GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LUSC-TP
Lung Squamous Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1T72GH6
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 LUSC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1T72GH6
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 LUSC-TP. This pipeline has the following features:

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

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

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

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

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

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

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 192
Number of samples: 501
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 ] 113
pheno.type: 2 - 4 :[ clus2 ] 153
pheno.type: 3 - 4 :[ clus3 ] 155
pheno.type: 4 - 4 :[ clus4 ] 80

For the expression subtypes of 18514 genes in 502 samples, GSEA found enriched gene sets in each cluster using 501 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA RACCYCD PATHWAY, BIOCARTA MAPK PATHWAY, BIOCARTA P38MAPK PATHWAY, BIOCARTA IL1R PATHWAY, BIOCARTA TNFR1 PATHWAY, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG OXIDATIVE PHOSPHORYLATION, KEGG LINOLEIC ACID METABOLISM, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG RETINOL METABOLISM

    • And common core enriched genes are RAC1, CHUK, HRAS, NFKB1, NFKBIA, RB1, MAPK8, TNF, TRADD, CDC42

  • clus2

    • Top enriched gene sets are BIOCARTA CHREBP2 PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG GLYCEROLIPID METABOLISM, KEGG GLYCEROPHOSPHOLIPID METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450

    • And common core enriched genes are RPA1, RPA4, MLXIPL, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R5A, PRKAA2, G6PD, GCLC

  • clus3

    • Top enriched gene sets are BIOCARTA AGR PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA MPR PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA NKT PATHWAY, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG N GLYCAN BIOSYNTHESIS, KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION

    • And common core enriched genes are APAF1, BCL2, BIRC2, BIRC3, CASP6, CASP9, DFFB, MAP3K14, TRAF2, DNMT3A

  • clus4

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA KERATINOCYTE PATHWAY

    • And common core enriched genes are PLA2G10, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G4E, PLA2G5, KDR, ACP2, ACP5

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 RACCYCD PATHWAY 25 genes.ES.table 0.48 1.9 0.01 0.21 0.15 0.48 0.23 0.37 0 0.064
BIOCARTA MAPK PATHWAY 86 genes.ES.table 0.27 1.3 0.15 0.73 0.98 0.3 0.21 0.24 0.61 0.25
BIOCARTA P38MAPK PATHWAY 39 genes.ES.table 0.37 1.4 0.11 1 0.95 0.33 0.21 0.26 1 0.56
BIOCARTA IL1R PATHWAY 31 genes.ES.table 0.57 1.6 0.042 0.91 0.82 0.19 0.035 0.19 0.57 0.3
BIOCARTA TNFR1 PATHWAY 28 genes.ES.table 0.43 1.7 0.03 0.44 0.49 0.43 0.27 0.32 0 0.12
KEGG STEROID HORMONE BIOSYNTHESIS 48 genes.ES.table 0.51 1.3 0.16 0.68 0.99 0.31 0.074 0.29 0.58 0.21
KEGG OXIDATIVE PHOSPHORYLATION 114 genes.ES.table 0.34 1.3 0.21 0.79 0.98 0.56 0.28 0.41 0.66 0.29
KEGG LINOLEIC ACID METABOLISM 25 genes.ES.table 0.55 1.3 0.17 0.66 0.99 0.32 0.041 0.31 0.56 0.19
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES 25 genes.ES.table 0.49 1.3 0.13 0.82 0.98 0.16 0.012 0.16 0.68 0.3
KEGG RETINOL METABOLISM 59 genes.ES.table 0.56 1.4 0.088 0.86 0.97 0.42 0.1 0.38 0.68 0.31
genes ES table in pathway: BIOCARTA RACCYCD 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 CDKN1A CDKN1A CDKN1A 1554 0.1 0.01 YES
2 CDK6 CDK6 CDK6 1557 0.1 0.1 YES
3 CCND1 CCND1 CCND1 1822 0.091 0.17 YES
4 RAC1 RAC1 RAC1 2001 0.084 0.24 YES
5 RB1 RB1 RB1 2533 0.067 0.27 YES
6 AKT1 AKT1 AKT1 2755 0.061 0.31 YES
7 NFKBIA NFKBIA NFKBIA 2896 0.058 0.36 YES
8 NFKB1 NFKB1 NFKB1 2922 0.057 0.41 YES
9 CHUK CHUK CHUK 3333 0.049 0.43 YES
10 HRAS HRAS HRAS 3861 0.04 0.44 YES
11 MAPK3 MAPK3 MAPK3 4180 0.035 0.45 YES
12 PIK3R1 PIK3R1 PIK3R1 4292 0.033 0.48 YES
13 IKBKB IKBKB IKBKB 5055 0.023 0.46 NO
14 TFDP1 TFDP1 TFDP1 5333 0.02 0.46 NO
15 RELA RELA RELA 5566 0.018 0.46 NO
16 PAK1 PAK1 PAK1 6607 0.0076 0.41 NO
17 RAF1 RAF1 RAF1 6705 0.0066 0.42 NO
18 RHOA RHOA RHOA 6941 0.0044 0.41 NO
19 CCNE1 CCNE1 CCNE1 7422 0.00019 0.38 NO
20 MAPK1 MAPK1 MAPK1 7548 -0.0012 0.37 NO
21 IKBKG IKBKG IKBKG 8591 -0.011 0.33 NO
22 CDK4 CDK4 CDK4 11747 -0.045 0.2 NO
23 CDK2 CDK2 CDK2 11947 -0.048 0.23 NO
24 PIK3CA PIK3CA PIK3CA 12002 -0.048 0.27 NO
25 CDKN1B CDKN1B CDKN1B 14226 -0.089 0.23 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 RACCYCD PATHWAY.

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

genes ES table in pathway: BIOCARTA MAPK PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TNF TNF TNF 640 0.19 0.15 YES
2 BAG4 BAG4 BAG4 1517 0.11 0.2 YES
3 RB1 RB1 RB1 2533 0.067 0.21 YES
4 DFFA DFFA DFFA 2713 0.062 0.26 YES
5 TNFRSF1A TNFRSF1A TNFRSF1A 3185 0.052 0.28 YES
6 FADD FADD FADD 3301 0.05 0.32 YES
7 TRADD TRADD TRADD 3611 0.044 0.35 YES
8 MAPK8 MAPK8 MAPK8 3786 0.041 0.38 YES
9 CASP8 CASP8 CASP8 4070 0.036 0.4 YES
10 RIPK1 RIPK1 RIPK1 4650 0.028 0.4 YES
11 MAP3K1 MAP3K1 MAP3K1 4788 0.027 0.41 YES
12 CASP3 CASP3 CASP3 4920 0.025 0.43 YES
13 PRKDC PRKDC PRKDC 5836 0.015 0.39 NO
14 LMNA LMNA LMNA 5939 0.014 0.4 NO
15 PAK2 PAK2 PAK2 5964 0.013 0.41 NO
16 PAK1 PAK1 PAK1 6607 0.0076 0.38 NO
17 JUN JUN JUN 6920 0.0047 0.37 NO
18 CRADD CRADD CRADD 7715 -0.0029 0.33 NO
19 LMNB2 LMNB2 LMNB2 7752 -0.0033 0.33 NO
20 CASP2 CASP2 CASP2 8307 -0.0083 0.31 NO
21 MAP3K7 MAP3K7 MAP3K7 8370 -0.0089 0.32 NO
22 DFFB DFFB DFFB 9248 -0.017 0.28 NO
23 SPTAN1 SPTAN1 SPTAN1 9327 -0.018 0.3 NO
24 MAP2K4 MAP2K4 MAP2K4 9632 -0.021 0.3 NO
25 ARHGDIB ARHGDIB ARHGDIB 10714 -0.033 0.27 NO
26 LMNB1 LMNB1 LMNB1 11829 -0.046 0.26 NO
27 PARP1 PARP1 PARP1 12091 -0.05 0.29 NO
28 MADD MADD MADD 12736 -0.059 0.31 NO

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

Figure S4.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MAPK 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 P38MAPK PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IL1RN IL1RN IL1RN 50 0.51 0.16 YES
2 IL1A IL1A IL1A 55 0.5 0.32 YES
3 IL1B IL1B IL1B 370 0.27 0.39 YES
4 IL1RAP IL1RAP IL1RAP 468 0.23 0.46 YES
5 IRAK2 IRAK2 IRAK2 612 0.2 0.51 YES
6 TNF TNF TNF 640 0.19 0.57 YES
7 TGFB1 TGFB1 TGFB1 1542 0.1 0.56 NO
8 TOLLIP TOLLIP TOLLIP 1941 0.086 0.56 NO
9 NFKBIA NFKBIA NFKBIA 2896 0.058 0.53 NO
10 NFKB1 NFKB1 NFKB1 2922 0.057 0.55 NO
11 CHUK CHUK CHUK 3333 0.049 0.54 NO
12 TGFB3 TGFB3 TGFB3 3734 0.042 0.53 NO
13 MAPK8 MAPK8 MAPK8 3786 0.041 0.54 NO
14 MAP2K3 MAP2K3 MAP2K3 4429 0.031 0.52 NO
15 MAP3K1 MAP3K1 MAP3K1 4788 0.027 0.51 NO
16 IKBKB IKBKB IKBKB 5055 0.023 0.5 NO
17 ECSIT ECSIT ECSIT 5276 0.02 0.5 NO
18 RELA RELA RELA 5566 0.018 0.48 NO
19 MAPK14 MAPK14 MAPK14 6043 0.013 0.46 NO
20 IRAK3 IRAK3 IRAK3 6347 0.01 0.45 NO
21 MYD88 MYD88 MYD88 6746 0.0063 0.43 NO
22 TAB1 TAB1 TAB1 6873 0.0052 0.42 NO
23 JUN JUN JUN 6920 0.0047 0.42 NO
24 MAP3K7 MAP3K7 MAP3K7 8370 -0.0089 0.35 NO
25 IRAK1 IRAK1 IRAK1 9332 -0.018 0.3 NO
26 TRAF6 TRAF6 TRAF6 10335 -0.029 0.26 NO
27 TGFB2 TGFB2 TGFB2 11424 -0.041 0.21 NO
28 MAP2K6 MAP2K6 MAP2K6 14531 -0.096 0.074 NO
29 MAP3K14 MAP3K14 MAP3K14 15091 -0.11 0.079 NO
30 IFNB1 IFNB1 IFNB1 15463 -0.12 0.099 NO
31 IL6 IL6 IL6 17249 -0.2 0.068 NO

Figure S5.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA P38MAPK PATHWAY.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA P38MAPK PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA IL1R PATHWAY

Table 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 MAP3K9 MAP3K9 MAP3K9 627 0.2 0.066 YES
2 HSPB1 HSPB1 HSPB1 885 0.16 0.13 YES
3 RPS6KA5 RPS6KA5 RPS6KA5 1181 0.13 0.18 YES
4 TGFB1 TGFB1 TGFB1 1542 0.1 0.22 YES
5 MAP3K5 MAP3K5 MAP3K5 1686 0.097 0.26 YES
6 RAC1 RAC1 RAC1 2001 0.084 0.29 YES
7 CDC42 CDC42 CDC42 2378 0.071 0.3 YES
8 PLA2G4A PLA2G4A PLA2G4A 2744 0.061 0.31 YES
9 MYC MYC MYC 2965 0.056 0.33 YES
10 TRADD TRADD TRADD 3611 0.044 0.32 YES
11 HSPB2 HSPB2 HSPB2 3719 0.042 0.33 YES
12 TGFB3 TGFB3 TGFB3 3734 0.042 0.35 YES
13 HRAS HRAS HRAS 3861 0.04 0.37 YES
14 RIPK1 RIPK1 RIPK1 4650 0.028 0.34 NO
15 MAP3K1 MAP3K1 MAP3K1 4788 0.027 0.34 NO
16 MAPKAPK2 MAPKAPK2 MAPKAPK2 4964 0.024 0.35 NO
17 MAX MAX MAX 5084 0.023 0.35 NO
18 CREB1 CREB1 CREB1 5393 0.019 0.35 NO
19 MKNK1 MKNK1 MKNK1 5491 0.018 0.35 NO
20 MAPK14 MAPK14 MAPK14 6043 0.013 0.33 NO
21 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 6299 0.01 0.32 NO
22 GRB2 GRB2 GRB2 6553 0.0081 0.31 NO
23 SHC1 SHC1 SHC1 6924 0.0046 0.29 NO
24 DAXX DAXX DAXX 6976 0.0041 0.29 NO
25 MAPKAPK5 MAPKAPK5 MAPKAPK5 8328 -0.0085 0.22 NO
26 MAP3K7 MAP3K7 MAP3K7 8370 -0.0089 0.22 NO
27 MEF2A MEF2A MEF2A 8875 -0.014 0.2 NO
28 MAP2K4 MAP2K4 MAP2K4 9632 -0.021 0.17 NO
29 ATF2 ATF2 ATF2 10237 -0.028 0.15 NO
30 ELK1 ELK1 ELK1 10323 -0.029 0.16 NO
31 TGFBR1 TGFBR1 TGFBR1 11364 -0.04 0.13 NO
32 MEF2D MEF2D MEF2D 11400 -0.041 0.15 NO
33 TGFB2 TGFB2 TGFB2 11424 -0.041 0.17 NO
34 DDIT3 DDIT3 DDIT3 12035 -0.049 0.16 NO
35 STAT1 STAT1 STAT1 12049 -0.049 0.18 NO
36 TRAF2 TRAF2 TRAF2 12423 -0.054 0.19 NO
37 MEF2C MEF2C MEF2C 13976 -0.083 0.15 NO
38 RAPGEF2 RAPGEF2 RAPGEF2 14385 -0.092 0.17 NO
39 MAP2K6 MAP2K6 MAP2K6 14531 -0.096 0.22 NO

Figure S7.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL1R PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA TNFR1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CXCL1 CXCL1 CXCL1 65 0.49 0.094 YES
2 IL8 IL8 IL8 107 0.42 0.18 YES
3 CXCR1 CXCR1 CXCR1 221 0.33 0.24 YES
4 CXCR2 CXCR2 CXCR2 250 0.32 0.3 YES
5 PTPRZ1 PTPRZ1 PTPRZ1 632 0.2 0.32 YES
6 MAPK10 MAPK10 MAPK10 1104 0.14 0.32 YES
7 EGFR EGFR EGFR 1640 0.099 0.31 YES
8 ATP6V1D ATP6V1D ATP6V1D 1786 0.093 0.32 YES
9 RAC1 RAC1 RAC1 2001 0.084 0.32 YES
10 MAPK11 MAPK11 MAPK11 2130 0.079 0.33 YES
11 CDC42 CDC42 CDC42 2378 0.071 0.33 YES
12 ATP6V0D1 ATP6V0D1 ATP6V0D1 2617 0.065 0.33 YES
13 ATP6V0B ATP6V0B ATP6V0B 2774 0.06 0.34 YES
14 NFKBIA NFKBIA NFKBIA 2896 0.058 0.34 YES
15 NFKB1 NFKB1 NFKB1 2922 0.057 0.35 YES
16 MAPK13 MAPK13 MAPK13 3173 0.052 0.35 YES
17 CHUK CHUK CHUK 3333 0.049 0.35 YES
18 HBEGF HBEGF HBEGF 3515 0.046 0.35 YES
19 MAPK8 MAPK8 MAPK8 3786 0.041 0.34 YES
20 ATP6V1E1 ATP6V1E1 ATP6V1E1 3969 0.038 0.34 YES
21 ATP6V0C ATP6V0C ATP6V0C 3991 0.038 0.35 YES
22 F11R F11R F11R 4027 0.037 0.35 YES
23 ATP6V1H ATP6V1H ATP6V1H 4325 0.033 0.34 NO
24 SRC SRC SRC 4507 0.03 0.34 NO
25 TCIRG1 TCIRG1 TCIRG1 4752 0.027 0.33 NO
26 CASP3 CASP3 CASP3 4920 0.025 0.33 NO
27 ATP6V1A ATP6V1A ATP6V1A 4998 0.024 0.33 NO
28 IKBKB IKBKB IKBKB 5055 0.023 0.33 NO
29 LYN LYN LYN 5240 0.021 0.32 NO
30 ATP6V1G1 ATP6V1G1 ATP6V1G1 5447 0.019 0.32 NO
31 RELA RELA RELA 5566 0.018 0.31 NO
32 ATP6V1C1 ATP6V1C1 ATP6V1C1 5850 0.014 0.3 NO
33 MAPK14 MAPK14 MAPK14 6043 0.013 0.29 NO
34 ATP6V1B2 ATP6V1B2 ATP6V1B2 6348 0.01 0.28 NO
35 MAPK12 MAPK12 MAPK12 6375 0.0098 0.28 NO
36 ATP6V1F ATP6V1F ATP6V1F 6388 0.0097 0.28 NO
37 PAK1 PAK1 PAK1 6607 0.0076 0.27 NO
38 JUN JUN JUN 6920 0.0047 0.25 NO
39 CSK CSK CSK 7773 -0.0035 0.21 NO
40 PLCG1 PLCG1 PLCG1 7803 -0.0038 0.21 NO
41 TJP1 TJP1 TJP1 7936 -0.0051 0.2 NO
42 ADAM10 ADAM10 ADAM10 8544 -0.011 0.17 NO
43 IKBKG IKBKG IKBKG 8591 -0.011 0.17 NO
44 MET MET MET 8727 -0.012 0.16 NO
45 ATP6AP1 ATP6AP1 ATP6AP1 9016 -0.015 0.15 NO
46 NOD1 NOD1 NOD1 9112 -0.016 0.15 NO
47 PTPN11 PTPN11 PTPN11 9150 -0.016 0.15 NO
48 ATP6V1C2 ATP6V1C2 ATP6V1C2 9219 -0.017 0.15 NO
49 MAP2K4 MAP2K4 MAP2K4 9632 -0.021 0.13 NO
50 ATP6V0A1 ATP6V0A1 ATP6V0A1 10362 -0.029 0.099 NO
51 PLCG2 PLCG2 PLCG2 11776 -0.046 0.031 NO
52 ATP6V0D2 ATP6V0D2 ATP6V0D2 11789 -0.046 0.04 NO
53 MAPK9 MAPK9 MAPK9 11938 -0.048 0.041 NO
54 ATP6V0A2 ATP6V0A2 ATP6V0A2 12039 -0.049 0.045 NO
55 ADAM17 ADAM17 ADAM17 12239 -0.052 0.045 NO
56 GIT1 GIT1 GIT1 13649 -0.076 -0.016 NO
57 JAM2 JAM2 JAM2 14305 -0.091 -0.034 NO
58 CCL5 CCL5 CCL5 14798 -0.1 -0.04 NO
59 MAP3K14 MAP3K14 MAP3K14 15091 -0.11 -0.034 NO
60 IGSF5 IGSF5 IGSF5 15236 -0.12 -0.019 NO
61 JAM3 JAM3 JAM3 15452 -0.12 -0.0062 NO
62 ATP6V1E2 ATP6V1E2 ATP6V1E2 16008 -0.14 -0.0083 NO
63 ATP6V1G2 ATP6V1G2 ATP6V1G2 16204 -0.15 0.011 NO
64 ATP6V0A4 ATP6V0A4 ATP6V0A4 16233 -0.15 0.039 NO
65 ATP6V1B1 ATP6V1B1 ATP6V1B1 17047 -0.19 0.033 NO
66 ATP6V0E2 ATP6V0E2 ATP6V0E2 17554 -0.23 0.051 NO

Figure S9.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TNFR1 PATHWAY.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 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 STEROID HORMONE BIOSYNTHESIS

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 TP53AIP1 TP53AIP1 TP53AIP1 29 0.58 0.12 YES
2 SERPINB5 SERPINB5 SERPINB5 272 0.31 0.17 YES
3 SFN SFN SFN 526 0.22 0.2 YES
4 SESN3 SESN3 SESN3 563 0.21 0.24 YES
5 TP73 TP73 TP73 584 0.2 0.28 YES
6 PERP PERP PERP 966 0.15 0.29 YES
7 CD82 CD82 CD82 1183 0.13 0.31 YES
8 CDKN1A CDKN1A CDKN1A 1554 0.1 0.31 YES
9 CDK6 CDK6 CDK6 1557 0.1 0.33 YES
10 CCND1 CCND1 CCND1 1822 0.091 0.34 YES
11 BID BID BID 2269 0.075 0.33 YES
12 DDB2 DDB2 DDB2 2288 0.074 0.34 YES
13 TNFRSF10B TNFRSF10B TNFRSF10B 2856 0.058 0.32 NO
14 EI24 EI24 EI24 3119 0.053 0.32 NO
15 SHISA5 SHISA5 SHISA5 3272 0.05 0.32 NO
16 CASP9 CASP9 CASP9 3457 0.047 0.32 NO
17 CYCS CYCS CYCS 3479 0.046 0.33 NO
18 SIAH1 SIAH1 SIAH1 3703 0.042 0.32 NO
19 GADD45A GADD45A GADD45A 3950 0.038 0.32 NO
20 CASP8 CASP8 CASP8 4070 0.036 0.32 NO
21 PTEN PTEN PTEN 4166 0.035 0.32 NO
22 SESN1 SESN1 SESN1 4282 0.033 0.32 NO
23 SERPINE1 SERPINE1 SERPINE1 4652 0.028 0.31 NO
24 RRM2B RRM2B RRM2B 4734 0.027 0.31 NO
25 CCNB1 CCNB1 CCNB1 4758 0.027 0.32 NO
26 SESN2 SESN2 SESN2 4844 0.026 0.32 NO
27 CASP3 CASP3 CASP3 4920 0.025 0.32 NO
28 CCNE2 CCNE2 CCNE2 5010 0.023 0.32 NO
29 CDK1 CDK1 CDK1 5049 0.023 0.32 NO
30 ATR ATR ATR 5794 0.015 0.28 NO
31 TP53I3 TP53I3 TP53I3 5966 0.013 0.28 NO
32 BAX BAX BAX 6099 0.012 0.27 NO
33 RRM2 RRM2 RRM2 6199 0.011 0.27 NO
34 TSC2 TSC2 TSC2 6500 0.0086 0.25 NO
35 RCHY1 RCHY1 RCHY1 6540 0.0083 0.25 NO
36 CCNE1 CCNE1 CCNE1 7422 0.00019 0.2 NO
37 ZMAT3 ZMAT3 ZMAT3 8049 -0.0062 0.17 NO
38 CHEK1 CHEK1 CHEK1 8109 -0.0067 0.17 NO
39 CDKN2A CDKN2A CDKN2A 8613 -0.011 0.15 NO
40 CHEK2 CHEK2 CHEK2 8773 -0.013 0.14 NO
41 MDM2 MDM2 MDM2 9529 -0.02 0.1 NO
42 APAF1 APAF1 APAF1 9624 -0.021 0.1 NO
43 CCNG2 CCNG2 CCNG2 9785 -0.023 0.098 NO
44 GTSE1 GTSE1 GTSE1 10023 -0.025 0.09 NO
45 FAS FAS FAS 10301 -0.028 0.081 NO
46 LRDD LRDD LRDD 10473 -0.03 0.078 NO
47 IGFBP3 IGFBP3 IGFBP3 10643 -0.032 0.076 NO
48 RPRM RPRM RPRM 10761 -0.034 0.076 NO
49 CCNB2 CCNB2 CCNB2 11002 -0.036 0.071 NO
50 BAI1 BAI1 BAI1 11212 -0.039 0.068 NO
51 CCNG1 CCNG1 CCNG1 11719 -0.045 0.049 NO
52 CDK4 CDK4 CDK4 11747 -0.045 0.057 NO
53 PMAIP1 PMAIP1 PMAIP1 11752 -0.045 0.066 NO
54 CDK2 CDK2 CDK2 11947 -0.048 0.066 NO
55 RFWD2 RFWD2 RFWD2 12202 -0.051 0.062 NO
56 THBS1 THBS1 THBS1 12213 -0.051 0.072 NO
57 GADD45B GADD45B GADD45B 12576 -0.057 0.064 NO
58 TP53 TP53 TP53 12592 -0.057 0.075 NO
59 MDM4 MDM4 MDM4 12869 -0.062 0.073 NO
60 ATM ATM ATM 13658 -0.076 0.046 NO
61 BBC3 BBC3 BBC3 14605 -0.098 0.015 NO
62 CCND2 CCND2 CCND2 14619 -0.098 0.035 NO
63 CCND3 CCND3 CCND3 14654 -0.099 0.053 NO
64 PPM1D PPM1D PPM1D 15168 -0.11 0.049 NO
65 IGF1 IGF1 IGF1 15778 -0.13 0.043 NO
66 CCNB3 CCNB3 CCNB3 16412 -0.16 0.041 NO
67 GADD45G GADD45G GADD45G 18277 -0.35 0.012 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 STEROID HORMONE BIOSYNTHESIS.

