GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LGG-TP
Brain Lower Grade Glioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LGG-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1N878VW
Overview
Introduction

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

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

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

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

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

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

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

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 191
Number of samples: 516
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 5 :[ clus1 ] 134
pheno.type: 2 - 5 :[ clus2 ] 109
pheno.type: 3 - 5 :[ clus3 ] 109
pheno.type: 4 - 5 :[ clus4 ] 134
pheno.type: 5 - 5 :[ clus5 ] 30

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

  • clus1

    • Top enriched gene sets are BIOCARTA BCR PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA GH PATHWAY, BIOCARTA VIP PATHWAY, BIOCARTA TOLL PATHWAY, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG RIBOSOME, KEGG RNA POLYMERASE, KEGG BASAL TRANSCRIPTION FACTORS

    • And common core enriched genes are RXRG, ACIN1, AQR, BAT1, BCAS2, CDC5L, CWC15, DDX42, DDX46, DDX5

  • clus2

    • Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA P38MAPK PATHWAY, BIOCARTA TCR PATHWAY, BIOCARTA TNFR1 PATHWAY, KEGG N GLYCAN BIOSYNTHESIS, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

    • And common core enriched genes are CASP3, CASP6, CASP7, CASP8, CFLAR, FADD, FAS, LMNA, MAP3K1, BIRC3

  • clus3

    • Top enriched gene sets are BIOCARTA CARM ER PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA RACCYCD PATHWAY, KEGG GALACTOSE METABOLISM, KEGG OXIDATIVE PHOSPHORYLATION, KEGG LYSINE DEGRADATION, KEGG SPHINGOLIPID METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME, KEGG RNA DEGRADATION

    • And common core enriched genes are CCND1, CREBBP, EP300, ERCC3, GRIP1, GTF2F1, HDAC10, HDAC4, HDAC6, HDAC8

  • clus4

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA ERK PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA NFAT PATHWAY, BIOCARTA PDGF PATHWAY

    • And common core enriched genes are CALM1, CALM3, CALM2, MAP2K1, MAPK1, MAPK3, MAPK8, PRKCB, PTK2B, GNAQ

  • clus5

    • Top enriched gene sets are BIOCARTA MYOSIN PATHWAY, KEGG FRUCTOSE AND MANNOSE METABOLISM, KEGG FATTY ACID METABOLISM, KEGG OXIDATIVE PHOSPHORYLATION, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG HISTIDINE METABOLISM, KEGG GLUTATHIONE METABOLISM, KEGG ETHER LIPID METABOLISM, KEGG PROPANOATE METABOLISM

    • And common core enriched genes are ACAA1, ALDH2, ALDH7A1, ALDH9A1, HMGCL, ACAA2, ACADS, AUH, BCAT2, BCKDHA

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.55 1.4 0.12 0.77 0.95 0.21 0.042 0.2 0.61 0.27
BIOCARTA HDAC PATHWAY 27 genes.ES.table 0.42 1.2 0.23 0.81 0.99 0.18 0.044 0.18 0.7 0.28
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.54 1.4 0.15 0.7 0.97 0.24 0.07 0.23 0.58 0.21
BIOCARTA GH PATHWAY 25 genes.ES.table 0.53 1.5 0.077 0.74 0.88 0.24 0.087 0.22 0.56 0.25
BIOCARTA VIP PATHWAY 25 genes.ES.table 0.46 1.3 0.2 0.76 0.99 0.24 0.068 0.22 0.66 0.25
BIOCARTA TOLL PATHWAY 36 genes.ES.table 0.55 1.4 0.13 0.7 0.97 0.56 0.26 0.41 0.57 0.23
KEGG PENTOSE PHOSPHATE PATHWAY 25 genes.ES.table 0.47 1.4 0.11 0.73 0.97 0.28 0.16 0.24 0.58 0.24
KEGG RIBOSOME 85 genes.ES.table 0.66 1.6 0.055 0.6 0.65 0.88 0.28 0.64 0.37 0.2
KEGG RNA POLYMERASE 28 genes.ES.table 0.36 1.3 0.22 0.75 0.99 0.5 0.32 0.34 0.65 0.24
KEGG BASAL TRANSCRIPTION FACTORS 34 genes.ES.table 0.39 1.3 0.19 0.8 0.98 0.53 0.38 0.33 0.68 0.27
genes ES table in pathway: BIOCARTA BCR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRPF38A PRPF38A PRPF38A 1655 0.14 -0.057 YES
2 PPIH PPIH PPIH 1972 0.12 -0.045 YES
3 SFRS4 SFRS4 SFRS4 1975 0.12 -0.016 YES
4 PRPF38B PRPF38B PRPF38B 2016 0.12 0.011 YES
5 SYF2 SYF2 SYF2 2307 0.11 0.021 YES
6 SNRNP40 SNRNP40 SNRNP40 2324 0.11 0.046 YES
7 RBM17 RBM17 RBM17 2489 0.1 0.061 YES
8 SF3A3 SF3A3 SF3A3 2775 0.094 0.068 YES
9 PPIE PPIE PPIE 3128 0.082 0.068 YES
10 SNRPA SNRPA SNRPA 3136 0.082 0.087 YES
11 SNRNP70 SNRNP70 SNRNP70 3254 0.079 0.099 YES
12 MAGOH MAGOH MAGOH 3279 0.078 0.12 YES
13 PRPF31 PRPF31 PRPF31 3362 0.076 0.13 YES
14 SMNDC1 SMNDC1 SMNDC1 3606 0.07 0.13 YES
15 THOC2 THOC2 THOC2 3840 0.065 0.14 YES
16 HNRNPA1L2 HNRNPA1L2 HNRNPA1L2 3909 0.064 0.15 YES
17 HSPA1L HSPA1L HSPA1L 4073 0.06 0.15 YES
18 LSM2 LSM2 LSM2 4074 0.06 0.17 YES
19 HNRNPA1 HNRNPA1 HNRNPA1 4098 0.06 0.18 YES
20 PRPF18 PRPF18 PRPF18 4221 0.058 0.19 YES
21 HNRNPC HNRNPC HNRNPC 4246 0.057 0.2 YES
22 SNRPD2 SNRPD2 SNRPD2 4341 0.056 0.21 YES
23 U2AF2 U2AF2 U2AF2 4347 0.056 0.22 YES
24 PUF60 PUF60 PUF60 4368 0.055 0.23 YES
25 PLRG1 PLRG1 PLRG1 4379 0.055 0.24 YES
26 SFRS13A SFRS13A SFRS13A 4394 0.055 0.26 YES
27 HSPA1A HSPA1A HSPA1A 4713 0.049 0.25 YES
28 PHF5A PHF5A PHF5A 4751 0.048 0.26 YES
29 HSPA6 HSPA6 HSPA6 4904 0.046 0.26 YES
30 EIF4A3 EIF4A3 EIF4A3 4989 0.045 0.27 YES
31 LSM6 LSM6 LSM6 5057 0.044 0.27 YES
32 ACIN1 ACIN1 ACIN1 5073 0.044 0.28 YES
33 PPIL1 PPIL1 PPIL1 5097 0.044 0.29 YES
34 HSPA1B HSPA1B HSPA1B 5255 0.041 0.29 YES
35 SFRS9 SFRS9 SFRS9 5259 0.041 0.3 YES
36 TRA2A TRA2A TRA2A 5342 0.04 0.31 YES
37 THOC1 THOC1 THOC1 5564 0.037 0.3 YES
38 PRPF40A PRPF40A PRPF40A 5608 0.036 0.31 YES
39 SNRPC SNRPC SNRPC 5610 0.036 0.32 YES
40 SF3B14 SF3B14 SF3B14 5684 0.036 0.32 YES
41 HNRNPM HNRNPM HNRNPM 5692 0.035 0.33 YES
42 RBM8A RBM8A RBM8A 5724 0.035 0.34 YES
43 BCAS2 BCAS2 BCAS2 5728 0.035 0.35 YES
44 SF3B3 SF3B3 SF3B3 5817 0.034 0.35 YES
45 DHX38 DHX38 DHX38 5958 0.032 0.35 YES
46 SF3B2 SF3B2 SF3B2 5960 0.032 0.36 YES
47 BAT1 BAT1 BAT1 5965 0.032 0.36 YES
48 SR140 SR140 SR140 5977 0.032 0.37 YES
49 SF3B1 SF3B1 SF3B1 6013 0.031 0.38 YES
50 LSM7 LSM7 LSM7 6355 0.027 0.36 YES
51 HNRNPU HNRNPU HNRNPU 6409 0.027 0.37 YES
52 DDX5 DDX5 DDX5 6440 0.026 0.37 YES
53 CDC5L CDC5L CDC5L 6471 0.026 0.38 YES
54 PQBP1 PQBP1 PQBP1 6598 0.025 0.38 YES
55 SNRPG SNRPG SNRPG 6607 0.024 0.38 YES
56 AQR AQR AQR 6626 0.024 0.39 YES
57 USP39 USP39 USP39 6631 0.024 0.39 YES
58 DDX42 DDX42 DDX42 6664 0.024 0.4 YES
59 SF3A1 SF3A1 SF3A1 6673 0.024 0.4 YES
60 RBMX RBMX RBMX 6750 0.023 0.4 YES
61 SNRPF SNRPF SNRPF 6791 0.022 0.4 YES
62 EFTUD2 EFTUD2 EFTUD2 6826 0.022 0.41 YES
63 SNW1 SNW1 SNW1 6861 0.022 0.41 YES
64 TCERG1 TCERG1 TCERG1 6929 0.021 0.41 YES
65 SNRPB SNRPB SNRPB 6965 0.02 0.42 YES
66 CWC15 CWC15 CWC15 6967 0.02 0.42 YES
67 NCBP1 NCBP1 NCBP1 7193 0.018 0.41 YES
68 DHX16 DHX16 DHX16 7230 0.018 0.42 YES
69 SNRPD3 SNRPD3 SNRPD3 7250 0.017 0.42 YES
70 SART1 SART1 SART1 7296 0.017 0.42 YES
71 SNRNP27 SNRNP27 SNRNP27 7319 0.017 0.42 YES
72 RBM25 RBM25 RBM25 7405 0.016 0.42 YES
73 DDX46 DDX46 DDX46 7441 0.015 0.42 YES
74 HNRNPK HNRNPK HNRNPK 7464 0.015 0.42 YES
75 DHX15 DHX15 DHX15 7615 0.014 0.42 NO
76 BUD31 BUD31 BUD31 7670 0.013 0.42 NO
77 THOC4 THOC4 THOC4 7754 0.012 0.42 NO
78 U2AF1 U2AF1 U2AF1 7771 0.012 0.42 NO
79 XAB2 XAB2 XAB2 7807 0.012 0.42 NO
80 SNRNP200 SNRNP200 SNRNP200 7824 0.011 0.42 NO
81 ISY1 ISY1 ISY1 7869 0.011 0.42 NO
82 CHERP CHERP CHERP 7959 0.01 0.42 NO
83 RBM22 RBM22 RBM22 7997 0.0096 0.42 NO
84 SFRS3 SFRS3 SFRS3 8224 0.0075 0.41 NO
85 SF3B4 SF3B4 SF3B4 8300 0.0067 0.41 NO
86 CCDC12 CCDC12 CCDC12 8321 0.0064 0.41 NO
87 SNRPA1 SNRPA1 SNRPA1 8351 0.0061 0.41 NO
88 HSPA2 HSPA2 HSPA2 8357 0.006 0.41 NO
89 SFRS5 SFRS5 SFRS5 8457 0.005 0.4 NO
90 HNRNPA3 HNRNPA3 HNRNPA3 8611 0.0034 0.4 NO
91 LSM3 LSM3 LSM3 8637 0.0031 0.4 NO
92 NAA38 NAA38 NAA38 8677 0.0026 0.4 NO
93 CRNKL1 CRNKL1 CRNKL1 8862 0.00092 0.38 NO
94 SF3A2 SF3A2 SF3A2 8877 0.00078 0.38 NO
95 ZMAT2 ZMAT2 ZMAT2 8890 0.00064 0.38 NO
96 SFRS2B SFRS2B SFRS2B 8979 -0.00026 0.38 NO
97 PRPF19 PRPF19 PRPF19 9013 -0.00055 0.38 NO
98 WBP11 WBP11 WBP11 9026 -0.00063 0.38 NO
99 TRA2B TRA2B TRA2B 9101 -0.0014 0.37 NO
100 SNRPE SNRPE SNRPE 9199 -0.0024 0.37 NO
101 NHP2L1 NHP2L1 NHP2L1 9321 -0.0036 0.36 NO
102 LSM5 LSM5 LSM5 9323 -0.0037 0.36 NO
103 SFRS2 SFRS2 SFRS2 9419 -0.0046 0.36 NO
104 SFRS1 SFRS1 SFRS1 9570 -0.0062 0.35 NO
105 CTNNBL1 CTNNBL1 CTNNBL1 9704 -0.008 0.35 NO
106 SF3B5 SF3B5 SF3B5 9765 -0.0086 0.35 NO
107 PCBP1 PCBP1 PCBP1 9787 -0.0089 0.35 NO
108 PRPF4 PRPF4 PRPF4 10159 -0.013 0.33 NO
109 SLU7 SLU7 SLU7 10202 -0.014 0.33 NO
110 PRPF8 PRPF8 PRPF8 10228 -0.014 0.33 NO
111 SFRS7 SFRS7 SFRS7 10270 -0.014 0.33 NO
112 PRPF6 PRPF6 PRPF6 10317 -0.015 0.34 NO
113 DDX23 DDX23 DDX23 10411 -0.016 0.33 NO
114 PRPF40B PRPF40B PRPF40B 10413 -0.016 0.34 NO
115 CDC40 CDC40 CDC40 10540 -0.018 0.33 NO
116 SNRPB2 SNRPB2 SNRPB2 10763 -0.021 0.33 NO
117 DHX8 DHX8 DHX8 11133 -0.026 0.31 NO
118 SNRPD1 SNRPD1 SNRPD1 11134 -0.026 0.32 NO
119 SFRS6 SFRS6 SFRS6 11288 -0.028 0.32 NO
120 HSPA8 HSPA8 HSPA8 11480 -0.031 0.31 NO
121 PRPF3 PRPF3 PRPF3 11599 -0.032 0.32 NO
122 LSM4 LSM4 LSM4 12253 -0.043 0.29 NO
123 TXNL4A TXNL4A TXNL4A 12395 -0.046 0.29 NO
124 THOC3 THOC3 THOC3 12778 -0.055 0.28 NO
125 MAGOHB MAGOHB MAGOHB 13781 -0.084 0.25 NO

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

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

genes ES table in pathway: BIOCARTA HDAC PATHWAY

Table 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 DLL3 DLL3 DLL3 356 0.31 0.079 YES
2 HES5 HES5 HES5 400 0.3 0.17 YES
3 DLL1 DLL1 DLL1 995 0.2 0.2 YES
4 NOTCH2 NOTCH2 NOTCH2 1125 0.19 0.26 YES
5 MAML2 MAML2 MAML2 1242 0.18 0.3 YES
6 HDAC1 HDAC1 HDAC1 1401 0.16 0.35 YES
7 DTX4 DTX4 DTX4 1976 0.12 0.36 YES
8 DVL1 DVL1 DVL1 3023 0.086 0.33 YES
9 CTBP2 CTBP2 CTBP2 3026 0.086 0.35 YES
10 RBPJ RBPJ RBPJ 3084 0.084 0.38 YES
11 PSENEN PSENEN PSENEN 3246 0.079 0.39 YES
12 NCOR2 NCOR2 NCOR2 3370 0.076 0.41 YES
13 NOTCH1 NOTCH1 NOTCH1 3685 0.068 0.42 YES
14 NOTCH3 NOTCH3 NOTCH3 3974 0.062 0.42 YES
15 MAML3 MAML3 MAML3 4683 0.05 0.4 YES
16 DTX2 DTX2 DTX2 4722 0.049 0.41 YES
17 MAML1 MAML1 MAML1 4918 0.046 0.41 YES
18 LFNG LFNG LFNG 5028 0.045 0.42 YES
19 DVL2 DVL2 DVL2 5044 0.044 0.44 YES
20 NUMB NUMB NUMB 5100 0.044 0.45 YES
21 HES1 HES1 HES1 5143 0.043 0.46 YES
22 EP300 EP300 EP300 5162 0.043 0.47 YES
23 RFNG RFNG RFNG 5829 0.034 0.44 NO
24 DVL3 DVL3 DVL3 5850 0.034 0.46 NO
25 CREBBP CREBBP CREBBP 6202 0.029 0.44 NO
26 ADAM17 ADAM17 ADAM17 6542 0.025 0.43 NO
27 APH1A APH1A APH1A 6696 0.024 0.43 NO
28 SNW1 SNW1 SNW1 6861 0.022 0.43 NO
29 KAT2B KAT2B KAT2B 7047 0.02 0.43 NO
30 NUMBL NUMBL NUMBL 7329 0.016 0.42 NO
31 HDAC2 HDAC2 HDAC2 7423 0.016 0.42 NO
32 CIR1 CIR1 CIR1 7549 0.014 0.42 NO
33 DTX3L DTX3L DTX3L 8109 0.0084 0.39 NO
34 KAT2A KAT2A KAT2A 8679 0.0026 0.36 NO
35 CTBP1 CTBP1 CTBP1 8767 0.0018 0.35 NO
36 NCSTN NCSTN NCSTN 8777 0.0017 0.35 NO
37 PSEN1 PSEN1 PSEN1 9048 -0.00086 0.34 NO
38 DTX3 DTX3 DTX3 9052 -0.00087 0.34 NO
39 JAG1 JAG1 JAG1 10829 -0.022 0.25 NO
40 DTX1 DTX1 DTX1 11151 -0.026 0.24 NO
41 DLL4 DLL4 DLL4 12092 -0.04 0.2 NO
42 PTCRA PTCRA PTCRA 12313 -0.044 0.2 NO
43 NOTCH4 NOTCH4 NOTCH4 13120 -0.063 0.18 NO
44 JAG2 JAG2 JAG2 13951 -0.09 0.16 NO
45 PSEN2 PSEN2 PSEN2 14235 -0.1 0.18 NO
46 RBPJL RBPJL RBPJL 15097 -0.14 0.18 NO

