GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in GBM-TP
Glioblastoma Multiforme (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1N015QT
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 GBM-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1N015QT
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 GBM-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: 190
Number of samples: 153
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 ] 47
pheno.type: 2 - 3 :[ clus2 ] 70
pheno.type: 3 - 3 :[ clus3 ] 36

For the expression subtypes of 18210 genes in 154 samples, GSEA found enriched gene sets in each cluster using 153 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA ALK PATHWAY, BIOCARTA CARM ER PATHWAY, BIOCARTA G1 PATHWAY, BIOCARTA MPR PATHWAY, BIOCARTA EDG1 PATHWAY, KEGG RNA DEGRADATION, KEGG BASAL TRANSCRIPTION FACTORS, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG HOMOLOGOUS RECOMBINATION

    • And common core enriched genes are CCNB1, CDC25C, CDK1, LSM2, LSM3, LSM7, BUB1, CCNA2, CCNB2, CCNB3

  • clus2

    • Top enriched gene sets are BIOCARTA FAS PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA IL1R PATHWAY, KEGG GLUTATHIONE METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG PROTEASOME, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG LYSOSOME

    • And common core enriched genes are CFLAR, NFKBIA, BIRC3, CASP3, CASP6, CASP7, CASP8, FAS, LMNA, NFKB1

  • clus3

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA FMLP PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA GPCR PATHWAY

    • And common core enriched genes are PRKCB, CAMK2A, CAMK2B, CAMK2G, PTK2B, STAT4, AQP2, AQP3, AQP4, CREB3L1

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 ALK PATHWAY 34 genes.ES.table 0.45 1.4 0.11 0.72 0.98 0.18 0.1 0.16 0.58 0.24
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.44 1.5 0.063 0.62 0.91 0.59 0.34 0.39 0.46 0.19
BIOCARTA G1 PATHWAY 27 genes.ES.table 0.45 1.3 0.14 0.7 0.99 0.48 0.27 0.35 0.58 0.21
BIOCARTA MPR PATHWAY 31 genes.ES.table 0.54 1.7 0.023 0.29 0.59 0.19 0.13 0.17 0.15 0.058
BIOCARTA EDG1 PATHWAY 25 genes.ES.table 0.53 1.5 0.053 0.64 0.9 0.2 0.1 0.18 0.46 0.21
KEGG RNA DEGRADATION 56 genes.ES.table 0.43 1.8 0.02 0.41 0.24 0.52 0.37 0.33 0 0.16
KEGG BASAL TRANSCRIPTION FACTORS 34 genes.ES.table 0.4 1.4 0.16 0.65 0.98 0.56 0.4 0.34 0.53 0.18
KEGG DNA REPLICATION 35 genes.ES.table 0.61 1.6 0.091 0.53 0.82 0.69 0.3 0.48 0.35 0.16
KEGG SPLICEOSOME 125 genes.ES.table 0.4 1.7 0.068 0.34 0.57 0.72 0.45 0.4 0.19 0.09
KEGG HOMOLOGOUS RECOMBINATION 27 genes.ES.table 0.5 1.4 0.18 0.68 0.98 0.26 0.16 0.22 0.55 0.21
genes ES table in pathway: BIOCARTA ALK 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 PAPOLB PAPOLB PAPOLB 1422 0.23 0.017 YES
2 CNOT6 CNOT6 CNOT6 3088 0.12 -0.027 YES
3 PAPD7 PAPD7 PAPD7 3438 0.1 -0.0033 YES
4 EXOSC2 EXOSC2 EXOSC2 3735 0.093 0.019 YES
5 LSM7 LSM7 LSM7 3738 0.093 0.057 YES
6 EDC4 EDC4 EDC4 4096 0.082 0.072 YES
7 EXOSC7 EXOSC7 EXOSC7 4263 0.078 0.094 YES
8 EDC3 EDC3 EDC3 4322 0.076 0.12 YES
9 ZCCHC7 ZCCHC7 ZCCHC7 4407 0.074 0.15 YES
10 EXOSC5 EXOSC5 EXOSC5 4462 0.073 0.18 YES
11 DCP1A DCP1A DCP1A 4511 0.072 0.2 YES
12 RQCD1 RQCD1 RQCD1 4813 0.065 0.21 YES
13 EXOSC1 EXOSC1 EXOSC1 4841 0.064 0.24 YES
14 LSM3 LSM3 LSM3 5146 0.058 0.24 YES
15 CNOT7 CNOT7 CNOT7 5206 0.057 0.27 YES
16 EXOSC9 EXOSC9 EXOSC9 5207 0.057 0.29 YES
17 EXOSC8 EXOSC8 EXOSC8 5316 0.055 0.31 YES
18 DDX6 DDX6 DDX6 5356 0.054 0.33 YES
19 EXOSC3 EXOSC3 EXOSC3 5379 0.054 0.35 YES
20 MPHOSPH6 MPHOSPH6 MPHOSPH6 5678 0.049 0.35 YES
21 PAPOLG PAPOLG PAPOLG 6062 0.043 0.35 YES
22 CNOT10 CNOT10 CNOT10 6108 0.042 0.36 YES
23 LSM2 LSM2 LSM2 6136 0.041 0.38 YES
24 EXOSC10 EXOSC10 EXOSC10 6228 0.04 0.39 YES
25 DCP2 DCP2 DCP2 6546 0.035 0.39 YES
26 EXOSC6 EXOSC6 EXOSC6 6556 0.035 0.4 YES
27 SKIV2L2 SKIV2L2 SKIV2L2 6564 0.035 0.42 YES
28 CNOT1 CNOT1 CNOT1 6671 0.034 0.42 YES
29 EXOSC4 EXOSC4 EXOSC4 6711 0.033 0.44 YES
30 XRN1 XRN1 XRN1 7364 0.026 0.41 NO
31 DCPS DCPS DCPS 7559 0.023 0.41 NO
32 XRN2 XRN2 XRN2 7705 0.021 0.41 NO
33 ENO3 ENO3 ENO3 7832 0.02 0.41 NO
34 PATL1 PATL1 PATL1 7864 0.019 0.42 NO
35 LSM4 LSM4 LSM4 8014 0.018 0.42 NO
36 CNOT3 CNOT3 CNOT3 8080 0.017 0.42 NO
37 CNOT6L CNOT6L CNOT6L 8135 0.016 0.42 NO
38 DIS3 DIS3 DIS3 8465 0.012 0.41 NO
39 HSPD1 HSPD1 HSPD1 8544 0.01 0.41 NO
40 ENO2 ENO2 ENO2 8572 0.01 0.41 NO
41 LSM1 LSM1 LSM1 8955 0.0054 0.39 NO
42 PAPOLA PAPOLA PAPOLA 8987 0.005 0.39 NO
43 ENO1 ENO1 ENO1 9249 0.0017 0.38 NO
44 TTC37 TTC37 TTC37 9288 0.0014 0.38 NO
45 PNPT1 PNPT1 PNPT1 9464 -0.0011 0.37 NO
46 SKIV2L SKIV2L SKIV2L 9560 -0.0025 0.36 NO
47 NAA38 NAA38 NAA38 9597 -0.0028 0.36 NO
48 CNOT2 CNOT2 CNOT2 9671 -0.0038 0.36 NO
49 DCP1B DCP1B DCP1B 9883 -0.0064 0.35 NO
50 LSM5 LSM5 LSM5 9937 -0.007 0.35 NO
51 CNOT4 CNOT4 CNOT4 11718 -0.031 0.27 NO
52 HSPA9 HSPA9 HSPA9 11931 -0.034 0.27 NO
53 LSM6 LSM6 LSM6 12322 -0.04 0.26 NO
54 PARN PARN PARN 12608 -0.045 0.27 NO
55 WDR61 WDR61 WDR61 12697 -0.046 0.28 NO
56 C1D C1D C1D 12977 -0.051 0.29 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 ALK PATHWAY.

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

genes ES table in pathway: BIOCARTA CARM ER 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 ADCY5 ADCY5 ADCY5 236 0.5 0.044 YES
2 CDC25C CDC25C CDC25C 379 0.43 0.086 YES
3 CDC25A CDC25A CDC25A 381 0.43 0.14 YES
4 PKMYT1 PKMYT1 PKMYT1 588 0.36 0.16 YES
5 GNAI1 GNAI1 GNAI1 678 0.34 0.2 YES
6 CCNB3 CCNB3 CCNB3 760 0.32 0.23 YES
7 PDE3B PDE3B PDE3B 869 0.3 0.26 YES
8 RPS6KA6 RPS6KA6 RPS6KA6 940 0.29 0.29 YES
9 PLK1 PLK1 PLK1 1026 0.28 0.32 YES
10 MAD2L1 MAD2L1 MAD2L1 1039 0.28 0.35 YES
11 CCNB2 CCNB2 CCNB2 1154 0.26 0.37 YES
12 BUB1 BUB1 BUB1 1301 0.24 0.39 YES
13 CCNA2 CCNA2 CCNA2 1313 0.24 0.42 YES
14 CDK1 CDK1 CDK1 1589 0.21 0.43 YES
15 MAPK8 MAPK8 MAPK8 1597 0.21 0.45 YES
16 PIK3R3 PIK3R3 PIK3R3 1912 0.19 0.46 YES
17 CCNB1 CCNB1 CCNB1 2312 0.16 0.45 YES
18 AKT3 AKT3 AKT3 2375 0.15 0.47 YES
19 PRKX PRKX PRKX 2618 0.14 0.47 YES
20 MAD2L2 MAD2L2 MAD2L2 2723 0.13 0.48 YES
21 CDC26 CDC26 CDC26 2962 0.12 0.48 YES
22 ADCY8 ADCY8 ADCY8 3118 0.12 0.48 YES
23 ADCY1 ADCY1 ADCY1 3257 0.11 0.49 YES
24 ADCY2 ADCY2 ADCY2 3367 0.11 0.5 YES
25 PIK3R2 PIK3R2 PIK3R2 3464 0.1 0.5 YES
26 RAF1 RAF1 RAF1 4015 0.084 0.48 NO
27 ADCY9 ADCY9 ADCY9 4442 0.073 0.46 NO
28 CCNA1 CCNA1 CCNA1 4485 0.072 0.47 NO
29 MAPK12 MAPK12 MAPK12 4794 0.065 0.46 NO
30 MAPK10 MAPK10 MAPK10 5170 0.058 0.45 NO
31 PIK3CA PIK3CA PIK3CA 5241 0.056 0.45 NO
32 BRAF BRAF BRAF 5453 0.053 0.44 NO
33 KRAS KRAS KRAS 5931 0.045 0.42 NO
34 ANAPC7 ANAPC7 ANAPC7 5977 0.044 0.43 NO
35 ANAPC1 ANAPC1 ANAPC1 5997 0.044 0.43 NO
36 CDC25B CDC25B CDC25B 6107 0.042 0.43 NO
37 FZR1 FZR1 FZR1 6430 0.037 0.42 NO
38 ANAPC13 ANAPC13 ANAPC13 6743 0.033 0.4 NO
39 ANAPC5 ANAPC5 ANAPC5 6826 0.032 0.4 NO
40 CDK2 CDK2 CDK2 6882 0.031 0.4 NO
41 CDC23 CDC23 CDC23 6938 0.03 0.4 NO
42 CDC27 CDC27 CDC27 7059 0.029 0.4 NO
43 ANAPC2 ANAPC2 ANAPC2 7323 0.026 0.39 NO
44 PRKACB PRKACB PRKACB 7445 0.024 0.38 NO
45 ANAPC11 ANAPC11 ANAPC11 7603 0.022 0.38 NO
46 IGF1R IGF1R IGF1R 7622 0.022 0.38 NO
47 PIK3R1 PIK3R1 PIK3R1 7711 0.021 0.38 NO
48 ADCY7 ADCY7 ADCY7 8696 0.0086 0.32 NO
49 ADCY6 ADCY6 ADCY6 9093 0.0037 0.3 NO
50 GNAI3 GNAI3 GNAI3 9106 0.0035 0.3 NO
51 MAPK14 MAPK14 MAPK14 9447 -0.00076 0.28 NO
52 MAPK9 MAPK9 MAPK9 9485 -0.0014 0.28 NO
53 MAPK11 MAPK11 MAPK11 10073 -0.0085 0.25 NO
54 MAPK1 MAPK1 MAPK1 10306 -0.012 0.24 NO
55 ANAPC4 ANAPC4 ANAPC4 10684 -0.017 0.22 NO
56 AKT2 AKT2 AKT2 11143 -0.022 0.2 NO
57 MAPK3 MAPK3 MAPK3 11418 -0.026 0.18 NO
58 MAP2K1 MAP2K1 MAP2K1 11425 -0.026 0.19 NO
59 HSP90AA1 HSP90AA1 HSP90AA1 11996 -0.035 0.16 NO
60 AKT1 AKT1 AKT1 12054 -0.036 0.16 NO
61 CDC16 CDC16 CDC16 12114 -0.037 0.16 NO
62 PDE3A PDE3A PDE3A 12286 -0.04 0.16 NO
63 ADCY4 ADCY4 ADCY4 12298 -0.04 0.16 NO
64 PRKACA PRKACA PRKACA 12338 -0.041 0.16 NO
65 GNAI2 GNAI2 GNAI2 12423 -0.042 0.16 NO
66 RPS6KA2 RPS6KA2 RPS6KA2 12653 -0.045 0.16 NO
67 PIK3CD PIK3CD PIK3CD 12701 -0.046 0.16 NO
68 ADCY3 ADCY3 ADCY3 12789 -0.048 0.16 NO
69 ARAF ARAF ARAF 13155 -0.055 0.14 NO
70 PIK3CB PIK3CB PIK3CB 13231 -0.056 0.15 NO
71 SPDYA SPDYA SPDYA 13526 -0.062 0.14 NO
72 ANAPC10 ANAPC10 ANAPC10 13670 -0.066 0.14 NO
73 RPS6KA1 RPS6KA1 RPS6KA1 13933 -0.073 0.13 NO
74 RPS6KA3 RPS6KA3 RPS6KA3 14516 -0.088 0.11 NO
75 PIK3R5 PIK3R5 PIK3R5 14776 -0.096 0.11 NO
76 CPEB1 CPEB1 CPEB1 15160 -0.11 0.097 NO
77 PGR PGR PGR 15719 -0.13 0.082 NO
78 IGF1 IGF1 IGF1 15830 -0.14 0.091 NO
79 PIK3CG PIK3CG PIK3CG 16464 -0.17 0.076 NO
80 MAPK13 MAPK13 MAPK13 16473 -0.17 0.095 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 CARM ER PATHWAY.

