GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in KIRP-TP
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1NP23TM
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in KIRP-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1NP23TM
Overview
Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes having more than three samples and the input expression file "KIRP-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:

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

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

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

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

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

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

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 707
Number of samples: 290
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 5 :[ clus1 ] 32
pheno.type: 2 - 5 :[ clus2 ] 91
pheno.type: 3 - 5 :[ clus3 ] 71
pheno.type: 4 - 5 :[ clus4 ] 32
pheno.type: 5 - 5 :[ clus5 ] 64

For the expression subtypes of 17999 genes in 291 samples, GSEA found enriched gene sets in each cluster using 290 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG GLYCEROPHOSPHOLIPID METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG ARACHIDONIC ACID METABOLISM, KEGG MAPK SIGNALING PATHWAY, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT

    • And common core enriched genes are AP1B1, AP1S2, CTSB, CTSK, CTSL1, CTSS, LGMN, CD4, FOS, ABCB9

  • clus2

    • Top enriched gene sets are KEGG HISTIDINE METABOLISM, KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, KEGG HEDGEHOG SIGNALING PATHWAY, KEGG TIGHT JUNCTION, KEGG TASTE TRANSDUCTION, BIOCARTA ALK PATHWAY, BIOCARTA DEATH PATHWAY, PID HDAC CLASSI PATHWAY, PID BMPPATHWAY, REACTOME SIGNALING BY FGFR1 MUTANTS

    • And common core enriched genes are CLDN15, CLDN18, CLDN19, CLDN20, CLDN3, CLDN6, CLDN7, CLDN9, SMAD7, GNAI1

  • clus3

    • Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

    • And common core enriched genes are EHHADH, PIPOX, AARS, CARS2, DARS2, EARS2, EPRS, FARS2, FARSA, FARSB

  • clus4

    • Top enriched gene sets are KEGG N GLYCAN BIOSYNTHESIS, KEGG O GLYCAN BIOSYNTHESIS, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG BASAL TRANSCRIPTION FACTORS, KEGG MAPK SIGNALING PATHWAY, KEGG ERBB SIGNALING PATHWAY, KEGG CALCIUM SIGNALING PATHWAY, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY

    • And common core enriched genes are PIK3CA, PIK3CG, HDAC1, CCND1, MAPK8, SHC3, SHC4, EP300, HIF1A, BIRC3

  • clus5

    • Top enriched gene sets are KEGG OOCYTE MEIOSIS, KEGG UBIQUITIN MEDIATED PROTEOLYSIS, KEGG ADHERENS JUNCTION, KEGG THYROID CANCER, BIOCARTA MPR PATHWAY, BIOCARTA VEGF PATHWAY, PID AURORA B PATHWAY, PID DELTANP63PATHWAY, PID AURORA A PATHWAY, REACTOME CELL CYCLE

    • And common core enriched genes are EIF4B, EIF4E, CDH1, LEF1, MYC, RET, RXRA, RXRG, TCF7L1, ADCY1

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.46 1.4 0.11 0.22 0.98 0.48 0.31 0.34 0.17 0.001
KEGG O GLYCAN BIOSYNTHESIS 29 genes.ES.table 0.55 1.5 0.025 0.14 0.94 0.34 0.15 0.29 0.1 0.001
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 44 genes.ES.table 0.54 1.8 0.0041 0.058 0.6 0.36 0.24 0.28 0.02 0.002
KEGG GLYCEROPHOSPHOLIPID METABOLISM 70 genes.ES.table 0.38 1.4 0.033 0.2 0.97 0.27 0.23 0.21 0.15 0.001
KEGG ETHER LIPID METABOLISM 27 genes.ES.table 0.61 1.7 0.0041 0.074 0.74 0.37 0.23 0.29 0.034 0
KEGG ARACHIDONIC ACID METABOLISM 50 genes.ES.table 0.55 1.4 0.054 0.21 0.97 0.28 0.11 0.25 0.16 0.001
KEGG MAPK SIGNALING PATHWAY 243 genes.ES.table 0.38 1.4 0.057 0.23 0.98 0.21 0.15 0.18 0.18 0.002
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION 231 genes.ES.table 0.7 1.7 0 0.064 0.66 0.57 0.16 0.48 0.026 0.002
KEGG CHEMOKINE SIGNALING PATHWAY 183 genes.ES.table 0.72 1.9 0 0.056 0.25 0.41 0.12 0.36 0 0.009
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT 38 genes.ES.table 0.35 1.4 0.12 0.25 0.99 0.21 0.24 0.16 0.2 0.002
genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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 DNASE2B DNASE2B DNASE2B 28 0.71 0.056 YES
2 ATP6V0D2 ATP6V0D2 ATP6V0D2 66 0.65 0.11 YES
3 CTSK CTSK CTSK 254 0.49 0.14 YES
4 CTSS CTSS CTSS 349 0.45 0.17 YES
5 SLC11A1 SLC11A1 SLC11A1 605 0.37 0.18 YES
6 CTSG CTSG CTSG 712 0.35 0.2 YES
7 ACP5 ACP5 ACP5 763 0.33 0.23 YES
8 AP1S2 AP1S2 AP1S2 811 0.32 0.25 YES
9 CTSW CTSW CTSW 837 0.32 0.28 YES
10 LAPTM5 LAPTM5 LAPTM5 846 0.31 0.3 YES
11 CTSE CTSE CTSE 964 0.29 0.32 YES
12 CD68 CD68 CD68 1150 0.26 0.33 YES
13 LIPA LIPA LIPA 1199 0.25 0.34 YES
14 CTSZ CTSZ CTSZ 1326 0.23 0.36 YES
15 LGMN LGMN LGMN 1407 0.22 0.37 YES
16 GM2A GM2A GM2A 1449 0.22 0.38 YES
17 MCOLN1 MCOLN1 MCOLN1 1520 0.21 0.4 YES
18 ARSG ARSG ARSG 1555 0.21 0.41 YES
19 FUCA1 FUCA1 FUCA1 1623 0.2 0.42 YES
20 LAMP3 LAMP3 LAMP3 2257 0.15 0.4 YES
21 CTSD CTSD CTSD 2346 0.14 0.41 YES
22 CTSF CTSF CTSF 2560 0.13 0.4 YES
23 NAPSA NAPSA NAPSA 2567 0.13 0.42 YES
24 PLA2G15 PLA2G15 PLA2G15 2651 0.12 0.42 YES
25 ATP6V0A4 ATP6V0A4 ATP6V0A4 2686 0.12 0.43 YES
26 TCIRG1 TCIRG1 TCIRG1 2702 0.12 0.44 YES
27 DNASE2 DNASE2 DNASE2 2769 0.12 0.44 YES
28 NPC2 NPC2 NPC2 2799 0.12 0.45 YES
29 AP1B1 AP1B1 AP1B1 2808 0.12 0.46 YES
30 CTSB CTSB CTSB 2828 0.11 0.47 YES
31 ACP2 ACP2 ACP2 2853 0.11 0.48 YES
32 GAA GAA GAA 2858 0.11 0.48 YES
33 CTSL1 CTSL1 CTSL1 2895 0.11 0.49 YES
34 MAN2B1 MAN2B1 MAN2B1 2922 0.11 0.5 YES
35 CTSH CTSH CTSH 3019 0.1 0.5 YES
36 GALC GALC GALC 3052 0.1 0.51 YES
37 PSAP PSAP PSAP 3100 0.1 0.51 YES
38 GALNS GALNS GALNS 3128 0.1 0.52 YES
39 SUMF1 SUMF1 SUMF1 3235 0.096 0.52 YES
40 NEU1 NEU1 NEU1 3257 0.096 0.53 YES
41 HEXB HEXB HEXB 3262 0.095 0.54 YES
42 AP4B1 AP4B1 AP4B1 3313 0.093 0.54 YES
43 PPT1 PPT1 PPT1 3547 0.084 0.54 YES
44 ARSA ARSA ARSA 3584 0.083 0.54 YES
45 HEXA HEXA HEXA 3586 0.082 0.55 YES
46 GLB1 GLB1 GLB1 3616 0.082 0.55 YES
47 MANBA MANBA MANBA 3624 0.081 0.56 YES
48 ATP6V0D1 ATP6V0D1 ATP6V0D1 3654 0.08 0.56 YES
49 GUSB GUSB GUSB 3660 0.08 0.57 YES
50 GGA1 GGA1 GGA1 3703 0.079 0.57 YES
51 HYAL1 HYAL1 HYAL1 3749 0.077 0.58 YES
52 ASAH1 ASAH1 ASAH1 3782 0.076 0.58 YES
53 GLA GLA GLA 3787 0.076 0.59 YES
54 ARSB ARSB ARSB 3788 0.076 0.59 YES
55 CLTCL1 CLTCL1 CLTCL1 3815 0.074 0.6 YES
56 SMPD1 SMPD1 SMPD1 3897 0.072 0.6 YES
57 NAGLU NAGLU NAGLU 3950 0.07 0.6 YES
58 CTSA CTSA CTSA 4054 0.067 0.6 YES
59 NAGPA NAGPA NAGPA 4078 0.067 0.6 YES
60 ATP6V0A1 ATP6V0A1 ATP6V0A1 4133 0.066 0.61 YES
61 GNS GNS GNS 4178 0.064 0.61 YES
62 PPT2 PPT2 PPT2 4316 0.06 0.61 YES
63 TPP1 TPP1 TPP1 4378 0.059 0.61 YES
64 CTSC CTSC CTSC 4442 0.057 0.61 YES
65 GBA GBA GBA 4453 0.057 0.61 YES
66 NAGA NAGA NAGA 4480 0.056 0.62 YES
67 AP3B2 AP3B2 AP3B2 4487 0.056 0.62 YES
68 CTSL2 CTSL2 CTSL2 4605 0.054 0.62 YES
69 ATP6V0B ATP6V0B ATP6V0B 4644 0.053 0.62 YES
70 ATP6V0C ATP6V0C ATP6V0C 4699 0.052 0.62 YES
71 ABCB9 ABCB9 ABCB9 4702 0.052 0.63 YES
72 NPC1 NPC1 NPC1 4714 0.052 0.63 YES
73 CD63 CD63 CD63 4767 0.05 0.63 YES
74 M6PR M6PR M6PR 4778 0.05 0.63 YES
75 GGA2 GGA2 GGA2 4879 0.048 0.63 YES
76 LAMP1 LAMP1 LAMP1 4958 0.047 0.63 YES
77 IDUA IDUA IDUA 5083 0.045 0.63 YES
78 CTSO CTSO CTSO 5139 0.044 0.63 YES
79 SGSH SGSH SGSH 5155 0.044 0.63 YES
80 GGA3 GGA3 GGA3 5157 0.044 0.64 YES
81 AP3S1 AP3S1 AP3S1 5228 0.042 0.63 NO
82 GNPTG GNPTG GNPTG 5408 0.04 0.63 NO
83 LAPTM4A LAPTM4A LAPTM4A 5791 0.034 0.61 NO
84 GNPTAB GNPTAB GNPTAB 5898 0.033 0.61 NO
85 SORT1 SORT1 SORT1 5996 0.031 0.6 NO
86 ATP6AP1 ATP6AP1 ATP6AP1 6024 0.031 0.6 NO
87 CLN5 CLN5 CLN5 6255 0.028 0.59 NO
88 ENTPD4 ENTPD4 ENTPD4 6315 0.028 0.59 NO
89 ATP6V1H ATP6V1H ATP6V1H 6480 0.026 0.58 NO
90 LAMP2 LAMP2 LAMP2 6714 0.024 0.57 NO
91 CLN3 CLN3 CLN3 6897 0.022 0.56 NO
92 AP4M1 AP4M1 AP4M1 7099 0.019 0.56 NO
93 AGA AGA AGA 7162 0.019 0.55 NO
94 CTNS CTNS CTNS 7245 0.018 0.55 NO
95 AP1S1 AP1S1 AP1S1 7356 0.017 0.55 NO
96 AP4S1 AP4S1 AP4S1 7436 0.016 0.54 NO
97 CLTB CLTB CLTB 7746 0.013 0.53 NO
98 AP3S2 AP3S2 AP3S2 7917 0.012 0.52 NO
99 IGF2R IGF2R IGF2R 7987 0.011 0.52 NO
100 AP4E1 AP4E1 AP4E1 8167 0.0089 0.5 NO
101 LAPTM4B LAPTM4B LAPTM4B 8376 0.007 0.49 NO
102 CLTA CLTA CLTA 8469 0.0061 0.49 NO
103 SCARB2 SCARB2 SCARB2 9073 0.00055 0.46 NO
104 ATP6V0A2 ATP6V0A2 ATP6V0A2 9247 -0.00097 0.45 NO
105 AP1G1 AP1G1 AP1G1 9416 -0.0027 0.44 NO
106 CLTC CLTC CLTC 9891 -0.0068 0.41 NO
107 AP1S3 AP1S3 AP1S3 10115 -0.0089 0.4 NO
108 SLC11A2 SLC11A2 SLC11A2 10183 -0.0096 0.4 NO
109 HGSNAT HGSNAT HGSNAT 10295 -0.011 0.39 NO
110 AP3B1 AP3B1 AP3B1 10319 -0.011 0.39 NO
111 AP3M1 AP3M1 AP3M1 11089 -0.018 0.35 NO
112 AP1M1 AP1M1 AP1M1 12213 -0.03 0.29 NO
113 AP3D1 AP3D1 AP3D1 12350 -0.032 0.28 NO
114 IDS IDS IDS 12670 -0.036 0.27 NO
115 CD164 CD164 CD164 12894 -0.038 0.26 NO
116 AP1M2 AP1M2 AP1M2 13613 -0.049 0.22 NO
117 MFSD8 MFSD8 MFSD8 14235 -0.059 0.19 NO
118 ABCA2 ABCA2 ABCA2 14292 -0.06 0.2 NO
119 SLC17A5 SLC17A5 SLC17A5 14859 -0.072 0.17 NO
120 AP3M2 AP3M2 AP3M2 14989 -0.076 0.17 NO

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

Figure S2.  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 O GLYCAN BIOSYNTHESIS

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 NCF1C NCF1C NCF1C 10 0.77 0.19 YES
2 FPR1 FPR1 FPR1 113 0.58 0.32 YES
3 NCF2 NCF2 NCF2 166 0.54 0.45 YES
4 CAMK1G CAMK1G CAMK1G 188 0.52 0.58 YES
5 GNA15 GNA15 GNA15 383 0.44 0.67 YES
6 NFATC4 NFATC4 NFATC4 2766 0.12 0.57 NO
7 NFATC1 NFATC1 NFATC1 3354 0.092 0.56 NO
8 GNGT1 GNGT1 GNGT1 3615 0.082 0.56 NO
9 NFATC3 NFATC3 NFATC3 3887 0.072 0.56 NO
10 NFKBIA NFKBIA NFKBIA 3904 0.072 0.58 NO
11 CAMK1 CAMK1 CAMK1 4197 0.064 0.58 NO
12 MAP2K3 MAP2K3 MAP2K3 4942 0.048 0.55 NO
13 NFATC2 NFATC2 NFATC2 5493 0.038 0.53 NO
14 PAK1 PAK1 PAK1 5556 0.038 0.54 NO
15 CALM3 CALM3 CALM3 5575 0.037 0.54 NO
16 RAC1 RAC1 RAC1 5724 0.035 0.54 NO
17 NFKB1 NFKB1 NFKB1 6143 0.03 0.53 NO
18 MAPK3 MAPK3 MAPK3 6174 0.029 0.53 NO
19 RAF1 RAF1 RAF1 6729 0.023 0.51 NO
20 MAPK14 MAPK14 MAPK14 7042 0.02 0.5 NO
21 CALM2 CALM2 CALM2 7677 0.014 0.46 NO
22 PPP3CB PPP3CB PPP3CB 7712 0.014 0.46 NO
23 GNB1 GNB1 GNB1 7779 0.013 0.46 NO
24 RELA RELA RELA 8154 0.0091 0.44 NO
25 PPP3CC PPP3CC PPP3CC 8478 0.006 0.43 NO
26 MAP2K1 MAP2K1 MAP2K1 8849 0.0025 0.41 NO
27 PPP3CA PPP3CA PPP3CA 9618 -0.0044 0.37 NO
28 MAPK1 MAPK1 MAPK1 10282 -0.01 0.33 NO
29 MAP3K1 MAP3K1 MAP3K1 10703 -0.014 0.31 NO
30 MAP2K2 MAP2K2 MAP2K2 10729 -0.015 0.32 NO
31 CALM1 CALM1 CALM1 11950 -0.027 0.25 NO
32 HRAS HRAS HRAS 12133 -0.029 0.25 NO
33 MAP2K6 MAP2K6 MAP2K6 12493 -0.033 0.24 NO
34 ELK1 ELK1 ELK1 13018 -0.04 0.22 NO
35 PLCB1 PLCB1 PLCB1 16048 -0.11 0.077 NO
36 PIK3C2G PIK3C2G PIK3C2G 16390 -0.13 0.089 NO

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

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

genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

Table 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 CR1 CR1 CR1 4 0.83 0.028 YES
2 MEFV MEFV MEFV 43 0.69 0.048 YES
3 CFD CFD CFD 49 0.68 0.071 YES
4 NLRC4 NLRC4 NLRC4 67 0.65 0.091 YES
5 CD180 CD180 CD180 77 0.63 0.11 YES
6 TLR8 TLR8 TLR8 101 0.59 0.13 YES
7 TLR7 TLR7 TLR7 131 0.56 0.15 YES
8 LY86 LY86 LY86 145 0.56 0.16 YES
9 ZBP1 ZBP1 ZBP1 194 0.52 0.18 YES
10 NOD2 NOD2 NOD2 218 0.5 0.2 YES
11 SAA1 SAA1 SAA1 224 0.5 0.21 YES
12 BTK BTK BTK 245 0.49 0.23 YES
13 CTSK CTSK CTSK 254 0.49 0.24 YES
14 RIPK3 RIPK3 RIPK3 258 0.49 0.26 YES
15 LY96 LY96 LY96 270 0.48 0.28 YES
16 NLRP3 NLRP3 NLRP3 273 0.48 0.29 YES
17 C4BPA C4BPA C4BPA 299 0.47 0.3 YES
18 CFH CFH CFH 338 0.45 0.32 YES
19 CTSS CTSS CTSS 349 0.45 0.33 YES
20 PSTPIP1 PSTPIP1 PSTPIP1 358 0.44 0.35 YES
21 C2 C2 C2 394 0.43 0.36 YES
22 CCR2 CCR2 CCR2 437 0.42 0.37 YES
23 C1QB C1QB C1QB 538 0.39 0.38 YES
24 DEFA1B DEFA1B DEFA1B 563 0.38 0.39 YES
25 IRAK3 IRAK3 IRAK3 574 0.38 0.4 YES
26 TLR5 TLR5 TLR5 606 0.37 0.41 YES
27 C1QA C1QA C1QA 615 0.37 0.42 YES
28 CD4 CD4 CD4 652 0.36 0.43 YES
29 C1QC C1QC C1QC 657 0.36 0.45 YES
30 TLR6 TLR6 TLR6 674 0.36 0.46 YES
31 CARD9 CARD9 CARD9 689 0.35 0.47 YES
32 CD14 CD14 CD14 692 0.35 0.48 YES
33 S100A12 S100A12 S100A12 705 0.35 0.49 YES
34 CASP1 CASP1 CASP1 754 0.34 0.5 YES
35 C3 C3 C3 765 0.33 0.51 YES
36 C1S C1S C1S 782 0.33 0.52 YES
37 P2RX7 P2RX7 P2RX7 802 0.32 0.53 YES
38 TLR1 TLR1 TLR1 851 0.31 0.54 YES
39 TLR4 TLR4 TLR4 932 0.29 0.54 YES
40 FOS FOS FOS 1040 0.27 0.55 YES
41 AIM2 AIM2 AIM2 1053 0.27 0.55 YES
42 DEFB1 DEFB1 DEFB1 1090 0.26 0.56 YES
43 BIRC3 BIRC3 BIRC3 1133 0.26 0.57 YES
44 TLR2 TLR2 TLR2 1146 0.26 0.57 YES
45 NLRP1 NLRP1 NLRP1 1173 0.25 0.58 YES
46 PYCARD PYCARD PYCARD 1248 0.24 0.59 YES
47 S100B S100B S100B 1327 0.23 0.59 YES
48 TLR10 TLR10 TLR10 1354 0.23 0.6 YES
49 LBP LBP LBP 1358 0.23 0.6 YES
50 RNF125 RNF125 RNF125 1365 0.23 0.61 YES
51 CFB CFB CFB 1377 0.23 0.62 YES
52 TLR9 TLR9 TLR9 1406 0.22 0.62 YES
53 LGMN LGMN LGMN 1407 0.22 0.63 YES
54 CFHR3 CFHR3 CFHR3 1518 0.21 0.63 YES
55 TNFAIP3 TNFAIP3 TNFAIP3 1720 0.19 0.63 YES
56 TICAM2 TICAM2 TICAM2 1750 0.19 0.63 YES
57 CCR6 CCR6 CCR6 2115 0.16 0.62 YES
58 MAPK11 MAPK11 MAPK11 2307 0.14 0.61 YES
59 C4A C4A C4A 2316 0.14 0.62 YES
60 NLRC5 NLRC5 NLRC5 2412 0.14 0.61 YES
61 MASP1 MASP1 MASP1 2429 0.14 0.62 YES
62 MAPK13 MAPK13 MAPK13 2430 0.14 0.62 YES
63 RPS6KA2 RPS6KA2 RPS6KA2 2540 0.13 0.62 YES
64 UNC93B1 UNC93B1 UNC93B1 2552 0.13 0.62 YES
65 CASP4 CASP4 CASP4 2592 0.13 0.63 YES
66 RPS6KA5 RPS6KA5 RPS6KA5 2618 0.12 0.63 YES
67 IRF1 IRF1 IRF1 2628 0.12 0.63 YES
68 C6 C6 C6 2676 0.12 0.63 YES
69 UBA7 UBA7 UBA7 2735 0.12 0.63 YES
70 ISG15 ISG15 ISG15 2748 0.12 0.64 YES
71 UBE2L6 UBE2L6 UBE2L6 2770 0.12 0.64 YES
72 CTSB CTSB CTSB 2828 0.11 0.64 YES
73 C7 C7 C7 2837 0.11 0.64 YES
74 C4BPB C4BPB C4BPB 2854 0.11 0.65 YES
75 CTSL1 CTSL1 CTSL1 2895 0.11 0.65 YES
76 CNPY3 CNPY3 CNPY3 3083 0.1 0.64 YES
77 LGALS3 LGALS3 LGALS3 3103 0.1 0.64 YES
78 PELI1 PELI1 PELI1 3111 0.1 0.65 YES
79 JUN JUN JUN 3209 0.097 0.64 YES
80 DEFB103B DEFB103B DEFB103B 3223 0.096 0.65 YES
81 MYD88 MYD88 MYD88 3280 0.095 0.65 YES
82 CFI CFI CFI 3303 0.094 0.65 YES
83 PROS1 PROS1 PROS1 3361 0.092 0.65 YES
84 TXNIP TXNIP TXNIP 3404 0.09 0.65 YES
85 RIPK2 RIPK2 RIPK2 3496 0.086 0.65 NO
86 MEF2C MEF2C MEF2C 3568 0.083 0.65 NO
87 RPS6KA1 RPS6KA1 RPS6KA1 3810 0.075 0.64 NO
88 IRAK2 IRAK2 IRAK2 3874 0.072 0.63 NO
89 NFKBIA NFKBIA NFKBIA 3904 0.072 0.64 NO
90 C9 C9 C9 3971 0.069 0.63 NO
91 AGER AGER AGER 4037 0.068 0.63 NO
92 IRF7 IRF7 IRF7 4069 0.067 0.63 NO
93 IKBKE IKBKE IKBKE 4082 0.067 0.63 NO
94 HERC5 HERC5 HERC5 4290 0.061 0.62 NO
95 DHX58 DHX58 DHX58 4364 0.059 0.62 NO
96 NOD1 NOD1 NOD1 4497 0.056 0.62 NO
97 CYLD CYLD CYLD 4560 0.055 0.62 NO
98 MBL2 MBL2 MBL2 4564 0.055 0.62 NO
99 TLR3 TLR3 TLR3 4569 0.055 0.62 NO
100 IRAK4 IRAK4 IRAK4 4658 0.053 0.62 NO
101 PLCG2 PLCG2 PLCG2 4673 0.052 0.62 NO
102 NFKB2 NFKB2 NFKB2 4710 0.052 0.62 NO
103 MAPK7 MAPK7 MAPK7 4737 0.051 0.62 NO
104 MAP2K3 MAP2K3 MAP2K3 4942 0.048 0.61 NO
105 NLRX1 NLRX1 NLRX1 5033 0.046 0.6 NO
106 DUSP4 DUSP4 DUSP4 5069 0.045 0.6 NO
107 CD55 CD55 CD55 5539 0.038 0.58 NO
108 UBE2D1 UBE2D1 UBE2D1 5586 0.037 0.58 NO
109 CASP10 CASP10 CASP10 5725 0.035 0.57 NO
110 IRF3 IRF3 IRF3 5825 0.034 0.56 NO
111 TRAF2 TRAF2 TRAF2 5960 0.032 0.56 NO
112 IKBKG IKBKG IKBKG 5982 0.032 0.56 NO
113 IKBKB IKBKB IKBKB 6018 0.031 0.56 NO
114 CRP CRP CRP 6023 0.031 0.56 NO
115 IRF2 IRF2 IRF2 6081 0.03 0.56 NO
116 HSP90B1 HSP90B1 HSP90B1 6135 0.03 0.55 NO
117 MAPK3 MAPK3 MAPK3 6174 0.029 0.55 NO
118 BCL2L1 BCL2L1 BCL2L1 6177 0.029 0.55 NO
119 DDOST DDOST DDOST 6265 0.028 0.55 NO
120 FADD FADD FADD 6484 0.026 0.54 NO
121 CAPZA1 CAPZA1 CAPZA1 6517 0.026 0.54 NO
122 UBA52 UBA52 UBA52 6549 0.025 0.54 NO
123 RNF135 RNF135 RNF135 6655 0.024 0.53 NO
124 OTUD5 OTUD5 OTUD5 7001 0.02 0.51 NO
125 MAPK14 MAPK14 MAPK14 7042 0.02 0.51 NO
126 IFNA1 IFNA1 IFNA1 7109 0.019 0.51 NO
127 ECSIT ECSIT ECSIT 7157 0.019 0.51 NO
128 ATG12 ATG12 ATG12 7241 0.018 0.5 NO
129 ZFYVE20 ZFYVE20 ZFYVE20 7272 0.018 0.5 NO
130 NFKBIB NFKBIB NFKBIB 7480 0.016 0.49 NO
131 IRAK1 IRAK1 IRAK1 7543 0.015 0.49 NO
132 RIPK1 RIPK1 RIPK1 7600 0.015 0.48 NO
133 TAB1 TAB1 TAB1 7601 0.015 0.48 NO
134 RPS27A RPS27A RPS27A 7758 0.013 0.48 NO
135 CASP9 CASP9 CASP9 7846 0.012 0.47 NO
136 TRAF3 TRAF3 TRAF3 8056 0.01 0.46 NO
137 RELA RELA RELA 8154 0.0091 0.46 NO
138 MAPKAPK3 MAPKAPK3 MAPKAPK3 8303 0.0076 0.45 NO
139 PIN1 PIN1 PIN1 8344 0.0073 0.44 NO
140 CASP8 CASP8 CASP8 8414 0.0066 0.44 NO
141 UBE2D2 UBE2D2 UBE2D2 8417 0.0066 0.44 NO
142 TANK TANK TANK 8524 0.0055 0.44 NO
143 TAB2 TAB2 TAB2 8549 0.0052 0.43 NO
144 UBE2N UBE2N UBE2N 8628 0.0045 0.43 NO
145 BCL2 BCL2 BCL2 8744 0.0036 0.42 NO
146 TBK1 TBK1 TBK1 8760 0.0034 0.42 NO
147 MAP2K1 MAP2K1 MAP2K1 8849 0.0025 0.42 NO
148 PIK3R4 PIK3R4 PIK3R4 8859 0.0024 0.42 NO
149 MAP2K4 MAP2K4 MAP2K4 8930 0.0018 0.41 NO
150 DAK DAK DAK 9006 0.0011 0.41 NO
151 UBE2D3 UBE2D3 UBE2D3 9044 0.00078 0.41 NO
152 TXN TXN TXN 9340 -0.0019 0.39 NO
153 DUSP7 DUSP7 DUSP7 9406 -0.0025 0.39 NO
154 ATG5 ATG5 ATG5 9646 -0.0047 0.37 NO
155 PRKCSH PRKCSH PRKCSH 9865 -0.0067 0.36 NO
156 APP APP APP 10072 -0.0085 0.35 NO
157 PPP2CB PPP2CB PPP2CB 10080 -0.0086 0.35 NO
158 BIRC2 BIRC2 BIRC2 10138 -0.0091 0.35 NO
159 CAPZA2 CAPZA2 CAPZA2 10247 -0.01 0.34 NO
160 MAPK1 MAPK1 MAPK1 10282 -0.01 0.34 NO
161 PIK3C3 PIK3C3 PIK3C3 10539 -0.013 0.33 NO
162 PPP2CA PPP2CA PPP2CA 10590 -0.013 0.32 NO
163 MAP3K1 MAP3K1 MAP3K1 10703 -0.014 0.32 NO
164 MAP2K2 MAP2K2 MAP2K2 10729 -0.015 0.32 NO
165 HSP90AB1 HSP90AB1 HSP90AB1 10773 -0.015 0.32 NO
166 TRAF6 TRAF6 TRAF6 10909 -0.016 0.31 NO
167 TICAM1 TICAM1 TICAM1 11027 -0.017 0.3 NO
168 RPS6KA3 RPS6KA3 RPS6KA3 11124 -0.018 0.3 NO
169 DUSP3 DUSP3 DUSP3 11242 -0.019 0.29 NO
170 PPP2R1A PPP2R1A PPP2R1A 11343 -0.02 0.29 NO
171 CHUK CHUK CHUK 11383 -0.021 0.28 NO
172 PCBP2 PCBP2 PCBP2 11421 -0.021 0.28 NO
173 UBE2K UBE2K UBE2K 11438 -0.021 0.28 NO
174 IFIH1 IFIH1 IFIH1 11532 -0.022 0.28 NO
175 PANX1 PANX1 PANX1 11607 -0.023 0.28 NO
176 HMGB1 HMGB1 HMGB1 11618 -0.023 0.28 NO
177 CASP2 CASP2 CASP2 11703 -0.024 0.27 NO
178 MAP3K7 MAP3K7 MAP3K7 11753 -0.024 0.27 NO
179 CREB1 CREB1 CREB1 11758 -0.024 0.27 NO
180 DDX58 DDX58 DDX58 12178 -0.029 0.25 NO
181 MAPK10 MAPK10 MAPK10 12254 -0.03 0.24 NO
182 MAPKAPK2 MAPKAPK2 MAPKAPK2 12364 -0.032 0.24 NO
183 CREBBP CREBBP CREBBP 12366 -0.032 0.24 NO
184 MAP2K6 MAP2K6 MAP2K6 12493 -0.033 0.24 NO
185 TAB3 TAB3 TAB3 12598 -0.035 0.23 NO
186 MAP2K7 MAP2K7 MAP2K7 12660 -0.036 0.23 NO
187 ATF1 ATF1 ATF1 12757 -0.037 0.22 NO
188 DNM1 DNM1 DNM1 12956 -0.039 0.21 NO
189 ELK1 ELK1 ELK1 13018 -0.04 0.21 NO
190 TRIM25 TRIM25 TRIM25 13024 -0.04 0.21 NO
191 PELI3 PELI3 PELI3 13046 -0.04 0.21 NO
192 MAPK9 MAPK9 MAPK9 13400 -0.045 0.2 NO
193 PPP2R1B PPP2R1B PPP2R1B 13462 -0.046 0.19 NO
194 CD46 CD46 CD46 13496 -0.047 0.19 NO
195 MAVS MAVS MAVS 13638 -0.049 0.19 NO
196 PPP2R5D PPP2R5D PPP2R5D 13860 -0.052 0.18 NO
197 MAPK12 MAPK12 MAPK12 13997 -0.055 0.17 NO
198 TAX1BP1 TAX1BP1 TAX1BP1 14068 -0.056 0.17 NO
199 PELI2 PELI2 PELI2 14134 -0.057 0.17 NO
200 SIGIRR SIGIRR SIGIRR 14344 -0.061 0.16 NO
201 EP300 EP300 EP300 14576 -0.066 0.14 NO
202 SIKE1 SIKE1 SIKE1 14695 -0.069 0.14 NO
203 C8G C8G C8G 14778 -0.071 0.14 NO
204 MEF2A MEF2A MEF2A 14990 -0.076 0.13 NO
205 MASP2 MASP2 MASP2 15173 -0.08 0.12 NO
206 DNM2 DNM2 DNM2 15507 -0.09 0.11 NO
207 EEA1 EEA1 EEA1 15562 -0.092 0.11 NO
208 ATF2 ATF2 ATF2 15611 -0.093 0.11 NO
209 TIRAP TIRAP TIRAP 15916 -0.1 0.093 NO
210 MAPK8 MAPK8 MAPK8 16073 -0.11 0.088 NO
211 DUSP6 DUSP6 DUSP6 16342 -0.12 0.077 NO
212 C5 C5 C5 17368 -0.2 0.026 NO
213 CDK1 CDK1 CDK1 17655 -0.25 0.018 NO

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

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

genes ES table in pathway: KEGG GLYCEROPHOSPHOLIPID METABOLISM

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 OSM OSM OSM 74 0.64 0.14 YES
2 IRF8 IRF8 IRF8 449 0.42 0.2 YES
3 CSF2RA CSF2RA CSF2RA 483 0.4 0.29 YES
4 CSF2RB CSF2RB CSF2RB 487 0.4 0.38 YES
5 CCL2 CCL2 CCL2 580 0.38 0.46 YES
6 INPP5D INPP5D INPP5D 921 0.3 0.5 YES
7 FOS FOS FOS 1040 0.27 0.56 YES
8 CISH CISH CISH 1203 0.25 0.6 YES
9 SYK SYK SYK 1397 0.22 0.64 YES
10 LYN LYN LYN 1867 0.18 0.65 YES
11 STAT5A STAT5A STAT5A 1907 0.18 0.69 YES
12 CSF2 CSF2 CSF2 2099 0.16 0.71 YES
13 GAB2 GAB2 GAB2 2419 0.14 0.72 YES
14 GRB2 GRB2 GRB2 4058 0.067 0.65 NO
15 STAT3 STAT3 STAT3 4893 0.048 0.61 NO
16 PRKACB PRKACB PRKACB 5003 0.046 0.62 NO
17 IKBKB IKBKB IKBKB 6018 0.031 0.57 NO
18 MAPK3 MAPK3 MAPK3 6174 0.029 0.56 NO
19 PIM1 PIM1 PIM1 6558 0.025 0.55 NO
20 RAF1 RAF1 RAF1 6729 0.023 0.54 NO
21 STAT5B STAT5B STAT5B 7271 0.018 0.52 NO
22 STAT1 STAT1 STAT1 7441 0.016 0.51 NO
23 MAP2K1 MAP2K1 MAP2K1 8849 0.0025 0.43 NO
24 PIK3R1 PIK3R1 PIK3R1 9374 -0.0023 0.4 NO
25 PRKACA PRKACA PRKACA 9680 -0.005 0.39 NO
26 YWHAZ YWHAZ YWHAZ 10256 -0.01 0.36 NO
27 MAPK1 MAPK1 MAPK1 10282 -0.01 0.36 NO
28 MAP2K2 MAP2K2 MAP2K2 10729 -0.015 0.34 NO
29 JAK2 JAK2 JAK2 11420 -0.021 0.3 NO
30 PTPN11 PTPN11 PTPN11 11699 -0.024 0.29 NO
31 HRAS HRAS HRAS 12133 -0.029 0.28 NO
32 NRAS NRAS NRAS 12310 -0.031 0.27 NO
33 KRAS KRAS KRAS 13155 -0.042 0.24 NO
34 SHC1 SHC1 SHC1 13338 -0.044 0.24 NO
35 PIK3CA PIK3CA PIK3CA 13417 -0.046 0.24 NO
36 SOS1 SOS1 SOS1 14418 -0.062 0.2 NO

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

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

genes ES table in pathway: KEGG ETHER LIPID METABOLISM

Table 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 CD28 CD28 CD28 157 0.55 0.066 YES
2 HCK HCK HCK 268 0.48 0.13 YES
3 CD8B CD8B CD8B 361 0.44 0.18 YES
4 LCK LCK LCK 371 0.44 0.24 YES
5 CD247 CD247 CD247 385 0.44 0.3 YES
6 DOCK2 DOCK2 DOCK2 417 0.42 0.36 YES
7 CD4 CD4 CD4 652 0.36 0.39 YES
8 AP1S2 AP1S2 AP1S2 811 0.32 0.43 YES
9 ELMO1 ELMO1 ELMO1 1151 0.26 0.44 YES
10 PSMB9 PSMB9 PSMB9 1979 0.17 0.42 YES
11 APOBEC3G APOBEC3G APOBEC3G 2003 0.17 0.44 YES
12 RCC1 RCC1 RCC1 2485 0.13 0.43 YES
13 B2M B2M B2M 2648 0.12 0.44 YES
14 PSMB10 PSMB10 PSMB10 2729 0.12 0.45 YES
15 AP1B1 AP1B1 AP1B1 2808 0.12 0.46 YES
16 HLA-A HLA-A HLA-A 3667 0.08 0.43 NO
17 PSMB8 PSMB8 PSMB8 3949 0.07 0.42 NO
18 AP2S1 AP2S1 AP2S1 4389 0.059 0.4 NO
19 PSMB3 PSMB3 PSMB3 4651 0.053 0.4 NO
20 HMGA1 HMGA1 HMGA1 4970 0.047 0.38 NO
21 PSMD2 PSMD2 PSMD2 5110 0.045 0.38 NO
22 PSME2 PSME2 PSME2 5144 0.044 0.39 NO
23 PSMB6 PSMB6 PSMB6 5205 0.043 0.39 NO
24 PSMC1 PSMC1 PSMC1 5304 0.041 0.39 NO
25 NUP85 NUP85 NUP85 5321 0.041 0.4 NO
26 PSMB2 PSMB2 PSMB2 5334 0.041 0.4 NO
27 NUP37 NUP37 NUP37 5515 0.038 0.4 NO
28 PSMD13 PSMD13 PSMD13 5717 0.035 0.39 NO
29 RAC1 RAC1 RAC1 5724 0.035 0.39 NO
30 PSME4 PSME4 PSME4 5885 0.033 0.39 NO
31 PSMD7 PSMD7 PSMD7 5968 0.032 0.39 NO
32 NUP93 NUP93 NUP93 5992 0.031 0.39 NO
33 PSMA2 PSMA2 PSMA2 6105 0.03 0.39 NO
34 PSMC2 PSMC2 PSMC2 6209 0.029 0.39 NO
35 PSMB1 PSMB1 PSMB1 6314 0.028 0.38 NO
36 RBX1 RBX1 RBX1 6382 0.027 0.38 NO
37 PSMD6 PSMD6 PSMD6 6407 0.027 0.39 NO
38 ATP6V1H ATP6V1H ATP6V1H 6480 0.026 0.39 NO
39 UBA52 UBA52 UBA52 6549 0.025 0.39 NO
40 PSMC5 PSMC5 PSMC5 6570 0.025 0.39 NO
41 PSMD9 PSMD9 PSMD9 6688 0.024 0.38 NO
42 RANBP1 RANBP1 RANBP1 6693 0.024 0.39 NO
43 AAAS AAAS AAAS 6835 0.022 0.38 NO
44 PSME1 PSME1 PSME1 6847 0.022 0.39 NO
45 CDK9 CDK9 CDK9 6873 0.022 0.39 NO
46 PSMA5 PSMA5 PSMA5 6925 0.021 0.39 NO
47 TCEB2 TCEB2 TCEB2 6933 0.021 0.39 NO
48 PSMC3 PSMC3 PSMC3 7112 0.019 0.38 NO
49 AP2M1 AP2M1 AP2M1 7130 0.019 0.38 NO
50 AP2A2 AP2A2 AP2A2 7292 0.018 0.38 NO
51 RANGAP1 RANGAP1 RANGAP1 7348 0.017 0.38 NO
52 AP1S1 AP1S1 AP1S1 7356 0.017 0.38 NO
53 PSMD11 PSMD11 PSMD11 7408 0.016 0.38 NO
54 PSMD3 PSMD3 PSMD3 7542 0.015 0.37 NO
55 NUP62 NUP62 NUP62 7561 0.015 0.37 NO
56 PSMD4 PSMD4 PSMD4 7566 0.015 0.38 NO
57 PSMD1 PSMD1 PSMD1 7628 0.014 0.38 NO
58 AP2B1 AP2B1 AP2B1 7748 0.013 0.37 NO
59 RPS27A RPS27A RPS27A 7758 0.013 0.37 NO
60 PSMA7 PSMA7 PSMA7 7929 0.011 0.36 NO
61 PAK2 PAK2 PAK2 7956 0.011 0.36 NO
62 PSMB4 PSMB4 PSMB4 8010 0.011 0.36 NO
63 PSMA6 PSMA6 PSMA6 8149 0.0091 0.36 NO
64 PSMD14 PSMD14 PSMD14 8153 0.0091 0.36 NO
65 BANF1 BANF1 BANF1 8158 0.009 0.36 NO
66 PSMA3 PSMA3 PSMA3 8168 0.0088 0.36 NO
67 PSMA1 PSMA1 PSMA1 8235 0.0082 0.36 NO
68 RAN RAN RAN 8322 0.0074 0.35 NO
69 PSMC4 PSMC4 PSMC4 8529 0.0054 0.34 NO
70 NUP188 NUP188 NUP188 8746 0.0035 0.33 NO
71 PPIA PPIA PPIA 8752 0.0035 0.33 NO
72 KPNA1 KPNA1 KPNA1 8780 0.0032 0.33 NO
73 PACS1 PACS1 PACS1 8860 0.0024 0.32 NO
74 PSMB5 PSMB5 PSMB5 8995 0.0012 0.32 NO
75 NUP107 NUP107 NUP107 9120 0.00013 0.31 NO
76 NUP88 NUP88 NUP88 9362 -0.0021 0.3 NO
77 PSMB7 PSMB7 PSMB7 9405 -0.0025 0.3 NO
78 AP1G1 AP1G1 AP1G1 9416 -0.0027 0.29 NO
79 NUP214 NUP214 NUP214 9622 -0.0044 0.28 NO
80 PSMA4 PSMA4 PSMA4 9625 -0.0044 0.28 NO
81 AP2A1 AP2A1 AP2A1 9833 -0.0064 0.27 NO
82 NUP210 NUP210 NUP210 9888 -0.0068 0.27 NO
83 ARF1 ARF1 ARF1 9920 -0.0071 0.27 NO
84 PSMD8 PSMD8 PSMD8 10120 -0.0089 0.26 NO
85 SKP1 SKP1 SKP1 10171 -0.0094 0.26 NO
86 BTRC BTRC BTRC 10258 -0.01 0.26 NO
87 PSMD10 PSMD10 PSMD10 10355 -0.011 0.25 NO
88 PSMD12 PSMD12 PSMD12 10553 -0.013 0.24 NO
89 PSMC6 PSMC6 PSMC6 10581 -0.013 0.24 NO
90 NUPL1 NUPL1 NUPL1 10669 -0.014 0.24 NO
91 SLC25A5 SLC25A5 SLC25A5 10801 -0.015 0.24 NO
92 NUP54 NUP54 NUP54 10822 -0.016 0.24 NO
93 RAE1 RAE1 RAE1 10874 -0.016 0.24 NO
94 NUP50 NUP50 NUP50 11026 -0.017 0.23 NO
95 NUPL2 NUPL2 NUPL2 11087 -0.018 0.23 NO
96 PSMD5 PSMD5 PSMD5 11105 -0.018 0.23 NO
97 TCEB1 TCEB1 TCEB1 11130 -0.018 0.23 NO
98 NUP133 NUP133 NUP133 11172 -0.019 0.23 NO
99 RANBP2 RANBP2 RANBP2 11230 -0.019 0.23 NO
100 XPO1 XPO1 XPO1 11872 -0.026 0.2 NO
101 AP1M1 AP1M1 AP1M1 12213 -0.03 0.18 NO
102 NUP153 NUP153 NUP153 12319 -0.031 0.18 NO
103 PSMF1 PSMF1 PSMF1 12360 -0.032 0.18 NO
104 POM121 POM121 POM121 12385 -0.032 0.19 NO
105 KPNB1 KPNB1 KPNB1 12609 -0.035 0.18 NO
106 NUP43 NUP43 NUP43 12863 -0.038 0.17 NO
107 NUP205 NUP205 NUP205 12919 -0.039 0.17 NO
108 SLC25A6 SLC25A6 SLC25A6 13124 -0.041 0.17 NO
109 NPM1 NPM1 NPM1 13255 -0.043 0.16 NO
110 SEH1L SEH1L SEH1L 13260 -0.043 0.17 NO
111 SLC25A4 SLC25A4 SLC25A4 13283 -0.044 0.18 NO
112 CUL5 CUL5 CUL5 13335 -0.044 0.18 NO
113 AP1M2 AP1M2 AP1M2 13613 -0.049 0.17 NO
114 NUP35 NUP35 NUP35 14645 -0.068 0.12 NO
115 PSIP1 PSIP1 PSIP1 14834 -0.072 0.12 NO
116 FYN FYN FYN 15324 -0.084 0.1 NO
117 NUP155 NUP155 NUP155 15328 -0.084 0.12 NO
118 TPR TPR TPR 15918 -0.1 0.097 NO
119 CCNT1 CCNT1 CCNT1 16483 -0.13 0.084 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: KEGG ETHER LIPID METABOLISM.

