GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in STES-TP
Stomach and Esophageal carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1PC31PK
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 STES-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1PC31PK
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 STES-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: 196
Number of samples: 184
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 ] 82
pheno.type: 2 - 4 :[ clus2 ] 69
pheno.type: 3 - 4 :[ clus3 ] 22
pheno.type: 4 - 4 :[ clus4 ] 11

For the expression subtypes of 18768 genes in 185 samples, GSEA found enriched gene sets in each cluster using 184 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA DEATH PATHWAY, BIOCARTA PPARA PATHWAY, BIOCARTA RHO PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG HISTIDINE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG N GLYCAN BIOSYNTHESIS, KEGG GLYCEROLIPID METABOLISM

    • And common core enriched genes are PRKACG, NOS2, PRKCA, ABCD1, ABCD3, ABCD4, ACAA1, ACOT8, ACOX1, ACSL5

  • clus2

    • Top enriched gene sets are BIOCARTA CARM ER PATHWAY, BIOCARTA G1 PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA INTEGRIN PATHWAY, KEGG RNA DEGRADATION, KEGG RNA POLYMERASE, KEGG BASAL TRANSCRIPTION FACTORS, KEGG SPLICEOSOME, KEGG PROTEASOME

    • And common core enriched genes are CCNB1, CCNB2, CCND1, CCNE2, CDK1, CDK2, CDK4, CDK6, CHEK1, CHEK2

  • clus3

    • Top enriched gene sets are BIOCARTA RACCYCD PATHWAY, BIOCARTA MAPK PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA IL1R PATHWAY, BIOCARTA WNT PATHWAY, KEGG OXIDATIVE PHOSPHORYLATION, KEGG GLYCEROPHOSPHOLIPID METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG ARACHIDONIC ACID METABOLISM, KEGG LINOLEIC ACID METABOLISM

    • And common core enriched genes are IKBKB, NFKBIA, RAC1, ATP6V0A1, ATP6V0A4, ATP6V0C, ATP6V0D1, ATP6V0E2, ATP6V1A, ATP6V1B1

  • clus4

    • Top enriched gene sets are BIOCARTA AGR PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA FMLP PATHWAY, BIOCARTA GH PATHWAY

    • And common core enriched genes are AKT3, PIK3CG, PIK3R1, PIK3CD, PIK3R5, PRKAA2, PRKCB, RXRG, CAB39L, FIGF

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.48 1.6 0.058 0.32 0.75 0.56 0.29 0.4 0.18 0.064
BIOCARTA PPARA PATHWAY 55 genes.ES.table 0.51 1.7 0 0.47 0.46 0.18 0.11 0.16 0 0.13
BIOCARTA RHO PATHWAY 31 genes.ES.table 0.44 1.7 0.013 0.35 0.47 0.064 0.033 0.062 0 0.096
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.49 1.6 0.059 0.34 0.82 0.33 0.17 0.28 0.21 0.067
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 29 genes.ES.table 0.54 1.6 0.027 0.32 0.82 0.28 0.091 0.25 0.2 0.053
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.51 1.7 0.027 0.28 0.52 0.49 0.27 0.36 0.12 0.064
KEGG HISTIDINE METABOLISM 28 genes.ES.table 0.59 1.6 0.03 0.32 0.83 0.18 0.034 0.17 0.2 0.051
KEGG STARCH AND SUCROSE METABOLISM 46 genes.ES.table 0.56 1.4 0.076 0.44 0.95 0.3 0.094 0.28 0.33 0.089
KEGG N GLYCAN BIOSYNTHESIS 45 genes.ES.table 0.44 1.6 0.064 0.35 0.75 0.42 0.26 0.31 0.2 0.075
KEGG GLYCEROLIPID METABOLISM 47 genes.ES.table 0.45 1.5 0.045 0.43 0.93 0.43 0.2 0.34 0.32 0.089
genes ES table in pathway: BIOCARTA DEATH PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACSL5 ACSL5 ACSL5 243 0.94 0.06 YES
2 BAAT BAAT BAAT 432 0.75 0.11 YES
3 NOS2 NOS2 NOS2 433 0.75 0.17 YES
4 FAR2 FAR2 FAR2 441 0.74 0.22 YES
5 SLC27A2 SLC27A2 SLC27A2 507 0.7 0.28 YES
6 AGXT AGXT AGXT 585 0.66 0.32 YES
7 HAO2 HAO2 HAO2 1054 0.46 0.33 YES
8 PECR PECR PECR 1521 0.35 0.34 YES
9 PHYH PHYH PHYH 1613 0.34 0.36 YES
10 PEX11A PEX11A PEX11A 1968 0.28 0.36 YES
11 EPHX2 EPHX2 EPHX2 2122 0.27 0.37 YES
12 PIPOX PIPOX PIPOX 2395 0.24 0.38 YES
13 DECR2 DECR2 DECR2 2477 0.23 0.39 YES
14 DDO DDO DDO 2536 0.23 0.41 YES
15 PEX11G PEX11G PEX11G 2715 0.21 0.41 YES
16 ABCD3 ABCD3 ABCD3 2771 0.21 0.43 YES
17 ABCD1 ABCD1 ABCD1 2787 0.2 0.44 YES
18 AMACR AMACR AMACR 2883 0.2 0.45 YES
19 HACL1 HACL1 HACL1 3135 0.18 0.45 YES
20 PEX7 PEX7 PEX7 3250 0.17 0.46 YES
21 CAT CAT CAT 3281 0.17 0.47 YES
22 ACAA1 ACAA1 ACAA1 3320 0.17 0.48 YES
23 ACOX1 ACOX1 ACOX1 3361 0.16 0.49 YES
24 NUDT12 NUDT12 NUDT12 3480 0.16 0.5 YES
25 CRAT CRAT CRAT 3592 0.15 0.5 YES
26 HMGCL HMGCL HMGCL 3682 0.15 0.51 YES
27 IDH1 IDH1 IDH1 3696 0.14 0.52 YES
28 MLYCD MLYCD MLYCD 3761 0.14 0.53 YES
29 PXMP4 PXMP4 PXMP4 3958 0.13 0.53 YES
30 PXMP2 PXMP2 PXMP2 3977 0.13 0.54 YES
31 ACOT8 ACOT8 ACOT8 4214 0.12 0.54 YES
32 SCP2 SCP2 SCP2 4282 0.12 0.54 YES
33 ABCD4 ABCD4 ABCD4 4370 0.11 0.55 YES
34 PEX1 PEX1 PEX1 4462 0.11 0.55 YES
35 GSTK1 GSTK1 GSTK1 4464 0.11 0.56 YES
36 IDH2 IDH2 IDH2 4889 0.094 0.54 NO
37 GNPAT GNPAT GNPAT 5410 0.077 0.52 NO
38 PECI PECI PECI 5753 0.067 0.51 NO
39 ABCD2 ABCD2 ABCD2 5872 0.064 0.5 NO
40 HSD17B4 HSD17B4 HSD17B4 6238 0.055 0.49 NO
41 ECH1 ECH1 ECH1 6355 0.052 0.49 NO
42 ACSL6 ACSL6 ACSL6 6416 0.05 0.49 NO
43 ACSL3 ACSL3 ACSL3 6513 0.048 0.49 NO
44 PEX16 PEX16 PEX16 6567 0.047 0.49 NO
45 ACSL4 ACSL4 ACSL4 6594 0.046 0.49 NO
46 PEX2 PEX2 PEX2 6647 0.045 0.49 NO
47 PEX6 PEX6 PEX6 7041 0.036 0.47 NO
48 PEX11B PEX11B PEX11B 7552 0.025 0.45 NO
49 AGPS AGPS AGPS 7640 0.023 0.44 NO
50 FAR1 FAR1 FAR1 8298 0.01 0.41 NO
51 ACOX3 ACOX3 ACOX3 8744 0.0018 0.39 NO
52 PEX26 PEX26 PEX26 8850 0.000053 0.38 NO
53 XDH XDH XDH 9256 -0.0074 0.36 NO
54 EHHADH EHHADH EHHADH 10167 -0.024 0.31 NO
55 PEX19 PEX19 PEX19 10415 -0.028 0.3 NO
56 SOD1 SOD1 SOD1 10486 -0.03 0.3 NO
57 PMVK PMVK PMVK 10635 -0.032 0.3 NO
58 PEX12 PEX12 PEX12 10985 -0.039 0.28 NO
59 PEX3 PEX3 PEX3 11315 -0.045 0.26 NO
60 PEX14 PEX14 PEX14 11369 -0.046 0.27 NO
61 PEX13 PEX13 PEX13 11515 -0.049 0.26 NO
62 PRDX5 PRDX5 PRDX5 11816 -0.056 0.25 NO
63 SOD2 SOD2 SOD2 11837 -0.057 0.25 NO
64 PEX5 PEX5 PEX5 11926 -0.058 0.25 NO
65 PEX10 PEX10 PEX10 12572 -0.073 0.22 NO
66 NUDT19 NUDT19 NUDT19 13366 -0.094 0.19 NO
67 PRDX1 PRDX1 PRDX1 13410 -0.096 0.2 NO
68 MPV17 MPV17 MPV17 13731 -0.11 0.19 NO
69 PAOX PAOX PAOX 14235 -0.12 0.17 NO
70 SLC25A17 SLC25A17 SLC25A17 14261 -0.12 0.18 NO
71 MPV17L MPV17L MPV17L 14313 -0.13 0.18 NO
72 DHRS4 DHRS4 DHRS4 14695 -0.14 0.18 NO
73 ACSL1 ACSL1 ACSL1 14974 -0.16 0.17 NO
74 MVK MVK MVK 15013 -0.16 0.18 NO
75 CROT CROT CROT 15921 -0.22 0.15 NO

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

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

genes ES table in pathway: BIOCARTA PPARA 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 CFTR CFTR CFTR 78 1.4 0.14 YES
2 KCNQ1 KCNQ1 KCNQ1 319 0.85 0.21 YES
3 PRKCG PRKCG PRKCG 405 0.77 0.28 YES
4 MUC2 MUC2 MUC2 494 0.71 0.35 YES
5 PRKACG PRKACG PRKACG 522 0.69 0.42 YES
6 SLC12A2 SLC12A2 SLC12A2 884 0.53 0.45 YES
7 PRKCA PRKCA PRKCA 1373 0.38 0.47 YES
8 KDELR3 KDELR3 KDELR3 1393 0.38 0.5 YES
9 TJP2 TJP2 TJP2 2636 0.22 0.46 NO
10 ATP6V1C2 ATP6V1C2 ATP6V1C2 2955 0.19 0.46 NO
11 TCIRG1 TCIRG1 TCIRG1 3632 0.15 0.44 NO
12 KDELR2 KDELR2 KDELR2 3653 0.15 0.46 NO
13 KDELR1 KDELR1 KDELR1 4665 0.1 0.41 NO
14 ATP6V0A2 ATP6V0A2 ATP6V0A2 4920 0.093 0.41 NO
15 PDIA4 PDIA4 PDIA4 5142 0.086 0.4 NO
16 ATP6V0E2 ATP6V0E2 ATP6V0E2 5865 0.064 0.37 NO
17 PRKCB PRKCB PRKCB 5893 0.063 0.38 NO
18 ATP6V0A1 ATP6V0A1 ATP6V0A1 5923 0.063 0.38 NO
19 ATP6V0B ATP6V0B ATP6V0B 5938 0.062 0.39 NO
20 SEC61A2 SEC61A2 SEC61A2 6093 0.058 0.39 NO
21 TJP1 TJP1 TJP1 7000 0.037 0.34 NO
22 ARF1 ARF1 ARF1 7198 0.032 0.33 NO
23 ATP6AP1 ATP6AP1 ATP6AP1 8043 0.015 0.29 NO
24 ATP6V1C1 ATP6V1C1 ATP6V1C1 8477 0.0068 0.27 NO
25 SEC61A1 SEC61A1 SEC61A1 8808 0.00066 0.25 NO
26 SEC61B SEC61B SEC61B 9203 -0.0065 0.23 NO
27 SEC61G SEC61G SEC61G 10012 -0.021 0.19 NO
28 ACTB ACTB ACTB 10068 -0.022 0.19 NO
29 ACTG1 ACTG1 ACTG1 10277 -0.026 0.18 NO
30 ATP6V0E1 ATP6V0E1 ATP6V0E1 10671 -0.033 0.16 NO
31 ATP6V1B2 ATP6V1B2 ATP6V1B2 10719 -0.033 0.16 NO
32 ATP6V0D1 ATP6V0D1 ATP6V0D1 10941 -0.038 0.16 NO
33 GNAS GNAS GNAS 11481 -0.048 0.13 NO
34 ERO1L ERO1L ERO1L 11611 -0.051 0.13 NO
35 ADCY9 ADCY9 ADCY9 12002 -0.06 0.12 NO
36 ATP6V0C ATP6V0C ATP6V0C 12366 -0.068 0.1 NO
37 ATP6V1A ATP6V1A ATP6V1A 12561 -0.073 0.1 NO
38 PRKACB PRKACB PRKACB 12646 -0.075 0.1 NO
39 ATP6V1G1 ATP6V1G1 ATP6V1G1 12655 -0.076 0.11 NO
40 ATP6V1D ATP6V1D ATP6V1D 12861 -0.081 0.11 NO
41 ATP6V1H ATP6V1H ATP6V1H 12985 -0.084 0.11 NO
42 PLCG1 PLCG1 PLCG1 13129 -0.088 0.11 NO
43 PRKACA PRKACA PRKACA 13401 -0.096 0.11 NO
44 ATP6V1G2 ATP6V1G2 ATP6V1G2 13675 -0.1 0.1 NO
45 ATP6V1F ATP6V1F ATP6V1F 13708 -0.11 0.11 NO
46 PLCG2 PLCG2 PLCG2 13723 -0.11 0.12 NO
47 ATP6V1E1 ATP6V1E1 ATP6V1E1 13925 -0.11 0.12 NO
48 ATP6V0D2 ATP6V0D2 ATP6V0D2 14950 -0.16 0.083 NO
49 ATP6V0A4 ATP6V0A4 ATP6V0A4 16007 -0.22 0.05 NO
50 PRKX PRKX PRKX 16097 -0.23 0.069 NO
51 ATP6V1E2 ATP6V1E2 ATP6V1E2 17116 -0.36 0.051 NO
52 ATP6V1B1 ATP6V1B1 ATP6V1B1 17127 -0.36 0.087 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 PPARA PATHWAY.

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

genes ES table in pathway: BIOCARTA RHO PATHWAY

Table 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 NR0B2 NR0B2 NR0B2 43 1.6 0.15 YES
2 FABP1 FABP1 FABP1 207 0.99 0.23 YES
3 NOS2 NOS2 NOS2 433 0.75 0.29 YES
4 PRKACG PRKACG PRKACG 522 0.69 0.36 YES
5 APOA1 APOA1 APOA1 731 0.59 0.4 YES
6 PPARGC1A PPARGC1A PPARGC1A 1105 0.45 0.42 YES
7 APOA2 APOA2 APOA2 1270 0.4 0.45 YES
8 PRKCA PRKCA PRKCA 1373 0.38 0.48 YES
9 NR1H3 NR1H3 NR1H3 1722 0.32 0.5 YES
10 PIK3CG PIK3CG PIK3CG 1991 0.28 0.51 YES
11 STAT5A STAT5A STAT5A 2670 0.22 0.49 NO
12 PRKAR2A PRKAR2A PRKAR2A 3862 0.14 0.44 NO
13 PDGFA PDGFA PDGFA 3931 0.13 0.45 NO
14 MAPK3 MAPK3 MAPK3 4048 0.13 0.46 NO
15 NR2F1 NR2F1 NR2F1 4527 0.11 0.44 NO
16 PPARA PPARA PPARA 4618 0.1 0.45 NO
17 NCOR1 NCOR1 NCOR1 5041 0.089 0.43 NO
18 MED1 MED1 MED1 5874 0.064 0.4 NO
19 PRKCB PRKCB PRKCB 5893 0.063 0.4 NO
20 HSD17B4 HSD17B4 HSD17B4 6238 0.055 0.39 NO
21 PTGS2 PTGS2 PTGS2 6351 0.052 0.39 NO
22 STAT5B STAT5B STAT5B 6745 0.043 0.37 NO
23 CPT1B CPT1B CPT1B 6780 0.042 0.37 NO
24 PRKAR1B PRKAR1B PRKAR1B 7002 0.037 0.36 NO
25 LPL LPL LPL 7485 0.026 0.34 NO
26 FAT1 FAT1 FAT1 7771 0.021 0.33 NO
27 SP1 SP1 SP1 8643 0.0038 0.28 NO
28 NCOA1 NCOA1 NCOA1 8753 0.0017 0.28 NO
29 PIK3R1 PIK3R1 PIK3R1 8780 0.0012 0.27 NO
30 HSP90AA1 HSP90AA1 HSP90AA1 9381 -0.0096 0.24 NO
31 NCOR2 NCOR2 NCOR2 9433 -0.01 0.24 NO
32 SRA1 SRA1 SRA1 9963 -0.02 0.22 NO
33 EHHADH EHHADH EHHADH 10167 -0.024 0.21 NO
34 PRKAR1A PRKAR1A PRKAR1A 10215 -0.025 0.21 NO
35 RELA RELA RELA 10240 -0.025 0.21 NO
36 MRPL11 MRPL11 MRPL11 10275 -0.026 0.21 NO
37 EP300 EP300 EP300 10512 -0.03 0.2 NO
38 RB1 RB1 RB1 11015 -0.039 0.18 NO
39 CREBBP CREBBP CREBBP 11877 -0.057 0.14 NO
40 MAPK1 MAPK1 MAPK1 12040 -0.061 0.13 NO
41 PRKACB PRKACB PRKACB 12646 -0.075 0.11 NO
42 CITED2 CITED2 CITED2 12974 -0.084 0.098 NO
43 TNF TNF TNF 13840 -0.11 0.062 NO
44 HSPA1A HSPA1A HSPA1A 13863 -0.11 0.071 NO
45 JUN JUN JUN 14035 -0.12 0.073 NO
46 MYC MYC MYC 14307 -0.13 0.071 NO
47 NRIP1 NRIP1 NRIP1 14440 -0.13 0.076 NO
48 DUT DUT DUT 14989 -0.16 0.062 NO
49 PRKAR2B PRKAR2B PRKAR2B 15190 -0.17 0.068 NO
50 NFKBIA NFKBIA NFKBIA 15298 -0.18 0.079 NO
51 ME1 ME1 ME1 15612 -0.2 0.081 NO
52 DUSP1 DUSP1 DUSP1 15710 -0.2 0.095 NO
53 RXRA RXRA RXRA 15737 -0.2 0.11 NO
54 PIK3CA PIK3CA PIK3CA 15746 -0.2 0.13 NO
55 CD36 CD36 CD36 16690 -0.3 0.11 NO

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

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PIP5K1B PIP5K1B PIP5K1B 81 1.3 0.32 YES
2 ARHGAP6 ARHGAP6 ARHGAP6 613 0.64 0.44 YES
3 ARHGAP4 ARHGAP4 ARHGAP4 2577 0.22 0.39 NO
4 SRC SRC SRC 3388 0.16 0.39 NO
5 ARPC1B ARPC1B ARPC1B 5474 0.075 0.29 NO
6 ARPC4 ARPC4 ARPC4 5588 0.071 0.3 NO
7 RHOA RHOA RHOA 5953 0.062 0.3 NO
8 ARHGEF11 ARHGEF11 ARHGEF11 6142 0.057 0.3 NO
9 ARHGEF1 ARHGEF1 ARHGEF1 6793 0.042 0.28 NO
10 PPP1R12B PPP1R12B PPP1R12B 7029 0.036 0.28 NO
11 ROCK1 ROCK1 ROCK1 7231 0.032 0.27 NO
12 DIAPH1 DIAPH1 DIAPH1 7385 0.029 0.27 NO
13 CFL1 CFL1 CFL1 8429 0.0077 0.22 NO
14 OPHN1 OPHN1 OPHN1 8495 0.0064 0.22 NO
15 ACTR2 ACTR2 ACTR2 8743 0.0018 0.2 NO
16 ARPC5 ARPC5 ARPC5 9078 -0.004 0.18 NO
17 ARHGAP5 ARHGAP5 ARHGAP5 9149 -0.0054 0.18 NO
18 ARPC1A ARPC1A ARPC1A 9441 -0.011 0.17 NO
19 PFN1 PFN1 PFN1 10317 -0.026 0.13 NO
20 ARPC3 ARPC3 ARPC3 10559 -0.031 0.12 NO
21 PIP5K1A PIP5K1A PIP5K1A 10643 -0.032 0.13 NO
22 MYL2 MYL2 MYL2 11370 -0.046 0.1 NO
23 VCL VCL VCL 11595 -0.051 0.1 NO
24 ARHGAP1 ARHGAP1 ARHGAP1 12198 -0.064 0.083 NO
25 GSN GSN GSN 12339 -0.068 0.092 NO
26 ACTR3 ACTR3 ACTR3 12504 -0.072 0.1 NO
27 ARPC2 ARPC2 ARPC2 12602 -0.074 0.11 NO
28 ARHGEF5 ARHGEF5 ARHGEF5 15003 -0.16 0.023 NO
29 LIMK1 LIMK1 LIMK1 15162 -0.17 0.055 NO
30 MYLK MYLK MYLK 16340 -0.26 0.054 NO
31 BAIAP2 BAIAP2 BAIAP2 16806 -0.31 0.1 NO

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

Figure S8.  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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CREB3L3 CREB3L3 CREB3L3 115 1.2 0.15 YES
2 CREB3L1 CREB3L1 CREB3L1 408 0.77 0.23 YES
3 AQP2 AQP2 AQP2 419 0.76 0.33 YES
4 PRKACG PRKACG PRKACG 522 0.69 0.41 YES
5 ADCY6 ADCY6 ADCY6 1100 0.45 0.44 YES
6 AVPR2 AVPR2 AVPR2 2447 0.23 0.4 NO
7 CREB3L4 CREB3L4 CREB3L4 3116 0.18 0.39 NO
8 NSF NSF NSF 4746 0.098 0.31 NO
9 CREB3 CREB3 CREB3 4913 0.094 0.32 NO
10 DYNC2LI1 DYNC2LI1 DYNC2LI1 5238 0.082 0.31 NO
11 RAB5C RAB5C RAB5C 6635 0.045 0.24 NO
12 CREB3L2 CREB3L2 CREB3L2 6661 0.045 0.24 NO
13 RAB11A RAB11A RAB11A 6692 0.044 0.25 NO
14 RAB5A RAB5A RAB5A 6763 0.042 0.25 NO
15 ARHGDIB ARHGDIB ARHGDIB 8002 0.016 0.19 NO
16 ARHGDIA ARHGDIA ARHGDIA 8345 0.0091 0.17 NO
17 STX4 STX4 STX4 9173 -0.006 0.13 NO
18 DYNC1I2 DYNC1I2 DYNC1I2 9577 -0.013 0.11 NO
19 DYNLL2 DYNLL2 DYNLL2 9689 -0.015 0.1 NO
20 DCTN6 DCTN6 DCTN6 9811 -0.018 0.098 NO
21 DYNC1LI2 DYNC1LI2 DYNC1LI2 9832 -0.018 0.099 NO
22 RAB5B RAB5B RAB5B 10364 -0.027 0.074 NO
23 CREB1 CREB1 CREB1 10507 -0.03 0.07 NO
24 DCTN5 DCTN5 DCTN5 11143 -0.041 0.042 NO
25 DCTN4 DCTN4 DCTN4 11373 -0.046 0.035 NO
26 GNAS GNAS GNAS 11481 -0.048 0.036 NO
27 RAB11B RAB11B RAB11B 11910 -0.058 0.02 NO
28 ADCY9 ADCY9 ADCY9 12002 -0.06 0.023 NO
29 DYNC1LI1 DYNC1LI1 DYNC1LI1 12298 -0.066 0.016 NO
30 DYNC1H1 DYNC1H1 DYNC1H1 12347 -0.068 0.022 NO
31 PRKACB PRKACB PRKACB 12646 -0.075 0.016 NO
32 DCTN1 DCTN1 DCTN1 12869 -0.081 0.015 NO
33 DCTN2 DCTN2 DCTN2 12987 -0.084 0.019 NO
34 DYNLL1 DYNLL1 DYNLL1 13084 -0.087 0.025 NO
35 VAMP2 VAMP2 VAMP2 13262 -0.092 0.028 NO
36 PRKACA PRKACA PRKACA 13401 -0.096 0.032 NO
37 AQP4 AQP4 AQP4 13647 -0.1 0.033 NO
38 PRKX PRKX PRKX 16097 -0.23 -0.068 NO
39 DYNC2H1 DYNC2H1 DYNC2H1 16959 -0.33 -0.072 NO
40 CREB5 CREB5 CREB5 17262 -0.38 -0.039 NO
41 AQP3 AQP3 AQP3 17440 -0.41 0.0047 NO
42 DYNC1I1 DYNC1I1 DYNC1I1 17861 -0.51 0.047 NO