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

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 708 0.24 -0.0034 YES
2 RPS8 RPS8 RPS8 1543 0.15 -0.027 YES
3 RPS16 RPS16 RPS16 1568 0.15 -0.0069 YES
4 RPL11 RPL11 RPL11 1578 0.15 0.014 YES
5 RPL9 RPL9 RPL9 1625 0.14 0.033 YES
6 RPL22 RPL22 RPL22 1626 0.14 0.054 YES
7 RPL13A RPL13A RPL13A 1688 0.14 0.071 YES
8 RPL5 RPL5 RPL5 1723 0.14 0.09 YES
9 RPS19 RPS19 RPS19 2167 0.12 0.082 YES
10 RPLP0 RPLP0 RPLP0 2214 0.11 0.097 YES
11 RPS5 RPS5 RPS5 2241 0.11 0.11 YES
12 RPS11 RPS11 RPS11 2308 0.11 0.12 YES
13 RPL7 RPL7 RPL7 2315 0.11 0.14 YES
14 RPS3 RPS3 RPS3 2341 0.11 0.16 YES
15 RPL17 RPL17 RPL17 2433 0.11 0.17 YES
16 RPS2 RPS2 RPS2 2499 0.1 0.18 YES
17 RPS10 RPS10 RPS10 2535 0.1 0.19 YES
18 RPL18A RPL18A RPL18A 2573 0.1 0.2 YES
19 RPL28 RPL28 RPL28 2681 0.097 0.21 YES
20 RPL7A RPL7A RPL7A 2686 0.097 0.23 YES
21 RPL30 RPL30 RPL30 2704 0.096 0.24 YES
22 RPS4Y1 RPS4Y1 RPS4Y1 2737 0.096 0.25 YES
23 RPL23 RPL23 RPL23 2738 0.096 0.26 YES
24 RPLP1 RPLP1 RPLP1 2754 0.095 0.28 YES
25 RPS17 RPS17 RPS17 2762 0.095 0.29 YES
26 RPS15A RPS15A RPS15A 2812 0.092 0.3 YES
27 RPS9 RPS9 RPS9 2822 0.092 0.32 YES
28 RPL39 RPL39 RPL39 2824 0.092 0.33 YES
29 RPL12 RPL12 RPL12 2950 0.088 0.34 YES
30 RPS27 RPS27 RPS27 2957 0.088 0.35 YES
31 RPS3A RPS3A RPS3A 2979 0.087 0.36 YES
32 RPS25 RPS25 RPS25 3067 0.084 0.37 YES
33 RPS29 RPS29 RPS29 3121 0.082 0.38 YES
34 RPL3 RPL3 RPL3 3162 0.081 0.39 YES
35 RPS24 RPS24 RPS24 3198 0.08 0.4 YES
36 RPS6 RPS6 RPS6 3281 0.078 0.4 YES
37 RPL27 RPL27 RPL27 3300 0.078 0.41 YES
38 RPSA RPSA RPSA 3331 0.077 0.42 YES
39 RPL4 RPL4 RPL4 3407 0.075 0.43 YES
40 RPL27A RPL27A RPL27A 3434 0.074 0.44 YES
41 RPL34 RPL34 RPL34 3505 0.073 0.45 YES
42 RPL26 RPL26 RPL26 3508 0.072 0.46 YES
43 RPL8 RPL8 RPL8 3510 0.072 0.47 YES
44 RPL19 RPL19 RPL19 3536 0.072 0.48 YES
45 RPL38 RPL38 RPL38 3560 0.071 0.48 YES
46 FAU FAU FAU 3621 0.07 0.49 YES
47 RPL32 RPL32 RPL32 3627 0.07 0.5 YES
48 RPL35A RPL35A RPL35A 3648 0.069 0.51 YES
49 RPL37A RPL37A RPL37A 3654 0.069 0.52 YES
50 RPL29 RPL29 RPL29 3665 0.068 0.53 YES
51 RPL10 RPL10 RPL10 3723 0.067 0.54 YES
52 RPS18 RPS18 RPS18 3727 0.067 0.55 YES
53 RPS15 RPS15 RPS15 3729 0.067 0.56 YES
54 RPLP2 RPLP2 RPLP2 3735 0.067 0.57 YES
55 RPS23 RPS23 RPS23 3784 0.066 0.57 YES
56 RPS27A RPS27A RPS27A 3945 0.063 0.57 YES
57 RPL15 RPL15 RPL15 3949 0.063 0.58 YES
58 RPS21 RPS21 RPS21 3953 0.063 0.59 YES
59 RPL6 RPL6 RPL6 4011 0.061 0.6 YES
60 RPS13 RPS13 RPS13 4095 0.06 0.6 YES
61 RPL13 RPL13 RPL13 4129 0.059 0.61 YES
62 RPL36 RPL36 RPL36 4229 0.058 0.61 YES
63 RPL35 RPL35 RPL35 4257 0.057 0.62 YES
64 RPS4X RPS4X RPS4X 4260 0.057 0.63 YES
65 RPL37 RPL37 RPL37 4325 0.056 0.63 YES
66 RPL14 RPL14 RPL14 4392 0.055 0.64 YES
67 RPL41 RPL41 RPL41 4455 0.054 0.64 YES
68 RPS12 RPS12 RPS12 4479 0.053 0.65 YES
69 RPL24 RPL24 RPL24 4766 0.048 0.64 YES
70 RPS20 RPS20 RPS20 4784 0.048 0.64 YES
71 RPL36A RPL36A RPL36A 4789 0.048 0.65 YES
72 RPL23A RPL23A RPL23A 4916 0.046 0.65 YES
73 RPL10A RPL10A RPL10A 4971 0.045 0.66 YES
74 UBA52 UBA52 UBA52 5078 0.044 0.66 YES
75 RPS7 RPS7 RPS7 5092 0.044 0.66 YES
76 RSL24D1 RSL24D1 RSL24D1 5501 0.038 0.64 NO
77 RPS26 RPS26 RPS26 5525 0.038 0.65 NO
78 RPL31 RPL31 RPL31 5681 0.036 0.64 NO
79 MRPL13 MRPL13 MRPL13 6173 0.029 0.62 NO
80 RPL10L RPL10L RPL10L 6593 0.025 0.6 NO
81 RPS28 RPS28 RPS28 7068 0.02 0.58 NO
82 RPL36AL RPL36AL RPL36AL 7403 0.016 0.56 NO
83 RPL26L1 RPL26L1 RPL26L1 10971 -0.024 0.37 NO
84 RPS27L RPS27L RPS27L 12194 -0.042 0.31 NO
85 RPL22L1 RPL22L1 RPL22L1 15490 -0.17 0.16 NO

Figure S5.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA GH PATHWAY

Table 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 PIK3CG PIK3CG PIK3CG 426 0.29 0.045 YES
2 RXRG RXRG RXRG 435 0.29 0.11 YES
3 PIK3R5 PIK3R5 PIK3R5 453 0.28 0.18 YES
4 EGF EGF EGF 456 0.28 0.25 YES
5 PLCG2 PLCG2 PLCG2 656 0.25 0.3 YES
6 CASP9 CASP9 CASP9 722 0.24 0.35 YES
7 E2F2 E2F2 E2F2 834 0.22 0.39 YES
8 CDKN2A CDKN2A CDKN2A 899 0.21 0.44 YES
9 NRAS NRAS NRAS 2981 0.087 0.35 NO
10 PIK3CD PIK3CD PIK3CD 4084 0.06 0.3 NO
11 CCND1 CCND1 CCND1 4137 0.059 0.31 NO
12 AKT2 AKT2 AKT2 4154 0.059 0.33 NO
13 RAF1 RAF1 RAF1 4620 0.051 0.31 NO
14 PIK3R1 PIK3R1 PIK3R1 4856 0.047 0.31 NO
15 BAD BAD BAD 4876 0.047 0.32 NO
16 RB1 RB1 RB1 5199 0.042 0.31 NO
17 E2F3 E2F3 E2F3 5397 0.039 0.31 NO
18 SOS2 SOS2 SOS2 5632 0.036 0.31 NO
19 RXRA RXRA RXRA 6046 0.031 0.29 NO
20 STK4 STK4 STK4 6116 0.03 0.3 NO
21 SOS1 SOS1 SOS1 6183 0.029 0.3 NO
22 PIK3CA PIK3CA PIK3CA 6318 0.028 0.3 NO
23 RASSF1 RASSF1 RASSF1 6364 0.027 0.3 NO
24 CDK6 CDK6 CDK6 6419 0.026 0.3 NO
25 RXRB RXRB RXRB 6760 0.023 0.29 NO
26 RASSF5 RASSF5 RASSF5 6783 0.022 0.3 NO
27 PRKCA PRKCA PRKCA 6867 0.022 0.3 NO
28 PIK3CB PIK3CB PIK3CB 6964 0.021 0.3 NO
29 GRB2 GRB2 GRB2 7015 0.02 0.3 NO
30 ARAF ARAF ARAF 7034 0.02 0.3 NO
31 AKT1 AKT1 AKT1 7096 0.019 0.3 NO
32 CDK4 CDK4 CDK4 7165 0.018 0.3 NO
33 AKT3 AKT3 AKT3 7745 0.012 0.27 NO
34 EGFR EGFR EGFR 7826 0.011 0.27 NO
35 MAPK1 MAPK1 MAPK1 7941 0.01 0.27 NO
36 FOXO3 FOXO3 FOXO3 8124 0.0084 0.26 NO
37 PLCG1 PLCG1 PLCG1 8558 0.004 0.24 NO
38 MAP2K2 MAP2K2 MAP2K2 8959 -0.000042 0.22 NO
39 MAPK3 MAPK3 MAPK3 9063 -0.0011 0.21 NO
40 PIK3R3 PIK3R3 PIK3R3 10236 -0.014 0.15 NO
41 KRAS KRAS KRAS 11016 -0.024 0.11 NO
42 PIK3R2 PIK3R2 PIK3R2 11445 -0.03 0.097 NO
43 PDPK1 PDPK1 PDPK1 12128 -0.041 0.069 NO
44 MAP2K1 MAP2K1 MAP2K1 12456 -0.047 0.062 NO
45 HRAS HRAS HRAS 12489 -0.048 0.072 NO
46 TP53 TP53 TP53 12715 -0.053 0.072 NO
47 BRAF BRAF BRAF 12726 -0.053 0.084 NO
48 RARB RARB RARB 13118 -0.063 0.078 NO
49 ERBB2 ERBB2 ERBB2 13687 -0.081 0.066 NO
50 FHIT FHIT FHIT 14576 -0.12 0.045 NO
51 PRKCB PRKCB PRKCB 15931 -0.2 0.018 NO
52 TGFA TGFA TGFA 16128 -0.22 0.058 NO
53 PRKCG PRKCG PRKCG 16581 -0.26 0.095 NO

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

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

genes ES table in pathway: BIOCARTA VIP PATHWAY

Table S5.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RET RET RET 39 0.53 0.22 YES
2 RXRG RXRG RXRG 435 0.29 0.33 YES
3 TCF7L1 TCF7L1 TCF7L1 1132 0.19 0.37 YES
4 MYC MYC MYC 1238 0.18 0.44 YES
5 NTRK1 NTRK1 NTRK1 2472 0.1 0.42 YES
6 CDH1 CDH1 CDH1 2541 0.1 0.46 YES
7 TCF7L2 TCF7L2 TCF7L2 2685 0.097 0.49 YES
8 NRAS NRAS NRAS 2981 0.087 0.51 YES
9 TCF7 TCF7 TCF7 3342 0.076 0.52 YES
10 CCND1 CCND1 CCND1 4137 0.059 0.51 NO
11 NCOA4 NCOA4 NCOA4 5244 0.042 0.46 NO
12 RXRA RXRA RXRA 6046 0.031 0.43 NO
13 RXRB RXRB RXRB 6760 0.023 0.4 NO
14 TPR TPR TPR 6825 0.022 0.41 NO
15 MAPK1 MAPK1 MAPK1 7941 0.01 0.35 NO
16 MAP2K2 MAP2K2 MAP2K2 8959 -0.000042 0.3 NO
17 MAPK3 MAPK3 MAPK3 9063 -0.0011 0.29 NO
18 CTNNB1 CTNNB1 CTNNB1 9388 -0.0042 0.28 NO
19 TPM3 TPM3 TPM3 10078 -0.012 0.24 NO
20 CCDC6 CCDC6 CCDC6 10314 -0.015 0.24 NO
21 TFG TFG TFG 10352 -0.016 0.24 NO
22 KRAS KRAS KRAS 11016 -0.024 0.22 NO
23 MAP2K1 MAP2K1 MAP2K1 12456 -0.047 0.16 NO
24 TP53 TP53 TP53 12715 -0.053 0.17 NO
25 BRAF BRAF BRAF 12726 -0.053 0.19 NO
26 PPARG PPARG PPARG 13211 -0.065 0.19 NO
27 LEF1 LEF1 LEF1 13542 -0.076 0.21 NO
28 PAX8 PAX8 PAX8 14828 -0.13 0.19 NO

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

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

genes ES table in pathway: BIOCARTA TOLL PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SLC2A4 SLC2A4 SLC2A4 88 0.45 0.18 YES
2 PIK3CG PIK3CG PIK3CG 426 0.29 0.28 YES
3 PTPN6 PTPN6 PTPN6 729 0.24 0.37 YES
4 GHR GHR GHR 1040 0.2 0.43 YES
5 STAT5A STAT5A STAT5A 1372 0.16 0.48 YES
6 RPS6KA1 RPS6KA1 RPS6KA1 1593 0.15 0.53 YES
7 JAK2 JAK2 JAK2 3951 0.063 0.43 NO
8 RAF1 RAF1 RAF1 4620 0.051 0.41 NO
9 STAT5B STAT5B STAT5B 4767 0.048 0.42 NO
10 PIK3R1 PIK3R1 PIK3R1 4856 0.047 0.44 NO
11 SOS1 SOS1 SOS1 6183 0.029 0.38 NO
12 PIK3CA PIK3CA PIK3CA 6318 0.028 0.38 NO
13 PRKCA PRKCA PRKCA 6867 0.022 0.36 NO
14 GRB2 GRB2 GRB2 7015 0.02 0.36 NO
15 MAPK1 MAPK1 MAPK1 7941 0.01 0.32 NO
16 PLCG1 PLCG1 PLCG1 8558 0.004 0.28 NO
17 IRS1 IRS1 IRS1 8605 0.0034 0.28 NO
18 MAPK3 MAPK3 MAPK3 9063 -0.0011 0.26 NO
19 INSR INSR INSR 9168 -0.0021 0.25 NO
20 SRF SRF SRF 9701 -0.008 0.23 NO
21 HNF1A HNF1A HNF1A 11446 -0.03 0.14 NO
22 MAP2K1 MAP2K1 MAP2K1 12456 -0.047 0.11 NO
23 SHC1 SHC1 SHC1 12597 -0.05 0.12 NO
24 PRKCB PRKCB PRKCB 15931 -0.2 0.022 NO
25 SOCS1 SOCS1 SOCS1 16560 -0.26 0.096 NO

