GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in UCS-TP
Uterine Carcinosarcoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C11N80NG
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in UCS-TP. Broad Institute of MIT and Harvard. doi:10.7908/C11N80NG
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 having more than three samples and the input expression file "UCS-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. 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: 723
Number of samples: 57
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 16
pheno.type: 2 - 4 :[ clus2 ] 19
pheno.type: 3 - 4 :[ clus3 ] 12
pheno.type: 4 - 4 :[ clus4 ] 10

For the expression subtypes of 18665 genes in 58 samples, GSEA found enriched gene sets in each cluster using 57 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RNA DEGRADATION, KEGG CARDIAC MUSCLE CONTRACTION, KEGG PARKINSONS DISEASE, BIOCARTA NO1 PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA CHREBP2 PATHWAY, PID HDAC CLASSIII PATHWAY, PID RB 1PATHWAY, REACTOME RNA POL II TRANSCRIPTION

    • And common core enriched genes are ACTA1, ACTN2, ACTN3, EIF4EBP1, PRKAA2, PRKAB2, PRKAG3, STRADB, ASB1, ASB12

  • clus2

    • Top enriched gene sets are KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY, BIOCARTA FAS PATHWAY, PID HIF2PATHWAY, PID AVB3 OPN PATHWAY, PID TRAIL PATHWAY, PID FASPATHWAY, PID IL1PATHWAY, PID ECADHERIN NASCENTAJ PATHWAY, PID PDGFRBPATHWAY, PID TAP63PATHWAY

    • And common core enriched genes are MAP3K1, PIK3R1, CASP10, CASP8, CFLAR, PIK3CB, PIK3R3, MAP2K6, MAPK10, SYK

  • clus3

    • Top enriched gene sets are KEGG SELENOAMINO ACID METABOLISM, KEGG STARCH AND SUCROSE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG RETINOL METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM CYTOCHROME P450, SIG IL4RECEPTOR IN B LYPHOCYTES, ST INTERLEUKIN 4 PATHWAY, PID CD40 PATHWAY

    • And common core enriched genes are UGT1A6, UGT1A9, UGT2B10, UGT2B11, UGT2B7, UGT2A3, UGT2B15, GSTO2, IRS2, JAK3

  • clus4

    • Top enriched gene sets are KEGG CELL CYCLE, ST WNT BETA CATENIN PATHWAY, PID AURORA B PATHWAY, PID PLK1 PATHWAY, PID FOXM1PATHWAY, PID AURORA A PATHWAY, REACTOME MEIOSIS, REACTOME CELL CYCLE, REACTOME SIGNALLING TO ERKS, REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS

    • And common core enriched genes are AURKA, BIRC5, CDC25B, CENPA, CKAP5, PPP2R5D, BUB1, CDC20, ERCC6L, INCENP

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
KEGG AMINOACYL TRNA BIOSYNTHESIS 41 genes.ES.table 0.47 1.7 0.045 0.35 0.71 0.61 0.37 0.39 0.12 0.095
KEGG RNA DEGRADATION 57 genes.ES.table 0.37 1.8 0.034 0.39 0.7 0.018 0.0024 0.018 0.13 0.1
KEGG CARDIAC MUSCLE CONTRACTION 70 genes.ES.table 0.71 1.9 0 0.42 0.39 0.29 0.046 0.27 0 0.08
KEGG PARKINSONS DISEASE 112 genes.ES.table 0.44 1.7 0.054 0.33 0.76 0.53 0.33 0.36 0.12 0.09
BIOCARTA NO1 PATHWAY 29 genes.ES.table 0.69 1.7 0.002 0.34 0.74 0.21 0.038 0.2 0.12 0.091
BIOCARTA INTEGRIN PATHWAY 38 genes.ES.table 0.58 2.1 0 0.2 0.064 0.079 0.0061 0.079 0 0.043
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.45 1.7 0.0021 0.36 0.7 0.22 0.16 0.19 0.12 0.095
PID HDAC CLASSIII PATHWAY 25 genes.ES.table 0.61 1.9 0.0058 0.36 0.41 0.4 0.16 0.34 0 0.076
PID RB 1PATHWAY 65 genes.ES.table 0.48 1.8 0 0.32 0.48 0.17 0.093 0.15 0 0.069
REACTOME RNA POL II TRANSCRIPTION 93 genes.ES.table 0.38 1.8 0.051 0.34 0.64 0.5 0.37 0.31 0.098 0.089
genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

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 ACTN2 ACTN2 ACTN2 23 1.5 0.22 YES
2 ACTA1 ACTA1 ACTA1 31 1.4 0.43 YES
3 ACTN3 ACTN3 ACTN3 113 1.1 0.58 YES
4 PPP1R12B PPP1R12B PPP1R12B 1688 0.23 0.53 NO
5 FYN FYN FYN 1971 0.2 0.55 NO
6 MAP2K1 MAP2K1 MAP2K1 2391 0.17 0.55 NO
7 HRAS HRAS HRAS 3248 0.12 0.52 NO
8 PXN PXN PXN 3495 0.11 0.52 NO
9 RAPGEF1 RAPGEF1 RAPGEF1 3521 0.11 0.54 NO
10 TNS1 TNS1 TNS1 4642 0.073 0.49 NO
11 MAP2K2 MAP2K2 MAP2K2 5930 0.047 0.43 NO
12 CRKL CRKL CRKL 6664 0.035 0.39 NO
13 SHC1 SHC1 SHC1 6711 0.034 0.4 NO
14 RAF1 RAF1 RAF1 6814 0.032 0.39 NO
15 MAPK8 MAPK8 MAPK8 6914 0.03 0.39 NO
16 ZYX ZYX ZYX 7465 0.022 0.37 NO
17 RAP1A RAP1A RAP1A 7725 0.018 0.36 NO
18 MAPK1 MAPK1 MAPK1 7853 0.016 0.35 NO
19 CSK CSK CSK 8559 0.0048 0.31 NO
20 RHOA RHOA RHOA 8652 0.003 0.31 NO
21 CAV1 CAV1 CAV1 9672 -0.013 0.26 NO
22 SRC SRC SRC 9947 -0.018 0.24 NO
23 GRB2 GRB2 GRB2 9989 -0.018 0.24 NO
24 SOS1 SOS1 SOS1 10077 -0.02 0.24 NO
25 CAPNS1 CAPNS1 CAPNS1 10250 -0.023 0.24 NO
26 BCAR1 BCAR1 BCAR1 10424 -0.025 0.23 NO
27 PTK2 PTK2 PTK2 11049 -0.036 0.2 NO
28 TLN1 TLN1 TLN1 11181 -0.039 0.2 NO
29 VCL VCL VCL 11359 -0.042 0.2 NO
30 ITGB1 ITGB1 ITGB1 12455 -0.064 0.15 NO
31 MAPK3 MAPK3 MAPK3 12657 -0.069 0.15 NO
32 ROCK1 ROCK1 ROCK1 12951 -0.076 0.14 NO
33 CAPN1 CAPN1 CAPN1 13736 -0.097 0.12 NO
34 ACTN1 ACTN1 ACTN1 14166 -0.11 0.11 NO
35 JUN JUN JUN 14534 -0.12 0.11 NO
36 ITGA1 ITGA1 ITGA1 14927 -0.14 0.11 NO
37 BCR BCR BCR 15371 -0.16 0.11 NO
38 CAPNS2 CAPNS2 CAPNS2 18090 -0.45 0.03 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: KEGG AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RNA DEGRADATION

Table 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 PRKAG3 PRKAG3 PRKAG3 27 1.4 0.42 YES
2 PRKAA2 PRKAA2 PRKAA2 1096 0.33 0.46 YES
3 STRADB STRADB STRADB 2185 0.19 0.46 YES
4 PRKAB2 PRKAB2 PRKAB2 2730 0.14 0.47 YES
5 EIF4EBP1 EIF4EBP1 EIF4EBP1 2747 0.14 0.51 YES
6 EEF2K EEF2K EEF2K 4692 0.072 0.43 NO
7 PRKAG1 PRKAG1 PRKAG1 5610 0.053 0.4 NO
8 STK11 STK11 STK11 5768 0.05 0.4 NO
9 AKT2 AKT2 AKT2 5822 0.049 0.41 NO
10 EIF4G1 EIF4G1 EIF4G1 5845 0.049 0.43 NO
11 RPS6 RPS6 RPS6 5981 0.046 0.43 NO
12 RPTOR RPTOR RPTOR 6051 0.046 0.44 NO
13 EIF4B EIF4B EIF4B 6358 0.04 0.44 NO
14 CAB39 CAB39 CAB39 6611 0.036 0.44 NO
15 PDE3B PDE3B PDE3B 6683 0.034 0.44 NO
16 RPS6KB1 RPS6KB1 RPS6KB1 7054 0.028 0.43 NO
17 TSC1 TSC1 TSC1 7593 0.019 0.41 NO
18 TSC2 TSC2 TSC2 8118 0.012 0.38 NO
19 MLST8 MLST8 MLST8 8373 0.0077 0.37 NO
20 RHEB RHEB RHEB 9726 -0.014 0.3 NO
21 MTOR MTOR MTOR 10160 -0.021 0.29 NO
22 PPM1A PPM1A PPM1A 10748 -0.031 0.26 NO
23 STRADA STRADA STRADA 10998 -0.035 0.26 NO
24 PRKAB1 PRKAB1 PRKAB1 12307 -0.061 0.21 NO
25 PRKAA1 PRKAA1 PRKAA1 12425 -0.064 0.22 NO
26 EIF4E EIF4E EIF4E 12852 -0.074 0.22 NO
27 CAB39L CAB39L CAB39L 14406 -0.12 0.17 NO
28 PRKAG2 PRKAG2 PRKAG2 15964 -0.19 0.14 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: KEGG RNA DEGRADATION.

Figure S4.  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 CARDIAC MUSCLE CONTRACTION

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 ASB4 ASB4 ASB4 50 1.3 0.07 YES
2 ASB5 ASB5 ASB5 60 1.3 0.14 YES
3 TRIM63 TRIM63 TRIM63 66 1.2 0.21 YES
4 SPSB4 SPSB4 SPSB4 237 0.73 0.24 YES
5 ASB2 ASB2 ASB2 468 0.53 0.26 YES
6 ZBTB16 ZBTB16 ZBTB16 506 0.51 0.28 YES
7 ASB16 ASB16 ASB16 1004 0.34 0.28 YES
8 SKP2 SKP2 SKP2 1050 0.34 0.29 YES
9 KLHL13 KLHL13 KLHL13 1322 0.28 0.29 YES
10 DET1 DET1 DET1 1338 0.28 0.31 YES
11 ASB12 ASB12 ASB12 1619 0.24 0.31 YES
12 FBXO17 FBXO17 FBXO17 2211 0.18 0.28 YES
13 TCEB1 TCEB1 TCEB1 2440 0.16 0.28 YES
14 UBE2E2 UBE2E2 UBE2E2 2533 0.16 0.29 YES
15 BTRC BTRC BTRC 2833 0.14 0.28 YES
16 DZIP3 DZIP3 DZIP3 2927 0.13 0.28 YES
17 UBE2D4 UBE2D4 UBE2D4 2947 0.13 0.29 YES
18 UBE2W UBE2W UBE2W 2977 0.13 0.29 YES
19 CDC34 CDC34 CDC34 2993 0.13 0.3 YES
20 ASB1 ASB1 ASB1 3002 0.13 0.3 YES
21 UBE2V2 UBE2V2 UBE2V2 3102 0.12 0.31 YES
22 PSMD6 PSMD6 PSMD6 3157 0.12 0.31 YES
23 UBE2G2 UBE2G2 UBE2G2 3526 0.11 0.3 NO
24 FBXW8 FBXW8 FBXW8 3622 0.1 0.3 NO
25 RNF6 RNF6 RNF6 3716 0.1 0.3 NO
26 ANAPC13 ANAPC13 ANAPC13 3945 0.093 0.29 NO
27 PSMC4 PSMC4 PSMC4 4079 0.089 0.29 NO
28 UBE3B UBE3B UBE3B 4220 0.085 0.28 NO
29 PSMC1 PSMC1 PSMC1 4246 0.084 0.29 NO
30 CUL5 CUL5 CUL5 4268 0.083 0.29 NO
31 TMEM189-UBE2V1 TMEM189-UBE2V1 TMEM189-UBE2V1 4312 0.082 0.29 NO
32 UBE2E3 UBE2E3 UBE2E3 4350 0.081 0.3 NO
33 PSMC2 PSMC2 PSMC2 4591 0.075 0.29 NO
34 UBA5 UBA5 UBA5 4604 0.074 0.29 NO
35 PJA2 PJA2 PJA2 4618 0.074 0.29 NO
36 ASB8 ASB8 ASB8 4682 0.072 0.3 NO
37 STUB1 STUB1 STUB1 4707 0.072 0.3 NO
38 UBA2 UBA2 UBA2 5049 0.064 0.28 NO
39 PSME4 PSME4 PSME4 5056 0.064 0.29 NO
40 PSMD14 PSMD14 PSMD14 5112 0.063 0.29 NO
41 UBE2J2 UBE2J2 UBE2J2 5120 0.063 0.29 NO
42 PSMD4 PSMD4 PSMD4 5162 0.062 0.29 NO
43 PSMA5 PSMA5 PSMA5 5202 0.061 0.29 NO
44 UBE2M UBE2M UBE2M 5264 0.06 0.29 NO
45 PSMD2 PSMD2 PSMD2 5283 0.06 0.3 NO
46 TPP2 TPP2 TPP2 5348 0.058 0.29 NO
47 RPS27A RPS27A RPS27A 5447 0.056 0.29 NO
48 UBA52 UBA52 UBA52 5448 0.056 0.3 NO
49 PSMD1 PSMD1 PSMD1 5499 0.056 0.3 NO
50 RNF123 RNF123 RNF123 5508 0.055 0.3 NO
51 BLMH BLMH BLMH 5524 0.055 0.3 NO
52 TRIM36 TRIM36 TRIM36 5551 0.054 0.3 NO
53 UBE4A UBE4A UBE4A 5623 0.053 0.3 NO
54 CUL2 CUL2 CUL2 5655 0.052 0.3 NO
55 CUL7 CUL7 CUL7 5656 0.052 0.3 NO
56 PSMD8 PSMD8 PSMD8 5669 0.052 0.31 NO
57 FBXW11 FBXW11 FBXW11 5721 0.051 0.31 NO
58 UBE2G1 UBE2G1 UBE2G1 5774 0.05 0.31 NO
59 ANAPC7 ANAPC7 ANAPC7 5846 0.049 0.31 NO
60 UBE2B UBE2B UBE2B 5946 0.047 0.3 NO
61 VPRBP VPRBP VPRBP 6124 0.044 0.3 NO
62 PSMD12 PSMD12 PSMD12 6178 0.043 0.3 NO
63 UBE2Q2 UBE2Q2 UBE2Q2 6182 0.043 0.3 NO
64 GAN GAN GAN 6183 0.043 0.3 NO
65 CUL1 CUL1 CUL1 6239 0.042 0.3 NO
66 PSMD3 PSMD3 PSMD3 6267 0.042 0.3 NO
67 WSB1 WSB1 WSB1 6470 0.038 0.29 NO
68 PSMA4 PSMA4 PSMA4 6542 0.037 0.29 NO
69 PSMD11 PSMD11 PSMD11 6557 0.037 0.29 NO
70 NEDD4 NEDD4 NEDD4 6600 0.036 0.29 NO
71 UBE3A UBE3A UBE3A 6638 0.035 0.29 NO
72 UBR2 UBR2 UBR2 6642 0.035 0.29 NO
73 CUL3 CUL3 CUL3 6719 0.034 0.29 NO
74 UBE2C UBE2C UBE2C 6722 0.034 0.29 NO
75 NPEPPS NPEPPS NPEPPS 6726 0.034 0.3 NO
76 ANAPC11 ANAPC11 ANAPC11 6764 0.033 0.29 NO
77 PSMD10 PSMD10 PSMD10 6771 0.033 0.3 NO
78 PSMA1 PSMA1 PSMA1 6834 0.032 0.29 NO
79 UBE2F UBE2F UBE2F 6835 0.032 0.3 NO
80 TRIP12 TRIP12 TRIP12 6839 0.031 0.3 NO
81 UBR4 UBR4 UBR4 6962 0.029 0.29 NO
82 ASB7 ASB7 ASB7 6992 0.029 0.29 NO
83 KEAP1 KEAP1 KEAP1 6996 0.029 0.29 NO
84 PSMB2 PSMB2 PSMB2 7021 0.028 0.29 NO
85 PSMB5 PSMB5 PSMB5 7105 0.027 0.29 NO
86 ARIH2 ARIH2 ARIH2 7150 0.027 0.29 NO
87 PSMC5 PSMC5 PSMC5 7182 0.026 0.29 NO
88 UBE2R2 UBE2R2 UBE2R2 7219 0.026 0.29 NO
89 PSMA7 PSMA7 PSMA7 7244 0.025 0.29 NO
90 UBE2N UBE2N UBE2N 7270 0.025 0.29 NO
91 UBE2J1 UBE2J1 UBE2J1 7354 0.023 0.29 NO
92 UBE2Q1 UBE2Q1 UBE2Q1 7399 0.022 0.29 NO
93 PSMB4 PSMB4 PSMB4 7409 0.022 0.29 NO
94 HECTD3 HECTD3 HECTD3 7412 0.022 0.29 NO
95 RBX1 RBX1 RBX1 7572 0.02 0.28 NO
96 PSMB7 PSMB7 PSMB7 7606 0.019 0.28 NO
97 KLHL20 KLHL20 KLHL20 7644 0.019 0.28 NO
98 RCHY1 RCHY1 RCHY1 7666 0.018 0.28 NO
99 PSMD13 PSMD13 PSMD13 7744 0.017 0.28 NO
100 PJA1 PJA1 PJA1 7759 0.017 0.28 NO
101 CDC20 CDC20 CDC20 7849 0.016 0.27 NO
102 PSMC6 PSMC6 PSMC6 7899 0.015 0.27 NO
103 RNF41 RNF41 RNF41 8000 0.014 0.26 NO
104 PSMB3 PSMB3 PSMB3 8002 0.014 0.26 NO
105 RNF220 RNF220 RNF220 8034 0.013 0.26 NO
106 RNF4 RNF4 RNF4 8061 0.013 0.26 NO
107 PSMA2 PSMA2 PSMA2 8100 0.012 0.26 NO
108 PSMD7 PSMD7 PSMD7 8133 0.011 0.26 NO
109 PSMA6 PSMA6 PSMA6 8263 0.0093 0.26 NO
110 CDC27 CDC27 CDC27 8271 0.0092 0.26 NO
111 UBR1 UBR1 UBR1 8345 0.0081 0.25 NO
112 UBE2D3 UBE2D3 UBE2D3 8403 0.0073 0.25 NO
113 PSMB1 PSMB1 PSMB1 8421 0.007 0.25 NO
114 FBXO4 FBXO4 FBXO4 8528 0.0052 0.24 NO
115 UBE2O UBE2O UBE2O 8585 0.0044 0.24 NO
116 SKP1 SKP1 SKP1 8595 0.0042 0.24 NO
117 UBE2S UBE2S UBE2S 8664 0.0029 0.24 NO
118 TRIM32 TRIM32 TRIM32 8668 0.0029 0.24 NO
119 UBA1 UBA1 UBA1 8722 0.002 0.23 NO
120 VHL VHL VHL 8738 0.0018 0.23 NO
121 ANAPC5 ANAPC5 ANAPC5 8820 0.00073 0.23 NO
122 SAE1 SAE1 SAE1 8832 0.00056 0.23 NO
123 ASB13 ASB13 ASB13 8864 0.000031 0.23 NO
124 RNF25 RNF25 RNF25 9295 -0.0072 0.2 NO
125 PSMC3 PSMC3 PSMC3 9349 -0.008 0.2 NO
126 UBOX5 UBOX5 UBOX5 9397 -0.0088 0.2 NO
127 ANAPC1 ANAPC1 ANAPC1 9477 -0.0098 0.2 NO
128 PSMA3 PSMA3 PSMA3 9479 -0.0098 0.2 NO
129 CBLB CBLB CBLB 9505 -0.01 0.2 NO
130 CDC23 CDC23 CDC23 9545 -0.011 0.19 NO
131 PSMB6 PSMB6 PSMB6 9600 -0.012 0.19 NO
132 MKRN1 MKRN1 MKRN1 9668 -0.013 0.19 NO
133 CDC16 CDC16 CDC16 9846 -0.016 0.18 NO
134 UBE2D1 UBE2D1 UBE2D1 9870 -0.016 0.18 NO
135 TCEB2 TCEB2 TCEB2 9906 -0.017 0.18 NO
136 UBE2A UBE2A UBE2A 9922 -0.017 0.18 NO
137 SPSB1 SPSB1 SPSB1 10185 -0.021 0.16 NO
138 FBXW7 FBXW7 FBXW7 10246 -0.022 0.16 NO
139 PARK2 PARK2 PARK2 10278 -0.023 0.16 NO
140 UBE2D2 UBE2D2 UBE2D2 10279 -0.023 0.16 NO
141 ANAPC4 ANAPC4 ANAPC4 10372 -0.024 0.16 NO
142 PSMD9 PSMD9 PSMD9 10577 -0.028 0.15 NO
143 CDC26 CDC26 CDC26 10585 -0.028 0.15 NO
144 KLHL9 KLHL9 KLHL9 10619 -0.029 0.15 NO
145 HERC2 HERC2 HERC2 10654 -0.03 0.15 NO
146 UBE2L3 UBE2L3 UBE2L3 10674 -0.03 0.15 NO
147 RNF182 RNF182 RNF182 10679 -0.03 0.15 NO
148 UBE2E1 UBE2E1 UBE2E1 10743 -0.031 0.15 NO
149 PSMD5 PSMD5 PSMD5 10751 -0.031 0.15 NO
150 UBE2K UBE2K UBE2K 10815 -0.032 0.15 NO
151 UBE2L6 UBE2L6 UBE2L6 11127 -0.038 0.14 NO
152 ASB3 ASB3 ASB3 11208 -0.039 0.14 NO
153 ANAPC10 ANAPC10 ANAPC10 11499 -0.045 0.12 NO
154 UBA7 UBA7 UBA7 11512 -0.045 0.12 NO
155 PSME1 PSME1 PSME1 11790 -0.051 0.11 NO
156 RNF138 RNF138 RNF138 11821 -0.051 0.11 NO
157 ASB6 ASB6 ASB6 11934 -0.053 0.11 NO
158 PSMF1 PSMF1 PSMF1 12011 -0.055 0.11 NO
159 TRIM9 TRIM9 TRIM9 12033 -0.055 0.11 NO
160 UBA3 UBA3 UBA3 12039 -0.055 0.11 NO
161 FBXO6 FBXO6 FBXO6 12043 -0.055 0.12 NO
162 SPSB2 SPSB2 SPSB2 12078 -0.056 0.12 NO
163 RNF34 RNF34 RNF34 12171 -0.058 0.12 NO
164 SOCS3 SOCS3 SOCS3 12250 -0.06 0.12 NO
165 UBE2Z UBE2Z UBE2Z 12375 -0.063 0.11 NO
166 ANAPC2 ANAPC2 ANAPC2 12541 -0.066 0.11 NO
167 HUWE1 HUWE1 HUWE1 12680 -0.07 0.1 NO
168 ATG7 ATG7 ATG7 12681 -0.07 0.11 NO
169 FBXO3 FBXO3 FBXO3 12778 -0.072 0.1 NO
170 PSMB10 PSMB10 PSMB10 12884 -0.074 0.1 NO
171 FBXO44 FBXO44 FBXO44 12978 -0.077 0.1 NO
172 TRIM11 TRIM11 TRIM11 13040 -0.078 0.1 NO
173 PSME2 PSME2 PSME2 13170 -0.081 0.1 NO
174 LRSAM1 LRSAM1 LRSAM1 13271 -0.084 0.1 NO
175 UBA6 UBA6 UBA6 13326 -0.086 0.1 NO
176 TRIM37 TRIM37 TRIM37 13467 -0.09 0.1 NO
177 RBCK1 RBCK1 RBCK1 13598 -0.094 0.098 NO
178 UBE3C UBE3C UBE3C 13649 -0.095 0.1 NO
179 SMURF2 SMURF2 SMURF2 13919 -0.1 0.092 NO
180 SMURF1 SMURF1 SMURF1 14078 -0.11 0.089 NO
181 DTX3L DTX3L DTX3L 14083 -0.11 0.095 NO
182 WWP1 WWP1 WWP1 14225 -0.11 0.094 NO
183 FBXO27 FBXO27 FBXO27 14260 -0.11 0.098 NO
184 UBE2H UBE2H UBE2H 14587 -0.12 0.087 NO
185 FBXO2 FBXO2 FBXO2 14983 -0.14 0.074 NO
186 LNPEP LNPEP LNPEP 15478 -0.16 0.056 NO
187 SOCS1 SOCS1 SOCS1 15553 -0.17 0.061 NO
188 LRRC41 LRRC41 LRRC41 15821 -0.18 0.057 NO
189 PSMB9 PSMB9 PSMB9 15858 -0.19 0.066 NO
190 PSMB8 PSMB8 PSMB8 16604 -0.24 0.038 NO
191 TRIM21 TRIM21 TRIM21 16731 -0.25 0.045 NO
192 ASB9 ASB9 ASB9 16939 -0.26 0.049 NO
193 RNF144B RNF144B RNF144B 17197 -0.29 0.051 NO
194 UBE2U UBE2U UBE2U 18211 -0.49 0.024 NO

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

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CARDIAC MUSCLE CONTRACTION, 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 PARKINSONS DISEASE

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 ACTC1 ACTC1 ACTC1 8 1.6 0.071 YES
2 CACNA1S CACNA1S CACNA1S 19 1.5 0.14 YES
3 CACNG1 CACNG1 CACNG1 47 1.3 0.19 YES
4 TNNC1 TNNC1 TNNC1 63 1.3 0.25 YES
5 ATP1B4 ATP1B4 ATP1B4 81 1.2 0.3 YES
6 COX6A2 COX6A2 COX6A2 93 1.1 0.35 YES
7 MYH7 MYH7 MYH7 98 1.1 0.4 YES
8 TNNT2 TNNT2 TNNT2 102 1.1 0.44 YES
9 MYL3 MYL3 MYL3 163 0.89 0.48 YES
10 MYH6 MYH6 MYH6 166 0.88 0.52 YES
11 MYL2 MYL2 MYL2 176 0.86 0.56 YES
12 CACNG6 CACNG6 CACNG6 276 0.7 0.58 YES
13 CACNB1 CACNB1 CACNB1 415 0.57 0.6 YES
14 RYR2 RYR2 RYR2 513 0.51 0.62 YES
15 CACNA2D1 CACNA2D1 CACNA2D1 571 0.48 0.64 YES
16 ATP1A3 ATP1A3 ATP1A3 604 0.46 0.66 YES
17 TPM2 TPM2 TPM2 698 0.43 0.67 YES
18 ATP1B2 ATP1B2 ATP1B2 705 0.42 0.69 YES
19 CACNA2D4 CACNA2D4 CACNA2D4 758 0.41 0.7 YES
20 TNNI3 TNNI3 TNNI3 858 0.38 0.71 YES
21 COX8C COX8C COX8C 1378 0.28 0.7 NO
22 ATP1A4 ATP1A4 ATP1A4 1401 0.27 0.71 NO
23 ATP2A2 ATP2A2 ATP2A2 1744 0.23 0.7 NO
24 ATP1A2 ATP1A2 ATP1A2 1969 0.2 0.7 NO
25 TPM1 TPM1 TPM1 2323 0.17 0.69 NO
26 UQCRFS1 UQCRFS1 UQCRFS1 2723 0.14 0.67 NO
27 CACNG8 CACNG8 CACNG8 2960 0.13 0.66 NO
28 COX7A1 COX7A1 COX7A1 3115 0.12 0.66 NO
29 UQCRC2 UQCRC2 UQCRC2 3154 0.12 0.66 NO
30 CACNA2D2 CACNA2D2 CACNA2D2 3597 0.1 0.65 NO
31 COX5A COX5A COX5A 3727 0.1 0.64 NO
32 COX5B COX5B COX5B 4073 0.089 0.63 NO
33 CYC1 CYC1 CYC1 4210 0.085 0.62 NO
34 UQCR11 UQCR11 UQCR11 4534 0.076 0.61 NO
35 COX6B1 COX6B1 COX6B1 4689 0.072 0.61 NO
36 TPM3 TPM3 TPM3 4780 0.07 0.6 NO
37 COX6C COX6C COX6C 4996 0.066 0.6 NO
38 COX7A2L COX7A2L COX7A2L 5278 0.06 0.58 NO
39 COX7B COX7B COX7B 5737 0.051 0.56 NO
40 COX8A COX8A COX8A 6045 0.046 0.55 NO
41 COX7A2 COX7A2 COX7A2 6054 0.045 0.55 NO
42 ATP1B3 ATP1B3 ATP1B3 6103 0.045 0.55 NO
43 UQCR10 UQCR10 UQCR10 6398 0.039 0.53 NO
44 COX4I1 COX4I1 COX4I1 6575 0.036 0.52 NO
45 UQCRB UQCRB UQCRB 6605 0.036 0.52 NO
46 CACNB4 CACNB4 CACNB4 6944 0.03 0.51 NO
47 CACNB2 CACNB2 CACNB2 7114 0.027 0.5 NO
48 UQCRC1 UQCRC1 UQCRC1 8904 -0.00059 0.4 NO
49 SLC9A1 SLC9A1 SLC9A1 9254 -0.0065 0.39 NO
50 CACNG7 CACNG7 CACNG7 9444 -0.0094 0.38 NO
51 COX6A1 COX6A1 COX6A1 9993 -0.018 0.35 NO
52 COX7C COX7C COX7C 10425 -0.025 0.32 NO
53 UQCRQ UQCRQ UQCRQ 11037 -0.036 0.29 NO
54 COX4I2 COX4I2 COX4I2 11607 -0.047 0.26 NO
55 UQCRHL UQCRHL UQCRHL 11744 -0.05 0.26 NO
56 CACNA1F CACNA1F CACNA1F 11750 -0.05 0.26 NO
57 CACNB3 CACNB3 CACNB3 11930 -0.053 0.26 NO
58 UQCRH UQCRH UQCRH 12829 -0.073 0.21 NO
59 TPM4 TPM4 TPM4 13295 -0.085 0.19 NO
60 ATP1A1 ATP1A1 ATP1A1 13345 -0.086 0.19 NO
61 SLC9A6 SLC9A6 SLC9A6 13991 -0.1 0.16 NO
62 CACNG4 CACNG4 CACNG4 14795 -0.13 0.12 NO
63 FXYD2 FXYD2 FXYD2 15024 -0.14 0.12 NO
64 COX6B2 COX6B2 COX6B2 15126 -0.15 0.12 NO
65 CACNA1C CACNA1C CACNA1C 15833 -0.18 0.087 NO
66 CACNG5 CACNG5 CACNG5 16024 -0.2 0.086 NO
67 CACNA2D3 CACNA2D3 CACNA2D3 16801 -0.25 0.055 NO
68 ATP1B1 ATP1B1 ATP1B1 17010 -0.27 0.056 NO
69 CACNA1D CACNA1D CACNA1D 17530 -0.34 0.043 NO
70 SLC8A1 SLC8A1 SLC8A1 17776 -0.38 0.047 NO

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

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PARKINSONS DISEASE, 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 NO1 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 MYOD1 MYOD1 MYOD1 17 1.5 0.32 YES
2 CDKN1A CDKN1A CDKN1A 780 0.4 0.37 YES
3 FOXO4 FOXO4 FOXO4 1482 0.26 0.39 YES
4 SIRT2 SIRT2 SIRT2 1491 0.26 0.44 YES
5 TUBB2A TUBB2A TUBB2A 1733 0.23 0.48 YES
6 FOXO1 FOXO1 FOXO1 1843 0.22 0.52 YES
7 ACSS2 ACSS2 ACSS2 1997 0.2 0.56 YES
8 PPARGC1A PPARGC1A PPARGC1A 2031 0.2 0.6 YES
9 MEF2D MEF2D MEF2D 2552 0.16 0.6 YES
10 FHL2 FHL2 FHL2 2975 0.13 0.61 YES
11 HDAC4 HDAC4 HDAC4 4025 0.09 0.57 NO
12 SIRT1 SIRT1 SIRT1 4437 0.078 0.57 NO
13 XRCC6 XRCC6 XRCC6 6738 0.034 0.45 NO
14 TUBA1B TUBA1B TUBA1B 6897 0.03 0.45 NO
15 FOXO3 FOXO3 FOXO3 7634 0.019 0.41 NO
16 CREBBP CREBBP CREBBP 7679 0.018 0.41 NO
17 HIST1H1E HIST1H1E HIST1H1E 8311 0.0085 0.38 NO
18 EP300 EP300 EP300 9751 -0.014 0.31 NO
19 SIRT3 SIRT3 SIRT3 10329 -0.024 0.28 NO
20 SIRT7 SIRT7 SIRT7 11977 -0.054 0.21 NO
21 TP53 TP53 TP53 12523 -0.066 0.19 NO
22 BAX BAX BAX 12666 -0.069 0.2 NO
23 ACSS1 ACSS1 ACSS1 13507 -0.091 0.17 NO
24 KAT2B KAT2B KAT2B 15728 -0.18 0.092 NO
25 HOXA10 HOXA10 HOXA10 17247 -0.3 0.075 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 NO1 PATHWAY.