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

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

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

Table 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 HMGCS2 HMGCS2 HMGCS2 130 1.2 0.18 YES
2 ACAA2 ACAA2 ACAA2 761 0.58 0.24 YES
3 BCKDHB BCKDHB BCKDHB 2213 0.26 0.2 YES
4 ACADS ACADS ACADS 2323 0.25 0.24 YES
5 ALDH2 ALDH2 ALDH2 2370 0.24 0.27 YES
6 IVD IVD IVD 2625 0.22 0.3 YES
7 HIBADH HIBADH HIBADH 2791 0.2 0.32 YES
8 ABAT ABAT ABAT 2969 0.19 0.34 YES
9 ACAD8 ACAD8 ACAD8 3002 0.19 0.37 YES
10 PCCA PCCA PCCA 3084 0.18 0.39 YES
11 ACAA1 ACAA1 ACAA1 3320 0.17 0.41 YES
12 ACADSB ACADSB ACADSB 3538 0.15 0.42 YES
13 ALDH1B1 ALDH1B1 ALDH1B1 3585 0.15 0.44 YES
14 HMGCL HMGCL HMGCL 3682 0.15 0.46 YES
15 ECHS1 ECHS1 ECHS1 4063 0.13 0.46 YES
16 ACAT1 ACAT1 ACAT1 4253 0.12 0.47 YES
17 HADH HADH HADH 4299 0.12 0.49 YES
18 HIBCH HIBCH HIBCH 4799 0.096 0.47 YES
19 MCCC2 MCCC2 MCCC2 4879 0.094 0.48 YES
20 ALDH6A1 ALDH6A1 ALDH6A1 4983 0.09 0.49 YES
21 AUH AUH AUH 4984 0.09 0.51 YES
22 MCEE MCEE MCEE 5661 0.07 0.48 NO
23 OXCT2 OXCT2 OXCT2 6464 0.05 0.45 NO
24 ALDH9A1 ALDH9A1 ALDH9A1 7851 0.019 0.38 NO
25 HADHA HADHA HADHA 7959 0.017 0.38 NO
26 BCAT2 BCAT2 BCAT2 7971 0.017 0.38 NO
27 ALDH7A1 ALDH7A1 ALDH7A1 8227 0.011 0.36 NO
28 ACADM ACADM ACADM 8396 0.0084 0.36 NO
29 MUT MUT MUT 8887 -0.00068 0.33 NO
30 HSD17B10 HSD17B10 HSD17B10 8916 -0.0011 0.33 NO
31 DLD DLD DLD 9855 -0.018 0.28 NO
32 EHHADH EHHADH EHHADH 10167 -0.024 0.27 NO
33 HMGCS1 HMGCS1 HMGCS1 10592 -0.031 0.25 NO
34 PCCB PCCB PCCB 11899 -0.058 0.19 NO
35 HADHB HADHB HADHB 12164 -0.063 0.19 NO
36 ACAT2 ACAT2 ACAT2 12308 -0.067 0.19 NO
37 AOX1 AOX1 AOX1 12794 -0.079 0.18 NO
38 IL4I1 IL4I1 IL4I1 12798 -0.079 0.19 NO
39 MCCC1 MCCC1 MCCC1 13822 -0.11 0.15 NO
40 ALDH3A2 ALDH3A2 ALDH3A2 14403 -0.13 0.14 NO
41 DBT DBT DBT 14448 -0.13 0.16 NO
42 BCKDHA BCKDHA BCKDHA 14596 -0.14 0.18 NO
43 OXCT1 OXCT1 OXCT1 16577 -0.28 0.12 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG HISTIDINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GAL3ST1 GAL3ST1 GAL3ST1 41 1.6 0.16 YES
2 SMPD3 SMPD3 SMPD3 182 1 0.26 YES
3 NEU4 NEU4 NEU4 370 0.79 0.33 YES
4 DEGS2 DEGS2 DEGS2 548 0.68 0.39 YES
5 UGT8 UGT8 UGT8 708 0.6 0.44 YES
6 GALC GALC GALC 1259 0.41 0.45 YES
7 ACER2 ACER2 ACER2 1335 0.39 0.49 YES
8 GLB1 GLB1 GLB1 2276 0.25 0.46 YES
9 NEU3 NEU3 NEU3 2505 0.23 0.47 YES
10 SMPD2 SMPD2 SMPD2 2633 0.22 0.49 YES
11 ASAH2 ASAH2 ASAH2 2889 0.2 0.5 YES
12 SGMS2 SGMS2 SGMS2 2947 0.19 0.51 YES
13 SPHK2 SPHK2 SPHK2 2948 0.19 0.53 YES
14 B4GALT6 B4GALT6 B4GALT6 3280 0.17 0.53 YES
15 SGPP2 SGPP2 SGPP2 3440 0.16 0.54 YES
16 PPAP2C PPAP2C PPAP2C 3672 0.15 0.54 YES
17 ASAH1 ASAH1 ASAH1 3890 0.14 0.54 YES
18 NEU1 NEU1 NEU1 4424 0.11 0.53 NO
19 SPTLC2 SPTLC2 SPTLC2 4449 0.11 0.54 NO
20 CERK CERK CERK 5305 0.081 0.5 NO
21 PPAP2A PPAP2A PPAP2A 5330 0.08 0.5 NO
22 GBA GBA GBA 5648 0.07 0.5 NO
23 PPAP2B PPAP2B PPAP2B 6275 0.054 0.47 NO
24 SMPD1 SMPD1 SMPD1 8154 0.013 0.37 NO
25 SGMS1 SGMS1 SGMS1 8470 0.0069 0.35 NO
26 ACER3 ACER3 ACER3 8994 -0.0024 0.32 NO
27 SMPD4 SMPD4 SMPD4 9680 -0.015 0.29 NO
28 SGPL1 SGPL1 SGPL1 10128 -0.024 0.27 NO
29 UGCG UGCG UGCG 10261 -0.026 0.26 NO
30 SGPP1 SGPP1 SGPP1 10489 -0.03 0.25 NO
31 GLA GLA GLA 10569 -0.031 0.25 NO
32 SPTLC1 SPTLC1 SPTLC1 10669 -0.033 0.25 NO
33 ARSA ARSA ARSA 11001 -0.039 0.24 NO
34 KDSR KDSR KDSR 14082 -0.12 0.084 NO
35 DEGS1 DEGS1 DEGS1 15774 -0.21 0.015 NO
36 ACER1 ACER1 ACER1 17276 -0.38 -0.026 NO
37 NEU2 NEU2 NEU2 17793 -0.49 -0.004 NO
38 SPHK1 SPHK1 SPHK1 17984 -0.54 0.041 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 HISTIDINE METABOLISM.

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

genes ES table in pathway: KEGG STARCH AND SUCROSE 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 ACACB ACACB ACACB 1246 0.41 0.032 YES
2 LDHAL6B LDHAL6B LDHAL6B 1325 0.39 0.12 YES
3 SUCLG2 SUCLG2 SUCLG2 1886 0.3 0.16 YES
4 LDHAL6A LDHAL6A LDHAL6A 2266 0.25 0.2 YES
5 ACSS1 ACSS1 ACSS1 2321 0.25 0.26 YES
6 ALDH2 ALDH2 ALDH2 2370 0.24 0.32 YES
7 ACSS2 ACSS2 ACSS2 2555 0.22 0.36 YES
8 ABAT ABAT ABAT 2969 0.19 0.38 YES
9 PCCA PCCA PCCA 3084 0.18 0.42 YES
10 ALDH1B1 ALDH1B1 ALDH1B1 3585 0.15 0.43 YES
11 MLYCD MLYCD MLYCD 3761 0.14 0.46 YES
12 ECHS1 ECHS1 ECHS1 4063 0.13 0.47 YES
13 SUCLG1 SUCLG1 SUCLG1 4240 0.12 0.49 YES
14 ACAT1 ACAT1 ACAT1 4253 0.12 0.52 YES
15 HIBCH HIBCH HIBCH 4799 0.096 0.51 YES
16 ALDH6A1 ALDH6A1 ALDH6A1 4983 0.09 0.52 YES
17 MCEE MCEE MCEE 5661 0.07 0.5 NO
18 ALDH9A1 ALDH9A1 ALDH9A1 7851 0.019 0.39 NO
19 HADHA HADHA HADHA 7959 0.017 0.39 NO
20 ALDH7A1 ALDH7A1 ALDH7A1 8227 0.011 0.38 NO
21 ACADM ACADM ACADM 8396 0.0084 0.37 NO
22 SUCLA2 SUCLA2 SUCLA2 8670 0.0032 0.36 NO
23 MUT MUT MUT 8887 -0.00068 0.35 NO
24 EHHADH EHHADH EHHADH 10167 -0.024 0.28 NO
25 ACSS3 ACSS3 ACSS3 10976 -0.039 0.25 NO
26 PCCB PCCB PCCB 11899 -0.058 0.22 NO
27 ACAT2 ACAT2 ACAT2 12308 -0.067 0.21 NO
28 ACACA ACACA ACACA 13119 -0.088 0.19 NO
29 LDHA LDHA LDHA 13156 -0.089 0.21 NO
30 ALDH3A2 ALDH3A2 ALDH3A2 14403 -0.13 0.17 NO
31 LDHB LDHB LDHB 16309 -0.25 0.13 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 STARCH AND SUCROSE METABOLISM.

Figure S16.  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 N GLYCAN BIOSYNTHESIS

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 MGAT3 MGAT3 MGAT3 345 0.82 0.092 YES
2 MGAT4A MGAT4A MGAT4A 603 0.64 0.16 YES
3 ALG11 ALG11 ALG11 1026 0.48 0.21 YES
4 ST6GAL1 ST6GAL1 ST6GAL1 1116 0.44 0.26 YES
5 FUT8 FUT8 FUT8 1489 0.36 0.29 YES
6 MAN1A1 MAN1A1 MAN1A1 1974 0.28 0.3 YES
7 MGAT5 MGAT5 MGAT5 2186 0.26 0.33 YES
8 MGAT4B MGAT4B MGAT4B 2406 0.24 0.35 YES
9 ALG5 ALG5 ALG5 2407 0.24 0.38 YES
10 MAN2A2 MAN2A2 MAN2A2 2628 0.22 0.4 YES
11 ALG14 ALG14 ALG14 2649 0.22 0.43 YES
12 DPAGT1 DPAGT1 DPAGT1 2940 0.19 0.44 YES
13 ALG1 ALG1 ALG1 3484 0.16 0.43 YES
14 MAN1C1 MAN1C1 MAN1C1 4151 0.12 0.41 YES
15 MAN2A1 MAN2A1 MAN2A1 4366 0.11 0.41 YES
16 STT3A STT3A STT3A 4388 0.11 0.43 YES
17 RPN2 RPN2 RPN2 4807 0.096 0.42 YES
18 ALG8 ALG8 ALG8 4878 0.094 0.43 YES
19 STT3B STT3B STT3B 4917 0.093 0.44 YES
20 ALG13 ALG13 ALG13 5528 0.073 0.42 NO
21 ALG2 ALG2 ALG2 5643 0.07 0.42 NO
22 DDOST DDOST DDOST 5752 0.067 0.42 NO
23 DPM3 DPM3 DPM3 5762 0.067 0.43 NO
24 ALG9 ALG9 ALG9 6473 0.049 0.4 NO
25 B4GALT3 B4GALT3 B4GALT3 6834 0.041 0.38 NO
26 MAN1A2 MAN1A2 MAN1A2 7685 0.022 0.34 NO
27 DOLPP1 DOLPP1 DOLPP1 7734 0.021 0.34 NO
28 DAD1 DAD1 DAD1 8046 0.015 0.33 NO
29 B4GALT1 B4GALT1 B4GALT1 8120 0.014 0.33 NO
30 RPN1 RPN1 RPN1 8252 0.011 0.32 NO
31 MOGS MOGS MOGS 8267 0.011 0.32 NO
32 DPM2 DPM2 DPM2 8401 0.0083 0.32 NO
33 ALG6 ALG6 ALG6 8629 0.0042 0.3 NO
34 MGAT2 MGAT2 MGAT2 8995 -0.0024 0.28 NO
35 GANAB GANAB GANAB 9031 -0.0031 0.28 NO
36 DPM1 DPM1 DPM1 9703 -0.016 0.25 NO
37 ALG12 ALG12 ALG12 9734 -0.016 0.25 NO
38 MGAT1 MGAT1 MGAT1 10360 -0.027 0.22 NO
39 MAN1B1 MAN1B1 MAN1B1 10578 -0.031 0.21 NO
40 ALG3 ALG3 ALG3 11970 -0.059 0.15 NO
41 ALG10 ALG10 ALG10 12470 -0.07 0.13 NO
42 ALG10B ALG10B ALG10B 12799 -0.079 0.12 NO
43 B4GALT2 B4GALT2 B4GALT2 15169 -0.17 0.019 NO
44 MGAT5B MGAT5B MGAT5B 17449 -0.41 -0.047 NO
45 TUSC3 TUSC3 TUSC3 18571 -0.86 0.0095 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 N GLYCAN BIOSYNTHESIS.

Figure S18.  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 GLYCEROLIPID 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 GAS2 GAS2 GAS2 402 0.78 0.12 YES
2 BIRC3 BIRC3 BIRC3 741 0.59 0.22 YES
3 CASP10 CASP10 CASP10 908 0.52 0.3 YES
4 DFFB DFFB DFFB 1407 0.37 0.35 YES
5 APAF1 APAF1 APAF1 1960 0.28 0.37 YES
6 CASP6 CASP6 CASP6 2388 0.24 0.39 YES
7 CASP8 CASP8 CASP8 3191 0.18 0.38 YES
8 CASP7 CASP7 CASP7 3791 0.14 0.38 YES
9 SPTAN1 SPTAN1 SPTAN1 4500 0.11 0.36 YES
10 MAP3K14 MAP3K14 MAP3K14 4553 0.11 0.38 YES
11 TNFRSF10A TNFRSF10A TNFRSF10A 4577 0.1 0.4 YES
12 TRAF2 TRAF2 TRAF2 4583 0.1 0.42 YES
13 CASP9 CASP9 CASP9 4589 0.1 0.44 YES
14 TNFRSF10B TNFRSF10B TNFRSF10B 4649 0.1 0.45 YES
15 CHUK CHUK CHUK 4801 0.096 0.46 YES
16 CFLAR CFLAR CFLAR 4968 0.091 0.47 YES
17 CYCS CYCS CYCS 5156 0.085 0.48 YES
18 CASP3 CASP3 CASP3 5397 0.077 0.48 YES
19 XIAP XIAP XIAP 5646 0.07 0.48 NO
20 RIPK1 RIPK1 RIPK1 6796 0.042 0.42 NO
21 TNFSF12 TNFSF12 TNFSF12 8239 0.011 0.35 NO
22 DFFA DFFA DFFA 8336 0.0092 0.34 NO
23 BIRC2 BIRC2 BIRC2 8587 0.0047 0.33 NO
24 TNFRSF25 TNFRSF25 TNFRSF25 10039 -0.022 0.26 NO
25 RELA RELA RELA 10240 -0.025 0.25 NO
26 NFKB1 NFKB1 NFKB1 10702 -0.033 0.24 NO
27 LMNA LMNA LMNA 11142 -0.041 0.22 NO
28 TRADD TRADD TRADD 14116 -0.12 0.083 NO
29 NFKBIA NFKBIA NFKBIA 15298 -0.18 0.052 NO
30 BCL2 BCL2 BCL2 15406 -0.18 0.081 NO
31 TNFSF10 TNFSF10 TNFSF10 16333 -0.26 0.079 NO
32 FADD FADD FADD 16425 -0.27 0.12 NO

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

Figure S20.  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

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 CARM ER PATHWAY 34 genes.ES.table 0.34 1.3 0.19 0.68 1 0.44 0.32 0.3 0.59 0.21
BIOCARTA G1 PATHWAY 27 genes.ES.table 0.44 1.4 0.12 0.67 0.98 0.37 0.22 0.29 0.54 0.22
BIOCARTA ERK PATHWAY 27 genes.ES.table 0.47 1.6 0.048 1 0.79 0.18 0.082 0.17 0.86 0.46
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.35 1.3 0.15 0.67 0.98 0.4 0.31 0.28 0.54 0.21
BIOCARTA INTEGRIN PATHWAY 37 genes.ES.table 0.34 1.3 0.17 0.66 0.99 0.49 0.35 0.32 0.54 0.21
KEGG RNA DEGRADATION 56 genes.ES.table 0.35 1.5 0.11 0.69 0.88 0.61 0.46 0.33 0.46 0.23
KEGG RNA POLYMERASE 28 genes.ES.table 0.43 1.4 0.14 0.83 0.95 0.64 0.39 0.39 0.64 0.29
KEGG BASAL TRANSCRIPTION FACTORS 34 genes.ES.table 0.4 1.5 0.061 0.82 0.83 0.44 0.35 0.29 0.51 0.27
KEGG SPLICEOSOME 125 genes.ES.table 0.41 1.6 0.088 1 0.69 0.61 0.43 0.35 1 0.51
KEGG PROTEASOME 42 genes.ES.table 0.44 1.4 0.2 0.68 0.98 0.64 0.43 0.37 0.54 0.22
genes ES table in pathway: BIOCARTA CARM ER 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 HSPA2 HSPA2 HSPA2 672 0.43 0.028 YES
2 HSPA6 HSPA6 HSPA6 1921 0.24 -0.0025 YES
3 PRPF40B PRPF40B PRPF40B 2284 0.21 0.0095 YES
4 THOC3 THOC3 THOC3 2933 0.17 -0.00024 YES
5 HSPA1A HSPA1A HSPA1A 3309 0.14 0.0015 YES
6 HSPA1B HSPA1B HSPA1B 3318 0.14 0.023 YES
7 PHF5A PHF5A PHF5A 3524 0.14 0.032 YES
8 SF3A2 SF3A2 SF3A2 3964 0.12 0.027 YES
9 ISY1 ISY1 ISY1 4035 0.12 0.041 YES
10 SNRPD3 SNRPD3 SNRPD3 4236 0.11 0.047 YES
11 SNRPF SNRPF SNRPF 4307 0.11 0.059 YES
12 PRPF4 PRPF4 PRPF4 4308 0.11 0.076 YES
13 PPIE PPIE PPIE 4389 0.11 0.087 YES
14 MAGOHB MAGOHB MAGOHB 4455 0.1 0.1 YES
15 XAB2 XAB2 XAB2 4485 0.1 0.11 YES
16 PUF60 PUF60 PUF60 4719 0.096 0.12 YES
17 SART1 SART1 SART1 4765 0.095 0.13 YES
18 PLRG1 PLRG1 PLRG1 4793 0.094 0.14 YES
19 EIF4A3 EIF4A3 EIF4A3 4876 0.093 0.15 YES
20 TRA2B TRA2B TRA2B 5223 0.083 0.14 YES
21 MAGOH MAGOH MAGOH 5255 0.082 0.15 YES
22 SNRNP40 SNRNP40 SNRNP40 5270 0.082 0.17 YES
23 SR140 SR140 SR140 5445 0.077 0.17 YES
24 LSM6 LSM6 LSM6 5449 0.077 0.18 YES
25 SNRPG SNRPG SNRPG 5565 0.074 0.18 YES
26 LSM4 LSM4 LSM4 5593 0.074 0.19 YES
27 SF3B4 SF3B4 SF3B4 5656 0.072 0.2 YES
28 PRPF19 PRPF19 PRPF19 5738 0.071 0.21 YES
29 SF3B14 SF3B14 SF3B14 5821 0.069 0.21 YES
30 SNRPB SNRPB SNRPB 5834 0.069 0.22 YES
31 SNW1 SNW1 SNW1 5914 0.067 0.23 YES
32 NHP2L1 NHP2L1 NHP2L1 5916 0.067 0.24 YES
33 SNRPD2 SNRPD2 SNRPD2 5968 0.066 0.25 YES
34 HNRNPC HNRNPC HNRNPC 6056 0.064 0.25 YES
35 THOC4 THOC4 THOC4 6119 0.063 0.26 YES
36 THOC1 THOC1 THOC1 6182 0.062 0.26 YES
37 WBP11 WBP11 WBP11 6186 0.062 0.27 YES
38 SFRS9 SFRS9 SFRS9 6209 0.061 0.28 YES
39 SNRPE SNRPE SNRPE 6227 0.061 0.29 YES
40 LSM7 LSM7 LSM7 6229 0.061 0.3 YES
41 SNRPD1 SNRPD1 SNRPD1 6383 0.058 0.3 YES
42 SFRS4 SFRS4 SFRS4 6678 0.052 0.29 YES
43 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 6721 0.051 0.3 YES
44 BUD31 BUD31 BUD31 6788 0.05 0.3 YES
45 SF3A3 SF3A3 SF3A3 6803 0.049 0.31 YES
46 USP39 USP39 USP39 6887 0.048 0.31 YES
47 SNRPA1 SNRPA1 SNRPA1 6941 0.047 0.31 YES
48 U2AF1 U2AF1 U2AF1 6979 0.046 0.32 YES
49 ZMAT2 ZMAT2 ZMAT2 7005 0.045 0.32 YES
50 SNRPA SNRPA SNRPA 7064 0.044 0.33 YES
51 PRPF8 PRPF8 PRPF8 7113 0.043 0.33 YES
52 SF3B3 SF3B3 SF3B3 7164 0.042 0.34 YES
53 HNRNPA3 HNRNPA3 HNRNPA3 7186 0.042 0.34 YES
54 EFTUD2 EFTUD2 EFTUD2 7244 0.041 0.34 YES
55 DHX38 DHX38 DHX38 7264 0.041 0.35 YES
56 BCAS2 BCAS2 BCAS2 7284 0.04 0.35 YES
57 PPIL1 PPIL1 PPIL1 7305 0.04 0.36 YES
58 HNRNPM HNRNPM HNRNPM 7383 0.038 0.36 YES
59 PPIH PPIH PPIH 7416 0.038 0.36 YES
60 HNRNPA1 HNRNPA1 HNRNPA1 7423 0.038 0.37 YES
61 RBM8A RBM8A RBM8A 7424 0.038 0.38 YES
62 SF3B2 SF3B2 SF3B2 7425 0.038 0.38 YES
63 SF3A1 SF3A1 SF3A1 7442 0.038 0.39 YES
64 SFRS7 SFRS7 SFRS7 7474 0.037 0.39 YES
65 PRPF31 PRPF31 PRPF31 7487 0.037 0.4 YES
66 SNRNP27 SNRNP27 SNRNP27 7541 0.036 0.4 YES
67 PCBP1 PCBP1 PCBP1 7613 0.035 0.4 YES
68 HNRNPK HNRNPK HNRNPK 7756 0.033 0.4 YES
69 SNRPC SNRPC SNRPC 7789 0.032 0.4 YES
70 HNRNPU HNRNPU HNRNPU 7841 0.031 0.4 YES
71 SFRS2 SFRS2 SFRS2 7865 0.031 0.4 YES
72 U2AF2 U2AF2 U2AF2 7923 0.03 0.41 YES
73 CWC15 CWC15 CWC15 7956 0.029 0.41 YES
74 RBM17 RBM17 RBM17 7981 0.029 0.41 YES
75 CHERP CHERP CHERP 8101 0.027 0.41 YES
76 SFRS1 SFRS1 SFRS1 8111 0.027 0.41 YES
77 SFRS3 SFRS3 SFRS3 8293 0.024 0.41 NO
78 ACIN1 ACIN1 ACIN1 8389 0.022 0.41 NO
79 SMNDC1 SMNDC1 SMNDC1 8547 0.019 0.4 NO
80 TCERG1 TCERG1 TCERG1 8680 0.017 0.4 NO
81 RBMX RBMX RBMX 8697 0.017 0.4 NO
82 PRPF40A PRPF40A PRPF40A 8748 0.016 0.4 NO
83 SNRNP70 SNRNP70 SNRNP70 8781 0.015 0.4 NO
84 LSM5 LSM5 LSM5 8814 0.015 0.4 NO
85 RBM22 RBM22 RBM22 8845 0.014 0.4 NO
86 SFRS13A SFRS13A SFRS13A 8922 0.013 0.4 NO
87 NAA38 NAA38 NAA38 9027 0.011 0.39 NO
88 AQR AQR AQR 9368 0.0053 0.38 NO
89 DDX5 DDX5 DDX5 9423 0.0044 0.37 NO
90 NCBP1 NCBP1 NCBP1 9545 0.0023 0.37 NO
91 DHX16 DHX16 DHX16 9597 0.0014 0.36 NO
92 TXNL4A TXNL4A TXNL4A 9652 0.00067 0.36 NO
93 CTNNBL1 CTNNBL1 CTNNBL1 9695 -0.00015 0.36 NO
94 SNRPB2 SNRPB2 SNRPB2 9745 -0.00099 0.36 NO
95 RBM25 RBM25 RBM25 9807 -0.0018 0.35 NO
96 SLU7 SLU7 SLU7 9812 -0.0019 0.35 NO
97 DHX8 DHX8 DHX8 9918 -0.0037 0.35 NO
98 PRPF38A PRPF38A PRPF38A 9942 -0.0042 0.35 NO
99 SFRS5 SFRS5 SFRS5 9953 -0.0043 0.35 NO
100 LSM2 LSM2 LSM2 10188 -0.0087 0.34 NO
101 SNRNP200 SNRNP200 SNRNP200 10208 -0.0091 0.34 NO
102 DDX42 DDX42 DDX42 10236 -0.0096 0.34 NO
103 PQBP1 PQBP1 PQBP1 10245 -0.0098 0.34 NO
104 HSPA8 HSPA8 HSPA8 10309 -0.011 0.34 NO
105 SYF2 SYF2 SYF2 10421 -0.013 0.33 NO
106 SF3B5 SF3B5 SF3B5 10425 -0.013 0.33 NO
107 DDX46 DDX46 DDX46 10464 -0.014 0.33 NO
108 BAT1 BAT1 BAT1 10554 -0.016 0.33 NO
109 CRNKL1 CRNKL1 CRNKL1 10584 -0.016 0.33 NO
110 CDC5L CDC5L CDC5L 10692 -0.018 0.33 NO
111 DDX23 DDX23 DDX23 10981 -0.024 0.32 NO
112 PRPF6 PRPF6 PRPF6 11086 -0.026 0.32 NO
113 TRA2A TRA2A TRA2A 11118 -0.027 0.32 NO
114 PRPF3 PRPF3 PRPF3 11175 -0.028 0.32 NO
115 SF3B1 SF3B1 SF3B1 11215 -0.028 0.32 NO
116 PRPF18 PRPF18 PRPF18 11326 -0.031 0.32 NO
117 SFRS6 SFRS6 SFRS6 11361 -0.031 0.32 NO
118 DHX15 DHX15 DHX15 11603 -0.036 0.32 NO
119 HSPA1L HSPA1L HSPA1L 11674 -0.038 0.32 NO
120 CDC40 CDC40 CDC40 11909 -0.043 0.31 NO
121 LSM3 LSM3 LSM3 12077 -0.048 0.31 NO
122 PRPF38B PRPF38B PRPF38B 12125 -0.049 0.32 NO
123 THOC2 THOC2 THOC2 12743 -0.063 0.29 NO
124 SFRS2B SFRS2B SFRS2B 13523 -0.086 0.26 NO
125 CCDC12 CCDC12 CCDC12 14347 -0.12 0.24 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 CARM ER PATHWAY.

