GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in COAD-TP
Colon Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1BC3XJF
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 COAD-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1BC3XJF
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 COAD-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: 191
Number of samples: 457
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 123
pheno.type: 2 - 4 :[ clus2 ] 108
pheno.type: 3 - 4 :[ clus3 ] 91
pheno.type: 4 - 4 :[ clus4 ] 135

For the expression subtypes of 18012 genes in 458 samples, GSEA found enriched gene sets in each cluster using 457 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA RACCYCD PATHWAY, BIOCARTA CHREBP2 PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG LYSINE DEGRADATION, KEGG SELENOAMINO ACID METABOLISM, KEGG PYRUVATE METABOLISM, KEGG PROPANOATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RNA DEGRADATION

    • And common core enriched genes are LSM3, LSM5, LSM6, NAA38, AADAT, AASDH, AASDHPPT, AASS, ACAT1, ACAT2

  • clus2

    • Top enriched gene sets are BIOCARTA FAS PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA KERATINOCYTE PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA TNFR1 PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG O GLYCAN BIOSYNTHESIS

    • And common core enriched genes are CASP3, CASP7, CASP8, LMNA, APAF1, BCL2, BIRC2, BIRC3, CASP9, CYCS

  • clus3

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA CARM ER PATHWAY, BIOCARTA G1 PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY

    • And common core enriched genes are PIK3CD, PIK3CG, PIK3R5, AKT3, PDGFB, PIK3CA, FGFR1, ARNT2, ETS1, FIGF

  • clus4

    • Top enriched gene sets are BIOCARTA FMLP PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG ARACHIDONIC ACID METABOLISM, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG RIBOSOME, KEGG COMPLEMENT AND COAGULATION CASCADES

    • And common core enriched genes are CD14, TUBA1A, TUBA1C, TUBA3D, TUBA3E, TUBAL3, TUBB2A, TUBB2B, TUBB3, TUBB4Q

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.25 1 0.38 0.79 1 1 0.75 0.25 0.73 0.25
BIOCARTA CHREBP2 PATHWAY 40 genes.ES.table 0.26 1 0.47 0.81 1 0.12 0.098 0.11 0.76 0.26
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.36 1.2 0.29 0.73 1 0.31 0.27 0.23 0.65 0.24
KEGG GLYCINE SERINE AND THREONINE METABOLISM 29 genes.ES.table 0.29 0.77 0.84 0.89 1 0.21 0.06 0.2 0.89 0.27
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.49 1.9 0.0079 0.086 0.15 0.46 0.28 0.34 0 0.02
KEGG SELENOAMINO ACID METABOLISM 25 genes.ES.table 0.39 1.2 0.23 0.65 0.99 0.56 0.29 0.4 0.55 0.19
KEGG PYRUVATE METABOLISM 37 genes.ES.table 0.26 0.88 0.58 0.83 1 0.46 0.26 0.34 0.81 0.24
KEGG PROPANOATE METABOLISM 31 genes.ES.table 0.33 1.1 0.38 0.81 1 0.42 0.27 0.3 0.75 0.26
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.42 1.5 0.11 0.39 0.87 0.65 0.37 0.41 0.26 0.087
KEGG RNA DEGRADATION 55 genes.ES.table 0.38 1.5 0.12 0.35 0.89 0.49 0.32 0.34 0.24 0.068
genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PIPOX PIPOX PIPOX 98 0.36 0.14 YES
2 OGDHL OGDHL OGDHL 270 0.27 0.24 YES
3 SETDB2 SETDB2 SETDB2 940 0.16 0.26 YES
4 SETMAR SETMAR SETMAR 1748 0.12 0.27 YES
5 AASDHPPT AASDHPPT AASDHPPT 2212 0.1 0.28 YES
6 AADAT AADAT AADAT 2480 0.092 0.3 YES
7 TMLHE TMLHE TMLHE 2564 0.09 0.33 YES
8 ALDH7A1 ALDH7A1 ALDH7A1 3144 0.076 0.33 YES
9 SETD2 SETD2 SETD2 3383 0.071 0.35 YES
10 SUV39H2 SUV39H2 SUV39H2 3466 0.069 0.37 YES
11 ASH1L ASH1L ASH1L 3638 0.065 0.38 YES
12 ALDH1B1 ALDH1B1 ALDH1B1 4126 0.056 0.38 YES
13 ACAT2 ACAT2 ACAT2 4156 0.056 0.4 YES
14 ACAT1 ACAT1 ACAT1 4213 0.055 0.42 YES
15 SUV420H1 SUV420H1 SUV420H1 4537 0.05 0.42 YES
16 WHSC1L1 WHSC1L1 WHSC1L1 4640 0.048 0.44 YES
17 AASS AASS AASS 4763 0.046 0.45 YES
18 PLOD2 PLOD2 PLOD2 4925 0.044 0.46 YES
19 AASDH AASDH AASDH 4960 0.043 0.47 YES
20 SUV39H1 SUV39H1 SUV39H1 4969 0.043 0.49 YES
21 SETDB1 SETDB1 SETDB1 5802 0.032 0.45 NO
22 ALDH2 ALDH2 ALDH2 6330 0.025 0.43 NO
23 SETD1A SETD1A SETD1A 6372 0.025 0.44 NO
24 EHMT2 EHMT2 EHMT2 6843 0.018 0.42 NO
25 PLOD3 PLOD3 PLOD3 6945 0.017 0.42 NO
26 HADHA HADHA HADHA 7193 0.014 0.42 NO
27 ALDH9A1 ALDH9A1 ALDH9A1 7406 0.012 0.41 NO
28 WHSC1 WHSC1 WHSC1 7664 0.0086 0.4 NO
29 HADH HADH HADH 7669 0.0085 0.4 NO
30 GCDH GCDH GCDH 7825 0.0068 0.39 NO
31 NSD1 NSD1 NSD1 8635 -0.0039 0.35 NO
32 SUV420H2 SUV420H2 SUV420H2 8807 -0.0064 0.34 NO
33 SETD1B SETD1B SETD1B 8869 -0.0071 0.34 NO
34 OGDH OGDH OGDH 9209 -0.012 0.33 NO
35 SETD8 SETD8 SETD8 9349 -0.014 0.33 NO
36 BBOX1 BBOX1 BBOX1 10143 -0.026 0.29 NO
37 EHMT1 EHMT1 EHMT1 10148 -0.026 0.3 NO
38 SETD7 SETD7 SETD7 10798 -0.037 0.28 NO
39 ECHS1 ECHS1 ECHS1 10815 -0.037 0.3 NO
40 ALDH3A2 ALDH3A2 ALDH3A2 11791 -0.058 0.26 NO
41 DOT1L DOT1L DOT1L 11880 -0.06 0.28 NO
42 DLST DLST DLST 12226 -0.069 0.29 NO
43 PLOD1 PLOD1 PLOD1 12467 -0.076 0.31 NO

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

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

genes ES table in pathway: BIOCARTA CHREBP2 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 NAA38 NAA38 NAA38 1277 0.14 -0.047 YES
2 PRPF40B PRPF40B PRPF40B 1304 0.14 -0.024 YES
3 CTNNBL1 CTNNBL1 CTNNBL1 1373 0.14 -0.0048 YES
4 THOC2 THOC2 THOC2 1403 0.13 0.017 YES
5 SR140 SR140 SR140 1466 0.13 0.036 YES
6 CWC15 CWC15 CWC15 1967 0.11 0.027 YES
7 PRPF6 PRPF6 PRPF6 2038 0.11 0.041 YES
8 LSM5 LSM5 LSM5 2049 0.11 0.059 YES
9 SNRNP27 SNRNP27 SNRNP27 2336 0.096 0.06 YES
10 SNRPB2 SNRPB2 SNRPB2 2441 0.093 0.07 YES
11 PRPF40A PRPF40A PRPF40A 2641 0.088 0.074 YES
12 PRPF3 PRPF3 PRPF3 2695 0.087 0.086 YES
13 PRPF38B PRPF38B PRPF38B 2804 0.084 0.095 YES
14 TCERG1 TCERG1 TCERG1 2860 0.083 0.11 YES
15 SNRPE SNRPE SNRPE 3008 0.079 0.11 YES
16 SNRPA1 SNRPA1 SNRPA1 3022 0.079 0.12 YES
17 LSM3 LSM3 LSM3 3128 0.076 0.13 YES
18 SYF2 SYF2 SYF2 3198 0.075 0.14 YES
19 SFRS6 SFRS6 SFRS6 3215 0.074 0.15 YES
20 ISY1 ISY1 ISY1 3258 0.073 0.16 YES
21 SF3B14 SF3B14 SF3B14 3262 0.073 0.18 YES
22 PPIH PPIH PPIH 3367 0.071 0.18 YES
23 CRNKL1 CRNKL1 CRNKL1 3379 0.071 0.19 YES
24 PQBP1 PQBP1 PQBP1 3386 0.07 0.21 YES
25 MAGOH MAGOH MAGOH 3552 0.067 0.21 YES
26 SNRPG SNRPG SNRPG 3696 0.064 0.21 YES
27 PRPF38A PRPF38A PRPF38A 3737 0.063 0.22 YES
28 SLU7 SLU7 SLU7 3935 0.06 0.22 YES
29 LSM6 LSM6 LSM6 3996 0.059 0.23 YES
30 PRPF18 PRPF18 PRPF18 4121 0.057 0.23 YES
31 SFRS13A SFRS13A SFRS13A 4139 0.056 0.24 YES
32 CDC5L CDC5L CDC5L 4283 0.054 0.24 YES
33 THOC1 THOC1 THOC1 4428 0.052 0.24 YES
34 CDC40 CDC40 CDC40 4441 0.051 0.25 YES
35 BCAS2 BCAS2 BCAS2 4447 0.051 0.26 YES
36 TRA2A TRA2A TRA2A 4458 0.051 0.26 YES
37 ZMAT2 ZMAT2 ZMAT2 4579 0.049 0.27 YES
38 RBM25 RBM25 RBM25 4590 0.049 0.28 YES
39 RBMX RBMX RBMX 4650 0.048 0.28 YES
40 DDX46 DDX46 DDX46 4655 0.048 0.29 YES
41 HNRNPK HNRNPK HNRNPK 4888 0.044 0.28 YES
42 NCBP1 NCBP1 NCBP1 4975 0.043 0.28 YES
43 SMNDC1 SMNDC1 SMNDC1 5090 0.041 0.29 YES
44 SNRPC SNRPC SNRPC 5169 0.04 0.29 YES
45 SF3B1 SF3B1 SF3B1 5190 0.04 0.29 YES
46 SFRS1 SFRS1 SFRS1 5202 0.04 0.3 YES
47 HNRNPU HNRNPU HNRNPU 5258 0.039 0.3 YES
48 SFRS3 SFRS3 SFRS3 5302 0.038 0.31 YES
49 USP39 USP39 USP39 5339 0.038 0.31 YES
50 PPIE PPIE PPIE 5405 0.037 0.32 YES
51 HNRNPA3 HNRNPA3 HNRNPA3 5433 0.037 0.32 YES
52 DDX42 DDX42 DDX42 5490 0.036 0.32 YES
53 RBM17 RBM17 RBM17 5605 0.035 0.32 YES
54 SNRPF SNRPF SNRPF 5623 0.034 0.33 YES
55 MAGOHB MAGOHB MAGOHB 5705 0.033 0.33 YES
56 PPIL1 PPIL1 PPIL1 5719 0.033 0.33 YES
57 SNRPD3 SNRPD3 SNRPD3 5775 0.032 0.34 YES
58 AQR AQR AQR 5786 0.032 0.34 YES
59 BUD31 BUD31 BUD31 5790 0.032 0.35 YES
60 SF3B2 SF3B2 SF3B2 5816 0.032 0.35 YES
61 SNRNP200 SNRNP200 SNRNP200 5903 0.031 0.35 YES
62 DHX8 DHX8 DHX8 5935 0.03 0.36 YES
63 PRPF19 PRPF19 PRPF19 6072 0.028 0.35 YES
64 CHERP CHERP CHERP 6091 0.028 0.36 YES
65 SNW1 SNW1 SNW1 6095 0.028 0.36 YES
66 SF3B3 SF3B3 SF3B3 6105 0.028 0.37 YES
67 SNRPA SNRPA SNRPA 6227 0.026 0.36 YES
68 SFRS5 SFRS5 SFRS5 6335 0.025 0.36 YES
69 SNRPD2 SNRPD2 SNRPD2 6347 0.025 0.36 YES
70 SART1 SART1 SART1 6396 0.024 0.37 YES
71 SF3A3 SF3A3 SF3A3 6626 0.021 0.36 NO
72 EFTUD2 EFTUD2 EFTUD2 6681 0.02 0.36 NO
73 SNRPB SNRPB SNRPB 6718 0.02 0.36 NO
74 DDX5 DDX5 DDX5 6734 0.02 0.36 NO
75 RBM22 RBM22 RBM22 6904 0.018 0.36 NO
76 BAT1 BAT1 BAT1 7040 0.016 0.35 NO
77 PLRG1 PLRG1 PLRG1 7042 0.016 0.35 NO
78 CCDC12 CCDC12 CCDC12 7263 0.013 0.34 NO
79 DHX15 DHX15 DHX15 7386 0.012 0.34 NO
80 WBP11 WBP11 WBP11 7412 0.012 0.34 NO
81 NHP2L1 NHP2L1 NHP2L1 7456 0.011 0.34 NO
82 THOC4 THOC4 THOC4 7479 0.011 0.34 NO
83 HNRNPC HNRNPC HNRNPC 7495 0.011 0.34 NO
84 ACIN1 ACIN1 ACIN1 7548 0.01 0.34 NO
85 SNRNP70 SNRNP70 SNRNP70 7610 0.0092 0.34 NO
86 U2AF1 U2AF1 U2AF1 7616 0.0092 0.34 NO
87 U2AF2 U2AF2 U2AF2 7625 0.0091 0.34 NO
88 SFRS4 SFRS4 SFRS4 7660 0.0086 0.34 NO
89 PUF60 PUF60 PUF60 7754 0.0076 0.34 NO
90 SFRS2B SFRS2B SFRS2B 7855 0.0063 0.33 NO
91 SF3B4 SF3B4 SF3B4 7858 0.0063 0.33 NO
92 TRA2B TRA2B TRA2B 7927 0.0054 0.33 NO
93 SF3A2 SF3A2 SF3A2 7992 0.0043 0.33 NO
94 DHX38 DHX38 DHX38 8024 0.004 0.33 NO
95 DDX23 DDX23 DDX23 8094 0.0032 0.32 NO
96 SFRS7 SFRS7 SFRS7 8157 0.0025 0.32 NO
97 LSM4 LSM4 LSM4 8239 0.0014 0.32 NO
98 SFRS2 SFRS2 SFRS2 8243 0.0013 0.32 NO
99 PCBP1 PCBP1 PCBP1 8358 -0.0003 0.31 NO
100 PRPF4 PRPF4 PRPF4 8359 -0.00031 0.31 NO
101 HSPA1A HSPA1A HSPA1A 8725 -0.005 0.29 NO
102 XAB2 XAB2 XAB2 8755 -0.0055 0.29 NO
103 RBM8A RBM8A RBM8A 8782 -0.0061 0.29 NO
104 HNRNPM HNRNPM HNRNPM 8883 -0.0073 0.28 NO
105 DHX16 DHX16 DHX16 8997 -0.009 0.28 NO
106 THOC3 THOC3 THOC3 9022 -0.0093 0.28 NO
107 LSM7 LSM7 LSM7 9180 -0.011 0.27 NO
108 LSM2 LSM2 LSM2 9183 -0.012 0.28 NO
109 SFRS9 SFRS9 SFRS9 9333 -0.014 0.27 NO
110 PHF5A PHF5A PHF5A 9620 -0.018 0.26 NO
111 SNRPD1 SNRPD1 SNRPD1 9624 -0.018 0.26 NO
112 HNRNPA1 HNRNPA1 HNRNPA1 9936 -0.022 0.24 NO
113 EIF4A3 EIF4A3 EIF4A3 10002 -0.023 0.25 NO
114 PRPF31 PRPF31 PRPF31 10051 -0.024 0.25 NO
115 SF3A1 SF3A1 SF3A1 10070 -0.024 0.25 NO
116 HSPA8 HSPA8 HSPA8 10276 -0.028 0.24 NO
117 SNRNP40 SNRNP40 SNRNP40 10374 -0.029 0.24 NO
118 SF3B5 SF3B5 SF3B5 10499 -0.032 0.24 NO
119 PRPF8 PRPF8 PRPF8 11814 -0.059 0.18 NO
120 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 12515 -0.078 0.15 NO
121 TXNL4A TXNL4A TXNL4A 12776 -0.085 0.15 NO
122 HSPA1B HSPA1B HSPA1B 13928 -0.13 0.11 NO
123 HSPA2 HSPA2 HSPA2 15023 -0.18 0.081 NO
124 HSPA6 HSPA6 HSPA6 15480 -0.21 0.091 NO
125 HSPA1L HSPA1L HSPA1L 16549 -0.29 0.081 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 CHREBP2 PATHWAY.

Figure S4.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

Table 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 XRCC2 XRCC2 XRCC2 606 0.2 0.068 YES
2 RPA4 RPA4 RPA4 642 0.2 0.16 YES
3 MRE11A MRE11A MRE11A 848 0.18 0.24 YES
4 BRCA2 BRCA2 BRCA2 912 0.17 0.32 YES
5 RAD54B RAD54B RAD54B 1101 0.15 0.39 YES
6 SHFM1 SHFM1 SHFM1 1885 0.11 0.4 YES
7 RAD50 RAD50 RAD50 1944 0.11 0.45 YES
8 BLM BLM BLM 2821 0.084 0.44 YES
9 SSBP1 SSBP1 SSBP1 3487 0.068 0.44 YES
10 EME1 EME1 EME1 3584 0.066 0.47 YES
11 RPA3 RPA3 RPA3 3782 0.063 0.49 YES
12 RAD51L3 RAD51L3 RAD51L3 4462 0.051 0.48 YES
13 NBN NBN NBN 4463 0.051 0.5 YES
14 RAD51L1 RAD51L1 RAD51L1 4503 0.05 0.52 YES
15 RAD52 RAD52 RAD52 4665 0.048 0.54 YES
16 POLD2 POLD2 POLD2 6155 0.027 0.47 NO
17 RAD54L RAD54L RAD54L 6530 0.023 0.46 NO
18 MUS81 MUS81 MUS81 8148 0.0026 0.37 NO
19 TOP3B TOP3B TOP3B 9009 -0.0091 0.33 NO
20 POLD3 POLD3 POLD3 9383 -0.014 0.32 NO
21 RPA2 RPA2 RPA2 9978 -0.023 0.3 NO
22 POLD1 POLD1 POLD1 10111 -0.025 0.3 NO
23 RAD51 RAD51 RAD51 10302 -0.028 0.3 NO
24 XRCC3 XRCC3 XRCC3 10716 -0.035 0.3 NO
25 RPA1 RPA1 RPA1 11789 -0.058 0.27 NO
26 POLD4 POLD4 POLD4 12032 -0.064 0.29 NO
27 TOP3A TOP3A TOP3A 12966 -0.092 0.28 NO

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

Figure S6.  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 GLYCINE SERINE AND THREONINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NARS2 NARS2 NARS2 1798 0.12 -0.025 YES
2 DARS DARS DARS 1979 0.11 0.035 YES
3 DARS2 DARS2 DARS2 3208 0.075 0.015 YES
4 LARS LARS LARS 3350 0.072 0.054 YES
5 GARS GARS GARS 3491 0.068 0.09 YES
6 MARS2 MARS2 MARS2 3511 0.068 0.13 YES
7 FARSB FARSB FARSB 3969 0.059 0.15 YES
8 CARS2 CARS2 CARS2 3995 0.059 0.18 YES
9 LARS2 LARS2 LARS2 4089 0.057 0.22 YES
10 TARS TARS TARS 4108 0.057 0.25 YES
11 SEPSECS SEPSECS SEPSECS 4357 0.053 0.27 YES
12 RARS2 RARS2 RARS2 4425 0.052 0.3 YES
13 KARS KARS KARS 5660 0.034 0.25 YES
14 EPRS EPRS EPRS 5663 0.034 0.28 YES
15 PSTK PSTK PSTK 5827 0.032 0.29 YES
16 CARS CARS CARS 5889 0.031 0.3 YES
17 EARS2 EARS2 EARS2 5892 0.031 0.32 YES
18 YARS YARS YARS 6181 0.027 0.32 YES
19 AARS AARS AARS 6304 0.026 0.34 YES
20 SARS SARS SARS 6362 0.025 0.35 YES
21 YARS2 YARS2 YARS2 6455 0.024 0.36 YES
22 HARS2 HARS2 HARS2 6468 0.024 0.37 YES
23 IARS IARS IARS 6482 0.023 0.39 YES
24 PARS2 PARS2 PARS2 6507 0.023 0.4 YES
25 VARS2 VARS2 VARS2 6620 0.021 0.41 YES
26 IARS2 IARS2 IARS2 6640 0.021 0.42 YES
27 RARS RARS RARS 7282 0.013 0.39 NO
28 WARS2 WARS2 WARS2 7561 0.0099 0.38 NO
29 HARS HARS HARS 7909 0.0056 0.37 NO
30 QARS QARS QARS 7980 0.0045 0.37 NO
31 MTFMT MTFMT MTFMT 8017 0.0041 0.37 NO
32 TARSL2 TARSL2 TARSL2 8188 0.002 0.36 NO
33 AARS2 AARS2 AARS2 8335 -4.4e-06 0.35 NO
34 MARS MARS MARS 8416 -0.0012 0.35 NO
35 VARS VARS VARS 8559 -0.0031 0.34 NO
36 FARSA FARSA FARSA 8645 -0.004 0.34 NO
37 NARS NARS NARS 9119 -0.011 0.32 NO
38 SARS2 SARS2 SARS2 9215 -0.012 0.32 NO
39 FARS2 FARS2 FARS2 12342 -0.073 0.2 NO
40 WARS WARS WARS 15060 -0.18 0.16 NO

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

Figure S8.  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 LYSINE DEGRADATION

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 NAA38 NAA38 NAA38 1277 0.14 -0.019 YES
2 PNPT1 PNPT1 PNPT1 1523 0.13 0.015 YES
3 C1D C1D C1D 1679 0.12 0.051 YES
4 MPHOSPH6 MPHOSPH6 MPHOSPH6 1870 0.11 0.082 YES
5 LSM5 LSM5 LSM5 2049 0.11 0.11 YES
6 EXOSC8 EXOSC8 EXOSC8 2196 0.1 0.14 YES
7 HSPD1 HSPD1 HSPD1 2313 0.097 0.17 YES
8 DIS3 DIS3 DIS3 2677 0.087 0.18 YES
9 TTC37 TTC37 TTC37 2926 0.081 0.2 YES
10 ZCCHC7 ZCCHC7 ZCCHC7 3024 0.079 0.22 YES
11 LSM3 LSM3 LSM3 3128 0.076 0.24 YES
12 CNOT4 CNOT4 CNOT4 3572 0.066 0.24 YES
13 EXOSC5 EXOSC5 EXOSC5 3603 0.066 0.27 YES
14 PAPOLG PAPOLG PAPOLG 3812 0.062 0.28 YES
15 LSM6 LSM6 LSM6 3996 0.059 0.29 YES
16 XRN2 XRN2 XRN2 4149 0.056 0.3 YES
17 SKIV2L2 SKIV2L2 SKIV2L2 4227 0.055 0.32 YES
18 EXOSC3 EXOSC3 EXOSC3 4492 0.05 0.32 YES
19 PAPOLA PAPOLA PAPOLA 4632 0.048 0.33 YES
20 HSPA9 HSPA9 HSPA9 5079 0.042 0.32 YES
21 CNOT10 CNOT10 CNOT10 5153 0.04 0.34 YES
22 PATL1 PATL1 PATL1 5250 0.039 0.34 YES
23 EXOSC9 EXOSC9 EXOSC9 5511 0.036 0.34 YES
24 LSM1 LSM1 LSM1 5578 0.035 0.35 YES
25 CNOT1 CNOT1 CNOT1 5617 0.034 0.36 YES
26 EXOSC7 EXOSC7 EXOSC7 5649 0.034 0.37 YES
27 EXOSC1 EXOSC1 EXOSC1 5715 0.033 0.38 YES
28 DCP1A DCP1A DCP1A 6163 0.027 0.37 NO
29 PARN PARN PARN 6248 0.026 0.37 NO
30 EXOSC2 EXOSC2 EXOSC2 6313 0.025 0.38 NO
31 PAPD7 PAPD7 PAPD7 6503 0.023 0.38 NO
32 DCP1B DCP1B DCP1B 6669 0.021 0.38 NO
33 EDC3 EDC3 EDC3 6717 0.02 0.38 NO
34 DCP2 DCP2 DCP2 6925 0.018 0.37 NO
35 CNOT2 CNOT2 CNOT2 7018 0.016 0.38 NO
36 XRN1 XRN1 XRN1 7069 0.016 0.38 NO
37 DDX6 DDX6 DDX6 7226 0.014 0.38 NO
38 EXOSC10 EXOSC10 EXOSC10 7459 0.011 0.37 NO
39 EDC4 EDC4 EDC4 7594 0.0095 0.36 NO
40 CNOT6L CNOT6L CNOT6L 7689 0.0083 0.36 NO
41 ENO3 ENO3 ENO3 7704 0.0082 0.36 NO
42 CNOT6 CNOT6 CNOT6 7807 0.007 0.36 NO
43 SKIV2L SKIV2L SKIV2L 7925 0.0054 0.36 NO
44 LSM4 LSM4 LSM4 8239 0.0014 0.34 NO
45 WDR61 WDR61 WDR61 8904 -0.0076 0.3 NO
46 CNOT7 CNOT7 CNOT7 9149 -0.011 0.29 NO
47 LSM7 LSM7 LSM7 9180 -0.011 0.3 NO
48 LSM2 LSM2 LSM2 9183 -0.012 0.3 NO
49 EXOSC4 EXOSC4 EXOSC4 9302 -0.013 0.3 NO
50 CNOT3 CNOT3 CNOT3 9902 -0.022 0.27 NO
51 ENO1 ENO1 ENO1 11210 -0.045 0.22 NO
52 RQCD1 RQCD1 RQCD1 11352 -0.048 0.23 NO
53 EXOSC6 EXOSC6 EXOSC6 11615 -0.054 0.23 NO
54 DCPS DCPS DCPS 11656 -0.055 0.25 NO
55 ENO2 ENO2 ENO2 16447 -0.28 0.086 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 LYSINE DEGRADATION.

