GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in READ-TP
Rectum Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C10K27TB
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in READ-TP. Broad Institute of MIT and Harvard. doi:10.7908/C10K27TB
Overview
Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes in READ-TP. This pipeline has the following features:

  1. For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.

  2. Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).

  3. Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).

  4. Checks if the top core genes are up-regulated or down-regulated.

  5. Checks if the top core genes are high expressed or low expressed.

  6. Checks if the top core genes are significantly differently expressed genes.

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 193
Number of samples: 166
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 5 :[ clus1 ] 29
pheno.type: 2 - 5 :[ clus5 ] 61
pheno.type: 3 - 5 :[ clus2 ] 14
pheno.type: 4 - 5 :[ clus3 ] 34
pheno.type: 5 - 5 :[ clus4 ] 28

For the expression subtypes of 18106 genes in 167 samples, GSEA found enriched gene sets in each cluster using 166 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA G1 PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA GH PATHWAY

    • And common core enriched genes are ACTN2, ACTN3, VCL, PIK3CA, EGFR, ITGA1, ROCK1, FYN, APC, CD14

  • clus2

    • Top enriched gene sets are BIOCARTA BCR PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA KERATINOCYTE PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA PPARA PATHWAY, BIOCARTA VIP PATHWAY

    • And common core enriched genes are MAPK8, PIK3CA, PIK3CG, PTEN, MAP3K1, RASA1, MAP2K1, MAPK1, MAPK3, PAK1

  • clus3

    • Top enriched gene sets are BIOCARTA FAS PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA TNFR1 PATHWAY, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG O GLYCAN BIOSYNTHESIS, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG PROPANOATE METABOLISM, KEGG BUTANOATE METABOLISM

    • And common core enriched genes are LSM3, LSM5, LSM6, NAA38, AARS2, DARS, DARS2, EARS2, EPRS, FARSB

  • clus4

    • Top enriched gene sets are BIOCARTA ERK PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA RACCYCD PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA WNT PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG LYSINE DEGRADATION, KEGG SELENOAMINO ACID METABOLISM, KEGG PROPANOATE METABOLISM

    • And common core enriched genes are PIPOX, LSM3, LSM5, LSM6, NAA38, AASDHPPT, AASS, ACAT1, BBOX1, OGDHL

  • clus5

    • Top enriched gene sets are BIOCARTA FMLP PATHWAY, KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG ARGININE AND PROLINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG GLYCEROPHOSPHOLIPID METABOLISM

    • And common core enriched genes are TUBA1A, TUBA3D, TUBA8, TUBAL3, TUBB2A, TUBB3, TUBB4Q, TUBB8, C8G, ELANE

Results
Subtype clus1 enriched pathways

Table 3.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA NO1 PATHWAY 29 genes.ES.table 0.51 1.3 0.14 0.25 0.98 0.28 0.14 0.24 0.19 0.006
BIOCARTA ALK PATHWAY 33 genes.ES.table 0.44 1.3 0.13 0.25 0.98 0.36 0.23 0.28 0.2 0.006
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.38 1.5 0.081 0.18 0.86 0.062 0.061 0.059 0.11 0.006
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.53 1.5 0.079 0.16 0.82 0.39 0.3 0.28 0.095 0.004
BIOCARTA BIOPEPTIDES PATHWAY 40 genes.ES.table 0.44 1.6 0.03 0.15 0.77 0.28 0.2 0.22 0.088 0.007
BIOCARTA G1 PATHWAY 27 genes.ES.table 0.48 1.6 0.039 0.15 0.77 0.15 0.097 0.13 0.085 0.007
BIOCARTA HDAC PATHWAY 26 genes.ES.table 0.49 1.5 0.12 0.2 0.9 0.54 0.37 0.34 0.13 0.006
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.47 1.6 0.061 0.17 0.74 0.7 0.46 0.38 0.092 0.012
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.54 1.6 0.062 0.15 0.79 0.43 0.31 0.3 0.092 0.004
BIOCARTA GH PATHWAY 25 genes.ES.table 0.49 1.5 0.071 0.17 0.86 0.28 0.18 0.23 0.11 0.006
genes ES table in pathway: BIOCARTA NO1 PATHWAY

Table S1.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 LY96 LY96 LY96 307 0.65 0.18 YES
2 GJA1 GJA1 GJA1 1882 0.3 0.18 YES
3 LEF1 LEF1 LEF1 2100 0.28 0.26 YES
4 TLR4 TLR4 TLR4 2160 0.27 0.34 YES
5 FZD1 FZD1 FZD1 2219 0.26 0.41 YES
6 GNAI1 GNAI1 GNAI1 2340 0.25 0.48 YES
7 CD14 CD14 CD14 3055 0.19 0.5 YES
8 PIK3CA PIK3CA PIK3CA 3142 0.18 0.55 YES
9 EIF2AK2 EIF2AK2 EIF2AK2 3418 0.16 0.58 YES
10 APC APC APC 3508 0.16 0.63 YES
11 PIK3R1 PIK3R1 PIK3R1 5574 0.085 0.54 NO
12 CCND1 CCND1 CCND1 6399 0.066 0.51 NO
13 WNT1 WNT1 WNT1 7036 0.054 0.49 NO
14 NFKB1 NFKB1 NFKB1 8473 0.029 0.42 NO
15 GSK3B GSK3B GSK3B 8561 0.028 0.43 NO
16 RELA RELA RELA 9233 0.016 0.39 NO
17 CTNNB1 CTNNB1 CTNNB1 9483 0.012 0.38 NO
18 MYD88 MYD88 MYD88 10056 0.0023 0.35 NO
19 PPP2CA PPP2CA PPP2CA 10802 -0.0099 0.31 NO
20 TIRAP TIRAP TIRAP 10821 -0.01 0.32 NO
21 PDPK1 PDPK1 PDPK1 10945 -0.013 0.31 NO
22 AKT1 AKT1 AKT1 11433 -0.022 0.29 NO
23 AXIN1 AXIN1 AXIN1 12051 -0.032 0.27 NO
24 IRAK1 IRAK1 IRAK1 12896 -0.048 0.24 NO
25 LBP LBP LBP 14237 -0.079 0.19 NO
26 DVL1 DVL1 DVL1 14623 -0.091 0.19 NO

Figure S1.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

Figure S2.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA ALK 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 FGF14 FGF14 FGF14 10 0.95 0.03 YES
2 FGF1 FGF1 FGF1 94 0.78 0.05 YES
3 CHRM2 CHRM2 CHRM2 102 0.77 0.074 YES
4 FGF7 FGF7 FGF7 121 0.76 0.097 YES
5 FGF2 FGF2 FGF2 303 0.65 0.11 YES
6 FGF10 FGF10 FGF10 355 0.62 0.12 YES
7 FGF5 FGF5 FGF5 436 0.59 0.14 YES
8 ITGAM ITGAM ITGAM 485 0.57 0.15 YES
9 PDGFC PDGFC PDGFC 628 0.52 0.16 YES
10 ITGA10 ITGA10 ITGA10 664 0.51 0.18 YES
11 MRAS MRAS MRAS 758 0.49 0.19 YES
12 ITGA11 ITGA11 ITGA11 849 0.47 0.2 YES
13 ACTN2 ACTN2 ACTN2 892 0.46 0.21 YES
14 PAK3 PAK3 PAK3 904 0.46 0.22 YES
15 MYLK MYLK MYLK 932 0.45 0.24 YES
16 CFL2 CFL2 CFL2 1013 0.43 0.24 YES
17 ITGAX ITGAX ITGAX 1141 0.41 0.25 YES
18 TIAM1 TIAM1 TIAM1 1196 0.4 0.26 YES
19 MYH10 MYH10 MYH10 1238 0.39 0.27 YES
20 ARHGEF6 ARHGEF6 ARHGEF6 1240 0.39 0.28 YES
21 RDX RDX RDX 1287 0.38 0.29 YES
22 FGF12 FGF12 FGF12 1333 0.38 0.3 YES
23 FGF13 FGF13 FGF13 1398 0.36 0.31 YES
24 ITGA4 ITGA4 ITGA4 1438 0.36 0.32 YES
25 PIK3CG PIK3CG PIK3CG 1455 0.36 0.33 YES
26 MYL9 MYL9 MYL9 1456 0.36 0.34 YES
27 FN1 FN1 FN1 1486 0.35 0.35 YES
28 FGFR1 FGFR1 FGFR1 1521 0.35 0.36 YES
29 ITGB3 ITGB3 ITGB3 1559 0.34 0.37 YES
30 NCKAP1L NCKAP1L NCKAP1L 1560 0.34 0.38 YES
31 PIK3R5 PIK3R5 PIK3R5 1567 0.34 0.39 YES
32 WAS WAS WAS 1742 0.32 0.39 YES
33 ITGA7 ITGA7 ITGA7 1743 0.32 0.4 YES
34 PDGFD PDGFD PDGFD 1801 0.31 0.41 YES
35 PDGFRB PDGFRB PDGFRB 1803 0.31 0.42 YES
36 ITGAL ITGAL ITGAL 1812 0.31 0.43 YES
37 ITGA5 ITGA5 ITGA5 1904 0.3 0.43 YES
38 CHRM4 CHRM4 CHRM4 1963 0.3 0.44 YES
39 ITGB2 ITGB2 ITGB2 1968 0.29 0.45 YES
40 F2R F2R F2R 1997 0.29 0.45 YES
41 FGF9 FGF9 FGF9 2018 0.29 0.46 YES
42 PIK3CD PIK3CD PIK3CD 2163 0.27 0.46 YES
43 ITGAV ITGAV ITGAV 2189 0.27 0.47 YES
44 FGFR2 FGFR2 FGFR2 2196 0.27 0.48 YES
45 ITGB8 ITGB8 ITGB8 2197 0.27 0.49 YES
46 ITGA1 ITGA1 ITGA1 2201 0.27 0.49 YES
47 TIAM2 TIAM2 TIAM2 2237 0.26 0.5 YES
48 PDGFRA PDGFRA PDGFRA 2405 0.24 0.5 YES
49 MSN MSN MSN 2664 0.22 0.49 YES
50 WASF1 WASF1 WASF1 2780 0.21 0.49 YES
51 PDGFB PDGFB PDGFB 2787 0.21 0.5 YES
52 CD14 CD14 CD14 3055 0.19 0.49 YES
53 PIP4K2A PIP4K2A PIP4K2A 3093 0.18 0.49 YES
54 PIK3CA PIK3CA PIK3CA 3142 0.18 0.5 YES
55 CHRM5 CHRM5 CHRM5 3315 0.17 0.49 YES
56 ENAH ENAH ENAH 3464 0.16 0.49 YES
57 BDKRB1 BDKRB1 BDKRB1 3499 0.16 0.49 YES
58 APC APC APC 3508 0.16 0.5 YES
59 PFN4 PFN4 PFN4 3598 0.15 0.5 YES
60 ROCK1 ROCK1 ROCK1 3615 0.15 0.5 YES
61 MYLK3 MYLK3 MYLK3 3679 0.15 0.5 YES
62 PDGFA PDGFA PDGFA 3713 0.15 0.5 YES
63 VCL VCL VCL 3750 0.15 0.51 YES
64 PIKFYVE PIKFYVE PIKFYVE 3809 0.14 0.51 YES
65 SSH1 SSH1 SSH1 3829 0.14 0.51 YES
66 ITGA9 ITGA9 ITGA9 3837 0.14 0.52 YES
67 ACTN3 ACTN3 ACTN3 3908 0.14 0.52 YES
68 ARHGEF4 ARHGEF4 ARHGEF4 3939 0.14 0.52 YES
69 VAV1 VAV1 VAV1 3960 0.14 0.52 YES
70 FGF11 FGF11 FGF11 4005 0.14 0.52 YES
71 SOS2 SOS2 SOS2 4099 0.13 0.52 YES
72 SCIN SCIN SCIN 4139 0.13 0.52 YES
73 PPP1R12A PPP1R12A PPP1R12A 4186 0.13 0.53 YES
74 ITGB5 ITGB5 ITGB5 4254 0.12 0.53 YES
75 EGFR EGFR EGFR 4305 0.12 0.53 YES
76 ABI2 ABI2 ABI2 4343 0.12 0.53 YES
77 ITGB1 ITGB1 ITGB1 4461 0.12 0.53 NO
78 SOS1 SOS1 SOS1 4575 0.11 0.52 NO
79 DOCK1 DOCK1 DOCK1 4784 0.11 0.52 NO
80 ACTN1 ACTN1 ACTN1 4867 0.1 0.52 NO
81 GNG12 GNG12 GNG12 4942 0.1 0.51 NO
82 ROCK2 ROCK2 ROCK2 4986 0.1 0.52 NO
83 WASL WASL WASL 5071 0.099 0.51 NO
84 BRAF BRAF BRAF 5099 0.098 0.52 NO
85 ARHGEF12 ARHGEF12 ARHGEF12 5169 0.096 0.51 NO
86 GSN GSN GSN 5335 0.091 0.51 NO
87 DIAPH2 DIAPH2 DIAPH2 5440 0.089 0.5 NO
88 PIK3R1 PIK3R1 PIK3R1 5574 0.085 0.5 NO
89 PIK3R3 PIK3R3 PIK3R3 5593 0.084 0.5 NO
90 FGF18 FGF18 FGF18 5657 0.082 0.5 NO
91 ITGA8 ITGA8 ITGA8 5676 0.082 0.5 NO
92 PPP1CB PPP1CB PPP1CB 5722 0.081 0.5 NO
93 INSRR INSRR INSRR 5936 0.076 0.49 NO
94 MYH9 MYH9 MYH9 5940 0.076 0.5 NO
95 PAK2 PAK2 PAK2 6049 0.073 0.49 NO
96 GNA12 GNA12 GNA12 6074 0.073 0.49 NO
97 GNA13 GNA13 GNA13 6219 0.07 0.49 NO
98 IQGAP1 IQGAP1 IQGAP1 6290 0.068 0.48 NO
99 SSH2 SSH2 SSH2 6412 0.066 0.48 NO
100 ARPC3 ARPC3 ARPC3 6577 0.062 0.47 NO
101 KRAS KRAS KRAS 6580 0.062 0.48 NO
102 PFN2 PFN2 PFN2 6599 0.062 0.48 NO
103 LIMK1 LIMK1 LIMK1 6640 0.061 0.48 NO
104 PIK3CB PIK3CB PIK3CB 6898 0.056 0.46 NO
105 NRAS NRAS NRAS 6951 0.056 0.46 NO
106 VAV2 VAV2 VAV2 6981 0.055 0.46 NO
107 NCKAP1 NCKAP1 NCKAP1 7046 0.054 0.46 NO
108 BDKRB2 BDKRB2 BDKRB2 7119 0.052 0.46 NO
109 CDC42 CDC42 CDC42 7140 0.052 0.46 NO
110 WASF2 WASF2 WASF2 7228 0.05 0.46 NO
111 PTK2 PTK2 PTK2 7335 0.048 0.45 NO
112 PIP4K2B PIP4K2B PIP4K2B 7345 0.048 0.45 NO
113 MAP2K1 MAP2K1 MAP2K1 7482 0.046 0.44 NO
114 PIP5K1C PIP5K1C PIP5K1C 7507 0.045 0.44 NO
115 ARHGEF7 ARHGEF7 ARHGEF7 7528 0.045 0.45 NO
116 MAPK1 MAPK1 MAPK1 7616 0.043 0.44 NO
117 ITGA2 ITGA2 ITGA2 7649 0.043 0.44 NO
118 FGF19 FGF19 FGF19 7697 0.042 0.44 NO
119 RAC1 RAC1 RAC1 7768 0.04 0.44 NO
120 MYL2 MYL2 MYL2 7799 0.04 0.44 NO
121 ARPC5 ARPC5 ARPC5 7915 0.038 0.43 NO
122 PIP5K1A PIP5K1A PIP5K1A 8138 0.034 0.42 NO
123 RHOA RHOA RHOA 8291 0.032 0.41 NO
124 BAIAP2 BAIAP2 BAIAP2 8355 0.031 0.41 NO
125 MYL12A MYL12A MYL12A 8710 0.025 0.39 NO
126 VAV3 VAV3 VAV3 8800 0.023 0.39 NO
127 PAK1 PAK1 PAK1 8925 0.021 0.38 NO
128 CRKL CRKL CRKL 8977 0.02 0.38 NO
129 EZR EZR EZR 9378 0.014 0.36 NO
130 DIAPH1 DIAPH1 DIAPH1 9515 0.011 0.35 NO
131 ITGAD ITGAD ITGAD 9527 0.011 0.35 NO
132 FGD1 FGD1 FGD1 9607 0.0099 0.35 NO
133 CRK CRK CRK 9611 0.0098 0.35 NO
134 ARPC2 ARPC2 ARPC2 9813 0.0061 0.34 NO
135 MYLK2 MYLK2 MYLK2 9819 0.006 0.34 NO
136 RAC2 RAC2 RAC2 9895 0.0047 0.33 NO
137 GRLF1 GRLF1 GRLF1 9916 0.0044 0.33 NO
138 ITGB6 ITGB6 ITGB6 9986 0.0034 0.33 NO
139 PXN PXN PXN 10057 0.0022 0.32 NO
140 RAF1 RAF1 RAF1 10109 0.0014 0.32 NO
141 ITGB7 ITGB7 ITGB7 10154 0.00058 0.32 NO
142 ARPC4 ARPC4 ARPC4 10313 -0.002 0.31 NO
143 CYFIP1 CYFIP1 CYFIP1 10326 -0.0022 0.31 NO
144 ACTB ACTB ACTB 10373 -0.0029 0.3 NO
145 IQGAP2 IQGAP2 IQGAP2 10384 -0.0032 0.3 NO
146 PPP1CC PPP1CC PPP1CC 10433 -0.004 0.3 NO
147 ACTN4 ACTN4 ACTN4 10523 -0.0055 0.3 NO
148 ARHGEF1 ARHGEF1 ARHGEF1 10741 -0.0091 0.28 NO
149 RRAS RRAS RRAS 10831 -0.011 0.28 NO
150 PIP4K2C PIP4K2C PIP4K2C 11063 -0.015 0.27 NO
151 SLC9A1 SLC9A1 SLC9A1 11165 -0.017 0.26 NO
152 CFL1 CFL1 CFL1 11218 -0.018 0.26 NO
153 ITGAE ITGAE ITGAE 11372 -0.02 0.25 NO
154 ITGA6 ITGA6 ITGA6 11479 -0.022 0.25 NO
155 LIMK2 LIMK2 LIMK2 11508 -0.023 0.25 NO
156 FGF23 FGF23 FGF23 11545 -0.024 0.25 NO
157 ARPC1B ARPC1B ARPC1B 11669 -0.026 0.24 NO
158 DIAPH3 DIAPH3 DIAPH3 11737 -0.027 0.24 NO
159 PIP5K1B PIP5K1B PIP5K1B 11800 -0.028 0.23 NO
160 MYH14 MYH14 MYH14 12103 -0.033 0.22 NO
161 FGF3 FGF3 FGF3 12139 -0.034 0.22 NO
162 SSH3 SSH3 SSH3 12148 -0.034 0.22 NO
163 BCAR1 BCAR1 BCAR1 12352 -0.038 0.21 NO
164 FGF20 FGF20 FGF20 12370 -0.038 0.21 NO
165 FGD3 FGD3 FGD3 12467 -0.04 0.2 NO
166 GIT1 GIT1 GIT1 12511 -0.041 0.2 NO
167 MAPK3 MAPK3 MAPK3 12556 -0.042 0.2 NO
168 ARPC1A ARPC1A ARPC1A 12595 -0.042 0.2 NO
169 ITGB4 ITGB4 ITGB4 12772 -0.045 0.19 NO
170 ACTG1 ACTG1 ACTG1 12783 -0.046 0.19 NO
171 ITGA3 ITGA3 ITGA3 12822 -0.046 0.19 NO
172 MYL12B MYL12B MYL12B 12843 -0.047 0.19 NO
173 TMSL3 TMSL3 TMSL3 12874 -0.047 0.19 NO
174 RRAS2 RRAS2 RRAS2 12925 -0.048 0.19 NO
175 TMSB4Y TMSB4Y TMSB4Y 13036 -0.051 0.19 NO
176 PAK4 PAK4 PAK4 13193 -0.054 0.18 NO
177 EGF EGF EGF 13212 -0.055 0.18 NO
178 CSK CSK CSK 13327 -0.058 0.18 NO
179 CYFIP2 CYFIP2 CYFIP2 13332 -0.058 0.18 NO
180 ARPC5L ARPC5L ARPC5L 13346 -0.058 0.18 NO
181 PFN1 PFN1 PFN1 13606 -0.064 0.17 NO
182 PPP1CA PPP1CA PPP1CA 13639 -0.064 0.17 NO
183 PAK6 PAK6 PAK6 13717 -0.066 0.16 NO
184 IQGAP3 IQGAP3 IQGAP3 13724 -0.066 0.17 NO
185 PIK3R2 PIK3R2 PIK3R2 14099 -0.075 0.15 NO
186 ITGA2B ITGA2B ITGA2B 14854 -0.098 0.11 NO
187 CHRM1 CHRM1 CHRM1 14856 -0.098 0.11 NO
188 MAP2K2 MAP2K2 MAP2K2 15004 -0.1 0.11 NO
189 FGF17 FGF17 FGF17 15020 -0.1 0.11 NO
190 ARAF ARAF ARAF 15092 -0.11 0.11 NO
191 FGF21 FGF21 FGF21 15096 -0.11 0.11 NO
192 RAC3 RAC3 RAC3 15589 -0.13 0.088 NO
193 FGF8 FGF8 FGF8 15845 -0.14 0.078 NO
194 CHRM3 CHRM3 CHRM3 15934 -0.14 0.078 NO
195 MYL5 MYL5 MYL5 16032 -0.15 0.077 NO
196 F2 F2 F2 16097 -0.15 0.078 NO
197 FGFR4 FGFR4 FGFR4 16591 -0.19 0.057 NO
198 FGFR3 FGFR3 FGFR3 17012 -0.23 0.04 NO
199 APC2 APC2 APC2 17250 -0.27 0.036 NO
200 MYLPF MYLPF MYLPF 17605 -0.35 0.027 NO

Figure S3.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA ALK PATHWAY.

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

genes ES table in pathway: BIOCARTA AT1R 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 ACTN2 ACTN2 ACTN2 892 0.46 0.014 YES
2 SNAI2 SNAI2 SNAI2 958 0.45 0.072 YES
3 CTNNA3 CTNNA3 CTNNA3 1048 0.43 0.12 YES
4 SORBS1 SORBS1 SORBS1 1483 0.35 0.15 YES
5 FGFR1 FGFR1 FGFR1 1521 0.35 0.2 YES
6 PTPRM PTPRM PTPRM 1693 0.32 0.23 YES
7 WAS WAS WAS 1742 0.32 0.27 YES
8 WASF3 WASF3 WASF3 1749 0.32 0.32 YES
9 LEF1 LEF1 LEF1 2100 0.28 0.34 YES
10 TCF7L1 TCF7L1 TCF7L1 2487 0.24 0.35 YES
11 WASF1 WASF1 WASF1 2780 0.21 0.36 YES
12 TGFBR1 TGFBR1 TGFBR1 3089 0.19 0.37 YES
13 FYN FYN FYN 3108 0.18 0.39 YES
14 VCL VCL VCL 3750 0.15 0.38 YES
15 ACTN3 ACTN3 ACTN3 3908 0.14 0.39 YES
16 TGFBR2 TGFBR2 TGFBR2 4234 0.13 0.39 YES
17 EGFR EGFR EGFR 4305 0.12 0.4 YES
18 FER FER FER 4380 0.12 0.41 YES
19 ACTN1 ACTN1 ACTN1 4867 0.1 0.4 YES
20 WASL WASL WASL 5071 0.099 0.4 YES
21 SNAI1 SNAI1 SNAI1 5375 0.09 0.4 YES
22 IGF1R IGF1R IGF1R 5477 0.087 0.4 YES
23 TJP1 TJP1 TJP1 5559 0.085 0.41 YES
24 CTNNA2 CTNNA2 CTNNA2 5798 0.079 0.41 YES
25 LMO7 LMO7 LMO7 5827 0.078 0.42 YES
26 EP300 EP300 EP300 6024 0.074 0.42 YES
27 SMAD2 SMAD2 SMAD2 6193 0.071 0.42 YES
28 MET MET MET 6251 0.069 0.42 YES
29 IQGAP1 IQGAP1 IQGAP1 6290 0.068 0.43 YES
30 PTPRJ PTPRJ PTPRJ 6514 0.064 0.43 YES
31 PTPRB PTPRB PTPRB 6570 0.062 0.43 YES
32 SMAD4 SMAD4 SMAD4 6621 0.061 0.44 YES
33 YES1 YES1 YES1 6888 0.057 0.43 YES
34 MAP3K7 MAP3K7 MAP3K7 7063 0.053 0.43 YES
35 CDC42 CDC42 CDC42 7140 0.052 0.43 YES
36 WASF2 WASF2 WASF2 7228 0.05 0.44 YES
37 CSNK2A1 CSNK2A1 CSNK2A1 7321 0.048 0.44 YES
38 SSX2IP SSX2IP SSX2IP 7361 0.048 0.44 YES
39 MLLT4 MLLT4 MLLT4 7395 0.047 0.45 YES
40 INSR INSR INSR 7439 0.046 0.45 YES
41 MAPK1 MAPK1 MAPK1 7616 0.043 0.45 YES
42 CREBBP CREBBP CREBBP 7651 0.042 0.45 YES
43 SMAD3 SMAD3 SMAD3 7666 0.042 0.46 YES
44 RAC1 RAC1 RAC1 7768 0.04 0.46 NO
45 CTNND1 CTNND1 CTNND1 8239 0.033 0.43 NO
46 RHOA RHOA RHOA 8291 0.032 0.44 NO
47 BAIAP2 BAIAP2 BAIAP2 8355 0.031 0.44 NO
48 NLK NLK NLK 8780 0.024 0.42 NO
49 TCF7 TCF7 TCF7 8941 0.021 0.41 NO
50 PARD3 PARD3 PARD3 9004 0.02 0.41 NO
51 CTNNB1 CTNNB1 CTNNB1 9483 0.012 0.38 NO
52 CDH1 CDH1 CDH1 9848 0.0056 0.36 NO
53 RAC2 RAC2 RAC2 9895 0.0047 0.36 NO
54 CTNNA1 CTNNA1 CTNNA1 9956 0.0038 0.36 NO
55 PTPN1 PTPN1 PTPN1 10052 0.0023 0.36 NO
56 ACTB ACTB ACTB 10373 -0.0029 0.34 NO
57 PVRL3 PVRL3 PVRL3 10489 -0.005 0.33 NO
58 TCF7L2 TCF7L2 TCF7L2 10507 -0.0054 0.33 NO
59 ACP1 ACP1 ACP1 10521 -0.0055 0.33 NO
60 ACTN4 ACTN4 ACTN4 10523 -0.0055 0.33 NO
61 PTPN6 PTPN6 PTPN6 10987 -0.013 0.31 NO
62 ERBB2 ERBB2 ERBB2 11296 -0.019 0.29 NO
63 PTPRF PTPRF PTPRF 11306 -0.019 0.3 NO
64 SRC SRC SRC 11558 -0.024 0.28 NO
65 FARP2 FARP2 FARP2 12476 -0.04 0.24 NO
66 MAPK3 MAPK3 MAPK3 12556 -0.042 0.24 NO
67 CSNK2A2 CSNK2A2 CSNK2A2 12738 -0.045 0.24 NO
68 ACTG1 ACTG1 ACTG1 12783 -0.046 0.24 NO
69 CSNK2B CSNK2B CSNK2B 12956 -0.049 0.24 NO
70 PVRL1 PVRL1 PVRL1 13041 -0.051 0.24 NO
71 PVRL2 PVRL2 PVRL2 13684 -0.065 0.21 NO
72 PVRL4 PVRL4 PVRL4 14747 -0.094 0.17 NO
73 RAC3 RAC3 RAC3 15589 -0.13 0.14 NO

Figure S5.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA AT1R PATHWAY.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA BCR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TNS1 TNS1 TNS1 791 0.48 0.072 YES
2 ACTN2 ACTN2 ACTN2 892 0.46 0.18 YES
3 PPP1R12B PPP1R12B PPP1R12B 1685 0.33 0.21 YES
4 ITGA1 ITGA1 ITGA1 2201 0.27 0.25 YES
5 CAV1 CAV1 CAV1 2233 0.26 0.31 YES
6 FYN FYN FYN 3108 0.18 0.31 YES
7 CAPNS2 CAPNS2 CAPNS2 3162 0.18 0.35 YES
8 ROCK1 ROCK1 ROCK1 3615 0.15 0.36 YES
9 VCL VCL VCL 3750 0.15 0.39 YES
10 ACTN3 ACTN3 ACTN3 3908 0.14 0.41 YES
11 RAP1A RAP1A RAP1A 4091 0.13 0.43 YES
12 ITGB1 ITGB1 ITGB1 4461 0.12 0.44 YES
13 SOS1 SOS1 SOS1 4575 0.11 0.46 YES
14 ACTN1 ACTN1 ACTN1 4867 0.1 0.47 YES
15 ACTA1 ACTA1 ACTA1 5191 0.095 0.48 YES
16 RAPGEF1 RAPGEF1 RAPGEF1 5260 0.093 0.5 YES
17 JUN JUN JUN 7148 0.052 0.4 NO
18 SHC1 SHC1 SHC1 7250 0.05 0.41 NO
19 PTK2 PTK2 PTK2 7335 0.048 0.42 NO
20 MAP2K1 MAP2K1 MAP2K1 7482 0.046 0.42 NO
21 MAPK1 MAPK1 MAPK1 7616 0.043 0.42 NO
22 ZYX ZYX ZYX 8040 0.036 0.41 NO
23 RHOA RHOA RHOA 8291 0.032 0.4 NO
24 CRKL CRKL CRKL 8977 0.02 0.37 NO
25 GRB2 GRB2 GRB2 8992 0.02 0.37 NO
26 MAPK8 MAPK8 MAPK8 9791 0.0065 0.33 NO
27 PXN PXN PXN 10057 0.0022 0.32 NO
28 RAF1 RAF1 RAF1 10109 0.0014 0.32 NO
29 SRC SRC SRC 11558 -0.024 0.24 NO
30 CAPN1 CAPN1 CAPN1 12211 -0.035 0.21 NO
31 BCAR1 BCAR1 BCAR1 12352 -0.038 0.21 NO
32 MAPK3 MAPK3 MAPK3 12556 -0.042 0.21 NO
33 BCR BCR BCR 13319 -0.058 0.18 NO
34 CSK CSK CSK 13327 -0.058 0.2 NO
35 CAPNS1 CAPNS1 CAPNS1 13989 -0.072 0.18 NO
36 HRAS HRAS HRAS 14840 -0.097 0.16 NO
37 MAP2K2 MAP2K2 MAP2K2 15004 -0.1 0.17 NO