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

genes ES table in pathway: KEGG ARACHIDONIC ACID METABOLISM

Table 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 IL1RN IL1RN IL1RN 133 0.56 0.014 YES
2 IL2RA IL2RA IL2RA 209 0.51 0.029 YES
3 NOD2 NOD2 NOD2 218 0.5 0.048 YES
4 VAV1 VAV1 VAV1 250 0.49 0.064 YES
5 HCK HCK HCK 268 0.48 0.082 YES
6 FCGR1A FCGR1A FCGR1A 339 0.45 0.095 YES
7 HGF HGF HGF 354 0.45 0.11 YES
8 LCK LCK LCK 371 0.44 0.13 YES
9 IL2RG IL2RG IL2RG 377 0.44 0.14 YES
10 HLA-DQA2 HLA-DQA2 HLA-DQA2 398 0.43 0.16 YES
11 GBP5 GBP5 GBP5 443 0.42 0.17 YES
12 IRF8 IRF8 IRF8 449 0.42 0.19 YES
13 HLA-G HLA-G HLA-G 455 0.41 0.2 YES
14 CSF2RA CSF2RA CSF2RA 483 0.4 0.22 YES
15 CSF2RB CSF2RB CSF2RB 487 0.4 0.23 YES
16 IRF4 IRF4 IRF4 489 0.4 0.25 YES
17 HLA-DQA1 HLA-DQA1 HLA-DQA1 497 0.4 0.26 YES
18 HLA-DRB5 HLA-DRB5 HLA-DRB5 534 0.39 0.27 YES
19 PTAFR PTAFR PTAFR 568 0.38 0.29 YES
20 FCGR1B FCGR1B FCGR1B 571 0.38 0.3 YES
21 IRAK3 IRAK3 IRAK3 574 0.38 0.32 YES
22 IL1B IL1B IL1B 671 0.36 0.32 YES
23 MX2 MX2 MX2 690 0.35 0.34 YES
24 CASP1 CASP1 CASP1 754 0.34 0.35 YES
25 IL7R IL7R IL7R 787 0.33 0.36 YES
26 IL2RB IL2RB IL2RB 792 0.33 0.37 YES
27 IL1A IL1A IL1A 793 0.33 0.38 YES
28 CIITA CIITA CIITA 806 0.32 0.39 YES
29 HLA-DRB1 HLA-DRB1 HLA-DRB1 889 0.3 0.4 YES
30 SOCS3 SOCS3 SOCS3 900 0.3 0.41 YES
31 HLA-DPB1 HLA-DPB1 HLA-DPB1 954 0.29 0.42 YES
32 OAS2 OAS2 OAS2 981 0.28 0.43 YES
33 CD44 CD44 CD44 1116 0.26 0.43 YES
34 HLA-DPA1 HLA-DPA1 HLA-DPA1 1171 0.25 0.44 YES
35 CISH CISH CISH 1203 0.25 0.44 YES
36 IL6 IL6 IL6 1257 0.24 0.45 YES
37 IL1R2 IL1R2 IL1R2 1337 0.23 0.45 YES
38 ICAM1 ICAM1 ICAM1 1351 0.23 0.46 YES
39 SYK SYK SYK 1397 0.22 0.47 YES
40 IL2 IL2 IL2 1410 0.22 0.48 YES
41 VCAM1 VCAM1 VCAM1 1631 0.2 0.47 YES
42 MT2A MT2A MT2A 1676 0.2 0.48 YES
43 IFI27 IFI27 IFI27 1700 0.19 0.48 YES
44 OASL OASL OASL 1717 0.19 0.49 YES
45 PIK3CD PIK3CD PIK3CD 1823 0.18 0.49 YES
46 LYN LYN LYN 1867 0.18 0.49 YES
47 STAT5A STAT5A STAT5A 1907 0.18 0.5 YES
48 IL1RAP IL1RAP IL1RAP 1942 0.17 0.5 YES
49 ISG20 ISG20 ISG20 1976 0.17 0.51 YES
50 MAP3K8 MAP3K8 MAP3K8 1978 0.17 0.51 YES
51 SOCS1 SOCS1 SOCS1 2012 0.17 0.52 YES
52 EGR1 EGR1 EGR1 2062 0.16 0.52 YES
53 HLA-F HLA-F HLA-F 2078 0.16 0.53 YES
54 CSF2 CSF2 CSF2 2099 0.16 0.53 YES
55 GAB2 GAB2 GAB2 2419 0.14 0.52 YES
56 BLNK BLNK BLNK 2522 0.13 0.52 YES
57 XAF1 XAF1 XAF1 2621 0.12 0.52 YES
58 IL5RA IL5RA IL5RA 2626 0.12 0.52 YES
59 IRF1 IRF1 IRF1 2628 0.12 0.53 YES
60 JAK3 JAK3 JAK3 2634 0.12 0.53 YES
61 IFI6 IFI6 IFI6 2635 0.12 0.54 YES
62 B2M B2M B2M 2648 0.12 0.54 YES
63 PTPN6 PTPN6 PTPN6 2652 0.12 0.54 YES
64 IL18 IL18 IL18 2681 0.12 0.55 YES
65 HLA-B HLA-B HLA-B 2725 0.12 0.55 YES
66 UBA7 UBA7 UBA7 2735 0.12 0.55 YES
67 ISG15 ISG15 ISG15 2748 0.12 0.56 YES
68 UBE2L6 UBE2L6 UBE2L6 2770 0.12 0.56 YES
69 PTK2B PTK2B PTK2B 2926 0.11 0.56 YES
70 GBP4 GBP4 GBP4 2967 0.11 0.56 YES
71 MX1 MX1 MX1 2973 0.11 0.56 YES
72 IFITM2 IFITM2 IFITM2 2979 0.11 0.56 YES
73 TEC TEC TEC 2991 0.11 0.57 YES
74 PELI1 PELI1 PELI1 3111 0.1 0.57 YES
75 IFNG IFNG IFNG 3130 0.1 0.57 YES
76 IRF6 IRF6 IRF6 3176 0.098 0.57 YES
77 MYD88 MYD88 MYD88 3280 0.095 0.57 YES
78 IFNAR2 IFNAR2 IFNAR2 3282 0.094 0.57 YES
79 IL3RA IL3RA IL3RA 3308 0.094 0.57 YES
80 IFNGR2 IFNGR2 IFNGR2 3336 0.093 0.57 YES
81 IFNGR1 IFNGR1 IFNGR1 3365 0.092 0.58 YES
82 HLA-C HLA-C HLA-C 3456 0.088 0.58 YES
83 RIPK2 RIPK2 RIPK2 3496 0.086 0.58 YES
84 NCAM1 NCAM1 NCAM1 3564 0.083 0.58 YES
85 PML PML PML 3594 0.082 0.58 YES
86 HLA-A HLA-A HLA-A 3667 0.08 0.58 YES
87 IFI35 IFI35 IFI35 3709 0.078 0.58 YES
88 IRF5 IRF5 IRF5 3717 0.078 0.58 YES
89 STAT2 STAT2 STAT2 3841 0.074 0.58 YES
90 IRAK2 IRAK2 IRAK2 3874 0.072 0.58 YES
91 IFITM3 IFITM3 IFITM3 3896 0.072 0.58 YES
92 OAS1 OAS1 OAS1 3934 0.07 0.58 YES
93 PSMB8 PSMB8 PSMB8 3949 0.07 0.58 YES
94 GRB2 GRB2 GRB2 4058 0.067 0.58 NO
95 IRF7 IRF7 IRF7 4069 0.067 0.58 NO
96 PRKCD PRKCD PRKCD 4123 0.066 0.58 NO
97 GBP1 GBP1 GBP1 4183 0.064 0.58 NO
98 HERC5 HERC5 HERC5 4290 0.061 0.57 NO
99 NOD1 NOD1 NOD1 4497 0.056 0.56 NO
100 PTPN2 PTPN2 PTPN2 4570 0.055 0.56 NO
101 PTPN1 PTPN1 PTPN1 4582 0.054 0.56 NO
102 IRAK4 IRAK4 IRAK4 4658 0.053 0.56 NO
103 NFKB2 NFKB2 NFKB2 4710 0.052 0.56 NO
104 IFIT2 IFIT2 IFIT2 4785 0.05 0.56 NO
105 STAT3 STAT3 STAT3 4893 0.048 0.55 NO
106 USP18 USP18 USP18 4940 0.048 0.55 NO
107 PRKACB PRKACB PRKACB 5003 0.046 0.55 NO
108 IFITM1 IFITM1 IFITM1 5259 0.042 0.54 NO
109 NUP85 NUP85 NUP85 5321 0.041 0.54 NO
110 NUP37 NUP37 NUP37 5515 0.038 0.53 NO
111 SOCS2 SOCS2 SOCS2 5548 0.038 0.53 NO
112 EIF4A3 EIF4A3 EIF4A3 5638 0.036 0.52 NO
113 RNASEL RNASEL RNASEL 5694 0.036 0.52 NO
114 GBP2 GBP2 GBP2 5698 0.036 0.52 NO
115 EIF4A1 EIF4A1 EIF4A1 5709 0.035 0.52 NO
116 IRF9 IRF9 IRF9 5740 0.035 0.52 NO
117 IRF3 IRF3 IRF3 5825 0.034 0.52 NO
118 IP6K2 IP6K2 IP6K2 5843 0.033 0.52 NO
119 OAS3 OAS3 OAS3 5970 0.032 0.52 NO
120 IKBKG IKBKG IKBKG 5982 0.032 0.52 NO
121 NUP93 NUP93 NUP93 5992 0.031 0.52 NO
122 IKBKB IKBKB IKBKB 6018 0.031 0.52 NO
123 IRF2 IRF2 IRF2 6081 0.03 0.51 NO
124 MAPK3 MAPK3 MAPK3 6174 0.029 0.51 NO
125 SQSTM1 SQSTM1 SQSTM1 6304 0.028 0.5 NO
126 RBX1 RBX1 RBX1 6382 0.027 0.5 NO
127 IL1R1 IL1R1 IL1R1 6438 0.026 0.5 NO
128 UBA52 UBA52 UBA52 6549 0.025 0.49 NO
129 RAF1 RAF1 RAF1 6729 0.023 0.48 NO
130 AAAS AAAS AAAS 6835 0.022 0.48 NO
131 EIF4G1 EIF4G1 EIF4G1 6884 0.022 0.48 NO
132 UBE2E1 UBE2E1 UBE2E1 6896 0.022 0.48 NO
133 IFNAR1 IFNAR1 IFNAR1 7076 0.02 0.47 NO
134 IRS2 IRS2 IRS2 7100 0.019 0.47 NO
135 IFNA1 IFNA1 IFNA1 7109 0.019 0.47 NO
136 RAPGEF1 RAPGEF1 RAPGEF1 7126 0.019 0.47 NO
137 TYK2 TYK2 TYK2 7206 0.018 0.46 NO
138 STAT5B STAT5B STAT5B 7271 0.018 0.46 NO
139 MAP3K3 MAP3K3 MAP3K3 7309 0.018 0.46 NO
140 TNIP2 TNIP2 TNIP2 7317 0.017 0.46 NO
141 EIF4E3 EIF4E3 EIF4E3 7354 0.017 0.46 NO
142 STAT1 STAT1 STAT1 7441 0.016 0.45 NO
143 IRAK1 IRAK1 IRAK1 7543 0.015 0.45 NO
144 NUP62 NUP62 NUP62 7561 0.015 0.45 NO
145 TAB1 TAB1 TAB1 7601 0.015 0.45 NO
146 RPS27A RPS27A RPS27A 7758 0.013 0.44 NO
147 KPNA4 KPNA4 KPNA4 7792 0.013 0.44 NO
148 IL6R IL6R IL6R 7804 0.013 0.44 NO
149 GBP6 GBP6 GBP6 7845 0.012 0.43 NO
150 IL7 IL7 IL7 7894 0.012 0.43 NO
151 ADAM17 ADAM17 ADAM17 7976 0.011 0.43 NO
152 JAK1 JAK1 JAK1 8104 0.0096 0.42 NO
153 SP100 SP100 SP100 8108 0.0095 0.42 NO
154 RELA RELA RELA 8154 0.0091 0.42 NO
155 PIN1 PIN1 PIN1 8344 0.0073 0.41 NO
156 TAB2 TAB2 TAB2 8549 0.0052 0.4 NO
157 UBE2N UBE2N UBE2N 8628 0.0045 0.39 NO
158 PIK3CB PIK3CB PIK3CB 8641 0.0044 0.39 NO
159 NUP188 NUP188 NUP188 8746 0.0035 0.39 NO
160 SH2B1 SH2B1 SH2B1 8764 0.0034 0.39 NO
161 KPNA1 KPNA1 KPNA1 8780 0.0032 0.38 NO
162 MAP2K1 MAP2K1 MAP2K1 8849 0.0025 0.38 NO
163 MAP2K4 MAP2K4 MAP2K4 8930 0.0018 0.38 NO
164 EIF4E2 EIF4E2 EIF4E2 9071 0.00056 0.37 NO
165 NUP107 NUP107 NUP107 9120 0.00013 0.37 NO
166 CRKL CRKL CRKL 9158 -0.00022 0.36 NO
167 IFIT3 IFIT3 IFIT3 9195 -0.00054 0.36 NO
168 NUP88 NUP88 NUP88 9362 -0.0021 0.35 NO
169 PIK3R1 PIK3R1 PIK3R1 9374 -0.0023 0.35 NO
170 KPNA3 KPNA3 KPNA3 9378 -0.0023 0.35 NO
171 EIF4A2 EIF4A2 EIF4A2 9582 -0.0041 0.34 NO
172 NUP214 NUP214 NUP214 9622 -0.0044 0.34 NO
173 NUP210 NUP210 NUP210 9888 -0.0068 0.32 NO
174 YWHAB YWHAB YWHAB 9907 -0.007 0.32 NO
175 SKP1 SKP1 SKP1 10171 -0.0094 0.31 NO
176 YWHAZ YWHAZ YWHAZ 10256 -0.01 0.3 NO
177 BTRC BTRC BTRC 10258 -0.01 0.3 NO
178 MAPK1 MAPK1 MAPK1 10282 -0.01 0.3 NO
179 INPPL1 INPPL1 INPPL1 10337 -0.011 0.3 NO
180 CAMK2D CAMK2D CAMK2D 10389 -0.012 0.3 NO
181 EIF4G2 EIF4G2 EIF4G2 10412 -0.012 0.3 NO
182 SUMO1 SUMO1 SUMO1 10521 -0.013 0.29 NO
183 NUPL1 NUPL1 NUPL1 10669 -0.014 0.28 NO
184 MAP2K2 MAP2K2 MAP2K2 10729 -0.015 0.28 NO
185 PIAS1 PIAS1 PIAS1 10795 -0.015 0.28 NO
186 NUP54 NUP54 NUP54 10822 -0.016 0.28 NO
187 ADAR ADAR ADAR 10869 -0.016 0.28 NO
188 RAE1 RAE1 RAE1 10874 -0.016 0.28 NO
189 EIF4E EIF4E EIF4E 10907 -0.016 0.28 NO
190 TRAF6 TRAF6 TRAF6 10909 -0.016 0.28 NO
191 NUP50 NUP50 NUP50 11026 -0.017 0.27 NO
192 NUPL2 NUPL2 NUPL2 11087 -0.018 0.27 NO
193 NUP133 NUP133 NUP133 11172 -0.019 0.26 NO
194 RANBP2 RANBP2 RANBP2 11230 -0.019 0.26 NO
195 CHUK CHUK CHUK 11383 -0.021 0.25 NO
196 KPNA2 KPNA2 KPNA2 11405 -0.021 0.25 NO
197 JAK2 JAK2 JAK2 11420 -0.021 0.25 NO
198 CUL1 CUL1 CUL1 11564 -0.022 0.25 NO
199 MAP3K7 MAP3K7 MAP3K7 11753 -0.024 0.24 NO
200 TOLLIP TOLLIP TOLLIP 11811 -0.025 0.23 NO
201 CBL CBL CBL 11882 -0.026 0.23 NO
202 PPM1B PPM1B PPM1B 12126 -0.029 0.22 NO
203 HRAS HRAS HRAS 12133 -0.029 0.22 NO
204 DDX58 DDX58 DDX58 12178 -0.029 0.22 NO
205 PLCG1 PLCG1 PLCG1 12183 -0.029 0.22 NO
206 NRAS NRAS NRAS 12310 -0.031 0.21 NO
207 PIK3R2 PIK3R2 PIK3R2 12317 -0.031 0.21 NO
208 NUP153 NUP153 NUP153 12319 -0.031 0.22 NO
209 ARIH1 ARIH1 ARIH1 12337 -0.031 0.22 NO
210 POM121 POM121 POM121 12385 -0.032 0.21 NO
211 IFIT1 IFIT1 IFIT1 12445 -0.033 0.21 NO
212 GHR GHR GHR 12488 -0.033 0.21 NO
213 MAP2K6 MAP2K6 MAP2K6 12493 -0.033 0.21 NO
214 CRK CRK CRK 12573 -0.034 0.21 NO
215 TAB3 TAB3 TAB3 12598 -0.035 0.21 NO
216 KPNB1 KPNB1 KPNB1 12609 -0.035 0.21 NO
217 NUP43 NUP43 NUP43 12863 -0.038 0.2 NO
218 NUP205 NUP205 NUP205 12919 -0.039 0.19 NO
219 TRIM25 TRIM25 TRIM25 13024 -0.04 0.19 NO
220 PELI3 PELI3 PELI3 13046 -0.04 0.19 NO
221 KRAS KRAS KRAS 13155 -0.042 0.19 NO
222 SEH1L SEH1L SEH1L 13260 -0.043 0.18 NO
223 SHC1 SHC1 SHC1 13338 -0.044 0.18 NO
224 PIK3CA PIK3CA PIK3CA 13417 -0.046 0.18 NO
225 EIF4G3 EIF4G3 EIF4G3 13617 -0.049 0.17 NO
226 FLNB FLNB FLNB 13931 -0.053 0.15 NO
227 GBP7 GBP7 GBP7 14114 -0.057 0.14 NO
228 PELI2 PELI2 PELI2 14134 -0.057 0.14 NO
229 SOS1 SOS1 SOS1 14418 -0.062 0.13 NO
230 CAMK2A CAMK2A CAMK2A 14421 -0.062 0.13 NO
231 PIK3R3 PIK3R3 PIK3R3 14526 -0.065 0.13 NO
232 NUP35 NUP35 NUP35 14645 -0.068 0.13 NO
233 YES1 YES1 YES1 14882 -0.073 0.12 NO
234 EIF2AK2 EIF2AK2 EIF2AK2 15051 -0.077 0.11 NO
235 IRS1 IRS1 IRS1 15165 -0.08 0.1 NO
236 FYN FYN FYN 15324 -0.084 0.099 NO
237 NUP155 NUP155 NUP155 15328 -0.084 0.1 NO
238 PRLR PRLR PRLR 15423 -0.088 0.1 NO
239 TPR TPR TPR 15918 -0.1 0.077 NO
240 NEDD4 NEDD4 NEDD4 16142 -0.11 0.068 NO
241 IL6ST IL6ST IL6ST 16865 -0.16 0.034 NO
242 KPNA5 KPNA5 KPNA5 17312 -0.2 0.016 NO
243 CDK1 CDK1 CDK1 17655 -0.25 0.0064 NO
244 CAMK2B CAMK2B CAMK2B 17848 -0.31 0.0075 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: KEGG ARACHIDONIC ACID METABOLISM.

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

genes ES table in pathway: KEGG MAPK SIGNALING 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 MEFV MEFV MEFV 43 0.69 0.11 YES
2 NLRC4 NLRC4 NLRC4 67 0.65 0.21 YES
3 NOD2 NOD2 NOD2 218 0.5 0.28 YES
4 NLRP3 NLRP3 NLRP3 273 0.48 0.36 YES
5 PSTPIP1 PSTPIP1 PSTPIP1 358 0.44 0.43 YES
6 CARD9 CARD9 CARD9 689 0.35 0.46 YES
7 CASP1 CASP1 CASP1 754 0.34 0.52 YES
8 P2RX7 P2RX7 P2RX7 802 0.32 0.57 YES
9 AIM2 AIM2 AIM2 1053 0.27 0.6 YES
10 BIRC3 BIRC3 BIRC3 1133 0.26 0.63 YES
11 NLRP1 NLRP1 NLRP1 1173 0.25 0.67 YES
12 PYCARD PYCARD PYCARD 1248 0.24 0.71 YES
13 TNFAIP3 TNFAIP3 TNFAIP3 1720 0.19 0.71 YES
14 MAPK11 MAPK11 MAPK11 2307 0.14 0.7 YES
15 MAPK13 MAPK13 MAPK13 2430 0.14 0.72 YES
16 CASP4 CASP4 CASP4 2592 0.13 0.73 YES
17 TXNIP TXNIP TXNIP 3404 0.09 0.7 NO
18 RIPK2 RIPK2 RIPK2 3496 0.086 0.71 NO
19 IRAK2 IRAK2 IRAK2 3874 0.072 0.7 NO
20 NOD1 NOD1 NOD1 4497 0.056 0.67 NO
21 CYLD CYLD CYLD 4560 0.055 0.68 NO
22 IKBKG IKBKG IKBKG 5982 0.032 0.6 NO
23 IKBKB IKBKB IKBKB 6018 0.031 0.6 NO
24 BCL2L1 BCL2L1 BCL2L1 6177 0.029 0.6 NO
25 MAPK14 MAPK14 MAPK14 7042 0.02 0.56 NO
26 IRAK1 IRAK1 IRAK1 7543 0.015 0.53 NO
27 TAB1 TAB1 TAB1 7601 0.015 0.53 NO
28 CASP9 CASP9 CASP9 7846 0.012 0.52 NO
29 CASP8 CASP8 CASP8 8414 0.0066 0.49 NO
30 TAB2 TAB2 TAB2 8549 0.0052 0.48 NO
31 UBE2N UBE2N UBE2N 8628 0.0045 0.48 NO
32 BCL2 BCL2 BCL2 8744 0.0036 0.47 NO
33 TXN TXN TXN 9340 -0.0019 0.44 NO
34 APP APP APP 10072 -0.0085 0.4 NO
35 BIRC2 BIRC2 BIRC2 10138 -0.0091 0.4 NO
36 HSP90AB1 HSP90AB1 HSP90AB1 10773 -0.015 0.36 NO
37 TRAF6 TRAF6 TRAF6 10909 -0.016 0.36 NO
38 CHUK CHUK CHUK 11383 -0.021 0.34 NO
39 PANX1 PANX1 PANX1 11607 -0.023 0.33 NO
40 CASP2 CASP2 CASP2 11703 -0.024 0.33 NO
41 MAP3K7 MAP3K7 MAP3K7 11753 -0.024 0.33 NO
42 MAP2K6 MAP2K6 MAP2K6 12493 -0.033 0.29 NO
43 TAB3 TAB3 TAB3 12598 -0.035 0.29 NO
44 MAPK12 MAPK12 MAPK12 13997 -0.055 0.22 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: KEGG MAPK SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

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 CD28 CD28 CD28 157 0.55 0.044 YES
2 HCK HCK HCK 268 0.48 0.085 YES
3 CCR5 CCR5 CCR5 355 0.45 0.12 YES
4 CD8B CD8B CD8B 361 0.44 0.17 YES
5 LCK LCK LCK 371 0.44 0.21 YES
6 CD247 CD247 CD247 385 0.44 0.25 YES
7 DOCK2 DOCK2 DOCK2 417 0.42 0.29 YES
8 CXCR4 CXCR4 CXCR4 578 0.38 0.32 YES
9 CD4 CD4 CD4 652 0.36 0.35 YES
10 AP1S2 AP1S2 AP1S2 811 0.32 0.37 YES
11 ELMO1 ELMO1 ELMO1 1151 0.26 0.37 YES
12 PSMB9 PSMB9 PSMB9 1979 0.17 0.34 NO
13 APOBEC3G APOBEC3G APOBEC3G 2003 0.17 0.36 NO
14 RCC1 RCC1 RCC1 2485 0.13 0.34 NO
15 B2M B2M B2M 2648 0.12 0.35 NO
16 PSMB10 PSMB10 PSMB10 2729 0.12 0.36 NO
17 AP1B1 AP1B1 AP1B1 2808 0.12 0.36 NO
18 GTF2H2B GTF2H2B GTF2H2B 2990 0.11 0.36 NO
19 GTF2E1 GTF2E1 GTF2E1 3649 0.08 0.33 NO
20 VPS37B VPS37B VPS37B 3652 0.08 0.34 NO
21 HLA-A HLA-A HLA-A 3667 0.08 0.35 NO
22 PSMB8 PSMB8 PSMB8 3949 0.07 0.34 NO
23 ELL ELL ELL 4350 0.06 0.32 NO
24 TAF13 TAF13 TAF13 4361 0.059 0.33 NO
25 AP2S1 AP2S1 AP2S1 4389 0.059 0.33 NO
26 PSMB3 PSMB3 PSMB3 4651 0.053 0.32 NO
27 POLR2L POLR2L POLR2L 4813 0.05 0.32 NO
28 HMGA1 HMGA1 HMGA1 4970 0.047 0.31 NO
29 PSMD2 PSMD2 PSMD2 5110 0.045 0.31 NO
30 PSME2 PSME2 PSME2 5144 0.044 0.31 NO
31 PSMB6 PSMB6 PSMB6 5205 0.043 0.31 NO
32 PSMC1 PSMC1 PSMC1 5304 0.041 0.31 NO
33 NUP85 NUP85 NUP85 5321 0.041 0.31 NO
34 PSMB2 PSMB2 PSMB2 5334 0.041 0.32 NO
35 TAF10 TAF10 TAF10 5366 0.04 0.32 NO
36 XRCC6 XRCC6 XRCC6 5411 0.04 0.32 NO
37 NUP37 NUP37 NUP37 5515 0.038 0.32 NO
38 PSMD13 PSMD13 PSMD13 5717 0.035 0.31 NO
39 RAC1 RAC1 RAC1 5724 0.035 0.31 NO
40 CTDP1 CTDP1 CTDP1 5739 0.035 0.32 NO
41 POLR2H POLR2H POLR2H 5875 0.033 0.31 NO
42 PSME4 PSME4 PSME4 5885 0.033 0.31 NO
43 VPS37D VPS37D VPS37D 5940 0.032 0.32 NO
44 PSMD7 PSMD7 PSMD7 5968 0.032 0.32 NO
45 NUP93 NUP93 NUP93 5992 0.031 0.32 NO
46 PSMA2 PSMA2 PSMA2 6105 0.03 0.31 NO
47 XRCC4 XRCC4 XRCC4 6134 0.03 0.32 NO
48 PSMC2 PSMC2 PSMC2 6209 0.029 0.31 NO
49 TCEB3 TCEB3 TCEB3 6291 0.028 0.31 NO
50 PSMB1 PSMB1 PSMB1 6314 0.028 0.31 NO
51 RBX1 RBX1 RBX1 6382 0.027 0.31 NO
52 PSMD6 PSMD6 PSMD6 6407 0.027 0.31 NO
53 GTF2F2 GTF2F2 GTF2F2 6449 0.026 0.31 NO
54 ATP6V1H ATP6V1H ATP6V1H 6480 0.026 0.32 NO
55 UBA52 UBA52 UBA52 6549 0.025 0.31 NO
56 PSMC5 PSMC5 PSMC5 6570 0.025 0.32 NO
57 GTF2B GTF2B GTF2B 6642 0.024 0.31 NO
58 PSMD9 PSMD9 PSMD9 6688 0.024 0.31 NO
59 RANBP1 RANBP1 RANBP1 6693 0.024 0.32 NO
60 AAAS AAAS AAAS 6835 0.022 0.31 NO
61 PSME1 PSME1 PSME1 6847 0.022 0.31 NO
62 CDK9 CDK9 CDK9 6873 0.022 0.31 NO
63 PSMA5 PSMA5 PSMA5 6925 0.021 0.31 NO
64 GTF2E2 GTF2E2 GTF2E2 6928 0.021 0.31 NO
65 TCEB2 TCEB2 TCEB2 6933 0.021 0.32 NO
66 VPS37C VPS37C VPS37C 6977 0.021 0.31 NO
67 PSMC3 PSMC3 PSMC3 7112 0.019 0.31 NO
68 AP2M1 AP2M1 AP2M1 7130 0.019 0.31 NO
69 GTF2H4 GTF2H4 GTF2H4 7195 0.019 0.31 NO
70 AP2A2 AP2A2 AP2A2 7292 0.018 0.3 NO
71 POLR2F POLR2F POLR2F 7318 0.017 0.3 NO
72 RANGAP1 RANGAP1 RANGAP1 7348 0.017 0.3 NO
73 AP1S1 AP1S1 AP1S1 7356 0.017 0.31 NO
74 PSMD11 PSMD11 PSMD11 7408 0.016 0.3 NO
75 NMT1 NMT1 NMT1 7505 0.016 0.3 NO
76 PSMD3 PSMD3 PSMD3 7542 0.015 0.3 NO
77 NUP62 NUP62 NUP62 7561 0.015 0.3 NO
78 PSMD4 PSMD4 PSMD4 7566 0.015 0.3 NO
79 PSMD1 PSMD1 PSMD1 7628 0.014 0.3 NO
80 AP2B1 AP2B1 AP2B1 7748 0.013 0.29 NO
81 TAF12 TAF12 TAF12 7755 0.013 0.3 NO
82 RPS27A RPS27A RPS27A 7758 0.013 0.3 NO
83 PSMA7 PSMA7 PSMA7 7929 0.011 0.29 NO
84 PAK2 PAK2 PAK2 7956 0.011 0.29 NO
85 PSMB4 PSMB4 PSMB4 8010 0.011 0.28 NO
86 PSMA6 PSMA6 PSMA6 8149 0.0091 0.28 NO
87 PSMD14 PSMD14 PSMD14 8153 0.0091 0.28 NO
88 BANF1 BANF1 BANF1 8158 0.009 0.28 NO
89 PSMA3 PSMA3 PSMA3 8168 0.0088 0.28 NO
90 RNGTT RNGTT RNGTT 8172 0.0088 0.28 NO
91 NCBP2 NCBP2 NCBP2 8187 0.0087 0.28 NO
92 PSMA1 PSMA1 PSMA1 8235 0.0082 0.28 NO
93 POLR2G POLR2G POLR2G 8301 0.0076 0.28 NO
94 RAN RAN RAN 8322 0.0074 0.28 NO
95 TAF11 TAF11 TAF11 8380 0.007 0.27 NO
96 COBRA1 COBRA1 COBRA1 8508 0.0056 0.27 NO
97 PSMC4 PSMC4 PSMC4 8529 0.0054 0.27 NO
98 SUPT4H1 SUPT4H1 SUPT4H1 8741 0.0036 0.25 NO
99 NUP188 NUP188 NUP188 8746 0.0035 0.26 NO
100 PPIA PPIA PPIA 8752 0.0035 0.26 NO
101 KPNA1 KPNA1 KPNA1 8780 0.0032 0.25 NO
102 POLR2C POLR2C POLR2C 8853 0.0025 0.25 NO
103 PACS1 PACS1 PACS1 8860 0.0024 0.25 NO
104 PSMB5 PSMB5 PSMB5 8995 0.0012 0.24 NO
105 NUP107 NUP107 NUP107 9120 0.00013 0.24 NO
106 POLR2B POLR2B POLR2B 9129 -5e-05 0.24 NO
107 TSG101 TSG101 TSG101 9133 -0.000058 0.24 NO
108 RDBP RDBP RDBP 9172 -0.00036 0.23 NO
109 VPS28 VPS28 VPS28 9263 -0.0011 0.23 NO
110 NUP88 NUP88 NUP88 9362 -0.0021 0.22 NO
111 PSMB7 PSMB7 PSMB7 9405 -0.0025 0.22 NO
112 AP1G1 AP1G1 AP1G1 9416 -0.0027 0.22 NO
113 XRCC5 XRCC5 XRCC5 9533 -0.0037 0.21 NO
114 TAF6 TAF6 TAF6 9545 -0.0038 0.21 NO
115 TBP TBP TBP 9560 -0.004 0.21 NO
116 POLR2J POLR2J POLR2J 9566 -0.004 0.21 NO
117 NUP214 NUP214 NUP214 9622 -0.0044 0.21 NO
118 PSMA4 PSMA4 PSMA4 9625 -0.0044 0.21 NO
119 ERCC2 ERCC2 ERCC2 9675 -0.005 0.21 NO
120 GTF2A2 GTF2A2 GTF2A2 9695 -0.0051 0.21 NO
121 AP2A1 AP2A1 AP2A1 9833 -0.0064 0.2 NO
122 POLR2E POLR2E POLR2E 9881 -0.0068 0.2 NO
123 NUP210 NUP210 NUP210 9888 -0.0068 0.2 NO
124 SSRP1 SSRP1 SSRP1 9919 -0.0071 0.2 NO
125 ARF1 ARF1 ARF1 9920 -0.0071 0.2 NO
126 WHSC2 WHSC2 WHSC2 10100 -0.0088 0.19 NO
127 PSMD8 PSMD8 PSMD8 10120 -0.0089 0.19 NO
128 SKP1 SKP1 SKP1 10171 -0.0094 0.19 NO
129 POLR2A POLR2A POLR2A 10176 -0.0095 0.19 NO
130 POLR2D POLR2D POLR2D 10216 -0.0098 0.19 NO
131 BTRC BTRC BTRC 10258 -0.01 0.19 NO
132 PSMD10 PSMD10 PSMD10 10355 -0.011 0.18 NO
133 NCBP1 NCBP1 NCBP1 10523 -0.013 0.17 NO
134 PSMD12 PSMD12 PSMD12 10553 -0.013 0.17 NO
135 PSMC6 PSMC6 PSMC6 10581 -0.013 0.17 NO
136 NUPL1 NUPL1 NUPL1 10669 -0.014 0.17 NO
137 SLC25A5 SLC25A5 SLC25A5 10801 -0.015 0.16 NO
138 NUP54 NUP54 NUP54 10822 -0.016 0.16 NO
139 RAE1 RAE1 RAE1 10874 -0.016 0.16 NO
140 ERCC3 ERCC3 ERCC3 10937 -0.016 0.16 NO
141 RNMT RNMT RNMT 10979 -0.017 0.16 NO
142 GTF2F1 GTF2F1 GTF2F1 10984 -0.017 0.16 NO
143 POLR2I POLR2I POLR2I 11010 -0.017 0.16 NO
144 NUP50 NUP50 NUP50 11026 -0.017 0.16 NO
145 NUPL2 NUPL2 NUPL2 11087 -0.018 0.16 NO
146 PSMD5 PSMD5 PSMD5 11105 -0.018 0.16 NO
147 TCEB1 TCEB1 TCEB1 11130 -0.018 0.16 NO
148 SUPT5H SUPT5H SUPT5H 11139 -0.018 0.16 NO
149 CCNH CCNH CCNH 11155 -0.019 0.16 NO
150 NUP133 NUP133 NUP133 11172 -0.019 0.16 NO
151 RANBP2 RANBP2 RANBP2 11230 -0.019 0.16 NO
152 GTF2H1 GTF2H1 GTF2H1 11251 -0.02 0.16 NO
153 NMT2 NMT2 NMT2 11444 -0.021 0.16 NO
154 XPO1 XPO1 XPO1 11872 -0.026 0.13 NO
155 TH1L TH1L TH1L 12077 -0.028 0.12 NO
156 POLR2K POLR2K POLR2K 12116 -0.029 0.13 NO
157 AP1M1 AP1M1 AP1M1 12213 -0.03 0.12 NO
158 NUP153 NUP153 NUP153 12319 -0.031 0.12 NO
159 PSMF1 PSMF1 PSMF1 12360 -0.032 0.12 NO
160 POM121 POM121 POM121 12385 -0.032 0.12 NO
161 KPNB1 KPNB1 KPNB1 12609 -0.035 0.11 NO
162 TAF5 TAF5 TAF5 12665 -0.036 0.11 NO
163 SUPT16H SUPT16H SUPT16H 12818 -0.037 0.11 NO
164 NUP43 NUP43 NUP43 12863 -0.038 0.11 NO
165 FEN1 FEN1 FEN1 12914 -0.038 0.11 NO
166 NUP205 NUP205 NUP205 12919 -0.039 0.12 NO
167 GTF2H3 GTF2H3 GTF2H3 12962 -0.039 0.12 NO
168 LIG1 LIG1 LIG1 13048 -0.04 0.12 NO
169 VPS37A VPS37A VPS37A 13074 -0.041 0.12 NO
170 SLC25A6 SLC25A6 SLC25A6 13124 -0.041 0.12 NO
171 NPM1 NPM1 NPM1 13255 -0.043 0.12 NO
172 SEH1L SEH1L SEH1L 13260 -0.043 0.12 NO
173 TAF9 TAF9 TAF9 13276 -0.044 0.12 NO
174 SLC25A4 SLC25A4 SLC25A4 13283 -0.044 0.13 NO
175 CUL5 CUL5 CUL5 13335 -0.044 0.13 NO
176 AP1M2 AP1M2 AP1M2 13613 -0.049 0.12 NO
177 LIG4 LIG4 LIG4 13849 -0.052 0.11 NO
178 CDK7 CDK7 CDK7 14055 -0.056 0.1 NO
179 GTF2H2 GTF2H2 GTF2H2 14387 -0.062 0.091 NO
180 CCNT2 CCNT2 CCNT2 14590 -0.066 0.086 NO
181 TAF1 TAF1 TAF1 14636 -0.067 0.09 NO
182 NUP35 NUP35 NUP35 14645 -0.068 0.096 NO
183 PSIP1 PSIP1 PSIP1 14834 -0.072 0.092 NO
184 MNAT1 MNAT1 MNAT1 14865 -0.072 0.098 NO
185 TCEA1 TCEA1 TCEA1 15063 -0.077 0.094 NO
186 TAF4B TAF4B TAF4B 15181 -0.08 0.095 NO
187 FYN FYN FYN 15324 -0.084 0.096 NO
188 NUP155 NUP155 NUP155 15328 -0.084 0.1 NO
189 TPR TPR TPR 15918 -0.1 0.081 NO
190 TAF4 TAF4 TAF4 16179 -0.12 0.077 NO
191 GTF2A1 GTF2A1 GTF2A1 16182 -0.12 0.088 NO
192 CCNT1 CCNT1 CCNT1 16483 -0.13 0.084 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: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION.