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

genes ES table in pathway: KEGG SELENOAMINO ACID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPA4 RPA4 RPA4 642 0.2 0.059 YES
2 RFC3 RFC3 RFC3 1404 0.13 0.08 YES
3 CUL4B CUL4B CUL4B 2190 0.1 0.085 YES
4 CETN2 CETN2 CETN2 2497 0.092 0.11 YES
5 CUL4A CUL4A CUL4A 2625 0.088 0.15 YES
6 RFC4 RFC4 RFC4 2858 0.083 0.17 YES
7 ERCC5 ERCC5 ERCC5 2920 0.081 0.21 YES
8 CCNH CCNH CCNH 2924 0.081 0.25 YES
9 CDK7 CDK7 CDK7 3029 0.078 0.28 YES
10 GTF2H5 GTF2H5 GTF2H5 3173 0.076 0.31 YES
11 GTF2H1 GTF2H1 GTF2H1 3673 0.064 0.31 YES
12 RPA3 RPA3 RPA3 3782 0.063 0.34 YES
13 ERCC8 ERCC8 ERCC8 4018 0.058 0.35 YES
14 RFC1 RFC1 RFC1 4777 0.046 0.33 YES
15 ERCC3 ERCC3 ERCC3 4939 0.043 0.34 YES
16 POLE4 POLE4 POLE4 5020 0.042 0.36 YES
17 ERCC4 ERCC4 ERCC4 5204 0.04 0.37 YES
18 RAD23A RAD23A RAD23A 5283 0.038 0.38 YES
19 ERCC6 ERCC6 ERCC6 5772 0.032 0.37 YES
20 RFC2 RFC2 RFC2 6020 0.029 0.37 YES
21 MNAT1 MNAT1 MNAT1 6076 0.028 0.38 YES
22 POLE POLE POLE 6094 0.028 0.39 YES
23 XPA XPA XPA 6138 0.028 0.4 YES
24 POLD2 POLD2 POLD2 6155 0.027 0.41 YES
25 POLE3 POLE3 POLE3 6821 0.019 0.39 NO
26 POLE2 POLE2 POLE2 7003 0.017 0.38 NO
27 GTF2H3 GTF2H3 GTF2H3 7147 0.015 0.38 NO
28 DDB1 DDB1 DDB1 7657 0.0086 0.36 NO
29 LIG1 LIG1 LIG1 7768 0.0075 0.36 NO
30 ERCC1 ERCC1 ERCC1 8391 -0.00078 0.32 NO
31 XPC XPC XPC 8452 -0.0017 0.32 NO
32 RFC5 RFC5 RFC5 8497 -0.0022 0.32 NO
33 RBX1 RBX1 RBX1 8611 -0.0036 0.31 NO
34 PCNA PCNA PCNA 8636 -0.0039 0.32 NO
35 ERCC2 ERCC2 ERCC2 9305 -0.013 0.28 NO
36 GTF2H4 GTF2H4 GTF2H4 9337 -0.014 0.29 NO
37 POLD3 POLD3 POLD3 9383 -0.014 0.29 NO
38 RPA2 RPA2 RPA2 9978 -0.023 0.27 NO
39 POLD1 POLD1 POLD1 10111 -0.025 0.28 NO
40 RPA1 RPA1 RPA1 11789 -0.058 0.21 NO
41 POLD4 POLD4 POLD4 12032 -0.064 0.23 NO
42 GTF2H2 GTF2H2 GTF2H2 12448 -0.076 0.24 NO
43 DDB2 DDB2 DDB2 14264 -0.14 0.21 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 SELENOAMINO ACID METABOLISM.

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

genes ES table in pathway: KEGG PYRUVATE 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 ACSL6 ACSL6 ACSL6 18 0.47 0.073 YES
2 PIPOX PIPOX PIPOX 98 0.36 0.12 YES
3 AGXT AGXT AGXT 153 0.32 0.17 YES
4 AMACR AMACR AMACR 294 0.26 0.21 YES
5 MPV17L MPV17L MPV17L 573 0.21 0.22 YES
6 PXMP4 PXMP4 PXMP4 1082 0.15 0.22 YES
7 PHYH PHYH PHYH 1085 0.15 0.24 YES
8 PEX12 PEX12 PEX12 1460 0.13 0.24 YES
9 PRDX5 PRDX5 PRDX5 1489 0.13 0.26 YES
10 CROT CROT CROT 1718 0.12 0.27 YES
11 BAAT BAAT BAAT 1961 0.11 0.27 YES
12 PECR PECR PECR 2011 0.11 0.28 YES
13 NUDT12 NUDT12 NUDT12 2033 0.11 0.3 YES
14 DDO DDO DDO 2116 0.1 0.31 YES
15 ACSL5 ACSL5 ACSL5 2144 0.1 0.33 YES
16 PEX1 PEX1 PEX1 2168 0.1 0.34 YES
17 ACOT8 ACOT8 ACOT8 2231 0.099 0.35 YES
18 PEX3 PEX3 PEX3 2655 0.088 0.34 NO
19 PEX13 PEX13 PEX13 3051 0.078 0.34 NO
20 NUDT19 NUDT19 NUDT19 3355 0.071 0.33 NO
21 ACOX1 ACOX1 ACOX1 3424 0.07 0.34 NO
22 PEX11A PEX11A PEX11A 3663 0.065 0.33 NO
23 EPHX2 EPHX2 EPHX2 4179 0.056 0.31 NO
24 DECR2 DECR2 DECR2 4262 0.054 0.32 NO
25 FAR2 FAR2 FAR2 4297 0.054 0.32 NO
26 PEX7 PEX7 PEX7 4334 0.053 0.33 NO
27 HACL1 HACL1 HACL1 4358 0.053 0.34 NO
28 CAT CAT CAT 4832 0.045 0.32 NO
29 HSD17B4 HSD17B4 HSD17B4 4879 0.044 0.32 NO
30 ACSL3 ACSL3 ACSL3 5000 0.042 0.32 NO
31 PEX5 PEX5 PEX5 5099 0.041 0.32 NO
32 PEX2 PEX2 PEX2 5159 0.04 0.33 NO
33 GNPAT GNPAT GNPAT 5286 0.038 0.32 NO
34 HAO2 HAO2 HAO2 5340 0.038 0.33 NO
35 PEX16 PEX16 PEX16 5361 0.038 0.33 NO
36 SCP2 SCP2 SCP2 5383 0.037 0.34 NO
37 IDH1 IDH1 IDH1 5476 0.036 0.34 NO
38 FAR1 FAR1 FAR1 5483 0.036 0.34 NO
39 AGPS AGPS AGPS 5849 0.031 0.33 NO
40 ACSL4 ACSL4 ACSL4 6149 0.027 0.32 NO
41 PEX11B PEX11B PEX11B 6478 0.023 0.3 NO
42 MPV17 MPV17 MPV17 6497 0.023 0.3 NO
43 PEX10 PEX10 PEX10 6512 0.023 0.31 NO
44 PEX19 PEX19 PEX19 6546 0.022 0.31 NO
45 SLC25A17 SLC25A17 SLC25A17 7318 0.013 0.27 NO
46 ABCD3 ABCD3 ABCD3 7425 0.011 0.26 NO
47 PRDX1 PRDX1 PRDX1 7448 0.011 0.26 NO
48 GSTK1 GSTK1 GSTK1 7667 0.0086 0.25 NO
49 MLYCD MLYCD MLYCD 7681 0.0084 0.25 NO
50 PEX6 PEX6 PEX6 8365 -0.00041 0.22 NO
51 EHHADH EHHADH EHHADH 8600 -0.0036 0.2 NO
52 ACOX3 ACOX3 ACOX3 8751 -0.0055 0.2 NO
53 ACAA1 ACAA1 ACAA1 8788 -0.0061 0.19 NO
54 MVK MVK MVK 8803 -0.0063 0.19 NO
55 IDH2 IDH2 IDH2 9310 -0.014 0.17 NO
56 SLC27A2 SLC27A2 SLC27A2 9392 -0.015 0.17 NO
57 PMVK PMVK PMVK 9511 -0.016 0.16 NO
58 PEX26 PEX26 PEX26 10145 -0.026 0.13 NO
59 HMGCL HMGCL HMGCL 10467 -0.031 0.12 NO
60 SOD1 SOD1 SOD1 10476 -0.031 0.12 NO
61 DHRS4 DHRS4 DHRS4 10808 -0.037 0.11 NO
62 ABCD1 ABCD1 ABCD1 11127 -0.043 0.098 NO
63 ECH1 ECH1 ECH1 11174 -0.044 0.1 NO
64 PEX14 PEX14 PEX14 11197 -0.044 0.11 NO
65 PECI PECI PECI 11305 -0.047 0.11 NO
66 PXMP2 PXMP2 PXMP2 11692 -0.055 0.097 NO
67 PEX11G PEX11G PEX11G 12081 -0.065 0.086 NO
68 ABCD4 ABCD4 ABCD4 12536 -0.078 0.073 NO
69 CRAT CRAT CRAT 13206 -0.1 0.051 NO
70 ACSL1 ACSL1 ACSL1 13219 -0.1 0.066 NO
71 SOD2 SOD2 SOD2 13385 -0.11 0.074 NO
72 PAOX PAOX PAOX 14062 -0.13 0.057 NO
73 XDH XDH XDH 14294 -0.14 0.067 NO
74 DAO DAO DAO 14913 -0.17 0.06 NO
75 NOS2 NOS2 NOS2 16907 -0.33 0.00047 NO
76 ABCD2 ABCD2 ABCD2 17290 -0.38 0.039 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 PYRUVATE METABOLISM.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRUVATE 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 PROPANOATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GGT7 GGT7 GGT7 205 0.29 0.14 YES
2 CBS CBS CBS 866 0.17 0.19 YES
3 MAT1A MAT1A MAT1A 1203 0.14 0.25 YES
4 METTL6 METTL6 METTL6 1951 0.11 0.26 YES
5 TRMT11 TRMT11 TRMT11 1958 0.11 0.32 YES
6 AHCY AHCY AHCY 3212 0.075 0.29 YES
7 LCMT2 LCMT2 LCMT2 3411 0.07 0.31 YES
8 MARS2 MARS2 MARS2 3511 0.068 0.34 YES
9 GGT1 GGT1 GGT1 3828 0.062 0.36 YES
10 CTH CTH CTH 3977 0.059 0.38 YES
11 SEPHS1 SEPHS1 SEPHS1 4591 0.049 0.37 YES
12 WBSCR22 WBSCR22 WBSCR22 4819 0.045 0.38 YES
13 HEMK1 HEMK1 HEMK1 5241 0.039 0.38 YES
14 METTL2B METTL2B METTL2B 5288 0.038 0.4 YES
15 LCMT1 LCMT1 LCMT1 6418 0.024 0.34 NO
16 SCLY SCLY SCLY 7081 0.016 0.32 NO
17 MAT2A MAT2A MAT2A 7692 0.0083 0.29 NO
18 MARS MARS MARS 8416 -0.0012 0.25 NO
19 GGT6 GGT6 GGT6 9186 -0.012 0.21 NO
20 MAT2B MAT2B MAT2B 10042 -0.024 0.17 NO
21 AHCYL1 AHCYL1 AHCYL1 10076 -0.024 0.18 NO
22 PAPSS1 PAPSS1 PAPSS1 11148 -0.043 0.15 NO
23 AHCYL2 AHCYL2 AHCYL2 13099 -0.096 0.089 NO
24 PAPSS2 PAPSS2 PAPSS2 13881 -0.13 0.11 NO
25 GGT5 GGT5 GGT5 15829 -0.23 0.12 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 PROPANOATE METABOLISM.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PROPANOATE 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 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 OGDHL OGDHL OGDHL 270 0.27 0.2 YES
2 PCK1 PCK1 PCK1 2170 0.1 0.18 YES
3 PDHA1 PDHA1 PDHA1 2384 0.095 0.25 YES
4 SUCLA2 SUCLA2 SUCLA2 3180 0.075 0.26 YES
5 SUCLG1 SUCLG1 SUCLG1 4384 0.052 0.24 YES
6 PC PC PC 4605 0.048 0.26 YES
7 DLD DLD DLD 4724 0.047 0.3 YES
8 DLAT DLAT DLAT 4740 0.046 0.33 YES
9 SUCLG2 SUCLG2 SUCLG2 4924 0.044 0.36 YES
10 IDH1 IDH1 IDH1 5476 0.036 0.36 NO
11 SDHD SDHD SDHD 6014 0.029 0.35 NO
12 PDHB PDHB PDHB 6385 0.024 0.35 NO
13 MDH1 MDH1 MDH1 6849 0.018 0.34 NO
14 ACLY ACLY ACLY 6879 0.018 0.35 NO
15 PCK2 PCK2 PCK2 7617 0.0091 0.32 NO
16 MDH2 MDH2 MDH2 8131 0.0027 0.29 NO
17 IDH3G IDH3G IDH3G 8341 -0.000064 0.28 NO
18 IDH3A IDH3A IDH3A 8524 -0.0026 0.27 NO
19 FH FH FH 8941 -0.0081 0.26 NO
20 OGDH OGDH OGDH 9209 -0.012 0.25 NO
21 IDH2 IDH2 IDH2 9310 -0.014 0.26 NO
22 SDHC SDHC SDHC 9432 -0.015 0.26 NO
23 CS CS CS 9462 -0.016 0.27 NO
24 IDH3B IDH3B IDH3B 9529 -0.017 0.28 NO
25 SDHB SDHB SDHB 9686 -0.019 0.29 NO
26 ACO2 ACO2 ACO2 9771 -0.02 0.3 NO
27 ACO1 ACO1 ACO1 11115 -0.043 0.26 NO
28 DLST DLST DLST 12226 -0.069 0.25 NO
29 SDHA SDHA SDHA 12724 -0.084 0.29 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 AMINOACYL TRNA BIOSYNTHESIS.

Figure S18.  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 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 RPA4 RPA4 RPA4 642 0.2 0.094 YES
2 RFC3 RFC3 RFC3 1404 0.13 0.14 YES
3 RNASEH2B RNASEH2B RNASEH2B 1409 0.13 0.22 YES
4 DNA2 DNA2 DNA2 1623 0.12 0.29 YES
5 RFC4 RFC4 RFC4 2858 0.083 0.28 YES
6 SSBP1 SSBP1 SSBP1 3487 0.068 0.29 YES
7 RPA3 RPA3 RPA3 3782 0.063 0.31 YES
8 PRIM1 PRIM1 PRIM1 4306 0.054 0.32 YES
9 RNASEH1 RNASEH1 RNASEH1 4713 0.047 0.33 YES
10 RFC1 RFC1 RFC1 4777 0.046 0.35 YES
11 POLE4 POLE4 POLE4 5020 0.042 0.37 YES
12 RFC2 RFC2 RFC2 6020 0.029 0.33 YES
13 PRIM2 PRIM2 PRIM2 6060 0.029 0.35 YES
14 POLE POLE POLE 6094 0.028 0.36 YES
15 POLD2 POLD2 POLD2 6155 0.027 0.38 YES
16 MCM3 MCM3 MCM3 6444 0.024 0.38 YES
17 POLE3 POLE3 POLE3 6821 0.019 0.37 YES
18 POLE2 POLE2 POLE2 7003 0.017 0.37 YES
19 MCM6 MCM6 MCM6 7078 0.016 0.38 YES
20 RNASEH2C RNASEH2C RNASEH2C 7264 0.013 0.38 YES
21 MCM7 MCM7 MCM7 7271 0.013 0.38 YES
22 MCM4 MCM4 MCM4 7581 0.0096 0.37 NO
23 FEN1 FEN1 FEN1 7743 0.0077 0.37 NO
24 LIG1 LIG1 LIG1 7768 0.0075 0.37 NO
25 RNASEH2A RNASEH2A RNASEH2A 8293 0.0005 0.34 NO
26 RFC5 RFC5 RFC5 8497 -0.0022 0.33 NO
27 PCNA PCNA PCNA 8636 -0.0039 0.33 NO
28 POLA2 POLA2 POLA2 9101 -0.01 0.31 NO
29 POLD3 POLD3 POLD3 9383 -0.014 0.3 NO
30 MCM2 MCM2 MCM2 9942 -0.022 0.29 NO
31 RPA2 RPA2 RPA2 9978 -0.023 0.3 NO
32 POLD1 POLD1 POLD1 10111 -0.025 0.31 NO
33 RPA1 RPA1 RPA1 11789 -0.058 0.25 NO
34 POLD4 POLD4 POLD4 12032 -0.064 0.28 NO
35 MCM5 MCM5 MCM5 12446 -0.076 0.31 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 RNA DEGRADATION.

Figure S20.  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

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 FAS PATHWAY 29 genes.ES.table 0.47 1.7 0.03 0.46 0.48 0.38 0.23 0.29 0 0.13
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.41 1.9 0.018 0.28 0.19 0.42 0.27 0.31 0 0.078
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.35 1.4 0.092 1 0.9 0.47 0.22 0.36 1 0.52
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.31 1.3 0.13 1 0.98 1 0.69 0.31 0.88 0.44
BIOCARTA KERATINOCYTE PATHWAY 45 genes.ES.table 0.35 1.3 0.22 1 0.99 0.36 0.22 0.28 0.85 0.41
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.31 1.3 0.22 1 0.98 0.41 0.25 0.3 0.88 0.43
BIOCARTA TNFR1 PATHWAY 28 genes.ES.table 0.34 1.3 0.16 1 0.97 0.39 0.27 0.29 1 0.55
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.4 1.3 0.12 1 0.96 0.36 0.14 0.31 1 0.57
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.33 1.1 0.32 1 1 0.67 0.26 0.5 0.91 0.43
KEGG O GLYCAN BIOSYNTHESIS 28 genes.ES.table 0.47 1.2 0.22 1 0.99 0.36 0.06 0.34 0.89 0.43
genes ES table in pathway: BIOCARTA FAS 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 MAP3K5 MAP3K5 MAP3K5 622 0.18 0.037 YES
2 FAS FAS FAS 737 0.17 0.096 YES
3 CASP7 CASP7 CASP7 754 0.16 0.16 YES
4 BCL2 BCL2 BCL2 962 0.14 0.2 YES
5 BIRC3 BIRC3 BIRC3 1118 0.13 0.24 YES
6 MDM2 MDM2 MDM2 1202 0.12 0.29 YES
7 APAF1 APAF1 APAF1 1660 0.096 0.3 YES
8 LMNA LMNA LMNA 2094 0.079 0.3 YES
9 CASP3 CASP3 CASP3 2575 0.064 0.3 YES
10 GSN GSN GSN 2746 0.06 0.32 YES
11 RIPK1 RIPK1 RIPK1 2790 0.059 0.34 YES
12 PSEN1 PSEN1 PSEN1 2993 0.055 0.35 YES
13 BAG4 BAG4 BAG4 3100 0.052 0.36 YES
14 LMNB1 LMNB1 LMNB1 3641 0.043 0.35 YES
15 CYCS CYCS CYCS 3691 0.042 0.36 YES
16 CASP8 CASP8 CASP8 3700 0.042 0.38 YES
17 MAPK8 MAPK8 MAPK8 3723 0.042 0.39 YES
18 CASP9 CASP9 CASP9 3895 0.039 0.4 YES
19 BIRC2 BIRC2 BIRC2 4027 0.037 0.4 YES
20 PARP1 PARP1 PARP1 4136 0.036 0.41 YES
21 CDK11B CDK11B CDK11B 4602 0.03 0.4 YES
22 CHUK CHUK CHUK 4727 0.028 0.4 YES
23 SPTAN1 SPTAN1 SPTAN1 4823 0.027 0.41 YES
24 MAP2K7 MAP2K7 MAP2K7 4894 0.026 0.41 YES
25 PAK2 PAK2 PAK2 5392 0.02 0.39 NO
26 NFKB1 NFKB1 NFKB1 5582 0.018 0.39 NO
27 ACTG1 ACTG1 ACTG1 5872 0.014 0.38 NO
28 CRADD CRADD CRADD 6018 0.013 0.38 NO
29 LMNB2 LMNB2 LMNB2 6254 0.01 0.37 NO
30 CASP2 CASP2 CASP2 6350 0.0093 0.36 NO
31 NFKBIA NFKBIA NFKBIA 6470 0.0079 0.36 NO
32 TRADD TRADD TRADD 6597 0.0065 0.36 NO
33 RASA1 RASA1 RASA1 6818 0.0041 0.35 NO
34 TRAF2 TRAF2 TRAF2 6835 0.0039 0.35 NO
35 MAP3K1 MAP3K1 MAP3K1 7128 0.00078 0.33 NO
36 DAXX DAXX DAXX 7160 0.00048 0.33 NO
37 CASP6 CASP6 CASP6 7480 -0.003 0.31 NO
38 DFFB DFFB DFFB 7554 -0.0038 0.31 NO
39 PRKCD PRKCD PRKCD 7566 -0.0039 0.31 NO
40 RB1 RB1 RB1 7589 -0.0042 0.31 NO
41 TNFRSF1A TNFRSF1A TNFRSF1A 7626 -0.0046 0.31 NO
42 ARHGDIB ARHGDIB ARHGDIB 8185 -0.011 0.28 NO
43 NUMA1 NUMA1 NUMA1 8459 -0.014 0.28 NO
44 RELA RELA RELA 8482 -0.014 0.28 NO
45 XIAP XIAP XIAP 8515 -0.014 0.28 NO
46 CDK11A CDK11A CDK11A 8737 -0.017 0.28 NO
47 FADD FADD FADD 9317 -0.025 0.25 NO
48 DFFA DFFA DFFA 9514 -0.027 0.25 NO
49 PTK2 PTK2 PTK2 9617 -0.029 0.26 NO
50 PRKDC PRKDC PRKDC 10549 -0.043 0.22 NO
51 TNFRSF1B TNFRSF1B TNFRSF1B 10719 -0.046 0.23 NO
52 MAP3K14 MAP3K14 MAP3K14 10968 -0.05 0.24 NO
53 CFLAR CFLAR CFLAR 11003 -0.05 0.26 NO
54 PSEN2 PSEN2 PSEN2 11166 -0.054 0.27 NO
55 BID BID BID 11315 -0.057 0.28 NO
56 TNF TNF TNF 12654 -0.092 0.24 NO
57 TRAF1 TRAF1 TRAF1 14093 -0.14 0.22 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 FAS PATHWAY.

Figure S22.  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 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 PTPN13 PTPN13 PTPN13 409 0.23 0.13 YES
2 FAS FAS FAS 737 0.17 0.23 YES
3 CASP7 CASP7 CASP7 754 0.16 0.34 YES
4 MAP2K4 MAP2K4 MAP2K4 1814 0.088 0.34 YES
5 CASP10 CASP10 CASP10 1869 0.087 0.4 YES
6 LMNA LMNA LMNA 2094 0.079 0.44 YES
7 CASP3 CASP3 CASP3 2575 0.064 0.45 YES
8 CASP8 CASP8 CASP8 3700 0.042 0.42 YES
9 MAPK8 MAPK8 MAPK8 3723 0.042 0.45 YES
10 FASLG FASLG FASLG 3857 0.04 0.46 YES
11 PARP1 PARP1 PARP1 4136 0.036 0.47 YES
12 SPTAN1 SPTAN1 SPTAN1 4823 0.027 0.45 NO
13 PAK2 PAK2 PAK2 5392 0.02 0.44 NO
14 PAK1 PAK1 PAK1 5787 0.015 0.42 NO
15 LMNB2 LMNB2 LMNB2 6254 0.01 0.4 NO
16 MAP3K1 MAP3K1 MAP3K1 7128 0.00078 0.36 NO
17 DAXX DAXX DAXX 7160 0.00048 0.36 NO
18 CASP6 CASP6 CASP6 7480 -0.003 0.34 NO
19 DFFB DFFB DFFB 7554 -0.0038 0.34 NO
20 RB1 RB1 RB1 7589 -0.0042 0.34 NO
21 ARHGDIB ARHGDIB ARHGDIB 8185 -0.011 0.31 NO
22 FADD FADD FADD 9317 -0.025 0.27 NO
23 DFFA DFFA DFFA 9514 -0.027 0.28 NO
24 JUN JUN JUN 9814 -0.032 0.28 NO
25 FAF1 FAF1 FAF1 10129 -0.036 0.29 NO
26 MAP3K7 MAP3K7 MAP3K7 10378 -0.04 0.3 NO
27 PRKDC PRKDC PRKDC 10549 -0.043 0.32 NO
28 CFLAR CFLAR CFLAR 11003 -0.05 0.33 NO
29 RIPK2 RIPK2 RIPK2 12581 -0.089 0.3 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 HIVNEF PATHWAY.

Figure S24.  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 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 CASP7 CASP7 CASP7 754 0.16 0.036 YES
2 BCL2 BCL2 BCL2 962 0.14 0.092 YES
3 BIRC3 BIRC3 BIRC3 1118 0.13 0.14 YES
4 APAF1 APAF1 APAF1 1660 0.096 0.16 YES
5 TNFRSF10A TNFRSF10A TNFRSF10A 1713 0.093 0.2 YES
6 CASP10 CASP10 CASP10 1869 0.087 0.24 YES
7 LMNA LMNA LMNA 2094 0.079 0.26 YES
8 TNFRSF10B TNFRSF10B TNFRSF10B 2286 0.072 0.28 YES
9 TNFSF10 TNFSF10 TNFSF10 2458 0.068 0.31 YES
10 CASP3 CASP3 CASP3 2575 0.064 0.33 YES
11 RIPK1 RIPK1 RIPK1 2790 0.059 0.35 YES
12 CYCS CYCS CYCS 3691 0.042 0.32 YES
13 CASP8 CASP8 CASP8 3700 0.042 0.34 YES
14 CASP9 CASP9 CASP9 3895 0.039 0.34 YES
15 BIRC2 BIRC2 BIRC2 4027 0.037 0.35 YES
16 CHUK CHUK CHUK 4727 0.028 0.33 NO
17 SPTAN1 SPTAN1 SPTAN1 4823 0.027 0.34 NO
18 NFKB1 NFKB1 NFKB1 5582 0.018 0.3 NO
19 NFKBIA NFKBIA NFKBIA 6470 0.0079 0.26 NO
20 TRADD TRADD TRADD 6597 0.0065 0.25 NO
21 TRAF2 TRAF2 TRAF2 6835 0.0039 0.24 NO
22 CASP6 CASP6 CASP6 7480 -0.003 0.21 NO
23 DFFB DFFB DFFB 7554 -0.0038 0.2 NO
24 RELA RELA RELA 8482 -0.014 0.16 NO
25 XIAP XIAP XIAP 8515 -0.014 0.16 NO
26 FADD FADD FADD 9317 -0.025 0.13 NO
27 DFFA DFFA DFFA 9514 -0.027 0.13 NO
28 MAP3K14 MAP3K14 MAP3K14 10968 -0.05 0.077 NO
29 CFLAR CFLAR CFLAR 11003 -0.05 0.099 NO
30 TNFSF12 TNFSF12 TNFSF12 12408 -0.084 0.061 NO
31 TNFRSF25 TNFRSF25 TNFRSF25 15893 -0.23 -0.022 NO
32 GAS2 GAS2 GAS2 16715 -0.29 0.071 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 DEATH PATHWAY.