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

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

genes ES table in pathway: BIOCARTA BIOPEPTIDES PATHWAY

Table 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 THBS4 THBS4 THBS4 9 0.97 0.027 YES
2 IGF1 IGF1 IGF1 186 0.71 0.038 YES
3 COMP COMP COMP 213 0.69 0.056 YES
4 COL11A1 COL11A1 COL11A1 336 0.63 0.067 YES
5 IBSP IBSP IBSP 468 0.57 0.076 YES
6 VEGFC VEGFC VEGFC 474 0.57 0.092 YES
7 THBS2 THBS2 THBS2 478 0.57 0.11 YES
8 SPP1 SPP1 SPP1 484 0.57 0.12 YES
9 RELN RELN RELN 495 0.56 0.14 YES
10 SHC4 SHC4 SHC4 504 0.56 0.16 YES
11 HGF HGF HGF 518 0.56 0.17 YES
12 AKT3 AKT3 AKT3 569 0.54 0.18 YES
13 MAPK10 MAPK10 MAPK10 600 0.53 0.2 YES
14 TNN TNN TNN 603 0.53 0.21 YES
15 PDGFC PDGFC PDGFC 628 0.52 0.23 YES
16 ITGA10 ITGA10 ITGA10 664 0.51 0.24 YES
17 TNXB TNXB TNXB 691 0.5 0.25 YES
18 LAMA2 LAMA2 LAMA2 748 0.49 0.26 YES
19 ITGA11 ITGA11 ITGA11 849 0.47 0.27 YES
20 ACTN2 ACTN2 ACTN2 892 0.46 0.28 YES
21 PAK3 PAK3 PAK3 904 0.46 0.29 YES
22 MYLK MYLK MYLK 932 0.45 0.3 YES
23 PRKCB PRKCB PRKCB 1108 0.41 0.31 YES
24 TNC TNC TNC 1144 0.41 0.32 YES
25 FLNC FLNC FLNC 1181 0.4 0.33 YES
26 COL6A6 COL6A6 COL6A6 1281 0.38 0.33 YES
27 COL4A4 COL4A4 COL4A4 1383 0.37 0.34 YES
28 COL5A2 COL5A2 COL5A2 1411 0.36 0.34 YES
29 ITGA4 ITGA4 ITGA4 1438 0.36 0.35 YES
30 PIK3CG PIK3CG PIK3CG 1455 0.36 0.36 YES
31 MYL9 MYL9 MYL9 1456 0.36 0.37 YES
32 FN1 FN1 FN1 1486 0.35 0.38 YES
33 ITGB3 ITGB3 ITGB3 1559 0.34 0.39 YES
34 PIK3R5 PIK3R5 PIK3R5 1567 0.34 0.4 YES
35 COL6A3 COL6A3 COL6A3 1647 0.33 0.4 YES
36 ITGA7 ITGA7 ITGA7 1743 0.32 0.41 YES
37 FIGF FIGF FIGF 1751 0.32 0.42 YES
38 PDGFD PDGFD PDGFD 1801 0.31 0.42 YES
39 PDGFRB PDGFRB PDGFRB 1803 0.31 0.43 YES
40 COL5A1 COL5A1 COL5A1 1855 0.3 0.44 YES
41 FLT4 FLT4 FLT4 1880 0.3 0.44 YES
42 ITGA5 ITGA5 ITGA5 1904 0.3 0.45 YES
43 COL1A2 COL1A2 COL1A2 1953 0.3 0.46 YES
44 COL3A1 COL3A1 COL3A1 1999 0.29 0.46 YES
45 PARVG PARVG PARVG 2003 0.29 0.47 YES
46 COL5A3 COL5A3 COL5A3 2052 0.28 0.48 YES
47 LAMA4 LAMA4 LAMA4 2118 0.28 0.48 YES
48 COL1A1 COL1A1 COL1A1 2140 0.27 0.49 YES
49 PIK3CD PIK3CD PIK3CD 2163 0.27 0.49 YES
50 ITGAV ITGAV ITGAV 2189 0.27 0.5 YES
51 KDR KDR KDR 2192 0.27 0.51 YES
52 ITGB8 ITGB8 ITGB8 2197 0.27 0.51 YES
53 ITGA1 ITGA1 ITGA1 2201 0.27 0.52 YES
54 CAV1 CAV1 CAV1 2233 0.26 0.53 YES
55 CAV2 CAV2 CAV2 2285 0.26 0.53 YES
56 THBS1 THBS1 THBS1 2321 0.25 0.54 YES
57 TNR TNR TNR 2384 0.25 0.54 YES
58 PDGFRA PDGFRA PDGFRA 2405 0.24 0.55 YES
59 FLNA FLNA FLNA 2417 0.24 0.55 YES
60 FLT1 FLT1 FLT1 2501 0.24 0.56 YES
61 COL6A1 COL6A1 COL6A1 2629 0.22 0.55 YES
62 COL6A2 COL6A2 COL6A2 2660 0.22 0.56 YES
63 BCL2 BCL2 BCL2 2698 0.22 0.56 YES
64 PDGFB PDGFB PDGFB 2787 0.21 0.56 YES
65 BIRC3 BIRC3 BIRC3 2903 0.2 0.56 YES
66 THBS3 THBS3 THBS3 2978 0.19 0.56 YES
67 COL4A1 COL4A1 COL4A1 2988 0.19 0.57 YES
68 COL4A2 COL4A2 COL4A2 2998 0.19 0.57 YES
69 LAMB2 LAMB2 LAMB2 3057 0.19 0.58 YES
70 FYN FYN FYN 3108 0.18 0.58 YES
71 PIK3CA PIK3CA PIK3CA 3142 0.18 0.58 YES
72 VTN VTN VTN 3301 0.17 0.58 YES
73 LAMC1 LAMC1 LAMC1 3385 0.16 0.58 YES
74 VWF VWF VWF 3504 0.16 0.58 YES
75 ROCK1 ROCK1 ROCK1 3615 0.15 0.57 YES
76 MYLK3 MYLK3 MYLK3 3679 0.15 0.58 YES
77 PDGFA PDGFA PDGFA 3713 0.15 0.58 YES
78 VCL VCL VCL 3750 0.15 0.58 YES
79 ITGA9 ITGA9 ITGA9 3837 0.14 0.58 YES
80 LAMB1 LAMB1 LAMB1 3874 0.14 0.58 YES
81 ACTN3 ACTN3 ACTN3 3908 0.14 0.58 YES
82 VAV1 VAV1 VAV1 3960 0.14 0.58 YES
83 BIRC2 BIRC2 BIRC2 4007 0.14 0.59 YES
84 RAP1A RAP1A RAP1A 4091 0.13 0.58 YES
85 SOS2 SOS2 SOS2 4099 0.13 0.59 YES
86 PPP1R12A PPP1R12A PPP1R12A 4186 0.13 0.59 YES
87 ITGB5 ITGB5 ITGB5 4254 0.12 0.59 YES
88 ARHGAP5 ARHGAP5 ARHGAP5 4265 0.12 0.59 YES
89 EGFR EGFR EGFR 4305 0.12 0.59 YES
90 PGF PGF PGF 4337 0.12 0.59 YES
91 ITGB1 ITGB1 ITGB1 4461 0.12 0.59 NO
92 TLN1 TLN1 TLN1 4562 0.11 0.59 NO
93 SOS1 SOS1 SOS1 4575 0.11 0.59 NO
94 DOCK1 DOCK1 DOCK1 4784 0.11 0.58 NO
95 ACTN1 ACTN1 ACTN1 4867 0.1 0.58 NO
96 ROCK2 ROCK2 ROCK2 4986 0.1 0.58 NO
97 BRAF BRAF BRAF 5099 0.098 0.57 NO
98 PARVA PARVA PARVA 5187 0.095 0.57 NO
99 RAPGEF1 RAPGEF1 RAPGEF1 5260 0.093 0.57 NO
100 LAMA1 LAMA1 LAMA1 5417 0.089 0.56 NO
101 IGF1R IGF1R IGF1R 5477 0.087 0.56 NO
102 LAMB4 LAMB4 LAMB4 5521 0.086 0.56 NO
103 PIK3R1 PIK3R1 PIK3R1 5574 0.085 0.56 NO
104 PIK3R3 PIK3R3 PIK3R3 5593 0.084 0.56 NO
105 ITGA8 ITGA8 ITGA8 5676 0.082 0.56 NO
106 PTEN PTEN PTEN 5692 0.082 0.56 NO
107 PPP1CB PPP1CB PPP1CB 5722 0.081 0.56 NO
108 SHC3 SHC3 SHC3 5969 0.075 0.55 NO
109 PAK2 PAK2 PAK2 6049 0.073 0.55 NO
110 LAMC2 LAMC2 LAMC2 6120 0.072 0.55 NO
111 VEGFB VEGFB VEGFB 6191 0.071 0.55 NO
112 MET MET MET 6251 0.069 0.54 NO
113 SHC2 SHC2 SHC2 6265 0.069 0.55 NO
114 LAMA3 LAMA3 LAMA3 6267 0.069 0.55 NO
115 CCND1 CCND1 CCND1 6399 0.066 0.54 NO
116 LAMA5 LAMA5 LAMA5 6616 0.061 0.53 NO
117 PIK3CB PIK3CB PIK3CB 6898 0.056 0.52 NO
118 VAV2 VAV2 VAV2 6981 0.055 0.52 NO
119 XIAP XIAP XIAP 7025 0.054 0.51 NO
120 CDC42 CDC42 CDC42 7140 0.052 0.51 NO
121 JUN JUN JUN 7148 0.052 0.51 NO
122 SHC1 SHC1 SHC1 7250 0.05 0.51 NO
123 PTK2 PTK2 PTK2 7335 0.048 0.5 NO
124 MAP2K1 MAP2K1 MAP2K1 7482 0.046 0.5 NO
125 PIP5K1C PIP5K1C PIP5K1C 7507 0.045 0.5 NO
126 MAPK1 MAPK1 MAPK1 7616 0.043 0.49 NO
127 ITGA2 ITGA2 ITGA2 7649 0.043 0.49 NO
128 ILK ILK ILK 7686 0.042 0.49 NO
129 MAPK9 MAPK9 MAPK9 7695 0.042 0.49 NO
130 RAC1 RAC1 RAC1 7768 0.04 0.49 NO
131 MYL2 MYL2 MYL2 7799 0.04 0.49 NO
132 CAPN2 CAPN2 CAPN2 7972 0.037 0.48 NO
133 ZYX ZYX ZYX 8040 0.036 0.48 NO
134 RHOA RHOA RHOA 8291 0.032 0.46 NO
135 GSK3B GSK3B GSK3B 8561 0.028 0.45 NO
136 MYL12A MYL12A MYL12A 8710 0.025 0.44 NO
137 VAV3 VAV3 VAV3 8800 0.023 0.44 NO
138 PAK1 PAK1 PAK1 8925 0.021 0.43 NO
139 CRKL CRKL CRKL 8977 0.02 0.43 NO
140 GRB2 GRB2 GRB2 8992 0.02 0.43 NO
141 TLN2 TLN2 TLN2 8995 0.02 0.43 NO
142 FLNB FLNB FLNB 9227 0.016 0.42 NO
143 LAMB3 LAMB3 LAMB3 9349 0.014 0.41 NO
144 CTNNB1 CTNNB1 CTNNB1 9483 0.012 0.4 NO
145 DIAPH1 DIAPH1 DIAPH1 9515 0.011 0.4 NO
146 CRK CRK CRK 9611 0.0098 0.4 NO
147 RAP1B RAP1B RAP1B 9615 0.0098 0.4 NO
148 MAPK8 MAPK8 MAPK8 9791 0.0065 0.39 NO
149 MYLK2 MYLK2 MYLK2 9819 0.006 0.38 NO
150 RAC2 RAC2 RAC2 9895 0.0047 0.38 NO
151 GRLF1 GRLF1 GRLF1 9916 0.0044 0.38 NO
152 ITGB6 ITGB6 ITGB6 9986 0.0034 0.38 NO
153 PXN PXN PXN 10057 0.0022 0.37 NO
154 RAF1 RAF1 RAF1 10109 0.0014 0.37 NO
155 ITGB7 ITGB7 ITGB7 10154 0.00058 0.37 NO
156 ELK1 ELK1 ELK1 10283 -0.0014 0.36 NO
157 VEGFA VEGFA VEGFA 10359 -0.0026 0.36 NO
158 ACTB ACTB ACTB 10373 -0.0029 0.36 NO
159 CCND2 CCND2 CCND2 10427 -0.0039 0.35 NO
160 PPP1CC PPP1CC PPP1CC 10433 -0.004 0.35 NO
161 ACTN4 ACTN4 ACTN4 10523 -0.0055 0.35 NO
162 PDPK1 PDPK1 PDPK1 10945 -0.013 0.32 NO
163 PRKCA PRKCA PRKCA 11032 -0.014 0.32 NO
164 ERBB2 ERBB2 ERBB2 11296 -0.019 0.3 NO
165 AKT1 AKT1 AKT1 11433 -0.022 0.3 NO
166 ITGA6 ITGA6 ITGA6 11479 -0.022 0.3 NO
167 VASP VASP VASP 11487 -0.022 0.3 NO
168 SRC SRC SRC 11558 -0.024 0.29 NO
169 PARVB PARVB PARVB 11707 -0.026 0.29 NO
170 LAMC3 LAMC3 LAMC3 11840 -0.029 0.28 NO
171 AKT2 AKT2 AKT2 11925 -0.03 0.28 NO
172 BCAR1 BCAR1 BCAR1 12352 -0.038 0.25 NO
173 MAPK3 MAPK3 MAPK3 12556 -0.042 0.24 NO
174 ITGB4 ITGB4 ITGB4 12772 -0.045 0.23 NO
175 ACTG1 ACTG1 ACTG1 12783 -0.046 0.23 NO
176 ITGA3 ITGA3 ITGA3 12822 -0.046 0.23 NO
177 MYL12B MYL12B MYL12B 12843 -0.047 0.23 NO
178 PAK4 PAK4 PAK4 13193 -0.054 0.21 NO
179 EGF EGF EGF 13212 -0.055 0.22 NO
180 CCND3 CCND3 CCND3 13498 -0.061 0.2 NO
181 PPP1CA PPP1CA PPP1CA 13639 -0.064 0.2 NO
182 PAK6 PAK6 PAK6 13717 -0.066 0.19 NO
183 PIK3R2 PIK3R2 PIK3R2 14099 -0.075 0.17 NO
184 RASGRF1 RASGRF1 RASGRF1 14244 -0.08 0.17 NO
185 CHAD CHAD CHAD 14397 -0.084 0.16 NO
186 BAD BAD BAD 14823 -0.097 0.14 NO
187 ITGA2B ITGA2B ITGA2B 14854 -0.098 0.14 NO
188 PRKCG PRKCG PRKCG 14986 -0.1 0.14 NO
189 COL11A2 COL11A2 COL11A2 15494 -0.12 0.11 NO
190 RAC3 RAC3 RAC3 15589 -0.13 0.11 NO
191 COL2A1 COL2A1 COL2A1 15801 -0.14 0.1 NO
192 MYL5 MYL5 MYL5 16032 -0.15 0.094 NO
193 MYLPF MYLPF MYLPF 17605 -0.35 0.016 NO
194 COL4A6 COL4A6 COL4A6 17689 -0.38 0.022 NO

Figure S9.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA BIOPEPTIDES PATHWAY.

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

genes ES table in pathway: BIOCARTA G1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FGF14 FGF14 FGF14 10 0.95 0.067 YES
2 FGF1 FGF1 FGF1 94 0.78 0.12 YES
3 FGF7 FGF7 FGF7 121 0.76 0.17 YES
4 MITF MITF MITF 152 0.73 0.22 YES
5 IGF1 IGF1 IGF1 186 0.71 0.27 YES
6 FGF2 FGF2 FGF2 303 0.65 0.31 YES
7 FGF10 FGF10 FGF10 355 0.62 0.35 YES
8 FGF5 FGF5 FGF5 436 0.59 0.39 YES
9 HGF HGF HGF 518 0.56 0.42 YES
10 AKT3 AKT3 AKT3 569 0.54 0.46 YES
11 PDGFC PDGFC PDGFC 628 0.52 0.49 YES
12 FGF12 FGF12 FGF12 1333 0.38 0.48 YES
13 FGF13 FGF13 FGF13 1398 0.36 0.5 YES
14 PIK3CG PIK3CG PIK3CG 1455 0.36 0.52 YES
15 FGFR1 FGFR1 FGFR1 1521 0.35 0.54 YES
16 PIK3R5 PIK3R5 PIK3R5 1567 0.34 0.56 YES
17 PDGFD PDGFD PDGFD 1801 0.31 0.57 YES
18 PDGFRB PDGFRB PDGFRB 1803 0.31 0.6 YES
19 FGF9 FGF9 FGF9 2018 0.29 0.6 YES
20 PIK3CD PIK3CD PIK3CD 2163 0.27 0.62 YES
21 PDGFRA PDGFRA PDGFRA 2405 0.24 0.62 YES
22 PDGFB PDGFB PDGFB 2787 0.21 0.61 NO
23 PIK3CA PIK3CA PIK3CA 3142 0.18 0.61 NO
24 PDGFA PDGFA PDGFA 3713 0.15 0.58 NO
25 FGF11 FGF11 FGF11 4005 0.14 0.58 NO
26 EGFR EGFR EGFR 4305 0.12 0.57 NO
27 CDK6 CDK6 CDK6 4511 0.12 0.57 NO
28 BRAF BRAF BRAF 5099 0.098 0.54 NO
29 RB1 RB1 RB1 5265 0.093 0.54 NO
30 IGF1R IGF1R IGF1R 5477 0.087 0.53 NO
31 PIK3R1 PIK3R1 PIK3R1 5574 0.085 0.53 NO
32 PIK3R3 PIK3R3 PIK3R3 5593 0.084 0.54 NO
33 FGF18 FGF18 FGF18 5657 0.082 0.54 NO
34 PTEN PTEN PTEN 5692 0.082 0.55 NO
35 MET MET MET 6251 0.069 0.52 NO
36 CCND1 CCND1 CCND1 6399 0.066 0.52 NO
37 KRAS KRAS KRAS 6580 0.062 0.51 NO
38 PIK3CB PIK3CB PIK3CB 6898 0.056 0.5 NO
39 NRAS NRAS NRAS 6951 0.056 0.5 NO
40 E2F3 E2F3 E2F3 7249 0.05 0.48 NO
41 MAP2K1 MAP2K1 MAP2K1 7482 0.046 0.48 NO
42 MAPK1 MAPK1 MAPK1 7616 0.043 0.47 NO
43 FGF19 FGF19 FGF19 7697 0.042 0.47 NO
44 MDM2 MDM2 MDM2 9399 0.013 0.38 NO
45 CDH1 CDH1 CDH1 9848 0.0056 0.35 NO
46 RAF1 RAF1 RAF1 10109 0.0014 0.34 NO
47 AKT1 AKT1 AKT1 11433 -0.022 0.26 NO
48 FGF23 FGF23 FGF23 11545 -0.024 0.26 NO
49 AKT2 AKT2 AKT2 11925 -0.03 0.24 NO
50 FGF3 FGF3 FGF3 12139 -0.034 0.23 NO
51 CDKN2A CDKN2A CDKN2A 12317 -0.037 0.22 NO
52 FGF20 FGF20 FGF20 12370 -0.038 0.22 NO
53 MAPK3 MAPK3 MAPK3 12556 -0.042 0.22 NO
54 EGF EGF EGF 13212 -0.055 0.18 NO
55 CDKN1A CDKN1A CDKN1A 13676 -0.065 0.16 NO
56 PIK3R2 PIK3R2 PIK3R2 14099 -0.075 0.14 NO
57 CDK4 CDK4 CDK4 14226 -0.079 0.14 NO
58 TP53 TP53 TP53 14292 -0.081 0.15 NO
59 BAD BAD BAD 14823 -0.097 0.12 NO
60 HRAS HRAS HRAS 14840 -0.097 0.13 NO
61 MAP2K2 MAP2K2 MAP2K2 15004 -0.1 0.13 NO
62 FGF17 FGF17 FGF17 15020 -0.1 0.13 NO
63 ARAF ARAF ARAF 15092 -0.11 0.14 NO
64 FGF21 FGF21 FGF21 15096 -0.11 0.14 NO
65 FGF8 FGF8 FGF8 15845 -0.14 0.11 NO
66 E2F2 E2F2 E2F2 16264 -0.16 0.1 NO

Figure S11.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA G1 PATHWAY.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA HDAC PATHWAY

Table S7.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FGF14 FGF14 FGF14 10 0.95 0.02 YES
2 RUNX1T1 RUNX1T1 RUNX1T1 70 0.8 0.033 YES
3 FGF1 FGF1 FGF1 94 0.78 0.048 YES
4 FGF7 FGF7 FGF7 121 0.76 0.063 YES
5 MITF MITF MITF 152 0.73 0.076 YES
6 TGFB3 TGFB3 TGFB3 154 0.73 0.092 YES
7 GLI3 GLI3 GLI3 162 0.73 0.11 YES
8 IGF1 IGF1 IGF1 186 0.71 0.12 YES
9 CCNA1 CCNA1 CCNA1 300 0.65 0.13 YES
10 FGF2 FGF2 FGF2 303 0.65 0.14 YES
11 AR AR AR 329 0.64 0.15 YES
12 FGF10 FGF10 FGF10 355 0.62 0.16 YES
13 FGF5 FGF5 FGF5 436 0.59 0.17 YES
14 VEGFC VEGFC VEGFC 474 0.57 0.18 YES
15 HGF HGF HGF 518 0.56 0.19 YES
16 GLI1 GLI1 GLI1 524 0.56 0.2 YES
17 RARB RARB RARB 533 0.55 0.21 YES
18 AKT3 AKT3 AKT3 569 0.54 0.22 YES
19 GLI2 GLI2 GLI2 597 0.53 0.23 YES
20 MAPK10 MAPK10 MAPK10 600 0.53 0.24 YES
21 TGFB2 TGFB2 TGFB2 639 0.52 0.25 YES
22 LAMA2 LAMA2 LAMA2 748 0.49 0.26 YES
23 ZBTB16 ZBTB16 ZBTB16 857 0.47 0.26 YES
24 HHIP HHIP HHIP 935 0.45 0.27 YES
25 WNT2 WNT2 WNT2 973 0.44 0.27 YES
26 CTNNA3 CTNNA3 CTNNA3 1048 0.43 0.28 YES
27 PRKCB PRKCB PRKCB 1108 0.41 0.28 YES
28 FGF12 FGF12 FGF12 1333 0.38 0.28 YES
29 PTCH2 PTCH2 PTCH2 1354 0.37 0.29 YES
30 COL4A4 COL4A4 COL4A4 1383 0.37 0.29 YES
31 FGF13 FGF13 FGF13 1398 0.36 0.3 YES
32 PIK3CG PIK3CG PIK3CG 1455 0.36 0.3 YES
33 FN1 FN1 FN1 1486 0.35 0.31 YES
34 FGFR1 FGFR1 FGFR1 1521 0.35 0.31 YES
35 PIK3R5 PIK3R5 PIK3R5 1567 0.34 0.32 YES
36 WNT9A WNT9A WNT9A 1598 0.34 0.32 YES
37 ARNT2 ARNT2 ARNT2 1651 0.33 0.33 YES
38 MMP9 MMP9 MMP9 1673 0.33 0.33 YES
39 FIGF FIGF FIGF 1751 0.32 0.34 YES
40 CDKN2B CDKN2B CDKN2B 1756 0.32 0.34 YES
41 MMP2 MMP2 MMP2 1776 0.31 0.35 YES
42 FZD8 FZD8 FZD8 1791 0.31 0.35 YES
43 PDGFRB PDGFRB PDGFRB 1803 0.31 0.36 YES
44 FZD4 FZD4 FZD4 1810 0.31 0.37 YES
45 CSF1R CSF1R CSF1R 1817 0.31 0.37 YES
46 WNT9B WNT9B WNT9B 1958 0.3 0.37 YES
47 IL6 IL6 IL6 1965 0.3 0.38 YES
48 FGF9 FGF9 FGF9 2018 0.29 0.38 YES
49 RET RET RET 2068 0.28 0.38 YES
50 LEF1 LEF1 LEF1 2100 0.28 0.39 YES
51 LAMA4 LAMA4 LAMA4 2118 0.28 0.39 YES
52 SPI1 SPI1 SPI1 2139 0.27 0.4 YES
53 PIK3CD PIK3CD PIK3CD 2163 0.27 0.4 YES
54 ITGAV ITGAV ITGAV 2189 0.27 0.4 YES
55 FGFR2 FGFR2 FGFR2 2196 0.27 0.41 YES
56 FZD1 FZD1 FZD1 2219 0.26 0.42 YES
57 NTRK1 NTRK1 NTRK1 2282 0.26 0.42 YES
58 ETS1 ETS1 ETS1 2290 0.26 0.42 YES
59 DAPK1 DAPK1 DAPK1 2381 0.25 0.42 YES
60 PDGFRA PDGFRA PDGFRA 2405 0.24 0.42 YES
61 FZD7 FZD7 FZD7 2406 0.24 0.43 YES
62 NKX3-1 NKX3-1 NKX3-1 2459 0.24 0.43 YES
63 TCF7L1 TCF7L1 TCF7L1 2487 0.24 0.44 YES
64 KIT KIT KIT 2561 0.23 0.44 YES
65 CSF2RA CSF2RA CSF2RA 2626 0.22 0.44 YES
66 FLT3 FLT3 FLT3 2647 0.22 0.44 YES
67 BCL2 BCL2 BCL2 2698 0.22 0.44 YES
68 PLCG2 PLCG2 PLCG2 2713 0.22 0.45 YES
69 WNT7A WNT7A WNT7A 2740 0.21 0.45 YES
70 CSF3R CSF3R CSF3R 2749 0.21 0.45 YES
71 FASLG FASLG FASLG 2772 0.21 0.46 YES
72 PDGFB PDGFB PDGFB 2787 0.21 0.46 YES
73 SMO SMO SMO 2790 0.21 0.46 YES
74 PTGS2 PTGS2 PTGS2 2795 0.21 0.47 YES
75 TRAF1 TRAF1 TRAF1 2868 0.2 0.47 YES
76 BIRC3 BIRC3 BIRC3 2903 0.2 0.47 YES
77 COL4A1 COL4A1 COL4A1 2988 0.19 0.47 YES
78 COL4A2 COL4A2 COL4A2 2998 0.19 0.48 YES
79 LAMB2 LAMB2 LAMB2 3057 0.19 0.48 YES
80 TGFBR1 TGFBR1 TGFBR1 3089 0.19 0.48 YES
81 RASSF5 RASSF5 RASSF5 3114 0.18 0.48 YES
82 PIK3CA PIK3CA PIK3CA 3142 0.18 0.48 YES
83 FOXO1 FOXO1 FOXO1 3236 0.18 0.48 YES
84 LAMC1 LAMC1 LAMC1 3385 0.16 0.48 YES
85 APC APC APC 3508 0.16 0.47 YES
86 TGFB1 TGFB1 TGFB1 3530 0.16 0.48 YES
87 STAT1 STAT1 STAT1 3550 0.16 0.48 YES
88 PDGFA PDGFA PDGFA 3713 0.15 0.47 YES
89 WNT5A WNT5A WNT5A 3724 0.15 0.47 YES
90 RUNX1 RUNX1 RUNX1 3796 0.14 0.47 YES
91 FOS FOS FOS 3800 0.14 0.48 YES
92 KITLG KITLG KITLG 3827 0.14 0.48 YES
93 WNT7B WNT7B WNT7B 3848 0.14 0.48 YES
94 LAMB1 LAMB1 LAMB1 3874 0.14 0.48 YES
95 WNT2B WNT2B WNT2B 3875 0.14 0.48 YES
96 APPL1 APPL1 APPL1 3942 0.14 0.48 YES
97 FGF11 FGF11 FGF11 4005 0.14 0.48 YES
98 BIRC2 BIRC2 BIRC2 4007 0.14 0.48 YES
99 FLT3LG FLT3LG FLT3LG 4047 0.13 0.48 YES
100 SOS2 SOS2 SOS2 4099 0.13 0.48 YES
101 WNT10B WNT10B WNT10B 4207 0.13 0.48 YES
102 HIF1A HIF1A HIF1A 4208 0.13 0.48 YES
103 TGFBR2 TGFBR2 TGFBR2 4234 0.13 0.49 YES
104 EGFR EGFR EGFR 4305 0.12 0.48 NO
105 PGF PGF PGF 4337 0.12 0.48 NO
106 ITGB1 ITGB1 ITGB1 4461 0.12 0.48 NO
107 CDK6 CDK6 CDK6 4511 0.12 0.48 NO
108 SOS1 SOS1 SOS1 4575 0.11 0.48 NO
109 FAS FAS FAS 4690 0.11 0.48 NO
110 CBL CBL CBL 4691 0.11 0.48 NO
111 FZD2 FZD2 FZD2 4731 0.11 0.48 NO
112 IL8 IL8 IL8 4950 0.1 0.47 NO
113 DCC DCC DCC 5040 0.1 0.46 NO
114 BRAF BRAF BRAF 5099 0.098 0.46 NO
115 CBLB CBLB CBLB 5162 0.096 0.46 NO
116 RB1 RB1 RB1 5265 0.093 0.46 NO
117 PTCH1 PTCH1 PTCH1 5412 0.089 0.45 NO
118 LAMA1 LAMA1 LAMA1 5417 0.089 0.45 NO
119 WNT11 WNT11 WNT11 5467 0.088 0.45 NO
120 IGF1R IGF1R IGF1R 5477 0.087 0.45 NO
121 CCNE2 CCNE2 CCNE2 5506 0.087 0.45 NO
122 LAMB4 LAMB4 LAMB4 5521 0.086 0.46 NO
123 PIK3R1 PIK3R1 PIK3R1 5574 0.085 0.45 NO
124 PIK3R3 PIK3R3 PIK3R3 5593 0.084 0.46 NO
125 JAK1 JAK1 JAK1 5625 0.083 0.46 NO
126 BMP2 BMP2 BMP2 5641 0.083 0.46 NO
127 FGF18 FGF18 FGF18 5657 0.082 0.46 NO
128 PTEN PTEN PTEN 5692 0.082 0.46 NO
129 RALA RALA RALA 5744 0.08 0.46 NO
130 CTNNA2 CTNNA2 CTNNA2 5798 0.079 0.45 NO
131 ARNT ARNT ARNT 5860 0.078 0.45 NO
132 BRCA2 BRCA2 BRCA2 6021 0.074 0.44 NO
133 EP300 EP300 EP300 6024 0.074 0.45 NO
134 PIAS3 PIAS3 PIAS3 6044 0.074 0.45 NO
135 TRAF5 TRAF5 TRAF5 6061 0.073 0.45 NO
136 LAMC2 LAMC2 LAMC2 6120 0.072 0.44 NO
137 PLD1 PLD1 PLD1 6146 0.072 0.44 NO
138 FZD6 FZD6 FZD6 6165 0.071 0.45 NO
139 VEGFB VEGFB VEGFB 6191 0.071 0.45 NO
140 SMAD2 SMAD2 SMAD2 6193 0.071 0.45 NO
141 NFKB2 NFKB2 NFKB2 6195 0.07 0.45 NO
142 CASP8 CASP8 CASP8 6206 0.07 0.45 NO
143 MET MET MET 6251 0.069 0.45 NO
144 LAMA3 LAMA3 LAMA3 6267 0.069 0.45 NO
145 STK4 STK4 STK4 6268 0.069 0.45 NO
146 TPR TPR TPR 6358 0.067 0.45 NO
147 RALB RALB RALB 6368 0.066 0.45 NO
148 CCND1 CCND1 CCND1 6399 0.066 0.45 NO
149 PIAS2 PIAS2 PIAS2 6513 0.064 0.44 NO
150 EPAS1 EPAS1 EPAS1 6525 0.063 0.44 NO
151 KRAS KRAS KRAS 6580 0.062 0.44 NO
152 LAMA5 LAMA5 LAMA5 6616 0.061 0.44 NO
153 SMAD4 SMAD4 SMAD4 6621 0.061 0.44 NO
154 STAT5B STAT5B STAT5B 6690 0.06 0.44 NO
155 MAX MAX MAX 6706 0.06 0.44 NO
156 ABL1 ABL1 ABL1 6764 0.059 0.44 NO
157 MMP1 MMP1 MMP1 6858 0.057 0.43 NO
158 PIK3CB PIK3CB PIK3CB 6898 0.056 0.43 NO
159 NRAS NRAS NRAS 6951 0.056 0.43 NO
160 CDKN1B CDKN1B CDKN1B 6979 0.055 0.43 NO
161 HSP90B1 HSP90B1 HSP90B1 7002 0.054 0.43 NO
162 XIAP XIAP XIAP 7025 0.054 0.43 NO
163 SUFU SUFU SUFU 7031 0.054 0.43 NO
164 WNT1 WNT1 WNT1 7036 0.054 0.43 NO
165 TGFA TGFA TGFA 7076 0.053 0.43 NO
166 CDC42 CDC42 CDC42 7140 0.052 0.43 NO
167 JUN JUN JUN 7148 0.052 0.43 NO
168 NFKBIA NFKBIA NFKBIA 7197 0.051 0.43 NO
169 E2F3 E2F3 E2F3 7249 0.05 0.43 NO
170 RARA RARA RARA 7288 0.049 0.42 NO
171 PTK2 PTK2 PTK2 7335 0.048 0.42 NO
172 NCOA4 NCOA4 NCOA4 7375 0.047 0.42 NO
173 MLH1 MLH1 MLH1 7429 0.046 0.42 NO
174 MAP2K1 MAP2K1 MAP2K1 7482 0.046 0.42 NO
175 TRAF6 TRAF6 TRAF6 7577 0.044 0.41 NO
176 HSP90AA1 HSP90AA1 HSP90AA1 7581 0.044 0.42 NO
177 MAPK1 MAPK1 MAPK1 7616 0.043 0.41 NO
178 ITGA2 ITGA2 ITGA2 7649 0.043 0.41 NO
179 CREBBP CREBBP CREBBP 7651 0.042 0.41 NO
180 MSH2 MSH2 MSH2 7653 0.042 0.41 NO
181 SMAD3 SMAD3 SMAD3 7666 0.042 0.42 NO
182 MAPK9 MAPK9 MAPK9 7695 0.042 0.41 NO
183 FGF19 FGF19 FGF19 7697 0.042 0.42 NO
184 RAC1 RAC1 RAC1 7768 0.04 0.41 NO
185 HDAC2 HDAC2 HDAC2 7828 0.039 0.41 NO
186 BMP4 BMP4 BMP4 7840 0.039 0.41 NO
187 STAT5A STAT5A STAT5A 7954 0.038 0.4 NO
188 CYCS CYCS CYCS 8045 0.036 0.4 NO
189 CUL2 CUL2 CUL2 8058 0.036 0.4 NO
190 RXRG RXRG RXRG 8102 0.035 0.4 NO
191 IKBKB IKBKB IKBKB 8179 0.034 0.39 NO
192 RHOA RHOA RHOA 8291 0.032 0.39 NO
193 PIAS1 PIAS1 PIAS1 8304 0.032 0.39 NO
194 MSH3 MSH3 MSH3 8307 0.032 0.39 NO
195 STAT3 STAT3 STAT3 8346 0.031 0.39 NO
196 PLCG1 PLCG1 PLCG1 8386 0.03 0.39 NO
197 NFKB1 NFKB1 NFKB1 8473 0.029 0.38 NO
198 CCDC6 CCDC6 CCDC6 8517 0.028 0.38 NO
199 GSK3B GSK3B GSK3B 8561 0.028 0.38 NO
200 TRAF2 TRAF2 TRAF2 8564 0.028 0.38 NO
201 CHUK CHUK CHUK 8569 0.028 0.38 NO
202 RALGDS RALGDS RALGDS 8597 0.027 0.38 NO
203 RXRA RXRA RXRA 8638 0.026 0.38 NO
204 WNT16 WNT16 WNT16 8724 0.025 0.37 NO
205 TCF7 TCF7 TCF7 8941 0.021 0.36 NO
206 EGLN1 EGLN1 EGLN1 8950 0.02 0.36 NO
207 CRKL CRKL CRKL 8977 0.02 0.36 NO
208 GRB2 GRB2 GRB2 8992 0.02 0.36 NO
209 TCEB1 TCEB1 TCEB1 9125 0.018 0.35 NO
210 PML PML PML 9130 0.018 0.35 NO
211 KLK3 KLK3 KLK3 9145 0.017 0.35 NO
212 HSP90AB1 HSP90AB1 HSP90AB1 9209 0.016 0.35 NO
213 RELA RELA RELA 9233 0.016 0.35 NO
214 MSH6 MSH6 MSH6 9268 0.015 0.35 NO
215 LAMB3 LAMB3 LAMB3 9349 0.014 0.34 NO
216 MDM2 MDM2 MDM2 9399 0.013 0.34 NO
217 CTNNB1 CTNNB1 CTNNB1 9483 0.012 0.34 NO
218 FZD10 FZD10 FZD10 9525 0.011 0.33 NO
219 TRAF3 TRAF3 TRAF3 9552 0.011 0.33 NO
220 CRK CRK CRK 9611 0.0098 0.33 NO
221 TPM3 TPM3 TPM3 9692 0.0082 0.32 NO
222 MAPK8 MAPK8 MAPK8 9791 0.0065 0.32 NO
223 MTOR MTOR MTOR 9823 0.006 0.32 NO
224 CDH1 CDH1 CDH1 9848 0.0056 0.32 NO
225 RAC2 RAC2 RAC2 9895 0.0047 0.31 NO
226 CTNNA1 CTNNA1 CTNNA1 9956 0.0038 0.31 NO
227 WNT10A WNT10A WNT10A 9964 0.0037 0.31 NO
228 BCL2L1 BCL2L1 BCL2L1 10017 0.003 0.31 NO
229 RAF1 RAF1 RAF1 10109 0.0014 0.3 NO
230 RBX1 RBX1 RBX1 10187 -1.1e-06 0.3 NO
231 CASP3 CASP3 CASP3 10199 -0.0002 0.3 NO
232 DVL3 DVL3 DVL3 10315 -0.002 0.29 NO
233 VEGFA VEGFA VEGFA 10359 -0.0026 0.29 NO
234 TCF7L2 TCF7L2 TCF7L2 10507 -0.0054 0.28 NO
235 PPARD PPARD PPARD 10607 -0.0069 0.28 NO
236 RALBP1 RALBP1 RALBP1 10611 -0.007 0.27 NO
237 WNT3A WNT3A WNT3A 10653 -0.0078 0.27 NO
238 VHL VHL VHL 10904 -0.012 0.26 NO
239 DVL2 DVL2 DVL2 10956 -0.013 0.26 NO
240 PRKCA PRKCA PRKCA 11032 -0.014 0.25 NO
241 EGLN2 EGLN2 EGLN2 11044 -0.014 0.25 NO
242 RXRB RXRB RXRB 11080 -0.015 0.25 NO
243 MECOM MECOM MECOM 11100 -0.016 0.25 NO
244 DAPK3 DAPK3 DAPK3 11230 -0.018 0.24 NO
245 WNT3 WNT3 WNT3 11279 -0.019 0.24 NO
246 ERBB2 ERBB2 ERBB2 11296 -0.019 0.24 NO
247 AKT1 AKT1 AKT1 11433 -0.022 0.23 NO
248 WNT5B WNT5B WNT5B 11435 -0.022 0.23 NO
249 ITGA6 ITGA6 ITGA6 11479 -0.022 0.23 NO
250 FGF23 FGF23 FGF23 11545 -0.024 0.23 NO
251 CDK2 CDK2 CDK2 11547 -0.024 0.23 NO
252 CASP9 CASP9 CASP9 11613 -0.025 0.22 NO
253 HDAC1 HDAC1 HDAC1 11617 -0.025 0.22 NO
254 DAPK2 DAPK2 DAPK2 11744 -0.027 0.22 NO
255 LAMC3 LAMC3 LAMC3 11840 -0.029 0.21 NO
256 AKT2 AKT2 AKT2 11925 -0.03 0.21 NO
257 FADD FADD FADD 12012 -0.032 0.21 NO
258 AXIN1 AXIN1 AXIN1 12051 -0.032 0.2 NO
259 EGLN3 EGLN3 EGLN3 12058 -0.033 0.2 NO
260 FGF3 FGF3 FGF3 12139 -0.034 0.2 NO
261 STK36 STK36 STK36 12235 -0.035 0.2 NO
262 TFG TFG TFG 12264 -0.036 0.2 NO
263 CDKN2A CDKN2A CDKN2A 12317 -0.037 0.19 NO
264 IKBKG IKBKG IKBKG 12339 -0.038 0.19 NO
265 PPARG PPARG PPARG 12360 -0.038 0.19 NO
266 FGF20 FGF20 FGF20 12370 -0.038 0.19 NO
267 RASSF1 RASSF1 RASSF1 12402 -0.039 0.19 NO
268 MAPK3 MAPK3 MAPK3 12556 -0.042 0.18 NO
269 CTBP2 CTBP2 CTBP2 12627 -0.043 0.18 NO
270 ITGA3 ITGA3 ITGA3 12822 -0.046 0.17 NO
271 RAD51 RAD51 RAD51 12904 -0.048 0.17 NO
272 CTBP1 CTBP1 CTBP1 13085 -0.052 0.16 NO
273 FZD5 FZD5 FZD5 13156 -0.054 0.16 NO
274 EGF EGF EGF 13212 -0.055 0.15 NO
275 JUP JUP JUP 13228 -0.055 0.15 NO
276 BCR BCR BCR 13319 -0.058 0.15 NO
277 CDKN1A CDKN1A CDKN1A 13676 -0.065 0.13 NO
278 SLC2A1 SLC2A1 SLC2A1 13992 -0.072 0.12 NO
279 MYC MYC MYC 14032 -0.074 0.12 NO
280 SKP2 SKP2 SKP2 14040 -0.074 0.12 NO
281 PIK3R2 PIK3R2 PIK3R2 14099 -0.075 0.11 NO
282 CEBPA CEBPA CEBPA 14215 -0.078 0.11 NO
283 CDK4 CDK4 CDK4 14226 -0.079 0.11 NO
284 BAX BAX BAX 14227 -0.079 0.11 NO
285 TP53 TP53 TP53 14292 -0.081 0.11 NO
286 FH FH FH 14363 -0.083 0.11 NO
287 DVL1 DVL1 DVL1 14623 -0.091 0.096 NO
288 E2F1 E2F1 E2F1 14631 -0.091 0.097 NO
289 BIRC5 BIRC5 BIRC5 14637 -0.091 0.099 NO
290 BAD BAD BAD 14823 -0.097 0.09 NO
291 PAX8 PAX8 PAX8 14829 -0.097 0.092 NO
292 ITGA2B ITGA2B ITGA2B 14854 -0.098 0.093 NO
293 PIAS4 PIAS4 PIAS4 14894 -0.099 0.093 NO
294 PRKCG PRKCG PRKCG 14986 -0.1 0.09 NO
295 MAP2K2 MAP2K2 MAP2K2 15004 -0.1 0.091 NO
296 FGF17 FGF17 FGF17 15020 -0.1 0.092 NO
297 TCEB2 TCEB2 TCEB2 15043 -0.1 0.093 NO
298 ARAF ARAF ARAF 15092 -0.11 0.093 NO
299 FGF21 FGF21 FGF21 15096 -0.11 0.095 NO
300 BID BID BID 15200 -0.11 0.091 NO
301 WNT6 WNT6 WNT6 15250 -0.11 0.091 NO
302 CKS1B CKS1B CKS1B 15313 -0.11 0.09 NO
303 AXIN2 AXIN2 AXIN2 15531 -0.12 0.08 NO
304 GSTP1 GSTP1 GSTP1 15532 -0.12 0.083 NO
305 CCNE1 CCNE1 CCNE1 15585 -0.12 0.082 NO
306 RAC3 RAC3 RAC3 15589 -0.13 0.085 NO
307 WNT8B WNT8B WNT8B 15601 -0.13 0.087 NO
308 TRAF4 TRAF4 TRAF4 15676 -0.13 0.085 NO
309 FGF8 FGF8 FGF8 15845 -0.14 0.079 NO
310 CBLC CBLC CBLC 16234 -0.16 0.06 NO
311 E2F2 E2F2 E2F2 16264 -0.16 0.062 NO
312 FZD3 FZD3 FZD3 16364 -0.17 0.06 NO
313 NOS2 NOS2 NOS2 16459 -0.18 0.058 NO
314 SHH SHH SHH 16560 -0.18 0.057 NO
315 FGFR3 FGFR3 FGFR3 17012 -0.23 0.036 NO
316 FZD9 FZD9 FZD9 17105 -0.24 0.036 NO
317 WNT4 WNT4 WNT4 17237 -0.27 0.034 NO
318 APC2 APC2 APC2 17250 -0.27 0.039 NO
319 COL4A6 COL4A6 COL4A6 17689 -0.38 0.023 NO