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

genes ES table in pathway: KEGG CHEMOKINE SIGNALING 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 IL1RN IL1RN IL1RN 133 0.56 0.16 YES
2 IRAK3 IRAK3 IRAK3 574 0.38 0.25 YES
3 IL1B IL1B IL1B 671 0.36 0.35 YES
4 CASP1 CASP1 CASP1 754 0.34 0.45 YES
5 IL1A IL1A IL1A 793 0.33 0.55 YES
6 IL1R2 IL1R2 IL1R2 1337 0.23 0.58 YES
7 TICAM2 TICAM2 TICAM2 1750 0.19 0.62 YES
8 IL1RAP IL1RAP IL1RAP 1942 0.17 0.66 YES
9 JUN JUN JUN 3209 0.097 0.62 NO
10 MYD88 MYD88 MYD88 3280 0.095 0.64 NO
11 IRAK4 IRAK4 IRAK4 4658 0.053 0.58 NO
12 IKBKG IKBKG IKBKG 5982 0.032 0.52 NO
13 IKBKB IKBKB IKBKB 6018 0.031 0.52 NO
14 NFKB1 NFKB1 NFKB1 6143 0.03 0.53 NO
15 SQSTM1 SQSTM1 SQSTM1 6304 0.028 0.53 NO
16 IL1R1 IL1R1 IL1R1 6438 0.026 0.53 NO
17 MAP3K3 MAP3K3 MAP3K3 7309 0.018 0.48 NO
18 IRAK1 IRAK1 IRAK1 7543 0.015 0.48 NO
19 TAB1 TAB1 TAB1 7601 0.015 0.48 NO
20 RELA RELA RELA 8154 0.0091 0.45 NO
21 TAB2 TAB2 TAB2 8549 0.0052 0.43 NO
22 ERC1 ERC1 ERC1 8561 0.0051 0.43 NO
23 UBE2N UBE2N UBE2N 8628 0.0045 0.43 NO
24 PRKCI PRKCI PRKCI 8910 0.002 0.41 NO
25 PIK3R1 PIK3R1 PIK3R1 9374 -0.0023 0.39 NO
26 PRKCZ PRKCZ PRKCZ 10899 -0.016 0.31 NO
27 TRAF6 TRAF6 TRAF6 10909 -0.016 0.31 NO
28 UBE2V1 UBE2V1 UBE2V1 10972 -0.017 0.31 NO
29 CHUK CHUK CHUK 11383 -0.021 0.3 NO
30 MAP3K7 MAP3K7 MAP3K7 11753 -0.024 0.28 NO
31 TOLLIP TOLLIP TOLLIP 11811 -0.025 0.29 NO
32 MAP2K6 MAP2K6 MAP2K6 12493 -0.033 0.26 NO
33 PIK3CA PIK3CA PIK3CA 13417 -0.046 0.22 NO
34 MAPK8 MAPK8 MAPK8 16073 -0.11 0.11 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: KEGG CHEMOKINE SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT

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 FAIM2 FAIM2 FAIM2 210 0.51 0.14 YES
2 BTK BTK BTK 245 0.49 0.29 YES
3 FASLG FASLG FASLG 699 0.35 0.37 YES
4 BIRC3 BIRC3 BIRC3 1133 0.26 0.42 YES
5 SYK SYK SYK 1397 0.22 0.48 YES
6 PIK3CD PIK3CD PIK3CD 1823 0.18 0.51 YES
7 BID BID BID 2079 0.16 0.54 YES
8 MAPK11 MAPK11 MAPK11 2307 0.14 0.57 YES
9 SMPD1 SMPD1 SMPD1 3897 0.072 0.5 NO
10 CASP3 CASP3 CASP3 4301 0.061 0.5 NO
11 FAS FAS FAS 4773 0.05 0.49 NO
12 CFLAR CFLAR CFLAR 5529 0.038 0.46 NO
13 CASP10 CASP10 CASP10 5725 0.035 0.46 NO
14 IKBKG IKBKG IKBKG 5982 0.032 0.46 NO
15 IKBKB IKBKB IKBKB 6018 0.031 0.46 NO
16 FADD FADD FADD 6484 0.026 0.44 NO
17 MAPK14 MAPK14 MAPK14 7042 0.02 0.42 NO
18 EZR EZR EZR 7426 0.016 0.4 NO
19 RIPK1 RIPK1 RIPK1 7600 0.015 0.4 NO
20 AKT1 AKT1 AKT1 8062 0.01 0.38 NO
21 CASP8 CASP8 CASP8 8414 0.0066 0.36 NO
22 PIK3CB PIK3CB PIK3CB 8641 0.0044 0.35 NO
23 PIK3R1 PIK3R1 PIK3R1 9374 -0.0023 0.31 NO
24 CLTC CLTC CLTC 9891 -0.0068 0.28 NO
25 BIRC2 BIRC2 BIRC2 10138 -0.0091 0.27 NO
26 SRC SRC SRC 10653 -0.014 0.24 NO
27 MAP3K1 MAP3K1 MAP3K1 10703 -0.014 0.24 NO
28 CHUK CHUK CHUK 11383 -0.021 0.21 NO
29 PDPK1 PDPK1 PDPK1 12186 -0.029 0.18 NO
30 MAPK10 MAPK10 MAPK10 12254 -0.03 0.18 NO
31 PIK3R2 PIK3R2 PIK3R2 12317 -0.031 0.19 NO
32 MAP2K6 MAP2K6 MAP2K6 12493 -0.033 0.19 NO
33 MAP2K7 MAP2K7 MAP2K7 12660 -0.036 0.19 NO
34 MAPK9 MAPK9 MAPK9 13400 -0.045 0.16 NO
35 PIK3CA PIK3CA PIK3CA 13417 -0.046 0.18 NO
36 PIK3R3 PIK3R3 PIK3R3 14526 -0.065 0.13 NO
37 RFC1 RFC1 RFC1 15252 -0.082 0.12 NO
38 MAPK8 MAPK8 MAPK8 16073 -0.11 0.11 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: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG HISTIDINE METABOLISM 29 genes.ES.table 0.41 0.97 0.51 1 1 0.45 0.26 0.33 1 0.93
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT 38 genes.ES.table 0.3 1.2 0.26 1 1 0.13 0.11 0.12 1 0.96
KEGG HEDGEHOG SIGNALING PATHWAY 54 genes.ES.table 0.37 1 0.43 1 1 0.24 0.13 0.21 1 0.92
KEGG TIGHT JUNCTION 125 genes.ES.table 0.32 1.3 0.12 1 1 0.17 0.12 0.15 1 0.98
KEGG TASTE TRANSDUCTION 35 genes.ES.table 0.41 0.97 0.5 1 1 0.31 0.11 0.28 1 0.92
BIOCARTA ALK PATHWAY 33 genes.ES.table 0.38 1.1 0.31 1 1 0.24 0.15 0.21 1 0.92
BIOCARTA DEATH PATHWAY 33 genes.ES.table 0.27 1 0.46 1 1 0.15 0.17 0.13 1 0.91
PID HDAC CLASSI PATHWAY 65 genes.ES.table 0.22 1.1 0.3 1 1 0.38 0.39 0.24 1 0.96
PID BMPPATHWAY 42 genes.ES.table 0.42 1.2 0.21 1 1 0.24 0.13 0.21 1 0.98
REACTOME SIGNALING BY FGFR1 MUTANTS 25 genes.ES.table 0.36 1.1 0.33 1 1 0.12 0.077 0.11 1 0.92
genes ES table in pathway: KEGG HISTIDINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CLDN9 CLDN9 CLDN9 624 0.4 0.065 YES
2 CLDN3 CLDN3 CLDN3 729 0.38 0.15 YES
3 CLDN7 CLDN7 CLDN7 780 0.37 0.24 YES
4 CLDN18 CLDN18 CLDN18 937 0.34 0.32 YES
5 CLDN15 CLDN15 CLDN15 1124 0.31 0.39 YES
6 CLDN20 CLDN20 CLDN20 1307 0.28 0.45 YES
7 CLDN6 CLDN6 CLDN6 1352 0.28 0.52 YES
8 CLDN19 CLDN19 CLDN19 1390 0.27 0.58 YES
9 CLDN4 CLDN4 CLDN4 2965 0.15 0.53 NO
10 PRKCI PRKCI PRKCI 4598 0.085 0.46 NO
11 PARD6B PARD6B PARD6B 4823 0.079 0.47 NO
12 CRB3 CRB3 CRB3 5321 0.065 0.46 NO
13 CLDN12 CLDN12 CLDN12 5337 0.065 0.47 NO
14 PARD6A PARD6A PARD6A 5355 0.064 0.49 NO
15 CLDN1 CLDN1 CLDN1 5878 0.052 0.47 NO
16 CLDN2 CLDN2 CLDN2 6751 0.034 0.43 NO
17 F11R F11R F11R 7841 0.013 0.38 NO
18 MPP5 MPP5 MPP5 7932 0.012 0.37 NO
19 CLDN10 CLDN10 CLDN10 8525 0.0021 0.34 NO
20 CLDN14 CLDN14 CLDN14 8711 -0.00093 0.33 NO
21 CLDN16 CLDN16 CLDN16 9894 -0.02 0.27 NO
22 PARD3 PARD3 PARD3 10748 -0.034 0.23 NO
23 INADL INADL INADL 10984 -0.038 0.23 NO
24 PARD6G PARD6G PARD6G 11803 -0.054 0.2 NO
25 CLDN8 CLDN8 CLDN8 14317 -0.12 0.087 NO
26 CLDN5 CLDN5 CLDN5 14941 -0.16 0.092 NO
27 CLDN11 CLDN11 CLDN11 16853 -0.31 0.063 NO

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

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

genes ES table in pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT

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 MYH3 MYH3 MYH3 113 0.55 0.028 YES
2 IGSF5 IGSF5 IGSF5 168 0.53 0.056 YES
3 PRKCG PRKCG PRKCG 284 0.48 0.079 YES
4 MYH8 MYH8 MYH8 290 0.48 0.11 YES
5 MYH7B MYH7B MYH7B 317 0.47 0.14 YES
6 CLDN9 CLDN9 CLDN9 624 0.4 0.14 YES
7 CLDN3 CLDN3 CLDN3 729 0.38 0.16 YES
8 CLDN7 CLDN7 CLDN7 780 0.37 0.18 YES
9 RAB3B RAB3B RAB3B 805 0.36 0.2 YES
10 PRKCQ PRKCQ PRKCQ 873 0.35 0.22 YES
11 CLDN18 CLDN18 CLDN18 937 0.34 0.23 YES
12 CLDN15 CLDN15 CLDN15 1124 0.31 0.24 YES
13 TJP3 TJP3 TJP3 1277 0.29 0.25 YES
14 CLDN20 CLDN20 CLDN20 1307 0.28 0.27 YES
15 CLDN6 CLDN6 CLDN6 1352 0.28 0.28 YES
16 CLDN19 CLDN19 CLDN19 1390 0.27 0.3 YES
17 GNAI1 GNAI1 GNAI1 1536 0.26 0.3 YES
18 MYH4 MYH4 MYH4 1919 0.22 0.3 YES
19 MAGI2 MAGI2 MAGI2 1940 0.22 0.31 YES
20 OCLN OCLN OCLN 2100 0.2 0.31 YES
21 MYH1 MYH1 MYH1 2125 0.2 0.32 YES
22 CLDN4 CLDN4 CLDN4 2965 0.15 0.28 NO
23 LLGL2 LLGL2 LLGL2 3028 0.15 0.29 NO
24 CLDN23 CLDN23 CLDN23 3335 0.13 0.28 NO
25 MYL5 MYL5 MYL5 3526 0.12 0.28 NO
26 PRKCZ PRKCZ PRKCZ 3583 0.12 0.28 NO
27 MLLT4 MLLT4 MLLT4 3754 0.11 0.28 NO
28 MYH14 MYH14 MYH14 4206 0.097 0.26 NO
29 MAGI1 MAGI1 MAGI1 4293 0.094 0.26 NO
30 PRKCI PRKCI PRKCI 4598 0.085 0.25 NO
31 TJP2 TJP2 TJP2 4658 0.083 0.25 NO
32 CASK CASK CASK 4717 0.082 0.25 NO
33 TJP1 TJP1 TJP1 4757 0.08 0.26 NO
34 PARD6B PARD6B PARD6B 4823 0.079 0.26 NO
35 KRAS KRAS KRAS 5005 0.074 0.25 NO
36 EXOC4 EXOC4 EXOC4 5066 0.072 0.25 NO
37 HRAS HRAS HRAS 5153 0.07 0.25 NO
38 CRB3 CRB3 CRB3 5321 0.065 0.25 NO
39 PARD6A PARD6A PARD6A 5355 0.064 0.25 NO
40 EPB41L1 EPB41L1 EPB41L1 5567 0.059 0.24 NO
41 MYL12B MYL12B MYL12B 5875 0.052 0.23 NO
42 CLDN1 CLDN1 CLDN1 5878 0.052 0.23 NO
43 AKT2 AKT2 AKT2 6016 0.049 0.22 NO
44 CSDA CSDA CSDA 6543 0.038 0.2 NO
45 MRAS MRAS MRAS 6572 0.037 0.2 NO
46 AMOTL1 AMOTL1 AMOTL1 6618 0.036 0.2 NO
47 AKT1 AKT1 AKT1 6640 0.036 0.2 NO
48 CLDN2 CLDN2 CLDN2 6751 0.034 0.19 NO
49 SYMPK SYMPK SYMPK 6833 0.032 0.19 NO
50 TJAP1 TJAP1 TJAP1 6888 0.031 0.19 NO
51 PRKCA PRKCA PRKCA 7256 0.024 0.17 NO
52 CTTN CTTN CTTN 7273 0.024 0.17 NO
53 LLGL1 LLGL1 LLGL1 7456 0.021 0.16 NO
54 F11R F11R F11R 7841 0.013 0.14 NO
55 EPB41L2 EPB41L2 EPB41L2 7903 0.012 0.14 NO
56 RHOA RHOA RHOA 7916 0.012 0.14 NO
57 MPP5 MPP5 MPP5 7932 0.012 0.14 NO
58 SPTAN1 SPTAN1 SPTAN1 8063 0.0094 0.13 NO
59 CTNNA1 CTNNA1 CTNNA1 8114 0.0085 0.13 NO
60 MYLPF MYLPF MYLPF 8264 0.006 0.12 NO
61 ACTB ACTB ACTB 8332 0.005 0.12 NO
62 MYL12A MYL12A MYL12A 8421 0.0035 0.12 NO
63 CLDN10 CLDN10 CLDN10 8525 0.0021 0.11 NO
64 MYH15 MYH15 MYH15 8646 0.00015 0.1 NO
65 CLDN14 CLDN14 CLDN14 8711 -0.00093 0.099 NO
66 RAB13 RAB13 RAB13 8716 -0.0011 0.098 NO
67 ASH1L ASH1L ASH1L 8732 -0.0012 0.098 NO
68 RRAS RRAS RRAS 8792 -0.0023 0.095 NO
69 SRC SRC SRC 8822 -0.0028 0.093 NO
70 CSNK2B CSNK2B CSNK2B 8897 -0.004 0.089 NO
71 MAGI3 MAGI3 MAGI3 9298 -0.01 0.068 NO
72 EXOC3 EXOC3 EXOC3 9302 -0.01 0.068 NO
73 PPP2R1A PPP2R1A PPP2R1A 9312 -0.011 0.068 NO
74 MYL9 MYL9 MYL9 9502 -0.014 0.058 NO
75 CDC42 CDC42 CDC42 9575 -0.015 0.055 NO
76 AKT3 AKT3 AKT3 9868 -0.02 0.04 NO
77 CLDN16 CLDN16 CLDN16 9894 -0.02 0.04 NO
78 RRAS2 RRAS2 RRAS2 9924 -0.02 0.04 NO
79 MYH10 MYH10 MYH10 9950 -0.021 0.039 NO
80 YES1 YES1 YES1 10277 -0.026 0.023 NO
81 CSNK2A2 CSNK2A2 CSNK2A2 10382 -0.028 0.019 NO
82 MYH2 MYH2 MYH2 10411 -0.028 0.019 NO
83 GNAI3 GNAI3 GNAI3 10441 -0.029 0.019 NO
84 PPP2R2D PPP2R2D PPP2R2D 10470 -0.029 0.019 NO
85 PTEN PTEN PTEN 10639 -0.032 0.012 NO
86 PARD3 PARD3 PARD3 10748 -0.034 0.0077 NO
87 CTNNB1 CTNNB1 CTNNB1 10869 -0.036 0.0031 NO
88 INADL INADL INADL 10984 -0.038 -0.00094 NO
89 VAPA VAPA VAPA 11297 -0.043 -0.016 NO
90 GNAI2 GNAI2 GNAI2 11375 -0.045 -0.017 NO
91 EPB41L3 EPB41L3 EPB41L3 11392 -0.045 -0.016 NO
92 ACTG1 ACTG1 ACTG1 11473 -0.047 -0.017 NO
93 ACTN4 ACTN4 ACTN4 11476 -0.047 -0.014 NO
94 PPP2R1B PPP2R1B PPP2R1B 11547 -0.049 -0.015 NO
95 PPP2CA PPP2CA PPP2CA 11620 -0.05 -0.016 NO
96 CSNK2A1 CSNK2A1 CSNK2A1 11709 -0.052 -0.018 NO
97 PARD6G PARD6G PARD6G 11803 -0.054 -0.02 NO
98 PPP2CB PPP2CB PPP2CB 12001 -0.058 -0.027 NO
99 MPDZ MPDZ MPDZ 12759 -0.074 -0.065 NO
100 MYH9 MYH9 MYH9 12895 -0.078 -0.068 NO
101 CGN CGN CGN 12909 -0.078 -0.064 NO
102 CDK4 CDK4 CDK4 13017 -0.081 -0.065 NO
103 EPB41 EPB41 EPB41 13563 -0.097 -0.09 NO
104 NRAS NRAS NRAS 13612 -0.098 -0.086 NO
105 ZAK ZAK ZAK 13629 -0.099 -0.081 NO
106 PRKCD PRKCD PRKCD 13701 -0.1 -0.079 NO
107 ACTN1 ACTN1 ACTN1 13711 -0.1 -0.073 NO
108 ACTN2 ACTN2 ACTN2 14186 -0.12 -0.093 NO
109 PPP2R2A PPP2R2A PPP2R2A 14296 -0.12 -0.091 NO
110 CLDN8 CLDN8 CLDN8 14317 -0.12 -0.085 NO
111 CLDN5 CLDN5 CLDN5 14941 -0.16 -0.11 NO
112 MYH7 MYH7 MYH7 15041 -0.16 -0.11 NO
113 ACTN3 ACTN3 ACTN3 15479 -0.2 -0.12 NO
114 HCLS1 HCLS1 HCLS1 15822 -0.22 -0.12 NO
115 CTNNA3 CTNNA3 CTNNA3 16536 -0.28 -0.15 NO
116 JAM2 JAM2 JAM2 16735 -0.3 -0.14 NO
117 CLDN11 CLDN11 CLDN11 16853 -0.31 -0.13 NO
118 JAM3 JAM3 JAM3 16873 -0.31 -0.11 NO
119 PRKCE PRKCE PRKCE 16999 -0.32 -0.097 NO
120 CTNNA2 CTNNA2 CTNNA2 17043 -0.33 -0.08 NO
121 PRKCH PRKCH PRKCH 17185 -0.35 -0.066 NO
122 PRKCB PRKCB PRKCB 17643 -0.44 -0.066 NO
123 MYH11 MYH11 MYH11 17661 -0.44 -0.04 NO
124 PPP2R2B PPP2R2B PPP2R2B 17669 -0.44 -0.013 NO
125 PPP2R2C PPP2R2C PPP2R2C 17798 -0.5 0.01 NO

Figure S23.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT.

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, 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 HEDGEHOG SIGNALING 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 SOSTDC1 SOSTDC1 SOSTDC1 66 0.6 0.089 YES
2 BMP6 BMP6 BMP6 154 0.53 0.16 YES
3 NOG NOG NOG 276 0.48 0.23 YES
4 BMP4 BMP4 BMP4 512 0.42 0.28 YES
5 SMAD6 SMAD6 SMAD6 577 0.41 0.34 YES
6 SMAD9 SMAD9 SMAD9 1275 0.29 0.35 YES
7 BAMBI BAMBI BAMBI 1344 0.28 0.39 YES
8 SMAD7 SMAD7 SMAD7 1971 0.22 0.38 YES
9 BMP7 BMP7 BMP7 2167 0.2 0.4 YES
10 BMP2 BMP2 BMP2 2350 0.19 0.42 YES
11 HFE2 HFE2 HFE2 3644 0.12 0.37 NO
12 SKI SKI SKI 4079 0.1 0.36 NO
13 SMURF2 SMURF2 SMURF2 4358 0.092 0.36 NO
14 TAB1 TAB1 TAB1 4806 0.079 0.35 NO
15 CER1 CER1 CER1 5206 0.068 0.33 NO
16 SMAD4 SMAD4 SMAD4 5430 0.062 0.33 NO
17 NUP214 NUP214 NUP214 6427 0.04 0.28 NO
18 SMURF1 SMURF1 SMURF1 6442 0.04 0.29 NO
19 PPP1R15A PPP1R15A PPP1R15A 6458 0.04 0.29 NO
20 BMPR1A BMPR1A BMPR1A 7697 0.016 0.23 NO
21 SMAD5 SMAD5 SMAD5 7715 0.016 0.23 NO
22 CTDSP1 CTDSP1 CTDSP1 7738 0.015 0.23 NO
23 ZFYVE16 ZFYVE16 ZFYVE16 8271 0.006 0.2 NO
24 PPP1CA PPP1CA PPP1CA 8738 -0.0014 0.17 NO
25 RGMB RGMB RGMB 8791 -0.0023 0.17 NO
26 GSK3B GSK3B GSK3B 9148 -0.0079 0.15 NO
27 CTDSPL CTDSPL CTDSPL 9199 -0.0089 0.15 NO
28 CTDSP2 CTDSP2 CTDSP2 9582 -0.015 0.13 NO
29 MAP3K7 MAP3K7 MAP3K7 9731 -0.018 0.13 NO
30 BMPR2 BMPR2 BMPR2 9866 -0.02 0.12 NO
31 XIAP XIAP XIAP 10096 -0.023 0.11 NO
32 SMAD1 SMAD1 SMAD1 10210 -0.025 0.11 NO
33 MAPK1 MAPK1 MAPK1 10337 -0.027 0.11 NO
34 PPM1A PPM1A PPM1A 10669 -0.032 0.094 NO
35 AHSG AHSG AHSG 14279 -0.12 -0.088 NO
36 TAB2 TAB2 TAB2 14367 -0.13 -0.074 NO
37 RGMA RGMA RGMA 14472 -0.13 -0.059 NO
38 CHRD CHRD CHRD 14595 -0.14 -0.045 NO
39 BMPR1B BMPR1B BMPR1B 16403 -0.27 -0.1 NO
40 CHRDL1 CHRDL1 CHRDL1 17508 -0.41 -0.1 NO
41 FST FST FST 17528 -0.41 -0.042 NO
42 GREM1 GREM1 GREM1 17654 -0.44 0.018 NO

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

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

genes ES table in pathway: KEGG TIGHT JUNCTION

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 VAMP1 VAMP1 VAMP1 1045 0.32 0.036 YES
2 STX1A STX1A STX1A 1163 0.3 0.12 YES
3 SNAP25 SNAP25 SNAP25 1272 0.29 0.2 YES
4 STX19 STX19 STX19 1705 0.24 0.24 YES
5 STX1B STX1B STX1B 1908 0.22 0.3 YES
6 STX2 STX2 STX2 3184 0.14 0.27 NO
7 STX16 STX16 STX16 3965 0.1 0.26 NO
8 STX10 STX10 STX10 5091 0.071 0.21 NO
9 VAMP2 VAMP2 VAMP2 5136 0.07 0.23 NO
10 STX8 STX8 STX8 5522 0.06 0.23 NO
11 VAMP5 VAMP5 VAMP5 5558 0.059 0.24 NO
12 VAMP4 VAMP4 VAMP4 5685 0.056 0.25 NO
13 YKT6 YKT6 YKT6 7080 0.028 0.18 NO
14 TSNARE1 TSNARE1 TSNARE1 7378 0.022 0.17 NO
15 STX18 STX18 STX18 7551 0.019 0.17 NO
16 STX17 STX17 STX17 8151 0.0079 0.14 NO
17 BET1 BET1 BET1 8218 0.0068 0.14 NO
18 VAMP8 VAMP8 VAMP8 8326 0.0051 0.13 NO
19 GOSR1 GOSR1 GOSR1 8468 0.0028 0.13 NO
20 STX4 STX4 STX4 8477 0.0026 0.13 NO
21 BET1L BET1L BET1L 9211 -0.0091 0.088 NO
22 VTI1B VTI1B VTI1B 9754 -0.018 0.063 NO
23 STX5 STX5 STX5 9873 -0.02 0.062 NO
24 SNAP47 SNAP47 SNAP47 10143 -0.024 0.054 NO
25 STX3 STX3 STX3 10282 -0.026 0.054 NO
26 STX7 STX7 STX7 10538 -0.03 0.049 NO
27 VAMP3 VAMP3 VAMP3 10853 -0.036 0.042 NO
28 SNAP29 SNAP29 SNAP29 10986 -0.038 0.046 NO
29 USE1 USE1 USE1 11180 -0.041 0.047 NO
30 STX12 STX12 STX12 12049 -0.059 0.016 NO
31 SNAP23 SNAP23 SNAP23 12147 -0.061 0.029 NO
32 GOSR2 GOSR2 GOSR2 12475 -0.068 0.03 NO
33 STX6 STX6 STX6 13557 -0.096 -0.0014 NO
34 SEC22B SEC22B SEC22B 14171 -0.12 -0.00064 NO
35 BNIP1 BNIP1 BNIP1 14193 -0.12 0.033 NO
36 VTI1A VTI1A VTI1A 14372 -0.13 0.061 NO
37 VAMP7 VAMP7 VAMP7 14431 -0.13 0.096 NO
38 STX11 STX11 STX11 17182 -0.35 0.044 NO

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

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

genes ES table in pathway: KEGG TASTE TRANSDUCTION

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 NR2E3 NR2E3 NR2E3 83 0.58 0.01 YES
2 ZNF577 ZNF577 ZNF577 124 0.55 0.022 YES
3 ZNF167 ZNF167 ZNF167 363 0.46 0.02 YES
4 ZNF334 ZNF334 ZNF334 399 0.45 0.03 YES
5 ZNF300 ZNF300 ZNF300 649 0.39 0.026 YES
6 ZNF540 ZNF540 ZNF540 680 0.39 0.034 YES
7 ZFP2 ZFP2 ZFP2 712 0.38 0.042 YES
8 ZNF439 ZNF439 ZNF439 761 0.37 0.049 YES
9 ZNF596 ZNF596 ZNF596 826 0.36 0.055 YES
10 ZNF273 ZNF273 ZNF273 1010 0.33 0.053 YES
11 ZNF471 ZNF471 ZNF471 1060 0.32 0.058 YES
12 ZNF23 ZNF23 ZNF23 1073 0.32 0.066 YES
13 ZNF157 ZNF157 ZNF157 1118 0.31 0.071 YES
14 ZFP28 ZFP28 ZFP28 1138 0.31 0.078 YES
15 ZNF547 ZNF547 ZNF547 1180 0.3 0.084 YES
16 ZNF625 ZNF625 ZNF625 1228 0.29 0.088 YES
17 ZNF141 ZNF141 ZNF141 1419 0.27 0.085 YES
18 MAMLD1 MAMLD1 MAMLD1 1442 0.27 0.09 YES
19 ZNF519 ZNF519 ZNF519 1472 0.26 0.096 YES
20 ZNF169 ZNF169 ZNF169 1528 0.26 0.099 YES
21 ZNF493 ZNF493 ZNF493 1552 0.26 0.1 YES
22 ZNF433 ZNF433 ZNF433 1562 0.26 0.11 YES
23 TEAD2 TEAD2 TEAD2 1570 0.26 0.12 YES
24 ZNF454 ZNF454 ZNF454 1579 0.25 0.12 YES
25 ZNF337 ZNF337 ZNF337 1599 0.25 0.13 YES
26 ZNF320 ZNF320 ZNF320 1713 0.24 0.13 YES
27 ZNF599 ZNF599 ZNF599 1736 0.24 0.13 YES
28 ZNF425 ZNF425 ZNF425 1774 0.24 0.14 YES
29 RORA RORA RORA 1840 0.23 0.14 YES
30 ZNF558 ZNF558 ZNF558 1841 0.23 0.14 YES
31 ZNF311 ZNF311 ZNF311 1844 0.23 0.15 YES
32 ESR2 ESR2 ESR2 1871 0.23 0.16 YES
33 ZNF443 ZNF443 ZNF443 1894 0.23 0.16 YES
34 ZNF354B ZNF354B ZNF354B 1947 0.22 0.16 YES
35 ZNF214 ZNF214 ZNF214 1952 0.22 0.17 YES
36 ZNF530 ZNF530 ZNF530 1957 0.22 0.17 YES
37 ZNF287 ZNF287 ZNF287 1961 0.22 0.18 YES
38 SMAD7 SMAD7 SMAD7 1971 0.22 0.18 YES
39 KAT2A KAT2A KAT2A 1973 0.22 0.19 YES
40 ZNF442 ZNF442 ZNF442 1982 0.22 0.2 YES
41 ZNF19 ZNF19 ZNF19 1999 0.22 0.2 YES
42 ZNF441 ZNF441 ZNF441 2002 0.22 0.2 YES
43 ZNF620 ZNF620 ZNF620 2006 0.22 0.21 YES
44 ZNF382 ZNF382 ZNF382 2022 0.21 0.22 YES
45 HNF4A HNF4A HNF4A 2042 0.21 0.22 YES
46 ZNF546 ZNF546 ZNF546 2051 0.21 0.22 YES
47 NPPA NPPA NPPA 2066 0.21 0.23 YES
48 ZFP37 ZFP37 ZFP37 2104 0.2 0.23 YES
49 ZNF266 ZNF266 ZNF266 2111 0.2 0.24 YES
50 NR1I2 NR1I2 NR1I2 2204 0.2 0.24 YES
51 ZNF211 ZNF211 ZNF211 2254 0.19 0.24 YES
52 SMARCD3 SMARCD3 SMARCD3 2285 0.19 0.24 YES
53 ZNF498 ZNF498 ZNF498 2287 0.19 0.25 YES
54 ZNF483 ZNF483 ZNF483 2363 0.18 0.25 YES
55 HNF4G HNF4G HNF4G 2382 0.18 0.25 YES
56 ZNF160 ZNF160 ZNF160 2386 0.18 0.26 YES
57 ZNF514 ZNF514 ZNF514 2392 0.18 0.26 YES
58 ZNF92 ZNF92 ZNF92 2423 0.18 0.26 YES
59 ZNF606 ZNF606 ZNF606 2453 0.18 0.27 YES
60 ZNF10 ZNF10 ZNF10 2455 0.18 0.27 YES
61 RARA RARA RARA 2500 0.18 0.27 YES
62 ZNF517 ZNF517 ZNF517 2532 0.17 0.28 YES
63 ZNF212 ZNF212 ZNF212 2611 0.17 0.28 YES
64 ZNF224 ZNF224 ZNF224 2631 0.17 0.28 YES
65 ZNF655 ZNF655 ZNF655 2678 0.16 0.28 YES
66 ZNF419 ZNF419 ZNF419 2803 0.16 0.28 YES
67 ZNF250 ZNF250 ZNF250 2815 0.16 0.28 YES
68 ZNF354C ZNF354C ZNF354C 2842 0.16 0.28 YES
69 ZNF708 ZNF708 ZNF708 2886 0.15 0.28 YES
70 ZNF446 ZNF446 ZNF446 2906 0.15 0.29 YES
71 ZNF3 ZNF3 ZNF3 2973 0.15 0.29 YES
72 ZNF235 ZNF235 ZNF235 2974 0.15 0.29 YES
73 ZNF43 ZNF43 ZNF43 2983 0.15 0.3 YES
74 ZNF621 ZNF621 ZNF621 3006 0.15 0.3 YES
75 ZNF624 ZNF624 ZNF624 3021 0.15 0.3 YES
76 ZNF234 ZNF234 ZNF234 3059 0.14 0.3 YES
77 ZNF605 ZNF605 ZNF605 3069 0.14 0.3 YES
78 PPARD PPARD PPARD 3092 0.14 0.31 YES
79 ZKSCAN5 ZKSCAN5 ZKSCAN5 3135 0.14 0.31 YES
80 ZNF415 ZNF415 ZNF415 3182 0.14 0.31 YES
81 ZNF559 ZNF559 ZNF559 3251 0.14 0.31 YES
82 ZNF26 ZNF26 ZNF26 3269 0.14 0.31 YES
83 ZNF12 ZNF12 ZNF12 3311 0.13 0.31 YES
84 ZFP90 ZFP90 ZFP90 3367 0.13 0.31 YES
85 ZNF528 ZNF528 ZNF528 3370 0.13 0.32 YES
86 ZNF285 ZNF285 ZNF285 3442 0.13 0.32 YES
87 ZNF30 ZNF30 ZNF30 3497 0.12 0.32 YES
88 ZNF248 ZNF248 ZNF248 3508 0.12 0.32 YES
89 ZNF100 ZNF100 ZNF100 3514 0.12 0.32 YES
90 ZNF610 ZNF610 ZNF610 3519 0.12 0.32 YES
91 ZNF226 ZNF226 ZNF226 3579 0.12 0.32 YES
92 ZNF18 ZNF18 ZNF18 3595 0.12 0.33 YES
93 ZNF221 ZNF221 ZNF221 3606 0.12 0.33 YES
94 ZNF582 ZNF582 ZNF582 3609 0.12 0.33 YES
95 ZNF347 ZNF347 ZNF347 3647 0.12 0.33 YES
96 ZKSCAN3 ZKSCAN3 ZKSCAN3 3660 0.12 0.34 YES
97 AR AR AR 3661 0.12 0.34 YES
98 ZNF202 ZNF202 ZNF202 3700 0.12 0.34 YES
99 THRA THRA THRA 3713 0.12 0.34 YES
100 ZNF658 ZNF658 ZNF658 3715 0.12 0.34 YES
101 ZNF440 ZNF440 ZNF440 3743 0.11 0.35 YES
102 ZNF607 ZNF607 ZNF607 3763 0.11 0.35 YES
103 ZNF571 ZNF571 ZNF571 3764 0.11 0.35 YES
104 CCNT2 CCNT2 CCNT2 3864 0.11 0.35 YES
105 ZNF600 ZNF600 ZNF600 3926 0.11 0.35 YES
106 ZNF642 ZNF642 ZNF642 3937 0.11 0.35 YES
107 ZNF138 ZNF138 ZNF138 3980 0.1 0.35 YES
108 ZNF417 ZNF417 ZNF417 3993 0.1 0.35 YES
109 ZNF506 ZNF506 ZNF506 4030 0.1 0.35 YES
110 ZNF274 ZNF274 ZNF274 4077 0.1 0.35 YES
111 SP1 SP1 SP1 4078 0.1 0.36 YES
112 SKI SKI SKI 4079 0.1 0.36 YES
113 ZNF264 ZNF264 ZNF264 4154 0.098 0.36 YES
114 ZNF175 ZNF175 ZNF175 4181 0.098 0.36 YES
115 ZNF282 ZNF282 ZNF282 4225 0.096 0.36 YES
116 ZNF155 ZNF155 ZNF155 4237 0.096 0.36 YES
117 ZNF529 ZNF529 ZNF529 4274 0.095 0.36 YES
118 CDK9 CDK9 CDK9 4301 0.094 0.36 YES
119 ZNF286A ZNF286A ZNF286A 4324 0.093 0.36 YES
120 ZKSCAN1 ZKSCAN1 ZKSCAN1 4327 0.093 0.36 YES
121 ZNF418 ZNF418 ZNF418 4328 0.093 0.37 YES
122 NR2C2AP NR2C2AP NR2C2AP 4347 0.092 0.37 YES
123 ZNF585B ZNF585B ZNF585B 4356 0.092 0.37 YES
124 SMURF2 SMURF2 SMURF2 4358 0.092 0.37 YES
125 ZNF544 ZNF544 ZNF544 4360 0.092 0.37 YES
126 MED31 MED31 MED31 4441 0.09 0.37 YES
127 ZNF354A ZNF354A ZNF354A 4459 0.089 0.37 YES
128 TGIF1 TGIF1 TGIF1 4485 0.088 0.37 YES
129 ZNF140 ZNF140 ZNF140 4505 0.088 0.38 YES
130 ZNF205 ZNF205 ZNF205 4571 0.086 0.37 YES
131 RARG RARG RARG 4604 0.085 0.37 YES
132 ZIK1 ZIK1 ZIK1 4607 0.085 0.38 YES
133 ZNF394 ZNF394 ZNF394 4630 0.084 0.38 YES
134 ZNF432 ZNF432 ZNF432 4663 0.083 0.38 YES
135 ZNF256 ZNF256 ZNF256 4671 0.083 0.38 YES
136 ZNF569 ZNF569 ZNF569 4704 0.082 0.38 YES
137 ZNF333 ZNF333 ZNF333 4718 0.082 0.38 YES
138 ZNF611 ZNF611 ZNF611 4767 0.08 0.38 YES
139 ZNF223 ZNF223 ZNF223 4886 0.077 0.38 YES
140 ZNF2 ZNF2 ZNF2 4930 0.076 0.38 YES
141 ZNF215 ZNF215 ZNF215 4943 0.075 0.38 YES
142 ZNF587 ZNF587 ZNF587 4970 0.075 0.38 YES
143 ZNF254 ZNF254 ZNF254 5014 0.073 0.38 YES
144 ZNF566 ZNF566 ZNF566 5080 0.072 0.37 YES
145 ZNF343 ZNF343 ZNF343 5084 0.072 0.38 YES
146 ZNF33B ZNF33B ZNF33B 5102 0.071 0.38 YES
147 ZNF510 ZNF510 ZNF510 5103 0.071 0.38 YES
148 ZNF20 ZNF20 ZNF20 5124 0.07 0.38 YES
149 NR1D1 NR1D1 NR1D1 5126 0.07 0.38 YES
150 ZNF213 ZNF213 ZNF213 5127 0.07 0.38 YES
151 ZNF398 ZNF398 ZNF398 5195 0.069 0.38 NO
152 ZFP112 ZFP112 ZFP112 5213 0.068 0.38 NO
153 NR6A1 NR6A1 NR6A1 5313 0.065 0.38 NO
154 TEAD4 TEAD4 TEAD4 5384 0.064 0.38 NO
155 TEAD3 TEAD3 TEAD3 5402 0.063 0.38 NO
156 SMAD4 SMAD4 SMAD4 5430 0.062 0.38 NO
157 ZNF37A ZNF37A ZNF37A 5436 0.062 0.38 NO
158 NCOR1 NCOR1 NCOR1 5583 0.059 0.37 NO
159 MED4 MED4 MED4 5605 0.058 0.37 NO
160 ZNF589 ZNF589 ZNF589 5606 0.058 0.37 NO
161 ZNF557 ZNF557 ZNF557 5608 0.058 0.37 NO
162 ZNF551 ZNF551 ZNF551 5698 0.056 0.37 NO
163 ZNF431 ZNF431 ZNF431 5706 0.056 0.37 NO
164 ZNF567 ZNF567 ZNF567 5772 0.054 0.37 NO
165 ZKSCAN4 ZKSCAN4 ZKSCAN4 5804 0.054 0.37 NO
166 ZNF383 ZNF383 ZNF383 5834 0.053 0.37 NO
167 ZNF500 ZNF500 ZNF500 5902 0.051 0.37 NO
168 ZNF33A ZNF33A ZNF33A 5907 0.051 0.37 NO
169 ZNF434 ZNF434 ZNF434 5948 0.051 0.37 NO
170 MEN1 MEN1 MEN1 5972 0.05 0.37 NO
171 MAML3 MAML3 MAML3 6042 0.049 0.36 NO
172 ZNF445 ZNF445 ZNF445 6083 0.048 0.36 NO
173 ZNF17 ZNF17 ZNF17 6143 0.047 0.36 NO
174 ZNF480 ZNF480 ZNF480 6156 0.046 0.36 NO
175 NOTCH2 NOTCH2 NOTCH2 6191 0.046 0.36 NO
176 ZFP1 ZFP1 ZFP1 6201 0.046 0.36 NO
177 ZNF564 ZNF564 ZNF564 6219 0.045 0.36 NO
178 MED17 MED17 MED17 6275 0.044 0.36 NO
179 NR1D2 NR1D2 NR1D2 6304 0.043 0.36 NO
180 HDAC1 HDAC1 HDAC1 6307 0.043 0.36 NO
181 ZNF649 ZNF649 ZNF649 6328 0.043 0.36 NO
182 ZNF197 ZNF197 ZNF197 6336 0.043 0.36 NO
183 ZNF225 ZNF225 ZNF225 6397 0.041 0.36 NO
184 ZNF263 ZNF263 ZNF263 6605 0.036 0.35 NO
185 ZNF773 ZNF773 ZNF773 6615 0.036 0.35 NO
186 MED15 MED15 MED15 6660 0.035 0.35 NO
187 ZNF565 ZNF565 ZNF565 6680 0.035 0.34 NO
188 MED24 MED24 MED24 6777 0.033 0.34 NO
189 ZNF485 ZNF485 ZNF485 6804 0.032 0.34 NO
190 ZNF25 ZNF25 ZNF25 6830 0.032 0.34 NO
191 SMAD3 SMAD3 SMAD3 6845 0.032 0.34 NO
192 ZNF627 ZNF627 ZNF627 6846 0.032 0.34 NO
193 MAML2 MAML2 MAML2 6853 0.032 0.34 NO
194 PPARG PPARG PPARG 6890 0.031 0.34 NO
195 NCOA3 NCOA3 NCOA3 7044 0.028 0.33 NO
196 ZNF136 ZNF136 ZNF136 7071 0.028 0.33 NO
197 NR2F6 NR2F6 NR2F6 7097 0.027 0.33 NO
198 ZNF304 ZNF304 ZNF304 7100 0.027 0.33 NO
199 MED23 MED23 MED23 7187 0.026 0.33 NO
200 ZNF331 ZNF331 ZNF331 7254 0.024 0.32 NO
201 TRIM33 TRIM33 TRIM33 7264 0.024 0.32 NO
202 ESRRG ESRRG ESRRG 7278 0.024 0.32 NO
203 ZNF585A ZNF585A ZNF585A 7302 0.023 0.32 NO
204 RXRB RXRB RXRB 7482 0.02 0.31 NO
205 ESRRA ESRRA ESRRA 7530 0.019 0.31 NO
206 RBPJ RBPJ RBPJ 7564 0.018 0.31 NO
207 ZNF570 ZNF570 ZNF570 7567 0.018 0.31 NO
208 MED7 MED7 MED7 7635 0.017 0.31 NO
209 ZNF548 ZNF548 ZNF548 7696 0.016 0.3 NO
210 MED26 MED26 MED26 7781 0.014 0.3 NO
211 MED27 MED27 MED27 7834 0.014 0.3 NO
212 NRBP1 NRBP1 NRBP1 7848 0.013 0.3 NO
213 ZNF490 ZNF490 ZNF490 7872 0.013 0.3 NO
214 ZNF324 ZNF324 ZNF324 7873 0.013 0.3 NO
215 ZNF563 ZNF563 ZNF563 7885 0.013 0.3 NO
216 MED25 MED25 MED25 8013 0.01 0.29 NO
217 ZNF200 ZNF200 ZNF200 8066 0.0093 0.29 NO
218 TBL1XR1 TBL1XR1 TBL1XR1 8094 0.0089 0.28 NO
219 ZNF101 ZNF101 ZNF101 8103 0.0086 0.28 NO
220 NR1H2 NR1H2 NR1H2 8117 0.0084 0.28 NO
221 ZNF230 ZNF230 ZNF230 8220 0.0066 0.28 NO
222 ZNF595 ZNF595 ZNF595 8221 0.0066 0.28 NO
223 CREBBP CREBBP CREBBP 8279 0.0058 0.28 NO
224 NCOA6 NCOA6 NCOA6 8321 0.0052 0.27 NO
225 MAML1 MAML1 MAML1 8416 0.0036 0.27 NO
226 ZNF615 ZNF615 ZNF615 8427 0.0034 0.27 NO
227 ZNF556 ZNF556 ZNF556 8476 0.0026 0.26 NO
228 E2F4 E2F4 E2F4 8533 0.0019 0.26 NO
229 ZNF180 ZNF180 ZNF180 8590 0.0011 0.26 NO
230 ZNF468 ZNF468 ZNF468 8619 0.00063 0.26 NO
231 ZNF436 ZNF436 ZNF436 8701 -0.0008 0.25 NO
232 ZNF555 ZNF555 ZNF555 8707 -0.00087 0.25 NO
233 ZNF583 ZNF583 ZNF583 8825 -0.0029 0.24 NO
234 ZNF192 ZNF192 ZNF192 8927 -0.0044 0.24 NO
235 ZNF543 ZNF543 ZNF543 8961 -0.0048 0.24 NO
236 ZNF267 ZNF267 ZNF267 9095 -0.0071 0.23 NO
237 RUNX2 RUNX2 RUNX2 9252 -0.0096 0.22 NO
238 ZNF28 ZNF28 ZNF28 9256 -0.0096 0.22 NO
239 TFDP1 TFDP1 TFDP1 9311 -0.011 0.22 NO
240 ZNF597 ZNF597 ZNF597 9314 -0.011 0.22 NO
241 ZNF613 ZNF613 ZNF613 9381 -0.012 0.22 NO
242 TBL1X TBL1X TBL1X 9386 -0.012 0.22 NO
243 ZNF189 ZNF189 ZNF189 9408 -0.012 0.22 NO
244 MED6 MED6 MED6 9505 -0.014 0.21 NO
245 CTGF CTGF CTGF 9595 -0.016 0.21 NO
246 ZNF561 ZNF561 ZNF561 9764 -0.018 0.2 NO
247 SMAD2 SMAD2 SMAD2 9784 -0.018 0.2 NO
248 MED1 MED1 MED1 9793 -0.019 0.2 NO
249 TGIF2 TGIF2 TGIF2 9833 -0.019 0.19 NO
250 ZNF154 ZNF154 ZNF154 9884 -0.02 0.19 NO
251 ZNF317 ZNF317 ZNF317 9904 -0.02 0.19 NO
252 ZIM2 ZIM2 ZIM2 9905 -0.02 0.19 NO
253 MED12 MED12 MED12 9915 -0.02 0.19 NO
254 TRIM28 TRIM28 TRIM28 9917 -0.02 0.19 NO
255 TEAD1 TEAD1 TEAD1 9956 -0.021 0.19 NO
256 ZNF184 ZNF184 ZNF184 10082 -0.023 0.18 NO
257 ZNF208 ZNF208 ZNF208 10126 -0.024 0.18 NO
258 ZNF492 ZNF492 ZNF492 10179 -0.024 0.18 NO
259 MED16 MED16 MED16 10276 -0.026 0.18 NO
260 ZNF484 ZNF484 ZNF484 10297 -0.026 0.18 NO
261 ZNF584 ZNF584 ZNF584 10333 -0.027 0.17 NO
262 PPARA PPARA PPARA 10431 -0.029 0.17 NO
263 SNW1 SNW1 SNW1 10463 -0.029 0.17 NO
264 RORC RORC RORC 10483 -0.03 0.17 NO
265 WWTR1 WWTR1 WWTR1 10605 -0.031 0.16 NO
266 PPM1A PPM1A PPM1A 10669 -0.032 0.16 NO
267 ZNF227 ZNF227 ZNF227 10674 -0.033 0.16 NO
268 ZNF416 ZNF416 ZNF416 10761 -0.034 0.16 NO
269 MED14 MED14 MED14 10782 -0.034 0.16 NO
270 MED8 MED8 MED8 10891 -0.036 0.15 NO
271 ZNF45 ZNF45 ZNF45 10919 -0.037 0.15 NO
272 NCOR2 NCOR2 NCOR2 10987 -0.038 0.15 NO
273 YAP1 YAP1 YAP1 11057 -0.039 0.14 NO
274 ZNF14 ZNF14 ZNF14 11077 -0.039 0.14 NO
275 ZNF614 ZNF614 ZNF614 11200 -0.042 0.14 NO
276 ZNF222 ZNF222 ZNF222 11207 -0.042 0.14 NO
277 MED10 MED10 MED10 11219 -0.042 0.14 NO
278 CCNC CCNC CCNC 11526 -0.048 0.12 NO
279 E2F5 E2F5 E2F5 11563 -0.049 0.12 NO
280 UBE2D3 UBE2D3 UBE2D3 11585 -0.05 0.12 NO
281 NCOA1 NCOA1 NCOA1 11611 -0.05 0.12 NO
282 UBA52 UBA52 UBA52 11636 -0.051 0.12 NO
283 THRB THRB THRB 11656 -0.051 0.12 NO
284 PRIC285 PRIC285 PRIC285 11754 -0.053 0.12 NO
285 ZNF473 ZNF473 ZNF473 11949 -0.057 0.11 NO
286 ZNF496 ZNF496 ZNF496 12076 -0.06 0.1 NO
287 ZNF616 ZNF616 ZNF616 12081 -0.06 0.1 NO
288 NR1I3 NR1I3 NR1I3 12127 -0.061 0.1 NO
289 ZNF114 ZNF114 ZNF114 12190 -0.062 0.1 NO
290 ZNF552 ZNF552 ZNF552 12238 -0.063 0.1 NO
291 TGS1 TGS1 TGS1 12453 -0.068 0.09 NO
292 ZNF350 ZNF350 ZNF350 12492 -0.068 0.09 NO
293 RPS27A RPS27A RPS27A 12534 -0.069 0.089 NO
294 MED20 MED20 MED20 12628 -0.071 0.086 NO
295 NR3C2 NR3C2 NR3C2 12674 -0.072 0.085 NO
296 NR3C1 NR3C1 NR3C1 12902 -0.078 0.074 NO
297 NR1H3 NR1H3 NR1H3 12960 -0.08 0.073 NO
298 RBL1 RBL1 RBL1 12988 -0.08 0.073 NO
299 ZNF641 ZNF641 ZNF641 13033 -0.081 0.073 NO
300 ZNF420 ZNF420 ZNF420 13176 -0.085 0.067 NO
301 UBE2D1 UBE2D1 UBE2D1 13180 -0.085 0.069 NO
302 ZNF619 ZNF619 ZNF619 13234 -0.086 0.068 NO
303 CCNT1 CCNT1 CCNT1 13289 -0.088 0.068 NO
304 USP9X USP9X USP9X 13476 -0.094 0.06 NO
305 CDK8 CDK8 CDK8 13489 -0.094 0.061 NO
306 MED30 MED30 MED30 13687 -0.1 0.053 NO
307 SKIL SKIL SKIL 13778 -0.1 0.05 NO
308 ZNF643 ZNF643 ZNF643 13797 -0.1 0.052 NO
309 ZNF430 ZNF430 ZNF430 13970 -0.11 0.045 NO
310 ZNF460 ZNF460 ZNF460 13973 -0.11 0.048 NO
311 ZNF426 ZNF426 ZNF426 14030 -0.11 0.048 NO
312 ESRRB ESRRB ESRRB 14353 -0.13 0.033 NO
313 PARP1 PARP1 PARP1 14643 -0.14 0.02 NO
314 JUNB JUNB JUNB 14810 -0.15 0.014 NO
315 NRBF2 NRBF2 NRBF2 14850 -0.15 0.016 NO
316 KAT2B KAT2B KAT2B 14855 -0.15 0.02 NO
317 NCOA2 NCOA2 NCOA2 14869 -0.15 0.023 NO
318 NR2E1 NR2E1 NR2E1 14887 -0.16 0.026 NO
319 NOTCH4 NOTCH4 NOTCH4 15138 -0.17 0.016 NO
320 CDKN2B CDKN2B CDKN2B 15374 -0.19 0.0078 NO
321 ZNF98 ZNF98 ZNF98 15532 -0.2 0.004 NO
322 NR4A2 NR4A2 NR4A2 15676 -0.21 0.0012 NO
323 NR4A1 NR4A1 NR4A1 15928 -0.23 -0.0072 NO
324 RXRA RXRA RXRA 16239 -0.25 -0.018 NO
325 NR0B2 NR0B2 NR0B2 16351 -0.26 -0.018 NO
326 NR0B1 NR0B1 NR0B1 16535 -0.28 -0.021 NO
327 NR5A2 NR5A2 NR5A2 16551 -0.28 -0.015 NO
328 ESR1 ESR1 ESR1 16741 -0.3 -0.018 NO
329 RXRG RXRG RXRG 16810 -0.3 -0.014 NO
330 VDR VDR VDR 16838 -0.31 -0.0074 NO
331 NR4A3 NR4A3 NR4A3 16961 -0.32 -0.006 NO
332 NR2F1 NR2F1 NR2F1 17272 -0.36 -0.014 NO
333 MYC MYC MYC 17337 -0.37 -0.0084 NO
334 SERPINE1 SERPINE1 SERPINE1 17424 -0.39 -0.0032 NO
335 NOTCH3 NOTCH3 NOTCH3 17552 -0.42 0.00028 NO
336 RORB RORB RORB 17708 -0.46 0.0033 NO
337 PGR PGR PGR 17730 -0.47 0.014 NO

