GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in ACC-TP
Adrenocortical Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1TH8KTH
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 ACC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1TH8KTH
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 ACC-TP. This pipeline has the following features:

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

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

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

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

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

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

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 192
Number of samples: 79
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 ] 24
pheno.type: 2 - 4 :[ clus2 ] 14
pheno.type: 3 - 4 :[ clus3 ] 18
pheno.type: 4 - 4 :[ clus4 ] 23

For the expression subtypes of 17733 genes in 80 samples, GSEA found enriched gene sets in each cluster using 79 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA MPR PATHWAY, KEGG PYRIMIDINE METABOLISM, KEGG LYSINE DEGRADATION, KEGG SELENOAMINO ACID METABOLISM, KEGG PYRUVATE METABOLISM, KEGG RIBOSOME, KEGG RNA DEGRADATION, KEGG RNA POLYMERASE, KEGG DNA REPLICATION

    • And common core enriched genes are IFNG, POMP, PSMA1, PSMA3, PSMA4, PSMA5, PSMA6, PSMA8, PSMB1, PSMB11

  • clus2

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA VIP PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA WNT PATHWAY, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG MAPK SIGNALING PATHWAY, KEGG WNT SIGNALING PATHWAY

    • And common core enriched genes are CTNNB1, LEF1, BMP4, APC, BTRC, CCND1, CREBBP, CSNK1A1, FRAT1, FZD1

  • clus3

    • Top enriched gene sets are BIOCARTA AT1R PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA GH PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA CREB PATHWAY, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG O GLYCAN BIOSYNTHESIS, KEGG BUTANOATE METABOLISM

    • And common core enriched genes are CUL4A, CUL4B, ERCC8, CCNH, CDK7, ERCC2, ERCC4, ERCC5, GTF2H2, GTF2H3

  • clus4

    • Top enriched gene sets are BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA CARM ER PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA GH PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA GSK3 PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA KERATINOCYTE PATHWAY

    • And common core enriched genes are PIK3CG, PIK3R1, PTPN6, STAT5A, NFATC2, BCL2, FAS, FASLG, IKZF3, IL2RA

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 G1 PATHWAY 27 genes.ES.table 0.49 1.4 0.18 0.64 0.95 0.48 0.3 0.34 0.52 0.19
BIOCARTA MPR PATHWAY 32 genes.ES.table 0.43 1.4 0.12 0.58 0.95 0.41 0.18 0.33 0.47 0.15
KEGG PYRIMIDINE METABOLISM 97 genes.ES.table 0.28 1.2 0.23 0.89 1 0.26 0.16 0.22 0.78 0.35
KEGG LYSINE DEGRADATION 42 genes.ES.table 0.22 0.98 0.44 1 1 0.17 0.12 0.15 1 0.66
KEGG SELENOAMINO ACID METABOLISM 25 genes.ES.table 0.38 1.2 0.26 0.84 1 0.28 0.13 0.24 0.74 0.3
KEGG PYRUVATE METABOLISM 37 genes.ES.table 0.31 0.98 0.47 1 1 0.24 0.17 0.2 1 0.71
KEGG RIBOSOME 84 genes.ES.table 0.57 1.6 0.075 0.41 0.68 0.73 0.29 0.52 0.26 0.11
KEGG RNA DEGRADATION 56 genes.ES.table 0.29 1.4 0.12 0.5 0.9 0.38 0.26 0.28 0.38 0.11
KEGG RNA POLYMERASE 28 genes.ES.table 0.31 1.2 0.26 0.9 1 0.46 0.28 0.34 0.79 0.36
KEGG DNA REPLICATION 35 genes.ES.table 0.57 1.5 0.14 0.53 0.87 0.54 0.22 0.42 0.4 0.14
genes ES table in pathway: BIOCARTA G1 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 PSME4 PSME4 PSME4 1376 0.22 -0.01 YES
2 PSMD4 PSMD4 PSMD4 1650 0.2 0.034 YES
3 PSMB9 PSMB9 PSMB9 1983 0.18 0.068 YES
4 PSMD13 PSMD13 PSMD13 2328 0.16 0.095 YES
5 PSMC3 PSMC3 PSMC3 2489 0.15 0.13 YES
6 PSMD1 PSMD1 PSMD1 2660 0.14 0.16 YES
7 PSMA8 PSMA8 PSMA8 2734 0.14 0.2 YES
8 PSMB4 PSMB4 PSMB4 2757 0.13 0.24 YES
9 PSMD14 PSMD14 PSMD14 2916 0.13 0.27 YES
10 PSMC1 PSMC1 PSMC1 3248 0.12 0.28 YES
11 PSMC5 PSMC5 PSMC5 3270 0.11 0.32 YES
12 PSMA4 PSMA4 PSMA4 3457 0.11 0.34 YES
13 PSME2 PSME2 PSME2 3463 0.11 0.37 YES
14 PSMD11 PSMD11 PSMD11 3532 0.1 0.4 YES
15 PSMA1 PSMA1 PSMA1 3842 0.095 0.41 YES
16 PSMB5 PSMB5 PSMB5 3913 0.092 0.43 YES
17 PSMB3 PSMB3 PSMB3 4061 0.088 0.45 YES
18 PSMA5 PSMA5 PSMA5 4206 0.084 0.47 YES
19 PSMD2 PSMD2 PSMD2 4300 0.081 0.49 YES
20 PSMB11 PSMB11 PSMB11 4623 0.072 0.49 YES
21 PSMD12 PSMD12 PSMD12 4875 0.065 0.5 YES
22 PSMB7 PSMB7 PSMB7 5071 0.06 0.5 YES
23 POMP POMP POMP 5259 0.056 0.51 YES
24 PSMA6 PSMA6 PSMA6 5425 0.052 0.52 YES
25 PSMC6 PSMC6 PSMC6 5427 0.052 0.53 YES
26 PSMB1 PSMB1 PSMB1 5759 0.043 0.52 YES
27 PSMA3 PSMA3 PSMA3 5824 0.041 0.53 YES
28 PSME3 PSME3 PSME3 6028 0.036 0.53 YES
29 PSMD3 PSMD3 PSMD3 6039 0.036 0.54 YES
30 PSMC4 PSMC4 PSMC4 6156 0.034 0.55 YES
31 PSMD6 PSMD6 PSMD6 6170 0.033 0.56 YES
32 PSME1 PSME1 PSME1 6256 0.031 0.56 YES
33 IFNG IFNG IFNG 6322 0.029 0.57 YES
34 PSMB6 PSMB6 PSMB6 6329 0.029 0.57 YES
35 PSMB2 PSMB2 PSMB2 6872 0.017 0.55 NO
36 PSMA7 PSMA7 PSMA7 7461 0.0041 0.52 NO
37 PSMA2 PSMA2 PSMA2 7554 0.0021 0.51 NO
38 PSMF1 PSMF1 PSMF1 8465 -0.018 0.47 NO
39 PSMB8 PSMB8 PSMB8 8609 -0.021 0.46 NO
40 PSMD7 PSMD7 PSMD7 8689 -0.023 0.47 NO
41 PSMD8 PSMD8 PSMD8 8968 -0.029 0.46 NO
42 PSMC2 PSMC2 PSMC2 9757 -0.049 0.43 NO
43 SHFM1 SHFM1 SHFM1 10522 -0.068 0.41 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 G1 PATHWAY.

Figure S2.  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 MPR 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 POLE2 POLE2 POLE2 347 0.41 0.089 YES
2 NEIL1 NEIL1 NEIL1 613 0.33 0.16 YES
3 FEN1 FEN1 FEN1 687 0.32 0.24 YES
4 NEIL3 NEIL3 NEIL3 734 0.31 0.32 YES
5 POLE4 POLE4 POLE4 1451 0.22 0.34 YES
6 MUTYH MUTYH MUTYH 2039 0.17 0.35 YES
7 POLD3 POLD3 POLD3 2402 0.15 0.37 YES
8 POLD1 POLD1 POLD1 2471 0.15 0.41 YES
9 PARP1 PARP1 PARP1 2762 0.13 0.43 YES
10 NTHL1 NTHL1 NTHL1 2871 0.13 0.46 YES
11 POLD2 POLD2 POLD2 3619 0.1 0.44 YES
12 PARP2 PARP2 PARP2 3869 0.094 0.45 YES
13 OGG1 OGG1 OGG1 4185 0.085 0.46 YES
14 POLB POLB POLB 4561 0.073 0.45 YES
15 APEX1 APEX1 APEX1 4621 0.072 0.47 YES
16 TDG TDG TDG 4741 0.069 0.48 YES
17 LIG1 LIG1 LIG1 5040 0.061 0.48 YES
18 POLE3 POLE3 POLE3 5258 0.056 0.48 YES
19 PCNA PCNA PCNA 6243 0.032 0.44 NO
20 POLD4 POLD4 POLD4 6406 0.027 0.43 NO
21 MPG MPG MPG 6529 0.024 0.43 NO
22 POLE POLE POLE 6826 0.018 0.42 NO
23 SMUG1 SMUG1 SMUG1 7820 -0.004 0.37 NO
24 MBD4 MBD4 MBD4 8024 -0.0082 0.36 NO
25 POLL POLL POLL 8394 -0.017 0.34 NO
26 XRCC1 XRCC1 XRCC1 9523 -0.043 0.29 NO
27 UNG UNG UNG 9915 -0.053 0.28 NO
28 LIG3 LIG3 LIG3 10004 -0.055 0.29 NO
29 NEIL2 NEIL2 NEIL2 10762 -0.074 0.27 NO
30 PARP3 PARP3 PARP3 10782 -0.074 0.28 NO
31 PARP4 PARP4 PARP4 11490 -0.093 0.27 NO
32 APEX2 APEX2 APEX2 15978 -0.31 0.098 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 MPR PATHWAY.

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

genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 446 0.38 0.022 YES
2 RPS27A RPS27A RPS27A 1532 0.21 -0.014 YES
3 RPS7 RPS7 RPS7 1694 0.2 0.0018 YES
4 RPL37A RPL37A RPL37A 1726 0.19 0.024 YES
5 RPL27A RPL27A RPL27A 1760 0.19 0.046 YES
6 RPL27 RPL27 RPL27 1891 0.18 0.061 YES
7 RPL23A RPL23A RPL23A 2104 0.17 0.07 YES
8 RPS3 RPS3 RPS3 2214 0.16 0.084 YES
9 RPL31 RPL31 RPL31 2312 0.16 0.098 YES
10 RPS25 RPS25 RPS25 2368 0.15 0.11 YES
11 RPS18 RPS18 RPS18 2411 0.15 0.13 YES
12 RPL17 RPL17 RPL17 2456 0.15 0.15 YES
13 RPLP2 RPLP2 RPLP2 2540 0.14 0.16 YES
14 RPS29 RPS29 RPS29 2715 0.14 0.17 YES
15 RPSA RPSA RPSA 2849 0.13 0.18 YES
16 RPS13 RPS13 RPS13 2859 0.13 0.19 YES
17 RPS19 RPS19 RPS19 2868 0.13 0.21 YES
18 RPS12 RPS12 RPS12 2925 0.13 0.22 YES
19 RPS24 RPS24 RPS24 2954 0.13 0.23 YES
20 RPL36 RPL36 RPL36 2974 0.12 0.25 YES
21 RPLP1 RPLP1 RPLP1 2990 0.12 0.26 YES
22 RPS17 RPS17 RPS17 3027 0.12 0.28 YES
23 FAU FAU FAU 3183 0.12 0.28 YES
24 RPL29 RPL29 RPL29 3247 0.12 0.29 YES
25 RPL22 RPL22 RPL22 3374 0.11 0.3 YES
26 RPS8 RPS8 RPS8 3415 0.11 0.31 YES
27 RPL18A RPL18A RPL18A 3454 0.11 0.32 YES
28 RPL4 RPL4 RPL4 3459 0.11 0.34 YES
29 RPL35 RPL35 RPL35 3533 0.1 0.34 YES
30 RPS10 RPS10 RPS10 3548 0.1 0.36 YES
31 RPL32 RPL32 RPL32 3653 0.1 0.36 YES
32 RPS9 RPS9 RPS9 3655 0.1 0.38 YES
33 RPLP0 RPLP0 RPLP0 3724 0.099 0.38 YES
34 RPL11 RPL11 RPL11 3795 0.096 0.39 YES
35 RPS2 RPS2 RPS2 3875 0.094 0.4 YES
36 RPL22L1 RPL22L1 RPL22L1 3924 0.092 0.41 YES
37 RPL14 RPL14 RPL14 3983 0.091 0.42 YES
38 RPL35A RPL35A RPL35A 3987 0.091 0.43 YES
39 RPL13A RPL13A RPL13A 4140 0.086 0.43 YES
40 RPS27 RPS27 RPS27 4182 0.085 0.44 YES
41 RPL23 RPL23 RPL23 4220 0.084 0.44 YES
42 RPL8 RPL8 RPL8 4290 0.082 0.45 YES
43 RPL30 RPL30 RPL30 4293 0.082 0.46 YES
44 RPS20 RPS20 RPS20 4315 0.081 0.47 YES
45 RPS16 RPS16 RPS16 4332 0.08 0.48 YES
46 RPL12 RPL12 RPL12 4379 0.079 0.49 YES
47 RPL26 RPL26 RPL26 4544 0.074 0.49 YES
48 RPL19 RPL19 RPL19 4565 0.073 0.5 YES
49 RPS11 RPS11 RPS11 4597 0.072 0.5 YES
50 UBA52 UBA52 UBA52 4612 0.072 0.51 YES
51 RPL5 RPL5 RPL5 4634 0.072 0.52 YES
52 RPL24 RPL24 RPL24 4668 0.071 0.52 YES
53 RPS26 RPS26 RPS26 4736 0.069 0.53 YES
54 RPL3 RPL3 RPL3 4831 0.066 0.53 YES
55 RPS15 RPS15 RPS15 4845 0.066 0.54 YES
56 RPL28 RPL28 RPL28 4862 0.066 0.55 YES
57 RPL10A RPL10A RPL10A 4930 0.064 0.55 YES
58 RPL38 RPL38 RPL38 4979 0.062 0.56 YES
59 RPL7 RPL7 RPL7 5008 0.062 0.56 YES
60 RPL36AL RPL36AL RPL36AL 5086 0.06 0.57 YES
61 RPL7A RPL7A RPL7A 5145 0.059 0.57 YES
62 RPS3A RPS3A RPS3A 5454 0.051 0.56 NO
63 RPS15A RPS15A RPS15A 5465 0.051 0.56 NO
64 RPL13 RPL13 RPL13 5603 0.047 0.56 NO
65 RPL15 RPL15 RPL15 5625 0.046 0.57 NO
66 RPS5 RPS5 RPS5 5701 0.044 0.57 NO
67 RPL41 RPL41 RPL41 5783 0.042 0.57 NO
68 RPS21 RPS21 RPS21 6403 0.027 0.54 NO
69 RPS6 RPS6 RPS6 6663 0.022 0.52 NO
70 RPL37 RPL37 RPL37 6817 0.018 0.52 NO
71 MRPL13 MRPL13 MRPL13 6880 0.017 0.52 NO
72 RPL39 RPL39 RPL39 7139 0.011 0.5 NO
73 RPL6 RPL6 RPL6 7234 0.0091 0.5 NO
74 RSL24D1 RSL24D1 RSL24D1 7518 0.003 0.48 NO
75 RPS4X RPS4X RPS4X 7716 -0.0016 0.47 NO
76 RPL34 RPL34 RPL34 8102 -0.01 0.45 NO
77 RPL10 RPL10 RPL10 8258 -0.014 0.45 NO
78 RPS27L RPS27L RPS27L 8532 -0.02 0.43 NO
79 RPS23 RPS23 RPS23 8692 -0.023 0.43 NO
80 RPS28 RPS28 RPS28 10647 -0.071 0.32 NO
81 RPL26L1 RPL26L1 RPL26L1 10697 -0.072 0.33 NO
82 RPS4Y1 RPS4Y1 RPS4Y1 11213 -0.085 0.31 NO
83 RPL9 RPL9 RPL9 13932 -0.18 0.18 NO
84 RPL36A RPL36A RPL36A 15622 -0.28 0.12 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 PYRIMIDINE METABOLISM.

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

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 CDC20 CDC20 CDC20 83 0.57 0.026 YES
2 CDC25A CDC25A CDC25A 109 0.54 0.054 YES
3 BUB1 BUB1 BUB1 128 0.53 0.082 YES
4 CDC45 CDC45 CDC45 130 0.52 0.11 YES
5 E2F2 E2F2 E2F2 135 0.52 0.14 YES
6 ORC1L ORC1L ORC1L 263 0.44 0.16 YES
7 PLK1 PLK1 PLK1 285 0.43 0.18 YES
8 CCNB2 CCNB2 CCNB2 298 0.42 0.2 YES
9 BUB1B BUB1B BUB1B 351 0.4 0.22 YES
10 CDK1 CDK1 CDK1 365 0.4 0.24 YES
11 CDC7 CDC7 CDC7 469 0.37 0.25 YES
12 PTTG1 PTTG1 PTTG1 470 0.37 0.27 YES
13 CCNA2 CCNA2 CCNA2 505 0.36 0.29 YES
14 PKMYT1 PKMYT1 PKMYT1 590 0.34 0.3 YES
15 CDC25C CDC25C CDC25C 751 0.31 0.31 YES
16 CCNE2 CCNE2 CCNE2 779 0.3 0.33 YES
17 TTK TTK TTK 781 0.3 0.34 YES
18 CHEK2 CHEK2 CHEK2 920 0.28 0.35 YES
19 CHEK1 CHEK1 CHEK1 959 0.28 0.36 YES
20 ESPL1 ESPL1 ESPL1 997 0.27 0.38 YES
21 CDC6 CDC6 CDC6 1019 0.27 0.39 YES
22 CDK6 CDK6 CDK6 1021 0.27 0.4 YES
23 MCM6 MCM6 MCM6 1046 0.26 0.42 YES
24 MYC MYC MYC 1117 0.25 0.43 YES
25 MCM2 MCM2 MCM2 1182 0.25 0.44 YES
26 TGFB2 TGFB2 TGFB2 1233 0.24 0.45 YES
27 MCM5 MCM5 MCM5 1270 0.24 0.46 YES
28 SFN SFN SFN 1288 0.23 0.47 YES
29 GADD45A GADD45A GADD45A 1476 0.21 0.47 YES
30 SKP2 SKP2 SKP2 1495 0.21 0.48 YES
31 CCNB1 CCNB1 CCNB1 1566 0.21 0.49 YES
32 MCM7 MCM7 MCM7 1634 0.2 0.5 YES
33 RBX1 RBX1 RBX1 2125 0.17 0.48 YES
34 ORC2L ORC2L ORC2L 2184 0.16 0.48 YES
35 SMC1B SMC1B SMC1B 2385 0.15 0.48 YES
36 YWHAH YWHAH YWHAH 2515 0.14 0.48 YES
37 CDKN2C CDKN2C CDKN2C 2643 0.14 0.48 YES
38 MCM4 MCM4 MCM4 2694 0.14 0.48 YES
39 MAD2L2 MAD2L2 MAD2L2 2780 0.13 0.49 YES
40 CCND1 CCND1 CCND1 2782 0.13 0.49 YES
41 ORC6L ORC6L ORC6L 3016 0.12 0.49 YES
42 SMAD3 SMAD3 SMAD3 3021 0.12 0.49 YES
43 SMAD2 SMAD2 SMAD2 3060 0.12 0.5 YES
44 ANAPC1 ANAPC1 ANAPC1 3099 0.12 0.5 YES
45 MCM3 MCM3 MCM3 3110 0.12 0.51 YES
46 MAD1L1 MAD1L1 MAD1L1 3189 0.12 0.51 YES
47 WEE1 WEE1 WEE1 3241 0.12 0.51 YES
48 CDC25B CDC25B CDC25B 3272 0.11 0.52 YES
49 BUB3 BUB3 BUB3 3379 0.11 0.52 YES
50 E2F1 E2F1 E2F1 3398 0.11 0.52 YES
51 ANAPC11 ANAPC11 ANAPC11 3430 0.11 0.53 YES
52 CDC26 CDC26 CDC26 3732 0.099 0.52 NO
53 HDAC2 HDAC2 HDAC2 3754 0.098 0.52 NO
54 ORC4L ORC4L ORC4L 3852 0.095 0.52 NO
55 YWHAQ YWHAQ YWHAQ 3877 0.094 0.52 NO
56 MAD2L1 MAD2L1 MAD2L1 4086 0.088 0.52 NO
57 CDKN1C CDKN1C CDKN1C 4343 0.08 0.5 NO
58 CDKN2A CDKN2A CDKN2A 4437 0.077 0.5 NO
59 TFDP1 TFDP1 TFDP1 4472 0.076 0.51 NO
60 SMAD4 SMAD4 SMAD4 4814 0.067 0.49 NO
61 TGFB3 TGFB3 TGFB3 5229 0.056 0.47 NO
62 PRKDC PRKDC PRKDC 5251 0.056 0.47 NO
63 CDK2 CDK2 CDK2 5385 0.053 0.47 NO
64 ZBTB17 ZBTB17 ZBTB17 5435 0.052 0.47 NO
65 CDKN2D CDKN2D CDKN2D 5463 0.051 0.47 NO
66 CCNE1 CCNE1 CCNE1 6213 0.032 0.43 NO
67 PCNA PCNA PCNA 6243 0.032 0.43 NO
68 CDKN1A CDKN1A CDKN1A 6292 0.03 0.43 NO
69 MDM2 MDM2 MDM2 6349 0.029 0.42 NO
70 CDC16 CDC16 CDC16 6455 0.026 0.42 NO
71 ANAPC7 ANAPC7 ANAPC7 6541 0.024 0.42 NO
72 TGFB1 TGFB1 TGFB1 6567 0.024 0.42 NO
73 ORC3L ORC3L ORC3L 6893 0.016 0.4 NO
74 SMC3 SMC3 SMC3 6983 0.014 0.4 NO
75 TFDP2 TFDP2 TFDP2 7109 0.012 0.39 NO
76 CDK4 CDK4 CDK4 7239 0.0089 0.38 NO
77 TP53 TP53 TP53 7338 0.0068 0.38 NO
78 YWHAZ YWHAZ YWHAZ 7370 0.0061 0.38 NO
79 YWHAE YWHAE YWHAE 7472 0.0038 0.37 NO
80 CDC27 CDC27 CDC27 7522 0.0029 0.37 NO
81 HDAC1 HDAC1 HDAC1 7532 0.0027 0.37 NO
82 PTTG2 PTTG2 PTTG2 7572 0.0017 0.36 NO
83 E2F5 E2F5 E2F5 7675 -0.0004 0.36 NO
84 E2F4 E2F4 E2F4 8061 -0.0093 0.34 NO
85 CCND3 CCND3 CCND3 8164 -0.012 0.33 NO
86 GSK3B GSK3B GSK3B 8169 -0.012 0.33 NO
87 ANAPC2 ANAPC2 ANAPC2 8293 -0.014 0.33 NO
88 ATM ATM ATM 8503 -0.019 0.32 NO
89 ABL1 ABL1 ABL1 8542 -0.02 0.31 NO
90 ANAPC5 ANAPC5 ANAPC5 8543 -0.02 0.32 NO
91 RAD21 RAD21 RAD21 8761 -0.024 0.3 NO
92 SMC1A SMC1A SMC1A 8816 -0.026 0.3 NO
93 ANAPC10 ANAPC10 ANAPC10 8944 -0.028 0.3 NO
94 FZR1 FZR1 FZR1 9079 -0.032 0.29 NO
95 CCNA1 CCNA1 CCNA1 9427 -0.041 0.27 NO
96 ATR ATR ATR 9603 -0.045 0.27 NO
97 CDC14A CDC14A CDC14A 9684 -0.047 0.26 NO
98 YWHAB YWHAB YWHAB 9778 -0.05 0.26 NO
99 EP300 EP300 EP300 9891 -0.052 0.26 NO
100 CCNB3 CCNB3 CCNB3 10017 -0.055 0.25 NO
101 ORC5L ORC5L ORC5L 10091 -0.057 0.25 NO
102 ANAPC13 ANAPC13 ANAPC13 10165 -0.059 0.25 NO
103 CUL1 CUL1 CUL1 10600 -0.07 0.23 NO
104 E2F3 E2F3 E2F3 10696 -0.072 0.23 NO
105 CDKN1B CDKN1B CDKN1B 10878 -0.077 0.22 NO
106 CDC23 CDC23 CDC23 11409 -0.091 0.2 NO
107 STAG1 STAG1 STAG1 11500 -0.093 0.2 NO
108 CCNH CCNH CCNH 12171 -0.11 0.17 NO
109 RB1 RB1 RB1 12214 -0.11 0.17 NO
110 YWHAG YWHAG YWHAG 12323 -0.12 0.17 NO
111 CDC14B CDC14B CDC14B 12362 -0.12 0.17 NO
112 SKP1 SKP1 SKP1 12508 -0.12 0.17 NO
113 GADD45B GADD45B GADD45B 12597 -0.13 0.18 NO
114 ANAPC4 ANAPC4 ANAPC4 12869 -0.14 0.17 NO
115 CREBBP CREBBP CREBBP 12946 -0.14 0.17 NO
116 CDK7 CDK7 CDK7 13380 -0.15 0.15 NO
117 STAG2 STAG2 STAG2 13582 -0.16 0.15 NO
118 CDKN2B CDKN2B CDKN2B 13643 -0.16 0.16 NO
119 RBL1 RBL1 RBL1 13913 -0.18 0.15 NO
120 GADD45G GADD45G GADD45G 14893 -0.23 0.11 NO
121 CCND2 CCND2 CCND2 15253 -0.25 0.1 NO
122 RBL2 RBL2 RBL2 15586 -0.27 0.096 NO
123 WEE2 WEE2 WEE2 16994 -0.46 0.041 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 LYSINE DEGRADATION.