Figure S13.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA HDAC PATHWAY.

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

genes ES table in pathway: BIOCARTA EGF PATHWAY

Table 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 AKT3 AKT3 AKT3 569 0.54 0.041 YES
2 MAPK10 MAPK10 MAPK10 600 0.53 0.11 YES
3 ADIPOQ ADIPOQ ADIPOQ 611 0.53 0.18 YES
4 CD36 CD36 CD36 634 0.52 0.25 YES
5 LEP LEP LEP 1015 0.43 0.28 YES
6 CPT1C CPT1C CPT1C 1243 0.39 0.32 YES
7 SLC2A4 SLC2A4 SLC2A4 1804 0.31 0.34 YES
8 LEPR LEPR LEPR 1816 0.31 0.38 YES
9 POMC POMC POMC 1978 0.29 0.41 YES
10 NPY NPY NPY 2152 0.27 0.43 YES
11 JAK2 JAK2 JAK2 2293 0.26 0.46 YES
12 PRKAA2 PRKAA2 PRKAA2 2566 0.23 0.47 YES
13 TNF TNF TNF 3135 0.18 0.47 YES
14 IRS1 IRS1 IRS1 3158 0.18 0.49 YES
15 SOCS3 SOCS3 SOCS3 3286 0.17 0.51 YES
16 PRKAB2 PRKAB2 PRKAB2 4039 0.13 0.48 NO
17 AGRP AGRP AGRP 4438 0.12 0.48 NO
18 PCK1 PCK1 PCK1 4666 0.11 0.48 NO
19 PRKAA1 PRKAA1 PRKAA1 4685 0.11 0.49 NO
20 ACSL4 ACSL4 ACSL4 5067 0.099 0.48 NO
21 ACSL1 ACSL1 ACSL1 5820 0.078 0.45 NO
22 ACSL3 ACSL3 ACSL3 6684 0.06 0.41 NO
23 PTPN11 PTPN11 PTPN11 6751 0.059 0.42 NO
24 PRKAG2 PRKAG2 PRKAG2 6938 0.056 0.41 NO
25 G6PC2 G6PC2 G6PC2 6996 0.055 0.42 NO
26 ACSL6 ACSL6 ACSL6 7043 0.054 0.42 NO
27 NFKBIA NFKBIA NFKBIA 7197 0.051 0.42 NO
28 PPARA PPARA PPARA 7564 0.044 0.41 NO
29 MAPK9 MAPK9 MAPK9 7695 0.042 0.4 NO
30 IRS2 IRS2 IRS2 7772 0.04 0.41 NO
31 RXRG RXRG RXRG 8102 0.035 0.39 NO
32 IKBKB IKBKB IKBKB 8179 0.034 0.39 NO
33 STAT3 STAT3 STAT3 8346 0.031 0.39 NO
34 NFKB1 NFKB1 NFKB1 8473 0.029 0.38 NO
35 TRAF2 TRAF2 TRAF2 8564 0.028 0.38 NO
36 CHUK CHUK CHUK 8569 0.028 0.39 NO
37 RXRA RXRA RXRA 8638 0.026 0.39 NO
38 ACACB ACACB ACACB 8952 0.02 0.37 NO
39 CAMKK2 CAMKK2 CAMKK2 8984 0.02 0.37 NO
40 RELA RELA RELA 9233 0.016 0.36 NO
41 NFKBIE NFKBIE NFKBIE 9407 0.013 0.35 NO
42 TNFRSF1B TNFRSF1B TNFRSF1B 9479 0.012 0.35 NO
43 MAPK8 MAPK8 MAPK8 9791 0.0065 0.33 NO
44 MTOR MTOR MTOR 9823 0.006 0.33 NO
45 ACSL5 ACSL5 ACSL5 10071 0.0021 0.32 NO
46 ADIPOR1 ADIPOR1 ADIPOR1 10341 -0.0023 0.3 NO
47 ADIPOR2 ADIPOR2 ADIPOR2 10380 -0.0031 0.3 NO
48 PPARGC1A PPARGC1A PPARGC1A 10525 -0.0056 0.3 NO
49 RXRB RXRB RXRB 11080 -0.015 0.27 NO
50 G6PC G6PC G6PC 11084 -0.015 0.27 NO
51 CAMKK1 CAMKK1 CAMKK1 11112 -0.016 0.27 NO
52 AKT1 AKT1 AKT1 11433 -0.022 0.26 NO
53 TNFRSF1A TNFRSF1A TNFRSF1A 11562 -0.024 0.25 NO
54 CPT1A CPT1A CPT1A 11663 -0.026 0.25 NO
55 PRKAG1 PRKAG1 PRKAG1 11769 -0.028 0.25 NO
56 AKT2 AKT2 AKT2 11925 -0.03 0.24 NO
57 IKBKG IKBKG IKBKG 12339 -0.038 0.22 NO
58 PRKCQ PRKCQ PRKCQ 12351 -0.038 0.23 NO
59 NFKBIB NFKBIB NFKBIB 13180 -0.054 0.19 NO
60 PRKAB1 PRKAB1 PRKAB1 13925 -0.07 0.16 NO
61 SLC2A1 SLC2A1 SLC2A1 13992 -0.072 0.16 NO
62 PCK2 PCK2 PCK2 14175 -0.077 0.16 NO
63 TRADD TRADD TRADD 14218 -0.079 0.17 NO
64 STK11 STK11 STK11 15640 -0.13 0.11 NO
65 CPT1B CPT1B CPT1B 16606 -0.19 0.082 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: BIOCARTA EGF PATHWAY.

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

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 CACNA2D1 CACNA2D1 CACNA2D1 80 0.79 0.051 YES
2 CDH2 CDH2 CDH2 118 0.76 0.1 YES
3 SGCD SGCD SGCD 202 0.7 0.15 YES
4 DES DES DES 364 0.62 0.18 YES
5 ITGA10 ITGA10 ITGA10 664 0.51 0.2 YES
6 SGCG SGCG SGCG 695 0.5 0.23 YES
7 LAMA2 LAMA2 LAMA2 748 0.49 0.26 YES
8 ITGA11 ITGA11 ITGA11 849 0.47 0.29 YES
9 ACTN2 ACTN2 ACTN2 892 0.46 0.32 YES
10 SGCA SGCA SGCA 895 0.46 0.35 YES
11 CACNB4 CACNB4 CACNB4 937 0.45 0.38 YES
12 SLC8A1 SLC8A1 SLC8A1 967 0.44 0.41 YES
13 CTNNA3 CTNNA3 CTNNA3 1048 0.43 0.44 YES
14 ITGA4 ITGA4 ITGA4 1438 0.36 0.44 YES
15 ITGB3 ITGB3 ITGB3 1559 0.34 0.46 YES
16 ITGA7 ITGA7 ITGA7 1743 0.32 0.47 YES
17 RYR2 RYR2 RYR2 1774 0.32 0.49 YES
18 GJA1 GJA1 GJA1 1882 0.3 0.51 YES
19 ITGA5 ITGA5 ITGA5 1904 0.3 0.53 YES
20 DMD DMD DMD 1947 0.3 0.55 YES
21 LEF1 LEF1 LEF1 2100 0.28 0.56 YES
22 ITGAV ITGAV ITGAV 2189 0.27 0.57 YES
23 ITGB8 ITGB8 ITGB8 2197 0.27 0.59 YES
24 ITGA1 ITGA1 ITGA1 2201 0.27 0.61 YES
25 CACNB2 CACNB2 CACNB2 2434 0.24 0.61 YES
26 TCF7L1 TCF7L1 TCF7L1 2487 0.24 0.62 YES
27 CACNA1C CACNA1C CACNA1C 2697 0.22 0.63 YES
28 CACNG4 CACNG4 CACNG4 2885 0.2 0.63 YES
29 SGCB SGCB SGCB 3501 0.16 0.61 NO
30 ITGA9 ITGA9 ITGA9 3837 0.14 0.6 NO
31 ACTN3 ACTN3 ACTN3 3908 0.14 0.61 NO
32 ITGB5 ITGB5 ITGB5 4254 0.12 0.6 NO
33 ITGB1 ITGB1 ITGB1 4461 0.12 0.59 NO
34 ACTN1 ACTN1 ACTN1 4867 0.1 0.58 NO
35 ITGA8 ITGA8 ITGA8 5676 0.082 0.54 NO
36 CACNG6 CACNG6 CACNG6 5680 0.082 0.54 NO
37 CTNNA2 CTNNA2 CTNNA2 5798 0.079 0.54 NO
38 CACNA2D4 CACNA2D4 CACNA2D4 6284 0.068 0.52 NO
39 CACNG1 CACNG1 CACNG1 6683 0.06 0.5 NO
40 DSP DSP DSP 7469 0.046 0.46 NO
41 CACNB1 CACNB1 CACNB1 7493 0.045 0.46 NO
42 CACNA2D3 CACNA2D3 CACNA2D3 7621 0.043 0.46 NO
43 ITGA2 ITGA2 ITGA2 7649 0.043 0.46 NO
44 LMNA LMNA LMNA 8269 0.032 0.43 NO
45 DSC2 DSC2 DSC2 8322 0.031 0.43 NO
46 TCF7 TCF7 TCF7 8941 0.021 0.4 NO
47 CACNB3 CACNB3 CACNB3 9063 0.019 0.39 NO
48 DAG1 DAG1 DAG1 9193 0.017 0.38 NO
49 CTNNB1 CTNNB1 CTNNB1 9483 0.012 0.37 NO
50 CTNNA1 CTNNA1 CTNNA1 9956 0.0038 0.34 NO
51 ITGB6 ITGB6 ITGB6 9986 0.0034 0.34 NO
52 ITGB7 ITGB7 ITGB7 10154 0.00058 0.33 NO
53 ATP2A2 ATP2A2 ATP2A2 10161 0.00038 0.33 NO
54 DSG2 DSG2 DSG2 10279 -0.0013 0.33 NO
55 ACTB ACTB ACTB 10373 -0.0029 0.32 NO
56 TCF7L2 TCF7L2 TCF7L2 10507 -0.0054 0.31 NO
57 ACTN4 ACTN4 ACTN4 10523 -0.0055 0.31 NO
58 ITGA6 ITGA6 ITGA6 11479 -0.022 0.26 NO
59 CACNA1D CACNA1D CACNA1D 12269 -0.036 0.22 NO
60 ITGB4 ITGB4 ITGB4 12772 -0.045 0.2 NO
61 ACTG1 ACTG1 ACTG1 12783 -0.046 0.2 NO
62 ITGA3 ITGA3 ITGA3 12822 -0.046 0.2 NO
63 JUP JUP JUP 13228 -0.055 0.18 NO
64 EMD EMD EMD 13292 -0.057 0.18 NO
65 PKP2 PKP2 PKP2 13731 -0.066 0.16 NO
66 ITGA2B ITGA2B ITGA2B 14854 -0.098 0.11 NO
67 CACNA2D2 CACNA2D2 CACNA2D2 16640 -0.19 0.021 NO
68 CACNG8 CACNG8 CACNG8 17214 -0.26 0.0076 NO
69 CACNA1S CACNA1S CACNA1S 17301 -0.28 0.022 NO
70 CACNA1F CACNA1F CACNA1F 17447 -0.31 0.036 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: BIOCARTA FCER1 PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 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 GH PATHWAY

Table S10.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RUNX1T1 RUNX1T1 RUNX1T1 70 0.8 0.1 YES
2 CCNA1 CCNA1 CCNA1 300 0.65 0.17 YES
3 AKT3 AKT3 AKT3 569 0.54 0.23 YES
4 ZBTB16 ZBTB16 ZBTB16 857 0.47 0.28 YES
5 PIK3CG PIK3CG PIK3CG 1455 0.36 0.29 YES
6 PIK3R5 PIK3R5 PIK3R5 1567 0.34 0.33 YES
7 LEF1 LEF1 LEF1 2100 0.28 0.33 YES
8 SPI1 SPI1 SPI1 2139 0.27 0.37 YES
9 PIK3CD PIK3CD PIK3CD 2163 0.27 0.4 YES
10 TCF7L1 TCF7L1 TCF7L1 2487 0.24 0.42 YES
11 KIT KIT KIT 2561 0.23 0.44 YES
12 FLT3 FLT3 FLT3 2647 0.22 0.47 YES
13 PIK3CA PIK3CA PIK3CA 3142 0.18 0.46 YES
14 PIM1 PIM1 PIM1 3183 0.18 0.48 YES
15 RUNX1 RUNX1 RUNX1 3796 0.14 0.47 NO
16 SOS2 SOS2 SOS2 4099 0.13 0.47 NO
17 SOS1 SOS1 SOS1 4575 0.11 0.46 NO
18 BRAF BRAF BRAF 5099 0.098 0.44 NO
19 PIK3R1 PIK3R1 PIK3R1 5574 0.085 0.43 NO
20 PIK3R3 PIK3R3 PIK3R3 5593 0.084 0.44 NO
21 RPS6KB1 RPS6KB1 RPS6KB1 5631 0.083 0.44 NO
22 CCND1 CCND1 CCND1 6399 0.066 0.41 NO
23 KRAS KRAS KRAS 6580 0.062 0.41 NO
24 STAT5B STAT5B STAT5B 6690 0.06 0.41 NO
25 PIK3CB PIK3CB PIK3CB 6898 0.056 0.41 NO
26 NRAS NRAS NRAS 6951 0.056 0.41 NO
27 RARA RARA RARA 7288 0.049 0.4 NO
28 MAP2K1 MAP2K1 MAP2K1 7482 0.046 0.39 NO
29 MAPK1 MAPK1 MAPK1 7616 0.043 0.39 NO
30 STAT5A STAT5A STAT5A 7954 0.038 0.38 NO
31 IKBKB IKBKB IKBKB 8179 0.034 0.37 NO
32 STAT3 STAT3 STAT3 8346 0.031 0.37 NO
33 NFKB1 NFKB1 NFKB1 8473 0.029 0.36 NO
34 CHUK CHUK CHUK 8569 0.028 0.36 NO
35 TCF7 TCF7 TCF7 8941 0.021 0.34 NO
36 GRB2 GRB2 GRB2 8992 0.02 0.34 NO
37 PML PML PML 9130 0.018 0.34 NO
38 RELA RELA RELA 9233 0.016 0.33 NO
39 MTOR MTOR MTOR 9823 0.006 0.3 NO
40 RAF1 RAF1 RAF1 10109 0.0014 0.29 NO
41 TCF7L2 TCF7L2 TCF7L2 10507 -0.0054 0.26 NO
42 AKT1 AKT1 AKT1 11433 -0.022 0.22 NO
43 AKT2 AKT2 AKT2 11925 -0.03 0.19 NO
44 PIM2 PIM2 PIM2 12227 -0.035 0.18 NO
45 IKBKG IKBKG IKBKG 12339 -0.038 0.18 NO
46 MAPK3 MAPK3 MAPK3 12556 -0.042 0.17 NO
47 JUP JUP JUP 13228 -0.055 0.14 NO
48 MYC MYC MYC 14032 -0.074 0.11 NO
49 PIK3R2 PIK3R2 PIK3R2 14099 -0.075 0.12 NO
50 CEBPA CEBPA CEBPA 14215 -0.078 0.12 NO
51 BAD BAD BAD 14823 -0.097 0.098 NO
52 HRAS HRAS HRAS 14840 -0.097 0.11 NO
53 MAP2K2 MAP2K2 MAP2K2 15004 -0.1 0.11 NO
54 ARAF ARAF ARAF 15092 -0.11 0.12 NO
55 RPS6KB2 RPS6KB2 RPS6KB2 16063 -0.15 0.089 NO
56 EIF4EBP1 EIF4EBP1 EIF4EBP1 16515 -0.18 0.087 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: BIOCARTA GH PATHWAY.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.55 1.6 0.058 0.27 0.63 0.48 0.28 0.35 0.13 0.057
BIOCARTA HDAC PATHWAY 26 genes.ES.table 0.57 1.7 0.015 0.25 0.57 0.58 0.34 0.38 0.1 0.052
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.5 1.7 0.017 0.24 0.46 0.57 0.35 0.37 0 0.053
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.53 1.6 0.049 0.29 0.72 0.6 0.34 0.39 0.16 0.058
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.4 1.9 0.0099 0.29 0.16 0.49 0.36 0.31 0 0.089
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.43 1.7 0.017 0.27 0.44 0.53 0.32 0.36 0 0.064
BIOCARTA KERATINOCYTE PATHWAY 45 genes.ES.table 0.48 1.8 0.0085 0.25 0.35 0.49 0.29 0.35 0 0.061
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.47 1.9 0.0042 0.25 0.2 0.67 0.42 0.39 0 0.08
BIOCARTA PPARA PATHWAY 55 genes.ES.table 0.5 1.8 0.0022 0.22 0.36 0.62 0.32 0.42 0 0.047
BIOCARTA VIP PATHWAY 25 genes.ES.table 0.59 1.7 0.0086 0.25 0.55 0.6 0.28 0.43 0.1 0.057
genes ES table in pathway: BIOCARTA BCR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PIK3CG PIK3CG PIK3CG 200 0.52 0.099 YES
2 PLCE1 PLCE1 PLCE1 651 0.34 0.14 YES
3 PLCG2 PLCG2 PLCG2 968 0.27 0.18 YES
4 ITPKA ITPKA ITPKA 1067 0.25 0.23 YES
5 IPMK IPMK IPMK 1339 0.21 0.26 YES
6 IMPA1 IMPA1 IMPA1 1438 0.2 0.3 YES
7 SYNJ1 SYNJ1 SYNJ1 1520 0.19 0.33 YES
8 PIK3CD PIK3CD PIK3CD 1989 0.16 0.34 YES
9 PIP5K1B PIP5K1B PIP5K1B 2089 0.15 0.37 YES
10 PLCB1 PLCB1 PLCB1 2466 0.13 0.37 YES
11 PIKFYVE PIKFYVE PIKFYVE 2733 0.12 0.38 YES
12 INPP1 INPP1 INPP1 2916 0.12 0.4 YES
13 ALDH6A1 ALDH6A1 ALDH6A1 3289 0.1 0.4 YES
14 PLCD3 PLCD3 PLCD3 3393 0.1 0.41 YES
15 SYNJ2 SYNJ2 SYNJ2 3631 0.094 0.42 YES
16 PIK3CA PIK3CA PIK3CA 3678 0.093 0.44 YES
17 PIP4K2A PIP4K2A PIP4K2A 3907 0.087 0.44 YES
18 PIK3C2A PIK3C2A PIK3C2A 3932 0.086 0.46 YES
19 PIK3C3 PIK3C3 PIK3C3 4101 0.083 0.47 YES
20 PLCD1 PLCD1 PLCD1 4303 0.078 0.47 YES
21 PTEN PTEN PTEN 4332 0.078 0.49 YES
22 PIK3CB PIK3CB PIK3CB 4437 0.076 0.5 YES
23 MINPP1 MINPP1 MINPP1 5230 0.06 0.47 NO
24 PIP4K2C PIP4K2C PIP4K2C 5562 0.055 0.46 NO
25 INPP4B INPP4B INPP4B 5759 0.051 0.46 NO
26 PIK3C2B PIK3C2B PIK3C2B 5870 0.05 0.46 NO
27 PLCB4 PLCB4 PLCB4 5998 0.048 0.47 NO
28 PLCB2 PLCB2 PLCB2 6110 0.046 0.47 NO
29 IMPA2 IMPA2 IMPA2 6396 0.041 0.46 NO
30 PI4KA PI4KA PI4KA 6433 0.041 0.47 NO
31 ITPKB ITPKB ITPKB 6861 0.034 0.45 NO
32 PIP5K1A PIP5K1A PIP5K1A 6942 0.033 0.46 NO
33 INPP4A INPP4A INPP4A 7320 0.027 0.44 NO
34 IPPK IPPK IPPK 7763 0.02 0.42 NO
35 PI4KB PI4KB PI4KB 8029 0.017 0.41 NO
36 INPP5A INPP5A INPP5A 8240 0.014 0.4 NO
37 ITPK1 ITPK1 ITPK1 8493 0.01 0.39 NO
38 PLCB3 PLCB3 PLCB3 8558 0.0093 0.39 NO
39 INPP5K INPP5K INPP5K 9135 0.0015 0.35 NO
40 PIP4K2B PIP4K2B PIP4K2B 9902 -0.01 0.31 NO
41 OCRL OCRL OCRL 9961 -0.011 0.31 NO
42 PLCD4 PLCD4 PLCD4 10013 -0.012 0.31 NO
43 INPPL1 INPPL1 INPPL1 10483 -0.018 0.29 NO
44 PIP5K1C PIP5K1C PIP5K1C 11370 -0.032 0.25 NO
45 INPP5J INPP5J INPP5J 11951 -0.041 0.22 NO
46 PLCG1 PLCG1 PLCG1 12207 -0.046 0.22 NO
47 INPP5B INPP5B INPP5B 12231 -0.046 0.23 NO
48 TPI1 TPI1 TPI1 12790 -0.057 0.21 NO
49 CDIPT CDIPT CDIPT 13076 -0.062 0.21 NO
50 MIOX MIOX MIOX 14112 -0.087 0.17 NO
51 INPP5E INPP5E INPP5E 15200 -0.12 0.13 NO
52 ISYNA1 ISYNA1 ISYNA1 15385 -0.13 0.15 NO

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

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

genes ES table in pathway: BIOCARTA HDAC PATHWAY

Table 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 FAS FAS FAS 913 0.28 0.03 YES
2 BIRC3 BIRC3 BIRC3 1254 0.22 0.076 YES
3 CASP7 CASP7 CASP7 1280 0.22 0.14 YES
4 BCL2 BCL2 BCL2 1408 0.21 0.19 YES
5 GSN GSN GSN 2199 0.14 0.19 YES
6 CHUK CHUK CHUK 2745 0.12 0.19 YES
7 MAP3K5 MAP3K5 MAP3K5 3340 0.1 0.19 YES
8 PSEN1 PSEN1 PSEN1 3482 0.098 0.21 YES
9 MAP3K1 MAP3K1 MAP3K1 3605 0.095 0.23 YES
10 APAF1 APAF1 APAF1 3628 0.094 0.26 YES
11 CASP3 CASP3 CASP3 4027 0.085 0.26 YES
12 BIRC2 BIRC2 BIRC2 4162 0.081 0.27 YES
13 MAP3K14 MAP3K14 MAP3K14 4442 0.076 0.28 YES
14 RB1 RB1 RB1 4451 0.076 0.3 YES
15 NFKB1 NFKB1 NFKB1 4759 0.069 0.3 YES
16 RIPK1 RIPK1 RIPK1 4818 0.067 0.32 YES
17 CASP8 CASP8 CASP8 4831 0.067 0.34 YES
18 XIAP XIAP XIAP 5008 0.064 0.35 YES
19 MAPK8 MAPK8 MAPK8 5067 0.063 0.36 YES
20 CFLAR CFLAR CFLAR 5210 0.06 0.37 YES
21 RASA1 RASA1 RASA1 5293 0.059 0.38 YES
22 SPTAN1 SPTAN1 SPTAN1 5725 0.052 0.38 YES
23 CYCS CYCS CYCS 5760 0.051 0.39 YES
24 PAK2 PAK2 PAK2 6065 0.047 0.38 YES
25 MDM2 MDM2 MDM2 6361 0.042 0.38 YES
26 BAG4 BAG4 BAG4 6474 0.04 0.39 YES
27 TRAF1 TRAF1 TRAF1 6507 0.04 0.4 YES
28 CASP9 CASP9 CASP9 6601 0.038 0.4 YES
29 TNFRSF1B TNFRSF1B TNFRSF1B 7368 0.026 0.37 NO
30 PARP1 PARP1 PARP1 7513 0.024 0.37 NO
31 CRADD CRADD CRADD 7701 0.022 0.36 NO
32 PRKDC PRKDC PRKDC 7926 0.018 0.35 NO
33 MAP2K7 MAP2K7 MAP2K7 7967 0.017 0.36 NO
34 DAXX DAXX DAXX 8040 0.016 0.36 NO
35 PRKCD PRKCD PRKCD 8131 0.015 0.36 NO
36 TNF TNF TNF 8213 0.014 0.36 NO
37 TNFRSF1A TNFRSF1A TNFRSF1A 8226 0.014 0.36 NO
38 NUMA1 NUMA1 NUMA1 8420 0.011 0.35 NO
39 CASP6 CASP6 CASP6 8605 0.0086 0.34 NO
40 ARHGDIB ARHGDIB ARHGDIB 9186 0.0008 0.31 NO
41 CASP2 CASP2 CASP2 9331 -0.0013 0.3 NO
42 LMNA LMNA LMNA 9458 -0.0031 0.3 NO
43 LMNB1 LMNB1 LMNB1 9862 -0.0095 0.28 NO
44 CDK11B CDK11B CDK11B 10085 -0.013 0.27 NO
45 LMNB2 LMNB2 LMNB2 10104 -0.013 0.27 NO
46 TRAF2 TRAF2 TRAF2 10284 -0.016 0.27 NO
47 PTK2 PTK2 PTK2 10389 -0.017 0.27 NO
48 RELA RELA RELA 10621 -0.02 0.26 NO
49 PSEN2 PSEN2 PSEN2 10762 -0.022 0.26 NO
50 NFKBIA NFKBIA NFKBIA 10972 -0.026 0.26 NO
51 CDK11A CDK11A CDK11A 11534 -0.035 0.23 NO
52 ACTG1 ACTG1 ACTG1 12010 -0.042 0.22 NO
53 DFFA DFFA DFFA 12205 -0.046 0.22 NO
54 FADD FADD FADD 12867 -0.058 0.2 NO
55 DFFB DFFB DFFB 14078 -0.086 0.16 NO
56 BID BID BID 14446 -0.096 0.17 NO
57 TRADD TRADD TRADD 15115 -0.12 0.16 NO