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

genes ES table in pathway: BIOCARTA G1 PATHWAY

Table 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 E2F2 E2F2 E2F2 176 0.54 0.027 YES
2 GADD45G GADD45G GADD45G 305 0.46 0.051 YES
3 CDC25C CDC25C CDC25C 379 0.43 0.075 YES
4 CDC25A CDC25A CDC25A 381 0.43 0.1 YES
5 TTK TTK TTK 482 0.4 0.12 YES
6 PKMYT1 PKMYT1 PKMYT1 588 0.36 0.14 YES
7 CDK4 CDK4 CDK4 642 0.35 0.16 YES
8 ORC1L ORC1L ORC1L 644 0.35 0.19 YES
9 ESPL1 ESPL1 ESPL1 699 0.34 0.21 YES
10 CCNB3 CCNB3 CCNB3 760 0.32 0.22 YES
11 CDC45 CDC45 CDC45 769 0.32 0.25 YES
12 ORC6L ORC6L ORC6L 980 0.29 0.25 YES
13 PLK1 PLK1 PLK1 1026 0.28 0.27 YES
14 MAD2L1 MAD2L1 MAD2L1 1039 0.28 0.29 YES
15 CDKN2A CDKN2A CDKN2A 1100 0.27 0.3 YES
16 CCNB2 CCNB2 CCNB2 1154 0.26 0.32 YES
17 CDC7 CDC7 CDC7 1190 0.26 0.33 YES
18 BUB1B BUB1B BUB1B 1193 0.26 0.35 YES
19 CCND1 CCND1 CCND1 1256 0.25 0.36 YES
20 CDKN1C CDKN1C CDKN1C 1269 0.25 0.38 YES
21 BUB1 BUB1 BUB1 1301 0.24 0.39 YES
22 CCNA2 CCNA2 CCNA2 1313 0.24 0.41 YES
23 CDC20 CDC20 CDC20 1355 0.24 0.42 YES
24 E2F1 E2F1 E2F1 1523 0.22 0.43 YES
25 CDK1 CDK1 CDK1 1589 0.21 0.44 YES
26 PTTG1 PTTG1 PTTG1 1691 0.2 0.45 YES
27 CCNE2 CCNE2 CCNE2 1716 0.2 0.46 YES
28 CDC6 CDC6 CDC6 1766 0.2 0.47 YES
29 CHEK2 CHEK2 CHEK2 1914 0.19 0.48 YES
30 HDAC2 HDAC2 HDAC2 1943 0.18 0.49 YES
31 CDKN2B CDKN2B CDKN2B 1979 0.18 0.5 YES
32 CHEK1 CHEK1 CHEK1 2038 0.18 0.5 YES
33 E2F3 E2F3 E2F3 2118 0.17 0.51 YES
34 CCNB1 CCNB1 CCNB1 2312 0.16 0.51 YES
35 MDM2 MDM2 MDM2 2532 0.14 0.51 YES
36 MYC MYC MYC 2610 0.14 0.51 YES
37 MCM2 MCM2 MCM2 2644 0.14 0.52 YES
38 MAD2L2 MAD2L2 MAD2L2 2723 0.13 0.53 YES
39 MCM7 MCM7 MCM7 2764 0.13 0.53 YES
40 CDC26 CDC26 CDC26 2962 0.12 0.53 YES
41 RBL1 RBL1 RBL1 2969 0.12 0.54 YES
42 GSK3B GSK3B GSK3B 2977 0.12 0.55 YES
43 CDKN2D CDKN2D CDKN2D 3150 0.11 0.54 NO
44 CCND2 CCND2 CCND2 3341 0.11 0.54 NO
45 TFDP2 TFDP2 TFDP2 3384 0.11 0.55 NO
46 BUB3 BUB3 BUB3 3721 0.094 0.53 NO
47 SMC3 SMC3 SMC3 3792 0.091 0.54 NO
48 MCM4 MCM4 MCM4 3853 0.089 0.54 NO
49 ZBTB17 ZBTB17 ZBTB17 3970 0.085 0.54 NO
50 ABL1 ABL1 ABL1 4359 0.075 0.52 NO
51 MCM5 MCM5 MCM5 4411 0.074 0.52 NO
52 SKP2 SKP2 SKP2 4418 0.074 0.53 NO
53 CCNA1 CCNA1 CCNA1 4485 0.072 0.53 NO
54 RAD21 RAD21 RAD21 4687 0.068 0.52 NO
55 PTTG2 PTTG2 PTTG2 4762 0.066 0.52 NO
56 CCNE1 CCNE1 CCNE1 4784 0.066 0.53 NO
57 E2F5 E2F5 E2F5 4797 0.065 0.53 NO
58 MCM6 MCM6 MCM6 4819 0.065 0.53 NO
59 CDKN1B CDKN1B CDKN1B 4842 0.064 0.54 NO
60 MAD1L1 MAD1L1 MAD1L1 4852 0.064 0.54 NO
61 CREBBP CREBBP CREBBP 5088 0.059 0.53 NO
62 PCNA PCNA PCNA 5106 0.059 0.53 NO
63 SMC1A SMC1A SMC1A 5122 0.058 0.54 NO
64 EP300 EP300 EP300 5850 0.046 0.5 NO
65 ANAPC7 ANAPC7 ANAPC7 5977 0.044 0.5 NO
66 ANAPC1 ANAPC1 ANAPC1 5997 0.044 0.5 NO
67 PRKDC PRKDC PRKDC 6040 0.043 0.5 NO
68 CDC25B CDC25B CDC25B 6107 0.042 0.5 NO
69 YWHAQ YWHAQ YWHAQ 6305 0.038 0.49 NO
70 FZR1 FZR1 FZR1 6430 0.037 0.48 NO
71 MCM3 MCM3 MCM3 6557 0.035 0.48 NO
72 CCNH CCNH CCNH 6666 0.034 0.48 NO
73 ORC4L ORC4L ORC4L 6686 0.034 0.48 NO
74 ANAPC13 ANAPC13 ANAPC13 6743 0.033 0.48 NO
75 ANAPC5 ANAPC5 ANAPC5 6826 0.032 0.47 NO
76 CDK2 CDK2 CDK2 6882 0.031 0.47 NO
77 CDC23 CDC23 CDC23 6938 0.03 0.47 NO
78 CDC27 CDC27 CDC27 7059 0.029 0.47 NO
79 CDKN2C CDKN2C CDKN2C 7138 0.028 0.46 NO
80 ANAPC2 ANAPC2 ANAPC2 7323 0.026 0.46 NO
81 STAG1 STAG1 STAG1 7518 0.024 0.45 NO
82 ANAPC11 ANAPC11 ANAPC11 7603 0.022 0.44 NO
83 YWHAE YWHAE YWHAE 7733 0.021 0.44 NO
84 ORC3L ORC3L ORC3L 7738 0.021 0.44 NO
85 CDC14B CDC14B CDC14B 7753 0.021 0.44 NO
86 ATM ATM ATM 8154 0.016 0.42 NO
87 RBX1 RBX1 RBX1 8464 0.012 0.4 NO
88 CCND3 CCND3 CCND3 8481 0.011 0.4 NO
89 WEE2 WEE2 WEE2 8589 0.01 0.4 NO
90 YWHAG YWHAG YWHAG 8628 0.0096 0.4 NO
91 SMAD4 SMAD4 SMAD4 8631 0.0095 0.4 NO
92 YWHAB YWHAB YWHAB 8654 0.0092 0.4 NO
93 E2F4 E2F4 E2F4 8841 0.0068 0.39 NO
94 STAG2 STAG2 STAG2 8850 0.0067 0.39 NO
95 RBL2 RBL2 RBL2 9047 0.0043 0.38 NO
96 SMAD2 SMAD2 SMAD2 9344 0.00062 0.36 NO
97 ORC5L ORC5L ORC5L 9381 0.0002 0.36 NO
98 YWHAZ YWHAZ YWHAZ 10021 -0.008 0.32 NO
99 RB1 RB1 RB1 10146 -0.0099 0.32 NO
100 ATR ATR ATR 10464 -0.014 0.3 NO
101 ORC2L ORC2L ORC2L 10575 -0.016 0.29 NO
102 ANAPC4 ANAPC4 ANAPC4 10684 -0.017 0.29 NO
103 CDK6 CDK6 CDK6 10722 -0.017 0.29 NO
104 YWHAH YWHAH YWHAH 11097 -0.022 0.27 NO
105 TFDP1 TFDP1 TFDP1 11472 -0.027 0.25 NO
106 HDAC1 HDAC1 HDAC1 11630 -0.03 0.24 NO
107 CDC14A CDC14A CDC14A 11887 -0.034 0.23 NO
108 TP53 TP53 TP53 11926 -0.034 0.23 NO
109 SMC1B SMC1B SMC1B 12016 -0.036 0.23 NO
110 CDC16 CDC16 CDC16 12114 -0.037 0.23 NO
111 CDK7 CDK7 CDK7 12285 -0.04 0.22 NO
112 SKP1 SKP1 SKP1 12527 -0.043 0.21 NO
113 CUL1 CUL1 CUL1 12915 -0.05 0.19 NO
114 WEE1 WEE1 WEE1 13483 -0.061 0.16 NO
115 ANAPC10 ANAPC10 ANAPC10 13670 -0.066 0.16 NO
116 TGFB1 TGFB1 TGFB1 14850 -0.099 0.099 NO
117 SMAD3 SMAD3 SMAD3 15038 -0.1 0.096 NO
118 CDKN1A CDKN1A CDKN1A 15853 -0.14 0.06 NO
119 GADD45B GADD45B GADD45B 16177 -0.15 0.053 NO
120 TGFB2 TGFB2 TGFB2 16727 -0.19 0.035 NO
121 GADD45A GADD45A GADD45A 16771 -0.19 0.046 NO
122 TGFB3 TGFB3 TGFB3 17009 -0.21 0.047 NO
123 SFN SFN SFN 17595 -0.28 0.033 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 G1 PATHWAY.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA MPR PATHWAY

Table 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 TCERG1 TCERG1 TCERG1 3335 0.11 -0.16 YES
2 LSM7 LSM7 LSM7 3738 0.093 -0.16 YES
3 RBMX RBMX RBMX 3912 0.087 -0.15 YES
4 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 4143 0.081 -0.15 YES
5 PPIL1 PPIL1 PPIL1 4297 0.077 -0.14 YES
6 HNRNPA3 HNRNPA3 HNRNPA3 4362 0.075 -0.12 YES
7 THOC4 THOC4 THOC4 4450 0.073 -0.11 YES
8 HNRNPA1 HNRNPA1 HNRNPA1 4499 0.072 -0.098 YES
9 SF3A2 SF3A2 SF3A2 4508 0.072 -0.083 YES
10 NCBP1 NCBP1 NCBP1 4625 0.069 -0.074 YES
11 SART1 SART1 SART1 4710 0.067 -0.063 YES
12 SF3B3 SF3B3 SF3B3 4799 0.065 -0.053 YES
13 SNRPA SNRPA SNRPA 4815 0.065 -0.039 YES
14 PPIH PPIH PPIH 4934 0.062 -0.032 YES
15 HNRNPM HNRNPM HNRNPM 4954 0.062 -0.019 YES
16 CDC40 CDC40 CDC40 4960 0.062 -0.0052 YES
17 LSM3 LSM3 LSM3 5146 0.058 -0.0023 YES
18 THOC3 THOC3 THOC3 5199 0.057 0.0077 YES
19 SFRS3 SFRS3 SFRS3 5221 0.057 0.019 YES
20 SNRPC SNRPC SNRPC 5229 0.057 0.032 YES
21 SNRPD1 SNRPD1 SNRPD1 5311 0.055 0.04 YES
22 DDX46 DDX46 DDX46 5312 0.055 0.052 YES
23 DHX15 DHX15 DHX15 5411 0.053 0.059 YES
24 PRPF8 PRPF8 PRPF8 5432 0.053 0.07 YES
25 SFRS7 SFRS7 SFRS7 5478 0.052 0.079 YES
26 SNRPF SNRPF SNRPF 5483 0.052 0.09 YES
27 SR140 SR140 SR140 5549 0.051 0.098 YES
28 SNRPB SNRPB SNRPB 5607 0.05 0.11 YES
29 PRPF18 PRPF18 PRPF18 5749 0.048 0.11 YES
30 SNRPA1 SNRPA1 SNRPA1 5755 0.047 0.12 YES
31 SFRS1 SFRS1 SFRS1 5768 0.047 0.13 YES
32 BAT1 BAT1 BAT1 5772 0.047 0.14 YES
33 TRA2B TRA2B TRA2B 5819 0.046 0.15 YES
34 DHX38 DHX38 DHX38 5840 0.046 0.16 YES
35 RBM8A RBM8A RBM8A 5916 0.045 0.16 YES
36 SFRS2B SFRS2B SFRS2B 5972 0.044 0.17 YES
37 PRPF38A PRPF38A PRPF38A 5992 0.044 0.18 YES
38 TRA2A TRA2A TRA2A 6010 0.043 0.19 YES
39 PQBP1 PQBP1 PQBP1 6071 0.042 0.2 YES
40 XAB2 XAB2 XAB2 6092 0.042 0.2 YES
41 SNRPD3 SNRPD3 SNRPD3 6120 0.042 0.21 YES
42 LSM2 LSM2 LSM2 6136 0.041 0.22 YES
43 SNRNP200 SNRNP200 SNRNP200 6177 0.041 0.23 YES
44 SFRS6 SFRS6 SFRS6 6233 0.04 0.23 YES
45 SMNDC1 SMNDC1 SMNDC1 6332 0.038 0.24 YES
46 DHX8 DHX8 DHX8 6388 0.037 0.24 YES
47 SNRNP40 SNRNP40 SNRNP40 6403 0.037 0.25 YES
48 SNRPB2 SNRPB2 SNRPB2 6489 0.036 0.25 YES
49 ACIN1 ACIN1 ACIN1 6522 0.036 0.26 YES
50 CHERP CHERP CHERP 6535 0.036 0.26 YES
51 WBP11 WBP11 WBP11 6543 0.036 0.27 YES
52 CDC5L CDC5L CDC5L 6544 0.035 0.28 YES
53 DHX16 DHX16 DHX16 6607 0.035 0.28 YES
54 CTNNBL1 CTNNBL1 CTNNBL1 6610 0.034 0.29 YES
55 PUF60 PUF60 PUF60 6645 0.034 0.3 YES
56 PRPF19 PRPF19 PRPF19 6684 0.034 0.3 YES
57 SFRS2 SFRS2 SFRS2 6714 0.033 0.31 YES
58 RBM17 RBM17 RBM17 6715 0.033 0.32 YES
59 PRPF4 PRPF4 PRPF4 6723 0.033 0.32 YES
60 PRPF6 PRPF6 PRPF6 6823 0.032 0.33 YES
61 SNRPE SNRPE SNRPE 6867 0.031 0.33 YES
62 PHF5A PHF5A PHF5A 6885 0.031 0.34 YES
63 CCDC12 CCDC12 CCDC12 6887 0.031 0.34 YES
64 MAGOHB MAGOHB MAGOHB 6937 0.03 0.35 YES
65 SF3B5 SF3B5 SF3B5 7043 0.029 0.35 YES
66 SFRS9 SFRS9 SFRS9 7063 0.029 0.36 YES
67 SF3B2 SF3B2 SF3B2 7252 0.027 0.35 YES
68 EFTUD2 EFTUD2 EFTUD2 7281 0.027 0.36 YES
69 HNRNPU HNRNPU HNRNPU 7314 0.026 0.36 YES
70 HNRNPK HNRNPK HNRNPK 7350 0.026 0.36 YES
71 U2AF1 U2AF1 U2AF1 7369 0.026 0.37 YES
72 SF3A1 SF3A1 SF3A1 7432 0.025 0.37 YES
73 SF3B4 SF3B4 SF3B4 7462 0.024 0.37 YES
74 NHP2L1 NHP2L1 NHP2L1 7612 0.022 0.37 YES
75 SNRPG SNRPG SNRPG 7632 0.022 0.37 YES
76 RBM22 RBM22 RBM22 7658 0.022 0.38 YES
77 SFRS13A SFRS13A SFRS13A 7742 0.021 0.38 YES
78 PRPF40A PRPF40A PRPF40A 7820 0.02 0.38 YES
79 PRPF3 PRPF3 PRPF3 7844 0.02 0.38 YES
80 USP39 USP39 USP39 7847 0.02 0.39 YES
81 TXNL4A TXNL4A TXNL4A 7859 0.019 0.39 YES
82 U2AF2 U2AF2 U2AF2 7899 0.019 0.39 YES
83 SNRNP27 SNRNP27 SNRNP27 7941 0.018 0.39 YES
84 SF3B14 SF3B14 SF3B14 8009 0.018 0.39 YES
85 LSM4 LSM4 LSM4 8014 0.018 0.4 YES
86 THOC1 THOC1 THOC1 8104 0.016 0.4 YES
87 DDX42 DDX42 DDX42 8107 0.016 0.4 YES
88 SFRS4 SFRS4 SFRS4 8113 0.016 0.4 YES
89 DDX5 DDX5 DDX5 8209 0.015 0.4 YES
90 SF3B1 SF3B1 SF3B1 8218 0.015 0.4 YES
91 CRNKL1 CRNKL1 CRNKL1 8519 0.011 0.39 NO
92 CWC15 CWC15 CWC15 8549 0.01 0.39 NO
93 HNRNPC HNRNPC HNRNPC 8561 0.01 0.39 NO
94 EIF4A3 EIF4A3 EIF4A3 8579 0.01 0.39 NO
95 PPIE PPIE PPIE 8735 0.0082 0.39 NO
96 SF3A3 SF3A3 SF3A3 8840 0.0068 0.38 NO
97 ISY1 ISY1 ISY1 8961 0.0053 0.38 NO
98 SNRNP70 SNRNP70 SNRNP70 8974 0.0052 0.38 NO
99 PRPF38B PRPF38B PRPF38B 9293 0.0013 0.36 NO
100 PCBP1 PCBP1 PCBP1 9379 0.00022 0.36 NO
101 ZMAT2 ZMAT2 ZMAT2 9398 -5.2e-06 0.36 NO
102 HSPA1L HSPA1L HSPA1L 9446 -0.00074 0.35 NO
103 BCAS2 BCAS2 BCAS2 9474 -0.0012 0.35 NO
104 NAA38 NAA38 NAA38 9597 -0.0028 0.34 NO
105 DDX23 DDX23 DDX23 9665 -0.0037 0.34 NO
106 LSM5 LSM5 LSM5 9937 -0.007 0.33 NO
107 THOC2 THOC2 THOC2 10117 -0.0093 0.32 NO
108 SFRS5 SFRS5 SFRS5 10412 -0.013 0.31 NO
109 RBM25 RBM25 RBM25 10440 -0.014 0.31 NO
110 HSPA1A HSPA1A HSPA1A 10502 -0.015 0.31 NO
111 HSPA8 HSPA8 HSPA8 10513 -0.015 0.31 NO
112 PRPF40B PRPF40B PRPF40B 10651 -0.017 0.31 NO
113 MAGOH MAGOH MAGOH 10831 -0.019 0.3 NO
114 PLRG1 PLRG1 PLRG1 10847 -0.019 0.31 NO
115 SLU7 SLU7 SLU7 10938 -0.02 0.31 NO
116 SNRPD2 SNRPD2 SNRPD2 10970 -0.02 0.31 NO
117 SNW1 SNW1 SNW1 11056 -0.022 0.31 NO
118 SYF2 SYF2 SYF2 11396 -0.026 0.3 NO
119 BUD31 BUD31 BUD31 11468 -0.027 0.3 NO
120 AQR AQR AQR 11503 -0.028 0.3 NO
121 HSPA1B HSPA1B HSPA1B 11566 -0.029 0.31 NO
122 PRPF31 PRPF31 PRPF31 11853 -0.033 0.3 NO
123 HSPA6 HSPA6 HSPA6 11987 -0.035 0.3 NO
124 LSM6 LSM6 LSM6 12322 -0.04 0.29 NO
125 HSPA2 HSPA2 HSPA2 16303 -0.16 0.1 NO