Figure S26.  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 RACCYCD PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 UGT1A1 UGT1A1 UGT1A1 130 0.34 0.11 YES
2 UGT1A10 UGT1A10 UGT1A10 320 0.26 0.19 YES
3 UGT2B4 UGT2B4 UGT2B4 452 0.22 0.26 YES
4 UGT2B7 UGT2B7 UGT2B7 545 0.2 0.32 YES
5 UGT1A6 UGT1A6 UGT1A6 897 0.15 0.35 YES
6 BLVRA BLVRA BLVRA 1104 0.13 0.38 YES
7 UGT1A9 UGT1A9 UGT1A9 1111 0.13 0.43 YES
8 UGT2B15 UGT2B15 UGT2B15 1180 0.12 0.46 YES
9 FECH FECH FECH 1293 0.11 0.5 YES
10 BLVRB BLVRB BLVRB 1889 0.086 0.49 YES
11 UGT1A8 UGT1A8 UGT1A8 1912 0.085 0.52 YES
12 ALAS1 ALAS1 ALAS1 2011 0.082 0.55 YES
13 COX10 COX10 COX10 2402 0.069 0.55 YES
14 EPRS EPRS EPRS 2923 0.056 0.54 NO
15 CPOX CPOX CPOX 3159 0.051 0.54 NO
16 COX15 COX15 COX15 4410 0.032 0.48 NO
17 GUSB GUSB GUSB 5496 0.018 0.43 NO
18 UGT1A3 UGT1A3 UGT1A3 6894 0.0033 0.35 NO
19 ALAD ALAD ALAD 7363 -0.0017 0.33 NO
20 EARS2 EARS2 EARS2 7395 -0.002 0.33 NO
21 HMOX2 HMOX2 HMOX2 7752 -0.0058 0.31 NO
22 HMBS HMBS HMBS 7993 -0.0086 0.3 NO
23 UGT2B11 UGT2B11 UGT2B11 8087 -0.0097 0.3 NO
24 HMOX1 HMOX1 HMOX1 8584 -0.015 0.27 NO
25 MMAB MMAB MMAB 8806 -0.018 0.27 NO
26 UROD UROD UROD 9480 -0.027 0.24 NO
27 UROS UROS UROS 9533 -0.028 0.25 NO
28 ALAS2 ALAS2 ALAS2 11436 -0.059 0.16 NO
29 FTH1 FTH1 FTH1 11468 -0.06 0.18 NO
30 PPOX PPOX PPOX 11705 -0.066 0.19 NO
31 UGT2B10 UGT2B10 UGT2B10 13483 -0.12 0.13 NO
32 CP CP CP 13503 -0.12 0.17 NO
33 UGT2A3 UGT2A3 UGT2A3 15845 -0.23 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 RACCYCD PATHWAY.

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

genes ES table in pathway: BIOCARTA KERATINOCYTE PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AKR1B10 AKR1B10 AKR1B10 254 0.28 0.088 YES
2 ALDOB ALDOB ALDOB 634 0.18 0.13 YES
3 PFKFB4 PFKFB4 PFKFB4 951 0.14 0.17 YES
4 GMDS GMDS GMDS 1018 0.14 0.21 YES
5 HK2 HK2 HK2 1103 0.13 0.26 YES
6 MTMR7 MTMR7 MTMR7 1128 0.13 0.3 YES
7 PFKP PFKP PFKP 1268 0.12 0.34 YES
8 PFKFB2 PFKFB2 PFKFB2 1630 0.097 0.35 YES
9 MPI MPI MPI 1969 0.083 0.36 YES
10 TSTA3 TSTA3 TSTA3 2074 0.079 0.39 YES
11 PFKFB3 PFKFB3 PFKFB3 2536 0.065 0.38 YES
12 FPGT FPGT FPGT 2611 0.064 0.4 YES
13 GMPPB GMPPB GMPPB 3084 0.053 0.4 NO
14 GMPPA GMPPA GMPPA 3466 0.046 0.39 NO
15 PMM2 PMM2 PMM2 3896 0.039 0.38 NO
16 HK1 HK1 HK1 4157 0.035 0.38 NO
17 TPI1 TPI1 TPI1 4334 0.033 0.38 NO
18 PFKL PFKL PFKL 5483 0.019 0.32 NO
19 PMM1 PMM1 PMM1 6512 0.0075 0.27 NO
20 SORD SORD SORD 6839 0.0039 0.25 NO
21 ALDOC ALDOC ALDOC 7690 -0.0052 0.21 NO
22 MTMR2 MTMR2 MTMR2 7713 -0.0054 0.21 NO
23 PHPT1 PHPT1 PHPT1 7901 -0.0077 0.2 NO
24 MTMR6 MTMR6 MTMR6 10040 -0.034 0.095 NO
25 FBP1 FBP1 FBP1 10077 -0.035 0.11 NO
26 MTMR1 MTMR1 MTMR1 10123 -0.036 0.12 NO
27 PFKM PFKM PFKM 10432 -0.041 0.11 NO
28 FUK FUK FUK 10702 -0.045 0.12 NO
29 KHK KHK KHK 11967 -0.073 0.072 NO
30 FBP2 FBP2 FBP2 13056 -0.1 0.049 NO
31 PFKFB1 PFKFB1 PFKFB1 14953 -0.18 0.0092 NO
32 HK3 HK3 HK3 15502 -0.21 0.055 NO
33 AKR1B1 AKR1B1 AKR1B1 15836 -0.23 0.12 NO

Figure S29.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA KERATINOCYTE PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 PATHWAY

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 MAP2K4 MAP2K4 MAP2K4 1814 0.088 -0.004 YES
2 LMNA LMNA LMNA 2094 0.079 0.067 YES
3 CASP3 CASP3 CASP3 2575 0.064 0.11 YES
4 RIPK1 RIPK1 RIPK1 2790 0.059 0.16 YES
5 BAG4 BAG4 BAG4 3100 0.052 0.2 YES
6 LMNB1 LMNB1 LMNB1 3641 0.043 0.22 YES
7 CASP8 CASP8 CASP8 3700 0.042 0.26 YES
8 MAPK8 MAPK8 MAPK8 3723 0.042 0.31 YES
9 PARP1 PARP1 PARP1 4136 0.036 0.32 YES
10 SPTAN1 SPTAN1 SPTAN1 4823 0.027 0.32 YES
11 MADD MADD MADD 4932 0.025 0.34 YES
12 PAK2 PAK2 PAK2 5392 0.02 0.33 NO
13 PAK1 PAK1 PAK1 5787 0.015 0.33 NO
14 CRADD CRADD CRADD 6018 0.013 0.33 NO
15 LMNB2 LMNB2 LMNB2 6254 0.01 0.33 NO
16 CASP2 CASP2 CASP2 6350 0.0093 0.33 NO
17 TRADD TRADD TRADD 6597 0.0065 0.32 NO
18 MAP3K1 MAP3K1 MAP3K1 7128 0.00078 0.3 NO
19 DFFB DFFB DFFB 7554 -0.0038 0.28 NO
20 RB1 RB1 RB1 7589 -0.0042 0.28 NO
21 TNFRSF1A TNFRSF1A TNFRSF1A 7626 -0.0046 0.28 NO
22 ARHGDIB ARHGDIB ARHGDIB 8185 -0.011 0.26 NO
23 FADD FADD FADD 9317 -0.025 0.23 NO
24 DFFA DFFA DFFA 9514 -0.027 0.25 NO
25 JUN JUN JUN 9814 -0.032 0.26 NO
26 MAP3K7 MAP3K7 MAP3K7 10378 -0.04 0.28 NO
27 PRKDC PRKDC PRKDC 10549 -0.043 0.31 NO
28 TNF TNF TNF 12654 -0.092 0.3 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: BIOCARTA PYK2 PATHWAY.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA TNFR1 PATHWAY

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 NEIL2 NEIL2 NEIL2 1647 0.096 0.006 YES
2 POLD3 POLD3 POLD3 1668 0.095 0.1 YES
3 POLE2 POLE2 POLE2 2921 0.056 0.089 YES
4 MBD4 MBD4 MBD4 3406 0.047 0.11 YES
5 LIG1 LIG1 LIG1 3463 0.046 0.15 YES
6 POLD4 POLD4 POLD4 3570 0.044 0.19 YES
7 FEN1 FEN1 FEN1 3858 0.04 0.22 YES
8 PARP1 PARP1 PARP1 4136 0.036 0.24 YES
9 PARP3 PARP3 PARP3 4235 0.034 0.27 YES
10 PARP2 PARP2 PARP2 4267 0.034 0.3 YES
11 POLE POLE POLE 4581 0.03 0.31 YES
12 TDG TDG TDG 5274 0.021 0.3 YES
13 UNG UNG UNG 5551 0.018 0.3 YES
14 POLE3 POLE3 POLE3 5656 0.017 0.31 YES
15 POLL POLL POLL 6107 0.012 0.3 YES
16 POLE4 POLE4 POLE4 6334 0.0094 0.29 YES
17 APEX1 APEX1 APEX1 6524 0.0074 0.29 YES
18 XRCC1 XRCC1 XRCC1 6696 0.0056 0.29 YES
19 NEIL3 NEIL3 NEIL3 7077 0.0015 0.27 YES
20 MPG MPG MPG 7676 -0.005 0.24 YES
21 POLD2 POLD2 POLD2 7735 -0.0057 0.24 YES
22 POLD1 POLD1 POLD1 8118 -0.01 0.23 YES
23 PCNA PCNA PCNA 8317 -0.012 0.23 YES
24 SMUG1 SMUG1 SMUG1 8553 -0.015 0.23 YES
25 PARP4 PARP4 PARP4 9152 -0.023 0.22 YES
26 MUTYH MUTYH MUTYH 9239 -0.024 0.24 YES
27 NEIL1 NEIL1 NEIL1 9326 -0.025 0.26 YES
28 APEX2 APEX2 APEX2 9374 -0.026 0.28 YES
29 LIG3 LIG3 LIG3 10095 -0.035 0.28 YES
30 NTHL1 NTHL1 NTHL1 10986 -0.05 0.28 YES
31 OGG1 OGG1 OGG1 11056 -0.052 0.33 YES
32 POLB POLB POLB 11216 -0.055 0.38 YES

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: BIOCARTA TNFR1 PATHWAY.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CDKN1A CDKN1A CDKN1A 1336 0.11 0.084 YES
2 AKT1 AKT1 AKT1 4002 0.038 -0.011 YES
3 MAPK3 MAPK3 MAPK3 4030 0.037 0.04 YES
4 CHUK CHUK CHUK 4727 0.028 0.04 YES
5 NFKB1 NFKB1 NFKB1 5582 0.018 0.018 YES
6 RAC1 RAC1 RAC1 5617 0.017 0.04 YES
7 RHOA RHOA RHOA 5634 0.017 0.063 YES
8 MAPK1 MAPK1 MAPK1 5738 0.016 0.079 YES
9 PAK1 PAK1 PAK1 5787 0.015 0.098 YES
10 CDK6 CDK6 CDK6 5818 0.015 0.12 YES
11 CDK2 CDK2 CDK2 6173 0.011 0.11 YES
12 NFKBIA NFKBIA NFKBIA 6470 0.0079 0.11 YES
13 RAF1 RAF1 RAF1 6844 0.0038 0.093 YES
14 RB1 RB1 RB1 7589 -0.0042 0.058 YES
15 PIK3CA PIK3CA PIK3CA 7618 -0.0045 0.062 YES
16 RELA RELA RELA 8482 -0.014 0.034 YES
17 HRAS HRAS HRAS 8898 -0.019 0.038 YES
18 CCND1 CCND1 CCND1 9338 -0.025 0.049 YES
19 CDKN1B CDKN1B CDKN1B 9635 -0.029 0.074 YES
20 IKBKB IKBKB IKBKB 9826 -0.032 0.11 YES
21 TFDP1 TFDP1 TFDP1 9853 -0.032 0.15 YES
22 PIK3R1 PIK3R1 PIK3R1 10074 -0.035 0.19 YES
23 CCNE1 CCNE1 CCNE1 10714 -0.046 0.22 YES
24 CDK4 CDK4 CDK4 10844 -0.048 0.28 YES
25 IKBKG IKBKG IKBKG 12438 -0.085 0.31 YES

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 FRUCTOSE AND MANNOSE METABOLISM.

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

genes ES table in pathway: KEGG VALINE LEUCINE AND ISOLEUCINE 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 DEGS2 DEGS2 DEGS2 371 0.24 0.051 YES
2 SGMS2 SGMS2 SGMS2 400 0.23 0.12 YES
3 ACER2 ACER2 ACER2 554 0.2 0.17 YES
4 UGT8 UGT8 UGT8 570 0.19 0.23 YES
5 B4GALT6 B4GALT6 B4GALT6 734 0.17 0.27 YES
6 SGMS1 SGMS1 SGMS1 1005 0.14 0.3 YES
7 SGPP2 SGPP2 SGPP2 1025 0.14 0.34 YES
8 SPTLC2 SPTLC2 SPTLC2 1217 0.12 0.36 YES
9 SGPP1 SGPP1 SGPP1 1431 0.11 0.38 YES
10 SMPD3 SMPD3 SMPD3 2531 0.066 0.34 NO
11 ACER3 ACER3 ACER3 2565 0.065 0.36 NO
12 KDSR KDSR KDSR 2682 0.061 0.37 NO
13 ARSA ARSA ARSA 2849 0.058 0.38 NO
14 ASAH1 ASAH1 ASAH1 4341 0.033 0.31 NO
15 SPTLC1 SPTLC1 SPTLC1 5560 0.018 0.24 NO
16 SGPL1 SGPL1 SGPL1 5568 0.018 0.25 NO
17 PPAP2C PPAP2C PPAP2C 6150 0.012 0.22 NO
18 SMPD2 SMPD2 SMPD2 6379 0.0091 0.21 NO
19 DEGS1 DEGS1 DEGS1 6544 0.0072 0.2 NO
20 UGCG UGCG UGCG 8265 -0.012 0.11 NO
21 GAL3ST1 GAL3ST1 GAL3ST1 8509 -0.014 0.1 NO
22 GBA GBA GBA 9068 -0.021 0.077 NO
23 SMPD4 SMPD4 SMPD4 9337 -0.025 0.07 NO
24 GLB1 GLB1 GLB1 9490 -0.027 0.07 NO
25 SPHK2 SPHK2 SPHK2 10216 -0.037 0.04 NO
26 GLA GLA GLA 10903 -0.049 0.017 NO
27 SPHK1 SPHK1 SPHK1 11687 -0.066 -0.0067 NO
28 NEU4 NEU4 NEU4 11845 -0.07 0.0056 NO
29 GALC GALC GALC 12647 -0.092 -0.011 NO
30 SMPD1 SMPD1 SMPD1 12891 -0.099 0.0051 NO
31 NEU3 NEU3 NEU3 13263 -0.11 0.018 NO
32 PPAP2A PPAP2A PPAP2A 13535 -0.12 0.039 NO
33 PPAP2B PPAP2B PPAP2B 14096 -0.14 0.051 NO
34 NEU1 NEU1 NEU1 14134 -0.14 0.093 NO
35 CERK CERK CERK 14725 -0.17 0.11 NO
36 ASAH2 ASAH2 ASAH2 15871 -0.23 0.12 NO

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

Figure S38.  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 O GLYCAN BIOSYNTHESIS

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 GNAQ GNAQ GNAQ 1196 0.12 0.039 YES
2 MAP2K4 MAP2K4 MAP2K4 1814 0.088 0.082 YES
3 PRKCA PRKCA PRKCA 2126 0.077 0.13 YES
4 MAP2K1 MAP2K1 MAP2K1 2578 0.064 0.16 YES
5 PTK2B PTK2B PTK2B 2803 0.059 0.2 YES
6 CALM3 CALM3 CALM3 3362 0.048 0.21 YES
7 MAP2K3 MAP2K3 MAP2K3 3422 0.047 0.25 YES
8 MAPK8 MAPK8 MAPK8 3723 0.042 0.27 YES
9 MAPK3 MAPK3 MAPK3 4030 0.037 0.28 YES
10 CALM2 CALM2 CALM2 4120 0.036 0.31 YES
11 BCAR1 BCAR1 BCAR1 4562 0.03 0.31 YES
12 RAC1 RAC1 RAC1 5617 0.017 0.27 NO
13 MAPK1 MAPK1 MAPK1 5738 0.016 0.28 NO
14 PAK1 PAK1 PAK1 5787 0.015 0.29 NO
15 SOS1 SOS1 SOS1 6213 0.011 0.27 NO
16 CALM1 CALM1 CALM1 6642 0.0061 0.25 NO
17 MAP2K2 MAP2K2 MAP2K2 6734 0.0051 0.25 NO
18 RAF1 RAF1 RAF1 6844 0.0038 0.25 NO
19 GRB2 GRB2 GRB2 7122 0.00084 0.24 NO
20 MAP3K1 MAP3K1 MAP3K1 7128 0.00078 0.24 NO
21 CRKL CRKL CRKL 7238 -0.00043 0.23 NO
22 SHC1 SHC1 SHC1 9065 -0.021 0.15 NO
23 SRC SRC SRC 9578 -0.028 0.14 NO
24 JUN JUN JUN 9814 -0.032 0.16 NO
25 MAPK14 MAPK14 MAPK14 11620 -0.064 0.11 NO
26 PRKCB PRKCB PRKCB 13909 -0.14 0.1 NO
27 PLCG1 PLCG1 PLCG1 14082 -0.14 0.22 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 O GLYCAN BIOSYNTHESIS.

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

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 28 genes.ES.table 0.57 1.5 0.068 0.11 0.88 0.32 0.16 0.27 0.072 0
BIOCARTA AGR PATHWAY 34 genes.ES.table 0.5 1.5 0.059 0.1 0.85 0.41 0.29 0.29 0.064 0.001
BIOCARTA ALK PATHWAY 32 genes.ES.table 0.51 1.5 0.026 0.1 0.84 0.44 0.27 0.32 0.062 0.001
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.45 1.7 0.019 0.062 0.46 0.28 0.28 0.2 0 0.005
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.59 1.7 0.021 0.06 0.47 0.21 0.12 0.19 0 0.003
BIOCARTA BIOPEPTIDES PATHWAY 40 genes.ES.table 0.44 1.5 0.047 0.11 0.88 0.28 0.22 0.21 0.072 0
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.37 1.4 0.1 0.14 0.94 0.47 0.36 0.3 0.1 0
BIOCARTA G1 PATHWAY 27 genes.ES.table 0.46 1.5 0.082 0.11 0.88 0.18 0.16 0.16 0.074 0
BIOCARTA HDAC PATHWAY 26 genes.ES.table 0.57 1.7 0.011 0.067 0.61 0.69 0.38 0.43 0.028 0.002
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.47 1.6 0.03 0.074 0.68 0.8 0.45 0.44 0.038 0.001
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 TGFB3 TGFB3 TGFB3 133 0.76 0.069 YES
2 VEGFC VEGFC VEGFC 267 0.69 0.13 YES
3 HGF HGF HGF 409 0.63 0.19 YES
4 AKT3 AKT3 AKT3 589 0.58 0.24 YES
5 PIK3R5 PIK3R5 PIK3R5 599 0.58 0.29 YES
6 PIK3CG PIK3CG PIK3CG 627 0.57 0.35 YES
7 PAK3 PAK3 PAK3 829 0.52 0.39 YES
8 TGFB2 TGFB2 TGFB2 871 0.52 0.44 YES
9 PIK3CD PIK3CD PIK3CD 1278 0.45 0.46 YES
10 ARNT2 ARNT2 ARNT2 1606 0.4 0.49 YES
11 ETS1 ETS1 ETS1 2218 0.32 0.48 YES
12 PDGFB PDGFB PDGFB 2363 0.31 0.51 YES
13 FIGF FIGF FIGF 2395 0.3 0.54 YES
14 TGFB1 TGFB1 TGFB1 2855 0.26 0.54 YES
15 PGF PGF PGF 2954 0.24 0.56 YES
16 PIK3CA PIK3CA PIK3CA 3553 0.18 0.54 NO
17 HIF1A HIF1A HIF1A 4015 0.15 0.53 NO
18 EPAS1 EPAS1 EPAS1 4644 0.12 0.51 NO
19 EP300 EP300 EP300 4834 0.11 0.51 NO
20 RAPGEF1 RAPGEF1 RAPGEF1 4917 0.11 0.52 NO
21 SOS1 SOS1 SOS1 4964 0.11 0.52 NO
22 PIK3R3 PIK3R3 PIK3R3 5084 0.1 0.53 NO
23 CREBBP CREBBP CREBBP 5369 0.091 0.52 NO
24 ARNT ARNT ARNT 5501 0.087 0.52 NO
25 PIK3R1 PIK3R1 PIK3R1 5698 0.081 0.52 NO
26 SOS2 SOS2 SOS2 5736 0.08 0.52 NO
27 RAP1A RAP1A RAP1A 5836 0.077 0.53 NO
28 BRAF BRAF BRAF 6011 0.072 0.52 NO
29 PTPN11 PTPN11 PTPN11 6079 0.071 0.53 NO
30 GRB2 GRB2 GRB2 6836 0.054 0.49 NO
31 VEGFB VEGFB VEGFB 6843 0.054 0.5 NO
32 FLCN FLCN FLCN 6924 0.052 0.5 NO
33 PIK3CB PIK3CB PIK3CB 7306 0.045 0.48 NO
34 CRK CRK CRK 7342 0.044 0.48 NO
35 PAK2 PAK2 PAK2 7367 0.043 0.49 NO
36 KRAS KRAS KRAS 7391 0.043 0.49 NO
37 GAB1 GAB1 GAB1 7733 0.037 0.47 NO
38 CDC42 CDC42 CDC42 8026 0.033 0.46 NO
39 MAP2K1 MAP2K1 MAP2K1 8051 0.032 0.46 NO
40 CRKL CRKL CRKL 8241 0.03 0.46 NO
41 NRAS NRAS NRAS 8595 0.024 0.44 NO
42 MAPK1 MAPK1 MAPK1 8628 0.024 0.44 NO
43 MET MET MET 9106 0.016 0.41 NO
44 JUN JUN JUN 9240 0.014 0.41 NO
45 TGFA TGFA TGFA 9565 0.0099 0.39 NO
46 CUL2 CUL2 CUL2 9809 0.0064 0.38 NO
47 EGLN2 EGLN2 EGLN2 9876 0.0054 0.37 NO
48 AKT1 AKT1 AKT1 10068 0.0026 0.36 NO
49 RAF1 RAF1 RAF1 10189 0.00062 0.36 NO
50 VHL VHL VHL 10501 -0.0038 0.34 NO
51 AKT2 AKT2 AKT2 10721 -0.0078 0.33 NO
52 VEGFA VEGFA VEGFA 10940 -0.011 0.32 NO
53 EGLN1 EGLN1 EGLN1 10944 -0.011 0.32 NO
54 EGLN3 EGLN3 EGLN3 11166 -0.014 0.31 NO
55 SLC2A1 SLC2A1 SLC2A1 11167 -0.014 0.31 NO
56 TCEB1 TCEB1 TCEB1 11802 -0.024 0.28 NO
57 PAK1 PAK1 PAK1 11955 -0.027 0.27 NO
58 ARAF ARAF ARAF 12085 -0.029 0.27 NO
59 RAC1 RAC1 RAC1 12125 -0.03 0.27 NO
60 PIK3R2 PIK3R2 PIK3R2 12385 -0.034 0.26 NO
61 RAP1B RAP1B RAP1B 12414 -0.035 0.26 NO
62 RBX1 RBX1 RBX1 13047 -0.045 0.23 NO
63 PAK4 PAK4 PAK4 13209 -0.048 0.22 NO
64 MAPK3 MAPK3 MAPK3 13939 -0.062 0.19 NO
65 MAP2K2 MAP2K2 MAP2K2 13995 -0.063 0.19 NO
66 FH FH FH 15150 -0.093 0.14 NO
67 TCEB2 TCEB2 TCEB2 15406 -0.1 0.13 NO
68 PAK6 PAK6 PAK6 15686 -0.11 0.13 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 AGR 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 WAS WAS WAS 1010 0.49 0.0056 YES
2 SNAI2 SNAI2 SNAI2 1110 0.47 0.06 YES
3 FGFR1 FGFR1 FGFR1 1452 0.42 0.094 YES
4 PTPRM PTPRM PTPRM 1637 0.4 0.13 YES
5 WASF3 WASF3 WASF3 1706 0.39 0.18 YES
6 SORBS1 SORBS1 SORBS1 2085 0.34 0.2 YES
7 FYN FYN FYN 2311 0.31 0.23 YES
8 TCF7L1 TCF7L1 TCF7L1 2325 0.31 0.27 YES
9 ACTN2 ACTN2 ACTN2 2376 0.31 0.3 YES
10 WASF1 WASF1 WASF1 2458 0.3 0.34 YES
11 ACTN3 ACTN3 ACTN3 2575 0.28 0.36 YES
12 SNAI1 SNAI1 SNAI1 2641 0.28 0.4 YES
13 CTNNA3 CTNNA3 CTNNA3 2693 0.27 0.43 YES
14 LEF1 LEF1 LEF1 2767 0.26 0.46 YES
15 FER FER FER 3091 0.23 0.47 YES
16 TGFBR1 TGFBR1 TGFBR1 3935 0.16 0.44 YES
17 VCL VCL VCL 4131 0.14 0.45 YES
18 EGFR EGFR EGFR 4510 0.12 0.44 YES
19 ACTN1 ACTN1 ACTN1 4525 0.12 0.46 YES
20 TGFBR2 TGFBR2 TGFBR2 4543 0.12 0.47 YES
21 RAC2 RAC2 RAC2 4559 0.12 0.49 YES
22 EP300 EP300 EP300 4834 0.11 0.48 YES
23 IGF1R IGF1R IGF1R 5054 0.1 0.49 YES
24 PTPRJ PTPRJ PTPRJ 5096 0.1 0.5 YES
25 CREBBP CREBBP CREBBP 5369 0.091 0.49 YES
26 TJP1 TJP1 TJP1 5823 0.078 0.48 YES
27 PTPRB PTPRB PTPRB 5827 0.077 0.49 YES
28 CTNNA2 CTNNA2 CTNNA2 5964 0.074 0.49 YES
29 BAIAP2 BAIAP2 BAIAP2 6064 0.071 0.49 YES
30 WASF2 WASF2 WASF2 6123 0.07 0.5 YES
31 SMAD3 SMAD3 SMAD3 6408 0.064 0.49 YES
32 MAP3K7 MAP3K7 MAP3K7 6613 0.059 0.48 YES
33 LMO7 LMO7 LMO7 6662 0.058 0.49 YES
34 IQGAP1 IQGAP1 IQGAP1 6733 0.056 0.49 YES
35 SMAD2 SMAD2 SMAD2 6759 0.056 0.5 YES
36 PTPN6 PTPN6 PTPN6 6963 0.052 0.49 NO
37 PTPN1 PTPN1 PTPN1 7439 0.042 0.47 NO
38 MLLT4 MLLT4 MLLT4 7571 0.04 0.47 NO
39 INSR INSR INSR 7659 0.038 0.47 NO
40 CTNND1 CTNND1 CTNND1 8009 0.033 0.46 NO
41 CDC42 CDC42 CDC42 8026 0.033 0.46 NO
42 PARD3 PARD3 PARD3 8188 0.03 0.45 NO
43 SSX2IP SSX2IP SSX2IP 8215 0.03 0.46 NO
44 MAPK1 MAPK1 MAPK1 8628 0.024 0.44 NO
45 SMAD4 SMAD4 SMAD4 8664 0.023 0.44 NO
46 ACTN4 ACTN4 ACTN4 8897 0.019 0.43 NO
47 RHOA RHOA RHOA 9105 0.016 0.42 NO
48 MET MET MET 9106 0.016 0.42 NO
49 CSNK2A1 CSNK2A1 CSNK2A1 9295 0.014 0.41 NO
50 PVRL2 PVRL2 PVRL2 9399 0.012 0.41 NO
51 WASL WASL WASL 9700 0.0081 0.39 NO
52 YES1 YES1 YES1 9726 0.0077 0.39 NO
53 ACTB ACTB ACTB 9764 0.0071 0.39 NO
54 CTNNB1 CTNNB1 CTNNB1 10115 0.0019 0.37 NO
55 PTPRF PTPRF PTPRF 10192 0.0006 0.36 NO
56 PVRL3 PVRL3 PVRL3 10463 -0.0033 0.35 NO
57 CTNNA1 CTNNA1 CTNNA1 10564 -0.0052 0.34 NO
58 PVRL1 PVRL1 PVRL1 10746 -0.0081 0.34 NO
59 RAC3 RAC3 RAC3 11127 -0.014 0.32 NO
60 CDH1 CDH1 CDH1 11193 -0.015 0.32 NO
61 TCF7L2 TCF7L2 TCF7L2 11393 -0.018 0.31 NO
62 SRC SRC SRC 11624 -0.022 0.3 NO
63 ERBB2 ERBB2 ERBB2 11814 -0.024 0.29 NO
64 NLK NLK NLK 11845 -0.025 0.29 NO
65 ACTG1 ACTG1 ACTG1 11985 -0.027 0.29 NO
66 TCF7 TCF7 TCF7 11988 -0.027 0.29 NO
67 FARP2 FARP2 FARP2 12039 -0.028 0.29 NO
68 RAC1 RAC1 RAC1 12125 -0.03 0.29 NO
69 ACP1 ACP1 ACP1 13287 -0.05 0.23 NO
70 MAPK3 MAPK3 MAPK3 13939 -0.062 0.2 NO
71 CSNK2B CSNK2B CSNK2B 14017 -0.064 0.2 NO
72 CSNK2A2 CSNK2A2 CSNK2A2 14047 -0.064 0.21 NO
73 PVRL4 PVRL4 PVRL4 14163 -0.067 0.21 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 AGR PATHWAY.