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

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

genes ES table in pathway: BIOCARTA EGF PATHWAY

Table 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 PRKCB PRKCB PRKCB 507 0.38 0.19 YES
2 PTK2B PTK2B PTK2B 1671 0.18 0.23 YES
3 GNAQ GNAQ GNAQ 2508 0.13 0.26 YES
4 SOS1 SOS1 SOS1 3531 0.096 0.26 YES
5 MAP3K1 MAP3K1 MAP3K1 3605 0.095 0.31 YES
6 PRKCA PRKCA PRKCA 3679 0.093 0.36 YES
7 MAPK3 MAPK3 MAPK3 4650 0.071 0.34 YES
8 CALM2 CALM2 CALM2 4913 0.066 0.36 YES
9 MAP2K1 MAP2K1 MAP2K1 4988 0.064 0.4 YES
10 MAPK8 MAPK8 MAPK8 5067 0.063 0.43 YES
11 MAPK1 MAPK1 MAPK1 5534 0.055 0.44 YES
12 PAK1 PAK1 PAK1 5919 0.049 0.44 YES
13 MAPK14 MAPK14 MAPK14 6186 0.044 0.45 YES
14 CALM1 CALM1 CALM1 6689 0.037 0.45 YES
15 GRB2 GRB2 GRB2 6983 0.032 0.45 YES
16 SHC1 SHC1 SHC1 7007 0.032 0.46 YES
17 CRKL CRKL CRKL 7322 0.027 0.46 YES
18 MAP2K4 MAP2K4 MAP2K4 7518 0.024 0.47 YES
19 SRC SRC SRC 8149 0.015 0.44 NO
20 RAF1 RAF1 RAF1 8377 0.012 0.43 NO
21 CALM3 CALM3 CALM3 8595 0.0088 0.43 NO
22 RAC1 RAC1 RAC1 9404 -0.0024 0.38 NO
23 MAP2K3 MAP2K3 MAP2K3 9486 -0.0036 0.38 NO
24 BCAR1 BCAR1 BCAR1 9906 -0.01 0.36 NO
25 MAP2K2 MAP2K2 MAP2K2 11467 -0.034 0.3 NO
26 PLCG1 PLCG1 PLCG1 12207 -0.046 0.28 NO
27 JUN JUN JUN 13628 -0.075 0.25 NO

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

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TUSC3 TUSC3 TUSC3 725 0.32 0.065 YES
2 MGAT5 MGAT5 MGAT5 1523 0.19 0.085 YES
3 MGAT3 MGAT3 MGAT3 1598 0.19 0.14 YES
4 MAN2A1 MAN2A1 MAN2A1 1630 0.19 0.2 YES
5 MAN1A2 MAN1A2 MAN1A2 1631 0.19 0.26 YES
6 MGAT4A MGAT4A MGAT4A 2101 0.15 0.29 YES
7 ALG11 ALG11 ALG11 2104 0.15 0.34 YES
8 MAN1A1 MAN1A1 MAN1A1 2410 0.14 0.36 YES
9 MAN1C1 MAN1C1 MAN1C1 3201 0.11 0.36 YES
10 ALG6 ALG6 ALG6 3440 0.099 0.38 YES
11 ST6GAL1 ST6GAL1 ST6GAL1 4148 0.082 0.36 YES
12 DOLPP1 DOLPP1 DOLPP1 4185 0.081 0.39 YES
13 B4GALT1 B4GALT1 B4GALT1 4283 0.079 0.41 YES
14 MGAT2 MGAT2 MGAT2 5372 0.057 0.37 NO
15 ALG10 ALG10 ALG10 5424 0.057 0.38 NO
16 ALG10B ALG10B ALG10B 5790 0.051 0.38 NO
17 ALG14 ALG14 ALG14 6084 0.046 0.38 NO
18 STT3B STT3B STT3B 6273 0.043 0.38 NO
19 ALG5 ALG5 ALG5 6323 0.043 0.4 NO
20 MAN2A2 MAN2A2 MAN2A2 7145 0.03 0.36 NO
21 ALG13 ALG13 ALG13 7775 0.02 0.33 NO
22 ALG2 ALG2 ALG2 7791 0.02 0.34 NO
23 STT3A STT3A STT3A 8441 0.011 0.3 NO
24 ALG8 ALG8 ALG8 8840 0.0054 0.28 NO
25 DPM1 DPM1 DPM1 9422 -0.0026 0.25 NO
26 GANAB GANAB GANAB 9513 -0.0041 0.25 NO
27 FUT8 FUT8 FUT8 9669 -0.0064 0.24 NO
28 MOGS MOGS MOGS 9693 -0.0067 0.24 NO
29 B4GALT3 B4GALT3 B4GALT3 9757 -0.0076 0.24 NO
30 ALG1 ALG1 ALG1 10627 -0.02 0.2 NO
31 MGAT1 MGAT1 MGAT1 10637 -0.021 0.21 NO
32 RPN2 RPN2 RPN2 10669 -0.021 0.21 NO
33 ALG9 ALG9 ALG9 10832 -0.024 0.21 NO
34 MGAT4B MGAT4B MGAT4B 10836 -0.024 0.22 NO
35 DAD1 DAD1 DAD1 10910 -0.025 0.22 NO
36 DDOST DDOST DDOST 11022 -0.026 0.23 NO
37 MAN1B1 MAN1B1 MAN1B1 11029 -0.026 0.23 NO
38 DPAGT1 DPAGT1 DPAGT1 11499 -0.034 0.22 NO
39 RPN1 RPN1 RPN1 11786 -0.039 0.22 NO
40 MGAT5B MGAT5B MGAT5B 12247 -0.047 0.21 NO
41 ALG12 ALG12 ALG12 12823 -0.058 0.19 NO
42 B4GALT2 B4GALT2 B4GALT2 13093 -0.063 0.2 NO
43 ALG3 ALG3 ALG3 13649 -0.075 0.19 NO
44 DPM2 DPM2 DPM2 13650 -0.075 0.22 NO
45 DPM3 DPM3 DPM3 13979 -0.083 0.23 NO

Figure S27.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

Table 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 PIK3CG PIK3CG PIK3CG 200 0.52 0.15 YES
2 MAP4K1 MAP4K1 MAP4K1 930 0.28 0.19 YES
3 HGF HGF HGF 1029 0.26 0.26 YES
4 PTK2B PTK2B PTK2B 1671 0.18 0.28 YES
5 GAB1 GAB1 GAB1 1812 0.17 0.32 YES
6 ITGA1 ITGA1 ITGA1 2655 0.12 0.32 YES
7 RAP1A RAP1A RAP1A 2683 0.12 0.35 YES
8 SOS1 SOS1 SOS1 3531 0.096 0.33 YES
9 PIK3CA PIK3CA PIK3CA 3678 0.093 0.35 YES
10 DOCK1 DOCK1 DOCK1 4222 0.08 0.35 YES
11 PTEN PTEN PTEN 4332 0.078 0.36 YES
12 STAT3 STAT3 STAT3 4390 0.077 0.38 YES
13 MAPK3 MAPK3 MAPK3 4650 0.071 0.39 YES
14 RAPGEF1 RAPGEF1 RAPGEF1 4652 0.071 0.41 YES
15 CRK CRK CRK 4716 0.07 0.43 YES
16 MAP2K1 MAP2K1 MAP2K1 4988 0.064 0.44 YES
17 MAPK8 MAPK8 MAPK8 5067 0.063 0.45 YES
18 RASA1 RASA1 RASA1 5293 0.059 0.46 YES
19 MAPK1 MAPK1 MAPK1 5534 0.055 0.46 YES
20 PIK3R1 PIK3R1 PIK3R1 5695 0.053 0.47 YES
21 RAP1B RAP1B RAP1B 5811 0.05 0.47 YES
22 PTPN11 PTPN11 PTPN11 5899 0.049 0.48 YES
23 PAK1 PAK1 PAK1 5919 0.049 0.5 YES
24 PXN PXN PXN 5987 0.048 0.51 YES
25 FOS FOS FOS 6146 0.045 0.51 YES
26 ITGB1 ITGB1 ITGB1 6747 0.036 0.49 NO
27 GRB2 GRB2 GRB2 6983 0.032 0.49 NO
28 CRKL CRKL CRKL 7322 0.027 0.48 NO
29 SRC SRC SRC 8149 0.015 0.44 NO
30 MET MET MET 8219 0.014 0.44 NO
31 RAF1 RAF1 RAF1 8377 0.012 0.43 NO
32 PTK2 PTK2 PTK2 10389 -0.017 0.32 NO
33 MAP2K2 MAP2K2 MAP2K2 11467 -0.034 0.28 NO
34 ELK1 ELK1 ELK1 11878 -0.04 0.26 NO
35 JUN JUN JUN 13628 -0.075 0.19 NO
36 ACTA1 ACTA1 ACTA1 16304 -0.19 0.099 NO

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

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

genes ES table in pathway: BIOCARTA DEATH PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 507 0.38 0.071 YES
2 FAS FAS FAS 913 0.28 0.12 YES
3 FASLG FASLG FASLG 1019 0.26 0.18 YES
4 BCL2 BCL2 BCL2 1408 0.21 0.22 YES
5 EGFR EGFR EGFR 1719 0.18 0.25 YES
6 ETS1 ETS1 ETS1 1969 0.16 0.28 YES
7 HOXA7 HOXA7 HOXA7 2032 0.16 0.31 YES
8 EGF EGF EGF 2289 0.14 0.34 YES
9 CHUK CHUK CHUK 2745 0.12 0.34 YES
10 PRKCH PRKCH PRKCH 2773 0.12 0.37 YES
11 MAP3K5 MAP3K5 MAP3K5 3340 0.1 0.37 YES
12 MAP3K1 MAP3K1 MAP3K1 3605 0.095 0.38 YES
13 PRKCA PRKCA PRKCA 3679 0.093 0.4 YES
14 PRKCE PRKCE PRKCE 3935 0.086 0.41 YES
15 MAP3K14 MAP3K14 MAP3K14 4442 0.076 0.4 YES
16 MAP2K6 MAP2K6 MAP2K6 4525 0.074 0.41 YES
17 MAPK3 MAPK3 MAPK3 4650 0.071 0.42 YES
18 NFKB1 NFKB1 NFKB1 4759 0.069 0.44 YES
19 RIPK1 RIPK1 RIPK1 4818 0.067 0.45 YES
20 MAP2K1 MAP2K1 MAP2K1 4988 0.064 0.46 YES
21 MAPK8 MAPK8 MAPK8 5067 0.063 0.47 YES
22 SP1 SP1 SP1 5189 0.061 0.48 YES
23 MAPK1 MAPK1 MAPK1 5534 0.055 0.48 NO
24 FOS FOS FOS 6146 0.045 0.45 NO
25 MAPK14 MAPK14 MAPK14 6186 0.044 0.46 NO
26 MAPK13 MAPK13 MAPK13 6252 0.044 0.47 NO
27 TNFRSF1B TNFRSF1B TNFRSF1B 7368 0.026 0.42 NO
28 MAP2K4 MAP2K4 MAP2K4 7518 0.024 0.41 NO
29 MAP2K7 MAP2K7 MAP2K7 7967 0.017 0.39 NO
30 DAXX DAXX DAXX 8040 0.016 0.39 NO
31 PRKCD PRKCD PRKCD 8131 0.015 0.39 NO
32 TNF TNF TNF 8213 0.014 0.39 NO
33 TNFRSF1A TNFRSF1A TNFRSF1A 8226 0.014 0.4 NO
34 RAF1 RAF1 RAF1 8377 0.012 0.39 NO
35 CEBPA CEBPA CEBPA 9316 -0.0011 0.34 NO
36 MAP2K3 MAP2K3 MAP2K3 9486 -0.0036 0.33 NO
37 ETS2 ETS2 ETS2 9699 -0.0068 0.32 NO
38 PPP2CA PPP2CA PPP2CA 9803 -0.0084 0.32 NO
39 IKBKB IKBKB IKBKB 9979 -0.011 0.31 NO
40 RELA RELA RELA 10621 -0.02 0.28 NO
41 NFKBIA NFKBIA NFKBIA 10972 -0.026 0.27 NO
42 PRKCQ PRKCQ PRKCQ 12509 -0.051 0.2 NO
43 JUN JUN JUN 13628 -0.075 0.15 NO
44 HRAS HRAS HRAS 15203 -0.12 0.098 NO
45 PRKCG PRKCG PRKCG 16873 -0.24 0.067 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: BIOCARTA DEATH PATHWAY.

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

genes ES table in pathway: BIOCARTA KERATINOCYTE PATHWAY

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 PIK3CG PIK3CG PIK3CG 200 0.52 0.074 YES
2 PRKAR2B PRKAR2B PRKAR2B 403 0.42 0.13 YES
3 PRKCB PRKCB PRKCB 507 0.38 0.19 YES
4 PPARGC1A PPARGC1A PPARGC1A 512 0.38 0.25 YES
5 CD36 CD36 CD36 532 0.37 0.31 YES
6 NOS2 NOS2 NOS2 554 0.36 0.36 YES
7 PRKACB PRKACB PRKACB 951 0.27 0.39 YES
8 FABP1 FABP1 FABP1 1735 0.18 0.37 YES
9 CITED2 CITED2 CITED2 2395 0.14 0.36 YES
10 EHHADH EHHADH EHHADH 2428 0.13 0.38 YES
11 PDGFA PDGFA PDGFA 2763 0.12 0.38 YES
12 PTGS2 PTGS2 PTGS2 2791 0.12 0.4 YES
13 NRIP1 NRIP1 NRIP1 2930 0.11 0.41 YES
14 NCOA1 NCOA1 NCOA1 3124 0.11 0.41 YES
15 PIK3CA PIK3CA PIK3CA 3678 0.093 0.4 YES
16 PRKCA PRKCA PRKCA 3679 0.093 0.41 YES
17 FAT1 FAT1 FAT1 3838 0.089 0.42 YES
18 PPARA PPARA PPARA 3918 0.087 0.43 YES
19 MED1 MED1 MED1 3951 0.086 0.44 YES
20 ME1 ME1 ME1 3985 0.086 0.45 YES
21 NR0B2 NR0B2 NR0B2 4120 0.083 0.46 YES
22 EP300 EP300 EP300 4337 0.078 0.46 YES
23 NCOR1 NCOR1 NCOR1 4381 0.077 0.47 YES
24 RB1 RB1 RB1 4451 0.076 0.48 YES
25 MAPK3 MAPK3 MAPK3 4650 0.071 0.48 YES
26 PRKAR1A PRKAR1A PRKAR1A 4987 0.064 0.47 YES
27 PRKAR2A PRKAR2A PRKAR2A 5104 0.062 0.47 YES
28 RXRA RXRA RXRA 5139 0.062 0.48 YES
29 SP1 SP1 SP1 5189 0.061 0.49 YES
30 CREBBP CREBBP CREBBP 5439 0.056 0.48 YES
31 HSD17B4 HSD17B4 HSD17B4 5441 0.056 0.49 YES
32 MAPK1 MAPK1 MAPK1 5534 0.055 0.5 YES
33 PRKACG PRKACG PRKACG 5657 0.053 0.5 YES
34 PIK3R1 PIK3R1 PIK3R1 5695 0.053 0.5 YES
35 HSP90AA1 HSP90AA1 HSP90AA1 7464 0.025 0.41 NO
36 DUSP1 DUSP1 DUSP1 7814 0.02 0.4 NO
37 STAT5B STAT5B STAT5B 8098 0.016 0.38 NO
38 TNF TNF TNF 8213 0.014 0.38 NO
39 HSPA1A HSPA1A HSPA1A 8650 0.0081 0.35 NO
40 MYC MYC MYC 9940 -0.011 0.28 NO
41 APOA1 APOA1 APOA1 10053 -0.013 0.28 NO
42 NCOR2 NCOR2 NCOR2 10089 -0.013 0.28 NO
43 STAT5A STAT5A STAT5A 10425 -0.018 0.26 NO
44 RELA RELA RELA 10621 -0.02 0.26 NO
45 NFKBIA NFKBIA NFKBIA 10972 -0.026 0.24 NO
46 NR2F1 NR2F1 NR2F1 12386 -0.049 0.17 NO
47 PRKAR1B PRKAR1B PRKAR1B 13082 -0.063 0.14 NO
48 SRA1 SRA1 SRA1 13627 -0.075 0.12 NO
49 JUN JUN JUN 13628 -0.075 0.14 NO
50 NR1H3 NR1H3 NR1H3 13993 -0.083 0.13 NO
51 LPL LPL LPL 14431 -0.096 0.12 NO
52 MRPL11 MRPL11 MRPL11 14472 -0.097 0.14 NO
53 DUT DUT DUT 14727 -0.1 0.14 NO
54 APOA2 APOA2 APOA2 15026 -0.12 0.14 NO
55 CPT1B CPT1B CPT1B 16203 -0.18 0.1 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: BIOCARTA KERATINOCYTE PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 PATHWAY

Table 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 BIRC3 BIRC3 BIRC3 1254 0.22 0.019 YES
2 CASP7 CASP7 CASP7 1280 0.22 0.1 YES
3 BCL2 BCL2 BCL2 1408 0.21 0.18 YES
4 CASP10 CASP10 CASP10 1558 0.19 0.24 YES
5 TNFSF10 TNFSF10 TNFSF10 1780 0.17 0.3 YES
6 CHUK CHUK CHUK 2745 0.12 0.3 YES
7 APAF1 APAF1 APAF1 3628 0.094 0.28 YES
8 CASP3 CASP3 CASP3 4027 0.085 0.29 YES
9 BIRC2 BIRC2 BIRC2 4162 0.081 0.32 YES
10 MAP3K14 MAP3K14 MAP3K14 4442 0.076 0.33 YES
11 NFKB1 NFKB1 NFKB1 4759 0.069 0.34 YES
12 RIPK1 RIPK1 RIPK1 4818 0.067 0.37 YES
13 CASP8 CASP8 CASP8 4831 0.067 0.39 YES
14 XIAP XIAP XIAP 5008 0.064 0.41 YES
15 CFLAR CFLAR CFLAR 5210 0.06 0.42 YES
16 SPTAN1 SPTAN1 SPTAN1 5725 0.052 0.41 YES
17 CYCS CYCS CYCS 5760 0.051 0.43 YES
18 CASP9 CASP9 CASP9 6601 0.038 0.4 NO
19 TNFRSF10A TNFRSF10A TNFRSF10A 7959 0.018 0.33 NO
20 CASP6 CASP6 CASP6 8605 0.0086 0.3 NO
21 TNFRSF10B TNFRSF10B TNFRSF10B 9272 -0.00059 0.26 NO
22 LMNA LMNA LMNA 9458 -0.0031 0.25 NO
23 TRAF2 TRAF2 TRAF2 10284 -0.016 0.21 NO
24 RELA RELA RELA 10621 -0.02 0.2 NO
25 TNFSF12 TNFSF12 TNFSF12 10680 -0.021 0.21 NO
26 NFKBIA NFKBIA NFKBIA 10972 -0.026 0.2 NO
27 DFFA DFFA DFFA 12205 -0.046 0.15 NO
28 TNFRSF25 TNFRSF25 TNFRSF25 12682 -0.054 0.15 NO
29 FADD FADD FADD 12867 -0.058 0.16 NO
30 DFFB DFFB DFFB 14078 -0.086 0.13 NO
31 TRADD TRADD TRADD 15115 -0.12 0.12 NO
32 GAS2 GAS2 GAS2 15236 -0.12 0.16 NO

Figure S35.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PYK2 PATHWAY.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA PPARA PATHWAY

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 PRKAR2B PRKAR2B PRKAR2B 403 0.42 0.14 YES
2 PRKCB PRKCB PRKCB 507 0.38 0.27 YES
3 PRKACB PRKACB PRKACB 951 0.27 0.35 YES
4 RPS6KA5 RPS6KA5 RPS6KA5 1248 0.22 0.42 YES
5 CAMK2D CAMK2D CAMK2D 2593 0.13 0.39 YES
6 SOS1 SOS1 SOS1 3531 0.096 0.38 YES
7 PIK3CA PIK3CA PIK3CA 3678 0.093 0.4 YES
8 PRKCA PRKCA PRKCA 3679 0.093 0.44 YES
9 CAMK2B CAMK2B CAMK2B 4075 0.084 0.45 YES
10 MAPK3 MAPK3 MAPK3 4650 0.071 0.44 YES
11 PRKAR1A PRKAR1A PRKAR1A 4987 0.064 0.45 YES
12 CREB1 CREB1 CREB1 5069 0.063 0.47 YES
13 PRKAR2A PRKAR2A PRKAR2A 5104 0.062 0.49 YES
14 MAPK1 MAPK1 MAPK1 5534 0.055 0.49 YES
15 PRKACG PRKACG PRKACG 5657 0.053 0.5 YES
16 PIK3R1 PIK3R1 PIK3R1 5695 0.053 0.52 YES
17 CAMK2A CAMK2A CAMK2A 5717 0.052 0.54 YES
18 MAPK14 MAPK14 MAPK14 6186 0.044 0.53 NO
19 RPS6KA1 RPS6KA1 RPS6KA1 6636 0.038 0.52 NO
20 GRB2 GRB2 GRB2 6983 0.032 0.51 NO
21 CAMK2G CAMK2G CAMK2G 8847 0.0053 0.41 NO
22 RAC1 RAC1 RAC1 9404 -0.0024 0.38 NO
23 AKT1 AKT1 AKT1 9581 -0.005 0.37 NO
24 PRKAR1B PRKAR1B PRKAR1B 13082 -0.063 0.2 NO
25 GNAS GNAS GNAS 13560 -0.073 0.2 NO
26 HRAS HRAS HRAS 15203 -0.12 0.16 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: BIOCARTA PPARA PATHWAY.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PPARA 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 VIP PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 507 0.38 0.14 YES
2 STAT4 STAT4 STAT4 1264 0.22 0.2 YES
3 EGFR EGFR EGFR 1719 0.18 0.26 YES
4 EGF EGF EGF 2289 0.14 0.29 YES
5 SOS1 SOS1 SOS1 3531 0.096 0.27 YES
6 MAP3K1 MAP3K1 MAP3K1 3605 0.095 0.31 YES
7 PIK3CA PIK3CA PIK3CA 3678 0.093 0.35 YES
8 PRKCA PRKCA PRKCA 3679 0.093 0.39 YES
9 JAK1 JAK1 JAK1 3850 0.088 0.42 YES
10 STAT3 STAT3 STAT3 4390 0.077 0.42 YES
11 MAPK3 MAPK3 MAPK3 4650 0.071 0.44 YES
12 MAP2K1 MAP2K1 MAP2K1 4988 0.064 0.45 YES
13 MAPK8 MAPK8 MAPK8 5067 0.063 0.48 YES
14 RASA1 RASA1 RASA1 5293 0.059 0.49 YES
15 PIK3R1 PIK3R1 PIK3R1 5695 0.053 0.49 YES
16 FOS FOS FOS 6146 0.045 0.49 YES
17 STAT1 STAT1 STAT1 6272 0.043 0.5 YES
18 GRB2 GRB2 GRB2 6983 0.032 0.48 NO
19 SHC1 SHC1 SHC1 7007 0.032 0.49 NO
20 MAP2K4 MAP2K4 MAP2K4 7518 0.024 0.47 NO
21 STAT5B STAT5B STAT5B 8098 0.016 0.45 NO
22 SRF SRF SRF 8329 0.012 0.44 NO
23 RAF1 RAF1 RAF1 8377 0.012 0.44 NO
24 CSNK2A1 CSNK2A1 CSNK2A1 8395 0.012 0.45 NO
25 STAT2 STAT2 STAT2 8545 0.0094 0.44 NO
26 STAT6 STAT6 STAT6 9477 -0.0035 0.4 NO
27 STAT5A STAT5A STAT5A 10425 -0.018 0.35 NO
28 ELK1 ELK1 ELK1 11878 -0.04 0.29 NO
29 PLCG1 PLCG1 PLCG1 12207 -0.046 0.29 NO
30 JUN JUN JUN 13628 -0.075 0.25 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: BIOCARTA VIP PATHWAY.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA FAS PATHWAY 29 genes.ES.table 0.48 1.6 0.048 0.65 0.68 0.59 0.33 0.39 0.33 0.21
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.24 1.1 0.33 1 1 0.44 0.32 0.3 1 0.8
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.25 1.1 0.39 1 1 1 0.75 0.25 1 0.79
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.27 1.1 0.36 1 1 1 0.73 0.27 1 0.76
BIOCARTA TNFR1 PATHWAY 28 genes.ES.table 0.31 1.2 0.21 1 1 0.61 0.34 0.4 1 0.68
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.26 0.94 0.52 1 1 0.46 0.26 0.35 1 0.82
KEGG O GLYCAN BIOSYNTHESIS 28 genes.ES.table 0.37 0.96 0.53 1 1 0.39 0.12 0.34 1 0.85
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES 25 genes.ES.table 0.33 0.92 0.58 1 1 0.32 0.1 0.29 1 0.77
KEGG PROPANOATE METABOLISM 31 genes.ES.table 0.32 1 0.44 1 1 0.48 0.26 0.36 1 0.74
KEGG BUTANOATE METABOLISM 29 genes.ES.table 0.29 0.87 0.63 1 1 0.17 0.087 0.16 1 0.85
genes ES table in pathway: BIOCARTA FAS PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 EPRS EPRS EPRS 2056 0.095 -0.051 YES
2 DARS2 DARS2 DARS2 2199 0.091 0.00097 YES
3 NARS NARS NARS 2296 0.088 0.054 YES
4 SEPSECS SEPSECS SEPSECS 2344 0.087 0.11 YES
5 WARS2 WARS2 WARS2 2563 0.082 0.15 YES
6 RARS RARS RARS 2569 0.081 0.2 YES
7 YARS2 YARS2 YARS2 2761 0.076 0.24 YES
8 HARS2 HARS2 HARS2 3419 0.064 0.25 YES
9 AARS2 AARS2 AARS2 3533 0.062 0.28 YES
10 MTFMT MTFMT MTFMT 3868 0.056 0.3 YES
11 IARS2 IARS2 IARS2 3888 0.056 0.34 YES
12 TARS TARS TARS 4121 0.052 0.36 YES
13 YARS YARS YARS 4817 0.041 0.35 YES
14 LARS LARS LARS 4829 0.04 0.37 YES
15 FARSB FARSB FARSB 4969 0.038 0.39 YES
16 DARS DARS DARS 5461 0.031 0.38 YES
17 TARSL2 TARSL2 TARSL2 5467 0.031 0.41 YES
18 RARS2 RARS2 RARS2 5490 0.031 0.42 YES
19 IARS IARS IARS 5685 0.028 0.43 YES
20 SARS2 SARS2 SARS2 5730 0.027 0.45 YES
21 PSTK PSTK PSTK 5823 0.026 0.46 YES
22 MARS2 MARS2 MARS2 6029 0.023 0.46 YES
23 EARS2 EARS2 EARS2 6158 0.021 0.47 YES
24 PARS2 PARS2 PARS2 6490 0.016 0.46 YES
25 LARS2 LARS2 LARS2 6518 0.016 0.47 YES
26 HARS HARS HARS 6587 0.015 0.48 YES
27 QARS QARS QARS 6751 0.013 0.48 YES
28 KARS KARS KARS 6865 0.011 0.48 YES
29 VARS2 VARS2 VARS2 6915 0.01 0.48 YES
30 MARS MARS MARS 7224 0.0057 0.47 NO
31 GARS GARS GARS 7434 0.0029 0.46 NO
32 VARS VARS VARS 7816 -0.0022 0.44 NO
33 WARS WARS WARS 8144 -0.0072 0.43 NO
34 FARS2 FARS2 FARS2 8765 -0.016 0.4 NO
35 CARS CARS CARS 8827 -0.017 0.41 NO
36 AARS AARS AARS 8865 -0.018 0.42 NO
37 SARS SARS SARS 9012 -0.02 0.42 NO
38 FARSA FARSA FARSA 9129 -0.022 0.43 NO
39 NARS2 NARS2 NARS2 9833 -0.032 0.42 NO
40 CARS2 CARS2 CARS2 11532 -0.063 0.36 NO

Figure S41.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FAS PATHWAY.

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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

Table 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 PTPN13 PTPN13 PTPN13 133 0.29 0.19 YES
2 MAP2K4 MAP2K4 MAP2K4 1794 0.1 0.17 YES
3 PARP1 PARP1 PARP1 2021 0.096 0.22 YES
4 CASP3 CASP3 CASP3 2416 0.085 0.26 YES
5 CASP7 CASP7 CASP7 2964 0.072 0.28 YES
6 MAP3K1 MAP3K1 MAP3K1 2966 0.072 0.33 YES
7 PAK2 PAK2 PAK2 3352 0.065 0.35 YES
8 RB1 RB1 RB1 3557 0.061 0.38 YES
9 MAPK8 MAPK8 MAPK8 3880 0.056 0.4 YES
10 PRKDC PRKDC PRKDC 4165 0.051 0.42 YES
11 CASP10 CASP10 CASP10 4671 0.043 0.42 YES
12 CASP8 CASP8 CASP8 4843 0.04 0.44 YES
13 FAS FAS FAS 5194 0.035 0.44 YES
14 LMNA LMNA LMNA 5449 0.031 0.45 YES
15 LMNB2 LMNB2 LMNB2 5598 0.029 0.46 YES
16 SPTAN1 SPTAN1 SPTAN1 5865 0.025 0.46 YES
17 MAP3K7 MAP3K7 MAP3K7 5947 0.024 0.48 YES
18 FAF1 FAF1 FAF1 7075 0.008 0.42 NO
19 CASP6 CASP6 CASP6 7282 0.005 0.41 NO
20 DFFA DFFA DFFA 7394 0.0035 0.41 NO
21 DAXX DAXX DAXX 7440 0.0029 0.41 NO
22 DFFB DFFB DFFB 7735 -0.0013 0.39 NO
23 ARHGDIB ARHGDIB ARHGDIB 7739 -0.0013 0.39 NO
24 PAK1 PAK1 PAK1 9096 -0.021 0.33 NO
25 RIPK2 RIPK2 RIPK2 9111 -0.022 0.34 NO
26 FASLG FASLG FASLG 10598 -0.045 0.29 NO
27 JUN JUN JUN 10633 -0.046 0.32 NO
28 CFLAR CFLAR CFLAR 10761 -0.049 0.35 NO
29 FADD FADD FADD 12448 -0.084 0.31 NO

