GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LGG-TP
Brain Lower Grade Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1TX3DTP
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 LGG-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1TX3DTP
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 "LGG-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: 516
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 5 :[ clus1 ] 130
pheno.type: 2 - 5 :[ clus2 ] 115
pheno.type: 3 - 5 :[ clus3 ] 106
pheno.type: 4 - 5 :[ clus4 ] 135
pheno.type: 5 - 5 :[ clus5 ] 30

For the expression subtypes of 18334 genes in 517 samples, GSEA found enriched gene sets in each cluster using 516 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG RIBOSOME, KEGG SPLICEOSOME, KEGG NOTCH SIGNALING PATHWAY, PID HDAC CLASSI PATHWAY, PID AR NONGENOMIC PATHWAY, REACTOME TRANSLATION, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

    • And common core enriched genes are EIF4B, RPS6, AKT2, CAB39L, EEF2K, EIF4EBP1, MLST8, MTOR, PDE3B, PPM1A

  • clus2

    • Top enriched gene sets are KEGG PYRIMIDINE METABOLISM, KEGG N GLYCAN BIOSYNTHESIS, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG DNA REPLICATION, KEGG PROTEASOME, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CELL CYCLE, KEGG P53 SIGNALING PATHWAY

    • And common core enriched genes are IKBKE, IRF3, DDX58, HERC5, IFIH1, IRF7, ISG15, NFKB2, NFKBIB, NLRC5

  • clus3

    • Top enriched gene sets are KEGG RIBOSOME, BIOCARTA CARM ER PATHWAY, PID HDAC CLASSII PATHWAY, PID RET PATHWAY, PID BMPPATHWAY, REACTOME TRANSLATION, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, REACTOME MITOCHONDRIAL PROTEIN IMPORT, REACTOME SIGNALLING TO ERKS, REACTOME PI3K AKT ACTIVATION

    • And common core enriched genes are HDAC10, HDAC4, HDAC9, ERCC3, GTF2F1, ANKRA2, CAMK4, GATA1, GATA2, GNG2

  • clus4

    • Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG PURINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG ARGININE AND PROLINE METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG GLYCEROLIPID METABOLISM, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG GLYCEROPHOSPHOLIPID METABOLISM, KEGG PYRUVATE METABOLISM

    • And common core enriched genes are CALM1, CALM2, CALM3, MAP2K1, MAPK1, MAPK3, ADCY1, ADCY2, ADCY3, ADCY5

  • clus5

    • Top enriched gene sets are KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG HISTIDINE METABOLISM, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG PPAR SIGNALING PATHWAY, KEGG PEROXISOME, KEGG TIGHT JUNCTION, KEGG PARKINSONS DISEASE, BIOCARTA MYOSIN PATHWAY

    • And common core enriched genes are ALDH2, ALDH7A1, ALDH9A1, ALDOB, ALDOC, ENO3, FBP1, PC, PCK2, PFKFB1

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 RIBOSOME 86 genes.ES.table 0.65 1.6 0.075 0.43 0.91 0.88 0.29 0.63 0.24 0.11
KEGG SPLICEOSOME 114 genes.ES.table 0.43 1.7 0.076 0.46 0.85 0.62 0.4 0.37 0.22 0.12
KEGG NOTCH SIGNALING PATHWAY 47 genes.ES.table 0.46 1.6 0.036 0.45 0.91 0.49 0.29 0.35 0.24 0.11
PID HDAC CLASSI PATHWAY 65 genes.ES.table 0.38 1.8 0.03 0.62 0.62 0.32 0.26 0.24 0.23 0.16
PID AR NONGENOMIC PATHWAY 31 genes.ES.table 0.53 1.9 0.002 0.51 0.36 0.58 0.32 0.4 0 0.12
REACTOME TRANSLATION 146 genes.ES.table 0.56 1.7 0.06 0.5 0.68 0.68 0.29 0.48 0.19 0.13
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 49 genes.ES.table 0.62 1.6 0.067 0.44 0.86 0.84 0.31 0.58 0.21 0.12
REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES 47 genes.ES.table 0.54 1.7 0.016 0.54 0.65 0.064 0.015 0.063 0.21 0.14
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 109 genes.ES.table 0.58 1.6 0.076 0.39 0.87 0.74 0.29 0.53 0.19 0.098
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 57 genes.ES.table 0.61 1.7 0.06 0.49 0.76 0.77 0.31 0.54 0.2 0.13
genes ES table in pathway: KEGG RIBOSOME

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 PRKAG2 PRKAG2 PRKAG2 2166 0.12 -0.012 YES
2 CAB39L CAB39L CAB39L 2435 0.1 0.07 YES
3 MTOR MTOR MTOR 2991 0.085 0.12 YES
4 EIF4EBP1 EIF4EBP1 EIF4EBP1 3337 0.075 0.17 YES
5 RPS6 RPS6 RPS6 3381 0.074 0.24 YES
6 STRADB STRADB STRADB 3523 0.071 0.3 YES
7 EIF4B EIF4B EIF4B 4010 0.061 0.33 YES
8 AKT2 AKT2 AKT2 4118 0.059 0.38 YES
9 PRKAA2 PRKAA2 PRKAA2 4143 0.058 0.43 YES
10 EEF2K EEF2K EEF2K 4203 0.057 0.48 YES
11 STRADA STRADA STRADA 4446 0.053 0.52 YES
12 MLST8 MLST8 MLST8 6085 0.03 0.45 YES
13 PDE3B PDE3B PDE3B 6341 0.027 0.46 YES
14 TSC2 TSC2 TSC2 6623 0.024 0.47 YES
15 RPS6KB1 RPS6KB1 RPS6KB1 6678 0.023 0.49 YES
16 PPM1A PPM1A PPM1A 7026 0.019 0.49 YES
17 STK11 STK11 STK11 7229 0.017 0.49 YES
18 TSC1 TSC1 TSC1 7378 0.015 0.5 YES
19 RHEB RHEB RHEB 7445 0.015 0.51 YES
20 PRKAB1 PRKAB1 PRKAB1 7557 0.014 0.52 YES
21 PRKAG1 PRKAG1 PRKAG1 7931 0.0096 0.51 NO
22 RPTOR RPTOR RPTOR 8039 0.0084 0.51 NO
23 PRKAB2 PRKAB2 PRKAB2 8491 0.0036 0.49 NO
24 PRKAA1 PRKAA1 PRKAA1 8897 -0.00023 0.46 NO
25 EIF4G1 EIF4G1 EIF4G1 9418 -0.0056 0.44 NO
26 CAB39 CAB39 CAB39 10534 -0.019 0.4 NO
27 EIF4E EIF4E EIF4E 11322 -0.03 0.38 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 RIBOSOME.

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

genes ES table in pathway: KEGG SPLICEOSOME

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 AR AR AR 38 0.53 0.22 YES
2 PLCG2 PLCG2 PLCG2 695 0.24 0.29 YES
3 PLCB2 PLCB2 PLCB2 1002 0.2 0.36 YES
4 GNRH1 GNRH1 GNRH1 1013 0.2 0.44 YES
5 PLCB1 PLCB1 PLCB1 1747 0.14 0.46 YES
6 GNAI3 GNAI3 GNAI3 1876 0.13 0.5 YES
7 FOS FOS FOS 2908 0.087 0.48 YES
8 PLCB3 PLCB3 PLCB3 4041 0.06 0.45 YES
9 SHBG SHBG SHBG 4060 0.06 0.47 YES
10 PIK3R1 PIK3R1 PIK3R1 4306 0.055 0.48 YES
11 RAF1 RAF1 RAF1 4498 0.052 0.49 YES
12 CDC42 CDC42 CDC42 4818 0.048 0.5 YES
13 GNB1 GNB1 GNB1 5129 0.043 0.5 YES
14 GNAI2 GNAI2 GNAI2 5455 0.038 0.5 YES
15 PTK2 PTK2 PTK2 5560 0.037 0.51 YES
16 SRC SRC SRC 5654 0.036 0.52 YES
17 PIK3CA PIK3CA PIK3CA 5688 0.035 0.53 YES
18 CREB1 CREB1 CREB1 5874 0.033 0.53 YES
19 GNAO1 GNAO1 GNAO1 6121 0.03 0.53 NO
20 AKT1 AKT1 AKT1 7035 0.019 0.49 NO
21 MAPK1 MAPK1 MAPK1 7479 0.014 0.47 NO
22 PELP1 PELP1 PELP1 7574 0.013 0.47 NO
23 GNAI1 GNAI1 GNAI1 7664 0.012 0.47 NO
24 PLCG1 PLCG1 PLCG1 8420 0.0044 0.43 NO
25 RAC1 RAC1 RAC1 8465 0.004 0.43 NO
26 MAP2K2 MAP2K2 MAP2K2 9175 -0.003 0.4 NO
27 MAPK3 MAPK3 MAPK3 9218 -0.0034 0.39 NO
28 MAP2K1 MAP2K1 MAP2K1 12304 -0.046 0.24 NO
29 HRAS HRAS HRAS 12522 -0.051 0.26 NO
30 GNAZ GNAZ GNAZ 12755 -0.056 0.27 NO
31 GNG2 GNG2 GNG2 13863 -0.089 0.24 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 SPLICEOSOME.

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

genes ES table in pathway: KEGG NOTCH SIGNALING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 660 0.24 -0.014 YES
2 RPS8 RPS8 RPS8 1575 0.15 -0.051 YES
3 RPL22 RPL22 RPL22 1592 0.14 -0.039 YES
4 RPS16 RPS16 RPS16 1623 0.14 -0.028 YES
5 RPL18 RPL18 RPL18 1633 0.14 -0.015 YES
6 RPL11 RPL11 RPL11 1635 0.14 -0.0023 YES
7 RPL13A RPL13A RPL13A 1674 0.14 0.0083 YES
8 RPL5 RPL5 RPL5 1705 0.14 0.019 YES
9 RPL9 RPL9 RPL9 1806 0.13 0.026 YES
10 EXOSC5 EXOSC5 EXOSC5 1845 0.13 0.035 YES
11 ZFP36L1 ZFP36L1 ZFP36L1 1992 0.12 0.038 YES
12 PABPC1 PABPC1 PABPC1 2139 0.12 0.041 YES
13 RPSAP9 RPSAP9 RPSAP9 2160 0.12 0.05 YES
14 RPS5 RPS5 RPS5 2199 0.11 0.058 YES
15 RPS19 RPS19 RPS19 2204 0.11 0.068 YES
16 RPLP0 RPLP0 RPLP0 2213 0.11 0.078 YES
17 RPL7 RPL7 RPL7 2267 0.11 0.085 YES
18 RPS11 RPS11 RPS11 2293 0.11 0.094 YES
19 RPS3 RPS3 RPS3 2356 0.11 0.1 YES
20 RPL17 RPL17 RPL17 2469 0.1 0.1 YES
21 RPS10 RPS10 RPS10 2521 0.1 0.11 YES
22 RPS2 RPS2 RPS2 2564 0.099 0.12 YES
23 RPL28 RPL28 RPL28 2651 0.096 0.12 YES
24 RPL18A RPL18A RPL18A 2663 0.095 0.13 YES
25 RPL7A RPL7A RPL7A 2714 0.094 0.13 YES
26 RPL30 RPL30 RPL30 2725 0.093 0.14 YES
27 RPLP1 RPLP1 RPLP1 2760 0.092 0.15 YES
28 RPS17 RPS17 RPS17 2776 0.092 0.16 YES
29 RPL23 RPL23 RPL23 2781 0.092 0.16 YES
30 RPS9 RPS9 RPS9 2800 0.091 0.17 YES
31 UPF3A UPF3A UPF3A 2846 0.089 0.18 YES
32 RPL39 RPL39 RPL39 2873 0.088 0.18 YES
33 RPS15A RPS15A RPS15A 2879 0.088 0.19 YES
34 RPS3A RPS3A RPS3A 2920 0.087 0.2 YES
35 RPS4Y1 RPS4Y1 RPS4Y1 2924 0.087 0.2 YES
36 RPS25 RPS25 RPS25 3040 0.084 0.21 YES
37 RPL12 RPL12 RPL12 3046 0.084 0.21 YES
38 PRKCD PRKCD PRKCD 3066 0.083 0.22 YES
39 RPL3 RPL3 RPL3 3183 0.08 0.22 YES
40 RPS29 RPS29 RPS29 3189 0.08 0.23 YES
41 RPS27 RPS27 RPS27 3246 0.078 0.23 YES
42 RPS24 RPS24 RPS24 3248 0.078 0.24 YES
43 RPL27 RPL27 RPL27 3255 0.078 0.24 YES
44 UPF2 UPF2 UPF2 3309 0.076 0.25 YES
45 RPSA RPSA RPSA 3331 0.076 0.26 YES
46 EXOSC7 EXOSC7 EXOSC7 3339 0.075 0.26 YES
47 ZFP36 ZFP36 ZFP36 3372 0.075 0.27 YES
48 RPS6 RPS6 RPS6 3381 0.074 0.27 YES
49 RPL4 RPL4 RPL4 3402 0.074 0.28 YES
50 RPL27A RPL27A RPL27A 3440 0.073 0.28 YES
51 PSMA5 PSMA5 PSMA5 3454 0.072 0.29 YES
52 RPL26 RPL26 RPL26 3525 0.071 0.29 YES
53 MAGOH MAGOH MAGOH 3526 0.071 0.3 YES
54 RPL8 RPL8 RPL8 3575 0.069 0.3 YES
55 RPL34 RPL34 RPL34 3580 0.069 0.31 YES
56 RPL19 RPL19 RPL19 3592 0.069 0.31 YES
57 CNOT3 CNOT3 CNOT3 3596 0.069 0.32 YES
58 RPS14 RPS14 RPS14 3631 0.068 0.32 YES
59 RPL32 RPL32 RPL32 3633 0.068 0.33 YES
60 PSMB2 PSMB2 PSMB2 3663 0.067 0.34 YES
61 FAU FAU FAU 3684 0.067 0.34 YES
62 RPL38 RPL38 RPL38 3699 0.067 0.34 YES
63 RPL29 RPL29 RPL29 3722 0.066 0.35 YES
64 RPL37A RPL37A RPL37A 3725 0.066 0.36 YES
65 EXOSC1 EXOSC1 EXOSC1 3741 0.066 0.36 YES
66 RPL35A RPL35A RPL35A 3757 0.066 0.37 YES
67 RPLP2 RPLP2 RPLP2 3772 0.065 0.37 YES
68 RPL10 RPL10 RPL10 3800 0.065 0.38 YES
69 RPL15 RPL15 RPL15 3858 0.064 0.38 YES
70 RPS23 RPS23 RPS23 3865 0.064 0.38 YES
71 RPS18 RPS18 RPS18 3885 0.063 0.39 YES
72 RPS15 RPS15 RPS15 3907 0.063 0.39 YES
73 EIF4B EIF4B EIF4B 4010 0.061 0.39 YES
74 RPS27A RPS27A RPS27A 4026 0.06 0.4 YES
75 RPS21 RPS21 RPS21 4051 0.06 0.4 YES
76 RPL6 RPL6 RPL6 4110 0.059 0.4 YES
77 RPS13 RPS13 RPS13 4180 0.058 0.4 YES
78 RPL13 RPL13 RPL13 4237 0.057 0.41 YES
79 ANP32A ANP32A ANP32A 4243 0.056 0.41 YES
80 LSM2 LSM2 LSM2 4263 0.056 0.42 YES
81 RPL36 RPL36 RPL36 4337 0.055 0.42 YES
82 EXOSC8 EXOSC8 EXOSC8 4340 0.055 0.42 YES
83 KHSRP KHSRP KHSRP 4345 0.055 0.43 YES
84 RPS4X RPS4X RPS4X 4348 0.055 0.43 YES
85 RPL36A RPL36A RPL36A 4350 0.055 0.44 YES
86 DDX6 DDX6 DDX6 4422 0.054 0.44 YES
87 RPL37 RPL37 RPL37 4443 0.053 0.44 YES
88 RPL35 RPL35 RPL35 4517 0.052 0.44 YES
89 RPL14 RPL14 RPL14 4519 0.052 0.45 YES
90 XRN1 XRN1 XRN1 4532 0.052 0.45 YES
91 RPS12 RPS12 RPS12 4574 0.051 0.45 YES
92 RPL41 RPL41 RPL41 4640 0.05 0.45 YES
93 PATL1 PATL1 PATL1 4768 0.048 0.45 YES
94 PSMC4 PSMC4 PSMC4 4796 0.048 0.45 YES
95 UPF3B UPF3B UPF3B 4842 0.047 0.46 YES
96 RPL24 RPL24 RPL24 4931 0.046 0.46 YES
97 RPL23A RPL23A RPL23A 4989 0.045 0.46 YES
98 RPS20 RPS20 RPS20 5060 0.044 0.46 YES
99 DCP1A DCP1A DCP1A 5088 0.044 0.46 YES
100 EIF4A3 EIF4A3 EIF4A3 5162 0.042 0.46 YES
101 LSM6 LSM6 LSM6 5195 0.042 0.46 YES
102 RPL10A RPL10A RPL10A 5285 0.041 0.46 YES
103 EXOSC4 EXOSC4 EXOSC4 5287 0.041 0.46 YES
104 RPS7 RPS7 RPS7 5305 0.04 0.47 YES
105 UBA52 UBA52 UBA52 5314 0.04 0.47 YES
106 DCP1B DCP1B DCP1B 5441 0.038 0.47 NO
107 RBM8A RBM8A RBM8A 5484 0.038 0.47 NO
108 RPS26 RPS26 RPS26 5648 0.036 0.46 NO
109 RPL31 RPL31 RPL31 5743 0.034 0.46 NO
110 CASC3 CASC3 CASC3 5856 0.033 0.46 NO
111 PSME1 PSME1 PSME1 5879 0.032 0.46 NO
112 HSPA1B HSPA1B HSPA1B 5937 0.032 0.46 NO
113 SMG6 SMG6 SMG6 5946 0.032 0.46 NO
114 XPO1 XPO1 XPO1 6049 0.03 0.46 NO
115 NUP214 NUP214 NUP214 6113 0.03 0.46 NO
116 PSMA7 PSMA7 PSMA7 6219 0.029 0.45 NO
117 LSM1 LSM1 LSM1 6223 0.029 0.46 NO
118 PSMA3 PSMA3 PSMA3 6286 0.028 0.46 NO
119 HNRNPD HNRNPD HNRNPD 6323 0.027 0.46 NO
120 CNOT10 CNOT10 CNOT10 6331 0.027 0.46 NO
121 PRKCA PRKCA PRKCA 6420 0.026 0.46 NO
122 NCBP2 NCBP2 NCBP2 6454 0.026 0.46 NO
123 PSMA6 PSMA6 PSMA6 6603 0.024 0.45 NO
124 CNOT6 CNOT6 CNOT6 6679 0.023 0.45 NO
125 NCBP1 NCBP1 NCBP1 6891 0.021 0.44 NO
126 PARN PARN PARN 6937 0.02 0.44 NO
127 CNOT8 CNOT8 CNOT8 6944 0.02 0.44 NO
128 AKT1 AKT1 AKT1 7035 0.019 0.44 NO
129 EXOSC2 EXOSC2 EXOSC2 7045 0.019 0.44 NO
130 EDC3 EDC3 EDC3 7057 0.019 0.44 NO
131 PSME4 PSME4 PSME4 7232 0.017 0.43 NO
132 CNOT4 CNOT4 CNOT4 7290 0.016 0.43 NO
133 EDC4 EDC4 EDC4 7370 0.015 0.42 NO
134 PSMD9 PSMD9 PSMD9 7502 0.014 0.42 NO
135 PPP2R1A PPP2R1A PPP2R1A 7602 0.013 0.42 NO
136 EIF4A1 EIF4A1 EIF4A1 7637 0.013 0.41 NO
137 PSMC6 PSMC6 PSMC6 7647 0.013 0.42 NO
138 RPS28 RPS28 RPS28 7758 0.012 0.41 NO
139 SMG1 SMG1 SMG1 7768 0.011 0.41 NO
140 TNPO1 TNPO1 TNPO1 7806 0.011 0.41 NO
141 PSMD8 PSMD8 PSMD8 7920 0.0097 0.4 NO
142 PAIP1 PAIP1 PAIP1 8007 0.0086 0.4 NO
143 PSMB10 PSMB10 PSMB10 8074 0.0081 0.4 NO
144 CNOT7 CNOT7 CNOT7 8202 0.0067 0.39 NO
145 PSMF1 PSMF1 PSMF1 8227 0.0064 0.39 NO
146 C2orf29 C2orf29 C2orf29 8376 0.0049 0.38 NO
147 SMG5 SMG5 SMG5 8441 0.0043 0.38 NO
148 PSMB3 PSMB3 PSMB3 8444 0.0042 0.38 NO
149 PSMB4 PSMB4 PSMB4 8473 0.0038 0.38 NO
150 ELAVL1 ELAVL1 ELAVL1 8499 0.0035 0.38 NO
151 MAPK14 MAPK14 MAPK14 8501 0.0035 0.38 NO
152 LSM3 LSM3 LSM3 8518 0.0033 0.38 NO
153 RNPS1 RNPS1 RNPS1 8551 0.0031 0.38 NO
154 EIF4A2 EIF4A2 EIF4A2 8588 0.0028 0.37 NO
155 MAPKAPK2 MAPKAPK2 MAPKAPK2 8607 0.0026 0.37 NO
156 PSME2 PSME2 PSME2 8664 0.002 0.37 NO
157 PSMB6 PSMB6 PSMB6 8673 0.0019 0.37 NO
158 PSMD4 PSMD4 PSMD4 8721 0.0015 0.37 NO
159 TNKS1BP1 TNKS1BP1 TNKS1BP1 8789 0.00095 0.36 NO
160 PSMD2 PSMD2 PSMD2 9012 -0.0015 0.35 NO
161 GSPT2 GSPT2 GSPT2 9025 -0.0016 0.35 NO
162 LSM5 LSM5 LSM5 9117 -0.0025 0.35 NO
163 PSMD3 PSMD3 PSMD3 9119 -0.0025 0.35 NO
164 RQCD1 RQCD1 RQCD1 9148 -0.0028 0.34 NO
165 PSMD10 PSMD10 PSMD10 9186 -0.0032 0.34 NO
166 PSMC1 PSMC1 PSMC1 9216 -0.0034 0.34 NO
167 CNOT2 CNOT2 CNOT2 9222 -0.0035 0.34 NO
168 PSMD11 PSMD11 PSMD11 9254 -0.0038 0.34 NO
169 PSMD5 PSMD5 PSMD5 9341 -0.0047 0.34 NO
170 PSMA4 PSMA4 PSMA4 9352 -0.0048 0.34 NO
171 PSMA2 PSMA2 PSMA2 9359 -0.0049 0.34 NO
172 EXOSC3 EXOSC3 EXOSC3 9398 -0.0053 0.33 NO
173 PSMB5 PSMB5 PSMB5 9400 -0.0053 0.34 NO
174 EIF4G1 EIF4G1 EIF4G1 9418 -0.0056 0.33 NO
175 PSMD6 PSMD6 PSMD6 9473 -0.0063 0.33 NO
176 PSMC2 PSMC2 PSMC2 9486 -0.0064 0.33 NO
177 PPP2R2A PPP2R2A PPP2R2A 9525 -0.007 0.33 NO
178 PSMA1 PSMA1 PSMA1 9664 -0.0085 0.32 NO
179 ETF1 ETF1 ETF1 9712 -0.0089 0.32 NO
180 PSMB7 PSMB7 PSMB7 9744 -0.0093 0.32 NO
181 PSMC3 PSMC3 PSMC3 9767 -0.0096 0.32 NO
182 SMG7 SMG7 SMG7 9902 -0.011 0.31 NO
183 PSMC5 PSMC5 PSMC5 10123 -0.014 0.3 NO
184 DCP2 DCP2 DCP2 10555 -0.019 0.28 NO
185 PSMD13 PSMD13 PSMD13 10742 -0.022 0.27 NO
186 TNFSF13 TNFSF13 TNFSF13 10818 -0.023 0.27 NO
187 PSMB8 PSMB8 PSMB8 10852 -0.023 0.27 NO
188 PPP2CA PPP2CA PPP2CA 10894 -0.024 0.27 NO
189 PSMD7 PSMD7 PSMD7 10920 -0.024 0.27 NO
190 PSMB1 PSMB1 PSMB1 10965 -0.025 0.27 NO
191 RPL26L1 RPL26L1 RPL26L1 11124 -0.027 0.26 NO
192 HSPA8 HSPA8 HSPA8 11187 -0.028 0.26 NO
193 DIS3 DIS3 DIS3 11311 -0.03 0.26 NO
194 EIF4E EIF4E EIF4E 11322 -0.03 0.26 NO
195 PSMB9 PSMB9 PSMB9 11501 -0.032 0.26 NO
196 DCPS DCPS DCPS 11958 -0.04 0.23 NO
197 EXOSC9 EXOSC9 EXOSC9 11997 -0.04 0.24 NO
198 PSMD1 PSMD1 PSMD1 12024 -0.041 0.24 NO
199 PSMD12 PSMD12 PSMD12 12049 -0.041 0.24 NO
200 EXOSC6 EXOSC6 EXOSC6 12231 -0.044 0.23 NO
201 YWHAZ YWHAZ YWHAZ 12397 -0.048 0.23 NO
202 LSM4 LSM4 LSM4 12430 -0.049 0.23 NO
203 PSMD14 PSMD14 PSMD14 12851 -0.059 0.21 NO
204 YWHAB YWHAB YWHAB 12949 -0.061 0.22 NO
205 PSMA8 PSMA8 PSMA8 14627 -0.12 0.13 NO
206 HSPB1 HSPB1 HSPB1 15226 -0.15 0.11 NO
207 MAPK11 MAPK11 MAPK11 15619 -0.18 0.11 NO
208 FAM153A FAM153A FAM153A 17676 -0.44 0.035 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 NOTCH SIGNALING PATHWAY.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOTCH 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: PID HDAC CLASSI 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 TNF TNF TNF 272 0.33 0.086 YES
2 SSPO SSPO SSPO 915 0.21 0.11 YES
3 GATA2 GATA2 GATA2 966 0.2 0.17 YES
4 HDAC1 HDAC1 HDAC1 1440 0.16 0.19 YES
5 SIRT4 SIRT4 SIRT4 1805 0.13 0.21 YES
6 SIRT2 SIRT2 SIRT2 1933 0.12 0.24 YES
7 RBBP4 RBBP4 RBBP4 2652 0.096 0.23 YES
8 SMAD7 SMAD7 SMAD7 3078 0.083 0.24 YES
9 SIRT1 SIRT1 SIRT1 3126 0.081 0.26 YES
10 NCOR2 NCOR2 NCOR2 3233 0.078 0.28 YES
11 WDR77 WDR77 WDR77 3437 0.073 0.29 YES
12 SAP30 SAP30 SAP30 3670 0.067 0.29 YES
13 CHD4 CHD4 CHD4 3913 0.063 0.3 YES
14 PRMT5 PRMT5 PRMT5 4068 0.06 0.31 YES
15 NFKBIA NFKBIA NFKBIA 4158 0.058 0.32 YES
16 NR2C1 NR2C1 NR2C1 4275 0.056 0.33 YES
17 MTA2 MTA2 MTA2 4335 0.055 0.35 YES
18 GATA1 GATA1 GATA1 4359 0.054 0.36 YES
19 NFKB1 NFKB1 NFKB1 4420 0.054 0.37 YES
20 RELA RELA RELA 4752 0.048 0.37 YES
21 EP300 EP300 EP300 4806 0.048 0.38 YES
22 HDAC5 HDAC5 HDAC5 5409 0.039 0.36 NO
23 CREBBP CREBBP CREBBP 5772 0.034 0.35 NO
24 MAX MAX MAX 5789 0.034 0.36 NO
25 SIN3A SIN3A SIN3A 6037 0.031 0.36 NO
26 XPO1 XPO1 XPO1 6049 0.03 0.36 NO
27 KAT2B KAT2B KAT2B 6467 0.026 0.35 NO
28 HDAC4 HDAC4 HDAC4 6490 0.026 0.36 NO
29 SAP18 SAP18 SAP18 6547 0.025 0.36 NO
30 GATAD2B GATAD2B GATAD2B 6553 0.025 0.37 NO
31 STAT3 STAT3 STAT3 6692 0.023 0.37 NO
32 YY1 YY1 YY1 6695 0.023 0.38 NO
33 UBE2I UBE2I UBE2I 6776 0.022 0.38 NO
34 SIRT7 SIRT7 SIRT7 6868 0.021 0.38 NO
35 MXD1 MXD1 MXD1 7237 0.017 0.36 NO
36 GATAD2A GATAD2A GATAD2A 7390 0.015 0.36 NO
37 HDAC2 HDAC2 HDAC2 7509 0.014 0.36 NO
38 TFCP2 TFCP2 TFCP2 7520 0.014 0.36 NO
39 MBD3 MBD3 MBD3 7541 0.014 0.36 NO
40 HDAC3 HDAC3 HDAC3 7730 0.012 0.36 NO
41 TNFRSF1A TNFRSF1A TNFRSF1A 7734 0.012 0.36 NO
42 SIRT6 SIRT6 SIRT6 8036 0.0084 0.35 NO
43 RBBP7 RBBP7 RBBP7 8327 0.0054 0.33 NO
44 SMG5 SMG5 SMG5 8441 0.0043 0.33 NO
45 NCOR1 NCOR1 NCOR1 8480 0.0037 0.33 NO
46 HDAC6 HDAC6 HDAC6 8602 0.0027 0.32 NO
47 RANBP2 RANBP2 RANBP2 8948 -0.00076 0.3 NO
48 SMURF1 SMURF1 SMURF1 8956 -0.00088 0.3 NO
49 HDAC8 HDAC8 HDAC8 8989 -0.0012 0.3 NO
50 MBD2 MBD2 MBD2 9080 -0.0021 0.3 NO
51 RAN RAN RAN 9550 -0.0073 0.27 NO
52 FKBP3 FKBP3 FKBP3 9929 -0.011 0.26 NO
53 SUMO1 SUMO1 SUMO1 10048 -0.013 0.25 NO
54 SIRT3 SIRT3 SIRT3 10223 -0.015 0.25 NO
55 HDAC7 HDAC7 HDAC7 10296 -0.016 0.25 NO
56 HDAC10 HDAC10 HDAC10 11008 -0.025 0.22 NO
57 ZFPM1 ZFPM1 ZFPM1 11327 -0.03 0.21 NO
58 CHD3 CHD3 CHD3 11393 -0.031 0.22 NO
59 RANGAP1 RANGAP1 RANGAP1 11636 -0.034 0.21 NO
60 PRKACA PRKACA PRKACA 12375 -0.048 0.19 NO
61 SIN3B SIN3B SIN3B 12562 -0.052 0.19 NO
62 HDAC11 HDAC11 HDAC11 12747 -0.056 0.2 NO
63 PPARG PPARG PPARG 13611 -0.081 0.18 NO
64 SIRT5 SIRT5 SIRT5 13996 -0.095 0.18 NO
65 HDAC9 HDAC9 HDAC9 15528 -0.18 0.15 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 HDAC CLASSI PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: PID HDAC CLASSI 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 NONGENOMIC 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 MRC1 MRC1 MRC1 44 0.51 0.24 YES
2 FCGR1A FCGR1A FCGR1A 251 0.34 0.39 YES
3 FCGR1B FCGR1B FCGR1B 281 0.33 0.54 YES
4 PSMA5 PSMA5 PSMA5 3454 0.072 0.4 NO
5 PSMB2 PSMB2 PSMB2 3663 0.067 0.42 NO
6 CD207 CD207 CD207 4171 0.058 0.42 NO
7 PSMC4 PSMC4 PSMC4 4796 0.048 0.41 NO
8 PSME1 PSME1 PSME1 5879 0.032 0.37 NO
9 PSMA7 PSMA7 PSMA7 6219 0.029 0.36 NO
10 PSMA3 PSMA3 PSMA3 6286 0.028 0.37 NO
11 PSMA6 PSMA6 PSMA6 6603 0.024 0.37 NO
12 MRC2 MRC2 MRC2 7198 0.017 0.34 NO
13 PSME4 PSME4 PSME4 7232 0.017 0.35 NO
14 PSMD9 PSMD9 PSMD9 7502 0.014 0.34 NO
15 PSMC6 PSMC6 PSMC6 7647 0.013 0.34 NO
16 PSMD8 PSMD8 PSMD8 7920 0.0097 0.33 NO
17 PSMB10 PSMB10 PSMB10 8074 0.0081 0.32 NO
18 PSMF1 PSMF1 PSMF1 8227 0.0064 0.32 NO
19 PSMB3 PSMB3 PSMB3 8444 0.0042 0.31 NO
20 PSMB4 PSMB4 PSMB4 8473 0.0038 0.31 NO
21 PSME2 PSME2 PSME2 8664 0.002 0.3 NO
22 PSMB6 PSMB6 PSMB6 8673 0.0019 0.3 NO
23 PSMD4 PSMD4 PSMD4 8721 0.0015 0.3 NO
24 PSMD2 PSMD2 PSMD2 9012 -0.0015 0.28 NO
25 PSMD3 PSMD3 PSMD3 9119 -0.0025 0.28 NO
26 PSMD10 PSMD10 PSMD10 9186 -0.0032 0.28 NO
27 PSMC1 PSMC1 PSMC1 9216 -0.0034 0.28 NO
28 PSMD11 PSMD11 PSMD11 9254 -0.0038 0.28 NO
29 PSMD5 PSMD5 PSMD5 9341 -0.0047 0.27 NO
30 PSMA4 PSMA4 PSMA4 9352 -0.0048 0.28 NO
31 PSMA2 PSMA2 PSMA2 9359 -0.0049 0.28 NO
32 PSMB5 PSMB5 PSMB5 9400 -0.0053 0.28 NO
33 PSMD6 PSMD6 PSMD6 9473 -0.0063 0.28 NO
34 PSMC2 PSMC2 PSMC2 9486 -0.0064 0.28 NO
35 PSMA1 PSMA1 PSMA1 9664 -0.0085 0.27 NO
36 PSMB7 PSMB7 PSMB7 9744 -0.0093 0.27 NO
37 PSMC3 PSMC3 PSMC3 9767 -0.0096 0.28 NO
38 PSMC5 PSMC5 PSMC5 10123 -0.014 0.26 NO
39 PSMD13 PSMD13 PSMD13 10742 -0.022 0.24 NO
40 PSMB8 PSMB8 PSMB8 10852 -0.023 0.24 NO
41 PSMD7 PSMD7 PSMD7 10920 -0.024 0.25 NO
42 PSMB1 PSMB1 PSMB1 10965 -0.025 0.26 NO
43 PSMB9 PSMB9 PSMB9 11501 -0.032 0.25 NO
44 PSMD1 PSMD1 PSMD1 12024 -0.041 0.24 NO
45 PSMD12 PSMD12 PSMD12 12049 -0.041 0.26 NO
46 PSMD14 PSMD14 PSMD14 12851 -0.059 0.24 NO
47 PSMA8 PSMA8 PSMA8 14627 -0.12 0.2 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 AR NONGENOMIC PATHWAY.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AR NONGENOMIC PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TRANSLATION

