GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in GBMLGG-TP
Glioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1MS3RS4
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 GBMLGG-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1MS3RS4
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 GBMLGG-TP. This pipeline has the following features:

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

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

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

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

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

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

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 191
Number of samples: 669
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 239
pheno.type: 2 - 3 :[ clus2 ] 236
pheno.type: 3 - 3 :[ clus3 ] 194

For the expression subtypes of 18325 genes in 670 samples, GSEA found enriched gene sets in each cluster using 669 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA TNFR1 PATHWAY, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG DNA REPLICATION, KEGG BASE EXCISION REPAIR, KEGG NUCLEOTIDE EXCISION REPAIR

    • And common core enriched genes are MDM2, PCNA, CHIT1, CYB5R1, FPGT, GALE, GALK1, GCK, GMDS, GMPPA

  • clus2

    • Top enriched gene sets are BIOCARTA CARM ER PATHWAY, BIOCARTA VIP PATHWAY, BIOCARTA EDG1 PATHWAY, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG LYSINE DEGRADATION, KEGG SPHINGOLIPID METABOLISM, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME

    • And common core enriched genes are CCND1, CREBBP, EP300, NCOR2, FAU, RPL10, RPL10L, RPL11, RPL12, RPL13

  • clus3

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA GPCR PATHWAY, BIOCARTA CREB PATHWAY, KEGG CITRATE CYCLE TCA CYCLE

    • And common core enriched genes are CACNA1C, CACNA1D, CACNA1F, CACNA1S, RYR2, CAMK2A, CAMK2B, CAMK2G, PRKCB, PTK2B

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 0.57 1.5 0.062 0.56 0.88 0.48 0.2 0.38 0.38 0.15
BIOCARTA FAS PATHWAY 29 genes.ES.table 0.55 1.5 0.071 0.6 0.84 0.45 0.21 0.35 0.4 0.17
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.46 1.6 0.075 1 0.77 0.42 0.28 0.3 0.67 0.37
BIOCARTA IL2RB PATHWAY 37 genes.ES.table 0.64 1.5 0.064 0.6 0.87 0.46 0.2 0.37 0.41 0.18
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.56 1.5 0.049 0.7 0.82 0.44 0.2 0.35 0.47 0.22
BIOCARTA TNFR1 PATHWAY 28 genes.ES.table 0.5 1.5 0.059 0.63 0.83 0.43 0.21 0.34 0.42 0.2
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 43 genes.ES.table 0.53 1.6 0.038 1 0.65 0.56 0.3 0.39 1 0.61
KEGG DNA REPLICATION 35 genes.ES.table 0.61 1.5 0.15 0.5 0.9 0.74 0.31 0.51 0.36 0.13
KEGG BASE EXCISION REPAIR 32 genes.ES.table 0.5 1.5 0.11 0.53 0.88 0.56 0.35 0.37 0.36 0.14
KEGG NUCLEOTIDE EXCISION REPAIR 43 genes.ES.table 0.48 1.6 0.081 1 0.71 0.54 0.34 0.35 0.64 0.37
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 HK3 HK3 HK3 301 0.8 0.092 YES
2 GCK GCK GCK 895 0.57 0.14 YES
3 FPGT FPGT FPGT 1927 0.38 0.13 YES
4 NANP NANP NANP 2059 0.36 0.18 YES
5 HEXB HEXB HEXB 2379 0.32 0.2 YES
6 HK2 HK2 HK2 2445 0.32 0.24 YES
7 PMM2 PMM2 PMM2 2600 0.3 0.27 YES
8 CHIT1 CHIT1 CHIT1 2647 0.29 0.31 YES
9 PGM2 PGM2 PGM2 2883 0.27 0.34 YES
10 GMPPB GMPPB GMPPB 3168 0.25 0.35 YES
11 CYB5R1 CYB5R1 CYB5R1 3334 0.23 0.38 YES
12 RENBP RENBP RENBP 3750 0.2 0.38 YES
13 GALE GALE GALE 3928 0.19 0.4 YES
14 GMPPA GMPPA GMPPA 3999 0.19 0.42 YES
15 NPL NPL NPL 4324 0.17 0.42 YES
16 GMDS GMDS GMDS 4674 0.15 0.42 YES
17 PGM1 PGM1 PGM1 4676 0.15 0.45 YES
18 HEXA HEXA HEXA 4700 0.15 0.46 YES
19 UAP1 UAP1 UAP1 4794 0.14 0.48 YES
20 UGP2 UGP2 UGP2 4804 0.14 0.5 YES
21 GNPDA1 GNPDA1 GNPDA1 5096 0.13 0.5 YES
22 GALK1 GALK1 GALK1 5173 0.13 0.51 YES
23 TSTA3 TSTA3 TSTA3 5303 0.12 0.52 YES
24 GPI GPI GPI 5555 0.12 0.53 YES
25 NANS NANS NANS 5929 0.1 0.52 NO
26 UGDH UGDH UGDH 6728 0.077 0.49 NO
27 UXS1 UXS1 UXS1 6824 0.074 0.49 NO
28 GNPNAT1 GNPNAT1 GNPNAT1 6947 0.071 0.49 NO
29 GFPT2 GFPT2 GFPT2 7028 0.068 0.5 NO
30 NAGK NAGK NAGK 7149 0.065 0.5 NO
31 AMDHD2 AMDHD2 AMDHD2 8033 0.04 0.46 NO
32 FUK FUK FUK 8740 0.023 0.42 NO
33 PGM3 PGM3 PGM3 9082 0.014 0.41 NO
34 GALK2 GALK2 GALK2 9513 0.0035 0.38 NO
35 CMAS CMAS CMAS 10500 -0.021 0.33 NO
36 HK1 HK1 HK1 10985 -0.033 0.31 NO
37 PMM1 PMM1 PMM1 11852 -0.056 0.27 NO
38 MPI MPI MPI 11887 -0.057 0.28 NO
39 GALT GALT GALT 12266 -0.068 0.26 NO
40 GFPT1 GFPT1 GFPT1 12305 -0.07 0.27 NO
41 GNPDA2 GNPDA2 GNPDA2 12439 -0.074 0.27 NO
42 GNE GNE GNE 13322 -0.1 0.24 NO
43 CHIA CHIA CHIA 15775 -0.24 0.14 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 FAS 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 CDC20 CDC20 CDC20 130 0.94 0.024 YES
2 PTTG1 PTTG1 PTTG1 180 0.89 0.05 YES
3 ORC1L ORC1L ORC1L 182 0.89 0.079 YES
4 CCNB2 CCNB2 CCNB2 237 0.85 0.1 YES
5 CDC25C CDC25C CDC25C 274 0.82 0.13 YES
6 CDC6 CDC6 CDC6 279 0.82 0.16 YES
7 CCNA2 CCNA2 CCNA2 289 0.81 0.18 YES
8 BUB1 BUB1 BUB1 312 0.8 0.21 YES
9 TTK TTK TTK 318 0.79 0.23 YES
10 CDC45 CDC45 CDC45 338 0.78 0.26 YES
11 ESPL1 ESPL1 ESPL1 401 0.75 0.28 YES
12 BUB1B BUB1B BUB1B 492 0.71 0.3 YES
13 CDK1 CDK1 CDK1 543 0.69 0.32 YES
14 CCNB1 CCNB1 CCNB1 573 0.68 0.34 YES
15 WEE1 WEE1 WEE1 628 0.66 0.36 YES
16 CHEK2 CHEK2 CHEK2 690 0.64 0.37 YES
17 TGFB2 TGFB2 TGFB2 714 0.63 0.39 YES
18 PLK1 PLK1 PLK1 764 0.61 0.41 YES
19 CDKN2C CDKN2C CDKN2C 866 0.58 0.42 YES
20 E2F2 E2F2 E2F2 978 0.55 0.44 YES
21 CDK2 CDK2 CDK2 1165 0.51 0.44 YES
22 PKMYT1 PKMYT1 PKMYT1 1203 0.5 0.46 YES
23 ORC6L ORC6L ORC6L 1244 0.49 0.47 YES
24 GADD45A GADD45A GADD45A 1363 0.47 0.48 YES
25 MAD2L1 MAD2L1 MAD2L1 1607 0.43 0.48 YES
26 MCM2 MCM2 MCM2 1618 0.43 0.49 YES
27 SFN SFN SFN 1749 0.41 0.5 YES
28 CDC25A CDC25A CDC25A 1771 0.4 0.51 YES
29 E2F1 E2F1 E2F1 1789 0.4 0.52 YES
30 CHEK1 CHEK1 CHEK1 1845 0.39 0.53 YES
31 CCNE1 CCNE1 CCNE1 2167 0.35 0.53 YES
32 PCNA PCNA PCNA 2534 0.31 0.52 YES
33 CDK6 CDK6 CDK6 2700 0.29 0.52 YES
34 RBL1 RBL1 RBL1 2760 0.28 0.52 YES
35 SKP2 SKP2 SKP2 2781 0.28 0.53 YES
36 CDKN1A CDKN1A CDKN1A 3064 0.26 0.52 YES
37 CCNA1 CCNA1 CCNA1 3073 0.26 0.53 YES
38 CDK4 CDK4 CDK4 3082 0.26 0.54 YES
39 TGFB1 TGFB1 TGFB1 3146 0.25 0.55 YES
40 HDAC1 HDAC1 HDAC1 3191 0.24 0.55 YES
41 MCM6 MCM6 MCM6 3345 0.23 0.55 YES
42 CDC7 CDC7 CDC7 3351 0.23 0.56 YES
43 CCNE2 CCNE2 CCNE2 3355 0.23 0.56 YES
44 MCM5 MCM5 MCM5 3439 0.22 0.57 YES
45 TGFB3 TGFB3 TGFB3 3691 0.21 0.56 YES
46 GADD45B GADD45B GADD45B 3780 0.2 0.56 YES
47 ORC5L ORC5L ORC5L 3821 0.2 0.57 YES
48 MCM4 MCM4 MCM4 3927 0.19 0.57 YES
49 SMC1B SMC1B SMC1B 3976 0.19 0.57 YES
50 MAD2L2 MAD2L2 MAD2L2 4141 0.18 0.57 YES
51 MCM3 MCM3 MCM3 4241 0.17 0.57 YES
52 MDM2 MDM2 MDM2 4244 0.17 0.57 YES
53 ANAPC10 ANAPC10 ANAPC10 4643 0.15 0.56 NO
54 TP53 TP53 TP53 4791 0.14 0.55 NO
55 CDC25B CDC25B CDC25B 5498 0.12 0.52 NO
56 ANAPC11 ANAPC11 ANAPC11 5548 0.12 0.52 NO
57 PTTG2 PTTG2 PTTG2 5634 0.11 0.52 NO
58 RB1 RB1 RB1 5654 0.11 0.52 NO
59 CDK7 CDK7 CDK7 5957 0.1 0.51 NO
60 E2F4 E2F4 E2F4 6159 0.094 0.5 NO
61 E2F5 E2F5 E2F5 6193 0.094 0.5 NO
62 ANAPC7 ANAPC7 ANAPC7 6344 0.089 0.5 NO
63 MCM7 MCM7 MCM7 6774 0.075 0.47 NO
64 ORC2L ORC2L ORC2L 6801 0.075 0.48 NO
65 CUL1 CUL1 CUL1 6864 0.073 0.47 NO
66 CDC23 CDC23 CDC23 7103 0.066 0.46 NO
67 CDC14A CDC14A CDC14A 7168 0.064 0.46 NO
68 CCND2 CCND2 CCND2 7236 0.062 0.46 NO
69 YWHAQ YWHAQ YWHAQ 7336 0.059 0.46 NO
70 ATR ATR ATR 7471 0.056 0.45 NO
71 MAD1L1 MAD1L1 MAD1L1 7661 0.051 0.44 NO
72 RBX1 RBX1 RBX1 7710 0.05 0.44 NO
73 CDC16 CDC16 CDC16 7757 0.048 0.44 NO
74 E2F3 E2F3 E2F3 8159 0.037 0.42 NO
75 ANAPC4 ANAPC4 ANAPC4 8373 0.032 0.41 NO
76 ANAPC1 ANAPC1 ANAPC1 8521 0.028 0.4 NO
77 YWHAZ YWHAZ YWHAZ 8632 0.025 0.4 NO
78 CCNH CCNH CCNH 8657 0.025 0.4 NO
79 TFDP2 TFDP2 TFDP2 8851 0.02 0.39 NO
80 HDAC2 HDAC2 HDAC2 9052 0.015 0.38 NO
81 ANAPC5 ANAPC5 ANAPC5 9139 0.013 0.37 NO
82 CDC27 CDC27 CDC27 9230 0.01 0.37 NO
83 YWHAH YWHAH YWHAH 9333 0.008 0.36 NO
84 ANAPC13 ANAPC13 ANAPC13 9423 0.0058 0.36 NO
85 ORC4L ORC4L ORC4L 9692 -0.00094 0.34 NO
86 FZR1 FZR1 FZR1 9780 -0.0032 0.34 NO
87 CCND3 CCND3 CCND3 9781 -0.0032 0.34 NO
88 SKP1 SKP1 SKP1 9802 -0.0038 0.34 NO
89 YWHAE YWHAE YWHAE 9839 -0.0044 0.33 NO
90 TFDP1 TFDP1 TFDP1 9852 -0.0048 0.33 NO
91 YWHAG YWHAG YWHAG 10049 -0.01 0.32 NO
92 PRKDC PRKDC PRKDC 10054 -0.01 0.32 NO
93 SMAD2 SMAD2 SMAD2 10282 -0.016 0.31 NO
94 YWHAB YWHAB YWHAB 10327 -0.017 0.31 NO
95 SMAD4 SMAD4 SMAD4 10468 -0.02 0.3 NO
96 ZBTB17 ZBTB17 ZBTB17 10522 -0.022 0.3 NO
97 SMC1A SMC1A SMC1A 10615 -0.024 0.3 NO
98 STAG1 STAG1 STAG1 11138 -0.037 0.27 NO
99 ORC3L ORC3L ORC3L 11275 -0.04 0.26 NO
100 STAG2 STAG2 STAG2 11349 -0.042 0.26 NO
101 CCND1 CCND1 CCND1 11596 -0.049 0.25 NO
102 CDKN2A CDKN2A CDKN2A 11700 -0.052 0.24 NO
103 RAD21 RAD21 RAD21 11781 -0.054 0.24 NO
104 BUB3 BUB3 BUB3 11904 -0.057 0.24 NO
105 ABL1 ABL1 ABL1 12202 -0.067 0.22 NO
106 CDC14B CDC14B CDC14B 12408 -0.073 0.21 NO
107 RBL2 RBL2 RBL2 12556 -0.078 0.21 NO
108 ANAPC2 ANAPC2 ANAPC2 12813 -0.086 0.2 NO
109 SMAD3 SMAD3 SMAD3 13066 -0.094 0.19 NO
110 GSK3B GSK3B GSK3B 13225 -0.1 0.18 NO
111 CDKN1B CDKN1B CDKN1B 13351 -0.1 0.18 NO
112 MYC MYC MYC 13811 -0.12 0.16 NO
113 CDKN2D CDKN2D CDKN2D 13839 -0.12 0.16 NO
114 ATM ATM ATM 14161 -0.14 0.14 NO
115 CDKN1C CDKN1C CDKN1C 14264 -0.14 0.14 NO
116 CREBBP CREBBP CREBBP 14328 -0.15 0.14 NO
117 EP300 EP300 EP300 14587 -0.16 0.14 NO
118 WEE2 WEE2 WEE2 15184 -0.2 0.11 NO
119 SMC3 SMC3 SMC3 15469 -0.22 0.1 NO
120 CDKN2B CDKN2B CDKN2B 16051 -0.27 0.078 NO
121 GADD45G GADD45G GADD45G 16558 -0.32 0.061 NO
122 CDC26 CDC26 CDC26 17312 -0.45 0.034 NO
123 CCNB3 CCNB3 CCNB3 17906 -0.62 0.022 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 FAS PATHWAY.

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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

