GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in OV-TP
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1FJ2G1M
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 OV-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1FJ2G1M
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 OV-TP. This pipeline has the following features:

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

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

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

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

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

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

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 192
Number of samples: 303
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 79
pheno.type: 2 - 3 :[ clus2 ] 109
pheno.type: 3 - 3 :[ clus3 ] 115

For the expression subtypes of 18585 genes in 304 samples, GSEA found enriched gene sets in each cluster using 303 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA FAS PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA TOLL PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG GLUTATHIONE METABOLISM, KEGG PEROXISOME, KEGG APOPTOSIS, KEGG ANTIGEN PROCESSING AND PRESENTATION

    • And common core enriched genes are CASP8, CXCL10, IFNB1, IKBKE, IRF7, NFKB1, NFKBIA, TMEM173, TNF, TRADD

  • clus2

    • Top enriched gene sets are BIOCARTA CARM ER PATHWAY, BIOCARTA MPR PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA WNT PATHWAY, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RNA DEGRADATION, KEGG BASAL TRANSCRIPTION FACTORS

    • And common core enriched genes are LSM2, LSM4, LSM5, NAA38, CNOT10, CNOT2, CNOT3, CNOT7, DCP1A, DCP1B

  • clus3

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA FMLP PATHWAY

    • And common core enriched genes are AKT3, PIK3CD, PIK3CG, PIK3R5, MAPK1, PGF, TGFB1, TGFB3, VEGFC, CCND1

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 FAS PATHWAY 29 genes.ES.table 0.38 1.4 0.15 0.53 0.98 0.31 0.19 0.25 0.42 0.13
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.39 1.7 0.06 0.5 0.58 0.46 0.28 0.33 0.26 0.15
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.43 1.5 0.089 0.51 0.87 0.56 0.28 0.41 0.34 0.15
BIOCARTA TOLL PATHWAY 36 genes.ES.table 0.48 1.4 0.17 0.5 0.97 0.44 0.2 0.36 0.39 0.11
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.45 1.5 0.12 0.55 0.87 0.66 0.34 0.43 0.37 0.16
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.38 1.4 0.15 0.53 0.97 0.26 0.2 0.21 0.41 0.13
KEGG GLUTATHIONE METABOLISM 46 genes.ES.table 0.43 1.4 0.086 0.59 0.96 0.48 0.25 0.36 0.46 0.16
KEGG PEROXISOME 75 genes.ES.table 0.5 2 0.004 0.14 0.099 0.48 0.28 0.35 0 0.053
KEGG APOPTOSIS 83 genes.ES.table 0.37 1.3 0.19 0.58 0.99 0.41 0.22 0.32 0.47 0.16
KEGG ANTIGEN PROCESSING AND PRESENTATION 66 genes.ES.table 0.7 1.6 0.045 0.38 0.67 0.61 0.17 0.5 0.22 0.096
genes ES table in pathway: BIOCARTA FAS 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 PIPOX PIPOX PIPOX 179 0.29 0.066 YES
2 DDO DDO DDO 183 0.29 0.14 YES
3 ACSL5 ACSL5 ACSL5 425 0.23 0.19 YES
4 PEX11G PEX11G PEX11G 1091 0.16 0.19 YES
5 PEX11A PEX11A PEX11A 1639 0.12 0.2 YES
6 MPV17L MPV17L MPV17L 1776 0.12 0.22 YES
7 SOD2 SOD2 SOD2 2447 0.092 0.21 YES
8 MLYCD MLYCD MLYCD 2459 0.092 0.23 YES
9 IDH2 IDH2 IDH2 2495 0.09 0.25 YES
10 GSTK1 GSTK1 GSTK1 2521 0.09 0.28 YES
11 SCP2 SCP2 SCP2 2903 0.078 0.28 YES
12 PAOX PAOX PAOX 2950 0.077 0.29 YES
13 PEX6 PEX6 PEX6 3024 0.075 0.31 YES
14 PEX16 PEX16 PEX16 3054 0.074 0.33 YES
15 ACAA1 ACAA1 ACAA1 3387 0.066 0.33 YES
16 EPHX2 EPHX2 EPHX2 3448 0.064 0.34 YES
17 PECR PECR PECR 3475 0.064 0.36 YES
18 CAT CAT CAT 3529 0.062 0.37 YES
19 PEX7 PEX7 PEX7 3638 0.06 0.38 YES
20 DHRS4 DHRS4 DHRS4 3663 0.059 0.39 YES
21 ABCD1 ABCD1 ABCD1 3697 0.059 0.41 YES
22 IDH1 IDH1 IDH1 3769 0.057 0.42 YES
23 PXMP4 PXMP4 PXMP4 4065 0.052 0.42 YES
24 PMVK PMVK PMVK 4344 0.048 0.41 YES
25 CRAT CRAT CRAT 4355 0.047 0.42 YES
26 HMGCL HMGCL HMGCL 4419 0.046 0.43 YES
27 HACL1 HACL1 HACL1 4468 0.046 0.44 YES
28 PRDX5 PRDX5 PRDX5 4546 0.044 0.45 YES
29 SOD1 SOD1 SOD1 4702 0.042 0.45 YES
30 NUDT12 NUDT12 NUDT12 4765 0.041 0.46 YES
31 ABCD2 ABCD2 ABCD2 4793 0.041 0.47 YES
32 PEX11B PEX11B PEX11B 4806 0.041 0.48 YES
33 HAO2 HAO2 HAO2 4867 0.04 0.49 YES
34 ACOX3 ACOX3 ACOX3 4911 0.039 0.5 YES
35 PRDX1 PRDX1 PRDX1 5085 0.036 0.5 YES
36 ACSL6 ACSL6 ACSL6 5216 0.034 0.5 YES
37 XDH XDH XDH 5527 0.031 0.49 NO
38 PEX10 PEX10 PEX10 5559 0.03 0.49 NO
39 ACOT8 ACOT8 ACOT8 5712 0.028 0.49 NO
40 PEX12 PEX12 PEX12 5958 0.025 0.49 NO
41 NUDT19 NUDT19 NUDT19 6273 0.022 0.48 NO
42 PEX2 PEX2 PEX2 6275 0.022 0.48 NO
43 ACOX1 ACOX1 ACOX1 6520 0.019 0.47 NO
44 AGPS AGPS AGPS 6737 0.017 0.47 NO
45 PEX26 PEX26 PEX26 6763 0.016 0.47 NO
46 SLC25A17 SLC25A17 SLC25A17 6779 0.016 0.47 NO
47 MVK MVK MVK 6826 0.016 0.47 NO
48 AMACR AMACR AMACR 6965 0.014 0.47 NO
49 FAR2 FAR2 FAR2 7382 0.01 0.45 NO
50 SLC27A2 SLC27A2 SLC27A2 8013 0.0038 0.42 NO
51 EHHADH EHHADH EHHADH 8164 0.0022 0.41 NO
52 ACSL4 ACSL4 ACSL4 8386 -0.000048 0.4 NO
53 DECR2 DECR2 DECR2 8574 -0.002 0.39 NO
54 HSD17B4 HSD17B4 HSD17B4 8675 -0.0031 0.38 NO
55 PEX13 PEX13 PEX13 8716 -0.0034 0.38 NO
56 PXMP2 PXMP2 PXMP2 8782 -0.004 0.38 NO
57 PEX1 PEX1 PEX1 9228 -0.0078 0.36 NO
58 GNPAT GNPAT GNPAT 9286 -0.0083 0.36 NO
59 ACSL3 ACSL3 ACSL3 9723 -0.012 0.34 NO
60 MPV17 MPV17 MPV17 9731 -0.012 0.34 NO
61 PEX14 PEX14 PEX14 9785 -0.013 0.34 NO
62 ECH1 ECH1 ECH1 9795 -0.013 0.34 NO
63 ACSL1 ACSL1 ACSL1 9900 -0.014 0.34 NO
64 ABCD3 ABCD3 ABCD3 10086 -0.016 0.33 NO
65 FAR1 FAR1 FAR1 10724 -0.022 0.31 NO
66 PEX19 PEX19 PEX19 11105 -0.026 0.29 NO
67 PEX5 PEX5 PEX5 11459 -0.03 0.28 NO
68 BAAT BAAT BAAT 11600 -0.032 0.28 NO
69 CROT CROT CROT 12065 -0.037 0.27 NO
70 PEX3 PEX3 PEX3 12390 -0.041 0.26 NO
71 PECI PECI PECI 12444 -0.042 0.27 NO
72 PHYH PHYH PHYH 12812 -0.047 0.26 NO
73 ABCD4 ABCD4 ABCD4 12813 -0.047 0.27 NO
74 AGXT AGXT AGXT 13242 -0.054 0.26 NO
75 NOS2 NOS2 NOS2 14895 -0.093 0.2 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 FAS PATHWAY.

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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

Table 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 IL12A IL12A IL12A 105 0.33 0.066 YES
2 CXCL10 CXCL10 CXCL10 409 0.23 0.1 YES
3 TMEM173 TMEM173 TMEM173 692 0.2 0.13 YES
4 RNF125 RNF125 RNF125 884 0.18 0.16 YES
5 IFIH1 IFIH1 IFIH1 909 0.18 0.19 YES
6 IFNE IFNE IFNE 1134 0.16 0.22 YES
7 IRF7 IRF7 IRF7 1144 0.16 0.25 YES
8 IL8 IL8 IL8 1243 0.15 0.28 YES
9 TNF TNF TNF 1318 0.14 0.3 YES
10 IFNB1 IFNB1 IFNB1 1415 0.14 0.33 YES
11 ISG15 ISG15 ISG15 1535 0.13 0.35 YES
12 DHX58 DHX58 DHX58 1552 0.13 0.38 YES
13 CASP10 CASP10 CASP10 1553 0.13 0.41 YES
14 IKBKE IKBKE IKBKE 1595 0.13 0.43 YES
15 IL12B IL12B IL12B 1602 0.13 0.46 YES
16 TRADD TRADD TRADD 1681 0.12 0.48 YES
17 MAPK13 MAPK13 MAPK13 1862 0.12 0.5 YES
18 DDX58 DDX58 DDX58 2249 0.099 0.5 YES
19 TANK TANK TANK 2828 0.08 0.49 YES
20 CASP8 CASP8 CASP8 2981 0.076 0.5 YES
21 NLRX1 NLRX1 NLRX1 3013 0.075 0.51 YES
22 IKBKB IKBKB IKBKB 3241 0.069 0.51 YES
23 IKBKG IKBKG IKBKG 3423 0.065 0.52 YES
24 NFKBIA NFKBIA NFKBIA 3584 0.061 0.52 YES
25 DAK DAK DAK 3731 0.058 0.53 YES
26 NFKB1 NFKB1 NFKB1 3761 0.057 0.54 YES
27 FADD FADD FADD 4066 0.052 0.53 NO
28 IFNW1 IFNW1 IFNW1 4306 0.049 0.53 NO
29 TRAF2 TRAF2 TRAF2 4834 0.04 0.51 NO
30 RELA RELA RELA 4908 0.039 0.52 NO
31 MAPK11 MAPK11 MAPK11 5195 0.035 0.51 NO
32 MAP3K1 MAP3K1 MAP3K1 5290 0.034 0.51 NO
33 CYLD CYLD CYLD 5838 0.027 0.49 NO
34 TBK1 TBK1 TBK1 6135 0.023 0.48 NO
35 TRAF3 TRAF3 TRAF3 6585 0.018 0.46 NO
36 TRAF6 TRAF6 TRAF6 6759 0.016 0.45 NO
37 IRF3 IRF3 IRF3 6783 0.016 0.45 NO
38 DDX3X DDX3X DDX3X 7555 0.0082 0.41 NO
39 PIN1 PIN1 PIN1 8106 0.0028 0.38 NO
40 MAVS MAVS MAVS 8138 0.0025 0.38 NO
41 MAPK9 MAPK9 MAPK9 8434 -0.00056 0.37 NO
42 TRIM25 TRIM25 TRIM25 8833 -0.0045 0.35 NO
43 OTUD5 OTUD5 OTUD5 9041 -0.0062 0.34 NO
44 RIPK1 RIPK1 RIPK1 9130 -0.007 0.33 NO
45 MAPK14 MAPK14 MAPK14 9432 -0.0097 0.32 NO
46 ATG12 ATG12 ATG12 9510 -0.01 0.32 NO
47 ATG5 ATG5 ATG5 10697 -0.022 0.26 NO
48 AZI2 AZI2 AZI2 11054 -0.026 0.24 NO
49 NFKBIB NFKBIB NFKBIB 11913 -0.035 0.2 NO
50 SIKE1 SIKE1 SIKE1 13177 -0.053 0.15 NO
51 CHUK CHUK CHUK 13532 -0.059 0.14 NO
52 MAPK8 MAPK8 MAPK8 14079 -0.071 0.13 NO
53 MAPK12 MAPK12 MAPK12 14120 -0.072 0.14 NO
54 MAP3K7 MAP3K7 MAP3K7 14478 -0.081 0.14 NO
55 TBKBP1 TBKBP1 TBKBP1 16466 -0.16 0.069 NO
56 MAPK10 MAPK10 MAPK10 17113 -0.2 0.078 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 HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA DEATH PATHWAY

Table 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 BIRC3 BIRC3 BIRC3 300 0.25 0.069 YES
2 TNF TNF TNF 1318 0.14 0.063 YES
3 TRAF1 TRAF1 TRAF1 1658 0.12 0.086 YES
4 TRADD TRADD TRADD 1681 0.12 0.13 YES
5 ARHGDIB ARHGDIB ARHGDIB 1767 0.12 0.16 YES
6 PRKCD PRKCD PRKCD 2080 0.11 0.18 YES
7 BID BID BID 2426 0.093 0.19 YES
8 TNFRSF1B TNFRSF1B TNFRSF1B 2479 0.091 0.22 YES
9 FAS FAS FAS 2544 0.089 0.25 YES
10 CRADD CRADD CRADD 2864 0.079 0.26 YES
11 CASP8 CASP8 CASP8 2981 0.076 0.28 YES
12 CASP7 CASP7 CASP7 3090 0.073 0.3 YES
13 LMNA LMNA LMNA 3262 0.069 0.31 YES
14 CFLAR CFLAR CFLAR 3489 0.063 0.32 YES
15 NFKBIA NFKBIA NFKBIA 3584 0.061 0.34 YES
16 NFKB1 NFKB1 NFKB1 3761 0.057 0.34 YES
17 FADD FADD FADD 4066 0.052 0.35 YES
18 XIAP XIAP XIAP 4541 0.044 0.34 YES
19 TRAF2 TRAF2 TRAF2 4834 0.04 0.33 YES
20 RELA RELA RELA 4908 0.039 0.34 YES
21 MAP3K5 MAP3K5 MAP3K5 4958 0.038 0.35 YES
22 GSN GSN GSN 5029 0.037 0.36 YES
23 MAP3K14 MAP3K14 MAP3K14 5055 0.037 0.37 YES
24 CYCS CYCS CYCS 5199 0.035 0.38 YES
25 TNFRSF1A TNFRSF1A TNFRSF1A 5244 0.034 0.38 YES
26 MAP3K1 MAP3K1 MAP3K1 5290 0.034 0.39 YES
27 DFFB DFFB DFFB 6314 0.021 0.35 NO
28 PTK2 PTK2 PTK2 6321 0.021 0.35 NO
29 BCL2 BCL2 BCL2 6503 0.019 0.35 NO
30 CASP6 CASP6 CASP6 6517 0.019 0.36 NO
31 NUMA1 NUMA1 NUMA1 8584 -0.0021 0.24 NO
32 RIPK1 RIPK1 RIPK1 9130 -0.007 0.22 NO
33 DAXX DAXX DAXX 9156 -0.0073 0.22 NO
34 ACTG1 ACTG1 ACTG1 9671 -0.012 0.2 NO
35 CASP2 CASP2 CASP2 9672 -0.012 0.2 NO
36 CDK11A CDK11A CDK11A 9752 -0.012 0.2 NO
37 BIRC2 BIRC2 BIRC2 10254 -0.017 0.18 NO
38 PSEN2 PSEN2 PSEN2 10460 -0.02 0.17 NO
39 MDM2 MDM2 MDM2 10776 -0.023 0.16 NO
40 BAG4 BAG4 BAG4 10872 -0.024 0.17 NO
41 MAP2K7 MAP2K7 MAP2K7 11012 -0.025 0.17 NO
42 PAK2 PAK2 PAK2 11152 -0.027 0.17 NO
43 PRKDC PRKDC PRKDC 11209 -0.027 0.18 NO
44 RB1 RB1 RB1 11281 -0.028 0.18 NO
45 LMNB2 LMNB2 LMNB2 11613 -0.032 0.17 NO
46 CDK11B CDK11B CDK11B 11792 -0.034 0.18 NO
47 PSEN1 PSEN1 PSEN1 11834 -0.034 0.18 NO
48 PARP1 PARP1 PARP1 12016 -0.036 0.19 NO
49 SPTAN1 SPTAN1 SPTAN1 12507 -0.043 0.18 NO
50 CASP3 CASP3 CASP3 12527 -0.043 0.19 NO
51 DFFA DFFA DFFA 12545 -0.043 0.2 NO
52 LMNB1 LMNB1 LMNB1 12661 -0.045 0.21 NO
53 CASP9 CASP9 CASP9 13155 -0.052 0.2 NO
54 RASA1 RASA1 RASA1 13362 -0.056 0.21 NO
55 CHUK CHUK CHUK 13532 -0.059 0.22 NO
56 MAPK8 MAPK8 MAPK8 14079 -0.071 0.22 NO
57 APAF1 APAF1 APAF1 14326 -0.077 0.23 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 DEATH PATHWAY.