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 RPL21 RPL21 RPL21 660 0.24 -0.01 YES
2 RPS8 RPS8 RPS8 1575 0.15 -0.045 YES
3 RPL22 RPL22 RPL22 1592 0.14 -0.03 YES
4 RPS16 RPS16 RPS16 1623 0.14 -0.017 YES
5 RPL18 RPL18 RPL18 1633 0.14 -0.002 YES
6 RPL11 RPL11 RPL11 1635 0.14 0.013 YES
7 RPL13A RPL13A RPL13A 1674 0.14 0.026 YES
8 RPL5 RPL5 RPL5 1705 0.14 0.039 YES
9 RPL9 RPL9 RPL9 1806 0.13 0.048 YES
10 EEF1G EEF1G EEF1G 1951 0.12 0.053 YES
11 PABPC1 PABPC1 PABPC1 2139 0.12 0.055 YES
12 RPSAP9 RPSAP9 RPSAP9 2160 0.12 0.066 YES
13 RPS5 RPS5 RPS5 2199 0.11 0.076 YES
14 RPS19 RPS19 RPS19 2204 0.11 0.088 YES
15 RPLP0 RPLP0 RPLP0 2213 0.11 0.1 YES
16 RPL7 RPL7 RPL7 2267 0.11 0.11 YES
17 RPS11 RPS11 RPS11 2293 0.11 0.12 YES
18 RPS3 RPS3 RPS3 2356 0.11 0.13 YES
19 RPL17 RPL17 RPL17 2469 0.1 0.13 YES
20 RPS10 RPS10 RPS10 2521 0.1 0.14 YES
21 RPS2 RPS2 RPS2 2564 0.099 0.15 YES
22 RPL28 RPL28 RPL28 2651 0.096 0.15 YES
23 RPL18A RPL18A RPL18A 2663 0.095 0.16 YES
24 RPL7A RPL7A RPL7A 2714 0.094 0.17 YES
25 RPL30 RPL30 RPL30 2725 0.093 0.18 YES
26 RPLP1 RPLP1 RPLP1 2760 0.092 0.19 YES
27 RPS17 RPS17 RPS17 2776 0.092 0.2 YES
28 RPL23 RPL23 RPL23 2781 0.092 0.21 YES
29 RPS9 RPS9 RPS9 2800 0.091 0.21 YES
30 RPL39 RPL39 RPL39 2873 0.088 0.22 YES
31 RPS15A RPS15A RPS15A 2879 0.088 0.23 YES
32 RPS3A RPS3A RPS3A 2920 0.087 0.24 YES
33 RPS4Y1 RPS4Y1 RPS4Y1 2924 0.087 0.24 YES
34 RPS25 RPS25 RPS25 3040 0.084 0.25 YES
35 RPL12 RPL12 RPL12 3046 0.084 0.26 YES
36 EIF3H EIF3H EIF3H 3052 0.083 0.26 YES
37 SEC11A SEC11A SEC11A 3080 0.083 0.27 YES
38 EEF1D EEF1D EEF1D 3083 0.083 0.28 YES
39 RPL3 RPL3 RPL3 3183 0.08 0.28 YES
40 RPS29 RPS29 RPS29 3189 0.08 0.29 YES
41 RPS27 RPS27 RPS27 3246 0.078 0.3 YES
42 RPS24 RPS24 RPS24 3248 0.078 0.31 YES
43 RPL27 RPL27 RPL27 3255 0.078 0.31 YES
44 RPSA RPSA RPSA 3331 0.076 0.32 YES
45 EIF4EBP1 EIF4EBP1 EIF4EBP1 3337 0.075 0.33 YES
46 EIF3E EIF3E EIF3E 3343 0.075 0.33 YES
47 RPS6 RPS6 RPS6 3381 0.074 0.34 YES
48 EIF3I EIF3I EIF3I 3390 0.074 0.35 YES
49 RPL4 RPL4 RPL4 3402 0.074 0.35 YES
50 RPL27A RPL27A RPL27A 3440 0.073 0.36 YES
51 EEF1A1 EEF1A1 EEF1A1 3520 0.071 0.36 YES
52 RPL26 RPL26 RPL26 3525 0.071 0.37 YES
53 EEF1B2 EEF1B2 EEF1B2 3570 0.07 0.38 YES
54 RPL8 RPL8 RPL8 3575 0.069 0.38 YES
55 RPL34 RPL34 RPL34 3580 0.069 0.39 YES
56 RPL19 RPL19 RPL19 3592 0.069 0.4 YES
57 RPS14 RPS14 RPS14 3631 0.068 0.4 YES
58 RPL32 RPL32 RPL32 3633 0.068 0.41 YES
59 FAU FAU FAU 3684 0.067 0.41 YES
60 RPL38 RPL38 RPL38 3699 0.067 0.42 YES
61 RPL29 RPL29 RPL29 3722 0.066 0.42 YES
62 RPL37A RPL37A RPL37A 3725 0.066 0.43 YES
63 RPL35A RPL35A RPL35A 3757 0.066 0.44 YES
64 RPLP2 RPLP2 RPLP2 3772 0.065 0.44 YES
65 RPL10 RPL10 RPL10 3800 0.065 0.45 YES
66 RPL15 RPL15 RPL15 3858 0.064 0.45 YES
67 RPS23 RPS23 RPS23 3865 0.064 0.46 YES
68 RPS18 RPS18 RPS18 3885 0.063 0.46 YES
69 RPS15 RPS15 RPS15 3907 0.063 0.47 YES
70 EEF2 EEF2 EEF2 3933 0.062 0.48 YES
71 EIF4B EIF4B EIF4B 4010 0.061 0.48 YES
72 RPS27A RPS27A RPS27A 4026 0.06 0.48 YES
73 RPS21 RPS21 RPS21 4051 0.06 0.49 YES
74 EIF3D EIF3D EIF3D 4094 0.059 0.49 YES
75 RPL6 RPL6 RPL6 4110 0.059 0.5 YES
76 RPS13 RPS13 RPS13 4180 0.058 0.5 YES
77 RPL13 RPL13 RPL13 4237 0.057 0.5 YES
78 EIF2B4 EIF2B4 EIF2B4 4295 0.056 0.51 YES
79 RPL36 RPL36 RPL36 4337 0.055 0.51 YES
80 RPS4X RPS4X RPS4X 4348 0.055 0.52 YES
81 RPL36A RPL36A RPL36A 4350 0.055 0.52 YES
82 RPL37 RPL37 RPL37 4443 0.053 0.52 YES
83 RPL35 RPL35 RPL35 4517 0.052 0.52 YES
84 RPL14 RPL14 RPL14 4519 0.052 0.53 YES
85 RPS12 RPS12 RPS12 4574 0.051 0.53 YES
86 RPL41 RPL41 RPL41 4640 0.05 0.53 YES
87 EIF2B3 EIF2B3 EIF2B3 4669 0.05 0.54 YES
88 EIF5B EIF5B EIF5B 4691 0.049 0.54 YES
89 EIF3F EIF3F EIF3F 4853 0.047 0.54 YES
90 EIF3J EIF3J EIF3J 4917 0.046 0.54 YES
91 RPL24 RPL24 RPL24 4931 0.046 0.54 YES
92 RPL23A RPL23A RPL23A 4989 0.045 0.54 YES
93 DDOST DDOST DDOST 5041 0.044 0.55 YES
94 SRP14 SRP14 SRP14 5046 0.044 0.55 YES
95 RPS20 RPS20 RPS20 5060 0.044 0.56 YES
96 EIF3A EIF3A EIF3A 5109 0.043 0.56 YES
97 RPL10A RPL10A RPL10A 5285 0.041 0.55 YES
98 RPS7 RPS7 RPS7 5305 0.04 0.56 YES
99 UBA52 UBA52 UBA52 5314 0.04 0.56 YES
100 EIF3G EIF3G EIF3G 5576 0.036 0.55 NO
101 RPS26 RPS26 RPS26 5648 0.036 0.55 NO
102 RPL31 RPL31 RPL31 5743 0.034 0.55 NO
103 EIF2B5 EIF2B5 EIF2B5 5864 0.033 0.54 NO
104 EIF3K EIF3K EIF3K 6193 0.029 0.53 NO
105 SEC61A2 SEC61A2 SEC61A2 6878 0.021 0.49 NO
106 EIF2B2 EIF2B2 EIF2B2 6881 0.021 0.5 NO
107 SEC61B SEC61B SEC61B 7537 0.014 0.46 NO
108 EIF4A1 EIF4A1 EIF4A1 7637 0.013 0.46 NO
109 RPS28 RPS28 RPS28 7758 0.012 0.45 NO
110 RPN2 RPN2 RPN2 7915 0.0097 0.44 NO
111 EIF3B EIF3B EIF3B 7982 0.009 0.44 NO
112 SRP72 SRP72 SRP72 8023 0.0085 0.44 NO
113 EIF4H EIF4H EIF4H 8147 0.0072 0.43 NO
114 EIF2S2 EIF2S2 EIF2S2 8260 0.006 0.43 NO
115 SPCS1 SPCS1 SPCS1 8302 0.0056 0.43 NO
116 SRP9 SRP9 SRP9 8387 0.0048 0.42 NO
117 SSR1 SSR1 SSR1 8494 0.0036 0.42 NO
118 EIF4A2 EIF4A2 EIF4A2 8588 0.0028 0.41 NO
119 EIF2S3 EIF2S3 EIF2S3 8655 0.0021 0.41 NO
120 EIF2B1 EIF2B1 EIF2B1 8660 0.002 0.41 NO
121 EIF1AX EIF1AX EIF1AX 8667 0.002 0.41 NO
122 GSPT2 GSPT2 GSPT2 9025 -0.0016 0.39 NO
123 SRP68 SRP68 SRP68 9082 -0.0021 0.39 NO
124 LOC653566 LOC653566 LOC653566 9145 -0.0027 0.38 NO
125 SRP54 SRP54 SRP54 9195 -0.0032 0.38 NO
126 SSR4 SSR4 SSR4 9305 -0.0043 0.38 NO
127 SSR2 SSR2 SSR2 9414 -0.0055 0.37 NO
128 EIF4G1 EIF4G1 EIF4G1 9418 -0.0056 0.37 NO
129 SEC11C SEC11C SEC11C 9496 -0.0066 0.37 NO
130 SPCS2 SPCS2 SPCS2 9694 -0.0087 0.36 NO
131 ETF1 ETF1 ETF1 9712 -0.0089 0.36 NO
132 RPN1 RPN1 RPN1 10039 -0.013 0.34 NO
133 EIF2S1 EIF2S1 EIF2S1 10138 -0.014 0.34 NO
134 TRAM1 TRAM1 TRAM1 10312 -0.016 0.33 NO
135 SEC61A1 SEC61A1 SEC61A1 10490 -0.018 0.32 NO
136 SRP19 SRP19 SRP19 10648 -0.02 0.31 NO
137 EIF5 EIF5 EIF5 10860 -0.023 0.3 NO
138 SRPR SRPR SRPR 10979 -0.025 0.3 NO
139 RPL26L1 RPL26L1 RPL26L1 11124 -0.027 0.3 NO
140 SSR3 SSR3 SSR3 11307 -0.03 0.29 NO
141 EIF4E EIF4E EIF4E 11322 -0.03 0.29 NO
142 SPCS3 SPCS3 SPCS3 12190 -0.044 0.25 NO
143 SRPRB SRPRB SRPRB 13677 -0.083 0.18 NO
144 SEC61G SEC61G SEC61G 14561 -0.12 0.14 NO
145 EIF3C EIF3C EIF3C 15690 -0.18 0.098 NO
146 FAM153A FAM153A FAM153A 17676 -0.44 0.035 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: REACTOME TRANSLATION.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSLATION, 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 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX

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 RPL21 RPL21 RPL21 660 0.24 -0.017 YES
2 RPS8 RPS8 RPS8 1575 0.15 -0.056 YES
3 RPL22 RPL22 RPL22 1592 0.14 -0.045 YES
4 RPS16 RPS16 RPS16 1623 0.14 -0.035 YES
5 RPL18 RPL18 RPL18 1633 0.14 -0.024 YES
6 RPL11 RPL11 RPL11 1635 0.14 -0.013 YES
7 RPL13A RPL13A RPL13A 1674 0.14 -0.0036 YES
8 RPL5 RPL5 RPL5 1705 0.14 0.0059 YES
9 DDX20 DDX20 DDX20 1783 0.13 0.012 YES
10 RPL9 RPL9 RPL9 1806 0.13 0.022 YES
11 EXOSC5 EXOSC5 EXOSC5 1845 0.13 0.03 YES
12 ZFP36L1 ZFP36L1 ZFP36L1 1992 0.12 0.032 YES
13 PABPC1 PABPC1 PABPC1 2139 0.12 0.033 YES
14 RPSAP9 RPSAP9 RPSAP9 2160 0.12 0.041 YES
15 RPS5 RPS5 RPS5 2199 0.11 0.048 YES
16 RPS19 RPS19 RPS19 2204 0.11 0.057 YES
17 RPLP0 RPLP0 RPLP0 2213 0.11 0.066 YES
18 RPL7 RPL7 RPL7 2267 0.11 0.072 YES
19 RPS11 RPS11 RPS11 2293 0.11 0.079 YES
20 RPS3 RPS3 RPS3 2356 0.11 0.084 YES
21 RPL17 RPL17 RPL17 2469 0.1 0.086 YES
22 RPS10 RPS10 RPS10 2521 0.1 0.091 YES
23 RPS2 RPS2 RPS2 2564 0.099 0.097 YES
24 RPL28 RPL28 RPL28 2651 0.096 0.1 YES
25 RPL18A RPL18A RPL18A 2663 0.095 0.11 YES
26 RPL7A RPL7A RPL7A 2714 0.094 0.11 YES
27 RPL30 RPL30 RPL30 2725 0.093 0.12 YES
28 RPLP1 RPLP1 RPLP1 2760 0.092 0.12 YES
29 RPS17 RPS17 RPS17 2776 0.092 0.13 YES
30 RPL23 RPL23 RPL23 2781 0.092 0.14 YES
31 RPS9 RPS9 RPS9 2800 0.091 0.14 YES
32 UPF3A UPF3A UPF3A 2846 0.089 0.15 YES
33 NUP62 NUP62 NUP62 2853 0.089 0.16 YES
34 RPL39 RPL39 RPL39 2873 0.088 0.16 YES
35 RPS15A RPS15A RPS15A 2879 0.088 0.17 YES
36 RPS3A RPS3A RPS3A 2920 0.087 0.17 YES
37 RPS4Y1 RPS4Y1 RPS4Y1 2924 0.087 0.18 YES
38 RPS25 RPS25 RPS25 3040 0.084 0.18 YES
39 RPL12 RPL12 RPL12 3046 0.084 0.19 YES
40 PRKCD PRKCD PRKCD 3066 0.083 0.19 YES
41 RPL3 RPL3 RPL3 3183 0.08 0.19 YES
42 RPS29 RPS29 RPS29 3189 0.08 0.2 YES
43 RPS27 RPS27 RPS27 3246 0.078 0.2 YES
44 RPS24 RPS24 RPS24 3248 0.078 0.21 YES
45 RPL27 RPL27 RPL27 3255 0.078 0.21 YES
46 UPF2 UPF2 UPF2 3309 0.076 0.22 YES
47 RPSA RPSA RPSA 3331 0.076 0.22 YES
48 EXOSC7 EXOSC7 EXOSC7 3339 0.075 0.23 YES
49 ZFP36 ZFP36 ZFP36 3372 0.075 0.23 YES
50 RPS6 RPS6 RPS6 3381 0.074 0.24 YES
51 RPL4 RPL4 RPL4 3402 0.074 0.24 YES
52 WDR77 WDR77 WDR77 3437 0.073 0.25 YES
53 RPL27A RPL27A RPL27A 3440 0.073 0.25 YES
54 PSMA5 PSMA5 PSMA5 3454 0.072 0.26 YES
55 RPL26 RPL26 RPL26 3525 0.071 0.26 YES
56 MAGOH MAGOH MAGOH 3526 0.071 0.26 YES
57 RPL8 RPL8 RPL8 3575 0.069 0.27 YES
58 RPL34 RPL34 RPL34 3580 0.069 0.27 YES
59 RPL19 RPL19 RPL19 3592 0.069 0.28 YES
60 CNOT3 CNOT3 CNOT3 3596 0.069 0.28 YES
61 RPS14 RPS14 RPS14 3631 0.068 0.29 YES
62 RPL32 RPL32 RPL32 3633 0.068 0.29 YES
63 PSMB2 PSMB2 PSMB2 3663 0.067 0.3 YES
64 FAU FAU FAU 3684 0.067 0.3 YES
65 RPL38 RPL38 RPL38 3699 0.067 0.3 YES
66 RPL29 RPL29 RPL29 3722 0.066 0.31 YES
67 RPL37A RPL37A RPL37A 3725 0.066 0.31 YES
68 EXOSC1 EXOSC1 EXOSC1 3741 0.066 0.32 YES
69 RPL35A RPL35A RPL35A 3757 0.066 0.32 YES
70 RPLP2 RPLP2 RPLP2 3772 0.065 0.33 YES
71 RPL10 RPL10 RPL10 3800 0.065 0.33 YES
72 RPL15 RPL15 RPL15 3858 0.064 0.33 YES
73 RPS23 RPS23 RPS23 3865 0.064 0.34 YES
74 RPS18 RPS18 RPS18 3885 0.063 0.34 YES
75 RPS15 RPS15 RPS15 3907 0.063 0.35 YES
76 EIF4B EIF4B EIF4B 4010 0.061 0.35 YES
77 RPS27A RPS27A RPS27A 4026 0.06 0.35 YES
78 RPS21 RPS21 RPS21 4051 0.06 0.35 YES
79 PRMT5 PRMT5 PRMT5 4068 0.06 0.36 YES
80 RPL6 RPL6 RPL6 4110 0.059 0.36 YES
81 RPS13 RPS13 RPS13 4180 0.058 0.36 YES
82 RPL13 RPL13 RPL13 4237 0.057 0.36 YES
83 ANP32A ANP32A ANP32A 4243 0.056 0.37 YES
84 LSM2 LSM2 LSM2 4263 0.056 0.37 YES
85 GEMIN7 GEMIN7 GEMIN7 4307 0.055 0.37 YES
86 RPL36 RPL36 RPL36 4337 0.055 0.37 YES
87 EXOSC8 EXOSC8 EXOSC8 4340 0.055 0.38 YES
88 KHSRP KHSRP KHSRP 4345 0.055 0.38 YES
89 RPS4X RPS4X RPS4X 4348 0.055 0.39 YES
90 RPL36A RPL36A RPL36A 4350 0.055 0.39 YES
91 DDX6 DDX6 DDX6 4422 0.054 0.39 YES
92 SNRPD2 SNRPD2 SNRPD2 4437 0.053 0.4 YES
93 RPL37 RPL37 RPL37 4443 0.053 0.4 YES
94 RPL35 RPL35 RPL35 4517 0.052 0.4 YES
95 RPL14 RPL14 RPL14 4519 0.052 0.4 YES
96 XRN1 XRN1 XRN1 4532 0.052 0.41 YES
97 RPS12 RPS12 RPS12 4574 0.051 0.41 YES
98 RPL41 RPL41 RPL41 4640 0.05 0.41 YES
99 NUP188 NUP188 NUP188 4700 0.049 0.41 YES
100 PATL1 PATL1 PATL1 4768 0.048 0.41 YES
101 PSMC4 PSMC4 PSMC4 4796 0.048 0.41 YES
102 UPF3B UPF3B UPF3B 4842 0.047 0.41 YES
103 RPL24 RPL24 RPL24 4931 0.046 0.41 YES
104 RPL23A RPL23A RPL23A 4989 0.045 0.41 YES
105 RPS20 RPS20 RPS20 5060 0.044 0.41 YES
106 GEMIN4 GEMIN4 GEMIN4 5087 0.044 0.42 YES
107 DCP1A DCP1A DCP1A 5088 0.044 0.42 YES
108 EIF4A3 EIF4A3 EIF4A3 5162 0.042 0.42 YES
109 LSM6 LSM6 LSM6 5195 0.042 0.42 YES
110 RPL10A RPL10A RPL10A 5285 0.041 0.42 YES
111 EXOSC4 EXOSC4 EXOSC4 5287 0.041 0.42 YES
112 RPS7 RPS7 RPS7 5305 0.04 0.42 YES
113 UBA52 UBA52 UBA52 5314 0.04 0.43 YES
114 DCP1B DCP1B DCP1B 5441 0.038 0.42 NO
115 CLNS1A CLNS1A CLNS1A 5457 0.038 0.42 NO
116 RBM8A RBM8A RBM8A 5484 0.038 0.43 NO
117 RPS26 RPS26 RPS26 5648 0.036 0.42 NO
118 RPL31 RPL31 RPL31 5743 0.034 0.42 NO
119 CASC3 CASC3 CASC3 5856 0.033 0.41 NO
120 PSME1 PSME1 PSME1 5879 0.032 0.42 NO
121 HSPA1B HSPA1B HSPA1B 5937 0.032 0.42 NO
122 SMG6 SMG6 SMG6 5946 0.032 0.42 NO
123 XPO1 XPO1 XPO1 6049 0.03 0.41 NO
124 NUP205 NUP205 NUP205 6071 0.03 0.42 NO
125 NUP214 NUP214 NUP214 6113 0.03 0.42 NO
126 PSMA7 PSMA7 PSMA7 6219 0.029 0.41 NO
127 LSM1 LSM1 LSM1 6223 0.029 0.41 NO
128 PSMA3 PSMA3 PSMA3 6286 0.028 0.41 NO
129 HNRNPD HNRNPD HNRNPD 6323 0.027 0.41 NO
130 CNOT10 CNOT10 CNOT10 6331 0.027 0.42 NO
131 AAAS AAAS AAAS 6345 0.027 0.42 NO
132 TPR TPR TPR 6395 0.026 0.42 NO
133 PRKCA PRKCA PRKCA 6420 0.026 0.42 NO
134 NUP93 NUP93 NUP93 6435 0.026 0.42 NO
135 NCBP2 NCBP2 NCBP2 6454 0.026 0.42 NO
136 PSMA6 PSMA6 PSMA6 6603 0.024 0.41 NO
137 NUP153 NUP153 NUP153 6607 0.024 0.41 NO
138 POM121 POM121 POM121 6676 0.023 0.41 NO
139 CNOT6 CNOT6 CNOT6 6679 0.023 0.41 NO
140 NUP133 NUP133 NUP133 6798 0.022 0.41 NO
141 GEMIN5 GEMIN5 GEMIN5 6808 0.022 0.41 NO
142 NCBP1 NCBP1 NCBP1 6891 0.021 0.41 NO
143 PARN PARN PARN 6937 0.02 0.41 NO
144 SNRPG SNRPG SNRPG 6939 0.02 0.41 NO
145 CNOT8 CNOT8 CNOT8 6944 0.02 0.41 NO
146 SNRPF SNRPF SNRPF 6956 0.02 0.41 NO
147 AKT1 AKT1 AKT1 7035 0.019 0.41 NO
148 EXOSC2 EXOSC2 EXOSC2 7045 0.019 0.41 NO
149 EDC3 EDC3 EDC3 7057 0.019 0.41 NO
150 NUP85 NUP85 NUP85 7061 0.019 0.41 NO
151 PSME4 PSME4 PSME4 7232 0.017 0.4 NO
152 CNOT4 CNOT4 CNOT4 7290 0.016 0.4 NO
153 NUP54 NUP54 NUP54 7319 0.016 0.4 NO
154 SMN2 SMN2 SMN2 7354 0.016 0.4 NO
155 EDC4 EDC4 EDC4 7370 0.015 0.4 NO
156 SNRPD3 SNRPD3 SNRPD3 7401 0.015 0.4 NO
157 PSMD9 PSMD9 PSMD9 7502 0.014 0.4 NO
158 SNRPB SNRPB SNRPB 7571 0.013 0.39 NO
159 NUP107 NUP107 NUP107 7572 0.013 0.39 NO
160 PPP2R1A PPP2R1A PPP2R1A 7602 0.013 0.39 NO
161 EIF4A1 EIF4A1 EIF4A1 7637 0.013 0.39 NO
162 PSMC6 PSMC6 PSMC6 7647 0.013 0.39 NO
163 RPS28 RPS28 RPS28 7758 0.012 0.39 NO
164 SMG1 SMG1 SMG1 7768 0.011 0.39 NO
165 TNPO1 TNPO1 TNPO1 7806 0.011 0.39 NO
166 PSMD8 PSMD8 PSMD8 7920 0.0097 0.38 NO
167 TGS1 TGS1 TGS1 7941 0.0095 0.38 NO
168 NUP88 NUP88 NUP88 7944 0.0095 0.38 NO
169 PAIP1 PAIP1 PAIP1 8007 0.0086 0.38 NO
170 PSMB10 PSMB10 PSMB10 8074 0.0081 0.38 NO
171 CNOT7 CNOT7 CNOT7 8202 0.0067 0.37 NO
172 PSMF1 PSMF1 PSMF1 8227 0.0064 0.37 NO
173 C2orf29 C2orf29 C2orf29 8376 0.0049 0.36 NO
174 SMG5 SMG5 SMG5 8441 0.0043 0.36 NO
175 PSMB3 PSMB3 PSMB3 8444 0.0042 0.36 NO
176 PSMB4 PSMB4 PSMB4 8473 0.0038 0.36 NO
177 ELAVL1 ELAVL1 ELAVL1 8499 0.0035 0.36 NO
178 MAPK14 MAPK14 MAPK14 8501 0.0035 0.36 NO
179 LSM3 LSM3 LSM3 8518 0.0033 0.36 NO
180 RNPS1 RNPS1 RNPS1 8551 0.0031 0.35 NO
181 EIF4A2 EIF4A2 EIF4A2 8588 0.0028 0.35 NO
182 MAPKAPK2 MAPKAPK2 MAPKAPK2 8607 0.0026 0.35 NO
183 PSME2 PSME2 PSME2 8664 0.002 0.35 NO
184 PSMB6 PSMB6 PSMB6 8673 0.0019 0.35 NO
185 PSMD4 PSMD4 PSMD4 8721 0.0015 0.35 NO
186 TNKS1BP1 TNKS1BP1 TNKS1BP1 8789 0.00095 0.34 NO
187 RANBP2 RANBP2 RANBP2 8948 -0.00076 0.33 NO
188 PSMD2 PSMD2 PSMD2 9012 -0.0015 0.33 NO
189 GSPT2 GSPT2 GSPT2 9025 -0.0016 0.33 NO
190 SNRPE SNRPE SNRPE 9026 -0.0016 0.33 NO
191 LSM5 LSM5 LSM5 9117 -0.0025 0.32 NO
192 PSMD3 PSMD3 PSMD3 9119 -0.0025 0.32 NO
193 RQCD1 RQCD1 RQCD1 9148 -0.0028 0.32 NO
194 PSMD10 PSMD10 PSMD10 9186 -0.0032 0.32 NO
195 PSMC1 PSMC1 PSMC1 9216 -0.0034 0.32 NO
196 CNOT2 CNOT2 CNOT2 9222 -0.0035 0.32 NO
197 PSMD11 PSMD11 PSMD11 9254 -0.0038 0.32 NO
198 PSMD5 PSMD5 PSMD5 9341 -0.0047 0.32 NO
199 PSMA4 PSMA4 PSMA4 9352 -0.0048 0.32 NO
200 PSMA2 PSMA2 PSMA2 9359 -0.0049 0.32 NO
201 EXOSC3 EXOSC3 EXOSC3 9398 -0.0053 0.31 NO
202 PSMB5 PSMB5 PSMB5 9400 -0.0053 0.31 NO
203 EIF4G1 EIF4G1 EIF4G1 9418 -0.0056 0.31 NO
204 RAE1 RAE1 RAE1 9467 -0.0062 0.31 NO
205 PSMD6 PSMD6 PSMD6 9473 -0.0063 0.31 NO
206 PSMC2 PSMC2 PSMC2 9486 -0.0064 0.31 NO
207 PPP2R2A PPP2R2A PPP2R2A 9525 -0.007 0.31 NO
208 PSMA1 PSMA1 PSMA1 9664 -0.0085 0.3 NO
209 NUP50 NUP50 NUP50 9682 -0.0086 0.3 NO
210 NUP155 NUP155 NUP155 9708 -0.0089 0.3 NO
211 ETF1 ETF1 ETF1 9712 -0.0089 0.3 NO
212 PSMB7 PSMB7 PSMB7 9744 -0.0093 0.3 NO
213 PSMC3 PSMC3 PSMC3 9767 -0.0096 0.3 NO
214 SMG7 SMG7 SMG7 9902 -0.011 0.29 NO
215 PSMC5 PSMC5 PSMC5 10123 -0.014 0.28 NO
216 NUP43 NUP43 NUP43 10160 -0.014 0.28 NO
217 NUPL2 NUPL2 NUPL2 10356 -0.017 0.27 NO
218 NUP37 NUP37 NUP37 10401 -0.017 0.27 NO
219 PHAX PHAX PHAX 10429 -0.018 0.27 NO
220 DCP2 DCP2 DCP2 10555 -0.019 0.27 NO
221 PSMD13 PSMD13 PSMD13 10742 -0.022 0.26 NO
222 TNFSF13 TNFSF13 TNFSF13 10818 -0.023 0.26 NO
223 PSMB8 PSMB8 PSMB8 10852 -0.023 0.26 NO
224 PPP2CA PPP2CA PPP2CA 10894 -0.024 0.26 NO
225 PSMD7 PSMD7 PSMD7 10920 -0.024 0.26 NO
226 GEMIN6 GEMIN6 GEMIN6 10921 -0.024 0.26 NO
227 NUP35 NUP35 NUP35 10935 -0.024 0.26 NO
228 PSMB1 PSMB1 PSMB1 10965 -0.025 0.26 NO
229 SMN1 SMN1 SMN1 10966 -0.025 0.26 NO
230 NUPL1 NUPL1 NUPL1 11041 -0.026 0.26 NO
231 RPL26L1 RPL26L1 RPL26L1 11124 -0.027 0.26 NO
232 SNRPD1 SNRPD1 SNRPD1 11146 -0.027 0.26 NO
233 HSPA8 HSPA8 HSPA8 11187 -0.028 0.26 NO
234 DIS3 DIS3 DIS3 11311 -0.03 0.25 NO
235 EIF4E EIF4E EIF4E 11322 -0.03 0.26 NO
236 PSMB9 PSMB9 PSMB9 11501 -0.032 0.25 NO
237 DCPS DCPS DCPS 11958 -0.04 0.23 NO
238 EXOSC9 EXOSC9 EXOSC9 11997 -0.04 0.23 NO
239 PSMD1 PSMD1 PSMD1 12024 -0.041 0.23 NO
240 PSMD12 PSMD12 PSMD12 12049 -0.041 0.23 NO
241 SEH1L SEH1L SEH1L 12163 -0.043 0.23 NO
242 EXOSC6 EXOSC6 EXOSC6 12231 -0.044 0.23 NO
243 YWHAZ YWHAZ YWHAZ 12397 -0.048 0.22 NO
244 SNUPN SNUPN SNUPN 12426 -0.049 0.22 NO
245 LSM4 LSM4 LSM4 12430 -0.049 0.23 NO
246 PSMD14 PSMD14 PSMD14 12851 -0.059 0.21 NO
247 YWHAB YWHAB YWHAB 12949 -0.061 0.21 NO
248 PSMA8 PSMA8 PSMA8 14627 -0.12 0.13 NO
249 HSPB1 HSPB1 HSPB1 15226 -0.15 0.11 NO
250 MAPK11 MAPK11 MAPK11 15619 -0.18 0.099 NO
251 NUP210 NUP210 NUP210 15691 -0.18 0.11 NO
252 FAM153A FAM153A FAM153A 17676 -0.44 0.035 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: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, 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 CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES

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 RPS8 RPS8 RPS8 1575 0.15 -0.047 YES
2 RPS16 RPS16 RPS16 1623 0.14 -0.011 YES
3 PABPC1 PABPC1 PABPC1 2139 0.12 -0.0082 YES
4 RPSAP9 RPSAP9 RPSAP9 2160 0.12 0.022 YES
5 RPS5 RPS5 RPS5 2199 0.11 0.05 YES
6 RPS19 RPS19 RPS19 2204 0.11 0.08 YES
7 RPS11 RPS11 RPS11 2293 0.11 0.1 YES
8 RPS3 RPS3 RPS3 2356 0.11 0.13 YES
9 RPS10 RPS10 RPS10 2521 0.1 0.15 YES
10 RPS2 RPS2 RPS2 2564 0.099 0.17 YES
11 RPS17 RPS17 RPS17 2776 0.092 0.18 YES
12 RPS9 RPS9 RPS9 2800 0.091 0.21 YES
13 RPS15A RPS15A RPS15A 2879 0.088 0.23 YES
14 RPS3A RPS3A RPS3A 2920 0.087 0.25 YES
15 RPS4Y1 RPS4Y1 RPS4Y1 2924 0.087 0.27 YES
16 RPS25 RPS25 RPS25 3040 0.084 0.29 YES
17 EIF3H EIF3H EIF3H 3052 0.083 0.31 YES
18 RPS29 RPS29 RPS29 3189 0.08 0.32 YES
19 RPS27 RPS27 RPS27 3246 0.078 0.34 YES
20 RPS24 RPS24 RPS24 3248 0.078 0.36 YES
21 RPSA RPSA RPSA 3331 0.076 0.38 YES
22 EIF4EBP1 EIF4EBP1 EIF4EBP1 3337 0.075 0.4 YES
23 EIF3E EIF3E EIF3E 3343 0.075 0.42 YES
24 RPS6 RPS6 RPS6 3381 0.074 0.44 YES
25 EIF3I EIF3I EIF3I 3390 0.074 0.46 YES
26 RPS14 RPS14 RPS14 3631 0.068 0.46 YES
27 FAU FAU FAU 3684 0.067 0.48 YES
28 RPS23 RPS23 RPS23 3865 0.064 0.48 YES
29 RPS18 RPS18 RPS18 3885 0.063 0.5 YES
30 RPS15 RPS15 RPS15 3907 0.063 0.52 YES
31 EIF4B EIF4B EIF4B 4010 0.061 0.53 YES
32 RPS27A RPS27A RPS27A 4026 0.06 0.54 YES
33 RPS21 RPS21 RPS21 4051 0.06 0.56 YES
34 EIF3D EIF3D EIF3D 4094 0.059 0.57 YES
35 RPS13 RPS13 RPS13 4180 0.058 0.58 YES
36 RPS4X RPS4X RPS4X 4348 0.055 0.59 YES
37 RPS12 RPS12 RPS12 4574 0.051 0.59 YES
38 EIF3F EIF3F EIF3F 4853 0.047 0.58 YES
39 EIF3J EIF3J EIF3J 4917 0.046 0.59 YES
40 RPS20 RPS20 RPS20 5060 0.044 0.6 YES
41 EIF3A EIF3A EIF3A 5109 0.043 0.61 YES
42 RPS7 RPS7 RPS7 5305 0.04 0.61 YES
43 EIF3G EIF3G EIF3G 5576 0.036 0.6 YES
44 RPS26 RPS26 RPS26 5648 0.036 0.61 YES
45 EIF3K EIF3K EIF3K 6193 0.029 0.59 NO
46 EIF4A1 EIF4A1 EIF4A1 7637 0.013 0.51 NO
47 RPS28 RPS28 RPS28 7758 0.012 0.51 NO
48 EIF3B EIF3B EIF3B 7982 0.009 0.5 NO
49 EIF4H EIF4H EIF4H 8147 0.0072 0.49 NO
50 EIF2S2 EIF2S2 EIF2S2 8260 0.006 0.49 NO
51 EIF4A2 EIF4A2 EIF4A2 8588 0.0028 0.47 NO
52 EIF2S3 EIF2S3 EIF2S3 8655 0.0021 0.46 NO
53 EIF1AX EIF1AX EIF1AX 8667 0.002 0.46 NO
54 EIF4G1 EIF4G1 EIF4G1 9418 -0.0056 0.43 NO
55 EIF2S1 EIF2S1 EIF2S1 10138 -0.014 0.39 NO
56 EIF4E EIF4E EIF4E 11322 -0.03 0.33 NO
57 EIF3C EIF3C EIF3C 15690 -0.18 0.14 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: REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME CROSS PRESENTATION OF SOLUBLE EXOGENOUS ANTIGENS ENDOSOMES, 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 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE

