PARP2 PARP2 9430 -0.022 0.33 NO
28 APEX2 APEX2 APEX2 10543 -0.045 0.28 NO
29 LIG3 LIG3 LIG3 10937 -0.054 0.28 NO
30 PARP1 PARP1 PARP1 11975 -0.082 0.24 NO
31 PARP4 PARP4 PARP4 12146 -0.086 0.26 NO
32 PARP3 PARP3 PARP3 15828 -0.28 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 RIBOSOME.

Figure S30.  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 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 AQP2 AQP2 AQP2 41 0.68 0.12 YES
2 CREB3L3 CREB3L3 CREB3L3 66 0.62 0.23 YES
3 AVPR2 AVPR2 AVPR2 300 0.45 0.3 YES
4 CREB3L1 CREB3L1 CREB3L1 1042 0.29 0.31 YES
5 ARHGDIB ARHGDIB ARHGDIB 1620 0.22 0.32 YES
6 PRKACB PRKACB PRKACB 3654 0.11 0.23 NO
7 DYNLL1 DYNLL1 DYNLL1 3866 0.1 0.24 NO
8 AQP3 AQP3 AQP3 4639 0.081 0.21 NO
9 VAMP2 VAMP2 VAMP2 4883 0.074 0.21 NO
10 RAB11B RAB11B RAB11B 5060 0.07 0.21 NO
11 DCTN2 DCTN2 DCTN2 5184 0.068 0.22 NO
12 ARHGDIA ARHGDIA ARHGDIA 5430 0.062 0.22 NO
13 GNAS GNAS GNAS 5462 0.06 0.22 NO
14 DYNC2LI1 DYNC2LI1 DYNC2LI1 5580 0.058 0.23 NO
15 CREB3L4 CREB3L4 CREB3L4 5596 0.057 0.24 NO
16 DCTN1 DCTN1 DCTN1 6866 0.031 0.18 NO
17 DYNC1LI1 DYNC1LI1 DYNC1LI1 6952 0.03 0.18 NO
18 CREB3 CREB3 CREB3 7264 0.023 0.16 NO
19 PRKACA PRKACA PRKACA 7747 0.013 0.14 NO
20 STX4 STX4 STX4 8233 0.0032 0.11 NO
21 RAB5A RAB5A RAB5A 8890 -0.01 0.079 NO
22 CREB1 CREB1 CREB1 9078 -0.014 0.071 NO
23 DYNC2H1 DYNC2H1 DYNC2H1 9486 -0.023 0.053 NO
24 DCTN5 DCTN5 DCTN5 9534 -0.024 0.055 NO
25 DYNC1H1 DYNC1H1 DYNC1H1 10170 -0.037 0.026 NO
26 RAB5B RAB5B RAB5B 10203 -0.037 0.032 NO
27 RAB5C RAB5C RAB5C 10251 -0.039 0.036 NO
28 DYNC1I2 DYNC1I2 DYNC1I2 10256 -0.039 0.043 NO
29 RAB11A RAB11A RAB11A 10702 -0.049 0.027 NO
30 DCTN4 DCTN4 DCTN4 10934 -0.054 0.025 NO
31 DCTN6 DCTN6 DCTN6 11264 -0.062 0.018 NO
32 CREB3L2 CREB3L2 CREB3L2 11266 -0.062 0.029 NO
33 DYNC1LI2 DYNC1LI2 DYNC1LI2 11379 -0.066 0.035 NO
34 PRKX PRKX PRKX 12125 -0.086 0.0099 NO
35 NSF NSF NSF 12486 -0.096 0.0077 NO
36 ADCY9 ADCY9 ADCY9 13061 -0.12 -0.0026 NO
37 DYNLL2 DYNLL2 DYNLL2 13636 -0.14 -0.0087 NO
38 ADCY6 ADCY6 ADCY6 14111 -0.16 -0.0053 NO
39 AQP4 AQP4 AQP4 14452 -0.18 0.0087 NO
40 CREB5 CREB5 CREB5 16661 -0.36 -0.047 NO
41 DYNC1I1 DYNC1I1 DYNC1I1 18166 -0.74 0.0064 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 RNA DEGRADATION.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA 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 RNA POLYMERASE

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 SLC6A3 SLC6A3 SLC6A3 97 0.59 0.049 YES
2 COX4I2 COX4I2 COX4I2 389 0.42 0.072 YES
3 SNCA SNCA SNCA 403 0.41 0.11 YES
4 SNCAIP SNCAIP SNCAIP 820 0.32 0.12 YES
5 COX6B2 COX6B2 COX6B2 880 0.31 0.14 YES
6 NDUFA4L2 NDUFA4L2 NDUFA4L2 2534 0.15 0.065 YES
7 NDUFS6 NDUFS6 NDUFS6 2562 0.15 0.078 YES
8 ATP5J ATP5J ATP5J 2661 0.15 0.086 YES
9 NDUFB7 NDUFB7 NDUFB7 2925 0.13 0.084 YES
10 NDUFA7 NDUFA7 NDUFA7 2929 0.13 0.096 YES
11 COX4I1 COX4I1 COX4I1 2992 0.13 0.1 YES
12 NDUFS8 NDUFS8 NDUFS8 3031 0.13 0.11 YES
13 NDUFA3 NDUFA3 NDUFA3 3137 0.12 0.12 YES
14 NDUFB1 NDUFB1 NDUFB1 3141 0.12 0.13 YES
15 NDUFS5 NDUFS5 NDUFS5 3161 0.12 0.14 YES
16 NDUFA2 NDUFA2 NDUFA2 3211 0.12 0.15 YES
17 COX7A2 COX7A2 COX7A2 3289 0.12 0.16 YES
18 UBE2J2 UBE2J2 UBE2J2 3321 0.12 0.17 YES
19 NDUFB10 NDUFB10 NDUFB10 3337 0.12 0.18 YES
20 NDUFB8 NDUFB8 NDUFB8 3387 0.12 0.18 YES
21 NDUFS3 NDUFS3 NDUFS3 3410 0.12 0.19 YES
22 UQCR10 UQCR10 UQCR10 3428 0.11 0.2 YES
23 ATP5O ATP5O ATP5O 3479 0.11 0.21 YES
24 COX6B1 COX6B1 COX6B1 3650 0.11 0.21 YES
25 HTRA2 HTRA2 HTRA2 3651 0.11 0.22 YES
26 NDUFV2 NDUFV2 NDUFV2 3653 0.11 0.23 YES
27 ATP5E ATP5E ATP5E 3897 0.1 0.23 YES
28 ATP5D ATP5D ATP5D 3958 0.098 0.23 YES
29 NDUFB2 NDUFB2 NDUFB2 3973 0.098 0.24 YES
30 UBB UBB UBB 4129 0.094 0.24 YES
31 ATP5G2 ATP5G2 ATP5G2 4135 0.094 0.25 YES
32 UBE2L3 UBE2L3 UBE2L3 4277 0.09 0.25 YES
33 UQCRQ UQCRQ UQCRQ 4293 0.09 0.26 YES
34 NDUFS7 NDUFS7 NDUFS7 4394 0.087 0.26 YES
35 UCHL1 UCHL1 UCHL1 4443 0.086 0.27 YES
36 UBE2J1 UBE2J1 UBE2J1 4485 0.085 0.27 YES
37 PARK7 PARK7 PARK7 4521 0.084 0.28 YES
38 ATP5C1 ATP5C1 ATP5C1 4560 0.083 0.28 YES
39 NDUFB9 NDUFB9 NDUFB9 4608 0.081 0.29 YES
40 COX8A COX8A COX8A 4678 0.08 0.29 YES
41 COX6C COX6C COX6C 4735 0.078 0.3 YES
42 NDUFB6 NDUFB6 NDUFB6 4791 0.077 0.3 YES
43 COX6A1 COX6A1 COX6A1 4829 0.076 0.3 YES
44 NDUFAB1 NDUFAB1 NDUFAB1 4837 0.076 0.31 YES
45 NDUFC2 NDUFC2 NDUFC2 5091 0.07 0.3 YES
46 NDUFA6 NDUFA6 NDUFA6 5128 0.069 0.31 YES
47 NDUFA9 NDUFA9 NDUFA9 5185 0.068 0.31 YES
48 PINK1 PINK1 PINK1 5250 0.066 0.31 YES
49 NDUFB4 NDUFB4 NDUFB4 5306 0.065 0.32 YES
50 NDUFV1 NDUFV1 NDUFV1 5365 0.063 0.32 YES
51 NDUFS4 NDUFS4 NDUFS4 5401 0.062 0.32 YES
52 UQCRH UQCRH UQCRH 5428 0.062 0.33 YES
53 NDUFB3 NDUFB3 NDUFB3 5471 0.06 0.33 YES
54 UQCRHL UQCRHL UQCRHL 5481 0.06 0.34 YES
55 VDAC3 VDAC3 VDAC3 5536 0.059 0.34 YES
56 CASP3 CASP3 CASP3 5586 0.058 0.34 YES
57 COX5B COX5B COX5B 5665 0.056 0.34 YES
58 UQCR11 UQCR11 UQCR11 5701 0.055 0.35 YES
59 COX7C COX7C COX7C 5706 0.055 0.35 YES
60 UQCRC1 UQCRC1 UQCRC1 5793 0.053 0.35 YES
61 UQCRB UQCRB UQCRB 5814 0.053 0.36 YES
62 ATP5H ATP5H ATP5H 5839 0.052 0.36 YES
63 SDHB SDHB SDHB 5914 0.05 0.36 YES
64 NDUFA1 NDUFA1 NDUFA1 5954 0.049 0.36 YES
65 COX5A COX5A COX5A 6083 0.047 0.36 YES
66 NDUFA4 NDUFA4 NDUFA4 6133 0.046 0.36 YES
67 SLC25A6 SLC25A6 SLC25A6 6135 0.046 0.36 YES
68 ATP5G3 ATP5G3 ATP5G3 6254 0.043 0.36 YES
69 UQCRFS1 UQCRFS1 UQCRFS1 6293 0.042 0.36 YES
70 ATP5A1 ATP5A1 ATP5A1 6328 0.042 0.36 YES
71 SDHA SDHA SDHA 6494 0.039 0.36 YES
72 SLC25A5 SLC25A5 SLC25A5 6569 0.037 0.36 YES
73 NDUFC1 NDUFC1 NDUFC1 6579 0.037 0.36 YES
74 UBE2L6 UBE2L6 UBE2L6 6622 0.036 0.36 YES
75 COX7B COX7B COX7B 6626 0.036 0.37 YES
76 TH TH TH 6635 0.036 0.37 YES
77 ATP5F1 ATP5F1 ATP5F1 6759 0.033 0.37 NO
78 ATP5G1 ATP5G1 ATP5G1 6798 0.032 0.37 NO
79 NDUFA8 NDUFA8 NDUFA8 6950 0.03 0.36 NO
80 COX7A2L COX7A2L COX7A2L 6985 0.029 0.36 NO
81 CYC1 CYC1 CYC1 7114 0.026 0.36 NO
82 PPID PPID PPID 7174 0.025 0.36 NO
83 COX6A2 COX6A2 COX6A2 7364 0.021 0.35 NO
84 ATP5B ATP5B ATP5B 7646 0.015 0.33 NO
85 NDUFA10 NDUFA10 NDUFA10 7725 0.014 0.33 NO
86 PARK2 PARK2 PARK2 7814 0.012 0.33 NO
87 VDAC2 VDAC2 VDAC2 7837 0.011 0.33 NO
88 UBE2G2 UBE2G2 UBE2G2 7929 0.0096 0.32 NO
89 NDUFB5 NDUFB5 NDUFB5 7931 0.0096 0.32 NO
90 NDUFV3 NDUFV3 NDUFV3 7990 0.0084 0.32 NO
91 NDUFA5 NDUFA5 NDUFA5 8137 0.0051 0.31 NO
92 UBA1 UBA1 UBA1 8323 0.0015 0.3 NO
93 COX7A1 COX7A1 COX7A1 8405 -0.00032 0.3 NO
94 VDAC1 VDAC1 VDAC1 8524 -0.0028 0.29 NO
95 UBE2G1 UBE2G1 UBE2G1 8724 -0.0071 0.28 NO
96 UQCRC2 UQCRC2 UQCRC2 9500 -0.023 0.24 NO
97 UBA7 UBA7 UBA7 9658 -0.026 0.24 NO
98 CYCS CYCS CYCS 9988 -0.033 0.22 NO
99 CASP9 CASP9 CASP9 10118 -0.036 0.22 NO
100 SDHD SDHD SDHD 10694 -0.049 0.19 NO
101 APAF1 APAF1 APAF1 10886 -0.053 0.18 NO
102 SLC25A31 SLC25A31 SLC25A31 10927 -0.054 0.19 NO
103 SDHC SDHC SDHC 11394 -0.066 0.17 NO
104 NDUFS2 NDUFS2 NDUFS2 11561 -0.07 0.16 NO
105 COX8C COX8C COX8C 12301 -0.091 0.13 NO
106 NDUFS1 NDUFS1 NDUFS1 12596 -0.099 0.13 NO
107 SLC25A4 SLC25A4 SLC25A4 13902 -0.15 0.068 NO
108 SLC18A2 SLC18A2 SLC18A2 14171 -0.16 0.068 NO
109 SLC18A1 SLC18A1 SLC18A1 15805 -0.27 0.0036 NO
110 LRRK2 LRRK2 LRRK2 18051 -0.65 -0.059 NO
111 GPR37 GPR37 GPR37 18206 -0.78 0.0042 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 RNA POLYMERASE.