Figure S8.  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 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 HSPA6 HSPA6 HSPA6 402 0.39 0.018 YES
2 THOC4 THOC4 THOC4 1165 0.25 0.00095 YES
3 SF3B4 SF3B4 SF3B4 1350 0.23 0.014 YES
4 SNRPA1 SNRPA1 SNRPA1 1445 0.22 0.032 YES
5 SNRPG SNRPG SNRPG 1608 0.2 0.044 YES
6 EIF4A3 EIF4A3 EIF4A3 1627 0.2 0.064 YES
7 SNRPD1 SNRPD1 SNRPD1 1835 0.18 0.072 YES
8 PHF5A PHF5A PHF5A 1866 0.18 0.089 YES
9 SNRPE SNRPE SNRPE 2531 0.14 0.067 YES
10 SF3B14 SF3B14 SF3B14 2551 0.14 0.081 YES
11 RBM8A RBM8A RBM8A 2650 0.14 0.09 YES
12 SART1 SART1 SART1 2657 0.14 0.1 YES
13 PRPF3 PRPF3 PRPF3 2760 0.13 0.11 YES
14 PRPF40A PRPF40A PRPF40A 2840 0.13 0.12 YES
15 HSPA1B HSPA1B HSPA1B 2922 0.13 0.13 YES
16 SNRPD3 SNRPD3 SNRPD3 3125 0.12 0.13 YES
17 SNRNP40 SNRNP40 SNRNP40 3196 0.12 0.14 YES
18 HNRNPA3 HNRNPA3 HNRNPA3 3246 0.12 0.15 YES
19 PUF60 PUF60 PUF60 3308 0.11 0.16 YES
20 PRPF38A PRPF38A PRPF38A 3330 0.11 0.17 YES
21 SFRS7 SFRS7 SFRS7 3527 0.1 0.17 YES
22 SF3B2 SF3B2 SF3B2 3549 0.1 0.18 YES
23 CCDC12 CCDC12 CCDC12 3595 0.1 0.19 YES
24 SNRPC SNRPC SNRPC 3632 0.1 0.2 YES
25 LSM2 LSM2 LSM2 3773 0.097 0.2 YES
26 SNRNP27 SNRNP27 SNRNP27 3800 0.096 0.2 YES
27 USP39 USP39 USP39 3876 0.094 0.21 YES
28 LSM4 LSM4 LSM4 3964 0.091 0.22 YES
29 LSM3 LSM3 LSM3 3968 0.091 0.22 YES
30 DHX16 DHX16 DHX16 3986 0.091 0.23 YES
31 SMNDC1 SMNDC1 SMNDC1 3995 0.09 0.24 YES
32 NHP2L1 NHP2L1 NHP2L1 4024 0.089 0.25 YES
33 U2AF1 U2AF1 U2AF1 4040 0.089 0.26 YES
34 PRPF4 PRPF4 PRPF4 4068 0.088 0.27 YES
35 LSM7 LSM7 LSM7 4099 0.087 0.27 YES
36 THOC1 THOC1 THOC1 4166 0.085 0.28 YES
37 SFRS3 SFRS3 SFRS3 4370 0.08 0.28 YES
38 TXNL4A TXNL4A TXNL4A 4466 0.076 0.28 YES
39 CWC15 CWC15 CWC15 4477 0.076 0.29 YES
40 SF3A2 SF3A2 SF3A2 4581 0.073 0.29 YES
41 ISY1 ISY1 ISY1 4722 0.069 0.29 YES
42 SNRPA SNRPA SNRPA 4732 0.069 0.29 YES
43 SF3B5 SF3B5 SF3B5 4834 0.066 0.3 YES
44 SF3B1 SF3B1 SF3B1 4906 0.064 0.3 YES
45 HNRNPU HNRNPU HNRNPU 4929 0.064 0.3 YES
46 HSPA1A HSPA1A HSPA1A 4952 0.063 0.31 YES
47 SFRS2 SFRS2 SFRS2 4986 0.062 0.31 YES
48 NCBP1 NCBP1 NCBP1 5107 0.06 0.31 YES
49 SNRNP70 SNRNP70 SNRNP70 5183 0.058 0.32 YES
50 RBM17 RBM17 RBM17 5242 0.056 0.32 YES
51 CDC40 CDC40 CDC40 5453 0.051 0.31 YES
52 TRA2A TRA2A TRA2A 5552 0.048 0.31 YES
53 EFTUD2 EFTUD2 EFTUD2 5693 0.044 0.31 YES
54 TRA2B TRA2B TRA2B 5702 0.044 0.31 YES
55 SFRS1 SFRS1 SFRS1 5769 0.042 0.31 YES
56 HSPA1L HSPA1L HSPA1L 5793 0.042 0.32 YES
57 SNW1 SNW1 SNW1 5814 0.041 0.32 YES
58 BUD31 BUD31 BUD31 5833 0.041 0.32 YES
59 PCBP1 PCBP1 PCBP1 5854 0.04 0.32 YES
60 HNRNPM HNRNPM HNRNPM 5887 0.039 0.33 YES
61 SF3A3 SF3A3 SF3A3 5934 0.039 0.33 YES
62 HNRNPC HNRNPC HNRNPC 5948 0.038 0.33 YES
63 BAT1 BAT1 BAT1 5966 0.038 0.34 YES
64 PPIE PPIE PPIE 6038 0.036 0.34 YES
65 NAA38 NAA38 NAA38 6076 0.035 0.34 YES
66 SNRNP200 SNRNP200 SNRNP200 6090 0.035 0.34 YES
67 SFRS9 SFRS9 SFRS9 6097 0.035 0.34 YES
68 HNRNPA1 HNRNPA1 HNRNPA1 6175 0.033 0.34 NO
69 PRPF19 PRPF19 PRPF19 6299 0.03 0.34 NO
70 SFRS6 SFRS6 SFRS6 6411 0.027 0.34 NO
71 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 6430 0.027 0.34 NO
72 SNRPD2 SNRPD2 SNRPD2 6436 0.026 0.34 NO
73 SF3A1 SF3A1 SF3A1 6671 0.021 0.33 NO
74 MAGOH MAGOH MAGOH 6730 0.02 0.33 NO
75 DDX42 DDX42 DDX42 6752 0.02 0.33 NO
76 SNRPB SNRPB SNRPB 6803 0.018 0.33 NO
77 SNRPF SNRPF SNRPF 6855 0.017 0.33 NO
78 PPIH PPIH PPIH 7147 0.011 0.31 NO
79 LSM6 LSM6 LSM6 7273 0.0082 0.3 NO
80 HSPA8 HSPA8 HSPA8 7364 0.0062 0.3 NO
81 LSM5 LSM5 LSM5 7406 0.0051 0.3 NO
82 CDC5L CDC5L CDC5L 7463 0.004 0.3 NO
83 PPIL1 PPIL1 PPIL1 7499 0.0033 0.29 NO
84 DHX8 DHX8 DHX8 7600 0.0012 0.29 NO
85 DDX5 DDX5 DDX5 7622 0.00078 0.29 NO
86 ACIN1 ACIN1 ACIN1 7704 -0.0012 0.28 NO
87 HNRNPK HNRNPK HNRNPK 7857 -0.0047 0.27 NO
88 RBMX RBMX RBMX 8083 -0.0099 0.26 NO
89 SFRS13A SFRS13A SFRS13A 8115 -0.011 0.26 NO
90 SFRS4 SFRS4 SFRS4 8167 -0.012 0.26 NO
91 CTNNBL1 CTNNBL1 CTNNBL1 8196 -0.012 0.26 NO
92 RBM25 RBM25 RBM25 8306 -0.015 0.26 NO
93 PRPF38B PRPF38B PRPF38B 8320 -0.015 0.26 NO
94 PRPF31 PRPF31 PRPF31 8343 -0.015 0.26 NO
95 CHERP CHERP CHERP 8413 -0.017 0.25 NO
96 SF3B3 SF3B3 SF3B3 8548 -0.02 0.25 NO
97 XAB2 XAB2 XAB2 8613 -0.021 0.25 NO
98 PRPF8 PRPF8 PRPF8 8649 -0.022 0.25 NO
99 SFRS2B SFRS2B SFRS2B 8725 -0.024 0.25 NO
100 PRPF6 PRPF6 PRPF6 8984 -0.029 0.23 NO
101 DDX46 DDX46 DDX46 9000 -0.029 0.24 NO
102 PQBP1 PQBP1 PQBP1 9057 -0.031 0.24 NO
103 BCAS2 BCAS2 BCAS2 9110 -0.032 0.24 NO
104 SYF2 SYF2 SYF2 9152 -0.033 0.24 NO
105 DDX23 DDX23 DDX23 9246 -0.036 0.24 NO
106 SR140 SR140 SR140 9483 -0.042 0.23 NO
107 DHX38 DHX38 DHX38 9494 -0.042 0.23 NO
108 DHX15 DHX15 DHX15 9573 -0.044 0.23 NO
109 U2AF2 U2AF2 U2AF2 9664 -0.047 0.23 NO
110 PRPF18 PRPF18 PRPF18 9669 -0.047 0.24 NO
111 AQR AQR AQR 10566 -0.069 0.19 NO
112 WBP11 WBP11 WBP11 10812 -0.075 0.19 NO
113 SNRPB2 SNRPB2 SNRPB2 11037 -0.081 0.18 NO
114 TCERG1 TCERG1 TCERG1 11051 -0.081 0.19 NO
115 SFRS5 SFRS5 SFRS5 11237 -0.086 0.19 NO
116 ZMAT2 ZMAT2 ZMAT2 11428 -0.091 0.19 NO
117 RBM22 RBM22 RBM22 11684 -0.099 0.18 NO
118 MAGOHB MAGOHB MAGOHB 11729 -0.1 0.19 NO
119 PLRG1 PLRG1 PLRG1 12062 -0.11 0.18 NO
120 PRPF40B PRPF40B PRPF40B 12211 -0.11 0.19 NO
121 CRNKL1 CRNKL1 CRNKL1 12482 -0.12 0.18 NO
122 SLU7 SLU7 SLU7 12873 -0.14 0.18 NO
123 THOC3 THOC3 THOC3 13220 -0.15 0.17 NO
124 THOC2 THOC2 THOC2 13726 -0.17 0.16 NO
125 HSPA2 HSPA2 HSPA2 17472 -0.62 0.014 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 SELENOAMINO ACID METABOLISM.

Figure S10.  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 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 POLE2 POLE2 POLE2 347 0.41 0.069 YES
2 DNA2 DNA2 DNA2 652 0.32 0.12 YES
3 FEN1 FEN1 FEN1 687 0.32 0.19 YES
4 MCM6 MCM6 MCM6 1046 0.26 0.23 YES
5 MCM2 MCM2 MCM2 1182 0.25 0.27 YES
6 MCM5 MCM5 MCM5 1270 0.24 0.32 YES
7 POLE4 POLE4 POLE4 1451 0.22 0.36 YES
8 MCM7 MCM7 MCM7 1634 0.2 0.39 YES
9 RNASEH1 RNASEH1 RNASEH1 1849 0.18 0.42 YES
10 POLA2 POLA2 POLA2 2264 0.16 0.43 YES
11 POLD3 POLD3 POLD3 2402 0.15 0.45 YES
12 POLD1 POLD1 POLD1 2471 0.15 0.48 YES
13 MCM4 MCM4 MCM4 2694 0.14 0.5 YES
14 RFC4 RFC4 RFC4 2777 0.13 0.52 YES
15 MCM3 MCM3 MCM3 3110 0.12 0.53 YES
16 RFC2 RFC2 RFC2 3302 0.11 0.54 YES
17 PRIM2 PRIM2 PRIM2 3564 0.1 0.55 YES
18 POLD2 POLD2 POLD2 3619 0.1 0.57 YES
19 PRIM1 PRIM1 PRIM1 3936 0.092 0.57 YES
20 RNASEH2A RNASEH2A RNASEH2A 4529 0.074 0.55 NO
21 RFC3 RFC3 RFC3 4738 0.069 0.56 NO
22 LIG1 LIG1 LIG1 5040 0.061 0.55 NO
23 POLE3 POLE3 POLE3 5258 0.056 0.55 NO
24 RNASEH2B RNASEH2B RNASEH2B 6223 0.032 0.5 NO
25 PCNA PCNA PCNA 6243 0.032 0.51 NO
26 POLD4 POLD4 POLD4 6406 0.027 0.51 NO
27 RNASEH2C RNASEH2C RNASEH2C 6655 0.022 0.5 NO
28 RFC5 RFC5 RFC5 6738 0.02 0.5 NO
29 POLE POLE POLE 6826 0.018 0.5 NO
30 RPA3 RPA3 RPA3 8119 -0.011 0.43 NO
31 RPA1 RPA1 RPA1 8295 -0.014 0.42 NO
32 RPA2 RPA2 RPA2 8717 -0.023 0.4 NO
33 SSBP1 SSBP1 SSBP1 10423 -0.065 0.32 NO
34 RFC1 RFC1 RFC1 11238 -0.086 0.29 NO
35 RPA4 RPA4 RPA4 16301 -0.35 0.08 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 PYRUVATE METABOLISM.

Figure S12.  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 RIBOSOME

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 TP53I3 TP53I3 TP53I3 30 0.66 0.057 YES
2 TP73 TP73 TP73 104 0.55 0.1 YES
3 RRM2 RRM2 RRM2 132 0.52 0.15 YES
4 GTSE1 GTSE1 GTSE1 155 0.5 0.19 YES
5 CCNB2 CCNB2 CCNB2 298 0.42 0.22 YES
6 CDK1 CDK1 CDK1 365 0.4 0.25 YES
7 TP53AIP1 TP53AIP1 TP53AIP1 665 0.32 0.26 YES
8 CCNE2 CCNE2 CCNE2 779 0.3 0.28 YES
9 PERP PERP PERP 877 0.29 0.3 YES
10 CHEK2 CHEK2 CHEK2 920 0.28 0.33 YES
11 CHEK1 CHEK1 CHEK1 959 0.28 0.35 YES
12 CDK6 CDK6 CDK6 1021 0.27 0.37 YES
13 LRDD LRDD LRDD 1099 0.26 0.39 YES
14 SFN SFN SFN 1288 0.23 0.4 YES
15 GADD45A GADD45A GADD45A 1476 0.21 0.41 YES
16 CCNB1 CCNB1 CCNB1 1566 0.21 0.42 YES
17 CASP9 CASP9 CASP9 1585 0.2 0.44 YES
18 SERPINE1 SERPINE1 SERPINE1 1930 0.18 0.44 YES
19 TNFRSF10B TNFRSF10B TNFRSF10B 2307 0.16 0.43 YES
20 BID BID BID 2538 0.14 0.43 YES
21 CASP8 CASP8 CASP8 2574 0.14 0.44 YES
22 CASP3 CASP3 CASP3 2652 0.14 0.45 YES
23 CCND1 CCND1 CCND1 2782 0.13 0.45 YES
24 EI24 EI24 EI24 3058 0.12 0.45 NO
25 RFWD2 RFWD2 RFWD2 3192 0.12 0.45 NO
26 BAX BAX BAX 3652 0.1 0.43 NO
27 DDB2 DDB2 DDB2 3658 0.1 0.44 NO
28 THBS1 THBS1 THBS1 4238 0.083 0.42 NO
29 CDKN2A CDKN2A CDKN2A 4437 0.077 0.41 NO
30 SESN1 SESN1 SESN1 4734 0.069 0.4 NO
31 SHISA5 SHISA5 SHISA5 5140 0.059 0.38 NO
32 MDM4 MDM4 MDM4 5177 0.058 0.39 NO
33 CDK2 CDK2 CDK2 5385 0.053 0.38 NO
34 BBC3 BBC3 BBC3 5462 0.051 0.38 NO
35 SESN3 SESN3 SESN3 5883 0.04 0.36 NO
36 RRM2B RRM2B RRM2B 6168 0.033 0.34 NO
37 CCNE1 CCNE1 CCNE1 6213 0.032 0.35 NO
38 CDKN1A CDKN1A CDKN1A 6292 0.03 0.34 NO
39 MDM2 MDM2 MDM2 6349 0.029 0.34 NO
40 PTEN PTEN PTEN 6877 0.017 0.32 NO
41 SERPINB5 SERPINB5 SERPINB5 7224 0.0093 0.3 NO
42 CDK4 CDK4 CDK4 7239 0.0089 0.3 NO
43 TP53 TP53 TP53 7338 0.0068 0.29 NO
44 RPRM RPRM RPRM 7610 0.00096 0.28 NO
45 CCND3 CCND3 CCND3 8164 -0.012 0.25 NO
46 ATM ATM ATM 8503 -0.019 0.23 NO
47 CYCS CYCS CYCS 8663 -0.022 0.22 NO
48 PPM1D PPM1D PPM1D 8743 -0.024 0.22 NO
49 IGFBP3 IGFBP3 IGFBP3 8849 -0.026 0.22 NO
50 ATR ATR ATR 9603 -0.045 0.18 NO
51 CCNB3 CCNB3 CCNB3 10017 -0.055 0.16 NO
52 SESN2 SESN2 SESN2 10923 -0.078 0.11 NO
53 TSC2 TSC2 TSC2 11005 -0.08 0.12 NO
54 CCNG1 CCNG1 CCNG1 11741 -0.1 0.084 NO
55 FAS FAS FAS 12535 -0.12 0.05 NO
56 GADD45B GADD45B GADD45B 12597 -0.13 0.058 NO
57 BAI1 BAI1 BAI1 12947 -0.14 0.05 NO
58 SIAH1 SIAH1 SIAH1 13595 -0.16 0.028 NO
59 RCHY1 RCHY1 RCHY1 13686 -0.17 0.038 NO
60 APAF1 APAF1 APAF1 14034 -0.18 0.034 NO
61 ZMAT3 ZMAT3 ZMAT3 14728 -0.22 0.015 NO
62 GADD45G GADD45G GADD45G 14893 -0.23 0.026 NO
63 CCND2 CCND2 CCND2 15253 -0.25 0.027 NO
64 CCNG2 CCNG2 CCNG2 15263 -0.25 0.049 NO
65 PMAIP1 PMAIP1 PMAIP1 15519 -0.27 0.059 NO
66 IGF1 IGF1 IGF1 16389 -0.36 0.041 NO
67 CD82 CD82 CD82 16538 -0.38 0.067 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 RIBOSOME.