Figure S10.  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 INTEGRIN PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ENO3 ENO3 ENO3 44 1.4 0.12 YES
2 FBP2 FBP2 FBP2 117 1 0.21 YES
3 PYGM PYGM PYGM 135 0.97 0.29 YES
4 PGAM2 PGAM2 PGAM2 191 0.82 0.36 YES
5 PHKG1 PHKG1 PHKG1 201 0.79 0.44 YES
6 PFKFB1 PFKFB1 PFKFB1 820 0.39 0.44 YES
7 GYS2 GYS2 GYS2 937 0.36 0.46 YES
8 PKLR PKLR PKLR 1341 0.28 0.47 YES
9 GYG1 GYG1 GYG1 1349 0.28 0.49 YES
10 AGL AGL AGL 1605 0.24 0.5 YES
11 PFKM PFKM PFKM 1975 0.2 0.5 YES
12 PC PC PC 1981 0.2 0.52 YES
13 PRKACA PRKACA PRKACA 2160 0.19 0.52 YES
14 GOT1 GOT1 GOT1 2338 0.17 0.53 YES
15 GAPDHS GAPDHS GAPDHS 2580 0.16 0.53 YES
16 GYS1 GYS1 GYS1 3182 0.12 0.51 NO
17 ALDOA ALDOA ALDOA 4080 0.089 0.47 NO
18 MDH2 MDH2 MDH2 4156 0.087 0.47 NO
19 MDH1 MDH1 MDH1 4235 0.084 0.47 NO
20 UGP2 UGP2 UGP2 4462 0.078 0.47 NO
21 GPI GPI GPI 4757 0.071 0.46 NO
22 SLC25A12 SLC25A12 SLC25A12 5001 0.066 0.45 NO
23 SLC25A11 SLC25A11 SLC25A11 5069 0.064 0.45 NO
24 PYGL PYGL PYGL 5341 0.059 0.44 NO
25 PGM1 PGM1 PGM1 5515 0.055 0.44 NO
26 PGAM1 PGAM1 PGAM1 6807 0.032 0.37 NO
27 PRKACB PRKACB PRKACB 7497 0.021 0.34 NO
28 PKM2 PKM2 PKM2 7985 0.014 0.31 NO
29 PFKFB2 PFKFB2 PFKFB2 8282 0.009 0.3 NO
30 PPP2CA PPP2CA PPP2CA 8519 0.0053 0.29 NO
31 PPP2R5D PPP2R5D PPP2R5D 8761 0.0014 0.27 NO
32 PPP2CB PPP2CB PPP2CB 9119 -0.0041 0.25 NO
33 GAPDH GAPDH GAPDH 9208 -0.0057 0.25 NO
34 TPI1 TPI1 TPI1 9278 -0.0069 0.25 NO
35 PHKA1 PHKA1 PHKA1 9409 -0.0089 0.24 NO
36 GYG2 GYG2 GYG2 9608 -0.012 0.23 NO
37 PGK1 PGK1 PGK1 9908 -0.017 0.22 NO
38 PFKFB3 PFKFB3 PFKFB3 9965 -0.018 0.22 NO
39 ALDOC ALDOC ALDOC 10168 -0.021 0.21 NO
40 SLC25A13 SLC25A13 SLC25A13 10415 -0.025 0.2 NO
41 PPP2R1A PPP2R1A PPP2R1A 10449 -0.026 0.2 NO
42 CALM1 CALM1 CALM1 10663 -0.03 0.19 NO
43 GOT2 GOT2 GOT2 10826 -0.032 0.18 NO
44 PHKG2 PHKG2 PHKG2 11070 -0.037 0.17 NO
45 CALM2 CALM2 CALM2 11554 -0.046 0.15 NO
46 ENO1 ENO1 ENO1 11649 -0.048 0.15 NO
47 GBE1 GBE1 GBE1 11713 -0.049 0.15 NO
48 PPP2R1B PPP2R1B PPP2R1B 11887 -0.052 0.14 NO
49 CALM3 CALM3 CALM3 12045 -0.055 0.14 NO
50 ALDOB ALDOB ALDOB 13700 -0.096 0.061 NO
51 PFKL PFKL PFKL 14077 -0.11 0.05 NO
52 PHKA2 PHKA2 PHKA2 14109 -0.11 0.059 NO
53 PCK2 PCK2 PCK2 14458 -0.12 0.051 NO
54 PFKP PFKP PFKP 14501 -0.12 0.059 NO
55 PHKB PHKB PHKB 14515 -0.12 0.069 NO
56 ENO2 ENO2 ENO2 14662 -0.13 0.073 NO
57 PGM2 PGM2 PGM2 14896 -0.14 0.072 NO
58 SLC25A1 SLC25A1 SLC25A1 15192 -0.15 0.07 NO
59 PYGB PYGB PYGB 15269 -0.15 0.08 NO
60 PFKFB4 PFKFB4 PFKFB4 15377 -0.16 0.088 NO
61 SLC25A10 SLC25A10 SLC25A10 16502 -0.23 0.048 NO
62 FBP1 FBP1 FBP1 17341 -0.31 0.03 NO
63 PCK1 PCK1 PCK1 18068 -0.45 0.031 NO

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

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA INTEGRIN 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 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 MYOD1 MYOD1 MYOD1 17 1.5 0.14 YES
2 CKM CKM CKM 25 1.4 0.27 YES
3 MEF2C MEF2C MEF2C 420 0.56 0.3 YES
4 PAX3 PAX3 PAX3 597 0.47 0.34 YES
5 CCND2 CCND2 CCND2 739 0.41 0.37 YES
6 CDKN1A CDKN1A CDKN1A 780 0.4 0.4 YES
7 SKP2 SKP2 SKP2 1050 0.34 0.42 YES
8 GSC GSC GSC 1266 0.29 0.44 YES
9 CCND3 CCND3 CCND3 1385 0.27 0.45 YES
10 PPP2R3B PPP2R3B PPP2R3B 1564 0.25 0.47 YES
11 CEBPD CEBPD CEBPD 1728 0.23 0.48 YES
12 CDK6 CDK6 CDK6 2280 0.18 0.47 NO
13 RB1 RB1 RB1 2370 0.17 0.48 NO
14 TGFB2 TGFB2 TGFB2 3491 0.11 0.43 NO
15 BGLAP BGLAP BGLAP 3669 0.1 0.43 NO
16 CCNE1 CCNE1 CCNE1 3815 0.098 0.43 NO
17 TBP TBP TBP 4255 0.084 0.41 NO
18 AATF AATF AATF 4307 0.082 0.42 NO
19 SIRT1 SIRT1 SIRT1 4437 0.078 0.42 NO
20 ATF7 ATF7 ATF7 4833 0.069 0.4 NO
21 CDK4 CDK4 CDK4 6343 0.04 0.32 NO
22 ATF2 ATF2 ATF2 6592 0.036 0.32 NO
23 SMARCA4 SMARCA4 SMARCA4 6627 0.035 0.32 NO
24 RAF1 RAF1 RAF1 6814 0.032 0.31 NO
25 CBX4 CBX4 CBX4 6906 0.03 0.31 NO
26 E2F4 E2F4 E2F4 7201 0.026 0.29 NO
27 TAF1 TAF1 TAF1 7446 0.022 0.28 NO
28 CREBBP CREBBP CREBBP 7679 0.018 0.27 NO
29 E2F2 E2F2 E2F2 7736 0.017 0.27 NO
30 CEBPA CEBPA CEBPA 7896 0.015 0.26 NO
31 ABL1 ABL1 ABL1 8077 0.012 0.26 NO
32 RBBP4 RBBP4 RBBP4 8099 0.012 0.26 NO
33 CTBP1 CTBP1 CTBP1 8334 0.0082 0.24 NO
34 PPP2CA PPP2CA PPP2CA 8519 0.0053 0.23 NO
35 SMARCB1 SMARCB1 SMARCB1 9228 -0.0061 0.2 NO
36 MDM2 MDM2 MDM2 9390 -0.0087 0.19 NO
37 MET MET MET 9399 -0.0088 0.19 NO
38 EP300 EP300 EP300 9751 -0.014 0.17 NO
39 MITF MITF MITF 10241 -0.022 0.15 NO
40 E2F1 E2F1 E2F1 10265 -0.023 0.15 NO
41 DNMT1 DNMT1 DNMT1 10651 -0.029 0.13 NO
42 MAPK14 MAPK14 MAPK14 10794 -0.032 0.12 NO
43 TFDP1 TFDP1 TFDP1 10910 -0.034 0.12 NO
44 SUV39H1 SUV39H1 SUV39H1 11026 -0.036 0.12 NO
45 CCNA2 CCNA2 CCNA2 11142 -0.038 0.12 NO
46 BRD2 BRD2 BRD2 11464 -0.044 0.1 NO
47 CDKN2A CDKN2A CDKN2A 11504 -0.045 0.1 NO
48 CDK2 CDK2 CDK2 11679 -0.048 0.1 NO
49 UBTF UBTF UBTF 11682 -0.048 0.1 NO
50 E2F3 E2F3 E2F3 11700 -0.049 0.11 NO
51 CEBPB CEBPB CEBPB 12061 -0.056 0.094 NO
52 MAPK9 MAPK9 MAPK9 12145 -0.058 0.095 NO
53 HDAC3 HDAC3 HDAC3 12181 -0.059 0.098 NO
54 CDKN1B CDKN1B CDKN1B 12471 -0.065 0.089 NO
55 HDAC1 HDAC1 HDAC1 13489 -0.09 0.042 NO
56 ELF1 ELF1 ELF1 13951 -0.1 0.027 NO
57 MAPK11 MAPK11 MAPK11 14353 -0.12 0.016 NO
58 JUN JUN JUN 14534 -0.12 0.018 NO
59 SPI1 SPI1 SPI1 15188 -0.15 -0.0032 NO
60 RBP2 RBP2 RBP2 16122 -0.2 -0.034 NO
61 CCND1 CCND1 CCND1 16568 -0.23 -0.037 NO
62 PPARG PPARG PPARG 17234 -0.3 -0.045 NO
63 CSF2 CSF2 CSF2 17641 -0.36 -0.034 NO
64 SFTPD SFTPD SFTPD 17779 -0.38 -0.0061 NO
65 RUNX2 RUNX2 RUNX2 18383 -0.57 0.014 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: BIOCARTA CHREBP2 PATHWAY.

Figure S14.  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: PID HDAC CLASSIII PATHWAY

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 CDKN1A CDKN1A CDKN1A 780 0.4 0.14 YES
2 FOXO4 FOXO4 FOXO4 1482 0.26 0.22 YES
3 FOXO1 FOXO1 FOXO1 1843 0.22 0.29 YES
4 THEM4 THEM4 THEM4 2030 0.2 0.37 YES
5 CASP9 CASP9 CASP9 2272 0.18 0.44 YES
6 TRIB3 TRIB3 TRIB3 2820 0.14 0.47 YES
7 PDPK1 PDPK1 PDPK1 5605 0.054 0.35 NO
8 CHUK CHUK CHUK 5751 0.051 0.36 NO
9 AKT2 AKT2 AKT2 5822 0.049 0.38 NO
10 RICTOR RICTOR RICTOR 6473 0.038 0.36 NO
11 AKT1S1 AKT1S1 AKT1S1 6649 0.035 0.37 NO
12 RPS6KB2 RPS6KB2 RPS6KB2 6660 0.035 0.38 NO
13 MAPKAP1 MAPKAP1 MAPKAP1 7190 0.026 0.37 NO
14 FOXO3 FOXO3 FOXO3 7634 0.019 0.35 NO
15 AKT1 AKT1 AKT1 7994 0.014 0.34 NO
16 TSC2 TSC2 TSC2 8118 0.012 0.34 NO
17 MLST8 MLST8 MLST8 8373 0.0077 0.33 NO
18 NR4A1 NR4A1 NR4A1 8776 0.0012 0.31 NO
19 MDM2 MDM2 MDM2 9390 -0.0087 0.28 NO
20 MTOR MTOR MTOR 10160 -0.021 0.25 NO
21 BAD BAD BAD 11424 -0.043 0.2 NO
22 AKT3 AKT3 AKT3 11623 -0.047 0.21 NO
23 GSK3A GSK3A GSK3A 12184 -0.059 0.2 NO
24 CREB1 CREB1 CREB1 12383 -0.063 0.22 NO
25 CDKN1B CDKN1B CDKN1B 12471 -0.065 0.25 NO
26 PTEN PTEN PTEN 13003 -0.077 0.25 NO
27 PHLPP1 PHLPP1 PHLPP1 14189 -0.11 0.24 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: PID HDAC CLASSIII PATHWAY.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: PID HDAC CLASSIII 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: PID RB 1PATHWAY

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 TAF13 TAF13 TAF13 1799 0.22 -0.032 YES
2 TCEB1 TCEB1 TCEB1 2440 0.16 -0.018 YES
3 GTF2H2B GTF2H2B GTF2H2B 2546 0.16 0.022 YES
4 GTF2E1 GTF2E1 GTF2E1 3319 0.12 0.014 YES
5 GTF2B GTF2B GTF2B 3343 0.11 0.046 YES
6 POLR2D POLR2D POLR2D 3376 0.11 0.077 YES
7 TAF10 TAF10 TAF10 3409 0.11 0.11 YES
8 NCBP2 NCBP2 NCBP2 3579 0.11 0.13 YES
9 GTF2H2 GTF2H2 GTF2H2 3721 0.1 0.15 YES
10 TAF5 TAF5 TAF5 3799 0.098 0.18 YES
11 GTF2F2 GTF2F2 GTF2F2 3809 0.098 0.2 YES
12 TAF12 TAF12 TAF12 3985 0.092 0.22 YES
13 TBP TBP TBP 4255 0.084 0.23 YES
14 POLR2B POLR2B POLR2B 4338 0.081 0.25 YES
15 ELL ELL ELL 4504 0.077 0.26 YES
16 TCEA1 TCEA1 TCEA1 4527 0.076 0.28 YES
17 NCBP1 NCBP1 NCBP1 4895 0.068 0.28 YES
18 POLR2J POLR2J POLR2J 5210 0.061 0.28 YES
19 POLR2I POLR2I POLR2I 5297 0.059 0.3 YES
20 SUPT16H SUPT16H SUPT16H 5344 0.058 0.31 YES
21 TCEB3 TCEB3 TCEB3 5541 0.055 0.32 YES
22 SUPT5H SUPT5H SUPT5H 5579 0.054 0.33 YES
23 RDBP RDBP RDBP 5633 0.053 0.34 YES
24 TAF11 TAF11 TAF11 5637 0.053 0.36 YES
25 MNAT1 MNAT1 MNAT1 5716 0.051 0.37 YES
26 GTF2H3 GTF2H3 GTF2H3 5886 0.048 0.38 YES
27 TAF9 TAF9 TAF9 6014 0.046 0.38 YES
28 ERCC3 ERCC3 ERCC3 6408 0.039 0.37 YES
29 POLR2H POLR2H POLR2H 6448 0.038 0.38 YES
30 SSRP1 SSRP1 SSRP1 6585 0.036 0.38 YES
31 POLR2E POLR2E POLR2E 6597 0.036 0.39 YES
32 GTF2A2 GTF2A2 GTF2A2 6657 0.035 0.4 YES
33 POLR2G POLR2G POLR2G 6782 0.033 0.4 YES
34 SUPT4H1 SUPT4H1 SUPT4H1 6840 0.031 0.41 YES
35 GTF2H1 GTF2H1 GTF2H1 6877 0.031 0.42 YES
36 TAF1 TAF1 TAF1 7446 0.022 0.39 NO
37 TAF6 TAF6 TAF6 7571 0.02 0.39 NO
38 CCNT2 CCNT2 CCNT2 7747 0.017 0.39 NO
39 POLR2A POLR2A POLR2A 8178 0.011 0.37 NO
40 WHSC2 WHSC2 WHSC2 8463 0.0063 0.35 NO
41 POLR2F POLR2F POLR2F 8725 0.002 0.34 NO
42 CCNT1 CCNT1 CCNT1 9074 -0.0036 0.32 NO
43 POLR2K POLR2K POLR2K 9090 -0.0038 0.32 NO
44 GTF2E2 GTF2E2 GTF2E2 9167 -0.0048 0.32 NO
45 GTF2F1 GTF2F1 GTF2F1 9200 -0.0056 0.32 NO
46 POLR2C POLR2C POLR2C 9256 -0.0066 0.32 NO
47 CDK9 CDK9 CDK9 9454 -0.0095 0.31 NO
48 GTF2A1 GTF2A1 GTF2A1 9619 -0.012 0.31 NO
49 TCEB2 TCEB2 TCEB2 9906 -0.017 0.3 NO
50 TAF4 TAF4 TAF4 10830 -0.033 0.26 NO
51 POLR2L POLR2L POLR2L 11220 -0.039 0.25 NO
52 COBRA1 COBRA1 COBRA1 11397 -0.043 0.25 NO
53 TH1L TH1L TH1L 11428 -0.043 0.26 NO
54 ERCC2 ERCC2 ERCC2 11876 -0.052 0.25 NO
55 CTDP1 CTDP1 CTDP1 11979 -0.054 0.26 NO
56 CCNH CCNH CCNH 12601 -0.068 0.25 NO
57 CDK7 CDK7 CDK7 12901 -0.074 0.25 NO
58 TAF4B TAF4B TAF4B 13415 -0.088 0.25 NO
59 GTF2H4 GTF2H4 GTF2H4 13897 -0.1 0.26 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: PID RB 1PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: PID RB 1PATHWAY, 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: REACTOME RNA POL II TRANSCRIPTION

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 MYL1 MYL1 MYL1 6 1.6 0.06 YES
2 TNNC2 TNNC2 TNNC2 12 1.5 0.12 YES
3 ACTN2 ACTN2 ACTN2 23 1.5 0.17 YES
4 MYBPC1 MYBPC1 MYBPC1 35 1.4 0.22 YES
5 MYL4 MYL4 MYL4 36 1.4 0.28 YES
6 MYH3 MYH3 MYH3 41 1.4 0.33 YES
7 NEB NEB NEB 42 1.4 0.38 YES
8 MYH8 MYH8 MYH8 58 1.3 0.43 YES
9 TNNC1 TNNC1 TNNC1 63 1.3 0.47 YES
10 TNNI2 TNNI2 TNNI2 83 1.2 0.52 YES
11 TNNI1 TNNI1 TNNI1 96 1.1 0.56 YES
12 TNNT2 TNNT2 TNNT2 102 1.1 0.6 YES
13 DES DES DES 108 1.1 0.64 YES
14 MYBPC2 MYBPC2 MYBPC2 116 1 0.68 YES
15 MYL3 MYL3 MYL3 163 0.89 0.71 YES
16 MYH6 MYH6 MYH6 166 0.88 0.74 YES
17 TCAP TCAP TCAP 170 0.86 0.77 YES
18 MYL2 MYL2 MYL2 176 0.86 0.8 YES
19 TNNT1 TNNT1 TNNT1 182 0.85 0.84 YES
20 TPM2 TPM2 TPM2 698 0.43 0.82 YES
21 TNNI3 TNNI3 TNNI3 858 0.38 0.83 YES
22 TMOD1 TMOD1 TMOD1 915 0.36 0.84 YES
23 MYL6B MYL6B MYL6B 964 0.35 0.85 YES
24 DMD DMD DMD 2048 0.2 0.8 NO
25 TPM1 TPM1 TPM1 2323 0.17 0.79 NO
26 MYL9 MYL9 MYL9 2593 0.15 0.78 NO
27 LMOD1 LMOD1 LMOD1 3607 0.1 0.73 NO
28 TPM3 TPM3 TPM3 4780 0.07 0.67 NO
29 SORBS1 SORBS1 SORBS1 5310 0.059 0.65 NO
30 SORBS3 SORBS3 SORBS3 6205 0.043 0.6 NO
31 VIM VIM VIM 7284 0.024 0.54 NO
32 MYL6 MYL6 MYL6 10132 -0.021 0.39 NO
33 CALM1 CALM1 CALM1 10663 -0.03 0.36 NO
34 TLN1 TLN1 TLN1 11181 -0.039 0.34 NO
35 VCL VCL VCL 11359 -0.042 0.33 NO
36 CALM2 CALM2 CALM2 11554 -0.046 0.32 NO
37 CALM3 CALM3 CALM3 12045 -0.055 0.3 NO
38 TPM4 TPM4 TPM4 13295 -0.085 0.23 NO
39 ACTA2 ACTA2 ACTA2 13817 -0.099 0.21 NO
40 MYL12B MYL12B MYL12B 14027 -0.11 0.2 NO
41 CALD1 CALD1 CALD1 14433 -0.12 0.18 NO
42 ITGA1 ITGA1 ITGA1 14927 -0.14 0.16 NO
43 MYLK MYLK MYLK 15414 -0.16 0.14 NO
44 ITGB5 ITGB5 ITGB5 15748 -0.18 0.13 NO
45 ACTG2 ACTG2 ACTG2 16232 -0.21 0.11 NO
46 MYH11 MYH11 MYH11 18084 -0.45 0.03 NO

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

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME RNA POL II TRANSCRIPTION, 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
KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY 89 genes.ES.table 0.63 1.7 0.004 0.39 0.74 0.51 0.21 0.4 0.13 0.099
BIOCARTA FAS PATHWAY 30 genes.ES.table 0.51 1.8 0.022 0.5 0.69 0.37 0.2 0.29 0.15 0.12
PID HIF2PATHWAY 34 genes.ES.table 0.52 1.7 0.01 0.43 0.72 0.41 0.2 0.33 0.14 0.11
PID AVB3 OPN PATHWAY 31 genes.ES.table 0.68 1.9 0 0.56 0.27 0.48 0.2 0.39 0 0.099
PID TRAIL PATHWAY 28 genes.ES.table 0.7 2 0 0.9 0.15 0.36 0.16 0.3 0 0.12
PID FASPATHWAY 38 genes.ES.table 0.64 2 0 0.54 0.18 0.4 0.19 0.32 0 0.081
PID IL1PATHWAY 34 genes.ES.table 0.56 1.7 0.022 0.41 0.72 0.38 0.2 0.31 0.13 0.1
PID ECADHERIN NASCENTAJ PATHWAY 39 genes.ES.table 0.42 1.7 0.016 0.4 0.74 0.36 0.29 0.25 0.13 0.1
PID PDGFRBPATHWAY 127 genes.ES.table 0.42 1.8 0.028 0.47 0.7 0.23 0.2 0.18 0.14 0.12
PID TAP63PATHWAY 54 genes.ES.table 0.59 1.8 0 0.43 0.53 0.35 0.15 0.3 0.097 0.093
genes ES table in pathway: KEGG TOLL LIKE RECEPTOR SIGNALING 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 TNFRSF10A TNFRSF10A TNFRSF10A 145 0.6 0.15 YES
2 TNFSF10 TNFSF10 TNFSF10 210 0.55 0.3 YES
3 CASP8 CASP8 CASP8 588 0.4 0.38 YES
4 TNFRSF10C TNFRSF10C TNFRSF10C 730 0.37 0.47 YES
5 CASP10 CASP10 CASP10 851 0.34 0.56 YES
6 PIK3R1 PIK3R1 PIK3R1 1685 0.23 0.57 YES
7 PIK3R3 PIK3R3 PIK3R3 1801 0.22 0.63 YES
8 PIK3CB PIK3CB PIK3CB 2070 0.2 0.67 YES
9 CFLAR CFLAR CFLAR 2424 0.18 0.69 YES
10 MAP3K1 MAP3K1 MAP3K1 3055 0.14 0.7 YES
11 TRADD TRADD TRADD 4475 0.083 0.64 NO
12 IKBKB IKBKB IKBKB 4540 0.081 0.66 NO
13 RIPK1 RIPK1 RIPK1 4869 0.072 0.66 NO
14 PIK3R2 PIK3R2 PIK3R2 7184 0.024 0.54 NO
15 SMPD1 SMPD1 SMPD1 7799 0.014 0.52 NO
16 PIK3CA PIK3CA PIK3CA 7976 0.011 0.51 NO
17 IKBKG IKBKG IKBKG 8001 0.011 0.51 NO
18 MAPK3 MAPK3 MAPK3 8354 0.0053 0.49 NO
19 FADD FADD FADD 8488 0.0035 0.49 NO
20 MAPK8 MAPK8 MAPK8 9321 -0.0091 0.44 NO
21 TNFRSF10B TNFRSF10B TNFRSF10B 9882 -0.017 0.42 NO
22 TRAF2 TRAF2 TRAF2 9995 -0.019 0.42 NO
23 PIK3CD PIK3CD PIK3CD 10080 -0.02 0.42 NO
24 MAP2K4 MAP2K4 MAP2K4 10493 -0.026 0.4 NO
25 DAP3 DAP3 DAP3 10538 -0.026 0.41 NO
26 CHUK CHUK CHUK 10701 -0.029 0.41 NO
27 MAPK1 MAPK1 MAPK1 11100 -0.035 0.39 NO
28 TNFRSF10D TNFRSF10D TNFRSF10D 11492 -0.041 0.38 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: KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY.