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

genes ES table in pathway: BIOCARTA ALK PATHWAY

Table 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 NGFR NGFR NGFR 274 0.69 0.032 YES
2 AKT3 AKT3 AKT3 589 0.58 0.053 YES
3 PIK3R5 PIK3R5 PIK3R5 599 0.58 0.092 YES
4 PIK3CG PIK3CG PIK3CG 627 0.57 0.13 YES
5 NTRK3 NTRK3 NTRK3 684 0.56 0.16 YES
6 NGF NGF NGF 832 0.52 0.19 YES
7 SHC4 SHC4 SHC4 833 0.52 0.23 YES
8 CAMK2A CAMK2A CAMK2A 1109 0.47 0.24 YES
9 NTRK1 NTRK1 NTRK1 1177 0.46 0.27 YES
10 MAPK10 MAPK10 MAPK10 1191 0.46 0.3 YES
11 PIK3CD PIK3CD PIK3CD 1278 0.45 0.33 YES
12 PLCG2 PLCG2 PLCG2 1331 0.44 0.36 YES
13 IRAK3 IRAK3 IRAK3 1393 0.43 0.38 YES
14 MAPK11 MAPK11 MAPK11 1586 0.4 0.4 YES
15 CAMK4 CAMK4 CAMK4 1850 0.37 0.41 YES
16 FASLG FASLG FASLG 2748 0.27 0.38 YES
17 BDNF BDNF BDNF 2786 0.26 0.39 YES
18 NTRK2 NTRK2 NTRK2 2823 0.26 0.41 YES
19 BCL2 BCL2 BCL2 2877 0.25 0.42 YES
20 MAP3K3 MAP3K3 MAP3K3 2946 0.24 0.44 YES
21 CAMK2B CAMK2B CAMK2B 3028 0.24 0.45 YES
22 RPS6KA2 RPS6KA2 RPS6KA2 3104 0.23 0.46 YES
23 IRS1 IRS1 IRS1 3260 0.21 0.46 YES
24 SH2B3 SH2B3 SH2B3 3540 0.18 0.46 YES
25 PIK3CA PIK3CA PIK3CA 3553 0.18 0.47 YES
26 MAPK12 MAPK12 MAPK12 3599 0.18 0.48 YES
27 IRAK2 IRAK2 IRAK2 3731 0.17 0.49 YES
28 MAP3K1 MAP3K1 MAP3K1 4321 0.14 0.46 NO
29 KIDINS220 KIDINS220 KIDINS220 4393 0.13 0.47 NO
30 ARHGDIB ARHGDIB ARHGDIB 4466 0.13 0.47 NO
31 RAPGEF1 RAPGEF1 RAPGEF1 4917 0.11 0.45 NO
32 SOS1 SOS1 SOS1 4964 0.11 0.46 NO
33 NTF4 NTF4 NTF4 5026 0.1 0.46 NO
34 PIK3R3 PIK3R3 PIK3R3 5084 0.1 0.47 NO
35 NTF3 NTF3 NTF3 5346 0.092 0.46 NO
36 PIK3R1 PIK3R1 PIK3R1 5698 0.081 0.44 NO
37 SOS2 SOS2 SOS2 5736 0.08 0.45 NO
38 NGFRAP1 NGFRAP1 NGFRAP1 5825 0.077 0.45 NO
39 RAP1A RAP1A RAP1A 5836 0.077 0.45 NO
40 SHC2 SHC2 SHC2 5885 0.076 0.46 NO
41 FRS2 FRS2 FRS2 5924 0.074 0.46 NO
42 MAP3K5 MAP3K5 MAP3K5 5977 0.073 0.46 NO
43 BRAF BRAF BRAF 6011 0.072 0.46 NO
44 PTPN11 PTPN11 PTPN11 6079 0.071 0.46 NO
45 NFKBIA NFKBIA NFKBIA 6188 0.068 0.46 NO
46 ABL1 ABL1 ABL1 6215 0.067 0.47 NO
47 SHC1 SHC1 SHC1 6272 0.066 0.47 NO
48 PLCG1 PLCG1 PLCG1 6291 0.066 0.47 NO
49 MAPK7 MAPK7 MAPK7 6681 0.057 0.45 NO
50 TRAF6 TRAF6 TRAF6 6810 0.055 0.45 NO
51 GRB2 GRB2 GRB2 6836 0.054 0.45 NO
52 NFKBIE NFKBIE NFKBIE 7016 0.05 0.44 NO
53 ZNF274 ZNF274 ZNF274 7063 0.05 0.45 NO
54 RPS6KA5 RPS6KA5 RPS6KA5 7080 0.049 0.45 NO
55 NFKB1 NFKB1 NFKB1 7091 0.049 0.45 NO
56 YWHAG YWHAG YWHAG 7140 0.048 0.45 NO
57 MAPKAPK2 MAPKAPK2 MAPKAPK2 7151 0.048 0.45 NO
58 MAP2K7 MAP2K7 MAP2K7 7182 0.047 0.46 NO
59 PIK3CB PIK3CB PIK3CB 7306 0.045 0.45 NO
60 YWHAH YWHAH YWHAH 7317 0.045 0.45 NO
61 MAPK8 MAPK8 MAPK8 7328 0.044 0.46 NO
62 CRK CRK CRK 7342 0.044 0.46 NO
63 KRAS KRAS KRAS 7391 0.043 0.46 NO
64 IKBKB IKBKB IKBKB 7582 0.04 0.45 NO
65 TP73 TP73 TP73 7698 0.038 0.45 NO
66 GAB1 GAB1 GAB1 7733 0.037 0.45 NO
67 RIPK2 RIPK2 RIPK2 7889 0.035 0.44 NO
68 CDC42 CDC42 CDC42 8026 0.033 0.44 NO
69 MAP2K1 MAP2K1 MAP2K1 8051 0.032 0.44 NO
70 RELA RELA RELA 8140 0.031 0.44 NO
71 MAGED1 MAGED1 MAGED1 8216 0.03 0.43 NO
72 CRKL CRKL CRKL 8241 0.03 0.43 NO
73 CAMK2D CAMK2D CAMK2D 8379 0.027 0.43 NO
74 IRS2 IRS2 IRS2 8488 0.026 0.42 NO
75 FOXO3 FOXO3 FOXO3 8525 0.025 0.42 NO
76 NRAS NRAS NRAS 8595 0.024 0.42 NO
77 MAPK1 MAPK1 MAPK1 8628 0.024 0.42 NO
78 CAMK2G CAMK2G CAMK2G 8645 0.023 0.42 NO
79 GSK3B GSK3B GSK3B 8699 0.022 0.42 NO
80 RHOA RHOA RHOA 9105 0.016 0.4 NO
81 JUN JUN JUN 9240 0.014 0.39 NO
82 PSEN1 PSEN1 PSEN1 9306 0.013 0.39 NO
83 SORT1 SORT1 SORT1 9376 0.012 0.39 NO
84 SHC3 SHC3 SHC3 9508 0.011 0.38 NO
85 YWHAB YWHAB YWHAB 9557 0.01 0.38 NO
86 IRAK4 IRAK4 IRAK4 9651 0.0088 0.37 NO
87 CALM3 CALM3 CALM3 9675 0.0084 0.37 NO
88 IRAK1 IRAK1 IRAK1 9730 0.0076 0.37 NO
89 PRDM4 PRDM4 PRDM4 9836 0.006 0.36 NO
90 YWHAZ YWHAZ YWHAZ 9898 0.0051 0.36 NO
91 CALM1 CALM1 CALM1 9903 0.0051 0.36 NO
92 MAPK14 MAPK14 MAPK14 9936 0.0045 0.36 NO
93 AKT1 AKT1 AKT1 10068 0.0026 0.35 NO
94 RAF1 RAF1 RAF1 10189 0.00062 0.35 NO
95 CSK CSK CSK 10563 -0.0052 0.32 NO
96 CALM2 CALM2 CALM2 10573 -0.0054 0.32 NO
97 PRKCD PRKCD PRKCD 10643 -0.0065 0.32 NO
98 AKT2 AKT2 AKT2 10721 -0.0078 0.32 NO
99 RPS6KA3 RPS6KA3 RPS6KA3 10736 -0.0079 0.32 NO
100 RPS6KA4 RPS6KA4 RPS6KA4 10749 -0.0082 0.32 NO
101 SH2B1 SH2B1 SH2B1 10844 -0.0096 0.31 NO
102 ARHGDIA ARHGDIA ARHGDIA 11022 -0.012 0.3 NO
103 NFKBIB NFKBIB NFKBIB 11331 -0.017 0.29 NO
104 ATF4 ATF4 ATF4 11585 -0.021 0.28 NO
105 YWHAE YWHAE YWHAE 11643 -0.022 0.27 NO
106 YWHAQ YWHAQ YWHAQ 11686 -0.022 0.27 NO
107 MAPK9 MAPK9 MAPK9 11891 -0.026 0.26 NO
108 BAX BAX BAX 11905 -0.026 0.26 NO
109 RAC1 RAC1 RAC1 12125 -0.03 0.25 NO
110 PDK1 PDK1 PDK1 12282 -0.032 0.25 NO
111 PIK3R2 PIK3R2 PIK3R2 12385 -0.034 0.24 NO
112 RAP1B RAP1B RAP1B 12414 -0.035 0.24 NO
113 MAP2K5 MAP2K5 MAP2K5 12426 -0.035 0.25 NO
114 RPS6KA6 RPS6KA6 RPS6KA6 13349 -0.051 0.2 NO
115 BAD BAD BAD 13682 -0.057 0.18 NO
116 MAPK3 MAPK3 MAPK3 13939 -0.062 0.17 NO
117 TP53 TP53 TP53 13975 -0.063 0.18 NO
118 MAP2K2 MAP2K2 MAP2K2 13995 -0.063 0.18 NO
119 RPS6KA1 RPS6KA1 RPS6KA1 14208 -0.068 0.17 NO
120 MAPK13 MAPK13 MAPK13 14560 -0.077 0.16 NO
121 CALML3 CALML3 CALML3 15239 -0.096 0.13 NO
122 SH2B2 SH2B2 SH2B2 15795 -0.12 0.1 NO
123 CALML6 CALML6 CALML6 17529 -0.3 0.026 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 ALK PATHWAY.

Figure S46.  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 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 FGF1 FGF1 FGF1 38 0.85 0.022 YES
2 ITGAM ITGAM ITGAM 251 0.7 0.031 YES
3 FGF14 FGF14 FGF14 261 0.69 0.05 YES
4 FGF5 FGF5 FGF5 262 0.69 0.07 YES
5 FGF7 FGF7 FGF7 276 0.69 0.089 YES
6 CHRM2 CHRM2 CHRM2 387 0.64 0.1 YES
7 FGF2 FGF2 FGF2 496 0.6 0.11 YES
8 MRAS MRAS MRAS 520 0.59 0.13 YES
9 PIK3R5 PIK3R5 PIK3R5 599 0.58 0.14 YES
10 FGF10 FGF10 FGF10 611 0.57 0.16 YES
11 TIAM1 TIAM1 TIAM1 615 0.57 0.17 YES
12 PIK3CG PIK3CG PIK3CG 627 0.57 0.19 YES
13 ITGA11 ITGA11 ITGA11 710 0.55 0.2 YES
14 PAK3 PAK3 PAK3 829 0.52 0.21 YES
15 ITGAX ITGAX ITGAX 844 0.52 0.22 YES
16 ITGA10 ITGA10 ITGA10 922 0.51 0.23 YES
17 ITGAL ITGAL ITGAL 935 0.5 0.25 YES
18 NCKAP1L NCKAP1L NCKAP1L 953 0.5 0.26 YES
19 WAS WAS WAS 1010 0.49 0.27 YES
20 PDGFC PDGFC PDGFC 1058 0.48 0.28 YES
21 ITGB3 ITGB3 ITGB3 1070 0.48 0.3 YES
22 ARHGEF6 ARHGEF6 ARHGEF6 1091 0.48 0.31 YES
23 MYH10 MYH10 MYH10 1147 0.47 0.32 YES
24 PIK3CD PIK3CD PIK3CD 1278 0.45 0.32 YES
25 MYLK MYLK MYLK 1332 0.44 0.34 YES
26 FN1 FN1 FN1 1370 0.44 0.35 YES
27 ITGB2 ITGB2 ITGB2 1381 0.43 0.36 YES
28 ITGA7 ITGA7 ITGA7 1394 0.43 0.37 YES
29 FGFR1 FGFR1 FGFR1 1452 0.42 0.38 YES
30 ITGA4 ITGA4 ITGA4 1598 0.4 0.38 YES
31 FGF12 FGF12 FGF12 1614 0.4 0.39 YES
32 ITGA5 ITGA5 ITGA5 1764 0.38 0.4 YES
33 MYL9 MYL9 MYL9 1774 0.38 0.41 YES
34 CFL2 CFL2 CFL2 1812 0.37 0.42 YES
35 PDGFRB PDGFRB PDGFRB 1852 0.37 0.42 YES
36 RDX RDX RDX 1911 0.36 0.43 YES
37 FGF11 FGF11 FGF11 2191 0.33 0.42 YES
38 VAV1 VAV1 VAV1 2243 0.32 0.43 YES
39 PDGFB PDGFB PDGFB 2363 0.31 0.43 YES
40 CD14 CD14 CD14 2372 0.31 0.44 YES
41 ACTN2 ACTN2 ACTN2 2376 0.31 0.45 YES
42 ITGA9 ITGA9 ITGA9 2387 0.31 0.46 YES
43 F2R F2R F2R 2450 0.3 0.46 YES
44 WASF1 WASF1 WASF1 2458 0.3 0.47 YES
45 MSN MSN MSN 2486 0.3 0.48 YES
46 PDGFRA PDGFRA PDGFRA 2510 0.29 0.49 YES
47 PDGFD PDGFD PDGFD 2529 0.29 0.49 YES
48 ACTN3 ACTN3 ACTN3 2575 0.28 0.5 YES
49 CHRM4 CHRM4 CHRM4 2731 0.27 0.5 YES
50 TIAM2 TIAM2 TIAM2 2978 0.24 0.49 YES
51 ITGA1 ITGA1 ITGA1 3011 0.24 0.5 YES
52 FGF13 FGF13 FGF13 3012 0.24 0.5 YES
53 ITGAV ITGAV ITGAV 3067 0.23 0.51 YES
54 CHRM5 CHRM5 CHRM5 3115 0.23 0.51 YES
55 ARHGEF4 ARHGEF4 ARHGEF4 3157 0.22 0.51 YES
56 ITGA8 ITGA8 ITGA8 3216 0.21 0.52 YES
57 INSRR INSRR INSRR 3266 0.21 0.52 YES
58 PIP4K2A PIP4K2A PIP4K2A 3269 0.21 0.53 YES
59 FGD1 FGD1 FGD1 3344 0.2 0.53 YES
60 FGF9 FGF9 FGF9 3440 0.19 0.53 YES
61 APC APC APC 3462 0.19 0.53 YES
62 BDKRB1 BDKRB1 BDKRB1 3467 0.19 0.54 YES
63 ITGB7 ITGB7 ITGB7 3490 0.19 0.54 YES
64 PIK3CA PIK3CA PIK3CA 3553 0.18 0.54 YES
65 SSH1 SSH1 SSH1 3586 0.18 0.55 YES
66 ROCK1 ROCK1 ROCK1 3775 0.17 0.54 YES
67 MYLK3 MYLK3 MYLK3 3860 0.16 0.54 YES
68 ITGB8 ITGB8 ITGB8 3901 0.16 0.54 YES
69 ITGAD ITGAD ITGAD 3961 0.16 0.55 YES
70 FGF18 FGF18 FGF18 3974 0.15 0.55 YES
71 VCL VCL VCL 4131 0.14 0.54 YES
72 MYLK2 MYLK2 MYLK2 4163 0.14 0.55 YES
73 PIKFYVE PIKFYVE PIKFYVE 4179 0.14 0.55 YES
74 FGFR2 FGFR2 FGFR2 4426 0.13 0.54 YES
75 PPP1R12A PPP1R12A PPP1R12A 4440 0.13 0.54 YES
76 EGFR EGFR EGFR 4510 0.12 0.54 YES
77 ACTN1 ACTN1 ACTN1 4525 0.12 0.55 YES
78 RAC2 RAC2 RAC2 4559 0.12 0.55 YES
79 GSN GSN GSN 4604 0.12 0.55 YES
80 GNA12 GNA12 GNA12 4811 0.11 0.54 YES
81 ENAH ENAH ENAH 4836 0.11 0.54 YES
82 DOCK1 DOCK1 DOCK1 4840 0.11 0.55 YES
83 ABI2 ABI2 ABI2 4844 0.11 0.55 YES
84 ITGB5 ITGB5 ITGB5 4854 0.11 0.55 YES
85 PIP5K1C PIP5K1C PIP5K1C 4862 0.11 0.55 YES
86 MYH9 MYH9 MYH9 4958 0.11 0.55 YES
87 SOS1 SOS1 SOS1 4964 0.11 0.55 YES
88 ITGB1 ITGB1 ITGB1 5023 0.1 0.55 YES
89 FGD3 FGD3 FGD3 5078 0.1 0.55 YES
90 PIK3R3 PIK3R3 PIK3R3 5084 0.1 0.56 YES
91 SSH2 SSH2 SSH2 5300 0.093 0.55 NO
92 ARHGEF12 ARHGEF12 ARHGEF12 5387 0.091 0.54 NO
93 LIMK1 LIMK1 LIMK1 5504 0.087 0.54 NO
94 PIP4K2B PIP4K2B PIP4K2B 5568 0.084 0.54 NO
95 PIK3R1 PIK3R1 PIK3R1 5698 0.081 0.53 NO
96 SOS2 SOS2 SOS2 5736 0.08 0.53 NO
97 VAV2 VAV2 VAV2 6007 0.072 0.52 NO
98 BRAF BRAF BRAF 6011 0.072 0.52 NO
99 FGF19 FGF19 FGF19 6046 0.072 0.52 NO
100 ITGA2 ITGA2 ITGA2 6061 0.071 0.52 NO
101 BAIAP2 BAIAP2 BAIAP2 6064 0.071 0.53 NO
102 WASF2 WASF2 WASF2 6123 0.07 0.52 NO
103 ROCK2 ROCK2 ROCK2 6184 0.068 0.52 NO
104 BDKRB2 BDKRB2 BDKRB2 6279 0.066 0.52 NO
105 GNA13 GNA13 GNA13 6286 0.066 0.52 NO
106 PDGFA PDGFA PDGFA 6324 0.065 0.52 NO
107 ARHGEF1 ARHGEF1 ARHGEF1 6352 0.065 0.52 NO
108 GRLF1 GRLF1 GRLF1 6376 0.064 0.52 NO
109 IQGAP1 IQGAP1 IQGAP1 6733 0.056 0.5 NO
110 FGF20 FGF20 FGF20 7230 0.046 0.48 NO
111 PIK3CB PIK3CB PIK3CB 7306 0.045 0.48 NO
112 CRK CRK CRK 7342 0.044 0.47 NO
113 PAK2 PAK2 PAK2 7367 0.043 0.47 NO
114 KRAS KRAS KRAS 7391 0.043 0.47 NO
115 PIP5K1A PIP5K1A PIP5K1A 7394 0.043 0.48 NO
116 RRAS RRAS RRAS 7599 0.039 0.46 NO
117 FGF23 FGF23 FGF23 7616 0.039 0.46 NO
118 NCKAP1 NCKAP1 NCKAP1 7877 0.035 0.45 NO
119 SLC9A1 SLC9A1 SLC9A1 7896 0.035 0.45 NO
120 CDC42 CDC42 CDC42 8026 0.033 0.44 NO
121 MAP2K1 MAP2K1 MAP2K1 8051 0.032 0.44 NO
122 PIP4K2C PIP4K2C PIP4K2C 8075 0.032 0.44 NO
123 LIMK2 LIMK2 LIMK2 8121 0.031 0.44 NO
124 CHRM3 CHRM3 CHRM3 8125 0.031 0.44 NO
125 PTK2 PTK2 PTK2 8169 0.031 0.44 NO
126 FGF3 FGF3 FGF3 8235 0.03 0.44 NO
127 CRKL CRKL CRKL 8241 0.03 0.44 NO
128 ARPC3 ARPC3 ARPC3 8457 0.026 0.43 NO
129 NRAS NRAS NRAS 8595 0.024 0.42 NO
130 MAPK1 MAPK1 MAPK1 8628 0.024 0.42 NO
131 ITGAE ITGAE ITGAE 8694 0.023 0.42 NO
132 ARHGEF7 ARHGEF7 ARHGEF7 8828 0.02 0.41 NO
133 BCAR1 BCAR1 BCAR1 8845 0.02 0.41 NO
134 PFN2 PFN2 PFN2 8874 0.02 0.41 NO
135 ACTN4 ACTN4 ACTN4 8897 0.019 0.41 NO
136 ARPC2 ARPC2 ARPC2 9054 0.017 0.4 NO
137 DIAPH1 DIAPH1 DIAPH1 9069 0.017 0.4 NO
138 CYFIP1 CYFIP1 CYFIP1 9086 0.016 0.4 NO
139 RHOA RHOA RHOA 9105 0.016 0.4 NO
140 ARPC1B ARPC1B ARPC1B 9117 0.016 0.4 NO
141 GNG12 GNG12 GNG12 9146 0.016 0.4 NO
142 ITGB4 ITGB4 ITGB4 9155 0.016 0.4 NO
143 MYL12A MYL12A MYL12A 9182 0.015 0.4 NO
144 PXN PXN PXN 9220 0.015 0.4 NO
145 EZR EZR EZR 9266 0.014 0.39 NO
146 RRAS2 RRAS2 RRAS2 9448 0.011 0.38 NO
147 PPP1CB PPP1CB PPP1CB 9449 0.011 0.38 NO
148 DIAPH2 DIAPH2 DIAPH2 9677 0.0083 0.37 NO
149 WASL WASL WASL 9700 0.0081 0.37 NO
150 ACTB ACTB ACTB 9764 0.0071 0.37 NO
151 IQGAP2 IQGAP2 IQGAP2 10099 0.0021 0.35 NO
152 RAF1 RAF1 RAF1 10189 0.00062 0.34 NO
153 ITGA3 ITGA3 ITGA3 10195 0.00054 0.34 NO
154 ARPC5 ARPC5 ARPC5 10555 -0.005 0.32 NO
155 CSK CSK CSK 10563 -0.0052 0.32 NO
156 ITGA6 ITGA6 ITGA6 11073 -0.013 0.29 NO
157 RAC3 RAC3 RAC3 11127 -0.014 0.29 NO
158 CYFIP2 CYFIP2 CYFIP2 11159 -0.014 0.29 NO
159 CFL1 CFL1 CFL1 11161 -0.014 0.29 NO
160 GIT1 GIT1 GIT1 11235 -0.015 0.29 NO
161 ARPC4 ARPC4 ARPC4 11297 -0.016 0.28 NO
162 SCIN SCIN SCIN 11422 -0.018 0.28 NO
163 MYH14 MYH14 MYH14 11496 -0.019 0.27 NO
164 PPP1CC PPP1CC PPP1CC 11642 -0.022 0.27 NO
165 DIAPH3 DIAPH3 DIAPH3 11759 -0.024 0.26 NO
166 ITGB6 ITGB6 ITGB6 11887 -0.026 0.25 NO
167 PAK1 PAK1 PAK1 11955 -0.027 0.25 NO
168 PFN1 PFN1 PFN1 11965 -0.027 0.25 NO
169 ACTG1 ACTG1 ACTG1 11985 -0.027 0.25 NO
170 ARAF ARAF ARAF 12085 -0.029 0.25 NO
171 RAC1 RAC1 RAC1 12125 -0.03 0.24 NO
172 APC2 APC2 APC2 12194 -0.031 0.24 NO
173 MYL12B MYL12B MYL12B 12223 -0.032 0.24 NO
174 PIK3R2 PIK3R2 PIK3R2 12385 -0.034 0.23 NO
175 FGF8 FGF8 FGF8 12817 -0.041 0.21 NO
176 IQGAP3 IQGAP3 IQGAP3 13139 -0.047 0.19 NO
177 SSH3 SSH3 SSH3 13157 -0.047 0.19 NO
178 PAK4 PAK4 PAK4 13209 -0.048 0.19 NO
179 ARPC1A ARPC1A ARPC1A 13321 -0.05 0.19 NO
180 TMSB4Y TMSB4Y TMSB4Y 13698 -0.058 0.17 NO
181 MAPK3 MAPK3 MAPK3 13939 -0.062 0.16 NO
182 PPP1CA PPP1CA PPP1CA 13984 -0.063 0.16 NO
183 MAP2K2 MAP2K2 MAP2K2 13995 -0.063 0.16 NO
184 TMSL3 TMSL3 TMSL3 14221 -0.069 0.15 NO
185 CHRM1 CHRM1 CHRM1 14486 -0.075 0.13 NO
186 ARPC5L ARPC5L ARPC5L 14827 -0.084 0.12 NO
187 PFN4 PFN4 PFN4 14849 -0.084 0.12 NO
188 PAK6 PAK6 PAK6 15686 -0.11 0.075 NO
189 PIP5K1B PIP5K1B PIP5K1B 15770 -0.11 0.074 NO
190 ITGA2B ITGA2B ITGA2B 15889 -0.12 0.07 NO
191 FGFR4 FGFR4 FGFR4 15947 -0.12 0.071 NO
192 VAV3 VAV3 VAV3 15975 -0.12 0.073 NO
193 EGF EGF EGF 16378 -0.15 0.054 NO
194 MYL5 MYL5 MYL5 17028 -0.21 0.024 NO
195 F2 F2 F2 17167 -0.22 0.023 NO
196 FGF17 FGF17 FGF17 17196 -0.23 0.028 NO
197 FGFR3 FGFR3 FGFR3 17423 -0.27 0.023 NO
198 MYLPF MYLPF MYLPF 17596 -0.32 0.022 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 AT1R PATHWAY.