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

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TASTE TRANSDUCTION, 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 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 OR2A1 OR2A1 OR2A1 51 0.62 0.13 YES
2 OR2A25 OR2A25 OR2A25 1168 0.3 0.13 YES
3 OR10AD1 OR10AD1 OR10AD1 1301 0.28 0.18 YES
4 OR2A4 OR2A4 OR2A4 1379 0.27 0.23 YES
5 OR4F29 OR4F29 OR4F29 1382 0.27 0.29 YES
6 GNGT1 GNGT1 GNGT1 1426 0.27 0.34 YES
7 OR5K2 OR5K2 OR5K2 1589 0.25 0.39 YES
8 OR56B1 OR56B1 OR56B1 1959 0.22 0.41 YES
9 OR2T10 OR2T10 OR2T10 2660 0.17 0.41 YES
10 OR2AE1 OR2AE1 OR2AE1 2696 0.16 0.44 YES
11 OR52N4 OR52N4 OR52N4 2960 0.15 0.46 YES
12 OR2A7 OR2A7 OR2A7 3163 0.14 0.48 YES
13 GNAL GNAL GNAL 3321 0.13 0.5 YES
14 OR2T5 OR2T5 OR2T5 4330 0.093 0.46 NO
15 OR51B5 OR51B5 OR51B5 7667 0.016 0.28 NO
16 OR56B4 OR56B4 OR56B4 8757 -0.0016 0.22 NO
17 OR1J2 OR1J2 OR1J2 9360 -0.012 0.18 NO
18 OR1L8 OR1L8 OR1L8 9537 -0.015 0.18 NO
19 OR52N2 OR52N2 OR52N2 9922 -0.02 0.16 NO
20 GNB1 GNB1 GNB1 10087 -0.023 0.16 NO
21 OR4C6 OR4C6 OR4C6 10140 -0.024 0.16 NO
22 OR7D2 OR7D2 OR7D2 11481 -0.047 0.094 NO
23 OR2B11 OR2B11 OR2B11 11541 -0.049 0.1 NO
24 OR3A2 OR3A2 OR3A2 11908 -0.056 0.092 NO
25 OR2C1 OR2C1 OR2C1 13253 -0.087 0.035 NO
26 OR2B6 OR2B6 OR2B6 13714 -0.1 0.031 NO
27 OR2L13 OR2L13 OR2L13 14718 -0.14 0.0055 NO
28 OR2W3 OR2W3 OR2W3 14777 -0.15 0.033 NO
29 OR51E2 OR51E2 OR51E2 16061 -0.24 0.011 NO
30 OR51E1 OR51E1 OR51E1 17706 -0.46 0.015 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 ALK PATHWAY.

Figure S32.  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 DEATH 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 GATA1 GATA1 GATA1 462 0.43 0.078 YES
2 SSPO SSPO SSPO 1800 0.23 0.059 YES
3 SMAD7 SMAD7 SMAD7 1971 0.22 0.1 YES
4 ZFPM1 ZFPM1 ZFPM1 2336 0.19 0.13 YES
5 HDAC9 HDAC9 HDAC9 2729 0.16 0.14 YES
6 NR2C1 NR2C1 NR2C1 3072 0.14 0.16 YES
7 HDAC11 HDAC11 HDAC11 3096 0.14 0.19 YES
8 GATA2 GATA2 GATA2 3884 0.11 0.17 YES
9 SIRT3 SIRT3 SIRT3 3934 0.11 0.2 YES
10 SIRT5 SIRT5 SIRT5 4805 0.079 0.17 YES
11 SIRT6 SIRT6 SIRT6 5031 0.073 0.17 YES
12 HDAC7 HDAC7 HDAC7 5192 0.069 0.18 YES
13 MBD2 MBD2 MBD2 5534 0.06 0.18 YES
14 NCOR1 NCOR1 NCOR1 5583 0.059 0.19 YES
15 SIRT7 SIRT7 SIRT7 5788 0.054 0.19 YES
16 XPO1 XPO1 XPO1 5896 0.052 0.2 YES
17 MBD3 MBD3 MBD3 6026 0.049 0.2 YES
18 FKBP3 FKBP3 FKBP3 6221 0.045 0.2 YES
19 HDAC1 HDAC1 HDAC1 6307 0.043 0.2 YES
20 SMURF1 SMURF1 SMURF1 6442 0.04 0.21 YES
21 SIN3B SIN3B SIN3B 6721 0.034 0.2 YES
22 HDAC6 HDAC6 HDAC6 6767 0.033 0.21 YES
23 PPARG PPARG PPARG 6890 0.031 0.21 YES
24 CHD3 CHD3 CHD3 6979 0.029 0.21 YES
25 HDAC4 HDAC4 HDAC4 6986 0.029 0.22 YES
26 SIRT4 SIRT4 SIRT4 7281 0.024 0.2 NO
27 TNFRSF1A TNFRSF1A TNFRSF1A 7539 0.019 0.2 NO
28 EP300 EP300 EP300 7861 0.013 0.18 NO
29 UBE2I UBE2I UBE2I 8038 0.0098 0.17 NO
30 RANGAP1 RANGAP1 RANGAP1 8197 0.0071 0.16 NO
31 CREBBP CREBBP CREBBP 8279 0.0058 0.16 NO
32 NFKB1 NFKB1 NFKB1 8382 0.0042 0.16 NO
33 SIN3A SIN3A SIN3A 8383 0.0042 0.16 NO
34 TNF TNF TNF 8396 0.004 0.16 NO
35 MTA2 MTA2 MTA2 8610 0.00073 0.15 NO
36 HDAC10 HDAC10 HDAC10 8647 0.00015 0.14 NO
37 TFCP2 TFCP2 TFCP2 8658 -0.000065 0.14 NO
38 RBBP4 RBBP4 RBBP4 9248 -0.0095 0.11 NO
39 SMG5 SMG5 SMG5 9577 -0.015 0.099 NO
40 HDAC8 HDAC8 HDAC8 9633 -0.016 0.1 NO
41 PRKACA PRKACA PRKACA 9635 -0.016 0.1 NO
42 GATAD2A GATAD2A GATAD2A 9720 -0.018 0.1 NO
43 SAP18 SAP18 SAP18 9759 -0.018 0.11 NO
44 RELA RELA RELA 9762 -0.018 0.11 NO
45 STAT3 STAT3 STAT3 9899 -0.02 0.11 NO
46 GATAD2B GATAD2B GATAD2B 10241 -0.026 0.094 NO
47 CHD4 CHD4 CHD4 10507 -0.03 0.087 NO
48 HDAC2 HDAC2 HDAC2 10888 -0.036 0.074 NO
49 NCOR2 NCOR2 NCOR2 10987 -0.038 0.078 NO
50 MAX MAX MAX 11049 -0.039 0.084 NO
51 NFKBIA NFKBIA NFKBIA 11598 -0.05 0.065 NO
52 SIRT1 SIRT1 SIRT1 11770 -0.054 0.068 NO
53 PRMT5 PRMT5 PRMT5 11919 -0.057 0.074 NO
54 HDAC5 HDAC5 HDAC5 12133 -0.061 0.076 NO
55 SUMO1 SUMO1 SUMO1 12203 -0.062 0.088 NO
56 RANBP2 RANBP2 RANBP2 12340 -0.065 0.096 NO
57 HDAC3 HDAC3 HDAC3 12594 -0.071 0.098 NO
58 YY1 YY1 YY1 12614 -0.071 0.11 NO
59 RBBP7 RBBP7 RBBP7 12688 -0.073 0.13 NO
60 SIRT2 SIRT2 SIRT2 12858 -0.077 0.14 NO
61 WDR77 WDR77 WDR77 13152 -0.084 0.14 NO
62 SAP30 SAP30 SAP30 13439 -0.092 0.15 NO
63 RAN RAN RAN 13898 -0.11 0.15 NO
64 KAT2B KAT2B KAT2B 14855 -0.15 0.13 NO
65 MXD1 MXD1 MXD1 15263 -0.18 0.15 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 DEATH PATHWAY.

Figure S34.  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: PID HDAC CLASSI 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 ENO3 ENO3 ENO3 543 0.42 0.11 YES
2 PGAM2 PGAM2 PGAM2 669 0.39 0.24 YES
3 GAPDHS GAPDHS GAPDHS 1303 0.28 0.3 YES
4 PFKFB1 PFKFB1 PFKFB1 1449 0.27 0.38 YES
5 ENO2 ENO2 ENO2 7123 0.027 0.073 NO
6 ALDOC ALDOC ALDOC 7415 0.021 0.064 NO
7 PFKP PFKP PFKP 8125 0.0083 0.028 NO
8 PPP2R1A PPP2R1A PPP2R1A 9312 -0.011 -0.035 NO
9 ENO1 ENO1 ENO1 9748 -0.018 -0.053 NO
10 PKLR PKLR PKLR 9909 -0.02 -0.055 NO
11 GAPDH GAPDH GAPDH 10704 -0.033 -0.088 NO
12 PKM2 PKM2 PKM2 10979 -0.038 -0.09 NO
13 TPI1 TPI1 TPI1 11183 -0.041 -0.088 NO
14 PFKM PFKM PFKM 11380 -0.045 -0.083 NO
15 PPP2R5D PPP2R5D PPP2R5D 11529 -0.048 -0.075 NO
16 PPP2R1B PPP2R1B PPP2R1B 11547 -0.049 -0.059 NO
17 PPP2CA PPP2CA PPP2CA 11620 -0.05 -0.046 NO
18 PPP2CB PPP2CB PPP2CB 12001 -0.058 -0.048 NO
19 ALDOA ALDOA ALDOA 12185 -0.062 -0.037 NO
20 PGAM1 PGAM1 PGAM1 12700 -0.073 -0.04 NO
21 PFKL PFKL PFKL 12757 -0.074 -0.018 NO
22 PFKFB4 PFKFB4 PFKFB4 12910 -0.079 0.000028 NO
23 GPI GPI GPI 13343 -0.09 0.0065 NO
24 PGK1 PGK1 PGK1 13934 -0.11 0.011 NO
25 PFKFB2 PFKFB2 PFKFB2 14080 -0.12 0.042 NO
26 PFKFB3 PFKFB3 PFKFB3 14909 -0.16 0.05 NO
27 ALDOB ALDOB ALDOB 17254 -0.36 0.04 NO

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

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

genes ES table in pathway: PID BMPPATHWAY

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 SPHK1 SPHK1 SPHK1 354 0.46 0.11 YES
2 TUBB1 TUBB1 TUBB1 902 0.35 0.18 YES
3 TUBB3 TUBB3 TUBB3 1153 0.31 0.25 YES
4 TUBB2B TUBB2B TUBB2B 4039 0.1 0.12 NO
5 TUBB6 TUBB6 TUBB6 4105 0.1 0.15 NO
6 FBXW4 FBXW4 FBXW4 4760 0.08 0.13 NO
7 FKBP9 FKBP9 FKBP9 5644 0.057 0.1 NO
8 FBXW7 FBXW7 FBXW7 5889 0.052 0.1 NO
9 KIFC3 KIFC3 KIFC3 6284 0.044 0.092 NO
10 PFDN6 PFDN6 PFDN6 6698 0.035 0.078 NO
11 USP11 USP11 USP11 7158 0.026 0.06 NO
12 TUBA1A TUBA1A TUBA1A 7498 0.02 0.047 NO
13 FBXO6 FBXO6 FBXO6 8140 0.0081 0.014 NO
14 FBXW2 FBXW2 FBXW2 8242 0.0063 0.0099 NO
15 TBCD TBCD TBCD 8276 0.0059 0.0097 NO
16 ACTB ACTB ACTB 8332 0.005 0.0081 NO
17 PFDN5 PFDN5 PFDN5 8360 0.0046 0.0079 NO
18 TBCB TBCB TBCB 8362 0.0045 0.0091 NO
19 FBXW5 FBXW5 FBXW5 8414 0.0036 0.0073 NO
20 TBCC TBCC TBCC 8982 -0.0052 -0.023 NO
21 FBXL3 FBXL3 FBXL3 9110 -0.0073 -0.028 NO
22 PFDN1 PFDN1 PFDN1 9487 -0.014 -0.045 NO
23 XRN2 XRN2 XRN2 9743 -0.018 -0.054 NO
24 NOP56 NOP56 NOP56 9871 -0.02 -0.056 NO
25 TUBA1C TUBA1C TUBA1C 9955 -0.021 -0.054 NO
26 TUBB2A TUBB2A TUBB2A 10025 -0.022 -0.052 NO
27 PFDN4 PFDN4 PFDN4 10191 -0.025 -0.054 NO
28 PFDN2 PFDN2 PFDN2 10293 -0.026 -0.052 NO
29 CCT6A CCT6A CCT6A 10398 -0.028 -0.05 NO
30 FBXL5 FBXL5 FBXL5 10830 -0.035 -0.064 NO
31 TUBA1B TUBA1B TUBA1B 10911 -0.037 -0.058 NO
32 ARFGEF2 ARFGEF2 ARFGEF2 10973 -0.038 -0.05 NO
33 FBXO4 FBXO4 FBXO4 11758 -0.053 -0.079 NO
34 TBCA TBCA TBCA 11798 -0.054 -0.066 NO
35 CCT2 CCT2 CCT2 12499 -0.068 -0.085 NO
36 AP3M1 AP3M1 AP3M1 12553 -0.07 -0.068 NO
37 CCT7 CCT7 CCT7 12689 -0.073 -0.055 NO
38 KIF13A KIF13A KIF13A 13056 -0.082 -0.052 NO
39 CCT3 CCT3 CCT3 13067 -0.082 -0.029 NO
40 CCT8 CCT8 CCT8 13166 -0.085 -0.01 NO
41 TCP1 TCP1 TCP1 13200 -0.086 0.012 NO
42 TUBA3D TUBA3D TUBA3D 13353 -0.09 0.029 NO
43 CCT5 CCT5 CCT5 13654 -0.1 0.041 NO
44 TBCE TBCE TBCE 13981 -0.11 0.055 NO
45 CCT4 CCT4 CCT4 14125 -0.12 0.08 NO
46 LONP2 LONP2 LONP2 14142 -0.12 0.11 NO
47 VBP1 VBP1 VBP1 14782 -0.15 0.12 NO
48 TUBA4A TUBA4A TUBA4A 15634 -0.21 0.13 NO

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

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

genes ES table in pathway: REACTOME SIGNALING BY FGFR1 MUTANTS

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 NOG NOG NOG 276 0.48 0.099 YES
2 BMP4 BMP4 BMP4 512 0.42 0.18 YES
3 SMAD6 SMAD6 SMAD6 577 0.41 0.28 YES
4 NPPA NPPA NPPA 2066 0.21 0.24 YES
5 BMP7 BMP7 BMP7 2167 0.2 0.29 YES
6 FZD1 FZD1 FZD1 2301 0.19 0.32 YES
7 BMP2 BMP2 BMP2 2350 0.19 0.37 YES
8 HNF1A HNF1A HNF1A 2749 0.16 0.38 YES
9 WNT1 WNT1 WNT1 4853 0.078 0.28 NO
10 TGFB2 TGFB2 TGFB2 5416 0.063 0.27 NO
11 SMAD4 SMAD4 SMAD4 5430 0.062 0.28 NO
12 AXIN1 AXIN1 AXIN1 5623 0.058 0.28 NO
13 DVL1 DVL1 DVL1 5746 0.055 0.29 NO
14 TGFBR3 TGFBR3 TGFBR3 6573 0.037 0.25 NO
15 BMPR1A BMPR1A BMPR1A 7697 0.016 0.2 NO
16 SMAD5 SMAD5 SMAD5 7715 0.016 0.2 NO
17 TGFBR2 TGFBR2 TGFBR2 8821 -0.0028 0.14 NO
18 GSK3B GSK3B GSK3B 9148 -0.0079 0.12 NO
19 MAP3K7 MAP3K7 MAP3K7 9731 -0.018 0.092 NO
20 BMPR2 BMPR2 BMPR2 9866 -0.02 0.089 NO
21 SMAD1 SMAD1 SMAD1 10210 -0.025 0.076 NO
22 CTNNB1 CTNNB1 CTNNB1 10869 -0.036 0.048 NO
23 RFC1 RFC1 RFC1 10909 -0.037 0.054 NO
24 TGFB3 TGFB3 TGFB3 11982 -0.058 0.0085 NO
25 TGFBR1 TGFBR1 TGFBR1 12979 -0.08 -0.028 NO
26 APC APC APC 13399 -0.091 -0.03 NO
27 ACVR1 ACVR1 ACVR1 14459 -0.13 -0.057 NO
28 CHRD CHRD CHRD 14595 -0.14 -0.032 NO
29 TGFB1 TGFB1 TGFB1 14702 -0.14 -0.0036 NO
30 GATA4 GATA4 GATA4 14764 -0.15 0.028 NO
31 ATF2 ATF2 ATF2 15111 -0.17 0.049 NO
32 BMP5 BMP5 BMP5 15218 -0.18 0.085 NO
33 MEF2C MEF2C MEF2C 16694 -0.29 0.072 NO

Figure S39.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME SIGNALING BY FGFR1 MUTANTS.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SIGNALING BY FGFR1 MUTANTS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG GLYCOLYSIS GLUCONEOGENESIS 58 genes.ES.table 0.57 1.8 0.0021 0.086 0.55 0.55 0.18 0.45 0.025 0.011
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.81 2 0.002 0.033 0.17 0.9 0.17 0.75 0 0.004
KEGG PENTOSE PHOSPHATE PATHWAY 26 genes.ES.table 0.53 1.6 0.035 0.16 0.88 0.69 0.21 0.55 0.087 0.009
KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS 25 genes.ES.table 0.81 1.7 0 0.11 0.65 0.68 0.12 0.6 0.039 0.013
KEGG FRUCTOSE AND MANNOSE METABOLISM 33 genes.ES.table 0.54 1.6 0.026 0.16 0.87 0.27 0.096 0.25 0.083 0.011
KEGG FATTY ACID METABOLISM 39 genes.ES.table 0.73 2 0.0022 0.034 0.2 0.74 0.13 0.65 0 0.003
KEGG STEROID HORMONE BIOSYNTHESIS 49 genes.ES.table 0.69 1.7 0 0.12 0.74 0.41 0.065 0.38 0.054 0.01
KEGG OXIDATIVE PHOSPHORYLATION 112 genes.ES.table 0.57 1.6 0.08 0.15 0.81 0.75 0.22 0.59 0.071 0.013
KEGG PYRIMIDINE METABOLISM 97 genes.ES.table 0.36 1.5 0.071 0.22 0.93 0.42 0.27 0.31 0.14 0.014
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 31 genes.ES.table 0.68 1.8 0.004 0.1 0.63 0.52 0.1 0.46 0.038 0.012
genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 HAO2 HAO2 HAO2 4 0.88 0.083 YES
2 PIPOX PIPOX PIPOX 15 0.76 0.15 YES
3 DAO DAO DAO 19 0.74 0.22 YES
4 AGXT AGXT AGXT 80 0.54 0.27 YES
5 EHHADH EHHADH EHHADH 293 0.35 0.29 YES
6 SLC27A2 SLC27A2 SLC27A2 347 0.31 0.32 YES
7 MPV17L MPV17L MPV17L 355 0.31 0.35 YES
8 ACOX2 ACOX2 ACOX2 377 0.3 0.37 YES
9 PXMP2 PXMP2 PXMP2 420 0.28 0.4 YES
10 DHRS4 DHRS4 DHRS4 454 0.27 0.42 YES
11 EPHX2 EPHX2 EPHX2 641 0.22 0.43 YES
12 DDO DDO DDO 666 0.22 0.45 YES
13 ACSL1 ACSL1 ACSL1 712 0.21 0.47 YES
14 DECR2 DECR2 DECR2 713 0.21 0.49 YES
15 MLYCD MLYCD MLYCD 750 0.2 0.5 YES
16 FAR2 FAR2 FAR2 774 0.2 0.52 YES
17 PAOX PAOX PAOX 890 0.18 0.53 YES
18 HMGCL HMGCL HMGCL 999 0.17 0.54 YES
19 PHYH PHYH PHYH 1001 0.17 0.56 YES
20 ACAA1 ACAA1 ACAA1 1045 0.16 0.57 YES
21 IDH2 IDH2 IDH2 1141 0.15 0.58 YES
22 PEX11A PEX11A PEX11A 1206 0.14 0.59 YES
23 BAAT BAAT BAAT 1234 0.14 0.6 YES
24 HACL1 HACL1 HACL1 1260 0.14 0.61 YES
25 CAT CAT CAT 1270 0.14 0.62 YES
26 CRAT CRAT CRAT 1360 0.13 0.63 YES
27 SCP2 SCP2 SCP2 1495 0.12 0.64 YES
28 PEX3 PEX3 PEX3 1598 0.12 0.64 YES
29 PEX7 PEX7 PEX7 1606 0.12 0.65 YES
30 ECH1 ECH1 ECH1 1608 0.12 0.66 YES
31 PEX26 PEX26 PEX26 1618 0.12 0.67 YES
32 NUDT12 NUDT12 NUDT12 1774 0.11 0.68 YES
33 ABCD3 ABCD3 ABCD3 1801 0.1 0.68 YES
34 IDH1 IDH1 IDH1 1826 0.1 0.69 YES
35 MVK MVK MVK 1839 0.1 0.7 YES
36 PRDX1 PRDX1 PRDX1 1846 0.1 0.71 YES
37 SOD2 SOD2 SOD2 2038 0.096 0.71 YES
38 ACOX3 ACOX3 ACOX3 2055 0.095 0.72 YES
39 HSD17B4 HSD17B4 HSD17B4 2162 0.09 0.72 YES
40 ACOX1 ACOX1 ACOX1 2276 0.087 0.72 YES
41 PEX11G PEX11G PEX11G 2350 0.084 0.72 YES
42 SOD1 SOD1 SOD1 2681 0.074 0.71 NO
43 PEX5 PEX5 PEX5 2809 0.07 0.71 NO
44 NUDT19 NUDT19 NUDT19 2891 0.068 0.72 NO
45 PRDX5 PRDX5 PRDX5 3308 0.058 0.7 NO
46 PECR PECR PECR 3451 0.054 0.69 NO
47 GSTK1 GSTK1 GSTK1 3724 0.049 0.68 NO
48 ABCD4 ABCD4 ABCD4 3745 0.048 0.69 NO
49 MPV17 MPV17 MPV17 3756 0.048 0.69 NO
50 ACOT8 ACOT8 ACOT8 3870 0.046 0.69 NO
51 PEX10 PEX10 PEX10 4020 0.043 0.68 NO
52 PEX19 PEX19 PEX19 4111 0.041 0.68 NO
53 PMVK PMVK PMVK 4231 0.039 0.68 NO
54 PEX13 PEX13 PEX13 4245 0.039 0.68 NO
55 ABCD1 ABCD1 ABCD1 4633 0.032 0.66 NO
56 PEX11B PEX11B PEX11B 4937 0.027 0.65 NO
57 PEX16 PEX16 PEX16 5126 0.024 0.64 NO
58 AGPS AGPS AGPS 5130 0.024 0.64 NO
59 GNPAT GNPAT GNPAT 5729 0.016 0.61 NO
60 PEX14 PEX14 PEX14 6773 0.0022 0.56 NO
61 ABCD2 ABCD2 ABCD2 6991 -0.00078 0.54 NO
62 AMACR AMACR AMACR 7125 -0.0026 0.54 NO
63 PEX2 PEX2 PEX2 7787 -0.011 0.5 NO
64 ACSL3 ACSL3 ACSL3 7903 -0.013 0.49 NO
65 SLC25A17 SLC25A17 SLC25A17 8177 -0.016 0.48 NO
66 PEX6 PEX6 PEX6 8368 -0.019 0.47 NO
67 ACSL5 ACSL5 ACSL5 8820 -0.026 0.45 NO
68 PEX12 PEX12 PEX12 8848 -0.026 0.45 NO
69 PXMP4 PXMP4 PXMP4 8889 -0.027 0.45 NO
70 ACSL6 ACSL6 ACSL6 9233 -0.032 0.43 NO
71 PEX1 PEX1 PEX1 9601 -0.037 0.42 NO
72 XDH XDH XDH 11181 -0.065 0.34 NO
73 CROT CROT CROT 12849 -0.1 0.25 NO
74 ACSL4 ACSL4 ACSL4 13116 -0.11 0.25 NO
75 FAR1 FAR1 FAR1 13506 -0.12 0.24 NO
76 NOS2 NOS2 NOS2 14254 -0.14 0.21 NO

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

Figure S42.  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 CITRATE CYCLE TCA CYCLE

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 PIPOX PIPOX PIPOX 15 0.76 0.14 YES
2 BBOX1 BBOX1 BBOX1 79 0.54 0.23 YES
3 ALDH1B1 ALDH1B1 ALDH1B1 238 0.38 0.29 YES
4 EHHADH EHHADH EHHADH 293 0.35 0.35 YES
5 ACAT1 ACAT1 ACAT1 619 0.23 0.38 YES
6 OGDHL OGDHL OGDHL 760 0.2 0.4 YES
7 ECHS1 ECHS1 ECHS1 865 0.18 0.43 YES
8 GCDH GCDH GCDH 932 0.18 0.46 YES
9 HADH HADH HADH 986 0.17 0.49 YES
10 AADAT AADAT AADAT 1019 0.16 0.52 YES
11 ACAT2 ACAT2 ACAT2 1085 0.16 0.54 YES
12 ALDH7A1 ALDH7A1 ALDH7A1 1108 0.16 0.57 YES
13 ALDH2 ALDH2 ALDH2 1187 0.15 0.59 YES
14 ALDH9A1 ALDH9A1 ALDH9A1 1229 0.14 0.62 YES
15 TMLHE TMLHE TMLHE 1444 0.13 0.63 YES
16 ALDH3A2 ALDH3A2 ALDH3A2 1903 0.1 0.62 YES
17 OGDH OGDH OGDH 2155 0.09 0.62 YES
18 PLOD1 PLOD1 PLOD1 2269 0.087 0.63 YES
19 DLST DLST DLST 2319 0.085 0.64 YES
20 HADHA HADHA HADHA 2343 0.085 0.66 YES
21 AASDHPPT AASDHPPT AASDHPPT 3837 0.046 0.58 NO
22 AASS AASS AASS 6086 0.011 0.46 NO
23 PLOD3 PLOD3 PLOD3 6205 0.0095 0.46 NO
24 SETDB2 SETDB2 SETDB2 6371 0.0074 0.45 NO
25 EHMT2 EHMT2 EHMT2 7914 -0.013 0.36 NO
26 NSD1 NSD1 NSD1 8168 -0.016 0.35 NO
27 SETDB1 SETDB1 SETDB1 8221 -0.017 0.35 NO
28 SETD7 SETD7 SETD7 8248 -0.018 0.36 NO
29 AASDH AASDH AASDH 8495 -0.021 0.35 NO
30 SUV39H2 SUV39H2 SUV39H2 8592 -0.022 0.34 NO
31 SETD1A SETD1A SETD1A 8880 -0.027 0.33 NO
32 SUV39H1 SUV39H1 SUV39H1 9259 -0.032 0.32 NO
33 SETD2 SETD2 SETD2 9861 -0.042 0.29 NO
34 ASH1L ASH1L ASH1L 10031 -0.045 0.29 NO
35 PLOD2 PLOD2 PLOD2 10271 -0.048 0.29 NO
36 EHMT1 EHMT1 EHMT1 11305 -0.067 0.24 NO
37 SUV420H1 SUV420H1 SUV420H1 11400 -0.069 0.25 NO
38 SETMAR SETMAR SETMAR 12108 -0.084 0.22 NO
39 WHSC1 WHSC1 WHSC1 12161 -0.085 0.24 NO
40 DOT1L DOT1L DOT1L 12230 -0.087 0.25 NO
41 SUV420H2 SUV420H2 SUV420H2 12238 -0.087 0.26 NO
42 WHSC1L1 WHSC1L1 WHSC1L1 12355 -0.09 0.28 NO
43 SETD8 SETD8 SETD8 12570 -0.094 0.28 NO
44 SETD1B SETD1B SETD1B 13493 -0.12 0.25 NO

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

Figure S44.  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 PENTOSE PHOSPHATE 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 MARS2 MARS2 MARS2 1425 0.13 -0.017 YES
2 WARS2 WARS2 WARS2 1718 0.11 0.02 YES
3 EARS2 EARS2 EARS2 1767 0.11 0.07 YES
4 LARS2 LARS2 LARS2 1836 0.1 0.12 YES
5 DARS2 DARS2 DARS2 1923 0.1 0.16 YES
6 PARS2 PARS2 PARS2 1966 0.098 0.21 YES
7 FARS2 FARS2 FARS2 2062 0.095 0.25 YES
8 AARS AARS AARS 2444 0.081 0.27 YES
9 TARS2 TARS2 TARS2 2485 0.08 0.3 YES
10 NARS NARS NARS 2822 0.07 0.32 YES
11 YARS YARS YARS 2840 0.07 0.35 YES
12 IARS2 IARS2 IARS2 2905 0.067 0.38 YES
13 NARS2 NARS2 NARS2 2933 0.067 0.41 YES
14 SEPSECS SEPSECS SEPSECS 3029 0.064 0.44 YES
15 YARS2 YARS2 YARS2 3144 0.062 0.46 YES
16 IARS IARS IARS 3268 0.058 0.48 YES
17 HARS2 HARS2 HARS2 3681 0.05 0.49 YES
18 SARS SARS SARS 3961 0.044 0.49 YES
19 MTFMT MTFMT MTFMT 4126 0.041 0.5 YES
20 RARS RARS RARS 4131 0.041 0.52 YES
21 KARS KARS KARS 4167 0.04 0.54 YES
22 RARS2 RARS2 RARS2 4316 0.038 0.55 YES
23 TARS TARS TARS 4351 0.037 0.57 YES
24 VARS VARS VARS 4466 0.035 0.58 YES
25 FARSA FARSA FARSA 4724 0.03 0.58 YES
26 QARS QARS QARS 4819 0.029 0.59 YES
27 EPRS EPRS EPRS 4918 0.027 0.6 YES
28 GARS GARS GARS 4922 0.027 0.61 YES
29 FARSB FARSB FARSB 4938 0.027 0.62 YES
30 HARS HARS HARS 4941 0.027 0.63 YES
31 CARS2 CARS2 CARS2 4949 0.027 0.65 YES
32 WARS WARS WARS 5017 0.026 0.66 YES
33 VARS2 VARS2 VARS2 5021 0.026 0.67 YES
34 PSTK PSTK PSTK 5023 0.026 0.68 YES
35 SARS2 SARS2 SARS2 5135 0.024 0.69 YES
36 DARS DARS DARS 5519 0.019 0.67 NO
37 TARSL2 TARSL2 TARSL2 5577 0.018 0.68 NO
38 CARS CARS CARS 6081 0.011 0.66 NO
39 LARS LARS LARS 6466 0.0062 0.64 NO
40 AARS2 AARS2 AARS2 7069 -0.0018 0.6 NO
41 MARS MARS MARS 7362 -0.0056 0.59 NO

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

Figure S46.  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 PENTOSE AND GLUCURONATE INTERCONVERSIONS

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 TPD52L1 TPD52L1 TPD52L1 824 0.19 0.011 YES
2 FTL FTL FTL 832 0.19 0.067 YES
3 AP1M2 AP1M2 AP1M2 990 0.17 0.11 YES
4 SH3GL2 SH3GL2 SH3GL2 991 0.17 0.16 YES
5 DNAJC6 DNAJC6 DNAJC6 1152 0.15 0.19 YES
6 SH3D19 SH3D19 SH3D19 1843 0.1 0.19 YES
7 YIPF6 YIPF6 YIPF6 2076 0.094 0.2 YES
8 IGF2R IGF2R IGF2R 2090 0.093 0.23 YES
9 AP1S1 AP1S1 AP1S1 2310 0.086 0.24 YES
10 SNX5 SNX5 SNX5 2379 0.083 0.26 YES
11 HSPA8 HSPA8 HSPA8 2390 0.083 0.29 YES
12 SNX2 SNX2 SNX2 2410 0.082 0.31 YES
13 FTH1 FTH1 FTH1 2892 0.068 0.3 YES
14 SNX9 SNX9 SNX9 3077 0.063 0.31 YES
15 GAK GAK GAK 3112 0.062 0.33 YES
16 AP1M1 AP1M1 AP1M1 3123 0.062 0.35 YES
17 DTNBP1 DTNBP1 DTNBP1 3186 0.06 0.36 YES
18 PLDN PLDN PLDN 3252 0.059 0.38 YES
19 TGOLN2 TGOLN2 TGOLN2 3267 0.058 0.39 YES
20 CLTC CLTC CLTC 3355 0.056 0.4 YES
21 AP3S1 AP3S1 AP3S1 3373 0.056 0.42 YES
22 GNS GNS GNS 3476 0.054 0.43 YES
23 VAMP7 VAMP7 VAMP7 3522 0.053 0.44 YES
24 RAB5C RAB5C RAB5C 3631 0.051 0.45 YES
25 AP1G1 AP1G1 AP1G1 3718 0.049 0.46 YES
26 BLOC1S1 BLOC1S1 BLOC1S1 3964 0.044 0.46 YES
27 STX4 STX4 STX4 3973 0.043 0.47 YES
28 AP1B1 AP1B1 AP1B1 4012 0.043 0.48 YES
29 VAMP8 VAMP8 VAMP8 4017 0.043 0.5 YES
30 DNASE2 DNASE2 DNASE2 4142 0.041 0.5 YES
31 NAPA NAPA NAPA 4246 0.039 0.51 YES
32 SNAP23 SNAP23 SNAP23 4321 0.038 0.52 YES
33 AP3B1 AP3B1 AP3B1 4496 0.034 0.52 YES
34 CLTA CLTA CLTA 4596 0.032 0.52 YES
35 TBC1D8B TBC1D8B TBC1D8B 4701 0.031 0.52 YES
36 NECAP1 NECAP1 NECAP1 4862 0.028 0.52 NO
37 PICALM PICALM PICALM 6078 0.011 0.46 NO
38 M6PR M6PR M6PR 6412 0.0069 0.44 NO
39 CNO CNO CNO 6656 0.0037 0.43 NO
40 PUM1 PUM1 PUM1 6745 0.0026 0.42 NO
41 ARRB1 ARRB1 ARRB1 6787 0.0019 0.42 NO
42 CTSZ CTSZ CTSZ 7208 -0.0038 0.4 NO
43 AP1S2 AP1S2 AP1S2 7295 -0.0046 0.4 NO
44 ARF1 ARF1 ARF1 7755 -0.011 0.38 NO
45 SNAPIN SNAPIN SNAPIN 8001 -0.014 0.36 NO
46 AP4E1 AP4E1 AP4E1 8057 -0.015 0.37 NO
47 TPD52 TPD52 TPD52 8614 -0.023 0.34 NO
48 SORT1 SORT1 SORT1 8672 -0.024 0.35 NO
49 OCRL OCRL OCRL 8765 -0.025 0.35 NO
50 GBF1 GBF1 GBF1 8768 -0.025 0.36 NO
51 BLOC1S3 BLOC1S3 BLOC1S3 9053 -0.029 0.35 NO
52 TXNDC5 TXNDC5 TXNDC5 9108 -0.03 0.35 NO
53 PIK3C2A PIK3C2A PIK3C2A 9743 -0.04 0.33 NO
54 VAMP2 VAMP2 VAMP2 10231 -0.048 0.32 NO
55 CPD CPD CPD 10288 -0.049 0.33 NO
56 DNM2 DNM2 DNM2 10792 -0.057 0.32 NO
57 AP4B1 AP4B1 AP4B1 10822 -0.058 0.33 NO
58 HIP1R HIP1R HIP1R 12115 -0.084 0.29 NO
59 TFRC TFRC TFRC 14043 -0.14 0.22 NO

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

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MARS2 MARS2 MARS2 1425 0.13 -0.021 YES
2 WARS2 WARS2 WARS2 1718 0.11 0.012 YES
3 PPA2 PPA2 PPA2 1742 0.11 0.06 YES
4 EARS2 EARS2 EARS2 1767 0.11 0.11 YES
5 LARS2 LARS2 LARS2 1836 0.1 0.15 YES
6 DARS2 DARS2 DARS2 1923 0.1 0.19 YES
7 PARS2 PARS2 PARS2 1966 0.098 0.23 YES
8 FARS2 FARS2 FARS2 2062 0.095 0.27 YES
9 AIMP2 AIMP2 AIMP2 2067 0.095 0.32 YES
10 PPA1 PPA1 PPA1 2180 0.09 0.35 YES
11 AARS AARS AARS 2444 0.081 0.37 YES
12 TARS2 TARS2 TARS2 2485 0.08 0.41 YES
13 NARS NARS NARS 2822 0.07 0.42 YES
14 YARS YARS YARS 2840 0.07 0.45 YES
15 IARS2 IARS2 IARS2 2905 0.067 0.48 YES
16 NARS2 NARS2 NARS2 2933 0.067 0.51 YES
17 YARS2 YARS2 YARS2 3144 0.062 0.52 YES
18 IARS IARS IARS 3268 0.058 0.54 YES
19 HARS2 HARS2 HARS2 3681 0.05 0.54 YES
20 SARS SARS SARS 3961 0.044 0.55 YES
21 RARS RARS RARS 4131 0.041 0.56 YES
22 KARS KARS KARS 4167 0.04 0.57 YES
23 RARS2 RARS2 RARS2 4316 0.038 0.58 YES
24 TARS TARS TARS 4351 0.037 0.6 YES
25 VARS VARS VARS 4466 0.035 0.6 YES
26 FARSA FARSA FARSA 4724 0.03 0.6 YES
27 QARS QARS QARS 4819 0.029 0.61 YES
28 EPRS EPRS EPRS 4918 0.027 0.62 YES
29 GARS GARS GARS 4922 0.027 0.63 YES
30 FARSB FARSB FARSB 4938 0.027 0.64 YES
31 HARS HARS HARS 4941 0.027 0.66 YES
32 CARS2 CARS2 CARS2 4949 0.027 0.67 YES
33 WARS WARS WARS 5017 0.026 0.68 YES
34 VARS2 VARS2 VARS2 5021 0.026 0.69 YES
35 SARS2 SARS2 SARS2 5135 0.024 0.69 YES
36 DARS DARS DARS 5519 0.019 0.68 NO
37 CARS CARS CARS 6081 0.011 0.65 NO
38 LARS LARS LARS 6466 0.0062 0.63 NO
39 AIMP1 AIMP1 AIMP1 6551 0.0051 0.63 NO
40 AARS2 AARS2 AARS2 7069 -0.0018 0.6 NO
41 EEF1E1 EEF1E1 EEF1E1 7337 -0.0052 0.59 NO
42 MARS MARS MARS 7362 -0.0056 0.59 NO

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

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

genes ES table in pathway: KEGG FATTY ACID METABOLISM

Table 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 PKLR PKLR PKLR 9 0.8 0.13 YES
2 PCK1 PCK1 PCK1 56 0.6 0.22 YES
3 ALDH1B1 ALDH1B1 ALDH1B1 238 0.38 0.27 YES
4 LDHD LDHD LDHD 242 0.37 0.33 YES
5 PC PC PC 263 0.36 0.39 YES
6 ME1 ME1 ME1 333 0.32 0.44 YES
7 ACOT12 ACOT12 ACOT12 444 0.27 0.47 YES
8 PCK2 PCK2 PCK2 465 0.26 0.51 YES
9 ACAT1 ACAT1 ACAT1 619 0.23 0.54 YES
10 GRHPR GRHPR GRHPR 814 0.19 0.56 YES
11 LDHC LDHC LDHC 857 0.19 0.59 YES
12 HAGH HAGH HAGH 945 0.17 0.61 YES
13 ACAT2 ACAT2 ACAT2 1085 0.16 0.63 YES
14 HAGHL HAGHL HAGHL 1106 0.16 0.65 YES
15 ALDH7A1 ALDH7A1 ALDH7A1 1108 0.16 0.68 YES
16 ALDH2 ALDH2 ALDH2 1187 0.15 0.7 YES
17 ALDH9A1 ALDH9A1 ALDH9A1 1229 0.14 0.72 YES
18 MDH1 MDH1 MDH1 1265 0.14 0.74 YES
19 ALDH3A2 ALDH3A2 ALDH3A2 1903 0.1 0.72 YES
20 ACSS2 ACSS2 ACSS2 1945 0.099 0.73 YES
21 ACSS1 ACSS1 ACSS1 1956 0.099 0.75 YES
22 DLAT DLAT DLAT 2191 0.089 0.75 YES
23 LDHB LDHB LDHB 2216 0.088 0.76 YES
24 PDHA1 PDHA1 PDHA1 2599 0.077 0.75 YES
25 MDH2 MDH2 MDH2 2641 0.075 0.76 YES
26 DLD DLD DLD 2877 0.068 0.76 YES
27 PDHB PDHB PDHB 2914 0.067 0.77 YES
28 ME2 ME2 ME2 4399 0.036 0.69 NO
29 ME3 ME3 ME3 4579 0.033 0.69 NO
30 ACACB ACACB ACACB 6020 0.012 0.61 NO
31 AKR1B1 AKR1B1 AKR1B1 6576 0.0048 0.58 NO
32 PKM2 PKM2 PKM2 6874 0.00084 0.56 NO
33 LDHA LDHA LDHA 7973 -0.014 0.5 NO
34 ACYP2 ACYP2 ACYP2 8159 -0.016 0.5 NO
35 ACACA ACACA ACACA 8332 -0.019 0.49 NO
36 GLO1 GLO1 GLO1 8936 -0.027 0.46 NO
37 LDHAL6B LDHAL6B LDHAL6B 11228 -0.066 0.34 NO
38 ACYP1 ACYP1 ACYP1 11262 -0.066 0.35 NO
39 LDHAL6A LDHAL6A LDHAL6A 14291 -0.15 0.21 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 FATTY ACID METABOLISM.