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

genes ES table in pathway: BIOCARTA FAS 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 SYK SYK SYK 281 0.51 0.1 YES
2 MAPK10 MAPK10 MAPK10 543 0.42 0.18 YES
3 CASP8 CASP8 CASP8 588 0.4 0.27 YES
4 CASP10 CASP10 CASP10 851 0.34 0.33 YES
5 FAS FAS FAS 1047 0.31 0.39 YES
6 PIK3R1 PIK3R1 PIK3R1 1685 0.23 0.41 YES
7 PIK3R3 PIK3R3 PIK3R3 1801 0.22 0.46 YES
8 PIK3CB PIK3CB PIK3CB 2070 0.2 0.49 YES
9 MAP2K6 MAP2K6 MAP2K6 2265 0.19 0.52 YES
10 CFLAR CFLAR CFLAR 2424 0.18 0.55 YES
11 BIRC3 BIRC3 BIRC3 2807 0.15 0.56 YES
12 MAP3K1 MAP3K1 MAP3K1 3055 0.14 0.58 YES
13 EZR EZR EZR 3349 0.12 0.6 YES
14 FASLG FASLG FASLG 3452 0.12 0.62 YES
15 BTK BTK BTK 3551 0.12 0.64 YES
16 IKBKB IKBKB IKBKB 4540 0.081 0.6 NO
17 RIPK1 RIPK1 RIPK1 4869 0.072 0.6 NO
18 RFC1 RFC1 RFC1 6723 0.033 0.51 NO
19 PIK3R2 PIK3R2 PIK3R2 7184 0.024 0.49 NO
20 CASP3 CASP3 CASP3 7304 0.022 0.49 NO
21 SMPD1 SMPD1 SMPD1 7799 0.014 0.47 NO
22 PIK3CA PIK3CA PIK3CA 7976 0.011 0.46 NO
23 IKBKG IKBKG IKBKG 8001 0.011 0.46 NO
24 AKT1 AKT1 AKT1 8029 0.011 0.46 NO
25 CLTC CLTC CLTC 8482 0.0036 0.44 NO
26 FADD FADD FADD 8488 0.0035 0.44 NO
27 MAP2K7 MAP2K7 MAP2K7 8526 0.003 0.44 NO
28 BIRC2 BIRC2 BIRC2 8973 -0.0042 0.42 NO
29 MAPK9 MAPK9 MAPK9 9190 -0.0073 0.4 NO
30 MAPK8 MAPK8 MAPK8 9321 -0.0091 0.4 NO
31 PIK3CD PIK3CD PIK3CD 10080 -0.02 0.36 NO
32 BID BID BID 10192 -0.021 0.36 NO
33 MAPK14 MAPK14 MAPK14 10638 -0.028 0.34 NO
34 CHUK CHUK CHUK 10701 -0.029 0.35 NO
35 MAPK11 MAPK11 MAPK11 11967 -0.048 0.29 NO
36 PDPK1 PDPK1 PDPK1 12670 -0.062 0.27 NO
37 SRC SRC SRC 13785 -0.086 0.23 NO
38 FAIM2 FAIM2 FAIM2 15517 -0.15 0.17 NO

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

Figure S24.  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: PID HIF2PATHWAY

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 VAV3 VAV3 VAV3 190 0.57 0.13 YES
2 SYK SYK SYK 281 0.51 0.25 YES
3 CD44 CD44 CD44 901 0.33 0.29 YES
4 PLAU PLAU PLAU 1039 0.31 0.36 YES
5 FOS FOS FOS 1151 0.29 0.42 YES
6 ITGB3 ITGB3 ITGB3 1438 0.26 0.47 YES
7 PIK3R1 PIK3R1 PIK3R1 1685 0.23 0.51 YES
8 PTK2B PTK2B PTK2B 2029 0.2 0.55 YES
9 NFKBIA NFKBIA NFKBIA 2493 0.17 0.56 YES
10 MMP9 MMP9 MMP9 2859 0.15 0.58 YES
11 ITGAV ITGAV ITGAV 3010 0.14 0.6 YES
12 MAP3K1 MAP3K1 MAP3K1 3055 0.14 0.63 YES
13 MMP2 MMP2 MMP2 3271 0.13 0.65 YES
14 SPP1 SPP1 SPP1 3643 0.11 0.66 YES
15 JUN JUN JUN 3757 0.11 0.68 YES
16 GSN GSN GSN 4666 0.077 0.65 NO
17 NFKB1 NFKB1 NFKB1 5025 0.068 0.65 NO
18 RHOA RHOA RHOA 5113 0.066 0.66 NO
19 ILK ILK ILK 5903 0.049 0.63 NO
20 PIK3CA PIK3CA PIK3CA 7976 0.011 0.52 NO
21 ROCK2 ROCK2 ROCK2 8047 0.01 0.52 NO
22 RELA RELA RELA 8074 0.01 0.52 NO
23 BCAR1 BCAR1 BCAR1 8349 0.0054 0.5 NO
24 MAPK3 MAPK3 MAPK3 8354 0.0053 0.51 NO
25 CDC42 CDC42 CDC42 8629 0.0013 0.49 NO
26 RAC1 RAC1 RAC1 8804 -0.0012 0.48 NO
27 MAPK8 MAPK8 MAPK8 9321 -0.0091 0.46 NO
28 CHUK CHUK CHUK 10701 -0.029 0.39 NO
29 MAPK1 MAPK1 MAPK1 11100 -0.035 0.38 NO
30 PIP5K1A PIP5K1A PIP5K1A 11318 -0.038 0.37 NO
31 MAP3K14 MAP3K14 MAP3K14 13569 -0.08 0.27 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: PID HIF2PATHWAY.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: PID HIF2PATHWAY, 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: PID AVB3 OPN 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 TLR3 TLR3 TLR3 192 0.57 0.06 YES
2 RIPK3 RIPK3 RIPK3 418 0.45 0.1 YES
3 RPS6KA5 RPS6KA5 RPS6KA5 489 0.43 0.15 YES
4 MAPK10 MAPK10 MAPK10 543 0.42 0.2 YES
5 SAA1 SAA1 SAA1 669 0.38 0.24 YES
6 S100B S100B S100B 913 0.33 0.27 YES
7 FOS FOS FOS 1151 0.29 0.3 YES
8 RPS6KA2 RPS6KA2 RPS6KA2 1197 0.29 0.33 YES
9 IRF7 IRF7 IRF7 1228 0.28 0.36 YES
10 TICAM1 TICAM1 TICAM1 1475 0.26 0.38 YES
11 DUSP4 DUSP4 DUSP4 1785 0.23 0.39 YES
12 MAP2K6 MAP2K6 MAP2K6 2265 0.19 0.39 YES
13 RIPK2 RIPK2 RIPK2 2307 0.18 0.41 YES
14 RPS6KA1 RPS6KA1 RPS6KA1 2317 0.18 0.43 YES
15 IKBKE IKBKE IKBKE 2456 0.17 0.45 YES
16 NFKBIA NFKBIA NFKBIA 2493 0.17 0.47 YES
17 IRAK2 IRAK2 IRAK2 2966 0.14 0.46 YES
18 ZBP1 ZBP1 ZBP1 3365 0.12 0.45 YES
19 MAP2K3 MAP2K3 MAP2K3 3544 0.12 0.46 YES
20 PPP2CB PPP2CB PPP2CB 3717 0.11 0.46 YES
21 JUN JUN JUN 3757 0.11 0.47 YES
22 DUSP6 DUSP6 DUSP6 4168 0.093 0.46 NO
23 IKBKB IKBKB IKBKB 4540 0.081 0.45 NO
24 RIPK1 RIPK1 RIPK1 4869 0.072 0.44 NO
25 PPP2R1B PPP2R1B PPP2R1B 5137 0.065 0.44 NO
26 APP APP APP 5186 0.064 0.44 NO
27 TRAF6 TRAF6 TRAF6 6010 0.046 0.4 NO
28 CREB1 CREB1 CREB1 6264 0.041 0.4 NO
29 IRF3 IRF3 IRF3 6717 0.033 0.38 NO
30 UBA52 UBA52 UBA52 7115 0.025 0.36 NO
31 MAPKAPK2 MAPKAPK2 MAPKAPK2 7143 0.025 0.36 NO
32 NOD2 NOD2 NOD2 7889 0.013 0.32 NO
33 IKBKG IKBKG IKBKG 8001 0.011 0.32 NO
34 RELA RELA RELA 8074 0.01 0.31 NO
35 NOD1 NOD1 NOD1 8094 0.0096 0.31 NO
36 PPP2CA PPP2CA PPP2CA 8313 0.006 0.3 NO
37 MAPK3 MAPK3 MAPK3 8354 0.0053 0.3 NO
38 MAP2K7 MAP2K7 MAP2K7 8526 0.003 0.29 NO
39 TBK1 TBK1 TBK1 8710 0.00027 0.28 NO
40 PPP2R1A PPP2R1A PPP2R1A 8782 -0.00082 0.28 NO
41 TAB2 TAB2 TAB2 9183 -0.0072 0.26 NO
42 MAPK9 MAPK9 MAPK9 9190 -0.0073 0.26 NO
43 IRAK1 IRAK1 IRAK1 9233 -0.0078 0.26 NO
44 MAPK8 MAPK8 MAPK8 9321 -0.0091 0.25 NO
45 DUSP3 DUSP3 DUSP3 9886 -0.017 0.22 NO
46 CDK1 CDK1 CDK1 10001 -0.019 0.22 NO
47 HMGB1 HMGB1 HMGB1 10049 -0.02 0.22 NO
48 MAP2K2 MAP2K2 MAP2K2 10081 -0.02 0.22 NO
49 MAP2K4 MAP2K4 MAP2K4 10493 -0.026 0.2 NO
50 MAPK14 MAPK14 MAPK14 10638 -0.028 0.2 NO
51 CHUK CHUK CHUK 10701 -0.029 0.2 NO
52 MAPK1 MAPK1 MAPK1 11100 -0.035 0.18 NO
53 MAPK7 MAPK7 MAPK7 11257 -0.037 0.18 NO
54 TAB1 TAB1 TAB1 11475 -0.04 0.17 NO
55 RPS27A RPS27A RPS27A 11845 -0.046 0.16 NO
56 PPP2R5D PPP2R5D PPP2R5D 11947 -0.048 0.16 NO
57 MAPK11 MAPK11 MAPK11 11967 -0.048 0.16 NO
58 MAPKAPK3 MAPKAPK3 MAPKAPK3 12047 -0.05 0.16 NO
59 TAB3 TAB3 TAB3 12152 -0.052 0.16 NO
60 NFKB2 NFKB2 NFKB2 12851 -0.065 0.14 NO
61 MEF2A MEF2A MEF2A 12921 -0.067 0.14 NO
62 RPS6KA3 RPS6KA3 RPS6KA3 12945 -0.067 0.15 NO
63 ELK1 ELK1 ELK1 13429 -0.077 0.13 NO
64 MAP2K1 MAP2K1 MAP2K1 13529 -0.079 0.14 NO
65 S100A12 S100A12 S100A12 13695 -0.083 0.14 NO
66 MAP3K7 MAP3K7 MAP3K7 13740 -0.084 0.14 NO
67 ATF2 ATF2 ATF2 14231 -0.099 0.13 NO
68 ATF1 ATF1 ATF1 15089 -0.13 0.1 NO
69 DUSP7 DUSP7 DUSP7 15224 -0.14 0.11 NO
70 AGER AGER AGER 15246 -0.14 0.13 NO
71 NFKBIB NFKBIB NFKBIB 16249 -0.2 0.097 NO
72 MEF2C MEF2C MEF2C 16865 -0.25 0.096 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: PID AVB3 OPN PATHWAY.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AVB3 OPN 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: PID TRAIL 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 AP1M2 AP1M2 AP1M2 39 0.76 0.089 YES
2 KLC3 KLC3 KLC3 825 0.34 0.088 YES
3 HLA-DRB5 HLA-DRB5 HLA-DRB5 869 0.34 0.13 YES
4 CTSK CTSK CTSK 1142 0.3 0.15 YES
5 HLA-DMA HLA-DMA HLA-DMA 1202 0.29 0.18 YES
6 SH3GL2 SH3GL2 SH3GL2 1285 0.28 0.21 YES
7 HLA-DQA2 HLA-DQA2 HLA-DQA2 1292 0.28 0.24 YES
8 HLA-DRB1 HLA-DRB1 HLA-DRB1 1352 0.27 0.27 YES
9 CTSO CTSO CTSO 1427 0.26 0.3 YES
10 HLA-DOB HLA-DOB HLA-DOB 1428 0.26 0.33 YES
11 DYNC1I1 DYNC1I1 DYNC1I1 1450 0.26 0.36 YES
12 HLA-DQA1 HLA-DQA1 HLA-DQA1 1664 0.24 0.38 YES
13 CTSH CTSH CTSH 2073 0.2 0.38 YES
14 CD74 CD74 CD74 2104 0.2 0.4 YES
15 HLA-DPA1 HLA-DPA1 HLA-DPA1 2164 0.19 0.42 YES
16 CTSS CTSS CTSS 2214 0.19 0.44 YES
17 HLA-DPB1 HLA-DPB1 HLA-DPB1 2351 0.18 0.46 YES
18 CTSB CTSB CTSB 2598 0.16 0.46 YES
19 HLA-DMB HLA-DMB HLA-DMB 2782 0.15 0.47 YES
20 RILP RILP RILP 3160 0.13 0.46 NO
21 CTSD CTSD CTSD 3830 0.1 0.44 NO
22 CTSC CTSC CTSC 4057 0.096 0.44 NO
23 DCTN6 DCTN6 DCTN6 4808 0.073 0.41 NO
24 SAR1B SAR1B SAR1B 5725 0.052 0.37 NO
25 LGMN LGMN LGMN 5837 0.05 0.37 NO
26 SEC24D SEC24D SEC24D 5948 0.048 0.37 NO
27 AP2S1 AP2S1 AP2S1 6172 0.043 0.36 NO
28 AP1S1 AP1S1 AP1S1 6340 0.04 0.36 NO
29 SPTBN2 SPTBN2 SPTBN2 6564 0.036 0.35 NO
30 SEC24B SEC24B SEC24B 6665 0.034 0.35 NO
31 AP1G1 AP1G1 AP1G1 6781 0.032 0.34 NO
32 CANX CANX CANX 6975 0.028 0.34 NO
33 DYNC1LI2 DYNC1LI2 DYNC1LI2 7102 0.026 0.33 NO
34 CLTA CLTA CLTA 7258 0.022 0.33 NO
35 DYNLL1 DYNLL1 DYNLL1 7352 0.021 0.32 NO
36 SEC24C SEC24C SEC24C 7355 0.021 0.33 NO
37 CTSA CTSA CTSA 7562 0.018 0.32 NO
38 DYNLL2 DYNLL2 DYNLL2 7759 0.015 0.31 NO
39 KIF4B KIF4B KIF4B 7876 0.013 0.3 NO
40 DCTN3 DCTN3 DCTN3 8014 0.011 0.3 NO
41 CTSL2 CTSL2 CTSL2 8070 0.01 0.3 NO
42 KIF2A KIF2A KIF2A 8082 0.0098 0.3 NO
43 KIFAP3 KIFAP3 KIFAP3 8100 0.0095 0.3 NO
44 AP1B1 AP1B1 AP1B1 8122 0.0091 0.3 NO
45 KIF5A KIF5A KIF5A 8241 0.0071 0.29 NO
46 CLTC CLTC CLTC 8482 0.0036 0.28 NO
47 DCTN4 DCTN4 DCTN4 8494 0.0034 0.28 NO
48 DYNC1H1 DYNC1H1 DYNC1H1 8599 0.0018 0.27 NO
49 DCTN5 DCTN5 DCTN5 8748 -0.00049 0.27 NO
50 AP2M1 AP2M1 AP2M1 8850 -0.002 0.26 NO
51 AP2A1 AP2A1 AP2A1 9036 -0.0052 0.25 NO
52 KIF3B KIF3B KIF3B 9127 -0.0065 0.25 NO
53 ARF1 ARF1 ARF1 9417 -0.01 0.23 NO
54 AP2A2 AP2A2 AP2A2 9492 -0.012 0.23 NO
55 DNM2 DNM2 DNM2 9573 -0.013 0.23 NO
56 OSBPL1A OSBPL1A OSBPL1A 9653 -0.014 0.22 NO
57 RACGAP1 RACGAP1 RACGAP1 9709 -0.015 0.22 NO
58 SEC31A SEC31A SEC31A 9834 -0.016 0.22 NO
59 CTSF CTSF CTSF 10011 -0.019 0.21 NO
60 ACTR1B ACTR1B ACTR1B 10029 -0.019 0.21 NO
61 DCTN2 DCTN2 DCTN2 10190 -0.021 0.21 NO
62 KLC1 KLC1 KLC1 10539 -0.026 0.19 NO
63 ACTR1A ACTR1A ACTR1A 10559 -0.027 0.19 NO
64 KIF5B KIF5B KIF5B 10718 -0.029 0.19 NO
65 RAB7A RAB7A RAB7A 10719 -0.029 0.19 NO
66 DYNC2LI1 DYNC2LI1 DYNC2LI1 10732 -0.029 0.2 NO
67 KLC2 KLC2 KLC2 10827 -0.031 0.19 NO
68 AP2B1 AP2B1 AP2B1 11037 -0.034 0.19 NO
69 DCTN1 DCTN1 DCTN1 11246 -0.037 0.18 NO
70 SEC23A SEC23A SEC23A 11308 -0.038 0.18 NO
71 DYNC1I2 DYNC1I2 DYNC1I2 11400 -0.039 0.18 NO
72 CTSL1 CTSL1 CTSL1 11498 -0.041 0.18 NO
73 KIF4A KIF4A KIF4A 11545 -0.041 0.18 NO
74 AP1S2 AP1S2 AP1S2 11651 -0.043 0.18 NO
75 SEC13 SEC13 SEC13 11820 -0.046 0.18 NO
76 KIF20A KIF20A KIF20A 12010 -0.049 0.18 NO
77 KLC4 KLC4 KLC4 12044 -0.05 0.18 NO
78 KIF18A KIF18A KIF18A 12503 -0.058 0.16 NO
79 KIF3C KIF3C KIF3C 13099 -0.07 0.14 NO
80 KIF22 KIF22 KIF22 13800 -0.086 0.11 NO
81 KIF23 KIF23 KIF23 13956 -0.09 0.11 NO
82 KIF11 KIF11 KIF11 14341 -0.1 0.1 NO
83 KIF2C KIF2C KIF2C 14422 -0.1 0.11 NO
84 DYNC2H1 DYNC2H1 DYNC2H1 14546 -0.11 0.12 NO
85 KIF15 KIF15 KIF15 14575 -0.11 0.13 NO
86 AP1M1 AP1M1 AP1M1 14934 -0.12 0.13 NO
87 DNM1 DNM1 DNM1 15457 -0.15 0.12 NO
88 HLA-DOA HLA-DOA HLA-DOA 15977 -0.18 0.11 NO
89 KIF26A KIF26A KIF26A 17124 -0.28 0.082 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: PID TRAIL PATHWAY.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: PID TRAIL 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: PID FASPATHWAY

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 TLR3 TLR3 TLR3 192 0.57 0.063 YES
2 RPS6KA5 RPS6KA5 RPS6KA5 489 0.43 0.1 YES
3 MAPK10 MAPK10 MAPK10 543 0.42 0.15 YES
4 SAA1 SAA1 SAA1 669 0.38 0.2 YES
5 S100B S100B S100B 913 0.33 0.23 YES
6 FOS FOS FOS 1151 0.29 0.25 YES
7 RPS6KA2 RPS6KA2 RPS6KA2 1197 0.29 0.29 YES
8 TLR4 TLR4 TLR4 1437 0.26 0.31 YES
9 TICAM2 TICAM2 TICAM2 1464 0.26 0.34 YES
10 TICAM1 TICAM1 TICAM1 1475 0.26 0.37 YES
11 DUSP4 DUSP4 DUSP4 1785 0.23 0.38 YES
12 MAP2K6 MAP2K6 MAP2K6 2265 0.19 0.38 YES
13 RIPK2 RIPK2 RIPK2 2307 0.18 0.4 YES
14 RPS6KA1 RPS6KA1 RPS6KA1 2317 0.18 0.43 YES
15 NFKBIA NFKBIA NFKBIA 2493 0.17 0.44 YES
16 CD14 CD14 CD14 2691 0.16 0.45 YES
17 IRAK2 IRAK2 IRAK2 2966 0.14 0.45 YES
18 MAP2K3 MAP2K3 MAP2K3 3544 0.12 0.44 YES
19 PPP2CB PPP2CB PPP2CB 3717 0.11 0.44 YES
20 JUN JUN JUN 3757 0.11 0.45 YES
21 DUSP6 DUSP6 DUSP6 4168 0.093 0.44 NO
22 IKBKB IKBKB IKBKB 4540 0.081 0.43 NO
23 LY96 LY96 LY96 4852 0.072 0.43 NO
24 RIPK1 RIPK1 RIPK1 4869 0.072 0.44 NO
25 PPP2R1B PPP2R1B PPP2R1B 5137 0.065 0.43 NO
26 APP APP APP 5186 0.064 0.44 NO
27 TRAF6 TRAF6 TRAF6 6010 0.046 0.4 NO
28 CREB1 CREB1 CREB1 6264 0.041 0.39 NO
29 UBA52 UBA52 UBA52 7115 0.025 0.35 NO
30 MAPKAPK2 MAPKAPK2 MAPKAPK2 7143 0.025 0.35 NO
31 NOD2 NOD2 NOD2 7889 0.013 0.31 NO
32 IKBKG IKBKG IKBKG 8001 0.011 0.3 NO
33 RELA RELA RELA 8074 0.01 0.3 NO
34 NOD1 NOD1 NOD1 8094 0.0096 0.3 NO
35 PPP2CA PPP2CA PPP2CA 8313 0.006 0.29 NO
36 MAPK3 MAPK3 MAPK3 8354 0.0053 0.29 NO
37 MAP2K7 MAP2K7 MAP2K7 8526 0.003 0.28 NO
38 PPP2R1A PPP2R1A PPP2R1A 8782 -0.00082 0.27 NO
39 TAB2 TAB2 TAB2 9183 -0.0072 0.25 NO
40 MAPK9 MAPK9 MAPK9 9190 -0.0073 0.25 NO
41 IRAK1 IRAK1 IRAK1 9233 -0.0078 0.25 NO
42 MAPK8 MAPK8 MAPK8 9321 -0.0091 0.24 NO
43 DUSP3 DUSP3 DUSP3 9886 -0.017 0.22 NO
44 CDK1 CDK1 CDK1 10001 -0.019 0.21 NO
45 HMGB1 HMGB1 HMGB1 10049 -0.02 0.21 NO
46 MAP2K2 MAP2K2 MAP2K2 10081 -0.02 0.21 NO
47 MAP2K4 MAP2K4 MAP2K4 10493 -0.026 0.19 NO
48 MAPK14 MAPK14 MAPK14 10638 -0.028 0.19 NO
49 CHUK CHUK CHUK 10701 -0.029 0.19 NO
50 MAPK1 MAPK1 MAPK1 11100 -0.035 0.17 NO
51 MAPK7 MAPK7 MAPK7 11257 -0.037 0.17 NO
52 TAB1 TAB1 TAB1 11475 -0.04 0.16 NO
53 RPS27A RPS27A RPS27A 11845 -0.046 0.15 NO
54 PPP2R5D PPP2R5D PPP2R5D 11947 -0.048 0.15 NO
55 MAPK11 MAPK11 MAPK11 11967 -0.048 0.16 NO
56 MAPKAPK3 MAPKAPK3 MAPKAPK3 12047 -0.05 0.16 NO
57 TAB3 TAB3 TAB3 12152 -0.052 0.16 NO
58 NFKB2 NFKB2 NFKB2 12851 -0.065 0.13 NO
59 MEF2A MEF2A MEF2A 12921 -0.067 0.13 NO
60 RPS6KA3 RPS6KA3 RPS6KA3 12945 -0.067 0.14 NO
61 ELK1 ELK1 ELK1 13429 -0.077 0.12 NO
62 MAP2K1 MAP2K1 MAP2K1 13529 -0.079 0.13 NO
63 S100A12 S100A12 S100A12 13695 -0.083 0.13 NO
64 MAP3K7 MAP3K7 MAP3K7 13740 -0.084 0.14 NO
65 ATF2 ATF2 ATF2 14231 -0.099 0.13 NO
66 ATF1 ATF1 ATF1 15089 -0.13 0.097 NO
67 DUSP7 DUSP7 DUSP7 15224 -0.14 0.11 NO
68 AGER AGER AGER 15246 -0.14 0.12 NO
69 NFKBIB NFKBIB NFKBIB 16249 -0.2 0.096 NO
70 MEF2C MEF2C MEF2C 16865 -0.25 0.096 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: PID FASPATHWAY.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: PID FASPATHWAY, 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: PID IL1PATHWAY

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 TLR3 TLR3 TLR3 192 0.57 0.044 YES
2 RPS6KA5 RPS6KA5 RPS6KA5 489 0.43 0.068 YES
3 MAPK10 MAPK10 MAPK10 543 0.42 0.1 YES
4 SAA1 SAA1 SAA1 669 0.38 0.13 YES
5 TLR1 TLR1 TLR1 684 0.38 0.17 YES
6 S100B S100B S100B 913 0.33 0.19 YES
7 FOS FOS FOS 1151 0.29 0.2 YES
8 SIGIRR SIGIRR SIGIRR 1176 0.29 0.23 YES
9 RPS6KA2 RPS6KA2 RPS6KA2 1197 0.29 0.26 YES
10 IRF7 IRF7 IRF7 1228 0.28 0.28 YES
11 TLR4 TLR4 TLR4 1437 0.26 0.29 YES
12 TICAM2 TICAM2 TICAM2 1464 0.26 0.32 YES
13 TICAM1 TICAM1 TICAM1 1475 0.26 0.34 YES
14 DUSP4 DUSP4 DUSP4 1785 0.23 0.35 YES
15 TLR2 TLR2 TLR2 1903 0.22 0.36 YES
16 PELI2 PELI2 PELI2 1977 0.21 0.38 YES
17 MAP2K6 MAP2K6 MAP2K6 2265 0.19 0.38 YES
18 RIPK2 RIPK2 RIPK2 2307 0.18 0.39 YES
19 RPS6KA1 RPS6KA1 RPS6KA1 2317 0.18 0.41 YES
20 IKBKE IKBKE IKBKE 2456 0.17 0.42 YES
21 NFKBIA NFKBIA NFKBIA 2493 0.17 0.43 YES
22 TLR6 TLR6 TLR6 2576 0.16 0.44 YES
23 CD14 CD14 CD14 2691 0.16 0.45 YES
24 MYD88 MYD88 MYD88 2798 0.15 0.46 YES
25 IRAK2 IRAK2 IRAK2 2966 0.14 0.47 YES
26 MAP3K1 MAP3K1 MAP3K1 3055 0.14 0.47 YES
27 IRAK4 IRAK4 IRAK4 3421 0.12 0.47 YES
28 MAP2K3 MAP2K3 MAP2K3 3544 0.12 0.47 YES
29 BTK BTK BTK 3551 0.12 0.48 YES
30 PPP2CB PPP2CB PPP2CB 3717 0.11 0.48 YES
31 JUN JUN JUN 3757 0.11 0.49 YES
32 DUSP6 DUSP6 DUSP6 4168 0.093 0.48 NO
33 IKBKB IKBKB IKBKB 4540 0.081 0.46 NO
34 LY96 LY96 LY96 4852 0.072 0.46 NO
35 RIPK1 RIPK1 RIPK1 4869 0.072 0.46 NO
36 PPP2R1B PPP2R1B PPP2R1B 5137 0.065 0.45 NO
37 APP APP APP 5186 0.064 0.46 NO
38 TRAF6 TRAF6 TRAF6 6010 0.046 0.42 NO
39 TMEM189-UBE2V1 TMEM189-UBE2V1 TMEM189-UBE2V1 6188 0.043 0.41 NO
40 CREB1 CREB1 CREB1 6264 0.041 0.41 NO
41 IRF3 IRF3 IRF3 6717 0.033 0.39 NO
42 TIRAP TIRAP TIRAP 6832 0.031 0.39 NO
43 UBA52 UBA52 UBA52 7115 0.025 0.37 NO
44 MAPKAPK2 MAPKAPK2 MAPKAPK2 7143 0.025 0.37 NO
45 UBE2N UBE2N UBE2N 7390 0.02 0.36 NO
46 PELI1 PELI1 PELI1 7593 0.017 0.35 NO
47 NOD2 NOD2 NOD2 7889 0.013 0.34 NO
48 IKBKG IKBKG IKBKG 8001 0.011 0.33 NO
49 RELA RELA RELA 8074 0.01 0.33 NO
50 NOD1 NOD1 NOD1 8094 0.0096 0.33 NO
51 PPP2CA PPP2CA PPP2CA 8313 0.006 0.32 NO
52 MAPK3 MAPK3 MAPK3 8354 0.0053 0.32 NO
53 MAP2K7 MAP2K7 MAP2K7 8526 0.003 0.31 NO
54 TBK1 TBK1 TBK1 8710 0.00027 0.3 NO
55 PPP2R1A PPP2R1A PPP2R1A 8782 -0.00082 0.3 NO
56 TAB2 TAB2 TAB2 9183 -0.0072 0.28 NO
57 MAPK9 MAPK9 MAPK9 9190 -0.0073 0.28 NO
58 IRAK1 IRAK1 IRAK1 9233 -0.0078 0.27 NO
59 MAPK8 MAPK8 MAPK8 9321 -0.0091 0.27 NO
60 TRAF3 TRAF3 TRAF3 9662 -0.014 0.25 NO
61 DUSP3 DUSP3 DUSP3 9886 -0.017 0.24 NO
62 CDK1 CDK1 CDK1 10001 -0.019 0.24 NO
63 HMGB1 HMGB1 HMGB1 10049 -0.02 0.24 NO
64 MAP2K2 MAP2K2 MAP2K2 10081 -0.02 0.24 NO
65 MAP2K4 MAP2K4 MAP2K4 10493 -0.026 0.22 NO
66 MAPK14 MAPK14 MAPK14 10638 -0.028 0.21 NO
67 CHUK CHUK CHUK 10701 -0.029 0.21 NO
68 ECSIT ECSIT ECSIT 10956 -0.032 0.2 NO
69 MAPK1 MAPK1 MAPK1 11100 -0.035 0.2 NO
70 MAPK7 MAPK7 MAPK7 11257 -0.037 0.19 NO
71 PELI3 PELI3 PELI3 11460 -0.04 0.18 NO
72 TAB1 TAB1 TAB1 11475 -0.04 0.19 NO
73 RPS27A RPS27A RPS27A 11845 -0.046 0.17 NO
74 PPP2R5D PPP2R5D PPP2R5D 11947 -0.048 0.17 NO
75 MAPK11 MAPK11 MAPK11 11967 -0.048 0.18 NO
76 MAPKAPK3 MAPKAPK3 MAPKAPK3 12047 -0.05 0.18 NO
77 TAB3 TAB3 TAB3 12152 -0.052 0.18 NO
78 NFKB2 NFKB2 NFKB2 12851 -0.065 0.14 NO
79 MEF2A MEF2A MEF2A 12921 -0.067 0.15 NO
80 RPS6KA3 RPS6KA3 RPS6KA3 12945 -0.067 0.15 NO
81 ELK1 ELK1 ELK1 13429 -0.077 0.13 NO
82 MAP2K1 MAP2K1 MAP2K1 13529 -0.079 0.14 NO
83 S100A12 S100A12 S100A12 13695 -0.083 0.13 NO
84 MAP3K7 MAP3K7 MAP3K7 13740 -0.084 0.14 NO
85 ATF2 ATF2 ATF2 14231 -0.099 0.12 NO
86 ATF1 ATF1 ATF1 15089 -0.13 0.088 NO
87 DUSP7 DUSP7 DUSP7 15224 -0.14 0.094 NO
88 AGER AGER AGER 15246 -0.14 0.11 NO
89 NFKBIB NFKBIB NFKBIB 16249 -0.2 0.07 NO
90 MEF2C MEF2C MEF2C 16865 -0.25 0.061 NO
91 IRAK3 IRAK3 IRAK3 17737 -0.36 0.049 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: PID IL1PATHWAY.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: PID IL1PATHWAY, 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: PID ECADHERIN NASCENTAJ PATHWAY

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 NOXA1 NOXA1 NOXA1 287 0.51 0.096 YES
2 CDH1 CDH1 CDH1 410 0.46 0.19 YES
3 PIP5K1B PIP5K1B PIP5K1B 1568 0.25 0.18 YES
4 CYBB CYBB CYBB 1841 0.22 0.22 YES
5 MAP2K6 MAP2K6 MAP2K6 2265 0.19 0.23 YES
6 CYBA CYBA CYBA 2286 0.18 0.27 YES
7 NCF2 NCF2 NCF2 2328 0.18 0.31 YES
8 NCF1 NCF1 NCF1 2471 0.17 0.34 YES
9 IQGAP1 IQGAP1 IQGAP1 2521 0.17 0.38 YES
10 MAP3K1 MAP3K1 MAP3K1 3055 0.14 0.38 YES
11 ARPC1B ARPC1B ARPC1B 3386 0.12 0.39 YES
12 MAP2K3 MAP2K3 MAP2K3 3544 0.12 0.4 YES
13 CTNNA1 CTNNA1 CTNNA1 3682 0.11 0.42 YES
14 JUN JUN JUN 3757 0.11 0.44 YES
15 NOXO1 NOXO1 NOXO1 3965 0.099 0.45 YES
16 ARHGAP5 ARHGAP5 ARHGAP5 4539 0.081 0.44 YES
17 ABI1 ABI1 ABI1 4741 0.075 0.44 YES
18 CRK CRK CRK 4884 0.071 0.45 YES
19 NOX1 NOX1 NOX1 4935 0.07 0.46 YES
20 ARPC5 ARPC5 ARPC5 5070 0.067 0.47 YES
21 ACTR3 ACTR3 ACTR3 5385 0.059 0.47 YES
22 MAP3K11 MAP3K11 MAP3K11 5489 0.057 0.48 YES
23 STAT3 STAT3 STAT3 5634 0.054 0.48 YES
24 PAK1 PAK1 PAK1 5732 0.052 0.48 YES
25 ARPC3 ARPC3 ARPC3 5817 0.051 0.49 YES
26 CTNNB1 CTNNB1 CTNNB1 6328 0.04 0.47 NO
27 IQGAP3 IQGAP3 IQGAP3 6533 0.036 0.47 NO
28 WASF1 WASF1 WASF1 7762 0.015 0.41 NO
29 CFL1 CFL1 CFL1 7924 0.012 0.4 NO
30 BCAR1 BCAR1 BCAR1 8349 0.0054 0.38 NO
31 ARPC2 ARPC2 ARPC2 8461 0.0039 0.38 NO
32 ACTR2 ACTR2 ACTR2 8500 0.0033 0.37 NO
33 MAP2K7 MAP2K7 MAP2K7 8526 0.003 0.37 NO
34 NCKAP1 NCKAP1 NCKAP1 8661 0.00094 0.37 NO
35 RAC1 RAC1 RAC1 8804 -0.0012 0.36 NO
36 PIP5K1C PIP5K1C PIP5K1C 9003 -0.0047 0.35 NO
37 MAPK9 MAPK9 MAPK9 9190 -0.0073 0.34 NO
38 MAPK8 MAPK8 MAPK8 9321 -0.0091 0.34 NO
39 CYFIP2 CYFIP2 CYFIP2 9517 -0.012 0.33 NO
40 RACGAP1 RACGAP1 RACGAP1 9709 -0.015 0.32 NO
41 ARPC4 ARPC4 ARPC4 9863 -0.017 0.32 NO
42 MAP2K4 MAP2K4 MAP2K4 10493 -0.026 0.29 NO
43 MAPK14 MAPK14 MAPK14 10638 -0.028 0.29 NO
44 STAT5A STAT5A STAT5A 10663 -0.028 0.29 NO
45 ABI2 ABI2 ABI2 10913 -0.032 0.28 NO
46 PIP5K1A PIP5K1A PIP5K1A 11318 -0.038 0.27 NO
47 PAK2 PAK2 PAK2 11409 -0.039 0.28 NO
48 ARHGDIA ARHGDIA ARHGDIA 11764 -0.045 0.27 NO
49 WASF2 WASF2 WASF2 12283 -0.054 0.25 NO
50 BAIAP2 BAIAP2 BAIAP2 13585 -0.08 0.2 NO
51 ATF2 ATF2 ATF2 14231 -0.099 0.18 NO
52 LIMK1 LIMK1 LIMK1 14380 -0.1 0.2 NO
53 PLCB2 PLCB2 PLCB2 15223 -0.14 0.18 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: PID ECADHERIN NASCENTAJ PATHWAY.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ECADHERIN NASCENTAJ 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: PID PDGFRBPATHWAY