Figure S6.  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 TOLL PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ZBP1 ZBP1 ZBP1 132 0.31 0.065 YES
2 CCL4L2 CCL4L2 CCL4L2 173 0.29 0.13 YES
3 CXCL10 CXCL10 CXCL10 409 0.23 0.17 YES
4 CCL4 CCL4 CCL4 531 0.21 0.22 YES
5 CCL5 CCL5 CCL5 532 0.21 0.26 YES
6 CASP1 CASP1 CASP1 543 0.21 0.31 YES
7 RIPK3 RIPK3 RIPK3 623 0.2 0.36 YES
8 TMEM173 TMEM173 TMEM173 692 0.2 0.4 YES
9 IL1B IL1B IL1B 694 0.2 0.44 YES
10 IL33 IL33 IL33 927 0.17 0.47 YES
11 PYCARD PYCARD PYCARD 1099 0.16 0.5 YES
12 IL18 IL18 IL18 1140 0.16 0.53 YES
13 IRF7 IRF7 IRF7 1144 0.16 0.57 YES
14 TREX1 TREX1 TREX1 1388 0.14 0.59 YES
15 IFNB1 IFNB1 IFNB1 1415 0.14 0.62 YES
16 IKBKE IKBKE IKBKE 1595 0.13 0.64 YES
17 AIM2 AIM2 AIM2 1623 0.13 0.67 YES
18 DDX58 DDX58 DDX58 2249 0.099 0.66 NO
19 IKBKB IKBKB IKBKB 3241 0.069 0.62 NO
20 IKBKG IKBKG IKBKG 3423 0.065 0.62 NO
21 NFKBIA NFKBIA NFKBIA 3584 0.061 0.63 NO
22 NFKB1 NFKB1 NFKB1 3761 0.057 0.63 NO
23 POLR3K POLR3K POLR3K 4282 0.049 0.62 NO
24 POLR1C POLR1C POLR1C 4484 0.045 0.62 NO
25 RELA RELA RELA 4908 0.039 0.6 NO
26 TBK1 TBK1 TBK1 6135 0.023 0.54 NO
27 POLR1D POLR1D POLR1D 6234 0.022 0.54 NO
28 POLR3H POLR3H POLR3H 6433 0.02 0.53 NO
29 IRF3 IRF3 IRF3 6783 0.016 0.52 NO
30 ADAR ADAR ADAR 7756 0.0062 0.47 NO
31 MAVS MAVS MAVS 8138 0.0025 0.45 NO
32 POLR3GL POLR3GL POLR3GL 8430 -0.00048 0.43 NO
33 RIPK1 RIPK1 RIPK1 9130 -0.007 0.4 NO
34 POLR3C POLR3C POLR3C 9773 -0.013 0.36 NO
35 NFKBIB NFKBIB NFKBIB 11913 -0.035 0.26 NO
36 POLR3B POLR3B POLR3B 12860 -0.048 0.22 NO
37 POLR3F POLR3F POLR3F 13325 -0.055 0.2 NO
38 CHUK CHUK CHUK 13532 -0.059 0.21 NO
39 POLR3A POLR3A POLR3A 13767 -0.064 0.21 NO
40 IL6 IL6 IL6 13816 -0.065 0.22 NO
41 POLR3D POLR3D POLR3D 13997 -0.069 0.23 NO
42 POLR3G POLR3G POLR3G 14386 -0.078 0.23 NO

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

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

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

Table 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 KIR2DL4 KIR2DL4 KIR2DL4 103 0.33 0.041 YES
2 CIITA CIITA CIITA 142 0.3 0.082 YES
3 HLA-DRB5 HLA-DRB5 HLA-DRB5 151 0.3 0.12 YES
4 HLA-DOB HLA-DOB HLA-DOB 340 0.24 0.15 YES
5 KLRC1 KLRC1 KLRC1 386 0.23 0.18 YES
6 LTA LTA LTA 446 0.23 0.21 YES
7 HLA-DMA HLA-DMA HLA-DMA 450 0.23 0.24 YES
8 HLA-DRB1 HLA-DRB1 HLA-DRB1 462 0.22 0.27 YES
9 HLA-DOA HLA-DOA HLA-DOA 739 0.19 0.28 YES
10 HLA-F HLA-F HLA-F 744 0.19 0.31 YES
11 HLA-DQA1 HLA-DQA1 HLA-DQA1 748 0.19 0.34 YES
12 TAP1 TAP1 TAP1 764 0.19 0.36 YES
13 HLA-DPA1 HLA-DPA1 HLA-DPA1 779 0.19 0.39 YES
14 TAP2 TAP2 TAP2 782 0.19 0.42 YES
15 HLA-DPB1 HLA-DPB1 HLA-DPB1 791 0.19 0.44 YES
16 HLA-DRA HLA-DRA HLA-DRA 1011 0.17 0.46 YES
17 HLA-DMB HLA-DMB HLA-DMB 1021 0.17 0.48 YES
18 HLA-DQB1 HLA-DQB1 HLA-DQB1 1022 0.17 0.5 YES
19 KLRC2 KLRC2 KLRC2 1039 0.16 0.52 YES
20 CD74 CD74 CD74 1242 0.15 0.53 YES
21 PSME2 PSME2 PSME2 1309 0.14 0.55 YES
22 CTSS CTSS CTSS 1434 0.14 0.56 YES
23 PSME1 PSME1 PSME1 1667 0.12 0.57 YES
24 HLA-B HLA-B HLA-B 1847 0.12 0.57 YES
25 HLA-C HLA-C HLA-C 1876 0.11 0.59 YES
26 B2M B2M B2M 1892 0.11 0.6 YES
27 KLRC3 KLRC3 KLRC3 1894 0.11 0.62 YES
28 IFI30 IFI30 IFI30 2229 0.1 0.62 YES
29 HLA-E HLA-E HLA-E 2248 0.099 0.63 YES
30 CD8A CD8A CD8A 2382 0.095 0.64 YES
31 HLA-G HLA-G HLA-G 2663 0.085 0.63 YES
32 HLA-DQA2 HLA-DQA2 HLA-DQA2 2682 0.084 0.64 YES
33 TAPBP TAPBP TAPBP 2738 0.082 0.65 YES
34 HSPA1L HSPA1L HSPA1L 2924 0.077 0.65 YES
35 HLA-A HLA-A HLA-A 2936 0.077 0.66 YES
36 CD4 CD4 CD4 3044 0.074 0.67 YES
37 KIR3DL2 KIR3DL2 KIR3DL2 3075 0.074 0.68 YES
38 KIR2DL3 KIR2DL3 KIR2DL3 3132 0.072 0.68 YES
39 KIR3DL1 KIR3DL1 KIR3DL1 3135 0.072 0.7 YES
40 KLRC4 KLRC4 KLRC4 3194 0.07 0.7 YES
41 HSPA1B HSPA1B HSPA1B 4008 0.053 0.67 NO
42 KLRD1 KLRD1 KLRD1 4173 0.05 0.66 NO
43 KIR2DS4 KIR2DS4 KIR2DS4 4680 0.042 0.64 NO
44 PDIA3 PDIA3 PDIA3 4722 0.042 0.65 NO
45 CTSL1 CTSL1 CTSL1 5030 0.037 0.64 NO
46 RFX5 RFX5 RFX5 5068 0.037 0.64 NO
47 CTSB CTSB CTSB 5089 0.036 0.64 NO
48 HSPA1A HSPA1A HSPA1A 5170 0.035 0.64 NO
49 HSP90AA1 HSP90AA1 HSP90AA1 5461 0.031 0.63 NO
50 HSPA8 HSPA8 HSPA8 6860 0.015 0.56 NO
51 NFYB NFYB NFYB 6977 0.014 0.55 NO
52 CANX CANX CANX 7266 0.011 0.54 NO
53 RFXANK RFXANK RFXANK 8671 -0.003 0.46 NO
54 CALR CALR CALR 8703 -0.0033 0.46 NO
55 HSPA5 HSPA5 HSPA5 8841 -0.0045 0.46 NO
56 HSPA4 HSPA4 HSPA4 9233 -0.0078 0.44 NO
57 NFYC NFYC NFYC 9476 -0.01 0.42 NO
58 RFXAP RFXAP RFXAP 9886 -0.014 0.4 NO
59 HSPA6 HSPA6 HSPA6 9944 -0.014 0.4 NO
60 PSME3 PSME3 PSME3 10716 -0.022 0.36 NO
61 KIR2DL1 KIR2DL1 KIR2DL1 11044 -0.026 0.35 NO
62 LGMN LGMN LGMN 11080 -0.026 0.35 NO
63 CD8B CD8B CD8B 12650 -0.045 0.27 NO
64 CREB1 CREB1 CREB1 13758 -0.064 0.22 NO
65 NFYA NFYA NFYA 14410 -0.079 0.2 NO
66 HSPA2 HSPA2 HSPA2 16712 -0.18 0.1 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 CITRATE CYCLE TCA CYCLE.

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

genes ES table in pathway: KEGG 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 IL12A IL12A IL12A 105 0.33 0.058 YES
2 HLA-DRB5 HLA-DRB5 HLA-DRB5 151 0.3 0.12 YES
3 FASLG FASLG FASLG 166 0.29 0.17 YES
4 HLA-DOB HLA-DOB HLA-DOB 340 0.24 0.21 YES
5 HLA-DMA HLA-DMA HLA-DMA 450 0.23 0.25 YES
6 HLA-DRB1 HLA-DRB1 HLA-DRB1 462 0.22 0.29 YES
7 PRF1 PRF1 PRF1 710 0.2 0.32 YES
8 HLA-DOA HLA-DOA HLA-DOA 739 0.19 0.35 YES
9 HLA-F HLA-F HLA-F 744 0.19 0.39 YES
10 HLA-DQA1 HLA-DQA1 HLA-DQA1 748 0.19 0.43 YES
11 HLA-DPA1 HLA-DPA1 HLA-DPA1 779 0.19 0.46 YES
12 HLA-DPB1 HLA-DPB1 HLA-DPB1 791 0.19 0.5 YES
13 GZMB GZMB GZMB 798 0.19 0.54 YES
14 CD86 CD86 CD86 829 0.18 0.57 YES
15 HLA-DRA HLA-DRA HLA-DRA 1011 0.17 0.59 YES
16 HLA-DMB HLA-DMB HLA-DMB 1021 0.17 0.62 YES
17 CD80 CD80 CD80 1033 0.16 0.66 YES
18 IFNG IFNG IFNG 1166 0.15 0.68 YES
19 CD40 CD40 CD40 1238 0.15 0.7 YES
20 TNF TNF TNF 1318 0.14 0.73 YES
21 IL12B IL12B IL12B 1602 0.13 0.74 YES
22 HLA-B HLA-B HLA-B 1847 0.12 0.75 YES
23 CD40LG CD40LG CD40LG 1869 0.12 0.77 YES
24 HLA-C HLA-C HLA-C 1876 0.11 0.79 YES
25 HLA-E HLA-E HLA-E 2248 0.099 0.79 YES
26 FAS FAS FAS 2544 0.089 0.79 YES
27 HLA-G HLA-G HLA-G 2663 0.085 0.8 YES
28 HLA-DQA2 HLA-DQA2 HLA-DQA2 2682 0.084 0.82 YES
29 HLA-A HLA-A HLA-A 2936 0.077 0.82 YES
30 IL10 IL10 IL10 9208 -0.0076 0.48 NO
31 CD28 CD28 CD28 13424 -0.057 0.27 NO
32 IL5 IL5 IL5 13501 -0.058 0.27 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 GLUTATHIONE 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 HLA-DRB5 HLA-DRB5 HLA-DRB5 151 0.3 0.049 YES
2 FASLG FASLG FASLG 166 0.29 0.1 YES
3 HLA-DOB HLA-DOB HLA-DOB 340 0.24 0.14 YES
4 KLRC1 KLRC1 KLRC1 386 0.23 0.18 YES
5 HLA-DMA HLA-DMA HLA-DMA 450 0.23 0.22 YES
6 HLA-DRB1 HLA-DRB1 HLA-DRB1 462 0.22 0.26 YES
7 IL1B IL1B IL1B 694 0.2 0.29 YES
8 PRF1 PRF1 PRF1 710 0.2 0.32 YES
9 HLA-DOA HLA-DOA HLA-DOA 739 0.19 0.36 YES
10 HLA-F HLA-F HLA-F 744 0.19 0.4 YES
11 HLA-DQA1 HLA-DQA1 HLA-DQA1 748 0.19 0.43 YES
12 HLA-DPA1 HLA-DPA1 HLA-DPA1 779 0.19 0.46 YES
13 HLA-DPB1 HLA-DPB1 HLA-DPB1 791 0.19 0.5 YES
14 GZMB GZMB GZMB 798 0.19 0.54 YES
15 CD86 CD86 CD86 829 0.18 0.57 YES
16 IL1A IL1A IL1A 887 0.18 0.6 YES
17 HLA-DRA HLA-DRA HLA-DRA 1011 0.17 0.62 YES
18 HLA-DMB HLA-DMB HLA-DMB 1021 0.17 0.65 YES
19 CD80 CD80 CD80 1033 0.16 0.68 YES
20 IFNG IFNG IFNG 1166 0.15 0.71 YES
21 TNF TNF TNF 1318 0.14 0.73 YES
22 HLA-B HLA-B HLA-B 1847 0.12 0.72 YES
23 HLA-C HLA-C HLA-C 1876 0.11 0.74 YES
24 HLA-E HLA-E HLA-E 2248 0.099 0.74 YES
25 FAS FAS FAS 2544 0.089 0.74 YES
26 HLA-G HLA-G HLA-G 2663 0.085 0.75 YES
27 HLA-DQA2 HLA-DQA2 HLA-DQA2 2682 0.084 0.76 YES
28 HLA-A HLA-A HLA-A 2936 0.077 0.76 YES
29 KIR3DL2 KIR3DL2 KIR3DL2 3075 0.074 0.77 YES
30 KIR2DL3 KIR2DL3 KIR2DL3 3132 0.072 0.78 YES
31 KIR3DL1 KIR3DL1 KIR3DL1 3135 0.072 0.8 YES
32 KLRD1 KLRD1 KLRD1 4173 0.05 0.75 NO
33 KIR2DL1 KIR2DL1 KIR2DL1 11044 -0.026 0.38 NO
34 CD28 CD28 CD28 13424 -0.057 0.26 NO
35 IL6 IL6 IL6 13816 -0.065 0.26 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 GLUTATHIONE METABOLISM.

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

genes ES table in pathway: KEGG PEROXISOME

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 PCK1 PCK1 PCK1 1102 0.16 0.044 YES
2 IDH3A IDH3A IDH3A 1775 0.12 0.086 YES
3 SUCLG2 SUCLG2 SUCLG2 2346 0.096 0.12 YES
4 IDH2 IDH2 IDH2 2495 0.09 0.17 YES
5 PDHA1 PDHA1 PDHA1 2756 0.082 0.21 YES
6 IDH3G IDH3G IDH3G 2826 0.08 0.26 YES
7 PCK2 PCK2 PCK2 3288 0.068 0.28 YES
8 SDHA SDHA SDHA 3473 0.064 0.31 YES
9 ACO2 ACO2 ACO2 3554 0.062 0.35 YES
10 SDHD SDHD SDHD 3660 0.059 0.38 YES
11 IDH1 IDH1 IDH1 3769 0.057 0.41 YES
12 MDH2 MDH2 MDH2 3853 0.056 0.44 YES
13 SDHB SDHB SDHB 4852 0.04 0.42 YES
14 SUCLG1 SUCLG1 SUCLG1 4953 0.038 0.43 YES
15 FH FH FH 5267 0.034 0.44 YES
16 DLAT DLAT DLAT 5473 0.031 0.45 YES
17 PC PC PC 5936 0.026 0.44 YES
18 SDHC SDHC SDHC 6113 0.023 0.45 YES
19 OGDH OGDH OGDH 6277 0.022 0.45 YES
20 PDHB PDHB PDHB 6727 0.017 0.44 NO
21 MDH1 MDH1 MDH1 6886 0.015 0.44 NO
22 CS CS CS 6945 0.014 0.45 NO
23 DLD DLD DLD 7355 0.01 0.43 NO
24 DLST DLST DLST 8469 -0.001 0.37 NO
25 IDH3B IDH3B IDH3B 10447 -0.02 0.28 NO
26 ACLY ACLY ACLY 12426 -0.042 0.2 NO
27 ACO1 ACO1 ACO1 12671 -0.046 0.22 NO
28 SUCLA2 SUCLA2 SUCLA2 12986 -0.05 0.23 NO
29 OGDHL OGDHL OGDHL 15316 -0.11 0.18 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 PEROXISOME.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PEROXISOME, 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 APOPTOSIS