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

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

genes ES table in pathway: BIOCARTA EDG1 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 MYT1 MYT1 MYT1 16 0.84 0.26 YES
2 CDC25C CDC25C CDC25C 379 0.43 0.37 YES
3 GNAI1 GNAI1 GNAI1 678 0.34 0.46 YES
4 CDK1 CDK1 CDK1 1589 0.21 0.47 YES
5 SRC SRC SRC 1827 0.19 0.52 YES
6 CCNB1 CCNB1 CCNB1 2312 0.16 0.54 YES
7 PRKAR2A PRKAR2A PRKAR2A 3507 0.1 0.51 NO
8 PRKAR2B PRKAR2B PRKAR2B 3835 0.09 0.52 NO
9 GNB1 GNB1 GNB1 7103 0.029 0.34 NO
10 PRKACB PRKACB PRKACB 7445 0.024 0.33 NO
11 GNAS GNAS GNAS 7861 0.019 0.32 NO
12 PRKAR1B PRKAR1B PRKAR1B 8636 0.0095 0.28 NO
13 ACTA1 ACTA1 ACTA1 8920 0.0058 0.26 NO
14 PIN1 PIN1 PIN1 9161 0.0028 0.25 NO
15 ACTR2 ACTR2 ACTR2 9551 -0.0023 0.23 NO
16 ARPC5 ARPC5 ARPC5 9654 -0.0036 0.23 NO
17 MAPK1 MAPK1 MAPK1 10306 -0.012 0.19 NO
18 PRKAR1A PRKAR1A PRKAR1A 10579 -0.016 0.18 NO
19 ACTR3 ACTR3 ACTR3 10649 -0.016 0.18 NO
20 ARPC4 ARPC4 ARPC4 10843 -0.019 0.18 NO
21 ARPC2 ARPC2 ARPC2 10971 -0.02 0.18 NO
22 PAQR7 PAQR7 PAQR7 11152 -0.023 0.18 NO
23 MAPK3 MAPK3 MAPK3 11418 -0.026 0.17 NO
24 CAP1 CAP1 CAP1 11614 -0.029 0.17 NO
25 ARPC1A ARPC1A ARPC1A 11621 -0.03 0.18 NO
26 HRAS HRAS HRAS 11872 -0.034 0.17 NO
27 ARPC3 ARPC3 ARPC3 12630 -0.045 0.14 NO
28 RPS6KA1 RPS6KA1 RPS6KA1 13933 -0.073 0.096 NO
29 PGR PGR PGR 15719 -0.13 0.038 NO
30 ARPC1B ARPC1B ARPC1B 15757 -0.13 0.077 NO
31 PAQR5 PAQR5 PAQR5 16667 -0.18 0.084 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 EDG1 PATHWAY.

Figure S10.  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 RNA DEGRADATION

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 DNA2 DNA2 DNA2 580 0.36 0.084 YES
2 RFC3 RFC3 RFC3 2126 0.17 0.053 YES
3 POLE POLE POLE 2176 0.17 0.1 YES
4 PRIM1 PRIM1 PRIM1 2220 0.16 0.15 YES
5 RPA4 RPA4 RPA4 2299 0.16 0.2 YES
6 POLE2 POLE2 POLE2 2505 0.14 0.23 YES
7 MCM2 MCM2 MCM2 2644 0.14 0.27 YES
8 POLA2 POLA2 POLA2 2734 0.13 0.31 YES
9 MCM7 MCM7 MCM7 2764 0.13 0.35 YES
10 PRIM2 PRIM2 PRIM2 2780 0.13 0.39 YES
11 RFC4 RFC4 RFC4 3018 0.12 0.42 YES
12 RNASEH2A RNASEH2A RNASEH2A 3022 0.12 0.45 YES
13 FEN1 FEN1 FEN1 3495 0.1 0.46 YES
14 MCM4 MCM4 MCM4 3853 0.089 0.47 YES
15 RFC5 RFC5 RFC5 3857 0.089 0.5 YES
16 POLD1 POLD1 POLD1 3998 0.084 0.52 YES
17 LIG1 LIG1 LIG1 4116 0.081 0.54 YES
18 MCM5 MCM5 MCM5 4411 0.074 0.54 YES
19 RNASEH2B RNASEH2B RNASEH2B 4532 0.071 0.56 YES
20 POLE4 POLE4 POLE4 4609 0.07 0.58 YES
21 MCM6 MCM6 MCM6 4819 0.065 0.59 YES
22 POLE3 POLE3 POLE3 4981 0.061 0.6 YES
23 PCNA PCNA PCNA 5106 0.059 0.61 YES
24 POLD3 POLD3 POLD3 5412 0.053 0.61 YES
25 MCM3 MCM3 MCM3 6557 0.035 0.56 NO
26 RNASEH1 RNASEH1 RNASEH1 7219 0.028 0.53 NO
27 RNASEH2C RNASEH2C RNASEH2C 7496 0.024 0.52 NO
28 RFC1 RFC1 RFC1 8167 0.016 0.49 NO
29 RPA1 RPA1 RPA1 9265 0.0015 0.43 NO
30 RPA2 RPA2 RPA2 9736 -0.0046 0.4 NO
31 RPA3 RPA3 RPA3 10006 -0.0079 0.39 NO
32 POLD2 POLD2 POLD2 10326 -0.012 0.38 NO
33 RFC2 RFC2 RFC2 10522 -0.015 0.37 NO
34 SSBP1 SSBP1 SSBP1 11868 -0.034 0.31 NO
35 POLD4 POLD4 POLD4 15455 -0.12 0.15 NO

Figure S11.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RNA DEGRADATION.

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

genes ES table in pathway: KEGG BASAL TRANSCRIPTION FACTORS

Table 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 SPHKAP SPHKAP SPHKAP 196 0.53 0.17 YES
2 PDGFRA PDGFRA PDGFRA 409 0.42 0.3 YES
3 PLCB1 PLCB1 PLCB1 599 0.36 0.41 YES
4 GNAI1 GNAI1 GNAI1 678 0.34 0.53 YES
5 SRC SRC SRC 1827 0.19 0.53 YES
6 PIK3CA PIK3CA PIK3CA 5241 0.056 0.36 NO
7 PTK2 PTK2 PTK2 5502 0.052 0.36 NO
8 GNB1 GNB1 GNB1 7103 0.029 0.29 NO
9 PIK3R1 PIK3R1 PIK3R1 7711 0.021 0.26 NO
10 ITGB3 ITGB3 ITGB3 8212 0.015 0.24 NO
11 SPHK1 SPHK1 SPHK1 8414 0.012 0.23 NO
12 MAPK1 MAPK1 MAPK1 10306 -0.012 0.13 NO
13 ASAH1 ASAH1 ASAH1 10401 -0.013 0.13 NO
14 RHOA RHOA RHOA 10738 -0.018 0.12 NO
15 MAPK3 MAPK3 MAPK3 11418 -0.026 0.089 NO
16 RAC1 RAC1 RAC1 11658 -0.03 0.086 NO
17 SMPD2 SMPD2 SMPD2 11920 -0.034 0.083 NO
18 PRKCA PRKCA PRKCA 11978 -0.035 0.092 NO
19 AKT1 AKT1 AKT1 12054 -0.036 0.1 NO
20 S1PR1 S1PR1 S1PR1 13825 -0.07 0.027 NO
21 ITGAV ITGAV ITGAV 14287 -0.082 0.029 NO
22 SMPD1 SMPD1 SMPD1 14813 -0.097 0.034 NO
23 PRKCB PRKCB PRKCB 15105 -0.11 0.054 NO
24 PDGFA PDGFA PDGFA 16431 -0.17 0.039 NO
25 PIK3CG PIK3CG PIK3CG 16464 -0.17 0.095 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 BASAL TRANSCRIPTION FACTORS.

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

genes ES table in pathway: KEGG 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 NR0B1 NR0B1 NR0B1 205 0.52 0.15 YES
2 HIST2H3C HIST2H3C HIST2H3C 672 0.34 0.24 YES
3 CCND1 CCND1 CCND1 1256 0.25 0.28 YES
4 GRIP1 GRIP1 GRIP1 1357 0.24 0.36 YES
5 HDAC2 HDAC2 HDAC2 1943 0.18 0.38 YES
6 HDAC5 HDAC5 HDAC5 3992 0.084 0.3 YES
7 BRCA1 BRCA1 BRCA1 4004 0.084 0.32 YES
8 MED1 MED1 MED1 4098 0.082 0.34 YES
9 HDAC4 HDAC4 HDAC4 4159 0.08 0.36 YES
10 SPEN SPEN SPEN 4267 0.078 0.38 YES
11 GTF2A1 GTF2A1 GTF2A1 4354 0.075 0.4 YES
12 PELP1 PELP1 PELP1 4857 0.064 0.39 YES
13 GTF2E1 GTF2E1 GTF2E1 4914 0.063 0.41 YES
14 CREBBP CREBBP CREBBP 5088 0.059 0.42 YES
15 HDAC8 HDAC8 HDAC8 5682 0.049 0.4 YES
16 POLR2A POLR2A POLR2A 5738 0.048 0.42 YES
17 EP300 EP300 EP300 5850 0.046 0.42 YES
18 ERCC3 ERCC3 ERCC3 6048 0.043 0.43 YES
19 TBP TBP TBP 6140 0.041 0.44 YES
20 HDAC9 HDAC9 HDAC9 6266 0.039 0.44 YES
21 PHB2 PHB2 PHB2 6963 0.03 0.41 NO
22 HDAC6 HDAC6 HDAC6 7427 0.025 0.39 NO
23 NCOR2 NCOR2 NCOR2 7689 0.021 0.39 NO
24 CARM1 CARM1 CARM1 7952 0.018 0.38 NO
25 HDAC11 HDAC11 HDAC11 9719 -0.0044 0.28 NO
26 GTF2F1 GTF2F1 GTF2F1 9922 -0.0068 0.27 NO
27 HDAC3 HDAC3 HDAC3 9958 -0.0072 0.27 NO
28 SRA1 SRA1 SRA1 10704 -0.017 0.24 NO
29 HDAC1 HDAC1 HDAC1 11630 -0.03 0.2 NO
30 NRIP1 NRIP1 NRIP1 12932 -0.05 0.14 NO
31 HDAC10 HDAC10 HDAC10 13963 -0.073 0.11 NO
32 HDAC7 HDAC7 HDAC7 15086 -0.11 0.079 NO
33 ESR1 ESR1 ESR1 15372 -0.12 0.1 NO
34 PPARGC1A PPARGC1A PPARGC1A 16519 -0.17 0.092 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 SPLICEOSOME

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 DLL3 DLL3 DLL3 156 0.55 0.1 YES
2 HES5 HES5 HES5 170 0.54 0.21 YES
3 RBPJL RBPJL RBPJL 366 0.44 0.29 YES
4 DLL1 DLL1 DLL1 700 0.34 0.34 YES
5 DTX4 DTX4 DTX4 1414 0.23 0.34 YES
6 DTX3 DTX3 DTX3 1477 0.22 0.39 YES
7 RBPJ RBPJ RBPJ 1873 0.19 0.4 YES
8 HDAC2 HDAC2 HDAC2 1943 0.18 0.44 YES
9 MAML2 MAML2 MAML2 2493 0.15 0.44 NO
10 NOTCH1 NOTCH1 NOTCH1 3385 0.11 0.41 NO
11 CTBP2 CTBP2 CTBP2 4207 0.079 0.38 NO
12 DVL3 DVL3 DVL3 4790 0.065 0.36 NO
13 CREBBP CREBBP CREBBP 5088 0.059 0.36 NO
14 MAML1 MAML1 MAML1 5300 0.055 0.35 NO
15 DVL2 DVL2 DVL2 5605 0.05 0.35 NO
16 EP300 EP300 EP300 5850 0.046 0.34 NO
17 DLL4 DLL4 DLL4 6060 0.043 0.34 NO
18 CTBP1 CTBP1 CTBP1 6802 0.032 0.31 NO
19 DVL1 DVL1 DVL1 7425 0.025 0.28 NO
20 NCOR2 NCOR2 NCOR2 7689 0.021 0.27 NO
21 DTX1 DTX1 DTX1 7776 0.02 0.27 NO
22 JAG2 JAG2 JAG2 9440 -0.00065 0.18 NO
23 RFNG RFNG RFNG 9618 -0.0031 0.16 NO
24 KAT2A KAT2A KAT2A 9687 -0.004 0.16 NO
25 NOTCH4 NOTCH4 NOTCH4 9866 -0.0062 0.15 NO
26 APH1A APH1A APH1A 9976 -0.0075 0.15 NO
27 CIR1 CIR1 CIR1 10598 -0.016 0.12 NO
28 JAG1 JAG1 JAG1 10916 -0.02 0.1 NO
29 SNW1 SNW1 SNW1 11056 -0.022 0.1 NO
30 ADAM17 ADAM17 ADAM17 11403 -0.026 0.088 NO
31 NOTCH2 NOTCH2 NOTCH2 11592 -0.029 0.083 NO
32 HDAC1 HDAC1 HDAC1 11630 -0.03 0.087 NO
33 PSEN1 PSEN1 PSEN1 12028 -0.036 0.073 NO
34 NCSTN NCSTN NCSTN 12855 -0.049 0.037 NO
35 KAT2B KAT2B KAT2B 13289 -0.058 0.025 NO
36 NOTCH3 NOTCH3 NOTCH3 13352 -0.059 0.033 NO
37 DTX2 DTX2 DTX2 13837 -0.07 0.02 NO
38 MAML3 MAML3 MAML3 14118 -0.077 0.02 NO
39 NUMB NUMB NUMB 14393 -0.084 0.022 NO
40 PSENEN PSENEN PSENEN 14611 -0.091 0.028 NO
41 PTCRA PTCRA PTCRA 14972 -0.1 0.029 NO
42 HES1 HES1 HES1 15277 -0.11 0.035 NO
43 NUMBL NUMBL NUMBL 15503 -0.12 0.048 NO
44 PSEN2 PSEN2 PSEN2 16193 -0.16 0.041 NO
45 LFNG LFNG LFNG 16468 -0.17 0.06 NO
46 DTX3L DTX3L DTX3L 16535 -0.17 0.091 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 SPLICEOSOME.

