GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LIHC-TP
Liver Hepatocellular Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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 LIHC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1DJ5F2G
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 "LIHC-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: 702
Number of samples: 371
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 ] 68
pheno.type: 2 - 5 :[ clus2 ] 88
pheno.type: 3 - 5 :[ clus3 ] 74
pheno.type: 4 - 5 :[ clus4 ] 71
pheno.type: 5 - 5 :[ clus5 ] 70

For the expression subtypes of 17745 genes in 372 samples, GSEA found enriched gene sets in each cluster using 371 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG CELL CYCLE, KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, BIOCARTA FMLP PATHWAY, PID IL2 PI3KPATHWAY, PID CASPASE PATHWAY, REACTOME CELL CYCLE, REACTOME MHC CLASS II ANTIGEN PRESENTATION, REACTOME RNA POL II TRANSCRIPTION, REACTOME CELL CYCLE MITOTIC, REACTOME CELL CYCLE CHECKPOINTS

    • And common core enriched genes are TCEB1, AAAS, BANF1, CD4, COBRA1, CTDP1, GTF2B, GTF2E1, GTF2E2, GTF2F2

  • clus2

    • Top enriched gene sets are KEGG CITRATE CYCLE TCA CYCLE, KEGG FATTY ACID METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION, KEGG STARCH AND SUCROSE METABOLISM, KEGG PYRUVATE METABOLISM, KEGG PROPANOATE METABOLISM, KEGG RETINOL METABOLISM

    • And common core enriched genes are ACAT1, ACAT2, ALDH2, ALDH7A1, ALDH9A1, EHHADH, PIPOX, ACACB, ACSS2, LDHAL6B

  • clus3

    • Top enriched gene sets are KEGG RIBOSOME, PID ATM PATHWAY, REACTOME TRANSLATION, REACTOME METABOLISM OF NON CODING RNA, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME SIGNALLING TO RAS, REACTOME SIGNALLING TO ERKS, REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, REACTOME PEPTIDE CHAIN ELONGATION

    • And common core enriched genes are FAM153A, RPL10, RPL10A, RPL12, RPL13A, RPL14, RPL15, RPL17, RPL18, RPL18A

  • clus4

    • Top enriched gene sets are KEGG GALACTOSE METABOLISM, KEGG PURINE METABOLISM, KEGG SELENOAMINO ACID METABOLISM, KEGG N GLYCAN BIOSYNTHESIS, KEGG O GLYCAN BIOSYNTHESIS, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG GLYCEROPHOSPHOLIPID METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG ARACHIDONIC ACID METABOLISM

    • And common core enriched genes are ADCY2, ADCY3, ADCY4, ADCY5, AKT3, CAMK4, ITPR3, PDE1A, PDE1B, PRKAR2B

  • clus5

    • Top enriched gene sets are KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG LYSINE DEGRADATION, KEGG TYROSINE METABOLISM, KEGG BUTANOATE METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM CYTOCHROME P450

    • And common core enriched genes are UGT1A1, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A8, UGT1A9, UGT2B10, UGT2B11, UGT2B28

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 CELL CYCLE 118 genes.ES.table 0.59 1.8 0.0058 0.32 0.57 0.33 0.14 0.29 0.084 0.078
KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY 60 genes.ES.table 0.67 1.8 0.01 0.35 0.51 0.38 0.14 0.33 0.095 0.083
BIOCARTA FMLP PATHWAY 36 genes.ES.table 0.55 1.8 0.01 0.22 0.66 0.28 0.22 0.22 0.076 0.054
PID IL2 PI3KPATHWAY 33 genes.ES.table 0.66 2 0 0.28 0.13 0.24 0.094 0.22 0 0.077
PID CASPASE PATHWAY 51 genes.ES.table 0.46 1.8 0.0042 0.26 0.6 0.51 0.37 0.32 0.07 0.07
REACTOME CELL CYCLE 376 genes.ES.table 0.56 1.8 0.017 0.39 0.47 0.46 0.27 0.34 0 0.09
REACTOME MHC CLASS II ANTIGEN PRESENTATION 89 genes.ES.table 0.52 1.8 0.004 0.25 0.6 0.32 0.2 0.25 0.067 0.063
REACTOME RNA POL II TRANSCRIPTION 93 genes.ES.table 0.4 1.9 0.012 0.37 0.28 0.73 0.52 0.35 0 0.081
REACTOME CELL CYCLE MITOTIC 297 genes.ES.table 0.6 1.8 0.0097 0.31 0.52 0.33 0.15 0.28 0.083 0.072
REACTOME CELL CYCLE CHECKPOINTS 105 genes.ES.table 0.56 1.8 0.027 0.3 0.59 0.4 0.27 0.29 0.081 0.074
genes ES table in pathway: KEGG CELL CYCLE

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 PSMA8 PSMA8 PSMA8 220 0.47 0.022 YES
2 CCR5 CCR5 CCR5 832 0.33 0.012 YES
3 CD8B CD8B CD8B 948 0.32 0.028 YES
4 HCK HCK HCK 1253 0.29 0.032 YES
5 AP1M2 AP1M2 AP1M2 1275 0.28 0.052 YES
6 DOCK2 DOCK2 DOCK2 1450 0.27 0.062 YES
7 LCK LCK LCK 1530 0.26 0.076 YES
8 APOBEC3G APOBEC3G APOBEC3G 1567 0.26 0.093 YES
9 PSMB9 PSMB9 PSMB9 1778 0.24 0.099 YES
10 HMGA1 HMGA1 HMGA1 1784 0.24 0.12 YES
11 CD28 CD28 CD28 1858 0.24 0.13 YES
12 RCC1 RCC1 RCC1 1941 0.23 0.14 YES
13 TAF4B TAF4B TAF4B 2370 0.2 0.13 YES
14 FEN1 FEN1 FEN1 2433 0.2 0.14 YES
15 CD247 CD247 CD247 2505 0.19 0.15 YES
16 XRCC4 XRCC4 XRCC4 2622 0.19 0.16 YES
17 CXCR4 CXCR4 CXCR4 3007 0.17 0.15 YES
18 NUP37 NUP37 NUP37 3033 0.17 0.16 YES
19 NUP188 NUP188 NUP188 3118 0.16 0.17 YES
20 NUP93 NUP93 NUP93 3299 0.15 0.17 YES
21 NUP210 NUP210 NUP210 3337 0.15 0.18 YES
22 NUP62 NUP62 NUP62 3421 0.15 0.18 YES
23 NUP107 NUP107 NUP107 3450 0.15 0.19 YES
24 PSMB8 PSMB8 PSMB8 3634 0.14 0.19 YES
25 GTF2H2B GTF2H2B GTF2H2B 3651 0.14 0.2 YES
26 NUP43 NUP43 NUP43 3727 0.14 0.21 YES
27 GTF2H2 GTF2H2 GTF2H2 3730 0.14 0.22 YES
28 PSMB10 PSMB10 PSMB10 3811 0.13 0.22 YES
29 RAN RAN RAN 3951 0.13 0.23 YES
30 NUP205 NUP205 NUP205 3971 0.13 0.23 YES
31 LIG1 LIG1 LIG1 4146 0.12 0.23 YES
32 PSMD14 PSMD14 PSMD14 4220 0.12 0.24 YES
33 NUP155 NUP155 NUP155 4261 0.12 0.24 YES
34 VPS37C VPS37C VPS37C 4280 0.12 0.25 YES
35 TAF12 TAF12 TAF12 4377 0.12 0.26 YES
36 TAF6 TAF6 TAF6 4439 0.11 0.26 YES
37 PSMA5 PSMA5 PSMA5 4626 0.11 0.26 YES
38 AP1S2 AP1S2 AP1S2 4636 0.11 0.26 YES
39 PSMB2 PSMB2 PSMB2 4724 0.1 0.27 YES
40 NUP85 NUP85 NUP85 4786 0.1 0.27 YES
41 TCEB1 TCEB1 TCEB1 4897 0.1 0.27 YES
42 POLR2D POLR2D POLR2D 5178 0.092 0.26 YES
43 TBP TBP TBP 5225 0.091 0.27 YES
44 NPM1 NPM1 NPM1 5312 0.089 0.27 YES
45 ELMO1 ELMO1 ELMO1 5353 0.088 0.27 YES
46 HLA-A HLA-A HLA-A 5381 0.087 0.28 YES
47 RNGTT RNGTT RNGTT 5400 0.087 0.28 YES
48 RANBP1 RANBP1 RANBP1 5401 0.087 0.29 YES
49 GTF2E2 GTF2E2 GTF2E2 5434 0.086 0.29 YES
50 SSRP1 SSRP1 SSRP1 5545 0.083 0.29 YES
51 PSMD2 PSMD2 PSMD2 5622 0.081 0.3 YES
52 CD4 CD4 CD4 5637 0.081 0.3 YES
53 PSIP1 PSIP1 PSIP1 5643 0.081 0.31 YES
54 PACS1 PACS1 PACS1 5797 0.077 0.3 YES
55 KPNB1 KPNB1 KPNB1 5866 0.076 0.3 YES
56 RDBP RDBP RDBP 5906 0.075 0.31 YES
57 GTF2H1 GTF2H1 GTF2H1 5939 0.074 0.31 YES
58 POLR2H POLR2H POLR2H 5946 0.074 0.32 YES
59 POLR2G POLR2G POLR2G 5971 0.074 0.32 YES
60 GTF2H3 GTF2H3 GTF2H3 6050 0.072 0.32 YES
61 SEH1L SEH1L SEH1L 6075 0.072 0.33 YES
62 PSMD10 PSMD10 PSMD10 6085 0.072 0.33 YES
63 NCBP2 NCBP2 NCBP2 6133 0.071 0.33 YES
64 TCEB3 TCEB3 TCEB3 6253 0.069 0.33 YES
65 PSMD12 PSMD12 PSMD12 6318 0.067 0.33 YES
66 RAC1 RAC1 RAC1 6340 0.067 0.34 YES
67 NUPL1 NUPL1 NUPL1 6360 0.067 0.34 YES
68 VPS37A VPS37A VPS37A 6415 0.066 0.34 YES
69 TAF9 TAF9 TAF9 6583 0.063 0.34 YES
70 PPIA PPIA PPIA 6587 0.062 0.34 YES
71 BANF1 BANF1 BANF1 6621 0.062 0.34 YES
72 PSMD13 PSMD13 PSMD13 6700 0.061 0.34 YES
73 PSMB3 PSMB3 PSMB3 6741 0.06 0.35 YES
74 PSMA1 PSMA1 PSMA1 6781 0.059 0.35 YES
75 NUP35 NUP35 NUP35 6783 0.059 0.35 YES
76 NCBP1 NCBP1 NCBP1 6825 0.059 0.36 YES
77 PSMC4 PSMC4 PSMC4 6990 0.055 0.35 YES
78 PSMD1 PSMD1 PSMD1 7002 0.055 0.35 YES
79 AP2S1 AP2S1 AP2S1 7020 0.055 0.36 YES
80 TAF13 TAF13 TAF13 7047 0.055 0.36 YES
81 SUPT5H SUPT5H SUPT5H 7092 0.054 0.36 YES
82 POLR2K POLR2K POLR2K 7315 0.05 0.35 YES
83 CTDP1 CTDP1 CTDP1 7329 0.05 0.35 YES
84 RAE1 RAE1 RAE1 7340 0.05 0.36 YES
85 MNAT1 MNAT1 MNAT1 7354 0.049 0.36 YES
86 PSMD7 PSMD7 PSMD7 7381 0.049 0.36 YES
87 PSMB1 PSMB1 PSMB1 7387 0.049 0.36 YES
88 SLC25A6 SLC25A6 SLC25A6 7439 0.048 0.37 YES
89 PSMD3 PSMD3 PSMD3 7449 0.048 0.37 YES
90 GTF2E1 GTF2E1 GTF2E1 7523 0.047 0.37 YES
91 RNMT RNMT RNMT 7527 0.047 0.37 YES
92 GTF2F2 GTF2F2 GTF2F2 7571 0.046 0.37 YES
93 SUPT16H SUPT16H SUPT16H 7609 0.046 0.37 YES
94 GTF2B GTF2B GTF2B 7628 0.045 0.38 YES
95 PSMD9 PSMD9 PSMD9 7683 0.045 0.38 YES
96 AP1B1 AP1B1 AP1B1 7735 0.044 0.38 YES
97 PSMD11 PSMD11 PSMD11 7789 0.043 0.38 YES
98 COBRA1 COBRA1 COBRA1 7831 0.042 0.38 YES
99 NUPL2 NUPL2 NUPL2 7842 0.042 0.38 YES
100 PSMA4 PSMA4 PSMA4 7875 0.042 0.38 YES
101 TAF10 TAF10 TAF10 7879 0.042 0.38 YES
102 AAAS AAAS AAAS 7913 0.041 0.38 YES
103 VPS37B VPS37B VPS37B 7927 0.041 0.39 YES
104 POLR2I POLR2I POLR2I 7971 0.04 0.39 YES
105 PSMA3 PSMA3 PSMA3 7979 0.04 0.39 YES
106 POLR2B POLR2B POLR2B 8051 0.039 0.39 YES
107 POLR2L POLR2L POLR2L 8131 0.038 0.39 YES
108 PAK2 PAK2 PAK2 8140 0.038 0.39 YES
109 RBX1 RBX1 RBX1 8167 0.038 0.39 YES
110 WHSC2 WHSC2 WHSC2 8171 0.038 0.39 YES
111 PSMD8 PSMD8 PSMD8 8176 0.037 0.4 YES
112 PSMD5 PSMD5 PSMD5 8290 0.036 0.39 YES
113 ATP6V1H ATP6V1H ATP6V1H 8320 0.035 0.39 YES
114 CDK7 CDK7 CDK7 8343 0.035 0.39 YES
115 PSMC5 PSMC5 PSMC5 8363 0.035 0.4 YES
116 PSME2 PSME2 PSME2 8417 0.034 0.4 YES
117 PSMC3 PSMC3 PSMC3 8446 0.034 0.4 YES
118 XRCC6 XRCC6 XRCC6 8459 0.034 0.4 YES
119 XPO1 XPO1 XPO1 8557 0.032 0.4 NO
120 AP2M1 AP2M1 AP2M1 8661 0.03 0.39 NO
121 TCEB2 TCEB2 TCEB2 8675 0.03 0.39 NO
122 RPS27A RPS27A RPS27A 8697 0.03 0.39 NO
123 PSMB4 PSMB4 PSMB4 8722 0.03 0.39 NO
124 XRCC5 XRCC5 XRCC5 8783 0.029 0.39 NO
125 RANGAP1 RANGAP1 RANGAP1 8813 0.028 0.39 NO
126 NUP54 NUP54 NUP54 8872 0.027 0.39 NO
127 NUP214 NUP214 NUP214 8905 0.027 0.39 NO
128 PSMB7 PSMB7 PSMB7 8968 0.026 0.39 NO
129 PSMA7 PSMA7 PSMA7 8973 0.026 0.39 NO
130 PSMA6 PSMA6 PSMA6 9021 0.025 0.39 NO
131 TAF11 TAF11 TAF11 9154 0.024 0.39 NO
132 ERCC2 ERCC2 ERCC2 9218 0.023 0.38 NO
133 ERCC3 ERCC3 ERCC3 9288 0.022 0.38 NO
134 POLR2J POLR2J POLR2J 9297 0.022 0.38 NO
135 PSMC1 PSMC1 PSMC1 9404 0.02 0.38 NO
136 PSMC2 PSMC2 PSMC2 9407 0.02 0.38 NO
137 SUPT4H1 SUPT4H1 SUPT4H1 9417 0.02 0.38 NO
138 PSMD4 PSMD4 PSMD4 9467 0.019 0.38 NO
139 PSME4 PSME4 PSME4 9480 0.019 0.38 NO
140 TSG101 TSG101 TSG101 9509 0.018 0.38 NO
141 GTF2F1 GTF2F1 GTF2F1 9571 0.017 0.38 NO
142 NUP153 NUP153 NUP153 9575 0.017 0.38 NO
143 PSMD6 PSMD6 PSMD6 9653 0.016 0.38 NO
144 SLC25A5 SLC25A5 SLC25A5 9722 0.015 0.37 NO
145 AP2B1 AP2B1 AP2B1 9752 0.015 0.37 NO
146 TAF4 TAF4 TAF4 9774 0.014 0.37 NO
147 TAF5 TAF5 TAF5 9784 0.014 0.37 NO
148 CDK9 CDK9 CDK9 9806 0.014 0.37 NO
149 TCEA1 TCEA1 TCEA1 9863 0.013 0.37 NO
150 AP1S1 AP1S1 AP1S1 9938 0.012 0.37 NO
151 CCNH CCNH CCNH 9975 0.011 0.36 NO
152 GTF2H4 GTF2H4 GTF2H4 9995 0.011 0.36 NO
153 UBA52 UBA52 UBA52 10003 0.011 0.36 NO
154 NUP50 NUP50 NUP50 10014 0.011 0.36 NO
155 POLR2A POLR2A POLR2A 10130 0.0091 0.36 NO
156 PSMB6 PSMB6 PSMB6 10219 0.0077 0.36 NO
157 B2M B2M B2M 10267 0.0071 0.35 NO
158 AP1M1 AP1M1 AP1M1 10452 0.0045 0.34 NO
159 AP2A2 AP2A2 AP2A2 10576 0.0029 0.34 NO
160 PSMC6 PSMC6 PSMC6 10581 0.0028 0.34 NO
161 GTF2A2 GTF2A2 GTF2A2 10595 0.0026 0.34 NO
162 CCNT2 CCNT2 CCNT2 10601 0.0024 0.34 NO
163 PSMB5 PSMB5 PSMB5 10629 0.0022 0.33 NO
164 AP2A1 AP2A1 AP2A1 10647 0.0018 0.33 NO
165 PSME1 PSME1 PSME1 10693 0.0011 0.33 NO
166 TPR TPR TPR 10709 0.00086 0.33 NO
167 SKP1 SKP1 SKP1 10734 0.00053 0.33 NO
168 NMT1 NMT1 NMT1 10786 -0.00027 0.33 NO
169 POLR2C POLR2C POLR2C 11031 -0.004 0.31 NO
170 POM121 POM121 POM121 11050 -0.0044 0.31 NO
171 AP1G1 AP1G1 AP1G1 11051 -0.0044 0.31 NO
172 NUP133 NUP133 NUP133 11195 -0.0066 0.3 NO
173 RANBP2 RANBP2 RANBP2 11229 -0.007 0.3 NO
174 VPS28 VPS28 VPS28 11317 -0.0084 0.3 NO
175 ARF1 ARF1 ARF1 11364 -0.009 0.3 NO
176 PSMF1 PSMF1 PSMF1 11406 -0.0096 0.3 NO
177 PSMA2 PSMA2 PSMA2 11435 -0.01 0.29 NO
178 TH1L TH1L TH1L 11439 -0.01 0.29 NO
179 POLR2E POLR2E POLR2E 11449 -0.01 0.3 NO
180 ELL ELL ELL 11557 -0.012 0.29 NO
181 TAF1 TAF1 TAF1 11569 -0.012 0.29 NO
182 CUL5 CUL5 CUL5 12048 -0.02 0.26 NO
183 NUP88 NUP88 NUP88 12072 -0.021 0.26 NO
184 CCNT1 CCNT1 CCNT1 12282 -0.025 0.25 NO
185 POLR2F POLR2F POLR2F 12287 -0.025 0.26 NO
186 KPNA1 KPNA1 KPNA1 12769 -0.034 0.23 NO
187 BTRC BTRC BTRC 13409 -0.048 0.2 NO
188 GTF2A1 GTF2A1 GTF2A1 13556 -0.052 0.19 NO
189 LIG4 LIG4 LIG4 14291 -0.072 0.16 NO
190 SLC25A4 SLC25A4 SLC25A4 14552 -0.08 0.15 NO
191 NMT2 NMT2 NMT2 14951 -0.097 0.13 NO
192 FYN FYN FYN 15313 -0.11 0.12 NO
193 VPS37D VPS37D VPS37D 16923 -0.24 0.046 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 CELL CYCLE.

Figure S2.  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 NOD LIKE RECEPTOR SIGNALING PATHWAY

Table S2.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MYB MYB MYB 203 0.47 0.11 YES
2 IL2RA IL2RA IL2RA 247 0.46 0.23 YES
3 IL2RG IL2RG IL2RG 253 0.46 0.35 YES
4 JAK3 JAK3 JAK3 543 0.38 0.43 YES
5 IL2RB IL2RB IL2RB 861 0.33 0.5 YES
6 E2F1 E2F1 E2F1 1194 0.29 0.56 YES
7 LCK LCK LCK 1530 0.26 0.61 YES
8 TERT TERT TERT 1671 0.25 0.66 YES
9 RAC1 RAC1 RAC1 6340 0.067 0.42 NO
10 GRB2 GRB2 GRB2 6666 0.061 0.42 NO
11 RPS6KB1 RPS6KB1 RPS6KB1 7090 0.054 0.41 NO
12 HSP90AA1 HSP90AA1 HSP90AA1 7854 0.042 0.37 NO
13 UGCG UGCG UGCG 8163 0.038 0.37 NO
14 MTOR MTOR MTOR 8379 0.035 0.36 NO
15 SHC1 SHC1 SHC1 8406 0.034 0.37 NO
16 RPS6 RPS6 RPS6 8792 0.028 0.36 NO
17 JAK1 JAK1 JAK1 9654 0.016 0.31 NO
18 RELA RELA RELA 9664 0.016 0.32 NO
19 MYC MYC MYC 9782 0.014 0.31 NO
20 NFKB1 NFKB1 NFKB1 9885 0.013 0.31 NO
21 PIK3CA PIK3CA PIK3CA 10261 0.0072 0.29 NO
22 GAB2 GAB2 GAB2 10350 0.0061 0.29 NO
23 FOXO3 FOXO3 FOXO3 10963 -0.003 0.25 NO
24 EIF3A EIF3A EIF3A 11041 -0.0042 0.25 NO
25 AKT1 AKT1 AKT1 11480 -0.011 0.23 NO
26 SOS1 SOS1 SOS1 11761 -0.016 0.22 NO
27 PTPN11 PTPN11 PTPN11 12284 -0.025 0.19 NO
28 PRKCZ PRKCZ PRKCZ 12826 -0.036 0.17 NO
29 BCL2 BCL2 BCL2 12850 -0.036 0.18 NO
30 SGMS1 SGMS1 SGMS1 12946 -0.038 0.18 NO
31 BCL2L1 BCL2L1 BCL2L1 14117 -0.067 0.14 NO
32 SMPD1 SMPD1 SMPD1 14192 -0.069 0.15 NO
33 PIK3R1 PIK3R1 PIK3R1 16441 -0.19 0.073 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 NOD LIKE RECEPTOR SIGNALING PATHWAY.

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

genes ES table in pathway: BIOCARTA FMLP 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 CCR5 CCR5 CCR5 832 0.33 -0.0039 YES
2 HMGA1 HMGA1 HMGA1 1784 0.24 -0.027 YES
3 RCC1 RCC1 RCC1 1941 0.23 -0.0058 YES
4 TAF4B TAF4B TAF4B 2370 0.2 -0.004 YES
5 FEN1 FEN1 FEN1 2433 0.2 0.018 YES
6 XRCC4 XRCC4 XRCC4 2622 0.19 0.031 YES
7 CXCR4 CXCR4 CXCR4 3007 0.17 0.031 YES
8 NUP37 NUP37 NUP37 3033 0.17 0.051 YES
9 NUP188 NUP188 NUP188 3118 0.16 0.068 YES
10 NUP93 NUP93 NUP93 3299 0.15 0.077 YES
11 NUP210 NUP210 NUP210 3337 0.15 0.095 YES
12 NUP62 NUP62 NUP62 3421 0.15 0.11 YES
13 NUP107 NUP107 NUP107 3450 0.15 0.13 YES
14 GTF2H2B GTF2H2B GTF2H2B 3651 0.14 0.13 YES
15 NUP43 NUP43 NUP43 3727 0.14 0.15 YES
16 GTF2H2 GTF2H2 GTF2H2 3730 0.14 0.16 YES
17 RAN RAN RAN 3951 0.13 0.17 YES
18 NUP205 NUP205 NUP205 3971 0.13 0.18 YES
19 LIG1 LIG1 LIG1 4146 0.12 0.19 YES
20 NUP155 NUP155 NUP155 4261 0.12 0.2 YES
21 VPS37C VPS37C VPS37C 4280 0.12 0.21 YES
22 TAF12 TAF12 TAF12 4377 0.12 0.22 YES
23 TAF6 TAF6 TAF6 4439 0.11 0.24 YES
24 NUP85 NUP85 NUP85 4786 0.1 0.23 YES
25 TCEB1 TCEB1 TCEB1 4897 0.1 0.24 YES
26 POLR2D POLR2D POLR2D 5178 0.092 0.23 YES
27 TBP TBP TBP 5225 0.091 0.24 YES
28 RNGTT RNGTT RNGTT 5400 0.087 0.24 YES
29 RANBP1 RANBP1 RANBP1 5401 0.087 0.25 YES
30 GTF2E2 GTF2E2 GTF2E2 5434 0.086 0.26 YES
31 SSRP1 SSRP1 SSRP1 5545 0.083 0.27 YES
32 CD4 CD4 CD4 5637 0.081 0.27 YES
33 PSIP1 PSIP1 PSIP1 5643 0.081 0.28 YES
34 RDBP RDBP RDBP 5906 0.075 0.28 YES
35 GTF2H1 GTF2H1 GTF2H1 5939 0.074 0.28 YES
36 POLR2H POLR2H POLR2H 5946 0.074 0.3 YES
37 POLR2G POLR2G POLR2G 5971 0.074 0.3 YES
38 GTF2H3 GTF2H3 GTF2H3 6050 0.072 0.31 YES
39 SEH1L SEH1L SEH1L 6075 0.072 0.32 YES
40 NCBP2 NCBP2 NCBP2 6133 0.071 0.32 YES
41 TCEB3 TCEB3 TCEB3 6253 0.069 0.32 YES
42 NUPL1 NUPL1 NUPL1 6360 0.067 0.33 YES
43 VPS37A VPS37A VPS37A 6415 0.066 0.33 YES
44 TAF9 TAF9 TAF9 6583 0.063 0.33 YES
45 PPIA PPIA PPIA 6587 0.062 0.34 YES
46 BANF1 BANF1 BANF1 6621 0.062 0.34 YES
47 NUP35 NUP35 NUP35 6783 0.059 0.34 YES
48 NCBP1 NCBP1 NCBP1 6825 0.059 0.35 YES
49 TAF13 TAF13 TAF13 7047 0.055 0.34 YES
50 SUPT5H SUPT5H SUPT5H 7092 0.054 0.35 YES
51 POLR2K POLR2K POLR2K 7315 0.05 0.34 YES
52 CTDP1 CTDP1 CTDP1 7329 0.05 0.35 YES
53 RAE1 RAE1 RAE1 7340 0.05 0.35 YES
54 MNAT1 MNAT1 MNAT1 7354 0.049 0.36 YES
55 GTF2E1 GTF2E1 GTF2E1 7523 0.047 0.36 YES
56 RNMT RNMT RNMT 7527 0.047 0.36 YES
57 GTF2F2 GTF2F2 GTF2F2 7571 0.046 0.36 YES
58 SUPT16H SUPT16H SUPT16H 7609 0.046 0.37 YES
59 GTF2B GTF2B GTF2B 7628 0.045 0.37 YES
60 COBRA1 COBRA1 COBRA1 7831 0.042 0.37 YES
61 NUPL2 NUPL2 NUPL2 7842 0.042 0.37 YES
62 TAF10 TAF10 TAF10 7879 0.042 0.38 YES
63 AAAS AAAS AAAS 7913 0.041 0.38 YES
64 VPS37B VPS37B VPS37B 7927 0.041 0.38 YES
65 POLR2I POLR2I POLR2I 7971 0.04 0.39 YES
66 POLR2B POLR2B POLR2B 8051 0.039 0.39 YES
67 POLR2L POLR2L POLR2L 8131 0.038 0.39 YES
68 WHSC2 WHSC2 WHSC2 8171 0.038 0.39 YES
69 CDK7 CDK7 CDK7 8343 0.035 0.38 NO
70 XRCC6 XRCC6 XRCC6 8459 0.034 0.38 NO
71 XPO1 XPO1 XPO1 8557 0.032 0.38 NO
72 TCEB2 TCEB2 TCEB2 8675 0.03 0.38 NO
73 RPS27A RPS27A RPS27A 8697 0.03 0.38 NO
74 XRCC5 XRCC5 XRCC5 8783 0.029 0.38 NO
75 RANGAP1 RANGAP1 RANGAP1 8813 0.028 0.38 NO
76 NUP54 NUP54 NUP54 8872 0.027 0.38 NO
77 NUP214 NUP214 NUP214 8905 0.027 0.38 NO
78 TAF11 TAF11 TAF11 9154 0.024 0.37 NO
79 ERCC2 ERCC2 ERCC2 9218 0.023 0.37 NO
80 ERCC3 ERCC3 ERCC3 9288 0.022 0.37 NO
81 POLR2J POLR2J POLR2J 9297 0.022 0.37 NO
82 SUPT4H1 SUPT4H1 SUPT4H1 9417 0.02 0.37 NO
83 TSG101 TSG101 TSG101 9509 0.018 0.37 NO
84 GTF2F1 GTF2F1 GTF2F1 9571 0.017 0.36 NO
85 NUP153 NUP153 NUP153 9575 0.017 0.37 NO
86 TAF4 TAF4 TAF4 9774 0.014 0.36 NO
87 TAF5 TAF5 TAF5 9784 0.014 0.36 NO
88 CDK9 CDK9 CDK9 9806 0.014 0.36 NO
89 TCEA1 TCEA1 TCEA1 9863 0.013 0.36 NO
90 CCNH CCNH CCNH 9975 0.011 0.35 NO
91 GTF2H4 GTF2H4 GTF2H4 9995 0.011 0.35 NO
92 UBA52 UBA52 UBA52 10003 0.011 0.36 NO
93 NUP50 NUP50 NUP50 10014 0.011 0.36 NO
94 POLR2A POLR2A POLR2A 10130 0.0091 0.35 NO
95 GTF2A2 GTF2A2 GTF2A2 10595 0.0026 0.32 NO
96 CCNT2 CCNT2 CCNT2 10601 0.0024 0.32 NO
97 TPR TPR TPR 10709 0.00086 0.32 NO
98 NMT1 NMT1 NMT1 10786 -0.00027 0.31 NO
99 POLR2C POLR2C POLR2C 11031 -0.004 0.3 NO
100 POM121 POM121 POM121 11050 -0.0044 0.3 NO
101 NUP133 NUP133 NUP133 11195 -0.0066 0.29 NO
102 RANBP2 RANBP2 RANBP2 11229 -0.007 0.29 NO
103 VPS28 VPS28 VPS28 11317 -0.0084 0.29 NO
104 TH1L TH1L TH1L 11439 -0.01 0.28 NO
105 POLR2E POLR2E POLR2E 11449 -0.01 0.28 NO
106 ELL ELL ELL 11557 -0.012 0.28 NO
107 TAF1 TAF1 TAF1 11569 -0.012 0.28 NO
108 NUP88 NUP88 NUP88 12072 -0.021 0.25 NO
109 CCNT1 CCNT1 CCNT1 12282 -0.025 0.25 NO
110 POLR2F POLR2F POLR2F 12287 -0.025 0.25 NO
111 GTF2A1 GTF2A1 GTF2A1 13556 -0.052 0.18 NO
112 LIG4 LIG4 LIG4 14291 -0.072 0.15 NO
113 NMT2 NMT2 NMT2 14951 -0.097 0.13 NO
114 VPS37D VPS37D VPS37D 16923 -0.24 0.046 NO

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

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

genes ES table in pathway: PID IL2 PI3KPATHWAY

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 CSTF2 CSTF2 CSTF2 1782 0.24 -0.054 YES
2 TAF4B TAF4B TAF4B 2370 0.2 -0.048 YES
3 UPF3B UPF3B UPF3B 2645 0.18 -0.027 YES
4 THOC4 THOC4 THOC4 3349 0.15 -0.037 YES
5 GTF2H2B GTF2H2B GTF2H2B 3651 0.14 -0.027 YES
6 GTF2H2 GTF2H2 GTF2H2 3730 0.14 -0.0043 YES
7 SNRPB SNRPB SNRPB 4003 0.13 0.0052 YES
8 TAF12 TAF12 TAF12 4377 0.12 0.0067 YES
9 SNRPF SNRPF SNRPF 4393 0.12 0.028 YES
10 TAF6 TAF6 TAF6 4439 0.11 0.048 YES
11 TCEB1 TCEB1 TCEB1 4897 0.1 0.042 YES
12 LSM10 LSM10 LSM10 4982 0.098 0.056 YES
13 POLR2D POLR2D POLR2D 5178 0.092 0.063 YES
14 TBP TBP TBP 5225 0.091 0.078 YES
15 RNPS1 RNPS1 RNPS1 5348 0.088 0.088 YES
16 RNGTT RNGTT RNGTT 5400 0.087 0.1 YES
17 GTF2E2 GTF2E2 GTF2E2 5434 0.086 0.12 YES
18 MAGOH MAGOH MAGOH 5494 0.084 0.13 YES
19 SSRP1 SSRP1 SSRP1 5545 0.083 0.14 YES
20 CPSF3 CPSF3 CPSF3 5554 0.083 0.16 YES
21 SLBP SLBP SLBP 5795 0.077 0.16 YES
22 RDBP RDBP RDBP 5906 0.075 0.17 YES
23 GTF2H1 GTF2H1 GTF2H1 5939 0.074 0.18 YES
24 POLR2H POLR2H POLR2H 5946 0.074 0.2 YES
25 POLR2G POLR2G POLR2G 5971 0.074 0.21 YES
26 ZNF473 ZNF473 ZNF473 5987 0.074 0.22 YES
27 U2AF2 U2AF2 U2AF2 6026 0.073 0.24 YES
28 GTF2H3 GTF2H3 GTF2H3 6050 0.072 0.25 YES
29 SNRPG SNRPG SNRPG 6125 0.071 0.26 YES
30 NCBP2 NCBP2 NCBP2 6133 0.071 0.27 YES
31 TCEB3 TCEB3 TCEB3 6253 0.069 0.28 YES
32 TAF9 TAF9 TAF9 6583 0.063 0.27 YES
33 NCBP1 NCBP1 NCBP1 6825 0.059 0.27 YES
34 SNRPE SNRPE SNRPE 6925 0.057 0.28 YES
35 TAF13 TAF13 TAF13 7047 0.055 0.28 YES
36 RBM8A RBM8A RBM8A 7060 0.054 0.29 YES
37 U2AF1 U2AF1 U2AF1 7076 0.054 0.3 YES
38 SUPT5H SUPT5H SUPT5H 7092 0.054 0.31 YES
39 POLR2K POLR2K POLR2K 7315 0.05 0.31 YES
40 CTDP1 CTDP1 CTDP1 7329 0.05 0.32 YES
41 MNAT1 MNAT1 MNAT1 7354 0.049 0.32 YES
42 GTF2E1 GTF2E1 GTF2E1 7523 0.047 0.32 YES
43 RNMT RNMT RNMT 7527 0.047 0.33 YES
44 GTF2F2 GTF2F2 GTF2F2 7571 0.046 0.34 YES
45 SUPT16H SUPT16H SUPT16H 7609 0.046 0.34 YES
46 CSTF3 CSTF3 CSTF3 7614 0.046 0.35 YES
47 GTF2B GTF2B GTF2B 7628 0.045 0.36 YES
48 SRRM1 SRRM1 SRRM1 7701 0.044 0.37 YES
49 COBRA1 COBRA1 COBRA1 7831 0.042 0.37 YES
50 TAF10 TAF10 TAF10 7879 0.042 0.37 YES
51 POLR2I POLR2I POLR2I 7971 0.04 0.38 YES
52 POLR2B POLR2B POLR2B 8051 0.039 0.38 YES
53 POLR2L POLR2L POLR2L 8131 0.038 0.38 YES
54 WHSC2 WHSC2 WHSC2 8171 0.038 0.39 YES
55 DHX38 DHX38 DHX38 8288 0.036 0.39 YES
56 CDK7 CDK7 CDK7 8343 0.035 0.39 YES
57 CPSF1 CPSF1 CPSF1 8500 0.033 0.39 YES
58 PAPOLA PAPOLA PAPOLA 8562 0.032 0.39 YES
59 TCEB2 TCEB2 TCEB2 8675 0.03 0.39 YES
60 PABPN1 PABPN1 PABPN1 8693 0.03 0.4 YES
61 NUDT21 NUDT21 NUDT21 8825 0.028 0.39 YES
62 CPSF2 CPSF2 CPSF2 9041 0.025 0.39 YES
63 TAF11 TAF11 TAF11 9154 0.024 0.38 YES
64 CDC40 CDC40 CDC40 9196 0.023 0.39 YES
65 ERCC2 ERCC2 ERCC2 9218 0.023 0.39 YES
66 ERCC3 ERCC3 ERCC3 9288 0.022 0.39 YES
67 POLR2J POLR2J POLR2J 9297 0.022 0.4 YES
68 CLP1 CLP1 CLP1 9306 0.021 0.4 YES
69 SUPT4H1 SUPT4H1 SUPT4H1 9417 0.02 0.4 NO
70 GTF2F1 GTF2F1 GTF2F1 9571 0.017 0.39 NO
71 TAF4 TAF4 TAF4 9774 0.014 0.38 NO
72 TAF5 TAF5 TAF5 9784 0.014 0.38 NO
73 CDK9 CDK9 CDK9 9806 0.014 0.39 NO
74 TCEA1 TCEA1 TCEA1 9863 0.013 0.38 NO
75 CCNH CCNH CCNH 9975 0.011 0.38 NO
76 GTF2H4 GTF2H4 GTF2H4 9995 0.011 0.38 NO
77 CPSF7 CPSF7 CPSF7 10105 0.0096 0.38 NO
78 POLR2A POLR2A POLR2A 10130 0.0091 0.38 NO
79 GTF2A2 GTF2A2 GTF2A2 10595 0.0026 0.35 NO
80 CCNT2 CCNT2 CCNT2 10601 0.0024 0.35 NO
81 SNRPD3 SNRPD3 SNRPD3 10702 0.00097 0.35 NO
82 POLR2C POLR2C POLR2C 11031 -0.004 0.33 NO
83 TH1L TH1L TH1L 11439 -0.01 0.31 NO
84 POLR2E POLR2E POLR2E 11449 -0.01 0.31 NO
85 LSM11 LSM11 LSM11 11473 -0.011 0.31 NO
86 ELL ELL ELL 11557 -0.012 0.31 NO
87 TAF1 TAF1 TAF1 11569 -0.012 0.31 NO
88 NFX1 NFX1 NFX1 12262 -0.024 0.28 NO
89 CCNT1 CCNT1 CCNT1 12282 -0.025 0.28 NO
90 POLR2F POLR2F POLR2F 12287 -0.025 0.28 NO
91 CSTF1 CSTF1 CSTF1 12322 -0.026 0.29 NO
92 PCF11 PCF11 PCF11 13281 -0.046 0.24 NO
93 GTF2A1 GTF2A1 GTF2A1 13556 -0.052 0.24 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 IL2 PI3KPATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: PID IL2 PI3KPATHWAY, 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 CASPASE 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 PSMA8 PSMA8 PSMA8 220 0.47 0.039 YES
2 CD8B CD8B CD8B 948 0.32 0.034 YES
3 HCK HCK HCK 1253 0.29 0.048 YES
4 AP1M2 AP1M2 AP1M2 1275 0.28 0.078 YES
5 DOCK2 DOCK2 DOCK2 1450 0.27 0.098 YES
6 LCK LCK LCK 1530 0.26 0.12 YES
7 APOBEC3G APOBEC3G APOBEC3G 1567 0.26 0.15 YES
8 PSMB9 PSMB9 PSMB9 1778 0.24 0.16 YES
9 HMGA1 HMGA1 HMGA1 1784 0.24 0.19 YES
10 CD28 CD28 CD28 1858 0.24 0.21 YES
11 RCC1 RCC1 RCC1 1941 0.23 0.23 YES
12 CD247 CD247 CD247 2505 0.19 0.22 YES
13 NUP37 NUP37 NUP37 3033 0.17 0.21 YES
14 NUP188 NUP188 NUP188 3118 0.16 0.22 YES
15 NUP93 NUP93 NUP93 3299 0.15 0.23 YES
16 NUP210 NUP210 NUP210 3337 0.15 0.25 YES
17 NUP62 NUP62 NUP62 3421 0.15 0.26 YES
18 NUP107 NUP107 NUP107 3450 0.15 0.27 YES
19 PSMB8 PSMB8 PSMB8 3634 0.14 0.28 YES
20 NUP43 NUP43 NUP43 3727 0.14 0.29 YES
21 PSMB10 PSMB10 PSMB10 3811 0.13 0.3 YES
22 RAN RAN RAN 3951 0.13 0.3 YES
23 NUP205 NUP205 NUP205 3971 0.13 0.32 YES
24 PSMD14 PSMD14 PSMD14 4220 0.12 0.32 YES
25 NUP155 NUP155 NUP155 4261 0.12 0.33 YES
26 PSMA5 PSMA5 PSMA5 4626 0.11 0.32 YES
27 AP1S2 AP1S2 AP1S2 4636 0.11 0.33 YES
28 PSMB2 PSMB2 PSMB2 4724 0.1 0.34 YES
29 NUP85 NUP85 NUP85 4786 0.1 0.34 YES
30 TCEB1 TCEB1 TCEB1 4897 0.1 0.35 YES
31 NPM1 NPM1 NPM1 5312 0.089 0.34 YES
32 ELMO1 ELMO1 ELMO1 5353 0.088 0.34 YES
33 HLA-A HLA-A HLA-A 5381 0.087 0.35 YES
34 RANBP1 RANBP1 RANBP1 5401 0.087 0.36 YES
35 PSMD2 PSMD2 PSMD2 5622 0.081 0.36 YES
36 CD4 CD4 CD4 5637 0.081 0.36 YES
37 PSIP1 PSIP1 PSIP1 5643 0.081 0.37 YES
38 PACS1 PACS1 PACS1 5797 0.077 0.37 YES
39 KPNB1 KPNB1 KPNB1 5866 0.076 0.38 YES
40 SEH1L SEH1L SEH1L 6075 0.072 0.37 YES
41 PSMD10 PSMD10 PSMD10 6085 0.072 0.38 YES
42 PSMD12 PSMD12 PSMD12 6318 0.067 0.38 YES
43 RAC1 RAC1 RAC1 6340 0.067 0.38 YES
44 NUPL1 NUPL1 NUPL1 6360 0.067 0.39 YES
45 PPIA PPIA PPIA 6587 0.062 0.38 YES
46 BANF1 BANF1 BANF1 6621 0.062 0.39 YES
47 PSMD13 PSMD13 PSMD13 6700 0.061 0.39 YES
48 PSMB3 PSMB3 PSMB3 6741 0.06 0.39 YES
49 PSMA1 PSMA1 PSMA1 6781 0.059 0.4 YES
50 NUP35 NUP35 NUP35 6783 0.059 0.4 YES
51 PSMC4 PSMC4 PSMC4 6990 0.055 0.4 YES
52 PSMD1 PSMD1 PSMD1 7002 0.055 0.4 YES
53 AP2S1 AP2S1 AP2S1 7020 0.055 0.41 YES
54 RAE1 RAE1 RAE1 7340 0.05 0.4 YES
55 PSMD7 PSMD7 PSMD7 7381 0.049 0.4 YES
56 PSMB1 PSMB1 PSMB1 7387 0.049 0.41 YES
57 SLC25A6 SLC25A6 SLC25A6 7439 0.048 0.41 YES
58 PSMD3 PSMD3 PSMD3 7449 0.048 0.41 YES
59 PSMD9 PSMD9 PSMD9 7683 0.045 0.4 YES
60 AP1B1 AP1B1 AP1B1 7735 0.044 0.41 YES
61 PSMD11 PSMD11 PSMD11 7789 0.043 0.41 YES
62 NUPL2 NUPL2 NUPL2 7842 0.042 0.41 YES
63 PSMA4 PSMA4 PSMA4 7875 0.042 0.41 YES
64 AAAS AAAS AAAS 7913 0.041 0.42 YES
65 PSMA3 PSMA3 PSMA3 7979 0.04 0.42 YES
66 PAK2 PAK2 PAK2 8140 0.038 0.41 YES
67 RBX1 RBX1 RBX1 8167 0.038 0.41 YES
68 PSMD8 PSMD8 PSMD8 8176 0.037 0.42 YES
69 PSMD5 PSMD5 PSMD5 8290 0.036 0.42 YES
70 ATP6V1H ATP6V1H ATP6V1H 8320 0.035 0.42 YES
71 PSMC5 PSMC5 PSMC5 8363 0.035 0.42 YES
72 PSME2 PSME2 PSME2 8417 0.034 0.42 YES
73 PSMC3 PSMC3 PSMC3 8446 0.034 0.42 YES
74 XPO1 XPO1 XPO1 8557 0.032 0.42 YES
75 AP2M1 AP2M1 AP2M1 8661 0.03 0.42 YES
76 TCEB2 TCEB2 TCEB2 8675 0.03 0.42 YES
77 RPS27A RPS27A RPS27A 8697 0.03 0.42 YES
78 PSMB4 PSMB4 PSMB4 8722 0.03 0.42 YES
79 RANGAP1 RANGAP1 RANGAP1 8813 0.028 0.42 YES
80 NUP54 NUP54 NUP54 8872 0.027 0.42 YES
81 NUP214 NUP214 NUP214 8905 0.027 0.42 YES
82 PSMB7 PSMB7 PSMB7 8968 0.026 0.42 YES
83 PSMA7 PSMA7 PSMA7 8973 0.026 0.42 YES
84 PSMA6 PSMA6 PSMA6 9021 0.025 0.42 YES
85 PSMC1 PSMC1 PSMC1 9404 0.02 0.4 NO
86 PSMC2 PSMC2 PSMC2 9407 0.02 0.41 NO
87 PSMD4 PSMD4 PSMD4 9467 0.019 0.41 NO
88 PSME4 PSME4 PSME4 9480 0.019 0.41 NO
89 NUP153 NUP153 NUP153 9575 0.017 0.4 NO
90 PSMD6 PSMD6 PSMD6 9653 0.016 0.4 NO
91 SLC25A5 SLC25A5 SLC25A5 9722 0.015 0.4 NO
92 AP2B1 AP2B1 AP2B1 9752 0.015 0.4 NO
93 CDK9 CDK9 CDK9 9806 0.014 0.4 NO
94 AP1S1 AP1S1 AP1S1 9938 0.012 0.39 NO
95 UBA52 UBA52 UBA52 10003 0.011 0.39 NO
96 NUP50 NUP50 NUP50 10014 0.011 0.39 NO
97 PSMB6 PSMB6 PSMB6 10219 0.0077 0.38 NO
98 B2M B2M B2M 10267 0.0071 0.38 NO
99 AP1M1 AP1M1 AP1M1 10452 0.0045 0.37 NO
100 AP2A2 AP2A2 AP2A2 10576 0.0029 0.36 NO
101 PSMC6 PSMC6 PSMC6 10581 0.0028 0.36 NO
102 PSMB5 PSMB5 PSMB5 10629 0.0022 0.36 NO
103 AP2A1 AP2A1 AP2A1 10647 0.0018 0.36 NO
104 PSME1 PSME1 PSME1 10693 0.0011 0.36 NO
105 TPR TPR TPR 10709 0.00086 0.35 NO
106 SKP1 SKP1 SKP1 10734 0.00053 0.35 NO
107 POM121 POM121 POM121 11050 -0.0044 0.34 NO
108 AP1G1 AP1G1 AP1G1 11051 -0.0044 0.34 NO
109 NUP133 NUP133 NUP133 11195 -0.0066 0.33 NO
110 RANBP2 RANBP2 RANBP2 11229 -0.007 0.33 NO
111 ARF1 ARF1 ARF1 11364 -0.009 0.32 NO
112 PSMF1 PSMF1 PSMF1 11406 -0.0096 0.32 NO
113 PSMA2 PSMA2 PSMA2 11435 -0.01 0.32 NO
114 CUL5 CUL5 CUL5 12048 -0.02 0.29 NO
115 NUP88 NUP88 NUP88 12072 -0.021 0.29 NO
116 CCNT1 CCNT1 CCNT1 12282 -0.025 0.28 NO
117 KPNA1 KPNA1 KPNA1 12769 -0.034 0.26 NO
118 BTRC BTRC BTRC 13409 -0.048 0.22 NO
119 SLC25A4 SLC25A4 SLC25A4 14552 -0.08 0.17 NO
120 FYN FYN FYN 15313 -0.11 0.14 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 CASPASE PATHWAY.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: PID CASPASE 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 CELL CYCLE