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 BIRC3 BIRC3 BIRC3 300 0.25 0.097 YES
2 TNFSF10 TNFSF10 TNFSF10 741 0.19 0.16 YES
3 TNFRSF10A TNFRSF10A TNFRSF10A 1054 0.16 0.22 YES
4 CASP10 CASP10 CASP10 1553 0.13 0.25 YES
5 TRADD TRADD TRADD 1681 0.12 0.3 YES
6 TNFRSF25 TNFRSF25 TNFRSF25 2799 0.081 0.27 YES
7 CASP8 CASP8 CASP8 2981 0.076 0.3 YES
8 CASP7 CASP7 CASP7 3090 0.073 0.32 YES
9 LMNA LMNA LMNA 3262 0.069 0.35 YES
10 CFLAR CFLAR CFLAR 3489 0.063 0.36 YES
11 NFKBIA NFKBIA NFKBIA 3584 0.061 0.38 YES
12 NFKB1 NFKB1 NFKB1 3761 0.057 0.4 YES
13 FADD FADD FADD 4066 0.052 0.41 YES
14 XIAP XIAP XIAP 4541 0.044 0.4 YES
15 TRAF2 TRAF2 TRAF2 4834 0.04 0.4 YES
16 RELA RELA RELA 4908 0.039 0.42 YES
17 MAP3K14 MAP3K14 MAP3K14 5055 0.037 0.43 YES
18 CYCS CYCS CYCS 5199 0.035 0.44 YES
19 DFFB DFFB DFFB 6314 0.021 0.38 NO
20 TNFSF12 TNFSF12 TNFSF12 6337 0.021 0.39 NO
21 BCL2 BCL2 BCL2 6503 0.019 0.39 NO
22 CASP6 CASP6 CASP6 6517 0.019 0.4 NO
23 RIPK1 RIPK1 RIPK1 9130 -0.007 0.26 NO
24 TNFRSF10B TNFRSF10B TNFRSF10B 10020 -0.015 0.22 NO
25 BIRC2 BIRC2 BIRC2 10254 -0.017 0.22 NO
26 SPTAN1 SPTAN1 SPTAN1 12507 -0.043 0.11 NO
27 CASP3 CASP3 CASP3 12527 -0.043 0.13 NO
28 DFFA DFFA DFFA 12545 -0.043 0.15 NO
29 CASP9 CASP9 CASP9 13155 -0.052 0.14 NO
30 CHUK CHUK CHUK 13532 -0.059 0.15 NO
31 APAF1 APAF1 APAF1 14326 -0.077 0.14 NO
32 GAS2 GAS2 GAS2 17026 -0.2 0.083 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 APOPTOSIS.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG APOPTOSIS, 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 ANTIGEN PROCESSING AND PRESENTATION

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 IL12A IL12A IL12A 105 0.33 0.048 YES
2 HLA-DRB5 HLA-DRB5 HLA-DRB5 151 0.3 0.094 YES
3 FASLG FASLG FASLG 166 0.29 0.14 YES
4 HLA-DOB HLA-DOB HLA-DOB 340 0.24 0.17 YES
5 LTA LTA LTA 446 0.23 0.2 YES
6 HLA-DMA HLA-DMA HLA-DMA 450 0.23 0.24 YES
7 HLA-DRB1 HLA-DRB1 HLA-DRB1 462 0.22 0.28 YES
8 IL1B IL1B IL1B 694 0.2 0.3 YES
9 PRF1 PRF1 PRF1 710 0.2 0.33 YES
10 HLA-DOA HLA-DOA HLA-DOA 739 0.19 0.36 YES
11 HLA-F HLA-F HLA-F 744 0.19 0.39 YES
12 HLA-DQA1 HLA-DQA1 HLA-DQA1 748 0.19 0.42 YES
13 HLA-DPA1 HLA-DPA1 HLA-DPA1 779 0.19 0.45 YES
14 HLA-DPB1 HLA-DPB1 HLA-DPB1 791 0.19 0.48 YES
15 GZMB GZMB GZMB 798 0.19 0.51 YES
16 CD86 CD86 CD86 829 0.18 0.54 YES
17 IL1A IL1A IL1A 887 0.18 0.56 YES
18 HLA-DRA HLA-DRA HLA-DRA 1011 0.17 0.58 YES
19 HLA-DMB HLA-DMB HLA-DMB 1021 0.17 0.61 YES
20 CD80 CD80 CD80 1033 0.16 0.64 YES
21 IFNG IFNG IFNG 1166 0.15 0.65 YES
22 PTPRN2 PTPRN2 PTPRN2 1298 0.14 0.67 YES
23 TNF TNF TNF 1318 0.14 0.69 YES
24 IL12B IL12B IL12B 1602 0.13 0.7 YES
25 HLA-B HLA-B HLA-B 1847 0.12 0.7 YES
26 HLA-C HLA-C HLA-C 1876 0.11 0.72 YES
27 HLA-E HLA-E HLA-E 2248 0.099 0.72 YES
28 FAS FAS FAS 2544 0.089 0.71 YES
29 HLA-G HLA-G HLA-G 2663 0.085 0.72 YES
30 HLA-DQA2 HLA-DQA2 HLA-DQA2 2682 0.084 0.74 YES
31 HLA-A HLA-A HLA-A 2936 0.077 0.73 NO
32 HSPD1 HSPD1 HSPD1 5363 0.033 0.61 NO
33 ICA1 ICA1 ICA1 7022 0.014 0.52 NO
34 CD28 CD28 CD28 13424 -0.057 0.18 NO
35 GAD1 GAD1 GAD1 13731 -0.063 0.18 NO
36 CPE CPE CPE 17121 -0.2 0.029 NO
37 PTPRN PTPRN PTPRN 18005 -0.3 0.03 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 ANTIGEN PROCESSING AND PRESENTATION.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION, 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 0.36 1.3 0.14 1 0.99 0.5 0.37 0.32 1 0.78
BIOCARTA MPR PATHWAY 32 genes.ES.table 0.36 1.2 0.24 0.93 1 0.16 0.13 0.14 0.81 0.36
BIOCARTA CHREBP2 PATHWAY 40 genes.ES.table 0.31 1.3 0.21 1 1 0.075 0.068 0.07 0.9 0.43
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.33 1.1 0.34 0.99 1 0.44 0.36 0.28 0.91 0.41
KEGG GLYCINE SERINE AND THREONINE METABOLISM 28 genes.ES.table 0.48 1.2 0.17 0.95 1 0.5 0.2 0.4 0.83 0.37
KEGG STARCH AND SUCROSE METABOLISM 33 genes.ES.table 0.46 1.3 0.14 1 0.99 0.24 0.098 0.22 0.92 0.45
KEGG BUTANOATE METABOLISM 29 genes.ES.table 0.38 1.1 0.36 0.98 1 0.28 0.24 0.21 0.91 0.42
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.3 1.2 0.3 0.95 1 0.55 0.48 0.29 0.88 0.38
KEGG RNA DEGRADATION 56 genes.ES.table 0.32 1.5 0.12 1 0.92 0.59 0.5 0.29 1 0.8
KEGG BASAL TRANSCRIPTION FACTORS 34 genes.ES.table 0.33 1.2 0.25 0.89 1 0.5 0.42 0.29 0.79 0.34
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 ENO3 ENO3 ENO3 1265 0.25 0.036 YES
2 DCP1B DCP1B DCP1B 2885 0.15 0.01 YES
3 ENO2 ENO2 ENO2 3682 0.12 0.016 YES
4 PAPOLB PAPOLB PAPOLB 4150 0.1 0.034 YES
5 PAPOLG PAPOLG PAPOLG 4479 0.096 0.056 YES
6 LSM5 LSM5 LSM5 5139 0.081 0.054 YES
7 DCP1A DCP1A DCP1A 5543 0.072 0.062 YES
8 XRN2 XRN2 XRN2 5694 0.07 0.082 YES
9 CNOT2 CNOT2 CNOT2 5835 0.067 0.1 YES
10 RQCD1 RQCD1 RQCD1 5838 0.067 0.13 YES
11 EXOSC6 EXOSC6 EXOSC6 5882 0.066 0.16 YES
12 EXOSC7 EXOSC7 EXOSC7 6052 0.064 0.17 YES
13 PNPT1 PNPT1 PNPT1 6179 0.062 0.19 YES
14 CNOT7 CNOT7 CNOT7 6375 0.058 0.2 YES
15 EXOSC10 EXOSC10 EXOSC10 6829 0.052 0.2 YES
16 EXOSC1 EXOSC1 EXOSC1 6862 0.051 0.22 YES
17 EXOSC9 EXOSC9 EXOSC9 7194 0.047 0.22 YES
18 EDC4 EDC4 EDC4 7257 0.046 0.24 YES
19 MPHOSPH6 MPHOSPH6 MPHOSPH6 7274 0.046 0.26 YES
20 LSM2 LSM2 LSM2 7420 0.044 0.26 YES
21 DIS3 DIS3 DIS3 7489 0.042 0.28 YES
22 SKIV2L SKIV2L SKIV2L 7553 0.042 0.29 YES
23 HSPD1 HSPD1 HSPD1 7865 0.038 0.29 YES
24 LSM4 LSM4 LSM4 7995 0.036 0.3 YES
25 TTC37 TTC37 TTC37 8200 0.033 0.3 YES
26 PARN PARN PARN 8356 0.032 0.31 YES
27 EDC3 EDC3 EDC3 8455 0.03 0.31 YES
28 CNOT10 CNOT10 CNOT10 8760 0.027 0.31 YES
29 CNOT3 CNOT3 CNOT3 9067 0.023 0.3 YES
30 ZCCHC7 ZCCHC7 ZCCHC7 9095 0.023 0.31 YES
31 NAA38 NAA38 NAA38 9172 0.022 0.31 YES
32 DDX6 DDX6 DDX6 9304 0.02 0.32 YES
33 DCP2 DCP2 DCP2 9359 0.019 0.32 YES
34 EXOSC8 EXOSC8 EXOSC8 9719 0.014 0.31 NO
35 CNOT6 CNOT6 CNOT6 9733 0.014 0.31 NO
36 CNOT1 CNOT1 CNOT1 9863 0.012 0.31 NO
37 EXOSC2 EXOSC2 EXOSC2 9995 0.011 0.31 NO
38 LSM6 LSM6 LSM6 10079 0.01 0.31 NO
39 LSM7 LSM7 LSM7 10250 0.0079 0.3 NO
40 EXOSC3 EXOSC3 EXOSC3 10311 0.0073 0.3 NO
41 LSM1 LSM1 LSM1 10323 0.0072 0.3 NO
42 PAPOLA PAPOLA PAPOLA 10374 0.0062 0.3 NO
43 PATL1 PATL1 PATL1 10496 0.0049 0.3 NO
44 SKIV2L2 SKIV2L2 SKIV2L2 10513 0.0047 0.3 NO
45 CNOT4 CNOT4 CNOT4 10522 0.0046 0.3 NO
46 EXOSC5 EXOSC5 EXOSC5 11097 -0.0035 0.27 NO
47 C1D C1D C1D 11159 -0.0045 0.27 NO
48 WDR61 WDR61 WDR61 11163 -0.0046 0.27 NO
49 LSM3 LSM3 LSM3 11290 -0.0062 0.27 NO
50 PAPD7 PAPD7 PAPD7 11493 -0.0088 0.26 NO
51 ENO1 ENO1 ENO1 12414 -0.022 0.22 NO
52 CNOT6L CNOT6L CNOT6L 13074 -0.034 0.2 NO
53 XRN1 XRN1 XRN1 13109 -0.035 0.21 NO
54 HSPA9 HSPA9 HSPA9 13166 -0.036 0.22 NO
55 DCPS DCPS DCPS 13644 -0.045 0.21 NO
56 EXOSC4 EXOSC4 EXOSC4 15971 -0.13 0.14 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 MPR 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 PRPF40B PRPF40B PRPF40B 3599 0.12 -0.17 YES
2 CHERP CHERP CHERP 4040 0.11 -0.17 YES
3 SNRPE SNRPE SNRPE 4044 0.11 -0.15 YES
4 SNRNP200 SNRNP200 SNRNP200 4272 0.1 -0.14 YES
5 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 4407 0.098 -0.13 YES
6 SNRPF SNRPF SNRPF 4815 0.088 -0.13 YES
7 CTNNBL1 CTNNBL1 CTNNBL1 4964 0.085 -0.12 YES
8 CRNKL1 CRNKL1 CRNKL1 4976 0.084 -0.11 YES
9 WBP11 WBP11 WBP11 5083 0.082 -0.095 YES
10 LSM5 LSM5 LSM5 5139 0.081 -0.082 YES
11 MAGOHB MAGOHB MAGOHB 5263 0.078 -0.072 YES
12 THOC1 THOC1 THOC1 5613 0.071 -0.077 YES
13 CDC40 CDC40 CDC40 5717 0.069 -0.068 YES
14 RBM8A RBM8A RBM8A 5745 0.069 -0.055 YES
15 HSPA2 HSPA2 HSPA2 5815 0.068 -0.045 YES
16 HNRNPA1 HNRNPA1 HNRNPA1 5871 0.067 -0.034 YES
17 CDC5L CDC5L CDC5L 5947 0.065 -0.025 YES
18 SNRPG SNRPG SNRPG 6170 0.062 -0.025 YES
19 HSPA1L HSPA1L HSPA1L 6331 0.059 -0.021 YES
20 USP39 USP39 USP39 6342 0.059 -0.0096 YES
21 SNRPB SNRPB SNRPB 6356 0.059 0.0018 YES
22 SF3B1 SF3B1 SF3B1 6368 0.058 0.013 YES
23 SF3B3 SF3B3 SF3B3 6572 0.056 0.014 YES
24 RBMX RBMX RBMX 6641 0.054 0.021 YES
25 PPIL1 PPIL1 PPIL1 6645 0.054 0.032 YES
26 ACIN1 ACIN1 ACIN1 6715 0.053 0.039 YES
27 SFRS9 SFRS9 SFRS9 6755 0.053 0.048 YES
28 SNRPD1 SNRPD1 SNRPD1 6788 0.052 0.057 YES
29 ISY1 ISY1 ISY1 6892 0.051 0.062 YES
30 HNRNPU HNRNPU HNRNPU 6904 0.051 0.072 YES
31 PRPF8 PRPF8 PRPF8 6947 0.05 0.08 YES
32 PRPF40A PRPF40A PRPF40A 6948 0.05 0.09 YES
33 SFRS7 SFRS7 SFRS7 7133 0.048 0.09 YES
34 SNRNP40 SNRNP40 SNRNP40 7160 0.047 0.098 YES
35 SNRPB2 SNRPB2 SNRPB2 7198 0.046 0.11 YES
36 HNRNPA3 HNRNPA3 HNRNPA3 7245 0.046 0.11 YES
37 RBM17 RBM17 RBM17 7251 0.046 0.12 YES
38 DHX16 DHX16 DHX16 7282 0.046 0.13 YES
39 SF3B14 SF3B14 SF3B14 7293 0.045 0.14 YES
40 SFRS6 SFRS6 SFRS6 7326 0.045 0.15 YES
41 SMNDC1 SMNDC1 SMNDC1 7344 0.045 0.15 YES
42 SF3A3 SF3A3 SF3A3 7345 0.045 0.16 YES
43 SFRS13A SFRS13A SFRS13A 7348 0.045 0.17 YES
44 EFTUD2 EFTUD2 EFTUD2 7368 0.044 0.18 YES
45 MAGOH MAGOH MAGOH 7376 0.044 0.19 YES
46 LSM2 LSM2 LSM2 7420 0.044 0.2 YES
47 SR140 SR140 SR140 7531 0.042 0.2 YES
48 HNRNPM HNRNPM HNRNPM 7545 0.042 0.21 YES
49 SNRPC SNRPC SNRPC 7616 0.041 0.21 YES
50 TRA2B TRA2B TRA2B 7642 0.04 0.22 YES
51 DDX23 DDX23 DDX23 7667 0.04 0.22 YES
52 DHX38 DHX38 DHX38 7790 0.038 0.23 YES
53 TCERG1 TCERG1 TCERG1 7958 0.036 0.22 YES
54 LSM4 LSM4 LSM4 7995 0.036 0.23 YES
55 SNRPA SNRPA SNRPA 8027 0.036 0.24 YES
56 SFRS3 SFRS3 SFRS3 8131 0.034 0.24 YES
57 DHX15 DHX15 DHX15 8219 0.033 0.24 YES
58 HNRNPC HNRNPC HNRNPC 8376 0.032 0.24 YES
59 BCAS2 BCAS2 BCAS2 8418 0.031 0.24 YES
60 SFRS1 SFRS1 SFRS1 8507 0.03 0.24 YES
61 PRPF6 PRPF6 PRPF6 8512 0.03 0.25 YES
62 RBM25 RBM25 RBM25 8597 0.029 0.25 YES
63 BAT1 BAT1 BAT1 8607 0.029 0.26 YES
64 CCDC12 CCDC12 CCDC12 8650 0.028 0.26 YES
65 XAB2 XAB2 XAB2 8666 0.028 0.26 YES
66 DDX46 DDX46 DDX46 8773 0.027 0.26 YES
67 PRPF38A PRPF38A PRPF38A 8787 0.027 0.27 YES
68 SNRNP27 SNRNP27 SNRNP27 8795 0.026 0.27 YES
69 PPIE PPIE PPIE 8855 0.026 0.28 YES
70 PRPF19 PRPF19 PRPF19 8873 0.026 0.28 YES
71 PRPF3 PRPF3 PRPF3 8893 0.025 0.28 YES
72 SF3B4 SF3B4 SF3B4 8911 0.025 0.29 YES
73 DHX8 DHX8 DHX8 8932 0.025 0.29 YES
74 NAA38 NAA38 NAA38 9172 0.022 0.28 YES
75 SFRS2B SFRS2B SFRS2B 9209 0.021 0.29 YES
76 PRPF38B PRPF38B PRPF38B 9221 0.021 0.29 YES
77 PRPF31 PRPF31 PRPF31 9275 0.02 0.29 YES
78 SFRS4 SFRS4 SFRS4 9288 0.02 0.29 YES
79 SNRPD2 SNRPD2 SNRPD2 9314 0.02 0.3 YES
80 SF3B5 SF3B5 SF3B5 9339 0.02 0.3 YES
81 U2AF1 U2AF1 U2AF1 9375 0.019 0.3 YES
82 PQBP1 PQBP1 PQBP1 9401 0.019 0.3 YES
83 TRA2A TRA2A TRA2A 9414 0.018 0.31 YES
84 HNRNPK HNRNPK HNRNPK 9505 0.017 0.31 YES
85 U2AF2 U2AF2 U2AF2 9576 0.016 0.31 YES
86 SF3B2 SF3B2 SF3B2 9598 0.016 0.31 YES
87 PRPF18 PRPF18 PRPF18 9614 0.016 0.31 YES
88 SART1 SART1 SART1 9680 0.015 0.31 NO
89 PPIH PPIH PPIH 10014 0.011 0.29 NO
90 NCBP1 NCBP1 NCBP1 10064 0.01 0.29 NO
91 PRPF4 PRPF4 PRPF4 10077 0.01 0.3 NO
92 LSM6 LSM6 LSM6 10079 0.01 0.3 NO
93 THOC4 THOC4 THOC4 10135 0.0093 0.3 NO
94 PCBP1 PCBP1 PCBP1 10161 0.009 0.3 NO
95 SF3A2 SF3A2 SF3A2 10199 0.0086 0.3 NO
96 SFRS5 SFRS5 SFRS5 10229 0.0082 0.3 NO
97 LSM7 LSM7 LSM7 10250 0.0079 0.3 NO
98 BUD31 BUD31 BUD31 10265 0.0078 0.3 NO
99 TXNL4A TXNL4A TXNL4A 10319 0.0072 0.3 NO
100 SF3A1 SF3A1 SF3A1 10348 0.0068 0.3 NO
101 SNW1 SNW1 SNW1 10390 0.0061 0.3 NO
102 SFRS2 SFRS2 SFRS2 10587 0.0038 0.28 NO
103 SYF2 SYF2 SYF2 10686 0.0025 0.28 NO
104 DDX42 DDX42 DDX42 10717 0.002 0.28 NO
105 SNRNP70 SNRNP70 SNRNP70 10785 0.001 0.28 NO
106 CWC15 CWC15 CWC15 11038 -0.0027 0.26 NO
107 THOC2 THOC2 THOC2 11062 -0.003 0.26 NO
108 RBM22 RBM22 RBM22 11107 -0.0036 0.26 NO
109 LSM3 LSM3 LSM3 11290 -0.0062 0.25 NO
110 AQR AQR AQR 11488 -0.0088 0.24 NO
111 SNRPA1 SNRPA1 SNRPA1 11768 -0.013 0.23 NO
112 SNRPD3 SNRPD3 SNRPD3 11974 -0.016 0.22 NO
113 THOC3 THOC3 THOC3 12293 -0.02 0.21 NO
114 HSPA1B HSPA1B HSPA1B 12483 -0.023 0.2 NO
115 DDX5 DDX5 DDX5 12489 -0.023 0.21 NO
116 HSPA8 HSPA8 HSPA8 12821 -0.029 0.2 NO
117 NHP2L1 NHP2L1 NHP2L1 12896 -0.03 0.2 NO
118 HSPA1A HSPA1A HSPA1A 12910 -0.03 0.2 NO
119 SLU7 SLU7 SLU7 13088 -0.034 0.2 NO
120 PHF5A PHF5A PHF5A 13094 -0.034 0.21 NO
121 EIF4A3 EIF4A3 EIF4A3 13104 -0.034 0.22 NO
122 PLRG1 PLRG1 PLRG1 13920 -0.051 0.18 NO
123 ZMAT2 ZMAT2 ZMAT2 13927 -0.051 0.19 NO
124 PUF60 PUF60 PUF60 13968 -0.052 0.2 NO
125 HSPA6 HSPA6 HSPA6 17244 -0.24 0.072 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 MPR PATHWAY.