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

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TOLL 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 PHOSPHATE 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 PIK3CG PIK3CG PIK3CG 426 0.29 0.061 YES
2 PIK3R5 PIK3R5 PIK3R5 453 0.28 0.14 YES
3 EGF EGF EGF 456 0.28 0.22 YES
4 CASP9 CASP9 CASP9 722 0.24 0.28 YES
5 TCF7L1 TCF7L1 TCF7L1 1132 0.19 0.31 YES
6 MYC MYC MYC 1238 0.18 0.36 YES
7 CTNNA3 CTNNA3 CTNNA3 2353 0.11 0.33 YES
8 CDH1 CDH1 CDH1 2541 0.1 0.35 YES
9 TCF7L2 TCF7L2 TCF7L2 2685 0.097 0.37 YES
10 NRAS NRAS NRAS 2981 0.087 0.38 YES
11 TCF7 TCF7 TCF7 3342 0.076 0.38 YES
12 PIK3CD PIK3CD PIK3CD 4084 0.06 0.36 YES
13 CCND1 CCND1 CCND1 4137 0.059 0.37 YES
14 AKT2 AKT2 AKT2 4154 0.059 0.38 YES
15 AXIN2 AXIN2 AXIN2 4570 0.052 0.38 YES
16 RAF1 RAF1 RAF1 4620 0.051 0.39 YES
17 PIK3R1 PIK3R1 PIK3R1 4856 0.047 0.39 YES
18 BAD BAD BAD 4876 0.047 0.4 YES
19 AXIN1 AXIN1 AXIN1 5227 0.042 0.4 NO
20 SOS2 SOS2 SOS2 5632 0.036 0.38 NO
21 APC2 APC2 APC2 5795 0.034 0.38 NO
22 SOS1 SOS1 SOS1 6183 0.029 0.37 NO
23 PIK3CA PIK3CA PIK3CA 6318 0.028 0.37 NO
24 PIK3CB PIK3CB PIK3CB 6964 0.021 0.34 NO
25 GRB2 GRB2 GRB2 7015 0.02 0.35 NO
26 ARAF ARAF ARAF 7034 0.02 0.35 NO
27 AKT1 AKT1 AKT1 7096 0.019 0.35 NO
28 AKT3 AKT3 AKT3 7745 0.012 0.32 NO
29 EGFR EGFR EGFR 7826 0.011 0.32 NO
30 MAPK1 MAPK1 MAPK1 7941 0.01 0.32 NO
31 FOXO3 FOXO3 FOXO3 8124 0.0084 0.31 NO
32 PTEN PTEN PTEN 8349 0.0061 0.3 NO
33 MAP2K2 MAP2K2 MAP2K2 8959 -0.000042 0.27 NO
34 MAPK3 MAPK3 MAPK3 9063 -0.0011 0.26 NO
35 CTNNB1 CTNNB1 CTNNB1 9388 -0.0042 0.24 NO
36 ILK ILK ILK 9688 -0.0078 0.23 NO
37 PIK3R3 PIK3R3 PIK3R3 10236 -0.014 0.2 NO
38 CTNNA1 CTNNA1 CTNNA1 10812 -0.022 0.18 NO
39 KRAS KRAS KRAS 11016 -0.024 0.18 NO
40 PIK3R2 PIK3R2 PIK3R2 11445 -0.03 0.16 NO
41 APC APC APC 11937 -0.038 0.14 NO
42 GSK3B GSK3B GSK3B 12041 -0.04 0.15 NO
43 PDPK1 PDPK1 PDPK1 12128 -0.041 0.16 NO
44 MAP2K1 MAP2K1 MAP2K1 12456 -0.047 0.15 NO
45 MLH1 MLH1 MLH1 12554 -0.05 0.16 NO
46 TP53 TP53 TP53 12715 -0.053 0.17 NO
47 BRAF BRAF BRAF 12726 -0.053 0.18 NO
48 LEF1 LEF1 LEF1 13542 -0.076 0.16 NO
49 ERBB2 ERBB2 ERBB2 13687 -0.081 0.18 NO
50 CTNNA2 CTNNA2 CTNNA2 14580 -0.12 0.16 NO
51 ELK1 ELK1 ELK1 15187 -0.15 0.17 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 PENTOSE PHOSPHATE PATHWAY.

Figure S14.  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 RIBOSOME

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 PIK3CG PIK3CG PIK3CG 426 0.29 0.046 YES
2 PIK3R5 PIK3R5 PIK3R5 453 0.28 0.11 YES
3 CASP9 CASP9 CASP9 722 0.24 0.16 YES
4 TGFB1 TGFB1 TGFB1 1051 0.2 0.18 YES
5 TCF7L1 TCF7L1 TCF7L1 1132 0.19 0.22 YES
6 RAC2 RAC2 RAC2 1168 0.18 0.27 YES
7 MYC MYC MYC 1238 0.18 0.3 YES
8 RAC3 RAC3 RAC3 1635 0.14 0.32 YES
9 SMAD3 SMAD3 SMAD3 2183 0.12 0.31 YES
10 TCF7L2 TCF7L2 TCF7L2 2685 0.097 0.31 YES
11 FOS FOS FOS 2730 0.096 0.33 YES
12 JUN JUN JUN 3161 0.081 0.33 YES
13 TCF7 TCF7 TCF7 3342 0.076 0.33 YES
14 TGFBR2 TGFBR2 TGFBR2 3391 0.075 0.35 YES
15 SMAD4 SMAD4 SMAD4 3596 0.07 0.36 YES
16 PIK3CD PIK3CD PIK3CD 4084 0.06 0.34 YES
17 CCND1 CCND1 CCND1 4137 0.059 0.36 YES
18 AKT2 AKT2 AKT2 4154 0.059 0.37 YES
19 TGFBR1 TGFBR1 TGFBR1 4409 0.054 0.37 YES
20 AXIN2 AXIN2 AXIN2 4570 0.052 0.37 YES
21 RAF1 RAF1 RAF1 4620 0.051 0.38 YES
22 MAPK8 MAPK8 MAPK8 4679 0.05 0.39 YES
23 PIK3R1 PIK3R1 PIK3R1 4856 0.047 0.39 YES
24 BAD BAD BAD 4876 0.047 0.4 YES
25 RHOA RHOA RHOA 5039 0.044 0.4 YES
26 BCL2 BCL2 BCL2 5094 0.044 0.41 YES
27 AXIN1 AXIN1 AXIN1 5227 0.042 0.41 YES
28 SMAD2 SMAD2 SMAD2 5438 0.039 0.41 NO
29 DCC DCC DCC 5690 0.036 0.4 NO
30 APC2 APC2 APC2 5795 0.034 0.41 NO
31 PIK3CA PIK3CA PIK3CA 6318 0.028 0.38 NO
32 APPL1 APPL1 APPL1 6527 0.026 0.38 NO
33 RALGDS RALGDS RALGDS 6843 0.022 0.37 NO
34 PIK3CB PIK3CB PIK3CB 6964 0.021 0.37 NO
35 ARAF ARAF ARAF 7034 0.02 0.37 NO
36 AKT1 AKT1 AKT1 7096 0.019 0.37 NO
37 BAX BAX BAX 7157 0.018 0.37 NO
38 AKT3 AKT3 AKT3 7745 0.012 0.34 NO
39 MAPK1 MAPK1 MAPK1 7941 0.01 0.33 NO
40 MSH6 MSH6 MSH6 8303 0.0066 0.31 NO
41 RAC1 RAC1 RAC1 8507 0.0045 0.3 NO
42 MAPK3 MAPK3 MAPK3 9063 -0.0011 0.27 NO
43 CTNNB1 CTNNB1 CTNNB1 9388 -0.0042 0.26 NO
44 MAPK10 MAPK10 MAPK10 9562 -0.0062 0.25 NO
45 PIK3R3 PIK3R3 PIK3R3 10236 -0.014 0.22 NO
46 KRAS KRAS KRAS 11016 -0.024 0.18 NO
47 MSH3 MSH3 MSH3 11255 -0.028 0.17 NO
48 PIK3R2 PIK3R2 PIK3R2 11445 -0.03 0.17 NO
49 APC APC APC 11937 -0.038 0.15 NO
50 GSK3B GSK3B GSK3B 12041 -0.04 0.16 NO
51 MSH2 MSH2 MSH2 12337 -0.045 0.15 NO
52 MAP2K1 MAP2K1 MAP2K1 12456 -0.047 0.15 NO
53 MLH1 MLH1 MLH1 12554 -0.05 0.16 NO
54 TP53 TP53 TP53 12715 -0.053 0.16 NO
55 BRAF BRAF BRAF 12726 -0.053 0.18 NO
56 BIRC5 BIRC5 BIRC5 13008 -0.06 0.18 NO
57 MAPK9 MAPK9 MAPK9 13259 -0.067 0.18 NO
58 CASP3 CASP3 CASP3 13521 -0.076 0.18 NO
59 LEF1 LEF1 LEF1 13542 -0.076 0.2 NO
60 CYCS CYCS CYCS 14696 -0.12 0.16 NO
61 TGFB2 TGFB2 TGFB2 15081 -0.14 0.18 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 RIBOSOME.

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

genes ES table in pathway: KEGG RNA POLYMERASE

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 BLNK BLNK BLNK 195 0.37 0.097 YES
2 VAV1 VAV1 VAV1 353 0.31 0.18 YES
3 CD79A CD79A CD79A 361 0.31 0.26 YES
4 SYK SYK SYK 445 0.29 0.34 YES
5 BTK BTK BTK 511 0.27 0.42 YES
6 NFATC1 NFATC1 NFATC1 587 0.26 0.49 YES
7 NFATC2 NFATC2 NFATC2 776 0.23 0.55 YES
8 FOS FOS FOS 2730 0.096 0.47 NO
9 LYN LYN LYN 2988 0.087 0.48 NO
10 JUN JUN JUN 3161 0.081 0.49 NO
11 NFATC3 NFATC3 NFATC3 4551 0.052 0.43 NO
12 RAF1 RAF1 RAF1 4620 0.051 0.44 NO
13 MAPK8 MAPK8 MAPK8 4679 0.05 0.45 NO
14 PPP3CC PPP3CC PPP3CC 5677 0.036 0.41 NO
15 SOS1 SOS1 SOS1 6183 0.029 0.39 NO
16 PRKCA PRKCA PRKCA 6867 0.022 0.36 NO
17 GRB2 GRB2 GRB2 7015 0.02 0.36 NO
18 NFATC4 NFATC4 NFATC4 7599 0.014 0.33 NO
19 MAP3K1 MAP3K1 MAP3K1 8365 0.006 0.29 NO
20 RAC1 RAC1 RAC1 8507 0.0045 0.28 NO
21 PLCG1 PLCG1 PLCG1 8558 0.004 0.28 NO
22 MAPK14 MAPK14 MAPK14 8668 0.0028 0.27 NO
23 MAPK3 MAPK3 MAPK3 9063 -0.0011 0.25 NO
24 PPP3CB PPP3CB PPP3CB 12044 -0.04 0.1 NO
25 MAP2K1 MAP2K1 MAP2K1 12456 -0.047 0.092 NO
26 CALM2 CALM2 CALM2 12591 -0.05 0.1 NO
27 SHC1 SHC1 SHC1 12597 -0.05 0.11 NO
28 CALM3 CALM3 CALM3 12752 -0.054 0.12 NO
29 PPP3CA PPP3CA PPP3CA 12992 -0.06 0.12 NO
30 CALM1 CALM1 CALM1 13728 -0.082 0.11 NO
31 ELK1 ELK1 ELK1 15187 -0.15 0.071 NO
32 CD79B CD79B CD79B 15247 -0.15 0.11 NO
33 PRKCB PRKCB PRKCB 15931 -0.2 0.13 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 RNA POLYMERASE.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA POLYMERASE, 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 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 LEFTY2 LEFTY2 LEFTY2 25 0.56 0.06 YES
2 BMP8B BMP8B BMP8B 124 0.41 0.099 YES
3 CDKN2B CDKN2B CDKN2B 219 0.36 0.13 YES
4 LEFTY1 LEFTY1 LEFTY1 269 0.34 0.17 YES
5 TNF TNF TNF 282 0.33 0.2 YES
6 ID3 ID3 ID3 300 0.32 0.24 YES
7 GDF7 GDF7 GDF7 533 0.27 0.25 YES
8 ID4 ID4 ID4 701 0.24 0.27 YES
9 BMP4 BMP4 BMP4 888 0.21 0.28 YES
10 TGFB1 TGFB1 TGFB1 1051 0.2 0.3 YES
11 SMAD6 SMAD6 SMAD6 1076 0.19 0.32 YES
12 BMPR1B BMPR1B BMPR1B 1109 0.19 0.33 YES
13 BMP2 BMP2 BMP2 1147 0.18 0.35 YES
14 INHBC INHBC INHBC 1187 0.18 0.37 YES
15 ID1 ID1 ID1 1225 0.18 0.39 YES
16 MYC MYC MYC 1238 0.18 0.4 YES
17 SMAD9 SMAD9 SMAD9 1472 0.16 0.41 YES
18 ROCK1 ROCK1 ROCK1 1777 0.14 0.41 YES
19 AMH AMH AMH 1953 0.13 0.41 YES
20 ACVR2B ACVR2B ACVR2B 2071 0.12 0.42 YES
21 SMAD3 SMAD3 SMAD3 2183 0.12 0.42 YES
22 BMPR1A BMPR1A BMPR1A 2570 0.1 0.41 NO
23 E2F5 E2F5 E2F5 2715 0.096 0.42 NO
24 SMAD7 SMAD7 SMAD7 3164 0.081 0.4 NO
25 TGFBR2 TGFBR2 TGFBR2 3391 0.075 0.4 NO
26 SMAD4 SMAD4 SMAD4 3596 0.07 0.39 NO
27 SMAD1 SMAD1 SMAD1 3943 0.063 0.38 NO
28 SP1 SP1 SP1 4039 0.061 0.38 NO
29 ZFYVE16 ZFYVE16 ZFYVE16 4369 0.055 0.37 NO
30 TGFBR1 TGFBR1 TGFBR1 4409 0.054 0.37 NO
31 RBL2 RBL2 RBL2 4521 0.052 0.37 NO
32 ID2 ID2 ID2 4861 0.047 0.36 NO
33 SMAD5 SMAD5 SMAD5 4864 0.047 0.36 NO
34 RHOA RHOA RHOA 5039 0.044 0.36 NO
35 LTBP1 LTBP1 LTBP1 5043 0.044 0.36 NO
36 EP300 EP300 EP300 5162 0.043 0.36 NO
37 SMAD2 SMAD2 SMAD2 5438 0.039 0.35 NO
38 TFDP1 TFDP1 TFDP1 5869 0.033 0.33 NO
39 CREBBP CREBBP CREBBP 6202 0.029 0.32 NO
40 SMURF2 SMURF2 SMURF2 6373 0.027 0.31 NO
41 INHBA INHBA INHBA 6623 0.024 0.3 NO
42 RPS6KB2 RPS6KB2 RPS6KB2 6858 0.022 0.29 NO
43 RPS6KB1 RPS6KB1 RPS6KB1 6990 0.02 0.28 NO
44 ZFYVE9 ZFYVE9 ZFYVE9 7062 0.02 0.28 NO
45 INHBB INHBB INHBB 7492 0.015 0.26 NO
46 INHBE INHBE INHBE 7610 0.014 0.26 NO
47 PPP2R1A PPP2R1A PPP2R1A 7729 0.012 0.25 NO
48 E2F4 E2F4 E2F4 7898 0.011 0.24 NO
49 MAPK1 MAPK1 MAPK1 7941 0.01 0.24 NO
50 PPP2CB PPP2CB PPP2CB 8482 0.0047 0.21 NO
51 BMPR2 BMPR2 BMPR2 8592 0.0036 0.21 NO
52 RBX1 RBX1 RBX1 8712 0.0023 0.2 NO
53 SMURF1 SMURF1 SMURF1 8715 0.0022 0.2 NO
54 MAPK3 MAPK3 MAPK3 9063 -0.0011 0.18 NO
55 SKP1 SKP1 SKP1 9374 -0.0042 0.16 NO
56 CUL1 CUL1 CUL1 9563 -0.0062 0.16 NO
57 PPP2R1B PPP2R1B PPP2R1B 10119 -0.013 0.13 NO
58 THBS3 THBS3 THBS3 10196 -0.014 0.12 NO
59 PPP2CA PPP2CA PPP2CA 11008 -0.024 0.082 NO
60 ACVR1 ACVR1 ACVR1 11795 -0.035 0.042 NO
61 ROCK2 ROCK2 ROCK2 12090 -0.04 0.03 NO
62 ACVR2A ACVR2A ACVR2A 12159 -0.042 0.031 NO
63 RBL1 RBL1 RBL1 12294 -0.044 0.029 NO
64 CHRD CHRD CHRD 12326 -0.044 0.032 NO
65 ACVRL1 ACVRL1 ACVRL1 12606 -0.051 0.022 NO
66 BMP6 BMP6 BMP6 12812 -0.055 0.017 NO
67 BMP8A BMP8A BMP8A 12867 -0.057 0.02 NO
68 BMP7 BMP7 BMP7 12995 -0.06 0.019 NO
69 COMP COMP COMP 13376 -0.071 0.0063 NO
70 TGFB3 TGFB3 TGFB3 13630 -0.079 0.00097 NO
71 NODAL NODAL NODAL 13886 -0.087 -0.0036 NO
72 PITX2 PITX2 PITX2 14361 -0.11 -0.018 NO
73 DCN DCN DCN 14972 -0.13 -0.037 NO
74 THBS4 THBS4 THBS4 15039 -0.14 -0.026 NO
75 TGFB2 TGFB2 TGFB2 15081 -0.14 -0.012 NO
76 THBS2 THBS2 THBS2 15422 -0.16 -0.014 NO
77 GDF6 GDF6 GDF6 15751 -0.18 -0.012 NO
78 BMP5 BMP5 BMP5 15863 -0.19 0.003 NO
79 THBS1 THBS1 THBS1 15990 -0.2 0.018 NO
80 GDF5 GDF5 GDF5 16024 -0.21 0.039 NO
81 FST FST FST 16462 -0.25 0.042 NO
82 ACVR1C ACVR1C ACVR1C 18095 -0.55 0.012 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 BASAL TRANSCRIPTION FACTORS.