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 CDC25A CDC25A CDC25A 114 0.52 0.034 YES
2 CDC45 CDC45 CDC45 158 0.5 0.071 YES
3 PSMA8 PSMA8 PSMA8 220 0.47 0.1 YES
4 CDC6 CDC6 CDC6 305 0.44 0.13 YES
5 GINS1 GINS1 GINS1 331 0.43 0.17 YES
6 CDT1 CDT1 CDT1 358 0.42 0.2 YES
7 CCNE1 CCNE1 CCNE1 563 0.38 0.22 YES
8 CCNE2 CCNE2 CCNE2 675 0.36 0.24 YES
9 POLE2 POLE2 POLE2 729 0.35 0.26 YES
10 CCNA2 CCNA2 CCNA2 746 0.35 0.29 YES
11 GINS4 GINS4 GINS4 757 0.35 0.32 YES
12 MCM8 MCM8 MCM8 1049 0.31 0.32 YES
13 GINS2 GINS2 GINS2 1164 0.29 0.34 YES
14 MCM2 MCM2 MCM2 1213 0.29 0.36 YES
15 CDC25B CDC25B CDC25B 1399 0.27 0.37 YES
16 PRIM1 PRIM1 PRIM1 1641 0.25 0.38 YES
17 RFC4 RFC4 RFC4 1766 0.24 0.39 YES
18 PSMB9 PSMB9 PSMB9 1778 0.24 0.41 YES
19 POLA2 POLA2 POLA2 1986 0.23 0.41 YES
20 DNA2 DNA2 DNA2 2017 0.22 0.43 YES
21 MCM6 MCM6 MCM6 2057 0.22 0.44 YES
22 MCM4 MCM4 MCM4 2098 0.22 0.46 YES
23 FEN1 FEN1 FEN1 2433 0.2 0.46 YES
24 MCM7 MCM7 MCM7 2511 0.19 0.47 YES
25 PRIM2 PRIM2 PRIM2 2547 0.19 0.48 YES
26 POLA1 POLA1 POLA1 2568 0.19 0.49 YES
27 POLD1 POLD1 POLD1 2647 0.18 0.5 YES
28 MCM5 MCM5 MCM5 3333 0.15 0.48 YES
29 MCM3 MCM3 MCM3 3454 0.15 0.48 YES
30 POLD3 POLD3 POLD3 3496 0.15 0.49 YES
31 PSMB8 PSMB8 PSMB8 3634 0.14 0.49 YES
32 CKS1B CKS1B CKS1B 3666 0.14 0.5 YES
33 SKP2 SKP2 SKP2 3700 0.14 0.51 YES
34 CDK4 CDK4 CDK4 3779 0.14 0.52 YES
35 PSMB10 PSMB10 PSMB10 3811 0.13 0.53 YES
36 CCNA1 CCNA1 CCNA1 3998 0.13 0.53 YES
37 RFC3 RFC3 RFC3 4037 0.13 0.53 YES
38 LIG1 LIG1 LIG1 4146 0.12 0.54 YES
39 PCNA PCNA PCNA 4148 0.12 0.55 YES
40 PSMD14 PSMD14 PSMD14 4220 0.12 0.55 YES
41 RFC2 RFC2 RFC2 4288 0.12 0.56 YES
42 RPA2 RPA2 RPA2 4335 0.12 0.56 YES
43 CDK2 CDK2 CDK2 4374 0.12 0.57 YES
44 RFC5 RFC5 RFC5 4574 0.11 0.57 YES
45 PSMA5 PSMA5 PSMA5 4626 0.11 0.57 YES
46 PSMB2 PSMB2 PSMB2 4724 0.1 0.58 YES
47 RPA3 RPA3 RPA3 5359 0.087 0.55 NO
48 PSMD2 PSMD2 PSMD2 5622 0.081 0.54 NO
49 PSMD10 PSMD10 PSMD10 6085 0.072 0.52 NO
50 POLE POLE POLE 6157 0.07 0.52 NO
51 PSMD12 PSMD12 PSMD12 6318 0.067 0.52 NO
52 MAX MAX MAX 6397 0.066 0.52 NO
53 PSMD13 PSMD13 PSMD13 6700 0.061 0.5 NO
54 PSMB3 PSMB3 PSMB3 6741 0.06 0.51 NO
55 PSMA1 PSMA1 PSMA1 6781 0.059 0.51 NO
56 PSMC4 PSMC4 PSMC4 6990 0.055 0.5 NO
57 PSMD1 PSMD1 PSMD1 7002 0.055 0.51 NO
58 RPA1 RPA1 RPA1 7222 0.052 0.5 NO
59 MNAT1 MNAT1 MNAT1 7354 0.049 0.5 NO
60 PSMD7 PSMD7 PSMD7 7381 0.049 0.5 NO
61 PSMB1 PSMB1 PSMB1 7387 0.049 0.5 NO
62 PSMD3 PSMD3 PSMD3 7449 0.048 0.5 NO
63 PSMD9 PSMD9 PSMD9 7683 0.045 0.49 NO
64 PSMD11 PSMD11 PSMD11 7789 0.043 0.49 NO
65 PSMA4 PSMA4 PSMA4 7875 0.042 0.49 NO
66 PSMA3 PSMA3 PSMA3 7979 0.04 0.48 NO
67 PSMD8 PSMD8 PSMD8 8176 0.037 0.48 NO
68 PSMD5 PSMD5 PSMD5 8290 0.036 0.47 NO
69 WEE1 WEE1 WEE1 8316 0.036 0.47 NO
70 POLD2 POLD2 POLD2 8327 0.035 0.48 NO
71 CDK7 CDK7 CDK7 8343 0.035 0.48 NO
72 PSMC5 PSMC5 PSMC5 8363 0.035 0.48 NO
73 PSME2 PSME2 PSME2 8417 0.034 0.48 NO
74 PSMC3 PSMC3 PSMC3 8446 0.034 0.48 NO
75 RPS27A RPS27A RPS27A 8697 0.03 0.47 NO
76 PSMB4 PSMB4 PSMB4 8722 0.03 0.47 NO
77 PSMB7 PSMB7 PSMB7 8968 0.026 0.46 NO
78 PSMA7 PSMA7 PSMA7 8973 0.026 0.46 NO
79 PSMA6 PSMA6 PSMA6 9021 0.025 0.46 NO
80 PSMC1 PSMC1 PSMC1 9404 0.02 0.44 NO
81 PSMC2 PSMC2 PSMC2 9407 0.02 0.44 NO
82 PSMD4 PSMD4 PSMD4 9467 0.019 0.44 NO
83 PSME4 PSME4 PSME4 9480 0.019 0.44 NO
84 PSMD6 PSMD6 PSMD6 9653 0.016 0.43 NO
85 MYC MYC MYC 9782 0.014 0.42 NO
86 CCNH CCNH CCNH 9975 0.011 0.41 NO
87 UBA52 UBA52 UBA52 10003 0.011 0.41 NO
88 PSMB6 PSMB6 PSMB6 10219 0.0077 0.4 NO
89 PSMC6 PSMC6 PSMC6 10581 0.0028 0.38 NO
90 PSMB5 PSMB5 PSMB5 10629 0.0022 0.38 NO
91 PSME1 PSME1 PSME1 10693 0.0011 0.38 NO
92 SKP1 SKP1 SKP1 10734 0.00053 0.37 NO
93 CUL1 CUL1 CUL1 11082 -0.0049 0.35 NO
94 PSMF1 PSMF1 PSMF1 11406 -0.0096 0.34 NO
95 PSMA2 PSMA2 PSMA2 11435 -0.01 0.34 NO
96 POLD4 POLD4 POLD4 11922 -0.018 0.31 NO
97 RB1 RB1 RB1 12314 -0.025 0.29 NO
98 CDKN1B CDKN1B CDKN1B 12848 -0.036 0.26 NO
99 CDKN1A CDKN1A CDKN1A 13155 -0.043 0.25 NO
100 CCND1 CCND1 CCND1 15847 -0.14 0.11 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 CELL CYCLE.

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

genes ES table in pathway: REACTOME MHC CLASS II ANTIGEN PRESENTATION

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 E2F2 E2F2 E2F2 29 0.61 0.033 YES
2 MCM10 MCM10 MCM10 58 0.57 0.063 YES
3 MYBL2 MYBL2 MYBL2 60 0.57 0.095 YES
4 CDC25A CDC25A CDC25A 114 0.52 0.12 YES
5 PKMYT1 PKMYT1 PKMYT1 140 0.5 0.15 YES
6 CDC45 CDC45 CDC45 158 0.5 0.17 YES
7 CDC7 CDC7 CDC7 289 0.44 0.19 YES
8 CDC6 CDC6 CDC6 305 0.44 0.22 YES
9 CDT1 CDT1 CDT1 358 0.42 0.24 YES
10 CDKN2A CDKN2A CDKN2A 361 0.42 0.26 YES
11 CCNB1 CCNB1 CCNB1 455 0.4 0.28 YES
12 CDK1 CDK1 CDK1 477 0.4 0.3 YES
13 CCNE1 CCNE1 CCNE1 563 0.38 0.31 YES
14 FBXO5 FBXO5 FBXO5 595 0.37 0.33 YES
15 RRM2 RRM2 RRM2 661 0.36 0.35 YES
16 CCNE2 CCNE2 CCNE2 675 0.36 0.37 YES
17 POLE2 POLE2 POLE2 729 0.35 0.38 YES
18 CCNA2 CCNA2 CCNA2 746 0.35 0.4 YES
19 RBL1 RBL1 RBL1 964 0.32 0.41 YES
20 MCM8 MCM8 MCM8 1049 0.31 0.42 YES
21 E2F1 E2F1 E2F1 1194 0.29 0.43 YES
22 MCM2 MCM2 MCM2 1213 0.29 0.44 YES
23 E2F5 E2F5 E2F5 1303 0.28 0.46 YES
24 DBF4 DBF4 DBF4 1389 0.27 0.47 YES
25 PRIM1 PRIM1 PRIM1 1641 0.25 0.47 YES
26 PSMB9 PSMB9 PSMB9 1778 0.24 0.47 YES
27 TYMS TYMS TYMS 1841 0.24 0.48 YES
28 CDKN2C CDKN2C CDKN2C 1943 0.23 0.49 YES
29 POLA2 POLA2 POLA2 1986 0.23 0.5 YES
30 MCM6 MCM6 MCM6 2057 0.22 0.51 YES
31 MCM4 MCM4 MCM4 2098 0.22 0.52 YES
32 RPA4 RPA4 RPA4 2328 0.2 0.52 YES
33 CDKN2B CDKN2B CDKN2B 2343 0.2 0.53 YES
34 CDKN2D CDKN2D CDKN2D 2344 0.2 0.54 YES
35 LIN9 LIN9 LIN9 2449 0.2 0.54 YES
36 MCM7 MCM7 MCM7 2511 0.19 0.55 YES
37 PRIM2 PRIM2 PRIM2 2547 0.19 0.56 YES
38 POLA1 POLA1 POLA1 2568 0.19 0.57 YES
39 E2F3 E2F3 E2F3 2690 0.18 0.57 YES
40 MCM5 MCM5 MCM5 3333 0.15 0.54 YES
41 MCM3 MCM3 MCM3 3454 0.15 0.55 YES
42 PSMB8 PSMB8 PSMB8 3634 0.14 0.54 YES
43 CKS1B CKS1B CKS1B 3666 0.14 0.55 YES
44 SKP2 SKP2 SKP2 3700 0.14 0.55 YES
45 CDK4 CDK4 CDK4 3779 0.14 0.56 YES
46 PSMB10 PSMB10 PSMB10 3811 0.13 0.56 YES
47 CCNA1 CCNA1 CCNA1 3998 0.13 0.56 YES
48 PCNA PCNA PCNA 4148 0.12 0.56 YES
49 HDAC1 HDAC1 HDAC1 4197 0.12 0.56 YES
50 PSMD14 PSMD14 PSMD14 4220 0.12 0.57 YES
51 RPA2 RPA2 RPA2 4335 0.12 0.57 YES
52 CDK2 CDK2 CDK2 4374 0.12 0.57 YES
53 PSMA5 PSMA5 PSMA5 4626 0.11 0.56 NO
54 PSMB2 PSMB2 PSMB2 4724 0.1 0.56 NO
55 CCND2 CCND2 CCND2 5006 0.097 0.55 NO
56 E2F4 E2F4 E2F4 5241 0.09 0.55 NO
57 RPA3 RPA3 RPA3 5359 0.087 0.54 NO
58 PSMD2 PSMD2 PSMD2 5622 0.081 0.53 NO
59 RBBP4 RBBP4 RBBP4 5722 0.079 0.53 NO
60 PSMD10 PSMD10 PSMD10 6085 0.072 0.52 NO
61 POLE POLE POLE 6157 0.07 0.52 NO
62 PSMD12 PSMD12 PSMD12 6318 0.067 0.51 NO
63 PPP2R3B PPP2R3B PPP2R3B 6322 0.067 0.51 NO
64 MAX MAX MAX 6397 0.066 0.51 NO
65 CCND3 CCND3 CCND3 6468 0.065 0.51 NO
66 PSMD13 PSMD13 PSMD13 6700 0.061 0.5 NO
67 PSMB3 PSMB3 PSMB3 6741 0.06 0.5 NO
68 PSMA1 PSMA1 PSMA1 6781 0.059 0.5 NO
69 PSMC4 PSMC4 PSMC4 6990 0.055 0.5 NO
70 PSMD1 PSMD1 PSMD1 7002 0.055 0.5 NO
71 LIN37 LIN37 LIN37 7021 0.055 0.5 NO
72 RPA1 RPA1 RPA1 7222 0.052 0.49 NO
73 MNAT1 MNAT1 MNAT1 7354 0.049 0.49 NO
74 PSMD7 PSMD7 PSMD7 7381 0.049 0.49 NO
75 PSMB1 PSMB1 PSMB1 7387 0.049 0.49 NO
76 PSMD3 PSMD3 PSMD3 7449 0.048 0.49 NO
77 LIN54 LIN54 LIN54 7592 0.046 0.48 NO
78 PSMD9 PSMD9 PSMD9 7683 0.045 0.48 NO
79 PSMD11 PSMD11 PSMD11 7789 0.043 0.48 NO
80 PSMA4 PSMA4 PSMA4 7875 0.042 0.48 NO
81 PPP2R1A PPP2R1A PPP2R1A 7883 0.042 0.48 NO
82 PSMA3 PSMA3 PSMA3 7979 0.04 0.48 NO
83 PSMD8 PSMD8 PSMD8 8176 0.037 0.47 NO
84 PSMD5 PSMD5 PSMD5 8290 0.036 0.46 NO
85 WEE1 WEE1 WEE1 8316 0.036 0.46 NO
86 CDK7 CDK7 CDK7 8343 0.035 0.46 NO
87 PSMC5 PSMC5 PSMC5 8363 0.035 0.46 NO
88 PSME2 PSME2 PSME2 8417 0.034 0.46 NO
89 PSMC3 PSMC3 PSMC3 8446 0.034 0.46 NO
90 PPP2CA PPP2CA PPP2CA 8533 0.032 0.46 NO
91 RPS27A RPS27A RPS27A 8697 0.03 0.45 NO
92 PSMB4 PSMB4 PSMB4 8722 0.03 0.45 NO
93 TFDP1 TFDP1 TFDP1 8914 0.027 0.44 NO
94 PSMB7 PSMB7 PSMB7 8968 0.026 0.44 NO
95 PSMA7 PSMA7 PSMA7 8973 0.026 0.44 NO
96 PSMA6 PSMA6 PSMA6 9021 0.025 0.44 NO
97 PPP2R2A PPP2R2A PPP2R2A 9071 0.024 0.44 NO
98 DHFR DHFR DHFR 9114 0.024 0.44 NO
99 PSMC1 PSMC1 PSMC1 9404 0.02 0.42 NO
100 PSMC2 PSMC2 PSMC2 9407 0.02 0.42 NO
101 PSMD4 PSMD4 PSMD4 9467 0.019 0.42 NO
102 PSMD6 PSMD6 PSMD6 9653 0.016 0.41 NO
103 MYC MYC MYC 9782 0.014 0.41 NO
104 CCNH CCNH CCNH 9975 0.011 0.4 NO
105 UBA52 UBA52 UBA52 10003 0.011 0.4 NO
106 PSMB6 PSMB6 PSMB6 10219 0.0077 0.38 NO
107 PSMC6 PSMC6 PSMC6 10581 0.0028 0.36 NO
108 PSMB5 PSMB5 PSMB5 10629 0.0022 0.36 NO
109 PSME1 PSME1 PSME1 10693 0.0011 0.36 NO
110 SKP1 SKP1 SKP1 10734 0.00053 0.36 NO
111 CUL1 CUL1 CUL1 11082 -0.0049 0.34 NO
112 PSMF1 PSMF1 PSMF1 11406 -0.0096 0.32 NO
113 PSMA2 PSMA2 PSMA2 11435 -0.01 0.32 NO
114 PPP2CB PPP2CB PPP2CB 11558 -0.012 0.31 NO
115 CDK6 CDK6 CDK6 12086 -0.021 0.28 NO
116 RB1 RB1 RB1 12314 -0.025 0.27 NO
117 CDKN1B CDKN1B CDKN1B 12848 -0.036 0.24 NO
118 CDKN1A CDKN1A CDKN1A 13155 -0.043 0.23 NO
119 DYRK1A DYRK1A DYRK1A 13306 -0.046 0.22 NO
120 TK2 TK2 TK2 14701 -0.086 0.15 NO
121 RBL2 RBL2 RBL2 14964 -0.098 0.14 NO
122 LIN52 LIN52 LIN52 15083 -0.1 0.14 NO
123 PPP2R1B PPP2R1B PPP2R1B 15145 -0.1 0.14 NO
124 CCND1 CCND1 CCND1 15847 -0.14 0.11 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 MHC CLASS II ANTIGEN PRESENTATION.

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

genes ES table in pathway: REACTOME RNA POL II TRANSCRIPTION

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 KIF2C KIF2C KIF2C 19 0.63 0.01 YES
2 E2F2 E2F2 E2F2 29 0.61 0.02 YES
3 CDC20 CDC20 CDC20 49 0.58 0.029 YES
4 CENPA CENPA CENPA 51 0.58 0.04 YES
5 ERCC6L ERCC6L ERCC6L 53 0.58 0.05 YES
6 MCM10 MCM10 MCM10 58 0.57 0.059 YES
7 MYBL2 MYBL2 MYBL2 60 0.57 0.069 YES
8 SGOL1 SGOL1 SGOL1 74 0.56 0.078 YES
9 KIF18A KIF18A KIF18A 78 0.55 0.088 YES
10 SKA1 SKA1 SKA1 86 0.54 0.097 YES
11 BIRC5 BIRC5 BIRC5 99 0.53 0.11 YES
12 CDC25A CDC25A CDC25A 114 0.52 0.11 YES
13 PLK1 PLK1 PLK1 128 0.51 0.12 YES
14 BUB1 BUB1 BUB1 131 0.51 0.13 YES
15 KIF23 KIF23 KIF23 133 0.51 0.14 YES
16 PKMYT1 PKMYT1 PKMYT1 140 0.5 0.15 YES
17 CDCA8 CDCA8 CDCA8 146 0.5 0.16 YES
18 BUB1B BUB1B BUB1B 147 0.5 0.16 YES
19 PLK4 PLK4 PLK4 149 0.5 0.17 YES
20 CDC45 CDC45 CDC45 158 0.5 0.18 YES
21 PTTG1 PTTG1 PTTG1 165 0.49 0.19 YES
22 CENPM CENPM CENPM 168 0.49 0.2 YES
23 NDC80 NDC80 NDC80 171 0.49 0.21 YES
24 SPC25 SPC25 SPC25 173 0.49 0.22 YES
25 CDC25C CDC25C CDC25C 186 0.48 0.22 YES
26 NUF2 NUF2 NUF2 197 0.47 0.23 YES
27 CENPI CENPI CENPI 218 0.47 0.24 YES
28 PSMA8 PSMA8 PSMA8 220 0.47 0.25 YES
29 CENPK CENPK CENPK 229 0.46 0.25 YES
30 HJURP HJURP HJURP 250 0.46 0.26 YES
31 AURKB AURKB AURKB 256 0.46 0.27 YES
32 KIF20A KIF20A KIF20A 264 0.45 0.28 YES
33 SGOL2 SGOL2 SGOL2 279 0.45 0.28 YES
34 OIP5 OIP5 OIP5 288 0.44 0.29 YES
35 CDC7 CDC7 CDC7 289 0.44 0.3 YES
36 CCNB2 CCNB2 CCNB2 293 0.44 0.31 YES
37 CDC6 CDC6 CDC6 305 0.44 0.31 YES
38 NEK2 NEK2 NEK2 321 0.43 0.32 YES
39 GINS1 GINS1 GINS1 331 0.43 0.33 YES
40 CDT1 CDT1 CDT1 358 0.42 0.33 YES
41 CDKN2A CDKN2A CDKN2A 361 0.42 0.34 YES
42 MAD2L1 MAD2L1 MAD2L1 398 0.41 0.34 YES
43 CCNB1 CCNB1 CCNB1 455 0.4 0.35 YES
44 CDK1 CDK1 CDK1 477 0.4 0.35 YES
45 CENPO CENPO CENPO 485 0.39 0.36 YES
46 CENPH CENPH CENPH 510 0.39 0.37 YES
47 CCNE1 CCNE1 CCNE1 563 0.38 0.37 YES
48 UBE2C UBE2C UBE2C 589 0.37 0.38 YES
49 FBXO5 FBXO5 FBXO5 595 0.37 0.38 YES
50 RRM2 RRM2 RRM2 661 0.36 0.38 YES
51 CCNE2 CCNE2 CCNE2 675 0.36 0.39 YES
52 POLE2 POLE2 POLE2 729 0.35 0.39 YES
53 CCNA2 CCNA2 CCNA2 746 0.35 0.4 YES
54 GINS4 GINS4 GINS4 757 0.35 0.4 YES
55 SMC1B SMC1B SMC1B 819 0.34 0.41 YES
56 RBL1 RBL1 RBL1 964 0.32 0.4 YES
57 MCM8 MCM8 MCM8 1049 0.31 0.4 YES
58 KNTC1 KNTC1 KNTC1 1072 0.31 0.41 YES
59 CHEK1 CHEK1 CHEK1 1102 0.3 0.41 YES
60 MLF1IP MLF1IP MLF1IP 1127 0.3 0.42 YES
61 ZWINT ZWINT ZWINT 1151 0.3 0.42 YES
62 GINS2 GINS2 GINS2 1164 0.29 0.42 YES
63 E2F1 E2F1 E2F1 1194 0.29 0.43 YES
64 LMNB1 LMNB1 LMNB1 1196 0.29 0.43 YES
65 MCM2 MCM2 MCM2 1213 0.29 0.44 YES
66 BRCA1 BRCA1 BRCA1 1229 0.29 0.44 YES
67 CENPJ CENPJ CENPJ 1262 0.28 0.44 YES
68 E2F5 E2F5 E2F5 1303 0.28 0.45 YES
69 CEP135 CEP135 CEP135 1360 0.28 0.45 YES
70 SPC24 SPC24 SPC24 1386 0.27 0.45 YES
71 DBF4 DBF4 DBF4 1389 0.27 0.46 YES
72 CDC25B CDC25B CDC25B 1399 0.27 0.46 YES
73 CDC14A CDC14A CDC14A 1454 0.27 0.46 YES
74 CCDC99 CCDC99 CCDC99 1469 0.27 0.46 YES
75 CENPL CENPL CENPL 1616 0.25 0.46 YES
76 KIF2A KIF2A KIF2A 1634 0.25 0.46 YES
77 PRIM1 PRIM1 PRIM1 1641 0.25 0.47 YES
78 PRKAR2B PRKAR2B PRKAR2B 1667 0.25 0.47 YES
79 TERT TERT TERT 1671 0.25 0.48 YES
80 RFC4 RFC4 RFC4 1766 0.24 0.48 YES
81 PSMB9 PSMB9 PSMB9 1778 0.24 0.48 YES
82 TYMS TYMS TYMS 1841 0.24 0.48 YES
83 HIST1H4D HIST1H4D HIST1H4D 1882 0.23 0.48 YES
84 TUBA4A TUBA4A TUBA4A 1899 0.23 0.48 YES
85 ITGB3BP ITGB3BP ITGB3BP 1912 0.23 0.49 YES
86 CENPP CENPP CENPP 1935 0.23 0.49 YES
87 CDKN2C CDKN2C CDKN2C 1943 0.23 0.49 YES
88 POLA2 POLA2 POLA2 1986 0.23 0.5 YES
89 HIST1H2AB HIST1H2AB HIST1H2AB 2010 0.22 0.5 YES
90 AURKA AURKA AURKA 2016 0.22 0.5 YES
91 DNA2 DNA2 DNA2 2017 0.22 0.5 YES
92 INCENP INCENP INCENP 2027 0.22 0.51 YES
93 MCM6 MCM6 MCM6 2057 0.22 0.51 YES
94 MCM4 MCM4 MCM4 2098 0.22 0.51 YES
95 HIST1H2AD HIST1H2AD HIST1H2AD 2140 0.22 0.51 YES
96 AZI1 AZI1 AZI1 2170 0.21 0.52 YES
97 H2AFX H2AFX H2AFX 2177 0.21 0.52 YES
98 HIST1H2BL HIST1H2BL HIST1H2BL 2268 0.21 0.52 YES
99 HIST1H4E HIST1H4E HIST1H4E 2291 0.21 0.52 YES
100 RPA4 RPA4 RPA4 2328 0.2 0.52 YES
101 CDKN2B CDKN2B CDKN2B 2343 0.2 0.52 YES
102 CDKN2D CDKN2D CDKN2D 2344 0.2 0.53 YES
103 CENPQ CENPQ CENPQ 2415 0.2 0.53 YES
104 FEN1 FEN1 FEN1 2433 0.2 0.53 YES
105 RCC2 RCC2 RCC2 2437 0.2 0.53 YES
106 HIST1H2AJ HIST1H2AJ HIST1H2AJ 2444 0.2 0.54 YES
107 LIN9 LIN9 LIN9 2449 0.2 0.54 YES
108 MCM7 MCM7 MCM7 2511 0.19 0.54 YES
109 PRIM2 PRIM2 PRIM2 2547 0.19 0.54 YES
110 POLA1 POLA1 POLA1 2568 0.19 0.54 YES
111 H2AFZ H2AFZ H2AFZ 2579 0.19 0.55 YES
112 REC8 REC8 REC8 2643 0.18 0.55 YES
113 POLD1 POLD1 POLD1 2647 0.18 0.55 YES
114 E2F3 E2F3 E2F3 2690 0.18 0.55 YES
115 HIST1H4A HIST1H4A HIST1H4A 2701 0.18 0.55 YES
116 HIST1H4H HIST1H4H HIST1H4H 2741 0.18 0.55 YES
117 ZWILCH ZWILCH ZWILCH 2827 0.17 0.55 YES
118 APITD1 APITD1 APITD1 2828 0.17 0.55 YES
119 HIST1H2BG HIST1H2BG HIST1H2BG 2942 0.17 0.55 YES
120 NUP37 NUP37 NUP37 3033 0.17 0.55 YES
121 NEDD1 NEDD1 NEDD1 3135 0.16 0.55 YES
122 HIST1H2BN HIST1H2BN HIST1H2BN 3177 0.16 0.55 YES
123 HIST1H4C HIST1H4C HIST1H4C 3262 0.16 0.54 YES
124 ACD ACD ACD 3279 0.16 0.55 YES
125 HIST1H2BO HIST1H2BO HIST1H2BO 3283 0.16 0.55 YES
126 MCM5 MCM5 MCM5 3333 0.15 0.55 YES
127 B9D2 B9D2 B9D2 3352 0.15 0.55 YES
128 CEP72 CEP72 CEP72 3400 0.15 0.55 YES
129 HIST4H4 HIST4H4 HIST4H4 3403 0.15 0.55 YES
130 NUP107 NUP107 NUP107 3450 0.15 0.55 YES
131 MCM3 MCM3 MCM3 3454 0.15 0.55 YES
132 TUBG1 TUBG1 TUBG1 3456 0.15 0.56 YES
133 HIST1H2BM HIST1H2BM HIST1H2BM 3491 0.15 0.56 YES
134 POLD3 POLD3 POLD3 3496 0.15 0.56 YES
135 SYCP2 SYCP2 SYCP2 3603 0.14 0.56 YES
136 PSMB8 PSMB8 PSMB8 3634 0.14 0.56 YES
137 CKS1B CKS1B CKS1B 3666 0.14 0.56 YES
138 SKP2 SKP2 SKP2 3700 0.14 0.56 YES
139 NUP43 NUP43 NUP43 3727 0.14 0.56 YES
140 CDK4 CDK4 CDK4 3779 0.14 0.56 YES
141 DKC1 DKC1 DKC1 3783 0.14 0.56 YES
142 PSMB10 PSMB10 PSMB10 3811 0.13 0.56 YES
143 CENPN CENPN CENPN 3852 0.13 0.56 YES
144 CCNA1 CCNA1 CCNA1 3998 0.13 0.56 YES
145 UBE2D1 UBE2D1 UBE2D1 4001 0.13 0.56 YES
146 UBE2I UBE2I UBE2I 4007 0.13 0.56 YES
147 RFC3 RFC3 RFC3 4037 0.13 0.56 YES
148 CASC5 CASC5 CASC5 4059 0.13 0.56 YES
149 WRAP53 WRAP53 WRAP53 4093 0.12 0.56 YES
150 MAPRE1 MAPRE1 MAPRE1 4115 0.12 0.56 YES
151 LIG1 LIG1 LIG1 4146 0.12 0.56 YES
152 PCNA PCNA PCNA 4148 0.12 0.56 YES
153 HDAC1 HDAC1 HDAC1 4197 0.12 0.56 YES
154 PSMD14 PSMD14 PSMD14 4220 0.12 0.56 YES
155 RFC2 RFC2 RFC2 4288 0.12 0.56 YES
156 RPA2 RPA2 RPA2 4335 0.12 0.56 YES
157 CHEK2 CHEK2 CHEK2 4370 0.12 0.56 YES
158 CDK2 CDK2 CDK2 4374 0.12 0.56 YES
159 RUVBL1 RUVBL1 RUVBL1 4501 0.11 0.56 YES
160 RFC5 RFC5 RFC5 4574 0.11 0.56 YES
161 RAD9A RAD9A RAD9A 4621 0.11 0.56 YES
162 PSMA5 PSMA5 PSMA5 4626 0.11 0.56 YES
163 CKAP5 CKAP5 CKAP5 4658 0.11 0.56 YES
164 SMARCA5 SMARCA5 SMARCA5 4661 0.11 0.56 YES
165 PPP1CC PPP1CC PPP1CC 4672 0.11 0.56 YES
166 HIST1H2BF HIST1H2BF HIST1H2BF 4680 0.11 0.56 YES
167 DSN1 DSN1 DSN1 4714 0.1 0.56 YES
168 RAD1 RAD1 RAD1 4719 0.1 0.56 YES
169 PSMB2 PSMB2 PSMB2 4724 0.1 0.56 YES
170 NUDC NUDC NUDC 4777 0.1 0.56 YES
171 NUP85 NUP85 NUP85 4786 0.1 0.56 YES
172 ANAPC7 ANAPC7 ANAPC7 4821 0.1 0.56 NO
173 TUBB TUBB TUBB 4868 0.1 0.56 NO
174 TUBG2 TUBG2 TUBG2 4964 0.098 0.56 NO
175 CCND2 CCND2 CCND2 5006 0.097 0.56 NO
176 HIST1H4B HIST1H4B HIST1H4B 5017 0.096 0.56 NO
177 CEP164 CEP164 CEP164 5042 0.096 0.56 NO
178 HIST1H2BJ HIST1H2BJ HIST1H2BJ 5079 0.095 0.56 NO
179 E2F4 E2F4 E2F4 5241 0.09 0.55 NO
180 NPM1 NPM1 NPM1 5312 0.089 0.55 NO
181 ATRIP ATRIP ATRIP 5325 0.088 0.55 NO
182 HSPA2 HSPA2 HSPA2 5346 0.088 0.55 NO
183 RPA3 RPA3 RPA3 5359 0.087 0.55 NO
184 HIST2H2AC HIST2H2AC HIST2H2AC 5476 0.085 0.55 NO
185 RPS27 RPS27 RPS27 5510 0.084 0.55 NO
186 UBE2E1 UBE2E1 UBE2E1 5548 0.083 0.55 NO
187 PSMD2 PSMD2 PSMD2 5622 0.081 0.54 NO
188 CEP250 CEP250 CEP250 5697 0.08 0.54 NO
189 RBBP4 RBBP4 RBBP4 5722 0.079 0.54 NO
190 DYNLL1 DYNLL1 DYNLL1 5728 0.079 0.54 NO
191 CSNK1D CSNK1D CSNK1D 5729 0.079 0.54 NO
192 TUBA1A TUBA1A TUBA1A 5733 0.079 0.54 NO
193 DYNC1H1 DYNC1H1 DYNC1H1 5780 0.078 0.54 NO
194 RUVBL2 RUVBL2 RUVBL2 5876 0.076 0.54 NO
195 TEX12 TEX12 TEX12 5897 0.075 0.54 NO
196 RAD21 RAD21 RAD21 6028 0.073 0.53 NO
197 SEH1L SEH1L SEH1L 6075 0.072 0.53 NO
198 PSMD10 PSMD10 PSMD10 6085 0.072 0.53 NO
199 POLE POLE POLE 6157 0.07 0.53 NO
200 DCTN2 DCTN2 DCTN2 6174 0.07 0.53 NO
201 SSNA1 SSNA1 SSNA1 6314 0.067 0.52 NO
202 PSMD12 PSMD12 PSMD12 6318 0.067 0.52 NO
203 PPP2R3B PPP2R3B PPP2R3B 6322 0.067 0.52 NO
204 CDC27 CDC27 CDC27 6332 0.067 0.52 NO
205 OFD1 OFD1 OFD1 6344 0.067 0.53 NO
206 MAX MAX MAX 6397 0.066 0.52 NO
207 HIST1H2BH HIST1H2BH HIST1H2BH 6466 0.065 0.52 NO
208 CCND3 CCND3 CCND3 6468 0.065 0.52 NO
209 TAOK1 TAOK1 TAOK1 6694 0.061 0.51 NO
210 PSMD13 PSMD13 PSMD13 6700 0.061 0.51 NO
211 PSMB3 PSMB3 PSMB3 6741 0.06 0.51 NO
212 BUB3 BUB3 BUB3 6749 0.06 0.51 NO
213 RBBP7 RBBP7 RBBP7 6764 0.06 0.51 NO
214 CDK5RAP2 CDK5RAP2 CDK5RAP2 6777 0.059 0.51 NO
215 PSMA1 PSMA1 PSMA1 6781 0.059 0.51 NO
216 HIST1H2BC HIST1H2BC HIST1H2BC 6798 0.059 0.51 NO
217 SMC1A SMC1A SMC1A 6821 0.059 0.51 NO
218 ANAPC1 ANAPC1 ANAPC1 6840 0.058 0.51 NO
219 ANAPC11 ANAPC11 ANAPC11 6903 0.057 0.51 NO
220 GMNN GMNN GMNN 6955 0.056 0.51 NO
221 HIST2H4A HIST2H4A HIST2H4A 6978 0.056 0.51 NO
222 PSMC4 PSMC4 PSMC4 6990 0.055 0.51 NO
223 PSMD1 PSMD1 PSMD1 7002 0.055 0.51 NO
224 LIN37 LIN37 LIN37 7021 0.055 0.51 NO
225 SEC13 SEC13 SEC13 7039 0.055 0.51 NO
226 CEP290 CEP290 CEP290 7048 0.055 0.51 NO
227 ATR ATR ATR 7117 0.054 0.5 NO
228 ANAPC4 ANAPC4 ANAPC4 7169 0.053 0.5 NO
229 DCTN1 DCTN1 DCTN1 7187 0.052 0.5 NO
230 RPA1 RPA1 RPA1 7222 0.052 0.5 NO
231 ATM ATM ATM 7350 0.049 0.5 NO
232 MNAT1 MNAT1 MNAT1 7354 0.049 0.5 NO
233 PSMD7 PSMD7 PSMD7 7381 0.049 0.5 NO
234 PSMB1 PSMB1 PSMB1 7387 0.049 0.5 NO
235 PSMD3 PSMD3 PSMD3 7449 0.048 0.49 NO
236 LIN54 LIN54 LIN54 7592 0.046 0.49 NO
237 NHP2 NHP2 NHP2 7608 0.046 0.49 NO
238 PCNT PCNT PCNT 7619 0.046 0.49 NO
239 PSMD9 PSMD9 PSMD9 7683 0.045 0.48 NO
240 CENPT CENPT CENPT 7692 0.044 0.48 NO
241 ALMS1 ALMS1 ALMS1 7728 0.044 0.48 NO
242 FGFR1OP FGFR1OP FGFR1OP 7772 0.043 0.48 NO
243 PSMD11 PSMD11 PSMD11 7789 0.043 0.48 NO
244 CSNK1E CSNK1E CSNK1E 7818 0.042 0.48 NO
245 HSP90AA1 HSP90AA1 HSP90AA1 7854 0.042 0.48 NO
246 ANAPC5 ANAPC5 ANAPC5 7860 0.042 0.48 NO
247 PSMA4 PSMA4 PSMA4 7875 0.042 0.48 NO
248 PPP2R1A PPP2R1A PPP2R1A 7883 0.042 0.48 NO
249 PSMA3 PSMA3 PSMA3 7979 0.04 0.47 NO
250 PPP2R5E PPP2R5E PPP2R5E 8010 0.04 0.47 NO
251 YWHAG YWHAG YWHAG 8059 0.039 0.47 NO
252 CDC26 CDC26 CDC26 8080 0.039 0.47 NO
253 PSMD8 PSMD8 PSMD8 8176 0.037 0.47 NO
254 SKA2 SKA2 SKA2 8191 0.037 0.47 NO
255 LMNA LMNA LMNA 8251 0.036 0.46 NO
256 PPP2R5B PPP2R5B PPP2R5B 8265 0.036 0.46 NO
257 PSMD5 PSMD5 PSMD5 8290 0.036 0.46 NO
258 WEE1 WEE1 WEE1 8316 0.036 0.46 NO
259 POLD2 POLD2 POLD2 8327 0.035 0.46 NO
260 CDK7 CDK7 CDK7 8343 0.035 0.46 NO
261 PSMC5 PSMC5 PSMC5 8363 0.035 0.46 NO
262 HIST3H2BB HIST3H2BB HIST3H2BB 8400 0.034 0.46 NO
263 PSME2 PSME2 PSME2 8417 0.034 0.46 NO
264 PSMC3 PSMC3 PSMC3 8446 0.034 0.46 NO
265 PPP2CA PPP2CA PPP2CA 8533 0.032 0.45 NO
266 XPO1 XPO1 XPO1 8557 0.032 0.45 NO
267 RPS27A RPS27A RPS27A 8697 0.03 0.44 NO
268 TERF1 TERF1 TERF1 8710 0.03 0.44 NO
269 PSMB4 PSMB4 PSMB4 8722 0.03 0.44 NO
270 RANGAP1 RANGAP1 RANGAP1 8813 0.028 0.44 NO
271 TFDP1 TFDP1 TFDP1 8914 0.027 0.44 NO
272 PSMB7 PSMB7 PSMB7 8968 0.026 0.43 NO
273 PSMA7 PSMA7 PSMA7 8973 0.026 0.43 NO
274 CDC23 CDC23 CDC23 8980 0.026 0.43 NO
275 PSMA6 PSMA6 PSMA6 9021 0.025 0.43 NO
276 PPP2R2A PPP2R2A PPP2R2A 9071 0.024 0.43 NO
277 DCTN3 DCTN3 DCTN3 9090 0.024 0.43 NO
278 DHFR DHFR DHFR 9114 0.024 0.43 NO
279 DYNC1I2 DYNC1I2 DYNC1I2 9220 0.022 0.42 NO
280 PCM1 PCM1 PCM1 9317 0.021 0.42 NO
281 RSF1 RSF1 RSF1 9396 0.02 0.41 NO
282 PSMC1 PSMC1 PSMC1 9404 0.02 0.41 NO
283 PSMC2 PSMC2 PSMC2 9407 0.02 0.41 NO
284 CEP76 CEP76 CEP76 9421 0.02 0.41 NO
285 HUS1 HUS1 HUS1 9440 0.019 0.41 NO
286 PSMD4 PSMD4 PSMD4 9467 0.019 0.41 NO
287 PSME4 PSME4 PSME4 9480 0.019 0.41 NO
288 CETN2 CETN2 CETN2 9547 0.018 0.41 NO
289 HAUS2 HAUS2 HAUS2 9550 0.018 0.41 NO
290 CEP192 CEP192 CEP192 9574 0.017 0.4 NO
291 PSMD6 PSMD6 PSMD6 9653 0.016 0.4 NO
292 ZW10 ZW10 ZW10 9665 0.016 0.4 NO
293 PPP2R5D PPP2R5D PPP2R5D 9750 0.015 0.4 NO
294 MYC MYC MYC 9782 0.014 0.39 NO
295 STAG2 STAG2 STAG2 9835 0.013 0.39 NO
296 PMF1 PMF1 PMF1 9856 0.013 0.39 NO
297 CCNH CCNH CCNH 9975 0.011 0.38 NO
298 UBA52 UBA52 UBA52 10003 0.011 0.38 NO
299 YWHAE YWHAE YWHAE 10008 0.011 0.38 NO
300 GORASP1 GORASP1 GORASP1 10161 0.0086 0.37 NO
301 POT1 POT1 POT1 10213 0.0078 0.37 NO
302 PSMB6 PSMB6 PSMB6 10219 0.0077 0.37 NO
303 MAD1L1 MAD1L1 MAD1L1 10510 0.0038 0.36 NO
304 PSMC6 PSMC6 PSMC6 10581 0.0028 0.35 NO
305 PSMB5 PSMB5 PSMB5 10629 0.0022 0.35 NO
306 PSME1 PSME1 PSME1 10693 0.0011 0.34 NO
307 SKP1 SKP1 SKP1 10734 0.00053 0.34 NO
308 CLIP1 CLIP1 CLIP1 10753 0.00018 0.34 NO
309 NSL1 NSL1 NSL1 10758 0.000067 0.34 NO
310 CDC16 CDC16 CDC16 10778 -0.00015 0.34 NO
311 ACTR1A ACTR1A ACTR1A 10901 -0.002 0.33 NO
312 NUMA1 NUMA1 NUMA1 10911 -0.0022 0.33 NO
313 TUBGCP2 TUBGCP2 TUBGCP2 11012 -0.0037 0.33 NO
314 CEP63 CEP63 CEP63 11028 -0.0039 0.33 NO
315 RFWD2 RFWD2 RFWD2 11030 -0.004 0.33 NO
316 CUL1 CUL1 CUL1 11082 -0.0049 0.32 NO
317 ANAPC10 ANAPC10 ANAPC10 11087 -0.005 0.32 NO
318 DIDO1 DIDO1 DIDO1 11131 -0.0056 0.32 NO
319 MDM2 MDM2 MDM2 11147 -0.0058 0.32 NO
320 NUP133 NUP133 NUP133 11195 -0.0066 0.32 NO
321 RANBP2 RANBP2 RANBP2 11229 -0.007 0.32 NO
322 SMC3 SMC3 SMC3 11239 -0.0072 0.32 NO
323 SDCCAG8 SDCCAG8 SDCCAG8 11242 -0.0072 0.32 NO
324 TUBGCP3 TUBGCP3 TUBGCP3 11400 -0.0096 0.31 NO
325 PSMF1 PSMF1 PSMF1 11406 -0.0096 0.31 NO
326 PSMA2 PSMA2 PSMA2 11435 -0.01 0.3 NO
327 PPP2CB PPP2CB PPP2CB 11558 -0.012 0.3 NO
328 AHCTF1 AHCTF1 AHCTF1 11598 -0.013 0.3 NO
329 AKAP9 AKAP9 AKAP9 11630 -0.014 0.29 NO
330 RAD17 RAD17 RAD17 11668 -0.014 0.29 NO
331 ANAPC2 ANAPC2 ANAPC2 11787 -0.016 0.29 NO
332 HIST1H2BK HIST1H2BK HIST1H2BK 11891 -0.018 0.28 NO
333 POLD4 POLD4 POLD4 11922 -0.018 0.28 NO
334 CDK6 CDK6 CDK6 12086 -0.021 0.27 NO
335 STAG1 STAG1 STAG1 12089 -0.021 0.27 NO
336 RB1 RB1 RB1 12314 -0.025 0.26 NO
337 HIST1H4K HIST1H4K HIST1H4K 12391 -0.027 0.25 NO
338 TERF2 TERF2 TERF2 12401 -0.027 0.25 NO
339 HIST1H4I HIST1H4I HIST1H4I 12568 -0.03 0.24 NO
340 HIST1H2BE HIST1H2BE HIST1H2BE 12669 -0.032 0.24 NO
341 TINF2 TINF2 TINF2 12691 -0.033 0.24 NO
342 MIS12 MIS12 MIS12 12743 -0.034 0.24 NO
343 CLASP1 CLASP1 CLASP1 12808 -0.035 0.23 NO
344 CDKN1B CDKN1B CDKN1B 12848 -0.036 0.23 NO
345 PAFAH1B1 PAFAH1B1 PAFAH1B1 12863 -0.036 0.23 NO
346 TERF2IP TERF2IP TERF2IP 12970 -0.038 0.23 NO
347 CEP70 CEP70 CEP70 13019 -0.04 0.22 NO
348 CDKN1A CDKN1A CDKN1A 13155 -0.043 0.22 NO
349 CEP57 CEP57 CEP57 13178 -0.044 0.22 NO
350 PPP2R5C PPP2R5C PPP2R5C 13195 -0.044 0.22 NO
351 DYRK1A DYRK1A DYRK1A 13306 -0.046 0.21 NO
352 HIST2H2BE HIST2H2BE HIST2H2BE 13336 -0.047 0.21 NO
353 HIST1H2AE HIST1H2AE HIST1H2AE 13349 -0.047 0.21 NO
354 BTRC BTRC BTRC 13409 -0.048 0.21 NO
355 TUBGCP6 TUBGCP6 TUBGCP6 13415 -0.048 0.21 NO
356 TP53 TP53 TP53 13854 -0.06 0.18 NO
357 HIST1H2BD HIST1H2BD HIST1H2BD 13993 -0.063 0.18 NO
358 SYNE1 SYNE1 SYNE1 14060 -0.065 0.17 NO
359 SYNE2 SYNE2 SYNE2 14243 -0.071 0.16 NO
360 PPP2R5A PPP2R5A PPP2R5A 14363 -0.075 0.16 NO
361 HIST1H2AC HIST1H2AC HIST1H2AC 14383 -0.075 0.16 NO
362 HIST2H2AA3 HIST2H2AA3 HIST2H2AA3 14419 -0.077 0.16 NO
363 PRKACA PRKACA PRKACA 14668 -0.085 0.15 NO
364 TK2 TK2 TK2 14701 -0.086 0.15 NO
365 TUBGCP5 TUBGCP5 TUBGCP5 14723 -0.087 0.15 NO
366 CENPC1 CENPC1 CENPC1 14733 -0.088 0.15 NO
367 RBL2 RBL2 RBL2 14964 -0.098 0.14 NO
368 LIN52 LIN52 LIN52 15083 -0.1 0.13 NO
369 PPP2R1B PPP2R1B PPP2R1B 15145 -0.1 0.13 NO
370 NDEL1 NDEL1 NDEL1 15228 -0.11 0.13 NO
371 SUN2 SUN2 SUN2 15485 -0.12 0.11 NO
372 CCND1 CCND1 CCND1 15847 -0.14 0.095 NO
373 NINL NINL NINL 15861 -0.14 0.097 NO
374 STAG3 STAG3 STAG3 16042 -0.16 0.089 NO
375 HIST1H4J HIST1H4J HIST1H4J 16660 -0.21 0.057 NO
376 FKBP6 FKBP6 FKBP6 16918 -0.24 0.047 NO