Figure S34.  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

genes ES table in pathway: KEGG DNA REPLICATION

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 CREB3L3 CREB3L3 CREB3L3 66 0.62 0.035 YES
2 COX4I2 COX4I2 COX4I2 389 0.42 0.043 YES
3 COX6B2 COX6B2 COX6B2 880 0.31 0.035 YES
4 CREB3L1 CREB3L1 CREB3L1 1042 0.29 0.044 YES
5 GRIN1 GRIN1 GRIN1 1414 0.24 0.038 YES
6 PLCB4 PLCB4 PLCB4 1636 0.22 0.04 YES
7 TGM2 TGM2 TGM2 1740 0.21 0.047 YES
8 HAP1 HAP1 HAP1 1902 0.19 0.05 YES
9 BAX BAX BAX 1962 0.19 0.058 YES
10 NDUFA4L2 NDUFA4L2 NDUFA4L2 2534 0.15 0.036 YES
11 NDUFS6 NDUFS6 NDUFS6 2562 0.15 0.044 YES
12 AP2S1 AP2S1 AP2S1 2650 0.15 0.048 YES
13 ATP5J ATP5J ATP5J 2661 0.15 0.056 YES
14 POLR2I POLR2I POLR2I 2798 0.14 0.058 YES
15 BBC3 BBC3 BBC3 2812 0.14 0.065 YES
16 POLR2F POLR2F POLR2F 2911 0.13 0.068 YES
17 NDUFB7 NDUFB7 NDUFB7 2925 0.13 0.076 YES
18 NDUFA7 NDUFA7 NDUFA7 2929 0.13 0.084 YES
19 COX4I1 COX4I1 COX4I1 2992 0.13 0.088 YES
20 NDUFS8 NDUFS8 NDUFS8 3031 0.13 0.094 YES
21 NDUFA3 NDUFA3 NDUFA3 3137 0.12 0.096 YES
22 NDUFB1 NDUFB1 NDUFB1 3141 0.12 0.1 YES
23 POLR2L POLR2L POLR2L 3159 0.12 0.11 YES
24 NDUFS5 NDUFS5 NDUFS5 3161 0.12 0.12 YES
25 NDUFA2 NDUFA2 NDUFA2 3211 0.12 0.12 YES
26 COX7A2 COX7A2 COX7A2 3289 0.12 0.13 YES
27 NDUFB10 NDUFB10 NDUFB10 3337 0.12 0.13 YES
28 NDUFB8 NDUFB8 NDUFB8 3387 0.12 0.14 YES
29 NDUFS3 NDUFS3 NDUFS3 3410 0.12 0.14 YES
30 UQCR10 UQCR10 UQCR10 3428 0.11 0.15 YES
31 ATP5O ATP5O ATP5O 3479 0.11 0.15 YES
32 POLR2J2 POLR2J2 POLR2J2 3547 0.11 0.16 YES
33 POLR2J POLR2J POLR2J 3643 0.11 0.16 YES
34 COX6B1 COX6B1 COX6B1 3650 0.11 0.16 YES
35 NDUFV2 NDUFV2 NDUFV2 3653 0.11 0.17 YES
36 TP53 TP53 TP53 3693 0.11 0.17 YES
37 TBPL1 TBPL1 TBPL1 3758 0.1 0.18 YES
38 POLR2G POLR2G POLR2G 3767 0.1 0.18 YES
39 POLR2D POLR2D POLR2D 3872 0.1 0.18 YES
40 DLG4 DLG4 DLG4 3896 0.1 0.19 YES
41 ATP5E ATP5E ATP5E 3897 0.1 0.19 YES
42 ATP5D ATP5D ATP5D 3958 0.098 0.2 YES
43 NDUFB2 NDUFB2 NDUFB2 3973 0.098 0.2 YES
44 POLR2H POLR2H POLR2H 3979 0.098 0.21 YES
45 ATP5G2 ATP5G2 ATP5G2 4135 0.094 0.2 YES
46 UQCRQ UQCRQ UQCRQ 4293 0.09 0.2 YES
47 NDUFS7 NDUFS7 NDUFS7 4394 0.087 0.2 YES
48 AP2A2 AP2A2 AP2A2 4438 0.086 0.2 YES
49 HDAC2 HDAC2 HDAC2 4456 0.086 0.21 YES
50 HDAC1 HDAC1 HDAC1 4532 0.083 0.21 YES
51 ATP5C1 ATP5C1 ATP5C1 4560 0.083 0.21 YES
52 NDUFB9 NDUFB9 NDUFB9 4608 0.081 0.22 YES
53 CLTB CLTB CLTB 4654 0.08 0.22 YES
54 COX8A COX8A COX8A 4678 0.08 0.22 YES
55 POLR2E POLR2E POLR2E 4688 0.08 0.23 YES
56 COX6C COX6C COX6C 4735 0.078 0.23 YES
57 NRF1 NRF1 NRF1 4750 0.078 0.23 YES
58 NDUFB6 NDUFB6 NDUFB6 4791 0.077 0.24 YES
59 COX6A1 COX6A1 COX6A1 4829 0.076 0.24 YES
60 NDUFAB1 NDUFAB1 NDUFAB1 4837 0.076 0.24 YES
61 GPX1 GPX1 GPX1 5031 0.071 0.24 YES
62 NDUFC2 NDUFC2 NDUFC2 5091 0.07 0.24 YES
63 NDUFA6 NDUFA6 NDUFA6 5128 0.069 0.24 YES
64 DCTN2 DCTN2 DCTN2 5184 0.068 0.24 YES
65 NDUFA9 NDUFA9 NDUFA9 5185 0.068 0.24 YES
66 NDUFB4 NDUFB4 NDUFB4 5306 0.065 0.24 YES
67 NDUFV1 NDUFV1 NDUFV1 5365 0.063 0.24 YES
68 NDUFS4 NDUFS4 NDUFS4 5401 0.062 0.24 YES
69 UQCRH UQCRH UQCRH 5428 0.062 0.25 YES
70 NDUFB3 NDUFB3 NDUFB3 5471 0.06 0.25 YES
71 UQCRHL UQCRHL UQCRHL 5481 0.06 0.25 YES
72 VDAC3 VDAC3 VDAC3 5536 0.059 0.25 YES
73 CASP3 CASP3 CASP3 5586 0.058 0.25 YES
74 CREB3L4 CREB3L4 CREB3L4 5596 0.057 0.26 YES
75 AP2M1 AP2M1 AP2M1 5661 0.056 0.26 YES
76 COX5B COX5B COX5B 5665 0.056 0.26 YES
77 UQCR11 UQCR11 UQCR11 5701 0.055 0.26 YES
78 COX7C COX7C COX7C 5706 0.055 0.26 YES
79 DNAL4 DNAL4 DNAL4 5778 0.054 0.26 YES
80 UQCRC1 UQCRC1 UQCRC1 5793 0.053 0.27 YES
81 IFT57 IFT57 IFT57 5806 0.053 0.27 YES
82 UQCRB UQCRB UQCRB 5814 0.053 0.27 YES
83 ATP5H ATP5H ATP5H 5839 0.052 0.27 YES
84 SDHB SDHB SDHB 5914 0.05 0.27 YES
85 NDUFA1 NDUFA1 NDUFA1 5954 0.049 0.27 YES
86 SOD1 SOD1 SOD1 6021 0.048 0.27 YES
87 DNAI2 DNAI2 DNAI2 6077 0.047 0.27 YES
88 COX5A COX5A COX5A 6083 0.047 0.28 YES
89 NDUFA4 NDUFA4 NDUFA4 6133 0.046 0.28 YES
90 SLC25A6 SLC25A6 SLC25A6 6135 0.046 0.28 YES
91 CLTA CLTA CLTA 6165 0.045 0.28 YES
92 ATP5G3 ATP5G3 ATP5G3 6254 0.043 0.28 NO
93 UQCRFS1 UQCRFS1 UQCRFS1 6293 0.042 0.28 NO
94 ATP5A1 ATP5A1 ATP5A1 6328 0.042 0.28 NO
95 POLR2K POLR2K POLR2K 6398 0.04 0.28 NO
96 PPARG PPARG PPARG 6448 0.04 0.28 NO
97 POLR2C POLR2C POLR2C 6487 0.039 0.28 NO
98 SDHA SDHA SDHA 6494 0.039 0.28 NO
99 SLC25A5 SLC25A5 SLC25A5 6569 0.037 0.28 NO
100 NDUFC1 NDUFC1 NDUFC1 6579 0.037 0.28 NO
101 COX7B COX7B COX7B 6626 0.036 0.28 NO
102 ATP5F1 ATP5F1 ATP5F1 6759 0.033 0.27 NO
103 ATP5G1 ATP5G1 ATP5G1 6798 0.032 0.27 NO
104 CASP8 CASP8 CASP8 6851 0.031 0.27 NO
105 DCTN1 DCTN1 DCTN1 6866 0.031 0.27 NO
106 NDUFA8 NDUFA8 NDUFA8 6950 0.03 0.27 NO
107 COX7A2L COX7A2L COX7A2L 6985 0.029 0.27 NO
108 PLCB2 PLCB2 PLCB2 7021 0.028 0.27 NO
109 CYC1 CYC1 CYC1 7114 0.026 0.27 NO
110 PPID PPID PPID 7174 0.025 0.26 NO
111 TBP TBP TBP 7197 0.024 0.26 NO
112 CREB3 CREB3 CREB3 7264 0.023 0.26 NO
113 COX6A2 COX6A2 COX6A2 7364 0.021 0.26 NO
114 ATP5B ATP5B ATP5B 7646 0.015 0.24 NO
115 NDUFA10 NDUFA10 NDUFA10 7725 0.014 0.24 NO
116 DNALI1 DNALI1 DNALI1 7830 0.012 0.24 NO
117 VDAC2 VDAC2 VDAC2 7837 0.011 0.24 NO
118 NDUFB5 NDUFB5 NDUFB5 7931 0.0096 0.23 NO
119 NDUFV3 NDUFV3 NDUFV3 7990 0.0084 0.23 NO
120 NDUFA5 NDUFA5 NDUFA5 8137 0.0051 0.22 NO
121 COX7A1 COX7A1 COX7A1 8405 -0.00032 0.21 NO
122 VDAC1 VDAC1 VDAC1 8524 -0.0028 0.2 NO
123 POLR2A POLR2A POLR2A 8745 -0.0077 0.19 NO
124 AP2A1 AP2A1 AP2A1 8868 -0.0098 0.18 NO
125 SIN3A SIN3A SIN3A 8940 -0.011 0.18 NO
126 TFAM TFAM TFAM 9051 -0.014 0.17 NO
127 CREB1 CREB1 CREB1 9078 -0.014 0.17 NO
128 RCOR1 RCOR1 RCOR1 9190 -0.016 0.17 NO
129 SP1 SP1 SP1 9257 -0.018 0.17 NO
130 POLR2J3 POLR2J3 POLR2J3 9264 -0.018 0.17 NO
131 HTT HTT HTT 9305 -0.019 0.16 NO
132 UQCRC2 UQCRC2 UQCRC2 9500 -0.023 0.16 NO
133 CYCS CYCS CYCS 9988 -0.033 0.13 NO
134 DNAH2 DNAH2 DNAH2 10052 -0.034 0.13 NO
135 CASP9 CASP9 CASP9 10118 -0.036 0.13 NO
136 GNAQ GNAQ GNAQ 10365 -0.041 0.12 NO
137 POLR2B POLR2B POLR2B 10560 -0.045 0.11 NO
138 AP2B1 AP2B1 AP2B1 10569 -0.045 0.11 NO
139 TAF4B TAF4B TAF4B 10644 -0.048 0.11 NO
140 SDHD SDHD SDHD 10694 -0.049 0.11 NO
141 CREBBP CREBBP CREBBP 10801 -0.051 0.11 NO
142 APAF1 APAF1 APAF1 10886 -0.053 0.11 NO
143 SLC25A31 SLC25A31 SLC25A31 10927 -0.054 0.11 NO
144 DCTN4 DCTN4 DCTN4 10934 -0.054 0.11 NO
145 CREB3L2 CREB3L2 CREB3L2 11266 -0.062 0.097 NO
146 SDHC SDHC SDHC 11394 -0.066 0.094 NO
147 CLTCL1 CLTCL1 CLTCL1 11400 -0.066 0.098 NO
148 CLTC CLTC CLTC 11517 -0.069 0.096 NO
149 NDUFS2 NDUFS2 NDUFS2 11561 -0.07 0.098 NO
150 ITPR1 ITPR1 ITPR1 11941 -0.08 0.082 NO
151 TAF4 TAF4 TAF4 12032 -0.083 0.082 NO
152 COX8C COX8C COX8C 12301 -0.091 0.072 NO
153 DNAL1 DNAL1 DNAL1 12408 -0.094 0.072 NO
154 NDUFS1 NDUFS1 NDUFS1 12596 -0.099 0.068 NO
155 PLCB1 PLCB1 PLCB1 12686 -0.1 0.07 NO
156 SOD2 SOD2 SOD2 12707 -0.1 0.075 NO
157 DNAH1 DNAH1 DNAH1 13121 -0.12 0.06 NO
158 EP300 EP300 EP300 13277 -0.12 0.059 NO
159 PLCB3 PLCB3 PLCB3 13441 -0.13 0.058 NO
160 SLC25A4 SLC25A4 SLC25A4 13902 -0.15 0.042 NO
161 GRM5 GRM5 GRM5 15590 -0.26 -0.036 NO
162 DNAH3 DNAH3 DNAH3 15889 -0.28 -0.035 NO
163 CREB5 CREB5 CREB5 16661 -0.36 -0.055 NO
164 DNAI1 DNAI1 DNAI1 16760 -0.37 -0.037 NO
165 REST REST REST 16986 -0.4 -0.025 NO
166 HIP1 HIP1 HIP1 16990 -0.4 0.000014 NO
167 PPARGC1A PPARGC1A PPARGC1A 17240 -0.44 0.014 NO
168 BDNF BDNF BDNF 18129 -0.71 0.0085 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 DNA REPLICATION.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DNA REPLICATION, 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 SPLICEOSOME

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 POLE2 POLE2 POLE2 942 0.3 0.012 YES
2 RNASEH2B RNASEH2B RNASEH2B 1196 0.27 0.054 YES
3 FEN1 FEN1 FEN1 1668 0.21 0.073 YES
4 RNASEH2A RNASEH2A RNASEH2A 1804 0.2 0.11 YES
5 MCM7 MCM7 MCM7 2127 0.18 0.13 YES
6 RNASEH2C RNASEH2C RNASEH2C 2138 0.17 0.16 YES
7 MCM5 MCM5 MCM5 2225 0.17 0.19 YES
8 RPA3 RPA3 RPA3 2342 0.16 0.22 YES
9 MCM6 MCM6 MCM6 2416 0.16 0.25 YES
10 POLD1 POLD1 POLD1 2481 0.15 0.28 YES
11 PCNA PCNA PCNA 2549 0.15 0.3 YES
12 POLD2 POLD2 POLD2 2720 0.14 0.33 YES
13 POLE POLE POLE 2733 0.14 0.36 YES
14 POLA2 POLA2 POLA2 2750 0.14 0.38 YES
15 RFC4 RFC4 RFC4 2897 0.14 0.4 YES
16 LIG1 LIG1 LIG1 2962 0.13 0.43 YES
17 PRIM1 PRIM1 PRIM1 3099 0.13 0.45 YES
18 RFC2 RFC2 RFC2 3207 0.12 0.47 YES
19 MCM3 MCM3 MCM3 3386 0.12 0.48 YES
20 MCM2 MCM2 MCM2 3446 0.11 0.5 YES
21 DNA2 DNA2 DNA2 3621 0.11 0.51 YES
22 RFC5 RFC5 RFC5 3678 0.11 0.53 YES
23 PRIM2 PRIM2 PRIM2 3729 0.1 0.55 YES
24 SSBP1 SSBP1 SSBP1 4462 0.085 0.53 NO
25 POLD4 POLD4 POLD4 5170 0.068 0.51 NO
26 RFC3 RFC3 RFC3 5394 0.063 0.51 NO
27 POLD3 POLD3 POLD3 5722 0.055 0.5 NO
28 POLE4 POLE4 POLE4 5743 0.054 0.51 NO
29 POLE3 POLE3 POLE3 5991 0.049 0.51 NO
30 RPA1 RPA1 RPA1 6211 0.044 0.5 NO
31 RPA2 RPA2 RPA2 6315 0.042 0.51 NO
32 RFC1 RFC1 RFC1 8771 -0.0081 0.37 NO
33 MCM4 MCM4 MCM4 9218 -0.017 0.35 NO
34 RNASEH1 RNASEH1 RNASEH1 12957 -0.11 0.17 NO
35 RPA4 RPA4 RPA4 17843 -0.57 0.024 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 SPLICEOSOME.

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

genes ES table in pathway: KEGG PROTEASOME

Table 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 E2F2 E2F2 E2F2 467 0.39 -0.0041 YES
2 CCNA1 CCNA1 CCNA1 540 0.38 0.013 YES
3 CDKN2D CDKN2D CDKN2D 563 0.37 0.032 YES
4 CDC25C CDC25C CDC25C 626 0.36 0.048 YES
5 CDC20 CDC20 CDC20 646 0.36 0.066 YES
6 PTTG2 PTTG2 PTTG2 667 0.35 0.085 YES
7 CDC45 CDC45 CDC45 718 0.34 0.1 YES
8 TTK TTK TTK 796 0.33 0.11 YES
9 TFDP2 TFDP2 TFDP2 813 0.32 0.13 YES
10 CCNB2 CCNB2 CCNB2 859 0.32 0.15 YES
11 CDKN2C CDKN2C CDKN2C 860 0.32 0.16 YES
12 CDC25A CDC25A CDC25A 871 0.31 0.18 YES
13 PKMYT1 PKMYT1 PKMYT1 901 0.31 0.2 YES
14 PLK1 PLK1 PLK1 962 0.3 0.21 YES
15 E2F1 E2F1 E2F1 1034 0.29 0.22 YES
16 MAD2L2 MAD2L2 MAD2L2 1076 0.28 0.23 YES
17 ORC1L ORC1L ORC1L 1101 0.28 0.25 YES
18 PTTG1 PTTG1 PTTG1 1145 0.28 0.26 YES
19 CCNA2 CCNA2 CCNA2 1284 0.26 0.27 YES
20 CDKN1C CDKN1C CDKN1C 1294 0.26 0.28 YES
21 BUB1 BUB1 BUB1 1329 0.25 0.29 YES
22 CHEK1 CHEK1 CHEK1 1427 0.24 0.3 YES
23 ESPL1 ESPL1 ESPL1 1451 0.24 0.31 YES
24 CDK6 CDK6 CDK6 1478 0.23 0.32 YES
25 CDC6 CDC6 CDC6 1543 0.22 0.33 YES
26 CCNB1 CCNB1 CCNB1 1653 0.22 0.34 YES
27 BUB1B BUB1B BUB1B 1694 0.21 0.35 YES
28 CDK1 CDK1 CDK1 1802 0.2 0.35 YES
29 CCNE2 CCNE2 CCNE2 1856 0.2 0.36 YES
30 CCND3 CCND3 CCND3 1910 0.19 0.37 YES
31 MCM7 MCM7 MCM7 2127 0.18 0.36 YES
32 MCM5 MCM5 MCM5 2225 0.17 0.37 YES
33 CHEK2 CHEK2 CHEK2 2289 0.16 0.38 YES
34 MCM6 MCM6 MCM6 2416 0.16 0.38 YES
35 RBX1 RBX1 RBX1 2499 0.15 0.38 YES
36 PCNA PCNA PCNA 2549 0.15 0.39 YES
37 MAD2L1 MAD2L1 MAD2L1 2576 0.15 0.39 YES
38 CDC25B CDC25B CDC25B 2692 0.14 0.39 YES
39 MAD1L1 MAD1L1 MAD1L1 2854 0.14 0.39 NO
40 ANAPC11 ANAPC11 ANAPC11 2984 0.13 0.39 NO
41 CCNE1 CCNE1 CCNE1 3148 0.12 0.39 NO
42 MCM3 MCM3 MCM3 3386 0.12 0.38 NO
43 MCM2 MCM2 MCM2 3446 0.11 0.39 NO
44 TP53 TP53 TP53 3693 0.11 0.38 NO
45 CDC7 CDC7 CDC7 3743 0.1 0.38 NO
46 ORC6L ORC6L ORC6L 4265 0.09 0.36 NO
47 CCND2 CCND2 CCND2 4315 0.089 0.36 NO
48 HDAC2 HDAC2 HDAC2 4456 0.086 0.36 NO
49 HDAC1 HDAC1 HDAC1 4532 0.083 0.36 NO
50 CDC26 CDC26 CDC26 4582 0.082 0.36 NO
51 CDK2 CDK2 CDK2 4647 0.08 0.36 NO
52 CDC16 CDC16 CDC16 4690 0.079 0.36 NO
53 CDK4 CDK4 CDK4 4884 0.074 0.36 NO
54 ZBTB17 ZBTB17 ZBTB17 5066 0.07 0.35 NO
55 ANAPC2 ANAPC2 ANAPC2 5313 0.065 0.34 NO
56 CCNH CCNH CCNH 5335 0.064 0.34 NO
57 CDKN2A CDKN2A CDKN2A 5480 0.06 0.34 NO
58 FZR1 FZR1 FZR1 5501 0.059 0.34 NO
59 YWHAE YWHAE YWHAE 5566 0.058 0.34 NO
60 E2F4 E2F4 E2F4 5700 0.055 0.34 NO
61 BUB3 BUB3 BUB3 5711 0.055 0.34 NO
62 ANAPC5 ANAPC5 ANAPC5 5818 0.053 0.34 NO
63 SKP1 SKP1 SKP1 6298 0.042 0.31 NO
64 YWHAQ YWHAQ YWHAQ 6396 0.04 0.31 NO
65 CDKN1B CDKN1B CDKN1B 6443 0.04 0.31 NO
66 YWHAH YWHAH YWHAH 6552 0.037 0.3 NO
67 ANAPC4 ANAPC4 ANAPC4 6565 0.037 0.3 NO
68 GADD45B GADD45B GADD45B 6940 0.03 0.29 NO
69 MYC MYC MYC 7057 0.027 0.28 NO
70 ANAPC7 ANAPC7 ANAPC7 7077 0.027 0.28 NO
71 TFDP1 TFDP1 TFDP1 7288 0.023 0.27 NO
72 SMAD4 SMAD4 SMAD4 7377 0.021 0.27 NO
73 E2F5 E2F5 E2F5 7522 0.018 0.26 NO
74 TGFB1 TGFB1 TGFB1 7600 0.016 0.26 NO
75 WEE1 WEE1 WEE1 7856 0.011 0.24 NO
76 RAD21 RAD21 RAD21 7920 0.0098 0.24 NO
77 ORC3L ORC3L ORC3L 7955 0.0091 0.24 NO
78 YWHAB YWHAB YWHAB 8103 0.0059 0.23 NO
79 SMAD2 SMAD2 SMAD2 8169 0.0045 0.23 NO
80 ANAPC10 ANAPC10 ANAPC10 8559 -0.0034 0.21 NO
81 ANAPC13 ANAPC13 ANAPC13 8577 -0.004 0.21 NO
82 YWHAZ YWHAZ YWHAZ 8744 -0.0077 0.2 NO
83 SFN SFN SFN 8866 -0.0098 0.19 NO
84 ORC4L ORC4L ORC4L 8947 -0.011 0.19 NO
85 MDM2 MDM2 MDM2 9141 -0.016 0.18 NO
86 ORC5L ORC5L ORC5L 9195 -0.017 0.18 NO
87 MCM4 MCM4 MCM4 9218 -0.017 0.18 NO
88 SMAD3 SMAD3 SMAD3 9703 -0.027 0.15 NO
89 SMC1A SMC1A SMC1A 9837 -0.029 0.14 NO
90 STAG2 STAG2 STAG2 9964 -0.032 0.14 NO
91 CDK7 CDK7 CDK7 10064 -0.034 0.14 NO
92 SKP2 SKP2 SKP2 10138 -0.036 0.13 NO
93 RB1 RB1 RB1 10279 -0.039 0.13 NO
94 ABL1 ABL1 ABL1 10326 -0.04 0.13 NO
95 E2F3 E2F3 E2F3 10402 -0.042 0.13 NO
96 SMC3 SMC3 SMC3 10454 -0.043 0.13 NO
97 CDC27 CDC27 CDC27 10511 -0.044 0.12 NO
98 GADD45A GADD45A GADD45A 10710 -0.049 0.12 NO
99 CREBBP CREBBP CREBBP 10801 -0.051 0.12 NO
100 ORC2L ORC2L ORC2L 11224 -0.062 0.095 NO
101 CUL1 CUL1 CUL1 11260 -0.062 0.097 NO
102 CDC23 CDC23 CDC23 11458 -0.068 0.09 NO
103 ANAPC1 ANAPC1 ANAPC1 11506 -0.069 0.091 NO
104 CCND1 CCND1 CCND1 12073 -0.084 0.064 NO
105 PRKDC PRKDC PRKDC 12167 -0.087 0.064 NO
106 YWHAG YWHAG YWHAG 12823 -0.11 0.034 NO
107 TGFB3 TGFB3 TGFB3 12999 -0.11 0.03 NO
108 RBL2 RBL2 RBL2 13043 -0.12 0.034 NO
109 EP300 EP300 EP300 13277 -0.12 0.028 NO
110 ATR ATR ATR 13478 -0.13 0.024 NO
111 GSK3B GSK3B GSK3B 13497 -0.13 0.031 NO
112 CDC14A CDC14A CDC14A 13763 -0.14 0.024 NO
113 TGFB2 TGFB2 TGFB2 14081 -0.16 0.015 NO
114 ATM ATM ATM 14294 -0.17 0.013 NO
115 STAG1 STAG1 STAG1 14526 -0.18 0.01 NO
116 RBL1 RBL1 RBL1 15007 -0.21 -0.0045 NO
117 CDKN1A CDKN1A CDKN1A 15255 -0.23 -0.0055 NO
118 SMC1B SMC1B SMC1B 15282 -0.23 0.0058 NO
119 CDC14B CDC14B CDC14B 15436 -0.24 0.011 NO
120 GADD45G GADD45G GADD45G 16292 -0.32 -0.019 NO
121 WEE2 WEE2 WEE2 17913 -0.59 -0.076 NO
122 CCNB3 CCNB3 CCNB3 18114 -0.7 -0.048 NO
123 CDKN2B CDKN2B CDKN2B 18280 -1 0.00016 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 PROTEASOME.