Figure S48.  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 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 FGF1 FGF1 FGF1 38 0.85 0.014 YES
2 GLI3 GLI3 GLI3 59 0.82 0.029 YES
3 RUNX1T1 RUNX1T1 RUNX1T1 64 0.81 0.045 YES
4 TGFB3 TGFB3 TGFB3 133 0.76 0.056 YES
5 IGF1 IGF1 IGF1 161 0.74 0.068 YES
6 FGF14 FGF14 FGF14 261 0.69 0.076 YES
7 FGF5 FGF5 FGF5 262 0.69 0.09 YES
8 VEGFC VEGFC VEGFC 267 0.69 0.1 YES
9 FGF7 FGF7 FGF7 276 0.69 0.12 YES
10 MITF MITF MITF 310 0.67 0.13 YES
11 GLI2 GLI2 GLI2 397 0.64 0.14 YES
12 HGF HGF HGF 409 0.63 0.15 YES
13 FGF2 FGF2 FGF2 496 0.6 0.15 YES
14 AKT3 AKT3 AKT3 589 0.58 0.16 YES
15 PIK3R5 PIK3R5 PIK3R5 599 0.58 0.17 YES
16 AR AR AR 607 0.57 0.18 YES
17 FGF10 FGF10 FGF10 611 0.57 0.19 YES
18 RARB RARB RARB 614 0.57 0.2 YES
19 PIK3CG PIK3CG PIK3CG 627 0.57 0.21 YES
20 LAMA2 LAMA2 LAMA2 672 0.56 0.22 YES
21 PRKCB PRKCB PRKCB 681 0.56 0.23 YES
22 ZBTB16 ZBTB16 ZBTB16 742 0.55 0.24 YES
23 GLI1 GLI1 GLI1 775 0.54 0.25 YES
24 TGFB2 TGFB2 TGFB2 871 0.52 0.25 YES
25 WNT9B WNT9B WNT9B 971 0.5 0.26 YES
26 CSF3R CSF3R CSF3R 1080 0.48 0.26 YES
27 NTRK1 NTRK1 NTRK1 1177 0.46 0.26 YES
28 MAPK10 MAPK10 MAPK10 1191 0.46 0.27 YES
29 WNT9A WNT9A WNT9A 1266 0.45 0.28 YES
30 PIK3CD PIK3CD PIK3CD 1278 0.45 0.28 YES
31 MMP9 MMP9 MMP9 1290 0.45 0.29 YES
32 PLCG2 PLCG2 PLCG2 1331 0.44 0.3 YES
33 CSF1R CSF1R CSF1R 1349 0.44 0.31 YES
34 FN1 FN1 FN1 1370 0.44 0.31 YES
35 PTCH2 PTCH2 PTCH2 1439 0.43 0.32 YES
36 FGFR1 FGFR1 FGFR1 1452 0.42 0.33 YES
37 SPI1 SPI1 SPI1 1458 0.42 0.33 YES
38 CCNA1 CCNA1 CCNA1 1578 0.41 0.34 YES
39 ARNT2 ARNT2 ARNT2 1606 0.4 0.34 YES
40 FGF12 FGF12 FGF12 1614 0.4 0.35 YES
41 CSF2RA CSF2RA CSF2RA 1758 0.38 0.35 YES
42 WNT2 WNT2 WNT2 1788 0.38 0.35 YES
43 PDGFRB PDGFRB PDGFRB 1852 0.37 0.36 YES
44 MMP2 MMP2 MMP2 1855 0.37 0.36 YES
45 DAPK1 DAPK1 DAPK1 1885 0.36 0.37 YES
46 COL4A4 COL4A4 COL4A4 1902 0.36 0.38 YES
47 FLT3 FLT3 FLT3 1953 0.36 0.38 YES
48 RASSF5 RASSF5 RASSF5 2092 0.34 0.38 YES
49 FGF11 FGF11 FGF11 2191 0.33 0.38 YES
50 ETS1 ETS1 ETS1 2218 0.32 0.38 YES
51 FZD4 FZD4 FZD4 2229 0.32 0.39 YES
52 CDKN2B CDKN2B CDKN2B 2241 0.32 0.4 YES
53 LAMA4 LAMA4 LAMA4 2309 0.31 0.4 YES
54 TCF7L1 TCF7L1 TCF7L1 2325 0.31 0.4 YES
55 SMO SMO SMO 2329 0.31 0.41 YES
56 IL6 IL6 IL6 2359 0.31 0.41 YES
57 PDGFB PDGFB PDGFB 2363 0.31 0.42 YES
58 FIGF FIGF FIGF 2395 0.3 0.42 YES
59 PDGFRA PDGFRA PDGFRA 2510 0.29 0.42 YES
60 KIT KIT KIT 2597 0.28 0.42 YES
61 WNT7B WNT7B WNT7B 2659 0.28 0.43 YES
62 FZD2 FZD2 FZD2 2660 0.28 0.43 YES
63 CTNNA3 CTNNA3 CTNNA3 2693 0.27 0.44 YES
64 FLT3LG FLT3LG FLT3LG 2723 0.27 0.44 YES
65 FASLG FASLG FASLG 2748 0.27 0.44 YES
66 LEF1 LEF1 LEF1 2767 0.26 0.45 YES
67 HHIP HHIP HHIP 2805 0.26 0.45 YES
68 NKX3-1 NKX3-1 NKX3-1 2849 0.26 0.45 YES
69 TGFB1 TGFB1 TGFB1 2855 0.26 0.46 YES
70 BCL2 BCL2 BCL2 2877 0.25 0.46 YES
71 PGF PGF PGF 2954 0.24 0.46 YES
72 FZD1 FZD1 FZD1 2960 0.24 0.46 YES
73 COL4A2 COL4A2 COL4A2 2969 0.24 0.47 YES
74 LAMB2 LAMB2 LAMB2 3005 0.24 0.47 YES
75 FGF13 FGF13 FGF13 3012 0.24 0.48 YES
76 ITGAV ITGAV ITGAV 3067 0.23 0.48 YES
77 COL4A1 COL4A1 COL4A1 3092 0.23 0.48 YES
78 FZD8 FZD8 FZD8 3094 0.23 0.49 YES
79 DCC DCC DCC 3140 0.22 0.49 YES
80 TRAF1 TRAF1 TRAF1 3238 0.21 0.49 YES
81 WNT7A WNT7A WNT7A 3254 0.21 0.49 YES
82 MMP1 MMP1 MMP1 3255 0.21 0.49 YES
83 RET RET RET 3268 0.21 0.5 YES
84 PTGS2 PTGS2 PTGS2 3412 0.2 0.49 YES
85 BIRC3 BIRC3 BIRC3 3415 0.19 0.5 YES
86 FGF9 FGF9 FGF9 3440 0.19 0.5 YES
87 APC APC APC 3462 0.19 0.5 YES
88 LAMC1 LAMC1 LAMC1 3472 0.19 0.5 YES
89 RUNX1 RUNX1 RUNX1 3502 0.19 0.51 YES
90 FZD7 FZD7 FZD7 3527 0.18 0.51 YES
91 PIK3CA PIK3CA PIK3CA 3553 0.18 0.51 YES
92 WNT1 WNT1 WNT1 3697 0.17 0.51 YES
93 FOXO1 FOXO1 FOXO1 3722 0.17 0.51 YES
94 WNT16 WNT16 WNT16 3752 0.17 0.51 YES
95 IL8 IL8 IL8 3756 0.17 0.51 YES
96 PIAS3 PIAS3 PIAS3 3838 0.16 0.51 YES
97 LAMB1 LAMB1 LAMB1 3911 0.16 0.51 YES
98 TGFBR1 TGFBR1 TGFBR1 3935 0.16 0.51 YES
99 LAMA1 LAMA1 LAMA1 3945 0.16 0.52 YES
100 LAMA5 LAMA5 LAMA5 3949 0.16 0.52 YES
101 FGF18 FGF18 FGF18 3974 0.15 0.52 YES
102 STAT1 STAT1 STAT1 4005 0.15 0.52 YES
103 WNT10B WNT10B WNT10B 4008 0.15 0.52 YES
104 HIF1A HIF1A HIF1A 4015 0.15 0.53 YES
105 LAMB4 LAMB4 LAMB4 4051 0.15 0.53 YES
106 WNT10A WNT10A WNT10A 4068 0.15 0.53 YES
107 CBL CBL CBL 4071 0.15 0.53 YES
108 CBLB CBLB CBLB 4155 0.14 0.53 NO
109 SUFU SUFU SUFU 4221 0.14 0.53 NO
110 FGFR2 FGFR2 FGFR2 4426 0.13 0.52 NO
111 EGFR EGFR EGFR 4510 0.12 0.52 NO
112 TGFBR2 TGFBR2 TGFBR2 4543 0.12 0.52 NO
113 RAC2 RAC2 RAC2 4559 0.12 0.52 NO
114 WNT6 WNT6 WNT6 4608 0.12 0.52 NO
115 NFKB2 NFKB2 NFKB2 4612 0.12 0.52 NO
116 EPAS1 EPAS1 EPAS1 4644 0.12 0.52 NO
117 FAS FAS FAS 4814 0.11 0.52 NO
118 KITLG KITLG KITLG 4830 0.11 0.52 NO
119 EP300 EP300 EP300 4834 0.11 0.52 NO
120 LAMC2 LAMC2 LAMC2 4848 0.11 0.52 NO
121 SOS1 SOS1 SOS1 4964 0.11 0.52 NO
122 ITGB1 ITGB1 ITGB1 5023 0.1 0.51 NO
123 IGF1R IGF1R IGF1R 5054 0.1 0.51 NO
124 WNT2B WNT2B WNT2B 5076 0.1 0.52 NO
125 FZD10 FZD10 FZD10 5079 0.1 0.52 NO
126 PIK3R3 PIK3R3 PIK3R3 5084 0.1 0.52 NO
127 WNT5A WNT5A WNT5A 5166 0.097 0.52 NO
128 LAMA3 LAMA3 LAMA3 5281 0.094 0.51 NO
129 CREBBP CREBBP CREBBP 5369 0.091 0.51 NO
130 JAK1 JAK1 JAK1 5459 0.088 0.5 NO
131 ARNT ARNT ARNT 5501 0.087 0.5 NO
132 BIRC2 BIRC2 BIRC2 5526 0.086 0.5 NO
133 RXRG RXRG RXRG 5541 0.085 0.5 NO
134 PIK3R1 PIK3R1 PIK3R1 5698 0.081 0.5 NO
135 STAT5A STAT5A STAT5A 5731 0.08 0.5 NO
136 SOS2 SOS2 SOS2 5736 0.08 0.5 NO
137 TRAF3 TRAF3 TRAF3 5749 0.079 0.5 NO
138 WNT5B WNT5B WNT5B 5777 0.079 0.5 NO
139 STK4 STK4 STK4 5807 0.078 0.5 NO
140 STAT5B STAT5B STAT5B 5838 0.077 0.5 NO
141 PML PML PML 5864 0.076 0.5 NO
142 CDK6 CDK6 CDK6 5930 0.074 0.5 NO
143 RARA RARA RARA 5934 0.074 0.5 NO
144 TPR TPR TPR 5955 0.074 0.5 NO
145 CTNNA2 CTNNA2 CTNNA2 5964 0.074 0.5 NO
146 BRAF BRAF BRAF 6011 0.072 0.5 NO
147 APPL1 APPL1 APPL1 6015 0.072 0.5 NO
148 FGF19 FGF19 FGF19 6046 0.072 0.5 NO
149 ITGA2 ITGA2 ITGA2 6061 0.071 0.5 NO
150 MTOR MTOR MTOR 6187 0.068 0.49 NO
151 NFKBIA NFKBIA NFKBIA 6188 0.068 0.5 NO
152 ABL1 ABL1 ABL1 6215 0.067 0.5 NO
153 PLCG1 PLCG1 PLCG1 6291 0.066 0.49 NO
154 PDGFA PDGFA PDGFA 6324 0.065 0.49 NO
155 CCND1 CCND1 CCND1 6381 0.064 0.49 NO
156 SMAD3 SMAD3 SMAD3 6408 0.064 0.49 NO
157 PTCH1 PTCH1 PTCH1 6451 0.063 0.49 NO
158 PTEN PTEN PTEN 6703 0.057 0.48 NO
159 LAMC3 LAMC3 LAMC3 6729 0.056 0.48 NO
160 SMAD2 SMAD2 SMAD2 6759 0.056 0.48 NO
161 PIAS1 PIAS1 PIAS1 6799 0.055 0.47 NO
162 TRAF6 TRAF6 TRAF6 6810 0.055 0.47 NO
163 GRB2 GRB2 GRB2 6836 0.054 0.47 NO
164 VEGFB VEGFB VEGFB 6843 0.054 0.48 NO
165 RB1 RB1 RB1 6889 0.053 0.47 NO
166 MAX MAX MAX 6899 0.053 0.47 NO
167 PLD1 PLD1 PLD1 6913 0.053 0.47 NO
168 E2F3 E2F3 E2F3 6917 0.053 0.48 NO
169 FOS FOS FOS 7068 0.05 0.47 NO
170 PRKCG PRKCG PRKCG 7086 0.049 0.47 NO
171 NFKB1 NFKB1 NFKB1 7091 0.049 0.47 NO
172 FGF20 FGF20 FGF20 7230 0.046 0.46 NO
173 STAT3 STAT3 STAT3 7235 0.046 0.46 NO
174 PIAS2 PIAS2 PIAS2 7256 0.046 0.46 NO
175 HSP90B1 HSP90B1 HSP90B1 7271 0.046 0.46 NO
176 MLH1 MLH1 MLH1 7281 0.045 0.46 NO
177 PIK3CB PIK3CB PIK3CB 7306 0.045 0.46 NO
178 MAPK8 MAPK8 MAPK8 7328 0.044 0.46 NO
179 CRK CRK CRK 7342 0.044 0.46 NO
180 KRAS KRAS KRAS 7391 0.043 0.46 NO
181 PRKCA PRKCA PRKCA 7450 0.042 0.46 NO
182 BMP4 BMP4 BMP4 7460 0.042 0.46 NO
183 LAMB3 LAMB3 LAMB3 7555 0.04 0.45 NO
184 IKBKB IKBKB IKBKB 7582 0.04 0.45 NO
185 CDKN1B CDKN1B CDKN1B 7597 0.039 0.45 NO
186 HSP90AA1 HSP90AA1 HSP90AA1 7610 0.039 0.45 NO
187 FGF23 FGF23 FGF23 7616 0.039 0.45 NO
188 XIAP XIAP XIAP 7687 0.038 0.45 NO
189 CHUK CHUK CHUK 7758 0.037 0.45 NO
190 PPARD PPARD PPARD 7816 0.036 0.44 NO
191 BCL2L1 BCL2L1 BCL2L1 7830 0.036 0.44 NO
192 RALGDS RALGDS RALGDS 7834 0.036 0.44 NO
193 RALB RALB RALB 7841 0.036 0.44 NO
194 CDC42 CDC42 CDC42 8026 0.033 0.44 NO
195 MAP2K1 MAP2K1 MAP2K1 8051 0.032 0.43 NO
196 FZD6 FZD6 FZD6 8060 0.032 0.43 NO
197 DAPK3 DAPK3 DAPK3 8127 0.031 0.43 NO
198 RELA RELA RELA 8140 0.031 0.43 NO
199 PTK2 PTK2 PTK2 8169 0.031 0.43 NO
200 DVL2 DVL2 DVL2 8182 0.03 0.43 NO
201 BRCA2 BRCA2 BRCA2 8231 0.03 0.43 NO
202 FGF3 FGF3 FGF3 8235 0.03 0.43 NO
203 CRKL CRKL CRKL 8241 0.03 0.43 NO
204 DVL3 DVL3 DVL3 8282 0.029 0.43 NO
205 RALBP1 RALBP1 RALBP1 8347 0.028 0.42 NO
206 CDKN2A CDKN2A CDKN2A 8385 0.027 0.42 NO
207 NRAS NRAS NRAS 8595 0.024 0.41 NO
208 MAPK1 MAPK1 MAPK1 8628 0.024 0.41 NO
209 SMAD4 SMAD4 SMAD4 8664 0.023 0.41 NO
210 GSK3B GSK3B GSK3B 8699 0.022 0.41 NO
211 NCOA4 NCOA4 NCOA4 8848 0.02 0.4 NO
212 WNT3A WNT3A WNT3A 8903 0.019 0.4 NO
213 WNT8B WNT8B WNT8B 8904 0.019 0.4 NO
214 HSP90AB1 HSP90AB1 HSP90AB1 8920 0.019 0.4 NO
215 WNT11 WNT11 WNT11 8930 0.019 0.4 NO
216 MSH3 MSH3 MSH3 8942 0.019 0.4 NO
217 MSH6 MSH6 MSH6 8987 0.018 0.39 NO
218 CASP8 CASP8 CASP8 9082 0.017 0.39 NO
219 RHOA RHOA RHOA 9105 0.016 0.39 NO
220 MET MET MET 9106 0.016 0.39 NO
221 RXRB RXRB RXRB 9211 0.015 0.38 NO
222 JUN JUN JUN 9240 0.014 0.38 NO
223 MDM2 MDM2 MDM2 9478 0.011 0.37 NO
224 TGFA TGFA TGFA 9565 0.0099 0.36 NO
225 BCR BCR BCR 9734 0.0076 0.35 NO
226 CUL2 CUL2 CUL2 9809 0.0064 0.35 NO
227 EGLN2 EGLN2 EGLN2 9876 0.0054 0.35 NO
228 TRAF2 TRAF2 TRAF2 10031 0.0032 0.34 NO
229 AKT1 AKT1 AKT1 10068 0.0026 0.34 NO
230 CTNNB1 CTNNB1 CTNNB1 10115 0.0019 0.33 NO
231 CASP9 CASP9 CASP9 10141 0.0015 0.33 NO
232 CDK2 CDK2 CDK2 10151 0.0013 0.33 NO
233 RAF1 RAF1 RAF1 10189 0.00062 0.33 NO
234 ITGA3 ITGA3 ITGA3 10195 0.00054 0.33 NO
235 CCDC6 CCDC6 CCDC6 10219 0.00014 0.33 NO
236 CCNE2 CCNE2 CCNE2 10294 -0.0011 0.32 NO
237 RXRA RXRA RXRA 10382 -0.0022 0.32 NO
238 VHL VHL VHL 10501 -0.0038 0.31 NO
239 PIAS4 PIAS4 PIAS4 10533 -0.0045 0.31 NO
240 RALA RALA RALA 10538 -0.0046 0.31 NO
241 CTNNA1 CTNNA1 CTNNA1 10564 -0.0052 0.31 NO
242 MSH2 MSH2 MSH2 10577 -0.0055 0.31 NO
243 AKT2 AKT2 AKT2 10721 -0.0078 0.3 NO
244 TPM3 TPM3 TPM3 10758 -0.0084 0.3 NO
245 STK36 STK36 STK36 10805 -0.0091 0.3 NO
246 HDAC2 HDAC2 HDAC2 10859 -0.0098 0.29 NO
247 CASP3 CASP3 CASP3 10881 -0.01 0.29 NO
248 VEGFA VEGFA VEGFA 10940 -0.011 0.29 NO
249 EGLN1 EGLN1 EGLN1 10944 -0.011 0.29 NO
250 IKBKG IKBKG IKBKG 11005 -0.012 0.28 NO
251 ITGA6 ITGA6 ITGA6 11073 -0.013 0.28 NO
252 RAC3 RAC3 RAC3 11127 -0.014 0.28 NO
253 EGLN3 EGLN3 EGLN3 11166 -0.014 0.28 NO
254 SLC2A1 SLC2A1 SLC2A1 11167 -0.014 0.28 NO
255 CDH1 CDH1 CDH1 11193 -0.015 0.28 NO
256 BMP2 BMP2 BMP2 11295 -0.016 0.27 NO
257 TRAF5 TRAF5 TRAF5 11304 -0.016 0.27 NO
258 CDKN1A CDKN1A CDKN1A 11341 -0.017 0.27 NO
259 TCF7L2 TCF7L2 TCF7L2 11393 -0.018 0.27 NO
260 RASSF1 RASSF1 RASSF1 11431 -0.018 0.26 NO
261 MYC MYC MYC 11600 -0.021 0.26 NO
262 JUP JUP JUP 11604 -0.021 0.26 NO
263 TCEB1 TCEB1 TCEB1 11802 -0.024 0.24 NO
264 ERBB2 ERBB2 ERBB2 11814 -0.024 0.24 NO
265 HDAC1 HDAC1 HDAC1 11853 -0.025 0.24 NO
266 MAPK9 MAPK9 MAPK9 11891 -0.026 0.24 NO
267 BAX BAX BAX 11905 -0.026 0.24 NO
268 TCF7 TCF7 TCF7 11988 -0.027 0.24 NO
269 ARAF ARAF ARAF 12085 -0.029 0.23 NO
270 CTBP1 CTBP1 CTBP1 12105 -0.03 0.23 NO
271 RAC1 RAC1 RAC1 12125 -0.03 0.23 NO
272 CTBP2 CTBP2 CTBP2 12160 -0.03 0.23 NO
273 APC2 APC2 APC2 12194 -0.031 0.23 NO
274 AXIN1 AXIN1 AXIN1 12197 -0.031 0.23 NO
275 PIK3R2 PIK3R2 PIK3R2 12385 -0.034 0.22 NO
276 MECOM MECOM MECOM 12386 -0.034 0.22 NO
277 FGF8 FGF8 FGF8 12817 -0.041 0.2 NO
278 FADD FADD FADD 12992 -0.044 0.19 NO
279 RBX1 RBX1 RBX1 13047 -0.045 0.19 NO
280 DVL1 DVL1 DVL1 13210 -0.048 0.18 NO
281 FZD3 FZD3 FZD3 13390 -0.051 0.17 NO
282 TFG TFG TFG 13466 -0.053 0.16 NO
283 CDK4 CDK4 CDK4 13579 -0.055 0.16 NO
284 BAD BAD BAD 13682 -0.057 0.16 NO
285 CYCS CYCS CYCS 13688 -0.057 0.16 NO
286 FZD9 FZD9 FZD9 13902 -0.061 0.14 NO
287 MAPK3 MAPK3 MAPK3 13939 -0.062 0.14 NO
288 TP53 TP53 TP53 13975 -0.063 0.14 NO
289 MAP2K2 MAP2K2 MAP2K2 13995 -0.063 0.14 NO
290 PAX8 PAX8 PAX8 14085 -0.065 0.14 NO
291 FZD5 FZD5 FZD5 14113 -0.066 0.14 NO
292 SKP2 SKP2 SKP2 14123 -0.067 0.14 NO
293 GSTP1 GSTP1 GSTP1 14550 -0.077 0.12 NO
294 WNT3 WNT3 WNT3 14926 -0.087 0.098 NO
295 BIRC5 BIRC5 BIRC5 15003 -0.089 0.096 NO
296 FH FH FH 15150 -0.093 0.089 NO
297 E2F1 E2F1 E2F1 15158 -0.094 0.091 NO
298 CEBPA CEBPA CEBPA 15332 -0.099 0.083 NO
299 TCEB2 TCEB2 TCEB2 15406 -0.1 0.081 NO
300 TRAF4 TRAF4 TRAF4 15484 -0.1 0.078 NO
301 RAD51 RAD51 RAD51 15604 -0.11 0.074 NO
302 BID BID BID 15626 -0.11 0.075 NO
303 E2F2 E2F2 E2F2 15817 -0.12 0.066 NO
304 ITGA2B ITGA2B ITGA2B 15889 -0.12 0.065 NO
305 CKS1B CKS1B CKS1B 16145 -0.13 0.053 NO
306 CBLC CBLC CBLC 16213 -0.14 0.052 NO
307 AXIN2 AXIN2 AXIN2 16219 -0.14 0.054 NO
308 EGF EGF EGF 16378 -0.15 0.048 NO
309 PPARG PPARG PPARG 16395 -0.15 0.05 NO
310 DAPK2 DAPK2 DAPK2 16442 -0.15 0.05 NO
311 CCNE1 CCNE1 CCNE1 16605 -0.16 0.044 NO
312 NOS2 NOS2 NOS2 17082 -0.21 0.021 NO
313 FGF17 FGF17 FGF17 17196 -0.23 0.02 NO
314 KLK3 KLK3 KLK3 17223 -0.23 0.023 NO
315 COL4A6 COL4A6 COL4A6 17378 -0.26 0.019 NO
316 SHH SHH SHH 17394 -0.26 0.023 NO
317 FGFR3 FGFR3 FGFR3 17423 -0.27 0.027 NO
318 WNT4 WNT4 WNT4 17434 -0.27 0.032 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 BCR PATHWAY.