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 TFAP2C TFAP2C TFAP2C 53 0.73 0.074 YES
2 S100A2 S100A2 S100A2 95 0.66 0.14 YES
3 ITGB4 ITGB4 ITGB4 142 0.6 0.2 YES
4 PERP PERP PERP 269 0.52 0.25 YES
5 VDR VDR VDR 312 0.5 0.3 YES
6 CLCA2 CLCA2 CLCA2 314 0.5 0.35 YES
7 EVPL EVPL EVPL 352 0.48 0.4 YES
8 SERPINB5 SERPINB5 SERPINB5 656 0.38 0.43 YES
9 SPATA18 SPATA18 SPATA18 944 0.32 0.44 YES
10 FAS FAS FAS 1047 0.31 0.47 YES
11 GDF15 GDF15 GDF15 1085 0.3 0.5 YES
12 NQO1 NQO1 NQO1 1106 0.3 0.53 YES
13 ITGA3 ITGA3 ITGA3 1746 0.23 0.52 YES
14 WWP1 WWP1 WWP1 1807 0.22 0.54 YES
15 PRKCD PRKCD PRKCD 1829 0.22 0.56 YES
16 DHRS3 DHRS3 DHRS3 2012 0.21 0.58 YES
17 DST DST DST 2356 0.18 0.58 YES
18 IGFBP3 IGFBP3 IGFBP3 2642 0.16 0.58 YES
19 JAG1 JAG1 JAG1 2772 0.15 0.59 YES
20 CABLES1 CABLES1 CABLES1 3320 0.13 0.57 NO
21 PML PML PML 4176 0.093 0.54 NO
22 MFGE8 MFGE8 MFGE8 4293 0.088 0.54 NO
23 TP53I3 TP53I3 TP53I3 4471 0.083 0.54 NO
24 IKBKB IKBKB IKBKB 4540 0.081 0.54 NO
25 GADD45A GADD45A GADD45A 4652 0.078 0.55 NO
26 BAX BAX BAX 5299 0.061 0.52 NO
27 YWHAQ YWHAQ YWHAQ 5622 0.055 0.51 NO
28 BBC3 BBC3 BBC3 6046 0.046 0.49 NO
29 TRAF4 TRAF4 TRAF4 6275 0.041 0.48 NO
30 HBP1 HBP1 HBP1 6321 0.04 0.48 NO
31 EGR2 EGR2 EGR2 6662 0.034 0.47 NO
32 FDXR FDXR FDXR 6878 0.03 0.46 NO
33 MDM2 MDM2 MDM2 7398 0.02 0.43 NO
34 CDKN1A CDKN1A CDKN1A 7661 0.016 0.42 NO
35 SP1 SP1 SP1 9053 -0.0054 0.35 NO
36 EP300 EP300 EP300 9294 -0.0087 0.34 NO
37 SHH SHH SHH 10362 -0.024 0.28 NO
38 CHUK CHUK CHUK 10701 -0.029 0.26 NO
39 ITCH ITCH ITCH 10934 -0.032 0.26 NO
40 FLOT2 FLOT2 FLOT2 11077 -0.034 0.25 NO
41 GPX2 GPX2 GPX2 11592 -0.042 0.23 NO
42 DICER1 DICER1 DICER1 12080 -0.051 0.21 NO
43 ABL1 ABL1 ABL1 12129 -0.051 0.21 NO
44 TP63 TP63 TP63 12391 -0.056 0.2 NO
45 PMAIP1 PMAIP1 PMAIP1 12764 -0.063 0.19 NO
46 SSRP1 SSRP1 SSRP1 12957 -0.067 0.19 NO
47 CDKN2A CDKN2A CDKN2A 13381 -0.076 0.17 NO
48 PLK1 PLK1 PLK1 13789 -0.086 0.16 NO
49 OGG1 OGG1 OGG1 13823 -0.086 0.17 NO
50 NOC2L NOC2L NOC2L 14609 -0.11 0.14 NO
51 AEN AEN AEN 15072 -0.13 0.12 NO
52 SMARCD3 SMARCD3 SMARCD3 15515 -0.15 0.12 NO
53 ADA ADA ADA 16735 -0.24 0.076 NO
54 SSPO SSPO SSPO 16813 -0.25 0.099 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: PID PDGFRBPATHWAY.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: PID PDGFRBPATHWAY, 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: PID TAP63PATHWAY

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 TLR3 TLR3 TLR3 192 0.57 0.032 YES
2 RPS6KA5 RPS6KA5 RPS6KA5 489 0.43 0.049 YES
3 MAPK10 MAPK10 MAPK10 543 0.42 0.077 YES
4 TLR5 TLR5 TLR5 654 0.38 0.1 YES
5 SAA1 SAA1 SAA1 669 0.38 0.13 YES
6 TLR1 TLR1 TLR1 684 0.38 0.16 YES
7 S100B S100B S100B 913 0.33 0.17 YES
8 CTSK CTSK CTSK 1142 0.3 0.18 YES
9 FOS FOS FOS 1151 0.29 0.2 YES
10 SIGIRR SIGIRR SIGIRR 1176 0.29 0.22 YES
11 RPS6KA2 RPS6KA2 RPS6KA2 1197 0.29 0.24 YES
12 IRF7 IRF7 IRF7 1228 0.28 0.26 YES
13 UNC93B1 UNC93B1 UNC93B1 1351 0.27 0.27 YES
14 TLR4 TLR4 TLR4 1437 0.26 0.29 YES
15 TICAM2 TICAM2 TICAM2 1464 0.26 0.31 YES
16 TICAM1 TICAM1 TICAM1 1475 0.26 0.33 YES
17 DUSP4 DUSP4 DUSP4 1785 0.23 0.33 YES
18 TLR7 TLR7 TLR7 1890 0.22 0.34 YES
19 TLR2 TLR2 TLR2 1903 0.22 0.35 YES
20 CD180 CD180 CD180 1950 0.21 0.36 YES
21 PELI2 PELI2 PELI2 1977 0.21 0.38 YES
22 CTSS CTSS CTSS 2214 0.19 0.38 YES
23 MAP2K6 MAP2K6 MAP2K6 2265 0.19 0.39 YES
24 RIPK2 RIPK2 RIPK2 2307 0.18 0.4 YES
25 RPS6KA1 RPS6KA1 RPS6KA1 2317 0.18 0.42 YES
26 PLCG2 PLCG2 PLCG2 2323 0.18 0.43 YES
27 IKBKE IKBKE IKBKE 2456 0.17 0.44 YES
28 NFKBIA NFKBIA NFKBIA 2493 0.17 0.45 YES
29 TLR6 TLR6 TLR6 2576 0.16 0.46 YES
30 CTSB CTSB CTSB 2598 0.16 0.47 YES
31 CD14 CD14 CD14 2691 0.16 0.47 YES
32 LY86 LY86 LY86 2722 0.16 0.48 YES
33 MYD88 MYD88 MYD88 2798 0.15 0.49 YES
34 IRAK2 IRAK2 IRAK2 2966 0.14 0.49 YES
35 MAP3K1 MAP3K1 MAP3K1 3055 0.14 0.5 YES
36 IRAK4 IRAK4 IRAK4 3421 0.12 0.49 YES
37 MAP2K3 MAP2K3 MAP2K3 3544 0.12 0.49 YES
38 BTK BTK BTK 3551 0.12 0.5 YES
39 PPP2CB PPP2CB PPP2CB 3717 0.11 0.5 YES
40 JUN JUN JUN 3757 0.11 0.5 YES
41 TLR8 TLR8 TLR8 3808 0.1 0.51 YES
42 TLR10 TLR10 TLR10 3828 0.1 0.52 YES
43 DUSP6 DUSP6 DUSP6 4168 0.093 0.5 NO
44 IKBKB IKBKB IKBKB 4540 0.081 0.49 NO
45 TLR9 TLR9 TLR9 4651 0.078 0.49 NO
46 LY96 LY96 LY96 4852 0.072 0.48 NO
47 RIPK1 RIPK1 RIPK1 4869 0.072 0.49 NO
48 PPP2R1B PPP2R1B PPP2R1B 5137 0.065 0.48 NO
49 APP APP APP 5186 0.064 0.48 NO
50 LGMN LGMN LGMN 5837 0.05 0.45 NO
51 TRAF6 TRAF6 TRAF6 6010 0.046 0.44 NO
52 TMEM189-UBE2V1 TMEM189-UBE2V1 TMEM189-UBE2V1 6188 0.043 0.44 NO
53 CREB1 CREB1 CREB1 6264 0.041 0.44 NO
54 IRF3 IRF3 IRF3 6717 0.033 0.42 NO
55 TIRAP TIRAP TIRAP 6832 0.031 0.41 NO
56 UBA52 UBA52 UBA52 7115 0.025 0.4 NO
57 MAPKAPK2 MAPKAPK2 MAPKAPK2 7143 0.025 0.4 NO
58 UBE2N UBE2N UBE2N 7390 0.02 0.39 NO
59 PELI1 PELI1 PELI1 7593 0.017 0.38 NO
60 NOD2 NOD2 NOD2 7889 0.013 0.36 NO
61 IKBKG IKBKG IKBKG 8001 0.011 0.36 NO
62 RELA RELA RELA 8074 0.01 0.35 NO
63 NOD1 NOD1 NOD1 8094 0.0096 0.35 NO
64 LBP LBP LBP 8140 0.0087 0.35 NO
65 PPP2CA PPP2CA PPP2CA 8313 0.006 0.34 NO
66 MAPK3 MAPK3 MAPK3 8354 0.0053 0.34 NO
67 MAP2K7 MAP2K7 MAP2K7 8526 0.003 0.33 NO
68 TBK1 TBK1 TBK1 8710 0.00027 0.32 NO
69 PPP2R1A PPP2R1A PPP2R1A 8782 -0.00082 0.32 NO
70 HSP90B1 HSP90B1 HSP90B1 9034 -0.0052 0.3 NO
71 TAB2 TAB2 TAB2 9183 -0.0072 0.3 NO
72 MAPK9 MAPK9 MAPK9 9190 -0.0073 0.3 NO
73 IRAK1 IRAK1 IRAK1 9233 -0.0078 0.3 NO
74 MAPK8 MAPK8 MAPK8 9321 -0.0091 0.29 NO
75 DNM2 DNM2 DNM2 9573 -0.013 0.28 NO
76 TRAF3 TRAF3 TRAF3 9662 -0.014 0.28 NO
77 DUSP3 DUSP3 DUSP3 9886 -0.017 0.26 NO
78 CDK1 CDK1 CDK1 10001 -0.019 0.26 NO
79 HMGB1 HMGB1 HMGB1 10049 -0.02 0.26 NO
80 MAP2K2 MAP2K2 MAP2K2 10081 -0.02 0.26 NO
81 PIK3R4 PIK3R4 PIK3R4 10104 -0.02 0.26 NO
82 PIK3C3 PIK3C3 PIK3C3 10274 -0.022 0.25 NO
83 CNPY3 CNPY3 CNPY3 10396 -0.024 0.25 NO
84 MAP2K4 MAP2K4 MAP2K4 10493 -0.026 0.24 NO
85 MAPK14 MAPK14 MAPK14 10638 -0.028 0.24 NO
86 CHUK CHUK CHUK 10701 -0.029 0.24 NO
87 ZFYVE20 ZFYVE20 ZFYVE20 10830 -0.031 0.23 NO
88 ECSIT ECSIT ECSIT 10956 -0.032 0.23 NO
89 MAPK1 MAPK1 MAPK1 11100 -0.035 0.22 NO
90 MAPK7 MAPK7 MAPK7 11257 -0.037 0.22 NO
91 EEA1 EEA1 EEA1 11361 -0.038 0.22 NO
92 PELI3 PELI3 PELI3 11460 -0.04 0.21 NO
93 TAB1 TAB1 TAB1 11475 -0.04 0.22 NO
94 CTSL1 CTSL1 CTSL1 11498 -0.041 0.22 NO
95 RPS27A RPS27A RPS27A 11845 -0.046 0.2 NO
96 PPP2R5D PPP2R5D PPP2R5D 11947 -0.048 0.2 NO
97 MAPK11 MAPK11 MAPK11 11967 -0.048 0.2 NO
98 MAPKAPK3 MAPKAPK3 MAPKAPK3 12047 -0.05 0.2 NO
99 TAB3 TAB3 TAB3 12152 -0.052 0.2 NO
100 NFKB2 NFKB2 NFKB2 12851 -0.065 0.17 NO
101 MEF2A MEF2A MEF2A 12921 -0.067 0.17 NO
102 RPS6KA3 RPS6KA3 RPS6KA3 12945 -0.067 0.17 NO
103 ELK1 ELK1 ELK1 13429 -0.077 0.15 NO
104 MAP2K1 MAP2K1 MAP2K1 13529 -0.079 0.15 NO
105 S100A12 S100A12 S100A12 13695 -0.083 0.15 NO
106 MAP3K7 MAP3K7 MAP3K7 13740 -0.084 0.15 NO
107 ATF2 ATF2 ATF2 14231 -0.099 0.14 NO
108 ATF1 ATF1 ATF1 15089 -0.13 0.099 NO
109 DUSP7 DUSP7 DUSP7 15224 -0.14 0.1 NO
110 AGER AGER AGER 15246 -0.14 0.11 NO
111 DNM1 DNM1 DNM1 15457 -0.15 0.11 NO
112 NFKBIB NFKBIB NFKBIB 16249 -0.2 0.083 NO
113 MEF2C MEF2C MEF2C 16865 -0.25 0.069 NO
114 IRAK3 IRAK3 IRAK3 17737 -0.36 0.049 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: PID TAP63PATHWAY.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: PID TAP63PATHWAY, 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
KEGG SELENOAMINO ACID METABOLISM 26 genes.ES.table 0.45 1.5 0.099 1 0.98 0.46 0.35 0.3 1 0.61
KEGG STARCH AND SUCROSE METABOLISM 40 genes.ES.table 0.62 1.6 0.017 1 0.9 0.28 0.072 0.26 1 0.55
KEGG BUTANOATE METABOLISM 32 genes.ES.table 0.51 1.5 0.064 1 0.98 0.19 0.03 0.18 1 0.64
KEGG RETINOL METABOLISM 53 genes.ES.table 0.67 1.7 0.0024 1 0.86 0.4 0.077 0.37 1 0.68
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 32 genes.ES.table 0.59 1.6 0.03 1 0.91 0.22 0.06 0.21 0.91 0.47
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 59 genes.ES.table 0.58 1.5 0.03 1 0.98 0.36 0.1 0.32 1 0.62
KEGG DRUG METABOLISM CYTOCHROME P450 60 genes.ES.table 0.58 1.5 0.039 1 0.98 0.35 0.1 0.32 1 0.58
SIG IL4RECEPTOR IN B LYPHOCYTES 27 genes.ES.table 0.53 1.7 0.012 1 0.76 0.22 0.091 0.2 1 0.69
ST INTERLEUKIN 4 PATHWAY 25 genes.ES.table 0.54 1.5 0.082 1 0.98 0.16 0.09 0.15 1 0.56
PID CD40 PATHWAY 30 genes.ES.table 0.55 1.5 0.11 1 0.98 0.2 0.079 0.18 1 0.64
genes ES table in pathway: KEGG SELENOAMINO ACID METABOLISM

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 IRS2 IRS2 IRS2 554 0.38 0.1 YES
2 MAP4K1 MAP4K1 MAP4K1 923 0.32 0.2 YES
3 SOCS1 SOCS1 SOCS1 958 0.32 0.3 YES
4 JAK3 JAK3 JAK3 1242 0.28 0.39 YES
5 STAT6 STAT6 STAT6 1675 0.24 0.45 YES
6 PIK3CD PIK3CD PIK3CD 1700 0.24 0.53 YES
7 IRS1 IRS1 IRS1 5223 0.083 0.37 NO
8 BAD BAD BAD 5554 0.076 0.37 NO
9 AKT3 AKT3 AKT3 5914 0.068 0.38 NO
10 SHC1 SHC1 SHC1 6345 0.06 0.38 NO
11 GRB2 GRB2 GRB2 6372 0.059 0.4 NO
12 MAPK3 MAPK3 MAPK3 7317 0.043 0.36 NO
13 GSK3A GSK3A GSK3A 7407 0.042 0.37 NO
14 SOS1 SOS1 SOS1 7483 0.04 0.38 NO
15 IL4R IL4R IL4R 7599 0.039 0.39 NO
16 AKT2 AKT2 AKT2 9450 0.012 0.29 NO
17 PPP1R13B PPP1R13B PPP1R13B 9962 0.0056 0.26 NO
18 JAK1 JAK1 JAK1 10025 0.0046 0.26 NO
19 MAPK1 MAPK1 MAPK1 10537 -0.0028 0.24 NO
20 SOS2 SOS2 SOS2 10691 -0.0052 0.23 NO
21 AKT1 AKT1 AKT1 12373 -0.031 0.15 NO
22 PDK1 PDK1 PDK1 12656 -0.036 0.15 NO
23 GSK3B GSK3B GSK3B 13441 -0.05 0.12 NO
24 RAF1 RAF1 RAF1 13977 -0.06 0.12 NO
25 PIK3R1 PIK3R1 PIK3R1 15032 -0.088 0.089 NO
26 PIK3CA PIK3CA PIK3CA 15343 -0.098 0.11 NO
27 BCL2 BCL2 BCL2 17234 -0.21 0.076 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: KEGG SELENOAMINO ACID METABOLISM.

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

genes ES table in pathway: KEGG STARCH AND SUCROSE METABOLISM

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 UGT2A3 UGT2A3 UGT2A3 51 0.71 0.06 YES
2 CYP2B6 CYP2B6 CYP2B6 54 0.7 0.12 YES
3 UGT2B10 UGT2B10 UGT2B10 145 0.56 0.17 YES
4 UGT2B7 UGT2B7 UGT2B7 163 0.54 0.21 YES
5 CYP26C1 CYP26C1 CYP26C1 316 0.46 0.24 YES
6 UGT2B15 UGT2B15 UGT2B15 399 0.43 0.28 YES
7 UGT1A6 UGT1A6 UGT1A6 429 0.42 0.31 YES
8 CYP3A5 CYP3A5 CYP3A5 489 0.4 0.35 YES
9 BCMO1 BCMO1 BCMO1 492 0.4 0.38 YES
10 CYP2C18 CYP2C18 CYP2C18 504 0.4 0.42 YES
11 ALDH1A1 ALDH1A1 ALDH1A1 728 0.35 0.44 YES
12 UGT1A9 UGT1A9 UGT1A9 743 0.35 0.47 YES
13 CYP2C9 CYP2C9 CYP2C9 764 0.35 0.5 YES
14 ALDH1A2 ALDH1A2 ALDH1A2 810 0.34 0.52 YES
15 ADH1B ADH1B ADH1B 831 0.34 0.55 YES
16 CYP26A1 CYP26A1 CYP26A1 881 0.33 0.58 YES
17 ADH6 ADH6 ADH6 997 0.32 0.6 YES
18 UGT2B11 UGT2B11 UGT2B11 1124 0.3 0.62 YES
19 ADH1C ADH1C ADH1C 1355 0.27 0.63 YES
20 RDH16 RDH16 RDH16 1362 0.27 0.65 YES
21 CYP3A7 CYP3A7 CYP3A7 1433 0.26 0.67 YES
22 ADH1A ADH1A ADH1A 2427 0.19 0.64 NO
23 UGT1A1 UGT1A1 UGT1A1 4115 0.11 0.56 NO
24 CYP4A11 CYP4A11 CYP4A11 4329 0.1 0.55 NO
25 RPE65 RPE65 RPE65 4557 0.099 0.55 NO
26 CYP4A22 CYP4A22 CYP4A22 4975 0.089 0.54 NO
27 CYP2C8 CYP2C8 CYP2C8 5332 0.08 0.52 NO
28 RDH5 RDH5 RDH5 6130 0.064 0.49 NO
29 RETSAT RETSAT RETSAT 6616 0.055 0.46 NO
30 RDH8 RDH8 RDH8 6647 0.055 0.47 NO
31 UGT2B4 UGT2B4 UGT2B4 6706 0.054 0.47 NO
32 DGAT2 DGAT2 DGAT2 6735 0.053 0.47 NO
33 CYP3A43 CYP3A43 CYP3A43 7844 0.035 0.42 NO
34 CYP1A2 CYP1A2 CYP1A2 9825 0.0071 0.31 NO
35 DHRS3 DHRS3 DHRS3 10347 -0.00022 0.28 NO
36 DGAT1 DGAT1 DGAT1 10602 -0.0038 0.27 NO
37 RDH10 RDH10 RDH10 11444 -0.016 0.23 NO
38 ADH5 ADH5 ADH5 11562 -0.018 0.22 NO
39 LRAT LRAT LRAT 11667 -0.02 0.22 NO
40 DHRS4 DHRS4 DHRS4 11812 -0.022 0.21 NO
41 PNPLA4 PNPLA4 PNPLA4 11903 -0.024 0.21 NO
42 ADH4 ADH4 ADH4 12130 -0.027 0.2 NO
43 CYP2A13 CYP2A13 CYP2A13 12231 -0.029 0.2 NO
44 RDH11 RDH11 RDH11 13956 -0.06 0.11 NO
45 DHRS9 DHRS9 DHRS9 14422 -0.071 0.09 NO
46 DHRS4L2 DHRS4L2 DHRS4L2 14607 -0.076 0.086 NO
47 CYP3A4 CYP3A4 CYP3A4 14667 -0.078 0.09 NO
48 CYP26B1 CYP26B1 CYP26B1 15675 -0.11 0.046 NO
49 UGT2A1 UGT2A1 UGT2A1 17380 -0.22 -0.026 NO
50 CYP2A6 CYP2A6 CYP2A6 17405 -0.23 -0.0075 NO
51 CYP1A1 CYP1A1 CYP1A1 17540 -0.24 0.0068 NO
52 RDH12 RDH12 RDH12 17774 -0.28 0.018 NO
53 AWAT2 AWAT2 AWAT2 18047 -0.32 0.032 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: KEGG STARCH AND SUCROSE METABOLISM.

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

Table 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 NMNAT2 NMNAT2 NMNAT2 202 0.52 0.076 YES
2 SLC19A3 SLC19A3 SLC19A3 431 0.42 0.13 YES
3 TPK1 TPK1 TPK1 564 0.38 0.19 YES
4 QPRT QPRT QPRT 953 0.32 0.22 YES
5 SLC23A1 SLC23A1 SLC23A1 1475 0.26 0.24 YES
6 GSTO2 GSTO2 GSTO2 1814 0.23 0.26 YES
7 CYB5A CYB5A CYB5A 2553 0.18 0.25 YES
8 PNPO PNPO PNPO 2593 0.18 0.28 YES
9 NADSYN1 NADSYN1 NADSYN1 2673 0.17 0.3 YES
10 SHMT1 SHMT1 SHMT1 2773 0.17 0.33 YES
11 SLC5A6 SLC5A6 SLC5A6 2987 0.16 0.34 YES
12 PPCDC PPCDC PPCDC 3241 0.14 0.35 YES
13 FASN FASN FASN 3324 0.14 0.37 YES
14 MOCS3 MOCS3 MOCS3 3375 0.14 0.39 YES
15 SLC2A3 SLC2A3 SLC2A3 3595 0.13 0.4 YES
16 PANK1 PANK1 PANK1 3608 0.13 0.42 YES
17 SLC46A1 SLC46A1 SLC46A1 3685 0.13 0.44 YES
18 SLC19A2 SLC19A2 SLC19A2 4336 0.1 0.42 NO
19 SLC2A1 SLC2A1 SLC2A1 4749 0.094 0.42 NO
20 NADK NADK NADK 4899 0.091 0.42 NO
21 SLC19A1 SLC19A1 SLC19A1 5305 0.081 0.42 NO
22 COASY COASY COASY 5334 0.08 0.43 NO
23 GPHN GPHN GPHN 6018 0.066 0.4 NO
24 AASDHPPT AASDHPPT AASDHPPT 6079 0.064 0.41 NO
25 FLAD1 FLAD1 FLAD1 6277 0.061 0.41 NO
26 RFK RFK RFK 6282 0.061 0.42 NO
27 SLC25A16 SLC25A16 SLC25A16 6690 0.054 0.41 NO
28 GSTO1 GSTO1 GSTO1 7015 0.048 0.4 NO
29 MTHFR MTHFR MTHFR 7117 0.047 0.4 NO
30 NMNAT3 NMNAT3 NMNAT3 7181 0.046 0.4 NO
31 FPGS FPGS FPGS 7474 0.041 0.4 NO
32 NFS1 NFS1 NFS1 7890 0.034 0.38 NO
33 ACP5 ACP5 ACP5 8932 0.019 0.32 NO
34 NMNAT1 NMNAT1 NMNAT1 9101 0.016 0.32 NO
35 SLC23A2 SLC23A2 SLC23A2 10079 0.0039 0.27 NO
36 PPCS PPCS PPCS 10789 -0.0066 0.23 NO
37 PANK2 PANK2 PANK2 10933 -0.0089 0.22 NO
38 DHFR DHFR DHFR 11454 -0.016 0.2 NO
39 PDXK PDXK PDXK 11623 -0.019 0.19 NO
40 PANK4 PANK4 PANK4 11710 -0.02 0.19 NO
41 CYB5R3 CYB5R3 CYB5R3 12073 -0.026 0.18 NO
42 THTPA THTPA THTPA 12553 -0.034 0.16 NO
43 PANK3 PANK3 PANK3 12884 -0.04 0.15 NO
44 MTHFD1 MTHFD1 MTHFD1 13512 -0.051 0.12 NO
45 NAMPT NAMPT NAMPT 14046 -0.062 0.1 NO
46 MOCS2 MOCS2 MOCS2 15764 -0.11 0.029 NO
47 SLC25A32 SLC25A32 SLC25A32 16076 -0.13 0.034 NO
48 ENPP1 ENPP1 ENPP1 16263 -0.14 0.048 NO
49 MOCS1 MOCS1 MOCS1 16786 -0.17 0.048 NO
50 MOCOS MOCOS MOCOS 17968 -0.31 0.036 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: KEGG BUTANOATE METABOLISM.

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

genes ES table in pathway: KEGG RETINOL METABOLISM

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 SULT1C2 SULT1C2 SULT1C2 53 0.7 0.071 YES
2 GLYAT GLYAT GLYAT 102 0.6 0.13 YES
3 UGT2B10 UGT2B10 UGT2B10 145 0.56 0.19 YES
4 UGT2B7 UGT2B7 UGT2B7 163 0.54 0.24 YES
5 GGT1 GGT1 GGT1 338 0.45 0.28 YES
6 ACSM1 ACSM1 ACSM1 347 0.45 0.33 YES
7 UGT1A6 UGT1A6 UGT1A6 429 0.42 0.37 YES
8 MAT1A MAT1A MAT1A 433 0.42 0.41 YES
9 SULT1E1 SULT1E1 SULT1E1 482 0.4 0.45 YES
10 UGT1A9 UGT1A9 UGT1A9 743 0.35 0.48 YES
11 SULT1C4 SULT1C4 SULT1C4 994 0.32 0.5 YES
12 UGT2B11 UGT2B11 UGT2B11 1124 0.3 0.52 YES
13 GSTA1 GSTA1 GSTA1 1633 0.25 0.52 YES
14 MGST1 MGST1 MGST1 1649 0.24 0.55 YES
15 GSTO2 GSTO2 GSTO2 1814 0.23 0.56 YES
16 GSTA2 GSTA2 GSTA2 1942 0.22 0.58 YES
17 SULT1B1 SULT1B1 SULT1B1 2359 0.19 0.57 NO
18 SULT1A1 SULT1A1 SULT1A1 3427 0.14 0.53 NO
19 AHCY AHCY AHCY 3622 0.13 0.53 NO
20 SULT1A2 SULT1A2 SULT1A2 3631 0.13 0.55 NO
21 GSTM5 GSTM5 GSTM5 3747 0.12 0.55 NO
22 UGT1A1 UGT1A1 UGT1A1 4115 0.11 0.55 NO
23 CNDP2 CNDP2 CNDP2 4917 0.09 0.51 NO
24 GSS GSS GSS 5203 0.083 0.51 NO
25 MAT2A MAT2A MAT2A 5277 0.082 0.51 NO
26 GSTP1 GSTP1 GSTP1 5394 0.079 0.51 NO
27 UGDH UGDH UGDH 5637 0.074 0.51 NO
28 SULT1A3 SULT1A3 SULT1A3 6027 0.065 0.49 NO
29 PAPSS1 PAPSS1 PAPSS1 6243 0.062 0.49 NO
30 NAT2 NAT2 NAT2 6626 0.055 0.47 NO
31 UGT2B4 UGT2B4 UGT2B4 6706 0.054 0.48 NO
32 GSTO1 GSTO1 GSTO1 7015 0.048 0.46 NO
33 MAT2B MAT2B MAT2B 7707 0.037 0.43 NO
34 TPMT TPMT TPMT 7990 0.032 0.42 NO
35 BPNT1 BPNT1 BPNT1 8029 0.032 0.42 NO
36 MTR MTR MTR 8261 0.028 0.41 NO
37 GSTM4 GSTM4 GSTM4 8357 0.027 0.41 NO
38 GCLC GCLC GCLC 8955 0.019 0.38 NO
39 MGST3 MGST3 MGST3 9084 0.017 0.37 NO
40 COMT COMT COMT 9663 0.0092 0.34 NO
41 CYP1A2 CYP1A2 CYP1A2 9825 0.0071 0.33 NO
42 MGST2 MGST2 MGST2 10236 0.0014 0.31 NO
43 NAT1 NAT1 NAT1 10570 -0.0034 0.3 NO
44 PAPSS2 PAPSS2 PAPSS2 10574 -0.0034 0.3 NO
45 GGCT GGCT GGCT 11191 -0.012 0.26 NO
46 GSTA4 GSTA4 GSTA4 11887 -0.024 0.23 NO
47 SULT2B1 SULT2B1 SULT2B1 12796 -0.038 0.18 NO
48 SULT4A1 SULT4A1 SULT4A1 12968 -0.041 0.18 NO
49 GGT7 GGT7 GGT7 13423 -0.049 0.16 NO
50 GCLM GCLM GCLM 13896 -0.059 0.14 NO
51 GGT5 GGT5 GGT5 14612 -0.076 0.11 NO
52 UGP2 UGP2 UGP2 14864 -0.083 0.1 NO
53 SLC35D1 SLC35D1 SLC35D1 15039 -0.088 0.1 NO
54 GSTA3 GSTA3 GSTA3 15652 -0.11 0.084 NO
55 GSTM1 GSTM1 GSTM1 16120 -0.13 0.072 NO
56 OPLAH OPLAH OPLAH 16983 -0.19 0.046 NO
57 NNMT NNMT NNMT 17056 -0.19 0.062 NO
58 UGT2A1 UGT2A1 UGT2A1 17380 -0.22 0.068 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: KEGG RETINOL METABOLISM.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RETINOL 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 PORPHYRIN AND CHLOROPHYLL METABOLISM

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 MGAM MGAM MGAM 43 0.72 0.09 YES
2 UGT2A3 UGT2A3 UGT2A3 51 0.71 0.18 YES
3 ENPP3 ENPP3 ENPP3 122 0.58 0.25 YES
4 UGT2B10 UGT2B10 UGT2B10 145 0.56 0.32 YES
5 UGT2B7 UGT2B7 UGT2B7 163 0.54 0.39 YES
6 AMY2B AMY2B AMY2B 194 0.52 0.46 YES
7 UGT2B15 UGT2B15 UGT2B15 399 0.43 0.5 YES
8 UGT1A6 UGT1A6 UGT1A6 429 0.42 0.56 YES
9 UGT1A9 UGT1A9 UGT1A9 743 0.35 0.58 YES
10 UGT2B11 UGT2B11 UGT2B11 1124 0.3 0.6 YES
11 AMY2A AMY2A AMY2A 1350 0.27 0.62 YES
12 UGT1A1 UGT1A1 UGT1A1 4115 0.11 0.49 NO
13 AMY1A AMY1A AMY1A 4118 0.11 0.5 NO
14 G6PC G6PC G6PC 4819 0.093 0.48 NO
15 GCK GCK GCK 4882 0.091 0.49 NO
16 HK3 HK3 HK3 5089 0.086 0.49 NO
17 HK2 HK2 HK2 5344 0.08 0.48 NO
18 UGDH UGDH UGDH 5637 0.074 0.48 NO
19 GAA GAA GAA 6302 0.061 0.45 NO
20 UGT2B4 UGT2B4 UGT2B4 6706 0.054 0.44 NO
21 UXS1 UXS1 UXS1 6736 0.053 0.44 NO
22 GPI GPI GPI 6899 0.05 0.44 NO
23 TREH TREH TREH 7079 0.048 0.44 NO
24 GBA3 GBA3 GBA3 7800 0.036 0.4 NO
25 PYGB PYGB PYGB 7904 0.034 0.4 NO
26 GYS1 GYS1 GYS1 8761 0.022 0.36 NO
27 GYS2 GYS2 GYS2 9444 0.012 0.32 NO
28 HK1 HK1 HK1 10455 -0.0018 0.27 NO
29 GANC GANC GANC 10524 -0.0026 0.26 NO
30 GUSB GUSB GUSB 11861 -0.023 0.2 NO
31 PYGM PYGM PYGM 14015 -0.061 0.087 NO
32 UGP2 UGP2 UGP2 14864 -0.083 0.052 NO
33 PGM2 PGM2 PGM2 15030 -0.088 0.055 NO
34 PGM1 PGM1 PGM1 15479 -0.1 0.044 NO
35 PGM2L1 PGM2L1 PGM2L1 15538 -0.11 0.055 NO
36 AGL AGL AGL 15901 -0.12 0.051 NO
37 ENPP1 ENPP1 ENPP1 16263 -0.14 0.049 NO
38 PYGL PYGL PYGL 16853 -0.18 0.04 NO
39 GBE1 GBE1 GBE1 17292 -0.21 0.044 NO
40 UGT2A1 UGT2A1 UGT2A1 17380 -0.22 0.068 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: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM.