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

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 AGR PATHWAY 35 genes.ES.table 0.52 1.3 0.15 0.78 0.97 0.46 0.23 0.35 0.7 0.3
BIOCARTA ERK PATHWAY 27 genes.ES.table 0.46 1.3 0.12 0.81 0.96 0.44 0.32 0.3 0.71 0.32
BIOCARTA EDG1 PATHWAY 26 genes.ES.table 0.53 1.4 0.052 0.96 0.91 0.5 0.28 0.36 0.77 0.39
KEGG N GLYCAN BIOSYNTHESIS 45 genes.ES.table 0.35 1.3 0.18 0.86 0.97 0.2 0.17 0.17 0.76 0.35
KEGG O GLYCAN BIOSYNTHESIS 27 genes.ES.table 0.58 1.5 0.021 1 0.85 0.44 0.25 0.33 1 0.72
KEGG WNT SIGNALING PATHWAY 145 genes.ES.table 0.39 1.3 0.088 0.85 0.96 0.32 0.24 0.24 0.74 0.34
KEGG TGF BETA SIGNALING PATHWAY 84 genes.ES.table 0.56 1.4 0.036 1 0.88 0.58 0.3 0.41 0.84 0.44
KEGG AXON GUIDANCE 127 genes.ES.table 0.48 1.4 0.033 0.92 0.92 0.4 0.24 0.31 0.73 0.38
KEGG FOCAL ADHESION 195 genes.ES.table 0.52 1.5 0.037 1 0.82 0.46 0.23 0.36 1 0.8
KEGG ECM RECEPTOR INTERACTION 80 genes.ES.table 0.61 1.4 0.057 0.97 0.89 0.61 0.23 0.47 0.75 0.38
genes ES table in pathway: BIOCARTA AGR 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 ITGB8 ITGB8 ITGB8 44 1.1 0.017 YES
2 MYLK3 MYLK3 MYLK3 61 1.1 0.035 YES
3 ITGA9 ITGA9 ITGA9 96 1 0.051 YES
4 IBSP IBSP IBSP 155 0.96 0.065 YES
5 ITGA1 ITGA1 ITGA1 172 0.94 0.08 YES
6 LAMA1 LAMA1 LAMA1 219 0.9 0.093 YES
7 ROCK2 ROCK2 ROCK2 287 0.85 0.1 YES
8 LAMB4 LAMB4 LAMB4 293 0.85 0.12 YES
9 ITGB3 ITGB3 ITGB3 366 0.81 0.13 YES
10 ITGA8 ITGA8 ITGA8 472 0.76 0.14 YES
11 MYLK MYLK MYLK 488 0.76 0.15 YES
12 COL11A1 COL11A1 COL11A1 497 0.75 0.16 YES
13 ITGA2 ITGA2 ITGA2 536 0.74 0.17 YES
14 EGFR EGFR EGFR 689 0.69 0.18 YES
15 FN1 FN1 FN1 887 0.65 0.18 YES
16 LAMA2 LAMA2 LAMA2 921 0.64 0.19 YES
17 HGF HGF HGF 967 0.63 0.2 YES
18 VEGFC VEGFC VEGFC 985 0.63 0.2 YES
19 ITGA2B ITGA2B ITGA2B 1007 0.62 0.21 YES
20 COL2A1 COL2A1 COL2A1 1008 0.62 0.22 YES
21 MYLK2 MYLK2 MYLK2 1029 0.62 0.24 YES
22 FLNC FLNC FLNC 1061 0.61 0.24 YES
23 KDR KDR KDR 1090 0.6 0.25 YES
24 MET MET MET 1244 0.57 0.25 YES
25 CHAD CHAD CHAD 1314 0.56 0.26 YES
26 FLT1 FLT1 FLT1 1351 0.56 0.27 YES
27 THBS1 THBS1 THBS1 1432 0.54 0.27 YES
28 LAMA4 LAMA4 LAMA4 1475 0.53 0.28 YES
29 VEGFA VEGFA VEGFA 1497 0.53 0.29 YES
30 PDGFC PDGFC PDGFC 1536 0.52 0.3 YES
31 ITGA10 ITGA10 ITGA10 1581 0.51 0.3 YES
32 THBS4 THBS4 THBS4 1583 0.51 0.31 YES
33 ERBB2 ERBB2 ERBB2 1659 0.5 0.32 YES
34 ITGA3 ITGA3 ITGA3 1707 0.5 0.32 YES
35 MYL9 MYL9 MYL9 1804 0.48 0.32 YES
36 DOCK1 DOCK1 DOCK1 1887 0.47 0.33 YES
37 PAK6 PAK6 PAK6 1889 0.47 0.34 YES
38 SHC4 SHC4 SHC4 1930 0.47 0.34 YES
39 COL11A2 COL11A2 COL11A2 1942 0.47 0.35 YES
40 PARVA PARVA PARVA 1976 0.46 0.36 YES
41 PDGFD PDGFD PDGFD 1978 0.46 0.36 YES
42 LAMB2 LAMB2 LAMB2 2096 0.44 0.36 YES
43 MAPK8 MAPK8 MAPK8 2134 0.44 0.37 YES
44 PDGFB PDGFB PDGFB 2223 0.43 0.37 YES
45 SPP1 SPP1 SPP1 2297 0.42 0.38 YES
46 PDGFRA PDGFRA PDGFRA 2312 0.42 0.38 YES
47 ITGB4 ITGB4 ITGB4 2331 0.41 0.39 YES
48 COL4A6 COL4A6 COL4A6 2469 0.4 0.39 YES
49 COL5A1 COL5A1 COL5A1 2483 0.4 0.4 YES
50 ITGAV ITGAV ITGAV 2493 0.39 0.4 YES
51 PDGFA PDGFA PDGFA 2548 0.39 0.4 YES
52 CCND2 CCND2 CCND2 2695 0.38 0.4 YES
53 COL4A1 COL4A1 COL4A1 2696 0.37 0.41 YES
54 PDGFRB PDGFRB PDGFRB 2703 0.37 0.42 YES
55 PIK3CA PIK3CA PIK3CA 2724 0.37 0.42 YES
56 ITGB5 ITGB5 ITGB5 2757 0.37 0.43 YES
57 LAMA5 LAMA5 LAMA5 2801 0.36 0.43 YES
58 ACTN3 ACTN3 ACTN3 2842 0.36 0.43 YES
59 VCL VCL VCL 2905 0.36 0.44 YES
60 LAMC1 LAMC1 LAMC1 2909 0.35 0.44 YES
61 ITGA6 ITGA6 ITGA6 2920 0.35 0.45 YES
62 IGF1R IGF1R IGF1R 3069 0.34 0.45 YES
63 FLT4 FLT4 FLT4 3090 0.34 0.45 YES
64 TNC TNC TNC 3111 0.34 0.46 YES
65 LAMA3 LAMA3 LAMA3 3174 0.33 0.46 YES
66 ARHGAP5 ARHGAP5 ARHGAP5 3313 0.32 0.46 YES
67 CCND1 CCND1 CCND1 3360 0.32 0.46 YES
68 PDPK1 PDPK1 PDPK1 3382 0.31 0.46 YES
69 COL1A2 COL1A2 COL1A2 3411 0.31 0.47 YES
70 COL5A2 COL5A2 COL5A2 3509 0.3 0.47 YES
71 LAMC3 LAMC3 LAMC3 3605 0.29 0.47 YES
72 ITGB1 ITGB1 ITGB1 3611 0.29 0.47 YES
73 CRK CRK CRK 3665 0.29 0.47 YES
74 RASGRF1 RASGRF1 RASGRF1 3666 0.29 0.48 YES
75 PRKCA PRKCA PRKCA 3742 0.28 0.48 YES
76 PTK2 PTK2 PTK2 3804 0.28 0.48 YES
77 BCAR1 BCAR1 BCAR1 3820 0.28 0.49 YES
78 COL1A1 COL1A1 COL1A1 3852 0.28 0.49 YES
79 BCL2 BCL2 BCL2 3938 0.27 0.49 YES
80 CAPN2 CAPN2 CAPN2 3967 0.27 0.49 YES
81 TLN2 TLN2 TLN2 3970 0.27 0.5 YES
82 CAV2 CAV2 CAV2 3976 0.27 0.5 YES
83 MYL7 MYL7 MYL7 4008 0.27 0.5 YES
84 COL4A2 COL4A2 COL4A2 4045 0.26 0.51 YES
85 CTNNB1 CTNNB1 CTNNB1 4060 0.26 0.51 YES
86 COL5A3 COL5A3 COL5A3 4080 0.26 0.51 YES
87 MAPK10 MAPK10 MAPK10 4086 0.26 0.52 YES
88 COL6A3 COL6A3 COL6A3 4108 0.26 0.52 YES
89 PAK3 PAK3 PAK3 4176 0.25 0.52 YES
90 BRAF BRAF BRAF 4238 0.25 0.52 YES
91 SHC2 SHC2 SHC2 4452 0.24 0.52 NO
92 COL3A1 COL3A1 COL3A1 4474 0.24 0.52 NO
93 GRLF1 GRLF1 GRLF1 4617 0.23 0.51 NO
94 LAMB1 LAMB1 LAMB1 4786 0.22 0.51 NO
95 SOS2 SOS2 SOS2 4843 0.21 0.51 NO
96 TNN TNN TNN 4924 0.21 0.51 NO
97 ITGA11 ITGA11 ITGA11 4949 0.21 0.51 NO
98 ACTN4 ACTN4 ACTN4 5035 0.2 0.51 NO
99 MAPK1 MAPK1 MAPK1 5082 0.2 0.51 NO
100 IGF1 IGF1 IGF1 5177 0.2 0.51 NO
101 COL6A2 COL6A2 COL6A2 5190 0.2 0.51 NO
102 PXN PXN PXN 5456 0.18 0.5 NO
103 ROCK1 ROCK1 ROCK1 5459 0.18 0.5 NO
104 PPP1R12A PPP1R12A PPP1R12A 5478 0.18 0.51 NO
105 COL4A4 COL4A4 COL4A4 5765 0.17 0.49 NO
106 SOS1 SOS1 SOS1 5768 0.17 0.5 NO
107 VWF VWF VWF 5813 0.16 0.5 NO
108 TNXB TNXB TNXB 5827 0.16 0.5 NO
109 XIAP XIAP XIAP 5878 0.16 0.5 NO
110 CRKL CRKL CRKL 6011 0.16 0.49 NO
111 VAV2 VAV2 VAV2 6098 0.15 0.49 NO
112 FLNA FLNA FLNA 6383 0.14 0.48 NO
113 COL6A1 COL6A1 COL6A1 6414 0.14 0.48 NO
114 CAV1 CAV1 CAV1 6718 0.12 0.46 NO
115 THBS2 THBS2 THBS2 6824 0.12 0.46 NO
116 FLNB FLNB FLNB 6905 0.12 0.46 NO
117 PAK4 PAK4 PAK4 6939 0.11 0.46 NO
118 ACTN1 ACTN1 ACTN1 6955 0.11 0.46 NO
119 TLN1 TLN1 TLN1 6996 0.11 0.46 NO
120 SHC1 SHC1 SHC1 7132 0.11 0.45 NO
121 GSK3B GSK3B GSK3B 7193 0.1 0.45 NO
122 RAPGEF1 RAPGEF1 RAPGEF1 7374 0.097 0.44 NO
123 JUN JUN JUN 7411 0.095 0.44 NO
124 MAP2K1 MAP2K1 MAP2K1 7580 0.088 0.44 NO
125 ITGB6 ITGB6 ITGB6 7662 0.085 0.43 NO
126 MAPK3 MAPK3 MAPK3 7931 0.075 0.42 NO
127 BIRC2 BIRC2 BIRC2 8069 0.069 0.41 NO
128 PAK1 PAK1 PAK1 8130 0.067 0.41 NO
129 AKT3 AKT3 AKT3 8375 0.058 0.4 NO
130 AKT2 AKT2 AKT2 8598 0.05 0.39 NO
131 PAK7 PAK7 PAK7 8665 0.048 0.38 NO
132 PIK3R1 PIK3R1 PIK3R1 8731 0.045 0.38 NO
133 VTN VTN VTN 8867 0.04 0.38 NO
134 PIP5K1C PIP5K1C PIP5K1C 8925 0.038 0.37 NO
135 PIK3CB PIK3CB PIK3CB 8934 0.038 0.37 NO
136 SRC SRC SRC 9095 0.033 0.36 NO
137 COL6A6 COL6A6 COL6A6 9329 0.026 0.35 NO
138 RAC1 RAC1 RAC1 9377 0.024 0.35 NO
139 ZYX ZYX ZYX 9408 0.023 0.35 NO
140 SHC3 SHC3 SHC3 9415 0.022 0.35 NO
141 RAF1 RAF1 RAF1 9537 0.017 0.34 NO
142 ITGA5 ITGA5 ITGA5 9550 0.017 0.34 NO
143 RAP1A RAP1A RAP1A 9614 0.015 0.34 NO
144 PIK3R3 PIK3R3 PIK3R3 9687 0.012 0.34 NO
145 PIK3R2 PIK3R2 PIK3R2 9818 0.0067 0.33 NO
146 MAPK9 MAPK9 MAPK9 9983 0.0017 0.32 NO
147 CDC42 CDC42 CDC42 9987 0.0014 0.32 NO
148 PARVB PARVB PARVB 10056 -0.0011 0.32 NO
149 PGF PGF PGF 10057 -0.0012 0.32 NO
150 RHOA RHOA RHOA 10107 -0.0026 0.31 NO
151 ILK ILK ILK 10324 -0.011 0.3 NO
152 GRB2 GRB2 GRB2 10467 -0.016 0.29 NO
153 MYL12A MYL12A MYL12A 10607 -0.02 0.28 NO
154 PAK2 PAK2 PAK2 10656 -0.022 0.28 NO
155 ELK1 ELK1 ELK1 10689 -0.023 0.28 NO
156 PIK3CG PIK3CG PIK3CG 10942 -0.032 0.27 NO
157 PPP1CC PPP1CC PPP1CC 11053 -0.036 0.26 NO
158 PPP1CB PPP1CB PPP1CB 11117 -0.038 0.26 NO
159 MYL12B MYL12B MYL12B 11378 -0.047 0.25 NO
160 RAP1B RAP1B RAP1B 11822 -0.063 0.22 NO
161 ACTG1 ACTG1 ACTG1 11878 -0.065 0.22 NO
162 THBS3 THBS3 THBS3 12012 -0.07 0.22 NO
163 ITGA7 ITGA7 ITGA7 12024 -0.071 0.22 NO
164 COMP COMP COMP 12251 -0.08 0.2 NO
165 DIAPH1 DIAPH1 DIAPH1 12284 -0.081 0.2 NO
166 RELN RELN RELN 12405 -0.086 0.2 NO
167 AKT1 AKT1 AKT1 12631 -0.096 0.19 NO
168 PTEN PTEN PTEN 13056 -0.11 0.17 NO
169 ACTB ACTB ACTB 13084 -0.12 0.17 NO
170 ITGA4 ITGA4 ITGA4 13123 -0.12 0.17 NO
171 FIGF FIGF FIGF 13180 -0.12 0.17 NO
172 PIK3CD PIK3CD PIK3CD 13247 -0.12 0.16 NO
173 RAC3 RAC3 RAC3 13515 -0.13 0.15 NO
174 MYL2 MYL2 MYL2 13523 -0.13 0.15 NO
175 BIRC3 BIRC3 BIRC3 13813 -0.14 0.14 NO
176 VASP VASP VASP 13858 -0.15 0.14 NO
177 ITGB7 ITGB7 ITGB7 13928 -0.15 0.14 NO
178 VEGFB VEGFB VEGFB 13958 -0.15 0.14 NO
179 PPP1CA PPP1CA PPP1CA 14636 -0.19 0.11 NO
180 LAMB3 LAMB3 LAMB3 14710 -0.19 0.11 NO
181 FYN FYN FYN 14922 -0.2 0.098 NO
182 LAMC2 LAMC2 LAMC2 15035 -0.21 0.095 NO
183 BAD BAD BAD 15050 -0.21 0.098 NO
184 PIK3R5 PIK3R5 PIK3R5 15092 -0.21 0.1 NO
185 ACTN2 ACTN2 ACTN2 15558 -0.24 0.078 NO
186 CCND3 CCND3 CCND3 16155 -0.29 0.05 NO
187 MYL5 MYL5 MYL5 16405 -0.31 0.042 NO
188 PARVG PARVG PARVG 16650 -0.34 0.034 NO
189 PRKCG PRKCG PRKCG 16740 -0.35 0.036 NO
190 MYLPF MYLPF MYLPF 17129 -0.42 0.022 NO
191 EGF EGF EGF 17176 -0.42 0.026 NO
192 VAV1 VAV1 VAV1 17256 -0.44 0.03 NO
193 PRKCB PRKCB PRKCB 17269 -0.44 0.037 NO
194 RAC2 RAC2 RAC2 17501 -0.49 0.032 NO
195 VAV3 VAV3 VAV3 17925 -0.61 0.02 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 AGR PATHWAY.