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

genes ES table in pathway: BIOCARTA BIOPEPTIDES PATHWAY

Table 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 THBS4 THBS4 THBS4 39 0.85 0.019 YES
2 COMP COMP COMP 93 0.79 0.036 YES
3 IGF1 IGF1 IGF1 161 0.74 0.05 YES
4 VEGFC VEGFC VEGFC 267 0.69 0.062 YES
5 COL11A1 COL11A1 COL11A1 278 0.69 0.078 YES
6 RELN RELN RELN 353 0.65 0.09 YES
7 TNXB TNXB TNXB 377 0.65 0.1 YES
8 HGF HGF HGF 409 0.63 0.12 YES
9 THBS2 THBS2 THBS2 505 0.6 0.13 YES
10 AKT3 AKT3 AKT3 589 0.58 0.14 YES
11 PIK3R5 PIK3R5 PIK3R5 599 0.58 0.15 YES
12 PIK3CG PIK3CG PIK3CG 627 0.57 0.17 YES
13 LAMA2 LAMA2 LAMA2 672 0.56 0.18 YES
14 PRKCB PRKCB PRKCB 681 0.56 0.19 YES
15 IBSP IBSP IBSP 706 0.55 0.2 YES
16 ITGA11 ITGA11 ITGA11 710 0.55 0.22 YES
17 PAK3 PAK3 PAK3 829 0.52 0.22 YES
18 SHC4 SHC4 SHC4 833 0.52 0.24 YES
19 COL6A6 COL6A6 COL6A6 860 0.52 0.25 YES
20 SPP1 SPP1 SPP1 886 0.51 0.26 YES
21 ITGA10 ITGA10 ITGA10 922 0.51 0.27 YES
22 FLT4 FLT4 FLT4 948 0.5 0.28 YES
23 TNN TNN TNN 1033 0.49 0.29 YES
24 PDGFC PDGFC PDGFC 1058 0.48 0.3 YES
25 ITGB3 ITGB3 ITGB3 1070 0.48 0.31 YES
26 TNC TNC TNC 1097 0.48 0.32 YES
27 MAPK10 MAPK10 MAPK10 1191 0.46 0.33 YES
28 PARVG PARVG PARVG 1244 0.45 0.34 YES
29 PIK3CD PIK3CD PIK3CD 1278 0.45 0.34 YES
30 FLNC FLNC FLNC 1301 0.45 0.36 YES
31 MYLK MYLK MYLK 1332 0.44 0.36 YES
32 FN1 FN1 FN1 1370 0.44 0.37 YES
33 ITGA7 ITGA7 ITGA7 1394 0.43 0.38 YES
34 COL5A3 COL5A3 COL5A3 1486 0.42 0.39 YES
35 COL5A2 COL5A2 COL5A2 1589 0.4 0.39 YES
36 ITGA4 ITGA4 ITGA4 1598 0.4 0.4 YES
37 TNR TNR TNR 1654 0.39 0.41 YES
38 COL6A3 COL6A3 COL6A3 1681 0.39 0.42 YES
39 ITGA5 ITGA5 ITGA5 1764 0.38 0.42 YES
40 MYL9 MYL9 MYL9 1774 0.38 0.43 YES
41 PDGFRB PDGFRB PDGFRB 1852 0.37 0.44 YES
42 COL4A4 COL4A4 COL4A4 1902 0.36 0.44 YES
43 COL5A1 COL5A1 COL5A1 1922 0.36 0.45 YES
44 COL1A1 COL1A1 COL1A1 2109 0.34 0.45 YES
45 COL1A2 COL1A2 COL1A2 2125 0.34 0.46 YES
46 COL3A1 COL3A1 COL3A1 2167 0.33 0.46 YES
47 VAV1 VAV1 VAV1 2243 0.32 0.47 YES
48 KDR KDR KDR 2264 0.32 0.47 YES
49 LAMA4 LAMA4 LAMA4 2309 0.31 0.48 YES
50 FYN FYN FYN 2311 0.31 0.49 YES
51 VTN VTN VTN 2320 0.31 0.49 YES
52 PDGFB PDGFB PDGFB 2363 0.31 0.5 YES
53 ACTN2 ACTN2 ACTN2 2376 0.31 0.5 YES
54 ITGA9 ITGA9 ITGA9 2387 0.31 0.51 YES
55 FIGF FIGF FIGF 2395 0.3 0.52 YES
56 VWF VWF VWF 2407 0.3 0.53 YES
57 CAV2 CAV2 CAV2 2415 0.3 0.53 YES
58 CAV1 CAV1 CAV1 2425 0.3 0.54 YES
59 FLNA FLNA FLNA 2430 0.3 0.55 YES
60 COL6A2 COL6A2 COL6A2 2433 0.3 0.56 YES
61 PDGFRA PDGFRA PDGFRA 2510 0.29 0.56 YES
62 PDGFD PDGFD PDGFD 2529 0.29 0.56 YES
63 COL6A1 COL6A1 COL6A1 2534 0.29 0.57 YES
64 FLT1 FLT1 FLT1 2555 0.29 0.58 YES
65 ACTN3 ACTN3 ACTN3 2575 0.28 0.58 YES
66 THBS1 THBS1 THBS1 2800 0.26 0.58 YES
67 BCL2 BCL2 BCL2 2877 0.25 0.58 YES
68 PGF PGF PGF 2954 0.24 0.58 YES
69 COL4A2 COL4A2 COL4A2 2969 0.24 0.59 YES
70 LAMB2 LAMB2 LAMB2 3005 0.24 0.59 YES
71 ITGA1 ITGA1 ITGA1 3011 0.24 0.6 YES
72 ITGAV ITGAV ITGAV 3067 0.23 0.6 YES
73 THBS3 THBS3 THBS3 3077 0.23 0.6 YES
74 COL4A1 COL4A1 COL4A1 3092 0.23 0.61 YES
75 ITGA8 ITGA8 ITGA8 3216 0.21 0.61 YES
76 BIRC3 BIRC3 BIRC3 3415 0.19 0.6 YES
77 LAMC1 LAMC1 LAMC1 3472 0.19 0.6 YES
78 ITGB7 ITGB7 ITGB7 3490 0.19 0.61 YES
79 PIK3CA PIK3CA PIK3CA 3553 0.18 0.61 YES
80 ROCK1 ROCK1 ROCK1 3775 0.17 0.6 YES
81 MYLK3 MYLK3 MYLK3 3860 0.16 0.6 YES
82 ITGB8 ITGB8 ITGB8 3901 0.16 0.6 YES
83 LAMB1 LAMB1 LAMB1 3911 0.16 0.6 YES
84 TLN1 TLN1 TLN1 3923 0.16 0.61 YES
85 LAMA1 LAMA1 LAMA1 3945 0.16 0.61 YES
86 LAMA5 LAMA5 LAMA5 3949 0.16 0.61 YES
87 LAMB4 LAMB4 LAMB4 4051 0.15 0.61 NO
88 VCL VCL VCL 4131 0.14 0.61 NO
89 MYLK2 MYLK2 MYLK2 4163 0.14 0.61 NO
90 PPP1R12A PPP1R12A PPP1R12A 4440 0.13 0.6 NO
91 PARVB PARVB PARVB 4454 0.13 0.6 NO
92 EGFR EGFR EGFR 4510 0.12 0.6 NO
93 ACTN1 ACTN1 ACTN1 4525 0.12 0.61 NO
94 RAC2 RAC2 RAC2 4559 0.12 0.61 NO
95 DOCK1 DOCK1 DOCK1 4840 0.11 0.59 NO
96 LAMC2 LAMC2 LAMC2 4848 0.11 0.6 NO
97 ITGB5 ITGB5 ITGB5 4854 0.11 0.6 NO
98 PIP5K1C PIP5K1C PIP5K1C 4862 0.11 0.6 NO
99 RAPGEF1 RAPGEF1 RAPGEF1 4917 0.11 0.6 NO
100 SOS1 SOS1 SOS1 4964 0.11 0.6 NO
101 RASGRF1 RASGRF1 RASGRF1 5007 0.1 0.6 NO
102 ITGB1 ITGB1 ITGB1 5023 0.1 0.6 NO
103 IGF1R IGF1R IGF1R 5054 0.1 0.6 NO
104 PIK3R3 PIK3R3 PIK3R3 5084 0.1 0.6 NO
105 LAMA3 LAMA3 LAMA3 5281 0.094 0.6 NO
106 ARHGAP5 ARHGAP5 ARHGAP5 5359 0.091 0.59 NO
107 BIRC2 BIRC2 BIRC2 5526 0.086 0.59 NO
108 PIK3R1 PIK3R1 PIK3R1 5698 0.081 0.58 NO
109 SOS2 SOS2 SOS2 5736 0.08 0.58 NO
110 PARVA PARVA PARVA 5792 0.078 0.58 NO
111 RAP1A RAP1A RAP1A 5836 0.077 0.58 NO
112 SHC2 SHC2 SHC2 5885 0.076 0.58 NO
113 VAV2 VAV2 VAV2 6007 0.072 0.57 NO
114 BRAF BRAF BRAF 6011 0.072 0.57 NO
115 ITGA2 ITGA2 ITGA2 6061 0.071 0.57 NO
116 ROCK2 ROCK2 ROCK2 6184 0.068 0.57 NO
117 SHC1 SHC1 SHC1 6272 0.066 0.56 NO
118 PDGFA PDGFA PDGFA 6324 0.065 0.56 NO
119 GRLF1 GRLF1 GRLF1 6376 0.064 0.56 NO
120 CCND1 CCND1 CCND1 6381 0.064 0.56 NO
121 ZYX ZYX ZYX 6620 0.059 0.55 NO
122 PTEN PTEN PTEN 6703 0.057 0.55 NO
123 ILK ILK ILK 6711 0.057 0.55 NO
124 LAMC3 LAMC3 LAMC3 6729 0.056 0.55 NO
125 GRB2 GRB2 GRB2 6836 0.054 0.55 NO
126 VEGFB VEGFB VEGFB 6843 0.054 0.55 NO
127 PRKCG PRKCG PRKCG 7086 0.049 0.53 NO
128 TLN2 TLN2 TLN2 7250 0.046 0.53 NO
129 PIK3CB PIK3CB PIK3CB 7306 0.045 0.52 NO
130 MAPK8 MAPK8 MAPK8 7328 0.044 0.52 NO
131 CRK CRK CRK 7342 0.044 0.52 NO
132 PAK2 PAK2 PAK2 7367 0.043 0.52 NO
133 PDPK1 PDPK1 PDPK1 7370 0.043 0.52 NO
134 PRKCA PRKCA PRKCA 7450 0.042 0.52 NO
135 LAMB3 LAMB3 LAMB3 7555 0.04 0.52 NO
136 FLNB FLNB FLNB 7643 0.039 0.51 NO
137 CAPN2 CAPN2 CAPN2 7645 0.039 0.51 NO
138 XIAP XIAP XIAP 7687 0.038 0.51 NO
139 ELK1 ELK1 ELK1 7785 0.037 0.51 NO
140 CDC42 CDC42 CDC42 8026 0.033 0.5 NO
141 MAP2K1 MAP2K1 MAP2K1 8051 0.032 0.49 NO
142 PTK2 PTK2 PTK2 8169 0.031 0.49 NO
143 CRKL CRKL CRKL 8241 0.03 0.48 NO
144 MAPK1 MAPK1 MAPK1 8628 0.024 0.46 NO
145 GSK3B GSK3B GSK3B 8699 0.022 0.46 NO
146 BCAR1 BCAR1 BCAR1 8845 0.02 0.45 NO
147 ACTN4 ACTN4 ACTN4 8897 0.019 0.45 NO
148 DIAPH1 DIAPH1 DIAPH1 9069 0.017 0.44 NO
149 RHOA RHOA RHOA 9105 0.016 0.44 NO
150 MET MET MET 9106 0.016 0.44 NO
151 ITGB4 ITGB4 ITGB4 9155 0.016 0.44 NO
152 MYL12A MYL12A MYL12A 9182 0.015 0.44 NO
153 PXN PXN PXN 9220 0.015 0.44 NO
154 JUN JUN JUN 9240 0.014 0.44 NO
155 PPP1CB PPP1CB PPP1CB 9449 0.011 0.42 NO
156 SHC3 SHC3 SHC3 9508 0.011 0.42 NO
157 ACTB ACTB ACTB 9764 0.0071 0.41 NO
158 AKT1 AKT1 AKT1 10068 0.0026 0.39 NO
159 CTNNB1 CTNNB1 CTNNB1 10115 0.0019 0.39 NO
160 RAF1 RAF1 RAF1 10189 0.00062 0.38 NO
161 ITGA3 ITGA3 ITGA3 10195 0.00054 0.38 NO
162 VASP VASP VASP 10224 -0.000019 0.38 NO
163 COL11A2 COL11A2 COL11A2 10231 -0.00012 0.38 NO
164 CCND3 CCND3 CCND3 10615 -0.006 0.36 NO
165 AKT2 AKT2 AKT2 10721 -0.0078 0.35 NO
166 VEGFA VEGFA VEGFA 10940 -0.011 0.34 NO
167 ITGA6 ITGA6 ITGA6 11073 -0.013 0.33 NO
168 RAC3 RAC3 RAC3 11127 -0.014 0.33 NO
169 SRC SRC SRC 11624 -0.022 0.3 NO
170 PPP1CC PPP1CC PPP1CC 11642 -0.022 0.3 NO
171 ERBB2 ERBB2 ERBB2 11814 -0.024 0.3 NO
172 ITGB6 ITGB6 ITGB6 11887 -0.026 0.29 NO
173 MAPK9 MAPK9 MAPK9 11891 -0.026 0.29 NO
174 PAK1 PAK1 PAK1 11955 -0.027 0.29 NO
175 ACTG1 ACTG1 ACTG1 11985 -0.027 0.29 NO
176 RAC1 RAC1 RAC1 12125 -0.03 0.28 NO
177 MYL12B MYL12B MYL12B 12223 -0.032 0.28 NO
178 PIK3R2 PIK3R2 PIK3R2 12385 -0.034 0.27 NO
179 RAP1B RAP1B RAP1B 12414 -0.035 0.27 NO
180 PAK4 PAK4 PAK4 13209 -0.048 0.22 NO
181 COL2A1 COL2A1 COL2A1 13368 -0.051 0.22 NO
182 BAD BAD BAD 13682 -0.057 0.2 NO
183 MAPK3 MAPK3 MAPK3 13939 -0.062 0.19 NO
184 PPP1CA PPP1CA PPP1CA 13984 -0.063 0.19 NO
185 CCND2 CCND2 CCND2 15228 -0.096 0.12 NO
186 PAK6 PAK6 PAK6 15686 -0.11 0.096 NO
187 ITGA2B ITGA2B ITGA2B 15889 -0.12 0.088 NO
188 VAV3 VAV3 VAV3 15975 -0.12 0.086 NO
189 CHAD CHAD CHAD 16376 -0.15 0.067 NO
190 EGF EGF EGF 16378 -0.15 0.071 NO
191 MYL5 MYL5 MYL5 17028 -0.21 0.04 NO
192 COL4A6 COL4A6 COL4A6 17378 -0.26 0.027 NO
193 MYLPF MYLPF MYLPF 17596 -0.32 0.022 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 BIOPEPTIDES PATHWAY.

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

genes ES table in pathway: BIOCARTA CARM ER PATHWAY

Table 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 133 0.76 0.079 YES
2 TGFB2 TGFB2 TGFB2 871 0.52 0.096 YES
3 MAP3K12 MAP3K12 MAP3K12 1043 0.48 0.14 YES
4 MAPK10 MAPK10 MAPK10 1191 0.46 0.19 YES
5 MAP4K1 MAP4K1 MAP4K1 1382 0.43 0.22 YES
6 MAPK4 MAPK4 MAPK4 1546 0.41 0.26 YES
7 MAPK11 MAPK11 MAPK11 1586 0.4 0.31 YES
8 TGFB1 TGFB1 TGFB1 2855 0.26 0.26 YES
9 MAP3K3 MAP3K3 MAP3K3 2946 0.24 0.29 YES
10 RPS6KA2 RPS6KA2 RPS6KA2 3104 0.23 0.3 YES
11 MAPK12 MAPK12 MAPK12 3599 0.18 0.3 YES
12 MAP4K4 MAP4K4 MAP4K4 3774 0.17 0.31 YES
13 TGFBR1 TGFBR1 TGFBR1 3935 0.16 0.32 YES
14 STAT1 STAT1 STAT1 4005 0.15 0.33 YES
15 MEF2A MEF2A MEF2A 4151 0.14 0.34 YES
16 MAP3K2 MAP3K2 MAP3K2 4188 0.14 0.35 YES
17 MAP4K5 MAP4K5 MAP4K5 4287 0.14 0.36 YES
18 MAP3K1 MAP3K1 MAP3K1 4321 0.14 0.37 YES
19 MEF2D MEF2D MEF2D 4481 0.13 0.38 YES
20 ATF2 ATF2 ATF2 4609 0.12 0.39 YES
21 MAP3K8 MAP3K8 MAP3K8 4673 0.12 0.4 YES
22 RAPGEF2 RAPGEF2 RAPGEF2 4747 0.11 0.4 YES
23 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 4756 0.11 0.42 YES
24 MAP3K6 MAP3K6 MAP3K6 4897 0.11 0.42 YES
25 MAP3K9 MAP3K9 MAP3K9 5213 0.096 0.42 YES
26 MAP3K14 MAP3K14 MAP3K14 5429 0.09 0.41 YES
27 CREB1 CREB1 CREB1 5448 0.089 0.42 YES
28 MAP3K5 MAP3K5 MAP3K5 5977 0.073 0.4 YES
29 BRAF BRAF BRAF 6011 0.072 0.41 YES
30 RPS6KB1 RPS6KB1 RPS6KB1 6036 0.072 0.42 YES
31 NFKBIA NFKBIA NFKBIA 6188 0.068 0.41 YES
32 SHC1 SHC1 SHC1 6272 0.066 0.42 YES
33 MAP3K7 MAP3K7 MAP3K7 6613 0.059 0.4 YES
34 MAPK7 MAPK7 MAPK7 6681 0.057 0.41 YES
35 GRB2 GRB2 GRB2 6836 0.054 0.4 YES
36 MAX MAX MAX 6899 0.053 0.41 YES
37 FOS FOS FOS 7068 0.05 0.4 YES
38 RPS6KA5 RPS6KA5 RPS6KA5 7080 0.049 0.41 YES
39 NFKB1 NFKB1 NFKB1 7091 0.049 0.41 YES
40 MAPKAPK2 MAPKAPK2 MAPKAPK2 7151 0.048 0.42 YES
41 MAP2K7 MAP2K7 MAP2K7 7182 0.047 0.42 YES
42 SP1 SP1 SP1 7312 0.045 0.42 YES
43 MAPK8 MAPK8 MAPK8 7328 0.044 0.42 YES
44 PAK2 PAK2 PAK2 7367 0.043 0.42 YES
45 MAP4K2 MAP4K2 MAP4K2 7518 0.041 0.42 YES
46 IKBKB IKBKB IKBKB 7582 0.04 0.42 YES
47 RIPK1 RIPK1 RIPK1 7634 0.039 0.42 YES
48 MAP3K4 MAP3K4 MAP3K4 7700 0.038 0.42 YES
49 CHUK CHUK CHUK 7758 0.037 0.42 YES
50 ELK1 ELK1 ELK1 7785 0.037 0.43 YES
51 MAP4K3 MAP4K3 MAP4K3 7930 0.034 0.42 NO
52 MAP2K4 MAP2K4 MAP2K4 7971 0.034 0.42 NO
53 MAP2K1 MAP2K1 MAP2K1 8051 0.032 0.42 NO
54 RELA RELA RELA 8140 0.031 0.42 NO
55 DAXX DAXX DAXX 8268 0.029 0.42 NO
56 MAPK1 MAPK1 MAPK1 8628 0.024 0.4 NO
57 MKNK1 MKNK1 MKNK1 8834 0.02 0.39 NO
58 MAPK6 MAPK6 MAPK6 9209 0.015 0.37 NO
59 JUN JUN JUN 9240 0.014 0.37 NO
60 MAP3K10 MAP3K10 MAP3K10 9502 0.011 0.36 NO
61 MAPK14 MAPK14 MAPK14 9936 0.0045 0.34 NO
62 TRAF2 TRAF2 TRAF2 10031 0.0032 0.33 NO
63 MAP3K13 MAP3K13 MAP3K13 10041 0.003 0.33 NO
64 RAF1 RAF1 RAF1 10189 0.00062 0.32 NO
65 MAP2K3 MAP2K3 MAP2K3 10290 -0.001 0.32 NO
66 RPS6KA3 RPS6KA3 RPS6KA3 10736 -0.0079 0.29 NO
67 RPS6KA4 RPS6KA4 RPS6KA4 10749 -0.0082 0.29 NO
68 MKNK2 MKNK2 MKNK2 10795 -0.009 0.29 NO
69 MAP3K11 MAP3K11 MAP3K11 11595 -0.021 0.25 NO
70 MYC MYC MYC 11600 -0.021 0.25 NO
71 MAPK9 MAPK9 MAPK9 11891 -0.026 0.24 NO
72 PAK1 PAK1 PAK1 11955 -0.027 0.24 NO
73 TRADD TRADD TRADD 11999 -0.028 0.24 NO
74 ARAF ARAF ARAF 12085 -0.029 0.24 NO
75 RAC1 RAC1 RAC1 12125 -0.03 0.24 NO
76 MAP2K5 MAP2K5 MAP2K5 12426 -0.035 0.23 NO
77 MAPKAPK3 MAPKAPK3 MAPKAPK3 13130 -0.047 0.19 NO
78 MAPKAPK5 MAPKAPK5 MAPKAPK5 13320 -0.05 0.19 NO
79 HRAS HRAS HRAS 13670 -0.057 0.18 NO
80 MAPK3 MAPK3 MAPK3 13939 -0.062 0.17 NO
81 MAP2K2 MAP2K2 MAP2K2 13995 -0.063 0.17 NO
82 RPS6KA1 RPS6KA1 RPS6KA1 14208 -0.068 0.17 NO
83 MAPK13 MAPK13 MAPK13 14560 -0.077 0.16 NO
84 CEBPA CEBPA CEBPA 15332 -0.099 0.12 NO
85 RPS6KB2 RPS6KB2 RPS6KB2 15387 -0.1 0.13 NO
86 MAP2K6 MAP2K6 MAP2K6 15743 -0.11 0.13 NO

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

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

genes ES table in pathway: BIOCARTA G1 PATHWAY

Table 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 AKT3 AKT3 AKT3 589 0.58 0.05 YES
2 PIK3R5 PIK3R5 PIK3R5 599 0.58 0.13 YES
3 PIK3CG PIK3CG PIK3CG 627 0.57 0.21 YES
4 TGFB2 TGFB2 TGFB2 871 0.52 0.27 YES
5 MAPK10 MAPK10 MAPK10 1191 0.46 0.32 YES
6 PIK3CD PIK3CD PIK3CD 1278 0.45 0.38 YES
7 TCF7L1 TCF7L1 TCF7L1 2325 0.31 0.37 YES
8 LEF1 LEF1 LEF1 2767 0.26 0.38 YES
9 TGFB1 TGFB1 TGFB1 2855 0.26 0.41 YES
10 BCL2 BCL2 BCL2 2877 0.25 0.45 YES
11 DCC DCC DCC 3140 0.22 0.47 YES
12 APC APC APC 3462 0.19 0.48 YES
13 PIK3CA PIK3CA PIK3CA 3553 0.18 0.5 YES
14 TGFBR1 TGFBR1 TGFBR1 3935 0.16 0.5 YES
15 TGFBR2 TGFBR2 TGFBR2 4543 0.12 0.48 YES
16 RAC2 RAC2 RAC2 4559 0.12 0.5 YES
17 PIK3R3 PIK3R3 PIK3R3 5084 0.1 0.48 NO
18 PIK3R1 PIK3R1 PIK3R1 5698 0.081 0.46 NO
19 BRAF BRAF BRAF 6011 0.072 0.46 NO
20 APPL1 APPL1 APPL1 6015 0.072 0.46 NO
21 CCND1 CCND1 CCND1 6381 0.064 0.45 NO
22 SMAD3 SMAD3 SMAD3 6408 0.064 0.46 NO
23 SMAD2 SMAD2 SMAD2 6759 0.056 0.45 NO
24 FOS FOS FOS 7068 0.05 0.44 NO
25 MLH1 MLH1 MLH1 7281 0.045 0.44 NO
26 PIK3CB PIK3CB PIK3CB 7306 0.045 0.44 NO
27 MAPK8 MAPK8 MAPK8 7328 0.044 0.44 NO
28 KRAS KRAS KRAS 7391 0.043 0.45 NO
29 RALGDS RALGDS RALGDS 7834 0.036 0.43 NO
30 MAP2K1 MAP2K1 MAP2K1 8051 0.032 0.42 NO
31 MAPK1 MAPK1 MAPK1 8628 0.024 0.39 NO
32 SMAD4 SMAD4 SMAD4 8664 0.023 0.39 NO
33 GSK3B GSK3B GSK3B 8699 0.022 0.4 NO
34 MSH3 MSH3 MSH3 8942 0.019 0.38 NO
35 MSH6 MSH6 MSH6 8987 0.018 0.38 NO
36 RHOA RHOA RHOA 9105 0.016 0.38 NO
37 JUN JUN JUN 9240 0.014 0.38 NO
38 AKT1 AKT1 AKT1 10068 0.0026 0.33 NO
39 CTNNB1 CTNNB1 CTNNB1 10115 0.0019 0.33 NO
40 CASP9 CASP9 CASP9 10141 0.0015 0.32 NO
41 RAF1 RAF1 RAF1 10189 0.00062 0.32 NO
42 MSH2 MSH2 MSH2 10577 -0.0055 0.3 NO
43 AKT2 AKT2 AKT2 10721 -0.0078 0.3 NO
44 CASP3 CASP3 CASP3 10881 -0.01 0.29 NO
45 RAC3 RAC3 RAC3 11127 -0.014 0.28 NO
46 TCF7L2 TCF7L2 TCF7L2 11393 -0.018 0.26 NO
47 MYC MYC MYC 11600 -0.021 0.26 NO
48 MAPK9 MAPK9 MAPK9 11891 -0.026 0.24 NO
49 BAX BAX BAX 11905 -0.026 0.25 NO
50 TCF7 TCF7 TCF7 11988 -0.027 0.24 NO
51 ARAF ARAF ARAF 12085 -0.029 0.24 NO
52 RAC1 RAC1 RAC1 12125 -0.03 0.25 NO
53 APC2 APC2 APC2 12194 -0.031 0.25 NO
54 AXIN1 AXIN1 AXIN1 12197 -0.031 0.25 NO
55 PIK3R2 PIK3R2 PIK3R2 12385 -0.034 0.25 NO
56 BAD BAD BAD 13682 -0.057 0.18 NO
57 CYCS CYCS CYCS 13688 -0.057 0.19 NO
58 MAPK3 MAPK3 MAPK3 13939 -0.062 0.18 NO
59 TP53 TP53 TP53 13975 -0.063 0.19 NO
60 BIRC5 BIRC5 BIRC5 15003 -0.089 0.15 NO
61 AXIN2 AXIN2 AXIN2 16219 -0.14 0.099 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 G1 PATHWAY.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA HDAC 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 TGFB3 TGFB3 TGFB3 133 0.76 0.087 YES
2 AKT3 AKT3 AKT3 589 0.58 0.13 YES
3 PIK3R5 PIK3R5 PIK3R5 599 0.58 0.2 YES
4 PIK3CG PIK3CG PIK3CG 627 0.57 0.28 YES
5 SHC4 SHC4 SHC4 833 0.52 0.33 YES
6 TGFB2 TGFB2 TGFB2 871 0.52 0.39 YES
7 PIK3CD PIK3CD PIK3CD 1278 0.45 0.42 YES
8 TGFB1 TGFB1 TGFB1 2855 0.26 0.37 YES
9 RUNX1 RUNX1 RUNX1 3502 0.19 0.36 YES
10 PIK3CA PIK3CA PIK3CA 3553 0.18 0.38 YES
11 TGFBR1 TGFBR1 TGFBR1 3935 0.16 0.37 YES
12 CBL CBL CBL 4071 0.15 0.38 YES
13 CBLB CBLB CBLB 4155 0.14 0.4 YES
14 GAB2 GAB2 GAB2 4416 0.13 0.4 YES
15 TGFBR2 TGFBR2 TGFBR2 4543 0.12 0.41 YES
16 SOS1 SOS1 SOS1 4964 0.11 0.4 YES
17 PIK3R3 PIK3R3 PIK3R3 5084 0.1 0.4 YES
18 PIK3R1 PIK3R1 PIK3R1 5698 0.081 0.38 YES
19 STAT5A STAT5A STAT5A 5731 0.08 0.39 YES
20 SOS2 SOS2 SOS2 5736 0.08 0.4 YES
21 STAT5B STAT5B STAT5B 5838 0.077 0.4 YES
22 SHC2 SHC2 SHC2 5885 0.076 0.41 YES
23 CDK6 CDK6 CDK6 5930 0.074 0.42 YES
24 BRAF BRAF BRAF 6011 0.072 0.42 YES
25 PTPN11 PTPN11 PTPN11 6079 0.071 0.42 YES
26 NFKBIA NFKBIA NFKBIA 6188 0.068 0.43 YES
27 ABL1 ABL1 ABL1 6215 0.067 0.43 YES
28 SHC1 SHC1 SHC1 6272 0.066 0.44 YES
29 CCND1 CCND1 CCND1 6381 0.064 0.44 YES
30 SMAD3 SMAD3 SMAD3 6408 0.064 0.45 YES
31 GRB2 GRB2 GRB2 6836 0.054 0.43 NO
32 RB1 RB1 RB1 6889 0.053 0.43 NO
33 E2F3 E2F3 E2F3 6917 0.053 0.44 NO
34 NFKB1 NFKB1 NFKB1 7091 0.049 0.44 NO
35 PIK3CB PIK3CB PIK3CB 7306 0.045 0.43 NO
36 CRK CRK CRK 7342 0.044 0.43 NO
37 KRAS KRAS KRAS 7391 0.043 0.44 NO
38 IKBKB IKBKB IKBKB 7582 0.04 0.43 NO
39 CDKN1B CDKN1B CDKN1B 7597 0.039 0.43 NO
40 CHUK CHUK CHUK 7758 0.037 0.43 NO
41 BCL2L1 BCL2L1 BCL2L1 7830 0.036 0.43 NO
42 MAP2K1 MAP2K1 MAP2K1 8051 0.032 0.42 NO
43 RELA RELA RELA 8140 0.031 0.42 NO
44 CRKL CRKL CRKL 8241 0.03 0.42 NO
45 CDKN2A CDKN2A CDKN2A 8385 0.027 0.42 NO
46 NRAS NRAS NRAS 8595 0.024 0.41 NO
47 MAPK1 MAPK1 MAPK1 8628 0.024 0.41 NO
48 SMAD4 SMAD4 SMAD4 8664 0.023 0.41 NO
49 MDM2 MDM2 MDM2 9478 0.011 0.36 NO
50 SHC3 SHC3 SHC3 9508 0.011 0.36 NO
51 BCR BCR BCR 9734 0.0076 0.35 NO
52 AKT1 AKT1 AKT1 10068 0.0026 0.33 NO
53 RAF1 RAF1 RAF1 10189 0.00062 0.33 NO
54 AKT2 AKT2 AKT2 10721 -0.0078 0.3 NO
55 HDAC2 HDAC2 HDAC2 10859 -0.0098 0.29 NO
56 IKBKG IKBKG IKBKG 11005 -0.012 0.29 NO
57 CDKN1A CDKN1A CDKN1A 11341 -0.017 0.27 NO
58 MYC MYC MYC 11600 -0.021 0.26 NO
59 HDAC1 HDAC1 HDAC1 11853 -0.025 0.25 NO
60 ARAF ARAF ARAF 12085 -0.029 0.24 NO
61 CTBP1 CTBP1 CTBP1 12105 -0.03 0.24 NO
62 CTBP2 CTBP2 CTBP2 12160 -0.03 0.24 NO
63 PIK3R2 PIK3R2 PIK3R2 12385 -0.034 0.23 NO
64 MECOM MECOM MECOM 12386 -0.034 0.24 NO
65 CDK4 CDK4 CDK4 13579 -0.055 0.18 NO
66 HRAS HRAS HRAS 13670 -0.057 0.18 NO
67 BAD BAD BAD 13682 -0.057 0.19 NO
68 MAPK3 MAPK3 MAPK3 13939 -0.062 0.18 NO
69 TP53 TP53 TP53 13975 -0.063 0.18 NO
70 MAP2K2 MAP2K2 MAP2K2 13995 -0.063 0.19 NO
71 E2F2 E2F2 E2F2 15817 -0.12 0.1 NO
72 CBLC CBLC CBLC 16213 -0.14 0.1 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 HDAC PATHWAY.