Table 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 POLE2 POLE2 POLE2 181 0.89 0.13 YES
2 DDB2 DDB2 DDB2 1107 0.52 0.17 YES
3 RPA3 RPA3 RPA3 1805 0.4 0.19 YES
4 PCNA PCNA PCNA 2534 0.31 0.2 YES
5 RFC2 RFC2 RFC2 2620 0.3 0.24 YES
6 RFC3 RFC3 RFC3 2817 0.28 0.28 YES
7 POLD1 POLD1 POLD1 3006 0.26 0.31 YES
8 RFC4 RFC4 RFC4 3192 0.24 0.34 YES
9 LIG1 LIG1 LIG1 3865 0.2 0.33 YES
10 POLD3 POLD3 POLD3 3946 0.19 0.36 YES
11 GTF2H2 GTF2H2 GTF2H2 4260 0.17 0.37 YES
12 CETN2 CETN2 CETN2 5079 0.13 0.34 YES
13 ERCC1 ERCC1 ERCC1 5154 0.13 0.36 YES
14 POLE4 POLE4 POLE4 5163 0.13 0.38 YES
15 RPA2 RPA2 RPA2 5408 0.12 0.39 YES
16 POLD4 POLD4 POLD4 5415 0.12 0.41 YES
17 RFC5 RFC5 RFC5 5427 0.12 0.43 YES
18 POLE POLE POLE 5488 0.12 0.44 YES
19 POLE3 POLE3 POLE3 5625 0.11 0.45 YES
20 ERCC8 ERCC8 ERCC8 5907 0.1 0.45 YES
21 CDK7 CDK7 CDK7 5957 0.1 0.47 YES
22 RPA4 RPA4 RPA4 6289 0.091 0.46 YES
23 POLD2 POLD2 POLD2 6311 0.09 0.48 YES
24 GTF2H3 GTF2H3 GTF2H3 6936 0.071 0.45 NO
25 RPA1 RPA1 RPA1 6946 0.071 0.46 NO
26 RBX1 RBX1 RBX1 7710 0.05 0.43 NO
27 CUL4A CUL4A CUL4A 7741 0.049 0.44 NO
28 ERCC2 ERCC2 ERCC2 7881 0.045 0.44 NO
29 CCNH CCNH CCNH 8657 0.025 0.4 NO
30 RAD23A RAD23A RAD23A 8941 0.018 0.38 NO
31 GTF2H4 GTF2H4 GTF2H4 8993 0.016 0.38 NO
32 GTF2H1 GTF2H1 GTF2H1 9288 0.0092 0.37 NO
33 ERCC4 ERCC4 ERCC4 9934 -0.0066 0.34 NO
34 CUL4B CUL4B CUL4B 10014 -0.0087 0.33 NO
35 ERCC3 ERCC3 ERCC3 10108 -0.011 0.33 NO
36 MNAT1 MNAT1 MNAT1 10200 -0.014 0.33 NO
37 RFC1 RFC1 RFC1 10764 -0.028 0.3 NO
38 GTF2H5 GTF2H5 GTF2H5 11326 -0.042 0.28 NO
39 XPC XPC XPC 12107 -0.064 0.24 NO
40 DDB1 DDB1 DDB1 12382 -0.072 0.24 NO
41 XPA XPA XPA 13404 -0.11 0.2 NO
42 ERCC5 ERCC5 ERCC5 14427 -0.15 0.17 NO
43 ERCC6 ERCC6 ERCC6 16082 -0.27 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: BIOCARTA HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CASP8 CASP8 CASP8 651 0.65 0.032 YES
2 CASP6 CASP6 CASP6 752 0.62 0.09 YES
3 BIRC3 BIRC3 BIRC3 893 0.57 0.14 YES
4 FAS FAS FAS 1070 0.53 0.19 YES
5 TNFRSF1A TNFRSF1A TNFRSF1A 1833 0.39 0.18 YES
6 LMNB1 LMNB1 LMNB1 2087 0.36 0.21 YES
7 TRADD TRADD TRADD 2112 0.36 0.24 YES
8 CASP7 CASP7 CASP7 2219 0.34 0.27 YES
9 CASP3 CASP3 CASP3 2645 0.3 0.28 YES
10 ARHGDIB ARHGDIB ARHGDIB 2692 0.29 0.31 YES
11 TRAF1 TRAF1 TRAF1 2908 0.27 0.32 YES
12 LMNA LMNA LMNA 3359 0.23 0.32 YES
13 RIPK1 RIPK1 RIPK1 3516 0.22 0.34 YES
14 FADD FADD FADD 3542 0.22 0.36 YES
15 CASP2 CASP2 CASP2 3619 0.21 0.38 YES
16 CFLAR CFLAR CFLAR 3654 0.21 0.4 YES
17 TNFRSF1B TNFRSF1B TNFRSF1B 3836 0.2 0.41 YES
18 MAP3K1 MAP3K1 MAP3K1 3907 0.19 0.42 YES
19 PSEN2 PSEN2 PSEN2 4216 0.18 0.42 YES
20 MDM2 MDM2 MDM2 4244 0.17 0.44 YES
21 MAP3K14 MAP3K14 MAP3K14 4272 0.17 0.46 YES
22 LMNB2 LMNB2 LMNB2 4614 0.16 0.45 YES
23 PRKCD PRKCD PRKCD 4845 0.14 0.46 YES
24 NFKB1 NFKB1 NFKB1 5074 0.13 0.46 YES
25 RB1 RB1 RB1 5654 0.11 0.44 NO
26 CYCS CYCS CYCS 5729 0.11 0.44 NO
27 DFFB DFFB DFFB 6343 0.089 0.42 NO
28 ACTG1 ACTG1 ACTG1 6536 0.083 0.42 NO
29 BIRC2 BIRC2 BIRC2 7337 0.059 0.38 NO
30 DFFA DFFA DFFA 7348 0.059 0.38 NO
31 DAXX DAXX DAXX 7700 0.05 0.37 NO
32 GSN GSN GSN 7924 0.044 0.36 NO
33 TRAF2 TRAF2 TRAF2 8648 0.025 0.33 NO
34 CRADD CRADD CRADD 8697 0.024 0.33 NO
35 RELA RELA RELA 9064 0.015 0.31 NO
36 CDK11B CDK11B CDK11B 9799 -0.0037 0.27 NO
37 CDK11A CDK11A CDK11A 9840 -0.0044 0.27 NO
38 PRKDC PRKDC PRKDC 10054 -0.01 0.26 NO
39 PAK2 PAK2 PAK2 10149 -0.012 0.25 NO
40 PSEN1 PSEN1 PSEN1 10270 -0.015 0.25 NO
41 APAF1 APAF1 APAF1 10331 -0.017 0.24 NO
42 PARP1 PARP1 PARP1 10578 -0.023 0.23 NO
43 RASA1 RASA1 RASA1 10843 -0.03 0.22 NO
44 NFKBIA NFKBIA NFKBIA 11274 -0.04 0.2 NO
45 MAP2K7 MAP2K7 MAP2K7 11638 -0.05 0.19 NO
46 XIAP XIAP XIAP 11787 -0.054 0.19 NO
47 BAG4 BAG4 BAG4 11851 -0.056 0.19 NO
48 TNF TNF TNF 12120 -0.064 0.18 NO
49 CHUK CHUK CHUK 12316 -0.07 0.18 NO
50 PTK2 PTK2 PTK2 12334 -0.071 0.18 NO
51 BCL2 BCL2 BCL2 14100 -0.14 0.1 NO
52 SPTAN1 SPTAN1 SPTAN1 14569 -0.16 0.091 NO
53 CASP9 CASP9 CASP9 14806 -0.17 0.095 NO
54 BID BID BID 15020 -0.18 0.1 NO
55 NUMA1 NUMA1 NUMA1 15538 -0.22 0.097 NO
56 MAP3K5 MAP3K5 MAP3K5 15864 -0.25 0.1 NO
57 MAPK8 MAPK8 MAPK8 16186 -0.28 0.12 NO

Figure S7.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL2RB PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA DEATH PATHWAY

Table 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 CLCF1 CLCF1 CLCF1 24 1.2 0.036 YES
2 LIF LIF LIF 43 1.1 0.07 YES
3 SOCS1 SOCS1 SOCS1 73 1 0.1 YES
4 CISH CISH CISH 94 1 0.13 YES
5 SOCS3 SOCS3 SOCS3 202 0.88 0.15 YES
6 IL7 IL7 IL7 217 0.87 0.18 YES
7 IL13RA2 IL13RA2 IL13RA2 262 0.84 0.2 YES
8 IL15 IL15 IL15 309 0.8 0.23 YES
9 IL2RB IL2RB IL2RB 392 0.76 0.24 YES
10 IL2RG IL2RG IL2RG 416 0.74 0.27 YES
11 SPRY1 SPRY1 SPRY1 471 0.72 0.29 YES
12 OSMR OSMR OSMR 473 0.72 0.31 YES
13 SPRY4 SPRY4 SPRY4 537 0.69 0.33 YES
14 SOCS2 SOCS2 SOCS2 544 0.69 0.35 YES
15 IL2RA IL2RA IL2RA 554 0.68 0.37 YES
16 CTF1 CTF1 CTF1 609 0.67 0.39 YES
17 IL6 IL6 IL6 843 0.59 0.39 YES
18 IL10 IL10 IL10 952 0.56 0.4 YES
19 IL7R IL7R IL7R 1166 0.5 0.41 YES
20 OSM OSM OSM 1283 0.48 0.42 YES
21 JAK3 JAK3 JAK3 1294 0.48 0.43 YES
22 PIK3CG PIK3CG PIK3CG 1397 0.46 0.44 YES
23 CSF2RB CSF2RB CSF2RB 1527 0.44 0.45 YES
24 IL22RA1 IL22RA1 IL22RA1 1610 0.43 0.46 YES
25 IL28RA IL28RA IL28RA 1879 0.39 0.46 YES
26 EPO EPO EPO 1905 0.38 0.46 YES
27 IL24 IL24 IL24 1973 0.38 0.47 YES
28 IL15RA IL15RA IL15RA 1991 0.37 0.48 YES
29 LEP LEP LEP 2070 0.36 0.49 YES
30 IL12RB1 IL12RB1 IL12RB1 2149 0.35 0.5 YES
31 IL23A IL23A IL23A 2422 0.32 0.49 YES
32 SPRY2 SPRY2 SPRY2 2480 0.31 0.5 YES
33 IL11 IL11 IL11 2489 0.31 0.51 YES
34 IFNGR2 IFNGR2 IFNGR2 2524 0.31 0.52 YES
35 CSF3 CSF3 CSF3 2734 0.29 0.52 YES
36 IL10RA IL10RA IL10RA 2783 0.28 0.52 YES
37 PIK3R5 PIK3R5 PIK3R5 2795 0.28 0.53 YES
38 CSF3R CSF3R CSF3R 2843 0.27 0.54 YES
39 STAT5A STAT5A STAT5A 2942 0.27 0.54 YES
40 IL10RB IL10RB IL10RB 2981 0.26 0.54 YES
41 PTPN6 PTPN6 PTPN6 3003 0.26 0.55 YES
42 PIM1 PIM1 PIM1 3052 0.26 0.56 YES
43 SPRED2 SPRED2 SPRED2 3170 0.25 0.56 YES
44 IL13RA1 IL13RA1 IL13RA1 3222 0.24 0.56 YES
45 IL21R IL21R IL21R 3235 0.24 0.57 YES
46 IL4R IL4R IL4R 3323 0.23 0.57 YES
47 STAT1 STAT1 STAT1 3490 0.22 0.57 YES
48 IL5RA IL5RA IL5RA 3543 0.22 0.57 YES
49 TSLP TSLP TSLP 3884 0.19 0.56 NO
50 IL20RA IL20RA IL20RA 3994 0.19 0.56 NO
51 PIK3CD PIK3CD PIK3CD 4079 0.18 0.56 NO
52 SPRED1 SPRED1 SPRED1 4099 0.18 0.57 NO
53 STAT6 STAT6 STAT6 4435 0.16 0.55 NO
54 IFNAR2 IFNAR2 IFNAR2 4799 0.14 0.54 NO
55 MPL MPL MPL 4884 0.14 0.54 NO
56 AKT2 AKT2 AKT2 5299 0.12 0.52 NO
57 IL12B IL12B IL12B 5363 0.12 0.52 NO
58 STAT3 STAT3 STAT3 5617 0.11 0.51 NO
59 STAT2 STAT2 STAT2 5651 0.11 0.51 NO
60 CSF2RA CSF2RA CSF2RA 5722 0.11 0.51 NO
61 PIK3R3 PIK3R3 PIK3R3 6087 0.096 0.49 NO
62 PRLR PRLR PRLR 6171 0.094 0.49 NO
63 IL20RB IL20RB IL20RB 6183 0.094 0.5 NO
64 PIAS2 PIAS2 PIAS2 6385 0.087 0.49 NO
65 IL6R IL6R IL6R 6877 0.072 0.46 NO
66 PIAS3 PIAS3 PIAS3 6962 0.07 0.46 NO
67 CCND2 CCND2 CCND2 7236 0.062 0.45 NO
68 IFNGR1 IFNGR1 IFNGR1 7495 0.055 0.43 NO
69 AKT1 AKT1 AKT1 7672 0.05 0.43 NO
70 IFNAR1 IFNAR1 IFNAR1 7975 0.042 0.41 NO
71 EPOR EPOR EPOR 8038 0.04 0.41 NO
72 BCL2L1 BCL2L1 BCL2L1 8122 0.038 0.4 NO
73 IRF9 IRF9 IRF9 8141 0.038 0.4 NO
74 SOCS4 SOCS4 SOCS4 8191 0.037 0.4 NO
75 TYK2 TYK2 TYK2 8333 0.033 0.4 NO
76 STAM2 STAM2 STAM2 8495 0.029 0.39 NO
77 TPO TPO TPO 9075 0.014 0.36 NO
78 IFNE IFNE IFNE 9432 0.0055 0.34 NO
79 SOCS5 SOCS5 SOCS5 9491 0.004 0.34 NO
80 JAK2 JAK2 JAK2 9653 -0.00011 0.33 NO
81 PIAS4 PIAS4 PIAS4 9765 -0.003 0.32 NO
82 CCND3 CCND3 CCND3 9781 -0.0032 0.32 NO
83 GRB2 GRB2 GRB2 10395 -0.019 0.29 NO
84 IL3RA IL3RA IL3RA 10907 -0.031 0.26 NO
85 PIAS1 PIAS1 PIAS1 11264 -0.04 0.24 NO
86 PIK3R2 PIK3R2 PIK3R2 11499 -0.047 0.23 NO
87 IL13 IL13 IL13 11534 -0.048 0.23 NO
88 STAT4 STAT4 STAT4 11575 -0.049 0.23 NO
89 CCND1 CCND1 CCND1 11596 -0.049 0.23 NO
90 IL11RA IL11RA IL11RA 11678 -0.051 0.23 NO
91 IL6ST IL6ST IL6ST 11703 -0.052 0.23 NO
92 IFNA13 IFNA13 IFNA13 11774 -0.054 0.22 NO
93 JAK1 JAK1 JAK1 11943 -0.059 0.22 NO
94 CNTF CNTF CNTF 11969 -0.06 0.22 NO
95 SPRY3 SPRY3 SPRY3 12478 -0.076 0.19 NO
96 IFNW1 IFNW1 IFNW1 12594 -0.079 0.19 NO
97 STAT5B STAT5B STAT5B 12654 -0.081 0.19 NO
98 LEPR LEPR LEPR 12674 -0.082 0.19 NO
99 SOS1 SOS1 SOS1 12711 -0.083 0.19 NO
100 PIK3CA PIK3CA PIK3CA 12934 -0.09 0.18 NO
101 CBL CBL CBL 13219 -0.1 0.17 NO
102 PTPN11 PTPN11 PTPN11 13777 -0.12 0.14 NO
103 MYC MYC MYC 13811 -0.12 0.14 NO
104 PIK3CB PIK3CB PIK3CB 14130 -0.14 0.13 NO
105 CBLB CBLB CBLB 14323 -0.14 0.12 NO
106 CREBBP CREBBP CREBBP 14328 -0.15 0.13 NO
107 GHR GHR GHR 14380 -0.15 0.13 NO
108 SOS2 SOS2 SOS2 14432 -0.15 0.13 NO
109 EP300 EP300 EP300 14587 -0.16 0.13 NO
110 LIFR LIFR LIFR 14613 -0.16 0.13 NO
111 IL5 IL5 IL5 14719 -0.16 0.13 NO
112 IL12A IL12A IL12A 14976 -0.18 0.12 NO
113 STAM STAM STAM 14996 -0.18 0.13 NO
114 PIK3R1 PIK3R1 PIK3R1 15489 -0.22 0.11 NO
115 IL12RB2 IL12RB2 IL12RB2 15673 -0.23 0.1 NO
116 AKT3 AKT3 AKT3 15862 -0.25 0.1 NO
117 IFNA21 IFNA21 IFNA21 16060 -0.27 0.1 NO
118 CNTFR CNTFR CNTFR 16540 -0.32 0.083 NO
119 SOCS7 SOCS7 SOCS7 17277 -0.44 0.057 NO

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

Figure S10.  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 TNFR1 PATHWAY

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 COL4A1 COL4A1 COL4A1 303 0.8 0.028 YES
2 COL4A2 COL4A2 COL4A2 631 0.66 0.046 YES
3 LAMB4 LAMB4 LAMB4 636 0.66 0.083 YES
4 LAMB1 LAMB1 LAMB1 857 0.58 0.1 YES
5 BIRC3 BIRC3 BIRC3 893 0.57 0.13 YES
6 E2F2 E2F2 E2F2 978 0.55 0.16 YES
7 CDK2 CDK2 CDK2 1165 0.51 0.18 YES
8 TRAF5 TRAF5 TRAF5 1222 0.49 0.2 YES
9 ITGA2 ITGA2 ITGA2 1374 0.46 0.22 YES
10 PIK3CG PIK3CG PIK3CG 1397 0.46 0.24 YES
11 LAMC1 LAMC1 LAMC1 1430 0.46 0.27 YES
12 LAMA2 LAMA2 LAMA2 1485 0.45 0.29 YES
13 LAMC3 LAMC3 LAMC3 1549 0.44 0.31 YES
14 LAMC2 LAMC2 LAMC2 1625 0.42 0.33 YES
15 CKS1B CKS1B CKS1B 1754 0.4 0.34 YES
16 ITGA3 ITGA3 ITGA3 1924 0.38 0.36 YES
17 FN1 FN1 FN1 2015 0.37 0.37 YES
18 PTGS2 PTGS2 PTGS2 2154 0.35 0.38 YES
19 CCNE1 CCNE1 CCNE1 2167 0.35 0.4 YES
20 LAMA4 LAMA4 LAMA4 2591 0.3 0.4 YES
21 CDK6 CDK6 CDK6 2700 0.29 0.4 YES
22 NOS2 NOS2 NOS2 2723 0.29 0.42 YES
23 SKP2 SKP2 SKP2 2781 0.28 0.43 YES
24 PIK3R5 PIK3R5 PIK3R5 2795 0.28 0.45 YES
25 TRAF1 TRAF1 TRAF1 2908 0.27 0.46 YES
26 COL4A6 COL4A6 COL4A6 2984 0.26 0.47 YES
27 CDK4 CDK4 CDK4 3082 0.26 0.48 YES
28 ITGB1 ITGB1 ITGB1 3291 0.24 0.48 YES
29 CCNE2 CCNE2 CCNE2 3355 0.23 0.49 YES
30 LAMB2 LAMB2 LAMB2 3875 0.19 0.47 NO
31 PIK3CD PIK3CD PIK3CD 4079 0.18 0.47 NO
32 TP53 TP53 TP53 4791 0.14 0.44 NO
33 RARB RARB RARB 4831 0.14 0.44 NO
34 TRAF4 TRAF4 TRAF4 4922 0.14 0.44 NO
35 NFKB1 NFKB1 NFKB1 5074 0.13 0.44 NO
36 AKT2 AKT2 AKT2 5299 0.12 0.44 NO
37 RB1 RB1 RB1 5654 0.11 0.43 NO
38 CYCS CYCS CYCS 5729 0.11 0.43 NO
39 PIK3R3 PIK3R3 PIK3R3 6087 0.096 0.41 NO
40 PIAS2 PIAS2 PIAS2 6385 0.087 0.4 NO
41 ITGA6 ITGA6 ITGA6 6532 0.083 0.4 NO
42 IKBKB IKBKB IKBKB 6727 0.077 0.39 NO
43 PIAS3 PIAS3 PIAS3 6962 0.07 0.38 NO
44 ITGAV ITGAV ITGAV 7039 0.068 0.38 NO
45 LAMB3 LAMB3 LAMB3 7043 0.068 0.39 NO
46 LAMA1 LAMA1 LAMA1 7122 0.066 0.39 NO
47 BIRC2 BIRC2 BIRC2 7337 0.059 0.38 NO
48 LAMA5 LAMA5 LAMA5 7346 0.059 0.38 NO
49 AKT1 AKT1 AKT1 7672 0.05 0.36 NO
50 TRAF6 TRAF6 TRAF6 7851 0.046 0.36 NO
51 BCL2L1 BCL2L1 BCL2L1 8122 0.038 0.34 NO
52 E2F3 E2F3 E2F3 8159 0.037 0.34 NO
53 TRAF2 TRAF2 TRAF2 8648 0.025 0.32 NO
54 RELA RELA RELA 9064 0.015 0.3 NO
55 IKBKG IKBKG IKBKG 9536 0.0029 0.27 NO
56 PIAS4 PIAS4 PIAS4 9765 -0.003 0.26 NO
57 FHIT FHIT FHIT 10147 -0.012 0.24 NO
58 APAF1 APAF1 APAF1 10331 -0.017 0.23 NO
59 MAX MAX MAX 10739 -0.027 0.21 NO
60 PIAS1 PIAS1 PIAS1 11264 -0.04 0.18 NO
61 NFKBIA NFKBIA NFKBIA 11274 -0.04 0.18 NO
62 PIK3R2 PIK3R2 PIK3R2 11499 -0.047 0.18 NO
63 CCND1 CCND1 CCND1 11596 -0.049 0.17 NO
64 XIAP XIAP XIAP 11787 -0.054 0.16 NO
65 TRAF3 TRAF3 TRAF3 12315 -0.07 0.14 NO
66 CHUK CHUK CHUK 12316 -0.07 0.14 NO
67 PTK2 PTK2 PTK2 12334 -0.071 0.15 NO
68 RXRB RXRB RXRB 12697 -0.082 0.13 NO
69 RXRA RXRA RXRA 12851 -0.088 0.13 NO
70 PIK3CA PIK3CA PIK3CA 12934 -0.09 0.13 NO
71 CDKN1B CDKN1B CDKN1B 13351 -0.1 0.11 NO
72 PTEN PTEN PTEN 13686 -0.12 0.1 NO
73 MYC MYC MYC 13811 -0.12 0.1 NO
74 BCL2 BCL2 BCL2 14100 -0.14 0.092 NO
75 PIK3CB PIK3CB PIK3CB 14130 -0.14 0.098 NO
76 CASP9 CASP9 CASP9 14806 -0.17 0.07 NO
77 PIK3R1 PIK3R1 PIK3R1 15489 -0.22 0.045 NO
78 ITGA2B ITGA2B ITGA2B 15709 -0.23 0.046 NO
79 AKT3 AKT3 AKT3 15862 -0.25 0.051 NO
80 CDKN2B CDKN2B CDKN2B 16051 -0.27 0.056 NO
81 LAMA3 LAMA3 LAMA3 16366 -0.3 0.055 NO
82 COL4A4 COL4A4 COL4A4 16780 -0.36 0.052 NO
83 RXRG RXRG RXRG 17793 -0.57 0.028 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: BIOCARTA TNFR1 PATHWAY.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CASP8 CASP8 CASP8 651 0.65 0.067 YES
2 CASP6 CASP6 CASP6 752 0.62 0.16 YES
3 BIRC3 BIRC3 BIRC3 893 0.57 0.24 YES
4 TRADD TRADD TRADD 2112 0.36 0.23 YES
5 CASP7 CASP7 CASP7 2219 0.34 0.28 YES
6 TNFSF10 TNFSF10 TNFSF10 2372 0.32 0.32 YES
7 TNFRSF10A TNFRSF10A TNFRSF10A 2533 0.31 0.36 YES
8 CASP3 CASP3 CASP3 2645 0.3 0.4 YES
9 TNFRSF10B TNFRSF10B TNFRSF10B 3218 0.24 0.41 YES
10 CASP10 CASP10 CASP10 3265 0.24 0.44 YES
11 LMNA LMNA LMNA 3359 0.23 0.47 YES
12 RIPK1 RIPK1 RIPK1 3516 0.22 0.5 YES
13 FADD FADD FADD 3542 0.22 0.53 YES
14 CFLAR CFLAR CFLAR 3654 0.21 0.56 YES
15 MAP3K14 MAP3K14 MAP3K14 4272 0.17 0.55 NO
16 NFKB1 NFKB1 NFKB1 5074 0.13 0.53 NO
17 TNFRSF25 TNFRSF25 TNFRSF25 5455 0.12 0.53 NO
18 CYCS CYCS CYCS 5729 0.11 0.53 NO
19 TNFSF12 TNFSF12 TNFSF12 6141 0.095 0.52 NO
20 DFFB DFFB DFFB 6343 0.089 0.52 NO
21 BIRC2 BIRC2 BIRC2 7337 0.059 0.48 NO
22 DFFA DFFA DFFA 7348 0.059 0.49 NO
23 TRAF2 TRAF2 TRAF2 8648 0.025 0.42 NO
24 GAS2 GAS2 GAS2 8848 0.02 0.41 NO
25 RELA RELA RELA 9064 0.015 0.4 NO
26 APAF1 APAF1 APAF1 10331 -0.017 0.34 NO
27 NFKBIA NFKBIA NFKBIA 11274 -0.04 0.29 NO
28 XIAP XIAP XIAP 11787 -0.054 0.27 NO
29 CHUK CHUK CHUK 12316 -0.07 0.26 NO
30 BCL2 BCL2 BCL2 14100 -0.14 0.18 NO
31 SPTAN1 SPTAN1 SPTAN1 14569 -0.16 0.18 NO
32 CASP9 CASP9 CASP9 14806 -0.17 0.19 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR 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 DNA REPLICATION