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 RPL21 RPL21 RPL21 660 0.24 -0.0046 YES
2 RPS8 RPS8 RPS8 1575 0.15 -0.036 YES
3 RPL22 RPL22 RPL22 1592 0.14 -0.018 YES
4 RPS16 RPS16 RPS16 1623 0.14 -0.0012 YES
5 RPL18 RPL18 RPL18 1633 0.14 0.017 YES
6 RPL11 RPL11 RPL11 1635 0.14 0.035 YES
7 RPL13A RPL13A RPL13A 1674 0.14 0.051 YES
8 RPL5 RPL5 RPL5 1705 0.14 0.067 YES
9 RPL9 RPL9 RPL9 1806 0.13 0.079 YES
10 PABPC1 PABPC1 PABPC1 2139 0.12 0.076 YES
11 RPSAP9 RPSAP9 RPSAP9 2160 0.12 0.089 YES
12 RPS5 RPS5 RPS5 2199 0.11 0.1 YES
13 RPS19 RPS19 RPS19 2204 0.11 0.12 YES
14 RPLP0 RPLP0 RPLP0 2213 0.11 0.13 YES
15 RPL7 RPL7 RPL7 2267 0.11 0.14 YES
16 RPS11 RPS11 RPS11 2293 0.11 0.15 YES
17 RPS3 RPS3 RPS3 2356 0.11 0.16 YES
18 RPL17 RPL17 RPL17 2469 0.1 0.17 YES
19 RPS10 RPS10 RPS10 2521 0.1 0.18 YES
20 RPS2 RPS2 RPS2 2564 0.099 0.19 YES
21 RPL28 RPL28 RPL28 2651 0.096 0.2 YES
22 RPL18A RPL18A RPL18A 2663 0.095 0.21 YES
23 RPL7A RPL7A RPL7A 2714 0.094 0.22 YES
24 RPL30 RPL30 RPL30 2725 0.093 0.23 YES
25 RPLP1 RPLP1 RPLP1 2760 0.092 0.24 YES
26 RPS17 RPS17 RPS17 2776 0.092 0.25 YES
27 RPL23 RPL23 RPL23 2781 0.092 0.26 YES
28 RPS9 RPS9 RPS9 2800 0.091 0.28 YES
29 UPF3A UPF3A UPF3A 2846 0.089 0.28 YES
30 RPL39 RPL39 RPL39 2873 0.088 0.3 YES
31 RPS15A RPS15A RPS15A 2879 0.088 0.31 YES
32 RPS3A RPS3A RPS3A 2920 0.087 0.32 YES
33 RPS4Y1 RPS4Y1 RPS4Y1 2924 0.087 0.33 YES
34 RPS25 RPS25 RPS25 3040 0.084 0.33 YES
35 RPL12 RPL12 RPL12 3046 0.084 0.34 YES
36 RPL3 RPL3 RPL3 3183 0.08 0.34 YES
37 RPS29 RPS29 RPS29 3189 0.08 0.35 YES
38 RPS27 RPS27 RPS27 3246 0.078 0.36 YES
39 RPS24 RPS24 RPS24 3248 0.078 0.37 YES
40 RPL27 RPL27 RPL27 3255 0.078 0.38 YES
41 UPF2 UPF2 UPF2 3309 0.076 0.39 YES
42 RPSA RPSA RPSA 3331 0.076 0.4 YES
43 RPS6 RPS6 RPS6 3381 0.074 0.4 YES
44 RPL4 RPL4 RPL4 3402 0.074 0.41 YES
45 RPL27A RPL27A RPL27A 3440 0.073 0.42 YES
46 RPL26 RPL26 RPL26 3525 0.071 0.42 YES
47 MAGOH MAGOH MAGOH 3526 0.071 0.43 YES
48 RPL8 RPL8 RPL8 3575 0.069 0.44 YES
49 RPL34 RPL34 RPL34 3580 0.069 0.45 YES
50 RPL19 RPL19 RPL19 3592 0.069 0.46 YES
51 RPS14 RPS14 RPS14 3631 0.068 0.46 YES
52 RPL32 RPL32 RPL32 3633 0.068 0.47 YES
53 FAU FAU FAU 3684 0.067 0.48 YES
54 RPL38 RPL38 RPL38 3699 0.067 0.49 YES
55 RPL29 RPL29 RPL29 3722 0.066 0.49 YES
56 RPL37A RPL37A RPL37A 3725 0.066 0.5 YES
57 RPL35A RPL35A RPL35A 3757 0.066 0.51 YES
58 RPLP2 RPLP2 RPLP2 3772 0.065 0.52 YES
59 RPL10 RPL10 RPL10 3800 0.065 0.52 YES
60 RPL15 RPL15 RPL15 3858 0.064 0.53 YES
61 RPS23 RPS23 RPS23 3865 0.064 0.54 YES
62 RPS18 RPS18 RPS18 3885 0.063 0.54 YES
63 RPS15 RPS15 RPS15 3907 0.063 0.55 YES
64 RPS27A RPS27A RPS27A 4026 0.06 0.55 YES
65 RPS21 RPS21 RPS21 4051 0.06 0.56 YES
66 RPL6 RPL6 RPL6 4110 0.059 0.56 YES
67 RPS13 RPS13 RPS13 4180 0.058 0.57 YES
68 RPL13 RPL13 RPL13 4237 0.057 0.57 YES
69 RPL36 RPL36 RPL36 4337 0.055 0.57 YES
70 RPS4X RPS4X RPS4X 4348 0.055 0.58 YES
71 RPL36A RPL36A RPL36A 4350 0.055 0.58 YES
72 RPL37 RPL37 RPL37 4443 0.053 0.59 YES
73 RPL35 RPL35 RPL35 4517 0.052 0.59 YES
74 RPL14 RPL14 RPL14 4519 0.052 0.6 YES
75 RPS12 RPS12 RPS12 4574 0.051 0.6 YES
76 RPL41 RPL41 RPL41 4640 0.05 0.6 YES
77 UPF3B UPF3B UPF3B 4842 0.047 0.6 YES
78 RPL24 RPL24 RPL24 4931 0.046 0.6 YES
79 RPL23A RPL23A RPL23A 4989 0.045 0.6 YES
80 RPS20 RPS20 RPS20 5060 0.044 0.6 YES
81 EIF4A3 EIF4A3 EIF4A3 5162 0.042 0.6 YES
82 RPL10A RPL10A RPL10A 5285 0.041 0.6 YES
83 RPS7 RPS7 RPS7 5305 0.04 0.61 YES
84 UBA52 UBA52 UBA52 5314 0.04 0.61 YES
85 RBM8A RBM8A RBM8A 5484 0.038 0.61 NO
86 RPS26 RPS26 RPS26 5648 0.036 0.6 NO
87 RPL31 RPL31 RPL31 5743 0.034 0.6 NO
88 CASC3 CASC3 CASC3 5856 0.033 0.6 NO
89 SMG6 SMG6 SMG6 5946 0.032 0.6 NO
90 NCBP2 NCBP2 NCBP2 6454 0.026 0.57 NO
91 NCBP1 NCBP1 NCBP1 6891 0.021 0.55 NO
92 PPP2R1A PPP2R1A PPP2R1A 7602 0.013 0.52 NO
93 RPS28 RPS28 RPS28 7758 0.012 0.51 NO
94 SMG1 SMG1 SMG1 7768 0.011 0.51 NO
95 SMG5 SMG5 SMG5 8441 0.0043 0.47 NO
96 RNPS1 RNPS1 RNPS1 8551 0.0031 0.47 NO
97 GSPT2 GSPT2 GSPT2 9025 -0.0016 0.44 NO
98 EIF4G1 EIF4G1 EIF4G1 9418 -0.0056 0.42 NO
99 PPP2R2A PPP2R2A PPP2R2A 9525 -0.007 0.42 NO
100 ETF1 ETF1 ETF1 9712 -0.0089 0.41 NO
101 SMG7 SMG7 SMG7 9902 -0.011 0.4 NO
102 PPP2CA PPP2CA PPP2CA 10894 -0.024 0.35 NO
103 RPL26L1 RPL26L1 RPL26L1 11124 -0.027 0.34 NO
104 FAM153A FAM153A FAM153A 17676 -0.44 0.035 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: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, 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 THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

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 SRRM1 SRRM1 SRRM1 2842 0.09 -0.039 YES
2 MAGOH MAGOH MAGOH 3526 0.071 0.016 YES
3 U2AF2 U2AF2 U2AF2 4222 0.057 0.052 YES
4 CPSF7 CPSF7 CPSF7 4503 0.052 0.1 YES
5 CPSF1 CPSF1 CPSF1 4504 0.052 0.17 YES
6 CPSF2 CPSF2 CPSF2 4575 0.051 0.24 YES
7 PABPN1 PABPN1 PABPN1 4790 0.048 0.29 YES
8 UPF3B UPF3B UPF3B 4842 0.047 0.34 YES
9 RBM8A RBM8A RBM8A 5484 0.038 0.36 YES
10 PCF11 PCF11 PCF11 5626 0.036 0.4 YES
11 DHX38 DHX38 DHX38 5834 0.033 0.43 YES
12 CSTF2 CSTF2 CSTF2 6417 0.026 0.43 YES
13 NCBP2 NCBP2 NCBP2 6454 0.026 0.46 YES
14 PAPOLA PAPOLA PAPOLA 6464 0.026 0.5 YES
15 NFX1 NFX1 NFX1 6624 0.024 0.52 YES
16 NCBP1 NCBP1 NCBP1 6891 0.021 0.53 YES
17 CSTF3 CSTF3 CSTF3 7508 0.014 0.52 NO
18 CLP1 CLP1 CLP1 7642 0.013 0.53 NO
19 U2AF1 U2AF1 U2AF1 7969 0.0092 0.52 NO
20 THOC4 THOC4 THOC4 8246 0.0062 0.51 NO
21 CPSF3 CPSF3 CPSF3 8303 0.0056 0.52 NO
22 RNPS1 RNPS1 RNPS1 8551 0.0031 0.51 NO
23 NUDT21 NUDT21 NUDT21 8587 0.0028 0.51 NO
24 CSTF1 CSTF1 CSTF1 9129 -0.0026 0.48 NO
25 CDC40 CDC40 CDC40 10185 -0.014 0.44 NO

Figure S19.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, 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 PYRIMIDINE METABOLISM 98 genes.ES.table 0.34 1.4 0.1 0.21 1 0.44 0.36 0.28 0.16 0.001
KEGG N GLYCAN BIOSYNTHESIS 46 genes.ES.table 0.4 1.5 0.091 0.2 0.98 0.72 0.4 0.44 0.13 0.008
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 44 genes.ES.table 0.49 1.6 0.042 0.22 0.94 0.61 0.36 0.4 0.12 0.023
KEGG DNA REPLICATION 36 genes.ES.table 0.57 1.4 0.17 0.21 1 0.5 0.23 0.38 0.16 0.001
KEGG PROTEASOME 43 genes.ES.table 0.43 1.4 0.18 0.23 1 0.49 0.39 0.3 0.19 0.001
KEGG NUCLEOTIDE EXCISION REPAIR 44 genes.ES.table 0.45 1.6 0.075 0.22 0.92 0.41 0.34 0.27 0.12 0.023
KEGG HOMOLOGOUS RECOMBINATION 26 genes.ES.table 0.66 1.5 0.063 0.2 0.99 0.35 0.14 0.3 0.13 0.004
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION 222 genes.ES.table 0.6 1.5 0.044 0.2 0.99 0.56 0.23 0.44 0.14 0.004
KEGG CELL CYCLE 118 genes.ES.table 0.57 1.6 0.076 0.21 0.96 0.41 0.23 0.32 0.13 0.017
KEGG P53 SIGNALING PATHWAY 67 genes.ES.table 0.53 1.5 0.043 0.2 0.98 0.37 0.18 0.31 0.13 0.007
genes ES table in pathway: KEGG PYRIMIDINE 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 288 0.64 0.062 YES
2 CASP8 CASP8 CASP8 427 0.58 0.12 YES
3 RNF135 RNF135 RNF135 860 0.46 0.16 YES
4 HERC5 HERC5 HERC5 919 0.46 0.21 YES
5 IRF1 IRF1 IRF1 1127 0.42 0.25 YES
6 ISG15 ISG15 ISG15 1224 0.4 0.29 YES
7 IRF7 IRF7 IRF7 1261 0.39 0.34 YES
8 NLRC5 NLRC5 NLRC5 1431 0.36 0.38 YES
9 IFIH1 IFIH1 IFIH1 1617 0.34 0.41 YES
10 IKBKE IKBKE IKBKE 1802 0.32 0.44 YES
11 TNFAIP3 TNFAIP3 TNFAIP3 2076 0.29 0.46 YES
12 CASP10 CASP10 CASP10 2570 0.24 0.46 YES
13 MAP3K1 MAP3K1 MAP3K1 2752 0.23 0.48 YES
14 UBA7 UBA7 UBA7 2903 0.22 0.49 YES
15 DHX58 DHX58 DHX58 3262 0.19 0.5 YES
16 RIPK1 RIPK1 RIPK1 3400 0.18 0.51 YES
17 NFKB2 NFKB2 NFKB2 3642 0.17 0.52 YES
18 NFKBIB NFKBIB NFKBIB 3687 0.16 0.54 YES
19 DDX58 DDX58 DDX58 3727 0.16 0.56 YES
20 IRF3 IRF3 IRF3 3783 0.16 0.57 YES
21 FADD FADD FADD 3851 0.15 0.59 YES
22 SIKE1 SIKE1 SIKE1 4669 0.12 0.56 NO
23 IRF2 IRF2 IRF2 5063 0.1 0.55 NO
24 S100A12 S100A12 S100A12 5107 0.099 0.56 NO
25 TRAF2 TRAF2 TRAF2 5455 0.086 0.55 NO
26 IKBKB IKBKB IKBKB 5555 0.084 0.55 NO
27 TANK TANK TANK 5967 0.072 0.54 NO
28 TRIM25 TRIM25 TRIM25 6165 0.067 0.54 NO
29 S100B S100B S100B 6344 0.062 0.54 NO
30 UBE2L6 UBE2L6 UBE2L6 6576 0.057 0.53 NO
31 TBK1 TBK1 TBK1 7426 0.038 0.49 NO
32 TRAF6 TRAF6 TRAF6 8582 0.018 0.43 NO
33 ATG5 ATG5 ATG5 8624 0.018 0.43 NO
34 UBA52 UBA52 UBA52 8661 0.017 0.43 NO
35 UBE2D3 UBE2D3 UBE2D3 8674 0.017 0.43 NO
36 MAVS MAVS MAVS 8690 0.017 0.43 NO
37 RNF125 RNF125 RNF125 8758 0.015 0.43 NO
38 CYLD CYLD CYLD 9072 0.01 0.41 NO
39 TAX1BP1 TAX1BP1 TAX1BP1 9284 0.0063 0.4 NO
40 RELA RELA RELA 9414 0.0041 0.39 NO
41 UBE2D2 UBE2D2 UBE2D2 9671 0.000065 0.38 NO
42 IKBKG IKBKG IKBKG 9731 -0.00092 0.38 NO
43 HMGB1 HMGB1 HMGB1 9921 -0.0048 0.37 NO
44 APP APP APP 10248 -0.011 0.35 NO
45 UBE2K UBE2K UBE2K 10257 -0.011 0.35 NO
46 ATG12 ATG12 ATG12 10259 -0.011 0.35 NO
47 AGER AGER AGER 10402 -0.013 0.35 NO
48 DAK DAK DAK 10836 -0.021 0.32 NO
49 PCBP2 PCBP2 PCBP2 11239 -0.027 0.31 NO
50 UBE2D1 UBE2D1 UBE2D1 11425 -0.03 0.3 NO
51 PIN1 PIN1 PIN1 11782 -0.037 0.28 NO
52 CHUK CHUK CHUK 11874 -0.038 0.28 NO
53 NFKBIA NFKBIA NFKBIA 12313 -0.047 0.27 NO
54 CREBBP CREBBP CREBBP 13162 -0.065 0.23 NO
55 TRAF3 TRAF3 TRAF3 13166 -0.065 0.24 NO
56 RPS27A RPS27A RPS27A 13221 -0.066 0.24 NO
57 NLRX1 NLRX1 NLRX1 13261 -0.067 0.25 NO
58 OTUD5 OTUD5 OTUD5 13612 -0.076 0.24 NO
59 EP300 EP300 EP300 13814 -0.081 0.24 NO
60 IFNA21 IFNA21 IFNA21 13998 -0.087 0.24 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 PYRIMIDINE METABOLISM.

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

genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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 PLAUR PLAUR PLAUR 236 0.65 0.27 YES
2 PIGB PIGB PIGB 3778 0.16 0.14 YES
3 PIGT PIGT PIGT 4076 0.14 0.19 YES
4 PIGK PIGK PIGK 4398 0.13 0.22 YES
5 PIGW PIGW PIGW 4524 0.12 0.27 YES
6 PIGG PIGG PIGG 4873 0.11 0.3 YES
7 PIGL PIGL PIGL 4931 0.11 0.34 YES
8 PIGN PIGN PIGN 5043 0.1 0.38 YES
9 DPM3 DPM3 DPM3 5605 0.083 0.38 YES
10 SEMA6D SEMA6D SEMA6D 5718 0.079 0.41 YES
11 PIGP PIGP PIGP 5973 0.072 0.43 YES
12 DPM1 DPM1 DPM1 5985 0.072 0.46 YES
13 PIGC PIGC PIGC 6058 0.07 0.48 YES
14 PIGA PIGA PIGA 6198 0.066 0.5 YES
15 PIGU PIGU PIGU 6359 0.062 0.52 YES
16 PIGF PIGF PIGF 6630 0.056 0.53 YES
17 DPM2 DPM2 DPM2 7245 0.042 0.52 NO
18 PIGV PIGV PIGV 7513 0.037 0.52 NO
19 PIGQ PIGQ PIGQ 8172 0.026 0.49 NO
20 PIGO PIGO PIGO 8685 0.017 0.47 NO
21 GPAA1 GPAA1 GPAA1 9626 0.00066 0.42 NO
22 PIGX PIGX PIGX 10324 -0.012 0.39 NO
23 PGAP1 PGAP1 PGAP1 10788 -0.02 0.37 NO
24 PIGM PIGM PIGM 11420 -0.03 0.35 NO
25 PIGH PIGH PIGH 11456 -0.031 0.36 NO
26 PIGS PIGS PIGS 11743 -0.036 0.36 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: KEGG N GLYCAN BIOSYNTHESIS.

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG N 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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 IL2RG IL2RG IL2RG 96 0.75 0.08 YES
2 SOCS3 SOCS3 SOCS3 105 0.74 0.16 YES
3 IL2RB IL2RB IL2RB 111 0.74 0.24 YES
4 SOCS1 SOCS1 SOCS1 215 0.67 0.32 YES
5 FASLG FASLG FASLG 324 0.62 0.38 YES
6 JAK3 JAK3 JAK3 619 0.52 0.42 YES
7 IKZF3 IKZF3 IKZF3 649 0.52 0.48 YES
8 PIK3CG PIK3CG PIK3CG 863 0.46 0.52 YES
9 NMI NMI NMI 917 0.46 0.57 YES
10 IL2RA IL2RA IL2RA 1107 0.42 0.6 YES
11 FAS FAS FAS 1538 0.35 0.62 YES
12 STAT5A STAT5A STAT5A 1918 0.3 0.63 YES
13 PTPN6 PTPN6 PTPN6 1984 0.3 0.66 YES
14 E2F1 E2F1 E2F1 2202 0.28 0.68 YES
15 SYK SYK SYK 2450 0.25 0.7 YES
16 SHC1 SHC1 SHC1 2673 0.23 0.71 YES
17 FOS FOS FOS 2728 0.23 0.73 YES
18 CFLAR CFLAR CFLAR 3416 0.18 0.72 NO
19 BCL2L1 BCL2L1 BCL2L1 7675 0.034 0.49 NO
20 AKT1 AKT1 AKT1 7717 0.033 0.49 NO
21 PPIA PPIA PPIA 8090 0.027 0.47 NO
22 BAD BAD BAD 8723 0.016 0.44 NO
23 GRB2 GRB2 GRB2 8778 0.015 0.44 NO
24 JAK1 JAK1 JAK1 9162 0.0084 0.42 NO
25 CBL CBL CBL 9622 0.00076 0.39 NO
26 RPS6KB1 RPS6KB1 RPS6KB1 9958 -0.0055 0.38 NO
27 RAF1 RAF1 RAF1 10373 -0.013 0.35 NO
28 SOS1 SOS1 SOS1 10910 -0.022 0.33 NO
29 PIK3CA PIK3CA PIK3CA 10999 -0.023 0.32 NO
30 BCL2 BCL2 BCL2 11075 -0.024 0.32 NO
31 STAT5B STAT5B STAT5B 11309 -0.028 0.31 NO
32 HRAS HRAS HRAS 11882 -0.039 0.29 NO
33 CRKL CRKL CRKL 12618 -0.053 0.25 NO
34 MAPK1 MAPK1 MAPK1 12887 -0.059 0.24 NO
35 IRS1 IRS1 IRS1 13738 -0.079 0.21 NO
36 MAPK3 MAPK3 MAPK3 13869 -0.083 0.21 NO
37 MYC MYC MYC 15292 -0.14 0.15 NO
38 PIK3R1 PIK3R1 PIK3R1 15743 -0.16 0.14 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: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

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

genes ES table in pathway: KEGG DNA REPLICATION

Table 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 SAA1 SAA1 SAA1 288 0.64 0.05 YES
2 RIPK3 RIPK3 RIPK3 543 0.54 0.092 YES
3 ZBP1 ZBP1 ZBP1 677 0.51 0.14 YES
4 CDK1 CDK1 CDK1 921 0.46 0.17 YES
5 TLR3 TLR3 TLR3 1098 0.42 0.2 YES
6 IRF7 IRF7 IRF7 1261 0.39 0.24 YES
7 RPS6KA1 RPS6KA1 RPS6KA1 1732 0.33 0.24 YES
8 IKBKE IKBKE IKBKE 1802 0.32 0.27 YES
9 IRAK2 IRAK2 IRAK2 1860 0.31 0.3 YES
10 NOD1 NOD1 NOD1 1946 0.3 0.33 YES
11 MAP2K3 MAP2K3 MAP2K3 2022 0.29 0.36 YES
12 DUSP6 DUSP6 DUSP6 2099 0.28 0.38 YES
13 NOD2 NOD2 NOD2 2284 0.27 0.4 YES
14 DUSP4 DUSP4 DUSP4 2372 0.26 0.42 YES
15 FOS FOS FOS 2728 0.23 0.42 YES
16 JUN JUN JUN 3029 0.21 0.43 YES
17 RIPK1 RIPK1 RIPK1 3400 0.18 0.43 YES
18 NFKB2 NFKB2 NFKB2 3642 0.17 0.43 YES
19 NFKBIB NFKBIB NFKBIB 3687 0.16 0.45 YES
20 RPS6KA3 RPS6KA3 RPS6KA3 3769 0.16 0.46 YES
21 IRF3 IRF3 IRF3 3783 0.16 0.47 YES
22 MAPKAPK3 MAPKAPK3 MAPKAPK3 4079 0.14 0.47 NO
23 MAPKAPK2 MAPKAPK2 MAPKAPK2 4522 0.12 0.46 NO
24 S100A12 S100A12 S100A12 5107 0.099 0.44 NO
25 IKBKB IKBKB IKBKB 5555 0.084 0.42 NO
26 IRAK1 IRAK1 IRAK1 5841 0.076 0.42 NO
27 S100B S100B S100B 6344 0.062 0.4 NO
28 MAPK7 MAPK7 MAPK7 6780 0.053 0.38 NO
29 TAB2 TAB2 TAB2 7100 0.045 0.36 NO
30 ATF1 ATF1 ATF1 7322 0.04 0.36 NO
31 TBK1 TBK1 TBK1 7426 0.038 0.35 NO
32 DUSP3 DUSP3 DUSP3 7837 0.031 0.34 NO
33 PPP2R1B PPP2R1B PPP2R1B 7945 0.03 0.33 NO
34 CREB1 CREB1 CREB1 8011 0.028 0.33 NO
35 TICAM1 TICAM1 TICAM1 8350 0.022 0.32 NO
36 ELK1 ELK1 ELK1 8447 0.021 0.31 NO
37 MAP3K7 MAP3K7 MAP3K7 8466 0.02 0.31 NO
38 TRAF6 TRAF6 TRAF6 8582 0.018 0.31 NO
39 MEF2A MEF2A MEF2A 8602 0.018 0.31 NO
40 UBA52 UBA52 UBA52 8661 0.017 0.31 NO
41 MAP2K2 MAP2K2 MAP2K2 8776 0.015 0.3 NO
42 MAPK14 MAPK14 MAPK14 8814 0.014 0.3 NO
43 RELA RELA RELA 9414 0.0041 0.27 NO
44 TAB3 TAB3 TAB3 9533 0.0024 0.26 NO
45 IKBKG IKBKG IKBKG 9731 -0.00092 0.25 NO
46 MAP2K7 MAP2K7 MAP2K7 9851 -0.0032 0.25 NO
47 HMGB1 HMGB1 HMGB1 9921 -0.0048 0.24 NO
48 APP APP APP 10248 -0.011 0.23 NO
49 AGER AGER AGER 10402 -0.013 0.22 NO
50 PPP2R1A PPP2R1A PPP2R1A 10558 -0.016 0.21 NO
51 PPP2CA PPP2CA PPP2CA 10560 -0.016 0.22 NO
52 PPP2CB PPP2CB PPP2CB 10592 -0.017 0.22 NO
53 MEF2C MEF2C MEF2C 10921 -0.022 0.2 NO
54 MAP2K6 MAP2K6 MAP2K6 11363 -0.029 0.18 NO
55 PPP2R5D PPP2R5D PPP2R5D 11861 -0.038 0.16 NO
56 CHUK CHUK CHUK 11874 -0.038 0.16 NO
57 NFKBIA NFKBIA NFKBIA 12313 -0.047 0.14 NO
58 MAPK1 MAPK1 MAPK1 12887 -0.059 0.11 NO
59 RPS6KA2 RPS6KA2 RPS6KA2 13071 -0.063 0.11 NO
60 RPS27A RPS27A RPS27A 13221 -0.066 0.11 NO
61 ATF2 ATF2 ATF2 13271 -0.067 0.11 NO
62 RIPK2 RIPK2 RIPK2 13625 -0.076 0.1 NO
63 MAP2K1 MAP2K1 MAP2K1 13802 -0.081 0.1 NO
64 MAPK3 MAPK3 MAPK3 13869 -0.083 0.1 NO
65 TAB1 TAB1 TAB1 14108 -0.091 0.1 NO
66 MAPK11 MAPK11 MAPK11 14117 -0.091 0.11 NO
67 MAP2K4 MAP2K4 MAP2K4 14924 -0.12 0.079 NO
68 DUSP7 DUSP7 DUSP7 14967 -0.12 0.09 NO
69 MAPK9 MAPK9 MAPK9 15195 -0.14 0.091 NO
70 MAPK10 MAPK10 MAPK10 16561 -0.23 0.04 NO
71 MAPK8 MAPK8 MAPK8 16652 -0.25 0.061 NO
72 RPS6KA5 RPS6KA5 RPS6KA5 17019 -0.29 0.071 NO

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

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

genes ES table in pathway: KEGG PROTEASOME

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 RNF135 RNF135 RNF135 860 0.46 0.075 YES
2 HERC5 HERC5 HERC5 919 0.46 0.19 YES
3 ISG15 ISG15 ISG15 1224 0.4 0.28 YES
4 NLRC5 NLRC5 NLRC5 1431 0.36 0.36 YES
5 IFIH1 IFIH1 IFIH1 1617 0.34 0.44 YES
6 IKBKE IKBKE IKBKE 1802 0.32 0.52 YES
7 TNFAIP3 TNFAIP3 TNFAIP3 2076 0.29 0.58 YES
8 UBA7 UBA7 UBA7 2903 0.22 0.59 YES
9 DDX58 DDX58 DDX58 3727 0.16 0.58 YES
10 IRF3 IRF3 IRF3 3783 0.16 0.62 YES
11 TRIM25 TRIM25 TRIM25 6165 0.067 0.51 NO
12 UBE2L6 UBE2L6 UBE2L6 6576 0.057 0.5 NO
13 TBK1 TBK1 TBK1 7426 0.038 0.47 NO
14 ATG5 ATG5 ATG5 8624 0.018 0.4 NO
15 UBA52 UBA52 UBA52 8661 0.017 0.41 NO
16 UBE2D3 UBE2D3 UBE2D3 8674 0.017 0.41 NO
17 MAVS MAVS MAVS 8690 0.017 0.42 NO
18 RNF125 RNF125 RNF125 8758 0.015 0.42 NO
19 CYLD CYLD CYLD 9072 0.01 0.4 NO
20 TAX1BP1 TAX1BP1 TAX1BP1 9284 0.0063 0.39 NO
21 UBE2D2 UBE2D2 UBE2D2 9671 0.000065 0.37 NO
22 UBE2K UBE2K UBE2K 10257 -0.011 0.34 NO
23 ATG12 ATG12 ATG12 10259 -0.011 0.34 NO
24 PCBP2 PCBP2 PCBP2 11239 -0.027 0.3 NO
25 UBE2D1 UBE2D1 UBE2D1 11425 -0.03 0.3 NO
26 PIN1 PIN1 PIN1 11782 -0.037 0.28 NO
27 TRAF3 TRAF3 TRAF3 13166 -0.065 0.23 NO
28 RPS27A RPS27A RPS27A 13221 -0.066 0.24 NO
29 NLRX1 NLRX1 NLRX1 13261 -0.067 0.26 NO
30 OTUD5 OTUD5 OTUD5 13612 -0.076 0.26 NO

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

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

genes ES table in pathway: KEGG NUCLEOTIDE EXCISION REPAIR

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 FASLG FASLG FASLG 324 0.62 0.095 YES
2 CASP8 CASP8 CASP8 427 0.58 0.19 YES
3 CASP6 CASP6 CASP6 808 0.48 0.26 YES
4 FAS FAS FAS 1538 0.35 0.28 YES
5 LMNB1 LMNB1 LMNB1 1952 0.3 0.32 YES
6 CASP7 CASP7 CASP7 2003 0.3 0.37 YES
7 CASP10 CASP10 CASP10 2570 0.24 0.38 YES
8 ARHGDIB ARHGDIB ARHGDIB 2702 0.23 0.41 YES
9 MAP3K1 MAP3K1 MAP3K1 2752 0.23 0.45 YES
10 JUN JUN JUN 3029 0.21 0.48 YES
11 LMNA LMNA LMNA 3053 0.2 0.51 YES
12 CASP3 CASP3 CASP3 3305 0.19 0.53 YES
13 CFLAR CFLAR CFLAR 3416 0.18 0.56 YES
14 LMNB2 LMNB2 LMNB2 3528 0.17 0.58 YES
15 PTPN13 PTPN13 PTPN13 3738 0.16 0.6 YES
16 FADD FADD FADD 3851 0.15 0.62 YES
17 RB1 RB1 RB1 5019 0.1 0.58 NO
18 FAF1 FAF1 FAF1 5589 0.083 0.56 NO
19 DFFB DFFB DFFB 5966 0.072 0.55 NO
20 DFFA DFFA DFFA 7316 0.04 0.49 NO
21 PRKDC PRKDC PRKDC 7578 0.036 0.48 NO
22 DAXX DAXX DAXX 7843 0.031 0.47 NO
23 MAP3K7 MAP3K7 MAP3K7 8466 0.02 0.44 NO
24 PARP1 PARP1 PARP1 8858 0.014 0.42 NO
25 PAK2 PAK2 PAK2 9034 0.011 0.41 NO
26 PAK1 PAK1 PAK1 10684 -0.018 0.33 NO
27 SPTAN1 SPTAN1 SPTAN1 12649 -0.054 0.23 NO
28 RIPK2 RIPK2 RIPK2 13625 -0.076 0.19 NO
29 MAP2K4 MAP2K4 MAP2K4 14924 -0.12 0.14 NO
30 MAPK8 MAPK8 MAPK8 16652 -0.25 0.091 NO

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

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

genes ES table in pathway: KEGG HOMOLOGOUS RECOMBINATION

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 ALG6 ALG6 ALG6 2615 0.24 -0.046 YES
2 PMM2 PMM2 PMM2 3224 0.19 -0.0011 YES
3 ALG10 ALG10 ALG10 3457 0.18 0.058 YES
4 ALG14 ALG14 ALG14 3565 0.17 0.12 YES
5 GMPPB GMPPB GMPPB 3729 0.16 0.18 YES
6 GMPPA GMPPA GMPPA 4083 0.14 0.22 YES
7 ALG12 ALG12 ALG12 4233 0.14 0.26 YES
8 ALG3 ALG3 ALG3 4296 0.13 0.31 YES
9 ALG1 ALG1 ALG1 4708 0.11 0.34 YES
10 DPAGT1 DPAGT1 DPAGT1 4860 0.11 0.37 YES
11 ALG2 ALG2 ALG2 4868 0.11 0.42 YES
12 ALG8 ALG8 ALG8 5598 0.083 0.41 YES
13 DPM3 DPM3 DPM3 5605 0.083 0.44 YES
14 DPM1 DPM1 DPM1 5985 0.072 0.45 YES
15 GFPT2 GFPT2 GFPT2 6092 0.069 0.47 YES
16 ALG5 ALG5 ALG5 6345 0.062 0.48 YES
17 RFT1 RFT1 RFT1 6748 0.054 0.48 YES
18 DOLK DOLK DOLK 6798 0.052 0.5 YES
19 ALG11 ALG11 ALG11 7031 0.047 0.51 YES
20 DPM2 DPM2 DPM2 7245 0.042 0.51 YES
21 ALG10B ALG10B ALG10B 9325 0.0056 0.4 NO
22 GNPNAT1 GNPNAT1 GNPNAT1 9434 0.0039 0.4 NO
23 PGM3 PGM3 PGM3 9898 -0.0042 0.38 NO
24 DOLPP1 DOLPP1 DOLPP1 10368 -0.013 0.35 NO
25 ALG13 ALG13 ALG13 10422 -0.014 0.36 NO
26 ALG9 ALG9 ALG9 10688 -0.018 0.35 NO
27 MPI MPI MPI 13385 -0.07 0.23 NO
28 PMM1 PMM1 PMM1 14254 -0.096 0.22 NO