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

genes ES table in pathway: KEGG RNA DEGRADATION

Table 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 EXOSC8 EXOSC8 EXOSC8 1030 0.27 -0.0038 YES
2 ENO3 ENO3 ENO3 1359 0.23 0.024 YES
3 RQCD1 RQCD1 RQCD1 1468 0.21 0.062 YES
4 HSPD1 HSPD1 HSPD1 1937 0.18 0.072 YES
5 DCPS DCPS DCPS 1964 0.18 0.11 YES
6 EXOSC4 EXOSC4 EXOSC4 2570 0.14 0.1 YES
7 EXOSC1 EXOSC1 EXOSC1 2798 0.13 0.12 YES
8 EXOSC2 EXOSC2 EXOSC2 3037 0.12 0.13 YES
9 PATL1 PATL1 PATL1 3147 0.12 0.14 YES
10 EDC3 EDC3 EDC3 3229 0.12 0.16 YES
11 ENO1 ENO1 ENO1 3604 0.1 0.16 YES
12 EXOSC6 EXOSC6 EXOSC6 3683 0.1 0.18 YES
13 LSM2 LSM2 LSM2 3773 0.097 0.2 YES
14 LSM4 LSM4 LSM4 3964 0.091 0.2 YES
15 LSM3 LSM3 LSM3 3968 0.091 0.22 YES
16 LSM1 LSM1 LSM1 4077 0.088 0.23 YES
17 LSM7 LSM7 LSM7 4099 0.087 0.25 YES
18 EXOSC7 EXOSC7 EXOSC7 4167 0.085 0.26 YES
19 PNPT1 PNPT1 PNPT1 4237 0.083 0.28 YES
20 CNOT3 CNOT3 CNOT3 4406 0.078 0.28 YES
21 PAPOLG PAPOLG PAPOLG 4539 0.074 0.29 YES
22 DCP2 DCP2 DCP2 4889 0.065 0.28 NO
23 C1D C1D C1D 5109 0.06 0.28 NO
24 EXOSC10 EXOSC10 EXOSC10 5517 0.05 0.27 NO
25 EXOSC3 EXOSC3 EXOSC3 5588 0.047 0.28 NO
26 CNOT10 CNOT10 CNOT10 5886 0.039 0.27 NO
27 NAA38 NAA38 NAA38 6076 0.035 0.26 NO
28 EDC4 EDC4 EDC4 6352 0.029 0.26 NO
29 CNOT2 CNOT2 CNOT2 6457 0.026 0.25 NO
30 ENO2 ENO2 ENO2 7041 0.013 0.22 NO
31 WDR61 WDR61 WDR61 7173 0.01 0.22 NO
32 LSM6 LSM6 LSM6 7273 0.0082 0.22 NO
33 LSM5 LSM5 LSM5 7406 0.0051 0.21 NO
34 EXOSC9 EXOSC9 EXOSC9 7576 0.0017 0.2 NO
35 SKIV2L SKIV2L SKIV2L 7753 -0.0024 0.19 NO
36 DCP1A DCP1A DCP1A 7847 -0.0045 0.18 NO
37 CNOT7 CNOT7 CNOT7 7882 -0.0053 0.18 NO
38 EXOSC5 EXOSC5 EXOSC5 7999 -0.0077 0.18 NO
39 PAPOLA PAPOLA PAPOLA 8150 -0.011 0.17 NO
40 CNOT6L CNOT6L CNOT6L 8634 -0.022 0.15 NO
41 DIS3 DIS3 DIS3 8726 -0.024 0.15 NO
42 CNOT1 CNOT1 CNOT1 8798 -0.025 0.15 NO
43 DDX6 DDX6 DDX6 9368 -0.039 0.13 NO
44 CNOT6 CNOT6 CNOT6 10018 -0.055 0.1 NO
45 XRN1 XRN1 XRN1 10457 -0.066 0.09 NO
46 PAPOLB PAPOLB PAPOLB 10759 -0.074 0.088 NO
47 SKIV2L2 SKIV2L2 SKIV2L2 11091 -0.082 0.087 NO
48 PARN PARN PARN 11123 -0.083 0.1 NO
49 MPHOSPH6 MPHOSPH6 MPHOSPH6 11754 -0.1 0.087 NO
50 ZCCHC7 ZCCHC7 ZCCHC7 12053 -0.11 0.092 NO
51 XRN2 XRN2 XRN2 12850 -0.13 0.075 NO
52 PAPD7 PAPD7 PAPD7 13017 -0.14 0.094 NO
53 DCP1B DCP1B DCP1B 13910 -0.18 0.079 NO
54 HSPA9 HSPA9 HSPA9 13961 -0.18 0.11 NO
55 CNOT4 CNOT4 CNOT4 14389 -0.2 0.13 NO
56 TTC37 TTC37 TTC37 15769 -0.29 0.11 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 RNA DEGRADATION.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA DEGRADATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG RNA POLYMERASE

Table 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 CDC25A CDC25A CDC25A 109 0.54 0.18 YES
2 CDK1 CDK1 CDK1 365 0.4 0.3 YES
3 CDK6 CDK6 CDK6 1021 0.27 0.36 YES
4 TGFB2 TGFB2 TGFB2 1233 0.24 0.42 YES
5 SKP2 SKP2 SKP2 1495 0.21 0.48 YES
6 CCND1 CCND1 CCND1 2782 0.13 0.46 YES
7 SMAD3 SMAD3 SMAD3 3021 0.12 0.48 YES
8 DHFR DHFR DHFR 4181 0.085 0.45 YES
9 CDKN2A CDKN2A CDKN2A 4437 0.077 0.46 YES
10 TFDP1 TFDP1 TFDP1 4472 0.076 0.48 YES
11 SMAD4 SMAD4 SMAD4 4814 0.067 0.49 YES
12 TGFB3 TGFB3 TGFB3 5229 0.056 0.48 YES
13 CDK2 CDK2 CDK2 5385 0.053 0.49 YES
14 CCNE1 CCNE1 CCNE1 6213 0.032 0.46 NO
15 CDKN1A CDKN1A CDKN1A 6292 0.03 0.46 NO
16 TGFB1 TGFB1 TGFB1 6567 0.024 0.46 NO
17 CDK4 CDK4 CDK4 7239 0.0089 0.42 NO
18 TP53 TP53 TP53 7338 0.0068 0.42 NO
19 HDAC1 HDAC1 HDAC1 7532 0.0027 0.41 NO
20 GSK3B GSK3B GSK3B 8169 -0.012 0.38 NO
21 ATM ATM ATM 8503 -0.019 0.36 NO
22 ABL1 ABL1 ABL1 8542 -0.02 0.37 NO
23 CCNA1 CCNA1 CCNA1 9427 -0.041 0.33 NO
24 ATR ATR ATR 9603 -0.045 0.34 NO
25 CDKN1B CDKN1B CDKN1B 10878 -0.077 0.29 NO
26 RB1 RB1 RB1 12214 -0.11 0.26 NO
27 CDKN2B CDKN2B CDKN2B 13643 -0.16 0.23 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 RNA POLYMERASE.

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

genes ES table in pathway: KEGG DNA REPLICATION

Table 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 CDK1 CDK1 CDK1 365 0.4 0.071 YES
2 CDC25C CDC25C CDC25C 751 0.31 0.12 YES
3 RPS6KA1 RPS6KA1 RPS6KA1 1114 0.25 0.16 YES
4 HRAS HRAS HRAS 1160 0.25 0.21 YES
5 ACTA1 ACTA1 ACTA1 1456 0.22 0.24 YES
6 ARPC2 ARPC2 ARPC2 1561 0.21 0.28 YES
7 CCNB1 CCNB1 CCNB1 1566 0.21 0.33 YES
8 ACTR3 ACTR3 ACTR3 2128 0.17 0.34 YES
9 PAQR7 PAQR7 PAQR7 2301 0.16 0.36 YES
10 ARPC1B ARPC1B ARPC1B 2607 0.14 0.38 YES
11 PAQR5 PAQR5 PAQR5 2725 0.14 0.4 YES
12 ARPC5 ARPC5 ARPC5 3068 0.12 0.41 YES
13 ARPC4 ARPC4 ARPC4 3282 0.11 0.42 YES
14 ACTR2 ACTR2 ACTR2 4403 0.079 0.38 NO
15 PRKAR2B PRKAR2B PRKAR2B 5300 0.055 0.34 NO
16 PIN1 PIN1 PIN1 5393 0.053 0.35 NO
17 MAPK1 MAPK1 MAPK1 5704 0.044 0.34 NO
18 GNB1 GNB1 GNB1 5711 0.044 0.35 NO
19 ARPC1A ARPC1A ARPC1A 8519 -0.019 0.2 NO
20 CAP1 CAP1 CAP1 8864 -0.027 0.18 NO
21 PRKAR1B PRKAR1B PRKAR1B 8969 -0.029 0.18 NO
22 ARPC3 ARPC3 ARPC3 10140 -0.058 0.13 NO
23 PRKACB PRKACB PRKACB 10493 -0.067 0.13 NO
24 MAPK3 MAPK3 MAPK3 10570 -0.069 0.14 NO
25 GNAS GNAS GNAS 10723 -0.073 0.15 NO
26 PRKAR1A PRKAR1A PRKAR1A 10768 -0.074 0.16 NO
27 PRKAR2A PRKAR2A PRKAR2A 10996 -0.08 0.17 NO
28 PGR PGR PGR 11313 -0.088 0.17 NO
29 SRC SRC SRC 13200 -0.15 0.095 NO
30 GNAI1 GNAI1 GNAI1 13465 -0.16 0.12 NO
31 MYT1 MYT1 MYT1 15487 -0.27 0.062 NO
32 PRKACG PRKACG PRKACG 15671 -0.28 0.12 NO

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

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA NO1 PATHWAY 27 genes.ES.table 0.59 1.6 0.024 0.8 0.65 0.33 0.15 0.28 0.48 0.29
BIOCARTA AGR PATHWAY 33 genes.ES.table 0.39 1.3 0.16 0.68 0.99 0.24 0.12 0.21 0.6 0.19
BIOCARTA ALK PATHWAY 34 genes.ES.table 0.52 1.5 0.028 0.8 0.81 0.29 0.21 0.23 0.56 0.29
BIOCARTA VIP PATHWAY 25 genes.ES.table 0.48 1.4 0.13 0.65 0.95 0.44 0.33 0.3 0.52 0.19
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.38 1.3 0.16 0.63 0.98 0.12 0.091 0.11 0.55 0.16
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.52 1.8 0.013 0.53 0.34 0.6 0.38 0.37 0 0.19
KEGG CYSTEINE AND METHIONINE METABOLISM 32 genes.ES.table 0.43 1.4 0.08 0.65 0.94 0.16 0.1 0.14 0.51 0.2
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE 25 genes.ES.table 0.46 1.3 0.16 0.61 0.98 0.2 0.13 0.18 0.53 0.15
KEGG MAPK SIGNALING PATHWAY 246 genes.ES.table 0.34 1.3 0.064 0.66 0.97 0.22 0.16 0.19 0.56 0.18
KEGG WNT SIGNALING PATHWAY 144 genes.ES.table 0.39 1.5 0.038 0.84 0.91 0.33 0.22 0.26 0.64 0.31
genes ES table in pathway: BIOCARTA NO1 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 WIF1 WIF1 WIF1 204 0.57 0.19 YES
2 LEF1 LEF1 LEF1 218 0.57 0.39 YES
3 TLE1 TLE1 TLE1 2162 0.22 0.35 YES
4 MYC MYC MYC 2845 0.18 0.38 YES
5 CTNNB1 CTNNB1 CTNNB1 3473 0.15 0.4 YES
6 CCND1 CCND1 CCND1 3579 0.14 0.44 YES
7 FRAT1 FRAT1 FRAT1 4165 0.12 0.45 YES
8 BTRC BTRC BTRC 4421 0.11 0.48 YES
9 APC APC APC 5010 0.097 0.48 YES
10 GSK3B GSK3B GSK3B 5332 0.088 0.49 YES
11 FZD1 FZD1 FZD1 5728 0.078 0.49 YES
12 CSNK1A1 CSNK1A1 CSNK1A1 5853 0.075 0.51 YES
13 WNT1 WNT1 WNT1 6283 0.066 0.51 YES
14 NLK NLK NLK 6569 0.059 0.52 YES
15 CREBBP CREBBP CREBBP 6766 0.055 0.52 YES
16 CSNK2A1 CSNK2A1 CSNK2A1 8245 0.026 0.45 NO
17 AXIN1 AXIN1 AXIN1 8325 0.025 0.45 NO
18 MAP3K7 MAP3K7 MAP3K7 9085 0.011 0.41 NO
19 PPP2CA PPP2CA PPP2CA 9144 0.0098 0.41 NO
20 CSNK1D CSNK1D CSNK1D 9591 0.0015 0.39 NO
21 CTBP1 CTBP1 CTBP1 10485 -0.016 0.34 NO
22 SMAD4 SMAD4 SMAD4 10531 -0.017 0.35 NO
23 DVL1 DVL1 DVL1 11135 -0.028 0.32 NO
24 TAB1 TAB1 TAB1 11317 -0.032 0.32 NO
25 HDAC1 HDAC1 HDAC1 14183 -0.11 0.2 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 NO1 PATHWAY.

Figure S22.  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 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 PDE2A PDE2A PDE2A 54 0.73 0.18 YES
2 RYR2 RYR2 RYR2 589 0.42 0.26 YES
3 SLC7A1 SLC7A1 SLC7A1 1092 0.33 0.31 YES
4 PRKAR1B PRKAR1B PRKAR1B 1343 0.3 0.37 YES
5 PDE3A PDE3A PDE3A 1533 0.28 0.43 YES
6 PRKAR2B PRKAR2B PRKAR2B 1609 0.27 0.5 YES
7 PRKG1 PRKG1 PRKG1 1808 0.25 0.55 YES
8 PDE3B PDE3B PDE3B 2652 0.19 0.55 YES
9 PRKAR2A PRKAR2A PRKAR2A 2689 0.19 0.59 YES
10 FLT1 FLT1 FLT1 5329 0.088 0.46 NO
11 PRKACG PRKACG PRKACG 5438 0.085 0.48 NO
12 VEGFA VEGFA VEGFA 5499 0.084 0.5 NO
13 CALM1 CALM1 CALM1 7458 0.042 0.4 NO
14 CALM3 CALM3 CALM3 8416 0.023 0.35 NO
15 AKT1 AKT1 AKT1 8859 0.015 0.33 NO
16 CALM2 CALM2 CALM2 8948 0.014 0.33 NO
17 PRKAR1A PRKAR1A PRKAR1A 9822 -0.0028 0.28 NO
18 HSP90AA1 HSP90AA1 HSP90AA1 10070 -0.0077 0.26 NO
19 PRKACB PRKACB PRKACB 10326 -0.012 0.25 NO
20 KNG1 KNG1 KNG1 10603 -0.018 0.24 NO
21 KDR KDR KDR 10775 -0.021 0.24 NO
22 NOS3 NOS3 NOS3 12342 -0.054 0.16 NO
23 FLT4 FLT4 FLT4 12359 -0.055 0.18 NO
24 PRKG2 PRKG2 PRKG2 13074 -0.072 0.15 NO
25 ACTA1 ACTA1 ACTA1 14350 -0.11 0.11 NO
26 BDKRB2 BDKRB2 BDKRB2 14719 -0.13 0.12 NO
27 CHRNA1 CHRNA1 CHRNA1 15744 -0.19 0.11 NO

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

Figure S24.  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 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 WNT4 WNT4 WNT4 108 0.65 0.055 YES
2 LEF1 LEF1 LEF1 218 0.57 0.1 YES
3 AXIN2 AXIN2 AXIN2 350 0.5 0.14 YES
4 GLI1 GLI1 GLI1 368 0.49 0.19 YES
5 SHH SHH SHH 487 0.46 0.22 YES
6 BMP4 BMP4 BMP4 556 0.43 0.26 YES
7 SMO SMO SMO 656 0.41 0.29 YES
8 WNT9A WNT9A WNT9A 1076 0.34 0.3 YES
9 TCF7 TCF7 TCF7 1094 0.33 0.33 YES
10 FZD10 FZD10 FZD10 1125 0.33 0.36 YES
11 WNT10B WNT10B WNT10B 1336 0.3 0.38 YES
12 FZD7 FZD7 FZD7 1362 0.3 0.4 YES
13 FZD6 FZD6 FZD6 1551 0.28 0.42 YES
14 PTCH2 PTCH2 PTCH2 1585 0.28 0.44 YES
15 FZD9 FZD9 FZD9 1621 0.27 0.46 YES
16 GLI3 GLI3 GLI3 1651 0.27 0.49 YES
17 HHIP HHIP HHIP 2052 0.23 0.49 YES
18 APC2 APC2 APC2 2133 0.23 0.5 YES
19 PTCH1 PTCH1 PTCH1 2185 0.22 0.52 YES
20 WNT5A WNT5A WNT5A 2446 0.2 0.52 YES
21 FZD8 FZD8 FZD8 2592 0.2 0.54 YES
22 WNT3 WNT3 WNT3 2981 0.17 0.53 YES
23 TCF7L2 TCF7L2 TCF7L2 3024 0.17 0.54 YES
24 WNT16 WNT16 WNT16 3241 0.16 0.55 YES
25 WNT2 WNT2 WNT2 3359 0.15 0.55 YES
26 CTNNB1 CTNNB1 CTNNB1 3473 0.15 0.56 YES
27 GLI2 GLI2 GLI2 4049 0.13 0.54 NO
28 TCF7L1 TCF7L1 TCF7L1 4210 0.12 0.54 NO
29 WNT6 WNT6 WNT6 4856 0.1 0.52 NO
30 APC APC APC 5010 0.097 0.52 NO
31 SUFU SUFU SUFU 5171 0.092 0.52 NO
32 GSK3B GSK3B GSK3B 5332 0.088 0.52 NO
33 TP53 TP53 TP53 5427 0.086 0.52 NO
34 FZD3 FZD3 FZD3 5537 0.082 0.52 NO
35 WNT11 WNT11 WNT11 5672 0.08 0.52 NO
36 FZD1 FZD1 FZD1 5728 0.078 0.52 NO
37 DVL3 DVL3 DVL3 5971 0.073 0.52 NO
38 WNT1 WNT1 WNT1 6283 0.066 0.5 NO
39 WNT7B WNT7B WNT7B 6321 0.065 0.51 NO
40 BMP2 BMP2 BMP2 6924 0.052 0.48 NO
41 FZD5 FZD5 FZD5 7375 0.043 0.46 NO
42 AXIN1 AXIN1 AXIN1 8325 0.025 0.41 NO
43 WNT8B WNT8B WNT8B 9877 -0.004 0.32 NO
44 DVL1 DVL1 DVL1 11135 -0.028 0.25 NO
45 DVL2 DVL2 DVL2 12119 -0.049 0.2 NO
46 WNT10A WNT10A WNT10A 12752 -0.064 0.17 NO
47 STK36 STK36 STK36 12829 -0.066 0.17 NO
48 FZD2 FZD2 FZD2 12974 -0.07 0.17 NO
49 FZD4 FZD4 FZD4 13521 -0.086 0.15 NO
50 WNT2B WNT2B WNT2B 14533 -0.12 0.1 NO
51 WNT9B WNT9B WNT9B 15392 -0.17 0.068 NO
52 WNT7A WNT7A WNT7A 15580 -0.18 0.074 NO
53 WNT5B WNT5B WNT5B 17580 -0.5 0.0078 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 ALK PATHWAY.