Figure S20.  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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA G1 PATHWAY 27 genes.ES.table 0.58 1.6 0.033 0.41 0.79 0.48 0.22 0.38 0.28 0.097
BIOCARTA FAS PATHWAY 29 genes.ES.table 0.61 1.7 0.0039 1 0.46 0.52 0.21 0.41 0 0.39
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.48 1.6 0.025 0.46 0.63 0.47 0.29 0.34 0.28 0.12
BIOCARTA IL2RB PATHWAY 37 genes.ES.table 0.72 1.7 0.0078 0.76 0.5 0.43 0.16 0.37 0.37 0.27
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.59 1.6 0.019 0.5 0.59 0.5 0.23 0.38 0.28 0.14
BIOCARTA P38MAPK PATHWAY 39 genes.ES.table 0.41 1.5 0.064 0.34 0.88 0.38 0.25 0.29 0.24 0.05
BIOCARTA TCR PATHWAY 43 genes.ES.table 0.57 1.5 0.075 0.36 0.9 0.37 0.18 0.3 0.27 0.057
BIOCARTA TNFR1 PATHWAY 28 genes.ES.table 0.5 1.6 0.042 0.45 0.72 0.46 0.22 0.36 0.28 0.11
KEGG N GLYCAN BIOSYNTHESIS 45 genes.ES.table 0.41 1.6 0.066 0.35 0.8 0.64 0.35 0.42 0.24 0.072
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 43 genes.ES.table 0.49 1.5 0.068 0.35 0.84 0.65 0.37 0.41 0.25 0.065
genes ES table in pathway: BIOCARTA G1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CASP8 CASP8 CASP8 416 0.59 0.09 YES
2 FASLG FASLG FASLG 446 0.57 0.2 YES
3 CASP6 CASP6 CASP6 781 0.49 0.27 YES
4 FAS FAS FAS 1444 0.37 0.31 YES
5 CASP7 CASP7 CASP7 2103 0.29 0.33 YES
6 ARHGDIB ARHGDIB ARHGDIB 2769 0.23 0.34 YES
7 CASP10 CASP10 CASP10 2776 0.23 0.38 YES
8 MAP3K1 MAP3K1 MAP3K1 2822 0.23 0.42 YES
9 JUN JUN JUN 3096 0.2 0.44 YES
10 LMNA LMNA LMNA 3114 0.2 0.48 YES
11 CASP3 CASP3 CASP3 3210 0.2 0.52 YES
12 CFLAR CFLAR CFLAR 3435 0.18 0.54 YES
13 PTPN13 PTPN13 PTPN13 3506 0.18 0.57 YES
14 LMNB2 LMNB2 LMNB2 3735 0.16 0.59 YES
15 FADD FADD FADD 3888 0.16 0.61 YES
16 RB1 RB1 RB1 4840 0.11 0.58 NO
17 FAF1 FAF1 FAF1 5650 0.082 0.55 NO
18 DFFB DFFB DFFB 6140 0.069 0.54 NO
19 DFFA DFFA DFFA 7070 0.046 0.49 NO
20 PRKDC PRKDC PRKDC 7490 0.037 0.48 NO
21 DAXX DAXX DAXX 8345 0.022 0.44 NO
22 MAP3K7 MAP3K7 MAP3K7 8356 0.022 0.44 NO
23 PAK2 PAK2 PAK2 8810 0.014 0.42 NO
24 PARP1 PARP1 PARP1 8820 0.014 0.42 NO
25 PAK1 PAK1 PAK1 9938 -0.0062 0.36 NO
26 SPTAN1 SPTAN1 SPTAN1 12566 -0.054 0.22 NO
27 RIPK2 RIPK2 RIPK2 14059 -0.091 0.16 NO
28 MAP2K4 MAP2K4 MAP2K4 14740 -0.12 0.15 NO
29 MAPK8 MAPK8 MAPK8 16711 -0.26 0.088 NO

Figure S21.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA G1 PATHWAY.

Figure S22.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA G1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA FAS PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SOCS3 SOCS3 SOCS3 106 0.75 0.082 YES
2 IL2RG IL2RG IL2RG 163 0.71 0.16 YES
3 IL2RB IL2RB IL2RB 181 0.69 0.24 YES
4 SOCS1 SOCS1 SOCS1 190 0.69 0.32 YES
5 FASLG FASLG FASLG 446 0.57 0.38 YES
6 JAK3 JAK3 JAK3 628 0.52 0.43 YES
7 IKZF3 IKZF3 IKZF3 729 0.5 0.48 YES
8 PIK3CG PIK3CG PIK3CG 812 0.48 0.53 YES
9 NMI NMI NMI 958 0.45 0.58 YES
10 IL2RA IL2RA IL2RA 1335 0.39 0.6 YES
11 FAS FAS FAS 1444 0.37 0.64 YES
12 STAT5A STAT5A STAT5A 1833 0.32 0.66 YES
13 PTPN6 PTPN6 PTPN6 2047 0.29 0.68 YES
14 SYK SYK SYK 2460 0.26 0.69 YES
15 SHC1 SHC1 SHC1 2731 0.23 0.7 YES
16 FOS FOS FOS 2844 0.22 0.72 YES
17 CFLAR CFLAR CFLAR 3435 0.18 0.71 NO
18 BCL2L1 BCL2L1 BCL2L1 7668 0.034 0.48 NO
19 AKT1 AKT1 AKT1 7750 0.032 0.48 NO
20 PPIA PPIA PPIA 7946 0.029 0.47 NO
21 GRB2 GRB2 GRB2 8816 0.014 0.43 NO
22 BAD BAD BAD 8879 0.013 0.43 NO
23 JAK1 JAK1 JAK1 8974 0.011 0.42 NO
24 CBL CBL CBL 9423 0.0034 0.4 NO
25 RPS6KB1 RPS6KB1 RPS6KB1 10036 -0.008 0.36 NO
26 BCL2 BCL2 BCL2 10077 -0.0086 0.36 NO
27 RAF1 RAF1 RAF1 10575 -0.017 0.34 NO
28 PIK3CA PIK3CA PIK3CA 10748 -0.02 0.33 NO
29 SOS1 SOS1 SOS1 10917 -0.023 0.32 NO
30 STAT5B STAT5B STAT5B 11367 -0.03 0.3 NO
31 HRAS HRAS HRAS 11935 -0.041 0.28 NO
32 CRKL CRKL CRKL 12454 -0.051 0.26 NO
33 MAPK1 MAPK1 MAPK1 12544 -0.053 0.26 NO
34 IRS1 IRS1 IRS1 13583 -0.077 0.21 NO
35 MAPK3 MAPK3 MAPK3 13812 -0.084 0.21 NO
36 PIK3R1 PIK3R1 PIK3R1 15698 -0.17 0.12 NO
37 MYC MYC MYC 15730 -0.17 0.14 NO

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

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

genes ES table in pathway: BIOCARTA HIVNEF PATHWAY

Table 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 SOCS3 SOCS3 SOCS3 106 0.75 0.064 YES
2 SOCS1 SOCS1 SOCS1 190 0.69 0.12 YES
3 CDC20 CDC20 CDC20 228 0.66 0.18 YES
4 UBE2C UBE2C UBE2C 981 0.44 0.18 YES
5 DDB2 DDB2 DDB2 1204 0.41 0.21 YES
6 BIRC3 BIRC3 BIRC3 1765 0.33 0.21 YES
7 BRCA1 BRCA1 BRCA1 2030 0.3 0.22 YES
8 CUL7 CUL7 CUL7 2511 0.25 0.22 YES
9 MAP3K1 MAP3K1 MAP3K1 2822 0.23 0.22 YES
10 UBE2S UBE2S UBE2S 2960 0.22 0.24 YES
11 FBXO4 FBXO4 FBXO4 3044 0.21 0.25 YES
12 UBA7 UBA7 UBA7 3045 0.21 0.27 YES
13 SKP2 SKP2 SKP2 3100 0.2 0.29 YES
14 MID1 MID1 MID1 4040 0.15 0.25 NO
15 UBE2J2 UBE2J2 UBE2J2 4882 0.11 0.21 NO
16 CDC26 CDC26 CDC26 4998 0.1 0.22 NO
17 MDM2 MDM2 MDM2 5153 0.099 0.22 NO
18 NEDD4 NEDD4 NEDD4 5465 0.088 0.21 NO
19 UBA6 UBA6 UBA6 5859 0.076 0.19 NO
20 UBE2F UBE2F UBE2F 6134 0.069 0.18 NO
21 CUL4A CUL4A CUL4A 6135 0.069 0.19 NO
22 ANAPC10 ANAPC10 ANAPC10 6190 0.067 0.2 NO
23 UBE3C UBE3C UBE3C 6334 0.064 0.19 NO
24 PML PML PML 6454 0.06 0.19 NO
25 UBE2A UBE2A UBE2A 6510 0.059 0.19 NO
26 PIAS3 PIAS3 PIAS3 6518 0.058 0.2 NO
27 CUL1 CUL1 CUL1 6540 0.058 0.2 NO
28 UBE2NL UBE2NL UBE2NL 6570 0.057 0.21 NO
29 UBE2D4 UBE2D4 UBE2D4 6614 0.056 0.21 NO
30 SAE1 SAE1 SAE1 6694 0.055 0.21 NO
31 TRIP12 TRIP12 TRIP12 6836 0.052 0.21 NO
32 ANAPC4 ANAPC4 ANAPC4 6843 0.051 0.21 NO
33 UBE2L6 UBE2L6 UBE2L6 6916 0.05 0.21 NO
34 UBE2H UBE2H UBE2H 7101 0.045 0.21 NO
35 UBE2I UBE2I UBE2I 7145 0.044 0.21 NO
36 SMURF1 SMURF1 SMURF1 7333 0.04 0.2 NO
37 ANAPC7 ANAPC7 ANAPC7 7421 0.039 0.2 NO
38 BIRC2 BIRC2 BIRC2 7455 0.038 0.2 NO
39 RNF7 RNF7 RNF7 7465 0.038 0.21 NO
40 UBE2E3 UBE2E3 UBE2E3 7508 0.037 0.21 NO
41 CDC34 CDC34 CDC34 7587 0.036 0.21 NO
42 UBE2Z UBE2Z UBE2Z 7780 0.032 0.2 NO
43 ERCC8 ERCC8 ERCC8 7787 0.032 0.2 NO
44 UBE2M UBE2M UBE2M 7911 0.029 0.2 NO
45 CDC23 CDC23 CDC23 7924 0.029 0.2 NO
46 ANAPC11 ANAPC11 ANAPC11 7933 0.029 0.2 NO
47 CDC16 CDC16 CDC16 7967 0.028 0.2 NO
48 ITCH ITCH ITCH 8168 0.025 0.19 NO
49 UBA3 UBA3 UBA3 8238 0.023 0.19 NO
50 PIAS2 PIAS2 PIAS2 8398 0.021 0.18 NO
51 TRAF6 TRAF6 TRAF6 8458 0.02 0.18 NO
52 UBE2D3 UBE2D3 UBE2D3 8525 0.019 0.18 NO
53 FANCL FANCL FANCL 8573 0.018 0.18 NO
54 RFWD2 RFWD2 RFWD2 8581 0.018 0.18 NO
55 UBA2 UBA2 UBA2 8615 0.017 0.18 NO
56 ANAPC1 ANAPC1 ANAPC1 8678 0.016 0.18 NO
57 WWP1 WWP1 WWP1 8944 0.012 0.17 NO
58 PIAS4 PIAS4 PIAS4 9005 0.011 0.16 NO
59 FZR1 FZR1 FZR1 9090 0.0093 0.16 NO
60 SYVN1 SYVN1 SYVN1 9197 0.0076 0.16 NO
61 UBE2J1 UBE2J1 UBE2J1 9359 0.0046 0.15 NO
62 UBE2N UBE2N UBE2N 9361 0.0045 0.15 NO
63 CBL CBL CBL 9423 0.0034 0.14 NO
64 CDC27 CDC27 CDC27 9438 0.0031 0.14 NO
65 UBE2B UBE2B UBE2B 9581 0.00036 0.14 NO
66 FBXW8 FBXW8 FBXW8 9595 0.000032 0.14 NO
67 UBE2D2 UBE2D2 UBE2D2 9623 -0.00037 0.13 NO
68 UBA1 UBA1 UBA1 9701 -0.0016 0.13 NO
69 CUL4B CUL4B CUL4B 9789 -0.0034 0.13 NO
70 TCEB2 TCEB2 TCEB2 9837 -0.0044 0.12 NO
71 PPIL2 PPIL2 PPIL2 9851 -0.0047 0.12 NO
72 VHL VHL VHL 9943 -0.0062 0.12 NO
73 UBE2L3 UBE2L3 UBE2L3 9988 -0.0072 0.12 NO
74 UBE3A UBE3A UBE3A 10042 -0.0081 0.12 NO
75 UBE4B UBE4B UBE4B 10143 -0.0098 0.11 NO
76 UBE2K UBE2K UBE2K 10237 -0.012 0.11 NO
77 TCEB1 TCEB1 TCEB1 10256 -0.012 0.11 NO
78 UBE3B UBE3B UBE3B 10364 -0.014 0.1 NO
79 NEDD4L NEDD4L NEDD4L 10391 -0.014 0.1 NO
80 KEAP1 KEAP1 KEAP1 10407 -0.014 0.1 NO
81 SMURF2 SMURF2 SMURF2 10427 -0.015 0.1 NO
82 UBE2E1 UBE2E1 UBE2E1 10473 -0.015 0.1 NO
83 AIRE AIRE AIRE 10502 -0.016 0.1 NO
84 UBOX5 UBOX5 UBOX5 10561 -0.017 0.1 NO
85 CUL5 CUL5 CUL5 10587 -0.017 0.1 NO
86 CUL3 CUL3 CUL3 10595 -0.017 0.1 NO
87 ANAPC5 ANAPC5 ANAPC5 10611 -0.018 0.1 NO
88 UBE2Q1 UBE2Q1 UBE2Q1 10824 -0.021 0.092 NO
89 PIAS1 PIAS1 PIAS1 10849 -0.022 0.093 NO
90 UBE2G1 UBE2G1 UBE2G1 10850 -0.022 0.095 NO
91 UBE4A UBE4A UBE4A 10989 -0.024 0.09 NO
92 UBE2G2 UBE2G2 UBE2G2 11118 -0.026 0.085 NO
93 RBX1 RBX1 RBX1 11264 -0.028 0.08 NO
94 XIAP XIAP XIAP 11277 -0.028 0.082 NO
95 SKP1 SKP1 SKP1 11432 -0.031 0.076 NO
96 MGRN1 MGRN1 MGRN1 11448 -0.032 0.078 NO
97 UBR5 UBR5 UBR5 11548 -0.033 0.076 NO
98 UBE2D1 UBE2D1 UBE2D1 11560 -0.034 0.079 NO
99 ANAPC2 ANAPC2 ANAPC2 11563 -0.034 0.082 NO
100 DDB1 DDB1 DDB1 11603 -0.034 0.083 NO
101 UBE2Q2 UBE2Q2 UBE2Q2 11692 -0.036 0.081 NO
102 ANAPC13 ANAPC13 ANAPC13 11920 -0.041 0.072 NO
103 UBE2W UBE2W UBE2W 12010 -0.042 0.072 NO
104 SIAH1 SIAH1 SIAH1 12114 -0.044 0.07 NO
105 UBE2R2 UBE2R2 UBE2R2 12139 -0.045 0.073 NO
106 KLHL13 KLHL13 KLHL13 12205 -0.046 0.074 NO
107 RHOBTB2 RHOBTB2 RHOBTB2 12370 -0.049 0.069 NO
108 RCHY1 RCHY1 RCHY1 12554 -0.054 0.064 NO
109 HUWE1 HUWE1 HUWE1 12735 -0.057 0.06 NO
110 HERC4 HERC4 HERC4 12793 -0.058 0.062 NO
111 PRPF19 PRPF19 PRPF19 12801 -0.058 0.067 NO
112 HERC2 HERC2 HERC2 12944 -0.061 0.065 NO
113 TRIM32 TRIM32 TRIM32 13040 -0.064 0.066 NO
114 BIRC6 BIRC6 BIRC6 13225 -0.068 0.062 NO
115 STUB1 STUB1 STUB1 13395 -0.072 0.059 NO
116 TRIM37 TRIM37 TRIM37 13717 -0.08 0.049 NO
117 HERC3 HERC3 HERC3 13937 -0.087 0.045 NO
118 FBXW11 FBXW11 FBXW11 13957 -0.087 0.052 NO
119 FBXW7 FBXW7 FBXW7 13991 -0.088 0.059 NO
120 NHLRC1 NHLRC1 NHLRC1 14023 -0.09 0.066 NO
121 WWP2 WWP2 WWP2 14108 -0.092 0.069 NO
122 CUL2 CUL2 CUL2 14141 -0.093 0.076 NO
123 UBE2O UBE2O UBE2O 14355 -0.1 0.074 NO
124 DET1 DET1 DET1 14514 -0.11 0.075 NO
125 CBLB CBLB CBLB 14834 -0.12 0.069 NO
126 HERC1 HERC1 HERC1 15117 -0.13 0.066 NO
127 KLHL9 KLHL9 KLHL9 15126 -0.13 0.078 NO
128 FBXO2 FBXO2 FBXO2 15278 -0.14 0.083 NO
129 UBE2E2 UBE2E2 UBE2E2 15641 -0.16 0.078 NO
130 PARK2 PARK2 PARK2 16479 -0.23 0.054 NO
131 UBE2QL1 UBE2QL1 UBE2QL1 17948 -0.5 0.02 NO