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

genes ES table in pathway: KEGG STEROID HORMONE BIOSYNTHESIS

Table 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 AOX1 AOX1 AOX1 135 0.47 0.056 YES
2 ABAT ABAT ABAT 155 0.45 0.12 YES
3 ALDH6A1 ALDH6A1 ALDH6A1 161 0.44 0.18 YES
4 ALDH1B1 ALDH1B1 ALDH1B1 238 0.38 0.22 YES
5 EHHADH EHHADH EHHADH 293 0.35 0.27 YES
6 ACAT1 ACAT1 ACAT1 619 0.23 0.28 YES
7 PCCA PCCA PCCA 664 0.22 0.31 YES
8 OXCT1 OXCT1 OXCT1 773 0.2 0.33 YES
9 HIBCH HIBCH HIBCH 836 0.19 0.35 YES
10 ACADM ACADM ACADM 837 0.19 0.38 YES
11 ACADS ACADS ACADS 846 0.19 0.4 YES
12 ECHS1 ECHS1 ECHS1 865 0.18 0.43 YES
13 HMGCS2 HMGCS2 HMGCS2 915 0.18 0.45 YES
14 MCCC1 MCCC1 MCCC1 930 0.18 0.47 YES
15 HADH HADH HADH 986 0.17 0.49 YES
16 HMGCL HMGCL HMGCL 999 0.17 0.52 YES
17 ACAA1 ACAA1 ACAA1 1045 0.16 0.53 YES
18 ACAA2 ACAA2 ACAA2 1048 0.16 0.56 YES
19 AUH AUH AUH 1060 0.16 0.58 YES
20 BCAT2 BCAT2 BCAT2 1066 0.16 0.6 YES
21 ACAT2 ACAT2 ACAT2 1085 0.16 0.62 YES
22 ALDH7A1 ALDH7A1 ALDH7A1 1108 0.16 0.64 YES
23 ACADSB ACADSB ACADSB 1111 0.16 0.66 YES
24 PCCB PCCB PCCB 1143 0.15 0.68 YES
25 ALDH2 ALDH2 ALDH2 1187 0.15 0.7 YES
26 ALDH9A1 ALDH9A1 ALDH9A1 1229 0.14 0.72 YES
27 MUT MUT MUT 1277 0.14 0.73 YES
28 MCCC2 MCCC2 MCCC2 1460 0.12 0.74 YES
29 MCEE MCEE MCEE 1487 0.12 0.75 YES
30 IL4I1 IL4I1 IL4I1 1663 0.11 0.76 YES
31 HIBADH HIBADH HIBADH 1724 0.11 0.77 YES
32 BCAT1 BCAT1 BCAT1 1772 0.11 0.78 YES
33 IVD IVD IVD 1787 0.11 0.8 YES
34 ACAD8 ACAD8 ACAD8 1854 0.1 0.81 YES
35 ALDH3A2 ALDH3A2 ALDH3A2 1903 0.1 0.82 YES
36 DBT DBT DBT 1918 0.1 0.83 YES
37 HADHB HADHB HADHB 2339 0.085 0.82 YES
38 HADHA HADHA HADHA 2343 0.085 0.83 YES
39 BCKDHA BCKDHA BCKDHA 2462 0.081 0.83 YES
40 DLD DLD DLD 2877 0.068 0.82 NO
41 BCKDHB BCKDHB BCKDHB 2959 0.066 0.82 NO
42 HSD17B10 HSD17B10 HSD17B10 3187 0.06 0.82 NO
43 OXCT2 OXCT2 OXCT2 5028 0.026 0.72 NO
44 HMGCS1 HMGCS1 HMGCS1 6712 0.0031 0.63 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 STEROID HORMONE BIOSYNTHESIS.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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 TPD52L1 TPD52L1 TPD52L1 824 0.19 0.014 YES
2 FTL FTL FTL 832 0.19 0.074 YES
3 AP1M2 AP1M2 AP1M2 990 0.17 0.12 YES
4 SH3GL2 SH3GL2 SH3GL2 991 0.17 0.17 YES
5 DNAJC6 DNAJC6 DNAJC6 1152 0.15 0.21 YES
6 SH3D19 SH3D19 SH3D19 1843 0.1 0.21 YES
7 YIPF6 YIPF6 YIPF6 2076 0.094 0.22 YES
8 IGF2R IGF2R IGF2R 2090 0.093 0.25 YES
9 AP1S1 AP1S1 AP1S1 2310 0.086 0.27 YES
10 SNX5 SNX5 SNX5 2379 0.083 0.29 YES
11 HSPA8 HSPA8 HSPA8 2390 0.083 0.32 YES
12 SNX2 SNX2 SNX2 2410 0.082 0.34 YES
13 FTH1 FTH1 FTH1 2892 0.068 0.34 YES
14 SNX9 SNX9 SNX9 3077 0.063 0.34 YES
15 GAK GAK GAK 3112 0.062 0.36 YES
16 AP1M1 AP1M1 AP1M1 3123 0.062 0.38 YES
17 DTNBP1 DTNBP1 DTNBP1 3186 0.06 0.4 YES
18 PLDN PLDN PLDN 3252 0.059 0.41 YES
19 TGOLN2 TGOLN2 TGOLN2 3267 0.058 0.43 YES
20 CLTC CLTC CLTC 3355 0.056 0.44 YES
21 AP3S1 AP3S1 AP3S1 3373 0.056 0.46 YES
22 VAMP7 VAMP7 VAMP7 3522 0.053 0.47 YES
23 RAB5C RAB5C RAB5C 3631 0.051 0.48 YES
24 AP1G1 AP1G1 AP1G1 3718 0.049 0.49 YES
25 BLOC1S1 BLOC1S1 BLOC1S1 3964 0.044 0.49 YES
26 AP1B1 AP1B1 AP1B1 4012 0.043 0.5 YES
27 VAMP8 VAMP8 VAMP8 4017 0.043 0.51 YES
28 NAPA NAPA NAPA 4246 0.039 0.51 YES
29 AP3B1 AP3B1 AP3B1 4496 0.034 0.51 YES
30 CLTA CLTA CLTA 4596 0.032 0.52 YES
31 TBC1D8B TBC1D8B TBC1D8B 4701 0.031 0.52 YES
32 NECAP1 NECAP1 NECAP1 4862 0.028 0.52 NO
33 PICALM PICALM PICALM 6078 0.011 0.46 NO
34 CNO CNO CNO 6656 0.0037 0.42 NO
35 PUM1 PUM1 PUM1 6745 0.0026 0.42 NO
36 ARRB1 ARRB1 ARRB1 6787 0.0019 0.42 NO
37 AP1S2 AP1S2 AP1S2 7295 -0.0046 0.39 NO
38 ARF1 ARF1 ARF1 7755 -0.011 0.37 NO
39 SNAPIN SNAPIN SNAPIN 8001 -0.014 0.36 NO
40 AP4E1 AP4E1 AP4E1 8057 -0.015 0.36 NO
41 TPD52 TPD52 TPD52 8614 -0.023 0.34 NO
42 SORT1 SORT1 SORT1 8672 -0.024 0.34 NO
43 OCRL OCRL OCRL 8765 -0.025 0.34 NO
44 BLOC1S3 BLOC1S3 BLOC1S3 9053 -0.029 0.34 NO
45 TXNDC5 TXNDC5 TXNDC5 9108 -0.03 0.34 NO
46 PIK3C2A PIK3C2A PIK3C2A 9743 -0.04 0.32 NO
47 VAMP2 VAMP2 VAMP2 10231 -0.048 0.31 NO
48 CPD CPD CPD 10288 -0.049 0.32 NO
49 DNM2 DNM2 DNM2 10792 -0.057 0.31 NO
50 AP4B1 AP4B1 AP4B1 10822 -0.058 0.33 NO
51 HIP1R HIP1R HIP1R 12115 -0.084 0.28 NO
52 TFRC TFRC TFRC 14043 -0.14 0.22 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 OXIDATIVE PHOSPHORYLATION.

Figure S56.  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 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 QPRT QPRT QPRT 66 0.57 0.11 YES
2 ENPP1 ENPP1 ENPP1 97 0.52 0.21 YES
3 SLC23A1 SLC23A1 SLC23A1 337 0.32 0.26 YES
4 ACP5 ACP5 ACP5 359 0.31 0.32 YES
5 PANK1 PANK1 PANK1 451 0.27 0.37 YES
6 SLC19A3 SLC19A3 SLC19A3 663 0.22 0.4 YES
7 CYB5A CYB5A CYB5A 901 0.18 0.42 YES
8 MTHFD1 MTHFD1 MTHFD1 1010 0.17 0.45 YES
9 SHMT1 SHMT1 SHMT1 1107 0.16 0.47 YES
10 PNPO PNPO PNPO 1310 0.14 0.49 YES
11 MTHFR MTHFR MTHFR 1352 0.13 0.51 YES
12 GPHN GPHN GPHN 1463 0.12 0.53 YES
13 PANK3 PANK3 PANK3 1838 0.1 0.53 YES
14 PPCS PPCS PPCS 1938 0.099 0.54 YES
15 GSTO1 GSTO1 GSTO1 2243 0.088 0.54 YES
16 RFK RFK RFK 2512 0.079 0.54 YES
17 NMNAT1 NMNAT1 NMNAT1 2626 0.076 0.55 YES
18 NFS1 NFS1 NFS1 2638 0.075 0.57 YES
19 DHFR DHFR DHFR 2703 0.074 0.58 YES
20 SLC46A1 SLC46A1 SLC46A1 2770 0.072 0.59 YES
21 MOCS2 MOCS2 MOCS2 2991 0.065 0.59 YES
22 MOCS3 MOCS3 MOCS3 3040 0.064 0.6 YES
23 THTPA THTPA THTPA 3168 0.061 0.6 YES
24 SLC25A16 SLC25A16 SLC25A16 3315 0.058 0.61 YES
25 AASDHPPT AASDHPPT AASDHPPT 3837 0.046 0.59 NO
26 FLAD1 FLAD1 FLAD1 3948 0.044 0.59 NO
27 COASY COASY COASY 4081 0.042 0.59 NO
28 MOCS1 MOCS1 MOCS1 4505 0.034 0.57 NO
29 FPGS FPGS FPGS 4769 0.03 0.56 NO
30 NADK NADK NADK 4886 0.028 0.56 NO
31 NMNAT3 NMNAT3 NMNAT3 5447 0.02 0.54 NO
32 FASN FASN FASN 5454 0.02 0.54 NO
33 SLC25A32 SLC25A32 SLC25A32 5844 0.014 0.52 NO
34 TPK1 TPK1 TPK1 5969 0.012 0.52 NO
35 SLC19A1 SLC19A1 SLC19A1 6142 0.01 0.51 NO
36 PANK2 PANK2 PANK2 6549 0.0051 0.49 NO
37 MOCOS MOCOS MOCOS 6744 0.0026 0.48 NO
38 PPCDC PPCDC PPCDC 7496 -0.0073 0.44 NO
39 PDXK PDXK PDXK 7749 -0.011 0.42 NO
40 SLC19A2 SLC19A2 SLC19A2 8002 -0.014 0.41 NO
41 PANK4 PANK4 PANK4 8436 -0.02 0.39 NO
42 SLC5A6 SLC5A6 SLC5A6 8547 -0.022 0.39 NO
43 NADSYN1 NADSYN1 NADSYN1 8551 -0.022 0.4 NO
44 CYB5R3 CYB5R3 CYB5R3 8729 -0.024 0.39 NO
45 GSTO2 GSTO2 GSTO2 8794 -0.025 0.39 NO
46 NAMPT NAMPT NAMPT 10563 -0.053 0.3 NO
47 SLC2A1 SLC2A1 SLC2A1 10855 -0.058 0.3 NO
48 SLC23A2 SLC23A2 SLC23A2 12709 -0.098 0.22 NO
49 NMNAT2 NMNAT2 NMNAT2 15415 -0.19 0.1 NO
50 SLC2A3 SLC2A3 SLC2A3 15689 -0.21 0.13 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 PYRIMIDINE METABOLISM.

Figure S58.  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 ALANINE ASPARTATE AND GLUTAMATE 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 PCK1 PCK1 PCK1 56 0.6 0.15 YES
2 PC PC PC 263 0.36 0.24 YES
3 PCK2 PCK2 PCK2 465 0.26 0.29 YES
4 OGDHL OGDHL OGDHL 760 0.2 0.33 YES
5 ACO1 ACO1 ACO1 1088 0.16 0.35 YES
6 SUCLG2 SUCLG2 SUCLG2 1118 0.16 0.39 YES
7 IDH2 IDH2 IDH2 1141 0.15 0.43 YES
8 SDHB SDHB SDHB 1174 0.15 0.47 YES
9 ACO2 ACO2 ACO2 1251 0.14 0.5 YES
10 MDH1 MDH1 MDH1 1265 0.14 0.53 YES
11 SUCLG1 SUCLG1 SUCLG1 1420 0.13 0.56 YES
12 SDHD SDHD SDHD 1587 0.12 0.58 YES
13 SDHA SDHA SDHA 1653 0.11 0.61 YES
14 IDH1 IDH1 IDH1 1826 0.1 0.62 YES
15 FH FH FH 1922 0.1 0.64 YES
16 SDHC SDHC SDHC 1924 0.1 0.67 YES
17 OGDH OGDH OGDH 2155 0.09 0.68 YES
18 SUCLA2 SUCLA2 SUCLA2 2167 0.09 0.7 YES
19 DLAT DLAT DLAT 2191 0.089 0.72 YES
20 DLST DLST DLST 2319 0.085 0.74 YES
21 PDHA1 PDHA1 PDHA1 2599 0.077 0.74 YES
22 MDH2 MDH2 MDH2 2641 0.075 0.76 YES
23 IDH3B IDH3B IDH3B 2670 0.074 0.78 YES
24 DLD DLD DLD 2877 0.068 0.79 YES
25 PDHB PDHB PDHB 2914 0.067 0.8 YES
26 IDH3G IDH3G IDH3G 2997 0.065 0.81 YES
27 CS CS CS 3647 0.05 0.79 NO
28 ACLY ACLY ACLY 5702 0.016 0.68 NO
29 IDH3A IDH3A IDH3A 5710 0.016 0.68 NO

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

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus4 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG N GLYCAN BIOSYNTHESIS 46 genes.ES.table 0.43 1.5 0.09 0.14 0.96 0.22 0.23 0.17 0.095 0.001
KEGG O GLYCAN BIOSYNTHESIS 29 genes.ES.table 0.47 1.3 0.11 0.23 0.99 0.31 0.15 0.26 0.19 0
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE 25 genes.ES.table 0.49 1.3 0.16 0.23 0.99 0.56 0.34 0.37 0.19 0
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES 26 genes.ES.table 0.51 1.4 0.093 0.2 0.99 0.27 0.13 0.24 0.16 0
KEGG BASAL TRANSCRIPTION FACTORS 34 genes.ES.table 0.42 1.3 0.22 0.23 1 0.38 0.3 0.27 0.2 0
KEGG MAPK SIGNALING PATHWAY 243 genes.ES.table 0.45 1.6 0.002 0.13 0.83 0.28 0.18 0.23 0.066 0.007
KEGG ERBB SIGNALING PATHWAY 87 genes.ES.table 0.41 1.6 0.008 0.13 0.93 0.39 0.33 0.26 0.08 0.002
KEGG CALCIUM SIGNALING PATHWAY 166 genes.ES.table 0.57 1.6 0 0.13 0.87 0.37 0.16 0.31 0.073 0.004
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION 231 genes.ES.table 0.61 1.5 0.042 0.14 0.96 0.58 0.21 0.46 0.092 0.001
KEGG CHEMOKINE SIGNALING PATHWAY 183 genes.ES.table 0.55 1.5 0.093 0.16 0.98 0.43 0.22 0.34 0.11 0.001
genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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 CNTN1 CNTN1 CNTN1 4 0.83 0.099 YES
2 HEYL HEYL HEYL 520 0.46 0.12 YES
3 DLL1 DLL1 DLL1 662 0.42 0.17 YES
4 DLL4 DLL4 DLL4 1061 0.36 0.19 YES
5 MAML2 MAML2 MAML2 1207 0.34 0.22 YES
6 HEY1 HEY1 HEY1 1274 0.33 0.26 YES
7 HEY2 HEY2 HEY2 1646 0.29 0.27 YES
8 MAML3 MAML3 MAML3 1668 0.29 0.3 YES
9 DTX1 DTX1 DTX1 1965 0.26 0.32 YES
10 NEURL NEURL NEURL 2025 0.26 0.35 YES
11 ADAM10 ADAM10 ADAM10 2955 0.19 0.32 YES
12 HES1 HES1 HES1 3094 0.18 0.33 YES
13 ADAM17 ADAM17 ADAM17 3469 0.16 0.33 YES
14 JAG2 JAG2 JAG2 3546 0.16 0.34 YES
15 JAG1 JAG1 JAG1 3575 0.16 0.36 YES
16 HES5 HES5 HES5 3705 0.15 0.37 YES
17 MIB1 MIB1 MIB1 3756 0.15 0.39 YES
18 MAMLD1 MAMLD1 MAMLD1 3792 0.15 0.4 YES
19 HDAC4 HDAC4 HDAC4 3905 0.14 0.42 YES
20 ARRB1 ARRB1 ARRB1 3948 0.14 0.43 YES
21 TLE2 TLE2 TLE2 3990 0.14 0.44 YES
22 EP300 EP300 EP300 4158 0.14 0.45 YES
23 TLE3 TLE3 TLE3 4284 0.13 0.46 YES
24 FBXW7 FBXW7 FBXW7 4296 0.13 0.48 YES
25 HIF1A HIF1A HIF1A 4370 0.13 0.49 YES
26 HDAC1 HDAC1 HDAC1 4871 0.11 0.47 YES
27 MAML1 MAML1 MAML1 4880 0.11 0.48 YES
28 KAT2B KAT2B KAT2B 4885 0.11 0.5 YES
29 HDAC9 HDAC9 HDAC9 5126 0.1 0.5 YES
30 APH1B APH1B APH1B 5214 0.099 0.5 YES
31 NCOR2 NCOR2 NCOR2 5278 0.097 0.51 YES
32 DTX4 DTX4 DTX4 5516 0.09 0.51 NO
33 TLE4 TLE4 TLE4 5713 0.085 0.51 NO
34 HDAC2 HDAC2 HDAC2 5907 0.081 0.51 NO
35 NCOR1 NCOR1 NCOR1 6379 0.071 0.49 NO
36 CDK8 CDK8 CDK8 6649 0.065 0.48 NO
37 NCSTN NCSTN NCSTN 7098 0.056 0.46 NO
38 HDAC7 HDAC7 HDAC7 7254 0.053 0.46 NO
39 SNW1 SNW1 SNW1 7431 0.05 0.46 NO
40 RBPJ RBPJ RBPJ 7466 0.049 0.46 NO
41 CREBBP CREBBP CREBBP 7530 0.048 0.46 NO
42 TBL1X TBL1X TBL1X 7532 0.048 0.47 NO
43 TBL1XR1 TBL1XR1 TBL1XR1 7694 0.045 0.47 NO
44 CUL1 CUL1 CUL1 8271 0.036 0.44 NO
45 TLE1 TLE1 TLE1 8607 0.03 0.42 NO
46 CCNC CCNC CCNC 8687 0.029 0.42 NO
47 MYC MYC MYC 8752 0.028 0.42 NO
48 PSEN1 PSEN1 PSEN1 8850 0.026 0.42 NO
49 DTX2 DTX2 DTX2 8957 0.025 0.42 NO
50 APH1A APH1A APH1A 9856 0.01 0.37 NO
51 DNER DNER DNER 10115 0.006 0.35 NO
52 RPS27A RPS27A RPS27A 10303 0.0027 0.34 NO
53 SKP1 SKP1 SKP1 10565 -0.0014 0.33 NO
54 RBX1 RBX1 RBX1 10746 -0.0046 0.32 NO
55 HDAC3 HDAC3 HDAC3 11055 -0.0098 0.3 NO
56 PSEN2 PSEN2 PSEN2 11247 -0.013 0.3 NO
57 HDAC5 HDAC5 HDAC5 11427 -0.016 0.29 NO
58 UBA52 UBA52 UBA52 11621 -0.019 0.28 NO
59 NUMB NUMB NUMB 11839 -0.023 0.27 NO
60 MIB2 MIB2 MIB2 11916 -0.024 0.27 NO
61 ARRB2 ARRB2 ARRB2 12408 -0.034 0.24 NO
62 HDAC8 HDAC8 HDAC8 13460 -0.054 0.19 NO
63 PSENEN PSENEN PSENEN 14134 -0.07 0.16 NO
64 HDAC6 HDAC6 HDAC6 14241 -0.073 0.17 NO
65 HDAC11 HDAC11 HDAC11 15275 -0.1 0.12 NO
66 HDAC10 HDAC10 HDAC10 15560 -0.11 0.12 NO
67 KAT2A KAT2A KAT2A 16176 -0.14 0.1 NO

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

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

genes ES table in pathway: KEGG O GLYCAN BIOSYNTHESIS

Table 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 GLI2 GLI2 GLI2 6 0.83 0.017 YES
2 PDGFRA PDGFRA PDGFRA 20 0.76 0.033 YES
3 PTGS2 PTGS2 PTGS2 56 0.69 0.046 YES
4 FGF7 FGF7 FGF7 69 0.68 0.06 YES
5 LEF1 LEF1 LEF1 73 0.67 0.074 YES
6 FZD10 FZD10 FZD10 96 0.65 0.087 YES
7 RUNX1T1 RUNX1T1 RUNX1T1 169 0.59 0.095 YES
8 GLI1 GLI1 GLI1 183 0.58 0.11 YES
9 LAMC3 LAMC3 LAMC3 204 0.57 0.12 YES
10 WNT10A WNT10A WNT10A 213 0.57 0.13 YES
11 WNT4 WNT4 WNT4 236 0.55 0.14 YES
12 LAMB3 LAMB3 LAMB3 273 0.54 0.15 YES
13 IL6 IL6 IL6 280 0.53 0.16 YES
14 HGF HGF HGF 299 0.53 0.17 YES
15 PIK3CG PIK3CG PIK3CG 308 0.52 0.18 YES
16 CDKN2B CDKN2B CDKN2B 312 0.52 0.19 YES
17 PDGFRB PDGFRB PDGFRB 337 0.51 0.2 YES
18 FGF1 FGF1 FGF1 417 0.48 0.21 YES
19 RUNX1 RUNX1 RUNX1 458 0.48 0.22 YES
20 CCNA1 CCNA1 CCNA1 476 0.47 0.23 YES
21 IGF1 IGF1 IGF1 501 0.46 0.23 YES
22 TGFB2 TGFB2 TGFB2 588 0.44 0.24 YES
23 FGF18 FGF18 FGF18 601 0.44 0.25 YES
24 LAMA2 LAMA2 LAMA2 618 0.43 0.26 YES
25 MMP2 MMP2 MMP2 640 0.43 0.26 YES
26 WNT7A WNT7A WNT7A 654 0.42 0.27 YES
27 LAMA4 LAMA4 LAMA4 685 0.42 0.28 YES
28 DAPK2 DAPK2 DAPK2 693 0.42 0.29 YES
29 WNT9B WNT9B WNT9B 710 0.41 0.3 YES
30 FGF14 FGF14 FGF14 790 0.4 0.3 YES
31 WNT9A WNT9A WNT9A 844 0.39 0.3 YES
32 BRCA2 BRCA2 BRCA2 848 0.39 0.31 YES
33 FZD7 FZD7 FZD7 894 0.38 0.32 YES
34 RET RET RET 935 0.38 0.32 YES
35 FOS FOS FOS 974 0.37 0.33 YES
36 IL8 IL8 IL8 980 0.37 0.34 YES
37 LAMC2 LAMC2 LAMC2 1035 0.36 0.34 YES
38 TGFB3 TGFB3 TGFB3 1098 0.35 0.35 YES
39 HHIP HHIP HHIP 1138 0.35 0.35 YES
40 SLC2A1 SLC2A1 SLC2A1 1170 0.34 0.36 YES
41 ITGA2 ITGA2 ITGA2 1182 0.34 0.36 YES
42 ETS1 ETS1 ETS1 1199 0.34 0.37 YES
43 WNT6 WNT6 WNT6 1278 0.33 0.37 YES
44 RASSF5 RASSF5 RASSF5 1297 0.33 0.38 YES
45 TCF7 TCF7 TCF7 1311 0.32 0.39 YES
46 KIT KIT KIT 1332 0.32 0.39 YES
47 FN1 FN1 FN1 1446 0.31 0.39 YES
48 PTCH1 PTCH1 PTCH1 1451 0.31 0.4 YES
49 NOS2 NOS2 NOS2 1471 0.31 0.4 YES
50 DCC DCC DCC 1601 0.29 0.4 YES
51 TCF7L1 TCF7L1 TCF7L1 1727 0.28 0.4 YES
52 COL4A1 COL4A1 COL4A1 1802 0.28 0.4 YES
53 WNT7B WNT7B WNT7B 1898 0.27 0.4 YES
54 PRKCB PRKCB PRKCB 1909 0.27 0.41 YES
55 VEGFA VEGFA VEGFA 1922 0.26 0.41 YES
56 FASLG FASLG FASLG 1937 0.26 0.42 YES
57 MECOM MECOM MECOM 1962 0.26 0.42 YES
58 WNT8B WNT8B WNT8B 1967 0.26 0.43 YES
59 CDH1 CDH1 CDH1 1995 0.26 0.43 YES
60 PDGFB PDGFB PDGFB 2170 0.25 0.43 YES
61 CCNE2 CCNE2 CCNE2 2178 0.24 0.43 YES
62 NTRK1 NTRK1 NTRK1 2315 0.24 0.43 YES
63 CTNNA3 CTNNA3 CTNNA3 2346 0.23 0.43 YES
64 BIRC3 BIRC3 BIRC3 2414 0.23 0.44 YES
65 TGFB1 TGFB1 TGFB1 2461 0.22 0.44 YES
66 MAPK8 MAPK8 MAPK8 2503 0.22 0.44 YES
67 LAMA3 LAMA3 LAMA3 2527 0.22 0.44 YES
68 PGF PGF PGF 2613 0.21 0.44 YES
69 CCND1 CCND1 CCND1 2662 0.21 0.44 YES
70 TRAF3 TRAF3 TRAF3 2686 0.21 0.45 YES
71 EPAS1 EPAS1 EPAS1 2696 0.21 0.45 YES
72 COL4A6 COL4A6 COL4A6 2724 0.21 0.45 YES
73 PLCG2 PLCG2 PLCG2 2762 0.2 0.46 YES
74 RAC2 RAC2 RAC2 2846 0.2 0.46 YES
75 SKP2 SKP2 SKP2 2870 0.2 0.46 YES
76 TGFBR2 TGFBR2 TGFBR2 2889 0.2 0.46 YES
77 RXRG RXRG RXRG 2911 0.19 0.46 YES
78 VEGFC VEGFC VEGFC 2940 0.19 0.47 YES
79 NKX3-1 NKX3-1 NKX3-1 2957 0.19 0.47 YES
80 TGFA TGFA TGFA 3027 0.19 0.47 YES
81 PIK3CA PIK3CA PIK3CA 3044 0.19 0.47 YES
82 FOXO1 FOXO1 FOXO1 3062 0.18 0.48 YES
83 EGLN3 EGLN3 EGLN3 3084 0.18 0.48 YES
84 FLT3 FLT3 FLT3 3095 0.18 0.48 YES
85 ITGAV ITGAV ITGAV 3137 0.18 0.48 YES
86 BMP2 BMP2 BMP2 3187 0.18 0.49 YES
87 KITLG KITLG KITLG 3204 0.18 0.49 YES
88 FGF13 FGF13 FGF13 3249 0.17 0.49 YES
89 MMP1 MMP1 MMP1 3309 0.17 0.49 YES
90 DAPK1 DAPK1 DAPK1 3317 0.17 0.49 YES
91 PTCH2 PTCH2 PTCH2 3320 0.17 0.5 YES
92 FZD3 FZD3 FZD3 3445 0.16 0.49 YES
93 CSF1R CSF1R CSF1R 3509 0.16 0.49 YES
94 COL4A2 COL4A2 COL4A2 3595 0.16 0.49 YES
95 BMP4 BMP4 BMP4 3686 0.15 0.49 YES
96 COL4A4 COL4A4 COL4A4 3769 0.15 0.49 YES
97 PIAS2 PIAS2 PIAS2 3777 0.15 0.49 YES
98 MMP9 MMP9 MMP9 3797 0.15 0.49 YES
99 PIAS3 PIAS3 PIAS3 3821 0.15 0.5 YES
100 CBLB CBLB CBLB 3855 0.15 0.5 YES
101 ITGB1 ITGB1 ITGB1 3869 0.15 0.5 YES
102 PPARD PPARD PPARD 3924 0.14 0.5 YES
103 FGF12 FGF12 FGF12 3937 0.14 0.5 YES
104 PIK3R5 PIK3R5 PIK3R5 3956 0.14 0.5 YES
105 TRAF6 TRAF6 TRAF6 4078 0.14 0.5 YES
106 SHH SHH SHH 4079 0.14 0.5 YES
107 WNT3A WNT3A WNT3A 4083 0.14 0.51 YES
108 E2F2 E2F2 E2F2 4088 0.14 0.51 YES
109 TRAF5 TRAF5 TRAF5 4089 0.14 0.51 YES
110 EP300 EP300 EP300 4158 0.14 0.51 YES
111 RXRA RXRA RXRA 4184 0.13 0.51 YES
112 PIAS1 PIAS1 PIAS1 4266 0.13 0.51 YES
113 WNT1 WNT1 WNT1 4332 0.13 0.51 YES
114 HIF1A HIF1A HIF1A 4370 0.13 0.51 YES
115 EGFR EGFR EGFR 4399 0.13 0.51 YES
116 FZD6 FZD6 FZD6 4407 0.13 0.51 YES
117 WNT2 WNT2 WNT2 4437 0.12 0.52 YES
118 LAMC1 LAMC1 LAMC1 4484 0.12 0.52 YES
119 MSH6 MSH6 MSH6 4545 0.12 0.51 YES
120 FGF9 FGF9 FGF9 4559 0.12 0.52 YES
121 TGFBR1 TGFBR1 TGFBR1 4669 0.12 0.51 YES
122 WNT16 WNT16 WNT16 4689 0.12 0.51 YES
123 JUN JUN JUN 4720 0.12 0.51 YES
124 SPI1 SPI1 SPI1 4739 0.11 0.52 YES
125 VHL VHL VHL 4800 0.11 0.52 YES
126 MSH2 MSH2 MSH2 4855 0.11 0.51 YES
127 HDAC1 HDAC1 HDAC1 4871 0.11 0.52 YES
128 CBL CBL CBL 4887 0.11 0.52 YES
129 CDKN2A CDKN2A CDKN2A 4933 0.11 0.52 YES
130 RAD51 RAD51 RAD51 4945 0.11 0.52 YES
131 FAS FAS FAS 4980 0.11 0.52 YES
132 RALGDS RALGDS RALGDS 5030 0.1 0.52 YES
133 CSF2RA CSF2RA CSF2RA 5051 0.1 0.52 YES
134 TCF7L2 TCF7L2 TCF7L2 5069 0.1 0.52 YES
135 RB1 RB1 RB1 5073 0.1 0.52 YES
136 RALBP1 RALBP1 RALBP1 5139 0.1 0.52 NO
137 ARNT2 ARNT2 ARNT2 5185 0.1 0.52 NO
138 PTEN PTEN PTEN 5398 0.094 0.51 NO
139 SOS1 SOS1 SOS1 5404 0.094 0.51 NO
140 MAP2K1 MAP2K1 MAP2K1 5407 0.094 0.51 NO
141 CDKN1B CDKN1B CDKN1B 5434 0.093 0.52 NO
142 BRAF BRAF BRAF 5446 0.092 0.52 NO
143 CSF3R CSF3R CSF3R 5509 0.091 0.52 NO
144 CRKL CRKL CRKL 5518 0.09 0.52 NO
145 TPR TPR TPR 5618 0.088 0.51 NO
146 NFKB1 NFKB1 NFKB1 5646 0.087 0.51 NO
147 CTNNB1 CTNNB1 CTNNB1 5708 0.086 0.51 NO
148 FIGF FIGF FIGF 5756 0.084 0.51 NO
149 AKT3 AKT3 AKT3 5768 0.084 0.51 NO
150 PIK3CD PIK3CD PIK3CD 5819 0.083 0.51 NO
151 RARB RARB RARB 5821 0.083 0.51 NO
152 HDAC2 HDAC2 HDAC2 5907 0.081 0.51 NO
153 STAT1 STAT1 STAT1 5926 0.08 0.51 NO
154 FGF11 FGF11 FGF11 5930 0.08 0.51 NO
155 RARA RARA RARA 5955 0.08 0.51 NO
156 XIAP XIAP XIAP 5990 0.079 0.51 NO
157 NFKBIA NFKBIA NFKBIA 5995 0.079 0.51 NO
158 STAT3 STAT3 STAT3 6195 0.075 0.5 NO
159 JAK1 JAK1 JAK1 6235 0.074 0.5 NO
160 ITGA3 ITGA3 ITGA3 6247 0.074 0.5 NO
161 SMAD3 SMAD3 SMAD3 6276 0.073 0.5 NO
162 PIAS4 PIAS4 PIAS4 6319 0.072 0.5 NO
163 STK4 STK4 STK4 6321 0.072 0.5 NO
164 RELA RELA RELA 6404 0.07 0.5 NO
165 NRAS NRAS NRAS 6436 0.07 0.5 NO
166 SMAD2 SMAD2 SMAD2 6463 0.069 0.5 NO
167 CRK CRK CRK 6505 0.068 0.5 NO
168 IGF1R IGF1R IGF1R 6594 0.066 0.5 NO
169 APPL1 APPL1 APPL1 6621 0.066 0.5 NO
170 CTBP2 CTBP2 CTBP2 6826 0.061 0.49 NO
171 BIRC2 BIRC2 BIRC2 6870 0.06 0.48 NO
172 APC APC APC 6873 0.06 0.49 NO
173 CASP3 CASP3 CASP3 6967 0.059 0.48 NO
174 BCR BCR BCR 6968 0.059 0.48 NO
175 FGF20 FGF20 FGF20 7112 0.056 0.48 NO
176 AXIN2 AXIN2 AXIN2 7142 0.055 0.48 NO
177 CDK6 CDK6 CDK6 7150 0.055 0.48 NO
178 PTK2 PTK2 PTK2 7167 0.055 0.48 NO
179 NFKB2 NFKB2 NFKB2 7172 0.055 0.48 NO
180 PML PML PML 7185 0.054 0.48 NO
181 LAMA5 LAMA5 LAMA5 7211 0.054 0.48 NO
182 ARNT ARNT ARNT 7217 0.054 0.48 NO
183 GLI3 GLI3 GLI3 7257 0.053 0.48 NO
184 MAPK1 MAPK1 MAPK1 7286 0.052 0.48 NO
185 E2F3 E2F3 E2F3 7340 0.052 0.48 NO
186 CDK2 CDK2 CDK2 7456 0.049 0.47 NO
187 WNT10B WNT10B WNT10B 7490 0.049 0.47 NO
188 EGLN1 EGLN1 EGLN1 7493 0.049 0.47 NO
189 CDC42 CDC42 CDC42 7513 0.048 0.47 NO
190 SOS2 SOS2 SOS2 7514 0.048 0.47 NO
191 CREBBP CREBBP CREBBP 7530 0.048 0.47 NO
192 FGF2 FGF2 FGF2 7555 0.048 0.47 NO
193 FGFR1 FGFR1 FGFR1 7626 0.046 0.47 NO
194 JUP JUP JUP 7663 0.046 0.47 NO
195 CDKN1A CDKN1A CDKN1A 7688 0.045 0.47 NO
196 PIK3R1 PIK3R1 PIK3R1 7744 0.044 0.46 NO
197 ABL1 ABL1 ABL1 7762 0.044 0.46 NO
198 GSK3B GSK3B GSK3B 7929 0.041 0.46 NO
199 MSH3 MSH3 MSH3 7999 0.04 0.45 NO
200 AKT1 AKT1 AKT1 8012 0.04 0.45 NO
201 CKS1B CKS1B CKS1B 8068 0.039 0.45 NO
202 SMAD4 SMAD4 SMAD4 8086 0.039 0.45 NO
203 CCDC6 CCDC6 CCDC6 8175 0.038 0.45 NO
204 AR AR AR 8216 0.037 0.44 NO
205 CUL2 CUL2 CUL2 8227 0.037 0.44 NO
206 MTOR MTOR MTOR 8328 0.035 0.44 NO
207 TPM3 TPM3 TPM3 8430 0.033 0.44 NO
208 DVL1 DVL1 DVL1 8606 0.03 0.43 NO
209 RASSF1 RASSF1 RASSF1 8677 0.029 0.42 NO
210 PIK3CB PIK3CB PIK3CB 8701 0.028 0.42 NO
211 MYC MYC MYC 8752 0.028 0.42 NO
212 KLK3 KLK3 KLK3 8774 0.027 0.42 NO
213 ERBB2 ERBB2 ERBB2 8805 0.027 0.42 NO
214 LAMB2 LAMB2 LAMB2 8813 0.027 0.42 NO
215 PIK3R3 PIK3R3 PIK3R3 9002 0.024 0.41 NO
216 BID BID BID 9048 0.023 0.41 NO
217 MAPK10 MAPK10 MAPK10 9218 0.02 0.4 NO
218 HSP90B1 HSP90B1 HSP90B1 9228 0.02 0.4 NO
219 KRAS KRAS KRAS 9234 0.02 0.4 NO
220 BIRC5 BIRC5 BIRC5 9252 0.02 0.4 NO
221 SUFU SUFU SUFU 9367 0.018 0.39 NO
222 ARAF ARAF ARAF 9405 0.017 0.39 NO
223 MDM2 MDM2 MDM2 9442 0.017 0.39 NO
224 RHOA RHOA RHOA 9523 0.016 0.38 NO
225 RXRB RXRB RXRB 9531 0.015 0.38 NO
226 DVL3 DVL3 DVL3 9533 0.015 0.38 NO
227 FZD8 FZD8 FZD8 9581 0.014 0.38 NO
228 PDGFA PDGFA PDGFA 9608 0.014 0.38 NO
229 DAPK3 DAPK3 DAPK3 9615 0.014 0.38 NO
230 AKT2 AKT2 AKT2 9624 0.014 0.38 NO
231 TP53 TP53 TP53 9629 0.014 0.38 NO
232 RAF1 RAF1 RAF1 9646 0.014 0.38 NO
233 CCNE1 CCNE1 CCNE1 9848 0.01 0.37 NO
234 STAT5B STAT5B STAT5B 9877 0.01 0.37 NO
235 FLT3LG FLT3LG FLT3LG 9888 0.0098 0.37 NO
236 RALA RALA RALA 9938 0.0089 0.36 NO
237 HSP90AB1 HSP90AB1 HSP90AB1 9939 0.0089 0.36 NO
238 HSP90AA1 HSP90AA1 HSP90AA1 9952 0.0087 0.36 NO
239 NCOA4 NCOA4 NCOA4 10024 0.0075 0.36 NO
240 CTNNA1 CTNNA1 CTNNA1 10107 0.006 0.36 NO
241 IKBKB IKBKB IKBKB 10283 0.0031 0.34 NO
242 CASP9 CASP9 CASP9 10360 0.0016 0.34 NO
243 BCL2 BCL2 BCL2 10423 0.00083 0.34 NO
244 FGFR2 FGFR2 FGFR2 10500 -0.00067 0.33 NO
245 MLH1 MLH1 MLH1 10501 -0.00068 0.33 NO
246 ITGA6 ITGA6 ITGA6 10573 -0.0016 0.33 NO
247 GSTP1 GSTP1 GSTP1 10591 -0.0019 0.33 NO
248 MET MET MET 10604 -0.0021 0.33 NO
249 RBX1 RBX1 RBX1 10746 -0.0046 0.32 NO
250 IKBKG IKBKG IKBKG 10750 -0.0046 0.32 NO
251 MAPK3 MAPK3 MAPK3 10867 -0.0068 0.31 NO
252 MAX MAX MAX 10909 -0.0075 0.31 NO
253 EGLN2 EGLN2 EGLN2 10916 -0.0076 0.31 NO
254 FZD2 FZD2 FZD2 10951 -0.0082 0.31 NO
255 RALB RALB RALB 10976 -0.0087 0.31 NO
256 WNT5B WNT5B WNT5B 11042 -0.0096 0.3 NO
257 FZD4 FZD4 FZD4 11051 -0.0098 0.3 NO
258 WNT3 WNT3 WNT3 11076 -0.01 0.3 NO
259 CHUK CHUK CHUK 11102 -0.01 0.3 NO
260 CASP8 CASP8 CASP8 11193 -0.012 0.3 NO
261 ZBTB16 ZBTB16 ZBTB16 11291 -0.013 0.29 NO
262 TRAF1 TRAF1 TRAF1 11338 -0.014 0.29 NO
263 MAPK9 MAPK9 MAPK9 11373 -0.015 0.29 NO
264 STAT5A STAT5A STAT5A 11375 -0.015 0.29 NO
265 E2F1 E2F1 E2F1 11598 -0.019 0.28 NO
266 ITGA2B ITGA2B ITGA2B 11604 -0.019 0.28 NO
267 RAC1 RAC1 RAC1 11607 -0.019 0.28 NO
268 FZD5 FZD5 FZD5 11681 -0.02 0.27 NO
269 CBLC CBLC CBLC 11768 -0.022 0.27 NO
270 LAMB1 LAMB1 LAMB1 11824 -0.022 0.26 NO
271 MITF MITF MITF 11984 -0.026 0.26 NO
272 FZD9 FZD9 FZD9 11988 -0.026 0.26 NO
273 PIK3R2 PIK3R2 PIK3R2 12062 -0.027 0.25 NO
274 PRKCA PRKCA PRKCA 12074 -0.027 0.25 NO
275 CTBP1 CTBP1 CTBP1 12192 -0.03 0.25 NO
276 LAMB4 LAMB4 LAMB4 12540 -0.036 0.23 NO
277 TFG TFG TFG 12678 -0.039 0.22 NO
278 CDK4 CDK4 CDK4 12681 -0.039 0.22 NO
279 FADD FADD FADD 12695 -0.039 0.22 NO
280 HRAS HRAS HRAS 12706 -0.039 0.22 NO
281 BCL2L1 BCL2L1 BCL2L1 12774 -0.041 0.22 NO
282 DVL2 DVL2 DVL2 12897 -0.043 0.21 NO
283 PLCG1 PLCG1 PLCG1 13005 -0.045 0.21 NO
284 GRB2 GRB2 GRB2 13043 -0.046 0.21 NO
285 FZD1 FZD1 FZD1 13052 -0.046 0.21 NO
286 TCEB1 TCEB1 TCEB1 13084 -0.047 0.21 NO
287 BAX BAX BAX 13168 -0.049 0.2 NO
288 MAP2K2 MAP2K2 MAP2K2 13169 -0.049 0.2 NO
289 AXIN1 AXIN1 AXIN1 13270 -0.05 0.2 NO
290 FGFR3 FGFR3 FGFR3 13315 -0.052 0.2 NO
291 STK36 STK36 STK36 13327 -0.052 0.2 NO
292 TRAF4 TRAF4 TRAF4 13556 -0.056 0.19 NO
293 FGF5 FGF5 FGF5 13593 -0.057 0.19 NO
294 PAX8 PAX8 PAX8 13601 -0.057 0.19 NO
295 FGF22 FGF22 FGF22 13617 -0.058 0.19 NO
296 BAD BAD BAD 13942 -0.065 0.17 NO
297 WNT5A WNT5A WNT5A 14514 -0.081 0.14 NO
298 TRAF2 TRAF2 TRAF2 14583 -0.083 0.14 NO
299 WNT11 WNT11 WNT11 14618 -0.084 0.14 NO
300 PLD1 PLD1 PLD1 14682 -0.086 0.14 NO
301 PPARG PPARG PPARG 14913 -0.092 0.13 NO
302 WNT2B WNT2B WNT2B 14946 -0.093 0.13 NO
303 VEGFB VEGFB VEGFB 15263 -0.1 0.11 NO
304 CEBPA CEBPA CEBPA 15309 -0.1 0.11 NO
305 APC2 APC2 APC2 15344 -0.11 0.11 NO
306 FH FH FH 15579 -0.12 0.1 NO
307 CYCS CYCS CYCS 15724 -0.12 0.094 NO
308 FGF17 FGF17 FGF17 15844 -0.12 0.09 NO
309 SMO SMO SMO 16055 -0.14 0.081 NO
310 LAMA1 LAMA1 LAMA1 16177 -0.14 0.077 NO
311 TCEB2 TCEB2 TCEB2 16270 -0.15 0.075 NO
312 CTNNA2 CTNNA2 CTNNA2 16772 -0.18 0.051 NO
313 EGF EGF EGF 16931 -0.19 0.046 NO
314 PRKCG PRKCG PRKCG 16936 -0.19 0.05 NO
315 FGF8 FGF8 FGF8 17088 -0.21 0.046 NO
316 RAC3 RAC3 RAC3 17236 -0.23 0.042 NO