Figure S26.  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 VIP 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 CHRD CHRD CHRD 144 0.62 0.13 YES
2 TGFB2 TGFB2 TGFB2 299 0.52 0.24 YES
3 NOG NOG NOG 395 0.48 0.34 YES
4 BMP4 BMP4 BMP4 556 0.43 0.42 YES
5 BMP7 BMP7 BMP7 1029 0.34 0.47 YES
6 NKX2-5 NKX2-5 NKX2-5 1873 0.25 0.48 YES
7 TGFB3 TGFB3 TGFB3 2437 0.2 0.5 YES
8 CTNNB1 CTNNB1 CTNNB1 3473 0.15 0.47 YES
9 RFC1 RFC1 RFC1 3656 0.14 0.49 YES
10 SMAD5 SMAD5 SMAD5 3710 0.14 0.52 YES
11 SMAD1 SMAD1 SMAD1 4907 0.1 0.47 NO
12 APC APC APC 5010 0.097 0.49 NO
13 GSK3B GSK3B GSK3B 5332 0.088 0.49 NO
14 FZD1 FZD1 FZD1 5728 0.078 0.48 NO
15 ATF2 ATF2 ATF2 5739 0.078 0.5 NO
16 BMPR1A BMPR1A BMPR1A 5987 0.072 0.5 NO
17 WNT1 WNT1 WNT1 6283 0.066 0.5 NO
18 BMP2 BMP2 BMP2 6924 0.052 0.48 NO
19 HNF1A HNF1A HNF1A 7956 0.032 0.43 NO
20 GATA4 GATA4 GATA4 7959 0.032 0.43 NO
21 BMPR2 BMPR2 BMPR2 7999 0.031 0.44 NO
22 AXIN1 AXIN1 AXIN1 8325 0.025 0.42 NO
23 NPPB NPPB NPPB 8726 0.018 0.41 NO
24 MAP3K7 MAP3K7 MAP3K7 9085 0.011 0.39 NO
25 TGFBR2 TGFBR2 TGFBR2 9502 0.003 0.36 NO
26 SMAD6 SMAD6 SMAD6 9791 -0.0024 0.35 NO
27 SMAD4 SMAD4 SMAD4 10531 -0.017 0.31 NO
28 MYL2 MYL2 MYL2 10625 -0.019 0.31 NO
29 TGFBR1 TGFBR1 TGFBR1 10908 -0.024 0.3 NO
30 TGFBR3 TGFBR3 TGFBR3 11034 -0.026 0.3 NO
31 DVL1 DVL1 DVL1 11135 -0.028 0.3 NO
32 TGFB1 TGFB1 TGFB1 12082 -0.048 0.26 NO
33 ACVR1 ACVR1 ACVR1 13232 -0.077 0.21 NO
34 NPPA NPPA NPPA 15905 -0.21 0.1 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 VIP PATHWAY.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA VIP 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 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 TAS2R31 TAS2R31 TAS2R31 48 0.76 0.076 YES
2 CACNA1B CACNA1B CACNA1B 84 0.67 0.14 YES
3 TAS2R14 TAS2R14 TAS2R14 97 0.66 0.21 YES
4 TAS2R46 TAS2R46 TAS2R46 327 0.51 0.25 YES
5 TAS2R43 TAS2R43 TAS2R43 349 0.5 0.3 YES
6 KCNB1 KCNB1 KCNB1 408 0.48 0.35 YES
7 TAS2R10 TAS2R10 TAS2R10 431 0.47 0.4 YES
8 GNB3 GNB3 GNB3 535 0.44 0.44 YES
9 TAS2R19 TAS2R19 TAS2R19 536 0.44 0.48 YES
10 TAS2R13 TAS2R13 TAS2R13 660 0.41 0.52 YES
11 TAS2R42 TAS2R42 TAS2R42 757 0.39 0.55 YES
12 TAS2R20 TAS2R20 TAS2R20 1469 0.28 0.54 YES
13 TAS2R50 TAS2R50 TAS2R50 1696 0.26 0.56 YES
14 CACNA1A CACNA1A CACNA1A 2413 0.21 0.54 YES
15 TAS2R5 TAS2R5 TAS2R5 2414 0.21 0.56 YES
16 PRKX PRKX PRKX 2544 0.2 0.57 YES
17 ADCY6 ADCY6 ADCY6 3791 0.14 0.52 NO
18 PRKACG PRKACG PRKACG 5438 0.085 0.43 NO
19 ACCN1 ACCN1 ACCN1 6660 0.057 0.37 NO
20 PRKACA PRKACA PRKACA 6667 0.057 0.38 NO
21 ADCY8 ADCY8 ADCY8 7530 0.04 0.33 NO
22 SCNN1B SCNN1B SCNN1B 7545 0.04 0.33 NO
23 GRM4 GRM4 GRM4 8667 0.019 0.27 NO
24 SCNN1G SCNN1G SCNN1G 9447 0.0039 0.23 NO
25 PRKACB PRKACB PRKACB 10326 -0.012 0.18 NO
26 TAS1R1 TAS1R1 TAS1R1 11260 -0.03 0.13 NO
27 TAS2R4 TAS2R4 TAS2R4 11995 -0.046 0.094 NO
28 TRPM5 TRPM5 TRPM5 12459 -0.057 0.074 NO
29 GNAS GNAS GNAS 12830 -0.066 0.06 NO
30 GNB1 GNB1 GNB1 13288 -0.078 0.042 NO
31 PDE1A PDE1A PDE1A 14985 -0.14 -0.039 NO
32 TAS1R3 TAS1R3 TAS1R3 15936 -0.21 -0.072 NO
33 GNG3 GNG3 GNG3 15955 -0.21 -0.05 NO
34 SCNN1A SCNN1A SCNN1A 15970 -0.21 -0.029 NO
35 ADCY4 ADCY4 ADCY4 16192 -0.24 -0.017 NO
36 PLCB2 PLCB2 PLCB2 16947 -0.32 -0.026 NO
37 ITPR3 ITPR3 ITPR3 17695 -0.67 0.0012 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 CHREBP2 PATHWAY.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA WNT PATHWAY

Table 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 NKD1 NKD1 NKD1 52 0.74 0.03 YES
2 WNT4 WNT4 WNT4 108 0.65 0.056 YES
3 NFATC4 NFATC4 NFATC4 180 0.59 0.079 YES
4 WIF1 WIF1 WIF1 204 0.57 0.1 YES
5 LEF1 LEF1 LEF1 218 0.57 0.13 YES
6 PRICKLE1 PRICKLE1 PRICKLE1 246 0.55 0.15 YES
7 AXIN2 AXIN2 AXIN2 350 0.5 0.17 YES
8 VANGL2 VANGL2 VANGL2 549 0.44 0.18 YES
9 CAMK2B CAMK2B CAMK2B 573 0.43 0.19 YES
10 CSNK1A1L CSNK1A1L CSNK1A1L 750 0.39 0.2 YES
11 SFRP5 SFRP5 SFRP5 859 0.37 0.21 YES
12 NFATC2 NFATC2 NFATC2 869 0.37 0.23 YES
13 PRKCG PRKCG PRKCG 1002 0.35 0.24 YES
14 WNT9A WNT9A WNT9A 1076 0.34 0.25 YES
15 TCF7 TCF7 TCF7 1094 0.33 0.26 YES
16 FZD10 FZD10 FZD10 1125 0.33 0.27 YES
17 SFRP4 SFRP4 SFRP4 1322 0.3 0.28 YES
18 WNT10B WNT10B WNT10B 1336 0.3 0.29 YES
19 FZD7 FZD7 FZD7 1362 0.3 0.3 YES
20 MAPK8 MAPK8 MAPK8 1399 0.29 0.31 YES
21 FZD6 FZD6 FZD6 1551 0.28 0.32 YES
22 FZD9 FZD9 FZD9 1621 0.27 0.32 YES
23 TBL1X TBL1X TBL1X 1980 0.24 0.31 YES
24 APC2 APC2 APC2 2133 0.23 0.32 YES
25 LRP5 LRP5 LRP5 2209 0.22 0.32 YES
26 WNT5A WNT5A WNT5A 2446 0.2 0.32 YES
27 CXXC4 CXXC4 CXXC4 2458 0.2 0.33 YES
28 PRKX PRKX PRKX 2544 0.2 0.33 YES
29 FZD8 FZD8 FZD8 2592 0.2 0.34 YES
30 PLCB4 PLCB4 PLCB4 2619 0.19 0.34 YES
31 MYC MYC MYC 2845 0.18 0.34 YES
32 WNT3 WNT3 WNT3 2981 0.17 0.34 YES
33 CTBP2 CTBP2 CTBP2 2998 0.17 0.34 YES
34 TCF7L2 TCF7L2 TCF7L2 3024 0.17 0.35 YES
35 CAMK2G CAMK2G CAMK2G 3053 0.17 0.36 YES
36 SFRP1 SFRP1 SFRP1 3163 0.16 0.36 YES
37 PPP2R5E PPP2R5E PPP2R5E 3210 0.16 0.36 YES
38 WNT16 WNT16 WNT16 3241 0.16 0.37 YES
39 PLCB1 PLCB1 PLCB1 3301 0.16 0.37 YES
40 WNT2 WNT2 WNT2 3359 0.15 0.38 YES
41 CTNNB1 CTNNB1 CTNNB1 3473 0.15 0.38 YES
42 CCND1 CCND1 CCND1 3579 0.14 0.38 YES
43 LRP6 LRP6 LRP6 3602 0.14 0.38 YES
44 NKD2 NKD2 NKD2 3704 0.14 0.38 YES
45 FBXW11 FBXW11 FBXW11 3752 0.14 0.39 YES
46 FRAT2 FRAT2 FRAT2 3766 0.14 0.39 YES
47 DAAM2 DAAM2 DAAM2 3845 0.13 0.39 YES
48 DAAM1 DAAM1 DAAM1 4159 0.12 0.38 NO
49 FRAT1 FRAT1 FRAT1 4165 0.12 0.38 NO
50 TCF7L1 TCF7L1 TCF7L1 4210 0.12 0.39 NO
51 NFATC1 NFATC1 NFATC1 4384 0.12 0.38 NO
52 BTRC BTRC BTRC 4421 0.11 0.39 NO
53 NFAT5 NFAT5 NFAT5 4595 0.11 0.38 NO
54 SMAD3 SMAD3 SMAD3 4734 0.1 0.38 NO
55 MAPK10 MAPK10 MAPK10 4794 0.1 0.38 NO
56 WNT6 WNT6 WNT6 4856 0.1 0.38 NO
57 PPP3R1 PPP3R1 PPP3R1 4903 0.1 0.38 NO
58 PPP3CA PPP3CA PPP3CA 4977 0.098 0.38 NO
59 APC APC APC 5010 0.097 0.39 NO
60 PPP3CB PPP3CB PPP3CB 5186 0.092 0.38 NO
61 GSK3B GSK3B GSK3B 5332 0.088 0.38 NO
62 TBL1XR1 TBL1XR1 TBL1XR1 5351 0.088 0.38 NO
63 SKP1 SKP1 SKP1 5414 0.086 0.38 NO
64 TP53 TP53 TP53 5427 0.086 0.38 NO
65 PRKACG PRKACG PRKACG 5438 0.085 0.38 NO
66 FZD3 FZD3 FZD3 5537 0.082 0.38 NO
67 WNT11 WNT11 WNT11 5672 0.08 0.38 NO
68 CCND2 CCND2 CCND2 5680 0.079 0.38 NO
69 PPP2R5C PPP2R5C PPP2R5C 5696 0.079 0.38 NO
70 FZD1 FZD1 FZD1 5728 0.078 0.39 NO
71 CUL1 CUL1 CUL1 5820 0.076 0.38 NO
72 CSNK1A1 CSNK1A1 CSNK1A1 5853 0.075 0.39 NO
73 DVL3 DVL3 DVL3 5971 0.073 0.38 NO
74 EP300 EP300 EP300 5989 0.072 0.38 NO
75 PRICKLE2 PRICKLE2 PRICKLE2 6142 0.069 0.38 NO
76 CHD8 CHD8 CHD8 6162 0.069 0.38 NO
77 WNT1 WNT1 WNT1 6283 0.066 0.38 NO
78 WNT7B WNT7B WNT7B 6321 0.065 0.38 NO
79 SENP2 SENP2 SENP2 6374 0.064 0.38 NO
80 NLK NLK NLK 6569 0.059 0.37 NO
81 PRKACA PRKACA PRKACA 6667 0.057 0.37 NO
82 SMAD2 SMAD2 SMAD2 6705 0.056 0.37 NO
83 CSNK1E CSNK1E CSNK1E 6707 0.056 0.37 NO
84 CREBBP CREBBP CREBBP 6766 0.055 0.37 NO
85 MAPK9 MAPK9 MAPK9 6851 0.053 0.37 NO
86 PRKCB PRKCB PRKCB 6914 0.052 0.37 NO
87 SIAH1 SIAH1 SIAH1 7075 0.048 0.36 NO
88 FZD5 FZD5 FZD5 7375 0.043 0.34 NO
89 VANGL1 VANGL1 VANGL1 7656 0.037 0.33 NO
90 ROCK2 ROCK2 ROCK2 7797 0.035 0.32 NO
91 RAC1 RAC1 RAC1 7907 0.032 0.32 NO
92 PPP2R1A PPP2R1A PPP2R1A 7976 0.031 0.32 NO
93 DKK1 DKK1 DKK1 8103 0.029 0.31 NO
94 CSNK2A2 CSNK2A2 CSNK2A2 8173 0.028 0.31 NO
95 CTNNBIP1 CTNNBIP1 CTNNBIP1 8198 0.027 0.31 NO
96 CSNK2A1 CSNK2A1 CSNK2A1 8245 0.026 0.31 NO
97 AXIN1 AXIN1 AXIN1 8325 0.025 0.3 NO
98 CHP CHP CHP 8901 0.014 0.27 NO
99 MAP3K7 MAP3K7 MAP3K7 9085 0.011 0.26 NO
100 ROCK1 ROCK1 ROCK1 9110 0.01 0.26 NO
101 PPP2CA PPP2CA PPP2CA 9144 0.0098 0.26 NO
102 CAMK2D CAMK2D CAMK2D 9173 0.0093 0.26 NO
103 RHOA RHOA RHOA 9196 0.0089 0.26 NO
104 RAC3 RAC3 RAC3 9518 0.0027 0.24 NO
105 PSEN1 PSEN1 PSEN1 9832 -0.0031 0.22 NO
106 WNT8B WNT8B WNT8B 9877 -0.004 0.22 NO
107 PPP3CC PPP3CC PPP3CC 10241 -0.011 0.2 NO
108 PRKACB PRKACB PRKACB 10326 -0.012 0.19 NO
109 CTBP1 CTBP1 CTBP1 10485 -0.016 0.18 NO
110 SMAD4 SMAD4 SMAD4 10531 -0.017 0.18 NO
111 FOSL1 FOSL1 FOSL1 10890 -0.023 0.16 NO
112 NFATC3 NFATC3 NFATC3 10901 -0.023 0.16 NO
113 DVL1 DVL1 DVL1 11135 -0.028 0.15 NO
114 PPP2R5A PPP2R5A PPP2R5A 11211 -0.029 0.15 NO
115 RUVBL1 RUVBL1 RUVBL1 11442 -0.035 0.14 NO
116 PPP2CB PPP2CB PPP2CB 11552 -0.037 0.13 NO
117 WNT3A WNT3A WNT3A 11609 -0.038 0.13 NO
118 DVL2 DVL2 DVL2 12119 -0.049 0.1 NO
119 WNT10A WNT10A WNT10A 12752 -0.064 0.072 NO
120 PPP2R5D PPP2R5D PPP2R5D 12811 -0.066 0.072 NO
121 CHP2 CHP2 CHP2 12953 -0.069 0.067 NO
122 FZD2 FZD2 FZD2 12974 -0.07 0.069 NO
123 RBX1 RBX1 RBX1 13122 -0.074 0.064 NO
124 CSNK2B CSNK2B CSNK2B 13428 -0.083 0.05 NO
125 PORCN PORCN PORCN 13483 -0.084 0.051 NO
126 FZD4 FZD4 FZD4 13521 -0.086 0.053 NO
127 PLCB3 PLCB3 PLCB3 13681 -0.09 0.048 NO
128 SOX17 SOX17 SOX17 14435 -0.12 0.01 NO
129 MMP7 MMP7 MMP7 14520 -0.12 0.011 NO
130 WNT2B WNT2B WNT2B 14533 -0.12 0.015 NO
131 CACYBP CACYBP CACYBP 15062 -0.15 -0.0081 NO
132 JUN JUN JUN 15116 -0.15 -0.0044 NO
133 WNT9B WNT9B WNT9B 15392 -0.17 -0.013 NO
134 CCND3 CCND3 CCND3 15519 -0.17 -0.012 NO
135 WNT7A WNT7A WNT7A 15580 -0.18 -0.0074 NO
136 DKK2 DKK2 DKK2 15932 -0.21 -0.018 NO
137 PPP2R1B PPP2R1B PPP2R1B 15943 -0.21 -0.0092 NO
138 CAMK2A CAMK2A CAMK2A 15992 -0.21 -0.0024 NO
139 PPARD PPARD PPARD 16062 -0.22 0.0037 NO
140 PLCB2 PLCB2 PLCB2 16947 -0.32 -0.032 NO
141 SFRP2 SFRP2 SFRP2 17229 -0.37 -0.032 NO
142 RAC2 RAC2 RAC2 17321 -0.39 -0.019 NO
143 PRKCA PRKCA PRKCA 17451 -0.44 -0.0071 NO
144 WNT5B WNT5B WNT5B 17580 -0.5 0.0078 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 WNT PATHWAY.

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

genes ES table in pathway: KEGG CYSTEINE AND METHIONINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CTNNA2 CTNNA2 CTNNA2 86 0.66 0.039 YES
2 CACNA2D2 CACNA2D2 CACNA2D2 116 0.64 0.079 YES
3 CACNG2 CACNG2 CACNG2 133 0.63 0.12 YES
4 CACNB2 CACNB2 CACNB2 188 0.58 0.16 YES
5 LEF1 LEF1 LEF1 218 0.57 0.19 YES
6 CACNA2D1 CACNA2D1 CACNA2D1 286 0.52 0.22 YES
7 RYR2 RYR2 RYR2 589 0.42 0.23 YES
8 ITGA8 ITGA8 ITGA8 604 0.42 0.26 YES
9 CACNA1S CACNA1S CACNA1S 652 0.41 0.28 YES
10 ITGA9 ITGA9 ITGA9 777 0.38 0.3 YES
11 ITGB8 ITGB8 ITGB8 778 0.38 0.33 YES
12 CACNA1D CACNA1D CACNA1D 877 0.37 0.34 YES
13 LAMA2 LAMA2 LAMA2 1058 0.34 0.36 YES
14 TCF7 TCF7 TCF7 1094 0.33 0.38 YES
15 CACNA1C CACNA1C CACNA1C 1201 0.32 0.39 YES
16 DMD DMD DMD 1619 0.27 0.39 YES
17 CACNG7 CACNG7 CACNG7 1748 0.26 0.4 YES
18 ITGA1 ITGA1 ITGA1 1787 0.25 0.41 YES
19 SGCD SGCD SGCD 1895 0.24 0.42 YES
20 CACNB1 CACNB1 CACNB1 2119 0.23 0.42 YES
21 ITGA2 ITGA2 ITGA2 2126 0.23 0.44 YES
22 CDH2 CDH2 CDH2 2163 0.22 0.45 YES
23 ITGA7 ITGA7 ITGA7 2179 0.22 0.46 YES
24 CACNB3 CACNB3 CACNB3 2201 0.22 0.48 YES
25 ACTN1 ACTN1 ACTN1 2237 0.22 0.49 YES
26 PKP2 PKP2 PKP2 2786 0.18 0.47 NO
27 TCF7L2 TCF7L2 TCF7L2 3024 0.17 0.47 NO
28 ITGB5 ITGB5 ITGB5 3057 0.17 0.48 NO
29 CTNNB1 CTNNB1 CTNNB1 3473 0.15 0.46 NO
30 CACNB4 CACNB4 CACNB4 4065 0.13 0.44 NO
31 TCF7L1 TCF7L1 TCF7L1 4210 0.12 0.44 NO
32 SGCB SGCB SGCB 4274 0.12 0.44 NO
33 SGCA SGCA SGCA 4925 0.099 0.41 NO
34 ITGA11 ITGA11 ITGA11 5080 0.095 0.41 NO
35 ITGA10 ITGA10 ITGA10 5304 0.089 0.4 NO
36 SGCG SGCG SGCG 6571 0.059 0.33 NO
37 ITGA2B ITGA2B ITGA2B 7205 0.046 0.3 NO
38 ITGB1 ITGB1 ITGB1 7295 0.044 0.3 NO
39 DES DES DES 7682 0.037 0.28 NO
40 ITGA6 ITGA6 ITGA6 9037 0.012 0.2 NO
41 EMD EMD EMD 9105 0.011 0.2 NO
42 CTNNA1 CTNNA1 CTNNA1 9577 0.0017 0.17 NO
43 ACTN3 ACTN3 ACTN3 9812 -0.0026 0.16 NO
44 CACNG4 CACNG4 CACNG4 10121 -0.0086 0.14 NO
45 ACTN2 ACTN2 ACTN2 10857 -0.023 0.1 NO
46 DAG1 DAG1 DAG1 10977 -0.025 0.098 NO
47 JUP JUP JUP 11558 -0.037 0.068 NO
48 ACTN4 ACTN4 ACTN4 12412 -0.056 0.023 NO
49 ITGAV ITGAV ITGAV 12710 -0.063 0.011 NO
50 ACTB ACTB ACTB 12718 -0.063 0.014 NO
51 ACTG1 ACTG1 ACTG1 12796 -0.065 0.014 NO
52 CTNNA3 CTNNA3 CTNNA3 13198 -0.076 -0.0035 NO
53 DSP DSP DSP 13284 -0.078 -0.0032 NO
54 LMNA LMNA LMNA 13782 -0.093 -0.025 NO
55 ATP2A2 ATP2A2 ATP2A2 14250 -0.11 -0.044 NO
56 DSG2 DSG2 DSG2 14332 -0.11 -0.042 NO
57 ITGA3 ITGA3 ITGA3 14530 -0.12 -0.045 NO
58 ITGB7 ITGB7 ITGB7 14814 -0.13 -0.052 NO
59 ITGB3 ITGB3 ITGB3 15039 -0.14 -0.056 NO
60 CACNA2D3 CACNA2D3 CACNA2D3 15071 -0.15 -0.048 NO
61 CACNA1F CACNA1F CACNA1F 15302 -0.16 -0.05 NO
62 ITGA5 ITGA5 ITGA5 16012 -0.22 -0.076 NO
63 CACNG1 CACNG1 CACNG1 16184 -0.24 -0.07 NO
64 GJA1 GJA1 GJA1 16378 -0.25 -0.065 NO
65 ITGB4 ITGB4 ITGB4 16511 -0.27 -0.055 NO
66 ITGA4 ITGA4 ITGA4 16548 -0.27 -0.039 NO
67 SLC8A1 SLC8A1 SLC8A1 16920 -0.32 -0.039 NO
68 DSC2 DSC2 DSC2 17068 -0.34 -0.025 NO
69 CACNA2D4 CACNA2D4 CACNA2D4 17327 -0.39 -0.014 NO
70 ITGB6 ITGB6 ITGB6 17634 -0.55 0.0047 NO