Figure S12.  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 OXIDATIVE PHOSPHORYLATION

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 CALML3 CALML3 CALML3 204 0.34 0.026 YES
2 CALML5 CALML5 CALML5 282 0.3 0.054 YES
3 IL1B IL1B IL1B 370 0.27 0.078 YES
4 COX6B2 COX6B2 COX6B2 505 0.22 0.095 YES
5 TNF TNF TNF 640 0.19 0.11 YES
6 NDUFA4L2 NDUFA4L2 NDUFA4L2 732 0.18 0.12 YES
7 GRIN2D GRIN2D GRIN2D 877 0.16 0.13 YES
8 BACE2 BACE2 BACE2 1050 0.14 0.14 YES
9 PLCB3 PLCB3 PLCB3 1644 0.099 0.12 YES
10 CAPN2 CAPN2 CAPN2 1810 0.092 0.12 YES
11 UQCRHL UQCRHL UQCRHL 1812 0.092 0.13 YES
12 CALM1 CALM1 CALM1 1817 0.091 0.14 YES
13 CHP2 CHP2 CHP2 1826 0.091 0.15 YES
14 CAPN1 CAPN1 CAPN1 2025 0.083 0.14 YES
15 CDK5R1 CDK5R1 CDK5R1 2118 0.079 0.15 YES
16 NDUFB1 NDUFB1 NDUFB1 2249 0.075 0.15 YES
17 UQCRH UQCRH UQCRH 2254 0.075 0.16 YES
18 BID BID BID 2269 0.075 0.16 YES
19 NDUFB3 NDUFB3 NDUFB3 2294 0.074 0.17 YES
20 ATP5F1 ATP5F1 ATP5F1 2300 0.074 0.18 YES
21 NDUFS5 NDUFS5 NDUFS5 2352 0.072 0.18 YES
22 NDUFS4 NDUFS4 NDUFS4 2684 0.063 0.17 YES
23 NDUFA6 NDUFA6 NDUFA6 2797 0.06 0.17 YES
24 CASP7 CASP7 CASP7 2859 0.058 0.18 YES
25 NDUFC1 NDUFC1 NDUFC1 2881 0.058 0.18 YES
26 NDUFS6 NDUFS6 NDUFS6 2975 0.056 0.18 YES
27 CYC1 CYC1 CYC1 3114 0.053 0.18 YES
28 PSEN1 PSEN1 PSEN1 3135 0.053 0.18 YES
29 PPP3CA PPP3CA PPP3CA 3144 0.053 0.19 YES
30 NDUFB9 NDUFB9 NDUFB9 3180 0.052 0.19 YES
31 COX7B COX7B COX7B 3181 0.052 0.2 YES
32 TNFRSF1A TNFRSF1A TNFRSF1A 3185 0.052 0.2 YES
33 ATP5C1 ATP5C1 ATP5C1 3237 0.051 0.21 YES
34 COX8A COX8A COX8A 3269 0.05 0.21 YES
35 FADD FADD FADD 3301 0.05 0.21 YES
36 NDUFS7 NDUFS7 NDUFS7 3352 0.049 0.22 YES
37 CHP CHP CHP 3399 0.048 0.22 YES
38 GSK3B GSK3B GSK3B 3408 0.048 0.22 YES
39 SDHB SDHB SDHB 3420 0.048 0.23 YES
40 CASP9 CASP9 CASP9 3457 0.047 0.23 YES
41 NDUFV1 NDUFV1 NDUFV1 3474 0.046 0.24 YES
42 CYCS CYCS CYCS 3479 0.046 0.24 YES
43 UQCR10 UQCR10 UQCR10 3501 0.046 0.24 YES
44 NDUFB4 NDUFB4 NDUFB4 3564 0.045 0.24 YES
45 BAD BAD BAD 3613 0.044 0.25 YES
46 PPP3CC PPP3CC PPP3CC 3646 0.043 0.25 YES
47 ATP5H ATP5H ATP5H 3695 0.043 0.25 YES
48 COX6C COX6C COX6C 3704 0.042 0.26 YES
49 NDUFA10 NDUFA10 NDUFA10 3849 0.04 0.25 YES
50 NDUFAB1 NDUFAB1 NDUFAB1 3856 0.04 0.26 YES
51 SDHD SDHD SDHD 4014 0.037 0.25 YES
52 COX7A2 COX7A2 COX7A2 4062 0.036 0.25 YES
53 CASP8 CASP8 CASP8 4070 0.036 0.26 YES
54 NDUFS8 NDUFS8 NDUFS8 4097 0.036 0.26 YES
55 ATP5O ATP5O ATP5O 4110 0.036 0.26 YES
56 ATP5E ATP5E ATP5E 4154 0.035 0.26 YES
57 MAPK3 MAPK3 MAPK3 4180 0.035 0.27 YES
58 NDUFB7 NDUFB7 NDUFB7 4181 0.035 0.27 YES
59 APP APP APP 4232 0.034 0.27 YES
60 SDHA SDHA SDHA 4298 0.033 0.27 YES
61 UQCRQ UQCRQ UQCRQ 4351 0.032 0.27 YES
62 PSENEN PSENEN PSENEN 4364 0.032 0.28 YES
63 UQCRC2 UQCRC2 UQCRC2 4407 0.032 0.28 YES
64 NDUFA3 NDUFA3 NDUFA3 4413 0.031 0.28 YES
65 GRIN2C GRIN2C GRIN2C 4544 0.03 0.28 YES
66 UQCRB UQCRB UQCRB 4612 0.029 0.28 YES
67 COX7B2 COX7B2 COX7B2 4646 0.028 0.28 YES
68 ATP5D ATP5D ATP5D 4655 0.028 0.28 YES
69 COX4I1 COX4I1 COX4I1 4707 0.028 0.28 YES
70 COX6A1 COX6A1 COX6A1 4761 0.027 0.28 YES
71 UQCR11 UQCR11 UQCR11 4804 0.026 0.28 YES
72 NDUFB8 NDUFB8 NDUFB8 4841 0.026 0.28 YES
73 ATP5J ATP5J ATP5J 4899 0.025 0.28 YES
74 SDHC SDHC SDHC 4915 0.025 0.28 YES
75 CASP3 CASP3 CASP3 4920 0.025 0.28 YES
76 NDUFB10 NDUFB10 NDUFB10 4948 0.024 0.28 YES
77 ATP5G3 ATP5G3 ATP5G3 5051 0.023 0.28 NO
78 NDUFV2 NDUFV2 NDUFV2 5078 0.023 0.28 NO
79 UQCRC1 UQCRC1 UQCRC1 5374 0.02 0.27 NO
80 ATP2A2 ATP2A2 ATP2A2 5382 0.02 0.27 NO
81 NDUFV3 NDUFV3 NDUFV3 5417 0.019 0.27 NO
82 NDUFA1 NDUFA1 NDUFA1 5443 0.019 0.27 NO
83 COX7C COX7C COX7C 5725 0.016 0.26 NO
84 NDUFC2 NDUFC2 NDUFC2 5761 0.016 0.26 NO
85 MME MME MME 5955 0.013 0.25 NO
86 NDUFB2 NDUFB2 NDUFB2 6020 0.013 0.25 NO
87 NDUFA7 NDUFA7 NDUFA7 6117 0.012 0.24 NO
88 NDUFS1 NDUFS1 NDUFS1 6213 0.011 0.24 NO
89 NDUFB6 NDUFB6 NDUFB6 6349 0.01 0.23 NO
90 GAPDH GAPDH GAPDH 6429 0.0092 0.23 NO
91 NDUFA5 NDUFA5 NDUFA5 6431 0.0092 0.23 NO
92 PPP3CB PPP3CB PPP3CB 6512 0.0085 0.23 NO
93 COX6B1 COX6B1 COX6B1 6536 0.0083 0.23 NO
94 HSD17B10 HSD17B10 HSD17B10 6723 0.0065 0.22 NO
95 ATP5G1 ATP5G1 ATP5G1 6736 0.0064 0.22 NO
96 NDUFB5 NDUFB5 NDUFB5 6783 0.0059 0.22 NO
97 NDUFA4 NDUFA4 NDUFA4 6843 0.0054 0.21 NO
98 ATP5B ATP5B ATP5B 6944 0.0044 0.21 NO
99 LRP1 LRP1 LRP1 7057 0.0034 0.2 NO
100 NDUFA9 NDUFA9 NDUFA9 7148 0.0027 0.2 NO
101 NDUFA2 NDUFA2 NDUFA2 7415 0.00024 0.18 NO
102 GNAQ GNAQ GNAQ 7487 -0.00042 0.18 NO
103 MAPK1 MAPK1 MAPK1 7548 -0.0012 0.18 NO
104 UQCRFS1 UQCRFS1 UQCRFS1 7591 -0.0016 0.17 NO
105 NDUFS3 NDUFS3 NDUFS3 7592 -0.0017 0.17 NO
106 COX5A COX5A COX5A 8108 -0.0067 0.15 NO
107 ATP5A1 ATP5A1 ATP5A1 8164 -0.0071 0.14 NO
108 COX5B COX5B COX5B 8301 -0.0082 0.14 NO
109 NDUFS2 NDUFS2 NDUFS2 8525 -0.01 0.13 NO
110 CALML6 CALML6 CALML6 8534 -0.011 0.13 NO
111 COX7A2L COX7A2L COX7A2L 8536 -0.011 0.13 NO
112 ADAM10 ADAM10 ADAM10 8544 -0.011 0.13 NO
113 NCSTN NCSTN NCSTN 8593 -0.011 0.13 NO
114 IDE IDE IDE 8596 -0.011 0.13 NO
115 RYR3 RYR3 RYR3 8611 -0.011 0.13 NO
116 ITPR3 ITPR3 ITPR3 8638 -0.011 0.13 NO
117 ATP2A1 ATP2A1 ATP2A1 8806 -0.013 0.12 NO
118 APH1A APH1A APH1A 8906 -0.014 0.12 NO
119 ATP5G2 ATP5G2 ATP5G2 8970 -0.015 0.12 NO
120 EIF2AK3 EIF2AK3 EIF2AK3 9076 -0.016 0.11 NO
121 COX8C COX8C COX8C 9169 -0.016 0.11 NO
122 CALM3 CALM3 CALM3 9265 -0.017 0.1 NO
123 CDK5 CDK5 CDK5 9272 -0.017 0.11 NO
124 COX7A1 COX7A1 COX7A1 9289 -0.018 0.11 NO
125 NAE1 NAE1 NAE1 9619 -0.021 0.092 NO
126 APAF1 APAF1 APAF1 9624 -0.021 0.094 NO
127 GRIN2A GRIN2A GRIN2A 9667 -0.022 0.094 NO
128 BACE1 BACE1 BACE1 9695 -0.022 0.094 NO
129 NDUFA8 NDUFA8 NDUFA8 10140 -0.027 0.073 NO
130 FAS FAS FAS 10301 -0.028 0.068 NO
131 PPP3R1 PPP3R1 PPP3R1 10361 -0.029 0.067 NO
132 ATF6 ATF6 ATF6 10766 -0.034 0.049 NO
133 CALM2 CALM2 CALM2 10826 -0.034 0.05 NO
134 COX4I2 COX4I2 COX4I2 11933 -0.047 -0.0058 NO
135 ADAM17 ADAM17 ADAM17 12239 -0.052 -0.017 NO
136 ERN1 ERN1 ERN1 12289 -0.052 -0.014 NO
137 CACNA1C CACNA1C CACNA1C 12536 -0.056 -0.021 NO
138 ITPR1 ITPR1 ITPR1 13513 -0.074 -0.067 NO
139 LPL LPL LPL 13743 -0.078 -0.071 NO
140 CACNA1D CACNA1D CACNA1D 14095 -0.086 -0.081 NO
141 PSEN2 PSEN2 PSEN2 14188 -0.088 -0.076 NO
142 ATP2A3 ATP2A3 ATP2A3 14568 -0.097 -0.086 NO
143 PLCB2 PLCB2 PLCB2 14796 -0.1 -0.088 NO
144 PLCB1 PLCB1 PLCB1 15324 -0.12 -0.1 NO
145 ITPR2 ITPR2 ITPR2 15368 -0.12 -0.093 NO
146 GRIN2B GRIN2B GRIN2B 15421 -0.12 -0.083 NO
147 APOE APOE APOE 15517 -0.12 -0.075 NO
148 SNCA SNCA SNCA 15872 -0.14 -0.079 NO
149 NOS1 NOS1 NOS1 16952 -0.18 -0.12 NO
150 CACNA1F CACNA1F CACNA1F 17058 -0.19 -0.1 NO
151 GRIN1 GRIN1 GRIN1 17470 -0.22 -0.1 NO
152 APBB1 APBB1 APBB1 17842 -0.26 -0.094 NO
153 CACNA1S CACNA1S CACNA1S 18046 -0.29 -0.074 NO
154 MAPT MAPT MAPT 18359 -0.37 -0.05 NO
155 PLCB4 PLCB4 PLCB4 18489 -0.54 0.00038 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 OXIDATIVE PHOSPHORYLATION.

Figure S14.  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 LINOLEIC ACID 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 CYP3A5 CYP3A5 CYP3A5 189 0.36 0.04 YES
2 CYP2C18 CYP2C18 CYP2C18 207 0.34 0.086 YES
3 RDH16 RDH16 RDH16 233 0.33 0.13 YES
4 ADH1C ADH1C ADH1C 283 0.3 0.17 YES
5 DHRS9 DHRS9 DHRS9 326 0.28 0.21 YES
6 RDH12 RDH12 RDH12 416 0.25 0.24 YES
7 CYP2C9 CYP2C9 CYP2C9 507 0.22 0.26 YES
8 UGT2B7 UGT2B7 UGT2B7 515 0.22 0.29 YES
9 UGT2B15 UGT2B15 UGT2B15 551 0.21 0.32 YES
10 CYP2C19 CYP2C19 CYP2C19 585 0.2 0.35 YES
11 UGT2A1 UGT2A1 UGT2A1 586 0.2 0.38 YES
12 UGT1A10 UGT1A10 UGT1A10 604 0.2 0.4 YES
13 DHRS3 DHRS3 DHRS3 751 0.18 0.42 YES
14 RDH10 RDH10 RDH10 950 0.15 0.43 YES
15 ADH6 ADH6 ADH6 992 0.15 0.45 YES
16 UGT2A3 UGT2A3 UGT2A3 1011 0.15 0.47 YES
17 ADH7 ADH7 ADH7 1125 0.14 0.48 YES
18 RDH8 RDH8 RDH8 1267 0.12 0.49 YES
19 UGT2B28 UGT2B28 UGT2B28 1364 0.12 0.5 YES
20 CYP4A11 CYP4A11 CYP4A11 1393 0.11 0.52 YES
21 CYP2A13 CYP2A13 CYP2A13 1396 0.11 0.53 YES
22 DGAT1 DGAT1 DGAT1 1525 0.11 0.54 YES
23 ADH1A ADH1A ADH1A 1668 0.098 0.55 YES
24 RETSAT RETSAT RETSAT 1706 0.096 0.56 YES
25 UGT1A8 UGT1A8 UGT1A8 1847 0.09 0.56 YES
26 DGAT2 DGAT2 DGAT2 2117 0.079 0.56 NO
27 RDH11 RDH11 RDH11 2358 0.072 0.56 NO
28 ADH5 ADH5 ADH5 2449 0.069 0.56 NO
29 PNPLA4 PNPLA4 PNPLA4 3042 0.055 0.54 NO
30 CYP2A6 CYP2A6 CYP2A6 3208 0.052 0.54 NO
31 CYP2C8 CYP2C8 CYP2C8 4438 0.031 0.47 NO
32 DHRS4 DHRS4 DHRS4 5273 0.02 0.43 NO
33 CYP3A7 CYP3A7 CYP3A7 5300 0.02 0.43 NO
34 DHRS4L2 DHRS4L2 DHRS4L2 5342 0.02 0.43 NO
35 CYP26B1 CYP26B1 CYP26B1 5666 0.016 0.42 NO
36 UGT1A6 UGT1A6 UGT1A6 6368 0.0099 0.38 NO
37 ADH4 ADH4 ADH4 6455 0.009 0.38 NO
38 AWAT2 AWAT2 AWAT2 6542 0.0083 0.37 NO
39 LRAT LRAT LRAT 7794 -0.0038 0.31 NO
40 CYP3A43 CYP3A43 CYP3A43 8218 -0.0076 0.28 NO
41 CYP2A7 CYP2A7 CYP2A7 10134 -0.027 0.18 NO
42 CYP2B6 CYP2B6 CYP2B6 10405 -0.03 0.17 NO
43 UGT1A1 UGT1A1 UGT1A1 10700 -0.033 0.16 NO
44 RPE65 RPE65 RPE65 11057 -0.037 0.15 NO
45 CYP26C1 CYP26C1 CYP26C1 11070 -0.037 0.15 NO
46 UGT2B4 UGT2B4 UGT2B4 11476 -0.042 0.14 NO
47 UGT1A4 UGT1A4 UGT1A4 12182 -0.051 0.11 NO
48 UGT1A9 UGT1A9 UGT1A9 12744 -0.059 0.084 NO
49 ADH1B ADH1B ADH1B 13988 -0.083 0.028 NO
50 BCMO1 BCMO1 BCMO1 15102 -0.11 -0.016 NO
51 CYP1A1 CYP1A1 CYP1A1 15197 -0.11 -0.0057 NO
52 UGT1A3 UGT1A3 UGT1A3 15369 -0.12 0.0018 NO
53 CYP1A2 CYP1A2 CYP1A2 15428 -0.12 0.016 NO
54 ALDH1A1 ALDH1A1 ALDH1A1 15770 -0.13 0.016 NO
55 UGT1A5 UGT1A5 UGT1A5 16049 -0.14 0.021 NO
56 UGT1A7 UGT1A7 UGT1A7 16094 -0.14 0.038 NO
57 RDH5 RDH5 RDH5 16454 -0.16 0.041 NO
58 ALDH1A2 ALDH1A2 ALDH1A2 17377 -0.22 0.021 NO
59 CYP26A1 CYP26A1 CYP26A1 17983 -0.28 0.028 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 LINOLEIC ACID METABOLISM.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LINOLEIC 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

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 CYP3A5 CYP3A5 CYP3A5 189 0.36 0.038 YES
2 CYP2C18 CYP2C18 CYP2C18 207 0.34 0.082 YES
3 FMO4 FMO4 FMO4 246 0.32 0.12 YES
4 ALDH3B2 ALDH3B2 ALDH3B2 269 0.31 0.16 YES
5 ADH1C ADH1C ADH1C 283 0.3 0.2 YES
6 CYP2C9 CYP2C9 CYP2C9 507 0.22 0.22 YES
7 UGT2B7 UGT2B7 UGT2B7 515 0.22 0.25 YES
8 ALDH1A3 ALDH1A3 ALDH1A3 521 0.22 0.28 YES
9 UGT2B15 UGT2B15 UGT2B15 551 0.21 0.3 YES
10 MAOA MAOA MAOA 579 0.2 0.33 YES
11 CYP2C19 CYP2C19 CYP2C19 585 0.2 0.36 YES
12 UGT2A1 UGT2A1 UGT2A1 586 0.2 0.38 YES
13 UGT1A10 UGT1A10 UGT1A10 604 0.2 0.41 YES
14 CYP2E1 CYP2E1 CYP2E1 625 0.2 0.44 YES
15 FMO3 FMO3 FMO3 947 0.15 0.44 YES
16 GSTO2 GSTO2 GSTO2 979 0.15 0.46 YES
17 GSTA3 GSTA3 GSTA3 986 0.15 0.48 YES
18 ADH6 ADH6 ADH6 992 0.15 0.5 YES
19 UGT2A3 UGT2A3 UGT2A3 1011 0.15 0.52 YES
20 FMO1 FMO1 FMO1 1032 0.14 0.53 YES
21 ADH7 ADH7 ADH7 1125 0.14 0.55 YES
22 UGT2B28 UGT2B28 UGT2B28 1364 0.12 0.55 YES
23 CYP2A13 CYP2A13 CYP2A13 1396 0.11 0.56 YES
24 ADH1A ADH1A ADH1A 1668 0.098 0.56 YES
25 MGST2 MGST2 MGST2 1760 0.094 0.57 YES
26 UGT1A8 UGT1A8 UGT1A8 1847 0.09 0.58 YES
27 GSTP1 GSTP1 GSTP1 2035 0.082 0.58 YES
28 ADH5 ADH5 ADH5 2449 0.069 0.56 NO
29 CYP2A6 CYP2A6 CYP2A6 3208 0.052 0.53 NO
30 ALDH3A1 ALDH3A1 ALDH3A1 3366 0.049 0.53 NO
31 GSTZ1 GSTZ1 GSTZ1 3441 0.047 0.53 NO
32 FMO2 FMO2 FMO2 3990 0.038 0.51 NO
33 CYP2C8 CYP2C8 CYP2C8 4438 0.031 0.49 NO
34 MGST1 MGST1 MGST1 4820 0.026 0.47 NO
35 GSTT1 GSTT1 GSTT1 5244 0.021 0.45 NO
36 GSTK1 GSTK1 GSTK1 5283 0.02 0.45 NO
37 CYP3A7 CYP3A7 CYP3A7 5300 0.02 0.45 NO
38 UGT1A6 UGT1A6 UGT1A6 6368 0.0099 0.4 NO
39 ADH4 ADH4 ADH4 6455 0.009 0.39 NO
40 GSTA1 GSTA1 GSTA1 8173 -0.0072 0.3 NO
41 CYP3A43 CYP3A43 CYP3A43 8218 -0.0076 0.3 NO
42 GSTA2 GSTA2 GSTA2 8243 -0.0078 0.3 NO
43 CYP2D6 CYP2D6 CYP2D6 8410 -0.0093 0.29 NO
44 GSTO1 GSTO1 GSTO1 9216 -0.017 0.25 NO
45 MGST3 MGST3 MGST3 9796 -0.023 0.22 NO
46 GSTM1 GSTM1 GSTM1 9951 -0.024 0.22 NO
47 CYP2A7 CYP2A7 CYP2A7 10134 -0.027 0.21 NO
48 GSTA4 GSTA4 GSTA4 10167 -0.027 0.21 NO
49 CYP2B6 CYP2B6 CYP2B6 10405 -0.03 0.2 NO
50 MAOB MAOB MAOB 10619 -0.032 0.19 NO
51 UGT1A1 UGT1A1 UGT1A1 10700 -0.033 0.19 NO
52 UGT2B4 UGT2B4 UGT2B4 11476 -0.042 0.16 NO
53 UGT1A4 UGT1A4 UGT1A4 12182 -0.051 0.13 NO
54 GSTM3 GSTM3 GSTM3 12445 -0.055 0.12 NO
55 GSTM5 GSTM5 GSTM5 12721 -0.059 0.11 NO
56 UGT1A9 UGT1A9 UGT1A9 12744 -0.059 0.12 NO
57 AOX1 AOX1 AOX1 13986 -0.083 0.063 NO
58 ADH1B ADH1B ADH1B 13988 -0.083 0.074 NO
59 ALDH3B1 ALDH3B1 ALDH3B1 15074 -0.11 0.03 NO
60 UGT1A3 UGT1A3 UGT1A3 15369 -0.12 0.03 NO
61 CYP1A2 CYP1A2 CYP1A2 15428 -0.12 0.043 NO
62 GSTT2 GSTT2 GSTT2 15596 -0.13 0.051 NO
63 UGT1A5 UGT1A5 UGT1A5 16049 -0.14 0.046 NO
64 UGT1A7 UGT1A7 UGT1A7 16094 -0.14 0.062 NO
65 FMO5 FMO5 FMO5 16334 -0.15 0.07 NO
66 GSTM4 GSTM4 GSTM4 16599 -0.17 0.078 NO
67 GSTM2 GSTM2 GSTM2 16978 -0.19 0.082 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