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

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME RNA POL II TRANSCRIPTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME CELL CYCLE MITOTIC

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 RCC1 RCC1 RCC1 1941 0.23 -0.072 YES
2 TAF4B TAF4B TAF4B 2370 0.2 -0.063 YES
3 NUP37 NUP37 NUP37 3033 0.17 -0.073 YES
4 NUP188 NUP188 NUP188 3118 0.16 -0.051 YES
5 NUP93 NUP93 NUP93 3299 0.15 -0.036 YES
6 NUP210 NUP210 NUP210 3337 0.15 -0.013 YES
7 NUP62 NUP62 NUP62 3421 0.15 0.0072 YES
8 NUP107 NUP107 NUP107 3450 0.15 0.03 YES
9 GTF2H2B GTF2H2B GTF2H2B 3651 0.14 0.042 YES
10 NUP43 NUP43 NUP43 3727 0.14 0.06 YES
11 GTF2H2 GTF2H2 GTF2H2 3730 0.14 0.083 YES
12 RAN RAN RAN 3951 0.13 0.092 YES
13 NUP205 NUP205 NUP205 3971 0.13 0.11 YES
14 NUP155 NUP155 NUP155 4261 0.12 0.12 YES
15 VPS37C VPS37C VPS37C 4280 0.12 0.13 YES
16 TAF12 TAF12 TAF12 4377 0.12 0.15 YES
17 TAF6 TAF6 TAF6 4439 0.11 0.16 YES
18 NUP85 NUP85 NUP85 4786 0.1 0.16 YES
19 TCEB1 TCEB1 TCEB1 4897 0.1 0.17 YES
20 POLR2D POLR2D POLR2D 5178 0.092 0.17 YES
21 TBP TBP TBP 5225 0.091 0.18 YES
22 RNGTT RNGTT RNGTT 5400 0.087 0.19 YES
23 RANBP1 RANBP1 RANBP1 5401 0.087 0.2 YES
24 GTF2E2 GTF2E2 GTF2E2 5434 0.086 0.21 YES
25 SSRP1 SSRP1 SSRP1 5545 0.083 0.22 YES
26 RDBP RDBP RDBP 5906 0.075 0.21 YES
27 GTF2H1 GTF2H1 GTF2H1 5939 0.074 0.22 YES
28 POLR2H POLR2H POLR2H 5946 0.074 0.24 YES
29 POLR2G POLR2G POLR2G 5971 0.074 0.25 YES
30 GTF2H3 GTF2H3 GTF2H3 6050 0.072 0.25 YES
31 SEH1L SEH1L SEH1L 6075 0.072 0.26 YES
32 NCBP2 NCBP2 NCBP2 6133 0.071 0.27 YES
33 TCEB3 TCEB3 TCEB3 6253 0.069 0.28 YES
34 NUPL1 NUPL1 NUPL1 6360 0.067 0.28 YES
35 VPS37A VPS37A VPS37A 6415 0.066 0.29 YES
36 TAF9 TAF9 TAF9 6583 0.063 0.29 YES
37 NUP35 NUP35 NUP35 6783 0.059 0.29 YES
38 NCBP1 NCBP1 NCBP1 6825 0.059 0.3 YES
39 TAF13 TAF13 TAF13 7047 0.055 0.29 YES
40 SUPT5H SUPT5H SUPT5H 7092 0.054 0.3 YES
41 POLR2K POLR2K POLR2K 7315 0.05 0.3 YES
42 CTDP1 CTDP1 CTDP1 7329 0.05 0.3 YES
43 RAE1 RAE1 RAE1 7340 0.05 0.31 YES
44 MNAT1 MNAT1 MNAT1 7354 0.049 0.32 YES
45 GTF2E1 GTF2E1 GTF2E1 7523 0.047 0.32 YES
46 RNMT RNMT RNMT 7527 0.047 0.32 YES
47 GTF2F2 GTF2F2 GTF2F2 7571 0.046 0.33 YES
48 SUPT16H SUPT16H SUPT16H 7609 0.046 0.33 YES
49 GTF2B GTF2B GTF2B 7628 0.045 0.34 YES
50 COBRA1 COBRA1 COBRA1 7831 0.042 0.34 YES
51 NUPL2 NUPL2 NUPL2 7842 0.042 0.34 YES
52 TAF10 TAF10 TAF10 7879 0.042 0.35 YES
53 AAAS AAAS AAAS 7913 0.041 0.35 YES
54 VPS37B VPS37B VPS37B 7927 0.041 0.36 YES
55 POLR2I POLR2I POLR2I 7971 0.04 0.36 YES
56 POLR2B POLR2B POLR2B 8051 0.039 0.36 YES
57 POLR2L POLR2L POLR2L 8131 0.038 0.37 YES
58 WHSC2 WHSC2 WHSC2 8171 0.038 0.37 YES
59 CDK7 CDK7 CDK7 8343 0.035 0.37 NO
60 XPO1 XPO1 XPO1 8557 0.032 0.36 NO
61 TCEB2 TCEB2 TCEB2 8675 0.03 0.36 NO
62 RPS27A RPS27A RPS27A 8697 0.03 0.36 NO
63 RANGAP1 RANGAP1 RANGAP1 8813 0.028 0.36 NO
64 NUP54 NUP54 NUP54 8872 0.027 0.36 NO
65 NUP214 NUP214 NUP214 8905 0.027 0.36 NO
66 TAF11 TAF11 TAF11 9154 0.024 0.35 NO
67 ERCC2 ERCC2 ERCC2 9218 0.023 0.35 NO
68 ERCC3 ERCC3 ERCC3 9288 0.022 0.35 NO
69 POLR2J POLR2J POLR2J 9297 0.022 0.36 NO
70 SUPT4H1 SUPT4H1 SUPT4H1 9417 0.02 0.35 NO
71 TSG101 TSG101 TSG101 9509 0.018 0.35 NO
72 GTF2F1 GTF2F1 GTF2F1 9571 0.017 0.35 NO
73 NUP153 NUP153 NUP153 9575 0.017 0.35 NO
74 TAF4 TAF4 TAF4 9774 0.014 0.34 NO
75 TAF5 TAF5 TAF5 9784 0.014 0.35 NO
76 CDK9 CDK9 CDK9 9806 0.014 0.35 NO
77 TCEA1 TCEA1 TCEA1 9863 0.013 0.35 NO
78 CCNH CCNH CCNH 9975 0.011 0.34 NO
79 GTF2H4 GTF2H4 GTF2H4 9995 0.011 0.34 NO
80 UBA52 UBA52 UBA52 10003 0.011 0.34 NO
81 NUP50 NUP50 NUP50 10014 0.011 0.34 NO
82 POLR2A POLR2A POLR2A 10130 0.0091 0.34 NO
83 GTF2A2 GTF2A2 GTF2A2 10595 0.0026 0.31 NO
84 CCNT2 CCNT2 CCNT2 10601 0.0024 0.31 NO
85 TPR TPR TPR 10709 0.00086 0.31 NO
86 NMT1 NMT1 NMT1 10786 -0.00027 0.3 NO
87 POLR2C POLR2C POLR2C 11031 -0.004 0.29 NO
88 POM121 POM121 POM121 11050 -0.0044 0.29 NO
89 NUP133 NUP133 NUP133 11195 -0.0066 0.28 NO
90 RANBP2 RANBP2 RANBP2 11229 -0.007 0.28 NO
91 VPS28 VPS28 VPS28 11317 -0.0084 0.28 NO
92 TH1L TH1L TH1L 11439 -0.01 0.27 NO
93 POLR2E POLR2E POLR2E 11449 -0.01 0.28 NO
94 ELL ELL ELL 11557 -0.012 0.27 NO
95 TAF1 TAF1 TAF1 11569 -0.012 0.27 NO
96 NUP88 NUP88 NUP88 12072 -0.021 0.25 NO
97 CCNT1 CCNT1 CCNT1 12282 -0.025 0.24 NO
98 POLR2F POLR2F POLR2F 12287 -0.025 0.24 NO
99 GTF2A1 GTF2A1 GTF2A1 13556 -0.052 0.18 NO
100 NMT2 NMT2 NMT2 14951 -0.097 0.12 NO
101 VPS37D VPS37D VPS37D 16923 -0.24 0.046 NO

Figure S17.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME CELL CYCLE MITOTIC.

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

genes ES table in pathway: REACTOME CELL CYCLE CHECKPOINTS

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 CARD18 CARD18 CARD18 137 0.5 0.048 YES
2 CASP5 CASP5 CASP5 257 0.46 0.091 YES
3 CCL13 CCL13 CCL13 439 0.4 0.12 YES
4 CXCL1 CXCL1 CXCL1 457 0.4 0.17 YES
5 IL18 IL18 IL18 520 0.39 0.21 YES
6 MAPK13 MAPK13 MAPK13 560 0.38 0.25 YES
7 IL1B IL1B IL1B 638 0.36 0.28 YES
8 IL8 IL8 IL8 782 0.34 0.31 YES
9 PYCARD PYCARD PYCARD 800 0.34 0.35 YES
10 PSTPIP1 PSTPIP1 PSTPIP1 907 0.32 0.38 YES
11 NLRC4 NLRC4 NLRC4 976 0.32 0.41 YES
12 BIRC3 BIRC3 BIRC3 1035 0.31 0.44 YES
13 CARD9 CARD9 CARD9 1036 0.31 0.47 YES
14 TNF TNF TNF 1046 0.31 0.51 YES
15 NOD2 NOD2 NOD2 1074 0.31 0.54 YES
16 CARD6 CARD6 CARD6 1221 0.29 0.56 YES
17 CASP1 CASP1 CASP1 1235 0.29 0.59 YES
18 CCL5 CCL5 CCL5 1500 0.26 0.61 YES
19 CCL8 CCL8 CCL8 1862 0.24 0.61 YES
20 NLRP3 NLRP3 NLRP3 1933 0.23 0.64 YES
21 RIPK2 RIPK2 RIPK2 2024 0.22 0.65 YES
22 NAIP NAIP NAIP 2382 0.2 0.66 YES
23 MEFV MEFV MEFV 2502 0.19 0.67 YES
24 NLRP1 NLRP1 NLRP1 3304 0.15 0.64 NO
25 CASP8 CASP8 CASP8 4134 0.12 0.61 NO
26 IL6 IL6 IL6 4587 0.11 0.6 NO
27 NOD1 NOD1 NOD1 4941 0.099 0.59 NO
28 MAP3K7 MAP3K7 MAP3K7 5063 0.095 0.59 NO
29 MAPK12 MAPK12 MAPK12 5577 0.082 0.57 NO
30 MAPK3 MAPK3 MAPK3 5609 0.082 0.58 NO
31 IKBKG IKBKG IKBKG 5771 0.078 0.58 NO
32 NFKBIB NFKBIB NFKBIB 6539 0.063 0.54 NO
33 HSP90AB1 HSP90AB1 HSP90AB1 7256 0.051 0.5 NO
34 TNFAIP3 TNFAIP3 TNFAIP3 7548 0.046 0.49 NO
35 HSP90B1 HSP90B1 HSP90B1 7804 0.043 0.48 NO
36 HSP90AA1 HSP90AA1 HSP90AA1 7854 0.042 0.49 NO
37 XIAP XIAP XIAP 9455 0.019 0.4 NO
38 SUGT1 SUGT1 SUGT1 9506 0.018 0.4 NO
39 CCL2 CCL2 CCL2 9545 0.018 0.4 NO
40 RELA RELA RELA 9664 0.016 0.39 NO
41 NFKB1 NFKB1 NFKB1 9885 0.013 0.38 NO
42 IKBKB IKBKB IKBKB 9916 0.012 0.38 NO
43 CXCL2 CXCL2 CXCL2 10615 0.0023 0.34 NO
44 ERBB2IP ERBB2IP ERBB2IP 10934 -0.0025 0.32 NO
45 TAB2 TAB2 TAB2 11209 -0.0068 0.31 NO
46 MAPK1 MAPK1 MAPK1 11247 -0.0072 0.31 NO
47 BIRC2 BIRC2 BIRC2 11284 -0.0079 0.31 NO
48 MAPK9 MAPK9 MAPK9 11597 -0.013 0.29 NO
49 MAPK14 MAPK14 MAPK14 11602 -0.013 0.29 NO
50 CARD8 CARD8 CARD8 11620 -0.013 0.29 NO
51 TAB3 TAB3 TAB3 11793 -0.016 0.28 NO
52 TRIP6 TRIP6 TRIP6 12491 -0.028 0.25 NO
53 TAB1 TAB1 TAB1 13035 -0.04 0.22 NO
54 TRAF6 TRAF6 TRAF6 13407 -0.048 0.2 NO
55 CCL11 CCL11 CCL11 13445 -0.049 0.21 NO
56 NFKBIA NFKBIA NFKBIA 13481 -0.05 0.21 NO
57 MAPK10 MAPK10 MAPK10 13524 -0.051 0.22 NO
58 CHUK CHUK CHUK 13904 -0.061 0.2 NO
59 MAPK11 MAPK11 MAPK11 14030 -0.064 0.2 NO
60 MAPK8 MAPK8 MAPK8 14556 -0.081 0.18 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 CELL CYCLE CHECKPOINTS.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME CELL CYCLE CHECKPOINTS, 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 CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.62 1.7 0.032 0.3 0.77 0.55 0.21 0.44 0.13 0.071
KEGG FATTY ACID METABOLISM 40 genes.ES.table 0.7 1.6 0.038 0.35 0.9 0.72 0.17 0.6 0.18 0.076
KEGG GLYCINE SERINE AND THREONINE METABOLISM 31 genes.ES.table 0.78 1.7 0.0058 0.28 0.82 0.84 0.18 0.69 0.13 0.059
KEGG CYSTEINE AND METHIONINE METABOLISM 34 genes.ES.table 0.57 1.7 0.018 0.29 0.78 0.38 0.11 0.34 0.12 0.067
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 44 genes.ES.table 0.62 1.7 0.035 0.31 0.82 0.73 0.17 0.61 0.14 0.067
KEGG LYSINE DEGRADATION 44 genes.ES.table 0.59 2 0.0019 0.21 0.17 0.32 0.12 0.28 0 0.057
KEGG STARCH AND SUCROSE METABOLISM 48 genes.ES.table 0.65 1.6 0.032 0.36 0.96 0.52 0.11 0.46 0.21 0.073
KEGG PYRUVATE METABOLISM 39 genes.ES.table 0.59 1.8 0.008 0.28 0.44 0.46 0.11 0.41 0 0.059
KEGG PROPANOATE METABOLISM 32 genes.ES.table 0.72 1.9 0 0.22 0.3 0.75 0.17 0.62 0 0.049
KEGG RETINOL METABOLISM 62 genes.ES.table 0.77 1.6 0.006 0.34 0.91 0.61 0.1 0.55 0.18 0.071
genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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 AADAT AADAT AADAT 27 0.61 0.11 YES
2 BBOX1 BBOX1 BBOX1 51 0.56 0.21 YES
3 AASS AASS AASS 136 0.45 0.29 YES
4 OGDHL OGDHL OGDHL 443 0.32 0.33 YES
5 EHHADH EHHADH EHHADH 472 0.31 0.39 YES
6 PIPOX PIPOX PIPOX 523 0.3 0.44 YES
7 GCDH GCDH GCDH 952 0.22 0.46 YES
8 ALDH7A1 ALDH7A1 ALDH7A1 1138 0.19 0.48 YES
9 ALDH2 ALDH2 ALDH2 1329 0.18 0.5 YES
10 ACAT1 ACAT1 ACAT1 1540 0.16 0.52 YES
11 ACAT2 ACAT2 ACAT2 1658 0.15 0.54 YES
12 ALDH9A1 ALDH9A1 ALDH9A1 1827 0.14 0.55 YES
13 SETD7 SETD7 SETD7 1834 0.14 0.58 YES
14 HADH HADH HADH 2072 0.12 0.59 YES
15 ALDH1B1 ALDH1B1 ALDH1B1 2519 0.1 0.58 NO
16 ECHS1 ECHS1 ECHS1 2984 0.082 0.57 NO
17 OGDH OGDH OGDH 3145 0.077 0.57 NO
18 TMLHE TMLHE TMLHE 3714 0.059 0.55 NO
19 HADHA HADHA HADHA 4099 0.049 0.54 NO
20 DLST DLST DLST 4217 0.047 0.54 NO
21 PLOD1 PLOD1 PLOD1 4516 0.04 0.53 NO
22 SETD2 SETD2 SETD2 4849 0.033 0.52 NO
23 AASDH AASDH AASDH 5874 0.014 0.46 NO
24 SUV39H1 SUV39H1 SUV39H1 5928 0.014 0.46 NO
25 AASDHPPT AASDHPPT AASDHPPT 6249 0.0082 0.45 NO
26 PLOD3 PLOD3 PLOD3 6909 -0.0016 0.41 NO
27 SUV420H1 SUV420H1 SUV420H1 7096 -0.0044 0.4 NO
28 ALDH3A2 ALDH3A2 ALDH3A2 7358 -0.0084 0.39 NO
29 EHMT1 EHMT1 EHMT1 8100 -0.019 0.35 NO
30 SETD1A SETD1A SETD1A 8348 -0.022 0.34 NO
31 DOT1L DOT1L DOT1L 8929 -0.031 0.31 NO
32 WHSC1L1 WHSC1L1 WHSC1L1 9053 -0.032 0.31 NO
33 ASH1L ASH1L ASH1L 9157 -0.034 0.31 NO
34 NSD1 NSD1 NSD1 9723 -0.043 0.29 NO
35 SETMAR SETMAR SETMAR 10680 -0.058 0.24 NO
36 SETD1B SETD1B SETD1B 10964 -0.063 0.24 NO
37 SETDB2 SETDB2 SETDB2 11093 -0.065 0.24 NO
38 PLOD2 PLOD2 PLOD2 11783 -0.08 0.22 NO
39 SETD8 SETD8 SETD8 12034 -0.085 0.22 NO
40 WHSC1 WHSC1 WHSC1 12251 -0.09 0.22 NO
41 SUV39H2 SUV39H2 SUV39H2 12970 -0.11 0.2 NO
42 SETDB1 SETDB1 SETDB1 13020 -0.11 0.22 NO
43 SUV420H2 SUV420H2 SUV420H2 13276 -0.12 0.23 NO
44 EHMT2 EHMT2 EHMT2 13591 -0.13 0.23 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 CITRATE CYCLE TCA CYCLE.

Figure S22.  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 FATTY ACID METABOLISM

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 ALDH6A1 ALDH6A1 ALDH6A1 407 0.33 0.046 YES
2 ABAT ABAT ABAT 434 0.32 0.11 YES
3 ACACB ACACB ACACB 470 0.31 0.18 YES
4 EHHADH EHHADH EHHADH 472 0.31 0.24 YES
5 MUT MUT MUT 847 0.23 0.27 YES
6 ACADM ACADM ACADM 1048 0.2 0.3 YES
7 ALDH7A1 ALDH7A1 ALDH7A1 1138 0.19 0.33 YES
8 ACSS2 ACSS2 ACSS2 1195 0.19 0.37 YES
9 MLYCD MLYCD MLYCD 1299 0.18 0.4 YES
10 ALDH2 ALDH2 ALDH2 1329 0.18 0.44 YES
11 LDHC LDHC LDHC 1449 0.16 0.46 YES
12 ACAT1 ACAT1 ACAT1 1540 0.16 0.49 YES
13 MCEE MCEE MCEE 1550 0.15 0.52 YES
14 LDHAL6B LDHAL6B LDHAL6B 1598 0.15 0.55 YES
15 ACAT2 ACAT2 ACAT2 1658 0.15 0.58 YES
16 SUCLG2 SUCLG2 SUCLG2 1793 0.14 0.6 YES
17 ALDH9A1 ALDH9A1 ALDH9A1 1827 0.14 0.63 YES
18 PCCA PCCA PCCA 1855 0.13 0.65 YES
19 PCCB PCCB PCCB 2044 0.12 0.67 YES
20 HIBCH HIBCH HIBCH 2181 0.12 0.68 YES
21 SUCLG1 SUCLG1 SUCLG1 2286 0.11 0.7 YES
22 ALDH1B1 ALDH1B1 ALDH1B1 2519 0.1 0.71 YES
23 ACSS3 ACSS3 ACSS3 2794 0.089 0.71 YES
24 ECHS1 ECHS1 ECHS1 2984 0.082 0.72 YES
25 HADHA HADHA HADHA 4099 0.049 0.67 NO
26 ALDH3A2 ALDH3A2 ALDH3A2 7358 -0.0084 0.48 NO
27 LDHA LDHA LDHA 7840 -0.016 0.46 NO
28 SUCLA2 SUCLA2 SUCLA2 7956 -0.017 0.46 NO
29 LDHAL6A LDHAL6A LDHAL6A 9038 -0.032 0.4 NO
30 ACACA ACACA ACACA 10802 -0.06 0.32 NO
31 LDHB LDHB LDHB 13920 -0.14 0.17 NO
32 ACSS1 ACSS1 ACSS1 15739 -0.22 0.11 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 FATTY ACID METABOLISM.

Figure S24.  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 GLYCINE SERINE AND THREONINE 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 ACOT12 ACOT12 ACOT12 104 0.48 0.078 YES
2 PCK1 PCK1 PCK1 180 0.43 0.15 YES
3 ACACB ACACB ACACB 470 0.31 0.19 YES
4 PCK2 PCK2 PCK2 471 0.31 0.24 YES
5 LDHD LDHD LDHD 663 0.26 0.28 YES
6 PKLR PKLR PKLR 730 0.25 0.32 YES
7 HAGH HAGH HAGH 861 0.23 0.35 YES
8 ALDH7A1 ALDH7A1 ALDH7A1 1138 0.19 0.37 YES
9 ACYP2 ACYP2 ACYP2 1154 0.19 0.4 YES
10 ACSS2 ACSS2 ACSS2 1195 0.19 0.43 YES
11 ALDH2 ALDH2 ALDH2 1329 0.18 0.45 YES
12 LDHC LDHC LDHC 1449 0.16 0.47 YES
13 GRHPR GRHPR GRHPR 1523 0.16 0.5 YES
14 ACAT1 ACAT1 ACAT1 1540 0.16 0.52 YES
15 LDHAL6B LDHAL6B LDHAL6B 1598 0.15 0.55 YES
16 ACAT2 ACAT2 ACAT2 1658 0.15 0.57 YES
17 ALDH9A1 ALDH9A1 ALDH9A1 1827 0.14 0.58 YES
18 PC PC PC 2018 0.12 0.59 YES
19 ALDH1B1 ALDH1B1 ALDH1B1 2519 0.1 0.58 NO
20 MDH1 MDH1 MDH1 3259 0.073 0.55 NO
21 DLD DLD DLD 3771 0.057 0.54 NO
22 PDHB PDHB PDHB 4935 0.031 0.47 NO
23 PDHA1 PDHA1 PDHA1 5542 0.02 0.44 NO
24 GLO1 GLO1 GLO1 5549 0.02 0.45 NO
25 ME3 ME3 ME3 6620 0.0029 0.39 NO
26 ME1 ME1 ME1 6789 0.00032 0.38 NO
27 ALDH3A2 ALDH3A2 ALDH3A2 7358 -0.0084 0.35 NO
28 MDH2 MDH2 MDH2 7820 -0.015 0.32 NO
29 LDHA LDHA LDHA 7840 -0.016 0.32 NO
30 DLAT DLAT DLAT 8323 -0.022 0.3 NO
31 LDHAL6A LDHAL6A LDHAL6A 9038 -0.032 0.27 NO
32 ME2 ME2 ME2 10097 -0.049 0.22 NO
33 ACACA ACACA ACACA 10802 -0.06 0.19 NO
34 ACYP1 ACYP1 ACYP1 12175 -0.088 0.12 NO
35 LDHB LDHB LDHB 13920 -0.14 0.049 NO
36 AKR1B1 AKR1B1 AKR1B1 14188 -0.15 0.06 NO
37 ACSS1 ACSS1 ACSS1 15739 -0.22 0.011 NO
38 PKM2 PKM2 PKM2 16111 -0.25 0.033 NO
39 HAGHL HAGHL HAGHL 17012 -0.33 0.04 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 GLYCINE SERINE AND THREONINE METABOLISM.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCINE SERINE AND THREONINE 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 CYSTEINE AND METHIONINE METABOLISM

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 FOXO1 FOXO1 FOXO1 1734 0.14 0.0034 YES
2 CDKN1A CDKN1A CDKN1A 1971 0.13 0.082 YES
3 MTOR MTOR MTOR 1982 0.13 0.17 YES
4 CASP9 CASP9 CASP9 2594 0.097 0.21 YES
5 FOXO4 FOXO4 FOXO4 3257 0.073 0.22 YES
6 BAD BAD BAD 3376 0.069 0.27 YES
7 NR4A1 NR4A1 NR4A1 3454 0.067 0.31 YES
8 AKT1 AKT1 AKT1 3694 0.059 0.34 YES
9 PHLPP1 PHLPP1 PHLPP1 3706 0.059 0.38 YES
10 CDKN1B CDKN1B CDKN1B 3744 0.058 0.42 YES
11 AKT2 AKT2 AKT2 3910 0.053 0.45 YES
12 MDM2 MDM2 MDM2 4626 0.038 0.44 NO
13 TSC2 TSC2 TSC2 5515 0.021 0.4 NO
14 AKT3 AKT3 AKT3 5569 0.02 0.41 NO
15 RPS6KB2 RPS6KB2 RPS6KB2 5654 0.018 0.42 NO
16 PDPK1 PDPK1 PDPK1 6166 0.0097 0.4 NO
17 PTEN PTEN PTEN 6792 0.00028 0.36 NO
18 MAPKAP1 MAPKAP1 MAPKAP1 7328 -0.008 0.34 NO
19 FOXO3 FOXO3 FOXO3 7455 -0.0098 0.34 NO
20 MLST8 MLST8 MLST8 7575 -0.012 0.34 NO
21 RICTOR RICTOR RICTOR 7726 -0.014 0.34 NO
22 CHUK CHUK CHUK 7870 -0.016 0.35 NO
23 AKT1S1 AKT1S1 AKT1S1 8853 -0.03 0.31 NO
24 CREB1 CREB1 CREB1 9884 -0.046 0.29 NO
25 GSK3A GSK3A GSK3A 10493 -0.055 0.29 NO
26 TRIB3 TRIB3 TRIB3 10936 -0.062 0.31 NO
27 THEM4 THEM4 THEM4 12555 -0.097 0.29 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 CYSTEINE AND METHIONINE METABOLISM.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYSTEINE AND METHIONINE 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 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 HAO2 HAO2 HAO2 9 0.74 0.064 YES
2 XDH XDH XDH 37 0.59 0.11 YES
3 DAO DAO DAO 90 0.5 0.15 YES
4 SLC27A2 SLC27A2 SLC27A2 266 0.38 0.18 YES
5 AGXT AGXT AGXT 272 0.37 0.21 YES
6 PEX11G PEX11G PEX11G 337 0.35 0.24 YES
7 HAO1 HAO1 HAO1 438 0.32 0.26 YES
8 EHHADH EHHADH EHHADH 472 0.31 0.28 YES
9 EPHX2 EPHX2 EPHX2 477 0.31 0.31 YES
10 ACOX2 ACOX2 ACOX2 511 0.3 0.33 YES
11 PIPOX PIPOX PIPOX 523 0.3 0.36 YES
12 PXMP2 PXMP2 PXMP2 588 0.28 0.38 YES
13 ACSL1 ACSL1 ACSL1 673 0.26 0.4 YES
14 SCP2 SCP2 SCP2 706 0.26 0.42 YES
15 BAAT BAAT BAAT 793 0.24 0.43 YES
16 NOS2 NOS2 NOS2 829 0.23 0.45 YES
17 CAT CAT CAT 938 0.22 0.46 YES
18 NUDT12 NUDT12 NUDT12 961 0.21 0.48 YES
19 PHYH PHYH PHYH 1212 0.19 0.48 YES
20 ACOX1 ACOX1 ACOX1 1249 0.18 0.5 YES
21 DHRS4 DHRS4 DHRS4 1282 0.18 0.51 YES
22 MLYCD MLYCD MLYCD 1299 0.18 0.53 YES
23 HACL1 HACL1 HACL1 1614 0.15 0.52 YES
24 ACAA1 ACAA1 ACAA1 1723 0.14 0.53 YES
25 PEX1 PEX1 PEX1 1762 0.14 0.54 YES
26 PECR PECR PECR 1780 0.14 0.55 YES
27 HMGCL HMGCL HMGCL 1881 0.13 0.55 YES
28 GSTK1 GSTK1 GSTK1 1913 0.13 0.56 YES
29 MPV17L MPV17L MPV17L 1966 0.13 0.57 YES
30 PAOX PAOX PAOX 2077 0.12 0.58 YES
31 PEX7 PEX7 PEX7 2313 0.11 0.57 YES
32 PEX14 PEX14 PEX14 2316 0.11 0.58 YES
33 DDO DDO DDO 2504 0.1 0.58 YES
34 HSD17B4 HSD17B4 HSD17B4 2581 0.098 0.58 YES
35 SOD1 SOD1 SOD1 2615 0.096 0.59 YES
36 PXMP4 PXMP4 PXMP4 2679 0.094 0.6 YES
37 SLC25A17 SLC25A17 SLC25A17 2742 0.091 0.6 YES
38 CRAT CRAT CRAT 2757 0.09 0.61 YES
39 PEX12 PEX12 PEX12 2816 0.088 0.61 YES
40 PEX19 PEX19 PEX19 2851 0.087 0.62 YES
41 PEX16 PEX16 PEX16 2875 0.086 0.62 YES
42 CROT CROT CROT 2887 0.085 0.63 YES
43 ACOX3 ACOX3 ACOX3 2983 0.082 0.63 YES
44 PEX3 PEX3 PEX3 2994 0.082 0.64 YES
45 ACOT8 ACOT8 ACOT8 3566 0.063 0.61 NO
46 IDH1 IDH1 IDH1 3633 0.061 0.61 NO
47 PEX6 PEX6 PEX6 3778 0.057 0.61 NO
48 DECR2 DECR2 DECR2 3797 0.056 0.61 NO
49 ECH1 ECH1 ECH1 3900 0.054 0.61 NO
50 ABCD4 ABCD4 ABCD4 3901 0.054 0.62 NO
51 PEX13 PEX13 PEX13 4143 0.048 0.61 NO
52 ABCD3 ABCD3 ABCD3 4203 0.047 0.61 NO
53 AMACR AMACR AMACR 4214 0.047 0.61 NO
54 PEX10 PEX10 PEX10 4496 0.04 0.6 NO
55 PRDX5 PRDX5 PRDX5 4981 0.031 0.57 NO
56 ACSL5 ACSL5 ACSL5 4992 0.03 0.58 NO
57 PEX26 PEX26 PEX26 5173 0.027 0.57 NO
58 PMVK PMVK PMVK 5488 0.021 0.55 NO
59 IDH2 IDH2 IDH2 5651 0.019 0.55 NO
60 PRDX1 PRDX1 PRDX1 6115 0.01 0.52 NO
61 MVK MVK MVK 6374 0.0063 0.5 NO
62 SOD2 SOD2 SOD2 6554 0.0038 0.5 NO
63 PEX11A PEX11A PEX11A 6769 0.0006 0.48 NO
64 PEX5 PEX5 PEX5 6929 -0.0019 0.48 NO
65 PEX11B PEX11B PEX11B 8066 -0.019 0.41 NO
66 NUDT19 NUDT19 NUDT19 9018 -0.032 0.36 NO
67 PEX2 PEX2 PEX2 9882 -0.046 0.32 NO
68 AGPS AGPS AGPS 11088 -0.065 0.25 NO
69 ACSL6 ACSL6 ACSL6 12659 -0.1 0.17 NO
70 ABCD1 ABCD1 ABCD1 13026 -0.11 0.16 NO
71 GNPAT GNPAT GNPAT 13918 -0.14 0.12 NO
72 ACSL3 ACSL3 ACSL3 14202 -0.15 0.12 NO
73 FAR1 FAR1 FAR1 14287 -0.15 0.13 NO
74 MPV17 MPV17 MPV17 14387 -0.16 0.14 NO
75 ABCD2 ABCD2 ABCD2 15162 -0.19 0.11 NO
76 ACSL4 ACSL4 ACSL4 15436 -0.2 0.11 NO
77 FAR2 FAR2 FAR2 15524 -0.21 0.12 NO

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

Figure S30.  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 LYSINE DEGRADATION

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GYS2 GYS2 GYS2 19 0.63 0.066 YES
2 PFKFB1 PFKFB1 PFKFB1 52 0.56 0.12 YES
3 ALDOB ALDOB ALDOB 140 0.45 0.16 YES
4 PCK1 PCK1 PCK1 180 0.43 0.21 YES
5 FBP1 FBP1 FBP1 189 0.42 0.25 YES
6 ENO3 ENO3 ENO3 342 0.35 0.28 YES
7 PCK2 PCK2 PCK2 471 0.31 0.3 YES
8 AGL AGL AGL 676 0.26 0.32 YES
9 PHKG1 PHKG1 PHKG1 683 0.26 0.35 YES
10 PKLR PKLR PKLR 730 0.25 0.37 YES
11 FBP2 FBP2 FBP2 903 0.22 0.38 YES
12 UGP2 UGP2 UGP2 1021 0.21 0.4 YES
13 PGM2 PGM2 PGM2 1113 0.2 0.42 YES
14 ALDOC ALDOC ALDOC 1114 0.2 0.44 YES
15 PYGL PYGL PYGL 1189 0.19 0.45 YES
16 SLC25A10 SLC25A10 SLC25A10 1469 0.16 0.45 YES
17 PGM1 PGM1 PGM1 1521 0.16 0.47 YES
18 GOT1 GOT1 GOT1 1617 0.15 0.48 YES
19 GOT2 GOT2 GOT2 1896 0.13 0.48 YES
20 GBE1 GBE1 GBE1 1987 0.13 0.48 YES
21 PC PC PC 2018 0.12 0.5 YES
22 PPP2R1B PPP2R1B PPP2R1B 2890 0.085 0.45 NO
23 PHKA1 PHKA1 PHKA1 3110 0.078 0.45 NO
24 MDH1 MDH1 MDH1 3259 0.073 0.45 NO
25 SLC25A13 SLC25A13 SLC25A13 3540 0.064 0.44 NO
26 PHKG2 PHKG2 PHKG2 3631 0.061 0.44 NO
27 CALM1 CALM1 CALM1 4442 0.042 0.4 NO
28 PPP2CB PPP2CB PPP2CB 4616 0.038 0.39 NO
29 PFKL PFKL PFKL 5109 0.028 0.37 NO
30 SLC25A11 SLC25A11 SLC25A11 5268 0.025 0.36 NO
31 SLC25A1 SLC25A1 SLC25A1 5472 0.021 0.35 NO
32 PRKACA PRKACA PRKACA 5666 0.018 0.34 NO
33 PHKB PHKB PHKB 6131 0.01 0.32 NO
34 GPI GPI GPI 6307 0.0073 0.31 NO
35 TPI1 TPI1 TPI1 6686 0.002 0.29 NO
36 PGAM1 PGAM1 PGAM1 6727 0.0012 0.29 NO
37 PRKACB PRKACB PRKACB 6859 -0.00077 0.28 NO
38 PPP2CA PPP2CA PPP2CA 7017 -0.0032 0.27 NO
39 PPP2R5D PPP2R5D PPP2R5D 7127 -0.005 0.27 NO
40 PGK1 PGK1 PGK1 7286 -0.0073 0.26 NO
41 MDH2 MDH2 MDH2 7820 -0.015 0.23 NO
42 PHKA2 PHKA2 PHKA2 8107 -0.019 0.22 NO
43 CALM2 CALM2 CALM2 8576 -0.026 0.19 NO
44 PYGB PYGB PYGB 10296 -0.052 0.099 NO
45 ENO1 ENO1 ENO1 10555 -0.056 0.09 NO
46 GAPDH GAPDH GAPDH 10813 -0.06 0.082 NO
47 GAPDHS GAPDHS GAPDHS 11767 -0.079 0.036 NO
48 PYGM PYGM PYGM 12075 -0.086 0.028 NO
49 GYS1 GYS1 GYS1 12091 -0.086 0.036 NO
50 PPP2R1A PPP2R1A PPP2R1A 12160 -0.088 0.042 NO
51 CALM3 CALM3 CALM3 12203 -0.089 0.049 NO
52 GYG2 GYG2 GYG2 12472 -0.095 0.043 NO
53 PFKFB4 PFKFB4 PFKFB4 13653 -0.13 -0.0099 NO
54 SLC25A12 SLC25A12 SLC25A12 13658 -0.13 0.0034 NO
55 ALDOA ALDOA ALDOA 13724 -0.13 0.014 NO
56 PGAM2 PGAM2 PGAM2 14335 -0.15 -0.0049 NO
57 PFKFB2 PFKFB2 PFKFB2 14492 -0.16 0.0032 NO
58 GYG1 GYG1 GYG1 14670 -0.17 0.011 NO
59 PFKFB3 PFKFB3 PFKFB3 14941 -0.18 0.015 NO
60 PFKM PFKM PFKM 15212 -0.2 0.02 NO
61 PKM2 PKM2 PKM2 16111 -0.25 -0.0051 NO
62 PFKP PFKP PFKP 17509 -0.44 -0.038 NO
63 ENO2 ENO2 ENO2 17602 -0.48 0.0071 NO

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

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

genes ES table in pathway: KEGG STARCH AND SUCROSE METABOLISM

Table S17.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PFKFB1 PFKFB1 PFKFB1 52 0.56 0.11 YES
2 ALDOB ALDOB ALDOB 140 0.45 0.2 YES
3 PCK1 PCK1 PCK1 180 0.43 0.29 YES
4 FBP1 FBP1 FBP1 189 0.42 0.37 YES
5 ENO3 ENO3 ENO3 342 0.35 0.44 YES
6 PCK2 PCK2 PCK2 471 0.31 0.5 YES
7 FBP2 FBP2 FBP2 903 0.22 0.52 YES
8 ALDOC ALDOC ALDOC 1114 0.2 0.55 YES
9 SLC25A10 SLC25A10 SLC25A10 1469 0.16 0.56 YES
10 GOT1 GOT1 GOT1 1617 0.15 0.58 YES
11 GOT2 GOT2 GOT2 1896 0.13 0.59 YES
12 PC PC PC 2018 0.12 0.61 YES
13 MDH1 MDH1 MDH1 3259 0.073 0.56 NO
14 SLC25A13 SLC25A13 SLC25A13 3540 0.064 0.55 NO
15 SLC25A11 SLC25A11 SLC25A11 5268 0.025 0.46 NO
16 SLC25A1 SLC25A1 SLC25A1 5472 0.021 0.46 NO
17 PRKACA PRKACA PRKACA 5666 0.018 0.45 NO
18 GPI GPI GPI 6307 0.0073 0.41 NO
19 TPI1 TPI1 TPI1 6686 0.002 0.39 NO
20 PGAM1 PGAM1 PGAM1 6727 0.0012 0.39 NO
21 PRKACB PRKACB PRKACB 6859 -0.00077 0.38 NO
22 PGK1 PGK1 PGK1 7286 -0.0073 0.36 NO
23 MDH2 MDH2 MDH2 7820 -0.015 0.33 NO
24 ENO1 ENO1 ENO1 10555 -0.056 0.19 NO
25 GAPDH GAPDH GAPDH 10813 -0.06 0.19 NO
26 GAPDHS GAPDHS GAPDHS 11767 -0.079 0.15 NO
27 SLC25A12 SLC25A12 SLC25A12 13658 -0.13 0.071 NO
28 ALDOA ALDOA ALDOA 13724 -0.13 0.095 NO
29 PGAM2 PGAM2 PGAM2 14335 -0.15 0.092 NO
30 ENO2 ENO2 ENO2 17602 -0.48 0.0071 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 STARCH AND SUCROSE METABOLISM.