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

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

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

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 CD247 CD247 CD247 220 0.66 0.052 YES
2 LCK LCK LCK 281 0.64 0.11 YES
3 APOBEC3G APOBEC3G APOBEC3G 318 0.62 0.17 YES
4 CD28 CD28 CD28 898 0.46 0.18 YES
5 RCC1 RCC1 RCC1 1212 0.4 0.2 YES
6 PSMB9 PSMB9 PSMB9 1851 0.31 0.2 YES
7 DOCK2 DOCK2 DOCK2 2122 0.28 0.21 YES
8 HCK HCK HCK 2178 0.28 0.23 YES
9 CD8B CD8B CD8B 2495 0.25 0.24 YES
10 PSMB8 PSMB8 PSMB8 2768 0.22 0.24 YES
11 NUP37 NUP37 NUP37 2979 0.21 0.25 YES
12 HLA-A HLA-A HLA-A 3055 0.2 0.27 YES
13 CD4 CD4 CD4 3133 0.2 0.28 YES
14 PSMA8 PSMA8 PSMA8 3413 0.18 0.29 YES
15 B2M B2M B2M 3607 0.17 0.29 YES
16 NUP210 NUP210 NUP210 3663 0.16 0.3 YES
17 PSME2 PSME2 PSME2 3821 0.16 0.31 YES
18 PSMB10 PSMB10 PSMB10 4144 0.14 0.31 YES
19 NUP85 NUP85 NUP85 4433 0.13 0.3 YES
20 AP1S2 AP1S2 AP1S2 4496 0.12 0.31 YES
21 PSMD5 PSMD5 PSMD5 4502 0.12 0.32 YES
22 NUP107 NUP107 NUP107 4552 0.12 0.33 YES
23 PSMC2 PSMC2 PSMC2 4734 0.11 0.33 YES
24 NUP62 NUP62 NUP62 4762 0.11 0.34 YES
25 NUP205 NUP205 NUP205 4844 0.11 0.35 YES
26 AP2S1 AP2S1 AP2S1 4978 0.1 0.35 YES
27 PSMD9 PSMD9 PSMD9 5034 0.1 0.36 YES
28 NUP54 NUP54 NUP54 5059 0.1 0.37 YES
29 PSMA5 PSMA5 PSMA5 5064 0.1 0.38 YES
30 PSMC4 PSMC4 PSMC4 5090 0.1 0.38 YES
31 HMGA1 HMGA1 HMGA1 5131 0.098 0.39 YES
32 PSME4 PSME4 PSME4 5468 0.086 0.38 YES
33 PSMD8 PSMD8 PSMD8 5652 0.081 0.38 YES
34 NUP188 NUP188 NUP188 5666 0.081 0.38 YES
35 PSMA2 PSMA2 PSMA2 5952 0.073 0.38 YES
36 NUP93 NUP93 NUP93 5971 0.072 0.38 YES
37 PSMB2 PSMB2 PSMB2 5992 0.072 0.39 YES
38 PSMD12 PSMD12 PSMD12 6038 0.071 0.39 YES
39 PSMB3 PSMB3 PSMB3 6445 0.06 0.38 NO
40 PSMA7 PSMA7 PSMA7 6471 0.06 0.38 NO
41 PSMD11 PSMD11 PSMD11 6540 0.058 0.38 NO
42 PSMA4 PSMA4 PSMA4 6627 0.056 0.38 NO
43 PSMA3 PSMA3 PSMA3 6663 0.056 0.39 NO
44 AP1M1 AP1M1 AP1M1 6683 0.055 0.39 NO
45 NUP155 NUP155 NUP155 6825 0.052 0.39 NO
46 PSMB4 PSMB4 PSMB4 6962 0.049 0.38 NO
47 RAE1 RAE1 RAE1 7045 0.047 0.38 NO
48 PSME1 PSME1 PSME1 7070 0.046 0.39 NO
49 NUP43 NUP43 NUP43 7091 0.046 0.39 NO
50 NUP88 NUP88 NUP88 7335 0.04 0.38 NO
51 NUPL2 NUPL2 NUPL2 7684 0.034 0.37 NO
52 XPO1 XPO1 XPO1 7720 0.033 0.37 NO
53 PSMA1 PSMA1 PSMA1 7779 0.032 0.37 NO
54 POM121 POM121 POM121 7813 0.032 0.37 NO
55 RAN RAN RAN 7814 0.032 0.37 NO
56 PSMC1 PSMC1 PSMC1 7920 0.03 0.37 NO
57 RAC1 RAC1 RAC1 8031 0.028 0.36 NO
58 PPIA PPIA PPIA 8090 0.027 0.36 NO
59 NUP153 NUP153 NUP153 8193 0.025 0.36 NO
60 KPNB1 KPNB1 KPNB1 8263 0.024 0.36 NO
61 PSMB1 PSMB1 PSMB1 8382 0.022 0.36 NO
62 PSMD2 PSMD2 PSMD2 8407 0.021 0.36 NO
63 PSMD14 PSMD14 PSMD14 8495 0.02 0.35 NO
64 UBA52 UBA52 UBA52 8661 0.017 0.35 NO
65 ARF1 ARF1 ARF1 8833 0.014 0.34 NO
66 AP1B1 AP1B1 AP1B1 8908 0.013 0.34 NO
67 BANF1 BANF1 BANF1 8909 0.013 0.34 NO
68 PSMD6 PSMD6 PSMD6 8986 0.012 0.33 NO
69 NUP35 NUP35 NUP35 9009 0.011 0.33 NO
70 PAK2 PAK2 PAK2 9034 0.011 0.33 NO
71 PSMF1 PSMF1 PSMF1 9055 0.01 0.33 NO
72 PSMB6 PSMB6 PSMB6 9086 0.0098 0.33 NO
73 TPR TPR TPR 9220 0.0074 0.32 NO
74 PSMD7 PSMD7 PSMD7 9231 0.0072 0.32 NO
75 NUP214 NUP214 NUP214 9293 0.0061 0.32 NO
76 RANBP2 RANBP2 RANBP2 9355 0.005 0.32 NO
77 KPNA1 KPNA1 KPNA1 9370 0.0048 0.32 NO
78 PACS1 PACS1 PACS1 9461 0.0035 0.32 NO
79 AP1G1 AP1G1 AP1G1 9542 0.0023 0.31 NO
80 PSMD1 PSMD1 PSMD1 9646 0.00037 0.3 NO
81 TCEB2 TCEB2 TCEB2 9724 -0.00079 0.3 NO
82 AP2A1 AP2A1 AP2A1 9743 -0.0012 0.3 NO
83 RANBP1 RANBP1 RANBP1 9802 -0.0023 0.3 NO
84 PSMD3 PSMD3 PSMD3 9834 -0.003 0.3 NO
85 PSMD13 PSMD13 PSMD13 9876 -0.0036 0.29 NO
86 NUP50 NUP50 NUP50 10072 -0.0075 0.28 NO
87 TCEB1 TCEB1 TCEB1 10120 -0.0085 0.28 NO
88 AP2M1 AP2M1 AP2M1 10140 -0.0088 0.28 NO
89 AP1S1 AP1S1 AP1S1 10301 -0.012 0.27 NO
90 CUL5 CUL5 CUL5 10603 -0.017 0.26 NO
91 SEH1L SEH1L SEH1L 10752 -0.019 0.25 NO
92 RBX1 RBX1 RBX1 10830 -0.021 0.25 NO
93 NUP133 NUP133 NUP133 10859 -0.021 0.25 NO
94 AAAS AAAS AAAS 10879 -0.021 0.25 NO
95 PSMB7 PSMB7 PSMB7 10909 -0.022 0.25 NO
96 SLC25A6 SLC25A6 SLC25A6 10968 -0.023 0.25 NO
97 PSMC3 PSMC3 PSMC3 11085 -0.025 0.25 NO
98 PSMD4 PSMD4 PSMD4 11251 -0.027 0.24 NO
99 PSMA6 PSMA6 PSMA6 11593 -0.033 0.23 NO
100 SLC25A5 SLC25A5 SLC25A5 11610 -0.034 0.23 NO
101 PSMC5 PSMC5 PSMC5 11627 -0.034 0.23 NO
102 SKP1 SKP1 SKP1 11754 -0.036 0.23 NO
103 NPM1 NPM1 NPM1 11790 -0.037 0.23 NO
104 NUPL1 NUPL1 NUPL1 12058 -0.042 0.22 NO
105 AP2A2 AP2A2 AP2A2 12166 -0.044 0.22 NO
106 SLC25A4 SLC25A4 SLC25A4 12188 -0.045 0.22 NO
107 PSMC6 PSMC6 PSMC6 12245 -0.046 0.22 NO
108 PSMB5 PSMB5 PSMB5 12434 -0.05 0.22 NO
109 CDK9 CDK9 CDK9 12462 -0.05 0.22 NO
110 RANGAP1 RANGAP1 RANGAP1 12766 -0.056 0.21 NO
111 CCNT1 CCNT1 CCNT1 12829 -0.058 0.21 NO
112 FYN FYN FYN 12968 -0.06 0.21 NO
113 PSMD10 PSMD10 PSMD10 13028 -0.062 0.21 NO
114 RPS27A RPS27A RPS27A 13221 -0.066 0.21 NO
115 PSIP1 PSIP1 PSIP1 13320 -0.069 0.21 NO
116 AP2B1 AP2B1 AP2B1 14186 -0.093 0.17 NO
117 ATP6V1H ATP6V1H ATP6V1H 14249 -0.095 0.17 NO
118 AP1M2 AP1M2 AP1M2 15433 -0.15 0.12 NO
119 BTRC BTRC BTRC 15834 -0.17 0.12 NO
120 ELMO1 ELMO1 ELMO1 16080 -0.19 0.12 NO

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

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

genes ES table in pathway: KEGG CELL CYCLE

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 FASLG FASLG FASLG 324 0.62 0.054 YES
2 CASP8 CASP8 CASP8 427 0.58 0.12 YES
3 CASP6 CASP6 CASP6 808 0.48 0.15 YES
4 FAS FAS FAS 1538 0.35 0.15 YES
5 BIRC3 BIRC3 BIRC3 1690 0.33 0.18 YES
6 TNFRSF1A TNFRSF1A TNFRSF1A 1857 0.31 0.21 YES
7 LMNB1 LMNB1 LMNB1 1952 0.3 0.24 YES
8 CASP7 CASP7 CASP7 2003 0.3 0.27 YES
9 TRADD TRADD TRADD 2146 0.28 0.3 YES
10 TRAF1 TRAF1 TRAF1 2578 0.24 0.3 YES
11 TNFRSF1B TNFRSF1B TNFRSF1B 2629 0.24 0.32 YES
12 ARHGDIB ARHGDIB ARHGDIB 2702 0.23 0.35 YES
13 MAP3K1 MAP3K1 MAP3K1 2752 0.23 0.37 YES
14 LMNA LMNA LMNA 3053 0.2 0.38 YES
15 CASP3 CASP3 CASP3 3305 0.19 0.39 YES
16 PRKCD PRKCD PRKCD 3330 0.19 0.41 YES
17 MAP3K14 MAP3K14 MAP3K14 3381 0.18 0.42 YES
18 RIPK1 RIPK1 RIPK1 3400 0.18 0.44 YES
19 CFLAR CFLAR CFLAR 3416 0.18 0.46 YES
20 LMNB2 LMNB2 LMNB2 3528 0.17 0.48 YES
21 FADD FADD FADD 3851 0.15 0.48 YES
22 CASP2 CASP2 CASP2 3881 0.15 0.5 YES
23 NFKB1 NFKB1 NFKB1 4195 0.14 0.49 YES
24 PSEN2 PSEN2 PSEN2 4646 0.12 0.48 YES
25 GSN GSN GSN 4870 0.11 0.48 YES
26 RB1 RB1 RB1 5019 0.1 0.49 YES
27 CDK11A CDK11A CDK11A 5025 0.1 0.5 YES
28 MDM2 MDM2 MDM2 5146 0.098 0.5 YES
29 TRAF2 TRAF2 TRAF2 5455 0.086 0.5 NO
30 DFFB DFFB DFFB 5966 0.072 0.48 NO
31 CDK11B CDK11B CDK11B 6364 0.062 0.46 NO
32 TNF TNF TNF 6814 0.052 0.44 NO
33 ACTG1 ACTG1 ACTG1 7273 0.041 0.42 NO
34 DFFA DFFA DFFA 7316 0.04 0.43 NO
35 BIRC2 BIRC2 BIRC2 7443 0.038 0.42 NO
36 PRKDC PRKDC PRKDC 7578 0.036 0.42 NO
37 DAXX DAXX DAXX 7843 0.031 0.41 NO
38 CYCS CYCS CYCS 7889 0.03 0.41 NO
39 APAF1 APAF1 APAF1 8699 0.016 0.37 NO
40 PARP1 PARP1 PARP1 8858 0.014 0.36 NO
41 PAK2 PAK2 PAK2 9034 0.011 0.35 NO
42 RELA RELA RELA 9414 0.0041 0.33 NO
43 RASA1 RASA1 RASA1 9568 0.0017 0.32 NO
44 MAP2K7 MAP2K7 MAP2K7 9851 -0.0032 0.31 NO
45 PSEN1 PSEN1 PSEN1 10007 -0.0064 0.3 NO
46 BCL2 BCL2 BCL2 11075 -0.024 0.25 NO
47 XIAP XIAP XIAP 11360 -0.029 0.23 NO
48 CHUK CHUK CHUK 11874 -0.038 0.21 NO
49 PTK2 PTK2 PTK2 12179 -0.045 0.2 NO
50 NFKBIA NFKBIA NFKBIA 12313 -0.047 0.2 NO
51 SPTAN1 SPTAN1 SPTAN1 12649 -0.054 0.18 NO
52 CRADD CRADD CRADD 13192 -0.066 0.16 NO
53 NUMA1 NUMA1 NUMA1 14391 -0.1 0.11 NO
54 BAG4 BAG4 BAG4 15419 -0.15 0.07 NO
55 MAP3K5 MAP3K5 MAP3K5 15471 -0.15 0.084 NO
56 CASP9 CASP9 CASP9 15543 -0.15 0.098 NO
57 BID BID BID 16341 -0.21 0.08 NO
58 MAPK8 MAPK8 MAPK8 16652 -0.25 0.091 NO

Figure S37.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG CELL CYCLE.

Figure S38.  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 P53 SIGNALING PATHWAY

Table S20.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IL2RG IL2RG IL2RG 96 0.75 0.1 YES
2 IL2RB IL2RB IL2RB 111 0.74 0.2 YES
3 LCK LCK LCK 281 0.64 0.29 YES
4 JAK3 JAK3 JAK3 619 0.52 0.34 YES
5 CSF2RB CSF2RB CSF2RB 683 0.51 0.41 YES
6 CDK1 CDK1 CDK1 921 0.46 0.46 YES
7 IL2RA IL2RA IL2RA 1107 0.42 0.51 YES
8 STAT5A STAT5A STAT5A 1918 0.3 0.51 YES
9 PTPN6 PTPN6 PTPN6 1984 0.3 0.55 YES
10 SYK SYK SYK 2450 0.25 0.56 YES
11 SHC1 SHC1 SHC1 2673 0.23 0.58 YES
12 PIK3CD PIK3CD PIK3CD 2687 0.23 0.61 YES
13 IL5RA IL5RA IL5RA 2747 0.23 0.64 YES
14 CSF2RA CSF2RA CSF2RA 3030 0.21 0.65 YES
15 PIK3R3 PIK3R3 PIK3R3 4656 0.12 0.58 NO
16 NRAS NRAS NRAS 4992 0.1 0.58 NO
17 JAK2 JAK2 JAK2 5450 0.087 0.56 NO
18 INPPL1 INPPL1 INPPL1 5887 0.074 0.55 NO
19 IL3RA IL3RA IL3RA 7734 0.033 0.46 NO
20 MAP2K2 MAP2K2 MAP2K2 8776 0.015 0.4 NO
21 GRB2 GRB2 GRB2 8778 0.015 0.4 NO
22 JAK1 JAK1 JAK1 9162 0.0084 0.38 NO
23 RAF1 RAF1 RAF1 10373 -0.013 0.32 NO
24 SOS1 SOS1 SOS1 10910 -0.022 0.29 NO
25 YWHAB YWHAB YWHAB 10978 -0.023 0.29 NO
26 PIK3CA PIK3CA PIK3CA 10999 -0.023 0.29 NO
27 KRAS KRAS KRAS 11195 -0.026 0.29 NO
28 STAT5B STAT5B STAT5B 11309 -0.028 0.28 NO
29 PTK2B PTK2B PTK2B 11624 -0.034 0.27 NO
30 HRAS HRAS HRAS 11882 -0.039 0.26 NO
31 IL5 IL5 IL5 12100 -0.043 0.26 NO
32 PIK3R2 PIK3R2 PIK3R2 12187 -0.045 0.26 NO
33 GAB2 GAB2 GAB2 12415 -0.05 0.25 NO
34 MAPK1 MAPK1 MAPK1 12887 -0.059 0.24 NO
35 MAP2K1 MAP2K1 MAP2K1 13802 -0.081 0.2 NO
36 MAPK3 MAPK3 MAPK3 13869 -0.083 0.21 NO
37 PIK3CB PIK3CB PIK3CB 14262 -0.096 0.2 NO
38 PIK3R1 PIK3R1 PIK3R1 15743 -0.16 0.14 NO

Figure S39.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG P53 SIGNALING PATHWAY.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG P53 SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG RIBOSOME 86 genes.ES.table 0.49 1.2 0.32 1 1 0.66 0.32 0.45 1 0.93
BIOCARTA CARM ER PATHWAY 35 genes.ES.table 0.38 1.4 0.14 1 1 0.46 0.24 0.35 1 0.91
PID HDAC CLASSII PATHWAY 34 genes.ES.table 0.45 1.8 0.015 1 0.62 0.24 0.14 0.2 0.46 0.29
PID RET PATHWAY 39 genes.ES.table 0.35 1.2 0.23 1 1 0.23 0.17 0.19 1 0.89
PID BMPPATHWAY 42 genes.ES.table 0.46 1.4 0.068 1 1 0.24 0.086 0.22 1 0.83
REACTOME TRANSLATION 146 genes.ES.table 0.37 1.1 0.38 1 1 0.56 0.34 0.37 1 0.85
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 49 genes.ES.table 0.44 1.2 0.36 1 1 0.65 0.33 0.44 1 0.94
REACTOME MITOCHONDRIAL PROTEIN IMPORT 49 genes.ES.table 0.5 1.6 0.073 1 0.85 0.57 0.34 0.38 0.69 0.38
REACTOME SIGNALLING TO ERKS 36 genes.ES.table 0.33 1.1 0.31 1 1 0.14 0.11 0.12 1 0.88
REACTOME PI3K AKT ACTIVATION 36 genes.ES.table 0.31 1.1 0.3 1 1 0.47 0.3 0.33 1 0.91
genes ES table in pathway: KEGG RIBOSOME

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 CAMK4 CAMK4 CAMK4 89 0.56 0.19 YES
2 GATA1 GATA1 GATA1 1022 0.22 0.21 YES
3 HDAC4 HDAC4 HDAC4 1139 0.21 0.28 YES
4 HDAC9 HDAC9 HDAC9 1141 0.21 0.35 YES
5 GATA2 GATA2 GATA2 2106 0.13 0.34 YES
6 GNG2 GNG2 GNG2 2127 0.13 0.39 YES
7 ANKRA2 ANKRA2 ANKRA2 2231 0.12 0.42 YES
8 HDAC10 HDAC10 HDAC10 2484 0.11 0.45 YES
9 HDAC6 HDAC6 HDAC6 3826 0.075 0.4 NO
10 NCOR2 NCOR2 NCOR2 4239 0.067 0.4 NO
11 HDAC5 HDAC5 HDAC5 6175 0.035 0.31 NO
12 BCOR BCOR BCOR 6309 0.033 0.31 NO
13 NR3C1 NR3C1 NR3C1 7712 0.013 0.24 NO
14 SRF SRF SRF 7738 0.012 0.24 NO
15 YWHAE YWHAE YWHAE 7971 0.0087 0.24 NO
16 RAN RAN RAN 8241 0.0048 0.22 NO
17 UBE2I UBE2I UBE2I 9263 -0.011 0.17 NO
18 ESR1 ESR1 ESR1 9531 -0.015 0.16 NO
19 SUMO1 SUMO1 SUMO1 9565 -0.016 0.16 NO
20 YWHAB YWHAB YWHAB 9680 -0.018 0.16 NO
21 RFXANK RFXANK RFXANK 9785 -0.02 0.16 NO
22 XPO1 XPO1 XPO1 9800 -0.02 0.17 NO
23 HDAC11 HDAC11 HDAC11 9805 -0.02 0.18 NO
24 BCL6 BCL6 BCL6 10030 -0.025 0.18 NO
25 RANBP2 RANBP2 RANBP2 10174 -0.028 0.18 NO
26 HDAC7 HDAC7 HDAC7 10213 -0.029 0.18 NO
27 HSP90AA1 HSP90AA1 HSP90AA1 10428 -0.034 0.18 NO
28 RANGAP1 RANGAP1 RANGAP1 10478 -0.035 0.19 NO
29 HDAC3 HDAC3 HDAC3 10524 -0.036 0.2 NO
30 TUBB2A TUBB2A TUBB2A 11064 -0.048 0.19 NO
31 ADRBK1 ADRBK1 ADRBK1 11110 -0.05 0.21 NO
32 TUBA1B TUBA1B TUBA1B 13009 -0.11 0.14 NO
33 GNB1 GNB1 GNB1 13569 -0.14 0.16 NO
34 MEF2C MEF2C MEF2C 16395 -0.29 0.1 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 RIBOSOME.

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

genes ES table in pathway: BIOCARTA CARM ER PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GRPEL2 GRPEL2 GRPEL2 1252 0.19 0.014 YES
2 TIMM8A TIMM8A TIMM8A 2421 0.12 -0.0015 YES
3 SAMM50 SAMM50 SAMM50 2454 0.11 0.045 YES
4 FXC1 FXC1 FXC1 2476 0.11 0.092 YES
5 TIMM10 TIMM10 TIMM10 2527 0.11 0.14 YES
6 COQ2 COQ2 COQ2 2930 0.097 0.16 YES
7 TOMM20 TOMM20 TOMM20 3207 0.09 0.18 YES
8 TOMM22 TOMM22 TOMM22 3396 0.085 0.2 YES
9 COX17 COX17 COX17 3563 0.081 0.23 YES
10 TIMM8B TIMM8B TIMM8B 3690 0.078 0.26 YES
11 TOMM70A TOMM70A TOMM70A 3707 0.078 0.29 YES
12 TIMM9 TIMM9 TIMM9 3905 0.074 0.31 YES
13 IDH3G IDH3G IDH3G 4073 0.07 0.33 YES
14 TIMM17B TIMM17B TIMM17B 4273 0.067 0.35 YES
15 SLC25A6 SLC25A6 SLC25A6 4607 0.06 0.35 YES
16 TIMM13 TIMM13 TIMM13 4655 0.059 0.38 YES
17 SLC25A12 SLC25A12 SLC25A12 4851 0.055 0.39 YES
18 LDHD LDHD LDHD 5097 0.052 0.4 YES
19 BCS1L BCS1L BCS1L 5391 0.047 0.4 YES
20 HSPA9 HSPA9 HSPA9 5662 0.043 0.4 YES
21 CS CS CS 5744 0.042 0.42 YES
22 GFER GFER GFER 5748 0.042 0.44 YES
23 ATP5B ATP5B ATP5B 5866 0.04 0.45 YES
24 CYC1 CYC1 CYC1 5870 0.04 0.46 YES
25 TAZ TAZ TAZ 5908 0.039 0.48 YES
26 MTX1 MTX1 MTX1 5992 0.038 0.49 YES
27 CHCHD4 CHCHD4 CHCHD4 6097 0.036 0.5 YES
28 FXN FXN FXN 6253 0.034 0.5 YES
29 TOMM7 TOMM7 TOMM7 6679 0.028 0.49 NO
30 HSPD1 HSPD1 HSPD1 7129 0.021 0.48 NO
31 ATP5G1 ATP5G1 ATP5G1 7565 0.015 0.46 NO
32 C18orf55 C18orf55 C18orf55 7661 0.013 0.46 NO
33 SLC25A4 SLC25A4 SLC25A4 7775 0.012 0.46 NO
34 PMPCB PMPCB PMPCB 7822 0.011 0.46 NO
35 TIMM22 TIMM22 TIMM22 7870 0.01 0.46 NO
36 ACO2 ACO2 ACO2 7982 0.0085 0.46 NO
37 HSCB HSCB HSCB 8024 0.0078 0.46 NO
38 ATP5A1 ATP5A1 ATP5A1 8038 0.0076 0.46 NO
39 TIMM44 TIMM44 TIMM44 8067 0.0071 0.47 NO
40 TOMM5 TOMM5 TOMM5 8505 0.00075 0.44 NO
41 GRPEL1 GRPEL1 GRPEL1 8557 0.000064 0.44 NO
42 MTX2 MTX2 MTX2 8659 -0.0014 0.43 NO
43 SLC25A13 SLC25A13 SLC25A13 8957 -0.0059 0.42 NO
44 DNAJC19 DNAJC19 DNAJC19 9024 -0.0072 0.42 NO
45 TIMM17A TIMM17A TIMM17A 9893 -0.022 0.38 NO
46 VDAC1 VDAC1 VDAC1 9907 -0.022 0.39 NO
47 PMPCA PMPCA PMPCA 10036 -0.025 0.39 NO
48 TIMM50 TIMM50 TIMM50 10807 -0.042 0.37 NO
49 TOMM40 TOMM40 TOMM40 12573 -0.097 0.31 NO

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

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

genes ES table in pathway: PID HDAC CLASSII PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 AHSG AHSG AHSG 50 0.62 0.1 YES
2 NOG NOG NOG 58 0.61 0.2 YES
3 BMP2 BMP2 BMP2 231 0.44 0.27 YES
4 CHRDL1 CHRDL1 CHRDL1 616 0.3 0.3 YES
5 RGMB RGMB RGMB 655 0.29 0.35 YES
6 BMP4 BMP4 BMP4 876 0.24 0.38 YES
7 FST FST FST 1154 0.21 0.4 YES
8 SMAD9 SMAD9 SMAD9 1303 0.19 0.42 YES
9 BMP7 BMP7 BMP7 1441 0.18 0.44 YES
10 BMP6 BMP6 BMP6 1581 0.16 0.46 YES
11 HFE2 HFE2 HFE2 2567 0.11 0.42 NO
12 TAB1 TAB1 TAB1 3391 0.085 0.4 NO
13 GSK3B GSK3B GSK3B 4041 0.071 0.37 NO
14 SMAD7 SMAD7 SMAD7 4336 0.065 0.37 NO
15 SMURF2 SMURF2 SMURF2 5306 0.048 0.32 NO
16 XIAP XIAP XIAP 5504 0.045 0.32 NO
17 SMAD5 SMAD5 SMAD5 6022 0.038 0.3 NO
18 NUP214 NUP214 NUP214 6581 0.029 0.27 NO
19 BMPR1A BMPR1A BMPR1A 6588 0.029 0.28 NO
20 ZFYVE16 ZFYVE16 ZFYVE16 6811 0.026 0.27 NO
21 BMPR2 BMPR2 BMPR2 7212 0.02 0.25 NO
22 BAMBI BAMBI BAMBI 7408 0.017 0.24 NO
23 MAP3K7 MAP3K7 MAP3K7 7554 0.015 0.24 NO
24 SMAD4 SMAD4 SMAD4 7571 0.015 0.24 NO
25 SMAD1 SMAD1 SMAD1 8096 0.0067 0.21 NO
26 CTDSP2 CTDSP2 CTDSP2 10304 -0.031 0.094 NO
27 PPM1A PPM1A PPM1A 10554 -0.037 0.086 NO
28 MAPK1 MAPK1 MAPK1 10633 -0.038 0.088 NO
29 PPP1CA PPP1CA PPP1CA 10736 -0.041 0.09 NO
30 CHRD CHRD CHRD 11043 -0.048 0.081 NO
31 CTDSP1 CTDSP1 CTDSP1 11420 -0.058 0.07 NO
32 SMURF1 SMURF1 SMURF1 11641 -0.065 0.069 NO
33 RGMA RGMA RGMA 11648 -0.065 0.08 NO
34 SKI SKI SKI 12228 -0.084 0.062 NO
35 CTDSPL CTDSPL CTDSPL 12668 -0.1 0.055 NO
36 TAB2 TAB2 TAB2 13007 -0.11 0.056 NO
37 SMAD6 SMAD6 SMAD6 14261 -0.17 0.016 NO
38 SOSTDC1 SOSTDC1 SOSTDC1 14937 -0.2 0.012 NO
39 PPP1R15A PPP1R15A PPP1R15A 15107 -0.21 0.038 NO
40 GREM1 GREM1 GREM1 15579 -0.24 0.052 NO
41 BMPR1B BMPR1B BMPR1B 15850 -0.25 0.08 NO
42 CER1 CER1 CER1 16737 -0.33 0.086 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: PID HDAC CLASSII PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: PID HDAC CLASSII 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 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 GRIP1 GRIP1 GRIP1 198 0.46 0.12 YES
2 NR0B1 NR0B1 NR0B1 719 0.28 0.18 YES
3 HDAC4 HDAC4 HDAC4 1139 0.21 0.21 YES
4 HDAC9 HDAC9 HDAC9 1141 0.21 0.27 YES
5 CCND1 CCND1 CCND1 2137 0.13 0.26 YES
6 HDAC10 HDAC10 HDAC10 2484 0.11 0.27 YES
7 GTF2F1 GTF2F1 GTF2F1 2879 0.099 0.28 YES
8 TBP TBP TBP 3023 0.095 0.3 YES
9 CREBBP CREBBP CREBBP 3439 0.084 0.3 YES
10 HDAC6 HDAC6 HDAC6 3826 0.075 0.3 YES
11 PHB2 PHB2 PHB2 4182 0.068 0.3 YES
12 NCOR2 NCOR2 NCOR2 4239 0.067 0.32 YES
13 EP300 EP300 EP300 4319 0.066 0.33 YES
14 PELP1 PELP1 PELP1 4332 0.066 0.35 YES
15 ERCC3 ERCC3 ERCC3 4371 0.064 0.36 YES
16 HDAC8 HDAC8 HDAC8 4481 0.062 0.38 YES
17 MED1 MED1 MED1 5776 0.041 0.32 NO
18 POLR2A POLR2A POLR2A 5973 0.038 0.32 NO
19 HDAC2 HDAC2 HDAC2 5998 0.038 0.33 NO
20 HDAC5 HDAC5 HDAC5 6175 0.035 0.33 NO
21 GTF2E1 GTF2E1 GTF2E1 6872 0.025 0.3 NO
22 PPARGC1A PPARGC1A PPARGC1A 7451 0.016 0.27 NO
23 GTF2A1 GTF2A1 GTF2A1 8177 0.0057 0.23 NO
24 SRA1 SRA1 SRA1 9153 -0.0092 0.18 NO
25 NRIP1 NRIP1 NRIP1 9450 -0.014 0.17 NO
26 ESR1 ESR1 ESR1 9531 -0.015 0.17 NO
27 HDAC11 HDAC11 HDAC11 9805 -0.02 0.16 NO
28 HDAC7 HDAC7 HDAC7 10213 -0.029 0.15 NO
29 HDAC3 HDAC3 HDAC3 10524 -0.036 0.14 NO
30 SPEN SPEN SPEN 12361 -0.089 0.066 NO
31 CARM1 CARM1 CARM1 12431 -0.091 0.089 NO
32 HIST2H3C HIST2H3C HIST2H3C 12547 -0.095 0.11 NO
33 BRCA1 BRCA1 BRCA1 12952 -0.11 0.12 NO
34 MEF2C MEF2C MEF2C 16395 -0.29 0.018 NO
35 HDAC1 HDAC1 HDAC1 16481 -0.3 0.1 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: PID RET PATHWAY.

Figure S48.  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 BMPPATHWAY

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 POLR2F POLR2F POLR2F 1196 0.2 0.058 YES
2 GTF2H2B GTF2H2B GTF2H2B 1791 0.15 0.12 YES
3 GTF2F1 GTF2F1 GTF2F1 2879 0.099 0.12 YES
4 GTF2F2 GTF2F2 GTF2F2 3650 0.079 0.12 YES
5 GTF2H4 GTF2H4 GTF2H4 3795 0.076 0.16 YES
6 POLR2H POLR2H POLR2H 4035 0.071 0.19 YES
7 GTF2H2 GTF2H2 GTF2H2 4121 0.07 0.23 YES
8 ERCC3 ERCC3 ERCC3 4371 0.064 0.26 YES
9 CCNH CCNH CCNH 4454 0.063 0.29 YES
10 RNGTT RNGTT RNGTT 4715 0.058 0.31 YES
11 GTF2H1 GTF2H1 GTF2H1 4823 0.056 0.34 YES
12 POLR2A POLR2A POLR2A 5973 0.038 0.3 NO
13 POLR2D POLR2D POLR2D 6227 0.034 0.31 NO
14 NCBP2 NCBP2 NCBP2 6325 0.033 0.32 NO
15 MNAT1 MNAT1 MNAT1 7965 0.0089 0.24 NO
16 POLR2G POLR2G POLR2G 8230 0.005 0.23 NO
17 POLR2C POLR2C POLR2C 8327 0.0035 0.23 NO
18 POLR2E POLR2E POLR2E 8591 -0.00047 0.21 NO
19 RNMT RNMT RNMT 8868 -0.0046 0.2 NO
20 CDK7 CDK7 CDK7 9198 -0.01 0.19 NO
21 POLR2B POLR2B POLR2B 9366 -0.012 0.19 NO
22 GTF2H3 GTF2H3 GTF2H3 9660 -0.017 0.18 NO
23 POLR2K POLR2K POLR2K 10584 -0.038 0.15 NO
24 POLR2L POLR2L POLR2L 10602 -0.038 0.18 NO
25 NCBP1 NCBP1 NCBP1 10681 -0.039 0.2 NO
26 SUPT5H SUPT5H SUPT5H 11462 -0.059 0.19 NO
27 ERCC2 ERCC2 ERCC2 11589 -0.063 0.22 NO
28 POLR2J POLR2J POLR2J 11859 -0.071 0.25 NO
29 POLR2I POLR2I POLR2I 14221 -0.17 0.22 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: PID BMPPATHWAY.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: PID BMPPATHWAY, 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 TRANSLATION

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 POLR2F POLR2F POLR2F 1196 0.2 0.026 YES
2 GTF2H2B GTF2H2B GTF2H2B 1791 0.15 0.061 YES
3 GTF2F1 GTF2F1 GTF2F1 2879 0.099 0.047 YES
4 GTF2F2 GTF2F2 GTF2F2 3650 0.079 0.041 YES
5 GTF2H4 GTF2H4 GTF2H4 3795 0.076 0.068 YES
6 POLR2H POLR2H POLR2H 4035 0.071 0.087 YES
7 GTF2H2 GTF2H2 GTF2H2 4121 0.07 0.11 YES
8 ERCC3 ERCC3 ERCC3 4371 0.064 0.13 YES
9 CCNT2 CCNT2 CCNT2 4435 0.063 0.16 YES
10 CCNH CCNH CCNH 4454 0.063 0.18 YES
11 GTF2H1 GTF2H1 GTF2H1 4823 0.056 0.19 YES
12 SUPT4H1 SUPT4H1 SUPT4H1 5049 0.052 0.2 YES
13 SUPT16H SUPT16H SUPT16H 5154 0.05 0.22 YES
14 CCNT1 CCNT1 CCNT1 5627 0.043 0.21 YES
15 CDK9 CDK9 CDK9 5644 0.043 0.23 YES
16 SSRP1 SSRP1 SSRP1 5705 0.042 0.25 YES
17 RDBP RDBP RDBP 5849 0.04 0.26 YES
18 POLR2A POLR2A POLR2A 5973 0.038 0.27 YES
19 POLR2D POLR2D POLR2D 6227 0.034 0.27 YES
20 TCEB1 TCEB1 TCEB1 6239 0.034 0.28 YES
21 NCBP2 NCBP2 NCBP2 6325 0.033 0.3 YES
22 WHSC2 WHSC2 WHSC2 6582 0.029 0.3 YES
23 COBRA1 COBRA1 COBRA1 6800 0.026 0.29 YES
24 TH1L TH1L TH1L 6972 0.023 0.3 YES
25 TCEA1 TCEA1 TCEA1 6988 0.023 0.3 YES
26 CTDP1 CTDP1 CTDP1 7142 0.021 0.31 YES
27 MNAT1 MNAT1 MNAT1 7965 0.0089 0.27 NO
28 ELL ELL ELL 8066 0.0071 0.26 NO
29 POLR2G POLR2G POLR2G 8230 0.005 0.26 NO
30 POLR2C POLR2C POLR2C 8327 0.0035 0.25 NO
31 POLR2E POLR2E POLR2E 8591 -0.00047 0.24 NO
32 CDK7 CDK7 CDK7 9198 -0.01 0.21 NO
33 TCEB2 TCEB2 TCEB2 9208 -0.01 0.22 NO
34 POLR2B POLR2B POLR2B 9366 -0.012 0.21 NO
35 GTF2H3 GTF2H3 GTF2H3 9660 -0.017 0.2 NO
36 POLR2K POLR2K POLR2K 10584 -0.038 0.17 NO
37 POLR2L POLR2L POLR2L 10602 -0.038 0.19 NO
38 NCBP1 NCBP1 NCBP1 10681 -0.039 0.2 NO
39 SUPT5H SUPT5H SUPT5H 11462 -0.059 0.18 NO
40 ERCC2 ERCC2 ERCC2 11589 -0.063 0.21 NO
41 POLR2J POLR2J POLR2J 11859 -0.071 0.22 NO
42 TCEB3 TCEB3 TCEB3 13050 -0.11 0.21 NO
43 POLR2I POLR2I POLR2I 14221 -0.17 0.22 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: REACTOME TRANSLATION.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSLATION, 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 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX

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 POLR2F POLR2F POLR2F 1196 0.2 0.038 YES
2 POLR3D POLR3D POLR3D 1532 0.17 0.11 YES
3 TBP TBP TBP 3023 0.095 0.074 YES
4 GTF3C3 GTF3C3 GTF3C3 3279 0.088 0.11 YES
5 SNAPC3 SNAPC3 SNAPC3 3614 0.08 0.13 YES
6 GTF3C5 GTF3C5 GTF3C5 3949 0.073 0.15 YES
7 POLR2H POLR2H POLR2H 4035 0.071 0.18 YES
8 POLR3F POLR3F POLR3F 4116 0.07 0.21 YES
9 POLR3GL POLR3GL POLR3GL 4236 0.067 0.24 YES
10 NFIB NFIB NFIB 4374 0.064 0.27 YES
11 GTF3C2 GTF3C2 GTF3C2 4640 0.059 0.28 YES
12 GTF3C4 GTF3C4 GTF3C4 4818 0.056 0.3 YES
13 SNAPC4 SNAPC4 SNAPC4 5591 0.044 0.28 NO
14 POLR3K POLR3K POLR3K 5754 0.042 0.3 NO
15 ZNF143 ZNF143 ZNF143 6087 0.036 0.3 NO
16 BRF1 BRF1 BRF1 6613 0.028 0.28 NO
17 POLR3E POLR3E POLR3E 6956 0.023 0.28 NO
18 POLR1C POLR1C POLR1C 6978 0.023 0.29 NO
19 POLR3C POLR3C POLR3C 8203 0.0054 0.22 NO
20 POLR3B POLR3B POLR3B 8225 0.0051 0.22 NO
21 BRF2 BRF2 BRF2 8402 0.0024 0.22 NO
22 SNAPC1 SNAPC1 SNAPC1 8552 0.000096 0.21 NO
23 POLR2E POLR2E POLR2E 8591 -0.00047 0.2 NO
24 POU2F1 POU2F1 POU2F1 8792 -0.0033 0.2 NO
25 SSB SSB SSB 9786 -0.02 0.15 NO
26 POLR3H POLR3H POLR3H 9894 -0.022 0.16 NO
27 POLR3A POLR3A POLR3A 9967 -0.024 0.16 NO
28 POLR2K POLR2K POLR2K 10584 -0.038 0.15 NO
29 POLR2L POLR2L POLR2L 10602 -0.038 0.17 NO
30 SNAPC5 SNAPC5 SNAPC5 11548 -0.062 0.15 NO
31 POLR1D POLR1D POLR1D 12063 -0.078 0.16 NO
32 LZTS1 LZTS1 LZTS1 12233 -0.084 0.2 NO
33 SNAPC2 SNAPC2 SNAPC2 15989 -0.26 0.13 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: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.