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

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

genes ES table in pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

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 WNT4 WNT4 WNT4 108 0.65 0.056 YES
2 BMP6 BMP6 BMP6 230 0.56 0.1 YES
3 GLI1 GLI1 GLI1 368 0.49 0.14 YES
4 SHH SHH SHH 487 0.46 0.18 YES
5 BMP4 BMP4 BMP4 556 0.43 0.22 YES
6 IHH IHH IHH 591 0.42 0.25 YES
7 SMO SMO SMO 656 0.41 0.29 YES
8 CSNK1A1L CSNK1A1L CSNK1A1L 750 0.39 0.32 YES
9 BMP7 BMP7 BMP7 1029 0.34 0.34 YES
10 WNT9A WNT9A WNT9A 1076 0.34 0.37 YES
11 WNT10B WNT10B WNT10B 1336 0.3 0.38 YES
12 PTCH2 PTCH2 PTCH2 1585 0.28 0.39 YES
13 GLI3 GLI3 GLI3 1651 0.27 0.42 YES
14 HHIP HHIP HHIP 2052 0.23 0.42 YES
15 PTCH1 PTCH1 PTCH1 2185 0.22 0.43 YES
16 WNT5A WNT5A WNT5A 2446 0.2 0.43 YES
17 BMP8B BMP8B BMP8B 2478 0.2 0.45 YES
18 PRKX PRKX PRKX 2544 0.2 0.47 YES
19 ZIC2 ZIC2 ZIC2 2867 0.18 0.47 YES
20 WNT3 WNT3 WNT3 2981 0.17 0.48 YES
21 LRP2 LRP2 LRP2 3078 0.17 0.49 YES
22 WNT16 WNT16 WNT16 3241 0.16 0.49 YES
23 WNT2 WNT2 WNT2 3359 0.15 0.5 YES
24 BMP8A BMP8A BMP8A 3592 0.14 0.5 YES
25 FBXW11 FBXW11 FBXW11 3752 0.14 0.5 YES
26 GLI2 GLI2 GLI2 4049 0.13 0.5 NO
27 CSNK1G3 CSNK1G3 CSNK1G3 4417 0.11 0.49 NO
28 BTRC BTRC BTRC 4421 0.11 0.5 NO
29 WNT6 WNT6 WNT6 4856 0.1 0.49 NO
30 SUFU SUFU SUFU 5171 0.092 0.48 NO
31 GSK3B GSK3B GSK3B 5332 0.088 0.48 NO
32 PRKACG PRKACG PRKACG 5438 0.085 0.48 NO
33 WNT11 WNT11 WNT11 5672 0.08 0.47 NO
34 CSNK1A1 CSNK1A1 CSNK1A1 5853 0.075 0.47 NO
35 WNT1 WNT1 WNT1 6283 0.066 0.45 NO
36 WNT7B WNT7B WNT7B 6321 0.065 0.46 NO
37 PRKACA PRKACA PRKACA 6667 0.057 0.44 NO
38 CSNK1E CSNK1E CSNK1E 6707 0.056 0.44 NO
39 BMP2 BMP2 BMP2 6924 0.052 0.44 NO
40 GAS1 GAS1 GAS1 7380 0.043 0.42 NO
41 CSNK1G1 CSNK1G1 CSNK1G1 7846 0.034 0.39 NO
42 CSNK1G2 CSNK1G2 CSNK1G2 8304 0.025 0.37 NO
43 CSNK1D CSNK1D CSNK1D 9591 0.0015 0.3 NO
44 WNT8B WNT8B WNT8B 9877 -0.004 0.28 NO
45 PRKACB PRKACB PRKACB 10326 -0.012 0.26 NO
46 WNT10A WNT10A WNT10A 12752 -0.064 0.13 NO
47 STK36 STK36 STK36 12829 -0.066 0.13 NO
48 WNT2B WNT2B WNT2B 14533 -0.12 0.043 NO
49 RAB23 RAB23 RAB23 14845 -0.14 0.039 NO
50 WNT9B WNT9B WNT9B 15392 -0.17 0.024 NO
51 WNT7A WNT7A WNT7A 15580 -0.18 0.03 NO
52 DHH DHH DHH 17509 -0.46 -0.036 NO
53 WNT5B WNT5B WNT5B 17580 -0.5 0.0078 NO

Figure S35.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, 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 MAPK SIGNALING PATHWAY

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 NKD1 NKD1 NKD1 52 0.74 0.054 YES
2 WNT4 WNT4 WNT4 108 0.65 0.1 YES
3 WIF1 WIF1 WIF1 204 0.57 0.14 YES
4 LEF1 LEF1 LEF1 218 0.57 0.18 YES
5 PYGO1 PYGO1 PYGO1 277 0.53 0.22 YES
6 WISP1 WISP1 WISP1 540 0.44 0.24 YES
7 WNT9A WNT9A WNT9A 1076 0.34 0.23 YES
8 TCF7 TCF7 TCF7 1094 0.33 0.26 YES
9 RHOU RHOU RHOU 1286 0.31 0.27 YES
10 SFRP4 SFRP4 SFRP4 1322 0.3 0.29 YES
11 FZD7 FZD7 FZD7 1362 0.3 0.31 YES
12 FZD6 FZD6 FZD6 1551 0.28 0.32 YES
13 TLE1 TLE1 TLE1 2162 0.22 0.3 YES
14 LRP5 LRP5 LRP5 2209 0.22 0.32 YES
15 WNT5A WNT5A WNT5A 2446 0.2 0.32 YES
16 CXXC4 CXXC4 CXXC4 2458 0.2 0.33 YES
17 FZD8 FZD8 FZD8 2592 0.2 0.34 YES
18 MYC MYC MYC 2845 0.18 0.34 YES
19 WNT3 WNT3 WNT3 2981 0.17 0.35 YES
20 CTBP2 CTBP2 CTBP2 2998 0.17 0.36 YES
21 SFRP1 SFRP1 SFRP1 3163 0.16 0.36 YES
22 WNT16 WNT16 WNT16 3241 0.16 0.37 YES
23 FRZB FRZB FRZB 3336 0.16 0.38 YES
24 WNT2 WNT2 WNT2 3359 0.15 0.39 YES
25 CTNNB1 CTNNB1 CTNNB1 3473 0.15 0.39 YES
26 CCND1 CCND1 CCND1 3579 0.14 0.4 YES
27 LRP6 LRP6 LRP6 3602 0.14 0.41 YES
28 FBXW11 FBXW11 FBXW11 3752 0.14 0.41 YES
29 DAAM1 DAAM1 DAAM1 4159 0.12 0.39 YES
30 FRAT1 FRAT1 FRAT1 4165 0.12 0.4 YES
31 TCF7L1 TCF7L1 TCF7L1 4210 0.12 0.41 YES
32 BTRC BTRC BTRC 4421 0.11 0.41 NO
33 WNT6 WNT6 WNT6 4856 0.1 0.39 NO
34 APC APC APC 5010 0.097 0.39 NO
35 GSK3B GSK3B GSK3B 5332 0.088 0.38 NO
36 FZD3 FZD3 FZD3 5537 0.082 0.37 NO
37 WNT11 WNT11 WNT11 5672 0.08 0.37 NO
38 CCND2 CCND2 CCND2 5680 0.079 0.38 NO
39 FZD1 FZD1 FZD1 5728 0.078 0.38 NO
40 CSNK1A1 CSNK1A1 CSNK1A1 5853 0.075 0.38 NO
41 EP300 EP300 EP300 5989 0.072 0.38 NO
42 FBXW2 FBXW2 FBXW2 6214 0.068 0.37 NO
43 GSK3A GSK3A GSK3A 6218 0.068 0.37 NO
44 WNT1 WNT1 WNT1 6283 0.066 0.37 NO
45 DIXDC1 DIXDC1 DIXDC1 6315 0.065 0.38 NO
46 WNT7B WNT7B WNT7B 6321 0.065 0.38 NO
47 FBXW4 FBXW4 FBXW4 6344 0.064 0.39 NO
48 SENP2 SENP2 SENP2 6374 0.064 0.39 NO
49 NLK NLK NLK 6569 0.059 0.38 NO
50 RPL13A RPL13A RPL13A 6921 0.052 0.37 NO
51 FZD5 FZD5 FZD5 7375 0.043 0.34 NO
52 CSNK1G1 CSNK1G1 CSNK1G1 7846 0.034 0.32 NO
53 PPP2R1A PPP2R1A PPP2R1A 7976 0.031 0.32 NO
54 DKK1 DKK1 DKK1 8103 0.029 0.31 NO
55 CTNNBIP1 CTNNBIP1 CTNNBIP1 8198 0.027 0.31 NO
56 CSNK2A1 CSNK2A1 CSNK2A1 8245 0.026 0.31 NO
57 AXIN1 AXIN1 AXIN1 8325 0.025 0.3 NO
58 HPRT1 HPRT1 HPRT1 8456 0.023 0.3 NO
59 PPP2CA PPP2CA PPP2CA 9144 0.0098 0.26 NO
60 CSNK1D CSNK1D CSNK1D 9591 0.0015 0.24 NO
61 GAPDH GAPDH GAPDH 10234 -0.011 0.2 NO
62 CTBP1 CTBP1 CTBP1 10485 -0.016 0.19 NO
63 FOSL1 FOSL1 FOSL1 10890 -0.023 0.16 NO
64 DVL1 DVL1 DVL1 11135 -0.028 0.15 NO
65 DVL2 DVL2 DVL2 12119 -0.049 0.1 NO
66 BCL9 BCL9 BCL9 12250 -0.052 0.098 NO
67 ACTB ACTB ACTB 12718 -0.063 0.076 NO
68 WNT10A WNT10A WNT10A 12752 -0.064 0.079 NO
69 FZD2 FZD2 FZD2 12974 -0.07 0.072 NO
70 AES AES AES 13114 -0.074 0.07 NO
71 PORCN PORCN PORCN 13483 -0.084 0.055 NO
72 FZD4 FZD4 FZD4 13521 -0.086 0.06 NO
73 SOX17 SOX17 SOX17 14435 -0.12 0.017 NO
74 TLE2 TLE2 TLE2 14460 -0.12 0.024 NO
75 SLC9A3R1 SLC9A3R1 SLC9A3R1 14493 -0.12 0.032 NO
76 WNT2B WNT2B WNT2B 14533 -0.12 0.039 NO
77 JUN JUN JUN 15116 -0.15 0.017 NO
78 CCND3 CCND3 CCND3 15519 -0.17 0.0074 NO
79 B2M B2M B2M 15543 -0.18 0.02 NO
80 WNT7A WNT7A WNT7A 15580 -0.18 0.031 NO
81 KREMEN1 KREMEN1 KREMEN1 16232 -0.24 0.012 NO
82 PITX2 PITX2 PITX2 17476 -0.45 -0.024 NO
83 WNT5B WNT5B WNT5B 17580 -0.5 0.0078 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 MAPK SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG WNT SIGNALING PATHWAY

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 CDO1 CDO1 CDO1 156 0.61 0.17 YES
2 CBS CBS CBS 546 0.44 0.27 YES
3 SMS SMS SMS 1687 0.26 0.28 YES
4 TRDMT1 TRDMT1 TRDMT1 1722 0.26 0.36 YES
5 TAT TAT TAT 1814 0.25 0.43 YES
6 BHMT BHMT BHMT 4028 0.13 0.34 NO
7 MAT2B MAT2B MAT2B 5604 0.081 0.27 NO
8 MPST MPST MPST 5766 0.077 0.29 NO
9 LDHB LDHB LDHB 6316 0.065 0.27 NO
10 AHCYL2 AHCYL2 AHCYL2 6516 0.06 0.28 NO
11 DNMT3A DNMT3A DNMT3A 6653 0.058 0.29 NO
12 GOT1 GOT1 GOT1 6659 0.057 0.3 NO
13 CTH CTH CTH 7673 0.037 0.26 NO
14 GOT2 GOT2 GOT2 8365 0.024 0.23 NO
15 DNMT1 DNMT1 DNMT1 8502 0.022 0.22 NO
16 LDHAL6B LDHAL6B LDHAL6B 8591 0.02 0.23 NO
17 AHCY AHCY AHCY 8746 0.017 0.22 NO
18 MTR MTR MTR 8835 0.016 0.22 NO
19 MTAP MTAP MTAP 9559 0.002 0.18 NO
20 MAT2A MAT2A MAT2A 9771 -0.0019 0.17 NO
21 AMD1 AMD1 AMD1 10253 -0.011 0.15 NO
22 AHCYL1 AHCYL1 AHCYL1 10286 -0.012 0.15 NO
23 ENOPH1 ENOPH1 ENOPH1 10332 -0.013 0.15 NO
24 LDHAL6A LDHAL6A LDHAL6A 10942 -0.024 0.12 NO
25 APIP APIP APIP 12767 -0.064 0.037 NO
26 ADI1 ADI1 ADI1 12857 -0.067 0.052 NO
27 SRM SRM SRM 13000 -0.07 0.064 NO
28 LDHA LDHA LDHA 13583 -0.087 0.057 NO
29 SDS SDS SDS 14622 -0.12 0.034 NO
30 MAT1A MAT1A MAT1A 14695 -0.13 0.067 NO
31 IL4I1 IL4I1 IL4I1 15388 -0.17 0.076 NO
32 DNMT3B DNMT3B DNMT3B 15734 -0.19 0.11 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 WNT SIGNALING PATHWAY.

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

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 AT1R PATHWAY 32 genes.ES.table 0.34 1.3 0.18 1 0.98 0.28 0.3 0.2 0.89 0.42
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.46 1.4 0.15 1 0.96 0.17 0.072 0.16 0.81 0.4
BIOCARTA GH PATHWAY 26 genes.ES.table 0.43 1.4 0.083 1 0.95 0.15 0.054 0.15 1 0.52
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.32 1.3 0.22 0.82 0.99 0.22 0.3 0.16 0.71 0.3
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.34 1.2 0.24 0.79 0.99 0.32 0.27 0.23 0.69 0.27
BIOCARTA CREB PATHWAY 26 genes.ES.table 0.51 1.6 0.021 0.88 0.76 0.23 0.16 0.19 0.57 0.31
KEGG PENTOSE PHOSPHATE PATHWAY 25 genes.ES.table 0.42 1.3 0.17 0.87 0.99 0.48 0.34 0.32 0.75 0.34
KEGG STEROID HORMONE BIOSYNTHESIS 41 genes.ES.table 0.56 1.4 0.062 1 0.95 0.51 0.15 0.44 0.9 0.44
KEGG O GLYCAN BIOSYNTHESIS 27 genes.ES.table 0.45 1.3 0.12 0.78 0.99 0.41 0.2 0.33 0.67 0.28
KEGG BUTANOATE METABOLISM 30 genes.ES.table 0.57 1.5 0.044 0.81 0.8 0.6 0.29 0.42 0.53 0.29
genes ES table in pathway: BIOCARTA AT1R 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 RPA4 RPA4 RPA4 127 0.48 0.14 YES
2 ERCC4 ERCC4 ERCC4 1037 0.26 0.17 YES
3 ERCC8 ERCC8 ERCC8 2425 0.16 0.14 YES
4 GTF2H3 GTF2H3 GTF2H3 2734 0.14 0.17 YES
5 ERCC2 ERCC2 ERCC2 3079 0.13 0.19 YES
6 CDK7 CDK7 CDK7 3265 0.12 0.22 YES
7 GTF2H2 GTF2H2 GTF2H2 3407 0.12 0.24 YES
8 RPA3 RPA3 RPA3 3472 0.12 0.28 YES
9 LIG1 LIG1 LIG1 3639 0.11 0.3 YES
10 RPA2 RPA2 RPA2 3667 0.11 0.33 YES
11 POLE2 POLE2 POLE2 3781 0.11 0.36 YES
12 CUL4B CUL4B CUL4B 4248 0.097 0.36 YES
13 CUL4A CUL4A CUL4A 4256 0.096 0.39 YES
14 ERCC5 ERCC5 ERCC5 4634 0.088 0.4 YES
15 CCNH CCNH CCNH 4792 0.084 0.42 YES
16 RFC2 RFC2 RFC2 5625 0.067 0.39 NO
17 GTF2H5 GTF2H5 GTF2H5 5629 0.067 0.41 NO
18 CETN2 CETN2 CETN2 6064 0.059 0.4 NO
19 MNAT1 MNAT1 MNAT1 6213 0.056 0.41 NO
20 RFC1 RFC1 RFC1 6663 0.048 0.4 NO
21 RFC3 RFC3 RFC3 6930 0.043 0.4 NO
22 POLD1 POLD1 POLD1 7285 0.037 0.39 NO
23 GTF2H4 GTF2H4 GTF2H4 7626 0.031 0.38 NO
24 RFC5 RFC5 RFC5 7665 0.031 0.39 NO
25 POLE4 POLE4 POLE4 7798 0.029 0.39 NO
26 POLE3 POLE3 POLE3 7905 0.027 0.39 NO
27 POLD2 POLD2 POLD2 8191 0.022 0.38 NO
28 POLE POLE POLE 8248 0.021 0.39 NO
29 PCNA PCNA PCNA 8729 0.013 0.36 NO
30 POLD3 POLD3 POLD3 8924 0.0096 0.36 NO
31 RAD23A RAD23A RAD23A 9678 -0.0028 0.32 NO
32 DDB1 DDB1 DDB1 9815 -0.0048 0.31 NO
33 ERCC6 ERCC6 ERCC6 10019 -0.0078 0.3 NO
34 GTF2H1 GTF2H1 GTF2H1 10262 -0.012 0.29 NO
35 ERCC1 ERCC1 ERCC1 10697 -0.019 0.27 NO
36 ERCC3 ERCC3 ERCC3 10741 -0.02 0.28 NO
37 XPC XPC XPC 11060 -0.026 0.26 NO
38 RBX1 RBX1 RBX1 11852 -0.039 0.23 NO
39 POLD4 POLD4 POLD4 12096 -0.044 0.23 NO
40 RPA1 RPA1 RPA1 12994 -0.064 0.2 NO
41 RFC4 RFC4 RFC4 13072 -0.066 0.22 NO
42 XPA XPA XPA 13357 -0.073 0.22 NO
43 DDB2 DDB2 DDB2 13536 -0.077 0.24 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 AT1R PATHWAY.