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

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

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 THOC1 THOC1 THOC1 717 0.17 -0.013 YES
2 RBM25 RBM25 RBM25 1089 0.14 -0.012 YES
3 SNRPD1 SNRPD1 SNRPD1 1190 0.13 0.0031 YES
4 SNRPE SNRPE SNRPE 1285 0.12 0.018 YES
5 CDC5L CDC5L CDC5L 1770 0.1 0.0073 YES
6 RBM8A RBM8A RBM8A 1922 0.099 0.015 YES
7 BCAS2 BCAS2 BCAS2 1948 0.098 0.029 YES
8 SYF2 SYF2 SYF2 1950 0.098 0.044 YES
9 PRPF38B PRPF38B PRPF38B 1974 0.098 0.059 YES
10 SNRNP27 SNRNP27 SNRNP27 1984 0.097 0.074 YES
11 LSM6 LSM6 LSM6 1998 0.097 0.088 YES
12 SNRPA1 SNRPA1 SNRPA1 2101 0.094 0.098 YES
13 PRPF18 PRPF18 PRPF18 2273 0.089 0.1 YES
14 SNRPB2 SNRPB2 SNRPB2 2357 0.087 0.11 YES
15 CDC40 CDC40 CDC40 2467 0.084 0.12 YES
16 SNW1 SNW1 SNW1 2478 0.083 0.13 YES
17 TCERG1 TCERG1 TCERG1 2531 0.082 0.14 YES
18 NCBP1 NCBP1 NCBP1 2551 0.082 0.15 YES
19 SLU7 SLU7 SLU7 2596 0.08 0.16 YES
20 HNRNPU HNRNPU HNRNPU 2741 0.077 0.17 YES
21 DDX46 DDX46 DDX46 2747 0.077 0.18 YES
22 MAGOHB MAGOHB MAGOHB 2813 0.076 0.19 YES
23 CRNKL1 CRNKL1 CRNKL1 2845 0.075 0.2 YES
24 PRPF40A PRPF40A PRPF40A 2917 0.074 0.21 YES
25 SR140 SR140 SR140 2993 0.072 0.21 YES
26 HNRNPC HNRNPC HNRNPC 3117 0.069 0.22 YES
27 SNRPF SNRPF SNRPF 3154 0.069 0.23 YES
28 HNRNPA3 HNRNPA3 HNRNPA3 3190 0.068 0.24 YES
29 LSM3 LSM3 LSM3 3284 0.066 0.24 YES
30 THOC2 THOC2 THOC2 3328 0.066 0.25 YES
31 DHX15 DHX15 DHX15 3404 0.064 0.26 YES
32 SF3A3 SF3A3 SF3A3 3418 0.064 0.26 YES
33 HNRNPK HNRNPK HNRNPK 3429 0.064 0.27 YES
34 SMNDC1 SMNDC1 SMNDC1 3488 0.062 0.28 YES
35 SFRS13A SFRS13A SFRS13A 3653 0.06 0.28 YES
36 AQR AQR AQR 3716 0.058 0.29 YES
37 HNRNPA1 HNRNPA1 HNRNPA1 3820 0.057 0.29 YES
38 PPIH PPIH PPIH 3967 0.054 0.29 YES
39 ACIN1 ACIN1 ACIN1 4016 0.054 0.3 YES
40 SF3B1 SF3B1 SF3B1 4068 0.053 0.3 YES
41 LSM5 LSM5 LSM5 4114 0.052 0.31 YES
42 SFRS3 SFRS3 SFRS3 4172 0.051 0.31 YES
43 SFRS4 SFRS4 SFRS4 4195 0.051 0.32 YES
44 SFRS1 SFRS1 SFRS1 4296 0.049 0.32 YES
45 PRPF38A PRPF38A PRPF38A 4317 0.049 0.33 YES
46 PPIL1 PPIL1 PPIL1 4331 0.048 0.34 YES
47 SF3B14 SF3B14 SF3B14 4334 0.048 0.34 YES
48 TRA2B TRA2B TRA2B 4528 0.045 0.34 YES
49 RBM17 RBM17 RBM17 4672 0.043 0.34 YES
50 PRPF40B PRPF40B PRPF40B 4787 0.041 0.34 YES
51 SNRPG SNRPG SNRPG 4789 0.041 0.34 YES
52 DDX5 DDX5 DDX5 4814 0.041 0.35 YES
53 WBP11 WBP11 WBP11 4889 0.04 0.35 YES
54 MAGOH MAGOH MAGOH 5014 0.038 0.35 YES
55 DDX23 DDX23 DDX23 5022 0.038 0.36 YES
56 DDX42 DDX42 DDX42 5056 0.037 0.36 YES
57 NAA38 NAA38 NAA38 5189 0.035 0.36 YES
58 RBMX RBMX RBMX 5205 0.035 0.36 YES
59 SNRNP40 SNRNP40 SNRNP40 5297 0.033 0.36 YES
60 SFRS9 SFRS9 SFRS9 5486 0.031 0.36 YES
61 U2AF1 U2AF1 U2AF1 5669 0.028 0.35 YES
62 PRPF4 PRPF4 PRPF4 5701 0.027 0.36 YES
63 RBM22 RBM22 RBM22 5808 0.026 0.35 YES
64 TXNL4A TXNL4A TXNL4A 5851 0.025 0.36 YES
65 HNRNPM HNRNPM HNRNPM 5861 0.025 0.36 YES
66 TRA2A TRA2A TRA2A 5945 0.024 0.36 YES
67 ZMAT2 ZMAT2 ZMAT2 5949 0.024 0.36 YES
68 SF3B3 SF3B3 SF3B3 5950 0.024 0.36 YES
69 THOC3 THOC3 THOC3 6002 0.023 0.37 YES
70 PRPF3 PRPF3 PRPF3 6018 0.023 0.37 YES
71 SNRPA SNRPA SNRPA 6027 0.023 0.37 YES
72 BAT1 BAT1 BAT1 6107 0.021 0.37 NO
73 SFRS2B SFRS2B SFRS2B 6242 0.02 0.37 NO
74 SFRS5 SFRS5 SFRS5 6330 0.018 0.36 NO
75 SNRNP70 SNRNP70 SNRNP70 6397 0.017 0.36 NO
76 PLRG1 PLRG1 PLRG1 6411 0.017 0.36 NO
77 SNRPD3 SNRPD3 SNRPD3 6428 0.017 0.37 NO
78 PRPF8 PRPF8 PRPF8 6486 0.016 0.37 NO
79 ISY1 ISY1 ISY1 6673 0.014 0.36 NO
80 SNRPB SNRPB SNRPB 6750 0.013 0.36 NO
81 HSPA8 HSPA8 HSPA8 6809 0.012 0.36 NO
82 USP39 USP39 USP39 6843 0.011 0.36 NO
83 PPIE PPIE PPIE 6950 0.0098 0.35 NO
84 SNRPC SNRPC SNRPC 6959 0.0096 0.35 NO
85 CCDC12 CCDC12 CCDC12 7024 0.0086 0.35 NO
86 SFRS7 SFRS7 SFRS7 7088 0.0078 0.35 NO
87 PRPF31 PRPF31 PRPF31 7114 0.0074 0.35 NO
88 LSM2 LSM2 LSM2 7205 0.0059 0.34 NO
89 DHX8 DHX8 DHX8 7208 0.0059 0.34 NO
90 SNRPD2 SNRPD2 SNRPD2 7368 0.0038 0.34 NO
91 HSPA2 HSPA2 HSPA2 7601 0.00083 0.32 NO
92 EFTUD2 EFTUD2 EFTUD2 7916 -0.0038 0.31 NO
93 DHX16 DHX16 DHX16 7950 -0.0042 0.3 NO
94 CWC15 CWC15 CWC15 7967 -0.0045 0.3 NO
95 SF3A1 SF3A1 SF3A1 7976 -0.0046 0.3 NO
96 THOC4 THOC4 THOC4 8101 -0.0066 0.3 NO
97 SF3B4 SF3B4 SF3B4 8364 -0.01 0.29 NO
98 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 8386 -0.011 0.29 NO
99 SF3B2 SF3B2 SF3B2 8411 -0.011 0.29 NO
100 U2AF2 U2AF2 U2AF2 8502 -0.012 0.28 NO
101 LSM4 LSM4 LSM4 8577 -0.014 0.28 NO
102 CHERP CHERP CHERP 8756 -0.016 0.28 NO
103 SFRS2 SFRS2 SFRS2 8759 -0.016 0.28 NO
104 SNRNP200 SNRNP200 SNRNP200 8843 -0.018 0.28 NO
105 PRPF19 PRPF19 PRPF19 8941 -0.019 0.27 NO
106 SFRS6 SFRS6 SFRS6 8955 -0.019 0.28 NO
107 PCBP1 PCBP1 PCBP1 9297 -0.024 0.26 NO
108 BUD31 BUD31 BUD31 9319 -0.024 0.26 NO
109 NHP2L1 NHP2L1 NHP2L1 9340 -0.025 0.27 NO
110 EIF4A3 EIF4A3 EIF4A3 9343 -0.025 0.27 NO
111 DHX38 DHX38 DHX38 9507 -0.027 0.26 NO
112 SF3B5 SF3B5 SF3B5 9738 -0.031 0.26 NO
113 PHF5A PHF5A PHF5A 10466 -0.043 0.22 NO
114 SF3A2 SF3A2 SF3A2 10527 -0.044 0.23 NO
115 HSPA1A HSPA1A HSPA1A 10801 -0.049 0.22 NO
116 SART1 SART1 SART1 11022 -0.053 0.22 NO
117 CTNNBL1 CTNNBL1 CTNNBL1 11842 -0.07 0.18 NO
118 PUF60 PUF60 PUF60 12003 -0.073 0.18 NO
119 XAB2 XAB2 XAB2 12103 -0.075 0.19 NO
120 LSM7 LSM7 LSM7 12398 -0.082 0.19 NO
121 PRPF6 PRPF6 PRPF6 12606 -0.088 0.19 NO
122 PQBP1 PQBP1 PQBP1 12725 -0.091 0.2 NO
123 HSPA6 HSPA6 HSPA6 14519 -0.15 0.12 NO
124 HSPA1B HSPA1B HSPA1B 14722 -0.16 0.14 NO
125 HSPA1L HSPA1L HSPA1L 17366 -0.33 0.04 NO

Figure S45.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA RACCYCD PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 PATHWAY

Table 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 ENO3 ENO3 ENO3 718 0.17 0.016 YES
2 C1D C1D C1D 1707 0.11 -0.0039 YES
3 CNOT7 CNOT7 CNOT7 1881 0.1 0.02 YES
4 LSM6 LSM6 LSM6 1998 0.097 0.045 YES
5 EXOSC9 EXOSC9 EXOSC9 2000 0.097 0.077 YES
6 MPHOSPH6 MPHOSPH6 MPHOSPH6 2045 0.095 0.11 YES
7 CNOT6 CNOT6 CNOT6 2144 0.092 0.13 YES
8 ENO2 ENO2 ENO2 2174 0.091 0.16 YES
9 DCP2 DCP2 DCP2 2631 0.079 0.16 YES
10 SKIV2L2 SKIV2L2 SKIV2L2 2738 0.077 0.18 YES
11 CNOT2 CNOT2 CNOT2 2772 0.076 0.2 YES
12 PAPOLA PAPOLA PAPOLA 3042 0.071 0.21 YES
13 DCP1A DCP1A DCP1A 3099 0.07 0.23 YES
14 CNOT6L CNOT6L CNOT6L 3148 0.069 0.25 YES
15 LSM3 LSM3 LSM3 3284 0.066 0.27 YES
16 ZCCHC7 ZCCHC7 ZCCHC7 3787 0.057 0.26 YES
17 LSM1 LSM1 LSM1 3876 0.056 0.27 YES
18 CNOT10 CNOT10 CNOT10 3898 0.055 0.29 YES
19 DDX6 DDX6 DDX6 4075 0.053 0.3 YES
20 LSM5 LSM5 LSM5 4114 0.052 0.31 YES
21 EXOSC10 EXOSC10 EXOSC10 4131 0.052 0.33 YES
22 DIS3 DIS3 DIS3 4272 0.05 0.34 YES
23 PAPOLG PAPOLG PAPOLG 4279 0.049 0.35 YES
24 XRN2 XRN2 XRN2 4436 0.047 0.36 YES
25 HSPD1 HSPD1 HSPD1 4522 0.045 0.37 YES
26 ENO1 ENO1 ENO1 4772 0.042 0.37 YES
27 HSPA9 HSPA9 HSPA9 5041 0.037 0.37 YES
28 NAA38 NAA38 NAA38 5189 0.035 0.37 YES
29 XRN1 XRN1 XRN1 5225 0.034 0.38 YES
30 DCP1B DCP1B DCP1B 5952 0.024 0.35 NO
31 CNOT1 CNOT1 CNOT1 6054 0.022 0.35 NO
32 CNOT4 CNOT4 CNOT4 6075 0.022 0.36 NO
33 PAPD7 PAPD7 PAPD7 6077 0.022 0.36 NO
34 PNPT1 PNPT1 PNPT1 6197 0.02 0.36 NO
35 PARN PARN PARN 6498 0.016 0.35 NO
36 EXOSC2 EXOSC2 EXOSC2 6602 0.015 0.35 NO
37 EXOSC3 EXOSC3 EXOSC3 6695 0.013 0.35 NO
38 PATL1 PATL1 PATL1 6776 0.012 0.35 NO
39 LSM2 LSM2 LSM2 7205 0.0059 0.33 NO
40 RQCD1 RQCD1 RQCD1 7371 0.0038 0.32 NO
41 DCPS DCPS DCPS 7400 0.0034 0.32 NO
42 TTC37 TTC37 TTC37 7472 0.0024 0.32 NO
43 CNOT3 CNOT3 CNOT3 7841 -0.0026 0.3 NO
44 EXOSC7 EXOSC7 EXOSC7 7897 -0.0034 0.29 NO
45 EDC3 EDC3 EDC3 8304 -0.0096 0.28 NO
46 LSM4 LSM4 LSM4 8577 -0.014 0.26 NO
47 SKIV2L SKIV2L SKIV2L 8893 -0.018 0.25 NO
48 EXOSC8 EXOSC8 EXOSC8 9100 -0.022 0.25 NO
49 WDR61 WDR61 WDR61 9489 -0.027 0.24 NO
50 EXOSC1 EXOSC1 EXOSC1 9759 -0.031 0.23 NO
51 EDC4 EDC4 EDC4 11336 -0.059 0.16 NO
52 LSM7 LSM7 LSM7 12398 -0.082 0.13 NO
53 EXOSC6 EXOSC6 EXOSC6 12684 -0.09 0.15 NO
54 EXOSC4 EXOSC4 EXOSC4 12952 -0.096 0.16 NO
55 EXOSC5 EXOSC5 EXOSC5 13036 -0.099 0.19 NO
56 PAPOLB PAPOLB PAPOLB 16737 -0.27 0.075 NO

Figure S47.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA PYK2 PATHWAY.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA TNFR1 PATHWAY

Table S25.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MNAT1 MNAT1 MNAT1 1657 0.11 -0.027 YES
2 RFC1 RFC1 RFC1 2956 0.073 -0.056 YES
3 GTF2H3 GTF2H3 GTF2H3 3074 0.07 -0.02 YES
4 GTF2H5 GTF2H5 GTF2H5 3124 0.069 0.019 YES
5 POLD3 POLD3 POLD3 3178 0.068 0.057 YES
6 ERCC6 ERCC6 ERCC6 3367 0.065 0.085 YES
7 ERCC4 ERCC4 ERCC4 3584 0.061 0.11 YES
8 RFC4 RFC4 RFC4 3609 0.06 0.14 YES
9 CDK7 CDK7 CDK7 3713 0.058 0.17 YES
10 ERCC8 ERCC8 ERCC8 3734 0.058 0.21 YES
11 RPA2 RPA2 RPA2 3790 0.057 0.24 YES
12 PCNA PCNA PCNA 3918 0.055 0.26 YES
13 RFC5 RFC5 RFC5 3968 0.054 0.29 YES
14 RPA1 RPA1 RPA1 4129 0.052 0.32 YES
15 XPA XPA XPA 4303 0.049 0.34 YES
16 POLE2 POLE2 POLE2 4443 0.046 0.36 YES
17 DDB2 DDB2 DDB2 4993 0.038 0.35 YES
18 POLE3 POLE3 POLE3 5064 0.037 0.37 YES
19 POLE POLE POLE 5222 0.034 0.38 YES
20 ERCC5 ERCC5 ERCC5 5425 0.032 0.39 YES
21 GTF2H4 GTF2H4 GTF2H4 5528 0.03 0.4 YES
22 RFC3 RFC3 RFC3 5770 0.026 0.4 YES
23 LIG1 LIG1 LIG1 5843 0.025 0.41 YES
24 CCNH CCNH CCNH 6594 0.015 0.38 NO
25 CUL4B CUL4B CUL4B 7117 0.0074 0.36 NO
26 CUL4A CUL4A CUL4A 7423 0.0032 0.34 NO
27 GTF2H1 GTF2H1 GTF2H1 7604 0.00079 0.33 NO
28 CETN2 CETN2 CETN2 7807 -0.0022 0.32 NO
29 POLE4 POLE4 POLE4 8012 -0.0053 0.31 NO
30 DDB1 DDB1 DDB1 8021 -0.0055 0.32 NO
31 RBX1 RBX1 RBX1 8218 -0.0082 0.31 NO
32 XPC XPC XPC 8378 -0.011 0.31 NO
33 RPA3 RPA3 RPA3 8533 -0.013 0.31 NO
34 RAD23A RAD23A RAD23A 8667 -0.015 0.31 NO
35 RFC2 RFC2 RFC2 8692 -0.015 0.32 NO
36 POLD1 POLD1 POLD1 9263 -0.024 0.3 NO
37 POLD2 POLD2 POLD2 9782 -0.032 0.29 NO
38 ERCC3 ERCC3 ERCC3 9842 -0.032 0.3 NO
39 GTF2H2 GTF2H2 GTF2H2 10017 -0.035 0.32 NO
40 ERCC2 ERCC2 ERCC2 10070 -0.036 0.34 NO
41 ERCC1 ERCC1 ERCC1 10313 -0.04 0.34 NO
42 RPA4 RPA4 RPA4 11425 -0.061 0.32 NO
43 POLD4 POLD4 POLD4 12370 -0.082 0.32 NO

Figure S49.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TNFR1 PATHWAY.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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

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 MAP2K4 MAP2K4 MAP2K4 1794 0.1 -0.027 YES
2 PARP1 PARP1 PARP1 2021 0.096 0.028 YES
3 CASP3 CASP3 CASP3 2416 0.085 0.065 YES
4 MAP3K1 MAP3K1 MAP3K1 2966 0.072 0.086 YES
5 PAK2 PAK2 PAK2 3352 0.065 0.11 YES
6 RB1 RB1 RB1 3557 0.061 0.14 YES
7 LMNB1 LMNB1 LMNB1 3725 0.058 0.17 YES
8 MAPK8 MAPK8 MAPK8 3880 0.056 0.2 YES
9 BAG4 BAG4 BAG4 3998 0.054 0.24 YES
10 PRKDC PRKDC PRKDC 4165 0.051 0.26 YES
11 RIPK1 RIPK1 RIPK1 4266 0.05 0.29 YES
12 CASP8 CASP8 CASP8 4843 0.04 0.29 YES
13 LMNA LMNA LMNA 5449 0.031 0.28 YES
14 LMNB2 LMNB2 LMNB2 5598 0.029 0.29 YES
15 SPTAN1 SPTAN1 SPTAN1 5865 0.025 0.29 YES
16 MAP3K7 MAP3K7 MAP3K7 5947 0.024 0.3 YES
17 CASP2 CASP2 CASP2 6126 0.021 0.31 YES
18 DFFA DFFA DFFA 7394 0.0035 0.24 NO
19 DFFB DFFB DFFB 7735 -0.0013 0.22 NO
20 ARHGDIB ARHGDIB ARHGDIB 7739 -0.0013 0.22 NO
21 MADD MADD MADD 8191 -0.0078 0.2 NO
22 PAK1 PAK1 PAK1 9096 -0.021 0.17 NO
23 JUN JUN JUN 10633 -0.046 0.12 NO
24 TRADD TRADD TRADD 11482 -0.062 0.11 NO
25 CRADD CRADD CRADD 11492 -0.062 0.16 NO
26 TNFRSF1A TNFRSF1A TNFRSF1A 11785 -0.069 0.19 NO
27 FADD FADD FADD 12448 -0.084 0.21 NO
28 TNF TNF TNF 14469 -0.15 0.2 NO

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

Figure S52.  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 O GLYCAN BIOSYNTHESIS

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 BLM BLM BLM 791 0.16 0.047 YES
2 RAD54B RAD54B RAD54B 850 0.16 0.13 YES
3 XRCC2 XRCC2 XRCC2 1036 0.14 0.2 YES
4 BRCA2 BRCA2 BRCA2 1090 0.14 0.28 YES
5 EME1 EME1 EME1 1884 0.1 0.29 YES
6 RAD54L RAD54L RAD54L 2191 0.091 0.32 YES
7 POLD3 POLD3 POLD3 3178 0.068 0.31 YES
8 RAD51 RAD51 RAD51 3309 0.066 0.34 YES
9 NBN NBN NBN 3376 0.065 0.37 YES
10 RPA2 RPA2 RPA2 3790 0.057 0.38 YES
11 TOP3A TOP3A TOP3A 3997 0.054 0.4 YES
12 RPA1 RPA1 RPA1 4129 0.052 0.42 YES
13 RAD50 RAD50 RAD50 5110 0.036 0.39 NO
14 SSBP1 SSBP1 SSBP1 6586 0.015 0.32 NO
15 MRE11A MRE11A MRE11A 6667 0.014 0.32 NO
16 SHFM1 SHFM1 SHFM1 6859 0.011 0.31 NO
17 XRCC3 XRCC3 XRCC3 8358 -0.01 0.24 NO
18 RPA3 RPA3 RPA3 8533 -0.013 0.24 NO
19 RAD52 RAD52 RAD52 9037 -0.02 0.22 NO
20 POLD1 POLD1 POLD1 9263 -0.024 0.22 NO
21 POLD2 POLD2 POLD2 9782 -0.032 0.21 NO
22 TOP3B TOP3B TOP3B 11387 -0.06 0.15 NO
23 RPA4 RPA4 RPA4 11425 -0.061 0.19 NO
24 RAD51L3 RAD51L3 RAD51L3 11744 -0.068 0.21 NO
25 RAD51L1 RAD51L1 RAD51L1 12199 -0.078 0.23 NO
26 POLD4 POLD4 POLD4 12370 -0.082 0.26 NO
27 MUS81 MUS81 MUS81 12903 -0.095 0.29 NO

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

Figure S54.  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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

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 MDM2 MDM2 MDM2 885 0.15 0.0032 YES
2 MAP3K5 MAP3K5 MAP3K5 1509 0.11 0.0077 YES
3 BCL2 BCL2 BCL2 1577 0.11 0.042 YES
4 APAF1 APAF1 APAF1 1651 0.11 0.075 YES
5 PARP1 PARP1 PARP1 2021 0.096 0.088 YES
6 CASP3 CASP3 CASP3 2416 0.085 0.095 YES
7 CASP7 CASP7 CASP7 2964 0.072 0.089 YES
8 MAP3K1 MAP3K1 MAP3K1 2966 0.072 0.11 YES
9 PAK2 PAK2 PAK2 3352 0.065 0.12 YES
10 CYCS CYCS CYCS 3447 0.063 0.13 YES
11 RB1 RB1 RB1 3557 0.061 0.15 YES
12 BIRC3 BIRC3 BIRC3 3703 0.059 0.16 YES
13 LMNB1 LMNB1 LMNB1 3725 0.058 0.18 YES
14 MAPK8 MAPK8 MAPK8 3880 0.056 0.19 YES
15 BAG4 BAG4 BAG4 3998 0.054 0.2 YES
16 PRKDC PRKDC PRKDC 4165 0.051 0.21 YES
17 RASA1 RASA1 RASA1 4180 0.051 0.22 YES
18 RIPK1 RIPK1 RIPK1 4266 0.05 0.24 YES
19 CHUK CHUK CHUK 4553 0.045 0.24 YES
20 CASP8 CASP8 CASP8 4843 0.04 0.23 YES
21 BIRC2 BIRC2 BIRC2 5134 0.036 0.23 YES
22 FAS FAS FAS 5194 0.035 0.24 YES
23 LMNA LMNA LMNA 5449 0.031 0.24 YES
24 LMNB2 LMNB2 LMNB2 5598 0.029 0.24 YES
25 PSEN1 PSEN1 PSEN1 5698 0.028 0.24 YES
26 SPTAN1 SPTAN1 SPTAN1 5865 0.025 0.24 NO
27 CASP2 CASP2 CASP2 6126 0.021 0.23 NO
28 XIAP XIAP XIAP 6582 0.015 0.21 NO
29 CASP6 CASP6 CASP6 7282 0.005 0.18 NO
30 PTK2 PTK2 PTK2 7329 0.0044 0.18 NO
31 DFFA DFFA DFFA 7394 0.0035 0.17 NO
32 DAXX DAXX DAXX 7440 0.0029 0.17 NO
33 DFFB DFFB DFFB 7735 -0.0013 0.16 NO
34 ARHGDIB ARHGDIB ARHGDIB 7739 -0.0013 0.16 NO
35 PSEN2 PSEN2 PSEN2 7863 -0.0029 0.15 NO
36 CDK11B CDK11B CDK11B 7998 -0.0049 0.14 NO
37 NFKB1 NFKB1 NFKB1 8023 -0.0055 0.14 NO
38 MAP2K7 MAP2K7 MAP2K7 8143 -0.0072 0.14 NO
39 CASP9 CASP9 CASP9 8312 -0.0098 0.14 NO
40 CDK11A CDK11A CDK11A 9054 -0.021 0.1 NO
41 ACTG1 ACTG1 ACTG1 9061 -0.021 0.11 NO
42 TRAF2 TRAF2 TRAF2 9544 -0.028 0.09 NO
43 PRKCD PRKCD PRKCD 9783 -0.032 0.088 NO
44 GSN GSN GSN 9847 -0.032 0.096 NO
45 CFLAR CFLAR CFLAR 10761 -0.049 0.062 NO
46 NUMA1 NUMA1 NUMA1 10937 -0.052 0.069 NO
47 TNFRSF1B TNFRSF1B TNFRSF1B 10962 -0.052 0.086 NO
48 NFKBIA NFKBIA NFKBIA 11359 -0.059 0.084 NO
49 TRADD TRADD TRADD 11482 -0.062 0.099 NO
50 CRADD CRADD CRADD 11492 -0.062 0.12 NO
51 RELA RELA RELA 11667 -0.066 0.13 NO
52 TNFRSF1A TNFRSF1A TNFRSF1A 11785 -0.069 0.15 NO
53 FADD FADD FADD 12448 -0.084 0.14 NO
54 MAP3K14 MAP3K14 MAP3K14 12756 -0.091 0.16 NO
55 BID BID BID 12853 -0.094 0.18 NO
56 TNF TNF TNF 14469 -0.15 0.14 NO
57 TRAF1 TRAF1 TRAF1 14847 -0.17 0.18 NO

Figure S55.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES.

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

genes ES table in pathway: KEGG PROPANOATE METABOLISM

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 CDC7 CDC7 CDC7 313 0.23 0.014 YES
2 CCNB3 CCNB3 CCNB3 828 0.16 0.0061 YES
3 MDM2 MDM2 MDM2 885 0.15 0.023 YES
4 TTK TTK TTK 942 0.15 0.04 YES
5 BUB1B BUB1B BUB1B 1126 0.13 0.048 YES
6 CDC25A CDC25A CDC25A 1173 0.13 0.063 YES
7 PTTG1 PTTG1 PTTG1 1345 0.12 0.07 YES
8 MAD2L1 MAD2L1 MAD2L1 1553 0.11 0.073 YES
9 CDK1 CDK1 CDK1 1569 0.11 0.087 YES
10 BUB1 BUB1 BUB1 1614 0.11 0.1 YES
11 E2F2 E2F2 E2F2 1678 0.11 0.11 YES
12 SMAD2 SMAD2 SMAD2 1736 0.1 0.12 YES
13 E2F3 E2F3 E2F3 2040 0.096 0.12 YES
14 SKP2 SKP2 SKP2 2042 0.096 0.13 YES
15 SMC1B SMC1B SMC1B 2176 0.091 0.14 YES
16 ORC1L ORC1L ORC1L 2246 0.09 0.14 YES
17 CDK6 CDK6 CDK6 2549 0.082 0.14 YES
18 CDC20 CDC20 CDC20 2712 0.078 0.14 YES
19 CCNA2 CCNA2 CCNA2 2783 0.076 0.14 YES
20 ANAPC4 ANAPC4 ANAPC4 2977 0.072 0.14 YES
21 CDC25C CDC25C CDC25C 2994 0.072 0.15 YES
22 CDC27 CDC27 CDC27 3097 0.07 0.16 YES
23 HDAC2 HDAC2 HDAC2 3180 0.068 0.16 YES
24 CCNB2 CCNB2 CCNB2 3208 0.068 0.17 YES
25 CHEK1 CHEK1 CHEK1 3278 0.066 0.17 YES
26 MCM3 MCM3 MCM3 3311 0.066 0.18 YES
27 ORC2L ORC2L ORC2L 3400 0.064 0.18 YES
28 RB1 RB1 RB1 3557 0.061 0.18 YES
29 YWHAE YWHAE YWHAE 3586 0.061 0.19 YES
30 CCNE2 CCNE2 CCNE2 3587 0.061 0.2 YES
31 MCM6 MCM6 MCM6 3649 0.06 0.2 YES
32 HDAC1 HDAC1 HDAC1 3677 0.059 0.21 YES
33 CDC6 CDC6 CDC6 3688 0.059 0.22 YES
34 CDK7 CDK7 CDK7 3713 0.058 0.22 YES
35 PTTG2 PTTG2 PTTG2 3715 0.058 0.23 YES
36 CDK2 CDK2 CDK2 3742 0.058 0.24 YES
37 PCNA PCNA PCNA 3918 0.055 0.24 YES
38 ESPL1 ESPL1 ESPL1 3975 0.054 0.24 YES
39 CCNB1 CCNB1 CCNB1 4044 0.053 0.24 YES
40 PRKDC PRKDC PRKDC 4165 0.051 0.24 YES
41 CDC14B CDC14B CDC14B 4398 0.047 0.24 YES
42 GSK3B GSK3B GSK3B 4777 0.041 0.22 YES
43 CDC25B CDC25B CDC25B 4791 0.041 0.22 YES
44 CDC23 CDC23 CDC23 4896 0.04 0.22 YES
45 TGFB2 TGFB2 TGFB2 4935 0.039 0.23 YES
46 ATM ATM ATM 4941 0.039 0.23 YES
47 MCM4 MCM4 MCM4 4975 0.038 0.24 YES
48 SKP1 SKP1 SKP1 5067 0.037 0.24 YES
49 ORC4L ORC4L ORC4L 5080 0.036 0.24 YES
50 SMAD4 SMAD4 SMAD4 5239 0.034 0.24 YES
51 ANAPC10 ANAPC10 ANAPC10 5303 0.033 0.24 YES
52 BUB3 BUB3 BUB3 5335 0.033 0.24 YES
53 YWHAZ YWHAZ YWHAZ 5373 0.032 0.24 YES
54 CHEK2 CHEK2 CHEK2 5386 0.032 0.25 YES
55 RAD21 RAD21 RAD21 5395 0.032 0.25 YES
56 MAD2L2 MAD2L2 MAD2L2 5512 0.03 0.25 NO
57 CDKN1B CDKN1B CDKN1B 5852 0.025 0.23 NO
58 SMC1A SMC1A SMC1A 5899 0.025 0.23 NO
59 SFN SFN SFN 5919 0.024 0.24 NO
60 STAG1 STAG1 STAG1 6182 0.02 0.22 NO
61 ATR ATR ATR 6189 0.02 0.22 NO
62 ANAPC7 ANAPC7 ANAPC7 6351 0.018 0.22 NO
63 CCNH CCNH CCNH 6594 0.015 0.21 NO
64 ANAPC13 ANAPC13 ANAPC13 6689 0.013 0.2 NO
65 SMC3 SMC3 SMC3 6798 0.012 0.2 NO
66 YWHAQ YWHAQ YWHAQ 6907 0.01 0.2 NO
67 STAG2 STAG2 STAG2 6969 0.0094 0.19 NO
68 CDKN1A CDKN1A CDKN1A 6977 0.0092 0.19 NO
69 GADD45A GADD45A GADD45A 7063 0.0081 0.19 NO
70 WEE1 WEE1 WEE1 7173 0.0064 0.18 NO
71 CUL1 CUL1 CUL1 7180 0.0062 0.18 NO
72 CCNE1 CCNE1 CCNE1 7237 0.0055 0.18 NO
73 CDC45 CDC45 CDC45 7297 0.0047 0.18 NO
74 TFDP1 TFDP1 TFDP1 7411 0.0033 0.17 NO
75 CDKN2C CDKN2C CDKN2C 7609 0.00076 0.16 NO
76 ORC3L ORC3L ORC3L 7715 -0.001 0.16 NO
77 EP300 EP300 EP300 7757 -0.0016 0.16 NO
78 CCND2 CCND2 CCND2 7855 -0.0028 0.15 NO
79 YWHAG YWHAG YWHAG 7913 -0.0038 0.15 NO
80 ORC6L ORC6L ORC6L 7990 -0.0048 0.14 NO
81 E2F5 E2F5 E2F5 8070 -0.0061 0.14 NO
82 ANAPC1 ANAPC1 ANAPC1 8188 -0.0078 0.14 NO
83 RBX1 RBX1 RBX1 8218 -0.0082 0.14 NO
84 RBL2 RBL2 RBL2 8232 -0.0084 0.14 NO
85 ORC5L ORC5L ORC5L 8292 -0.0095 0.13 NO
86 CCND1 CCND1 CCND1 8353 -0.01 0.13 NO
87 PLK1 PLK1 PLK1 8436 -0.011 0.13 NO
88 CREBBP CREBBP CREBBP 8574 -0.014 0.12 NO
89 YWHAH YWHAH YWHAH 8731 -0.016 0.12 NO
90 ANAPC5 ANAPC5 ANAPC5 8790 -0.017 0.12 NO
91 ZBTB17 ZBTB17 ZBTB17 9058 -0.021 0.1 NO
92 CDK4 CDK4 CDK4 9094 -0.021 0.1 NO
93 YWHAB YWHAB YWHAB 9214 -0.023 0.1 NO
94 CDC16 CDC16 CDC16 9386 -0.025 0.094 NO
95 PKMYT1 PKMYT1 PKMYT1 9425 -0.026 0.095 NO
96 SMAD3 SMAD3 SMAD3 9571 -0.028 0.091 NO
97 MCM5 MCM5 MCM5 9726 -0.031 0.086 NO
98 MCM7 MCM7 MCM7 9728 -0.031 0.091 NO
99 MCM2 MCM2 MCM2 9743 -0.031 0.094 NO
100 CDC14A CDC14A CDC14A 9900 -0.033 0.09 NO
101 ABL1 ABL1 ABL1 10037 -0.035 0.087 NO
102 FZR1 FZR1 FZR1 10232 -0.039 0.081 NO
103 CCND3 CCND3 CCND3 10266 -0.039 0.085 NO
104 TP53 TP53 TP53 10371 -0.041 0.084 NO
105 RBL1 RBL1 RBL1 10492 -0.044 0.084 NO
106 TFDP2 TFDP2 TFDP2 10500 -0.044 0.089 NO
107 ANAPC2 ANAPC2 ANAPC2 10884 -0.051 0.074 NO
108 E2F4 E2F4 E2F4 11087 -0.054 0.07 NO
109 GADD45G GADD45G GADD45G 11797 -0.069 0.04 NO
110 CDC26 CDC26 CDC26 12151 -0.077 0.031 NO
111 MAD1L1 MAD1L1 MAD1L1 12310 -0.08 0.033 NO
112 MYC MYC MYC 12700 -0.09 0.023 NO
113 E2F1 E2F1 E2F1 13132 -0.1 0.013 NO
114 WEE2 WEE2 WEE2 13218 -0.1 0.022 NO
115 ANAPC11 ANAPC11 ANAPC11 13832 -0.12 0.0045 NO
116 CDKN2D CDKN2D CDKN2D 13865 -0.12 0.019 NO
117 CDKN2A CDKN2A CDKN2A 14312 -0.14 0.014 NO
118 CDKN2B CDKN2B CDKN2B 15112 -0.18 -0.0071 NO
119 GADD45B GADD45B GADD45B 15745 -0.21 -0.014 NO
120 CDKN1C CDKN1C CDKN1C 15792 -0.21 0.012 NO
121 TGFB1 TGFB1 TGFB1 15884 -0.22 0.036 NO
122 CCNA1 CCNA1 CCNA1 17262 -0.32 0.0014 NO
123 TGFB3 TGFB3 TGFB3 17406 -0.33 0.038 NO

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

Figure S58.  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 BUTANOATE METABOLISM