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

genes ES table in pathway: BIOCARTA CHREBP2 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 TAS1R1 TAS1R1 TAS1R1 293 0.4 0.042 YES
2 TAS2R19 TAS2R19 TAS2R19 489 0.36 0.082 YES
3 GNG3 GNG3 GNG3 737 0.31 0.11 YES
4 GNB3 GNB3 GNB3 781 0.31 0.16 YES
5 ADCY8 ADCY8 ADCY8 937 0.28 0.19 YES
6 TAS2R31 TAS2R31 TAS2R31 986 0.28 0.22 YES
7 TAS2R38 TAS2R38 TAS2R38 1041 0.28 0.26 YES
8 TAS2R60 TAS2R60 TAS2R60 1052 0.27 0.3 YES
9 TAS2R14 TAS2R14 TAS2R14 1171 0.26 0.33 YES
10 TRPM5 TRPM5 TRPM5 1196 0.26 0.37 YES
11 GRM4 GRM4 GRM4 1243 0.26 0.4 YES
12 TAS2R13 TAS2R13 TAS2R13 1483 0.24 0.42 YES
13 TAS2R50 TAS2R50 TAS2R50 1567 0.23 0.45 YES
14 CACNA1A CACNA1A CACNA1A 1587 0.23 0.48 YES
15 TAS2R10 TAS2R10 TAS2R10 1907 0.2 0.49 YES
16 TAS2R5 TAS2R5 TAS2R5 2075 0.19 0.51 YES
17 TAS2R20 TAS2R20 TAS2R20 2227 0.18 0.53 YES
18 TAS2R3 TAS2R3 TAS2R3 2638 0.16 0.53 YES
19 CACNA1B CACNA1B CACNA1B 2745 0.16 0.55 YES
20 TAS2R43 TAS2R43 TAS2R43 3679 0.12 0.51 NO
21 TAS2R4 TAS2R4 TAS2R4 3730 0.12 0.53 NO
22 TAS2R42 TAS2R42 TAS2R42 3942 0.11 0.53 NO
23 TAS1R3 TAS1R3 TAS1R3 4508 0.095 0.52 NO
24 TAS2R40 TAS2R40 TAS2R40 5017 0.083 0.5 NO
25 PRKACB PRKACB PRKACB 5413 0.075 0.49 NO
26 ADCY6 ADCY6 ADCY6 6889 0.051 0.42 NO
27 PRKACA PRKACA PRKACA 7560 0.042 0.39 NO
28 GNAS GNAS GNAS 8498 0.03 0.34 NO
29 SCNN1G SCNN1G SCNN1G 8742 0.027 0.33 NO
30 GNG13 GNG13 GNG13 8809 0.026 0.33 NO
31 GNB1 GNB1 GNB1 9210 0.021 0.31 NO
32 KCNB1 KCNB1 KCNB1 12278 -0.02 0.15 NO
33 ITPR3 ITPR3 ITPR3 13308 -0.038 0.1 NO
34 SCNN1A SCNN1A SCNN1A 13545 -0.043 0.094 NO
35 PRKX PRKX PRKX 14815 -0.076 0.036 NO
36 SCNN1B SCNN1B SCNN1B 15743 -0.11 0.0023 NO
37 ACCN1 ACCN1 ACCN1 15869 -0.12 0.013 NO
38 ADCY4 ADCY4 ADCY4 17539 -0.28 -0.037 NO
39 PLCB2 PLCB2 PLCB2 17662 -0.31 0.00041 NO
40 PDE1A PDE1A PDE1A 17795 -0.34 0.042 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 CHREBP2 PATHWAY.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA WNT PATHWAY

Table 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 BRCA1 BRCA1 BRCA1 1786 0.21 -0.001 YES
2 NR0B1 NR0B1 NR0B1 2331 0.18 0.05 YES
3 GRIP1 GRIP1 GRIP1 2678 0.16 0.1 YES
4 HDAC2 HDAC2 HDAC2 3581 0.12 0.11 YES
5 HDAC6 HDAC6 HDAC6 4201 0.1 0.12 YES
6 PELP1 PELP1 PELP1 4234 0.1 0.17 YES
7 HDAC4 HDAC4 HDAC4 4463 0.096 0.2 YES
8 TBP TBP TBP 4577 0.094 0.23 YES
9 PPARGC1A PPARGC1A PPARGC1A 5557 0.072 0.21 YES
10 POLR2A POLR2A POLR2A 5641 0.071 0.24 YES
11 ERCC3 ERCC3 ERCC3 5716 0.069 0.27 YES
12 CREBBP CREBBP CREBBP 6162 0.062 0.27 YES
13 NRIP1 NRIP1 NRIP1 6202 0.061 0.3 YES
14 GTF2A1 GTF2A1 GTF2A1 6557 0.056 0.3 YES
15 HDAC1 HDAC1 HDAC1 6604 0.055 0.32 YES
16 GTF2E1 GTF2E1 GTF2E1 6675 0.054 0.35 YES
17 CARM1 CARM1 CARM1 6905 0.051 0.36 YES
18 HDAC8 HDAC8 HDAC8 7573 0.041 0.34 NO
19 PHB2 PHB2 PHB2 7648 0.04 0.35 NO
20 MED1 MED1 MED1 8140 0.034 0.34 NO
21 HDAC5 HDAC5 HDAC5 8714 0.027 0.32 NO
22 EP300 EP300 EP300 8917 0.025 0.32 NO
23 SPEN SPEN SPEN 9273 0.02 0.31 NO
24 NCOR2 NCOR2 NCOR2 9640 0.016 0.3 NO
25 HDAC3 HDAC3 HDAC3 9801 0.013 0.3 NO
26 GTF2F1 GTF2F1 GTF2F1 10776 0.0011 0.25 NO
27 HIST2H3C HIST2H3C HIST2H3C 10799 0.00082 0.24 NO
28 CCND1 CCND1 CCND1 12435 -0.022 0.17 NO
29 HDAC11 HDAC11 HDAC11 12706 -0.027 0.16 NO
30 ESR1 ESR1 ESR1 13128 -0.035 0.16 NO
31 HDAC7 HDAC7 HDAC7 13164 -0.036 0.17 NO
32 HDAC9 HDAC9 HDAC9 13439 -0.041 0.18 NO
33 SRA1 SRA1 SRA1 14760 -0.074 0.14 NO
34 HDAC10 HDAC10 HDAC10 16357 -0.15 0.12 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 WNT PATHWAY.

Figure S28.  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 GLYCINE SERINE AND THREONINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MYH6 MYH6 MYH6 37 0.54 0.061 YES
2 CACNA2D2 CACNA2D2 CACNA2D2 96 0.49 0.12 YES
3 ATP1B2 ATP1B2 ATP1B2 152 0.46 0.17 YES
4 ATP1A2 ATP1A2 ATP1A2 177 0.45 0.22 YES
5 MYH7 MYH7 MYH7 226 0.42 0.26 YES
6 CACNB4 CACNB4 CACNB4 571 0.34 0.28 YES
7 COX6A2 COX6A2 COX6A2 610 0.33 0.32 YES
8 RYR2 RYR2 RYR2 977 0.28 0.33 YES
9 CACNA1D CACNA1D CACNA1D 1348 0.24 0.34 YES
10 CACNA1S CACNA1S CACNA1S 1800 0.21 0.34 YES
11 CACNG5 CACNG5 CACNG5 1884 0.21 0.36 YES
12 FXYD2 FXYD2 FXYD2 2013 0.2 0.38 YES
13 CACNG6 CACNG6 CACNG6 2252 0.18 0.39 YES
14 COX6B2 COX6B2 COX6B2 2278 0.18 0.41 YES
15 ATP1A4 ATP1A4 ATP1A4 2447 0.17 0.42 YES
16 COX8C COX8C COX8C 2557 0.17 0.43 YES
17 ACTC1 ACTC1 ACTC1 2696 0.16 0.44 YES
18 TNNT2 TNNT2 TNNT2 3181 0.14 0.43 NO
19 COX4I2 COX4I2 COX4I2 3450 0.13 0.43 NO
20 CACNB3 CACNB3 CACNB3 4248 0.1 0.4 NO
21 CACNA1F CACNA1F CACNA1F 5123 0.081 0.36 NO
22 MYL3 MYL3 MYL3 6113 0.063 0.32 NO
23 CACNB2 CACNB2 CACNB2 6114 0.063 0.32 NO
24 ATP1B1 ATP1B1 ATP1B1 6937 0.05 0.28 NO
25 CACNG8 CACNG8 CACNG8 7035 0.049 0.29 NO
26 CACNA2D1 CACNA2D1 CACNA2D1 7136 0.047 0.29 NO
27 CACNB1 CACNB1 CACNB1 7312 0.045 0.28 NO
28 TNNC1 TNNC1 TNNC1 8075 0.035 0.24 NO
29 COX7A2L COX7A2L COX7A2L 8304 0.032 0.24 NO
30 TNNI3 TNNI3 TNNI3 8407 0.031 0.23 NO
31 ATP1B3 ATP1B3 ATP1B3 11193 -0.005 0.084 NO
32 COX6B1 COX6B1 COX6B1 11589 -0.01 0.064 NO
33 COX7C COX7C COX7C 11609 -0.01 0.064 NO
34 UQCRC1 UQCRC1 UQCRC1 11886 -0.014 0.051 NO
35 SLC8A1 SLC8A1 SLC8A1 12013 -0.016 0.046 NO
36 ATP1A1 ATP1A1 ATP1A1 12017 -0.016 0.048 NO
37 UQCRFS1 UQCRFS1 UQCRFS1 12125 -0.018 0.044 NO
38 TPM3 TPM3 TPM3 12198 -0.019 0.042 NO
39 ATP2A2 ATP2A2 ATP2A2 12213 -0.019 0.044 NO
40 COX7A2 COX7A2 COX7A2 12333 -0.021 0.04 NO
41 COX5B COX5B COX5B 12369 -0.021 0.041 NO
42 CACNA2D3 CACNA2D3 CACNA2D3 12695 -0.026 0.026 NO
43 COX4I1 COX4I1 COX4I1 12716 -0.027 0.028 NO
44 CACNG4 CACNG4 CACNG4 12867 -0.03 0.024 NO
45 COX6A1 COX6A1 COX6A1 12926 -0.031 0.024 NO
46 SLC9A1 SLC9A1 SLC9A1 13064 -0.034 0.02 NO
47 SLC9A6 SLC9A6 SLC9A6 13532 -0.043 0.00022 NO
48 TPM4 TPM4 TPM4 13651 -0.045 -0.00089 NO
49 CACNA1C CACNA1C CACNA1C 14407 -0.064 -0.034 NO
50 UQCRQ UQCRQ UQCRQ 14769 -0.075 -0.045 NO
51 COX8A COX8A COX8A 14822 -0.076 -0.039 NO
52 COX5A COX5A COX5A 14880 -0.078 -0.033 NO
53 UQCR10 UQCR10 UQCR10 14911 -0.079 -0.025 NO
54 UQCRHL UQCRHL UQCRHL 14970 -0.081 -0.019 NO
55 UQCR11 UQCR11 UQCR11 15024 -0.083 -0.012 NO
56 UQCRH UQCRH UQCRH 15319 -0.093 -0.017 NO
57 COX7B COX7B COX7B 15602 -0.11 -0.02 NO
58 UQCRB UQCRB UQCRB 15619 -0.11 -0.0085 NO
59 TPM1 TPM1 TPM1 15628 -0.11 0.0036 NO
60 TPM2 TPM2 TPM2 16113 -0.13 -0.0071 NO
61 CYC1 CYC1 CYC1 16295 -0.15 0.00033 NO
62 CACNG1 CACNG1 CACNG1 16542 -0.16 0.0063 NO
63 COX6C COX6C COX6C 16699 -0.18 0.019 NO
64 COX7A1 COX7A1 COX7A1 16906 -0.2 0.031 NO
65 ATP1A3 ATP1A3 ATP1A3 17088 -0.22 0.047 NO
66 CACNA2D4 CACNA2D4 CACNA2D4 17526 -0.28 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: KEGG GLYCINE SERINE AND THREONINE METABOLISM.