Figure S42.  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 EGF 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 SOCS1 SOCS1 SOCS1 163 0.46 0.04 YES
2 PARK2 PARK2 PARK2 533 0.34 0.055 YES
3 NHLRC1 NHLRC1 NHLRC1 576 0.33 0.088 YES
4 UBE2NL UBE2NL UBE2NL 776 0.29 0.11 YES
5 HERC3 HERC3 HERC3 996 0.26 0.12 YES
6 UBE2QL1 UBE2QL1 UBE2QL1 1558 0.21 0.11 YES
7 ERCC8 ERCC8 ERCC8 2425 0.16 0.082 YES
8 UBE2D4 UBE2D4 UBE2D4 2654 0.15 0.084 YES
9 XIAP XIAP XIAP 3298 0.12 0.061 YES
10 UBE2C UBE2C UBE2C 3379 0.12 0.069 YES
11 CDC23 CDC23 CDC23 3499 0.12 0.074 YES
12 NEDD4 NEDD4 NEDD4 3550 0.11 0.084 YES
13 FBXO4 FBXO4 FBXO4 3644 0.11 0.09 YES
14 KLHL9 KLHL9 KLHL9 3882 0.11 0.088 YES
15 ANAPC10 ANAPC10 ANAPC10 3924 0.1 0.097 YES
16 UBE3C UBE3C UBE3C 4026 0.1 0.1 YES
17 UBA6 UBA6 UBA6 4062 0.1 0.11 YES
18 UBE2A UBE2A UBE2A 4198 0.098 0.11 YES
19 CUL4B CUL4B CUL4B 4248 0.097 0.12 YES
20 CUL4A CUL4A CUL4A 4256 0.096 0.13 YES
21 RCHY1 RCHY1 RCHY1 4286 0.096 0.14 YES
22 SAE1 SAE1 SAE1 4287 0.096 0.15 YES
23 UBE2B UBE2B UBE2B 4357 0.094 0.16 YES
24 CDC20 CDC20 CDC20 4406 0.093 0.16 YES
25 NEDD4L NEDD4L NEDD4L 4644 0.088 0.16 YES
26 UBE2K UBE2K UBE2K 4683 0.087 0.17 YES
27 UBE2H UBE2H UBE2H 4782 0.085 0.17 YES
28 MGRN1 MGRN1 MGRN1 4897 0.082 0.17 YES
29 UBE2D2 UBE2D2 UBE2D2 4958 0.08 0.18 YES
30 BIRC3 BIRC3 BIRC3 4968 0.08 0.18 YES
31 SKP1 SKP1 SKP1 5111 0.077 0.19 YES
32 RHOBTB2 RHOBTB2 RHOBTB2 5118 0.077 0.19 YES
33 UBE2D3 UBE2D3 UBE2D3 5150 0.076 0.2 YES
34 FZR1 FZR1 FZR1 5162 0.076 0.21 YES
35 SMURF1 SMURF1 SMURF1 5298 0.073 0.21 YES
36 ANAPC4 ANAPC4 ANAPC4 5385 0.072 0.21 YES
37 HUWE1 HUWE1 HUWE1 5476 0.07 0.21 YES
38 UBOX5 UBOX5 UBOX5 5547 0.068 0.22 YES
39 FBXW8 FBXW8 FBXW8 5658 0.066 0.22 YES
40 UBE2N UBE2N UBE2N 5705 0.066 0.22 YES
41 FBXW11 FBXW11 FBXW11 5753 0.064 0.22 YES
42 UBE2I UBE2I UBE2I 5802 0.064 0.23 YES
43 TCEB2 TCEB2 TCEB2 5881 0.062 0.23 YES
44 UBE3B UBE3B UBE3B 5921 0.061 0.24 YES
45 UBA1 UBA1 UBA1 6011 0.06 0.24 YES
46 ANAPC5 ANAPC5 ANAPC5 6116 0.058 0.24 YES
47 UBE2S UBE2S UBE2S 6128 0.058 0.24 YES
48 SIAH1 SIAH1 SIAH1 6175 0.057 0.25 YES
49 FANCL FANCL FANCL 6189 0.056 0.25 YES
50 UBE2M UBE2M UBE2M 6253 0.055 0.25 YES
51 UBE2E2 UBE2E2 UBE2E2 6364 0.053 0.25 YES
52 SKP2 SKP2 SKP2 6494 0.051 0.25 YES
53 UBE3A UBE3A UBE3A 6580 0.05 0.25 YES
54 CUL1 CUL1 CUL1 6622 0.049 0.26 YES
55 PIAS4 PIAS4 PIAS4 6702 0.047 0.26 YES
56 SYVN1 SYVN1 SYVN1 7042 0.042 0.24 NO
57 CDC16 CDC16 CDC16 7071 0.041 0.24 NO
58 UBE2G2 UBE2G2 UBE2G2 7075 0.041 0.25 NO
59 HERC1 HERC1 HERC1 7286 0.037 0.24 NO
60 KEAP1 KEAP1 KEAP1 7425 0.035 0.24 NO
61 PPIL2 PPIL2 PPIL2 7587 0.032 0.23 NO
62 WWP2 WWP2 WWP2 7590 0.032 0.23 NO
63 ANAPC13 ANAPC13 ANAPC13 7751 0.03 0.23 NO
64 MAP3K1 MAP3K1 MAP3K1 7805 0.029 0.23 NO
65 ANAPC7 ANAPC7 ANAPC7 7837 0.028 0.23 NO
66 BIRC6 BIRC6 BIRC6 7943 0.026 0.22 NO
67 UBA2 UBA2 UBA2 7945 0.026 0.23 NO
68 MID1 MID1 MID1 8049 0.024 0.22 NO
69 UBE2R2 UBE2R2 UBE2R2 8186 0.022 0.22 NO
70 UBE4A UBE4A UBE4A 8276 0.02 0.22 NO
71 FBXW7 FBXW7 FBXW7 8324 0.019 0.22 NO
72 HERC2 HERC2 HERC2 8387 0.018 0.21 NO
73 STUB1 STUB1 STUB1 8412 0.018 0.22 NO
74 CUL3 CUL3 CUL3 8537 0.016 0.21 NO
75 UBE2J1 UBE2J1 UBE2J1 8833 0.011 0.19 NO
76 TCEB1 TCEB1 TCEB1 8851 0.011 0.19 NO
77 ANAPC2 ANAPC2 ANAPC2 8923 0.0096 0.19 NO
78 CDC26 CDC26 CDC26 9091 0.0067 0.18 NO
79 CUL2 CUL2 CUL2 9226 0.0044 0.18 NO
80 CDC34 CDC34 CDC34 9451 0.00056 0.16 NO
81 BRCA1 BRCA1 BRCA1 9473 0.00023 0.16 NO
82 DDB1 DDB1 DDB1 9815 -0.0048 0.14 NO
83 CUL7 CUL7 CUL7 9819 -0.0048 0.14 NO
84 RNF7 RNF7 RNF7 9941 -0.0067 0.14 NO
85 UBE2O UBE2O UBE2O 10175 -0.01 0.12 NO
86 UBE2W UBE2W UBE2W 10185 -0.011 0.12 NO
87 UBE2J2 UBE2J2 UBE2J2 10680 -0.019 0.099 NO
88 ANAPC11 ANAPC11 ANAPC11 10756 -0.02 0.097 NO
89 KLHL13 KLHL13 KLHL13 10779 -0.021 0.098 NO
90 SOCS3 SOCS3 SOCS3 10890 -0.022 0.094 NO
91 PIAS1 PIAS1 PIAS1 10909 -0.023 0.096 NO
92 UBE2F UBE2F UBE2F 11129 -0.026 0.086 NO
93 TRIP12 TRIP12 TRIP12 11292 -0.03 0.08 NO
94 PIAS2 PIAS2 PIAS2 11294 -0.03 0.083 NO
95 CDC27 CDC27 CDC27 11322 -0.03 0.085 NO
96 UBE2G1 UBE2G1 UBE2G1 11338 -0.03 0.087 NO
97 DET1 DET1 DET1 11345 -0.03 0.09 NO
98 CUL5 CUL5 CUL5 11395 -0.031 0.09 NO
99 UBE2Z UBE2Z UBE2Z 11465 -0.032 0.09 NO
100 UBE2L3 UBE2L3 UBE2L3 11525 -0.034 0.09 NO
101 UBE2Q2 UBE2Q2 UBE2Q2 11658 -0.036 0.086 NO
102 ITCH ITCH ITCH 11719 -0.037 0.087 NO
103 UBA3 UBA3 UBA3 11794 -0.038 0.087 NO
104 RBX1 RBX1 RBX1 11852 -0.039 0.088 NO
105 PML PML PML 11913 -0.041 0.089 NO
106 UBR5 UBR5 UBR5 12246 -0.047 0.075 NO
107 TRIM32 TRIM32 TRIM32 12374 -0.05 0.073 NO
108 UBE2Q1 UBE2Q1 UBE2Q1 12398 -0.051 0.077 NO
109 HERC4 HERC4 HERC4 12518 -0.053 0.076 NO
110 CBL CBL CBL 12732 -0.058 0.07 NO
111 TRIM37 TRIM37 TRIM37 12839 -0.06 0.071 NO
112 ANAPC1 ANAPC1 ANAPC1 12957 -0.063 0.071 NO
113 UBE2L6 UBE2L6 UBE2L6 12990 -0.064 0.076 NO
114 RFWD2 RFWD2 RFWD2 13053 -0.065 0.079 NO
115 UBE2D1 UBE2D1 UBE2D1 13112 -0.067 0.083 NO
116 TRAF6 TRAF6 TRAF6 13116 -0.067 0.09 NO
117 UBE4B UBE4B UBE4B 13314 -0.072 0.086 NO
118 PIAS3 PIAS3 PIAS3 13332 -0.072 0.093 NO
119 WWP1 WWP1 WWP1 13336 -0.072 0.1 NO
120 DDB2 DDB2 DDB2 13536 -0.077 0.098 NO
121 BIRC2 BIRC2 BIRC2 13606 -0.079 0.1 NO
122 PRPF19 PRPF19 PRPF19 13807 -0.084 0.1 NO
123 UBE2E3 UBE2E3 UBE2E3 13904 -0.087 0.1 NO
124 AIRE AIRE AIRE 14166 -0.094 0.099 NO
125 UBE2E1 UBE2E1 UBE2E1 14372 -0.1 0.098 NO
126 UBA7 UBA7 UBA7 14511 -0.1 0.1 NO
127 VHL VHL VHL 14675 -0.11 0.1 NO
128 MDM2 MDM2 MDM2 14696 -0.11 0.11 NO
129 CBLB CBLB CBLB 14868 -0.12 0.12 NO
130 FBXO2 FBXO2 FBXO2 16057 -0.18 0.069 NO
131 SMURF2 SMURF2 SMURF2 16585 -0.24 0.064 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 EGF PATHWAY.

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

genes ES table in pathway: BIOCARTA GH 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 PRKCB PRKCB PRKCB 111 0.5 0.2 YES
2 CAMK2B CAMK2B CAMK2B 739 0.3 0.3 YES
3 PIK3R1 PIK3R1 PIK3R1 957 0.27 0.4 YES
4 PRKAR2B PRKAR2B PRKAR2B 1360 0.23 0.47 YES
5 RPS6KA5 RPS6KA5 RPS6KA5 2646 0.15 0.46 YES
6 PRKCA PRKCA PRKCA 2879 0.14 0.51 YES
7 PRKAR1B PRKAR1B PRKAR1B 4760 0.085 0.44 NO
8 CAMK2D CAMK2D CAMK2D 5264 0.074 0.44 NO
9 PRKACG PRKACG PRKACG 5796 0.064 0.44 NO
10 PRKAR2A PRKAR2A PRKAR2A 8427 0.018 0.29 NO
11 GNAS GNAS GNAS 8593 0.015 0.29 NO
12 AKT1 AKT1 AKT1 8685 0.014 0.29 NO
13 PRKACB PRKACB PRKACB 9213 0.0047 0.26 NO
14 RAC1 RAC1 RAC1 9464 0.00038 0.25 NO
15 SOS1 SOS1 SOS1 9786 -0.0044 0.23 NO
16 MAPK14 MAPK14 MAPK14 9830 -0.005 0.23 NO
17 MAPK3 MAPK3 MAPK3 9833 -0.005 0.24 NO
18 GRB2 GRB2 GRB2 10200 -0.011 0.22 NO
19 CAMK2G CAMK2G CAMK2G 10576 -0.017 0.21 NO
20 MAPK1 MAPK1 MAPK1 10708 -0.019 0.21 NO
21 RPS6KA1 RPS6KA1 RPS6KA1 11996 -0.042 0.15 NO
22 CREB1 CREB1 CREB1 12133 -0.045 0.16 NO
23 PRKAR1A PRKAR1A PRKAR1A 13265 -0.071 0.13 NO
24 PIK3CA PIK3CA PIK3CA 13737 -0.083 0.14 NO
25 CAMK2A CAMK2A CAMK2A 14364 -0.1 0.14 NO
26 HRAS HRAS HRAS 14538 -0.11 0.18 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 GH PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 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 ACSM1 ACSM1 ACSM1 12 0.72 0.16 YES
2 ACSM3 ACSM3 ACSM3 55 0.57 0.28 YES
3 GAD1 GAD1 GAD1 283 0.41 0.36 YES
4 ABAT ABAT ABAT 619 0.32 0.41 YES
5 ACSM5 ACSM5 ACSM5 894 0.28 0.45 YES
6 L2HGDH L2HGDH L2HGDH 1134 0.25 0.49 YES
7 ACSM2A ACSM2A ACSM2A 1657 0.2 0.51 YES
8 HMGCS1 HMGCS1 HMGCS1 1673 0.2 0.55 YES
9 ALDH5A1 ALDH5A1 ALDH5A1 2338 0.16 0.55 YES
10 AACS AACS AACS 3292 0.12 0.52 YES
11 HMGCS2 HMGCS2 HMGCS2 3581 0.11 0.53 YES
12 HADH HADH HADH 3720 0.11 0.54 YES
13 OXCT1 OXCT1 OXCT1 3756 0.11 0.56 YES
14 ALDH1B1 ALDH1B1 ALDH1B1 4497 0.091 0.54 YES
15 ACAT2 ACAT2 ACAT2 4531 0.09 0.56 YES
16 AKR1B10 AKR1B10 AKR1B10 5079 0.078 0.55 YES
17 ACADS ACADS ACADS 5113 0.077 0.56 YES
18 PDHA1 PDHA1 PDHA1 5204 0.075 0.57 YES
19 ALDH3A2 ALDH3A2 ALDH3A2 5676 0.066 0.56 NO
20 BDH2 BDH2 BDH2 5776 0.064 0.57 NO
21 ALDH9A1 ALDH9A1 ALDH9A1 7111 0.04 0.5 NO
22 ECHS1 ECHS1 ECHS1 8106 0.024 0.45 NO
23 HMGCL HMGCL HMGCL 8148 0.023 0.45 NO
24 ALDH7A1 ALDH7A1 ALDH7A1 8205 0.022 0.46 NO
25 ALDH2 ALDH2 ALDH2 8376 0.018 0.45 NO
26 OXCT2 OXCT2 OXCT2 9321 0.0028 0.4 NO
27 HADHA HADHA HADHA 10980 -0.024 0.31 NO
28 ACAT1 ACAT1 ACAT1 13376 -0.073 0.19 NO
29 PDHB PDHB PDHB 14552 -0.11 0.15 NO
30 BDH1 BDH1 BDH1 15501 -0.15 0.12 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 PYK2 PATHWAY.

Figure S48.  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 CHREBP2 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 MARS2 MARS2 MARS2 1805 0.19 -0.013 YES
2 TARSL2 TARSL2 TARSL2 2707 0.14 0.0029 YES
3 RARS RARS RARS 3921 0.1 -0.017 YES
4 HARS2 HARS2 HARS2 4007 0.1 0.026 YES
5 HARS HARS HARS 4010 0.1 0.074 YES
6 VARS2 VARS2 VARS2 4044 0.1 0.12 YES
7 PSTK PSTK PSTK 4509 0.091 0.14 YES
8 MTFMT MTFMT MTFMT 4589 0.089 0.17 YES
9 LARS LARS LARS 4623 0.088 0.21 YES
10 GARS GARS GARS 4945 0.081 0.23 YES
11 SEPSECS SEPSECS SEPSECS 5015 0.079 0.26 YES
12 EARS2 EARS2 EARS2 5020 0.079 0.3 YES
13 YARS2 YARS2 YARS2 5667 0.066 0.3 YES
14 AARS2 AARS2 AARS2 5839 0.063 0.32 YES
15 SARS2 SARS2 SARS2 5854 0.063 0.34 YES
16 MARS MARS MARS 5906 0.062 0.37 YES
17 FARS2 FARS2 FARS2 5933 0.061 0.4 YES
18 VARS VARS VARS 6871 0.044 0.36 NO
19 FARSA FARSA FARSA 7482 0.034 0.35 NO
20 KARS KARS KARS 7637 0.031 0.35 NO
21 SARS SARS SARS 7723 0.03 0.36 NO
22 LARS2 LARS2 LARS2 8460 0.017 0.33 NO
23 IARS2 IARS2 IARS2 8767 0.012 0.32 NO
24 IARS IARS IARS 8768 0.012 0.32 NO
25 WARS WARS WARS 8773 0.012 0.33 NO
26 FARSB FARSB FARSB 8932 0.0095 0.32 NO
27 EPRS EPRS EPRS 9028 0.0078 0.32 NO
28 NARS NARS NARS 9050 0.0075 0.32 NO
29 PARS2 PARS2 PARS2 9070 0.0071 0.32 NO
30 TARS TARS TARS 9122 0.0062 0.32 NO
31 NARS2 NARS2 NARS2 10337 -0.013 0.26 NO
32 CARS2 CARS2 CARS2 10398 -0.014 0.27 NO
33 DARS DARS DARS 10614 -0.018 0.26 NO
34 DARS2 DARS2 DARS2 11100 -0.026 0.25 NO
35 YARS YARS YARS 11330 -0.03 0.25 NO
36 RARS2 RARS2 RARS2 11974 -0.042 0.23 NO
37 AARS AARS AARS 11990 -0.042 0.25 NO
38 CARS CARS CARS 12010 -0.043 0.27 NO
39 WARS2 WARS2 WARS2 12108 -0.044 0.28 NO
40 QARS QARS QARS 13281 -0.071 0.25 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 CHREBP2 PATHWAY.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA CREB 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 PRKCB PRKCB PRKCB 111 0.5 0.14 YES
2 SOCS1 SOCS1 SOCS1 163 0.46 0.28 YES
3 GHR GHR GHR 352 0.38 0.38 YES
4 PIK3R1 PIK3R1 PIK3R1 957 0.27 0.43 YES
5 HNF1A HNF1A HNF1A 2333 0.16 0.4 NO
6 PRKCA PRKCA PRKCA 2879 0.14 0.41 NO
7 MAP2K1 MAP2K1 MAP2K1 4819 0.084 0.32 NO
8 INSR INSR INSR 6005 0.06 0.28 NO
9 JAK2 JAK2 JAK2 8743 0.013 0.12 NO
10 SRF SRF SRF 9318 0.0029 0.094 NO
11 SOS1 SOS1 SOS1 9786 -0.0044 0.069 NO
12 MAPK3 MAPK3 MAPK3 9833 -0.005 0.068 NO
13 GRB2 GRB2 GRB2 10200 -0.011 0.05 NO
14 IRS1 IRS1 IRS1 10525 -0.016 0.037 NO
15 MAPK1 MAPK1 MAPK1 10708 -0.019 0.032 NO
16 STAT5B STAT5B STAT5B 11160 -0.027 0.015 NO
17 RAF1 RAF1 RAF1 11552 -0.034 0.0032 NO
18 RPS6KA1 RPS6KA1 RPS6KA1 11996 -0.042 -0.0092 NO
19 SHC1 SHC1 SHC1 12134 -0.045 -0.0034 NO
20 STAT5A STAT5A STAT5A 12798 -0.059 -0.023 NO
21 PTPN6 PTPN6 PTPN6 13285 -0.071 -0.029 NO
22 PLCG1 PLCG1 PLCG1 13290 -0.071 -0.0082 NO
23 PIK3CA PIK3CA PIK3CA 13737 -0.083 -0.0086 NO
24 GH1 GH1 GH1 16502 -0.22 -0.098 NO
25 PIK3CG PIK3CG PIK3CG 16917 -0.28 -0.039 NO
26 SLC2A4 SLC2A4 SLC2A4 16948 -0.28 0.044 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 CREB PATHWAY.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CREB 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 PENTOSE PHOSPHATE 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 CYP19A1 CYP19A1 CYP19A1 28 0.63 0.083 YES
2 CYP17A1 CYP17A1 CYP17A1 219 0.44 0.13 YES
3 AKR1D1 AKR1D1 AKR1D1 279 0.41 0.18 YES
4 CYP3A5 CYP3A5 CYP3A5 409 0.37 0.23 YES
5 CYP11A1 CYP11A1 CYP11A1 733 0.3 0.25 YES
6 STS STS STS 943 0.27 0.27 YES
7 CYP3A43 CYP3A43 CYP3A43 1027 0.26 0.3 YES
8 SRD5A2 SRD5A2 SRD5A2 1221 0.24 0.32 YES
9 CYP3A7 CYP3A7 CYP3A7 1432 0.22 0.34 YES
10 SRD5A1 SRD5A1 SRD5A1 1595 0.2 0.36 YES
11 HSD17B6 HSD17B6 HSD17B6 1675 0.2 0.38 YES
12 AKR1C3 AKR1C3 AKR1C3 1691 0.2 0.41 YES
13 SULT1E1 SULT1E1 SULT1E1 1773 0.19 0.43 YES
14 AKR1C1 AKR1C1 AKR1C1 1923 0.18 0.45 YES
15 CYP7B1 CYP7B1 CYP7B1 1968 0.18 0.47 YES
16 CYP21A2 CYP21A2 CYP21A2 2022 0.18 0.49 YES
17 UGT2A1 UGT2A1 UGT2A1 2055 0.18 0.51 YES
18 CYP1A1 CYP1A1 CYP1A1 2123 0.17 0.53 YES
19 HSD17B3 HSD17B3 HSD17B3 2245 0.16 0.55 YES
20 UGT1A7 UGT1A7 UGT1A7 2574 0.15 0.55 YES
21 HSD3B2 HSD3B2 HSD3B2 2630 0.15 0.56 YES
22 HSD3B1 HSD3B1 HSD3B1 2970 0.13 0.56 NO
23 UGT2A3 UGT2A3 UGT2A3 3396 0.12 0.56 NO
24 CYP7A1 CYP7A1 CYP7A1 4493 0.091 0.5 NO
25 UGT1A6 UGT1A6 UGT1A6 5349 0.072 0.47 NO
26 AKR1C2 AKR1C2 AKR1C2 6556 0.05 0.4 NO
27 SRD5A3 SRD5A3 SRD5A3 7068 0.041 0.38 NO
28 HSD17B7 HSD17B7 HSD17B7 8296 0.02 0.32 NO
29 UGT2B4 UGT2B4 UGT2B4 8696 0.013 0.29 NO
30 CYP11B1 CYP11B1 CYP11B1 9734 -0.0036 0.24 NO
31 COMT COMT COMT 10863 -0.022 0.18 NO
32 HSD17B8 HSD17B8 HSD17B8 13093 -0.066 0.058 NO
33 CYP11B2 CYP11B2 CYP11B2 13519 -0.077 0.044 NO
34 HSD17B12 HSD17B12 HSD17B12 14160 -0.094 0.02 NO
35 CYP1B1 CYP1B1 CYP1B1 15350 -0.14 -0.028 NO
36 SULT2B1 SULT2B1 SULT2B1 15572 -0.15 -0.02 NO
37 HSD17B2 HSD17B2 HSD17B2 15610 -0.16 -0.00094 NO
38 HSD11B2 HSD11B2 HSD11B2 15641 -0.16 0.018 NO
39 UGT1A9 UGT1A9 UGT1A9 16195 -0.19 0.013 NO
40 HSD17B1 HSD17B1 HSD17B1 16858 -0.27 0.012 NO
41 HSD11B1 HSD11B1 HSD11B1 16898 -0.27 0.046 NO

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

Figure S54.  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 STEROID HORMONE BIOSYNTHESIS

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 POLR2J2 POLR2J2 POLR2J2 1346 0.23 0.048 YES
2 POLR3G POLR3G POLR3G 1575 0.21 0.15 YES
3 POLR1E POLR1E POLR1E 2798 0.14 0.16 YES
4 ZNRD1 ZNRD1 ZNRD1 2976 0.13 0.22 YES
5 POLR2J3 POLR2J3 POLR2J3 3204 0.12 0.28 YES
6 POLR3B POLR3B POLR3B 3646 0.11 0.31 YES
7 POLR2B POLR2B POLR2B 5090 0.078 0.27 YES
8 POLR2J POLR2J POLR2J 5405 0.071 0.29 YES
9 POLR3K POLR3K POLR3K 5503 0.069 0.33 YES
10 POLR2C POLR2C POLR2C 5999 0.06 0.33 YES
11 POLR2F POLR2F POLR2F 6160 0.057 0.35 YES
12 POLR2I POLR2I POLR2I 6677 0.048 0.35 NO
13 POLR1C POLR1C POLR1C 7939 0.026 0.29 NO
14 POLR3D POLR3D POLR3D 8596 0.015 0.26 NO
15 POLR2E POLR2E POLR2E 8895 0.01 0.25 NO
16 POLR1D POLR1D POLR1D 9146 0.0058 0.24 NO
17 POLR2K POLR2K POLR2K 9164 0.0056 0.24 NO
18 POLR2D POLR2D POLR2D 9879 -0.0058 0.21 NO
19 POLR2A POLR2A POLR2A 9934 -0.0066 0.21 NO
20 POLR3F POLR3F POLR3F 10504 -0.016 0.18 NO
21 POLR2L POLR2L POLR2L 10520 -0.016 0.19 NO
22 POLR3A POLR3A POLR3A 11007 -0.024 0.18 NO
23 POLR1B POLR1B POLR1B 11946 -0.041 0.15 NO
24 POLR1A POLR1A POLR1A 11984 -0.042 0.17 NO
25 POLR3GL POLR3GL POLR3GL 12519 -0.053 0.17 NO
26 POLR3H POLR3H POLR3H 12943 -0.063 0.18 NO
27 POLR2G POLR2G POLR2G 13561 -0.078 0.19 NO
28 POLR3C POLR3C POLR3C 13940 -0.088 0.21 NO

Figure S55.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS.