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 CASP8 CASP8 CASP8 651 0.65 0.092 YES
2 TNFRSF1A TNFRSF1A TNFRSF1A 1833 0.39 0.1 YES
3 LMNB1 LMNB1 LMNB1 2087 0.36 0.16 YES
4 TRADD TRADD TRADD 2112 0.36 0.23 YES
5 CASP3 CASP3 CASP3 2645 0.3 0.26 YES
6 ARHGDIB ARHGDIB ARHGDIB 2692 0.29 0.31 YES
7 LMNA LMNA LMNA 3359 0.23 0.32 YES
8 RIPK1 RIPK1 RIPK1 3516 0.22 0.36 YES
9 FADD FADD FADD 3542 0.22 0.4 YES
10 CASP2 CASP2 CASP2 3619 0.21 0.44 YES
11 JUN JUN JUN 3683 0.21 0.47 YES
12 MAP3K1 MAP3K1 MAP3K1 3907 0.19 0.5 YES
13 LMNB2 LMNB2 LMNB2 4614 0.16 0.49 NO
14 RB1 RB1 RB1 5654 0.11 0.46 NO
15 DFFB DFFB DFFB 6343 0.089 0.44 NO
16 DFFA DFFA DFFA 7348 0.059 0.39 NO
17 PAK1 PAK1 PAK1 7909 0.044 0.37 NO
18 CRADD CRADD CRADD 8697 0.024 0.33 NO
19 MAP3K7 MAP3K7 MAP3K7 9084 0.014 0.31 NO
20 PRKDC PRKDC PRKDC 10054 -0.01 0.26 NO
21 PAK2 PAK2 PAK2 10149 -0.012 0.26 NO
22 PARP1 PARP1 PARP1 10578 -0.023 0.24 NO
23 BAG4 BAG4 BAG4 11851 -0.056 0.18 NO
24 TNF TNF TNF 12120 -0.064 0.18 NO
25 MAP2K4 MAP2K4 MAP2K4 13215 -0.1 0.14 NO
26 SPTAN1 SPTAN1 SPTAN1 14569 -0.16 0.098 NO
27 MADD MADD MADD 16037 -0.26 0.069 NO
28 MAPK8 MAPK8 MAPK8 16186 -0.28 0.12 NO

Figure S15.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG DNA REPLICATION.

Figure S16.  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

genes ES table in pathway: KEGG BASE EXCISION REPAIR

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 CASP8 CASP8 CASP8 651 0.65 0.073 YES
2 CASP6 CASP6 CASP6 752 0.62 0.17 YES
3 FAS FAS FAS 1070 0.53 0.24 YES
4 FASLG FASLG FASLG 1087 0.53 0.33 YES
5 CASP7 CASP7 CASP7 2219 0.34 0.32 YES
6 CASP3 CASP3 CASP3 2645 0.3 0.35 YES
7 ARHGDIB ARHGDIB ARHGDIB 2692 0.29 0.4 YES
8 CASP10 CASP10 CASP10 3265 0.24 0.41 YES
9 LMNA LMNA LMNA 3359 0.23 0.44 YES
10 FADD FADD FADD 3542 0.22 0.47 YES
11 CFLAR CFLAR CFLAR 3654 0.21 0.5 YES
12 JUN JUN JUN 3683 0.21 0.53 YES
13 MAP3K1 MAP3K1 MAP3K1 3907 0.19 0.55 YES
14 LMNB2 LMNB2 LMNB2 4614 0.16 0.54 NO
15 FAF1 FAF1 FAF1 4948 0.14 0.54 NO
16 RB1 RB1 RB1 5654 0.11 0.52 NO
17 PTPN13 PTPN13 PTPN13 6029 0.098 0.52 NO
18 DFFB DFFB DFFB 6343 0.089 0.51 NO
19 DFFA DFFA DFFA 7348 0.059 0.47 NO
20 DAXX DAXX DAXX 7700 0.05 0.46 NO
21 PAK1 PAK1 PAK1 7909 0.044 0.45 NO
22 MAP3K7 MAP3K7 MAP3K7 9084 0.014 0.39 NO
23 PRKDC PRKDC PRKDC 10054 -0.01 0.34 NO
24 PAK2 PAK2 PAK2 10149 -0.012 0.34 NO
25 PARP1 PARP1 PARP1 10578 -0.023 0.32 NO
26 RIPK2 RIPK2 RIPK2 12957 -0.091 0.2 NO
27 MAP2K4 MAP2K4 MAP2K4 13215 -0.1 0.2 NO
28 SPTAN1 SPTAN1 SPTAN1 14569 -0.16 0.16 NO
29 MAPK8 MAPK8 MAPK8 16186 -0.28 0.12 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 BASE EXCISION REPAIR.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BASE EXCISION REPAIR, 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 NUCLEOTIDE EXCISION REPAIR

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 SOCS1 SOCS1 SOCS1 73 1 0.099 YES
2 SOCS3 SOCS3 SOCS3 202 0.88 0.18 YES
3 IL2RB IL2RB IL2RB 392 0.76 0.24 YES
4 IL2RG IL2RG IL2RG 416 0.74 0.32 YES
5 IL2RA IL2RA IL2RA 554 0.68 0.38 YES
6 FAS FAS FAS 1070 0.53 0.4 YES
7 FASLG FASLG FASLG 1087 0.53 0.45 YES
8 NMI NMI NMI 1110 0.52 0.5 YES
9 JAK3 JAK3 JAK3 1294 0.48 0.54 YES
10 PIK3CG PIK3CG PIK3CG 1397 0.46 0.58 YES
11 SHC1 SHC1 SHC1 2382 0.32 0.56 YES
12 IKZF3 IKZF3 IKZF3 2477 0.31 0.58 YES
13 STAT5A STAT5A STAT5A 2942 0.27 0.58 YES
14 PTPN6 PTPN6 PTPN6 3003 0.26 0.61 YES
15 FOS FOS FOS 3470 0.22 0.6 YES
16 SYK SYK SYK 3650 0.21 0.62 YES
17 CFLAR CFLAR CFLAR 3654 0.21 0.64 YES
18 PPIA PPIA PPIA 4124 0.18 0.63 NO
19 AKT1 AKT1 AKT1 7672 0.05 0.44 NO
20 BCL2L1 BCL2L1 BCL2L1 8122 0.038 0.42 NO
21 BAD BAD BAD 8179 0.037 0.42 NO
22 HRAS HRAS HRAS 9741 -0.0023 0.33 NO
23 RAF1 RAF1 RAF1 9935 -0.0066 0.32 NO
24 GRB2 GRB2 GRB2 10395 -0.019 0.3 NO
25 RPS6KB1 RPS6KB1 RPS6KB1 10852 -0.03 0.28 NO
26 JAK1 JAK1 JAK1 11943 -0.059 0.22 NO
27 MAPK1 MAPK1 MAPK1 12486 -0.076 0.2 NO
28 STAT5B STAT5B STAT5B 12654 -0.081 0.2 NO
29 SOS1 SOS1 SOS1 12711 -0.083 0.21 NO
30 MAPK3 MAPK3 MAPK3 12876 -0.088 0.2 NO
31 PIK3CA PIK3CA PIK3CA 12934 -0.09 0.21 NO
32 CRKL CRKL CRKL 13011 -0.092 0.22 NO
33 CBL CBL CBL 13219 -0.1 0.22 NO
34 MYC MYC MYC 13811 -0.12 0.19 NO
35 BCL2 BCL2 BCL2 14100 -0.14 0.19 NO
36 IRS1 IRS1 IRS1 14733 -0.17 0.17 NO
37 PIK3R1 PIK3R1 PIK3R1 15489 -0.22 0.15 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 NUCLEOTIDE EXCISION REPAIR.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.4 1.4 0.14 1 0.96 0.35 0.18 0.29 1 0.63
BIOCARTA VIP PATHWAY 25 genes.ES.table 0.34 0.99 0.47 1 1 0.12 0.055 0.11 1 0.89
BIOCARTA EDG1 PATHWAY 25 genes.ES.table 0.31 0.96 0.52 1 1 0.36 0.2 0.29 1 0.75
KEGG PENTOSE PHOSPHATE PATHWAY 25 genes.ES.table 0.24 0.74 0.84 1 1 0.2 0.098 0.18 1 0.91
KEGG STEROID HORMONE BIOSYNTHESIS 30 genes.ES.table 0.31 0.79 0.84 1 1 0.33 0.12 0.29 1 0.95
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.22 1 0.41 1 1 0.49 0.27 0.36 1 0.9
KEGG SPHINGOLIPID METABOLISM 37 genes.ES.table 0.31 0.93 0.55 1 1 0.16 0.08 0.15 1 0.76
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES 25 genes.ES.table 0.3 0.76 0.82 1 1 0.12 0.006 0.12 1 0.92
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.22 0.9 0.55 1 1 1 0.78 0.22 1 0.71
KEGG RIBOSOME 85 genes.ES.table 0.65 1.7 0.064 0.44 0.54 0.69 0.25 0.52 0.22 0.14
genes ES table in pathway: BIOCARTA CARM ER PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 56 0.48 0.065 YES
2 RPL17 RPL17 RPL17 685 0.25 0.065 YES
3 RPL7 RPL7 RPL7 744 0.24 0.095 YES
4 RPS28 RPS28 RPS28 926 0.21 0.12 YES
5 RPL9 RPL9 RPL9 1098 0.2 0.13 YES
6 RPL18A RPL18A RPL18A 1215 0.18 0.15 YES
7 RPL12 RPL12 RPL12 1302 0.18 0.17 YES
8 RPL13A RPL13A RPL13A 1382 0.17 0.19 YES
9 RPS27A RPS27A RPS27A 1753 0.14 0.19 YES
10 RPS25 RPS25 RPS25 1769 0.14 0.21 YES
11 RPL3 RPL3 RPL3 1818 0.14 0.23 YES
12 RPS12 RPS12 RPS12 1848 0.14 0.24 YES
13 RPL7A RPL7A RPL7A 1853 0.14 0.26 YES
14 RPL4 RPL4 RPL4 1924 0.13 0.28 YES
15 RPS24 RPS24 RPS24 2006 0.13 0.29 YES
16 RPL10 RPL10 RPL10 2203 0.12 0.3 YES
17 RPL10L RPL10L RPL10L 2222 0.12 0.31 YES
18 RPL6 RPL6 RPL6 2312 0.12 0.32 YES
19 RPL22 RPL22 RPL22 2366 0.11 0.34 YES
20 RPSA RPSA RPSA 2570 0.1 0.34 YES
21 RPS18 RPS18 RPS18 2628 0.1 0.35 YES
22 RPS3 RPS3 RPS3 2680 0.1 0.36 YES
23 RPL34 RPL34 RPL34 2807 0.096 0.37 YES
24 RPS7 RPS7 RPS7 2820 0.096 0.38 YES
25 RPL30 RPL30 RPL30 2837 0.095 0.4 YES
26 RPS13 RPS13 RPS13 2934 0.092 0.4 YES
27 RPL26 RPL26 RPL26 2965 0.091 0.41 YES
28 RPL27A RPL27A RPL27A 3042 0.089 0.42 YES
29 RPL5 RPL5 RPL5 3050 0.089 0.43 YES
30 RPL19 RPL19 RPL19 3085 0.088 0.44 YES
31 RPL24 RPL24 RPL24 3096 0.088 0.46 YES
32 RPS23 RPS23 RPS23 3128 0.087 0.47 YES
33 RPL13 RPL13 RPL13 3198 0.085 0.48 YES
34 RPL37 RPL37 RPL37 3210 0.085 0.49 YES
35 RPS6 RPS6 RPS6 3241 0.084 0.5 YES
36 RPS10 RPS10 RPS10 3245 0.084 0.51 YES
37 RPS20 RPS20 RPS20 3267 0.084 0.52 YES
38 RPL23 RPL23 RPL23 3291 0.083 0.53 YES
39 RPLP0 RPLP0 RPLP0 3337 0.082 0.54 YES
40 FAU FAU FAU 3483 0.078 0.54 YES
41 RPS2 RPS2 RPS2 3528 0.077 0.55 YES
42 RPL11 RPL11 RPL11 3576 0.076 0.56 YES
43 RPLP1 RPLP1 RPLP1 3675 0.073 0.56 YES
44 RPS17 RPS17 RPS17 3771 0.071 0.57 YES
45 RPS16 RPS16 RPS16 3883 0.068 0.57 YES
46 RPL15 RPL15 RPL15 3891 0.068 0.58 YES
47 RPS8 RPS8 RPS8 3969 0.067 0.58 YES
48 RPL36AL RPL36AL RPL36AL 4043 0.065 0.59 YES
49 RPL29 RPL29 RPL29 4056 0.065 0.6 YES
50 RPL14 RPL14 RPL14 4066 0.065 0.61 YES
51 RPS4X RPS4X RPS4X 4070 0.065 0.62 YES
52 RPL32 RPL32 RPL32 4286 0.06 0.61 YES
53 RPL8 RPL8 RPL8 4318 0.06 0.62 YES
54 RPS29 RPS29 RPS29 4407 0.058 0.62 YES
55 RPL37A RPL37A RPL37A 4426 0.058 0.63 YES
56 RPS9 RPS9 RPS9 4506 0.056 0.63 YES
57 RPLP2 RPLP2 RPLP2 4522 0.056 0.64 YES
58 RPS3A RPS3A RPS3A 4606 0.054 0.64 YES
59 RPS15A RPS15A RPS15A 4643 0.053 0.65 YES
60 RPL10A RPL10A RPL10A 5052 0.046 0.63 NO
61 RPL39 RPL39 RPL39 5090 0.045 0.64 NO
62 RPS11 RPS11 RPS11 5279 0.042 0.63 NO
63 RPL31 RPL31 RPL31 5296 0.042 0.64 NO
64 RSL24D1 RSL24D1 RSL24D1 5309 0.042 0.64 NO
65 RPS21 RPS21 RPS21 5385 0.04 0.64 NO
66 RPS27 RPS27 RPS27 5592 0.037 0.64 NO
67 RPS15 RPS15 RPS15 5638 0.036 0.64 NO
68 RPL35 RPL35 RPL35 5650 0.036 0.64 NO
69 RPL35A RPL35A RPL35A 5977 0.031 0.63 NO
70 RPL38 RPL38 RPL38 6043 0.03 0.63 NO
71 RPS19 RPS19 RPS19 6194 0.028 0.63 NO
72 RPL36 RPL36 RPL36 6559 0.023 0.61 NO
73 RPL23A RPL23A RPL23A 6819 0.019 0.6 NO
74 RPL28 RPL28 RPL28 7031 0.016 0.59 NO
75 RPL36A RPL36A RPL36A 7072 0.015 0.59 NO
76 RPS4Y1 RPS4Y1 RPS4Y1 7659 0.007 0.56 NO
77 RPL27 RPL27 RPL27 7754 0.0058 0.55 NO
78 UBA52 UBA52 UBA52 7864 0.0041 0.55 NO
79 RPS5 RPS5 RPS5 7962 0.0025 0.54 NO
80 RPL22L1 RPL22L1 RPL22L1 8169 -0.0002 0.53 NO
81 RPL26L1 RPL26L1 RPL26L1 8249 -0.001 0.53 NO
82 RPL41 RPL41 RPL41 9635 -0.022 0.45 NO
83 RPS26 RPS26 RPS26 10477 -0.036 0.41 NO
84 RPS27L RPS27L RPS27L 10691 -0.039 0.41 NO
85 MRPL13 MRPL13 MRPL13 12493 -0.077 0.32 NO