Figure S42.  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 ERK 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 GALNT13 GALNT13 GALNT13 522 0.74 0.081 YES
2 GCNT1 GCNT1 GCNT1 727 0.69 0.17 YES
3 GALNT5 GALNT5 GALNT5 779 0.68 0.27 YES
4 GALNTL6 GALNTL6 GALNTL6 1093 0.6 0.34 YES
5 WBSCR17 WBSCR17 WBSCR17 1649 0.5 0.38 YES
6 GALNT8 GALNT8 GALNT8 1962 0.46 0.44 YES
7 GALNT4 GALNT4 GALNT4 2123 0.44 0.49 YES
8 GALNTL2 GALNTL2 GALNTL2 2139 0.44 0.56 YES
9 B4GALT5 B4GALT5 B4GALT5 3442 0.31 0.53 YES
10 GALNT9 GALNT9 GALNT9 3526 0.3 0.57 YES
11 GALNT10 GALNT10 GALNT10 4235 0.25 0.57 YES
12 GALNTL4 GALNTL4 GALNTL4 4556 0.23 0.58 YES
13 GALNT11 GALNT11 GALNT11 5327 0.19 0.57 NO
14 GALNTL1 GALNTL1 GALNTL1 6489 0.13 0.52 NO
15 GALNT14 GALNT14 GALNT14 7037 0.11 0.51 NO
16 GALNT1 GALNT1 GALNT1 8145 0.066 0.46 NO
17 C1GALT1 C1GALT1 C1GALT1 9143 0.031 0.41 NO
18 C1GALT1C1 C1GALT1C1 C1GALT1C1 9216 0.029 0.41 NO
19 GCNT3 GCNT3 GCNT3 9235 0.028 0.41 NO
20 ST3GAL2 ST3GAL2 ST3GAL2 9806 0.0072 0.38 NO
21 GCNT4 GCNT4 GCNT4 10260 -0.0084 0.36 NO
22 GALNT2 GALNT2 GALNT2 10516 -0.017 0.35 NO
23 GALNT7 GALNT7 GALNT7 10757 -0.026 0.34 NO
24 ST6GALNAC1 ST6GALNAC1 ST6GALNAC1 11140 -0.039 0.32 NO
25 GALNT12 GALNT12 GALNT12 11370 -0.047 0.32 NO
26 ST3GAL1 ST3GAL1 ST3GAL1 14425 -0.18 0.18 NO
27 GALNT6 GALNT6 GALNT6 15387 -0.23 0.16 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 ERK PATHWAY.

Figure S44.  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 EDG1 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 PVRL3 PVRL3 PVRL3 64 1.1 0.053 YES
2 EGFR EGFR EGFR 689 0.69 0.055 YES
3 MET MET MET 1244 0.57 0.054 YES
4 FER FER FER 1328 0.56 0.079 YES
5 TCF7L1 TCF7L1 TCF7L1 1578 0.52 0.092 YES
6 WASF3 WASF3 WASF3 1582 0.51 0.12 YES
7 ERBB2 ERBB2 ERBB2 1659 0.5 0.14 YES
8 PTPRB PTPRB PTPRB 1692 0.5 0.16 YES
9 TCF7L2 TCF7L2 TCF7L2 2109 0.44 0.16 YES
10 TJP1 TJP1 TJP1 2259 0.42 0.18 YES
11 CTNNA2 CTNNA2 CTNNA2 2293 0.42 0.2 YES
12 MLLT4 MLLT4 MLLT4 2395 0.41 0.22 YES
13 PVRL2 PVRL2 PVRL2 2715 0.37 0.22 YES
14 TGFBR2 TGFBR2 TGFBR2 2814 0.36 0.23 YES
15 ACTN3 ACTN3 ACTN3 2842 0.36 0.25 YES
16 VCL VCL VCL 2905 0.36 0.26 YES
17 TGFBR1 TGFBR1 TGFBR1 2957 0.35 0.28 YES
18 SNAI2 SNAI2 SNAI2 3021 0.34 0.29 YES
19 INSR INSR INSR 3068 0.34 0.31 YES
20 IGF1R IGF1R IGF1R 3069 0.34 0.32 YES
21 YES1 YES1 YES1 3117 0.34 0.34 YES
22 FARP2 FARP2 FARP2 3165 0.33 0.36 YES
23 SORBS1 SORBS1 SORBS1 3406 0.31 0.36 YES
24 FGFR1 FGFR1 FGFR1 3550 0.3 0.37 YES
25 CTNND1 CTNND1 CTNND1 3567 0.3 0.38 YES
26 WASL WASL WASL 3617 0.29 0.39 YES
27 LMO7 LMO7 LMO7 3623 0.29 0.41 YES
28 PTPRM PTPRM PTPRM 3676 0.29 0.42 YES
29 SMAD3 SMAD3 SMAD3 3988 0.27 0.42 YES
30 PVRL1 PVRL1 PVRL1 4044 0.26 0.43 YES
31 CTNNB1 CTNNB1 CTNNB1 4060 0.26 0.44 YES
32 CDH1 CDH1 CDH1 4114 0.26 0.45 YES
33 EP300 EP300 EP300 4220 0.25 0.46 YES
34 CTNNA1 CTNNA1 CTNNA1 4222 0.25 0.47 YES
35 PVRL4 PVRL4 PVRL4 4721 0.22 0.46 NO
36 PTPRF PTPRF PTPRF 4747 0.22 0.47 NO
37 ACTN4 ACTN4 ACTN4 5035 0.2 0.46 NO
38 MAPK1 MAPK1 MAPK1 5082 0.2 0.47 NO
39 CREBBP CREBBP CREBBP 5660 0.17 0.45 NO
40 MAP3K7 MAP3K7 MAP3K7 5667 0.17 0.46 NO
41 PTPRJ PTPRJ PTPRJ 6233 0.15 0.43 NO
42 BAIAP2 BAIAP2 BAIAP2 6315 0.14 0.43 NO
43 PARD3 PARD3 PARD3 6736 0.12 0.42 NO
44 WASF2 WASF2 WASF2 6759 0.12 0.42 NO
45 ACTN1 ACTN1 ACTN1 6955 0.11 0.42 NO
46 SMAD4 SMAD4 SMAD4 7001 0.11 0.42 NO
47 SNAI1 SNAI1 SNAI1 7092 0.11 0.42 NO
48 IQGAP1 IQGAP1 IQGAP1 7331 0.098 0.41 NO
49 MAPK3 MAPK3 MAPK3 7931 0.075 0.38 NO
50 CSNK2A2 CSNK2A2 CSNK2A2 8397 0.057 0.36 NO
51 CSNK2A1 CSNK2A1 CSNK2A1 8499 0.053 0.36 NO
52 CTNNA3 CTNNA3 CTNNA3 8789 0.043 0.35 NO
53 SMAD2 SMAD2 SMAD2 8891 0.039 0.34 NO
54 NLK NLK NLK 8989 0.036 0.34 NO
55 SRC SRC SRC 9095 0.033 0.34 NO
56 RAC1 RAC1 RAC1 9377 0.024 0.32 NO
57 WASF1 WASF1 WASF1 9775 0.0084 0.3 NO
58 PTPN1 PTPN1 PTPN1 9950 0.0027 0.29 NO
59 CDC42 CDC42 CDC42 9987 0.0014 0.29 NO
60 RHOA RHOA RHOA 10107 -0.0026 0.28 NO
61 ACTG1 ACTG1 ACTG1 11878 -0.065 0.19 NO
62 ACP1 ACP1 ACP1 12519 -0.091 0.16 NO
63 SSX2IP SSX2IP SSX2IP 12702 -0.099 0.15 NO
64 ACTB ACTB ACTB 13084 -0.12 0.14 NO
65 RAC3 RAC3 RAC3 13515 -0.13 0.12 NO
66 CSNK2B CSNK2B CSNK2B 13692 -0.14 0.12 NO
67 FYN FYN FYN 14922 -0.2 0.062 NO
68 ACTN2 ACTN2 ACTN2 15558 -0.24 0.04 NO
69 PTPN6 PTPN6 PTPN6 15649 -0.25 0.048 NO
70 LEF1 LEF1 LEF1 17294 -0.45 -0.02 NO
71 WAS WAS WAS 17347 -0.45 0.0013 NO
72 TCF7 TCF7 TCF7 17418 -0.47 0.022 NO
73 RAC2 RAC2 RAC2 17501 -0.49 0.043 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 EDG1 PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EDG1 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 N GLYCAN BIOSYNTHESIS

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 CACNA2D1 CACNA2D1 CACNA2D1 26 1.2 0.041 YES
2 ITGB8 ITGB8 ITGB8 44 1.1 0.08 YES
3 ITGA9 ITGA9 ITGA9 96 1 0.11 YES
4 ITGA1 ITGA1 ITGA1 172 0.94 0.14 YES
5 TGFB2 TGFB2 TGFB2 178 0.92 0.18 YES
6 ITGB3 ITGB3 ITGB3 366 0.81 0.19 YES
7 ITGA8 ITGA8 ITGA8 472 0.76 0.21 YES
8 ITGA2 ITGA2 ITGA2 536 0.74 0.24 YES
9 DMD DMD DMD 615 0.71 0.26 YES
10 LAMA2 LAMA2 LAMA2 921 0.64 0.26 YES
11 ADCY2 ADCY2 ADCY2 943 0.64 0.28 YES
12 ITGA2B ITGA2B ITGA2B 1007 0.62 0.3 YES
13 ADCY5 ADCY5 ADCY5 1251 0.57 0.31 YES
14 SLC8A1 SLC8A1 SLC8A1 1341 0.56 0.33 YES
15 CACNA1C CACNA1C CACNA1C 1375 0.55 0.34 YES
16 ITGA10 ITGA10 ITGA10 1581 0.51 0.35 YES
17 CACNB4 CACNB4 CACNB4 1705 0.5 0.36 YES
18 ITGA3 ITGA3 ITGA3 1707 0.5 0.38 YES
19 TNNT2 TNNT2 TNNT2 1815 0.48 0.39 YES
20 MYH6 MYH6 MYH6 1915 0.47 0.4 YES
21 CACNA1D CACNA1D CACNA1D 2056 0.45 0.41 YES
22 SGCB SGCB SGCB 2280 0.42 0.41 YES
23 ITGB4 ITGB4 ITGB4 2331 0.41 0.42 YES
24 CACNA2D2 CACNA2D2 CACNA2D2 2338 0.41 0.44 YES
25 CACNB2 CACNB2 CACNB2 2432 0.4 0.45 YES
26 SGCA SGCA SGCA 2481 0.4 0.46 YES
27 ITGAV ITGAV ITGAV 2493 0.39 0.47 YES
28 ADCY6 ADCY6 ADCY6 2645 0.38 0.48 YES
29 ITGB5 ITGB5 ITGB5 2757 0.37 0.48 YES
30 DAG1 DAG1 DAG1 2818 0.36 0.49 YES
31 MYL3 MYL3 MYL3 2859 0.36 0.5 YES
32 ITGA6 ITGA6 ITGA6 2920 0.35 0.51 YES
33 RYR2 RYR2 RYR2 2970 0.35 0.52 YES
34 SGCG SGCG SGCG 3013 0.34 0.53 YES
35 ADCY4 ADCY4 ADCY4 3033 0.34 0.54 YES
36 ATP2A2 ATP2A2 ATP2A2 3179 0.33 0.55 YES
37 ADCY9 ADCY9 ADCY9 3217 0.33 0.56 YES
38 ADCY1 ADCY1 ADCY1 3327 0.32 0.56 YES
39 TPM1 TPM1 TPM1 3475 0.31 0.56 YES
40 ITGB1 ITGB1 ITGB1 3611 0.29 0.57 YES
41 MYH7 MYH7 MYH7 4202 0.25 0.55 NO
42 ACTC1 ACTC1 ACTC1 4673 0.22 0.53 NO
43 ADCY8 ADCY8 ADCY8 4690 0.22 0.53 NO
44 ADRB1 ADRB1 ADRB1 4862 0.21 0.53 NO
45 ITGA11 ITGA11 ITGA11 4949 0.21 0.54 NO
46 IGF1 IGF1 IGF1 5177 0.2 0.53 NO
47 TNNC1 TNNC1 TNNC1 5359 0.19 0.53 NO
48 PLN PLN PLN 5366 0.19 0.53 NO
49 TNF TNF TNF 5821 0.16 0.51 NO
50 TGFB3 TGFB3 TGFB3 6330 0.14 0.49 NO
51 TPM4 TPM4 TPM4 6957 0.11 0.46 NO
52 TTN TTN TTN 6983 0.11 0.46 NO
53 ITGB6 ITGB6 ITGB6 7662 0.085 0.43 NO
54 PRKX PRKX PRKX 7705 0.084 0.43 NO
55 ADCY7 ADCY7 ADCY7 7835 0.079 0.42 NO
56 PRKACA PRKACA PRKACA 8158 0.066 0.41 NO
57 CACNA2D3 CACNA2D3 CACNA2D3 8248 0.062 0.41 NO
58 TPM2 TPM2 TPM2 8473 0.054 0.4 NO
59 DES DES DES 8928 0.038 0.37 NO
60 LMNA LMNA LMNA 9067 0.034 0.37 NO
61 ITGA5 ITGA5 ITGA5 9550 0.017 0.34 NO
62 GNAS GNAS GNAS 10138 -0.0036 0.31 NO
63 CACNG4 CACNG4 CACNG4 11320 -0.045 0.24 NO
64 TGFB1 TGFB1 TGFB1 11577 -0.054 0.23 NO
65 CACNA2D4 CACNA2D4 CACNA2D4 11647 -0.056 0.23 NO
66 CACNA1S CACNA1S CACNA1S 11787 -0.061 0.22 NO
67 ACTG1 ACTG1 ACTG1 11878 -0.065 0.22 NO
68 ITGA7 ITGA7 ITGA7 12024 -0.071 0.22 NO
69 PRKACB PRKACB PRKACB 12182 -0.078 0.21 NO
70 ACTB ACTB ACTB 13084 -0.12 0.17 NO
71 ITGA4 ITGA4 ITGA4 13123 -0.12 0.17 NO
72 CACNB1 CACNB1 CACNB1 13236 -0.12 0.17 NO
73 TPM3 TPM3 TPM3 13253 -0.12 0.17 NO
74 MYL2 MYL2 MYL2 13523 -0.13 0.16 NO
75 TNNI3 TNNI3 TNNI3 13693 -0.14 0.16 NO
76 MYBPC3 MYBPC3 MYBPC3 13856 -0.15 0.15 NO
77 ITGB7 ITGB7 ITGB7 13928 -0.15 0.15 NO
78 EMD EMD EMD 14578 -0.18 0.12 NO
79 SGCD SGCD SGCD 15029 -0.21 0.11 NO
80 CACNG2 CACNG2 CACNG2 15390 -0.23 0.095 NO
81 CACNG3 CACNG3 CACNG3 15986 -0.28 0.072 NO
82 CACNB3 CACNB3 CACNB3 16089 -0.28 0.076 NO
83 CACNG1 CACNG1 CACNG1 17166 -0.42 0.032 NO
84 CACNA1F CACNA1F CACNA1F 18231 -0.82 0.0029 NO

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

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG N GLYCAN 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 O GLYCAN BIOSYNTHESIS