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

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

Table 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 CASP8 CASP8 CASP8 416 0.59 0.094 YES
2 CASP6 CASP6 CASP6 781 0.49 0.17 YES
3 BIRC3 BIRC3 BIRC3 1765 0.33 0.18 YES
4 TNFRSF10A TNFRSF10A TNFRSF10A 1774 0.33 0.25 YES
5 CASP7 CASP7 CASP7 2103 0.29 0.29 YES
6 TRADD TRADD TRADD 2301 0.27 0.33 YES
7 TNFSF10 TNFSF10 TNFSF10 2357 0.26 0.38 YES
8 CASP10 CASP10 CASP10 2776 0.23 0.4 YES
9 LMNA LMNA LMNA 3114 0.2 0.42 YES
10 CASP3 CASP3 CASP3 3210 0.2 0.46 YES
11 RIPK1 RIPK1 RIPK1 3344 0.19 0.49 YES
12 CFLAR CFLAR CFLAR 3435 0.18 0.52 YES
13 MAP3K14 MAP3K14 MAP3K14 3490 0.18 0.55 YES
14 FADD FADD FADD 3888 0.16 0.56 YES
15 TNFRSF10B TNFRSF10B TNFRSF10B 3986 0.15 0.58 YES
16 NFKB1 NFKB1 NFKB1 4288 0.14 0.59 YES
17 TNFRSF25 TNFRSF25 TNFRSF25 5536 0.086 0.54 NO
18 TNFSF12 TNFSF12 TNFSF12 5616 0.083 0.56 NO
19 TRAF2 TRAF2 TRAF2 5787 0.078 0.56 NO
20 DFFB DFFB DFFB 6140 0.069 0.56 NO
21 DFFA DFFA DFFA 7070 0.046 0.51 NO
22 BIRC2 BIRC2 BIRC2 7455 0.038 0.5 NO
23 CYCS CYCS CYCS 7462 0.038 0.51 NO
24 APAF1 APAF1 APAF1 8866 0.013 0.43 NO
25 RELA RELA RELA 9589 0.00021 0.39 NO
26 BCL2 BCL2 BCL2 10077 -0.0086 0.37 NO
27 XIAP XIAP XIAP 11277 -0.028 0.31 NO
28 CHUK CHUK CHUK 11912 -0.041 0.28 NO
29 SPTAN1 SPTAN1 SPTAN1 12566 -0.054 0.26 NO
30 NFKBIA NFKBIA NFKBIA 12695 -0.056 0.26 NO
31 GAS2 GAS2 GAS2 12764 -0.058 0.27 NO
32 CASP9 CASP9 CASP9 15770 -0.17 0.14 NO

Figure S27.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL2RB PATHWAY.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA DEATH PATHWAY

Table 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 CASP8 CASP8 CASP8 416 0.59 0.05 YES
2 CASP6 CASP6 CASP6 781 0.49 0.091 YES
3 FAS FAS FAS 1444 0.37 0.1 YES
4 BIRC3 BIRC3 BIRC3 1765 0.33 0.12 YES
5 TNFRSF1A TNFRSF1A TNFRSF1A 1846 0.32 0.16 YES
6 CASP7 CASP7 CASP7 2103 0.29 0.18 YES
7 LMNB1 LMNB1 LMNB1 2219 0.28 0.21 YES
8 TRADD TRADD TRADD 2301 0.27 0.24 YES
9 TRAF1 TRAF1 TRAF1 2449 0.26 0.26 YES
10 TNFRSF1B TNFRSF1B TNFRSF1B 2732 0.23 0.28 YES
11 ARHGDIB ARHGDIB ARHGDIB 2769 0.23 0.3 YES
12 MAP3K1 MAP3K1 MAP3K1 2822 0.23 0.33 YES
13 LMNA LMNA LMNA 3114 0.2 0.34 YES
14 CASP3 CASP3 CASP3 3210 0.2 0.36 YES
15 PRKCD PRKCD PRKCD 3270 0.19 0.38 YES
16 RIPK1 RIPK1 RIPK1 3344 0.19 0.4 YES
17 CFLAR CFLAR CFLAR 3435 0.18 0.41 YES
18 MAP3K14 MAP3K14 MAP3K14 3490 0.18 0.43 YES
19 LMNB2 LMNB2 LMNB2 3735 0.16 0.44 YES
20 FADD FADD FADD 3888 0.16 0.45 YES
21 CASP2 CASP2 CASP2 4039 0.15 0.46 YES
22 NFKB1 NFKB1 NFKB1 4288 0.14 0.46 YES
23 PSEN2 PSEN2 PSEN2 4489 0.12 0.47 YES
24 RB1 RB1 RB1 4840 0.11 0.46 YES
25 GSN GSN GSN 4884 0.11 0.47 YES
26 MDM2 MDM2 MDM2 5153 0.099 0.47 YES
27 CDK11A CDK11A CDK11A 5258 0.095 0.48 YES
28 TRAF2 TRAF2 TRAF2 5787 0.078 0.46 NO
29 DFFB DFFB DFFB 6140 0.069 0.45 NO
30 CDK11B CDK11B CDK11B 6480 0.059 0.44 NO
31 TNF TNF TNF 6515 0.058 0.44 NO
32 DFFA DFFA DFFA 7070 0.046 0.42 NO
33 ACTG1 ACTG1 ACTG1 7236 0.042 0.41 NO
34 BIRC2 BIRC2 BIRC2 7455 0.038 0.41 NO
35 CYCS CYCS CYCS 7462 0.038 0.41 NO
36 PRKDC PRKDC PRKDC 7490 0.037 0.41 NO
37 DAXX DAXX DAXX 8345 0.022 0.37 NO
38 PAK2 PAK2 PAK2 8810 0.014 0.35 NO
39 PARP1 PARP1 PARP1 8820 0.014 0.35 NO
40 APAF1 APAF1 APAF1 8866 0.013 0.35 NO
41 RASA1 RASA1 RASA1 9355 0.0047 0.32 NO
42 RELA RELA RELA 9589 0.00021 0.31 NO
43 PSEN1 PSEN1 PSEN1 9637 -0.00064 0.31 NO
44 MAP2K7 MAP2K7 MAP2K7 9917 -0.0058 0.29 NO
45 BCL2 BCL2 BCL2 10077 -0.0086 0.28 NO
46 XIAP XIAP XIAP 11277 -0.028 0.22 NO
47 CHUK CHUK CHUK 11912 -0.041 0.19 NO
48 PTK2 PTK2 PTK2 12229 -0.047 0.18 NO
49 SPTAN1 SPTAN1 SPTAN1 12566 -0.054 0.17 NO
50 NFKBIA NFKBIA NFKBIA 12695 -0.056 0.17 NO
51 CRADD CRADD CRADD 13043 -0.064 0.16 NO
52 NUMA1 NUMA1 NUMA1 14596 -0.11 0.086 NO
53 BAG4 BAG4 BAG4 15269 -0.14 0.067 NO
54 MAP3K5 MAP3K5 MAP3K5 15390 -0.15 0.079 NO
55 CASP9 CASP9 CASP9 15770 -0.17 0.079 NO
56 BID BID BID 16446 -0.23 0.07 NO
57 MAPK8 MAPK8 MAPK8 16711 -0.26 0.088 NO

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

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

genes ES table in pathway: BIOCARTA P38MAPK 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 CLCF1 CLCF1 CLCF1 11 0.97 0.036 YES
2 LIF LIF LIF 33 0.87 0.069 YES
3 CISH CISH CISH 39 0.86 0.1 YES
4 SOCS3 SOCS3 SOCS3 106 0.75 0.13 YES
5 IL2RG IL2RG IL2RG 163 0.71 0.15 YES
6 IL2RB IL2RB IL2RB 181 0.69 0.18 YES
7 SOCS1 SOCS1 SOCS1 190 0.69 0.2 YES
8 IL15 IL15 IL15 200 0.68 0.23 YES
9 IL7 IL7 IL7 252 0.65 0.25 YES
10 CTF1 CTF1 CTF1 372 0.6 0.27 YES
11 IL13RA2 IL13RA2 IL13RA2 388 0.6 0.29 YES
12 OSMR OSMR OSMR 395 0.6 0.31 YES
13 SPRY1 SPRY1 SPRY1 519 0.55 0.32 YES
14 SPRY4 SPRY4 SPRY4 593 0.53 0.34 YES
15 JAK3 JAK3 JAK3 628 0.52 0.36 YES
16 SOCS2 SOCS2 SOCS2 656 0.51 0.38 YES
17 CSF2RB CSF2RB CSF2RB 717 0.5 0.39 YES
18 PIK3CG PIK3CG PIK3CG 812 0.48 0.41 YES
19 IL28RA IL28RA IL28RA 870 0.47 0.42 YES
20 IL6 IL6 IL6 899 0.46 0.44 YES
21 IL7R IL7R IL7R 979 0.44 0.45 YES
22 IL10 IL10 IL10 1162 0.42 0.46 YES
23 IL12RB1 IL12RB1 IL12RB1 1247 0.4 0.47 YES
24 IL2RA IL2RA IL2RA 1335 0.39 0.48 YES
25 PIK3R5 PIK3R5 PIK3R5 1681 0.34 0.47 YES
26 IL22RA1 IL22RA1 IL22RA1 1787 0.32 0.48 YES
27 STAT5A STAT5A STAT5A 1833 0.32 0.49 YES
28 OSM OSM OSM 1965 0.3 0.49 YES
29 CSF3R CSF3R CSF3R 1971 0.3 0.5 YES
30 IL15RA IL15RA IL15RA 2003 0.3 0.51 YES
31 PTPN6 PTPN6 PTPN6 2047 0.29 0.52 YES
32 IL10RA IL10RA IL10RA 2270 0.27 0.52 YES
33 IL13RA1 IL13RA1 IL13RA1 2461 0.26 0.52 YES
34 PIM1 PIM1 PIM1 2480 0.25 0.53 YES
35 SPRY2 SPRY2 SPRY2 2639 0.24 0.53 YES
36 IL5RA IL5RA IL5RA 2707 0.24 0.54 YES
37 PIK3CD PIK3CD PIK3CD 2709 0.24 0.54 YES
38 IL4R IL4R IL4R 2713 0.24 0.55 YES
39 SPRED2 SPRED2 SPRED2 2786 0.23 0.56 YES
40 IFNGR2 IFNGR2 IFNGR2 2803 0.23 0.56 YES
41 IL24 IL24 IL24 2804 0.23 0.57 YES
42 STAT1 STAT1 STAT1 2869 0.22 0.58 YES
43 CNTF CNTF CNTF 2878 0.22 0.59 YES
44 IL21R IL21R IL21R 2938 0.22 0.59 YES
45 CSF2RA CSF2RA CSF2RA 3001 0.21 0.6 YES
46 IL10RB IL10RB IL10RB 3417 0.18 0.58 NO
47 PRLR PRLR PRLR 3806 0.16 0.57 NO
48 SPRED1 SPRED1 SPRED1 3868 0.16 0.57 NO
49 IL6R IL6R IL6R 3905 0.15 0.57 NO
50 EPO EPO EPO 3983 0.15 0.57 NO
51 LEP LEP LEP 4000 0.15 0.58 NO
52 STAT6 STAT6 STAT6 4091 0.14 0.58 NO
53 MPL MPL MPL 4286 0.14 0.57 NO
54 IL20RA IL20RA IL20RA 4488 0.12 0.57 NO
55 AKT2 AKT2 AKT2 4573 0.12 0.57 NO
56 STAT3 STAT3 STAT3 4582 0.12 0.57 NO
57 PIK3R3 PIK3R3 PIK3R3 4859 0.11 0.56 NO
58 IL23A IL23A IL23A 5243 0.096 0.54 NO
59 STAT2 STAT2 STAT2 5323 0.093 0.54 NO
60 IFNAR2 IFNAR2 IFNAR2 5367 0.092 0.54 NO
61 JAK2 JAK2 JAK2 5414 0.09 0.55 NO
62 IRF9 IRF9 IRF9 5718 0.08 0.53 NO
63 CCND2 CCND2 CCND2 5739 0.08 0.53 NO
64 IFNE IFNE IFNE 5945 0.074 0.52 NO
65 TYK2 TYK2 TYK2 6176 0.067 0.52 NO
66 PIAS3 PIAS3 PIAS3 6518 0.058 0.5 NO
67 IL11 IL11 IL11 6696 0.055 0.49 NO
68 IFNAR1 IFNAR1 IFNAR1 6884 0.05 0.48 NO
69 SOCS4 SOCS4 SOCS4 6969 0.048 0.48 NO
70 IFNGR1 IFNGR1 IFNGR1 6986 0.048 0.48 NO
71 TPO TPO TPO 7380 0.04 0.46 NO
72 CCND1 CCND1 CCND1 7386 0.039 0.46 NO
73 BCL2L1 BCL2L1 BCL2L1 7668 0.034 0.45 NO
74 AKT1 AKT1 AKT1 7750 0.032 0.44 NO
75 PIAS2 PIAS2 PIAS2 8398 0.021 0.41 NO
76 IL6ST IL6ST IL6ST 8688 0.016 0.39 NO
77 IL3RA IL3RA IL3RA 8729 0.015 0.39 NO
78 STAM2 STAM2 STAM2 8762 0.015 0.39 NO
79 GRB2 GRB2 GRB2 8816 0.014 0.39 NO
80 JAK1 JAK1 JAK1 8974 0.011 0.38 NO
81 PIAS4 PIAS4 PIAS4 9005 0.011 0.38 NO
82 IFNA13 IFNA13 IFNA13 9011 0.011 0.38 NO
83 TSLP TSLP TSLP 9074 0.0096 0.38 NO
84 CBL CBL CBL 9423 0.0034 0.36 NO
85 GHR GHR GHR 9802 -0.0038 0.34 NO
86 IL13 IL13 IL13 10157 -0.01 0.32 NO
87 PIK3CA PIK3CA PIK3CA 10748 -0.02 0.29 NO
88 EPOR EPOR EPOR 10815 -0.021 0.28 NO
89 SOCS5 SOCS5 SOCS5 10820 -0.021 0.28 NO
90 PIAS1 PIAS1 PIAS1 10849 -0.022 0.28 NO
91 SOS1 SOS1 SOS1 10917 -0.023 0.28 NO
92 CSF3 CSF3 CSF3 11007 -0.024 0.28 NO
93 CCND3 CCND3 CCND3 11343 -0.03 0.26 NO
94 STAT5B STAT5B STAT5B 11367 -0.03 0.26 NO
95 PTPN11 PTPN11 PTPN11 11698 -0.036 0.24 NO
96 IL20RB IL20RB IL20RB 11848 -0.039 0.24 NO
97 LEPR LEPR LEPR 12126 -0.044 0.22 NO
98 STAT4 STAT4 STAT4 12306 -0.048 0.21 NO
99 PIK3R2 PIK3R2 PIK3R2 12448 -0.051 0.21 NO
100 IFNW1 IFNW1 IFNW1 12697 -0.056 0.2 NO
101 SPRY3 SPRY3 SPRY3 13030 -0.063 0.18 NO
102 IL5 IL5 IL5 13085 -0.065 0.18 NO
103 CREBBP CREBBP CREBBP 13179 -0.066 0.18 NO
104 SOS2 SOS2 SOS2 13664 -0.079 0.15 NO
105 EP300 EP300 EP300 13750 -0.082 0.15 NO
106 LIFR LIFR LIFR 14123 -0.092 0.14 NO
107 PIK3CB PIK3CB PIK3CB 14310 -0.099 0.13 NO
108 IFNA21 IFNA21 IFNA21 14371 -0.1 0.13 NO
109 IL11RA IL11RA IL11RA 14595 -0.11 0.12 NO
110 STAM STAM STAM 14736 -0.12 0.12 NO
111 CBLB CBLB CBLB 14834 -0.12 0.12 NO
112 PIK3R1 PIK3R1 PIK3R1 15698 -0.17 0.077 NO
113 MYC MYC MYC 15730 -0.17 0.082 NO
114 AKT3 AKT3 AKT3 15834 -0.18 0.083 NO
115 IL12RB2 IL12RB2 IL12RB2 16158 -0.2 0.073 NO
116 SOCS7 SOCS7 SOCS7 16213 -0.2 0.078 NO
117 IL12A IL12A IL12A 16663 -0.25 0.063 NO
118 CNTFR CNTFR CNTFR 16686 -0.25 0.071 NO
119 IL9 IL9 IL9 17853 -0.47 0.025 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 P38MAPK PATHWAY.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA P38MAPK 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 TCR 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 CASP8 CASP8 CASP8 416 0.59 0.11 YES
2 TNFRSF1A TNFRSF1A TNFRSF1A 1846 0.32 0.11 YES
3 LMNB1 LMNB1 LMNB1 2219 0.28 0.15 YES
4 TRADD TRADD TRADD 2301 0.27 0.21 YES
5 ARHGDIB ARHGDIB ARHGDIB 2769 0.23 0.23 YES
6 MAP3K1 MAP3K1 MAP3K1 2822 0.23 0.28 YES
7 JUN JUN JUN 3096 0.2 0.31 YES
8 LMNA LMNA LMNA 3114 0.2 0.36 YES
9 CASP3 CASP3 CASP3 3210 0.2 0.4 YES
10 RIPK1 RIPK1 RIPK1 3344 0.19 0.44 YES
11 LMNB2 LMNB2 LMNB2 3735 0.16 0.45 YES
12 FADD FADD FADD 3888 0.16 0.48 YES
13 CASP2 CASP2 CASP2 4039 0.15 0.5 YES
14 RB1 RB1 RB1 4840 0.11 0.48 NO
15 DFFB DFFB DFFB 6140 0.069 0.43 NO
16 TNF TNF TNF 6515 0.058 0.42 NO
17 DFFA DFFA DFFA 7070 0.046 0.4 NO
18 PRKDC PRKDC PRKDC 7490 0.037 0.39 NO
19 MAP3K7 MAP3K7 MAP3K7 8356 0.022 0.35 NO
20 PAK2 PAK2 PAK2 8810 0.014 0.32 NO
21 PARP1 PARP1 PARP1 8820 0.014 0.33 NO
22 PAK1 PAK1 PAK1 9938 -0.0062 0.27 NO
23 SPTAN1 SPTAN1 SPTAN1 12566 -0.054 0.14 NO
24 CRADD CRADD CRADD 13043 -0.064 0.12 NO
25 MAP2K4 MAP2K4 MAP2K4 14740 -0.12 0.059 NO
26 BAG4 BAG4 BAG4 15269 -0.14 0.063 NO
27 MADD MADD MADD 16129 -0.2 0.061 NO
28 MAPK8 MAPK8 MAPK8 16711 -0.26 0.088 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 TCR PATHWAY.