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

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

genes ES table in pathway: BIOCARTA VIP 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 NR0B1 NR0B1 NR0B1 509 0.28 0.062 YES
2 HIST2H3C HIST2H3C HIST2H3C 567 0.27 0.15 YES
3 GRIP1 GRIP1 GRIP1 927 0.21 0.2 YES
4 HDAC4 HDAC4 HDAC4 964 0.21 0.26 YES
5 SPEN SPEN SPEN 2277 0.12 0.23 YES
6 CCND1 CCND1 CCND1 2334 0.12 0.26 YES
7 HDAC5 HDAC5 HDAC5 2371 0.11 0.3 YES
8 NCOR2 NCOR2 NCOR2 2551 0.1 0.32 YES
9 EP300 EP300 EP300 2682 0.1 0.34 YES
10 CREBBP CREBBP CREBBP 2741 0.099 0.37 YES
11 PELP1 PELP1 PELP1 2862 0.094 0.4 YES
12 HDAC11 HDAC11 HDAC11 3321 0.082 0.4 YES
13 MED1 MED1 MED1 3832 0.069 0.39 NO
14 HDAC6 HDAC6 HDAC6 4300 0.06 0.39 NO
15 PHB2 PHB2 PHB2 4635 0.053 0.38 NO
16 GTF2A1 GTF2A1 GTF2A1 4717 0.052 0.4 NO
17 POLR2A POLR2A POLR2A 5410 0.04 0.37 NO
18 GTF2F1 GTF2F1 GTF2F1 5715 0.035 0.37 NO
19 TBP TBP TBP 6348 0.026 0.34 NO
20 HDAC10 HDAC10 HDAC10 6655 0.021 0.33 NO
21 HDAC2 HDAC2 HDAC2 6774 0.02 0.33 NO
22 HDAC8 HDAC8 HDAC8 7350 0.011 0.3 NO
23 ERCC3 ERCC3 ERCC3 7787 0.0052 0.28 NO
24 NRIP1 NRIP1 NRIP1 8938 -0.011 0.22 NO
25 GTF2E1 GTF2E1 GTF2E1 9869 -0.025 0.18 NO
26 HDAC7 HDAC7 HDAC7 11393 -0.052 0.11 NO
27 HDAC1 HDAC1 HDAC1 11677 -0.058 0.12 NO
28 SRA1 SRA1 SRA1 11994 -0.065 0.12 NO
29 HDAC3 HDAC3 HDAC3 12426 -0.075 0.12 NO
30 CARM1 CARM1 CARM1 12778 -0.085 0.13 NO
31 HDAC9 HDAC9 HDAC9 13135 -0.097 0.14 NO
32 BRCA1 BRCA1 BRCA1 13286 -0.1 0.16 NO
33 PPARGC1A PPARGC1A PPARGC1A 14329 -0.15 0.15 NO
34 ESR1 ESR1 ESR1 15226 -0.2 0.17 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 VIP PATHWAY.

Figure S24.  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 EDG1 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 DLL3 DLL3 DLL3 77 0.46 0.093 YES
2 DLL1 DLL1 DLL1 214 0.37 0.16 YES
3 HES5 HES5 HES5 418 0.3 0.22 YES
4 MAML2 MAML2 MAML2 884 0.22 0.24 YES
5 DTX4 DTX4 DTX4 1198 0.19 0.26 YES
6 RBPJ RBPJ RBPJ 1529 0.16 0.28 YES
7 NOTCH1 NOTCH1 NOTCH1 2014 0.13 0.28 YES
8 CTBP2 CTBP2 CTBP2 2106 0.12 0.3 YES
9 NCOR2 NCOR2 NCOR2 2551 0.1 0.3 YES
10 EP300 EP300 EP300 2682 0.1 0.31 YES
11 CREBBP CREBBP CREBBP 2741 0.099 0.33 YES
12 KAT2A KAT2A KAT2A 2758 0.098 0.35 YES
13 DVL2 DVL2 DVL2 3469 0.078 0.32 NO
14 KAT2B KAT2B KAT2B 3707 0.072 0.33 NO
15 CIR1 CIR1 CIR1 3849 0.069 0.33 NO
16 NOTCH2 NOTCH2 NOTCH2 4591 0.054 0.3 NO
17 DVL3 DVL3 DVL3 4770 0.051 0.3 NO
18 DVL1 DVL1 DVL1 4846 0.05 0.31 NO
19 MAML1 MAML1 MAML1 4997 0.047 0.31 NO
20 DTX1 DTX1 DTX1 6588 0.022 0.23 NO
21 SNW1 SNW1 SNW1 6646 0.021 0.23 NO
22 PSEN1 PSEN1 PSEN1 6653 0.021 0.24 NO
23 DTX3 DTX3 DTX3 6688 0.02 0.24 NO
24 HDAC2 HDAC2 HDAC2 6774 0.02 0.24 NO
25 RFNG RFNG RFNG 6969 0.017 0.23 NO
26 CTBP1 CTBP1 CTBP1 7646 0.0072 0.2 NO
27 APH1A APH1A APH1A 9295 -0.016 0.11 NO
28 NOTCH4 NOTCH4 NOTCH4 9478 -0.019 0.1 NO
29 ADAM17 ADAM17 ADAM17 9580 -0.021 0.1 NO
30 NCSTN NCSTN NCSTN 10833 -0.042 0.041 NO
31 LFNG LFNG LFNG 11026 -0.045 0.04 NO
32 PSENEN PSENEN PSENEN 11417 -0.052 0.03 NO
33 NUMB NUMB NUMB 11447 -0.053 0.04 NO
34 DTX2 DTX2 DTX2 11584 -0.056 0.044 NO
35 HDAC1 HDAC1 HDAC1 11677 -0.058 0.051 NO
36 NOTCH3 NOTCH3 NOTCH3 12372 -0.074 0.029 NO
37 DTX3L DTX3L DTX3L 12582 -0.08 0.034 NO
38 JAG2 JAG2 JAG2 12652 -0.081 0.047 NO
39 HES1 HES1 HES1 13294 -0.1 0.034 NO
40 MAML3 MAML3 MAML3 13803 -0.12 0.031 NO
41 JAG1 JAG1 JAG1 14134 -0.14 0.042 NO
42 DLL4 DLL4 DLL4 14519 -0.16 0.054 NO
43 PSEN2 PSEN2 PSEN2 14657 -0.17 0.082 NO
44 NUMBL NUMBL NUMBL 14714 -0.17 0.11 NO
45 RBPJL RBPJL RBPJL 14866 -0.18 0.14 NO
46 PTCRA PTCRA PTCRA 15404 -0.21 0.16 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 EDG1 PATHWAY.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EDG1 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 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 CTNNA3 CTNNA3 CTNNA3 100 0.44 0.1 YES
2 MYC MYC MYC 1003 0.21 0.1 YES
3 CASP9 CASP9 CASP9 1169 0.19 0.14 YES
4 TCF7L1 TCF7L1 TCF7L1 1217 0.18 0.18 YES
5 APC2 APC2 APC2 1604 0.15 0.2 YES
6 TCF7L2 TCF7L2 TCF7L2 1994 0.13 0.21 YES
7 PIK3R1 PIK3R1 PIK3R1 2186 0.12 0.23 YES
8 SOS2 SOS2 SOS2 2290 0.12 0.25 YES
9 CCND1 CCND1 CCND1 2334 0.12 0.28 YES
10 AKT3 AKT3 AKT3 3207 0.085 0.25 YES
11 AXIN1 AXIN1 AXIN1 3211 0.085 0.27 YES
12 AXIN2 AXIN2 AXIN2 3265 0.084 0.29 YES
13 PIK3CA PIK3CA PIK3CA 3721 0.072 0.28 YES
14 FOXO3 FOXO3 FOXO3 3874 0.069 0.29 YES
15 SOS1 SOS1 SOS1 3911 0.068 0.31 YES
16 RAF1 RAF1 RAF1 5158 0.044 0.25 NO
17 PIK3R5 PIK3R5 PIK3R5 5253 0.042 0.25 NO
18 PTEN PTEN PTEN 5539 0.038 0.25 NO
19 PIK3CB PIK3CB PIK3CB 6286 0.026 0.21 NO
20 PIK3R2 PIK3R2 PIK3R2 6312 0.026 0.22 NO
21 GSK3B GSK3B GSK3B 6466 0.024 0.22 NO
22 APC APC APC 6907 0.018 0.2 NO
23 GRB2 GRB2 GRB2 7090 0.015 0.19 NO
24 MAPK1 MAPK1 MAPK1 7889 0.0036 0.15 NO
25 MAPK3 MAPK3 MAPK3 7955 0.0026 0.14 NO
26 PDPK1 PDPK1 PDPK1 8054 0.0013 0.14 NO
27 MAP2K2 MAP2K2 MAP2K2 8209 -0.00057 0.13 NO
28 KRAS KRAS KRAS 8298 -0.0016 0.13 NO
29 BAD BAD BAD 8302 -0.0017 0.13 NO
30 AKT1 AKT1 AKT1 8655 -0.0066 0.11 NO
31 CDH1 CDH1 CDH1 8985 -0.011 0.093 NO
32 ARAF ARAF ARAF 9315 -0.017 0.079 NO
33 CTNNA2 CTNNA2 CTNNA2 9790 -0.024 0.059 NO
34 TP53 TP53 TP53 9881 -0.026 0.06 NO
35 MLH1 MLH1 MLH1 10595 -0.038 0.03 NO
36 AKT2 AKT2 AKT2 10722 -0.04 0.033 NO
37 CTNNB1 CTNNB1 CTNNB1 10795 -0.042 0.04 NO
38 NRAS NRAS NRAS 11470 -0.054 0.016 NO
39 CTNNA1 CTNNA1 CTNNA1 11505 -0.054 0.027 NO
40 ILK ILK ILK 11542 -0.055 0.039 NO
41 EGF EGF EGF 12178 -0.069 0.021 NO
42 BRAF BRAF BRAF 12281 -0.071 0.033 NO
43 EGFR EGFR EGFR 12352 -0.073 0.047 NO
44 PIK3R3 PIK3R3 PIK3R3 12861 -0.088 0.041 NO
45 MAP2K1 MAP2K1 MAP2K1 13092 -0.095 0.051 NO
46 PIK3CG PIK3CG PIK3CG 13230 -0.1 0.068 NO
47 ERBB2 ERBB2 ERBB2 13507 -0.11 0.08 NO
48 PIK3CD PIK3CD PIK3CD 14455 -0.15 0.066 NO
49 LEF1 LEF1 LEF1 15100 -0.19 0.078 NO
50 ELK1 ELK1 ELK1 15202 -0.2 0.12 NO
51 TCF7 TCF7 TCF7 15228 -0.2 0.17 NO

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

Figure S28.  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 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 TAS2R4 TAS2R4 TAS2R4 131 0.42 0.046 YES
2 TAS2R19 TAS2R19 TAS2R19 201 0.38 0.09 YES
3 TAS2R31 TAS2R31 TAS2R31 251 0.36 0.13 YES
4 KCNB1 KCNB1 KCNB1 255 0.35 0.18 YES
5 TAS2R14 TAS2R14 TAS2R14 277 0.34 0.22 YES
6 PRKACG PRKACG PRKACG 499 0.28 0.24 YES
7 TAS2R3 TAS2R3 TAS2R3 502 0.28 0.28 YES
8 GNB3 GNB3 GNB3 593 0.26 0.31 YES
9 PRKX PRKX PRKX 724 0.24 0.33 YES
10 TAS2R20 TAS2R20 TAS2R20 857 0.22 0.35 YES
11 ADCY8 ADCY8 ADCY8 888 0.22 0.38 YES
12 TAS1R3 TAS1R3 TAS1R3 1052 0.2 0.39 YES
13 TAS2R5 TAS2R5 TAS2R5 1123 0.19 0.41 YES
14 TAS2R43 TAS2R43 TAS2R43 1148 0.19 0.44 YES
15 CACNA1A CACNA1A CACNA1A 1168 0.19 0.46 YES
16 TAS2R13 TAS2R13 TAS2R13 1932 0.13 0.44 NO
17 TAS2R10 TAS2R10 TAS2R10 2081 0.12 0.44 NO
18 TAS2R50 TAS2R50 TAS2R50 2099 0.12 0.46 NO
19 TAS2R46 TAS2R46 TAS2R46 2456 0.11 0.45 NO
20 PLCB2 PLCB2 PLCB2 5666 0.036 0.28 NO
21 CACNA1B CACNA1B CACNA1B 6966 0.017 0.21 NO
22 TRPM5 TRPM5 TRPM5 7308 0.012 0.2 NO
23 GNAS GNAS GNAS 9195 -0.015 0.093 NO
24 PRKACB PRKACB PRKACB 9484 -0.019 0.08 NO
25 TAS2R42 TAS2R42 TAS2R42 10060 -0.028 0.052 NO
26 ADCY6 ADCY6 ADCY6 10220 -0.031 0.047 NO
27 GNB1 GNB1 GNB1 10750 -0.041 0.023 NO
28 GRM4 GRM4 GRM4 11603 -0.056 -0.016 NO
29 ADCY4 ADCY4 ADCY4 12139 -0.068 -0.037 NO
30 PDE1A PDE1A PDE1A 12290 -0.072 -0.036 NO
31 SCNN1A SCNN1A SCNN1A 12766 -0.085 -0.051 NO
32 PRKACA PRKACA PRKACA 13028 -0.093 -0.054 NO
33 ITPR3 ITPR3 ITPR3 14020 -0.13 -0.092 NO
34 TAS1R1 TAS1R1 TAS1R1 14663 -0.17 -0.1 NO
35 ACCN1 ACCN1 ACCN1 15669 -0.23 -0.13 NO
36 GNG13 GNG13 GNG13 16555 -0.32 -0.14 NO
37 SCNN1B SCNN1B SCNN1B 17832 -0.54 -0.14 NO
38 GNG3 GNG3 GNG3 17927 -0.57 -0.073 NO
39 SCNN1G SCNN1G SCNN1G 18205 -0.74 0.0056 NO

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

Figure S30.  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 LYSINE DEGRADATION