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 PIK3R1 PIK3R1 PIK3R1 2306 0.088 -0.035 YES
2 CDK6 CDK6 CDK6 2549 0.082 0.038 YES
3 RB1 RB1 RB1 3557 0.061 0.047 YES
4 PIK3CA PIK3CA PIK3CA 3723 0.058 0.1 YES
5 CDK2 CDK2 CDK2 3742 0.058 0.16 YES
6 CHUK CHUK CHUK 4553 0.045 0.16 YES
7 RHOA RHOA RHOA 5829 0.026 0.12 YES
8 CDKN1B CDKN1B CDKN1B 5852 0.025 0.14 YES
9 CDKN1A CDKN1A CDKN1A 6977 0.0092 0.092 YES
10 CCNE1 CCNE1 CCNE1 7237 0.0055 0.083 YES
11 MAPK1 MAPK1 MAPK1 7351 0.0039 0.081 YES
12 RAC1 RAC1 RAC1 7386 0.0036 0.083 YES
13 TFDP1 TFDP1 TFDP1 7411 0.0033 0.085 YES
14 AKT1 AKT1 AKT1 7778 -0.0018 0.067 YES
15 NFKB1 NFKB1 NFKB1 8023 -0.0055 0.059 YES
16 CCND1 CCND1 CCND1 8353 -0.01 0.052 YES
17 RAF1 RAF1 RAF1 8857 -0.018 0.043 YES
18 CDK4 CDK4 CDK4 9094 -0.021 0.052 YES
19 PAK1 PAK1 PAK1 9096 -0.021 0.075 YES
20 HRAS HRAS HRAS 10746 -0.048 0.034 YES
21 IKBKB IKBKB IKBKB 11127 -0.055 0.071 YES
22 MAPK3 MAPK3 MAPK3 11323 -0.058 0.12 YES
23 NFKBIA NFKBIA NFKBIA 11359 -0.059 0.18 YES
24 RELA RELA RELA 11667 -0.066 0.24 YES
25 IKBKG IKBKG IKBKG 13519 -0.11 0.25 YES

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

Figure S60.  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

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
BIOCARTA ERK PATHWAY 27 genes.ES.table 0.22 0.75 0.75 1 1 1 0.78 0.22 1 0.88
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.23 0.9 0.56 1 1 0.031 0.00028 0.031 1 0.71
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.21 0.9 0.59 1 1 1 0.79 0.21 1 0.64
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.26 1 0.44 1 1 0.098 0.099 0.088 0.99 0.49
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.3 1.1 0.36 0.99 1 0.04 0.00061 0.04 0.9 0.4
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.28 0.89 0.56 1 1 1 0.72 0.28 1 0.57
KEGG CYSTEINE AND METHIONINE METABOLISM 32 genes.ES.table 0.22 0.75 0.85 1 1 0.12 0.073 0.12 1 0.84
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.52 2.1 0.0039 0.021 0.036 0.23 0.14 0.2 0 0.006
KEGG SELENOAMINO ACID METABOLISM 25 genes.ES.table 0.35 1.1 0.32 1 0.99 0.2 0.16 0.17 0.94 0.45
KEGG PROPANOATE METABOLISM 31 genes.ES.table 0.37 1.2 0.25 0.99 0.99 0.58 0.32 0.4 0.85 0.41
genes ES table in pathway: BIOCARTA ERK PATHWAY

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 PIPOX PIPOX PIPOX 1 0.58 0.2 YES
2 AASS AASS AASS 201 0.28 0.28 YES
3 BBOX1 BBOX1 BBOX1 510 0.2 0.33 YES
4 SETDB2 SETDB2 SETDB2 868 0.16 0.37 YES
5 PLOD2 PLOD2 PLOD2 894 0.16 0.42 YES
6 AASDHPPT AASDHPPT AASDHPPT 1125 0.14 0.46 YES
7 OGDHL OGDHL OGDHL 1477 0.12 0.48 YES
8 ACAT1 ACAT1 ACAT1 1908 0.11 0.49 YES
9 WHSC1L1 WHSC1L1 WHSC1L1 2189 0.098 0.51 YES
10 SUV420H1 SUV420H1 SUV420H1 2563 0.087 0.52 YES
11 SETD2 SETD2 SETD2 3211 0.073 0.51 NO
12 ALDH2 ALDH2 ALDH2 3527 0.066 0.51 NO
13 ALDH7A1 ALDH7A1 ALDH7A1 4118 0.055 0.5 NO
14 PLOD3 PLOD3 PLOD3 4561 0.047 0.49 NO
15 ASH1L ASH1L ASH1L 5225 0.036 0.47 NO
16 SUV39H2 SUV39H2 SUV39H2 5641 0.03 0.45 NO
17 ALDH3A2 ALDH3A2 ALDH3A2 5652 0.03 0.46 NO
18 ACAT2 ACAT2 ACAT2 5796 0.028 0.46 NO
19 SETMAR SETMAR SETMAR 6095 0.023 0.46 NO
20 ALDH9A1 ALDH9A1 ALDH9A1 6177 0.022 0.46 NO
21 GCDH GCDH GCDH 6194 0.022 0.46 NO
22 ALDH1B1 ALDH1B1 ALDH1B1 6600 0.016 0.45 NO
23 NSD1 NSD1 NSD1 7191 0.0078 0.42 NO
24 SETD1A SETD1A SETD1A 7441 0.004 0.41 NO
25 AASDH AASDH AASDH 7638 0.0012 0.4 NO
26 EHMT2 EHMT2 EHMT2 7976 -0.0036 0.38 NO
27 SETD7 SETD7 SETD7 8028 -0.0041 0.38 NO
28 SETD8 SETD8 SETD8 8201 -0.0066 0.37 NO
29 HADHA HADHA HADHA 8260 -0.0075 0.37 NO
30 WHSC1 WHSC1 WHSC1 8261 -0.0075 0.37 NO
31 SETD1B SETD1B SETD1B 8292 -0.008 0.37 NO
32 SUV39H1 SUV39H1 SUV39H1 8710 -0.014 0.35 NO
33 HADH HADH HADH 8826 -0.015 0.35 NO
34 PLOD1 PLOD1 PLOD1 8953 -0.017 0.35 NO
35 TMLHE TMLHE TMLHE 9151 -0.02 0.35 NO
36 SETDB1 SETDB1 SETDB1 9178 -0.02 0.35 NO
37 OGDH OGDH OGDH 9336 -0.023 0.35 NO
38 ECHS1 ECHS1 ECHS1 9821 -0.03 0.34 NO
39 SUV420H2 SUV420H2 SUV420H2 10311 -0.037 0.32 NO
40 AADAT AADAT AADAT 10562 -0.041 0.32 NO
41 DOT1L DOT1L DOT1L 12727 -0.086 0.23 NO
42 DLST DLST DLST 13020 -0.095 0.25 NO
43 EHMT1 EHMT1 EHMT1 13040 -0.095 0.28 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: BIOCARTA ERK PATHWAY.

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

genes ES table in pathway: BIOCARTA DEATH PATHWAY

Table 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 C1D C1D C1D 485 0.2 0.031 YES
2 NAA38 NAA38 NAA38 614 0.18 0.077 YES
3 MPHOSPH6 MPHOSPH6 MPHOSPH6 1066 0.14 0.094 YES
4 LSM6 LSM6 LSM6 1482 0.12 0.11 YES
5 PNPT1 PNPT1 PNPT1 1525 0.12 0.14 YES
6 DIS3 DIS3 DIS3 1545 0.12 0.17 YES
7 LSM5 LSM5 LSM5 1607 0.12 0.2 YES
8 HSPD1 HSPD1 HSPD1 1761 0.11 0.23 YES
9 EXOSC9 EXOSC9 EXOSC9 2318 0.093 0.22 YES
10 CNOT4 CNOT4 CNOT4 2840 0.08 0.22 YES
11 XRN1 XRN1 XRN1 2875 0.08 0.24 YES
12 CNOT6L CNOT6L CNOT6L 3098 0.075 0.25 YES
13 DCP2 DCP2 DCP2 3116 0.075 0.27 YES
14 LSM3 LSM3 LSM3 3117 0.075 0.29 YES
15 DDX6 DDX6 DDX6 3239 0.072 0.3 YES
16 PARN PARN PARN 3273 0.072 0.32 YES
17 HSPA9 HSPA9 HSPA9 3275 0.072 0.34 YES
18 EXOSC8 EXOSC8 EXOSC8 3282 0.071 0.36 YES
19 LSM1 LSM1 LSM1 3291 0.071 0.38 YES
20 PAPOLG PAPOLG PAPOLG 3788 0.061 0.37 YES
21 SKIV2L2 SKIV2L2 SKIV2L2 3884 0.059 0.39 YES
22 PAPOLA PAPOLA PAPOLA 4069 0.056 0.39 YES
23 CNOT6 CNOT6 CNOT6 4377 0.05 0.39 YES
24 ZCCHC7 ZCCHC7 ZCCHC7 4445 0.049 0.4 YES
25 EXOSC5 EXOSC5 EXOSC5 4485 0.048 0.41 YES
26 XRN2 XRN2 XRN2 4951 0.04 0.4 NO
27 PATL1 PATL1 PATL1 5034 0.039 0.4 NO
28 CNOT2 CNOT2 CNOT2 5383 0.033 0.4 NO
29 CNOT7 CNOT7 CNOT7 5833 0.027 0.38 NO
30 CNOT1 CNOT1 CNOT1 6329 0.02 0.36 NO
31 PAPOLB PAPOLB PAPOLB 6916 0.012 0.33 NO
32 LSM4 LSM4 LSM4 7118 0.009 0.32 NO
33 EXOSC7 EXOSC7 EXOSC7 7188 0.0079 0.32 NO
34 DCP1A DCP1A DCP1A 7358 0.0052 0.31 NO
35 EXOSC1 EXOSC1 EXOSC1 7596 0.0017 0.3 NO
36 CNOT10 CNOT10 CNOT10 7914 -0.0026 0.28 NO
37 TTC37 TTC37 TTC37 7942 -0.003 0.28 NO
38 EXOSC10 EXOSC10 EXOSC10 7988 -0.0036 0.28 NO
39 ENO2 ENO2 ENO2 8060 -0.0044 0.28 NO
40 DCP1B DCP1B DCP1B 8105 -0.0052 0.27 NO
41 EXOSC3 EXOSC3 EXOSC3 8688 -0.013 0.25 NO
42 PAPD7 PAPD7 PAPD7 9037 -0.018 0.23 NO
43 SKIV2L SKIV2L SKIV2L 9200 -0.021 0.23 NO
44 ENO1 ENO1 ENO1 9542 -0.026 0.22 NO
45 EDC4 EDC4 EDC4 9905 -0.031 0.21 NO
46 EXOSC2 EXOSC2 EXOSC2 10324 -0.038 0.19 NO
47 EDC3 EDC3 EDC3 10466 -0.04 0.2 NO
48 LSM7 LSM7 LSM7 10868 -0.046 0.19 NO
49 WDR61 WDR61 WDR61 10869 -0.046 0.2 NO
50 CNOT3 CNOT3 CNOT3 11008 -0.049 0.21 NO
51 LSM2 LSM2 LSM2 11343 -0.055 0.21 NO
52 DCPS DCPS DCPS 11367 -0.056 0.22 NO
53 EXOSC4 EXOSC4 EXOSC4 12616 -0.083 0.18 NO
54 EXOSC6 EXOSC6 EXOSC6 14011 -0.13 0.14 NO
55 ENO3 ENO3 ENO3 14452 -0.15 0.16 NO
56 RQCD1 RQCD1 RQCD1 14715 -0.16 0.19 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: BIOCARTA DEATH PATHWAY.

Figure S64.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA DEATH PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CTNNBL1 CTNNBL1 CTNNBL1 597 0.18 -0.0074 YES
2 NAA38 NAA38 NAA38 614 0.18 0.017 YES
3 CWC15 CWC15 CWC15 710 0.17 0.036 YES
4 SYF2 SYF2 SYF2 813 0.16 0.052 YES
5 SR140 SR140 SR140 986 0.15 0.064 YES
6 SNRNP27 SNRNP27 SNRNP27 1127 0.14 0.076 YES
7 PRPF6 PRPF6 PRPF6 1151 0.14 0.094 YES
8 MAGOHB MAGOHB MAGOHB 1166 0.14 0.11 YES
9 ISY1 ISY1 ISY1 1343 0.13 0.12 YES
10 THOC2 THOC2 THOC2 1452 0.12 0.13 YES
11 LSM6 LSM6 LSM6 1482 0.12 0.15 YES
12 LSM5 LSM5 LSM5 1607 0.12 0.16 YES
13 SNRPA1 SNRPA1 SNRPA1 1724 0.11 0.16 YES
14 CDC40 CDC40 CDC40 1822 0.11 0.17 YES
15 CRNKL1 CRNKL1 CRNKL1 1843 0.11 0.19 YES
16 SNRPE SNRPE SNRPE 1949 0.1 0.2 YES
17 SLU7 SLU7 SLU7 2151 0.098 0.2 YES
18 SART1 SART1 SART1 2210 0.097 0.21 YES
19 PRPF40A PRPF40A PRPF40A 2331 0.093 0.22 YES
20 SNRPG SNRPG SNRPG 2366 0.092 0.23 YES
21 PRPF38B PRPF38B PRPF38B 2518 0.088 0.23 YES
22 SNRPB2 SNRPB2 SNRPB2 2583 0.087 0.24 YES
23 SMNDC1 SMNDC1 SMNDC1 2618 0.086 0.25 YES
24 SNRPF SNRPF SNRPF 2728 0.083 0.26 YES
25 SF3B14 SF3B14 SF3B14 2731 0.083 0.27 YES
26 ZMAT2 ZMAT2 ZMAT2 3054 0.076 0.26 YES
27 BUD31 BUD31 BUD31 3075 0.075 0.27 YES
28 LSM3 LSM3 LSM3 3117 0.075 0.28 YES
29 DDX46 DDX46 DDX46 3296 0.071 0.28 YES
30 TRA2A TRA2A TRA2A 3336 0.07 0.28 YES
31 PRPF40B PRPF40B PRPF40B 3561 0.066 0.28 YES
32 SNW1 SNW1 SNW1 3570 0.065 0.29 YES
33 SF3B2 SF3B2 SF3B2 3597 0.064 0.3 YES
34 HNRNPA3 HNRNPA3 HNRNPA3 3889 0.059 0.29 YES
35 PRPF18 PRPF18 PRPF18 3904 0.058 0.3 YES
36 SNRPD3 SNRPD3 SNRPD3 3908 0.058 0.3 YES
37 HNRNPK HNRNPK HNRNPK 3911 0.058 0.31 YES
38 SFRS6 SFRS6 SFRS6 4053 0.056 0.31 YES
39 DDX42 DDX42 DDX42 4072 0.056 0.32 YES
40 PQBP1 PQBP1 PQBP1 4100 0.055 0.32 YES
41 SFRS13A SFRS13A SFRS13A 4157 0.054 0.33 YES
42 THOC1 THOC1 THOC1 4175 0.054 0.34 YES
43 MAGOH MAGOH MAGOH 4262 0.052 0.34 YES
44 HNRNPU HNRNPU HNRNPU 4426 0.049 0.34 YES
45 SFRS1 SFRS1 SFRS1 4483 0.048 0.34 YES
46 TCERG1 TCERG1 TCERG1 4526 0.047 0.34 YES
47 PRPF3 PRPF3 PRPF3 4762 0.044 0.34 YES
48 PLRG1 PLRG1 PLRG1 4870 0.042 0.34 YES
49 SNRNP200 SNRNP200 SNRNP200 4911 0.041 0.34 YES
50 RBM25 RBM25 RBM25 4942 0.04 0.34 YES
51 RBM17 RBM17 RBM17 4966 0.04 0.35 YES
52 CDC5L CDC5L CDC5L 5016 0.039 0.35 YES
53 SFRS3 SFRS3 SFRS3 5157 0.037 0.35 YES
54 BCAS2 BCAS2 BCAS2 5270 0.035 0.35 YES
55 NHP2L1 NHP2L1 NHP2L1 5475 0.032 0.34 YES
56 SFRS4 SFRS4 SFRS4 5506 0.032 0.34 YES
57 SNRPD2 SNRPD2 SNRPD2 5582 0.03 0.34 YES
58 RBM22 RBM22 RBM22 5658 0.029 0.34 YES
59 PRPF19 PRPF19 PRPF19 5666 0.029 0.35 YES
60 THOC4 THOC4 THOC4 5711 0.029 0.35 YES
61 RBMX RBMX RBMX 5743 0.028 0.35 YES
62 USP39 USP39 USP39 5770 0.028 0.35 YES
63 SFRS5 SFRS5 SFRS5 6078 0.023 0.34 NO
64 SFRS2B SFRS2B SFRS2B 6211 0.021 0.34 NO
65 CHERP CHERP CHERP 6221 0.021 0.34 NO
66 DHX8 DHX8 DHX8 6331 0.02 0.34 NO
67 CCDC12 CCDC12 CCDC12 6349 0.019 0.34 NO
68 SF3A2 SF3A2 SF3A2 6466 0.018 0.33 NO
69 SF3B3 SF3B3 SF3B3 6528 0.017 0.33 NO
70 DDX5 DDX5 DDX5 6529 0.017 0.33 NO
71 SF3A3 SF3A3 SF3A3 6585 0.016 0.33 NO
72 DDX23 DDX23 DDX23 6625 0.016 0.33 NO
73 NCBP1 NCBP1 NCBP1 6715 0.014 0.33 NO
74 PPIH PPIH PPIH 6756 0.014 0.33 NO
75 SF3B1 SF3B1 SF3B1 6761 0.014 0.33 NO
76 U2AF1 U2AF1 U2AF1 6970 0.011 0.32 NO
77 RBM8A RBM8A RBM8A 7004 0.01 0.32 NO
78 LSM4 LSM4 LSM4 7118 0.009 0.32 NO
79 SFRS9 SFRS9 SFRS9 7203 0.0077 0.31 NO
80 SNRPD1 SNRPD1 SNRPD1 7273 0.0065 0.31 NO
81 ACIN1 ACIN1 ACIN1 7411 0.0045 0.3 NO
82 WBP11 WBP11 WBP11 7437 0.004 0.3 NO
83 SNRPC SNRPC SNRPC 7461 0.0037 0.3 NO
84 PRPF38A PRPF38A PRPF38A 7483 0.0034 0.3 NO
85 U2AF2 U2AF2 U2AF2 7626 0.0013 0.29 NO
86 PCBP1 PCBP1 PCBP1 7644 0.0011 0.29 NO
87 DHX15 DHX15 DHX15 7735 0.000066 0.29 NO
88 HNRNPC HNRNPC HNRNPC 7748 -0.00015 0.29 NO
89 DHX38 DHX38 DHX38 7773 -0.00054 0.28 NO
90 AQR AQR AQR 7955 -0.0032 0.28 NO
91 EFTUD2 EFTUD2 EFTUD2 8043 -0.0043 0.27 NO
92 SNRPA SNRPA SNRPA 8112 -0.0053 0.27 NO
93 TRA2B TRA2B TRA2B 8127 -0.0055 0.27 NO
94 PRPF8 PRPF8 PRPF8 8179 -0.0062 0.27 NO
95 HNRNPM HNRNPM HNRNPM 8182 -0.0064 0.27 NO
96 HSPA1A HSPA1A HSPA1A 8366 -0.009 0.26 NO
97 PHF5A PHF5A PHF5A 8494 -0.011 0.25 NO
98 SFRS7 SFRS7 SFRS7 8509 -0.011 0.25 NO
99 SF3A1 SF3A1 SF3A1 8556 -0.012 0.25 NO
100 SNRNP70 SNRNP70 SNRNP70 8674 -0.013 0.25 NO
101 DHX16 DHX16 DHX16 8746 -0.014 0.24 NO
102 XAB2 XAB2 XAB2 9102 -0.019 0.23 NO
103 BAT1 BAT1 BAT1 9245 -0.021 0.22 NO
104 HNRNPA1 HNRNPA1 HNRNPA1 9288 -0.022 0.22 NO
105 PRPF4 PRPF4 PRPF4 9339 -0.023 0.22 NO
106 PPIE PPIE PPIE 9495 -0.025 0.22 NO
107 PRPF31 PRPF31 PRPF31 9701 -0.028 0.21 NO
108 SF3B4 SF3B4 SF3B4 9797 -0.029 0.21 NO
109 SFRS2 SFRS2 SFRS2 10254 -0.036 0.19 NO
110 EIF4A3 EIF4A3 EIF4A3 10307 -0.037 0.19 NO
111 THOC3 THOC3 THOC3 10462 -0.04 0.19 NO
112 HSPA8 HSPA8 HSPA8 10531 -0.041 0.19 NO
113 PUF60 PUF60 PUF60 10567 -0.041 0.2 NO
114 LSM7 LSM7 LSM7 10868 -0.046 0.18 NO
115 LSM2 LSM2 LSM2 11343 -0.055 0.17 NO
116 PPIL1 PPIL1 PPIL1 11458 -0.058 0.17 NO
117 SNRPB SNRPB SNRPB 11761 -0.064 0.16 NO
118 SF3B5 SF3B5 SF3B5 12189 -0.074 0.15 NO
119 TXNL4A TXNL4A TXNL4A 12225 -0.075 0.16 NO
120 HSPA6 HSPA6 HSPA6 12304 -0.076 0.16 NO
121 SNRNP40 SNRNP40 SNRNP40 12467 -0.08 0.16 NO
122 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 13234 -0.1 0.14 NO
123 HSPA1B HSPA1B HSPA1B 15249 -0.19 0.049 NO
124 HSPA2 HSPA2 HSPA2 16600 -0.3 0.015 NO
125 HSPA1L HSPA1L HSPA1L 17692 -0.49 0.022 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: BIOCARTA RACCYCD PATHWAY.

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

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

Table 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 PIPOX PIPOX PIPOX 1 0.58 0.089 YES
2 BAAT BAAT BAAT 36 0.41 0.15 YES
3 ACSL6 ACSL6 ACSL6 48 0.39 0.21 YES
4 DDO DDO DDO 223 0.27 0.24 YES
5 PECR PECR PECR 270 0.25 0.28 YES
6 AMACR AMACR AMACR 661 0.18 0.28 YES
7 CROT CROT CROT 705 0.17 0.31 YES
8 PEX12 PEX12 PEX12 764 0.17 0.33 YES
9 NUDT12 NUDT12 NUDT12 885 0.16 0.35 YES
10 HAO2 HAO2 HAO2 1398 0.12 0.34 YES
11 PEX1 PEX1 PEX1 1478 0.12 0.35 YES
12 ACSL4 ACSL4 ACSL4 1526 0.12 0.37 YES
13 PRDX5 PRDX5 PRDX5 1795 0.11 0.37 YES
14 PXMP4 PXMP4 PXMP4 1861 0.11 0.38 YES
15 FAR1 FAR1 FAR1 1978 0.1 0.39 YES
16 ACOT8 ACOT8 ACOT8 2181 0.098 0.4 YES
17 PEX3 PEX3 PEX3 2535 0.088 0.39 YES
18 AGXT AGXT AGXT 2584 0.087 0.4 YES
19 PHYH PHYH PHYH 2757 0.083 0.41 YES
20 ACSL3 ACSL3 ACSL3 3533 0.066 0.37 NO
21 ACSL5 ACSL5 ACSL5 3790 0.061 0.37 NO
22 PEX16 PEX16 PEX16 3947 0.058 0.37 NO
23 PEX13 PEX13 PEX13 4335 0.051 0.36 NO
24 AGPS AGPS AGPS 4502 0.048 0.35 NO
25 SCP2 SCP2 SCP2 4536 0.047 0.36 NO
26 ACOX1 ACOX1 ACOX1 4789 0.043 0.35 NO
27 HSD17B4 HSD17B4 HSD17B4 4994 0.04 0.35 NO
28 SLC25A17 SLC25A17 SLC25A17 5011 0.039 0.35 NO
29 NUDT19 NUDT19 NUDT19 5056 0.038 0.36 NO
30 EHHADH EHHADH EHHADH 5101 0.038 0.36 NO
31 GSTK1 GSTK1 GSTK1 5121 0.038 0.36 NO
32 SOD1 SOD1 SOD1 5391 0.033 0.35 NO
33 PEX5 PEX5 PEX5 5537 0.031 0.35 NO
34 PEX7 PEX7 PEX7 5639 0.03 0.35 NO
35 HACL1 HACL1 HACL1 5981 0.025 0.33 NO
36 PRDX1 PRDX1 PRDX1 6198 0.022 0.33 NO
37 FAR2 FAR2 FAR2 6283 0.02 0.32 NO
38 PEX2 PEX2 PEX2 6342 0.019 0.32 NO
39 IDH1 IDH1 IDH1 6599 0.016 0.31 NO
40 ACSL1 ACSL1 ACSL1 6790 0.013 0.3 NO
41 EPHX2 EPHX2 EPHX2 6844 0.013 0.3 NO
42 GNPAT GNPAT GNPAT 6845 0.013 0.3 NO
43 CAT CAT CAT 7129 0.0088 0.29 NO
44 PEX11B PEX11B PEX11B 7576 0.0019 0.27 NO
45 ACOX3 ACOX3 ACOX3 7680 0.00073 0.26 NO
46 PMVK PMVK PMVK 7689 0.00068 0.26 NO
47 PEX11A PEX11A PEX11A 8040 -0.0043 0.24 NO
48 MPV17 MPV17 MPV17 8157 -0.006 0.24 NO
49 ABCD3 ABCD3 ABCD3 8404 -0.0095 0.22 NO
50 SOD2 SOD2 SOD2 8419 -0.0097 0.22 NO
51 IDH2 IDH2 IDH2 8736 -0.014 0.21 NO
52 PEX10 PEX10 PEX10 9014 -0.018 0.2 NO
53 PEX19 PEX19 PEX19 9235 -0.021 0.19 NO
54 MLYCD MLYCD MLYCD 9338 -0.023 0.18 NO
55 DHRS4 DHRS4 DHRS4 9361 -0.023 0.19 NO
56 PEX14 PEX14 PEX14 9434 -0.024 0.19 NO
57 DECR2 DECR2 DECR2 9444 -0.024 0.19 NO
58 MPV17L MPV17L MPV17L 9545 -0.026 0.19 NO
59 ABCD1 ABCD1 ABCD1 9620 -0.026 0.19 NO
60 PAOX PAOX PAOX 9838 -0.03 0.18 NO
61 SLC27A2 SLC27A2 SLC27A2 10013 -0.032 0.18 NO
62 HMGCL HMGCL HMGCL 10121 -0.034 0.18 NO
63 ECH1 ECH1 ECH1 10273 -0.037 0.17 NO
64 MVK MVK MVK 10930 -0.048 0.14 NO
65 ACAA1 ACAA1 ACAA1 11355 -0.056 0.13 NO
66 PEX6 PEX6 PEX6 11453 -0.057 0.13 NO
67 PEX26 PEX26 PEX26 11651 -0.062 0.13 NO
68 CRAT CRAT CRAT 12291 -0.076 0.11 NO
69 PEX11G PEX11G PEX11G 12910 -0.091 0.088 NO
70 ABCD4 ABCD4 ABCD4 12920 -0.092 0.1 NO
71 PXMP2 PXMP2 PXMP2 13068 -0.096 0.11 NO
72 PECI PECI PECI 13885 -0.12 0.082 NO
73 XDH XDH XDH 15259 -0.19 0.036 NO
74 ABCD2 ABCD2 ABCD2 16029 -0.24 0.03 NO
75 DAO DAO DAO 16095 -0.25 0.065 NO
76 NOS2 NOS2 NOS2 16591 -0.29 0.083 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: BIOCARTA CHREBP2 PATHWAY.

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA WNT PATHWAY

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 RPA4 RPA4 RPA4 385 0.22 0.082 YES
2 SHFM1 SHFM1 SHFM1 567 0.19 0.16 YES
3 MRE11A MRE11A MRE11A 921 0.15 0.22 YES
4 BRCA2 BRCA2 BRCA2 1228 0.13 0.26 YES
5 XRCC2 XRCC2 XRCC2 1263 0.13 0.33 YES
6 RPA3 RPA3 RPA3 2070 0.1 0.33 YES
7 RAD50 RAD50 RAD50 2104 0.1 0.38 YES
8 SSBP1 SSBP1 SSBP1 2157 0.098 0.42 YES
9 NBN NBN NBN 2726 0.083 0.43 YES
10 BLM BLM BLM 3342 0.07 0.43 NO
11 RAD54B RAD54B RAD54B 4625 0.046 0.38 NO
12 RAD51L3 RAD51L3 RAD51L3 5923 0.025 0.32 NO
13 EME1 EME1 EME1 7646 0.0011 0.22 NO
14 POLD4 POLD4 POLD4 7658 0.00096 0.22 NO
15 POLD2 POLD2 POLD2 8026 -0.0041 0.21 NO
16 RPA1 RPA1 RPA1 8571 -0.012 0.18 NO
17 POLD3 POLD3 POLD3 8759 -0.014 0.18 NO
18 RPA2 RPA2 RPA2 9337 -0.023 0.16 NO
19 RAD51L1 RAD51L1 RAD51L1 10504 -0.04 0.11 NO
20 RAD52 RAD52 RAD52 10509 -0.041 0.13 NO
21 MUS81 MUS81 MUS81 10553 -0.041 0.15 NO
22 RAD54L RAD54L RAD54L 10851 -0.046 0.15 NO
23 TOP3A TOP3A TOP3A 11342 -0.055 0.15 NO
24 RAD51 RAD51 RAD51 12657 -0.084 0.12 NO
25 TOP3B TOP3B TOP3B 12700 -0.086 0.16 NO
26 POLD1 POLD1 POLD1 13298 -0.1 0.18 NO
27 XRCC3 XRCC3 XRCC3 15174 -0.18 0.16 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: BIOCARTA WNT PATHWAY.

Figure S70.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA WNT PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CITRATE CYCLE TCA CYCLE

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPA4 RPA4 RPA4 385 0.22 0.062 YES
2 ERCC5 ERCC5 ERCC5 1726 0.11 0.031 YES
3 CETN2 CETN2 CETN2 1790 0.11 0.07 YES
4 CDK7 CDK7 CDK7 1819 0.11 0.11 YES
5 CUL4B CUL4B CUL4B 1852 0.11 0.15 YES
6 RFC3 RFC3 RFC3 1911 0.11 0.19 YES
7 GTF2H5 GTF2H5 GTF2H5 2068 0.1 0.22 YES
8 RPA3 RPA3 RPA3 2070 0.1 0.26 YES
9 RFC1 RFC1 RFC1 2976 0.078 0.24 YES
10 CUL4A CUL4A CUL4A 3099 0.075 0.26 YES
11 XPA XPA XPA 3163 0.074 0.28 YES
12 CCNH CCNH CCNH 3247 0.072 0.31 YES
13 XPC XPC XPC 3658 0.063 0.31 YES
14 GTF2H1 GTF2H1 GTF2H1 4058 0.056 0.31 YES
15 RFC4 RFC4 RFC4 4167 0.054 0.32 YES
16 RFC5 RFC5 RFC5 4909 0.041 0.3 NO
17 RAD23A RAD23A RAD23A 5032 0.039 0.31 NO
18 ERCC6 ERCC6 ERCC6 5320 0.034 0.3 NO
19 RFC2 RFC2 RFC2 5350 0.034 0.32 NO
20 MNAT1 MNAT1 MNAT1 6048 0.024 0.29 NO
21 ERCC4 ERCC4 ERCC4 6067 0.024 0.29 NO
22 DDB1 DDB1 DDB1 6713 0.014 0.26 NO
23 RBX1 RBX1 RBX1 6759 0.014 0.27 NO
24 ERCC3 ERCC3 ERCC3 7226 0.0073 0.24 NO
25 POLE4 POLE4 POLE4 7384 0.0049 0.24 NO
26 POLD4 POLD4 POLD4 7658 0.00096 0.22 NO
27 POLE POLE POLE 7887 -0.0022 0.21 NO
28 POLD2 POLD2 POLD2 8026 -0.0041 0.2 NO
29 LIG1 LIG1 LIG1 8101 -0.0052 0.2 NO
30 RPA1 RPA1 RPA1 8571 -0.012 0.18 NO
31 POLD3 POLD3 POLD3 8759 -0.014 0.18 NO
32 ERCC8 ERCC8 ERCC8 9062 -0.018 0.17 NO
33 RPA2 RPA2 RPA2 9337 -0.023 0.16 NO
34 POLE3 POLE3 POLE3 9415 -0.024 0.16 NO
35 GTF2H3 GTF2H3 GTF2H3 9965 -0.032 0.15 NO
36 ERCC1 ERCC1 ERCC1 10721 -0.044 0.12 NO
37 POLE2 POLE2 POLE2 11263 -0.054 0.11 NO
38 GTF2H4 GTF2H4 GTF2H4 11884 -0.067 0.1 NO
39 PCNA PCNA PCNA 12206 -0.074 0.12 NO
40 DDB2 DDB2 DDB2 12908 -0.091 0.11 NO
41 ERCC2 ERCC2 ERCC2 13267 -0.1 0.13 NO
42 POLD1 POLD1 POLD1 13298 -0.1 0.17 NO
43 GTF2H2 GTF2H2 GTF2H2 16099 -0.25 0.11 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 CITRATE CYCLE TCA CYCLE.