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

genes ES table in pathway: KEGG STARCH AND SUCROSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PTCH2 PTCH2 PTCH2 86 0.5 0.057 YES
2 WNT2B WNT2B WNT2B 206 0.43 0.1 YES
3 TCF7L1 TCF7L1 TCF7L1 261 0.41 0.15 YES
4 GLI1 GLI1 GLI1 273 0.41 0.2 YES
5 WNT8B WNT8B WNT8B 605 0.33 0.22 YES
6 GLI2 GLI2 GLI2 675 0.32 0.26 YES
7 WNT6 WNT6 WNT6 868 0.29 0.29 YES
8 FZD2 FZD2 FZD2 966 0.28 0.32 YES
9 FZD10 FZD10 FZD10 1178 0.26 0.34 YES
10 WNT11 WNT11 WNT11 1361 0.24 0.36 YES
11 SMO SMO SMO 1372 0.24 0.39 YES
12 LEF1 LEF1 LEF1 1452 0.24 0.41 YES
13 WNT5A WNT5A WNT5A 1891 0.2 0.41 YES
14 WNT8A WNT8A WNT8A 1904 0.2 0.44 YES
15 SHH SHH SHH 2631 0.16 0.42 YES
16 WNT10B WNT10B WNT10B 2788 0.16 0.43 YES
17 PTCH1 PTCH1 PTCH1 2976 0.15 0.44 YES
18 STK36 STK36 STK36 3069 0.14 0.45 YES
19 WNT5B WNT5B WNT5B 3183 0.14 0.46 YES
20 WNT3 WNT3 WNT3 3213 0.14 0.48 YES
21 FZD9 FZD9 FZD9 3466 0.13 0.48 YES
22 FZD5 FZD5 FZD5 3526 0.12 0.49 YES
23 FZD7 FZD7 FZD7 3554 0.12 0.5 YES
24 APC2 APC2 APC2 3667 0.12 0.51 YES
25 DVL2 DVL2 DVL2 4260 0.1 0.49 NO
26 GSK3B GSK3B GSK3B 5697 0.07 0.42 NO
27 FZD3 FZD3 FZD3 5873 0.067 0.42 NO
28 TCF7 TCF7 TCF7 6178 0.062 0.41 NO
29 AXIN2 AXIN2 AXIN2 6228 0.06 0.42 NO
30 WNT10A WNT10A WNT10A 6930 0.05 0.39 NO
31 SUFU SUFU SUFU 7086 0.048 0.38 NO
32 DVL1 DVL1 DVL1 7656 0.04 0.36 NO
33 CTNNB1 CTNNB1 CTNNB1 7672 0.04 0.36 NO
34 TCF7L2 TCF7L2 TCF7L2 7704 0.04 0.37 NO
35 WNT4 WNT4 WNT4 7903 0.037 0.36 NO
36 WNT9B WNT9B WNT9B 8009 0.036 0.36 NO
37 DVL3 DVL3 DVL3 8637 0.028 0.33 NO
38 AXIN1 AXIN1 AXIN1 9307 0.02 0.3 NO
39 TP53 TP53 TP53 9701 0.015 0.28 NO
40 WNT1 WNT1 WNT1 9963 0.011 0.26 NO
41 WNT16 WNT16 WNT16 11196 -0.005 0.2 NO
42 APC APC APC 11372 -0.0072 0.19 NO
43 GLI3 GLI3 GLI3 11514 -0.0092 0.18 NO
44 WNT9A WNT9A WNT9A 11574 -0.0099 0.18 NO
45 WNT2 WNT2 WNT2 12015 -0.016 0.16 NO
46 FZD4 FZD4 FZD4 14732 -0.073 0.021 NO
47 WNT7A WNT7A WNT7A 15435 -0.098 -0.0051 NO
48 FZD6 FZD6 FZD6 15542 -0.1 0.002 NO
49 BMP4 BMP4 BMP4 16375 -0.15 -0.024 NO
50 FZD8 FZD8 FZD8 16411 -0.16 -0.0069 NO
51 FZD1 FZD1 FZD1 16723 -0.18 -0.0015 NO
52 BMP2 BMP2 BMP2 17065 -0.22 0.0069 NO
53 HHIP HHIP HHIP 17254 -0.24 0.027 NO
54 WNT7B WNT7B WNT7B 17871 -0.36 0.038 NO

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

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PTCH2 PTCH2 PTCH2 86 0.5 0.06 YES
2 WNT2B WNT2B WNT2B 206 0.43 0.11 YES
3 GLI1 GLI1 GLI1 273 0.41 0.16 YES
4 BMP7 BMP7 BMP7 479 0.36 0.2 YES
5 WNT8B WNT8B WNT8B 605 0.33 0.23 YES
6 BMP6 BMP6 BMP6 632 0.33 0.27 YES
7 GLI2 GLI2 GLI2 675 0.32 0.31 YES
8 WNT6 WNT6 WNT6 868 0.29 0.34 YES
9 IHH IHH IHH 1154 0.26 0.36 YES
10 WNT11 WNT11 WNT11 1361 0.24 0.38 YES
11 SMO SMO SMO 1372 0.24 0.41 YES
12 WNT5A WNT5A WNT5A 1891 0.2 0.41 YES
13 WNT8A WNT8A WNT8A 1904 0.2 0.44 YES
14 ZIC2 ZIC2 ZIC2 1943 0.2 0.46 YES
15 SHH SHH SHH 2631 0.16 0.44 YES
16 WNT10B WNT10B WNT10B 2788 0.16 0.46 YES
17 PTCH1 PTCH1 PTCH1 2976 0.15 0.46 YES
18 STK36 STK36 STK36 3069 0.14 0.48 YES
19 WNT5B WNT5B WNT5B 3183 0.14 0.49 YES
20 WNT3 WNT3 WNT3 3213 0.14 0.51 YES
21 LRP2 LRP2 LRP2 4288 0.1 0.46 NO
22 BTRC BTRC BTRC 4893 0.086 0.44 NO
23 PRKACB PRKACB PRKACB 5413 0.075 0.42 NO
24 CSNK1A1L CSNK1A1L CSNK1A1L 5441 0.075 0.43 NO
25 GSK3B GSK3B GSK3B 5697 0.07 0.43 NO
26 BMP8A BMP8A BMP8A 5773 0.068 0.43 NO
27 RAB23 RAB23 RAB23 6879 0.051 0.38 NO
28 WNT10A WNT10A WNT10A 6930 0.05 0.38 NO
29 SUFU SUFU SUFU 7086 0.048 0.38 NO
30 BMP8B BMP8B BMP8B 7324 0.045 0.37 NO
31 CSNK1E CSNK1E CSNK1E 7365 0.044 0.38 NO
32 PRKACA PRKACA PRKACA 7560 0.042 0.37 NO
33 WNT4 WNT4 WNT4 7903 0.037 0.36 NO
34 WNT9B WNT9B WNT9B 8009 0.036 0.36 NO
35 WNT1 WNT1 WNT1 9963 0.011 0.25 NO
36 FBXW11 FBXW11 FBXW11 10517 0.0046 0.22 NO
37 CSNK1G1 CSNK1G1 CSNK1G1 10568 0.004 0.22 NO
38 CSNK1G3 CSNK1G3 CSNK1G3 10750 0.0015 0.21 NO
39 CSNK1G2 CSNK1G2 CSNK1G2 10935 -0.0012 0.2 NO
40 CSNK1D CSNK1D CSNK1D 11177 -0.0047 0.19 NO
41 WNT16 WNT16 WNT16 11196 -0.005 0.19 NO
42 GLI3 GLI3 GLI3 11514 -0.0092 0.17 NO
43 WNT9A WNT9A WNT9A 11574 -0.0099 0.17 NO
44 WNT2 WNT2 WNT2 12015 -0.016 0.15 NO
45 CSNK1A1 CSNK1A1 CSNK1A1 13709 -0.046 0.064 NO
46 PRKX PRKX PRKX 14815 -0.076 0.014 NO
47 WNT7A WNT7A WNT7A 15435 -0.098 -0.0065 NO
48 BMP4 BMP4 BMP4 16375 -0.15 -0.037 NO
49 DHH DHH DHH 16600 -0.17 -0.027 NO
50 GAS1 GAS1 GAS1 16954 -0.21 -0.02 NO
51 BMP2 BMP2 BMP2 17065 -0.22 0.0028 NO
52 HHIP HHIP HHIP 17254 -0.24 0.024 NO
53 WNT7B WNT7B WNT7B 17871 -0.36 0.038 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 BUTANOATE METABOLISM.

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

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 GCK GCK GCK 40 0.54 0.13 YES
2 UGT1A6 UGT1A6 UGT1A6 686 0.32 0.17 YES
3 ENPP3 ENPP3 ENPP3 741 0.31 0.24 YES
4 GYS2 GYS2 GYS2 1279 0.25 0.28 YES
5 UGT2A1 UGT2A1 UGT2A1 1412 0.24 0.33 YES
6 GBA3 GBA3 GBA3 1432 0.24 0.38 YES
7 UGT2B15 UGT2B15 UGT2B15 1778 0.21 0.42 YES
8 UGT2B11 UGT2B11 UGT2B11 1825 0.21 0.46 YES
9 MGAM MGAM MGAM 3637 0.12 0.4 NO
10 HK2 HK2 HK2 4030 0.11 0.4 NO
11 PYGM PYGM PYGM 4370 0.098 0.41 NO
12 PYGB PYGB PYGB 7568 0.041 0.24 NO
13 PYGL PYGL PYGL 7598 0.041 0.25 NO
14 AGL AGL AGL 7855 0.038 0.25 NO
15 TREH TREH TREH 8805 0.026 0.2 NO
16 UGDH UGDH UGDH 9043 0.024 0.2 NO
17 GUSB GUSB GUSB 9948 0.012 0.15 NO
18 GBE1 GBE1 GBE1 10472 0.0052 0.12 NO
19 GPI GPI GPI 12025 -0.016 0.043 NO
20 HK1 HK1 HK1 12250 -0.02 0.036 NO
21 UGP2 UGP2 UGP2 13312 -0.038 -0.012 NO
22 AMY2A AMY2A AMY2A 13451 -0.041 -0.0094 NO
23 GANC GANC GANC 13464 -0.041 -0.000093 NO
24 ENPP1 ENPP1 ENPP1 13467 -0.041 0.0098 NO
25 PGM2 PGM2 PGM2 13486 -0.042 0.019 NO
26 PGM1 PGM1 PGM1 13529 -0.043 0.027 NO
27 UGT2B7 UGT2B7 UGT2B7 13731 -0.047 0.028 NO
28 GYS1 GYS1 GYS1 14273 -0.06 0.013 NO
29 GAA GAA GAA 14761 -0.074 0.0047 NO
30 PGM2L1 PGM2L1 PGM2L1 14903 -0.079 0.016 NO
31 AMY2B AMY2B AMY2B 15798 -0.12 -0.0038 NO
32 AMY1A AMY1A AMY1A 15827 -0.12 0.023 NO
33 HK3 HK3 HK3 18349 -0.51 0.012 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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RNA DEGRADATION

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 RXRG RXRG RXRG 90 0.49 0.2 YES
2 TCF7L1 TCF7L1 TCF7L1 261 0.41 0.36 YES
3 LEF1 LEF1 LEF1 1452 0.24 0.39 YES
4 KRAS KRAS KRAS 4151 0.1 0.29 NO
5 TPR TPR TPR 5115 0.081 0.27 NO
6 RET RET RET 5615 0.071 0.27 NO
7 TCF7 TCF7 TCF7 6178 0.062 0.26 NO
8 NRAS NRAS NRAS 6417 0.058 0.28 NO
9 CTNNB1 CTNNB1 CTNNB1 7672 0.04 0.22 NO
10 TCF7L2 TCF7L2 TCF7L2 7704 0.04 0.24 NO
11 TFG TFG TFG 7886 0.037 0.24 NO
12 BRAF BRAF BRAF 8179 0.034 0.24 NO
13 RXRB RXRB RXRB 9008 0.024 0.21 NO
14 PAX8 PAX8 PAX8 9420 0.018 0.19 NO
15 TP53 TP53 TP53 9701 0.015 0.18 NO
16 NTRK1 NTRK1 NTRK1 9972 0.011 0.17 NO
17 CDH1 CDH1 CDH1 10523 0.0046 0.15 NO
18 MAP2K2 MAP2K2 MAP2K2 11891 -0.014 0.078 NO
19 TPM3 TPM3 TPM3 12198 -0.019 0.07 NO
20 CCND1 CCND1 CCND1 12435 -0.022 0.066 NO
21 MAP2K1 MAP2K1 MAP2K1 12708 -0.027 0.062 NO
22 CCDC6 CCDC6 CCDC6 12814 -0.029 0.068 NO
23 NCOA4 NCOA4 NCOA4 12883 -0.03 0.077 NO
24 RXRA RXRA RXRA 12992 -0.032 0.084 NO
25 MAPK1 MAPK1 MAPK1 13359 -0.039 0.08 NO
26 MYC MYC MYC 14466 -0.065 0.048 NO
27 MAPK3 MAPK3 MAPK3 14618 -0.07 0.068 NO
28 PPARG PPARG PPARG 17858 -0.36 0.038 NO

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

Figure S38.  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 BASAL TRANSCRIPTION FACTORS

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 GCK GCK GCK 40 0.54 0.18 YES
2 MLXIPL MLXIPL MLXIPL 633 0.33 0.26 YES
3 PRKAA2 PRKAA2 PRKAA2 1269 0.25 0.31 YES
4 PKLR PKLR PKLR 2766 0.16 0.28 NO
5 PRKAB2 PRKAB2 PRKAB2 4682 0.091 0.21 NO
6 PRKAR1B PRKAR1B PRKAR1B 4823 0.088 0.23 NO
7 PRKACB PRKACB PRKACB 5413 0.075 0.23 NO
8 PRKAB1 PRKAB1 PRKAB1 5606 0.072 0.24 NO
9 PRKAR2B PRKAR2B PRKAR2B 6103 0.063 0.24 NO
10 YWHAE YWHAE YWHAE 6720 0.053 0.22 NO
11 PPP2R3A PPP2R3A PPP2R3A 6958 0.05 0.22 NO
12 PPP2R5D PPP2R5D PPP2R5D 7352 0.045 0.22 NO
13 YWHAQ YWHAQ YWHAQ 7401 0.044 0.23 NO
14 PPP2R3B PPP2R3B PPP2R3B 7488 0.042 0.24 NO
15 PPP2R5E PPP2R5E PPP2R5E 7541 0.042 0.25 NO
16 PRKACA PRKACA PRKACA 7560 0.042 0.26 NO
17 ACACA ACACA ACACA 8108 0.035 0.25 NO
18 PPP2R2D PPP2R2D PPP2R2D 8284 0.032 0.25 NO
19 PPP2CB PPP2CB PPP2CB 8449 0.031 0.25 NO
20 PRKAR2A PRKAR2A PRKAR2A 8582 0.029 0.25 NO
21 PPP2R1A PPP2R1A PPP2R1A 8689 0.028 0.26 NO
22 PRKAG1 PRKAG1 PRKAG1 9392 0.019 0.23 NO
23 PPP2R2C PPP2R2C PPP2R2C 9689 0.015 0.22 NO
24 PPP2R2A PPP2R2A PPP2R2A 9763 0.014 0.22 NO
25 YWHAG YWHAG YWHAG 10605 0.0034 0.17 NO
26 FASN FASN FASN 10791 0.00097 0.16 NO
27 YWHAB YWHAB YWHAB 11590 -0.01 0.12 NO
28 PRKAR1A PRKAR1A PRKAR1A 11714 -0.012 0.12 NO
29 PPP2R5C PPP2R5C PPP2R5C 11718 -0.012 0.12 NO
30 PPP2CA PPP2CA PPP2CA 12582 -0.024 0.085 NO
31 PPP2R1B PPP2R1B PPP2R1B 12711 -0.027 0.087 NO
32 PPP2R4 PPP2R4 PPP2R4 13050 -0.033 0.08 NO
33 PRKAA1 PRKAA1 PRKAA1 13519 -0.043 0.069 NO
34 PRKAG2 PRKAG2 PRKAG2 13541 -0.043 0.083 NO
35 PPP2R5A PPP2R5A PPP2R5A 14039 -0.054 0.074 NO
36 MLX MLX MLX 14442 -0.065 0.074 NO
37 PPP2R5B PPP2R5B PPP2R5B 14698 -0.072 0.085 NO
38 YWHAZ YWHAZ YWHAZ 15259 -0.091 0.086 NO
39 YWHAH YWHAH YWHAH 15958 -0.12 0.09 NO
40 PPP2R2B PPP2R2B PPP2R2B 16323 -0.15 0.12 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 BASAL TRANSCRIPTION FACTORS.