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

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

Table 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 CLDN19 CLDN19 CLDN19 35 0.75 0.11 YES
2 PARD6B PARD6B PARD6B 108 0.6 0.19 YES
3 CLDN2 CLDN2 CLDN2 172 0.54 0.27 YES
4 CLDN6 CLDN6 CLDN6 179 0.53 0.34 YES
5 CLDN11 CLDN11 CLDN11 222 0.5 0.42 YES
6 CRB3 CRB3 CRB3 459 0.42 0.46 YES
7 CLDN3 CLDN3 CLDN3 469 0.41 0.52 YES
8 CLDN7 CLDN7 CLDN7 1246 0.28 0.52 YES
9 PARD6A PARD6A PARD6A 1290 0.28 0.56 YES
10 CLDN4 CLDN4 CLDN4 1338 0.27 0.6 YES
11 CLDN20 CLDN20 CLDN20 1938 0.22 0.6 YES
12 CLDN9 CLDN9 CLDN9 2345 0.19 0.6 YES
13 CLDN14 CLDN14 CLDN14 2358 0.19 0.63 YES
14 CLDN18 CLDN18 CLDN18 2433 0.19 0.66 YES
15 F11R F11R F11R 2514 0.18 0.68 YES
16 INADL INADL INADL 2668 0.17 0.7 YES
17 CLDN8 CLDN8 CLDN8 3485 0.13 0.67 YES
18 CLDN1 CLDN1 CLDN1 3492 0.13 0.69 YES
19 CLDN16 CLDN16 CLDN16 3541 0.13 0.71 YES
20 CLDN15 CLDN15 CLDN15 3623 0.13 0.72 YES
21 PRKCI PRKCI PRKCI 5643 0.074 0.62 NO
22 CLDN12 CLDN12 CLDN12 6452 0.058 0.59 NO
23 MPP5 MPP5 MPP5 6532 0.056 0.59 NO
24 PARD3 PARD3 PARD3 9004 0.018 0.46 NO
25 PARD6G PARD6G PARD6G 14300 -0.068 0.19 NO
26 CLDN5 CLDN5 CLDN5 14453 -0.072 0.19 NO
27 CLDN10 CLDN10 CLDN10 17529 -0.24 0.06 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: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG DRUG METABOLISM CYTOCHROME P450

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 UGT2A3 UGT2A3 UGT2A3 51 0.71 0.14 YES
2 UGT2B10 UGT2B10 UGT2B10 145 0.56 0.24 YES
3 UGT2B7 UGT2B7 UGT2B7 163 0.54 0.34 YES
4 UGT2B15 UGT2B15 UGT2B15 399 0.43 0.42 YES
5 UGT1A6 UGT1A6 UGT1A6 429 0.42 0.5 YES
6 UGT1A9 UGT1A9 UGT1A9 743 0.35 0.55 YES
7 UGT2B11 UGT2B11 UGT2B11 1124 0.3 0.59 YES
8 PPOX PPOX PPOX 2298 0.19 0.56 NO
9 ALAS2 ALAS2 ALAS2 3533 0.13 0.52 NO
10 UGT1A1 UGT1A1 UGT1A1 4115 0.11 0.51 NO
11 UGT2B4 UGT2B4 UGT2B4 6706 0.054 0.38 NO
12 CPOX CPOX CPOX 6905 0.05 0.38 NO
13 UROD UROD UROD 7371 0.042 0.36 NO
14 EARS2 EARS2 EARS2 7538 0.04 0.36 NO
15 HMBS HMBS HMBS 7776 0.036 0.36 NO
16 COX15 COX15 COX15 7830 0.035 0.36 NO
17 HMOX2 HMOX2 HMOX2 9059 0.017 0.3 NO
18 ALAD ALAD ALAD 10165 0.0026 0.24 NO
19 EPRS EPRS EPRS 11610 -0.019 0.17 NO
20 GUSB GUSB GUSB 11861 -0.023 0.16 NO
21 BLVRB BLVRB BLVRB 11969 -0.025 0.16 NO
22 FECH FECH FECH 12012 -0.026 0.16 NO
23 UROS UROS UROS 12175 -0.028 0.16 NO
24 COX10 COX10 COX10 12268 -0.03 0.16 NO
25 BLVRA BLVRA BLVRA 13408 -0.049 0.11 NO
26 FTH1 FTH1 FTH1 14256 -0.067 0.073 NO
27 MMAB MMAB MMAB 14953 -0.085 0.053 NO
28 ALAS1 ALAS1 ALAS1 15640 -0.11 0.037 NO
29 HMOX1 HMOX1 HMOX1 16008 -0.13 0.042 NO
30 HCCS HCCS HCCS 16305 -0.14 0.053 NO
31 CP CP CP 16423 -0.15 0.076 NO
32 UGT2A1 UGT2A1 UGT2A1 17380 -0.22 0.068 NO

Figure S53.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450.

Figure S54.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: SIG IL4RECEPTOR IN B LYPHOCYTES

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 PLA2G4F PLA2G4F PLA2G4F 164 0.54 0.053 YES
2 SLC44A5 SLC44A5 SLC44A5 415 0.42 0.088 YES
3 SLC44A3 SLC44A3 SLC44A3 829 0.34 0.1 YES
4 LPIN3 LPIN3 LPIN3 920 0.32 0.14 YES
5 PLD4 PLD4 PLD4 1156 0.29 0.16 YES
6 GPD1 GPD1 GPD1 1464 0.26 0.17 YES
7 PLA2G3 PLA2G3 PLA2G3 1478 0.26 0.2 YES
8 CHAT CHAT CHAT 1697 0.24 0.21 YES
9 SLC44A4 SLC44A4 SLC44A4 1739 0.24 0.24 YES
10 PNPLA3 PNPLA3 PNPLA3 1982 0.22 0.25 YES
11 PCYT1B PCYT1B PCYT1B 2147 0.2 0.26 YES
12 CDS1 CDS1 CDS1 2327 0.19 0.28 YES
13 PLA2G4C PLA2G4C PLA2G4C 2389 0.19 0.3 YES
14 LPCAT3 LPCAT3 LPCAT3 2507 0.18 0.31 YES
15 LPCAT2 LPCAT2 LPCAT2 2606 0.18 0.32 YES
16 ETNK1 ETNK1 ETNK1 2607 0.18 0.34 YES
17 PLA2G1B PLA2G1B PLA2G1B 2669 0.17 0.36 YES
18 AGPAT2 AGPAT2 AGPAT2 2867 0.16 0.37 YES
19 PLA2G2D PLA2G2D PLA2G2D 2891 0.16 0.38 YES
20 PLBD1 PLBD1 PLBD1 2991 0.16 0.4 YES
21 CHKB CHKB CHKB 3160 0.15 0.4 YES
22 PLD2 PLD2 PLD2 3275 0.14 0.41 YES
23 PLA2G6 PLA2G6 PLA2G6 3834 0.12 0.4 NO
24 MBOAT7 MBOAT7 MBOAT7 3883 0.12 0.41 NO
25 PCYT2 PCYT2 PCYT2 4440 0.1 0.39 NO
26 PGS1 PGS1 PGS1 4510 0.1 0.4 NO
27 EPT1 EPT1 EPT1 4606 0.098 0.4 NO
28 TAZ TAZ TAZ 4986 0.089 0.39 NO
29 CHKA CHKA CHKA 5413 0.078 0.38 NO
30 CRLS1 CRLS1 CRLS1 5419 0.078 0.39 NO
31 PTDSS2 PTDSS2 PTDSS2 6292 0.061 0.35 NO
32 PLD3 PLD3 PLD3 6688 0.054 0.33 NO
33 DGAT2 DGAT2 DGAT2 6735 0.053 0.34 NO
34 LCLAT1 LCLAT1 LCLAT1 6804 0.052 0.34 NO
35 PEMT PEMT PEMT 6843 0.051 0.34 NO
36 AGPAT9 AGPAT9 AGPAT9 7011 0.048 0.34 NO
37 AGPAT1 AGPAT1 AGPAT1 7571 0.039 0.31 NO
38 ETNK2 ETNK2 ETNK2 7815 0.035 0.3 NO
39 MBOAT1 MBOAT1 MBOAT1 7901 0.034 0.3 NO
40 LPIN1 LPIN1 LPIN1 7979 0.032 0.3 NO
41 PNPLA2 PNPLA2 PNPLA2 8120 0.03 0.3 NO
42 CDIPT CDIPT CDIPT 8301 0.028 0.29 NO
43 PLA2G12A PLA2G12A PLA2G12A 8327 0.028 0.3 NO
44 GPAT2 GPAT2 GPAT2 8691 0.022 0.28 NO
45 HADHA HADHA HADHA 9355 0.013 0.24 NO
46 CDS2 CDS2 CDS2 9525 0.011 0.24 NO
47 PLA2G4D PLA2G4D PLA2G4D 9565 0.01 0.24 NO
48 LPCAT4 LPCAT4 LPCAT4 9765 0.0079 0.22 NO
49 CEPT1 CEPT1 CEPT1 9845 0.0068 0.22 NO
50 LPCAT1 LPCAT1 LPCAT1 9854 0.0067 0.22 NO
51 MBOAT2 MBOAT2 MBOAT2 9884 0.0064 0.22 NO
52 PITPNB PITPNB PITPNB 9947 0.0058 0.22 NO
53 AGPAT4 AGPAT4 AGPAT4 10020 0.0047 0.22 NO
54 PLA2G2F PLA2G2F PLA2G2F 10256 0.0011 0.2 NO
55 DGAT1 DGAT1 DGAT1 10602 -0.0038 0.18 NO
56 LPIN2 LPIN2 LPIN2 10725 -0.0057 0.18 NO
57 PLA2G5 PLA2G5 PLA2G5 10861 -0.0078 0.17 NO
58 GNPAT GNPAT GNPAT 10866 -0.0078 0.17 NO
59 PLA2G16 PLA2G16 PLA2G16 10905 -0.0084 0.17 NO
60 HADHB HADHB HADHB 11192 -0.013 0.16 NO
61 GPCPD1 GPCPD1 GPCPD1 11877 -0.023 0.12 NO
62 AGPAT3 AGPAT3 AGPAT3 11952 -0.025 0.12 NO
63 AGPAT6 AGPAT6 AGPAT6 12160 -0.028 0.11 NO
64 SLC44A1 SLC44A1 SLC44A1 12406 -0.032 0.1 NO
65 GPAM GPAM GPAM 12508 -0.034 0.1 NO
66 GPD1L GPD1L GPD1L 12547 -0.034 0.1 NO
67 AGPAT5 AGPAT5 AGPAT5 13114 -0.043 0.079 NO
68 PLD6 PLD6 PLD6 13164 -0.044 0.082 NO
69 MGLL MGLL MGLL 13760 -0.056 0.056 NO
70 CHPT1 CHPT1 CHPT1 14140 -0.065 0.043 NO
71 PCYT1A PCYT1A PCYT1A 14215 -0.066 0.046 NO
72 PTDSS1 PTDSS1 PTDSS1 14856 -0.082 0.021 NO
73 PLA2G10 PLA2G10 PLA2G10 14945 -0.085 0.026 NO
74 SLC44A2 SLC44A2 SLC44A2 15103 -0.09 0.028 NO
75 LPGAT1 LPGAT1 LPGAT1 15315 -0.098 0.028 NO
76 PNPLA8 PNPLA8 PNPLA8 15814 -0.12 0.014 NO
77 PLA2G4A PLA2G4A PLA2G4A 16563 -0.16 -0.0086 NO
78 PLD1 PLD1 PLD1 16642 -0.16 0.0056 NO
79 ACHE ACHE ACHE 16889 -0.18 0.012 NO
80 PLA2G2A PLA2G2A PLA2G2A 17607 -0.25 0.0024 NO
81 PHOSPHO1 PHOSPHO1 PHOSPHO1 18507 -0.47 0.0075 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: SIG IL4RECEPTOR IN B LYPHOCYTES.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: SIG IL4RECEPTOR IN B LYPHOCYTES, 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: ST INTERLEUKIN 4 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 HNF4A HNF4A HNF4A 24 0.8 0.081 YES
2 HNF1B HNF1B HNF1B 33 0.75 0.16 YES
3 HNF1A HNF1A HNF1A 39 0.73 0.23 YES
4 AFP AFP AFP 149 0.55 0.28 YES
5 FOXA2 FOXA2 FOXA2 156 0.55 0.34 YES
6 FOXA3 FOXA3 FOXA3 270 0.48 0.38 YES
7 SLC2A2 SLC2A2 SLC2A2 278 0.48 0.43 YES
8 PCK1 PCK1 PCK1 336 0.45 0.47 YES
9 TTR TTR TTR 356 0.44 0.52 YES
10 PDX1 PDX1 PDX1 539 0.39 0.55 YES
11 F2 F2 F2 761 0.35 0.57 YES
12 ALB ALB ALB 974 0.32 0.59 YES
13 ALDOB ALDOB ALDOB 1035 0.31 0.62 YES
14 APOA1 APOA1 APOA1 1411 0.27 0.63 YES
15 NKX2-1 NKX2-1 NKX2-1 1890 0.22 0.63 NO
16 ABCC8 ABCC8 ABCC8 2257 0.2 0.63 NO
17 DLK1 DLK1 DLK1 2793 0.17 0.62 NO
18 PKLR PKLR PKLR 3260 0.14 0.6 NO
19 CPT1B CPT1B CPT1B 3314 0.14 0.62 NO
20 FOXA1 FOXA1 FOXA1 3822 0.12 0.6 NO
21 KCNJ11 KCNJ11 KCNJ11 3867 0.12 0.61 NO
22 G6PC G6PC G6PC 4819 0.093 0.57 NO
23 GCK GCK GCK 4882 0.091 0.58 NO
24 CPT1C CPT1C CPT1C 5800 0.07 0.53 NO
25 BDH1 BDH1 BDH1 6059 0.065 0.53 NO
26 NF1 NF1 NF1 6138 0.063 0.53 NO
27 CEBPB CEBPB CEBPB 7877 0.034 0.44 NO
28 SP1 SP1 SP1 8135 0.03 0.43 NO
29 ACADVL ACADVL ACADVL 8646 0.023 0.4 NO
30 CREB1 CREB1 CREB1 8746 0.022 0.4 NO
31 ACADM ACADM ACADM 9739 0.0081 0.35 NO
32 UCP2 UCP2 UCP2 9848 0.0068 0.34 NO
33 AKT1 AKT1 AKT1 12373 -0.031 0.21 NO
34 NR3C1 NR3C1 NR3C1 13695 -0.055 0.14 NO
35 IGFBP1 IGFBP1 IGFBP1 14340 -0.069 0.12 NO
36 CPT1A CPT1A CPT1A 14409 -0.071 0.12 NO
37 HMGCS1 HMGCS1 HMGCS1 14444 -0.072 0.13 NO
38 ALAS1 ALAS1 ALAS1 15640 -0.11 0.074 NO
39 TFRC TFRC TFRC 15857 -0.12 0.074 NO
40 CEBPA CEBPA CEBPA 15946 -0.12 0.082 NO
41 FOXF1 FOXF1 FOXF1 16126 -0.13 0.086 NO
42 HADH HADH HADH 16346 -0.14 0.088 NO
43 TAT TAT TAT 16714 -0.17 0.086 NO
44 CEBPD CEBPD CEBPD 16858 -0.18 0.096 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: ST INTERLEUKIN 4 PATHWAY.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: ST INTERLEUKIN 4 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: PID CD40 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 PIP5K1B PIP5K1B PIP5K1B 905 0.33 0.036 YES
2 MAP3K1 MAP3K1 MAP3K1 1071 0.31 0.11 YES
3 CDH1 CDH1 CDH1 1385 0.27 0.16 YES
4 NOXA1 NOXA1 NOXA1 1493 0.26 0.22 YES
5 NCF1 NCF1 NCF1 1687 0.24 0.27 YES
6 CYFIP2 CYFIP2 CYFIP2 2718 0.17 0.26 YES
7 BAIAP2 BAIAP2 BAIAP2 3149 0.15 0.28 YES
8 NOXO1 NOXO1 NOXO1 3391 0.14 0.3 YES
9 PLCB2 PLCB2 PLCB2 3612 0.13 0.32 YES
10 MAP2K6 MAP2K6 MAP2K6 3690 0.13 0.35 YES
11 ABI1 ABI1 ABI1 4097 0.11 0.36 YES
12 MAP3K11 MAP3K11 MAP3K11 4136 0.11 0.38 YES
13 STAT5A STAT5A STAT5A 4575 0.098 0.39 YES
14 ABI2 ABI2 ABI2 4780 0.094 0.4 YES
15 ATF2 ATF2 ATF2 5350 0.08 0.39 YES
16 ARHGDIA ARHGDIA ARHGDIA 5490 0.077 0.4 YES
17 CYBA CYBA CYBA 6095 0.064 0.39 YES
18 CYBB CYBB CYBB 6157 0.063 0.4 YES
19 LIMK1 LIMK1 LIMK1 6209 0.062 0.41 YES
20 MAPK9 MAPK9 MAPK9 6555 0.056 0.41 YES
21 BCAR1 BCAR1 BCAR1 6644 0.055 0.42 YES
22 MAP2K3 MAP2K3 MAP2K3 7413 0.042 0.39 NO
23 JUN JUN JUN 7614 0.039 0.39 NO
24 NCKAP1 NCKAP1 NCKAP1 7762 0.036 0.39 NO
25 MAPK8 MAPK8 MAPK8 8122 0.03 0.38 NO
26 ACTR2 ACTR2 ACTR2 8578 0.024 0.36 NO
27 PAK1 PAK1 PAK1 8587 0.024 0.37 NO
28 ACTR3 ACTR3 ACTR3 8753 0.022 0.36 NO
29 WASF2 WASF2 WASF2 8941 0.019 0.36 NO
30 ARHGAP5 ARHGAP5 ARHGAP5 8968 0.018 0.36 NO
31 ARPC4 ARPC4 ARPC4 9088 0.017 0.36 NO
32 STAT3 STAT3 STAT3 9449 0.012 0.34 NO
33 PAK2 PAK2 PAK2 9457 0.012 0.34 NO
34 NCF2 NCF2 NCF2 9461 0.012 0.35 NO
35 ARPC2 ARPC2 ARPC2 9786 0.0076 0.33 NO
36 RAC1 RAC1 RAC1 9872 0.0065 0.33 NO
37 PIP5K1A PIP5K1A PIP5K1A 9990 0.0051 0.32 NO
38 CTNNA1 CTNNA1 CTNNA1 10148 0.0029 0.32 NO
39 MAP2K4 MAP2K4 MAP2K4 10421 -0.0013 0.3 NO
40 MAPK14 MAPK14 MAPK14 10652 -0.0046 0.29 NO
41 ARPC5 ARPC5 ARPC5 10855 -0.0076 0.28 NO
42 NOX1 NOX1 NOX1 11408 -0.016 0.26 NO
43 IQGAP1 IQGAP1 IQGAP1 11678 -0.02 0.25 NO
44 CFL1 CFL1 CFL1 11739 -0.021 0.25 NO
45 ARPC1B ARPC1B ARPC1B 12010 -0.026 0.24 NO
46 ARPC3 ARPC3 ARPC3 12359 -0.031 0.23 NO
47 IQGAP3 IQGAP3 IQGAP3 12515 -0.034 0.23 NO
48 MAP2K7 MAP2K7 MAP2K7 12578 -0.035 0.24 NO
49 PIP5K1C PIP5K1C PIP5K1C 12888 -0.04 0.23 NO
50 CTNNB1 CTNNB1 CTNNB1 13035 -0.042 0.23 NO
51 WASF1 WASF1 WASF1 13474 -0.05 0.22 NO
52 CRK CRK CRK 14814 -0.082 0.17 NO
53 RACGAP1 RACGAP1 RACGAP1 16017 -0.13 0.14 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: PID CD40 PATHWAY.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: PID CD40 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus4 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG CELL CYCLE 118 genes.ES.table 0.36 1.6 0.042 0.75 0.88 0.42 0.28 0.3 0.34 0.2
ST WNT BETA CATENIN PATHWAY 33 genes.ES.table 0.54 1.5 0.065 0.84 0.97 0.42 0.21 0.34 0.53 0.28
PID AURORA B PATHWAY 39 genes.ES.table 0.45 1.6 0.079 0.77 0.91 0.51 0.24 0.39 0.39 0.22
PID PLK1 PATHWAY 45 genes.ES.table 0.53 1.8 0.032 1 0.58 0.44 0.19 0.36 0.33 0.25
PID FOXM1PATHWAY 39 genes.ES.table 0.41 1.6 0.028 0.9 0.96 0.56 0.3 0.4 0.52 0.27
PID AURORA A PATHWAY 31 genes.ES.table 0.51 2 0.008 0.75 0.22 0.39 0.24 0.29 0 0.12
REACTOME MEIOSIS 103 genes.ES.table 0.55 1.5 0.091 0.85 0.98 0.4 0.19 0.32 0.56 0.29
REACTOME CELL CYCLE 380 genes.ES.table 0.38 1.7 0.058 0.79 0.7 0.41 0.28 0.3 0.22 0.18
REACTOME SIGNALLING TO ERKS 36 genes.ES.table 0.42 1.5 0.067 0.88 0.96 0.33 0.22 0.26 0.53 0.28
REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 25 genes.ES.table 0.59 1.5 0.024 0.89 0.97 0.56 0.19 0.45 0.54 0.3
genes ES table in pathway: KEGG CELL CYCLE

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CPEB1 CPEB1 CPEB1 190 0.4 0.17 YES
2 CENPA CENPA CENPA 1671 0.17 0.17 YES
3 TACC3 TACC3 TACC3 1783 0.16 0.24 YES
4 DLGAP5 DLGAP5 DLGAP5 1903 0.15 0.3 YES
5 TPX2 TPX2 TPX2 2356 0.13 0.34 YES
6 CDC25B CDC25B CDC25B 2737 0.11 0.37 YES
7 CKAP5 CKAP5 CKAP5 3043 0.1 0.4 YES
8 BIRC5 BIRC5 BIRC5 3259 0.096 0.43 YES
9 AURKA AURKA AURKA 3404 0.091 0.46 YES
10 PPP2R5D PPP2R5D PPP2R5D 3425 0.09 0.5 YES
11 TP53 TP53 TP53 4180 0.071 0.5 YES
12 FZR1 FZR1 FZR1 4517 0.064 0.51 YES
13 AURKB AURKB AURKB 5304 0.05 0.49 NO
14 RAN RAN RAN 5924 0.04 0.47 NO
15 GADD45A GADD45A GADD45A 6686 0.028 0.44 NO
16 RASA1 RASA1 RASA1 7097 0.022 0.43 NO
17 MDM2 MDM2 MDM2 7163 0.021 0.44 NO
18 TACC1 TACC1 TACC1 7171 0.021 0.45 NO
19 PRKACA PRKACA PRKACA 7253 0.02 0.45 NO
20 BRCA1 BRCA1 BRCA1 8211 0.0075 0.4 NO
21 AURKAIP1 AURKAIP1 AURKAIP1 8221 0.0074 0.41 NO
22 GSK3B GSK3B GSK3B 8251 0.007 0.41 NO
23 ARHGEF7 ARHGEF7 ARHGEF7 8636 0.002 0.39 NO
24 AKT1 AKT1 AKT1 8741 0.0005 0.38 NO
25 GIT1 GIT1 GIT1 8897 -0.0012 0.38 NO
26 PAK1 PAK1 PAK1 10096 -0.017 0.32 NO
27 NDEL1 NDEL1 NDEL1 10164 -0.017 0.32 NO
28 OAZ1 OAZ1 OAZ1 10458 -0.021 0.32 NO
29 NFKBIA NFKBIA NFKBIA 12284 -0.051 0.24 NO
30 TDRD7 TDRD7 TDRD7 13092 -0.067 0.23 NO
31 JUB JUB JUB 15597 -0.15 0.16 NO

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

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

genes ES table in pathway: ST WNT BETA CATENIN PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CLSPN CLSPN CLSPN 963 0.24 0.018 YES
2 NDC80 NDC80 NDC80 1594 0.17 0.035 YES
3 SGOL1 SGOL1 SGOL1 1937 0.15 0.061 YES
4 FBXO5 FBXO5 FBXO5 1950 0.15 0.1 YES
5 ERCC6L ERCC6L ERCC6L 2253 0.14 0.13 YES
6 CENPE CENPE CENPE 2266 0.14 0.17 YES
7 TPX2 TPX2 TPX2 2356 0.13 0.2 YES
8 KIF20A KIF20A KIF20A 2461 0.13 0.23 YES
9 PRC1 PRC1 PRC1 2605 0.12 0.26 YES
10 INCENP INCENP INCENP 2608 0.12 0.29 YES
11 CDC25B CDC25B CDC25B 2737 0.11 0.32 YES
12 ODF2 ODF2 ODF2 2847 0.11 0.35 YES
13 MLF1IP MLF1IP MLF1IP 3110 0.1 0.36 YES
14 GOLGA2 GOLGA2 GOLGA2 3182 0.098 0.39 YES
15 CDC20 CDC20 CDC20 3237 0.096 0.41 YES
16 CDC25C CDC25C CDC25C 3339 0.092 0.43 YES
17 SPC24 SPC24 SPC24 3390 0.091 0.46 YES
18 AURKA AURKA AURKA 3404 0.091 0.48 YES
19 BUB1 BUB1 BUB1 3429 0.09 0.51 YES
20 PLK1 PLK1 PLK1 3481 0.088 0.53 YES
21 NINL NINL NINL 4199 0.071 0.51 NO
22 FZR1 FZR1 FZR1 4517 0.064 0.52 NO
23 CDC14B CDC14B CDC14B 4749 0.06 0.52 NO
24 BUB1B BUB1B BUB1B 5954 0.039 0.47 NO
25 PLK1S1 PLK1S1 PLK1S1 5986 0.039 0.48 NO
26 PPP1R12A PPP1R12A PPP1R12A 6329 0.033 0.47 NO
27 STAG2 STAG2 STAG2 6410 0.032 0.47 NO
28 TUBG1 TUBG1 TUBG1 7135 0.022 0.44 NO
29 CCNB1 CCNB1 CCNB1 7358 0.019 0.44 NO
30 ECT2 ECT2 ECT2 7431 0.018 0.44 NO
31 PPP2CA PPP2CA PPP2CA 7776 0.014 0.42 NO
32 CDK1 CDK1 CDK1 7814 0.013 0.42 NO
33 NUDC NUDC NUDC 8273 0.0068 0.4 NO
34 FBXW11 FBXW11 FBXW11 8305 0.0063 0.4 NO
35 SSPO SSPO SSPO 9009 -0.0027 0.36 NO
36 PAK1 PAK1 PAK1 10096 -0.017 0.31 NO
37 GORASP1 GORASP1 GORASP1 10321 -0.019 0.3 NO
38 PPP2R1A PPP2R1A PPP2R1A 10379 -0.02 0.31 NO
39 PPP1CB PPP1CB PPP1CB 11004 -0.029 0.28 NO
40 WEE1 WEE1 WEE1 12424 -0.053 0.22 NO
41 RAB1A RAB1A RAB1A 12569 -0.056 0.23 NO
42 RHOA RHOA RHOA 13272 -0.071 0.21 NO
43 KIF2A KIF2A KIF2A 13302 -0.072 0.23 NO
44 ROCK2 ROCK2 ROCK2 13445 -0.075 0.25 NO
45 TPT1 TPT1 TPT1 14644 -0.11 0.22 NO