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

genes ES table in pathway: BIOCARTA G1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GNGT1 GNGT1 GNGT1 214 0.6 0.13 YES
2 NGF NGF NGF 287 0.56 0.26 YES
3 NGFR NGFR NGFR 373 0.52 0.38 YES
4 EGFR EGFR EGFR 1049 0.35 0.42 YES
5 IGF1R IGF1R IGF1R 1530 0.28 0.47 YES
6 SHC1 SHC1 SHC1 3880 0.12 0.37 NO
7 MYC MYC MYC 4655 0.098 0.35 NO
8 MKNK1 MKNK1 MKNK1 4948 0.091 0.36 NO
9 MKNK2 MKNK2 MKNK2 5913 0.067 0.32 NO
10 MAP2K1 MAP2K1 MAP2K1 6094 0.063 0.33 NO
11 ITGB1 ITGB1 ITGB1 6277 0.06 0.33 NO
12 MAPK1 MAPK1 MAPK1 6549 0.054 0.33 NO
13 GNAS GNAS GNAS 6581 0.054 0.34 NO
14 PPP2CA PPP2CA PPP2CA 7217 0.042 0.32 NO
15 GNB1 GNB1 GNB1 7303 0.04 0.32 NO
16 RPS6KA5 RPS6KA5 RPS6KA5 7583 0.035 0.32 NO
17 MAP2K2 MAP2K2 MAP2K2 8177 0.025 0.29 NO
18 SOS1 SOS1 SOS1 8948 0.012 0.25 NO
19 ELK1 ELK1 ELK1 10644 -0.017 0.16 NO
20 STAT3 STAT3 STAT3 10982 -0.024 0.15 NO
21 GRB2 GRB2 GRB2 11064 -0.025 0.15 NO
22 RPS6KA1 RPS6KA1 RPS6KA1 11880 -0.043 0.12 NO
23 RAF1 RAF1 RAF1 12305 -0.053 0.11 NO
24 SRC SRC SRC 14511 -0.12 0.022 NO
25 MAPK3 MAPK3 MAPK3 14995 -0.15 0.031 NO
26 PDGFRA PDGFRA PDGFRA 16167 -0.22 0.021 NO
27 PTPRR PTPRR PTPRR 17925 -0.49 0.044 NO

Figure S23.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA G1 PATHWAY.

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA ERK 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 CCNA1 CCNA1 CCNA1 45 0.8 0.054 YES
2 SFN SFN SFN 732 0.41 0.046 YES
3 TGFB3 TGFB3 TGFB3 803 0.4 0.07 YES
4 TGFB1 TGFB1 TGFB1 1399 0.29 0.059 YES
5 PKMYT1 PKMYT1 PKMYT1 1598 0.27 0.067 YES
6 ORC6L ORC6L ORC6L 1672 0.26 0.082 YES
7 CDC45 CDC45 CDC45 1709 0.26 0.098 YES
8 TGFB2 TGFB2 TGFB2 2160 0.22 0.089 YES
9 MAD2L2 MAD2L2 MAD2L2 2169 0.22 0.1 YES
10 CDKN2D CDKN2D CDKN2D 2258 0.21 0.11 YES
11 MCM2 MCM2 MCM2 2357 0.2 0.12 YES
12 ORC1L ORC1L ORC1L 2408 0.2 0.13 YES
13 MCM5 MCM5 MCM5 2435 0.2 0.15 YES
14 PTTG1 PTTG1 PTTG1 2443 0.2 0.16 YES
15 CDC7 CDC7 CDC7 2583 0.19 0.16 YES
16 SKP2 SKP2 SKP2 2601 0.18 0.18 YES
17 CCNE2 CCNE2 CCNE2 2773 0.17 0.18 YES
18 CDC20 CDC20 CDC20 2836 0.17 0.19 YES
19 CCNB1 CCNB1 CCNB1 2975 0.16 0.19 YES
20 MCM4 MCM4 MCM4 3036 0.16 0.2 YES
21 ANAPC10 ANAPC10 ANAPC10 3075 0.16 0.21 YES
22 CHEK2 CHEK2 CHEK2 3161 0.15 0.22 YES
23 CCNA2 CCNA2 CCNA2 3189 0.15 0.23 YES
24 CCND1 CCND1 CCND1 3359 0.14 0.23 YES
25 YWHAQ YWHAQ YWHAQ 3388 0.14 0.24 YES
26 BUB1B BUB1B BUB1B 3423 0.14 0.24 YES
27 RBX1 RBX1 RBX1 3444 0.14 0.25 YES
28 YWHAG YWHAG YWHAG 3563 0.14 0.26 YES
29 GADD45A GADD45A GADD45A 3590 0.13 0.26 YES
30 CCNB2 CCNB2 CCNB2 3599 0.13 0.27 YES
31 RBL1 RBL1 RBL1 3615 0.13 0.28 YES
32 CHEK1 CHEK1 CHEK1 3699 0.13 0.28 YES
33 TTK TTK TTK 3857 0.12 0.29 YES
34 CDK2 CDK2 CDK2 3882 0.12 0.29 YES
35 CDKN2C CDKN2C CDKN2C 4034 0.12 0.29 YES
36 CDK1 CDK1 CDK1 4137 0.11 0.3 YES
37 PLK1 PLK1 PLK1 4171 0.11 0.3 YES
38 CDK6 CDK6 CDK6 4172 0.11 0.31 YES
39 MAD2L1 MAD2L1 MAD2L1 4181 0.11 0.32 YES
40 CDK4 CDK4 CDK4 4214 0.11 0.32 YES
41 FZR1 FZR1 FZR1 4452 0.1 0.32 YES
42 SMAD2 SMAD2 SMAD2 4468 0.1 0.32 YES
43 MCM7 MCM7 MCM7 4484 0.1 0.33 YES
44 TFDP2 TFDP2 TFDP2 4563 0.1 0.33 YES
45 YWHAE YWHAE YWHAE 4575 0.1 0.34 YES
46 MYC MYC MYC 4655 0.098 0.34 YES
47 PCNA PCNA PCNA 4665 0.097 0.35 YES
48 ANAPC7 ANAPC7 ANAPC7 4953 0.09 0.34 YES
49 ORC5L ORC5L ORC5L 5000 0.089 0.34 YES
50 ZBTB17 ZBTB17 ZBTB17 5100 0.086 0.34 YES
51 PRKDC PRKDC PRKDC 5113 0.086 0.35 YES
52 CDC27 CDC27 CDC27 5145 0.085 0.35 YES
53 GSK3B GSK3B GSK3B 5154 0.084 0.36 YES
54 WEE1 WEE1 WEE1 5297 0.081 0.36 YES
55 MCM6 MCM6 MCM6 5314 0.08 0.36 YES
56 ORC3L ORC3L ORC3L 5420 0.078 0.36 YES
57 SMC1B SMC1B SMC1B 5502 0.076 0.36 YES
58 CDC23 CDC23 CDC23 5574 0.074 0.36 YES
59 TFDP1 TFDP1 TFDP1 5577 0.074 0.37 YES
60 CDC6 CDC6 CDC6 5657 0.072 0.37 YES
61 CDKN1A CDKN1A CDKN1A 5691 0.072 0.37 YES
62 STAG1 STAG1 STAG1 5873 0.068 0.37 YES
63 RAD21 RAD21 RAD21 5906 0.067 0.37 YES
64 E2F4 E2F4 E2F4 5978 0.066 0.37 YES
65 MAD1L1 MAD1L1 MAD1L1 6001 0.065 0.38 YES
66 CDKN1C CDKN1C CDKN1C 6032 0.065 0.38 YES
67 YWHAZ YWHAZ YWHAZ 6163 0.062 0.38 YES
68 BUB1 BUB1 BUB1 6175 0.062 0.38 YES
69 SMAD3 SMAD3 SMAD3 6224 0.061 0.38 YES
70 CUL1 CUL1 CUL1 6233 0.06 0.38 YES
71 CDC25B CDC25B CDC25B 6239 0.06 0.39 YES
72 ATR ATR ATR 6384 0.058 0.38 NO
73 TP53 TP53 TP53 6636 0.053 0.38 NO
74 ANAPC13 ANAPC13 ANAPC13 6719 0.051 0.38 NO
75 CDC25C CDC25C CDC25C 6824 0.049 0.37 NO
76 ANAPC11 ANAPC11 ANAPC11 6839 0.049 0.38 NO
77 SKP1 SKP1 SKP1 6907 0.047 0.38 NO
78 CREBBP CREBBP CREBBP 6965 0.046 0.38 NO
79 YWHAH YWHAH YWHAH 7016 0.045 0.38 NO
80 E2F2 E2F2 E2F2 7109 0.044 0.37 NO
81 E2F1 E2F1 E2F1 7123 0.043 0.38 NO
82 ABL1 ABL1 ABL1 7406 0.038 0.36 NO
83 SMAD4 SMAD4 SMAD4 7461 0.037 0.36 NO
84 SMC3 SMC3 SMC3 7505 0.036 0.36 NO
85 GADD45B GADD45B GADD45B 7579 0.035 0.36 NO
86 RBL2 RBL2 RBL2 7673 0.034 0.36 NO
87 ESPL1 ESPL1 ESPL1 7737 0.033 0.36 NO
88 CDK7 CDK7 CDK7 7862 0.031 0.35 NO
89 STAG2 STAG2 STAG2 7969 0.029 0.35 NO
90 MCM3 MCM3 MCM3 8113 0.027 0.34 NO
91 E2F3 E2F3 E2F3 8175 0.025 0.34 NO
92 ANAPC5 ANAPC5 ANAPC5 8260 0.024 0.34 NO
93 HDAC2 HDAC2 HDAC2 8497 0.02 0.33 NO
94 RB1 RB1 RB1 8505 0.02 0.33 NO
95 ANAPC4 ANAPC4 ANAPC4 8789 0.015 0.32 NO
96 EP300 EP300 EP300 8921 0.013 0.31 NO
97 ANAPC2 ANAPC2 ANAPC2 9089 0.0099 0.3 NO
98 BUB3 BUB3 BUB3 9345 0.0057 0.29 NO
99 SMC1A SMC1A SMC1A 9676 0.00016 0.27 NO
100 ANAPC1 ANAPC1 ANAPC1 10137 -0.0079 0.25 NO
101 MDM2 MDM2 MDM2 10324 -0.012 0.24 NO
102 CDKN1B CDKN1B CDKN1B 10553 -0.016 0.23 NO
103 CDC25A CDC25A CDC25A 10642 -0.017 0.22 NO
104 YWHAB YWHAB YWHAB 11644 -0.037 0.17 NO
105 CDC16 CDC16 CDC16 11789 -0.041 0.17 NO
106 ORC4L ORC4L ORC4L 11813 -0.041 0.17 NO
107 CCNE1 CCNE1 CCNE1 11886 -0.043 0.17 NO
108 ORC2L ORC2L ORC2L 11906 -0.043 0.17 NO
109 CCNH CCNH CCNH 12105 -0.048 0.16 NO
110 WEE2 WEE2 WEE2 12198 -0.05 0.16 NO
111 HDAC1 HDAC1 HDAC1 12321 -0.053 0.16 NO
112 ATM ATM ATM 12579 -0.059 0.15 NO
113 PTTG2 PTTG2 PTTG2 13306 -0.079 0.12 NO
114 CDC14A CDC14A CDC14A 13886 -0.098 0.09 NO
115 CCND3 CCND3 CCND3 14296 -0.12 0.077 NO
116 CCND2 CCND2 CCND2 14891 -0.14 0.055 NO
117 CDC26 CDC26 CDC26 16059 -0.21 0.0068 NO
118 CDC14B CDC14B CDC14B 16158 -0.22 0.017 NO
119 CDKN2B CDKN2B CDKN2B 16359 -0.24 0.023 NO
120 GADD45G GADD45G GADD45G 16587 -0.26 0.029 NO
121 CDKN2A CDKN2A CDKN2A 17313 -0.35 0.015 NO
122 CCNB3 CCNB3 CCNB3 17697 -0.43 0.024 NO
123 E2F5 E2F5 E2F5 17789 -0.46 0.052 NO

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

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

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

Table 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 GTF2A1L GTF2A1L GTF2A1L 899 0.38 0.11 YES
2 STON1 STON1 STON1 1113 0.34 0.24 YES
3 GTF2H3 GTF2H3 GTF2H3 3862 0.12 0.15 YES
4 GTF2E1 GTF2E1 GTF2E1 3936 0.12 0.2 YES
5 TAF4B TAF4B TAF4B 4102 0.12 0.24 YES
6 TAF12 TAF12 TAF12 4703 0.096 0.25 YES
7 GTF2A1 GTF2A1 GTF2A1 5143 0.085 0.26 YES
8 GTF2IRD1 GTF2IRD1 GTF2IRD1 5781 0.07 0.25 YES
9 TAF6 TAF6 TAF6 5824 0.069 0.28 YES
10 GTF2H4 GTF2H4 GTF2H4 5874 0.068 0.31 YES
11 TAF6L TAF6L TAF6L 5890 0.067 0.34 YES
12 TAF2 TAF2 TAF2 5917 0.067 0.36 YES
13 TAF5 TAF5 TAF5 5950 0.066 0.39 YES
14 GTF2F2 GTF2F2 GTF2F2 6165 0.062 0.4 YES
15 TAF13 TAF13 TAF13 6590 0.054 0.4 YES
16 GTF2F1 GTF2F1 GTF2F1 7851 0.031 0.35 NO
17 TBPL1 TBPL1 TBPL1 7868 0.031 0.36 NO
18 GTF2H2 GTF2H2 GTF2H2 8082 0.027 0.36 NO
19 TAF9B TAF9B TAF9B 8364 0.022 0.36 NO
20 GTF2A2 GTF2A2 GTF2A2 8450 0.021 0.36 NO
21 GTF2I GTF2I GTF2I 8621 0.018 0.36 NO
22 TBP TBP TBP 8747 0.016 0.36 NO
23 TAF5L TAF5L TAF5L 8794 0.015 0.36 NO
24 GTF2H1 GTF2H1 GTF2H1 8897 0.013 0.36 NO
25 GTF2E2 GTF2E2 GTF2E2 9013 0.011 0.36 NO
26 TAF7 TAF7 TAF7 9225 0.0077 0.35 NO
27 TAF9 TAF9 TAF9 9351 0.0056 0.35 NO
28 TAF11 TAF11 TAF11 10143 -0.008 0.31 NO
29 TAF10 TAF10 TAF10 10166 -0.0083 0.31 NO
30 TAF7L TAF7L TAF7L 10851 -0.021 0.29 NO
31 GTF2B GTF2B GTF2B 11423 -0.033 0.27 NO
32 TAF4 TAF4 TAF4 12667 -0.061 0.23 NO
33 TAF1 TAF1 TAF1 13483 -0.085 0.22 NO
34 TAF1L TAF1L TAF1L 14904 -0.14 0.2 NO

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

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

genes ES table in pathway: BIOCARTA INTEGRIN PATHWAY

Table 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 TP53AIP1 TP53AIP1 TP53AIP1 136 0.67 0.056 YES
2 TP73 TP73 TP73 240 0.59 0.11 YES
3 SESN3 SESN3 SESN3 460 0.49 0.14 YES
4 BAI1 BAI1 BAI1 574 0.46 0.18 YES
5 SFN SFN SFN 732 0.41 0.21 YES
6 RPRM RPRM RPRM 1044 0.35 0.22 YES
7 SERPINE1 SERPINE1 SERPINE1 1058 0.34 0.26 YES
8 SERPINB5 SERPINB5 SERPINB5 1235 0.32 0.28 YES
9 PMAIP1 PMAIP1 PMAIP1 1251 0.31 0.3 YES
10 PERP PERP PERP 1475 0.28 0.32 YES
11 DDB2 DDB2 DDB2 2365 0.2 0.29 YES
12 SIAH1 SIAH1 SIAH1 2668 0.18 0.29 YES
13 CCNE2 CCNE2 CCNE2 2773 0.17 0.3 YES
14 CCNB1 CCNB1 CCNB1 2975 0.16 0.31 YES
15 CHEK2 CHEK2 CHEK2 3161 0.15 0.31 YES
16 CCND1 CCND1 CCND1 3359 0.14 0.32 YES
17 GADD45A GADD45A GADD45A 3590 0.13 0.32 YES
18 CCNB2 CCNB2 CCNB2 3599 0.13 0.33 YES
19 CHEK1 CHEK1 CHEK1 3699 0.13 0.34 YES
20 THBS1 THBS1 THBS1 3796 0.13 0.34 YES
21 CDK2 CDK2 CDK2 3882 0.12 0.35 YES
22 CDK1 CDK1 CDK1 4137 0.11 0.34 YES
23 GTSE1 GTSE1 GTSE1 4151 0.11 0.36 YES
24 CDK6 CDK6 CDK6 4172 0.11 0.36 YES
25 CDK4 CDK4 CDK4 4214 0.11 0.37 YES
26 RRM2 RRM2 RRM2 4328 0.11 0.38 YES
27 IGFBP3 IGFBP3 IGFBP3 4914 0.092 0.36 NO
28 FAS FAS FAS 4978 0.09 0.36 NO
29 RRM2B RRM2B RRM2B 5563 0.074 0.34 NO
30 ZMAT3 ZMAT3 ZMAT3 5596 0.074 0.34 NO
31 CDKN1A CDKN1A CDKN1A 5691 0.072 0.34 NO
32 ATR ATR ATR 6384 0.058 0.31 NO
33 TP53 TP53 TP53 6636 0.053 0.3 NO
34 LRDD LRDD LRDD 7192 0.042 0.28 NO
35 BID BID BID 7350 0.039 0.27 NO
36 GADD45B GADD45B GADD45B 7579 0.035 0.26 NO
37 PTEN PTEN PTEN 8480 0.02 0.22 NO
38 TSC2 TSC2 TSC2 8488 0.02 0.22 NO
39 RFWD2 RFWD2 RFWD2 9364 0.0054 0.17 NO
40 IGF1 IGF1 IGF1 9882 -0.0031 0.14 NO
41 TNFRSF10B TNFRSF10B TNFRSF10B 9916 -0.0037 0.14 NO
42 CD82 CD82 CD82 10133 -0.0078 0.13 NO
43 MDM2 MDM2 MDM2 10324 -0.012 0.12 NO
44 EI24 EI24 EI24 10325 -0.012 0.12 NO
45 SHISA5 SHISA5 SHISA5 10707 -0.018 0.11 NO
46 CCNE1 CCNE1 CCNE1 11886 -0.043 0.047 NO
47 BAX BAX BAX 11962 -0.045 0.047 NO
48 CYCS CYCS CYCS 12246 -0.051 0.037 NO
49 ATM ATM ATM 12579 -0.059 0.024 NO
50 CASP3 CASP3 CASP3 12754 -0.064 0.021 NO
51 MDM4 MDM4 MDM4 13659 -0.09 -0.019 NO
52 RCHY1 RCHY1 RCHY1 13752 -0.093 -0.015 NO
53 CCNG2 CCNG2 CCNG2 13846 -0.097 -0.011 NO
54 CCND3 CCND3 CCND3 14296 -0.12 -0.024 NO
55 PPM1D PPM1D PPM1D 14451 -0.12 -0.021 NO
56 SESN2 SESN2 SESN2 14665 -0.13 -0.02 NO
57 CASP9 CASP9 CASP9 14856 -0.14 -0.017 NO
58 CCND2 CCND2 CCND2 14891 -0.14 -0.0055 NO
59 CASP8 CASP8 CASP8 15082 -0.15 -0.0015 NO
60 CCNG1 CCNG1 CCNG1 15131 -0.15 0.01 NO
61 BBC3 BBC3 BBC3 15537 -0.18 0.0054 NO
62 APAF1 APAF1 APAF1 16089 -0.21 -0.0039 NO
63 SESN1 SESN1 SESN1 16215 -0.22 0.011 NO
64 GADD45G GADD45G GADD45G 16587 -0.26 0.015 NO
65 TP53I3 TP53I3 TP53I3 16775 -0.28 0.032 NO
66 CDKN2A CDKN2A CDKN2A 17313 -0.35 0.036 NO
67 CCNB3 CCNB3 CCNB3 17697 -0.43 0.056 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: BIOCARTA INTEGRIN PATHWAY.

Figure S30.  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: KEGG RNA DEGRADATION

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ENO2 ENO2 ENO2 1264 0.31 0.03 YES
2 MPHOSPH6 MPHOSPH6 MPHOSPH6 2534 0.19 0.021 YES
3 PAPOLB PAPOLB PAPOLB 2743 0.18 0.065 YES
4 EXOSC6 EXOSC6 EXOSC6 3018 0.16 0.1 YES
5 ENO1 ENO1 ENO1 3680 0.13 0.11 YES
6 EXOSC4 EXOSC4 EXOSC4 3736 0.13 0.14 YES
7 PAPD7 PAPD7 PAPD7 4313 0.11 0.15 YES
8 EXOSC9 EXOSC9 EXOSC9 4487 0.1 0.17 YES
9 PAPOLG PAPOLG PAPOLG 4608 0.099 0.19 YES
10 PARN PARN PARN 4626 0.098 0.22 YES
11 EXOSC2 EXOSC2 EXOSC2 4629 0.098 0.26 YES
12 C1D C1D C1D 4933 0.091 0.27 YES
13 LSM6 LSM6 LSM6 5449 0.077 0.26 YES
14 LSM4 LSM4 LSM4 5593 0.074 0.28 YES
15 EDC3 EDC3 EDC3 5723 0.071 0.3 YES
16 EXOSC3 EXOSC3 EXOSC3 6105 0.063 0.29 YES
17 LSM7 LSM7 LSM7 6229 0.061 0.31 YES
18 LSM1 LSM1 LSM1 6237 0.06 0.32 YES
19 PATL1 PATL1 PATL1 6980 0.046 0.3 YES
20 CNOT3 CNOT3 CNOT3 7081 0.044 0.31 YES
21 WDR61 WDR61 WDR61 7312 0.04 0.31 YES
22 PNPT1 PNPT1 PNPT1 7346 0.039 0.32 YES
23 CNOT2 CNOT2 CNOT2 7630 0.035 0.32 YES
24 RQCD1 RQCD1 RQCD1 7643 0.034 0.32 YES
25 EXOSC5 EXOSC5 EXOSC5 7749 0.033 0.33 YES
26 XRN2 XRN2 XRN2 7958 0.029 0.33 YES
27 EDC4 EDC4 EDC4 8094 0.027 0.33 YES
28 XRN1 XRN1 XRN1 8237 0.024 0.33 YES
29 CNOT4 CNOT4 CNOT4 8239 0.024 0.34 YES
30 EXOSC1 EXOSC1 EXOSC1 8321 0.023 0.34 YES
31 ZCCHC7 ZCCHC7 ZCCHC7 8445 0.021 0.34 YES
32 DCPS DCPS DCPS 8451 0.021 0.34 YES
33 EXOSC8 EXOSC8 EXOSC8 8551 0.019 0.35 YES
34 EXOSC10 EXOSC10 EXOSC10 8555 0.019 0.35 YES
35 LSM5 LSM5 LSM5 8814 0.015 0.34 NO
36 NAA38 NAA38 NAA38 9027 0.011 0.34 NO
37 PAPOLA PAPOLA PAPOLA 9190 0.0085 0.33 NO
38 HSPA9 HSPA9 HSPA9 9252 0.0073 0.33 NO
39 CNOT6 CNOT6 CNOT6 9440 0.0042 0.32 NO
40 CNOT7 CNOT7 CNOT7 9594 0.0014 0.31 NO
41 SKIV2L2 SKIV2L2 SKIV2L2 9808 -0.0019 0.3 NO
42 EXOSC7 EXOSC7 EXOSC7 9861 -0.0028 0.3 NO
43 DCP2 DCP2 DCP2 10069 -0.0065 0.29 NO
44 LSM2 LSM2 LSM2 10188 -0.0087 0.29 NO
45 DDX6 DDX6 DDX6 10561 -0.016 0.27 NO
46 TTC37 TTC37 TTC37 10718 -0.019 0.27 NO
47 DIS3 DIS3 DIS3 10759 -0.019 0.27 NO
48 HSPD1 HSPD1 HSPD1 10890 -0.022 0.27 NO
49 SKIV2L SKIV2L SKIV2L 11116 -0.027 0.27 NO
50 CNOT1 CNOT1 CNOT1 11187 -0.028 0.27 NO
51 ENO3 ENO3 ENO3 11873 -0.042 0.25 NO
52 LSM3 LSM3 LSM3 12077 -0.048 0.25 NO
53 DCP1B DCP1B DCP1B 12657 -0.061 0.24 NO
54 CNOT6L CNOT6L CNOT6L 12720 -0.062 0.26 NO
55 CNOT10 CNOT10 CNOT10 12760 -0.064 0.28 NO
56 DCP1A DCP1A DCP1A 14869 -0.14 0.21 NO

