GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in GBM-TP
Glioblastoma Multiforme (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1513XKW
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 GBM-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1513XKW
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 "GBM-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: 709
Number of samples: 153
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 48
pheno.type: 2 - 3 :[ clus2 ] 71
pheno.type: 3 - 3 :[ clus3 ] 34

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

  • clus1

    • Top enriched gene sets are KEGG RNA DEGRADATION, KEGG CELL CYCLE, KEGG PROGESTERONE MEDIATED OOCYTE MATURATION, PID ATR PATHWAY, PID RET PATHWAY, PID ATM PATHWAY, PID PLK1 PATHWAY, PID AR TF PATHWAY, PID LIS1PATHWAY, PID ERA GENOMIC PATHWAY

    • And common core enriched genes are CCNA2, CDC25A, CDC25C, PLK1, LSM2, ADCY1, ADCY5, ADCY8, AKT3, BUB1

  • clus2

    • Top enriched gene sets are KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, BIOCARTA HIVNEF PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA DEATH PATHWAY, ST TUMOR NECROSIS FACTOR PATHWAY, PID SYNDECAN 4 PATHWAY, PID HIVNEFPATHWAY, REACTOME ANTIGEN PROCESSING CROSS PRESENTATION, REACTOME TRIF MEDIATED TLR3 SIGNALING, REACTOME ACTIVATION OF CHAPERONE GENES BY XBP1S

    • And common core enriched genes are DDX58, HERC5, IFNB1, IRF1, IRF2, IRF3, IRF7, ISG15, UBA7, UBE2L6

  • clus3

    • Top enriched gene sets are KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG BUTANOATE METABOLISM, KEGG MAPK SIGNALING PATHWAY, KEGG ERBB SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION

    • And common core enriched genes are CAMK2A, CAMK2B, GRIN1, GRIN2A, GRIN2C, NEFL, ACTN2, RASGRF1, RASGRF2, CAMK2G

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 RNA DEGRADATION 57 genes.ES.table 0.43 1.8 0.026 1 0.52 0.53 0.37 0.33 0.35 0.27
KEGG CELL CYCLE 118 genes.ES.table 0.54 1.7 0.046 0.45 0.82 0.35 0.17 0.29 0.2 0.12
KEGG PROGESTERONE MEDIATED OOCYTE MATURATION 81 genes.ES.table 0.51 1.8 0 1 0.5 0.28 0.16 0.24 0.27 0.39
PID ATR PATHWAY 39 genes.ES.table 0.7 1.8 0.015 0.86 0.65 0.44 0.18 0.36 0.31 0.22
PID RET PATHWAY 39 genes.ES.table 0.49 1.8 0.0059 0.67 0.7 0.18 0.1 0.16 0.26 0.17
PID ATM PATHWAY 34 genes.ES.table 0.52 1.7 0.048 0.44 0.86 0.44 0.29 0.32 0.2 0.11
PID PLK1 PATHWAY 45 genes.ES.table 0.73 1.7 0.027 0.44 0.78 0.53 0.17 0.44 0.18 0.11
PID AR TF PATHWAY 50 genes.ES.table 0.48 1.7 0.012 0.43 0.82 0.52 0.33 0.35 0.19 0.11
PID LIS1PATHWAY 28 genes.ES.table 0.55 1.7 0.018 0.41 0.87 0.25 0.15 0.21 0.2 0.1
PID ERA GENOMIC PATHWAY 62 genes.ES.table 0.46 1.7 0.0084 0.47 0.78 0.13 0.066 0.12 0.19 0.12
genes ES table in pathway: KEGG RNA DEGRADATION

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 ADCY5 ADCY5 ADCY5 236 0.5 0.044 YES
2 CDC25C CDC25C CDC25C 381 0.43 0.086 YES
3 CDC25A CDC25A CDC25A 383 0.43 0.14 YES
4 PKMYT1 PKMYT1 PKMYT1 565 0.37 0.17 YES
5 GNAI1 GNAI1 GNAI1 664 0.34 0.2 YES
6 CCNB3 CCNB3 CCNB3 831 0.31 0.23 YES
7 PDE3B PDE3B PDE3B 936 0.29 0.25 YES
8 PLK1 PLK1 PLK1 988 0.28 0.28 YES
9 RPS6KA6 RPS6KA6 RPS6KA6 989 0.28 0.32 YES
10 MAD2L1 MAD2L1 MAD2L1 1060 0.27 0.34 YES
11 CCNB2 CCNB2 CCNB2 1115 0.27 0.37 YES
12 BUB1 BUB1 BUB1 1291 0.24 0.39 YES
13 CCNA2 CCNA2 CCNA2 1313 0.24 0.42 YES
14 CDK1 CDK1 CDK1 1599 0.21 0.42 YES
15 MAPK8 MAPK8 MAPK8 1658 0.21 0.44 YES
16 PIK3R3 PIK3R3 PIK3R3 1926 0.18 0.45 YES
17 CCNB1 CCNB1 CCNB1 2331 0.16 0.45 YES
18 AKT3 AKT3 AKT3 2415 0.15 0.46 YES
19 MAD2L2 MAD2L2 MAD2L2 2632 0.14 0.46 YES
20 PRKX PRKX PRKX 2639 0.14 0.48 YES
21 ADCY8 ADCY8 ADCY8 2797 0.13 0.48 YES
22 CDC26 CDC26 CDC26 2879 0.12 0.5 YES
23 ADCY1 ADCY1 ADCY1 2914 0.12 0.51 YES
24 PIK3R2 PIK3R2 PIK3R2 3399 0.1 0.49 NO
25 ADCY2 ADCY2 ADCY2 3647 0.095 0.49 NO
26 RAF1 RAF1 RAF1 3993 0.084 0.48 NO
27 ADCY9 ADCY9 ADCY9 4281 0.076 0.47 NO
28 MAPK12 MAPK12 MAPK12 4514 0.07 0.47 NO
29 CCNA1 CCNA1 CCNA1 4801 0.064 0.46 NO
30 MAPK10 MAPK10 MAPK10 5214 0.055 0.44 NO
31 BRAF BRAF BRAF 5592 0.049 0.43 NO
32 PIK3CA PIK3CA PIK3CA 5616 0.049 0.43 NO
33 CDC25B CDC25B CDC25B 5946 0.043 0.42 NO
34 ANAPC1 ANAPC1 ANAPC1 5969 0.043 0.42 NO
35 ANAPC7 ANAPC7 ANAPC7 5975 0.043 0.43 NO
36 KRAS KRAS KRAS 6004 0.043 0.43 NO
37 HSP90AB1 HSP90AB1 HSP90AB1 6237 0.039 0.42 NO
38 FZR1 FZR1 FZR1 6295 0.038 0.42 NO
39 CDC23 CDC23 CDC23 6843 0.03 0.4 NO
40 ANAPC13 ANAPC13 ANAPC13 6879 0.03 0.4 NO
41 CDC27 CDC27 CDC27 6980 0.029 0.4 NO
42 ANAPC5 ANAPC5 ANAPC5 6998 0.029 0.4 NO
43 ANAPC2 ANAPC2 ANAPC2 7118 0.027 0.4 NO
44 CDK2 CDK2 CDK2 7151 0.027 0.4 NO
45 PRKACB PRKACB PRKACB 7428 0.023 0.38 NO
46 IGF1R IGF1R IGF1R 7514 0.022 0.38 NO
47 ANAPC11 ANAPC11 ANAPC11 7649 0.02 0.38 NO
48 PIK3R1 PIK3R1 PIK3R1 7809 0.019 0.37 NO
49 ADCY7 ADCY7 ADCY7 8427 0.011 0.34 NO
50 ADCY6 ADCY6 ADCY6 8607 0.0083 0.33 NO
51 MAPK11 MAPK11 MAPK11 9127 0.0017 0.3 NO
52 GNAI3 GNAI3 GNAI3 9186 0.00096 0.3 NO
53 MAPK9 MAPK9 MAPK9 9470 -0.0025 0.28 NO
54 MAPK14 MAPK14 MAPK14 9593 -0.004 0.28 NO
55 MAPK1 MAPK1 MAPK1 9920 -0.0081 0.26 NO
56 AKT2 AKT2 AKT2 10960 -0.022 0.2 NO
57 ANAPC4 ANAPC4 ANAPC4 11228 -0.025 0.19 NO
58 MAPK3 MAPK3 MAPK3 11233 -0.025 0.19 NO
59 MAP2K1 MAP2K1 MAP2K1 11414 -0.028 0.19 NO
60 AKT1 AKT1 AKT1 11636 -0.031 0.18 NO
61 CDC16 CDC16 CDC16 11943 -0.036 0.17 NO
62 ADCY4 ADCY4 ADCY4 11954 -0.036 0.17 NO
63 HSP90AA1 HSP90AA1 HSP90AA1 11967 -0.036 0.17 NO
64 RPS6KA2 RPS6KA2 RPS6KA2 12020 -0.037 0.17 NO
65 PRKACA PRKACA PRKACA 12068 -0.038 0.18 NO
66 GNAI2 GNAI2 GNAI2 12115 -0.038 0.18 NO
67 PIK3CD PIK3CD PIK3CD 12324 -0.041 0.17 NO
68 ADCY3 ADCY3 ADCY3 12706 -0.048 0.16 NO
69 ARAF ARAF ARAF 13101 -0.056 0.14 NO
70 PIK3CB PIK3CB PIK3CB 13129 -0.056 0.14 NO
71 PDE3A PDE3A PDE3A 13494 -0.063 0.13 NO
72 RPS6KA1 RPS6KA1 RPS6KA1 13716 -0.068 0.13 NO
73 ANAPC10 ANAPC10 ANAPC10 13778 -0.07 0.13 NO
74 SPDYA SPDYA SPDYA 13801 -0.07 0.14 NO
75 RPS6KA3 RPS6KA3 RPS6KA3 14415 -0.086 0.12 NO
76 PIK3R5 PIK3R5 PIK3R5 14891 -0.1 0.1 NO
77 CPEB1 CPEB1 CPEB1 15340 -0.12 0.089 NO
78 IGF1 IGF1 IGF1 15506 -0.12 0.094 NO
79 PGR PGR PGR 15717 -0.13 0.098 NO
80 PIK3CG PIK3CG PIK3CG 16330 -0.16 0.083 NO
81 MAPK13 MAPK13 MAPK13 16522 -0.18 0.092 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 RNA DEGRADATION.

Figure S2.  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 CELL CYCLE

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 PAPOLB PAPOLB PAPOLB 1540 0.22 0.0055 YES
2 CNOT6 CNOT6 CNOT6 3104 0.11 -0.033 YES
3 PAPD7 PAPD7 PAPD7 3416 0.1 -0.0069 YES
4 EXOSC2 EXOSC2 EXOSC2 3758 0.091 0.012 YES
5 LSM7 LSM7 LSM7 3825 0.089 0.046 YES
6 EDC4 EDC4 EDC4 3980 0.084 0.072 YES
7 EDC3 EDC3 EDC3 4222 0.077 0.092 YES
8 EXOSC7 EXOSC7 EXOSC7 4319 0.075 0.12 YES
9 EXOSC5 EXOSC5 EXOSC5 4483 0.071 0.14 YES
10 DCP1A DCP1A DCP1A 4567 0.069 0.16 YES
11 ZCCHC7 ZCCHC7 ZCCHC7 4578 0.068 0.19 YES
12 RQCD1 RQCD1 RQCD1 4752 0.064 0.21 YES
13 EXOSC1 EXOSC1 EXOSC1 5041 0.059 0.22 YES
14 CNOT7 CNOT7 CNOT7 5292 0.054 0.22 YES
15 DDX6 DDX6 DDX6 5317 0.054 0.25 YES
16 EXOSC3 EXOSC3 EXOSC3 5323 0.054 0.27 YES
17 LSM3 LSM3 LSM3 5365 0.053 0.29 YES
18 EXOSC9 EXOSC9 EXOSC9 5420 0.052 0.31 YES
19 EXOSC8 EXOSC8 EXOSC8 5436 0.052 0.33 YES
20 MPHOSPH6 MPHOSPH6 MPHOSPH6 5761 0.046 0.33 YES
21 CNOT8 CNOT8 CNOT8 5974 0.043 0.34 YES
22 CNOT10 CNOT10 CNOT10 6149 0.04 0.34 YES
23 EXOSC10 EXOSC10 EXOSC10 6168 0.04 0.36 YES
24 PAPOLG PAPOLG PAPOLG 6271 0.038 0.37 YES
25 LSM2 LSM2 LSM2 6317 0.037 0.38 YES
26 EXOSC6 EXOSC6 EXOSC6 6429 0.036 0.39 YES
27 DCP2 DCP2 DCP2 6534 0.034 0.4 YES
28 CNOT1 CNOT1 CNOT1 6609 0.034 0.41 YES
29 EXOSC4 EXOSC4 EXOSC4 6710 0.032 0.42 YES
30 SKIV2L2 SKIV2L2 SKIV2L2 6743 0.032 0.43 YES
31 DCPS DCPS DCPS 7302 0.025 0.41 NO
32 XRN1 XRN1 XRN1 7592 0.021 0.4 NO
33 PATL1 PATL1 PATL1 7708 0.02 0.4 NO
34 ENO3 ENO3 ENO3 7800 0.019 0.41 NO
35 XRN2 XRN2 XRN2 7859 0.018 0.41 NO
36 CNOT3 CNOT3 CNOT3 7951 0.017 0.41 NO
37 CNOT6L CNOT6L CNOT6L 8090 0.015 0.41 NO
38 LSM4 LSM4 LSM4 8097 0.015 0.42 NO
39 DIS3 DIS3 DIS3 8437 0.011 0.4 NO
40 ENO2 ENO2 ENO2 8685 0.0073 0.39 NO
41 HSPD1 HSPD1 HSPD1 8688 0.0072 0.4 NO
42 PAPOLA PAPOLA PAPOLA 8940 0.0041 0.38 NO
43 LSM1 LSM1 LSM1 8998 0.0034 0.38 NO
44 ENO1 ENO1 ENO1 9211 0.00073 0.37 NO
45 PNPT1 PNPT1 PNPT1 9231 0.00051 0.37 NO
46 TTC37 TTC37 TTC37 9285 -0.00022 0.37 NO
47 SKIV2L SKIV2L SKIV2L 9504 -0.0029 0.36 NO
48 NAA38 NAA38 NAA38 9569 -0.0037 0.35 NO
49 CNOT2 CNOT2 CNOT2 9754 -0.0058 0.35 NO
50 DCP1B DCP1B DCP1B 9937 -0.0084 0.34 NO
51 LSM5 LSM5 LSM5 10307 -0.013 0.32 NO
52 CNOT4 CNOT4 CNOT4 11447 -0.028 0.27 NO
53 HSPA9 HSPA9 HSPA9 11896 -0.035 0.26 NO
54 PARN PARN PARN 12502 -0.044 0.25 NO
55 LSM6 LSM6 LSM6 12604 -0.046 0.26 NO
56 WDR61 WDR61 WDR61 12690 -0.048 0.28 NO
57 C1D C1D C1D 13367 -0.061 0.27 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 CELL CYCLE.

Figure S4.  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: KEGG PROGESTERONE MEDIATED OOCYTE MATURATION

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 E2F2 E2F2 E2F2 166 0.55 0.15 YES
2 CDK4 CDK4 CDK4 683 0.34 0.22 YES
3 PPP2R3B PPP2R3B PPP2R3B 1073 0.27 0.27 YES
4 CDKN2A CDKN2A CDKN2A 1179 0.26 0.34 YES
5 CCND1 CCND1 CCND1 1210 0.25 0.41 YES
6 E2F1 E2F1 E2F1 1521 0.22 0.46 YES
7 CDKN2B CDKN2B CDKN2B 2110 0.17 0.48 YES
8 E2F3 E2F3 E2F3 2128 0.17 0.52 YES
9 RBL1 RBL1 RBL1 3017 0.12 0.51 YES
10 CDKN2D CDKN2D CDKN2D 3170 0.11 0.53 YES
11 CCND2 CCND2 CCND2 3306 0.11 0.56 YES
12 PPP2R2A PPP2R2A PPP2R2A 3503 0.1 0.57 YES
13 CKS1B CKS1B CKS1B 3555 0.098 0.6 YES
14 SKP2 SKP2 SKP2 4324 0.075 0.58 NO
15 E2F5 E2F5 E2F5 4735 0.065 0.57 NO
16 CDKN1B CDKN1B CDKN1B 5078 0.058 0.57 NO
17 CCNH CCNH CCNH 6757 0.032 0.49 NO
18 CDKN2C CDKN2C CDKN2C 6817 0.031 0.49 NO
19 PPP2R1A PPP2R1A PPP2R1A 7103 0.028 0.49 NO
20 PPP2R1B PPP2R1B PPP2R1B 7139 0.027 0.49 NO
21 PPP2CA PPP2CA PPP2CA 8148 0.015 0.44 NO
22 CCND3 CCND3 CCND3 8398 0.011 0.43 NO
23 E2F4 E2F4 E2F4 8769 0.0062 0.41 NO
24 RBL2 RBL2 RBL2 9141 0.0015 0.39 NO
25 MNAT1 MNAT1 MNAT1 9747 -0.0057 0.36 NO
26 CDK6 CDK6 CDK6 9867 -0.0073 0.36 NO
27 RB1 RB1 RB1 9968 -0.0088 0.35 NO
28 UBA52 UBA52 UBA52 10240 -0.012 0.34 NO
29 PPP2CB PPP2CB PPP2CB 10382 -0.014 0.34 NO
30 RPS27A RPS27A RPS27A 11126 -0.024 0.3 NO
31 TFDP1 TFDP1 TFDP1 11264 -0.026 0.3 NO
32 CDK7 CDK7 CDK7 12501 -0.044 0.25 NO
33 SKP1 SKP1 SKP1 12556 -0.045 0.26 NO
34 CUL1 CUL1 CUL1 12808 -0.05 0.26 NO
35 CDKN1A CDKN1A CDKN1A 15669 -0.13 0.14 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 PROGESTERONE MEDIATED OOCYTE MATURATION.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PROGESTERONE MEDIATED OOCYTE MATURATION, 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 ATR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CDC25C CDC25C CDC25C 381 0.43 0.078 YES
2 CDC25A CDC25A CDC25A 383 0.43 0.18 YES
3 CLSPN CLSPN CLSPN 554 0.37 0.25 YES
4 PLK1 PLK1 PLK1 988 0.28 0.29 YES
5 RAD51 RAD51 RAD51 1072 0.27 0.35 YES
6 FANCD2 FANCD2 FANCD2 1186 0.26 0.4 YES
7 CCNA2 CCNA2 CCNA2 1313 0.24 0.45 YES
8 BRCA2 BRCA2 BRCA2 1337 0.24 0.51 YES
9 CDC6 CDC6 CDC6 1737 0.2 0.53 YES
10 CHEK1 CHEK1 CHEK1 2070 0.17 0.55 YES
11 RFC3 RFC3 RFC3 2112 0.17 0.59 YES
12 MDM2 MDM2 MDM2 2567 0.14 0.6 YES
13 MCM2 MCM2 MCM2 2642 0.14 0.62 YES
14 MCM7 MCM7 MCM7 2726 0.13 0.65 YES
15 TIMELESS TIMELESS TIMELESS 2925 0.12 0.66 YES
16 RFC4 RFC4 RFC4 3053 0.12 0.68 YES
17 TOPBP1 TOPBP1 TOPBP1 3244 0.11 0.7 YES
18 RFC5 RFC5 RFC5 3996 0.083 0.68 NO
19 RAD1 RAD1 RAD1 4744 0.065 0.65 NO
20 ATRIP ATRIP ATRIP 4957 0.06 0.65 NO
21 FBXW11 FBXW11 FBXW11 6171 0.04 0.6 NO
22 PPP2R1A PPP2R1A PPP2R1A 7103 0.028 0.55 NO
23 CDK2 CDK2 CDK2 7151 0.027 0.55 NO
24 RAD9A RAD9A RAD9A 7625 0.021 0.53 NO
25 PPP2CA PPP2CA PPP2CA 8148 0.015 0.51 NO
26 YWHAB YWHAB YWHAB 8514 0.0096 0.49 NO
27 CEP164 CEP164 CEP164 8868 0.0049 0.47 NO
28 PPP2R2B PPP2R2B PPP2R2B 8884 0.0048 0.47 NO
29 RAD17 RAD17 RAD17 9216 0.00066 0.45 NO
30 RPA1 RPA1 RPA1 9256 0.00022 0.45 NO
31 SSPO SSPO SSPO 9862 -0.0072 0.42 NO
32 RPA2 RPA2 RPA2 10018 -0.0096 0.41 NO
33 YWHAZ YWHAZ YWHAZ 10093 -0.01 0.41 NO
34 SMARCAL1 SMARCAL1 SMARCAL1 10195 -0.012 0.41 NO
35 RFC2 RFC2 RFC2 10352 -0.014 0.4 NO
36 ATR ATR ATR 10455 -0.015 0.4 NO
37 NBN NBN NBN 10567 -0.017 0.4 NO
38 TIPIN TIPIN TIPIN 11758 -0.033 0.34 NO
39 HUS1 HUS1 HUS1 13406 -0.062 0.26 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: PID ATR PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ATR 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 RET 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 POLR2F POLR2F POLR2F 2938 0.12 -0.14 YES
2 NUP107 NUP107 NUP107 3390 0.1 -0.14 YES
3 NUP188 NUP188 NUP188 3582 0.098 -0.13 YES
4 HNRNPA0 HNRNPA0 HNRNPA0 3694 0.093 -0.12 YES
5 NUP93 NUP93 NUP93 3699 0.093 -0.1 YES
6 NUP35 NUP35 NUP35 3707 0.093 -0.082 YES
7 NUP88 NUP88 NUP88 3743 0.092 -0.065 YES
8 YBX1 YBX1 YBX1 3809 0.089 -0.05 YES
9 POLR2D POLR2D POLR2D 3869 0.087 -0.036 YES
10 RBMX RBMX RBMX 3971 0.084 -0.024 YES
11 NUP155 NUP155 NUP155 4191 0.078 -0.02 YES
12 HNRNPD HNRNPD HNRNPD 4204 0.078 -0.0047 YES
13 HNRNPA3 HNRNPA3 HNRNPA3 4305 0.075 0.0052 YES
14 NUP50 NUP50 NUP50 4412 0.072 0.014 YES
15 AAAS AAAS AAAS 4416 0.072 0.029 YES
16 HNRNPA1 HNRNPA1 HNRNPA1 4467 0.071 0.04 YES
17 THOC4 THOC4 THOC4 4471 0.071 0.055 YES
18 SF3A2 SF3A2 SF3A2 4525 0.07 0.066 YES
19 NCBP1 NCBP1 NCBP1 4599 0.068 0.076 YES
20 SF3B3 SF3B3 SF3B3 4649 0.067 0.087 YES
21 FUS FUS FUS 4665 0.066 0.1 YES
22 RNPS1 RNPS1 RNPS1 4707 0.066 0.11 YES
23 SNRPA SNRPA SNRPA 4819 0.063 0.12 YES
24 NUPL2 NUPL2 NUPL2 4901 0.062 0.13 YES
25 HNRNPM HNRNPM HNRNPM 4909 0.061 0.14 YES
26 CDC40 CDC40 CDC40 4975 0.06 0.15 YES
27 POLR2B POLR2B POLR2B 5029 0.059 0.16 YES
28 NFX1 NFX1 NFX1 5043 0.059 0.17 YES
29 HNRNPR HNRNPR HNRNPR 5056 0.058 0.18 YES
30 CPSF1 CPSF1 CPSF1 5060 0.058 0.19 YES
31 SMC1A SMC1A SMC1A 5224 0.055 0.19 YES
32 HNRNPH1 HNRNPH1 HNRNPH1 5283 0.054 0.2 YES
33 PRPF8 PRPF8 PRPF8 5347 0.053 0.21 YES
34 SNRPD1 SNRPD1 SNRPD1 5386 0.053 0.22 YES
35 POLR2A POLR2A POLR2A 5442 0.052 0.22 YES
36 SNRPF SNRPF SNRPF 5544 0.05 0.23 YES
37 NUP43 NUP43 NUP43 5611 0.049 0.24 YES
38 HNRNPL HNRNPL HNRNPL 5635 0.048 0.24 YES
39 DHX38 DHX38 DHX38 5672 0.048 0.25 YES
40 DHX9 DHX9 DHX9 5691 0.047 0.26 YES
41 CPSF3 CPSF3 CPSF3 5744 0.046 0.27 YES
42 CSTF3 CSTF3 CSTF3 5747 0.046 0.28 YES
43 SNRPA1 SNRPA1 SNRPA1 5763 0.046 0.28 YES
44 HNRNPUL1 HNRNPUL1 HNRNPUL1 5799 0.046 0.29 YES
45 SNRPB SNRPB SNRPB 5818 0.045 0.3 YES
46 NUPL1 NUPL1 NUPL1 5908 0.044 0.3 YES
47 RBM8A RBM8A RBM8A 5930 0.044 0.31 YES
48 CCAR1 CCAR1 CCAR1 5994 0.043 0.32 YES
49 RBM5 RBM5 RBM5 6051 0.042 0.32 YES
50 SNRNP200 SNRNP200 SNRNP200 6099 0.041 0.33 YES
51 NUDT21 NUDT21 NUDT21 6122 0.041 0.34 YES
52 SNRPD3 SNRPD3 SNRPD3 6145 0.04 0.34 YES
53 CPSF7 CPSF7 CPSF7 6160 0.04 0.35 YES
54 NUP214 NUP214 NUP214 6201 0.04 0.36 YES
55 LSM2 LSM2 LSM2 6317 0.037 0.36 YES
56 PABPN1 PABPN1 PABPN1 6420 0.036 0.36 YES
57 SNRNP40 SNRNP40 SNRNP40 6505 0.035 0.36 YES
58 CSTF2 CSTF2 CSTF2 6537 0.034 0.37 YES
59 NUP62 NUP62 NUP62 6541 0.034 0.37 YES
60 CLP1 CLP1 CLP1 6629 0.033 0.38 YES
61 SNRPB2 SNRPB2 SNRPB2 6666 0.033 0.38 YES
62 PRPF4 PRPF4 PRPF4 6747 0.032 0.38 YES
63 PRPF6 PRPF6 PRPF6 6793 0.031 0.39 YES
64 RAE1 RAE1 RAE1 6892 0.03 0.39 YES
65 PHF5A PHF5A PHF5A 6914 0.03 0.39 YES
66 NUP153 NUP153 NUP153 7044 0.028 0.39 YES
67 SF3B5 SF3B5 SF3B5 7064 0.028 0.4 YES
68 SF3B2 SF3B2 SF3B2 7087 0.028 0.4 YES
69 EFTUD2 EFTUD2 EFTUD2 7133 0.027 0.4 YES
70 U2AF1 U2AF1 U2AF1 7260 0.026 0.4 YES
71 HNRNPU HNRNPU HNRNPU 7268 0.026 0.41 YES
72 SNRPE SNRPE SNRPE 7283 0.025 0.41 YES
73 SF3B4 SF3B4 SF3B4 7309 0.025 0.41 YES
74 SF3A1 SF3A1 SF3A1 7357 0.024 0.42 YES
75 POLR2E POLR2E POLR2E 7367 0.024 0.42 YES
76 HNRNPK HNRNPK HNRNPK 7372 0.024 0.42 YES
77 CD2BP2 CD2BP2 CD2BP2 7521 0.022 0.42 YES
78 NHP2L1 NHP2L1 NHP2L1 7590 0.021 0.42 YES
79 NUP205 NUP205 NUP205 7660 0.02 0.42 YES
80 GTF2F2 GTF2F2 GTF2F2 7684 0.02 0.42 YES
81 HNRNPA2B1 HNRNPA2B1 HNRNPA2B1 7699 0.02 0.43 YES
82 PTBP1 PTBP1 PTBP1 7825 0.018 0.43 YES
83 U2AF2 U2AF2 U2AF2 7829 0.018 0.43 YES
84 TXNL4A TXNL4A TXNL4A 7830 0.018 0.43 YES
85 PCF11 PCF11 PCF11 8043 0.016 0.42 YES
86 SNRPG SNRPG SNRPG 8084 0.015 0.42 YES
87 NUP85 NUP85 NUP85 8109 0.015 0.43 YES
88 NXF1 NXF1 NXF1 8112 0.015 0.43 YES
89 SF3B14 SF3B14 SF3B14 8121 0.015 0.43 YES
90 NUP133 NUP133 NUP133 8173 0.014 0.43 YES
91 PCBP2 PCBP2 PCBP2 8221 0.014 0.43 YES
92 SF3B1 SF3B1 SF3B1 8236 0.014 0.44 YES
93 POM121 POM121 POM121 8360 0.012 0.43 NO
94 UPF3B UPF3B UPF3B 8509 0.0096 0.42 NO
95 HNRNPC HNRNPC HNRNPC 8558 0.0089 0.42 NO
96 METTL3 METTL3 METTL3 8595 0.0085 0.42 NO
97 CSTF1 CSTF1 CSTF1 8640 0.0079 0.42 NO
98 NCBP2 NCBP2 NCBP2 8686 0.0073 0.42 NO
99 SNRNP70 SNRNP70 SNRNP70 8751 0.0064 0.42 NO
100 SF3A3 SF3A3 SF3A3 8754 0.0064 0.42 NO
101 PAPOLA PAPOLA PAPOLA 8940 0.0041 0.41 NO
102 TPR TPR TPR 9247 0.00035 0.39 NO
103 POLR2C POLR2C POLR2C 9350 -0.001 0.39 NO
104 PCBP1 PCBP1 PCBP1 9369 -0.0013 0.39 NO
105 DNAJC8 DNAJC8 DNAJC8 9380 -0.0014 0.39 NO
106 POLR2K POLR2K POLR2K 9494 -0.0028 0.38 NO
107 POLR2H POLR2H POLR2H 9634 -0.0044 0.38 NO
108 DDX23 DDX23 DDX23 9649 -0.0045 0.38 NO
109 POLR2G POLR2G POLR2G 9823 -0.0067 0.37 NO
110 SRRM1 SRRM1 SRRM1 9857 -0.0072 0.37 NO
111 GTF2F1 GTF2F1 GTF2F1 9865 -0.0073 0.37 NO
112 EIF4E EIF4E EIF4E 9883 -0.0075 0.37 NO
113 NUP54 NUP54 NUP54 10003 -0.0093 0.36 NO
114 SEH1L SEH1L SEH1L 10071 -0.01 0.36 NO
115 HNRNPH2 HNRNPH2 HNRNPH2 10463 -0.015 0.34 NO
116 RANBP2 RANBP2 RANBP2 10508 -0.016 0.34 NO
117 HNRNPF HNRNPF HNRNPF 10593 -0.017 0.34 NO
118 SLBP SLBP SLBP 10816 -0.02 0.34 NO
119 MAGOH MAGOH MAGOH 11015 -0.023 0.33 NO
120 SNRPD2 SNRPD2 SNRPD2 11189 -0.025 0.32 NO
121 NUP210 NUP210 NUP210 11384 -0.027 0.32 NO
122 POLR2I POLR2I POLR2I 11694 -0.032 0.31 NO
123 POLR2J POLR2J POLR2J 11746 -0.033 0.31 NO
124 CPSF2 CPSF2 CPSF2 11974 -0.036 0.31 NO
125 NUP37 NUP37 NUP37 13141 -0.056 0.25 NO
126 POLR2L POLR2L POLR2L 15488 -0.12 0.15 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: PID RET PATHWAY.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: PID RET 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 ATM 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 GFRA1 GFRA1 GFRA1 22 0.8 0.17 YES
2 GDNF GDNF GDNF 31 0.75 0.34 YES
3 DOK6 DOK6 DOK6 674 0.34 0.38 YES
4 DOK4 DOK4 DOK4 1385 0.23 0.39 YES
5 MAPK8 MAPK8 MAPK8 1658 0.21 0.42 YES
6 SRC SRC SRC 1772 0.2 0.45 YES
7 RET RET RET 1835 0.19 0.49 YES
8 BCAR1 BCAR1 BCAR1 3319 0.11 0.43 NO
9 GAB1 GAB1 GAB1 4186 0.078 0.4 NO
10 SHANK3 SHANK3 SHANK3 4264 0.076 0.41 NO
11 IRS1 IRS1 IRS1 4761 0.064 0.4 NO
12 PTK2 PTK2 PTK2 5422 0.052 0.38 NO
13 PIK3CA PIK3CA PIK3CA 5616 0.049 0.38 NO
14 SOS1 SOS1 SOS1 6118 0.041 0.36 NO
15 FRS2 FRS2 FRS2 6477 0.035 0.34 NO
16 CREB1 CREB1 CREB1 6764 0.032 0.34 NO
17 PIK3R1 PIK3R1 PIK3R1 7809 0.019 0.28 NO
18 CRK CRK CRK 9511 -0.003 0.19 NO
19 PTPN11 PTPN11 PTPN11 9898 -0.0078 0.17 NO
20 MAPK1 MAPK1 MAPK1 9920 -0.0081 0.17 NO
21 GRB2 GRB2 GRB2 10308 -0.013 0.15 NO
22 RHOA RHOA RHOA 10623 -0.018 0.14 NO
23 MAPK3 MAPK3 MAPK3 11233 -0.025 0.11 NO
24 HRAS HRAS HRAS 11609 -0.031 0.096 NO
25 RAC1 RAC1 RAC1 11682 -0.032 0.099 NO
26 PRKCA PRKCA PRKCA 11898 -0.035 0.095 NO
27 PRKACA PRKACA PRKACA 12068 -0.038 0.094 NO
28 JUN JUN JUN 12676 -0.047 0.07 NO
29 PXN PXN PXN 12813 -0.05 0.074 NO
30 NCK1 NCK1 NCK1 12851 -0.051 0.083 NO
31 RASA1 RASA1 RASA1 12900 -0.052 0.091 NO
32 RAP1A RAP1A RAP1A 12934 -0.052 0.1 NO
33 DOK5 DOK5 DOK5 13553 -0.065 0.081 NO
34 PDLIM7 PDLIM7 PDLIM7 14061 -0.077 0.07 NO
35 DOK1 DOK1 DOK1 14601 -0.092 0.06 NO
36 GRB10 GRB10 GRB10 15516 -0.12 0.036 NO
37 SHC1 SHC1 SHC1 16184 -0.16 0.034 NO
38 IRS2 IRS2 IRS2 16318 -0.16 0.062 NO
39 GRB7 GRB7 GRB7 16730 -0.19 0.08 NO