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

Figure S64.  Get High-res Image For the top 5 core enriched genes in the pathway: ST WNT BETA CATENIN 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: PID AURORA B PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CENPP CENPP CENPP 822 0.26 -0.0062 YES
2 NDC80 NDC80 NDC80 1594 0.17 -0.022 YES
3 CASC5 CASC5 CASC5 1596 0.17 0.0037 YES
4 CENPA CENPA CENPA 1671 0.17 0.025 YES
5 PPP2R5B PPP2R5B PPP2R5B 1760 0.16 0.044 YES
6 CENPO CENPO CENPO 1766 0.16 0.068 YES
7 SPC25 SPC25 SPC25 1778 0.16 0.091 YES
8 APITD1 APITD1 APITD1 1787 0.16 0.11 YES
9 SMC1A SMC1A SMC1A 1894 0.15 0.13 YES
10 KIF18A KIF18A KIF18A 1917 0.15 0.15 YES
11 SGOL1 SGOL1 SGOL1 1937 0.15 0.17 YES
12 CENPI CENPI CENPI 2215 0.14 0.18 YES
13 ERCC6L ERCC6L ERCC6L 2253 0.14 0.2 YES
14 SKA1 SKA1 SKA1 2322 0.13 0.21 YES
15 KIF2C KIF2C KIF2C 2488 0.12 0.22 YES
16 CDCA8 CDCA8 CDCA8 2515 0.12 0.24 YES
17 CENPQ CENPQ CENPQ 2532 0.12 0.26 YES
18 INCENP INCENP INCENP 2608 0.12 0.27 YES
19 NUF2 NUF2 NUF2 2651 0.12 0.29 YES
20 CENPL CENPL CENPL 2652 0.12 0.3 YES
21 MAD2L1 MAD2L1 MAD2L1 2928 0.11 0.3 YES
22 CENPN CENPN CENPN 2965 0.1 0.32 YES
23 SGOL2 SGOL2 SGOL2 3007 0.1 0.33 YES
24 CKAP5 CKAP5 CKAP5 3043 0.1 0.34 YES
25 MLF1IP MLF1IP MLF1IP 3110 0.1 0.36 YES
26 SMC3 SMC3 SMC3 3164 0.098 0.37 YES
27 CDC20 CDC20 CDC20 3237 0.096 0.38 YES
28 BIRC5 BIRC5 BIRC5 3259 0.096 0.39 YES
29 SPC24 SPC24 SPC24 3390 0.091 0.4 YES
30 PPP2R5D PPP2R5D PPP2R5D 3425 0.09 0.41 YES
31 BUB1 BUB1 BUB1 3429 0.09 0.42 YES
32 PLK1 PLK1 PLK1 3481 0.088 0.43 YES
33 MAD1L1 MAD1L1 MAD1L1 3555 0.086 0.44 YES
34 CENPC1 CENPC1 CENPC1 3616 0.085 0.45 YES
35 RAD21 RAD21 RAD21 3786 0.08 0.45 YES
36 CCDC99 CCDC99 CCDC99 3828 0.079 0.46 YES
37 SEC13 SEC13 SEC13 4125 0.072 0.46 YES
38 STAG1 STAG1 STAG1 4184 0.071 0.47 YES
39 KNTC1 KNTC1 KNTC1 4572 0.063 0.45 YES
40 BUB3 BUB3 BUB3 4610 0.062 0.46 YES
41 ZWILCH ZWILCH ZWILCH 4741 0.06 0.46 YES
42 ZWINT ZWINT ZWINT 4805 0.059 0.47 YES
43 AURKB AURKB AURKB 5304 0.05 0.45 NO
44 PAFAH1B1 PAFAH1B1 PAFAH1B1 5381 0.048 0.45 NO
45 SKA2 SKA2 SKA2 5467 0.047 0.46 NO
46 BUB1B BUB1B BUB1B 5954 0.039 0.43 NO
47 NUP107 NUP107 NUP107 6038 0.038 0.44 NO
48 AHCTF1 AHCTF1 AHCTF1 6213 0.035 0.43 NO
49 ITGB3BP ITGB3BP ITGB3BP 6223 0.035 0.44 NO
50 PPP1CC PPP1CC PPP1CC 6295 0.034 0.44 NO
51 STAG2 STAG2 STAG2 6410 0.032 0.44 NO
52 SEH1L SEH1L SEH1L 6483 0.031 0.44 NO
53 NUP37 NUP37 NUP37 6627 0.029 0.43 NO
54 RCC2 RCC2 RCC2 6638 0.028 0.44 NO
55 NUP43 NUP43 NUP43 6678 0.028 0.44 NO
56 CENPT CENPT CENPT 6748 0.027 0.44 NO
57 PPP2R5C PPP2R5C PPP2R5C 6918 0.025 0.43 NO
58 PMF1 PMF1 PMF1 7229 0.02 0.42 NO
59 DSN1 DSN1 DSN1 7371 0.018 0.42 NO
60 RANGAP1 RANGAP1 RANGAP1 7482 0.017 0.41 NO
61 NSL1 NSL1 NSL1 7591 0.016 0.41 NO
62 CENPH CENPH CENPH 7600 0.016 0.41 NO
63 PPP2CA PPP2CA PPP2CA 7776 0.014 0.4 NO
64 NUP85 NUP85 NUP85 7945 0.011 0.4 NO
65 XPO1 XPO1 XPO1 8090 0.0091 0.39 NO
66 NUDC NUDC NUDC 8273 0.0068 0.38 NO
67 MAPRE1 MAPRE1 MAPRE1 8357 0.0056 0.38 NO
68 PPP2R5E PPP2R5E PPP2R5E 8930 -0.0017 0.35 NO
69 NUP133 NUP133 NUP133 9516 -0.0092 0.32 NO
70 CLIP1 CLIP1 CLIP1 9924 -0.014 0.3 NO
71 NDEL1 NDEL1 NDEL1 10164 -0.017 0.29 NO
72 PPP2R1A PPP2R1A PPP2R1A 10379 -0.02 0.28 NO
73 CLASP1 CLASP1 CLASP1 10585 -0.023 0.27 NO
74 TAOK1 TAOK1 TAOK1 11044 -0.03 0.25 NO
75 PPP2R1B PPP2R1B PPP2R1B 11430 -0.036 0.23 NO
76 ZW10 ZW10 ZW10 12386 -0.053 0.19 NO
77 MIS12 MIS12 MIS12 12691 -0.059 0.18 NO
78 PPP2R5A PPP2R5A PPP2R5A 13062 -0.066 0.17 NO
79 KIF2A KIF2A KIF2A 13302 -0.072 0.17 NO
80 RANBP2 RANBP2 RANBP2 13540 -0.078 0.17 NO
81 CENPK CENPK CENPK 13704 -0.082 0.17 NO
82 PPP2CB PPP2CB PPP2CB 14713 -0.11 0.14 NO
83 B9D2 B9D2 B9D2 15050 -0.12 0.14 NO
84 CENPM CENPM CENPM 15068 -0.13 0.15 NO
85 RPS27 RPS27 RPS27 17443 -0.27 0.065 NO

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

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AURORA B 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: PID PLK1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FBXO6 FBXO6 FBXO6 1980 0.15 0.022 YES
2 FBXO4 FBXO4 FBXO4 2321 0.13 0.12 YES
3 FKBP9 FKBP9 FKBP9 2379 0.13 0.23 YES
4 USP11 USP11 USP11 3652 0.084 0.23 YES
5 KIF13A KIF13A KIF13A 3813 0.079 0.29 YES
6 FBXW2 FBXW2 FBXW2 4178 0.071 0.33 YES
7 FBXW5 FBXW5 FBXW5 5269 0.05 0.32 YES
8 XRN2 XRN2 XRN2 5480 0.047 0.35 YES
9 FBXL3 FBXL3 FBXL3 5916 0.04 0.36 YES
10 TCP1 TCP1 TCP1 6224 0.035 0.37 YES
11 FBXW7 FBXW7 FBXW7 6314 0.034 0.4 YES
12 NOP56 NOP56 NOP56 6577 0.029 0.41 YES
13 KIFC3 KIFC3 KIFC3 6816 0.026 0.42 YES
14 CCT4 CCT4 CCT4 7656 0.015 0.38 NO
15 CCT5 CCT5 CCT5 7854 0.012 0.38 NO
16 CCT6A CCT6A CCT6A 8420 0.0048 0.36 NO
17 CCT2 CCT2 CCT2 8545 0.0032 0.36 NO
18 CCT8 CCT8 CCT8 8671 0.0014 0.35 NO
19 CCT7 CCT7 CCT7 9207 -0.0051 0.32 NO
20 CCT3 CCT3 CCT3 9334 -0.007 0.32 NO
21 FBXL5 FBXL5 FBXL5 9627 -0.011 0.32 NO
22 ARFGEF2 ARFGEF2 ARFGEF2 9747 -0.012 0.32 NO
23 LONP2 LONP2 LONP2 10116 -0.017 0.32 NO
24 FBXW4 FBXW4 FBXW4 10831 -0.026 0.3 NO
25 AP3M1 AP3M1 AP3M1 11628 -0.039 0.29 NO
26 SPHK1 SPHK1 SPHK1 14283 -0.098 0.23 NO

Figure S67.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID PLK1 PATHWAY.

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: PID PLK1 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: PID FOXM1PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HIST1H2BN HIST1H2BN HIST1H2BN 38 0.54 0.017 YES
2 SYCP1 SYCP1 SYCP1 130 0.44 0.028 YES
3 CDKN2C CDKN2C CDKN2C 154 0.43 0.042 YES
4 RPA4 RPA4 RPA4 413 0.33 0.04 YES
5 HIST1H2BB HIST1H2BB HIST1H2BB 430 0.33 0.051 YES
6 STAG3 STAG3 STAG3 491 0.31 0.059 YES
7 HIST1H2BC HIST1H2BC HIST1H2BC 589 0.29 0.064 YES
8 HIST1H2BE HIST1H2BE HIST1H2BE 592 0.29 0.075 YES
9 HIST1H2BO HIST1H2BO HIST1H2BO 610 0.29 0.084 YES
10 PRIM1 PRIM1 PRIM1 731 0.27 0.087 YES
11 CENPP CENPP CENPP 822 0.26 0.092 YES
12 HIST1H2BI HIST1H2BI HIST1H2BI 936 0.24 0.094 YES
13 SYCP3 SYCP3 SYCP3 1021 0.23 0.098 YES
14 SYCP2 SYCP2 SYCP2 1046 0.23 0.1 YES
15 HIST2H4A HIST2H4A HIST2H4A 1249 0.2 0.1 YES
16 CCNE2 CCNE2 CCNE2 1344 0.19 0.1 YES
17 HIST1H2BK HIST1H2BK HIST1H2BK 1353 0.19 0.11 YES
18 HIST1H4J HIST1H4J HIST1H4J 1453 0.18 0.11 YES
19 NDC80 NDC80 NDC80 1594 0.17 0.11 YES
20 CASC5 CASC5 CASC5 1596 0.17 0.12 YES
21 HIST1H2AD HIST1H2AD HIST1H2AD 1620 0.17 0.12 YES
22 CENPA CENPA CENPA 1671 0.17 0.12 YES
23 PPP2R3B PPP2R3B PPP2R3B 1714 0.16 0.13 YES
24 PPP2R5B PPP2R5B PPP2R5B 1760 0.16 0.13 YES
25 CENPO CENPO CENPO 1766 0.16 0.14 YES
26 SPC25 SPC25 SPC25 1778 0.16 0.14 YES
27 APITD1 APITD1 APITD1 1787 0.16 0.15 YES
28 HIST2H2BE HIST2H2BE HIST2H2BE 1794 0.16 0.15 YES
29 HIST1H2BJ HIST1H2BJ HIST1H2BJ 1800 0.16 0.16 YES
30 HIST2H2AA3 HIST2H2AA3 HIST2H2AA3 1826 0.16 0.16 YES
31 CDKN2A CDKN2A CDKN2A 1834 0.16 0.17 YES
32 CCNA2 CCNA2 CCNA2 1868 0.16 0.17 YES
33 SMC1A SMC1A SMC1A 1894 0.15 0.17 YES
34 KIF18A KIF18A KIF18A 1917 0.15 0.18 YES
35 SGOL1 SGOL1 SGOL1 1937 0.15 0.18 YES
36 FBXO5 FBXO5 FBXO5 1950 0.15 0.19 YES
37 ANAPC10 ANAPC10 ANAPC10 1952 0.15 0.19 YES
38 MCM8 MCM8 MCM8 2007 0.15 0.2 YES
39 CDKN1B CDKN1B CDKN1B 2068 0.14 0.2 YES
40 TYMS TYMS TYMS 2098 0.14 0.2 YES
41 DBF4 DBF4 DBF4 2115 0.14 0.2 YES
42 CENPI CENPI CENPI 2215 0.14 0.2 YES
43 ERCC6L ERCC6L ERCC6L 2253 0.14 0.21 YES
44 SKA1 SKA1 SKA1 2322 0.13 0.21 YES
45 CDC45 CDC45 CDC45 2381 0.13 0.21 YES
46 NEK2 NEK2 NEK2 2411 0.13 0.21 YES
47 KIF20A KIF20A KIF20A 2461 0.13 0.22 YES
48 KIF2C KIF2C KIF2C 2488 0.12 0.22 YES
49 CDCA8 CDCA8 CDCA8 2515 0.12 0.22 YES
50 CENPQ CENPQ CENPQ 2532 0.12 0.22 YES
51 KIF23 KIF23 KIF23 2543 0.12 0.23 YES
52 CDC26 CDC26 CDC26 2574 0.12 0.23 YES
53 INCENP INCENP INCENP 2608 0.12 0.23 YES
54 RBBP7 RBBP7 RBBP7 2637 0.12 0.24 YES
55 NUF2 NUF2 NUF2 2651 0.12 0.24 YES
56 CENPL CENPL CENPL 2652 0.12 0.24 YES
57 CDC25B CDC25B CDC25B 2737 0.11 0.24 YES
58 POLA1 POLA1 POLA1 2743 0.11 0.25 YES
59 GINS1 GINS1 GINS1 2779 0.11 0.25 YES
60 CCNB2 CCNB2 CCNB2 2786 0.11 0.25 YES
61 CDKN2D CDKN2D CDKN2D 2826 0.11 0.26 YES
62 HIST1H4I HIST1H4I HIST1H4I 2837 0.11 0.26 YES
63 CDKN2B CDKN2B CDKN2B 2868 0.11 0.26 YES
64 MAD2L1 MAD2L1 MAD2L1 2928 0.11 0.26 YES
65 HIST1H2AB HIST1H2AB HIST1H2AB 2940 0.11 0.26 YES
66 CENPN CENPN CENPN 2965 0.1 0.27 YES
67 SGOL2 SGOL2 SGOL2 3007 0.1 0.27 YES
68 CDK2 CDK2 CDK2 3020 0.1 0.27 YES
69 HIST2H2AC HIST2H2AC HIST2H2AC 3033 0.1 0.28 YES
70 CKAP5 CKAP5 CKAP5 3043 0.1 0.28 YES
71 LIN52 LIN52 LIN52 3087 0.1 0.28 YES
72 HIST1H4E HIST1H4E HIST1H4E 3091 0.1 0.28 YES
73 HIST1H2AE HIST1H2AE HIST1H2AE 3097 0.1 0.29 YES
74 MLF1IP MLF1IP MLF1IP 3110 0.1 0.29 YES
75 HIST4H4 HIST4H4 HIST4H4 3117 0.099 0.29 YES
76 SUN2 SUN2 SUN2 3121 0.099 0.3 YES
77 SMC3 SMC3 SMC3 3164 0.098 0.3 YES
78 CDC20 CDC20 CDC20 3237 0.096 0.3 YES
79 UBE2C UBE2C UBE2C 3242 0.096 0.3 YES
80 BIRC5 BIRC5 BIRC5 3259 0.096 0.3 YES
81 POLE POLE POLE 3269 0.095 0.3 YES
82 CEP76 CEP76 CEP76 3273 0.095 0.31 YES
83 CDC25C CDC25C CDC25C 3339 0.092 0.31 YES
84 ANAPC2 ANAPC2 ANAPC2 3369 0.092 0.31 YES
85 SPC24 SPC24 SPC24 3390 0.091 0.31 YES
86 CEP135 CEP135 CEP135 3403 0.091 0.31 YES
87 AURKA AURKA AURKA 3404 0.091 0.32 YES
88 PPP2R5D PPP2R5D PPP2R5D 3425 0.09 0.32 YES
89 BUB1 BUB1 BUB1 3429 0.09 0.32 YES
90 CDK5RAP2 CDK5RAP2 CDK5RAP2 3432 0.09 0.33 YES
91 OIP5 OIP5 OIP5 3444 0.09 0.33 YES
92 SMC1B SMC1B SMC1B 3472 0.088 0.33 YES
93 PLK1 PLK1 PLK1 3481 0.088 0.33 YES
94 PSMC3 PSMC3 PSMC3 3492 0.088 0.34 YES
95 CDC6 CDC6 CDC6 3547 0.086 0.34 YES
96 MAD1L1 MAD1L1 MAD1L1 3555 0.086 0.34 YES
97 PLK4 PLK4 PLK4 3567 0.086 0.34 YES
98 CENPC1 CENPC1 CENPC1 3616 0.085 0.34 YES
99 TUBGCP3 TUBGCP3 TUBGCP3 3633 0.084 0.34 YES
100 PSMC4 PSMC4 PSMC4 3677 0.083 0.34 YES
101 RAD1 RAD1 RAD1 3707 0.082 0.35 YES
102 LIN54 LIN54 LIN54 3767 0.08 0.34 YES
103 RAD21 RAD21 RAD21 3786 0.08 0.35 YES
104 PSMD8 PSMD8 PSMD8 3801 0.08 0.35 YES
105 CCDC99 CCDC99 CCDC99 3828 0.079 0.35 YES
106 SYNE1 SYNE1 SYNE1 3926 0.076 0.35 YES
107 E2F4 E2F4 E2F4 3967 0.076 0.35 YES
108 GINS2 GINS2 GINS2 3981 0.076 0.35 YES
109 SDCCAG8 SDCCAG8 SDCCAG8 4111 0.073 0.35 YES
110 SEC13 SEC13 SEC13 4125 0.072 0.35 YES
111 TP53 TP53 TP53 4180 0.071 0.35 YES
112 STAG1 STAG1 STAG1 4184 0.071 0.35 YES
113 NINL NINL NINL 4199 0.071 0.35 YES
114 DCTN3 DCTN3 DCTN3 4217 0.07 0.35 YES
115 TUBG2 TUBG2 TUBG2 4262 0.069 0.35 YES
116 RBL1 RBL1 RBL1 4295 0.069 0.35 YES
117 FEN1 FEN1 FEN1 4315 0.068 0.36 YES
118 HJURP HJURP HJURP 4400 0.066 0.35 YES
119 ALMS1 ALMS1 ALMS1 4432 0.066 0.35 YES
120 PRIM2 PRIM2 PRIM2 4446 0.066 0.36 YES
121 RRM2 RRM2 RRM2 4476 0.065 0.36 YES
122 E2F1 E2F1 E2F1 4500 0.064 0.36 YES
123 TUBGCP5 TUBGCP5 TUBGCP5 4524 0.064 0.36 YES
124 POLE2 POLE2 POLE2 4564 0.063 0.36 YES
125 KNTC1 KNTC1 KNTC1 4572 0.063 0.36 YES
126 PSMD3 PSMD3 PSMD3 4587 0.063 0.36 YES
127 CEP72 CEP72 CEP72 4597 0.062 0.36 YES
128 BUB3 BUB3 BUB3 4610 0.062 0.36 YES
129 LIN37 LIN37 LIN37 4622 0.062 0.37 YES
130 CEP192 CEP192 CEP192 4642 0.062 0.37 YES
131 PSMD13 PSMD13 PSMD13 4681 0.061 0.37 YES
132 MCM5 MCM5 MCM5 4718 0.06 0.37 YES
133 HIST1H4B HIST1H4B HIST1H4B 4727 0.06 0.37 YES
134 ZWILCH ZWILCH ZWILCH 4741 0.06 0.37 YES
135 LMNB1 LMNB1 LMNB1 4766 0.06 0.37 YES
136 TERF2IP TERF2IP TERF2IP 4786 0.059 0.37 YES
137 RPA3 RPA3 RPA3 4798 0.059 0.38 YES
138 PSMD7 PSMD7 PSMD7 4800 0.059 0.38 YES
139 ZWINT ZWINT ZWINT 4805 0.059 0.38 YES
140 HUS1 HUS1 HUS1 4861 0.058 0.38 YES
141 NEDD1 NEDD1 NEDD1 4884 0.057 0.38 YES
142 TEX12 TEX12 TEX12 4920 0.056 0.38 YES
143 TFDP1 TFDP1 TFDP1 4949 0.056 0.38 YES
144 SKP2 SKP2 SKP2 4985 0.055 0.38 YES
145 RFC2 RFC2 RFC2 5038 0.054 0.38 YES
146 PSMB7 PSMB7 PSMB7 5067 0.054 0.38 YES
147 MCM6 MCM6 MCM6 5102 0.053 0.38 YES
148 HIST1H4H HIST1H4H HIST1H4H 5130 0.053 0.38 YES
149 RFC4 RFC4 RFC4 5137 0.053 0.38 YES
150 GMNN GMNN GMNN 5246 0.051 0.38 YES
151 CDT1 CDT1 CDT1 5272 0.05 0.38 YES
152 PTTG1 PTTG1 PTTG1 5285 0.05 0.38 YES
153 PSMB1 PSMB1 PSMB1 5290 0.05 0.38 YES
154 OFD1 OFD1 OFD1 5300 0.05 0.38 YES
155 AURKB AURKB AURKB 5304 0.05 0.38 YES
156 PAFAH1B1 PAFAH1B1 PAFAH1B1 5381 0.048 0.38 NO
157 LIN9 LIN9 LIN9 5412 0.048 0.38 NO
158 CSNK1E CSNK1E CSNK1E 5461 0.047 0.38 NO
159 SKA2 SKA2 SKA2 5467 0.047 0.38 NO
160 CDK4 CDK4 CDK4 5495 0.046 0.38 NO
161 CEP250 CEP250 CEP250 5588 0.045 0.38 NO
162 H2AFZ H2AFZ H2AFZ 5623 0.044 0.38 NO
163 TUBGCP2 TUBGCP2 TUBGCP2 5659 0.044 0.38 NO
164 MYBL2 MYBL2 MYBL2 5662 0.044 0.38 NO
165 PCNA PCNA PCNA 5678 0.044 0.38 NO
166 CDC25A CDC25A CDC25A 5702 0.043 0.38 NO
167 CEP63 CEP63 CEP63 5717 0.043 0.38 NO
168 CDC27 CDC27 CDC27 5718 0.043 0.38 NO
169 TINF2 TINF2 TINF2 5815 0.042 0.38 NO
170 RAD9A RAD9A RAD9A 5860 0.041 0.38 NO
171 SMARCA5 SMARCA5 SMARCA5 5880 0.041 0.38 NO
172 PCNT PCNT PCNT 5941 0.04 0.38 NO
173 BUB1B BUB1B BUB1B 5954 0.039 0.38 NO
174 PSMA7 PSMA7 PSMA7 6019 0.038 0.38 NO
175 POLA2 POLA2 POLA2 6032 0.038 0.38 NO
176 NUP107 NUP107 NUP107 6038 0.038 0.38 NO
177 SSNA1 SSNA1 SSNA1 6086 0.037 0.38 NO
178 POLD1 POLD1 POLD1 6121 0.037 0.38 NO
179 ACD ACD ACD 6159 0.036 0.37 NO
180 AHCTF1 AHCTF1 AHCTF1 6213 0.035 0.37 NO
181 ITGB3BP ITGB3BP ITGB3BP 6223 0.035 0.37 NO
182 MCM10 MCM10 MCM10 6249 0.035 0.37 NO
183 PPP1CC PPP1CC PPP1CC 6295 0.034 0.37 NO
184 TK2 TK2 TK2 6308 0.034 0.37 NO
185 MCM2 MCM2 MCM2 6309 0.034 0.37 NO
186 RPA2 RPA2 RPA2 6388 0.032 0.37 NO
187 RPA1 RPA1 RPA1 6399 0.032 0.37 NO
188 STAG2 STAG2 STAG2 6410 0.032 0.37 NO
189 LMNA LMNA LMNA 6416 0.032 0.37 NO
190 PSMD6 PSMD6 PSMD6 6423 0.032 0.37 NO
191 CEP70 CEP70 CEP70 6456 0.031 0.37 NO
192 SEH1L SEH1L SEH1L 6483 0.031 0.37 NO
193 NUP37 NUP37 NUP37 6627 0.029 0.36 NO
194 DYRK1A DYRK1A DYRK1A 6635 0.028 0.37 NO
195 RCC2 RCC2 RCC2 6638 0.028 0.37 NO
196 NUP43 NUP43 NUP43 6678 0.028 0.37 NO
197 PSMC2 PSMC2 PSMC2 6713 0.027 0.36 NO
198 HIST1H2BG HIST1H2BG HIST1H2BG 6722 0.027 0.36 NO
199 CENPT CENPT CENPT 6748 0.027 0.36 NO
200 PSMF1 PSMF1 PSMF1 6801 0.026 0.36 NO
201 DYNC1H1 DYNC1H1 DYNC1H1 6803 0.026 0.36 NO
202 ANAPC7 ANAPC7 ANAPC7 6847 0.026 0.36 NO
203 CEP290 CEP290 CEP290 6907 0.025 0.36 NO
204 ATR ATR ATR 6912 0.025 0.36 NO
205 CDC16 CDC16 CDC16 6913 0.025 0.36 NO
206 PPP2R5C PPP2R5C PPP2R5C 6918 0.025 0.36 NO
207 RFC5 RFC5 RFC5 6994 0.024 0.36 NO
208 ACTR1A ACTR1A ACTR1A 7021 0.023 0.36 NO
209 PSMD10 PSMD10 PSMD10 7024 0.023 0.36 NO
210 PSMA2 PSMA2 PSMA2 7057 0.023 0.36 NO
211 RSF1 RSF1 RSF1 7064 0.023 0.36 NO
212 TUBG1 TUBG1 TUBG1 7135 0.022 0.36 NO
213 DCTN2 DCTN2 DCTN2 7148 0.022 0.36 NO
214 MDM2 MDM2 MDM2 7163 0.021 0.36 NO
215 CDC23 CDC23 CDC23 7177 0.021 0.36 NO
216 PSMB6 PSMB6 PSMB6 7210 0.021 0.36 NO
217 PMF1 PMF1 PMF1 7229 0.02 0.36 NO
218 PRKACA PRKACA PRKACA 7253 0.02 0.35 NO
219 PSMD2 PSMD2 PSMD2 7266 0.02 0.35 NO
220 PSMD11 PSMD11 PSMD11 7279 0.02 0.35 NO
221 TUBB TUBB TUBB 7285 0.02 0.36 NO
222 MCM7 MCM7 MCM7 7296 0.02 0.36 NO
223 MCM3 MCM3 MCM3 7306 0.02 0.36 NO
224 DCTN1 DCTN1 DCTN1 7341 0.019 0.35 NO
225 ANAPC4 ANAPC4 ANAPC4 7350 0.019 0.35 NO
226 CCNB1 CCNB1 CCNB1 7358 0.019 0.36 NO
227 DSN1 DSN1 DSN1 7371 0.018 0.36 NO
228 NUMA1 NUMA1 NUMA1 7414 0.018 0.35 NO
229 PSMA1 PSMA1 PSMA1 7436 0.018 0.35 NO
230 FGFR1OP FGFR1OP FGFR1OP 7452 0.018 0.35 NO
231 RANGAP1 RANGAP1 RANGAP1 7482 0.017 0.35 NO
232 DHFR DHFR DHFR 7489 0.017 0.35 NO
233 CDC7 CDC7 CDC7 7568 0.016 0.35 NO
234 NSL1 NSL1 NSL1 7591 0.016 0.35 NO
235 CENPH CENPH CENPH 7600 0.016 0.35 NO
236 DYNLL1 DYNLL1 DYNLL1 7642 0.015 0.35 NO
237 PSMD1 PSMD1 PSMD1 7682 0.015 0.34 NO
238 PPP2CA PPP2CA PPP2CA 7776 0.014 0.34 NO
239 CDK1 CDK1 CDK1 7814 0.013 0.34 NO
240 POT1 POT1 POT1 7890 0.012 0.33 NO
241 NUP85 NUP85 NUP85 7945 0.011 0.33 NO
242 PSMA4 PSMA4 PSMA4 7957 0.011 0.33 NO
243 HAUS2 HAUS2 HAUS2 7987 0.011 0.33 NO
244 E2F3 E2F3 E2F3 7994 0.011 0.33 NO
245 PSMD14 PSMD14 PSMD14 8020 0.01 0.33 NO
246 RFWD2 RFWD2 RFWD2 8040 0.0098 0.33 NO
247 XPO1 XPO1 XPO1 8090 0.0091 0.33 NO
248 POLD3 POLD3 POLD3 8115 0.0089 0.32 NO
249 ATRIP ATRIP ATRIP 8149 0.0083 0.32 NO
250 BRCA1 BRCA1 BRCA1 8211 0.0075 0.32 NO
251 NUDC NUDC NUDC 8273 0.0068 0.32 NO
252 YWHAE YWHAE YWHAE 8286 0.0066 0.32 NO
253 YWHAG YWHAG YWHAG 8316 0.0062 0.32 NO
254 PSMC1 PSMC1 PSMC1 8323 0.006 0.32 NO
255 MAPRE1 MAPRE1 MAPRE1 8357 0.0056 0.31 NO
256 UBE2E1 UBE2E1 UBE2E1 8497 0.0038 0.31 NO
257 ANAPC5 ANAPC5 ANAPC5 8513 0.0036 0.31 NO
258 PSMB9 PSMB9 PSMB9 8528 0.0034 0.3 NO
259 TUBA1A TUBA1A TUBA1A 8550 0.0031 0.3 NO
260 CKS1B CKS1B CKS1B 8565 0.0028 0.3 NO
261 RBBP4 RBBP4 RBBP4 8637 0.002 0.3 NO
262 CEP164 CEP164 CEP164 8641 0.0019 0.3 NO
263 TERF2 TERF2 TERF2 8701 0.001 0.3 NO
264 CENPJ CENPJ CENPJ 8712 0.00085 0.3 NO
265 H2AFX H2AFX H2AFX 8807 -0.00012 0.29 NO
266 BTRC BTRC BTRC 8845 -0.0006 0.29 NO
267 PPP2R5E PPP2R5E PPP2R5E 8930 -0.0017 0.28 NO
268 CUL1 CUL1 CUL1 8953 -0.0019 0.28 NO
269 PSMA3 PSMA3 PSMA3 8981 -0.0023 0.28 NO
270 HSP90AA1 HSP90AA1 HSP90AA1 8987 -0.0023 0.28 NO
271 CCNE1 CCNE1 CCNE1 9036 -0.003 0.28 NO
272 PSMB2 PSMB2 PSMB2 9105 -0.0038 0.28 NO
273 POLD2 POLD2 POLD2 9239 -0.0056 0.27 NO
274 NHP2 NHP2 NHP2 9243 -0.0056 0.27 NO
275 RBL2 RBL2 RBL2 9268 -0.0061 0.27 NO
276 PSMD9 PSMD9 PSMD9 9296 -0.0065 0.27 NO
277 CCNH CCNH CCNH 9339 -0.007 0.26 NO
278 UBE2I UBE2I UBE2I 9447 -0.0085 0.26 NO
279 LIG1 LIG1 LIG1 9499 -0.009 0.26 NO
280 NUP133 NUP133 NUP133 9516 -0.0092 0.26 NO
281 MCM4 MCM4 MCM4 9529 -0.0093 0.26 NO
282 PSMC6 PSMC6 PSMC6 9566 -0.0099 0.25 NO
283 DIDO1 DIDO1 DIDO1 9573 -0.01 0.25 NO
284 CHEK2 CHEK2 CHEK2 9591 -0.01 0.25 NO
285 RUVBL1 RUVBL1 RUVBL1 9594 -0.01 0.25 NO
286 PSMB4 PSMB4 PSMB4 9664 -0.011 0.25 NO
287 RUVBL2 RUVBL2 RUVBL2 9749 -0.012 0.25 NO
288 CCND3 CCND3 CCND3 9829 -0.013 0.24 NO
289 PSMC5 PSMC5 PSMC5 9854 -0.013 0.24 NO
290 HIST1H2BF HIST1H2BF HIST1H2BF 9908 -0.014 0.24 NO
291 NPM1 NPM1 NPM1 9916 -0.014 0.24 NO
292 CLIP1 CLIP1 CLIP1 9924 -0.014 0.24 NO
293 SKP1 SKP1 SKP1 9965 -0.015 0.24 NO
294 HSPA2 HSPA2 HSPA2 10062 -0.016 0.23 NO
295 NDEL1 NDEL1 NDEL1 10164 -0.017 0.23 NO
296 UBA52 UBA52 UBA52 10204 -0.018 0.23 NO
297 E2F2 E2F2 E2F2 10206 -0.018 0.23 NO
298 AZI1 AZI1 AZI1 10243 -0.018 0.22 NO
299 GORASP1 GORASP1 GORASP1 10321 -0.019 0.22 NO
300 PPP2R1A PPP2R1A PPP2R1A 10379 -0.02 0.22 NO
301 HIST1H2BL HIST1H2BL HIST1H2BL 10427 -0.021 0.22 NO
302 PSMB5 PSMB5 PSMB5 10454 -0.021 0.22 NO
303 MNAT1 MNAT1 MNAT1 10490 -0.022 0.22 NO
304 HIST1H4C HIST1H4C HIST1H4C 10522 -0.022 0.22 NO
305 CLASP1 CLASP1 CLASP1 10585 -0.023 0.21 NO
306 DKC1 DKC1 DKC1 10597 -0.023 0.21 NO
307 MAX MAX MAX 10617 -0.023 0.21 NO
308 HIST1H2AJ HIST1H2AJ HIST1H2AJ 10711 -0.025 0.21 NO
309 PSMA6 PSMA6 PSMA6 10746 -0.025 0.21 NO
310 PSMB3 PSMB3 PSMB3 10811 -0.026 0.2 NO
311 HIST1H4K HIST1H4K HIST1H4K 10926 -0.028 0.2 NO
312 PSME2 PSME2 PSME2 10986 -0.029 0.2 NO
313 SYNE2 SYNE2 SYNE2 11040 -0.03 0.2 NO
314 TAOK1 TAOK1 TAOK1 11044 -0.03 0.2 NO
315 HIST1H4L HIST1H4L HIST1H4L 11080 -0.03 0.2 NO
316 AKAP9 AKAP9 AKAP9 11235 -0.032 0.19 NO
317 DYNC1I2 DYNC1I2 DYNC1I2 11303 -0.033 0.19 NO
318 PSME4 PSME4 PSME4 11425 -0.035 0.18 NO
319 PPP2R1B PPP2R1B PPP2R1B 11430 -0.036 0.18 NO
320 PSMD4 PSMD4 PSMD4 11490 -0.037 0.18 NO
321 PSMB8 PSMB8 PSMB8 11591 -0.039 0.18 NO
322 GINS4 GINS4 GINS4 11609 -0.039 0.18 NO
323 CETN2 CETN2 CETN2 11942 -0.044 0.16 NO
324 UBE2D1 UBE2D1 UBE2D1 11957 -0.045 0.16 NO
325 ANAPC11 ANAPC11 ANAPC11 11983 -0.045 0.16 NO
326 ANAPC1 ANAPC1 ANAPC1 11987 -0.045 0.16 NO
327 PCM1 PCM1 PCM1 12020 -0.046 0.16 NO
328 PSMD12 PSMD12 PSMD12 12043 -0.046 0.16 NO
329 HDAC1 HDAC1 HDAC1 12114 -0.048 0.16 NO
330 TUBGCP6 TUBGCP6 TUBGCP6 12297 -0.051 0.15 NO
331 DNA2 DNA2 DNA2 12364 -0.052 0.15 NO
332 ZW10 ZW10 ZW10 12386 -0.053 0.15 NO
333 WEE1 WEE1 WEE1 12424 -0.053 0.15 NO
334 HIST1H2AC HIST1H2AC HIST1H2AC 12559 -0.056 0.15 NO
335 PSMA5 PSMA5 PSMA5 12579 -0.057 0.15 NO
336 CSNK1D CSNK1D CSNK1D 12595 -0.057 0.15 NO
337 TUBA4A TUBA4A TUBA4A 12633 -0.057 0.15 NO
338 HIST1H2BD HIST1H2BD HIST1H2BD 12668 -0.058 0.15 NO
339 MIS12 MIS12 MIS12 12691 -0.059 0.15 NO
340 RAD17 RAD17 RAD17 12814 -0.062 0.14 NO
341 HIST1H4A HIST1H4A HIST1H4A 12831 -0.062 0.15 NO
342 HIST3H2BB HIST3H2BB HIST3H2BB 12875 -0.063 0.15 NO
343 RFC3 RFC3 RFC3 12945 -0.064 0.14 NO
344 PPP2R5A PPP2R5A PPP2R5A 13062 -0.066 0.14 NO
345 CDK6 CDK6 CDK6 13149 -0.068 0.14 NO
346 WRAP53 WRAP53 WRAP53 13252 -0.07 0.14 NO
347 KIF2A KIF2A KIF2A 13302 -0.072 0.14 NO
348 HIST1H2BH HIST1H2BH HIST1H2BH 13314 -0.072 0.14 NO
349 CEP57 CEP57 CEP57 13446 -0.075 0.13 NO
350 RANBP2 RANBP2 RANBP2 13540 -0.078 0.13 NO
351 PKMYT1 PKMYT1 PKMYT1 13586 -0.079 0.13 NO
352 RPS27A RPS27A RPS27A 13660 -0.081 0.13 NO
353 CENPK CENPK CENPK 13704 -0.082 0.13 NO
354 PPP2R2A PPP2R2A PPP2R2A 13749 -0.083 0.13 NO
355 TERF1 TERF1 TERF1 13791 -0.085 0.13 NO
356 PSME1 PSME1 PSME1 14099 -0.093 0.12 NO
357 TERT TERT TERT 14102 -0.093 0.12 NO
358 POLD4 POLD4 POLD4 14192 -0.096 0.12 NO
359 PSMD5 PSMD5 PSMD5 14232 -0.097 0.12 NO
360 CCNA1 CCNA1 CCNA1 14312 -0.099 0.12 NO
361 PRKAR2B PRKAR2B PRKAR2B 14367 -0.1 0.12 NO
362 CHEK1 CHEK1 CHEK1 14381 -0.1 0.12 NO
363 CCND1 CCND1 CCND1 14514 -0.11 0.12 NO
364 FKBP6 FKBP6 FKBP6 14545 -0.11 0.12 NO
365 PPP2CB PPP2CB PPP2CB 14713 -0.11 0.12 NO
366 B9D2 B9D2 B9D2 15050 -0.12 0.1 NO
367 CENPM CENPM CENPM 15068 -0.13 0.11 NO
368 HIST1H2BM HIST1H2BM HIST1H2BM 15272 -0.14 0.1 NO
369 ATM ATM ATM 15287 -0.14 0.1 NO
370 MYC MYC MYC 15517 -0.15 0.098 NO
371 CDKN1A CDKN1A CDKN1A 15730 -0.16 0.092 NO
372 CDK7 CDK7 CDK7 15848 -0.16 0.091 NO
373 RB1 RB1 RB1 15924 -0.16 0.093 NO
374 PSMB10 PSMB10 PSMB10 16018 -0.17 0.094 NO
375 CCND2 CCND2 CCND2 16505 -0.2 0.074 NO
376 E2F5 E2F5 E2F5 16623 -0.2 0.075 NO
377 CDC14A CDC14A CDC14A 16627 -0.2 0.082 NO
378 REC8 REC8 REC8 17021 -0.23 0.069 NO
379 RPS27 RPS27 RPS27 17443 -0.27 0.056 NO
380 HIST1H4D HIST1H4D HIST1H4D 17506 -0.28 0.062 NO