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

genes ES table in pathway: KEGG PYRUVATE METABOLISM

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 GLS2 GLS2 GLS2 10 0.72 0.022 YES
2 TAT TAT TAT 21 0.63 0.042 YES
3 AADAT AADAT AADAT 27 0.61 0.061 YES
4 BBOX1 BBOX1 BBOX1 51 0.56 0.078 YES
5 IDO2 IDO2 IDO2 71 0.52 0.093 YES
6 IYD IYD IYD 81 0.51 0.11 YES
7 DAO DAO DAO 90 0.5 0.12 YES
8 BHMT BHMT BHMT 105 0.48 0.14 YES
9 TDO2 TDO2 TDO2 123 0.46 0.15 YES
10 AASS AASS AASS 136 0.45 0.17 YES
11 ACMSD ACMSD ACMSD 146 0.45 0.18 YES
12 HAL HAL HAL 154 0.44 0.19 YES
13 PRODH PRODH PRODH 163 0.44 0.21 YES
14 UROC1 UROC1 UROC1 167 0.43 0.22 YES
15 ARG1 ARG1 ARG1 188 0.42 0.23 YES
16 KMO KMO KMO 250 0.38 0.24 YES
17 CTH CTH CTH 255 0.38 0.25 YES
18 AGXT AGXT AGXT 272 0.37 0.26 YES
19 INHBC INHBC INHBC 307 0.36 0.27 YES
20 AGXT2 AGXT2 AGXT2 336 0.35 0.28 YES
21 HAAO HAAO HAAO 382 0.34 0.29 YES
22 DIO1 DIO1 DIO1 386 0.34 0.3 YES
23 OTC OTC OTC 388 0.34 0.31 YES
24 CPS1 CPS1 CPS1 394 0.33 0.32 YES
25 ALDH6A1 ALDH6A1 ALDH6A1 407 0.33 0.33 YES
26 DBH DBH DBH 413 0.33 0.34 YES
27 SLC25A15 SLC25A15 SLC25A15 421 0.33 0.35 YES
28 GSTZ1 GSTZ1 GSTZ1 431 0.32 0.36 YES
29 HAO1 HAO1 HAO1 438 0.32 0.37 YES
30 HPD HPD HPD 467 0.31 0.38 YES
31 AMDHD1 AMDHD1 AMDHD1 483 0.31 0.39 YES
32 CBS CBS CBS 506 0.3 0.4 YES
33 HDC HDC HDC 508 0.3 0.41 YES
34 CDO1 CDO1 CDO1 554 0.29 0.41 YES
35 SHMT1 SHMT1 SHMT1 594 0.28 0.42 YES
36 PNMT PNMT PNMT 625 0.27 0.43 YES
37 GPT GPT GPT 738 0.25 0.43 YES
38 BCKDHB BCKDHB BCKDHB 770 0.24 0.44 YES
39 FTCD FTCD FTCD 785 0.24 0.44 YES
40 GCDH GCDH GCDH 952 0.22 0.44 YES
41 MAT1A MAT1A MAT1A 986 0.21 0.44 YES
42 HGD HGD HGD 1080 0.2 0.45 YES
43 ALDH7A1 ALDH7A1 ALDH7A1 1138 0.19 0.45 YES
44 PAH PAH PAH 1206 0.19 0.45 YES
45 GATM GATM GATM 1230 0.18 0.46 YES
46 CCBL1 CCBL1 CCBL1 1283 0.18 0.46 YES
47 IVD IVD IVD 1303 0.18 0.46 YES
48 GPT2 GPT2 GPT2 1328 0.18 0.47 YES
49 INHBE INHBE INHBE 1332 0.17 0.47 YES
50 ASL ASL ASL 1359 0.17 0.48 YES
51 DIO2 DIO2 DIO2 1372 0.17 0.48 YES
52 AGMAT AGMAT AGMAT 1376 0.17 0.49 YES
53 FAH FAH FAH 1440 0.17 0.49 YES
54 SLC25A10 SLC25A10 SLC25A10 1469 0.16 0.49 YES
55 NAGS NAGS NAGS 1491 0.16 0.5 YES
56 DBT DBT DBT 1497 0.16 0.5 YES
57 ASS1 ASS1 ASS1 1499 0.16 0.5 YES
58 GRHPR GRHPR GRHPR 1523 0.16 0.51 YES
59 ACAT1 ACAT1 ACAT1 1540 0.16 0.51 YES
60 ADI1 ADI1 ADI1 1579 0.15 0.52 YES
61 GOT1 GOT1 GOT1 1617 0.15 0.52 YES
62 ACADSB ACADSB ACADSB 1621 0.15 0.52 YES
63 QDPR QDPR QDPR 1656 0.15 0.52 YES
64 PHGDH PHGDH PHGDH 1773 0.14 0.52 YES
65 ALDH9A1 ALDH9A1 ALDH9A1 1827 0.14 0.52 YES
66 SUOX SUOX SUOX 1839 0.13 0.53 YES
67 TST TST TST 1886 0.13 0.53 YES
68 GOT2 GOT2 GOT2 1896 0.13 0.53 YES
69 PAOX PAOX PAOX 2077 0.12 0.53 YES
70 ETHE1 ETHE1 ETHE1 2089 0.12 0.53 YES
71 INHBA INHBA INHBA 2114 0.12 0.53 YES
72 HSD17B10 HSD17B10 HSD17B10 2131 0.12 0.54 YES
73 CSAD CSAD CSAD 2141 0.12 0.54 YES
74 HIBCH HIBCH HIBCH 2181 0.12 0.54 YES
75 ACAD8 ACAD8 ACAD8 2263 0.11 0.54 YES
76 MCCC1 MCCC1 MCCC1 2340 0.11 0.54 YES
77 GAMT GAMT GAMT 2362 0.11 0.54 YES
78 DDC DDC DDC 2403 0.11 0.54 YES
79 CGA CGA CGA 2503 0.1 0.54 NO
80 GCLC GCLC GCLC 2712 0.092 0.53 NO
81 BCKDHA BCKDHA BCKDHA 2822 0.088 0.53 NO
82 MCCC2 MCCC2 MCCC2 2993 0.082 0.52 NO
83 OGDH OGDH OGDH 3145 0.077 0.51 NO
84 OAZ2 OAZ2 OAZ2 3266 0.073 0.51 NO
85 PCBD1 PCBD1 PCBD1 3354 0.07 0.51 NO
86 INHBB INHBB INHBB 3464 0.066 0.5 NO
87 ADC ADC ADC 3580 0.063 0.5 NO
88 MAT2B MAT2B MAT2B 3614 0.062 0.5 NO
89 HIBADH HIBADH HIBADH 3646 0.061 0.5 NO
90 TMLHE TMLHE TMLHE 3714 0.059 0.5 NO
91 PSMB8 PSMB8 PSMB8 3753 0.058 0.5 NO
92 DLD DLD DLD 3771 0.057 0.5 NO
93 PSMA2 PSMA2 PSMA2 3842 0.055 0.49 NO
94 ALDH4A1 ALDH4A1 ALDH4A1 4148 0.048 0.48 NO
95 DLST DLST DLST 4217 0.047 0.48 NO
96 BCAT2 BCAT2 BCAT2 4226 0.046 0.48 NO
97 GCLM GCLM GCLM 4235 0.046 0.48 NO
98 AHCY AHCY AHCY 4299 0.045 0.48 NO
99 PSAT1 PSAT1 PSAT1 4368 0.043 0.47 NO
100 PSMC3 PSMC3 PSMC3 4380 0.043 0.47 NO
101 PSME4 PSME4 PSME4 4591 0.039 0.46 NO
102 CNDP2 CNDP2 CNDP2 4617 0.038 0.46 NO
103 CCBL2 CCBL2 CCBL2 4639 0.037 0.46 NO
104 SAT1 SAT1 SAT1 4641 0.037 0.46 NO
105 AUH AUH AUH 4656 0.037 0.46 NO
106 SLC25A2 SLC25A2 SLC25A2 4711 0.036 0.46 NO
107 PSME1 PSME1 PSME1 4800 0.034 0.46 NO
108 AFMID AFMID AFMID 4826 0.034 0.46 NO
109 ARG2 ARG2 ARG2 4858 0.033 0.46 NO
110 KYNU KYNU KYNU 4887 0.032 0.46 NO
111 PSMA7 PSMA7 PSMA7 5040 0.03 0.45 NO
112 PSMC5 PSMC5 PSMC5 5113 0.028 0.45 NO
113 PSMC2 PSMC2 PSMC2 5156 0.028 0.44 NO
114 MAT2A MAT2A MAT2A 5162 0.027 0.44 NO
115 PSMD12 PSMD12 PSMD12 5611 0.019 0.42 NO
116 ODC1 ODC1 ODC1 5684 0.018 0.42 NO
117 PSMD6 PSMD6 PSMD6 5962 0.013 0.4 NO
118 MTAP MTAP MTAP 6011 0.012 0.4 NO
119 PSMB2 PSMB2 PSMB2 6092 0.011 0.39 NO
120 PSMD2 PSMD2 PSMD2 6096 0.011 0.4 NO
121 PSMF1 PSMF1 PSMF1 6138 0.01 0.39 NO
122 PSMC1 PSMC1 PSMC1 6359 0.0066 0.38 NO
123 PSMA6 PSMA6 PSMA6 6408 0.0057 0.38 NO
124 PSMC4 PSMC4 PSMC4 6422 0.0055 0.38 NO
125 PSMC6 PSMC6 PSMC6 6456 0.0051 0.38 NO
126 PSMB9 PSMB9 PSMB9 6458 0.0051 0.38 NO
127 PSMD9 PSMD9 PSMD9 6590 0.0033 0.37 NO
128 PSMD8 PSMD8 PSMD8 6640 0.0027 0.36 NO
129 PSMA3 PSMA3 PSMA3 6683 0.002 0.36 NO
130 PSMB7 PSMB7 PSMB7 6702 0.0017 0.36 NO
131 PSMB1 PSMB1 PSMB1 6767 0.00062 0.36 NO
132 PSMD3 PSMD3 PSMD3 6794 0.00023 0.36 NO
133 PSMD7 PSMD7 PSMD7 6832 -0.00016 0.36 NO
134 PSME2 PSME2 PSME2 6850 -0.00053 0.35 NO
135 PSMD13 PSMD13 PSMD13 7048 -0.0037 0.34 NO
136 PSMD11 PSMD11 PSMD11 7091 -0.0043 0.34 NO
137 MRI1 MRI1 MRI1 7285 -0.0073 0.33 NO
138 PSMA4 PSMA4 PSMA4 7374 -0.0086 0.32 NO
139 PSMA1 PSMA1 PSMA1 7839 -0.016 0.3 NO
140 PSMB3 PSMB3 PSMB3 7962 -0.017 0.29 NO
141 OAZ1 OAZ1 OAZ1 8007 -0.018 0.29 NO
142 PSMB6 PSMB6 PSMB6 8096 -0.019 0.29 NO
143 PSMA5 PSMA5 PSMA5 8343 -0.022 0.27 NO
144 PSMB10 PSMB10 PSMB10 8628 -0.027 0.26 NO
145 PSMB5 PSMB5 PSMB5 8744 -0.028 0.25 NO
146 PSMD5 PSMD5 PSMD5 8882 -0.03 0.24 NO
147 PSMD1 PSMD1 PSMD1 9008 -0.032 0.24 NO
148 SQRDL SQRDL SQRDL 9786 -0.044 0.2 NO
149 APIP APIP APIP 9943 -0.046 0.19 NO
150 PSMD10 PSMD10 PSMD10 9955 -0.047 0.19 NO
151 PSMB4 PSMB4 PSMB4 10041 -0.048 0.19 NO
152 CKMT2 CKMT2 CKMT2 10294 -0.052 0.17 NO
153 PSMD14 PSMD14 PSMD14 10679 -0.058 0.15 NO
154 ENOPH1 ENOPH1 ENOPH1 11034 -0.064 0.14 NO
155 GLUD1 GLUD1 GLUD1 11339 -0.07 0.12 NO
156 SRM SRM SRM 11631 -0.076 0.11 NO
157 AMD1 AMD1 AMD1 11720 -0.078 0.1 NO
158 PSMD4 PSMD4 PSMD4 11803 -0.08 0.1 NO
159 TH TH TH 12159 -0.088 0.084 NO
160 SMS SMS SMS 12252 -0.09 0.082 NO
161 ALDH18A1 ALDH18A1 ALDH18A1 12677 -0.1 0.061 NO
162 GLS GLS GLS 13159 -0.11 0.037 NO
163 AZIN1 AZIN1 AZIN1 13274 -0.12 0.034 NO
164 IDO1 IDO1 IDO1 13352 -0.12 0.033 NO
165 MTR MTR MTR 13478 -0.12 0.03 NO
166 TPH1 TPH1 TPH1 13787 -0.13 0.017 NO
167 OAZ3 OAZ3 OAZ3 13832 -0.14 0.019 NO
168 PSPH PSPH PSPH 13878 -0.14 0.02 NO
169 POMC POMC POMC 14310 -0.15 0.00068 NO
170 CKM CKM CKM 14463 -0.16 -0.0029 NO
171 SLC25A21 SLC25A21 SLC25A21 14824 -0.18 -0.018 NO
172 PSMA8 PSMA8 PSMA8 15049 -0.19 -0.025 NO
173 GLUL GLUL GLUL 15121 -0.19 -0.023 NO
174 LHB LHB LHB 15366 -0.2 -0.03 NO
175 PCSK1 PCSK1 PCSK1 15398 -0.2 -0.026 NO
176 AANAT AANAT AANAT 15742 -0.22 -0.038 NO
177 CKB CKB CKB 15806 -0.23 -0.034 NO
178 CKMT1A CKMT1A CKMT1A 15810 -0.23 -0.027 NO
179 BCAT1 BCAT1 BCAT1 16158 -0.25 -0.039 NO
180 DIO3 DIO3 DIO3 16561 -0.28 -0.053 NO
181 CKMT1B CKMT1B CKMT1B 16597 -0.29 -0.046 NO
182 NQO1 NQO1 NQO1 16630 -0.29 -0.039 NO
183 SLC5A5 SLC5A5 SLC5A5 17179 -0.36 -0.058 NO
184 OAT OAT OAT 17213 -0.37 -0.048 NO
185 INHA INHA INHA 17215 -0.37 -0.037 NO
186 ASNS ASNS ASNS 17475 -0.42 -0.038 NO
187 PYCR1 PYCR1 PYCR1 17490 -0.43 -0.025 NO
188 SMOX SMOX SMOX 17646 -0.52 -0.018 NO
189 SLC6A8 SLC6A8 SLC6A8 17722 -0.7 0.00034 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 PYRUVATE METABOLISM.

Figure S36.  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

genes ES table in pathway: KEGG PROPANOATE METABOLISM

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 PCK1 PCK1 PCK1 180 0.43 0.14 YES
2 OGDHL OGDHL OGDHL 443 0.32 0.24 YES
3 PCK2 PCK2 PCK2 471 0.31 0.34 YES
4 ACO1 ACO1 ACO1 1276 0.18 0.36 YES
5 SDHD SDHD SDHD 1767 0.14 0.38 YES
6 SUCLG2 SUCLG2 SUCLG2 1793 0.14 0.43 YES
7 PC PC PC 2018 0.12 0.46 YES
8 SDHB SDHB SDHB 2250 0.11 0.48 YES
9 SUCLG1 SUCLG1 SUCLG1 2286 0.11 0.52 YES
10 FH FH FH 2392 0.11 0.55 YES
11 OGDH OGDH OGDH 3145 0.077 0.54 YES
12 SDHA SDHA SDHA 3177 0.076 0.56 YES
13 MDH1 MDH1 MDH1 3259 0.073 0.58 YES
14 ACO2 ACO2 ACO2 3483 0.066 0.59 YES
15 IDH1 IDH1 IDH1 3633 0.061 0.6 YES
16 DLD DLD DLD 3771 0.057 0.62 YES
17 DLST DLST DLST 4217 0.047 0.61 NO
18 IDH3A IDH3A IDH3A 4530 0.04 0.6 NO
19 SDHC SDHC SDHC 4925 0.032 0.59 NO
20 PDHB PDHB PDHB 4935 0.031 0.6 NO
21 PDHA1 PDHA1 PDHA1 5542 0.02 0.58 NO
22 IDH2 IDH2 IDH2 5651 0.019 0.58 NO
23 IDH3B IDH3B IDH3B 6355 0.0067 0.54 NO
24 MDH2 MDH2 MDH2 7820 -0.015 0.46 NO
25 SUCLA2 SUCLA2 SUCLA2 7956 -0.017 0.46 NO
26 DLAT DLAT DLAT 8323 -0.022 0.45 NO
27 IDH3G IDH3G IDH3G 9025 -0.032 0.42 NO
28 ACLY ACLY ACLY 11279 -0.069 0.32 NO
29 CS CS CS 13950 -0.14 0.21 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 PROPANOATE METABOLISM.

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

genes ES table in pathway: KEGG RETINOL METABOLISM

Table 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 TAT TAT TAT 21 0.63 0.1 YES
2 SDS SDS SDS 22 0.63 0.2 YES
3 DNMT3L DNMT3L DNMT3L 66 0.54 0.29 YES
4 BHMT BHMT BHMT 105 0.48 0.36 YES
5 CTH CTH CTH 255 0.38 0.42 YES
6 CBS CBS CBS 506 0.3 0.45 YES
7 CDO1 CDO1 CDO1 554 0.29 0.49 YES
8 MAT1A MAT1A MAT1A 986 0.21 0.5 YES
9 LDHC LDHC LDHC 1449 0.16 0.5 YES
10 ADI1 ADI1 ADI1 1579 0.15 0.52 YES
11 LDHAL6B LDHAL6B LDHAL6B 1598 0.15 0.55 YES
12 GOT1 GOT1 GOT1 1617 0.15 0.57 YES
13 GOT2 GOT2 GOT2 1896 0.13 0.57 YES
14 AHCYL2 AHCYL2 AHCYL2 2253 0.11 0.57 NO
15 MAT2B MAT2B MAT2B 3614 0.062 0.5 NO
16 MPST MPST MPST 4105 0.049 0.48 NO
17 AHCY AHCY AHCY 4299 0.045 0.48 NO
18 MAT2A MAT2A MAT2A 5162 0.027 0.44 NO
19 AHCYL1 AHCYL1 AHCYL1 5983 0.012 0.39 NO
20 MTAP MTAP MTAP 6011 0.012 0.39 NO
21 LDHA LDHA LDHA 7840 -0.016 0.29 NO
22 LDHAL6A LDHAL6A LDHAL6A 9038 -0.032 0.23 NO
23 DNMT1 DNMT1 DNMT1 9575 -0.04 0.21 NO
24 APIP APIP APIP 9943 -0.046 0.19 NO
25 TRDMT1 TRDMT1 TRDMT1 10963 -0.063 0.14 NO
26 ENOPH1 ENOPH1 ENOPH1 11034 -0.064 0.15 NO
27 SRM SRM SRM 11631 -0.076 0.13 NO
28 AMD1 AMD1 AMD1 11720 -0.078 0.14 NO
29 SMS SMS SMS 12252 -0.09 0.12 NO
30 MTR MTR MTR 13478 -0.12 0.073 NO
31 LDHB LDHB LDHB 13920 -0.14 0.07 NO
32 DNMT3B DNMT3B DNMT3B 14753 -0.17 0.051 NO
33 DNMT3A DNMT3A DNMT3A 16352 -0.27 0.0039 NO
34 IL4I1 IL4I1 IL4I1 17561 -0.46 0.0094 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 RETINOL METABOLISM.

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

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 0.59 1.5 0.17 1 0.98 0.8 0.29 0.57 0.79 0.4
PID ATM PATHWAY 34 genes.ES.table 0.52 1.5 0.12 1 0.98 0.47 0.27 0.34 0.84 0.43
REACTOME TRANSLATION 146 genes.ES.table 0.53 1.7 0.089 1 0.85 0.7 0.34 0.47 1 0.74
REACTOME METABOLISM OF NON CODING RNA 47 genes.ES.table 0.48 1.7 0.061 1 0.86 0.64 0.4 0.38 1 0.59
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 109 genes.ES.table 0.58 1.6 0.11 1 0.93 0.8 0.33 0.54 0.8 0.42
REACTOME SIGNALLING TO RAS 27 genes.ES.table 0.46 1.4 0.098 1 0.99 0.11 0.064 0.1 0.85 0.42
REACTOME SIGNALLING TO ERKS 35 genes.ES.table 0.43 1.5 0.063 1 0.97 0.43 0.37 0.27 0.78 0.41
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 126 genes.ES.table 0.38 1.5 0.096 1 0.98 0.59 0.4 0.35 0.79 0.41
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 57 genes.ES.table 0.5 1.5 0.14 1 0.98 0.7 0.34 0.47 0.79 0.4
REACTOME PEPTIDE CHAIN ELONGATION 85 genes.ES.table 0.62 1.5 0.13 1 0.97 0.85 0.29 0.6 0.91 0.46
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 RPL21 RPL21 RPL21 884 0.26 -0.027 YES
2 RPL36A RPL36A RPL36A 1468 0.2 -0.043 YES
3 RPL9 RPL9 RPL9 1788 0.17 -0.046 YES
4 GSPT2 GSPT2 GSPT2 1932 0.16 -0.04 YES
5 FAM153A FAM153A FAM153A 1939 0.16 -0.026 YES
6 RPS24 RPS24 RPS24 1956 0.16 -0.013 YES
7 RPS19 RPS19 RPS19 2207 0.15 -0.014 YES
8 RPSA RPSA RPSA 2217 0.15 -0.0016 YES
9 RPSAP9 RPSAP9 RPSAP9 2231 0.15 0.01 YES
10 RPLP0 RPLP0 RPLP0 2454 0.14 0.0098 YES
11 RPS21 RPS21 RPS21 2515 0.13 0.018 YES
12 SEC11C SEC11C SEC11C 2517 0.13 0.03 YES
13 SSR2 SSR2 SSR2 2580 0.13 0.038 YES
14 RPL39 RPL39 RPL39 2600 0.13 0.048 YES
15 RPL27A RPL27A RPL27A 2612 0.13 0.058 YES
16 RPS10 RPS10 RPS10 2613 0.13 0.07 YES
17 RPS12 RPS12 RPS12 2677 0.13 0.077 YES
18 RPS27 RPS27 RPS27 2735 0.12 0.085 YES
19 RPS17 RPS17 RPS17 2737 0.12 0.096 YES
20 RPS3 RPS3 RPS3 2761 0.12 0.1 YES
21 RPL23A RPL23A RPL23A 2768 0.12 0.12 YES
22 RPS7 RPS7 RPS7 2788 0.12 0.12 YES
23 RPS18 RPS18 RPS18 2794 0.12 0.14 YES
24 RPL26 RPL26 RPL26 2852 0.12 0.14 YES
25 RPS5 RPS5 RPS5 2871 0.12 0.15 YES
26 RPS27A RPS27A RPS27A 2884 0.12 0.16 YES
27 RPS15 RPS15 RPS15 2892 0.12 0.17 YES
28 RPL18A RPL18A RPL18A 2917 0.12 0.18 YES
29 RPS29 RPS29 RPS29 2934 0.12 0.19 YES
30 RPL28 RPL28 RPL28 2952 0.12 0.2 YES
31 RPL37A RPL37A RPL37A 3192 0.11 0.2 YES
32 EEF1B2 EEF1B2 EEF1B2 3243 0.11 0.2 YES
33 RPL36 RPL36 RPL36 3272 0.11 0.21 YES
34 RPS28 RPS28 RPS28 3286 0.1 0.22 YES
35 RPL7 RPL7 RPL7 3288 0.1 0.23 YES
36 RPLP2 RPLP2 RPLP2 3289 0.1 0.24 YES
37 RPS4X RPS4X RPS4X 3293 0.1 0.25 YES
38 RPL32 RPL32 RPL32 3331 0.1 0.25 YES
39 RPL18 RPL18 RPL18 3335 0.1 0.26 YES
40 RPL6 RPL6 RPL6 3358 0.1 0.27 YES
41 EEF1G EEF1G EEF1G 3365 0.1 0.28 YES
42 RPL31 RPL31 RPL31 3366 0.1 0.29 YES
43 RPL7A RPL7A RPL7A 3376 0.1 0.3 YES
44 RPL27 RPL27 RPL27 3384 0.1 0.3 YES
45 RPL38 RPL38 RPL38 3414 0.1 0.31 YES
46 RPL17 RPL17 RPL17 3417 0.1 0.32 YES
47 RPL13A RPL13A RPL13A 3488 0.1 0.32 YES
48 RPS16 RPS16 RPS16 3532 0.099 0.33 YES
49 RPL35A RPL35A RPL35A 3619 0.097 0.34 YES
50 RPL14 RPL14 RPL14 3627 0.096 0.34 YES
51 SEC61A2 SEC61A2 SEC61A2 3647 0.096 0.35 YES
52 RPL3 RPL3 RPL3 3661 0.095 0.36 YES
53 RPL10A RPL10A RPL10A 3670 0.095 0.36 YES
54 RPS11 RPS11 RPS11 3681 0.094 0.37 YES
55 RPL4 RPL4 RPL4 3741 0.093 0.38 YES
56 RPL23 RPL23 RPL23 4022 0.085 0.37 YES
57 RPL35 RPL35 RPL35 4077 0.084 0.37 YES
58 RPS9 RPS9 RPS9 4088 0.084 0.38 YES
59 SSR4 SSR4 SSR4 4105 0.083 0.39 YES
60 RPL8 RPL8 RPL8 4107 0.083 0.39 YES
61 RPL41 RPL41 RPL41 4108 0.083 0.4 YES
62 RPS6 RPS6 RPS6 4116 0.083 0.41 YES
63 RPS2 RPS2 RPS2 4195 0.081 0.41 YES
64 RPL37 RPL37 RPL37 4259 0.08 0.41 YES
65 RPS23 RPS23 RPS23 4261 0.08 0.42 YES
66 RPL24 RPL24 RPL24 4266 0.08 0.43 YES
67 SEC11A SEC11A SEC11A 4272 0.08 0.44 YES
68 RPL30 RPL30 RPL30 4292 0.079 0.44 YES
69 RPS13 RPS13 RPS13 4332 0.078 0.44 YES
70 RPS25 RPS25 RPS25 4342 0.078 0.45 YES
71 EIF3D EIF3D EIF3D 4456 0.075 0.45 YES
72 EIF2S3 EIF2S3 EIF2S3 4494 0.074 0.46 YES
73 RPLP1 RPLP1 RPLP1 4504 0.074 0.46 YES
74 PABPC1 PABPC1 PABPC1 4626 0.072 0.46 YES
75 RPL29 RPL29 RPL29 4630 0.072 0.47 YES
76 EIF2S2 EIF2S2 EIF2S2 4715 0.07 0.47 YES
77 RPL12 RPL12 RPL12 4729 0.07 0.47 YES
78 SPCS2 SPCS2 SPCS2 4844 0.068 0.47 YES
79 SRP9 SRP9 SRP9 4864 0.067 0.48 YES
80 RPL15 RPL15 RPL15 4885 0.067 0.48 YES
81 RPS20 RPS20 RPS20 4902 0.066 0.49 YES
82 EIF4A1 EIF4A1 EIF4A1 4963 0.065 0.49 YES
83 EIF4A2 EIF4A2 EIF4A2 4972 0.065 0.5 YES
84 EEF1A1 EEF1A1 EEF1A1 4988 0.064 0.5 YES
85 RPS14 RPS14 RPS14 5088 0.062 0.5 YES
86 LOC653566 LOC653566 LOC653566 5174 0.061 0.5 YES
87 RPS3A RPS3A RPS3A 5206 0.06 0.5 YES
88 RPL10 RPL10 RPL10 5212 0.06 0.51 YES
89 RPL5 RPL5 RPL5 5219 0.06 0.51 YES
90 SEC61G SEC61G SEC61G 5265 0.059 0.52 YES
91 UBA52 UBA52 UBA52 5362 0.057 0.52 YES
92 RPL34 RPL34 RPL34 5551 0.054 0.51 YES
93 RPL19 RPL19 RPL19 5664 0.052 0.51 YES
94 EEF1D EEF1D EEF1D 5669 0.052 0.51 YES
95 EIF4B EIF4B EIF4B 5738 0.051 0.51 YES
96 RPS8 RPS8 RPS8 5783 0.05 0.52 YES
97 RPN2 RPN2 RPN2 5793 0.05 0.52 YES
98 RPS15A RPS15A RPS15A 5804 0.05 0.52 YES
99 SSR1 SSR1 SSR1 5816 0.049 0.53 YES
100 EIF3K EIF3K EIF3K 5900 0.048 0.53 YES
101 EIF3F EIF3F EIF3F 5948 0.047 0.53 YES
102 RPL13 RPL13 RPL13 5986 0.046 0.53 YES
103 RPS26 RPS26 RPS26 6149 0.044 0.52 NO
104 SRPRB SRPRB SRPRB 6241 0.042 0.52 NO
105 EIF3G EIF3G EIF3G 6317 0.041 0.52 NO
106 FAU FAU FAU 6458 0.039 0.52 NO
107 EIF3E EIF3E EIF3E 6583 0.036 0.51 NO
108 EIF3B EIF3B EIF3B 6773 0.034 0.5 NO
109 SRP14 SRP14 SRP14 7002 0.03 0.5 NO
110 RPL11 RPL11 RPL11 7214 0.027 0.48 NO
111 RPL22 RPL22 RPL22 7268 0.026 0.48 NO
112 SRP68 SRP68 SRP68 7408 0.024 0.48 NO
113 SSR3 SSR3 SSR3 7590 0.021 0.47 NO
114 SEC61B SEC61B SEC61B 7976 0.015 0.45 NO
115 RPN1 RPN1 RPN1 7994 0.014 0.45 NO
116 EEF2 EEF2 EEF2 8073 0.013 0.45 NO
117 EIF1AX EIF1AX EIF1AX 8327 0.01 0.43 NO
118 EIF5B EIF5B EIF5B 8410 0.0087 0.43 NO
119 SRP72 SRP72 SRP72 8414 0.0086 0.43 NO
120 EIF2B4 EIF2B4 EIF2B4 8535 0.0068 0.42 NO
121 EIF3A EIF3A EIF3A 8556 0.0066 0.42 NO
122 SEC61A1 SEC61A1 SEC61A1 8632 0.0052 0.42 NO
123 EIF3J EIF3J EIF3J 8723 0.0038 0.41 NO
124 EIF3H EIF3H EIF3H 8844 0.0019 0.41 NO
125 TRAM1 TRAM1 TRAM1 9035 -0.00076 0.4 NO
126 EIF2B5 EIF2B5 EIF2B5 9167 -0.0028 0.39 NO
127 EIF2B1 EIF2B1 EIF2B1 9362 -0.0057 0.38 NO
128 SRP19 SRP19 SRP19 9449 -0.0073 0.38 NO
129 EIF5 EIF5 EIF5 9797 -0.013 0.36 NO
130 EIF4E EIF4E EIF4E 9994 -0.016 0.35 NO
131 EIF4H EIF4H EIF4H 10191 -0.02 0.34 NO
132 EIF2B2 EIF2B2 EIF2B2 10407 -0.023 0.33 NO
133 SPCS1 SPCS1 SPCS1 10513 -0.025 0.32 NO
134 DDOST DDOST DDOST 10683 -0.028 0.32 NO
135 EIF2S1 EIF2S1 EIF2S1 10844 -0.03 0.31 NO
136 ETF1 ETF1 ETF1 11080 -0.034 0.3 NO
137 EIF3C EIF3C EIF3C 11701 -0.046 0.27 NO
138 SRP54 SRP54 SRP54 11703 -0.046 0.27 NO
139 EIF4EBP1 EIF4EBP1 EIF4EBP1 11826 -0.048 0.27 NO
140 EIF4G1 EIF4G1 EIF4G1 12581 -0.064 0.23 NO
141 EIF3I EIF3I EIF3I 12667 -0.066 0.23 NO
142 SRPR SRPR SRPR 12687 -0.066 0.24 NO
143 SPCS3 SPCS3 SPCS3 13086 -0.075 0.22 NO
144 RPL26L1 RPL26L1 RPL26L1 13573 -0.087 0.2 NO
145 EIF2B3 EIF2B3 EIF2B3 15494 -0.16 0.11 NO
146 RPS4Y1 RPS4Y1 RPS4Y1 16645 -0.24 0.062 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: PID ATM 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 SMN1 SMN1 SMN1 1945 0.16 -0.048 YES
2 GEMIN7 GEMIN7 GEMIN7 2025 0.16 0.0064 YES
3 SNRPE SNRPE SNRPE 2268 0.14 0.047 YES
4 SNRPD1 SNRPD1 SNRPD1 2587 0.13 0.078 YES
5 NUP210 NUP210 NUP210 2790 0.12 0.11 YES
6 SNRPF SNRPF SNRPF 2829 0.12 0.16 YES
7 NUP133 NUP133 NUP133 3352 0.1 0.17 YES
8 SNRPB SNRPB SNRPB 3425 0.1 0.2 YES
9 NUP50 NUP50 NUP50 3689 0.094 0.22 YES
10 TPR TPR TPR 3693 0.094 0.26 YES
11 RAE1 RAE1 RAE1 3982 0.086 0.27 YES
12 SNRPG SNRPG SNRPG 4041 0.085 0.3 YES
13 NUP88 NUP88 NUP88 4204 0.081 0.32 YES
14 SMN2 SMN2 SMN2 4271 0.08 0.35 YES
15 NCBP2 NCBP2 NCBP2 4440 0.076 0.37 YES
16 SNRPD3 SNRPD3 SNRPD3 4545 0.073 0.39 YES
17 POM121 POM121 POM121 4614 0.072 0.41 YES
18 SNRPD2 SNRPD2 SNRPD2 4777 0.069 0.43 YES
19 NUP43 NUP43 NUP43 5203 0.06 0.43 YES
20 NUP85 NUP85 NUP85 5425 0.056 0.44 YES
21 GEMIN4 GEMIN4 GEMIN4 5684 0.052 0.44 YES
22 NUP37 NUP37 NUP37 5781 0.05 0.46 YES
23 NUP62 NUP62 NUP62 6439 0.039 0.43 YES
24 NUP205 NUP205 NUP205 6454 0.039 0.45 YES
25 AAAS AAAS AAAS 6673 0.035 0.45 YES
26 NUP214 NUP214 NUP214 6834 0.033 0.45 YES
27 SEH1L SEH1L SEH1L 6848 0.032 0.46 YES
28 NUP107 NUP107 NUP107 6928 0.031 0.47 YES
29 SNUPN SNUPN SNUPN 7047 0.029 0.48 YES
30 NUP35 NUP35 NUP35 7132 0.028 0.48 YES
31 CLNS1A CLNS1A CLNS1A 7375 0.025 0.48 NO
32 NUPL2 NUPL2 NUPL2 7769 0.018 0.46 NO
33 NUP155 NUP155 NUP155 7775 0.018 0.47 NO
34 NUP153 NUP153 NUP153 8016 0.014 0.46 NO
35 NUP188 NUP188 NUP188 8129 0.013 0.46 NO
36 RANBP2 RANBP2 RANBP2 8408 0.0088 0.44 NO
37 TGS1 TGS1 TGS1 8764 0.0032 0.43 NO
38 WDR77 WDR77 WDR77 8983 0.000074 0.41 NO
39 GEMIN6 GEMIN6 GEMIN6 8994 -0.00014 0.41 NO
40 NUPL1 NUPL1 NUPL1 9184 -0.003 0.4 NO
41 GEMIN5 GEMIN5 GEMIN5 9812 -0.013 0.37 NO
42 PHAX PHAX PHAX 10484 -0.024 0.34 NO
43 NCBP1 NCBP1 NCBP1 10645 -0.027 0.35 NO
44 PRMT5 PRMT5 PRMT5 10737 -0.029 0.35 NO
45 DDX20 DDX20 DDX20 10819 -0.03 0.36 NO
46 NUP54 NUP54 NUP54 11550 -0.043 0.33 NO
47 NUP93 NUP93 NUP93 11578 -0.043 0.35 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: PID ATM PATHWAY.

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

genes ES table in pathway: REACTOME TRANSLATION

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 RPL21 RPL21 RPL21 884 0.26 -0.023 YES
2 RPL36A RPL36A RPL36A 1468 0.2 -0.035 YES
3 RPL9 RPL9 RPL9 1788 0.17 -0.035 YES
4 GSPT2 GSPT2 GSPT2 1932 0.16 -0.026 YES
5 FAM153A FAM153A FAM153A 1939 0.16 -0.009 YES
6 RPS24 RPS24 RPS24 1956 0.16 0.007 YES
7 RPS19 RPS19 RPS19 2207 0.15 0.0083 YES
8 RPSA RPSA RPSA 2217 0.15 0.023 YES
9 RPSAP9 RPSAP9 RPSAP9 2231 0.15 0.038 YES
10 RPLP0 RPLP0 RPLP0 2454 0.14 0.04 YES
11 RPS21 RPS21 RPS21 2515 0.13 0.05 YES
12 RPL39 RPL39 RPL39 2600 0.13 0.059 YES
13 RPL27A RPL27A RPL27A 2612 0.13 0.072 YES
14 RPS10 RPS10 RPS10 2613 0.13 0.085 YES
15 RPS12 RPS12 RPS12 2677 0.13 0.095 YES
16 RPS27 RPS27 RPS27 2735 0.12 0.1 YES
17 RPS17 RPS17 RPS17 2737 0.12 0.12 YES
18 RPS3 RPS3 RPS3 2761 0.12 0.13 YES
19 RPL23A RPL23A RPL23A 2768 0.12 0.14 YES
20 RPS7 RPS7 RPS7 2788 0.12 0.15 YES
21 RPS18 RPS18 RPS18 2794 0.12 0.17 YES
22 RPL26 RPL26 RPL26 2852 0.12 0.18 YES
23 RPS5 RPS5 RPS5 2871 0.12 0.19 YES
24 RPS27A RPS27A RPS27A 2884 0.12 0.2 YES
25 RPS15 RPS15 RPS15 2892 0.12 0.21 YES
26 RPL18A RPL18A RPL18A 2917 0.12 0.22 YES
27 RPS29 RPS29 RPS29 2934 0.12 0.23 YES
28 RPL28 RPL28 RPL28 2952 0.12 0.24 YES
29 RPL37A RPL37A RPL37A 3192 0.11 0.24 YES
30 RPL36 RPL36 RPL36 3272 0.11 0.25 YES
31 RPS28 RPS28 RPS28 3286 0.1 0.26 YES
32 RPL7 RPL7 RPL7 3288 0.1 0.27 YES
33 RPLP2 RPLP2 RPLP2 3289 0.1 0.28 YES
34 RPS4X RPS4X RPS4X 3293 0.1 0.29 YES
35 RPL32 RPL32 RPL32 3331 0.1 0.3 YES
36 RPL18 RPL18 RPL18 3335 0.1 0.31 YES
37 UPF3A UPF3A UPF3A 3350 0.1 0.32 YES
38 RPL6 RPL6 RPL6 3358 0.1 0.33 YES
39 RPL31 RPL31 RPL31 3366 0.1 0.34 YES
40 RPL7A RPL7A RPL7A 3376 0.1 0.35 YES
41 RPL27 RPL27 RPL27 3384 0.1 0.36 YES
42 RPL38 RPL38 RPL38 3414 0.1 0.37 YES
43 RPL17 RPL17 RPL17 3417 0.1 0.38 YES
44 RPL13A RPL13A RPL13A 3488 0.1 0.39 YES
45 RPS16 RPS16 RPS16 3532 0.099 0.4 YES
46 RPL35A RPL35A RPL35A 3619 0.097 0.4 YES
47 RPL14 RPL14 RPL14 3627 0.096 0.41 YES
48 RPL3 RPL3 RPL3 3661 0.095 0.42 YES
49 RPL10A RPL10A RPL10A 3670 0.095 0.43 YES
50 RPS11 RPS11 RPS11 3681 0.094 0.44 YES
51 RPL4 RPL4 RPL4 3741 0.093 0.44 YES
52 SMG5 SMG5 SMG5 3809 0.091 0.45 YES
53 RPL23 RPL23 RPL23 4022 0.085 0.45 YES
54 RPL35 RPL35 RPL35 4077 0.084 0.45 YES
55 RPS9 RPS9 RPS9 4088 0.084 0.46 YES
56 RPL8 RPL8 RPL8 4107 0.083 0.47 YES
57 RPL41 RPL41 RPL41 4108 0.083 0.48 YES
58 RPS6 RPS6 RPS6 4116 0.083 0.49 YES
59 RPS2 RPS2 RPS2 4195 0.081 0.49 YES
60 RPL37 RPL37 RPL37 4259 0.08 0.5 YES
61 RPS23 RPS23 RPS23 4261 0.08 0.5 YES
62 RPL24 RPL24 RPL24 4266 0.08 0.51 YES
63 RPL30 RPL30 RPL30 4292 0.079 0.52 YES
64 RPS13 RPS13 RPS13 4332 0.078 0.52 YES
65 RPS25 RPS25 RPS25 4342 0.078 0.53 YES
66 NCBP2 NCBP2 NCBP2 4440 0.076 0.54 YES
67 RBM8A RBM8A RBM8A 4488 0.074 0.54 YES
68 RPLP1 RPLP1 RPLP1 4504 0.074 0.55 YES
69 PABPC1 PABPC1 PABPC1 4626 0.072 0.55 YES
70 RPL29 RPL29 RPL29 4630 0.072 0.56 YES
71 RPL12 RPL12 RPL12 4729 0.07 0.56 YES
72 RPL15 RPL15 RPL15 4885 0.067 0.55 YES
73 SMG7 SMG7 SMG7 4892 0.067 0.56 YES
74 RPS20 RPS20 RPS20 4902 0.066 0.57 YES
75 RPS14 RPS14 RPS14 5088 0.062 0.56 YES
76 RPS3A RPS3A RPS3A 5206 0.06 0.56 YES
77 RPL10 RPL10 RPL10 5212 0.06 0.57 YES
78 RPL5 RPL5 RPL5 5219 0.06 0.57 YES
79 PPP2R1A PPP2R1A PPP2R1A 5230 0.06 0.58 YES
80 UBA52 UBA52 UBA52 5362 0.057 0.58 NO
81 RPL34 RPL34 RPL34 5551 0.054 0.57 NO
82 RPL19 RPL19 RPL19 5664 0.052 0.57 NO
83 RPS8 RPS8 RPS8 5783 0.05 0.57 NO
84 RPS15A RPS15A RPS15A 5804 0.05 0.58 NO
85 SMG6 SMG6 SMG6 5933 0.047 0.57 NO
86 RPL13 RPL13 RPL13 5986 0.046 0.58 NO
87 UPF2 UPF2 UPF2 6013 0.046 0.58 NO
88 RPS26 RPS26 RPS26 6149 0.044 0.58 NO
89 FAU FAU FAU 6458 0.039 0.56 NO
90 RPL11 RPL11 RPL11 7214 0.027 0.52 NO
91 RPL22 RPL22 RPL22 7268 0.026 0.52 NO
92 CASC3 CASC3 CASC3 7763 0.018 0.5 NO
93 EIF4A3 EIF4A3 EIF4A3 8136 0.012 0.48 NO
94 UPF3B UPF3B UPF3B 8568 0.0063 0.45 NO
95 PPP2CA PPP2CA PPP2CA 8969 0.00031 0.43 NO
96 RNPS1 RNPS1 RNPS1 10306 -0.022 0.36 NO
97 NCBP1 NCBP1 NCBP1 10645 -0.027 0.34 NO
98 ETF1 ETF1 ETF1 11080 -0.034 0.32 NO
99 MAGOH MAGOH MAGOH 11661 -0.045 0.29 NO
100 SMG1 SMG1 SMG1 11991 -0.051 0.28 NO
101 EIF4G1 EIF4G1 EIF4G1 12581 -0.064 0.25 NO
102 PPP2R2A PPP2R2A PPP2R2A 12599 -0.064 0.26 NO
103 RPL26L1 RPL26L1 RPL26L1 13573 -0.087 0.21 NO
104 RPS4Y1 RPS4Y1 RPS4Y1 16645 -0.24 0.062 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: REACTOME TRANSLATION.

Figure S46.  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 METABOLISM OF NON CODING RNA