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RBM17 RBM17 RBM17 1735 0.14 -0.07 YES
2 HSPA1L HSPA1L HSPA1L 1937 0.13 -0.058 YES
3 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 1955 0.13 -0.036 YES
4 PRPF18 PRPF18 PRPF18 2303 0.12 -0.034 YES
5 SART1 SART1 SART1 2311 0.12 -0.014 YES
6 HNRNPA1 HNRNPA1 HNRNPA1 2438 0.11 -0.0018 YES
7 DHX38 DHX38 DHX38 2774 0.098 -0.0031 YES
8 PQBP1 PQBP1 PQBP1 2950 0.092 0.0034 YES
9 PRPF6 PRPF6 PRPF6 3048 0.089 0.014 YES
10 DDX42 DDX42 DDX42 3182 0.085 0.022 YES
11 XAB2 XAB2 XAB2 3203 0.085 0.035 YES
12 SF3B2 SF3B2 SF3B2 3247 0.084 0.048 YES
13 SF3A2 SF3A2 SF3A2 3381 0.08 0.055 YES
14 TCERG1 TCERG1 TCERG1 3457 0.078 0.064 YES
15 PRPF40B PRPF40B PRPF40B 3595 0.075 0.07 YES
16 ACIN1 ACIN1 ACIN1 3611 0.074 0.082 YES
17 SF3A1 SF3A1 SF3A1 3778 0.071 0.086 YES
18 PUF60 PUF60 PUF60 4279 0.06 0.069 YES
19 SR140 SR140 SR140 4409 0.058 0.072 YES
20 SNRNP200 SNRNP200 SNRNP200 4435 0.057 0.08 YES
21 THOC2 THOC2 THOC2 4441 0.057 0.09 YES
22 SYF2 SYF2 SYF2 4746 0.051 0.082 YES
23 DDX46 DDX46 DDX46 4789 0.051 0.089 YES
24 HNRNPM HNRNPM HNRNPM 4839 0.05 0.095 YES
25 RBM25 RBM25 RBM25 4879 0.049 0.1 YES
26 SNRNP70 SNRNP70 SNRNP70 4951 0.048 0.11 YES
27 THOC1 THOC1 THOC1 4999 0.047 0.11 YES
28 CWC15 CWC15 CWC15 5075 0.046 0.12 YES
29 HSPA2 HSPA2 HSPA2 5083 0.045 0.12 YES
30 SFRS5 SFRS5 SFRS5 5109 0.045 0.13 YES
31 SNRPE SNRPE SNRPE 5167 0.044 0.13 YES
32 U2AF1 U2AF1 U2AF1 5180 0.044 0.14 YES
33 CTNNBL1 CTNNBL1 CTNNBL1 5183 0.043 0.15 YES
34 CDC5L CDC5L CDC5L 5188 0.043 0.16 YES
35 CHERP CHERP CHERP 5207 0.043 0.16 YES
36 PRPF40A PRPF40A PRPF40A 5243 0.043 0.17 YES
37 HNRNPU HNRNPU HNRNPU 5351 0.041 0.17 YES
38 CCDC12 CCDC12 CCDC12 5353 0.041 0.18 YES
39 ISY1 ISY1 ISY1 5383 0.04 0.18 YES
40 SFRS2B SFRS2B SFRS2B 5389 0.04 0.19 YES
41 SLU7 SLU7 SLU7 5414 0.04 0.2 YES
42 PRPF8 PRPF8 PRPF8 5512 0.038 0.2 YES
43 SF3B1 SF3B1 SF3B1 5551 0.038 0.2 YES
44 HNRNPA3 HNRNPA3 HNRNPA3 5564 0.038 0.21 YES
45 RBM8A RBM8A RBM8A 5578 0.037 0.21 YES
46 HNRNPC HNRNPC HNRNPC 5631 0.036 0.22 YES
47 PRPF38A PRPF38A PRPF38A 5635 0.036 0.22 YES
48 SF3B3 SF3B3 SF3B3 5737 0.035 0.22 YES
49 AQR AQR AQR 5763 0.034 0.23 YES
50 RBMX RBMX RBMX 5876 0.032 0.23 YES
51 BAT1 BAT1 BAT1 5934 0.032 0.23 YES
52 PRPF38B PRPF38B PRPF38B 5952 0.031 0.23 YES
53 PRPF3 PRPF3 PRPF3 6005 0.031 0.24 YES
54 SNRPA SNRPA SNRPA 6150 0.028 0.23 YES
55 SNRNP27 SNRNP27 SNRNP27 6180 0.028 0.24 YES
56 PLRG1 PLRG1 PLRG1 6238 0.027 0.24 YES
57 DHX16 DHX16 DHX16 6326 0.026 0.24 YES
58 NHP2L1 NHP2L1 NHP2L1 6356 0.026 0.24 YES
59 HNRNPK HNRNPK HNRNPK 6368 0.025 0.24 YES
60 RBM22 RBM22 RBM22 6542 0.023 0.24 YES
61 SNRPF SNRPF SNRPF 6553 0.023 0.24 YES
62 WBP11 WBP11 WBP11 6630 0.022 0.24 YES
63 SNW1 SNW1 SNW1 6646 0.021 0.25 YES
64 SFRS6 SFRS6 SFRS6 6691 0.02 0.25 YES
65 SF3B14 SF3B14 SF3B14 6814 0.019 0.24 NO
66 DDX23 DDX23 DDX23 6934 0.017 0.24 NO
67 ZMAT2 ZMAT2 ZMAT2 6937 0.017 0.24 NO
68 SMNDC1 SMNDC1 SMNDC1 6984 0.016 0.24 NO
69 SNRPD3 SNRPD3 SNRPD3 7058 0.015 0.24 NO
70 SF3B4 SF3B4 SF3B4 7101 0.015 0.24 NO
71 PRPF19 PRPF19 PRPF19 7156 0.014 0.24 NO
72 CDC40 CDC40 CDC40 7160 0.014 0.24 NO
73 DDX5 DDX5 DDX5 7216 0.013 0.24 NO
74 HSPA1A HSPA1A HSPA1A 7316 0.012 0.24 NO
75 CRNKL1 CRNKL1 CRNKL1 7361 0.011 0.24 NO
76 SFRS1 SFRS1 SFRS1 7549 0.0086 0.23 NO
77 TRA2A TRA2A TRA2A 7628 0.0074 0.23 NO
78 SFRS4 SFRS4 SFRS4 7833 0.0046 0.22 NO
79 NAA38 NAA38 NAA38 7839 0.0046 0.22 NO
80 SNRPA1 SNRPA1 SNRPA1 7887 0.0037 0.22 NO
81 EFTUD2 EFTUD2 EFTUD2 7917 0.0031 0.22 NO
82 EIF4A3 EIF4A3 EIF4A3 8081 0.00092 0.21 NO
83 LSM2 LSM2 LSM2 8145 0.000091 0.2 NO
84 PPIL1 PPIL1 PPIL1 8176 -0.00026 0.2 NO
85 U2AF2 U2AF2 U2AF2 8505 -0.0043 0.18 NO
86 LSM6 LSM6 LSM6 8516 -0.0046 0.18 NO
87 SF3B5 SF3B5 SF3B5 8618 -0.0061 0.18 NO
88 PCBP1 PCBP1 PCBP1 8674 -0.007 0.18 NO
89 USP39 USP39 USP39 8730 -0.0078 0.18 NO
90 SFRS3 SFRS3 SFRS3 8743 -0.008 0.18 NO
91 THOC4 THOC4 THOC4 8778 -0.0085 0.18 NO
92 LSM7 LSM7 LSM7 8839 -0.0093 0.18 NO
93 NCBP1 NCBP1 NCBP1 8967 -0.011 0.17 NO
94 SNRPD1 SNRPD1 SNRPD1 9166 -0.014 0.16 NO
95 DHX8 DHX8 DHX8 9214 -0.015 0.16 NO
96 SNRPG SNRPG SNRPG 9227 -0.015 0.16 NO
97 PPIE PPIE PPIE 9279 -0.016 0.16 NO
98 PRPF31 PRPF31 PRPF31 9609 -0.022 0.15 NO
99 LSM3 LSM3 LSM3 9636 -0.022 0.15 NO
100 PHF5A PHF5A PHF5A 9880 -0.026 0.14 NO
101 SF3A3 SF3A3 SF3A3 10116 -0.03 0.14 NO
102 TRA2B TRA2B TRA2B 10182 -0.03 0.14 NO
103 DHX15 DHX15 DHX15 10192 -0.031 0.14 NO
104 SFRS13A SFRS13A SFRS13A 10306 -0.032 0.14 NO
105 PRPF4 PRPF4 PRPF4 10318 -0.033 0.15 NO
106 SFRS9 SFRS9 SFRS9 10320 -0.033 0.15 NO
107 SNRPB2 SNRPB2 SNRPB2 10409 -0.035 0.15 NO
108 HSPA8 HSPA8 HSPA8 10534 -0.037 0.15 NO
109 SNRPC SNRPC SNRPC 10567 -0.037 0.16 NO
110 SFRS2 SFRS2 SFRS2 10754 -0.041 0.16 NO
111 TXNL4A TXNL4A TXNL4A 10909 -0.043 0.15 NO
112 SFRS7 SFRS7 SFRS7 11249 -0.049 0.14 NO
113 SNRPB SNRPB SNRPB 11521 -0.054 0.14 NO
114 MAGOHB MAGOHB MAGOHB 11690 -0.058 0.14 NO
115 BUD31 BUD31 BUD31 12173 -0.069 0.12 NO
116 SNRNP40 SNRNP40 SNRNP40 12513 -0.078 0.12 NO
117 LSM5 LSM5 LSM5 12833 -0.087 0.12 NO
118 LSM4 LSM4 LSM4 12920 -0.09 0.13 NO
119 PPIH PPIH PPIH 12956 -0.091 0.14 NO
120 BCAS2 BCAS2 BCAS2 13240 -0.1 0.14 NO
121 THOC3 THOC3 THOC3 13347 -0.1 0.16 NO
122 SNRPD2 SNRPD2 SNRPD2 13348 -0.1 0.18 NO
123 MAGOH MAGOH MAGOH 13445 -0.11 0.19 NO
124 HSPA1B HSPA1B HSPA1B 13909 -0.12 0.19 NO
125 HSPA6 HSPA6 HSPA6 16537 -0.32 0.097 NO

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

Figure S32.  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 SPHINGOLIPID 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 ALDH2 ALDH2 ALDH2 1794 0.14 -0.053 YES
2 SUV420H1 SUV420H1 SUV420H1 2609 0.1 -0.065 YES
3 EHMT2 EHMT2 EHMT2 2895 0.093 -0.05 YES
4 GCDH GCDH GCDH 3175 0.086 -0.038 YES
5 SETD1A SETD1A SETD1A 3228 0.084 -0.014 YES
6 TMLHE TMLHE TMLHE 3512 0.077 -0.005 YES
7 ACAT1 ACAT1 ACAT1 3599 0.075 0.014 YES
8 ASH1L ASH1L ASH1L 3620 0.074 0.037 YES
9 HADHA HADHA HADHA 3705 0.072 0.056 YES
10 SUV39H2 SUV39H2 SUV39H2 3728 0.072 0.077 YES
11 SETD7 SETD7 SETD7 3848 0.069 0.093 YES
12 WHSC1L1 WHSC1L1 WHSC1L1 3898 0.068 0.11 YES
13 SUV420H2 SUV420H2 SUV420H2 3927 0.067 0.13 YES
14 SETDB1 SETDB1 SETDB1 4015 0.066 0.15 YES
15 AADAT AADAT AADAT 4041 0.065 0.17 YES
16 DOT1L DOT1L DOT1L 4047 0.065 0.19 YES
17 SETD1B SETD1B SETD1B 4149 0.063 0.2 YES
18 EHMT1 EHMT1 EHMT1 4338 0.059 0.21 YES
19 SETD2 SETD2 SETD2 4612 0.054 0.21 YES
20 AASS AASS AASS 4845 0.05 0.22 YES
21 BBOX1 BBOX1 BBOX1 4992 0.047 0.22 YES
22 AASDH AASDH AASDH 5502 0.038 0.21 NO
23 ALDH3A2 ALDH3A2 ALDH3A2 5651 0.036 0.21 NO
24 ALDH9A1 ALDH9A1 ALDH9A1 5789 0.034 0.22 NO
25 SETMAR SETMAR SETMAR 6260 0.027 0.2 NO
26 ALDH1B1 ALDH1B1 ALDH1B1 6457 0.024 0.2 NO
27 HADH HADH HADH 7139 0.014 0.16 NO
28 WHSC1 WHSC1 WHSC1 7218 0.013 0.16 NO
29 AASDHPPT AASDHPPT AASDHPPT 7541 0.0087 0.15 NO
30 ECHS1 ECHS1 ECHS1 7607 0.0077 0.15 NO
31 NSD1 NSD1 NSD1 7973 0.0023 0.13 NO
32 DLST DLST DLST 8997 -0.012 0.075 NO
33 SETDB2 SETDB2 SETDB2 9123 -0.014 0.072 NO
34 OGDH OGDH OGDH 11256 -0.049 -0.028 NO
35 ACAT2 ACAT2 ACAT2 11452 -0.053 -0.022 NO
36 SETD8 SETD8 SETD8 11595 -0.056 -0.012 NO
37 SUV39H1 SUV39H1 SUV39H1 11642 -0.057 0.0038 NO
38 ALDH7A1 ALDH7A1 ALDH7A1 11649 -0.057 0.022 NO
39 PLOD3 PLOD3 PLOD3 12370 -0.074 0.0058 NO
40 PLOD1 PLOD1 PLOD1 12998 -0.092 0.0011 NO
41 PLOD2 PLOD2 PLOD2 15044 -0.19 -0.05 NO
42 PIPOX PIPOX PIPOX 16357 -0.3 -0.027 NO
43 OGDHL OGDHL OGDHL 17297 -0.42 0.055 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 SPHINGOLIPID METABOLISM.

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

genes ES table in pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

Table 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 VIPR2 VIPR2 VIPR2 29 0.51 0.2 YES
2 PRKACG PRKACG PRKACG 499 0.28 0.29 YES
3 MYC MYC MYC 1003 0.21 0.34 YES
4 NFKBIA NFKBIA NFKBIA 3447 0.079 0.24 NO
5 CHUK CHUK CHUK 4337 0.059 0.22 NO
6 RELA RELA RELA 5012 0.047 0.2 NO
7 PPP3CC PPP3CC PPP3CC 6101 0.029 0.15 NO
8 PPP3CB PPP3CB PPP3CB 7731 0.0063 0.062 NO
9 GNAQ GNAQ GNAQ 9301 -0.016 -0.018 NO
10 NFKB1 NFKB1 NFKB1 9309 -0.016 -0.011 NO
11 NFATC2 NFATC2 NFATC2 9330 -0.017 -0.0059 NO
12 PRKACB PRKACB PRKACB 9484 -0.019 -0.0066 NO
13 PRKAR1A PRKAR1A PRKAR1A 9569 -0.021 -0.0029 NO
14 PLCG1 PLCG1 PLCG1 9721 -0.024 -0.0019 NO
15 PPP3CA PPP3CA PPP3CA 10370 -0.034 -0.024 NO
16 PRKAR2A PRKAR2A PRKAR2A 10948 -0.044 -0.038 NO
17 NFATC1 NFATC1 NFATC1 11644 -0.057 -0.054 NO
18 CALM2 CALM2 CALM2 12327 -0.073 -0.062 NO
19 MAP3K1 MAP3K1 MAP3K1 12346 -0.073 -0.034 NO
20 CALM1 CALM1 CALM1 12670 -0.082 -0.02 NO
21 EGR2 EGR2 EGR2 12881 -0.088 0.004 NO
22 CALM3 CALM3 CALM3 12943 -0.09 0.036 NO
23 PRKAR2B PRKAR2B PRKAR2B 15333 -0.21 -0.012 NO
24 PRKAR1B PRKAR1B PRKAR1B 15477 -0.22 0.067 NO
25 EGR3 EGR3 EGR3 15518 -0.22 0.15 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

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 ENO3 ENO3 ENO3 1845 0.14 -0.038 YES
2 EXOSC4 EXOSC4 EXOSC4 3234 0.084 -0.075 YES
3 CNOT6L CNOT6L CNOT6L 3299 0.083 -0.041 YES
4 DDX6 DDX6 DDX6 3353 0.081 -0.0066 YES
5 XRN1 XRN1 XRN1 3365 0.081 0.03 YES
6 EXOSC7 EXOSC7 EXOSC7 3377 0.08 0.066 YES
7 CNOT6 CNOT6 CNOT6 3589 0.075 0.089 YES
8 EXOSC1 EXOSC1 EXOSC1 4454 0.057 0.068 YES
9 EDC3 EDC3 EDC3 4470 0.057 0.093 YES
10 EDC4 EDC4 EDC4 4583 0.054 0.11 YES
11 EXOSC5 EXOSC5 EXOSC5 4771 0.051 0.12 YES
12 ZCCHC7 ZCCHC7 ZCCHC7 4814 0.05 0.14 YES
13 EXOSC6 EXOSC6 EXOSC6 5142 0.044 0.15 YES
14 DIS3 DIS3 DIS3 6006 0.031 0.12 YES
15 PATL1 PATL1 PATL1 6157 0.028 0.12 YES
16 EXOSC2 EXOSC2 EXOSC2 6231 0.027 0.13 YES
17 HSPD1 HSPD1 HSPD1 6261 0.027 0.14 YES
18 CNOT1 CNOT1 CNOT1 6363 0.025 0.14 YES
19 SKIV2L2 SKIV2L2 SKIV2L2 6585 0.022 0.14 YES
20 PARN PARN PARN 6831 0.019 0.14 YES
21 DCP1A DCP1A DCP1A 6851 0.018 0.14 YES
22 PNPT1 PNPT1 PNPT1 7172 0.014 0.13 YES
23 EXOSC8 EXOSC8 EXOSC8 7176 0.014 0.14 YES
24 PAPD7 PAPD7 PAPD7 7319 0.012 0.14 YES
25 SKIV2L SKIV2L SKIV2L 7603 0.0078 0.13 YES
26 HSPA9 HSPA9 HSPA9 7654 0.0071 0.13 YES
27 MPHOSPH6 MPHOSPH6 MPHOSPH6 7812 0.0049 0.12 YES
28 NAA38 NAA38 NAA38 7839 0.0046 0.12 YES
29 LSM2 LSM2 LSM2 8145 0.000091 0.1 YES
30 CNOT10 CNOT10 CNOT10 8291 -0.0016 0.097 YES
31 PAPOLA PAPOLA PAPOLA 8351 -0.0023 0.095 YES
32 CNOT2 CNOT2 CNOT2 8408 -0.0031 0.093 YES
33 LSM6 LSM6 LSM6 8516 -0.0046 0.089 YES
34 DCP1B DCP1B DCP1B 8593 -0.0056 0.088 YES
35 TTC37 TTC37 TTC37 8834 -0.0092 0.079 YES
36 LSM7 LSM7 LSM7 8839 -0.0093 0.083 YES
37 CNOT4 CNOT4 CNOT4 8864 -0.0097 0.086 YES
38 PAPOLG PAPOLG PAPOLG 8948 -0.011 0.086 YES
39 LSM1 LSM1 LSM1 9286 -0.016 0.075 YES
40 LSM3 LSM3 LSM3 9636 -0.022 0.066 YES
41 EXOSC3 EXOSC3 EXOSC3 9719 -0.023 0.072 YES
42 CNOT3 CNOT3 CNOT3 9750 -0.024 0.082 YES
43 EXOSC10 EXOSC10 EXOSC10 9969 -0.027 0.082 YES
44 CNOT7 CNOT7 CNOT7 10025 -0.028 0.092 YES
45 C1D C1D C1D 10213 -0.031 0.096 YES
46 DCPS DCPS DCPS 10458 -0.035 0.099 YES
47 DCP2 DCP2 DCP2 10539 -0.037 0.11 YES
48 ENO2 ENO2 ENO2 10564 -0.037 0.13 YES
49 EXOSC9 EXOSC9 EXOSC9 10922 -0.044 0.13 YES
50 XRN2 XRN2 XRN2 11206 -0.048 0.13 YES
51 ENO1 ENO1 ENO1 12247 -0.071 0.11 YES
52 RQCD1 RQCD1 RQCD1 12576 -0.079 0.13 YES
53 LSM5 LSM5 LSM5 12833 -0.087 0.15 YES
54 WDR61 WDR61 WDR61 12845 -0.087 0.19 YES
55 LSM4 LSM4 LSM4 12920 -0.09 0.23 YES
56 PAPOLB PAPOLB PAPOLB 14263 -0.14 0.22 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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RIBOSOME

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 RET RET RET 284 0.34 0.1 YES
2 RXRG RXRG RXRG 401 0.31 0.2 YES
3 MYC MYC MYC 1003 0.21 0.24 YES
4 TCF7L1 TCF7L1 TCF7L1 1217 0.18 0.29 YES
5 TCF7L2 TCF7L2 TCF7L2 1994 0.13 0.29 YES
6 CCND1 CCND1 CCND1 2334 0.12 0.31 YES
7 NCOA4 NCOA4 NCOA4 3215 0.085 0.29 NO
8 TPR TPR TPR 4316 0.06 0.25 NO
9 RXRB RXRB RXRB 4523 0.056 0.26 NO
10 RXRA RXRA RXRA 4995 0.047 0.25 NO
11 CCDC6 CCDC6 CCDC6 5050 0.046 0.26 NO
12 MAPK1 MAPK1 MAPK1 7889 0.0036 0.11 NO
13 MAPK3 MAPK3 MAPK3 7955 0.0026 0.11 NO
14 MAP2K2 MAP2K2 MAP2K2 8209 -0.00057 0.093 NO
15 KRAS KRAS KRAS 8298 -0.0016 0.088 NO
16 CDH1 CDH1 CDH1 8985 -0.011 0.055 NO
17 NTRK1 NTRK1 NTRK1 9212 -0.015 0.047 NO
18 TP53 TP53 TP53 9881 -0.026 0.02 NO
19 TFG TFG TFG 9901 -0.026 0.028 NO
20 CTNNB1 CTNNB1 CTNNB1 10795 -0.042 -0.0072 NO
21 NRAS NRAS NRAS 11470 -0.054 -0.026 NO
22 BRAF BRAF BRAF 12281 -0.071 -0.046 NO
23 TPM3 TPM3 TPM3 12315 -0.072 -0.023 NO
24 MAP2K1 MAP2K1 MAP2K1 13092 -0.095 -0.033 NO
25 LEF1 LEF1 LEF1 15100 -0.19 -0.077 NO
26 TCF7 TCF7 TCF7 15228 -0.2 -0.016 NO
27 PPARG PPARG PPARG 16022 -0.27 0.032 NO
28 PAX8 PAX8 PAX8 16098 -0.27 0.12 NO