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

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

genes ES table in pathway: KEGG RNA POLYMERASE

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PITX2 PITX2 PITX2 118 0.69 0.038 YES
2 WNT9A WNT9A WNT9A 143 0.67 0.079 YES
3 WNT7B WNT7B WNT7B 191 0.62 0.12 YES
4 WNT7A WNT7A WNT7A 211 0.61 0.15 YES
5 FOXN1 FOXN1 FOXN1 410 0.51 0.18 YES
6 TCF7L1 TCF7L1 TCF7L1 841 0.39 0.18 YES
7 WNT2B WNT2B WNT2B 968 0.36 0.19 YES
8 FZD6 FZD6 FZD6 999 0.36 0.22 YES
9 WISP1 WISP1 WISP1 1035 0.35 0.24 YES
10 WNT3 WNT3 WNT3 1121 0.34 0.25 YES
11 WNT10A WNT10A WNT10A 1150 0.33 0.27 YES
12 PYGO1 PYGO1 PYGO1 1311 0.3 0.28 YES
13 WNT6 WNT6 WNT6 1494 0.28 0.29 YES
14 KREMEN1 KREMEN1 KREMEN1 1542 0.28 0.31 YES
15 FZD1 FZD1 FZD1 1656 0.26 0.32 YES
16 SFRP1 SFRP1 SFRP1 1736 0.26 0.33 YES
17 T T T 1812 0.25 0.34 YES
18 WNT2 WNT2 WNT2 1821 0.25 0.36 YES
19 FOSL1 FOSL1 FOSL1 1876 0.24 0.37 YES
20 DVL2 DVL2 DVL2 2085 0.22 0.37 YES
21 WNT4 WNT4 WNT4 2111 0.22 0.38 YES
22 FZD7 FZD7 FZD7 2159 0.22 0.4 YES
23 FZD2 FZD2 FZD2 2217 0.21 0.41 YES
24 WNT5A WNT5A WNT5A 2516 0.19 0.4 YES
25 SFRP4 SFRP4 SFRP4 2658 0.18 0.41 YES
26 CTNNBIP1 CTNNBIP1 CTNNBIP1 2760 0.18 0.41 YES
27 DKK1 DKK1 DKK1 3096 0.16 0.4 YES
28 NKD1 NKD1 NKD1 3151 0.15 0.41 YES
29 WNT16 WNT16 WNT16 3341 0.14 0.41 YES
30 CCND1 CCND1 CCND1 3359 0.14 0.42 YES
31 HPRT1 HPRT1 HPRT1 3540 0.14 0.42 YES
32 LEF1 LEF1 LEF1 3583 0.13 0.42 YES
33 GAPDH GAPDH GAPDH 3601 0.13 0.43 YES
34 PORCN PORCN PORCN 3704 0.13 0.44 YES
35 SENP2 SENP2 SENP2 4076 0.12 0.42 NO
36 CSNK1A1 CSNK1A1 CSNK1A1 4500 0.1 0.41 NO
37 MYC MYC MYC 4655 0.098 0.4 NO
38 WNT5B WNT5B WNT5B 4671 0.097 0.41 NO
39 JUN JUN JUN 4688 0.097 0.42 NO
40 GSK3B GSK3B GSK3B 5154 0.084 0.4 NO
41 DAAM1 DAAM1 DAAM1 5244 0.082 0.4 NO
42 CSNK1G1 CSNK1G1 CSNK1G1 5823 0.069 0.37 NO
43 AXIN1 AXIN1 AXIN1 6183 0.062 0.35 NO
44 FBXW4 FBXW4 FBXW4 6379 0.058 0.35 NO
45 DVL1 DVL1 DVL1 7151 0.043 0.31 NO
46 PPP2CA PPP2CA PPP2CA 7217 0.042 0.31 NO
47 FZD3 FZD3 FZD3 7411 0.038 0.3 NO
48 WIF1 WIF1 WIF1 7608 0.035 0.29 NO
49 ACTB ACTB ACTB 7831 0.031 0.28 NO
50 FBXW2 FBXW2 FBXW2 8192 0.025 0.26 NO
51 EP300 EP300 EP300 8921 0.013 0.23 NO
52 BTRC BTRC BTRC 8968 0.012 0.22 NO
53 CSNK2A1 CSNK2A1 CSNK2A1 9016 0.011 0.22 NO
54 AES AES AES 9054 0.01 0.22 NO
55 FZD8 FZD8 FZD8 9295 0.0066 0.21 NO
56 WNT11 WNT11 WNT11 9847 -0.0025 0.18 NO
57 FGF4 FGF4 FGF4 10110 -0.0073 0.16 NO
58 GSK3A GSK3A GSK3A 10280 -0.011 0.16 NO
59 APC APC APC 10693 -0.018 0.14 NO
60 B2M B2M B2M 10736 -0.019 0.14 NO
61 PPP2R1A PPP2R1A PPP2R1A 10761 -0.019 0.14 NO
62 SLC9A3R1 SLC9A3R1 SLC9A3R1 10908 -0.022 0.13 NO
63 CTBP1 CTBP1 CTBP1 11551 -0.035 0.096 NO
64 FBXW11 FBXW11 FBXW11 12158 -0.05 0.067 NO
65 CTNNB1 CTNNB1 CTNNB1 12186 -0.05 0.069 NO
66 CSNK1D CSNK1D CSNK1D 12291 -0.052 0.067 NO
67 DIXDC1 DIXDC1 DIXDC1 12994 -0.07 0.034 NO
68 BCL9 BCL9 BCL9 13005 -0.07 0.037 NO
69 RPL13A RPL13A RPL13A 13340 -0.08 0.025 NO
70 TLE1 TLE1 TLE1 13875 -0.098 0.0022 NO
71 LRP6 LRP6 LRP6 14285 -0.11 -0.012 NO
72 CCND3 CCND3 CCND3 14296 -0.12 -0.0056 NO
73 CTBP2 CTBP2 CTBP2 14422 -0.12 -0.0047 NO
74 NLK NLK NLK 14426 -0.12 0.0028 NO
75 LRP5 LRP5 LRP5 14616 -0.13 0.00083 NO
76 CCND2 CCND2 CCND2 14891 -0.14 -0.0049 NO
77 CXXC4 CXXC4 CXXC4 15226 -0.16 -0.013 NO
78 TCF7 TCF7 TCF7 15685 -0.19 -0.025 NO
79 TLE2 TLE2 TLE2 16224 -0.22 -0.04 NO
80 FRAT1 FRAT1 FRAT1 16331 -0.24 -0.03 NO
81 WNT1 WNT1 WNT1 16723 -0.27 -0.034 NO
82 SOX17 SOX17 SOX17 16922 -0.3 -0.026 NO
83 FZD4 FZD4 FZD4 16983 -0.3 -0.0095 NO
84 FZD5 FZD5 FZD5 17921 -0.49 -0.028 NO
85 FRZB FRZB FRZB 18043 -0.53 -0.00094 NO
86 RHOU RHOU RHOU 18214 -0.61 0.029 NO

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

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

genes ES table in pathway: KEGG BASAL TRANSCRIPTION FACTORS

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 POLR3G POLR3G POLR3G 2618 0.18 -0.037 YES
2 POLR2J3 POLR2J3 POLR2J3 3183 0.15 0.018 YES
3 POLR2J2 POLR2J2 POLR2J2 3242 0.15 0.098 YES
4 POLR2F POLR2F POLR2F 3903 0.12 0.13 YES
5 POLR3H POLR3H POLR3H 4601 0.099 0.15 YES
6 POLR2A POLR2A POLR2A 5151 0.084 0.17 YES
7 POLR2G POLR2G POLR2G 5619 0.073 0.18 YES
8 POLR2J POLR2J POLR2J 5628 0.073 0.22 YES
9 POLR2E POLR2E POLR2E 5800 0.069 0.25 YES
10 POLR3B POLR3B POLR3B 5954 0.066 0.28 YES
11 POLR3D POLR3D POLR3D 6098 0.063 0.31 YES
12 POLR1E POLR1E POLR1E 6180 0.062 0.34 YES
13 POLR3F POLR3F POLR3F 6600 0.054 0.35 YES
14 POLR2K POLR2K POLR2K 6920 0.047 0.36 YES
15 POLR3K POLR3K POLR3K 7189 0.042 0.36 YES
16 POLR2D POLR2D POLR2D 7202 0.042 0.39 YES
17 POLR2C POLR2C POLR2C 7215 0.042 0.41 YES
18 POLR2L POLR2L POLR2L 7308 0.04 0.43 YES
19 POLR1D POLR1D POLR1D 7811 0.032 0.42 NO
20 POLR2B POLR2B POLR2B 8575 0.019 0.39 NO
21 POLR2I POLR2I POLR2I 9363 0.0054 0.35 NO
22 POLR1A POLR1A POLR1A 10269 -0.01 0.31 NO
23 POLR3C POLR3C POLR3C 10346 -0.012 0.31 NO
24 POLR3A POLR3A POLR3A 10824 -0.021 0.3 NO
25 POLR1B POLR1B POLR1B 11083 -0.026 0.3 NO
26 ZNRD1 ZNRD1 ZNRD1 12073 -0.048 0.27 NO
27 POLR3GL POLR3GL POLR3GL 12699 -0.062 0.27 NO
28 POLR1C POLR1C POLR1C 13748 -0.093 0.27 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 BASAL TRANSCRIPTION FACTORS.

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

genes ES table in pathway: KEGG SPLICEOSOME

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PGF PGF PGF 711 0.42 0.018 YES
2 TGFB3 TGFB3 TGFB3 803 0.4 0.067 YES
3 VEGFC VEGFC VEGFC 909 0.38 0.11 YES
4 SLC2A1 SLC2A1 SLC2A1 961 0.36 0.16 YES
5 TGFB1 TGFB1 TGFB1 1399 0.29 0.17 YES
6 PIK3CD PIK3CD PIK3CD 1527 0.28 0.2 YES
7 PAK6 PAK6 PAK6 1749 0.26 0.23 YES
8 AKT3 AKT3 AKT3 1795 0.25 0.26 YES
9 PAK7 PAK7 PAK7 2061 0.23 0.28 YES
10 TGFB2 TGFB2 TGFB2 2160 0.22 0.3 YES
11 TGFA TGFA TGFA 2600 0.18 0.3 YES
12 PIK3CA PIK3CA PIK3CA 3016 0.16 0.3 YES
13 CRKL CRKL CRKL 3331 0.14 0.3 YES
14 RBX1 RBX1 RBX1 3444 0.14 0.32 YES
15 VEGFB VEGFB VEGFB 3721 0.13 0.32 YES
16 EGLN3 EGLN3 EGLN3 3933 0.12 0.32 YES
17 HIF1A HIF1A HIF1A 4082 0.12 0.33 YES
18 PAK2 PAK2 PAK2 4187 0.11 0.34 YES
19 JUN JUN JUN 4688 0.097 0.32 YES
20 TCEB1 TCEB1 TCEB1 4711 0.096 0.34 YES
21 PIK3R2 PIK3R2 PIK3R2 4804 0.094 0.34 YES
22 MAP2K1 MAP2K1 MAP2K1 6094 0.063 0.28 NO
23 MAPK1 MAPK1 MAPK1 6549 0.054 0.27 NO
24 CREBBP CREBBP CREBBP 6965 0.046 0.25 NO
25 AKT1 AKT1 AKT1 7280 0.04 0.24 NO
26 ARNT2 ARNT2 ARNT2 7382 0.039 0.24 NO
27 CRK CRK CRK 7638 0.034 0.23 NO
28 RAPGEF1 RAPGEF1 RAPGEF1 7704 0.034 0.23 NO
29 BRAF BRAF BRAF 7821 0.031 0.23 NO
30 PDGFB PDGFB PDGFB 7829 0.031 0.23 NO
31 AKT2 AKT2 AKT2 7869 0.031 0.24 NO
32 MAP2K2 MAP2K2 MAP2K2 8177 0.025 0.22 NO
33 NRAS NRAS NRAS 8179 0.025 0.23 NO
34 SOS2 SOS2 SOS2 8280 0.024 0.22 NO
35 FH FH FH 8401 0.022 0.22 NO
36 RAP1B RAP1B RAP1B 8456 0.021 0.22 NO
37 FIGF FIGF FIGF 8570 0.019 0.22 NO
38 TCEB2 TCEB2 TCEB2 8605 0.018 0.22 NO
39 CDC42 CDC42 CDC42 8836 0.014 0.21 NO
40 PTPN11 PTPN11 PTPN11 8898 0.013 0.2 NO
41 EP300 EP300 EP300 8921 0.013 0.21 NO
42 SOS1 SOS1 SOS1 8948 0.012 0.21 NO
43 ARNT ARNT ARNT 9330 0.006 0.19 NO
44 FLCN FLCN FLCN 9476 0.0034 0.18 NO
45 CUL2 CUL2 CUL2 9670 0.00029 0.17 NO
46 EGLN1 EGLN1 EGLN1 9698 -0.00025 0.17 NO
47 RAC1 RAC1 RAC1 9827 -0.0021 0.16 NO
48 PAK4 PAK4 PAK4 10097 -0.007 0.15 NO
49 PAK1 PAK1 PAK1 10290 -0.011 0.14 NO
50 MET MET MET 10457 -0.014 0.13 NO
51 GRB2 GRB2 GRB2 11064 -0.025 0.1 NO
52 RAP1A RAP1A RAP1A 11532 -0.035 0.082 NO
53 GAB1 GAB1 GAB1 11999 -0.046 0.063 NO
54 PIK3R1 PIK3R1 PIK3R1 12151 -0.049 0.062 NO
55 RAF1 RAF1 RAF1 12305 -0.053 0.061 NO
56 VEGFA VEGFA VEGFA 12600 -0.059 0.053 NO
57 EPAS1 EPAS1 EPAS1 12774 -0.064 0.052 NO
58 EGLN2 EGLN2 EGLN2 13119 -0.074 0.044 NO
59 PIK3CB PIK3CB PIK3CB 13216 -0.077 0.049 NO
60 VHL VHL VHL 13530 -0.086 0.044 NO
61 KRAS KRAS KRAS 13602 -0.089 0.052 NO
62 ARAF ARAF ARAF 13759 -0.093 0.056 NO
63 ETS1 ETS1 ETS1 13880 -0.098 0.063 NO
64 MAPK3 MAPK3 MAPK3 14995 -0.15 0.023 NO
65 PIK3R3 PIK3R3 PIK3R3 15382 -0.17 0.025 NO
66 PIK3R5 PIK3R5 PIK3R5 15386 -0.17 0.047 NO
67 PAK3 PAK3 PAK3 16364 -0.24 0.026 NO
68 HGF HGF HGF 17426 -0.37 0.02 NO
69 PIK3CG PIK3CG PIK3CG 17485 -0.38 0.068 NO

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

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

genes ES table in pathway: KEGG PROTEASOME

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NTF4 NTF4 NTF4 12 0.91 0.056 YES
2 CALML3 CALML3 CALML3 71 0.74 0.1 YES
3 TP73 TP73 TP73 240 0.59 0.13 YES
4 MAPK12 MAPK12 MAPK12 278 0.56 0.16 YES
5 NGF NGF NGF 287 0.56 0.2 YES
6 NGFR NGFR NGFR 373 0.52 0.22 YES
7 NGFRAP1 NGFRAP1 NGFRAP1 487 0.48 0.25 YES
8 CALML5 CALML5 CALML5 704 0.42 0.26 YES
9 NTRK2 NTRK2 NTRK2 746 0.41 0.29 YES
10 MAPK11 MAPK11 MAPK11 756 0.41 0.31 YES
11 CAMK2B CAMK2B CAMK2B 1270 0.31 0.3 YES
12 PIK3CD PIK3CD PIK3CD 1527 0.28 0.31 YES
13 MAPK10 MAPK10 MAPK10 1597 0.27 0.32 YES
14 CAMK2A CAMK2A CAMK2A 1649 0.26 0.33 YES
15 CAMK4 CAMK4 CAMK4 1705 0.26 0.35 YES
16 AKT3 AKT3 AKT3 1795 0.25 0.36 YES
17 IRS4 IRS4 IRS4 2535 0.19 0.33 NO
18 PDK1 PDK1 PDK1 2577 0.19 0.34 NO
19 PIK3CA PIK3CA PIK3CA 3016 0.16 0.33 NO
20 SHC4 SHC4 SHC4 3253 0.15 0.32 NO
21 CRKL CRKL CRKL 3331 0.14 0.33 NO
22 YWHAQ YWHAQ YWHAQ 3388 0.14 0.33 NO
23 YWHAG YWHAG YWHAG 3563 0.14 0.33 NO
24 NFKBIA NFKBIA NFKBIA 3690 0.13 0.33 NO
25 SHC1 SHC1 SHC1 3880 0.12 0.33 NO
26 IRS2 IRS2 IRS2 4027 0.12 0.33 NO
27 NTRK1 NTRK1 NTRK1 4099 0.12 0.34 NO
28 IRS1 IRS1 IRS1 4179 0.11 0.34 NO
29 RPS6KA6 RPS6KA6 RPS6KA6 4376 0.11 0.33 NO
30 BDNF BDNF BDNF 4562 0.1 0.33 NO
31 YWHAE YWHAE YWHAE 4575 0.1 0.34 NO
32 SH2B2 SH2B2 SH2B2 4587 0.1 0.34 NO
33 JUN JUN JUN 4688 0.097 0.34 NO
34 MAPK7 MAPK7 MAPK7 4791 0.094 0.34 NO
35 PIK3R2 PIK3R2 PIK3R2 4804 0.094 0.35 NO
36 CALML6 CALML6 CALML6 4868 0.093 0.35 NO
37 PLCG1 PLCG1 PLCG1 4981 0.089 0.35 NO
38 KIDINS220 KIDINS220 KIDINS220 5104 0.086 0.35 NO
39 GSK3B GSK3B GSK3B 5154 0.084 0.35 NO
40 RPS6KA4 RPS6KA4 RPS6KA4 5580 0.074 0.33 NO
41 MAP2K7 MAP2K7 MAP2K7 5591 0.074 0.34 NO
42 BAD BAD BAD 5592 0.074 0.34 NO
43 SHC3 SHC3 SHC3 5670 0.072 0.34 NO
44 MAP2K1 MAP2K1 MAP2K1 6094 0.063 0.32 NO
45 YWHAZ YWHAZ YWHAZ 6163 0.062 0.32 NO
46 ZNF274 ZNF274 ZNF274 6211 0.061 0.32 NO
47 MAPK1 MAPK1 MAPK1 6549 0.054 0.31 NO
48 TP53 TP53 TP53 6636 0.053 0.31 NO
49 YWHAH YWHAH YWHAH 7016 0.045 0.29 NO
50 FRS2 FRS2 FRS2 7176 0.042 0.29 NO
51 AKT1 AKT1 AKT1 7280 0.04 0.28 NO
52 ABL1 ABL1 ABL1 7406 0.038 0.28 NO
53 RPS6KA5 RPS6KA5 RPS6KA5 7583 0.035 0.27 NO
54 CRK CRK CRK 7638 0.034 0.27 NO
55 RAPGEF1 RAPGEF1 RAPGEF1 7704 0.034 0.27 NO
56 BRAF BRAF BRAF 7821 0.031 0.26 NO
57 AKT2 AKT2 AKT2 7869 0.031 0.26 NO
58 MAP2K2 MAP2K2 MAP2K2 8177 0.025 0.25 NO
59 NRAS NRAS NRAS 8179 0.025 0.25 NO
60 SOS2 SOS2 SOS2 8280 0.024 0.25 NO
61 PRDM4 PRDM4 PRDM4 8319 0.023 0.25 NO
62 RAP1B RAP1B RAP1B 8456 0.021 0.24 NO
63 RELA RELA RELA 8514 0.02 0.24 NO
64 CDC42 CDC42 CDC42 8836 0.014 0.22 NO
65 PTPN11 PTPN11 PTPN11 8898 0.013 0.22 NO
66 SOS1 SOS1 SOS1 8948 0.012 0.22 NO
67 NFKB1 NFKB1 NFKB1 8992 0.012 0.22 NO
68 MAP2K5 MAP2K5 MAP2K5 9007 0.011 0.22 NO
69 ARHGDIA ARHGDIA ARHGDIA 9202 0.0082 0.21 NO
70 CALM1 CALM1 CALM1 9333 0.0059 0.2 NO
71 BCL2 BCL2 BCL2 9573 0.0018 0.19 NO
72 IRAK1 IRAK1 IRAK1 9743 -0.00094 0.18 NO
73 RAC1 RAC1 RAC1 9827 -0.0021 0.17 NO
74 ATF4 ATF4 ATF4 10054 -0.0062 0.16 NO
75 MAP3K3 MAP3K3 MAP3K3 10530 -0.015 0.14 NO
76 CAMK2D CAMK2D CAMK2D 10601 -0.017 0.14 NO
77 MAPKAPK2 MAPKAPK2 MAPKAPK2 10636 -0.017 0.13 NO
78 IRAK4 IRAK4 IRAK4 10925 -0.022 0.12 NO
79 MAPK14 MAPK14 MAPK14 10978 -0.024 0.12 NO
80 GRB2 GRB2 GRB2 11064 -0.025 0.12 NO
81 PLCG2 PLCG2 PLCG2 11138 -0.027 0.11 NO
82 CALM2 CALM2 CALM2 11456 -0.033 0.098 NO
83 RAP1A RAP1A RAP1A 11532 -0.035 0.096 NO
84 YWHAB YWHAB YWHAB 11644 -0.037 0.093 NO
85 MAGED1 MAGED1 MAGED1 11668 -0.038 0.094 NO
86 SH2B1 SH2B1 SH2B1 11705 -0.039 0.094 NO
87 CAMK2G CAMK2G CAMK2G 11755 -0.04 0.094 NO
88 MAPK9 MAPK9 MAPK9 11860 -0.042 0.092 NO
89 RPS6KA1 RPS6KA1 RPS6KA1 11880 -0.043 0.093 NO
90 BAX BAX BAX 11962 -0.045 0.092 NO
91 IKBKB IKBKB IKBKB 11989 -0.045 0.093 NO
92 GAB1 GAB1 GAB1 11999 -0.046 0.095 NO
93 MAP3K1 MAP3K1 MAP3K1 12007 -0.046 0.098 NO
94 PSEN1 PSEN1 PSEN1 12048 -0.047 0.099 NO
95 CSK CSK CSK 12144 -0.049 0.097 NO
96 PIK3R1 PIK3R1 PIK3R1 12151 -0.049 0.099 NO
97 RAF1 RAF1 RAF1 12305 -0.053 0.094 NO
98 ARHGDIB ARHGDIB ARHGDIB 12336 -0.054 0.096 NO
99 NFKBIB NFKBIB NFKBIB 12448 -0.056 0.094 NO
100 TRAF6 TRAF6 TRAF6 12598 -0.059 0.09 NO
101 MAP3K5 MAP3K5 MAP3K5 12643 -0.06 0.091 NO
102 MAPK8 MAPK8 MAPK8 12800 -0.065 0.087 NO
103 RIPK2 RIPK2 RIPK2 12812 -0.065 0.09 NO
104 MAPK13 MAPK13 MAPK13 12865 -0.067 0.092 NO
105 FOXO3 FOXO3 FOXO3 12960 -0.069 0.091 NO
106 RHOA RHOA RHOA 13180 -0.076 0.084 NO
107 PIK3CB PIK3CB PIK3CB 13216 -0.077 0.087 NO
108 KRAS KRAS KRAS 13602 -0.089 0.072 NO
109 SH2B3 SH2B3 SH2B3 13608 -0.089 0.077 NO
110 CALM3 CALM3 CALM3 14407 -0.12 0.042 NO
111 FASLG FASLG FASLG 14833 -0.14 0.027 NO
112 NTF3 NTF3 NTF3 14939 -0.14 0.031 NO
113 MAPK3 MAPK3 MAPK3 14995 -0.15 0.037 NO
114 SHC2 SHC2 SHC2 15027 -0.15 0.045 NO
115 IRAK3 IRAK3 IRAK3 15032 -0.15 0.054 NO
116 RPS6KA3 RPS6KA3 RPS6KA3 15057 -0.15 0.062 NO
117 NTRK3 NTRK3 NTRK3 15358 -0.17 0.056 NO
118 PIK3R3 PIK3R3 PIK3R3 15382 -0.17 0.065 NO
119 PIK3R5 PIK3R5 PIK3R5 15386 -0.17 0.076 NO
120 PRKCD PRKCD PRKCD 15474 -0.17 0.082 NO
121 NFKBIE NFKBIE NFKBIE 15805 -0.19 0.076 NO
122 RPS6KA2 RPS6KA2 RPS6KA2 16614 -0.26 0.049 NO
123 SORT1 SORT1 SORT1 16689 -0.27 0.062 NO
124 PIK3CG PIK3CG PIK3CG 17485 -0.38 0.043 NO
125 IRAK2 IRAK2 IRAK2 17514 -0.39 0.066 NO

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

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.41 1.6 0.049 0.87 0.75 0.4 0.24 0.3 0.52 0.3
BIOCARTA MAPK PATHWAY 86 genes.ES.table 0.38 1.8 0.0063 0.29 0.3 0.44 0.28 0.32 0 0.08
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.34 1.3 0.18 1 0.99 0.39 0.27 0.28 0.9 0.43
BIOCARTA IL1R PATHWAY 32 genes.ES.table 0.42 1.2 0.25 0.87 1 0.28 0.18 0.23 0.78 0.31
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.4 1.5 0.053 0.75 0.84 0.36 0.23 0.28 0.51 0.25
KEGG OXIDATIVE PHOSPHORYLATION 113 genes.ES.table 0.42 1.6 0.097 0.67 0.75 0.51 0.34 0.34 0.39 0.22
KEGG GLYCEROPHOSPHOLIPID METABOLISM 71 genes.ES.table 0.32 1.2 0.16 0.96 1 0.16 0.09 0.14 0.86 0.39
KEGG ETHER LIPID METABOLISM 29 genes.ES.table 0.41 1.2 0.18 0.93 1 0.21 0.083 0.19 0.83 0.37
KEGG ARACHIDONIC ACID METABOLISM 52 genes.ES.table 0.57 1.5 0.043 0.81 0.93 0.4 0.095 0.37 0.59 0.29
KEGG LINOLEIC ACID METABOLISM 25 genes.ES.table 0.6 1.4 0.1 1 0.97 0.44 0.084 0.4 0.82 0.39
genes ES table in pathway: BIOCARTA RACCYCD 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 CXCR2 CXCR2 CXCR2 117 0.82 0.1 YES
2 ATP6V0A4 ATP6V0A4 ATP6V0A4 126 0.8 0.2 YES
3 PTPRZ1 PTPRZ1 PTPRZ1 339 0.57 0.27 YES
4 MAPK10 MAPK10 MAPK10 601 0.43 0.31 YES
5 ATP6V1B1 ATP6V1B1 ATP6V1B1 1466 0.24 0.3 YES
6 HBEGF HBEGF HBEGF 1532 0.23 0.32 YES
7 ATP6V1C2 ATP6V1C2 ATP6V1C2 1620 0.22 0.34 YES
8 MAPK13 MAPK13 MAPK13 2213 0.16 0.33 YES
9 MAP2K4 MAP2K4 MAP2K4 2392 0.15 0.34 YES
10 ADAM17 ADAM17 ADAM17 2799 0.12 0.34 YES
11 ATP6V1D ATP6V1D ATP6V1D 2807 0.12 0.36 YES
12 TJP1 TJP1 TJP1 2994 0.12 0.36 YES
13 CSK CSK CSK 3030 0.11 0.37 YES
14 NFKBIA NFKBIA NFKBIA 3125 0.11 0.38 YES
15 PLCG2 PLCG2 PLCG2 3198 0.11 0.39 YES
16 ATP6V1F ATP6V1F ATP6V1F 3287 0.1 0.4 YES
17 ATP6V0D1 ATP6V0D1 ATP6V0D1 3579 0.091 0.4 YES
18 ATP6V0C ATP6V0C ATP6V0C 3612 0.09 0.41 YES
19 EGFR EGFR EGFR 3660 0.088 0.42 YES
20 ATP6V0A1 ATP6V0A1 ATP6V0A1 3783 0.084 0.42 YES
21 ATP6V1E1 ATP6V1E1 ATP6V1E1 3925 0.078 0.42 YES
22 ATP6V1A ATP6V1A ATP6V1A 3966 0.077 0.43 YES
23 IKBKB IKBKB IKBKB 4012 0.076 0.44 YES
24 F11R F11R F11R 4119 0.073 0.44 YES
25 IKBKG IKBKG IKBKG 4186 0.071 0.45 YES
26 ATP6V0E2 ATP6V0E2 ATP6V0E2 4227 0.07 0.46 YES
27 MAPK11 MAPK11 MAPK11 4320 0.067 0.46 YES
28 RAC1 RAC1 RAC1 4425 0.065 0.46 YES
29 ATP6V1H ATP6V1H ATP6V1H 4429 0.065 0.47 YES
30 MAPK14 MAPK14 MAPK14 5040 0.049 0.44 NO
31 JUN JUN JUN 5106 0.048 0.45 NO
32 ATP6V1B2 ATP6V1B2 ATP6V1B2 5368 0.042 0.44 NO
33 ATP6V1G1 ATP6V1G1 ATP6V1G1 5931 0.032 0.41 NO
34 RELA RELA RELA 6106 0.028 0.41 NO
35 NFKB1 NFKB1 NFKB1 6475 0.023 0.39 NO
36 ATP6V1E2 ATP6V1E2 ATP6V1E2 7384 0.0095 0.34 NO
37 CXCR1 CXCR1 CXCR1 8053 0.00023 0.31 NO
38 GIT1 GIT1 GIT1 8077 -0.00012 0.31 NO
39 ATP6V0B ATP6V0B ATP6V0B 8182 -0.0016 0.3 NO
40 PAK1 PAK1 PAK1 8276 -0.0029 0.3 NO
41 ATP6AP1 ATP6AP1 ATP6AP1 8419 -0.0048 0.29 NO
42 CDC42 CDC42 CDC42 9278 -0.017 0.25 NO
43 NOD1 NOD1 NOD1 9678 -0.024 0.23 NO
44 CASP3 CASP3 CASP3 10039 -0.029 0.21 NO
45 PTPN11 PTPN11 PTPN11 10631 -0.038 0.19 NO
46 CCL5 CCL5 CCL5 10826 -0.041 0.18 NO
47 MAPK8 MAPK8 MAPK8 10848 -0.041 0.18 NO
48 SRC SRC SRC 11118 -0.046 0.18 NO
49 MAPK12 MAPK12 MAPK12 11437 -0.052 0.17 NO
50 ADAM10 ADAM10 ADAM10 11652 -0.056 0.16 NO
51 CXCL1 CXCL1 CXCL1 11655 -0.056 0.17 NO
52 PLCG1 PLCG1 PLCG1 11669 -0.056 0.18 NO
53 CHUK CHUK CHUK 11796 -0.058 0.18 NO
54 ATP6V0A2 ATP6V0A2 ATP6V0A2 11913 -0.06 0.18 NO
55 ATP6V1C1 ATP6V1C1 ATP6V1C1 12155 -0.064 0.17 NO
56 LYN LYN LYN 12233 -0.066 0.18 NO
57 TCIRG1 TCIRG1 TCIRG1 12604 -0.074 0.17 NO
58 MAPK9 MAPK9 MAPK9 12828 -0.078 0.17 NO
59 JAM2 JAM2 JAM2 13163 -0.086 0.16 NO
60 MAP3K14 MAP3K14 MAP3K14 13378 -0.091 0.16 NO
61 ATP6V1G2 ATP6V1G2 ATP6V1G2 14148 -0.11 0.14 NO
62 IGSF5 IGSF5 IGSF5 14277 -0.12 0.14 NO
63 ATP6V0D2 ATP6V0D2 ATP6V0D2 14668 -0.13 0.14 NO
64 IL8 IL8 IL8 15077 -0.14 0.14 NO
65 MET MET MET 16303 -0.2 0.096 NO
66 JAM3 JAM3 JAM3 17317 -0.27 0.077 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 RACCYCD PATHWAY.