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 RPL21 RPL21 RPL21 884 0.26 -0.026 YES
2 RPL36A RPL36A RPL36A 1468 0.2 -0.04 YES
3 RPL9 RPL9 RPL9 1788 0.17 -0.042 YES
4 FAM153A FAM153A FAM153A 1939 0.16 -0.036 YES
5 RPS24 RPS24 RPS24 1956 0.16 -0.022 YES
6 RPS19 RPS19 RPS19 2207 0.15 -0.022 YES
7 RPSA RPSA RPSA 2217 0.15 -0.0091 YES
8 RPSAP9 RPSAP9 RPSAP9 2231 0.15 0.0038 YES
9 RPLP0 RPLP0 RPLP0 2454 0.14 0.0038 YES
10 RPS21 RPS21 RPS21 2515 0.13 0.013 YES
11 RPL39 RPL39 RPL39 2600 0.13 0.02 YES
12 RPL27A RPL27A RPL27A 2612 0.13 0.031 YES
13 RPS10 RPS10 RPS10 2613 0.13 0.043 YES
14 RPS12 RPS12 RPS12 2677 0.13 0.052 YES
15 RPS27 RPS27 RPS27 2735 0.12 0.06 YES
16 RPS17 RPS17 RPS17 2737 0.12 0.071 YES
17 RPS3 RPS3 RPS3 2761 0.12 0.082 YES
18 RPL23A RPL23A RPL23A 2768 0.12 0.093 YES
19 RPS7 RPS7 RPS7 2788 0.12 0.1 YES
20 NUP210 NUP210 NUP210 2790 0.12 0.11 YES
21 RPS18 RPS18 RPS18 2794 0.12 0.13 YES
22 RPL26 RPL26 RPL26 2852 0.12 0.13 YES
23 RPS5 RPS5 RPS5 2871 0.12 0.14 YES
24 RPS27A RPS27A RPS27A 2884 0.12 0.15 YES
25 RPS15 RPS15 RPS15 2892 0.12 0.16 YES
26 RPL18A RPL18A RPL18A 2917 0.12 0.17 YES
27 RPS29 RPS29 RPS29 2934 0.12 0.18 YES
28 RPL28 RPL28 RPL28 2952 0.12 0.19 YES
29 IPO5 IPO5 IPO5 3030 0.11 0.2 YES
30 RPL37A RPL37A RPL37A 3192 0.11 0.2 YES
31 RPL36 RPL36 RPL36 3272 0.11 0.21 YES
32 RPS28 RPS28 RPS28 3286 0.1 0.22 YES
33 RPL7 RPL7 RPL7 3288 0.1 0.22 YES
34 RPLP2 RPLP2 RPLP2 3289 0.1 0.24 YES
35 RPS4X RPS4X RPS4X 3293 0.1 0.24 YES
36 RPL32 RPL32 RPL32 3331 0.1 0.25 YES
37 RPL18 RPL18 RPL18 3335 0.1 0.26 YES
38 NUP133 NUP133 NUP133 3352 0.1 0.27 YES
39 RPL6 RPL6 RPL6 3358 0.1 0.28 YES
40 RPL31 RPL31 RPL31 3366 0.1 0.29 YES
41 RPL7A RPL7A RPL7A 3376 0.1 0.3 YES
42 RPL27 RPL27 RPL27 3384 0.1 0.31 YES
43 RPL38 RPL38 RPL38 3414 0.1 0.32 YES
44 RPL17 RPL17 RPL17 3417 0.1 0.32 YES
45 RPL13A RPL13A RPL13A 3488 0.1 0.33 YES
46 POLR2H POLR2H POLR2H 3505 0.1 0.34 YES
47 RPS16 RPS16 RPS16 3532 0.099 0.35 YES
48 RPL35A RPL35A RPL35A 3619 0.097 0.35 YES
49 RPL14 RPL14 RPL14 3627 0.096 0.36 YES
50 RPL3 RPL3 RPL3 3661 0.095 0.36 YES
51 RPL10A RPL10A RPL10A 3670 0.095 0.37 YES
52 RPS11 RPS11 RPS11 3681 0.094 0.38 YES
53 NUP50 NUP50 NUP50 3689 0.094 0.39 YES
54 TPR TPR TPR 3693 0.094 0.4 YES
55 RPL4 RPL4 RPL4 3741 0.093 0.4 YES
56 RAE1 RAE1 RAE1 3982 0.086 0.4 YES
57 RPL23 RPL23 RPL23 4022 0.085 0.4 YES
58 RPL35 RPL35 RPL35 4077 0.084 0.41 YES
59 RPS9 RPS9 RPS9 4088 0.084 0.42 YES
60 RPL8 RPL8 RPL8 4107 0.083 0.42 YES
61 RPL41 RPL41 RPL41 4108 0.083 0.43 YES
62 RPS6 RPS6 RPS6 4116 0.083 0.44 YES
63 RPS2 RPS2 RPS2 4195 0.081 0.44 YES
64 NUP88 NUP88 NUP88 4204 0.081 0.45 YES
65 RPL37 RPL37 RPL37 4259 0.08 0.45 YES
66 RPS23 RPS23 RPS23 4261 0.08 0.46 YES
67 RPL24 RPL24 RPL24 4266 0.08 0.47 YES
68 RPL30 RPL30 RPL30 4292 0.079 0.47 YES
69 RPS13 RPS13 RPS13 4332 0.078 0.48 YES
70 RPS25 RPS25 RPS25 4342 0.078 0.48 YES
71 RPLP1 RPLP1 RPLP1 4504 0.074 0.48 YES
72 POM121 POM121 POM121 4614 0.072 0.48 YES
73 RPL29 RPL29 RPL29 4630 0.072 0.49 YES
74 RPL12 RPL12 RPL12 4729 0.07 0.49 YES
75 POLR2D POLR2D POLR2D 4858 0.067 0.49 YES
76 RPL15 RPL15 RPL15 4885 0.067 0.49 YES
77 RPS20 RPS20 RPS20 4902 0.066 0.5 YES
78 RPS14 RPS14 RPS14 5088 0.062 0.49 YES
79 POLR2F POLR2F POLR2F 5124 0.062 0.5 YES
80 NUP43 NUP43 NUP43 5203 0.06 0.5 YES
81 RPS3A RPS3A RPS3A 5206 0.06 0.5 YES
82 RPL10 RPL10 RPL10 5212 0.06 0.51 YES
83 RPL5 RPL5 RPL5 5219 0.06 0.52 YES
84 UBA52 UBA52 UBA52 5362 0.057 0.51 YES
85 GTF2F2 GTF2F2 GTF2F2 5412 0.056 0.52 YES
86 NUP85 NUP85 NUP85 5425 0.056 0.52 YES
87 RPL34 RPL34 RPL34 5551 0.054 0.52 YES
88 RPL19 RPL19 RPL19 5664 0.052 0.52 YES
89 NUP37 NUP37 NUP37 5781 0.05 0.51 YES
90 RPS8 RPS8 RPS8 5783 0.05 0.52 YES
91 RPS15A RPS15A RPS15A 5804 0.05 0.52 YES
92 RPL13 RPL13 RPL13 5986 0.046 0.52 NO
93 RPS26 RPS26 RPS26 6149 0.044 0.51 NO
94 RAN RAN RAN 6180 0.043 0.51 NO
95 GTF2F1 GTF2F1 GTF2F1 6267 0.042 0.51 NO
96 CLTA CLTA CLTA 6330 0.041 0.51 NO
97 NUP62 NUP62 NUP62 6439 0.039 0.51 NO
98 NUP205 NUP205 NUP205 6454 0.039 0.51 NO
99 FAU FAU FAU 6458 0.039 0.52 NO
100 POLR2I POLR2I POLR2I 6615 0.036 0.51 NO
101 HSP90AA1 HSP90AA1 HSP90AA1 6669 0.035 0.51 NO
102 AAAS AAAS AAAS 6673 0.035 0.51 NO
103 NUP214 NUP214 NUP214 6834 0.033 0.51 NO
104 SEH1L SEH1L SEH1L 6848 0.032 0.51 NO
105 NUP107 NUP107 NUP107 6928 0.031 0.51 NO
106 XPO1 XPO1 XPO1 6991 0.03 0.51 NO
107 NUP35 NUP35 NUP35 7132 0.028 0.5 NO
108 RPL11 RPL11 RPL11 7214 0.027 0.5 NO
109 RPL22 RPL22 RPL22 7268 0.026 0.5 NO
110 POLR2J POLR2J POLR2J 7462 0.023 0.49 NO
111 KPNB1 KPNB1 KPNB1 7521 0.022 0.49 NO
112 NUPL2 NUPL2 NUPL2 7769 0.018 0.48 NO
113 NUP155 NUP155 NUP155 7775 0.018 0.48 NO
114 CALR CALR CALR 7999 0.014 0.47 NO
115 NUP153 NUP153 NUP153 8016 0.014 0.47 NO
116 NUP188 NUP188 NUP188 8129 0.013 0.46 NO
117 POLR2G POLR2G POLR2G 8198 0.012 0.46 NO
118 POLR2B POLR2B POLR2B 8200 0.012 0.46 NO
119 RANBP2 RANBP2 RANBP2 8408 0.0088 0.45 NO
120 NUPL1 NUPL1 NUPL1 9184 -0.003 0.41 NO
121 POLR2A POLR2A POLR2A 9461 -0.0075 0.39 NO
122 KPNA1 KPNA1 KPNA1 9467 -0.0076 0.39 NO
123 POLR2E POLR2E POLR2E 9788 -0.013 0.37 NO
124 DNAJC3 DNAJC3 DNAJC3 9816 -0.013 0.37 NO
125 CANX CANX CANX 9887 -0.014 0.37 NO
126 POLR2K POLR2K POLR2K 10232 -0.02 0.35 NO
127 CLTC CLTC CLTC 10471 -0.024 0.34 NO
128 POLR2L POLR2L POLR2L 11359 -0.04 0.3 NO
129 NUP54 NUP54 NUP54 11550 -0.043 0.29 NO
130 NUP93 NUP93 NUP93 11578 -0.043 0.29 NO
131 GRSF1 GRSF1 GRSF1 12923 -0.071 0.22 NO
132 POLR2C POLR2C POLR2C 13546 -0.087 0.19 NO
133 RPL26L1 RPL26L1 RPL26L1 13573 -0.087 0.2 NO
134 HSPA1B HSPA1B HSPA1B 15062 -0.14 0.13 NO
135 RPS4Y1 RPS4Y1 RPS4Y1 16645 -0.24 0.062 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: REACTOME METABOLISM OF NON CODING RNA.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME METABOLISM OF NON CODING RNA, 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 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 LSM11 LSM11 LSM11 1211 0.22 -0.04 YES
2 GTF2H2B GTF2H2B GTF2H2B 1713 0.18 -0.045 YES
3 ZNF473 ZNF473 ZNF473 1903 0.16 -0.034 YES
4 SNRPA1 SNRPA1 SNRPA1 2054 0.16 -0.022 YES
5 SNRPE SNRPE SNRPE 2268 0.14 -0.016 YES
6 SF3A2 SF3A2 SF3A2 2304 0.14 0.00092 YES
7 SNRPD1 SNRPD1 SNRPD1 2587 0.13 0.0019 YES
8 CDK7 CDK7 CDK7 2609 0.13 0.018 YES
9 NUP210 NUP210 NUP210 2790 0.12 0.023 YES
10 SNRPF SNRPF SNRPF 2829 0.12 0.037 YES
11 LSM2 LSM2 LSM2 2950 0.12 0.045 YES
12 THOC4 THOC4 THOC4 3135 0.11 0.049 YES
13 NUP133 NUP133 NUP133 3352 0.1 0.05 YES
14 SNRPB SNRPB SNRPB 3425 0.1 0.06 YES
15 POLR2H POLR2H POLR2H 3505 0.1 0.068 YES
16 HNRNPA0 HNRNPA0 HNRNPA0 3555 0.098 0.078 YES
17 HNRNPA1 HNRNPA1 HNRNPA1 3571 0.098 0.09 YES
18 NUP50 NUP50 NUP50 3689 0.094 0.096 YES
19 TPR TPR TPR 3693 0.094 0.11 YES
20 NHP2L1 NHP2L1 NHP2L1 3823 0.09 0.11 YES
21 RAE1 RAE1 RAE1 3982 0.086 0.11 YES
22 SNRPG SNRPG SNRPG 4041 0.085 0.12 YES
23 U2AF1 U2AF1 U2AF1 4153 0.082 0.13 YES
24 NUP88 NUP88 NUP88 4204 0.081 0.13 YES
25 NCBP2 NCBP2 NCBP2 4440 0.076 0.13 YES
26 RBM8A RBM8A RBM8A 4488 0.074 0.14 YES
27 SNRPA SNRPA SNRPA 4492 0.074 0.15 YES
28 SNRPD3 SNRPD3 SNRPD3 4545 0.073 0.15 YES
29 SNRNP70 SNRNP70 SNRNP70 4590 0.072 0.16 YES
30 POM121 POM121 POM121 4614 0.072 0.17 YES
31 SNRPD2 SNRPD2 SNRPD2 4777 0.069 0.17 YES
32 POLR2D POLR2D POLR2D 4858 0.067 0.17 YES
33 RBMX RBMX RBMX 4863 0.067 0.18 YES
34 HNRNPUL1 HNRNPUL1 HNRNPUL1 4866 0.067 0.19 YES
35 CCAR1 CCAR1 CCAR1 4920 0.066 0.2 YES
36 FUS FUS FUS 4923 0.066 0.2 YES
37 A1CF A1CF A1CF 4978 0.065 0.21 YES
38 PRPF6 PRPF6 PRPF6 5004 0.064 0.22 YES
39 PABPN1 PABPN1 PABPN1 5038 0.063 0.22 YES
40 SF3B4 SF3B4 SF3B4 5039 0.063 0.23 YES
41 PHF5A PHF5A PHF5A 5040 0.063 0.24 YES
42 HNRNPA3 HNRNPA3 HNRNPA3 5060 0.063 0.25 YES
43 POLR2F POLR2F POLR2F 5124 0.062 0.25 YES
44 RBM5 RBM5 RBM5 5195 0.06 0.26 YES
45 NUP43 NUP43 NUP43 5203 0.06 0.26 YES
46 SLBP SLBP SLBP 5213 0.06 0.27 YES
47 HNRNPH1 HNRNPH1 HNRNPH1 5261 0.059 0.27 YES
48 SUPT5H SUPT5H SUPT5H 5359 0.057 0.28 YES
49 GTF2F2 GTF2F2 GTF2F2 5412 0.056 0.28 YES
50 NUP85 NUP85 NUP85 5425 0.056 0.29 YES
51 HNRNPU HNRNPU HNRNPU 5503 0.055 0.29 YES
52 ERCC2 ERCC2 ERCC2 5564 0.054 0.29 YES
53 PTBP1 PTBP1 PTBP1 5611 0.053 0.3 YES
54 SNRPB2 SNRPB2 SNRPB2 5718 0.051 0.3 YES
55 CPSF1 CPSF1 CPSF1 5773 0.05 0.3 YES
56 NUP37 NUP37 NUP37 5781 0.05 0.31 YES
57 PCF11 PCF11 PCF11 5909 0.048 0.31 YES
58 GTF2H4 GTF2H4 GTF2H4 5918 0.048 0.31 YES
59 RNMT RNMT RNMT 5954 0.047 0.32 YES
60 U2AF2 U2AF2 U2AF2 6004 0.046 0.32 YES
61 DHX9 DHX9 DHX9 6022 0.046 0.32 YES
62 HNRNPL HNRNPL HNRNPL 6030 0.046 0.33 YES
63 TXNL4A TXNL4A TXNL4A 6162 0.044 0.33 YES
64 NXF1 NXF1 NXF1 6238 0.042 0.33 YES
65 GTF2F1 GTF2F1 GTF2F1 6267 0.042 0.33 YES
66 CPSF7 CPSF7 CPSF7 6313 0.041 0.34 YES
67 NUP62 NUP62 NUP62 6439 0.039 0.34 YES
68 NUP205 NUP205 NUP205 6454 0.039 0.34 YES
69 GTF2H1 GTF2H1 GTF2H1 6460 0.039 0.34 YES
70 HNRNPC HNRNPC HNRNPC 6537 0.037 0.34 YES
71 POLR2I POLR2I POLR2I 6615 0.036 0.34 YES
72 HNRNPM HNRNPM HNRNPM 6653 0.036 0.35 YES
73 AAAS AAAS AAAS 6673 0.035 0.35 YES
74 NUP214 NUP214 NUP214 6834 0.033 0.35 YES
75 PAPOLA PAPOLA PAPOLA 6845 0.032 0.35 YES
76 SEH1L SEH1L SEH1L 6848 0.032 0.35 YES
77 SF3B14 SF3B14 SF3B14 6878 0.032 0.36 YES
78 NUP107 NUP107 NUP107 6928 0.031 0.36 YES
79 HNRNPF HNRNPF HNRNPF 6943 0.031 0.36 YES
80 METTL3 METTL3 METTL3 6981 0.03 0.36 YES
81 CSTF3 CSTF3 CSTF3 6984 0.03 0.37 YES
82 SF3B5 SF3B5 SF3B5 7005 0.03 0.37 YES
83 HNRNPD HNRNPD HNRNPD 7096 0.029 0.37 YES
84 NUP35 NUP35 NUP35 7132 0.028 0.37 YES
85 POLR2J POLR2J POLR2J 7462 0.023 0.35 NO
86 ERCC3 ERCC3 ERCC3 7684 0.02 0.34 NO
87 EFTUD2 EFTUD2 EFTUD2 7711 0.019 0.34 NO
88 NUPL2 NUPL2 NUPL2 7769 0.018 0.34 NO
89 NUP155 NUP155 NUP155 7775 0.018 0.35 NO
90 ADARB1 ADARB1 ADARB1 7819 0.017 0.35 NO
91 PRPF8 PRPF8 PRPF8 7846 0.017 0.35 NO
92 CPSF3 CPSF3 CPSF3 8002 0.014 0.34 NO
93 NUP153 NUP153 NUP153 8016 0.014 0.34 NO
94 SF3B1 SF3B1 SF3B1 8060 0.014 0.34 NO
95 NUP188 NUP188 NUP188 8129 0.013 0.34 NO
96 DDX23 DDX23 DDX23 8165 0.012 0.34 NO
97 POLR2G POLR2G POLR2G 8198 0.012 0.34 NO
98 POLR2B POLR2B POLR2B 8200 0.012 0.34 NO
99 PCBP2 PCBP2 PCBP2 8205 0.012 0.34 NO
100 HNRNPA2B1 HNRNPA2B1 HNRNPA2B1 8348 0.0098 0.33 NO
101 CSTF1 CSTF1 CSTF1 8369 0.0095 0.33 NO
102 RANBP2 RANBP2 RANBP2 8408 0.0088 0.33 NO
103 UPF3B UPF3B UPF3B 8568 0.0063 0.32 NO
104 ADAR ADAR ADAR 8583 0.0061 0.32 NO
105 SF3B2 SF3B2 SF3B2 8767 0.0032 0.31 NO
106 PRPF4 PRPF4 PRPF4 8951 0.00049 0.3 NO
107 NFX1 NFX1 NFX1 9037 -0.00077 0.3 NO
108 NUPL1 NUPL1 NUPL1 9184 -0.003 0.29 NO
109 HNRNPK HNRNPK HNRNPK 9265 -0.0042 0.29 NO
110 SNRNP200 SNRNP200 SNRNP200 9301 -0.0047 0.28 NO
111 POLR2A POLR2A POLR2A 9461 -0.0075 0.28 NO
112 PCBP1 PCBP1 PCBP1 9474 -0.0078 0.28 NO
113 SNRNP40 SNRNP40 SNRNP40 9574 -0.0092 0.27 NO
114 CLP1 CLP1 CLP1 9643 -0.01 0.27 NO
115 MNAT1 MNAT1 MNAT1 9722 -0.012 0.27 NO
116 POLR2E POLR2E POLR2E 9788 -0.013 0.27 NO
117 RNGTT RNGTT RNGTT 9938 -0.015 0.26 NO
118 EIF4E EIF4E EIF4E 9994 -0.016 0.26 NO
119 SF3A1 SF3A1 SF3A1 10204 -0.02 0.25 NO
120 CPSF2 CPSF2 CPSF2 10206 -0.02 0.25 NO
121 POLR2K POLR2K POLR2K 10232 -0.02 0.25 NO
122 RNPS1 RNPS1 RNPS1 10306 -0.022 0.25 NO
123 GTF2H2 GTF2H2 GTF2H2 10477 -0.024 0.24 NO
124 NCBP1 NCBP1 NCBP1 10645 -0.027 0.24 NO
125 SMC1A SMC1A SMC1A 10867 -0.031 0.23 NO
126 POLR2L POLR2L POLR2L 11359 -0.04 0.21 NO
127 HNRNPR HNRNPR HNRNPR 11478 -0.042 0.21 NO
128 NUP54 NUP54 NUP54 11550 -0.043 0.21 NO
129 NUP93 NUP93 NUP93 11578 -0.043 0.21 NO
130 YBX1 YBX1 YBX1 11655 -0.045 0.21 NO
131 MAGOH MAGOH MAGOH 11661 -0.045 0.22 NO
132 CDC40 CDC40 CDC40 11761 -0.047 0.22 NO
133 CD2BP2 CD2BP2 CD2BP2 11803 -0.047 0.22 NO
134 SF3A3 SF3A3 SF3A3 11879 -0.049 0.23 NO
135 SF3B3 SF3B3 SF3B3 11927 -0.05 0.23 NO
136 NUDT21 NUDT21 NUDT21 11931 -0.05 0.24 NO
137 HNRNPH2 HNRNPH2 HNRNPH2 11943 -0.05 0.24 NO
138 DNAJC8 DNAJC8 DNAJC8 12013 -0.051 0.24 NO
139 SRRM1 SRRM1 SRRM1 12978 -0.072 0.2 NO
140 DHX38 DHX38 DHX38 13133 -0.076 0.2 NO
141 GTF2H3 GTF2H3 GTF2H3 13272 -0.08 0.2 NO
142 POLR2C POLR2C POLR2C 13546 -0.087 0.2 NO
143 CCNH CCNH CCNH 13982 -0.098 0.19 NO
144 CSTF2 CSTF2 CSTF2 14018 -0.099 0.2 NO
145 LSM10 LSM10 LSM10 14219 -0.1 0.2 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: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S50.  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 SIGNALLING TO RAS

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 RPL21 RPL21 RPL21 884 0.26 -0.023 YES
2 RPL36A RPL36A RPL36A 1468 0.2 -0.036 YES
3 RPL9 RPL9 RPL9 1788 0.17 -0.036 YES
4 FAM153A FAM153A FAM153A 1939 0.16 -0.028 YES
5 RPS24 RPS24 RPS24 1956 0.16 -0.012 YES
6 RPS19 RPS19 RPS19 2207 0.15 -0.011 YES
7 RPSA RPSA RPSA 2217 0.15 0.0041 YES
8 RPSAP9 RPSAP9 RPSAP9 2231 0.15 0.018 YES
9 RPLP0 RPLP0 RPLP0 2454 0.14 0.02 YES
10 RPS21 RPS21 RPS21 2515 0.13 0.03 YES
11 SEC11C SEC11C SEC11C 2517 0.13 0.044 YES
12 SSR2 SSR2 SSR2 2580 0.13 0.054 YES
13 RPL39 RPL39 RPL39 2600 0.13 0.066 YES
14 RPL27A RPL27A RPL27A 2612 0.13 0.079 YES
15 RPS10 RPS10 RPS10 2613 0.13 0.092 YES
16 RPS12 RPS12 RPS12 2677 0.13 0.1 YES
17 RPS27 RPS27 RPS27 2735 0.12 0.11 YES
18 RPS17 RPS17 RPS17 2737 0.12 0.12 YES
19 RPS3 RPS3 RPS3 2761 0.12 0.14 YES
20 RPL23A RPL23A RPL23A 2768 0.12 0.15 YES
21 RPS7 RPS7 RPS7 2788 0.12 0.16 YES
22 RPS18 RPS18 RPS18 2794 0.12 0.17 YES
23 RPL26 RPL26 RPL26 2852 0.12 0.18 YES
24 RPS5 RPS5 RPS5 2871 0.12 0.19 YES
25 RPS27A RPS27A RPS27A 2884 0.12 0.2 YES
26 RPS15 RPS15 RPS15 2892 0.12 0.22 YES
27 RPL18A RPL18A RPL18A 2917 0.12 0.23 YES
28 RPS29 RPS29 RPS29 2934 0.12 0.24 YES
29 RPL28 RPL28 RPL28 2952 0.12 0.25 YES
30 RPL37A RPL37A RPL37A 3192 0.11 0.25 YES
31 RPL36 RPL36 RPL36 3272 0.11 0.25 YES
32 RPS28 RPS28 RPS28 3286 0.1 0.26 YES
33 RPL7 RPL7 RPL7 3288 0.1 0.27 YES
34 RPLP2 RPLP2 RPLP2 3289 0.1 0.28 YES
35 RPS4X RPS4X RPS4X 3293 0.1 0.3 YES
36 RPL32 RPL32 RPL32 3331 0.1 0.3 YES
37 RPL18 RPL18 RPL18 3335 0.1 0.32 YES
38 RPL6 RPL6 RPL6 3358 0.1 0.32 YES
39 RPL31 RPL31 RPL31 3366 0.1 0.33 YES
40 RPL7A RPL7A RPL7A 3376 0.1 0.34 YES
41 RPL27 RPL27 RPL27 3384 0.1 0.36 YES
42 RPL38 RPL38 RPL38 3414 0.1 0.36 YES
43 RPL17 RPL17 RPL17 3417 0.1 0.37 YES
44 RPL13A RPL13A RPL13A 3488 0.1 0.38 YES
45 RPS16 RPS16 RPS16 3532 0.099 0.39 YES
46 RPL35A RPL35A RPL35A 3619 0.097 0.39 YES
47 RPL14 RPL14 RPL14 3627 0.096 0.4 YES
48 SEC61A2 SEC61A2 SEC61A2 3647 0.096 0.41 YES
49 RPL3 RPL3 RPL3 3661 0.095 0.42 YES
50 RPL10A RPL10A RPL10A 3670 0.095 0.43 YES
51 RPS11 RPS11 RPS11 3681 0.094 0.44 YES
52 RPL4 RPL4 RPL4 3741 0.093 0.44 YES
53 RPL23 RPL23 RPL23 4022 0.085 0.44 YES
54 RPL35 RPL35 RPL35 4077 0.084 0.44 YES
55 RPS9 RPS9 RPS9 4088 0.084 0.45 YES
56 SSR4 SSR4 SSR4 4105 0.083 0.46 YES
57 RPL8 RPL8 RPL8 4107 0.083 0.47 YES
58 RPL41 RPL41 RPL41 4108 0.083 0.48 YES
59 RPS6 RPS6 RPS6 4116 0.083 0.48 YES
60 RPS2 RPS2 RPS2 4195 0.081 0.49 YES
61 RPL37 RPL37 RPL37 4259 0.08 0.49 YES
62 RPS23 RPS23 RPS23 4261 0.08 0.5 YES
63 RPL24 RPL24 RPL24 4266 0.08 0.51 YES
64 SEC11A SEC11A SEC11A 4272 0.08 0.52 YES
65 RPL30 RPL30 RPL30 4292 0.079 0.52 YES
66 RPS13 RPS13 RPS13 4332 0.078 0.53 YES
67 RPS25 RPS25 RPS25 4342 0.078 0.54 YES
68 RPLP1 RPLP1 RPLP1 4504 0.074 0.54 YES
69 RPL29 RPL29 RPL29 4630 0.072 0.54 YES
70 RPL12 RPL12 RPL12 4729 0.07 0.54 YES
71 SPCS2 SPCS2 SPCS2 4844 0.068 0.54 YES
72 SRP9 SRP9 SRP9 4864 0.067 0.55 YES
73 RPL15 RPL15 RPL15 4885 0.067 0.55 YES
74 RPS20 RPS20 RPS20 4902 0.066 0.56 YES
75 RPS14 RPS14 RPS14 5088 0.062 0.55 YES
76 LOC653566 LOC653566 LOC653566 5174 0.061 0.55 YES
77 RPS3A RPS3A RPS3A 5206 0.06 0.56 YES
78 RPL10 RPL10 RPL10 5212 0.06 0.56 YES
79 RPL5 RPL5 RPL5 5219 0.06 0.57 YES
80 SEC61G SEC61G SEC61G 5265 0.059 0.57 YES
81 UBA52 UBA52 UBA52 5362 0.057 0.57 YES
82 RPL34 RPL34 RPL34 5551 0.054 0.57 YES
83 RPL19 RPL19 RPL19 5664 0.052 0.57 YES
84 RPS8 RPS8 RPS8 5783 0.05 0.57 YES
85 RPN2 RPN2 RPN2 5793 0.05 0.57 YES
86 RPS15A RPS15A RPS15A 5804 0.05 0.58 YES
87 SSR1 SSR1 SSR1 5816 0.049 0.58 YES
88 RPL13 RPL13 RPL13 5986 0.046 0.57 NO
89 RPS26 RPS26 RPS26 6149 0.044 0.57 NO
90 SRPRB SRPRB SRPRB 6241 0.042 0.57 NO
91 FAU FAU FAU 6458 0.039 0.56 NO
92 SRP14 SRP14 SRP14 7002 0.03 0.53 NO
93 RPL11 RPL11 RPL11 7214 0.027 0.52 NO
94 RPL22 RPL22 RPL22 7268 0.026 0.52 NO
95 SRP68 SRP68 SRP68 7408 0.024 0.52 NO
96 SSR3 SSR3 SSR3 7590 0.021 0.51 NO
97 SEC61B SEC61B SEC61B 7976 0.015 0.49 NO
98 RPN1 RPN1 RPN1 7994 0.014 0.49 NO
99 SRP72 SRP72 SRP72 8414 0.0086 0.47 NO
100 SEC61A1 SEC61A1 SEC61A1 8632 0.0052 0.46 NO
101 TRAM1 TRAM1 TRAM1 9035 -0.00076 0.43 NO
102 SRP19 SRP19 SRP19 9449 -0.0073 0.41 NO
103 SPCS1 SPCS1 SPCS1 10513 -0.025 0.35 NO
104 DDOST DDOST DDOST 10683 -0.028 0.35 NO
105 SRP54 SRP54 SRP54 11703 -0.046 0.29 NO
106 SRPR SRPR SRPR 12687 -0.066 0.24 NO
107 SPCS3 SPCS3 SPCS3 13086 -0.075 0.23 NO
108 RPL26L1 RPL26L1 RPL26L1 13573 -0.087 0.21 NO
109 RPS4Y1 RPS4Y1 RPS4Y1 16645 -0.24 0.062 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 SIGNALLING TO RAS.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SIGNALLING TO RAS, 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 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 RPL21 RPL21 RPL21 884 0.26 -0.022 YES
2 RPL36A RPL36A RPL36A 1468 0.2 -0.034 YES
3 RPL9 RPL9 RPL9 1788 0.17 -0.033 YES
4 FAM153A FAM153A FAM153A 1939 0.16 -0.024 YES
5 RPS24 RPS24 RPS24 1956 0.16 -0.008 YES
6 RPS19 RPS19 RPS19 2207 0.15 -0.0064 YES
7 RPSA RPSA RPSA 2217 0.15 0.0089 YES
8 RPSAP9 RPSAP9 RPSAP9 2231 0.15 0.024 YES
9 RPLP0 RPLP0 RPLP0 2454 0.14 0.026 YES
10 RPS21 RPS21 RPS21 2515 0.13 0.037 YES
11 RPL39 RPL39 RPL39 2600 0.13 0.046 YES
12 RPL27A RPL27A RPL27A 2612 0.13 0.059 YES
13 RPS10 RPS10 RPS10 2613 0.13 0.073 YES
14 RPS12 RPS12 RPS12 2677 0.13 0.083 YES
15 RPS27 RPS27 RPS27 2735 0.12 0.093 YES
16 RPS17 RPS17 RPS17 2737 0.12 0.11 YES
17 RPS3 RPS3 RPS3 2761 0.12 0.12 YES
18 RPL23A RPL23A RPL23A 2768 0.12 0.13 YES
19 RPS7 RPS7 RPS7 2788 0.12 0.14 YES
20 RPS18 RPS18 RPS18 2794 0.12 0.16 YES
21 RPL26 RPL26 RPL26 2852 0.12 0.16 YES
22 RPS5 RPS5 RPS5 2871 0.12 0.18 YES
23 RPS27A RPS27A RPS27A 2884 0.12 0.19 YES
24 RPS15 RPS15 RPS15 2892 0.12 0.2 YES
25 RPL18A RPL18A RPL18A 2917 0.12 0.21 YES
26 RPS29 RPS29 RPS29 2934 0.12 0.22 YES
27 RPL28 RPL28 RPL28 2952 0.12 0.24 YES
28 RPL37A RPL37A RPL37A 3192 0.11 0.23 YES
29 RPL36 RPL36 RPL36 3272 0.11 0.24 YES
30 RPS28 RPS28 RPS28 3286 0.1 0.25 YES
31 RPL7 RPL7 RPL7 3288 0.1 0.26 YES
32 RPLP2 RPLP2 RPLP2 3289 0.1 0.27 YES
33 RPS4X RPS4X RPS4X 3293 0.1 0.28 YES
34 RPL32 RPL32 RPL32 3331 0.1 0.29 YES
35 RPL18 RPL18 RPL18 3335 0.1 0.3 YES
36 RPL6 RPL6 RPL6 3358 0.1 0.32 YES
37 RPL31 RPL31 RPL31 3366 0.1 0.32 YES
38 RPL7A RPL7A RPL7A 3376 0.1 0.34 YES
39 RPL27 RPL27 RPL27 3384 0.1 0.35 YES
40 RPL38 RPL38 RPL38 3414 0.1 0.36 YES
41 RPL17 RPL17 RPL17 3417 0.1 0.37 YES
42 RPL13A RPL13A RPL13A 3488 0.1 0.37 YES
43 RPS16 RPS16 RPS16 3532 0.099 0.38 YES
44 RPL35A RPL35A RPL35A 3619 0.097 0.39 YES
45 RPL14 RPL14 RPL14 3627 0.096 0.4 YES
46 RPL3 RPL3 RPL3 3661 0.095 0.4 YES
47 RPL10A RPL10A RPL10A 3670 0.095 0.42 YES
48 RPS11 RPS11 RPS11 3681 0.094 0.42 YES
49 RPL4 RPL4 RPL4 3741 0.093 0.43 YES
50 RPL23 RPL23 RPL23 4022 0.085 0.42 YES
51 RPL35 RPL35 RPL35 4077 0.084 0.43 YES
52 RPS9 RPS9 RPS9 4088 0.084 0.44 YES
53 RPL8 RPL8 RPL8 4107 0.083 0.45 YES
54 RPL41 RPL41 RPL41 4108 0.083 0.46 YES
55 RPS6 RPS6 RPS6 4116 0.083 0.46 YES
56 RPS2 RPS2 RPS2 4195 0.081 0.47 YES
57 RPL37 RPL37 RPL37 4259 0.08 0.47 YES
58 RPS23 RPS23 RPS23 4261 0.08 0.48 YES
59 RPL24 RPL24 RPL24 4266 0.08 0.49 YES
60 RPL30 RPL30 RPL30 4292 0.079 0.5 YES
61 RPS13 RPS13 RPS13 4332 0.078 0.5 YES
62 RPS25 RPS25 RPS25 4342 0.078 0.51 YES
63 EIF3D EIF3D EIF3D 4456 0.075 0.51 YES
64 EIF2S3 EIF2S3 EIF2S3 4494 0.074 0.52 YES
65 RPLP1 RPLP1 RPLP1 4504 0.074 0.52 YES
66 PABPC1 PABPC1 PABPC1 4626 0.072 0.53 YES
67 RPL29 RPL29 RPL29 4630 0.072 0.53 YES
68 EIF2S2 EIF2S2 EIF2S2 4715 0.07 0.54 YES
69 RPL12 RPL12 RPL12 4729 0.07 0.54 YES
70 RPL15 RPL15 RPL15 4885 0.067 0.54 YES
71 RPS20 RPS20 RPS20 4902 0.066 0.55 YES
72 EIF4A1 EIF4A1 EIF4A1 4963 0.065 0.55 YES
73 EIF4A2 EIF4A2 EIF4A2 4972 0.065 0.56 YES
74 RPS14 RPS14 RPS14 5088 0.062 0.56 YES
75 RPS3A RPS3A RPS3A 5206 0.06 0.56 YES
76 RPL10 RPL10 RPL10 5212 0.06 0.56 YES
77 RPL5 RPL5 RPL5 5219 0.06 0.57 YES
78 UBA52 UBA52 UBA52 5362 0.057 0.57 YES
79 RPL34 RPL34 RPL34 5551 0.054 0.56 YES
80 RPL19 RPL19 RPL19 5664 0.052 0.56 YES
81 EIF4B EIF4B EIF4B 5738 0.051 0.56 YES
82 RPS8 RPS8 RPS8 5783 0.05 0.57 YES
83 RPS15A RPS15A RPS15A 5804 0.05 0.57 YES
84 EIF3K EIF3K EIF3K 5900 0.048 0.57 YES
85 EIF3F EIF3F EIF3F 5948 0.047 0.57 YES
86 RPL13 RPL13 RPL13 5986 0.046 0.57 YES
87 RPS26 RPS26 RPS26 6149 0.044 0.57 NO
88 EIF3G EIF3G EIF3G 6317 0.041 0.57 NO
89 FAU FAU FAU 6458 0.039 0.56 NO
90 EIF3E EIF3E EIF3E 6583 0.036 0.56 NO
91 EIF3B EIF3B EIF3B 6773 0.034 0.55 NO
92 RPL11 RPL11 RPL11 7214 0.027 0.53 NO
93 RPL22 RPL22 RPL22 7268 0.026 0.53 NO
94 EIF1AX EIF1AX EIF1AX 8327 0.01 0.47 NO
95 EIF3A EIF3A EIF3A 8556 0.0066 0.46 NO
96 EIF3J EIF3J EIF3J 8723 0.0038 0.45 NO
97 EIF3H EIF3H EIF3H 8844 0.0019 0.44 NO
98 EIF4E EIF4E EIF4E 9994 -0.016 0.38 NO
99 EIF4H EIF4H EIF4H 10191 -0.02 0.37 NO
100 EIF2S1 EIF2S1 EIF2S1 10844 -0.03 0.34 NO
101 EIF3C EIF3C EIF3C 11701 -0.046 0.29 NO
102 EIF4G1 EIF4G1 EIF4G1 12581 -0.064 0.25 NO
103 EIF3I EIF3I EIF3I 12667 -0.066 0.25 NO
104 RPL26L1 RPL26L1 RPL26L1 13573 -0.087 0.21 NO
105 RPS4Y1 RPS4Y1 RPS4Y1 16645 -0.24 0.062 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 SIGNALLING TO ERKS.

Figure S54.  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 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA

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 RPL21 RPL21 RPL21 884 0.26 -0.036 YES
2 RPL36A RPL36A RPL36A 1468 0.2 -0.057 YES
3 RPL9 RPL9 RPL9 1788 0.17 -0.066 YES
4 C2orf29 C2orf29 C2orf29 1857 0.17 -0.06 YES
5 PRKCD PRKCD PRKCD 1858 0.17 -0.05 YES
6 GSPT2 GSPT2 GSPT2 1932 0.16 -0.045 YES
7 FAM153A FAM153A FAM153A 1939 0.16 -0.036 YES
8 SMN1 SMN1 SMN1 1945 0.16 -0.027 YES
9 RPS24 RPS24 RPS24 1956 0.16 -0.018 YES
10 GEMIN7 GEMIN7 GEMIN7 2025 0.16 -0.013 YES
11 RPS19 RPS19 RPS19 2207 0.15 -0.015 YES
12 RPSA RPSA RPSA 2217 0.15 -0.0072 YES
13 RPSAP9 RPSAP9 RPSAP9 2231 0.15 0.00051 YES
14 SNRPE SNRPE SNRPE 2268 0.14 0.0068 YES
15 RPLP0 RPLP0 RPLP0 2454 0.14 0.004 YES
16 RPS21 RPS21 RPS21 2515 0.13 0.0082 YES
17 SNRPD1 SNRPD1 SNRPD1 2587 0.13 0.012 YES
18 RPL39 RPL39 RPL39 2600 0.13 0.018 YES
19 RPL27A RPL27A RPL27A 2612 0.13 0.025 YES
20 RPS10 RPS10 RPS10 2613 0.13 0.032 YES
21 RPS12 RPS12 RPS12 2677 0.13 0.036 YES
22 RPS27 RPS27 RPS27 2735 0.12 0.04 YES
23 RPS17 RPS17 RPS17 2737 0.12 0.047 YES
24 RPS3 RPS3 RPS3 2761 0.12 0.053 YES
25 RPL23A RPL23A RPL23A 2768 0.12 0.06 YES
26 RPS7 RPS7 RPS7 2788 0.12 0.066 YES
27 NUP210 NUP210 NUP210 2790 0.12 0.073 YES
28 RPS18 RPS18 RPS18 2794 0.12 0.079 YES
29 SNRPF SNRPF SNRPF 2829 0.12 0.084 YES
30 RPL26 RPL26 RPL26 2852 0.12 0.09 YES
31 RPS5 RPS5 RPS5 2871 0.12 0.096 YES
32 RPS27A RPS27A RPS27A 2884 0.12 0.1 YES
33 CNOT6 CNOT6 CNOT6 2885 0.12 0.11 YES
34 RPS15 RPS15 RPS15 2892 0.12 0.12 YES
35 RPL18A RPL18A RPL18A 2917 0.12 0.12 YES
36 RPS29 RPS29 RPS29 2934 0.12 0.13 YES
37 LSM2 LSM2 LSM2 2950 0.12 0.13 YES
38 RPL28 RPL28 RPL28 2952 0.12 0.14 YES
39 EXOSC8 EXOSC8 EXOSC8 3160 0.11 0.13 YES
40 RPL37A RPL37A RPL37A 3192 0.11 0.14 YES
41 RPL36 RPL36 RPL36 3272 0.11 0.14 YES
42 RPS28 RPS28 RPS28 3286 0.1 0.14 YES
43 RPL7 RPL7 RPL7 3288 0.1 0.15 YES
44 RPLP2 RPLP2 RPLP2 3289 0.1 0.16 YES
45 RPS4X RPS4X RPS4X 3293 0.1 0.16 YES
46 RPL32 RPL32 RPL32 3331 0.1 0.17 YES
47 RPL18 RPL18 RPL18 3335 0.1 0.17 YES
48 UPF3A UPF3A UPF3A 3350 0.1 0.18 YES
49 NUP133 NUP133 NUP133 3352 0.1 0.18 YES
50 RPL6 RPL6 RPL6 3358 0.1 0.19 YES
51 RPL31 RPL31 RPL31 3366 0.1 0.19 YES
52 RPL7A RPL7A RPL7A 3376 0.1 0.2 YES
53 RPL27 RPL27 RPL27 3384 0.1 0.2 YES
54 RPL38 RPL38 RPL38 3414 0.1 0.21 YES
55 RPL17 RPL17 RPL17 3417 0.1 0.22 YES
56 SNRPB SNRPB SNRPB 3425 0.1 0.22 YES
57 RPL13A RPL13A RPL13A 3488 0.1 0.22 YES
58 RPS16 RPS16 RPS16 3532 0.099 0.23 YES
59 KHSRP KHSRP KHSRP 3609 0.097 0.23 YES
60 DCP2 DCP2 DCP2 3610 0.097 0.23 YES
61 RPL35A RPL35A RPL35A 3619 0.097 0.24 YES
62 RPL14 RPL14 RPL14 3627 0.096 0.24 YES
63 CNOT3 CNOT3 CNOT3 3645 0.096 0.25 YES
64 RPL3 RPL3 RPL3 3661 0.095 0.25 YES
65 RPL10A RPL10A RPL10A 3670 0.095 0.26 YES
66 RPS11 RPS11 RPS11 3681 0.094 0.26 YES
67 NUP50 NUP50 NUP50 3689 0.094 0.27 YES
68 TPR TPR TPR 3693 0.094 0.27 YES
69 RPL4 RPL4 RPL4 3741 0.093 0.28 YES
70 SMG5 SMG5 SMG5 3809 0.091 0.28 YES
71 EXOSC1 EXOSC1 EXOSC1 3811 0.091 0.28 YES
72 RAE1 RAE1 RAE1 3982 0.086 0.28 YES
73 RPL23 RPL23 RPL23 4022 0.085 0.28 YES
74 SNRPG SNRPG SNRPG 4041 0.085 0.28 YES
75 RPL35 RPL35 RPL35 4077 0.084 0.29 YES
76 RPS9 RPS9 RPS9 4088 0.084 0.29 YES
77 RPL8 RPL8 RPL8 4107 0.083 0.29 YES
78 RPL41 RPL41 RPL41 4108 0.083 0.3 YES
79 RPS6 RPS6 RPS6 4116 0.083 0.3 YES
80 RPS2 RPS2 RPS2 4195 0.081 0.3 YES
81 NUP88 NUP88 NUP88 4204 0.081 0.31 YES
82 RPL37 RPL37 RPL37 4259 0.08 0.31 YES
83 RPS23 RPS23 RPS23 4261 0.08 0.31 YES
84 RPL24 RPL24 RPL24 4266 0.08 0.32 YES
85 SMN2 SMN2 SMN2 4271 0.08 0.32 YES
86 RPL30 RPL30 RPL30 4292 0.079 0.32 YES
87 RPS13 RPS13 RPS13 4332 0.078 0.33 YES
88 RPS25 RPS25 RPS25 4342 0.078 0.33 YES
89 NCBP2 NCBP2 NCBP2 4440 0.076 0.33 YES
90 RBM8A RBM8A RBM8A 4488 0.074 0.33 YES
91 RPLP1 RPLP1 RPLP1 4504 0.074 0.34 YES
92 SNRPD3 SNRPD3 SNRPD3 4545 0.073 0.34 YES
93 POM121 POM121 POM121 4614 0.072 0.34 YES
94 PABPC1 PABPC1 PABPC1 4626 0.072 0.34 YES
95 RPL29 RPL29 RPL29 4630 0.072 0.34 YES
96 ANP32A ANP32A ANP32A 4633 0.072 0.35 YES
97 CNOT10 CNOT10 CNOT10 4635 0.072 0.35 YES
98 RPL12 RPL12 RPL12 4729 0.07 0.35 YES
99 SNRPD2 SNRPD2 SNRPD2 4777 0.069 0.35 YES
100 RPL15 RPL15 RPL15 4885 0.067 0.35 YES
101 SMG7 SMG7 SMG7 4892 0.067 0.35 YES
102 RPS20 RPS20 RPS20 4902 0.066 0.36 YES
103 EIF4A1 EIF4A1 EIF4A1 4963 0.065 0.36 YES
104 EIF4A2 EIF4A2 EIF4A2 4972 0.065 0.36 YES
105 RPS14 RPS14 RPS14 5088 0.062 0.36 YES
106 NUP43 NUP43 NUP43 5203 0.06 0.36 YES
107 RPS3A RPS3A RPS3A 5206 0.06 0.36 YES
108 RPL10 RPL10 RPL10 5212 0.06 0.36 YES
109 RPL5 RPL5 RPL5 5219 0.06 0.36 YES
110 DCPS DCPS DCPS 5225 0.06 0.37 YES
111 PPP2R1A PPP2R1A PPP2R1A 5230 0.06 0.37 YES
112 HSPB1 HSPB1 HSPB1 5257 0.059 0.37 YES
113 UBA52 UBA52 UBA52 5362 0.057 0.37 YES
114 NUP85 NUP85 NUP85 5425 0.056 0.37 YES
115 DCP1B DCP1B DCP1B 5517 0.054 0.37 YES
116 RPL34 RPL34 RPL34 5551 0.054 0.37 YES
117 CNOT2 CNOT2 CNOT2 5560 0.054 0.37 YES
118 EXOSC7 EXOSC7 EXOSC7 5563 0.054 0.37 YES
119 EDC3 EDC3 EDC3 5605 0.053 0.38 YES
120 RPL19 RPL19 RPL19 5664 0.052 0.38 YES
121 GEMIN4 GEMIN4 GEMIN4 5684 0.052 0.38 YES
122 LSM4 LSM4 LSM4 5722 0.051 0.38 YES
123 EIF4B EIF4B EIF4B 5738 0.051 0.38 YES
124 NUP37 NUP37 NUP37 5781 0.05 0.38 YES
125 RPS8 RPS8 RPS8 5783 0.05 0.38 YES
126 RPS15A RPS15A RPS15A 5804 0.05 0.38 YES
127 YWHAZ YWHAZ YWHAZ 5817 0.049 0.39 YES
128 SMG6 SMG6 SMG6 5933 0.047 0.38 NO
129 RPL13 RPL13 RPL13 5986 0.046 0.38 NO
130 UPF2 UPF2 UPF2 6013 0.046 0.38 NO
131 RPS26 RPS26 RPS26 6149 0.044 0.38 NO
132 NUP62 NUP62 NUP62 6439 0.039 0.36 NO
133 NUP205 NUP205 NUP205 6454 0.039 0.36 NO
134 FAU FAU FAU 6458 0.039 0.37 NO
135 MAPK14 MAPK14 MAPK14 6480 0.038 0.37 NO
136 ELAVL1 ELAVL1 ELAVL1 6557 0.037 0.37 NO
137 EXOSC3 EXOSC3 EXOSC3 6624 0.036 0.36 NO
138 AAAS AAAS AAAS 6673 0.035 0.36 NO
139 LSM3 LSM3 LSM3 6769 0.034 0.36 NO
140 NUP214 NUP214 NUP214 6834 0.033 0.36 NO
141 SEH1L SEH1L SEH1L 6848 0.032 0.36 NO
142 NUP107 NUP107 NUP107 6928 0.031 0.36 NO
143 XPO1 XPO1 XPO1 6991 0.03 0.36 NO
144 EXOSC4 EXOSC4 EXOSC4 6995 0.03 0.36 NO
145 SNUPN SNUPN SNUPN 7047 0.029 0.36 NO
146 HNRNPD HNRNPD HNRNPD 7096 0.029 0.35 NO
147 NUP35 NUP35 NUP35 7132 0.028 0.35 NO
148 PSMD4 PSMD4 PSMD4 7196 0.027 0.35 NO
149 RPL11 RPL11 RPL11 7214 0.027 0.35 NO
150 RPL22 RPL22 RPL22 7268 0.026 0.35 NO
151 PSMB5 PSMB5 PSMB5 7288 0.026 0.35 NO
152 CLNS1A CLNS1A CLNS1A 7375 0.025 0.35 NO
153 EXOSC2 EXOSC2 EXOSC2 7573 0.022 0.34 NO
154 CASC3 CASC3 CASC3 7763 0.018 0.33 NO
155 NUPL2 NUPL2 NUPL2 7769 0.018 0.33 NO
156 NUP155 NUP155 NUP155 7775 0.018 0.33 NO
157 PSMB4 PSMB4 PSMB4 7880 0.016 0.32 NO
158 PSMA4 PSMA4 PSMA4 7963 0.015 0.32 NO
159 NUP153 NUP153 NUP153 8016 0.014 0.32 NO
160 NUP188 NUP188 NUP188 8129 0.013 0.31 NO
161 EIF4A3 EIF4A3 EIF4A3 8136 0.012 0.31 NO
162 PSMC4 PSMC4 PSMC4 8152 0.012 0.31 NO
163 PSME4 PSME4 PSME4 8224 0.011 0.31 NO
164 DDX6 DDX6 DDX6 8257 0.011 0.31 NO
165 RANBP2 RANBP2 RANBP2 8408 0.0088 0.3 NO
166 DCP1A DCP1A DCP1A 8524 0.0071 0.29 NO
167 PSMC6 PSMC6 PSMC6 8545 0.0067 0.29 NO
168 UPF3B UPF3B UPF3B 8568 0.0063 0.29 NO
169 TGS1 TGS1 TGS1 8764 0.0032 0.28 NO
170 PSMF1 PSMF1 PSMF1 8789 0.0028 0.28 NO
171 AKT1 AKT1 AKT1 8877 0.0014 0.28 NO
172 LSM1 LSM1 LSM1 8900 0.0011 0.27 NO
173 PPP2CA PPP2CA PPP2CA 8969 0.00031 0.27 NO
174 WDR77 WDR77 WDR77 8983 0.000074 0.27 NO
175 PSMD5 PSMD5 PSMD5 8985 7.5e-06 0.27 NO
176 PSMB6 PSMB6 PSMB6 8992 -0.000072 0.27 NO
177 GEMIN6 GEMIN6 GEMIN6 8994 -0.00014 0.27 NO
178 LSM6 LSM6 LSM6 8996 -0.00015 0.27 NO
179 PSMD13 PSMD13 PSMD13 9126 -0.002 0.26 NO
180 EXOSC5 EXOSC5 EXOSC5 9144 -0.0024 0.26 NO
181 NUPL1 NUPL1 NUPL1 9184 -0.003 0.26 NO
182 PSMB1 PSMB1 PSMB1 9199 -0.0032 0.26 NO
183 PSMB3 PSMB3 PSMB3 9237 -0.0038 0.26 NO
184 PSMD8 PSMD8 PSMD8 9300 -0.0047 0.25 NO
185 PATL1 PATL1 PATL1 9429 -0.007 0.25 NO
186 PSMC1 PSMC1 PSMC1 9456 -0.0075 0.24 NO
187 PSMD6 PSMD6 PSMD6 9628 -0.01 0.24 NO
188 CNOT7 CNOT7 CNOT7 9659 -0.011 0.24 NO
189 GEMIN5 GEMIN5 GEMIN5 9812 -0.013 0.23 NO
190 YWHAB YWHAB YWHAB 9824 -0.013 0.23 NO
191 PSMA6 PSMA6 PSMA6 9826 -0.013 0.23 NO
192 PSMC5 PSMC5 PSMC5 9836 -0.014 0.23 NO
193 PSMA1 PSMA1 PSMA1 9874 -0.014 0.23 NO
194 PRKCA PRKCA PRKCA 9883 -0.014 0.23 NO
195 EIF4E EIF4E EIF4E 9994 -0.016 0.22 NO
196 PAIP1 PAIP1 PAIP1 10095 -0.018 0.22 NO
197 RQCD1 RQCD1 RQCD1 10174 -0.019 0.21 NO
198 PSMC3 PSMC3 PSMC3 10181 -0.019 0.21 NO
199 HSPA8 HSPA8 HSPA8 10198 -0.02 0.21 NO
200 RNPS1 RNPS1 RNPS1 10306 -0.022 0.21 NO
201 PHAX PHAX PHAX 10484 -0.024 0.2 NO
202 NCBP1 NCBP1 NCBP1 10645 -0.027 0.19 NO
203 MAPK11 MAPK11 MAPK11 10684 -0.028 0.19 NO
204 PSMD10 PSMD10 PSMD10 10730 -0.029 0.19 NO
205 EXOSC9 EXOSC9 EXOSC9 10736 -0.029 0.19 NO
206 PRMT5 PRMT5 PRMT5 10737 -0.029 0.2 NO
207 TNKS1BP1 TNKS1BP1 TNKS1BP1 10805 -0.03 0.19 NO
208 DDX20 DDX20 DDX20 10819 -0.03 0.19 NO
209 PSMB7 PSMB7 PSMB7 10865 -0.031 0.19 NO
210 PSMA2 PSMA2 PSMA2 10910 -0.032 0.19 NO
211 PSMD1 PSMD1 PSMD1 10985 -0.033 0.19 NO
212 PSMD11 PSMD11 PSMD11 11023 -0.034 0.19 NO
213 PSMD14 PSMD14 PSMD14 11076 -0.034 0.19 NO
214 ETF1 ETF1 ETF1 11080 -0.034 0.19 NO
215 CNOT4 CNOT4 CNOT4 11260 -0.038 0.18 NO
216 XRN1 XRN1 XRN1 11396 -0.04 0.18 NO
217 CNOT8 CNOT8 CNOT8 11449 -0.041 0.18 NO
218 PSME1 PSME1 PSME1 11460 -0.042 0.18 NO
219 PSMA3 PSMA3 PSMA3 11466 -0.042 0.18 NO
220 NUP54 NUP54 NUP54 11550 -0.043 0.18 NO
221 NUP93 NUP93 NUP93 11578 -0.043 0.18 NO
222 LSM5 LSM5 LSM5 11622 -0.044 0.18 NO
223 PSMD9 PSMD9 PSMD9 11641 -0.045 0.18 NO
224 PSMD3 PSMD3 PSMD3 11649 -0.045 0.18 NO
225 MAGOH MAGOH MAGOH 11661 -0.045 0.18 NO
226 TNPO1 TNPO1 TNPO1 11705 -0.046 0.18 NO
227 PSME2 PSME2 PSME2 11869 -0.048 0.18 NO
228 EDC4 EDC4 EDC4 11904 -0.049 0.18 NO
229 PSMC2 PSMC2 PSMC2 11946 -0.05 0.18 NO
230 ZFP36L1 ZFP36L1 ZFP36L1 11950 -0.05 0.18 NO
231 SMG1 SMG1 SMG1 11991 -0.051 0.18 NO
232 PSMA7 PSMA7 PSMA7 12022 -0.052 0.18 NO
233 PSMD2 PSMD2 PSMD2 12278 -0.057 0.17 NO
234 DIS3 DIS3 DIS3 12438 -0.06 0.17 NO
235 EIF4G1 EIF4G1 EIF4G1 12581 -0.064 0.16 NO
236 PPP2R2A PPP2R2A PPP2R2A 12599 -0.064 0.16 NO
237 PSMD12 PSMD12 PSMD12 13033 -0.074 0.14 NO
238 PSMA5 PSMA5 PSMA5 13093 -0.075 0.15 NO
239 MAPKAPK2 MAPKAPK2 MAPKAPK2 13314 -0.081 0.14 NO
240 RPL26L1 RPL26L1 RPL26L1 13573 -0.087 0.13 NO
241 PSMD7 PSMD7 PSMD7 14039 -0.1 0.11 NO
242 EXOSC6 EXOSC6 EXOSC6 14401 -0.11 0.093 NO
243 ZFP36 ZFP36 ZFP36 14454 -0.11 0.096 NO
244 PSMB2 PSMB2 PSMB2 14598 -0.12 0.095 NO
245 PARN PARN PARN 14941 -0.13 0.083 NO
246 PSMA8 PSMA8 PSMA8 15031 -0.14 0.086 NO
247 PSMB10 PSMB10 PSMB10 15061 -0.14 0.092 NO
248 HSPA1B HSPA1B HSPA1B 15062 -0.14 0.1 NO
249 TNFSF13 TNFSF13 TNFSF13 15753 -0.17 0.07 NO
250 RPS4Y1 RPS4Y1 RPS4Y1 16645 -0.24 0.033 NO
251 PSMB9 PSMB9 PSMB9 16704 -0.25 0.044 NO
252 PSMB8 PSMB8 PSMB8 16750 -0.25 0.056 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 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA, 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 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 884 0.26 -0.022 YES
2 RPL36A RPL36A RPL36A 1468 0.2 -0.033 YES
3 RPL9 RPL9 RPL9 1788 0.17 -0.032 YES
4 FAM153A FAM153A FAM153A 1939 0.16 -0.023 YES
5 RPS24 RPS24 RPS24 1956 0.16 -0.0065 YES
6 RPS19 RPS19 RPS19 2207 0.15 -0.0047 YES
7 RPSA RPSA RPSA 2217 0.15 0.011 YES
8 RPSAP9 RPSAP9 RPSAP9 2231 0.15 0.026 YES
9 RPLP0 RPLP0 RPLP0 2454 0.14 0.028 YES
10 RPS21 RPS21 RPS21 2515 0.13 0.039 YES
11 RPL39 RPL39 RPL39 2600 0.13 0.049 YES
12 RPL27A RPL27A RPL27A 2612 0.13 0.062 YES
13 RPS10 RPS10 RPS10 2613 0.13 0.076 YES
14 RPS12 RPS12 RPS12 2677 0.13 0.086 YES
15 RPS27 RPS27 RPS27 2735 0.12 0.096 YES
16 RPS17 RPS17 RPS17 2737 0.12 0.11 YES
17 RPS3 RPS3 RPS3 2761 0.12 0.12 YES
18 RPL23A RPL23A RPL23A 2768 0.12 0.14 YES
19 RPS7 RPS7 RPS7 2788 0.12 0.15 YES
20 RPS18 RPS18 RPS18 2794 0.12 0.16 YES
21 RPL26 RPL26 RPL26 2852 0.12 0.17 YES
22 RPS5 RPS5 RPS5 2871 0.12 0.18 YES
23 RPS27A RPS27A RPS27A 2884 0.12 0.19 YES
24 RPS15 RPS15 RPS15 2892 0.12 0.21 YES
25 RPL18A RPL18A RPL18A 2917 0.12 0.22 YES
26 RPS29 RPS29 RPS29 2934 0.12 0.23 YES
27 RPL28 RPL28 RPL28 2952 0.12 0.24 YES
28 IPO5 IPO5 IPO5 3030 0.11 0.25 YES
29 RPL37A RPL37A RPL37A 3192 0.11 0.25 YES
30 RPL36 RPL36 RPL36 3272 0.11 0.26 YES
31 RPS28 RPS28 RPS28 3286 0.1 0.27 YES
32 RPL7 RPL7 RPL7 3288 0.1 0.28 YES
33 RPLP2 RPLP2 RPLP2 3289 0.1 0.29 YES
34 RPS4X RPS4X RPS4X 3293 0.1 0.3 YES
35 RPL32 RPL32 RPL32 3331 0.1 0.31 YES
36 RPL18 RPL18 RPL18 3335 0.1 0.32 YES
37 RPL6 RPL6 RPL6 3358 0.1 0.33 YES
38 RPL31 RPL31 RPL31 3366 0.1 0.34 YES
39 RPL7A RPL7A RPL7A 3376 0.1 0.36 YES
40 RPL27 RPL27 RPL27 3384 0.1 0.37 YES
41 RPL38 RPL38 RPL38 3414 0.1 0.38 YES
42 RPL17 RPL17 RPL17 3417 0.1 0.39 YES
43 RPL13A RPL13A RPL13A 3488 0.1 0.39 YES
44 POLR2H POLR2H POLR2H 3505 0.1 0.4 YES
45 RPS16 RPS16 RPS16 3532 0.099 0.41 YES
46 RPL35A RPL35A RPL35A 3619 0.097 0.42 YES
47 RPL14 RPL14 RPL14 3627 0.096 0.43 YES
48 RPL3 RPL3 RPL3 3661 0.095 0.44 YES
49 RPL10A RPL10A RPL10A 3670 0.095 0.45 YES
50 RPS11 RPS11 RPS11 3681 0.094 0.46 YES
51 RPL4 RPL4 RPL4 3741 0.093 0.46 YES
52 RPL23 RPL23 RPL23 4022 0.085 0.46 YES
53 RPL35 RPL35 RPL35 4077 0.084 0.46 YES
54 RPS9 RPS9 RPS9 4088 0.084 0.47 YES
55 RPL8 RPL8 RPL8 4107 0.083 0.48 YES
56 RPL41 RPL41 RPL41 4108 0.083 0.49 YES
57 RPS6 RPS6 RPS6 4116 0.083 0.5 YES
58 RPS2 RPS2 RPS2 4195 0.081 0.5 YES
59 RPL37 RPL37 RPL37 4259 0.08 0.51 YES
60 RPS23 RPS23 RPS23 4261 0.08 0.52 YES
61 RPL24 RPL24 RPL24 4266 0.08 0.52 YES
62 RPL30 RPL30 RPL30 4292 0.079 0.53 YES
63 RPS13 RPS13 RPS13 4332 0.078 0.54 YES
64 RPS25 RPS25 RPS25 4342 0.078 0.55 YES
65 RPLP1 RPLP1 RPLP1 4504 0.074 0.54 YES
66 RPL29 RPL29 RPL29 4630 0.072 0.54 YES
67 RPL12 RPL12 RPL12 4729 0.07 0.55 YES
68 POLR2D POLR2D POLR2D 4858 0.067 0.55 YES
69 RPL15 RPL15 RPL15 4885 0.067 0.55 YES
70 RPS20 RPS20 RPS20 4902 0.066 0.56 YES
71 RPS14 RPS14 RPS14 5088 0.062 0.56 YES
72 POLR2F POLR2F POLR2F 5124 0.062 0.56 YES
73 RPS3A RPS3A RPS3A 5206 0.06 0.56 YES
74 RPL10 RPL10 RPL10 5212 0.06 0.57 YES
75 RPL5 RPL5 RPL5 5219 0.06 0.57 YES
76 UBA52 UBA52 UBA52 5362 0.057 0.57 YES
77 GTF2F2 GTF2F2 GTF2F2 5412 0.056 0.57 YES
78 RPL34 RPL34 RPL34 5551 0.054 0.57 YES
79 RPL19 RPL19 RPL19 5664 0.052 0.57 YES
80 RPS8 RPS8 RPS8 5783 0.05 0.57 YES
81 RPS15A RPS15A RPS15A 5804 0.05 0.57 YES
82 RPL13 RPL13 RPL13 5986 0.046 0.57 NO
83 RPS26 RPS26 RPS26 6149 0.044 0.57 NO
84 GTF2F1 GTF2F1 GTF2F1 6267 0.042 0.56 NO
85 FAU FAU FAU 6458 0.039 0.56 NO
86 POLR2I POLR2I POLR2I 6615 0.036 0.55 NO
87 HSP90AA1 HSP90AA1 HSP90AA1 6669 0.035 0.55 NO
88 RPL11 RPL11 RPL11 7214 0.027 0.52 NO
89 RPL22 RPL22 RPL22 7268 0.026 0.52 NO
90 POLR2J POLR2J POLR2J 7462 0.023 0.52 NO
91 POLR2G POLR2G POLR2G 8198 0.012 0.48 NO
92 POLR2B POLR2B POLR2B 8200 0.012 0.48 NO
93 POLR2A POLR2A POLR2A 9461 -0.0075 0.41 NO
94 POLR2E POLR2E POLR2E 9788 -0.013 0.39 NO
95 DNAJC3 DNAJC3 DNAJC3 9816 -0.013 0.39 NO
96 POLR2K POLR2K POLR2K 10232 -0.02 0.37 NO
97 POLR2L POLR2L POLR2L 11359 -0.04 0.31 NO
98 GRSF1 GRSF1 GRSF1 12923 -0.071 0.23 NO
99 POLR2C POLR2C POLR2C 13546 -0.087 0.2 NO
100 RPL26L1 RPL26L1 RPL26L1 13573 -0.087 0.21 NO
101 RPS4Y1 RPS4Y1 RPS4Y1 16645 -0.24 0.061 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 ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S58.  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