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

genes ES table in pathway: BIOCARTA TNFR1 PATHWAY

Table 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 COL4A1 COL4A1 COL4A1 267 0.64 0.033 YES
2 LAMB4 LAMB4 LAMB4 312 0.62 0.076 YES
3 COL4A2 COL4A2 COL4A2 530 0.55 0.1 YES
4 PIK3CG PIK3CG PIK3CG 812 0.48 0.12 YES
5 LAMB1 LAMB1 LAMB1 877 0.46 0.16 YES
6 CDK2 CDK2 CDK2 1226 0.4 0.16 YES
7 ITGA2 ITGA2 ITGA2 1232 0.4 0.2 YES
8 TRAF5 TRAF5 TRAF5 1297 0.39 0.22 YES
9 LAMA2 LAMA2 LAMA2 1430 0.37 0.24 YES
10 E2F2 E2F2 E2F2 1447 0.37 0.27 YES
11 LAMC1 LAMC1 LAMC1 1484 0.36 0.29 YES
12 PIK3R5 PIK3R5 PIK3R5 1681 0.34 0.3 YES
13 BIRC3 BIRC3 BIRC3 1765 0.33 0.32 YES
14 LAMC3 LAMC3 LAMC3 1828 0.32 0.34 YES
15 ITGA3 ITGA3 ITGA3 1980 0.3 0.36 YES
16 LAMC2 LAMC2 LAMC2 2191 0.28 0.37 YES
17 COL4A6 COL4A6 COL4A6 2279 0.27 0.38 YES
18 FN1 FN1 FN1 2423 0.26 0.39 YES
19 CDK6 CDK6 CDK6 2434 0.26 0.41 YES
20 TRAF1 TRAF1 TRAF1 2449 0.26 0.43 YES
21 CKS1B CKS1B CKS1B 2524 0.25 0.44 YES
22 PIK3CD PIK3CD PIK3CD 2709 0.24 0.45 YES
23 LAMA4 LAMA4 LAMA4 2743 0.23 0.47 YES
24 SKP2 SKP2 SKP2 3100 0.2 0.46 YES
25 LAMB2 LAMB2 LAMB2 3142 0.2 0.48 YES
26 ITGB1 ITGB1 ITGB1 3285 0.19 0.48 YES
27 CCNE1 CCNE1 CCNE1 3347 0.19 0.49 YES
28 CDK4 CDK4 CDK4 3984 0.15 0.47 NO
29 PTGS2 PTGS2 PTGS2 4151 0.14 0.47 NO
30 NFKB1 NFKB1 NFKB1 4288 0.14 0.47 NO
31 AKT2 AKT2 AKT2 4573 0.12 0.46 NO
32 RB1 RB1 RB1 4840 0.11 0.46 NO
33 PIK3R3 PIK3R3 PIK3R3 4859 0.11 0.47 NO
34 ITGAV ITGAV ITGAV 5485 0.088 0.44 NO
35 TP53 TP53 TP53 5518 0.086 0.44 NO
36 IKBKB IKBKB IKBKB 5599 0.084 0.44 NO
37 TRAF2 TRAF2 TRAF2 5787 0.078 0.44 NO
38 ITGA6 ITGA6 ITGA6 5870 0.076 0.44 NO
39 CCNE2 CCNE2 CCNE2 6043 0.071 0.44 NO
40 RARB RARB RARB 6132 0.069 0.44 NO
41 PIAS3 PIAS3 PIAS3 6518 0.058 0.42 NO
42 LAMA5 LAMA5 LAMA5 6612 0.056 0.42 NO
43 TRAF4 TRAF4 TRAF4 7133 0.045 0.39 NO
44 CCND1 CCND1 CCND1 7386 0.039 0.38 NO
45 E2F3 E2F3 E2F3 7411 0.039 0.38 NO
46 BIRC2 BIRC2 BIRC2 7455 0.038 0.38 NO
47 CYCS CYCS CYCS 7462 0.038 0.39 NO
48 BCL2L1 BCL2L1 BCL2L1 7668 0.034 0.38 NO
49 NOS2 NOS2 NOS2 7741 0.032 0.38 NO
50 AKT1 AKT1 AKT1 7750 0.032 0.38 NO
51 PIAS2 PIAS2 PIAS2 8398 0.021 0.34 NO
52 TRAF6 TRAF6 TRAF6 8458 0.02 0.34 NO
53 APAF1 APAF1 APAF1 8866 0.013 0.32 NO
54 PIAS4 PIAS4 PIAS4 9005 0.011 0.32 NO
55 RELA RELA RELA 9589 0.00021 0.28 NO
56 FHIT FHIT FHIT 9880 -0.0051 0.27 NO
57 IKBKG IKBKG IKBKG 10070 -0.0085 0.26 NO
58 BCL2 BCL2 BCL2 10077 -0.0086 0.26 NO
59 LAMA1 LAMA1 LAMA1 10273 -0.012 0.25 NO
60 LAMB3 LAMB3 LAMB3 10309 -0.013 0.25 NO
61 PIK3CA PIK3CA PIK3CA 10748 -0.02 0.22 NO
62 PIAS1 PIAS1 PIAS1 10849 -0.022 0.22 NO
63 RXRA RXRA RXRA 11052 -0.025 0.21 NO
64 MAX MAX MAX 11108 -0.026 0.21 NO
65 XIAP XIAP XIAP 11277 -0.028 0.2 NO
66 CHUK CHUK CHUK 11912 -0.041 0.17 NO
67 PTK2 PTK2 PTK2 12229 -0.047 0.16 NO
68 TRAF3 TRAF3 TRAF3 12388 -0.05 0.15 NO
69 PIK3R2 PIK3R2 PIK3R2 12448 -0.051 0.15 NO
70 NFKBIA NFKBIA NFKBIA 12695 -0.056 0.14 NO
71 CDKN1B CDKN1B CDKN1B 13146 -0.066 0.12 NO
72 PTEN PTEN PTEN 13570 -0.077 0.11 NO
73 RXRB RXRB RXRB 14223 -0.096 0.078 NO
74 PIK3CB PIK3CB PIK3CB 14310 -0.099 0.081 NO
75 CDKN2B CDKN2B CDKN2B 14752 -0.12 0.065 NO
76 COL4A4 COL4A4 COL4A4 15481 -0.15 0.036 NO
77 PIK3R1 PIK3R1 PIK3R1 15698 -0.17 0.037 NO
78 MYC MYC MYC 15730 -0.17 0.047 NO
79 CASP9 CASP9 CASP9 15770 -0.17 0.058 NO
80 AKT3 AKT3 AKT3 15834 -0.18 0.067 NO
81 LAMA3 LAMA3 LAMA3 16335 -0.22 0.056 NO
82 ITGA2B ITGA2B ITGA2B 16920 -0.28 0.044 NO
83 RXRG RXRG RXRG 17744 -0.43 0.031 NO

Figure S35.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TNFR1 PATHWAY.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TNFR1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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 SLC11A1 SLC11A1 SLC11A1 248 0.65 0.034 YES
2 AP1S3 AP1S3 AP1S3 314 0.62 0.074 YES
3 CTSW CTSW CTSW 345 0.61 0.12 YES
4 LAMP3 LAMP3 LAMP3 850 0.47 0.12 YES
5 TCIRG1 TCIRG1 TCIRG1 1453 0.37 0.12 YES
6 ACP5 ACP5 ACP5 1503 0.36 0.14 YES
7 CTSC CTSC CTSC 1563 0.35 0.16 YES
8 CTSS CTSS CTSS 1807 0.32 0.17 YES
9 CTSK CTSK CTSK 1964 0.3 0.18 YES
10 GLA GLA GLA 2278 0.27 0.19 YES
11 CTSZ CTSZ CTSZ 2363 0.26 0.2 YES
12 CD68 CD68 CD68 2583 0.24 0.21 YES
13 HEXB HEXB HEXB 2682 0.24 0.22 YES
14 FUCA1 FUCA1 FUCA1 2846 0.22 0.23 YES
15 NPC2 NPC2 NPC2 2867 0.22 0.24 YES
16 LAPTM5 LAPTM5 LAPTM5 2873 0.22 0.26 YES
17 GUSB GUSB GUSB 2874 0.22 0.27 YES
18 DNASE2B DNASE2B DNASE2B 2894 0.22 0.29 YES
19 NAGA NAGA NAGA 2935 0.22 0.3 YES
20 SUMF1 SUMF1 SUMF1 3349 0.19 0.29 YES
21 MAN2B1 MAN2B1 MAN2B1 3362 0.18 0.3 YES
22 CD63 CD63 CD63 3505 0.18 0.31 YES
23 GALNS GALNS GALNS 3525 0.18 0.32 YES
24 GNS GNS GNS 3530 0.17 0.33 YES
25 ARSA ARSA ARSA 3535 0.17 0.34 YES
26 CD164 CD164 CD164 3593 0.17 0.35 YES
27 AGA AGA AGA 3632 0.17 0.36 YES
28 CTSA CTSA CTSA 3714 0.16 0.37 YES
29 GLB1 GLB1 GLB1 4003 0.15 0.37 YES
30 SGSH SGSH SGSH 4278 0.14 0.36 YES
31 AP1S2 AP1S2 AP1S2 4402 0.13 0.36 YES
32 CTSB CTSB CTSB 4563 0.12 0.36 YES
33 CTSL2 CTSL2 CTSL2 4570 0.12 0.37 YES
34 CTSL1 CTSL1 CTSL1 4638 0.12 0.38 YES
35 GALC GALC GALC 4713 0.12 0.38 YES
36 CLN5 CLN5 CLN5 4805 0.11 0.38 YES
37 AP4M1 AP4M1 AP4M1 4874 0.11 0.39 YES
38 PLA2G15 PLA2G15 PLA2G15 4967 0.11 0.39 YES
39 IDUA IDUA IDUA 5056 0.1 0.39 YES
40 DNASE2 DNASE2 DNASE2 5064 0.1 0.4 YES
41 NAGLU NAGLU NAGLU 5136 0.1 0.4 YES
42 HEXA HEXA HEXA 5161 0.099 0.41 YES
43 CTNS CTNS CTNS 5378 0.091 0.4 YES
44 AP4B1 AP4B1 AP4B1 5431 0.09 0.41 YES
45 AP3B1 AP3B1 AP3B1 5645 0.083 0.4 YES
46 LAPTM4A LAPTM4A LAPTM4A 5706 0.081 0.4 YES
47 ATP6V0B ATP6V0B ATP6V0B 5770 0.079 0.41 YES
48 ATP6V0D2 ATP6V0D2 ATP6V0D2 5827 0.077 0.41 YES
49 MANBA MANBA MANBA 5830 0.077 0.42 YES
50 CTSD CTSD CTSD 5920 0.075 0.42 YES
51 LAMP1 LAMP1 LAMP1 5939 0.074 0.42 YES
52 ABCB9 ABCB9 ABCB9 5997 0.072 0.42 YES
53 GAA GAA GAA 6003 0.072 0.43 YES
54 CTSH CTSH CTSH 6037 0.071 0.43 YES
55 GGA2 GGA2 GGA2 6082 0.07 0.43 YES
56 CLN3 CLN3 CLN3 6343 0.063 0.42 NO
57 ATP6V0A2 ATP6V0A2 ATP6V0A2 6374 0.062 0.42 NO
58 GBA GBA GBA 6415 0.061 0.43 NO
59 LGMN LGMN LGMN 6660 0.056 0.42 NO
60 AP1M1 AP1M1 AP1M1 6710 0.054 0.42 NO
61 SMPD1 SMPD1 SMPD1 6782 0.052 0.42 NO
62 M6PR M6PR M6PR 6925 0.049 0.42 NO
63 LAMP2 LAMP2 LAMP2 6932 0.049 0.42 NO
64 PPT1 PPT1 PPT1 6963 0.049 0.42 NO
65 MCOLN1 MCOLN1 MCOLN1 7055 0.046 0.42 NO
66 SORT1 SORT1 SORT1 7092 0.046 0.42 NO
67 NEU1 NEU1 NEU1 7238 0.042 0.42 NO
68 SLC17A5 SLC17A5 SLC17A5 7276 0.042 0.42 NO
69 MFSD8 MFSD8 MFSD8 7342 0.04 0.42 NO
70 AP3S1 AP3S1 AP3S1 7399 0.039 0.42 NO
71 ACP2 ACP2 ACP2 7477 0.038 0.41 NO
72 ASAH1 ASAH1 ASAH1 7599 0.035 0.41 NO
73 IGF2R IGF2R IGF2R 7956 0.028 0.39 NO
74 AP4E1 AP4E1 AP4E1 8018 0.028 0.39 NO
75 NAGPA NAGPA NAGPA 8232 0.024 0.38 NO
76 ARSB ARSB ARSB 8433 0.02 0.37 NO
77 TPP1 TPP1 TPP1 8479 0.02 0.37 NO
78 LIPA LIPA LIPA 8700 0.016 0.36 NO
79 NAPSA NAPSA NAPSA 8731 0.015 0.36 NO
80 ATP6AP1 ATP6AP1 ATP6AP1 8787 0.014 0.36 NO
81 AP1B1 AP1B1 AP1B1 8922 0.012 0.35 NO
82 AP1G1 AP1G1 AP1G1 9434 0.0031 0.32 NO
83 CLTC CLTC CLTC 9537 0.0012 0.32 NO
84 LAPTM4B LAPTM4B LAPTM4B 9571 0.00056 0.32 NO
85 GM2A GM2A GM2A 9678 -0.0013 0.31 NO
86 PSAP PSAP PSAP 9796 -0.0036 0.3 NO
87 AP3D1 AP3D1 AP3D1 9878 -0.0051 0.3 NO
88 ATP6V0A4 ATP6V0A4 ATP6V0A4 10097 -0.009 0.29 NO
89 ENTPD4 ENTPD4 ENTPD4 10188 -0.01 0.28 NO
90 AP1S1 AP1S1 AP1S1 10193 -0.011 0.28 NO
91 GNPTAB GNPTAB GNPTAB 10862 -0.022 0.25 NO
92 SCARB2 SCARB2 SCARB2 10866 -0.022 0.25 NO
93 GGA3 GGA3 GGA3 11069 -0.025 0.24 NO
94 GNPTG GNPTG GNPTG 11083 -0.026 0.24 NO
95 NPC1 NPC1 NPC1 11365 -0.03 0.23 NO
96 CLTA CLTA CLTA 11897 -0.04 0.2 NO
97 CTSO CTSO CTSO 11917 -0.041 0.2 NO
98 AP3S2 AP3S2 AP3S2 12024 -0.043 0.2 NO
99 ATP6V0C ATP6V0C ATP6V0C 12124 -0.044 0.2 NO
100 AP3M1 AP3M1 AP3M1 12183 -0.046 0.2 NO
101 PPT2 PPT2 PPT2 12507 -0.052 0.18 NO
102 ATP6V0D1 ATP6V0D1 ATP6V0D1 12667 -0.056 0.18 NO
103 ABCA2 ABCA2 ABCA2 13201 -0.067 0.16 NO
104 CLTB CLTB CLTB 13436 -0.073 0.15 NO
105 GGA1 GGA1 GGA1 13454 -0.074 0.15 NO
106 SLC11A2 SLC11A2 SLC11A2 13536 -0.076 0.15 NO
107 AP3M2 AP3M2 AP3M2 13592 -0.077 0.16 NO
108 HYAL1 HYAL1 HYAL1 13784 -0.083 0.15 NO
109 ATP6V1H ATP6V1H ATP6V1H 14134 -0.093 0.14 NO
110 CTSF CTSF CTSF 14154 -0.093 0.14 NO
111 ARSG ARSG ARSG 14534 -0.11 0.13 NO
112 IDS IDS IDS 14856 -0.12 0.12 NO
113 ATP6V0A1 ATP6V0A1 ATP6V0A1 15141 -0.14 0.12 NO
114 AP1M2 AP1M2 AP1M2 15322 -0.14 0.12 NO
115 AP4S1 AP4S1 AP4S1 15569 -0.16 0.12 NO
116 CLTCL1 CLTCL1 CLTCL1 16084 -0.19 0.1 NO
117 AP3B2 AP3B2 AP3B2 17024 -0.3 0.071 NO