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

genes ES table in pathway: KEGG RETINOL METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 XDH XDH XDH 163 0.38 0.074 YES
2 CYP3A5 CYP3A5 CYP3A5 189 0.36 0.15 YES
3 UGT2B7 UGT2B7 UGT2B7 515 0.22 0.18 YES
4 UGT2B15 UGT2B15 UGT2B15 551 0.21 0.22 YES
5 UGT2A1 UGT2A1 UGT2A1 586 0.2 0.27 YES
6 UGT1A10 UGT1A10 UGT1A10 604 0.2 0.31 YES
7 UPP1 UPP1 UPP1 873 0.16 0.33 YES
8 TYMP TYMP TYMP 1009 0.15 0.36 YES
9 UGT2A3 UGT2A3 UGT2A3 1011 0.15 0.39 YES
10 DPYD DPYD DPYD 1332 0.12 0.4 YES
11 UGT2B28 UGT2B28 UGT2B28 1364 0.12 0.42 YES
12 CYP2A13 CYP2A13 CYP2A13 1396 0.11 0.44 YES
13 CES2 CES2 CES2 1597 0.1 0.46 YES
14 CES7 CES7 CES7 1695 0.097 0.47 YES
15 UGT1A8 UGT1A8 UGT1A8 1847 0.09 0.48 YES
16 NAT1 NAT1 NAT1 1863 0.09 0.5 YES
17 CYP2A6 CYP2A6 CYP2A6 3208 0.052 0.44 NO
18 CDA CDA CDA 3279 0.05 0.45 NO
19 UMPS UMPS UMPS 3468 0.047 0.45 NO
20 CYP3A7 CYP3A7 CYP3A7 5300 0.02 0.35 NO
21 IMPDH2 IMPDH2 IMPDH2 5316 0.02 0.36 NO
22 ITPA ITPA ITPA 5625 0.017 0.34 NO
23 UGT1A6 UGT1A6 UGT1A6 6368 0.0099 0.31 NO
24 TK1 TK1 TK1 6777 0.006 0.29 NO
25 TPMT TPMT TPMT 7299 0.0012 0.26 NO
26 UCKL1 UCKL1 UCKL1 7635 -0.0021 0.24 NO
27 HPRT1 HPRT1 HPRT1 7673 -0.0024 0.24 NO
28 NAT2 NAT2 NAT2 8121 -0.0068 0.22 NO
29 CYP3A43 CYP3A43 CYP3A43 8218 -0.0076 0.21 NO
30 GMPS GMPS GMPS 8231 -0.0077 0.21 NO
31 IMPDH1 IMPDH1 IMPDH1 8351 -0.0087 0.21 NO
32 UCK2 UCK2 UCK2 8776 -0.013 0.19 NO
33 UPP2 UPP2 UPP2 9421 -0.019 0.16 NO
34 CYP2A7 CYP2A7 CYP2A7 10134 -0.027 0.12 NO
35 TK2 TK2 TK2 10307 -0.028 0.12 NO
36 UGT1A1 UGT1A1 UGT1A1 10700 -0.033 0.11 NO
37 GUSB GUSB GUSB 11427 -0.041 0.078 NO
38 UGT2B4 UGT2B4 UGT2B4 11476 -0.042 0.084 NO
39 UGT1A4 UGT1A4 UGT1A4 12182 -0.051 0.057 NO
40 UGT1A9 UGT1A9 UGT1A9 12744 -0.059 0.04 NO
41 UCK1 UCK1 UCK1 12980 -0.064 0.041 NO
42 UGT1A3 UGT1A3 UGT1A3 15369 -0.12 -0.062 NO
43 UGT1A5 UGT1A5 UGT1A5 16049 -0.14 -0.068 NO
44 UGT1A7 UGT1A7 UGT1A7 16094 -0.14 -0.039 NO
45 UPB1 UPB1 UPB1 16197 -0.15 -0.012 NO
46 DPYS DPYS DPYS 18031 -0.29 -0.048 NO
47 CES1 CES1 CES1 18240 -0.33 0.014 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 RETINOL METABOLISM.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA CHREBP2 PATHWAY 40 genes.ES.table 0.55 2 0 0.11 0.086 0.15 0.086 0.14 0 0.041
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.4 1.3 0.2 1 0.98 0.38 0.23 0.29 0.84 0.41
KEGG PENTOSE PHOSPHATE PATHWAY 26 genes.ES.table 0.45 1.4 0.12 1 0.97 0.23 0.079 0.21 0.8 0.4
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.36 1.3 0.17 0.96 0.98 0.21 0.12 0.19 0.82 0.4
KEGG GLUTATHIONE METABOLISM 46 genes.ES.table 0.63 1.8 0.008 0.39 0.39 0.39 0.11 0.35 0 0.13
KEGG STARCH AND SUCROSE METABOLISM 43 genes.ES.table 0.52 1.3 0.086 0.97 0.98 0.21 0.037 0.2 0.79 0.39
KEGG GLYCEROLIPID METABOLISM 44 genes.ES.table 0.37 1.3 0.14 0.92 0.99 0.23 0.064 0.21 0.8 0.37
KEGG GLYCEROPHOSPHOLIPID METABOLISM 72 genes.ES.table 0.34 1.3 0.15 0.96 0.99 0.17 0.059 0.16 0.83 0.4
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 36 genes.ES.table 0.6 1.5 0.087 1 0.92 0.22 0.033 0.22 0.89 0.45
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 65 genes.ES.table 0.61 1.4 0.094 1 0.96 0.37 0.069 0.34 0.81 0.42
genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PPP2R2B PPP2R2B PPP2R2B 139 0.54 0.17 YES
2 PPP2R2C PPP2R2C PPP2R2C 289 0.41 0.3 YES
3 PRKAA2 PRKAA2 PRKAA2 355 0.38 0.42 YES
4 MLXIPL MLXIPL MLXIPL 804 0.26 0.48 YES
5 PPP2R5A PPP2R5A PPP2R5A 1205 0.2 0.52 YES
6 PPP2R3A PPP2R3A PPP2R3A 1587 0.16 0.55 YES
7 YWHAG YWHAG YWHAG 2772 0.096 0.52 NO
8 PRKAB2 PRKAB2 PRKAB2 3806 0.066 0.48 NO
9 GCK GCK GCK 3861 0.064 0.5 NO
10 MLX MLX MLX 4711 0.047 0.47 NO
11 YWHAQ YWHAQ YWHAQ 4888 0.044 0.47 NO
12 PPP2R4 PPP2R4 PPP2R4 5264 0.037 0.46 NO
13 PPP2R3B PPP2R3B PPP2R3B 5343 0.036 0.47 NO
14 ACACA ACACA ACACA 5369 0.035 0.48 NO
15 YWHAE YWHAE YWHAE 5484 0.034 0.49 NO
16 PRKAR2A PRKAR2A PRKAR2A 5563 0.032 0.49 NO
17 YWHAZ YWHAZ YWHAZ 6170 0.023 0.47 NO
18 PPP2R1B PPP2R1B PPP2R1B 6203 0.023 0.47 NO
19 PRKAG1 PRKAG1 PRKAG1 6238 0.022 0.48 NO
20 PRKACA PRKACA PRKACA 6739 0.015 0.46 NO
21 PPP2R5D PPP2R5D PPP2R5D 7007 0.011 0.45 NO
22 PKLR PKLR PKLR 7248 0.0073 0.44 NO
23 PPP2R2A PPP2R2A PPP2R2A 7465 0.004 0.42 NO
24 PPP2CA PPP2CA PPP2CA 7466 0.004 0.43 NO
25 YWHAH YWHAH YWHAH 7571 0.0026 0.42 NO
26 PPP2R5E PPP2R5E PPP2R5E 8144 -0.0058 0.39 NO
27 PPP2R5C PPP2R5C PPP2R5C 8177 -0.0063 0.39 NO
28 FASN FASN FASN 8517 -0.011 0.38 NO
29 PPP2CB PPP2CB PPP2CB 9340 -0.023 0.34 NO
30 PRKACB PRKACB PRKACB 9383 -0.024 0.35 NO
31 PRKAB1 PRKAB1 PRKAB1 9465 -0.025 0.35 NO
32 PRKAR1B PRKAR1B PRKAR1B 9553 -0.026 0.35 NO
33 PRKAR1A PRKAR1A PRKAR1A 9803 -0.03 0.35 NO
34 PPP2R2D PPP2R2D PPP2R2D 10003 -0.034 0.35 NO
35 YWHAB YWHAB YWHAB 10113 -0.036 0.36 NO
36 PRKAA1 PRKAA1 PRKAA1 10265 -0.038 0.36 NO
37 PPP2R1A PPP2R1A PPP2R1A 11177 -0.054 0.33 NO
38 PPP2R5B PPP2R5B PPP2R5B 11309 -0.056 0.34 NO
39 PRKAG2 PRKAG2 PRKAG2 11571 -0.062 0.34 NO
40 PRKAR2B PRKAR2B PRKAR2B 12836 -0.092 0.31 NO

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

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

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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 GPX2 GPX2 GPX2 79 0.64 0.075 YES
2 GSTM2 GSTM2 GSTM2 93 0.61 0.15 YES
3 GSTM3 GSTM3 GSTM3 103 0.59 0.22 YES
4 GSTA1 GSTA1 GSTA1 144 0.54 0.29 YES
5 GSTM4 GSTM4 GSTM4 219 0.47 0.34 YES
6 GCLM GCLM GCLM 252 0.44 0.39 YES
7 GCLC GCLC GCLC 280 0.42 0.44 YES
8 GSR GSR GSR 467 0.33 0.47 YES
9 ODC1 ODC1 ODC1 475 0.33 0.52 YES
10 GSTA4 GSTA4 GSTA4 591 0.3 0.55 YES
11 G6PD G6PD G6PD 605 0.3 0.58 YES
12 GSTM1 GSTM1 GSTM1 1169 0.2 0.58 YES
13 GSTA2 GSTA2 GSTA2 1281 0.19 0.59 YES
14 SMS SMS SMS 1715 0.15 0.59 YES
15 RRM1 RRM1 RRM1 1856 0.14 0.6 YES
16 GSTT2 GSTT2 GSTT2 2050 0.13 0.6 YES
17 GSTO1 GSTO1 GSTO1 2099 0.13 0.62 YES
18 IDH1 IDH1 IDH1 2117 0.13 0.63 YES
19 RRM2 RRM2 RRM2 2957 0.09 0.6 NO
20 GGCT GGCT GGCT 3021 0.087 0.6 NO
21 GSTP1 GSTP1 GSTP1 3455 0.074 0.59 NO
22 MGST2 MGST2 MGST2 4449 0.052 0.54 NO
23 GSTZ1 GSTZ1 GSTZ1 4868 0.044 0.52 NO
24 GGT6 GGT6 GGT6 5694 0.03 0.48 NO
25 MGST1 MGST1 MGST1 5719 0.03 0.49 NO
26 GSTT1 GSTT1 GSTT1 6206 0.022 0.46 NO
27 GSS GSS GSS 6367 0.02 0.46 NO
28 GPX4 GPX4 GPX4 6953 0.011 0.43 NO
29 TXNDC12 TXNDC12 TXNDC12 7790 -0.00061 0.38 NO
30 MGST3 MGST3 MGST3 8513 -0.011 0.34 NO
31 GGT7 GGT7 GGT7 10146 -0.036 0.26 NO
32 GSTK1 GSTK1 GSTK1 10828 -0.048 0.23 NO
33 GSTA3 GSTA3 GSTA3 10932 -0.049 0.23 NO
34 RRM2B RRM2B RRM2B 10966 -0.05 0.23 NO
35 GPX1 GPX1 GPX1 11381 -0.058 0.22 NO
36 LAP3 LAP3 LAP3 12244 -0.077 0.18 NO
37 GSTM5 GSTM5 GSTM5 12323 -0.079 0.19 NO
38 IDH2 IDH2 IDH2 12479 -0.083 0.19 NO
39 SRM SRM SRM 12814 -0.091 0.18 NO
40 GPX3 GPX3 GPX3 12927 -0.094 0.19 NO
41 OPLAH OPLAH OPLAH 12991 -0.096 0.2 NO
42 GSTO2 GSTO2 GSTO2 13289 -0.1 0.19 NO
43 GGT5 GGT5 GGT5 14228 -0.14 0.16 NO
44 ANPEP ANPEP ANPEP 15095 -0.17 0.13 NO
45 GPX7 GPX7 GPX7 15602 -0.19 0.13 NO
46 GGT1 GGT1 GGT1 16541 -0.23 0.11 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: KEGG CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

Table 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 RPA4 RPA4 RPA4 316 0.4 0.15 YES
2 RFC4 RFC4 RFC4 1141 0.2 0.19 YES
3 RFC5 RFC5 RFC5 1998 0.13 0.2 YES
4 POLE3 POLE3 POLE3 2380 0.11 0.22 YES
5 RPA1 RPA1 RPA1 2413 0.11 0.27 YES
6 PRIM1 PRIM1 PRIM1 3247 0.081 0.25 YES
7 POLA2 POLA2 POLA2 3277 0.08 0.28 YES
8 RNASEH2A RNASEH2A RNASEH2A 3466 0.074 0.31 YES
9 RNASEH1 RNASEH1 RNASEH1 3584 0.071 0.33 YES
10 RFC2 RFC2 RFC2 3601 0.071 0.36 YES
11 FEN1 FEN1 FEN1 3602 0.071 0.39 YES
12 RFC3 RFC3 RFC3 3667 0.07 0.41 YES
13 MCM7 MCM7 MCM7 4026 0.06 0.42 YES
14 MCM5 MCM5 MCM5 4033 0.06 0.44 YES
15 MCM3 MCM3 MCM3 4037 0.06 0.47 YES
16 MCM6 MCM6 MCM6 4132 0.058 0.49 YES
17 SSBP1 SSBP1 SSBP1 4368 0.054 0.5 YES
18 PRIM2 PRIM2 PRIM2 4581 0.05 0.5 YES
19 POLD2 POLD2 POLD2 4696 0.047 0.52 YES
20 RNASEH2B RNASEH2B RNASEH2B 4863 0.044 0.53 YES
21 PCNA PCNA PCNA 4869 0.044 0.55 YES
22 DNA2 DNA2 DNA2 4878 0.044 0.56 YES
23 MCM2 MCM2 MCM2 4989 0.042 0.57 YES
24 MCM4 MCM4 MCM4 5975 0.026 0.53 NO
25 RNASEH2C RNASEH2C RNASEH2C 6707 0.015 0.5 NO
26 RPA3 RPA3 RPA3 7228 0.0076 0.47 NO
27 POLD3 POLD3 POLD3 7818 -0.00095 0.44 NO
28 POLE4 POLE4 POLE4 7902 -0.0022 0.44 NO
29 POLE POLE POLE 8323 -0.0086 0.42 NO
30 RFC1 RFC1 RFC1 8676 -0.014 0.4 NO
31 POLE2 POLE2 POLE2 10408 -0.04 0.33 NO
32 LIG1 LIG1 LIG1 10584 -0.044 0.34 NO
33 POLD1 POLD1 POLD1 11703 -0.065 0.3 NO
34 RPA2 RPA2 RPA2 12272 -0.078 0.3 NO
35 POLD4 POLD4 POLD4 12322 -0.079 0.33 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 PENTOSE PHOSPHATE PATHWAY.

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

Table 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 UGT1A7 UGT1A7 UGT1A7 2 1.1 0.13 YES
2 UGT1A9 UGT1A9 UGT1A9 30 0.74 0.22 YES
3 UGT1A1 UGT1A1 UGT1A1 36 0.73 0.31 YES
4 UGT1A3 UGT1A3 UGT1A3 68 0.66 0.39 YES
5 UGT1A5 UGT1A5 UGT1A5 114 0.58 0.46 YES
6 UGT1A6 UGT1A6 UGT1A6 125 0.56 0.53 YES
7 UGT1A4 UGT1A4 UGT1A4 229 0.46 0.58 YES
8 UGT1A8 UGT1A8 UGT1A8 607 0.3 0.6 YES
9 FECH FECH FECH 1124 0.2 0.6 NO
10 HMOX1 HMOX1 HMOX1 1704 0.15 0.58 NO
11 BLVRB BLVRB BLVRB 2647 0.1 0.55 NO
12 BLVRA BLVRA BLVRA 3363 0.077 0.52 NO
13 ALAD ALAD ALAD 3647 0.07 0.51 NO
14 COX10 COX10 COX10 3696 0.069 0.52 NO
15 FTH1 FTH1 FTH1 3755 0.068 0.52 NO
16 EPRS EPRS EPRS 3850 0.065 0.52 NO
17 UGT1A10 UGT1A10 UGT1A10 4306 0.055 0.51 NO
18 MMAB MMAB MMAB 4392 0.053 0.51 NO
19 HMBS HMBS HMBS 5013 0.041 0.48 NO
20 CPOX CPOX CPOX 5412 0.035 0.46 NO
21 HMOX2 HMOX2 HMOX2 5536 0.033 0.46 NO
22 ALAS1 ALAS1 ALAS1 5680 0.03 0.46 NO
23 UROS UROS UROS 5770 0.029 0.45 NO
24 EARS2 EARS2 EARS2 6748 0.015 0.4 NO
25 COX15 COX15 COX15 7855 -0.0015 0.34 NO
26 GUSB GUSB GUSB 7981 -0.0036 0.34 NO
27 PPOX PPOX PPOX 8260 -0.0077 0.32 NO
28 ALAS2 ALAS2 ALAS2 10340 -0.039 0.22 NO
29 UGT2A1 UGT2A1 UGT2A1 13928 -0.12 0.036 NO
30 UROD UROD UROD 14160 -0.13 0.04 NO
31 UGT2A3 UGT2A3 UGT2A3 14600 -0.15 0.034 NO
32 UGT2B28 UGT2B28 UGT2B28 15264 -0.17 0.02 NO
33 UGT2B4 UGT2B4 UGT2B4 16667 -0.24 -0.026 NO
34 CP CP CP 17225 -0.28 -0.022 NO
35 UGT2B15 UGT2B15 UGT2B15 17271 -0.28 0.01 NO
36 UGT2B7 UGT2B7 UGT2B7 18338 -0.45 0.0086 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 FRUCTOSE AND MANNOSE METABOLISM.

Figure S28.  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 GLUTATHIONE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPA4 RPA4 RPA4 316 0.4 0.14 YES
2 XRCC2 XRCC2 XRCC2 821 0.26 0.21 YES
3 RAD51L3 RAD51L3 RAD51L3 1012 0.22 0.28 YES
4 EME1 EME1 EME1 1199 0.2 0.35 YES
5 BRCA2 BRCA2 BRCA2 1346 0.18 0.41 YES
6 BLM BLM BLM 1459 0.17 0.47 YES
7 RAD51 RAD51 RAD51 1717 0.15 0.51 YES
8 RPA1 RPA1 RPA1 2413 0.11 0.52 YES
9 SHFM1 SHFM1 SHFM1 2907 0.091 0.52 YES
10 RAD51L1 RAD51L1 RAD51L1 3025 0.087 0.55 YES
11 TOP3B TOP3B TOP3B 3843 0.065 0.53 NO
12 SSBP1 SSBP1 SSBP1 4368 0.054 0.52 NO
13 POLD2 POLD2 POLD2 4696 0.047 0.53 NO
14 TOP3A TOP3A TOP3A 5034 0.041 0.52 NO
15 RAD50 RAD50 RAD50 5068 0.04 0.54 NO
16 RAD54B RAD54B RAD54B 5087 0.04 0.55 NO
17 XRCC3 XRCC3 XRCC3 6082 0.024 0.51 NO
18 RAD54L RAD54L RAD54L 6183 0.023 0.51 NO
19 MRE11A MRE11A MRE11A 6541 0.017 0.5 NO
20 RPA3 RPA3 RPA3 7228 0.0076 0.46 NO
21 POLD3 POLD3 POLD3 7818 -0.00095 0.43 NO
22 RAD52 RAD52 RAD52 8532 -0.012 0.4 NO
23 POLD1 POLD1 POLD1 11703 -0.065 0.25 NO
24 MUS81 MUS81 MUS81 11912 -0.069 0.27 NO
25 NBN NBN NBN 12245 -0.077 0.28 NO
26 RPA2 RPA2 RPA2 12272 -0.078 0.31 NO
27 POLD4 POLD4 POLD4 12322 -0.079 0.33 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 GLUTATHIONE METABOLISM.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLUTATHIONE 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 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 RPA4 RPA4 RPA4 316 0.4 0.13 YES
2 XPA XPA XPA 612 0.3 0.22 YES
3 RFC4 RFC4 RFC4 1141 0.2 0.27 YES
4 RFC5 RFC5 RFC5 1998 0.13 0.27 YES
5 POLE3 POLE3 POLE3 2380 0.11 0.3 YES
6 RPA1 RPA1 RPA1 2413 0.11 0.33 YES
7 RAD23A RAD23A RAD23A 2514 0.1 0.37 YES
8 RFC2 RFC2 RFC2 3601 0.071 0.34 YES
9 RFC3 RFC3 RFC3 3667 0.07 0.36 YES
10 ERCC4 ERCC4 ERCC4 3930 0.063 0.37 YES
11 GTF2H1 GTF2H1 GTF2H1 4455 0.052 0.36 YES
12 POLD2 POLD2 POLD2 4696 0.047 0.36 YES
13 MNAT1 MNAT1 MNAT1 4763 0.046 0.38 YES
14 PCNA PCNA PCNA 4869 0.044 0.39 YES
15 ERCC3 ERCC3 ERCC3 5075 0.04 0.39 YES
16 GTF2H3 GTF2H3 GTF2H3 5802 0.028 0.36 NO
17 DDB2 DDB2 DDB2 5957 0.026 0.36 NO
18 GTF2H2 GTF2H2 GTF2H2 6017 0.025 0.37 NO
19 CUL4A CUL4A CUL4A 6305 0.021 0.36 NO
20 CUL4B CUL4B CUL4B 7046 0.01 0.32 NO
21 CCNH CCNH CCNH 7224 0.0077 0.32 NO
22 RPA3 RPA3 RPA3 7228 0.0076 0.32 NO
23 XPC XPC XPC 7419 0.0049 0.31 NO
24 POLD3 POLD3 POLD3 7818 -0.00095 0.29 NO
25 POLE4 POLE4 POLE4 7902 -0.0022 0.29 NO
26 CDK7 CDK7 CDK7 8235 -0.0074 0.27 NO
27 POLE POLE POLE 8323 -0.0086 0.27 NO
28 RFC1 RFC1 RFC1 8676 -0.014 0.26 NO
29 CETN2 CETN2 CETN2 8732 -0.014 0.26 NO
30 RBX1 RBX1 RBX1 9112 -0.02 0.24 NO
31 DDB1 DDB1 DDB1 9126 -0.02 0.25 NO
32 ERCC1 ERCC1 ERCC1 9354 -0.023 0.25 NO
33 ERCC8 ERCC8 ERCC8 9713 -0.029 0.24 NO
34 POLE2 POLE2 POLE2 10408 -0.04 0.22 NO
35 ERCC6 ERCC6 ERCC6 10565 -0.043 0.22 NO
36 LIG1 LIG1 LIG1 10584 -0.044 0.24 NO
37 GTF2H4 GTF2H4 GTF2H4 11047 -0.052 0.23 NO
38 ERCC5 ERCC5 ERCC5 11173 -0.054 0.25 NO
39 POLD1 POLD1 POLD1 11703 -0.065 0.24 NO
40 RPA2 RPA2 RPA2 12272 -0.078 0.24 NO
41 GTF2H5 GTF2H5 GTF2H5 12302 -0.078 0.27 NO
42 POLD4 POLD4 POLD4 12322 -0.079 0.3 NO
43 ERCC2 ERCC2 ERCC2 13233 -0.1 0.28 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 STARCH AND SUCROSE METABOLISM.