genes ES table in pathway: REACTOME PEPTIDE CHAIN ELONGATION

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 RPL21 RPL21 RPL21 884 0.26 -0.019 YES
2 RPL36A RPL36A RPL36A 1468 0.2 -0.029 YES
3 RPL9 RPL9 RPL9 1788 0.17 -0.026 YES
4 FAM153A FAM153A FAM153A 1939 0.16 -0.016 YES
5 RPS24 RPS24 RPS24 1956 0.16 0.0026 YES
6 RPS19 RPS19 RPS19 2207 0.15 0.0058 YES
7 RPSA RPSA RPSA 2217 0.15 0.023 YES
8 RPSAP9 RPSAP9 RPSAP9 2231 0.15 0.039 YES
9 RPLP0 RPLP0 RPLP0 2454 0.14 0.043 YES
10 RPS21 RPS21 RPS21 2515 0.13 0.055 YES
11 RPL39 RPL39 RPL39 2600 0.13 0.066 YES
12 RPL27A RPL27A RPL27A 2612 0.13 0.08 YES
13 RPS10 RPS10 RPS10 2613 0.13 0.095 YES
14 RPS12 RPS12 RPS12 2677 0.13 0.11 YES
15 RPS27 RPS27 RPS27 2735 0.12 0.12 YES
16 RPS17 RPS17 RPS17 2737 0.12 0.13 YES
17 RPS3 RPS3 RPS3 2761 0.12 0.15 YES
18 RPL23A RPL23A RPL23A 2768 0.12 0.16 YES
19 RPS7 RPS7 RPS7 2788 0.12 0.17 YES
20 RPS18 RPS18 RPS18 2794 0.12 0.19 YES
21 RPL26 RPL26 RPL26 2852 0.12 0.2 YES
22 RPS5 RPS5 RPS5 2871 0.12 0.21 YES
23 RPS27A RPS27A RPS27A 2884 0.12 0.22 YES
24 RPS15 RPS15 RPS15 2892 0.12 0.24 YES
25 RPL18A RPL18A RPL18A 2917 0.12 0.25 YES
26 RPS29 RPS29 RPS29 2934 0.12 0.26 YES
27 RPL28 RPL28 RPL28 2952 0.12 0.28 YES
28 RPL37A RPL37A RPL37A 3192 0.11 0.28 YES
29 RPL36 RPL36 RPL36 3272 0.11 0.28 YES
30 RPS28 RPS28 RPS28 3286 0.1 0.3 YES
31 RPL7 RPL7 RPL7 3288 0.1 0.31 YES
32 RPLP2 RPLP2 RPLP2 3289 0.1 0.32 YES
33 RPS4X RPS4X RPS4X 3293 0.1 0.33 YES
34 RPL32 RPL32 RPL32 3331 0.1 0.34 YES
35 RPL18 RPL18 RPL18 3335 0.1 0.36 YES
36 RPL6 RPL6 RPL6 3358 0.1 0.37 YES
37 RPL31 RPL31 RPL31 3366 0.1 0.38 YES
38 RPL7A RPL7A RPL7A 3376 0.1 0.39 YES
39 RPL27 RPL27 RPL27 3384 0.1 0.4 YES
40 RPL38 RPL38 RPL38 3414 0.1 0.41 YES
41 RPL17 RPL17 RPL17 3417 0.1 0.42 YES
42 RPL13A RPL13A RPL13A 3488 0.1 0.43 YES
43 RPS16 RPS16 RPS16 3532 0.099 0.44 YES
44 RPL35A RPL35A RPL35A 3619 0.097 0.45 YES
45 RPL14 RPL14 RPL14 3627 0.096 0.46 YES
46 RPL3 RPL3 RPL3 3661 0.095 0.47 YES
47 RPL10A RPL10A RPL10A 3670 0.095 0.48 YES
48 RPS11 RPS11 RPS11 3681 0.094 0.49 YES
49 RPL4 RPL4 RPL4 3741 0.093 0.5 YES
50 RPL23 RPL23 RPL23 4022 0.085 0.49 YES
51 RPL35 RPL35 RPL35 4077 0.084 0.5 YES
52 RPS9 RPS9 RPS9 4088 0.084 0.51 YES
53 RPL8 RPL8 RPL8 4107 0.083 0.52 YES
54 RPL41 RPL41 RPL41 4108 0.083 0.52 YES
55 RPS6 RPS6 RPS6 4116 0.083 0.53 YES
56 RPS2 RPS2 RPS2 4195 0.081 0.54 YES
57 RPL37 RPL37 RPL37 4259 0.08 0.55 YES
58 RPS23 RPS23 RPS23 4261 0.08 0.56 YES
59 RPL24 RPL24 RPL24 4266 0.08 0.56 YES
60 RPL30 RPL30 RPL30 4292 0.079 0.57 YES
61 RPS13 RPS13 RPS13 4332 0.078 0.58 YES
62 RPS25 RPS25 RPS25 4342 0.078 0.59 YES
63 RPLP1 RPLP1 RPLP1 4504 0.074 0.59 YES
64 RPL29 RPL29 RPL29 4630 0.072 0.59 YES
65 RPL12 RPL12 RPL12 4729 0.07 0.59 YES
66 RPL15 RPL15 RPL15 4885 0.067 0.59 YES
67 RPS20 RPS20 RPS20 4902 0.066 0.6 YES
68 EEF1A1 EEF1A1 EEF1A1 4988 0.064 0.6 YES
69 RPS14 RPS14 RPS14 5088 0.062 0.6 YES
70 RPS3A RPS3A RPS3A 5206 0.06 0.6 YES
71 RPL10 RPL10 RPL10 5212 0.06 0.61 YES
72 RPL5 RPL5 RPL5 5219 0.06 0.62 YES
73 UBA52 UBA52 UBA52 5362 0.057 0.61 NO
74 RPL34 RPL34 RPL34 5551 0.054 0.61 NO
75 RPL19 RPL19 RPL19 5664 0.052 0.61 NO
76 RPS8 RPS8 RPS8 5783 0.05 0.61 NO
77 RPS15A RPS15A RPS15A 5804 0.05 0.61 NO
78 RPL13 RPL13 RPL13 5986 0.046 0.61 NO
79 RPS26 RPS26 RPS26 6149 0.044 0.6 NO
80 FAU FAU FAU 6458 0.039 0.59 NO
81 RPL11 RPL11 RPL11 7214 0.027 0.55 NO
82 RPL22 RPL22 RPL22 7268 0.026 0.55 NO
83 EEF2 EEF2 EEF2 8073 0.013 0.51 NO
84 RPL26L1 RPL26L1 RPL26L1 13573 -0.087 0.21 NO
85 RPS4Y1 RPS4Y1 RPS4Y1 16645 -0.24 0.061 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 PEPTIDE CHAIN ELONGATION.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PEPTIDE CHAIN ELONGATION, 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 GALACTOSE METABOLISM 25 genes.ES.table 0.47 1.4 0.093 0.18 0.99 0.28 0.2 0.22 0.14 0
KEGG PURINE METABOLISM 154 genes.ES.table 0.4 1.7 0.002 0.074 0.72 0.21 0.19 0.17 0.025 0.004
KEGG SELENOAMINO ACID METABOLISM 26 genes.ES.table 0.49 1.7 0.026 0.071 0.82 0.12 0.092 0.1 0.029 0.001
KEGG N GLYCAN BIOSYNTHESIS 46 genes.ES.table 0.35 1.4 0.15 0.18 0.99 0.15 0.23 0.12 0.14 0
KEGG O GLYCAN BIOSYNTHESIS 27 genes.ES.table 0.66 1.7 0.0084 0.076 0.85 0.67 0.27 0.49 0.034 0.001
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 43 genes.ES.table 0.36 1.3 0.18 0.21 1 0.4 0.38 0.25 0.18 0
KEGG INOSITOL PHOSPHATE METABOLISM 53 genes.ES.table 0.51 1.7 0.0042 0.071 0.74 0.4 0.33 0.26 0.024 0.002
KEGG GLYCEROPHOSPHOLIPID METABOLISM 70 genes.ES.table 0.46 1.7 0.002 0.075 0.86 0.36 0.28 0.26 0.034 0.001
KEGG ETHER LIPID METABOLISM 27 genes.ES.table 0.5 1.4 0.064 0.16 0.99 0.52 0.3 0.36 0.12 0
KEGG ARACHIDONIC ACID METABOLISM 49 genes.ES.table 0.63 1.6 0.012 0.081 0.91 0.31 0.1 0.28 0.04 0
genes ES table in pathway: KEGG GALACTOSE METABOLISM

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 PDE1A PDE1A PDE1A 18 0.85 0.074 YES
2 FGF1 FGF1 FGF1 107 0.7 0.13 YES
3 ADCY5 ADCY5 ADCY5 290 0.58 0.17 YES
4 FGFR1 FGFR1 FGFR1 422 0.53 0.21 YES
5 FGF7 FGF7 FGF7 451 0.52 0.26 YES
6 FGF18 FGF18 FGF18 489 0.5 0.3 YES
7 PRKAR2B PRKAR2B PRKAR2B 509 0.5 0.34 YES
8 AKT3 AKT3 AKT3 693 0.45 0.37 YES
9 ADCY2 ADCY2 ADCY2 781 0.43 0.41 YES
10 ADCY4 ADCY4 ADCY4 988 0.4 0.43 YES
11 CAMK4 CAMK4 CAMK4 1018 0.39 0.46 YES
12 ITPR3 ITPR3 ITPR3 1059 0.39 0.49 YES
13 ADCY3 ADCY3 ADCY3 1078 0.38 0.53 YES
14 FGFR2 FGFR2 FGFR2 1471 0.34 0.54 YES
15 PDE1B PDE1B PDE1B 1715 0.31 0.55 YES
16 ADCY7 ADCY7 ADCY7 2157 0.27 0.55 NO
17 PRKAR1B PRKAR1B PRKAR1B 2663 0.23 0.54 NO
18 NR4A1 NR4A1 NR4A1 3130 0.2 0.53 NO
19 CDKN1A CDKN1A CDKN1A 4361 0.13 0.47 NO
20 FGF19 FGF19 FGF19 4478 0.12 0.48 NO
21 PRKCE PRKCE PRKCE 4698 0.11 0.48 NO
22 FGF9 FGF9 FGF9 4870 0.1 0.48 NO
23 ADCY1 ADCY1 ADCY1 5684 0.075 0.44 NO
24 MAPK3 MAPK3 MAPK3 6203 0.061 0.41 NO
25 FGF2 FGF2 FGF2 6332 0.058 0.41 NO
26 FOXO1 FOXO1 FOXO1 6344 0.058 0.41 NO
27 MAP2K1 MAP2K1 MAP2K1 6532 0.054 0.41 NO
28 KL KL KL 6620 0.051 0.41 NO
29 SHC1 SHC1 SHC1 6672 0.05 0.41 NO
30 CALM2 CALM2 CALM2 6772 0.048 0.41 NO
31 YWHAB YWHAB YWHAB 6957 0.045 0.4 NO
32 GAB1 GAB1 GAB1 7034 0.043 0.4 NO
33 CALM1 CALM1 CALM1 7105 0.042 0.4 NO
34 KRAS KRAS KRAS 7315 0.038 0.39 NO
35 ADCY9 ADCY9 ADCY9 7427 0.036 0.39 NO
36 PRKACA PRKACA PRKACA 7454 0.036 0.39 NO
37 AKT1 AKT1 AKT1 7500 0.035 0.39 NO
38 BAD BAD BAD 7526 0.034 0.39 NO
39 CREB1 CREB1 CREB1 8078 0.026 0.36 NO
40 FOXO3 FOXO3 FOXO3 8135 0.025 0.36 NO
41 PIK3CA PIK3CA PIK3CA 8146 0.024 0.36 NO
42 FGFR3 FGFR3 FGFR3 8179 0.024 0.36 NO
43 ADRBK1 ADRBK1 ADRBK1 8439 0.02 0.35 NO
44 RICTOR RICTOR RICTOR 8684 0.017 0.34 NO
45 TRIB3 TRIB3 TRIB3 8719 0.016 0.34 NO
46 GSK3A GSK3A GSK3A 8736 0.016 0.34 NO
47 TSC2 TSC2 TSC2 8966 0.013 0.33 NO
48 PTEN PTEN PTEN 9336 0.0085 0.31 NO
49 MLST8 MLST8 MLST8 9614 0.0054 0.29 NO
50 PDPK1 PDPK1 PDPK1 9655 0.0049 0.29 NO
51 ADCY6 ADCY6 ADCY6 9659 0.0049 0.29 NO
52 MAP2K2 MAP2K2 MAP2K2 9980 0.0005 0.27 NO
53 PRKCD PRKCD PRKCD 10070 -0.0005 0.27 NO
54 HRAS HRAS HRAS 10357 -0.0038 0.25 NO
55 MDM2 MDM2 MDM2 10436 -0.0048 0.25 NO
56 CHUK CHUK CHUK 10594 -0.0064 0.24 NO
57 PRKAR1A PRKAR1A PRKAR1A 10944 -0.01 0.22 NO
58 PRKACB PRKACB PRKACB 11062 -0.012 0.22 NO
59 CALM3 CALM3 CALM3 11068 -0.012 0.22 NO
60 AKT1S1 AKT1S1 AKT1S1 11225 -0.014 0.21 NO
61 ADCY8 ADCY8 ADCY8 11454 -0.016 0.2 NO
62 MAPK1 MAPK1 MAPK1 11516 -0.017 0.2 NO
63 PLCG1 PLCG1 PLCG1 11609 -0.018 0.19 NO
64 SOS1 SOS1 SOS1 11693 -0.019 0.19 NO
65 FRS2 FRS2 FRS2 11702 -0.019 0.19 NO
66 THEM4 THEM4 THEM4 12090 -0.024 0.17 NO
67 AKT2 AKT2 AKT2 12138 -0.025 0.17 NO
68 CDKN1B CDKN1B CDKN1B 12303 -0.027 0.16 NO
69 RPS6KB2 RPS6KB2 RPS6KB2 12462 -0.029 0.16 NO
70 MAPKAP1 MAPKAP1 MAPKAP1 12478 -0.029 0.16 NO
71 GRB2 GRB2 GRB2 12627 -0.031 0.15 NO
72 PRKCG PRKCG PRKCG 12791 -0.033 0.15 NO
73 MTOR MTOR MTOR 12792 -0.033 0.15 NO
74 NRAS NRAS NRAS 13024 -0.036 0.14 NO
75 CASP9 CASP9 CASP9 13317 -0.04 0.13 NO
76 FGF22 FGF22 FGF22 13588 -0.044 0.11 NO
77 FRS3 FRS3 FRS3 14394 -0.059 0.074 NO
78 FOXO4 FOXO4 FOXO4 14432 -0.06 0.077 NO
79 FGFR4 FGFR4 FGFR4 14458 -0.061 0.081 NO
80 PIK3R1 PIK3R1 PIK3R1 14604 -0.063 0.078 NO
81 RAF1 RAF1 RAF1 14721 -0.066 0.078 NO
82 PRKAR2A PRKAR2A PRKAR2A 15298 -0.081 0.052 NO
83 PRKCA PRKCA PRKCA 16077 -0.11 0.018 NO
84 PHLPP1 PHLPP1 PHLPP1 16197 -0.12 0.022 NO
85 ITPR2 ITPR2 ITPR2 16227 -0.12 0.032 NO
86 FGF17 FGF17 FGF17 16767 -0.16 0.015 NO
87 KLB KLB KLB 17188 -0.2 0.0098 NO
88 CDK1 CDK1 CDK1 17369 -0.23 0.02 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 GALACTOSE METABOLISM.

Figure S62.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GALACTOSE 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 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 PDE1A PDE1A PDE1A 18 0.85 0.067 YES
2 FGF1 FGF1 FGF1 107 0.7 0.12 YES
3 IL17RD IL17RD IL17RD 245 0.6 0.16 YES
4 ADCY5 ADCY5 ADCY5 290 0.58 0.2 YES
5 FGFR1 FGFR1 FGFR1 422 0.53 0.24 YES
6 FGF7 FGF7 FGF7 451 0.52 0.28 YES
7 FGF18 FGF18 FGF18 489 0.5 0.32 YES
8 PRKAR2B PRKAR2B PRKAR2B 509 0.5 0.36 YES
9 AKT3 AKT3 AKT3 693 0.45 0.38 YES
10 ADCY2 ADCY2 ADCY2 781 0.43 0.41 YES
11 ADCY4 ADCY4 ADCY4 988 0.4 0.43 YES
12 CAMK4 CAMK4 CAMK4 1018 0.39 0.46 YES
13 ITPR3 ITPR3 ITPR3 1059 0.39 0.49 YES
14 ADCY3 ADCY3 ADCY3 1078 0.38 0.52 YES
15 FGFR2 FGFR2 FGFR2 1471 0.34 0.52 YES
16 PDE1B PDE1B PDE1B 1715 0.31 0.53 YES
17 ADCY7 ADCY7 ADCY7 2157 0.27 0.53 NO
18 PRKAR1B PRKAR1B PRKAR1B 2663 0.23 0.52 NO
19 NR4A1 NR4A1 NR4A1 3130 0.2 0.51 NO
20 CBL CBL CBL 4136 0.14 0.46 NO
21 SPRY2 SPRY2 SPRY2 4356 0.13 0.46 NO
22 CDKN1A CDKN1A CDKN1A 4361 0.13 0.47 NO
23 FGF19 FGF19 FGF19 4478 0.12 0.48 NO
24 PRKCE PRKCE PRKCE 4698 0.11 0.47 NO
25 FGF9 FGF9 FGF9 4870 0.1 0.47 NO
26 SRC SRC SRC 5246 0.091 0.46 NO
27 PPP2CB PPP2CB PPP2CB 5670 0.076 0.44 NO
28 ADCY1 ADCY1 ADCY1 5684 0.075 0.44 NO
29 MAPK3 MAPK3 MAPK3 6203 0.061 0.42 NO
30 FGF2 FGF2 FGF2 6332 0.058 0.42 NO
31 FOXO1 FOXO1 FOXO1 6344 0.058 0.42 NO
32 MAP2K1 MAP2K1 MAP2K1 6532 0.054 0.42 NO
33 KL KL KL 6620 0.051 0.42 NO
34 SHC1 SHC1 SHC1 6672 0.05 0.42 NO
35 PPP2R1A PPP2R1A PPP2R1A 6706 0.05 0.42 NO
36 CALM2 CALM2 CALM2 6772 0.048 0.42 NO
37 YWHAB YWHAB YWHAB 6957 0.045 0.41 NO
38 GAB1 GAB1 GAB1 7034 0.043 0.41 NO
39 CALM1 CALM1 CALM1 7105 0.042 0.41 NO
40 KRAS KRAS KRAS 7315 0.038 0.4 NO
41 ADCY9 ADCY9 ADCY9 7427 0.036 0.4 NO
42 PRKACA PRKACA PRKACA 7454 0.036 0.4 NO
43 AKT1 AKT1 AKT1 7500 0.035 0.4 NO
44 BAD BAD BAD 7526 0.034 0.4 NO
45 CREB1 CREB1 CREB1 8078 0.026 0.37 NO
46 FOXO3 FOXO3 FOXO3 8135 0.025 0.37 NO
47 PIK3CA PIK3CA PIK3CA 8146 0.024 0.37 NO
48 FGFR3 FGFR3 FGFR3 8179 0.024 0.37 NO
49 ADRBK1 ADRBK1 ADRBK1 8439 0.02 0.36 NO
50 RICTOR RICTOR RICTOR 8684 0.017 0.35 NO
51 TRIB3 TRIB3 TRIB3 8719 0.016 0.34 NO
52 GSK3A GSK3A GSK3A 8736 0.016 0.35 NO
53 TSC2 TSC2 TSC2 8966 0.013 0.33 NO
54 PTEN PTEN PTEN 9336 0.0085 0.31 NO
55 MKNK1 MKNK1 MKNK1 9448 0.0073 0.31 NO
56 MLST8 MLST8 MLST8 9614 0.0054 0.3 NO
57 PDPK1 PDPK1 PDPK1 9655 0.0049 0.3 NO
58 ADCY6 ADCY6 ADCY6 9659 0.0049 0.3 NO
59 MAP2K2 MAP2K2 MAP2K2 9980 0.0005 0.28 NO
60 PRKCD PRKCD PRKCD 10070 -0.0005 0.27 NO
61 HRAS HRAS HRAS 10357 -0.0038 0.26 NO
62 PPP2CA PPP2CA PPP2CA 10385 -0.0042 0.26 NO
63 MDM2 MDM2 MDM2 10436 -0.0048 0.26 NO
64 CHUK CHUK CHUK 10594 -0.0064 0.25 NO
65 PRKAR1A PRKAR1A PRKAR1A 10944 -0.01 0.23 NO
66 PRKACB PRKACB PRKACB 11062 -0.012 0.22 NO
67 CALM3 CALM3 CALM3 11068 -0.012 0.22 NO
68 AKT1S1 AKT1S1 AKT1S1 11225 -0.014 0.22 NO
69 ADCY8 ADCY8 ADCY8 11454 -0.016 0.2 NO
70 MAPK1 MAPK1 MAPK1 11516 -0.017 0.2 NO
71 UBA52 UBA52 UBA52 11591 -0.018 0.2 NO
72 PLCG1 PLCG1 PLCG1 11609 -0.018 0.2 NO
73 SOS1 SOS1 SOS1 11693 -0.019 0.2 NO
74 FRS2 FRS2 FRS2 11702 -0.019 0.2 NO
75 RPS27A RPS27A RPS27A 11897 -0.022 0.19 NO
76 THEM4 THEM4 THEM4 12090 -0.024 0.18 NO
77 AKT2 AKT2 AKT2 12138 -0.025 0.18 NO
78 CDKN1B CDKN1B CDKN1B 12303 -0.027 0.17 NO
79 RPS6KB2 RPS6KB2 RPS6KB2 12462 -0.029 0.16 NO
80 MAPKAP1 MAPKAP1 MAPKAP1 12478 -0.029 0.16 NO
81 GRB2 GRB2 GRB2 12627 -0.031 0.16 NO
82 PRKCG PRKCG PRKCG 12791 -0.033 0.15 NO
83 MTOR MTOR MTOR 12792 -0.033 0.16 NO
84 NRAS NRAS NRAS 13024 -0.036 0.14 NO
85 CASP9 CASP9 CASP9 13317 -0.04 0.13 NO
86 FGF22 FGF22 FGF22 13588 -0.044 0.12 NO
87 FRS3 FRS3 FRS3 14394 -0.059 0.079 NO
88 FOXO4 FOXO4 FOXO4 14432 -0.06 0.082 NO
89 FGFR4 FGFR4 FGFR4 14458 -0.061 0.085 NO
90 PIK3R1 PIK3R1 PIK3R1 14604 -0.063 0.082 NO
91 RAF1 RAF1 RAF1 14721 -0.066 0.081 NO
92 BRAF BRAF BRAF 15109 -0.075 0.065 NO
93 PRKAR2A PRKAR2A PRKAR2A 15298 -0.081 0.061 NO
94 PRKCA PRKCA PRKCA 16077 -0.11 0.026 NO
95 PHLPP1 PHLPP1 PHLPP1 16197 -0.12 0.029 NO
96 ITPR2 ITPR2 ITPR2 16227 -0.12 0.037 NO
97 FGF17 FGF17 FGF17 16767 -0.16 0.019 NO
98 KLB KLB KLB 17188 -0.2 0.012 NO
99 CDK1 CDK1 CDK1 17369 -0.23 0.02 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 SELENOAMINO ACID 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 PDE1A PDE1A PDE1A 18 0.85 0.082 YES
2 PDGFRA PDGFRA PDGFRA 142 0.67 0.14 YES
3 ADCY5 ADCY5 ADCY5 290 0.58 0.19 YES
4 PRKAR2B PRKAR2B PRKAR2B 509 0.5 0.22 YES
5 AKT3 AKT3 AKT3 693 0.45 0.26 YES
6 ADCY2 ADCY2 ADCY2 781 0.43 0.3 YES
7 ADCY4 ADCY4 ADCY4 988 0.4 0.32 YES
8 CAMK4 CAMK4 CAMK4 1018 0.39 0.36 YES
9 ITPR3 ITPR3 ITPR3 1059 0.39 0.4 YES
10 ADCY3 ADCY3 ADCY3 1078 0.38 0.43 YES
11 PDE1B PDE1B PDE1B 1715 0.31 0.42 YES
12 PDGFA PDGFA PDGFA 1897 0.29 0.44 YES
13 ADCY7 ADCY7 ADCY7 2157 0.27 0.46 YES
14 NCK2 NCK2 NCK2 2175 0.27 0.48 YES
15 PDGFRB PDGFRB PDGFRB 2202 0.27 0.5 YES
16 PRKAR1B PRKAR1B PRKAR1B 2663 0.23 0.5 NO
17 NR4A1 NR4A1 NR4A1 3130 0.2 0.5 NO
18 PDGFB PDGFB PDGFB 3314 0.19 0.5 NO
19 CDKN1A CDKN1A CDKN1A 4361 0.13 0.46 NO
20 BCAR1 BCAR1 BCAR1 4488 0.12 0.46 NO
21 PRKCE PRKCE PRKCE 4698 0.11 0.46 NO
22 STAT5A STAT5A STAT5A 4974 0.1 0.46 NO
23 SRC SRC SRC 5246 0.091 0.45 NO
24 STAT3 STAT3 STAT3 5331 0.088 0.45 NO
25 CRK CRK CRK 5648 0.076 0.44 NO
26 ADCY1 ADCY1 ADCY1 5684 0.075 0.45 NO
27 STAT1 STAT1 STAT1 5965 0.068 0.44 NO
28 MAPK3 MAPK3 MAPK3 6203 0.061 0.43 NO
29 FOXO1 FOXO1 FOXO1 6344 0.058 0.43 NO
30 MAP2K1 MAP2K1 MAP2K1 6532 0.054 0.42 NO
31 NCK1 NCK1 NCK1 6647 0.051 0.42 NO
32 CALM2 CALM2 CALM2 6772 0.048 0.42 NO
33 YWHAB YWHAB YWHAB 6957 0.045 0.41 NO
34 CALM1 CALM1 CALM1 7105 0.042 0.41 NO
35 STAT6 STAT6 STAT6 7228 0.04 0.4 NO
36 KRAS KRAS KRAS 7315 0.038 0.4 NO
37 ADCY9 ADCY9 ADCY9 7427 0.036 0.4 NO
38 PRKACA PRKACA PRKACA 7454 0.036 0.4 NO
39 AKT1 AKT1 AKT1 7500 0.035 0.4 NO
40 BAD BAD BAD 7526 0.034 0.41 NO
41 RAPGEF1 RAPGEF1 RAPGEF1 7573 0.033 0.41 NO
42 RASA1 RASA1 RASA1 7789 0.03 0.4 NO
43 CREB1 CREB1 CREB1 8078 0.026 0.38 NO
44 FOXO3 FOXO3 FOXO3 8135 0.025 0.38 NO
45 PIK3CA PIK3CA PIK3CA 8146 0.024 0.38 NO
46 ADRBK1 ADRBK1 ADRBK1 8439 0.02 0.37 NO
47 RICTOR RICTOR RICTOR 8684 0.017 0.36 NO
48 TRIB3 TRIB3 TRIB3 8719 0.016 0.36 NO
49 GSK3A GSK3A GSK3A 8736 0.016 0.36 NO
50 TSC2 TSC2 TSC2 8966 0.013 0.35 NO
51 PIK3CB PIK3CB PIK3CB 9266 0.0094 0.33 NO
52 PTEN PTEN PTEN 9336 0.0085 0.33 NO
53 MLST8 MLST8 MLST8 9614 0.0054 0.31 NO
54 PDPK1 PDPK1 PDPK1 9655 0.0049 0.31 NO
55 ADCY6 ADCY6 ADCY6 9659 0.0049 0.31 NO
56 MAP2K2 MAP2K2 MAP2K2 9980 0.0005 0.29 NO
57 PRKCD PRKCD PRKCD 10070 -0.0005 0.29 NO
58 HRAS HRAS HRAS 10357 -0.0038 0.27 NO
59 MDM2 MDM2 MDM2 10436 -0.0048 0.27 NO
60 CHUK CHUK CHUK 10594 -0.0064 0.26 NO
61 PRKAR1A PRKAR1A PRKAR1A 10944 -0.01 0.24 NO
62 PRKACB PRKACB PRKACB 11062 -0.012 0.24 NO
63 CALM3 CALM3 CALM3 11068 -0.012 0.24 NO
64 AKT1S1 AKT1S1 AKT1S1 11225 -0.014 0.23 NO
65 ADCY8 ADCY8 ADCY8 11454 -0.016 0.22 NO
66 MAPK1 MAPK1 MAPK1 11516 -0.017 0.22 NO
67 PLCG1 PLCG1 PLCG1 11609 -0.018 0.21 NO
68 SOS1 SOS1 SOS1 11693 -0.019 0.21 NO
69 THEM4 THEM4 THEM4 12090 -0.024 0.19 NO
70 AKT2 AKT2 AKT2 12138 -0.025 0.19 NO
71 CDKN1B CDKN1B CDKN1B 12303 -0.027 0.18 NO
72 PIK3R2 PIK3R2 PIK3R2 12460 -0.029 0.18 NO
73 RPS6KB2 RPS6KB2 RPS6KB2 12462 -0.029 0.18 NO
74 MAPKAP1 MAPKAP1 MAPKAP1 12478 -0.029 0.18 NO
75 GRB2 GRB2 GRB2 12627 -0.031 0.18 NO
76 PRKCG PRKCG PRKCG 12791 -0.033 0.17 NO
77 MTOR MTOR MTOR 12792 -0.033 0.17 NO
78 STAT5B STAT5B STAT5B 12851 -0.034 0.17 NO
79 NRAS NRAS NRAS 13024 -0.036 0.17 NO
80 CASP9 CASP9 CASP9 13317 -0.04 0.15 NO
81 GRB7 GRB7 GRB7 14375 -0.059 0.1 NO
82 FOXO4 FOXO4 FOXO4 14432 -0.06 0.1 NO
83 CRKL CRKL CRKL 14581 -0.063 0.1 NO
84 PIK3R1 PIK3R1 PIK3R1 14604 -0.063 0.1 NO
85 RAF1 RAF1 RAF1 14721 -0.066 0.1 NO
86 PRKAR2A PRKAR2A PRKAR2A 15298 -0.081 0.08 NO
87 PRKCA PRKCA PRKCA 16077 -0.11 0.047 NO
88 PHLPP1 PHLPP1 PHLPP1 16197 -0.12 0.052 NO
89 ITPR2 ITPR2 ITPR2 16227 -0.12 0.062 NO
90 CDK1 CDK1 CDK1 17369 -0.23 0.02 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 SELENOAMINO ACID METABOLISM.

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SELENOAMINO ACID METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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 PDE1A PDE1A PDE1A 18 0.85 0.064 YES
2 FGF1 FGF1 FGF1 107 0.7 0.11 YES
3 IL17RD IL17RD IL17RD 245 0.6 0.15 YES
4 ADCY5 ADCY5 ADCY5 290 0.58 0.19 YES
5 FGFR1 FGFR1 FGFR1 422 0.53 0.22 YES
6 FGF7 FGF7 FGF7 451 0.52 0.26 YES
7 FGF18 FGF18 FGF18 489 0.5 0.3 YES
8 PRKAR2B PRKAR2B PRKAR2B 509 0.5 0.34 YES
9 AKT3 AKT3 AKT3 693 0.45 0.36 YES
10 ADCY2 ADCY2 ADCY2 781 0.43 0.39 YES
11 ADCY4 ADCY4 ADCY4 988 0.4 0.4 YES
12 CAMK4 CAMK4 CAMK4 1018 0.39 0.43 YES
13 ITPR3 ITPR3 ITPR3 1059 0.39 0.46 YES
14 ADCY3 ADCY3 ADCY3 1078 0.38 0.49 YES
15 FGFR2 FGFR2 FGFR2 1471 0.34 0.49 YES
16 PDE1B PDE1B PDE1B 1715 0.31 0.5 YES
17 ADCY7 ADCY7 ADCY7 2157 0.27 0.5 NO
18 PRKAR1B PRKAR1B PRKAR1B 2663 0.23 0.49 NO
19 NR4A1 NR4A1 NR4A1 3130 0.2 0.48 NO
20 CBL CBL CBL 4136 0.14 0.43 NO
21 SPRY2 SPRY2 SPRY2 4356 0.13 0.43 NO
22 CDKN1A CDKN1A CDKN1A 4361 0.13 0.44 NO
23 FGF19 FGF19 FGF19 4478 0.12 0.44 NO
24 PRKCE PRKCE PRKCE 4698 0.11 0.44 NO
25 FGF9 FGF9 FGF9 4870 0.1 0.43 NO
26 STAT5A STAT5A STAT5A 4974 0.1 0.44 NO
27 SRC SRC SRC 5246 0.091 0.43 NO
28 STAT3 STAT3 STAT3 5331 0.088 0.43 NO
29 PPP2CB PPP2CB PPP2CB 5670 0.076 0.42 NO
30 ADCY1 ADCY1 ADCY1 5684 0.075 0.42 NO
31 STAT1 STAT1 STAT1 5965 0.068 0.41 NO
32 MAPK3 MAPK3 MAPK3 6203 0.061 0.4 NO
33 FGF2 FGF2 FGF2 6332 0.058 0.4 NO
34 FOXO1 FOXO1 FOXO1 6344 0.058 0.4 NO
35 CUX1 CUX1 CUX1 6385 0.057 0.4 NO
36 MAP2K1 MAP2K1 MAP2K1 6532 0.054 0.4 NO
37 KL KL KL 6620 0.051 0.4 NO
38 SHC1 SHC1 SHC1 6672 0.05 0.4 NO
39 PPP2R1A PPP2R1A PPP2R1A 6706 0.05 0.4 NO
40 CALM2 CALM2 CALM2 6772 0.048 0.4 NO
41 BCR BCR BCR 6814 0.048 0.4 NO
42 GAB2 GAB2 GAB2 6936 0.045 0.4 NO
43 YWHAB YWHAB YWHAB 6957 0.045 0.4 NO
44 GAB1 GAB1 GAB1 7034 0.043 0.4 NO
45 CALM1 CALM1 CALM1 7105 0.042 0.4 NO
46 KRAS KRAS KRAS 7315 0.038 0.39 NO
47 ADCY9 ADCY9 ADCY9 7427 0.036 0.39 NO
48 PRKACA PRKACA PRKACA 7454 0.036 0.39 NO
49 AKT1 AKT1 AKT1 7500 0.035 0.39 NO
50 BAD BAD BAD 7526 0.034 0.39 NO
51 CREB1 CREB1 CREB1 8078 0.026 0.36 NO
52 FOXO3 FOXO3 FOXO3 8135 0.025 0.36 NO
53 PIK3CA PIK3CA PIK3CA 8146 0.024 0.36 NO
54 FGFR3 FGFR3 FGFR3 8179 0.024 0.36 NO
55 ADRBK1 ADRBK1 ADRBK1 8439 0.02 0.35 NO
56 RICTOR RICTOR RICTOR 8684 0.017 0.33 NO
57 TRIB3 TRIB3 TRIB3 8719 0.016 0.33 NO
58 GSK3A GSK3A GSK3A 8736 0.016 0.33 NO
59 FGFR1OP2 FGFR1OP2 FGFR1OP2 8858 0.014 0.33 NO
60 TSC2 TSC2 TSC2 8966 0.013 0.32 NO
61 PTEN PTEN PTEN 9336 0.0085 0.3 NO
62 MKNK1 MKNK1 MKNK1 9448 0.0073 0.3 NO
63 MLST8 MLST8 MLST8 9614 0.0054 0.29 NO
64 PDPK1 PDPK1 PDPK1 9655 0.0049 0.29 NO
65 ADCY6 ADCY6 ADCY6 9659 0.0049 0.29 NO
66 ZMYM2 ZMYM2 ZMYM2 9663 0.0048 0.29 NO
67 CPSF6 CPSF6 CPSF6 9939 0.001 0.27 NO
68 MAP2K2 MAP2K2 MAP2K2 9980 0.0005 0.27 NO
69 PRKCD PRKCD PRKCD 10070 -0.0005 0.26 NO
70 HRAS HRAS HRAS 10357 -0.0038 0.25 NO
71 PPP2CA PPP2CA PPP2CA 10385 -0.0042 0.25 NO
72 MDM2 MDM2 MDM2 10436 -0.0048 0.24 NO
73 MYO18A MYO18A MYO18A 10443 -0.0049 0.24 NO
74 CHUK CHUK CHUK 10594 -0.0064 0.24 NO
75 PRKAR1A PRKAR1A PRKAR1A 10944 -0.01 0.22 NO
76 PRKACB PRKACB PRKACB 11062 -0.012 0.21 NO
77 CALM3 CALM3 CALM3 11068 -0.012 0.21 NO
78 AKT1S1 AKT1S1 AKT1S1 11225 -0.014 0.2 NO
79 ADCY8 ADCY8 ADCY8 11454 -0.016 0.19 NO
80 MAPK1 MAPK1 MAPK1 11516 -0.017 0.19 NO
81 UBA52 UBA52 UBA52 11591 -0.018 0.19 NO
82 PLCG1 PLCG1 PLCG1 11609 -0.018 0.19 NO
83 SOS1 SOS1 SOS1 11693 -0.019 0.18 NO
84 FRS2 FRS2 FRS2 11702 -0.019 0.19 NO
85 FGFR1OP FGFR1OP FGFR1OP 11805 -0.021 0.18 NO
86 RPS27A RPS27A RPS27A 11897 -0.022 0.18 NO
87 THEM4 THEM4 THEM4 12090 -0.024 0.17 NO
88 AKT2 AKT2 AKT2 12138 -0.025 0.17 NO
89 CDKN1B CDKN1B CDKN1B 12303 -0.027 0.16 NO
90 RPS6KB2 RPS6KB2 RPS6KB2 12462 -0.029 0.15 NO
91 MAPKAP1 MAPKAP1 MAPKAP1 12478 -0.029 0.16 NO
92 GRB2 GRB2 GRB2 12627 -0.031 0.15 NO
93 PRKCG PRKCG PRKCG 12791 -0.033 0.14 NO
94 MTOR MTOR MTOR 12792 -0.033 0.14 NO
95 STAT5B STAT5B STAT5B 12851 -0.034 0.14 NO
96 NRAS NRAS NRAS 13024 -0.036 0.14 NO
97 CASP9 CASP9 CASP9 13317 -0.04 0.12 NO
98 FGF22 FGF22 FGF22 13588 -0.044 0.11 NO
99 FRS3 FRS3 FRS3 14394 -0.059 0.071 NO
100 FOXO4 FOXO4 FOXO4 14432 -0.06 0.073 NO
101 FGFR4 FGFR4 FGFR4 14458 -0.061 0.076 NO
102 PIK3R1 PIK3R1 PIK3R1 14604 -0.063 0.073 NO
103 RAF1 RAF1 RAF1 14721 -0.066 0.071 NO
104 BRAF BRAF BRAF 15109 -0.075 0.055 NO
105 PRKAR2A PRKAR2A PRKAR2A 15298 -0.081 0.051 NO
106 PRKCA PRKCA PRKCA 16077 -0.11 0.015 NO
107 PHLPP1 PHLPP1 PHLPP1 16197 -0.12 0.018 NO
108 ITPR2 ITPR2 ITPR2 16227 -0.12 0.025 NO
109 FGF17 FGF17 FGF17 16767 -0.16 0.007 NO
110 TRIM24 TRIM24 TRIM24 17010 -0.18 0.0073 NO
111 KLB KLB KLB 17188 -0.2 0.013 NO
112 CDK1 CDK1 CDK1 17369 -0.23 0.02 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 N GLYCAN BIOSYNTHESIS.