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

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

Table S29.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 111 0.5 0.14 YES
2 EGF EGF EGF 156 0.46 0.27 YES
3 EGFR EGFR EGFR 526 0.34 0.35 YES
4 PIK3R1 PIK3R1 PIK3R1 957 0.27 0.41 YES
5 RASA1 RASA1 RASA1 1280 0.23 0.46 YES
6 ELK1 ELK1 ELK1 2631 0.15 0.42 NO
7 PRKCA PRKCA PRKCA 2879 0.14 0.45 NO
8 MAPK8 MAPK8 MAPK8 3572 0.11 0.44 NO
9 MAP2K1 MAP2K1 MAP2K1 4819 0.084 0.4 NO
10 STAT6 STAT6 STAT6 5495 0.07 0.38 NO
11 JAK1 JAK1 JAK1 7313 0.037 0.29 NO
12 MAP3K1 MAP3K1 MAP3K1 7805 0.029 0.27 NO
13 CSNK2A1 CSNK2A1 CSNK2A1 8436 0.018 0.24 NO
14 STAT3 STAT3 STAT3 8680 0.014 0.23 NO
15 JUN JUN JUN 8887 0.01 0.22 NO
16 SRF SRF SRF 9318 0.0029 0.2 NO
17 SOS1 SOS1 SOS1 9786 -0.0044 0.17 NO
18 MAPK3 MAPK3 MAPK3 9833 -0.005 0.17 NO
19 GRB2 GRB2 GRB2 10200 -0.011 0.15 NO
20 MAP2K4 MAP2K4 MAP2K4 10579 -0.017 0.14 NO
21 STAT5B STAT5B STAT5B 11160 -0.027 0.11 NO
22 RAF1 RAF1 RAF1 11552 -0.034 0.1 NO
23 SHC1 SHC1 SHC1 12134 -0.045 0.081 NO
24 STAT5A STAT5A STAT5A 12798 -0.059 0.061 NO
25 PLCG1 PLCG1 PLCG1 13290 -0.071 0.054 NO
26 STAT2 STAT2 STAT2 13334 -0.072 0.073 NO
27 PIK3CA PIK3CA PIK3CA 13737 -0.083 0.075 NO
28 STAT1 STAT1 STAT1 14123 -0.093 0.08 NO
29 FOS FOS FOS 14794 -0.12 0.076 NO
30 STAT4 STAT4 STAT4 17116 -0.3 0.034 NO

Figure S57.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG O GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CES7 CES7 CES7 2 0.89 0.16 YES
2 UPP2 UPP2 UPP2 317 0.4 0.21 YES
3 CYP3A5 CYP3A5 CYP3A5 409 0.37 0.27 YES
4 CYP2A6 CYP2A6 CYP2A6 567 0.33 0.32 YES
5 CYP3A43 CYP3A43 CYP3A43 1027 0.26 0.34 YES
6 CYP2A7 CYP2A7 CYP2A7 1063 0.26 0.39 YES
7 CYP3A7 CYP3A7 CYP3A7 1432 0.22 0.41 YES
8 XDH XDH XDH 1503 0.21 0.44 YES
9 UGT2A1 UGT2A1 UGT2A1 2055 0.18 0.44 YES
10 DPYD DPYD DPYD 2348 0.16 0.45 YES
11 HPRT1 HPRT1 HPRT1 2497 0.15 0.47 YES
12 UGT1A7 UGT1A7 UGT1A7 2574 0.15 0.5 YES
13 TPMT TPMT TPMT 2717 0.14 0.51 YES
14 DPYS DPYS DPYS 3240 0.12 0.5 YES
15 UGT2A3 UGT2A3 UGT2A3 3396 0.12 0.52 YES
16 NAT1 NAT1 NAT1 3771 0.11 0.52 YES
17 CES2 CES2 CES2 3939 0.1 0.52 YES
18 UPP1 UPP1 UPP1 4988 0.08 0.48 NO
19 UGT1A6 UGT1A6 UGT1A6 5349 0.072 0.47 NO
20 GUSB GUSB GUSB 5577 0.068 0.47 NO
21 NAT2 NAT2 NAT2 8198 0.022 0.33 NO
22 CDA CDA CDA 8317 0.02 0.32 NO
23 TK1 TK1 TK1 8347 0.019 0.33 NO
24 UGT2B4 UGT2B4 UGT2B4 8696 0.013 0.31 NO
25 ITPA ITPA ITPA 8705 0.013 0.31 NO
26 TK2 TK2 TK2 8795 0.012 0.31 NO
27 CES1 CES1 CES1 9144 0.0058 0.29 NO
28 UCK1 UCK1 UCK1 10124 -0.0096 0.24 NO
29 UPB1 UPB1 UPB1 10883 -0.022 0.2 NO
30 UMPS UMPS UMPS 11419 -0.032 0.17 NO
31 UCKL1 UCKL1 UCKL1 12595 -0.055 0.12 NO
32 IMPDH2 IMPDH2 IMPDH2 14616 -0.11 0.021 NO
33 UCK2 UCK2 UCK2 14993 -0.12 0.022 NO
34 GMPS GMPS GMPS 15308 -0.14 0.029 NO
35 IMPDH1 IMPDH1 IMPDH1 15843 -0.17 0.029 NO
36 UGT1A9 UGT1A9 UGT1A9 16195 -0.19 0.044 NO
37 TYMP TYMP TYMP 16598 -0.24 0.063 NO

Figure S59.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BUTANOATE METABOLISM.

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

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 BIOPEPTIDES PATHWAY 38 genes.ES.table 0.45 1.5 0.056 0.2 0.87 0.24 0.19 0.19 0.15 0.004
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.41 1.5 0.054 0.21 0.85 0.12 0.07 0.11 0.15 0.011
BIOCARTA HDAC PATHWAY 26 genes.ES.table 0.55 1.7 0.004 0.5 0.47 0.27 0.18 0.22 0 0.18
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.53 1.6 0.039 0.32 0.77 0.47 0.29 0.33 0.21 0.058
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.53 1.5 0.067 0.21 0.84 0.27 0.12 0.24 0.15 0.013
BIOCARTA GH PATHWAY 26 genes.ES.table 0.47 1.5 0.04 0.2 0.86 0.19 0.094 0.18 0.15 0.005
BIOCARTA IL2RB PATHWAY 37 genes.ES.table 0.72 1.9 0.002 0.18 0.089 0.35 0.097 0.32 0 0.072
BIOCARTA GSK3 PATHWAY 26 genes.ES.table 0.51 1.6 0.021 0.36 0.73 0.19 0.12 0.17 0.23 0.08
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.44 1.4 0.1 0.21 0.91 0.41 0.29 0.29 0.16 0.001
BIOCARTA KERATINOCYTE PATHWAY 45 genes.ES.table 0.44 1.4 0.1 0.24 0.94 0.49 0.28 0.35 0.2 0.004
genes ES table in pathway: BIOCARTA BIOPEPTIDES 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 IL2RB IL2RB IL2RB 31 0.88 0.11 YES
2 FASLG FASLG FASLG 138 0.68 0.19 YES
3 PIK3CG PIK3CG PIK3CG 163 0.66 0.27 YES
4 IL2RG IL2RG IL2RG 202 0.64 0.35 YES
5 IL2RA IL2RA IL2RA 336 0.58 0.41 YES
6 IKZF3 IKZF3 IKZF3 395 0.55 0.48 YES
7 SYK SYK SYK 545 0.5 0.53 YES
8 JAK3 JAK3 JAK3 794 0.44 0.58 YES
9 BCL2 BCL2 BCL2 1394 0.33 0.58 YES
10 PTPN6 PTPN6 PTPN6 1559 0.31 0.61 YES
11 STAT5A STAT5A STAT5A 1627 0.3 0.65 YES
12 PIK3R1 PIK3R1 PIK3R1 1657 0.3 0.68 YES
13 FAS FAS FAS 1721 0.29 0.72 YES
14 STAT5B STAT5B STAT5B 2744 0.2 0.68 NO
15 MAPK3 MAPK3 MAPK3 4472 0.11 0.6 NO
16 JAK1 JAK1 JAK1 4779 0.097 0.6 NO
17 FOS FOS FOS 6045 0.06 0.53 NO
18 CFLAR CFLAR CFLAR 6344 0.052 0.52 NO
19 SOS1 SOS1 SOS1 6990 0.037 0.49 NO
20 BAD BAD BAD 7089 0.034 0.49 NO
21 RPS6KB1 RPS6KB1 RPS6KB1 7186 0.032 0.49 NO
22 BCL2L1 BCL2L1 BCL2L1 7288 0.03 0.48 NO
23 SOCS3 SOCS3 SOCS3 7444 0.027 0.48 NO
24 GRB2 GRB2 GRB2 8173 0.012 0.44 NO
25 RAF1 RAF1 RAF1 8205 0.012 0.44 NO
26 PIK3CA PIK3CA PIK3CA 8369 0.0084 0.43 NO
27 SHC1 SHC1 SHC1 8921 -0.0026 0.4 NO
28 NMI NMI NMI 8928 -0.0029 0.4 NO
29 AKT1 AKT1 AKT1 9017 -0.0045 0.4 NO
30 IRS1 IRS1 IRS1 10772 -0.038 0.3 NO
31 CBL CBL CBL 11295 -0.049 0.28 NO
32 MAPK1 MAPK1 MAPK1 11645 -0.056 0.26 NO
33 CRKL CRKL CRKL 11706 -0.058 0.27 NO
34 SOCS1 SOCS1 SOCS1 12933 -0.088 0.21 NO
35 PPIA PPIA PPIA 13454 -0.1 0.19 NO
36 HRAS HRAS HRAS 13470 -0.1 0.21 NO
37 MYC MYC MYC 16006 -0.27 0.097 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 BIOPEPTIDES PATHWAY.

Figure S62.  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 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 UGT1A6 UGT1A6 UGT1A6 3 1 0.12 YES
2 UGT1A9 UGT1A9 UGT1A9 16 0.92 0.23 YES
3 UGT1A7 UGT1A7 UGT1A7 45 0.82 0.32 YES
4 AMY2A AMY2A AMY2A 231 0.62 0.39 YES
5 AMY2B AMY2B AMY2B 504 0.51 0.43 YES
6 ENPP1 ENPP1 ENPP1 526 0.51 0.49 YES
7 HK2 HK2 HK2 641 0.48 0.54 YES
8 UGT2A3 UGT2A3 UGT2A3 891 0.42 0.58 YES
9 AMY1A AMY1A AMY1A 949 0.41 0.62 YES
10 UGT2A1 UGT2A1 UGT2A1 1083 0.38 0.66 YES
11 UGT2B4 UGT2B4 UGT2B4 2128 0.25 0.63 NO
12 GYS2 GYS2 GYS2 2244 0.24 0.65 NO
13 PYGB PYGB PYGB 3516 0.15 0.6 NO
14 UGDH UGDH UGDH 5625 0.071 0.49 NO
15 HK3 HK3 HK3 5732 0.068 0.49 NO
16 GAA GAA GAA 6606 0.045 0.44 NO
17 PYGL PYGL PYGL 6798 0.041 0.44 NO
18 AGL AGL AGL 7755 0.02 0.39 NO
19 GANC GANC GANC 7846 0.018 0.38 NO
20 UGP2 UGP2 UGP2 8066 0.014 0.37 NO
21 PGM1 PGM1 PGM1 8220 0.012 0.37 NO
22 GBE1 GBE1 GBE1 8642 0.0031 0.34 NO
23 GPI GPI GPI 9033 -0.0046 0.32 NO
24 GYS1 GYS1 GYS1 10842 -0.04 0.22 NO
25 PGM2 PGM2 PGM2 11103 -0.045 0.22 NO
26 MGAM MGAM MGAM 12063 -0.066 0.17 NO
27 HK1 HK1 HK1 13339 -0.1 0.11 NO
28 PYGM PYGM PYGM 13419 -0.1 0.12 NO
29 GUSB GUSB GUSB 13561 -0.11 0.12 NO
30 G6PC2 G6PC2 G6PC2 14535 -0.15 0.083 NO
31 GBA3 GBA3 GBA3 14730 -0.16 0.091 NO
32 GCK GCK GCK 15429 -0.21 0.076 NO
33 PGM2L1 PGM2L1 PGM2L1 15507 -0.22 0.097 NO
34 ENPP3 ENPP3 ENPP3 15716 -0.24 0.11 NO

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

Figure S64.  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 HDAC 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 IGF1 IGF1 IGF1 95 0.72 0.19 YES
2 PIK3CG PIK3CG PIK3CG 163 0.66 0.36 YES
3 MAP2K6 MAP2K6 MAP2K6 1006 0.4 0.42 YES
4 PIK3R1 PIK3R1 PIK3R1 1657 0.3 0.47 YES
5 NFATC2 NFATC2 NFATC2 2108 0.25 0.51 YES
6 HDAC5 HDAC5 HDAC5 2984 0.18 0.51 YES
7 CAMK1G CAMK1G CAMK1G 3168 0.17 0.55 YES
8 NFATC1 NFATC1 NFATC1 4772 0.097 0.48 NO
9 IGF1R IGF1R IGF1R 6025 0.06 0.43 NO
10 PPP3CA PPP3CA PPP3CA 6175 0.056 0.44 NO
11 PPP3CC PPP3CC PPP3CC 7429 0.027 0.37 NO
12 MEF2A MEF2A MEF2A 7868 0.018 0.35 NO
13 PIK3CA PIK3CA PIK3CA 8369 0.0084 0.32 NO
14 MAPK7 MAPK7 MAPK7 8375 0.0082 0.33 NO
15 AKT1 AKT1 AKT1 9017 -0.0045 0.29 NO
16 CABIN1 CABIN1 CABIN1 9655 -0.016 0.26 NO
17 PPP3CB PPP3CB PPP3CB 10164 -0.026 0.24 NO
18 CALM1 CALM1 CALM1 10276 -0.029 0.24 NO
19 MEF2D MEF2D MEF2D 10534 -0.034 0.24 NO
20 CAMK1 CAMK1 CAMK1 11781 -0.06 0.18 NO
21 INSR INSR INSR 12175 -0.069 0.18 NO
22 YWHAH YWHAH YWHAH 12597 -0.079 0.18 NO
23 CALM3 CALM3 CALM3 12638 -0.08 0.19 NO
24 CALM2 CALM2 CALM2 12956 -0.089 0.2 NO
25 MAPK14 MAPK14 MAPK14 13897 -0.12 0.18 NO
26 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 14241 -0.14 0.2 NO

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

Figure S66.  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 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 STAT4 STAT4 STAT4 122 0.7 0.16 YES
2 PIK3CG PIK3CG PIK3CG 163 0.66 0.31 YES
3 PRKCA PRKCA PRKCA 301 0.59 0.44 YES
4 STAT5A STAT5A STAT5A 1627 0.3 0.43 YES
5 PIK3R1 PIK3R1 PIK3R1 1657 0.3 0.5 YES
6 STAT5B STAT5B STAT5B 2744 0.2 0.49 YES
7 STAT6 STAT6 STAT6 3336 0.16 0.49 YES
8 MAPK3 MAPK3 MAPK3 4472 0.11 0.45 YES
9 MAP3K1 MAP3K1 MAP3K1 4767 0.097 0.46 YES
10 MAP2K4 MAP2K4 MAP2K4 4774 0.097 0.48 YES
11 JAK1 JAK1 JAK1 4779 0.097 0.5 YES
12 JUN JUN JUN 4911 0.093 0.52 YES
13 STAT2 STAT2 STAT2 4938 0.091 0.54 YES
14 STAT3 STAT3 STAT3 5143 0.085 0.55 YES
15 CSNK2A1 CSNK2A1 CSNK2A1 5932 0.062 0.52 NO
16 RASA1 RASA1 RASA1 5938 0.062 0.53 NO
17 FOS FOS FOS 6045 0.06 0.54 NO
18 PRKCB PRKCB PRKCB 6978 0.037 0.5 NO
19 SOS1 SOS1 SOS1 6990 0.037 0.5 NO
20 PDGFRA PDGFRA PDGFRA 8054 0.014 0.45 NO
21 PLCG1 PLCG1 PLCG1 8085 0.014 0.45 NO
22 GRB2 GRB2 GRB2 8173 0.012 0.45 NO
23 RAF1 RAF1 RAF1 8205 0.012 0.45 NO
24 PIK3CA PIK3CA PIK3CA 8369 0.0084 0.44 NO
25 SHC1 SHC1 SHC1 8921 -0.0026 0.41 NO
26 SRF SRF SRF 9251 -0.0085 0.39 NO
27 STAT1 STAT1 STAT1 9907 -0.022 0.36 NO
28 PDGFA PDGFA PDGFA 11262 -0.048 0.3 NO
29 MAP2K1 MAP2K1 MAP2K1 12405 -0.074 0.25 NO
30 ELK1 ELK1 ELK1 12692 -0.081 0.25 NO
31 MAPK8 MAPK8 MAPK8 14381 -0.14 0.19 NO