Figure S32.  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 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 UGT1A7 UGT1A7 UGT1A7 2 1.1 0.056 YES
2 ADH7 ADH7 ADH7 17 0.81 0.099 YES
3 UGT1A9 UGT1A9 UGT1A9 30 0.74 0.14 YES
4 AKR1C1 AKR1C1 AKR1C1 32 0.74 0.18 YES
5 UGT1A1 UGT1A1 UGT1A1 36 0.73 0.22 YES
6 ALDH3A1 ALDH3A1 ALDH3A1 38 0.72 0.25 YES
7 AKR1C3 AKR1C3 AKR1C3 52 0.69 0.29 YES
8 UGT1A3 UGT1A3 UGT1A3 68 0.66 0.32 YES
9 AKR1C2 AKR1C2 AKR1C2 77 0.65 0.36 YES
10 GSTM2 GSTM2 GSTM2 93 0.61 0.39 YES
11 GSTM3 GSTM3 GSTM3 103 0.59 0.42 YES
12 UGT1A5 UGT1A5 UGT1A5 114 0.58 0.45 YES
13 UGT1A6 UGT1A6 UGT1A6 125 0.56 0.48 YES
14 GSTA1 GSTA1 GSTA1 144 0.54 0.51 YES
15 GSTM4 GSTM4 GSTM4 219 0.47 0.53 YES
16 UGT1A4 UGT1A4 UGT1A4 229 0.46 0.55 YES
17 CYP2S1 CYP2S1 CYP2S1 301 0.41 0.57 YES
18 CYP2C18 CYP2C18 CYP2C18 374 0.37 0.58 YES
19 GSTA4 GSTA4 GSTA4 591 0.3 0.59 YES
20 UGT1A8 UGT1A8 UGT1A8 607 0.3 0.6 YES
21 EPHX1 EPHX1 EPHX1 1033 0.22 0.59 YES
22 AKR1C4 AKR1C4 AKR1C4 1099 0.21 0.6 YES
23 GSTM1 GSTM1 GSTM1 1169 0.2 0.61 YES
24 GSTA2 GSTA2 GSTA2 1281 0.19 0.61 YES
25 CYP2C19 CYP2C19 CYP2C19 1463 0.17 0.61 NO
26 GSTT2 GSTT2 GSTT2 2050 0.13 0.58 NO
27 GSTO1 GSTO1 GSTO1 2099 0.13 0.59 NO
28 GSTP1 GSTP1 GSTP1 3455 0.074 0.52 NO
29 CYP2C9 CYP2C9 CYP2C9 3749 0.068 0.51 NO
30 UGT1A10 UGT1A10 UGT1A10 4306 0.055 0.48 NO
31 MGST2 MGST2 MGST2 4449 0.052 0.48 NO
32 GSTZ1 GSTZ1 GSTZ1 4868 0.044 0.46 NO
33 ALDH3B2 ALDH3B2 ALDH3B2 5549 0.032 0.42 NO
34 MGST1 MGST1 MGST1 5719 0.03 0.41 NO
35 GSTT1 GSTT1 GSTT1 6206 0.022 0.39 NO
36 ADH5 ADH5 ADH5 6631 0.016 0.36 NO
37 ADH4 ADH4 ADH4 7897 -0.0021 0.3 NO
38 MGST3 MGST3 MGST3 8513 -0.011 0.26 NO
39 CYP1A1 CYP1A1 CYP1A1 9647 -0.028 0.2 NO
40 GSTK1 GSTK1 GSTK1 10828 -0.048 0.14 NO
41 GSTA3 GSTA3 GSTA3 10932 -0.049 0.14 NO
42 DHDH DHDH DHDH 12311 -0.079 0.068 NO
43 GSTM5 GSTM5 GSTM5 12323 -0.079 0.072 NO
44 CYP3A43 CYP3A43 CYP3A43 12429 -0.082 0.071 NO
45 GSTO2 GSTO2 GSTO2 13289 -0.1 0.03 NO
46 ADH1C ADH1C ADH1C 13740 -0.12 0.012 NO
47 UGT2A1 UGT2A1 UGT2A1 13928 -0.12 0.0079 NO
48 CYP2C8 CYP2C8 CYP2C8 14175 -0.13 0.0016 NO
49 ADH1B ADH1B ADH1B 14521 -0.15 -0.0093 NO
50 UGT2A3 UGT2A3 UGT2A3 14600 -0.15 -0.0057 NO
51 UGT2B28 UGT2B28 UGT2B28 15264 -0.17 -0.032 NO
52 ADH6 ADH6 ADH6 15377 -0.18 -0.029 NO
53 ADH1A ADH1A ADH1A 15716 -0.19 -0.037 NO
54 CYP2E1 CYP2E1 CYP2E1 16498 -0.23 -0.068 NO
55 UGT2B4 UGT2B4 UGT2B4 16667 -0.24 -0.064 NO
56 CYP1A2 CYP1A2 CYP1A2 16673 -0.24 -0.051 NO
57 CYP1B1 CYP1B1 CYP1B1 16687 -0.24 -0.039 NO
58 CYP2F1 CYP2F1 CYP2F1 17185 -0.27 -0.052 NO
59 UGT2B15 UGT2B15 UGT2B15 17271 -0.28 -0.041 NO
60 CYP3A5 CYP3A5 CYP3A5 17303 -0.28 -0.028 NO
61 CYP2B6 CYP2B6 CYP2B6 17577 -0.31 -0.027 NO
62 ALDH3B1 ALDH3B1 ALDH3B1 17670 -0.32 -0.015 NO
63 CYP3A7 CYP3A7 CYP3A7 17724 -0.32 -0.00068 NO
64 ALDH1A3 ALDH1A3 ALDH1A3 17916 -0.35 0.0073 NO
65 UGT2B7 UGT2B7 UGT2B7 18338 -0.45 0.0086 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 GLYCEROLIPID METABOLISM.

Figure S34.  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 GLYCEROPHOSPHOLIPID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADCY8 ADCY8 ADCY8 18 0.81 0.088 YES
2 CCNA1 CCNA1 CCNA1 169 0.51 0.14 YES
3 RPS6KA6 RPS6KA6 RPS6KA6 387 0.36 0.16 YES
4 PRKX PRKX PRKX 484 0.33 0.2 YES
5 MAPK10 MAPK10 MAPK10 671 0.28 0.22 YES
6 PIK3CA PIK3CA PIK3CA 976 0.23 0.23 YES
7 ADCY3 ADCY3 ADCY3 1139 0.2 0.24 YES
8 CDC26 CDC26 CDC26 1328 0.18 0.25 YES
9 MAPK12 MAPK12 MAPK12 1380 0.18 0.27 YES
10 ADCY5 ADCY5 ADCY5 1381 0.18 0.29 YES
11 SPDYA SPDYA SPDYA 1486 0.17 0.3 YES
12 CDC25A CDC25A CDC25A 1669 0.15 0.31 YES
13 AKT3 AKT3 AKT3 1879 0.14 0.31 YES
14 BRAF BRAF BRAF 2147 0.12 0.31 YES
15 CCNB2 CCNB2 CCNB2 2590 0.1 0.3 YES
16 IGF1R IGF1R IGF1R 2842 0.094 0.29 YES
17 PDE3B PDE3B PDE3B 2882 0.092 0.3 YES
18 PIK3R2 PIK3R2 PIK3R2 3056 0.086 0.3 YES
19 KRAS KRAS KRAS 3162 0.083 0.3 YES
20 CCNA2 CCNA2 CCNA2 3169 0.082 0.31 YES
21 CPEB1 CPEB1 CPEB1 3204 0.082 0.32 YES
22 BUB1 BUB1 BUB1 3238 0.081 0.33 YES
23 ANAPC1 ANAPC1 ANAPC1 3340 0.078 0.33 YES
24 RPS6KA3 RPS6KA3 RPS6KA3 3359 0.077 0.34 YES
25 CDC25C CDC25C CDC25C 3427 0.075 0.34 YES
26 PLK1 PLK1 PLK1 3769 0.067 0.33 NO
27 ANAPC2 ANAPC2 ANAPC2 3909 0.063 0.33 NO
28 MAD2L1 MAD2L1 MAD2L1 3928 0.063 0.34 NO
29 ANAPC7 ANAPC7 ANAPC7 3981 0.061 0.34 NO
30 CDK1 CDK1 CDK1 4269 0.056 0.33 NO
31 MAPK1 MAPK1 MAPK1 4314 0.055 0.34 NO
32 CCNB1 CCNB1 CCNB1 4590 0.05 0.33 NO
33 CDC27 CDC27 CDC27 4620 0.049 0.33 NO
34 ANAPC11 ANAPC11 ANAPC11 5103 0.04 0.31 NO
35 FZR1 FZR1 FZR1 5202 0.038 0.31 NO
36 HSP90AA1 HSP90AA1 HSP90AA1 5477 0.034 0.3 NO
37 MAPK9 MAPK9 MAPK9 5516 0.033 0.3 NO
38 CDC23 CDC23 CDC23 5758 0.029 0.29 NO
39 CDK2 CDK2 CDK2 5786 0.028 0.29 NO
40 ANAPC13 ANAPC13 ANAPC13 6179 0.023 0.27 NO
41 ADCY2 ADCY2 ADCY2 6364 0.02 0.26 NO
42 ADCY9 ADCY9 ADCY9 6410 0.019 0.26 NO
43 GNAI1 GNAI1 GNAI1 6526 0.017 0.26 NO
44 PRKACA PRKACA PRKACA 6739 0.015 0.25 NO
45 PKMYT1 PKMYT1 PKMYT1 6892 0.012 0.24 NO
46 CDC25B CDC25B CDC25B 7012 0.011 0.24 NO
47 MAP2K1 MAP2K1 MAP2K1 7160 0.0087 0.23 NO
48 MAPK13 MAPK13 MAPK13 7627 0.002 0.2 NO
49 ANAPC5 ANAPC5 ANAPC5 7968 -0.0033 0.19 NO
50 AKT1 AKT1 AKT1 8482 -0.011 0.16 NO
51 RAF1 RAF1 RAF1 8526 -0.011 0.16 NO
52 MAPK11 MAPK11 MAPK11 9215 -0.022 0.12 NO
53 PRKACB PRKACB PRKACB 9383 -0.024 0.12 NO
54 AKT2 AKT2 AKT2 9958 -0.033 0.09 NO
55 MAPK14 MAPK14 MAPK14 10287 -0.038 0.076 NO
56 CDC16 CDC16 CDC16 10356 -0.039 0.077 NO
57 PIK3CB PIK3CB PIK3CB 10524 -0.042 0.073 NO
58 ANAPC10 ANAPC10 ANAPC10 10540 -0.043 0.076 NO
59 ANAPC4 ANAPC4 ANAPC4 10808 -0.048 0.067 NO
60 GNAI3 GNAI3 GNAI3 10846 -0.048 0.071 NO
61 ARAF ARAF ARAF 11179 -0.054 0.058 NO
62 ADCY7 ADCY7 ADCY7 11262 -0.056 0.06 NO
63 MAPK3 MAPK3 MAPK3 11343 -0.057 0.062 NO
64 CCNB3 CCNB3 CCNB3 11802 -0.067 0.045 NO
65 GNAI2 GNAI2 GNAI2 12075 -0.073 0.038 NO
66 PIK3R1 PIK3R1 PIK3R1 12327 -0.079 0.033 NO
67 IGF1 IGF1 IGF1 12362 -0.08 0.04 NO
68 ADCY6 ADCY6 ADCY6 13351 -0.11 -0.0016 NO
69 RPS6KA1 RPS6KA1 RPS6KA1 13591 -0.11 -0.002 NO
70 PIK3CD PIK3CD PIK3CD 14121 -0.13 -0.016 NO
71 MAPK8 MAPK8 MAPK8 14516 -0.15 -0.022 NO
72 ADCY1 ADCY1 ADCY1 14557 -0.15 -0.0074 NO
73 MAD2L2 MAD2L2 MAD2L2 14955 -0.16 -0.011 NO
74 RPS6KA2 RPS6KA2 RPS6KA2 15125 -0.17 -0.0018 NO
75 PGR PGR PGR 15592 -0.18 -0.0065 NO
76 PIK3R3 PIK3R3 PIK3R3 15821 -0.2 0.0028 NO
77 PIK3CG PIK3CG PIK3CG 16347 -0.22 -0.00097 NO
78 PIK3R5 PIK3R5 PIK3R5 16645 -0.24 0.0094 NO
79 ADCY4 ADCY4 ADCY4 16961 -0.26 0.021 NO
80 SPDYC SPDYC SPDYC 17247 -0.28 0.036 NO
81 PDE3A PDE3A PDE3A 17340 -0.28 0.063 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 GLYCEROPHOSPHOLIPID METABOLISM.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCEROPHOSPHOLIPID 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 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 PGD PGD PGD 562 0.31 0.082 YES
2 G6PD G6PD G6PD 605 0.3 0.19 YES
3 TALDO1 TALDO1 TALDO1 807 0.26 0.27 YES
4 ALDOC ALDOC ALDOC 1158 0.2 0.33 YES
5 TKT TKT TKT 1206 0.2 0.4 YES
6 GPI GPI GPI 1457 0.17 0.45 YES
7 RPIA RPIA RPIA 2294 0.12 0.44 NO
8 DERA DERA DERA 3035 0.087 0.44 NO
9 PGLS PGLS PGLS 4396 0.053 0.38 NO
10 PFKM PFKM PFKM 5096 0.04 0.36 NO
11 ALDOB ALDOB ALDOB 5228 0.038 0.36 NO
12 PGM2 PGM2 PGM2 6418 0.019 0.31 NO
13 PRPS2 PRPS2 PRPS2 6804 0.014 0.29 NO
14 PFKP PFKP PFKP 7106 0.0095 0.28 NO
15 PRPS1 PRPS1 PRPS1 8217 -0.0071 0.22 NO
16 RPE RPE RPE 8870 -0.017 0.19 NO
17 H6PD H6PD H6PD 9388 -0.024 0.17 NO
18 TKTL2 TKTL2 TKTL2 9626 -0.028 0.17 NO
19 LOC729020 LOC729020 LOC729020 9690 -0.028 0.18 NO
20 PFKL PFKL PFKL 10055 -0.034 0.17 NO
21 TKTL1 TKTL1 TKTL1 12068 -0.073 0.089 NO
22 PRPS1L1 PRPS1L1 PRPS1L1 12143 -0.075 0.11 NO
23 PGM1 PGM1 PGM1 13573 -0.11 0.076 NO
24 FBP2 FBP2 FBP2 14022 -0.13 0.099 NO
25 FBP1 FBP1 FBP1 15124 -0.17 0.1 NO
26 RBKS RBKS RBKS 16335 -0.22 0.12 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 PORPHYRIN AND CHLOROPHYLL METABOLISM.

Figure S38.  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

genes ES table in pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450

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 UGT1A7 UGT1A7 UGT1A7 2 1.1 0.11 YES
2 UGT1A9 UGT1A9 UGT1A9 30 0.74 0.19 YES
3 UGT1A1 UGT1A1 UGT1A1 36 0.73 0.26 YES
4 UGT1A3 UGT1A3 UGT1A3 68 0.66 0.33 YES
5 UGT1A5 UGT1A5 UGT1A5 114 0.58 0.39 YES
6 UGT1A6 UGT1A6 UGT1A6 125 0.56 0.44 YES
7 UGT1A4 UGT1A4 UGT1A4 229 0.46 0.49 YES
8 UGT1A8 UGT1A8 UGT1A8 607 0.3 0.5 YES
9 UGDH UGDH UGDH 683 0.28 0.52 YES
10 GPI GPI GPI 1457 0.17 0.5 NO
11 HK1 HK1 HK1 1739 0.15 0.5 NO
12 HK2 HK2 HK2 2122 0.13 0.49 NO
13 GAA GAA GAA 3129 0.084 0.44 NO
14 GCK GCK GCK 3861 0.064 0.41 NO
15 GBE1 GBE1 GBE1 4179 0.057 0.4 NO
16 UGT1A10 UGT1A10 UGT1A10 4306 0.055 0.4 NO
17 UGP2 UGP2 UGP2 4638 0.048 0.38 NO
18 PGM2 PGM2 PGM2 6418 0.019 0.29 NO
19 PYGL PYGL PYGL 6584 0.017 0.28 NO
20 PYGB PYGB PYGB 7394 0.0051 0.24 NO
21 GUSB GUSB GUSB 7981 -0.0036 0.21 NO
22 AGL AGL AGL 8229 -0.0073 0.2 NO
23 GYS1 GYS1 GYS1 8836 -0.016 0.16 NO
24 GBA3 GBA3 GBA3 10090 -0.035 0.1 NO
25 GANC GANC GANC 11410 -0.059 0.035 NO
26 ENPP1 ENPP1 ENPP1 11903 -0.069 0.016 NO
27 GYS2 GYS2 GYS2 12551 -0.085 -0.011 NO
28 AMY2B AMY2B AMY2B 13331 -0.11 -0.042 NO
29 PGM1 PGM1 PGM1 13573 -0.11 -0.043 NO
30 UGT2A1 UGT2A1 UGT2A1 13928 -0.12 -0.05 NO
31 TREH TREH TREH 13947 -0.12 -0.038 NO
32 PGM2L1 PGM2L1 PGM2L1 14407 -0.14 -0.048 NO
33 UGT2A3 UGT2A3 UGT2A3 14600 -0.15 -0.043 NO
34 HK3 HK3 HK3 15044 -0.16 -0.05 NO
35 UGT2B28 UGT2B28 UGT2B28 15264 -0.17 -0.044 NO
36 PYGM PYGM PYGM 15858 -0.2 -0.055 NO
37 AMY2A AMY2A AMY2A 15923 -0.2 -0.038 NO
38 AMY1A AMY1A AMY1A 16456 -0.23 -0.043 NO
39 MGAM MGAM MGAM 16603 -0.24 -0.026 NO
40 UGT2B4 UGT2B4 UGT2B4 16667 -0.24 -0.005 NO
41 ENPP3 ENPP3 ENPP3 17138 -0.27 -0.0025 NO
42 UGT2B15 UGT2B15 UGT2B15 17271 -0.28 0.019 NO
43 UGT2B7 UGT2B7 UGT2B7 18338 -0.45 0.0086 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 METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, 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 0.39 1.2 0.22 1 1 0.17 0.068 0.16 1 0.97
BIOCARTA ALK PATHWAY 34 genes.ES.table 0.41 1.2 0.25 1 1 0.29 0.2 0.24 1 0.94
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.31 1.3 0.21 1 0.99 0.35 0.32 0.24 1 0.88
BIOCARTA MPR PATHWAY 32 genes.ES.table 0.33 1.2 0.22 1 1 0.22 0.25 0.16 1 0.95
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.43 1.4 0.12 1 0.96 0.34 0.29 0.24 1 0.9
BIOCARTA NKT PATHWAY 25 genes.ES.table 0.6 1.1 0.39 1 1 0.56 0.25 0.42 1 0.89
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 29 genes.ES.table 0.37 1.1 0.34 1 1 0.24 0.13 0.21 1 0.9
KEGG CYSTEINE AND METHIONINE METABOLISM 32 genes.ES.table 0.45 1.5 0.059 1 0.93 0.22 0.14 0.19 1 0.92
KEGG N GLYCAN BIOSYNTHESIS 45 genes.ES.table 0.33 1.4 0.13 1 0.97 0.18 0.22 0.14 1 0.89
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION 232 genes.ES.table 0.42 1.2 0.23 1 1 0.38 0.17 0.31 1 0.92
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 TRDMT1 TRDMT1 TRDMT1 1247 0.21 0.034 YES
2 IL4I1 IL4I1 IL4I1 1260 0.21 0.13 YES
3 TAT TAT TAT 1704 0.19 0.2 YES
4 MAT1A MAT1A MAT1A 2267 0.16 0.24 YES
5 LDHAL6A LDHAL6A LDHAL6A 2383 0.16 0.31 YES
6 DNMT3A DNMT3A DNMT3A 2446 0.15 0.38 YES
7 DNMT3B DNMT3B DNMT3B 2512 0.15 0.45 YES
8 LDHAL6B LDHAL6B LDHAL6B 3963 0.1 0.42 NO
9 DNMT1 DNMT1 DNMT1 7778 0.037 0.23 NO
10 MAT2B MAT2B MAT2B 8114 0.033 0.23 NO
11 SRM SRM SRM 8301 0.031 0.23 NO
12 CBS CBS CBS 8702 0.027 0.22 NO
13 APIP APIP APIP 8823 0.026 0.23 NO
14 CTH CTH CTH 10131 0.013 0.17 NO
15 MTR MTR MTR 10230 0.012 0.17 NO
16 CDO1 CDO1 CDO1 10563 0.0088 0.15 NO
17 ENOPH1 ENOPH1 ENOPH1 10733 0.0072 0.15 NO
18 AHCY AHCY AHCY 11108 0.0036 0.13 NO
19 MAT2A MAT2A MAT2A 11215 0.0026 0.12 NO
20 AHCYL1 AHCYL1 AHCYL1 12185 -0.0072 0.074 NO
21 ADI1 ADI1 ADI1 12633 -0.012 0.056 NO
22 MTAP MTAP MTAP 13105 -0.018 0.039 NO
23 LDHB LDHB LDHB 13733 -0.025 0.017 NO
24 SDS SDS SDS 13900 -0.028 0.021 NO
25 LDHA LDHA LDHA 13973 -0.029 0.031 NO
26 GOT1 GOT1 GOT1 14466 -0.036 0.021 NO
27 AMD1 AMD1 AMD1 14902 -0.043 0.018 NO
28 AHCYL2 AHCYL2 AHCYL2 15016 -0.045 0.034 NO
29 SMS SMS SMS 15134 -0.048 0.05 NO
30 MPST MPST MPST 15660 -0.061 0.051 NO
31 GOT2 GOT2 GOT2 16169 -0.077 0.06 NO
32 BHMT BHMT BHMT 17228 -0.14 0.069 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 ALK 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 GAS2 GAS2 GAS2 38 0.43 0.18 YES
2 BIRC3 BIRC3 BIRC3 1447 0.2 0.19 YES
3 TNFRSF25 TNFRSF25 TNFRSF25 1680 0.19 0.26 YES
4 BCL2 BCL2 BCL2 1925 0.18 0.32 YES
5 DFFB DFFB DFFB 2557 0.15 0.35 YES
6 MAP3K14 MAP3K14 MAP3K14 3584 0.11 0.35 YES
7 APAF1 APAF1 APAF1 4146 0.099 0.36 YES
8 TRAF2 TRAF2 TRAF2 4648 0.087 0.37 YES
9 CASP6 CASP6 CASP6 4984 0.079 0.38 YES
10 CASP9 CASP9 CASP9 5231 0.074 0.4 YES
11 BIRC2 BIRC2 BIRC2 5334 0.072 0.43 YES
12 DFFA DFFA DFFA 5938 0.061 0.42 NO
13 TNFSF12 TNFSF12 TNFSF12 6946 0.047 0.39 NO
14 FADD FADD FADD 7665 0.038 0.36 NO
15 RIPK1 RIPK1 RIPK1 9238 0.022 0.29 NO
16 RELA RELA RELA 10073 0.013 0.25 NO
17 SPTAN1 SPTAN1 SPTAN1 10385 0.01 0.24 NO
18 TNFRSF10B TNFRSF10B TNFRSF10B 10746 0.007 0.22 NO
19 CFLAR CFLAR CFLAR 11519 -0.00024 0.18 NO
20 CHUK CHUK CHUK 11678 -0.0019 0.17 NO
21 NFKBIA NFKBIA NFKBIA 11994 -0.0053 0.16 NO
22 NFKB1 NFKB1 NFKB1 12141 -0.0066 0.15 NO
23 CASP7 CASP7 CASP7 12682 -0.013 0.13 NO
24 CASP3 CASP3 CASP3 13351 -0.021 0.099 NO
25 CASP8 CASP8 CASP8 13527 -0.023 0.1 NO
26 LMNA LMNA LMNA 13951 -0.028 0.089 NO
27 XIAP XIAP XIAP 14150 -0.031 0.091 NO
28 CASP10 CASP10 CASP10 14790 -0.041 0.074 NO
29 CYCS CYCS CYCS 15275 -0.051 0.07 NO
30 TRADD TRADD TRADD 15447 -0.055 0.084 NO
31 TNFSF10 TNFSF10 TNFSF10 16181 -0.078 0.078 NO
32 TNFRSF10A TNFRSF10A TNFRSF10A 16845 -0.11 0.089 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 ALK PATHWAY.