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

Figure S40.  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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA NO1 PATHWAY 28 genes.ES.table 0.54 1.4 0.087 0.21 0.95 0.39 0.19 0.32 0.16 0.002
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.56 1.6 0.028 0.15 0.7 0.23 0.08 0.21 0.093 0.006
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.44 1.6 0.06 0.13 0.74 0.5 0.29 0.36 0.084 0.001
BIOCARTA BIOPEPTIDES PATHWAY 38 genes.ES.table 0.57 1.8 0.0021 0.11 0.22 0.32 0.18 0.26 0 0.024
BIOCARTA HDAC PATHWAY 27 genes.ES.table 0.44 1.3 0.15 0.25 0.98 0.48 0.26 0.36 0.2 0.002
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.45 1.6 0.06 0.14 0.66 0.44 0.27 0.32 0.088 0.009
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.55 1.9 0 0.17 0.12 0.58 0.32 0.4 0 0.064
BIOCARTA GPCR PATHWAY 32 genes.ES.table 0.49 1.5 0.055 0.15 0.86 0.5 0.26 0.37 0.1 0
BIOCARTA CREB PATHWAY 26 genes.ES.table 0.6 1.7 0.012 0.11 0.49 0.27 0.13 0.24 0 0.006
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.43 1.5 0.13 0.17 0.9 0.24 0.24 0.18 0.13 0
genes ES table in pathway: BIOCARTA NO1 PATHWAY

Table S21.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PPP2R2C PPP2R2C PPP2R2C 439 0.71 0.13 YES
2 PKLR PKLR PKLR 995 0.47 0.2 YES
3 PRKAR1B PRKAR1B PRKAR1B 1320 0.38 0.27 YES
4 PRKAR2B PRKAR2B PRKAR2B 1647 0.32 0.32 YES
5 YWHAH YWHAH YWHAH 2329 0.24 0.34 YES
6 YWHAG YWHAG YWHAG 2996 0.18 0.34 YES
7 PRKAA2 PRKAA2 PRKAA2 3039 0.17 0.37 YES
8 FASN FASN FASN 3647 0.14 0.37 YES
9 PRKACB PRKACB PRKACB 3874 0.12 0.38 YES
10 ACACA ACACA ACACA 4016 0.12 0.4 YES
11 PPP2R2B PPP2R2B PPP2R2B 4066 0.12 0.42 YES
12 PPP2R2D PPP2R2D PPP2R2D 4117 0.11 0.44 YES
13 PRKACG PRKACG PRKACG 4188 0.11 0.46 YES
14 PRKAG2 PRKAG2 PRKAG2 4243 0.11 0.48 YES
15 MLXIPL MLXIPL MLXIPL 4343 0.1 0.5 YES
16 PPP2R5B PPP2R5B PPP2R5B 4580 0.094 0.51 YES
17 YWHAB YWHAB YWHAB 4983 0.08 0.5 YES
18 PPP2R3A PPP2R3A PPP2R3A 4998 0.08 0.52 YES
19 YWHAZ YWHAZ YWHAZ 5755 0.056 0.49 YES
20 PPP2R5A PPP2R5A PPP2R5A 5757 0.056 0.5 YES
21 PRKAR1A PRKAR1A PRKAR1A 5766 0.056 0.52 YES
22 PPP2R5D PPP2R5D PPP2R5D 5775 0.056 0.53 YES
23 PPP2R5C PPP2R5C PPP2R5C 5835 0.054 0.54 YES
24 PRKAB2 PRKAB2 PRKAB2 5868 0.053 0.55 YES
25 PPP2R4 PPP2R4 PPP2R4 6598 0.036 0.52 NO
26 PPP2R1A PPP2R1A PPP2R1A 6968 0.029 0.5 NO
27 PPP2CA PPP2CA PPP2CA 7518 0.018 0.48 NO
28 PPP2R5E PPP2R5E PPP2R5E 8023 0.0099 0.45 NO
29 PRKACA PRKACA PRKACA 8049 0.0096 0.45 NO
30 PPP2CB PPP2CB PPP2CB 8493 0.0017 0.43 NO
31 YWHAE YWHAE YWHAE 9028 -0.0075 0.4 NO
32 PPP2R3B PPP2R3B PPP2R3B 9110 -0.0087 0.4 NO
33 YWHAQ YWHAQ YWHAQ 10209 -0.026 0.34 NO
34 PPP2R2A PPP2R2A PPP2R2A 10729 -0.035 0.32 NO
35 PPP2R1B PPP2R1B PPP2R1B 10934 -0.038 0.32 NO
36 PRKAG1 PRKAG1 PRKAG1 11467 -0.047 0.3 NO
37 PRKAR2A PRKAR2A PRKAR2A 11517 -0.048 0.31 NO
38 GCK GCK GCK 11775 -0.053 0.3 NO
39 PRKAA1 PRKAA1 PRKAA1 12148 -0.06 0.3 NO
40 PRKAB1 PRKAB1 PRKAB1 12384 -0.064 0.3 NO
41 MLX MLX MLX 14587 -0.12 0.2 NO

Figure S41.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

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

genes ES table in pathway: BIOCARTA AGR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TNNT2 TNNT2 TNNT2 28 1.2 0.073 YES
2 CACNG3 CACNG3 CACNG3 33 1.2 0.15 YES
3 RYR2 RYR2 RYR2 44 1.2 0.22 YES
4 CACNA2D3 CACNA2D3 CACNA2D3 309 0.82 0.25 YES
5 CACNG2 CACNG2 CACNG2 384 0.75 0.3 YES
6 CACNA1F CACNA1F CACNA1F 405 0.74 0.34 YES
7 CACNG8 CACNG8 CACNG8 447 0.7 0.38 YES
8 CACNA1S CACNA1S CACNA1S 701 0.57 0.4 YES
9 CACNA2D1 CACNA2D1 CACNA2D1 847 0.51 0.42 YES
10 CACNA2D2 CACNA2D2 CACNA2D2 850 0.51 0.45 YES
11 CACNB2 CACNB2 CACNB2 1061 0.45 0.47 YES
12 ATP1A3 ATP1A3 ATP1A3 1122 0.43 0.49 YES
13 COX7A1 COX7A1 COX7A1 1171 0.42 0.52 YES
14 CACNB1 CACNB1 CACNB1 1195 0.41 0.54 YES
15 CACNB4 CACNB4 CACNB4 1341 0.38 0.56 YES
16 CACNA1D CACNA1D CACNA1D 1425 0.36 0.57 YES
17 CACNA1C CACNA1C CACNA1C 1440 0.36 0.59 YES
18 MYL3 MYL3 MYL3 1503 0.35 0.61 YES
19 CACNB3 CACNB3 CACNB3 1731 0.31 0.62 YES
20 ATP1B1 ATP1B1 ATP1B1 1738 0.31 0.64 YES
21 MYH6 MYH6 MYH6 1903 0.29 0.65 YES
22 ACTC1 ACTC1 ACTC1 2120 0.26 0.65 YES
23 MYH7 MYH7 MYH7 2145 0.26 0.66 YES
24 ATP1A2 ATP1A2 ATP1A2 2436 0.22 0.66 YES
25 ATP1A4 ATP1A4 ATP1A4 2503 0.22 0.67 YES
26 SLC9A6 SLC9A6 SLC9A6 2515 0.22 0.68 YES
27 TNNI3 TNNI3 TNNI3 3579 0.14 0.63 NO
28 CACNG7 CACNG7 CACNG7 4298 0.11 0.6 NO
29 CACNG5 CACNG5 CACNG5 4405 0.1 0.6 NO
30 ATP1B4 ATP1B4 ATP1B4 4675 0.09 0.59 NO
31 ATP2A2 ATP2A2 ATP2A2 4982 0.08 0.58 NO
32 UQCRB UQCRB UQCRB 5374 0.068 0.56 NO
33 SLC8A1 SLC8A1 SLC8A1 5960 0.051 0.53 NO
34 CACNG4 CACNG4 CACNG4 6214 0.045 0.52 NO
35 SLC9A1 SLC9A1 SLC9A1 6226 0.044 0.52 NO
36 TNNC1 TNNC1 TNNC1 6311 0.042 0.52 NO
37 ATP1A1 ATP1A1 ATP1A1 6506 0.038 0.52 NO
38 ATP1B2 ATP1B2 ATP1B2 6607 0.036 0.51 NO
39 COX4I1 COX4I1 COX4I1 6699 0.034 0.51 NO
40 COX7C COX7C COX7C 6810 0.032 0.5 NO
41 COX7A2L COX7A2L COX7A2L 6950 0.029 0.5 NO
42 COX6A1 COX6A1 COX6A1 7493 0.019 0.47 NO
43 UQCRC1 UQCRC1 UQCRC1 7700 0.015 0.46 NO
44 COX6C COX6C COX6C 8000 0.01 0.44 NO
45 UQCRH UQCRH UQCRH 8188 0.0073 0.43 NO
46 TPM1 TPM1 TPM1 8567 0.00069 0.41 NO
47 COX5A COX5A COX5A 8749 -0.0025 0.4 NO
48 COX7A2 COX7A2 COX7A2 9284 -0.012 0.38 NO
49 UQCR10 UQCR10 UQCR10 9329 -0.012 0.37 NO
50 COX6A2 COX6A2 COX6A2 9653 -0.017 0.36 NO
51 CYC1 CYC1 CYC1 9655 -0.017 0.36 NO
52 CACNG1 CACNG1 CACNG1 9678 -0.018 0.36 NO
53 COX5B COX5B COX5B 9798 -0.02 0.35 NO
54 UQCRFS1 UQCRFS1 UQCRFS1 10387 -0.029 0.32 NO
55 COX8A COX8A COX8A 10777 -0.036 0.3 NO
56 TPM3 TPM3 TPM3 11217 -0.043 0.28 NO
57 COX7B COX7B COX7B 11701 -0.051 0.26 NO
58 CACNG6 CACNG6 CACNG6 11824 -0.054 0.26 NO
59 COX6B1 COX6B1 COX6B1 12137 -0.06 0.24 NO
60 UQCR11 UQCR11 UQCR11 12399 -0.065 0.23 NO
61 ATP1B3 ATP1B3 ATP1B3 12786 -0.073 0.21 NO
62 UQCRHL UQCRHL UQCRHL 13430 -0.087 0.18 NO
63 UQCRQ UQCRQ UQCRQ 13444 -0.087 0.19 NO
64 TPM2 TPM2 TPM2 13600 -0.091 0.19 NO
65 FXYD2 FXYD2 FXYD2 13938 -0.1 0.17 NO
66 COX8C COX8C COX8C 14241 -0.11 0.16 NO
67 COX4I2 COX4I2 COX4I2 14805 -0.13 0.14 NO
68 TPM4 TPM4 TPM4 15542 -0.16 0.11 NO
69 COX6B2 COX6B2 COX6B2 15946 -0.19 0.1 NO
70 CACNA2D4 CACNA2D4 CACNA2D4 18079 -0.49 0.012 NO

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

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

genes ES table in pathway: BIOCARTA AT1R PATHWAY

Table S23.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CAMK2A CAMK2A CAMK2A 123 1 0.16 YES
2 STAT4 STAT4 STAT4 262 0.86 0.29 YES
3 PRKCB PRKCB PRKCB 621 0.61 0.36 YES
4 CAMK2B CAMK2B CAMK2B 720 0.56 0.45 YES
5 PTK2B PTK2B PTK2B 1949 0.28 0.43 YES
6 CAMK2G CAMK2G CAMK2G 2370 0.23 0.44 YES
7 GNAI1 GNAI1 GNAI1 2521 0.22 0.47 YES
8 CALM3 CALM3 CALM3 2799 0.19 0.48 YES
9 MAPK8 MAPK8 MAPK8 2803 0.19 0.51 YES
10 MAPT MAPT MAPT 3083 0.17 0.52 YES
11 MAP2K1 MAP2K1 MAP2K1 3189 0.16 0.54 YES
12 CALM1 CALM1 CALM1 3234 0.16 0.57 YES
13 F2 F2 F2 3887 0.12 0.55 NO
14 PRKCA PRKCA PRKCA 3970 0.12 0.57 NO
15 MAPK3 MAPK3 MAPK3 4581 0.094 0.55 NO
16 MAPK1 MAPK1 MAPK1 4988 0.08 0.54 NO
17 CDK5 CDK5 CDK5 5244 0.071 0.54 NO
18 GNA11 GNA11 GNA11 5489 0.064 0.53 NO
19 CALM2 CALM2 CALM2 6334 0.042 0.49 NO
20 SOS1 SOS1 SOS1 7632 0.016 0.42 NO
21 MYLK MYLK MYLK 7690 0.016 0.42 NO
22 GNB1 GNB1 GNB1 7878 0.012 0.42 NO
23 STAT5B STAT5B STAT5B 7903 0.012 0.42 NO
24 FYN FYN FYN 8311 0.0051 0.4 NO
25 GRB2 GRB2 GRB2 8364 0.0041 0.39 NO
26 AGT AGT AGT 8495 0.0016 0.39 NO
27 STAT6 STAT6 STAT6 9001 -0.0069 0.36 NO
28 MAP2K2 MAP2K2 MAP2K2 9098 -0.0084 0.36 NO
29 JAK2 JAK2 JAK2 9969 -0.022 0.31 NO
30 MAPK14 MAPK14 MAPK14 10472 -0.03 0.29 NO
31 CAMK2D CAMK2D CAMK2D 10649 -0.034 0.28 NO
32 PLCG1 PLCG1 PLCG1 10881 -0.037 0.28 NO
33 RAF1 RAF1 RAF1 11147 -0.042 0.27 NO
34 STAT2 STAT2 STAT2 13113 -0.08 0.18 NO
35 STAT3 STAT3 STAT3 14003 -0.1 0.14 NO
36 STAT1 STAT1 STAT1 14672 -0.12 0.13 NO
37 SHC1 SHC1 SHC1 16019 -0.19 0.083 NO
38 STAT5A STAT5A STAT5A 16810 -0.26 0.082 NO