Figure S72.  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 CYSTEINE AND METHIONINE 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 ABAT ABAT ABAT 64 0.36 0.19 YES
2 ACAT1 ACAT1 ACAT1 1908 0.11 0.14 YES
3 ACSS1 ACSS1 ACSS1 1962 0.1 0.2 YES
4 SUCLA2 SUCLA2 SUCLA2 2971 0.078 0.18 YES
5 HIBCH HIBCH HIBCH 3167 0.074 0.21 YES
6 ACSS2 ACSS2 ACSS2 3518 0.066 0.22 YES
7 ALDH2 ALDH2 ALDH2 3527 0.066 0.26 YES
8 ACACB ACACB ACACB 4040 0.056 0.26 YES
9 MCEE MCEE MCEE 4065 0.056 0.29 YES
10 ALDH7A1 ALDH7A1 ALDH7A1 4118 0.055 0.32 YES
11 LDHB LDHB LDHB 4575 0.047 0.32 YES
12 SUCLG2 SUCLG2 SUCLG2 5076 0.038 0.31 YES
13 EHHADH EHHADH EHHADH 5101 0.038 0.33 YES
14 SUCLG1 SUCLG1 SUCLG1 5262 0.036 0.34 YES
15 LDHA LDHA LDHA 5392 0.033 0.35 YES
16 ACADM ACADM ACADM 5574 0.031 0.35 YES
17 ALDH3A2 ALDH3A2 ALDH3A2 5652 0.03 0.36 YES
18 ACAT2 ACAT2 ACAT2 5796 0.028 0.37 YES
19 ALDH9A1 ALDH9A1 ALDH9A1 6177 0.022 0.36 NO
20 MUT MUT MUT 6376 0.019 0.36 NO
21 ALDH1B1 ALDH1B1 ALDH1B1 6600 0.016 0.36 NO
22 LDHAL6A LDHAL6A LDHAL6A 6743 0.014 0.36 NO
23 ACACA ACACA ACACA 8100 -0.0052 0.28 NO
24 HADHA HADHA HADHA 8260 -0.0075 0.28 NO
25 MLYCD MLYCD MLYCD 9338 -0.023 0.23 NO
26 PCCA PCCA PCCA 9384 -0.023 0.24 NO
27 ECHS1 ECHS1 ECHS1 9821 -0.03 0.23 NO
28 PCCB PCCB PCCB 10588 -0.042 0.21 NO
29 ACSS3 ACSS3 ACSS3 13685 -0.12 0.1 NO
30 ALDH6A1 ALDH6A1 ALDH6A1 13706 -0.12 0.16 NO
31 LDHAL6B LDHAL6B LDHAL6B 14422 -0.15 0.2 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 CYSTEINE AND METHIONINE METABOLISM.

Figure S74.  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 LYSINE DEGRADATION

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 MAT1A MAT1A MAT1A 160 0.29 0.18 YES
2 GGT7 GGT7 GGT7 456 0.2 0.29 YES
3 TRMT11 TRMT11 TRMT11 1412 0.12 0.32 YES
4 WBSCR22 WBSCR22 WBSCR22 2416 0.091 0.32 YES
5 METTL6 METTL6 METTL6 2795 0.082 0.35 YES
6 AHCY AHCY AHCY 3710 0.062 0.34 NO
7 PAPSS1 PAPSS1 PAPSS1 5195 0.037 0.28 NO
8 LCMT1 LCMT1 LCMT1 5670 0.029 0.28 NO
9 SEPHS1 SEPHS1 SEPHS1 6504 0.018 0.24 NO
10 MAT2B MAT2B MAT2B 6517 0.017 0.25 NO
11 HEMK1 HEMK1 HEMK1 6597 0.016 0.26 NO
12 MARS2 MARS2 MARS2 7194 0.0078 0.23 NO
13 METTL2B METTL2B METTL2B 8299 -0.0081 0.17 NO
14 GGT1 GGT1 GGT1 8539 -0.011 0.17 NO
15 MARS MARS MARS 8643 -0.013 0.17 NO
16 AHCYL1 AHCYL1 AHCYL1 9192 -0.02 0.15 NO
17 CTH CTH CTH 9711 -0.028 0.14 NO
18 LCMT2 LCMT2 LCMT2 9825 -0.03 0.16 NO
19 MAT2A MAT2A MAT2A 9958 -0.031 0.17 NO
20 GGT5 GGT5 GGT5 9960 -0.032 0.19 NO
21 SCLY SCLY SCLY 10157 -0.034 0.2 NO
22 CBS CBS CBS 10902 -0.047 0.19 NO
23 GGT6 GGT6 GGT6 11824 -0.066 0.18 NO
24 AHCYL2 AHCYL2 AHCYL2 12818 -0.089 0.18 NO
25 PAPSS2 PAPSS2 PAPSS2 14948 -0.17 0.17 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 LYSINE DEGRADATION.

Figure S76.  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 SELENOAMINO ACID 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 FBXO2 FBXO2 FBXO2 123 0.31 0.031 YES
2 NEDD4 NEDD4 NEDD4 676 0.17 0.021 YES
3 AIRE AIRE AIRE 1021 0.15 0.02 YES
4 CUL5 CUL5 CUL5 1211 0.14 0.026 YES
5 UBE2C UBE2C UBE2C 1348 0.13 0.034 YES
6 ITCH ITCH ITCH 1436 0.12 0.044 YES
7 UBE2B UBE2B UBE2B 1551 0.12 0.052 YES
8 HERC3 HERC3 HERC3 1622 0.12 0.062 YES
9 CUL4B CUL4B CUL4B 1852 0.11 0.062 YES
10 ANAPC10 ANAPC10 ANAPC10 1921 0.11 0.071 YES
11 ANAPC13 ANAPC13 ANAPC13 2019 0.1 0.078 YES
12 TCEB1 TCEB1 TCEB1 2185 0.098 0.08 YES
13 UBE2W UBE2W UBE2W 2272 0.095 0.087 YES
14 FANCL FANCL FANCL 2349 0.092 0.094 YES
15 FBXW7 FBXW7 FBXW7 2381 0.092 0.1 YES
16 MID1 MID1 MID1 2443 0.09 0.11 YES
17 UBE4A UBE4A UBE4A 2479 0.089 0.12 YES
18 XIAP XIAP XIAP 2489 0.089 0.13 YES
19 CBL CBL CBL 2643 0.085 0.13 YES
20 BRCA1 BRCA1 BRCA1 2648 0.085 0.14 YES
21 PARK2 PARK2 PARK2 2676 0.084 0.15 YES
22 WWP1 WWP1 WWP1 2724 0.083 0.16 YES
23 CUL1 CUL1 CUL1 2885 0.079 0.16 YES
24 UBE2H UBE2H UBE2H 3053 0.076 0.16 YES
25 CUL4A CUL4A CUL4A 3099 0.075 0.16 YES
26 CDC16 CDC16 CDC16 3248 0.072 0.16 YES
27 UBA6 UBA6 UBA6 3260 0.072 0.17 YES
28 UBA2 UBA2 UBA2 3680 0.063 0.16 YES
29 SYVN1 SYVN1 SYVN1 3690 0.063 0.16 YES
30 SIAH1 SIAH1 SIAH1 3866 0.059 0.16 YES
31 UBE2N UBE2N UBE2N 3901 0.058 0.17 YES
32 UBE2D1 UBE2D1 UBE2D1 3962 0.058 0.17 YES
33 ANAPC4 ANAPC4 ANAPC4 4135 0.054 0.17 YES
34 FBXO4 FBXO4 FBXO4 4139 0.054 0.17 YES
35 HERC4 HERC4 HERC4 4142 0.054 0.18 YES
36 RNF7 RNF7 RNF7 4186 0.054 0.18 YES
37 UBE2K UBE2K UBE2K 4371 0.05 0.18 YES
38 UBE3A UBE3A UBE3A 4396 0.05 0.18 YES
39 CDC27 CDC27 CDC27 4466 0.048 0.19 YES
40 BIRC2 BIRC2 BIRC2 4555 0.047 0.19 YES
41 CUL3 CUL3 CUL3 4570 0.047 0.19 YES
42 RHOBTB2 RHOBTB2 RHOBTB2 4620 0.046 0.2 YES
43 MAP3K1 MAP3K1 MAP3K1 4811 0.043 0.19 YES
44 HUWE1 HUWE1 HUWE1 4975 0.04 0.19 YES
45 UBE2D4 UBE2D4 UBE2D4 4976 0.04 0.19 YES
46 CDC23 CDC23 CDC23 5027 0.039 0.19 YES
47 UBR5 UBR5 UBR5 5063 0.038 0.2 YES
48 UBE2E3 UBE2E3 UBE2E3 5179 0.037 0.19 YES
49 SMURF2 SMURF2 SMURF2 5200 0.036 0.2 YES
50 BIRC6 BIRC6 BIRC6 5307 0.035 0.2 YES
51 DET1 DET1 DET1 5345 0.034 0.2 YES
52 TRIM37 TRIM37 TRIM37 5456 0.032 0.2 YES
53 UBE2A UBE2A UBE2A 5469 0.032 0.2 YES
54 PRPF19 PRPF19 PRPF19 5666 0.029 0.19 NO
55 SKP1 SKP1 SKP1 5863 0.026 0.18 NO
56 SMURF1 SMURF1 SMURF1 5878 0.026 0.18 NO
57 UBA3 UBA3 UBA3 6172 0.022 0.17 NO
58 UBE2E1 UBE2E1 UBE2E1 6174 0.022 0.17 NO
59 UBE2O UBE2O UBE2O 6287 0.02 0.17 NO
60 UBE2Q1 UBE2Q1 UBE2Q1 6350 0.019 0.17 NO
61 UBE2I UBE2I UBE2I 6386 0.019 0.17 NO
62 UBE4B UBE4B UBE4B 6402 0.019 0.17 NO
63 UBE3C UBE3C UBE3C 6445 0.018 0.17 NO
64 DDB1 DDB1 DDB1 6713 0.014 0.16 NO
65 RBX1 RBX1 RBX1 6759 0.014 0.16 NO
66 UBE2M UBE2M UBE2M 6887 0.012 0.15 NO
67 UBE2G2 UBE2G2 UBE2G2 6895 0.012 0.15 NO
68 UBE2G1 UBE2G1 UBE2G1 6917 0.012 0.15 NO
69 ANAPC7 ANAPC7 ANAPC7 7046 0.01 0.15 NO
70 CUL2 CUL2 CUL2 7119 0.009 0.14 NO
71 UBA1 UBA1 UBA1 7144 0.0086 0.14 NO
72 FBXW11 FBXW11 FBXW11 7260 0.0067 0.14 NO
73 UBE2D3 UBE2D3 UBE2D3 7275 0.0064 0.14 NO
74 UBE2J1 UBE2J1 UBE2J1 7381 0.0049 0.13 NO
75 UBE2D2 UBE2D2 UBE2D2 7464 0.0036 0.13 NO
76 MDM2 MDM2 MDM2 7546 0.0024 0.12 NO
77 TRIP12 TRIP12 TRIP12 7561 0.0021 0.12 NO
78 FBXW8 FBXW8 FBXW8 7585 0.0018 0.12 NO
79 UBE3B UBE3B UBE3B 7691 0.00066 0.12 NO
80 UBE2L3 UBE2L3 UBE2L3 7754 -0.00025 0.11 NO
81 RFWD2 RFWD2 RFWD2 7876 -0.0021 0.11 NO
82 UBE2F UBE2F UBE2F 8116 -0.0053 0.094 NO
83 CDC34 CDC34 CDC34 8165 -0.0061 0.092 NO
84 PPIL2 PPIL2 PPIL2 8170 -0.0061 0.093 NO
85 HERC2 HERC2 HERC2 8526 -0.011 0.074 NO
86 UBE2Z UBE2Z UBE2Z 8750 -0.014 0.064 NO
87 SAE1 SAE1 SAE1 8766 -0.014 0.065 NO
88 UBE2R2 UBE2R2 UBE2R2 8866 -0.016 0.061 NO
89 TCEB2 TCEB2 TCEB2 8899 -0.016 0.061 NO
90 TRAF6 TRAF6 TRAF6 9022 -0.018 0.057 NO
91 FZR1 FZR1 FZR1 9027 -0.018 0.058 NO
92 ERCC8 ERCC8 ERCC8 9062 -0.018 0.059 NO
93 KLHL9 KLHL9 KLHL9 9219 -0.021 0.053 NO
94 NEDD4L NEDD4L NEDD4L 9373 -0.023 0.047 NO
95 ANAPC5 ANAPC5 ANAPC5 9518 -0.025 0.042 NO
96 RCHY1 RCHY1 RCHY1 9605 -0.026 0.04 NO
97 UBE2Q2 UBE2Q2 UBE2Q2 9615 -0.026 0.043 NO
98 ANAPC1 ANAPC1 ANAPC1 9618 -0.026 0.046 NO
99 UBE2E2 UBE2E2 UBE2E2 9654 -0.027 0.047 NO
100 CUL7 CUL7 CUL7 9699 -0.028 0.048 NO
101 CBLB CBLB CBLB 9761 -0.029 0.048 NO
102 HERC1 HERC1 HERC1 9796 -0.029 0.05 NO
103 WWP2 WWP2 WWP2 9946 -0.031 0.046 NO
104 BIRC3 BIRC3 BIRC3 10054 -0.033 0.044 NO
105 KEAP1 KEAP1 KEAP1 10109 -0.034 0.045 NO
106 ANAPC11 ANAPC11 ANAPC11 11171 -0.052 -0.0082 NO
107 VHL VHL VHL 11328 -0.055 -0.01 NO
108 MGRN1 MGRN1 MGRN1 11463 -0.058 -0.011 NO
109 UBE2QL1 UBE2QL1 UBE2QL1 11535 -0.059 -0.0076 NO
110 SKP2 SKP2 SKP2 11641 -0.062 -0.0059 NO
111 STUB1 STUB1 STUB1 11808 -0.065 -0.0073 NO
112 UBE2J2 UBE2J2 UBE2J2 12335 -0.077 -0.027 NO
113 UBA7 UBA7 UBA7 12360 -0.078 -0.019 NO
114 UBE2L6 UBE2L6 UBE2L6 12528 -0.081 -0.019 NO
115 SOCS3 SOCS3 SOCS3 12538 -0.082 -0.0094 NO
116 UBOX5 UBOX5 UBOX5 12606 -0.083 -0.0031 NO
117 PIAS1 PIAS1 PIAS1 12838 -0.089 -0.0052 NO
118 DDB2 DDB2 DDB2 12908 -0.091 0.002 NO
119 TRIM32 TRIM32 TRIM32 12997 -0.094 0.0084 NO
120 PIAS3 PIAS3 PIAS3 13221 -0.1 0.0082 NO
121 NHLRC1 NHLRC1 NHLRC1 13330 -0.1 0.015 NO
122 PIAS4 PIAS4 PIAS4 13366 -0.1 0.026 NO
123 ANAPC2 ANAPC2 ANAPC2 13455 -0.11 0.034 NO
124 PML PML PML 13465 -0.11 0.046 NO
125 CDC20 CDC20 CDC20 13589 -0.11 0.053 NO
126 CBLC CBLC CBLC 13630 -0.12 0.065 NO
127 CDC26 CDC26 CDC26 14554 -0.15 0.032 NO
128 PIAS2 PIAS2 PIAS2 14871 -0.17 0.035 NO
129 UBE2S UBE2S UBE2S 15332 -0.19 0.032 NO
130 KLHL13 KLHL13 KLHL13 16116 -0.25 0.019 NO
131 UBE2NL UBE2NL UBE2NL 17205 -0.37 0.0029 NO
132 SOCS1 SOCS1 SOCS1 17284 -0.38 0.045 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 SELENOAMINO ACID METABOLISM.

Figure S78.  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 PROPANOATE 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 WIF1 WIF1 WIF1 11 0.48 0.3 YES
2 LEF1 LEF1 LEF1 1653 0.12 0.29 NO
3 GSK3B GSK3B GSK3B 4170 0.054 0.18 NO
4 NLK NLK NLK 4176 0.054 0.22 NO
5 CCND1 CCND1 CCND1 4328 0.051 0.24 NO
6 APC APC APC 4954 0.04 0.23 NO
7 AXIN1 AXIN1 AXIN1 5212 0.036 0.24 NO
8 TAB1 TAB1 TAB1 5370 0.034 0.25 NO
9 MYC MYC MYC 5754 0.028 0.25 NO
10 MAP3K7 MAP3K7 MAP3K7 5821 0.027 0.26 NO
11 CSNK1A1 CSNK1A1 CSNK1A1 6303 0.02 0.25 NO
12 HDAC1 HDAC1 HDAC1 6920 0.012 0.22 NO
13 BTRC BTRC BTRC 7217 0.0074 0.21 NO
14 CSNK1D CSNK1D CSNK1D 7581 0.0019 0.19 NO
15 CREBBP CREBBP CREBBP 7643 0.0011 0.19 NO
16 CTNNB1 CTNNB1 CTNNB1 8263 -0.0075 0.16 NO
17 CTBP1 CTBP1 CTBP1 8505 -0.011 0.15 NO
18 PPP2CA PPP2CA PPP2CA 8583 -0.012 0.16 NO
19 SMAD4 SMAD4 SMAD4 8684 -0.013 0.16 NO
20 CSNK2A1 CSNK2A1 CSNK2A1 10106 -0.034 0.1 NO
21 FRAT1 FRAT1 FRAT1 10429 -0.039 0.11 NO
22 DVL1 DVL1 DVL1 11957 -0.069 0.066 NO
23 FZD1 FZD1 FZD1 12783 -0.088 0.076 NO
24 TLE1 TLE1 TLE1 14483 -0.15 0.076 NO
25 WNT1 WNT1 WNT1 15346 -0.19 0.15 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 PROPANOATE METABOLISM.

Figure S80.  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

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
BIOCARTA FMLP PATHWAY 34 genes.ES.table 0.41 1.4 0.15 1 0.97 0.088 0.084 0.081 1 0.69
KEGG GLYCOLYSIS GLUCONEOGENESIS 58 genes.ES.table 0.37 1.2 0.22 1 0.99 0.31 0.26 0.23 1 0.69
KEGG PENTOSE PHOSPHATE PATHWAY 26 genes.ES.table 0.47 1.4 0.11 1 0.95 0.58 0.37 0.37 1 0.76
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.35 1.2 0.21 1 0.99 0.58 0.3 0.4 1 0.61
KEGG OXIDATIVE PHOSPHORYLATION 112 genes.ES.table 0.32 1.1 0.39 1 1 0.4 0.31 0.28 1 0.74
KEGG PYRIMIDINE METABOLISM 96 genes.ES.table 0.28 1.3 0.21 1 0.99 0.42 0.31 0.29 1 0.74
KEGG ARGININE AND PROLINE METABOLISM 52 genes.ES.table 0.36 1.2 0.17 1 0.99 0.35 0.26 0.26 1 0.68
KEGG TYROSINE METABOLISM 39 genes.ES.table 0.39 1.1 0.33 1 1 0.46 0.28 0.33 1 0.73
KEGG GLUTATHIONE METABOLISM 45 genes.ES.table 0.38 1.3 0.2 1 0.99 0.38 0.27 0.28 1 0.7
KEGG GLYCEROPHOSPHOLIPID METABOLISM 71 genes.ES.table 0.31 1.2 0.17 1 0.99 0.3 0.22 0.23 1 0.56
genes ES table in pathway: BIOCARTA FMLP PATHWAY

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 TUBB4Q TUBB4Q TUBB4Q 22 1.6 0.16 YES
2 TUBB8 TUBB8 TUBB8 46 1.4 0.3 YES
3 TUBA3D TUBA3D TUBA3D 337 0.71 0.35 YES
4 TUBA1A TUBA1A TUBA1A 599 0.49 0.39 YES
5 TUBB2A TUBB2A TUBB2A 601 0.49 0.44 YES
6 TUBB3 TUBB3 TUBB3 1143 0.32 0.44 YES
7 TUBA8 TUBA8 TUBA8 1875 0.23 0.43 YES
8 TUBAL3 TUBAL3 TUBAL3 1970 0.22 0.44 YES
9 TUBA1C TUBA1C TUBA1C 3041 0.16 0.4 NO
10 TUBA3E TUBA3E TUBA3E 3395 0.15 0.4 NO
11 CD14 CD14 CD14 3878 0.13 0.38 NO
12 TUBB6 TUBB6 TUBB6 3929 0.13 0.39 NO
13 TUBA4A TUBA4A TUBA4A 4137 0.12 0.4 NO
14 TUBB2C TUBB2C TUBB2C 4546 0.11 0.38 NO
15 TUBB4 TUBB4 TUBB4 4727 0.1 0.38 NO
16 ACTG1 ACTG1 ACTG1 5502 0.081 0.35 NO
17 ACTB ACTB ACTB 5873 0.072 0.34 NO
18 ARPC1A ARPC1A ARPC1A 6239 0.063 0.32 NO
19 ARPC1B ARPC1B ARPC1B 6262 0.062 0.33 NO
20 TUBB2B TUBB2B TUBB2B 6556 0.055 0.32 NO
21 TUBA1B TUBA1B TUBA1B 6697 0.052 0.32 NO
22 ARPC5L ARPC5L ARPC5L 6888 0.048 0.31 NO
23 NCK2 NCK2 NCK2 7072 0.044 0.3 NO
24 TUBB TUBB TUBB 7353 0.037 0.29 NO
25 OCLN OCLN OCLN 7672 0.03 0.28 NO
26 CTTN CTTN CTTN 7776 0.028 0.27 NO
27 KRT18 KRT18 KRT18 7969 0.023 0.27 NO
28 ARPC4 ARPC4 ARPC4 8376 0.014 0.24 NO
29 TUBA3C TUBA3C TUBA3C 8591 0.0095 0.23 NO
30 WAS WAS WAS 8708 0.0074 0.23 NO
31 YWHAQ YWHAQ YWHAQ 8836 0.0044 0.22 NO
32 CTNNB1 CTNNB1 CTNNB1 8855 0.0039 0.22 NO
33 ARPC2 ARPC2 ARPC2 8867 0.0037 0.22 NO
34 ABL1 ABL1 ABL1 9176 -0.0034 0.2 NO
35 RHOA RHOA RHOA 10371 -0.028 0.14 NO
36 EZR EZR EZR 11659 -0.057 0.075 NO
37 CDH1 CDH1 CDH1 11813 -0.06 0.073 NO
38 TUBB1 TUBB1 TUBB1 12083 -0.066 0.065 NO
39 ARHGEF2 ARHGEF2 ARHGEF2 12209 -0.069 0.065 NO
40 YWHAZ YWHAZ YWHAZ 12618 -0.078 0.05 NO
41 ARPC5 ARPC5 ARPC5 12792 -0.082 0.049 NO
42 ITGB1 ITGB1 ITGB1 13042 -0.088 0.044 NO
43 HCLS1 HCLS1 HCLS1 13678 -0.1 0.02 NO
44 CLDN1 CLDN1 CLDN1 13769 -0.11 0.026 NO
45 NCK1 NCK1 NCK1 14182 -0.12 0.015 NO
46 PRKCA PRKCA PRKCA 14204 -0.12 0.026 NO
47 WASL WASL WASL 14227 -0.12 0.036 NO
48 CDC42 CDC42 CDC42 14317 -0.12 0.044 NO
49 NCL NCL NCL 15015 -0.14 0.02 NO
50 ARPC3 ARPC3 ARPC3 15902 -0.17 -0.012 NO
51 TLR5 TLR5 TLR5 16162 -0.18 -0.0079 NO
52 FYN FYN FYN 16333 -0.19 0.0019 NO
53 ROCK2 ROCK2 ROCK2 16622 -0.2 0.0066 NO
54 ROCK1 ROCK1 ROCK1 16656 -0.2 0.026 NO
55 LY96 LY96 LY96 17314 -0.25 0.014 NO
56 TLR4 TLR4 TLR4 17568 -0.28 0.029 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: BIOCARTA FMLP PATHWAY.

Figure S82.  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: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 HIST1H4K HIST1H4K HIST1H4K 4 1.8 0.059 YES
2 HIST1H2BO HIST1H2BO HIST1H2BO 50 1.4 0.1 YES
3 HIST2H2AC HIST2H2AC HIST2H2AC 64 1.3 0.14 YES
4 HIST1H2AJ HIST1H2AJ HIST1H2AJ 142 1 0.17 YES
5 HIST2H3C HIST2H3C HIST2H3C 148 0.98 0.2 YES
6 HIST3H2A HIST3H2A HIST3H2A 237 0.83 0.22 YES
7 HIST1H2BN HIST1H2BN HIST1H2BN 260 0.8 0.25 YES
8 HIST2H3D HIST2H3D HIST2H3D 290 0.76 0.27 YES
9 HIST1H2BE HIST1H2BE HIST1H2BE 304 0.74 0.3 YES
10 FCGR2C FCGR2C FCGR2C 326 0.72 0.32 YES
11 HIST1H2BL HIST1H2BL HIST1H2BL 379 0.65 0.34 YES
12 HIST1H4J HIST1H4J HIST1H4J 409 0.62 0.36 YES
13 H2AFB1 H2AFB1 H2AFB1 508 0.55 0.37 YES
14 HIST2H4A HIST2H4A HIST2H4A 628 0.48 0.38 YES
15 HIST1H4I HIST1H4I HIST1H4I 653 0.47 0.39 YES
16 HIST1H3H HIST1H3H HIST1H3H 673 0.46 0.41 YES
17 HIST2H2BF HIST2H2BF HIST2H2BF 677 0.46 0.42 YES
18 H3F3C H3F3C H3F3C 697 0.45 0.44 YES
19 HIST1H4B HIST1H4B HIST1H4B 705 0.45 0.45 YES
20 FCGR3B FCGR3B FCGR3B 736 0.44 0.46 YES
21 FCGR1A FCGR1A FCGR1A 761 0.42 0.48 YES
22 HLA-DRB5 HLA-DRB5 HLA-DRB5 764 0.42 0.49 YES
23 C8G C8G C8G 776 0.42 0.5 YES
24 HIST1H4A HIST1H4A HIST1H4A 820 0.4 0.51 YES
25 HIST1H2AG HIST1H2AG HIST1H2AG 823 0.4 0.53 YES
26 HLA-DQA2 HLA-DQA2 HLA-DQA2 860 0.39 0.54 YES
27 HIST1H2AM HIST1H2AM HIST1H2AM 869 0.39 0.55 YES
28 HIST1H4E HIST1H4E HIST1H4E 893 0.38 0.56 YES
29 HIST1H2BH HIST1H2BH HIST1H2BH 935 0.37 0.57 YES
30 HIST1H3D HIST1H3D HIST1H3D 1025 0.35 0.58 YES
31 HIST3H2BB HIST3H2BB HIST3H2BB 1050 0.35 0.59 YES
32 HIST1H2BJ HIST1H2BJ HIST1H2BJ 1193 0.32 0.59 YES
33 HIST1H2BG HIST1H2BG HIST1H2BG 1333 0.29 0.59 YES
34 HIST3H3 HIST3H3 HIST3H3 1339 0.29 0.6 YES
35 FCGR2B FCGR2B FCGR2B 1343 0.29 0.61 YES
36 HIST1H2AL HIST1H2AL HIST1H2AL 1399 0.28 0.62 YES
37 HIST1H2BF HIST1H2BF HIST1H2BF 1462 0.28 0.62 YES
38 HIST1H2AB HIST1H2AB HIST1H2AB 1576 0.26 0.62 YES
39 ELANE ELANE ELANE 1647 0.26 0.63 YES
40 H2AFX H2AFX H2AFX 1714 0.25 0.63 YES
41 HIST1H3G HIST1H3G HIST1H3G 1720 0.25 0.64 YES
42 HIST1H2BI HIST1H2BI HIST1H2BI 1771 0.24 0.65 YES
43 HIST1H2AE HIST1H2AE HIST1H2AE 1886 0.23 0.65 YES
44 HIST1H3B HIST1H3B HIST1H3B 1897 0.23 0.66 YES
45 HIST1H2BC HIST1H2BC HIST1H2BC 2045 0.22 0.65 YES
46 HLA-DQB1 HLA-DQB1 HLA-DQB1 2085 0.22 0.66 YES
47 HLA-DRB1 HLA-DRB1 HLA-DRB1 2090 0.22 0.67 YES
48 HIST1H4C HIST1H4C HIST1H4C 2115 0.21 0.67 YES
49 HIST1H3F HIST1H3F HIST1H3F 2139 0.21 0.68 YES
50 HIST1H3J HIST1H3J HIST1H3J 2309 0.2 0.67 YES
51 HIST1H2AH HIST1H2AH HIST1H2AH 2381 0.2 0.68 YES
52 HIST1H2AK HIST1H2AK HIST1H2AK 2455 0.19 0.68 YES
53 C1QC C1QC C1QC 2763 0.18 0.67 NO
54 C1QB C1QB C1QB 2928 0.17 0.66 NO
55 HLA-DQA1 HLA-DQA1 HLA-DQA1 3138 0.16 0.66 NO
56 H2AFJ H2AFJ H2AFJ 3271 0.15 0.66 NO
57 HIST1H4D HIST1H4D HIST1H4D 3497 0.14 0.65 NO
58 TNF TNF TNF 3554 0.14 0.65 NO
59 HIST1H2BK HIST1H2BK HIST1H2BK 3734 0.14 0.64 NO
60 HIST2H2AB HIST2H2AB HIST2H2AB 3847 0.13 0.64 NO
61 HLA-DPB1 HLA-DPB1 HLA-DPB1 4164 0.12 0.63 NO
62 HLA-DMB HLA-DMB HLA-DMB 4222 0.12 0.63 NO
63 HIST1H3I HIST1H3I HIST1H3I 4589 0.11 0.61 NO
64 HIST1H3A HIST1H3A HIST1H3A 4736 0.1 0.61 NO
65 C4A C4A C4A 5055 0.094 0.59 NO
66 GRIN2B GRIN2B GRIN2B 5369 0.085 0.58 NO
67 HIST1H3C HIST1H3C HIST1H3C 5709 0.076 0.56 NO
68 H3F3A H3F3A H3F3A 5714 0.076 0.56 NO
69 SNRPB SNRPB SNRPB 5732 0.075 0.56 NO
70 HIST1H2BD HIST1H2BD HIST1H2BD 5743 0.075 0.57 NO
71 HIST1H4H HIST1H4H HIST1H4H 5842 0.072 0.56 NO
72 CD40 CD40 CD40 5856 0.072 0.57 NO
73 HLA-DMA HLA-DMA HLA-DMA 5966 0.069 0.56 NO
74 C1QA C1QA C1QA 6007 0.068 0.56 NO
75 CD80 CD80 CD80 6062 0.067 0.56 NO
76 HLA-DPA1 HLA-DPA1 HLA-DPA1 6083 0.066 0.56 NO
77 IL10 IL10 IL10 6103 0.066 0.56 NO
78 H2AFY2 H2AFY2 H2AFY2 6227 0.063 0.56 NO
79 HLA-DRA HLA-DRA HLA-DRA 6447 0.057 0.55 NO
80 HIST1H2BM HIST1H2BM HIST1H2BM 7370 0.037 0.5 NO
81 HIST1H2AC HIST1H2AC HIST1H2AC 7750 0.028 0.48 NO
82 HLA-DOB HLA-DOB HLA-DOB 7959 0.023 0.47 NO
83 C9 C9 C9 8047 0.021 0.46 NO
84 HIST1H3E HIST1H3E HIST1H3E 8501 0.012 0.44 NO
85 H2AFZ H2AFZ H2AFZ 8833 0.0044 0.42 NO
86 H2AFY H2AFY H2AFY 8858 0.0038 0.42 NO
87 FCGR2A FCGR2A FCGR2A 9013 0.00087 0.41 NO
88 HLA-DOA HLA-DOA HLA-DOA 9054 -0.00026 0.41 NO
89 ACTN4 ACTN4 ACTN4 9284 -0.0058 0.4 NO
90 TRIM21 TRIM21 TRIM21 9412 -0.0084 0.39 NO
91 C2 C2 C2 9429 -0.0087 0.39 NO
92 ACTN1 ACTN1 ACTN1 9993 -0.021 0.36 NO
93 ACTN2 ACTN2 ACTN2 10045 -0.022 0.36 NO
94 HIST1H2AD HIST1H2AD HIST1H2AD 10435 -0.03 0.33 NO
95 C1R C1R C1R 10569 -0.032 0.33 NO
96 H2AFV H2AFV H2AFV 10751 -0.036 0.32 NO
97 HIST2H2BE HIST2H2BE HIST2H2BE 10976 -0.042 0.31 NO
98 ACTN3 ACTN3 ACTN3 11026 -0.043 0.31 NO
99 SNRPD3 SNRPD3 SNRPD3 11166 -0.046 0.3 NO
100 CD40LG CD40LG CD40LG 11176 -0.046 0.3 NO
101 C3 C3 C3 11188 -0.046 0.3 NO
102 CTSG CTSG CTSG 11297 -0.049 0.3 NO
103 C1S C1S C1S 12342 -0.072 0.24 NO
104 SNRPD1 SNRPD1 SNRPD1 12879 -0.084 0.22 NO
105 CD86 CD86 CD86 13107 -0.09 0.21 NO
106 FCGR3A FCGR3A FCGR3A 13141 -0.091 0.21 NO
107 H3F3B H3F3B H3F3B 13164 -0.091 0.21 NO
108 HIST4H4 HIST4H4 HIST4H4 15234 -0.15 0.098 NO
109 CD28 CD28 CD28 15561 -0.16 0.085 NO
110 C5 C5 C5 16264 -0.18 0.052 NO
111 C7 C7 C7 16342 -0.19 0.054 NO
112 IFNG IFNG IFNG 16388 -0.19 0.058 NO
113 C6 C6 C6 16982 -0.22 0.032 NO
114 TROVE2 TROVE2 TROVE2 17127 -0.23 0.032 NO
115 SSB SSB SSB 17743 -0.3 0.0075 NO
116 GRIN2A GRIN2A GRIN2A 17953 -0.36 0.0076 NO

Figure S83.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS.