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

genes ES table in pathway: BIOCARTA HIVNEF 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 MGAT3 MGAT3 MGAT3 479 0.29 0.094 YES
2 ALG11 ALG11 ALG11 765 0.25 0.18 YES
3 MGAT5B MGAT5B MGAT5B 1613 0.19 0.22 YES
4 MGAT4A MGAT4A MGAT4A 2663 0.14 0.22 YES
5 MAN1C1 MAN1C1 MAN1C1 3497 0.12 0.23 YES
6 MAN1A1 MAN1A1 MAN1A1 3510 0.12 0.27 YES
7 TUSC3 TUSC3 TUSC3 3572 0.11 0.32 YES
8 ST6GAL1 ST6GAL1 ST6GAL1 4124 0.1 0.33 YES
9 DDOST DDOST DDOST 6560 0.052 0.22 NO
10 ALG14 ALG14 ALG14 7222 0.043 0.2 NO
11 B4GALT3 B4GALT3 B4GALT3 7551 0.039 0.2 NO
12 GANAB GANAB GANAB 7568 0.039 0.22 NO
13 RPN2 RPN2 RPN2 8423 0.03 0.18 NO
14 ALG10B ALG10B ALG10B 8484 0.029 0.19 NO
15 ALG9 ALG9 ALG9 9251 0.021 0.16 NO
16 MAN1B1 MAN1B1 MAN1B1 9340 0.02 0.16 NO
17 B4GALT1 B4GALT1 B4GALT1 9466 0.019 0.16 NO
18 MAN2A2 MAN2A2 MAN2A2 9754 0.016 0.16 NO
19 MGAT1 MGAT1 MGAT1 9960 0.014 0.15 NO
20 DPM1 DPM1 DPM1 10280 0.011 0.14 NO
21 ALG6 ALG6 ALG6 10585 0.0086 0.12 NO
22 MOGS MOGS MOGS 11004 0.0046 0.1 NO
23 ALG8 ALG8 ALG8 11114 0.0036 0.099 NO
24 ALG13 ALG13 ALG13 11786 -0.0032 0.064 NO
25 ALG5 ALG5 ALG5 11863 -0.004 0.062 NO
26 RPN1 RPN1 RPN1 11985 -0.0052 0.058 NO
27 DPAGT1 DPAGT1 DPAGT1 12078 -0.006 0.055 NO
28 DPM3 DPM3 DPM3 12118 -0.0063 0.056 NO
29 B4GALT2 B4GALT2 B4GALT2 12145 -0.0067 0.057 NO
30 ALG10 ALG10 ALG10 12501 -0.011 0.042 NO
31 STT3A STT3A STT3A 13003 -0.017 0.022 NO
32 MGAT4B MGAT4B MGAT4B 13065 -0.018 0.026 NO
33 ALG1 ALG1 ALG1 13594 -0.023 0.0072 NO
34 FUT8 FUT8 FUT8 13732 -0.025 0.01 NO
35 DAD1 DAD1 DAD1 14097 -0.03 0.0033 NO
36 MAN2A1 MAN2A1 MAN2A1 14245 -0.032 0.0088 NO
37 DPM2 DPM2 DPM2 14424 -0.035 0.014 NO
38 ALG12 ALG12 ALG12 14885 -0.043 0.0068 NO
39 MAN1A2 MAN1A2 MAN1A2 14994 -0.045 0.02 NO
40 MGAT5 MGAT5 MGAT5 15193 -0.049 0.03 NO
41 STT3B STT3B STT3B 15218 -0.05 0.049 NO
42 MGAT2 MGAT2 MGAT2 15235 -0.05 0.069 NO
43 ALG2 ALG2 ALG2 15684 -0.062 0.071 NO
44 DOLPP1 DOLPP1 DOLPP1 16053 -0.072 0.081 NO
45 ALG3 ALG3 ALG3 17027 -0.12 0.08 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 HIVNEF PATHWAY.

Figure S46.  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 MPR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TNF TNF TNF 999 0.23 0.015 YES
2 BIRC3 BIRC3 BIRC3 1447 0.2 0.051 YES
3 BCL2 BCL2 BCL2 1925 0.18 0.078 YES
4 DFFB DFFB DFFB 2557 0.15 0.088 YES
5 TRAF1 TRAF1 TRAF1 2853 0.14 0.11 YES
6 MAP3K14 MAP3K14 MAP3K14 3584 0.11 0.11 YES
7 MAPK8 MAPK8 MAPK8 3702 0.11 0.14 YES
8 APAF1 APAF1 APAF1 4146 0.099 0.14 YES
9 CDK11A CDK11A CDK11A 4359 0.094 0.16 YES
10 TNFRSF1B TNFRSF1B TNFRSF1B 4604 0.088 0.17 YES
11 TRAF2 TRAF2 TRAF2 4648 0.087 0.2 YES
12 CASP6 CASP6 CASP6 4984 0.079 0.2 YES
13 CASP9 CASP9 CASP9 5231 0.074 0.21 YES
14 CDK11B CDK11B CDK11B 5276 0.073 0.23 YES
15 BIRC2 BIRC2 BIRC2 5334 0.072 0.25 YES
16 PSEN2 PSEN2 PSEN2 5403 0.071 0.27 YES
17 ARHGDIB ARHGDIB ARHGDIB 5794 0.063 0.26 YES
18 DFFA DFFA DFFA 5938 0.061 0.27 YES
19 NUMA1 NUMA1 NUMA1 5951 0.061 0.29 YES
20 FAS FAS FAS 5996 0.06 0.31 YES
21 LMNB1 LMNB1 LMNB1 6766 0.049 0.28 NO
22 DAXX DAXX DAXX 6900 0.047 0.29 NO
23 PARP1 PARP1 PARP1 7190 0.044 0.28 NO
24 FADD FADD FADD 7665 0.038 0.27 NO
25 PRKDC PRKDC PRKDC 8383 0.03 0.24 NO
26 RIPK1 RIPK1 RIPK1 9238 0.022 0.2 NO
27 PTK2 PTK2 PTK2 9513 0.019 0.19 NO
28 MAP2K7 MAP2K7 MAP2K7 10039 0.014 0.17 NO
29 RELA RELA RELA 10073 0.013 0.17 NO
30 SPTAN1 SPTAN1 SPTAN1 10385 0.01 0.16 NO
31 RASA1 RASA1 RASA1 11123 0.0035 0.12 NO
32 CFLAR CFLAR CFLAR 11519 -0.00024 0.096 NO
33 CHUK CHUK CHUK 11678 -0.0019 0.088 NO
34 LMNB2 LMNB2 LMNB2 11992 -0.0053 0.072 NO
35 NFKBIA NFKBIA NFKBIA 11994 -0.0053 0.074 NO
36 NFKB1 NFKB1 NFKB1 12141 -0.0066 0.068 NO
37 CASP7 CASP7 CASP7 12682 -0.013 0.042 NO
38 CASP2 CASP2 CASP2 12860 -0.015 0.037 NO
39 MAP3K1 MAP3K1 MAP3K1 13235 -0.019 0.023 NO
40 CASP3 CASP3 CASP3 13351 -0.021 0.023 NO
41 ACTG1 ACTG1 ACTG1 13424 -0.022 0.025 NO
42 CASP8 CASP8 CASP8 13527 -0.023 0.027 NO
43 LMNA LMNA LMNA 13951 -0.028 0.012 NO
44 XIAP XIAP XIAP 14150 -0.031 0.011 NO
45 MDM2 MDM2 MDM2 14272 -0.033 0.014 NO
46 PRKCD PRKCD PRKCD 14409 -0.035 0.017 NO
47 TNFRSF1A TNFRSF1A TNFRSF1A 14633 -0.038 0.017 NO
48 RB1 RB1 RB1 14850 -0.042 0.018 NO
49 PSEN1 PSEN1 PSEN1 15092 -0.047 0.019 NO
50 PAK2 PAK2 PAK2 15253 -0.051 0.025 NO
51 CYCS CYCS CYCS 15275 -0.051 0.039 NO
52 TRADD TRADD TRADD 15447 -0.055 0.047 NO
53 BID BID BID 15503 -0.056 0.061 NO
54 MAP3K5 MAP3K5 MAP3K5 15888 -0.067 0.06 NO
55 BAG4 BAG4 BAG4 16296 -0.082 0.063 NO
56 GSN GSN GSN 16430 -0.088 0.082 NO
57 CRADD CRADD CRADD 16680 -0.1 0.098 NO

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

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MPR 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 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 CTNNA3 CTNNA3 CTNNA3 62 0.41 0.055 YES
2 DMD DMD DMD 147 0.36 0.1 YES
3 CACNB2 CACNB2 CACNB2 275 0.32 0.14 YES
4 CDH2 CDH2 CDH2 330 0.31 0.18 YES
5 ACTN2 ACTN2 ACTN2 541 0.28 0.21 YES
6 TCF7 TCF7 TCF7 1206 0.22 0.2 YES
7 CACNA1F CACNA1F CACNA1F 1289 0.21 0.23 YES
8 ITGB3 ITGB3 ITGB3 1348 0.2 0.26 YES
9 CACNA1C CACNA1C CACNA1C 1387 0.2 0.28 YES
10 ITGA7 ITGA7 ITGA7 1420 0.2 0.31 YES
11 ITGA9 ITGA9 ITGA9 1926 0.18 0.31 YES
12 SGCG SGCG SGCG 1981 0.17 0.33 YES
13 ITGA10 ITGA10 ITGA10 2333 0.16 0.33 YES
14 PKP2 PKP2 PKP2 2588 0.15 0.34 YES
15 LAMA2 LAMA2 LAMA2 2661 0.14 0.36 YES
16 CTNNA2 CTNNA2 CTNNA2 2691 0.14 0.37 YES
17 ITGA11 ITGA11 ITGA11 2700 0.14 0.39 YES
18 CACNG1 CACNG1 CACNG1 3047 0.13 0.39 YES
19 ACTN3 ACTN3 ACTN3 3098 0.13 0.41 YES
20 CACNA1D CACNA1D CACNA1D 3290 0.12 0.42 YES
21 CACNG4 CACNG4 CACNG4 3422 0.12 0.42 YES
22 CACNA1S CACNA1S CACNA1S 3544 0.12 0.44 YES
23 ITGA2B ITGA2B ITGA2B 3653 0.11 0.44 YES
24 SLC8A1 SLC8A1 SLC8A1 3848 0.11 0.45 YES
25 ITGA4 ITGA4 ITGA4 4028 0.1 0.45 YES
26 TCF7L1 TCF7L1 TCF7L1 4048 0.1 0.47 YES
27 SGCD SGCD SGCD 4078 0.1 0.48 YES
28 CACNB3 CACNB3 CACNB3 4713 0.086 0.46 NO
29 ITGB6 ITGB6 ITGB6 4714 0.085 0.47 NO
30 SGCA SGCA SGCA 5575 0.068 0.43 NO
31 CACNA2D4 CACNA2D4 CACNA2D4 5649 0.066 0.44 NO
32 CACNB1 CACNB1 CACNB1 5855 0.062 0.44 NO
33 TCF7L2 TCF7L2 TCF7L2 5958 0.061 0.44 NO
34 SGCB SGCB SGCB 6004 0.06 0.44 NO
35 ITGB7 ITGB7 ITGB7 6350 0.054 0.43 NO
36 ITGB1 ITGB1 ITGB1 6618 0.051 0.43 NO
37 RYR2 RYR2 RYR2 7129 0.044 0.41 NO
38 ITGA1 ITGA1 ITGA1 7376 0.041 0.4 NO
39 ITGA5 ITGA5 ITGA5 8362 0.03 0.35 NO
40 ITGA3 ITGA3 ITGA3 10250 0.012 0.25 NO
41 ITGA8 ITGA8 ITGA8 10269 0.012 0.25 NO
42 ITGAV ITGAV ITGAV 10758 0.0069 0.22 NO
43 DAG1 DAG1 DAG1 10812 0.0065 0.22 NO
44 CACNA2D1 CACNA2D1 CACNA2D1 10941 0.0052 0.22 NO
45 ACTB ACTB ACTB 11042 0.0042 0.21 NO
46 ACTN1 ACTN1 ACTN1 11081 0.0039 0.21 NO
47 CACNB4 CACNB4 CACNB4 11082 0.0039 0.21 NO
48 ACTN4 ACTN4 ACTN4 11485 0.000092 0.19 NO
49 CTNNA1 CTNNA1 CTNNA1 11668 -0.0018 0.18 NO
50 CACNG6 CACNG6 CACNG6 12227 -0.0076 0.15 NO
51 EMD EMD EMD 12732 -0.013 0.12 NO
52 CTNNB1 CTNNB1 CTNNB1 12838 -0.015 0.12 NO
53 DSG2 DSG2 DSG2 13022 -0.017 0.11 NO
54 ACTG1 ACTG1 ACTG1 13424 -0.022 0.094 NO
55 CACNA2D2 CACNA2D2 CACNA2D2 13565 -0.023 0.089 NO
56 DES DES DES 13692 -0.025 0.086 NO
57 LEF1 LEF1 LEF1 13821 -0.027 0.083 NO
58 LMNA LMNA LMNA 13951 -0.028 0.08 NO
59 ITGB5 ITGB5 ITGB5 15122 -0.047 0.023 NO
60 GJA1 GJA1 GJA1 15152 -0.048 0.028 NO
61 DSP DSP DSP 15386 -0.054 0.023 NO
62 ATP2A2 ATP2A2 ATP2A2 15883 -0.067 0.0059 NO
63 ITGA6 ITGA6 ITGA6 16423 -0.087 -0.011 NO
64 ITGA2 ITGA2 ITGA2 16442 -0.088 0.00057 NO
65 DSC2 DSC2 DSC2 16701 -0.1 0.00093 NO
66 JUP JUP JUP 17098 -0.13 -0.0025 NO
67 ITGB4 ITGB4 ITGB4 17143 -0.13 0.014 NO
68 ITGB8 ITGB8 ITGB8 17508 -0.17 0.018 NO
69 CACNA2D3 CACNA2D3 CACNA2D3 18006 -0.25 0.027 NO

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

Figure S50.  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: BIOCARTA NKT 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 PAK3 PAK3 PAK3 78 0.4 0.098 YES
2 DMD DMD DMD 147 0.36 0.19 YES
3 NRG2 NRG2 NRG2 244 0.33 0.27 YES
4 ACTA1 ACTA1 ACTA1 823 0.25 0.3 YES
5 RAPSN RAPSN RAPSN 1185 0.22 0.34 YES
6 CHRNA1 CHRNA1 CHRNA1 1259 0.21 0.39 YES
7 LAMA2 LAMA2 LAMA2 2661 0.14 0.35 NO
8 MAPK8 MAPK8 MAPK8 3702 0.11 0.32 NO
9 LAMA4 LAMA4 LAMA4 4646 0.087 0.29 NO
10 CHRM1 CHRM1 CHRM1 4776 0.084 0.31 NO
11 PXN PXN PXN 6561 0.052 0.22 NO
12 ITGB1 ITGB1 ITGB1 6618 0.051 0.23 NO
13 ITGA1 ITGA1 ITGA1 7376 0.041 0.2 NO
14 DVL1 DVL1 DVL1 7391 0.041 0.21 NO
15 PAK4 PAK4 PAK4 8312 0.031 0.17 NO
16 GIT2 GIT2 GIT2 8469 0.029 0.17 NO
17 JUN JUN JUN 8674 0.027 0.17 NO
18 PTK2 PTK2 PTK2 9513 0.019 0.13 NO
19 CTTN CTTN CTTN 10170 0.012 0.094 NO
20 CDC42 CDC42 CDC42 10383 0.01 0.085 NO
21 SRC SRC SRC 10398 0.01 0.087 NO
22 DAG1 DAG1 DAG1 10812 0.0065 0.066 NO
23 MAPK3 MAPK3 MAPK3 11249 0.0023 0.043 NO
24 UTRN UTRN UTRN 11853 -0.0039 0.012 NO
25 SP1 SP1 SP1 11923 -0.0045 0.009 NO
26 RAC1 RAC1 RAC1 13854 -0.027 -0.088 NO
27 MAPK1 MAPK1 MAPK1 14472 -0.036 -0.11 NO
28 PAK2 PAK2 PAK2 15253 -0.051 -0.14 NO
29 PAK1 PAK1 PAK1 16354 -0.084 -0.18 NO
30 EGFR EGFR EGFR 16693 -0.1 -0.17 NO
31 LAMA3 LAMA3 LAMA3 16847 -0.11 -0.15 NO
32 PAK6 PAK6 PAK6 17095 -0.13 -0.13 NO
33 MUSK MUSK MUSK 17692 -0.19 -0.12 NO
34 PAK7 PAK7 PAK7 17695 -0.19 -0.065 NO
35 NRG1 NRG1 NRG1 18378 -0.42 0.0064 NO

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

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NKT 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MYT1 MYT1 MYT1 102 0.39 0.18 YES
2 ACTA1 ACTA1 ACTA1 823 0.25 0.27 YES
3 CDC25C CDC25C CDC25C 2726 0.14 0.24 YES
4 PRKAR2B PRKAR2B PRKAR2B 3124 0.13 0.28 YES
5 GNGT1 GNGT1 GNGT1 3949 0.1 0.28 YES
6 PRKAR1B PRKAR1B PRKAR1B 4301 0.096 0.31 YES
7 PGR PGR PGR 4682 0.086 0.33 YES
8 GNB1 GNB1 GNB1 6695 0.05 0.25 NO
9 PRKACB PRKACB PRKACB 6852 0.048 0.26 NO
10 RPS6KA1 RPS6KA1 RPS6KA1 8146 0.033 0.21 NO
11 PRKAR1A PRKAR1A PRKAR1A 9054 0.023 0.17 NO
12 GNAS GNAS GNAS 9160 0.022 0.18 NO
13 CDK1 CDK1 CDK1 9317 0.021 0.18 NO
14 CCNB1 CCNB1 CCNB1 9693 0.017 0.17 NO
15 CAP1 CAP1 CAP1 9967 0.014 0.16 NO
16 ARPC4 ARPC4 ARPC4 10164 0.012 0.16 NO
17 SRC SRC SRC 10398 0.01 0.15 NO
18 PAQR7 PAQR7 PAQR7 11177 0.0029 0.11 NO
19 MAPK3 MAPK3 MAPK3 11249 0.0023 0.1 NO
20 ACTR2 ACTR2 ACTR2 11944 -0.0047 0.07 NO
21 PIN1 PIN1 PIN1 12028 -0.0056 0.068 NO
22 ARPC1B ARPC1B ARPC1B 12432 -0.0099 0.051 NO
23 ARPC2 ARPC2 ARPC2 12648 -0.012 0.046 NO
24 ARPC5 ARPC5 ARPC5 13786 -0.026 -0.0032 NO
25 ARPC3 ARPC3 ARPC3 14043 -0.03 -0.0024 NO
26 MAPK1 MAPK1 MAPK1 14472 -0.036 -0.0079 NO
27 HRAS HRAS HRAS 15437 -0.054 -0.033 NO
28 PAQR5 PAQR5 PAQR5 15540 -0.057 -0.01 NO
29 ARPC1A ARPC1A ARPC1A 15819 -0.066 0.0068 NO
30 PRKAR2A PRKAR2A PRKAR2A 16083 -0.073 0.029 NO
31 ACTR3 ACTR3 ACTR3 16126 -0.075 0.064 NO
32 GNAI1 GNAI1 GNAI1 17140 -0.13 0.073 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

genes ES table in pathway: KEGG CYSTEINE AND METHIONINE METABOLISM

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 TGFB2 TGFB2 TGFB2 514 0.28 0.066 YES
2 WNT1 WNT1 WNT1 666 0.26 0.14 YES
3 NOG NOG NOG 682 0.26 0.23 YES
4 SMAD6 SMAD6 SMAD6 1548 0.19 0.25 YES
5 BMP5 BMP5 BMP5 2291 0.16 0.26 YES
6 NPPA NPPA NPPA 2317 0.16 0.31 YES
7 HNF1A HNF1A HNF1A 2856 0.14 0.33 YES
8 CHRD CHRD CHRD 3061 0.13 0.36 YES
9 NKX2-5 NKX2-5 NKX2-5 3331 0.12 0.39 YES
10 TGFB3 TGFB3 TGFB3 3603 0.11 0.41 YES
11 BMPR1A BMPR1A BMPR1A 5217 0.075 0.35 NO
12 BMP2 BMP2 BMP2 5504 0.069 0.36 NO
13 GATA4 GATA4 GATA4 5526 0.068 0.38 NO
14 MAP3K7 MAP3K7 MAP3K7 5994 0.06 0.37 NO
15 FZD1 FZD1 FZD1 6551 0.052 0.36 NO
16 RFC1 RFC1 RFC1 6670 0.05 0.37 NO
17 DVL1 DVL1 DVL1 7391 0.041 0.34 NO
18 BMPR2 BMPR2 BMPR2 7910 0.035 0.33 NO
19 TGFBR2 TGFBR2 TGFBR2 7981 0.034 0.34 NO
20 BMP4 BMP4 BMP4 8221 0.032 0.33 NO
21 ATF2 ATF2 ATF2 8547 0.028 0.32 NO
22 SMAD4 SMAD4 SMAD4 9583 0.018 0.28 NO
23 AXIN1 AXIN1 AXIN1 10902 0.0056 0.21 NO
24 SMAD1 SMAD1 SMAD1 11973 -0.005 0.15 NO
25 SMAD5 SMAD5 SMAD5 12418 -0.0097 0.13 NO
26 CTNNB1 CTNNB1 CTNNB1 12838 -0.015 0.11 NO
27 GSK3B GSK3B GSK3B 13434 -0.022 0.086 NO
28 APC APC APC 13457 -0.022 0.092 NO
29 TGFBR1 TGFBR1 TGFBR1 13633 -0.024 0.09 NO
30 MYL2 MYL2 MYL2 13719 -0.025 0.094 NO
31 TGFB1 TGFB1 TGFB1 15083 -0.047 0.036 NO
32 ACVR1 ACVR1 ACVR1 15749 -0.063 0.021 NO
33 TGFBR3 TGFBR3 TGFBR3 16964 -0.12 -0.0051 NO
34 BMP7 BMP7 BMP7 18033 -0.26 0.025 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 CYSTEINE AND METHIONINE METABOLISM.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYSTEINE AND METHIONINE 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 N GLYCAN BIOSYNTHESIS

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 E2F5 E2F5 E2F5 167 0.36 0.042 YES
2 TGFB2 TGFB2 TGFB2 514 0.28 0.063 YES
3 GDF5 GDF5 GDF5 654 0.26 0.093 YES
4 GDF6 GDF6 GDF6 824 0.25 0.12 YES
5 TNF TNF TNF 999 0.23 0.14 YES
6 NODAL NODAL NODAL 1121 0.22 0.17 YES
7 GDF7 GDF7 GDF7 1541 0.2 0.17 YES
8 SMAD6 SMAD6 SMAD6 1548 0.19 0.2 YES
9 THBS4 THBS4 THBS4 1691 0.19 0.22 YES
10 COMP COMP COMP 1726 0.19 0.24 YES
11 INHBA INHBA INHBA 2286 0.16 0.24 YES
12 BMP5 BMP5 BMP5 2291 0.16 0.26 YES
13 SMAD7 SMAD7 SMAD7 2369 0.16 0.28 YES
14 BMPR1B BMPR1B BMPR1B 2641 0.14 0.28 YES
15 LEFTY1 LEFTY1 LEFTY1 2838 0.14 0.29 YES
16 CHRD CHRD CHRD 3061 0.13 0.3 YES
17 IFNG IFNG IFNG 3297 0.12 0.3 YES
18 ACVR2B ACVR2B ACVR2B 3368 0.12 0.32 YES
19 ID2 ID2 ID2 3485 0.12 0.33 YES
20 TGFB3 TGFB3 TGFB3 3603 0.11 0.34 YES
21 LTBP1 LTBP1 LTBP1 3798 0.11 0.34 YES
22 BMP8B BMP8B BMP8B 3992 0.1 0.34 YES
23 BMP8A BMP8A BMP8A 4277 0.096 0.34 YES
24 INHBC INHBC INHBC 4336 0.094 0.35 YES
25 THBS2 THBS2 THBS2 4587 0.088 0.35 NO
26 THBS3 THBS3 THBS3 5169 0.076 0.33 NO
27 BMPR1A BMPR1A BMPR1A 5217 0.075 0.34 NO
28 ID4 ID4 ID4 5464 0.07 0.34 NO
29 BMP2 BMP2 BMP2 5504 0.069 0.34 NO
30 LEFTY2 LEFTY2 LEFTY2 5773 0.064 0.34 NO
31 AMH AMH AMH 5869 0.062 0.34 NO
32 ACVRL1 ACVRL1 ACVRL1 5881 0.062 0.35 NO
33 SMAD9 SMAD9 SMAD9 6457 0.053 0.33 NO
34 PPP2R1A PPP2R1A PPP2R1A 6716 0.05 0.32 NO
35 ZFYVE16 ZFYVE16 ZFYVE16 6859 0.048 0.32 NO
36 AMHR2 AMHR2 AMHR2 7324 0.042 0.3 NO
37 INHBE INHBE INHBE 7504 0.04 0.3 NO
38 DCN DCN DCN 7733 0.037 0.29 NO
39 BMPR2 BMPR2 BMPR2 7910 0.035 0.28 NO
40 TGFBR2 TGFBR2 TGFBR2 7981 0.034 0.29 NO
41 ID3 ID3 ID3 8177 0.032 0.28 NO
42 BMP4 BMP4 BMP4 8221 0.032 0.28 NO
43 THBS1 THBS1 THBS1 9157 0.022 0.23 NO
44 SMAD4 SMAD4 SMAD4 9583 0.018 0.21 NO
45 RPS6KB2 RPS6KB2 RPS6KB2 9896 0.015 0.2 NO
46 ROCK1 ROCK1 ROCK1 9922 0.015 0.2 NO
47 SMURF2 SMURF2 SMURF2 9976 0.014 0.2 NO
48 ACVR2A ACVR2A ACVR2A 10343 0.011 0.18 NO
49 CREBBP CREBBP CREBBP 10643 0.008 0.17 NO
50 RBL1 RBL1 RBL1 11227 0.0024 0.13 NO
51 MAPK3 MAPK3 MAPK3 11249 0.0023 0.13 NO
52 RHOA RHOA RHOA 11451 0.00041 0.12 NO
53 RPS6KB1 RPS6KB1 RPS6KB1 11667 -0.0018 0.11 NO
54 SKP1 SKP1 SKP1 11687 -0.002 0.11 NO
55 SP1 SP1 SP1 11923 -0.0045 0.098 NO
56 SMAD1 SMAD1 SMAD1 11973 -0.005 0.096 NO
57 PITX2 PITX2 PITX2 12021 -0.0055 0.095 NO
58 PPP2R1B PPP2R1B PPP2R1B 12155 -0.0068 0.088 NO
59 EP300 EP300 EP300 12287 -0.0084 0.082 NO
60 RBX1 RBX1 RBX1 12354 -0.0091 0.08 NO
61 ROCK2 ROCK2 ROCK2 12398 -0.0094 0.079 NO
62 SMAD5 SMAD5 SMAD5 12418 -0.0097 0.08 NO
63 PPP2CA PPP2CA PPP2CA 12542 -0.011 0.074 NO
64 TFDP1 TFDP1 TFDP1 12613 -0.012 0.072 NO
65 RBL2 RBL2 RBL2 13546 -0.023 0.025 NO
66 TGFBR1 TGFBR1 TGFBR1 13633 -0.024 0.024 NO
67 PPP2CB PPP2CB PPP2CB 13735 -0.025 0.022 NO
68 SMAD2 SMAD2 SMAD2 13842 -0.027 0.02 NO
69 ZFYVE9 ZFYVE9 ZFYVE9 13884 -0.028 0.022 NO
70 E2F4 E2F4 E2F4 14059 -0.03 0.016 NO
71 ACVR1C ACVR1C ACVR1C 14371 -0.034 0.0044 NO
72 MAPK1 MAPK1 MAPK1 14472 -0.036 0.0041 NO
73 CUL1 CUL1 CUL1 14906 -0.043 -0.013 NO
74 TGFB1 TGFB1 TGFB1 15083 -0.047 -0.016 NO
75 ACVR1 ACVR1 ACVR1 15749 -0.063 -0.043 NO
76 INHBB INHBB INHBB 16240 -0.08 -0.058 NO
77 SMAD3 SMAD3 SMAD3 16506 -0.092 -0.06 NO
78 SMURF1 SMURF1 SMURF1 16655 -0.099 -0.054 NO
79 CDKN2B CDKN2B CDKN2B 16670 -0.1 -0.04 NO
80 BMP6 BMP6 BMP6 16717 -0.1 -0.028 NO
81 ID1 ID1 ID1 17327 -0.15 -0.04 NO
82 MYC MYC MYC 17481 -0.16 -0.025 NO
83 BMP7 BMP7 BMP7 18033 -0.26 -0.017 NO
84 FST FST FST 18141 -0.3 0.019 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 N GLYCAN BIOSYNTHESIS.