Figure S54.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, 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 MITOCHONDRIAL PROTEIN IMPORT

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 G6PC2 G6PC2 G6PC2 2 0.95 0.2 YES
2 G6PC G6PC G6PC 41 0.65 0.34 YES
3 NUP35 NUP35 NUP35 1970 0.14 0.26 NO
4 AAAS AAAS AAAS 2685 0.11 0.25 NO
5 NUP210 NUP210 NUP210 2969 0.096 0.25 NO
6 NUP43 NUP43 NUP43 3786 0.076 0.22 NO
7 NUPL1 NUPL1 NUPL1 4039 0.071 0.23 NO
8 NUPL2 NUPL2 NUPL2 4118 0.07 0.24 NO
9 NUP155 NUP155 NUP155 4269 0.067 0.24 NO
10 GCKR GCKR GCKR 4401 0.064 0.25 NO
11 NUP107 NUP107 NUP107 5348 0.048 0.21 NO
12 NUP50 NUP50 NUP50 5482 0.046 0.21 NO
13 SLC37A4 SLC37A4 SLC37A4 5786 0.041 0.2 NO
14 NUP88 NUP88 NUP88 6397 0.032 0.18 NO
15 NUP214 NUP214 NUP214 6581 0.029 0.17 NO
16 TPR TPR TPR 7105 0.021 0.15 NO
17 G6PC3 G6PC3 G6PC3 7248 0.019 0.14 NO
18 NUP188 NUP188 NUP188 7468 0.016 0.14 NO
19 NUP37 NUP37 NUP37 7545 0.015 0.14 NO
20 NUP133 NUP133 NUP133 7637 0.014 0.13 NO
21 NUP153 NUP153 NUP153 8440 0.0019 0.09 NO
22 POM121 POM121 POM121 8535 0.00031 0.085 NO
23 SEH1L SEH1L SEH1L 9432 -0.014 0.039 NO
24 RAE1 RAE1 RAE1 9493 -0.015 0.039 NO
25 NUP205 NUP205 NUP205 9495 -0.015 0.042 NO
26 NUP93 NUP93 NUP93 9712 -0.018 0.034 NO
27 SLC2A1 SLC2A1 SLC2A1 9796 -0.02 0.034 NO
28 HK1 HK1 HK1 10129 -0.027 0.022 NO
29 RANBP2 RANBP2 RANBP2 10174 -0.028 0.025 NO
30 NUP54 NUP54 NUP54 10543 -0.036 0.013 NO
31 NUP85 NUP85 NUP85 10628 -0.038 0.016 NO
32 NUP62 NUP62 NUP62 13363 -0.13 -0.11 NO
33 SLC2A3 SLC2A3 SLC2A3 14359 -0.17 -0.12 NO
34 HK3 HK3 HK3 14756 -0.19 -0.1 NO
35 SLC2A4 SLC2A4 SLC2A4 15867 -0.25 -0.11 NO
36 HK2 HK2 HK2 17281 -0.4 -0.1 NO
37 GCK GCK GCK 18276 -0.74 0.0021 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: REACTOME MITOCHONDRIAL PROTEIN IMPORT.

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

genes ES table in pathway: REACTOME SIGNALLING TO ERKS

Table 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 RPL21 RPL21 RPL21 65 0.6 0.097 YES
2 RPL22L1 RPL22L1 RPL22L1 468 0.34 0.13 YES
3 RPS28 RPS28 RPS28 1850 0.14 0.081 YES
4 RPL36A RPL36A RPL36A 2065 0.13 0.091 YES
5 RPS13 RPS13 RPS13 2438 0.11 0.09 YES
6 RPS27 RPS27 RPS27 2562 0.11 0.1 YES
7 RPL10L RPL10L RPL10L 2683 0.11 0.11 YES
8 RPL36AL RPL36AL RPL36AL 2699 0.1 0.13 YES
9 RPS12 RPS12 RPS12 2711 0.1 0.15 YES
10 RPL26L1 RPL26L1 RPL26L1 2931 0.097 0.15 YES
11 RPL7 RPL7 RPL7 2940 0.097 0.17 YES
12 RPL6 RPL6 RPL6 2995 0.096 0.18 YES
13 RPS26 RPS26 RPS26 3256 0.088 0.18 YES
14 RPL4 RPL4 RPL4 3299 0.087 0.19 YES
15 RPL13 RPL13 RPL13 3365 0.086 0.2 YES
16 RPL39 RPL39 RPL39 3385 0.085 0.22 YES
17 RPL3 RPL3 RPL3 3502 0.083 0.22 YES
18 RPS24 RPS24 RPS24 3513 0.083 0.24 YES
19 RPS23 RPS23 RPS23 3628 0.08 0.25 YES
20 RPL24 RPL24 RPL24 3645 0.079 0.26 YES
21 RPS25 RPS25 RPS25 3663 0.079 0.27 YES
22 RPS6 RPS6 RPS6 3711 0.078 0.28 YES
23 RPL10A RPL10A RPL10A 3877 0.074 0.28 YES
24 RPL34 RPL34 RPL34 3912 0.074 0.3 YES
25 RPS20 RPS20 RPS20 3929 0.073 0.31 YES
26 RPL10 RPL10 RPL10 4055 0.071 0.31 YES
27 RPL18A RPL18A RPL18A 4072 0.07 0.32 YES
28 RPLP2 RPLP2 RPLP2 4113 0.07 0.33 YES
29 RSL24D1 RSL24D1 RSL24D1 4166 0.069 0.34 YES
30 RPL29 RPL29 RPL29 4209 0.068 0.35 YES
31 RPS3 RPS3 RPS3 4249 0.067 0.36 YES
32 RPS4X RPS4X RPS4X 4306 0.066 0.37 YES
33 RPSA RPSA RPSA 4383 0.064 0.37 YES
34 RPS3A RPS3A RPS3A 4416 0.064 0.38 YES
35 RPL37 RPL37 RPL37 4543 0.061 0.39 YES
36 RPL23A RPL23A RPL23A 4548 0.061 0.4 YES
37 RPS29 RPS29 RPS29 4653 0.059 0.4 YES
38 RPL31 RPL31 RPL31 4670 0.059 0.41 YES
39 RPL23 RPL23 RPL23 4686 0.058 0.42 YES
40 RPL15 RPL15 RPL15 4737 0.058 0.43 YES
41 RPL17 RPL17 RPL17 4965 0.053 0.42 YES
42 RPS15A RPS15A RPS15A 5012 0.052 0.43 YES
43 RPL27A RPL27A RPL27A 5080 0.052 0.43 YES
44 RPS27A RPS27A RPS27A 5108 0.051 0.44 YES
45 RPS21 RPS21 RPS21 5149 0.051 0.45 YES
46 RPL37A RPL37A RPL37A 5185 0.05 0.45 YES
47 RPL32 RPL32 RPL32 5263 0.049 0.46 YES
48 FAU FAU FAU 5326 0.048 0.46 YES
49 RPLP0 RPLP0 RPLP0 5331 0.048 0.47 YES
50 RPL9 RPL9 RPL9 5367 0.047 0.48 YES
51 RPL7A RPL7A RPL7A 5616 0.044 0.47 YES
52 RPS18 RPS18 RPS18 5632 0.043 0.48 YES
53 RPL30 RPL30 RPL30 5690 0.043 0.48 YES
54 RPS27L RPS27L RPS27L 5697 0.042 0.49 YES
55 RPL19 RPL19 RPL19 5761 0.042 0.49 YES
56 RPL14 RPL14 RPL14 5860 0.04 0.49 YES
57 RPL35A RPL35A RPL35A 5959 0.039 0.49 YES
58 RPL8 RPL8 RPL8 6077 0.037 0.49 NO
59 RPL36 RPL36 RPL36 6392 0.032 0.48 NO
60 RPS7 RPS7 RPS7 6436 0.031 0.48 NO
61 RPL41 RPL41 RPL41 6475 0.031 0.49 NO
62 RPL12 RPL12 RPL12 6741 0.027 0.48 NO
63 RPS15 RPS15 RPS15 6967 0.023 0.47 NO
64 RPL38 RPL38 RPL38 7024 0.022 0.47 NO
65 RPL26 RPL26 RPL26 7028 0.022 0.47 NO
66 RPL27 RPL27 RPL27 7500 0.016 0.45 NO
67 RPS10 RPS10 RPS10 8228 0.005 0.41 NO
68 RPS9 RPS9 RPS9 8645 -0.0013 0.39 NO
69 RPS17 RPS17 RPS17 8679 -0.0016 0.39 NO
70 RPL35 RPL35 RPL35 8718 -0.0022 0.38 NO
71 UBA52 UBA52 UBA52 8848 -0.0044 0.38 NO
72 RPLP1 RPLP1 RPLP1 8922 -0.0054 0.38 NO
73 RPS2 RPS2 RPS2 9076 -0.008 0.37 NO
74 RPL5 RPL5 RPL5 10779 -0.042 0.28 NO
75 RPS5 RPS5 RPS5 10820 -0.042 0.29 NO
76 RPL22 RPL22 RPL22 10943 -0.046 0.29 NO
77 RPS4Y1 RPS4Y1 RPS4Y1 11120 -0.05 0.29 NO
78 RPS11 RPS11 RPS11 11308 -0.055 0.29 NO
79 RPL13A RPL13A RPL13A 11324 -0.056 0.3 NO
80 RPL28 RPL28 RPL28 11485 -0.06 0.3 NO
81 RPS8 RPS8 RPS8 11550 -0.062 0.3 NO
82 RPS16 RPS16 RPS16 11883 -0.072 0.3 NO
83 RPS19 RPS19 RPS19 11966 -0.074 0.3 NO
84 RPL18 RPL18 RPL18 12049 -0.077 0.31 NO
85 MRPL13 MRPL13 MRPL13 12313 -0.087 0.31 NO
86 RPL11 RPL11 RPL11 12459 -0.093 0.32 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: REACTOME SIGNALLING TO ERKS.

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

genes ES table in pathway: REACTOME PI3K AKT ACTIVATION

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 GFRA1 GFRA1 GFRA1 80 0.56 0.13 YES
2 GDNF GDNF GDNF 126 0.52 0.26 YES
3 DOK4 DOK4 DOK4 605 0.3 0.3 YES
4 DOK6 DOK6 DOK6 1002 0.23 0.34 YES
5 GRB10 GRB10 GRB10 1862 0.14 0.32 YES
6 SHANK3 SHANK3 SHANK3 2368 0.12 0.32 YES
7 BCAR1 BCAR1 BCAR1 2727 0.1 0.33 YES
8 IRS1 IRS1 IRS1 3104 0.093 0.33 YES
9 PIK3R1 PIK3R1 PIK3R1 3168 0.091 0.35 YES
10 SRC SRC SRC 4136 0.069 0.31 NO
11 MAPK8 MAPK8 MAPK8 4277 0.067 0.32 NO
12 PRKCA PRKCA PRKCA 4457 0.063 0.33 NO
13 PIK3CA PIK3CA PIK3CA 4475 0.062 0.34 NO
14 SOS1 SOS1 SOS1 5938 0.039 0.27 NO
15 HRAS HRAS HRAS 7268 0.019 0.2 NO
16 CRK CRK CRK 7410 0.017 0.2 NO
17 NCK1 NCK1 NCK1 7928 0.0094 0.17 NO
18 GAB1 GAB1 GAB1 8044 0.0075 0.17 NO
19 FRS2 FRS2 FRS2 9458 -0.014 0.095 NO
20 CREB1 CREB1 CREB1 9476 -0.014 0.098 NO
21 DOK5 DOK5 DOK5 9903 -0.022 0.08 NO
22 RAC1 RAC1 RAC1 10016 -0.025 0.08 NO
23 PXN PXN PXN 10132 -0.027 0.08 NO
24 PTK2 PTK2 PTK2 10203 -0.028 0.083 NO
25 RHOA RHOA RHOA 10429 -0.034 0.079 NO
26 SHC1 SHC1 SHC1 10440 -0.034 0.086 NO
27 PTPN11 PTPN11 PTPN11 10458 -0.035 0.094 NO
28 MAPK1 MAPK1 MAPK1 10633 -0.038 0.094 NO
29 GRB2 GRB2 GRB2 10662 -0.039 0.1 NO
30 MAPK3 MAPK3 MAPK3 10669 -0.039 0.11 NO
31 RASA1 RASA1 RASA1 10688 -0.04 0.12 NO
32 DOK1 DOK1 DOK1 10912 -0.045 0.12 NO
33 IRS2 IRS2 IRS2 11838 -0.07 0.084 NO
34 PRKACA PRKACA PRKACA 12508 -0.094 0.07 NO
35 PDLIM7 PDLIM7 PDLIM7 14046 -0.16 0.024 NO
36 JUN JUN JUN 15192 -0.21 0.013 NO
37 GRB7 GRB7 GRB7 15284 -0.22 0.06 NO
38 RAP1A RAP1A RAP1A 15313 -0.22 0.11 NO
39 RET RET RET 15323 -0.22 0.16 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: REACTOME PI3K AKT ACTIVATION.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PI3K AKT ACTIVATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus4 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.48 1.5 0.09 0.15 0.96 0.17 0.19 0.14 0.087 0.002
KEGG PURINE METABOLISM 156 genes.ES.table 0.42 1.6 0 0.12 0.86 0.15 0.13 0.14 0.054 0.006
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 30 genes.ES.table 0.58 1.6 0.027 0.13 0.94 0.53 0.25 0.4 0.075 0.002
KEGG ARGININE AND PROLINE METABOLISM 53 genes.ES.table 0.53 1.6 0.018 0.13 0.93 0.43 0.23 0.33 0.072 0.002
KEGG O GLYCAN BIOSYNTHESIS 30 genes.ES.table 0.58 1.5 0.02 0.15 0.97 0.33 0.16 0.28 0.098 0.002
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE 26 genes.ES.table 0.68 1.7 0.004 0.087 0.64 0.27 0.12 0.24 0.029 0.006
KEGG GLYCEROLIPID METABOLISM 45 genes.ES.table 0.46 1.5 0.02 0.15 0.97 0.33 0.2 0.27 0.097 0.003
KEGG INOSITOL PHOSPHATE METABOLISM 52 genes.ES.table 0.48 1.6 0.037 0.12 0.9 0.27 0.18 0.22 0.063 0.003
KEGG GLYCEROPHOSPHOLIPID METABOLISM 72 genes.ES.table 0.43 1.5 0.036 0.17 0.98 0.28 0.2 0.22 0.11 0.002
KEGG PYRUVATE METABOLISM 39 genes.ES.table 0.53 1.7 0.014 0.11 0.78 0.56 0.32 0.39 0.043 0.005
genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 115 1.1 0.057 YES
2 ADCYAP1 ADCYAP1 ADCYAP1 361 0.83 0.092 YES
3 DNM1 DNM1 DNM1 508 0.72 0.13 YES
4 PDE1A PDE1A PDE1A 609 0.66 0.16 YES
5 CAMK4 CAMK4 CAMK4 610 0.66 0.2 YES
6 PDE1B PDE1B PDE1B 611 0.66 0.24 YES
7 ADCY1 ADCY1 ADCY1 630 0.65 0.27 YES
8 MAPK13 MAPK13 MAPK13 881 0.52 0.29 YES
9 RIT2 RIT2 RIT2 886 0.52 0.32 YES
10 PRKAR1B PRKAR1B PRKAR1B 1177 0.43 0.33 YES
11 NGF NGF NGF 1323 0.39 0.34 YES
12 MEF2C MEF2C MEF2C 1395 0.37 0.36 YES
13 PRKCE PRKCE PRKCE 1464 0.36 0.38 YES
14 PRKAR2B PRKAR2B PRKAR2B 1572 0.34 0.39 YES
15 SH3GL2 SH3GL2 SH3GL2 1610 0.33 0.41 YES
16 SHC3 SHC3 SHC3 1714 0.31 0.42 YES
17 CALM3 CALM3 CALM3 2142 0.24 0.41 YES
18 ADCY5 ADCY5 ADCY5 2156 0.24 0.43 YES
19 MAP2K1 MAP2K1 MAP2K1 2409 0.21 0.42 YES
20 ELK1 ELK1 ELK1 2457 0.21 0.44 YES
21 CALM1 CALM1 CALM1 2691 0.18 0.43 YES
22 MAPK11 MAPK11 MAPK11 2800 0.18 0.44 YES
23 ADCYAP1R1 ADCYAP1R1 ADCYAP1R1 3051 0.15 0.43 YES
24 PRKCD PRKCD PRKCD 3086 0.15 0.44 YES
25 DUSP3 DUSP3 DUSP3 3127 0.15 0.45 YES
26 PRKACB PRKACB PRKACB 3370 0.13 0.44 YES
27 RPS6KA5 RPS6KA5 RPS6KA5 3399 0.13 0.45 YES
28 BRAF BRAF BRAF 3403 0.13 0.45 YES
29 AKT3 AKT3 AKT3 3437 0.13 0.46 YES
30 RALB RALB RALB 3503 0.12 0.46 YES
31 PIK3CB PIK3CB PIK3CB 3627 0.12 0.46 YES
32 PDPK1 PDPK1 PDPK1 3647 0.12 0.47 YES
33 RPS6KA2 RPS6KA2 RPS6KA2 3760 0.11 0.47 YES
34 YWHAB YWHAB YWHAB 3768 0.11 0.48 YES
35 GSK3A GSK3A GSK3A 3781 0.11 0.48 YES
36 MEF2A MEF2A MEF2A 3946 0.1 0.48 YES
37 AP2A1 AP2A1 AP2A1 4038 0.098 0.48 YES
38 MAPK3 MAPK3 MAPK3 4102 0.096 0.48 YES
39 ADRBK1 ADRBK1 ADRBK1 4130 0.094 0.48 YES
40 ADCY2 ADCY2 ADCY2 4192 0.091 0.49 YES
41 MAPK1 MAPK1 MAPK1 4317 0.086 0.48 YES
42 DUSP7 DUSP7 DUSP7 4334 0.086 0.49 YES
43 CALM2 CALM2 CALM2 4343 0.085 0.49 YES
44 ADCY8 ADCY8 ADCY8 4423 0.082 0.49 YES
45 ADCY3 ADCY3 ADCY3 4452 0.081 0.5 YES
46 AP2A2 AP2A2 AP2A2 4481 0.08 0.5 YES
47 NTRK2 NTRK2 NTRK2 4609 0.076 0.5 YES
48 PPP2R5D PPP2R5D PPP2R5D 4631 0.075 0.5 YES
49 KRAS KRAS KRAS 4769 0.07 0.5 YES
50 ADCY9 ADCY9 ADCY9 4773 0.07 0.5 YES
51 AP2S1 AP2S1 AP2S1 4789 0.069 0.5 YES
52 AP2M1 AP2M1 AP2M1 4797 0.069 0.51 YES
53 DNAL4 DNAL4 DNAL4 4907 0.066 0.5 YES
54 PRKACA PRKACA PRKACA 4908 0.066 0.51 YES
55 PRKAR1A PRKAR1A PRKAR1A 5169 0.057 0.5 NO
56 PTEN PTEN PTEN 5175 0.056 0.5 NO
57 CLTC CLTC CLTC 5259 0.054 0.5 NO
58 PPP2R1A PPP2R1A PPP2R1A 5287 0.053 0.5 NO
59 PPP2CA PPP2CA PPP2CA 5474 0.048 0.49 NO
60 HRAS HRAS HRAS 5522 0.047 0.49 NO
61 MTOR MTOR MTOR 5637 0.044 0.49 NO
62 PIK3R1 PIK3R1 PIK3R1 5842 0.039 0.48 NO
63 IRS1 IRS1 IRS1 5901 0.037 0.48 NO
64 PRKCA PRKCA PRKCA 5907 0.037 0.48 NO
65 FOXO4 FOXO4 FOXO4 6004 0.035 0.48 NO
66 RPS6KA3 RPS6KA3 RPS6KA3 6131 0.032 0.47 NO
67 FOXO3 FOXO3 FOXO3 6297 0.029 0.47 NO
68 PRKAR2A PRKAR2A PRKAR2A 6303 0.029 0.47 NO
69 AP2B1 AP2B1 AP2B1 6441 0.026 0.46 NO
70 MAP2K5 MAP2K5 MAP2K5 6465 0.026 0.46 NO
71 PRKACG PRKACG PRKACG 6609 0.023 0.46 NO
72 NR4A1 NR4A1 NR4A1 6940 0.016 0.44 NO
73 DUSP4 DUSP4 DUSP4 7130 0.012 0.43 NO
74 THEM4 THEM4 THEM4 7411 0.0077 0.41 NO
75 GRB2 GRB2 GRB2 7541 0.0056 0.41 NO
76 MAPK14 MAPK14 MAPK14 7588 0.005 0.4 NO
77 KIDINS220 KIDINS220 KIDINS220 7601 0.0047 0.4 NO
78 PPP2CB PPP2CB PPP2CB 7704 0.0031 0.4 NO
79 PHLPP1 PHLPP1 PHLPP1 7774 0.0018 0.4 NO
80 ITPR2 ITPR2 ITPR2 7791 0.0016 0.4 NO
81 SRC SRC SRC 7947 -0.0013 0.39 NO
82 CLTA CLTA CLTA 7974 -0.0017 0.38 NO
83 MAPK12 MAPK12 MAPK12 7983 -0.0018 0.38 NO
84 RAPGEF1 RAPGEF1 RAPGEF1 8009 -0.0022 0.38 NO
85 PIK3R2 PIK3R2 PIK3R2 8039 -0.0026 0.38 NO
86 IRS2 IRS2 IRS2 8057 -0.0029 0.38 NO
87 MLST8 MLST8 MLST8 8383 -0.0078 0.36 NO
88 CHUK CHUK CHUK 8496 -0.0092 0.36 NO
89 MAP2K2 MAP2K2 MAP2K2 8542 -0.0099 0.36 NO
90 RICTOR RICTOR RICTOR 8575 -0.01 0.36 NO
91 FOXO1 FOXO1 FOXO1 8682 -0.012 0.35 NO
92 MAPKAP1 MAPKAP1 MAPKAP1 8791 -0.013 0.34 NO
93 CRK CRK CRK 8921 -0.014 0.34 NO
94 PIK3CA PIK3CA PIK3CA 8957 -0.015 0.34 NO
95 ADCY6 ADCY6 ADCY6 9112 -0.017 0.33 NO
96 TSC2 TSC2 TSC2 9165 -0.018 0.33 NO
97 BAD BAD BAD 9205 -0.019 0.33 NO
98 FRS2 FRS2 FRS2 9292 -0.02 0.32 NO
99 CDKN1B CDKN1B CDKN1B 9585 -0.024 0.31 NO
100 SOS1 SOS1 SOS1 9742 -0.026 0.3 NO
101 ADORA2A ADORA2A ADORA2A 10003 -0.029 0.29 NO
102 ITPR3 ITPR3 ITPR3 10014 -0.029 0.29 NO
103 CREB1 CREB1 CREB1 10115 -0.03 0.29 NO
104 RALGDS RALGDS RALGDS 10498 -0.035 0.27 NO
105 PLCG1 PLCG1 PLCG1 10501 -0.035 0.27 NO
106 SHC2 SHC2 SHC2 11190 -0.044 0.23 NO
107 AKT1 AKT1 AKT1 11486 -0.048 0.22 NO
108 RHOA RHOA RHOA 11509 -0.048 0.22 NO
109 RALA RALA RALA 11652 -0.05 0.22 NO
110 PPP2R1B PPP2R1B PPP2R1B 11821 -0.053 0.21 NO
111 CASP9 CASP9 CASP9 12163 -0.057 0.2 NO
112 NRAS NRAS NRAS 12363 -0.06 0.19 NO
113 RAF1 RAF1 RAF1 12443 -0.061 0.19 NO
114 AKT1S1 AKT1S1 AKT1S1 12589 -0.063 0.18 NO
115 DNM2 DNM2 DNM2 12806 -0.067 0.18 NO
116 AKT2 AKT2 AKT2 12936 -0.069 0.17 NO
117 RAP1A RAP1A RAP1A 13023 -0.07 0.17 NO
118 MDM2 MDM2 MDM2 13140 -0.072 0.17 NO
119 DUSP6 DUSP6 DUSP6 13450 -0.077 0.16 NO
120 CDKN1A CDKN1A CDKN1A 13462 -0.077 0.16 NO
121 ADCY4 ADCY4 ADCY4 13542 -0.078 0.16 NO
122 STAT3 STAT3 STAT3 13708 -0.082 0.16 NO
123 ATF1 ATF1 ATF1 14388 -0.094 0.12 NO
124 MAPKAPK3 MAPKAPK3 MAPKAPK3 14487 -0.097 0.12 NO
125 ADCY7 ADCY7 ADCY7 14920 -0.11 0.11 NO
126 RPS6KB2 RPS6KB2 RPS6KB2 15049 -0.11 0.11 NO
127 MAPKAPK2 MAPKAPK2 MAPKAPK2 15092 -0.11 0.11 NO
128 SHC1 SHC1 SHC1 15124 -0.11 0.12 NO
129 RIT1 RIT1 RIT1 15467 -0.12 0.1 NO
130 MAPK7 MAPK7 MAPK7 15469 -0.12 0.11 NO
131 TRIB3 TRIB3 TRIB3 15538 -0.13 0.12 NO
132 RPS6KA1 RPS6KA1 RPS6KA1 16145 -0.15 0.091 NO
133 NTRK1 NTRK1 NTRK1 17201 -0.22 0.046 NO
134 CDK1 CDK1 CDK1 17661 -0.27 0.036 NO

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

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

genes ES table in pathway: KEGG PURINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 115 1.1 0.098 YES
2 PDE1A PDE1A PDE1A 609 0.66 0.13 YES
3 CAMK4 CAMK4 CAMK4 610 0.66 0.2 YES
4 PDE1B PDE1B PDE1B 611 0.66 0.26 YES
5 ADCY1 ADCY1 ADCY1 630 0.65 0.32 YES
6 PRKAR1B PRKAR1B PRKAR1B 1177 0.43 0.33 YES
7 GRB7 GRB7 GRB7 1359 0.38 0.36 YES
8 PRKCE PRKCE PRKCE 1464 0.36 0.39 YES
9 PRKAR2B PRKAR2B PRKAR2B 1572 0.34 0.42 YES
10 CALM3 CALM3 CALM3 2142 0.24 0.41 YES
11 ADCY5 ADCY5 ADCY5 2156 0.24 0.43 YES
12 MAP2K1 MAP2K1 MAP2K1 2409 0.21 0.44 YES
13 CALM1 CALM1 CALM1 2691 0.18 0.44 YES
14 PRKCD PRKCD PRKCD 3086 0.15 0.43 YES
15 PRKACB PRKACB PRKACB 3370 0.13 0.43 YES
16 AKT3 AKT3 AKT3 3437 0.13 0.44 YES
17 PIK3CB PIK3CB PIK3CB 3627 0.12 0.44 YES
18 PDPK1 PDPK1 PDPK1 3647 0.12 0.45 YES
19 YWHAB YWHAB YWHAB 3768 0.11 0.45 YES
20 GSK3A GSK3A GSK3A 3781 0.11 0.46 YES
21 STAT6 STAT6 STAT6 4046 0.098 0.46 YES
22 MAPK3 MAPK3 MAPK3 4102 0.096 0.46 YES
23 ADRBK1 ADRBK1 ADRBK1 4130 0.094 0.47 YES
24 ADCY2 ADCY2 ADCY2 4192 0.091 0.48 YES
25 MAPK1 MAPK1 MAPK1 4317 0.086 0.48 YES
26 CALM2 CALM2 CALM2 4343 0.085 0.48 YES
27 ADCY8 ADCY8 ADCY8 4423 0.082 0.49 YES
28 ADCY3 ADCY3 ADCY3 4452 0.081 0.49 YES
29 KRAS KRAS KRAS 4769 0.07 0.48 NO
30 ADCY9 ADCY9 ADCY9 4773 0.07 0.49 NO
31 PRKACA PRKACA PRKACA 4908 0.066 0.49 NO
32 PRKAR1A PRKAR1A PRKAR1A 5169 0.057 0.48 NO
33 PTEN PTEN PTEN 5175 0.056 0.48 NO
34 RASA1 RASA1 RASA1 5200 0.056 0.49 NO
35 HRAS HRAS HRAS 5522 0.047 0.48 NO
36 MTOR MTOR MTOR 5637 0.044 0.47 NO
37 PIK3R1 PIK3R1 PIK3R1 5842 0.039 0.46 NO
38 PRKCA PRKCA PRKCA 5907 0.037 0.46 NO
39 FOXO4 FOXO4 FOXO4 6004 0.035 0.46 NO
40 FOXO3 FOXO3 FOXO3 6297 0.029 0.45 NO
41 PRKAR2A PRKAR2A PRKAR2A 6303 0.029 0.45 NO
42 PRKACG PRKACG PRKACG 6609 0.023 0.44 NO
43 NR4A1 NR4A1 NR4A1 6940 0.016 0.42 NO
44 THEM4 THEM4 THEM4 7411 0.0077 0.4 NO
45 GRB2 GRB2 GRB2 7541 0.0056 0.39 NO
46 CRKL CRKL CRKL 7670 0.0036 0.38 NO
47 PHLPP1 PHLPP1 PHLPP1 7774 0.0018 0.38 NO
48 ITPR2 ITPR2 ITPR2 7791 0.0016 0.38 NO
49 SRC SRC SRC 7947 -0.0013 0.37 NO
50 RAPGEF1 RAPGEF1 RAPGEF1 8009 -0.0022 0.36 NO
51 PIK3R2 PIK3R2 PIK3R2 8039 -0.0026 0.36 NO
52 MLST8 MLST8 MLST8 8383 -0.0078 0.35 NO
53 CHUK CHUK CHUK 8496 -0.0092 0.34 NO
54 MAP2K2 MAP2K2 MAP2K2 8542 -0.0099 0.34 NO
55 RICTOR RICTOR RICTOR 8575 -0.01 0.34 NO
56 FOXO1 FOXO1 FOXO1 8682 -0.012 0.33 NO
57 PDGFA PDGFA PDGFA 8781 -0.013 0.33 NO
58 MAPKAP1 MAPKAP1 MAPKAP1 8791 -0.013 0.33 NO
59 PDGFRB PDGFRB PDGFRB 8823 -0.013 0.33 NO
60 PDGFB PDGFB PDGFB 8869 -0.014 0.33 NO
61 CRK CRK CRK 8921 -0.014 0.33 NO
62 PIK3CA PIK3CA PIK3CA 8957 -0.015 0.33 NO
63 ADCY6 ADCY6 ADCY6 9112 -0.017 0.32 NO
64 TSC2 TSC2 TSC2 9165 -0.018 0.32 NO
65 BAD BAD BAD 9205 -0.019 0.32 NO
66 NCK2 NCK2 NCK2 9507 -0.023 0.3 NO
67 CDKN1B CDKN1B CDKN1B 9585 -0.024 0.3 NO
68 SOS1 SOS1 SOS1 9742 -0.026 0.3 NO
69 ITPR3 ITPR3 ITPR3 10014 -0.029 0.28 NO
70 CREB1 CREB1 CREB1 10115 -0.03 0.28 NO
71 STAT5B STAT5B STAT5B 10117 -0.03 0.28 NO
72 PLCG1 PLCG1 PLCG1 10501 -0.035 0.27 NO
73 BCAR1 BCAR1 BCAR1 10886 -0.04 0.25 NO
74 AKT1 AKT1 AKT1 11486 -0.048 0.22 NO
75 PDGFRA PDGFRA PDGFRA 11998 -0.055 0.2 NO
76 STAT1 STAT1 STAT1 12059 -0.056 0.2 NO
77 CASP9 CASP9 CASP9 12163 -0.057 0.2 NO
78 NRAS NRAS NRAS 12363 -0.06 0.2 NO
79 RAF1 RAF1 RAF1 12443 -0.061 0.2 NO
80 AKT1S1 AKT1S1 AKT1S1 12589 -0.063 0.2 NO
81 NCK1 NCK1 NCK1 12637 -0.064 0.2 NO
82 AKT2 AKT2 AKT2 12936 -0.069 0.19 NO
83 MDM2 MDM2 MDM2 13140 -0.072 0.18 NO
84 CDKN1A CDKN1A CDKN1A 13462 -0.077 0.17 NO
85 ADCY4 ADCY4 ADCY4 13542 -0.078 0.18 NO
86 STAT3 STAT3 STAT3 13708 -0.082 0.18 NO
87 ADCY7 ADCY7 ADCY7 14920 -0.11 0.12 NO
88 RPS6KB2 RPS6KB2 RPS6KB2 15049 -0.11 0.12 NO
89 TRIB3 TRIB3 TRIB3 15538 -0.13 0.11 NO
90 STAT5A STAT5A STAT5A 16807 -0.19 0.057 NO
91 CDK1 CDK1 CDK1 17661 -0.27 0.036 NO