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

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ATM 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 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 CENPJ CENPJ CENPJ 672 0.34 0.042 YES
2 NEK2 NEK2 NEK2 804 0.31 0.11 YES
3 PLK1 PLK1 PLK1 988 0.28 0.16 YES
4 PLK4 PLK4 PLK4 1103 0.27 0.22 YES
5 CEP135 CEP135 CEP135 1583 0.21 0.24 YES
6 CDK1 CDK1 CDK1 1599 0.21 0.29 YES
7 CEP72 CEP72 CEP72 1744 0.2 0.32 YES
8 CSNK1E CSNK1E CSNK1E 2086 0.17 0.35 YES
9 AZI1 AZI1 AZI1 2430 0.15 0.36 YES
10 DCTN2 DCTN2 DCTN2 2585 0.14 0.38 YES
11 NINL NINL NINL 2986 0.12 0.39 YES
12 TUBB TUBB TUBB 3674 0.094 0.37 YES
13 DCTN3 DCTN3 DCTN3 3713 0.093 0.39 YES
14 ACTR1A ACTR1A ACTR1A 3714 0.093 0.41 YES
15 TUBA1A TUBA1A TUBA1A 3738 0.092 0.43 YES
16 CEP57 CEP57 CEP57 3827 0.089 0.45 YES
17 PRKAR2B PRKAR2B PRKAR2B 4012 0.083 0.46 YES
18 CEP63 CEP63 CEP63 4180 0.078 0.47 YES
19 TUBG1 TUBG1 TUBG1 4370 0.073 0.47 YES
20 CEP70 CEP70 CEP70 4628 0.067 0.48 YES
21 ALMS1 ALMS1 ALMS1 5034 0.059 0.47 NO
22 CKAP5 CKAP5 CKAP5 5376 0.053 0.46 NO
23 MAPRE1 MAPRE1 MAPRE1 5500 0.05 0.46 NO
24 CEP76 CEP76 CEP76 5810 0.045 0.46 NO
25 CLASP1 CLASP1 CLASP1 5913 0.044 0.46 NO
26 CDK5RAP2 CDK5RAP2 CDK5RAP2 6146 0.04 0.46 NO
27 DCTN1 DCTN1 DCTN1 6543 0.034 0.44 NO
28 CEP250 CEP250 CEP250 6601 0.034 0.45 NO
29 PAFAH1B1 PAFAH1B1 PAFAH1B1 6705 0.032 0.45 NO
30 PCNT PCNT PCNT 6799 0.031 0.45 NO
31 PPP2R1A PPP2R1A PPP2R1A 7103 0.028 0.44 NO
32 CEP192 CEP192 CEP192 7145 0.027 0.45 NO
33 DYNC1I2 DYNC1I2 DYNC1I2 7275 0.025 0.44 NO
34 CEP290 CEP290 CEP290 7398 0.024 0.44 NO
35 YWHAE YWHAE YWHAE 7564 0.022 0.44 NO
36 SSNA1 SSNA1 SSNA1 8001 0.016 0.42 NO
37 NEDD1 NEDD1 NEDD1 8230 0.014 0.41 NO
38 DYNC1H1 DYNC1H1 DYNC1H1 8317 0.012 0.41 NO
39 YWHAG YWHAG YWHAG 8521 0.0094 0.4 NO
40 CEP164 CEP164 CEP164 8868 0.0049 0.38 NO
41 PCM1 PCM1 PCM1 8959 0.0039 0.38 NO
42 DYNLL1 DYNLL1 DYNLL1 9371 -0.0013 0.36 NO
43 FGFR1OP FGFR1OP FGFR1OP 9648 -0.0045 0.34 NO
44 AKAP9 AKAP9 AKAP9 9941 -0.0084 0.33 NO
45 CSNK1D CSNK1D CSNK1D 10609 -0.017 0.29 NO
46 HSP90AA1 HSP90AA1 HSP90AA1 11967 -0.036 0.23 NO
47 PRKACA PRKACA PRKACA 12068 -0.038 0.23 NO
48 HAUS2 HAUS2 HAUS2 12193 -0.039 0.23 NO
49 SDCCAG8 SDCCAG8 SDCCAG8 12351 -0.042 0.23 NO
50 OFD1 OFD1 OFD1 12404 -0.042 0.24 NO
51 CETN2 CETN2 CETN2 14640 -0.093 0.14 NO
52 TUBA4A TUBA4A TUBA4A 17350 -0.25 0.046 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: PID PLK1 PATHWAY.

Figure S14.  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 AR TF 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 E2F2 E2F2 E2F2 166 0.55 0.0083 YES
2 MCM10 MCM10 MCM10 248 0.49 0.02 YES
3 SGOL1 SGOL1 SGOL1 294 0.47 0.032 YES
4 CDC25C CDC25C CDC25C 381 0.43 0.041 YES
5 CDC25A CDC25A CDC25A 383 0.43 0.055 YES
6 CASC5 CASC5 CASC5 397 0.42 0.067 YES
7 SPC24 SPC24 SPC24 450 0.4 0.078 YES
8 AURKB AURKB AURKB 502 0.39 0.087 YES
9 PKMYT1 PKMYT1 PKMYT1 565 0.37 0.095 YES
10 MYBL2 MYBL2 MYBL2 571 0.36 0.11 YES
11 DNA2 DNA2 DNA2 662 0.34 0.11 YES
12 CENPJ CENPJ CENPJ 672 0.34 0.12 YES
13 CDK4 CDK4 CDK4 683 0.34 0.13 YES
14 CDC45 CDC45 CDC45 738 0.32 0.14 YES
15 CENPI CENPI CENPI 753 0.32 0.15 YES
16 SPC25 SPC25 SPC25 765 0.32 0.16 YES
17 CDCA8 CDCA8 CDCA8 802 0.31 0.17 YES
18 NEK2 NEK2 NEK2 804 0.31 0.18 YES
19 CENPM CENPM CENPM 850 0.3 0.19 YES
20 CENPA CENPA CENPA 860 0.3 0.2 YES
21 NUF2 NUF2 NUF2 869 0.3 0.2 YES
22 SKA1 SKA1 SKA1 870 0.3 0.21 YES
23 UBE2C UBE2C UBE2C 937 0.29 0.22 YES
24 BIRC5 BIRC5 BIRC5 956 0.29 0.23 YES
25 KIF2C KIF2C KIF2C 967 0.29 0.24 YES
26 PLK1 PLK1 PLK1 988 0.28 0.24 YES
27 KIF20A KIF20A KIF20A 996 0.28 0.25 YES
28 MAD2L1 MAD2L1 MAD2L1 1060 0.27 0.26 YES
29 PPP2R3B PPP2R3B PPP2R3B 1073 0.27 0.27 YES
30 PLK4 PLK4 PLK4 1103 0.27 0.27 YES
31 CCNB2 CCNB2 CCNB2 1115 0.27 0.28 YES
32 BUB1B BUB1B BUB1B 1159 0.26 0.29 YES
33 CDKN2A CDKN2A CDKN2A 1179 0.26 0.29 YES
34 CCND1 CCND1 CCND1 1210 0.25 0.3 YES
35 KIF18A KIF18A KIF18A 1213 0.25 0.31 YES
36 ERCC6L ERCC6L ERCC6L 1227 0.25 0.32 YES
37 CENPH CENPH CENPH 1281 0.25 0.32 YES
38 CDC7 CDC7 CDC7 1288 0.24 0.33 YES
39 BUB1 BUB1 BUB1 1291 0.24 0.34 YES
40 CCNA2 CCNA2 CCNA2 1313 0.24 0.34 YES
41 NDC80 NDC80 NDC80 1334 0.24 0.35 YES
42 CDT1 CDT1 CDT1 1340 0.24 0.36 YES
43 CDC20 CDC20 CDC20 1343 0.24 0.36 YES
44 ZWINT ZWINT ZWINT 1354 0.24 0.37 YES
45 MLF1IP MLF1IP MLF1IP 1375 0.23 0.38 YES
46 E2F1 E2F1 E2F1 1521 0.22 0.38 YES
47 CEP135 CEP135 CEP135 1583 0.21 0.38 YES
48 CDK1 CDK1 CDK1 1599 0.21 0.39 YES
49 SGOL2 SGOL2 SGOL2 1640 0.21 0.39 YES
50 AURKA AURKA AURKA 1649 0.21 0.4 YES
51 LIN9 LIN9 LIN9 1664 0.21 0.4 YES
52 PTTG1 PTTG1 PTTG1 1680 0.2 0.41 YES
53 CCNE2 CCNE2 CCNE2 1707 0.2 0.41 YES
54 CDC6 CDC6 CDC6 1737 0.2 0.42 YES
55 CEP72 CEP72 CEP72 1744 0.2 0.42 YES
56 GINS2 GINS2 GINS2 1775 0.2 0.43 YES
57 KIF23 KIF23 KIF23 1814 0.19 0.43 YES
58 FBXO5 FBXO5 FBXO5 1862 0.19 0.44 YES
59 INCENP INCENP INCENP 1985 0.18 0.44 YES
60 MCM8 MCM8 MCM8 1990 0.18 0.44 YES
61 CSNK1E CSNK1E CSNK1E 2086 0.17 0.44 YES
62 CDKN2B CDKN2B CDKN2B 2110 0.17 0.44 YES
63 RFC3 RFC3 RFC3 2112 0.17 0.45 YES
64 E2F3 E2F3 E2F3 2128 0.17 0.46 YES
65 POLE POLE POLE 2133 0.17 0.46 YES
66 RRM2 RRM2 RRM2 2148 0.17 0.46 YES
67 DBF4 DBF4 DBF4 2235 0.16 0.46 YES
68 RPA4 RPA4 RPA4 2268 0.16 0.47 YES
69 PRIM1 PRIM1 PRIM1 2270 0.16 0.47 YES
70 GINS1 GINS1 GINS1 2301 0.16 0.48 YES
71 CCNB1 CCNB1 CCNB1 2331 0.16 0.48 YES
72 DHFR DHFR DHFR 2410 0.15 0.48 YES
73 CCDC99 CCDC99 CCDC99 2424 0.15 0.48 YES
74 AZI1 AZI1 AZI1 2430 0.15 0.49 YES
75 CENPK CENPK CENPK 2444 0.15 0.49 YES
76 POLE2 POLE2 POLE2 2477 0.14 0.5 YES
77 CENPN CENPN CENPN 2561 0.14 0.5 YES
78 DCTN2 DCTN2 DCTN2 2585 0.14 0.5 YES
79 CENPO CENPO CENPO 2592 0.14 0.5 YES
80 MCM2 MCM2 MCM2 2642 0.14 0.5 YES
81 ZWILCH ZWILCH ZWILCH 2649 0.14 0.51 YES
82 MCM7 MCM7 MCM7 2726 0.13 0.51 YES
83 POLA2 POLA2 POLA2 2727 0.13 0.51 YES
84 MYC MYC MYC 2730 0.13 0.52 YES
85 TYMS TYMS TYMS 2846 0.13 0.51 YES
86 CDC26 CDC26 CDC26 2879 0.12 0.52 YES
87 PRIM2 PRIM2 PRIM2 2916 0.12 0.52 YES
88 NINL NINL NINL 2986 0.12 0.52 YES
89 RBL1 RBL1 RBL1 3017 0.12 0.52 YES
90 RFC4 RFC4 RFC4 3053 0.12 0.52 YES
91 GINS4 GINS4 GINS4 3108 0.11 0.52 YES
92 KIF2A KIF2A KIF2A 3143 0.11 0.52 YES
93 CDKN2D CDKN2D CDKN2D 3170 0.11 0.53 YES
94 KNTC1 KNTC1 KNTC1 3293 0.11 0.52 YES
95 CCND2 CCND2 CCND2 3306 0.11 0.53 YES
96 NUP107 NUP107 NUP107 3390 0.1 0.52 YES
97 FEN1 FEN1 FEN1 3437 0.1 0.53 YES
98 PPP2R2A PPP2R2A PPP2R2A 3503 0.1 0.52 YES
99 CKS1B CKS1B CKS1B 3555 0.098 0.53 YES
100 RCC2 RCC2 RCC2 3556 0.098 0.53 YES
101 TUBB TUBB TUBB 3674 0.094 0.52 YES
102 DCTN3 DCTN3 DCTN3 3713 0.093 0.53 YES
103 ACTR1A ACTR1A ACTR1A 3714 0.093 0.53 YES
104 TUBA1A TUBA1A TUBA1A 3738 0.092 0.53 YES
105 BUB3 BUB3 BUB3 3776 0.09 0.53 YES
106 BTRC BTRC BTRC 3810 0.089 0.53 YES
107 MCM4 MCM4 MCM4 3820 0.089 0.54 YES
108 CEP57 CEP57 CEP57 3827 0.089 0.54 YES
109 SMC3 SMC3 SMC3 3845 0.088 0.54 YES
110 RANGAP1 RANGAP1 RANGAP1 3912 0.086 0.54 YES
111 CENPL CENPL CENPL 3948 0.085 0.54 YES
112 POLD1 POLD1 POLD1 3985 0.084 0.54 YES
113 RFC5 RFC5 RFC5 3996 0.083 0.54 YES
114 PRKAR2B PRKAR2B PRKAR2B 4012 0.083 0.54 YES
115 LIG1 LIG1 LIG1 4022 0.083 0.55 YES
116 DSN1 DSN1 DSN1 4064 0.082 0.55 YES
117 SKA2 SKA2 SKA2 4071 0.082 0.55 YES
118 CENPP CENPP CENPP 4078 0.082 0.55 YES
119 CEP63 CEP63 CEP63 4180 0.078 0.55 NO
120 SKP2 SKP2 SKP2 4324 0.075 0.54 NO
121 MCM5 MCM5 MCM5 4334 0.074 0.54 NO
122 TUBG1 TUBG1 TUBG1 4370 0.073 0.54 NO
123 TAOK1 TAOK1 TAOK1 4421 0.072 0.54 NO
124 PPP2R5D PPP2R5D PPP2R5D 4476 0.071 0.54 NO
125 CEP70 CEP70 CEP70 4628 0.067 0.54 NO
126 NUMA1 NUMA1 NUMA1 4693 0.066 0.54 NO
127 RAD21 RAD21 RAD21 4715 0.065 0.54 NO
128 E2F5 E2F5 E2F5 4735 0.065 0.54 NO
129 CCNA1 CCNA1 CCNA1 4801 0.064 0.54 NO
130 PSMD3 PSMD3 PSMD3 4810 0.063 0.54 NO
131 MCM6 MCM6 MCM6 4854 0.063 0.54 NO
132 CCNE1 CCNE1 CCNE1 4876 0.062 0.54 NO
133 PSMB7 PSMB7 PSMB7 4880 0.062 0.54 NO
134 MAD1L1 MAD1L1 MAD1L1 4921 0.061 0.54 NO
135 ALMS1 ALMS1 ALMS1 5034 0.059 0.54 NO
136 CENPC1 CENPC1 CENPC1 5058 0.058 0.54 NO
137 CDKN1B CDKN1B CDKN1B 5078 0.058 0.54 NO
138 CENPQ CENPQ CENPQ 5092 0.058 0.54 NO
139 PCNA PCNA PCNA 5204 0.055 0.53 NO
140 SMC1A SMC1A SMC1A 5224 0.055 0.53 NO
141 CENPT CENPT CENPT 5327 0.054 0.53 NO
142 CKAP5 CKAP5 CKAP5 5376 0.053 0.53 NO
143 ITGB3BP ITGB3BP ITGB3BP 5426 0.052 0.53 NO
144 MAPRE1 MAPRE1 MAPRE1 5500 0.05 0.52 NO
145 POLD3 POLD3 POLD3 5511 0.05 0.53 NO
146 TUBGCP6 TUBGCP6 TUBGCP6 5528 0.05 0.53 NO
147 UBE2D1 UBE2D1 UBE2D1 5553 0.05 0.53 NO
148 NUP43 NUP43 NUP43 5611 0.049 0.53 NO
149 PSMD11 PSMD11 PSMD11 5614 0.049 0.53 NO
150 RBBP4 RBBP4 RBBP4 5621 0.048 0.53 NO
151 POLA1 POLA1 POLA1 5765 0.046 0.52 NO
152 CEP76 CEP76 CEP76 5810 0.045 0.52 NO
153 GMNN GMNN GMNN 5874 0.044 0.52 NO
154 CLASP1 CLASP1 CLASP1 5913 0.044 0.52 NO
155 MIS12 MIS12 MIS12 5920 0.044 0.52 NO
156 CDC25B CDC25B CDC25B 5946 0.043 0.52 NO
157 ANAPC1 ANAPC1 ANAPC1 5969 0.043 0.52 NO
158 ANAPC7 ANAPC7 ANAPC7 5975 0.043 0.52 NO
159 TUBGCP3 TUBGCP3 TUBGCP3 6132 0.041 0.51 NO
160 CDK5RAP2 CDK5RAP2 CDK5RAP2 6146 0.04 0.51 NO
161 PPP2R5B PPP2R5B PPP2R5B 6273 0.038 0.51 NO
162 SEC13 SEC13 SEC13 6329 0.037 0.51 NO
163 DCTN1 DCTN1 DCTN1 6543 0.034 0.5 NO
164 ZW10 ZW10 ZW10 6580 0.034 0.49 NO
165 MCM3 MCM3 MCM3 6596 0.034 0.49 NO
166 CEP250 CEP250 CEP250 6601 0.034 0.5 NO
167 PAFAH1B1 PAFAH1B1 PAFAH1B1 6705 0.032 0.49 NO
168 LIN54 LIN54 LIN54 6721 0.032 0.49 NO
169 CCNH CCNH CCNH 6757 0.032 0.49 NO
170 PCNT PCNT PCNT 6799 0.031 0.49 NO
171 CDKN2C CDKN2C CDKN2C 6817 0.031 0.49 NO
172 CDC23 CDC23 CDC23 6843 0.03 0.49 NO
173 CDC27 CDC27 CDC27 6980 0.029 0.48 NO
174 ANAPC5 ANAPC5 ANAPC5 6998 0.029 0.48 NO
175 PSMD2 PSMD2 PSMD2 7102 0.028 0.48 NO
176 PPP2R1A PPP2R1A PPP2R1A 7103 0.028 0.48 NO
177 ANAPC2 ANAPC2 ANAPC2 7118 0.027 0.48 NO
178 PPP2R1B PPP2R1B PPP2R1B 7139 0.027 0.48 NO
179 CEP192 CEP192 CEP192 7145 0.027 0.48 NO
180 CDK2 CDK2 CDK2 7151 0.027 0.48 NO
181 PSMB6 PSMB6 PSMB6 7187 0.026 0.48 NO
182 TUBGCP2 TUBGCP2 TUBGCP2 7236 0.026 0.48 NO
183 DYNC1I2 DYNC1I2 DYNC1I2 7275 0.025 0.47 NO
184 CEP290 CEP290 CEP290 7398 0.024 0.47 NO
185 PSMB3 PSMB3 PSMB3 7447 0.023 0.47 NO
186 UBE2E1 UBE2E1 UBE2E1 7461 0.023 0.47 NO
187 PPP2R5E PPP2R5E PPP2R5E 7539 0.022 0.46 NO
188 PSMB2 PSMB2 PSMB2 7540 0.022 0.46 NO
189 YWHAE YWHAE YWHAE 7564 0.022 0.46 NO
190 STAG1 STAG1 STAG1 7627 0.021 0.46 NO
191 ANAPC11 ANAPC11 ANAPC11 7649 0.02 0.46 NO
192 NSL1 NSL1 NSL1 7726 0.02 0.46 NO
193 LIN52 LIN52 LIN52 7779 0.019 0.45 NO
194 PSMD10 PSMD10 PSMD10 7801 0.019 0.45 NO
195 PPP1CC PPP1CC PPP1CC 7828 0.018 0.45 NO
196 PMF1 PMF1 PMF1 7928 0.017 0.45 NO
197 PSMD4 PSMD4 PSMD4 7961 0.017 0.45 NO
198 XPO1 XPO1 XPO1 7986 0.016 0.44 NO
199 SSNA1 SSNA1 SSNA1 8001 0.016 0.44 NO
200 NUP85 NUP85 NUP85 8109 0.015 0.44 NO
201 PPP2CA PPP2CA PPP2CA 8148 0.015 0.44 NO
202 NUP133 NUP133 NUP133 8173 0.014 0.44 NO
203 NEDD1 NEDD1 NEDD1 8230 0.014 0.43 NO
204 PSMD6 PSMD6 PSMD6 8285 0.013 0.43 NO
205 DYNC1H1 DYNC1H1 DYNC1H1 8317 0.012 0.43 NO
206 CCND3 CCND3 CCND3 8398 0.011 0.43 NO
207 YWHAG YWHAG YWHAG 8521 0.0094 0.42 NO
208 NUDC NUDC NUDC 8662 0.0077 0.41 NO
209 DYRK1A DYRK1A DYRK1A 8718 0.0068 0.41 NO
210 E2F4 E2F4 E2F4 8769 0.0062 0.41 NO
211 STAG2 STAG2 STAG2 8809 0.0056 0.4 NO
212 LIN37 LIN37 LIN37 8814 0.0056 0.4 NO
213 PSMD1 PSMD1 PSMD1 8837 0.0053 0.4 NO
214 CEP164 CEP164 CEP164 8868 0.0049 0.4 NO
215 PCM1 PCM1 PCM1 8959 0.0039 0.4 NO
216 PSMB5 PSMB5 PSMB5 9004 0.0034 0.39 NO
217 RBL2 RBL2 RBL2 9141 0.0015 0.39 NO
218 RPA1 RPA1 RPA1 9256 0.00022 0.38 NO
219 PSMA7 PSMA7 PSMA7 9321 -0.00068 0.38 NO
220 PSMA4 PSMA4 PSMA4 9323 -0.0007 0.38 NO
221 DYNLL1 DYNLL1 DYNLL1 9371 -0.0013 0.37 NO
222 PSMD14 PSMD14 PSMD14 9469 -0.0025 0.37 NO
223 FGFR1OP FGFR1OP FGFR1OP 9648 -0.0045 0.36 NO
224 GORASP1 GORASP1 GORASP1 9735 -0.0056 0.36 NO
225 PSMD7 PSMD7 PSMD7 9742 -0.0056 0.35 NO
226 MNAT1 MNAT1 MNAT1 9747 -0.0057 0.35 NO
227 PSMB1 PSMB1 PSMB1 9812 -0.0065 0.35 NO
228 PPP2R5C PPP2R5C PPP2R5C 9860 -0.0072 0.35 NO
229 CDK6 CDK6 CDK6 9867 -0.0073 0.35 NO
230 PSME4 PSME4 PSME4 9874 -0.0074 0.35 NO
231 AKAP9 AKAP9 AKAP9 9941 -0.0084 0.34 NO
232 RB1 RB1 RB1 9968 -0.0088 0.34 NO
233 RPA2 RPA2 RPA2 10018 -0.0096 0.34 NO
234 PSMB4 PSMB4 PSMB4 10061 -0.01 0.34 NO
235 SEH1L SEH1L SEH1L 10071 -0.01 0.34 NO
236 PSMC3 PSMC3 PSMC3 10166 -0.012 0.33 NO
237 PSMF1 PSMF1 PSMF1 10206 -0.012 0.33 NO
238 UBA52 UBA52 UBA52 10240 -0.012 0.33 NO
239 PSMD8 PSMD8 PSMD8 10290 -0.013 0.33 NO
240 RFC2 RFC2 RFC2 10352 -0.014 0.33 NO
241 PPP2CB PPP2CB PPP2CB 10382 -0.014 0.32 NO
242 POLD2 POLD2 POLD2 10505 -0.016 0.32 NO
243 RANBP2 RANBP2 RANBP2 10508 -0.016 0.32 NO
244 PSMC4 PSMC4 PSMC4 10516 -0.016 0.32 NO
245 RPA3 RPA3 RPA3 10532 -0.016 0.32 NO
246 PSMA6 PSMA6 PSMA6 10533 -0.016 0.32 NO
247 CSNK1D CSNK1D CSNK1D 10609 -0.017 0.32 NO
248 PSMA5 PSMA5 PSMA5 10715 -0.019 0.31 NO
249 PSMD12 PSMD12 PSMD12 10787 -0.02 0.31 NO
250 PSMA2 PSMA2 PSMA2 10921 -0.022 0.3 NO
251 RPS27 RPS27 RPS27 11012 -0.023 0.3 NO
252 PSMC5 PSMC5 PSMC5 11025 -0.023 0.3 NO
253 RPS27A RPS27A RPS27A 11126 -0.024 0.29 NO
254 PSMD13 PSMD13 PSMD13 11151 -0.024 0.29 NO
255 ANAPC4 ANAPC4 ANAPC4 11228 -0.025 0.29 NO
256 TFDP1 TFDP1 TFDP1 11264 -0.026 0.29 NO
257 AHCTF1 AHCTF1 AHCTF1 11348 -0.027 0.28 NO
258 PSMC6 PSMC6 PSMC6 11658 -0.032 0.27 NO
259 HDAC1 HDAC1 HDAC1 11661 -0.032 0.27 NO
260 PSMC2 PSMC2 PSMC2 11763 -0.033 0.26 NO
261 APITD1 APITD1 APITD1 11842 -0.034 0.26 NO
262 CDC16 CDC16 CDC16 11943 -0.036 0.25 NO
263 HSP90AA1 HSP90AA1 HSP90AA1 11967 -0.036 0.25 NO
264 PRKACA PRKACA PRKACA 12068 -0.038 0.25 NO
265 HAUS2 HAUS2 HAUS2 12193 -0.039 0.24 NO
266 NDEL1 NDEL1 NDEL1 12299 -0.041 0.24 NO
267 SDCCAG8 SDCCAG8 SDCCAG8 12351 -0.042 0.24 NO
268 OFD1 OFD1 OFD1 12404 -0.042 0.24 NO
269 PSMA1 PSMA1 PSMA1 12410 -0.043 0.24 NO
270 CDK7 CDK7 CDK7 12501 -0.044 0.23 NO
271 PSMC1 PSMC1 PSMC1 12549 -0.045 0.23 NO
272 SKP1 SKP1 SKP1 12556 -0.045 0.23 NO
273 TUBG2 TUBG2 TUBG2 12648 -0.047 0.23 NO
274 CDC14A CDC14A CDC14A 12726 -0.048 0.23 NO
275 CUL1 CUL1 CUL1 12808 -0.05 0.22 NO
276 PSMD5 PSMD5 PSMD5 12919 -0.052 0.22 NO
277 MAX MAX MAX 13086 -0.055 0.21 NO
278 NUP37 NUP37 NUP37 13141 -0.056 0.21 NO
279 PSMD9 PSMD9 PSMD9 13349 -0.06 0.2 NO
280 WEE1 WEE1 WEE1 13448 -0.062 0.2 NO
281 ANAPC10 ANAPC10 ANAPC10 13778 -0.07 0.18 NO
282 PSMA3 PSMA3 PSMA3 13897 -0.073 0.18 NO
283 TUBGCP5 TUBGCP5 TUBGCP5 13963 -0.074 0.18 NO
284 PPP2R5A PPP2R5A PPP2R5A 14000 -0.075 0.18 NO
285 TK2 TK2 TK2 14418 -0.086 0.16 NO
286 CETN2 CETN2 CETN2 14640 -0.093 0.15 NO
287 CLIP1 CLIP1 CLIP1 14808 -0.098 0.14 NO
288 PSMB10 PSMB10 PSMB10 15166 -0.11 0.12 NO
289 POLD4 POLD4 POLD4 15443 -0.12 0.11 NO
290 PSME1 PSME1 PSME1 15535 -0.12 0.11 NO
291 PSME2 PSME2 PSME2 15537 -0.12 0.12 NO
292 CDKN1A CDKN1A CDKN1A 15669 -0.13 0.11 NO
293 PSMA8 PSMA8 PSMA8 15685 -0.13 0.12 NO
294 PSMB8 PSMB8 PSMB8 15918 -0.14 0.11 NO
295 B9D2 B9D2 B9D2 15935 -0.14 0.11 NO
296 PSMB9 PSMB9 PSMB9 16846 -0.2 0.067 NO
297 TUBA4A TUBA4A TUBA4A 17350 -0.25 0.047 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 AR TF PATHWAY.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AR TF 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 LIS1PATHWAY