Figure S58.  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 NEUROACTIVE LIGAND 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 DMD DMD DMD 147 0.36 0.043 YES
2 CACNB2 CACNB2 CACNB2 275 0.32 0.081 YES
3 TGFB2 TGFB2 TGFB2 514 0.28 0.11 YES
4 MYH6 MYH6 MYH6 881 0.24 0.12 YES
5 TNF TNF TNF 999 0.23 0.15 YES
6 CACNA1F CACNA1F CACNA1F 1289 0.21 0.16 YES
7 ITGB3 ITGB3 ITGB3 1348 0.2 0.18 YES
8 CACNA1C CACNA1C CACNA1C 1387 0.2 0.21 YES
9 ITGA7 ITGA7 ITGA7 1420 0.2 0.24 YES
10 MYH7 MYH7 MYH7 1627 0.19 0.25 YES
11 ITGA9 ITGA9 ITGA9 1926 0.18 0.26 YES
12 SGCG SGCG SGCG 1981 0.17 0.28 YES
13 TPM2 TPM2 TPM2 2250 0.16 0.29 YES
14 ITGA10 ITGA10 ITGA10 2333 0.16 0.31 YES
15 LAMA2 LAMA2 LAMA2 2661 0.14 0.31 YES
16 ITGA11 ITGA11 ITGA11 2700 0.14 0.33 YES
17 TTN TTN TTN 2971 0.13 0.33 YES
18 CACNG1 CACNG1 CACNG1 3047 0.13 0.35 YES
19 CACNA1D CACNA1D CACNA1D 3290 0.12 0.35 YES
20 TPM1 TPM1 TPM1 3415 0.12 0.36 YES
21 CACNG4 CACNG4 CACNG4 3422 0.12 0.38 YES
22 CACNA1S CACNA1S CACNA1S 3544 0.12 0.38 YES
23 TGFB3 TGFB3 TGFB3 3603 0.11 0.4 YES
24 ITGA2B ITGA2B ITGA2B 3653 0.11 0.41 YES
25 SLC8A1 SLC8A1 SLC8A1 3848 0.11 0.42 YES
26 ITGA4 ITGA4 ITGA4 4028 0.1 0.42 YES
27 SGCD SGCD SGCD 4078 0.1 0.43 YES
28 MYL3 MYL3 MYL3 4234 0.097 0.44 YES
29 CACNB3 CACNB3 CACNB3 4713 0.086 0.42 NO
30 ITGB6 ITGB6 ITGB6 4714 0.085 0.43 NO
31 TNNI3 TNNI3 TNNI3 5367 0.072 0.41 NO
32 SGCA SGCA SGCA 5575 0.068 0.41 NO
33 CACNA2D4 CACNA2D4 CACNA2D4 5649 0.066 0.41 NO
34 CACNB1 CACNB1 CACNB1 5855 0.062 0.41 NO
35 SGCB SGCB SGCB 6004 0.06 0.41 NO
36 ACTC1 ACTC1 ACTC1 6298 0.055 0.4 NO
37 ITGB7 ITGB7 ITGB7 6350 0.054 0.41 NO
38 ITGB1 ITGB1 ITGB1 6618 0.051 0.4 NO
39 RYR2 RYR2 RYR2 7129 0.044 0.38 NO
40 ACE ACE ACE 7202 0.043 0.38 NO
41 ITGA1 ITGA1 ITGA1 7376 0.041 0.38 NO
42 ITGA5 ITGA5 ITGA5 8362 0.03 0.33 NO
43 TNNC1 TNNC1 TNNC1 9994 0.014 0.24 NO
44 ITGA3 ITGA3 ITGA3 10250 0.012 0.23 NO
45 ITGA8 ITGA8 ITGA8 10269 0.012 0.23 NO
46 ITGAV ITGAV ITGAV 10758 0.0069 0.2 NO
47 DAG1 DAG1 DAG1 10812 0.0065 0.2 NO
48 PRKAA1 PRKAA1 PRKAA1 10939 0.0052 0.2 NO
49 CACNA2D1 CACNA2D1 CACNA2D1 10941 0.0052 0.2 NO
50 ACTB ACTB ACTB 11042 0.0042 0.19 NO
51 CACNB4 CACNB4 CACNB4 11082 0.0039 0.19 NO
52 TPM3 TPM3 TPM3 11526 -0.00035 0.16 NO
53 PRKAG2 PRKAG2 PRKAG2 11626 -0.0014 0.16 NO
54 MYBPC3 MYBPC3 MYBPC3 11706 -0.0022 0.16 NO
55 PRKAB1 PRKAB1 PRKAB1 11913 -0.0044 0.15 NO
56 PRKAA2 PRKAA2 PRKAA2 12076 -0.0059 0.14 NO
57 CACNG6 CACNG6 CACNG6 12227 -0.0076 0.13 NO
58 PRKAG1 PRKAG1 PRKAG1 12488 -0.01 0.12 NO
59 EMD EMD EMD 12732 -0.013 0.11 NO
60 ACTG1 ACTG1 ACTG1 13424 -0.022 0.072 NO
61 CACNA2D2 CACNA2D2 CACNA2D2 13565 -0.023 0.068 NO
62 DES DES DES 13692 -0.025 0.064 NO
63 PRKAB2 PRKAB2 PRKAB2 13699 -0.025 0.067 NO
64 MYL2 MYL2 MYL2 13719 -0.025 0.07 NO
65 LMNA LMNA LMNA 13951 -0.028 0.061 NO
66 TGFB1 TGFB1 TGFB1 15083 -0.047 0.0064 NO
67 ITGB5 ITGB5 ITGB5 15122 -0.047 0.011 NO
68 IGF1 IGF1 IGF1 15186 -0.049 0.014 NO
69 TPM4 TPM4 TPM4 15432 -0.054 0.0086 NO
70 ATP2A2 ATP2A2 ATP2A2 15883 -0.067 -0.0064 NO
71 ITGA6 ITGA6 ITGA6 16423 -0.087 -0.024 NO
72 ITGA2 ITGA2 ITGA2 16442 -0.088 -0.012 NO
73 ITGB4 ITGB4 ITGB4 17143 -0.13 -0.032 NO
74 IL6 IL6 IL6 17218 -0.14 -0.017 NO
75 ITGB8 ITGB8 ITGB8 17508 -0.17 -0.0092 NO
76 TNNT2 TNNT2 TNNT2 17736 -0.2 0.0059 NO
77 CACNA2D3 CACNA2D3 CACNA2D3 18006 -0.25 0.027 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 NEUROACTIVE LIGAND RECEPTOR INTERACTION.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NEUROACTIVE LIGAND 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 NO1 PATHWAY 28 genes.ES.table 0.54 1.4 0.1 0.21 0.97 0.5 0.26 0.37 0.16 0.001
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.46 1.8 0.022 0.22 0.45 0.094 0.05 0.089 0 0.047
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.59 1.7 0.018 0.15 0.56 0.36 0.25 0.28 0.07 0.018
BIOCARTA BIOPEPTIDES PATHWAY 41 genes.ES.table 0.45 1.6 0.026 0.15 0.79 0.098 0.051 0.093 0.092 0.003
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.46 1.6 0.046 0.15 0.69 0.27 0.25 0.2 0.089 0.01
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.56 1.7 0.014 0.19 0.51 0.27 0.18 0.22 0.085 0.035
BIOCARTA IL2RB PATHWAY 37 genes.ES.table 0.54 1.6 0.063 0.14 0.75 0.4 0.24 0.31 0.087 0.004
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.41 1.4 0.14 0.22 0.96 0.56 0.38 0.35 0.16 0.002
BIOCARTA INTEGRIN PATHWAY 37 genes.ES.table 0.43 1.5 0.054 0.16 0.85 0.38 0.26 0.28 0.11 0.003
BIOCARTA KERATINOCYTE PATHWAY 45 genes.ES.table 0.44 1.5 0.058 0.17 0.89 0.51 0.35 0.33 0.12 0.002
genes ES table in pathway: BIOCARTA NO1 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 NAPSA NAPSA NAPSA 32 0.74 0.065 YES
2 CTSE CTSE CTSE 63 0.68 0.12 YES
3 CTSG CTSG CTSG 319 0.48 0.15 YES
4 HYAL1 HYAL1 HYAL1 1003 0.34 0.15 YES
5 DNASE2B DNASE2B DNASE2B 1220 0.32 0.16 YES
6 ATP6V0D2 ATP6V0D2 ATP6V0D2 1484 0.28 0.18 YES
7 CTSW CTSW CTSW 1566 0.28 0.2 YES
8 LAMP3 LAMP3 LAMP3 1599 0.27 0.22 YES
9 SLC11A1 SLC11A1 SLC11A1 1665 0.27 0.24 YES
10 CTSH CTSH CTSH 1856 0.25 0.25 YES
11 ATP6V0A4 ATP6V0A4 ATP6V0A4 1940 0.24 0.27 YES
12 CTSS CTSS CTSS 2395 0.21 0.26 YES
13 LAPTM5 LAPTM5 LAPTM5 2460 0.2 0.28 YES
14 NPC2 NPC2 NPC2 2786 0.18 0.28 YES
15 CTSO CTSO CTSO 2810 0.18 0.29 YES
16 ASAH1 ASAH1 ASAH1 3046 0.16 0.29 YES
17 FUCA1 FUCA1 FUCA1 3049 0.16 0.31 YES
18 CD68 CD68 CD68 3096 0.16 0.32 YES
19 GALC GALC GALC 3298 0.15 0.32 YES
20 TCIRG1 TCIRG1 TCIRG1 3395 0.14 0.33 YES
21 ACP5 ACP5 ACP5 3405 0.14 0.34 YES
22 IDUA IDUA IDUA 3461 0.14 0.35 YES
23 AP1S3 AP1S3 AP1S3 3594 0.13 0.35 YES
24 CTSL1 CTSL1 CTSL1 3656 0.13 0.36 YES
25 LIPA LIPA LIPA 3657 0.13 0.37 YES
26 CTSD CTSD CTSD 3712 0.12 0.38 YES
27 LGMN LGMN LGMN 3746 0.12 0.39 YES
28 SORT1 SORT1 SORT1 3765 0.12 0.4 YES
29 PLA2G15 PLA2G15 PLA2G15 4074 0.11 0.39 YES
30 ARSA ARSA ARSA 4076 0.11 0.4 YES
31 CTSZ CTSZ CTSZ 4193 0.1 0.4 YES
32 AP1S2 AP1S2 AP1S2 4300 0.098 0.41 YES
33 CTSA CTSA CTSA 4322 0.098 0.42 YES
34 AP4S1 AP4S1 AP4S1 4346 0.097 0.42 YES
35 ATP6V0D1 ATP6V0D1 ATP6V0D1 4347 0.097 0.43 YES
36 PSAPL1 PSAPL1 PSAPL1 4420 0.095 0.44 YES
37 CTNS CTNS CTNS 4439 0.094 0.44 YES
38 TPP1 TPP1 TPP1 4489 0.092 0.45 YES
39 SMPD1 SMPD1 SMPD1 4516 0.092 0.46 YES
40 CD63 CD63 CD63 4531 0.091 0.46 YES
41 GNS GNS GNS 4582 0.088 0.47 YES
42 GNPTG GNPTG GNPTG 4605 0.088 0.48 YES
43 CTSB CTSB CTSB 4615 0.087 0.48 YES
44 CTSC CTSC CTSC 4764 0.082 0.48 YES
45 ACP2 ACP2 ACP2 4840 0.08 0.48 YES
46 SGSH SGSH SGSH 5012 0.074 0.48 YES
47 ARSB ARSB ARSB 5049 0.073 0.49 YES
48 PSAP PSAP PSAP 5225 0.068 0.48 YES
49 CTSK CTSK CTSK 5239 0.067 0.49 YES
50 SUMF1 SUMF1 SUMF1 5335 0.065 0.49 YES
51 MCOLN1 MCOLN1 MCOLN1 5388 0.063 0.49 YES
52 MAN2B1 MAN2B1 MAN2B1 5403 0.063 0.5 YES
53 HEXA HEXA HEXA 5412 0.063 0.5 YES
54 SLC17A5 SLC17A5 SLC17A5 5480 0.061 0.5 YES
55 IDS IDS IDS 5667 0.056 0.5 NO
56 SLC11A2 SLC11A2 SLC11A2 5853 0.052 0.49 NO
57 NAGPA NAGPA NAGPA 5856 0.052 0.5 NO
58 CLN3 CLN3 CLN3 5886 0.051 0.5 NO
59 GLB1 GLB1 GLB1 5952 0.05 0.5 NO
60 HEXB HEXB HEXB 6180 0.045 0.49 NO
61 MANBA MANBA MANBA 6376 0.041 0.49 NO
62 AP1M2 AP1M2 AP1M2 6408 0.04 0.49 NO
63 GUSB GUSB GUSB 6472 0.039 0.49 NO
64 LAMP1 LAMP1 LAMP1 6622 0.036 0.48 NO
65 ATP6V0C ATP6V0C ATP6V0C 6770 0.033 0.48 NO
66 NAGLU NAGLU NAGLU 6816 0.033 0.48 NO
67 ARSG ARSG ARSG 6878 0.032 0.48 NO
68 AGA AGA AGA 6926 0.031 0.48 NO
69 AP4B1 AP4B1 AP4B1 6928 0.031 0.48 NO
70 GBA GBA GBA 7035 0.029 0.48 NO
71 NEU1 NEU1 NEU1 7071 0.028 0.48 NO
72 ATP6V0B ATP6V0B ATP6V0B 7095 0.028 0.48 NO
73 SCARB2 SCARB2 SCARB2 7300 0.024 0.47 NO
74 CTSF CTSF CTSF 7330 0.024 0.47 NO
75 AP1G1 AP1G1 AP1G1 7418 0.023 0.47 NO
76 GM2A GM2A GM2A 7472 0.022 0.47 NO
77 NAGA NAGA NAGA 7478 0.022 0.47 NO
78 CLN5 CLN5 CLN5 7706 0.019 0.46 NO
79 CD164 CD164 CD164 7719 0.018 0.46 NO
80 AP1B1 AP1B1 AP1B1 7817 0.017 0.46 NO
81 ATP6AP1 ATP6AP1 ATP6AP1 7931 0.016 0.45 NO
82 GNPTAB GNPTAB GNPTAB 7973 0.015 0.45 NO
83 ATP6V1H ATP6V1H ATP6V1H 8064 0.014 0.45 NO
84 ENTPD4 ENTPD4 ENTPD4 8082 0.014 0.45 NO
85 ATP6V0A1 ATP6V0A1 ATP6V0A1 8182 0.012 0.44 NO
86 ABCA2 ABCA2 ABCA2 8205 0.012 0.44 NO
87 IGF2R IGF2R IGF2R 8218 0.012 0.44 NO
88 AP3D1 AP3D1 AP3D1 8458 0.0089 0.43 NO
89 MFSD8 MFSD8 MFSD8 8500 0.0086 0.43 NO
90 LAPTM4A LAPTM4A LAPTM4A 8525 0.0083 0.43 NO
91 GALNS GALNS GALNS 8606 0.0072 0.43 NO
92 AP3S2 AP3S2 AP3S2 8700 0.0057 0.42 NO
93 GAA GAA GAA 8747 0.0051 0.42 NO
94 CLTC CLTC CLTC 8797 0.0045 0.42 NO
95 GGA3 GGA3 GGA3 9014 0.0017 0.41 NO
96 ATP6V0A2 ATP6V0A2 ATP6V0A2 9349 -0.002 0.39 NO
97 AP3M1 AP3M1 AP3M1 9420 -0.0027 0.38 NO
98 GGA2 GGA2 GGA2 9531 -0.0039 0.38 NO
99 GGA1 GGA1 GGA1 9543 -0.004 0.38 NO
100 AP3B1 AP3B1 AP3B1 9738 -0.0063 0.37 NO
101 M6PR M6PR M6PR 10356 -0.013 0.34 NO
102 AP4E1 AP4E1 AP4E1 10367 -0.013 0.34 NO
103 CLTB CLTB CLTB 10379 -0.013 0.34 NO
104 AP1M1 AP1M1 AP1M1 10516 -0.015 0.33 NO
105 PPT1 PPT1 PPT1 10579 -0.016 0.33 NO
106 AP3S1 AP3S1 AP3S1 10764 -0.018 0.32 NO
107 AP4M1 AP4M1 AP4M1 10936 -0.02 0.31 NO
108 ABCB9 ABCB9 ABCB9 11029 -0.02 0.31 NO
109 LAPTM4B LAPTM4B LAPTM4B 11318 -0.024 0.3 NO
110 LAMP2 LAMP2 LAMP2 11677 -0.028 0.28 NO
111 GLA GLA GLA 11971 -0.031 0.27 NO
112 CLTA CLTA CLTA 12367 -0.036 0.25 NO
113 DNASE2 DNASE2 DNASE2 12783 -0.041 0.23 NO
114 NPC1 NPC1 NPC1 12834 -0.042 0.23 NO
115 AP1S1 AP1S1 AP1S1 13193 -0.046 0.22 NO
116 PPT2 PPT2 PPT2 14964 -0.077 0.12 NO
117 AP3M2 AP3M2 AP3M2 15608 -0.094 0.099 NO
118 CTSL2 CTSL2 CTSL2 17684 -0.21 0.0046 NO
119 AP3B2 AP3B2 AP3B2 17731 -0.21 0.021 NO
120 CLTCL1 CLTCL1 CLTCL1 17866 -0.23 0.034 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 NO1 PATHWAY.

Figure S62.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA AT1R 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 AQP4 AQP4 AQP4 16 0.78 0.2 YES
2 CREB3L1 CREB3L1 CREB3L1 1014 0.34 0.24 YES
3 AVPR2 AVPR2 AVPR2 1119 0.33 0.32 YES
4 AQP3 AQP3 AQP3 1421 0.29 0.38 YES
5 CREB3L3 CREB3L3 CREB3L3 2322 0.21 0.39 YES
6 AQP2 AQP2 AQP2 2387 0.21 0.44 YES
7 ARHGDIB ARHGDIB ARHGDIB 2831 0.18 0.46 YES
8 DYNC2H1 DYNC2H1 DYNC2H1 3277 0.15 0.47 YES
9 ADCY6 ADCY6 ADCY6 3864 0.12 0.47 YES
10 CREB3L2 CREB3L2 CREB3L2 3884 0.12 0.5 YES
11 ADCY9 ADCY9 ADCY9 4338 0.097 0.5 YES
12 VAMP2 VAMP2 VAMP2 5858 0.051 0.43 NO
13 PRKACB PRKACB PRKACB 6501 0.039 0.41 NO
14 RAB5A RAB5A RAB5A 7067 0.028 0.39 NO
15 DYNC1LI2 DYNC1LI2 DYNC1LI2 7132 0.027 0.39 NO
16 DCTN6 DCTN6 DCTN6 7954 0.015 0.35 NO
17 NSF NSF NSF 8037 0.014 0.35 NO
18 CREB3 CREB3 CREB3 8079 0.014 0.35 NO
19 STX4 STX4 STX4 8122 0.013 0.35 NO
20 RAB5C RAB5C RAB5C 8126 0.013 0.36 NO
21 RAB5B RAB5B RAB5B 8313 0.011 0.35 NO
22 ARHGDIA ARHGDIA ARHGDIA 8666 0.0063 0.33 NO
23 DYNC1H1 DYNC1H1 DYNC1H1 9027 0.0016 0.31 NO
24 RAB11A RAB11A RAB11A 9102 0.00072 0.31 NO
25 RAB11B RAB11B RAB11B 9179 7e-05 0.3 NO
26 CREB1 CREB1 CREB1 9325 -0.0017 0.3 NO
27 DYNLL2 DYNLL2 DYNLL2 9765 -0.0067 0.27 NO
28 GNAS GNAS GNAS 9795 -0.0071 0.27 NO
29 DYNC1LI1 DYNC1LI1 DYNC1LI1 10087 -0.01 0.26 NO
30 DCTN1 DCTN1 DCTN1 10289 -0.012 0.25 NO
31 CREB5 CREB5 CREB5 10387 -0.013 0.25 NO
32 PRKACA PRKACA PRKACA 10848 -0.019 0.23 NO
33 DCTN2 DCTN2 DCTN2 11162 -0.022 0.22 NO
34 DCTN4 DCTN4 DCTN4 11254 -0.023 0.22 NO
35 DYNC1I2 DYNC1I2 DYNC1I2 11790 -0.029 0.2 NO
36 DCTN5 DCTN5 DCTN5 12457 -0.037 0.17 NO
37 DYNC2LI1 DYNC2LI1 DYNC2LI1 12575 -0.038 0.18 NO
38 CREB3L4 CREB3L4 CREB3L4 12671 -0.04 0.18 NO
39 DYNLL1 DYNLL1 DYNLL1 12774 -0.041 0.19 NO
40 PRKX PRKX PRKX 15845 -0.1 0.047 NO
41 DYNC1I1 DYNC1I1 DYNC1I1 18427 -0.37 0.0037 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 AT1R PATHWAY.