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

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

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

Table 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 TGFB2 TGFB2 TGFB2 198 0.68 0.15 YES
2 CDK1 CDK1 CDK1 1183 0.41 0.19 YES
3 CDK2 CDK2 CDK2 1226 0.4 0.28 YES
4 CDK6 CDK6 CDK6 2434 0.26 0.28 YES
5 CDC25A CDC25A CDC25A 2754 0.23 0.32 YES
6 TGFB1 TGFB1 TGFB1 3031 0.21 0.35 YES
7 HDAC1 HDAC1 HDAC1 3043 0.21 0.4 YES
8 SKP2 SKP2 SKP2 3100 0.2 0.44 YES
9 CCNE1 CCNE1 CCNE1 3347 0.19 0.48 YES
10 CCNA1 CCNA1 CCNA1 3395 0.18 0.52 YES
11 CDK4 CDK4 CDK4 3984 0.15 0.52 YES
12 CDKN1A CDKN1A CDKN1A 4030 0.15 0.55 YES
13 TGFB3 TGFB3 TGFB3 4053 0.15 0.58 YES
14 RB1 RB1 RB1 4840 0.11 0.57 NO
15 TP53 TP53 TP53 5518 0.086 0.55 NO
16 ATR ATR ATR 5676 0.082 0.56 NO
17 DHFR DHFR DHFR 5796 0.078 0.57 NO
18 CCND1 CCND1 CCND1 7386 0.039 0.5 NO
19 SMAD3 SMAD3 SMAD3 10159 -0.01 0.35 NO
20 ATM ATM ATM 11382 -0.03 0.29 NO
21 ABL1 ABL1 ABL1 11477 -0.032 0.29 NO
22 SMAD4 SMAD4 SMAD4 11948 -0.041 0.27 NO
23 CDKN2A CDKN2A CDKN2A 11960 -0.042 0.28 NO
24 TFDP1 TFDP1 TFDP1 12007 -0.042 0.29 NO
25 GSK3B GSK3B GSK3B 12398 -0.05 0.28 NO
26 CDKN1B CDKN1B CDKN1B 13146 -0.066 0.26 NO
27 CDKN2B CDKN2B CDKN2B 14752 -0.12 0.2 NO

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

Figure S40.  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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus3 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.45 1.5 0.057 0.75 0.82 0.47 0.24 0.36 0.52 0.25
BIOCARTA ERK PATHWAY 26 genes.ES.table 0.19 0.64 0.92 1 1 0.19 0.14 0.17 1 0.95
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.19 0.71 0.82 1 1 1 0.81 0.19 1 0.95
KEGG GALACTOSE METABOLISM 25 genes.ES.table 0.34 1.1 0.38 1 1 0.08 0.0026 0.08 1 0.94
KEGG OXIDATIVE PHOSPHORYLATION 114 genes.ES.table 0.13 0.47 0.93 0.99 1 0.035 0.049 0.034 0.99 0.44
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.16 0.72 0.81 1 1 0.28 0.26 0.21 1 0.97
KEGG SPHINGOLIPID METABOLISM 37 genes.ES.table 0.28 0.85 0.67 1 1 0.27 0.18 0.22 1 0.65
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.14 0.57 0.97 1 1 1 0.86 0.14 1 0.99
KEGG RIBOSOME 85 genes.ES.table 0.49 1.2 0.35 1 1 0.69 0.34 0.46 1 0.84
KEGG RNA DEGRADATION 56 genes.ES.table 0.25 1 0.4 1 1 0.41 0.32 0.28 1 0.88
genes ES table in pathway: BIOCARTA CARM ER PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GRIP1 GRIP1 GRIP1 204 0.46 0.14 YES
2 NR0B1 NR0B1 NR0B1 622 0.3 0.21 YES
3 HDAC9 HDAC9 HDAC9 1131 0.21 0.25 YES
4 HDAC4 HDAC4 HDAC4 1158 0.2 0.31 YES
5 CCND1 CCND1 CCND1 2100 0.13 0.3 YES
6 HDAC10 HDAC10 HDAC10 2586 0.11 0.31 YES
7 GTF2F1 GTF2F1 GTF2F1 2888 0.098 0.32 YES
8 TBP TBP TBP 3053 0.094 0.35 YES
9 CREBBP CREBBP CREBBP 3465 0.083 0.35 YES
10 HDAC6 HDAC6 HDAC6 3839 0.075 0.35 YES
11 PHB2 PHB2 PHB2 4040 0.071 0.37 YES
12 PELP1 PELP1 PELP1 4220 0.067 0.38 YES
13 ERCC3 ERCC3 ERCC3 4295 0.066 0.4 YES
14 HDAC8 HDAC8 HDAC8 4352 0.064 0.41 YES
15 NCOR2 NCOR2 NCOR2 4361 0.064 0.43 YES
16 EP300 EP300 EP300 4410 0.063 0.45 YES
17 MED1 MED1 MED1 5554 0.045 0.4 NO
18 HDAC2 HDAC2 HDAC2 5670 0.043 0.41 NO
19 POLR2A POLR2A POLR2A 6011 0.038 0.4 NO
20 HDAC5 HDAC5 HDAC5 6255 0.035 0.4 NO
21 GTF2E1 GTF2E1 GTF2E1 6527 0.03 0.4 NO
22 PPARGC1A PPARGC1A PPARGC1A 8041 0.0082 0.32 NO
23 GTF2A1 GTF2A1 GTF2A1 8172 0.0063 0.31 NO
24 ESR1 ESR1 ESR1 9142 -0.0082 0.26 NO
25 SRA1 SRA1 SRA1 9177 -0.0088 0.26 NO
26 NRIP1 NRIP1 NRIP1 9584 -0.015 0.24 NO
27 HDAC11 HDAC11 HDAC11 10125 -0.026 0.22 NO
28 HDAC7 HDAC7 HDAC7 10142 -0.027 0.23 NO
29 HDAC3 HDAC3 HDAC3 10512 -0.035 0.22 NO
30 HIST2H3C HIST2H3C HIST2H3C 12130 -0.08 0.16 NO
31 BRCA1 BRCA1 BRCA1 12340 -0.087 0.18 NO
32 SPEN SPEN SPEN 12359 -0.088 0.2 NO
33 CARM1 CARM1 CARM1 12363 -0.088 0.23 NO
34 HDAC1 HDAC1 HDAC1 16417 -0.29 0.1 NO

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

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

genes ES table in pathway: BIOCARTA ERK PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 89 0.55 0.092 YES
2 RPL22L1 RPL22L1 RPL22L1 472 0.34 0.13 YES
3 RPL36A RPL36A RPL36A 1787 0.15 0.083 YES
4 RPS28 RPS28 RPS28 1895 0.14 0.1 YES
5 RPL10L RPL10L RPL10L 2297 0.12 0.1 YES
6 RPS13 RPS13 RPS13 2581 0.11 0.1 YES
7 RPL36AL RPL36AL RPL36AL 2756 0.1 0.11 YES
8 RPS12 RPS12 RPS12 2792 0.1 0.13 YES
9 RPL26L1 RPL26L1 RPL26L1 2903 0.098 0.14 YES
10 RPS27 RPS27 RPS27 2904 0.098 0.16 YES
11 RPL6 RPL6 RPL6 3050 0.094 0.17 YES
12 RPL7 RPL7 RPL7 3083 0.093 0.18 YES
13 RPS26 RPS26 RPS26 3239 0.089 0.19 YES
14 RPL39 RPL39 RPL39 3305 0.087 0.2 YES
15 RPL13 RPL13 RPL13 3462 0.083 0.2 YES
16 RPL4 RPL4 RPL4 3476 0.082 0.22 YES
17 RPS24 RPS24 RPS24 3616 0.079 0.22 YES
18 RPL3 RPL3 RPL3 3685 0.078 0.24 YES
19 RPL24 RPL24 RPL24 3733 0.077 0.25 YES
20 RPS23 RPS23 RPS23 3746 0.077 0.26 YES
21 RPS25 RPS25 RPS25 3815 0.076 0.27 YES
22 RPS6 RPS6 RPS6 3903 0.074 0.28 YES
23 RPS20 RPS20 RPS20 3971 0.072 0.28 YES
24 RPL10A RPL10A RPL10A 4013 0.071 0.3 YES
25 RSL24D1 RSL24D1 RSL24D1 4113 0.069 0.3 YES
26 RPL10 RPL10 RPL10 4117 0.069 0.31 YES
27 RPL18A RPL18A RPL18A 4119 0.069 0.33 YES
28 RPL34 RPL34 RPL34 4166 0.068 0.34 YES
29 RPLP2 RPLP2 RPLP2 4224 0.067 0.34 YES
30 RPS4X RPS4X RPS4X 4324 0.065 0.35 YES
31 RPL29 RPL29 RPL29 4332 0.065 0.36 YES
32 RPS3 RPS3 RPS3 4342 0.065 0.37 YES
33 RPSA RPSA RPSA 4600 0.06 0.37 YES
34 RPL37 RPL37 RPL37 4624 0.06 0.38 YES
35 RPS3A RPS3A RPS3A 4629 0.06 0.39 YES
36 RPL23 RPL23 RPL23 4718 0.058 0.39 YES
37 RPS29 RPS29 RPS29 4725 0.058 0.4 YES
38 RPL23A RPL23A RPL23A 4778 0.057 0.41 YES
39 RPL31 RPL31 RPL31 4894 0.055 0.41 YES
40 RPL15 RPL15 RPL15 4959 0.054 0.42 YES
41 RPL17 RPL17 RPL17 5111 0.052 0.42 YES
42 RPS15A RPS15A RPS15A 5137 0.051 0.43 YES
43 RPL9 RPL9 RPL9 5143 0.051 0.44 YES
44 RPS21 RPS21 RPS21 5257 0.049 0.44 YES
45 RPL37A RPL37A RPL37A 5326 0.048 0.44 YES
46 RPL27A RPL27A RPL27A 5332 0.048 0.45 YES
47 RPL32 RPL32 RPL32 5347 0.048 0.46 YES
48 RPS27L RPS27L RPS27L 5356 0.048 0.47 YES
49 RPS27A RPS27A RPS27A 5361 0.048 0.48 YES
50 FAU FAU FAU 5474 0.046 0.48 YES
51 RPLP0 RPLP0 RPLP0 5495 0.046 0.48 YES
52 RPL7A RPL7A RPL7A 5732 0.042 0.48 YES
53 RPS18 RPS18 RPS18 5788 0.041 0.48 YES
54 RPL30 RPL30 RPL30 5821 0.041 0.49 YES
55 RPL19 RPL19 RPL19 5890 0.04 0.49 YES
56 RPL14 RPL14 RPL14 5992 0.038 0.49 YES
57 RPL8 RPL8 RPL8 6198 0.036 0.49 YES
58 RPL35A RPL35A RPL35A 6227 0.035 0.49 YES
59 RPS7 RPS7 RPS7 6322 0.034 0.49 YES
60 RPL36 RPL36 RPL36 6452 0.032 0.49 NO
61 RPL41 RPL41 RPL41 6658 0.028 0.48 NO
62 RPL12 RPL12 RPL12 6915 0.025 0.48 NO
63 RPS15 RPS15 RPS15 7010 0.023 0.47 NO
64 RPL38 RPL38 RPL38 7047 0.023 0.48 NO
65 RPL26 RPL26 RPL26 7108 0.022 0.48 NO
66 RPL27 RPL27 RPL27 7445 0.017 0.46 NO
67 RPS10 RPS10 RPS10 8349 0.0035 0.41 NO
68 RPL35 RPL35 RPL35 8767 -0.0022 0.39 NO
69 RPS17 RPS17 RPS17 8771 -0.0022 0.39 NO
70 RPS9 RPS9 RPS9 8848 -0.0035 0.39 NO
71 UBA52 UBA52 UBA52 8913 -0.0046 0.38 NO
72 RPLP1 RPLP1 RPLP1 9068 -0.007 0.38 NO
73 RPS2 RPS2 RPS2 9110 -0.0077 0.38 NO
74 RPS5 RPS5 RPS5 10862 -0.043 0.29 NO
75 RPL5 RPL5 RPL5 10881 -0.043 0.29 NO
76 RPS4Y1 RPS4Y1 RPS4Y1 10992 -0.046 0.3 NO
77 RPL22 RPL22 RPL22 11093 -0.049 0.3 NO
78 RPS11 RPS11 RPS11 11317 -0.055 0.3 NO
79 RPL13A RPL13A RPL13A 11388 -0.057 0.3 NO
80 RPL28 RPL28 RPL28 11558 -0.061 0.3 NO
81 RPS8 RPS8 RPS8 11577 -0.062 0.31 NO
82 RPS16 RPS16 RPS16 11916 -0.072 0.31 NO
83 RPS19 RPS19 RPS19 11935 -0.073 0.32 NO
84 MRPL13 MRPL13 MRPL13 12184 -0.081 0.32 NO
85 RPL11 RPL11 RPL11 12482 -0.093 0.32 NO

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

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

genes ES table in pathway: BIOCARTA RACCYCD PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 G6PC2 G6PC2 G6PC2 2 0.91 0.2 YES
2 G6PC G6PC G6PC 48 0.62 0.34 YES
3 PFKM PFKM PFKM 3572 0.08 0.17 NO
4 GANC GANC GANC 4341 0.065 0.14 NO
5 GALK1 GALK1 GALK1 5651 0.044 0.078 NO
6 GALT GALT GALT 6275 0.034 0.051 NO
7 GALK2 GALK2 GALK2 8194 0.0059 -0.052 NO
8 GAA GAA GAA 8403 0.0028 -0.063 NO
9 PFKL PFKL PFKL 9832 -0.02 -0.14 NO
10 PGM2 PGM2 PGM2 9876 -0.021 -0.13 NO
11 AKR1B1 AKR1B1 AKR1B1 9948 -0.022 -0.13 NO
12 PFKP PFKP PFKP 10344 -0.031 -0.15 NO
13 HK1 HK1 HK1 10382 -0.032 -0.14 NO
14 GLB1 GLB1 GLB1 10564 -0.036 -0.14 NO
15 GLA GLA GLA 11460 -0.058 -0.18 NO
16 LCT LCT LCT 11685 -0.065 -0.18 NO
17 PGM1 PGM1 PGM1 12350 -0.088 -0.2 NO
18 B4GALT2 B4GALT2 B4GALT2 13773 -0.14 -0.24 NO
19 UGP2 UGP2 UGP2 13857 -0.15 -0.21 NO
20 HK3 HK3 HK3 14221 -0.16 -0.19 NO
21 GALE GALE GALE 14978 -0.2 -0.19 NO
22 B4GALT1 B4GALT1 B4GALT1 15183 -0.21 -0.16 NO
23 MGAM MGAM MGAM 16531 -0.3 -0.16 NO
24 HK2 HK2 HK2 17329 -0.4 -0.12 NO
25 GCK GCK GCK 18277 -0.75 0.0021 NO