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

Figure S64.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PURINE 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 115 1.1 0.078 YES
2 MATK MATK MATK 426 0.78 0.12 YES
3 PDE1A PDE1A PDE1A 609 0.66 0.16 YES
4 CAMK4 CAMK4 CAMK4 610 0.66 0.21 YES
5 PDE1B PDE1B PDE1B 611 0.66 0.26 YES
6 ADCY1 ADCY1 ADCY1 630 0.65 0.31 YES
7 NRG4 NRG4 NRG4 760 0.58 0.35 YES
8 NRG1 NRG1 NRG1 793 0.56 0.39 YES
9 PRKAR1B PRKAR1B PRKAR1B 1177 0.43 0.4 YES
10 GRB7 GRB7 GRB7 1359 0.38 0.42 YES
11 PRKCE PRKCE PRKCE 1464 0.36 0.45 YES
12 PRKAR2B PRKAR2B PRKAR2B 1572 0.34 0.47 YES
13 CALM3 CALM3 CALM3 2142 0.24 0.45 YES
14 ADCY5 ADCY5 ADCY5 2156 0.24 0.47 YES
15 MAP2K1 MAP2K1 MAP2K1 2409 0.21 0.47 YES
16 ERBB4 ERBB4 ERBB4 2463 0.21 0.49 YES
17 CALM1 CALM1 CALM1 2691 0.18 0.49 YES
18 PRKCD PRKCD PRKCD 3086 0.15 0.48 YES
19 EREG EREG EREG 3110 0.15 0.49 YES
20 PRKACB PRKACB PRKACB 3370 0.13 0.48 YES
21 AKT3 AKT3 AKT3 3437 0.13 0.49 YES
22 PDPK1 PDPK1 PDPK1 3647 0.12 0.49 YES
23 RNF41 RNF41 RNF41 3756 0.11 0.49 YES
24 YWHAB YWHAB YWHAB 3768 0.11 0.5 YES
25 GSK3A GSK3A GSK3A 3781 0.11 0.51 YES
26 MAPK3 MAPK3 MAPK3 4102 0.096 0.5 YES
27 ADRBK1 ADRBK1 ADRBK1 4130 0.094 0.5 YES
28 ADCY2 ADCY2 ADCY2 4192 0.091 0.51 YES
29 MAPK1 MAPK1 MAPK1 4317 0.086 0.51 YES
30 CALM2 CALM2 CALM2 4343 0.085 0.51 YES
31 ADCY8 ADCY8 ADCY8 4423 0.082 0.51 YES
32 ADCY3 ADCY3 ADCY3 4452 0.081 0.52 YES
33 KRAS KRAS KRAS 4769 0.07 0.5 NO
34 ADCY9 ADCY9 ADCY9 4773 0.07 0.51 NO
35 PRKACA PRKACA PRKACA 4908 0.066 0.51 NO
36 HSP90AA1 HSP90AA1 HSP90AA1 5118 0.059 0.5 NO
37 PRKAR1A PRKAR1A PRKAR1A 5169 0.057 0.5 NO
38 PTEN PTEN PTEN 5175 0.056 0.51 NO
39 HRAS HRAS HRAS 5522 0.047 0.49 NO
40 MTOR MTOR MTOR 5637 0.044 0.49 NO
41 PIK3R1 PIK3R1 PIK3R1 5842 0.039 0.48 NO
42 STUB1 STUB1 STUB1 5896 0.037 0.48 NO
43 PRKCA PRKCA PRKCA 5907 0.037 0.48 NO
44 FOXO4 FOXO4 FOXO4 6004 0.035 0.48 NO
45 FOXO3 FOXO3 FOXO3 6297 0.029 0.47 NO
46 PRKAR2A PRKAR2A PRKAR2A 6303 0.029 0.47 NO
47 PRKACG PRKACG PRKACG 6609 0.023 0.45 NO
48 ERBB3 ERBB3 ERBB3 6905 0.017 0.44 NO
49 NR4A1 NR4A1 NR4A1 6940 0.016 0.44 NO
50 THEM4 THEM4 THEM4 7411 0.0077 0.41 NO
51 CUL5 CUL5 CUL5 7499 0.0063 0.41 NO
52 GRB2 GRB2 GRB2 7541 0.0056 0.41 NO
53 PHLPP1 PHLPP1 PHLPP1 7774 0.0018 0.39 NO
54 ITPR2 ITPR2 ITPR2 7791 0.0016 0.39 NO
55 SRC SRC SRC 7947 -0.0013 0.38 NO
56 USP8 USP8 USP8 7969 -0.0016 0.38 NO
57 MLST8 MLST8 MLST8 8383 -0.0078 0.36 NO
58 CDC37 CDC37 CDC37 8413 -0.0081 0.36 NO
59 CHUK CHUK CHUK 8496 -0.0092 0.36 NO
60 MAP2K2 MAP2K2 MAP2K2 8542 -0.0099 0.36 NO
61 RICTOR RICTOR RICTOR 8575 -0.01 0.35 NO
62 FOXO1 FOXO1 FOXO1 8682 -0.012 0.35 NO
63 MAPKAP1 MAPKAP1 MAPKAP1 8791 -0.013 0.34 NO
64 PIK3CA PIK3CA PIK3CA 8957 -0.015 0.34 NO
65 ADCY6 ADCY6 ADCY6 9112 -0.017 0.33 NO
66 TSC2 TSC2 TSC2 9165 -0.018 0.33 NO
67 BAD BAD BAD 9205 -0.019 0.33 NO
68 CDKN1B CDKN1B CDKN1B 9585 -0.024 0.31 NO
69 BTC BTC BTC 9619 -0.024 0.31 NO
70 SOS1 SOS1 SOS1 9742 -0.026 0.3 NO
71 ITPR3 ITPR3 ITPR3 10014 -0.029 0.29 NO
72 CREB1 CREB1 CREB1 10115 -0.03 0.29 NO
73 NRG2 NRG2 NRG2 10313 -0.033 0.28 NO
74 PLCG1 PLCG1 PLCG1 10501 -0.035 0.27 NO
75 FYN FYN FYN 10873 -0.04 0.26 NO
76 AKT1 AKT1 AKT1 11486 -0.048 0.22 NO
77 CASP9 CASP9 CASP9 12163 -0.057 0.19 NO
78 RPS27A RPS27A RPS27A 12165 -0.057 0.2 NO
79 UBA52 UBA52 UBA52 12197 -0.058 0.2 NO
80 NRAS NRAS NRAS 12363 -0.06 0.2 NO
81 RAF1 RAF1 RAF1 12443 -0.061 0.2 NO
82 YES1 YES1 YES1 12581 -0.063 0.19 NO
83 AKT1S1 AKT1S1 AKT1S1 12589 -0.063 0.2 NO
84 EGFR EGFR EGFR 12661 -0.064 0.2 NO
85 AKT2 AKT2 AKT2 12936 -0.069 0.19 NO
86 ERBB2 ERBB2 ERBB2 13054 -0.071 0.19 NO
87 MDM2 MDM2 MDM2 13140 -0.072 0.19 NO
88 CDKN1A CDKN1A CDKN1A 13462 -0.077 0.18 NO
89 ADCY4 ADCY4 ADCY4 13542 -0.078 0.18 NO
90 GAB1 GAB1 GAB1 14235 -0.091 0.15 NO
91 EGF EGF EGF 14913 -0.11 0.12 NO
92 ADCY7 ADCY7 ADCY7 14920 -0.11 0.13 NO
93 RPS6KB2 RPS6KB2 RPS6KB2 15049 -0.11 0.13 NO
94 SHC1 SHC1 SHC1 15124 -0.11 0.13 NO
95 TRIB3 TRIB3 TRIB3 15538 -0.13 0.12 NO
96 HBEGF HBEGF HBEGF 16173 -0.15 0.097 NO
97 CDK1 CDK1 CDK1 17661 -0.27 0.036 NO

Figure S65.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

Figure S66.  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 ARGININE AND PROLINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 115 1.1 0.089 YES
2 PDE1A PDE1A PDE1A 609 0.66 0.12 YES
3 CAMK4 CAMK4 CAMK4 610 0.66 0.18 YES
4 PDE1B PDE1B PDE1B 611 0.66 0.24 YES
5 ADCY1 ADCY1 ADCY1 630 0.65 0.29 YES
6 PRKAR1B PRKAR1B PRKAR1B 1177 0.43 0.3 YES
7 PRKCE PRKCE PRKCE 1464 0.36 0.32 YES
8 PRKAR2B PRKAR2B PRKAR2B 1572 0.34 0.34 YES
9 SH3GL2 SH3GL2 SH3GL2 1610 0.33 0.36 YES
10 CALM3 CALM3 CALM3 2142 0.24 0.36 YES
11 ADCY5 ADCY5 ADCY5 2156 0.24 0.38 YES
12 MAP2K1 MAP2K1 MAP2K1 2409 0.21 0.38 YES
13 CALM1 CALM1 CALM1 2691 0.18 0.38 YES
14 PRKCD PRKCD PRKCD 3086 0.15 0.37 YES
15 EPS15 EPS15 EPS15 3291 0.14 0.38 YES
16 PRKACB PRKACB PRKACB 3370 0.13 0.38 YES
17 AKT3 AKT3 AKT3 3437 0.13 0.39 YES
18 PDPK1 PDPK1 PDPK1 3647 0.12 0.39 YES
19 YWHAB YWHAB YWHAB 3768 0.11 0.39 YES
20 GSK3A GSK3A GSK3A 3781 0.11 0.4 YES
21 AP2A1 AP2A1 AP2A1 4038 0.098 0.4 YES
22 MAPK3 MAPK3 MAPK3 4102 0.096 0.4 YES
23 ADRBK1 ADRBK1 ADRBK1 4130 0.094 0.41 YES
24 ADCY2 ADCY2 ADCY2 4192 0.091 0.41 YES
25 MAPK1 MAPK1 MAPK1 4317 0.086 0.41 YES
26 CALM2 CALM2 CALM2 4343 0.085 0.42 YES
27 ADCY8 ADCY8 ADCY8 4423 0.082 0.42 YES
28 ADCY3 ADCY3 ADCY3 4452 0.081 0.43 YES
29 AP2A2 AP2A2 AP2A2 4481 0.08 0.43 YES
30 STAM STAM STAM 4625 0.075 0.43 YES
31 KRAS KRAS KRAS 4769 0.07 0.43 YES
32 ADCY9 ADCY9 ADCY9 4773 0.07 0.43 YES
33 AP2S1 AP2S1 AP2S1 4789 0.069 0.44 YES
34 AP2M1 AP2M1 AP2M1 4797 0.069 0.44 YES
35 PRKACA PRKACA PRKACA 4908 0.066 0.44 YES
36 HSP90AA1 HSP90AA1 HSP90AA1 5118 0.059 0.44 YES
37 PRKAR1A PRKAR1A PRKAR1A 5169 0.057 0.44 YES
38 PTEN PTEN PTEN 5175 0.056 0.44 YES
39 CLTC CLTC CLTC 5259 0.054 0.45 YES
40 EPN1 EPN1 EPN1 5274 0.054 0.45 YES
41 HRAS HRAS HRAS 5522 0.047 0.44 NO
42 MTOR MTOR MTOR 5637 0.044 0.44 NO
43 PIK3R1 PIK3R1 PIK3R1 5842 0.039 0.43 NO
44 PRKCA PRKCA PRKCA 5907 0.037 0.43 NO
45 FOXO4 FOXO4 FOXO4 6004 0.035 0.43 NO
46 EPS15L1 EPS15L1 EPS15L1 6249 0.03 0.42 NO
47 FOXO3 FOXO3 FOXO3 6297 0.029 0.42 NO
48 PRKAR2A PRKAR2A PRKAR2A 6303 0.029 0.42 NO
49 AP2B1 AP2B1 AP2B1 6441 0.026 0.41 NO
50 PRKACG PRKACG PRKACG 6609 0.023 0.41 NO
51 NR4A1 NR4A1 NR4A1 6940 0.016 0.39 NO
52 THEM4 THEM4 THEM4 7411 0.0077 0.36 NO
53 GRB2 GRB2 GRB2 7541 0.0056 0.36 NO
54 SH3KBP1 SH3KBP1 SH3KBP1 7552 0.0054 0.36 NO
55 PHLPP1 PHLPP1 PHLPP1 7774 0.0018 0.35 NO
56 ITPR2 ITPR2 ITPR2 7791 0.0016 0.34 NO
57 ADAM10 ADAM10 ADAM10 7824 0.00084 0.34 NO
58 LRIG1 LRIG1 LRIG1 7879 -0.00022 0.34 NO
59 SRC SRC SRC 7947 -0.0013 0.34 NO
60 CLTA CLTA CLTA 7974 -0.0017 0.34 NO
61 SPRY2 SPRY2 SPRY2 8270 -0.0062 0.32 NO
62 MLST8 MLST8 MLST8 8383 -0.0078 0.31 NO
63 CDC37 CDC37 CDC37 8413 -0.0081 0.31 NO
64 CHUK CHUK CHUK 8496 -0.0092 0.31 NO
65 MAP2K2 MAP2K2 MAP2K2 8542 -0.0099 0.31 NO
66 RICTOR RICTOR RICTOR 8575 -0.01 0.31 NO
67 FOXO1 FOXO1 FOXO1 8682 -0.012 0.3 NO
68 CBL CBL CBL 8787 -0.013 0.3 NO
69 MAPKAP1 MAPKAP1 MAPKAP1 8791 -0.013 0.3 NO
70 CDC42 CDC42 CDC42 8797 -0.013 0.3 NO
71 PIK3CA PIK3CA PIK3CA 8957 -0.015 0.29 NO
72 HGS HGS HGS 9009 -0.016 0.29 NO
73 ADCY6 ADCY6 ADCY6 9112 -0.017 0.29 NO
74 TSC2 TSC2 TSC2 9165 -0.018 0.29 NO
75 BAD BAD BAD 9205 -0.019 0.28 NO
76 CDKN1B CDKN1B CDKN1B 9585 -0.024 0.27 NO
77 SOS1 SOS1 SOS1 9742 -0.026 0.26 NO
78 STAM2 STAM2 STAM2 9798 -0.026 0.26 NO
79 ITPR3 ITPR3 ITPR3 10014 -0.029 0.25 NO
80 CREB1 CREB1 CREB1 10115 -0.03 0.25 NO
81 PLCG1 PLCG1 PLCG1 10501 -0.035 0.23 NO
82 AKT1 AKT1 AKT1 11486 -0.048 0.18 NO
83 CASP9 CASP9 CASP9 12163 -0.057 0.15 NO
84 RPS27A RPS27A RPS27A 12165 -0.057 0.15 NO
85 UBA52 UBA52 UBA52 12197 -0.058 0.16 NO
86 NRAS NRAS NRAS 12363 -0.06 0.15 NO
87 RAF1 RAF1 RAF1 12443 -0.061 0.15 NO
88 AKT1S1 AKT1S1 AKT1S1 12589 -0.063 0.15 NO
89 EGFR EGFR EGFR 12661 -0.064 0.15 NO
90 ADAM17 ADAM17 ADAM17 12741 -0.066 0.15 NO
91 AKT2 AKT2 AKT2 12936 -0.069 0.15 NO
92 MDM2 MDM2 MDM2 13140 -0.072 0.14 NO
93 CDKN1A CDKN1A CDKN1A 13462 -0.077 0.13 NO
94 ADCY4 ADCY4 ADCY4 13542 -0.078 0.14 NO
95 PAG1 PAG1 PAG1 14056 -0.088 0.12 NO
96 GAB1 GAB1 GAB1 14235 -0.091 0.11 NO
97 CSK CSK CSK 14368 -0.094 0.11 NO
98 EGF EGF EGF 14913 -0.11 0.094 NO
99 ADCY7 ADCY7 ADCY7 14920 -0.11 0.1 NO
100 RPS6KB2 RPS6KB2 RPS6KB2 15049 -0.11 0.11 NO
101 SHC1 SHC1 SHC1 15124 -0.11 0.11 NO
102 SPRY1 SPRY1 SPRY1 15250 -0.12 0.12 NO
103 TRIB3 TRIB3 TRIB3 15538 -0.13 0.11 NO
104 ADAM12 ADAM12 ADAM12 17176 -0.22 0.039 NO
105 CDK1 CDK1 CDK1 17661 -0.27 0.036 NO

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

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ARGININE AND PROLINE 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 S35.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 786 0.57 0.12 YES
2 PAK1 PAK1 PAK1 803 0.56 0.27 YES
3 PTK2B PTK2B PTK2B 1412 0.37 0.34 YES
4 MAP2K4 MAP2K4 MAP2K4 2135 0.24 0.37 YES
5 CALM3 CALM3 CALM3 2142 0.24 0.44 YES
6 MAP2K1 MAP2K1 MAP2K1 2409 0.21 0.48 YES
7 CALM1 CALM1 CALM1 2691 0.18 0.52 YES
8 MAPK8 MAPK8 MAPK8 3120 0.15 0.53 YES
9 MAPK3 MAPK3 MAPK3 4102 0.096 0.51 YES
10 GNAQ GNAQ GNAQ 4173 0.092 0.53 YES
11 MAPK1 MAPK1 MAPK1 4317 0.086 0.54 YES
12 CALM2 CALM2 CALM2 4343 0.085 0.57 YES
13 HRAS HRAS HRAS 5522 0.047 0.52 NO
14 PRKCA PRKCA PRKCA 5907 0.037 0.5 NO
15 GRB2 GRB2 GRB2 7541 0.0056 0.42 NO
16 MAPK14 MAPK14 MAPK14 7588 0.005 0.42 NO
17 CRKL CRKL CRKL 7670 0.0036 0.41 NO
18 SRC SRC SRC 7947 -0.0013 0.4 NO
19 MAP2K2 MAP2K2 MAP2K2 8542 -0.0099 0.37 NO
20 RAC1 RAC1 RAC1 9293 -0.02 0.33 NO
21 SOS1 SOS1 SOS1 9742 -0.026 0.32 NO
22 PLCG1 PLCG1 PLCG1 10501 -0.035 0.28 NO
23 BCAR1 BCAR1 BCAR1 10886 -0.04 0.27 NO
24 RAF1 RAF1 RAF1 12443 -0.061 0.2 NO
25 MAP2K3 MAP2K3 MAP2K3 13722 -0.082 0.16 NO
26 JUN JUN JUN 13842 -0.084 0.18 NO
27 SHC1 SHC1 SHC1 15124 -0.11 0.14 NO
28 MAP3K1 MAP3K1 MAP3K1 15771 -0.14 0.14 NO

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

Figure S70.  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 GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 115 1.1 0.065 YES
2 PDE1A PDE1A PDE1A 609 0.66 0.082 YES
3 CAMK4 CAMK4 CAMK4 610 0.66 0.12 YES
4 PDE1B PDE1B PDE1B 611 0.66 0.17 YES
5 ADCY1 ADCY1 ADCY1 630 0.65 0.21 YES
6 FGF5 FGF5 FGF5 637 0.65 0.25 YES
7 FGF9 FGF9 FGF9 834 0.54 0.28 YES
8 KLB KLB KLB 895 0.52 0.31 YES
9 KL KL KL 1144 0.44 0.32 YES
10 FGF18 FGF18 FGF18 1175 0.43 0.35 YES
11 PRKAR1B PRKAR1B PRKAR1B 1177 0.43 0.38 YES
12 PRKCE PRKCE PRKCE 1464 0.36 0.39 YES
13 FGF22 FGF22 FGF22 1546 0.34 0.4 YES
14 PRKAR2B PRKAR2B PRKAR2B 1572 0.34 0.42 YES
15 FGFR3 FGFR3 FGFR3 2005 0.26 0.42 YES
16 FGF8 FGF8 FGF8 2011 0.26 0.44 YES
17 CALM3 CALM3 CALM3 2142 0.24 0.44 YES
18 ADCY5 ADCY5 ADCY5 2156 0.24 0.46 YES
19 FGF10 FGF10 FGF10 2291 0.22 0.47 YES
20 MAP2K1 MAP2K1 MAP2K1 2409 0.21 0.47 YES
21 CALM1 CALM1 CALM1 2691 0.18 0.47 YES
22 FGF7 FGF7 FGF7 2909 0.16 0.47 YES
23 PRKCD PRKCD PRKCD 3086 0.15 0.47 YES
24 FGFR2 FGFR2 FGFR2 3267 0.14 0.47 YES
25 PRKACB PRKACB PRKACB 3370 0.13 0.47 YES
26 BRAF BRAF BRAF 3403 0.13 0.48 YES
27 FRS3 FRS3 FRS3 3423 0.13 0.49 YES
28 AKT3 AKT3 AKT3 3437 0.13 0.49 YES
29 PDPK1 PDPK1 PDPK1 3647 0.12 0.49 YES
30 YWHAB YWHAB YWHAB 3768 0.11 0.49 YES
31 GSK3A GSK3A GSK3A 3781 0.11 0.5 YES
32 MAPK3 MAPK3 MAPK3 4102 0.096 0.49 YES
33 ADRBK1 ADRBK1 ADRBK1 4130 0.094 0.49 YES
34 ADCY2 ADCY2 ADCY2 4192 0.091 0.49 YES
35 FGFR1OP2 FGFR1OP2 FGFR1OP2 4311 0.086 0.49 YES
36 MAPK1 MAPK1 MAPK1 4317 0.086 0.5 YES
37 CALM2 CALM2 CALM2 4343 0.085 0.5 YES
38 ADCY8 ADCY8 ADCY8 4423 0.082 0.5 YES
39 ADCY3 ADCY3 ADCY3 4452 0.081 0.51 YES
40 KRAS KRAS KRAS 4769 0.07 0.49 NO
41 ADCY9 ADCY9 ADCY9 4773 0.07 0.5 NO
42 FGF17 FGF17 FGF17 4818 0.068 0.5 NO
43 PRKACA PRKACA PRKACA 4908 0.066 0.5 NO
44 PRKAR1A PRKAR1A PRKAR1A 5169 0.057 0.49 NO
45 PTEN PTEN PTEN 5175 0.056 0.49 NO
46 FGF1 FGF1 FGF1 5251 0.054 0.49 NO
47 PPP2R1A PPP2R1A PPP2R1A 5287 0.053 0.49 NO
48 PPP2CA PPP2CA PPP2CA 5474 0.048 0.49 NO
49 HRAS HRAS HRAS 5522 0.047 0.49 NO
50 MTOR MTOR MTOR 5637 0.044 0.48 NO
51 PIK3R1 PIK3R1 PIK3R1 5842 0.039 0.48 NO
52 PRKCA PRKCA PRKCA 5907 0.037 0.47 NO
53 FOXO4 FOXO4 FOXO4 6004 0.035 0.47 NO
54 FOXO3 FOXO3 FOXO3 6297 0.029 0.46 NO
55 PRKAR2A PRKAR2A PRKAR2A 6303 0.029 0.46 NO
56 PRKACG PRKACG PRKACG 6609 0.023 0.44 NO
57 MYO18A MYO18A MYO18A 6627 0.023 0.44 NO
58 ZMYM2 ZMYM2 ZMYM2 6856 0.018 0.43 NO
59 NR4A1 NR4A1 NR4A1 6940 0.016 0.43 NO
60 BCR BCR BCR 7260 0.01 0.41 NO
61 THEM4 THEM4 THEM4 7411 0.0077 0.4 NO
62 GRB2 GRB2 GRB2 7541 0.0056 0.4 NO
63 PPP2CB PPP2CB PPP2CB 7704 0.0031 0.39 NO
64 PHLPP1 PHLPP1 PHLPP1 7774 0.0018 0.39 NO
65 ITPR2 ITPR2 ITPR2 7791 0.0016 0.38 NO
66 SRC SRC SRC 7947 -0.0013 0.38 NO
67 SPRY2 SPRY2 SPRY2 8270 -0.0062 0.36 NO
68 MLST8 MLST8 MLST8 8383 -0.0078 0.35 NO
69 CHUK CHUK CHUK 8496 -0.0092 0.35 NO
70 MAP2K2 MAP2K2 MAP2K2 8542 -0.0099 0.35 NO
71 RICTOR RICTOR RICTOR 8575 -0.01 0.34 NO
72 CPSF6 CPSF6 CPSF6 8670 -0.012 0.34 NO
73 FGFR1OP FGFR1OP FGFR1OP 8678 -0.012 0.34 NO
74 FOXO1 FOXO1 FOXO1 8682 -0.012 0.34 NO
75 CBL CBL CBL 8787 -0.013 0.34 NO
76 MAPKAP1 MAPKAP1 MAPKAP1 8791 -0.013 0.34 NO
77 PIK3CA PIK3CA PIK3CA 8957 -0.015 0.33 NO
78 ADCY6 ADCY6 ADCY6 9112 -0.017 0.32 NO
79 TSC2 TSC2 TSC2 9165 -0.018 0.32 NO
80 BAD BAD BAD 9205 -0.019 0.32 NO
81 FGFR1 FGFR1 FGFR1 9245 -0.019 0.32 NO
82 FRS2 FRS2 FRS2 9292 -0.02 0.32 NO
83 FGF2 FGF2 FGF2 9489 -0.022 0.31 NO
84 CDKN1B CDKN1B CDKN1B 9585 -0.024 0.3 NO
85 SOS1 SOS1 SOS1 9742 -0.026 0.3 NO
86 CUX1 CUX1 CUX1 9779 -0.026 0.3 NO
87 ITPR3 ITPR3 ITPR3 10014 -0.029 0.29 NO
88 CREB1 CREB1 CREB1 10115 -0.03 0.28 NO
89 STAT5B STAT5B STAT5B 10117 -0.03 0.28 NO
90 PLCG1 PLCG1 PLCG1 10501 -0.035 0.27 NO
91 AKT1 AKT1 AKT1 11486 -0.048 0.22 NO
92 GAB2 GAB2 GAB2 11712 -0.051 0.21 NO
93 STAT1 STAT1 STAT1 12059 -0.056 0.19 NO
94 CASP9 CASP9 CASP9 12163 -0.057 0.19 NO
95 RPS27A RPS27A RPS27A 12165 -0.057 0.19 NO
96 UBA52 UBA52 UBA52 12197 -0.058 0.2 NO
97 MKNK1 MKNK1 MKNK1 12319 -0.059 0.19 NO
98 NRAS NRAS NRAS 12363 -0.06 0.19 NO
99 RAF1 RAF1 RAF1 12443 -0.061 0.19 NO
100 AKT1S1 AKT1S1 AKT1S1 12589 -0.063 0.19 NO
101 AKT2 AKT2 AKT2 12936 -0.069 0.18 NO
102 MDM2 MDM2 MDM2 13140 -0.072 0.17 NO
103 IL17RD IL17RD IL17RD 13182 -0.072 0.17 NO
104 CDKN1A CDKN1A CDKN1A 13462 -0.077 0.16 NO
105 ADCY4 ADCY4 ADCY4 13542 -0.078 0.16 NO
106 TRIM24 TRIM24 TRIM24 13699 -0.081 0.16 NO
107 STAT3 STAT3 STAT3 13708 -0.082 0.16 NO
108 GAB1 GAB1 GAB1 14235 -0.091 0.14 NO
109 ADCY7 ADCY7 ADCY7 14920 -0.11 0.11 NO
110 RPS6KB2 RPS6KB2 RPS6KB2 15049 -0.11 0.11 NO
111 SHC1 SHC1 SHC1 15124 -0.11 0.11 NO
112 TRIB3 TRIB3 TRIB3 15538 -0.13 0.099 NO
113 FGF20 FGF20 FGF20 16209 -0.15 0.072 NO
114 STAT5A STAT5A STAT5A 16807 -0.19 0.052 NO
115 FGFR4 FGFR4 FGFR4 17054 -0.21 0.052 NO
116 CDK1 CDK1 CDK1 17661 -0.27 0.036 NO