Figure S68.  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 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 PDE1A PDE1A PDE1A 18 0.85 0.062 YES
2 NTRK2 NTRK2 NTRK2 34 0.81 0.12 YES
3 ADCY5 ADCY5 ADCY5 290 0.58 0.15 YES
4 PRKAR2B PRKAR2B PRKAR2B 509 0.5 0.17 YES
5 AKT3 AKT3 AKT3 693 0.45 0.2 YES
6 ADCY2 ADCY2 ADCY2 781 0.43 0.22 YES
7 ADCY4 ADCY4 ADCY4 988 0.4 0.24 YES
8 DUSP4 DUSP4 DUSP4 1002 0.39 0.27 YES
9 CAMK4 CAMK4 CAMK4 1018 0.39 0.3 YES
10 ITPR3 ITPR3 ITPR3 1059 0.39 0.32 YES
11 ADCY3 ADCY3 ADCY3 1078 0.38 0.35 YES
12 NGF NGF NGF 1254 0.36 0.37 YES
13 PDE1B PDE1B PDE1B 1715 0.31 0.36 YES
14 MAPK11 MAPK11 MAPK11 2027 0.28 0.37 YES
15 ADCY7 ADCY7 ADCY7 2157 0.27 0.38 YES
16 RPS6KA2 RPS6KA2 RPS6KA2 2317 0.26 0.39 YES
17 MAPK12 MAPK12 MAPK12 2323 0.26 0.41 YES
18 DNM1 DNM1 DNM1 2536 0.24 0.42 YES
19 NTRK1 NTRK1 NTRK1 2617 0.24 0.43 YES
20 PRKAR1B PRKAR1B PRKAR1B 2663 0.23 0.44 YES
21 MEF2C MEF2C MEF2C 2748 0.23 0.46 YES
22 NR4A1 NR4A1 NR4A1 3130 0.2 0.45 YES
23 MAPK13 MAPK13 MAPK13 3233 0.19 0.46 YES
24 RALGDS RALGDS RALGDS 3927 0.15 0.43 NO
25 CDKN1A CDKN1A CDKN1A 4361 0.13 0.41 NO
26 ADCYAP1 ADCYAP1 ADCYAP1 4440 0.12 0.42 NO
27 SH3GL2 SH3GL2 SH3GL2 4663 0.11 0.41 NO
28 RALB RALB RALB 4687 0.11 0.42 NO
29 PRKCE PRKCE PRKCE 4698 0.11 0.43 NO
30 SHC3 SHC3 SHC3 5236 0.091 0.4 NO
31 SRC SRC SRC 5246 0.091 0.41 NO
32 STAT3 STAT3 STAT3 5331 0.088 0.41 NO
33 RPS6KA5 RPS6KA5 RPS6KA5 5390 0.085 0.42 NO
34 MAPK7 MAPK7 MAPK7 5445 0.083 0.42 NO
35 MEF2A MEF2A MEF2A 5574 0.078 0.42 NO
36 MAPKAPK2 MAPKAPK2 MAPKAPK2 5645 0.076 0.42 NO
37 CRK CRK CRK 5648 0.076 0.42 NO
38 DUSP7 DUSP7 DUSP7 5650 0.076 0.43 NO
39 PPP2CB PPP2CB PPP2CB 5670 0.076 0.44 NO
40 ADCY1 ADCY1 ADCY1 5684 0.075 0.44 NO
41 MAPK3 MAPK3 MAPK3 6203 0.061 0.41 NO
42 SHC2 SHC2 SHC2 6228 0.061 0.42 NO
43 ADORA2A ADORA2A ADORA2A 6249 0.06 0.42 NO
44 DNAL4 DNAL4 DNAL4 6257 0.06 0.42 NO
45 RPS6KA1 RPS6KA1 RPS6KA1 6293 0.059 0.43 NO
46 DUSP6 DUSP6 DUSP6 6296 0.059 0.43 NO
47 FOXO1 FOXO1 FOXO1 6344 0.058 0.43 NO
48 MAP2K1 MAP2K1 MAP2K1 6532 0.054 0.43 NO
49 SHC1 SHC1 SHC1 6672 0.05 0.42 NO
50 PPP2R1A PPP2R1A PPP2R1A 6706 0.05 0.42 NO
51 CALM2 CALM2 CALM2 6772 0.048 0.42 NO
52 RIT1 RIT1 RIT1 6809 0.048 0.42 NO
53 YWHAB YWHAB YWHAB 6957 0.045 0.42 NO
54 CALM1 CALM1 CALM1 7105 0.042 0.42 NO
55 KRAS KRAS KRAS 7315 0.038 0.41 NO
56 KIDINS220 KIDINS220 KIDINS220 7331 0.038 0.41 NO
57 ADCY9 ADCY9 ADCY9 7427 0.036 0.4 NO
58 PRKACA PRKACA PRKACA 7454 0.036 0.41 NO
59 AKT1 AKT1 AKT1 7500 0.035 0.41 NO
60 BAD BAD BAD 7526 0.034 0.41 NO
61 RAPGEF1 RAPGEF1 RAPGEF1 7573 0.033 0.41 NO
62 DNM2 DNM2 DNM2 7942 0.028 0.39 NO
63 CREB1 CREB1 CREB1 8078 0.026 0.38 NO
64 FOXO3 FOXO3 FOXO3 8135 0.025 0.38 NO
65 PIK3CA PIK3CA PIK3CA 8146 0.024 0.38 NO
66 RAP1A RAP1A RAP1A 8233 0.023 0.38 NO
67 ADRBK1 ADRBK1 ADRBK1 8439 0.02 0.37 NO
68 AP2A2 AP2A2 AP2A2 8617 0.018 0.36 NO
69 RICTOR RICTOR RICTOR 8684 0.017 0.36 NO
70 TRIB3 TRIB3 TRIB3 8719 0.016 0.36 NO
71 GSK3A GSK3A GSK3A 8736 0.016 0.36 NO
72 MAP2K5 MAP2K5 MAP2K5 8828 0.015 0.35 NO
73 AP2M1 AP2M1 AP2M1 8874 0.014 0.35 NO
74 AP2B1 AP2B1 AP2B1 8886 0.014 0.35 NO
75 TSC2 TSC2 TSC2 8966 0.013 0.35 NO
76 RHOA RHOA RHOA 9181 0.01 0.34 NO
77 PIK3CB PIK3CB PIK3CB 9266 0.0094 0.33 NO
78 RALA RALA RALA 9329 0.0086 0.33 NO
79 PTEN PTEN PTEN 9336 0.0085 0.33 NO
80 MLST8 MLST8 MLST8 9614 0.0054 0.32 NO
81 PDPK1 PDPK1 PDPK1 9655 0.0049 0.31 NO
82 ADCY6 ADCY6 ADCY6 9659 0.0049 0.31 NO
83 MAP2K2 MAP2K2 MAP2K2 9980 0.0005 0.3 NO
84 PRKCD PRKCD PRKCD 10070 -0.0005 0.29 NO
85 HRAS HRAS HRAS 10357 -0.0038 0.27 NO
86 MAPKAPK3 MAPKAPK3 MAPKAPK3 10382 -0.0041 0.27 NO
87 PPP2CA PPP2CA PPP2CA 10385 -0.0042 0.27 NO
88 MDM2 MDM2 MDM2 10436 -0.0048 0.27 NO
89 CHUK CHUK CHUK 10594 -0.0064 0.26 NO
90 DUSP3 DUSP3 DUSP3 10606 -0.0066 0.26 NO
91 CLTC CLTC CLTC 10832 -0.0092 0.25 NO
92 PRKAR1A PRKAR1A PRKAR1A 10944 -0.01 0.24 NO
93 AP2S1 AP2S1 AP2S1 10969 -0.011 0.24 NO
94 CLTA CLTA CLTA 11042 -0.012 0.24 NO
95 PRKACB PRKACB PRKACB 11062 -0.012 0.24 NO
96 CALM3 CALM3 CALM3 11068 -0.012 0.24 NO
97 IRS2 IRS2 IRS2 11070 -0.012 0.24 NO
98 AKT1S1 AKT1S1 AKT1S1 11225 -0.014 0.24 NO
99 AP2A1 AP2A1 AP2A1 11277 -0.014 0.23 NO
100 ADCY8 ADCY8 ADCY8 11454 -0.016 0.22 NO
101 MAPK1 MAPK1 MAPK1 11516 -0.017 0.22 NO
102 PLCG1 PLCG1 PLCG1 11609 -0.018 0.22 NO
103 SOS1 SOS1 SOS1 11693 -0.019 0.22 NO
104 FRS2 FRS2 FRS2 11702 -0.019 0.22 NO
105 ELK1 ELK1 ELK1 11926 -0.022 0.2 NO
106 PPP2R1B PPP2R1B PPP2R1B 12000 -0.023 0.2 NO
107 THEM4 THEM4 THEM4 12090 -0.024 0.2 NO
108 AKT2 AKT2 AKT2 12138 -0.025 0.2 NO
109 CDKN1B CDKN1B CDKN1B 12303 -0.027 0.19 NO
110 PIK3R2 PIK3R2 PIK3R2 12460 -0.029 0.18 NO
111 RPS6KB2 RPS6KB2 RPS6KB2 12462 -0.029 0.19 NO
112 MAPKAP1 MAPKAP1 MAPKAP1 12478 -0.029 0.19 NO
113 GRB2 GRB2 GRB2 12627 -0.031 0.18 NO
114 PRKCG PRKCG PRKCG 12791 -0.033 0.17 NO
115 MTOR MTOR MTOR 12792 -0.033 0.18 NO
116 MAPK14 MAPK14 MAPK14 12970 -0.035 0.17 NO
117 NRAS NRAS NRAS 13024 -0.036 0.17 NO
118 CASP9 CASP9 CASP9 13317 -0.04 0.16 NO
119 RPS6KA3 RPS6KA3 RPS6KA3 13891 -0.049 0.13 NO
120 ATF1 ATF1 ATF1 13988 -0.051 0.12 NO
121 FOXO4 FOXO4 FOXO4 14432 -0.06 0.1 NO
122 PIK3R1 PIK3R1 PIK3R1 14604 -0.063 0.099 NO
123 RAF1 RAF1 RAF1 14721 -0.066 0.097 NO
124 BRAF BRAF BRAF 15109 -0.075 0.081 NO
125 PRKAR2A PRKAR2A PRKAR2A 15298 -0.081 0.076 NO
126 PPP2R5D PPP2R5D PPP2R5D 15351 -0.083 0.079 NO
127 PRKCA PRKCA PRKCA 16077 -0.11 0.046 NO
128 PHLPP1 PHLPP1 PHLPP1 16197 -0.12 0.048 NO
129 ITPR2 ITPR2 ITPR2 16227 -0.12 0.056 NO
130 IRS1 IRS1 IRS1 16780 -0.16 0.037 NO
131 CDK1 CDK1 CDK1 17369 -0.23 0.02 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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 PDE1A PDE1A PDE1A 18 0.85 0.043 YES
2 THBS2 THBS2 THBS2 121 0.69 0.072 YES
3 PDGFRA PDGFRA PDGFRA 142 0.67 0.11 YES
4 COL5A1 COL5A1 COL5A1 187 0.64 0.14 YES
5 ADCY5 ADCY5 ADCY5 290 0.58 0.16 YES
6 COL4A4 COL4A4 COL4A4 313 0.57 0.19 YES
7 PLAT PLAT PLAT 344 0.55 0.22 YES
8 COL1A1 COL1A1 COL1A1 402 0.53 0.24 YES
9 COL3A1 COL3A1 COL3A1 433 0.52 0.26 YES
10 PRKAR2B PRKAR2B PRKAR2B 509 0.5 0.28 YES
11 COL1A2 COL1A2 COL1A2 548 0.49 0.31 YES
12 SPP1 SPP1 SPP1 670 0.46 0.32 YES
13 AKT3 AKT3 AKT3 693 0.45 0.35 YES
14 ADCY2 ADCY2 ADCY2 781 0.43 0.36 YES
15 COL6A3 COL6A3 COL6A3 830 0.42 0.38 YES
16 PDGFD PDGFD PDGFD 904 0.41 0.4 YES
17 COL6A2 COL6A2 COL6A2 956 0.4 0.42 YES
18 ADCY4 ADCY4 ADCY4 988 0.4 0.44 YES
19 CAMK4 CAMK4 CAMK4 1018 0.39 0.45 YES
20 ITPR3 ITPR3 ITPR3 1059 0.39 0.47 YES
21 ADCY3 ADCY3 ADCY3 1078 0.38 0.49 YES
22 COL4A3 COL4A3 COL4A3 1086 0.38 0.51 YES
23 COL6A1 COL6A1 COL6A1 1491 0.33 0.5 YES
24 THBS1 THBS1 THBS1 1657 0.32 0.51 YES
25 PDE1B PDE1B PDE1B 1715 0.31 0.52 YES
26 PDGFA PDGFA PDGFA 1897 0.29 0.53 YES
27 COL4A2 COL4A2 COL4A2 2141 0.27 0.53 YES
28 ADCY7 ADCY7 ADCY7 2157 0.27 0.54 YES
29 NCK2 NCK2 NCK2 2175 0.27 0.56 YES
30 PDGFRB PDGFRB PDGFRB 2202 0.27 0.57 YES
31 COL5A2 COL5A2 COL5A2 2429 0.25 0.57 YES
32 COL4A1 COL4A1 COL4A1 2622 0.24 0.57 YES
33 PRKAR1B PRKAR1B PRKAR1B 2663 0.23 0.58 YES
34 COL9A2 COL9A2 COL9A2 2867 0.22 0.58 YES
35 COL9A1 COL9A1 COL9A1 3088 0.2 0.58 YES
36 NR4A1 NR4A1 NR4A1 3130 0.2 0.58 YES
37 PDGFB PDGFB PDGFB 3314 0.19 0.58 YES
38 COL4A5 COL4A5 COL4A5 3429 0.18 0.59 YES
39 PDGFC PDGFC PDGFC 4173 0.14 0.55 NO
40 CDKN1A CDKN1A CDKN1A 4361 0.13 0.55 NO
41 FURIN FURIN FURIN 4408 0.13 0.55 NO
42 BCAR1 BCAR1 BCAR1 4488 0.12 0.55 NO
43 PRKCE PRKCE PRKCE 4698 0.11 0.55 NO
44 STAT5A STAT5A STAT5A 4974 0.1 0.54 NO
45 SRC SRC SRC 5246 0.091 0.52 NO
46 STAT3 STAT3 STAT3 5331 0.088 0.52 NO
47 CRK CRK CRK 5648 0.076 0.51 NO
48 ADCY1 ADCY1 ADCY1 5684 0.075 0.51 NO
49 THBS3 THBS3 THBS3 5913 0.069 0.5 NO
50 STAT1 STAT1 STAT1 5965 0.068 0.5 NO
51 MAPK3 MAPK3 MAPK3 6203 0.061 0.49 NO
52 FOXO1 FOXO1 FOXO1 6344 0.058 0.49 NO
53 MAP2K1 MAP2K1 MAP2K1 6532 0.054 0.48 NO
54 NCK1 NCK1 NCK1 6647 0.051 0.48 NO
55 CALM2 CALM2 CALM2 6772 0.048 0.47 NO
56 YWHAB YWHAB YWHAB 6957 0.045 0.46 NO
57 CALM1 CALM1 CALM1 7105 0.042 0.46 NO
58 STAT6 STAT6 STAT6 7228 0.04 0.45 NO
59 KRAS KRAS KRAS 7315 0.038 0.45 NO
60 ADCY9 ADCY9 ADCY9 7427 0.036 0.45 NO
61 PRKACA PRKACA PRKACA 7454 0.036 0.45 NO
62 AKT1 AKT1 AKT1 7500 0.035 0.44 NO
63 BAD BAD BAD 7526 0.034 0.45 NO
64 RAPGEF1 RAPGEF1 RAPGEF1 7573 0.033 0.44 NO
65 RASA1 RASA1 RASA1 7789 0.03 0.43 NO
66 CREB1 CREB1 CREB1 8078 0.026 0.42 NO
67 FOXO3 FOXO3 FOXO3 8135 0.025 0.42 NO
68 PIK3CA PIK3CA PIK3CA 8146 0.024 0.42 NO
69 ADRBK1 ADRBK1 ADRBK1 8439 0.02 0.4 NO
70 RICTOR RICTOR RICTOR 8684 0.017 0.39 NO
71 TRIB3 TRIB3 TRIB3 8719 0.016 0.39 NO
72 GSK3A GSK3A GSK3A 8736 0.016 0.39 NO
73 TSC2 TSC2 TSC2 8966 0.013 0.38 NO
74 PIK3CB PIK3CB PIK3CB 9266 0.0094 0.36 NO
75 PTEN PTEN PTEN 9336 0.0085 0.36 NO
76 MLST8 MLST8 MLST8 9614 0.0054 0.34 NO
77 PDPK1 PDPK1 PDPK1 9655 0.0049 0.34 NO
78 ADCY6 ADCY6 ADCY6 9659 0.0049 0.34 NO
79 MAP2K2 MAP2K2 MAP2K2 9980 0.0005 0.32 NO
80 PRKCD PRKCD PRKCD 10070 -0.0005 0.32 NO
81 HRAS HRAS HRAS 10357 -0.0038 0.3 NO
82 MDM2 MDM2 MDM2 10436 -0.0048 0.3 NO
83 CHUK CHUK CHUK 10594 -0.0064 0.29 NO
84 PRKAR1A PRKAR1A PRKAR1A 10944 -0.01 0.27 NO
85 PRKACB PRKACB PRKACB 11062 -0.012 0.26 NO
86 CALM3 CALM3 CALM3 11068 -0.012 0.26 NO
87 AKT1S1 AKT1S1 AKT1S1 11225 -0.014 0.25 NO
88 ADCY8 ADCY8 ADCY8 11454 -0.016 0.24 NO
89 MAPK1 MAPK1 MAPK1 11516 -0.017 0.24 NO
90 PLCG1 PLCG1 PLCG1 11609 -0.018 0.23 NO
91 SOS1 SOS1 SOS1 11693 -0.019 0.23 NO
92 THEM4 THEM4 THEM4 12090 -0.024 0.21 NO
93 AKT2 AKT2 AKT2 12138 -0.025 0.21 NO
94 CDKN1B CDKN1B CDKN1B 12303 -0.027 0.2 NO
95 PIK3R2 PIK3R2 PIK3R2 12460 -0.029 0.19 NO
96 RPS6KB2 RPS6KB2 RPS6KB2 12462 -0.029 0.19 NO
97 MAPKAP1 MAPKAP1 MAPKAP1 12478 -0.029 0.2 NO
98 GRB2 GRB2 GRB2 12627 -0.031 0.19 NO
99 PRKCG PRKCG PRKCG 12791 -0.033 0.18 NO
100 MTOR MTOR MTOR 12792 -0.033 0.18 NO
101 STAT5B STAT5B STAT5B 12851 -0.034 0.18 NO
102 NRAS NRAS NRAS 13024 -0.036 0.17 NO
103 CASP9 CASP9 CASP9 13317 -0.04 0.16 NO
104 GRB7 GRB7 GRB7 14375 -0.059 0.1 NO
105 FOXO4 FOXO4 FOXO4 14432 -0.06 0.1 NO
106 CRKL CRKL CRKL 14581 -0.063 0.096 NO
107 PIK3R1 PIK3R1 PIK3R1 14604 -0.063 0.098 NO
108 RAF1 RAF1 RAF1 14721 -0.066 0.095 NO
109 COL9A3 COL9A3 COL9A3 15186 -0.078 0.072 NO
110 PRKAR2A PRKAR2A PRKAR2A 15298 -0.081 0.07 NO
111 PRKCA PRKCA PRKCA 16077 -0.11 0.032 NO
112 PHLPP1 PHLPP1 PHLPP1 16197 -0.12 0.031 NO
113 ITPR2 ITPR2 ITPR2 16227 -0.12 0.036 NO
114 PLG PLG PLG 16433 -0.14 0.031 NO
115 COL2A1 COL2A1 COL2A1 17336 -0.23 -0.0083 NO
116 CDK1 CDK1 CDK1 17369 -0.23 0.0019 NO
117 THBS4 THBS4 THBS4 17693 -0.36 0.002 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S72.  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 INOSITOL PHOSPHATE 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 PDE1A PDE1A PDE1A 18 0.85 0.037 YES
2 NTRK2 NTRK2 NTRK2 34 0.81 0.072 YES
3 NGFR NGFR NGFR 65 0.74 0.1 YES
4 ADCY5 ADCY5 ADCY5 290 0.58 0.12 YES
5 PRKAR2B PRKAR2B PRKAR2B 509 0.5 0.13 YES
6 ARHGEF4 ARHGEF4 ARHGEF4 589 0.48 0.14 YES
7 ABR ABR ABR 686 0.45 0.16 YES
8 AKT3 AKT3 AKT3 693 0.45 0.18 YES
9 ADCY2 ADCY2 ADCY2 781 0.43 0.19 YES
10 ADCY4 ADCY4 ADCY4 988 0.4 0.2 YES
11 DUSP4 DUSP4 DUSP4 1002 0.39 0.21 YES
12 CAMK4 CAMK4 CAMK4 1018 0.39 0.23 YES
13 ITPR3 ITPR3 ITPR3 1059 0.39 0.24 YES
14 ADCY3 ADCY3 ADCY3 1078 0.38 0.26 YES
15 ARHGEF17 ARHGEF17 ARHGEF17 1182 0.37 0.27 YES
16 PCSK5 PCSK5 PCSK5 1195 0.37 0.29 YES
17 OBSCN OBSCN OBSCN 1200 0.37 0.3 YES
18 NGF NGF NGF 1254 0.36 0.32 YES
19 FGD3 FGD3 FGD3 1312 0.35 0.33 YES
20 LINGO1 LINGO1 LINGO1 1384 0.34 0.34 YES
21 ARHGEF16 ARHGEF16 ARHGEF16 1438 0.34 0.35 YES
22 VAV1 VAV1 VAV1 1689 0.31 0.35 YES
23 PDE1B PDE1B PDE1B 1715 0.31 0.36 YES
24 VAV3 VAV3 VAV3 1894 0.29 0.36 YES
25 MAPK11 MAPK11 MAPK11 2027 0.28 0.37 YES
26 ADCY7 ADCY7 ADCY7 2157 0.27 0.38 YES
27 ARHGEF3 ARHGEF3 ARHGEF3 2311 0.26 0.38 YES
28 TIAM2 TIAM2 TIAM2 2314 0.26 0.39 YES
29 RPS6KA2 RPS6KA2 RPS6KA2 2317 0.26 0.4 YES
30 MAPK12 MAPK12 MAPK12 2323 0.26 0.41 YES
31 FGD2 FGD2 FGD2 2431 0.25 0.42 YES
32 PREX1 PREX1 PREX1 2518 0.24 0.42 YES
33 DNM1 DNM1 DNM1 2536 0.24 0.43 YES
34 NTRK1 NTRK1 NTRK1 2617 0.24 0.44 YES
35 PRKAR1B PRKAR1B PRKAR1B 2663 0.23 0.45 YES
36 ARHGEF6 ARHGEF6 ARHGEF6 2731 0.23 0.45 YES
37 MEF2C MEF2C MEF2C 2748 0.23 0.46 YES
38 NR4A1 NR4A1 NR4A1 3130 0.2 0.45 YES
39 MAPK13 MAPK13 MAPK13 3233 0.19 0.45 YES
40 ARHGAP4 ARHGAP4 ARHGAP4 3292 0.19 0.46 YES
41 RASGRF2 RASGRF2 RASGRF2 3355 0.19 0.46 YES
42 TIAM1 TIAM1 TIAM1 3420 0.18 0.46 YES
43 RALGDS RALGDS RALGDS 3927 0.15 0.44 YES
44 FGD4 FGD4 FGD4 4142 0.14 0.44 YES
45 APH1B APH1B APH1B 4150 0.14 0.44 YES
46 FGD1 FGD1 FGD1 4335 0.13 0.44 YES
47 CDKN1A CDKN1A CDKN1A 4361 0.13 0.44 YES
48 PLEKHG2 PLEKHG2 PLEKHG2 4367 0.13 0.45 YES
49 FURIN FURIN FURIN 4408 0.13 0.45 YES
50 ADCYAP1 ADCYAP1 ADCYAP1 4440 0.12 0.46 YES
51 ADAM17 ADAM17 ADAM17 4466 0.12 0.46 YES
52 MCF2 MCF2 MCF2 4585 0.12 0.46 YES
53 SH3GL2 SH3GL2 SH3GL2 4663 0.11 0.46 YES
54 RALB RALB RALB 4687 0.11 0.46 YES
55 PRKCE PRKCE PRKCE 4698 0.11 0.47 YES
56 PSEN2 PSEN2 PSEN2 5131 0.094 0.44 YES
57 SHC3 SHC3 SHC3 5236 0.091 0.44 YES
58 BCL2L11 BCL2L11 BCL2L11 5241 0.091 0.45 YES
59 SRC SRC SRC 5246 0.091 0.45 YES
60 STAT3 STAT3 STAT3 5331 0.088 0.45 YES
61 AKAP13 AKAP13 AKAP13 5368 0.086 0.45 YES
62 RPS6KA5 RPS6KA5 RPS6KA5 5390 0.085 0.46 YES
63 RIPK2 RIPK2 RIPK2 5405 0.084 0.46 YES
64 MAPK7 MAPK7 MAPK7 5445 0.083 0.46 YES
65 ARHGEF2 ARHGEF2 ARHGEF2 5554 0.079 0.46 YES
66 MEF2A MEF2A MEF2A 5574 0.078 0.46 YES
67 MAPKAPK2 MAPKAPK2 MAPKAPK2 5645 0.076 0.46 YES
68 CRK CRK CRK 5648 0.076 0.46 YES
69 DUSP7 DUSP7 DUSP7 5650 0.076 0.46 YES
70 PPP2CB PPP2CB PPP2CB 5670 0.076 0.47 YES
71 ADCY1 ADCY1 ADCY1 5684 0.075 0.47 YES
72 TRIO TRIO TRIO 6044 0.065 0.45 NO
73 ARHGEF12 ARHGEF12 ARHGEF12 6081 0.064 0.45 NO
74 IKBKB IKBKB IKBKB 6160 0.062 0.45 NO
75 MAPK3 MAPK3 MAPK3 6203 0.061 0.45 NO
76 SHC2 SHC2 SHC2 6228 0.061 0.45 NO
77 ADORA2A ADORA2A ADORA2A 6249 0.06 0.45 NO
78 DNAL4 DNAL4 DNAL4 6257 0.06 0.46 NO
79 KALRN KALRN KALRN 6284 0.059 0.46 NO
80 RPS6KA1 RPS6KA1 RPS6KA1 6293 0.059 0.46 NO
81 DUSP6 DUSP6 DUSP6 6296 0.059 0.46 NO
82 FOXO1 FOXO1 FOXO1 6344 0.058 0.46 NO
83 MAP2K1 MAP2K1 MAP2K1 6532 0.054 0.45 NO
84 NFKBIA NFKBIA NFKBIA 6618 0.052 0.45 NO
85 SHC1 SHC1 SHC1 6672 0.05 0.45 NO
86 PPP2R1A PPP2R1A PPP2R1A 6706 0.05 0.45 NO
87 CALM2 CALM2 CALM2 6772 0.048 0.45 NO
88 RIT1 RIT1 RIT1 6809 0.048 0.45 NO
89 YWHAB YWHAB YWHAB 6957 0.045 0.44 NO
90 PRDM4 PRDM4 PRDM4 7060 0.043 0.44 NO
91 MAG MAG MAG 7086 0.042 0.44 NO
92 CALM1 CALM1 CALM1 7105 0.042 0.44 NO
93 RAC1 RAC1 RAC1 7184 0.041 0.44 NO
94 TRAF6 TRAF6 TRAF6 7208 0.04 0.44 NO
95 NGFRAP1 NGFRAP1 NGFRAP1 7254 0.039 0.44 NO
96 KRAS KRAS KRAS 7315 0.038 0.44 NO
97 RTN4 RTN4 RTN4 7317 0.038 0.44 NO
98 KIDINS220 KIDINS220 KIDINS220 7331 0.038 0.44 NO
99 OMG OMG OMG 7366 0.037 0.44 NO
100 ADCY9 ADCY9 ADCY9 7427 0.036 0.44 NO
101 PRKACA PRKACA PRKACA 7454 0.036 0.44 NO
102 SOS2 SOS2 SOS2 7494 0.035 0.44 NO
103 AKT1 AKT1 AKT1 7500 0.035 0.44 NO
104 BAD BAD BAD 7526 0.034 0.44 NO
105 RAPGEF1 RAPGEF1 RAPGEF1 7573 0.033 0.44 NO
106 RASGRF1 RASGRF1 RASGRF1 7669 0.032 0.43 NO
107 DNM2 DNM2 DNM2 7942 0.028 0.42 NO
108 CREB1 CREB1 CREB1 8078 0.026 0.41 NO
109 FOXO3 FOXO3 FOXO3 8135 0.025 0.41 NO
110 PIK3CA PIK3CA PIK3CA 8146 0.024 0.41 NO
111 RAP1A RAP1A RAP1A 8233 0.023 0.4 NO
112 ITSN1 ITSN1 ITSN1 8256 0.023 0.4 NO
113 ARHGEF18 ARHGEF18 ARHGEF18 8296 0.022 0.4 NO
114 SMPD2 SMPD2 SMPD2 8299 0.022 0.4 NO
115 IRAK1 IRAK1 IRAK1 8340 0.022 0.4 NO
116 ADRBK1 ADRBK1 ADRBK1 8439 0.02 0.4 NO
117 ARHGEF1 ARHGEF1 ARHGEF1 8546 0.018 0.39 NO
118 AP2A2 AP2A2 AP2A2 8617 0.018 0.39 NO
119 CASP2 CASP2 CASP2 8658 0.017 0.39 NO
120 RICTOR RICTOR RICTOR 8684 0.017 0.39 NO
121 TRIB3 TRIB3 TRIB3 8719 0.016 0.39 NO
122 GSK3A GSK3A GSK3A 8736 0.016 0.39 NO
123 MAP2K5 MAP2K5 MAP2K5 8828 0.015 0.38 NO
124 YWHAE YWHAE YWHAE 8847 0.014 0.38 NO
125 AP2M1 AP2M1 AP2M1 8874 0.014 0.38 NO
126 AP2B1 AP2B1 AP2B1 8886 0.014 0.38 NO
127 TSC2 TSC2 TSC2 8966 0.013 0.38 NO
128 PSENEN PSENEN PSENEN 8983 0.013 0.38 NO
129 PSEN1 PSEN1 PSEN1 9100 0.011 0.37 NO
130 RHOA RHOA RHOA 9181 0.01 0.37 NO
131 PIK3CB PIK3CB PIK3CB 9266 0.0094 0.36 NO
132 MAPK8 MAPK8 MAPK8 9314 0.0088 0.36 NO
133 RALA RALA RALA 9329 0.0086 0.36 NO
134 PTEN PTEN PTEN 9336 0.0085 0.36 NO
135 MLST8 MLST8 MLST8 9614 0.0054 0.34 NO
136 PDPK1 PDPK1 PDPK1 9655 0.0049 0.34 NO
137 ADCY6 ADCY6 ADCY6 9659 0.0049 0.34 NO
138 SQSTM1 SQSTM1 SQSTM1 9861 0.0022 0.33 NO
139 ARHGEF9 ARHGEF9 ARHGEF9 9960 0.0008 0.32 NO
140 MAP2K2 MAP2K2 MAP2K2 9980 0.0005 0.32 NO
141 MAGED1 MAGED1 MAGED1 10006 0.00015 0.32 NO
142 PRKCD PRKCD PRKCD 10070 -0.0005 0.32 NO
143 NCSTN NCSTN NCSTN 10138 -0.0013 0.31 NO
144 PRKCI PRKCI PRKCI 10219 -0.0022 0.31 NO
145 CASP3 CASP3 CASP3 10238 -0.0024 0.31 NO
146 HRAS HRAS HRAS 10357 -0.0038 0.3 NO
147 MAPKAPK3 MAPKAPK3 MAPKAPK3 10382 -0.0041 0.3 NO
148 PPP2CA PPP2CA PPP2CA 10385 -0.0042 0.3 NO
149 MDM2 MDM2 MDM2 10436 -0.0048 0.3 NO
150 CHUK CHUK CHUK 10594 -0.0064 0.29 NO
151 DUSP3 DUSP3 DUSP3 10606 -0.0066 0.29 NO
152 HDAC1 HDAC1 HDAC1 10758 -0.0084 0.28 NO
153 CLTC CLTC CLTC 10832 -0.0092 0.28 NO
154 HDAC2 HDAC2 HDAC2 10850 -0.0094 0.28 NO
155 PRKAR1A PRKAR1A PRKAR1A 10944 -0.01 0.27 NO
156 HDAC3 HDAC3 HDAC3 10964 -0.011 0.27 NO
157 AP2S1 AP2S1 AP2S1 10969 -0.011 0.27 NO
158 CLTA CLTA CLTA 11042 -0.012 0.27 NO
159 PRKACB PRKACB PRKACB 11062 -0.012 0.27 NO
160 CALM3 CALM3 CALM3 11068 -0.012 0.27 NO
161 ARHGDIA ARHGDIA ARHGDIA 11069 -0.012 0.27 NO
162 IRS2 IRS2 IRS2 11070 -0.012 0.27 NO
163 RELA RELA RELA 11135 -0.013 0.27 NO
164 AKT1S1 AKT1S1 AKT1S1 11225 -0.014 0.26 NO
165 AP2A1 AP2A1 AP2A1 11277 -0.014 0.26 NO
166 ADCY8 ADCY8 ADCY8 11454 -0.016 0.25 NO
167 MAPK1 MAPK1 MAPK1 11516 -0.017 0.25 NO
168 UBA52 UBA52 UBA52 11591 -0.018 0.24 NO
169 PLCG1 PLCG1 PLCG1 11609 -0.018 0.24 NO
170 SOS1 SOS1 SOS1 11693 -0.019 0.24 NO
171 FRS2 FRS2 FRS2 11702 -0.019 0.24 NO
172 ARHGEF11 ARHGEF11 ARHGEF11 11816 -0.021 0.24 NO
173 RPS27A RPS27A RPS27A 11897 -0.022 0.23 NO
174 ELK1 ELK1 ELK1 11926 -0.022 0.23 NO
175 PPP2R1B PPP2R1B PPP2R1B 12000 -0.023 0.23 NO
176 THEM4 THEM4 THEM4 12090 -0.024 0.22 NO
177 AKT2 AKT2 AKT2 12138 -0.025 0.22 NO
178 APH1A APH1A APH1A 12139 -0.025 0.22 NO
179 CDKN1B CDKN1B CDKN1B 12303 -0.027 0.22 NO
180 PIK3R2 PIK3R2 PIK3R2 12460 -0.029 0.21 NO
181 RPS6KB2 RPS6KB2 RPS6KB2 12462 -0.029 0.21 NO
182 MAPKAP1 MAPKAP1 MAPKAP1 12478 -0.029 0.21 NO
183 GRB2 GRB2 GRB2 12627 -0.031 0.2 NO
184 PRKCG PRKCG PRKCG 12791 -0.033 0.19 NO
185 MTOR MTOR MTOR 12792 -0.033 0.2 NO
186 MYD88 MYD88 MYD88 12859 -0.034 0.19 NO
187 MAPK14 MAPK14 MAPK14 12970 -0.035 0.19 NO
188 NRAS NRAS NRAS 13024 -0.036 0.19 NO
189 CASP9 CASP9 CASP9 13317 -0.04 0.17 NO
190 RPS6KA3 RPS6KA3 RPS6KA3 13891 -0.049 0.14 NO
191 ATF1 ATF1 ATF1 13988 -0.051 0.14 NO
192 AATF AATF AATF 14016 -0.052 0.14 NO
193 FOXO4 FOXO4 FOXO4 14432 -0.06 0.12 NO
194 PIK3R1 PIK3R1 PIK3R1 14604 -0.063 0.11 NO
195 NGEF NGEF NGEF 14660 -0.064 0.11 NO
196 RAF1 RAF1 RAF1 14721 -0.066 0.11 NO
197 ECT2 ECT2 ECT2 14806 -0.068 0.11 NO
198 BRAF BRAF BRAF 15109 -0.075 0.094 NO
199 PRKAR2A PRKAR2A PRKAR2A 15298 -0.081 0.087 NO
200 PPP2R5D PPP2R5D PPP2R5D 15351 -0.083 0.088 NO
201 NET1 NET1 NET1 15463 -0.087 0.085 NO
202 PCSK6 PCSK6 PCSK6 15792 -0.099 0.071 NO
203 PRKCA PRKCA PRKCA 16077 -0.11 0.06 NO
204 PHLPP1 PHLPP1 PHLPP1 16197 -0.12 0.058 NO
205 ITPR2 ITPR2 ITPR2 16227 -0.12 0.062 NO
206 ITGB3BP ITGB3BP ITGB3BP 16351 -0.13 0.061 NO
207 IRS1 IRS1 IRS1 16780 -0.16 0.044 NO
208 CDK1 CDK1 CDK1 17369 -0.23 0.02 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 INOSITOL PHOSPHATE METABOLISM.

Figure S74.  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 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 PDE1A PDE1A PDE1A 18 0.85 0.15 YES
2 ADCY5 ADCY5 ADCY5 290 0.58 0.24 YES
3 PLA2G4A PLA2G4A PLA2G4A 325 0.56 0.34 YES
4 PRKAR2B PRKAR2B PRKAR2B 509 0.5 0.42 YES
5 ADCY2 ADCY2 ADCY2 781 0.43 0.49 YES
6 ADCY4 ADCY4 ADCY4 988 0.4 0.55 YES
7 CAMK4 CAMK4 CAMK4 1018 0.39 0.62 YES
8 ADCY3 ADCY3 ADCY3 1078 0.38 0.68 YES
9 PDE1B PDE1B PDE1B 1715 0.31 0.7 YES
10 ADCY7 ADCY7 ADCY7 2157 0.27 0.73 YES
11 PRKAR1B PRKAR1B PRKAR1B 2663 0.23 0.74 YES
12 ADCY1 ADCY1 ADCY1 5684 0.075 0.59 NO
13 CALM2 CALM2 CALM2 6772 0.048 0.53 NO
14 CALM1 CALM1 CALM1 7105 0.042 0.52 NO
15 ADCY9 ADCY9 ADCY9 7427 0.036 0.51 NO
16 PRKACA PRKACA PRKACA 7454 0.036 0.52 NO
17 CREB1 CREB1 CREB1 8078 0.026 0.49 NO
18 ADRBK1 ADRBK1 ADRBK1 8439 0.02 0.47 NO
19 ADCY6 ADCY6 ADCY6 9659 0.0049 0.4 NO
20 PRKCD PRKCD PRKCD 10070 -0.0005 0.38 NO
21 PRKAR1A PRKAR1A PRKAR1A 10944 -0.01 0.33 NO
22 PRKACB PRKACB PRKACB 11062 -0.012 0.33 NO
23 CALM3 CALM3 CALM3 11068 -0.012 0.33 NO
24 ADCY8 ADCY8 ADCY8 11454 -0.016 0.31 NO
25 MAPK1 MAPK1 MAPK1 11516 -0.017 0.31 NO
26 PRKCG PRKCG PRKCG 12791 -0.033 0.24 NO
27 PRKAR2A PRKAR2A PRKAR2A 15298 -0.081 0.12 NO
28 PRKCA PRKCA PRKCA 16077 -0.11 0.093 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 GLYCEROPHOSPHOLIPID METABOLISM.

Figure S76.  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 ETHER LIPID 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 GATA2 GATA2 GATA2 788 0.43 0.11 YES
2 HDAC9 HDAC9 HDAC9 868 0.42 0.25 YES
3 CAMK4 CAMK4 CAMK4 1018 0.39 0.38 YES
4 GNG2 GNG2 GNG2 2289 0.26 0.4 YES
5 HDAC7 HDAC7 HDAC7 2718 0.23 0.46 YES
6 MEF2C MEF2C MEF2C 2748 0.23 0.54 YES
7 ESR1 ESR1 ESR1 4058 0.14 0.51 NO
8 YWHAB YWHAB YWHAB 6957 0.045 0.36 NO
9 NCOR2 NCOR2 NCOR2 7033 0.043 0.38 NO
10 UBE2I UBE2I UBE2I 7365 0.037 0.37 NO
11 GATA1 GATA1 GATA1 7828 0.029 0.35 NO
12 GNB1 GNB1 GNB1 8072 0.026 0.35 NO
13 HDAC10 HDAC10 HDAC10 8098 0.025 0.36 NO
14 RANBP2 RANBP2 RANBP2 8437 0.02 0.34 NO
15 ADRBK1 ADRBK1 ADRBK1 8439 0.02 0.35 NO
16 YWHAE YWHAE YWHAE 8847 0.014 0.33 NO
17 RANGAP1 RANGAP1 RANGAP1 9340 0.0085 0.31 NO
18 SRF SRF SRF 9690 0.0044 0.29 NO
19 HSP90AA1 HSP90AA1 HSP90AA1 10040 -0.00018 0.27 NO
20 RAN RAN RAN 10156 -0.0015 0.27 NO
21 HDAC3 HDAC3 HDAC3 10964 -0.011 0.22 NO
22 NR3C1 NR3C1 NR3C1 11192 -0.014 0.22 NO
23 SUMO1 SUMO1 SUMO1 11308 -0.015 0.22 NO
24 HDAC11 HDAC11 HDAC11 11348 -0.015 0.22 NO
25 TUBA1B TUBA1B TUBA1B 11613 -0.018 0.21 NO
26 BCOR BCOR BCOR 12006 -0.023 0.2 NO
27 TUBB2A TUBB2A TUBB2A 12334 -0.027 0.19 NO
28 HDAC5 HDAC5 HDAC5 12590 -0.03 0.18 NO
29 XPO1 XPO1 XPO1 12868 -0.034 0.18 NO
30 HDAC4 HDAC4 HDAC4 12872 -0.034 0.19 NO
31 RFXANK RFXANK RFXANK 13078 -0.037 0.19 NO
32 ANKRA2 ANKRA2 ANKRA2 14306 -0.057 0.14 NO
33 BCL6 BCL6 BCL6 14324 -0.058 0.16 NO
34 HDAC6 HDAC6 HDAC6 15399 -0.084 0.13 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 ETHER LIPID METABOLISM.