Figure S64.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA BCR 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 PLA2G1B PLA2G1B PLA2G1B 7 0.84 0.15 YES
2 PLA2G10 PLA2G10 PLA2G10 118 0.62 0.26 YES
3 PLA2G12B PLA2G12B PLA2G12B 208 0.53 0.35 YES
4 PLA2G2A PLA2G2A PLA2G2A 366 0.46 0.43 YES
5 PLA2G4E PLA2G4E PLA2G4E 765 0.38 0.48 YES
6 PLA2G5 PLA2G5 PLA2G5 885 0.35 0.54 YES
7 ENPP2 ENPP2 ENPP2 1436 0.29 0.56 YES
8 PLA2G7 PLA2G7 PLA2G7 1531 0.28 0.61 YES
9 LPCAT1 LPCAT1 LPCAT1 1539 0.28 0.66 YES
10 PLA2G2D PLA2G2D PLA2G2D 1780 0.26 0.69 YES
11 PLA2G4A PLA2G4A PLA2G4A 3322 0.14 0.64 NO
12 PAFAH2 PAFAH2 PAFAH2 3690 0.12 0.64 NO
13 PPAP2B PPAP2B PPAP2B 4186 0.1 0.63 NO
14 PPAP2A PPAP2A PPAP2A 5130 0.07 0.59 NO
15 PLA2G12A PLA2G12A PLA2G12A 6171 0.045 0.55 NO
16 PAFAH1B2 PAFAH1B2 PAFAH1B2 6793 0.033 0.52 NO
17 CHPT1 CHPT1 CHPT1 7070 0.028 0.51 NO
18 PLD2 PLD2 PLD2 7208 0.026 0.5 NO
19 PAFAH1B1 PAFAH1B1 PAFAH1B1 8291 0.011 0.45 NO
20 PPAP2C PPAP2C PPAP2C 8503 0.0086 0.44 NO
21 PLA2G2F PLA2G2F PLA2G2F 8562 0.0078 0.44 NO
22 AGPS AGPS AGPS 8639 0.0067 0.43 NO
23 LPCAT4 LPCAT4 LPCAT4 10795 -0.018 0.32 NO
24 LPCAT2 LPCAT2 LPCAT2 11178 -0.022 0.3 NO
25 PLA2G3 PLA2G3 PLA2G3 12690 -0.04 0.23 NO
26 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 14760 -0.073 0.13 NO
27 PAFAH1B3 PAFAH1B3 PAFAH1B3 15471 -0.089 0.11 NO
28 PLA2G6 PLA2G6 PLA2G6 16523 -0.13 0.076 NO
29 PLD1 PLD1 PLD1 17194 -0.17 0.07 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 BCR PATHWAY.

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

genes ES table in pathway: BIOCARTA BIOPEPTIDES PATHWAY

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 PLA2G1B PLA2G1B PLA2G1B 7 0.84 0.094 YES
2 PLA2G10 PLA2G10 PLA2G10 118 0.62 0.16 YES
3 PLA2G12B PLA2G12B PLA2G12B 208 0.53 0.21 YES
4 PLA2G2A PLA2G2A PLA2G2A 366 0.46 0.26 YES
5 NFATC2 NFATC2 NFATC2 466 0.43 0.3 YES
6 PIK3CG PIK3CG PIK3CG 692 0.39 0.33 YES
7 PLA2G4E PLA2G4E PLA2G4E 765 0.38 0.37 YES
8 PLA2G5 PLA2G5 PLA2G5 885 0.35 0.4 YES
9 PRKCB PRKCB PRKCB 932 0.35 0.44 YES
10 PIK3R5 PIK3R5 PIK3R5 940 0.35 0.48 YES
11 PTGS2 PTGS2 PTGS2 1180 0.32 0.5 YES
12 PLA2G2D PLA2G2D PLA2G2D 1780 0.26 0.5 YES
13 KDR KDR KDR 1781 0.26 0.53 YES
14 NOS3 NOS3 NOS3 1951 0.24 0.55 YES
15 SHC2 SHC2 SHC2 2672 0.18 0.53 NO
16 RAC2 RAC2 RAC2 2869 0.17 0.54 NO
17 PLA2G4A PLA2G4A PLA2G4A 3322 0.14 0.53 NO
18 PIK3CD PIK3CD PIK3CD 3822 0.12 0.52 NO
19 PIK3R3 PIK3R3 PIK3R3 3926 0.11 0.52 NO
20 PLCG2 PLCG2 PLCG2 4151 0.1 0.52 NO
21 NFATC4 NFATC4 NFATC4 4277 0.1 0.53 NO
22 PRKCA PRKCA PRKCA 4416 0.095 0.53 NO
23 PXN PXN PXN 4588 0.088 0.53 NO
24 MAPKAPK3 MAPKAPK3 MAPKAPK3 4887 0.078 0.52 NO
25 CHP CHP CHP 4991 0.075 0.53 NO
26 PPP3CA PPP3CA PPP3CA 5075 0.072 0.53 NO
27 PPP3CC PPP3CC PPP3CC 5551 0.059 0.51 NO
28 NFATC1 NFATC1 NFATC1 5738 0.054 0.51 NO
29 CASP9 CASP9 CASP9 6067 0.047 0.5 NO
30 PLA2G12A PLA2G12A PLA2G12A 6171 0.045 0.5 NO
31 NFAT5 NFAT5 NFAT5 6326 0.042 0.49 NO
32 NFATC3 NFATC3 NFATC3 6375 0.041 0.49 NO
33 MAPK3 MAPK3 MAPK3 6391 0.04 0.5 NO
34 MAPK11 MAPK11 MAPK11 6752 0.034 0.48 NO
35 CDC42 CDC42 CDC42 7050 0.028 0.47 NO
36 PIK3R1 PIK3R1 PIK3R1 7068 0.028 0.47 NO
37 AKT1 AKT1 AKT1 7335 0.024 0.46 NO
38 SPHK2 SPHK2 SPHK2 7502 0.022 0.45 NO
39 PPP3CB PPP3CB PPP3CB 7517 0.021 0.46 NO
40 SH2D2A SH2D2A SH2D2A 7662 0.019 0.45 NO
41 AKT2 AKT2 AKT2 8068 0.014 0.43 NO
42 MAPK13 MAPK13 MAPK13 8071 0.014 0.43 NO
43 MAPKAPK2 MAPKAPK2 MAPKAPK2 8161 0.013 0.43 NO
44 MAPK14 MAPK14 MAPK14 8181 0.012 0.43 NO
45 RAF1 RAF1 RAF1 8469 0.0088 0.41 NO
46 PLA2G2F PLA2G2F PLA2G2F 8562 0.0078 0.41 NO
47 SRC SRC SRC 8694 0.0058 0.4 NO
48 NRAS NRAS NRAS 8859 0.0036 0.39 NO
49 VEGFA VEGFA VEGFA 9094 0.00077 0.38 NO
50 MAP2K1 MAP2K1 MAP2K1 9530 -0.0038 0.36 NO
51 CHP2 CHP2 CHP2 9792 -0.007 0.34 NO
52 BAD BAD BAD 10368 -0.013 0.32 NO
53 MAP2K2 MAP2K2 MAP2K2 10500 -0.014 0.31 NO
54 RAC1 RAC1 RAC1 10656 -0.017 0.3 NO
55 PIK3CB PIK3CB PIK3CB 10919 -0.019 0.29 NO
56 PTK2 PTK2 PTK2 11024 -0.02 0.29 NO
57 PLCG1 PLCG1 PLCG1 11314 -0.024 0.28 NO
58 MAPK1 MAPK1 MAPK1 11737 -0.029 0.26 NO
59 PPP3R1 PPP3R1 PPP3R1 12660 -0.039 0.21 NO
60 PLA2G3 PLA2G3 PLA2G3 12690 -0.04 0.21 NO
61 MAPK12 MAPK12 MAPK12 13801 -0.055 0.16 NO
62 SPHK1 SPHK1 SPHK1 13917 -0.056 0.16 NO
63 KRAS KRAS KRAS 14008 -0.058 0.16 NO
64 HSPB1 HSPB1 HSPB1 14273 -0.063 0.15 NO
65 PRKCG PRKCG PRKCG 14431 -0.066 0.15 NO
66 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 14760 -0.073 0.14 NO
67 AKT3 AKT3 AKT3 14822 -0.074 0.15 NO
68 PIK3R2 PIK3R2 PIK3R2 15017 -0.078 0.15 NO
69 RAC3 RAC3 RAC3 16198 -0.11 0.095 NO
70 PLA2G6 PLA2G6 PLA2G6 16523 -0.13 0.092 NO
71 PIK3CA PIK3CA PIK3CA 16596 -0.13 0.1 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: BIOCARTA BIOPEPTIDES PATHWAY.

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

genes ES table in pathway: BIOCARTA EGF PATHWAY

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 ERBB4 ERBB4 ERBB4 102 0.63 0.034 YES
2 CXCR1 CXCR1 CXCR1 314 0.48 0.053 YES
3 ARRB1 ARRB1 ARRB1 667 0.39 0.058 YES
4 ADRB1 ADRB1 ADRB1 854 0.36 0.07 YES
5 ADRB2 ADRB2 ADRB2 959 0.34 0.086 YES
6 KIT KIT KIT 1024 0.34 0.1 YES
7 IQSEC3 IQSEC3 IQSEC3 1100 0.33 0.12 YES
8 HLA-G HLA-G HLA-G 1167 0.32 0.14 YES
9 NTRK1 NTRK1 NTRK1 1232 0.31 0.15 YES
10 PIP5K1B PIP5K1B PIP5K1B 1327 0.3 0.17 YES
11 IL2RA IL2RA IL2RA 1385 0.3 0.18 YES
12 CCR5 CCR5 CCR5 1404 0.29 0.2 YES
13 CXCR2 CXCR2 CXCR2 1431 0.29 0.22 YES
14 AGAP2 AGAP2 AGAP2 1568 0.28 0.22 YES
15 ACAP1 ACAP1 ACAP1 1644 0.27 0.24 YES
16 CSF1R CSF1R CSF1R 1778 0.26 0.25 YES
17 KDR KDR KDR 1781 0.26 0.26 YES
18 DNM3 DNM3 DNM3 2062 0.23 0.26 YES
19 GRK5 GRK5 GRK5 2121 0.23 0.27 YES
20 IL2RB IL2RB IL2RB 2321 0.21 0.28 YES
21 IL2RG IL2RG IL2RG 2538 0.2 0.28 YES
22 CXCR4 CXCR4 CXCR4 2709 0.18 0.28 YES
23 SH3KBP1 SH3KBP1 SH3KBP1 2844 0.17 0.28 YES
24 PARD6B PARD6B PARD6B 2989 0.16 0.28 YES
25 EHD2 EHD2 EHD2 3097 0.16 0.29 YES
26 DAB2 DAB2 DAB2 3214 0.15 0.29 YES
27 RAB31 RAB31 RAB31 3229 0.15 0.3 YES
28 SMAP2 SMAP2 SMAP2 3327 0.14 0.3 YES
29 FLT1 FLT1 FLT1 3344 0.14 0.31 YES
30 EGF EGF EGF 3357 0.14 0.32 YES
31 ARRB2 ARRB2 ARRB2 3364 0.14 0.33 YES
32 ADRB3 ADRB3 ADRB3 3410 0.14 0.34 YES
33 HLA-F HLA-F HLA-F 3477 0.14 0.34 YES
34 EHD1 EHD1 EHD1 3505 0.14 0.35 YES
35 ERBB3 ERBB3 ERBB3 3592 0.13 0.35 YES
36 PDGFRA PDGFRA PDGFRA 3595 0.13 0.36 YES
37 EHD4 EHD4 EHD4 3740 0.12 0.36 YES
38 MET MET MET 3785 0.12 0.36 YES
39 PRKCZ PRKCZ PRKCZ 3834 0.12 0.37 YES
40 IQSEC1 IQSEC1 IQSEC1 3982 0.11 0.37 YES
41 FGFR4 FGFR4 FGFR4 4024 0.11 0.37 YES
42 RAB11FIP1 RAB11FIP1 RAB11FIP1 4109 0.11 0.37 YES
43 SH3GL2 SH3GL2 SH3GL2 4118 0.11 0.38 YES
44 HLA-E HLA-E HLA-E 4327 0.098 0.37 YES
45 ARAP3 ARAP3 ARAP3 4446 0.094 0.37 YES
46 PSD4 PSD4 PSD4 4450 0.094 0.38 YES
47 HLA-B HLA-B HLA-B 4500 0.092 0.38 YES
48 HLA-C HLA-C HLA-C 4641 0.086 0.38 YES
49 ASAP3 ASAP3 ASAP3 4789 0.081 0.38 YES
50 LDLRAP1 LDLRAP1 LDLRAP1 4826 0.08 0.38 YES
51 PARD6A PARD6A PARD6A 4888 0.078 0.38 YES
52 HLA-A HLA-A HLA-A 4984 0.075 0.38 YES
53 AP2A2 AP2A2 AP2A2 5028 0.073 0.38 YES
54 F2R F2R F2R 5152 0.07 0.38 YES
55 RUFY1 RUFY1 RUFY1 5324 0.065 0.38 YES
56 DNAJC6 DNAJC6 DNAJC6 5420 0.062 0.38 YES
57 CHMP2B CHMP2B CHMP2B 5464 0.061 0.38 YES
58 HSPA6 HSPA6 HSPA6 5513 0.06 0.38 YES
59 ZFYVE20 ZFYVE20 ZFYVE20 5547 0.059 0.38 YES
60 VPS37B VPS37B VPS37B 5566 0.059 0.38 YES
61 ARAP1 ARAP1 ARAP1 5567 0.059 0.39 YES
62 SH3GLB1 SH3GLB1 SH3GLB1 5609 0.057 0.39 YES
63 ADRBK2 ADRBK2 ADRBK2 5622 0.057 0.39 YES
64 GIT2 GIT2 GIT2 5746 0.054 0.39 YES
65 RAB11FIP2 RAB11FIP2 RAB11FIP2 5747 0.054 0.39 YES
66 ADRBK1 ADRBK1 ADRBK1 5788 0.053 0.39 YES
67 AGAP1 AGAP1 AGAP1 5825 0.052 0.39 YES
68 SMURF2 SMURF2 SMURF2 5866 0.051 0.39 YES
69 EPS15 EPS15 EPS15 5893 0.051 0.4 YES
70 STAM2 STAM2 STAM2 5935 0.05 0.4 YES
71 RAB11FIP4 RAB11FIP4 RAB11FIP4 6134 0.046 0.39 NO
72 ARFGAP1 ARFGAP1 ARFGAP1 6411 0.04 0.38 NO
73 CHMP4B CHMP4B CHMP4B 6457 0.039 0.38 NO
74 ARAP2 ARAP2 ARAP2 6510 0.038 0.38 NO
75 EPN1 EPN1 EPN1 6525 0.038 0.38 NO
76 PSD PSD PSD 6570 0.037 0.38 NO
77 AP2A1 AP2A1 AP2A1 6596 0.036 0.38 NO
78 FAM125B FAM125B FAM125B 6599 0.036 0.38 NO
79 PDCD6IP PDCD6IP PDCD6IP 6610 0.036 0.38 NO
80 PIP5K1C PIP5K1C PIP5K1C 6884 0.032 0.37 NO
81 STAM STAM STAM 6977 0.03 0.36 NO
82 MDM2 MDM2 MDM2 6997 0.029 0.37 NO
83 CDC42 CDC42 CDC42 7050 0.028 0.36 NO
84 RAB5A RAB5A RAB5A 7067 0.028 0.37 NO
85 PLD2 PLD2 PLD2 7208 0.026 0.36 NO
86 SMURF1 SMURF1 SMURF1 7277 0.025 0.36 NO
87 ARF6 ARF6 ARF6 7297 0.024 0.36 NO
88 CBL CBL CBL 7332 0.024 0.36 NO
89 USP8 USP8 USP8 7446 0.022 0.35 NO
90 VPS37C VPS37C VPS37C 7488 0.022 0.35 NO
91 DNM2 DNM2 DNM2 7547 0.021 0.35 NO
92 ITCH ITCH ITCH 7573 0.021 0.35 NO
93 CBLB CBLB CBLB 7597 0.02 0.35 NO
94 GRK4 GRK4 GRK4 7676 0.019 0.35 NO
95 ARFGAP3 ARFGAP3 ARFGAP3 7730 0.018 0.34 NO
96 IQSEC2 IQSEC2 IQSEC2 7832 0.017 0.34 NO
97 AP2B1 AP2B1 AP2B1 7852 0.017 0.34 NO
98 GRK6 GRK6 GRK6 7999 0.015 0.33 NO
99 EHD3 EHD3 EHD3 8081 0.014 0.33 NO
100 RAB5C RAB5C RAB5C 8126 0.013 0.33 NO
101 SH3GLB2 SH3GLB2 SH3GLB2 8139 0.013 0.33 NO
102 RAB22A RAB22A RAB22A 8202 0.012 0.33 NO
103 HSPA8 HSPA8 HSPA8 8226 0.012 0.33 NO
104 CHMP2A CHMP2A CHMP2A 8251 0.012 0.32 NO
105 RAB5B RAB5B RAB5B 8313 0.011 0.32 NO
106 RNF41 RNF41 RNF41 8318 0.011 0.32 NO
107 CHMP4A CHMP4A CHMP4A 8470 0.0088 0.32 NO
108 RAB11FIP5 RAB11FIP5 RAB11FIP5 8530 0.0082 0.31 NO
109 CHMP4C CHMP4C CHMP4C 8553 0.0078 0.31 NO
110 RABEP1 RABEP1 RABEP1 8691 0.0059 0.3 NO
111 SRC SRC SRC 8694 0.0058 0.3 NO
112 ARFGAP2 ARFGAP2 ARFGAP2 8755 0.005 0.3 NO
113 VPS24 VPS24 VPS24 8766 0.0048 0.3 NO
114 CLTC CLTC CLTC 8797 0.0045 0.3 NO
115 TSG101 TSG101 TSG101 8815 0.0042 0.3 NO
116 LDLR LDLR LDLR 9031 0.0015 0.29 NO
117 CHMP6 CHMP6 CHMP6 9095 0.00077 0.28 NO
118 RAB11A RAB11A RAB11A 9102 0.00072 0.28 NO
119 RAB11B RAB11B RAB11B 9179 7e-05 0.28 NO
120 NEDD4L NEDD4L NEDD4L 9207 -0.00031 0.28 NO
121 WWP1 WWP1 WWP1 9312 -0.0016 0.27 NO
122 VPS37A VPS37A VPS37A 9436 -0.0028 0.27 NO
123 CHMP5 CHMP5 CHMP5 9439 -0.0028 0.27 NO
124 PSD2 PSD2 PSD2 9594 -0.0046 0.26 NO
125 EEA1 EEA1 EEA1 9605 -0.0047 0.26 NO
126 NEDD4 NEDD4 NEDD4 9775 -0.0068 0.25 NO
127 VPS28 VPS28 VPS28 9783 -0.0069 0.25 NO
128 CHMP1B CHMP1B CHMP1B 9823 -0.0074 0.25 NO
129 PIKFYVE PIKFYVE PIKFYVE 9916 -0.0083 0.24 NO
130 RAB11FIP3 RAB11FIP3 RAB11FIP3 9940 -0.0086 0.24 NO
131 VPS4A VPS4A VPS4A 10171 -0.011 0.23 NO
132 CLTB CLTB CLTB 10379 -0.013 0.22 NO
133 VPS36 VPS36 VPS36 10449 -0.014 0.22 NO
134 AP2S1 AP2S1 AP2S1 10765 -0.018 0.2 NO
135 HGS HGS HGS 10959 -0.02 0.19 NO
136 ACAP3 ACAP3 ACAP3 11002 -0.02 0.19 NO
137 PIP4K2B PIP4K2B PIP4K2B 11026 -0.02 0.19 NO
138 VPS4B VPS4B VPS4B 11065 -0.021 0.19 NO
139 ASAP1 ASAP1 ASAP1 11103 -0.021 0.19 NO
140 SMAP1 SMAP1 SMAP1 11388 -0.024 0.18 NO
141 PSD3 PSD3 PSD3 11426 -0.025 0.18 NO
142 VPS45 VPS45 VPS45 11527 -0.026 0.17 NO
143 FGFR3 FGFR3 FGFR3 11543 -0.026 0.17 NO
144 FAM125A FAM125A FAM125A 11739 -0.029 0.16 NO
145 RET RET RET 11808 -0.03 0.16 NO
146 RAB4A RAB4A RAB4A 11984 -0.032 0.15 NO
147 HSPA2 HSPA2 HSPA2 12112 -0.033 0.15 NO
148 SNF8 SNF8 SNF8 12177 -0.034 0.15 NO
149 HSPA1L HSPA1L HSPA1L 12335 -0.036 0.14 NO
150 CLTA CLTA CLTA 12367 -0.036 0.14 NO
151 EPN2 EPN2 EPN2 12498 -0.038 0.14 NO
152 TRAF6 TRAF6 TRAF6 12560 -0.038 0.14 NO
153 GIT1 GIT1 GIT1 12847 -0.042 0.12 NO
154 SH3GL1 SH3GL1 SH3GL1 12855 -0.042 0.12 NO
155 EPN3 EPN3 EPN3 13053 -0.044 0.12 NO
156 PIP5K1A PIP5K1A PIP5K1A 13407 -0.049 0.1 NO
157 VPS25 VPS25 VPS25 13521 -0.051 0.098 NO
158 EGFR EGFR EGFR 13575 -0.051 0.099 NO
159 HSPA1A HSPA1A HSPA1A 13625 -0.052 0.099 NO
160 STAMBP STAMBP STAMBP 13665 -0.052 0.1 NO
161 VTA1 VTA1 VTA1 13682 -0.053 0.1 NO
162 AP2M1 AP2M1 AP2M1 13841 -0.055 0.098 NO
163 IGF1R IGF1R IGF1R 14847 -0.075 0.047 NO
164 DNM1 DNM1 DNM1 14860 -0.075 0.051 NO
165 GRK1 GRK1 GRK1 15201 -0.083 0.038 NO
166 CBLC CBLC CBLC 15299 -0.085 0.038 NO
167 DNM1L DNM1L DNM1L 15309 -0.085 0.043 NO
168 PARD3 PARD3 PARD3 15332 -0.086 0.047 NO
169 ASAP2 ASAP2 ASAP2 15349 -0.086 0.052 NO
170 HSPA1B HSPA1B HSPA1B 15661 -0.095 0.04 NO
171 PRKCI PRKCI PRKCI 16262 -0.12 0.015 NO
172 ACAP2 ACAP2 ACAP2 16501 -0.13 0.01 NO
173 FGFR2 FGFR2 FGFR2 17010 -0.16 -0.0081 NO
174 VPS37D VPS37D VPS37D 17051 -0.16 -0.00039 NO
175 PLD1 PLD1 PLD1 17194 -0.17 0.0024 NO
176 TFRC TFRC TFRC 17339 -0.18 0.0056 NO
177 PARD6G PARD6G PARD6G 17542 -0.2 0.0068 NO
178 SH3GL3 SH3GL3 SH3GL3 17576 -0.2 0.017 NO
179 CLTCL1 CLTCL1 CLTCL1 17866 -0.23 0.016 NO
180 GRK7 GRK7 GRK7 18277 -0.3 0.012 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: BIOCARTA EGF PATHWAY.