Figure S45.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA AT1R PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA BIOPEPTIDES 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 HTR5A HTR5A HTR5A 3 1.4 0.026 YES
2 CCKBR CCKBR CCKBR 26 1.2 0.048 YES
3 RYR2 RYR2 RYR2 44 1.2 0.069 YES
4 DRD5 DRD5 DRD5 71 1.1 0.089 YES
5 PRKCG PRKCG PRKCG 72 1.1 0.11 YES
6 DRD1 DRD1 DRD1 107 1 0.13 YES
7 CAMK2A CAMK2A CAMK2A 123 1 0.15 YES
8 ATP2B3 ATP2B3 ATP2B3 131 1 0.16 YES
9 CACNA1I CACNA1I CACNA1I 187 0.93 0.18 YES
10 CHRM1 CHRM1 CHRM1 215 0.9 0.2 YES
11 CACNA1B CACNA1B CACNA1B 241 0.87 0.21 YES
12 GRIN1 GRIN1 GRIN1 254 0.87 0.23 YES
13 CHRM2 CHRM2 CHRM2 265 0.85 0.24 YES
14 HTR2A HTR2A HTR2A 301 0.83 0.26 YES
15 HTR2C HTR2C HTR2C 311 0.82 0.27 YES
16 HTR6 HTR6 HTR6 314 0.82 0.28 YES
17 SLC8A2 SLC8A2 SLC8A2 329 0.8 0.3 YES
18 CAMK4 CAMK4 CAMK4 353 0.79 0.31 YES
19 GRIN2A GRIN2A GRIN2A 371 0.76 0.33 YES
20 GRM1 GRM1 GRM1 380 0.76 0.34 YES
21 GRM5 GRM5 GRM5 400 0.74 0.35 YES
22 CACNA1F CACNA1F CACNA1F 405 0.74 0.37 YES
23 ADRA1B ADRA1B ADRA1B 415 0.73 0.38 YES
24 ADRB3 ADRB3 ADRB3 534 0.65 0.39 YES
25 HTR4 HTR4 HTR4 541 0.65 0.4 YES
26 ITPKA ITPKA ITPKA 555 0.64 0.41 YES
27 PTGER3 PTGER3 PTGER3 558 0.64 0.42 YES
28 NTSR1 NTSR1 NTSR1 574 0.63 0.43 YES
29 PDE1A PDE1A PDE1A 593 0.62 0.44 YES
30 PRKCB PRKCB PRKCB 621 0.61 0.45 YES
31 CHRM3 CHRM3 CHRM3 637 0.6 0.46 YES
32 PDE1B PDE1B PDE1B 641 0.6 0.48 YES
33 ADCY1 ADCY1 ADCY1 665 0.58 0.48 YES
34 NOS1 NOS1 NOS1 666 0.58 0.5 YES
35 GNAL GNAL GNAL 667 0.58 0.51 YES
36 ADRB1 ADRB1 ADRB1 679 0.58 0.52 YES
37 CACNA1S CACNA1S CACNA1S 701 0.57 0.53 YES
38 CAMK2B CAMK2B CAMK2B 720 0.56 0.54 YES
39 TACR3 TACR3 TACR3 724 0.56 0.55 YES
40 CACNA1E CACNA1E CACNA1E 764 0.54 0.56 YES
41 ITPR1 ITPR1 ITPR1 840 0.52 0.56 YES
42 HRH2 HRH2 HRH2 844 0.51 0.57 YES
43 CACNA1G CACNA1G CACNA1G 924 0.49 0.57 YES
44 CHRNA7 CHRNA7 CHRNA7 985 0.47 0.58 YES
45 CALML3 CALML3 CALML3 1006 0.46 0.59 YES
46 PTGFR PTGFR PTGFR 1107 0.44 0.59 YES
47 ATP2B2 ATP2B2 ATP2B2 1145 0.43 0.6 YES
48 P2RX2 P2RX2 P2RX2 1204 0.41 0.6 YES
49 HTR7 HTR7 HTR7 1251 0.4 0.61 YES
50 TACR2 TACR2 TACR2 1310 0.39 0.61 YES
51 ADRA1A ADRA1A ADRA1A 1313 0.39 0.62 YES
52 GRIN2C GRIN2C GRIN2C 1364 0.38 0.62 YES
53 CACNA1A CACNA1A CACNA1A 1382 0.37 0.63 YES
54 CACNA1D CACNA1D CACNA1D 1425 0.36 0.63 YES
55 CACNA1C CACNA1C CACNA1C 1440 0.36 0.64 YES
56 GNA14 GNA14 GNA14 1539 0.34 0.64 YES
57 PPP3R2 PPP3R2 PPP3R2 1633 0.33 0.64 YES
58 P2RX5 P2RX5 P2RX5 1646 0.32 0.65 YES
59 PLCB4 PLCB4 PLCB4 1662 0.32 0.65 YES
60 CHP2 CHP2 CHP2 1684 0.32 0.66 YES
61 PLCB1 PLCB1 PLCB1 1734 0.31 0.66 YES
62 TACR1 TACR1 TACR1 1785 0.3 0.66 YES
63 ERBB4 ERBB4 ERBB4 1832 0.3 0.67 YES
64 TNNC2 TNNC2 TNNC2 1875 0.29 0.67 YES
65 PTK2B PTK2B PTK2B 1949 0.28 0.67 YES
66 P2RX6 P2RX6 P2RX6 1982 0.28 0.67 YES
67 PPP3CB PPP3CB PPP3CB 2096 0.26 0.67 YES
68 ATP2B1 ATP2B1 ATP2B1 2185 0.25 0.67 YES
69 CHRM5 CHRM5 CHRM5 2302 0.24 0.67 YES
70 CAMK2G CAMK2G CAMK2G 2370 0.23 0.67 YES
71 MYLK3 MYLK3 MYLK3 2374 0.23 0.68 YES
72 PPP3CA PPP3CA PPP3CA 2446 0.22 0.68 YES
73 AVPR1B AVPR1B AVPR1B 2460 0.22 0.68 YES
74 CACNA1H CACNA1H CACNA1H 2498 0.22 0.68 YES
75 PPP3R1 PPP3R1 PPP3R1 2748 0.2 0.67 NO
76 TRHR TRHR TRHR 2752 0.2 0.68 NO
77 ADORA2B ADORA2B ADORA2B 2761 0.2 0.68 NO
78 CALM3 CALM3 CALM3 2799 0.19 0.68 NO
79 RYR1 RYR1 RYR1 2944 0.18 0.68 NO
80 GRIN2D GRIN2D GRIN2D 3113 0.17 0.67 NO
81 CALM1 CALM1 CALM1 3234 0.16 0.66 NO
82 ADCY2 ADCY2 ADCY2 3352 0.15 0.66 NO
83 RYR3 RYR3 RYR3 3467 0.15 0.66 NO
84 TRPC1 TRPC1 TRPC1 3500 0.14 0.66 NO
85 SLC25A31 SLC25A31 SLC25A31 3631 0.14 0.66 NO
86 PRKACB PRKACB PRKACB 3874 0.12 0.64 NO
87 ERBB3 ERBB3 ERBB3 3880 0.12 0.65 NO
88 PRKCA PRKCA PRKCA 3970 0.12 0.64 NO
89 PRKACG PRKACG PRKACG 4188 0.11 0.63 NO
90 CD38 CD38 CD38 4541 0.096 0.62 NO
91 GNAQ GNAQ GNAQ 4710 0.089 0.61 NO
92 P2RX7 P2RX7 P2RX7 4727 0.089 0.61 NO
93 SLC25A4 SLC25A4 SLC25A4 4828 0.085 0.6 NO
94 AVPR1A AVPR1A AVPR1A 4981 0.08 0.6 NO
95 ATP2A2 ATP2A2 ATP2A2 4982 0.08 0.6 NO
96 LHCGR LHCGR LHCGR 5263 0.071 0.58 NO
97 PDGFRA PDGFRA PDGFRA 5335 0.069 0.58 NO
98 VDAC2 VDAC2 VDAC2 5421 0.066 0.58 NO
99 GNA11 GNA11 GNA11 5489 0.064 0.58 NO
100 NOS2 NOS2 NOS2 5613 0.061 0.57 NO
101 CHP CHP CHP 5618 0.06 0.57 NO
102 ADCY3 ADCY3 ADCY3 5710 0.058 0.57 NO
103 ADCY9 ADCY9 ADCY9 5841 0.054 0.56 NO
104 ADRA1D ADRA1D ADRA1D 5886 0.053 0.56 NO
105 PLN PLN PLN 5894 0.053 0.56 NO
106 SLC8A1 SLC8A1 SLC8A1 5960 0.051 0.56 NO
107 PDE1C PDE1C PDE1C 6158 0.047 0.55 NO
108 PLCD4 PLCD4 PLCD4 6164 0.046 0.55 NO
109 ATP2B4 ATP2B4 ATP2B4 6183 0.046 0.55 NO
110 ADRB2 ADRB2 ADRB2 6265 0.043 0.55 NO
111 TNNC1 TNNC1 TNNC1 6311 0.042 0.54 NO
112 CALM2 CALM2 CALM2 6334 0.042 0.54 NO
113 GRPR GRPR GRPR 6378 0.041 0.54 NO
114 VDAC3 VDAC3 VDAC3 6481 0.038 0.54 NO
115 CYSLTR2 CYSLTR2 CYSLTR2 6572 0.036 0.53 NO
116 ADCY8 ADCY8 ADCY8 6625 0.035 0.53 NO
117 ITPR2 ITPR2 ITPR2 7033 0.028 0.51 NO
118 EDNRB EDNRB EDNRB 7099 0.026 0.5 NO
119 ADORA2A ADORA2A ADORA2A 7224 0.024 0.5 NO
120 PPID PPID PPID 7563 0.018 0.48 NO
121 ITPR3 ITPR3 ITPR3 7600 0.017 0.48 NO
122 PRKX PRKX PRKX 7652 0.016 0.48 NO
123 VDAC1 VDAC1 VDAC1 7665 0.016 0.48 NO
124 MYLK MYLK MYLK 7690 0.016 0.48 NO
125 PRKACA PRKACA PRKACA 8049 0.0096 0.46 NO
126 SPHK2 SPHK2 SPHK2 8062 0.0094 0.46 NO
127 PHKA1 PHKA1 PHKA1 8068 0.0094 0.46 NO
128 GNAS GNAS GNAS 8083 0.0091 0.45 NO
129 PHKG2 PHKG2 PHKG2 8323 0.005 0.44 NO
130 NOS3 NOS3 NOS3 8432 0.0029 0.44 NO
131 P2RX1 P2RX1 P2RX1 8529 0.0013 0.43 NO
132 P2RX3 P2RX3 P2RX3 8578 0.00046 0.43 NO
133 OXTR OXTR OXTR 8613 -0.00012 0.43 NO
134 ITPKB ITPKB ITPKB 8761 -0.0027 0.42 NO
135 SLC25A6 SLC25A6 SLC25A6 9075 -0.0081 0.4 NO
136 CCKAR CCKAR CCKAR 9300 -0.012 0.39 NO
137 PPP3CC PPP3CC PPP3CC 9483 -0.015 0.38 NO
138 ADCY4 ADCY4 ADCY4 10169 -0.026 0.34 NO
139 SLC25A5 SLC25A5 SLC25A5 10249 -0.027 0.34 NO
140 PHKB PHKB PHKB 10565 -0.032 0.32 NO
141 CAMK2D CAMK2D CAMK2D 10649 -0.034 0.32 NO
142 BDKRB1 BDKRB1 BDKRB1 10811 -0.036 0.31 NO
143 PLCD3 PLCD3 PLCD3 10819 -0.037 0.31 NO
144 PLCG1 PLCG1 PLCG1 10881 -0.037 0.31 NO
145 PLCB3 PLCB3 PLCB3 11192 -0.042 0.29 NO
146 PHKA2 PHKA2 PHKA2 11662 -0.051 0.26 NO
147 MYLK2 MYLK2 MYLK2 11785 -0.053 0.26 NO
148 PLCD1 PLCD1 PLCD1 11939 -0.056 0.25 NO
149 ADCY7 ADCY7 ADCY7 12132 -0.059 0.24 NO
150 PDGFRB PDGFRB PDGFRB 12327 -0.063 0.23 NO
151 ATP2A3 ATP2A3 ATP2A3 12837 -0.074 0.21 NO
152 ERBB2 ERBB2 ERBB2 13124 -0.08 0.19 NO
153 CALML6 CALML6 CALML6 13996 -0.1 0.15 NO
154 EGFR EGFR EGFR 14315 -0.11 0.13 NO
155 PHKG1 PHKG1 PHKG1 14603 -0.12 0.12 NO
156 HRH1 HRH1 HRH1 14783 -0.13 0.11 NO
157 LTB4R2 LTB4R2 LTB4R2 14825 -0.13 0.11 NO
158 HTR2B HTR2B HTR2B 14833 -0.13 0.11 NO
159 BDKRB2 BDKRB2 BDKRB2 15380 -0.16 0.085 NO
160 PLCE1 PLCE1 PLCE1 15696 -0.17 0.07 NO
161 ATP2A1 ATP2A1 ATP2A1 15720 -0.18 0.073 NO
162 PLCB2 PLCB2 PLCB2 15954 -0.19 0.063 NO
163 P2RX4 P2RX4 P2RX4 16127 -0.2 0.058 NO
164 F2R F2R F2R 16247 -0.21 0.055 NO
165 AGTR1 AGTR1 AGTR1 16333 -0.22 0.054 NO
166 CYSLTR1 CYSLTR1 CYSLTR1 16491 -0.23 0.05 NO
167 SPHK1 SPHK1 SPHK1 16499 -0.23 0.054 NO
168 PLCG2 PLCG2 PLCG2 16652 -0.25 0.051 NO
169 EDNRA EDNRA EDNRA 16839 -0.27 0.045 NO
170 GNA15 GNA15 GNA15 16844 -0.27 0.05 NO
171 PTGER1 PTGER1 PTGER1 17129 -0.3 0.04 NO
172 TBXA2R TBXA2R TBXA2R 17493 -0.36 0.027 NO
173 PTAFR PTAFR PTAFR 17496 -0.36 0.034 NO
174 BST1 BST1 BST1 18245 -0.57 0.0034 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 BIOPEPTIDES PATHWAY.

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

genes ES table in pathway: BIOCARTA HDAC PATHWAY

Table 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 NEFM NEFM NEFM 59 1.1 0.083 YES
2 NEFL NEFL NEFL 144 0.99 0.15 YES
3 NEFH NEFH NEFH 161 0.96 0.23 YES
4 PRPH2 PRPH2 PRPH2 188 0.93 0.3 YES
5 GRIN1 GRIN1 GRIN1 254 0.87 0.36 YES
6 GRIN2A GRIN2A GRIN2A 371 0.76 0.41 YES
7 GRIN2B GRIN2B GRIN2B 390 0.75 0.47 YES
8 NOS1 NOS1 NOS1 666 0.58 0.5 YES
9 GRIN2C GRIN2C GRIN2C 1364 0.38 0.49 YES
10 SLC1A2 SLC1A2 SLC1A2 1520 0.34 0.5 YES
11 PPP3R2 PPP3R2 PPP3R2 1633 0.33 0.52 YES
12 CHP2 CHP2 CHP2 1684 0.32 0.55 YES
13 GRIA1 GRIA1 GRIA1 1895 0.29 0.56 YES
14 GRIA2 GRIA2 GRIA2 1961 0.28 0.57 YES
15 PPP3CB PPP3CB PPP3CB 2096 0.26 0.59 YES
16 PPP3CA PPP3CA PPP3CA 2446 0.22 0.58 YES
17 PPP3R1 PPP3R1 PPP3R1 2748 0.2 0.58 YES
18 MAPK11 MAPK11 MAPK11 2831 0.19 0.59 YES
19 GRIN2D GRIN2D GRIN2D 3113 0.17 0.59 NO
20 MAP3K5 MAP3K5 MAP3K5 4605 0.094 0.52 NO
21 BCL2 BCL2 BCL2 5229 0.072 0.49 NO
22 MAPK12 MAPK12 MAPK12 5430 0.066 0.48 NO
23 CHP CHP CHP 5618 0.06 0.48 NO
24 BID BID BID 5921 0.052 0.46 NO
25 TOMM40L TOMM40L TOMM40L 6094 0.048 0.46 NO
26 MAPK13 MAPK13 MAPK13 6232 0.044 0.45 NO
27 APAF1 APAF1 APAF1 6264 0.043 0.45 NO
28 SOD1 SOD1 SOD1 6459 0.039 0.45 NO
29 CYCS CYCS CYCS 7208 0.024 0.41 NO
30 RAB5A RAB5A RAB5A 8137 0.0083 0.36 NO
31 CCS CCS CCS 8765 -0.0028 0.32 NO
32 PPP3CC PPP3CC PPP3CC 9483 -0.015 0.28 NO
33 CASP9 CASP9 CASP9 10051 -0.024 0.26 NO
34 RAC1 RAC1 RAC1 10467 -0.03 0.24 NO
35 MAPK14 MAPK14 MAPK14 10472 -0.03 0.24 NO
36 BAD BAD BAD 10999 -0.039 0.21 NO
37 BCL2L1 BCL2L1 BCL2L1 11071 -0.04 0.21 NO
38 DERL1 DERL1 DERL1 11459 -0.047 0.19 NO
39 CAT CAT CAT 12006 -0.057 0.17 NO
40 MAP2K6 MAP2K6 MAP2K6 12097 -0.059 0.17 NO
41 TOMM40 TOMM40 TOMM40 12184 -0.06 0.17 NO
42 TNF TNF TNF 12474 -0.066 0.16 NO
43 DAXX DAXX DAXX 12584 -0.069 0.16 NO
44 TP53 TP53 TP53 14985 -0.14 0.034 NO
45 CASP3 CASP3 CASP3 15310 -0.15 0.028 NO
46 GPX1 GPX1 GPX1 15559 -0.16 0.027 NO
47 MAP2K3 MAP2K3 MAP2K3 15635 -0.17 0.036 NO
48 PRPH PRPH PRPH 15719 -0.18 0.045 NO
49 BAX BAX BAX 16047 -0.2 0.042 NO
50 TNFRSF1B TNFRSF1B TNFRSF1B 16795 -0.26 0.021 NO
51 TNFRSF1A TNFRSF1A TNFRSF1A 16953 -0.28 0.034 NO
52 CASP1 CASP1 CASP1 18159 -0.52 0.0081 NO

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

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

genes ES table in pathway: BIOCARTA PYK2 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 CREB3L3 CREB3L3 CREB3L3 348 0.79 0.16 YES
2 DYNC1I1 DYNC1I1 DYNC1I1 640 0.6 0.28 YES
3 NSF NSF NSF 1763 0.31 0.29 YES
4 AVPR2 AVPR2 AVPR2 1967 0.28 0.34 YES
5 AQP3 AQP3 AQP3 2060 0.27 0.4 YES
6 VAMP2 VAMP2 VAMP2 2428 0.22 0.43 YES
7 PRKACB PRKACB PRKACB 3874 0.12 0.38 YES
8 DYNLL2 DYNLL2 DYNLL2 3967 0.12 0.4 YES
9 DCTN1 DCTN1 DCTN1 4061 0.12 0.42 YES
10 PRKACG PRKACG PRKACG 4188 0.11 0.44 YES
11 DYNC1H1 DYNC1H1 DYNC1H1 4205 0.11 0.46 YES
12 DYNC2H1 DYNC2H1 DYNC2H1 5069 0.077 0.43 NO
13 CREB3L1 CREB3L1 CREB3L1 5407 0.067 0.43 NO
14 ADCY9 ADCY9 ADCY9 5841 0.054 0.42 NO
15 RAB5B RAB5B RAB5B 5990 0.051 0.42 NO
16 DYNC1LI1 DYNC1LI1 DYNC1LI1 6142 0.047 0.42 NO
17 AQP4 AQP4 AQP4 6230 0.044 0.43 NO
18 DYNC1I2 DYNC1I2 DYNC1I2 6463 0.039 0.42 NO
19 DCTN6 DCTN6 DCTN6 6574 0.036 0.42 NO
20 DYNC1LI2 DYNC1LI2 DYNC1LI2 7292 0.023 0.39 NO
21 PRKX PRKX PRKX 7652 0.016 0.37 NO
22 PRKACA PRKACA PRKACA 8049 0.0096 0.36 NO
23 GNAS GNAS GNAS 8083 0.0091 0.36 NO
24 RAB5A RAB5A RAB5A 8137 0.0083 0.35 NO
25 RAB11B RAB11B RAB11B 8165 0.0077 0.35 NO
26 ADCY6 ADCY6 ADCY6 8372 0.0039 0.34 NO
27 DCTN4 DCTN4 DCTN4 8744 -0.0024 0.32 NO
28 RAB11A RAB11A RAB11A 8774 -0.0029 0.32 NO
29 DYNLL1 DYNLL1 DYNLL1 8778 -0.003 0.32 NO
30 CREB3L4 CREB3L4 CREB3L4 9146 -0.0094 0.31 NO
31 DYNC2LI1 DYNC2LI1 DYNC2LI1 9253 -0.011 0.3 NO
32 CREB3 CREB3 CREB3 9459 -0.014 0.3 NO
33 RAB5C RAB5C RAB5C 9902 -0.021 0.28 NO
34 DCTN5 DCTN5 DCTN5 9950 -0.022 0.28 NO
35 CREB1 CREB1 CREB1 9956 -0.022 0.28 NO
36 DCTN2 DCTN2 DCTN2 10715 -0.035 0.25 NO
37 STX4 STX4 STX4 10954 -0.039 0.24 NO
38 ARHGDIA ARHGDIA ARHGDIA 11871 -0.054 0.21 NO
39 CREB5 CREB5 CREB5 14200 -0.11 0.1 NO
40 AQP2 AQP2 AQP2 14306 -0.11 0.12 NO
41 CREB3L2 CREB3L2 CREB3L2 15123 -0.14 0.11 NO
42 ARHGDIB ARHGDIB ARHGDIB 16928 -0.28 0.076 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 PYK2 PATHWAY.