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 CDC25C CDC25C CDC25C 381 0.43 0.038 YES
2 CDC25A CDC25A CDC25A 383 0.43 0.098 YES
3 PKMYT1 PKMYT1 PKMYT1 565 0.37 0.14 YES
4 CENPJ CENPJ CENPJ 672 0.34 0.18 YES
5 NEK2 NEK2 NEK2 804 0.31 0.22 YES
6 PLK1 PLK1 PLK1 988 0.28 0.24 YES
7 PLK4 PLK4 PLK4 1103 0.27 0.28 YES
8 CCNB2 CCNB2 CCNB2 1115 0.27 0.31 YES
9 CCNA2 CCNA2 CCNA2 1313 0.24 0.34 YES
10 E2F1 E2F1 E2F1 1521 0.22 0.35 YES
11 CEP135 CEP135 CEP135 1583 0.21 0.38 YES
12 CDK1 CDK1 CDK1 1599 0.21 0.41 YES
13 CEP72 CEP72 CEP72 1744 0.2 0.43 YES
14 CSNK1E CSNK1E CSNK1E 2086 0.17 0.43 YES
15 E2F3 E2F3 E2F3 2128 0.17 0.45 YES
16 CCNB1 CCNB1 CCNB1 2331 0.16 0.46 YES
17 AZI1 AZI1 AZI1 2430 0.15 0.48 YES
18 DCTN2 DCTN2 DCTN2 2585 0.14 0.49 YES
19 NINL NINL NINL 2986 0.12 0.48 YES
20 TUBB TUBB TUBB 3674 0.094 0.46 YES
21 DCTN3 DCTN3 DCTN3 3713 0.093 0.47 YES
22 ACTR1A ACTR1A ACTR1A 3714 0.093 0.48 YES
23 TUBA1A TUBA1A TUBA1A 3738 0.092 0.5 YES
24 CEP57 CEP57 CEP57 3827 0.089 0.5 YES
25 PRKAR2B PRKAR2B PRKAR2B 4012 0.083 0.5 YES
26 CEP63 CEP63 CEP63 4180 0.078 0.5 YES
27 TUBG1 TUBG1 TUBG1 4370 0.073 0.5 YES
28 CEP70 CEP70 CEP70 4628 0.067 0.5 YES
29 NUMA1 NUMA1 NUMA1 4693 0.066 0.51 YES
30 CCNA1 CCNA1 CCNA1 4801 0.064 0.51 YES
31 ALMS1 ALMS1 ALMS1 5034 0.059 0.5 NO
32 CKAP5 CKAP5 CKAP5 5376 0.053 0.49 NO
33 MAPRE1 MAPRE1 MAPRE1 5500 0.05 0.49 NO
34 TUBGCP6 TUBGCP6 TUBGCP6 5528 0.05 0.5 NO
35 CEP76 CEP76 CEP76 5810 0.045 0.49 NO
36 CLASP1 CLASP1 CLASP1 5913 0.044 0.49 NO
37 CDC25B CDC25B CDC25B 5946 0.043 0.49 NO
38 TUBGCP3 TUBGCP3 TUBGCP3 6132 0.041 0.49 NO
39 CDK5RAP2 CDK5RAP2 CDK5RAP2 6146 0.04 0.49 NO
40 DCTN1 DCTN1 DCTN1 6543 0.034 0.48 NO
41 CEP250 CEP250 CEP250 6601 0.034 0.48 NO
42 PAFAH1B1 PAFAH1B1 PAFAH1B1 6705 0.032 0.48 NO
43 CCNH CCNH CCNH 6757 0.032 0.48 NO
44 PCNT PCNT PCNT 6799 0.031 0.48 NO
45 PPP2R1A PPP2R1A PPP2R1A 7103 0.028 0.47 NO
46 CEP192 CEP192 CEP192 7145 0.027 0.47 NO
47 CDK2 CDK2 CDK2 7151 0.027 0.47 NO
48 TUBGCP2 TUBGCP2 TUBGCP2 7236 0.026 0.47 NO
49 DYNC1I2 DYNC1I2 DYNC1I2 7275 0.025 0.47 NO
50 CEP290 CEP290 CEP290 7398 0.024 0.47 NO
51 YWHAE YWHAE YWHAE 7564 0.022 0.46 NO
52 XPO1 XPO1 XPO1 7986 0.016 0.44 NO
53 SSNA1 SSNA1 SSNA1 8001 0.016 0.44 NO
54 NEDD1 NEDD1 NEDD1 8230 0.014 0.43 NO
55 DYNC1H1 DYNC1H1 DYNC1H1 8317 0.012 0.43 NO
56 YWHAG YWHAG YWHAG 8521 0.0094 0.42 NO
57 CEP164 CEP164 CEP164 8868 0.0049 0.4 NO
58 PCM1 PCM1 PCM1 8959 0.0039 0.4 NO
59 DYNLL1 DYNLL1 DYNLL1 9371 -0.0013 0.38 NO
60 FGFR1OP FGFR1OP FGFR1OP 9648 -0.0045 0.36 NO
61 MNAT1 MNAT1 MNAT1 9747 -0.0057 0.36 NO
62 AKAP9 AKAP9 AKAP9 9941 -0.0084 0.35 NO
63 CSNK1D CSNK1D CSNK1D 10609 -0.017 0.31 NO
64 HSP90AA1 HSP90AA1 HSP90AA1 11967 -0.036 0.24 NO
65 PRKACA PRKACA PRKACA 12068 -0.038 0.24 NO
66 HAUS2 HAUS2 HAUS2 12193 -0.039 0.24 NO
67 SDCCAG8 SDCCAG8 SDCCAG8 12351 -0.042 0.24 NO
68 OFD1 OFD1 OFD1 12404 -0.042 0.24 NO
69 CDK7 CDK7 CDK7 12501 -0.044 0.24 NO
70 TUBG2 TUBG2 TUBG2 12648 -0.047 0.24 NO
71 WEE1 WEE1 WEE1 13448 -0.062 0.2 NO
72 TUBGCP5 TUBGCP5 TUBGCP5 13963 -0.074 0.19 NO
73 CETN2 CETN2 CETN2 14640 -0.093 0.16 NO
74 TUBA4A TUBA4A TUBA4A 17350 -0.25 0.046 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 LIS1PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: PID LIS1PATHWAY, 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 ERA GENOMIC PATHWAY