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

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

genes ES table in pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

Table 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 PIK3CG PIK3CG PIK3CG 308 0.52 0.057 YES
2 RUNX1 RUNX1 RUNX1 458 0.48 0.12 YES
3 TGFB2 TGFB2 TGFB2 588 0.44 0.17 YES
4 SHC3 SHC3 SHC3 660 0.42 0.23 YES
5 TGFB3 TGFB3 TGFB3 1098 0.35 0.25 YES
6 SHC4 SHC4 SHC4 1236 0.34 0.29 YES
7 MECOM MECOM MECOM 1962 0.26 0.29 YES
8 TGFB1 TGFB1 TGFB1 2461 0.22 0.29 YES
9 CCND1 CCND1 CCND1 2662 0.21 0.31 YES
10 TGFBR2 TGFBR2 TGFBR2 2889 0.2 0.33 YES
11 PIK3CA PIK3CA PIK3CA 3044 0.19 0.35 YES
12 CBLB CBLB CBLB 3855 0.15 0.32 YES
13 PIK3R5 PIK3R5 PIK3R5 3956 0.14 0.34 YES
14 E2F2 E2F2 E2F2 4088 0.14 0.35 YES
15 TGFBR1 TGFBR1 TGFBR1 4669 0.12 0.33 YES
16 HDAC1 HDAC1 HDAC1 4871 0.11 0.34 YES
17 CBL CBL CBL 4887 0.11 0.35 YES
18 CDKN2A CDKN2A CDKN2A 4933 0.11 0.36 YES
19 RB1 RB1 RB1 5073 0.1 0.37 YES
20 SOS1 SOS1 SOS1 5404 0.094 0.37 YES
21 MAP2K1 MAP2K1 MAP2K1 5407 0.094 0.38 YES
22 CDKN1B CDKN1B CDKN1B 5434 0.093 0.39 YES
23 BRAF BRAF BRAF 5446 0.092 0.4 YES
24 CRKL CRKL CRKL 5518 0.09 0.41 YES
25 NFKB1 NFKB1 NFKB1 5646 0.087 0.42 YES
26 AKT3 AKT3 AKT3 5768 0.084 0.42 YES
27 PIK3CD PIK3CD PIK3CD 5819 0.083 0.43 YES
28 HDAC2 HDAC2 HDAC2 5907 0.081 0.44 YES
29 SHC1 SHC1 SHC1 5967 0.079 0.45 YES
30 NFKBIA NFKBIA NFKBIA 5995 0.079 0.46 YES
31 SMAD3 SMAD3 SMAD3 6276 0.073 0.45 YES
32 RELA RELA RELA 6404 0.07 0.45 YES
33 NRAS NRAS NRAS 6436 0.07 0.46 YES
34 CRK CRK CRK 6505 0.068 0.47 YES
35 CTBP2 CTBP2 CTBP2 6826 0.061 0.46 NO
36 BCR BCR BCR 6968 0.059 0.46 NO
37 CDK6 CDK6 CDK6 7150 0.055 0.46 NO
38 MAPK1 MAPK1 MAPK1 7286 0.052 0.46 NO
39 E2F3 E2F3 E2F3 7340 0.052 0.46 NO
40 SOS2 SOS2 SOS2 7514 0.048 0.46 NO
41 CDKN1A CDKN1A CDKN1A 7688 0.045 0.46 NO
42 PIK3R1 PIK3R1 PIK3R1 7744 0.044 0.46 NO
43 ABL1 ABL1 ABL1 7762 0.044 0.46 NO
44 GAB2 GAB2 GAB2 7911 0.042 0.46 NO
45 AKT1 AKT1 AKT1 8012 0.04 0.46 NO
46 SMAD4 SMAD4 SMAD4 8086 0.039 0.46 NO
47 PIK3CB PIK3CB PIK3CB 8701 0.028 0.43 NO
48 MYC MYC MYC 8752 0.028 0.43 NO
49 PIK3R3 PIK3R3 PIK3R3 9002 0.024 0.42 NO
50 KRAS KRAS KRAS 9234 0.02 0.41 NO
51 ARAF ARAF ARAF 9405 0.017 0.41 NO
52 MDM2 MDM2 MDM2 9442 0.017 0.41 NO
53 AKT2 AKT2 AKT2 9624 0.014 0.4 NO
54 TP53 TP53 TP53 9629 0.014 0.4 NO
55 RAF1 RAF1 RAF1 9646 0.014 0.4 NO
56 STAT5B STAT5B STAT5B 9877 0.01 0.39 NO
57 PTPN11 PTPN11 PTPN11 10221 0.0041 0.37 NO
58 IKBKB IKBKB IKBKB 10283 0.0031 0.37 NO
59 IKBKG IKBKG IKBKG 10750 -0.0046 0.34 NO
60 MAPK3 MAPK3 MAPK3 10867 -0.0068 0.34 NO
61 CHUK CHUK CHUK 11102 -0.01 0.32 NO
62 STAT5A STAT5A STAT5A 11375 -0.015 0.31 NO
63 E2F1 E2F1 E2F1 11598 -0.019 0.3 NO
64 SHC2 SHC2 SHC2 11635 -0.019 0.3 NO
65 CBLC CBLC CBLC 11768 -0.022 0.3 NO
66 PIK3R2 PIK3R2 PIK3R2 12062 -0.027 0.29 NO
67 CTBP1 CTBP1 CTBP1 12192 -0.03 0.28 NO
68 CDK4 CDK4 CDK4 12681 -0.039 0.26 NO
69 HRAS HRAS HRAS 12706 -0.039 0.27 NO
70 BCL2L1 BCL2L1 BCL2L1 12774 -0.041 0.27 NO
71 GRB2 GRB2 GRB2 13043 -0.046 0.26 NO
72 MAP2K2 MAP2K2 MAP2K2 13169 -0.049 0.26 NO
73 BAD BAD BAD 13942 -0.065 0.23 NO

Figure S65.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.

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

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

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 NTF3 NTF3 NTF3 156 0.6 0.036 YES
2 CAMK4 CAMK4 CAMK4 164 0.59 0.08 YES
3 PIK3CG PIK3CG PIK3CG 308 0.52 0.11 YES
4 RPS6KA5 RPS6KA5 RPS6KA5 362 0.5 0.14 YES
5 IRAK3 IRAK3 IRAK3 497 0.46 0.17 YES
6 NGFR NGFR NGFR 532 0.46 0.2 YES
7 SHC3 SHC3 SHC3 660 0.42 0.23 YES
8 CAMK2A CAMK2A CAMK2A 1005 0.36 0.24 YES
9 NGF NGF NGF 1100 0.35 0.26 YES
10 SHC4 SHC4 SHC4 1236 0.34 0.28 YES
11 NTRK3 NTRK3 NTRK3 1769 0.28 0.27 YES
12 MAP3K5 MAP3K5 MAP3K5 1786 0.28 0.29 YES
13 FASLG FASLG FASLG 1937 0.26 0.3 YES
14 IRAK2 IRAK2 IRAK2 1979 0.26 0.32 YES
15 IRS1 IRS1 IRS1 2138 0.25 0.32 YES
16 IRS2 IRS2 IRS2 2212 0.24 0.34 YES
17 NTRK1 NTRK1 NTRK1 2315 0.24 0.35 YES
18 MAPK13 MAPK13 MAPK13 2421 0.23 0.36 YES
19 RPS6KA6 RPS6KA6 RPS6KA6 2443 0.23 0.38 YES
20 PDK1 PDK1 PDK1 2469 0.22 0.39 YES
21 MAPK8 MAPK8 MAPK8 2503 0.22 0.41 YES
22 SH2B3 SH2B3 SH2B3 2570 0.22 0.42 YES
23 PLCG2 PLCG2 PLCG2 2762 0.2 0.42 YES
24 ARHGDIB ARHGDIB ARHGDIB 2915 0.19 0.43 YES
25 PIK3CA PIK3CA PIK3CA 3044 0.19 0.44 YES
26 SH2B2 SH2B2 SH2B2 3108 0.18 0.45 YES
27 RPS6KA2 RPS6KA2 RPS6KA2 3247 0.18 0.45 YES
28 RIPK2 RIPK2 RIPK2 3749 0.15 0.44 NO
29 PIK3R5 PIK3R5 PIK3R5 3956 0.14 0.44 NO
30 TRAF6 TRAF6 TRAF6 4078 0.14 0.44 NO
31 NTRK2 NTRK2 NTRK2 4267 0.13 0.44 NO
32 NTF4 NTF4 NTF4 4544 0.12 0.43 NO
33 JUN JUN JUN 4720 0.12 0.43 NO
34 MAP3K1 MAP3K1 MAP3K1 5011 0.1 0.42 NO
35 SORT1 SORT1 SORT1 5330 0.096 0.41 NO
36 SOS1 SOS1 SOS1 5404 0.094 0.42 NO
37 CALML3 CALML3 CALML3 5406 0.094 0.42 NO
38 MAP2K1 MAP2K1 MAP2K1 5407 0.094 0.43 NO
39 BRAF BRAF BRAF 5446 0.092 0.43 NO
40 CRKL CRKL CRKL 5518 0.09 0.44 NO
41 NFKB1 NFKB1 NFKB1 5646 0.087 0.44 NO
42 AKT3 AKT3 AKT3 5768 0.084 0.44 NO
43 PIK3CD PIK3CD PIK3CD 5819 0.083 0.44 NO
44 FRS2 FRS2 FRS2 5830 0.083 0.44 NO
45 SHC1 SHC1 SHC1 5967 0.079 0.44 NO
46 NFKBIA NFKBIA NFKBIA 5995 0.079 0.45 NO
47 FOXO3 FOXO3 FOXO3 6274 0.073 0.44 NO
48 GAB1 GAB1 GAB1 6403 0.07 0.44 NO
49 RELA RELA RELA 6404 0.07 0.44 NO
50 NRAS NRAS NRAS 6436 0.07 0.44 NO
51 RAP1A RAP1A RAP1A 6443 0.07 0.45 NO
52 CRK CRK CRK 6505 0.068 0.45 NO
53 KIDINS220 KIDINS220 KIDINS220 6551 0.067 0.45 NO
54 RPS6KA3 RPS6KA3 RPS6KA3 6634 0.066 0.45 NO
55 YWHAZ YWHAZ YWHAZ 6866 0.061 0.44 NO
56 ZNF274 ZNF274 ZNF274 7066 0.057 0.44 NO
57 MAP3K3 MAP3K3 MAP3K3 7134 0.055 0.44 NO
58 RAPGEF1 RAPGEF1 RAPGEF1 7252 0.053 0.44 NO
59 MAPK1 MAPK1 MAPK1 7286 0.052 0.44 NO
60 PRKCD PRKCD PRKCD 7473 0.049 0.43 NO
61 CDC42 CDC42 CDC42 7513 0.048 0.43 NO
62 SOS2 SOS2 SOS2 7514 0.048 0.44 NO
63 PIK3R1 PIK3R1 PIK3R1 7744 0.044 0.43 NO
64 ABL1 ABL1 ABL1 7762 0.044 0.43 NO
65 CSK CSK CSK 7765 0.044 0.43 NO
66 TP73 TP73 TP73 7823 0.043 0.43 NO
67 GSK3B GSK3B GSK3B 7929 0.041 0.43 NO
68 AKT1 AKT1 AKT1 8012 0.04 0.43 NO
69 NFKBIE NFKBIE NFKBIE 8021 0.04 0.43 NO
70 YWHAB YWHAB YWHAB 8500 0.032 0.41 NO
71 ATF4 ATF4 ATF4 8651 0.029 0.4 NO
72 PIK3CB PIK3CB PIK3CB 8701 0.028 0.4 NO
73 PSEN1 PSEN1 PSEN1 8850 0.026 0.39 NO
74 MAPK14 MAPK14 MAPK14 8871 0.026 0.39 NO
75 PIK3R3 PIK3R3 PIK3R3 9002 0.024 0.39 NO
76 MAPK10 MAPK10 MAPK10 9218 0.02 0.38 NO
77 KRAS KRAS KRAS 9234 0.02 0.38 NO
78 MAPKAPK2 MAPKAPK2 MAPKAPK2 9371 0.018 0.37 NO
79 IRAK4 IRAK4 IRAK4 9378 0.018 0.37 NO
80 CALM1 CALM1 CALM1 9493 0.016 0.37 NO
81 YWHAQ YWHAQ YWHAQ 9501 0.016 0.37 NO
82 MAP2K7 MAP2K7 MAP2K7 9504 0.016 0.37 NO
83 RHOA RHOA RHOA 9523 0.016 0.37 NO
84 AKT2 AKT2 AKT2 9624 0.014 0.36 NO
85 TP53 TP53 TP53 9629 0.014 0.37 NO
86 RAF1 RAF1 RAF1 9646 0.014 0.37 NO
87 MAGED1 MAGED1 MAGED1 9679 0.013 0.36 NO
88 RPS6KA4 RPS6KA4 RPS6KA4 9821 0.011 0.36 NO
89 CALM2 CALM2 CALM2 9831 0.011 0.36 NO
90 YWHAH YWHAH YWHAH 9870 0.01 0.36 NO
91 RAP1B RAP1B RAP1B 10049 0.0071 0.35 NO
92 CAMK2D CAMK2D CAMK2D 10117 0.006 0.34 NO
93 YWHAG YWHAG YWHAG 10141 0.0054 0.34 NO
94 CALM3 CALM3 CALM3 10214 0.0042 0.34 NO
95 PTPN11 PTPN11 PTPN11 10221 0.0041 0.34 NO
96 IKBKB IKBKB IKBKB 10283 0.0031 0.34 NO
97 BCL2 BCL2 BCL2 10423 0.00083 0.33 NO
98 CAMK2G CAMK2G CAMK2G 10465 -0.000041 0.33 NO
99 MAPK11 MAPK11 MAPK11 10523 -0.00091 0.32 NO
100 MAPK3 MAPK3 MAPK3 10867 -0.0068 0.3 NO
101 MAPK9 MAPK9 MAPK9 11373 -0.015 0.28 NO
102 MAPK7 MAPK7 MAPK7 11388 -0.015 0.28 NO
103 YWHAE YWHAE YWHAE 11529 -0.018 0.27 NO
104 RAC1 RAC1 RAC1 11607 -0.019 0.27 NO
105 SHC2 SHC2 SHC2 11635 -0.019 0.27 NO
106 NGFRAP1 NGFRAP1 NGFRAP1 11750 -0.021 0.26 NO
107 CALML6 CALML6 CALML6 12013 -0.026 0.25 NO
108 ARHGDIA ARHGDIA ARHGDIA 12046 -0.027 0.25 NO
109 PIK3R2 PIK3R2 PIK3R2 12062 -0.027 0.25 NO
110 PRDM4 PRDM4 PRDM4 12144 -0.028 0.25 NO
111 IRAK1 IRAK1 IRAK1 12303 -0.032 0.24 NO
112 MAP2K5 MAP2K5 MAP2K5 12352 -0.032 0.24 NO
113 HRAS HRAS HRAS 12706 -0.039 0.23 NO
114 PLCG1 PLCG1 PLCG1 13005 -0.045 0.21 NO
115 GRB2 GRB2 GRB2 13043 -0.046 0.21 NO
116 BAX BAX BAX 13168 -0.049 0.21 NO
117 MAP2K2 MAP2K2 MAP2K2 13169 -0.049 0.21 NO
118 RPS6KA1 RPS6KA1 RPS6KA1 13604 -0.057 0.19 NO
119 BDNF BDNF BDNF 13920 -0.065 0.18 NO
120 BAD BAD BAD 13942 -0.065 0.18 NO
121 NFKBIB NFKBIB NFKBIB 14192 -0.072 0.18 NO
122 SH2B1 SH2B1 SH2B1 15546 -0.11 0.11 NO
123 CAMK2B CAMK2B CAMK2B 16523 -0.16 0.067 NO
124 MAPK12 MAPK12 MAPK12 17008 -0.2 0.054 NO

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

Figure S68.  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 BASAL TRANSCRIPTION FACTORS

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 PDGFRA PDGFRA PDGFRA 20 0.76 0.022 YES
2 ITGA8 ITGA8 ITGA8 27 0.74 0.044 YES
3 ITGA9 ITGA9 ITGA9 84 0.66 0.061 YES
4 COL6A3 COL6A3 COL6A3 91 0.65 0.08 YES
5 COL5A1 COL5A1 COL5A1 123 0.62 0.097 YES
6 ITGA11 ITGA11 ITGA11 168 0.59 0.11 YES
7 COL3A1 COL3A1 COL3A1 178 0.59 0.13 YES
8 LAMC3 LAMC3 LAMC3 204 0.57 0.15 YES
9 LAMB3 LAMB3 LAMB3 273 0.54 0.16 YES
10 COL5A2 COL5A2 COL5A2 291 0.53 0.17 YES
11 HGF HGF HGF 299 0.53 0.19 YES
12 PIK3CG PIK3CG PIK3CG 308 0.52 0.2 YES
13 COMP COMP COMP 323 0.52 0.22 YES
14 ITGA10 ITGA10 ITGA10 334 0.51 0.23 YES
15 PDGFRB PDGFRB PDGFRB 337 0.51 0.25 YES
16 ITGB6 ITGB6 ITGB6 399 0.49 0.26 YES
17 IGF1 IGF1 IGF1 501 0.46 0.27 YES
18 KDR KDR KDR 515 0.46 0.28 YES
19 ITGA4 ITGA4 ITGA4 528 0.46 0.3 YES
20 COL11A1 COL11A1 COL11A1 541 0.45 0.31 YES
21 TNN TNN TNN 608 0.44 0.32 YES
22 COL1A1 COL1A1 COL1A1 616 0.43 0.33 YES
23 LAMA2 LAMA2 LAMA2 618 0.43 0.34 YES
24 SHC3 SHC3 SHC3 660 0.42 0.35 YES
25 LAMA4 LAMA4 LAMA4 685 0.42 0.37 YES
26 PAK6 PAK6 PAK6 698 0.42 0.38 YES
27 TNXB TNXB TNXB 749 0.41 0.39 YES
28 FLT4 FLT4 FLT4 853 0.39 0.39 YES
29 COL1A2 COL1A2 COL1A2 904 0.38 0.4 YES
30 LAMC2 LAMC2 LAMC2 1035 0.36 0.4 YES
31 TNC TNC TNC 1057 0.36 0.42 YES
32 IBSP IBSP IBSP 1090 0.35 0.42 YES
33 ITGA1 ITGA1 ITGA1 1144 0.35 0.43 YES
34 ITGA2 ITGA2 ITGA2 1182 0.34 0.44 YES
35 SHC4 SHC4 SHC4 1236 0.34 0.45 YES
36 FLT1 FLT1 FLT1 1307 0.33 0.45 YES
37 COL6A2 COL6A2 COL6A2 1342 0.32 0.46 YES
38 ITGB3 ITGB3 ITGB3 1356 0.32 0.47 YES
39 FN1 FN1 FN1 1446 0.31 0.47 YES
40 THBS1 THBS1 THBS1 1460 0.31 0.48 YES
41 COL6A6 COL6A6 COL6A6 1486 0.31 0.49 YES
42 COL5A3 COL5A3 COL5A3 1590 0.3 0.49 YES
43 COL4A1 COL4A1 COL4A1 1802 0.28 0.49 YES
44 PRKCB PRKCB PRKCB 1909 0.27 0.49 YES
45 VEGFA VEGFA VEGFA 1922 0.26 0.5 YES
46 VAV1 VAV1 VAV1 1952 0.26 0.51 YES
47 RASGRF1 RASGRF1 RASGRF1 1978 0.26 0.51 YES
48 PAK3 PAK3 PAK3 2081 0.25 0.51 YES
49 PDGFB PDGFB PDGFB 2170 0.25 0.52 YES
50 ROCK2 ROCK2 ROCK2 2216 0.24 0.52 YES
51 MYLK2 MYLK2 MYLK2 2332 0.23 0.52 YES
52 BIRC3 BIRC3 BIRC3 2414 0.23 0.52 YES
53 MAPK8 MAPK8 MAPK8 2503 0.22 0.53 YES
54 LAMA3 LAMA3 LAMA3 2527 0.22 0.53 YES
55 PGF PGF PGF 2613 0.21 0.53 YES
56 CCND1 CCND1 CCND1 2662 0.21 0.54 YES
57 ITGA5 ITGA5 ITGA5 2685 0.21 0.54 YES
58 COL4A6 COL4A6 COL4A6 2724 0.21 0.55 YES
59 MYLK MYLK MYLK 2735 0.21 0.55 YES
60 RAC2 RAC2 RAC2 2846 0.2 0.55 YES
61 VCL VCL VCL 2867 0.2 0.56 YES
62 VEGFC VEGFC VEGFC 2940 0.19 0.56 YES
63 PIK3CA PIK3CA PIK3CA 3044 0.19 0.56 YES
64 ITGB4 ITGB4 ITGB4 3092 0.18 0.56 YES
65 ITGAV ITGAV ITGAV 3137 0.18 0.56 YES
66 VWF VWF VWF 3141 0.18 0.57 YES
67 FLNA FLNA FLNA 3180 0.18 0.57 YES
68 ACTN1 ACTN1 ACTN1 3198 0.18 0.58 YES
69 COL4A2 COL4A2 COL4A2 3595 0.16 0.56 NO
70 COL4A4 COL4A4 COL4A4 3769 0.15 0.55 NO
71 ITGB1 ITGB1 ITGB1 3869 0.15 0.55 NO
72 ROCK1 ROCK1 ROCK1 3879 0.15 0.56 NO
73 PIK3R5 PIK3R5 PIK3R5 3956 0.14 0.56 NO
74 PDGFD PDGFD PDGFD 4199 0.13 0.55 NO
75 CAV1 CAV1 CAV1 4226 0.13 0.55 NO
76 EGFR EGFR EGFR 4399 0.13 0.54 NO
77 LAMC1 LAMC1 LAMC1 4484 0.12 0.54 NO
78 THBS4 THBS4 THBS4 4524 0.12 0.54 NO
79 THBS2 THBS2 THBS2 4610 0.12 0.54 NO
80 JUN JUN JUN 4720 0.12 0.54 NO
81 CCND3 CCND3 CCND3 4839 0.11 0.54 NO
82 DOCK1 DOCK1 DOCK1 4942 0.11 0.54 NO
83 FYN FYN FYN 5216 0.099 0.52 NO
84 COL6A1 COL6A1 COL6A1 5227 0.099 0.52 NO
85 ITGB5 ITGB5 ITGB5 5233 0.098 0.53 NO
86 MYL9 MYL9 MYL9 5299 0.097 0.53 NO
87 PTEN PTEN PTEN 5398 0.094 0.52 NO
88 SOS1 SOS1 SOS1 5404 0.094 0.53 NO
89 MAP2K1 MAP2K1 MAP2K1 5407 0.094 0.53 NO
90 BRAF BRAF BRAF 5446 0.092 0.53 NO
91 PPP1R12A PPP1R12A PPP1R12A 5487 0.091 0.53 NO
92 ARHGAP5 ARHGAP5 ARHGAP5 5517 0.09 0.53 NO
93 CRKL CRKL CRKL 5518 0.09 0.53 NO
94 VASP VASP VASP 5558 0.089 0.54 NO
95 CTNNB1 CTNNB1 CTNNB1 5708 0.086 0.53 NO
96 FIGF FIGF FIGF 5756 0.084 0.53 NO
97 AKT3 AKT3 AKT3 5768 0.084 0.53 NO
98 PARVA PARVA PARVA 5785 0.084 0.53 NO
99 PIK3CD PIK3CD PIK3CD 5819 0.083 0.53 NO
100 ELK1 ELK1 ELK1 5823 0.083 0.54 NO
101 SHC1 SHC1 SHC1 5967 0.079 0.53 NO
102 XIAP XIAP XIAP 5990 0.079 0.53 NO
103 ITGA3 ITGA3 ITGA3 6247 0.074 0.52 NO
104 ACTN2 ACTN2 ACTN2 6380 0.071 0.51 NO
105 RAP1A RAP1A RAP1A 6443 0.07 0.51 NO
106 CRK CRK CRK 6505 0.068 0.51 NO
107 IGF1R IGF1R IGF1R 6594 0.066 0.51 NO
108 PARVG PARVG PARVG 6625 0.066 0.51 NO
109 BIRC2 BIRC2 BIRC2 6870 0.06 0.5 NO
110 PTK2 PTK2 PTK2 7167 0.055 0.48 NO
111 LAMA5 LAMA5 LAMA5 7211 0.054 0.48 NO
112 RAPGEF1 RAPGEF1 RAPGEF1 7252 0.053 0.48 NO
113 MAPK1 MAPK1 MAPK1 7286 0.052 0.48 NO
114 TLN1 TLN1 TLN1 7455 0.049 0.47 NO
115 CDC42 CDC42 CDC42 7513 0.048 0.47 NO
116 SOS2 SOS2 SOS2 7514 0.048 0.47 NO
117 ACTN4 ACTN4 ACTN4 7531 0.048 0.47 NO
118 PIP5K1C PIP5K1C PIP5K1C 7627 0.046 0.47 NO
119 VAV2 VAV2 VAV2 7698 0.045 0.47 NO
120 MYL12A MYL12A MYL12A 7712 0.045 0.47 NO
121 PIK3R1 PIK3R1 PIK3R1 7744 0.044 0.47 NO
122 PAK2 PAK2 PAK2 7819 0.043 0.46 NO
123 GSK3B GSK3B GSK3B 7929 0.041 0.46 NO
124 AKT1 AKT1 AKT1 8012 0.04 0.46 NO
125 FLNB FLNB FLNB 8202 0.037 0.44 NO
126 COL11A2 COL11A2 COL11A2 8403 0.033 0.44 NO
127 PAK7 PAK7 PAK7 8407 0.033 0.44 NO
128 CAPN2 CAPN2 CAPN2 8458 0.032 0.43 NO
129 PPP1CB PPP1CB PPP1CB 8605 0.03 0.43 NO
130 PIK3CB PIK3CB PIK3CB 8701 0.028 0.42 NO
131 ERBB2 ERBB2 ERBB2 8805 0.027 0.42 NO
132 LAMB2 LAMB2 LAMB2 8813 0.027 0.42 NO
133 CCND2 CCND2 CCND2 8866 0.026 0.42 NO
134 ACTG1 ACTG1 ACTG1 8954 0.025 0.41 NO
135 PXN PXN PXN 8988 0.024 0.41 NO
136 PIK3R3 PIK3R3 PIK3R3 9002 0.024 0.41 NO
137 MAPK10 MAPK10 MAPK10 9218 0.02 0.4 NO
138 DIAPH1 DIAPH1 DIAPH1 9411 0.017 0.39 NO
139 COL2A1 COL2A1 COL2A1 9448 0.017 0.39 NO
140 RHOA RHOA RHOA 9523 0.016 0.38 NO
141 SRC SRC SRC 9601 0.014 0.38 NO
142 PDGFA PDGFA PDGFA 9608 0.014 0.38 NO
143 AKT2 AKT2 AKT2 9624 0.014 0.38 NO
144 ITGA7 ITGA7 ITGA7 9628 0.014 0.38 NO
145 ZYX ZYX ZYX 9643 0.014 0.38 NO
146 RAF1 RAF1 RAF1 9646 0.014 0.38 NO
147 ACTB ACTB ACTB 9732 0.012 0.38 NO
148 PDGFC PDGFC PDGFC 9869 0.01 0.37 NO
149 RAP1B RAP1B RAP1B 10049 0.0071 0.36 NO
150 SPP1 SPP1 SPP1 10406 0.001 0.34 NO
151 PDPK1 PDPK1 PDPK1 10415 0.00096 0.34 NO
152 BCL2 BCL2 BCL2 10423 0.00083 0.34 NO
153 PPP1CC PPP1CC PPP1CC 10490 -0.00054 0.33 NO
154 ITGA6 ITGA6 ITGA6 10573 -0.0016 0.33 NO
155 MET MET MET 10604 -0.0021 0.33 NO
156 MAPK3 MAPK3 MAPK3 10867 -0.0068 0.31 NO
157 MYL12B MYL12B MYL12B 11073 -0.01 0.3 NO
158 PAK1 PAK1 PAK1 11367 -0.015 0.28 NO
159 MAPK9 MAPK9 MAPK9 11373 -0.015 0.28 NO
160 ILK ILK ILK 11451 -0.016 0.28 NO
161 ITGA2B ITGA2B ITGA2B 11604 -0.019 0.27 NO
162 RAC1 RAC1 RAC1 11607 -0.019 0.27 NO
163 SHC2 SHC2 SHC2 11635 -0.019 0.27 NO
164 ACTN3 ACTN3 ACTN3 11707 -0.02 0.27 NO
165 PPP1CA PPP1CA PPP1CA 11786 -0.022 0.27 NO
166 LAMB1 LAMB1 LAMB1 11824 -0.022 0.26 NO
167 THBS3 THBS3 THBS3 11826 -0.023 0.26 NO
168 VAV3 VAV3 VAV3 11966 -0.025 0.26 NO
169 PIK3R2 PIK3R2 PIK3R2 12062 -0.027 0.25 NO
170 PRKCA PRKCA PRKCA 12074 -0.027 0.25 NO
171 PAK4 PAK4 PAK4 12118 -0.028 0.25 NO
172 LAMB4 LAMB4 LAMB4 12540 -0.036 0.23 NO
173 MYLPF MYLPF MYLPF 12671 -0.038 0.22 NO
174 HRAS HRAS HRAS 12706 -0.039 0.22 NO
175 CAV2 CAV2 CAV2 12727 -0.04 0.22 NO
176 ITGB8 ITGB8 ITGB8 12782 -0.041 0.22 NO
177 GRB2 GRB2 GRB2 13043 -0.046 0.21 NO
178 PARVB PARVB PARVB 13221 -0.05 0.2 NO
179 ITGB7 ITGB7 ITGB7 13893 -0.064 0.16 NO
180 BAD BAD BAD 13942 -0.065 0.16 NO
181 BCAR1 BCAR1 BCAR1 14755 -0.088 0.12 NO
182 VTN VTN VTN 14885 -0.091 0.12 NO
183 MYLK3 MYLK3 MYLK3 15079 -0.098 0.11 NO
184 TLN2 TLN2 TLN2 15136 -0.1 0.11 NO
185 VEGFB VEGFB VEGFB 15263 -0.1 0.1 NO
186 CHAD CHAD CHAD 15544 -0.11 0.091 NO
187 LAMA1 LAMA1 LAMA1 16177 -0.14 0.06 NO
188 RELN RELN RELN 16886 -0.19 0.026 NO
189 EGF EGF EGF 16931 -0.19 0.029 NO
190 PRKCG PRKCG PRKCG 16936 -0.19 0.035 NO
191 RAC3 RAC3 RAC3 17236 -0.23 0.025 NO
192 MYL5 MYL5 MYL5 17471 -0.27 0.02 NO
193 FLNC FLNC FLNC 17575 -0.29 0.023 NO

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

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

genes ES table in pathway: KEGG MAPK SIGNALING PATHWAY

Table 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 TCF4 TCF4 TCF4 508 0.46 0.047 YES
2 TGFB1I1 TGFB1I1 TGFB1I1 845 0.39 0.093 YES
3 MAK MAK MAK 1558 0.3 0.1 YES
4 TMPRSS2 TMPRSS2 TMPRSS2 1941 0.26 0.12 YES
5 SNURF SNURF SNURF 2164 0.25 0.15 YES
6 FHL2 FHL2 FHL2 2187 0.24 0.19 YES
7 NCOA2 NCOA2 NCOA2 2489 0.22 0.21 YES
8 CCND1 CCND1 CCND1 2662 0.21 0.24 YES
9 HIP1 HIP1 HIP1 2842 0.2 0.26 YES
10 NKX3-1 NKX3-1 NKX3-1 2957 0.19 0.28 YES
11 GSN GSN GSN 3351 0.17 0.29 YES
12 CMTM2 CMTM2 CMTM2 3505 0.16 0.31 YES
13 PIAS3 PIAS3 PIAS3 3821 0.15 0.31 YES
14 SVIL SVIL SVIL 4148 0.14 0.32 YES
15 PIAS1 PIAS1 PIAS1 4266 0.13 0.33 YES
16 TMF1 TMF1 TMF1 4269 0.13 0.35 YES
17 PAWR PAWR PAWR 4297 0.13 0.37 YES
18 KDM4C KDM4C KDM4C 4573 0.12 0.38 YES
19 SRF SRF SRF 4824 0.11 0.38 YES
20 CCND3 CCND3 CCND3 4839 0.11 0.4 YES
21 NRIP1 NRIP1 NRIP1 4912 0.11 0.41 YES
22 CDKN2A CDKN2A CDKN2A 4933 0.11 0.43 YES
23 ZMIZ1 ZMIZ1 ZMIZ1 4974 0.11 0.44 YES
24 CTDSP2 CTDSP2 CTDSP2 5202 0.099 0.45 YES
25 PRKDC PRKDC PRKDC 5648 0.087 0.44 YES
26 CTNNB1 CTNNB1 CTNNB1 5708 0.086 0.45 YES
27 RANBP9 RANBP9 RANBP9 5740 0.085 0.46 YES
28 LATS2 LATS2 LATS2 5961 0.08 0.46 YES
29 PIAS4 PIAS4 PIAS4 6319 0.072 0.45 YES
30 ZNF318 ZNF318 ZNF318 6526 0.068 0.45 YES
31 APPL1 APPL1 APPL1 6621 0.066 0.46 YES
32 RPS6KA3 RPS6KA3 RPS6KA3 6634 0.066 0.47 YES
33 UBE3A UBE3A UBE3A 6768 0.063 0.47 YES
34 PTK2B PTK2B PTK2B 6777 0.062 0.48 YES
35 MED1 MED1 MED1 6801 0.062 0.49 YES
36 KDM1A KDM1A KDM1A 6871 0.06 0.5 YES
37 BRCA1 BRCA1 BRCA1 7109 0.056 0.49 YES
38 CDK6 CDK6 CDK6 7150 0.055 0.5 YES
39 XRCC5 XRCC5 XRCC5 7359 0.051 0.5 YES
40 KDM3A KDM3A KDM3A 7372 0.051 0.5 YES
41 AKT1 AKT1 AKT1 8012 0.04 0.47 NO
42 AR AR AR 8216 0.037 0.47 NO
43 TGIF1 TGIF1 TGIF1 8236 0.036 0.47 NO
44 KLK3 KLK3 KLK3 8774 0.027 0.45 NO
45 NCOA6 NCOA6 NCOA6 9068 0.023 0.44 NO
46 CTDSP1 CTDSP1 CTDSP1 9071 0.023 0.44 NO
47 PATZ1 PATZ1 PATZ1 9271 0.02 0.43 NO
48 XRCC6 XRCC6 XRCC6 9398 0.018 0.43 NO
49 HNRNPA1 HNRNPA1 HNRNPA1 9467 0.016 0.43 NO
50 NCOA4 NCOA4 NCOA4 10024 0.0075 0.4 NO
51 UBA3 UBA3 UBA3 10038 0.0074 0.4 NO
52 CDK11B CDK11B CDK11B 10180 0.0047 0.39 NO
53 CARM1 CARM1 CARM1 10270 0.0033 0.38 NO
54 CASP8 CASP8 CASP8 11193 -0.012 0.34 NO
55 UBE2I UBE2I UBE2I 11541 -0.018 0.32 NO
56 KLK2 KLK2 KLK2 11806 -0.022 0.31 NO
57 VAV3 VAV3 VAV3 11966 -0.025 0.3 NO
58 PA2G4 PA2G4 PA2G4 12400 -0.033 0.28 NO
59 PELP1 PELP1 PELP1 12565 -0.036 0.28 NO
60 PRDX1 PRDX1 PRDX1 13540 -0.056 0.24 NO
61 FKBP4 FKBP4 FKBP4 14184 -0.072 0.21 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 MAPK SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG ERBB SIGNALING PATHWAY

Table 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 PDGFRA PDGFRA PDGFRA 20 0.76 0.2 YES
2 PIK3CG PIK3CG PIK3CG 308 0.52 0.32 YES
3 S1PR1 S1PR1 S1PR1 1167 0.34 0.36 YES
4 ITGB3 ITGB3 ITGB3 1356 0.32 0.44 YES
5 ADCY1 ADCY1 ADCY1 1561 0.3 0.5 YES
6 PLCB1 PLCB1 PLCB1 1593 0.29 0.58 YES
7 PRKCB PRKCB PRKCB 1909 0.27 0.63 YES
8 PIK3CA PIK3CA PIK3CA 3044 0.19 0.62 YES
9 ITGAV ITGAV ITGAV 3137 0.18 0.66 YES
10 GNAI1 GNAI1 GNAI1 6952 0.059 0.46 NO
11 GNB1 GNB1 GNB1 7020 0.057 0.47 NO
12 PTK2 PTK2 PTK2 7167 0.055 0.48 NO
13 MAPK1 MAPK1 MAPK1 7286 0.052 0.49 NO
14 PIK3R1 PIK3R1 PIK3R1 7744 0.044 0.47 NO
15 AKT1 AKT1 AKT1 8012 0.04 0.47 NO
16 RHOA RHOA RHOA 9523 0.016 0.39 NO
17 SRC SRC SRC 9601 0.014 0.39 NO
18 PDGFA PDGFA PDGFA 9608 0.014 0.39 NO
19 SPHK1 SPHK1 SPHK1 10239 0.0039 0.36 NO
20 MAPK3 MAPK3 MAPK3 10867 -0.0068 0.32 NO
21 ASAH1 ASAH1 ASAH1 11132 -0.011 0.31 NO
22 RAC1 RAC1 RAC1 11607 -0.019 0.29 NO
23 PRKCA PRKCA PRKCA 12074 -0.027 0.27 NO
24 SMPD2 SMPD2 SMPD2 13317 -0.052 0.22 NO
25 SMPD1 SMPD1 SMPD1 14413 -0.078 0.18 NO
26 GNGT1 GNGT1 GNGT1 14595 -0.083 0.19 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 ERBB SIGNALING PATHWAY.