Figure S69.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FOXM1PATHWAY.

Figure S70.  Get High-res Image For the top 5 core enriched genes in the pathway: PID FOXM1PATHWAY, 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: PID AURORA A PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPA4 RPA4 RPA4 413 0.33 0.0079 YES
2 PRIM1 PRIM1 PRIM1 731 0.27 0.015 YES
3 CENPP CENPP CENPP 822 0.26 0.034 YES
4 NDC80 NDC80 NDC80 1594 0.17 0.008 YES
5 CASC5 CASC5 CASC5 1596 0.17 0.024 YES
6 CENPA CENPA CENPA 1671 0.17 0.035 YES
7 PPP2R5B PPP2R5B PPP2R5B 1760 0.16 0.045 YES
8 CENPO CENPO CENPO 1766 0.16 0.06 YES
9 SPC25 SPC25 SPC25 1778 0.16 0.074 YES
10 APITD1 APITD1 APITD1 1787 0.16 0.088 YES
11 SMC1A SMC1A SMC1A 1894 0.15 0.096 YES
12 KIF18A KIF18A KIF18A 1917 0.15 0.11 YES
13 SGOL1 SGOL1 SGOL1 1937 0.15 0.12 YES
14 FBXO5 FBXO5 FBXO5 1950 0.15 0.14 YES
15 MCM8 MCM8 MCM8 2007 0.15 0.14 YES
16 DBF4 DBF4 DBF4 2115 0.14 0.15 YES
17 CENPI CENPI CENPI 2215 0.14 0.16 YES
18 ERCC6L ERCC6L ERCC6L 2253 0.14 0.17 YES
19 SKA1 SKA1 SKA1 2322 0.13 0.18 YES
20 CDC45 CDC45 CDC45 2381 0.13 0.19 YES
21 KIF20A KIF20A KIF20A 2461 0.13 0.19 YES
22 KIF2C KIF2C KIF2C 2488 0.12 0.2 YES
23 CDCA8 CDCA8 CDCA8 2515 0.12 0.21 YES
24 CENPQ CENPQ CENPQ 2532 0.12 0.22 YES
25 KIF23 KIF23 KIF23 2543 0.12 0.24 YES
26 INCENP INCENP INCENP 2608 0.12 0.24 YES
27 NUF2 NUF2 NUF2 2651 0.12 0.25 YES
28 CENPL CENPL CENPL 2652 0.12 0.26 YES
29 POLA1 POLA1 POLA1 2743 0.11 0.27 YES
30 MAD2L1 MAD2L1 MAD2L1 2928 0.11 0.27 YES
31 CENPN CENPN CENPN 2965 0.1 0.28 YES
32 SGOL2 SGOL2 SGOL2 3007 0.1 0.28 YES
33 CDK2 CDK2 CDK2 3020 0.1 0.29 YES
34 CKAP5 CKAP5 CKAP5 3043 0.1 0.3 YES
35 MLF1IP MLF1IP MLF1IP 3110 0.1 0.3 YES
36 SMC3 SMC3 SMC3 3164 0.098 0.31 YES
37 CDC20 CDC20 CDC20 3237 0.096 0.32 YES
38 BIRC5 BIRC5 BIRC5 3259 0.096 0.32 YES
39 POLE POLE POLE 3269 0.095 0.33 YES
40 SPC24 SPC24 SPC24 3390 0.091 0.33 YES
41 PPP2R5D PPP2R5D PPP2R5D 3425 0.09 0.34 YES
42 BUB1 BUB1 BUB1 3429 0.09 0.35 YES
43 PLK1 PLK1 PLK1 3481 0.088 0.35 YES
44 PSMC3 PSMC3 PSMC3 3492 0.088 0.36 YES
45 CDC6 CDC6 CDC6 3547 0.086 0.36 YES
46 MAD1L1 MAD1L1 MAD1L1 3555 0.086 0.37 YES
47 CENPC1 CENPC1 CENPC1 3616 0.085 0.38 YES
48 PSMC4 PSMC4 PSMC4 3677 0.083 0.38 YES
49 RAD21 RAD21 RAD21 3786 0.08 0.38 YES
50 PSMD8 PSMD8 PSMD8 3801 0.08 0.39 YES
51 CCDC99 CCDC99 CCDC99 3828 0.079 0.4 YES
52 SEC13 SEC13 SEC13 4125 0.072 0.39 YES
53 STAG1 STAG1 STAG1 4184 0.071 0.39 YES
54 PRIM2 PRIM2 PRIM2 4446 0.066 0.38 YES
55 E2F1 E2F1 E2F1 4500 0.064 0.38 YES
56 POLE2 POLE2 POLE2 4564 0.063 0.39 YES
57 KNTC1 KNTC1 KNTC1 4572 0.063 0.39 YES
58 PSMD3 PSMD3 PSMD3 4587 0.063 0.4 YES
59 BUB3 BUB3 BUB3 4610 0.062 0.4 YES
60 PSMD13 PSMD13 PSMD13 4681 0.061 0.4 YES
61 MCM5 MCM5 MCM5 4718 0.06 0.41 YES
62 ZWILCH ZWILCH ZWILCH 4741 0.06 0.41 YES
63 RPA3 RPA3 RPA3 4798 0.059 0.41 YES
64 PSMD7 PSMD7 PSMD7 4800 0.059 0.42 YES
65 ZWINT ZWINT ZWINT 4805 0.059 0.42 YES
66 PSMB7 PSMB7 PSMB7 5067 0.054 0.41 YES
67 MCM6 MCM6 MCM6 5102 0.053 0.42 YES
68 GMNN GMNN GMNN 5246 0.051 0.41 YES
69 CDT1 CDT1 CDT1 5272 0.05 0.42 YES
70 PSMB1 PSMB1 PSMB1 5290 0.05 0.42 YES
71 AURKB AURKB AURKB 5304 0.05 0.42 YES
72 PAFAH1B1 PAFAH1B1 PAFAH1B1 5381 0.048 0.42 YES
73 SKA2 SKA2 SKA2 5467 0.047 0.42 NO
74 BUB1B BUB1B BUB1B 5954 0.039 0.4 NO
75 PSMA7 PSMA7 PSMA7 6019 0.038 0.4 NO
76 POLA2 POLA2 POLA2 6032 0.038 0.4 NO
77 NUP107 NUP107 NUP107 6038 0.038 0.41 NO
78 AHCTF1 AHCTF1 AHCTF1 6213 0.035 0.4 NO
79 ITGB3BP ITGB3BP ITGB3BP 6223 0.035 0.4 NO
80 MCM10 MCM10 MCM10 6249 0.035 0.41 NO
81 PPP1CC PPP1CC PPP1CC 6295 0.034 0.41 NO
82 MCM2 MCM2 MCM2 6309 0.034 0.41 NO
83 RPA2 RPA2 RPA2 6388 0.032 0.41 NO
84 RPA1 RPA1 RPA1 6399 0.032 0.41 NO
85 STAG2 STAG2 STAG2 6410 0.032 0.41 NO
86 PSMD6 PSMD6 PSMD6 6423 0.032 0.42 NO
87 SEH1L SEH1L SEH1L 6483 0.031 0.42 NO
88 NUP37 NUP37 NUP37 6627 0.029 0.41 NO
89 RCC2 RCC2 RCC2 6638 0.028 0.41 NO
90 NUP43 NUP43 NUP43 6678 0.028 0.41 NO
91 PSMC2 PSMC2 PSMC2 6713 0.027 0.41 NO
92 CENPT CENPT CENPT 6748 0.027 0.41 NO
93 PSMF1 PSMF1 PSMF1 6801 0.026 0.41 NO
94 PPP2R5C PPP2R5C PPP2R5C 6918 0.025 0.41 NO
95 PSMD10 PSMD10 PSMD10 7024 0.023 0.41 NO
96 PSMA2 PSMA2 PSMA2 7057 0.023 0.41 NO
97 PSMB6 PSMB6 PSMB6 7210 0.021 0.4 NO
98 PMF1 PMF1 PMF1 7229 0.02 0.4 NO
99 PSMD2 PSMD2 PSMD2 7266 0.02 0.4 NO
100 PSMD11 PSMD11 PSMD11 7279 0.02 0.4 NO
101 MCM7 MCM7 MCM7 7296 0.02 0.4 NO
102 MCM3 MCM3 MCM3 7306 0.02 0.4 NO
103 DSN1 DSN1 DSN1 7371 0.018 0.4 NO
104 PSMA1 PSMA1 PSMA1 7436 0.018 0.4 NO
105 RANGAP1 RANGAP1 RANGAP1 7482 0.017 0.4 NO
106 CDC7 CDC7 CDC7 7568 0.016 0.4 NO
107 NSL1 NSL1 NSL1 7591 0.016 0.4 NO
108 CENPH CENPH CENPH 7600 0.016 0.4 NO
109 PSMD1 PSMD1 PSMD1 7682 0.015 0.39 NO
110 PPP2CA PPP2CA PPP2CA 7776 0.014 0.39 NO
111 NUP85 NUP85 NUP85 7945 0.011 0.38 NO
112 PSMA4 PSMA4 PSMA4 7957 0.011 0.38 NO
113 E2F3 E2F3 E2F3 7994 0.011 0.38 NO
114 PSMD14 PSMD14 PSMD14 8020 0.01 0.38 NO
115 XPO1 XPO1 XPO1 8090 0.0091 0.38 NO
116 NUDC NUDC NUDC 8273 0.0068 0.37 NO
117 PSMC1 PSMC1 PSMC1 8323 0.006 0.37 NO
118 MAPRE1 MAPRE1 MAPRE1 8357 0.0056 0.37 NO
119 PSMB9 PSMB9 PSMB9 8528 0.0034 0.36 NO
120 PPP2R5E PPP2R5E PPP2R5E 8930 -0.0017 0.34 NO
121 PSMA3 PSMA3 PSMA3 8981 -0.0023 0.33 NO
122 PSMB2 PSMB2 PSMB2 9105 -0.0038 0.33 NO
123 PSMD9 PSMD9 PSMD9 9296 -0.0065 0.32 NO
124 NUP133 NUP133 NUP133 9516 -0.0092 0.31 NO
125 MCM4 MCM4 MCM4 9529 -0.0093 0.31 NO
126 PSMC6 PSMC6 PSMC6 9566 -0.0099 0.3 NO
127 PSMB4 PSMB4 PSMB4 9664 -0.011 0.3 NO
128 PSMC5 PSMC5 PSMC5 9854 -0.013 0.29 NO
129 CLIP1 CLIP1 CLIP1 9924 -0.014 0.29 NO
130 NDEL1 NDEL1 NDEL1 10164 -0.017 0.28 NO
131 UBA52 UBA52 UBA52 10204 -0.018 0.28 NO
132 E2F2 E2F2 E2F2 10206 -0.018 0.28 NO
133 GORASP1 GORASP1 GORASP1 10321 -0.019 0.28 NO
134 PPP2R1A PPP2R1A PPP2R1A 10379 -0.02 0.27 NO
135 PSMB5 PSMB5 PSMB5 10454 -0.021 0.27 NO
136 CLASP1 CLASP1 CLASP1 10585 -0.023 0.27 NO
137 PSMA6 PSMA6 PSMA6 10746 -0.025 0.26 NO
138 PSMB3 PSMB3 PSMB3 10811 -0.026 0.26 NO
139 PSME2 PSME2 PSME2 10986 -0.029 0.25 NO
140 TAOK1 TAOK1 TAOK1 11044 -0.03 0.25 NO
141 PSME4 PSME4 PSME4 11425 -0.035 0.24 NO
142 PPP2R1B PPP2R1B PPP2R1B 11430 -0.036 0.24 NO
143 PSMD4 PSMD4 PSMD4 11490 -0.037 0.24 NO
144 PSMB8 PSMB8 PSMB8 11591 -0.039 0.24 NO
145 PSMD12 PSMD12 PSMD12 12043 -0.046 0.22 NO
146 ZW10 ZW10 ZW10 12386 -0.053 0.2 NO
147 PSMA5 PSMA5 PSMA5 12579 -0.057 0.2 NO
148 MIS12 MIS12 MIS12 12691 -0.059 0.2 NO
149 PPP2R5A PPP2R5A PPP2R5A 13062 -0.066 0.18 NO
150 KIF2A KIF2A KIF2A 13302 -0.072 0.18 NO
151 RANBP2 RANBP2 RANBP2 13540 -0.078 0.17 NO
152 RPS27A RPS27A RPS27A 13660 -0.081 0.17 NO
153 CENPK CENPK CENPK 13704 -0.082 0.18 NO
154 PSME1 PSME1 PSME1 14099 -0.093 0.16 NO
155 PSMD5 PSMD5 PSMD5 14232 -0.097 0.16 NO
156 PPP2CB PPP2CB PPP2CB 14713 -0.11 0.15 NO
157 B9D2 B9D2 B9D2 15050 -0.12 0.14 NO
158 CENPM CENPM CENPM 15068 -0.13 0.15 NO
159 PSMB10 PSMB10 PSMB10 16018 -0.17 0.12 NO
160 RPS27 RPS27 RPS27 17443 -0.27 0.065 NO