Figure S42.  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 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 MAPK10 MAPK10 MAPK10 601 0.43 0.026 YES
2 MAP3K9 MAP3K9 MAP3K9 882 0.34 0.057 YES
3 MAP3K6 MAP3K6 MAP3K6 1152 0.29 0.082 YES
4 CEBPA CEBPA CEBPA 1459 0.24 0.097 YES
5 MKNK2 MKNK2 MKNK2 1892 0.19 0.1 YES
6 TGFB1 TGFB1 TGFB1 2077 0.17 0.11 YES
7 RPS6KA5 RPS6KA5 RPS6KA5 2145 0.17 0.13 YES
8 HRAS HRAS HRAS 2177 0.16 0.15 YES
9 MAPK13 MAPK13 MAPK13 2213 0.16 0.17 YES
10 RPS6KB2 RPS6KB2 RPS6KB2 2292 0.16 0.19 YES
11 MAPK6 MAPK6 MAPK6 2296 0.16 0.21 YES
12 MAP2K4 MAP2K4 MAP2K4 2392 0.15 0.23 YES
13 MAP3K8 MAP3K8 MAP3K8 2436 0.15 0.24 YES
14 FOS FOS FOS 2496 0.14 0.26 YES
15 MAPK7 MAPK7 MAPK7 2517 0.14 0.28 YES
16 MAP3K1 MAP3K1 MAP3K1 2560 0.14 0.29 YES
17 MAP3K4 MAP3K4 MAP3K4 2638 0.13 0.31 YES
18 BRAF BRAF BRAF 2719 0.13 0.32 YES
19 MAPKAPK3 MAPKAPK3 MAPKAPK3 3045 0.11 0.32 YES
20 NFKBIA NFKBIA NFKBIA 3125 0.11 0.33 YES
21 MAP3K5 MAP3K5 MAP3K5 3182 0.11 0.34 YES
22 MYC MYC MYC 3199 0.11 0.36 YES
23 TRADD TRADD TRADD 3445 0.097 0.36 YES
24 RAF1 RAF1 RAF1 3808 0.083 0.35 YES
25 IKBKB IKBKB IKBKB 4012 0.076 0.35 YES
26 MAPK11 MAPK11 MAPK11 4320 0.067 0.34 YES
27 MAP2K2 MAP2K2 MAP2K2 4335 0.067 0.35 YES
28 RAC1 RAC1 RAC1 4425 0.065 0.35 YES
29 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 4469 0.064 0.36 YES
30 MAPK3 MAPK3 MAPK3 4498 0.063 0.36 YES
31 MAP4K5 MAP4K5 MAP4K5 4757 0.056 0.36 YES
32 RIPK1 RIPK1 RIPK1 4964 0.051 0.35 YES
33 MAX MAX MAX 4978 0.05 0.36 YES
34 RPS6KB1 RPS6KB1 RPS6KB1 5035 0.049 0.36 YES
35 MAPK14 MAPK14 MAPK14 5040 0.049 0.37 YES
36 JUN JUN JUN 5106 0.048 0.37 YES
37 MKNK1 MKNK1 MKNK1 5192 0.046 0.38 YES
38 MAPK4 MAPK4 MAPK4 5243 0.045 0.38 YES
39 MAP2K1 MAP2K1 MAP2K1 5447 0.041 0.37 NO
40 MEF2A MEF2A MEF2A 5763 0.035 0.36 NO
41 MAP2K5 MAP2K5 MAP2K5 5812 0.034 0.36 NO
42 MAP4K1 MAP4K1 MAP4K1 6040 0.03 0.36 NO
43 RELA RELA RELA 6106 0.028 0.36 NO
44 MAPK1 MAPK1 MAPK1 6249 0.026 0.35 NO
45 MAP4K4 MAP4K4 MAP4K4 6310 0.025 0.35 NO
46 NFKB1 NFKB1 NFKB1 6475 0.023 0.35 NO
47 MAPKAPK2 MAPKAPK2 MAPKAPK2 6589 0.021 0.34 NO
48 MAP2K7 MAP2K7 MAP2K7 6748 0.018 0.34 NO
49 RPS6KA4 RPS6KA4 RPS6KA4 6783 0.018 0.34 NO
50 SP1 SP1 SP1 6851 0.017 0.34 NO
51 MAP3K3 MAP3K3 MAP3K3 6934 0.016 0.33 NO
52 MAP3K10 MAP3K10 MAP3K10 7121 0.013 0.32 NO
53 MAP2K3 MAP2K3 MAP2K3 7527 0.0076 0.3 NO
54 DAXX DAXX DAXX 7976 0.0013 0.28 NO
55 GRB2 GRB2 GRB2 8128 -0.00085 0.27 NO
56 STAT1 STAT1 STAT1 8231 -0.0023 0.27 NO
57 PAK1 PAK1 PAK1 8276 -0.0029 0.27 NO
58 MAP3K7 MAP3K7 MAP3K7 8306 -0.0032 0.26 NO
59 MAP4K2 MAP4K2 MAP4K2 8400 -0.0046 0.26 NO
60 MAP3K11 MAP3K11 MAP3K11 9081 -0.015 0.23 NO
61 SHC1 SHC1 SHC1 9204 -0.016 0.22 NO
62 PAK2 PAK2 PAK2 9585 -0.022 0.2 NO
63 ARAF ARAF ARAF 10105 -0.03 0.18 NO
64 CREB1 CREB1 CREB1 10479 -0.035 0.16 NO
65 MAPK8 MAPK8 MAPK8 10848 -0.041 0.15 NO
66 MAP3K2 MAP3K2 MAP3K2 11369 -0.05 0.13 NO
67 MEF2D MEF2D MEF2D 11431 -0.052 0.13 NO
68 MAPK12 MAPK12 MAPK12 11437 -0.052 0.14 NO
69 MAP2K6 MAP2K6 MAP2K6 11540 -0.054 0.14 NO
70 RPS6KA3 RPS6KA3 RPS6KA3 11702 -0.056 0.14 NO
71 MAPKAPK5 MAPKAPK5 MAPKAPK5 11764 -0.058 0.15 NO
72 CHUK CHUK CHUK 11796 -0.058 0.15 NO
73 MAP4K3 MAP4K3 MAP4K3 12227 -0.066 0.14 NO
74 RPS6KA2 RPS6KA2 RPS6KA2 12480 -0.071 0.13 NO
75 TGFBR1 TGFBR1 TGFBR1 12526 -0.072 0.14 NO
76 MAPK9 MAPK9 MAPK9 12828 -0.078 0.14 NO
77 MAP3K14 MAP3K14 MAP3K14 13378 -0.091 0.12 NO
78 RPS6KA1 RPS6KA1 RPS6KA1 13399 -0.092 0.13 NO
79 ELK1 ELK1 ELK1 13436 -0.093 0.14 NO
80 ATF2 ATF2 ATF2 13712 -0.1 0.14 NO
81 MAP3K12 MAP3K12 MAP3K12 13921 -0.11 0.14 NO
82 TRAF2 TRAF2 TRAF2 13968 -0.11 0.16 NO
83 TGFB3 TGFB3 TGFB3 14792 -0.13 0.13 NO
84 RAPGEF2 RAPGEF2 RAPGEF2 14836 -0.13 0.14 NO
85 MAP3K13 MAP3K13 MAP3K13 16963 -0.24 0.063 NO
86 TGFB2 TGFB2 TGFB2 16989 -0.24 0.094 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 MAPK PATHWAY.

Figure S44.  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 CHREBP2 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 HRAS HRAS HRAS 2177 0.16 0.000082 YES
2 CDKN1A CDKN1A CDKN1A 2361 0.15 0.097 YES
3 NFKBIA NFKBIA NFKBIA 3125 0.11 0.13 YES
4 RAF1 RAF1 RAF1 3808 0.083 0.16 YES
5 CCND1 CCND1 CCND1 4011 0.076 0.2 YES
6 IKBKB IKBKB IKBKB 4012 0.076 0.25 YES
7 IKBKG IKBKG IKBKG 4186 0.071 0.29 YES
8 PIK3CA PIK3CA PIK3CA 4405 0.065 0.33 YES
9 RAC1 RAC1 RAC1 4425 0.065 0.37 YES
10 MAPK3 MAPK3 MAPK3 4498 0.063 0.41 YES
11 RB1 RB1 RB1 5502 0.04 0.39 NO
12 RELA RELA RELA 6106 0.028 0.37 NO
13 MAPK1 MAPK1 MAPK1 6249 0.026 0.38 NO
14 TFDP1 TFDP1 TFDP1 6293 0.025 0.4 NO
15 NFKB1 NFKB1 NFKB1 6475 0.023 0.41 NO
16 RHOA RHOA RHOA 6760 0.018 0.4 NO
17 CCNE1 CCNE1 CCNE1 7745 0.0044 0.35 NO
18 CDKN1B CDKN1B CDKN1B 8265 -0.0027 0.33 NO
19 PAK1 PAK1 PAK1 8276 -0.0029 0.33 NO
20 AKT1 AKT1 AKT1 9857 -0.026 0.26 NO
21 CDK6 CDK6 CDK6 10360 -0.033 0.26 NO
22 CDK4 CDK4 CDK4 11178 -0.047 0.25 NO
23 PIK3R1 PIK3R1 PIK3R1 11749 -0.057 0.26 NO
24 CHUK CHUK CHUK 11796 -0.058 0.3 NO
25 CDK2 CDK2 CDK2 13848 -0.1 0.26 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 CHREBP2 PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA IL1R PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ATP6V0A4 ATP6V0A4 ATP6V0A4 126 0.8 0.11 YES
2 ATP12A ATP12A ATP12A 234 0.65 0.2 YES
3 NDUFA4L2 NDUFA4L2 NDUFA4L2 720 0.39 0.23 YES
4 ATP6V1B1 ATP6V1B1 ATP6V1B1 1466 0.24 0.22 YES
5 ATP6V1C2 ATP6V1C2 ATP6V1C2 1620 0.22 0.25 YES
6 ATP6V1D ATP6V1D ATP6V1D 2807 0.12 0.2 YES
7 LHPP LHPP LHPP 3088 0.11 0.2 YES
8 ATP6V1F ATP6V1F ATP6V1F 3287 0.1 0.21 YES
9 ATP5A1 ATP5A1 ATP5A1 3488 0.094 0.21 YES
10 ATP6V0D1 ATP6V0D1 ATP6V0D1 3579 0.091 0.22 YES
11 NDUFS4 NDUFS4 NDUFS4 3604 0.09 0.23 YES
12 ATP6V0C ATP6V0C ATP6V0C 3612 0.09 0.24 YES
13 ATP6V0A1 ATP6V0A1 ATP6V0A1 3783 0.084 0.25 YES
14 NDUFA11 NDUFA11 NDUFA11 3874 0.08 0.25 YES
15 ATP6V1E1 ATP6V1E1 ATP6V1E1 3925 0.078 0.26 YES
16 ATP5H ATP5H ATP5H 3956 0.077 0.27 YES
17 ATP6V1A ATP6V1A ATP6V1A 3966 0.077 0.28 YES
18 NDUFS8 NDUFS8 NDUFS8 4010 0.076 0.29 YES
19 ATP5J ATP5J ATP5J 4217 0.07 0.29 YES
20 NDUFB4 NDUFB4 NDUFB4 4225 0.07 0.3 YES
21 ATP6V0E2 ATP6V0E2 ATP6V0E2 4227 0.07 0.31 YES
22 NDUFS7 NDUFS7 NDUFS7 4258 0.069 0.32 YES
23 ATP6V1H ATP6V1H ATP6V1H 4429 0.065 0.32 YES
24 ATP5D ATP5D ATP5D 4485 0.063 0.33 YES
25 ATP5I ATP5I ATP5I 4500 0.063 0.33 YES
26 ATP4A ATP4A ATP4A 4581 0.06 0.34 YES
27 NDUFV1 NDUFV1 NDUFV1 4727 0.057 0.34 YES
28 NDUFS5 NDUFS5 NDUFS5 4894 0.052 0.34 YES
29 NDUFA10 NDUFA10 NDUFA10 4974 0.051 0.34 YES
30 ATP6V0E1 ATP6V0E1 ATP6V0E1 5063 0.048 0.34 YES
31 UQCRC2 UQCRC2 UQCRC2 5112 0.048 0.35 YES
32 NDUFB3 NDUFB3 NDUFB3 5181 0.046 0.35 YES
33 UQCRFS1 UQCRFS1 UQCRFS1 5259 0.044 0.35 YES
34 NDUFB7 NDUFB7 NDUFB7 5358 0.043 0.35 YES
35 ATP6V1B2 ATP6V1B2 ATP6V1B2 5368 0.042 0.36 YES
36 NDUFV3 NDUFV3 NDUFV3 5390 0.042 0.36 YES
37 NDUFA9 NDUFA9 NDUFA9 5487 0.04 0.37 YES
38 UQCR11 UQCR11 UQCR11 5530 0.039 0.37 YES
39 COX6B1 COX6B1 COX6B1 5535 0.039 0.38 YES
40 COX5A COX5A COX5A 5559 0.038 0.38 YES
41 NDUFB1 NDUFB1 NDUFB1 5607 0.038 0.38 YES
42 COX7B COX7B COX7B 5644 0.037 0.38 YES
43 COX8A COX8A COX8A 5647 0.037 0.39 YES
44 UQCRQ UQCRQ UQCRQ 5697 0.036 0.39 YES
45 ATP5G3 ATP5G3 ATP5G3 5741 0.035 0.4 YES
46 ATP5O ATP5O ATP5O 5787 0.035 0.4 YES
47 PPA2 PPA2 PPA2 5811 0.034 0.4 YES
48 NDUFB5 NDUFB5 NDUFB5 5860 0.033 0.4 YES
49 UQCRHL UQCRHL UQCRHL 5929 0.032 0.41 YES
50 ATP6V1G1 ATP6V1G1 ATP6V1G1 5931 0.032 0.41 YES
51 SDHC SDHC SDHC 5994 0.031 0.41 YES
52 NDUFB10 NDUFB10 NDUFB10 6034 0.03 0.41 YES
53 ATP5F1 ATP5F1 ATP5F1 6116 0.028 0.41 YES
54 COX10 COX10 COX10 6153 0.028 0.42 YES
55 NDUFS6 NDUFS6 NDUFS6 6182 0.027 0.42 YES
56 NDUFA6 NDUFA6 NDUFA6 6230 0.026 0.42 YES
57 ATP5B ATP5B ATP5B 6281 0.026 0.42 YES
58 UQCR10 UQCR10 UQCR10 6306 0.025 0.42 YES
59 NDUFC1 NDUFC1 NDUFC1 6468 0.023 0.42 NO
60 NDUFV2 NDUFV2 NDUFV2 6616 0.02 0.41 NO
61 COX5B COX5B COX5B 6650 0.02 0.41 NO
62 COX4I1 COX4I1 COX4I1 6714 0.019 0.41 NO
63 ATP5G2 ATP5G2 ATP5G2 6879 0.017 0.41 NO
64 COX6A1 COX6A1 COX6A1 6890 0.016 0.41 NO
65 UQCRC1 UQCRC1 UQCRC1 6914 0.016 0.41 NO
66 COX6C COX6C COX6C 6946 0.016 0.41 NO
67 COX7C COX7C COX7C 6956 0.016 0.41 NO
68 ATP5L ATP5L ATP5L 6983 0.015 0.41 NO
69 COX7A2 COX7A2 COX7A2 6993 0.015 0.42 NO
70 ATP5C1 ATP5C1 ATP5C1 7277 0.011 0.4 NO
71 ATP5G1 ATP5G1 ATP5G1 7370 0.0097 0.4 NO
72 ATP6V1E2 ATP6V1E2 ATP6V1E2 7384 0.0095 0.4 NO
73 UQCRH UQCRH UQCRH 7453 0.0086 0.4 NO
74 SDHD SDHD SDHD 7528 0.0076 0.39 NO
75 NDUFA7 NDUFA7 NDUFA7 7615 0.0065 0.39 NO
76 NDUFC2 NDUFC2 NDUFC2 7734 0.0046 0.38 NO
77 NDUFS3 NDUFS3 NDUFS3 7886 0.0025 0.38 NO
78 NDUFB8 NDUFB8 NDUFB8 7893 0.0025 0.38 NO
79 NDUFB6 NDUFB6 NDUFB6 8176 -0.0015 0.36 NO
80 ATP6V0B ATP6V0B ATP6V0B 8182 -0.0016 0.36 NO
81 CYC1 CYC1 CYC1 8211 -0.0021 0.36 NO
82 NDUFAB1 NDUFAB1 NDUFAB1 8226 -0.0023 0.36 NO
83 NDUFB9 NDUFB9 NDUFB9 8285 -0.003 0.36 NO
84 ATP5E ATP5E ATP5E 8328 -0.0035 0.36 NO
85 ATP6AP1 ATP6AP1 ATP6AP1 8419 -0.0048 0.35 NO
86 NDUFS2 NDUFS2 NDUFS2 8481 -0.0058 0.35 NO
87 NDUFA1 NDUFA1 NDUFA1 8512 -0.0062 0.35 NO
88 NDUFA4 NDUFA4 NDUFA4 8673 -0.0086 0.34 NO
89 NDUFA2 NDUFA2 NDUFA2 8691 -0.0089 0.34 NO
90 NDUFS1 NDUFS1 NDUFS1 8716 -0.0093 0.34 NO
91 UQCRB UQCRB UQCRB 8760 -0.0099 0.34 NO
92 ATP5J2 ATP5J2 ATP5J2 8891 -0.012 0.34 NO
93 NDUFA3 NDUFA3 NDUFA3 9112 -0.015 0.33 NO
94 NDUFB2 NDUFB2 NDUFB2 9143 -0.016 0.33 NO
95 SDHB SDHB SDHB 9977 -0.028 0.29 NO
96 COX7A2L COX7A2L COX7A2L 10390 -0.034 0.27 NO
97 NDUFA8 NDUFA8 NDUFA8 10401 -0.034 0.27 NO
98 COX17 COX17 COX17 10499 -0.036 0.27 NO
99 PPA1 PPA1 PPA1 10535 -0.036 0.28 NO
100 COX15 COX15 COX15 10586 -0.037 0.28 NO
101 COX6B2 COX6B2 COX6B2 10865 -0.042 0.27 NO
102 ATP4B ATP4B ATP4B 10892 -0.042 0.28 NO
103 NDUFA5 NDUFA5 NDUFA5 11879 -0.06 0.23 NO
104 ATP6V0A2 ATP6V0A2 ATP6V0A2 11913 -0.06 0.24 NO
105 ATP6V1C1 ATP6V1C1 ATP6V1C1 12155 -0.064 0.23 NO
106 SDHA SDHA SDHA 12164 -0.065 0.24 NO
107 COX8C COX8C COX8C 12298 -0.067 0.25 NO
108 TCIRG1 TCIRG1 TCIRG1 12604 -0.074 0.24 NO
109 COX11 COX11 COX11 13686 -0.1 0.2 NO
110 ATP6V1G2 ATP6V1G2 ATP6V1G2 14148 -0.11 0.19 NO
111 COX7A1 COX7A1 COX7A1 14303 -0.12 0.2 NO
112 ATP6V0D2 ATP6V0D2 ATP6V0D2 14668 -0.13 0.2 NO
113 COX4I2 COX4I2 COX4I2 15399 -0.15 0.18 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 IL1R PATHWAY.