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

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

genes ES table in pathway: KEGG GLYCEROLIPID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 115 1.1 0.034 YES
2 ADCYAP1 ADCYAP1 ADCYAP1 361 0.83 0.052 YES
3 NGEF NGEF NGEF 445 0.76 0.075 YES
4 RASGRF2 RASGRF2 RASGRF2 503 0.73 0.099 YES
5 DNM1 DNM1 DNM1 508 0.72 0.12 YES
6 PDE1A PDE1A PDE1A 609 0.66 0.14 YES
7 CAMK4 CAMK4 CAMK4 610 0.66 0.17 YES
8 PDE1B PDE1B PDE1B 611 0.66 0.19 YES
9 ADCY1 ADCY1 ADCY1 630 0.65 0.22 YES
10 MAPK13 MAPK13 MAPK13 881 0.52 0.22 YES
11 RIT2 RIT2 RIT2 886 0.52 0.24 YES
12 RASGRF1 RASGRF1 RASGRF1 887 0.52 0.26 YES
13 MCF2 MCF2 MCF2 940 0.5 0.28 YES
14 TIAM2 TIAM2 TIAM2 1026 0.47 0.29 YES
15 PRKAR1B PRKAR1B PRKAR1B 1177 0.43 0.3 YES
16 NGF NGF NGF 1323 0.39 0.3 YES
17 KALRN KALRN KALRN 1376 0.38 0.32 YES
18 MEF2C MEF2C MEF2C 1395 0.37 0.33 YES
19 PRKCE PRKCE PRKCE 1464 0.36 0.34 YES
20 PRKAR2B PRKAR2B PRKAR2B 1572 0.34 0.34 YES
21 SH3GL2 SH3GL2 SH3GL2 1610 0.33 0.35 YES
22 SHC3 SHC3 SHC3 1714 0.31 0.36 YES
23 CALM3 CALM3 CALM3 2142 0.24 0.35 YES
24 ADCY5 ADCY5 ADCY5 2156 0.24 0.35 YES
25 OBSCN OBSCN OBSCN 2232 0.23 0.36 YES
26 MAP2K1 MAP2K1 MAP2K1 2409 0.21 0.36 YES
27 ELK1 ELK1 ELK1 2457 0.21 0.36 YES
28 MAG MAG MAG 2616 0.19 0.36 YES
29 CALM1 CALM1 CALM1 2691 0.18 0.36 YES
30 ARHGEF9 ARHGEF9 ARHGEF9 2698 0.18 0.37 YES
31 MAPK11 MAPK11 MAPK11 2800 0.18 0.37 YES
32 VAV3 VAV3 VAV3 2870 0.17 0.37 YES
33 ADCYAP1R1 ADCYAP1R1 ADCYAP1R1 3051 0.15 0.37 YES
34 LINGO1 LINGO1 LINGO1 3063 0.15 0.37 YES
35 PRKCD PRKCD PRKCD 3086 0.15 0.38 YES
36 MAPK8 MAPK8 MAPK8 3120 0.15 0.38 YES
37 DUSP3 DUSP3 DUSP3 3127 0.15 0.39 YES
38 SORCS3 SORCS3 SORCS3 3247 0.14 0.38 YES
39 ARHGEF3 ARHGEF3 ARHGEF3 3332 0.14 0.39 YES
40 ABR ABR ABR 3346 0.13 0.39 YES
41 PRKACB PRKACB PRKACB 3370 0.13 0.39 YES
42 RPS6KA5 RPS6KA5 RPS6KA5 3399 0.13 0.4 YES
43 BRAF BRAF BRAF 3403 0.13 0.4 YES
44 AKT3 AKT3 AKT3 3437 0.13 0.4 YES
45 RALB RALB RALB 3503 0.12 0.4 YES
46 ARHGEF4 ARHGEF4 ARHGEF4 3505 0.12 0.41 YES
47 OMG OMG OMG 3599 0.12 0.41 YES
48 PIK3CB PIK3CB PIK3CB 3627 0.12 0.41 YES
49 PDPK1 PDPK1 PDPK1 3647 0.12 0.42 YES
50 RPS6KA2 RPS6KA2 RPS6KA2 3760 0.11 0.41 YES
51 YWHAB YWHAB YWHAB 3768 0.11 0.42 YES
52 GSK3A GSK3A GSK3A 3781 0.11 0.42 YES
53 MEF2A MEF2A MEF2A 3946 0.1 0.42 YES
54 AP2A1 AP2A1 AP2A1 4038 0.098 0.41 YES
55 MAPK3 MAPK3 MAPK3 4102 0.096 0.41 YES
56 ADRBK1 ADRBK1 ADRBK1 4130 0.094 0.42 YES
57 ADCY2 ADCY2 ADCY2 4192 0.091 0.42 YES
58 TIAM1 TIAM1 TIAM1 4286 0.087 0.41 YES
59 RTN4 RTN4 RTN4 4289 0.087 0.42 YES
60 MAPK1 MAPK1 MAPK1 4317 0.086 0.42 YES
61 DUSP7 DUSP7 DUSP7 4334 0.086 0.42 YES
62 CALM2 CALM2 CALM2 4343 0.085 0.42 YES
63 ADCY8 ADCY8 ADCY8 4423 0.082 0.42 YES
64 ADCY3 ADCY3 ADCY3 4452 0.081 0.42 YES
65 AP2A2 AP2A2 AP2A2 4481 0.08 0.42 YES
66 NTRK2 NTRK2 NTRK2 4609 0.076 0.42 YES
67 PPP2R5D PPP2R5D PPP2R5D 4631 0.075 0.42 YES
68 ARHGEF11 ARHGEF11 ARHGEF11 4701 0.072 0.42 YES
69 ARHGEF17 ARHGEF17 ARHGEF17 4717 0.072 0.42 YES
70 KRAS KRAS KRAS 4769 0.07 0.42 YES
71 ADCY9 ADCY9 ADCY9 4773 0.07 0.42 YES
72 AP2S1 AP2S1 AP2S1 4789 0.069 0.43 YES
73 AP2M1 AP2M1 AP2M1 4797 0.069 0.43 YES
74 ARHGEF12 ARHGEF12 ARHGEF12 4848 0.067 0.43 YES
75 DNAL4 DNAL4 DNAL4 4907 0.066 0.43 YES
76 PRKACA PRKACA PRKACA 4908 0.066 0.43 YES
77 NET1 NET1 NET1 4973 0.063 0.43 NO
78 PSEN2 PSEN2 PSEN2 5027 0.061 0.43 NO
79 PRKAR1A PRKAR1A PRKAR1A 5169 0.057 0.42 NO
80 PRKCI PRKCI PRKCI 5172 0.056 0.42 NO
81 PTEN PTEN PTEN 5175 0.056 0.43 NO
82 CLTC CLTC CLTC 5259 0.054 0.42 NO
83 PPP2R1A PPP2R1A PPP2R1A 5287 0.053 0.42 NO
84 PCSK6 PCSK6 PCSK6 5369 0.051 0.42 NO
85 PPP2CA PPP2CA PPP2CA 5474 0.048 0.42 NO
86 HRAS HRAS HRAS 5522 0.047 0.42 NO
87 NGFRAP1 NGFRAP1 NGFRAP1 5576 0.046 0.42 NO
88 ITSN1 ITSN1 ITSN1 5617 0.045 0.42 NO
89 MTOR MTOR MTOR 5637 0.044 0.42 NO
90 PIK3R1 PIK3R1 PIK3R1 5842 0.039 0.41 NO
91 IRS1 IRS1 IRS1 5901 0.037 0.4 NO
92 PRKCA PRKCA PRKCA 5907 0.037 0.41 NO
93 FOXO4 FOXO4 FOXO4 6004 0.035 0.4 NO
94 PRDM4 PRDM4 PRDM4 6124 0.032 0.4 NO
95 RPS6KA3 RPS6KA3 RPS6KA3 6131 0.032 0.4 NO
96 FURIN FURIN FURIN 6208 0.031 0.39 NO
97 FOXO3 FOXO3 FOXO3 6297 0.029 0.39 NO
98 PRKAR2A PRKAR2A PRKAR2A 6303 0.029 0.39 NO
99 AP2B1 AP2B1 AP2B1 6441 0.026 0.38 NO
100 MAP2K5 MAP2K5 MAP2K5 6465 0.026 0.38 NO
101 FGD4 FGD4 FGD4 6470 0.026 0.38 NO
102 PRKACG PRKACG PRKACG 6609 0.023 0.38 NO
103 NR4A1 NR4A1 NR4A1 6940 0.016 0.36 NO
104 DUSP4 DUSP4 DUSP4 7130 0.012 0.35 NO
105 TRIO TRIO TRIO 7355 0.0087 0.34 NO
106 THEM4 THEM4 THEM4 7411 0.0077 0.34 NO
107 MAGED1 MAGED1 MAGED1 7460 0.0069 0.33 NO
108 GRB2 GRB2 GRB2 7541 0.0056 0.33 NO
109 MAPK14 MAPK14 MAPK14 7588 0.005 0.33 NO
110 KIDINS220 KIDINS220 KIDINS220 7601 0.0047 0.33 NO
111 PREX1 PREX1 PREX1 7668 0.0036 0.32 NO
112 PPP2CB PPP2CB PPP2CB 7704 0.0031 0.32 NO
113 PHLPP1 PHLPP1 PHLPP1 7774 0.0018 0.32 NO
114 ITPR2 ITPR2 ITPR2 7791 0.0016 0.32 NO
115 SRC SRC SRC 7947 -0.0013 0.31 NO
116 CLTA CLTA CLTA 7974 -0.0017 0.31 NO
117 YWHAE YWHAE YWHAE 7975 -0.0017 0.31 NO
118 MAPK12 MAPK12 MAPK12 7983 -0.0018 0.31 NO
119 RAPGEF1 RAPGEF1 RAPGEF1 8009 -0.0022 0.3 NO
120 PIK3R2 PIK3R2 PIK3R2 8039 -0.0026 0.3 NO
121 IRS2 IRS2 IRS2 8057 -0.0029 0.3 NO
122 MLST8 MLST8 MLST8 8383 -0.0078 0.28 NO
123 CHUK CHUK CHUK 8496 -0.0092 0.28 NO
124 MAP2K2 MAP2K2 MAP2K2 8542 -0.0099 0.28 NO
125 RICTOR RICTOR RICTOR 8575 -0.01 0.28 NO
126 FOXO1 FOXO1 FOXO1 8682 -0.012 0.27 NO
127 MAPKAP1 MAPKAP1 MAPKAP1 8791 -0.013 0.26 NO
128 CRK CRK CRK 8921 -0.014 0.26 NO
129 PIK3CA PIK3CA PIK3CA 8957 -0.015 0.26 NO
130 PSEN1 PSEN1 PSEN1 9095 -0.017 0.25 NO
131 ARHGEF2 ARHGEF2 ARHGEF2 9108 -0.017 0.25 NO
132 ADCY6 ADCY6 ADCY6 9112 -0.017 0.25 NO
133 TSC2 TSC2 TSC2 9165 -0.018 0.25 NO
134 BAD BAD BAD 9205 -0.019 0.25 NO
135 FRS2 FRS2 FRS2 9292 -0.02 0.24 NO
136 RAC1 RAC1 RAC1 9293 -0.02 0.24 NO
137 APH1B APH1B APH1B 9400 -0.021 0.24 NO
138 CDKN1B CDKN1B CDKN1B 9585 -0.024 0.23 NO
139 FGD1 FGD1 FGD1 9611 -0.024 0.23 NO
140 SOS1 SOS1 SOS1 9742 -0.026 0.22 NO
141 TRAF6 TRAF6 TRAF6 9899 -0.028 0.22 NO
142 ADORA2A ADORA2A ADORA2A 10003 -0.029 0.21 NO
143 ITPR3 ITPR3 ITPR3 10014 -0.029 0.21 NO
144 ARHGEF18 ARHGEF18 ARHGEF18 10015 -0.029 0.21 NO
145 SQSTM1 SQSTM1 SQSTM1 10078 -0.03 0.21 NO
146 CREB1 CREB1 CREB1 10115 -0.03 0.21 NO
147 ARHGDIA ARHGDIA ARHGDIA 10480 -0.035 0.19 NO
148 RALGDS RALGDS RALGDS 10498 -0.035 0.19 NO
149 PLCG1 PLCG1 PLCG1 10501 -0.035 0.19 NO
150 SOS2 SOS2 SOS2 10527 -0.036 0.19 NO
151 ECT2 ECT2 ECT2 10919 -0.041 0.17 NO
152 PCSK5 PCSK5 PCSK5 10979 -0.042 0.17 NO
153 HDAC2 HDAC2 HDAC2 11043 -0.043 0.17 NO
154 SHC2 SHC2 SHC2 11190 -0.044 0.16 NO
155 BCL2L11 BCL2L11 BCL2L11 11427 -0.048 0.15 NO
156 AKT1 AKT1 AKT1 11486 -0.048 0.15 NO
157 RHOA RHOA RHOA 11509 -0.048 0.15 NO
158 RALA RALA RALA 11652 -0.05 0.14 NO
159 PPP2R1B PPP2R1B PPP2R1B 11821 -0.053 0.14 NO
160 HDAC3 HDAC3 HDAC3 11881 -0.054 0.13 NO
161 NCSTN NCSTN NCSTN 11892 -0.054 0.14 NO
162 CASP9 CASP9 CASP9 12163 -0.057 0.12 NO
163 RPS27A RPS27A RPS27A 12165 -0.057 0.12 NO
164 PSENEN PSENEN PSENEN 12177 -0.058 0.13 NO
165 UBA52 UBA52 UBA52 12197 -0.058 0.13 NO
166 NRAS NRAS NRAS 12363 -0.06 0.12 NO
167 RAF1 RAF1 RAF1 12443 -0.061 0.12 NO
168 ARHGEF16 ARHGEF16 ARHGEF16 12561 -0.063 0.12 NO
169 AKT1S1 AKT1S1 AKT1S1 12589 -0.063 0.12 NO
170 ADAM17 ADAM17 ADAM17 12741 -0.066 0.11 NO
171 ARHGEF6 ARHGEF6 ARHGEF6 12757 -0.066 0.11 NO
172 DNM2 DNM2 DNM2 12806 -0.067 0.11 NO
173 AKT2 AKT2 AKT2 12936 -0.069 0.11 NO
174 RAP1A RAP1A RAP1A 13023 -0.07 0.1 NO
175 AKAP13 AKAP13 AKAP13 13124 -0.072 0.1 NO
176 MDM2 MDM2 MDM2 13140 -0.072 0.1 NO
177 NFKBIA NFKBIA NFKBIA 13142 -0.072 0.11 NO
178 APH1A APH1A APH1A 13395 -0.076 0.095 NO
179 CASP3 CASP3 CASP3 13432 -0.076 0.096 NO
180 DUSP6 DUSP6 DUSP6 13450 -0.077 0.098 NO
181 IRAK1 IRAK1 IRAK1 13454 -0.077 0.1 NO
182 CDKN1A CDKN1A CDKN1A 13462 -0.077 0.1 NO
183 ADCY4 ADCY4 ADCY4 13542 -0.078 0.1 NO
184 STAT3 STAT3 STAT3 13708 -0.082 0.095 NO
185 RELA RELA RELA 14156 -0.09 0.074 NO
186 ATF1 ATF1 ATF1 14388 -0.094 0.065 NO
187 MAPKAPK3 MAPKAPK3 MAPKAPK3 14487 -0.097 0.063 NO
188 AATF AATF AATF 14563 -0.099 0.062 NO
189 ADCY7 ADCY7 ADCY7 14920 -0.11 0.047 NO
190 RPS6KB2 RPS6KB2 RPS6KB2 15049 -0.11 0.044 NO
191 MAPKAPK2 MAPKAPK2 MAPKAPK2 15092 -0.11 0.046 NO
192 SHC1 SHC1 SHC1 15124 -0.11 0.048 NO
193 IKBKB IKBKB IKBKB 15161 -0.12 0.05 NO
194 RIPK2 RIPK2 RIPK2 15305 -0.12 0.047 NO
195 RIT1 RIT1 RIT1 15467 -0.12 0.043 NO
196 MAPK7 MAPK7 MAPK7 15469 -0.12 0.047 NO
197 HDAC1 HDAC1 HDAC1 15505 -0.13 0.05 NO
198 TRIB3 TRIB3 TRIB3 15538 -0.13 0.053 NO
199 SMPD2 SMPD2 SMPD2 15650 -0.13 0.052 NO
200 CASP2 CASP2 CASP2 15762 -0.14 0.05 NO
201 ARHGEF1 ARHGEF1 ARHGEF1 16028 -0.14 0.041 NO
202 RPS6KA1 RPS6KA1 RPS6KA1 16145 -0.15 0.04 NO
203 ITGB3BP ITGB3BP ITGB3BP 16317 -0.16 0.037 NO
204 FGD3 FGD3 FGD3 16768 -0.18 0.019 NO
205 MYD88 MYD88 MYD88 16844 -0.19 0.022 NO
206 NGFR NGFR NGFR 17052 -0.21 0.018 NO
207 FGD2 FGD2 FGD2 17161 -0.22 0.02 NO
208 NTRK1 NTRK1 NTRK1 17201 -0.22 0.026 NO
209 ARHGAP4 ARHGAP4 ARHGAP4 17204 -0.22 0.034 NO
210 PLEKHG2 PLEKHG2 PLEKHG2 17207 -0.22 0.042 NO
211 VAV1 VAV1 VAV1 17470 -0.24 0.037 NO
212 CDK1 CDK1 CDK1 17661 -0.27 0.036 NO

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

Figure S74.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCEROLIPID 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 INOSITOL PHOSPHATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 115 1.1 0.12 YES
2 AKAP5 AKAP5 AKAP5 430 0.77 0.19 YES
3 CAMK4 CAMK4 CAMK4 610 0.66 0.25 YES
4 PRKCB PRKCB PRKCB 786 0.57 0.31 YES
5 RCAN2 RCAN2 RCAN2 893 0.52 0.36 YES
6 PRKCZ PRKCZ PRKCZ 1363 0.38 0.38 YES
7 PRKCE PRKCE PRKCE 1464 0.36 0.41 YES
8 YWHAH YWHAH YWHAH 1565 0.34 0.45 YES
9 PPP3R1 PPP3R1 PPP3R1 1989 0.26 0.45 YES
10 PPP3CB PPP3CB PPP3CB 2088 0.25 0.48 YES
11 YWHAG YWHAG YWHAG 2128 0.24 0.5 YES
12 PPP3CA PPP3CA PPP3CA 2190 0.24 0.53 YES
13 MAPK9 MAPK9 MAPK9 2440 0.21 0.54 YES
14 MEF2D MEF2D MEF2D 2715 0.18 0.54 YES
15 PRKCQ PRKCQ PRKCQ 2967 0.16 0.55 YES
16 PRKCD PRKCD PRKCD 3086 0.15 0.56 YES
17 MAPK8 MAPK8 MAPK8 3120 0.15 0.57 YES
18 YWHAB YWHAB YWHAB 3768 0.11 0.55 NO
19 YWHAZ YWHAZ YWHAZ 3939 0.1 0.55 NO
20 MAPK3 MAPK3 MAPK3 4102 0.096 0.55 NO
21 FKBP8 FKBP8 FKBP8 4772 0.07 0.52 NO
22 PRKACA PRKACA PRKACA 4908 0.066 0.52 NO
23 GSK3B GSK3B GSK3B 5224 0.055 0.51 NO
24 CHP CHP CHP 5315 0.052 0.52 NO
25 PRKCA PRKCA PRKCA 5907 0.037 0.49 NO
26 FKBP1A FKBP1A FKBP1A 6541 0.024 0.46 NO
27 NR4A1 NR4A1 NR4A1 6940 0.016 0.44 NO
28 YWHAQ YWHAQ YWHAQ 7151 0.012 0.42 NO
29 BCL2 BCL2 BCL2 7283 0.0099 0.42 NO
30 MAPK14 MAPK14 MAPK14 7588 0.005 0.4 NO
31 EP300 EP300 EP300 7971 -0.0017 0.38 NO
32 YWHAE YWHAE YWHAE 7975 -0.0017 0.38 NO
33 CSNK2A1 CSNK2A1 CSNK2A1 8146 -0.0042 0.37 NO
34 RAN RAN RAN 8506 -0.0095 0.35 NO
35 BCL2L1 BCL2L1 BCL2L1 8676 -0.012 0.35 NO
36 KPNA2 KPNA2 KPNA2 8757 -0.013 0.34 NO
37 BAD BAD BAD 9205 -0.019 0.32 NO
38 CREBBP CREBBP CREBBP 9341 -0.021 0.32 NO
39 CABIN1 CABIN1 CABIN1 9688 -0.025 0.3 NO
40 XPO1 XPO1 XPO1 10281 -0.033 0.27 NO
41 KPNB1 KPNB1 KPNB1 10394 -0.034 0.27 NO
42 CSNK1A1 CSNK1A1 CSNK1A1 10523 -0.036 0.27 NO
43 PRKCH PRKCH PRKCH 11406 -0.047 0.22 NO
44 NUP214 NUP214 NUP214 11564 -0.05 0.22 NO
45 RCAN1 RCAN1 RCAN1 12631 -0.064 0.17 NO
46 CASP3 CASP3 CASP3 13432 -0.076 0.13 NO
47 SFN SFN SFN 14546 -0.098 0.084 NO
48 NFATC3 NFATC3 NFATC3 15080 -0.11 0.068 NO
49 PIM1 PIM1 PIM1 15316 -0.12 0.068 NO
50 MAP3K1 MAP3K1 MAP3K1 15771 -0.14 0.059 NO
51 NFATC2 NFATC2 NFATC2 16289 -0.16 0.048 NO
52 BAX BAX BAX 16561 -0.17 0.053 NO
53 NFATC1 NFATC1 NFATC1 16815 -0.19 0.06 NO
54 MAP3K8 MAP3K8 MAP3K8 16871 -0.19 0.079 NO

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

Figure S76.  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 GLYCEROPHOSPHOLIPID METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 115 1.1 0.069 YES
2 PDE1A PDE1A PDE1A 609 0.66 0.087 YES
3 CAMK4 CAMK4 CAMK4 610 0.66 0.13 YES
4 PDE1B PDE1B PDE1B 611 0.66 0.18 YES
5 ADCY1 ADCY1 ADCY1 630 0.65 0.22 YES
6 FGF5 FGF5 FGF5 637 0.65 0.27 YES
7 FGF9 FGF9 FGF9 834 0.54 0.29 YES
8 KLB KLB KLB 895 0.52 0.32 YES
9 KL KL KL 1144 0.44 0.34 YES
10 FGF18 FGF18 FGF18 1175 0.43 0.37 YES
11 PRKAR1B PRKAR1B PRKAR1B 1177 0.43 0.4 YES
12 PRKCE PRKCE PRKCE 1464 0.36 0.41 YES
13 FGF22 FGF22 FGF22 1546 0.34 0.43 YES
14 PRKAR2B PRKAR2B PRKAR2B 1572 0.34 0.45 YES
15 FGFR3 FGFR3 FGFR3 2005 0.26 0.44 YES
16 FGF8 FGF8 FGF8 2011 0.26 0.46 YES
17 CALM3 CALM3 CALM3 2142 0.24 0.47 YES
18 ADCY5 ADCY5 ADCY5 2156 0.24 0.49 YES
19 FGF10 FGF10 FGF10 2291 0.22 0.49 YES
20 MAP2K1 MAP2K1 MAP2K1 2409 0.21 0.5 YES
21 CALM1 CALM1 CALM1 2691 0.18 0.5 YES
22 FGF7 FGF7 FGF7 2909 0.16 0.5 YES
23 PRKCD PRKCD PRKCD 3086 0.15 0.5 YES
24 FGFR2 FGFR2 FGFR2 3267 0.14 0.5 YES
25 PRKACB PRKACB PRKACB 3370 0.13 0.5 YES
26 BRAF BRAF BRAF 3403 0.13 0.51 YES
27 FRS3 FRS3 FRS3 3423 0.13 0.52 YES
28 AKT3 AKT3 AKT3 3437 0.13 0.53 YES
29 PDPK1 PDPK1 PDPK1 3647 0.12 0.52 YES
30 YWHAB YWHAB YWHAB 3768 0.11 0.52 YES
31 GSK3A GSK3A GSK3A 3781 0.11 0.53 YES
32 MAPK3 MAPK3 MAPK3 4102 0.096 0.52 YES
33 ADRBK1 ADRBK1 ADRBK1 4130 0.094 0.52 YES
34 ADCY2 ADCY2 ADCY2 4192 0.091 0.53 YES
35 MAPK1 MAPK1 MAPK1 4317 0.086 0.53 YES
36 CALM2 CALM2 CALM2 4343 0.085 0.53 YES
37 ADCY8 ADCY8 ADCY8 4423 0.082 0.53 YES
38 ADCY3 ADCY3 ADCY3 4452 0.081 0.54 YES
39 KRAS KRAS KRAS 4769 0.07 0.52 NO
40 ADCY9 ADCY9 ADCY9 4773 0.07 0.53 NO
41 FGF17 FGF17 FGF17 4818 0.068 0.53 NO
42 PRKACA PRKACA PRKACA 4908 0.066 0.53 NO
43 PRKAR1A PRKAR1A PRKAR1A 5169 0.057 0.52 NO
44 PTEN PTEN PTEN 5175 0.056 0.52 NO
45 FGF1 FGF1 FGF1 5251 0.054 0.52 NO
46 PPP2R1A PPP2R1A PPP2R1A 5287 0.053 0.52 NO
47 PPP2CA PPP2CA PPP2CA 5474 0.048 0.52 NO
48 HRAS HRAS HRAS 5522 0.047 0.52 NO
49 MTOR MTOR MTOR 5637 0.044 0.52 NO
50 PIK3R1 PIK3R1 PIK3R1 5842 0.039 0.51 NO
51 PRKCA PRKCA PRKCA 5907 0.037 0.5 NO
52 FOXO4 FOXO4 FOXO4 6004 0.035 0.5 NO
53 FOXO3 FOXO3 FOXO3 6297 0.029 0.49 NO
54 PRKAR2A PRKAR2A PRKAR2A 6303 0.029 0.49 NO
55 PRKACG PRKACG PRKACG 6609 0.023 0.48 NO
56 NR4A1 NR4A1 NR4A1 6940 0.016 0.46 NO
57 THEM4 THEM4 THEM4 7411 0.0077 0.43 NO
58 GRB2 GRB2 GRB2 7541 0.0056 0.43 NO
59 PPP2CB PPP2CB PPP2CB 7704 0.0031 0.42 NO
60 PHLPP1 PHLPP1 PHLPP1 7774 0.0018 0.41 NO
61 ITPR2 ITPR2 ITPR2 7791 0.0016 0.41 NO
62 SRC SRC SRC 7947 -0.0013 0.4 NO
63 SPRY2 SPRY2 SPRY2 8270 -0.0062 0.39 NO
64 MLST8 MLST8 MLST8 8383 -0.0078 0.38 NO
65 CHUK CHUK CHUK 8496 -0.0092 0.38 NO
66 MAP2K2 MAP2K2 MAP2K2 8542 -0.0099 0.37 NO
67 RICTOR RICTOR RICTOR 8575 -0.01 0.37 NO
68 FOXO1 FOXO1 FOXO1 8682 -0.012 0.37 NO
69 CBL CBL CBL 8787 -0.013 0.36 NO
70 MAPKAP1 MAPKAP1 MAPKAP1 8791 -0.013 0.36 NO
71 PIK3CA PIK3CA PIK3CA 8957 -0.015 0.36 NO
72 ADCY6 ADCY6 ADCY6 9112 -0.017 0.35 NO
73 TSC2 TSC2 TSC2 9165 -0.018 0.35 NO
74 BAD BAD BAD 9205 -0.019 0.35 NO
75 FGFR1 FGFR1 FGFR1 9245 -0.019 0.35 NO
76 FRS2 FRS2 FRS2 9292 -0.02 0.34 NO
77 FGF2 FGF2 FGF2 9489 -0.022 0.34 NO
78 CDKN1B CDKN1B CDKN1B 9585 -0.024 0.33 NO
79 SOS1 SOS1 SOS1 9742 -0.026 0.32 NO
80 ITPR3 ITPR3 ITPR3 10014 -0.029 0.31 NO
81 CREB1 CREB1 CREB1 10115 -0.03 0.31 NO
82 PLCG1 PLCG1 PLCG1 10501 -0.035 0.29 NO
83 AKT1 AKT1 AKT1 11486 -0.048 0.24 NO
84 CASP9 CASP9 CASP9 12163 -0.057 0.21 NO
85 RPS27A RPS27A RPS27A 12165 -0.057 0.21 NO
86 UBA52 UBA52 UBA52 12197 -0.058 0.21 NO
87 MKNK1 MKNK1 MKNK1 12319 -0.059 0.21 NO
88 NRAS NRAS NRAS 12363 -0.06 0.21 NO
89 RAF1 RAF1 RAF1 12443 -0.061 0.21 NO
90 AKT1S1 AKT1S1 AKT1S1 12589 -0.063 0.21 NO
91 AKT2 AKT2 AKT2 12936 -0.069 0.19 NO
92 MDM2 MDM2 MDM2 13140 -0.072 0.19 NO
93 IL17RD IL17RD IL17RD 13182 -0.072 0.19 NO
94 CDKN1A CDKN1A CDKN1A 13462 -0.077 0.18 NO
95 ADCY4 ADCY4 ADCY4 13542 -0.078 0.18 NO
96 GAB1 GAB1 GAB1 14235 -0.091 0.15 NO
97 ADCY7 ADCY7 ADCY7 14920 -0.11 0.12 NO
98 RPS6KB2 RPS6KB2 RPS6KB2 15049 -0.11 0.12 NO
99 SHC1 SHC1 SHC1 15124 -0.11 0.12 NO
100 TRIB3 TRIB3 TRIB3 15538 -0.13 0.11 NO
101 FGF20 FGF20 FGF20 16209 -0.15 0.083 NO
102 FGFR4 FGFR4 FGFR4 17054 -0.21 0.051 NO
103 CDK1 CDK1 CDK1 17661 -0.27 0.036 NO

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

Figure S78.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCEROPHOSPHOLIPID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PYRUVATE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CACNA1F CACNA1F CACNA1F 268 0.91 0.041 YES
2 GRIN2A GRIN2A GRIN2A 414 0.78 0.081 YES
3 GRIN1 GRIN1 GRIN1 437 0.76 0.13 YES
4 GRIN2B GRIN2B GRIN2B 516 0.72 0.17 YES
5 SNCA SNCA SNCA 566 0.68 0.2 YES
6 ITPR1 ITPR1 ITPR1 641 0.64 0.24 YES
7 CACNA1S CACNA1S CACNA1S 708 0.61 0.27 YES
8 COX7A1 COX7A1 COX7A1 726 0.6 0.31 YES
9 CALML3 CALML3 CALML3 1015 0.48 0.32 YES
10 NOS1 NOS1 NOS1 1123 0.45 0.34 YES
11 CHP2 CHP2 CHP2 1924 0.28 0.32 YES
12 PPP3R2 PPP3R2 PPP3R2 1968 0.27 0.33 YES
13 CDK5R1 CDK5R1 CDK5R1 1987 0.27 0.34 YES
14 PPP3R1 PPP3R1 PPP3R1 1989 0.26 0.36 YES
15 CACNA1C CACNA1C CACNA1C 2012 0.26 0.38 YES
16 GRIN2C GRIN2C GRIN2C 2053 0.26 0.39 YES
17 PPP3CB PPP3CB PPP3CB 2088 0.25 0.4 YES
18 CALM3 CALM3 CALM3 2142 0.24 0.42 YES
19 RYR3 RYR3 RYR3 2161 0.24 0.43 YES
20 PPP3CA PPP3CA PPP3CA 2190 0.24 0.44 YES
21 CACNA1D CACNA1D CACNA1D 2393 0.21 0.44 YES
22 PLCB4 PLCB4 PLCB4 2534 0.2 0.45 YES
23 PLCB1 PLCB1 PLCB1 2543 0.2 0.46 YES
24 MME MME MME 2617 0.19 0.47 YES
25 CALM1 CALM1 CALM1 2691 0.18 0.48 YES
26 CDK5 CDK5 CDK5 3033 0.16 0.46 NO
27 APBB1 APBB1 APBB1 3590 0.12 0.44 NO
28 NDUFB8 NDUFB8 NDUFB8 3652 0.12 0.45 NO
29 GRIN2D GRIN2D GRIN2D 4008 0.099 0.43 NO
30 MAPK3 MAPK3 MAPK3 4102 0.096 0.43 NO
31 GNAQ GNAQ GNAQ 4173 0.092 0.44 NO
32 NDUFA4 NDUFA4 NDUFA4 4235 0.089 0.44 NO
33 MAPK1 MAPK1 MAPK1 4317 0.086 0.44 NO
34 CALM2 CALM2 CALM2 4343 0.085 0.44 NO
35 MAPT MAPT MAPT 4412 0.083 0.44 NO
36 NDUFA5 NDUFA5 NDUFA5 4450 0.081 0.44 NO
37 ATP2A2 ATP2A2 ATP2A2 4490 0.08 0.45 NO
38 CYCS CYCS CYCS 4573 0.077 0.45 NO
39 NDUFS1 NDUFS1 NDUFS1 4754 0.071 0.44 NO
40 COX7A2L COX7A2L COX7A2L 4830 0.068 0.44 NO
41 ATP5G3 ATP5G3 ATP5G3 4928 0.065 0.44 NO
42 PSEN2 PSEN2 PSEN2 5027 0.061 0.44 NO
43 NDUFA8 NDUFA8 NDUFA8 5030 0.061 0.44 NO
44 GSK3B GSK3B GSK3B 5224 0.055 0.44 NO
45 UQCRFS1 UQCRFS1 UQCRFS1 5265 0.054 0.44 NO
46 CHP CHP CHP 5315 0.052 0.44 NO
47 COX5A COX5A COX5A 5516 0.047 0.43 NO
48 SDHA SDHA SDHA 5571 0.046 0.43 NO
49 COX6A1 COX6A1 COX6A1 5585 0.046 0.43 NO
50 UQCRC2 UQCRC2 UQCRC2 5604 0.045 0.43 NO
51 ATP5B ATP5B ATP5B 5618 0.044 0.44 NO
52 UQCRH UQCRH UQCRH 5685 0.043 0.43 NO
53 IL1B IL1B IL1B 5771 0.04 0.43 NO
54 ATP5A1 ATP5A1 ATP5A1 5843 0.039 0.43 NO
55 APP APP APP 5938 0.036 0.43 NO
56 NDUFB9 NDUFB9 NDUFB9 5985 0.035 0.43 NO
57 UQCRC1 UQCRC1 UQCRC1 6179 0.031 0.42 NO
58 COX4I1 COX4I1 COX4I1 6185 0.031 0.42 NO
59 NDUFS5 NDUFS5 NDUFS5 6344 0.028 0.41 NO
60 NDUFA10 NDUFA10 NDUFA10 6456 0.026 0.41 NO
61 ATP5G1 ATP5G1 ATP5G1 6542 0.024 0.4 NO
62 NDUFA3 NDUFA3 NDUFA3 6596 0.023 0.4 NO
63 UQCR10 UQCR10 UQCR10 6602 0.023 0.4 NO
64 NDUFS2 NDUFS2 NDUFS2 6629 0.022 0.4 NO
65 NDUFAB1 NDUFAB1 NDUFAB1 6636 0.022 0.41 NO
66 SDHB SDHB SDHB 6749 0.02 0.4 NO
67 ATP5H ATP5H ATP5H 6757 0.02 0.4 NO
68 ATP2A3 ATP2A3 ATP2A3 6795 0.019 0.4 NO
69 ATP5C1 ATP5C1 ATP5C1 6803 0.019 0.4 NO
70 COX7A2 COX7A2 COX7A2 6847 0.018 0.4 NO
71 BACE1 BACE1 BACE1 6879 0.018 0.4 NO
72 NDUFV1 NDUFV1 NDUFV1 6914 0.017 0.4 NO
73 ATP5O ATP5O ATP5O 6917 0.017 0.4 NO
74 COX7C COX7C COX7C 6990 0.015 0.4 NO
75 COX6C COX6C COX6C 7027 0.014 0.4 NO
76 NDUFS3 NDUFS3 NDUFS3 7053 0.014 0.4 NO
77 UQCRHL UQCRHL UQCRHL 7080 0.013 0.4 NO
78 COX6B1 COX6B1 COX6B1 7091 0.013 0.4 NO
79 NDUFA1 NDUFA1 NDUFA1 7115 0.013 0.39 NO
80 APAF1 APAF1 APAF1 7123 0.013 0.4 NO
81 NDUFB1 NDUFB1 NDUFB1 7161 0.012 0.39 NO
82 UQCRB UQCRB UQCRB 7217 0.011 0.39 NO
83 COX6A2 COX6A2 COX6A2 7242 0.011 0.39 NO
84 COX7B COX7B COX7B 7271 0.01 0.39 NO
85 NDUFV2 NDUFV2 NDUFV2 7311 0.0094 0.39 NO
86 NDUFC2 NDUFC2 NDUFC2 7335 0.0091 0.39 NO
87 ATP5J ATP5J ATP5J 7337 0.009 0.39 NO
88 COX5B COX5B COX5B 7341 0.009 0.39 NO
89 NDUFB6 NDUFB6 NDUFB6 7344 0.009 0.39 NO
90 NDUFB5 NDUFB5 NDUFB5 7607 0.0046 0.37 NO
91 NDUFA6 NDUFA6 NDUFA6 7686 0.0034 0.37 NO
92 ATP5F1 ATP5F1 ATP5F1 7737 0.0025 0.37 NO
93 CYC1 CYC1 CYC1 7764 0.002 0.37 NO
94 ITPR2 ITPR2 ITPR2 7791 0.0016 0.36 NO
95 ADAM10 ADAM10 ADAM10 7824 0.00084 0.36 NO
96 NDUFB3 NDUFB3 NDUFB3 7848 0.00036 0.36 NO
97 CAPN1 CAPN1 CAPN1 7981 -0.0018 0.36 NO
98 NDUFB4 NDUFB4 NDUFB4 7982 -0.0018 0.36 NO
99 IDE IDE IDE 8067 -0.003 0.35 NO
100 GAPDH GAPDH GAPDH 8096 -0.0034 0.35 NO
101 ATF6 ATF6 ATF6 8149 -0.0042 0.35 NO
102 BID BID BID 8471 -0.0088 0.33 NO
103 SDHC SDHC SDHC 8620 -0.011 0.32 NO
104 PPP3CC PPP3CC PPP3CC 8674 -0.012 0.32 NO
105 ERN1 ERN1 ERN1 8700 -0.012 0.32 NO
106 NDUFS4 NDUFS4 NDUFS4 8776 -0.013 0.32 NO
107 NDUFV3 NDUFV3 NDUFV3 8958 -0.015 0.31 NO
108 UQCR11 UQCR11 UQCR11 8960 -0.015 0.31 NO
109 PSEN1 PSEN1 PSEN1 9095 -0.017 0.3 NO
110 BAD BAD BAD 9205 -0.019 0.3 NO
111 NDUFB2 NDUFB2 NDUFB2 9223 -0.019 0.3 NO
112 NDUFS8 NDUFS8 NDUFS8 9331 -0.02 0.29 NO
113 NDUFS7 NDUFS7 NDUFS7 9358 -0.021 0.29 NO
114 NDUFC1 NDUFC1 NDUFC1 9382 -0.021 0.29 NO
115 NDUFB10 NDUFB10 NDUFB10 9414 -0.022 0.29 NO
116 NDUFA2 NDUFA2 NDUFA2 9442 -0.022 0.29 NO
117 COX8A COX8A COX8A 9510 -0.023 0.29 NO
118 NDUFA9 NDUFA9 NDUFA9 9530 -0.023 0.29 NO
119 SDHD SDHD SDHD 9555 -0.023 0.29 NO
120 UQCRQ UQCRQ UQCRQ 9565 -0.024 0.29 NO
121 ATP5D ATP5D ATP5D 9604 -0.024 0.29 NO
122 ITPR3 ITPR3 ITPR3 10014 -0.029 0.27 NO
123 FAS FAS FAS 10080 -0.03 0.27 NO
124 NDUFB7 NDUFB7 NDUFB7 10223 -0.032 0.26 NO
125 LRP1 LRP1 LRP1 10258 -0.032 0.26 NO
126 LPL LPL LPL 10388 -0.034 0.26 NO
127 NAE1 NAE1 NAE1 10410 -0.034 0.26 NO
128 NDUFA7 NDUFA7 NDUFA7 10965 -0.041 0.23 NO
129 ATP5G2 ATP5G2 ATP5G2 11264 -0.045 0.22 NO
130 ATP5E ATP5E ATP5E 11637 -0.05 0.2 NO
131 APOE APOE APOE 11820 -0.053 0.19 NO
132 CALML6 CALML6 CALML6 11823 -0.053 0.2 NO
133 NCSTN NCSTN NCSTN 11892 -0.054 0.19 NO
134 NDUFS6 NDUFS6 NDUFS6 12142 -0.057 0.18 NO
135 CASP9 CASP9 CASP9 12163 -0.057 0.19 NO
136 PSENEN PSENEN PSENEN 12177 -0.058 0.19 NO
137 EIF2AK3 EIF2AK3 EIF2AK3 12182 -0.058 0.19 NO
138 CAPN2 CAPN2 CAPN2 12255 -0.059 0.19 NO
139 ADAM17 ADAM17 ADAM17 12741 -0.066 0.17 NO
140 NDUFA4L2 NDUFA4L2 NDUFA4L2 13014 -0.07 0.16 NO
141 COX4I2 COX4I2 COX4I2 13260 -0.074 0.15 NO
142 APH1A APH1A APH1A 13395 -0.076 0.15 NO
143 CASP3 CASP3 CASP3 13432 -0.076 0.15 NO
144 CASP7 CASP7 CASP7 14071 -0.088 0.12 NO
145 HSD17B10 HSD17B10 HSD17B10 14756 -0.1 0.088 NO
146 COX8C COX8C COX8C 15334 -0.12 0.064 NO
147 PLCB3 PLCB3 PLCB3 15542 -0.13 0.06 NO
148 TNF TNF TNF 15662 -0.13 0.062 NO
149 FADD FADD FADD 15735 -0.13 0.066 NO
150 TNFRSF1A TNFRSF1A TNFRSF1A 16005 -0.14 0.06 NO
151 PLCB2 PLCB2 PLCB2 16233 -0.16 0.057 NO
152 BACE2 BACE2 BACE2 16629 -0.18 0.046 NO
153 COX6B2 COX6B2 COX6B2 16663 -0.18 0.055 NO
154 ATP2A1 ATP2A1 ATP2A1 17844 -0.29 0.0077 NO
155 CASP8 CASP8 CASP8 17900 -0.3 0.023 NO

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

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

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 clus5 enriched pathways

Table 7.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. 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 FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.45 1.5 0.032 1 0.95 0.36 0.25 0.27 0.72 0.39
KEGG FATTY ACID METABOLISM 38 genes.ES.table 0.47 1.5 0.046 1 0.98 0.47 0.27 0.35 0.67 0.34
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 44 genes.ES.table 0.45 1.7 0.029 1 0.81 0.61 0.38 0.38 1 0.64
KEGG HISTIDINE METABOLISM 29 genes.ES.table 0.61 1.6 0.025 1 0.93 0.62 0.29 0.44 0.94 0.48
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 44 genes.ES.table 0.57 1.5 0.018 0.9 0.98 0.68 0.25 0.52 0.6 0.31
KEGG PPAR SIGNALING PATHWAY 64 genes.ES.table 0.54 1.6 0.011 1 0.94 0.34 0.15 0.29 0.75 0.41
KEGG PEROXISOME 76 genes.ES.table 0.41 1.5 0.072 1 0.97 0.28 0.18 0.23 0.71 0.37
KEGG TIGHT JUNCTION 124 genes.ES.table 0.4 1.5 0.031 0.78 0.99 0.35 0.24 0.27 0.55 0.26
KEGG PARKINSONS DISEASE 112 genes.ES.table 0.41 1.5 0.12 0.93 0.98 0.62 0.39 0.38 0.62 0.31
BIOCARTA MYOSIN PATHWAY 29 genes.ES.table 0.47 1.5 0.049 1 0.96 0.1 0.04 0.099 0.69 0.37
genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

Table S41.  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 ACADS ACADS ACADS 633 0.32 0.079 YES
2 ACAA2 ACAA2 ACAA2 1805 0.17 0.077 YES
3 ALDH7A1 ALDH7A1 ALDH7A1 2191 0.15 0.11 YES
4 IL4I1 IL4I1 IL4I1 2522 0.13 0.14 YES
5 ALDH2 ALDH2 ALDH2 2651 0.12 0.18 YES
6 ACAA1 ACAA1 ACAA1 2670 0.12 0.22 YES
7 MCEE MCEE MCEE 2857 0.12 0.25 YES
8 HMGCL HMGCL HMGCL 3069 0.11 0.28 YES
9 BCAT2 BCAT2 BCAT2 3080 0.11 0.31 YES
10 AUH AUH AUH 3567 0.09 0.32 YES
11 HADHB HADHB HADHB 3814 0.083 0.34 YES
12 BCKDHB BCKDHB BCKDHB 3858 0.082 0.36 YES
13 HIBCH HIBCH HIBCH 3865 0.082 0.39 YES
14 ECHS1 ECHS1 ECHS1 3957 0.079 0.41 YES
15 ALDH9A1 ALDH9A1 ALDH9A1 4697 0.062 0.4 YES
16 AOX1 AOX1 AOX1 4728 0.062 0.42 YES
17 HSD17B10 HSD17B10 HSD17B10 4732 0.062 0.44 YES
18 BCKDHA BCKDHA BCKDHA 4873 0.059 0.45 YES
19 ALDH6A1 ALDH6A1 ALDH6A1 5487 0.047 0.44 YES
20 ACAT1 ACAT1 ACAT1 6078 0.039 0.42 YES
21 ACADSB ACADSB ACADSB 6204 0.037 0.42 YES
22 ACADM ACADM ACADM 6259 0.036 0.43 YES
23 EHHADH EHHADH EHHADH 6355 0.034 0.44 YES
24 OXCT2 OXCT2 OXCT2 6570 0.032 0.44 YES
25 HADHA HADHA HADHA 6605 0.031 0.45 YES
26 PCCA PCCA PCCA 6793 0.028 0.45 YES
27 HIBADH HIBADH HIBADH 6898 0.027 0.45 YES
28 IVD IVD IVD 7228 0.022 0.44 NO
29 HMGCS2 HMGCS2 HMGCS2 8025 0.012 0.4 NO
30 MCCC1 MCCC1 MCCC1 8145 0.011 0.4 NO
31 ALDH3A2 ALDH3A2 ALDH3A2 8257 0.0092 0.4 NO
32 ACAT2 ACAT2 ACAT2 8477 0.0066 0.39 NO
33 HADH HADH HADH 8571 0.0053 0.38 NO
34 PCCB PCCB PCCB 9029 -0.00056 0.36 NO
35 ACAD8 ACAD8 ACAD8 9557 -0.0068 0.33 NO
36 OXCT1 OXCT1 OXCT1 10239 -0.015 0.3 NO
37 MCCC2 MCCC2 MCCC2 10288 -0.016 0.3 NO
38 DBT DBT DBT 10533 -0.019 0.3 NO
39 MUT MUT MUT 10686 -0.021 0.3 NO
40 ABAT ABAT ABAT 11140 -0.026 0.28 NO
41 DLD DLD DLD 12044 -0.039 0.24 NO
42 HMGCS1 HMGCS1 HMGCS1 12651 -0.048 0.23 NO
43 ALDH1B1 ALDH1B1 ALDH1B1 14288 -0.081 0.17 NO
44 BCAT1 BCAT1 BCAT1 16177 -0.15 0.12 NO

Figure S81.  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 FRUCTOSE AND MANNOSE METABOLISM.