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

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

Table 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 ITK ITK ITK 27 0.89 0.037 YES
2 CD247 CD247 CD247 62 0.78 0.07 YES
3 CD3E CD3E CD3E 64 0.78 0.1 YES
4 PTPRC PTPRC PTPRC 116 0.7 0.13 YES
5 CD40LG CD40LG CD40LG 142 0.68 0.16 YES
6 GRAP2 GRAP2 GRAP2 158 0.67 0.19 YES
7 PIK3CG PIK3CG PIK3CG 163 0.66 0.22 YES
8 CD28 CD28 CD28 183 0.65 0.24 YES
9 CD3G CD3G CD3G 213 0.64 0.27 YES
10 CD8B CD8B CD8B 242 0.62 0.3 YES
11 CD3D CD3D CD3D 265 0.6 0.32 YES
12 CD8A CD8A CD8A 279 0.6 0.35 YES
13 ICOS ICOS ICOS 306 0.59 0.37 YES
14 ZAP70 ZAP70 ZAP70 308 0.59 0.4 YES
15 VAV3 VAV3 VAV3 322 0.58 0.42 YES
16 CD4 CD4 CD4 328 0.58 0.45 YES
17 LCK LCK LCK 342 0.57 0.47 YES
18 LCP2 LCP2 LCP2 360 0.56 0.49 YES
19 PIK3CD PIK3CD PIK3CD 513 0.51 0.51 YES
20 VAV1 VAV1 VAV1 889 0.42 0.5 YES
21 CTLA4 CTLA4 CTLA4 961 0.41 0.52 YES
22 PDCD1 PDCD1 PDCD1 1042 0.39 0.53 YES
23 TNF TNF TNF 1337 0.34 0.53 YES
24 MAP3K8 MAP3K8 MAP3K8 1551 0.31 0.53 YES
25 PTPN6 PTPN6 PTPN6 1559 0.31 0.55 YES
26 LAT LAT LAT 1652 0.3 0.55 YES
27 PIK3R1 PIK3R1 PIK3R1 1657 0.3 0.57 YES
28 RASGRP1 RASGRP1 RASGRP1 1814 0.28 0.57 YES
29 PIK3R5 PIK3R5 PIK3R5 1998 0.26 0.57 YES
30 CARD11 CARD11 CARD11 2060 0.25 0.58 YES
31 NFATC2 NFATC2 NFATC2 2108 0.25 0.59 YES
32 IL10 IL10 IL10 2438 0.22 0.58 NO
33 CSF2 CSF2 CSF2 2535 0.22 0.58 NO
34 IKBKB IKBKB IKBKB 2693 0.21 0.58 NO
35 PAK7 PAK7 PAK7 2877 0.19 0.58 NO
36 AKT3 AKT3 AKT3 3103 0.18 0.57 NO
37 PIK3CB PIK3CB PIK3CB 3429 0.16 0.56 NO
38 IFNG IFNG IFNG 3532 0.15 0.56 NO
39 NFATC3 NFATC3 NFATC3 3724 0.14 0.56 NO
40 MAP3K14 MAP3K14 MAP3K14 3921 0.13 0.55 NO
41 FYN FYN FYN 4175 0.12 0.55 NO
42 MAPK3 MAPK3 MAPK3 4472 0.11 0.53 NO
43 PIK3R2 PIK3R2 PIK3R2 4715 0.099 0.52 NO
44 NFATC1 NFATC1 NFATC1 4772 0.097 0.52 NO
45 NFKBIA NFKBIA NFKBIA 4886 0.094 0.52 NO
46 JUN JUN JUN 4911 0.093 0.52 NO
47 NFKB1 NFKB1 NFKB1 4945 0.091 0.53 NO
48 DLG1 DLG1 DLG1 4994 0.089 0.53 NO
49 NCK1 NCK1 NCK1 5107 0.086 0.52 NO
50 NFAT5 NFAT5 NFAT5 5187 0.084 0.52 NO
51 MAPK9 MAPK9 MAPK9 5210 0.083 0.53 NO
52 PAK3 PAK3 PAK3 5469 0.075 0.52 NO
53 MALT1 MALT1 MALT1 5924 0.062 0.49 NO
54 FOS FOS FOS 6045 0.06 0.49 NO
55 PPP3CA PPP3CA PPP3CA 6175 0.056 0.48 NO
56 NFKBIE NFKBIE NFKBIE 6237 0.054 0.48 NO
57 PAK1 PAK1 PAK1 6317 0.053 0.48 NO
58 CDK4 CDK4 CDK4 6373 0.051 0.48 NO
59 NCK2 NCK2 NCK2 6388 0.051 0.48 NO
60 CBLB CBLB CBLB 6956 0.038 0.45 NO
61 SOS1 SOS1 SOS1 6990 0.037 0.45 NO
62 PPP3CC PPP3CC PPP3CC 7429 0.027 0.43 NO
63 IKBKG IKBKG IKBKG 7452 0.026 0.43 NO
64 TEC TEC TEC 7695 0.022 0.41 NO
65 PAK2 PAK2 PAK2 7769 0.02 0.41 NO
66 PLCG1 PLCG1 PLCG1 8085 0.014 0.39 NO
67 GRB2 GRB2 GRB2 8173 0.012 0.39 NO
68 PIK3R3 PIK3R3 PIK3R3 8181 0.012 0.39 NO
69 RAF1 RAF1 RAF1 8205 0.012 0.39 NO
70 PIK3CA PIK3CA PIK3CA 8369 0.0084 0.38 NO
71 RELA RELA RELA 8802 -0.00044 0.35 NO
72 SOS2 SOS2 SOS2 8805 -0.00059 0.35 NO
73 GSK3B GSK3B GSK3B 9003 -0.0042 0.34 NO
74 AKT1 AKT1 AKT1 9017 -0.0045 0.34 NO
75 RHOA RHOA RHOA 9240 -0.0083 0.33 NO
76 CHP2 CHP2 CHP2 9457 -0.013 0.32 NO
77 MAPK13 MAPK13 MAPK13 9640 -0.016 0.31 NO
78 MAP3K7 MAP3K7 MAP3K7 9753 -0.019 0.3 NO
79 MAP2K2 MAP2K2 MAP2K2 10117 -0.026 0.28 NO
80 PPP3CB PPP3CB PPP3CB 10164 -0.026 0.28 NO
81 NFKBIB NFKBIB NFKBIB 10189 -0.027 0.28 NO
82 CDC42 CDC42 CDC42 10489 -0.033 0.27 NO
83 BCL10 BCL10 BCL10 10492 -0.033 0.27 NO
84 PRKCQ PRKCQ PRKCQ 10545 -0.034 0.27 NO
85 PPP3R1 PPP3R1 PPP3R1 10684 -0.037 0.26 NO
86 MAP2K7 MAP2K7 MAP2K7 11117 -0.045 0.24 NO
87 CBL CBL CBL 11295 -0.049 0.23 NO
88 MAPK1 MAPK1 MAPK1 11645 -0.056 0.21 NO
89 CHUK CHUK CHUK 12387 -0.074 0.17 NO
90 MAP2K1 MAP2K1 MAP2K1 12405 -0.074 0.18 NO
91 NRAS NRAS NRAS 12488 -0.076 0.18 NO
92 KRAS KRAS KRAS 13044 -0.091 0.15 NO
93 MAPK11 MAPK11 MAPK11 13383 -0.1 0.13 NO
94 CHP CHP CHP 13741 -0.12 0.12 NO
95 MAPK14 MAPK14 MAPK14 13897 -0.12 0.11 NO
96 AKT2 AKT2 AKT2 14564 -0.15 0.083 NO
97 PAK4 PAK4 PAK4 14674 -0.16 0.084 NO
98 PDK1 PDK1 PDK1 15910 -0.26 0.025 NO
99 VAV2 VAV2 VAV2 16082 -0.28 0.027 NO
100 MAPK12 MAPK12 MAPK12 16616 -0.35 0.012 NO
101 PAK6 PAK6 PAK6 16712 -0.37 0.023 NO
102 NFATC4 NFATC4 NFATC4 17665 -0.77 0.003 NO

Figure S69.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.

Figure S70.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA GH PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HLA-DRB5 HLA-DRB5 HLA-DRB5 174 0.66 0.031 YES
2 HLA-DQA1 HLA-DQA1 HLA-DQA1 206 0.64 0.07 YES
3 HLA-DOA HLA-DOA HLA-DOA 221 0.63 0.11 YES
4 CD8B CD8B CD8B 242 0.62 0.15 YES
5 CD8A CD8A CD8A 279 0.6 0.18 YES
6 HLA-DQA2 HLA-DQA2 HLA-DQA2 284 0.6 0.22 YES
7 KLRD1 KLRD1 KLRD1 303 0.59 0.25 YES
8 CD4 CD4 CD4 328 0.58 0.29 YES
9 HLA-DQB1 HLA-DQB1 HLA-DQB1 455 0.53 0.31 YES
10 CTSS CTSS CTSS 562 0.5 0.34 YES
11 HLA-DRB1 HLA-DRB1 HLA-DRB1 584 0.49 0.37 YES
12 CIITA CIITA CIITA 598 0.49 0.4 YES
13 HLA-DPA1 HLA-DPA1 HLA-DPA1 666 0.47 0.42 YES
14 IFI30 IFI30 IFI30 795 0.44 0.44 YES
15 HLA-DPB1 HLA-DPB1 HLA-DPB1 865 0.43 0.47 YES
16 LTA LTA LTA 931 0.42 0.49 YES
17 HLA-DOB HLA-DOB HLA-DOB 939 0.41 0.51 YES
18 KIR2DS4 KIR2DS4 KIR2DS4 1052 0.39 0.53 YES
19 HLA-DRA HLA-DRA HLA-DRA 1065 0.39 0.56 YES
20 HLA-F HLA-F HLA-F 1179 0.37 0.57 YES
21 CD74 CD74 CD74 1207 0.36 0.59 YES
22 KIR2DL1 KIR2DL1 KIR2DL1 1230 0.36 0.62 YES
23 HLA-DMA HLA-DMA HLA-DMA 1492 0.32 0.62 YES
24 KIR3DL2 KIR3DL2 KIR3DL2 1493 0.32 0.64 YES
25 KIR3DL1 KIR3DL1 KIR3DL1 1778 0.28 0.64 YES
26 KLRC1 KLRC1 KLRC1 1887 0.27 0.65 YES
27 HLA-E HLA-E HLA-E 2286 0.24 0.64 YES
28 HLA-B HLA-B HLA-B 2307 0.24 0.66 YES
29 HLA-A HLA-A HLA-A 2371 0.23 0.67 YES
30 KLRC4 KLRC4 KLRC4 2750 0.2 0.66 YES
31 KIR2DL3 KIR2DL3 KIR2DL3 2806 0.2 0.67 YES
32 HLA-C HLA-C HLA-C 3011 0.18 0.67 YES
33 B2M B2M B2M 3070 0.18 0.68 YES
34 HLA-DMB HLA-DMB HLA-DMB 3348 0.16 0.67 YES
35 HLA-G HLA-G HLA-G 3427 0.16 0.68 YES
36 NFYB NFYB NFYB 3496 0.15 0.68 YES
37 CTSB CTSB CTSB 3624 0.15 0.68 YES
38 KLRC3 KLRC3 KLRC3 3992 0.13 0.67 NO
39 HSPA2 HSPA2 HSPA2 4193 0.12 0.67 NO
40 TAPBP TAPBP TAPBP 4406 0.11 0.66 NO
41 KIR2DL4 KIR2DL4 KIR2DL4 4593 0.1 0.66 NO
42 HSPA1L HSPA1L HSPA1L 4771 0.097 0.66 NO
43 RFXAP RFXAP RFXAP 5477 0.074 0.62 NO
44 TAP1 TAP1 TAP1 5513 0.073 0.62 NO
45 CTSL1 CTSL1 CTSL1 5530 0.073 0.63 NO
46 CANX CANX CANX 5899 0.063 0.61 NO
47 CREB1 CREB1 CREB1 6212 0.055 0.6 NO
48 CALR CALR CALR 6865 0.04 0.56 NO
49 HSP90AA1 HSP90AA1 HSP90AA1 7417 0.027 0.53 NO
50 LGMN LGMN LGMN 7582 0.024 0.52 NO
51 PDIA3 PDIA3 PDIA3 7817 0.019 0.51 NO
52 PSME3 PSME3 PSME3 7960 0.016 0.5 NO
53 KLRC2 KLRC2 KLRC2 8097 0.014 0.5 NO
54 HSPA6 HSPA6 HSPA6 9274 -0.0089 0.43 NO
55 HSPA4 HSPA4 HSPA4 9495 -0.013 0.42 NO
56 HSPA1B HSPA1B HSPA1B 9606 -0.016 0.41 NO
57 NFYC NFYC NFYC 9673 -0.017 0.41 NO
58 TAP2 TAP2 TAP2 9733 -0.018 0.41 NO
59 PSME1 PSME1 PSME1 10393 -0.031 0.37 NO
60 HSPA5 HSPA5 HSPA5 11030 -0.043 0.34 NO
61 HSPA8 HSPA8 HSPA8 11936 -0.063 0.29 NO
62 HSPA1A HSPA1A HSPA1A 12428 -0.075 0.27 NO
63 NFYA NFYA NFYA 12476 -0.076 0.27 NO
64 RFX5 RFX5 RFX5 13276 -0.098 0.23 NO
65 RFXANK RFXANK RFXANK 13869 -0.12 0.21 NO
66 PSME2 PSME2 PSME2 14962 -0.17 0.16 NO

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

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CCL5 CCL5 CCL5 119 0.7 0.09 YES
2 CASP1 CASP1 CASP1 152 0.67 0.18 YES
3 IL33 IL33 IL33 345 0.57 0.25 YES
4 PYCARD PYCARD PYCARD 390 0.55 0.32 YES
5 IKBKE IKBKE IKBKE 446 0.53 0.39 YES
6 RIPK3 RIPK3 RIPK3 797 0.44 0.43 YES
7 ZBP1 ZBP1 ZBP1 953 0.41 0.48 YES
8 CXCL10 CXCL10 CXCL10 989 0.4 0.54 YES
9 CCL4 CCL4 CCL4 1800 0.28 0.53 YES
10 IL18 IL18 IL18 1807 0.28 0.57 YES
11 TMEM173 TMEM173 TMEM173 2136 0.25 0.58 YES
12 IL1B IL1B IL1B 2463 0.22 0.59 YES
13 CCL4L2 CCL4L2 CCL4L2 2532 0.22 0.62 YES
14 IRF7 IRF7 IRF7 2641 0.21 0.64 YES
15 IKBKB IKBKB IKBKB 2693 0.21 0.67 YES
16 DDX58 DDX58 DDX58 4224 0.12 0.6 NO
17 AIM2 AIM2 AIM2 4852 0.094 0.58 NO
18 NFKBIA NFKBIA NFKBIA 4886 0.094 0.59 NO
19 NFKB1 NFKB1 NFKB1 4945 0.091 0.6 NO
20 IL6 IL6 IL6 5982 0.061 0.55 NO
21 POLR3F POLR3F POLR3F 6125 0.057 0.55 NO
22 POLR3GL POLR3GL POLR3GL 6512 0.048 0.53 NO
23 POLR3G POLR3G POLR3G 6687 0.044 0.53 NO
24 MAVS MAVS MAVS 7031 0.036 0.51 NO
25 IKBKG IKBKG IKBKG 7452 0.026 0.49 NO
26 RIPK1 RIPK1 RIPK1 7939 0.017 0.47 NO
27 POLR3B POLR3B POLR3B 7952 0.016 0.47 NO
28 TBK1 TBK1 TBK1 7991 0.016 0.47 NO
29 IRF3 IRF3 IRF3 8027 0.015 0.47 NO
30 POLR3K POLR3K POLR3K 8624 0.0035 0.44 NO
31 RELA RELA RELA 8802 -0.00044 0.43 NO
32 ADAR ADAR ADAR 8997 -0.0042 0.42 NO
33 TREX1 TREX1 TREX1 9786 -0.019 0.37 NO
34 NFKBIB NFKBIB NFKBIB 10189 -0.027 0.35 NO
35 POLR3C POLR3C POLR3C 11210 -0.047 0.3 NO
36 POLR3D POLR3D POLR3D 11802 -0.06 0.28 NO
37 POLR1C POLR1C POLR1C 12246 -0.07 0.26 NO
38 CHUK CHUK CHUK 12387 -0.074 0.26 NO
39 POLR1D POLR1D POLR1D 12900 -0.087 0.25 NO
40 POLR3A POLR3A POLR3A 12904 -0.088 0.26 NO
41 POLR3H POLR3H POLR3H 12940 -0.089 0.27 NO

Figure S73.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL2RB PATHWAY.

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

genes ES table in pathway: BIOCARTA GSK3 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 UGT1A6 UGT1A6 UGT1A6 3 1 0.18 YES
2 UGT1A9 UGT1A9 UGT1A9 16 0.92 0.33 YES
3 UGT1A7 UGT1A7 UGT1A7 45 0.82 0.47 YES
4 UGT2A3 UGT2A3 UGT2A3 891 0.42 0.5 YES
5 UGT2A1 UGT2A1 UGT2A1 1083 0.38 0.55 YES
6 UGT2B4 UGT2B4 UGT2B4 2128 0.25 0.53 YES
7 CP CP CP 2251 0.24 0.57 YES
8 BLVRB BLVRB BLVRB 2689 0.21 0.58 YES
9 ALAD ALAD ALAD 3263 0.17 0.57 YES
10 FTH1 FTH1 FTH1 3863 0.13 0.56 YES
11 BLVRA BLVRA BLVRA 4066 0.12 0.57 YES
12 COX10 COX10 COX10 4337 0.11 0.58 YES
13 UROD UROD UROD 4395 0.11 0.59 YES
14 EARS2 EARS2 EARS2 5418 0.076 0.55 NO
15 FECH FECH FECH 6913 0.039 0.47 NO
16 PPOX PPOX PPOX 7242 0.031 0.46 NO
17 HMOX1 HMOX1 HMOX1 7512 0.025 0.45 NO
18 COX15 COX15 COX15 9007 -0.0043 0.36 NO
19 ALAS2 ALAS2 ALAS2 9031 -0.0046 0.36 NO
20 HMOX2 HMOX2 HMOX2 11067 -0.044 0.25 NO
21 CPOX CPOX CPOX 11586 -0.055 0.23 NO
22 UROS UROS UROS 12262 -0.071 0.21 NO
23 MMAB MMAB MMAB 13111 -0.093 0.18 NO
24 ALAS1 ALAS1 ALAS1 13411 -0.1 0.18 NO
25 GUSB GUSB GUSB 13561 -0.11 0.19 NO
26 HMBS HMBS HMBS 14297 -0.14 0.17 NO
27 EPRS EPRS EPRS 14410 -0.14 0.19 NO

Figure S75.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA GSK3 PATHWAY.

Figure S76.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GSK3 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 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 CD247 CD247 CD247 62 0.78 0.08 YES
2 CD3E CD3E CD3E 64 0.78 0.16 YES
3 PIK3CG PIK3CG PIK3CG 163 0.66 0.23 YES
4 CD3G CD3G CD3G 213 0.64 0.29 YES
5 CD3D CD3D CD3D 265 0.6 0.36 YES
6 PRKCA PRKCA PRKCA 301 0.59 0.42 YES
7 ZAP70 ZAP70 ZAP70 308 0.59 0.48 YES
8 LCK LCK LCK 342 0.57 0.54 YES
9 VAV1 VAV1 VAV1 889 0.42 0.55 YES
10 LAT LAT LAT 1652 0.3 0.54 YES
11 PIK3R1 PIK3R1 PIK3R1 1657 0.3 0.57 YES
12 NFATC2 NFATC2 NFATC2 2108 0.25 0.58 YES
13 NFATC3 NFATC3 NFATC3 3724 0.14 0.5 NO
14 FYN FYN FYN 4175 0.12 0.49 NO
15 MAPK3 MAPK3 MAPK3 4472 0.11 0.48 NO
16 MAP3K1 MAP3K1 MAP3K1 4767 0.097 0.48 NO
17 NFATC1 NFATC1 NFATC1 4772 0.097 0.49 NO
18 MAP2K4 MAP2K4 MAP2K4 4774 0.097 0.5 NO
19 NFKBIA NFKBIA NFKBIA 4886 0.094 0.5 NO
20 JUN JUN JUN 4911 0.093 0.51 NO
21 NFKB1 NFKB1 NFKB1 4945 0.091 0.52 NO
22 RASA1 RASA1 RASA1 5938 0.062 0.47 NO
23 FOS FOS FOS 6045 0.06 0.47 NO
24 PPP3CA PPP3CA PPP3CA 6175 0.056 0.47 NO
25 PRKCB PRKCB PRKCB 6978 0.037 0.42 NO
26 SOS1 SOS1 SOS1 6990 0.037 0.43 NO
27 PPP3CC PPP3CC PPP3CC 7429 0.027 0.41 NO
28 PLCG1 PLCG1 PLCG1 8085 0.014 0.37 NO
29 GRB2 GRB2 GRB2 8173 0.012 0.37 NO
30 RAF1 RAF1 RAF1 8205 0.012 0.37 NO
31 PIK3CA PIK3CA PIK3CA 8369 0.0084 0.36 NO
32 RELA RELA RELA 8802 -0.00044 0.33 NO
33 SHC1 SHC1 SHC1 8921 -0.0026 0.33 NO
34 RAC1 RAC1 RAC1 9616 -0.016 0.29 NO
35 PPP3CB PPP3CB PPP3CB 10164 -0.026 0.26 NO
36 CALM1 CALM1 CALM1 10276 -0.029 0.26 NO
37 MAP2K1 MAP2K1 MAP2K1 12405 -0.074 0.15 NO
38 CALM3 CALM3 CALM3 12638 -0.08 0.14 NO
39 ELK1 ELK1 ELK1 12692 -0.081 0.15 NO
40 CALM2 CALM2 CALM2 12956 -0.089 0.14 NO
41 MAPK8 MAPK8 MAPK8 14381 -0.14 0.077 NO
42 PTPN7 PTPN7 PTPN7 15989 -0.27 0.015 NO
43 NFATC4 NFATC4 NFATC4 17665 -0.77 0.0029 NO

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

Figure S78.  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 KERATINOCYTE PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 LY96 LY96 LY96 51 0.79 0.2 YES
2 CD14 CD14 CD14 252 0.61 0.34 YES
3 TLR4 TLR4 TLR4 561 0.5 0.45 YES
4 PIK3R1 PIK3R1 PIK3R1 1657 0.3 0.46 YES
5 GJA1 GJA1 GJA1 2031 0.26 0.51 YES
6 MYD88 MYD88 MYD88 4115 0.12 0.42 NO
7 NFKB1 NFKB1 NFKB1 4945 0.091 0.4 NO
8 FZD1 FZD1 FZD1 5451 0.075 0.39 NO
9 WNT1 WNT1 WNT1 5893 0.063 0.38 NO
10 DVL1 DVL1 DVL1 6502 0.048 0.36 NO
11 TIRAP TIRAP TIRAP 6691 0.044 0.36 NO
12 APC APC APC 6769 0.042 0.36 NO
13 PDPK1 PDPK1 PDPK1 7074 0.035 0.36 NO
14 GNAI1 GNAI1 GNAI1 7799 0.02 0.32 NO
15 PIK3CA PIK3CA PIK3CA 8369 0.0084 0.29 NO
16 RELA RELA RELA 8802 -0.00044 0.27 NO
17 PPP2CA PPP2CA PPP2CA 8919 -0.0026 0.26 NO
18 GSK3B GSK3B GSK3B 9003 -0.0042 0.26 NO
19 AKT1 AKT1 AKT1 9017 -0.0045 0.26 NO
20 LBP LBP LBP 10154 -0.026 0.2 NO
21 AXIN1 AXIN1 AXIN1 10940 -0.041 0.17 NO
22 CCND1 CCND1 CCND1 12020 -0.065 0.12 NO
23 IRAK1 IRAK1 IRAK1 12302 -0.072 0.12 NO
24 EIF2AK2 EIF2AK2 EIF2AK2 13215 -0.096 0.097 NO
25 CTNNB1 CTNNB1 CTNNB1 14224 -0.14 0.074 NO
26 LEF1 LEF1 LEF1 17216 -0.49 0.028 NO

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

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

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input

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

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

  • Phenotype data file = ACC-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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