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

genes ES table in pathway: BIOCARTA WNT 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 WIF1 WIF1 WIF1 1352 0.25 0.082 YES
2 LEF1 LEF1 LEF1 2848 0.12 0.078 YES
3 CSNK1A1 CSNK1A1 CSNK1A1 2903 0.12 0.15 YES
4 BTRC BTRC BTRC 3192 0.11 0.2 YES
5 MYC MYC MYC 3199 0.11 0.26 YES
6 APC APC APC 3487 0.094 0.31 YES
7 FZD1 FZD1 FZD1 3837 0.082 0.34 YES
8 CCND1 CCND1 CCND1 4011 0.076 0.37 YES
9 PPP2CA PPP2CA PPP2CA 4243 0.07 0.4 YES
10 GSK3B GSK3B GSK3B 5503 0.04 0.36 NO
11 TAB1 TAB1 TAB1 5865 0.033 0.36 NO
12 DVL1 DVL1 DVL1 6706 0.019 0.33 NO
13 CREBBP CREBBP CREBBP 7253 0.011 0.31 NO
14 FRAT1 FRAT1 FRAT1 7447 0.0086 0.3 NO
15 SMAD4 SMAD4 SMAD4 7755 0.0041 0.29 NO
16 MAP3K7 MAP3K7 MAP3K7 8306 -0.0032 0.26 NO
17 HDAC1 HDAC1 HDAC1 9007 -0.014 0.23 NO
18 CSNK1D CSNK1D CSNK1D 9151 -0.016 0.23 NO
19 CSNK2A1 CSNK2A1 CSNK2A1 9646 -0.023 0.22 NO
20 AXIN1 AXIN1 AXIN1 9872 -0.026 0.22 NO
21 CTNNB1 CTNNB1 CTNNB1 10127 -0.03 0.23 NO
22 CTBP1 CTBP1 CTBP1 11793 -0.058 0.18 NO
23 TLE1 TLE1 TLE1 12832 -0.078 0.17 NO
24 NLK NLK NLK 14164 -0.11 0.17 NO
25 WNT1 WNT1 WNT1 14741 -0.13 0.21 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 WNT PATHWAY.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

Table 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 TP53AIP1 TP53AIP1 TP53AIP1 228 0.66 0.073 YES
2 SESN3 SESN3 SESN3 542 0.45 0.11 YES
3 SFN SFN SFN 616 0.42 0.16 YES
4 SERPINB5 SERPINB5 SERPINB5 727 0.38 0.21 YES
5 PERP PERP PERP 931 0.33 0.24 YES
6 TP73 TP73 TP73 1175 0.28 0.26 YES
7 TP53I3 TP53I3 TP53I3 1222 0.27 0.3 YES
8 RPRM RPRM RPRM 1417 0.24 0.32 YES
9 BAI1 BAI1 BAI1 1609 0.22 0.34 YES
10 DDB2 DDB2 DDB2 1955 0.18 0.34 YES
11 CDKN1A CDKN1A CDKN1A 2361 0.15 0.34 YES
12 CCNG2 CCNG2 CCNG2 2382 0.15 0.36 YES
13 PMAIP1 PMAIP1 PMAIP1 2539 0.14 0.37 YES
14 CD82 CD82 CD82 2796 0.12 0.37 YES
15 SESN2 SESN2 SESN2 2955 0.12 0.38 YES
16 MDM2 MDM2 MDM2 3667 0.088 0.35 NO
17 CCND1 CCND1 CCND1 4011 0.076 0.34 NO
18 IGF1 IGF1 IGF1 4373 0.066 0.33 NO
19 TSC2 TSC2 TSC2 4895 0.052 0.31 NO
20 SHISA5 SHISA5 SHISA5 4923 0.052 0.32 NO
21 CASP9 CASP9 CASP9 5492 0.04 0.29 NO
22 RFWD2 RFWD2 RFWD2 6190 0.027 0.26 NO
23 ZMAT3 ZMAT3 ZMAT3 6280 0.026 0.25 NO
24 PPM1D PPM1D PPM1D 6311 0.025 0.26 NO
25 PTEN PTEN PTEN 7382 0.0096 0.2 NO
26 CCNE1 CCNE1 CCNE1 7745 0.0044 0.18 NO
27 EI24 EI24 EI24 8094 -0.00039 0.16 NO
28 ATR ATR ATR 8099 -0.00044 0.16 NO
29 TP53 TP53 TP53 8118 -0.00073 0.16 NO
30 LRDD LRDD LRDD 8267 -0.0028 0.15 NO
31 CYCS CYCS CYCS 8723 -0.0093 0.13 NO
32 SIAH1 SIAH1 SIAH1 8766 -0.01 0.13 NO
33 RRM2B RRM2B RRM2B 9199 -0.016 0.11 NO
34 CCNG1 CCNG1 CCNG1 9587 -0.022 0.091 NO
35 SESN1 SESN1 SESN1 9631 -0.023 0.092 NO
36 GADD45A GADD45A GADD45A 9807 -0.026 0.086 NO
37 MDM4 MDM4 MDM4 9836 -0.026 0.088 NO
38 FAS FAS FAS 9902 -0.027 0.088 NO
39 CCND3 CCND3 CCND3 10020 -0.028 0.085 NO
40 CASP3 CASP3 CASP3 10039 -0.029 0.088 NO
41 CDK6 CDK6 CDK6 10360 -0.033 0.075 NO
42 GADD45B GADD45B GADD45B 10442 -0.035 0.075 NO
43 BAX BAX BAX 10501 -0.036 0.077 NO
44 CCND2 CCND2 CCND2 10521 -0.036 0.08 NO
45 RRM2 RRM2 RRM2 11020 -0.044 0.059 NO
46 CDK4 CDK4 CDK4 11178 -0.047 0.057 NO
47 RCHY1 RCHY1 RCHY1 11371 -0.05 0.053 NO
48 CHEK2 CHEK2 CHEK2 11401 -0.051 0.058 NO
49 CCNE2 CCNE2 CCNE2 11744 -0.057 0.047 NO
50 IGFBP3 IGFBP3 IGFBP3 11952 -0.061 0.044 NO
51 CCNB1 CCNB1 CCNB1 12531 -0.072 0.022 NO
52 CCNB2 CCNB2 CCNB2 13126 -0.085 0.0017 NO
53 CDKN2A CDKN2A CDKN2A 13198 -0.087 0.0092 NO
54 BID BID BID 13361 -0.091 0.012 NO
55 CASP8 CASP8 CASP8 13529 -0.095 0.016 NO
56 CDK2 CDK2 CDK2 13848 -0.1 0.012 NO
57 CHEK1 CHEK1 CHEK1 14730 -0.13 -0.018 NO
58 CDK1 CDK1 CDK1 14884 -0.14 -0.0092 NO
59 ATM ATM ATM 15176 -0.14 -0.0061 NO
60 SERPINE1 SERPINE1 SERPINE1 15258 -0.15 0.0088 NO
61 GADD45G GADD45G GADD45G 15426 -0.16 0.02 NO
62 GTSE1 GTSE1 GTSE1 15654 -0.16 0.029 NO
63 TNFRSF10B TNFRSF10B TNFRSF10B 16043 -0.18 0.032 NO
64 APAF1 APAF1 APAF1 16325 -0.2 0.043 NO
65 THBS1 THBS1 THBS1 16466 -0.21 0.062 NO
66 CCNB3 CCNB3 CCNB3 16566 -0.21 0.085 NO
67 BBC3 BBC3 BBC3 17062 -0.25 0.09 NO

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

Figure S52.  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 GLYCEROPHOSPHOLIPID 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 ALOX12 ALOX12 ALOX12 72 0.93 0.062 YES
2 PLA2G4E PLA2G4E PLA2G4E 109 0.84 0.12 YES
3 ALOX12B ALOX12B ALOX12B 153 0.75 0.17 YES
4 ALOX15B ALOX15B ALOX15B 155 0.75 0.22 YES
5 PLA2G3 PLA2G3 PLA2G3 204 0.69 0.27 YES
6 CBR3 CBR3 CBR3 307 0.59 0.3 YES
7 CYP2C18 CYP2C18 CYP2C18 350 0.56 0.34 YES
8 GGT6 GGT6 GGT6 385 0.54 0.38 YES
9 CYP2C19 CYP2C19 CYP2C19 554 0.44 0.4 YES
10 GPX3 GPX3 GPX3 654 0.41 0.42 YES
11 CYP4F3 CYP4F3 CYP4F3 704 0.39 0.45 YES
12 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 782 0.37 0.47 YES
13 CYP2C9 CYP2C9 CYP2C9 1061 0.3 0.48 YES
14 ALOX15 ALOX15 ALOX15 1253 0.27 0.49 YES
15 CBR1 CBR1 CBR1 1331 0.26 0.5 YES
16 PLA2G2F PLA2G2F PLA2G2F 1559 0.22 0.5 YES
17 CYP4A11 CYP4A11 CYP4A11 1560 0.22 0.52 YES
18 CYP2E1 CYP2E1 CYP2E1 1566 0.22 0.54 YES
19 EPHX2 EPHX2 EPHX2 1573 0.22 0.55 YES
20 CYP4A22 CYP4A22 CYP4A22 1634 0.21 0.56 YES
21 PTGS1 PTGS1 PTGS1 1775 0.2 0.57 YES
22 AKR1C3 AKR1C3 AKR1C3 2386 0.15 0.55 NO
23 LTA4H LTA4H LTA4H 2523 0.14 0.55 NO
24 PLA2G4A PLA2G4A PLA2G4A 3253 0.1 0.52 NO
25 PTGES PTGES PTGES 3320 0.1 0.52 NO
26 LTC4S LTC4S LTC4S 3873 0.08 0.5 NO
27 PLA2G2D PLA2G2D PLA2G2D 4339 0.066 0.48 NO
28 PTGDS PTGDS PTGDS 5057 0.048 0.44 NO
29 GPX2 GPX2 GPX2 5721 0.036 0.41 NO
30 PTGIS PTGIS PTGIS 6383 0.024 0.38 NO
31 GPX4 GPX4 GPX4 6516 0.022 0.37 NO
32 HPGDS HPGDS HPGDS 7218 0.012 0.33 NO
33 PLA2G12A PLA2G12A PLA2G12A 7299 0.011 0.33 NO
34 GPX1 GPX1 GPX1 8174 -0.0015 0.28 NO
35 PLA2G6 PLA2G6 PLA2G6 9298 -0.018 0.22 NO
36 GPX7 GPX7 GPX7 10811 -0.041 0.15 NO
37 PLA2G5 PLA2G5 PLA2G5 10869 -0.042 0.15 NO
38 PTGES2 PTGES2 PTGES2 12848 -0.079 0.047 NO
39 CYP2C8 CYP2C8 CYP2C8 13858 -0.1 0.00022 NO
40 PLA2G2A PLA2G2A PLA2G2A 14427 -0.12 -0.022 NO
41 GGT7 GGT7 GGT7 15509 -0.16 -0.068 NO
42 PTGS2 PTGS2 PTGS2 16031 -0.18 -0.083 NO
43 GGT1 GGT1 GGT1 17201 -0.26 -0.13 NO
44 CYP2U1 CYP2U1 CYP2U1 17220 -0.26 -0.11 NO
45 PLA2G1B PLA2G1B PLA2G1B 17432 -0.28 -0.1 NO
46 ALOX5 ALOX5 ALOX5 17508 -0.29 -0.085 NO
47 CYP4F2 CYP4F2 CYP4F2 17527 -0.29 -0.066 NO
48 GGT5 GGT5 GGT5 17599 -0.29 -0.049 NO
49 PLA2G12B PLA2G12B PLA2G12B 17745 -0.31 -0.035 NO
50 TBXAS1 TBXAS1 TBXAS1 18323 -0.4 -0.038 NO
51 PLA2G10 PLA2G10 PLA2G10 18341 -0.4 -0.01 NO
52 CYP2B6 CYP2B6 CYP2B6 18511 -0.45 0.013 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 GLYCEROPHOSPHOLIPID METABOLISM.

Figure S54.  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 ETHER LIPID 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 HES5 HES5 HES5 87 0.89 0.19 YES
2 NOTCH3 NOTCH3 NOTCH3 1591 0.22 0.16 YES
3 MAML3 MAML3 MAML3 1595 0.22 0.2 YES
4 KAT2B KAT2B KAT2B 1606 0.22 0.25 YES
5 DTX2 DTX2 DTX2 2577 0.14 0.23 YES
6 NOTCH2 NOTCH2 NOTCH2 2692 0.13 0.25 YES
7 ADAM17 ADAM17 ADAM17 2799 0.12 0.27 YES
8 JAG1 JAG1 JAG1 2878 0.12 0.29 YES
9 DTX1 DTX1 DTX1 2886 0.12 0.32 YES
10 HES1 HES1 HES1 2972 0.12 0.34 YES
11 JAG2 JAG2 JAG2 3401 0.098 0.34 YES
12 DVL3 DVL3 DVL3 4141 0.072 0.31 YES
13 DVL2 DVL2 DVL2 4180 0.071 0.33 YES
14 NUMBL NUMBL NUMBL 4213 0.07 0.34 YES
15 DLL3 DLL3 DLL3 4319 0.067 0.35 YES
16 DLL1 DLL1 DLL1 5651 0.037 0.28 NO
17 EP300 EP300 EP300 5760 0.035 0.29 NO
18 DTX3 DTX3 DTX3 6074 0.029 0.28 NO
19 DVL1 DVL1 DVL1 6706 0.019 0.25 NO
20 RFNG RFNG RFNG 6846 0.017 0.24 NO
21 NOTCH1 NOTCH1 NOTCH1 7197 0.012 0.23 NO
22 CREBBP CREBBP CREBBP 7253 0.011 0.23 NO
23 SNW1 SNW1 SNW1 7910 0.0023 0.19 NO
24 NUMB NUMB NUMB 8019 0.00062 0.19 NO
25 PSEN1 PSEN1 PSEN1 8263 -0.0027 0.17 NO
26 PSENEN PSENEN PSENEN 8278 -0.003 0.17 NO
27 APH1A APH1A APH1A 8302 -0.0032 0.17 NO
28 HDAC1 HDAC1 HDAC1 9007 -0.014 0.14 NO
29 MAML1 MAML1 MAML1 9178 -0.016 0.13 NO
30 HDAC2 HDAC2 HDAC2 9569 -0.022 0.12 NO
31 NCSTN NCSTN NCSTN 9663 -0.024 0.12 NO
32 PTCRA PTCRA PTCRA 9949 -0.028 0.11 NO
33 DTX3L DTX3L DTX3L 10137 -0.03 0.1 NO
34 PSEN2 PSEN2 PSEN2 10598 -0.037 0.088 NO
35 CIR1 CIR1 CIR1 10906 -0.042 0.081 NO
36 KAT2A KAT2A KAT2A 11138 -0.046 0.078 NO
37 CTBP1 CTBP1 CTBP1 11793 -0.058 0.056 NO
38 MAML2 MAML2 MAML2 11884 -0.06 0.064 NO
39 RBPJ RBPJ RBPJ 12260 -0.067 0.058 NO
40 NCOR2 NCOR2 NCOR2 12350 -0.069 0.068 NO
41 CTBP2 CTBP2 CTBP2 13115 -0.085 0.046 NO
42 RBPJL RBPJL RBPJL 13533 -0.095 0.044 NO
43 NOTCH4 NOTCH4 NOTCH4 14823 -0.13 0.004 NO
44 LFNG LFNG LFNG 17607 -0.3 -0.081 NO
45 DLL4 DLL4 DLL4 17811 -0.32 -0.023 NO
46 DTX4 DTX4 DTX4 17964 -0.34 0.042 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 ETHER LIPID METABOLISM.

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

genes ES table in pathway: KEGG ARACHIDONIC ACID METABOLISM

Table 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 PLA2G4E PLA2G4E PLA2G4E 109 0.84 0.12 YES
2 PLA2G3 PLA2G3 PLA2G3 204 0.69 0.22 YES
3 CYP2C18 CYP2C18 CYP2C18 350 0.56 0.29 YES
4 AKR1B10 AKR1B10 AKR1B10 481 0.48 0.36 YES
5 CYP2C19 CYP2C19 CYP2C19 554 0.44 0.42 YES
6 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 782 0.37 0.46 YES
7 CYP2C9 CYP2C9 CYP2C9 1061 0.3 0.49 YES
8 ALOX15 ALOX15 ALOX15 1253 0.27 0.52 YES
9 PLA2G2F PLA2G2F PLA2G2F 1559 0.22 0.54 YES
10 CYP2E1 CYP2E1 CYP2E1 1566 0.22 0.57 YES
11 CYP1A2 CYP1A2 CYP1A2 1584 0.22 0.6 YES
12 CYP2J2 CYP2J2 CYP2J2 2342 0.15 0.59 NO
13 PLA2G4A PLA2G4A PLA2G4A 3253 0.1 0.55 NO
14 CYP3A5 CYP3A5 CYP3A5 3983 0.077 0.53 NO
15 PLA2G2D PLA2G2D PLA2G2D 4339 0.066 0.52 NO
16 PLA2G12A PLA2G12A PLA2G12A 7299 0.011 0.36 NO
17 PLA2G6 PLA2G6 PLA2G6 9298 -0.018 0.26 NO
18 PLA2G5 PLA2G5 PLA2G5 10869 -0.042 0.18 NO
19 CYP2C8 CYP2C8 CYP2C8 13858 -0.1 0.035 NO
20 PLA2G2A PLA2G2A PLA2G2A 14427 -0.12 0.023 NO
21 CYP3A43 CYP3A43 CYP3A43 15701 -0.17 -0.02 NO
22 CYP3A7 CYP3A7 CYP3A7 16881 -0.23 -0.048 NO
23 PLA2G1B PLA2G1B PLA2G1B 17432 -0.28 -0.036 NO
24 PLA2G12B PLA2G12B PLA2G12B 17745 -0.31 -0.0064 NO
25 PLA2G10 PLA2G10 PLA2G10 18341 -0.4 0.022 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 ARACHIDONIC ACID METABOLISM.

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

genes ES table in pathway: KEGG LINOLEIC ACID METABOLISM

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 CALML3 CALML3 CALML3 171 0.72 0.046 YES
2 CALML5 CALML5 CALML5 194 0.7 0.099 YES
3 NTF4 NTF4 NTF4 316 0.59 0.14 YES
4 NTRK2 NTRK2 NTRK2 531 0.46 0.16 YES
5 MAPK10 MAPK10 MAPK10 601 0.43 0.19 YES
6 NGFR NGFR NGFR 812 0.36 0.21 YES
7 NGFRAP1 NGFRAP1 NGFRAP1 1002 0.32 0.22 YES
8 NTF3 NTF3 NTF3 1067 0.3 0.24 YES
9 TP73 TP73 TP73 1175 0.28 0.26 YES
10 BDNF BDNF BDNF 1230 0.27 0.28 YES
11 RPS6KA6 RPS6KA6 RPS6KA6 1531 0.23 0.28 YES
12 IRS4 IRS4 IRS4 1902 0.19 0.27 YES
13 RPS6KA5 RPS6KA5 RPS6KA5 2145 0.17 0.27 YES
14 MAPK13 MAPK13 MAPK13 2213 0.16 0.28 YES
15 MAPK7 MAPK7 MAPK7 2517 0.14 0.28 YES
16 GAB1 GAB1 GAB1 2519 0.14 0.28 YES
17 MAP3K1 MAP3K1 MAP3K1 2560 0.14 0.29 YES
18 SORT1 SORT1 SORT1 2693 0.13 0.3 YES
19 BRAF BRAF BRAF 2719 0.13 0.3 YES
20 ZNF274 ZNF274 ZNF274 3013 0.12 0.3 YES
21 CSK CSK CSK 3030 0.11 0.31 YES
22 CAMK2B CAMK2B CAMK2B 3096 0.11 0.31 YES
23 NFKBIA NFKBIA NFKBIA 3125 0.11 0.32 YES
24 MAP3K5 MAP3K5 MAP3K5 3182 0.11 0.32 YES
25 PLCG2 PLCG2 PLCG2 3198 0.11 0.33 YES
26 BCL2 BCL2 BCL2 3292 0.1 0.33 YES
27 CAMK2A CAMK2A CAMK2A 3418 0.098 0.34 YES
28 RAF1 RAF1 RAF1 3808 0.083 0.32 YES
29 CRKL CRKL CRKL 3890 0.08 0.32 YES
30 IKBKB IKBKB IKBKB 4012 0.076 0.32 YES
31 AKT2 AKT2 AKT2 4172 0.071 0.32 YES
32 YWHAQ YWHAQ YWHAQ 4189 0.071 0.32 YES
33 MAPK11 MAPK11 MAPK11 4320 0.067 0.32 YES
34 MAP2K2 MAP2K2 MAP2K2 4335 0.067 0.33 YES
35 PIK3CA PIK3CA PIK3CA 4405 0.065 0.33 YES
36 RAC1 RAC1 RAC1 4425 0.065 0.33 YES
37 YWHAZ YWHAZ YWHAZ 4433 0.064 0.34 YES
38 SOS2 SOS2 SOS2 4471 0.064 0.34 YES
39 MAPK3 MAPK3 MAPK3 4498 0.063 0.34 YES
40 PIK3R2 PIK3R2 PIK3R2 4758 0.056 0.33 NO
41 TRAF6 TRAF6 TRAF6 4764 0.056 0.34 NO
42 CAMK2D CAMK2D CAMK2D 4783 0.055 0.34 NO
43 KIDINS220 KIDINS220 KIDINS220 4821 0.054 0.34 NO
44 PIK3CD PIK3CD PIK3CD 5038 0.049 0.33 NO
45 MAPK14 MAPK14 MAPK14 5040 0.049 0.34 NO
46 JUN JUN JUN 5106 0.048 0.34 NO
47 CALM1 CALM1 CALM1 5422 0.041 0.32 NO
48 MAP2K1 MAP2K1 MAP2K1 5447 0.041 0.33 NO
49 GSK3B GSK3B GSK3B 5503 0.04 0.33 NO
50 MAP2K5 MAP2K5 MAP2K5 5812 0.034 0.31 NO
51 PRDM4 PRDM4 PRDM4 6039 0.03 0.3 NO
52 PRKCD PRKCD PRKCD 6065 0.029 0.3 NO
53 RELA RELA RELA 6106 0.028 0.3 NO
54 BAD BAD BAD 6114 0.028 0.3 NO
55 MAPK1 MAPK1 MAPK1 6249 0.026 0.3 NO
56 IRAK4 IRAK4 IRAK4 6290 0.026 0.3 NO
57 SOS1 SOS1 SOS1 6416 0.024 0.3 NO
58 NFKB1 NFKB1 NFKB1 6475 0.023 0.29 NO
59 ATF4 ATF4 ATF4 6576 0.021 0.29 NO
60 MAPKAPK2 MAPKAPK2 MAPKAPK2 6589 0.021 0.29 NO
61 MAP2K7 MAP2K7 MAP2K7 6748 0.018 0.28 NO
62 RHOA RHOA RHOA 6760 0.018 0.28 NO
63 RPS6KA4 RPS6KA4 RPS6KA4 6783 0.018 0.28 NO
64 MAP3K3 MAP3K3 MAP3K3 6934 0.016 0.28 NO
65 CAMK2G CAMK2G CAMK2G 7154 0.013 0.27 NO
66 NTRK3 NTRK3 NTRK3 7246 0.012 0.26 NO
67 YWHAE YWHAE YWHAE 7304 0.011 0.26 NO
68 ARHGDIA ARHGDIA ARHGDIA 7599 0.0066 0.25 NO
69 NGF NGF NGF 7835 0.0031 0.23 NO
70 FOXO3 FOXO3 FOXO3 8031 0.0005 0.22 NO
71 TP53 TP53 TP53 8118 -0.00073 0.22 NO
72 GRB2 GRB2 GRB2 8128 -0.00085 0.22 NO
73 SH2B1 SH2B1 SH2B1 8156 -0.0012 0.22 NO
74 CRK CRK CRK 8222 -0.0022 0.21 NO
75 PSEN1 PSEN1 PSEN1 8263 -0.0027 0.21 NO
76 NFKBIB NFKBIB NFKBIB 8465 -0.0055 0.2 NO
77 YWHAG YWHAG YWHAG 8615 -0.0078 0.19 NO
78 PDK1 PDK1 PDK1 8811 -0.011 0.18 NO
79 FRS2 FRS2 FRS2 8855 -0.011 0.18 NO
80 SHC3 SHC3 SHC3 8991 -0.013 0.18 NO
81 SHC1 SHC1 SHC1 9204 -0.016 0.17 NO
82 CDC42 CDC42 CDC42 9278 -0.017 0.16 NO
83 NRAS NRAS NRAS 9297 -0.018 0.16 NO
84 IRAK1 IRAK1 IRAK1 9368 -0.019 0.16 NO
85 IRS2 IRS2 IRS2 9502 -0.021 0.16 NO
86 PIK3CB PIK3CB PIK3CB 9818 -0.026 0.14 NO
87 AKT1 AKT1 AKT1 9857 -0.026 0.14 NO
88 YWHAB YWHAB YWHAB 10330 -0.033 0.12 NO
89 BAX BAX BAX 10501 -0.036 0.11 NO
90 PTPN11 PTPN11 PTPN11 10631 -0.038 0.11 NO
91 KRAS KRAS KRAS 10710 -0.039 0.11 NO
92 RAP1A RAP1A RAP1A 10715 -0.039 0.11 NO
93 MAPK8 MAPK8 MAPK8 10848 -0.041 0.11 NO
94 RAP1B RAP1B RAP1B 10979 -0.044 0.1 NO
95 PIK3R3 PIK3R3 PIK3R3 11068 -0.045 0.1 NO
96 MAGED1 MAGED1 MAGED1 11315 -0.049 0.091 NO
97 MAPK12 MAPK12 MAPK12 11437 -0.052 0.089 NO
98 PLCG1 PLCG1 PLCG1 11669 -0.056 0.081 NO
99 RPS6KA3 RPS6KA3 RPS6KA3 11702 -0.056 0.083 NO
100 PIK3R1 PIK3R1 PIK3R1 11749 -0.057 0.085 NO
101 IRAK2 IRAK2 IRAK2 11782 -0.058 0.088 NO
102 ABL1 ABL1 ABL1 12402 -0.07 0.06 NO
103 RPS6KA2 RPS6KA2 RPS6KA2 12480 -0.071 0.061 NO
104 MAPK9 MAPK9 MAPK9 12828 -0.078 0.049 NO
105 ARHGDIB ARHGDIB ARHGDIB 12926 -0.081 0.05 NO
106 FASLG FASLG FASLG 13107 -0.085 0.047 NO
107 YWHAH YWHAH YWHAH 13108 -0.085 0.053 NO
108 SH2B2 SH2B2 SH2B2 13222 -0.087 0.054 NO
109 CALM2 CALM2 CALM2 13228 -0.087 0.06 NO
110 NTRK1 NTRK1 NTRK1 13327 -0.09 0.062 NO
111 CALM3 CALM3 CALM3 13394 -0.092 0.066 NO
112 RPS6KA1 RPS6KA1 RPS6KA1 13399 -0.092 0.072 NO
113 RAPGEF1 RAPGEF1 RAPGEF1 13546 -0.096 0.072 NO
114 IRS1 IRS1 IRS1 13610 -0.098 0.076 NO
115 CAMK4 CAMK4 CAMK4 14290 -0.12 0.049 NO
116 RIPK2 RIPK2 RIPK2 14999 -0.14 0.021 NO
117 PIK3CG PIK3CG PIK3CG 15902 -0.18 -0.014 NO
118 PIK3R5 PIK3R5 PIK3R5 16452 -0.21 -0.027 NO
119 AKT3 AKT3 AKT3 16541 -0.21 -0.016 NO
120 NFKBIE NFKBIE NFKBIE 16833 -0.23 -0.013 NO
121 CALML6 CALML6 CALML6 16883 -0.23 0.0021 NO
122 SHC4 SHC4 SHC4 17679 -0.3 -0.017 NO
123 SHC2 SHC2 SHC2 17697 -0.3 0.0052 NO
124 IRAK3 IRAK3 IRAK3 17905 -0.33 0.02 NO
125 SH2B3 SH2B3 SH2B3 17938 -0.33 0.044 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 LINOLEIC ACID METABOLISM.