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FIGF FIGF FIGF 264 0.5 0.11 YES
2 IGF1 IGF1 IGF1 643 0.4 0.19 YES
3 PIK3CG PIK3CG PIK3CG 692 0.39 0.29 YES
4 PIK3R5 PIK3R5 PIK3R5 940 0.35 0.36 YES
5 RPS6KA2 RPS6KA2 RPS6KA2 1257 0.31 0.43 YES
6 VEGFC VEGFC VEGFC 2342 0.21 0.42 YES
7 CAB39L CAB39L CAB39L 2737 0.18 0.45 YES
8 PIK3CD PIK3CD PIK3CD 3822 0.12 0.42 NO
9 PIK3R3 PIK3R3 PIK3R3 3926 0.11 0.44 NO
10 RPS6KA1 RPS6KA1 RPS6KA1 4704 0.084 0.42 NO
11 CAB39 CAB39 CAB39 5213 0.068 0.41 NO
12 PRKAA2 PRKAA2 PRKAA2 5960 0.049 0.38 NO
13 MAPK3 MAPK3 MAPK3 6391 0.04 0.37 NO
14 PDPK1 PDPK1 PDPK1 6398 0.04 0.38 NO
15 VEGFB VEGFB VEGFB 6519 0.038 0.38 NO
16 PRKAA1 PRKAA1 PRKAA1 6797 0.033 0.38 NO
17 TSC2 TSC2 TSC2 6917 0.031 0.38 NO
18 PIK3R1 PIK3R1 PIK3R1 7068 0.028 0.38 NO
19 RPS6KA3 RPS6KA3 RPS6KA3 7080 0.028 0.38 NO
20 RICTOR RICTOR RICTOR 7092 0.028 0.39 NO
21 HIF1A HIF1A HIF1A 7093 0.028 0.4 NO
22 EIF4E2 EIF4E2 EIF4E2 7236 0.025 0.4 NO
23 AKT1 AKT1 AKT1 7335 0.024 0.4 NO
24 RPS6KB2 RPS6KB2 RPS6KB2 7375 0.024 0.4 NO
25 MTOR MTOR MTOR 7425 0.023 0.4 NO
26 DDIT4 DDIT4 DDIT4 7721 0.018 0.39 NO
27 RPS6 RPS6 RPS6 7922 0.016 0.38 NO
28 AKT2 AKT2 AKT2 8068 0.014 0.38 NO
29 EIF4B EIF4B EIF4B 8237 0.012 0.38 NO
30 VEGFA VEGFA VEGFA 9094 0.00077 0.33 NO
31 RPS6KA6 RPS6KA6 RPS6KA6 9125 0.00054 0.33 NO
32 STK11 STK11 STK11 9395 -0.0024 0.31 NO
33 EIF4E EIF4E EIF4E 9673 -0.0055 0.3 NO
34 RPTOR RPTOR RPTOR 9709 -0.006 0.3 NO
35 RHEB RHEB RHEB 10602 -0.016 0.26 NO
36 TSC1 TSC1 TSC1 10642 -0.016 0.26 NO
37 PIK3CB PIK3CB PIK3CB 10919 -0.019 0.25 NO
38 MLST8 MLST8 MLST8 11494 -0.026 0.22 NO
39 ULK3 ULK3 ULK3 11674 -0.028 0.22 NO
40 MAPK1 MAPK1 MAPK1 11737 -0.029 0.22 NO
41 RPS6KB1 RPS6KB1 RPS6KB1 12557 -0.038 0.19 NO
42 ULK2 ULK2 ULK2 12567 -0.038 0.2 NO
43 ULK1 ULK1 ULK1 12706 -0.04 0.2 NO
44 BRAF BRAF BRAF 12819 -0.041 0.21 NO
45 STRADA STRADA STRADA 13029 -0.044 0.21 NO
46 EIF4EBP1 EIF4EBP1 EIF4EBP1 14558 -0.068 0.14 NO
47 AKT3 AKT3 AKT3 14822 -0.074 0.14 NO
48 PIK3R2 PIK3R2 PIK3R2 15017 -0.078 0.16 NO
49 PIK3CA PIK3CA PIK3CA 16596 -0.13 0.1 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: BIOCARTA FCER1 PATHWAY.

Figure S72.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

Table 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 PLA2G1B PLA2G1B PLA2G1B 7 0.84 0.077 YES
2 PLA2G10 PLA2G10 PLA2G10 118 0.62 0.13 YES
3 PLA2G12B PLA2G12B PLA2G12B 208 0.53 0.17 YES
4 MS4A2 MS4A2 MS4A2 312 0.48 0.21 YES
5 PLA2G2A PLA2G2A PLA2G2A 366 0.46 0.25 YES
6 FCER1A FCER1A FCER1A 503 0.42 0.28 YES
7 PIK3CG PIK3CG PIK3CG 692 0.39 0.31 YES
8 BTK BTK BTK 716 0.38 0.34 YES
9 PLA2G4E PLA2G4E PLA2G4E 765 0.38 0.38 YES
10 PLA2G5 PLA2G5 PLA2G5 885 0.35 0.4 YES
11 PRKCB PRKCB PRKCB 932 0.35 0.43 YES
12 PIK3R5 PIK3R5 PIK3R5 940 0.35 0.46 YES
13 INPP5D INPP5D INPP5D 1341 0.3 0.47 YES
14 IL13 IL13 IL13 1753 0.26 0.47 YES
15 PLA2G2D PLA2G2D PLA2G2D 1780 0.26 0.49 YES
16 CSF2 CSF2 CSF2 1894 0.25 0.51 YES
17 VAV1 VAV1 VAV1 1926 0.24 0.53 YES
18 GAB2 GAB2 GAB2 2093 0.23 0.54 YES
19 LCP2 LCP2 LCP2 2098 0.23 0.56 YES
20 FCER1G FCER1G FCER1G 2397 0.21 0.57 YES
21 VAV3 VAV3 VAV3 2607 0.19 0.57 YES
22 RAC2 RAC2 RAC2 2869 0.17 0.58 YES
23 LYN LYN LYN 3273 0.15 0.57 YES
24 PLA2G4A PLA2G4A PLA2G4A 3322 0.14 0.58 YES
25 PRKCE PRKCE PRKCE 3404 0.14 0.59 YES
26 LAT LAT LAT 3417 0.14 0.6 YES
27 PIK3CD PIK3CD PIK3CD 3822 0.12 0.59 NO
28 PIK3R3 PIK3R3 PIK3R3 3926 0.11 0.59 NO
29 PLCG2 PLCG2 PLCG2 4151 0.1 0.59 NO
30 PRKCA PRKCA PRKCA 4416 0.095 0.59 NO
31 PRKCD PRKCD PRKCD 4457 0.093 0.59 NO
32 FYN FYN FYN 4819 0.08 0.58 NO
33 TNF TNF TNF 4982 0.075 0.58 NO
34 MAP2K3 MAP2K3 MAP2K3 5011 0.074 0.58 NO
35 VAV2 VAV2 VAV2 5154 0.07 0.58 NO
36 SOS2 SOS2 SOS2 5409 0.063 0.57 NO
37 PLA2G12A PLA2G12A PLA2G12A 6171 0.045 0.54 NO
38 MAPK3 MAPK3 MAPK3 6391 0.04 0.53 NO
39 SYK SYK SYK 6742 0.034 0.51 NO
40 MAPK11 MAPK11 MAPK11 6752 0.034 0.52 NO
41 PIK3R1 PIK3R1 PIK3R1 7068 0.028 0.5 NO
42 AKT1 AKT1 AKT1 7335 0.024 0.49 NO
43 MAPK9 MAPK9 MAPK9 7789 0.018 0.47 NO
44 MAPK10 MAPK10 MAPK10 7796 0.017 0.47 NO
45 AKT2 AKT2 AKT2 8068 0.014 0.45 NO
46 MAPK13 MAPK13 MAPK13 8071 0.014 0.46 NO
47 MAPK14 MAPK14 MAPK14 8181 0.012 0.45 NO
48 GRB2 GRB2 GRB2 8279 0.011 0.45 NO
49 RAF1 RAF1 RAF1 8469 0.0088 0.44 NO
50 PLA2G2F PLA2G2F PLA2G2F 8562 0.0078 0.43 NO
51 NRAS NRAS NRAS 8859 0.0036 0.42 NO
52 MAP2K4 MAP2K4 MAP2K4 9337 -0.0018 0.39 NO
53 MAPK8 MAPK8 MAPK8 9512 -0.0036 0.38 NO
54 MAP2K1 MAP2K1 MAP2K1 9530 -0.0038 0.38 NO
55 MAP2K2 MAP2K2 MAP2K2 10500 -0.014 0.33 NO
56 RAC1 RAC1 RAC1 10656 -0.017 0.32 NO
57 PIK3CB PIK3CB PIK3CB 10919 -0.019 0.31 NO
58 PLCG1 PLCG1 PLCG1 11314 -0.024 0.29 NO
59 MAPK1 MAPK1 MAPK1 11737 -0.029 0.27 NO
60 SOS1 SOS1 SOS1 11749 -0.029 0.27 NO
61 MAP2K7 MAP2K7 MAP2K7 12477 -0.037 0.24 NO
62 PLA2G3 PLA2G3 PLA2G3 12690 -0.04 0.23 NO
63 MAPK12 MAPK12 MAPK12 13801 -0.055 0.17 NO
64 KRAS KRAS KRAS 14008 -0.058 0.17 NO
65 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 14760 -0.073 0.13 NO
66 AKT3 AKT3 AKT3 14822 -0.074 0.14 NO
67 PIK3R2 PIK3R2 PIK3R2 15017 -0.078 0.14 NO
68 MAP2K6 MAP2K6 MAP2K6 15897 -0.1 0.096 NO
69 PDK1 PDK1 PDK1 15955 -0.1 0.1 NO
70 RAC3 RAC3 RAC3 16198 -0.11 0.1 NO
71 PLA2G6 PLA2G6 PLA2G6 16523 -0.13 0.095 NO
72 PIK3CA PIK3CA PIK3CA 16596 -0.13 0.1 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: BIOCARTA IL2RB PATHWAY.

Figure S74.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA DEATH PATHWAY

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 CLDN18 CLDN18 CLDN18 22 0.76 0.048 YES
2 CLDN2 CLDN2 CLDN2 142 0.59 0.08 YES
3 JAM2 JAM2 JAM2 656 0.39 0.078 YES
4 PIK3CG PIK3CG PIK3CG 692 0.39 0.1 YES
5 ITK ITK ITK 707 0.38 0.12 YES
6 CLDN9 CLDN9 CLDN9 750 0.38 0.15 YES
7 CLDN3 CLDN3 CLDN3 767 0.37 0.17 YES
8 CLDN5 CLDN5 CLDN5 840 0.36 0.19 YES
9 PRKCB PRKCB PRKCB 932 0.35 0.21 YES
10 PIK3R5 PIK3R5 PIK3R5 940 0.35 0.23 YES
11 CDH5 CDH5 CDH5 1066 0.33 0.24 YES
12 CLDN23 CLDN23 CLDN23 1194 0.32 0.26 YES
13 TXK TXK TXK 1209 0.32 0.28 YES
14 ESAM ESAM ESAM 1261 0.31 0.3 YES
15 CLDN10 CLDN10 CLDN10 1275 0.31 0.32 YES
16 RAPGEF3 RAPGEF3 RAPGEF3 1362 0.3 0.33 YES
17 NCF4 NCF4 NCF4 1382 0.3 0.35 YES
18 RHOH RHOH RHOH 1393 0.29 0.37 YES
19 ITGAL ITGAL ITGAL 1493 0.28 0.38 YES
20 CYBB CYBB CYBB 1628 0.27 0.39 YES
21 NCF1 NCF1 NCF1 1660 0.27 0.41 YES
22 ICAM1 ICAM1 ICAM1 1706 0.27 0.42 YES
23 ITGAM ITGAM ITGAM 1849 0.25 0.43 YES
24 VAV1 VAV1 VAV1 1926 0.24 0.44 YES
25 PECAM1 PECAM1 PECAM1 2051 0.24 0.45 YES
26 ITGB2 ITGB2 ITGB2 2318 0.21 0.45 YES
27 ITGA4 ITGA4 ITGA4 2357 0.21 0.46 YES
28 NCF2 NCF2 NCF2 2551 0.19 0.46 YES
29 VAV3 VAV3 VAV3 2607 0.19 0.47 YES
30 CXCR4 CXCR4 CXCR4 2709 0.18 0.48 YES
31 RAC2 RAC2 RAC2 2869 0.17 0.48 YES
32 CXCL12 CXCL12 CXCL12 2876 0.17 0.49 YES
33 ACTN2 ACTN2 ACTN2 2973 0.16 0.5 YES
34 SIPA1 SIPA1 SIPA1 3250 0.15 0.49 YES
35 CYBA CYBA CYBA 3463 0.14 0.49 YES
36 MMP2 MMP2 MMP2 3467 0.14 0.5 YES
37 MYL9 MYL9 MYL9 3547 0.13 0.5 YES
38 PIK3CD PIK3CD PIK3CD 3822 0.12 0.5 YES
39 ACTN3 ACTN3 ACTN3 3919 0.11 0.5 YES
40 PIK3R3 PIK3R3 PIK3R3 3926 0.11 0.5 YES
41 CLDN11 CLDN11 CLDN11 3960 0.11 0.51 YES
42 PTK2B PTK2B PTK2B 3981 0.11 0.52 YES
43 CLDN7 CLDN7 CLDN7 4004 0.11 0.52 YES
44 PLCG2 PLCG2 PLCG2 4151 0.1 0.52 YES
45 CLDN4 CLDN4 CLDN4 4265 0.1 0.52 YES
46 JAM3 JAM3 JAM3 4350 0.097 0.52 YES
47 PRKCA PRKCA PRKCA 4416 0.095 0.53 YES
48 NOX1 NOX1 NOX1 4421 0.095 0.53 YES
49 PXN PXN PXN 4588 0.088 0.53 YES
50 RAPGEF4 RAPGEF4 RAPGEF4 4646 0.086 0.53 YES
51 BCAR1 BCAR1 BCAR1 4731 0.083 0.53 YES
52 CLDN8 CLDN8 CLDN8 4740 0.083 0.54 YES
53 RAP1A RAP1A RAP1A 4768 0.082 0.54 YES
54 CLDN6 CLDN6 CLDN6 4787 0.081 0.55 YES
55 ACTN1 ACTN1 ACTN1 4845 0.08 0.55 YES
56 VASP VASP VASP 4850 0.08 0.55 YES
57 GNAI2 GNAI2 GNAI2 4884 0.079 0.56 YES
58 RASSF5 RASSF5 RASSF5 4885 0.078 0.56 YES
59 EZR EZR EZR 5001 0.075 0.56 YES
60 VCAM1 VCAM1 VCAM1 5019 0.074 0.56 YES
61 CLDN14 CLDN14 CLDN14 5118 0.071 0.56 YES
62 VAV2 VAV2 VAV2 5154 0.07 0.56 YES
63 MSN MSN MSN 5195 0.069 0.57 YES
64 THY1 THY1 THY1 5245 0.067 0.57 YES
65 MYL12A MYL12A MYL12A 5322 0.065 0.57 YES
66 MMP9 MMP9 MMP9 5330 0.065 0.57 YES
67 RHOA RHOA RHOA 5709 0.055 0.56 NO
68 ITGB1 ITGB1 ITGB1 5875 0.051 0.55 NO
69 MLLT4 MLLT4 MLLT4 6107 0.046 0.54 NO
70 ACTB ACTB ACTB 6572 0.037 0.52 NO
71 MAPK11 MAPK11 MAPK11 6752 0.034 0.51 NO
72 CTNNA1 CTNNA1 CTNNA1 6896 0.031 0.5 NO
73 CDC42 CDC42 CDC42 7050 0.028 0.5 NO
74 PIK3R1 PIK3R1 PIK3R1 7068 0.028 0.5 NO
75 VCL VCL VCL 7378 0.024 0.48 NO
76 ACTN4 ACTN4 ACTN4 7430 0.023 0.48 NO
77 ARHGAP5 ARHGAP5 ARHGAP5 7758 0.018 0.47 NO
78 MYL12B MYL12B MYL12B 7955 0.015 0.46 NO
79 ROCK2 ROCK2 ROCK2 7968 0.015 0.46 NO
80 CD99 CD99 CD99 7991 0.015 0.46 NO
81 MAPK13 MAPK13 MAPK13 8071 0.014 0.45 NO
82 GRLF1 GRLF1 GRLF1 8097 0.014 0.45 NO
83 MAPK14 MAPK14 MAPK14 8181 0.012 0.45 NO
84 CTNNB1 CTNNB1 CTNNB1 8352 0.01 0.44 NO
85 ROCK1 ROCK1 ROCK1 8487 0.0087 0.43 NO
86 ACTG1 ACTG1 ACTG1 8569 0.0077 0.43 NO
87 RAP1B RAP1B RAP1B 8671 0.0062 0.42 NO
88 MYLPF MYLPF MYLPF 8837 0.0039 0.42 NO
89 GNAI3 GNAI3 GNAI3 8861 0.0036 0.42 NO
90 CLDN17 CLDN17 CLDN17 9265 -0.001 0.39 NO
91 CTNND1 CTNND1 CTNND1 9466 -0.0032 0.38 NO
92 PTPN11 PTPN11 PTPN11 9563 -0.0042 0.38 NO
93 RAC1 RAC1 RAC1 10656 -0.017 0.32 NO
94 PIK3CB PIK3CB PIK3CB 10919 -0.019 0.31 NO
95 PTK2 PTK2 PTK2 11024 -0.02 0.3 NO
96 GNAI1 GNAI1 GNAI1 11173 -0.022 0.3 NO
97 PLCG1 PLCG1 PLCG1 11314 -0.024 0.29 NO
98 CLDN15 CLDN15 CLDN15 12377 -0.036 0.23 NO
99 MAPK12 MAPK12 MAPK12 13801 -0.055 0.16 NO
100 CLDN16 CLDN16 CLDN16 13923 -0.057 0.16 NO
101 PRKCG PRKCG PRKCG 14431 -0.066 0.13 NO
102 MYL7 MYL7 MYL7 14441 -0.066 0.14 NO
103 MYL2 MYL2 MYL2 14580 -0.069 0.13 NO
104 F11R F11R F11R 14767 -0.073 0.13 NO
105 PIK3R2 PIK3R2 PIK3R2 15017 -0.078 0.12 NO
106 MYL5 MYL5 MYL5 15031 -0.079 0.12 NO
107 CLDN1 CLDN1 CLDN1 15712 -0.096 0.094 NO
108 CLDN19 CLDN19 CLDN19 16017 -0.11 0.084 NO
109 PIK3CA PIK3CA PIK3CA 16596 -0.13 0.062 NO
110 CTNNA2 CTNNA2 CTNNA2 17130 -0.16 0.043 NO
111 CTNNA3 CTNNA3 CTNNA3 17714 -0.21 0.025 NO
112 CLDN20 CLDN20 CLDN20 18119 -0.26 0.02 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: BIOCARTA DEATH PATHWAY.

Figure S76.  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: BIOCARTA INTEGRIN PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AGTR1 AGTR1 AGTR1 492 0.42 0.17 YES
2 AGT AGT AGT 875 0.36 0.31 YES
3 PRKCB PRKCB PRKCB 932 0.35 0.46 YES
4 PTK2B PTK2B PTK2B 3981 0.11 0.35 NO
5 PRKCA PRKCA PRKCA 4416 0.095 0.36 NO
6 JUN JUN JUN 4545 0.09 0.4 NO
7 GNAQ GNAQ GNAQ 5015 0.074 0.41 NO
8 MEF2D MEF2D MEF2D 5942 0.05 0.38 NO
9 MAPK3 MAPK3 MAPK3 6391 0.04 0.37 NO
10 CALM1 CALM1 CALM1 7005 0.029 0.35 NO
11 MEF2A MEF2A MEF2A 7130 0.027 0.36 NO
12 CALM3 CALM3 CALM3 7159 0.026 0.37 NO
13 SHC1 SHC1 SHC1 7273 0.025 0.38 NO
14 MAP3K1 MAP3K1 MAP3K1 7679 0.019 0.36 NO
15 GRB2 GRB2 GRB2 8279 0.011 0.33 NO
16 RAF1 RAF1 RAF1 8469 0.0088 0.33 NO
17 ATF2 ATF2 ATF2 8578 0.0076 0.32 NO
18 SRC SRC SRC 8694 0.0058 0.32 NO
19 CALM2 CALM2 CALM2 8730 0.0053 0.32 NO
20 MAP2K4 MAP2K4 MAP2K4 9337 -0.0018 0.29 NO
21 MAPK8 MAPK8 MAPK8 9512 -0.0036 0.28 NO
22 MAP2K1 MAP2K1 MAP2K1 9530 -0.0038 0.28 NO
23 MAP2K2 MAP2K2 MAP2K2 10500 -0.014 0.24 NO
24 RAC1 RAC1 RAC1 10656 -0.017 0.24 NO
25 PTK2 PTK2 PTK2 11024 -0.02 0.23 NO
26 ELK1 ELK1 ELK1 11406 -0.025 0.22 NO
27 MAPK1 MAPK1 MAPK1 11737 -0.029 0.21 NO
28 SOS1 SOS1 SOS1 11749 -0.029 0.22 NO
29 EGFR EGFR EGFR 13575 -0.051 0.15 NO
30 PAK1 PAK1 PAK1 14667 -0.071 0.12 NO
31 HRAS HRAS HRAS 14775 -0.073 0.15 NO
32 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 16271 -0.12 0.12 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: BIOCARTA INTEGRIN PATHWAY.

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

genes ES table in pathway: BIOCARTA KERATINOCYTE PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NR0B2 NR0B2 NR0B2 110 0.62 0.1 YES
2 LPL LPL LPL 374 0.46 0.17 YES
3 CD36 CD36 CD36 669 0.39 0.22 YES
4 PIK3CG PIK3CG PIK3CG 692 0.39 0.28 YES
5 NR2F1 NR2F1 NR2F1 914 0.35 0.33 YES
6 PRKCB PRKCB PRKCB 932 0.35 0.39 YES
7 PTGS2 PTGS2 PTGS2 1180 0.32 0.43 YES
8 CITED2 CITED2 CITED2 1824 0.26 0.44 YES
9 DUSP1 DUSP1 DUSP1 1853 0.25 0.48 YES
10 PPARGC1A PPARGC1A PPARGC1A 3019 0.16 0.45 YES
11 PRKAR2B PRKAR2B PRKAR2B 3167 0.15 0.47 YES
12 NR1H3 NR1H3 NR1H3 3336 0.14 0.48 YES
13 STAT5A STAT5A STAT5A 3806 0.12 0.48 YES
14 HSD17B4 HSD17B4 HSD17B4 4385 0.096 0.46 YES
15 PRKAR2A PRKAR2A PRKAR2A 4411 0.095 0.48 YES
16 PRKCA PRKCA PRKCA 4416 0.095 0.5 YES
17 JUN JUN JUN 4545 0.09 0.5 YES
18 TNF TNF TNF 4982 0.075 0.49 YES
19 NCOR2 NCOR2 NCOR2 4999 0.075 0.5 YES
20 NRIP1 NRIP1 NRIP1 5613 0.057 0.48 NO
21 NFKBIA NFKBIA NFKBIA 5894 0.051 0.48 NO
22 APOA1 APOA1 APOA1 6079 0.047 0.47 NO
23 PRKAR1A PRKAR1A PRKAR1A 6169 0.045 0.48 NO
24 MAPK3 MAPK3 MAPK3 6391 0.04 0.47 NO
25 PRKACB PRKACB PRKACB 6501 0.039 0.47 NO
26 NCOR1 NCOR1 NCOR1 6786 0.033 0.46 NO
27 PIK3R1 PIK3R1 PIK3R1 7068 0.028 0.45 NO
28 SRA1 SRA1 SRA1 7272 0.025 0.45 NO
29 RELA RELA RELA 7956 0.015 0.41 NO
30 RXRA RXRA RXRA 8478 0.0088 0.38 NO
31 PPARA PPARA PPARA 8527 0.0083 0.38 NO
32 FAT1 FAT1 FAT1 8581 0.0075 0.38 NO
33 CREBBP CREBBP CREBBP 8838 0.0039 0.37 NO
34 STAT5B STAT5B STAT5B 9137 0.00045 0.35 NO
35 EP300 EP300 EP300 9944 -0.0087 0.31 NO
36 PDGFA PDGFA PDGFA 10150 -0.011 0.3 NO
37 MYC MYC MYC 10402 -0.013 0.29 NO
38 SP1 SP1 SP1 10418 -0.014 0.29 NO
39 MED1 MED1 MED1 11118 -0.022 0.26 NO
40 HSP90AA1 HSP90AA1 HSP90AA1 11315 -0.024 0.25 NO
41 RB1 RB1 RB1 11603 -0.027 0.24 NO
42 MAPK1 MAPK1 MAPK1 11737 -0.029 0.24 NO
43 MRPL11 MRPL11 MRPL11 11938 -0.031 0.23 NO
44 NCOA1 NCOA1 NCOA1 12505 -0.038 0.21 NO
45 PRKAR1B PRKAR1B PRKAR1B 12636 -0.039 0.21 NO
46 NOS2 NOS2 NOS2 12887 -0.042 0.2 NO
47 APOA2 APOA2 APOA2 12945 -0.043 0.21 NO
48 HSPA1A HSPA1A HSPA1A 13625 -0.052 0.18 NO
49 DUT DUT DUT 15142 -0.081 0.11 NO
50 ME1 ME1 ME1 15190 -0.082 0.12 NO
51 EHHADH EHHADH EHHADH 15839 -0.1 0.1 NO
52 CPT1B CPT1B CPT1B 15894 -0.1 0.12 NO
53 PIK3CA PIK3CA PIK3CA 16596 -0.13 0.1 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: BIOCARTA KERATINOCYTE PATHWAY.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input

  • Gene set database = c2.cp.v3.0-2.symbols.gmt

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

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

GSEA analysis

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

Download Results

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

References
[1] Subramanian, A. et al, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles., Proc. Natl. Acad. Sci. USA 102(43) (2005)
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