Figure S74.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ERBB SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG CALCIUM SIGNALING PATHWAY

Table 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 CDKN2B CDKN2B CDKN2B 312 0.52 0.068 YES
2 SERPINE1 SERPINE1 SERPINE1 838 0.39 0.1 YES
3 PMEPA1 PMEPA1 PMEPA1 875 0.38 0.16 YES
4 SKIL SKIL SKIL 944 0.37 0.22 YES
5 CCNT1 CCNT1 CCNT1 1775 0.28 0.22 YES
6 JUNB JUNB JUNB 1945 0.26 0.26 YES
7 CGN CGN CGN 2077 0.25 0.29 YES
8 TGFB1 TGFB1 TGFB1 2461 0.22 0.3 YES
9 RBL1 RBL1 RBL1 2873 0.2 0.31 YES
10 TGFBR2 TGFBR2 TGFBR2 2889 0.2 0.34 YES
11 SKI SKI SKI 3539 0.16 0.34 YES
12 SMURF2 SMURF2 SMURF2 3553 0.16 0.36 YES
13 ZFYVE9 ZFYVE9 ZFYVE9 3843 0.15 0.37 YES
14 FURIN FURIN FURIN 4181 0.13 0.37 YES
15 WWTR1 WWTR1 WWTR1 4615 0.12 0.37 YES
16 TGFBR1 TGFBR1 TGFBR1 4669 0.12 0.38 YES
17 HDAC1 HDAC1 HDAC1 4871 0.11 0.39 YES
18 SMAD7 SMAD7 SMAD7 5098 0.1 0.4 YES
19 NCOR2 NCOR2 NCOR2 5278 0.097 0.4 YES
20 UBE2D1 UBE2D1 UBE2D1 5483 0.091 0.4 YES
21 TRIM33 TRIM33 TRIM33 5597 0.088 0.41 YES
22 TFDP1 TFDP1 TFDP1 6022 0.078 0.4 YES
23 UCHL5 UCHL5 UCHL5 6136 0.076 0.41 YES
24 USP9X USP9X USP9X 6146 0.076 0.42 YES
25 PPP1R15A PPP1R15A PPP1R15A 6201 0.075 0.43 YES
26 SMAD3 SMAD3 SMAD3 6276 0.073 0.44 YES
27 F11R F11R F11R 6299 0.073 0.45 YES
28 PARP1 PARP1 PARP1 6373 0.071 0.46 YES
29 NCOR1 NCOR1 NCOR1 6379 0.071 0.47 YES
30 SMAD2 SMAD2 SMAD2 6463 0.069 0.47 YES
31 CCNT2 CCNT2 CCNT2 6499 0.068 0.48 YES
32 CDK8 CDK8 CDK8 6649 0.065 0.48 YES
33 E2F5 E2F5 E2F5 7014 0.058 0.48 NO
34 SMURF1 SMURF1 SMURF1 7208 0.054 0.47 NO
35 TGIF2 TGIF2 TGIF2 7619 0.046 0.46 NO
36 SMAD4 SMAD4 SMAD4 8086 0.039 0.44 NO
37 TGIF1 TGIF1 TGIF1 8236 0.036 0.44 NO
38 PARD3 PARD3 PARD3 8327 0.035 0.44 NO
39 PPP1CB PPP1CB PPP1CB 8605 0.03 0.43 NO
40 UBE2D3 UBE2D3 UBE2D3 8646 0.029 0.43 NO
41 CCNC CCNC CCNC 8687 0.029 0.43 NO
42 MYC MYC MYC 8752 0.028 0.43 NO
43 ARHGEF18 ARHGEF18 ARHGEF18 9473 0.016 0.39 NO
44 RHOA RHOA RHOA 9523 0.016 0.39 NO
45 PPM1A PPM1A PPM1A 10147 0.0053 0.36 NO
46 SP1 SP1 SP1 10235 0.0039 0.36 NO
47 RPS27A RPS27A RPS27A 10303 0.0027 0.35 NO
48 PPP1CC PPP1CC PPP1CC 10490 -0.00054 0.34 NO
49 XPO1 XPO1 XPO1 10563 -0.0014 0.34 NO
50 FKBP1A FKBP1A FKBP1A 11032 -0.0095 0.31 NO
51 PRKCZ PRKCZ PRKCZ 11235 -0.012 0.3 NO
52 STRAP STRAP STRAP 11583 -0.018 0.29 NO
53 UBA52 UBA52 UBA52 11621 -0.019 0.29 NO
54 PPP1CA PPP1CA PPP1CA 11786 -0.022 0.28 NO
55 CDK9 CDK9 CDK9 11914 -0.024 0.28 NO
56 MEN1 MEN1 MEN1 12032 -0.026 0.28 NO
57 MTMR4 MTMR4 MTMR4 12402 -0.033 0.26 NO
58 E2F4 E2F4 E2F4 12714 -0.04 0.25 NO
59 PARD6A PARD6A PARD6A 15830 -0.12 0.099 NO
60 STUB1 STUB1 STUB1 15898 -0.13 0.12 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 CALCIUM SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION

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 CNTN1 CNTN1 CNTN1 4 0.83 0.067 YES
2 NOTCH3 NOTCH3 NOTCH3 366 0.5 0.087 YES
3 HEYL HEYL HEYL 520 0.46 0.12 YES
4 DLL1 DLL1 DLL1 662 0.42 0.14 YES
5 EIF2C2 EIF2C2 EIF2C2 1017 0.36 0.15 YES
6 DLL4 DLL4 DLL4 1061 0.36 0.18 YES
7 MAML2 MAML2 MAML2 1207 0.34 0.2 YES
8 HEY1 HEY1 HEY1 1274 0.33 0.22 YES
9 ATP2A3 ATP2A3 ATP2A3 1412 0.32 0.24 YES
10 NOTCH4 NOTCH4 NOTCH4 1539 0.3 0.26 YES
11 HEY2 HEY2 HEY2 1646 0.29 0.27 YES
12 MAML3 MAML3 MAML3 1668 0.29 0.3 YES
13 DTX1 DTX1 DTX1 1965 0.26 0.3 YES
14 NEURL NEURL NEURL 2025 0.26 0.32 YES
15 CCND1 CCND1 CCND1 2662 0.21 0.3 YES
16 ADAM10 ADAM10 ADAM10 2955 0.19 0.3 YES
17 HES1 HES1 HES1 3094 0.18 0.31 YES
18 MFNG MFNG MFNG 3262 0.17 0.31 YES
19 ADAM17 ADAM17 ADAM17 3469 0.16 0.31 YES
20 JAG2 JAG2 JAG2 3546 0.16 0.32 YES
21 JAG1 JAG1 JAG1 3575 0.16 0.33 YES
22 HES5 HES5 HES5 3705 0.15 0.34 YES
23 MIB1 MIB1 MIB1 3756 0.15 0.35 YES
24 MAMLD1 MAMLD1 MAMLD1 3792 0.15 0.36 YES
25 EIF2C4 EIF2C4 EIF2C4 3793 0.15 0.37 YES
26 HDAC4 HDAC4 HDAC4 3905 0.14 0.38 YES
27 ARRB1 ARRB1 ARRB1 3948 0.14 0.39 YES
28 NOTCH2 NOTCH2 NOTCH2 3951 0.14 0.4 YES
29 TLE2 TLE2 TLE2 3990 0.14 0.41 YES
30 EP300 EP300 EP300 4158 0.14 0.41 YES
31 FURIN FURIN FURIN 4181 0.13 0.42 YES
32 TLE3 TLE3 TLE3 4284 0.13 0.42 YES
33 FBXW7 FBXW7 FBXW7 4296 0.13 0.43 YES
34 EIF2C3 EIF2C3 EIF2C3 4363 0.13 0.44 YES
35 HIF1A HIF1A HIF1A 4370 0.13 0.45 YES
36 SEL1L SEL1L SEL1L 4647 0.12 0.44 YES
37 JUN JUN JUN 4720 0.12 0.45 YES
38 HDAC1 HDAC1 HDAC1 4871 0.11 0.45 YES
39 MAML1 MAML1 MAML1 4880 0.11 0.46 YES
40 KAT2B KAT2B KAT2B 4885 0.11 0.47 YES
41 HDAC9 HDAC9 HDAC9 5126 0.1 0.46 YES
42 APH1B APH1B APH1B 5214 0.099 0.46 YES
43 NCOR2 NCOR2 NCOR2 5278 0.097 0.47 YES
44 DTX4 DTX4 DTX4 5516 0.09 0.46 NO
45 TLE4 TLE4 TLE4 5713 0.085 0.46 NO
46 HDAC2 HDAC2 HDAC2 5907 0.081 0.45 NO
47 TFDP1 TFDP1 TFDP1 6022 0.078 0.45 NO
48 B4GALT1 B4GALT1 B4GALT1 6151 0.076 0.45 NO
49 TNRC6B TNRC6B TNRC6B 6279 0.073 0.45 NO
50 TNRC6C TNRC6C TNRC6C 6290 0.073 0.46 NO
51 NCOR1 NCOR1 NCOR1 6379 0.071 0.46 NO
52 RAB6A RAB6A RAB6A 6632 0.066 0.45 NO
53 CDK8 CDK8 CDK8 6649 0.065 0.45 NO
54 EIF2C1 EIF2C1 EIF2C1 6928 0.059 0.44 NO
55 NCSTN NCSTN NCSTN 7098 0.056 0.44 NO
56 HDAC7 HDAC7 HDAC7 7254 0.053 0.43 NO
57 E2F3 E2F3 E2F3 7340 0.052 0.43 NO
58 SNW1 SNW1 SNW1 7431 0.05 0.43 NO
59 RBPJ RBPJ RBPJ 7466 0.049 0.44 NO
60 CREBBP CREBBP CREBBP 7530 0.048 0.44 NO
61 TBL1X TBL1X TBL1X 7532 0.048 0.44 NO
62 TBL1XR1 TBL1XR1 TBL1XR1 7694 0.045 0.43 NO
63 ATP2A2 ATP2A2 ATP2A2 7954 0.041 0.42 NO
64 TMED2 TMED2 TMED2 7958 0.041 0.43 NO
65 CUL1 CUL1 CUL1 8271 0.036 0.41 NO
66 TLE1 TLE1 TLE1 8607 0.03 0.4 NO
67 CCNC CCNC CCNC 8687 0.029 0.39 NO
68 MYC MYC MYC 8752 0.028 0.39 NO
69 PSEN1 PSEN1 PSEN1 8850 0.026 0.39 NO
70 DTX2 DTX2 DTX2 8957 0.025 0.38 NO
71 TP53 TP53 TP53 9629 0.014 0.35 NO
72 APH1A APH1A APH1A 9856 0.01 0.34 NO
73 DNER DNER DNER 10115 0.006 0.32 NO
74 RPS27A RPS27A RPS27A 10303 0.0027 0.31 NO
75 POFUT1 POFUT1 POFUT1 10339 0.002 0.31 NO
76 SKP1 SKP1 SKP1 10565 -0.0014 0.3 NO
77 RBX1 RBX1 RBX1 10746 -0.0046 0.29 NO
78 HDAC3 HDAC3 HDAC3 11055 -0.0098 0.27 NO
79 PSEN2 PSEN2 PSEN2 11247 -0.013 0.26 NO
80 HDAC5 HDAC5 HDAC5 11427 -0.016 0.25 NO
81 E2F1 E2F1 E2F1 11598 -0.019 0.24 NO
82 UBA52 UBA52 UBA52 11621 -0.019 0.24 NO
83 NUMB NUMB NUMB 11839 -0.023 0.24 NO
84 MIB2 MIB2 MIB2 11916 -0.024 0.23 NO
85 LFNG LFNG LFNG 11942 -0.025 0.23 NO
86 ARRB2 ARRB2 ARRB2 12408 -0.034 0.21 NO
87 MOV10 MOV10 MOV10 12430 -0.034 0.21 NO
88 ST3GAL6 ST3GAL6 ST3GAL6 12839 -0.042 0.19 NO
89 TNRC6A TNRC6A TNRC6A 13222 -0.05 0.18 NO
90 HDAC8 HDAC8 HDAC8 13460 -0.054 0.17 NO
91 ST3GAL3 ST3GAL3 ST3GAL3 13603 -0.057 0.16 NO
92 PSENEN PSENEN PSENEN 14134 -0.07 0.14 NO
93 HDAC6 HDAC6 HDAC6 14241 -0.073 0.14 NO
94 HDAC11 HDAC11 HDAC11 15275 -0.1 0.09 NO
95 HDAC10 HDAC10 HDAC10 15560 -0.11 0.083 NO
96 RFNG RFNG RFNG 15997 -0.13 0.069 NO
97 KAT2A KAT2A KAT2A 16176 -0.14 0.071 NO
98 ATP2A1 ATP2A1 ATP2A1 17795 -0.37 0.01 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 CYTOKINE CYTOKINE RECEPTOR INTERACTION.

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

genes ES table in pathway: KEGG CHEMOKINE SIGNALING PATHWAY

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 SFRP1 SFRP1 SFRP1 2 0.89 0.044 YES
2 LEF1 LEF1 LEF1 73 0.67 0.074 YES
3 FZD10 FZD10 FZD10 96 0.65 0.1 YES
4 NKD1 NKD1 NKD1 170 0.59 0.13 YES
5 WNT10A WNT10A WNT10A 213 0.57 0.16 YES
6 WNT4 WNT4 WNT4 236 0.55 0.18 YES
7 DAAM2 DAAM2 DAAM2 245 0.55 0.21 YES
8 DKK1 DKK1 DKK1 249 0.55 0.24 YES
9 NFATC2 NFATC2 NFATC2 352 0.5 0.26 YES
10 SFRP2 SFRP2 SFRP2 371 0.5 0.28 YES
11 WNT7A WNT7A WNT7A 654 0.42 0.28 YES
12 WNT9B WNT9B WNT9B 710 0.41 0.3 YES
13 DKK2 DKK2 DKK2 713 0.41 0.32 YES
14 WNT9A WNT9A WNT9A 844 0.39 0.33 YES
15 NFATC4 NFATC4 NFATC4 884 0.38 0.35 YES
16 FZD7 FZD7 FZD7 894 0.38 0.37 YES
17 SOX17 SOX17 SOX17 927 0.38 0.39 YES
18 CAMK2A CAMK2A CAMK2A 1005 0.36 0.4 YES
19 FOSL1 FOSL1 FOSL1 1105 0.35 0.41 YES
20 WNT6 WNT6 WNT6 1278 0.33 0.42 YES
21 TCF7 TCF7 TCF7 1311 0.32 0.43 YES
22 DAAM1 DAAM1 DAAM1 1537 0.3 0.44 YES
23 PLCB1 PLCB1 PLCB1 1593 0.29 0.45 YES
24 TCF7L1 TCF7L1 TCF7L1 1727 0.28 0.45 YES
25 WNT7B WNT7B WNT7B 1898 0.27 0.46 YES
26 PRKCB PRKCB PRKCB 1909 0.27 0.47 YES
27 WNT8B WNT8B WNT8B 1967 0.26 0.48 YES
28 SFRP4 SFRP4 SFRP4 2099 0.25 0.48 YES
29 ROCK2 ROCK2 ROCK2 2216 0.24 0.49 YES
30 MAPK8 MAPK8 MAPK8 2503 0.22 0.48 YES
31 CCND1 CCND1 CCND1 2662 0.21 0.49 YES
32 CXXC4 CXXC4 CXXC4 2698 0.21 0.5 YES
33 RAC2 RAC2 RAC2 2846 0.2 0.5 YES
34 FZD3 FZD3 FZD3 3445 0.16 0.47 YES
35 PPP2R5E PPP2R5E PPP2R5E 3467 0.16 0.48 YES
36 MMP7 MMP7 MMP7 3694 0.15 0.47 YES
37 ROCK1 ROCK1 ROCK1 3879 0.15 0.47 YES
38 PPARD PPARD PPARD 3924 0.14 0.48 YES
39 WNT3A WNT3A WNT3A 4083 0.14 0.47 YES
40 EP300 EP300 EP300 4158 0.14 0.48 YES
41 NKD2 NKD2 NKD2 4189 0.13 0.48 YES
42 PLCB2 PLCB2 PLCB2 4190 0.13 0.49 YES
43 WNT1 WNT1 WNT1 4332 0.13 0.49 YES
44 FZD6 FZD6 FZD6 4407 0.13 0.49 YES
45 WNT2 WNT2 WNT2 4437 0.12 0.49 YES
46 VANGL2 VANGL2 VANGL2 4665 0.12 0.48 YES
47 WNT16 WNT16 WNT16 4689 0.12 0.49 YES
48 CHP2 CHP2 CHP2 4706 0.12 0.5 YES
49 JUN JUN JUN 4720 0.12 0.5 YES
50 PORCN PORCN PORCN 4781 0.11 0.5 YES
51 CCND3 CCND3 CCND3 4839 0.11 0.5 YES
52 NFATC1 NFATC1 NFATC1 4971 0.11 0.5 YES
53 TCF7L2 TCF7L2 TCF7L2 5069 0.1 0.5 YES
54 PRKX PRKX PRKX 5136 0.1 0.5 YES
55 CSNK1E CSNK1E CSNK1E 5153 0.1 0.51 YES
56 PPP2R5C PPP2R5C PPP2R5C 5476 0.092 0.49 NO
57 VANGL1 VANGL1 VANGL1 5631 0.087 0.49 NO
58 CSNK1A1L CSNK1A1L CSNK1A1L 5660 0.087 0.49 NO
59 CTNNB1 CTNNB1 CTNNB1 5708 0.086 0.49 NO
60 PRICKLE1 PRICKLE1 PRICKLE1 5804 0.083 0.49 NO
61 CHD8 CHD8 CHD8 5809 0.083 0.5 NO
62 PPP3CC PPP3CC PPP3CC 5854 0.082 0.5 NO
63 PPP3CB PPP3CB PPP3CB 6066 0.077 0.49 NO
64 SMAD3 SMAD3 SMAD3 6276 0.073 0.48 NO
65 PPP3R1 PPP3R1 PPP3R1 6399 0.071 0.48 NO
66 SMAD2 SMAD2 SMAD2 6463 0.069 0.48 NO
67 PPP3CA PPP3CA PPP3CA 6749 0.063 0.47 NO
68 MAP3K7 MAP3K7 MAP3K7 6796 0.062 0.47 NO
69 CTBP2 CTBP2 CTBP2 6826 0.061 0.47 NO
70 CER1 CER1 CER1 6833 0.061 0.47 NO
71 PPP2R1B PPP2R1B PPP2R1B 6852 0.061 0.47 NO
72 APC APC APC 6873 0.06 0.47 NO
73 NFATC3 NFATC3 NFATC3 6993 0.058 0.47 NO
74 SENP2 SENP2 SENP2 7114 0.056 0.47 NO
75 AXIN2 AXIN2 AXIN2 7142 0.055 0.47 NO
76 PPP2R5A PPP2R5A PPP2R5A 7194 0.054 0.47 NO
77 LRP5 LRP5 LRP5 7275 0.053 0.47 NO
78 PRKACB PRKACB PRKACB 7384 0.051 0.46 NO
79 CSNK1A1 CSNK1A1 CSNK1A1 7462 0.049 0.46 NO
80 WNT10B WNT10B WNT10B 7490 0.049 0.46 NO
81 CREBBP CREBBP CREBBP 7530 0.048 0.46 NO
82 TBL1X TBL1X TBL1X 7532 0.048 0.46 NO
83 FBXW11 FBXW11 FBXW11 7600 0.047 0.46 NO
84 TBL1XR1 TBL1XR1 TBL1XR1 7694 0.045 0.46 NO
85 GSK3B GSK3B GSK3B 7929 0.041 0.45 NO
86 BTRC BTRC BTRC 7959 0.041 0.45 NO
87 SFRP5 SFRP5 SFRP5 7993 0.04 0.45 NO
88 SMAD4 SMAD4 SMAD4 8086 0.039 0.45 NO
89 LRP6 LRP6 LRP6 8245 0.036 0.44 NO
90 CUL1 CUL1 CUL1 8271 0.036 0.44 NO
91 CTNNBIP1 CTNNBIP1 CTNNBIP1 8390 0.034 0.43 NO
92 NFAT5 NFAT5 NFAT5 8524 0.031 0.43 NO
93 DVL1 DVL1 DVL1 8606 0.03 0.42 NO
94 PLCB3 PLCB3 PLCB3 8713 0.028 0.42 NO
95 FRAT1 FRAT1 FRAT1 8725 0.028 0.42 NO
96 MYC MYC MYC 8752 0.028 0.42 NO
97 PSEN1 PSEN1 PSEN1 8850 0.026 0.42 NO
98 CCND2 CCND2 CCND2 8866 0.026 0.42 NO
99 CSNK2A1 CSNK2A1 CSNK2A1 8891 0.025 0.42 NO
100 SIAH1 SIAH1 SIAH1 8936 0.025 0.42 NO
101 PRKACA PRKACA PRKACA 8984 0.024 0.42 NO
102 MAPK10 MAPK10 MAPK10 9218 0.02 0.4 NO
103 RHOA RHOA RHOA 9523 0.016 0.39 NO
104 DVL3 DVL3 DVL3 9533 0.015 0.39 NO
105 FZD8 FZD8 FZD8 9581 0.014 0.38 NO
106 TP53 TP53 TP53 9629 0.014 0.38 NO
107 PLCB4 PLCB4 PLCB4 9704 0.013 0.38 NO
108 PPP2R5B PPP2R5B PPP2R5B 9804 0.011 0.37 NO
109 PPP2R5D PPP2R5D PPP2R5D 9957 0.0086 0.37 NO
110 CAMK2D CAMK2D CAMK2D 10117 0.006 0.36 NO
111 CAMK2G CAMK2G CAMK2G 10465 -0.000041 0.34 NO
112 PRICKLE2 PRICKLE2 PRICKLE2 10496 -0.00061 0.34 NO
113 SKP1 SKP1 SKP1 10565 -0.0014 0.33 NO
114 RBX1 RBX1 RBX1 10746 -0.0046 0.32 NO
115 FZD2 FZD2 FZD2 10951 -0.0082 0.31 NO
116 PPP2CA PPP2CA PPP2CA 10981 -0.0088 0.31 NO
117 WNT5B WNT5B WNT5B 11042 -0.0096 0.31 NO
118 FZD4 FZD4 FZD4 11051 -0.0098 0.31 NO
119 WNT3 WNT3 WNT3 11076 -0.01 0.31 NO
120 PPP2CB PPP2CB PPP2CB 11155 -0.011 0.3 NO
121 FRAT2 FRAT2 FRAT2 11189 -0.012 0.3 NO
122 PPP2R1A PPP2R1A PPP2R1A 11221 -0.012 0.3 NO
123 MAPK9 MAPK9 MAPK9 11373 -0.015 0.29 NO
124 RAC1 RAC1 RAC1 11607 -0.019 0.28 NO
125 FZD5 FZD5 FZD5 11681 -0.02 0.28 NO
126 FZD9 FZD9 FZD9 11988 -0.026 0.26 NO
127 PRKCA PRKCA PRKCA 12074 -0.027 0.26 NO
128 CTBP1 CTBP1 CTBP1 12192 -0.03 0.25 NO
129 CACYBP CACYBP CACYBP 12195 -0.03 0.26 NO
130 CSNK2B CSNK2B CSNK2B 12248 -0.031 0.25 NO
131 NLK NLK NLK 12290 -0.031 0.25 NO
132 RUVBL1 RUVBL1 RUVBL1 12726 -0.04 0.23 NO
133 DVL2 DVL2 DVL2 12897 -0.043 0.22 NO
134 CHP CHP CHP 12924 -0.044 0.22 NO
135 FZD1 FZD1 FZD1 13052 -0.046 0.22 NO
136 AXIN1 AXIN1 AXIN1 13270 -0.05 0.21 NO
137 WIF1 WIF1 WIF1 14344 -0.076 0.15 NO
138 CSNK2A2 CSNK2A2 CSNK2A2 14427 -0.078 0.15 NO
139 WNT5A WNT5A WNT5A 14514 -0.081 0.15 NO
140 WNT11 WNT11 WNT11 14618 -0.084 0.15 NO
141 WNT2B WNT2B WNT2B 14946 -0.093 0.14 NO
142 APC2 APC2 APC2 15344 -0.11 0.12 NO
143 CAMK2B CAMK2B CAMK2B 16523 -0.16 0.061 NO
144 PRKCG PRKCG PRKCG 16936 -0.19 0.047 NO
145 RAC3 RAC3 RAC3 17236 -0.23 0.042 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 CHEMOKINE SIGNALING PATHWAY.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus5 enriched pathways

Table 7.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG OOCYTE MEIOSIS 106 genes.ES.table 0.5 1.7 0.016 1 0.78 0.27 0.14 0.24 0.56 0.34
KEGG UBIQUITIN MEDIATED PROTEOLYSIS 134 genes.ES.table 0.29 1.6 0.051 0.78 0.88 0.35 0.31 0.24 0.44 0.25
KEGG ADHERENS JUNCTION 73 genes.ES.table 0.44 1.6 0.025 1 0.84 0.19 0.13 0.17 0.59 0.34
KEGG THYROID CANCER 29 genes.ES.table 0.61 1.8 0.0021 1 0.49 0.24 0.13 0.21 0 0.44
BIOCARTA MPR PATHWAY 33 genes.ES.table 0.56 1.8 0.0021 1 0.58 0.21 0.083 0.2 0.59 0.38
BIOCARTA VEGF PATHWAY 29 genes.ES.table 0.56 1.6 0.053 0.77 0.88 0.34 0.19 0.28 0.45 0.25
PID AURORA B PATHWAY 39 genes.ES.table 0.71 1.6 0.034 1 0.86 0.51 0.14 0.44 0.61 0.34
PID DELTANP63PATHWAY 46 genes.ES.table 0.64 1.7 0.01 1 0.76 0.37 0.17 0.31 0.6 0.35
PID AURORA A PATHWAY 31 genes.ES.table 0.6 1.6 0.057 1 0.86 0.23 0.052 0.22 0.57 0.32
REACTOME CELL CYCLE 372 genes.ES.table 0.48 1.6 0.079 0.96 0.86 0.38 0.25 0.29 0.54 0.31
genes ES table in pathway: KEGG OOCYTE MEIOSIS

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 RET RET RET 356 0.37 0.13 YES
2 TCF7L1 TCF7L1 TCF7L1 456 0.35 0.26 YES
3 LEF1 LEF1 LEF1 497 0.34 0.39 YES
4 CDH1 CDH1 CDH1 1079 0.25 0.46 YES
5 RXRG RXRG RXRG 1264 0.23 0.54 YES
6 MYC MYC MYC 1922 0.18 0.57 YES
7 RXRA RXRA RXRA 2313 0.15 0.61 YES
8 CCND1 CCND1 CCND1 3678 0.094 0.57 NO
9 MAP2K1 MAP2K1 MAP2K1 4493 0.074 0.55 NO
10 BRAF BRAF BRAF 4896 0.066 0.56 NO
11 MAP2K2 MAP2K2 MAP2K2 5285 0.058 0.56 NO
12 TPR TPR TPR 5602 0.053 0.56 NO
13 CCDC6 CCDC6 CCDC6 7515 0.024 0.46 NO
14 NTRK1 NTRK1 NTRK1 8324 0.014 0.42 NO
15 NRAS NRAS NRAS 8337 0.014 0.43 NO
16 MAPK3 MAPK3 MAPK3 8769 0.0075 0.41 NO
17 TPM3 TPM3 TPM3 8888 0.006 0.4 NO
18 NCOA4 NCOA4 NCOA4 9430 -0.0015 0.37 NO
19 TP53 TP53 TP53 9503 -0.0025 0.37 NO
20 PPARG PPARG PPARG 9565 -0.0034 0.37 NO
21 TFG TFG TFG 9824 -0.0068 0.36 NO
22 TCF7L2 TCF7L2 TCF7L2 9898 -0.0079 0.36 NO
23 KRAS KRAS KRAS 10253 -0.014 0.34 NO
24 TCF7 TCF7 TCF7 10558 -0.018 0.33 NO
25 MAPK1 MAPK1 MAPK1 10625 -0.019 0.33 NO
26 RXRB RXRB RXRB 10629 -0.019 0.34 NO
27 HRAS HRAS HRAS 10648 -0.019 0.35 NO
28 CTNNB1 CTNNB1 CTNNB1 11801 -0.037 0.3 NO
29 PAX8 PAX8 PAX8 14948 -0.12 0.17 NO

Figure S81.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OOCYTE MEIOSIS.

Figure S82.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OOCYTE MEIOSIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS

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 ADCY1 ADCY1 ADCY1 138 0.45 0.12 YES
2 CDC25C CDC25C CDC25C 160 0.44 0.24 YES
3 CDK1 CDK1 CDK1 434 0.35 0.32 YES
4 CCNB1 CCNB1 CCNB1 656 0.31 0.39 YES
5 PGR PGR PGR 701 0.3 0.47 YES
6 MYT1 MYT1 MYT1 848 0.28 0.54 YES
7 PRKAR2B PRKAR2B PRKAR2B 1488 0.21 0.56 YES
8 ACTR3 ACTR3 ACTR3 5420 0.056 0.36 NO
9 ACTR2 ACTR2 ACTR2 5913 0.048 0.35 NO
10 PRKAR2A PRKAR2A PRKAR2A 6327 0.041 0.34 NO
11 ARPC2 ARPC2 ARPC2 6391 0.04 0.34 NO
12 GNAS GNAS GNAS 6686 0.036 0.34 NO
13 PIN1 PIN1 PIN1 6840 0.034 0.34 NO
14 PRKAR1A PRKAR1A PRKAR1A 7424 0.026 0.31 NO
15 ARPC5 ARPC5 ARPC5 7730 0.021 0.3 NO
16 ARPC3 ARPC3 ARPC3 8410 0.012 0.27 NO
17 ARPC1A ARPC1A ARPC1A 8720 0.0081 0.25 NO
18 MAPK3 MAPK3 MAPK3 8769 0.0075 0.25 NO
19 SRC SRC SRC 9533 -0.0029 0.21 NO
20 PAQR5 PAQR5 PAQR5 10214 -0.013 0.18 NO
21 CAP1 CAP1 CAP1 10355 -0.015 0.17 NO
22 MAPK1 MAPK1 MAPK1 10625 -0.019 0.16 NO
23 HRAS HRAS HRAS 10648 -0.019 0.17 NO
24 PRKAR1B PRKAR1B PRKAR1B 11445 -0.032 0.13 NO
25 GNB1 GNB1 GNB1 11959 -0.04 0.11 NO
26 ARPC4 ARPC4 ARPC4 12446 -0.049 0.099 NO
27 ACTA1 ACTA1 ACTA1 13103 -0.063 0.08 NO
28 PAQR7 PAQR7 PAQR7 13828 -0.08 0.062 NO
29 ARPC1B ARPC1B ARPC1B 14428 -0.099 0.056 NO
30 PRKACB PRKACB PRKACB 14642 -0.11 0.073 NO
31 RPS6KA1 RPS6KA1 RPS6KA1 14842 -0.11 0.093 NO
32 GNAI1 GNAI1 GNAI1 15154 -0.13 0.11 NO
33 GNGT1 GNGT1 GNGT1 16000 -0.17 0.11 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 UBIQUITIN MEDIATED PROTEOLYSIS.

Figure S84.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG UBIQUITIN MEDIATED PROTEOLYSIS, 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 ADHERENS JUNCTION

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 RQCD1 RQCD1 RQCD1 2146 0.16 -0.034 YES
2 DCPS DCPS DCPS 2482 0.14 0.022 YES
3 PABPC1 PABPC1 PABPC1 2876 0.12 0.065 YES
4 EIF4E EIF4E EIF4E 3192 0.11 0.11 YES
5 EXOSC5 EXOSC5 EXOSC5 3490 0.099 0.14 YES
6 PATL1 PATL1 PATL1 3600 0.096 0.19 YES
7 EIF4B EIF4B EIF4B 4298 0.078 0.19 YES
8 CNOT8 CNOT8 CNOT8 4735 0.069 0.2 YES
9 PAIP1 PAIP1 PAIP1 4833 0.067 0.23 YES
10 TNKS1BP1 TNKS1BP1 TNKS1BP1 5058 0.062 0.26 YES
11 EDC3 EDC3 EDC3 5548 0.054 0.26 YES
12 EXOSC4 EXOSC4 EXOSC4 5966 0.047 0.26 YES
13 EXOSC9 EXOSC9 EXOSC9 6009 0.047 0.28 YES
14 EXOSC7 EXOSC7 EXOSC7 6309 0.042 0.29 YES
15 EXOSC1 EXOSC1 EXOSC1 6510 0.038 0.3 YES
16 LSM1 LSM1 LSM1 6559 0.038 0.31 YES
17 EXOSC3 EXOSC3 EXOSC3 6773 0.034 0.32 YES
18 LSM6 LSM6 LSM6 6839 0.034 0.34 YES
19 EXOSC2 EXOSC2 EXOSC2 6896 0.033 0.35 YES
20 CNOT7 CNOT7 CNOT7 6913 0.032 0.37 YES
21 LSM2 LSM2 LSM2 6988 0.031 0.38 YES
22 EIF4A2 EIF4A2 EIF4A2 7058 0.03 0.39 YES
23 CNOT6 CNOT6 CNOT6 7176 0.029 0.4 YES
24 EXOSC6 EXOSC6 EXOSC6 7388 0.026 0.4 YES
25 C2orf29 C2orf29 C2orf29 7587 0.023 0.4 YES
26 EIF4A3 EIF4A3 EIF4A3 8252 0.015 0.37 NO
27 DCP1B DCP1B DCP1B 8375 0.013 0.38 NO
28 LSM4 LSM4 LSM4 8687 0.0085 0.36 NO
29 DIS3 DIS3 DIS3 8793 0.0072 0.36 NO
30 CNOT3 CNOT3 CNOT3 8933 0.0054 0.36 NO
31 PARN PARN PARN 8949 0.0051 0.36 NO
32 CNOT2 CNOT2 CNOT2 8996 0.0045 0.36 NO
33 CNOT10 CNOT10 CNOT10 9137 0.0028 0.35 NO
34 DDX6 DDX6 DDX6 9182 0.0021 0.35 NO
35 DCP2 DCP2 DCP2 9423 -0.0014 0.34 NO
36 EIF4G1 EIF4G1 EIF4G1 9447 -0.0018 0.34 NO
37 XRN1 XRN1 XRN1 9621 -0.004 0.33 NO
38 EIF4A1 EIF4A1 EIF4A1 10110 -0.011 0.31 NO
39 EDC4 EDC4 EDC4 10334 -0.014 0.3 NO
40 LSM3 LSM3 LSM3 10702 -0.02 0.29 NO
41 EXOSC8 EXOSC8 EXOSC8 11871 -0.038 0.25 NO
42 CNOT4 CNOT4 CNOT4 12596 -0.052 0.24 NO
43 DCP1A DCP1A DCP1A 12730 -0.055 0.26 NO
44 LSM5 LSM5 LSM5 13206 -0.065 0.27 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 ADHERENS JUNCTION.

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

genes ES table in pathway: KEGG THYROID CANCER

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 PDE3B PDE3B PDE3B 255 0.4 0.22 YES
2 STRADB STRADB STRADB 2645 0.13 0.16 YES
3 EIF4EBP1 EIF4EBP1 EIF4EBP1 2803 0.12 0.22 YES
4 PRKAG2 PRKAG2 PRKAG2 2980 0.12 0.28 YES
5 PRKAB2 PRKAB2 PRKAB2 3099 0.11 0.34 YES
6 EIF4E EIF4E EIF4E 3192 0.11 0.4 YES
7 EIF4B EIF4B EIF4B 4298 0.078 0.38 YES
8 PRKAA1 PRKAA1 PRKAA1 4626 0.071 0.4 YES
9 RHEB RHEB RHEB 5243 0.059 0.4 YES
10 PRKAG1 PRKAG1 PRKAG1 5377 0.056 0.43 YES
11 RPS6KB1 RPS6KB1 RPS6KB1 6231 0.043 0.4 YES
12 EEF2K EEF2K EEF2K 6280 0.042 0.43 YES
13 STK11 STK11 STK11 6820 0.034 0.42 YES
14 CAB39 CAB39 CAB39 6898 0.033 0.43 YES
15 RPS6 RPS6 RPS6 7040 0.031 0.44 YES
16 MLST8 MLST8 MLST8 7572 0.024 0.42 NO
17 CAB39L CAB39L CAB39L 8576 0.01 0.37 NO
18 TSC2 TSC2 TSC2 8982 0.0047 0.35 NO
19 RPTOR RPTOR RPTOR 9172 0.0022 0.34 NO
20 PPM1A PPM1A PPM1A 9256 0.00076 0.34 NO
21 AKT2 AKT2 AKT2 9303 0.00029 0.34 NO
22 EIF4G1 EIF4G1 EIF4G1 9447 -0.0018 0.33 NO
23 STRADA STRADA STRADA 10055 -0.01 0.3 NO
24 TSC1 TSC1 TSC1 10457 -0.016 0.29 NO
25 MTOR MTOR MTOR 12130 -0.043 0.22 NO
26 PRKAB1 PRKAB1 PRKAB1 13568 -0.073 0.18 NO
27 PRKAA2 PRKAA2 PRKAA2 14686 -0.11 0.18 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 THYROID CANCER.

Figure S88.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG THYROID CANCER, 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 MPR PATHWAY

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 LZTS1 LZTS1 LZTS1 1839 0.18 0.016 YES
2 SNAPC1 SNAPC1 SNAPC1 2338 0.15 0.085 YES
3 BRF2 BRF2 BRF2 2633 0.13 0.16 YES
4 POLR3D POLR3D POLR3D 2890 0.12 0.22 YES
5 POLR3C POLR3C POLR3C 3614 0.095 0.24 YES
6 POLR2K POLR2K POLR2K 3866 0.088 0.28 YES
7 POLR3A POLR3A POLR3A 4197 0.08 0.32 YES
8 SNAPC2 SNAPC2 SNAPC2 4372 0.076 0.36 YES
9 POLR3B POLR3B POLR3B 4460 0.075 0.4 YES
10 POLR3K POLR3K POLR3K 4773 0.068 0.43 YES
11 SNAPC3 SNAPC3 SNAPC3 4909 0.066 0.46 YES
12 SNAPC5 SNAPC5 SNAPC5 5695 0.051 0.46 NO
13 POLR1D POLR1D POLR1D 6492 0.039 0.44 NO
14 ZNF143 ZNF143 ZNF143 7302 0.027 0.41 NO
15 POLR3E POLR3E POLR3E 7657 0.022 0.4 NO
16 POLR1C POLR1C POLR1C 8235 0.015 0.38 NO
17 POLR2F POLR2F POLR2F 8742 0.0078 0.36 NO
18 POLR2E POLR2E POLR2E 9938 -0.0086 0.3 NO
19 TBP TBP TBP 10063 -0.01 0.3 NO
20 POLR3F POLR3F POLR3F 10390 -0.015 0.29 NO
21 POLR2L POLR2L POLR2L 10444 -0.016 0.3 NO
22 POLR3H POLR3H POLR3H 10569 -0.018 0.3 NO
23 POLR2H POLR2H POLR2H 10977 -0.024 0.29 NO
24 POLR3GL POLR3GL POLR3GL 11383 -0.03 0.29 NO
25 SNAPC4 SNAPC4 SNAPC4 12167 -0.044 0.28 NO
26 POU2F1 POU2F1 POU2F1 13516 -0.072 0.25 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: BIOCARTA MPR PATHWAY.

Figure S90.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA MPR 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 VEGF PATHWAY

Table S46.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GPX2 GPX2 GPX2 210 0.41 0.068 YES
2 CCNB2 CCNB2 CCNB2 244 0.4 0.14 YES
3 TCF7L1 TCF7L1 TCF7L1 456 0.35 0.2 YES
4 HELLS HELLS HELLS 470 0.34 0.26 YES
5 TOP2A TOP2A TOP2A 532 0.33 0.32 YES
6 DLX6 DLX6 DLX6 749 0.3 0.37 YES
7 COL5A1 COL5A1 COL5A1 931 0.27 0.41 YES
8 BDKRB2 BDKRB2 BDKRB2 1024 0.26 0.46 YES
9 BRCA2 BRCA2 BRCA2 1371 0.22 0.48 YES
10 DLX5 DLX5 DLX5 1577 0.2 0.51 YES
11 RAB38 RAB38 RAB38 1763 0.19 0.54 YES
12 STXBP4 STXBP4 STXBP4 1782 0.19 0.57 YES
13 NRG1 NRG1 NRG1 2141 0.16 0.58 YES
14 TP63 TP63 TP63 2174 0.16 0.61 YES
15 ADA ADA ADA 2337 0.15 0.63 YES
16 FASN FASN FASN 2853 0.12 0.62 YES
17 IGFBP3 IGFBP3 IGFBP3 3052 0.11 0.64 YES
18 KRT14 KRT14 KRT14 3989 0.085 0.6 NO
19 WWP1 WWP1 WWP1 4969 0.064 0.56 NO
20 YAP1 YAP1 YAP1 5341 0.057 0.55 NO
21 GNB2L1 GNB2L1 GNB2L1 5614 0.052 0.54 NO
22 MRE11A MRE11A MRE11A 5890 0.048 0.54 NO
23 RUNX1 RUNX1 RUNX1 5939 0.048 0.54 NO
24 NOTCH1 NOTCH1 NOTCH1 6519 0.038 0.52 NO
25 PPP2R5A PPP2R5A PPP2R5A 7252 0.028 0.48 NO
26 ITCH ITCH ITCH 7392 0.026 0.48 NO
27 POU2F2 POU2F2 POU2F2 7769 0.021 0.46 NO
28 CDKN2A CDKN2A CDKN2A 8464 0.012 0.43 NO
29 MDM2 MDM2 MDM2 8632 0.0093 0.42 NO
30 ADRM1 ADRM1 ADRM1 8673 0.0087 0.42 NO
31 FOSL2 FOSL2 FOSL2 9060 0.0037 0.4 NO
32 KRT5 KRT5 KRT5 9076 0.0035 0.4 NO
33 IL1A IL1A IL1A 9381 -0.00085 0.38 NO
34 FBXW7 FBXW7 FBXW7 9489 -0.0024 0.38 NO
35 GSK3B GSK3B GSK3B 9550 -0.0031 0.37 NO
36 CEBPD CEBPD CEBPD 9950 -0.0088 0.35 NO
37 VDR VDR VDR 10388 -0.015 0.33 NO
38 ATM ATM ATM 10588 -0.018 0.32 NO
39 ITGA3 ITGA3 ITGA3 10606 -0.018 0.33 NO
40 SFN SFN SFN 10793 -0.021 0.32 NO
41 PERP PERP PERP 11151 -0.027 0.3 NO
42 HBP1 HBP1 HBP1 11698 -0.035 0.28 NO
43 SEC14L2 SEC14L2 SEC14L2 13478 -0.071 0.2 NO
44 AXL AXL AXL 13671 -0.076 0.2 NO
45 RRAD RRAD RRAD 14498 -0.1 0.17 NO
46 HES1 HES1 HES1 14674 -0.11 0.18 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: BIOCARTA VEGF PATHWAY.

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

genes ES table in pathway: PID AURORA B PATHWAY

Table 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 BUB1 BUB1 BUB1 31 0.57 0.042 YES
2 CCNE1 CCNE1 CCNE1 110 0.46 0.073 YES
3 ADCY1 ADCY1 ADCY1 138 0.45 0.1 YES
4 CDC25C CDC25C CDC25C 160 0.44 0.14 YES
5 CCNB2 CCNB2 CCNB2 244 0.4 0.16 YES
6 PTTG1 PTTG1 PTTG1 299 0.39 0.19 YES
7 MAD2L1 MAD2L1 MAD2L1 426 0.35 0.21 YES
8 CDK1 CDK1 CDK1 434 0.35 0.24 YES
9 CPEB1 CPEB1 CPEB1 513 0.34 0.26 YES
10 CCNB1 CCNB1 CCNB1 656 0.31 0.27 YES
11 PGR PGR PGR 701 0.3 0.29 YES
12 SGOL1 SGOL1 SGOL1 704 0.3 0.32 YES
13 CHP2 CHP2 CHP2 716 0.3 0.34 YES
14 ADCY3 ADCY3 ADCY3 762 0.3 0.36 YES
15 AURKA AURKA AURKA 809 0.29 0.38 YES
16 CCNE2 CCNE2 CCNE2 1061 0.26 0.38 YES
17 PLK1 PLK1 PLK1 1108 0.25 0.4 YES
18 CDC20 CDC20 CDC20 1177 0.24 0.42 YES
19 ESPL1 ESPL1 ESPL1 1285 0.23 0.43 YES
20 PKMYT1 PKMYT1 PKMYT1 1390 0.22 0.44 YES
21 ADCY4 ADCY4 ADCY4 1507 0.21 0.45 YES
22 SMC1B SMC1B SMC1B 1587 0.2 0.46 YES
23 CAMK2A CAMK2A CAMK2A 1594 0.2 0.47 YES
24 ITPR2 ITPR2 ITPR2 1721 0.19 0.48 YES
25 PTTG2 PTTG2 PTTG2 1810 0.18 0.49 YES
26 FBXO43 FBXO43 FBXO43 1932 0.17 0.5 YES
27 RPS6KA6 RPS6KA6 RPS6KA6 2065 0.16 0.5 YES
28 ITPR1 ITPR1 ITPR1 2364 0.15 0.5 YES
29 MAPK12 MAPK12 MAPK12 2439 0.14 0.5 YES
30 ANAPC1 ANAPC1 ANAPC1 2787 0.12 0.49 NO
31 FBXO5 FBXO5 FBXO5 2852 0.12 0.5 NO
32 FBXW11 FBXW11 FBXW11 3441 0.1 0.48 NO
33 SKP1 SKP1 SKP1 3971 0.086 0.45 NO
34 CDC27 CDC27 CDC27 4040 0.084 0.45 NO
35 ANAPC10 ANAPC10 ANAPC10 4181 0.081 0.45 NO
36 PPP2R5D PPP2R5D PPP2R5D 4225 0.08 0.46 NO
37 MAD2L2 MAD2L2 MAD2L2 4266 0.078 0.46 NO
38 SMC3 SMC3 SMC3 4287 0.078 0.46 NO
39 MAP2K1 MAP2K1 MAP2K1 4493 0.074 0.46 NO
40 ADCY7 ADCY7 ADCY7 4927 0.065 0.44 NO
41 ADCY8 ADCY8 ADCY8 4998 0.064 0.44 NO
42 PPP3R1 PPP3R1 PPP3R1 5180 0.06 0.44 NO
43 PPP2R5E PPP2R5E PPP2R5E 5452 0.055 0.42 NO
44 PPP1CC PPP1CC PPP1CC 5779 0.05 0.41 NO
45 PPP1CB PPP1CB PPP1CB 5803 0.05 0.41 NO
46 CDC23 CDC23 CDC23 5914 0.048 0.41 NO
47 SMC1A SMC1A SMC1A 5932 0.048 0.41 NO
48 YWHAB YWHAB YWHAB 6062 0.046 0.41 NO
49 PPP2CA PPP2CA PPP2CA 6245 0.043 0.4 NO
50 ADCY6 ADCY6 ADCY6 6303 0.042 0.4 NO
51 RPS6KA3 RPS6KA3 RPS6KA3 6336 0.041 0.4 NO
52 CALML6 CALML6 CALML6 6613 0.037 0.39 NO
53 SLK SLK SLK 6618 0.037 0.39 NO
54 PPP2R1B PPP2R1B PPP2R1B 6682 0.036 0.39 NO
55 YWHAQ YWHAQ YWHAQ 7126 0.029 0.37 NO
56 ANAPC5 ANAPC5 ANAPC5 7245 0.028 0.36 NO
57 PPP2R5A PPP2R5A PPP2R5A 7252 0.028 0.37 NO
58 PPP2R5C PPP2R5C PPP2R5C 7330 0.027 0.36 NO
59 PPP3CC PPP3CC PPP3CC 7529 0.024 0.36 NO
60 YWHAZ YWHAZ YWHAZ 7774 0.021 0.34 NO
61 PRKACA PRKACA PRKACA 7814 0.02 0.34 NO
62 CALM3 CALM3 CALM3 7912 0.019 0.34 NO
63 CHP CHP CHP 8052 0.017 0.33 NO
64 CDK2 CDK2 CDK2 8309 0.014 0.32 NO
65 PPP2CB PPP2CB PPP2CB 8377 0.013 0.32 NO
66 YWHAG YWHAG YWHAG 8480 0.012 0.31 NO
67 ANAPC11 ANAPC11 ANAPC11 8499 0.011 0.31 NO
68 CAMK2G CAMK2G CAMK2G 8655 0.009 0.3 NO
69 MAPK3 MAPK3 MAPK3 8769 0.0075 0.3 NO
70 PPP2R1A PPP2R1A PPP2R1A 8830 0.0068 0.3 NO
71 ANAPC7 ANAPC7 ANAPC7 8834 0.0067 0.3 NO
72 PPP3CA PPP3CA PPP3CA 8952 0.0051 0.29 NO
73 SPDYA SPDYA SPDYA 9079 0.0035 0.28 NO
74 CALM2 CALM2 CALM2 9101 0.0033 0.28 NO
75 CDC26 CDC26 CDC26 9112 0.0032 0.28 NO
76 CUL1 CUL1 CUL1 9458 -0.0019 0.26 NO
77 PPP1CA PPP1CA PPP1CA 10038 -0.01 0.23 NO
78 BTRC BTRC BTRC 10041 -0.01 0.23 NO
79 PPP3CB PPP3CB PPP3CB 10431 -0.016 0.21 NO
80 MAPK1 MAPK1 MAPK1 10625 -0.019 0.2 NO
81 CDC16 CDC16 CDC16 10841 -0.022 0.19 NO
82 ADCY5 ADCY5 ADCY5 11252 -0.028 0.17 NO
83 RBX1 RBX1 RBX1 11259 -0.029 0.17 NO
84 IGF1R IGF1R IGF1R 11365 -0.03 0.17 NO
85 ANAPC4 ANAPC4 ANAPC4 11896 -0.039 0.14 NO
86 CAMK2D CAMK2D CAMK2D 11930 -0.04 0.14 NO
87 YWHAE YWHAE YWHAE 11943 -0.04 0.14 NO
88 YWHAH YWHAH YWHAH 12310 -0.047 0.13 NO
89 PPP2R5B PPP2R5B PPP2R5B 13166 -0.064 0.085 NO
90 CALM1 CALM1 CALM1 13370 -0.069 0.079 NO
91 ITPR3 ITPR3 ITPR3 13543 -0.073 0.075 NO
92 ANAPC13 ANAPC13 ANAPC13 13631 -0.075 0.076 NO
93 ANAPC2 ANAPC2 ANAPC2 13759 -0.079 0.075 NO
94 PRKX PRKX PRKX 13770 -0.079 0.08 NO
95 IGF1 IGF1 IGF1 14477 -0.1 0.048 NO
96 PRKACB PRKACB PRKACB 14642 -0.11 0.047 NO
97 REC8 REC8 REC8 14702 -0.11 0.052 NO
98 RPS6KA1 RPS6KA1 RPS6KA1 14842 -0.11 0.053 NO
99 ADCY9 ADCY9 ADCY9 14844 -0.11 0.062 NO
100 CALML3 CALML3 CALML3 14954 -0.12 0.064 NO
101 RPS6KA2 RPS6KA2 RPS6KA2 15239 -0.13 0.058 NO
102 PLCZ1 PLCZ1 PLCZ1 15852 -0.16 0.036 NO
103 ADCY2 ADCY2 ADCY2 16006 -0.17 0.041 NO
104 STAG3 STAG3 STAG3 16419 -0.2 0.034 NO
105 AR AR AR 16907 -0.25 0.026 NO
106 CAMK2B CAMK2B CAMK2B 17775 -0.45 0.012 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: PID AURORA B PATHWAY.