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

genes ES table in pathway: KEGG HOMOLOGOUS RECOMBINATION

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 RPRM RPRM RPRM 80 0.64 0.065 YES
2 GADD45G GADD45G GADD45G 305 0.46 0.1 YES
3 TP73 TP73 TP73 352 0.44 0.15 YES
4 CDK4 CDK4 CDK4 642 0.35 0.17 YES
5 CCNB3 CCNB3 CCNB3 760 0.32 0.2 YES
6 BAI1 BAI1 BAI1 854 0.3 0.22 YES
7 GTSE1 GTSE1 GTSE1 925 0.3 0.25 YES
8 CDKN2A CDKN2A CDKN2A 1100 0.27 0.27 YES
9 CCNB2 CCNB2 CCNB2 1154 0.26 0.3 YES
10 CCND1 CCND1 CCND1 1256 0.25 0.32 YES
11 CDK1 CDK1 CDK1 1589 0.21 0.32 YES
12 CCNE2 CCNE2 CCNE2 1716 0.2 0.34 YES
13 CCNG2 CCNG2 CCNG2 1882 0.19 0.35 YES
14 CHEK2 CHEK2 CHEK2 1914 0.19 0.37 YES
15 CHEK1 CHEK1 CHEK1 2038 0.18 0.38 YES
16 RRM2 RRM2 RRM2 2242 0.16 0.39 YES
17 CCNB1 CCNB1 CCNB1 2312 0.16 0.4 YES
18 PPM1D PPM1D PPM1D 2502 0.14 0.41 YES
19 MDM2 MDM2 MDM2 2532 0.14 0.42 YES
20 CCND2 CCND2 CCND2 3341 0.11 0.39 NO
21 APAF1 APAF1 APAF1 3361 0.11 0.4 NO
22 SIAH1 SIAH1 SIAH1 3911 0.087 0.38 NO
23 TSC2 TSC2 TSC2 3931 0.086 0.38 NO
24 MDM4 MDM4 MDM4 4023 0.084 0.39 NO
25 CCNE1 CCNE1 CCNE1 4784 0.066 0.35 NO
26 CASP9 CASP9 CASP9 5007 0.06 0.35 NO
27 BID BID BID 5042 0.06 0.35 NO
28 RFWD2 RFWD2 RFWD2 5578 0.05 0.33 NO
29 CDK2 CDK2 CDK2 6882 0.031 0.26 NO
30 SESN2 SESN2 SESN2 7185 0.028 0.25 NO
31 SESN3 SESN3 SESN3 7901 0.019 0.21 NO
32 EI24 EI24 EI24 7930 0.019 0.21 NO
33 TP53I3 TP53I3 TP53I3 7933 0.018 0.21 NO
34 ATM ATM ATM 8154 0.016 0.2 NO
35 CCND3 CCND3 CCND3 8481 0.011 0.18 NO
36 RCHY1 RCHY1 RCHY1 9640 -0.0034 0.12 NO
37 BBC3 BBC3 BBC3 9751 -0.0048 0.12 NO
38 TP53AIP1 TP53AIP1 TP53AIP1 10012 -0.008 0.1 NO
39 ATR ATR ATR 10464 -0.014 0.078 NO
40 CDK6 CDK6 CDK6 10722 -0.017 0.066 NO
41 CYCS CYCS CYCS 11060 -0.022 0.05 NO
42 PTEN PTEN PTEN 11285 -0.024 0.04 NO
43 LRDD LRDD LRDD 11627 -0.03 0.024 NO
44 SHISA5 SHISA5 SHISA5 11815 -0.032 0.018 NO
45 TP53 TP53 TP53 11926 -0.034 0.015 NO
46 CCNG1 CCNG1 CCNG1 12155 -0.038 0.0066 NO
47 SESN1 SESN1 SESN1 12478 -0.042 -0.0066 NO
48 BAX BAX BAX 13147 -0.055 -0.038 NO
49 ZMAT3 ZMAT3 ZMAT3 13883 -0.071 -0.07 NO
50 CASP3 CASP3 CASP3 13885 -0.071 -0.063 NO
51 TNFRSF10B TNFRSF10B TNFRSF10B 14378 -0.084 -0.081 NO
52 PMAIP1 PMAIP1 PMAIP1 15010 -0.1 -0.1 NO
53 CD82 CD82 CD82 15075 -0.11 -0.097 NO
54 THBS1 THBS1 THBS1 15093 -0.11 -0.086 NO
55 RRM2B RRM2B RRM2B 15327 -0.12 -0.086 NO
56 IGFBP3 IGFBP3 IGFBP3 15828 -0.14 -0.099 NO
57 IGF1 IGF1 IGF1 15830 -0.14 -0.084 NO
58 CDKN1A CDKN1A CDKN1A 15853 -0.14 -0.071 NO
59 GADD45B GADD45B GADD45B 16177 -0.15 -0.072 NO
60 DDB2 DDB2 DDB2 16710 -0.19 -0.081 NO
61 GADD45A GADD45A GADD45A 16771 -0.19 -0.063 NO
62 SERPINE1 SERPINE1 SERPINE1 16777 -0.2 -0.042 NO
63 CASP8 CASP8 CASP8 17493 -0.26 -0.053 NO
64 FAS FAS FAS 17592 -0.28 -0.029 NO
65 SFN SFN SFN 17595 -0.28 0.0012 NO
66 PERP PERP PERP 17687 -0.29 0.028 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 HOMOLOGOUS RECOMBINATION.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA FAS PATHWAY 29 genes.ES.table 0.46 1.6 0.062 0.41 0.78 0.34 0.18 0.28 0.26 0.11
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.43 1.8 0.014 0.36 0.37 0.3 0.19 0.24 0 0.1
BIOCARTA IL2RB PATHWAY 37 genes.ES.table 0.66 1.7 0.017 0.49 0.57 0.4 0.15 0.34 0.25 0.15
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.55 1.7 0.018 0.43 0.61 0.5 0.19 0.41 0.22 0.12
BIOCARTA IL1R PATHWAY 31 genes.ES.table 0.58 1.6 0.041 0.3 0.84 0.52 0.19 0.42 0.2 0.043
KEGG GLUTATHIONE METABOLISM 42 genes.ES.table 0.49 1.6 0.029 0.36 0.78 0.5 0.24 0.38 0.23 0.082
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 42 genes.ES.table 0.55 1.8 0.016 0.63 0.33 0.69 0.32 0.47 0 0.21
KEGG PROTEASOME 43 genes.ES.table 0.51 1.6 0.076 0.35 0.81 0.56 0.35 0.36 0.22 0.079
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION 222 genes.ES.table 0.61 1.4 0.084 0.43 0.98 0.54 0.13 0.47 0.34 0.071
KEGG LYSOSOME 117 genes.ES.table 0.41 1.6 0.078 0.46 0.77 0.48 0.22 0.38 0.29 0.12
genes ES table in pathway: BIOCARTA FAS PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HK3 HK3 HK3 388 0.28 0.072 YES
2 GCK GCK GCK 666 0.23 0.13 YES
3 GFPT2 GFPT2 GFPT2 1311 0.17 0.16 YES
4 CHIT1 CHIT1 CHIT1 1599 0.15 0.19 YES
5 HEXB HEXB HEXB 1640 0.15 0.24 YES
6 HEXA HEXA HEXA 1819 0.14 0.27 YES
7 FPGT FPGT FPGT 2141 0.12 0.3 YES
8 RENBP RENBP RENBP 2174 0.12 0.34 YES
9 GMPPA GMPPA GMPPA 2274 0.12 0.37 YES
10 CYB5R1 CYB5R1 CYB5R1 2336 0.11 0.4 YES
11 GALK1 GALK1 GALK1 2598 0.1 0.42 YES
12 UGP2 UGP2 UGP2 3017 0.088 0.43 YES
13 UAP1 UAP1 UAP1 3246 0.081 0.44 YES
14 NPL NPL NPL 3522 0.073 0.45 YES
15 AMDHD2 AMDHD2 AMDHD2 4042 0.061 0.44 YES
16 GALK2 GALK2 GALK2 4315 0.056 0.45 YES
17 GNPNAT1 GNPNAT1 GNPNAT1 4497 0.052 0.46 YES
18 GNPDA1 GNPDA1 GNPDA1 4548 0.051 0.47 YES
19 PMM2 PMM2 PMM2 4571 0.051 0.49 YES
20 GPI GPI GPI 4579 0.05 0.5 YES
21 PGM2 PGM2 PGM2 4644 0.05 0.52 YES
22 PMM1 PMM1 PMM1 4837 0.046 0.52 YES
23 HK2 HK2 HK2 5005 0.043 0.53 YES
24 NANP NANP NANP 5293 0.038 0.52 YES
25 TSTA3 TSTA3 TSTA3 5423 0.036 0.53 YES
26 GMDS GMDS GMDS 5512 0.035 0.54 YES
27 GMPPB GMPPB GMPPB 5532 0.035 0.55 YES
28 UXS1 UXS1 UXS1 5798 0.031 0.54 YES
29 MPI MPI MPI 5877 0.03 0.55 YES
30 GALE GALE GALE 6174 0.026 0.54 NO
31 HK1 HK1 HK1 6434 0.023 0.53 NO
32 NANS NANS NANS 6576 0.021 0.53 NO
33 PGM3 PGM3 PGM3 6608 0.021 0.54 NO
34 FUK FUK FUK 7001 0.015 0.52 NO
35 CMAS CMAS CMAS 7151 0.014 0.52 NO
36 NAGK NAGK NAGK 7385 0.011 0.51 NO
37 GNPDA2 GNPDA2 GNPDA2 8424 -0.0018 0.45 NO
38 PGM1 PGM1 PGM1 8994 -0.0087 0.42 NO
39 GALT GALT GALT 10106 -0.024 0.37 NO
40 GFPT1 GFPT1 GFPT1 10979 -0.036 0.34 NO
41 UGDH UGDH UGDH 11304 -0.041 0.33 NO
42 GNE GNE GNE 14951 -0.14 0.18 NO

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

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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BIRC3 BIRC3 BIRC3 138 0.34 0.071 YES
2 CASP7 CASP7 CASP7 478 0.26 0.11 YES
3 FAS FAS FAS 551 0.25 0.16 YES
4 CASP8 CASP8 CASP8 608 0.24 0.22 YES
5 TRADD TRADD TRADD 1137 0.18 0.23 YES
6 TNFRSF1A TNFRSF1A TNFRSF1A 1316 0.17 0.26 YES
7 CASP6 CASP6 CASP6 1506 0.16 0.28 YES
8 TNFRSF1B TNFRSF1B TNFRSF1B 1737 0.14 0.3 YES
9 NFKBIA NFKBIA NFKBIA 1747 0.14 0.34 YES
10 LMNA LMNA LMNA 1896 0.13 0.36 YES
11 CFLAR CFLAR CFLAR 2272 0.12 0.36 YES
12 TRAF1 TRAF1 TRAF1 2690 0.099 0.36 YES
13 PSEN2 PSEN2 PSEN2 2768 0.096 0.38 YES
14 ARHGDIB ARHGDIB ARHGDIB 2815 0.095 0.4 YES
15 RIPK1 RIPK1 RIPK1 3077 0.086 0.41 YES
16 CASP3 CASP3 CASP3 3281 0.08 0.41 YES
17 NFKB1 NFKB1 NFKB1 3375 0.077 0.43 YES
18 PRKCD PRKCD PRKCD 4195 0.058 0.4 NO
19 CYCS CYCS CYCS 4761 0.048 0.37 NO
20 FADD FADD FADD 4778 0.047 0.38 NO
21 MAP3K14 MAP3K14 MAP3K14 5498 0.035 0.35 NO
22 RB1 RB1 RB1 5649 0.033 0.35 NO
23 MAP3K5 MAP3K5 MAP3K5 5669 0.033 0.36 NO
24 BIRC2 BIRC2 BIRC2 5705 0.032 0.36 NO
25 RASA1 RASA1 RASA1 5758 0.032 0.37 NO
26 GSN GSN GSN 6439 0.023 0.34 NO
27 XIAP XIAP XIAP 6607 0.021 0.33 NO
28 ACTG1 ACTG1 ACTG1 6622 0.02 0.34 NO
29 BAG4 BAG4 BAG4 7635 0.0075 0.28 NO
30 RELA RELA RELA 7818 0.0051 0.27 NO
31 DFFA DFFA DFFA 7822 0.005 0.27 NO
32 CRADD CRADD CRADD 7863 0.0045 0.27 NO
33 PAK2 PAK2 PAK2 8006 0.0027 0.26 NO
34 DAXX DAXX DAXX 8068 0.0021 0.26 NO
35 CHUK CHUK CHUK 8120 0.0016 0.26 NO
36 BID BID BID 8727 -0.0058 0.23 NO
37 PSEN1 PSEN1 PSEN1 8737 -0.0058 0.23 NO
38 CDK11B CDK11B CDK11B 9463 -0.015 0.19 NO
39 CASP2 CASP2 CASP2 9691 -0.018 0.18 NO
40 MDM2 MDM2 MDM2 9717 -0.018 0.19 NO
41 PRKDC PRKDC PRKDC 9977 -0.022 0.18 NO
42 BCL2 BCL2 BCL2 10033 -0.023 0.18 NO
43 TRAF2 TRAF2 TRAF2 10404 -0.028 0.16 NO
44 PARP1 PARP1 PARP1 10735 -0.032 0.16 NO
45 CDK11A CDK11A CDK11A 10830 -0.033 0.16 NO
46 PTK2 PTK2 PTK2 12188 -0.056 0.095 NO
47 MAP2K7 MAP2K7 MAP2K7 12221 -0.057 0.11 NO
48 SPTAN1 SPTAN1 SPTAN1 12478 -0.062 0.11 NO
49 NUMA1 NUMA1 NUMA1 12689 -0.066 0.11 NO
50 CASP9 CASP9 CASP9 12804 -0.07 0.12 NO
51 MAP3K1 MAP3K1 MAP3K1 12902 -0.072 0.13 NO
52 APAF1 APAF1 APAF1 13384 -0.084 0.12 NO
53 LMNB2 LMNB2 LMNB2 13888 -0.1 0.12 NO
54 DFFB DFFB DFFB 13906 -0.1 0.14 NO
55 TNF TNF TNF 13908 -0.1 0.16 NO
56 LMNB1 LMNB1 LMNB1 14903 -0.14 0.14 NO
57 MAPK8 MAPK8 MAPK8 15467 -0.17 0.15 NO

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

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

genes ES table in pathway: BIOCARTA IL2RB 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 IL2RA IL2RA IL2RA 27 0.44 0.11 YES
2 SOCS1 SOCS1 SOCS1 168 0.33 0.19 YES
3 IL2RB IL2RB IL2RB 444 0.27 0.24 YES
4 FAS FAS FAS 551 0.25 0.3 YES
5 SOCS3 SOCS3 SOCS3 646 0.24 0.36 YES
6 NMI NMI NMI 828 0.21 0.4 YES
7 FASLG FASLG FASLG 854 0.21 0.46 YES
8 IL2RG IL2RG IL2RG 1029 0.19 0.5 YES
9 SHC1 SHC1 SHC1 1164 0.18 0.54 YES
10 IKZF3 IKZF3 IKZF3 1442 0.16 0.56 YES
11 JAK3 JAK3 JAK3 1595 0.15 0.6 YES
12 PIK3CG PIK3CG PIK3CG 1609 0.15 0.63 YES
13 STAT5A STAT5A STAT5A 1995 0.13 0.64 YES
14 CFLAR CFLAR CFLAR 2272 0.12 0.66 YES
15 PTPN6 PTPN6 PTPN6 2723 0.098 0.66 YES
16 SYK SYK SYK 3205 0.082 0.66 NO
17 BCL2L1 BCL2L1 BCL2L1 4288 0.056 0.61 NO
18 PPIA PPIA PPIA 4422 0.054 0.62 NO
19 FOS FOS FOS 5396 0.037 0.57 NO
20 BAD BAD BAD 6121 0.027 0.54 NO
21 GRB2 GRB2 GRB2 7300 0.012 0.48 NO
22 HRAS HRAS HRAS 7460 0.0096 0.47 NO
23 AKT1 AKT1 AKT1 7692 0.0066 0.46 NO
24 PIK3CA PIK3CA PIK3CA 8126 0.0014 0.44 NO
25 RPS6KB1 RPS6KB1 RPS6KB1 9358 -0.013 0.37 NO
26 MAPK3 MAPK3 MAPK3 9494 -0.015 0.37 NO
27 JAK1 JAK1 JAK1 9582 -0.017 0.37 NO
28 MAPK1 MAPK1 MAPK1 9598 -0.017 0.37 NO
29 BCL2 BCL2 BCL2 10033 -0.023 0.36 NO
30 MYC MYC MYC 10305 -0.026 0.35 NO
31 STAT5B STAT5B STAT5B 10486 -0.029 0.34 NO
32 IRS1 IRS1 IRS1 10627 -0.031 0.34 NO
33 SOS1 SOS1 SOS1 11519 -0.045 0.31 NO
34 CBL CBL CBL 11908 -0.052 0.3 NO
35 CRKL CRKL CRKL 12068 -0.054 0.3 NO
36 RAF1 RAF1 RAF1 12445 -0.061 0.3 NO
37 PIK3R1 PIK3R1 PIK3R1 12640 -0.066 0.31 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 IL2RB PATHWAY.