Figure S58.  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 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 TNS1 TNS1 TNS1 798 0.53 0.089 YES
2 FYN FYN FYN 2311 0.31 0.083 YES
3 ACTN2 ACTN2 ACTN2 2376 0.31 0.16 YES
4 CAV1 CAV1 CAV1 2425 0.3 0.23 YES
5 PPP1R12B PPP1R12B PPP1R12B 2432 0.3 0.3 YES
6 ACTN3 ACTN3 ACTN3 2575 0.28 0.37 YES
7 ITGA1 ITGA1 ITGA1 3011 0.24 0.4 YES
8 ROCK1 ROCK1 ROCK1 3775 0.17 0.4 YES
9 VCL VCL VCL 4131 0.14 0.42 YES
10 ACTA1 ACTA1 ACTA1 4418 0.13 0.44 YES
11 ACTN1 ACTN1 ACTN1 4525 0.12 0.46 YES
12 RAPGEF1 RAPGEF1 RAPGEF1 4917 0.11 0.47 YES
13 SOS1 SOS1 SOS1 4964 0.11 0.49 YES
14 ITGB1 ITGB1 ITGB1 5023 0.1 0.51 YES
15 RAP1A RAP1A RAP1A 5836 0.077 0.49 NO
16 CAPNS2 CAPNS2 CAPNS2 6181 0.068 0.48 NO
17 SHC1 SHC1 SHC1 6272 0.066 0.5 NO
18 ZYX ZYX ZYX 6620 0.059 0.49 NO
19 GRB2 GRB2 GRB2 6836 0.054 0.49 NO
20 MAPK8 MAPK8 MAPK8 7328 0.044 0.48 NO
21 MAP2K1 MAP2K1 MAP2K1 8051 0.032 0.44 NO
22 PTK2 PTK2 PTK2 8169 0.031 0.45 NO
23 CRKL CRKL CRKL 8241 0.03 0.45 NO
24 MAPK1 MAPK1 MAPK1 8628 0.024 0.43 NO
25 BCAR1 BCAR1 BCAR1 8845 0.02 0.43 NO
26 RHOA RHOA RHOA 9105 0.016 0.42 NO
27 PXN PXN PXN 9220 0.015 0.41 NO
28 JUN JUN JUN 9240 0.014 0.42 NO
29 BCR BCR BCR 9734 0.0076 0.39 NO
30 RAF1 RAF1 RAF1 10189 0.00062 0.37 NO
31 CSK CSK CSK 10563 -0.0052 0.35 NO
32 CAPN1 CAPN1 CAPN1 11241 -0.016 0.31 NO
33 SRC SRC SRC 11624 -0.022 0.3 NO
34 CAPNS1 CAPNS1 CAPNS1 13319 -0.05 0.22 NO
35 HRAS HRAS HRAS 13670 -0.057 0.21 NO
36 MAPK3 MAPK3 MAPK3 13939 -0.062 0.21 NO
37 MAP2K2 MAP2K2 MAP2K2 13995 -0.063 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 EGF PATHWAY.

Figure S60.  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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus4 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA FMLP PATHWAY 34 genes.ES.table 0.51 1.6 0.042 1 0.68 0.12 0.09 0.11 0.58 0.35
KEGG GLYCOLYSIS GLUCONEOGENESIS 57 genes.ES.table 0.45 1.5 0.07 0.8 0.91 0.37 0.3 0.26 0.55 0.28
KEGG PENTOSE PHOSPHATE PATHWAY 26 genes.ES.table 0.5 1.5 0.038 1 0.8 0.5 0.3 0.35 0.6 0.33
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.46 1.5 0.054 1 0.85 0.58 0.3 0.4 0.66 0.35
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 29 genes.ES.table 0.47 1.4 0.071 0.6 0.93 0.45 0.26 0.33 0.44 0.18
KEGG GLUTATHIONE METABOLISM 45 genes.ES.table 0.46 1.4 0.084 0.66 0.93 0.42 0.22 0.33 0.47 0.22
KEGG ARACHIDONIC ACID METABOLISM 51 genes.ES.table 0.56 1.5 0.024 0.9 0.88 0.47 0.23 0.36 0.6 0.31
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 59 genes.ES.table 0.58 1.4 0.075 0.65 0.93 0.46 0.22 0.36 0.46 0.21
KEGG RIBOSOME 85 genes.ES.table 0.55 1.5 0.16 0.99 0.87 0.18 0.12 0.16 0.63 0.35
KEGG COMPLEMENT AND COAGULATION CASCADES 62 genes.ES.table 0.55 1.4 0.078 0.62 0.94 0.47 0.25 0.35 0.47 0.19
genes ES table in pathway: BIOCARTA FMLP PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TUBB4Q TUBB4Q TUBB4Q 21 1.4 0.18 YES
2 TUBB8 TUBB8 TUBB8 55 1.2 0.33 YES
3 TUBA1A TUBA1A TUBA1A 446 0.5 0.37 YES
4 TUBB2A TUBB2A TUBB2A 496 0.46 0.43 YES
5 TUBA3D TUBA3D TUBA3D 665 0.38 0.46 YES
6 TUBB3 TUBB3 TUBB3 726 0.36 0.51 YES
7 TUBA3E TUBA3E TUBA3E 1439 0.22 0.49 YES
8 TUBAL3 TUBAL3 TUBAL3 1499 0.22 0.52 YES
9 TUBB2B TUBB2B TUBB2B 1662 0.2 0.53 YES
10 CD14 CD14 CD14 2205 0.16 0.52 YES
11 TUBA1C TUBA1C TUBA1C 2215 0.16 0.54 YES
12 WAS WAS WAS 2765 0.13 0.53 NO
13 TUBB4 TUBB4 TUBB4 3206 0.11 0.52 NO
14 TUBB6 TUBB6 TUBB6 3459 0.1 0.52 NO
15 TUBA8 TUBA8 TUBA8 3502 0.1 0.53 NO
16 TUBB2C TUBB2C TUBB2C 3744 0.095 0.53 NO
17 ARPC5L ARPC5L ARPC5L 4535 0.075 0.49 NO
18 TUBA4A TUBA4A TUBA4A 4834 0.068 0.48 NO
19 OCLN OCLN OCLN 5161 0.062 0.48 NO
20 TUBA1B TUBA1B TUBA1B 5306 0.058 0.47 NO
21 ACTB ACTB ACTB 5755 0.05 0.46 NO
22 ARPC1B ARPC1B ARPC1B 6043 0.045 0.44 NO
23 ACTG1 ACTG1 ACTG1 6445 0.037 0.43 NO
24 HCLS1 HCLS1 HCLS1 6954 0.03 0.4 NO
25 ARPC1A ARPC1A ARPC1A 7057 0.028 0.4 NO
26 YWHAQ YWHAQ YWHAQ 7168 0.026 0.4 NO
27 CTNNB1 CTNNB1 CTNNB1 7437 0.021 0.38 NO
28 LY96 LY96 LY96 7537 0.02 0.38 NO
29 TUBB TUBB TUBB 7594 0.019 0.38 NO
30 KRT18 KRT18 KRT18 7670 0.018 0.38 NO
31 ARPC2 ARPC2 ARPC2 7714 0.017 0.38 NO
32 NCK2 NCK2 NCK2 8236 0.0094 0.35 NO
33 CTTN CTTN CTTN 8273 0.009 0.35 NO
34 ARPC4 ARPC4 ARPC4 8295 0.0086 0.35 NO
35 RHOA RHOA RHOA 8751 0.0021 0.33 NO
36 ARPC5 ARPC5 ARPC5 9135 -0.0031 0.3 NO
37 EZR EZR EZR 9667 -0.01 0.28 NO
38 TUBB1 TUBB1 TUBB1 10755 -0.026 0.22 NO
39 ITGB1 ITGB1 ITGB1 11476 -0.036 0.18 NO
40 CLDN1 CLDN1 CLDN1 11928 -0.043 0.16 NO
41 ABL1 ABL1 ABL1 12364 -0.049 0.15 NO
42 YWHAZ YWHAZ YWHAZ 12372 -0.049 0.15 NO
43 TLR4 TLR4 TLR4 12554 -0.052 0.15 NO
44 FYN FYN FYN 12637 -0.053 0.15 NO
45 CDH1 CDH1 CDH1 12835 -0.056 0.15 NO
46 NCK1 NCK1 NCK1 13065 -0.06 0.14 NO
47 CDC42 CDC42 CDC42 13585 -0.068 0.12 NO
48 ARHGEF2 ARHGEF2 ARHGEF2 13657 -0.069 0.12 NO
49 WASL WASL WASL 13843 -0.072 0.12 NO
50 PRKCA PRKCA PRKCA 14941 -0.093 0.075 NO
51 NCL NCL NCL 15597 -0.11 0.052 NO
52 ARPC3 ARPC3 ARPC3 16579 -0.14 0.015 NO
53 ROCK1 ROCK1 ROCK1 16760 -0.14 0.023 NO
54 ROCK2 ROCK2 ROCK2 17223 -0.17 0.019 NO
55 TLR5 TLR5 TLR5 17523 -0.19 0.026 NO

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

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

genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HIST1H4K HIST1H4K HIST1H4K 3 1.7 0.059 YES
2 HIST2H2AC HIST2H2AC HIST2H2AC 47 1.2 0.099 YES
3 HIST1H2BO HIST1H2BO HIST1H2BO 85 1.1 0.13 YES
4 HIST1H2AJ HIST1H2AJ HIST1H2AJ 162 0.86 0.16 YES
5 HIST2H3C HIST2H3C HIST2H3C 185 0.81 0.19 YES
6 FCGR2C FCGR2C FCGR2C 198 0.78 0.21 YES
7 HIST2H3D HIST2H3D HIST2H3D 209 0.77 0.24 YES
8 FCGR3B FCGR3B FCGR3B 287 0.66 0.26 YES
9 HIST1H2BN HIST1H2BN HIST1H2BN 349 0.59 0.28 YES
10 HIST2H2BF HIST2H2BF HIST2H2BF 370 0.56 0.29 YES
11 FCGR1A FCGR1A FCGR1A 371 0.56 0.31 YES
12 HLA-DQA2 HLA-DQA2 HLA-DQA2 409 0.53 0.33 YES
13 HIST1H4J HIST1H4J HIST1H4J 414 0.52 0.35 YES
14 HIST3H2A HIST3H2A HIST3H2A 432 0.51 0.36 YES
15 HIST1H4I HIST1H4I HIST1H4I 543 0.44 0.37 YES
16 H3F3C H3F3C H3F3C 558 0.43 0.39 YES
17 HIST1H2BE HIST1H2BE HIST1H2BE 569 0.42 0.4 YES
18 HIST2H4A HIST2H4A HIST2H4A 571 0.42 0.42 YES
19 HLA-DRB5 HLA-DRB5 HLA-DRB5 601 0.4 0.43 YES
20 FCGR2B FCGR2B FCGR2B 605 0.4 0.44 YES
21 HIST1H4A HIST1H4A HIST1H4A 606 0.4 0.46 YES
22 HIST1H2BL HIST1H2BL HIST1H2BL 616 0.4 0.47 YES
23 HIST1H4B HIST1H4B HIST1H4B 730 0.36 0.47 YES
24 H2AFB1 H2AFB1 H2AFB1 799 0.33 0.48 YES
25 C8G C8G C8G 824 0.32 0.49 YES
26 HIST1H4D HIST1H4D HIST1H4D 841 0.32 0.5 YES
27 HIST1H4E HIST1H4E HIST1H4E 857 0.32 0.51 YES
28 HIST1H2BJ HIST1H2BJ HIST1H2BJ 871 0.31 0.52 YES
29 HIST1H4C HIST1H4C HIST1H4C 927 0.3 0.53 YES
30 HIST3H2BB HIST3H2BB HIST3H2BB 935 0.3 0.54 YES
31 HIST1H3B HIST1H3B HIST1H3B 937 0.3 0.55 YES
32 HIST1H3H HIST1H3H HIST1H3H 956 0.29 0.56 YES
33 HIST1H2AG HIST1H2AG HIST1H2AG 962 0.29 0.57 YES
34 HIST1H3D HIST1H3D HIST1H3D 1022 0.28 0.57 YES
35 HIST1H2AL HIST1H2AL HIST1H2AL 1028 0.28 0.58 YES
36 IL10 IL10 IL10 1056 0.28 0.59 YES
37 HLA-DQA1 HLA-DQA1 HLA-DQA1 1080 0.27 0.6 YES
38 HIST1H2AH HIST1H2AH HIST1H2AH 1138 0.26 0.61 YES
39 HIST1H2BI HIST1H2BI HIST1H2BI 1201 0.25 0.61 YES
40 HLA-DRB1 HLA-DRB1 HLA-DRB1 1216 0.25 0.62 YES
41 HIST2H2AB HIST2H2AB HIST2H2AB 1247 0.24 0.63 YES
42 HIST1H3I HIST1H3I HIST1H3I 1334 0.24 0.63 YES
43 HIST1H3J HIST1H3J HIST1H3J 1339 0.23 0.64 YES
44 HIST1H3F HIST1H3F HIST1H3F 1358 0.23 0.64 YES
45 C1QB C1QB C1QB 1414 0.23 0.65 YES
46 HLA-DQB1 HLA-DQB1 HLA-DQB1 1486 0.22 0.65 YES
47 HIST1H4H HIST1H4H HIST1H4H 1500 0.22 0.66 YES
48 C1QC C1QC C1QC 1526 0.21 0.67 YES
49 HLA-DPB1 HLA-DPB1 HLA-DPB1 1574 0.21 0.67 YES
50 HIST1H2AM HIST1H2AM HIST1H2AM 1638 0.2 0.67 YES
51 TNF TNF TNF 1672 0.2 0.68 YES
52 HIST1H2BF HIST1H2BF HIST1H2BF 1725 0.2 0.68 YES
53 HIST1H2BM HIST1H2BM HIST1H2BM 1755 0.19 0.69 YES
54 HIST1H2BG HIST1H2BG HIST1H2BG 1764 0.19 0.7 YES
55 HIST1H2BC HIST1H2BC HIST1H2BC 1771 0.19 0.7 YES
56 HIST1H2AK HIST1H2AK HIST1H2AK 1777 0.19 0.71 YES
57 HLA-DMB HLA-DMB HLA-DMB 1790 0.19 0.71 YES
58 HIST1H2AB HIST1H2AB HIST1H2AB 1807 0.19 0.72 YES
59 HIST1H3G HIST1H3G HIST1H3G 1849 0.18 0.72 YES
60 HIST1H3C HIST1H3C HIST1H3C 1856 0.18 0.73 YES
61 HIST1H3A HIST1H3A HIST1H3A 1919 0.18 0.73 YES
62 CD80 CD80 CD80 1971 0.18 0.74 YES
63 HIST1H2BH HIST1H2BH HIST1H2BH 2128 0.17 0.73 YES
64 ELANE ELANE ELANE 2140 0.16 0.74 YES
65 IFNG IFNG IFNG 2160 0.16 0.74 YES
66 HLA-DPA1 HLA-DPA1 HLA-DPA1 2280 0.16 0.74 YES
67 H3F3A H3F3A H3F3A 2405 0.15 0.74 YES
68 C1QA C1QA C1QA 2602 0.14 0.73 YES
69 HLA-DOA HLA-DOA HLA-DOA 2700 0.13 0.73 YES
70 H2AFX H2AFX H2AFX 2724 0.13 0.74 YES
71 CD86 CD86 CD86 2746 0.13 0.74 YES
72 C4A C4A C4A 2783 0.13 0.74 YES
73 CD40 CD40 CD40 2799 0.13 0.74 YES
74 CTSG CTSG CTSG 2829 0.13 0.75 YES
75 FCGR2A FCGR2A FCGR2A 2867 0.13 0.75 YES
76 HLA-DRA HLA-DRA HLA-DRA 2877 0.13 0.75 YES
77 FCGR3A FCGR3A FCGR3A 3125 0.12 0.74 NO
78 HLA-DMA HLA-DMA HLA-DMA 3318 0.11 0.74 NO
79 CD40LG CD40LG CD40LG 3345 0.11 0.74 NO
80 HIST1H2AE HIST1H2AE HIST1H2AE 3755 0.094 0.72 NO
81 HLA-DOB HLA-DOB HLA-DOB 3790 0.094 0.72 NO
82 HIST1H2BK HIST1H2BK HIST1H2BK 3814 0.093 0.72 NO
83 C2 C2 C2 4908 0.067 0.66 NO
84 H2AFJ H2AFJ H2AFJ 5205 0.061 0.65 NO
85 CD28 CD28 CD28 5420 0.056 0.64 NO
86 SNRPB SNRPB SNRPB 5462 0.056 0.64 NO
87 HIST1H2BD HIST1H2BD HIST1H2BD 6039 0.045 0.61 NO
88 C3 C3 C3 6666 0.034 0.57 NO
89 C1R C1R C1R 7595 0.019 0.52 NO
90 ACTN2 ACTN2 ACTN2 7689 0.018 0.52 NO
91 TRIM21 TRIM21 TRIM21 7842 0.015 0.51 NO
92 H2AFZ H2AFZ H2AFZ 7908 0.014 0.51 NO
93 H2AFY H2AFY H2AFY 8100 0.012 0.5 NO
94 H2AFV H2AFV H2AFV 8553 0.0049 0.47 NO
95 C1S C1S C1S 9875 -0.013 0.4 NO
96 HIST1H2AC HIST1H2AC HIST1H2AC 10275 -0.019 0.38 NO
97 C6 C6 C6 10641 -0.024 0.36 NO
98 ACTN4 ACTN4 ACTN4 11101 -0.03 0.33 NO
99 ACTN1 ACTN1 ACTN1 11251 -0.033 0.33 NO
100 H2AFY2 H2AFY2 H2AFY2 11275 -0.033 0.33 NO
101 GRIN2A GRIN2A GRIN2A 11849 -0.042 0.3 NO
102 SNRPD3 SNRPD3 SNRPD3 11979 -0.043 0.29 NO
103 SNRPD1 SNRPD1 SNRPD1 11994 -0.044 0.29 NO
104 C9 C9 C9 12999 -0.059 0.24 NO
105 H3F3B H3F3B H3F3B 13264 -0.063 0.22 NO
106 HIST2H2BE HIST2H2BE HIST2H2BE 13913 -0.074 0.19 NO
107 GRIN2B GRIN2B GRIN2B 14760 -0.09 0.15 NO
108 ACTN3 ACTN3 ACTN3 15105 -0.097 0.13 NO
109 C5 C5 C5 15360 -0.1 0.12 NO
110 HIST1H2AD HIST1H2AD HIST1H2AD 15420 -0.1 0.12 NO
111 TROVE2 TROVE2 TROVE2 15637 -0.11 0.11 NO
112 HIST1H3E HIST1H3E HIST1H3E 15808 -0.11 0.11 NO
113 HIST4H4 HIST4H4 HIST4H4 15812 -0.11 0.11 NO
114 C7 C7 C7 15818 -0.11 0.11 NO
115 SSB SSB SSB 17874 -0.25 0.0068 NO

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

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

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NCF1C NCF1C NCF1C 143 0.92 0.26 YES
2 GNGT1 GNGT1 GNGT1 391 0.54 0.41 YES
3 FPR1 FPR1 FPR1 684 0.37 0.5 YES
4 CAMK1G CAMK1G CAMK1G 1611 0.2 0.51 YES
5 NCF2 NCF2 NCF2 2719 0.13 0.49 NO
6 NFATC1 NFATC1 NFATC1 3799 0.093 0.45 NO
7 HRAS HRAS HRAS 3956 0.09 0.47 NO
8 NFATC3 NFATC3 NFATC3 4477 0.076 0.46 NO
9 MAPK3 MAPK3 MAPK3 4942 0.066 0.46 NO
10 MAP2K2 MAP2K2 MAP2K2 5546 0.054 0.44 NO
11 CAMK1 CAMK1 CAMK1 5713 0.051 0.44 NO
12 NFKBIA NFKBIA NFKBIA 7009 0.029 0.38 NO
13 PPP3CC PPP3CC PPP3CC 7105 0.027 0.38 NO
14 GNB1 GNB1 GNB1 7807 0.016 0.35 NO
15 CALM1 CALM1 CALM1 8161 0.011 0.33 NO
16 MAPK14 MAPK14 MAPK14 8341 0.008 0.33 NO
17 MAP2K3 MAP2K3 MAP2K3 8349 0.0078 0.33 NO
18 MAP2K6 MAP2K6 MAP2K6 8635 0.0038 0.31 NO
19 RAC1 RAC1 RAC1 8888 0.00019 0.3 NO
20 CALM3 CALM3 CALM3 9066 -0.0022 0.29 NO
21 RAF1 RAF1 RAF1 9269 -0.0051 0.28 NO
22 RELA RELA RELA 9274 -0.0051 0.28 NO
23 NFKB1 NFKB1 NFKB1 9341 -0.0059 0.28 NO
24 PAK1 PAK1 PAK1 10196 -0.018 0.24 NO
25 PPP3CB PPP3CB PPP3CB 10265 -0.019 0.24 NO
26 MAPK1 MAPK1 MAPK1 10531 -0.023 0.23 NO
27 CALM2 CALM2 CALM2 11035 -0.03 0.21 NO
28 ELK1 ELK1 ELK1 11343 -0.034 0.2 NO
29 MAP2K1 MAP2K1 MAP2K1 11788 -0.041 0.19 NO
30 NFATC2 NFATC2 NFATC2 12044 -0.044 0.19 NO
31 NFATC4 NFATC4 NFATC4 13576 -0.068 0.12 NO
32 PPP3CA PPP3CA PPP3CA 13958 -0.074 0.13 NO
33 MAP3K1 MAP3K1 MAP3K1 16154 -0.12 0.04 NO
34 PLCB1 PLCB1 PLCB1 17686 -0.22 0.017 NO