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 CACNA2D1 CACNA2D1 CACNA2D1 26 1.2 0.045 YES
2 ITGB8 ITGB8 ITGB8 44 1.1 0.088 YES
3 ITGA9 ITGA9 ITGA9 96 1 0.12 YES
4 ITGA1 ITGA1 ITGA1 172 0.94 0.16 YES
5 ITGB3 ITGB3 ITGB3 366 0.81 0.18 YES
6 ITGA8 ITGA8 ITGA8 472 0.76 0.2 YES
7 ITGA2 ITGA2 ITGA2 536 0.74 0.23 YES
8 DMD DMD DMD 615 0.71 0.25 YES
9 LAMA2 LAMA2 LAMA2 921 0.64 0.26 YES
10 ITGA2B ITGA2B ITGA2B 1007 0.62 0.28 YES
11 SLC8A1 SLC8A1 SLC8A1 1341 0.56 0.28 YES
12 CACNA1C CACNA1C CACNA1C 1375 0.55 0.3 YES
13 TCF7L1 TCF7L1 TCF7L1 1578 0.52 0.31 YES
14 ITGA10 ITGA10 ITGA10 1581 0.51 0.33 YES
15 CACNB4 CACNB4 CACNB4 1705 0.5 0.34 YES
16 ITGA3 ITGA3 ITGA3 1707 0.5 0.36 YES
17 CACNA1D CACNA1D CACNA1D 2056 0.45 0.36 YES
18 TCF7L2 TCF7L2 TCF7L2 2109 0.44 0.38 YES
19 SGCB SGCB SGCB 2280 0.42 0.38 YES
20 CTNNA2 CTNNA2 CTNNA2 2293 0.42 0.4 YES
21 ITGB4 ITGB4 ITGB4 2331 0.41 0.41 YES
22 CACNA2D2 CACNA2D2 CACNA2D2 2338 0.41 0.43 YES
23 CACNB2 CACNB2 CACNB2 2432 0.4 0.44 YES
24 SGCA SGCA SGCA 2481 0.4 0.45 YES
25 ITGAV ITGAV ITGAV 2493 0.39 0.47 YES
26 ITGB5 ITGB5 ITGB5 2757 0.37 0.47 YES
27 DAG1 DAG1 DAG1 2818 0.36 0.48 YES
28 ACTN3 ACTN3 ACTN3 2842 0.36 0.49 YES
29 ITGA6 ITGA6 ITGA6 2920 0.35 0.5 YES
30 DSG2 DSG2 DSG2 2969 0.35 0.51 YES
31 RYR2 RYR2 RYR2 2970 0.35 0.52 YES
32 SGCG SGCG SGCG 3013 0.34 0.54 YES
33 ATP2A2 ATP2A2 ATP2A2 3179 0.33 0.54 YES
34 PKP2 PKP2 PKP2 3376 0.31 0.54 YES
35 ITGB1 ITGB1 ITGB1 3611 0.29 0.54 YES
36 GJA1 GJA1 GJA1 3719 0.28 0.55 YES
37 CTNNB1 CTNNB1 CTNNB1 4060 0.26 0.54 NO
38 CTNNA1 CTNNA1 CTNNA1 4222 0.25 0.54 NO
39 DSP DSP DSP 4264 0.25 0.55 NO
40 JUP JUP JUP 4628 0.23 0.53 NO
41 ITGA11 ITGA11 ITGA11 4949 0.21 0.52 NO
42 ACTN4 ACTN4 ACTN4 5035 0.2 0.53 NO
43 CDH2 CDH2 CDH2 5213 0.2 0.52 NO
44 DSC2 DSC2 DSC2 6920 0.12 0.44 NO
45 ACTN1 ACTN1 ACTN1 6955 0.11 0.44 NO
46 ITGB6 ITGB6 ITGB6 7662 0.085 0.4 NO
47 CACNA2D3 CACNA2D3 CACNA2D3 8248 0.062 0.37 NO
48 CTNNA3 CTNNA3 CTNNA3 8789 0.043 0.35 NO
49 DES DES DES 8928 0.038 0.34 NO
50 LMNA LMNA LMNA 9067 0.034 0.33 NO
51 ITGA5 ITGA5 ITGA5 9550 0.017 0.31 NO
52 CACNG4 CACNG4 CACNG4 11320 -0.045 0.21 NO
53 CACNA2D4 CACNA2D4 CACNA2D4 11647 -0.056 0.2 NO
54 CACNA1S CACNA1S CACNA1S 11787 -0.061 0.19 NO
55 ACTG1 ACTG1 ACTG1 11878 -0.065 0.19 NO
56 ITGA7 ITGA7 ITGA7 12024 -0.071 0.18 NO
57 ACTB ACTB ACTB 13084 -0.12 0.13 NO
58 ITGA4 ITGA4 ITGA4 13123 -0.12 0.13 NO
59 CACNB1 CACNB1 CACNB1 13236 -0.12 0.13 NO
60 ITGB7 ITGB7 ITGB7 13928 -0.15 0.099 NO
61 EMD EMD EMD 14578 -0.18 0.07 NO
62 SGCD SGCD SGCD 15029 -0.21 0.054 NO
63 CACNG2 CACNG2 CACNG2 15390 -0.23 0.043 NO
64 ACTN2 ACTN2 ACTN2 15558 -0.24 0.043 NO
65 CACNG3 CACNG3 CACNG3 15986 -0.28 0.031 NO
66 CACNB3 CACNB3 CACNB3 16089 -0.28 0.036 NO
67 CACNG1 CACNG1 CACNG1 17166 -0.42 -0.0065 NO
68 LEF1 LEF1 LEF1 17294 -0.45 0.0039 NO
69 TCF7 TCF7 TCF7 17418 -0.47 0.016 NO
70 CACNA1F CACNA1F CACNA1F 18231 -0.82 0.0029 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 O GLYCAN BIOSYNTHESIS.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG O GLYCAN 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 WNT SIGNALING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CACNA2D1 CACNA2D1 CACNA2D1 26 1.2 0.044 YES
2 ITGB8 ITGB8 ITGB8 44 1.1 0.085 YES
3 ITGA9 ITGA9 ITGA9 96 1 0.12 YES
4 ITGA1 ITGA1 ITGA1 172 0.94 0.15 YES
5 TGFB2 TGFB2 TGFB2 178 0.92 0.19 YES
6 ITGB3 ITGB3 ITGB3 366 0.81 0.21 YES
7 ITGA8 ITGA8 ITGA8 472 0.76 0.23 YES
8 ITGA2 ITGA2 ITGA2 536 0.74 0.26 YES
9 DMD DMD DMD 615 0.71 0.28 YES
10 LAMA2 LAMA2 LAMA2 921 0.64 0.29 YES
11 ITGA2B ITGA2B ITGA2B 1007 0.62 0.3 YES
12 PRKAA2 PRKAA2 PRKAA2 1179 0.58 0.32 YES
13 SLC8A1 SLC8A1 SLC8A1 1341 0.56 0.33 YES
14 CACNA1C CACNA1C CACNA1C 1375 0.55 0.35 YES
15 ITGA10 ITGA10 ITGA10 1581 0.51 0.36 YES
16 CACNB4 CACNB4 CACNB4 1705 0.5 0.37 YES
17 ITGA3 ITGA3 ITGA3 1707 0.5 0.39 YES
18 TNNT2 TNNT2 TNNT2 1815 0.48 0.4 YES
19 MYH6 MYH6 MYH6 1915 0.47 0.41 YES
20 CACNA1D CACNA1D CACNA1D 2056 0.45 0.42 YES
21 SGCB SGCB SGCB 2280 0.42 0.43 YES
22 ITGB4 ITGB4 ITGB4 2331 0.41 0.44 YES
23 CACNA2D2 CACNA2D2 CACNA2D2 2338 0.41 0.45 YES
24 CACNB2 CACNB2 CACNB2 2432 0.4 0.46 YES
25 SGCA SGCA SGCA 2481 0.4 0.48 YES
26 ITGAV ITGAV ITGAV 2493 0.39 0.49 YES
27 ACE ACE ACE 2699 0.37 0.49 YES
28 ITGB5 ITGB5 ITGB5 2757 0.37 0.5 YES
29 DAG1 DAG1 DAG1 2818 0.36 0.52 YES
30 MYL3 MYL3 MYL3 2859 0.36 0.53 YES
31 ITGA6 ITGA6 ITGA6 2920 0.35 0.54 YES
32 RYR2 RYR2 RYR2 2970 0.35 0.55 YES
33 SGCG SGCG SGCG 3013 0.34 0.56 YES
34 ATP2A2 ATP2A2 ATP2A2 3179 0.33 0.56 YES
35 TPM1 TPM1 TPM1 3475 0.31 0.56 NO
36 ITGB1 ITGB1 ITGB1 3611 0.29 0.56 NO
37 MYH7 MYH7 MYH7 4202 0.25 0.54 NO
38 ACTC1 ACTC1 ACTC1 4673 0.22 0.52 NO
39 ITGA11 ITGA11 ITGA11 4949 0.21 0.51 NO
40 PRKAG2 PRKAG2 PRKAG2 5061 0.2 0.51 NO
41 IGF1 IGF1 IGF1 5177 0.2 0.52 NO
42 TNNC1 TNNC1 TNNC1 5359 0.19 0.51 NO
43 IL6 IL6 IL6 5609 0.17 0.5 NO
44 TNF TNF TNF 5821 0.16 0.5 NO
45 PRKAB2 PRKAB2 PRKAB2 6002 0.16 0.5 NO
46 TGFB3 TGFB3 TGFB3 6330 0.14 0.48 NO
47 TPM4 TPM4 TPM4 6957 0.11 0.45 NO
48 TTN TTN TTN 6983 0.11 0.46 NO
49 PRKAA1 PRKAA1 PRKAA1 7489 0.092 0.43 NO
50 ITGB6 ITGB6 ITGB6 7662 0.085 0.43 NO
51 CACNA2D3 CACNA2D3 CACNA2D3 8248 0.062 0.4 NO
52 TPM2 TPM2 TPM2 8473 0.054 0.39 NO
53 PRKAB1 PRKAB1 PRKAB1 8555 0.051 0.38 NO
54 DES DES DES 8928 0.038 0.36 NO
55 LMNA LMNA LMNA 9067 0.034 0.36 NO
56 ITGA5 ITGA5 ITGA5 9550 0.017 0.33 NO
57 PRKAG1 PRKAG1 PRKAG1 11308 -0.045 0.24 NO
58 CACNG4 CACNG4 CACNG4 11320 -0.045 0.24 NO
59 TGFB1 TGFB1 TGFB1 11577 -0.054 0.23 NO
60 CACNA2D4 CACNA2D4 CACNA2D4 11647 -0.056 0.22 NO
61 CACNA1S CACNA1S CACNA1S 11787 -0.061 0.22 NO
62 ACTG1 ACTG1 ACTG1 11878 -0.065 0.22 NO
63 ITGA7 ITGA7 ITGA7 12024 -0.071 0.21 NO
64 ACTB ACTB ACTB 13084 -0.12 0.16 NO
65 ITGA4 ITGA4 ITGA4 13123 -0.12 0.16 NO
66 CACNB1 CACNB1 CACNB1 13236 -0.12 0.16 NO
67 TPM3 TPM3 TPM3 13253 -0.12 0.16 NO
68 MYL2 MYL2 MYL2 13523 -0.13 0.15 NO
69 TNNI3 TNNI3 TNNI3 13693 -0.14 0.15 NO
70 MYBPC3 MYBPC3 MYBPC3 13856 -0.15 0.14 NO
71 ITGB7 ITGB7 ITGB7 13928 -0.15 0.15 NO
72 EMD EMD EMD 14578 -0.18 0.12 NO
73 SGCD SGCD SGCD 15029 -0.21 0.1 NO
74 CACNG2 CACNG2 CACNG2 15390 -0.23 0.09 NO
75 CACNG3 CACNG3 CACNG3 15986 -0.28 0.068 NO
76 CACNB3 CACNB3 CACNB3 16089 -0.28 0.073 NO
77 CACNG1 CACNG1 CACNG1 17166 -0.42 0.03 NO
78 CACNA1F CACNA1F CACNA1F 18231 -0.82 0.0029 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 WNT SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG TGF BETA SIGNALING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SMAD9 SMAD9 SMAD9 10 1.3 0.049 YES
2 TGFB2 TGFB2 TGFB2 178 0.92 0.075 YES
3 ID4 ID4 ID4 209 0.9 0.11 YES
4 ROCK2 ROCK2 ROCK2 287 0.85 0.14 YES
5 BMP8B BMP8B BMP8B 341 0.82 0.17 YES
6 GDF6 GDF6 GDF6 475 0.76 0.19 YES
7 BMP2 BMP2 BMP2 577 0.73 0.21 YES
8 LTBP1 LTBP1 LTBP1 636 0.71 0.23 YES
9 SMAD7 SMAD7 SMAD7 767 0.68 0.25 YES
10 LEFTY2 LEFTY2 LEFTY2 830 0.66 0.28 YES
11 BMP4 BMP4 BMP4 941 0.64 0.29 YES
12 FST FST FST 1022 0.62 0.31 YES
13 GDF7 GDF7 GDF7 1184 0.58 0.33 YES
14 ACVR1C ACVR1C ACVR1C 1196 0.58 0.35 YES
15 INHBB INHBB INHBB 1233 0.58 0.37 YES
16 GDF5 GDF5 GDF5 1257 0.57 0.39 YES
17 BMPR1A BMPR1A BMPR1A 1393 0.55 0.4 YES
18 THBS1 THBS1 THBS1 1432 0.54 0.42 YES
19 THBS4 THBS4 THBS4 1583 0.51 0.43 YES
20 INHBC INHBC INHBC 1653 0.5 0.45 YES
21 BMP6 BMP6 BMP6 1730 0.49 0.46 YES
22 SMAD6 SMAD6 SMAD6 1750 0.49 0.48 YES
23 ACVR1 ACVR1 ACVR1 2514 0.39 0.46 YES
24 TGFBR2 TGFBR2 TGFBR2 2814 0.36 0.45 YES
25 NODAL NODAL NODAL 2931 0.35 0.46 YES
26 TGFBR1 TGFBR1 TGFBR1 2957 0.35 0.47 YES
27 BMPR2 BMPR2 BMPR2 2985 0.35 0.48 YES
28 LEFTY1 LEFTY1 LEFTY1 3314 0.32 0.48 YES
29 ZFYVE9 ZFYVE9 ZFYVE9 3336 0.32 0.49 YES
30 SMAD5 SMAD5 SMAD5 3361 0.32 0.5 YES
31 INHBA INHBA INHBA 3388 0.31 0.51 YES
32 ACVR2A ACVR2A ACVR2A 3517 0.3 0.52 YES
33 SMURF2 SMURF2 SMURF2 3755 0.28 0.51 YES
34 SMURF1 SMURF1 SMURF1 3837 0.28 0.52 YES
35 ID1 ID1 ID1 3838 0.28 0.53 YES
36 SMAD3 SMAD3 SMAD3 3988 0.27 0.53 YES
37 ZFYVE16 ZFYVE16 ZFYVE16 4013 0.27 0.54 YES
38 BMP5 BMP5 BMP5 4087 0.26 0.55 YES
39 DCN DCN DCN 4132 0.26 0.56 YES
40 EP300 EP300 EP300 4220 0.25 0.56 YES
41 BMP7 BMP7 BMP7 4390 0.24 0.56 YES
42 ID2 ID2 ID2 4511 0.23 0.56 YES
43 PPP2CB PPP2CB PPP2CB 4692 0.22 0.56 YES
44 RBL1 RBL1 RBL1 4975 0.21 0.55 YES
45 MAPK1 MAPK1 MAPK1 5082 0.2 0.56 YES
46 RBL2 RBL2 RBL2 5211 0.2 0.56 YES
47 SMAD1 SMAD1 SMAD1 5339 0.19 0.56 YES
48 ACVR2B ACVR2B ACVR2B 5404 0.18 0.56 YES
49 ROCK1 ROCK1 ROCK1 5459 0.18 0.56 YES
50 CREBBP CREBBP CREBBP 5660 0.17 0.56 NO
51 TNF TNF TNF 5821 0.16 0.56 NO
52 AMH AMH AMH 5970 0.16 0.56 NO
53 TGFB3 TGFB3 TGFB3 6330 0.14 0.54 NO
54 AMHR2 AMHR2 AMHR2 6358 0.14 0.55 NO
55 SP1 SP1 SP1 6421 0.14 0.55 NO
56 RPS6KB1 RPS6KB1 RPS6KB1 6803 0.12 0.53 NO
57 THBS2 THBS2 THBS2 6824 0.12 0.53 NO
58 SMAD4 SMAD4 SMAD4 7001 0.11 0.53 NO
59 ID3 ID3 ID3 7102 0.11 0.53 NO
60 CHRD CHRD CHRD 7218 0.1 0.52 NO
61 ACVRL1 ACVRL1 ACVRL1 7381 0.097 0.52 NO
62 MAPK3 MAPK3 MAPK3 7931 0.075 0.49 NO
63 BMPR1B BMPR1B BMPR1B 8049 0.07 0.49 NO
64 TFDP1 TFDP1 TFDP1 8269 0.062 0.48 NO
65 E2F5 E2F5 E2F5 8576 0.051 0.46 NO
66 BMP8A BMP8A BMP8A 8827 0.042 0.45 NO
67 SMAD2 SMAD2 SMAD2 8891 0.039 0.45 NO
68 SKP1 SKP1 SKP1 8970 0.036 0.45 NO
69 CUL1 CUL1 CUL1 9444 0.021 0.42 NO
70 RHOA RHOA RHOA 10107 -0.0026 0.38 NO
71 PPP2R1A PPP2R1A PPP2R1A 10574 -0.019 0.36 NO
72 CDKN2B CDKN2B CDKN2B 10831 -0.028 0.35 NO
73 TGFB1 TGFB1 TGFB1 11577 -0.054 0.31 NO
74 IFNG IFNG IFNG 11642 -0.056 0.31 NO
75 PPP2R1B PPP2R1B PPP2R1B 11954 -0.068 0.29 NO
76 THBS3 THBS3 THBS3 12012 -0.07 0.29 NO
77 COMP COMP COMP 12251 -0.08 0.28 NO
78 PITX2 PITX2 PITX2 12722 -0.099 0.26 NO
79 E2F4 E2F4 E2F4 12726 -0.1 0.26 NO
80 PPP2CA PPP2CA PPP2CA 12933 -0.11 0.26 NO
81 INHBE INHBE INHBE 14932 -0.2 0.16 NO
82 RPS6KB2 RPS6KB2 RPS6KB2 15285 -0.22 0.14 NO
83 RBX1 RBX1 RBX1 15770 -0.26 0.13 NO
84 MYC MYC MYC 15937 -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 TGF BETA SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG AXON GUIDANCE