Figure S26.  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 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 BIRC3 BIRC3 BIRC3 138 0.34 0.092 YES
2 CASP7 CASP7 CASP7 478 0.26 0.15 YES
3 TNFRSF10A TNFRSF10A TNFRSF10A 550 0.25 0.22 YES
4 CASP8 CASP8 CASP8 608 0.24 0.28 YES
5 TNFSF10 TNFSF10 TNFSF10 959 0.2 0.32 YES
6 TRADD TRADD TRADD 1137 0.18 0.37 YES
7 CASP6 CASP6 CASP6 1506 0.16 0.39 YES
8 NFKBIA NFKBIA NFKBIA 1747 0.14 0.42 YES
9 LMNA LMNA LMNA 1896 0.13 0.45 YES
10 CFLAR CFLAR CFLAR 2272 0.12 0.46 YES
11 TNFRSF10B TNFRSF10B TNFRSF10B 2529 0.1 0.48 YES
12 CASP10 CASP10 CASP10 2755 0.096 0.49 YES
13 TNFSF12 TNFSF12 TNFSF12 3028 0.088 0.5 YES
14 RIPK1 RIPK1 RIPK1 3077 0.086 0.53 YES
15 CASP3 CASP3 CASP3 3281 0.08 0.54 YES
16 NFKB1 NFKB1 NFKB1 3375 0.077 0.56 YES
17 CYCS CYCS CYCS 4761 0.048 0.49 NO
18 FADD FADD FADD 4778 0.047 0.5 NO
19 MAP3K14 MAP3K14 MAP3K14 5498 0.035 0.48 NO
20 BIRC2 BIRC2 BIRC2 5705 0.032 0.47 NO
21 XIAP XIAP XIAP 6607 0.021 0.43 NO
22 RELA RELA RELA 7818 0.0051 0.36 NO
23 DFFA DFFA DFFA 7822 0.005 0.37 NO
24 CHUK CHUK CHUK 8120 0.0016 0.35 NO
25 BCL2 BCL2 BCL2 10033 -0.023 0.25 NO
26 TRAF2 TRAF2 TRAF2 10404 -0.028 0.24 NO
27 SPTAN1 SPTAN1 SPTAN1 12478 -0.062 0.14 NO
28 CASP9 CASP9 CASP9 12804 -0.07 0.14 NO
29 APAF1 APAF1 APAF1 13384 -0.084 0.14 NO
30 DFFB DFFB DFFB 13906 -0.1 0.14 NO
31 TNFRSF25 TNFRSF25 TNFRSF25 14196 -0.11 0.15 NO
32 GAS2 GAS2 GAS2 16188 -0.23 0.11 NO

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

Figure S28.  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 IL1R PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FCGR2C FCGR2C FCGR2C 20 0.45 0.06 YES
2 NOS2 NOS2 NOS2 347 0.28 0.08 YES
3 MAPK13 MAPK13 MAPK13 454 0.26 0.11 YES
4 IL10 IL10 IL10 641 0.24 0.13 YES
5 CR1 CR1 CR1 688 0.23 0.16 YES
6 NCF4 NCF4 NCF4 961 0.2 0.17 YES
7 ITGA4 ITGA4 ITGA4 1050 0.19 0.19 YES
8 TLR2 TLR2 TLR2 1101 0.19 0.21 YES
9 FCGR2A FCGR2A FCGR2A 1117 0.19 0.24 YES
10 IL1A IL1A IL1A 1139 0.18 0.26 YES
11 HLA-DQA2 HLA-DQA2 HLA-DQA2 1416 0.16 0.27 YES
12 NCF1 NCF1 NCF1 1607 0.15 0.28 YES
13 ITGAM ITGAM ITGAM 1642 0.15 0.3 YES
14 NFKBIA NFKBIA NFKBIA 1747 0.14 0.31 YES
15 HLA-DMA HLA-DMA HLA-DMA 1750 0.14 0.33 YES
16 HLA-DPB1 HLA-DPB1 HLA-DPB1 1767 0.14 0.35 YES
17 NCF2 NCF2 NCF2 1783 0.14 0.36 YES
18 HLA-DRA HLA-DRA HLA-DRA 1789 0.14 0.38 YES
19 FCGR1A FCGR1A FCGR1A 1816 0.14 0.4 YES
20 HLA-DOB HLA-DOB HLA-DOB 1831 0.14 0.42 YES
21 TGFB2 TGFB2 TGFB2 1906 0.13 0.43 YES
22 FCGR3A FCGR3A FCGR3A 1908 0.13 0.45 YES
23 TGFB3 TGFB3 TGFB3 1966 0.13 0.46 YES
24 HLA-DQA1 HLA-DQA1 HLA-DQA1 1978 0.13 0.48 YES
25 CYBA CYBA CYBA 2039 0.13 0.49 YES
26 HLA-DOA HLA-DOA HLA-DOA 2097 0.12 0.51 YES
27 C3 C3 C3 2126 0.12 0.52 YES
28 IL1B IL1B IL1B 2134 0.12 0.54 YES
29 HLA-DPA1 HLA-DPA1 HLA-DPA1 2222 0.12 0.55 YES
30 HLA-DRB1 HLA-DRB1 HLA-DRB1 2263 0.12 0.56 YES
31 ITGB2 ITGB2 ITGB2 2324 0.11 0.57 YES
32 HLA-DMB HLA-DMB HLA-DMB 2685 0.099 0.57 YES
33 TGFB1 TGFB1 TGFB1 2688 0.099 0.58 YES
34 ITGB1 ITGB1 ITGB1 2689 0.099 0.59 YES
35 PTPN6 PTPN6 PTPN6 2723 0.098 0.6 YES
36 IL12A IL12A IL12A 2741 0.097 0.62 YES
37 HLA-DQB1 HLA-DQB1 HLA-DQB1 2761 0.096 0.63 YES
38 TRAF6 TRAF6 TRAF6 2928 0.091 0.63 YES
39 MYD88 MYD88 MYD88 2975 0.089 0.64 YES
40 IFNGR2 IFNGR2 IFNGR2 3012 0.088 0.65 YES
41 IRAK4 IRAK4 IRAK4 3044 0.087 0.66 YES
42 HLA-DRB5 HLA-DRB5 HLA-DRB5 3093 0.085 0.67 YES
43 NFKB1 NFKB1 NFKB1 3375 0.077 0.66 NO
44 STAT1 STAT1 STAT1 3690 0.069 0.66 NO
45 FCGR3B FCGR3B FCGR3B 4217 0.058 0.64 NO
46 JAK2 JAK2 JAK2 4284 0.056 0.64 NO
47 JUN JUN JUN 4470 0.053 0.64 NO
48 IFNGR1 IFNGR1 IFNGR1 4962 0.044 0.62 NO
49 FOS FOS FOS 5396 0.037 0.6 NO
50 IRAK1 IRAK1 IRAK1 5833 0.03 0.58 NO
51 MAPK14 MAPK14 MAPK14 6614 0.02 0.54 NO
52 NFKBIB NFKBIB NFKBIB 7428 0.01 0.49 NO
53 TAB2 TAB2 TAB2 7477 0.0094 0.49 NO
54 ELK1 ELK1 ELK1 7758 0.0058 0.48 NO
55 TLR4 TLR4 TLR4 7817 0.0051 0.47 NO
56 RELA RELA RELA 7818 0.0051 0.47 NO
57 MAP3K7 MAP3K7 MAP3K7 8986 -0.0086 0.41 NO
58 MAPK3 MAPK3 MAPK3 9494 -0.015 0.38 NO
59 JAK1 JAK1 JAK1 9582 -0.017 0.38 NO
60 MAPK1 MAPK1 MAPK1 9598 -0.017 0.38 NO
61 IFNG IFNG IFNG 9791 -0.019 0.38 NO
62 IL12B IL12B IL12B 9988 -0.022 0.37 NO
63 TAB1 TAB1 TAB1 10152 -0.024 0.36 NO
64 MAPK11 MAPK11 MAPK11 12419 -0.061 0.24 NO
65 MAPK12 MAPK12 MAPK12 12695 -0.067 0.24 NO
66 TNF TNF TNF 13908 -0.1 0.19 NO
67 MARCKSL1 MARCKSL1 MARCKSL1 15430 -0.17 0.12 NO
68 PRKCB PRKCB PRKCB 15929 -0.21 0.12 NO

Figure S29.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL1R PATHWAY.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG GLUTATHIONE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 LAMP3 LAMP3 LAMP3 460 0.26 0.0015 YES
2 CTSW CTSW CTSW 491 0.26 0.026 YES
3 AP1S3 AP1S3 AP1S3 1322 0.17 -0.0026 YES
4 GUSB GUSB GUSB 1412 0.16 0.009 YES
5 SLC11A1 SLC11A1 SLC11A1 1443 0.16 0.024 YES
6 TCIRG1 TCIRG1 TCIRG1 1453 0.16 0.039 YES
7 CTSS CTSS CTSS 1514 0.16 0.052 YES
8 SUMF1 SUMF1 SUMF1 1528 0.16 0.067 YES
9 CTSZ CTSZ CTSZ 1571 0.15 0.08 YES
10 HEXB HEXB HEXB 1640 0.15 0.091 YES
11 CTSH CTSH CTSH 1701 0.14 0.1 YES
12 FUCA1 FUCA1 FUCA1 1716 0.14 0.12 YES
13 NPC2 NPC2 NPC2 1793 0.14 0.13 YES
14 HEXA HEXA HEXA 1819 0.14 0.14 YES
15 CD63 CD63 CD63 1994 0.13 0.14 YES
16 CTSC CTSC CTSC 2010 0.13 0.16 YES
17 ATP6V0D2 ATP6V0D2 ATP6V0D2 2067 0.12 0.16 YES
18 AGA AGA AGA 2135 0.12 0.17 YES
19 CTSL1 CTSL1 CTSL1 2176 0.12 0.18 YES
20 CD164 CD164 CD164 2278 0.11 0.19 YES
21 GALNS GALNS GALNS 2319 0.11 0.2 YES
22 LAPTM4A LAPTM4A LAPTM4A 2468 0.11 0.2 YES
23 TPP1 TPP1 TPP1 2475 0.11 0.21 YES
24 LAPTM5 LAPTM5 LAPTM5 2484 0.11 0.22 YES
25 DNASE2 DNASE2 DNASE2 2509 0.1 0.23 YES
26 CTSK CTSK CTSK 2544 0.1 0.24 YES
27 CTSA CTSA CTSA 2605 0.1 0.25 YES
28 NEU1 NEU1 NEU1 2638 0.1 0.26 YES
29 ACP5 ACP5 ACP5 2644 0.1 0.26 YES
30 MAN2B1 MAN2B1 MAN2B1 2679 0.099 0.27 YES
31 CD68 CD68 CD68 2746 0.097 0.28 YES
32 LAMP2 LAMP2 LAMP2 2764 0.096 0.29 YES
33 CTSB CTSB CTSB 2772 0.096 0.3 YES
34 MANBA MANBA MANBA 2891 0.092 0.3 YES
35 CTSO CTSO CTSO 2918 0.091 0.31 YES
36 AP1S2 AP1S2 AP1S2 2966 0.09 0.32 YES
37 ARSG ARSG ARSG 2973 0.089 0.32 YES
38 AP4M1 AP4M1 AP4M1 3021 0.088 0.33 YES
39 MFSD8 MFSD8 MFSD8 3098 0.085 0.34 YES
40 GBA GBA GBA 3121 0.085 0.34 YES
41 GLB1 GLB1 GLB1 3125 0.085 0.35 YES
42 NAGA NAGA NAGA 3247 0.081 0.35 YES
43 GAA GAA GAA 3337 0.078 0.36 YES
44 CLN5 CLN5 CLN5 3419 0.076 0.36 YES
45 GALC GALC GALC 3483 0.075 0.36 YES
46 ARSA ARSA ARSA 3532 0.073 0.37 YES
47 SGSH SGSH SGSH 3541 0.073 0.37 YES
48 NAGLU NAGLU NAGLU 3658 0.07 0.38 YES
49 SMPD1 SMPD1 SMPD1 3714 0.069 0.38 YES
50 NAGPA NAGPA NAGPA 3776 0.067 0.38 YES
51 LGMN LGMN LGMN 3800 0.067 0.39 YES
52 GNPTG GNPTG GNPTG 3806 0.067 0.39 YES
53 CTSD CTSD CTSD 3809 0.066 0.4 YES
54 IDUA IDUA IDUA 3812 0.066 0.41 YES
55 GNS GNS GNS 3884 0.065 0.41 YES
56 ACP2 ACP2 ACP2 3939 0.064 0.41 YES
57 AP3B1 AP3B1 AP3B1 4167 0.058 0.41 NO
58 GM2A GM2A GM2A 4608 0.05 0.39 NO
59 GLA GLA GLA 4616 0.05 0.39 NO
60 AP3S1 AP3S1 AP3S1 4718 0.048 0.39 NO
61 NPC1 NPC1 NPC1 4860 0.046 0.39 NO
62 PPT1 PPT1 PPT1 4870 0.046 0.39 NO
63 ABCB9 ABCB9 ABCB9 5044 0.042 0.39 NO
64 CTNS CTNS CTNS 5070 0.042 0.39 NO
65 LAMP1 LAMP1 LAMP1 5162 0.04 0.39 NO
66 M6PR M6PR M6PR 5235 0.039 0.39 NO
67 PLA2G15 PLA2G15 PLA2G15 5254 0.039 0.39 NO
68 CTSF CTSF CTSF 5315 0.038 0.39 NO
69 ATP6V0B ATP6V0B ATP6V0B 5393 0.037 0.39 NO
70 PSAP PSAP PSAP 5828 0.031 0.37 NO
71 MCOLN1 MCOLN1 MCOLN1 6023 0.028 0.36 NO
72 CLTC CLTC CLTC 6178 0.026 0.36 NO
73 IGF2R IGF2R IGF2R 6205 0.026 0.36 NO
74 AP1B1 AP1B1 AP1B1 6726 0.019 0.33 NO
75 ASAH1 ASAH1 ASAH1 6818 0.018 0.33 NO
76 NAPSA NAPSA NAPSA 6833 0.018 0.33 NO
77 CLN3 CLN3 CLN3 6886 0.017 0.33 NO
78 ATP6AP1 ATP6AP1 ATP6AP1 7011 0.015 0.32 NO
79 AP4S1 AP4S1 AP4S1 7206 0.013 0.32 NO
80 SORT1 SORT1 SORT1 7213 0.013 0.32 NO
81 AP1S1 AP1S1 AP1S1 7291 0.012 0.31 NO
82 ARSB ARSB ARSB 7408 0.01 0.31 NO
83 IDS IDS IDS 7966 0.0032 0.28 NO
84 SLC17A5 SLC17A5 SLC17A5 8230 0.00042 0.26 NO
85 AP4E1 AP4E1 AP4E1 8463 -0.0023 0.25 NO
86 CLTB CLTB CLTB 9010 -0.0089 0.22 NO
87 AP3S2 AP3S2 AP3S2 9073 -0.0098 0.22 NO
88 AP1M1 AP1M1 AP1M1 9229 -0.012 0.21 NO
89 SCARB2 SCARB2 SCARB2 9278 -0.012 0.21 NO
90 CLTA CLTA CLTA 9312 -0.013 0.21 NO
91 SLC11A2 SLC11A2 SLC11A2 9357 -0.013 0.21 NO
92 ATP6V0D1 ATP6V0D1 ATP6V0D1 9417 -0.014 0.21 NO
93 LIPA LIPA LIPA 9491 -0.015 0.2 NO
94 ATP6V0C ATP6V0C ATP6V0C 9897 -0.021 0.18 NO
95 ATP6V1H ATP6V1H ATP6V1H 9902 -0.021 0.18 NO
96 AP3D1 AP3D1 AP3D1 10341 -0.027 0.16 NO
97 AP1G1 AP1G1 AP1G1 10477 -0.029 0.16 NO
98 GNPTAB GNPTAB GNPTAB 10549 -0.03 0.16 NO
99 GGA2 GGA2 GGA2 10658 -0.031 0.16 NO
100 GGA1 GGA1 GGA1 10815 -0.033 0.15 NO
101 CLTCL1 CLTCL1 CLTCL1 11115 -0.038 0.14 NO
102 AP4B1 AP4B1 AP4B1 11286 -0.041 0.13 NO
103 AP3M1 AP3M1 AP3M1 11556 -0.046 0.12 NO
104 PPT2 PPT2 PPT2 12159 -0.056 0.094 NO
105 ATP6V0A2 ATP6V0A2 ATP6V0A2 12460 -0.061 0.084 NO
106 AP3M2 AP3M2 AP3M2 12569 -0.064 0.084 NO
107 GGA3 GGA3 GGA3 12644 -0.066 0.087 NO
108 ENTPD4 ENTPD4 ENTPD4 13112 -0.078 0.069 NO
109 AP1M2 AP1M2 AP1M2 13364 -0.084 0.064 NO
110 LAPTM4B LAPTM4B LAPTM4B 13469 -0.087 0.067 NO
111 ATP6V0A1 ATP6V0A1 ATP6V0A1 13909 -0.1 0.053 NO
112 DNASE2B DNASE2B DNASE2B 14057 -0.1 0.055 NO
113 ABCA2 ABCA2 ABCA2 14560 -0.12 0.04 NO
114 CTSL2 CTSL2 CTSL2 16662 -0.28 -0.048 NO
115 AP3B2 AP3B2 AP3B2 16927 -0.31 -0.03 NO
116 HYAL1 HYAL1 HYAL1 16957 -0.32 0.00021 NO
117 ATP6V0A4 ATP6V0A4 ATP6V0A4 18057 -0.67 0.0075 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 GLUTATHIONE METABOLISM.