Figure S60.  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

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 AGR PATHWAY 35 genes.ES.table 0.43 1.4 0.091 0.22 0.98 0.26 0.2 0.21 0.18 0
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.43 1.8 0.011 0.24 0.41 0.062 0.021 0.061 0 0.068
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.57 1.7 0.039 0.2 0.6 0.21 0.14 0.18 0.091 0.033
BIOCARTA BIOPEPTIDES PATHWAY 41 genes.ES.table 0.4 1.4 0.11 0.23 0.98 0.098 0.062 0.092 0.19 0
BIOCARTA HDAC PATHWAY 26 genes.ES.table 0.57 1.7 0.013 0.25 0.54 0.58 0.34 0.38 0.11 0.058
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.45 1.6 0.053 0.17 0.73 0.37 0.34 0.24 0.095 0.017
BIOCARTA ERK PATHWAY 27 genes.ES.table 0.41 1.3 0.19 0.25 0.99 0.15 0.18 0.12 0.21 0.001
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.58 1.8 0.0038 0.23 0.3 0.24 0.16 0.2 0 0.063
BIOCARTA FMLP PATHWAY 35 genes.ES.table 0.4 1.4 0.13 0.23 0.98 0.31 0.29 0.22 0.19 0
BIOCARTA GH PATHWAY 25 genes.ES.table 0.54 1.6 0.026 0.18 0.73 0.16 0.045 0.15 0.099 0.019
genes ES table in pathway: BIOCARTA AGR 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 IGF1 IGF1 IGF1 161 0.84 0.096 YES
2 RPS6KA6 RPS6KA6 RPS6KA6 369 0.72 0.18 YES
3 FIGF FIGF FIGF 647 0.62 0.24 YES
4 PIK3CG PIK3CG PIK3CG 840 0.57 0.3 YES
5 PIK3R5 PIK3R5 PIK3R5 893 0.56 0.36 YES
6 PRKAA2 PRKAA2 PRKAA2 1277 0.49 0.4 YES
7 AKT3 AKT3 AKT3 1399 0.47 0.46 YES
8 CAB39L CAB39L CAB39L 2561 0.32 0.44 YES
9 VEGFC VEGFC VEGFC 2671 0.31 0.47 YES
10 PIK3R1 PIK3R1 PIK3R1 2844 0.29 0.49 YES
11 PIK3CD PIK3CD PIK3CD 2972 0.28 0.52 YES
12 ULK2 ULK2 ULK2 4048 0.2 0.49 NO
13 RPS6KA2 RPS6KA2 RPS6KA2 4721 0.16 0.47 NO
14 VEGFB VEGFB VEGFB 5350 0.12 0.45 NO
15 PIK3R3 PIK3R3 PIK3R3 5653 0.11 0.45 NO
16 BRAF BRAF BRAF 5935 0.1 0.45 NO
17 PIK3CA PIK3CA PIK3CA 6353 0.09 0.44 NO
18 RICTOR RICTOR RICTOR 7097 0.067 0.41 NO
19 STRADA STRADA STRADA 7510 0.056 0.39 NO
20 EIF4B EIF4B EIF4B 8133 0.041 0.36 NO
21 AKT2 AKT2 AKT2 8181 0.04 0.37 NO
22 ULK1 ULK1 ULK1 8307 0.037 0.36 NO
23 TSC2 TSC2 TSC2 8449 0.034 0.36 NO
24 RPS6 RPS6 RPS6 8794 0.027 0.35 NO
25 TSC1 TSC1 TSC1 8831 0.027 0.35 NO
26 RPS6KB1 RPS6KB1 RPS6KB1 9371 0.016 0.32 NO
27 RPS6KA3 RPS6KA3 RPS6KA3 9385 0.016 0.32 NO
28 MTOR MTOR MTOR 9525 0.013 0.32 NO
29 RPTOR RPTOR RPTOR 9654 0.011 0.31 NO
30 PIK3CB PIK3CB PIK3CB 9678 0.011 0.31 NO
31 RHEB RHEB RHEB 9980 0.0055 0.3 NO
32 PDPK1 PDPK1 PDPK1 10265 -0.00038 0.28 NO
33 MAPK1 MAPK1 MAPK1 10795 -0.0096 0.25 NO
34 PRKAA1 PRKAA1 PRKAA1 10976 -0.013 0.24 NO
35 EIF4E EIF4E EIF4E 11306 -0.019 0.23 NO
36 CAB39 CAB39 CAB39 11395 -0.02 0.23 NO
37 STK11 STK11 STK11 12303 -0.037 0.18 NO
38 HIF1A HIF1A HIF1A 12605 -0.042 0.17 NO
39 AKT1 AKT1 AKT1 12804 -0.046 0.17 NO
40 RPS6KA1 RPS6KA1 RPS6KA1 12919 -0.049 0.17 NO
41 PIK3R2 PIK3R2 PIK3R2 12942 -0.049 0.17 NO
42 EIF4E2 EIF4E2 EIF4E2 13966 -0.07 0.13 NO
43 ULK3 ULK3 ULK3 14208 -0.076 0.12 NO
44 MAPK3 MAPK3 MAPK3 14344 -0.08 0.13 NO
45 DDIT4 DDIT4 DDIT4 14743 -0.09 0.12 NO
46 MLST8 MLST8 MLST8 15406 -0.11 0.094 NO
47 RPS6KB2 RPS6KB2 RPS6KB2 16389 -0.15 0.061 NO
48 VEGFA VEGFA VEGFA 17736 -0.26 0.022 NO
49 EIF4EBP1 EIF4EBP1 EIF4EBP1 17749 -0.26 0.053 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 AGR PATHWAY.

Figure S62.  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 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 RXRG RXRG RXRG 333 0.74 0.073 YES
2 PRKCB PRKCB PRKCB 391 0.71 0.16 YES
3 PIK3CG PIK3CG PIK3CG 840 0.57 0.2 YES
4 RARB RARB RARB 870 0.57 0.27 YES
5 PIK3R5 PIK3R5 PIK3R5 893 0.56 0.34 YES
6 AKT3 AKT3 AKT3 1399 0.47 0.37 YES
7 FHIT FHIT FHIT 1995 0.38 0.39 YES
8 PLCG2 PLCG2 PLCG2 2269 0.35 0.41 YES
9 PIK3R1 PIK3R1 PIK3R1 2844 0.29 0.42 YES
10 PIK3CD PIK3CD PIK3CD 2972 0.28 0.45 YES
11 RASSF5 RASSF5 RASSF5 3107 0.27 0.47 YES
12 PLCG1 PLCG1 PLCG1 5651 0.11 0.35 NO
13 PIK3R3 PIK3R3 PIK3R3 5653 0.11 0.36 NO
14 BRAF BRAF BRAF 5935 0.1 0.36 NO
15 PRKCG PRKCG PRKCG 6126 0.097 0.36 NO
16 PIK3CA PIK3CA PIK3CA 6353 0.09 0.36 NO
17 SOS2 SOS2 SOS2 6660 0.079 0.36 NO
18 STK4 STK4 STK4 6672 0.079 0.36 NO
19 PRKCA PRKCA PRKCA 7865 0.047 0.31 NO
20 FOXO3 FOXO3 FOXO3 7909 0.046 0.31 NO
21 AKT2 AKT2 AKT2 8181 0.04 0.3 NO
22 CASP9 CASP9 CASP9 8240 0.039 0.3 NO
23 SOS1 SOS1 SOS1 8280 0.038 0.3 NO
24 TP53 TP53 TP53 8629 0.031 0.29 NO
25 RASSF1 RASSF1 RASSF1 8680 0.03 0.29 NO
26 RXRB RXRB RXRB 9002 0.023 0.28 NO
27 RB1 RB1 RB1 9467 0.014 0.25 NO
28 RAF1 RAF1 RAF1 9478 0.014 0.26 NO
29 PIK3CB PIK3CB PIK3CB 9678 0.011 0.25 NO
30 EGF EGF EGF 10119 0.0024 0.22 NO
31 PDPK1 PDPK1 PDPK1 10265 -0.00038 0.22 NO
32 GRB2 GRB2 GRB2 10703 -0.0078 0.19 NO
33 MAPK1 MAPK1 MAPK1 10795 -0.0096 0.19 NO
34 EGFR EGFR EGFR 11089 -0.015 0.18 NO
35 KRAS KRAS KRAS 11141 -0.016 0.17 NO
36 BAD BAD BAD 11441 -0.021 0.16 NO
37 CCND1 CCND1 CCND1 12468 -0.04 0.11 NO
38 E2F3 E2F3 E2F3 12555 -0.041 0.11 NO
39 AKT1 AKT1 AKT1 12804 -0.046 0.1 NO
40 PIK3R2 PIK3R2 PIK3R2 12942 -0.049 0.1 NO
41 RXRA RXRA RXRA 13493 -0.059 0.08 NO
42 MAP2K2 MAP2K2 MAP2K2 13520 -0.06 0.086 NO
43 ARAF ARAF ARAF 13643 -0.063 0.087 NO
44 MAP2K1 MAP2K1 MAP2K1 13918 -0.069 0.081 NO
45 NRAS NRAS NRAS 13950 -0.07 0.088 NO
46 CDK6 CDK6 CDK6 14045 -0.072 0.092 NO
47 MAPK3 MAPK3 MAPK3 14344 -0.08 0.085 NO
48 CDK4 CDK4 CDK4 15176 -0.1 0.054 NO
49 E2F2 E2F2 E2F2 15752 -0.12 0.038 NO
50 HRAS HRAS HRAS 16464 -0.16 0.02 NO
51 ERBB2 ERBB2 ERBB2 17534 -0.24 -0.0082 NO
52 TGFA TGFA TGFA 17854 -0.28 0.0087 NO
53 CDKN2A CDKN2A CDKN2A 18136 -0.32 0.033 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 ZBTB16 ZBTB16 ZBTB16 47 0.97 0.098 YES
2 FLT3 FLT3 FLT3 112 0.89 0.19 YES
3 RUNX1T1 RUNX1T1 RUNX1T1 233 0.79 0.26 YES
4 PIK3CG PIK3CG PIK3CG 840 0.57 0.29 YES
5 KIT KIT KIT 847 0.57 0.35 YES
6 PIK3R5 PIK3R5 PIK3R5 893 0.56 0.4 YES
7 AKT3 AKT3 AKT3 1399 0.47 0.42 YES
8 SPI1 SPI1 SPI1 1789 0.41 0.45 YES
9 LEF1 LEF1 LEF1 2235 0.35 0.46 YES
10 PIK3R1 PIK3R1 PIK3R1 2844 0.29 0.46 YES
11 TCF7L1 TCF7L1 TCF7L1 2886 0.29 0.48 YES
12 PIK3CD PIK3CD PIK3CD 2972 0.28 0.51 YES
13 PIM2 PIM2 PIM2 4221 0.18 0.46 NO
14 TCF7 TCF7 TCF7 4925 0.14 0.44 NO
15 STAT5B STAT5B STAT5B 4933 0.14 0.45 NO
16 STAT5A STAT5A STAT5A 4956 0.14 0.47 NO
17 PIK3R3 PIK3R3 PIK3R3 5653 0.11 0.44 NO
18 IKBKB IKBKB IKBKB 5771 0.11 0.45 NO
19 RUNX1 RUNX1 RUNX1 5836 0.11 0.45 NO
20 BRAF BRAF BRAF 5935 0.1 0.46 NO
21 PIK3CA PIK3CA PIK3CA 6353 0.09 0.45 NO
22 SOS2 SOS2 SOS2 6660 0.079 0.44 NO
23 PIM1 PIM1 PIM1 6965 0.07 0.43 NO
24 NFKB1 NFKB1 NFKB1 7549 0.055 0.4 NO
25 AKT2 AKT2 AKT2 8181 0.04 0.37 NO
26 SOS1 SOS1 SOS1 8280 0.038 0.37 NO
27 RARA RARA RARA 8377 0.036 0.37 NO
28 PML PML PML 8641 0.031 0.36 NO
29 RPS6KB1 RPS6KB1 RPS6KB1 9371 0.016 0.32 NO
30 RAF1 RAF1 RAF1 9478 0.014 0.32 NO
31 MTOR MTOR MTOR 9525 0.013 0.32 NO
32 PIK3CB PIK3CB PIK3CB 9678 0.011 0.31 NO
33 STAT3 STAT3 STAT3 9679 0.011 0.31 NO
34 GRB2 GRB2 GRB2 10703 -0.0078 0.26 NO
35 MAPK1 MAPK1 MAPK1 10795 -0.0096 0.25 NO
36 KRAS KRAS KRAS 11141 -0.016 0.24 NO
37 BAD BAD BAD 11441 -0.021 0.22 NO
38 IKBKG IKBKG IKBKG 11619 -0.024 0.22 NO
39 CCNA1 CCNA1 CCNA1 11684 -0.025 0.22 NO
40 RELA RELA RELA 11726 -0.026 0.22 NO
41 CCND1 CCND1 CCND1 12468 -0.04 0.18 NO
42 AKT1 AKT1 AKT1 12804 -0.046 0.17 NO
43 PIK3R2 PIK3R2 PIK3R2 12942 -0.049 0.16 NO
44 CHUK CHUK CHUK 13284 -0.055 0.15 NO
45 MYC MYC MYC 13405 -0.058 0.15 NO
46 TCF7L2 TCF7L2 TCF7L2 13494 -0.059 0.15 NO
47 MAP2K2 MAP2K2 MAP2K2 13520 -0.06 0.16 NO
48 ARAF ARAF ARAF 13643 -0.063 0.16 NO
49 MAP2K1 MAP2K1 MAP2K1 13918 -0.069 0.15 NO
50 NRAS NRAS NRAS 13950 -0.07 0.16 NO
51 CEBPA CEBPA CEBPA 13969 -0.07 0.16 NO
52 MAPK3 MAPK3 MAPK3 14344 -0.08 0.15 NO
53 RPS6KB2 RPS6KB2 RPS6KB2 16389 -0.15 0.057 NO
54 HRAS HRAS HRAS 16464 -0.16 0.07 NO
55 JUP JUP JUP 17581 -0.24 0.035 NO
56 EIF4EBP1 EIF4EBP1 EIF4EBP1 17749 -0.26 0.053 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 SLC2A4 SLC2A4 SLC2A4 183 0.82 0.062 YES
2 RXRG RXRG RXRG 333 0.74 0.12 YES
3 ACSL6 ACSL6 ACSL6 613 0.62 0.16 YES
4 PRKCQ PRKCQ PRKCQ 777 0.59 0.2 YES
5 MAPK10 MAPK10 MAPK10 804 0.58 0.25 YES
6 LEPR LEPR LEPR 1267 0.49 0.27 YES
7 PRKAA2 PRKAA2 PRKAA2 1277 0.49 0.31 YES
8 IRS4 IRS4 IRS4 1363 0.48 0.35 YES
9 AKT3 AKT3 AKT3 1399 0.47 0.39 YES
10 POMC POMC POMC 1520 0.45 0.42 YES
11 ACACB ACACB ACACB 1560 0.44 0.46 YES
12 ADIPOQ ADIPOQ ADIPOQ 1823 0.41 0.48 YES
13 CPT1C CPT1C CPT1C 2114 0.37 0.49 YES
14 CD36 CD36 CD36 2236 0.35 0.52 YES
15 PPARGC1A PPARGC1A PPARGC1A 2733 0.3 0.52 YES
16 AGRP AGRP AGRP 3465 0.24 0.5 YES
17 IRS2 IRS2 IRS2 3542 0.23 0.52 YES
18 TNFRSF1B TNFRSF1B TNFRSF1B 3601 0.23 0.53 YES
19 PRKAG2 PRKAG2 PRKAG2 4321 0.18 0.51 NO
20 JAK2 JAK2 JAK2 4387 0.17 0.52 NO
21 ACSL1 ACSL1 ACSL1 5262 0.13 0.49 NO
22 SOCS3 SOCS3 SOCS3 5281 0.13 0.5 NO
23 IKBKB IKBKB IKBKB 5771 0.11 0.48 NO
24 ACSL4 ACSL4 ACSL4 6239 0.094 0.46 NO
25 NPY NPY NPY 6948 0.071 0.43 NO
26 CPT1B CPT1B CPT1B 7269 0.062 0.42 NO
27 NFKB1 NFKB1 NFKB1 7549 0.055 0.41 NO
28 PRKAB2 PRKAB2 PRKAB2 8023 0.044 0.39 NO
29 AKT2 AKT2 AKT2 8181 0.04 0.38 NO
30 PPARA PPARA PPARA 8524 0.033 0.37 NO
31 RXRB RXRB RXRB 9002 0.023 0.34 NO
32 TRADD TRADD TRADD 9147 0.02 0.34 NO
33 MAPK9 MAPK9 MAPK9 9152 0.02 0.34 NO
34 MTOR MTOR MTOR 9525 0.013 0.32 NO
35 IRS1 IRS1 IRS1 9563 0.013 0.32 NO
36 CAMKK2 CAMKK2 CAMKK2 9661 0.011 0.32 NO
37 STAT3 STAT3 STAT3 9679 0.011 0.32 NO
38 CAMKK1 CAMKK1 CAMKK1 9715 0.01 0.31 NO
39 NFKBIA NFKBIA NFKBIA 9733 0.0098 0.31 NO
40 PTPN11 PTPN11 PTPN11 9953 0.0061 0.3 NO
41 ADIPOR1 ADIPOR1 ADIPOR1 10746 -0.0087 0.26 NO
42 CPT1A CPT1A CPT1A 10844 -0.01 0.26 NO
43 PRKAA1 PRKAA1 PRKAA1 10976 -0.013 0.25 NO
44 TRAF2 TRAF2 TRAF2 11344 -0.02 0.23 NO
45 IKBKG IKBKG IKBKG 11619 -0.024 0.22 NO
46 RELA RELA RELA 11726 -0.026 0.22 NO
47 PRKAG1 PRKAG1 PRKAG1 11730 -0.026 0.22 NO
48 ACSL5 ACSL5 ACSL5 12087 -0.033 0.2 NO
49 PRKAB1 PRKAB1 PRKAB1 12172 -0.035 0.2 NO
50 STK11 STK11 STK11 12303 -0.037 0.2 NO
51 PCK2 PCK2 PCK2 12485 -0.04 0.19 NO
52 TNFRSF1A TNFRSF1A TNFRSF1A 12548 -0.041 0.19 NO
53 AKT1 AKT1 AKT1 12804 -0.046 0.18 NO
54 ADIPOR2 ADIPOR2 ADIPOR2 12926 -0.049 0.18 NO
55 PCK1 PCK1 PCK1 12959 -0.049 0.18 NO
56 ACSL3 ACSL3 ACSL3 13144 -0.052 0.18 NO
57 CHUK CHUK CHUK 13284 -0.055 0.18 NO
58 NFKBIE NFKBIE NFKBIE 13285 -0.055 0.18 NO
59 RXRA RXRA RXRA 13493 -0.059 0.17 NO
60 TNF TNF TNF 13916 -0.069 0.16 NO
61 MAPK8 MAPK8 MAPK8 14183 -0.076 0.15 NO
62 NFKBIB NFKBIB NFKBIB 15717 -0.12 0.078 NO
63 LEP LEP LEP 17008 -0.19 0.026 NO
64 SLC2A1 SLC2A1 SLC2A1 17069 -0.2 0.04 NO
65 G6PC G6PC G6PC 17913 -0.28 0.02 NO
66 G6PC2 G6PC2 G6PC2 17939 -0.29 0.043 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 HDAC 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 FCER1A FCER1A FCER1A 247 0.78 0.12 YES
2 PRKCB PRKCB PRKCB 391 0.71 0.23 YES
3 BTK BTK BTK 507 0.66 0.33 YES
4 PIK3CG PIK3CG PIK3CG 840 0.57 0.41 YES
5 VAV1 VAV1 VAV1 939 0.55 0.49 YES
6 NFATC4 NFATC4 NFATC4 2414 0.34 0.47 YES
7 NFATC2 NFATC2 NFATC2 2693 0.3 0.51 YES
8 PIK3R1 PIK3R1 PIK3R1 2844 0.29 0.55 YES
9 FCER1G FCER1G FCER1G 3098 0.27 0.58 YES
10 NFATC1 NFATC1 NFATC1 3959 0.2 0.56 NO
11 MAP3K1 MAP3K1 MAP3K1 5193 0.13 0.52 NO
12 PPP3CC PPP3CC PPP3CC 5426 0.12 0.53 NO
13 PLCG1 PLCG1 PLCG1 5651 0.11 0.54 NO
14 PPP3CB PPP3CB PPP3CB 6116 0.098 0.53 NO
15 NFATC3 NFATC3 NFATC3 6320 0.091 0.53 NO
16 PIK3CA PIK3CA PIK3CA 6353 0.09 0.54 NO
17 SYK SYK SYK 8175 0.04 0.45 NO
18 SOS1 SOS1 SOS1 8280 0.038 0.45 NO
19 PPP3CA PPP3CA PPP3CA 8430 0.035 0.45 NO
20 FOS FOS FOS 8556 0.032 0.45 NO
21 RAF1 RAF1 RAF1 9478 0.014 0.4 NO
22 MAP2K7 MAP2K7 MAP2K7 9501 0.014 0.4 NO
23 JUN JUN JUN 9662 0.011 0.4 NO
24 CALM2 CALM2 CALM2 9814 0.0086 0.39 NO
25 CALM1 CALM1 CALM1 10109 0.0025 0.38 NO
26 PAK2 PAK2 PAK2 10216 0.00054 0.37 NO
27 GRB2 GRB2 GRB2 10703 -0.0078 0.34 NO
28 ELK1 ELK1 ELK1 10780 -0.0093 0.34 NO
29 MAPK1 MAPK1 MAPK1 10795 -0.0096 0.34 NO
30 SHC1 SHC1 SHC1 11026 -0.014 0.33 NO
31 LYN LYN LYN 11085 -0.015 0.33 NO
32 MAP2K4 MAP2K4 MAP2K4 11334 -0.019 0.32 NO
33 CALM3 CALM3 CALM3 11681 -0.025 0.31 NO
34 MAP2K1 MAP2K1 MAP2K1 13918 -0.069 0.2 NO
35 MAPK8 MAPK8 MAPK8 14183 -0.076 0.2 NO
36 MAPK3 MAPK3 MAPK3 14344 -0.08 0.2 NO
37 PLA2G4A PLA2G4A PLA2G4A 17029 -0.19 0.092 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 HDAC PATHWAY.

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

genes ES table in pathway: BIOCARTA EGF PATHWAY

Table 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 CPEB1 CPEB1 CPEB1 81 0.92 0.054 YES
2 ADCY5 ADCY5 ADCY5 102 0.9 0.11 YES
3 PGR PGR PGR 129 0.87 0.16 YES
4 IGF1 IGF1 IGF1 161 0.84 0.22 YES
5 ADCY2 ADCY2 ADCY2 335 0.74 0.25 YES
6 RPS6KA6 RPS6KA6 RPS6KA6 369 0.72 0.3 YES
7 PDE3A PDE3A PDE3A 458 0.68 0.33 YES
8 MAPK10 MAPK10 MAPK10 804 0.58 0.35 YES
9 PIK3CG PIK3CG PIK3CG 840 0.57 0.39 YES
10 PIK3R5 PIK3R5 PIK3R5 893 0.56 0.42 YES
11 AKT3 AKT3 AKT3 1399 0.47 0.42 YES
12 ADCY4 ADCY4 ADCY4 1935 0.39 0.42 YES
13 ADCY1 ADCY1 ADCY1 2032 0.38 0.44 YES
14 PDE3B PDE3B PDE3B 2385 0.34 0.44 YES
15 PRKACB PRKACB PRKACB 2601 0.32 0.45 YES
16 PIK3R1 PIK3R1 PIK3R1 2844 0.29 0.45 YES
17 PIK3CD PIK3CD PIK3CD 2972 0.28 0.46 YES
18 RPS6KA2 RPS6KA2 RPS6KA2 4721 0.16 0.38 NO
19 PRKX PRKX PRKX 5299 0.13 0.36 NO
20 IGF1R IGF1R IGF1R 5601 0.12 0.35 NO
21 PIK3R3 PIK3R3 PIK3R3 5653 0.11 0.35 NO
22 GNAI2 GNAI2 GNAI2 5731 0.11 0.36 NO
23 MAPK11 MAPK11 MAPK11 5744 0.11 0.36 NO
24 ADCY9 ADCY9 ADCY9 5846 0.11 0.36 NO
25 BRAF BRAF BRAF 5935 0.1 0.36 NO
26 PIK3CA PIK3CA PIK3CA 6353 0.09 0.35 NO
27 ANAPC4 ANAPC4 ANAPC4 6854 0.074 0.32 NO
28 SPDYA SPDYA SPDYA 7607 0.054 0.29 NO
29 PRKACA PRKACA PRKACA 7844 0.048 0.28 NO
30 ADCY7 ADCY7 ADCY7 8126 0.041 0.27 NO
31 AKT2 AKT2 AKT2 8181 0.04 0.27 NO
32 ADCY3 ADCY3 ADCY3 8371 0.036 0.26 NO
33 GNAI1 GNAI1 GNAI1 8484 0.034 0.25 NO
34 ADCY8 ADCY8 ADCY8 8835 0.027 0.24 NO
35 CDC27 CDC27 CDC27 9136 0.02 0.22 NO
36 MAPK9 MAPK9 MAPK9 9152 0.02 0.22 NO
37 ADCY6 ADCY6 ADCY6 9359 0.016 0.21 NO
38 RPS6KA3 RPS6KA3 RPS6KA3 9385 0.016 0.21 NO
39 RAF1 RAF1 RAF1 9478 0.014 0.21 NO
40 PIK3CB PIK3CB PIK3CB 9678 0.011 0.2 NO
41 CDC23 CDC23 CDC23 9813 0.0086 0.19 NO
42 ANAPC10 ANAPC10 ANAPC10 10040 0.0042 0.18 NO
43 MAPK12 MAPK12 MAPK12 10411 -0.0029 0.16 NO
44 ANAPC1 ANAPC1 ANAPC1 10418 -0.003 0.16 NO
45 MAPK14 MAPK14 MAPK14 10545 -0.0052 0.15 NO
46 CDC16 CDC16 CDC16 10662 -0.0072 0.15 NO
47 MAPK1 MAPK1 MAPK1 10795 -0.0096 0.14 NO
48 KRAS KRAS KRAS 11141 -0.016 0.12 NO
49 FZR1 FZR1 FZR1 11269 -0.018 0.12 NO
50 ANAPC2 ANAPC2 ANAPC2 11627 -0.024 0.1 NO
51 CCNA1 CCNA1 CCNA1 11684 -0.025 0.099 NO
52 ANAPC5 ANAPC5 ANAPC5 12574 -0.042 0.054 NO
53 ANAPC7 ANAPC7 ANAPC7 12670 -0.044 0.052 NO
54 ANAPC13 ANAPC13 ANAPC13 12765 -0.046 0.05 NO
55 GNAI3 GNAI3 GNAI3 12802 -0.046 0.051 NO
56 AKT1 AKT1 AKT1 12804 -0.046 0.054 NO
57 RPS6KA1 RPS6KA1 RPS6KA1 12919 -0.049 0.05 NO
58 PIK3R2 PIK3R2 PIK3R2 12942 -0.049 0.052 NO
59 CCNB3 CCNB3 CCNB3 13481 -0.059 0.027 NO
60 ARAF ARAF ARAF 13643 -0.063 0.022 NO
61 MAP2K1 MAP2K1 MAP2K1 13918 -0.069 0.012 NO
62 MAPK8 MAPK8 MAPK8 14183 -0.076 0.0028 NO
63 MAPK3 MAPK3 MAPK3 14344 -0.08 -0.00073 NO
64 MAD2L2 MAD2L2 MAD2L2 14366 -0.08 0.0032 NO
65 ANAPC11 ANAPC11 ANAPC11 14764 -0.091 -0.012 NO
66 BUB1 BUB1 BUB1 14939 -0.097 -0.016 NO
67 MAD2L1 MAD2L1 MAD2L1 14987 -0.098 -0.012 NO
68 HSP90AA1 HSP90AA1 HSP90AA1 15059 -0.1 -0.0095 NO
69 CDK2 CDK2 CDK2 15128 -0.1 -0.0067 NO
70 CCNA2 CCNA2 CCNA2 15904 -0.13 -0.04 NO
71 CDK1 CDK1 CDK1 16249 -0.15 -0.049 NO
72 CCNB1 CCNB1 CCNB1 16847 -0.18 -0.07 NO
73 MAPK13 MAPK13 MAPK13 16866 -0.18 -0.059 NO
74 CDC25B CDC25B CDC25B 16883 -0.18 -0.049 NO
75 CCNB2 CCNB2 CCNB2 16911 -0.18 -0.038 NO
76 PLK1 PLK1 PLK1 17236 -0.21 -0.043 NO
77 CDC25C CDC25C CDC25C 17452 -0.23 -0.04 NO
78 CDC25A CDC25A CDC25A 17601 -0.25 -0.032 NO
79 PKMYT1 PKMYT1 PKMYT1 17640 -0.25 -0.018 NO
80 SPDYC SPDYC SPDYC 18024 -0.3 -0.02 NO
81 CDC26 CDC26 CDC26 18301 -0.35 -0.012 NO
82 PRKACG PRKACG PRKACG 18721 -0.58 0.0014 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 EGF PATHWAY.