Figure S40.  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

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 NO1 PATHWAY 27 genes.ES.table 0.6 1.6 0.016 0.069 0.74 0.26 0.09 0.24 0.041 0
BIOCARTA ALK PATHWAY 33 genes.ES.table 0.48 1.3 0.13 0.19 0.98 0.27 0.12 0.24 0.16 0
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.47 1.8 0.014 0.029 0.31 0.38 0.27 0.28 0 0
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.63 1.8 0.0062 0.028 0.26 0.39 0.2 0.32 0 0
BIOCARTA HDAC PATHWAY 27 genes.ES.table 0.41 1.4 0.13 0.19 0.98 0.15 0.08 0.14 0.15 0
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.5 1.7 0.024 0.047 0.52 0.57 0.34 0.38 0.025 0
BIOCARTA ERK PATHWAY 27 genes.ES.table 0.41 1.3 0.14 0.19 0.98 0.33 0.24 0.25 0.15 0
BIOCARTA FAS PATHWAY 29 genes.ES.table 0.45 1.6 0.052 0.059 0.67 0.28 0.21 0.22 0.033 0
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.62 1.9 0.002 0.03 0.17 0.24 0.1 0.22 0 0
BIOCARTA FMLP PATHWAY 34 genes.ES.table 0.39 1.4 0.14 0.18 0.98 0.15 0.08 0.14 0.14 0
genes ES table in pathway: BIOCARTA NO1 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 CTSK CTSK CTSK 51 0.74 0.09 YES
2 CTSW CTSW CTSW 603 0.35 0.1 YES
3 CLTCL1 CLTCL1 CLTCL1 1121 0.26 0.11 YES
4 CTSG CTSG CTSG 1164 0.25 0.14 YES
5 ATP6V0D2 ATP6V0D2 ATP6V0D2 1279 0.23 0.16 YES
6 CTSE CTSE CTSE 1283 0.23 0.19 YES
7 LAPTM5 LAPTM5 LAPTM5 1296 0.23 0.22 YES
8 CD68 CD68 CD68 1475 0.2 0.24 YES
9 CTSS CTSS CTSS 1501 0.2 0.26 YES
10 ARSB ARSB ARSB 1532 0.2 0.28 YES
11 SLC11A1 SLC11A1 SLC11A1 1857 0.17 0.29 YES
12 CTSO CTSO CTSO 2144 0.14 0.29 YES
13 SMPD1 SMPD1 SMPD1 2437 0.12 0.29 YES
14 ARSA ARSA ARSA 2586 0.11 0.29 YES
15 ACP5 ACP5 ACP5 2767 0.1 0.3 YES
16 NPC1 NPC1 NPC1 2796 0.098 0.31 YES
17 CLTB CLTB CLTB 2824 0.097 0.32 YES
18 CTSL1 CTSL1 CTSL1 2860 0.095 0.33 YES
19 TPP1 TPP1 TPP1 3049 0.086 0.33 YES
20 CTSZ CTSZ CTSZ 3126 0.083 0.34 YES
21 MCOLN1 MCOLN1 MCOLN1 3259 0.077 0.34 YES
22 NAGA NAGA NAGA 3261 0.077 0.35 YES
23 GM2A GM2A GM2A 3283 0.076 0.36 YES
24 GALNS GALNS GALNS 3289 0.076 0.36 YES
25 AP4E1 AP4E1 AP4E1 3304 0.076 0.37 YES
26 AP1B1 AP1B1 AP1B1 3316 0.075 0.38 YES
27 PSAPL1 PSAPL1 PSAPL1 3320 0.075 0.39 YES
28 CTSA CTSA CTSA 3391 0.073 0.4 YES
29 LGMN LGMN LGMN 3393 0.073 0.41 YES
30 GAA GAA GAA 3416 0.072 0.41 YES
31 LAPTM4B LAPTM4B LAPTM4B 3492 0.069 0.42 YES
32 AP1S2 AP1S2 AP1S2 3506 0.069 0.43 YES
33 CTSB CTSB CTSB 3507 0.069 0.44 YES
34 TCIRG1 TCIRG1 TCIRG1 3557 0.067 0.44 YES
35 GNPTAB GNPTAB GNPTAB 3562 0.067 0.45 YES
36 CTSD CTSD CTSD 3575 0.067 0.46 YES
37 LIPA LIPA LIPA 3601 0.066 0.46 YES
38 DNASE2B DNASE2B DNASE2B 3641 0.065 0.47 YES
39 HEXB HEXB HEXB 3680 0.064 0.48 YES
40 ASAH1 ASAH1 ASAH1 3744 0.061 0.48 YES
41 ENTPD4 ENTPD4 ENTPD4 3745 0.061 0.49 YES
42 ATP6AP1 ATP6AP1 ATP6AP1 3791 0.06 0.49 YES
43 AP3S1 AP3S1 AP3S1 3812 0.06 0.5 YES
44 CTSH CTSH CTSH 4201 0.049 0.48 YES
45 CTSC CTSC CTSC 4204 0.049 0.49 YES
46 PLA2G15 PLA2G15 PLA2G15 4212 0.049 0.5 YES
47 MANBA MANBA MANBA 4237 0.048 0.5 YES
48 ACP2 ACP2 ACP2 4397 0.045 0.5 YES
49 GNPTG GNPTG GNPTG 4534 0.042 0.5 YES
50 NPC2 NPC2 NPC2 4547 0.042 0.5 YES
51 SLC17A5 SLC17A5 SLC17A5 4560 0.042 0.5 YES
52 PSAP PSAP PSAP 4573 0.042 0.51 YES
53 GGA3 GGA3 GGA3 4690 0.039 0.51 YES
54 HEXA HEXA HEXA 4728 0.038 0.51 YES
55 IGF2R IGF2R IGF2R 4756 0.038 0.52 YES
56 NAGLU NAGLU NAGLU 4775 0.038 0.52 YES
57 CLTC CLTC CLTC 4932 0.035 0.51 YES
58 CTNS CTNS CTNS 4962 0.034 0.52 YES
59 SCARB2 SCARB2 SCARB2 5010 0.033 0.52 YES
60 IDS IDS IDS 5135 0.031 0.52 YES
61 LAMP1 LAMP1 LAMP1 5136 0.031 0.52 YES
62 FUCA1 FUCA1 FUCA1 5275 0.029 0.52 NO
63 CLN3 CLN3 CLN3 5308 0.028 0.52 NO
64 GBA GBA GBA 5473 0.026 0.51 NO
65 AGA AGA AGA 5552 0.025 0.51 NO
66 NEU1 NEU1 NEU1 5601 0.024 0.51 NO
67 ATP6V0C ATP6V0C ATP6V0C 5728 0.022 0.51 NO
68 LAMP3 LAMP3 LAMP3 5784 0.022 0.51 NO
69 ATP6V0B ATP6V0B ATP6V0B 5837 0.021 0.51 NO
70 ATP6V0D1 ATP6V0D1 ATP6V0D1 5873 0.02 0.51 NO
71 SGSH SGSH SGSH 5902 0.02 0.51 NO
72 GLA GLA GLA 6035 0.018 0.5 NO
73 CD63 CD63 CD63 6106 0.017 0.5 NO
74 GALC GALC GALC 6149 0.017 0.5 NO
75 GNS GNS GNS 6186 0.016 0.5 NO
76 CLN5 CLN5 CLN5 6265 0.016 0.5 NO
77 NAGPA NAGPA NAGPA 6341 0.014 0.5 NO
78 ATP6V0A1 ATP6V0A1 ATP6V0A1 6352 0.014 0.5 NO
79 MFSD8 MFSD8 MFSD8 6721 0.01 0.48 NO
80 AP3D1 AP3D1 AP3D1 6750 0.0098 0.48 NO
81 GGA1 GGA1 GGA1 6887 0.0081 0.47 NO
82 AP3B1 AP3B1 AP3B1 6963 0.0073 0.47 NO
83 LAPTM4A LAPTM4A LAPTM4A 7019 0.0067 0.47 NO
84 MAN2B1 MAN2B1 MAN2B1 7027 0.0066 0.47 NO
85 ATP6V0A2 ATP6V0A2 ATP6V0A2 7569 0.001 0.44 NO
86 SORT1 SORT1 SORT1 7582 0.00085 0.44 NO
87 ABCA2 ABCA2 ABCA2 7585 0.00082 0.44 NO
88 GGA2 GGA2 GGA2 7747 -0.00082 0.43 NO
89 IDUA IDUA IDUA 7914 -0.0022 0.42 NO
90 AP1M1 AP1M1 AP1M1 8008 -0.0032 0.42 NO
91 LAMP2 LAMP2 LAMP2 8104 -0.0041 0.41 NO
92 GUSB GUSB GUSB 8224 -0.0053 0.41 NO
93 ABCB9 ABCB9 ABCB9 8263 -0.0056 0.4 NO
94 PPT1 PPT1 PPT1 8471 -0.0076 0.4 NO
95 GLB1 GLB1 GLB1 8700 -0.0094 0.38 NO
96 AP3M1 AP3M1 AP3M1 8795 -0.01 0.38 NO
97 CTSF CTSF CTSF 9138 -0.014 0.36 NO
98 ATP6V0A4 ATP6V0A4 ATP6V0A4 9662 -0.018 0.34 NO
99 AP1G1 AP1G1 AP1G1 9734 -0.019 0.34 NO
100 DNASE2 DNASE2 DNASE2 9909 -0.02 0.33 NO
101 CD164 CD164 CD164 10119 -0.022 0.32 NO
102 AP4M1 AP4M1 AP4M1 10591 -0.026 0.3 NO
103 AP1M2 AP1M2 AP1M2 10600 -0.026 0.3 NO
104 NAPSA NAPSA NAPSA 10913 -0.029 0.29 NO
105 AP1S1 AP1S1 AP1S1 11240 -0.032 0.27 NO
106 CLTA CLTA CLTA 11293 -0.032 0.28 NO
107 M6PR M6PR M6PR 11515 -0.034 0.27 NO
108 ATP6V1H ATP6V1H ATP6V1H 11533 -0.035 0.27 NO
109 AP4S1 AP4S1 AP4S1 11540 -0.035 0.28 NO
110 AP4B1 AP4B1 AP4B1 11619 -0.036 0.28 NO
111 SLC11A2 SLC11A2 SLC11A2 11737 -0.037 0.27 NO
112 AP3S2 AP3S2 AP3S2 11772 -0.037 0.28 NO
113 SUMF1 SUMF1 SUMF1 12049 -0.04 0.27 NO
114 PPT2 PPT2 PPT2 13083 -0.052 0.22 NO
115 ARSG ARSG ARSG 13677 -0.06 0.19 NO
116 HYAL1 HYAL1 HYAL1 14454 -0.074 0.16 NO
117 CTSL2 CTSL2 CTSL2 14690 -0.079 0.16 NO
118 AP3M2 AP3M2 AP3M2 14778 -0.081 0.16 NO
119 AP1S3 AP1S3 AP1S3 15545 -0.1 0.13 NO
120 AP3B2 AP3B2 AP3B2 17788 -0.24 0.042 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 NO1 PATHWAY.

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA ALK PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HGF HGF HGF 435 0.4 0.058 YES
2 TGFB3 TGFB3 TGFB3 539 0.37 0.13 YES
3 PIK3CG PIK3CG PIK3CG 576 0.36 0.2 YES
4 PIK3R5 PIK3R5 PIK3R5 778 0.32 0.25 YES
5 AKT3 AKT3 AKT3 1068 0.27 0.29 YES
6 VEGFC VEGFC VEGFC 1420 0.21 0.32 YES
7 PGF PGF PGF 1425 0.21 0.36 YES
8 ETS1 ETS1 ETS1 1445 0.21 0.4 YES
9 TGFB1 TGFB1 TGFB1 1448 0.21 0.44 YES
10 PDGFB PDGFB PDGFB 1905 0.16 0.45 YES
11 PIK3CD PIK3CD PIK3CD 1978 0.15 0.48 YES
12 EPAS1 EPAS1 EPAS1 2123 0.14 0.5 YES
13 EGLN3 EGLN3 EGLN3 2380 0.12 0.51 YES
14 PAK3 PAK3 PAK3 2520 0.12 0.53 YES
15 VEGFB VEGFB VEGFB 3721 0.062 0.48 NO
16 GAB1 GAB1 GAB1 3901 0.057 0.48 NO
17 GRB2 GRB2 GRB2 4006 0.054 0.48 NO
18 MAPK1 MAPK1 MAPK1 4182 0.05 0.48 NO
19 RAPGEF1 RAPGEF1 RAPGEF1 4672 0.04 0.47 NO
20 HIF1A HIF1A HIF1A 4804 0.037 0.47 NO
21 RAP1A RAP1A RAP1A 4852 0.036 0.47 NO
22 TGFA TGFA TGFA 5020 0.033 0.47 NO
23 VEGFA VEGFA VEGFA 5213 0.03 0.46 NO
24 CRK CRK CRK 5348 0.028 0.46 NO
25 MET MET MET 5543 0.025 0.46 NO
26 CDC42 CDC42 CDC42 5982 0.019 0.44 NO
27 FLCN FLCN FLCN 5993 0.019 0.44 NO
28 MAPK3 MAPK3 MAPK3 6024 0.019 0.44 NO
29 EGLN2 EGLN2 EGLN2 6040 0.018 0.45 NO
30 CUL2 CUL2 CUL2 6048 0.018 0.45 NO
31 JUN JUN JUN 6127 0.017 0.45 NO
32 SOS2 SOS2 SOS2 6154 0.017 0.45 NO
33 PIK3CB PIK3CB PIK3CB 6351 0.014 0.44 NO
34 ARNT ARNT ARNT 6358 0.014 0.45 NO
35 ARAF ARAF ARAF 6448 0.013 0.44 NO
36 MAP2K1 MAP2K1 MAP2K1 6545 0.012 0.44 NO
37 PIK3CA PIK3CA PIK3CA 6849 0.0086 0.43 NO
38 SLC2A1 SLC2A1 SLC2A1 6851 0.0086 0.43 NO
39 TCEB1 TCEB1 TCEB1 6967 0.0073 0.42 NO
40 PAK2 PAK2 PAK2 7002 0.0069 0.42 NO
41 MAP2K2 MAP2K2 MAP2K2 7143 0.0055 0.42 NO
42 RAP1B RAP1B RAP1B 7173 0.005 0.42 NO
43 PIK3R3 PIK3R3 PIK3R3 7189 0.0049 0.42 NO
44 RAC1 RAC1 RAC1 7349 0.0033 0.41 NO
45 AKT1 AKT1 AKT1 7591 0.00072 0.4 NO
46 CRKL CRKL CRKL 7653 0.000059 0.39 NO
47 RBX1 RBX1 RBX1 7854 -0.0017 0.38 NO
48 PIK3R1 PIK3R1 PIK3R1 8196 -0.0051 0.36 NO
49 AKT2 AKT2 AKT2 8644 -0.009 0.34 NO
50 NRAS NRAS NRAS 8982 -0.012 0.33 NO
51 CREBBP CREBBP CREBBP 9119 -0.013 0.32 NO
52 SOS1 SOS1 SOS1 9226 -0.014 0.32 NO
53 FIGF FIGF FIGF 9603 -0.018 0.3 NO
54 PTPN11 PTPN11 PTPN11 9697 -0.018 0.3 NO
55 EGLN1 EGLN1 EGLN1 9712 -0.018 0.3 NO
56 RAF1 RAF1 RAF1 9732 -0.019 0.31 NO
57 EP300 EP300 EP300 10044 -0.021 0.29 NO
58 BRAF BRAF BRAF 10088 -0.022 0.3 NO
59 TCEB2 TCEB2 TCEB2 10538 -0.026 0.28 NO
60 FH FH FH 10873 -0.029 0.26 NO
61 PAK4 PAK4 PAK4 11903 -0.038 0.22 NO
62 KRAS KRAS KRAS 12196 -0.041 0.21 NO
63 VHL VHL VHL 12527 -0.045 0.2 NO
64 TGFB2 TGFB2 TGFB2 12741 -0.048 0.2 NO
65 PIK3R2 PIK3R2 PIK3R2 12955 -0.05 0.2 NO
66 PAK6 PAK6 PAK6 13279 -0.055 0.19 NO
67 PAK1 PAK1 PAK1 14566 -0.076 0.14 NO
68 ARNT2 ARNT2 ARNT2 15649 -0.11 0.1 NO
69 PAK7 PAK7 PAK7 18031 -0.28 0.029 NO

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

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

genes ES table in pathway: BIOCARTA AT1R 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 LY96 LY96 LY96 377 0.42 0.15 YES
2 LBP LBP LBP 725 0.33 0.27 YES
3 TLR4 TLR4 TLR4 901 0.3 0.38 YES
4 FZD1 FZD1 FZD1 1004 0.28 0.49 YES
5 GJA1 GJA1 GJA1 1182 0.25 0.58 YES
6 CD14 CD14 CD14 1299 0.23 0.68 YES
7 NFKB1 NFKB1 NFKB1 3288 0.076 0.6 NO
8 WNT1 WNT1 WNT1 3898 0.057 0.59 NO
9 APC APC APC 4048 0.053 0.6 NO
10 CCND1 CCND1 CCND1 4198 0.049 0.62 NO
11 MYD88 MYD88 MYD88 4280 0.047 0.63 NO
12 IRAK1 IRAK1 IRAK1 5098 0.032 0.6 NO
13 PPP2CA PPP2CA PPP2CA 5747 0.022 0.57 NO
14 PDPK1 PDPK1 PDPK1 5787 0.022 0.58 NO
15 PIK3CA PIK3CA PIK3CA 6849 0.0086 0.53 NO
16 RELA RELA RELA 7130 0.0056 0.52 NO
17 AKT1 AKT1 AKT1 7591 0.00072 0.49 NO
18 AXIN1 AXIN1 AXIN1 7884 -0.002 0.48 NO
19 PIK3R1 PIK3R1 PIK3R1 8196 -0.0051 0.46 NO
20 EIF2AK2 EIF2AK2 EIF2AK2 8423 -0.0071 0.45 NO
21 CTNNB1 CTNNB1 CTNNB1 9303 -0.015 0.41 NO
22 GNAI1 GNAI1 GNAI1 9529 -0.017 0.4 NO
23 TIRAP TIRAP TIRAP 9636 -0.018 0.41 NO
24 GSK3B GSK3B GSK3B 11151 -0.031 0.34 NO
25 DVL1 DVL1 DVL1 12608 -0.046 0.28 NO
26 LEF1 LEF1 LEF1 15538 -0.1 0.16 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 AT1R PATHWAY.