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

genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR 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 CASP7 CASP7 CASP7 478 0.26 0.075 YES
2 FAS FAS FAS 551 0.25 0.17 YES
3 CASP8 CASP8 CASP8 608 0.24 0.26 YES
4 FASLG FASLG FASLG 854 0.21 0.33 YES
5 CASP6 CASP6 CASP6 1506 0.16 0.35 YES
6 LMNA LMNA LMNA 1896 0.13 0.38 YES
7 CFLAR CFLAR CFLAR 2272 0.12 0.41 YES
8 CASP10 CASP10 CASP10 2755 0.096 0.42 YES
9 ARHGDIB ARHGDIB ARHGDIB 2815 0.095 0.45 YES
10 CASP3 CASP3 CASP3 3281 0.08 0.46 YES
11 JUN JUN JUN 4470 0.053 0.41 NO
12 FADD FADD FADD 4778 0.047 0.42 NO
13 RB1 RB1 RB1 5649 0.033 0.38 NO
14 FAF1 FAF1 FAF1 6171 0.026 0.36 NO
15 RIPK2 RIPK2 RIPK2 7121 0.014 0.31 NO
16 PTPN13 PTPN13 PTPN13 7461 0.0095 0.3 NO
17 DFFA DFFA DFFA 7822 0.005 0.28 NO
18 PAK2 PAK2 PAK2 8006 0.0027 0.27 NO
19 DAXX DAXX DAXX 8068 0.0021 0.27 NO
20 MAP3K7 MAP3K7 MAP3K7 8986 -0.0086 0.22 NO
21 PRKDC PRKDC PRKDC 9977 -0.022 0.18 NO
22 PARP1 PARP1 PARP1 10735 -0.032 0.15 NO
23 SPTAN1 SPTAN1 SPTAN1 12478 -0.062 0.076 NO
24 PAK1 PAK1 PAK1 12775 -0.069 0.086 NO
25 MAP3K1 MAP3K1 MAP3K1 12902 -0.072 0.11 NO
26 MAP2K4 MAP2K4 MAP2K4 13805 -0.097 0.096 NO
27 LMNB2 LMNB2 LMNB2 13888 -0.1 0.13 NO
28 DFFB DFFB DFFB 13906 -0.1 0.17 NO
29 MAPK8 MAPK8 MAPK8 15467 -0.17 0.15 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S34.  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 PROTEASOME

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 ANPEP ANPEP ANPEP 428 0.27 0.057 YES
2 OPLAH OPLAH OPLAH 971 0.2 0.086 YES
3 GSTM1 GSTM1 GSTM1 1267 0.17 0.12 YES
4 MGST1 MGST1 MGST1 1560 0.15 0.15 YES
5 GSTK1 GSTK1 GSTK1 1697 0.14 0.19 YES
6 MGST2 MGST2 MGST2 1762 0.14 0.23 YES
7 GCLM GCLM GCLM 1768 0.14 0.27 YES
8 GSTM5 GSTM5 GSTM5 1864 0.14 0.3 YES
9 LAP3 LAP3 LAP3 2269 0.12 0.31 YES
10 GGCT GGCT GGCT 2367 0.11 0.34 YES
11 GSTM4 GSTM4 GSTM4 2522 0.1 0.36 YES
12 GSTO1 GSTO1 GSTO1 2548 0.1 0.4 YES
13 GSTT1 GSTT1 GSTT1 2826 0.094 0.41 YES
14 RRM2B RRM2B RRM2B 2899 0.092 0.43 YES
15 SMS SMS SMS 2908 0.092 0.46 YES
16 GPX1 GPX1 GPX1 3501 0.074 0.45 YES
17 GPX7 GPX7 GPX7 3706 0.069 0.46 YES
18 G6PD G6PD G6PD 3769 0.067 0.47 YES
19 TXNDC12 TXNDC12 TXNDC12 3968 0.063 0.48 YES
20 GSTP1 GSTP1 GSTP1 4302 0.056 0.48 YES
21 IDH1 IDH1 IDH1 4453 0.053 0.49 YES
22 MGST3 MGST3 MGST3 5284 0.039 0.45 NO
23 GSR GSR GSR 5403 0.037 0.46 NO
24 GGT5 GGT5 GGT5 5438 0.036 0.47 NO
25 GPX4 GPX4 GPX4 5884 0.03 0.45 NO
26 GSTZ1 GSTZ1 GSTZ1 5977 0.029 0.46 NO
27 GSS GSS GSS 6841 0.018 0.41 NO
28 GPX3 GPX3 GPX3 6984 0.016 0.41 NO
29 GGT1 GGT1 GGT1 7303 0.012 0.4 NO
30 GSTM3 GSTM3 GSTM3 7944 0.0034 0.36 NO
31 RRM1 RRM1 RRM1 8173 0.00099 0.35 NO
32 SRM SRM SRM 8948 -0.0082 0.31 NO
33 GSTM2 GSTM2 GSTM2 9200 -0.011 0.3 NO
34 RRM2 RRM2 RRM2 10035 -0.023 0.26 NO
35 IDH2 IDH2 IDH2 10494 -0.029 0.24 NO
36 GCLC GCLC GCLC 10872 -0.034 0.23 NO
37 GSTT2 GSTT2 GSTT2 11555 -0.046 0.21 NO
38 GGT7 GGT7 GGT7 13314 -0.082 0.14 NO
39 ODC1 ODC1 ODC1 13456 -0.087 0.16 NO
40 GPX2 GPX2 GPX2 13607 -0.091 0.17 NO
41 GSTO2 GSTO2 GSTO2 13783 -0.096 0.19 NO
42 GSTA4 GSTA4 GSTA4 15365 -0.17 0.16 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 PROTEASOME.

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

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

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 PSMB9 PSMB9 PSMB9 852 0.21 0.063 YES
2 PSMA8 PSMA8 PSMA8 1389 0.16 0.12 YES
3 PSMB8 PSMB8 PSMB8 1436 0.16 0.2 YES
4 PSME2 PSME2 PSME2 1926 0.13 0.24 YES
5 PSME1 PSME1 PSME1 2240 0.12 0.29 YES
6 SHFM1 SHFM1 SHFM1 3222 0.082 0.27 YES
7 PSMA3 PSMA3 PSMA3 3294 0.08 0.31 YES
8 PSMA2 PSMA2 PSMA2 3882 0.065 0.31 YES
9 POMP POMP POMP 4162 0.058 0.33 YES
10 PSMC2 PSMC2 PSMC2 4313 0.056 0.35 YES
11 PSMD12 PSMD12 PSMD12 4336 0.056 0.38 YES
12 PSMA1 PSMA1 PSMA1 4362 0.055 0.4 YES
13 PSMA5 PSMA5 PSMA5 4432 0.054 0.43 YES
14 PSMA6 PSMA6 PSMA6 4657 0.049 0.44 YES
15 PSMC1 PSMC1 PSMC1 4985 0.043 0.45 YES
16 PSMD13 PSMD13 PSMD13 5090 0.042 0.46 YES
17 PSMB4 PSMB4 PSMB4 5420 0.036 0.46 YES
18 PSMC6 PSMC6 PSMC6 5525 0.035 0.48 YES
19 PSMA7 PSMA7 PSMA7 5549 0.035 0.49 YES
20 PSMB11 PSMB11 PSMB11 5914 0.029 0.49 YES
21 PSMD8 PSMD8 PSMD8 6153 0.026 0.49 YES
22 PSMD14 PSMD14 PSMD14 6167 0.026 0.5 YES
23 PSMA4 PSMA4 PSMA4 6286 0.025 0.51 YES
24 PSMB1 PSMB1 PSMB1 6419 0.023 0.51 YES
25 PSMB3 PSMB3 PSMB3 6736 0.019 0.5 NO
26 PSMC4 PSMC4 PSMC4 6911 0.016 0.5 NO
27 PSMD7 PSMD7 PSMD7 7025 0.015 0.5 NO
28 PSMC3 PSMC3 PSMC3 7159 0.013 0.5 NO
29 PSMF1 PSMF1 PSMF1 7223 0.013 0.51 NO
30 PSMB5 PSMB5 PSMB5 7447 0.0098 0.5 NO
31 PSMC5 PSMC5 PSMC5 7540 0.0086 0.5 NO
32 PSME4 PSME4 PSME4 7615 0.0077 0.5 NO
33 PSMB2 PSMB2 PSMB2 7840 0.0048 0.49 NO
34 PSMD4 PSMD4 PSMD4 7880 0.0043 0.49 NO
35 PSMD6 PSMD6 PSMD6 8644 -0.0046 0.45 NO
36 PSMB6 PSMB6 PSMB6 8899 -0.0078 0.44 NO
37 PSMD2 PSMD2 PSMD2 8920 -0.008 0.44 NO
38 PSMD1 PSMD1 PSMD1 9011 -0.0089 0.44 NO
39 PSME3 PSME3 PSME3 9176 -0.011 0.44 NO
40 PSMD11 PSMD11 PSMD11 9342 -0.013 0.44 NO
41 IFNG IFNG IFNG 9791 -0.019 0.42 NO
42 PSMD3 PSMD3 PSMD3 11019 -0.036 0.38 NO
43 PSMB7 PSMB7 PSMB7 11138 -0.038 0.39 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 CYTOKINE CYTOKINE RECEPTOR INTERACTION.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, 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 LYSOSOME

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 PRF1 PRF1 PRF1 186 0.32 0.06 YES
2 GZMB GZMB GZMB 488 0.26 0.099 YES
3 FAS FAS FAS 551 0.25 0.15 YES
4 IL10 IL10 IL10 641 0.24 0.2 YES
5 CD40LG CD40LG CD40LG 696 0.23 0.24 YES
6 FASLG FASLG FASLG 854 0.21 0.28 YES
7 HLA-G HLA-G HLA-G 1112 0.19 0.31 YES
8 CD86 CD86 CD86 1361 0.17 0.33 YES
9 HLA-DQA2 HLA-DQA2 HLA-DQA2 1416 0.16 0.36 YES
10 HLA-F HLA-F HLA-F 1437 0.16 0.39 YES
11 HLA-B HLA-B HLA-B 1573 0.15 0.42 YES
12 HLA-DMA HLA-DMA HLA-DMA 1750 0.14 0.44 YES
13 HLA-DPB1 HLA-DPB1 HLA-DPB1 1767 0.14 0.47 YES
14 HLA-DRA HLA-DRA HLA-DRA 1789 0.14 0.5 YES
15 CD40 CD40 CD40 1809 0.14 0.53 YES
16 HLA-DOB HLA-DOB HLA-DOB 1831 0.14 0.56 YES
17 HLA-A HLA-A HLA-A 1960 0.13 0.58 YES
18 HLA-DQA1 HLA-DQA1 HLA-DQA1 1978 0.13 0.6 YES
19 HLA-C HLA-C HLA-C 1982 0.13 0.63 YES
20 HLA-DOA HLA-DOA HLA-DOA 2097 0.12 0.65 YES
21 CD80 CD80 CD80 2143 0.12 0.68 YES
22 HLA-DPA1 HLA-DPA1 HLA-DPA1 2222 0.12 0.7 YES
23 HLA-DRB1 HLA-DRB1 HLA-DRB1 2263 0.12 0.72 YES
24 CD28 CD28 CD28 2555 0.1 0.72 YES
25 HLA-DMB HLA-DMB HLA-DMB 2685 0.099 0.74 YES
26 IL12A IL12A IL12A 2741 0.097 0.76 YES
27 HLA-E HLA-E HLA-E 2778 0.096 0.78 YES
28 HLA-DRB5 HLA-DRB5 HLA-DRB5 3093 0.085 0.78 YES
29 IFNG IFNG IFNG 9791 -0.019 0.41 NO
30 IL12B IL12B IL12B 9988 -0.022 0.41 NO
31 TNF TNF TNF 13908 -0.1 0.21 NO
32 IL5 IL5 IL5 14213 -0.11 0.22 NO