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 E2F2 E2F2 E2F2 166 0.55 0.0044 YES
2 MCM10 MCM10 MCM10 248 0.49 0.012 YES
3 SGOL1 SGOL1 SGOL1 294 0.47 0.022 YES
4 CDC25C CDC25C CDC25C 381 0.43 0.027 YES
5 CDC25A CDC25A CDC25A 383 0.43 0.038 YES
6 CASC5 CASC5 CASC5 397 0.42 0.048 YES
7 SPC24 SPC24 SPC24 450 0.4 0.055 YES
8 AURKB AURKB AURKB 502 0.39 0.062 YES
9 PKMYT1 PKMYT1 PKMYT1 565 0.37 0.068 YES
10 MYBL2 MYBL2 MYBL2 571 0.36 0.077 YES
11 HIST1H4A HIST1H4A HIST1H4A 605 0.36 0.084 YES
12 DNA2 DNA2 DNA2 662 0.34 0.089 YES
13 CENPJ CENPJ CENPJ 672 0.34 0.097 YES
14 CDK4 CDK4 CDK4 683 0.34 0.1 YES
15 HIST1H2BG HIST1H2BG HIST1H2BG 732 0.33 0.11 YES
16 CDC45 CDC45 CDC45 738 0.32 0.12 YES
17 CENPI CENPI CENPI 753 0.32 0.13 YES
18 SPC25 SPC25 SPC25 765 0.32 0.13 YES
19 CDCA8 CDCA8 CDCA8 802 0.31 0.14 YES
20 NEK2 NEK2 NEK2 804 0.31 0.15 YES
21 CENPM CENPM CENPM 850 0.3 0.15 YES
22 REC8 REC8 REC8 856 0.3 0.16 YES
23 CENPA CENPA CENPA 860 0.3 0.17 YES
24 NUF2 NUF2 NUF2 869 0.3 0.17 YES
25 SKA1 SKA1 SKA1 870 0.3 0.18 YES
26 HIST1H4E HIST1H4E HIST1H4E 886 0.3 0.19 YES
27 UBE2C UBE2C UBE2C 937 0.29 0.19 YES
28 BIRC5 BIRC5 BIRC5 956 0.29 0.2 YES
29 KIF2C KIF2C KIF2C 967 0.29 0.21 YES
30 PLK1 PLK1 PLK1 988 0.28 0.21 YES
31 KIF20A KIF20A KIF20A 996 0.28 0.22 YES
32 MAD2L1 MAD2L1 MAD2L1 1060 0.27 0.22 YES
33 PPP2R3B PPP2R3B PPP2R3B 1073 0.27 0.23 YES
34 PLK4 PLK4 PLK4 1103 0.27 0.23 YES
35 CCNB2 CCNB2 CCNB2 1115 0.27 0.24 YES
36 BUB1B BUB1B BUB1B 1159 0.26 0.24 YES
37 HJURP HJURP HJURP 1176 0.26 0.25 YES
38 CDKN2A CDKN2A CDKN2A 1179 0.26 0.26 YES
39 HIST1H4C HIST1H4C HIST1H4C 1191 0.26 0.26 YES
40 CCND1 CCND1 CCND1 1210 0.25 0.27 YES
41 KIF18A KIF18A KIF18A 1213 0.25 0.27 YES
42 ERCC6L ERCC6L ERCC6L 1227 0.25 0.28 YES
43 CENPH CENPH CENPH 1281 0.25 0.28 YES
44 CDC7 CDC7 CDC7 1288 0.24 0.29 YES
45 BUB1 BUB1 BUB1 1291 0.24 0.29 YES
46 CCNA2 CCNA2 CCNA2 1313 0.24 0.3 YES
47 LMNB1 LMNB1 LMNB1 1321 0.24 0.3 YES
48 HIST1H2BL HIST1H2BL HIST1H2BL 1327 0.24 0.31 YES
49 NDC80 NDC80 NDC80 1334 0.24 0.32 YES
50 CDT1 CDT1 CDT1 1340 0.24 0.32 YES
51 CDC20 CDC20 CDC20 1343 0.24 0.33 YES
52 HIST1H2AB HIST1H2AB HIST1H2AB 1350 0.24 0.33 YES
53 ZWINT ZWINT ZWINT 1354 0.24 0.34 YES
54 OIP5 OIP5 OIP5 1366 0.24 0.34 YES
55 MLF1IP MLF1IP MLF1IP 1375 0.23 0.35 YES
56 HIST1H2BF HIST1H2BF HIST1H2BF 1395 0.23 0.35 YES
57 HIST2H2AC HIST2H2AC HIST2H2AC 1409 0.23 0.36 YES
58 HIST1H2AE HIST1H2AE HIST1H2AE 1461 0.22 0.36 YES
59 HIST1H2BI HIST1H2BI HIST1H2BI 1499 0.22 0.36 YES
60 E2F1 E2F1 E2F1 1521 0.22 0.37 YES
61 HIST3H2BB HIST3H2BB HIST3H2BB 1535 0.22 0.37 YES
62 CEP135 CEP135 CEP135 1583 0.21 0.38 YES
63 CDK1 CDK1 CDK1 1599 0.21 0.38 YES
64 SGOL2 SGOL2 SGOL2 1640 0.21 0.38 YES
65 AURKA AURKA AURKA 1649 0.21 0.39 YES
66 LIN9 LIN9 LIN9 1664 0.21 0.39 YES
67 PTTG1 PTTG1 PTTG1 1680 0.2 0.4 YES
68 HIST1H2BH HIST1H2BH HIST1H2BH 1705 0.2 0.4 YES
69 CCNE2 CCNE2 CCNE2 1707 0.2 0.41 YES
70 CDC6 CDC6 CDC6 1737 0.2 0.41 YES
71 CEP72 CEP72 CEP72 1744 0.2 0.41 YES
72 GINS2 GINS2 GINS2 1775 0.2 0.42 YES
73 KIF23 KIF23 KIF23 1814 0.19 0.42 YES
74 HIST1H2BO HIST1H2BO HIST1H2BO 1851 0.19 0.42 YES
75 FBXO5 FBXO5 FBXO5 1862 0.19 0.43 YES
76 HIST1H2BN HIST1H2BN HIST1H2BN 1882 0.19 0.43 YES
77 CHEK2 CHEK2 CHEK2 1938 0.18 0.43 YES
78 INCENP INCENP INCENP 1985 0.18 0.43 YES
79 MCM8 MCM8 MCM8 1990 0.18 0.44 YES
80 HIST1H4F HIST1H4F HIST1H4F 2048 0.17 0.44 YES
81 CHEK1 CHEK1 CHEK1 2070 0.17 0.44 YES
82 CSNK1E CSNK1E CSNK1E 2086 0.17 0.45 YES
83 CDKN2B CDKN2B CDKN2B 2110 0.17 0.45 YES
84 RFC3 RFC3 RFC3 2112 0.17 0.45 YES
85 E2F3 E2F3 E2F3 2128 0.17 0.46 YES
86 POLE POLE POLE 2133 0.17 0.46 YES
87 RRM2 RRM2 RRM2 2148 0.17 0.46 YES
88 HIST1H4B HIST1H4B HIST1H4B 2162 0.17 0.47 YES
89 DBF4 DBF4 DBF4 2235 0.16 0.47 YES
90 RPA4 RPA4 RPA4 2268 0.16 0.47 YES
91 PRIM1 PRIM1 PRIM1 2270 0.16 0.47 YES
92 GINS1 GINS1 GINS1 2301 0.16 0.48 YES
93 CCNB1 CCNB1 CCNB1 2331 0.16 0.48 YES
94 DHFR DHFR DHFR 2410 0.15 0.48 YES
95 CCDC99 CCDC99 CCDC99 2424 0.15 0.48 YES
96 AZI1 AZI1 AZI1 2430 0.15 0.48 YES
97 CENPK CENPK CENPK 2444 0.15 0.49 YES
98 POLE2 POLE2 POLE2 2477 0.14 0.49 YES
99 HIST1H2BB HIST1H2BB HIST1H2BB 2508 0.14 0.49 YES
100 CENPN CENPN CENPN 2561 0.14 0.49 YES
101 MDM2 MDM2 MDM2 2567 0.14 0.5 YES
102 DCTN2 DCTN2 DCTN2 2585 0.14 0.5 YES
103 CENPO CENPO CENPO 2592 0.14 0.5 YES
104 HIST1H2BM HIST1H2BM HIST1H2BM 2623 0.14 0.5 YES
105 MCM2 MCM2 MCM2 2642 0.14 0.5 YES
106 ZWILCH ZWILCH ZWILCH 2649 0.14 0.51 YES
107 MCM7 MCM7 MCM7 2726 0.13 0.51 YES
108 POLA2 POLA2 POLA2 2727 0.13 0.51 YES
109 MYC MYC MYC 2730 0.13 0.51 YES
110 TYMS TYMS TYMS 2846 0.13 0.51 YES
111 CDC26 CDC26 CDC26 2879 0.12 0.51 YES
112 PRIM2 PRIM2 PRIM2 2916 0.12 0.51 YES
113 NINL NINL NINL 2986 0.12 0.51 YES
114 HIST1H2BJ HIST1H2BJ HIST1H2BJ 2999 0.12 0.51 YES
115 RBL1 RBL1 RBL1 3017 0.12 0.52 YES
116 RFC4 RFC4 RFC4 3053 0.12 0.52 YES
117 HIST2H4A HIST2H4A HIST2H4A 3095 0.12 0.52 YES
118 GINS4 GINS4 GINS4 3108 0.11 0.52 YES
119 KIF2A KIF2A KIF2A 3143 0.11 0.52 YES
120 HIST1H2AD HIST1H2AD HIST1H2AD 3158 0.11 0.52 YES
121 CDKN2D CDKN2D CDKN2D 3170 0.11 0.52 YES
122 WRAP53 WRAP53 WRAP53 3224 0.11 0.52 YES
123 KNTC1 KNTC1 KNTC1 3293 0.11 0.52 YES
124 CCND2 CCND2 CCND2 3306 0.11 0.52 YES
125 NUP107 NUP107 NUP107 3390 0.1 0.52 YES
126 FEN1 FEN1 FEN1 3437 0.1 0.52 YES
127 HIST1H2BE HIST1H2BE HIST1H2BE 3499 0.1 0.52 YES
128 PPP2R2A PPP2R2A PPP2R2A 3503 0.1 0.52 YES
129 H2AFX H2AFX H2AFX 3554 0.098 0.52 YES
130 CKS1B CKS1B CKS1B 3555 0.098 0.53 YES
131 RCC2 RCC2 RCC2 3556 0.098 0.53 YES
132 H2AFZ H2AFZ H2AFZ 3646 0.095 0.53 YES
133 TUBB TUBB TUBB 3674 0.094 0.53 YES
134 DCTN3 DCTN3 DCTN3 3713 0.093 0.53 YES
135 ACTR1A ACTR1A ACTR1A 3714 0.093 0.53 YES
136 SYNE1 SYNE1 SYNE1 3726 0.092 0.53 YES
137 TUBA1A TUBA1A TUBA1A 3738 0.092 0.53 YES
138 BUB3 BUB3 BUB3 3776 0.09 0.53 YES
139 HIST1H4D HIST1H4D HIST1H4D 3778 0.09 0.54 YES
140 BTRC BTRC BTRC 3810 0.089 0.54 YES
141 MCM4 MCM4 MCM4 3820 0.089 0.54 YES
142 CEP57 CEP57 CEP57 3827 0.089 0.54 YES
143 SMC3 SMC3 SMC3 3845 0.088 0.54 YES
144 STAG3 STAG3 STAG3 3901 0.086 0.54 YES
145 RANGAP1 RANGAP1 RANGAP1 3912 0.086 0.54 YES
146 CENPL CENPL CENPL 3948 0.085 0.54 YES
147 POLD1 POLD1 POLD1 3985 0.084 0.54 YES
148 RFC5 RFC5 RFC5 3996 0.083 0.54 YES
149 PRKAR2B PRKAR2B PRKAR2B 4012 0.083 0.55 YES
150 LIG1 LIG1 LIG1 4022 0.083 0.55 YES
151 DSN1 DSN1 DSN1 4064 0.082 0.55 YES
152 SKA2 SKA2 SKA2 4071 0.082 0.55 YES
153 BRCA1 BRCA1 BRCA1 4074 0.082 0.55 YES
154 CENPP CENPP CENPP 4078 0.082 0.55 YES
155 HIST2H2BE HIST2H2BE HIST2H2BE 4174 0.079 0.55 NO
156 CEP63 CEP63 CEP63 4180 0.078 0.55 NO
157 SKP2 SKP2 SKP2 4324 0.075 0.54 NO
158 MCM5 MCM5 MCM5 4334 0.074 0.55 NO
159 TUBG1 TUBG1 TUBG1 4370 0.073 0.55 NO
160 TAOK1 TAOK1 TAOK1 4421 0.072 0.54 NO
161 PPP2R5D PPP2R5D PPP2R5D 4476 0.071 0.54 NO
162 UBE2I UBE2I UBE2I 4610 0.068 0.54 NO
163 CEP70 CEP70 CEP70 4628 0.067 0.54 NO
164 NUMA1 NUMA1 NUMA1 4693 0.066 0.54 NO
165 RAD21 RAD21 RAD21 4715 0.065 0.54 NO
166 E2F5 E2F5 E2F5 4735 0.065 0.54 NO
167 RAD1 RAD1 RAD1 4744 0.065 0.54 NO
168 RSF1 RSF1 RSF1 4751 0.064 0.54 NO
169 CCNA1 CCNA1 CCNA1 4801 0.064 0.54 NO
170 PSMD3 PSMD3 PSMD3 4810 0.063 0.54 NO
171 MCM6 MCM6 MCM6 4854 0.063 0.54 NO
172 CCNE1 CCNE1 CCNE1 4876 0.062 0.54 NO
173 PSMB7 PSMB7 PSMB7 4880 0.062 0.54 NO
174 MAD1L1 MAD1L1 MAD1L1 4921 0.061 0.54 NO
175 ATRIP ATRIP ATRIP 4957 0.06 0.54 NO
176 ACD ACD ACD 4983 0.06 0.54 NO
177 ALMS1 ALMS1 ALMS1 5034 0.059 0.54 NO
178 CENPC1 CENPC1 CENPC1 5058 0.058 0.54 NO
179 CDKN1B CDKN1B CDKN1B 5078 0.058 0.54 NO
180 CENPQ CENPQ CENPQ 5092 0.058 0.54 NO
181 PCNA PCNA PCNA 5204 0.055 0.53 NO
182 SMC1A SMC1A SMC1A 5224 0.055 0.54 NO
183 CENPT CENPT CENPT 5327 0.054 0.53 NO
184 CKAP5 CKAP5 CKAP5 5376 0.053 0.53 NO
185 ITGB3BP ITGB3BP ITGB3BP 5426 0.052 0.53 NO
186 MAPRE1 MAPRE1 MAPRE1 5500 0.05 0.52 NO
187 POLD3 POLD3 POLD3 5511 0.05 0.52 NO
188 TUBGCP6 TUBGCP6 TUBGCP6 5528 0.05 0.53 NO
189 UBE2D1 UBE2D1 UBE2D1 5553 0.05 0.53 NO
190 NUP43 NUP43 NUP43 5611 0.049 0.52 NO
191 PSMD11 PSMD11 PSMD11 5614 0.049 0.52 NO
192 RFWD2 RFWD2 RFWD2 5620 0.048 0.53 NO
193 RBBP4 RBBP4 RBBP4 5621 0.048 0.53 NO
194 FKBP6 FKBP6 FKBP6 5663 0.048 0.53 NO
195 POLA1 POLA1 POLA1 5765 0.046 0.52 NO
196 CEP76 CEP76 CEP76 5810 0.045 0.52 NO
197 GMNN GMNN GMNN 5874 0.044 0.52 NO
198 CLASP1 CLASP1 CLASP1 5913 0.044 0.52 NO
199 MIS12 MIS12 MIS12 5920 0.044 0.52 NO
200 CDC25B CDC25B CDC25B 5946 0.043 0.52 NO
201 ANAPC1 ANAPC1 ANAPC1 5969 0.043 0.52 NO
202 ANAPC7 ANAPC7 ANAPC7 5975 0.043 0.52 NO
203 DKC1 DKC1 DKC1 6037 0.042 0.52 NO
204 SUN2 SUN2 SUN2 6060 0.042 0.52 NO
205 TERF2 TERF2 TERF2 6107 0.041 0.51 NO
206 TUBGCP3 TUBGCP3 TUBGCP3 6132 0.041 0.51 NO
207 CDK5RAP2 CDK5RAP2 CDK5RAP2 6146 0.04 0.51 NO
208 RUVBL1 RUVBL1 RUVBL1 6164 0.04 0.51 NO
209 HIST1H2AJ HIST1H2AJ HIST1H2AJ 6270 0.038 0.51 NO
210 PPP2R5B PPP2R5B PPP2R5B 6273 0.038 0.51 NO
211 SEC13 SEC13 SEC13 6329 0.037 0.51 NO
212 TERF2IP TERF2IP TERF2IP 6408 0.036 0.5 NO
213 DCTN1 DCTN1 DCTN1 6543 0.034 0.5 NO
214 ZW10 ZW10 ZW10 6580 0.034 0.5 NO
215 MCM3 MCM3 MCM3 6596 0.034 0.5 NO
216 CEP250 CEP250 CEP250 6601 0.034 0.5 NO
217 HIST1H4I HIST1H4I HIST1H4I 6630 0.033 0.5 NO
218 DIDO1 DIDO1 DIDO1 6663 0.033 0.5 NO
219 PAFAH1B1 PAFAH1B1 PAFAH1B1 6705 0.032 0.49 NO
220 SMARCA5 SMARCA5 SMARCA5 6712 0.032 0.49 NO
221 LIN54 LIN54 LIN54 6721 0.032 0.49 NO
222 CCNH CCNH CCNH 6757 0.032 0.49 NO
223 PCNT PCNT PCNT 6799 0.031 0.49 NO
224 CDKN2C CDKN2C CDKN2C 6817 0.031 0.49 NO
225 CDC23 CDC23 CDC23 6843 0.03 0.49 NO
226 TERF1 TERF1 TERF1 6924 0.03 0.49 NO
227 CDC27 CDC27 CDC27 6980 0.029 0.48 NO
228 ANAPC5 ANAPC5 ANAPC5 6998 0.029 0.48 NO
229 PSMD2 PSMD2 PSMD2 7102 0.028 0.48 NO
230 PPP2R1A PPP2R1A PPP2R1A 7103 0.028 0.48 NO
231 TERT TERT TERT 7105 0.028 0.48 NO
232 ANAPC2 ANAPC2 ANAPC2 7118 0.027 0.48 NO
233 PPP2R1B PPP2R1B PPP2R1B 7139 0.027 0.48 NO
234 CEP192 CEP192 CEP192 7145 0.027 0.48 NO
235 CDK2 CDK2 CDK2 7151 0.027 0.48 NO
236 PSMB6 PSMB6 PSMB6 7187 0.026 0.48 NO
237 TUBGCP2 TUBGCP2 TUBGCP2 7236 0.026 0.48 NO
238 DYNC1I2 DYNC1I2 DYNC1I2 7275 0.025 0.48 NO
239 TEX12 TEX12 TEX12 7286 0.025 0.48 NO
240 NHP2 NHP2 NHP2 7381 0.024 0.47 NO
241 CEP290 CEP290 CEP290 7398 0.024 0.47 NO
242 PSMB3 PSMB3 PSMB3 7447 0.023 0.47 NO
243 UBE2E1 UBE2E1 UBE2E1 7461 0.023 0.47 NO
244 HIST4H4 HIST4H4 HIST4H4 7474 0.023 0.47 NO
245 PPP2R5E PPP2R5E PPP2R5E 7539 0.022 0.47 NO
246 PSMB2 PSMB2 PSMB2 7540 0.022 0.47 NO
247 YWHAE YWHAE YWHAE 7564 0.022 0.47 NO
248 RAD9A RAD9A RAD9A 7625 0.021 0.46 NO
249 STAG1 STAG1 STAG1 7627 0.021 0.46 NO
250 ANAPC11 ANAPC11 ANAPC11 7649 0.02 0.46 NO
251 SYNE2 SYNE2 SYNE2 7703 0.02 0.46 NO
252 NSL1 NSL1 NSL1 7726 0.02 0.46 NO
253 LIN52 LIN52 LIN52 7779 0.019 0.46 NO
254 PSMD10 PSMD10 PSMD10 7801 0.019 0.46 NO
255 PPP1CC PPP1CC PPP1CC 7828 0.018 0.46 NO
256 PMF1 PMF1 PMF1 7928 0.017 0.45 NO
257 PSMD4 PSMD4 PSMD4 7961 0.017 0.45 NO
258 XPO1 XPO1 XPO1 7986 0.016 0.45 NO
259 SSNA1 SSNA1 SSNA1 8001 0.016 0.45 NO
260 NUP85 NUP85 NUP85 8109 0.015 0.44 NO
261 NPM1 NPM1 NPM1 8113 0.015 0.44 NO
262 PPP2CA PPP2CA PPP2CA 8148 0.015 0.44 NO
263 NUP133 NUP133 NUP133 8173 0.014 0.44 NO
264 NEDD1 NEDD1 NEDD1 8230 0.014 0.44 NO
265 ATM ATM ATM 8275 0.013 0.44 NO
266 PSMD6 PSMD6 PSMD6 8285 0.013 0.43 NO
267 DYNC1H1 DYNC1H1 DYNC1H1 8317 0.012 0.43 NO
268 CCND3 CCND3 CCND3 8398 0.011 0.43 NO
269 YWHAG YWHAG YWHAG 8521 0.0094 0.42 NO
270 RUVBL2 RUVBL2 RUVBL2 8533 0.0091 0.42 NO
271 HIST1H2BC HIST1H2BC HIST1H2BC 8581 0.0087 0.42 NO
272 NUDC NUDC NUDC 8662 0.0077 0.42 NO
273 DYRK1A DYRK1A DYRK1A 8718 0.0068 0.41 NO
274 E2F4 E2F4 E2F4 8769 0.0062 0.41 NO
275 STAG2 STAG2 STAG2 8809 0.0056 0.41 NO
276 LIN37 LIN37 LIN37 8814 0.0056 0.41 NO
277 PSMD1 PSMD1 PSMD1 8837 0.0053 0.41 NO
278 CEP164 CEP164 CEP164 8868 0.0049 0.4 NO
279 PCM1 PCM1 PCM1 8959 0.0039 0.4 NO
280 PSMB5 PSMB5 PSMB5 9004 0.0034 0.4 NO
281 RBL2 RBL2 RBL2 9141 0.0015 0.39 NO
282 RAD17 RAD17 RAD17 9216 0.00066 0.39 NO
283 RPA1 RPA1 RPA1 9256 0.00022 0.38 NO
284 PSMA7 PSMA7 PSMA7 9321 -0.00068 0.38 NO
285 PSMA4 PSMA4 PSMA4 9323 -0.0007 0.38 NO
286 DYNLL1 DYNLL1 DYNLL1 9371 -0.0013 0.38 NO
287 PSMD14 PSMD14 PSMD14 9469 -0.0025 0.37 NO
288 HIST1H4H HIST1H4H HIST1H4H 9581 -0.0038 0.37 NO
289 FGFR1OP FGFR1OP FGFR1OP 9648 -0.0045 0.36 NO
290 GORASP1 GORASP1 GORASP1 9735 -0.0056 0.36 NO
291 PSMD7 PSMD7 PSMD7 9742 -0.0056 0.36 NO
292 MNAT1 MNAT1 MNAT1 9747 -0.0057 0.36 NO
293 PSMB1 PSMB1 PSMB1 9812 -0.0065 0.35 NO
294 RBBP7 RBBP7 RBBP7 9839 -0.0069 0.35 NO
295 PPP2R5C PPP2R5C PPP2R5C 9860 -0.0072 0.35 NO
296 CDK6 CDK6 CDK6 9867 -0.0073 0.35 NO
297 PSME4 PSME4 PSME4 9874 -0.0074 0.35 NO
298 AKAP9 AKAP9 AKAP9 9941 -0.0084 0.35 NO
299 RB1 RB1 RB1 9968 -0.0088 0.35 NO
300 RPA2 RPA2 RPA2 10018 -0.0096 0.34 NO
301 PSMB4 PSMB4 PSMB4 10061 -0.01 0.34 NO
302 SEH1L SEH1L SEH1L 10071 -0.01 0.34 NO
303 PSMC3 PSMC3 PSMC3 10166 -0.012 0.34 NO
304 PSMF1 PSMF1 PSMF1 10206 -0.012 0.34 NO
305 UBA52 UBA52 UBA52 10240 -0.012 0.33 NO
306 PSMD8 PSMD8 PSMD8 10290 -0.013 0.33 NO
307 RFC2 RFC2 RFC2 10352 -0.014 0.33 NO
308 PPP2CB PPP2CB PPP2CB 10382 -0.014 0.33 NO
309 HIST1H2AC HIST1H2AC HIST1H2AC 10411 -0.015 0.32 NO
310 ATR ATR ATR 10455 -0.015 0.32 NO
311 POLD2 POLD2 POLD2 10505 -0.016 0.32 NO
312 RANBP2 RANBP2 RANBP2 10508 -0.016 0.32 NO
313 PSMC4 PSMC4 PSMC4 10516 -0.016 0.32 NO
314 RPA3 RPA3 RPA3 10532 -0.016 0.32 NO
315 PSMA6 PSMA6 PSMA6 10533 -0.016 0.32 NO
316 CSNK1D CSNK1D CSNK1D 10609 -0.017 0.32 NO
317 PSMA5 PSMA5 PSMA5 10715 -0.019 0.31 NO
318 PSMD12 PSMD12 PSMD12 10787 -0.02 0.31 NO
319 PSMA2 PSMA2 PSMA2 10921 -0.022 0.3 NO
320 HIST1H2BD HIST1H2BD HIST1H2BD 10941 -0.022 0.3 NO
321 RPS27 RPS27 RPS27 11012 -0.023 0.3 NO
322 PSMC5 PSMC5 PSMC5 11025 -0.023 0.3 NO
323 RPS27A RPS27A RPS27A 11126 -0.024 0.29 NO
324 PSMD13 PSMD13 PSMD13 11151 -0.024 0.29 NO
325 SMC1B SMC1B SMC1B 11153 -0.024 0.29 NO
326 ANAPC4 ANAPC4 ANAPC4 11228 -0.025 0.29 NO
327 HIST2H2AA3 HIST2H2AA3 HIST2H2AA3 11258 -0.026 0.29 NO
328 TFDP1 TFDP1 TFDP1 11264 -0.026 0.29 NO
329 AHCTF1 AHCTF1 AHCTF1 11348 -0.027 0.28 NO
330 PSMC6 PSMC6 PSMC6 11658 -0.032 0.27 NO
331 HDAC1 HDAC1 HDAC1 11661 -0.032 0.27 NO
332 PSMC2 PSMC2 PSMC2 11763 -0.033 0.26 NO
333 TP53 TP53 TP53 11824 -0.034 0.26 NO
334 HIST1H4J HIST1H4J HIST1H4J 11837 -0.034 0.26 NO
335 APITD1 APITD1 APITD1 11842 -0.034 0.26 NO
336 CDC16 CDC16 CDC16 11943 -0.036 0.26 NO
337 HSP90AA1 HSP90AA1 HSP90AA1 11967 -0.036 0.26 NO
338 PRKACA PRKACA PRKACA 12068 -0.038 0.25 NO
339 HAUS2 HAUS2 HAUS2 12193 -0.039 0.25 NO
340 NDEL1 NDEL1 NDEL1 12299 -0.041 0.24 NO
341 SDCCAG8 SDCCAG8 SDCCAG8 12351 -0.042 0.24 NO
342 OFD1 OFD1 OFD1 12404 -0.042 0.24 NO
343 PSMA1 PSMA1 PSMA1 12410 -0.043 0.24 NO
344 CDK7 CDK7 CDK7 12501 -0.044 0.23 NO
345 PSMC1 PSMC1 PSMC1 12549 -0.045 0.23 NO
346 SKP1 SKP1 SKP1 12556 -0.045 0.23 NO
347 TINF2 TINF2 TINF2 12647 -0.047 0.23 NO
348 TUBG2 TUBG2 TUBG2 12648 -0.047 0.23 NO
349 CDC14A CDC14A CDC14A 12726 -0.048 0.23 NO
350 CUL1 CUL1 CUL1 12808 -0.05 0.22 NO
351 PSMD5 PSMD5 PSMD5 12919 -0.052 0.22 NO
352 MAX MAX MAX 13086 -0.055 0.21 NO
353 NUP37 NUP37 NUP37 13141 -0.056 0.21 NO
354 POT1 POT1 POT1 13171 -0.057 0.21 NO
355 PSMD9 PSMD9 PSMD9 13349 -0.06 0.2 NO
356 HIST1H2BK HIST1H2BK HIST1H2BK 13383 -0.061 0.2 NO
357 HUS1 HUS1 HUS1 13406 -0.062 0.2 NO
358 WEE1 WEE1 WEE1 13448 -0.062 0.2 NO
359 ANAPC10 ANAPC10 ANAPC10 13778 -0.07 0.18 NO
360 PSMA3 PSMA3 PSMA3 13897 -0.073 0.18 NO
361 TUBGCP5 TUBGCP5 TUBGCP5 13963 -0.074 0.18 NO
362 PPP2R5A PPP2R5A PPP2R5A 14000 -0.075 0.18 NO
363 TK2 TK2 TK2 14418 -0.086 0.16 NO
364 CETN2 CETN2 CETN2 14640 -0.093 0.15 NO
365 CLIP1 CLIP1 CLIP1 14808 -0.098 0.14 NO
366 PSMB10 PSMB10 PSMB10 15166 -0.11 0.12 NO
367 POLD4 POLD4 POLD4 15443 -0.12 0.11 NO
368 PSME1 PSME1 PSME1 15535 -0.12 0.11 NO
369 PSME2 PSME2 PSME2 15537 -0.12 0.11 NO
370 CDKN1A CDKN1A CDKN1A 15669 -0.13 0.11 NO
371 PSMA8 PSMA8 PSMA8 15685 -0.13 0.11 NO
372 PSMB8 PSMB8 PSMB8 15918 -0.14 0.099 NO
373 B9D2 B9D2 B9D2 15935 -0.14 0.1 NO
374 LMNA LMNA LMNA 16004 -0.15 0.1 NO
375 HSPA2 HSPA2 HSPA2 16278 -0.16 0.091 NO
376 PSMB9 PSMB9 PSMB9 16846 -0.2 0.064 NO
377 SYCP2 SYCP2 SYCP2 16999 -0.21 0.061 NO
378 TUBA4A TUBA4A TUBA4A 17350 -0.25 0.047 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: PID ERA GENOMIC PATHWAY.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ERA GENOMIC 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 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 43 genes.ES.table 0.55 1.8 0.008 0.72 0.47 0.7 0.33 0.47 0 0.16
BIOCARTA HIVNEF PATHWAY 58 genes.ES.table 0.44 1.8 0.016 0.64 0.64 0.31 0.19 0.25 0.23 0.16
BIOCARTA IL2RB PATHWAY 38 genes.ES.table 0.64 1.7 0.02 0.5 0.85 0.4 0.14 0.34 0.24 0.13
BIOCARTA DEATH PATHWAY 33 genes.ES.table 0.55 1.7 0.012 0.42 0.73 0.48 0.19 0.39 0.16 0.092
ST TUMOR NECROSIS FACTOR PATHWAY 28 genes.ES.table 0.57 1.7 0.021 0.45 0.73 0.46 0.19 0.38 0.17 0.097
PID SYNDECAN 4 PATHWAY 28 genes.ES.table 0.71 1.8 0.002 0.55 0.64 0.68 0.22 0.53 0.2 0.13
PID HIVNEFPATHWAY 35 genes.ES.table 0.54 1.7 0.025 0.41 0.78 0.4 0.19 0.32 0.18 0.097
REACTOME ANTIGEN PROCESSING CROSS PRESENTATION 72 genes.ES.table 0.57 1.7 0.01 0.53 0.7 0.64 0.3 0.45 0.2 0.13
REACTOME TRIF MEDIATED TLR3 SIGNALING 72 genes.ES.table 0.43 1.7 0.022 0.54 0.73 0.35 0.22 0.27 0.21 0.13
REACTOME ACTIVATION OF CHAPERONE GENES BY XBP1S 44 genes.ES.table 0.42 1.7 0.077 0.48 0.86 0.3 0.18 0.24 0.23 0.12
genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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 SAA1 SAA1 SAA1 332 0.29 0.042 YES
2 CASP8 CASP8 CASP8 590 0.25 0.078 YES
3 IRF1 IRF1 IRF1 842 0.22 0.11 YES
4 TNFAIP3 TNFAIP3 TNFAIP3 1106 0.19 0.13 YES
5 IFNB1 IFNB1 IFNB1 1215 0.18 0.16 YES
6 DHX58 DHX58 DHX58 1247 0.18 0.2 YES
7 S100A12 S100A12 S100A12 1378 0.17 0.23 YES
8 IFIH1 IFIH1 IFIH1 1518 0.16 0.25 YES
9 IKBKE IKBKE IKBKE 1539 0.16 0.28 YES
10 IRF7 IRF7 IRF7 1616 0.15 0.31 YES
11 RNF135 RNF135 RNF135 1621 0.15 0.34 YES
12 NFKBIA NFKBIA NFKBIA 1772 0.14 0.36 YES
13 TANK TANK TANK 2061 0.13 0.37 YES
14 HERC5 HERC5 HERC5 2201 0.12 0.39 YES
15 IRF2 IRF2 IRF2 2250 0.12 0.41 YES
16 ISG15 ISG15 ISG15 2406 0.11 0.42 YES
17 NFKB2 NFKB2 NFKB2 2434 0.11 0.45 YES
18 CASP10 CASP10 CASP10 2574 0.11 0.46 YES
19 NLRC5 NLRC5 NLRC5 2755 0.1 0.47 YES
20 IRF3 IRF3 IRF3 2930 0.093 0.48 YES
21 DDX58 DDX58 DDX58 2961 0.092 0.5 YES
22 TRAF6 TRAF6 TRAF6 3120 0.087 0.51 YES
23 RIPK1 RIPK1 RIPK1 3235 0.084 0.52 YES
24 UBA7 UBA7 UBA7 3300 0.082 0.53 YES
25 UBE2L6 UBE2L6 UBE2L6 3377 0.08 0.54 YES
26 TBK1 TBK1 TBK1 3485 0.076 0.55 YES
27 TAX1BP1 TAX1BP1 TAX1BP1 3723 0.071 0.55 YES
28 NLRX1 NLRX1 NLRX1 4286 0.059 0.53 NO
29 FADD FADD FADD 4758 0.05 0.52 NO
30 RPS27A RPS27A RPS27A 4814 0.049 0.52 NO
31 APP APP APP 5104 0.044 0.52 NO
32 UBA52 UBA52 UBA52 5368 0.039 0.51 NO
33 TRIM25 TRIM25 TRIM25 5375 0.039 0.52 NO
34 CYLD CYLD CYLD 5518 0.037 0.52 NO
35 ATG5 ATG5 ATG5 6282 0.026 0.48 NO
36 IKBKB IKBKB IKBKB 6382 0.025 0.48 NO
37 DAK DAK DAK 6425 0.025 0.48 NO
38 IKBKG IKBKG IKBKG 6526 0.023 0.48 NO
39 TRAF3 TRAF3 TRAF3 6548 0.023 0.49 NO
40 UBE2D3 UBE2D3 UBE2D3 6559 0.023 0.49 NO
41 NFKBIB NFKBIB NFKBIB 7427 0.012 0.45 NO
42 ATG12 ATG12 ATG12 7593 0.0094 0.44 NO
43 HMGB1 HMGB1 HMGB1 7967 0.0046 0.42 NO
44 RELA RELA RELA 8026 0.0039 0.42 NO
45 SIKE1 SIKE1 SIKE1 8117 0.0028 0.41 NO
46 CHUK CHUK CHUK 8196 0.0016 0.41 NO
47 UBE2D2 UBE2D2 UBE2D2 8243 0.00087 0.41 NO
48 S100B S100B S100B 8291 0.00031 0.4 NO
49 UBE2K UBE2K UBE2K 8621 -0.0038 0.39 NO
50 PIN1 PIN1 PIN1 8836 -0.0066 0.38 NO
51 PCBP2 PCBP2 PCBP2 8918 -0.0076 0.37 NO
52 UBE2D1 UBE2D1 UBE2D1 9205 -0.011 0.36 NO
53 OTUD5 OTUD5 OTUD5 10030 -0.023 0.32 NO
54 TRAF2 TRAF2 TRAF2 10411 -0.028 0.3 NO
55 MAVS MAVS MAVS 10789 -0.033 0.29 NO
56 EP300 EP300 EP300 11075 -0.038 0.28 NO
57 MAP3K1 MAP3K1 MAP3K1 13045 -0.076 0.19 NO
58 CREBBP CREBBP CREBBP 13069 -0.077 0.2 NO
59 AGER AGER AGER 15533 -0.18 0.1 NO
60 RNF125 RNF125 RNF125 15962 -0.21 0.12 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BIRC3 BIRC3 BIRC3 183 0.33 0.094 YES
2 CASP1 CASP1 CASP1 265 0.31 0.19 YES
3 NOD2 NOD2 NOD2 386 0.28 0.27 YES
4 MAPK13 MAPK13 MAPK13 393 0.28 0.36 YES
5 CASP4 CASP4 CASP4 583 0.25 0.42 YES
6 CASP8 CASP8 CASP8 590 0.25 0.5 YES
7 NOD1 NOD1 NOD1 1052 0.2 0.54 YES
8 TNFAIP3 TNFAIP3 TNFAIP3 1106 0.19 0.59 YES
9 IRAK2 IRAK2 IRAK2 1255 0.18 0.64 YES
10 CARD9 CARD9 CARD9 1563 0.16 0.67 YES
11 TRAF6 TRAF6 TRAF6 3120 0.087 0.62 NO
12 CYLD CYLD CYLD 5518 0.037 0.49 NO
13 IRAK1 IRAK1 IRAK1 5877 0.032 0.48 NO
14 BIRC2 BIRC2 BIRC2 5922 0.031 0.49 NO
15 IKBKB IKBKB IKBKB 6382 0.025 0.48 NO
16 IKBKG IKBKG IKBKG 6526 0.023 0.47 NO
17 MAPK14 MAPK14 MAPK14 6661 0.021 0.47 NO
18 RIPK2 RIPK2 RIPK2 7049 0.016 0.46 NO
19 TAB2 TAB2 TAB2 7665 0.0083 0.43 NO
20 CHUK CHUK CHUK 8196 0.0016 0.4 NO
21 UBE2N UBE2N UBE2N 8230 0.0011 0.4 NO
22 MAP3K7 MAP3K7 MAP3K7 9323 -0.013 0.34 NO
23 CASP2 CASP2 CASP2 9854 -0.02 0.32 NO
24 TAB1 TAB1 TAB1 10033 -0.023 0.31 NO
25 TAB3 TAB3 TAB3 11157 -0.039 0.26 NO
26 MAP2K6 MAP2K6 MAP2K6 11839 -0.051 0.24 NO
27 MAPK11 MAPK11 MAPK11 12420 -0.062 0.23 NO
28 MAPK12 MAPK12 MAPK12 12435 -0.062 0.25 NO
29 CASP9 CASP9 CASP9 12543 -0.064 0.26 NO
30 TMEM189-UBE2V1 TMEM189-UBE2V1 TMEM189-UBE2V1 15064 -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 HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