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 ITGB8 ITGB8 ITGB8 44 1.1 0.035 YES
2 ITGA9 ITGA9 ITGA9 96 1 0.067 YES
3 IBSP IBSP IBSP 155 0.96 0.096 YES
4 ITGA1 ITGA1 ITGA1 172 0.94 0.13 YES
5 LAMA1 LAMA1 LAMA1 219 0.9 0.15 YES
6 LAMB4 LAMB4 LAMB4 293 0.85 0.18 YES
7 ITGB3 ITGB3 ITGB3 366 0.81 0.2 YES
8 ITGA8 ITGA8 ITGA8 472 0.76 0.22 YES
9 COL11A1 COL11A1 COL11A1 497 0.75 0.24 YES
10 ITGA2 ITGA2 ITGA2 536 0.74 0.27 YES
11 SDC2 SDC2 SDC2 868 0.65 0.27 YES
12 FN1 FN1 FN1 887 0.65 0.29 YES
13 LAMA2 LAMA2 LAMA2 921 0.64 0.31 YES
14 ITGA2B ITGA2B ITGA2B 1007 0.62 0.33 YES
15 COL2A1 COL2A1 COL2A1 1008 0.62 0.35 YES
16 SDC4 SDC4 SDC4 1173 0.58 0.36 YES
17 CHAD CHAD CHAD 1314 0.56 0.37 YES
18 THBS1 THBS1 THBS1 1432 0.54 0.38 YES
19 LAMA4 LAMA4 LAMA4 1475 0.53 0.4 YES
20 ITGA10 ITGA10 ITGA10 1581 0.51 0.41 YES
21 THBS4 THBS4 THBS4 1583 0.51 0.42 YES
22 ITGA3 ITGA3 ITGA3 1707 0.5 0.44 YES
23 COL11A2 COL11A2 COL11A2 1942 0.47 0.44 YES
24 LAMB2 LAMB2 LAMB2 2096 0.44 0.44 YES
25 SPP1 SPP1 SPP1 2297 0.42 0.45 YES
26 ITGB4 ITGB4 ITGB4 2331 0.41 0.46 YES
27 COL4A6 COL4A6 COL4A6 2469 0.4 0.46 YES
28 COL5A1 COL5A1 COL5A1 2483 0.4 0.48 YES
29 ITGAV ITGAV ITGAV 2493 0.39 0.49 YES
30 AGRN AGRN AGRN 2604 0.38 0.5 YES
31 COL4A1 COL4A1 COL4A1 2696 0.37 0.5 YES
32 ITGB5 ITGB5 ITGB5 2757 0.37 0.51 YES
33 LAMA5 LAMA5 LAMA5 2801 0.36 0.52 YES
34 DAG1 DAG1 DAG1 2818 0.36 0.53 YES
35 LAMC1 LAMC1 LAMC1 2909 0.35 0.54 YES
36 ITGA6 ITGA6 ITGA6 2920 0.35 0.55 YES
37 TNC TNC TNC 3111 0.34 0.55 YES
38 LAMA3 LAMA3 LAMA3 3174 0.33 0.56 YES
39 COL1A2 COL1A2 COL1A2 3411 0.31 0.56 YES
40 COL5A2 COL5A2 COL5A2 3509 0.3 0.56 YES
41 HSPG2 HSPG2 HSPG2 3569 0.3 0.57 YES
42 LAMC3 LAMC3 LAMC3 3605 0.29 0.58 YES
43 ITGB1 ITGB1 ITGB1 3611 0.29 0.59 YES
44 GP1BA GP1BA GP1BA 3731 0.28 0.59 YES
45 COL1A1 COL1A1 COL1A1 3852 0.28 0.59 YES
46 COL4A2 COL4A2 COL4A2 4045 0.26 0.59 YES
47 COL5A3 COL5A3 COL5A3 4080 0.26 0.6 YES
48 COL6A3 COL6A3 COL6A3 4108 0.26 0.6 YES
49 SV2C SV2C SV2C 4217 0.25 0.61 YES
50 COL3A1 COL3A1 COL3A1 4474 0.24 0.6 NO
51 LAMB1 LAMB1 LAMB1 4786 0.22 0.59 NO
52 TNN TNN TNN 4924 0.21 0.59 NO
53 ITGA11 ITGA11 ITGA11 4949 0.21 0.6 NO
54 SDC1 SDC1 SDC1 4951 0.21 0.6 NO
55 CD36 CD36 CD36 5010 0.21 0.61 NO
56 COL6A2 COL6A2 COL6A2 5190 0.2 0.6 NO
57 COL4A4 COL4A4 COL4A4 5765 0.17 0.58 NO
58 VWF VWF VWF 5813 0.16 0.58 NO
59 TNXB TNXB TNXB 5827 0.16 0.59 NO
60 COL6A1 COL6A1 COL6A1 6414 0.14 0.56 NO
61 THBS2 THBS2 THBS2 6824 0.12 0.54 NO
62 GP6 GP6 GP6 7171 0.1 0.52 NO
63 CD47 CD47 CD47 7330 0.098 0.52 NO
64 SDC3 SDC3 SDC3 7347 0.098 0.52 NO
65 ITGB6 ITGB6 ITGB6 7662 0.085 0.51 NO
66 COL6A6 COL6A6 COL6A6 9329 0.026 0.42 NO
67 ITGA5 ITGA5 ITGA5 9550 0.017 0.4 NO
68 GP5 GP5 GP5 10083 -0.002 0.38 NO
69 THBS3 THBS3 THBS3 12012 -0.07 0.27 NO
70 ITGA7 ITGA7 ITGA7 12024 -0.071 0.27 NO
71 COMP COMP COMP 12251 -0.08 0.26 NO
72 RELN RELN RELN 12405 -0.086 0.26 NO
73 SV2A SV2A SV2A 12900 -0.11 0.24 NO
74 ITGA4 ITGA4 ITGA4 13123 -0.12 0.23 NO
75 ITGB7 ITGB7 ITGB7 13928 -0.15 0.19 NO
76 LAMB3 LAMB3 LAMB3 14710 -0.19 0.15 NO
77 LAMC2 LAMC2 LAMC2 15035 -0.21 0.14 NO
78 CD44 CD44 CD44 15150 -0.22 0.14 NO
79 SV2B SV2B SV2B 17338 -0.45 0.036 NO
80 HMMR HMMR HMMR 17437 -0.48 0.046 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 AXON GUIDANCE.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AXON GUIDANCE, 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 FOCAL ADHESION

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 ITGB3 ITGB3 ITGB3 366 0.81 0.11 YES
2 PLCB1 PLCB1 PLCB1 1619 0.51 0.13 YES
3 GNGT1 GNGT1 GNGT1 2010 0.46 0.18 YES
4 PDGFRA PDGFRA PDGFRA 2312 0.42 0.23 YES
5 ITGAV ITGAV ITGAV 2493 0.39 0.28 YES
6 PDGFA PDGFA PDGFA 2548 0.39 0.34 YES
7 PIK3CA PIK3CA PIK3CA 2724 0.37 0.4 YES
8 ASAH1 ASAH1 ASAH1 2964 0.35 0.44 YES
9 PRKCA PRKCA PRKCA 3742 0.28 0.44 YES
10 PTK2 PTK2 PTK2 3804 0.28 0.48 YES
11 GNAI1 GNAI1 GNAI1 4139 0.26 0.51 YES
12 SPHK1 SPHK1 SPHK1 4609 0.23 0.52 YES
13 MAPK1 MAPK1 MAPK1 5082 0.2 0.53 YES
14 S1PR1 S1PR1 S1PR1 7269 0.1 0.42 NO
15 MAPK3 MAPK3 MAPK3 7931 0.075 0.4 NO
16 PIK3R1 PIK3R1 PIK3R1 8731 0.045 0.36 NO
17 SRC SRC SRC 9095 0.033 0.35 NO
18 RAC1 RAC1 RAC1 9377 0.024 0.34 NO
19 GNB1 GNB1 GNB1 9557 0.017 0.33 NO
20 RHOA RHOA RHOA 10107 -0.0026 0.3 NO
21 PIK3CG PIK3CG PIK3CG 10942 -0.032 0.26 NO
22 SPHKAP SPHKAP SPHKAP 11396 -0.048 0.24 NO
23 SMPD1 SMPD1 SMPD1 11958 -0.068 0.22 NO
24 AKT1 AKT1 AKT1 12631 -0.096 0.2 NO
25 SMPD2 SMPD2 SMPD2 15127 -0.22 0.1 NO
26 PRKCB PRKCB PRKCB 17269 -0.44 0.056 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 FOCAL ADHESION.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FOCAL ADHESION, 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 ECM RECEPTOR INTERACTION

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 SEMA3D SEMA3D SEMA3D 43 1.1 0.028 YES
2 NFATC2 NFATC2 NFATC2 65 1.1 0.055 YES
3 SLIT2 SLIT2 SLIT2 90 1 0.081 YES
4 SEMA3E SEMA3E SEMA3E 98 1 0.11 YES
5 EPHA3 EPHA3 EPHA3 232 0.89 0.12 YES
6 ROCK2 ROCK2 ROCK2 287 0.85 0.14 YES
7 PLXNC1 PLXNC1 PLXNC1 300 0.84 0.16 YES
8 NGEF NGEF NGEF 327 0.83 0.19 YES
9 SEMA5B SEMA5B SEMA5B 372 0.8 0.2 YES
10 NTN4 NTN4 NTN4 465 0.76 0.22 YES
11 EFNB3 EFNB3 EFNB3 480 0.76 0.24 YES
12 EPHA2 EPHA2 EPHA2 584 0.72 0.25 YES
13 SEMA3C SEMA3C SEMA3C 622 0.71 0.27 YES
14 EPHB3 EPHB3 EPHB3 751 0.68 0.28 YES
15 NRP1 NRP1 NRP1 761 0.68 0.3 YES
16 SEMA6D SEMA6D SEMA6D 832 0.66 0.31 YES
17 UNC5C UNC5C UNC5C 840 0.66 0.33 YES
18 ROBO2 ROBO2 ROBO2 1072 0.61 0.33 YES
19 NTN1 NTN1 NTN1 1117 0.6 0.34 YES
20 SEMA3B SEMA3B SEMA3B 1219 0.58 0.36 YES
21 MET MET MET 1244 0.57 0.37 YES
22 EPHA4 EPHA4 EPHA4 1270 0.57 0.38 YES
23 UNC5D UNC5D UNC5D 1684 0.5 0.37 YES
24 SEMA5A SEMA5A SEMA5A 1812 0.48 0.38 YES
25 ROBO1 ROBO1 ROBO1 1852 0.48 0.39 YES
26 PAK6 PAK6 PAK6 1889 0.47 0.4 YES
27 ARHGEF12 ARHGEF12 ARHGEF12 1944 0.47 0.41 YES
28 EFNA5 EFNA5 EFNA5 1977 0.46 0.42 YES
29 UNC5B UNC5B UNC5B 2092 0.44 0.42 YES
30 NFAT5 NFAT5 NFAT5 2277 0.42 0.43 YES
31 SEMA4G SEMA4G SEMA4G 2335 0.41 0.43 YES
32 SRGAP1 SRGAP1 SRGAP1 2355 0.41 0.44 YES
33 SRGAP3 SRGAP3 SRGAP3 2535 0.39 0.44 YES
34 EFNB2 EFNB2 EFNB2 2608 0.38 0.45 YES
35 SEMA3F SEMA3F SEMA3F 2872 0.36 0.44 YES
36 SEMA4C SEMA4C SEMA4C 2938 0.35 0.45 YES
37 PLXNA2 PLXNA2 PLXNA2 3023 0.34 0.46 YES
38 PLXNB2 PLXNB2 PLXNB2 3038 0.34 0.46 YES
39 ITGB1 ITGB1 ITGB1 3611 0.29 0.44 YES
40 SEMA3A SEMA3A SEMA3A 3654 0.29 0.45 YES
41 NTN3 NTN3 NTN3 3791 0.28 0.44 YES
42 EPHA7 EPHA7 EPHA7 3800 0.28 0.45 YES
43 PTK2 PTK2 PTK2 3804 0.28 0.46 YES
44 EPHB4 EPHB4 EPHB4 3894 0.27 0.46 YES
45 SEMA6B SEMA6B SEMA6B 3902 0.27 0.47 YES
46 ABLIM1 ABLIM1 ABLIM1 3971 0.27 0.47 YES
47 EPHB1 EPHB1 EPHB1 4081 0.26 0.47 YES
48 GNAI1 GNAI1 GNAI1 4139 0.26 0.48 YES
49 PAK3 PAK3 PAK3 4176 0.25 0.48 YES
50 ABL1 ABL1 ABL1 4310 0.24 0.48 YES
51 RASA1 RASA1 RASA1 4363 0.24 0.48 YES
52 SEMA6A SEMA6A SEMA6A 4520 0.23 0.48 NO
53 NCK2 NCK2 NCK2 4948 0.21 0.46 NO
54 MAPK1 MAPK1 MAPK1 5082 0.2 0.46 NO
55 NTNG1 NTNG1 NTNG1 5218 0.2 0.46 NO
56 EPHA6 EPHA6 EPHA6 5302 0.19 0.46 NO
57 ROCK1 ROCK1 ROCK1 5459 0.18 0.46 NO
58 LIMK2 LIMK2 LIMK2 5567 0.18 0.46 NO
59 SLIT3 SLIT3 SLIT3 5618 0.17 0.46 NO
60 SEMA3G SEMA3G SEMA3G 5661 0.17 0.46 NO
61 CFL2 CFL2 CFL2 5665 0.17 0.46 NO
62 CHP CHP CHP 5713 0.17 0.46 NO
63 NFATC4 NFATC4 NFATC4 5718 0.17 0.47 NO
64 ABLIM2 ABLIM2 ABLIM2 5903 0.16 0.46 NO
65 PLXNA1 PLXNA1 PLXNA1 5999 0.16 0.46 NO
66 RHOD RHOD RHOD 6251 0.14 0.45 NO
67 EPHB2 EPHB2 EPHB2 6260 0.14 0.46 NO
68 PPP3CA PPP3CA PPP3CA 6702 0.12 0.44 NO
69 SEMA4F SEMA4F SEMA4F 6863 0.12 0.43 NO
70 SEMA4A SEMA4A SEMA4A 6913 0.12 0.43 NO
71 PAK4 PAK4 PAK4 6939 0.11 0.43 NO
72 PLXNB1 PLXNB1 PLXNB1 7062 0.11 0.43 NO
73 EFNA1 EFNA1 EFNA1 7101 0.11 0.43 NO
74 GSK3B GSK3B GSK3B 7193 0.1 0.43 NO
75 MAPK3 MAPK3 MAPK3 7931 0.075 0.39 NO
76 EPHA1 EPHA1 EPHA1 7988 0.072 0.39 NO
77 PAK1 PAK1 PAK1 8130 0.067 0.38 NO
78 PPP3R2 PPP3R2 PPP3R2 8247 0.062 0.38 NO
79 SRGAP2 SRGAP2 SRGAP2 8303 0.06 0.37 NO
80 FES FES FES 8447 0.055 0.37 NO
81 SEMA4B SEMA4B SEMA4B 8599 0.05 0.36 NO
82 PAK7 PAK7 PAK7 8665 0.048 0.36 NO
83 EFNB1 EFNB1 EFNB1 8695 0.047 0.36 NO
84 PLXNA3 PLXNA3 PLXNA3 8848 0.041 0.35 NO
85 SEMA6C SEMA6C SEMA6C 9010 0.035 0.34 NO
86 NCK1 NCK1 NCK1 9178 0.03 0.33 NO
87 LIMK1 LIMK1 LIMK1 9270 0.028 0.33 NO
88 PPP3CB PPP3CB PPP3CB 9336 0.025 0.33 NO
89 RAC1 RAC1 RAC1 9377 0.024 0.33 NO
90 KRAS KRAS KRAS 9778 0.0083 0.3 NO
91 PPP3R1 PPP3R1 PPP3R1 9844 0.006 0.3 NO
92 CDC42 CDC42 CDC42 9987 0.0014 0.29 NO
93 EFNA3 EFNA3 EFNA3 9994 0.0012 0.29 NO
94 GNAI3 GNAI3 GNAI3 10011 0.00031 0.29 NO
95 ROBO3 ROBO3 ROBO3 10047 -0.00082 0.29 NO
96 RHOA RHOA RHOA 10107 -0.0026 0.29 NO
97 NFATC1 NFATC1 NFATC1 10316 -0.011 0.28 NO
98 RGS3 RGS3 RGS3 10532 -0.018 0.26 NO
99 PAK2 PAK2 PAK2 10656 -0.022 0.26 NO
100 DCC DCC DCC 10687 -0.023 0.26 NO
101 CHP2 CHP2 CHP2 10818 -0.028 0.25 NO
102 GNAI2 GNAI2 GNAI2 10834 -0.028 0.25 NO
103 NRAS NRAS NRAS 11154 -0.04 0.23 NO
104 UNC5A UNC5A UNC5A 11451 -0.05 0.22 NO
105 RND1 RND1 RND1 12280 -0.081 0.18 NO
106 PPP3CC PPP3CC PPP3CC 12390 -0.086 0.17 NO
107 DPYSL2 DPYSL2 DPYSL2 12698 -0.099 0.16 NO
108 EFNA4 EFNA4 EFNA4 12780 -0.1 0.16 NO
109 SLIT1 SLIT1 SLIT1 13136 -0.12 0.14 NO
110 RAC3 RAC3 RAC3 13515 -0.13 0.12 NO
111 DPYSL5 DPYSL5 DPYSL5 13641 -0.14 0.12 NO
112 LRRC4C LRRC4C LRRC4C 13880 -0.15 0.11 NO
113 L1CAM L1CAM L1CAM 13914 -0.15 0.11 NO
114 SEMA4D SEMA4D SEMA4D 14630 -0.19 0.077 NO
115 FYN FYN FYN 14922 -0.2 0.066 NO
116 CFL1 CFL1 CFL1 15093 -0.21 0.062 NO
117 NFATC3 NFATC3 NFATC3 15345 -0.23 0.055 NO
118 EPHA8 EPHA8 EPHA8 15605 -0.24 0.047 NO
119 SEMA7A SEMA7A SEMA7A 16507 -0.32 0.0058 NO
120 ABLIM3 ABLIM3 ABLIM3 16538 -0.33 0.013 NO
121 EPHB6 EPHB6 EPHB6 16926 -0.38 0.0017 NO
122 CXCL12 CXCL12 CXCL12 17034 -0.4 0.0063 NO
123 CXCR4 CXCR4 CXCR4 17050 -0.4 0.016 NO
124 EPHA5 EPHA5 EPHA5 17100 -0.41 0.024 NO
125 CDK5 CDK5 CDK5 17126 -0.42 0.034 NO
126 RAC2 RAC2 RAC2 17501 -0.49 0.026 NO
127 PLXNB3 PLXNB3 PLXNB3 17997 -0.64 0.016 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 ECM RECEPTOR INTERACTION.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus4 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA FMLP PATHWAY 35 genes.ES.table 0.45 1.6 0.033 0.21 0.66 0.29 0.2 0.23 0.14 0.02
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.4 1.6 0.068 0.2 0.66 0.28 0.2 0.22 0.13 0.018
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.39 1.5 0.07 0.21 0.77 0.38 0.2 0.3 0.16 0.011
KEGG GLYCOLYSIS GLUCONEOGENESIS 56 genes.ES.table 0.53 1.8 0 0.34 0.29 0.43 0.23 0.33 0 0.13
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.51 1.6 0.043 0.21 0.63 0.48 0.22 0.38 0.14 0.019
KEGG ARGININE AND PROLINE METABOLISM 52 genes.ES.table 0.51 1.5 0.028 0.21 0.8 0.38 0.2 0.31 0.16 0.009
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 43 genes.ES.table 0.41 1.6 0.049 0.21 0.7 0.3 0.22 0.24 0.15 0.016
KEGG ETHER LIPID METABOLISM 26 genes.ES.table 0.6 1.6 0.013 0.24 0.61 0.27 0.066 0.25 0.15 0.033
KEGG ARACHIDONIC ACID METABOLISM 46 genes.ES.table 0.57 1.6 0.019 0.2 0.72 0.33 0.077 0.3 0.14 0.01
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 25 genes.ES.table 0.58 1.6 0.04 0.2 0.71 0.52 0.26 0.39 0.14 0.012
genes ES table in pathway: BIOCARTA FMLP PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CCL4 CCL4 CCL4 54 1 0.095 YES
2 ZBP1 ZBP1 ZBP1 60 1 0.19 YES
3 AIM2 AIM2 AIM2 130 0.89 0.28 YES
4 CXCL10 CXCL10 CXCL10 286 0.76 0.34 YES
5 CCL5 CCL5 CCL5 496 0.64 0.39 YES
6 IL6 IL6 IL6 837 0.53 0.42 YES
7 CCL4L2 CCL4L2 CCL4L2 953 0.5 0.46 YES
8 IL1B IL1B IL1B 1127 0.46 0.5 YES
9 IRF7 IRF7 IRF7 1284 0.43 0.53 YES
10 IL33 IL33 IL33 2011 0.32 0.52 YES
11 POLR3D POLR3D POLR3D 2179 0.3 0.55 YES
12 PYCARD PYCARD PYCARD 2494 0.27 0.55 YES
13 IL18 IL18 IL18 2566 0.26 0.57 YES
14 TBK1 TBK1 TBK1 2680 0.25 0.59 YES
15 IFNB1 IFNB1 IFNB1 2743 0.24 0.61 YES
16 CASP1 CASP1 CASP1 3190 0.2 0.61 YES
17 POLR3G POLR3G POLR3G 3240 0.2 0.62 YES
18 NFKBIA NFKBIA NFKBIA 3366 0.19 0.64 YES
19 RIPK3 RIPK3 RIPK3 3708 0.16 0.63 YES
20 NFKBIB NFKBIB NFKBIB 3777 0.16 0.64 YES
21 IKBKE IKBKE IKBKE 3915 0.15 0.65 YES
22 POLR1C POLR1C POLR1C 4825 0.11 0.61 NO
23 IRF3 IRF3 IRF3 4971 0.1 0.61 NO
24 TREX1 TREX1 TREX1 5447 0.083 0.6 NO
25 RELA RELA RELA 5511 0.08 0.6 NO
26 POLR3B POLR3B POLR3B 5517 0.08 0.61 NO
27 POLR3C POLR3C POLR3C 5693 0.074 0.6 NO
28 POLR3K POLR3K POLR3K 5736 0.073 0.61 NO
29 ADAR ADAR ADAR 5947 0.066 0.6 NO
30 POLR1D POLR1D POLR1D 6121 0.06 0.6 NO
31 TMEM173 TMEM173 TMEM173 6237 0.057 0.6 NO
32 IKBKB IKBKB IKBKB 6261 0.056 0.6 NO
33 POLR3H POLR3H POLR3H 7215 0.029 0.56 NO
34 IKBKG IKBKG IKBKG 7676 0.017 0.53 NO
35 POLR3F POLR3F POLR3F 7760 0.015 0.53 NO
36 POLR3A POLR3A POLR3A 8169 0.0053 0.51 NO
37 MAVS MAVS MAVS 8945 -0.013 0.46 NO
38 CHUK CHUK CHUK 10686 -0.053 0.38 NO
39 DDX58 DDX58 DDX58 11490 -0.072 0.34 NO
40 RIPK1 RIPK1 RIPK1 11918 -0.084 0.32 NO
41 POLR3GL POLR3GL POLR3GL 13534 -0.13 0.25 NO
42 NFKB1 NFKB1 NFKB1 13614 -0.14 0.26 NO