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

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA NO1 PATHWAY 27 genes.ES.table 0.59 1.5 0.063 0.21 0.94 0.15 0.036 0.14 0.17 0.003
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.53 1.5 0.027 0.19 0.87 0.2 0.12 0.18 0.13 0.003
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.48 1.9 0.014 0.08 0.22 0.53 0.35 0.35 0 0.008
BIOCARTA BIOPEPTIDES PATHWAY 37 genes.ES.table 0.57 2 0 0.088 0.044 0.16 0.13 0.14 0 0.033
BIOCARTA HDAC PATHWAY 27 genes.ES.table 0.5 1.6 0.035 0.15 0.76 0.44 0.27 0.32 0.098 0.004
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.47 1.6 0.051 0.14 0.73 0.4 0.34 0.27 0.085 0.003
BIOCARTA FMLP PATHWAY 34 genes.ES.table 0.42 1.5 0.09 0.21 0.94 0.029 0.0029 0.029 0.16 0.003
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.47 1.8 0.012 0.07 0.28 0.44 0.35 0.29 0 0.001
BIOCARTA CHREBP2 PATHWAY 40 genes.ES.table 0.47 1.7 0.018 0.089 0.47 0.22 0.25 0.17 0 0.001
BIOCARTA GPCR PATHWAY 31 genes.ES.table 0.52 1.8 0.016 0.07 0.32 0.52 0.34 0.34 0 0.001
genes ES table in pathway: BIOCARTA NO1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CAMK2A CAMK2A CAMK2A 96 0.78 0.24 YES
2 CAMK2B CAMK2B CAMK2B 543 0.39 0.34 YES
3 PRKCB PRKCB PRKCB 554 0.39 0.47 YES
4 STAT4 STAT4 STAT4 861 0.3 0.55 YES
5 CAMK2G CAMK2G CAMK2G 2118 0.16 0.53 YES
6 PTK2B PTK2B PTK2B 2359 0.15 0.57 YES
7 CALM1 CALM1 CALM1 3335 0.1 0.55 NO
8 MAPT MAPT MAPT 3957 0.083 0.54 NO
9 PRKCA PRKCA PRKCA 4229 0.076 0.55 NO
10 CALM3 CALM3 CALM3 4909 0.06 0.53 NO
11 MAPK3 MAPK3 MAPK3 5335 0.052 0.52 NO
12 AGT AGT AGT 5407 0.051 0.54 NO
13 STAT2 STAT2 STAT2 5681 0.046 0.54 NO
14 MAP2K1 MAP2K1 MAP2K1 6020 0.041 0.53 NO
15 PLCG1 PLCG1 PLCG1 6101 0.039 0.54 NO
16 MAPK1 MAPK1 MAPK1 6306 0.037 0.54 NO
17 CAMK2D CAMK2D CAMK2D 6778 0.03 0.52 NO
18 STAT1 STAT1 STAT1 7538 0.021 0.49 NO
19 GNA11 GNA11 GNA11 7556 0.021 0.49 NO
20 SOS1 SOS1 SOS1 8320 0.013 0.46 NO
21 FYN FYN FYN 8382 0.012 0.46 NO
22 MAP2K2 MAP2K2 MAP2K2 8805 0.008 0.43 NO
23 STAT5B STAT5B STAT5B 8934 0.0067 0.43 NO
24 JAK2 JAK2 JAK2 8948 0.0066 0.43 NO
25 STAT5A STAT5A STAT5A 9266 0.0036 0.41 NO
26 STAT6 STAT6 STAT6 9542 0.0011 0.4 NO
27 GRB2 GRB2 GRB2 9719 -0.00039 0.39 NO
28 CALM2 CALM2 CALM2 9810 -0.0011 0.38 NO
29 GNB1 GNB1 GNB1 10391 -0.0061 0.36 NO
30 STAT3 STAT3 STAT3 10885 -0.01 0.33 NO
31 RAF1 RAF1 RAF1 11501 -0.016 0.3 NO
32 MAPK8 MAPK8 MAPK8 11668 -0.017 0.3 NO
33 CDK5 CDK5 CDK5 11713 -0.018 0.3 NO
34 MYLK MYLK MYLK 12104 -0.021 0.29 NO
35 MAPK14 MAPK14 MAPK14 12758 -0.027 0.26 NO
36 GNAI1 GNAI1 GNAI1 15028 -0.055 0.15 NO
37 SHC1 SHC1 SHC1 15636 -0.067 0.14 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 CREB3L3 CREB3L3 CREB3L3 692 0.35 0.1 YES
2 DYNC1I1 DYNC1I1 DYNC1I1 727 0.34 0.24 YES
3 AQP3 AQP3 AQP3 1838 0.18 0.25 YES
4 AQP2 AQP2 AQP2 2428 0.15 0.28 YES
5 VAMP2 VAMP2 VAMP2 2591 0.14 0.32 YES
6 NSF NSF NSF 2985 0.12 0.35 YES
7 CREB3L1 CREB3L1 CREB3L1 3193 0.11 0.38 YES
8 AQP4 AQP4 AQP4 3244 0.11 0.42 YES
9 DYNC1LI2 DYNC1LI2 DYNC1LI2 4450 0.071 0.38 YES
10 PRKACB PRKACB PRKACB 4474 0.07 0.41 YES
11 DYNC1H1 DYNC1H1 DYNC1H1 4568 0.068 0.43 YES
12 DYNC2H1 DYNC2H1 DYNC2H1 4591 0.067 0.46 YES
13 DYNLL2 DYNLL2 DYNLL2 4595 0.067 0.48 YES
14 CREB5 CREB5 CREB5 5976 0.041 0.43 NO
15 DCTN1 DCTN1 DCTN1 6114 0.039 0.43 NO
16 RAB11B RAB11B RAB11B 6313 0.037 0.44 NO
17 RAB5B RAB5B RAB5B 6721 0.031 0.43 NO
18 RAB5A RAB5A RAB5A 6909 0.029 0.43 NO
19 ADCY6 ADCY6 ADCY6 6962 0.028 0.44 NO
20 DYNC2LI1 DYNC2LI1 DYNC2LI1 7094 0.027 0.44 NO
21 GNAS GNAS GNAS 7591 0.021 0.42 NO
22 PRKACA PRKACA PRKACA 8009 0.016 0.41 NO
23 PRKX PRKX PRKX 8095 0.015 0.41 NO
24 ADCY9 ADCY9 ADCY9 8455 0.011 0.39 NO
25 DCTN6 DCTN6 DCTN6 8506 0.011 0.39 NO
26 DYNC1I2 DYNC1I2 DYNC1I2 9551 0.0011 0.34 NO
27 RAB11A RAB11A RAB11A 9749 -0.00063 0.33 NO
28 ARHGDIA ARHGDIA ARHGDIA 10599 -0.008 0.28 NO
29 DYNC1LI1 DYNC1LI1 DYNC1LI1 10741 -0.0092 0.28 NO
30 DCTN4 DCTN4 DCTN4 11064 -0.012 0.26 NO
31 CREB1 CREB1 CREB1 11187 -0.013 0.26 NO
32 RAB5C RAB5C RAB5C 11190 -0.013 0.27 NO
33 DCTN2 DCTN2 DCTN2 11278 -0.014 0.27 NO
34 STX4 STX4 STX4 11637 -0.017 0.26 NO
35 DCTN5 DCTN5 DCTN5 11904 -0.019 0.25 NO
36 DYNLL1 DYNLL1 DYNLL1 12141 -0.022 0.25 NO
37 CREB3 CREB3 CREB3 12547 -0.025 0.23 NO
38 AVPR2 AVPR2 AVPR2 14106 -0.042 0.16 NO
39 CREB3L2 CREB3L2 CREB3L2 14612 -0.049 0.16 NO
40 ARHGDIB ARHGDIB ARHGDIB 14715 -0.05 0.17 NO
41 CREB3L4 CREB3L4 CREB3L4 14766 -0.051 0.19 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 SNAP25 SNAP25 SNAP25 252 0.58 0.18 YES
2 STX1B STX1B STX1B 493 0.42 0.3 YES
3 STX1A STX1A STX1A 668 0.36 0.41 YES
4 VAMP1 VAMP1 VAMP1 987 0.28 0.49 YES
5 STX19 STX19 STX19 1492 0.22 0.53 YES
6 VAMP2 VAMP2 VAMP2 2591 0.14 0.52 NO
7 TSNARE1 TSNARE1 TSNARE1 3154 0.11 0.52 NO
8 STX17 STX17 STX17 4908 0.06 0.44 NO
9 STX16 STX16 STX16 5955 0.042 0.4 NO
10 VTI1B VTI1B VTI1B 6421 0.036 0.39 NO
11 STX7 STX7 STX7 7101 0.026 0.36 NO
12 SNAP47 SNAP47 SNAP47 7640 0.02 0.34 NO
13 STX3 STX3 STX3 7816 0.018 0.33 NO
14 USE1 USE1 USE1 8932 0.0067 0.27 NO
15 STX2 STX2 STX2 9182 0.0043 0.26 NO
16 VAMP4 VAMP4 VAMP4 10125 -0.0039 0.21 NO
17 GOSR1 GOSR1 GOSR1 10632 -0.0083 0.18 NO
18 YKT6 YKT6 YKT6 10853 -0.01 0.18 NO
19 STX12 STX12 STX12 10950 -0.011 0.17 NO
20 VAMP3 VAMP3 VAMP3 11169 -0.013 0.17 NO
21 SNAP23 SNAP23 SNAP23 11274 -0.014 0.16 NO
22 BET1L BET1L BET1L 11446 -0.015 0.16 NO
23 STX18 STX18 STX18 11519 -0.016 0.16 NO
24 VTI1A VTI1A VTI1A 11590 -0.016 0.16 NO
25 GOSR2 GOSR2 GOSR2 11592 -0.016 0.17 NO
26 STX4 STX4 STX4 11637 -0.017 0.17 NO
27 STX6 STX6 STX6 11685 -0.017 0.18 NO
28 STX5 STX5 STX5 12187 -0.022 0.15 NO
29 STX10 STX10 STX10 12981 -0.03 0.12 NO
30 VAMP5 VAMP5 VAMP5 13620 -0.036 0.097 NO
31 STX8 STX8 STX8 13751 -0.038 0.1 NO
32 SEC22B SEC22B SEC22B 13969 -0.04 0.1 NO
33 VAMP7 VAMP7 VAMP7 14017 -0.041 0.12 NO
34 BET1 BET1 BET1 15506 -0.064 0.054 NO
35 BNIP1 BNIP1 BNIP1 16195 -0.083 0.044 NO
36 STX11 STX11 STX11 16462 -0.094 0.06 NO
37 VAMP8 VAMP8 VAMP8 16736 -0.11 0.08 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 GRIN1 GRIN1 GRIN1 24 0.98 0.13 YES
2 NEFM NEFM NEFM 78 0.81 0.24 YES
3 NEFH NEFH NEFH 191 0.64 0.32 YES
4 NEFL NEFL NEFL 195 0.64 0.4 YES
5 GRIN2A GRIN2A GRIN2A 304 0.53 0.47 YES
6 PRPH2 PRPH2 PRPH2 548 0.39 0.51 YES
7 GRIN2C GRIN2C GRIN2C 818 0.32 0.54 YES
8 NOS1 NOS1 NOS1 843 0.31 0.58 YES
9 CHP2 CHP2 CHP2 1075 0.26 0.6 YES
10 SLC1A2 SLC1A2 SLC1A2 1091 0.26 0.64 YES
11 GRIA2 GRIA2 GRIA2 1860 0.18 0.62 NO
12 TNF TNF TNF 2912 0.12 0.58 NO
13 GRIN2B GRIN2B GRIN2B 3208 0.11 0.58 NO
14 MAP3K5 MAP3K5 MAP3K5 3468 0.097 0.57 NO
15 MAPK11 MAPK11 MAPK11 3593 0.093 0.58 NO
16 BCL2 BCL2 BCL2 3791 0.087 0.58 NO
17 PPP3CB PPP3CB PPP3CB 3861 0.085 0.59 NO
18 GRIA1 GRIA1 GRIA1 3883 0.085 0.6 NO
19 GRIN2D GRIN2D GRIN2D 4277 0.075 0.59 NO
20 PPP3R1 PPP3R1 PPP3R1 4396 0.072 0.59 NO
21 PPP3CA PPP3CA PPP3CA 4531 0.069 0.59 NO
22 CHP CHP CHP 6742 0.031 0.48 NO
23 RAB5A RAB5A RAB5A 6909 0.029 0.47 NO
24 CCS CCS CCS 7238 0.025 0.46 NO
25 PRPH PRPH PRPH 7307 0.024 0.46 NO
26 CASP9 CASP9 CASP9 7328 0.024 0.46 NO
27 MAPK12 MAPK12 MAPK12 8176 0.014 0.41 NO
28 SOD1 SOD1 SOD1 9034 0.0059 0.37 NO
29 TP53 TP53 TP53 9428 0.0021 0.34 NO
30 BCL2L1 BCL2L1 BCL2L1 10423 -0.0064 0.29 NO
31 RAC1 RAC1 RAC1 10747 -0.0092 0.27 NO
32 BAD BAD BAD 10768 -0.0093 0.28 NO
33 APAF1 APAF1 APAF1 10884 -0.01 0.27 NO
34 MAP2K3 MAP2K3 MAP2K3 11035 -0.012 0.26 NO
35 TOMM40L TOMM40L TOMM40L 11212 -0.013 0.26 NO
36 CAT CAT CAT 11444 -0.015 0.24 NO
37 CASP3 CASP3 CASP3 12671 -0.027 0.18 NO
38 TNFRSF1A TNFRSF1A TNFRSF1A 12678 -0.027 0.18 NO
39 MAPK14 MAPK14 MAPK14 12758 -0.027 0.18 NO
40 CASP1 CASP1 CASP1 13298 -0.033 0.16 NO
41 TOMM40 TOMM40 TOMM40 13342 -0.034 0.16 NO
42 GPX1 GPX1 GPX1 13488 -0.035 0.16 NO
43 CYCS CYCS CYCS 13961 -0.04 0.14 NO
44 BAX BAX BAX 14161 -0.043 0.13 NO
45 DAXX DAXX DAXX 14677 -0.05 0.11 NO
46 PPP3CC PPP3CC PPP3CC 14810 -0.052 0.11 NO
47 DERL1 DERL1 DERL1 14902 -0.053 0.11 NO
48 BID BID BID 15495 -0.064 0.087 NO
49 MAP2K6 MAP2K6 MAP2K6 15632 -0.067 0.089 NO
50 TNFRSF1B TNFRSF1B TNFRSF1B 16314 -0.087 0.063 NO
51 PPP3R2 PPP3R2 PPP3R2 17061 -0.13 0.039 NO
52 MAPK13 MAPK13 MAPK13 17521 -0.17 0.037 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 PRKCG PRKCG PRKCG 68 0.83 0.072 YES
2 GJD2 GJD2 GJD2 173 0.67 0.13 YES
3 HTR2C HTR2C HTR2C 196 0.64 0.18 YES
4 HTR2A HTR2A HTR2A 199 0.63 0.24 YES
5 DRD1 DRD1 DRD1 219 0.61 0.3 YES
6 GRM1 GRM1 GRM1 313 0.52 0.34 YES
7 TUBA8 TUBA8 TUBA8 339 0.5 0.38 YES
8 GRM5 GRM5 GRM5 352 0.49 0.43 YES
9 PRKCB PRKCB PRKCB 554 0.39 0.45 YES
10 ADRB1 ADRB1 ADRB1 566 0.39 0.49 YES
11 TUBAL3 TUBAL3 TUBAL3 907 0.29 0.5 YES
12 TUBB4 TUBB4 TUBB4 1001 0.28 0.52 YES
13 TUBA3D TUBA3D TUBA3D 1002 0.28 0.54 YES
14 ADCY1 ADCY1 ADCY1 1283 0.24 0.55 YES
15 TUBA4A TUBA4A TUBA4A 1378 0.23 0.56 YES
16 ADCY5 ADCY5 ADCY5 1546 0.21 0.57 YES
17 EGFR EGFR EGFR 1708 0.2 0.58 YES
18 TUBA3E TUBA3E TUBA3E 1743 0.19 0.6 YES
19 GJA1 GJA1 GJA1 2407 0.15 0.58 NO
20 ADCY4 ADCY4 ADCY4 2736 0.13 0.57 NO
21 ADCY2 ADCY2 ADCY2 2865 0.12 0.57 NO
22 EGF EGF EGF 3444 0.098 0.55 NO
23 ITPR1 ITPR1 ITPR1 3465 0.097 0.56 NO
24 PLCB2 PLCB2 PLCB2 3606 0.092 0.56 NO
25 TJP1 TJP1 TJP1 3711 0.089 0.56 NO
26 GNAQ GNAQ GNAQ 3911 0.084 0.56 NO
27 GUCY1B3 GUCY1B3 GUCY1B3 4105 0.079 0.56 NO
28 PRKCA PRKCA PRKCA 4229 0.076 0.56 NO
29 LPAR1 LPAR1 LPAR1 4301 0.074 0.56 NO
30 PRKACB PRKACB PRKACB 4474 0.07 0.56 NO
31 PLCB4 PLCB4 PLCB4 4485 0.07 0.56 NO
32 ITPR2 ITPR2 ITPR2 4821 0.062 0.55 NO
33 MAPK3 MAPK3 MAPK3 5335 0.052 0.52 NO
34 TUBB1 TUBB1 TUBB1 5496 0.049 0.52 NO
35 ADCY8 ADCY8 ADCY8 5662 0.046 0.52 NO
36 TUBB2A TUBB2A TUBB2A 5782 0.045 0.51 NO
37 MAP2K1 MAP2K1 MAP2K1 6020 0.041 0.5 NO
38 PDGFA PDGFA PDGFA 6026 0.041 0.51 NO
39 MAPK1 MAPK1 MAPK1 6306 0.037 0.5 NO
40 PDGFB PDGFB PDGFB 6465 0.035 0.49 NO
41 ADCY6 ADCY6 ADCY6 6962 0.028 0.46 NO
42 TUBB2B TUBB2B TUBB2B 6985 0.028 0.47 NO
43 PLCB1 PLCB1 PLCB1 7053 0.027 0.46 NO
44 HRAS HRAS HRAS 7136 0.026 0.46 NO
45 SOS2 SOS2 SOS2 7445 0.023 0.45 NO
46 CSNK1D CSNK1D CSNK1D 7536 0.021 0.44 NO
47 GNA11 GNA11 GNA11 7556 0.021 0.45 NO
48 ITPR3 ITPR3 ITPR3 7581 0.021 0.45 NO
49 GNAS GNAS GNAS 7591 0.021 0.45 NO
50 MAP2K5 MAP2K5 MAP2K5 7794 0.018 0.44 NO
51 PRKACA PRKACA PRKACA 8009 0.016 0.43 NO
52 PRKX PRKX PRKX 8095 0.015 0.42 NO
53 SOS1 SOS1 SOS1 8320 0.013 0.41 NO
54 PRKG1 PRKG1 PRKG1 8374 0.012 0.41 NO
55 TUBB8 TUBB8 TUBB8 8422 0.012 0.41 NO
56 ADCY9 ADCY9 ADCY9 8455 0.011 0.41 NO
57 PRKG2 PRKG2 PRKG2 8674 0.0093 0.4 NO
58 MAP2K2 MAP2K2 MAP2K2 8805 0.008 0.39 NO
59 KRAS KRAS KRAS 9197 0.0042 0.37 NO
60 GRB2 GRB2 GRB2 9719 -0.00039 0.34 NO
61 GUCY1A3 GUCY1A3 GUCY1A3 9900 -0.0019 0.33 NO
62 GNAI2 GNAI2 GNAI2 9965 -0.0025 0.33 NO
63 ADCY7 ADCY7 ADCY7 10067 -0.0035 0.32 NO
64 TUBB3 TUBB3 TUBB3 10232 -0.0048 0.32 NO
65 PLCB3 PLCB3 PLCB3 10468 -0.0068 0.3 NO
66 TUBB2C TUBB2C TUBB2C 10743 -0.0092 0.29 NO
67 RAF1 RAF1 RAF1 11501 -0.016 0.25 NO
68 DRD2 DRD2 DRD2 11612 -0.017 0.24 NO
69 PDGFRB PDGFRB PDGFRB 12025 -0.02 0.22 NO
70 TUBA1A TUBA1A TUBA1A 12555 -0.026 0.2 NO
71 SRC SRC SRC 12724 -0.027 0.19 NO
72 MAP3K2 MAP3K2 MAP3K2 13339 -0.034 0.16 NO
73 TUBA1B TUBA1B TUBA1B 14005 -0.041 0.12 NO
74 MAPK7 MAPK7 MAPK7 14182 -0.043 0.12 NO
75 GNAI3 GNAI3 GNAI3 14783 -0.051 0.09 NO
76 GNAI1 GNAI1 GNAI1 15028 -0.055 0.082 NO
77 TUBB TUBB TUBB 15039 -0.055 0.086 NO
78 NRAS NRAS NRAS 15282 -0.06 0.078 NO
79 TUBA1C TUBA1C TUBA1C 15333 -0.061 0.081 NO
80 PDGFC PDGFC PDGFC 15622 -0.066 0.072 NO
81 GUCY1A2 GUCY1A2 GUCY1A2 15670 -0.068 0.075 NO
82 PDGFRA PDGFRA PDGFRA 16239 -0.084 0.052 NO
83 TUBB6 TUBB6 TUBB6 16482 -0.094 0.047 NO
84 PDGFD PDGFD PDGFD 17226 -0.14 0.019 NO
85 HTR2B HTR2B HTR2B 17489 -0.17 0.02 NO
86 CDK1 CDK1 CDK1 17799 -0.21 0.022 NO

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

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

genes ES table in pathway: BIOCARTA EGF PATHWAY

Table S26.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 554 0.39 0.17 YES
2 EGFR EGFR EGFR 1708 0.2 0.2 YES
3 PTK2B PTK2B PTK2B 2359 0.15 0.24 YES
4 CALM1 CALM1 CALM1 3335 0.1 0.24 YES
5 PAK1 PAK1 PAK1 3539 0.094 0.28 YES
6 GNAQ GNAQ GNAQ 3911 0.084 0.3 YES
7 PRKCA PRKCA PRKCA 4229 0.076 0.32 YES
8 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 4272 0.075 0.36 YES
9 MEF2D MEF2D MEF2D 4793 0.063 0.36 YES
10 MEF2A MEF2A MEF2A 4841 0.062 0.39 YES
11 CALM3 CALM3 CALM3 4909 0.06 0.42 YES
12 MAP2K4 MAP2K4 MAP2K4 4963 0.059 0.44 YES
13 MAPK3 MAPK3 MAPK3 5335 0.052 0.45 YES
14 AGT AGT AGT 5407 0.051 0.47 YES
15 MAP2K1 MAP2K1 MAP2K1 6020 0.041 0.46 YES
16 ELK1 ELK1 ELK1 6120 0.039 0.48 YES
17 MAPK1 MAPK1 MAPK1 6306 0.037 0.48 YES
18 HRAS HRAS HRAS 7136 0.026 0.45 NO
19 MAP3K1 MAP3K1 MAP3K1 7313 0.024 0.45 NO
20 PTK2 PTK2 PTK2 7988 0.016 0.42 NO
21 SOS1 SOS1 SOS1 8320 0.013 0.41 NO
22 MAP2K2 MAP2K2 MAP2K2 8805 0.008 0.39 NO
23 GRB2 GRB2 GRB2 9719 -0.00039 0.34 NO
24 CALM2 CALM2 CALM2 9810 -0.0011 0.34 NO
25 RAC1 RAC1 RAC1 10747 -0.0092 0.29 NO
26 RAF1 RAF1 RAF1 11501 -0.016 0.26 NO
27 MAPK8 MAPK8 MAPK8 11668 -0.017 0.26 NO
28 JUN JUN JUN 12008 -0.02 0.25 NO
29 ATF2 ATF2 ATF2 12069 -0.021 0.25 NO
30 SRC SRC SRC 12724 -0.027 0.23 NO
31 SHC1 SHC1 SHC1 15636 -0.067 0.1 NO
32 AGTR1 AGTR1 AGTR1 15741 -0.07 0.14 NO