Table S13.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HK3 HK3 HK3 378 0.28 0.071 YES
2 GCK GCK GCK 591 0.25 0.14 YES
3 CHIT1 CHIT1 CHIT1 1352 0.17 0.15 YES
4 GFPT2 GFPT2 GFPT2 1354 0.17 0.21 YES
5 HEXB HEXB HEXB 1644 0.15 0.24 YES
6 HEXA HEXA HEXA 1864 0.14 0.27 YES
7 FPGT FPGT FPGT 2109 0.13 0.3 YES
8 RENBP RENBP RENBP 2154 0.12 0.34 YES
9 GMPPA GMPPA GMPPA 2253 0.12 0.37 YES
10 CYB5R1 CYB5R1 CYB5R1 2295 0.12 0.41 YES
11 GALK1 GALK1 GALK1 2557 0.11 0.43 YES
12 UGP2 UGP2 UGP2 3092 0.088 0.42 YES
13 UAP1 UAP1 UAP1 3208 0.085 0.45 YES
14 NPL NPL NPL 3345 0.081 0.46 YES
15 AMDHD2 AMDHD2 AMDHD2 4032 0.064 0.45 YES
16 PMM2 PMM2 PMM2 4455 0.056 0.44 YES
17 GALK2 GALK2 GALK2 4480 0.056 0.46 YES
18 PMM1 PMM1 PMM1 4564 0.054 0.47 YES
19 GNPNAT1 GNPNAT1 GNPNAT1 4568 0.054 0.49 YES
20 GNPDA1 GNPDA1 GNPDA1 4600 0.053 0.5 YES
21 PGM2 PGM2 PGM2 4658 0.052 0.52 YES
22 GPI GPI GPI 4766 0.05 0.53 YES
23 TSTA3 TSTA3 TSTA3 5079 0.044 0.52 YES
24 GMDS GMDS GMDS 5439 0.038 0.52 YES
25 GMPPB GMPPB GMPPB 5460 0.038 0.53 YES
26 HK2 HK2 HK2 5463 0.038 0.54 YES
27 NANP NANP NANP 5642 0.035 0.54 YES
28 UXS1 UXS1 UXS1 5739 0.034 0.55 YES
29 GALE GALE GALE 5886 0.032 0.55 YES
30 MPI MPI MPI 6013 0.03 0.55 YES
31 NANS NANS NANS 6371 0.025 0.54 NO
32 PGM3 PGM3 PGM3 6729 0.02 0.53 NO
33 HK1 HK1 HK1 6814 0.019 0.53 NO
34 NAGK NAGK NAGK 6929 0.018 0.53 NO
35 FUK FUK FUK 7067 0.016 0.53 NO
36 CMAS CMAS CMAS 7519 0.01 0.51 NO
37 CYB5R3 CYB5R3 CYB5R3 7564 0.0098 0.51 NO
38 GNPDA2 GNPDA2 GNPDA2 8409 -0.0011 0.46 NO
39 PGM1 PGM1 PGM1 8759 -0.0056 0.44 NO
40 GALT GALT GALT 9708 -0.018 0.4 NO
41 GFPT1 GFPT1 GFPT1 11079 -0.038 0.33 NO
42 UGDH UGDH UGDH 11082 -0.038 0.35 NO
43 GNE GNE GNE 14913 -0.14 0.18 NO

Figure S25.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL2RB PATHWAY.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA DEATH PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GBP5 GBP5 GBP5 10 0.49 0.036 YES
2 SOCS1 SOCS1 SOCS1 123 0.36 0.056 YES
3 ISG20 ISG20 ISG20 368 0.28 0.064 YES
4 ICAM1 ICAM1 ICAM1 370 0.28 0.086 YES
5 GBP1 GBP1 GBP1 400 0.28 0.1 YES
6 OASL OASL OASL 471 0.26 0.12 YES
7 SP100 SP100 SP100 625 0.24 0.13 YES
8 SOCS3 SOCS3 SOCS3 647 0.24 0.15 YES
9 IRF6 IRF6 IRF6 653 0.24 0.16 YES
10 XAF1 XAF1 XAF1 730 0.23 0.18 YES
11 OAS1 OAS1 OAS1 735 0.23 0.2 YES
12 MT2A MT2A MT2A 818 0.22 0.21 YES
13 IRF1 IRF1 IRF1 842 0.22 0.22 YES
14 GBP2 GBP2 GBP2 843 0.22 0.24 YES
15 GBP4 GBP4 GBP4 862 0.21 0.25 YES
16 IFI35 IFI35 IFI35 911 0.21 0.27 YES
17 IFITM3 IFITM3 IFITM3 922 0.21 0.28 YES
18 HLA-G HLA-G HLA-G 929 0.21 0.3 YES
19 IFITM1 IFITM1 IFITM1 1088 0.19 0.3 YES
20 CIITA CIITA CIITA 1153 0.19 0.31 YES
21 IFNB1 IFNB1 IFNB1 1215 0.18 0.32 YES
22 IFITM2 IFITM2 IFITM2 1221 0.18 0.34 YES
23 OAS2 OAS2 OAS2 1320 0.17 0.34 YES
24 HLA-F HLA-F HLA-F 1346 0.17 0.36 YES
25 VCAM1 VCAM1 VCAM1 1356 0.17 0.37 YES
26 PSMB8 PSMB8 PSMB8 1359 0.17 0.38 YES
27 CD44 CD44 CD44 1467 0.16 0.39 YES
28 HLA-DQA2 HLA-DQA2 HLA-DQA2 1482 0.16 0.4 YES
29 HLA-B HLA-B HLA-B 1562 0.16 0.4 YES
30 IRF7 IRF7 IRF7 1616 0.15 0.41 YES
31 MX2 MX2 MX2 1735 0.15 0.42 YES
32 HLA-DPB1 HLA-DPB1 HLA-DPB1 1738 0.14 0.43 YES
33 FCGR1B FCGR1B FCGR1B 1788 0.14 0.44 YES
34 FCGR1A FCGR1A FCGR1A 1796 0.14 0.45 YES
35 MX1 MX1 MX1 1818 0.14 0.46 YES
36 PTPN2 PTPN2 PTPN2 1829 0.14 0.47 YES
37 HLA-DQA1 HLA-DQA1 HLA-DQA1 1858 0.14 0.48 YES
38 HLA-A HLA-A HLA-A 1936 0.14 0.48 YES
39 GBP6 GBP6 GBP6 2001 0.13 0.49 YES
40 HLA-C HLA-C HLA-C 2002 0.13 0.5 YES
41 OAS3 OAS3 OAS3 2031 0.13 0.51 YES
42 HLA-DRB1 HLA-DRB1 HLA-DRB1 2099 0.13 0.51 YES
43 HLA-DPA1 HLA-DPA1 HLA-DPA1 2177 0.12 0.52 YES
44 HERC5 HERC5 HERC5 2201 0.12 0.52 YES
45 IFI6 IFI6 IFI6 2216 0.12 0.53 YES
46 B2M B2M B2M 2237 0.12 0.54 YES
47 IRF2 IRF2 IRF2 2250 0.12 0.55 YES
48 IFIT3 IFIT3 IFIT3 2321 0.12 0.55 YES
49 ISG15 ISG15 ISG15 2406 0.11 0.56 YES
50 PTPN6 PTPN6 PTPN6 2568 0.11 0.56 YES
51 IRF5 IRF5 IRF5 2602 0.1 0.56 YES
52 HLA-DRB5 HLA-DRB5 HLA-DRB5 2609 0.1 0.57 YES
53 PML PML PML 2671 0.1 0.57 YES
54 USP18 USP18 USP18 2746 0.1 0.58 YES
55 IFI27 IFI27 IFI27 2865 0.095 0.58 YES
56 NUP37 NUP37 NUP37 2881 0.094 0.58 YES
57 IRF3 IRF3 IRF3 2930 0.093 0.59 YES
58 IFNGR2 IFNGR2 IFNGR2 2945 0.092 0.6 YES
59 DDX58 DDX58 DDX58 2961 0.092 0.6 YES
60 CAMK2D CAMK2D CAMK2D 2989 0.091 0.61 YES
61 RNASEL RNASEL RNASEL 3233 0.084 0.6 YES
62 EIF2AK2 EIF2AK2 EIF2AK2 3249 0.083 0.6 YES
63 UBA7 UBA7 UBA7 3300 0.082 0.61 YES
64 UBE2L6 UBE2L6 UBE2L6 3377 0.08 0.61 YES
65 STAT1 STAT1 STAT1 3588 0.074 0.6 NO
66 IRF9 IRF9 IRF9 3929 0.066 0.59 NO
67 PRKCD PRKCD PRKCD 4024 0.064 0.59 NO
68 IFIT1 IFIT1 IFIT1 4217 0.06 0.58 NO
69 JAK2 JAK2 JAK2 4291 0.059 0.58 NO
70 IRF8 IRF8 IRF8 4376 0.057 0.58 NO
71 IFIT2 IFIT2 IFIT2 4379 0.057 0.59 NO
72 STAT2 STAT2 STAT2 4443 0.056 0.59 NO
73 RPS27A RPS27A RPS27A 4814 0.049 0.57 NO
74 IFNGR1 IFNGR1 IFNGR1 4825 0.049 0.57 NO
75 NUP54 NUP54 NUP54 5268 0.041 0.55 NO
76 UBA52 UBA52 UBA52 5368 0.039 0.55 NO
77 IFNAR1 IFNAR1 IFNAR1 5373 0.039 0.55 NO
78 TRIM25 TRIM25 TRIM25 5375 0.039 0.56 NO
79 IRF4 IRF4 IRF4 5419 0.039 0.56 NO
80 SEH1L SEH1L SEH1L 5798 0.033 0.54 NO
81 KPNA4 KPNA4 KPNA4 5937 0.031 0.53 NO
82 NEDD4 NEDD4 NEDD4 6001 0.03 0.53 NO
83 EIF4E EIF4E EIF4E 6085 0.029 0.53 NO
84 EIF4A3 EIF4A3 EIF4A3 6289 0.026 0.52 NO
85 IFNAR2 IFNAR2 IFNAR2 6583 0.022 0.51 NO
86 UBE2E1 UBE2E1 UBE2E1 6799 0.02 0.5 NO
87 SUMO1 SUMO1 SUMO1 6841 0.019 0.49 NO
88 EIF4G2 EIF4G2 EIF4G2 7026 0.016 0.49 NO
89 NUP205 NUP205 NUP205 7244 0.014 0.48 NO
90 EIF4A1 EIF4A1 EIF4A1 7254 0.013 0.48 NO
91 PTPN1 PTPN1 PTPN1 7394 0.012 0.47 NO
92 PTAFR PTAFR PTAFR 7479 0.011 0.46 NO
93 NUP210 NUP210 NUP210 7550 0.01 0.46 NO
94 NUP85 NUP85 NUP85 7654 0.0085 0.46 NO
95 ARIH1 ARIH1 ARIH1 7927 0.0051 0.44 NO
96 TYK2 TYK2 TYK2 7945 0.0049 0.44 NO
97 EIF4E2 EIF4E2 EIF4E2 8072 0.0033 0.43 NO
98 EGR1 EGR1 EGR1 8093 0.0031 0.43 NO
99 UBE2N UBE2N UBE2N 8230 0.0011 0.43 NO
100 NUP62 NUP62 NUP62 8292 0.00031 0.42 NO
101 ADAR ADAR ADAR 8365 -0.00047 0.42 NO
102 RAE1 RAE1 RAE1 8366 -0.00047 0.42 NO
103 RANBP2 RANBP2 RANBP2 8482 -0.002 0.41 NO
104 CAMK2B CAMK2B CAMK2B 8549 -0.003 0.41 NO
105 TPR TPR TPR 8560 -0.0031 0.41 NO
106 EIF4E3 EIF4E3 EIF4E3 8575 -0.0034 0.41 NO
107 EIF4A2 EIF4A2 EIF4A2 8744 -0.0054 0.4 NO
108 EIF4G1 EIF4G1 EIF4G1 8834 -0.0066 0.4 NO
109 PIN1 PIN1 PIN1 8836 -0.0066 0.4 NO
110 PIAS1 PIAS1 PIAS1 8974 -0.0082 0.39 NO
111 PLCG1 PLCG1 PLCG1 9029 -0.0089 0.39 NO
112 NUPL2 NUPL2 NUPL2 9113 -0.0099 0.38 NO
113 NUP50 NUP50 NUP50 9358 -0.013 0.37 NO
114 KPNB1 KPNB1 KPNB1 9366 -0.013 0.37 NO
115 NUP153 NUP153 NUP153 9385 -0.014 0.37 NO
116 MAPK3 MAPK3 MAPK3 9399 -0.014 0.37 NO
117 FLNB FLNB FLNB 9566 -0.016 0.36 NO
118 NUP155 NUP155 NUP155 9674 -0.018 0.36 NO
119 JAK1 JAK1 JAK1 9768 -0.019 0.35 NO
120 KPNA2 KPNA2 KPNA2 10084 -0.023 0.34 NO
121 KPNA1 KPNA1 KPNA1 10115 -0.024 0.34 NO
122 NUPL1 NUPL1 NUPL1 10158 -0.024 0.34 NO
123 NUP133 NUP133 NUP133 10239 -0.025 0.34 NO
124 IFNG IFNG IFNG 10336 -0.026 0.33 NO
125 POM121 POM121 POM121 10381 -0.027 0.33 NO
126 KPNA3 KPNA3 KPNA3 10418 -0.028 0.33 NO
127 PPM1B PPM1B PPM1B 10550 -0.03 0.33 NO
128 NUP88 NUP88 NUP88 10911 -0.035 0.31 NO
129 NUP214 NUP214 NUP214 11172 -0.039 0.3 NO
130 NUP43 NUP43 NUP43 11364 -0.043 0.29 NO
131 NUP107 NUP107 NUP107 11465 -0.045 0.29 NO
132 EIF4G3 EIF4G3 EIF4G3 11609 -0.047 0.28 NO
133 NUP93 NUP93 NUP93 12060 -0.055 0.26 NO
134 NUP35 NUP35 NUP35 12071 -0.055 0.27 NO
135 IP6K2 IP6K2 IP6K2 12509 -0.064 0.25 NO
136 AAAS AAAS AAAS 12546 -0.064 0.25 NO
137 NUP188 NUP188 NUP188 12782 -0.07 0.24 NO
138 GBP7 GBP7 GBP7 12960 -0.074 0.24 NO
139 KPNA5 KPNA5 KPNA5 14470 -0.12 0.16 NO
140 NCAM1 NCAM1 NCAM1 15874 -0.2 0.1 NO
141 CAMK2A CAMK2A CAMK2A 17233 -0.36 0.053 NO