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

Figure S72.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AURORA A 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: REACTOME MEIOSIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CDKN2C CDKN2C CDKN2C 154 0.43 0.014 YES
2 RPA4 RPA4 RPA4 413 0.33 0.017 YES
3 PRIM1 PRIM1 PRIM1 731 0.27 0.013 YES
4 CENPP CENPP CENPP 822 0.26 0.021 YES
5 CCNE2 CCNE2 CCNE2 1344 0.19 0.0029 YES
6 NDC80 NDC80 NDC80 1594 0.17 -0.0018 YES
7 CASC5 CASC5 CASC5 1596 0.17 0.007 YES
8 CENPA CENPA CENPA 1671 0.17 0.012 YES
9 PPP2R3B PPP2R3B PPP2R3B 1714 0.16 0.018 YES
10 PPP2R5B PPP2R5B PPP2R5B 1760 0.16 0.024 YES
11 CENPO CENPO CENPO 1766 0.16 0.032 YES
12 SPC25 SPC25 SPC25 1778 0.16 0.039 YES
13 APITD1 APITD1 APITD1 1787 0.16 0.047 YES
14 CDKN2A CDKN2A CDKN2A 1834 0.16 0.053 YES
15 CCNA2 CCNA2 CCNA2 1868 0.16 0.059 YES
16 SMC1A SMC1A SMC1A 1894 0.15 0.065 YES
17 KIF18A KIF18A KIF18A 1917 0.15 0.072 YES
18 SGOL1 SGOL1 SGOL1 1937 0.15 0.079 YES
19 FBXO5 FBXO5 FBXO5 1950 0.15 0.086 YES
20 ANAPC10 ANAPC10 ANAPC10 1952 0.15 0.093 YES
21 MCM8 MCM8 MCM8 2007 0.15 0.098 YES
22 CDKN1B CDKN1B CDKN1B 2068 0.14 0.1 YES
23 TYMS TYMS TYMS 2098 0.14 0.11 YES
24 DBF4 DBF4 DBF4 2115 0.14 0.11 YES
25 CENPI CENPI CENPI 2215 0.14 0.12 YES
26 ERCC6L ERCC6L ERCC6L 2253 0.14 0.12 YES
27 SKA1 SKA1 SKA1 2322 0.13 0.12 YES
28 CDC45 CDC45 CDC45 2381 0.13 0.13 YES
29 NEK2 NEK2 NEK2 2411 0.13 0.13 YES
30 KIF20A KIF20A KIF20A 2461 0.13 0.14 YES
31 KIF2C KIF2C KIF2C 2488 0.12 0.14 YES
32 CDCA8 CDCA8 CDCA8 2515 0.12 0.15 YES
33 CENPQ CENPQ CENPQ 2532 0.12 0.15 YES
34 KIF23 KIF23 KIF23 2543 0.12 0.16 YES
35 CDC26 CDC26 CDC26 2574 0.12 0.16 YES
36 INCENP INCENP INCENP 2608 0.12 0.17 YES
37 NUF2 NUF2 NUF2 2651 0.12 0.17 YES
38 CENPL CENPL CENPL 2652 0.12 0.18 YES
39 CDC25B CDC25B CDC25B 2737 0.11 0.18 YES
40 POLA1 POLA1 POLA1 2743 0.11 0.18 YES
41 GINS1 GINS1 GINS1 2779 0.11 0.19 YES
42 CCNB2 CCNB2 CCNB2 2786 0.11 0.19 YES
43 CDKN2D CDKN2D CDKN2D 2826 0.11 0.2 YES
44 CDKN2B CDKN2B CDKN2B 2868 0.11 0.2 YES
45 MAD2L1 MAD2L1 MAD2L1 2928 0.11 0.2 YES
46 CENPN CENPN CENPN 2965 0.1 0.2 YES
47 SGOL2 SGOL2 SGOL2 3007 0.1 0.21 YES
48 CDK2 CDK2 CDK2 3020 0.1 0.21 YES
49 CKAP5 CKAP5 CKAP5 3043 0.1 0.22 YES
50 LIN52 LIN52 LIN52 3087 0.1 0.22 YES
51 MLF1IP MLF1IP MLF1IP 3110 0.1 0.22 YES
52 SMC3 SMC3 SMC3 3164 0.098 0.22 YES
53 CDC20 CDC20 CDC20 3237 0.096 0.23 YES
54 UBE2C UBE2C UBE2C 3242 0.096 0.23 YES
55 BIRC5 BIRC5 BIRC5 3259 0.096 0.24 YES
56 POLE POLE POLE 3269 0.095 0.24 YES
57 CEP76 CEP76 CEP76 3273 0.095 0.24 YES
58 CDC25C CDC25C CDC25C 3339 0.092 0.24 YES
59 ANAPC2 ANAPC2 ANAPC2 3369 0.092 0.25 YES
60 SPC24 SPC24 SPC24 3390 0.091 0.25 YES
61 CEP135 CEP135 CEP135 3403 0.091 0.26 YES
62 AURKA AURKA AURKA 3404 0.091 0.26 YES
63 PPP2R5D PPP2R5D PPP2R5D 3425 0.09 0.26 YES
64 BUB1 BUB1 BUB1 3429 0.09 0.27 YES
65 CDK5RAP2 CDK5RAP2 CDK5RAP2 3432 0.09 0.27 YES
66 PLK1 PLK1 PLK1 3481 0.088 0.28 YES
67 PSMC3 PSMC3 PSMC3 3492 0.088 0.28 YES
68 CDC6 CDC6 CDC6 3547 0.086 0.28 YES
69 MAD1L1 MAD1L1 MAD1L1 3555 0.086 0.28 YES
70 PLK4 PLK4 PLK4 3567 0.086 0.29 YES
71 CENPC1 CENPC1 CENPC1 3616 0.085 0.29 YES
72 TUBGCP3 TUBGCP3 TUBGCP3 3633 0.084 0.29 YES
73 PSMC4 PSMC4 PSMC4 3677 0.083 0.3 YES
74 LIN54 LIN54 LIN54 3767 0.08 0.3 YES
75 RAD21 RAD21 RAD21 3786 0.08 0.3 YES
76 PSMD8 PSMD8 PSMD8 3801 0.08 0.3 YES
77 CCDC99 CCDC99 CCDC99 3828 0.079 0.3 YES
78 E2F4 E2F4 E2F4 3967 0.076 0.3 YES
79 GINS2 GINS2 GINS2 3981 0.076 0.3 YES
80 SDCCAG8 SDCCAG8 SDCCAG8 4111 0.073 0.3 YES
81 SEC13 SEC13 SEC13 4125 0.072 0.3 YES
82 STAG1 STAG1 STAG1 4184 0.071 0.3 YES
83 NINL NINL NINL 4199 0.071 0.31 YES
84 DCTN3 DCTN3 DCTN3 4217 0.07 0.31 YES
85 TUBG2 TUBG2 TUBG2 4262 0.069 0.31 YES
86 RBL1 RBL1 RBL1 4295 0.069 0.31 YES
87 FEN1 FEN1 FEN1 4315 0.068 0.31 YES
88 ALMS1 ALMS1 ALMS1 4432 0.066 0.31 YES
89 PRIM2 PRIM2 PRIM2 4446 0.066 0.31 YES
90 RRM2 RRM2 RRM2 4476 0.065 0.32 YES
91 E2F1 E2F1 E2F1 4500 0.064 0.32 YES
92 TUBGCP5 TUBGCP5 TUBGCP5 4524 0.064 0.32 YES
93 POLE2 POLE2 POLE2 4564 0.063 0.32 YES
94 KNTC1 KNTC1 KNTC1 4572 0.063 0.32 YES
95 PSMD3 PSMD3 PSMD3 4587 0.063 0.33 YES
96 CEP72 CEP72 CEP72 4597 0.062 0.33 YES
97 BUB3 BUB3 BUB3 4610 0.062 0.33 YES
98 LIN37 LIN37 LIN37 4622 0.062 0.33 YES
99 CEP192 CEP192 CEP192 4642 0.062 0.34 YES
100 PSMD13 PSMD13 PSMD13 4681 0.061 0.34 YES
101 MCM5 MCM5 MCM5 4718 0.06 0.34 YES
102 ZWILCH ZWILCH ZWILCH 4741 0.06 0.34 YES
103 RPA3 RPA3 RPA3 4798 0.059 0.34 YES
104 PSMD7 PSMD7 PSMD7 4800 0.059 0.34 YES
105 ZWINT ZWINT ZWINT 4805 0.059 0.35 YES
106 NEDD1 NEDD1 NEDD1 4884 0.057 0.34 YES
107 TFDP1 TFDP1 TFDP1 4949 0.056 0.34 YES
108 SKP2 SKP2 SKP2 4985 0.055 0.34 YES
109 RFC2 RFC2 RFC2 5038 0.054 0.34 YES
110 PSMB7 PSMB7 PSMB7 5067 0.054 0.35 YES
111 MCM6 MCM6 MCM6 5102 0.053 0.35 YES
112 RFC4 RFC4 RFC4 5137 0.053 0.35 YES
113 GMNN GMNN GMNN 5246 0.051 0.34 YES
114 CDT1 CDT1 CDT1 5272 0.05 0.35 YES
115 PTTG1 PTTG1 PTTG1 5285 0.05 0.35 YES
116 PSMB1 PSMB1 PSMB1 5290 0.05 0.35 YES
117 OFD1 OFD1 OFD1 5300 0.05 0.35 YES
118 AURKB AURKB AURKB 5304 0.05 0.36 YES
119 PAFAH1B1 PAFAH1B1 PAFAH1B1 5381 0.048 0.35 YES
120 LIN9 LIN9 LIN9 5412 0.048 0.35 YES
121 CSNK1E CSNK1E CSNK1E 5461 0.047 0.35 YES
122 SKA2 SKA2 SKA2 5467 0.047 0.36 YES
123 CDK4 CDK4 CDK4 5495 0.046 0.36 YES
124 CEP250 CEP250 CEP250 5588 0.045 0.35 YES
125 TUBGCP2 TUBGCP2 TUBGCP2 5659 0.044 0.35 YES
126 MYBL2 MYBL2 MYBL2 5662 0.044 0.35 YES
127 PCNA PCNA PCNA 5678 0.044 0.36 YES
128 CDC25A CDC25A CDC25A 5702 0.043 0.36 YES
129 CEP63 CEP63 CEP63 5717 0.043 0.36 YES
130 CDC27 CDC27 CDC27 5718 0.043 0.36 YES
131 PCNT PCNT PCNT 5941 0.04 0.35 NO
132 BUB1B BUB1B BUB1B 5954 0.039 0.35 NO
133 PSMA7 PSMA7 PSMA7 6019 0.038 0.35 NO
134 POLA2 POLA2 POLA2 6032 0.038 0.35 NO
135 NUP107 NUP107 NUP107 6038 0.038 0.35 NO
136 SSNA1 SSNA1 SSNA1 6086 0.037 0.35 NO
137 POLD1 POLD1 POLD1 6121 0.037 0.35 NO
138 AHCTF1 AHCTF1 AHCTF1 6213 0.035 0.35 NO
139 ITGB3BP ITGB3BP ITGB3BP 6223 0.035 0.35 NO
140 MCM10 MCM10 MCM10 6249 0.035 0.35 NO
141 PPP1CC PPP1CC PPP1CC 6295 0.034 0.35 NO
142 TK2 TK2 TK2 6308 0.034 0.35 NO
143 MCM2 MCM2 MCM2 6309 0.034 0.35 NO
144 RPA2 RPA2 RPA2 6388 0.032 0.35 NO
145 RPA1 RPA1 RPA1 6399 0.032 0.35 NO
146 STAG2 STAG2 STAG2 6410 0.032 0.35 NO
147 PSMD6 PSMD6 PSMD6 6423 0.032 0.35 NO
148 CEP70 CEP70 CEP70 6456 0.031 0.35 NO
149 SEH1L SEH1L SEH1L 6483 0.031 0.35 NO
150 NUP37 NUP37 NUP37 6627 0.029 0.35 NO
151 DYRK1A DYRK1A DYRK1A 6635 0.028 0.35 NO
152 RCC2 RCC2 RCC2 6638 0.028 0.35 NO
153 NUP43 NUP43 NUP43 6678 0.028 0.35 NO
154 PSMC2 PSMC2 PSMC2 6713 0.027 0.35 NO
155 CENPT CENPT CENPT 6748 0.027 0.35 NO
156 PSMF1 PSMF1 PSMF1 6801 0.026 0.35 NO
157 DYNC1H1 DYNC1H1 DYNC1H1 6803 0.026 0.35 NO
158 ANAPC7 ANAPC7 ANAPC7 6847 0.026 0.35 NO
159 CEP290 CEP290 CEP290 6907 0.025 0.34 NO
160 CDC16 CDC16 CDC16 6913 0.025 0.35 NO
161 PPP2R5C PPP2R5C PPP2R5C 6918 0.025 0.35 NO
162 RFC5 RFC5 RFC5 6994 0.024 0.34 NO
163 ACTR1A ACTR1A ACTR1A 7021 0.023 0.34 NO
164 PSMD10 PSMD10 PSMD10 7024 0.023 0.34 NO
165 PSMA2 PSMA2 PSMA2 7057 0.023 0.34 NO
166 TUBG1 TUBG1 TUBG1 7135 0.022 0.34 NO
167 DCTN2 DCTN2 DCTN2 7148 0.022 0.34 NO
168 CDC23 CDC23 CDC23 7177 0.021 0.34 NO
169 PSMB6 PSMB6 PSMB6 7210 0.021 0.34 NO
170 PMF1 PMF1 PMF1 7229 0.02 0.34 NO
171 PRKACA PRKACA PRKACA 7253 0.02 0.34 NO
172 PSMD2 PSMD2 PSMD2 7266 0.02 0.34 NO
173 PSMD11 PSMD11 PSMD11 7279 0.02 0.34 NO
174 TUBB TUBB TUBB 7285 0.02 0.34 NO
175 MCM7 MCM7 MCM7 7296 0.02 0.34 NO
176 MCM3 MCM3 MCM3 7306 0.02 0.34 NO
177 DCTN1 DCTN1 DCTN1 7341 0.019 0.34 NO
178 ANAPC4 ANAPC4 ANAPC4 7350 0.019 0.34 NO
179 CCNB1 CCNB1 CCNB1 7358 0.019 0.34 NO
180 DSN1 DSN1 DSN1 7371 0.018 0.34 NO
181 NUMA1 NUMA1 NUMA1 7414 0.018 0.34 NO
182 PSMA1 PSMA1 PSMA1 7436 0.018 0.34 NO
183 FGFR1OP FGFR1OP FGFR1OP 7452 0.018 0.34 NO
184 RANGAP1 RANGAP1 RANGAP1 7482 0.017 0.34 NO
185 DHFR DHFR DHFR 7489 0.017 0.34 NO
186 CDC7 CDC7 CDC7 7568 0.016 0.34 NO
187 NSL1 NSL1 NSL1 7591 0.016 0.34 NO
188 CENPH CENPH CENPH 7600 0.016 0.34 NO
189 DYNLL1 DYNLL1 DYNLL1 7642 0.015 0.34 NO
190 PSMD1 PSMD1 PSMD1 7682 0.015 0.34 NO
191 PPP2CA PPP2CA PPP2CA 7776 0.014 0.33 NO
192 CDK1 CDK1 CDK1 7814 0.013 0.33 NO
193 NUP85 NUP85 NUP85 7945 0.011 0.32 NO
194 PSMA4 PSMA4 PSMA4 7957 0.011 0.32 NO
195 HAUS2 HAUS2 HAUS2 7987 0.011 0.32 NO
196 E2F3 E2F3 E2F3 7994 0.011 0.32 NO
197 PSMD14 PSMD14 PSMD14 8020 0.01 0.32 NO
198 XPO1 XPO1 XPO1 8090 0.0091 0.32 NO
199 POLD3 POLD3 POLD3 8115 0.0089 0.32 NO
200 NUDC NUDC NUDC 8273 0.0068 0.31 NO
201 YWHAE YWHAE YWHAE 8286 0.0066 0.31 NO
202 YWHAG YWHAG YWHAG 8316 0.0062 0.31 NO
203 PSMC1 PSMC1 PSMC1 8323 0.006 0.31 NO
204 MAPRE1 MAPRE1 MAPRE1 8357 0.0056 0.31 NO
205 UBE2E1 UBE2E1 UBE2E1 8497 0.0038 0.3 NO
206 ANAPC5 ANAPC5 ANAPC5 8513 0.0036 0.3 NO
207 PSMB9 PSMB9 PSMB9 8528 0.0034 0.3 NO
208 TUBA1A TUBA1A TUBA1A 8550 0.0031 0.3 NO
209 CKS1B CKS1B CKS1B 8565 0.0028 0.3 NO
210 RBBP4 RBBP4 RBBP4 8637 0.002 0.29 NO
211 CEP164 CEP164 CEP164 8641 0.0019 0.29 NO
212 CENPJ CENPJ CENPJ 8712 0.00085 0.29 NO
213 BTRC BTRC BTRC 8845 -0.0006 0.28 NO
214 PPP2R5E PPP2R5E PPP2R5E 8930 -0.0017 0.28 NO
215 CUL1 CUL1 CUL1 8953 -0.0019 0.28 NO
216 PSMA3 PSMA3 PSMA3 8981 -0.0023 0.28 NO
217 HSP90AA1 HSP90AA1 HSP90AA1 8987 -0.0023 0.27 NO
218 CCNE1 CCNE1 CCNE1 9036 -0.003 0.27 NO
219 PSMB2 PSMB2 PSMB2 9105 -0.0038 0.27 NO
220 POLD2 POLD2 POLD2 9239 -0.0056 0.26 NO
221 RBL2 RBL2 RBL2 9268 -0.0061 0.26 NO
222 PSMD9 PSMD9 PSMD9 9296 -0.0065 0.26 NO
223 CCNH CCNH CCNH 9339 -0.007 0.26 NO
224 LIG1 LIG1 LIG1 9499 -0.009 0.25 NO
225 NUP133 NUP133 NUP133 9516 -0.0092 0.25 NO
226 MCM4 MCM4 MCM4 9529 -0.0093 0.25 NO
227 PSMC6 PSMC6 PSMC6 9566 -0.0099 0.25 NO
228 PSMB4 PSMB4 PSMB4 9664 -0.011 0.24 NO
229 CCND3 CCND3 CCND3 9829 -0.013 0.23 NO
230 PSMC5 PSMC5 PSMC5 9854 -0.013 0.23 NO
231 CLIP1 CLIP1 CLIP1 9924 -0.014 0.23 NO
232 SKP1 SKP1 SKP1 9965 -0.015 0.23 NO
233 NDEL1 NDEL1 NDEL1 10164 -0.017 0.22 NO
234 UBA52 UBA52 UBA52 10204 -0.018 0.22 NO
235 E2F2 E2F2 E2F2 10206 -0.018 0.22 NO
236 AZI1 AZI1 AZI1 10243 -0.018 0.22 NO
237 GORASP1 GORASP1 GORASP1 10321 -0.019 0.21 NO
238 PPP2R1A PPP2R1A PPP2R1A 10379 -0.02 0.21 NO
239 PSMB5 PSMB5 PSMB5 10454 -0.021 0.21 NO
240 MNAT1 MNAT1 MNAT1 10490 -0.022 0.21 NO
241 CLASP1 CLASP1 CLASP1 10585 -0.023 0.2 NO
242 MAX MAX MAX 10617 -0.023 0.2 NO
243 PSMA6 PSMA6 PSMA6 10746 -0.025 0.2 NO
244 PSMB3 PSMB3 PSMB3 10811 -0.026 0.2 NO
245 PSME2 PSME2 PSME2 10986 -0.029 0.19 NO
246 TAOK1 TAOK1 TAOK1 11044 -0.03 0.19 NO
247 AKAP9 AKAP9 AKAP9 11235 -0.032 0.18 NO
248 DYNC1I2 DYNC1I2 DYNC1I2 11303 -0.033 0.18 NO
249 PSME4 PSME4 PSME4 11425 -0.035 0.17 NO
250 PPP2R1B PPP2R1B PPP2R1B 11430 -0.036 0.17 NO
251 PSMD4 PSMD4 PSMD4 11490 -0.037 0.17 NO
252 PSMB8 PSMB8 PSMB8 11591 -0.039 0.17 NO
253 GINS4 GINS4 GINS4 11609 -0.039 0.17 NO
254 CETN2 CETN2 CETN2 11942 -0.044 0.15 NO
255 UBE2D1 UBE2D1 UBE2D1 11957 -0.045 0.16 NO
256 ANAPC11 ANAPC11 ANAPC11 11983 -0.045 0.16 NO
257 ANAPC1 ANAPC1 ANAPC1 11987 -0.045 0.16 NO
258 PCM1 PCM1 PCM1 12020 -0.046 0.16 NO
259 PSMD12 PSMD12 PSMD12 12043 -0.046 0.16 NO
260 HDAC1 HDAC1 HDAC1 12114 -0.048 0.16 NO
261 TUBGCP6 TUBGCP6 TUBGCP6 12297 -0.051 0.15 NO
262 DNA2 DNA2 DNA2 12364 -0.052 0.15 NO
263 ZW10 ZW10 ZW10 12386 -0.053 0.15 NO
264 WEE1 WEE1 WEE1 12424 -0.053 0.15 NO
265 PSMA5 PSMA5 PSMA5 12579 -0.057 0.15 NO
266 CSNK1D CSNK1D CSNK1D 12595 -0.057 0.15 NO
267 TUBA4A TUBA4A TUBA4A 12633 -0.057 0.15 NO
268 MIS12 MIS12 MIS12 12691 -0.059 0.15 NO
269 RFC3 RFC3 RFC3 12945 -0.064 0.14 NO
270 PPP2R5A PPP2R5A PPP2R5A 13062 -0.066 0.14 NO
271 CDK6 CDK6 CDK6 13149 -0.068 0.14 NO
272 KIF2A KIF2A KIF2A 13302 -0.072 0.13 NO
273 CEP57 CEP57 CEP57 13446 -0.075 0.13 NO
274 RANBP2 RANBP2 RANBP2 13540 -0.078 0.13 NO
275 PKMYT1 PKMYT1 PKMYT1 13586 -0.079 0.13 NO
276 RPS27A RPS27A RPS27A 13660 -0.081 0.13 NO
277 CENPK CENPK CENPK 13704 -0.082 0.13 NO
278 PPP2R2A PPP2R2A PPP2R2A 13749 -0.083 0.13 NO
279 PSME1 PSME1 PSME1 14099 -0.093 0.12 NO
280 POLD4 POLD4 POLD4 14192 -0.096 0.12 NO
281 PSMD5 PSMD5 PSMD5 14232 -0.097 0.12 NO
282 CCNA1 CCNA1 CCNA1 14312 -0.099 0.12 NO
283 PRKAR2B PRKAR2B PRKAR2B 14367 -0.1 0.12 NO
284 CCND1 CCND1 CCND1 14514 -0.11 0.12 NO
285 PPP2CB PPP2CB PPP2CB 14713 -0.11 0.12 NO
286 B9D2 B9D2 B9D2 15050 -0.12 0.1 NO
287 CENPM CENPM CENPM 15068 -0.13 0.11 NO
288 MYC MYC MYC 15517 -0.15 0.092 NO
289 CDKN1A CDKN1A CDKN1A 15730 -0.16 0.088 NO
290 CDK7 CDK7 CDK7 15848 -0.16 0.09 NO
291 RB1 RB1 RB1 15924 -0.16 0.095 NO
292 PSMB10 PSMB10 PSMB10 16018 -0.17 0.098 NO
293 CCND2 CCND2 CCND2 16505 -0.2 0.082 NO
294 E2F5 E2F5 E2F5 16623 -0.2 0.086 NO
295 CDC14A CDC14A CDC14A 16627 -0.2 0.096 NO
296 RPS27 RPS27 RPS27 17443 -0.27 0.066 NO

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

Figure S74.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME MEIOSIS, 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: REACTOME CELL CYCLE

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NEK2 NEK2 NEK2 2411 0.13 -0.08 YES
2 CKAP5 CKAP5 CKAP5 3043 0.1 -0.075 YES
3 CEP76 CEP76 CEP76 3273 0.095 -0.05 YES
4 CEP135 CEP135 CEP135 3403 0.091 -0.022 YES
5 CDK5RAP2 CDK5RAP2 CDK5RAP2 3432 0.09 0.011 YES
6 PLK1 PLK1 PLK1 3481 0.088 0.042 YES
7 PLK4 PLK4 PLK4 3567 0.086 0.07 YES
8 TUBGCP3 TUBGCP3 TUBGCP3 3633 0.084 0.099 YES
9 SDCCAG8 SDCCAG8 SDCCAG8 4111 0.073 0.1 YES
10 NINL NINL NINL 4199 0.071 0.12 YES
11 DCTN3 DCTN3 DCTN3 4217 0.07 0.15 YES
12 TUBG2 TUBG2 TUBG2 4262 0.069 0.17 YES
13 ALMS1 ALMS1 ALMS1 4432 0.066 0.19 YES
14 TUBGCP5 TUBGCP5 TUBGCP5 4524 0.064 0.21 YES
15 CEP72 CEP72 CEP72 4597 0.062 0.23 YES
16 CEP192 CEP192 CEP192 4642 0.062 0.25 YES
17 NEDD1 NEDD1 NEDD1 4884 0.057 0.26 YES
18 OFD1 OFD1 OFD1 5300 0.05 0.26 YES
19 PAFAH1B1 PAFAH1B1 PAFAH1B1 5381 0.048 0.27 YES
20 CSNK1E CSNK1E CSNK1E 5461 0.047 0.29 YES
21 CEP250 CEP250 CEP250 5588 0.045 0.3 YES
22 TUBGCP2 TUBGCP2 TUBGCP2 5659 0.044 0.31 YES
23 CEP63 CEP63 CEP63 5717 0.043 0.32 YES
24 PCNT PCNT PCNT 5941 0.04 0.33 YES
25 SSNA1 SSNA1 SSNA1 6086 0.037 0.33 YES
26 CEP70 CEP70 CEP70 6456 0.031 0.32 YES
27 DYNC1H1 DYNC1H1 DYNC1H1 6803 0.026 0.32 YES
28 CEP290 CEP290 CEP290 6907 0.025 0.32 YES
29 ACTR1A ACTR1A ACTR1A 7021 0.023 0.32 YES
30 TUBG1 TUBG1 TUBG1 7135 0.022 0.32 YES
31 DCTN2 DCTN2 DCTN2 7148 0.022 0.33 YES
32 PRKACA PRKACA PRKACA 7253 0.02 0.34 YES
33 TUBB TUBB TUBB 7285 0.02 0.34 YES
34 DCTN1 DCTN1 DCTN1 7341 0.019 0.34 YES
35 CCNB1 CCNB1 CCNB1 7358 0.019 0.35 YES
36 NUMA1 NUMA1 NUMA1 7414 0.018 0.36 YES
37 FGFR1OP FGFR1OP FGFR1OP 7452 0.018 0.36 YES
38 DYNLL1 DYNLL1 DYNLL1 7642 0.015 0.36 NO
39 CDK1 CDK1 CDK1 7814 0.013 0.35 NO
40 HAUS2 HAUS2 HAUS2 7987 0.011 0.35 NO
41 YWHAE YWHAE YWHAE 8286 0.0066 0.33 NO
42 YWHAG YWHAG YWHAG 8316 0.0062 0.33 NO
43 MAPRE1 MAPRE1 MAPRE1 8357 0.0056 0.33 NO
44 TUBA1A TUBA1A TUBA1A 8550 0.0031 0.32 NO
45 CEP164 CEP164 CEP164 8641 0.0019 0.32 NO
46 CENPJ CENPJ CENPJ 8712 0.00085 0.32 NO
47 HSP90AA1 HSP90AA1 HSP90AA1 8987 -0.0023 0.3 NO
48 AZI1 AZI1 AZI1 10243 -0.018 0.24 NO
49 PPP2R1A PPP2R1A PPP2R1A 10379 -0.02 0.24 NO
50 CLASP1 CLASP1 CLASP1 10585 -0.023 0.24 NO
51 AKAP9 AKAP9 AKAP9 11235 -0.032 0.22 NO
52 DYNC1I2 DYNC1I2 DYNC1I2 11303 -0.033 0.23 NO
53 CETN2 CETN2 CETN2 11942 -0.044 0.21 NO
54 PCM1 PCM1 PCM1 12020 -0.046 0.22 NO
55 TUBGCP6 TUBGCP6 TUBGCP6 12297 -0.051 0.23 NO
56 CSNK1D CSNK1D CSNK1D 12595 -0.057 0.24 NO
57 TUBA4A TUBA4A TUBA4A 12633 -0.057 0.26 NO
58 CEP57 CEP57 CEP57 13446 -0.075 0.24 NO
59 PRKAR2B PRKAR2B PRKAR2B 14367 -0.1 0.23 NO

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

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

genes ES table in pathway: REACTOME SIGNALLING TO ERKS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FBXO6 FBXO6 FBXO6 1980 0.15 -0.033 YES
2 TUBA3C TUBA3C TUBA3C 2265 0.14 0.019 YES
3 FBXO4 FBXO4 FBXO4 2321 0.13 0.082 YES
4 FKBP9 FKBP9 FKBP9 2379 0.13 0.14 YES
5 USP11 USP11 USP11 3652 0.084 0.12 YES
6 TUBB1 TUBB1 TUBB1 3791 0.08 0.15 YES
7 KIF13A KIF13A KIF13A 3813 0.079 0.19 YES
8 VBP1 VBP1 VBP1 4012 0.074 0.21 YES
9 FBXW2 FBXW2 FBXW2 4178 0.071 0.24 YES
10 TUBB6 TUBB6 TUBB6 4290 0.069 0.27 YES
11 TBCB TBCB TBCB 4428 0.066 0.29 YES
12 TUBB2A TUBB2A TUBB2A 4464 0.065 0.32 YES
13 FBXW5 FBXW5 FBXW5 5269 0.05 0.3 YES
14 TUBA1B TUBA1B TUBA1B 5391 0.048 0.32 YES
15 XRN2 XRN2 XRN2 5480 0.047 0.34 YES
16 FBXL3 FBXL3 FBXL3 5916 0.04 0.34 YES
17 TCP1 TCP1 TCP1 6224 0.035 0.34 YES
18 FBXW7 FBXW7 FBXW7 6314 0.034 0.35 YES
19 PFDN4 PFDN4 PFDN4 6556 0.03 0.35 YES
20 NOP56 NOP56 NOP56 6577 0.029 0.36 YES
21 PFDN1 PFDN1 PFDN1 6712 0.027 0.37 YES
22 KIFC3 KIFC3 KIFC3 6816 0.026 0.38 YES
23 TBCD TBCD TBCD 7092 0.022 0.37 NO
24 CCT4 CCT4 CCT4 7656 0.015 0.35 NO
25 CCT5 CCT5 CCT5 7854 0.012 0.35 NO
26 PFDN2 PFDN2 PFDN2 8066 0.0094 0.34 NO
27 ACTB ACTB ACTB 8209 0.0076 0.34 NO
28 CCT6A CCT6A CCT6A 8420 0.0048 0.33 NO
29 CCT2 CCT2 CCT2 8545 0.0032 0.32 NO
30 TUBA1A TUBA1A TUBA1A 8550 0.0031 0.32 NO
31 CCT8 CCT8 CCT8 8671 0.0014 0.32 NO
32 TUBB3 TUBB3 TUBB3 8700 0.001 0.32 NO
33 TUBA1C TUBA1C TUBA1C 8947 -0.0018 0.3 NO
34 CCT7 CCT7 CCT7 9207 -0.0051 0.29 NO
35 CCT3 CCT3 CCT3 9334 -0.007 0.29 NO
36 TBCE TBCE TBCE 9345 -0.0071 0.29 NO
37 FBXL5 FBXL5 FBXL5 9627 -0.011 0.28 NO
38 ARFGEF2 ARFGEF2 ARFGEF2 9747 -0.012 0.28 NO
39 PFDN5 PFDN5 PFDN5 9806 -0.013 0.28 NO
40 LONP2 LONP2 LONP2 10116 -0.017 0.28 NO
41 TBCC TBCC TBCC 10350 -0.02 0.27 NO
42 PFDN6 PFDN6 PFDN6 10569 -0.023 0.27 NO
43 TUBA3D TUBA3D TUBA3D 10766 -0.025 0.28 NO
44 FBXW4 FBXW4 FBXW4 10831 -0.026 0.29 NO
45 TBCA TBCA TBCA 11302 -0.033 0.28 NO
46 AP3M1 AP3M1 AP3M1 11628 -0.039 0.28 NO
47 TUBB2B TUBB2B TUBB2B 11833 -0.043 0.29 NO
48 TUBA4A TUBA4A TUBA4A 12633 -0.057 0.28 NO
49 SPHK1 SPHK1 SPHK1 14283 -0.098 0.24 NO

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

Figure S78.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SIGNALLING TO ERKS, 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: REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CDKN2C CDKN2C CDKN2C 154 0.43 0.04 YES
2 CCNB3 CCNB3 CCNB3 211 0.4 0.082 YES
3 TGFB2 TGFB2 TGFB2 923 0.24 0.07 YES
4 TGFB3 TGFB3 TGFB3 997 0.23 0.092 YES
5 CCNE2 CCNE2 CCNE2 1344 0.19 0.096 YES
6 CDKN2A CDKN2A CDKN2A 1834 0.16 0.087 YES
7 CCNA2 CCNA2 CCNA2 1868 0.16 0.1 YES
8 SMC1A SMC1A SMC1A 1894 0.15 0.12 YES
9 ANAPC10 ANAPC10 ANAPC10 1952 0.15 0.13 YES
10 CDKN1B CDKN1B CDKN1B 2068 0.14 0.14 YES
11 DBF4 DBF4 DBF4 2115 0.14 0.16 YES
12 CDC45 CDC45 CDC45 2381 0.13 0.16 YES
13 CDC26 CDC26 CDC26 2574 0.12 0.16 YES
14 TGFB1 TGFB1 TGFB1 2713 0.12 0.16 YES
15 SMAD3 SMAD3 SMAD3 2728 0.12 0.18 YES
16 CDC25B CDC25B CDC25B 2737 0.11 0.19 YES
17 CCNB2 CCNB2 CCNB2 2786 0.11 0.2 YES
18 CDKN2D CDKN2D CDKN2D 2826 0.11 0.21 YES
19 CDKN2B CDKN2B CDKN2B 2868 0.11 0.22 YES
20 MAD2L1 MAD2L1 MAD2L1 2928 0.11 0.23 YES
21 CDK2 CDK2 CDK2 3020 0.1 0.24 YES
22 MAD2L2 MAD2L2 MAD2L2 3099 0.1 0.24 YES
23 SMC3 SMC3 SMC3 3164 0.098 0.25 YES
24 ESPL1 ESPL1 ESPL1 3191 0.098 0.26 YES
25 CDC20 CDC20 CDC20 3237 0.096 0.27 YES
26 CDC25C CDC25C CDC25C 3339 0.092 0.27 YES
27 ANAPC2 ANAPC2 ANAPC2 3369 0.092 0.28 YES
28 BUB1 BUB1 BUB1 3429 0.09 0.29 YES
29 SMC1B SMC1B SMC1B 3472 0.088 0.3 YES
30 PLK1 PLK1 PLK1 3481 0.088 0.3 YES
31 CDC6 CDC6 CDC6 3547 0.086 0.31 YES
32 MAD1L1 MAD1L1 MAD1L1 3555 0.086 0.32 YES
33 TTK TTK TTK 3730 0.082 0.32 YES
34 RAD21 RAD21 RAD21 3786 0.08 0.33 YES
35 E2F4 E2F4 E2F4 3967 0.076 0.32 YES
36 ABL1 ABL1 ABL1 3974 0.076 0.33 YES
37 TP53 TP53 TP53 4180 0.071 0.33 YES
38 STAG1 STAG1 STAG1 4184 0.071 0.34 YES
39 RBL1 RBL1 RBL1 4295 0.069 0.34 YES
40 E2F1 E2F1 E2F1 4500 0.064 0.34 YES
41 FZR1 FZR1 FZR1 4517 0.064 0.34 YES
42 BUB3 BUB3 BUB3 4610 0.062 0.34 YES
43 MCM5 MCM5 MCM5 4718 0.06 0.35 YES
44 CDC14B CDC14B CDC14B 4749 0.06 0.35 YES
45 TFDP1 TFDP1 TFDP1 4949 0.056 0.35 YES
46 SKP2 SKP2 SKP2 4985 0.055 0.35 YES
47 MCM6 MCM6 MCM6 5102 0.053 0.35 YES
48 SMAD2 SMAD2 SMAD2 5268 0.05 0.35 YES
49 PTTG1 PTTG1 PTTG1 5285 0.05 0.35 YES
50 HDAC2 HDAC2 HDAC2 5294 0.05 0.36 YES
51 CDK4 CDK4 CDK4 5495 0.046 0.35 NO
52 PCNA PCNA PCNA 5678 0.044 0.35 NO
53 CDC25A CDC25A CDC25A 5702 0.043 0.35 NO
54 CDC27 CDC27 CDC27 5718 0.043 0.35 NO
55 CREBBP CREBBP CREBBP 5900 0.04 0.35 NO
56 BUB1B BUB1B BUB1B 5954 0.039 0.35 NO
57 PRKDC PRKDC PRKDC 6214 0.035 0.34 NO
58 SMAD4 SMAD4 SMAD4 6296 0.034 0.34 NO
59 MCM2 MCM2 MCM2 6309 0.034 0.34 NO
60 STAG2 STAG2 STAG2 6410 0.032 0.34 NO
61 ZBTB17 ZBTB17 ZBTB17 6580 0.029 0.34 NO
62 GADD45A GADD45A GADD45A 6686 0.028 0.33 NO
63 YWHAH YWHAH YWHAH 6823 0.026 0.33 NO
64 ANAPC7 ANAPC7 ANAPC7 6847 0.026 0.33 NO
65 ATR ATR ATR 6912 0.025 0.33 NO
66 CDC16 CDC16 CDC16 6913 0.025 0.33 NO
67 MDM2 MDM2 MDM2 7163 0.021 0.32 NO
68 CDC23 CDC23 CDC23 7177 0.021 0.32 NO
69 MCM7 MCM7 MCM7 7296 0.02 0.32 NO
70 MCM3 MCM3 MCM3 7306 0.02 0.32 NO
71 ANAPC4 ANAPC4 ANAPC4 7350 0.019 0.32 NO
72 CCNB1 CCNB1 CCNB1 7358 0.019 0.32 NO
73 GADD45B GADD45B GADD45B 7370 0.018 0.32 NO
74 ANAPC13 ANAPC13 ANAPC13 7400 0.018 0.32 NO
75 CDC7 CDC7 CDC7 7568 0.016 0.32 NO
76 CDK1 CDK1 CDK1 7814 0.013 0.3 NO
77 EP300 EP300 EP300 7897 0.012 0.3 NO
78 E2F3 E2F3 E2F3 7994 0.011 0.3 NO
79 YWHAB YWHAB YWHAB 8046 0.0097 0.3 NO
80 SFN SFN SFN 8199 0.0078 0.29 NO
81 GSK3B GSK3B GSK3B 8251 0.007 0.29 NO
82 YWHAE YWHAE YWHAE 8286 0.0066 0.29 NO
83 YWHAG YWHAG YWHAG 8316 0.0062 0.28 NO
84 ANAPC5 ANAPC5 ANAPC5 8513 0.0036 0.28 NO
85 RBX1 RBX1 RBX1 8837 -0.0005 0.26 NO
86 CUL1 CUL1 CUL1 8953 -0.0019 0.25 NO
87 CCNE1 CCNE1 CCNE1 9036 -0.003 0.25 NO
88 RBL2 RBL2 RBL2 9268 -0.0061 0.24 NO
89 CCNH CCNH CCNH 9339 -0.007 0.23 NO
90 TFDP2 TFDP2 TFDP2 9487 -0.0089 0.23 NO
91 MCM4 MCM4 MCM4 9529 -0.0093 0.22 NO
92 CHEK2 CHEK2 CHEK2 9591 -0.01 0.22 NO
93 CCND3 CCND3 CCND3 9829 -0.013 0.21 NO
94 SKP1 SKP1 SKP1 9965 -0.015 0.2 NO
95 E2F2 E2F2 E2F2 10206 -0.018 0.19 NO
96 WEE2 WEE2 WEE2 10353 -0.02 0.19 NO
97 YWHAQ YWHAQ YWHAQ 11214 -0.032 0.15 NO
98 YWHAZ YWHAZ YWHAZ 11458 -0.036 0.14 NO
99 PTTG2 PTTG2 PTTG2 11960 -0.045 0.12 NO
100 CDKN1C CDKN1C CDKN1C 11972 -0.045 0.12 NO
101 ANAPC11 ANAPC11 ANAPC11 11983 -0.045 0.12 NO
102 ANAPC1 ANAPC1 ANAPC1 11987 -0.045 0.13 NO
103 HDAC1 HDAC1 HDAC1 12114 -0.048 0.13 NO
104 WEE1 WEE1 WEE1 12424 -0.053 0.12 NO
105 CDK6 CDK6 CDK6 13149 -0.068 0.085 NO
106 PKMYT1 PKMYT1 PKMYT1 13586 -0.079 0.07 NO
107 CCNA1 CCNA1 CCNA1 14312 -0.099 0.042 NO
108 CHEK1 CHEK1 CHEK1 14381 -0.1 0.05 NO
109 CCND1 CCND1 CCND1 14514 -0.11 0.055 NO
110 GADD45G GADD45G GADD45G 14960 -0.12 0.045 NO
111 ATM ATM ATM 15287 -0.14 0.042 NO
112 MYC MYC MYC 15517 -0.15 0.046 NO
113 CDKN1A CDKN1A CDKN1A 15730 -0.16 0.052 NO
114 CDK7 CDK7 CDK7 15848 -0.16 0.064 NO
115 RB1 RB1 RB1 15924 -0.16 0.079 NO
116 CCND2 CCND2 CCND2 16505 -0.2 0.07 NO
117 E2F5 E2F5 E2F5 16623 -0.2 0.086 NO
118 CDC14A CDC14A CDC14A 16627 -0.2 0.11 NO

Figure S79.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS.

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS, 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.v4.0.symbols.gmt

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

  • Phenotype data file = UCS-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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