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

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

genes ES table in pathway: BIOCARTA FMLP 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 CAMK2A CAMK2A CAMK2A 96 0.78 0.28 YES
2 CAMK2B CAMK2B CAMK2B 543 0.39 0.4 YES
3 PRKCB PRKCB PRKCB 554 0.39 0.55 YES
4 PRKAR1B PRKAR1B PRKAR1B 1980 0.17 0.53 YES
5 CAMK2G CAMK2G CAMK2G 2118 0.16 0.58 YES
6 RPS6KA5 RPS6KA5 RPS6KA5 2854 0.12 0.59 YES
7 PRKCA PRKCA PRKCA 4229 0.076 0.54 YES
8 PRKACB PRKACB PRKACB 4474 0.07 0.55 YES
9 PRKAR2B PRKAR2B PRKAR2B 4616 0.067 0.57 YES
10 PIK3R1 PIK3R1 PIK3R1 4683 0.065 0.59 YES
11 MAPK3 MAPK3 MAPK3 5335 0.052 0.57 NO
12 MAPK1 MAPK1 MAPK1 6306 0.037 0.53 NO
13 AKT1 AKT1 AKT1 6573 0.033 0.53 NO
14 CAMK2D CAMK2D CAMK2D 6778 0.03 0.53 NO
15 HRAS HRAS HRAS 7136 0.026 0.52 NO
16 GNAS GNAS GNAS 7591 0.021 0.5 NO
17 SOS1 SOS1 SOS1 8320 0.013 0.47 NO
18 PRKAR1A PRKAR1A PRKAR1A 8927 0.0068 0.44 NO
19 GRB2 GRB2 GRB2 9719 -0.00039 0.39 NO
20 RAC1 RAC1 RAC1 10747 -0.0092 0.34 NO
21 CREB1 CREB1 CREB1 11187 -0.013 0.32 NO
22 MAPK14 MAPK14 MAPK14 12758 -0.027 0.24 NO
23 PRKAR2A PRKAR2A PRKAR2A 13498 -0.035 0.22 NO
24 RPS6KA1 RPS6KA1 RPS6KA1 14140 -0.042 0.2 NO
25 PIK3CA PIK3CA PIK3CA 15730 -0.069 0.14 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 FMLP PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 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 68 0.83 0.12 YES
2 CDS1 CDS1 CDS1 476 0.42 0.15 YES
3 INPP5J INPP5J INPP5J 528 0.4 0.21 YES
4 PRKCB PRKCB PRKCB 554 0.39 0.26 YES
5 DGKE DGKE DGKE 589 0.38 0.32 YES
6 PIP5K1B PIP5K1B PIP5K1B 640 0.36 0.36 YES
7 ITPKA ITPKA ITPKA 886 0.3 0.39 YES
8 CALML6 CALML6 CALML6 1062 0.27 0.42 YES
9 SYNJ2 SYNJ2 SYNJ2 2064 0.17 0.39 YES
10 DGKZ DGKZ DGKZ 2361 0.15 0.4 YES
11 DGKB DGKB DGKB 2527 0.14 0.41 YES
12 PI4KA PI4KA PI4KA 2778 0.13 0.41 YES
13 SYNJ1 SYNJ1 SYNJ1 2920 0.12 0.42 YES
14 INPP4B INPP4B INPP4B 3034 0.11 0.43 YES
15 INPP5A INPP5A INPP5A 3147 0.11 0.44 YES
16 ITPK1 ITPK1 ITPK1 3159 0.11 0.46 YES
17 INPP5D INPP5D INPP5D 3239 0.11 0.47 YES
18 PIK3C2B PIK3C2B PIK3C2B 3245 0.11 0.48 YES
19 CALM1 CALM1 CALM1 3335 0.1 0.49 YES
20 DGKQ DGKQ DGKQ 3433 0.099 0.5 YES
21 PLCD1 PLCD1 PLCD1 3464 0.097 0.51 YES
22 ITPR1 ITPR1 ITPR1 3465 0.097 0.52 YES
23 PLCB2 PLCB2 PLCB2 3606 0.092 0.53 YES
24 PLCE1 PLCE1 PLCE1 3836 0.086 0.53 YES
25 ITPKB ITPKB ITPKB 4065 0.08 0.53 YES
26 PRKCA PRKCA PRKCA 4229 0.076 0.53 YES
27 PIP5K1C PIP5K1C PIP5K1C 4237 0.076 0.54 YES
28 INPP4A INPP4A INPP4A 4397 0.072 0.54 YES
29 PLCB4 PLCB4 PLCB4 4485 0.07 0.55 YES
30 INPP5E INPP5E INPP5E 4582 0.067 0.55 YES
31 PIK3R1 PIK3R1 PIK3R1 4683 0.065 0.56 YES
32 INPP1 INPP1 INPP1 4786 0.063 0.56 YES
33 ITPR2 ITPR2 ITPR2 4821 0.062 0.57 YES
34 CALM3 CALM3 CALM3 4909 0.06 0.57 YES
35 PIP4K2A PIP4K2A PIP4K2A 5067 0.057 0.57 YES
36 PLCD3 PLCD3 PLCD3 5406 0.051 0.56 YES
37 PIK3CB PIK3CB PIK3CB 5499 0.049 0.56 YES
38 PIKFYVE PIKFYVE PIKFYVE 5533 0.049 0.57 YES
39 PIP4K2B PIP4K2B PIP4K2B 5554 0.048 0.57 YES
40 PLCD4 PLCD4 PLCD4 5803 0.044 0.56 NO
41 PLCG1 PLCG1 PLCG1 6101 0.039 0.55 NO
42 PIK3C2A PIK3C2A PIK3C2A 6423 0.036 0.54 NO
43 INPPL1 INPPL1 INPPL1 6640 0.032 0.53 NO
44 IMPA1 IMPA1 IMPA1 6695 0.032 0.54 NO
45 PIP4K2C PIP4K2C PIP4K2C 6930 0.029 0.53 NO
46 PLCB1 PLCB1 PLCB1 7053 0.027 0.52 NO
47 INPP5K INPP5K INPP5K 7176 0.026 0.52 NO
48 IPPK IPPK IPPK 7375 0.024 0.51 NO
49 ITPR3 ITPR3 ITPR3 7581 0.021 0.5 NO
50 DGKG DGKG DGKG 7646 0.02 0.5 NO
51 PIK3CD PIK3CD PIK3CD 8010 0.016 0.49 NO
52 INPP5B INPP5B INPP5B 8014 0.016 0.49 NO
53 PLCG2 PLCG2 PLCG2 8235 0.014 0.48 NO
54 CDIPT CDIPT CDIPT 8704 0.009 0.45 NO
55 PI4KB PI4KB PI4KB 8965 0.0065 0.44 NO
56 DGKA DGKA DGKA 9527 0.0012 0.41 NO
57 DGKD DGKD DGKD 9752 -0.00064 0.4 NO
58 CALM2 CALM2 CALM2 9810 -0.0011 0.39 NO
59 PLCB3 PLCB3 PLCB3 10468 -0.0068 0.36 NO
60 PIK3CG PIK3CG PIK3CG 10606 -0.0081 0.35 NO
61 OCRL OCRL OCRL 10723 -0.009 0.35 NO
62 PTEN PTEN PTEN 10828 -0.01 0.34 NO
63 PIK3R2 PIK3R2 PIK3R2 11299 -0.014 0.32 NO
64 CDS2 CDS2 CDS2 12302 -0.023 0.27 NO
65 PIP5K1A PIP5K1A PIP5K1A 12607 -0.026 0.25 NO
66 PIK3C2G PIK3C2G PIK3C2G 12820 -0.028 0.25 NO
67 PIK3R5 PIK3R5 PIK3R5 13337 -0.034 0.22 NO
68 PIK3C3 PIK3C3 PIK3C3 13457 -0.035 0.22 NO
69 IMPA2 IMPA2 IMPA2 13559 -0.036 0.22 NO
70 PIK3R3 PIK3R3 PIK3R3 13706 -0.037 0.22 NO
71 DGKI DGKI DGKI 15521 -0.064 0.13 NO
72 PIK3CA PIK3CA PIK3CA 15730 -0.069 0.12 NO
73 DGKH DGKH DGKH 15891 -0.074 0.13 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 PYK2 PATHWAY.

Figure S56.  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 S29.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 554 0.39 0.24 YES
2 PTK2B PTK2B PTK2B 2359 0.15 0.24 YES
3 CALM1 CALM1 CALM1 3335 0.1 0.26 YES
4 PAK1 PAK1 PAK1 3539 0.094 0.31 YES
5 GNAQ GNAQ GNAQ 3911 0.084 0.35 YES
6 PRKCA PRKCA PRKCA 4229 0.076 0.39 YES
7 CALM3 CALM3 CALM3 4909 0.06 0.39 YES
8 MAP2K4 MAP2K4 MAP2K4 4963 0.059 0.43 YES
9 MAPK3 MAPK3 MAPK3 5335 0.052 0.44 YES
10 MAP2K1 MAP2K1 MAP2K1 6020 0.041 0.43 YES
11 PLCG1 PLCG1 PLCG1 6101 0.039 0.46 YES
12 MAPK1 MAPK1 MAPK1 6306 0.037 0.47 YES
13 MAP3K1 MAP3K1 MAP3K1 7313 0.024 0.43 NO
14 SOS1 SOS1 SOS1 8320 0.013 0.38 NO
15 MAP2K2 MAP2K2 MAP2K2 8805 0.008 0.36 NO
16 GRB2 GRB2 GRB2 9719 -0.00039 0.31 NO
17 CALM2 CALM2 CALM2 9810 -0.0011 0.31 NO
18 CRKL CRKL CRKL 10063 -0.0035 0.3 NO
19 RAC1 RAC1 RAC1 10747 -0.0092 0.27 NO
20 MAP2K3 MAP2K3 MAP2K3 11035 -0.012 0.26 NO
21 RAF1 RAF1 RAF1 11501 -0.016 0.24 NO
22 MAPK8 MAPK8 MAPK8 11668 -0.017 0.25 NO
23 JUN JUN JUN 12008 -0.02 0.24 NO
24 BCAR1 BCAR1 BCAR1 12085 -0.021 0.25 NO
25 SRC SRC SRC 12724 -0.027 0.24 NO
26 MAPK14 MAPK14 MAPK14 12758 -0.027 0.25 NO
27 SHC1 SHC1 SHC1 15636 -0.067 0.14 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 CHREBP2 PATHWAY.

Figure S58.  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 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 GRIN1 GRIN1 GRIN1 24 0.98 0.1 YES
2 PRKCG PRKCG PRKCG 68 0.83 0.18 YES
3 CAMK2A CAMK2A CAMK2A 96 0.78 0.26 YES
4 GRIN2A GRIN2A GRIN2A 304 0.53 0.31 YES
5 GRM1 GRM1 GRM1 313 0.52 0.36 YES
6 GRM5 GRM5 GRM5 352 0.49 0.41 YES
7 CAMK4 CAMK4 CAMK4 431 0.45 0.45 YES
8 CAMK2B CAMK2B CAMK2B 543 0.39 0.49 YES
9 PRKCB PRKCB PRKCB 554 0.39 0.53 YES
10 PPP1R1A PPP1R1A PPP1R1A 759 0.33 0.55 YES
11 GRIN2C GRIN2C GRIN2C 818 0.32 0.58 YES
12 CALML6 CALML6 CALML6 1062 0.27 0.59 YES
13 CHP2 CHP2 CHP2 1075 0.26 0.62 YES
14 RAPGEF3 RAPGEF3 RAPGEF3 1641 0.2 0.61 YES
15 CACNA1C CACNA1C CACNA1C 1724 0.2 0.63 YES
16 GRIA2 GRIA2 GRIA2 1860 0.18 0.64 YES
17 CAMK2G CAMK2G CAMK2G 2118 0.16 0.64 YES
18 GRIN2B GRIN2B GRIN2B 3208 0.11 0.59 NO
19 CALM1 CALM1 CALM1 3335 0.1 0.6 NO
20 ITPR1 ITPR1 ITPR1 3465 0.097 0.6 NO
21 PLCB2 PLCB2 PLCB2 3606 0.092 0.6 NO
22 PPP3CB PPP3CB PPP3CB 3861 0.085 0.6 NO
23 GRIA1 GRIA1 GRIA1 3883 0.085 0.6 NO
24 GNAQ GNAQ GNAQ 3911 0.084 0.61 NO
25 PRKCA PRKCA PRKCA 4229 0.076 0.6 NO
26 GRIN2D GRIN2D GRIN2D 4277 0.075 0.6 NO
27 RPS6KA2 RPS6KA2 RPS6KA2 4392 0.072 0.61 NO
28 PPP3R1 PPP3R1 PPP3R1 4396 0.072 0.61 NO
29 PRKACB PRKACB PRKACB 4474 0.07 0.62 NO
30 PLCB4 PLCB4 PLCB4 4485 0.07 0.62 NO
31 PPP3CA PPP3CA PPP3CA 4531 0.069 0.63 NO
32 RPS6KA6 RPS6KA6 RPS6KA6 4689 0.065 0.63 NO
33 ITPR2 ITPR2 ITPR2 4821 0.062 0.62 NO
34 CALM3 CALM3 CALM3 4909 0.06 0.63 NO
35 MAPK3 MAPK3 MAPK3 5335 0.052 0.61 NO
36 ADCY8 ADCY8 ADCY8 5662 0.046 0.6 NO
37 MAP2K1 MAP2K1 MAP2K1 6020 0.041 0.58 NO
38 MAPK1 MAPK1 MAPK1 6306 0.037 0.57 NO
39 CHP CHP CHP 6742 0.031 0.55 NO
40 CAMK2D CAMK2D CAMK2D 6778 0.03 0.55 NO
41 CREBBP CREBBP CREBBP 6938 0.028 0.54 NO
42 PLCB1 PLCB1 PLCB1 7053 0.027 0.54 NO
43 HRAS HRAS HRAS 7136 0.026 0.54 NO
44 ITPR3 ITPR3 ITPR3 7581 0.021 0.52 NO
45 PRKACA PRKACA PRKACA 8009 0.016 0.49 NO
46 PRKX PRKX PRKX 8095 0.015 0.49 NO
47 MAP2K2 MAP2K2 MAP2K2 8805 0.008 0.45 NO
48 KRAS KRAS KRAS 9197 0.0042 0.43 NO
49 PPP1R12A PPP1R12A PPP1R12A 9260 0.0037 0.43 NO
50 RPS6KA3 RPS6KA3 RPS6KA3 9333 0.003 0.42 NO
51 CALM2 CALM2 CALM2 9810 -0.0011 0.4 NO
52 PLCB3 PLCB3 PLCB3 10468 -0.0068 0.36 NO
53 EP300 EP300 EP300 10757 -0.0093 0.35 NO
54 ARAF ARAF ARAF 11442 -0.015 0.31 NO
55 RAF1 RAF1 RAF1 11501 -0.016 0.31 NO
56 PPP1CC PPP1CC PPP1CC 12327 -0.023 0.27 NO
57 ATF4 ATF4 ATF4 12716 -0.027 0.25 NO
58 RAP1A RAP1A RAP1A 13531 -0.036 0.21 NO
59 PPP1CB PPP1CB PPP1CB 13729 -0.038 0.2 NO
60 PPP1CA PPP1CA PPP1CA 13877 -0.039 0.2 NO
61 RPS6KA1 RPS6KA1 RPS6KA1 14140 -0.042 0.18 NO
62 PPP3CC PPP3CC PPP3CC 14810 -0.052 0.15 NO
63 BRAF BRAF BRAF 15150 -0.058 0.14 NO
64 NRAS NRAS NRAS 15282 -0.06 0.14 NO
65 RAP1B RAP1B RAP1B 15612 -0.066 0.13 NO
66 PPP3R2 PPP3R2 PPP3R2 17061 -0.13 0.062 NO

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

Figure S60.  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

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 = GBM-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = GBM-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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