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

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 COX4I2 COX4I2 COX4I2 737 0.36 0.003 YES
2 SLC18A2 SLC18A2 SLC18A2 1023 0.28 0.022 YES
3 COX7A1 COX7A1 COX7A1 1579 0.21 0.017 YES
4 NDUFS7 NDUFS7 NDUFS7 1754 0.19 0.031 YES
5 COX6A1 COX6A1 COX6A1 1861 0.18 0.048 YES
6 ATP5D ATP5D ATP5D 1917 0.18 0.067 YES
7 COX5B COX5B COX5B 2110 0.17 0.077 YES
8 TH TH TH 2155 0.16 0.095 YES
9 NDUFS8 NDUFS8 NDUFS8 2176 0.16 0.11 YES
10 CYC1 CYC1 CYC1 2251 0.16 0.13 YES
11 UQCR11 UQCR11 UQCR11 2435 0.15 0.14 YES
12 UQCRQ UQCRQ UQCRQ 2511 0.14 0.15 YES
13 SNCA SNCA SNCA 2677 0.14 0.16 YES
14 NDUFB10 NDUFB10 NDUFB10 2732 0.13 0.17 YES
15 NDUFA4L2 NDUFA4L2 NDUFA4L2 2808 0.13 0.18 YES
16 VDAC2 VDAC2 VDAC2 2813 0.13 0.2 YES
17 UBE2L6 UBE2L6 UBE2L6 2882 0.13 0.21 YES
18 NDUFS6 NDUFS6 NDUFS6 3041 0.12 0.22 YES
19 UQCR10 UQCR10 UQCR10 3147 0.12 0.23 YES
20 NDUFA9 NDUFA9 NDUFA9 3203 0.11 0.24 YES
21 NDUFB7 NDUFB7 NDUFB7 3299 0.11 0.24 YES
22 SLC25A5 SLC25A5 SLC25A5 3329 0.11 0.26 YES
23 NDUFA3 NDUFA3 NDUFA3 3355 0.11 0.27 YES
24 UQCRC1 UQCRC1 UQCRC1 3376 0.11 0.28 YES
25 COX8A COX8A COX8A 3464 0.1 0.29 YES
26 COX6B2 COX6B2 COX6B2 3476 0.1 0.3 YES
27 COX5A COX5A COX5A 3604 0.099 0.31 YES
28 NDUFA6 NDUFA6 NDUFA6 3620 0.099 0.32 YES
29 COX7B COX7B COX7B 3899 0.091 0.31 YES
30 NDUFS3 NDUFS3 NDUFS3 3939 0.09 0.32 YES
31 NDUFB8 NDUFB8 NDUFB8 3997 0.088 0.33 YES
32 UBB UBB UBB 4011 0.088 0.34 YES
33 UBE2J2 UBE2J2 UBE2J2 4119 0.085 0.34 YES
34 NDUFV1 NDUFV1 NDUFV1 4229 0.082 0.35 YES
35 NDUFA2 NDUFA2 NDUFA2 4236 0.082 0.36 YES
36 NDUFA7 NDUFA7 NDUFA7 4325 0.08 0.36 YES
37 UQCRFS1 UQCRFS1 UQCRFS1 4431 0.077 0.37 YES
38 COX4I1 COX4I1 COX4I1 4432 0.077 0.38 YES
39 SLC25A4 SLC25A4 SLC25A4 4700 0.071 0.37 YES
40 NDUFAB1 NDUFAB1 NDUFAB1 4826 0.068 0.37 YES
41 NDUFS5 NDUFS5 NDUFS5 5147 0.062 0.36 YES
42 UCHL1 UCHL1 UCHL1 5203 0.061 0.37 YES
43 UQCRHL UQCRHL UQCRHL 5208 0.061 0.38 YES
44 SDHA SDHA SDHA 5282 0.059 0.38 YES
45 ATP5B ATP5B ATP5B 5437 0.056 0.38 YES
46 COX7A2 COX7A2 COX7A2 5554 0.054 0.38 YES
47 UBA7 UBA7 UBA7 5639 0.052 0.38 YES
48 ATP5G3 ATP5G3 ATP5G3 5823 0.049 0.37 YES
49 HTRA2 HTRA2 HTRA2 5867 0.048 0.38 YES
50 NDUFA8 NDUFA8 NDUFA8 5974 0.046 0.38 YES
51 SDHB SDHB SDHB 5979 0.046 0.38 YES
52 ATP5C1 ATP5C1 ATP5C1 5996 0.046 0.39 YES
53 SDHC SDHC SDHC 6024 0.045 0.39 YES
54 NDUFS2 NDUFS2 NDUFS2 6029 0.045 0.4 YES
55 PINK1 PINK1 PINK1 6270 0.041 0.39 YES
56 COX6B1 COX6B1 COX6B1 6414 0.038 0.39 YES
57 NDUFB9 NDUFB9 NDUFB9 6456 0.037 0.39 YES
58 NDUFB2 NDUFB2 NDUFB2 6474 0.037 0.39 YES
59 SLC18A1 SLC18A1 SLC18A1 6547 0.036 0.39 YES
60 ATP5F1 ATP5F1 ATP5F1 6624 0.034 0.39 YES
61 SLC25A6 SLC25A6 SLC25A6 6657 0.034 0.39 YES
62 UQCRC2 UQCRC2 UQCRC2 6675 0.034 0.4 YES
63 ATP5A1 ATP5A1 ATP5A1 6829 0.031 0.39 NO
64 NDUFS4 NDUFS4 NDUFS4 6878 0.031 0.39 NO
65 ATP5G1 ATP5G1 ATP5G1 6998 0.029 0.39 NO
66 NDUFB4 NDUFB4 NDUFB4 7054 0.028 0.39 NO
67 UBA1 UBA1 UBA1 7153 0.026 0.39 NO
68 NDUFA10 NDUFA10 NDUFA10 7259 0.024 0.39 NO
69 NDUFB1 NDUFB1 NDUFB1 7402 0.022 0.38 NO
70 VDAC3 VDAC3 VDAC3 7525 0.02 0.38 NO
71 GPR37 GPR37 GPR37 7765 0.016 0.36 NO
72 ATP5O ATP5O ATP5O 7801 0.016 0.36 NO
73 CASP9 CASP9 CASP9 8008 0.013 0.36 NO
74 PARK7 PARK7 PARK7 8037 0.012 0.36 NO
75 PARK2 PARK2 PARK2 8173 0.01 0.35 NO
76 UBE2L3 UBE2L3 UBE2L3 8305 0.0084 0.34 NO
77 LRRK2 LRRK2 LRRK2 8515 0.0054 0.33 NO
78 COX7A2L COX7A2L COX7A2L 8966 -0.0009 0.31 NO
79 NDUFV3 NDUFV3 NDUFV3 9106 -0.0027 0.3 NO
80 NDUFC1 NDUFC1 NDUFC1 9394 -0.0066 0.28 NO
81 NDUFB6 NDUFB6 NDUFB6 9484 -0.0079 0.28 NO
82 NDUFC2 NDUFC2 NDUFC2 9716 -0.011 0.27 NO
83 ATP5G2 ATP5G2 ATP5G2 9906 -0.014 0.26 NO
84 VDAC1 VDAC1 VDAC1 10280 -0.02 0.24 NO
85 NDUFA1 NDUFA1 NDUFA1 10556 -0.023 0.23 NO
86 SLC6A3 SLC6A3 SLC6A3 10606 -0.024 0.23 NO
87 NDUFS1 NDUFS1 NDUFS1 10640 -0.024 0.23 NO
88 ATP5J ATP5J ATP5J 10656 -0.024 0.23 NO
89 SDHD SDHD SDHD 10769 -0.026 0.23 NO
90 UBE2G1 UBE2G1 UBE2G1 10793 -0.026 0.23 NO
91 NDUFB5 NDUFB5 NDUFB5 10850 -0.027 0.23 NO
92 NDUFB3 NDUFB3 NDUFB3 11154 -0.031 0.22 NO
93 CASP3 CASP3 CASP3 11224 -0.032 0.22 NO
94 COX6C COX6C COX6C 11655 -0.039 0.2 NO
95 UBE2J1 UBE2J1 UBE2J1 11988 -0.044 0.19 NO
96 COX7C COX7C COX7C 12086 -0.045 0.19 NO
97 SNCAIP SNCAIP SNCAIP 12361 -0.049 0.18 NO
98 UQCRH UQCRH UQCRH 12620 -0.053 0.17 NO
99 UBE2G2 UBE2G2 UBE2G2 13346 -0.064 0.14 NO
100 ATP5E ATP5E ATP5E 13633 -0.069 0.13 NO
101 CYCS CYCS CYCS 13893 -0.073 0.12 NO
102 PPID PPID PPID 13963 -0.075 0.13 NO
103 APAF1 APAF1 APAF1 14913 -0.092 0.088 NO
104 NDUFV2 NDUFV2 NDUFV2 15147 -0.098 0.087 NO
105 NDUFA4 NDUFA4 NDUFA4 15906 -0.12 0.059 NO
106 ATP5H ATP5H ATP5H 15929 -0.12 0.073 NO
107 UQCRB UQCRB UQCRB 16400 -0.13 0.063 NO
108 NDUFA5 NDUFA5 NDUFA5 17678 -0.21 0.018 NO

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

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRPS1L1 PRPS1L1 PRPS1L1 245 0.72 0.22 YES
2 LOC729020 LOC729020 LOC729020 374 0.56 0.4 YES
3 TKTL1 TKTL1 TKTL1 1389 0.23 0.42 YES
4 PGLS PGLS PGLS 2644 0.14 0.4 YES
5 ALDOB ALDOB ALDOB 2763 0.13 0.44 YES
6 FBP2 FBP2 FBP2 2914 0.12 0.47 YES
7 ALDOC ALDOC ALDOC 3294 0.11 0.48 YES
8 RBKS RBKS RBKS 4414 0.077 0.45 YES
9 PFKL PFKL PFKL 4795 0.069 0.45 YES
10 PGM1 PGM1 PGM1 4992 0.065 0.46 YES
11 PGD PGD PGD 5015 0.065 0.48 YES
12 FBP1 FBP1 FBP1 5217 0.06 0.49 YES
13 PFKP PFKP PFKP 5350 0.058 0.5 YES
14 TALDO1 TALDO1 TALDO1 5908 0.047 0.49 NO
15 GPI GPI GPI 6292 0.04 0.48 NO
16 G6PD G6PD G6PD 6535 0.036 0.48 NO
17 DERA DERA DERA 6706 0.033 0.48 NO
18 TKT TKT TKT 6919 0.03 0.48 NO
19 PRPS2 PRPS2 PRPS2 9122 -0.0029 0.36 NO
20 RPIA RPIA RPIA 9576 -0.0093 0.33 NO
21 PFKM PFKM PFKM 10562 -0.023 0.29 NO
22 PRPS1 PRPS1 PRPS1 10572 -0.023 0.29 NO
23 TKTL2 TKTL2 TKTL2 13001 -0.059 0.18 NO
24 H6PD H6PD H6PD 13583 -0.068 0.17 NO
25 PGM2 PGM2 PGM2 14718 -0.089 0.14 NO
26 RPE RPE RPE 16654 -0.14 0.075 NO

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

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

genes ES table in pathway: KEGG GLUTATHIONE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PFKFB1 PFKFB1 PFKFB1 1268 0.24 0.017 YES
2 HK3 HK3 HK3 1278 0.24 0.1 YES
3 SORD SORD SORD 2142 0.16 0.11 YES
4 GMPPB GMPPB GMPPB 2218 0.16 0.17 YES
5 AKR1B1 AKR1B1 AKR1B1 2723 0.13 0.19 YES
6 ALDOB ALDOB ALDOB 2763 0.13 0.23 YES
7 FBP2 FBP2 FBP2 2914 0.12 0.27 YES
8 PHPT1 PHPT1 PHPT1 3216 0.11 0.29 YES
9 ALDOC ALDOC ALDOC 3294 0.11 0.33 YES
10 PMM1 PMM1 PMM1 4248 0.082 0.3 YES
11 GMDS GMDS GMDS 4289 0.081 0.33 YES
12 TSTA3 TSTA3 TSTA3 4531 0.075 0.34 YES
13 FUK FUK FUK 4678 0.072 0.36 YES
14 PFKL PFKL PFKL 4795 0.069 0.38 YES
15 KHK KHK KHK 5064 0.064 0.39 YES
16 FBP1 FBP1 FBP1 5217 0.06 0.4 YES
17 TPI1 TPI1 TPI1 5225 0.06 0.42 YES
18 PFKFB4 PFKFB4 PFKFB4 5346 0.058 0.44 YES
19 PFKP PFKP PFKP 5350 0.058 0.46 YES
20 AKR1B10 AKR1B10 AKR1B10 5754 0.05 0.45 NO
21 GMPPA GMPPA GMPPA 6098 0.044 0.45 NO
22 MPI MPI MPI 7683 0.018 0.37 NO
23 HK1 HK1 HK1 8176 0.01 0.34 NO
24 PMM2 PMM2 PMM2 8372 0.0076 0.34 NO
25 MTMR1 MTMR1 MTMR1 9653 -0.01 0.27 NO
26 PFKM PFKM PFKM 10562 -0.023 0.23 NO
27 PFKFB2 PFKFB2 PFKFB2 11112 -0.031 0.21 NO
28 HK2 HK2 HK2 11607 -0.038 0.19 NO
29 PFKFB3 PFKFB3 PFKFB3 12148 -0.046 0.18 NO
30 MTMR2 MTMR2 MTMR2 13527 -0.067 0.13 NO
31 MTMR6 MTMR6 MTMR6 13534 -0.067 0.15 NO
32 FPGT FPGT FPGT 16360 -0.13 0.04 NO
33 MTMR7 MTMR7 MTMR7 16630 -0.14 0.076 NO

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

Figure S72.  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 ARACHIDONIC ACID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 20 1.4 0.12 YES
2 RPL36A RPL36A RPL36A 138 0.93 0.2 YES
3 RPL39 RPL39 RPL39 204 0.77 0.26 YES
4 RPS28 RPS28 RPS28 258 0.71 0.32 YES
5 RPS27 RPS27 RPS27 343 0.6 0.36 YES
6 RPL9 RPL9 RPL9 394 0.54 0.41 YES
7 RPS26 RPS26 RPS26 426 0.51 0.45 YES
8 RPL7 RPL7 RPL7 465 0.48 0.49 YES
9 RPL18A RPL18A RPL18A 551 0.43 0.52 YES
10 RPS3A RPS3A RPS3A 855 0.32 0.53 YES
11 RPL23A RPL23A RPL23A 1402 0.23 0.52 YES
12 RPSA RPSA RPSA 1419 0.23 0.54 YES
13 RPL10L RPL10L RPL10L 1959 0.18 0.53 YES
14 RPS15 RPS15 RPS15 1980 0.18 0.54 YES
15 RPS2 RPS2 RPS2 2078 0.17 0.55 YES
16 RPL41 RPL41 RPL41 2744 0.13 0.52 NO
17 RPL13 RPL13 RPL13 2769 0.13 0.53 NO
18 RPS5 RPS5 RPS5 3036 0.12 0.53 NO
19 RPLP0 RPLP0 RPLP0 3082 0.12 0.54 NO
20 RPL28 RPL28 RPL28 3385 0.11 0.53 NO
21 RPL29 RPL29 RPL29 3465 0.1 0.53 NO
22 RPL10 RPL10 RPL10 3629 0.098 0.53 NO
23 UBA52 UBA52 UBA52 3812 0.093 0.53 NO
24 RPL15 RPL15 RPL15 3927 0.09 0.53 NO
25 RPLP2 RPLP2 RPLP2 4182 0.083 0.52 NO
26 RPS21 RPS21 RPS21 4238 0.082 0.53 NO
27 RPS10 RPS10 RPS10 4703 0.071 0.51 NO
28 RPS3 RPS3 RPS3 4923 0.067 0.5 NO
29 RPL27 RPL27 RPL27 5134 0.062 0.5 NO
30 RPL8 RPL8 RPL8 5157 0.062 0.5 NO
31 RPS9 RPS9 RPS9 5163 0.062 0.5 NO
32 RPL36 RPL36 RPL36 5509 0.054 0.49 NO
33 RPL26L1 RPL26L1 RPL26L1 5535 0.054 0.49 NO
34 RPS4Y1 RPS4Y1 RPS4Y1 5608 0.052 0.49 NO
35 RPS16 RPS16 RPS16 5736 0.05 0.49 NO
36 RPL35 RPL35 RPL35 6052 0.045 0.48 NO
37 RPS6 RPS6 RPS6 6376 0.039 0.46 NO
38 FAU FAU FAU 6404 0.038 0.46 NO
39 RPLP1 RPLP1 RPLP1 6703 0.033 0.45 NO
40 RPS13 RPS13 RPS13 6801 0.032 0.45 NO
41 RPS8 RPS8 RPS8 6931 0.03 0.44 NO
42 RPL17 RPL17 RPL17 7252 0.024 0.43 NO
43 RPS11 RPS11 RPS11 7523 0.02 0.42 NO
44 RPL35A RPL35A RPL35A 7740 0.017 0.4 NO
45 RPL6 RPL6 RPL6 7958 0.014 0.39 NO
46 RPS15A RPS15A RPS15A 7971 0.013 0.39 NO
47 RPS19 RPS19 RPS19 8014 0.013 0.39 NO
48 RPS29 RPS29 RPS29 8178 0.01 0.38 NO
49 RPS4X RPS4X RPS4X 8222 0.0096 0.38 NO
50 RPL10A RPL10A RPL10A 8316 0.0083 0.38 NO
51 RPL3 RPL3 RPL3 8324 0.0081 0.38 NO
52 RPL38 RPL38 RPL38 8618 0.0041 0.36 NO
53 RPL7A RPL7A RPL7A 8644 0.0036 0.36 NO
54 RPL37A RPL37A RPL37A 8814 0.0011 0.35 NO
55 RPS17 RPS17 RPS17 8989 -0.0013 0.34 NO
56 MRPL13 MRPL13 MRPL13 9520 -0.0084 0.31 NO
57 RPL31 RPL31 RPL31 9695 -0.011 0.3 NO
58 RPL32 RPL32 RPL32 9800 -0.012 0.3 NO
59 RPL37 RPL37 RPL37 9940 -0.014 0.29 NO
60 RPL27A RPL27A RPL27A 10054 -0.016 0.29 NO
61 RPL34 RPL34 RPL34 10131 -0.017 0.29 NO
62 RPS23 RPS23 RPS23 10193 -0.018 0.28 NO
63 RPL22 RPL22 RPL22 10554 -0.023 0.27 NO
64 RPL5 RPL5 RPL5 10637 -0.024 0.26 NO
65 RPL36AL RPL36AL RPL36AL 10665 -0.025 0.26 NO
66 RPL23 RPL23 RPL23 10980 -0.029 0.25 NO
67 RPL30 RPL30 RPL30 11157 -0.031 0.24 NO
68 RPL19 RPL19 RPL19 11226 -0.032 0.24 NO
69 RPL11 RPL11 RPL11 11358 -0.035 0.24 NO
70 RPL4 RPL4 RPL4 12231 -0.047 0.19 NO
71 RPL14 RPL14 RPL14 12246 -0.047 0.2 NO
72 RPL13A RPL13A RPL13A 12279 -0.048 0.2 NO
73 RPS20 RPS20 RPS20 13196 -0.062 0.15 NO
74 RPL26 RPL26 RPL26 13398 -0.065 0.15 NO
75 RPS7 RPS7 RPS7 13551 -0.068 0.14 NO
76 RSL24D1 RSL24D1 RSL24D1 14565 -0.086 0.094 NO
77 RPS24 RPS24 RPS24 15907 -0.12 0.029 NO
78 RPL22L1 RPL22L1 RPL22L1 16032 -0.12 0.033 NO
79 RPL24 RPL24 RPL24 16045 -0.12 0.042 NO
80 RPS12 RPS12 RPS12 16059 -0.12 0.052 NO
81 RPS25 RPS25 RPS25 16085 -0.12 0.061 NO
82 RPS18 RPS18 RPS18 16134 -0.12 0.069 NO
83 RPS27L RPS27L RPS27L 16169 -0.12 0.077 NO
84 RPL12 RPL12 RPL12 16221 -0.12 0.085 NO
85 RPS27A RPS27A RPS27A 17022 -0.16 0.054 NO

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

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 LTC4S LTC4S LTC4S 278 0.67 0.11 YES
2 ALOX12 ALOX12 ALOX12 353 0.58 0.21 YES
3 PLA2G2A PLA2G2A PLA2G2A 1442 0.22 0.2 YES
4 PTGDS PTGDS PTGDS 1702 0.2 0.22 YES
5 PLA2G10 PLA2G10 PLA2G10 1810 0.19 0.25 YES
6 CYP4F2 CYP4F2 CYP4F2 1820 0.19 0.28 YES
7 CBR3 CBR3 CBR3 1996 0.17 0.3 YES
8 ALOX15 ALOX15 ALOX15 2105 0.17 0.33 YES
9 PLA2G2D PLA2G2D PLA2G2D 2172 0.16 0.36 YES
10 CYP2C18 CYP2C18 CYP2C18 2469 0.14 0.36 YES
11 GPX4 GPX4 GPX4 2578 0.14 0.38 YES
12 GPX1 GPX1 GPX1 2684 0.14 0.4 YES
13 GPX7 GPX7 GPX7 2747 0.13 0.43 YES
14 GPX3 GPX3 GPX3 2884 0.13 0.44 YES
15 ALOX12B ALOX12B ALOX12B 2927 0.12 0.46 YES
16 PLA2G12B PLA2G12B PLA2G12B 3159 0.11 0.47 YES
17 CYP2E1 CYP2E1 CYP2E1 3335 0.11 0.48 YES
18 PLA2G4E PLA2G4E PLA2G4E 3489 0.1 0.49 YES
19 CBR1 CBR1 CBR1 3513 0.1 0.51 YES
20 PTGES2 PTGES2 PTGES2 3588 0.1 0.52 YES
21 GGT1 GGT1 GGT1 3797 0.093 0.53 YES
22 GGT6 GGT6 GGT6 3827 0.092 0.55 YES
23 CYP2C9 CYP2C9 CYP2C9 3912 0.09 0.56 YES
24 ALOX15B ALOX15B ALOX15B 4074 0.086 0.56 YES
25 CYP2C19 CYP2C19 CYP2C19 4550 0.074 0.55 NO
26 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 4799 0.069 0.55 NO
27 PTGIS PTGIS PTGIS 5557 0.054 0.52 NO
28 PLA2G2F PLA2G2F PLA2G2F 5711 0.051 0.52 NO
29 CYP2B6 CYP2B6 CYP2B6 5752 0.05 0.53 NO
30 ALOX5 ALOX5 ALOX5 5887 0.048 0.53 NO
31 PLA2G1B PLA2G1B PLA2G1B 5983 0.046 0.53 NO
32 EPHX2 EPHX2 EPHX2 5992 0.046 0.54 NO
33 CYP4A11 CYP4A11 CYP4A11 6051 0.045 0.54 NO
34 PTGS1 PTGS1 PTGS1 6101 0.044 0.55 NO
35 GGT7 GGT7 GGT7 6539 0.036 0.53 NO
36 PTGS2 PTGS2 PTGS2 6540 0.036 0.54 NO
37 HPGDS HPGDS HPGDS 6903 0.03 0.52 NO
38 PLA2G3 PLA2G3 PLA2G3 6906 0.03 0.53 NO
39 PLA2G6 PLA2G6 PLA2G6 7047 0.028 0.53 NO
40 AKR1C3 AKR1C3 AKR1C3 7070 0.028 0.53 NO
41 TBXAS1 TBXAS1 TBXAS1 7399 0.022 0.52 NO
42 GPX2 GPX2 GPX2 7916 0.014 0.49 NO
43 PTGES PTGES PTGES 8397 0.0073 0.46 NO
44 CYP4F3 CYP4F3 CYP4F3 8660 0.0034 0.45 NO
45 CYP2C8 CYP2C8 CYP2C8 9318 -0.0056 0.42 NO
46 LTA4H LTA4H LTA4H 10841 -0.027 0.34 NO
47 GGT5 GGT5 GGT5 10877 -0.028 0.34 NO
48 PLA2G12A PLA2G12A PLA2G12A 10995 -0.029 0.34 NO
49 PLA2G4A PLA2G4A PLA2G4A 11107 -0.031 0.34 NO
50 PLA2G5 PLA2G5 PLA2G5 15496 -0.11 0.11 NO
51 CYP2U1 CYP2U1 CYP2U1 16676 -0.14 0.074 NO

Figure S75.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S76.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG RIBOSOME

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HLA-G HLA-G HLA-G 157 0.87 0.14 YES
2 HLA-DQA2 HLA-DQA2 HLA-DQA2 409 0.53 0.21 YES
3 HLA-DRB5 HLA-DRB5 HLA-DRB5 601 0.4 0.26 YES
4 IL10 IL10 IL10 1056 0.28 0.28 YES
5 HLA-DQA1 HLA-DQA1 HLA-DQA1 1080 0.27 0.33 YES
6 HLA-DRB1 HLA-DRB1 HLA-DRB1 1216 0.25 0.36 YES
7 CTLA4 CTLA4 CTLA4 1331 0.24 0.4 YES
8 HLA-DQB1 HLA-DQB1 HLA-DQB1 1486 0.22 0.42 YES
9 HLA-DPB1 HLA-DPB1 HLA-DPB1 1574 0.21 0.45 YES
10 HLA-DMB HLA-DMB HLA-DMB 1790 0.19 0.47 YES
11 CGA CGA CGA 1902 0.18 0.5 YES
12 CD80 CD80 CD80 1971 0.18 0.52 YES
13 GZMB GZMB GZMB 2011 0.17 0.55 YES
14 PRF1 PRF1 PRF1 2090 0.17 0.57 YES
15 HLA-DPA1 HLA-DPA1 HLA-DPA1 2280 0.16 0.58 YES
16 HLA-A HLA-A HLA-A 2646 0.14 0.59 YES
17 HLA-C HLA-C HLA-C 2647 0.14 0.61 YES
18 HLA-DOA HLA-DOA HLA-DOA 2700 0.13 0.63 YES
19 CD86 CD86 CD86 2746 0.13 0.65 YES
20 HLA-F HLA-F HLA-F 2759 0.13 0.67 YES
21 CD40 CD40 CD40 2799 0.13 0.69 YES
22 HLA-DRA HLA-DRA HLA-DRA 2877 0.13 0.7 YES
23 FASLG FASLG FASLG 2978 0.12 0.72 YES
24 HLA-DMA HLA-DMA HLA-DMA 3318 0.11 0.72 YES
25 CD40LG CD40LG CD40LG 3345 0.11 0.74 YES
26 HLA-B HLA-B HLA-B 3505 0.1 0.74 YES
27 HLA-DOB HLA-DOB HLA-DOB 3790 0.094 0.74 NO
28 HLA-E HLA-E HLA-E 4156 0.084 0.74 NO
29 TSHR TSHR TSHR 5151 0.062 0.69 NO
30 CD28 CD28 CD28 5420 0.056 0.69 NO
31 TPO TPO TPO 6099 0.044 0.66 NO
32 FAS FAS FAS 7865 0.015 0.56 NO
33 IL5 IL5 IL5 8878 0.00026 0.5 NO
34 TG TG TG 10829 -0.027 0.4 NO

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

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

genes ES table in pathway: KEGG COMPLEMENT AND COAGULATION CASCADES

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HLA-G HLA-G HLA-G 157 0.87 0.13 YES
2 HLA-DQA2 HLA-DQA2 HLA-DQA2 409 0.53 0.2 YES
3 HLA-DRB5 HLA-DRB5 HLA-DRB5 601 0.4 0.26 YES
4 HLA-DQA1 HLA-DQA1 HLA-DQA1 1080 0.27 0.27 YES
5 HLA-DRB1 HLA-DRB1 HLA-DRB1 1216 0.25 0.3 YES
6 HLA-DPB1 HLA-DPB1 HLA-DPB1 1574 0.21 0.32 YES
7 TNF TNF TNF 1672 0.2 0.35 YES
8 IL1B IL1B IL1B 1730 0.19 0.37 YES
9 HLA-DMB HLA-DMB HLA-DMB 1790 0.19 0.4 YES
10 PTPRN PTPRN PTPRN 1933 0.18 0.42 YES
11 CD80 CD80 CD80 1971 0.18 0.45 YES
12 GZMB GZMB GZMB 2011 0.17 0.47 YES
13 LTA LTA LTA 2035 0.17 0.5 YES
14 PRF1 PRF1 PRF1 2090 0.17 0.52 YES
15 IFNG IFNG IFNG 2160 0.16 0.55 YES
16 HLA-DPA1 HLA-DPA1 HLA-DPA1 2280 0.16 0.56 YES
17 HLA-A HLA-A HLA-A 2646 0.14 0.57 YES
18 HLA-C HLA-C HLA-C 2647 0.14 0.59 YES
19 HLA-DOA HLA-DOA HLA-DOA 2700 0.13 0.61 YES
20 CD86 CD86 CD86 2746 0.13 0.62 YES
21 HLA-F HLA-F HLA-F 2759 0.13 0.65 YES
22 HLA-DRA HLA-DRA HLA-DRA 2877 0.13 0.66 YES
23 FASLG FASLG FASLG 2978 0.12 0.67 YES
24 HLA-DMA HLA-DMA HLA-DMA 3318 0.11 0.67 YES
25 HLA-B HLA-B HLA-B 3505 0.1 0.68 YES
26 IL12A IL12A IL12A 3761 0.094 0.68 YES
27 HLA-DOB HLA-DOB HLA-DOB 3790 0.094 0.69 YES
28 IL1A IL1A IL1A 4049 0.087 0.69 YES
29 HLA-E HLA-E HLA-E 4156 0.084 0.7 YES
30 IL12B IL12B IL12B 4223 0.082 0.71 YES
31 CD28 CD28 CD28 5420 0.056 0.65 NO
32 GAD1 GAD1 GAD1 7409 0.022 0.54 NO
33 FAS FAS FAS 7865 0.015 0.52 NO
34 PTPRN2 PTPRN2 PTPRN2 12530 -0.052 0.27 NO
35 ICA1 ICA1 ICA1 13269 -0.063 0.24 NO
36 HSPD1 HSPD1 HSPD1 13308 -0.064 0.25 NO
37 CPE CPE CPE 14695 -0.088 0.18 NO

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

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG COMPLEMENT AND COAGULATION CASCADES, 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 = COAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = COAD-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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