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

Figure S62.  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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FBP1 FBP1 FBP1 208 0.82 0.075 YES
2 ALDH3B1 ALDH3B1 ALDH3B1 735 0.56 0.1 YES
3 ALDOC ALDOC ALDOC 857 0.53 0.15 YES
4 HK3 HK3 HK3 957 0.5 0.2 YES
5 ALDH3A1 ALDH3A1 ALDH3A1 988 0.49 0.25 YES
6 ALDOB ALDOB ALDOB 1672 0.37 0.25 YES
7 ADH6 ADH6 ADH6 2047 0.32 0.26 YES
8 PCK2 PCK2 PCK2 2106 0.31 0.29 YES
9 ADH1A ADH1A ADH1A 2233 0.29 0.32 YES
10 FBP2 FBP2 FBP2 2234 0.29 0.35 YES
11 ALDH1B1 ALDH1B1 ALDH1B1 2258 0.29 0.38 YES
12 ADH7 ADH7 ADH7 2335 0.28 0.4 YES
13 PKLR PKLR PKLR 2422 0.27 0.42 YES
14 PFKL PFKL PFKL 2853 0.23 0.43 YES
15 GALM GALM GALM 3117 0.21 0.43 YES
16 ENO2 ENO2 ENO2 3428 0.18 0.44 YES
17 HK2 HK2 HK2 3568 0.17 0.44 YES
18 TPI1 TPI1 TPI1 3613 0.17 0.46 YES
19 PFKP PFKP PFKP 3636 0.17 0.48 YES
20 ADH1C ADH1C ADH1C 3664 0.17 0.49 YES
21 PKM2 PKM2 PKM2 3721 0.16 0.51 YES
22 ACSS2 ACSS2 ACSS2 3811 0.16 0.52 YES
23 ACSS1 ACSS1 ACSS1 4179 0.14 0.51 YES
24 PCK1 PCK1 PCK1 4222 0.14 0.52 YES
25 HK1 HK1 HK1 4660 0.11 0.51 NO
26 ENO1 ENO1 ENO1 4788 0.11 0.52 NO
27 ALDOA ALDOA ALDOA 5607 0.077 0.48 NO
28 PGM2 PGM2 PGM2 5613 0.076 0.49 NO
29 ALDH3B2 ALDH3B2 ALDH3B2 5905 0.067 0.48 NO
30 GPI GPI GPI 6266 0.056 0.47 NO
31 GAPDH GAPDH GAPDH 6299 0.055 0.47 NO
32 PGAM1 PGAM1 PGAM1 6509 0.048 0.46 NO
33 LDHA LDHA LDHA 6943 0.036 0.44 NO
34 PGAM4 PGAM4 PGAM4 7667 0.017 0.4 NO
35 ADH1B ADH1B ADH1B 7730 0.016 0.4 NO
36 LDHAL6B LDHAL6B LDHAL6B 7943 0.01 0.39 NO
37 DLD DLD DLD 8553 -0.0035 0.36 NO
38 ALDH3A2 ALDH3A2 ALDH3A2 8682 -0.0067 0.35 NO
39 PGK1 PGK1 PGK1 8691 -0.0069 0.35 NO
40 AKR1A1 AKR1A1 AKR1A1 8971 -0.014 0.34 NO
41 ENO3 ENO3 ENO3 9194 -0.019 0.33 NO
42 ALDH2 ALDH2 ALDH2 9949 -0.036 0.29 NO
43 PFKM PFKM PFKM 10005 -0.037 0.29 NO
44 DLAT DLAT DLAT 10125 -0.04 0.29 NO
45 PDHA1 PDHA1 PDHA1 10291 -0.044 0.29 NO
46 PGAM2 PGAM2 PGAM2 10366 -0.046 0.29 NO
47 ALDH1A3 ALDH1A3 ALDH1A3 11145 -0.064 0.25 NO
48 ALDH9A1 ALDH9A1 ALDH9A1 11517 -0.073 0.24 NO
49 GCK GCK GCK 12298 -0.094 0.21 NO
50 PDHB PDHB PDHB 12311 -0.095 0.22 NO
51 LDHB LDHB LDHB 12513 -0.1 0.21 NO
52 BPGM BPGM BPGM 13288 -0.12 0.18 NO
53 ADH5 ADH5 ADH5 13320 -0.13 0.2 NO
54 PGM1 PGM1 PGM1 14158 -0.16 0.17 NO
55 ALDH7A1 ALDH7A1 ALDH7A1 15746 -0.25 0.11 NO
56 LDHAL6A LDHAL6A LDHAL6A 16511 -0.32 0.097 NO

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

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

genes ES table in pathway: BIOCARTA DEATH PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IFNG IFNG IFNG 76 0.98 0.048 YES
2 IL1A IL1A IL1A 345 0.72 0.072 YES
3 NCF1 NCF1 NCF1 414 0.67 0.1 YES
4 TNF TNF TNF 427 0.67 0.14 YES
5 FCGR1A FCGR1A FCGR1A 470 0.65 0.17 YES
6 IL10 IL10 IL10 612 0.6 0.2 YES
7 NOS2 NOS2 NOS2 687 0.57 0.22 YES
8 HLA-DOB HLA-DOB HLA-DOB 779 0.54 0.25 YES
9 IL1B IL1B IL1B 1127 0.46 0.25 YES
10 ITGAM ITGAM ITGAM 1169 0.46 0.28 YES
11 HLA-DOA HLA-DOA HLA-DOA 1300 0.43 0.29 YES
12 HLA-DQA2 HLA-DQA2 HLA-DQA2 1306 0.43 0.31 YES
13 NCF2 NCF2 NCF2 1355 0.42 0.33 YES
14 IL12A IL12A IL12A 1363 0.42 0.36 YES
15 FCGR3A FCGR3A FCGR3A 1368 0.42 0.38 YES
16 FCGR2C FCGR2C FCGR2C 1522 0.39 0.39 YES
17 TLR2 TLR2 TLR2 1585 0.38 0.41 YES
18 HLA-DQA1 HLA-DQA1 HLA-DQA1 1837 0.34 0.41 YES
19 MAPK12 MAPK12 MAPK12 1840 0.34 0.43 YES
20 HLA-DRB5 HLA-DRB5 HLA-DRB5 1856 0.34 0.45 YES
21 HLA-DMA HLA-DMA HLA-DMA 2031 0.32 0.45 YES
22 CR1 CR1 CR1 2197 0.3 0.46 YES
23 FCGR3B FCGR3B FCGR3B 2214 0.3 0.48 YES
24 HLA-DRB1 HLA-DRB1 HLA-DRB1 2470 0.27 0.48 YES
25 NCF4 NCF4 NCF4 2600 0.25 0.48 YES
26 C3 C3 C3 2653 0.25 0.49 YES
27 MAPK13 MAPK13 MAPK13 2715 0.24 0.5 YES
28 HLA-DRA HLA-DRA HLA-DRA 2740 0.24 0.52 YES
29 FCGR2A FCGR2A FCGR2A 2753 0.24 0.53 YES
30 HLA-DMB HLA-DMB HLA-DMB 2795 0.24 0.54 YES
31 FOS FOS FOS 2827 0.23 0.55 YES
32 MAPK11 MAPK11 MAPK11 2851 0.23 0.56 YES
33 HLA-DPA1 HLA-DPA1 HLA-DPA1 3060 0.21 0.56 YES
34 TLR4 TLR4 TLR4 3096 0.21 0.57 YES
35 IFNGR2 IFNGR2 IFNGR2 3176 0.2 0.57 YES
36 HLA-DPB1 HLA-DPB1 HLA-DPB1 3191 0.2 0.58 YES
37 STAT1 STAT1 STAT1 3217 0.2 0.6 YES
38 JAK2 JAK2 JAK2 3236 0.2 0.6 YES
39 CYBA CYBA CYBA 3365 0.19 0.61 YES
40 NFKBIA NFKBIA NFKBIA 3366 0.19 0.62 YES
41 HLA-DQB1 HLA-DQB1 HLA-DQB1 3589 0.17 0.62 YES
42 TGFB2 TGFB2 TGFB2 3648 0.17 0.62 YES
43 JUN JUN JUN 3699 0.16 0.63 YES
44 NFKBIB NFKBIB NFKBIB 3777 0.16 0.63 YES
45 IRAK1 IRAK1 IRAK1 3865 0.15 0.63 YES
46 IL12B IL12B IL12B 4810 0.11 0.59 NO
47 TGFB1 TGFB1 TGFB1 5149 0.094 0.57 NO
48 RELA RELA RELA 5511 0.08 0.56 NO
49 PTPN6 PTPN6 PTPN6 5670 0.075 0.56 NO
50 MYD88 MYD88 MYD88 6304 0.054 0.52 NO
51 ITGB1 ITGB1 ITGB1 6866 0.038 0.49 NO
52 ELK1 ELK1 ELK1 8125 0.0062 0.42 NO
53 TAB1 TAB1 TAB1 8911 -0.012 0.38 NO
54 MAPK3 MAPK3 MAPK3 8962 -0.013 0.38 NO
55 ITGB2 ITGB2 ITGB2 10004 -0.037 0.33 NO
56 JAK1 JAK1 JAK1 11112 -0.063 0.27 NO
57 IRAK4 IRAK4 IRAK4 11212 -0.065 0.27 NO
58 MARCKSL1 MARCKSL1 MARCKSL1 11568 -0.074 0.25 NO
59 TGFB3 TGFB3 TGFB3 12523 -0.1 0.2 NO
60 MAPK1 MAPK1 MAPK1 12925 -0.11 0.19 NO
61 NFKB1 NFKB1 NFKB1 13614 -0.14 0.16 NO
62 IFNGR1 IFNGR1 IFNGR1 13741 -0.14 0.16 NO
63 TAB2 TAB2 TAB2 13769 -0.14 0.16 NO
64 MAPK14 MAPK14 MAPK14 14222 -0.16 0.15 NO
65 TRAF6 TRAF6 TRAF6 14631 -0.18 0.14 NO
66 MAP3K7 MAP3K7 MAP3K7 15010 -0.2 0.12 NO
67 IL4 IL4 IL4 15305 -0.22 0.12 NO
68 PRKCB PRKCB PRKCB 16738 -0.34 0.06 NO
69 ITGA4 ITGA4 ITGA4 17440 -0.46 0.046 NO

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

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

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IFNG IFNG IFNG 76 0.98 0.06 YES
2 CD80 CD80 CD80 115 0.92 0.12 YES
3 GZMB GZMB GZMB 209 0.82 0.17 YES
4 IL1A IL1A IL1A 345 0.72 0.21 YES
5 TNF TNF TNF 427 0.67 0.25 YES
6 FASLG FASLG FASLG 673 0.58 0.27 YES
7 HLA-DOB HLA-DOB HLA-DOB 779 0.54 0.3 YES
8 HLA-G HLA-G HLA-G 854 0.53 0.33 YES
9 IL1B IL1B IL1B 1127 0.46 0.35 YES
10 CD86 CD86 CD86 1141 0.46 0.38 YES
11 GAD1 GAD1 GAD1 1147 0.46 0.41 YES
12 LTA LTA LTA 1162 0.46 0.44 YES
13 HLA-DOA HLA-DOA HLA-DOA 1300 0.43 0.46 YES
14 HLA-DQA2 HLA-DQA2 HLA-DQA2 1306 0.43 0.48 YES
15 IL12A IL12A IL12A 1363 0.42 0.51 YES
16 PTPRN PTPRN PTPRN 1398 0.41 0.53 YES
17 HLA-F HLA-F HLA-F 1437 0.4 0.56 YES
18 IL2 IL2 IL2 1474 0.4 0.58 YES
19 GAD2 GAD2 GAD2 1821 0.34 0.58 YES
20 HLA-DQA1 HLA-DQA1 HLA-DQA1 1837 0.34 0.61 YES
21 HLA-DRB5 HLA-DRB5 HLA-DRB5 1856 0.34 0.63 YES
22 PRF1 PRF1 PRF1 1980 0.32 0.64 YES
23 ICA1 ICA1 ICA1 1981 0.32 0.66 YES
24 HLA-DMA HLA-DMA HLA-DMA 2031 0.32 0.68 YES
25 HLA-DRB1 HLA-DRB1 HLA-DRB1 2470 0.27 0.68 YES
26 HLA-B HLA-B HLA-B 2475 0.27 0.69 YES
27 HLA-DRA HLA-DRA HLA-DRA 2740 0.24 0.69 YES
28 HLA-DMB HLA-DMB HLA-DMB 2795 0.24 0.71 YES
29 HLA-C HLA-C HLA-C 2972 0.22 0.71 YES
30 HLA-A HLA-A HLA-A 3013 0.22 0.72 YES
31 HLA-DPA1 HLA-DPA1 HLA-DPA1 3060 0.21 0.74 YES
32 HLA-DPB1 HLA-DPB1 HLA-DPB1 3191 0.2 0.74 YES
33 FAS FAS FAS 3262 0.2 0.75 YES
34 HLA-E HLA-E HLA-E 3421 0.18 0.75 YES
35 HSPD1 HSPD1 HSPD1 4133 0.14 0.72 NO
36 IL12B IL12B IL12B 4810 0.11 0.69 NO
37 CD28 CD28 CD28 14800 -0.19 0.16 NO
38 PTPRN2 PTPRN2 PTPRN2 15242 -0.22 0.15 NO
39 CPE CPE CPE 16046 -0.27 0.12 NO