Figure S52.  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 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 PRKCG PRKCG PRKCG 72 1.1 0.052 YES
2 DRD1 DRD1 DRD1 107 1 0.1 YES
3 HTR2A HTR2A HTR2A 301 0.83 0.13 YES
4 HTR2C HTR2C HTR2C 311 0.82 0.18 YES
5 TUBA8 TUBA8 TUBA8 360 0.78 0.21 YES
6 GRM1 GRM1 GRM1 380 0.76 0.25 YES
7 GJD2 GJD2 GJD2 383 0.75 0.29 YES
8 GRM5 GRM5 GRM5 400 0.74 0.32 YES
9 PRKCB PRKCB PRKCB 621 0.61 0.34 YES
10 ADCY1 ADCY1 ADCY1 665 0.58 0.37 YES
11 ADRB1 ADRB1 ADRB1 679 0.58 0.4 YES
12 TUBA4A TUBA4A TUBA4A 694 0.57 0.43 YES
13 ITPR1 ITPR1 ITPR1 840 0.52 0.44 YES
14 TUBA3D TUBA3D TUBA3D 1035 0.46 0.46 YES
15 PRKG2 PRKG2 PRKG2 1072 0.45 0.48 YES
16 GUCY1B3 GUCY1B3 GUCY1B3 1202 0.41 0.49 YES
17 ADCY5 ADCY5 ADCY5 1226 0.41 0.51 YES
18 GUCY1A3 GUCY1A3 GUCY1A3 1450 0.36 0.52 YES
19 PLCB4 PLCB4 PLCB4 1662 0.32 0.52 YES
20 PLCB1 PLCB1 PLCB1 1734 0.31 0.53 YES
21 TUBA3E TUBA3E TUBA3E 1839 0.3 0.54 YES
22 TUBB4 TUBB4 TUBB4 1872 0.29 0.56 YES
23 TUBA3C TUBA3C TUBA3C 1926 0.29 0.57 YES
24 TUBB4Q TUBB4Q TUBB4Q 2188 0.25 0.57 YES
25 PRKG1 PRKG1 PRKG1 2364 0.23 0.57 YES
26 GNAI1 GNAI1 GNAI1 2521 0.22 0.57 YES
27 MAP2K1 MAP2K1 MAP2K1 3189 0.16 0.54 NO
28 GUCY1A2 GUCY1A2 GUCY1A2 3270 0.16 0.55 NO
29 ADCY2 ADCY2 ADCY2 3352 0.15 0.55 NO
30 TUBB8 TUBB8 TUBB8 3462 0.15 0.55 NO
31 PRKACB PRKACB PRKACB 3874 0.12 0.53 NO
32 PRKCA PRKCA PRKCA 3970 0.12 0.54 NO
33 PRKACG PRKACG PRKACG 4188 0.11 0.53 NO
34 MAPK3 MAPK3 MAPK3 4581 0.094 0.51 NO
35 GNAQ GNAQ GNAQ 4710 0.089 0.51 NO
36 MAPK1 MAPK1 MAPK1 4988 0.08 0.5 NO
37 KRAS KRAS KRAS 5279 0.07 0.49 NO
38 PDGFRA PDGFRA PDGFRA 5335 0.069 0.49 NO
39 TUBB2A TUBB2A TUBB2A 5405 0.067 0.49 NO
40 GNA11 GNA11 GNA11 5489 0.064 0.48 NO
41 ADCY9 ADCY9 ADCY9 5841 0.054 0.47 NO
42 SRC SRC SRC 5993 0.051 0.46 NO
43 TJP1 TJP1 TJP1 6251 0.044 0.45 NO
44 HRAS HRAS HRAS 6452 0.039 0.44 NO
45 SOS2 SOS2 SOS2 6544 0.037 0.44 NO
46 ADCY8 ADCY8 ADCY8 6625 0.035 0.44 NO
47 TUBB3 TUBB3 TUBB3 6953 0.029 0.42 NO
48 ITPR2 ITPR2 ITPR2 7033 0.028 0.42 NO
49 MAP2K5 MAP2K5 MAP2K5 7523 0.018 0.39 NO
50 ITPR3 ITPR3 ITPR3 7600 0.017 0.39 NO
51 SOS1 SOS1 SOS1 7632 0.016 0.39 NO
52 TUBB1 TUBB1 TUBB1 7643 0.016 0.39 NO
53 PRKX PRKX PRKX 7652 0.016 0.39 NO
54 PRKACA PRKACA PRKACA 8049 0.0096 0.37 NO
55 GNAS GNAS GNAS 8083 0.0091 0.36 NO
56 GRB2 GRB2 GRB2 8364 0.0041 0.35 NO
57 ADCY6 ADCY6 ADCY6 8372 0.0039 0.35 NO
58 CSNK1D CSNK1D CSNK1D 8769 -0.0028 0.33 NO
59 MAP2K2 MAP2K2 MAP2K2 9098 -0.0084 0.31 NO
60 GJA1 GJA1 GJA1 9639 -0.017 0.28 NO
61 ADCY4 ADCY4 ADCY4 10169 -0.026 0.25 NO
62 TUBB2C TUBB2C TUBB2C 10313 -0.028 0.25 NO
63 TUBB2B TUBB2B TUBB2B 10541 -0.032 0.24 NO
64 RAF1 RAF1 RAF1 11147 -0.042 0.2 NO
65 PLCB3 PLCB3 PLCB3 11192 -0.042 0.2 NO
66 TUBA1B TUBA1B TUBA1B 11914 -0.055 0.17 NO
67 ADCY7 ADCY7 ADCY7 12132 -0.059 0.16 NO
68 MAP3K2 MAP3K2 MAP3K2 12198 -0.061 0.16 NO
69 PDGFRB PDGFRB PDGFRB 12327 -0.063 0.16 NO
70 GNAI2 GNAI2 GNAI2 12646 -0.07 0.14 NO
71 DRD2 DRD2 DRD2 12767 -0.073 0.14 NO
72 TUBAL3 TUBAL3 TUBAL3 13242 -0.083 0.12 NO
73 LPAR1 LPAR1 LPAR1 13304 -0.084 0.12 NO
74 PDGFB PDGFB PDGFB 13591 -0.091 0.11 NO
75 MAPK7 MAPK7 MAPK7 13886 -0.099 0.095 NO
76 TUBB TUBB TUBB 13941 -0.1 0.097 NO
77 EGFR EGFR EGFR 14315 -0.11 0.082 NO
78 TUBA1A TUBA1A TUBA1A 14396 -0.12 0.084 NO
79 PDGFC PDGFC PDGFC 14538 -0.12 0.082 NO
80 PDGFD PDGFD PDGFD 14816 -0.13 0.073 NO
81 HTR2B HTR2B HTR2B 14833 -0.13 0.079 NO
82 NRAS NRAS NRAS 14996 -0.14 0.077 NO
83 PDGFA PDGFA PDGFA 15230 -0.15 0.072 NO
84 GNAI3 GNAI3 GNAI3 15718 -0.18 0.054 NO
85 PLCB2 PLCB2 PLCB2 15954 -0.19 0.051 NO
86 EGF EGF EGF 16882 -0.27 0.014 NO
87 TUBB6 TUBB6 TUBB6 17435 -0.35 0.001 NO
88 CDK1 CDK1 CDK1 17851 -0.43 -0.000031 NO
89 TUBA1C TUBA1C TUBA1C 18093 -0.49 0.012 NO

Figure S53.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CHREBP2 PATHWAY.

Figure S54.  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 GPCR PATHWAY

Table S28.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 72 1.1 0.061 YES
2 CAMK2A CAMK2A CAMK2A 123 1 0.12 YES
3 GRIN1 GRIN1 GRIN1 254 0.87 0.16 YES
4 CAMK4 CAMK4 CAMK4 353 0.79 0.2 YES
5 GRIN2A GRIN2A GRIN2A 371 0.76 0.24 YES
6 GRM1 GRM1 GRM1 380 0.76 0.29 YES
7 GRIN2B GRIN2B GRIN2B 390 0.75 0.33 YES
8 GRM5 GRM5 GRM5 400 0.74 0.37 YES
9 PRKCB PRKCB PRKCB 621 0.61 0.4 YES
10 CAMK2B CAMK2B CAMK2B 720 0.56 0.42 YES
11 ITPR1 ITPR1 ITPR1 840 0.52 0.45 YES
12 RPS6KA6 RPS6KA6 RPS6KA6 956 0.48 0.47 YES
13 CALML3 CALML3 CALML3 1006 0.46 0.5 YES
14 PPP1R1A PPP1R1A PPP1R1A 1133 0.43 0.51 YES
15 GRIN2C GRIN2C GRIN2C 1364 0.38 0.52 YES
16 CACNA1C CACNA1C CACNA1C 1440 0.36 0.54 YES
17 PPP3R2 PPP3R2 PPP3R2 1633 0.33 0.55 YES
18 PLCB4 PLCB4 PLCB4 1662 0.32 0.56 YES
19 CHP2 CHP2 CHP2 1684 0.32 0.58 YES
20 PLCB1 PLCB1 PLCB1 1734 0.31 0.6 YES
21 GRIA1 GRIA1 GRIA1 1895 0.29 0.61 YES
22 GRIA2 GRIA2 GRIA2 1961 0.28 0.62 YES
23 PPP3CB PPP3CB PPP3CB 2096 0.26 0.63 YES
24 CAMK2G CAMK2G CAMK2G 2370 0.23 0.62 YES
25 RAPGEF3 RAPGEF3 RAPGEF3 2371 0.23 0.64 YES
26 PPP3CA PPP3CA PPP3CA 2446 0.22 0.65 YES
27 PPP3R1 PPP3R1 PPP3R1 2748 0.2 0.64 YES
28 CALM3 CALM3 CALM3 2799 0.19 0.65 YES
29 GRIN2D GRIN2D GRIN2D 3113 0.17 0.64 YES
30 MAP2K1 MAP2K1 MAP2K1 3189 0.16 0.65 YES
31 CALM1 CALM1 CALM1 3234 0.16 0.66 YES
32 RPS6KA2 RPS6KA2 RPS6KA2 3545 0.14 0.65 NO
33 PRKACB PRKACB PRKACB 3874 0.12 0.64 NO
34 PRKCA PRKCA PRKCA 3970 0.12 0.64 NO
35 PRKACG PRKACG PRKACG 4188 0.11 0.63 NO
36 MAPK3 MAPK3 MAPK3 4581 0.094 0.62 NO
37 GNAQ GNAQ GNAQ 4710 0.089 0.62 NO
38 BRAF BRAF BRAF 4901 0.083 0.61 NO
39 MAPK1 MAPK1 MAPK1 4988 0.08 0.61 NO
40 KRAS KRAS KRAS 5279 0.07 0.6 NO
41 EP300 EP300 EP300 5549 0.062 0.59 NO
42 CHP CHP CHP 5618 0.06 0.59 NO
43 CREBBP CREBBP CREBBP 5987 0.051 0.57 NO
44 CALM2 CALM2 CALM2 6334 0.042 0.55 NO
45 HRAS HRAS HRAS 6452 0.039 0.55 NO
46 ADCY8 ADCY8 ADCY8 6625 0.035 0.54 NO
47 PPP1R12A PPP1R12A PPP1R12A 6898 0.03 0.53 NO
48 ITPR2 ITPR2 ITPR2 7033 0.028 0.52 NO
49 ITPR3 ITPR3 ITPR3 7600 0.017 0.49 NO
50 PRKX PRKX PRKX 7652 0.016 0.49 NO
51 PRKACA PRKACA PRKACA 8049 0.0096 0.47 NO
52 MAP2K2 MAP2K2 MAP2K2 9098 -0.0084 0.41 NO
53 PPP3CC PPP3CC PPP3CC 9483 -0.015 0.39 NO
54 RPS6KA3 RPS6KA3 RPS6KA3 10473 -0.03 0.34 NO
55 CAMK2D CAMK2D CAMK2D 10649 -0.034 0.33 NO
56 RAF1 RAF1 RAF1 11147 -0.042 0.31 NO
57 PLCB3 PLCB3 PLCB3 11192 -0.042 0.31 NO
58 ATF4 ATF4 ATF4 11255 -0.044 0.31 NO
59 PPP1CC PPP1CC PPP1CC 11940 -0.056 0.27 NO
60 PPP1CB PPP1CB PPP1CB 12924 -0.076 0.22 NO
61 CALML6 CALML6 CALML6 13996 -0.1 0.17 NO
62 PPP1CA PPP1CA PPP1CA 14352 -0.11 0.16 NO
63 ARAF ARAF ARAF 14670 -0.12 0.15 NO
64 RAP1A RAP1A RAP1A 14882 -0.13 0.14 NO
65 NRAS NRAS NRAS 14996 -0.14 0.14 NO
66 RAP1B RAP1B RAP1B 15431 -0.16 0.13 NO
67 PLCB2 PLCB2 PLCB2 15954 -0.19 0.11 NO
68 RPS6KA1 RPS6KA1 RPS6KA1 17002 -0.29 0.072 NO

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

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GPCR 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 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 PRKCG PRKCG PRKCG 72 1.1 0.074 YES
2 DGKE DGKE DGKE 462 0.7 0.1 YES
3 ITPKA ITPKA ITPKA 555 0.64 0.14 YES
4 CDS1 CDS1 CDS1 568 0.63 0.19 YES
5 PRKCB PRKCB PRKCB 621 0.61 0.23 YES
6 PIP5K1B PIP5K1B PIP5K1B 654 0.59 0.27 YES
7 INPP5J INPP5J INPP5J 775 0.54 0.3 YES
8 ITPR1 ITPR1 ITPR1 840 0.52 0.33 YES
9 CALML3 CALML3 CALML3 1006 0.46 0.35 YES
10 INPP4B INPP4B INPP4B 1150 0.43 0.38 YES
11 DGKH DGKH DGKH 1466 0.35 0.38 YES
12 DGKB DGKB DGKB 1590 0.33 0.4 YES
13 PLCB4 PLCB4 PLCB4 1662 0.32 0.42 YES
14 DGKZ DGKZ DGKZ 1670 0.32 0.44 YES
15 PLCB1 PLCB1 PLCB1 1734 0.31 0.46 YES
16 DGKI DGKI DGKI 1818 0.3 0.48 YES
17 SYNJ2 SYNJ2 SYNJ2 2077 0.26 0.48 YES
18 SYNJ1 SYNJ1 SYNJ1 2093 0.26 0.5 YES
19 PI4KA PI4KA PI4KA 2187 0.25 0.51 YES
20 DGKG DGKG DGKG 2231 0.25 0.53 YES
21 INPP5A INPP5A INPP5A 2518 0.22 0.53 YES
22 CALM3 CALM3 CALM3 2799 0.19 0.52 YES
23 DGKQ DGKQ DGKQ 3213 0.16 0.51 YES
24 CALM1 CALM1 CALM1 3234 0.16 0.52 YES
25 ITPK1 ITPK1 ITPK1 3509 0.14 0.52 YES
26 PIP4K2A PIP4K2A PIP4K2A 3516 0.14 0.53 YES
27 INPP4A INPP4A INPP4A 3628 0.14 0.53 YES
28 PIP5K1C PIP5K1C PIP5K1C 3716 0.13 0.54 YES
29 PIK3C2B PIK3C2B PIK3C2B 3783 0.13 0.54 YES
30 PIK3CB PIK3CB PIK3CB 3905 0.12 0.54 YES
31 PRKCA PRKCA PRKCA 3970 0.12 0.55 YES
32 PIP4K2B PIP4K2B PIP4K2B 3971 0.12 0.56 YES
33 PIK3R1 PIK3R1 PIK3R1 4341 0.1 0.55 NO
34 PIK3C2G PIK3C2G PIK3C2G 4375 0.1 0.55 NO
35 PIKFYVE PIKFYVE PIKFYVE 4549 0.096 0.55 NO
36 PTEN PTEN PTEN 4761 0.087 0.54 NO
37 INPP1 INPP1 INPP1 4821 0.085 0.55 NO
38 PIP4K2C PIP4K2C PIP4K2C 5919 0.052 0.49 NO
39 PLCD4 PLCD4 PLCD4 6164 0.046 0.48 NO
40 CALM2 CALM2 CALM2 6334 0.042 0.47 NO
41 OCRL OCRL OCRL 6865 0.031 0.44 NO
42 CDIPT CDIPT CDIPT 6880 0.03 0.45 NO
43 IPPK IPPK IPPK 7020 0.028 0.44 NO
44 ITPR2 ITPR2 ITPR2 7033 0.028 0.44 NO
45 PIK3C2A PIK3C2A PIK3C2A 7214 0.024 0.43 NO
46 PIK3R2 PIK3R2 PIK3R2 7309 0.023 0.43 NO
47 PIK3CA PIK3CA PIK3CA 7440 0.02 0.42 NO
48 ITPR3 ITPR3 ITPR3 7600 0.017 0.42 NO
49 INPP5K INPP5K INPP5K 7881 0.012 0.4 NO
50 DGKA DGKA DGKA 7945 0.011 0.4 NO
51 CDS2 CDS2 CDS2 8104 0.0088 0.39 NO
52 DGKD DGKD DGKD 8350 0.0045 0.38 NO
53 ITPKB ITPKB ITPKB 8761 -0.0027 0.36 NO
54 INPP5E INPP5E INPP5E 9240 -0.011 0.33 NO
55 PIK3R3 PIK3R3 PIK3R3 9261 -0.011 0.33 NO
56 IMPA1 IMPA1 IMPA1 9578 -0.016 0.31 NO
57 PIK3C3 PIK3C3 PIK3C3 9668 -0.018 0.31 NO
58 PI4KB PI4KB PI4KB 9878 -0.021 0.3 NO
59 PIK3CD PIK3CD PIK3CD 10797 -0.036 0.25 NO
60 PLCD3 PLCD3 PLCD3 10819 -0.037 0.25 NO
61 PLCG1 PLCG1 PLCG1 10881 -0.037 0.25 NO
62 PLCB3 PLCB3 PLCB3 11192 -0.042 0.24 NO
63 PLCD1 PLCD1 PLCD1 11939 -0.056 0.2 NO
64 PIP5K1A PIP5K1A PIP5K1A 12146 -0.06 0.2 NO
65 INPPL1 INPPL1 INPPL1 13342 -0.085 0.14 NO
66 CALML6 CALML6 CALML6 13996 -0.1 0.11 NO
67 INPP5B INPP5B INPP5B 14129 -0.11 0.11 NO
68 IMPA2 IMPA2 IMPA2 15279 -0.15 0.055 NO
69 PLCE1 PLCE1 PLCE1 15696 -0.17 0.045 NO
70 PLCB2 PLCB2 PLCB2 15954 -0.19 0.044 NO
71 INPP5D INPP5D INPP5D 16013 -0.19 0.054 NO
72 PLCG2 PLCG2 PLCG2 16652 -0.25 0.037 NO
73 PIK3R5 PIK3R5 PIK3R5 17573 -0.38 0.013 NO
74 PIK3CG PIK3CG PIK3CG 17646 -0.39 0.036 NO

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

Figure S58.  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 CITRATE CYCLE TCA CYCLE

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 CAMK2A CAMK2A CAMK2A 123 1 0.21 YES
2 PRKCB PRKCB PRKCB 621 0.61 0.31 YES
3 CAMK2B CAMK2B CAMK2B 720 0.56 0.43 YES
4 PRKAR1B PRKAR1B PRKAR1B 1320 0.38 0.48 YES
5 PRKAR2B PRKAR2B PRKAR2B 1647 0.32 0.53 YES
6 RPS6KA5 RPS6KA5 RPS6KA5 1938 0.28 0.57 YES
7 CAMK2G CAMK2G CAMK2G 2370 0.23 0.6 YES
8 PRKACB PRKACB PRKACB 3874 0.12 0.54 NO
9 PRKCA PRKCA PRKCA 3970 0.12 0.56 NO
10 PRKACG PRKACG PRKACG 4188 0.11 0.57 NO
11 PIK3R1 PIK3R1 PIK3R1 4341 0.1 0.59 NO
12 MAPK3 MAPK3 MAPK3 4581 0.094 0.6 NO
13 MAPK1 MAPK1 MAPK1 4988 0.08 0.59 NO
14 PRKAR1A PRKAR1A PRKAR1A 5766 0.056 0.56 NO
15 HRAS HRAS HRAS 6452 0.039 0.53 NO
16 PIK3CA PIK3CA PIK3CA 7440 0.02 0.48 NO
17 SOS1 SOS1 SOS1 7632 0.016 0.47 NO
18 GNAS GNAS GNAS 8083 0.0091 0.45 NO
19 GRB2 GRB2 GRB2 8364 0.0041 0.44 NO
20 CREB1 CREB1 CREB1 9956 -0.022 0.35 NO
21 RAC1 RAC1 RAC1 10467 -0.03 0.33 NO
22 MAPK14 MAPK14 MAPK14 10472 -0.03 0.34 NO
23 CAMK2D CAMK2D CAMK2D 10649 -0.034 0.34 NO
24 PRKAR2A PRKAR2A PRKAR2A 11517 -0.048 0.3 NO
25 AKT1 AKT1 AKT1 11581 -0.049 0.31 NO
26 RPS6KA1 RPS6KA1 RPS6KA1 17002 -0.29 0.071 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 CITRATE CYCLE TCA CYCLE.

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

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 = GBMLGG-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = GBMLGG-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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