Figure S82.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FRUCTOSE AND MANNOSE 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 FATTY ACID METABOLISM

Table S42.  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 ALDOB ALDOB ALDOB 156 0.58 0.21 YES
2 PGAM2 PGAM2 PGAM2 973 0.26 0.27 YES
3 PFKFB1 PFKFB1 PFKFB1 1088 0.24 0.36 YES
4 SLC25A10 SLC25A10 SLC25A10 1205 0.23 0.44 YES
5 SLC25A13 SLC25A13 SLC25A13 2240 0.15 0.43 YES
6 FBP1 FBP1 FBP1 2253 0.14 0.49 YES
7 ALDOC ALDOC ALDOC 2958 0.11 0.49 YES
8 ENO3 ENO3 ENO3 3216 0.1 0.52 YES
9 PRKACG PRKACG PRKACG 3548 0.091 0.54 YES
10 PC PC PC 4198 0.074 0.53 YES
11 SLC25A1 SLC25A1 SLC25A1 4585 0.065 0.53 YES
12 PCK2 PCK2 PCK2 4710 0.062 0.55 YES
13 PRKACB PRKACB PRKACB 7132 0.024 0.42 NO
14 ENO1 ENO1 ENO1 7196 0.023 0.43 NO
15 ALDOA ALDOA ALDOA 7451 0.019 0.42 NO
16 PCK1 PCK1 PCK1 7602 0.017 0.42 NO
17 GAPDH GAPDH GAPDH 8347 0.0083 0.38 NO
18 SLC25A11 SLC25A11 SLC25A11 8654 0.0044 0.37 NO
19 PGAM1 PGAM1 PGAM1 9167 -0.002 0.34 NO
20 GOT2 GOT2 GOT2 9971 -0.012 0.3 NO
21 GAPDHS GAPDHS GAPDHS 10151 -0.014 0.3 NO
22 MDH1 MDH1 MDH1 10189 -0.014 0.3 NO
23 GOT1 GOT1 GOT1 10289 -0.016 0.3 NO
24 TPI1 TPI1 TPI1 10509 -0.018 0.3 NO
25 PRKACA PRKACA PRKACA 10772 -0.022 0.29 NO
26 MDH2 MDH2 MDH2 12451 -0.045 0.22 NO
27 GPI GPI GPI 12603 -0.048 0.23 NO
28 PGK1 PGK1 PGK1 13050 -0.055 0.22 NO
29 ENO2 ENO2 ENO2 13740 -0.068 0.21 NO
30 SLC25A12 SLC25A12 SLC25A12 14943 -0.1 0.18 NO

Figure S83.  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 FATTY ACID METABOLISM.

Figure S84.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FATTY ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION

Table S43.  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 ALDOB ALDOB ALDOB 156 0.58 0.11 YES
2 PYGM PYGM PYGM 492 0.36 0.16 YES
3 PGAM2 PGAM2 PGAM2 973 0.26 0.19 YES
4 GYG2 GYG2 GYG2 1051 0.25 0.23 YES
5 PFKFB1 PFKFB1 PFKFB1 1088 0.24 0.28 YES
6 SLC25A10 SLC25A10 SLC25A10 1205 0.23 0.32 YES
7 GYS2 GYS2 GYS2 1841 0.17 0.32 YES
8 SLC25A13 SLC25A13 SLC25A13 2240 0.15 0.33 YES
9 FBP1 FBP1 FBP1 2253 0.14 0.36 YES
10 PFKFB2 PFKFB2 PFKFB2 2826 0.12 0.35 YES
11 PPP2R1B PPP2R1B PPP2R1B 2832 0.12 0.37 YES
12 PHKA2 PHKA2 PHKA2 2932 0.11 0.39 YES
13 ALDOC ALDOC ALDOC 2958 0.11 0.41 YES
14 ENO3 ENO3 ENO3 3216 0.1 0.42 YES
15 PRKACG PRKACG PRKACG 3548 0.091 0.42 YES
16 GYG1 GYG1 GYG1 3867 0.082 0.42 YES
17 PHKG1 PHKG1 PHKG1 3892 0.081 0.43 YES
18 PPP2CB PPP2CB PPP2CB 4086 0.076 0.44 YES
19 PC PC PC 4198 0.074 0.45 YES
20 CALM2 CALM2 CALM2 4345 0.07 0.45 YES
21 SLC25A1 SLC25A1 SLC25A1 4585 0.065 0.45 YES
22 PCK2 PCK2 PCK2 4710 0.062 0.46 YES
23 PFKL PFKL PFKL 5775 0.043 0.41 NO
24 PHKG2 PHKG2 PHKG2 5905 0.041 0.41 NO
25 PYGB PYGB PYGB 6718 0.03 0.37 NO
26 PRKACB PRKACB PRKACB 7132 0.024 0.35 NO
27 ENO1 ENO1 ENO1 7196 0.023 0.35 NO
28 PYGL PYGL PYGL 7375 0.02 0.35 NO
29 ALDOA ALDOA ALDOA 7451 0.019 0.35 NO
30 PCK1 PCK1 PCK1 7602 0.017 0.34 NO
31 GYS1 GYS1 GYS1 7876 0.014 0.33 NO
32 PFKP PFKP PFKP 7893 0.014 0.33 NO
33 CALM1 CALM1 CALM1 7984 0.012 0.33 NO
34 GAPDH GAPDH GAPDH 8347 0.0083 0.31 NO
35 SLC25A11 SLC25A11 SLC25A11 8654 0.0044 0.3 NO
36 PFKFB4 PFKFB4 PFKFB4 8881 0.0014 0.28 NO
37 AGL AGL AGL 8966 0.00026 0.28 NO
38 PFKFB3 PFKFB3 PFKFB3 8994 -7e-05 0.28 NO
39 PGAM1 PGAM1 PGAM1 9167 -0.002 0.27 NO
40 PHKB PHKB PHKB 9682 -0.0085 0.24 NO
41 PHKA1 PHKA1 PHKA1 9961 -0.012 0.23 NO
42 GOT2 GOT2 GOT2 9971 -0.012 0.23 NO
43 GAPDHS GAPDHS GAPDHS 10151 -0.014 0.22 NO
44 MDH1 MDH1 MDH1 10189 -0.014 0.23 NO
45 GOT1 GOT1 GOT1 10289 -0.016 0.22 NO
46 PPP2R1A PPP2R1A PPP2R1A 10479 -0.018 0.22 NO
47 TPI1 TPI1 TPI1 10509 -0.018 0.22 NO
48 UGP2 UGP2 UGP2 10557 -0.019 0.22 NO
49 PPP2CA PPP2CA PPP2CA 10649 -0.02 0.22 NO
50 PRKACA PRKACA PRKACA 10772 -0.022 0.22 NO
51 PGM1 PGM1 PGM1 11134 -0.026 0.2 NO
52 PKM2 PKM2 PKM2 12241 -0.042 0.15 NO
53 MDH2 MDH2 MDH2 12451 -0.045 0.15 NO
54 GPI GPI GPI 12603 -0.048 0.15 NO
55 PGK1 PGK1 PGK1 13050 -0.055 0.14 NO
56 PFKM PFKM PFKM 13434 -0.062 0.13 NO
57 ENO2 ENO2 ENO2 13740 -0.068 0.12 NO
58 CALM3 CALM3 CALM3 14045 -0.075 0.12 NO
59 PPP2R5D PPP2R5D PPP2R5D 14119 -0.076 0.14 NO
60 GBE1 GBE1 GBE1 14763 -0.094 0.12 NO
61 SLC25A12 SLC25A12 SLC25A12 14943 -0.1 0.13 NO
62 PGM2 PGM2 PGM2 15247 -0.11 0.14 NO
63 PKLR PKLR PKLR 16513 -0.17 0.099 NO

Figure S85.  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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S86.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE 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 HISTIDINE METABOLISM

Table S44.  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 CNDP1 CNDP1 CNDP1 112 0.64 0.16 YES
2 ASPA ASPA ASPA 121 0.62 0.32 YES
3 ACY3 ACY3 ACY3 265 0.46 0.43 YES
4 MAOB MAOB MAOB 896 0.27 0.47 YES
5 ALDH3A1 ALDH3A1 ALDH3A1 1030 0.25 0.52 YES
6 AMDHD1 AMDHD1 AMDHD1 1700 0.18 0.54 YES
7 ALDH3B1 ALDH3B1 ALDH3B1 1911 0.17 0.57 YES
8 ALDH7A1 ALDH7A1 ALDH7A1 2191 0.15 0.59 YES
9 ALDH2 ALDH2 ALDH2 2651 0.12 0.6 YES
10 ALDH3B2 ALDH3B2 ALDH3B2 3520 0.092 0.57 YES
11 UROC1 UROC1 UROC1 4029 0.078 0.57 YES
12 HEMK1 HEMK1 HEMK1 4343 0.07 0.57 YES
13 HAL HAL HAL 4409 0.069 0.58 YES
14 MAOA MAOA MAOA 4577 0.065 0.59 YES
15 ALDH9A1 ALDH9A1 ALDH9A1 4697 0.062 0.6 YES
16 HNMT HNMT HNMT 4863 0.059 0.6 YES
17 FTCD FTCD FTCD 5021 0.056 0.61 YES
18 TRMT11 TRMT11 TRMT11 5257 0.051 0.61 YES
19 ALDH1A3 ALDH1A3 ALDH1A3 6514 0.032 0.55 NO
20 WBSCR22 WBSCR22 WBSCR22 6710 0.03 0.55 NO
21 ALDH3A2 ALDH3A2 ALDH3A2 8257 0.0092 0.47 NO
22 LCMT1 LCMT1 LCMT1 9090 -0.0012 0.42 NO
23 METTL6 METTL6 METTL6 10051 -0.013 0.37 NO
24 ABP1 ABP1 ABP1 10399 -0.017 0.36 NO
25 LCMT2 LCMT2 LCMT2 10435 -0.018 0.36 NO
26 DDC DDC DDC 11806 -0.036 0.29 NO
27 HDC HDC HDC 13379 -0.061 0.22 NO
28 ALDH1B1 ALDH1B1 ALDH1B1 14288 -0.081 0.2 NO
29 METTL2B METTL2B METTL2B 14900 -0.098 0.19 NO

Figure S87.  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 HISTIDINE METABOLISM.

Figure S88.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HISTIDINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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

Table S45.  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 SLC27A6 SLC27A6 SLC27A6 78 0.71 0.17 YES
2 SLCO1A2 SLCO1A2 SLCO1A2 336 0.41 0.26 YES
3 SLCO3A1 SLCO3A1 SLCO3A1 624 0.32 0.33 YES
4 ALB ALB ALB 672 0.31 0.4 YES
5 SLC28A1 SLC28A1 SLC28A1 1003 0.25 0.45 YES
6 SLC29A2 SLC29A2 SLC29A2 1628 0.19 0.46 YES
7 SLC27A1 SLC27A1 SLC27A1 1999 0.16 0.48 YES
8 SLC35D2 SLC35D2 SLC35D2 2085 0.16 0.52 YES
9 SLCO1C1 SLCO1C1 SLCO1C1 2365 0.14 0.54 YES
10 SLC29A3 SLC29A3 SLC29A3 4032 0.078 0.46 NO
11 SLC28A2 SLC28A2 SLC28A2 4230 0.073 0.47 NO
12 SLC27A4 SLC27A4 SLC27A4 4800 0.06 0.46 NO
13 SLC35B2 SLC35B2 SLC35B2 6179 0.037 0.39 NO
14 SLC35A2 SLC35A2 SLC35A2 6544 0.032 0.38 NO
15 SLCO4C1 SLCO4C1 SLCO4C1 7804 0.015 0.31 NO
16 SLCO2B1 SLCO2B1 SLCO2B1 8495 0.0064 0.28 NO
17 SLC35A1 SLC35A1 SLC35A1 11372 -0.03 0.13 NO
18 SLCO4A1 SLCO4A1 SLCO4A1 11478 -0.031 0.13 NO
19 SLC33A1 SLC33A1 SLC33A1 11650 -0.033 0.13 NO
20 SLC35C1 SLC35C1 SLC35C1 12185 -0.041 0.11 NO
21 SLC35D1 SLC35D1 SLC35D1 13060 -0.055 0.074 NO
22 SLC35B4 SLC35B4 SLC35B4 13550 -0.064 0.063 NO
23 SLC5A6 SLC5A6 SLC5A6 14294 -0.081 0.042 NO
24 SLC28A3 SLC28A3 SLC28A3 14351 -0.082 0.06 NO
25 SLC35A3 SLC35A3 SLC35A3 14506 -0.087 0.073 NO
26 SLC29A1 SLC29A1 SLC29A1 15622 -0.12 0.043 NO
27 SLC29A4 SLC29A4 SLC29A4 16801 -0.19 0.025 NO
28 SLCO2A1 SLCO2A1 SLCO2A1 17324 -0.23 0.054 NO

Figure S89.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S90.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PPAR SIGNALING PATHWAY

Table S46.  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 SLC27A6 SLC27A6 SLC27A6 78 0.71 0.09 YES
2 PLIN1 PLIN1 PLIN1 313 0.43 0.13 YES
3 RXRG RXRG RXRG 366 0.4 0.18 YES
4 CYP27A1 CYP27A1 CYP27A1 379 0.4 0.24 YES
5 CYP8B1 CYP8B1 CYP8B1 627 0.32 0.26 YES
6 ACSL1 ACSL1 ACSL1 959 0.26 0.28 YES
7 ANGPTL4 ANGPTL4 ANGPTL4 1213 0.22 0.3 YES
8 OLR1 OLR1 OLR1 1255 0.22 0.32 YES
9 FABP5 FABP5 FABP5 1317 0.22 0.35 YES
10 APOA1 APOA1 APOA1 1346 0.21 0.38 YES
11 ME1 ME1 ME1 1618 0.19 0.39 YES
12 FABP6 FABP6 FABP6 1748 0.18 0.4 YES
13 SCD SCD SCD 1790 0.18 0.42 YES
14 ACOX2 ACOX2 ACOX2 1947 0.16 0.44 YES
15 SLC27A1 SLC27A1 SLC27A1 1999 0.16 0.46 YES
16 CPT1B CPT1B CPT1B 2012 0.16 0.48 YES
17 SLC27A5 SLC27A5 SLC27A5 2024 0.16 0.5 YES
18 PPARG PPARG PPARG 2090 0.16 0.51 YES
19 FABP1 FABP1 FABP1 2220 0.15 0.52 YES
20 ACAA1 ACAA1 ACAA1 2670 0.12 0.52 YES
21 AQP7 AQP7 AQP7 2730 0.12 0.53 YES
22 ACADL ACADL ACADL 2790 0.12 0.54 YES
23 FABP4 FABP4 FABP4 3375 0.097 0.52 NO
24 DBI DBI DBI 3446 0.094 0.53 NO
25 FADS2 FADS2 FADS2 3890 0.081 0.52 NO
26 PCK2 PCK2 PCK2 4710 0.062 0.48 NO
27 SLC27A4 SLC27A4 SLC27A4 4800 0.06 0.48 NO
28 NR1H3 NR1H3 NR1H3 4908 0.058 0.49 NO
29 CPT2 CPT2 CPT2 4937 0.058 0.49 NO
30 PLTP PLTP PLTP 4973 0.057 0.5 NO
31 GK2 GK2 GK2 5076 0.055 0.5 NO
32 FABP7 FABP7 FABP7 5612 0.045 0.48 NO
33 SORBS1 SORBS1 SORBS1 5698 0.044 0.48 NO
34 ADIPOQ ADIPOQ ADIPOQ 5839 0.042 0.48 NO
35 ACADM ACADM ACADM 6259 0.036 0.46 NO
36 PPARA PPARA PPARA 6331 0.035 0.46 NO
37 EHHADH EHHADH EHHADH 6355 0.034 0.46 NO
38 SCD5 SCD5 SCD5 6700 0.03 0.45 NO
39 UBC UBC UBC 6705 0.03 0.45 NO
40 SCP2 SCP2 SCP2 7289 0.021 0.42 NO
41 ILK ILK ILK 7595 0.017 0.41 NO
42 PCK1 PCK1 PCK1 7602 0.017 0.41 NO
43 RXRA RXRA RXRA 7911 0.013 0.39 NO
44 HMGCS2 HMGCS2 HMGCS2 8025 0.012 0.39 NO
45 ACSL3 ACSL3 ACSL3 8102 0.011 0.39 NO
46 CYP7A1 CYP7A1 CYP7A1 8450 0.007 0.37 NO
47 APOA5 APOA5 APOA5 8715 0.0036 0.36 NO
48 LPL LPL LPL 8854 0.0018 0.35 NO
49 ACOX3 ACOX3 ACOX3 9018 -0.00037 0.34 NO
50 RXRB RXRB RXRB 9625 -0.0076 0.31 NO
51 ACSL5 ACSL5 ACSL5 9899 -0.011 0.29 NO
52 PPARD PPARD PPARD 10083 -0.013 0.28 NO
53 ACOX1 ACOX1 ACOX1 10682 -0.021 0.25 NO
54 ACSL6 ACSL6 ACSL6 11317 -0.029 0.22 NO
55 FABP3 FABP3 FABP3 11991 -0.038 0.19 NO
56 CYP4A11 CYP4A11 CYP4A11 12180 -0.041 0.19 NO
57 CPT1C CPT1C CPT1C 13222 -0.058 0.14 NO
58 MMP1 MMP1 MMP1 13984 -0.074 0.1 NO
59 GK GK GK 14168 -0.078 0.11 NO
60 PDPK1 PDPK1 PDPK1 14349 -0.082 0.11 NO
61 ACSL4 ACSL4 ACSL4 15136 -0.11 0.078 NO
62 CPT1A CPT1A CPT1A 15363 -0.11 0.08 NO
63 SLC27A2 SLC27A2 SLC27A2 17791 -0.3 -0.013 NO
64 CD36 CD36 CD36 17886 -0.32 0.024 NO

Figure S91.  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 PPAR SIGNALING PATHWAY.

Figure S92.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PPAR 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 PEROXISOME

Table S47.  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 ALDOB ALDOB ALDOB 156 0.58 0.21 YES
2 PFKFB1 PFKFB1 PFKFB1 1088 0.24 0.25 YES
3 MTMR7 MTMR7 MTMR7 2237 0.15 0.24 YES
4 FBP1 FBP1 FBP1 2253 0.14 0.3 YES
5 HK2 HK2 HK2 2384 0.14 0.34 YES
6 PFKFB2 PFKFB2 PFKFB2 2826 0.12 0.36 YES
7 ALDOC ALDOC ALDOC 2958 0.11 0.4 YES
8 FUK FUK FUK 3234 0.1 0.42 YES
9 PHPT1 PHPT1 PHPT1 3715 0.086 0.43 YES
10 KHK KHK KHK 4434 0.068 0.41 YES
11 GMPPA GMPPA GMPPA 4465 0.068 0.44 YES
12 MPI MPI MPI 4641 0.064 0.45 YES
13 FPGT FPGT FPGT 5034 0.056 0.45 NO
14 PFKL PFKL PFKL 5775 0.043 0.43 NO
15 PMM1 PMM1 PMM1 6018 0.039 0.43 NO
16 MTMR2 MTMR2 MTMR2 6519 0.032 0.41 NO
17 ALDOA ALDOA ALDOA 7451 0.019 0.37 NO
18 AKR1B10 AKR1B10 AKR1B10 7722 0.016 0.36 NO
19 PFKP PFKP PFKP 7893 0.014 0.36 NO
20 SORD SORD SORD 8005 0.012 0.35 NO
21 AKR1B1 AKR1B1 AKR1B1 8567 0.0053 0.32 NO
22 PFKFB4 PFKFB4 PFKFB4 8881 0.0014 0.31 NO
23 PFKFB3 PFKFB3 PFKFB3 8994 -7e-05 0.3 NO
24 TSTA3 TSTA3 TSTA3 10191 -0.014 0.24 NO
25 TPI1 TPI1 TPI1 10509 -0.018 0.23 NO
26 MTMR6 MTMR6 MTMR6 11014 -0.025 0.21 NO
27 GMPPB GMPPB GMPPB 11407 -0.03 0.2 NO
28 PMM2 PMM2 PMM2 11508 -0.032 0.21 NO
29 PFKM PFKM PFKM 13434 -0.062 0.13 NO
30 MTMR1 MTMR1 MTMR1 13998 -0.074 0.12 NO
31 GMDS GMDS GMDS 14361 -0.083 0.14 NO
32 HK1 HK1 HK1 14851 -0.097 0.15 NO
33 HK3 HK3 HK3 15410 -0.12 0.16 NO

Figure S93.  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 PEROXISOME.

Figure S94.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PEROXISOME, 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 TIGHT JUNCTION

Table S48.  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 ARHGEF16 ARHGEF16 ARHGEF16 58 0.74 0.24 YES
2 ARHGEF5 ARHGEF5 ARHGEF5 207 0.51 0.4 YES
3 MYLK MYLK MYLK 739 0.3 0.48 YES
4 ARHGEF10 ARHGEF10 ARHGEF10 1885 0.17 0.47 NO
5 ARHGEF1 ARHGEF1 ARHGEF1 2874 0.12 0.45 NO
6 ARHGEF19 ARHGEF19 ARHGEF19 3107 0.11 0.48 NO
7 ARHGEF4 ARHGEF4 ARHGEF4 4212 0.074 0.44 NO
8 ARHGEF2 ARHGEF2 ARHGEF2 6035 0.039 0.35 NO
9 PPP1R12B PPP1R12B PPP1R12B 6075 0.039 0.36 NO
10 GNA12 GNA12 GNA12 6739 0.029 0.34 NO
11 ARHGAP5 ARHGAP5 ARHGAP5 6931 0.026 0.33 NO
12 MYL7 MYL7 MYL7 8150 0.01 0.27 NO
13 ARHGEF6 ARHGEF6 ARHGEF6 8296 0.0089 0.27 NO
14 GNA13 GNA13 GNA13 8351 0.0083 0.27 NO
15 PKN1 PKN1 PKN1 8798 0.0026 0.24 NO
16 ARHGEF18 ARHGEF18 ARHGEF18 8983 5e-05 0.23 NO
17 GNAQ GNAQ GNAQ 9653 -0.0081 0.2 NO
18 ARHGEF17 ARHGEF17 ARHGEF17 10675 -0.021 0.15 NO
19 ARHGEF7 ARHGEF7 ARHGEF7 11267 -0.028 0.13 NO
20 GNB1 GNB1 GNB1 11597 -0.032 0.12 NO
21 PRKCA PRKCA PRKCA 11949 -0.038 0.11 NO
22 ROCK1 ROCK1 ROCK1 12288 -0.042 0.11 NO
23 ARHGEF12 ARHGEF12 ARHGEF12 13057 -0.055 0.084 NO
24 ARHGEF3 ARHGEF3 ARHGEF3 13677 -0.067 0.073 NO
25 PLCB1 PLCB1 PLCB1 14560 -0.088 0.054 NO
26 ARHGEF11 ARHGEF11 ARHGEF11 15006 -0.1 0.063 NO
27 ARHGEF15 ARHGEF15 ARHGEF15 15122 -0.11 0.092 NO
28 ARHGEF9 ARHGEF9 ARHGEF9 15299 -0.11 0.12 NO
29 PRKCB PRKCB PRKCB 15951 -0.14 0.13 NO

Figure S95.  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 TIGHT JUNCTION.

Figure S96.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TIGHT JUNCTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PARKINSONS DISEASE

Table S49.  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 DAO DAO DAO 235 0.48 0.059 YES
2 PAOX PAOX PAOX 359 0.4 0.11 YES
3 PEX11G PEX11G PEX11G 640 0.32 0.14 YES
4 EPHX2 EPHX2 EPHX2 706 0.3 0.19 YES
5 BAAT BAAT BAAT 835 0.28 0.22 YES
6 ACSL1 ACSL1 ACSL1 959 0.26 0.25 YES
7 MPV17L MPV17L MPV17L 1678 0.18 0.24 YES
8 DDO DDO DDO 1715 0.18 0.27 YES
9 HAO1 HAO1 HAO1 1761 0.18 0.29 YES
10 ACOX2 ACOX2 ACOX2 1947 0.16 0.3 YES
11 PRDX1 PRDX1 PRDX1 2084 0.16 0.32 YES
12 ACAA1 ACAA1 ACAA1 2670 0.12 0.31 YES
13 MVK MVK MVK 2892 0.12 0.31 YES
14 PEX16 PEX16 PEX16 2960 0.11 0.33 YES
15 PHYH PHYH PHYH 3037 0.11 0.34 YES
16 HMGCL HMGCL HMGCL 3069 0.11 0.35 YES
17 DHRS4 DHRS4 DHRS4 3110 0.11 0.37 YES
18 PEX7 PEX7 PEX7 3193 0.1 0.38 YES
19 PIPOX PIPOX PIPOX 3206 0.1 0.39 YES
20 FAR1 FAR1 FAR1 3230 0.1 0.4 YES
21 PMVK PMVK PMVK 3393 0.096 0.41 YES
22 ABCD4 ABCD4 ABCD4 4082 0.076 0.38 NO
23 HSD17B4 HSD17B4 HSD17B4 4519 0.066 0.37 NO
24 SOD1 SOD1 SOD1 4610 0.065 0.38 NO
25 PEX10 PEX10 PEX10 4689 0.063 0.38 NO
26 NUDT12 NUDT12 NUDT12 5027 0.056 0.37 NO
27 DECR2 DECR2 DECR2 5203 0.052 0.37 NO
28 IDH2 IDH2 IDH2 5224 0.052 0.38 NO
29 CAT CAT CAT 5252 0.052 0.38 NO
30 XDH XDH XDH 5351 0.05 0.38 NO
31 PXMP4 PXMP4 PXMP4 5634 0.045 0.38 NO
32 ACOT8 ACOT8 ACOT8 5683 0.044 0.38 NO
33 PEX2 PEX2 PEX2 5735 0.044 0.38 NO
34 ECH1 ECH1 ECH1 5788 0.043 0.39 NO
35 NUDT19 NUDT19 NUDT19 5866 0.042 0.39 NO
36 GSTK1 GSTK1 GSTK1 6105 0.038 0.38 NO
37 EHHADH EHHADH EHHADH 6355 0.034 0.37 NO
38 PEX11A PEX11A PEX11A 6498 0.032 0.37 NO
39 MPV17 MPV17 MPV17 6623 0.031 0.37 NO
40 PRDX5 PRDX5 PRDX5 6966 0.026 0.35 NO
41 SCP2 SCP2 SCP2 7289 0.021 0.34 NO
42 SOD2 SOD2 SOD2 7368 0.02 0.34 NO
43 PEX14 PEX14 PEX14 7387 0.02 0.34 NO
44 PEX1 PEX1 PEX1 7628 0.017 0.33 NO
45 PEX6 PEX6 PEX6 7919 0.013 0.31 NO
46 ABCD3 ABCD3 ABCD3 8098 0.011 0.31 NO
47 ACSL3 ACSL3 ACSL3 8102 0.011 0.31 NO
48 HACL1 HACL1 HACL1 8137 0.011 0.31 NO
49 GNPAT GNPAT GNPAT 8303 0.0088 0.3 NO
50 PEX12 PEX12 PEX12 8514 0.0061 0.29 NO
51 PEX3 PEX3 PEX3 8731 0.0034 0.28 NO
52 PEX5 PEX5 PEX5 8815 0.0023 0.27 NO
53 PEX19 PEX19 PEX19 8936 0.00062 0.27 NO
54 ACOX3 ACOX3 ACOX3 9018 -0.00037 0.26 NO
55 PXMP2 PXMP2 PXMP2 9062 -0.00094 0.26 NO
56 PECR PECR PECR 9307 -0.004 0.25 NO
57 CRAT CRAT CRAT 9316 -0.0041 0.25 NO
58 AGPS AGPS AGPS 9718 -0.0089 0.23 NO
59 PEX13 PEX13 PEX13 9873 -0.011 0.22 NO
60 ACSL5 ACSL5 ACSL5 9899 -0.011 0.22 NO
61 ABCD1 ABCD1 ABCD1 10543 -0.019 0.19 NO
62 ACOX1 ACOX1 ACOX1 10682 -0.021 0.18 NO
63 SLC25A17 SLC25A17 SLC25A17 11068 -0.026 0.17 NO
64 ACSL6 ACSL6 ACSL6 11317 -0.029 0.16 NO
65 PEX11B PEX11B PEX11B 11600 -0.032 0.15 NO
66 MLYCD MLYCD MLYCD 11613 -0.033 0.15 NO
67 CROT CROT CROT 13548 -0.064 0.054 NO
68 HAO2 HAO2 HAO2 13871 -0.071 0.047 NO
69 AMACR AMACR AMACR 13928 -0.072 0.054 NO
70 IDH1 IDH1 IDH1 14985 -0.1 0.011 NO
71 ACSL4 ACSL4 ACSL4 15136 -0.11 0.019 NO
72 PEX26 PEX26 PEX26 15226 -0.11 0.03 NO
73 ABCD2 ABCD2 ABCD2 17064 -0.2 -0.04 NO
74 NOS2 NOS2 NOS2 17113 -0.21 -0.011 NO
75 FAR2 FAR2 FAR2 17174 -0.22 0.018 NO
76 SLC27A2 SLC27A2 SLC27A2 17791 -0.3 0.029 NO

Figure S97.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PARKINSONS DISEASE.

Figure S98.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PARKINSONS DISEASE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA MYOSIN PATHWAY

Table S50.  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 HSD17B3 HSD17B3 HSD17B3 63 0.74 0.14 YES
2 LRP2 LRP2 LRP2 64 0.74 0.29 YES
3 HSD11B1 HSD11B1 HSD11B1 511 0.35 0.34 YES
4 LHB LHB LHB 576 0.33 0.4 YES
5 CYP11A1 CYP11A1 CYP11A1 625 0.32 0.46 YES
6 POMC POMC POMC 863 0.28 0.5 YES
7 LRAT LRAT LRAT 1303 0.22 0.52 YES
8 STARD6 STARD6 STARD6 1521 0.2 0.55 YES
9 CYP21A2 CYP21A2 CYP21A2 1788 0.18 0.57 YES
10 CYP17A1 CYP17A1 CYP17A1 1829 0.17 0.6 YES
11 BCMO1 BCMO1 BCMO1 2834 0.12 0.57 NO
12 SRD5A3 SRD5A3 SRD5A3 3029 0.11 0.58 NO
13 HSD17B1 HSD17B1 HSD17B1 4822 0.06 0.5 NO
14 CYP19A1 CYP19A1 CYP19A1 5666 0.045 0.46 NO
15 HSD3B2 HSD3B2 HSD3B2 5903 0.041 0.46 NO
16 RDH11 RDH11 RDH11 7604 0.017 0.37 NO
17 AKR1B1 AKR1B1 AKR1B1 8567 0.0053 0.32 NO
18 LGMN LGMN LGMN 9152 -0.0019 0.28 NO
19 RBP2 RBP2 RBP2 10657 -0.02 0.21 NO
20 CYP2R1 CYP2R1 CYP2R1 10892 -0.023 0.2 NO
21 STARD5 STARD5 STARD5 11125 -0.026 0.19 NO
22 SRD5A2 SRD5A2 SRD5A2 11336 -0.029 0.18 NO
23 CYP24A1 CYP24A1 CYP24A1 12487 -0.046 0.13 NO
24 SRD5A1 SRD5A1 SRD5A1 14526 -0.087 0.037 NO
25 CUBN CUBN CUBN 16089 -0.14 -0.02 NO
26 CYP27B1 CYP27B1 CYP27B1 16831 -0.19 -0.022 NO
27 STARD4 STARD4 STARD4 17421 -0.24 -0.0065 NO
28 STAR STAR STAR 17674 -0.28 0.035 NO

Figure S99.  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 MYOSIN PATHWAY.

Figure S100.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MYOSIN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input

  • Gene set database = c2.cp.v4.0.symbols.gmt

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

  • Phenotype data file = LGG-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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