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

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

genes ES table in pathway: ST TUMOR NECROSIS FACTOR 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 GBP5 GBP5 GBP5 10 0.49 0.02 YES
2 IL2RA IL2RA IL2RA 35 0.43 0.037 YES
3 SOCS1 SOCS1 SOCS1 123 0.36 0.047 YES
4 TEC TEC TEC 130 0.35 0.062 YES
5 IL7R IL7R IL7R 174 0.33 0.074 YES
6 LCK LCK LCK 245 0.31 0.083 YES
7 CASP1 CASP1 CASP1 265 0.31 0.095 YES
8 IL7 IL7 IL7 302 0.3 0.11 YES
9 ISG20 ISG20 ISG20 368 0.28 0.11 YES
10 ICAM1 ICAM1 ICAM1 370 0.28 0.13 YES
11 NOD2 NOD2 NOD2 386 0.28 0.14 YES
12 GBP1 GBP1 GBP1 400 0.28 0.15 YES
13 IL2RB IL2RB IL2RB 409 0.28 0.16 YES
14 MAP3K8 MAP3K8 MAP3K8 432 0.27 0.17 YES
15 OASL OASL OASL 471 0.26 0.18 YES
16 CISH CISH CISH 584 0.25 0.18 YES
17 IL1R1 IL1R1 IL1R1 588 0.25 0.19 YES
18 SP100 SP100 SP100 625 0.24 0.2 YES
19 SOCS3 SOCS3 SOCS3 647 0.24 0.21 YES
20 IRF6 IRF6 IRF6 653 0.24 0.22 YES
21 IL1RN IL1RN IL1RN 720 0.23 0.23 YES
22 XAF1 XAF1 XAF1 730 0.23 0.24 YES
23 OAS1 OAS1 OAS1 735 0.23 0.25 YES
24 MT2A MT2A MT2A 818 0.22 0.25 YES
25 IRF1 IRF1 IRF1 842 0.22 0.26 YES
26 GBP2 GBP2 GBP2 843 0.22 0.27 YES
27 GBP4 GBP4 GBP4 862 0.21 0.28 YES
28 IFI35 IFI35 IFI35 911 0.21 0.28 YES
29 IL1R2 IL1R2 IL1R2 919 0.21 0.29 YES
30 IFITM3 IFITM3 IFITM3 922 0.21 0.3 YES
31 IL1A IL1A IL1A 925 0.21 0.31 YES
32 HLA-G HLA-G HLA-G 929 0.21 0.32 YES
33 CSF2RB CSF2RB CSF2RB 942 0.2 0.32 YES
34 IL2RG IL2RG IL2RG 1002 0.2 0.33 YES
35 NOD1 NOD1 NOD1 1052 0.2 0.34 YES
36 IFITM1 IFITM1 IFITM1 1088 0.19 0.34 YES
37 CIITA CIITA CIITA 1153 0.19 0.35 YES
38 IFNB1 IFNB1 IFNB1 1215 0.18 0.35 YES
39 SHC1 SHC1 SHC1 1217 0.18 0.36 YES
40 IFITM2 IFITM2 IFITM2 1221 0.18 0.37 YES
41 IRAK2 IRAK2 IRAK2 1255 0.18 0.37 YES
42 OAS2 OAS2 OAS2 1320 0.17 0.38 YES
43 IL6 IL6 IL6 1345 0.17 0.38 YES
44 HLA-F HLA-F HLA-F 1346 0.17 0.39 YES
45 VCAM1 VCAM1 VCAM1 1356 0.17 0.4 YES
46 PSMB8 PSMB8 PSMB8 1359 0.17 0.4 YES
47 SOCS2 SOCS2 SOCS2 1410 0.17 0.41 YES
48 CD44 CD44 CD44 1467 0.16 0.41 YES
49 HLA-DQA2 HLA-DQA2 HLA-DQA2 1482 0.16 0.42 YES
50 HLA-B HLA-B HLA-B 1562 0.16 0.42 YES
51 IRF7 IRF7 IRF7 1616 0.15 0.42 YES
52 JAK3 JAK3 JAK3 1656 0.15 0.43 YES
53 IL18 IL18 IL18 1701 0.15 0.43 YES
54 VAV1 VAV1 VAV1 1726 0.15 0.44 YES
55 MX2 MX2 MX2 1735 0.15 0.44 YES
56 HLA-DPB1 HLA-DPB1 HLA-DPB1 1738 0.14 0.45 YES
57 IL1B IL1B IL1B 1749 0.14 0.45 YES
58 FCGR1B FCGR1B FCGR1B 1788 0.14 0.46 YES
59 FCGR1A FCGR1A FCGR1A 1796 0.14 0.46 YES
60 LYN LYN LYN 1802 0.14 0.47 YES
61 MX1 MX1 MX1 1818 0.14 0.47 YES
62 PTPN2 PTPN2 PTPN2 1829 0.14 0.48 YES
63 HLA-DQA1 HLA-DQA1 HLA-DQA1 1858 0.14 0.48 YES
64 HLA-A HLA-A HLA-A 1936 0.14 0.48 YES
65 IL1RAP IL1RAP IL1RAP 1945 0.14 0.49 YES
66 GBP6 GBP6 GBP6 2001 0.13 0.49 YES
67 HLA-C HLA-C HLA-C 2002 0.13 0.5 YES
68 OAS3 OAS3 OAS3 2031 0.13 0.5 YES
69 HCK HCK HCK 2040 0.13 0.51 YES
70 IRAK3 IRAK3 IRAK3 2057 0.13 0.51 YES
71 STAT5A STAT5A STAT5A 2062 0.13 0.52 YES
72 HLA-DRB1 HLA-DRB1 HLA-DRB1 2099 0.13 0.52 YES
73 HLA-DPA1 HLA-DPA1 HLA-DPA1 2177 0.12 0.52 YES
74 HERC5 HERC5 HERC5 2201 0.12 0.52 YES
75 IFI6 IFI6 IFI6 2216 0.12 0.53 YES
76 B2M B2M B2M 2237 0.12 0.53 YES
77 IRF2 IRF2 IRF2 2250 0.12 0.54 YES
78 IFIT3 IFIT3 IFIT3 2321 0.12 0.54 YES
79 ISG15 ISG15 ISG15 2406 0.11 0.54 YES
80 NFKB2 NFKB2 NFKB2 2434 0.11 0.54 YES
81 PTPN6 PTPN6 PTPN6 2568 0.11 0.54 YES
82 IRF5 IRF5 IRF5 2602 0.1 0.54 YES
83 HLA-DRB5 HLA-DRB5 HLA-DRB5 2609 0.1 0.55 YES
84 PML PML PML 2671 0.1 0.55 YES
85 USP18 USP18 USP18 2746 0.1 0.55 YES
86 IFI27 IFI27 IFI27 2865 0.095 0.54 YES
87 NUP37 NUP37 NUP37 2881 0.094 0.55 YES
88 SQSTM1 SQSTM1 SQSTM1 2929 0.093 0.55 YES
89 IRF3 IRF3 IRF3 2930 0.093 0.55 YES
90 IFNGR2 IFNGR2 IFNGR2 2945 0.092 0.56 YES
91 DDX58 DDX58 DDX58 2961 0.092 0.56 YES
92 IRAK4 IRAK4 IRAK4 2965 0.092 0.56 YES
93 MYD88 MYD88 MYD88 2966 0.092 0.57 YES
94 CAMK2D CAMK2D CAMK2D 2989 0.091 0.57 YES
95 IRS2 IRS2 IRS2 3068 0.089 0.57 YES
96 SYK SYK SYK 3096 0.088 0.57 YES
97 TRAF6 TRAF6 TRAF6 3120 0.087 0.57 YES
98 RNASEL RNASEL RNASEL 3233 0.084 0.57 YES
99 EIF2AK2 EIF2AK2 EIF2AK2 3249 0.083 0.57 YES
100 UBA7 UBA7 UBA7 3300 0.082 0.57 YES
101 CSF2RA CSF2RA CSF2RA 3335 0.081 0.58 YES
102 UBE2L6 UBE2L6 UBE2L6 3377 0.08 0.58 YES
103 STAT1 STAT1 STAT1 3588 0.074 0.57 NO
104 IL6R IL6R IL6R 3625 0.073 0.57 NO
105 IRF9 IRF9 IRF9 3929 0.066 0.56 NO
106 PRKCD PRKCD PRKCD 4024 0.064 0.55 NO
107 PTK2B PTK2B PTK2B 4106 0.062 0.55 NO
108 PRLR PRLR PRLR 4152 0.062 0.55 NO
109 IFIT1 IFIT1 IFIT1 4217 0.06 0.55 NO
110 JAK2 JAK2 JAK2 4291 0.059 0.55 NO
111 IRF8 IRF8 IRF8 4376 0.057 0.55 NO
112 IFIT2 IFIT2 IFIT2 4379 0.057 0.55 NO
113 STAT2 STAT2 STAT2 4443 0.056 0.55 NO
114 RBX1 RBX1 RBX1 4469 0.056 0.55 NO
115 CUL1 CUL1 CUL1 4793 0.049 0.53 NO
116 RPS27A RPS27A RPS27A 4814 0.049 0.53 NO
117 IFNGR1 IFNGR1 IFNGR1 4825 0.049 0.54 NO
118 BLNK BLNK BLNK 4869 0.048 0.53 NO
119 STAT3 STAT3 STAT3 4888 0.047 0.54 NO
120 ADAM17 ADAM17 ADAM17 5060 0.044 0.53 NO
121 NUP54 NUP54 NUP54 5268 0.041 0.52 NO
122 UBA52 UBA52 UBA52 5368 0.039 0.51 NO
123 IFNAR1 IFNAR1 IFNAR1 5373 0.039 0.52 NO
124 TRIM25 TRIM25 TRIM25 5375 0.039 0.52 NO
125 IRF4 IRF4 IRF4 5419 0.039 0.52 NO
126 SKP1 SKP1 SKP1 5672 0.035 0.5 NO
127 SEH1L SEH1L SEH1L 5798 0.033 0.5 NO
128 IRAK1 IRAK1 IRAK1 5877 0.032 0.5 NO
129 IL6ST IL6ST IL6ST 5887 0.032 0.5 NO
130 KPNA4 KPNA4 KPNA4 5937 0.031 0.5 NO
131 NEDD4 NEDD4 NEDD4 6001 0.03 0.49 NO
132 PIK3CD PIK3CD PIK3CD 6029 0.03 0.49 NO
133 TNIP2 TNIP2 TNIP2 6064 0.029 0.49 NO
134 EIF4E EIF4E EIF4E 6085 0.029 0.49 NO
135 EIF4A3 EIF4A3 EIF4A3 6289 0.026 0.48 NO
136 IKBKB IKBKB IKBKB 6382 0.025 0.48 NO
137 IKBKG IKBKG IKBKG 6526 0.023 0.47 NO
138 IFNAR2 IFNAR2 IFNAR2 6583 0.022 0.47 NO
139 UBE2E1 UBE2E1 UBE2E1 6799 0.02 0.46 NO
140 SUMO1 SUMO1 SUMO1 6841 0.019 0.46 NO
141 EIF4G2 EIF4G2 EIF4G2 7026 0.016 0.45 NO
142 RIPK2 RIPK2 RIPK2 7049 0.016 0.45 NO
143 YWHAZ YWHAZ YWHAZ 7211 0.014 0.44 NO
144 NUP205 NUP205 NUP205 7244 0.014 0.44 NO
145 EIF4A1 EIF4A1 EIF4A1 7254 0.013 0.44 NO
146 GRB2 GRB2 GRB2 7292 0.013 0.44 NO
147 PTPN1 PTPN1 PTPN1 7394 0.012 0.43 NO
148 YES1 YES1 YES1 7401 0.012 0.43 NO
149 PTAFR PTAFR PTAFR 7479 0.011 0.43 NO
150 NRAS NRAS NRAS 7535 0.01 0.42 NO
151 NUP210 NUP210 NUP210 7550 0.01 0.42 NO
152 HRAS HRAS HRAS 7626 0.009 0.42 NO
153 PIK3CB PIK3CB PIK3CB 7628 0.0089 0.42 NO
154 NUP85 NUP85 NUP85 7654 0.0085 0.42 NO
155 TAB2 TAB2 TAB2 7665 0.0083 0.42 NO
156 CRK CRK CRK 7833 0.0062 0.41 NO
157 ARIH1 ARIH1 ARIH1 7927 0.0051 0.4 NO
158 TYK2 TYK2 TYK2 7945 0.0049 0.4 NO
159 RELA RELA RELA 8026 0.0039 0.4 NO
160 EIF4E2 EIF4E2 EIF4E2 8072 0.0033 0.4 NO
161 EGR1 EGR1 EGR1 8093 0.0031 0.4 NO
162 CHUK CHUK CHUK 8196 0.0016 0.39 NO
163 UBE2N UBE2N UBE2N 8230 0.0011 0.39 NO
164 NUP62 NUP62 NUP62 8292 0.00031 0.38 NO
165 ADAR ADAR ADAR 8365 -0.00047 0.38 NO
166 RAE1 RAE1 RAE1 8366 -0.00047 0.38 NO
167 RANBP2 RANBP2 RANBP2 8482 -0.002 0.38 NO
168 PIK3CA PIK3CA PIK3CA 8531 -0.0027 0.37 NO
169 CAMK2B CAMK2B CAMK2B 8549 -0.003 0.37 NO
170 TPR TPR TPR 8560 -0.0031 0.37 NO
171 EIF4E3 EIF4E3 EIF4E3 8575 -0.0034 0.37 NO
172 EIF4A2 EIF4A2 EIF4A2 8744 -0.0054 0.36 NO
173 EIF4G1 EIF4G1 EIF4G1 8834 -0.0066 0.36 NO
174 PIN1 PIN1 PIN1 8836 -0.0066 0.36 NO
175 TOLLIP TOLLIP TOLLIP 8857 -0.0068 0.36 NO
176 IL3RA IL3RA IL3RA 8932 -0.0078 0.35 NO
177 MAP2K1 MAP2K1 MAP2K1 8969 -0.0081 0.35 NO
178 PIAS1 PIAS1 PIAS1 8974 -0.0082 0.35 NO
179 PLCG1 PLCG1 PLCG1 9029 -0.0089 0.35 NO
180 NUPL2 NUPL2 NUPL2 9113 -0.0099 0.34 NO
181 INPPL1 INPPL1 INPPL1 9176 -0.011 0.34 NO
182 MAP3K7 MAP3K7 MAP3K7 9323 -0.013 0.33 NO
183 NUP50 NUP50 NUP50 9358 -0.013 0.33 NO
184 KPNB1 KPNB1 KPNB1 9366 -0.013 0.33 NO
185 NUP153 NUP153 NUP153 9385 -0.014 0.33 NO
186 MAPK3 MAPK3 MAPK3 9399 -0.014 0.33 NO
187 FLNB FLNB FLNB 9566 -0.016 0.32 NO
188 NUP155 NUP155 NUP155 9674 -0.018 0.32 NO
189 MAP2K2 MAP2K2 MAP2K2 9725 -0.018 0.32 NO
190 JAK1 JAK1 JAK1 9768 -0.019 0.31 NO
191 MAPK1 MAPK1 MAPK1 9826 -0.02 0.31 NO
192 TAB1 TAB1 TAB1 10033 -0.023 0.3 NO
193 KPNA2 KPNA2 KPNA2 10084 -0.023 0.3 NO
194 KPNA1 KPNA1 KPNA1 10115 -0.024 0.3 NO
195 NUPL1 NUPL1 NUPL1 10158 -0.024 0.3 NO
196 NUP133 NUP133 NUP133 10239 -0.025 0.29 NO
197 IFNG IFNG IFNG 10336 -0.026 0.29 NO
198 POM121 POM121 POM121 10381 -0.027 0.29 NO
199 KPNA3 KPNA3 KPNA3 10418 -0.028 0.29 NO
200 YWHAB YWHAB YWHAB 10422 -0.028 0.29 NO
201 CDK1 CDK1 CDK1 10503 -0.029 0.28 NO
202 PPM1B PPM1B PPM1B 10550 -0.03 0.28 NO
203 STAT5B STAT5B STAT5B 10664 -0.031 0.28 NO
204 HGF HGF HGF 10779 -0.033 0.27 NO
205 IL5RA IL5RA IL5RA 10893 -0.035 0.27 NO
206 NUP88 NUP88 NUP88 10911 -0.035 0.27 NO
207 IRS1 IRS1 IRS1 11046 -0.037 0.26 NO
208 MAP3K3 MAP3K3 MAP3K3 11151 -0.039 0.26 NO
209 TAB3 TAB3 TAB3 11157 -0.039 0.26 NO
210 NUP214 NUP214 NUP214 11172 -0.039 0.26 NO
211 NUP43 NUP43 NUP43 11364 -0.043 0.25 NO
212 KRAS KRAS KRAS 11412 -0.044 0.25 NO
213 NUP107 NUP107 NUP107 11465 -0.045 0.25 NO
214 EIF4G3 EIF4G3 EIF4G3 11609 -0.047 0.25 NO
215 SOS1 SOS1 SOS1 11782 -0.05 0.24 NO
216 MAP2K6 MAP2K6 MAP2K6 11839 -0.051 0.24 NO
217 NUP93 NUP93 NUP93 12060 -0.055 0.23 NO
218 NUP35 NUP35 NUP35 12071 -0.055 0.23 NO
219 RAPGEF1 RAPGEF1 RAPGEF1 12092 -0.056 0.23 NO
220 CRKL CRKL CRKL 12099 -0.056 0.23 NO
221 GAB2 GAB2 GAB2 12194 -0.057 0.23 NO
222 SH2B1 SH2B1 SH2B1 12250 -0.058 0.23 NO
223 RAF1 RAF1 RAF1 12385 -0.061 0.22 NO
224 PELI2 PELI2 PELI2 12468 -0.063 0.22 NO
225 CBL CBL CBL 12478 -0.063 0.22 NO
226 IP6K2 IP6K2 IP6K2 12509 -0.064 0.22 NO
227 PIK3R1 PIK3R1 PIK3R1 12536 -0.064 0.23 NO
228 AAAS AAAS AAAS 12546 -0.064 0.23 NO
229 NUP188 NUP188 NUP188 12782 -0.07 0.22 NO
230 PRKACB PRKACB PRKACB 12789 -0.07 0.22 NO
231 PELI3 PELI3 PELI3 12840 -0.071 0.22 NO
232 GBP7 GBP7 GBP7 12960 -0.074 0.22 NO
233 PIK3R2 PIK3R2 PIK3R2 13126 -0.079 0.21 NO
234 PELI1 PELI1 PELI1 13646 -0.093 0.19 NO
235 FYN FYN FYN 13731 -0.096 0.19 NO
236 MAP2K4 MAP2K4 MAP2K4 13766 -0.097 0.19 NO
237 GHR GHR GHR 14098 -0.11 0.18 NO
238 IL5 IL5 IL5 14401 -0.12 0.16 NO
239 KPNA5 KPNA5 KPNA5 14470 -0.12 0.16 NO
240 PIK3R3 PIK3R3 PIK3R3 14862 -0.14 0.15 NO
241 BTRC BTRC BTRC 14930 -0.14 0.15 NO
242 TMEM189-UBE2V1 TMEM189-UBE2V1 TMEM189-UBE2V1 15064 -0.15 0.15 NO
243 NCAM1 NCAM1 NCAM1 15874 -0.2 0.11 NO
244 CAMK2A CAMK2A CAMK2A 17233 -0.36 0.053 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: ST TUMOR NECROSIS FACTOR PATHWAY.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: ST TUMOR NECROSIS FACTOR 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 SYNDECAN 4 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BIRC3 BIRC3 BIRC3 183 0.33 0.062 YES
2 CASP7 CASP7 CASP7 504 0.26 0.1 YES
3 FAS FAS FAS 543 0.26 0.15 YES
4 CASP8 CASP8 CASP8 590 0.25 0.2 YES
5 FASLG FASLG FASLG 824 0.22 0.24 YES
6 TRADD TRADD TRADD 1110 0.19 0.26 YES
7 TNFRSF1A TNFRSF1A TNFRSF1A 1333 0.17 0.29 YES
8 CASP6 CASP6 CASP6 1465 0.16 0.32 YES
9 TNFRSF1B TNFRSF1B TNFRSF1B 1751 0.14 0.33 YES
10 NFKBIA NFKBIA NFKBIA 1772 0.14 0.36 YES
11 LMNA LMNA LMNA 1956 0.13 0.38 YES
12 CFLAR CFLAR CFLAR 2266 0.12 0.39 YES
13 ARHGDIB ARHGDIB ARHGDIB 2715 0.1 0.39 YES
14 TRAF1 TRAF1 TRAF1 2819 0.097 0.4 YES
15 PSEN2 PSEN2 PSEN2 2882 0.094 0.42 YES
16 RIPK1 RIPK1 RIPK1 3235 0.084 0.42 YES
17 CASP3 CASP3 CASP3 3365 0.08 0.43 YES
18 NFKB1 NFKB1 NFKB1 3531 0.075 0.44 YES
19 PRKCD PRKCD PRKCD 4024 0.064 0.42 NO
20 FADD FADD FADD 4758 0.05 0.39 NO
21 CYCS CYCS CYCS 4958 0.046 0.39 NO
22 MAP3K14 MAP3K14 MAP3K14 5365 0.04 0.38 NO
23 RB1 RB1 RB1 5473 0.038 0.38 NO
24 BIRC2 BIRC2 BIRC2 5922 0.031 0.36 NO
25 MAP3K5 MAP3K5 MAP3K5 6130 0.029 0.36 NO
26 RASA1 RASA1 RASA1 6139 0.028 0.36 NO
27 GSN GSN GSN 6581 0.022 0.34 NO
28 ACTG1 ACTG1 ACTG1 6714 0.021 0.34 NO
29 XIAP XIAP XIAP 6825 0.019 0.34 NO
30 BAG4 BAG4 BAG4 7246 0.013 0.32 NO
31 DFFA DFFA DFFA 7663 0.0083 0.3 NO
32 CRADD CRADD CRADD 7692 0.0078 0.3 NO
33 RELA RELA RELA 8026 0.0039 0.28 NO
34 BID BID BID 8078 0.0032 0.28 NO
35 DAXX DAXX DAXX 8185 0.0017 0.27 NO
36 CHUK CHUK CHUK 8196 0.0016 0.27 NO
37 PAK2 PAK2 PAK2 8301 0.0002 0.27 NO
38 PSEN1 PSEN1 PSEN1 8732 -0.0053 0.24 NO
39 CDK11B CDK11B CDK11B 9611 -0.017 0.2 NO
40 CASP2 CASP2 CASP2 9854 -0.02 0.19 NO
41 PRKDC PRKDC PRKDC 10163 -0.024 0.18 NO
42 MDM2 MDM2 MDM2 10254 -0.025 0.18 NO
43 BCL2 BCL2 BCL2 10322 -0.026 0.18 NO
44 TRAF2 TRAF2 TRAF2 10411 -0.028 0.18 NO
45 PARP1 PARP1 PARP1 11036 -0.037 0.16 NO
46 CDK11A CDK11A CDK11A 11153 -0.039 0.16 NO
47 MAP2K7 MAP2K7 MAP2K7 12049 -0.055 0.12 NO
48 PTK2 PTK2 PTK2 12222 -0.058 0.12 NO
49 CASP9 CASP9 CASP9 12543 -0.064 0.12 NO
50 SPTAN1 SPTAN1 SPTAN1 12695 -0.068 0.12 NO
51 NUMA1 NUMA1 NUMA1 12980 -0.075 0.12 NO
52 MAP3K1 MAP3K1 MAP3K1 13045 -0.076 0.14 NO
53 TNF TNF TNF 13181 -0.08 0.15 NO
54 APAF1 APAF1 APAF1 13410 -0.086 0.15 NO
55 DFFB DFFB DFFB 13633 -0.093 0.16 NO
56 LMNB2 LMNB2 LMNB2 13881 -0.1 0.17 NO
57 LMNB1 LMNB1 LMNB1 14904 -0.14 0.14 NO
58 MAPK8 MAPK8 MAPK8 15394 -0.17 0.15 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 SYNDECAN 4 PATHWAY.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: PID SYNDECAN 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 HIVNEFPATHWAY

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 THBS1 THBS1 THBS1 159 0.34 0.094 YES
2 ADAM12 ADAM12 ADAM12 247 0.31 0.18 YES
3 FZD7 FZD7 FZD7 258 0.31 0.28 YES
4 CCL5 CCL5 CCL5 275 0.3 0.37 YES
5 SDC4 SDC4 SDC4 310 0.3 0.46 YES
6 ITGA5 ITGA5 ITGA5 1235 0.18 0.46 YES
7 TNC TNC TNC 1527 0.16 0.5 YES
8 CXCR4 CXCR4 CXCR4 1649 0.15 0.53 YES
9 LAMA3 LAMA3 LAMA3 2356 0.11 0.53 YES
10 LAMA1 LAMA1 LAMA1 2383 0.11 0.56 YES
11 ACTN1 ACTN1 ACTN1 2397 0.11 0.6 YES
12 ITGB1 ITGB1 ITGB1 2784 0.098 0.6 YES
13 MDK MDK MDK 2797 0.098 0.64 YES
14 FGFR1 FGFR1 FGFR1 2992 0.091 0.65 YES
15 FN1 FN1 FN1 3025 0.09 0.68 YES
16 FGF2 FGF2 FGF2 3292 0.082 0.69 YES
17 MMP9 MMP9 MMP9 3514 0.076 0.7 YES
18 SDCBP SDCBP SDCBP 3951 0.065 0.7 YES
19 PRKCD PRKCD PRKCD 4024 0.064 0.71 YES
20 TFPI TFPI TFPI 4391 0.057 0.71 NO
21 RAC1 RAC1 RAC1 5790 0.033 0.64 NO
22 RHOA RHOA RHOA 6157 0.028 0.63 NO
23 CXCL12 CXCL12 CXCL12 7882 0.0055 0.54 NO
24 GIPC1 GIPC1 GIPC1 8309 0.00013 0.51 NO
25 DNM2 DNM2 DNM2 8852 -0.0068 0.48 NO
26 NUDT16L1 NUDT16L1 NUDT16L1 8934 -0.0078 0.48 NO
27 PRKCA PRKCA PRKCA 10635 -0.031 0.4 NO
28 PTK2 PTK2 PTK2 12222 -0.058 0.33 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 HIVNEFPATHWAY.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: PID HIVNEFPATHWAY, 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 ANTIGEN PROCESSING CROSS PRESENTATION

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 KDELR3 KDELR3 KDELR3 9 0.49 0.095 YES
2 CCL2 CCL2 CCL2 142 0.35 0.16 YES
3 PDIA5 PDIA5 PDIA5 530 0.26 0.18 YES
4 IL8 IL8 IL8 696 0.23 0.22 YES
5 WIPI1 WIPI1 WIPI1 1124 0.19 0.23 YES
6 SHC1 SHC1 SHC1 1217 0.18 0.26 YES
7 LMNA LMNA LMNA 1956 0.13 0.25 YES
8 IGFBP1 IGFBP1 IGFBP1 2137 0.12 0.26 YES
9 CUL7 CUL7 CUL7 2255 0.12 0.28 YES
10 ATF3 ATF3 ATF3 2554 0.11 0.28 YES
11 FKBP14 FKBP14 FKBP14 2599 0.1 0.3 YES
12 TPP1 TPP1 TPP1 2689 0.1 0.32 YES
13 XBP1 XBP1 XBP1 2856 0.095 0.33 YES
14 C19orf10 C19orf10 C19orf10 2952 0.092 0.34 YES
15 PDIA6 PDIA6 PDIA6 3034 0.09 0.35 YES
16 DNAJC3 DNAJC3 DNAJC3 3211 0.085 0.36 YES
17 DNAJB9 DNAJB9 DNAJB9 3258 0.083 0.37 YES
18 HERPUD1 HERPUD1 HERPUD1 3321 0.081 0.39 YES
19 CALR CALR CALR 3362 0.08 0.4 YES
20 HSPA5 HSPA5 HSPA5 3560 0.074 0.4 YES
21 HSP90B1 HSP90B1 HSP90B1 3878 0.067 0.4 NO
22 EDEM1 EDEM1 EDEM1 4050 0.063 0.4 NO
23 EIF2S1 EIF2S1 EIF2S1 5489 0.038 0.33 NO
24 SRPRB SRPRB SRPRB 5676 0.035 0.33 NO
25 YIF1A YIF1A YIF1A 5785 0.033 0.33 NO
26 PREB PREB PREB 5844 0.032 0.33 NO
27 TLN1 TLN1 TLN1 6008 0.03 0.33 NO
28 SSR1 SSR1 SSR1 6042 0.03 0.33 NO
29 SRPR SRPR SRPR 6070 0.029 0.34 NO
30 SERP1 SERP1 SERP1 6164 0.028 0.34 NO
31 DNAJB11 DNAJB11 DNAJB11 6232 0.027 0.34 NO
32 SEC31A SEC31A SEC31A 6247 0.027 0.34 NO
33 EIF2AK3 EIF2AK3 EIF2AK3 6291 0.026 0.34 NO
34 ATF6 ATF6 ATF6 6353 0.026 0.35 NO
35 PARN PARN PARN 6395 0.025 0.35 NO
36 EXOSC4 EXOSC4 EXOSC4 6522 0.023 0.35 NO
37 ERN1 ERN1 ERN1 6643 0.022 0.34 NO
38 ACADVL ACADVL ACADVL 6660 0.021 0.35 NO
39 ATF4 ATF4 ATF4 6833 0.019 0.34 NO
40 MBTPS2 MBTPS2 MBTPS2 7037 0.016 0.33 NO
41 EXTL3 EXTL3 EXTL3 7296 0.013 0.32 NO
42 EXOSC3 EXOSC3 EXOSC3 7895 0.0053 0.29 NO
43 HDGF HDGF HDGF 8031 0.0037 0.28 NO
44 DIS3 DIS3 DIS3 8082 0.0032 0.28 NO
45 NFYB NFYB NFYB 8326 -0.000051 0.27 NO
46 GOSR2 GOSR2 GOSR2 8362 -0.00041 0.27 NO
47 EXOSC9 EXOSC9 EXOSC9 8486 -0.0021 0.26 NO
48 EXOSC1 EXOSC1 EXOSC1 8721 -0.0052 0.25 NO
49 ATP6V0D1 ATP6V0D1 ATP6V0D1 9210 -0.011 0.22 NO
50 DCP2 DCP2 DCP2 9386 -0.014 0.22 NO
51 SYVN1 SYVN1 SYVN1 9398 -0.014 0.22 NO
52 HYOU1 HYOU1 HYOU1 9520 -0.015 0.21 NO
53 EXOSC8 EXOSC8 EXOSC8 9636 -0.017 0.21 NO
54 EXOSC5 EXOSC5 EXOSC5 9801 -0.019 0.21 NO
55 WFS1 WFS1 WFS1 9907 -0.021 0.2 NO
56 MBTPS1 MBTPS1 MBTPS1 9968 -0.022 0.2 NO
57 GSK3A GSK3A GSK3A 9973 -0.022 0.21 NO
58 EXOSC7 EXOSC7 EXOSC7 9975 -0.022 0.21 NO
59 EXOSC6 EXOSC6 EXOSC6 10330 -0.026 0.2 NO
60 TATDN2 TATDN2 TATDN2 11198 -0.04 0.16 NO
61 CXXC1 CXXC1 CXXC1 11351 -0.043 0.16 NO
62 ASNS ASNS ASNS 11422 -0.044 0.16 NO
63 DDIT3 DDIT3 DDIT3 11536 -0.046 0.17 NO
64 ADD1 ADD1 ADD1 11652 -0.048 0.17 NO
65 KHSRP KHSRP KHSRP 11800 -0.05 0.17 NO
66 EXOSC2 EXOSC2 EXOSC2 12107 -0.056 0.16 NO
67 ARFGAP1 ARFGAP1 ARFGAP1 12391 -0.061 0.16 NO
68 DCTN1 DCTN1 DCTN1 12402 -0.061 0.17 NO
69 ZBTB17 ZBTB17 ZBTB17 12409 -0.062 0.18 NO
70 PPP2R5B PPP2R5B PPP2R5B 12580 -0.065 0.19 NO
71 KLHDC3 KLHDC3 KLHDC3 12828 -0.071 0.19 NO
72 DDX11 DDX11 DDX11 13106 -0.078 0.19 NO
73 NFYA NFYA NFYA 13542 -0.09 0.18 NO
74 TSPYL2 TSPYL2 TSPYL2 14508 -0.12 0.15 NO
75 CTDSP2 CTDSP2 CTDSP2 14659 -0.13 0.17 NO
76 SULT1A3 SULT1A3 SULT1A3 14744 -0.13 0.19 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: REACTOME ANTIGEN PROCESSING CROSS PRESENTATION.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ANTIGEN PROCESSING CROSS PRESENTATION, 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 TRIF MEDIATED TLR3 SIGNALING