Figure S78.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ETHER LIPID 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 ARACHIDONIC ACID 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 PRICKLE1 PRICKLE1 PRICKLE1 23 0.84 0.032 YES
2 SFRP4 SFRP4 SFRP4 44 0.77 0.062 YES
3 SFRP1 SFRP1 SFRP1 92 0.72 0.088 YES
4 MAPK10 MAPK10 MAPK10 129 0.68 0.11 YES
5 WNT2 WNT2 WNT2 163 0.66 0.14 YES
6 DKK2 DKK2 DKK2 167 0.66 0.16 YES
7 FZD2 FZD2 FZD2 217 0.62 0.19 YES
8 WNT4 WNT4 WNT4 227 0.61 0.21 YES
9 MMP7 MMP7 MMP7 246 0.6 0.23 YES
10 WNT2B WNT2B WNT2B 278 0.59 0.26 YES
11 NKD2 NKD2 NKD2 286 0.58 0.28 YES
12 PLCB4 PLCB4 PLCB4 346 0.55 0.3 YES
13 SFRP5 SFRP5 SFRP5 423 0.53 0.31 YES
14 FZD10 FZD10 FZD10 454 0.52 0.33 YES
15 VANGL2 VANGL2 VANGL2 555 0.49 0.35 YES
16 NFATC1 NFATC1 NFATC1 577 0.48 0.36 YES
17 WNT10A WNT10A WNT10A 592 0.48 0.38 YES
18 FZD8 FZD8 FZD8 722 0.44 0.39 YES
19 WNT9A WNT9A WNT9A 737 0.44 0.41 YES
20 FZD7 FZD7 FZD7 762 0.44 0.43 YES
21 FZD1 FZD1 FZD1 768 0.44 0.44 YES
22 SOX17 SOX17 SOX17 880 0.41 0.45 YES
23 PRKX PRKX PRKX 881 0.41 0.47 YES
24 WNT10B WNT10B WNT10B 912 0.41 0.48 YES
25 CTBP2 CTBP2 CTBP2 1010 0.39 0.5 YES
26 PRICKLE2 PRICKLE2 PRICKLE2 1043 0.39 0.51 YES
27 WNT7B WNT7B WNT7B 1053 0.39 0.52 YES
28 SFRP2 SFRP2 SFRP2 1069 0.39 0.54 YES
29 CCND2 CCND2 CCND2 1302 0.36 0.54 YES
30 NFATC4 NFATC4 NFATC4 1333 0.35 0.55 YES
31 FOSL1 FOSL1 FOSL1 1466 0.34 0.56 YES
32 PRKCB PRKCB PRKCB 1573 0.32 0.56 YES
33 WNT7A WNT7A WNT7A 1651 0.32 0.57 YES
34 WNT11 WNT11 WNT11 1706 0.31 0.58 YES
35 PLCB2 PLCB2 PLCB2 1713 0.31 0.59 YES
36 RAC2 RAC2 RAC2 1994 0.28 0.59 NO
37 WNT1 WNT1 WNT1 2204 0.27 0.59 NO
38 LEF1 LEF1 LEF1 2368 0.26 0.59 NO
39 WNT3A WNT3A WNT3A 2950 0.21 0.56 NO
40 FZD6 FZD6 FZD6 3333 0.19 0.55 NO
41 WNT9B WNT9B WNT9B 3524 0.18 0.55 NO
42 WNT6 WNT6 WNT6 3527 0.18 0.55 NO
43 CAMK2B CAMK2B CAMK2B 3529 0.18 0.56 NO
44 MYC MYC MYC 3924 0.15 0.55 NO
45 CAMK2A CAMK2A CAMK2A 4097 0.14 0.54 NO
46 TP53 TP53 TP53 4293 0.13 0.54 NO
47 FZD3 FZD3 FZD3 4381 0.13 0.54 NO
48 CCND3 CCND3 CCND3 4736 0.11 0.52 NO
49 APC2 APC2 APC2 4843 0.11 0.52 NO
50 WNT16 WNT16 WNT16 5066 0.097 0.51 NO
51 AXIN1 AXIN1 AXIN1 5208 0.092 0.5 NO
52 VANGL1 VANGL1 VANGL1 5260 0.09 0.5 NO
53 NFATC2 NFATC2 NFATC2 5290 0.09 0.51 NO
54 CCND1 CCND1 CCND1 5318 0.088 0.51 NO
55 PPARD PPARD PPARD 5335 0.088 0.51 NO
56 PORCN PORCN PORCN 5357 0.086 0.51 NO
57 PPP3CC PPP3CC PPP3CC 5660 0.076 0.5 NO
58 PPP3CA PPP3CA PPP3CA 5663 0.076 0.5 NO
59 PPP2CB PPP2CB PPP2CB 5670 0.076 0.5 NO
60 PLCB3 PLCB3 PLCB3 5700 0.075 0.51 NO
61 DAAM2 DAAM2 DAAM2 6004 0.067 0.49 NO
62 PPP2R5E PPP2R5E PPP2R5E 6053 0.065 0.49 NO
63 WNT5B WNT5B WNT5B 6054 0.065 0.5 NO
64 FBXW11 FBXW11 FBXW11 6330 0.058 0.48 NO
65 CSNK1E CSNK1E CSNK1E 6365 0.057 0.48 NO
66 WNT5A WNT5A WNT5A 6508 0.054 0.48 NO
67 FZD4 FZD4 FZD4 6565 0.053 0.48 NO
68 PPP2R1A PPP2R1A PPP2R1A 6706 0.05 0.47 NO
69 NFAT5 NFAT5 NFAT5 6844 0.047 0.46 NO
70 DAAM1 DAAM1 DAAM1 7004 0.044 0.46 NO
71 SMAD2 SMAD2 SMAD2 7165 0.041 0.45 NO
72 CAMK2D CAMK2D CAMK2D 7180 0.041 0.45 NO
73 RAC1 RAC1 RAC1 7184 0.041 0.45 NO
74 PRKACA PRKACA PRKACA 7454 0.036 0.44 NO
75 JUN JUN JUN 7666 0.032 0.43 NO
76 ROCK1 ROCK1 ROCK1 7688 0.032 0.43 NO
77 SKP1 SKP1 SKP1 7746 0.031 0.42 NO
78 PPP3CB PPP3CB PPP3CB 7852 0.029 0.42 NO
79 CHP2 CHP2 CHP2 8040 0.026 0.41 NO
80 CSNK1A1 CSNK1A1 CSNK1A1 8054 0.026 0.41 NO
81 CHP CHP CHP 8083 0.026 0.41 NO
82 APC APC APC 8139 0.025 0.41 NO
83 PPP2R5B PPP2R5B PPP2R5B 8310 0.022 0.4 NO
84 SIAH1 SIAH1 SIAH1 8398 0.021 0.39 NO
85 TCF7L1 TCF7L1 TCF7L1 8490 0.019 0.39 NO
86 MAPK9 MAPK9 MAPK9 8612 0.018 0.38 NO
87 TBL1XR1 TBL1XR1 TBL1XR1 9038 0.012 0.36 NO
88 PSEN1 PSEN1 PSEN1 9100 0.011 0.36 NO
89 CSNK2A1 CSNK2A1 CSNK2A1 9148 0.011 0.36 NO
90 RHOA RHOA RHOA 9181 0.01 0.35 NO
91 MAPK8 MAPK8 MAPK8 9314 0.0088 0.35 NO
92 CAMK2G CAMK2G CAMK2G 9412 0.0076 0.34 NO
93 RBX1 RBX1 RBX1 9603 0.0055 0.33 NO
94 CREBBP CREBBP CREBBP 9745 0.0037 0.32 NO
95 TCF7L2 TCF7L2 TCF7L2 9834 0.0026 0.32 NO
96 CSNK2A2 CSNK2A2 CSNK2A2 9904 0.0016 0.31 NO
97 WNT3 WNT3 WNT3 9961 0.00079 0.31 NO
98 RUVBL1 RUVBL1 RUVBL1 10292 -0.003 0.29 NO
99 PPP2CA PPP2CA PPP2CA 10385 -0.0042 0.29 NO
100 SMAD4 SMAD4 SMAD4 10554 -0.006 0.28 NO
101 SMAD3 SMAD3 SMAD3 10611 -0.0066 0.28 NO
102 PPP2R5C PPP2R5C PPP2R5C 10660 -0.0073 0.27 NO
103 CTBP1 CTBP1 CTBP1 10801 -0.0088 0.26 NO
104 LRP5 LRP5 LRP5 10873 -0.0096 0.26 NO
105 PRKACB PRKACB PRKACB 11062 -0.012 0.25 NO
106 CUL1 CUL1 CUL1 11290 -0.014 0.24 NO
107 GSK3B GSK3B GSK3B 11371 -0.016 0.23 NO
108 BTRC BTRC BTRC 11415 -0.016 0.23 NO
109 CHD8 CHD8 CHD8 11575 -0.018 0.22 NO
110 DVL3 DVL3 DVL3 11676 -0.019 0.22 NO
111 AXIN2 AXIN2 AXIN2 11886 -0.022 0.21 NO
112 PPP2R1B PPP2R1B PPP2R1B 12000 -0.023 0.2 NO
113 PPP3R1 PPP3R1 PPP3R1 12222 -0.026 0.19 NO
114 EP300 EP300 EP300 12280 -0.026 0.19 NO
115 DVL1 DVL1 DVL1 12691 -0.032 0.17 NO
116 LRP6 LRP6 LRP6 12744 -0.032 0.16 NO
117 MAP3K7 MAP3K7 MAP3K7 12788 -0.033 0.16 NO
118 PRKCG PRKCG PRKCG 12791 -0.033 0.16 NO
119 CTNNB1 CTNNB1 CTNNB1 12794 -0.033 0.17 NO
120 PPP2R5A PPP2R5A PPP2R5A 12850 -0.034 0.16 NO
121 FRAT2 FRAT2 FRAT2 12882 -0.034 0.16 NO
122 FZD9 FZD9 FZD9 12965 -0.035 0.16 NO
123 NLK NLK NLK 13325 -0.04 0.14 NO
124 DVL2 DVL2 DVL2 13504 -0.043 0.13 NO
125 NFATC3 NFATC3 NFATC3 13724 -0.046 0.12 NO
126 ROCK2 ROCK2 ROCK2 13989 -0.051 0.11 NO
127 CSNK1A1L CSNK1A1L CSNK1A1L 14097 -0.053 0.11 NO
128 CACYBP CACYBP CACYBP 14381 -0.059 0.093 NO
129 CSNK2B CSNK2B CSNK2B 14724 -0.066 0.076 NO
130 DKK1 DKK1 DKK1 14775 -0.067 0.076 NO
131 FRAT1 FRAT1 FRAT1 14920 -0.071 0.07 NO
132 SENP2 SENP2 SENP2 14951 -0.072 0.072 NO
133 FZD5 FZD5 FZD5 15058 -0.074 0.069 NO
134 TBL1X TBL1X TBL1X 15342 -0.083 0.056 NO
135 PPP2R5D PPP2R5D PPP2R5D 15351 -0.083 0.059 NO
136 CXXC4 CXXC4 CXXC4 15572 -0.091 0.05 NO
137 CTNNBIP1 CTNNBIP1 CTNNBIP1 15750 -0.097 0.044 NO
138 TBL1Y TBL1Y TBL1Y 15976 -0.11 0.035 NO
139 PLCB1 PLCB1 PLCB1 16060 -0.11 0.035 NO
140 PRKCA PRKCA PRKCA 16077 -0.11 0.039 NO
141 DKK4 DKK4 DKK4 16819 -0.16 0.0031 NO
142 NKD1 NKD1 NKD1 16854 -0.17 0.008 NO
143 WNT8B WNT8B WNT8B 17365 -0.23 -0.012 NO
144 TCF7 TCF7 TCF7 17390 -0.24 -0.0036 NO
145 RAC3 RAC3 RAC3 17526 -0.27 -0.0004 NO
146 WIF1 WIF1 WIF1 17588 -0.3 0.008 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 ARACHIDONIC ACID METABOLISM.

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ARACHIDONIC ACID 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS 27 genes.ES.table 0.7 1.4 0.1 1 0.99 0.52 0.089 0.47 0.85 0.43
KEGG FATTY ACID METABOLISM 40 genes.ES.table 0.67 1.5 0.047 1 0.97 0.7 0.2 0.56 1 0.57
KEGG STEROID HORMONE BIOSYNTHESIS 52 genes.ES.table 0.67 1.4 0.077 1 0.99 0.6 0.12 0.52 0.9 0.46
KEGG LYSINE DEGRADATION 44 genes.ES.table 0.42 1.4 0.17 1 1 0.39 0.2 0.31 0.84 0.42
KEGG TYROSINE METABOLISM 40 genes.ES.table 0.56 1.5 0.037 1 0.98 0.4 0.11 0.36 1 0.51
KEGG BUTANOATE METABOLISM 31 genes.ES.table 0.56 1.4 0.14 1 0.99 0.52 0.14 0.44 0.8 0.4
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 39 genes.ES.table 0.66 1.5 0.047 1 0.96 0.49 0.14 0.42 1 0.66
KEGG AMINOACYL TRNA BIOSYNTHESIS 41 genes.ES.table 0.38 1.4 0.15 1 0.99 1 0.62 0.38 0.92 0.46
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 66 genes.ES.table 0.65 1.5 0.048 1 0.99 0.61 0.13 0.53 0.92 0.46
KEGG DRUG METABOLISM CYTOCHROME P450 69 genes.ES.table 0.62 1.4 0.12 0.98 1 0.61 0.13 0.53 0.79 0.39
genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

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 AR AR AR 145 0.54 0.1 YES
2 CDK6 CDK6 CDK6 173 0.49 0.2 YES
3 KLK2 KLK2 KLK2 742 0.24 0.22 YES
4 NCOA2 NCOA2 NCOA2 869 0.22 0.25 YES
5 TGIF1 TGIF1 TGIF1 1130 0.19 0.28 YES
6 LATS2 LATS2 LATS2 1348 0.16 0.3 YES
7 CCND1 CCND1 CCND1 1500 0.15 0.32 YES
8 PIAS1 PIAS1 PIAS1 1771 0.13 0.33 YES
9 NRIP1 NRIP1 NRIP1 1778 0.13 0.35 YES
10 NCOA4 NCOA4 NCOA4 1973 0.11 0.36 YES
11 RPS6KA3 RPS6KA3 RPS6KA3 1989 0.11 0.38 YES
12 CTNNB1 CTNNB1 CTNNB1 2081 0.11 0.4 YES
13 KDM4C KDM4C KDM4C 2083 0.11 0.42 YES
14 NKX3-1 NKX3-1 NKX3-1 2254 0.099 0.43 YES
15 SVIL SVIL SVIL 3807 0.047 0.35 NO
16 KDM3A KDM3A KDM3A 4452 0.034 0.32 NO
17 CTDSP1 CTDSP1 CTDSP1 4599 0.031 0.32 NO
18 RANBP9 RANBP9 RANBP9 4601 0.031 0.33 NO
19 HIP1 HIP1 HIP1 4801 0.027 0.32 NO
20 PRDX1 PRDX1 PRDX1 4906 0.025 0.32 NO
21 ZNF318 ZNF318 ZNF318 5023 0.023 0.32 NO
22 MED1 MED1 MED1 5082 0.022 0.32 NO
23 UBE3A UBE3A UBE3A 5472 0.015 0.3 NO
24 UBA3 UBA3 UBA3 5778 0.0097 0.29 NO
25 TMF1 TMF1 TMF1 5988 0.0064 0.28 NO
26 PATZ1 PATZ1 PATZ1 6118 0.0044 0.27 NO
27 HNRNPA1 HNRNPA1 HNRNPA1 6262 0.0023 0.26 NO
28 KDM1A KDM1A KDM1A 6338 0.0012 0.26 NO
29 FKBP4 FKBP4 FKBP4 6469 -0.00085 0.25 NO
30 CDK11B CDK11B CDK11B 6476 -0.001 0.25 NO
31 XRCC6 XRCC6 XRCC6 6530 -0.0018 0.25 NO
32 CCND3 CCND3 CCND3 6831 -0.0065 0.23 NO
33 CTDSP2 CTDSP2 CTDSP2 7213 -0.012 0.21 NO
34 PELP1 PELP1 PELP1 7251 -0.013 0.21 NO
35 NCOA6 NCOA6 NCOA6 7335 -0.014 0.21 NO
36 SRF SRF SRF 7545 -0.017 0.2 NO
37 CDKN2A CDKN2A CDKN2A 8073 -0.025 0.18 NO
38 GSN GSN GSN 8123 -0.026 0.18 NO
39 CASP8 CASP8 CASP8 8375 -0.03 0.17 NO
40 PRKDC PRKDC PRKDC 8514 -0.032 0.17 NO
41 XRCC5 XRCC5 XRCC5 8521 -0.032 0.18 NO
42 PIAS4 PIAS4 PIAS4 8594 -0.034 0.18 NO
43 UBE2I UBE2I UBE2I 8731 -0.036 0.18 NO
44 CARM1 CARM1 CARM1 8741 -0.036 0.19 NO
45 FHL2 FHL2 FHL2 8883 -0.039 0.19 NO
46 PA2G4 PA2G4 PA2G4 9222 -0.044 0.18 NO
47 APPL1 APPL1 APPL1 9424 -0.048 0.18 NO
48 PIAS3 PIAS3 PIAS3 9495 -0.049 0.18 NO
49 PTK2B PTK2B PTK2B 9596 -0.051 0.19 NO
50 SNURF SNURF SNURF 9837 -0.056 0.18 NO
51 BRCA1 BRCA1 BRCA1 10001 -0.06 0.19 NO
52 TMPRSS2 TMPRSS2 TMPRSS2 10158 -0.063 0.19 NO
53 MAK MAK MAK 11178 -0.091 0.15 NO
54 AKT1 AKT1 AKT1 11395 -0.098 0.16 NO
55 PAWR PAWR PAWR 11737 -0.11 0.16 NO
56 TCF4 TCF4 TCF4 11994 -0.12 0.17 NO
57 CMTM2 CMTM2 CMTM2 12964 -0.16 0.15 NO
58 ZMIZ1 ZMIZ1 ZMIZ1 13221 -0.17 0.17 NO
59 TGFB1I1 TGFB1I1 TGFB1I1 13987 -0.21 0.17 NO
60 VAV3 VAV3 VAV3 14205 -0.22 0.2 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS.

Figure S82.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, 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 RDBP RDBP RDBP 3630 0.051 -0.14 YES
2 POLR2C POLR2C POLR2C 3748 0.048 -0.079 YES
3 TCEA1 TCEA1 TCEA1 4650 0.03 -0.09 YES
4 TCEB1 TCEB1 TCEB1 4847 0.026 -0.067 YES
5 POLR2F POLR2F POLR2F 5109 0.021 -0.054 YES
6 WHSC2 WHSC2 WHSC2 5158 0.02 -0.03 YES
7 TH1L TH1L TH1L 5257 0.018 -0.011 YES
8 SUPT4H1 SUPT4H1 SUPT4H1 5287 0.018 0.011 YES
9 POLR2J POLR2J POLR2J 5384 0.016 0.027 YES
10 TCEB2 TCEB2 TCEB2 5438 0.015 0.044 YES
11 POLR2L POLR2L POLR2L 5869 0.0084 0.031 YES
12 CDK9 CDK9 CDK9 5876 0.0082 0.042 YES
13 TCEB3 TCEB3 TCEB3 5902 0.0078 0.051 YES
14 CCNT1 CCNT1 CCNT1 6023 0.0058 0.052 YES
15 POLR2A POLR2A POLR2A 6049 0.0054 0.058 YES
16 POLR2K POLR2K POLR2K 6111 0.0045 0.06 YES
17 GTF2F2 GTF2F2 GTF2F2 6745 -0.0053 0.031 YES
18 POLR2B POLR2B POLR2B 6859 -0.0073 0.035 YES
19 POLR2E POLR2E POLR2E 6916 -0.008 0.042 YES
20 SUPT16H SUPT16H SUPT16H 7509 -0.017 0.031 YES
21 CTDP1 CTDP1 CTDP1 7652 -0.019 0.048 YES
22 CCNT2 CCNT2 CCNT2 7759 -0.02 0.069 YES
23 GTF2F1 GTF2F1 GTF2F1 7784 -0.021 0.096 YES
24 COBRA1 COBRA1 COBRA1 7892 -0.022 0.12 YES
25 POLR2G POLR2G POLR2G 8873 -0.038 0.12 YES
26 POLR2D POLR2D POLR2D 8992 -0.04 0.16 YES
27 POLR2H POLR2H POLR2H 9066 -0.042 0.21 YES
28 SUPT5H SUPT5H SUPT5H 9078 -0.042 0.27 YES
29 SSRP1 SSRP1 SSRP1 9303 -0.046 0.32 YES
30 POLR2I POLR2I POLR2I 9351 -0.047 0.38 YES
31 ELL ELL ELL 10554 -0.072 0.4 YES

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 STEROID HORMONE BIOSYNTHESIS

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 UGT1A3 UGT1A3 UGT1A3 57 0.77 0.1 YES
2 UGT1A5 UGT1A5 UGT1A5 63 0.76 0.21 YES
3 UGT1A4 UGT1A4 UGT1A4 76 0.69 0.3 YES
4 UGT1A1 UGT1A1 UGT1A1 178 0.49 0.36 YES
5 UGT1A9 UGT1A9 UGT1A9 318 0.38 0.41 YES
6 UGT2B28 UGT2B28 UGT2B28 485 0.31 0.44 YES
7 UGT1A6 UGT1A6 UGT1A6 492 0.31 0.49 YES
8 ALAS1 ALAS1 ALAS1 530 0.3 0.52 YES
9 UGT2B10 UGT2B10 UGT2B10 576 0.28 0.56 YES
10 UGT2B7 UGT2B7 UGT2B7 880 0.22 0.57 YES
11 ALAD ALAD ALAD 1075 0.19 0.59 YES
12 UGT2B11 UGT2B11 UGT2B11 1116 0.19 0.61 YES
13 UGT1A8 UGT1A8 UGT1A8 1251 0.17 0.63 YES
14 MMAB MMAB MMAB 1455 0.15 0.64 YES
15 UGT2B4 UGT2B4 UGT2B4 1580 0.14 0.65 YES
16 BLVRB BLVRB BLVRB 1867 0.12 0.65 YES
17 UGT2B15 UGT2B15 UGT2B15 2182 0.1 0.65 YES
18 HMOX2 HMOX2 HMOX2 2290 0.097 0.66 YES
19 EARS2 EARS2 EARS2 2411 0.091 0.66 YES
20 PPOX PPOX PPOX 2733 0.079 0.66 NO
21 FECH FECH FECH 2869 0.074 0.66 NO
22 COX15 COX15 COX15 3390 0.058 0.64 NO
23 UROS UROS UROS 3482 0.056 0.64 NO
24 UROD UROD UROD 5590 0.013 0.52 NO
25 CPOX CPOX CPOX 5875 0.0082 0.51 NO
26 EPRS EPRS EPRS 6012 0.0061 0.5 NO
27 HCCS HCCS HCCS 6213 0.003 0.49 NO
28 COX10 COX10 COX10 6252 0.0024 0.49 NO
29 UGT1A7 UGT1A7 UGT1A7 6794 -0.0059 0.46 NO
30 HMBS HMBS HMBS 7254 -0.013 0.43 NO
31 ALAS2 ALAS2 ALAS2 7491 -0.016 0.42 NO
32 FTH1 FTH1 FTH1 8711 -0.036 0.36 NO
33 GUSB GUSB GUSB 9784 -0.055 0.3 NO
34 HMOX1 HMOX1 HMOX1 11149 -0.09 0.24 NO
35 CP CP CP 12185 -0.13 0.2 NO
36 UGT2A1 UGT2A1 UGT2A1 12752 -0.15 0.19 NO
37 UGT1A10 UGT1A10 UGT1A10 12989 -0.16 0.2 NO
38 UGT2A3 UGT2A3 UGT2A3 13750 -0.2 0.18 NO
39 BLVRA BLVRA BLVRA 15725 -0.32 0.11 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 STEROID HORMONE BIOSYNTHESIS.

Figure S86.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG LYSINE DEGRADATION

Table 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 ACSL6 ACSL6 ACSL6 55 0.78 0.12 YES
2 ACSL5 ACSL5 ACSL5 176 0.49 0.18 YES
3 ADH1B ADH1B ADH1B 197 0.47 0.26 YES
4 ADH4 ADH4 ADH4 235 0.44 0.32 YES
5 ADH6 ADH6 ADH6 255 0.43 0.39 YES
6 EHHADH EHHADH EHHADH 644 0.26 0.4 YES
7 ADH1C ADH1C ADH1C 718 0.25 0.44 YES
8 ADH7 ADH7 ADH7 879 0.22 0.46 YES
9 ALDH3A2 ALDH3A2 ALDH3A2 886 0.22 0.5 YES
10 ACADL ACADL ACADL 1082 0.19 0.52 YES
11 HADH HADH HADH 1290 0.17 0.53 YES
12 ALDH1B1 ALDH1B1 ALDH1B1 1406 0.16 0.55 YES
13 ALDH2 ALDH2 ALDH2 1410 0.16 0.57 YES
14 GCDH GCDH GCDH 1450 0.15 0.59 YES
15 ACADSB ACADSB ACADSB 1566 0.14 0.61 YES
16 ACAA1 ACAA1 ACAA1 1682 0.13 0.62 YES
17 ADH5 ADH5 ADH5 1946 0.12 0.62 YES
18 ADH1A ADH1A ADH1A 1961 0.12 0.64 YES
19 CPT2 CPT2 CPT2 2074 0.11 0.65 YES
20 ACADM ACADM ACADM 2420 0.09 0.64 YES
21 ECHS1 ECHS1 ECHS1 2427 0.09 0.66 YES
22 CYP4A11 CYP4A11 CYP4A11 2874 0.074 0.64 YES
23 ACOX1 ACOX1 ACOX1 2962 0.071 0.65 YES
24 ALDH7A1 ALDH7A1 ALDH7A1 2998 0.07 0.66 YES
25 CPT1C CPT1C CPT1C 3085 0.067 0.66 YES
26 ALDH9A1 ALDH9A1 ALDH9A1 3220 0.062 0.66 YES
27 ACAA2 ACAA2 ACAA2 3471 0.056 0.66 YES
28 CYP4A22 CYP4A22 CYP4A22 3516 0.054 0.67 YES
29 ACSL1 ACSL1 ACSL1 4237 0.038 0.63 NO
30 ACADVL ACADVL ACADVL 4427 0.034 0.63 NO
31 ACAT1 ACAT1 ACAT1 4838 0.026 0.61 NO
32 ACSL3 ACSL3 ACSL3 5268 0.018 0.58 NO
33 HADHB HADHB HADHB 5635 0.012 0.57 NO
34 HADHA HADHA HADHA 5913 0.0076 0.55 NO
35 ACADS ACADS ACADS 8631 -0.034 0.4 NO
36 ACAT2 ACAT2 ACAT2 8904 -0.039 0.39 NO
37 ACOX3 ACOX3 ACOX3 9106 -0.042 0.39 NO
38 CPT1A CPT1A CPT1A 9209 -0.044 0.39 NO
39 CPT1B CPT1B CPT1B 12191 -0.13 0.24 NO
40 ACSL4 ACSL4 ACSL4 17151 -0.47 0.033 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 LYSINE DEGRADATION.

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

genes ES table in pathway: KEGG TYROSINE METABOLISM

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 SULT4A1 SULT4A1 SULT4A1 14 1 0.071 YES
2 UGT1A3 UGT1A3 UGT1A3 57 0.77 0.12 YES
3 UGT1A5 UGT1A5 UGT1A5 63 0.76 0.17 YES
4 CYP1A2 CYP1A2 CYP1A2 68 0.74 0.22 YES
5 UGT1A4 UGT1A4 UGT1A4 76 0.69 0.27 YES
6 SULT1B1 SULT1B1 SULT1B1 85 0.67 0.32 YES
7 UGT1A1 UGT1A1 UGT1A1 178 0.49 0.34 YES
8 GLYAT GLYAT GLYAT 184 0.48 0.38 YES
9 SULT2B1 SULT2B1 SULT2B1 285 0.41 0.4 YES
10 UGT1A9 UGT1A9 UGT1A9 318 0.38 0.42 YES
11 NAT2 NAT2 NAT2 382 0.35 0.45 YES
12 UGT2B28 UGT2B28 UGT2B28 485 0.31 0.46 YES
13 UGT1A6 UGT1A6 UGT1A6 492 0.31 0.48 YES
14 SULT2A1 SULT2A1 SULT2A1 533 0.3 0.5 YES
15 UGT2B10 UGT2B10 UGT2B10 576 0.28 0.52 YES
16 ACSM2B ACSM2B ACSM2B 591 0.28 0.54 YES
17 UGT2B7 UGT2B7 UGT2B7 880 0.22 0.54 YES
18 GCLC GCLC GCLC 1028 0.2 0.54 YES
19 MAT1A MAT1A MAT1A 1079 0.19 0.55 YES
20 UGT2B11 UGT2B11 UGT2B11 1116 0.19 0.56 YES
21 GSTM4 GSTM4 GSTM4 1216 0.18 0.57 YES
22 MGST1 MGST1 MGST1 1224 0.18 0.58 YES
23 UGT1A8 UGT1A8 UGT1A8 1251 0.17 0.59 YES
24 MTR MTR MTR 1299 0.17 0.6 YES
25 UGT2B4 UGT2B4 UGT2B4 1580 0.14 0.59 YES
26 MGST2 MGST2 MGST2 1626 0.14 0.6 YES
27 GCLM GCLM GCLM 1904 0.12 0.59 YES
28 SULT1E1 SULT1E1 SULT1E1 2132 0.1 0.59 YES
29 OPLAH OPLAH OPLAH 2143 0.1 0.59 YES
30 TPMT TPMT TPMT 2212 0.1 0.6 YES
31 GSTA4 GSTA4 GSTA4 2258 0.098 0.6 YES
32 MAT2B MAT2B MAT2B 2273 0.098 0.61 YES
33 ACSM1 ACSM1 ACSM1 2392 0.092 0.6 NO
34 GSTO1 GSTO1 GSTO1 2721 0.079 0.59 NO
35 CNDP2 CNDP2 CNDP2 2841 0.074 0.59 NO
36 GSTM1 GSTM1 GSTM1 2991 0.07 0.59 NO
37 SLC35D1 SLC35D1 SLC35D1 3747 0.048 0.55 NO
38 GSTA1 GSTA1 GSTA1 3918 0.044 0.54 NO
39 GSTA2 GSTA2 GSTA2 3940 0.044 0.54 NO
40 MGST3 MGST3 MGST3 4391 0.035 0.52 NO
41 COMT COMT COMT 4942 0.024 0.49 NO
42 GSS GSS GSS 5144 0.02 0.48 NO
43 PAPSS2 PAPSS2 PAPSS2 5482 0.015 0.46 NO
44 UGDH UGDH UGDH 6212 0.003 0.42 NO
45 UGT1A7 UGT1A7 UGT1A7 6794 -0.0059 0.39 NO
46 GGT7 GGT7 GGT7 6858 -0.0072 0.39 NO
47 GSTO2 GSTO2 GSTO2 7909 -0.022 0.33 NO
48 SULT1A3 SULT1A3 SULT1A3 7960 -0.024 0.33 NO
49 BPNT1 BPNT1 BPNT1 8189 -0.027 0.32 NO
50 AHCY AHCY AHCY 9095 -0.042 0.27 NO
51 UGP2 UGP2 UGP2 9256 -0.045 0.26 NO
52 PAPSS1 PAPSS1 PAPSS1 9542 -0.05 0.25 NO
53 NAT1 NAT1 NAT1 9629 -0.052 0.25 NO
54 GGCT GGCT GGCT 12216 -0.13 0.11 NO
55 SULT1A1 SULT1A1 SULT1A1 12297 -0.13 0.11 NO
56 MAT2A MAT2A MAT2A 12623 -0.14 0.11 NO
57 UGT2A1 UGT2A1 UGT2A1 12752 -0.15 0.11 NO
58 NNMT NNMT NNMT 14447 -0.24 0.029 NO
59 GSTM5 GSTM5 GSTM5 14772 -0.26 0.028 NO
60 SULT1A2 SULT1A2 SULT1A2 14875 -0.26 0.041 NO
61 SULT1C2 SULT1C2 SULT1C2 15647 -0.31 0.019 NO
62 SULT1C4 SULT1C4 SULT1C4 15728 -0.32 0.036 NO
63 GSTP1 GSTP1 GSTP1 16091 -0.35 0.04 NO
64 GGT1 GGT1 GGT1 16162 -0.35 0.06 NO
65 GGT5 GGT5 GGT5 16755 -0.41 0.055 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 TYROSINE METABOLISM.

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

Table 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 ALDH3A1 ALDH3A1 ALDH3A1 5 1.2 0.15 YES
2 AOX1 AOX1 AOX1 191 0.48 0.2 YES
3 ADH1B ADH1B ADH1B 197 0.47 0.27 YES
4 HPD HPD HPD 230 0.44 0.32 YES
5 ADH4 ADH4 ADH4 235 0.44 0.38 YES
6 ADH6 ADH6 ADH6 255 0.43 0.44 YES
7 ADH1C ADH1C ADH1C 718 0.25 0.44 YES
8 HGD HGD HGD 791 0.23 0.47 YES
9 ADH7 ADH7 ADH7 879 0.22 0.49 YES
10 NAT6 NAT6 NAT6 934 0.21 0.52 YES
11 DDC DDC DDC 1226 0.17 0.52 YES
12 MAOA MAOA MAOA 1549 0.14 0.52 YES
13 MAOB MAOB MAOB 1551 0.14 0.54 YES
14 AOC2 AOC2 AOC2 1847 0.12 0.54 YES
15 ADH5 ADH5 ADH5 1946 0.12 0.55 YES
16 ADH1A ADH1A ADH1A 1961 0.12 0.56 YES
17 GSTZ1 GSTZ1 GSTZ1 2218 0.1 0.56 NO
18 TAT TAT TAT 2534 0.086 0.56 NO
19 LCMT2 LCMT2 LCMT2 2710 0.079 0.56 NO
20 DCT DCT DCT 2911 0.072 0.56 NO
21 HEMK1 HEMK1 HEMK1 3396 0.058 0.54 NO
22 PNMT PNMT PNMT 3451 0.056 0.54 NO
23 WBSCR22 WBSCR22 WBSCR22 4350 0.036 0.49 NO
24 GOT2 GOT2 GOT2 4529 0.033 0.49 NO
25 COMT COMT COMT 4942 0.024 0.47 NO
26 FAH FAH FAH 5838 0.009 0.42 NO
27 METTL6 METTL6 METTL6 6266 0.0022 0.39 NO
28 MIF MIF MIF 6495 -0.0014 0.38 NO
29 METTL2B METTL2B METTL2B 6783 -0.0058 0.37 NO
30 TRMT11 TRMT11 TRMT11 7047 -0.0099 0.35 NO
31 LCMT1 LCMT1 LCMT1 10264 -0.066 0.18 NO
32 AOC3 AOC3 AOC3 10790 -0.079 0.16 NO
33 TYRP1 TYRP1 TYRP1 10852 -0.08 0.17 NO
34 DBH DBH DBH 12740 -0.15 0.08 NO
35 GOT1 GOT1 GOT1 13352 -0.18 0.069 NO
36 TH TH TH 13511 -0.19 0.084 NO
37 ALDH1A3 ALDH1A3 ALDH1A3 14394 -0.24 0.065 NO
38 ALDH3B1 ALDH3B1 ALDH3B1 14629 -0.25 0.084 NO
39 ALDH3B2 ALDH3B2 ALDH3B2 15991 -0.34 0.052 NO
40 IL4I1 IL4I1 IL4I1 16181 -0.35 0.088 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 BUTANOATE METABOLISM.

Figure S92.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BUTANOATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM

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 SLC5A6 SLC5A6 SLC5A6 335 0.37 0.048 YES
2 SLC23A2 SLC23A2 SLC23A2 420 0.34 0.1 YES
3 GPHN GPHN GPHN 468 0.32 0.16 YES
4 MTHFD1 MTHFD1 MTHFD1 539 0.29 0.2 YES
5 MOCS2 MOCS2 MOCS2 1268 0.17 0.19 YES
6 PNPO PNPO PNPO 1311 0.16 0.22 YES
7 PANK1 PANK1 PANK1 1527 0.14 0.23 YES
8 SLC19A2 SLC19A2 SLC19A2 1623 0.14 0.25 YES
9 QPRT QPRT QPRT 1719 0.13 0.27 YES
10 MOCS1 MOCS1 MOCS1 1721 0.13 0.29 YES
11 CYB5A CYB5A CYB5A 1807 0.12 0.31 YES
12 SLC23A1 SLC23A1 SLC23A1 2123 0.11 0.31 YES
13 MOCS3 MOCS3 MOCS3 2170 0.1 0.33 YES
14 MOCOS MOCOS MOCOS 2175 0.1 0.35 YES
15 THTPA THTPA THTPA 2226 0.1 0.36 YES
16 NMNAT3 NMNAT3 NMNAT3 2487 0.088 0.36 YES
17 NFS1 NFS1 NFS1 2510 0.087 0.38 YES
18 ENPP1 ENPP1 ENPP1 2565 0.085 0.39 YES
19 GSTO1 GSTO1 GSTO1 2721 0.079 0.39 YES
20 COASY COASY COASY 2812 0.076 0.4 YES
21 SLC25A32 SLC25A32 SLC25A32 2919 0.072 0.41 YES
22 NMNAT1 NMNAT1 NMNAT1 3137 0.065 0.41 NO
23 SHMT1 SHMT1 SHMT1 3659 0.051 0.39 NO
24 AASDHPPT AASDHPPT AASDHPPT 3778 0.048 0.39 NO
25 FASN FASN FASN 4464 0.034 0.36 NO
26 NADK NADK NADK 4513 0.033 0.36 NO
27 SLC19A1 SLC19A1 SLC19A1 4800 0.027 0.35 NO
28 FLAD1 FLAD1 FLAD1 4846 0.026 0.35 NO
29 PANK2 PANK2 PANK2 4861 0.026 0.36 NO
30 FPGS FPGS FPGS 4899 0.025 0.36 NO
31 CYB5R3 CYB5R3 CYB5R3 5460 0.015 0.33 NO
32 PPCS PPCS PPCS 5476 0.015 0.33 NO
33 SLC46A1 SLC46A1 SLC46A1 5600 0.013 0.33 NO
34 PDXK PDXK PDXK 6264 0.0022 0.29 NO
35 SLC2A1 SLC2A1 SLC2A1 7346 -0.014 0.23 NO
36 PANK3 PANK3 PANK3 7891 -0.022 0.2 NO
37 GSTO2 GSTO2 GSTO2 7909 -0.022 0.21 NO
38 PANK4 PANK4 PANK4 9252 -0.045 0.14 NO
39 DHFR DHFR DHFR 9598 -0.051 0.13 NO
40 NADSYN1 NADSYN1 NADSYN1 10302 -0.066 0.1 NO
41 MTHFR MTHFR MTHFR 10321 -0.067 0.11 NO
42 SLC25A16 SLC25A16 SLC25A16 10754 -0.078 0.1 NO
43 RFK RFK RFK 10961 -0.084 0.1 NO
44 TPK1 TPK1 TPK1 11483 -0.1 0.092 NO
45 NAMPT NAMPT NAMPT 12503 -0.14 0.059 NO
46 SLC2A3 SLC2A3 SLC2A3 12633 -0.14 0.077 NO
47 PPCDC PPCDC PPCDC 12662 -0.14 0.1 NO
48 SLC19A3 SLC19A3 SLC19A3 14954 -0.27 0.02 NO
49 NMNAT2 NMNAT2 NMNAT2 15905 -0.33 0.025 NO
50 ACP5 ACP5 ACP5 16941 -0.44 0.044 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 PORPHYRIN AND CHLOROPHYLL METABOLISM.

Figure S94.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

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 SLCO1B3 SLCO1B3 SLCO1B3 131 0.57 0.098 YES
2 AMACR AMACR AMACR 132 0.56 0.2 YES
3 CYP8B1 CYP8B1 CYP8B1 209 0.46 0.28 YES
4 SLC27A5 SLC27A5 SLC27A5 398 0.34 0.33 YES
5 CYP7B1 CYP7B1 CYP7B1 440 0.33 0.39 YES
6 ABCB11 ABCB11 ABCB11 453 0.32 0.45 YES
7 CH25H CH25H CH25H 553 0.29 0.5 YES
8 AKR1C4 AKR1C4 AKR1C4 723 0.25 0.53 YES
9 BAAT BAAT BAAT 884 0.22 0.56 YES
10 HSD17B4 HSD17B4 HSD17B4 918 0.21 0.6 YES
11 CYP27A1 CYP27A1 CYP27A1 926 0.21 0.64 YES
12 ACOX2 ACOX2 ACOX2 1163 0.18 0.66 YES
13 SLCO1B1 SLCO1B1 SLCO1B1 1334 0.16 0.68 YES
14 SLC10A1 SLC10A1 SLC10A1 1411 0.16 0.7 YES
15 CYP7A1 CYP7A1 CYP7A1 1920 0.12 0.69 YES
16 SCP2 SCP2 SCP2 2156 0.1 0.7 YES
17 CYP39A1 CYP39A1 CYP39A1 2312 0.096 0.71 YES
18 SLCO1A2 SLCO1A2 SLCO1A2 2326 0.095 0.72 YES
19 CYP46A1 CYP46A1 CYP46A1 3292 0.06 0.68 NO
20 SLC27A2 SLC27A2 SLC27A2 4782 0.027 0.6 NO
21 HSD3B7 HSD3B7 HSD3B7 5761 0.01 0.55 NO
22 ACOT8 ACOT8 ACOT8 8117 -0.026 0.42 NO
23 ALB ALB ALB 9661 -0.052 0.34 NO
24 ABCC3 ABCC3 ABCC3 12082 -0.12 0.23 NO
25 AKR1D1 AKR1D1 AKR1D1 12591 -0.14 0.22 NO
26 FABP6 FABP6 FABP6 16229 -0.36 0.085 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 AMINOACYL TRNA BIOSYNTHESIS.

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

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

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 ALDH3A1 ALDH3A1 ALDH3A1 5 1.2 0.064 YES
2 CYP1A1 CYP1A1 CYP1A1 18 1 0.12 YES
3 UGT1A3 UGT1A3 UGT1A3 57 0.77 0.16 YES
4 UGT1A5 UGT1A5 UGT1A5 63 0.76 0.2 YES
5 CYP1A2 CYP1A2 CYP1A2 68 0.74 0.24 YES
6 UGT1A4 UGT1A4 UGT1A4 76 0.69 0.28 YES
7 CYP3A4 CYP3A4 CYP3A4 87 0.66 0.32 YES
8 CYP2E1 CYP2E1 CYP2E1 92 0.65 0.35 YES
9 UGT1A1 UGT1A1 UGT1A1 178 0.49 0.37 YES
10 ADH1B ADH1B ADH1B 197 0.47 0.4 YES
11 ADH4 ADH4 ADH4 235 0.44 0.42 YES
12 ADH6 ADH6 ADH6 255 0.43 0.44 YES
13 UGT1A9 UGT1A9 UGT1A9 318 0.38 0.46 YES
14 CYP2C9 CYP2C9 CYP2C9 418 0.34 0.47 YES
15 CYP3A43 CYP3A43 CYP3A43 444 0.33 0.49 YES
16 UGT2B28 UGT2B28 UGT2B28 485 0.31 0.5 YES
17 UGT1A6 UGT1A6 UGT1A6 492 0.31 0.52 YES
18 AKR1C2 AKR1C2 AKR1C2 501 0.31 0.54 YES
19 UGT2B10 UGT2B10 UGT2B10 576 0.28 0.55 YES
20 AKR1C1 AKR1C1 AKR1C1 666 0.26 0.56 YES
21 ADH1C ADH1C ADH1C 718 0.25 0.57 YES
22 AKR1C4 AKR1C4 AKR1C4 723 0.25 0.58 YES
23 CYP2C19 CYP2C19 CYP2C19 758 0.24 0.59 YES
24 ADH7 ADH7 ADH7 879 0.22 0.6 YES
25 UGT2B7 UGT2B7 UGT2B7 880 0.22 0.61 YES
26 UGT2B11 UGT2B11 UGT2B11 1116 0.19 0.61 YES
27 GSTM4 GSTM4 GSTM4 1216 0.18 0.61 YES
28 MGST1 MGST1 MGST1 1224 0.18 0.62 YES
29 EPHX1 EPHX1 EPHX1 1229 0.17 0.63 YES
30 UGT1A8 UGT1A8 UGT1A8 1251 0.17 0.64 YES
31 GSTM3 GSTM3 GSTM3 1254 0.17 0.65 YES
32 UGT2B4 UGT2B4 UGT2B4 1580 0.14 0.64 YES
33 MGST2 MGST2 MGST2 1626 0.14 0.64 YES
34 CYP2C8 CYP2C8 CYP2C8 1912 0.12 0.63 YES
35 ADH5 ADH5 ADH5 1946 0.12 0.64 YES
36 ADH1A ADH1A ADH1A 1961 0.12 0.64 YES
37 GSTM2 GSTM2 GSTM2 1995 0.11 0.65 YES
38 UGT2B15 UGT2B15 UGT2B15 2182 0.1 0.64 YES
39 GSTZ1 GSTZ1 GSTZ1 2218 0.1 0.65 YES
40 GSTA4 GSTA4 GSTA4 2258 0.098 0.65 YES
41 GSTO1 GSTO1 GSTO1 2721 0.079 0.63 NO
42 CYP1B1 CYP1B1 CYP1B1 2766 0.077 0.63 NO
43 GSTM1 GSTM1 GSTM1 2991 0.07 0.62 NO
44 GSTK1 GSTK1 GSTK1 3147 0.065 0.62 NO
45 GSTT1 GSTT1 GSTT1 3915 0.044 0.57 NO
46 GSTA1 GSTA1 GSTA1 3918 0.044 0.58 NO
47 GSTA2 GSTA2 GSTA2 3940 0.044 0.58 NO
48 CYP3A5 CYP3A5 CYP3A5 4068 0.042 0.57 NO
49 MGST3 MGST3 MGST3 4391 0.035 0.56 NO
50 CYP2B6 CYP2B6 CYP2B6 5306 0.018 0.51 NO
51 AKR1C3 AKR1C3 AKR1C3 5355 0.017 0.5 NO
52 UGT1A7 UGT1A7 UGT1A7 6794 -0.0059 0.42 NO
53 GSTO2 GSTO2 GSTO2 7909 -0.022 0.36 NO
54 UGT2A1 UGT2A1 UGT2A1 12752 -0.15 0.096 NO
55 UGT1A10 UGT1A10 UGT1A10 12989 -0.16 0.091 NO
56 UGT2A3 UGT2A3 UGT2A3 13750 -0.2 0.059 NO
57 ALDH1A3 ALDH1A3 ALDH1A3 14394 -0.24 0.036 NO
58 ALDH3B1 ALDH3B1 ALDH3B1 14629 -0.25 0.036 NO
59 CYP2C18 CYP2C18 CYP2C18 14766 -0.26 0.043 NO
60 GSTM5 GSTM5 GSTM5 14772 -0.26 0.057 NO
61 GSTT2 GSTT2 GSTT2 15066 -0.28 0.055 NO
62 CYP2S1 CYP2S1 CYP2S1 15460 -0.3 0.05 NO
63 ALDH3B2 ALDH3B2 ALDH3B2 15991 -0.34 0.038 NO
64 GSTP1 GSTP1 GSTP1 16091 -0.35 0.052 NO
65 DHDH DHDH DHDH 16156 -0.35 0.068 NO
66 CYP3A7 CYP3A7 CYP3A7 16514 -0.38 0.069 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 METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S98.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG DRUG METABOLISM CYTOCHROME P450

Table 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 ACSL6 ACSL6 ACSL6 55 0.78 0.077 YES
2 AMACR AMACR AMACR 132 0.56 0.13 YES
3 ACSL5 ACSL5 ACSL5 176 0.49 0.18 YES
4 HAO1 HAO1 HAO1 602 0.27 0.18 YES
5 EHHADH EHHADH EHHADH 644 0.26 0.21 YES
6 PEX11G PEX11G PEX11G 715 0.25 0.23 YES
7 PEX12 PEX12 PEX12 810 0.23 0.25 YES
8 BAAT BAAT BAAT 884 0.22 0.27 YES
9 HSD17B4 HSD17B4 HSD17B4 918 0.21 0.29 YES
10 PEX11A PEX11A PEX11A 981 0.21 0.3 YES
11 DAO DAO DAO 1152 0.18 0.31 YES
12 ACOX2 ACOX2 ACOX2 1163 0.18 0.33 YES
13 PECR PECR PECR 1237 0.17 0.34 YES
14 MLYCD MLYCD MLYCD 1380 0.16 0.35 YES
15 GNPAT GNPAT GNPAT 1558 0.14 0.36 YES
16 DECR2 DECR2 DECR2 1591 0.14 0.37 YES
17 PIPOX PIPOX PIPOX 1632 0.14 0.38 YES
18 SOD1 SOD1 SOD1 1644 0.14 0.4 YES
19 ACAA1 ACAA1 ACAA1 1682 0.13 0.41 YES
20 PEX5 PEX5 PEX5 1780 0.13 0.41 YES
21 MVK MVK MVK 1864 0.12 0.42 YES
22 PAOX PAOX PAOX 1949 0.12 0.43 YES
23 PEX6 PEX6 PEX6 2013 0.11 0.44 YES
24 CAT CAT CAT 2045 0.11 0.45 YES
25 HMGCL HMGCL HMGCL 2082 0.11 0.46 YES
26 SCP2 SCP2 SCP2 2156 0.1 0.46 YES
27 EPHX2 EPHX2 EPHX2 2253 0.099 0.47 YES
28 PEX14 PEX14 PEX14 2315 0.096 0.47 YES
29 CRAT CRAT CRAT 2349 0.094 0.48 YES
30 IDH1 IDH1 IDH1 2387 0.092 0.49 YES
31 ABCD3 ABCD3 ABCD3 2780 0.076 0.47 YES
32 PEX2 PEX2 PEX2 2823 0.075 0.48 YES
33 PEX19 PEX19 PEX19 2855 0.074 0.48 YES
34 DHRS4 DHRS4 DHRS4 2904 0.073 0.49 YES
35 ACOX1 ACOX1 ACOX1 2962 0.071 0.49 YES
36 PMVK PMVK PMVK 2974 0.07 0.5 YES
37 PEX10 PEX10 PEX10 3048 0.068 0.5 YES
38 GSTK1 GSTK1 GSTK1 3147 0.065 0.5 YES
39 HACL1 HACL1 HACL1 3165 0.064 0.51 YES
40 ABCD2 ABCD2 ABCD2 3176 0.064 0.52 YES
41 PEX1 PEX1 PEX1 3505 0.055 0.5 NO
42 PXMP2 PXMP2 PXMP2 3937 0.044 0.48 NO
43 PEX11B PEX11B PEX11B 4040 0.042 0.48 NO
44 ACSL1 ACSL1 ACSL1 4237 0.038 0.48 NO
45 ECH1 ECH1 ECH1 4286 0.037 0.48 NO
46 SLC27A2 SLC27A2 SLC27A2 4782 0.027 0.45 NO
47 PRDX1 PRDX1 PRDX1 4906 0.025 0.45 NO
48 PEX13 PEX13 PEX13 5025 0.023 0.44 NO
49 NUDT12 NUDT12 NUDT12 5040 0.023 0.44 NO
50 ACSL3 ACSL3 ACSL3 5268 0.018 0.43 NO
51 DDO DDO DDO 5781 0.0096 0.4 NO
52 AGPS AGPS AGPS 5784 0.0096 0.41 NO
53 PEX26 PEX26 PEX26 6003 0.0062 0.39 NO
54 NUDT19 NUDT19 NUDT19 6588 -0.0028 0.36 NO
55 PEX16 PEX16 PEX16 6975 -0.009 0.34 NO
56 PEX3 PEX3 PEX3 7070 -0.01 0.34 NO
57 ABCD1 ABCD1 ABCD1 7242 -0.013 0.33 NO
58 ABCD4 ABCD4 ABCD4 7578 -0.018 0.31 NO
59 IDH2 IDH2 IDH2 7720 -0.02 0.3 NO
60 PEX7 PEX7 PEX7 7798 -0.021 0.3 NO
61 NOS2 NOS2 NOS2 8027 -0.025 0.29 NO
62 ACOT8 ACOT8 ACOT8 8117 -0.026 0.29 NO
63 PXMP4 PXMP4 PXMP4 8494 -0.032 0.27 NO
64 SLC25A17 SLC25A17 SLC25A17 8922 -0.039 0.25 NO
65 ACOX3 ACOX3 ACOX3 9106 -0.042 0.24 NO
66 SOD2 SOD2 SOD2 9777 -0.055 0.21 NO
67 AGXT AGXT AGXT 9844 -0.056 0.22 NO
68 PRDX5 PRDX5 PRDX5 10021 -0.06 0.21 NO
69 PHYH PHYH PHYH 10228 -0.065 0.21 NO
70 MPV17 MPV17 MPV17 10533 -0.072 0.2 NO
71 MPV17L MPV17L MPV17L 12209 -0.13 0.12 NO
72 CROT CROT CROT 14170 -0.22 0.026 NO
73 HAO2 HAO2 HAO2 14867 -0.26 0.014 NO
74 XDH XDH XDH 15083 -0.28 0.031 NO
75 FAR1 FAR1 FAR1 15459 -0.3 0.041 NO
76 FAR2 FAR2 FAR2 16490 -0.38 0.022 NO
77 ACSL4 ACSL4 ACSL4 17151 -0.47 0.033 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: KEGG DRUG METABOLISM CYTOCHROME P450.

Figure S100.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 = LIHC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = LIHC-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)