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

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IFNG IFNG IFNG 76 0.98 0.072 YES
2 CD80 CD80 CD80 115 0.92 0.14 YES
3 GZMB GZMB GZMB 209 0.82 0.2 YES
4 TNF TNF TNF 427 0.67 0.24 YES
5 IL10 IL10 IL10 612 0.6 0.28 YES
6 FASLG FASLG FASLG 673 0.58 0.32 YES
7 HLA-DOB HLA-DOB HLA-DOB 779 0.54 0.36 YES
8 HLA-G HLA-G HLA-G 854 0.53 0.39 YES
9 CD86 CD86 CD86 1141 0.46 0.41 YES
10 HLA-DOA HLA-DOA HLA-DOA 1300 0.43 0.44 YES
11 HLA-DQA2 HLA-DQA2 HLA-DQA2 1306 0.43 0.47 YES
12 IL12A IL12A IL12A 1363 0.42 0.5 YES
13 HLA-F HLA-F HLA-F 1437 0.4 0.53 YES
14 IL2 IL2 IL2 1474 0.4 0.56 YES
15 HLA-DQA1 HLA-DQA1 HLA-DQA1 1837 0.34 0.56 YES
16 HLA-DRB5 HLA-DRB5 HLA-DRB5 1856 0.34 0.59 YES
17 PRF1 PRF1 PRF1 1980 0.32 0.61 YES
18 HLA-DMA HLA-DMA HLA-DMA 2031 0.32 0.63 YES
19 CD40 CD40 CD40 2115 0.31 0.65 YES
20 HLA-DRB1 HLA-DRB1 HLA-DRB1 2470 0.27 0.65 YES
21 HLA-B HLA-B HLA-B 2475 0.27 0.67 YES
22 HLA-DRA HLA-DRA HLA-DRA 2740 0.24 0.68 YES
23 HLA-DMB HLA-DMB HLA-DMB 2795 0.24 0.69 YES
24 HLA-C HLA-C HLA-C 2972 0.22 0.7 YES
25 HLA-A HLA-A HLA-A 3013 0.22 0.71 YES
26 HLA-DPA1 HLA-DPA1 HLA-DPA1 3060 0.21 0.73 YES
27 HLA-DPB1 HLA-DPB1 HLA-DPB1 3191 0.2 0.74 YES
28 FAS FAS FAS 3262 0.2 0.75 YES
29 HLA-E HLA-E HLA-E 3421 0.18 0.75 YES
30 IL12B IL12B IL12B 4810 0.11 0.69 NO
31 CD40LG CD40LG CD40LG 11711 -0.078 0.32 NO
32 IL5 IL5 IL5 14475 -0.17 0.18 NO
33 CD28 CD28 CD28 14800 -0.19 0.17 NO
34 IL4 IL4 IL4 15305 -0.22 0.16 NO

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

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

genes ES table in pathway: KEGG ARGININE AND PROLINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IFNG IFNG IFNG 76 0.98 0.064 YES
2 CD80 CD80 CD80 115 0.92 0.13 YES
3 GZMB GZMB GZMB 209 0.82 0.18 YES
4 IL1A IL1A IL1A 345 0.72 0.22 YES
5 TNF TNF TNF 427 0.67 0.26 YES
6 KLRC1 KLRC1 KLRC1 437 0.66 0.31 YES
7 FASLG FASLG FASLG 673 0.58 0.34 YES
8 HLA-DOB HLA-DOB HLA-DOB 779 0.54 0.37 YES
9 IL6 IL6 IL6 837 0.53 0.4 YES
10 HLA-G HLA-G HLA-G 854 0.53 0.44 YES
11 IL1B IL1B IL1B 1127 0.46 0.46 YES
12 CD86 CD86 CD86 1141 0.46 0.49 YES
13 HLA-DOA HLA-DOA HLA-DOA 1300 0.43 0.51 YES
14 HLA-DQA2 HLA-DQA2 HLA-DQA2 1306 0.43 0.54 YES
15 HLA-F HLA-F HLA-F 1437 0.4 0.56 YES
16 IL2 IL2 IL2 1474 0.4 0.59 YES
17 HLA-DQA1 HLA-DQA1 HLA-DQA1 1837 0.34 0.59 YES
18 HLA-DRB5 HLA-DRB5 HLA-DRB5 1856 0.34 0.61 YES
19 PRF1 PRF1 PRF1 1980 0.32 0.63 YES
20 KLRD1 KLRD1 KLRD1 1985 0.32 0.65 YES
21 HLA-DMA HLA-DMA HLA-DMA 2031 0.32 0.67 YES
22 HLA-DRB1 HLA-DRB1 HLA-DRB1 2470 0.27 0.67 YES
23 HLA-B HLA-B HLA-B 2475 0.27 0.68 YES
24 HLA-DRA HLA-DRA HLA-DRA 2740 0.24 0.69 YES
25 HLA-DMB HLA-DMB HLA-DMB 2795 0.24 0.7 YES
26 HLA-C HLA-C HLA-C 2972 0.22 0.71 YES
27 KIR2DL1 KIR2DL1 KIR2DL1 2980 0.22 0.72 YES
28 HLA-A HLA-A HLA-A 3013 0.22 0.73 YES
29 HLA-DPA1 HLA-DPA1 HLA-DPA1 3060 0.21 0.75 YES
30 HLA-DPB1 HLA-DPB1 HLA-DPB1 3191 0.2 0.75 YES
31 FAS FAS FAS 3262 0.2 0.76 YES
32 HLA-E HLA-E HLA-E 3421 0.18 0.77 YES
33 KIR3DL1 KIR3DL1 KIR3DL1 3703 0.16 0.76 NO
34 KIR2DL3 KIR2DL3 KIR2DL3 4665 0.11 0.72 NO
35 CD28 CD28 CD28 14800 -0.19 0.18 NO
36 KIR3DL2 KIR3DL2 KIR3DL2 14983 -0.2 0.18 NO

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

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PYDC1 PYDC1 PYDC1 68 0.99 0.061 YES
2 CARD9 CARD9 CARD9 232 0.8 0.1 YES
3 NOD2 NOD2 NOD2 324 0.73 0.15 YES
4 CCL8 CCL8 CCL8 390 0.69 0.19 YES
5 TNF TNF TNF 427 0.67 0.23 YES
6 CCL5 CCL5 CCL5 496 0.64 0.27 YES
7 CCL13 CCL13 CCL13 538 0.62 0.3 YES
8 CASP5 CASP5 CASP5 632 0.59 0.34 YES
9 CCL11 CCL11 CCL11 649 0.58 0.38 YES
10 MEFV MEFV MEFV 800 0.54 0.4 YES
11 BIRC3 BIRC3 BIRC3 825 0.53 0.44 YES
12 IL6 IL6 IL6 837 0.53 0.47 YES
13 IL1B IL1B IL1B 1127 0.46 0.48 YES
14 CCL7 CCL7 CCL7 1633 0.37 0.48 YES
15 MAPK12 MAPK12 MAPK12 1840 0.34 0.49 YES
16 CCL2 CCL2 CCL2 1943 0.33 0.51 YES
17 CXCL2 CXCL2 CXCL2 2130 0.31 0.52 YES
18 NLRP3 NLRP3 NLRP3 2259 0.29 0.53 YES
19 RIPK2 RIPK2 RIPK2 2454 0.27 0.54 YES
20 PYCARD PYCARD PYCARD 2494 0.27 0.55 YES
21 PSTPIP1 PSTPIP1 PSTPIP1 2499 0.27 0.57 YES
22 IL18 IL18 IL18 2566 0.26 0.58 YES
23 MAPK13 MAPK13 MAPK13 2715 0.24 0.59 YES
24 MAPK11 MAPK11 MAPK11 2851 0.23 0.6 YES
25 CASP1 CASP1 CASP1 3190 0.2 0.59 NO
26 NFKBIA NFKBIA NFKBIA 3366 0.19 0.59 NO
27 NLRC4 NLRC4 NLRC4 3536 0.18 0.6 NO
28 NFKBIB NFKBIB NFKBIB 3777 0.16 0.59 NO
29 CXCL1 CXCL1 CXCL1 4532 0.12 0.56 NO
30 TNFAIP3 TNFAIP3 TNFAIP3 4675 0.11 0.56 NO
31 NLRP1 NLRP1 NLRP1 5021 0.099 0.55 NO
32 IL8 IL8 IL8 5377 0.086 0.53 NO
33 RELA RELA RELA 5511 0.08 0.53 NO
34 IKBKB IKBKB IKBKB 6261 0.056 0.49 NO
35 HSP90AA1 HSP90AA1 HSP90AA1 6435 0.05 0.49 NO
36 TRIP6 TRIP6 TRIP6 6704 0.042 0.48 NO
37 HSP90B1 HSP90B1 HSP90B1 6815 0.04 0.47 NO
38 IKBKG IKBKG IKBKG 7676 0.017 0.42 NO
39 SUGT1 SUGT1 SUGT1 7686 0.017 0.43 NO
40 MAPK10 MAPK10 MAPK10 8096 0.007 0.4 NO
41 TAB1 TAB1 TAB1 8911 -0.012 0.36 NO
42 MAPK3 MAPK3 MAPK3 8962 -0.013 0.36 NO
43 NOD1 NOD1 NOD1 9318 -0.022 0.34 NO
44 TAB3 TAB3 TAB3 10198 -0.042 0.29 NO
45 CHUK CHUK CHUK 10686 -0.053 0.27 NO
46 CASP8 CASP8 CASP8 11319 -0.068 0.24 NO
47 XIAP XIAP XIAP 11613 -0.076 0.23 NO
48 BIRC2 BIRC2 BIRC2 11963 -0.085 0.22 NO
49 CARD6 CARD6 CARD6 11981 -0.085 0.22 NO
50 MAPK9 MAPK9 MAPK9 12728 -0.11 0.19 NO
51 MAPK1 MAPK1 MAPK1 12925 -0.11 0.18 NO
52 CARD8 CARD8 CARD8 13272 -0.12 0.17 NO
53 NFKB1 NFKB1 NFKB1 13614 -0.14 0.16 NO
54 TAB2 TAB2 TAB2 13769 -0.14 0.16 NO
55 MAPK14 MAPK14 MAPK14 14222 -0.16 0.15 NO
56 TRAF6 TRAF6 TRAF6 14631 -0.18 0.14 NO
57 MAP3K7 MAP3K7 MAP3K7 15010 -0.2 0.13 NO
58 MAPK8 MAPK8 MAPK8 15463 -0.23 0.12 NO
59 ERBB2IP ERBB2IP ERBB2IP 15743 -0.25 0.12 NO
60 NAIP NAIP NAIP 16115 -0.28 0.12 NO

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

Figure S74.  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 S38.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CTLA4 CTLA4 CTLA4 35 1.1 0.082 YES
2 CD80 CD80 CD80 115 0.92 0.15 YES
3 GZMB GZMB GZMB 209 0.82 0.21 YES
4 IL10 IL10 IL10 612 0.6 0.23 YES
5 FASLG FASLG FASLG 673 0.58 0.27 YES
6 HLA-DOB HLA-DOB HLA-DOB 779 0.54 0.31 YES
7 HLA-G HLA-G HLA-G 854 0.53 0.34 YES
8 CD86 CD86 CD86 1141 0.46 0.36 YES
9 HLA-DOA HLA-DOA HLA-DOA 1300 0.43 0.39 YES
10 HLA-DQA2 HLA-DQA2 HLA-DQA2 1306 0.43 0.42 YES
11 HLA-F HLA-F HLA-F 1437 0.4 0.44 YES
12 IL2 IL2 IL2 1474 0.4 0.47 YES
13 HLA-DQA1 HLA-DQA1 HLA-DQA1 1837 0.34 0.48 YES
14 HLA-DRB5 HLA-DRB5 HLA-DRB5 1856 0.34 0.5 YES
15 PRF1 PRF1 PRF1 1980 0.32 0.52 YES
16 HLA-DMA HLA-DMA HLA-DMA 2031 0.32 0.55 YES
17 CD40 CD40 CD40 2115 0.31 0.56 YES
18 HLA-DRB1 HLA-DRB1 HLA-DRB1 2470 0.27 0.57 YES
19 HLA-B HLA-B HLA-B 2475 0.27 0.59 YES
20 HLA-DRA HLA-DRA HLA-DRA 2740 0.24 0.59 YES
21 HLA-DMB HLA-DMB HLA-DMB 2795 0.24 0.6 YES
22 CGA CGA CGA 2953 0.22 0.61 YES
23 HLA-C HLA-C HLA-C 2972 0.22 0.63 YES
24 HLA-A HLA-A HLA-A 3013 0.22 0.64 YES
25 HLA-DPA1 HLA-DPA1 HLA-DPA1 3060 0.21 0.66 YES
26 HLA-DPB1 HLA-DPB1 HLA-DPB1 3191 0.2 0.67 YES
27 FAS FAS FAS 3262 0.2 0.68 YES
28 HLA-E HLA-E HLA-E 3421 0.18 0.68 YES
29 HLA-DQB1 HLA-DQB1 HLA-DQB1 3589 0.17 0.69 YES
30 TPO TPO TPO 8135 0.006 0.44 NO
31 CD40LG CD40LG CD40LG 11711 -0.078 0.25 NO
32 TG TG TG 13151 -0.12 0.18 NO
33 IL5 IL5 IL5 14475 -0.17 0.12 NO
34 CD28 CD28 CD28 14800 -0.19 0.12 NO
35 IL4 IL4 IL4 15305 -0.22 0.11 NO
36 TSHR TSHR TSHR 18120 -0.74 0.0089 NO

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

Figure S76.  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 ARACHIDONIC ACID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SNAP25 SNAP25 SNAP25 704 0.57 0.1 YES
2 STX1A STX1A STX1A 768 0.55 0.24 YES
3 STX19 STX19 STX19 2218 0.3 0.24 YES
4 STX1B STX1B STX1B 2464 0.27 0.29 YES
5 STX11 STX11 STX11 2701 0.24 0.34 YES
6 VAMP5 VAMP5 VAMP5 4223 0.14 0.29 YES
7 VAMP8 VAMP8 VAMP8 4378 0.13 0.31 YES
8 STX4 STX4 STX4 4402 0.13 0.34 YES
9 STX3 STX3 STX3 4426 0.12 0.38 YES
10 SNAP47 SNAP47 SNAP47 6619 0.045 0.27 NO
11 BNIP1 BNIP1 BNIP1 6761 0.041 0.27 NO
12 GOSR1 GOSR1 GOSR1 6776 0.041 0.28 NO
13 VAMP3 VAMP3 VAMP3 7014 0.034 0.28 NO
14 TSNARE1 TSNARE1 TSNARE1 7166 0.03 0.27 NO
15 GOSR2 GOSR2 GOSR2 7384 0.025 0.27 NO
16 STX6 STX6 STX6 7570 0.02 0.26 NO
17 STX8 STX8 STX8 7615 0.019 0.27 NO
18 STX5 STX5 STX5 7697 0.017 0.27 NO
19 STX12 STX12 STX12 7791 0.015 0.26 NO
20 YKT6 YKT6 YKT6 8013 0.0089 0.25 NO
21 VTI1B VTI1B VTI1B 8406 0.00014 0.23 NO
22 STX18 STX18 STX18 8499 -0.0019 0.23 NO
23 VTI1A VTI1A VTI1A 8952 -0.013 0.21 NO
24 VAMP4 VAMP4 VAMP4 9123 -0.017 0.2 NO
25 SNAP23 SNAP23 SNAP23 9413 -0.024 0.19 NO
26 STX7 STX7 STX7 9586 -0.028 0.19 NO
27 BET1L BET1L BET1L 9696 -0.03 0.19 NO
28 STX10 STX10 STX10 9793 -0.033 0.2 NO
29 VAMP2 VAMP2 VAMP2 9931 -0.036 0.2 NO
30 USE1 USE1 USE1 9942 -0.036 0.2 NO
31 STX16 STX16 STX16 10152 -0.041 0.2 NO
32 STX17 STX17 STX17 11127 -0.064 0.17 NO
33 SEC22B SEC22B SEC22B 13268 -0.12 0.08 NO
34 BET1 BET1 BET1 13306 -0.12 0.11 NO
35 VAMP1 VAMP1 VAMP1 14006 -0.15 0.11 NO
36 VAMP7 VAMP7 VAMP7 15369 -0.22 0.092 NO
37 STX2 STX2 STX2 15984 -0.27 0.13 NO

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

Figure S78.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ARACHIDONIC 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 PORPHYRIN AND CHLOROPHYLL METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PLA2G3 PLA2G3 PLA2G3 11 1.2 0.18 YES
2 PLA2G2D PLA2G2D PLA2G2D 548 0.62 0.25 YES
3 PLA2G5 PLA2G5 PLA2G5 676 0.57 0.33 YES
4 PLA2G7 PLA2G7 PLA2G7 869 0.52 0.4 YES
5 PPAP2C PPAP2C PPAP2C 1008 0.49 0.47 YES
6 PLA2G2A PLA2G2A PLA2G2A 1037 0.48 0.54 YES
7 PLA2G10 PLA2G10 PLA2G10 1215 0.45 0.6 YES
8 CHPT1 CHPT1 CHPT1 3192 0.2 0.52 NO
9 PLA2G4A PLA2G4A PLA2G4A 3211 0.2 0.55 NO
10 ENPP2 ENPP2 ENPP2 3867 0.15 0.54 NO
11 PAFAH1B2 PAFAH1B2 PAFAH1B2 6049 0.062 0.43 NO
12 LPCAT1 LPCAT1 LPCAT1 7324 0.026 0.36 NO
13 PLA2G6 PLA2G6 PLA2G6 7393 0.024 0.36 NO
14 PPAP2A PPAP2A PPAP2A 8195 0.0048 0.32 NO
15 PAFAH1B3 PAFAH1B3 PAFAH1B3 8818 -0.0097 0.29 NO
16 PLD2 PLD2 PLD2 8860 -0.011 0.29 NO
17 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 9235 -0.02 0.27 NO
18 LPCAT4 LPCAT4 LPCAT4 10381 -0.046 0.22 NO
19 PLA2G12A PLA2G12A PLA2G12A 10895 -0.058 0.2 NO
20 PAFAH1B1 PAFAH1B1 PAFAH1B1 12240 -0.093 0.14 NO
21 LPCAT2 LPCAT2 LPCAT2 12806 -0.11 0.12 NO
22 PLD1 PLD1 PLD1 13497 -0.13 0.1 NO
23 AGPS AGPS AGPS 13815 -0.14 0.11 NO
24 PPAP2B PPAP2B PPAP2B 14640 -0.18 0.092 NO
25 PLA2G1B PLA2G1B PLA2G1B 15393 -0.22 0.086 NO
26 PAFAH2 PAFAH2 PAFAH2 17507 -0.47 0.042 NO

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

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL 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

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

  • Expression data file = THYM-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = THYM-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)