Figure S84.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS, 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 PENTOSE PHOSPHATE PATHWAY

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 PRPS1L1 PRPS1L1 PRPS1L1 239 0.82 0.23 YES
2 LOC729020 LOC729020 LOC729020 399 0.63 0.41 YES
3 PGLS PGLS PGLS 1601 0.26 0.42 YES
4 FBP2 FBP2 FBP2 3009 0.16 0.39 YES
5 ALDOC ALDOC ALDOC 3932 0.13 0.37 YES
6 G6PD G6PD G6PD 4206 0.12 0.39 YES
7 FBP1 FBP1 FBP1 4485 0.11 0.41 YES
8 PFKL PFKL PFKL 4670 0.1 0.43 YES
9 TKT TKT TKT 5311 0.087 0.42 YES
10 PGM1 PGM1 PGM1 5625 0.078 0.43 YES
11 PGD PGD PGD 5682 0.076 0.45 YES
12 PFKP PFKP PFKP 5930 0.07 0.45 YES
13 GPI GPI GPI 6175 0.064 0.46 YES
14 RBKS RBKS RBKS 6346 0.06 0.47 YES
15 ALDOB ALDOB ALDOB 6625 0.053 0.47 YES
16 TALDO1 TALDO1 TALDO1 7038 0.044 0.46 NO
17 TKTL1 TKTL1 TKTL1 7611 0.031 0.44 NO
18 PFKM PFKM PFKM 8273 0.016 0.4 NO
19 PRPS1 PRPS1 PRPS1 9089 -0.0012 0.36 NO
20 PRPS2 PRPS2 PRPS2 9569 -0.012 0.34 NO
21 DERA DERA DERA 10042 -0.022 0.32 NO
22 RPIA RPIA RPIA 10813 -0.038 0.28 NO
23 H6PD H6PD H6PD 11499 -0.053 0.26 NO
24 TKTL2 TKTL2 TKTL2 12818 -0.083 0.21 NO
25 PGM2 PGM2 PGM2 13668 -0.1 0.2 NO
26 RPE RPE RPE 15761 -0.16 0.13 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 PENTOSE PHOSPHATE PATHWAY.

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

Table S44.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ALOX12 ALOX12 ALOX12 111 1.1 0.14 YES
2 LTC4S LTC4S LTC4S 199 0.88 0.25 YES
3 CYP4F2 CYP4F2 CYP4F2 1270 0.3 0.23 YES
4 PLA2G4E PLA2G4E PLA2G4E 1448 0.28 0.25 YES
5 CBR3 CBR3 CBR3 2035 0.22 0.25 YES
6 GPX4 GPX4 GPX4 2216 0.21 0.27 YES
7 GGT1 GGT1 GGT1 2250 0.2 0.29 YES
8 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 2259 0.2 0.32 YES
9 GPX1 GPX1 GPX1 2277 0.2 0.34 YES
10 ALOX12B ALOX12B ALOX12B 2413 0.19 0.36 YES
11 PTGES2 PTGES2 PTGES2 2520 0.19 0.38 YES
12 PTGDS PTGDS PTGDS 2528 0.19 0.4 YES
13 CYP2C9 CYP2C9 CYP2C9 2794 0.17 0.41 YES
14 ALOX15 ALOX15 ALOX15 3366 0.15 0.4 YES
15 PLA2G12B PLA2G12B PLA2G12B 3394 0.15 0.42 YES
16 CBR1 CBR1 CBR1 3530 0.14 0.43 YES
17 PLA2G6 PLA2G6 PLA2G6 3749 0.14 0.44 YES
18 PLA2G1B PLA2G1B PLA2G1B 3873 0.13 0.45 YES
19 PLA2G10 PLA2G10 PLA2G10 4030 0.12 0.45 YES
20 CYP4F3 CYP4F3 CYP4F3 4055 0.12 0.47 YES
21 GPX7 GPX7 GPX7 4097 0.12 0.48 YES
22 CYP2C19 CYP2C19 CYP2C19 4195 0.12 0.49 YES
23 CYP2E1 CYP2E1 CYP2E1 4263 0.12 0.5 YES
24 PLA2G2A PLA2G2A PLA2G2A 4342 0.12 0.52 YES
25 ALOX5 ALOX5 ALOX5 4706 0.1 0.51 NO
26 CYP2C18 CYP2C18 CYP2C18 5481 0.082 0.48 NO
27 CYP2B6 CYP2B6 CYP2B6 5951 0.07 0.46 NO
28 GGT6 GGT6 GGT6 6214 0.063 0.45 NO
29 PLA2G2F PLA2G2F PLA2G2F 6414 0.058 0.45 NO
30 GPX3 GPX3 GPX3 6445 0.058 0.46 NO
31 GPX2 GPX2 GPX2 6815 0.05 0.44 NO
32 PLA2G3 PLA2G3 PLA2G3 7125 0.043 0.43 NO
33 GGT7 GGT7 GGT7 7143 0.042 0.44 NO
34 AKR1C3 AKR1C3 AKR1C3 7164 0.042 0.44 NO
35 PTGES PTGES PTGES 7520 0.034 0.42 NO
36 EPHX2 EPHX2 EPHX2 7807 0.027 0.41 NO
37 CYP2C8 CYP2C8 CYP2C8 9030 0.0004 0.34 NO
38 PLA2G2D PLA2G2D PLA2G2D 9242 -0.0049 0.33 NO
39 PLA2G12A PLA2G12A PLA2G12A 9402 -0.0082 0.32 NO
40 LTA4H LTA4H LTA4H 10823 -0.038 0.25 NO
41 PLA2G5 PLA2G5 PLA2G5 11072 -0.044 0.24 NO
42 GGT5 GGT5 GGT5 11186 -0.046 0.24 NO
43 ALOX15B ALOX15B ALOX15B 11243 -0.047 0.25 NO
44 TBXAS1 TBXAS1 TBXAS1 11363 -0.05 0.25 NO
45 PTGS1 PTGS1 PTGS1 11830 -0.061 0.23 NO
46 CYP4A11 CYP4A11 CYP4A11 12774 -0.082 0.19 NO
47 HPGDS HPGDS HPGDS 14090 -0.11 0.13 NO
48 PTGS2 PTGS2 PTGS2 15769 -0.16 0.058 NO
49 PTGIS PTGIS PTGIS 15846 -0.17 0.076 NO
50 PLA2G4A PLA2G4A PLA2G4A 16033 -0.18 0.089 NO
51 CYP2U1 CYP2U1 CYP2U1 16446 -0.19 0.091 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 FRUCTOSE AND MANNOSE METABOLISM.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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 NCF1C NCF1C NCF1C 149 0.98 0.24 YES
2 GNGT1 GNGT1 GNGT1 330 0.72 0.41 YES
3 FPR1 FPR1 FPR1 1522 0.27 0.41 YES
4 HRAS HRAS HRAS 3665 0.14 0.33 NO
5 MAP2K2 MAP2K2 MAP2K2 4098 0.12 0.33 NO
6 MAPK3 MAPK3 MAPK3 4479 0.11 0.34 NO
7 CAMK1G CAMK1G CAMK1G 5302 0.087 0.32 NO
8 CAMK1 CAMK1 CAMK1 5468 0.082 0.33 NO
9 ELK1 ELK1 ELK1 6762 0.051 0.27 NO
10 NFKBIA NFKBIA NFKBIA 6929 0.047 0.27 NO
11 NFATC3 NFATC3 NFATC3 7091 0.043 0.27 NO
12 NFATC4 NFATC4 NFATC4 7317 0.038 0.27 NO
13 CALM3 CALM3 CALM3 7429 0.036 0.27 NO
14 RELA RELA RELA 7570 0.032 0.27 NO
15 RAF1 RAF1 RAF1 7646 0.031 0.28 NO
16 MAP2K3 MAP2K3 MAP2K3 7937 0.024 0.27 NO
17 NFATC1 NFATC1 NFATC1 8289 0.016 0.25 NO
18 MAP2K6 MAP2K6 MAP2K6 8461 0.012 0.25 NO
19 GNB1 GNB1 GNB1 8525 0.011 0.24 NO
20 NCF2 NCF2 NCF2 8972 0.0017 0.22 NO
21 NFATC2 NFATC2 NFATC2 9420 -0.0086 0.2 NO
22 MAPK14 MAPK14 MAPK14 9670 -0.014 0.19 NO
23 NFKB1 NFKB1 NFKB1 9880 -0.018 0.18 NO
24 CALM1 CALM1 CALM1 10583 -0.033 0.15 NO
25 PAK1 PAK1 PAK1 11006 -0.042 0.14 NO
26 PPP3CB PPP3CB PPP3CB 11139 -0.045 0.14 NO
27 RAC1 RAC1 RAC1 11233 -0.047 0.15 NO
28 PPP3CC PPP3CC PPP3CC 11281 -0.048 0.16 NO
29 MAPK1 MAPK1 MAPK1 11712 -0.058 0.15 NO
30 MAP2K1 MAP2K1 MAP2K1 12012 -0.064 0.15 NO
31 CALM2 CALM2 CALM2 12394 -0.073 0.15 NO
32 PPP3CA PPP3CA PPP3CA 14952 -0.14 0.039 NO
33 MAP3K1 MAP3K1 MAP3K1 15933 -0.17 0.028 NO
34 PLCB1 PLCB1 PLCB1 17966 -0.36 0.0069 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 OXIDATIVE PHOSPHORYLATION.

Figure S90.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, 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 PYRIMIDINE 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 RPL21 RPL21 RPL21 37 1.4 0.11 YES
2 RPL36A RPL36A RPL36A 140 1 0.18 YES
3 RPS28 RPS28 RPS28 318 0.73 0.23 YES
4 RPL39 RPL39 RPL39 327 0.72 0.28 YES
5 RPL9 RPL9 RPL9 451 0.59 0.32 YES
6 RPL7 RPL7 RPL7 562 0.51 0.36 YES
7 RPS26 RPS26 RPS26 588 0.49 0.39 YES
8 RPS27 RPS27 RPS27 619 0.48 0.43 YES
9 RPL18A RPL18A RPL18A 699 0.45 0.46 YES
10 RPS3A RPS3A RPS3A 1215 0.31 0.45 YES
11 RPSA RPSA RPSA 1652 0.26 0.45 YES
12 RPL23A RPL23A RPL23A 1804 0.24 0.46 YES
13 RPS15 RPS15 RPS15 1993 0.22 0.47 YES
14 RPL10L RPL10L RPL10L 2229 0.21 0.47 YES
15 RPS2 RPS2 RPS2 2261 0.2 0.48 YES
16 RPS5 RPS5 RPS5 2705 0.18 0.47 YES
17 RPL13 RPL13 RPL13 2880 0.17 0.48 YES
18 RPL29 RPL29 RPL29 3123 0.16 0.48 YES
19 RPL10 RPL10 RPL10 3168 0.16 0.48 YES
20 RPLP0 RPLP0 RPLP0 3276 0.15 0.49 YES
21 RPL28 RPL28 RPL28 3461 0.14 0.49 YES
22 RPL41 RPL41 RPL41 4194 0.12 0.46 NO
23 UBA52 UBA52 UBA52 4353 0.11 0.46 NO
24 RPLP2 RPLP2 RPLP2 5002 0.095 0.43 NO
25 RPL8 RPL8 RPL8 5111 0.092 0.43 NO
26 RPS3 RPS3 RPS3 5146 0.091 0.44 NO
27 RPS10 RPS10 RPS10 5230 0.089 0.44 NO
28 RPL15 RPL15 RPL15 5388 0.084 0.44 NO
29 RPS9 RPS9 RPS9 5460 0.083 0.44 NO
30 RPL36 RPL36 RPL36 5632 0.078 0.44 NO
31 RPS16 RPS16 RPS16 6150 0.065 0.41 NO
32 RPS6 RPS6 RPS6 6308 0.061 0.41 NO
33 FAU FAU FAU 6372 0.059 0.41 NO
34 RPL27 RPL27 RPL27 6745 0.051 0.39 NO
35 RPLP1 RPLP1 RPLP1 7062 0.044 0.38 NO
36 RPL3 RPL3 RPL3 7161 0.042 0.38 NO
37 RPS21 RPS21 RPS21 7286 0.039 0.37 NO
38 RPL26L1 RPL26L1 RPL26L1 7289 0.039 0.38 NO
39 RPS11 RPS11 RPS11 7407 0.036 0.37 NO
40 RPL7A RPL7A RPL7A 7572 0.032 0.37 NO
41 RPL10A RPL10A RPL10A 7676 0.03 0.36 NO
42 RPL35 RPL35 RPL35 7727 0.029 0.36 NO
43 RPS13 RPS13 RPS13 7868 0.025 0.36 NO
44 RPS8 RPS8 RPS8 7919 0.024 0.36 NO
45 RPS19 RPS19 RPS19 8008 0.022 0.35 NO
46 RPS4X RPS4X RPS4X 8057 0.021 0.35 NO
47 RPL27A RPL27A RPL27A 8324 0.016 0.34 NO
48 RPL17 RPL17 RPL17 8331 0.015 0.34 NO
49 RPL38 RPL38 RPL38 8341 0.015 0.34 NO
50 RPS15A RPS15A RPS15A 8487 0.012 0.33 NO
51 RPS4Y1 RPS4Y1 RPS4Y1 8553 0.011 0.33 NO
52 RPL32 RPL32 RPL32 8711 0.0074 0.32 NO
53 RPL19 RPL19 RPL19 9234 -0.0048 0.29 NO
54 RPL6 RPL6 RPL6 9303 -0.0062 0.29 NO
55 RPL37A RPL37A RPL37A 9445 -0.0091 0.28 NO
56 RPL13A RPL13A RPL13A 9741 -0.016 0.27 NO
57 RPL23 RPL23 RPL23 9995 -0.021 0.25 NO
58 RPL30 RPL30 RPL30 10003 -0.021 0.26 NO
59 RPL37 RPL37 RPL37 10128 -0.024 0.25 NO
60 RPS17 RPS17 RPS17 10303 -0.027 0.24 NO
61 MRPL13 MRPL13 MRPL13 10470 -0.03 0.24 NO
62 RPL35A RPL35A RPL35A 10540 -0.032 0.24 NO
63 RPL31 RPL31 RPL31 10902 -0.04 0.22 NO
64 RPS29 RPS29 RPS29 10967 -0.041 0.22 NO
65 RPL5 RPL5 RPL5 11019 -0.042 0.22 NO
66 RPS23 RPS23 RPS23 11197 -0.046 0.21 NO
67 RPL11 RPL11 RPL11 11230 -0.047 0.21 NO
68 RPL4 RPL4 RPL4 11395 -0.051 0.21 NO
69 RPL36AL RPL36AL RPL36AL 11617 -0.056 0.2 NO
70 RPL34 RPL34 RPL34 11791 -0.06 0.2 NO
71 RPL14 RPL14 RPL14 11809 -0.06 0.2 NO
72 RPL22 RPL22 RPL22 12535 -0.076 0.16 NO
73 RPL26 RPL26 RPL26 12636 -0.079 0.16 NO
74 RPS20 RPS20 RPS20 13097 -0.09 0.15 NO
75 RPS7 RPS7 RPS7 13431 -0.097 0.14 NO
76 RPS18 RPS18 RPS18 14034 -0.11 0.11 NO
77 RPS24 RPS24 RPS24 14272 -0.12 0.11 NO
78 RPL12 RPL12 RPL12 14677 -0.13 0.095 NO
79 RSL24D1 RSL24D1 RSL24D1 14843 -0.14 0.096 NO
80 RPL24 RPL24 RPL24 15139 -0.14 0.091 NO
81 RPS25 RPS25 RPS25 15256 -0.15 0.096 NO
82 RPS12 RPS12 RPS12 15468 -0.16 0.097 NO
83 RPS27L RPS27L RPS27L 16405 -0.19 0.059 NO
84 RPS27A RPS27A RPS27A 16464 -0.19 0.071 NO
85 RPL22L1 RPL22L1 RPL22L1 17299 -0.25 0.044 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 PYRIMIDINE METABOLISM.

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

genes ES table in pathway: KEGG ARGININE AND PROLINE 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 POLR2J2 POLR2J2 POLR2J2 285 0.77 0.19 YES
2 POLR2J3 POLR2J3 POLR2J3 813 0.41 0.27 YES
3 POLR2I POLR2I POLR2I 1635 0.26 0.3 YES
4 POLR2L POLR2L POLR2L 2608 0.18 0.29 YES
5 POLR2G POLR2G POLR2G 2659 0.18 0.34 YES
6 ZNRD1 ZNRD1 ZNRD1 4588 0.11 0.26 YES
7 POLR3K POLR3K POLR3K 4760 0.1 0.28 YES
8 POLR3H POLR3H POLR3H 4775 0.1 0.31 YES
9 POLR1C POLR1C POLR1C 4897 0.098 0.33 YES
10 POLR2J POLR2J POLR2J 5007 0.095 0.35 YES
11 POLR2F POLR2F POLR2F 5290 0.087 0.35 YES
12 POLR2E POLR2E POLR2E 5371 0.085 0.37 YES
13 POLR2C POLR2C POLR2C 7073 0.044 0.29 NO
14 POLR3D POLR3D POLR3D 7753 0.028 0.26 NO
15 POLR2D POLR2D POLR2D 7790 0.027 0.27 NO
16 POLR3C POLR3C POLR3C 8398 0.014 0.24 NO
17 POLR3B POLR3B POLR3B 9236 -0.0049 0.19 NO
18 POLR3A POLR3A POLR3A 9258 -0.0052 0.19 NO
19 POLR1E POLR1E POLR1E 9516 -0.011 0.18 NO
20 POLR1B POLR1B POLR1B 10485 -0.031 0.13 NO
21 POLR1A POLR1A POLR1A 11399 -0.051 0.098 NO
22 POLR2B POLR2B POLR2B 11702 -0.058 0.097 NO
23 POLR2A POLR2A POLR2A 11801 -0.06 0.11 NO
24 POLR1D POLR1D POLR1D 12276 -0.071 0.1 NO
25 POLR3F POLR3F POLR3F 15281 -0.15 -0.026 NO
26 POLR2K POLR2K POLR2K 16131 -0.18 -0.024 NO
27 POLR3GL POLR3GL POLR3GL 17062 -0.23 -0.014 NO
28 POLR3G POLR3G POLR3G 17446 -0.26 0.036 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 ARGININE AND PROLINE METABOLISM.

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

genes ES table in pathway: KEGG TYROSINE METABOLISM

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 POLR2J2 POLR2J2 POLR2J2 285 0.77 0.054 YES
2 POLR2J3 POLR2J3 POLR2J3 813 0.41 0.061 YES
3 NT5C1B NT5C1B NT5C1B 1102 0.33 0.076 YES
4 TYMP TYMP TYMP 1245 0.31 0.095 YES
5 NME1-NME2 NME1-NME2 NME1-NME2 1430 0.28 0.11 YES
6 NME3 NME3 NME3 1614 0.26 0.12 YES
7 POLR2I POLR2I POLR2I 1635 0.26 0.15 YES
8 CDA CDA CDA 2046 0.22 0.14 YES
9 NT5C NT5C NT5C 2306 0.2 0.15 YES
10 POLD1 POLD1 POLD1 2326 0.2 0.16 YES
11 UCKL1 UCKL1 UCKL1 2591 0.18 0.17 YES
12 POLR2L POLR2L POLR2L 2608 0.18 0.18 YES
13 POLR2G POLR2G POLR2G 2659 0.18 0.2 YES
14 TK1 TK1 TK1 2860 0.17 0.2 YES
15 DTYMK DTYMK DTYMK 3783 0.13 0.16 YES
16 NME1 NME1 NME1 4162 0.12 0.15 YES
17 POLR2H POLR2H POLR2H 4391 0.11 0.15 YES
18 TXNRD2 TXNRD2 TXNRD2 4409 0.11 0.16 YES
19 NME4 NME4 NME4 4417 0.11 0.17 YES
20 ZNRD1 ZNRD1 ZNRD1 4588 0.11 0.17 YES
21 NT5M NT5M NT5M 4597 0.11 0.18 YES
22 UPP1 UPP1 UPP1 4719 0.1 0.18 YES
23 POLR3K POLR3K POLR3K 4760 0.1 0.19 YES
24 ENTPD8 ENTPD8 ENTPD8 4773 0.1 0.2 YES
25 POLR3H POLR3H POLR3H 4775 0.1 0.2 YES
26 TYMS TYMS TYMS 4881 0.098 0.21 YES
27 POLR1C POLR1C POLR1C 4897 0.098 0.22 YES
28 ENTPD6 ENTPD6 ENTPD6 4950 0.096 0.22 YES
29 POLD2 POLD2 POLD2 4961 0.096 0.23 YES
30 NME6 NME6 NME6 4975 0.096 0.24 YES
31 POLR2J POLR2J POLR2J 5007 0.095 0.24 YES
32 DUT DUT DUT 5069 0.093 0.25 YES
33 UPB1 UPB1 UPB1 5225 0.089 0.25 YES
34 POLR2F POLR2F POLR2F 5290 0.087 0.25 YES
35 POLR2E POLR2E POLR2E 5371 0.085 0.26 YES
36 NUDT2 NUDT2 NUDT2 5401 0.084 0.26 YES
37 PNP PNP PNP 5448 0.083 0.27 YES
38 UCK1 UCK1 UCK1 5567 0.08 0.27 YES
39 UCK2 UCK2 UCK2 5650 0.077 0.27 YES
40 POLA2 POLA2 POLA2 5667 0.077 0.28 YES
41 POLE4 POLE4 POLE4 6095 0.066 0.26 NO
42 POLD4 POLD4 POLD4 6270 0.062 0.25 NO
43 POLE2 POLE2 POLE2 6377 0.059 0.25 NO
44 CAD CAD CAD 6758 0.051 0.24 NO
45 NME2 NME2 NME2 6784 0.05 0.24 NO
46 DHODH DHODH DHODH 6789 0.05 0.24 NO
47 POLR2C POLR2C POLR2C 7073 0.044 0.23 NO
48 CANT1 CANT1 CANT1 7327 0.038 0.22 NO
49 CMPK2 CMPK2 CMPK2 7641 0.031 0.21 NO
50 POLR3D POLR3D POLR3D 7753 0.028 0.2 NO
51 ITPA ITPA ITPA 7771 0.028 0.21 NO
52 POLR2D POLR2D POLR2D 7790 0.027 0.21 NO
53 DCTD DCTD DCTD 8016 0.022 0.2 NO
54 PRIM2 PRIM2 PRIM2 8111 0.02 0.19 NO
55 POLE POLE POLE 8237 0.017 0.19 NO
56 POLR3C POLR3C POLR3C 8398 0.014 0.18 NO
57 RRM2 RRM2 RRM2 9044 0.000025 0.14 NO
58 POLR3B POLR3B POLR3B 9236 -0.0049 0.13 NO
59 POLR3A POLR3A POLR3A 9258 -0.0052 0.13 NO
60 POLR1E POLR1E POLR1E 9516 -0.011 0.12 NO
61 ENTPD5 ENTPD5 ENTPD5 9700 -0.015 0.11 NO
62 TK2 TK2 TK2 9846 -0.018 0.1 NO
63 POLE3 POLE3 POLE3 9953 -0.02 0.1 NO
64 UMPS UMPS UMPS 10424 -0.03 0.077 NO
65 POLR1B POLR1B POLR1B 10485 -0.031 0.077 NO
66 CTPS2 CTPS2 CTPS2 11016 -0.042 0.051 NO
67 AK3 AK3 AK3 11179 -0.046 0.046 NO
68 POLR1A POLR1A POLR1A 11399 -0.051 0.039 NO
69 POLR2B POLR2B POLR2B 11702 -0.058 0.027 NO
70 POLR2A POLR2A POLR2A 11801 -0.06 0.027 NO
71 NT5C2 NT5C2 NT5C2 11942 -0.063 0.025 NO
72 POLR1D POLR1D POLR1D 12276 -0.071 0.013 NO
73 UPP2 UPP2 UPP2 12290 -0.071 0.019 NO
74 TXNRD1 TXNRD1 TXNRD1 12320 -0.072 0.024 NO
75 RRM1 RRM1 RRM1 13075 -0.089 -0.01 NO
76 POLD3 POLD3 POLD3 13311 -0.095 -0.015 NO
77 PRIM1 PRIM1 PRIM1 13337 -0.096 -0.0075 NO
78 POLA1 POLA1 POLA1 13491 -0.099 -0.0071 NO
79 ENTPD1 ENTPD1 ENTPD1 13655 -0.1 -0.0068 NO
80 NT5E NT5E NT5E 13730 -0.1 -0.0015 NO
81 DPYD DPYD DPYD 13745 -0.1 0.0073 NO
82 PNPT1 PNPT1 PNPT1 13765 -0.11 0.016 NO
83 UPRT UPRT UPRT 13965 -0.11 0.015 NO
84 DPYS DPYS DPYS 14630 -0.13 -0.01 NO
85 ENTPD3 ENTPD3 ENTPD3 14880 -0.14 -0.012 NO
86 NME7 NME7 NME7 15016 -0.14 -0.0066 NO
87 DCK DCK DCK 15202 -0.15 -0.0036 NO
88 POLR3F POLR3F POLR3F 15281 -0.15 0.0056 NO
89 ENTPD4 ENTPD4 ENTPD4 15319 -0.15 0.017 NO
90 CMPK1 CMPK1 CMPK1 15702 -0.16 0.011 NO
91 POLR2K POLR2K POLR2K 16131 -0.18 0.0031 NO
92 NME5 NME5 NME5 16187 -0.18 0.016 NO
93 POLR3GL POLR3GL POLR3GL 17062 -0.23 -0.012 NO
94 NT5C3 NT5C3 NT5C3 17085 -0.23 0.008 NO
95 POLR3G POLR3G POLR3G 17446 -0.26 0.012 NO
96 RRM2B RRM2B RRM2B 17489 -0.27 0.033 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 TYROSINE METABOLISM.

Figure S96.  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 GLUTATHIONE METABOLISM

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 GSTM1 GSTM1 GSTM1 402 0.63 0.09 YES
2 GSTT2 GSTT2 GSTT2 1053 0.35 0.12 YES
3 GSTA2 GSTA2 GSTA2 1216 0.31 0.16 YES
4 GSTM2 GSTM2 GSTM2 1631 0.26 0.19 YES
5 GSTO2 GSTO2 GSTO2 1988 0.22 0.21 YES
6 SRM SRM SRM 2145 0.21 0.24 YES
7 GPX4 GPX4 GPX4 2216 0.21 0.27 YES
8 GGT1 GGT1 GGT1 2250 0.2 0.3 YES
9 GPX1 GPX1 GPX1 2277 0.2 0.34 YES
10 OPLAH OPLAH OPLAH 2353 0.2 0.37 YES
11 GSTP1 GSTP1 GSTP1 3178 0.16 0.35 YES
12 ANPEP ANPEP ANPEP 3406 0.15 0.36 YES
13 GPX7 GPX7 GPX7 4097 0.12 0.35 YES
14 G6PD G6PD G6PD 4206 0.12 0.36 YES
15 GSTZ1 GSTZ1 GSTZ1 4644 0.1 0.36 YES
16 IDH2 IDH2 IDH2 4717 0.1 0.37 YES
17 GSTM3 GSTM3 GSTM3 4872 0.098 0.38 YES
18 GSS GSS GSS 6011 0.068 0.33 NO
19 GSTT1 GSTT1 GSTT1 6047 0.067 0.34 NO
20 GGT6 GGT6 GGT6 6214 0.063 0.34 NO
21 GPX3 GPX3 GPX3 6445 0.058 0.34 NO
22 GSTM5 GSTM5 GSTM5 6672 0.052 0.34 NO
23 GPX2 GPX2 GPX2 6815 0.05 0.34 NO
24 GSR GSR GSR 6990 0.046 0.34 NO
25 ODC1 ODC1 ODC1 7045 0.044 0.34 NO
26 GGT7 GGT7 GGT7 7143 0.042 0.34 NO
27 GSTK1 GSTK1 GSTK1 7154 0.042 0.35 NO
28 MGST3 MGST3 MGST3 7469 0.035 0.34 NO
29 GSTM4 GSTM4 GSTM4 7474 0.035 0.35 NO
30 MGST1 MGST1 MGST1 7758 0.028 0.34 NO
31 GSTO1 GSTO1 GSTO1 8236 0.017 0.31 NO
32 RRM2 RRM2 RRM2 9044 0.000025 0.27 NO
33 GSTA1 GSTA1 GSTA1 9331 -0.0067 0.25 NO
34 LAP3 LAP3 LAP3 10327 -0.028 0.2 NO
35 IDH1 IDH1 IDH1 10996 -0.042 0.17 NO
36 GGT5 GGT5 GGT5 11186 -0.046 0.17 NO
37 TXNDC12 TXNDC12 TXNDC12 11938 -0.063 0.14 NO
38 MGST2 MGST2 MGST2 12532 -0.076 0.12 NO
39 RRM1 RRM1 RRM1 13075 -0.089 0.11 NO
40 GCLC GCLC GCLC 13347 -0.096 0.11 NO
41 GCLM GCLM GCLM 14240 -0.12 0.081 NO
42 GGCT GGCT GGCT 15244 -0.15 0.052 NO
43 GSTA4 GSTA4 GSTA4 15273 -0.15 0.077 NO
44 SMS SMS SMS 16073 -0.18 0.064 NO
45 RRM2B RRM2B RRM2B 17489 -0.27 0.033 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 GLUTATHIONE METABOLISM.

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

genes ES table in pathway: KEGG GLYCEROPHOSPHOLIPID METABOLISM

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 GSTM1 GSTM1 GSTM1 402 0.63 0.05 YES
2 AKR1C2 AKR1C2 AKR1C2 483 0.57 0.11 YES
3 CYP2F1 CYP2F1 CYP2F1 514 0.54 0.17 YES
4 DHDH DHDH DHDH 718 0.44 0.21 YES
5 ADH1A ADH1A ADH1A 801 0.41 0.26 YES
6 AKR1C4 AKR1C4 AKR1C4 979 0.36 0.29 YES
7 ALDH3B2 ALDH3B2 ALDH3B2 998 0.36 0.33 YES
8 GSTT2 GSTT2 GSTT2 1053 0.35 0.36 YES
9 GSTA2 GSTA2 GSTA2 1216 0.31 0.39 YES
10 AKR1C1 AKR1C1 AKR1C1 1230 0.31 0.43 YES
11 UGT2B11 UGT2B11 UGT2B11 1619 0.26 0.44 YES
12 GSTM2 GSTM2 GSTM2 1631 0.26 0.46 YES
13 GSTO2 GSTO2 GSTO2 1988 0.22 0.47 YES
14 UGT1A9 UGT1A9 UGT1A9 2288 0.2 0.48 YES
15 UGT1A8 UGT1A8 UGT1A8 2764 0.18 0.47 YES
16 CYP2C9 CYP2C9 CYP2C9 2794 0.17 0.49 YES
17 GSTP1 GSTP1 GSTP1 3178 0.16 0.49 YES
18 ADH1B ADH1B ADH1B 3319 0.15 0.5 YES
19 ADH1C ADH1C ADH1C 3334 0.15 0.51 YES
20 CYP2C19 CYP2C19 CYP2C19 4195 0.12 0.48 NO
21 CYP2E1 CYP2E1 CYP2E1 4263 0.12 0.49 NO
22 CYP2S1 CYP2S1 CYP2S1 4406 0.11 0.49 NO
23 ALDH3B1 ALDH3B1 ALDH3B1 4552 0.11 0.5 NO
24 GSTZ1 GSTZ1 GSTZ1 4644 0.1 0.5 NO
25 GSTM3 GSTM3 GSTM3 4872 0.098 0.5 NO
26 CYP2C18 CYP2C18 CYP2C18 5481 0.082 0.48 NO
27 CYP1A1 CYP1A1 CYP1A1 5589 0.079 0.48 NO
28 UGT2B15 UGT2B15 UGT2B15 5819 0.073 0.48 NO
29 CYP2B6 CYP2B6 CYP2B6 5951 0.07 0.48 NO
30 GSTT1 GSTT1 GSTT1 6047 0.067 0.48 NO
31 ALDH3A1 ALDH3A1 ALDH3A1 6381 0.059 0.47 NO
32 GSTM5 GSTM5 GSTM5 6672 0.052 0.46 NO
33 ADH4 ADH4 ADH4 6783 0.05 0.46 NO
34 CYP3A43 CYP3A43 CYP3A43 6960 0.046 0.46 NO
35 GSTK1 GSTK1 GSTK1 7154 0.042 0.45 NO
36 AKR1C3 AKR1C3 AKR1C3 7164 0.042 0.45 NO
37 UGT1A10 UGT1A10 UGT1A10 7361 0.037 0.45 NO
38 MGST3 MGST3 MGST3 7469 0.035 0.45 NO
39 GSTM4 GSTM4 GSTM4 7474 0.035 0.45 NO
40 MGST1 MGST1 MGST1 7758 0.028 0.44 NO
41 GSTO1 GSTO1 GSTO1 8236 0.017 0.41 NO
42 UGT2B10 UGT2B10 UGT2B10 8968 0.0018 0.37 NO
43 CYP2C8 CYP2C8 CYP2C8 9030 0.0004 0.37 NO
44 ADH5 ADH5 ADH5 9238 -0.0049 0.36 NO
45 GSTA1 GSTA1 GSTA1 9331 -0.0067 0.35 NO
46 UGT1A6 UGT1A6 UGT1A6 9432 -0.0087 0.35 NO
47 ADH6 ADH6 ADH6 9708 -0.015 0.34 NO
48 EPHX1 EPHX1 EPHX1 9874 -0.018 0.33 NO
49 UGT1A1 UGT1A1 UGT1A1 9879 -0.018 0.33 NO
50 UGT2B7 UGT2B7 UGT2B7 10278 -0.027 0.31 NO
51 UGT2A3 UGT2A3 UGT2A3 11278 -0.048 0.26 NO
52 UGT2B4 UGT2B4 UGT2B4 11609 -0.056 0.25 NO
53 MGST2 MGST2 MGST2 12532 -0.076 0.21 NO
54 CYP3A7 CYP3A7 CYP3A7 12642 -0.079 0.21 NO
55 CYP3A5 CYP3A5 CYP3A5 12768 -0.082 0.21 NO
56 UGT1A3 UGT1A3 UGT1A3 12886 -0.085 0.22 NO
57 GSTA4 GSTA4 GSTA4 15273 -0.15 0.1 NO
58 ALDH1A3 ALDH1A3 ALDH1A3 16408 -0.19 0.061 NO
59 CYP1B1 CYP1B1 CYP1B1 17599 -0.28 0.027 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 GLYCEROPHOSPHOLIPID METABOLISM.

Figure S100.  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

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input

  • Gene set database = c2.cp.v3.0-2.symbols.gmt

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

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

GSEA analysis

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

Download Results

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

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