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 MRC1 MRC1 MRC1 330 0.29 0.029 YES
2 PSMB9 PSMB9 PSMB9 785 0.22 0.039 YES
3 NCF4 NCF4 NCF4 859 0.21 0.069 YES
4 HLA-G HLA-G HLA-G 929 0.21 0.098 YES
5 MRC2 MRC2 MRC2 993 0.2 0.13 YES
6 PSMA8 PSMA8 PSMA8 1282 0.18 0.14 YES
7 HLA-F HLA-F HLA-F 1346 0.17 0.16 YES
8 PSMB8 PSMB8 PSMB8 1359 0.17 0.19 YES
9 LNPEP LNPEP LNPEP 1438 0.16 0.21 YES
10 SEC61G SEC61G SEC61G 1453 0.16 0.24 YES
11 TAP1 TAP1 TAP1 1457 0.16 0.26 YES
12 CTSS CTSS CTSS 1463 0.16 0.29 YES
13 HLA-B HLA-B HLA-B 1562 0.16 0.31 YES
14 NCF2 NCF2 NCF2 1719 0.15 0.32 YES
15 CD36 CD36 CD36 1746 0.14 0.34 YES
16 FCGR1B FCGR1B FCGR1B 1788 0.14 0.36 YES
17 FCGR1A FCGR1A FCGR1A 1796 0.14 0.39 YES
18 PSME2 PSME2 PSME2 1836 0.14 0.41 YES
19 CYBA CYBA CYBA 1905 0.14 0.42 YES
20 HLA-A HLA-A HLA-A 1936 0.14 0.44 YES
21 HLA-C HLA-C HLA-C 2002 0.13 0.46 YES
22 PSMB10 PSMB10 PSMB10 2076 0.13 0.48 YES
23 PSME1 PSME1 PSME1 2122 0.12 0.5 YES
24 B2M B2M B2M 2237 0.12 0.51 YES
25 ITGB5 ITGB5 ITGB5 2352 0.12 0.52 YES
26 CYBB CYBB CYBB 2414 0.11 0.53 YES
27 PDIA3 PDIA3 PDIA3 2549 0.11 0.54 YES
28 ITGAV ITGAV ITGAV 3162 0.086 0.52 YES
29 PSMA3 PSMA3 PSMA3 3190 0.085 0.54 YES
30 CALR CALR CALR 3362 0.08 0.54 YES
31 TAP2 TAP2 TAP2 3577 0.074 0.54 YES
32 PSMD9 PSMD9 PSMD9 3737 0.07 0.54 YES
33 PSMA2 PSMA2 PSMA2 3851 0.068 0.55 YES
34 PSMA5 PSMA5 PSMA5 4155 0.062 0.54 YES
35 PSMC2 PSMC2 PSMC2 4308 0.058 0.54 YES
36 PSMA1 PSMA1 PSMA1 4313 0.058 0.55 YES
37 PSMA6 PSMA6 PSMA6 4433 0.056 0.55 YES
38 PSMD12 PSMD12 PSMD12 4527 0.055 0.56 YES
39 PSMD5 PSMD5 PSMD5 4617 0.053 0.56 YES
40 RPS27A RPS27A RPS27A 4814 0.049 0.56 YES
41 PSMC1 PSMC1 PSMC1 4846 0.048 0.56 YES
42 PSMD13 PSMD13 PSMD13 4991 0.046 0.56 YES
43 PSMB4 PSMB4 PSMB4 5187 0.042 0.56 YES
44 PSMC6 PSMC6 PSMC6 5270 0.041 0.56 YES
45 PSMA7 PSMA7 PSMA7 5322 0.04 0.56 YES
46 UBA52 UBA52 UBA52 5368 0.039 0.57 YES
47 PSMD8 PSMD8 PSMD8 5794 0.033 0.55 NO
48 SEC61B SEC61B SEC61B 5902 0.031 0.55 NO
49 PSMD14 PSMD14 PSMD14 5988 0.03 0.55 NO
50 PSMA4 PSMA4 PSMA4 6126 0.029 0.54 NO
51 SEC61A1 SEC61A1 SEC61A1 6152 0.028 0.55 NO
52 PSMB1 PSMB1 PSMB1 6205 0.028 0.55 NO
53 PSMB3 PSMB3 PSMB3 6310 0.026 0.55 NO
54 PSMC4 PSMC4 PSMC4 6646 0.022 0.53 NO
55 PSMD7 PSMD7 PSMD7 7009 0.017 0.52 NO
56 PSMD10 PSMD10 PSMD10 7092 0.015 0.51 NO
57 PSMC3 PSMC3 PSMC3 7111 0.015 0.51 NO
58 PSMB5 PSMB5 PSMB5 7215 0.014 0.51 NO
59 PSMF1 PSMF1 PSMF1 7369 0.012 0.5 NO
60 PSMB2 PSMB2 PSMB2 7675 0.008 0.49 NO
61 PSMD4 PSMD4 PSMD4 7689 0.0078 0.49 NO
62 PSMC5 PSMC5 PSMC5 7811 0.0064 0.48 NO
63 PSME4 PSME4 PSME4 7818 0.0064 0.48 NO
64 PSMD6 PSMD6 PSMD6 8392 -0.00078 0.45 NO
65 PSMB6 PSMB6 PSMB6 8569 -0.0032 0.44 NO
66 PSMD2 PSMD2 PSMD2 8995 -0.0084 0.42 NO
67 PSMD11 PSMD11 PSMD11 9211 -0.011 0.41 NO
68 PSMD1 PSMD1 PSMD1 9297 -0.012 0.41 NO
69 PSMD3 PSMD3 PSMD3 10820 -0.034 0.33 NO
70 PSMB7 PSMB7 PSMB7 10852 -0.034 0.33 NO
71 CD207 CD207 CD207 15860 -0.2 0.09 NO
72 SEC61A2 SEC61A2 SEC61A2 16349 -0.24 0.1 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: REACTOME TRIF MEDIATED TLR3 SIGNALING.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRIF MEDIATED TLR3 SIGNALING, 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 ACTIVATION OF CHAPERONE GENES BY XBP1S

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 SAA1 SAA1 SAA1 332 0.29 0.035 YES
2 NOD2 NOD2 NOD2 386 0.28 0.084 YES
3 DUSP4 DUSP4 DUSP4 407 0.28 0.13 YES
4 NOD1 NOD1 NOD1 1052 0.2 0.13 YES
5 ZBP1 ZBP1 ZBP1 1082 0.19 0.17 YES
6 TLR3 TLR3 TLR3 1208 0.18 0.19 YES
7 IRAK2 IRAK2 IRAK2 1255 0.18 0.22 YES
8 S100A12 S100A12 S100A12 1378 0.17 0.25 YES
9 RIPK3 RIPK3 RIPK3 1409 0.17 0.28 YES
10 IKBKE IKBKE IKBKE 1539 0.16 0.3 YES
11 IRF7 IRF7 IRF7 1616 0.15 0.32 YES
12 NFKBIA NFKBIA NFKBIA 1772 0.14 0.34 YES
13 TICAM1 TICAM1 TICAM1 2151 0.12 0.34 YES
14 NFKB2 NFKB2 NFKB2 2434 0.11 0.34 YES
15 RPS6KA1 RPS6KA1 RPS6KA1 2700 0.1 0.35 YES
16 IRF3 IRF3 IRF3 2930 0.093 0.35 YES
17 MAP2K3 MAP2K3 MAP2K3 3048 0.09 0.36 YES
18 TRAF6 TRAF6 TRAF6 3120 0.087 0.38 YES
19 ATF1 ATF1 ATF1 3192 0.085 0.39 YES
20 RIPK1 RIPK1 RIPK1 3235 0.084 0.4 YES
21 TBK1 TBK1 TBK1 3485 0.076 0.4 YES
22 DUSP6 DUSP6 DUSP6 3580 0.074 0.41 YES
23 RPS6KA3 RPS6KA3 RPS6KA3 3739 0.07 0.41 YES
24 MAPKAPK3 MAPKAPK3 MAPKAPK3 3879 0.067 0.42 YES
25 MAPKAPK2 MAPKAPK2 MAPKAPK2 3942 0.066 0.43 YES
26 JUN JUN JUN 4557 0.054 0.4 NO
27 DUSP3 DUSP3 DUSP3 4683 0.052 0.4 NO
28 RPS27A RPS27A RPS27A 4814 0.049 0.41 NO
29 APP APP APP 5104 0.044 0.4 NO
30 FOS FOS FOS 5212 0.042 0.4 NO
31 UBA52 UBA52 UBA52 5368 0.039 0.4 NO
32 IRAK1 IRAK1 IRAK1 5877 0.032 0.38 NO
33 IKBKB IKBKB IKBKB 6382 0.025 0.35 NO
34 IKBKG IKBKG IKBKG 6526 0.023 0.35 NO
35 MAPK14 MAPK14 MAPK14 6661 0.021 0.35 NO
36 RIPK2 RIPK2 RIPK2 7049 0.016 0.33 NO
37 MEF2A MEF2A MEF2A 7263 0.013 0.32 NO
38 NFKBIB NFKBIB NFKBIB 7427 0.012 0.31 NO
39 TAB2 TAB2 TAB2 7665 0.0083 0.3 NO
40 PPP2CA PPP2CA PPP2CA 7667 0.0082 0.3 NO
41 ELK1 ELK1 ELK1 7683 0.0079 0.3 NO
42 HMGB1 HMGB1 HMGB1 7967 0.0046 0.29 NO
43 RELA RELA RELA 8026 0.0039 0.28 NO
44 PPP2CB PPP2CB PPP2CB 8069 0.0033 0.28 NO
45 CHUK CHUK CHUK 8196 0.0016 0.28 NO
46 S100B S100B S100B 8291 0.00031 0.27 NO
47 ATF2 ATF2 ATF2 8388 -0.00072 0.27 NO
48 MAP2K1 MAP2K1 MAP2K1 8969 -0.0081 0.24 NO
49 MAP3K7 MAP3K7 MAP3K7 9323 -0.013 0.22 NO
50 MAPK3 MAPK3 MAPK3 9399 -0.014 0.22 NO
51 PPP2R1B PPP2R1B PPP2R1B 9706 -0.018 0.2 NO
52 MAP2K2 MAP2K2 MAP2K2 9725 -0.018 0.2 NO
53 MAPK1 MAPK1 MAPK1 9826 -0.02 0.2 NO
54 CREB1 CREB1 CREB1 9879 -0.02 0.2 NO
55 RPS6KA2 RPS6KA2 RPS6KA2 9920 -0.021 0.21 NO
56 PPP2R1A PPP2R1A PPP2R1A 9983 -0.022 0.21 NO
57 TAB1 TAB1 TAB1 10033 -0.023 0.21 NO
58 CDK1 CDK1 CDK1 10503 -0.029 0.19 NO
59 MAPK7 MAPK7 MAPK7 10816 -0.034 0.18 NO
60 MAPK9 MAPK9 MAPK9 10848 -0.034 0.18 NO
61 TAB3 TAB3 TAB3 11157 -0.039 0.17 NO
62 MEF2C MEF2C MEF2C 11217 -0.04 0.18 NO
63 MAP2K6 MAP2K6 MAP2K6 11839 -0.051 0.15 NO
64 MAP2K7 MAP2K7 MAP2K7 12049 -0.055 0.15 NO
65 PPP2R5D PPP2R5D PPP2R5D 12406 -0.061 0.14 NO
66 MAPK11 MAPK11 MAPK11 12420 -0.062 0.15 NO
67 MAP2K4 MAP2K4 MAP2K4 13766 -0.097 0.094 NO
68 DUSP7 DUSP7 DUSP7 14700 -0.13 0.066 NO
69 MAPK10 MAPK10 MAPK10 15005 -0.15 0.076 NO
70 MAPK8 MAPK8 MAPK8 15394 -0.17 0.086 NO
71 AGER AGER AGER 15533 -0.18 0.11 NO
72 RPS6KA5 RPS6KA5 RPS6KA5 15776 -0.2 0.13 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: REACTOME ACTIVATION OF CHAPERONE GENES BY XBP1S.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF CHAPERONE GENES BY XBP1S, 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM 31 genes.ES.table 0.54 1.5 0.031 0.2 0.96 0.26 0.15 0.22 0.13 0.012
KEGG O GLYCAN BIOSYNTHESIS 30 genes.ES.table 0.66 1.7 0 0.15 0.84 0.17 0.022 0.16 0.078 0.017
KEGG INOSITOL PHOSPHATE METABOLISM 53 genes.ES.table 0.47 1.6 0.026 0.16 0.92 0.51 0.31 0.35 0.092 0.013
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES 25 genes.ES.table 0.62 1.6 0.016 0.17 0.94 0.28 0.078 0.26 0.1 0.013
KEGG BUTANOATE METABOLISM 30 genes.ES.table 0.53 1.6 0.034 0.19 0.95 0.47 0.28 0.33 0.11 0.013
KEGG MAPK SIGNALING PATHWAY 252 genes.ES.table 0.48 1.7 0.0021 0.15 0.78 0.3 0.23 0.23 0.069 0.021
KEGG ERBB SIGNALING PATHWAY 86 genes.ES.table 0.48 1.7 0.0019 0.16 0.73 0.15 0.11 0.14 0.066 0.025
KEGG CALCIUM SIGNALING PATHWAY 172 genes.ES.table 0.66 1.7 0 0.16 0.72 0.38 0.14 0.33 0.065 0.028
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM 73 genes.ES.table 0.57 1.8 0.0042 0.28 0.52 0.55 0.3 0.38 0.092 0.066
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION 241 genes.ES.table 0.66 1.6 0 0.16 0.9 0.46 0.16 0.39 0.092 0.016
genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE 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 CAMK2A CAMK2A CAMK2A 102 0.79 0.24 YES
2 CAMK2B CAMK2B CAMK2B 546 0.41 0.34 YES
3 PRKCB PRKCB PRKCB 576 0.4 0.46 YES
4 STAT4 STAT4 STAT4 842 0.32 0.54 YES
5 CAMK2G CAMK2G CAMK2G 2070 0.18 0.53 YES
6 PTK2B PTK2B PTK2B 2348 0.16 0.56 YES
7 CALM1 CALM1 CALM1 3455 0.1 0.53 NO
8 MAPT MAPT MAPT 3761 0.094 0.54 NO
9 PRKCA PRKCA PRKCA 3986 0.087 0.56 NO
10 CALM3 CALM3 CALM3 5028 0.062 0.52 NO
11 AGT AGT AGT 5168 0.059 0.53 NO
12 MAPK3 MAPK3 MAPK3 5591 0.051 0.52 NO
13 PLCG1 PLCG1 PLCG1 5688 0.049 0.53 NO
14 MAP2K1 MAP2K1 MAP2K1 5877 0.046 0.53 NO
15 STAT2 STAT2 STAT2 5990 0.044 0.54 NO
16 MAPK1 MAPK1 MAPK1 6398 0.038 0.53 NO
17 CAMK2D CAMK2D CAMK2D 6931 0.031 0.51 NO
18 HRAS HRAS HRAS 7361 0.025 0.49 NO
19 GNA11 GNA11 GNA11 7699 0.021 0.48 NO
20 SOS1 SOS1 SOS1 7754 0.021 0.48 NO
21 FYN FYN FYN 8397 0.014 0.45 NO
22 STAT5B STAT5B STAT5B 8438 0.013 0.46 NO
23 JAK2 JAK2 JAK2 9264 0.0044 0.41 NO
24 STAT5A STAT5A STAT5A 9391 0.0032 0.4 NO
25 MAP2K2 MAP2K2 MAP2K2 9418 0.003 0.4 NO
26 STAT1 STAT1 STAT1 9429 0.0028 0.4 NO
27 STAT6 STAT6 STAT6 9713 0.00028 0.39 NO
28 GRB2 GRB2 GRB2 9969 -0.002 0.38 NO
29 CALM2 CALM2 CALM2 10046 -0.0028 0.37 NO
30 MYLK MYLK MYLK 10486 -0.0072 0.35 NO
31 GNB1 GNB1 GNB1 10611 -0.0083 0.35 NO
32 STAT3 STAT3 STAT3 10983 -0.012 0.33 NO
33 MAPK8 MAPK8 MAPK8 11395 -0.016 0.31 NO
34 RAF1 RAF1 RAF1 11525 -0.017 0.31 NO
35 MAPK14 MAPK14 MAPK14 12406 -0.026 0.27 NO
36 CDK5 CDK5 CDK5 12648 -0.028 0.26 NO
37 GNAI1 GNAI1 GNAI1 15188 -0.062 0.14 NO
38 SHC1 SHC1 SHC1 15576 -0.07 0.14 NO

Figure S41.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

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

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

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 GRIN1 GRIN1 GRIN1 25 0.99 0.13 YES
2 CAMK2A CAMK2A CAMK2A 102 0.79 0.24 YES
3 RASGRF1 RASGRF1 RASGRF1 167 0.7 0.33 YES
4 NEFL NEFL NEFL 203 0.65 0.41 YES
5 GRIN2A GRIN2A GRIN2A 284 0.56 0.48 YES
6 CAMK4 CAMK4 CAMK4 379 0.49 0.55 YES
7 RASGRF2 RASGRF2 RASGRF2 452 0.46 0.6 YES
8 CAMK2B CAMK2B CAMK2B 546 0.41 0.65 YES
9 CAMKK1 CAMKK1 CAMKK1 560 0.4 0.71 YES
10 GRIN2C GRIN2C GRIN2C 740 0.35 0.74 YES
11 ACTN2 ACTN2 ACTN2 1167 0.26 0.76 YES
12 ADCY1 ADCY1 ADCY1 1227 0.26 0.79 YES
13 GRIN2B GRIN2B GRIN2B 3305 0.11 0.69 NO
14 CALM1 CALM1 CALM1 3455 0.1 0.7 NO
15 RPS6KA6 RPS6KA6 RPS6KA6 3612 0.099 0.7 NO
16 GRIN2D GRIN2D GRIN2D 3874 0.09 0.7 NO
17 RPS6KA2 RPS6KA2 RPS6KA2 4404 0.076 0.68 NO
18 PDPK1 PDPK1 PDPK1 4524 0.073 0.68 NO
19 PRKACB PRKACB PRKACB 4583 0.071 0.69 NO
20 CALM3 CALM3 CALM3 5028 0.062 0.67 NO
21 MAPK1 MAPK1 MAPK1 6398 0.038 0.6 NO
22 ADCY3 ADCY3 ADCY3 6537 0.036 0.6 NO
23 CAMK2D CAMK2D CAMK2D 6931 0.031 0.58 NO
24 HRAS HRAS HRAS 7361 0.025 0.56 NO
25 ADCY8 ADCY8 ADCY8 7557 0.023 0.55 NO
26 AKAP9 AKAP9 AKAP9 8653 0.011 0.5 NO
27 RPS6KA3 RPS6KA3 RPS6KA3 9176 0.0052 0.47 NO
28 CALM2 CALM2 CALM2 10046 -0.0028 0.42 NO
29 CREB1 CREB1 CREB1 10811 -0.01 0.38 NO
30 RAF1 RAF1 RAF1 11525 -0.017 0.34 NO
31 BRAF BRAF BRAF 14260 -0.048 0.2 NO
32 RPS6KA1 RPS6KA1 RPS6KA1 15195 -0.062 0.16 NO
33 RRAS RRAS RRAS 15850 -0.076 0.13 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 O GLYCAN BIOSYNTHESIS.

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

genes ES table in pathway: KEGG INOSITOL PHOSPHATE 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 GRIN1 GRIN1 GRIN1 25 0.99 0.16 YES
2 CAMK2A CAMK2A CAMK2A 102 0.79 0.29 YES
3 RASGRF1 RASGRF1 RASGRF1 167 0.7 0.4 YES
4 NEFL NEFL NEFL 203 0.65 0.5 YES
5 GRIN2A GRIN2A GRIN2A 284 0.56 0.59 YES
6 RASGRF2 RASGRF2 RASGRF2 452 0.46 0.65 YES
7 CAMK2B CAMK2B CAMK2B 546 0.41 0.72 YES
8 GRIN2C GRIN2C GRIN2C 740 0.35 0.76 YES
9 ACTN2 ACTN2 ACTN2 1167 0.26 0.78 YES
10 GRIN2B GRIN2B GRIN2B 3305 0.11 0.68 NO
11 CALM1 CALM1 CALM1 3455 0.1 0.69 NO
12 RPS6KA6 RPS6KA6 RPS6KA6 3612 0.099 0.7 NO
13 GRIN2D GRIN2D GRIN2D 3874 0.09 0.7 NO
14 RPS6KA2 RPS6KA2 RPS6KA2 4404 0.076 0.68 NO
15 PDPK1 PDPK1 PDPK1 4524 0.073 0.69 NO
16 CALM3 CALM3 CALM3 5028 0.062 0.67 NO
17 MAPK1 MAPK1 MAPK1 6398 0.038 0.6 NO
18 CAMK2D CAMK2D CAMK2D 6931 0.031 0.58 NO
19 HRAS HRAS HRAS 7361 0.025 0.56 NO
20 AKAP9 AKAP9 AKAP9 8653 0.011 0.49 NO
21 RPS6KA3 RPS6KA3 RPS6KA3 9176 0.0052 0.46 NO
22 CALM2 CALM2 CALM2 10046 -0.0028 0.41 NO
23 CREB1 CREB1 CREB1 10811 -0.01 0.37 NO
24 RAF1 RAF1 RAF1 11525 -0.017 0.34 NO
25 BRAF BRAF BRAF 14260 -0.048 0.19 NO
26 RPS6KA1 RPS6KA1 RPS6KA1 15195 -0.062 0.15 NO
27 RRAS RRAS RRAS 15850 -0.076 0.13 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 INOSITOL PHOSPHATE METABOLISM.