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

genes ES table in pathway: PID DELTANP63PATHWAY

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 CCNE1 CCNE1 CCNE1 110 0.46 0.036 YES
2 CDK1 CDK1 CDK1 434 0.35 0.05 YES
3 MCM10 MCM10 MCM10 437 0.35 0.083 YES
4 CCNB1 CCNB1 CCNB1 656 0.31 0.099 YES
5 RRM2 RRM2 RRM2 680 0.31 0.13 YES
6 CDC6 CDC6 CDC6 703 0.3 0.15 YES
7 CCNA2 CCNA2 CCNA2 806 0.29 0.17 YES
8 CCNE2 CCNE2 CCNE2 1061 0.26 0.18 YES
9 E2F1 E2F1 E2F1 1196 0.24 0.2 YES
10 CDKN2C CDKN2C CDKN2C 1249 0.24 0.22 YES
11 RBL1 RBL1 RBL1 1307 0.23 0.23 YES
12 MYBL2 MYBL2 MYBL2 1313 0.23 0.26 YES
13 CDC45 CDC45 CDC45 1358 0.22 0.27 YES
14 PKMYT1 PKMYT1 PKMYT1 1390 0.22 0.29 YES
15 RPA4 RPA4 RPA4 1431 0.22 0.31 YES
16 MCM4 MCM4 MCM4 1655 0.2 0.31 YES
17 LIN9 LIN9 LIN9 1766 0.19 0.32 YES
18 SKP2 SKP2 SKP2 1778 0.19 0.34 YES
19 E2F2 E2F2 E2F2 1836 0.18 0.36 YES
20 CDT1 CDT1 CDT1 1845 0.18 0.37 YES
21 MYC MYC MYC 1922 0.18 0.38 YES
22 MCM6 MCM6 MCM6 2063 0.17 0.39 YES
23 DBF4 DBF4 DBF4 2248 0.15 0.39 YES
24 POLE2 POLE2 POLE2 2382 0.15 0.4 YES
25 POLA1 POLA1 POLA1 2790 0.12 0.39 YES
26 CDK7 CDK7 CDK7 2831 0.12 0.4 YES
27 FBXO5 FBXO5 FBXO5 2852 0.12 0.41 YES
28 PRIM1 PRIM1 PRIM1 2855 0.12 0.42 YES
29 CDC25A CDC25A CDC25A 2868 0.12 0.43 YES
30 CKS1B CKS1B CKS1B 3233 0.11 0.42 YES
31 WEE1 WEE1 WEE1 3335 0.1 0.42 YES
32 CDK4 CDK4 CDK4 3410 0.1 0.43 YES
33 CCNH CCNH CCNH 3469 0.1 0.43 YES
34 PSMD10 PSMD10 PSMD10 3520 0.098 0.44 YES
35 MCM2 MCM2 MCM2 3558 0.097 0.45 YES
36 CCND1 CCND1 CCND1 3678 0.094 0.45 YES
37 PPP2R3B PPP2R3B PPP2R3B 3807 0.09 0.45 YES
38 RPS27A RPS27A RPS27A 3903 0.087 0.45 YES
39 POLA2 POLA2 POLA2 3920 0.087 0.46 YES
40 PSMD14 PSMD14 PSMD14 3937 0.087 0.47 YES
41 SKP1 SKP1 SKP1 3971 0.086 0.47 YES
42 PPP2R2A PPP2R2A PPP2R2A 3992 0.085 0.48 YES
43 LIN54 LIN54 LIN54 3998 0.085 0.49 YES
44 DHFR DHFR DHFR 4131 0.082 0.49 YES
45 MCM8 MCM8 MCM8 4132 0.082 0.5 YES
46 E2F5 E2F5 E2F5 4148 0.082 0.5 YES
47 PSMD8 PSMD8 PSMD8 4360 0.077 0.5 NO
48 CCNA1 CCNA1 CCNA1 4478 0.074 0.5 NO
49 PSMD11 PSMD11 PSMD11 4836 0.067 0.48 NO
50 PSMD1 PSMD1 PSMD1 4992 0.064 0.48 NO
51 E2F3 E2F3 E2F3 5208 0.059 0.47 NO
52 CDKN2B CDKN2B CDKN2B 5505 0.054 0.46 NO
53 PCNA PCNA PCNA 5535 0.054 0.47 NO
54 PSMA1 PSMA1 PSMA1 5743 0.051 0.46 NO
55 PRIM2 PRIM2 PRIM2 5801 0.05 0.46 NO
56 UBA52 UBA52 UBA52 5820 0.05 0.46 NO
57 PSMD12 PSMD12 PSMD12 5893 0.048 0.46 NO
58 PSMD4 PSMD4 PSMD4 5983 0.047 0.46 NO
59 PSMB4 PSMB4 PSMB4 6199 0.044 0.46 NO
60 PPP2CA PPP2CA PPP2CA 6245 0.043 0.46 NO
61 MNAT1 MNAT1 MNAT1 6264 0.042 0.46 NO
62 PSMD3 PSMD3 PSMD3 6342 0.041 0.46 NO
63 PSMA6 PSMA6 PSMA6 6464 0.039 0.46 NO
64 PSMA7 PSMA7 PSMA7 6517 0.038 0.46 NO
65 PPP2R1B PPP2R1B PPP2R1B 6682 0.036 0.45 NO
66 PSMA4 PSMA4 PSMA4 6701 0.036 0.45 NO
67 CDKN1B CDKN1B CDKN1B 7006 0.031 0.44 NO
68 DYRK1A DYRK1A DYRK1A 7211 0.028 0.43 NO
69 CCND3 CCND3 CCND3 7352 0.026 0.42 NO
70 PSMA3 PSMA3 PSMA3 7546 0.024 0.42 NO
71 PSMD2 PSMD2 PSMD2 7549 0.024 0.42 NO
72 CDKN2D CDKN2D CDKN2D 7619 0.023 0.42 NO
73 PSMC4 PSMC4 PSMC4 7669 0.022 0.42 NO
74 PSMF1 PSMF1 PSMF1 7742 0.021 0.41 NO
75 E2F4 E2F4 E2F4 7844 0.02 0.41 NO
76 LIN52 LIN52 LIN52 7945 0.019 0.41 NO
77 PSMC6 PSMC6 PSMC6 8041 0.018 0.4 NO
78 PSMB5 PSMB5 PSMB5 8161 0.016 0.4 NO
79 PSMB2 PSMB2 PSMB2 8282 0.014 0.39 NO
80 CDK2 CDK2 CDK2 8309 0.014 0.39 NO
81 PPP2CB PPP2CB PPP2CB 8377 0.013 0.39 NO
82 POLE POLE POLE 8433 0.012 0.39 NO
83 CDKN2A CDKN2A CDKN2A 8464 0.012 0.39 NO
84 MCM3 MCM3 MCM3 8671 0.0087 0.38 NO
85 PSMD13 PSMD13 PSMD13 8787 0.0072 0.37 NO
86 PPP2R1A PPP2R1A PPP2R1A 8830 0.0068 0.37 NO
87 PSMD7 PSMD7 PSMD7 9118 0.0031 0.35 NO
88 LIN37 LIN37 LIN37 9240 0.0011 0.35 NO
89 PSMA5 PSMA5 PSMA5 9415 -0.0014 0.34 NO
90 CUL1 CUL1 CUL1 9458 -0.0019 0.33 NO
91 PSMD9 PSMD9 PSMD9 9517 -0.0027 0.33 NO
92 PSMB3 PSMB3 PSMB3 9689 -0.0049 0.32 NO
93 PSMC3 PSMC3 PSMC3 9730 -0.0056 0.32 NO
94 PSMB7 PSMB7 PSMB7 9891 -0.0077 0.31 NO
95 CDC7 CDC7 CDC7 9945 -0.0087 0.31 NO
96 PSMB1 PSMB1 PSMB1 10138 -0.012 0.3 NO
97 PSMD6 PSMD6 PSMD6 10197 -0.013 0.3 NO
98 PSMC5 PSMC5 PSMC5 10396 -0.015 0.29 NO
99 MAX MAX MAX 10463 -0.016 0.29 NO
100 PSME2 PSME2 PSME2 10552 -0.018 0.28 NO
101 RBBP4 RBBP4 RBBP4 10693 -0.02 0.28 NO
102 PSMC2 PSMC2 PSMC2 10711 -0.02 0.28 NO
103 TFDP1 TFDP1 TFDP1 10764 -0.021 0.28 NO
104 RB1 RB1 RB1 10916 -0.023 0.27 NO
105 PSMA2 PSMA2 PSMA2 10948 -0.024 0.27 NO
106 PSMC1 PSMC1 PSMC1 11020 -0.025 0.27 NO
107 PSME1 PSME1 PSME1 11351 -0.03 0.25 NO
108 RBL2 RBL2 RBL2 11425 -0.031 0.25 NO
109 RPA1 RPA1 RPA1 11511 -0.033 0.25 NO
110 HDAC1 HDAC1 HDAC1 11785 -0.037 0.24 NO
111 PSMB8 PSMB8 PSMB8 12008 -0.041 0.23 NO
112 PSMB10 PSMB10 PSMB10 12056 -0.042 0.23 NO
113 PSMD5 PSMD5 PSMD5 12195 -0.044 0.23 NO
114 PSMB6 PSMB6 PSMB6 12557 -0.052 0.21 NO
115 MCM5 MCM5 MCM5 12565 -0.052 0.22 NO
116 CDK6 CDK6 CDK6 12732 -0.055 0.21 NO
117 RPA2 RPA2 RPA2 12805 -0.056 0.21 NO
118 TYMS TYMS TYMS 12820 -0.057 0.22 NO
119 PSMB9 PSMB9 PSMB9 13666 -0.076 0.18 NO
120 CDKN1A CDKN1A CDKN1A 13890 -0.082 0.17 NO
121 TK2 TK2 TK2 14512 -0.1 0.15 NO
122 RPA3 RPA3 RPA3 14688 -0.11 0.15 NO
123 MCM7 MCM7 MCM7 14711 -0.11 0.16 NO
124 CCND2 CCND2 CCND2 17262 -0.3 0.04 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: PID DELTANP63PATHWAY.

Figure S96.  Get High-res Image For the top 5 core enriched genes in the pathway: PID DELTANP63PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID AURORA A PATHWAY

Table 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 BUB1 BUB1 BUB1 31 0.57 0.017 YES
2 CCNE1 CCNE1 CCNE1 110 0.46 0.028 YES
3 CDC25C CDC25C CDC25C 160 0.44 0.04 YES
4 CENPI CENPI CENPI 162 0.44 0.054 YES
5 BUB1B BUB1B BUB1B 167 0.43 0.069 YES
6 SPC24 SPC24 SPC24 212 0.41 0.08 YES
7 CCNB2 CCNB2 CCNB2 244 0.4 0.092 YES
8 KIF18A KIF18A KIF18A 273 0.4 0.1 YES
9 PTTG1 PTTG1 PTTG1 299 0.39 0.12 YES
10 UBE2C UBE2C UBE2C 343 0.38 0.12 YES
11 ERCC6L ERCC6L ERCC6L 349 0.37 0.14 YES
12 KIF20A KIF20A KIF20A 382 0.36 0.15 YES
13 CENPA CENPA CENPA 405 0.36 0.16 YES
14 NUF2 NUF2 NUF2 412 0.36 0.17 YES
15 MAD2L1 MAD2L1 MAD2L1 426 0.35 0.18 YES
16 CDK1 CDK1 CDK1 434 0.35 0.19 YES
17 MCM10 MCM10 MCM10 437 0.35 0.2 YES
18 SKA1 SKA1 SKA1 580 0.32 0.21 YES
19 CENPK CENPK CENPK 603 0.32 0.22 YES
20 NEK2 NEK2 NEK2 612 0.32 0.23 YES
21 KIF2C KIF2C KIF2C 652 0.31 0.23 YES
22 CCNB1 CCNB1 CCNB1 656 0.31 0.24 YES
23 RRM2 RRM2 RRM2 680 0.31 0.25 YES
24 CDC6 CDC6 CDC6 703 0.3 0.26 YES
25 SGOL1 SGOL1 SGOL1 704 0.3 0.27 YES
26 BIRC5 BIRC5 BIRC5 717 0.3 0.28 YES
27 SGOL2 SGOL2 SGOL2 720 0.3 0.29 YES
28 CCNA2 CCNA2 CCNA2 806 0.29 0.3 YES
29 AURKA AURKA AURKA 809 0.29 0.31 YES
30 AURKB AURKB AURKB 926 0.27 0.31 YES
31 CENPM CENPM CENPM 948 0.27 0.32 YES
32 CCNE2 CCNE2 CCNE2 1061 0.26 0.32 YES
33 CDCA8 CDCA8 CDCA8 1107 0.25 0.32 YES
34 PLK1 PLK1 PLK1 1108 0.25 0.33 YES
35 NDC80 NDC80 NDC80 1129 0.25 0.34 YES
36 KIF23 KIF23 KIF23 1135 0.25 0.35 YES
37 CDC20 CDC20 CDC20 1177 0.24 0.35 YES
38 E2F1 E2F1 E2F1 1196 0.24 0.36 YES
39 CDKN2C CDKN2C CDKN2C 1249 0.24 0.37 YES
40 RBL1 RBL1 RBL1 1307 0.23 0.37 YES
41 MYBL2 MYBL2 MYBL2 1313 0.23 0.38 YES
42 PLK4 PLK4 PLK4 1352 0.22 0.38 YES
43 CDC45 CDC45 CDC45 1358 0.22 0.39 YES
44 PKMYT1 PKMYT1 PKMYT1 1390 0.22 0.4 YES
45 SPC25 SPC25 SPC25 1404 0.22 0.4 YES
46 RPA4 RPA4 RPA4 1431 0.22 0.41 YES
47 PRKAR2B PRKAR2B PRKAR2B 1488 0.21 0.41 YES
48 CASC5 CASC5 CASC5 1533 0.21 0.42 YES
49 MCM4 MCM4 MCM4 1655 0.2 0.42 YES
50 CENPL CENPL CENPL 1729 0.19 0.42 YES
51 LIN9 LIN9 LIN9 1766 0.19 0.42 YES
52 SKP2 SKP2 SKP2 1778 0.19 0.43 YES
53 E2F2 E2F2 E2F2 1836 0.18 0.43 YES
54 CDT1 CDT1 CDT1 1845 0.18 0.44 YES
55 MLF1IP MLF1IP MLF1IP 1915 0.18 0.44 YES
56 MYC MYC MYC 1922 0.18 0.44 YES
57 GINS4 GINS4 GINS4 1942 0.17 0.45 YES
58 CENPQ CENPQ CENPQ 2014 0.17 0.45 YES
59 GINS1 GINS1 GINS1 2019 0.17 0.46 YES
60 CENPP CENPP CENPP 2046 0.17 0.46 YES
61 MCM6 MCM6 MCM6 2063 0.17 0.46 YES
62 CCDC99 CCDC99 CCDC99 2124 0.16 0.47 YES
63 CENPO CENPO CENPO 2152 0.16 0.47 YES
64 CENPN CENPN CENPN 2157 0.16 0.48 YES
65 DBF4 DBF4 DBF4 2248 0.15 0.48 YES
66 POLE2 POLE2 POLE2 2382 0.15 0.47 YES
67 TUBA4A TUBA4A TUBA4A 2387 0.14 0.48 YES
68 KIF2A KIF2A KIF2A 2493 0.14 0.48 YES
69 GINS2 GINS2 GINS2 2604 0.13 0.47 YES
70 CDC25B CDC25B CDC25B 2641 0.13 0.48 YES
71 ANAPC1 ANAPC1 ANAPC1 2787 0.12 0.47 YES
72 POLA1 POLA1 POLA1 2790 0.12 0.48 YES
73 CDK7 CDK7 CDK7 2831 0.12 0.48 YES
74 FBXO5 FBXO5 FBXO5 2852 0.12 0.48 YES
75 PRIM1 PRIM1 PRIM1 2855 0.12 0.48 YES
76 CDC25A CDC25A CDC25A 2868 0.12 0.49 YES
77 CKAP5 CKAP5 CKAP5 3007 0.12 0.48 YES
78 RFC3 RFC3 RFC3 3131 0.11 0.48 YES
79 CKS1B CKS1B CKS1B 3233 0.11 0.48 YES
80 AHCTF1 AHCTF1 AHCTF1 3240 0.11 0.48 YES
81 WEE1 WEE1 WEE1 3335 0.1 0.48 YES
82 NEDD1 NEDD1 NEDD1 3338 0.1 0.48 YES
83 UBE2D1 UBE2D1 UBE2D1 3349 0.1 0.49 YES
84 CDK4 CDK4 CDK4 3410 0.1 0.49 YES
85 CCNH CCNH CCNH 3469 0.1 0.49 YES
86 PSMD10 PSMD10 PSMD10 3520 0.098 0.49 YES
87 CEP135 CEP135 CEP135 3523 0.098 0.49 YES
88 MCM2 MCM2 MCM2 3558 0.097 0.49 YES
89 CENPH CENPH CENPH 3588 0.096 0.49 YES
90 FEN1 FEN1 FEN1 3675 0.094 0.49 YES
91 CCND1 CCND1 CCND1 3678 0.094 0.49 YES
92 RFC4 RFC4 RFC4 3691 0.093 0.5 YES
93 TAOK1 TAOK1 TAOK1 3736 0.092 0.5 YES
94 PPP2R3B PPP2R3B PPP2R3B 3807 0.09 0.5 YES
95 ZWINT ZWINT ZWINT 3829 0.089 0.5 YES
96 INCENP INCENP INCENP 3845 0.089 0.5 YES
97 RPS27A RPS27A RPS27A 3903 0.087 0.5 YES
98 POLA2 POLA2 POLA2 3920 0.087 0.5 YES
99 PSMD14 PSMD14 PSMD14 3937 0.087 0.5 YES
100 SKP1 SKP1 SKP1 3971 0.086 0.5 YES
101 PPP2R2A PPP2R2A PPP2R2A 3992 0.085 0.51 YES
102 LIN54 LIN54 LIN54 3998 0.085 0.51 YES
103 CDC27 CDC27 CDC27 4040 0.084 0.51 YES
104 DHFR DHFR DHFR 4131 0.082 0.51 YES
105 MCM8 MCM8 MCM8 4132 0.082 0.51 YES
106 E2F5 E2F5 E2F5 4148 0.082 0.51 YES
107 ANAPC10 ANAPC10 ANAPC10 4181 0.081 0.51 YES
108 DNA2 DNA2 DNA2 4205 0.08 0.51 YES
109 PPP2R5D PPP2R5D PPP2R5D 4225 0.08 0.52 YES
110 SMC3 SMC3 SMC3 4287 0.078 0.52 NO
111 PSMD8 PSMD8 PSMD8 4360 0.077 0.51 NO
112 CEP76 CEP76 CEP76 4371 0.076 0.52 NO
113 GMNN GMNN GMNN 4464 0.075 0.51 NO
114 CCNA1 CCNA1 CCNA1 4478 0.074 0.51 NO
115 NUP133 NUP133 NUP133 4698 0.07 0.5 NO
116 ZW10 ZW10 ZW10 4736 0.069 0.5 NO
117 PSME4 PSME4 PSME4 4827 0.067 0.5 NO
118 PSMD11 PSMD11 PSMD11 4836 0.067 0.5 NO
119 KNTC1 KNTC1 KNTC1 4847 0.067 0.5 NO
120 PCNT PCNT PCNT 4877 0.066 0.51 NO
121 PSMD1 PSMD1 PSMD1 4992 0.064 0.5 NO
122 CLIP1 CLIP1 CLIP1 5035 0.063 0.5 NO
123 CEP290 CEP290 CEP290 5200 0.06 0.49 NO
124 E2F3 E2F3 E2F3 5208 0.059 0.5 NO
125 CEP250 CEP250 CEP250 5297 0.058 0.49 NO
126 PPP2R5E PPP2R5E PPP2R5E 5452 0.055 0.49 NO
127 SEH1L SEH1L SEH1L 5477 0.055 0.49 NO
128 SKA2 SKA2 SKA2 5487 0.055 0.49 NO
129 CDKN2B CDKN2B CDKN2B 5505 0.054 0.49 NO
130 PCNA PCNA PCNA 5535 0.054 0.49 NO
131 RANBP2 RANBP2 RANBP2 5647 0.052 0.48 NO
132 PSMA1 PSMA1 PSMA1 5743 0.051 0.48 NO
133 PPP1CC PPP1CC PPP1CC 5779 0.05 0.48 NO
134 PRIM2 PRIM2 PRIM2 5801 0.05 0.48 NO
135 UBA52 UBA52 UBA52 5820 0.05 0.48 NO
136 AZI1 AZI1 AZI1 5848 0.049 0.48 NO
137 DSN1 DSN1 DSN1 5876 0.049 0.48 NO
138 PSMD12 PSMD12 PSMD12 5893 0.048 0.48 NO
139 CDC23 CDC23 CDC23 5914 0.048 0.48 NO
140 SMC1A SMC1A SMC1A 5932 0.048 0.48 NO
141 PSMD4 PSMD4 PSMD4 5983 0.047 0.48 NO
142 PSMB4 PSMB4 PSMB4 6199 0.044 0.47 NO
143 PPP2CA PPP2CA PPP2CA 6245 0.043 0.47 NO
144 MNAT1 MNAT1 MNAT1 6264 0.042 0.47 NO
145 PCM1 PCM1 PCM1 6275 0.042 0.47 NO
146 CLASP1 CLASP1 CLASP1 6335 0.041 0.47 NO
147 PSMD3 PSMD3 PSMD3 6342 0.041 0.47 NO
148 RPS27 RPS27 RPS27 6416 0.04 0.47 NO
149 RAD21 RAD21 RAD21 6421 0.04 0.47 NO
150 PSMA6 PSMA6 PSMA6 6464 0.039 0.47 NO
151 NUP43 NUP43 NUP43 6477 0.039 0.47 NO
152 NUP37 NUP37 NUP37 6496 0.039 0.47 NO
153 DYNC1I2 DYNC1I2 DYNC1I2 6501 0.039 0.47 NO
154 MAPRE1 MAPRE1 MAPRE1 6515 0.038 0.47 NO
155 PSMA7 PSMA7 PSMA7 6517 0.038 0.47 NO
156 BUB3 BUB3 BUB3 6549 0.038 0.47 NO
157 HSP90AA1 HSP90AA1 HSP90AA1 6550 0.038 0.47 NO
158 PMF1 PMF1 PMF1 6642 0.036 0.47 NO
159 PPP2R1B PPP2R1B PPP2R1B 6682 0.036 0.47 NO
160 PSMA4 PSMA4 PSMA4 6701 0.036 0.47 NO
161 ALMS1 ALMS1 ALMS1 6715 0.035 0.47 NO
162 TUBGCP5 TUBGCP5 TUBGCP5 6752 0.035 0.47 NO
163 STAG2 STAG2 STAG2 6934 0.032 0.46 NO
164 CDKN1B CDKN1B CDKN1B 7006 0.031 0.46 NO
165 HAUS2 HAUS2 HAUS2 7179 0.029 0.45 NO
166 DYRK1A DYRK1A DYRK1A 7211 0.028 0.44 NO
167 ANAPC5 ANAPC5 ANAPC5 7245 0.028 0.44 NO
168 PPP2R5A PPP2R5A PPP2R5A 7252 0.028 0.44 NO
169 CEP63 CEP63 CEP63 7280 0.027 0.44 NO
170 DYNLL1 DYNLL1 DYNLL1 7320 0.027 0.44 NO
171 PPP2R5C PPP2R5C PPP2R5C 7330 0.027 0.44 NO
172 CCND3 CCND3 CCND3 7352 0.026 0.44 NO
173 UBE2E1 UBE2E1 UBE2E1 7448 0.025 0.44 NO
174 PSMA3 PSMA3 PSMA3 7546 0.024 0.43 NO
175 PSMD2 PSMD2 PSMD2 7549 0.024 0.43 NO
176 ZWILCH ZWILCH ZWILCH 7564 0.024 0.43 NO
177 CENPC1 CENPC1 CENPC1 7579 0.024 0.43 NO
178 CDKN2D CDKN2D CDKN2D 7619 0.023 0.43 NO
179 CDK5RAP2 CDK5RAP2 CDK5RAP2 7652 0.022 0.43 NO
180 NUP107 NUP107 NUP107 7668 0.022 0.43 NO
181 PSMC4 PSMC4 PSMC4 7669 0.022 0.43 NO
182 PSMF1 PSMF1 PSMF1 7742 0.021 0.43 NO
183 PRKACA PRKACA PRKACA 7814 0.02 0.43 NO
184 E2F4 E2F4 E2F4 7844 0.02 0.42 NO
185 NSL1 NSL1 NSL1 7891 0.02 0.42 NO
186 LIN52 LIN52 LIN52 7945 0.019 0.42 NO
187 POLD3 POLD3 POLD3 7967 0.018 0.42 NO
188 SDCCAG8 SDCCAG8 SDCCAG8 7993 0.018 0.42 NO
189 PSMC6 PSMC6 PSMC6 8041 0.018 0.42 NO
190 OFD1 OFD1 OFD1 8051 0.017 0.42 NO
191 PSMB5 PSMB5 PSMB5 8161 0.016 0.41 NO
192 PSMB2 PSMB2 PSMB2 8282 0.014 0.4 NO
193 CDK2 CDK2 CDK2 8309 0.014 0.4 NO
194 CENPJ CENPJ CENPJ 8327 0.014 0.4 NO
195 PPP2CB PPP2CB PPP2CB 8377 0.013 0.4 NO
196 XPO1 XPO1 XPO1 8409 0.012 0.4 NO
197 POLE POLE POLE 8433 0.012 0.4 NO
198 CDKN2A CDKN2A CDKN2A 8464 0.012 0.4 NO
199 YWHAG YWHAG YWHAG 8480 0.012 0.4 NO
200 ANAPC11 ANAPC11 ANAPC11 8499 0.011 0.4 NO
201 DCTN2 DCTN2 DCTN2 8540 0.011 0.4 NO
202 MCM3 MCM3 MCM3 8671 0.0087 0.39 NO
203 RFC5 RFC5 RFC5 8718 0.0082 0.38 NO
204 PSMD13 PSMD13 PSMD13 8787 0.0072 0.38 NO
205 PPP2R1A PPP2R1A PPP2R1A 8830 0.0068 0.38 NO
206 ANAPC7 ANAPC7 ANAPC7 8834 0.0067 0.38 NO
207 NUMA1 NUMA1 NUMA1 8836 0.0067 0.38 NO
208 STAG1 STAG1 STAG1 8840 0.0066 0.38 NO
209 RANGAP1 RANGAP1 RANGAP1 8911 0.0057 0.38 NO
210 TUBB TUBB TUBB 9106 0.0033 0.36 NO
211 CDC26 CDC26 CDC26 9112 0.0032 0.36 NO
212 PSMD7 PSMD7 PSMD7 9118 0.0031 0.36 NO
213 DCTN1 DCTN1 DCTN1 9186 0.0021 0.36 NO
214 LIN37 LIN37 LIN37 9240 0.0011 0.36 NO
215 CEP57 CEP57 CEP57 9414 -0.0014 0.35 NO
216 PSMA5 PSMA5 PSMA5 9415 -0.0014 0.35 NO
217 POLD4 POLD4 POLD4 9420 -0.0014 0.35 NO
218 CUL1 CUL1 CUL1 9458 -0.0019 0.35 NO
219 PSMD9 PSMD9 PSMD9 9517 -0.0027 0.34 NO
220 SEC13 SEC13 SEC13 9575 -0.0035 0.34 NO
221 PSMB3 PSMB3 PSMB3 9689 -0.0049 0.33 NO
222 PSMC3 PSMC3 PSMC3 9730 -0.0056 0.33 NO
223 PSMB7 PSMB7 PSMB7 9891 -0.0077 0.32 NO
224 CDC7 CDC7 CDC7 9945 -0.0087 0.32 NO
225 BTRC BTRC BTRC 10041 -0.01 0.32 NO
226 PSMB1 PSMB1 PSMB1 10138 -0.012 0.31 NO
227 CEP192 CEP192 CEP192 10194 -0.012 0.31 NO
228 PSMD6 PSMD6 PSMD6 10197 -0.013 0.31 NO
229 PSMC5 PSMC5 PSMC5 10396 -0.015 0.3 NO
230 CSNK1D CSNK1D CSNK1D 10452 -0.016 0.29 NO
231 MAX MAX MAX 10463 -0.016 0.29 NO
232 PSME2 PSME2 PSME2 10552 -0.018 0.29 NO
233 RBBP4 RBBP4 RBBP4 10693 -0.02 0.28 NO
234 PSMC2 PSMC2 PSMC2 10711 -0.02 0.28 NO
235 TFDP1 TFDP1 TFDP1 10764 -0.021 0.28 NO
236 TUBA1A TUBA1A TUBA1A 10799 -0.021 0.28 NO
237 CSNK1E CSNK1E CSNK1E 10803 -0.021 0.28 NO
238 SSNA1 SSNA1 SSNA1 10820 -0.022 0.28 NO
239 CDC16 CDC16 CDC16 10841 -0.022 0.28 NO
240 ACTR1A ACTR1A ACTR1A 10878 -0.023 0.28 NO
241 NUDC NUDC NUDC 10888 -0.023 0.28 NO
242 RB1 RB1 RB1 10916 -0.023 0.28 NO
243 TUBGCP3 TUBGCP3 TUBGCP3 10923 -0.023 0.28 NO
244 PSMA2 PSMA2 PSMA2 10948 -0.024 0.28 NO
245 DYNC1H1 DYNC1H1 DYNC1H1 10951 -0.024 0.28 NO
246 PSMC1 PSMC1 PSMC1 11020 -0.025 0.28 NO
247 AKAP9 AKAP9 AKAP9 11109 -0.026 0.27 NO
248 NUP85 NUP85 NUP85 11225 -0.028 0.26 NO
249 POLD1 POLD1 POLD1 11271 -0.029 0.26 NO
250 CETN2 CETN2 CETN2 11309 -0.03 0.26 NO
251 PSME1 PSME1 PSME1 11351 -0.03 0.26 NO
252 RBL2 RBL2 RBL2 11425 -0.031 0.26 NO
253 TUBG2 TUBG2 TUBG2 11459 -0.032 0.26 NO
254 RPA1 RPA1 RPA1 11511 -0.033 0.26 NO
255 TUBG1 TUBG1 TUBG1 11652 -0.035 0.25 NO
256 CDC14A CDC14A CDC14A 11721 -0.036 0.25 NO
257 B9D2 B9D2 B9D2 11780 -0.037 0.24 NO
258 HDAC1 HDAC1 HDAC1 11785 -0.037 0.24 NO
259 DCTN3 DCTN3 DCTN3 11810 -0.038 0.24 NO
260 ANAPC4 ANAPC4 ANAPC4 11896 -0.039 0.24 NO
261 YWHAE YWHAE YWHAE 11943 -0.04 0.24 NO
262 PSMB8 PSMB8 PSMB8 12008 -0.041 0.24 NO
263 PSMB10 PSMB10 PSMB10 12056 -0.042 0.24 NO
264 POLD2 POLD2 POLD2 12060 -0.042 0.24 NO
265 PSMD5 PSMD5 PSMD5 12195 -0.044 0.23 NO
266 CEP164 CEP164 CEP164 12231 -0.045 0.23 NO
267 CEP72 CEP72 CEP72 12313 -0.047 0.23 NO
268 PAFAH1B1 PAFAH1B1 PAFAH1B1 12486 -0.05 0.22 NO
269 LIG1 LIG1 LIG1 12540 -0.051 0.22 NO
270 PSMB6 PSMB6 PSMB6 12557 -0.052 0.22 NO
271 MCM5 MCM5 MCM5 12565 -0.052 0.22 NO
272 RFC2 RFC2 RFC2 12648 -0.053 0.22 NO
273 RCC2 RCC2 RCC2 12659 -0.054 0.22 NO
274 CDK6 CDK6 CDK6 12732 -0.055 0.22 NO
275 RPA2 RPA2 RPA2 12805 -0.056 0.22 NO
276 TYMS TYMS TYMS 12820 -0.057 0.22 NO
277 ITGB3BP ITGB3BP ITGB3BP 12980 -0.06 0.21 NO
278 PPP2R5B PPP2R5B PPP2R5B 13166 -0.064 0.2 NO
279 TUBGCP2 TUBGCP2 TUBGCP2 13276 -0.067 0.2 NO
280 PSMB9 PSMB9 PSMB9 13666 -0.076 0.18 NO
281 CENPT CENPT CENPT 13685 -0.077 0.18 NO
282 ANAPC2 ANAPC2 ANAPC2 13759 -0.079 0.18 NO
283 CDKN1A CDKN1A CDKN1A 13890 -0.082 0.17 NO
284 NDEL1 NDEL1 NDEL1 13927 -0.083 0.17 NO
285 MIS12 MIS12 MIS12 14090 -0.087 0.17 NO
286 GORASP1 GORASP1 GORASP1 14092 -0.087 0.17 NO
287 FGFR1OP FGFR1OP FGFR1OP 14122 -0.088 0.17 NO
288 TUBGCP6 TUBGCP6 TUBGCP6 14397 -0.098 0.16 NO
289 TK2 TK2 TK2 14512 -0.1 0.16 NO
290 RPA3 RPA3 RPA3 14688 -0.11 0.15 NO
291 MCM7 MCM7 MCM7 14711 -0.11 0.15 NO
292 NINL NINL NINL 15308 -0.13 0.12 NO
293 CEP70 CEP70 CEP70 15909 -0.16 0.094 NO
294 APITD1 APITD1 APITD1 16210 -0.19 0.084 NO
295 MAD1L1 MAD1L1 MAD1L1 16324 -0.2 0.084 NO
296 CCND2 CCND2 CCND2 17262 -0.3 0.041 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: PID AURORA A PATHWAY.

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

genes ES table in pathway: REACTOME CELL CYCLE

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 BUB1B BUB1B BUB1B 167 0.43 0.059 YES
2 PTTG1 PTTG1 PTTG1 299 0.39 0.11 YES
3 UBE2C UBE2C UBE2C 343 0.38 0.17 YES
4 MAD2L1 MAD2L1 MAD2L1 426 0.35 0.22 YES
5 CDK1 CDK1 CDK1 434 0.35 0.28 YES
6 CCNB1 CCNB1 CCNB1 656 0.31 0.32 YES
7 CCNA2 CCNA2 CCNA2 806 0.29 0.35 YES
8 AURKA AURKA AURKA 809 0.29 0.4 YES
9 AURKB AURKB AURKB 926 0.27 0.44 YES
10 PLK1 PLK1 PLK1 1108 0.25 0.46 YES
11 CDC20 CDC20 CDC20 1177 0.24 0.5 YES
12 SKP2 SKP2 SKP2 1778 0.19 0.5 YES
13 ANAPC1 ANAPC1 ANAPC1 2787 0.12 0.46 YES
14 FBXO5 FBXO5 FBXO5 2852 0.12 0.48 YES
15 UBE2D1 UBE2D1 UBE2D1 3349 0.1 0.46 YES
16 PSMD10 PSMD10 PSMD10 3520 0.098 0.47 YES
17 RPS27A RPS27A RPS27A 3903 0.087 0.46 YES
18 PSMD14 PSMD14 PSMD14 3937 0.087 0.47 YES
19 SKP1 SKP1 SKP1 3971 0.086 0.49 YES
20 CDC27 CDC27 CDC27 4040 0.084 0.5 YES
21 ANAPC10 ANAPC10 ANAPC10 4181 0.081 0.5 YES
22 PSMD8 PSMD8 PSMD8 4360 0.077 0.5 YES
23 CCNA1 CCNA1 CCNA1 4478 0.074 0.51 YES
24 PSME4 PSME4 PSME4 4827 0.067 0.5 YES
25 PSMD11 PSMD11 PSMD11 4836 0.067 0.51 YES
26 PSMD1 PSMD1 PSMD1 4992 0.064 0.51 YES
27 PSMA1 PSMA1 PSMA1 5743 0.051 0.48 NO
28 UBA52 UBA52 UBA52 5820 0.05 0.48 NO
29 PSMD12 PSMD12 PSMD12 5893 0.048 0.48 NO
30 CDC23 CDC23 CDC23 5914 0.048 0.49 NO
31 PSMD4 PSMD4 PSMD4 5983 0.047 0.49 NO
32 PSMB4 PSMB4 PSMB4 6199 0.044 0.49 NO
33 PSMD3 PSMD3 PSMD3 6342 0.041 0.49 NO
34 PSMA6 PSMA6 PSMA6 6464 0.039 0.49 NO
35 PSMA7 PSMA7 PSMA7 6517 0.038 0.49 NO
36 BUB3 BUB3 BUB3 6549 0.038 0.5 NO
37 PSMA4 PSMA4 PSMA4 6701 0.036 0.49 NO
38 ANAPC5 ANAPC5 ANAPC5 7245 0.028 0.47 NO
39 UBE2E1 UBE2E1 UBE2E1 7448 0.025 0.46 NO
40 PSMA3 PSMA3 PSMA3 7546 0.024 0.46 NO
41 PSMD2 PSMD2 PSMD2 7549 0.024 0.46 NO
42 PSMC4 PSMC4 PSMC4 7669 0.022 0.46 NO
43 PSMF1 PSMF1 PSMF1 7742 0.021 0.46 NO
44 PSMC6 PSMC6 PSMC6 8041 0.018 0.44 NO
45 PSMB5 PSMB5 PSMB5 8161 0.016 0.44 NO
46 PSMB2 PSMB2 PSMB2 8282 0.014 0.43 NO
47 CDK2 CDK2 CDK2 8309 0.014 0.44 NO
48 ANAPC11 ANAPC11 ANAPC11 8499 0.011 0.43 NO
49 PSMD13 PSMD13 PSMD13 8787 0.0072 0.41 NO
50 ANAPC7 ANAPC7 ANAPC7 8834 0.0067 0.41 NO
51 CDC26 CDC26 CDC26 9112 0.0032 0.4 NO
52 PSMD7 PSMD7 PSMD7 9118 0.0031 0.4 NO
53 PSMA5 PSMA5 PSMA5 9415 -0.0014 0.38 NO
54 CUL1 CUL1 CUL1 9458 -0.0019 0.38 NO
55 PSMD9 PSMD9 PSMD9 9517 -0.0027 0.37 NO
56 PSMB3 PSMB3 PSMB3 9689 -0.0049 0.36 NO
57 PSMC3 PSMC3 PSMC3 9730 -0.0056 0.36 NO
58 PSMB7 PSMB7 PSMB7 9891 -0.0077 0.36 NO
59 BTRC BTRC BTRC 10041 -0.01 0.35 NO
60 PSMB1 PSMB1 PSMB1 10138 -0.012 0.35 NO
61 PSMD6 PSMD6 PSMD6 10197 -0.013 0.34 NO
62 PSMC5 PSMC5 PSMC5 10396 -0.015 0.34 NO
63 PSME2 PSME2 PSME2 10552 -0.018 0.33 NO
64 PSMC2 PSMC2 PSMC2 10711 -0.02 0.32 NO
65 CDC16 CDC16 CDC16 10841 -0.022 0.32 NO
66 PSMA2 PSMA2 PSMA2 10948 -0.024 0.32 NO
67 PSMC1 PSMC1 PSMC1 11020 -0.025 0.32 NO
68 PSME1 PSME1 PSME1 11351 -0.03 0.3 NO
69 CDC14A CDC14A CDC14A 11721 -0.036 0.29 NO
70 ANAPC4 ANAPC4 ANAPC4 11896 -0.039 0.29 NO
71 PSMB8 PSMB8 PSMB8 12008 -0.041 0.29 NO
72 PSMB10 PSMB10 PSMB10 12056 -0.042 0.29 NO
73 PSMD5 PSMD5 PSMD5 12195 -0.044 0.29 NO
74 PSMB6 PSMB6 PSMB6 12557 -0.052 0.28 NO
75 PSMB9 PSMB9 PSMB9 13666 -0.076 0.23 NO
76 ANAPC2 ANAPC2 ANAPC2 13759 -0.079 0.24 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: REACTOME CELL CYCLE.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input

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

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

  • Phenotype data file = KIRP-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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