Figure S46.  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 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 TGFB3 TGFB3 TGFB3 539 0.37 0.051 YES
2 PIK3CG PIK3CG PIK3CG 576 0.36 0.13 YES
3 PIK3R5 PIK3R5 PIK3R5 778 0.32 0.18 YES
4 AKT3 AKT3 AKT3 1068 0.27 0.22 YES
5 ARHGEF6 ARHGEF6 ARHGEF6 1171 0.25 0.27 YES
6 RAC2 RAC2 RAC2 1310 0.23 0.31 YES
7 VEGFC VEGFC VEGFC 1420 0.21 0.35 YES
8 PGF PGF PGF 1425 0.21 0.4 YES
9 TGFB1 TGFB1 TGFB1 1448 0.21 0.44 YES
10 PIK3CD PIK3CD PIK3CD 1978 0.15 0.45 YES
11 TGFBR2 TGFBR2 TGFBR2 2071 0.15 0.47 YES
12 EGFR EGFR EGFR 2872 0.094 0.45 YES
13 NFKB1 NFKB1 NFKB1 3288 0.076 0.44 YES
14 MAPK9 MAPK9 MAPK9 3360 0.074 0.46 YES
15 CDKN2A CDKN2A CDKN2A 3635 0.065 0.45 YES
16 VEGFB VEGFB VEGFB 3721 0.062 0.46 YES
17 RALB RALB RALB 3818 0.06 0.47 YES
18 RB1 RB1 RB1 3939 0.056 0.48 YES
19 RAC3 RAC3 RAC3 3981 0.055 0.48 YES
20 TGFBR1 TGFBR1 TGFBR1 4049 0.053 0.49 YES
21 MAPK1 MAPK1 MAPK1 4182 0.05 0.5 YES
22 CCND1 CCND1 CCND1 4198 0.049 0.51 YES
23 STAT3 STAT3 STAT3 4428 0.044 0.5 NO
24 PLD1 PLD1 PLD1 4632 0.04 0.5 NO
25 IKBKG IKBKG IKBKG 4954 0.034 0.49 NO
26 TGFA TGFA TGFA 5020 0.033 0.5 NO
27 JAK1 JAK1 JAK1 5172 0.031 0.49 NO
28 VEGFA VEGFA VEGFA 5213 0.03 0.5 NO
29 RALBP1 RALBP1 RALBP1 5359 0.027 0.5 NO
30 BCL2L1 BCL2L1 BCL2L1 5361 0.027 0.5 NO
31 SMAD2 SMAD2 SMAD2 5497 0.026 0.5 NO
32 STAT1 STAT1 STAT1 5970 0.019 0.48 NO
33 CDC42 CDC42 CDC42 5982 0.019 0.48 NO
34 MAPK3 MAPK3 MAPK3 6024 0.019 0.48 NO
35 PIK3CB PIK3CB PIK3CB 6351 0.014 0.47 NO
36 ARAF ARAF ARAF 6448 0.013 0.47 NO
37 MAP2K1 MAP2K1 MAP2K1 6545 0.012 0.46 NO
38 PIK3CA PIK3CA PIK3CA 6849 0.0086 0.45 NO
39 BAD BAD BAD 6889 0.008 0.45 NO
40 CHUK CHUK CHUK 7117 0.0057 0.44 NO
41 RELA RELA RELA 7130 0.0056 0.44 NO
42 PIK3R3 PIK3R3 PIK3R3 7189 0.0049 0.44 NO
43 RAC1 RAC1 RAC1 7349 0.0033 0.43 NO
44 AKT1 AKT1 AKT1 7591 0.00072 0.42 NO
45 PIK3R1 PIK3R1 PIK3R1 8196 -0.0051 0.38 NO
46 RAD51 RAD51 RAD51 8274 -0.0057 0.38 NO
47 AKT2 AKT2 AKT2 8644 -0.009 0.36 NO
48 RALA RALA RALA 9265 -0.015 0.33 NO
49 EGF EGF EGF 9602 -0.018 0.32 NO
50 FIGF FIGF FIGF 9603 -0.018 0.32 NO
51 RAF1 RAF1 RAF1 9732 -0.019 0.32 NO
52 RALGDS RALGDS RALGDS 9889 -0.02 0.32 NO
53 SMAD4 SMAD4 SMAD4 10043 -0.021 0.31 NO
54 BRAF BRAF BRAF 10088 -0.022 0.31 NO
55 ERBB2 ERBB2 ERBB2 10488 -0.025 0.3 NO
56 E2F2 E2F2 E2F2 10811 -0.028 0.29 NO
57 E2F3 E2F3 E2F3 11017 -0.03 0.28 NO
58 TP53 TP53 TP53 11038 -0.03 0.29 NO
59 MAPK8 MAPK8 MAPK8 11165 -0.031 0.29 NO
60 IKBKB IKBKB IKBKB 11314 -0.033 0.28 NO
61 MAPK10 MAPK10 MAPK10 11458 -0.034 0.28 NO
62 KRAS KRAS KRAS 12196 -0.041 0.25 NO
63 TGFB2 TGFB2 TGFB2 12741 -0.048 0.23 NO
64 PIK3R2 PIK3R2 PIK3R2 12955 -0.05 0.23 NO
65 SMAD3 SMAD3 SMAD3 13441 -0.057 0.22 NO
66 CDK6 CDK6 CDK6 13469 -0.057 0.23 NO
67 CDK4 CDK4 CDK4 14066 -0.066 0.21 NO
68 BRCA2 BRCA2 BRCA2 14349 -0.072 0.21 NO
69 CASP9 CASP9 CASP9 14373 -0.072 0.23 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 BCR PATHWAY.

Figure S48.  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 HDAC 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 RUNX1T1 RUNX1T1 RUNX1T1 205 0.52 0.13 YES
2 PIK3CG PIK3CG PIK3CG 576 0.36 0.2 YES
3 PIK3R5 PIK3R5 PIK3R5 778 0.32 0.28 YES
4 AKT3 AKT3 AKT3 1068 0.27 0.34 YES
5 SPI1 SPI1 SPI1 1084 0.26 0.4 YES
6 RUNX1 RUNX1 RUNX1 1327 0.23 0.45 YES
7 PIK3CD PIK3CD PIK3CD 1978 0.15 0.46 YES
8 ZBTB16 ZBTB16 ZBTB16 2261 0.13 0.48 YES
9 FLT3 FLT3 FLT3 2774 0.099 0.48 YES
10 PIM1 PIM1 PIM1 3237 0.078 0.47 YES
11 NFKB1 NFKB1 NFKB1 3288 0.076 0.49 YES
12 PIM2 PIM2 PIM2 3747 0.061 0.48 YES
13 GRB2 GRB2 GRB2 4006 0.054 0.48 YES
14 MAPK1 MAPK1 MAPK1 4182 0.05 0.49 YES
15 CCND1 CCND1 CCND1 4198 0.049 0.5 YES
16 STAT3 STAT3 STAT3 4428 0.044 0.5 YES
17 CEBPA CEBPA CEBPA 4710 0.039 0.49 YES
18 IKBKG IKBKG IKBKG 4954 0.034 0.49 YES
19 HRAS HRAS HRAS 4961 0.034 0.5 YES
20 RARA RARA RARA 4993 0.034 0.51 YES
21 RPS6KB1 RPS6KB1 RPS6KB1 5156 0.031 0.51 NO
22 STAT5A STAT5A STAT5A 5351 0.027 0.5 NO
23 PML PML PML 6000 0.019 0.47 NO
24 MAPK3 MAPK3 MAPK3 6024 0.019 0.48 NO
25 SOS2 SOS2 SOS2 6154 0.017 0.47 NO
26 STAT5B STAT5B STAT5B 6198 0.016 0.48 NO
27 PIK3CB PIK3CB PIK3CB 6351 0.014 0.47 NO
28 ARAF ARAF ARAF 6448 0.013 0.47 NO
29 JUP JUP JUP 6484 0.013 0.47 NO
30 MAP2K1 MAP2K1 MAP2K1 6545 0.012 0.47 NO
31 PIK3CA PIK3CA PIK3CA 6849 0.0086 0.46 NO
32 BAD BAD BAD 6889 0.008 0.46 NO
33 CHUK CHUK CHUK 7117 0.0057 0.45 NO
34 RELA RELA RELA 7130 0.0056 0.45 NO
35 MAP2K2 MAP2K2 MAP2K2 7143 0.0055 0.45 NO
36 PIK3R3 PIK3R3 PIK3R3 7189 0.0049 0.45 NO
37 AKT1 AKT1 AKT1 7591 0.00072 0.43 NO
38 PIK3R1 PIK3R1 PIK3R1 8196 -0.0051 0.4 NO
39 RPS6KB2 RPS6KB2 RPS6KB2 8199 -0.0051 0.4 NO
40 AKT2 AKT2 AKT2 8644 -0.009 0.37 NO
41 NRAS NRAS NRAS 8982 -0.012 0.36 NO
42 SOS1 SOS1 SOS1 9226 -0.014 0.35 NO
43 RAF1 RAF1 RAF1 9732 -0.019 0.33 NO
44 KIT KIT KIT 10021 -0.021 0.32 NO
45 MTOR MTOR MTOR 10029 -0.021 0.32 NO
46 BRAF BRAF BRAF 10088 -0.022 0.33 NO
47 MYC MYC MYC 10193 -0.023 0.33 NO
48 EIF4EBP1 EIF4EBP1 EIF4EBP1 10400 -0.025 0.32 NO
49 IKBKB IKBKB IKBKB 11314 -0.033 0.28 NO
50 TCF7L2 TCF7L2 TCF7L2 11796 -0.037 0.26 NO
51 KRAS KRAS KRAS 12196 -0.041 0.26 NO
52 PIK3R2 PIK3R2 PIK3R2 12955 -0.05 0.23 NO
53 TCF7 TCF7 TCF7 12962 -0.05 0.24 NO
54 CCNA1 CCNA1 CCNA1 13349 -0.056 0.23 NO
55 TCF7L1 TCF7L1 TCF7L1 14468 -0.074 0.19 NO
56 LEF1 LEF1 LEF1 15538 -0.1 0.16 NO

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

Figure S50.  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 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 VCAM1 VCAM1 VCAM1 113 0.62 0.038 YES
2 ITK ITK ITK 165 0.55 0.074 YES
3 CXCL12 CXCL12 CXCL12 194 0.53 0.11 YES
4 RHOH RHOH RHOH 263 0.47 0.14 YES
5 MMP2 MMP2 MMP2 331 0.44 0.17 YES
6 JAM2 JAM2 JAM2 479 0.39 0.19 YES
7 PIK3CG PIK3CG PIK3CG 576 0.36 0.21 YES
8 ITGAL ITGAL ITGAL 676 0.34 0.23 YES
9 MMP9 MMP9 MMP9 711 0.33 0.25 YES
10 PRKCB PRKCB PRKCB 726 0.33 0.27 YES
11 ITGAM ITGAM ITGAM 728 0.33 0.29 YES
12 NCF1 NCF1 NCF1 741 0.32 0.32 YES
13 PIK3R5 PIK3R5 PIK3R5 778 0.32 0.34 YES
14 ITGA4 ITGA4 ITGA4 876 0.3 0.35 YES
15 NCF4 NCF4 NCF4 893 0.3 0.37 YES
16 CYBB CYBB CYBB 957 0.28 0.39 YES
17 MAPK11 MAPK11 MAPK11 1008 0.28 0.41 YES
18 NCF2 NCF2 NCF2 1010 0.28 0.43 YES
19 VAV1 VAV1 VAV1 1096 0.26 0.44 YES
20 ITGB2 ITGB2 ITGB2 1116 0.26 0.46 YES
21 CLDN14 CLDN14 CLDN14 1163 0.25 0.47 YES
22 PECAM1 PECAM1 PECAM1 1270 0.23 0.48 YES
23 RAC2 RAC2 RAC2 1310 0.23 0.5 YES
24 ICAM1 ICAM1 ICAM1 1443 0.21 0.5 YES
25 VAV3 VAV3 VAV3 1498 0.2 0.52 YES
26 JAM3 JAM3 JAM3 1522 0.2 0.53 YES
27 THY1 THY1 THY1 1610 0.19 0.54 YES
28 CLDN16 CLDN16 CLDN16 1688 0.18 0.55 YES
29 ESAM ESAM ESAM 1854 0.17 0.55 YES
30 MAPK12 MAPK12 MAPK12 1864 0.16 0.56 YES
31 CLDN5 CLDN5 CLDN5 1918 0.16 0.57 YES
32 CLDN11 CLDN11 CLDN11 1942 0.16 0.58 YES
33 CDH5 CDH5 CDH5 1972 0.16 0.59 YES
34 PIK3CD PIK3CD PIK3CD 1978 0.15 0.6 YES
35 RASSF5 RASSF5 RASSF5 2247 0.14 0.6 YES
36 PRKCA PRKCA PRKCA 2341 0.13 0.6 YES
37 CD99 CD99 CD99 2376 0.12 0.61 YES
38 MYL9 MYL9 MYL9 2561 0.11 0.6 YES
39 CLDN1 CLDN1 CLDN1 2655 0.11 0.61 YES
40 PTK2B PTK2B PTK2B 2690 0.1 0.61 YES
41 ACTN1 ACTN1 ACTN1 2910 0.092 0.61 YES
42 MSN MSN MSN 2955 0.09 0.61 YES
43 VASP VASP VASP 3096 0.084 0.61 YES
44 CLDN23 CLDN23 CLDN23 3109 0.084 0.62 YES
45 PLCG2 PLCG2 PLCG2 3112 0.084 0.62 YES
46 RAPGEF3 RAPGEF3 RAPGEF3 3220 0.079 0.62 YES
47 ITGB1 ITGB1 ITGB1 3229 0.078 0.62 YES
48 BCAR1 BCAR1 BCAR1 3375 0.073 0.62 NO
49 SIPA1 SIPA1 SIPA1 3499 0.069 0.62 NO
50 VCL VCL VCL 3634 0.065 0.62 NO
51 VAV2 VAV2 VAV2 3782 0.06 0.62 NO
52 MYL12A MYL12A MYL12A 3891 0.057 0.61 NO
53 ACTB ACTB ACTB 4013 0.054 0.61 NO
54 RAPGEF4 RAPGEF4 RAPGEF4 4346 0.046 0.6 NO
55 ACTN4 ACTN4 ACTN4 4371 0.046 0.6 NO
56 PTK2 PTK2 PTK2 4683 0.039 0.58 NO
57 CXCR4 CXCR4 CXCR4 4731 0.038 0.58 NO
58 RAP1A RAP1A RAP1A 4852 0.036 0.58 NO
59 ACTG1 ACTG1 ACTG1 4965 0.034 0.58 NO
60 GNAI2 GNAI2 GNAI2 4979 0.034 0.58 NO
61 GRLF1 GRLF1 GRLF1 5014 0.033 0.58 NO
62 ROCK1 ROCK1 ROCK1 5236 0.03 0.57 NO
63 CLDN7 CLDN7 CLDN7 5485 0.026 0.56 NO
64 PXN PXN PXN 5525 0.025 0.56 NO
65 CTNNA1 CTNNA1 CTNNA1 5622 0.024 0.55 NO
66 CLDN10 CLDN10 CLDN10 5703 0.023 0.55 NO
67 RHOA RHOA RHOA 5785 0.022 0.55 NO
68 CYBA CYBA CYBA 5847 0.021 0.55 NO
69 CDC42 CDC42 CDC42 5982 0.019 0.54 NO
70 CLDN8 CLDN8 CLDN8 6161 0.017 0.53 NO
71 PIK3CB PIK3CB PIK3CB 6351 0.014 0.52 NO
72 GNAI3 GNAI3 GNAI3 6416 0.014 0.52 NO
73 MAPK14 MAPK14 MAPK14 6429 0.014 0.52 NO
74 CLDN3 CLDN3 CLDN3 6509 0.013 0.52 NO
75 PIK3CA PIK3CA PIK3CA 6849 0.0086 0.5 NO
76 MYL12B MYL12B MYL12B 7053 0.0064 0.49 NO
77 RAP1B RAP1B RAP1B 7173 0.005 0.48 NO
78 PIK3R3 PIK3R3 PIK3R3 7189 0.0049 0.48 NO
79 RAC1 RAC1 RAC1 7349 0.0033 0.47 NO
80 CTNND1 CTNND1 CTNND1 7359 0.0032 0.47 NO
81 MYL5 MYL5 MYL5 7496 0.0018 0.46 NO
82 ROCK2 ROCK2 ROCK2 7839 -0.0016 0.45 NO
83 F11R F11R F11R 7872 -0.0019 0.44 NO
84 CLDN4 CLDN4 CLDN4 7900 -0.0021 0.44 NO
85 PIK3R1 PIK3R1 PIK3R1 8196 -0.0051 0.43 NO
86 EZR EZR EZR 8979 -0.012 0.39 NO
87 CTNNB1 CTNNB1 CTNNB1 9303 -0.015 0.37 NO
88 CLDN6 CLDN6 CLDN6 9357 -0.015 0.37 NO
89 GNAI1 GNAI1 GNAI1 9529 -0.017 0.36 NO
90 PLCG1 PLCG1 PLCG1 9667 -0.018 0.36 NO
91 PTPN11 PTPN11 PTPN11 9697 -0.018 0.35 NO
92 MAPK13 MAPK13 MAPK13 10564 -0.026 0.31 NO
93 ARHGAP5 ARHGAP5 ARHGAP5 11325 -0.033 0.27 NO
94 CLDN9 CLDN9 CLDN9 11717 -0.037 0.25 NO
95 NOX1 NOX1 NOX1 11927 -0.039 0.24 NO
96 MYL7 MYL7 MYL7 12033 -0.04 0.24 NO
97 MLLT4 MLLT4 MLLT4 12775 -0.048 0.2 NO
98 PIK3R2 PIK3R2 PIK3R2 12955 -0.05 0.2 NO
99 CLDN18 CLDN18 CLDN18 13115 -0.052 0.19 NO
100 CLDN20 CLDN20 CLDN20 13119 -0.052 0.2 NO
101 PRKCG PRKCG PRKCG 14364 -0.072 0.13 NO
102 CLDN15 CLDN15 CLDN15 14480 -0.074 0.13 NO
103 MYLPF MYLPF MYLPF 14685 -0.079 0.13 NO
104 TXK TXK TXK 15200 -0.092 0.11 NO
105 ACTN2 ACTN2 ACTN2 15779 -0.11 0.083 NO
106 ACTN3 ACTN3 ACTN3 16546 -0.14 0.052 NO
107 CTNNA2 CTNNA2 CTNNA2 17037 -0.17 0.037 NO
108 CLDN2 CLDN2 CLDN2 17283 -0.19 0.037 NO
109 CTNNA3 CTNNA3 CTNNA3 17625 -0.22 0.035 NO
110 CLDN19 CLDN19 CLDN19 17698 -0.23 0.047 NO