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

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

Table 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 DYNC1I1 DYNC1I1 DYNC1I1 682 0.36 0.1 YES
2 CREB3L3 CREB3L3 CREB3L3 726 0.35 0.23 YES
3 AQP3 AQP3 AQP3 2336 0.16 0.2 YES
4 AQP2 AQP2 AQP2 2436 0.15 0.26 YES
5 VAMP2 VAMP2 VAMP2 2571 0.14 0.3 YES
6 NSF NSF NSF 2975 0.12 0.33 YES
7 AQP4 AQP4 AQP4 3382 0.11 0.34 YES
8 CREB3L1 CREB3L1 CREB3L1 3640 0.098 0.37 YES
9 DYNC2H1 DYNC2H1 DYNC2H1 4277 0.079 0.36 YES
10 DYNC1LI2 DYNC1LI2 DYNC1LI2 4365 0.076 0.39 YES
11 DYNLL2 DYNLL2 DYNLL2 4463 0.074 0.41 YES
12 PRKACB PRKACB PRKACB 4583 0.071 0.43 YES
13 DYNC1H1 DYNC1H1 DYNC1H1 4633 0.07 0.45 YES
14 CREB5 CREB5 CREB5 5128 0.06 0.45 NO
15 DCTN1 DCTN1 DCTN1 5942 0.045 0.42 NO
16 RAB11B RAB11B RAB11B 6447 0.038 0.41 NO
17 RAB5B RAB5B RAB5B 6484 0.037 0.42 NO
18 ADCY3 ADCY3 ADCY3 6537 0.036 0.43 NO
19 ADCY6 ADCY6 ADCY6 6683 0.035 0.44 NO
20 RAB5A RAB5A RAB5A 6813 0.033 0.44 NO
21 DYNC2LI1 DYNC2LI1 DYNC2LI1 6848 0.032 0.45 NO
22 GNAS GNAS GNAS 7760 0.02 0.41 NO
23 ADCY9 ADCY9 ADCY9 7958 0.018 0.41 NO
24 PRKX PRKX PRKX 8035 0.018 0.41 NO
25 PRKACA PRKACA PRKACA 8454 0.013 0.39 NO
26 DCTN6 DCTN6 DCTN6 8993 0.0073 0.36 NO
27 DYNC1I2 DYNC1I2 DYNC1I2 9659 0.00083 0.33 NO
28 RAB11A RAB11A RAB11A 9792 -0.00041 0.32 NO
29 ARHGDIA ARHGDIA ARHGDIA 10808 -0.01 0.27 NO
30 CREB1 CREB1 CREB1 10811 -0.01 0.27 NO
31 DCTN4 DCTN4 DCTN4 10843 -0.01 0.27 NO
32 DYNC1LI1 DYNC1LI1 DYNC1LI1 11023 -0.012 0.27 NO
33 DCTN2 DCTN2 DCTN2 11124 -0.013 0.27 NO
34 STX4 STX4 STX4 11141 -0.013 0.27 NO
35 RAB5C RAB5C RAB5C 11488 -0.017 0.26 NO
36 DCTN5 DCTN5 DCTN5 12096 -0.023 0.24 NO
37 DYNLL1 DYNLL1 DYNLL1 12475 -0.027 0.22 NO
38 CREB3 CREB3 CREB3 13082 -0.033 0.2 NO
39 AVPR2 AVPR2 AVPR2 13880 -0.043 0.18 NO
40 CREB3L2 CREB3L2 CREB3L2 14276 -0.048 0.17 NO
41 CREB3L4 CREB3L4 CREB3L4 14726 -0.054 0.17 NO
42 ARHGDIB ARHGDIB ARHGDIB 15179 -0.062 0.17 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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

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

genes ES table in pathway: KEGG BUTANOATE 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 GRIN1 GRIN1 GRIN1 25 0.99 0.13 YES
2 NEFM NEFM NEFM 70 0.84 0.24 YES
3 NEFL NEFL NEFL 203 0.65 0.31 YES
4 NEFH NEFH NEFH 204 0.65 0.4 YES
5 GRIN2A GRIN2A GRIN2A 284 0.56 0.47 YES
6 PRPH2 PRPH2 PRPH2 659 0.37 0.5 YES
7 GRIN2C GRIN2C GRIN2C 740 0.35 0.54 YES
8 NOS1 NOS1 NOS1 763 0.34 0.58 YES
9 SLC1A2 SLC1A2 SLC1A2 1091 0.28 0.6 YES
10 CHP2 CHP2 CHP2 1322 0.24 0.62 YES
11 GRIA2 GRIA2 GRIA2 2112 0.17 0.6 NO
12 GRIN2B GRIN2B GRIN2B 3305 0.11 0.54 NO
13 TNF TNF TNF 3509 0.1 0.55 NO
14 MAP3K5 MAP3K5 MAP3K5 3600 0.1 0.55 NO
15 GRIA1 GRIA1 GRIA1 3678 0.097 0.56 NO
16 BCL2 BCL2 BCL2 3703 0.096 0.57 NO
17 GRIN2D GRIN2D GRIN2D 3874 0.09 0.58 NO
18 PPP3CB PPP3CB PPP3CB 3935 0.088 0.58 NO
19 MAPK11 MAPK11 MAPK11 4023 0.086 0.59 NO
20 PPP3CA PPP3CA PPP3CA 4465 0.074 0.58 NO
21 PPP3R1 PPP3R1 PPP3R1 4511 0.073 0.58 NO
22 CHP CHP CHP 6725 0.034 0.47 NO
23 RAB5A RAB5A RAB5A 6813 0.033 0.46 NO
24 CCS CCS CCS 7074 0.029 0.46 NO
25 ALS2 ALS2 ALS2 7127 0.029 0.46 NO
26 PRPH PRPH PRPH 7659 0.022 0.43 NO
27 CASP9 CASP9 CASP9 7802 0.02 0.42 NO
28 TP53 TP53 TP53 8157 0.016 0.41 NO
29 SOD1 SOD1 SOD1 8865 0.0085 0.37 NO
30 MAPK12 MAPK12 MAPK12 9600 0.0014 0.33 NO
31 BCL2L1 BCL2L1 BCL2L1 10080 -0.0031 0.3 NO
32 APAF1 APAF1 APAF1 10237 -0.0046 0.29 NO
33 RAC1 RAC1 RAC1 10594 -0.0082 0.28 NO
34 BAD BAD BAD 11291 -0.015 0.24 NO
35 CAT CAT CAT 11346 -0.015 0.24 NO
36 MAP2K3 MAP2K3 MAP2K3 11467 -0.017 0.23 NO
37 TOMM40L TOMM40L TOMM40L 11804 -0.02 0.22 NO
38 MAPK14 MAPK14 MAPK14 12406 -0.026 0.19 NO
39 TNFRSF1A TNFRSF1A TNFRSF1A 12945 -0.032 0.16 NO
40 CASP3 CASP3 CASP3 12984 -0.032 0.16 NO
41 CYCS CYCS CYCS 13150 -0.034 0.16 NO
42 TOMM40 TOMM40 TOMM40 13453 -0.038 0.15 NO
43 GPX1 GPX1 GPX1 14255 -0.047 0.11 NO
44 BAX BAX BAX 14456 -0.05 0.11 NO
45 DAXX DAXX DAXX 14538 -0.051 0.11 NO
46 PPP3CC PPP3CC PPP3CC 14614 -0.052 0.11 NO
47 DERL1 DERL1 DERL1 14895 -0.057 0.1 NO
48 CASP1 CASP1 CASP1 15097 -0.06 0.099 NO
49 MAP2K6 MAP2K6 MAP2K6 15709 -0.073 0.075 NO
50 BID BID BID 16013 -0.081 0.069 NO
51 TNFRSF1B TNFRSF1B TNFRSF1B 16273 -0.091 0.067 NO
52 PPP3R2 PPP3R2 PPP3R2 16669 -0.11 0.059 NO
53 MAPK13 MAPK13 MAPK13 17650 -0.19 0.03 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 BUTANOATE METABOLISM.

Figure S50.  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 MAPK SIGNALING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 576 0.4 0.16 YES
2 EGFR EGFR EGFR 1945 0.18 0.18 YES
3 PTK2B PTK2B PTK2B 2348 0.16 0.23 YES
4 CALM1 CALM1 CALM1 3455 0.1 0.22 YES
5 MEF2C MEF2C MEF2C 3698 0.096 0.26 YES
6 PAK1 PAK1 PAK1 3710 0.096 0.3 YES
7 GNAQ GNAQ GNAQ 3851 0.091 0.34 YES
8 PRKCA PRKCA PRKCA 3986 0.087 0.37 YES
9 MEF2D MEF2D MEF2D 4688 0.069 0.37 YES
10 MEF2A MEF2A MEF2A 4838 0.066 0.39 YES
11 MAP2K4 MAP2K4 MAP2K4 4955 0.063 0.42 YES
12 CALM3 CALM3 CALM3 5028 0.062 0.44 YES
13 AGT AGT AGT 5168 0.059 0.46 YES
14 MAPK3 MAPK3 MAPK3 5591 0.051 0.46 YES
15 MAP2K1 MAP2K1 MAP2K1 5877 0.046 0.47 YES
16 ELK1 ELK1 ELK1 6322 0.039 0.46 YES
17 MAPK1 MAPK1 MAPK1 6398 0.038 0.48 YES
18 MAP3K1 MAP3K1 MAP3K1 7315 0.026 0.44 NO
19 HRAS HRAS HRAS 7361 0.025 0.45 NO
20 SOS1 SOS1 SOS1 7754 0.021 0.44 NO
21 PTK2 PTK2 PTK2 7999 0.018 0.44 NO
22 MAP2K2 MAP2K2 MAP2K2 9418 0.003 0.36 NO
23 GRB2 GRB2 GRB2 9969 -0.002 0.33 NO
24 CALM2 CALM2 CALM2 10046 -0.0028 0.33 NO
25 RAC1 RAC1 RAC1 10594 -0.0082 0.3 NO
26 MAPK8 MAPK8 MAPK8 11395 -0.016 0.26 NO
27 RAF1 RAF1 RAF1 11525 -0.017 0.26 NO
28 ATF2 ATF2 ATF2 11699 -0.019 0.26 NO
29 JUN JUN JUN 11722 -0.019 0.27 NO
30 SRC SRC SRC 12696 -0.029 0.23 NO
31 SHC1 SHC1 SHC1 15576 -0.07 0.11 NO
32 AGTR1 AGTR1 AGTR1 15698 -0.073 0.14 NO

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

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

genes ES table in pathway: KEGG ERBB SIGNALING PATHWAY

Table S27.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SNAP25 SNAP25 SNAP25 257 0.59 0.17 YES
2 STX1B STX1B STX1B 504 0.43 0.29 YES
3 STX1A STX1A STX1A 666 0.37 0.4 YES
4 VAMP1 VAMP1 VAMP1 974 0.29 0.48 YES
5 STX19 STX19 STX19 1746 0.2 0.5 YES
6 VAMP2 VAMP2 VAMP2 2571 0.14 0.5 YES
7 TSNARE1 TSNARE1 TSNARE1 3277 0.11 0.5 NO
8 STX17 STX17 STX17 4881 0.065 0.43 NO
9 STX16 STX16 STX16 5726 0.049 0.4 NO
10 VTI1B VTI1B VTI1B 6736 0.034 0.35 NO
11 STX7 STX7 STX7 7023 0.03 0.34 NO
12 SNAP47 SNAP47 SNAP47 7701 0.021 0.31 NO
13 STX3 STX3 STX3 8007 0.018 0.3 NO
14 STX2 STX2 STX2 9267 0.0043 0.24 NO
15 USE1 USE1 USE1 9769 -0.00025 0.21 NO
16 YKT6 YKT6 YKT6 10047 -0.0028 0.19 NO
17 GOSR1 GOSR1 GOSR1 10068 -0.003 0.19 NO
18 VAMP4 VAMP4 VAMP4 10099 -0.0032 0.19 NO
19 VTI1A VTI1A VTI1A 10985 -0.012 0.15 NO
20 SNAP23 SNAP23 SNAP23 11130 -0.013 0.14 NO
21 STX4 STX4 STX4 11141 -0.013 0.15 NO
22 STX12 STX12 STX12 11215 -0.014 0.15 NO
23 BET1L BET1L BET1L 11221 -0.014 0.15 NO
24 STX18 STX18 STX18 11356 -0.016 0.15 NO
25 STX6 STX6 STX6 11433 -0.016 0.15 NO
26 GOSR2 GOSR2 GOSR2 11501 -0.017 0.15 NO
27 VAMP3 VAMP3 VAMP3 11815 -0.02 0.14 NO
28 STX5 STX5 STX5 12339 -0.025 0.12 NO
29 SNAP29 SNAP29 SNAP29 12378 -0.026 0.13 NO
30 STX10 STX10 STX10 13486 -0.038 0.077 NO
31 VAMP7 VAMP7 VAMP7 13897 -0.043 0.068 NO
32 SEC22B SEC22B SEC22B 14044 -0.045 0.074 NO
33 VAMP5 VAMP5 VAMP5 14085 -0.045 0.086 NO
34 STX8 STX8 STX8 14268 -0.048 0.091 NO
35 BET1 BET1 BET1 15409 -0.066 0.049 NO
36 BNIP1 BNIP1 BNIP1 16352 -0.094 0.027 NO
37 STX11 STX11 STX11 16685 -0.11 0.043 NO
38 VAMP8 VAMP8 VAMP8 16976 -0.13 0.067 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 ERBB SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG CALCIUM SIGNALING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 86 0.82 0.11 YES
2 CDS1 CDS1 CDS1 424 0.46 0.15 YES
3 INPP5J INPP5J INPP5J 545 0.41 0.2 YES
4 DGKE DGKE DGKE 566 0.4 0.25 YES
5 PRKCB PRKCB PRKCB 576 0.4 0.31 YES
6 PIP5K1B PIP5K1B PIP5K1B 773 0.34 0.34 YES
7 ITPKA ITPKA ITPKA 937 0.3 0.38 YES
8 CALML6 CALML6 CALML6 1245 0.25 0.39 YES
9 SYNJ2 SYNJ2 SYNJ2 1907 0.19 0.38 YES
10 DGKZ DGKZ DGKZ 2397 0.15 0.38 YES
11 INPP4B INPP4B INPP4B 2420 0.15 0.4 YES
12 DGKB DGKB DGKB 2447 0.15 0.41 YES
13 SYNJ1 SYNJ1 SYNJ1 2777 0.13 0.41 YES
14 PI4KA PI4KA PI4KA 2811 0.13 0.43 YES
15 INPP5A INPP5A INPP5A 3006 0.12 0.44 YES
16 PIK3C2B PIK3C2B PIK3C2B 3227 0.11 0.44 YES
17 ITPR1 ITPR1 ITPR1 3257 0.11 0.45 YES
18 ITPK1 ITPK1 ITPK1 3262 0.11 0.47 YES
19 DGKQ DGKQ DGKQ 3402 0.11 0.47 YES
20 CALM1 CALM1 CALM1 3455 0.1 0.49 YES
21 PLCB4 PLCB4 PLCB4 3556 0.1 0.49 YES
22 ITPKB ITPKB ITPKB 3602 0.099 0.5 YES
23 INPP5D INPP5D INPP5D 3606 0.099 0.52 YES
24 PLCD1 PLCD1 PLCD1 3719 0.095 0.52 YES
25 PLCE1 PLCE1 PLCE1 3933 0.089 0.52 YES
26 PRKCA PRKCA PRKCA 3986 0.087 0.53 YES
27 PLCB2 PLCB2 PLCB2 4194 0.081 0.53 YES
28 PIP5K1C PIP5K1C PIP5K1C 4309 0.078 0.54 YES
29 INPP4A INPP4A INPP4A 4334 0.077 0.55 YES
30 ITPR2 ITPR2 ITPR2 4594 0.071 0.54 YES
31 INPP5E INPP5E INPP5E 4663 0.07 0.55 YES
32 PIK3R1 PIK3R1 PIK3R1 4716 0.068 0.56 YES
33 PIP4K2A PIP4K2A PIP4K2A 4823 0.066 0.56 YES
34 CALM3 CALM3 CALM3 5028 0.062 0.56 YES
35 PLCD4 PLCD4 PLCD4 5080 0.061 0.56 YES
36 INPP1 INPP1 INPP1 5153 0.059 0.56 YES
37 PIKFYVE PIKFYVE PIKFYVE 5255 0.057 0.57 YES
38 PIK3CB PIK3CB PIK3CB 5294 0.056 0.57 YES
39 PLCD3 PLCD3 PLCD3 5439 0.054 0.57 YES
40 PIP4K2B PIP4K2B PIP4K2B 5552 0.052 0.57 YES
41 PLCG1 PLCG1 PLCG1 5688 0.049 0.57 NO
42 PIK3C2A PIK3C2A PIK3C2A 5917 0.046 0.56 NO
43 DGKG DGKG DGKG 6221 0.041 0.55 NO
44 INPPL1 INPPL1 INPPL1 6237 0.04 0.56 NO
45 PIP4K2C PIP4K2C PIP4K2C 6456 0.038 0.55 NO
46 ITPR3 ITPR3 ITPR3 6508 0.037 0.55 NO
47 PLCB1 PLCB1 PLCB1 6644 0.035 0.55 NO
48 IMPA1 IMPA1 IMPA1 6646 0.035 0.56 NO
49 IPPK IPPK IPPK 7379 0.025 0.52 NO
50 INPP5K INPP5K INPP5K 7393 0.025 0.52 NO
51 INPP5B INPP5B INPP5B 8632 0.011 0.46 NO
52 CDIPT CDIPT CDIPT 8760 0.0095 0.45 NO
53 PIK3CD PIK3CD PIK3CD 8902 0.0082 0.44 NO
54 DGKA DGKA DGKA 8924 0.008 0.44 NO
55 DGKD DGKD DGKD 9223 0.0047 0.43 NO
56 PI4KB PI4KB PI4KB 9246 0.0045 0.43 NO
57 PLCG2 PLCG2 PLCG2 9917 -0.0015 0.39 NO
58 CALM2 CALM2 CALM2 10046 -0.0028 0.38 NO
59 OCRL OCRL OCRL 10097 -0.0032 0.38 NO
60 PLCB3 PLCB3 PLCB3 10256 -0.0048 0.37 NO
61 PTEN PTEN PTEN 10752 -0.0095 0.35 NO
62 PIK3C2G PIK3C2G PIK3C2G 11198 -0.014 0.32 NO
63 PIK3R2 PIK3R2 PIK3R2 11487 -0.017 0.31 NO
64 CDS2 CDS2 CDS2 12170 -0.024 0.28 NO
65 PIP5K1A PIP5K1A PIP5K1A 12763 -0.03 0.25 NO
66 PIK3C3 PIK3C3 PIK3C3 12906 -0.031 0.24 NO
67 PIK3R5 PIK3R5 PIK3R5 13102 -0.034 0.24 NO
68 PIK3R3 PIK3R3 PIK3R3 13190 -0.035 0.24 NO
69 PIK3CG PIK3CG PIK3CG 13533 -0.038 0.22 NO
70 IMPA2 IMPA2 IMPA2 13633 -0.04 0.22 NO
71 PIK3CA PIK3CA PIK3CA 14929 -0.057 0.16 NO
72 DGKI DGKI DGKI 15779 -0.075 0.12 NO
73 DGKH DGKH DGKH 15872 -0.077 0.13 NO

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

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

genes ES table in pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

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 RASAL1 RASAL1 RASAL1 43 0.94 0.18 YES
2 RASGRF1 RASGRF1 RASGRF1 167 0.7 0.31 YES
3 RASGRF2 RASGRF2 RASGRF2 452 0.46 0.38 YES
4 CAMK2B CAMK2B CAMK2B 546 0.41 0.46 YES
5 PRKCB PRKCB PRKCB 576 0.4 0.54 YES
6 RASGRP1 RASGRP1 RASGRP1 804 0.33 0.59 YES
7 PRKCZ PRKCZ PRKCZ 979 0.29 0.64 YES
8 RIN1 RIN1 RIN1 2158 0.17 0.61 YES
9 PRKCE PRKCE PRKCE 2224 0.16 0.63 YES
10 SYNGAP1 SYNGAP1 SYNGAP1 2836 0.13 0.63 YES
11 RASGRP2 RASGRP2 RASGRP2 2939 0.12 0.64 YES
12 RASA4 RASA4 RASA4 3002 0.12 0.67 YES
13 RASGRP3 RASGRP3 RASGRP3 3212 0.11 0.68 YES
14 PLCE1 PLCE1 PLCE1 3933 0.089 0.65 NO
15 PRKCA PRKCA PRKCA 3986 0.087 0.67 NO
16 NF1 NF1 NF1 5309 0.056 0.61 NO
17 DAB2IP DAB2IP DAB2IP 5539 0.052 0.6 NO
18 HRAS HRAS HRAS 7361 0.025 0.51 NO
19 SOS2 SOS2 SOS2 7454 0.024 0.51 NO
20 RASA1 RASA1 RASA1 7565 0.023 0.51 NO
21 RASGRP4 RASGRP4 RASGRP4 7663 0.022 0.51 NO
22 SOS1 SOS1 SOS1 7754 0.021 0.5 NO
23 KRAS KRAS KRAS 8756 0.0095 0.45 NO
24 RABGEF1 RABGEF1 RABGEF1 8992 0.0073 0.44 NO
25 GRB2 GRB2 GRB2 9969 -0.002 0.39 NO
26 RASA2 RASA2 RASA2 10207 -0.0044 0.37 NO
27 NRAS NRAS NRAS 14931 -0.057 0.13 NO
28 RRAS RRAS RRAS 15850 -0.076 0.09 NO
29 LGALS3 LGALS3 LGALS3 16427 -0.097 0.077 NO
30 LGALS1 LGALS1 LGALS1 16547 -0.1 0.091 NO

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

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, 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 NEUROACTIVE LIGAND RECEPTOR INTERACTION

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 PRKCG PRKCG PRKCG 86 0.82 0.17 YES
2 CAMK4 CAMK4 CAMK4 379 0.49 0.26 YES
3 PRKCB PRKCB PRKCB 576 0.4 0.34 YES
4 AKAP5 AKAP5 AKAP5 667 0.37 0.42 YES
5 PRKCZ PRKCZ PRKCZ 979 0.29 0.46 YES
6 RCAN2 RCAN2 RCAN2 1196 0.26 0.51 YES
7 PRKCE PRKCE PRKCE 2224 0.16 0.48 YES
8 BCL2 BCL2 BCL2 3703 0.096 0.42 YES
9 PPP3CB PPP3CB PPP3CB 3935 0.088 0.43 YES
10 PRKCA PRKCA PRKCA 3986 0.087 0.45 YES
11 NFATC2 NFATC2 NFATC2 3992 0.087 0.47 YES
12 PPP3CA PPP3CA PPP3CA 4465 0.074 0.46 YES
13 PPP3R1 PPP3R1 PPP3R1 4511 0.073 0.47 YES
14 PRKCQ PRKCQ PRKCQ 4542 0.072 0.48 YES
15 MEF2D MEF2D MEF2D 4688 0.069 0.49 YES
16 PRKCD PRKCD PRKCD 4774 0.067 0.5 YES
17 YWHAH YWHAH YWHAH 4805 0.066 0.51 YES
18 MAPK9 MAPK9 MAPK9 5530 0.052 0.48 NO
19 MAPK3 MAPK3 MAPK3 5591 0.051 0.49 NO
20 PRKCH PRKCH PRKCH 6170 0.041 0.47 NO
21 FKBP8 FKBP8 FKBP8 6568 0.036 0.46 NO
22 CREBBP CREBBP CREBBP 6652 0.035 0.46 NO
23 CHP CHP CHP 6725 0.034 0.46 NO
24 YWHAB YWHAB YWHAB 7180 0.028 0.44 NO
25 YWHAG YWHAG YWHAG 7301 0.026 0.44 NO
26 MAP3K1 MAP3K1 MAP3K1 7315 0.026 0.45 NO
27 NR4A1 NR4A1 NR4A1 7815 0.02 0.42 NO
28 NFATC1 NFATC1 NFATC1 8342 0.014 0.4 NO
29 SFN SFN SFN 8404 0.013 0.4 NO
30 PRKACA PRKACA PRKACA 8454 0.013 0.4 NO
31 GSK3B GSK3B GSK3B 8842 0.0088 0.38 NO
32 CABIN1 CABIN1 CABIN1 8978 0.0074 0.37 NO
33 NUP214 NUP214 NUP214 8984 0.0074 0.37 NO
34 NFATC3 NFATC3 NFATC3 9356 0.0036 0.35 NO
35 CSNK2A1 CSNK2A1 CSNK2A1 9647 0.00097 0.34 NO
36 BCL2L1 BCL2L1 BCL2L1 10080 -0.0031 0.32 NO
37 YWHAZ YWHAZ YWHAZ 10456 -0.0068 0.3 NO
38 PIM1 PIM1 PIM1 10471 -0.007 0.3 NO
39 EP300 EP300 EP300 10585 -0.0081 0.29 NO
40 YWHAE YWHAE YWHAE 11033 -0.012 0.27 NO
41 FKBP1A FKBP1A FKBP1A 11216 -0.014 0.26 NO
42 KPNB1 KPNB1 KPNB1 11250 -0.014 0.26 NO
43 BAD BAD BAD 11291 -0.015 0.27 NO
44 YWHAQ YWHAQ YWHAQ 11358 -0.016 0.26 NO
45 MAPK8 MAPK8 MAPK8 11395 -0.016 0.27 NO
46 XPO1 XPO1 XPO1 12253 -0.024 0.22 NO
47 MAPK14 MAPK14 MAPK14 12406 -0.026 0.22 NO
48 CSNK1A1 CSNK1A1 CSNK1A1 12868 -0.031 0.2 NO
49 CASP3 CASP3 CASP3 12984 -0.032 0.2 NO
50 RAN RAN RAN 13972 -0.044 0.16 NO
51 BAX BAX BAX 14456 -0.05 0.14 NO
52 KPNA2 KPNA2 KPNA2 16103 -0.084 0.071 NO
53 RCAN1 RCAN1 RCAN1 16110 -0.084 0.089 NO
54 MAP3K8 MAP3K8 MAP3K8 16840 -0.12 0.074 NO

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

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION, 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 = GBM-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = GBM-TP.mergedcluster.txt

GSEA analysis

For the Gene Set Enrichment Analysis (GSEA), Broad GSEA-P-R.1.0 version is used with class2: canonical pathways geneses from MSigDB. Further details about statistics are available inThe Broad GSEA website.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Subramanian, A. et al, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles., Proc. Natl. Acad. Sci. USA 102(43) (2005)
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