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

genes ES table in pathway: BIOCARTA ERK PATHWAY

Table 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 PRKCB PRKCB PRKCB 391 0.71 0.2 YES
2 AGTR1 AGTR1 AGTR1 393 0.71 0.43 YES
3 MEF2A MEF2A MEF2A 4775 0.15 0.24 NO
4 MAP3K1 MAP3K1 MAP3K1 5193 0.13 0.26 NO
5 ATF2 ATF2 ATF2 5402 0.12 0.29 NO
6 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 5677 0.11 0.31 NO
7 MEF2D MEF2D MEF2D 6198 0.095 0.31 NO
8 AGT AGT AGT 6867 0.073 0.3 NO
9 GNAQ GNAQ GNAQ 7247 0.063 0.3 NO
10 PRKCA PRKCA PRKCA 7865 0.047 0.28 NO
11 SOS1 SOS1 SOS1 8280 0.038 0.27 NO
12 PTK2B PTK2B PTK2B 9258 0.018 0.22 NO
13 RAF1 RAF1 RAF1 9478 0.014 0.21 NO
14 JUN JUN JUN 9662 0.011 0.21 NO
15 CALM2 CALM2 CALM2 9814 0.0086 0.2 NO
16 CALM1 CALM1 CALM1 10109 0.0025 0.19 NO
17 GRB2 GRB2 GRB2 10703 -0.0078 0.16 NO
18 ELK1 ELK1 ELK1 10780 -0.0093 0.16 NO
19 MAPK1 MAPK1 MAPK1 10795 -0.0096 0.16 NO
20 PTK2 PTK2 PTK2 10930 -0.012 0.16 NO
21 SHC1 SHC1 SHC1 11026 -0.014 0.15 NO
22 EGFR EGFR EGFR 11089 -0.015 0.16 NO
23 MAP2K4 MAP2K4 MAP2K4 11334 -0.019 0.15 NO
24 CALM3 CALM3 CALM3 11681 -0.025 0.14 NO
25 MAP2K2 MAP2K2 MAP2K2 13520 -0.06 0.059 NO
26 MAP2K1 MAP2K1 MAP2K1 13918 -0.069 0.059 NO
27 MAPK8 MAPK8 MAPK8 14183 -0.076 0.069 NO
28 MAPK3 MAPK3 MAPK3 14344 -0.08 0.086 NO
29 PAK1 PAK1 PAK1 14405 -0.081 0.11 NO
30 RAC1 RAC1 RAC1 15579 -0.12 0.082 NO
31 SRC SRC SRC 15621 -0.12 0.12 NO
32 HRAS HRAS HRAS 16464 -0.16 0.12 NO

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

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

genes ES table in pathway: BIOCARTA FCER1 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 CADM3 CADM3 CADM3 17 1.1 0.022 YES
2 NRXN1 NRXN1 NRXN1 35 0.99 0.042 YES
3 NRXN3 NRXN3 NRXN3 94 0.91 0.059 YES
4 JAM2 JAM2 JAM2 135 0.87 0.075 YES
5 NEGR1 NEGR1 NEGR1 159 0.84 0.092 YES
6 NRXN2 NRXN2 NRXN2 196 0.81 0.11 YES
7 ITGA8 ITGA8 ITGA8 213 0.8 0.12 YES
8 NCAM1 NCAM1 NCAM1 221 0.8 0.14 YES
9 ITGA9 ITGA9 ITGA9 225 0.8 0.16 YES
10 CLDN11 CLDN11 CLDN11 248 0.78 0.17 YES
11 NLGN3 NLGN3 NLGN3 265 0.77 0.19 YES
12 CNTN2 CNTN2 CNTN2 285 0.76 0.2 YES
13 CD28 CD28 CD28 328 0.74 0.22 YES
14 SELP SELP SELP 351 0.73 0.23 YES
15 CDH2 CDH2 CDH2 370 0.72 0.25 YES
16 NLGN1 NLGN1 NLGN1 398 0.71 0.26 YES
17 SELL SELL SELL 484 0.67 0.27 YES
18 CD226 CD226 CD226 499 0.67 0.28 YES
19 NFASC NFASC NFASC 545 0.65 0.29 YES
20 SPN SPN SPN 565 0.64 0.31 YES
21 MPZ MPZ MPZ 586 0.63 0.32 YES
22 HLA-DOA HLA-DOA HLA-DOA 631 0.62 0.33 YES
23 HLA-DQA2 HLA-DQA2 HLA-DQA2 706 0.6 0.34 YES
24 ITGAL ITGAL ITGAL 739 0.59 0.35 YES
25 NCAM2 NCAM2 NCAM2 748 0.59 0.36 YES
26 CD22 CD22 CD22 761 0.59 0.37 YES
27 SIGLEC1 SIGLEC1 SIGLEC1 787 0.58 0.38 YES
28 CD8A CD8A CD8A 920 0.56 0.39 YES
29 NLGN4X NLGN4X NLGN4X 950 0.55 0.4 YES
30 CD2 CD2 CD2 958 0.55 0.41 YES
31 ITGAM ITGAM ITGAM 989 0.54 0.42 YES
32 ICOS ICOS ICOS 1006 0.54 0.43 YES
33 JAM3 JAM3 JAM3 1008 0.54 0.44 YES
34 CTLA4 CTLA4 CTLA4 1037 0.53 0.45 YES
35 PTPRC PTPRC PTPRC 1041 0.53 0.46 YES
36 HLA-DOB HLA-DOB HLA-DOB 1100 0.52 0.47 YES
37 CD80 CD80 CD80 1137 0.52 0.48 YES
38 CD8B CD8B CD8B 1148 0.52 0.49 YES
39 CNTN1 CNTN1 CNTN1 1160 0.51 0.5 YES
40 CADM1 CADM1 CADM1 1185 0.51 0.51 YES
41 HLA-DQA1 HLA-DQA1 HLA-DQA1 1225 0.5 0.52 YES
42 PDCD1LG2 PDCD1LG2 PDCD1LG2 1270 0.49 0.53 YES
43 CLDN5 CLDN5 CLDN5 1416 0.47 0.53 YES
44 CD40LG CD40LG CD40LG 1506 0.45 0.54 YES
45 CD6 CD6 CD6 1538 0.45 0.54 YES
46 ITGB2 ITGB2 ITGB2 1589 0.44 0.55 YES
47 CDH4 CDH4 CDH4 1593 0.44 0.56 YES
48 CD4 CD4 CD4 1598 0.44 0.57 YES
49 CD86 CD86 CD86 1599 0.44 0.58 YES
50 PDCD1 PDCD1 PDCD1 1643 0.43 0.59 YES
51 SELE SELE SELE 1644 0.43 0.6 YES
52 VCAM1 VCAM1 VCAM1 1645 0.43 0.6 YES
53 ITGB7 ITGB7 ITGB7 1669 0.43 0.61 YES
54 ICAM2 ICAM2 ICAM2 1723 0.42 0.62 YES
55 CNTNAP1 CNTNAP1 CNTNAP1 1746 0.42 0.63 YES
56 ITGA4 ITGA4 ITGA4 1803 0.41 0.63 YES
57 HLA-DPB1 HLA-DPB1 HLA-DPB1 1885 0.4 0.64 YES
58 HLA-DMB HLA-DMB HLA-DMB 1917 0.39 0.64 YES
59 SELPLG SELPLG SELPLG 1999 0.38 0.65 YES
60 CD40 CD40 CD40 2034 0.38 0.65 YES
61 PTPRM PTPRM PTPRM 2050 0.38 0.66 YES
62 HLA-DPA1 HLA-DPA1 HLA-DPA1 2241 0.35 0.66 YES
63 HLA-DQB1 HLA-DQB1 HLA-DQB1 2275 0.35 0.66 YES
64 CLDN16 CLDN16 CLDN16 2405 0.34 0.66 YES
65 NLGN2 NLGN2 NLGN2 2421 0.33 0.67 YES
66 CD34 CD34 CD34 2535 0.32 0.67 YES
67 PECAM1 PECAM1 PECAM1 2564 0.32 0.68 YES
68 L1CAM L1CAM L1CAM 2790 0.3 0.67 YES
69 CLDN20 CLDN20 CLDN20 2932 0.28 0.67 YES
70 CDH5 CDH5 CDH5 2976 0.28 0.67 YES
71 SDC2 SDC2 SDC2 3045 0.27 0.68 YES
72 HLA-DRA HLA-DRA HLA-DRA 3127 0.26 0.68 YES
73 VCAN VCAN VCAN 3308 0.25 0.67 YES
74 HLA-DMA HLA-DMA HLA-DMA 3311 0.25 0.68 YES
75 CD274 CD274 CD274 3319 0.25 0.68 YES
76 HLA-DRB1 HLA-DRB1 HLA-DRB1 3437 0.24 0.68 YES
77 ICAM3 ICAM3 ICAM3 3494 0.24 0.68 YES
78 HLA-DRB5 HLA-DRB5 HLA-DRB5 3849 0.21 0.67 NO
79 SDC3 SDC3 SDC3 3866 0.21 0.67 NO
80 CLDN8 CLDN8 CLDN8 4513 0.17 0.64 NO
81 ICOSLG ICOSLG ICOSLG 4927 0.14 0.62 NO
82 HLA-F HLA-F HLA-F 5486 0.12 0.59 NO
83 ITGAV ITGAV ITGAV 5491 0.12 0.6 NO
84 ICAM1 ICAM1 ICAM1 5542 0.12 0.6 NO
85 ESAM ESAM ESAM 5641 0.11 0.59 NO
86 NEO1 NEO1 NEO1 5693 0.11 0.59 NO
87 CNTNAP2 CNTNAP2 CNTNAP2 5824 0.11 0.59 NO
88 MADCAM1 MADCAM1 MADCAM1 5971 0.1 0.58 NO
89 HLA-G HLA-G HLA-G 5996 0.1 0.58 NO
90 ALCAM ALCAM ALCAM 6144 0.097 0.58 NO
91 HLA-E HLA-E HLA-E 6170 0.096 0.58 NO
92 CD99 CD99 CD99 6396 0.088 0.57 NO
93 NRCAM NRCAM NRCAM 6461 0.086 0.57 NO
94 CD58 CD58 CD58 8067 0.043 0.48 NO
95 GLG1 GLG1 GLG1 8113 0.042 0.48 NO
96 HLA-B HLA-B HLA-B 8435 0.035 0.46 NO
97 CLDN1 CLDN1 CLDN1 8458 0.034 0.46 NO
98 ITGB8 ITGB8 ITGB8 8825 0.027 0.44 NO
99 ITGB1 ITGB1 ITGB1 8867 0.026 0.44 NO
100 HLA-C HLA-C HLA-C 9219 0.019 0.42 NO
101 PVRL3 PVRL3 PVRL3 9537 0.013 0.41 NO
102 HLA-A HLA-A HLA-A 10157 0.0017 0.37 NO
103 MPZL1 MPZL1 MPZL1 12061 -0.032 0.27 NO
104 CDH15 CDH15 CDH15 12124 -0.034 0.27 NO
105 CLDN15 CLDN15 CLDN15 12269 -0.036 0.26 NO
106 PTPRF PTPRF PTPRF 13240 -0.054 0.21 NO
107 CLDN10 CLDN10 CLDN10 13295 -0.055 0.21 NO
108 SDC4 SDC4 SDC4 13970 -0.07 0.18 NO
109 CLDN14 CLDN14 CLDN14 14142 -0.075 0.17 NO
110 ITGA6 ITGA6 ITGA6 14453 -0.082 0.15 NO
111 CD276 CD276 CD276 14714 -0.089 0.14 NO
112 F11R F11R F11R 14828 -0.093 0.14 NO
113 MAG MAG MAG 15039 -0.099 0.13 NO
114 CLDN19 CLDN19 CLDN19 15095 -0.1 0.13 NO
115 CLDN9 CLDN9 CLDN9 15518 -0.12 0.11 NO
116 PVRL2 PVRL2 PVRL2 15813 -0.13 0.093 NO
117 CDH1 CDH1 CDH1 15874 -0.13 0.093 NO
118 CLDN18 CLDN18 CLDN18 15876 -0.13 0.096 NO
119 PVRL1 PVRL1 PVRL1 16256 -0.15 0.078 NO
120 CDH3 CDH3 CDH3 16503 -0.16 0.068 NO
121 CLDN23 CLDN23 CLDN23 16524 -0.16 0.071 NO
122 SDC1 SDC1 SDC1 16656 -0.17 0.068 NO
123 CLDN17 CLDN17 CLDN17 16937 -0.19 0.056 NO
124 CLDN2 CLDN2 CLDN2 17378 -0.22 0.038 NO
125 CLDN3 CLDN3 CLDN3 17426 -0.23 0.04 NO
126 OCLN OCLN OCLN 17582 -0.24 0.037 NO
127 CLDN4 CLDN4 CLDN4 17823 -0.27 0.03 NO
128 CLDN7 CLDN7 CLDN7 18411 -0.38 0.0063 NO
129 CLDN6 CLDN6 CLDN6 18706 -0.55 0.0023 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 FCER1 PATHWAY.

Figure S76.  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 FMLP 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 NTRK3 NTRK3 NTRK3 231 0.79 0.036 YES
2 RPS6KA6 RPS6KA6 RPS6KA6 369 0.72 0.073 YES
3 NGFR NGFR NGFR 541 0.65 0.1 YES
4 MAPK10 MAPK10 MAPK10 804 0.58 0.12 YES
5 CAMK4 CAMK4 CAMK4 828 0.58 0.16 YES
6 PIK3CG PIK3CG PIK3CG 840 0.57 0.19 YES
7 PIK3R5 PIK3R5 PIK3R5 893 0.56 0.23 YES
8 BCL2 BCL2 BCL2 1028 0.54 0.25 YES
9 IRS4 IRS4 IRS4 1363 0.48 0.26 YES
10 AKT3 AKT3 AKT3 1399 0.47 0.29 YES
11 SHC4 SHC4 SHC4 2159 0.36 0.27 YES
12 PLCG2 PLCG2 PLCG2 2269 0.35 0.29 YES
13 FASLG FASLG FASLG 2484 0.33 0.3 YES
14 NGF NGF NGF 2673 0.31 0.3 YES
15 PIK3R1 PIK3R1 PIK3R1 2844 0.29 0.31 YES
16 ARHGDIB ARHGDIB ARHGDIB 2910 0.29 0.33 YES
17 PIK3CD PIK3CD PIK3CD 2972 0.28 0.34 YES
18 NTRK2 NTRK2 NTRK2 3259 0.25 0.34 YES
19 RPS6KA5 RPS6KA5 RPS6KA5 3280 0.25 0.36 YES
20 IRS2 IRS2 IRS2 3542 0.23 0.36 YES
21 MAP3K3 MAP3K3 MAP3K3 3604 0.23 0.37 YES
22 NTF3 NTF3 NTF3 3882 0.21 0.36 YES
23 GAB1 GAB1 GAB1 3901 0.21 0.38 YES
24 NGFRAP1 NGFRAP1 NGFRAP1 3908 0.21 0.39 YES
25 CALML6 CALML6 CALML6 3942 0.2 0.4 YES
26 SHC2 SHC2 SHC2 3955 0.2 0.41 YES
27 SH2B2 SH2B2 SH2B2 4354 0.18 0.4 YES
28 CAMK2B CAMK2B CAMK2B 4501 0.17 0.4 YES
29 RPS6KA2 RPS6KA2 RPS6KA2 4721 0.16 0.4 YES
30 CAMK2A CAMK2A CAMK2A 4791 0.15 0.4 YES
31 SH2B3 SH2B3 SH2B3 4867 0.15 0.41 YES
32 RAP1A RAP1A RAP1A 5063 0.14 0.41 YES
33 NTRK1 NTRK1 NTRK1 5139 0.13 0.41 YES
34 MAP3K1 MAP3K1 MAP3K1 5193 0.13 0.42 YES
35 TP73 TP73 TP73 5237 0.13 0.42 YES
36 RAPGEF1 RAPGEF1 RAPGEF1 5276 0.13 0.43 YES
37 PLCG1 PLCG1 PLCG1 5651 0.11 0.42 YES
38 PIK3R3 PIK3R3 PIK3R3 5653 0.11 0.42 YES
39 MAPK11 MAPK11 MAPK11 5744 0.11 0.42 YES
40 IKBKB IKBKB IKBKB 5771 0.11 0.43 YES
41 IRAK3 IRAK3 IRAK3 5879 0.1 0.43 YES
42 BRAF BRAF BRAF 5935 0.1 0.43 YES
43 CALML5 CALML5 CALML5 6070 0.099 0.43 YES
44 SH2B1 SH2B1 SH2B1 6248 0.093 0.43 YES
45 CAMK2G CAMK2G CAMK2G 6315 0.091 0.43 YES
46 PIK3CA PIK3CA PIK3CA 6353 0.09 0.43 YES
47 ABL1 ABL1 ABL1 6357 0.09 0.44 YES
48 SOS2 SOS2 SOS2 6660 0.079 0.43 NO
49 ZNF274 ZNF274 ZNF274 6711 0.078 0.43 NO
50 NTF4 NTF4 NTF4 6725 0.077 0.43 NO
51 IRAK4 IRAK4 IRAK4 7145 0.066 0.42 NO
52 TRAF6 TRAF6 TRAF6 7337 0.06 0.41 NO
53 CAMK2D CAMK2D CAMK2D 7454 0.058 0.41 NO
54 NFKB1 NFKB1 NFKB1 7549 0.055 0.4 NO
55 MAP3K5 MAP3K5 MAP3K5 7585 0.054 0.41 NO
56 FOXO3 FOXO3 FOXO3 7909 0.046 0.39 NO
57 AKT2 AKT2 AKT2 8181 0.04 0.38 NO
58 SOS1 SOS1 SOS1 8280 0.038 0.38 NO
59 TP53 TP53 TP53 8629 0.031 0.36 NO
60 MAP2K5 MAP2K5 MAP2K5 8660 0.03 0.36 NO
61 FRS2 FRS2 FRS2 8752 0.028 0.36 NO
62 KIDINS220 KIDINS220 KIDINS220 8895 0.026 0.35 NO
63 MAGED1 MAGED1 MAGED1 8994 0.024 0.35 NO
64 MAPK9 MAPK9 MAPK9 9152 0.02 0.34 NO
65 PDK1 PDK1 PDK1 9242 0.018 0.34 NO
66 RPS6KA3 RPS6KA3 RPS6KA3 9385 0.016 0.33 NO
67 CALML3 CALML3 CALML3 9435 0.015 0.33 NO
68 RAF1 RAF1 RAF1 9478 0.014 0.33 NO
69 MAP2K7 MAP2K7 MAP2K7 9501 0.014 0.33 NO
70 ATF4 ATF4 ATF4 9543 0.013 0.32 NO
71 IRS1 IRS1 IRS1 9563 0.013 0.32 NO
72 SORT1 SORT1 SORT1 9564 0.013 0.33 NO
73 JUN JUN JUN 9662 0.011 0.32 NO
74 PIK3CB PIK3CB PIK3CB 9678 0.011 0.32 NO
75 NFKBIA NFKBIA NFKBIA 9733 0.0098 0.32 NO
76 CALM2 CALM2 CALM2 9814 0.0086 0.32 NO
77 MAPKAPK2 MAPKAPK2 MAPKAPK2 9853 0.0079 0.31 NO
78 RHOA RHOA RHOA 9864 0.0078 0.31 NO
79 PTPN11 PTPN11 PTPN11 9953 0.0061 0.31 NO
80 CALM1 CALM1 CALM1 10109 0.0025 0.3 NO
81 RAP1B RAP1B RAP1B 10405 -0.0028 0.28 NO
82 MAPK12 MAPK12 MAPK12 10411 -0.0029 0.28 NO
83 MAPK14 MAPK14 MAPK14 10545 -0.0052 0.28 NO
84 CRK CRK CRK 10638 -0.0066 0.27 NO
85 GRB2 GRB2 GRB2 10703 -0.0078 0.27 NO
86 MAPK1 MAPK1 MAPK1 10795 -0.0096 0.27 NO
87 SHC1 SHC1 SHC1 11026 -0.014 0.26 NO
88 KRAS KRAS KRAS 11141 -0.016 0.25 NO
89 MAPK7 MAPK7 MAPK7 11202 -0.017 0.25 NO
90 YWHAH YWHAH YWHAH 11423 -0.021 0.24 NO
91 BAD BAD BAD 11441 -0.021 0.24 NO
92 CDC42 CDC42 CDC42 11541 -0.023 0.23 NO
93 CALM3 CALM3 CALM3 11681 -0.025 0.23 NO
94 RELA RELA RELA 11726 -0.026 0.23 NO
95 YWHAB YWHAB YWHAB 11767 -0.027 0.23 NO
96 CRKL CRKL CRKL 12288 -0.037 0.2 NO
97 GSK3B GSK3B GSK3B 12467 -0.04 0.19 NO
98 AKT1 AKT1 AKT1 12804 -0.046 0.18 NO
99 PRDM4 PRDM4 PRDM4 12809 -0.046 0.18 NO
100 RPS6KA1 RPS6KA1 RPS6KA1 12919 -0.049 0.18 NO
101 PIK3R2 PIK3R2 PIK3R2 12942 -0.049 0.18 NO
102 CSK CSK CSK 13111 -0.052 0.17 NO
103 YWHAQ YWHAQ YWHAQ 13127 -0.052 0.18 NO
104 NFKBIE NFKBIE NFKBIE 13285 -0.055 0.17 NO
105 SHC3 SHC3 SHC3 13467 -0.059 0.16 NO
106 MAP2K2 MAP2K2 MAP2K2 13520 -0.06 0.17 NO
107 RIPK2 RIPK2 RIPK2 13672 -0.064 0.16 NO
108 YWHAE YWHAE YWHAE 13877 -0.068 0.16 NO
109 MAP2K1 MAP2K1 MAP2K1 13918 -0.069 0.16 NO
110 PSEN1 PSEN1 PSEN1 13937 -0.07 0.16 NO
111 NRAS NRAS NRAS 13950 -0.07 0.16 NO
112 BAX BAX BAX 14021 -0.072 0.16 NO
113 MAPK8 MAPK8 MAPK8 14183 -0.076 0.16 NO
114 MAPK3 MAPK3 MAPK3 14344 -0.08 0.16 NO
115 PRKCD PRKCD PRKCD 14419 -0.081 0.16 NO
116 YWHAG YWHAG YWHAG 14592 -0.086 0.15 NO
117 IRAK1 IRAK1 IRAK1 14673 -0.088 0.16 NO
118 ARHGDIA ARHGDIA ARHGDIA 14674 -0.088 0.16 NO
119 BDNF BDNF BDNF 14967 -0.097 0.15 NO
120 YWHAZ YWHAZ YWHAZ 15217 -0.1 0.14 NO
121 RAC1 RAC1 RAC1 15579 -0.12 0.13 NO
122 NFKBIB NFKBIB NFKBIB 15717 -0.12 0.13 NO
123 IRAK2 IRAK2 IRAK2 16262 -0.15 0.11 NO
124 RPS6KA4 RPS6KA4 RPS6KA4 16754 -0.18 0.096 NO
125 MAPK13 MAPK13 MAPK13 16866 -0.18 0.1 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 FMLP PATHWAY.

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

genes ES table in pathway: BIOCARTA GH 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 IGF1 IGF1 IGF1 161 0.84 0.21 YES
2 PIK3CG PIK3CG PIK3CG 840 0.57 0.32 YES
3 NFATC2 NFATC2 NFATC2 2693 0.3 0.3 YES
4 PIK3R1 PIK3R1 PIK3R1 2844 0.29 0.37 YES
5 CAMK1 CAMK1 CAMK1 3455 0.24 0.4 YES
6 CAMK1G CAMK1G CAMK1G 3509 0.24 0.45 YES
7 NFATC1 NFATC1 NFATC1 3959 0.2 0.48 YES
8 MEF2A MEF2A MEF2A 4775 0.15 0.48 YES
9 PPP3CC PPP3CC PPP3CC 5426 0.12 0.47 YES
10 IGF1R IGF1R IGF1R 5601 0.12 0.49 YES
11 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 5677 0.11 0.52 YES
12 PPP3CB PPP3CB PPP3CB 6116 0.098 0.52 YES
13 MEF2D MEF2D MEF2D 6198 0.095 0.54 YES
14 PIK3CA PIK3CA PIK3CA 6353 0.09 0.55 YES
15 HDAC5 HDAC5 HDAC5 6440 0.087 0.57 YES
16 INSR INSR INSR 7961 0.045 0.5 NO
17 CABIN1 CABIN1 CABIN1 8071 0.043 0.51 NO
18 PPP3CA PPP3CA PPP3CA 8430 0.035 0.5 NO
19 CALM2 CALM2 CALM2 9814 0.0086 0.42 NO
20 CALM1 CALM1 CALM1 10109 0.0025 0.41 NO
21 MAPK14 MAPK14 MAPK14 10545 -0.0052 0.39 NO
22 MAPK7 MAPK7 MAPK7 11202 -0.017 0.36 NO
23 YWHAH YWHAH YWHAH 11423 -0.021 0.35 NO
24 CALM3 CALM3 CALM3 11681 -0.025 0.34 NO
25 AKT1 AKT1 AKT1 12804 -0.046 0.3 NO
26 MAP2K6 MAP2K6 MAP2K6 14577 -0.086 0.22 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 GH PATHWAY.

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

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 = STES-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = STES-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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