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

Figure S52.  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 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 TGFB3 TGFB3 TGFB3 539 0.37 0.055 YES
2 PIK3CG PIK3CG PIK3CG 576 0.36 0.14 YES
3 PIK3R5 PIK3R5 PIK3R5 778 0.32 0.2 YES
4 AKT3 AKT3 AKT3 1068 0.27 0.24 YES
5 RUNX1 RUNX1 RUNX1 1327 0.23 0.28 YES
6 TGFB1 TGFB1 TGFB1 1448 0.21 0.32 YES
7 PIK3CD PIK3CD PIK3CD 1978 0.15 0.33 YES
8 TGFBR2 TGFBR2 TGFBR2 2071 0.15 0.35 YES
9 CDKN1A CDKN1A CDKN1A 2157 0.14 0.38 YES
10 SHC2 SHC2 SHC2 2221 0.14 0.41 YES
11 CBLC CBLC CBLC 2244 0.14 0.44 YES
12 NFKB1 NFKB1 NFKB1 3288 0.076 0.4 YES
13 CDKN2A CDKN2A CDKN2A 3635 0.065 0.4 YES
14 SHC1 SHC1 SHC1 3658 0.064 0.41 YES
15 NFKBIA NFKBIA NFKBIA 3712 0.062 0.42 YES
16 RB1 RB1 RB1 3939 0.056 0.42 YES
17 GRB2 GRB2 GRB2 4006 0.054 0.43 YES
18 TGFBR1 TGFBR1 TGFBR1 4049 0.053 0.44 YES
19 MAPK1 MAPK1 MAPK1 4182 0.05 0.44 YES
20 CCND1 CCND1 CCND1 4198 0.049 0.45 YES
21 SHC4 SHC4 SHC4 4418 0.044 0.45 YES
22 BCR BCR BCR 4689 0.039 0.45 YES
23 IKBKG IKBKG IKBKG 4954 0.034 0.44 YES
24 HRAS HRAS HRAS 4961 0.034 0.45 YES
25 GAB2 GAB2 GAB2 5088 0.032 0.45 YES
26 CRK CRK CRK 5348 0.028 0.44 YES
27 STAT5A STAT5A STAT5A 5351 0.027 0.44 YES
28 BCL2L1 BCL2L1 BCL2L1 5361 0.027 0.45 YES
29 SHC3 SHC3 SHC3 5397 0.027 0.46 YES
30 MAPK3 MAPK3 MAPK3 6024 0.019 0.43 NO
31 SOS2 SOS2 SOS2 6154 0.017 0.42 NO
32 STAT5B STAT5B STAT5B 6198 0.016 0.42 NO
33 PIK3CB PIK3CB PIK3CB 6351 0.014 0.42 NO
34 ABL1 ABL1 ABL1 6401 0.014 0.42 NO
35 ARAF ARAF ARAF 6448 0.013 0.42 NO
36 MAP2K1 MAP2K1 MAP2K1 6545 0.012 0.42 NO
37 PIK3CA PIK3CA PIK3CA 6849 0.0086 0.4 NO
38 BAD BAD BAD 6889 0.008 0.4 NO
39 CHUK CHUK CHUK 7117 0.0057 0.39 NO
40 RELA RELA RELA 7130 0.0056 0.39 NO
41 MAP2K2 MAP2K2 MAP2K2 7143 0.0055 0.39 NO
42 PIK3R3 PIK3R3 PIK3R3 7189 0.0049 0.39 NO
43 AKT1 AKT1 AKT1 7591 0.00072 0.37 NO
44 CBLB CBLB CBLB 7612 0.00046 0.37 NO
45 CRKL CRKL CRKL 7653 0.000059 0.37 NO
46 PIK3R1 PIK3R1 PIK3R1 8196 -0.0051 0.34 NO
47 CTBP2 CTBP2 CTBP2 8519 -0.008 0.32 NO
48 AKT2 AKT2 AKT2 8644 -0.009 0.32 NO
49 NRAS NRAS NRAS 8982 -0.012 0.3 NO
50 CBL CBL CBL 9116 -0.013 0.3 NO
51 SOS1 SOS1 SOS1 9226 -0.014 0.3 NO
52 PTPN11 PTPN11 PTPN11 9697 -0.018 0.28 NO
53 RAF1 RAF1 RAF1 9732 -0.019 0.28 NO
54 SMAD4 SMAD4 SMAD4 10043 -0.021 0.27 NO
55 BRAF BRAF BRAF 10088 -0.022 0.27 NO
56 MYC MYC MYC 10193 -0.023 0.27 NO
57 E2F2 E2F2 E2F2 10811 -0.028 0.24 NO
58 E2F3 E2F3 E2F3 11017 -0.03 0.24 NO
59 TP53 TP53 TP53 11038 -0.03 0.24 NO
60 IKBKB IKBKB IKBKB 11314 -0.033 0.24 NO
61 CTBP1 CTBP1 CTBP1 11846 -0.038 0.22 NO
62 KRAS KRAS KRAS 12196 -0.041 0.2 NO
63 TGFB2 TGFB2 TGFB2 12741 -0.048 0.19 NO
64 PIK3R2 PIK3R2 PIK3R2 12955 -0.05 0.19 NO
65 CDKN1B CDKN1B CDKN1B 12982 -0.051 0.2 NO
66 HDAC1 HDAC1 HDAC1 13205 -0.054 0.2 NO
67 SMAD3 SMAD3 SMAD3 13441 -0.057 0.2 NO
68 CDK6 CDK6 CDK6 13469 -0.057 0.21 NO
69 CDK4 CDK4 CDK4 14066 -0.066 0.19 NO
70 HDAC2 HDAC2 HDAC2 14128 -0.068 0.2 NO
71 MDM2 MDM2 MDM2 14449 -0.074 0.2 NO
72 MECOM MECOM MECOM 15053 -0.088 0.19 NO

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

Figure S54.  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 FAS PATHWAY

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 HGF HGF HGF 435 0.4 0.16 YES
2 PIK3CG PIK3CG PIK3CG 576 0.36 0.32 YES
3 ITGA1 ITGA1 ITGA1 1340 0.22 0.38 YES
4 FOS FOS FOS 1913 0.16 0.43 YES
5 PTK2B PTK2B PTK2B 2690 0.1 0.44 YES
6 ITGB1 ITGB1 ITGB1 3229 0.078 0.44 YES
7 GAB1 GAB1 GAB1 3901 0.057 0.43 YES
8 GRB2 GRB2 GRB2 4006 0.054 0.45 YES
9 MAPK1 MAPK1 MAPK1 4182 0.05 0.47 YES
10 PTEN PTEN PTEN 4217 0.049 0.49 YES
11 STAT3 STAT3 STAT3 4428 0.044 0.5 YES
12 RAPGEF1 RAPGEF1 RAPGEF1 4672 0.04 0.5 YES
13 PTK2 PTK2 PTK2 4683 0.039 0.52 YES
14 RAP1A RAP1A RAP1A 4852 0.036 0.53 YES
15 CRK CRK CRK 5348 0.028 0.51 NO
16 PXN PXN PXN 5525 0.025 0.52 NO
17 MET MET MET 5543 0.025 0.53 NO
18 MAPK3 MAPK3 MAPK3 6024 0.019 0.51 NO
19 JUN JUN JUN 6127 0.017 0.51 NO
20 RASA1 RASA1 RASA1 6234 0.016 0.51 NO
21 MAP2K1 MAP2K1 MAP2K1 6545 0.012 0.5 NO
22 DOCK1 DOCK1 DOCK1 6630 0.011 0.5 NO
23 PIK3CA PIK3CA PIK3CA 6849 0.0086 0.5 NO
24 MAP2K2 MAP2K2 MAP2K2 7143 0.0055 0.48 NO
25 RAP1B RAP1B RAP1B 7173 0.005 0.48 NO
26 ACTA1 ACTA1 ACTA1 7603 0.00057 0.46 NO
27 CRKL CRKL CRKL 7653 0.000059 0.46 NO
28 PIK3R1 PIK3R1 PIK3R1 8196 -0.0051 0.43 NO
29 SOS1 SOS1 SOS1 9226 -0.014 0.38 NO
30 PTPN11 PTPN11 PTPN11 9697 -0.018 0.36 NO
31 RAF1 RAF1 RAF1 9732 -0.019 0.37 NO
32 SRC SRC SRC 10396 -0.025 0.35 NO
33 MAPK8 MAPK8 MAPK8 11165 -0.031 0.32 NO
34 MAP4K1 MAP4K1 MAP4K1 11256 -0.032 0.33 NO
35 ELK1 ELK1 ELK1 13835 -0.063 0.22 NO
36 PAK1 PAK1 PAK1 14566 -0.076 0.22 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: BIOCARTA FAS PATHWAY.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FAS 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 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 ITK ITK ITK 165 0.55 0.032 YES
2 CD3D CD3D CD3D 217 0.51 0.066 YES
3 GRAP2 GRAP2 GRAP2 236 0.49 0.1 YES
4 CD3E CD3E CD3E 279 0.46 0.13 YES
5 CD247 CD247 CD247 300 0.45 0.17 YES
6 ZAP70 ZAP70 ZAP70 343 0.43 0.2 YES
7 IL10 IL10 IL10 351 0.43 0.23 YES
8 CD40LG CD40LG CD40LG 352 0.43 0.26 YES
9 ICOS ICOS ICOS 410 0.41 0.29 YES
10 CD3G CD3G CD3G 421 0.4 0.32 YES
11 CTLA4 CTLA4 CTLA4 483 0.39 0.34 YES
12 CD8A CD8A CD8A 486 0.39 0.37 YES
13 PTPRC PTPRC PTPRC 524 0.38 0.39 YES
14 PIK3CG PIK3CG PIK3CG 576 0.36 0.42 YES
15 LCP2 LCP2 LCP2 772 0.32 0.43 YES
16 PIK3R5 PIK3R5 PIK3R5 778 0.32 0.45 YES
17 CD28 CD28 CD28 829 0.31 0.47 YES
18 LCK LCK LCK 974 0.28 0.49 YES
19 MAPK11 MAPK11 MAPK11 1008 0.28 0.51 YES
20 AKT3 AKT3 AKT3 1068 0.27 0.52 YES
21 VAV1 VAV1 VAV1 1096 0.26 0.54 YES
22 CD8B CD8B CD8B 1120 0.26 0.56 YES
23 IFNG IFNG IFNG 1126 0.26 0.58 YES
24 PDCD1 PDCD1 PDCD1 1159 0.25 0.59 YES
25 TNF TNF TNF 1202 0.24 0.61 YES
26 NFATC1 NFATC1 NFATC1 1378 0.22 0.62 YES
27 PPP3CC PPP3CC PPP3CC 1483 0.2 0.62 YES
28 VAV3 VAV3 VAV3 1498 0.2 0.64 YES
29 CD4 CD4 CD4 1788 0.17 0.64 YES
30 MAPK12 MAPK12 MAPK12 1864 0.16 0.64 YES
31 FOS FOS FOS 1913 0.16 0.65 YES
32 PIK3CD PIK3CD PIK3CD 1978 0.15 0.66 YES
33 LAT LAT LAT 2239 0.14 0.66 YES
34 CBLC CBLC CBLC 2244 0.14 0.67 YES
35 CARD11 CARD11 CARD11 2454 0.12 0.66 YES
36 PAK3 PAK3 PAK3 2520 0.12 0.67 YES
37 CSF2 CSF2 CSF2 3007 0.088 0.65 NO
38 NFKBIE NFKBIE NFKBIE 3122 0.083 0.65 NO
39 NFKB1 NFKB1 NFKB1 3288 0.076 0.65 NO
40 PPP3CA PPP3CA PPP3CA 3341 0.074 0.65 NO
41 MAPK9 MAPK9 MAPK9 3360 0.074 0.65 NO
42 RASGRP1 RASGRP1 RASGRP1 3445 0.071 0.65 NO
43 NFKBIA NFKBIA NFKBIA 3712 0.062 0.64 NO
44 VAV2 VAV2 VAV2 3782 0.06 0.64 NO
45 GRB2 GRB2 GRB2 4006 0.054 0.64 NO
46 MALT1 MALT1 MALT1 4055 0.053 0.64 NO
47 MAPK1 MAPK1 MAPK1 4182 0.05 0.64 NO
48 NFATC2 NFATC2 NFATC2 4257 0.048 0.64 NO
49 CHP CHP CHP 4279 0.047 0.64 NO
50 NCK1 NCK1 NCK1 4828 0.037 0.61 NO
51 IKBKG IKBKG IKBKG 4954 0.034 0.61 NO
52 NFKBIB NFKBIB NFKBIB 5306 0.028 0.59 NO
53 MAP3K8 MAP3K8 MAP3K8 5509 0.025 0.58 NO
54 RHOA RHOA RHOA 5785 0.022 0.57 NO
55 CDC42 CDC42 CDC42 5982 0.019 0.56 NO
56 MAPK3 MAPK3 MAPK3 6024 0.019 0.56 NO
57 MAP3K14 MAP3K14 MAP3K14 6043 0.018 0.56 NO
58 JUN JUN JUN 6127 0.017 0.55 NO
59 SOS2 SOS2 SOS2 6154 0.017 0.55 NO
60 PPP3CB PPP3CB PPP3CB 6314 0.015 0.55 NO
61 PIK3CB PIK3CB PIK3CB 6351 0.014 0.55 NO
62 BCL10 BCL10 BCL10 6360 0.014 0.55 NO
63 NFATC4 NFATC4 NFATC4 6391 0.014 0.55 NO
64 MAPK14 MAPK14 MAPK14 6429 0.014 0.54 NO
65 MAP2K1 MAP2K1 MAP2K1 6545 0.012 0.54 NO
66 MAP2K7 MAP2K7 MAP2K7 6665 0.011 0.53 NO
67 PIK3CA PIK3CA PIK3CA 6849 0.0086 0.52 NO
68 PAK2 PAK2 PAK2 7002 0.0069 0.52 NO
69 CHUK CHUK CHUK 7117 0.0057 0.51 NO
70 RELA RELA RELA 7130 0.0056 0.51 NO
71 MAP2K2 MAP2K2 MAP2K2 7143 0.0055 0.51 NO
72 PIK3R3 PIK3R3 PIK3R3 7189 0.0049 0.51 NO
73 AKT1 AKT1 AKT1 7591 0.00072 0.49 NO
74 CBLB CBLB CBLB 7612 0.00046 0.48 NO
75 PPP3R1 PPP3R1 PPP3R1 7996 -0.003 0.46 NO
76 NCK2 NCK2 NCK2 8066 -0.0038 0.46 NO
77 PTPN6 PTPN6 PTPN6 8080 -0.0038 0.46 NO
78 PIK3R1 PIK3R1 PIK3R1 8196 -0.0051 0.46 NO
79 AKT2 AKT2 AKT2 8644 -0.009 0.43 NO
80 NRAS NRAS NRAS 8982 -0.012 0.41 NO
81 CBL CBL CBL 9116 -0.013 0.41 NO
82 SOS1 SOS1 SOS1 9226 -0.014 0.4 NO
83 DLG1 DLG1 DLG1 9635 -0.018 0.38 NO
84 PLCG1 PLCG1 PLCG1 9667 -0.018 0.38 NO
85 RAF1 RAF1 RAF1 9732 -0.019 0.38 NO
86 MAP3K7 MAP3K7 MAP3K7 10027 -0.021 0.37 NO
87 NFAT5 NFAT5 NFAT5 10535 -0.026 0.34 NO
88 MAPK13 MAPK13 MAPK13 10564 -0.026 0.34 NO
89 GSK3B GSK3B GSK3B 11151 -0.031 0.31 NO
90 IKBKB IKBKB IKBKB 11314 -0.033 0.3 NO
91 PAK4 PAK4 PAK4 11903 -0.038 0.28 NO
92 PDK1 PDK1 PDK1 12032 -0.04 0.27 NO
93 KRAS KRAS KRAS 12196 -0.041 0.27 NO
94 PIK3R2 PIK3R2 PIK3R2 12955 -0.05 0.23 NO
95 PAK6 PAK6 PAK6 13279 -0.055 0.22 NO
96 PRKCQ PRKCQ PRKCQ 13953 -0.065 0.18 NO
97 CDK4 CDK4 CDK4 14066 -0.066 0.18 NO
98 FYN FYN FYN 14311 -0.071 0.17 NO
99 NFATC3 NFATC3 NFATC3 14369 -0.072 0.18 NO
100 TEC TEC TEC 14494 -0.075 0.18 NO
101 PAK1 PAK1 PAK1 14566 -0.076 0.18 NO
102 CHP2 CHP2 CHP2 16047 -0.12 0.11 NO
103 IL5 IL5 IL5 16439 -0.14 0.095 NO
104 PAK7 PAK7 PAK7 18031 -0.28 0.029 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: BIOCARTA FCER1 PATHWAY.

Figure S58.  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 S30.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 726 0.33 0.23 YES
2 PRKCA PRKCA PRKCA 2341 0.13 0.25 YES
3 PTK2B PTK2B PTK2B 2690 0.1 0.32 YES
4 BCAR1 BCAR1 BCAR1 3375 0.073 0.35 YES
5 SHC1 SHC1 SHC1 3658 0.064 0.38 YES
6 GRB2 GRB2 GRB2 4006 0.054 0.41 YES
7 MAPK1 MAPK1 MAPK1 4182 0.05 0.44 YES
8 GNAQ GNAQ GNAQ 4287 0.047 0.48 YES
9 MAPK3 MAPK3 MAPK3 6024 0.019 0.4 NO
10 JUN JUN JUN 6127 0.017 0.41 NO
11 CALM1 CALM1 CALM1 6164 0.017 0.42 NO
12 CALM3 CALM3 CALM3 6296 0.015 0.43 NO
13 MAPK14 MAPK14 MAPK14 6429 0.014 0.43 NO
14 MAP2K1 MAP2K1 MAP2K1 6545 0.012 0.43 NO
15 MAP2K2 MAP2K2 MAP2K2 7143 0.0055 0.41 NO
16 RAC1 RAC1 RAC1 7349 0.0033 0.4 NO
17 MAP2K3 MAP2K3 MAP2K3 7597 0.0006 0.38 NO
18 CRKL CRKL CRKL 7653 0.000059 0.38 NO
19 MAP2K4 MAP2K4 MAP2K4 8296 -0.006 0.35 NO
20 SOS1 SOS1 SOS1 9226 -0.014 0.32 NO
21 CALM2 CALM2 CALM2 9409 -0.016 0.32 NO
22 PLCG1 PLCG1 PLCG1 9667 -0.018 0.32 NO
23 RAF1 RAF1 RAF1 9732 -0.019 0.33 NO
24 SRC SRC SRC 10396 -0.025 0.32 NO
25 MAPK8 MAPK8 MAPK8 11165 -0.031 0.3 NO
26 MAP3K1 MAP3K1 MAP3K1 12136 -0.041 0.28 NO
27 PAK1 PAK1 PAK1 14566 -0.076 0.22 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: BIOCARTA FMLP PATHWAY.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input

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

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

  • Phenotype data file = OV-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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