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

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

genes ES table in pathway: KEGG GALACTOSE METABOLISM

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 ZCCHC7 ZCCHC7 ZCCHC7 2071 0.13 -0.07 YES
2 CNOT6 CNOT6 CNOT6 2397 0.12 -0.05 YES
3 DIS3 DIS3 DIS3 2423 0.12 -0.013 YES
4 EXOSC4 EXOSC4 EXOSC4 2434 0.11 0.024 YES
5 DCPS DCPS DCPS 2585 0.11 0.052 YES
6 EDC3 EDC3 EDC3 2862 0.099 0.07 YES
7 SKIV2L SKIV2L SKIV2L 2867 0.099 0.1 YES
8 EXOSC2 EXOSC2 EXOSC2 3276 0.088 0.11 YES
9 EXOSC6 EXOSC6 EXOSC6 3656 0.079 0.11 YES
10 NAA38 NAA38 NAA38 3864 0.074 0.13 YES
11 LSM7 LSM7 LSM7 4302 0.066 0.13 YES
12 CNOT2 CNOT2 CNOT2 4415 0.063 0.14 YES
13 EXOSC8 EXOSC8 EXOSC8 4453 0.063 0.16 YES
14 PAPD7 PAPD7 PAPD7 4858 0.056 0.16 YES
15 LSM2 LSM2 LSM2 4948 0.054 0.17 YES
16 MPHOSPH6 MPHOSPH6 MPHOSPH6 5093 0.052 0.18 YES
17 XRN1 XRN1 XRN1 5216 0.05 0.19 YES
18 SKIV2L2 SKIV2L2 SKIV2L2 5225 0.05 0.2 YES
19 WDR61 WDR61 WDR61 5524 0.045 0.2 YES
20 LSM3 LSM3 LSM3 5572 0.044 0.22 YES
21 HSPA9 HSPA9 HSPA9 5702 0.043 0.22 YES
22 EXOSC9 EXOSC9 EXOSC9 5742 0.042 0.23 YES
23 CNOT10 CNOT10 CNOT10 5779 0.042 0.25 YES
24 EDC4 EDC4 EDC4 6269 0.034 0.23 NO
25 EXOSC7 EXOSC7 EXOSC7 6396 0.032 0.23 NO
26 ENO3 ENO3 ENO3 6478 0.031 0.24 NO
27 PNPT1 PNPT1 PNPT1 6781 0.027 0.23 NO
28 PATL1 PATL1 PATL1 6938 0.024 0.23 NO
29 EXOSC3 EXOSC3 EXOSC3 6941 0.024 0.24 NO
30 HSPD1 HSPD1 HSPD1 7098 0.022 0.24 NO
31 PAPOLG PAPOLG PAPOLG 7385 0.018 0.23 NO
32 CNOT6L CNOT6L CNOT6L 7425 0.018 0.23 NO
33 C1D C1D C1D 7468 0.017 0.24 NO
34 RQCD1 RQCD1 RQCD1 7515 0.016 0.24 NO
35 LSM5 LSM5 LSM5 7526 0.016 0.24 NO
36 DDX6 DDX6 DDX6 7656 0.014 0.24 NO
37 DCP1A DCP1A DCP1A 7817 0.012 0.24 NO
38 CNOT1 CNOT1 CNOT1 7934 0.0098 0.23 NO
39 XRN2 XRN2 XRN2 8122 0.0071 0.22 NO
40 ENO2 ENO2 ENO2 8288 0.0045 0.22 NO
41 LSM6 LSM6 LSM6 8779 -0.0024 0.19 NO
42 EXOSC1 EXOSC1 EXOSC1 8792 -0.0026 0.19 NO
43 CNOT7 CNOT7 CNOT7 8976 -0.0056 0.18 NO
44 LSM4 LSM4 LSM4 9568 -0.015 0.16 NO
45 PAPOLA PAPOLA PAPOLA 9709 -0.018 0.15 NO
46 CNOT4 CNOT4 CNOT4 9790 -0.019 0.16 NO
47 TTC37 TTC37 TTC37 9826 -0.02 0.16 NO
48 LSM1 LSM1 LSM1 9932 -0.022 0.16 NO
49 PARN PARN PARN 10302 -0.03 0.15 NO
50 DCP2 DCP2 DCP2 10838 -0.042 0.14 NO
51 DCP1B DCP1B DCP1B 11714 -0.065 0.11 NO
52 CNOT3 CNOT3 CNOT3 12819 -0.1 0.085 NO
53 ENO1 ENO1 ENO1 13381 -0.13 0.096 NO
54 EXOSC5 EXOSC5 EXOSC5 13434 -0.13 0.14 NO
55 EXOSC10 EXOSC10 EXOSC10 14543 -0.18 0.14 NO
56 PAPOLB PAPOLB PAPOLB 15308 -0.22 0.16 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 GALACTOSE METABOLISM.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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 MYH6 MYH6 MYH6 8 0.81 0.072 YES
2 CACNG2 CACNG2 CACNG2 15 0.76 0.14 YES
3 CACNG1 CACNG1 CACNG1 67 0.59 0.19 YES
4 MYH7 MYH7 MYH7 102 0.54 0.24 YES
5 FXYD2 FXYD2 FXYD2 235 0.44 0.27 YES
6 CACNG4 CACNG4 CACNG4 314 0.39 0.3 YES
7 TNNI3 TNNI3 TNNI3 393 0.36 0.33 YES
8 CACNA2D2 CACNA2D2 CACNA2D2 830 0.25 0.32 YES
9 COX4I2 COX4I2 COX4I2 893 0.24 0.34 YES
10 CACNG8 CACNG8 CACNG8 1172 0.2 0.34 YES
11 CACNA2D1 CACNA2D1 CACNA2D1 1783 0.15 0.32 NO
12 CACNG6 CACNG6 CACNG6 1788 0.15 0.34 NO
13 TPM2 TPM2 TPM2 1975 0.14 0.34 NO
14 CACNA1D CACNA1D CACNA1D 2234 0.12 0.34 NO
15 CACNA2D3 CACNA2D3 CACNA2D3 2702 0.1 0.32 NO
16 CACNA1C CACNA1C CACNA1C 3237 0.089 0.3 NO
17 SLC8A1 SLC8A1 SLC8A1 4493 0.062 0.24 NO
18 CACNB4 CACNB4 CACNB4 4660 0.059 0.23 NO
19 COX7A2 COX7A2 COX7A2 5125 0.051 0.21 NO
20 ATP2A2 ATP2A2 ATP2A2 5127 0.051 0.22 NO
21 COX8A COX8A COX8A 5567 0.045 0.2 NO
22 UQCRC1 UQCRC1 UQCRC1 5616 0.044 0.2 NO
23 UQCRB UQCRB UQCRB 5677 0.043 0.2 NO
24 CYC1 CYC1 CYC1 5911 0.04 0.19 NO
25 COX7B COX7B COX7B 6012 0.038 0.18 NO
26 COX4I1 COX4I1 COX4I1 6538 0.03 0.16 NO
27 ATP1B3 ATP1B3 ATP1B3 6607 0.029 0.16 NO
28 COX7C COX7C COX7C 7088 0.022 0.13 NO
29 COX5B COX5B COX5B 7284 0.019 0.12 NO
30 ATP1A3 ATP1A3 ATP1A3 7465 0.017 0.12 NO
31 MYL3 MYL3 MYL3 8427 0.0025 0.064 NO
32 CACNG7 CACNG7 CACNG7 8607 -0.00022 0.054 NO
33 UQCR10 UQCR10 UQCR10 8851 -0.0035 0.041 NO
34 ATP1B2 ATP1B2 ATP1B2 9189 -0.0089 0.024 NO
35 UQCRQ UQCRQ UQCRQ 9515 -0.014 0.007 NO
36 COX5A COX5A COX5A 9641 -0.016 0.0016 NO
37 COX6A1 COX6A1 COX6A1 9648 -0.016 0.0027 NO
38 COX7A2L COX7A2L COX7A2L 9859 -0.02 -0.007 NO
39 UQCR11 UQCR11 UQCR11 9962 -0.023 -0.01 NO
40 SLC9A6 SLC9A6 SLC9A6 10007 -0.024 -0.011 NO
41 COX6C COX6C COX6C 10473 -0.034 -0.033 NO
42 TPM4 TPM4 TPM4 10571 -0.036 -0.035 NO
43 CACNB1 CACNB1 CACNB1 10748 -0.04 -0.041 NO
44 TPM1 TPM1 TPM1 11140 -0.05 -0.058 NO
45 CACNG3 CACNG3 CACNG3 11625 -0.063 -0.079 NO
46 ACTC1 ACTC1 ACTC1 11961 -0.074 -0.091 NO
47 TPM3 TPM3 TPM3 12026 -0.076 -0.088 NO
48 TNNC1 TNNC1 TNNC1 12701 -0.1 -0.12 NO
49 COX8C COX8C COX8C 12737 -0.1 -0.11 NO
50 UQCRH UQCRH UQCRH 12919 -0.11 -0.11 NO
51 UQCRFS1 UQCRFS1 UQCRFS1 13007 -0.11 -0.1 NO
52 UQCRHL UQCRHL UQCRHL 13093 -0.12 -0.098 NO
53 COX6B2 COX6B2 COX6B2 13410 -0.13 -0.1 NO
54 CACNB3 CACNB3 CACNB3 13595 -0.14 -0.1 NO
55 COX6B1 COX6B1 COX6B1 13639 -0.14 -0.092 NO
56 ATP1B4 ATP1B4 ATP1B4 13729 -0.14 -0.084 NO
57 ATP1A1 ATP1A1 ATP1A1 13769 -0.14 -0.073 NO
58 ATP1A2 ATP1A2 ATP1A2 13801 -0.15 -0.062 NO
59 TNNT2 TNNT2 TNNT2 14693 -0.19 -0.094 NO
60 ATP1B1 ATP1B1 ATP1B1 14923 -0.2 -0.089 NO
61 SLC9A1 SLC9A1 SLC9A1 15209 -0.21 -0.086 NO
62 RYR2 RYR2 RYR2 15445 -0.22 -0.078 NO
63 COX7A1 COX7A1 COX7A1 15745 -0.24 -0.073 NO
64 CACNA1S CACNA1S CACNA1S 15924 -0.26 -0.06 NO
65 CACNG5 CACNG5 CACNG5 16210 -0.28 -0.051 NO
66 ATP1A4 ATP1A4 ATP1A4 16237 -0.28 -0.028 NO
67 COX6A2 COX6A2 COX6A2 16366 -0.29 -0.0088 NO
68 CACNB2 CACNB2 CACNB2 16487 -0.3 0.011 NO
69 CACNA2D4 CACNA2D4 CACNA2D4 17810 -0.49 -0.017 NO
70 CACNA1F CACNA1F CACNA1F 17858 -0.5 0.025 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 OXIDATIVE PHOSPHORYLATION.

Figure S50.  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 LYSINE DEGRADATION

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CREB3L1 CREB3L1 CREB3L1 114 0.53 0.14 YES
2 CREB3L4 CREB3L4 CREB3L4 245 0.43 0.25 YES
3 AVPR2 AVPR2 AVPR2 1399 0.18 0.23 NO
4 DCTN4 DCTN4 DCTN4 3352 0.086 0.15 NO
5 ADCY6 ADCY6 ADCY6 3506 0.082 0.16 NO
6 DCTN6 DCTN6 DCTN6 4184 0.068 0.14 NO
7 DCTN5 DCTN5 DCTN5 4565 0.061 0.14 NO
8 RAB11B RAB11B RAB11B 4970 0.054 0.13 NO
9 PRKX PRKX PRKX 5537 0.045 0.12 NO
10 STX4 STX4 STX4 6792 0.026 0.053 NO
11 CREB3 CREB3 CREB3 7011 0.023 0.048 NO
12 DYNC1LI1 DYNC1LI1 DYNC1LI1 7213 0.02 0.042 NO
13 RAB5C RAB5C RAB5C 7271 0.019 0.044 NO
14 RAB5B RAB5B RAB5B 7289 0.019 0.049 NO
15 RAB5A RAB5A RAB5A 7430 0.018 0.046 NO
16 DCTN1 DCTN1 DCTN1 8081 0.0076 0.012 NO
17 DYNC1I2 DYNC1I2 DYNC1I2 8373 0.0032 -0.0029 NO
18 GNAS GNAS GNAS 8414 0.0026 -0.0043 NO
19 DYNC1H1 DYNC1H1 DYNC1H1 8457 0.002 -0.0061 NO
20 ARHGDIA ARHGDIA ARHGDIA 8791 -0.0026 -0.024 NO
21 VAMP2 VAMP2 VAMP2 8829 -0.0032 -0.025 NO
22 CREB1 CREB1 CREB1 9459 -0.013 -0.056 NO
23 DCTN2 DCTN2 DCTN2 9466 -0.013 -0.052 NO
24 NSF NSF NSF 9616 -0.016 -0.056 NO
25 DYNLL2 DYNLL2 DYNLL2 9719 -0.018 -0.057 NO
26 DYNC1I1 DYNC1I1 DYNC1I1 10438 -0.033 -0.087 NO
27 RAB11A RAB11A RAB11A 10959 -0.045 -0.1 NO
28 DYNC1LI2 DYNC1LI2 DYNC1LI2 11220 -0.052 -0.1 NO
29 DYNC2LI1 DYNC2LI1 DYNC2LI1 11466 -0.059 -0.1 NO
30 DYNLL1 DYNLL1 DYNLL1 11803 -0.068 -0.1 NO
31 DYNC2H1 DYNC2H1 DYNC2H1 11845 -0.07 -0.084 NO
32 CREB3L2 CREB3L2 CREB3L2 11949 -0.073 -0.069 NO
33 PRKACB PRKACB PRKACB 12043 -0.076 -0.054 NO
34 ADCY9 ADCY9 ADCY9 12215 -0.083 -0.04 NO
35 AQP2 AQP2 AQP2 12234 -0.083 -0.019 NO
36 PRKACA PRKACA PRKACA 12441 -0.091 -0.0051 NO
37 CREB3L3 CREB3L3 CREB3L3 12573 -0.096 0.014 NO
38 CREB5 CREB5 CREB5 13178 -0.12 0.013 NO
39 AQP3 AQP3 AQP3 14514 -0.18 -0.011 NO
40 AQP4 AQP4 AQP4 14886 -0.2 0.022 NO
41 ARHGDIB ARHGDIB ARHGDIB 15351 -0.22 0.056 NO
42 PRKACG PRKACG PRKACG 17241 -0.39 0.059 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 LYSINE DEGRADATION.

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

genes ES table in pathway: KEGG SPHINGOLIPID METABOLISM

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 POLE2 POLE2 POLE2 818 0.25 0.08 YES
2 POLL POLL POLL 2079 0.13 0.074 YES
3 PARP3 PARP3 PARP3 2111 0.13 0.14 YES
4 SMUG1 SMUG1 SMUG1 2955 0.097 0.14 YES
5 PARP2 PARP2 PARP2 3108 0.092 0.17 YES
6 FEN1 FEN1 FEN1 3203 0.089 0.21 YES
7 NEIL2 NEIL2 NEIL2 3531 0.081 0.23 YES
8 APEX1 APEX1 APEX1 3869 0.074 0.25 YES
9 NEIL1 NEIL1 NEIL1 4287 0.066 0.26 YES
10 NTHL1 NTHL1 NTHL1 4582 0.06 0.28 YES
11 POLE POLE POLE 4591 0.06 0.3 YES
12 OGG1 OGG1 OGG1 5135 0.051 0.3 YES
13 TDG TDG TDG 5389 0.047 0.31 YES
14 POLD2 POLD2 POLD2 6358 0.033 0.27 NO
15 POLB POLB POLB 6504 0.03 0.28 NO
16 PARP4 PARP4 PARP4 7491 0.017 0.23 NO
17 APEX2 APEX2 APEX2 7980 0.0091 0.21 NO
18 NEIL3 NEIL3 NEIL3 8389 0.003 0.19 NO
19 MPG MPG MPG 8546 0.00068 0.18 NO
20 PCNA PCNA PCNA 8772 -0.0022 0.17 NO
21 PARP1 PARP1 PARP1 8941 -0.0051 0.16 NO
22 POLD3 POLD3 POLD3 9289 -0.01 0.15 NO
23 LIG3 LIG3 LIG3 9573 -0.015 0.14 NO
24 POLE3 POLE3 POLE3 9730 -0.018 0.14 NO
25 POLD4 POLD4 POLD4 9919 -0.022 0.14 NO
26 MBD4 MBD4 MBD4 10844 -0.042 0.11 NO
27 LIG1 LIG1 LIG1 11165 -0.051 0.12 NO
28 UNG UNG UNG 12101 -0.078 0.11 NO
29 XRCC1 XRCC1 XRCC1 12284 -0.085 0.14 NO
30 POLD1 POLD1 POLD1 12395 -0.089 0.18 NO
31 MUTYH MUTYH MUTYH 13395 -0.13 0.18 NO
32 POLE4 POLE4 POLE4 14426 -0.17 0.21 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 SPHINGOLIPID METABOLISM.

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

Table 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 POLR2F POLR2F POLR2F 1235 0.19 0.05 YES
2 POLR3D POLR3D POLR3D 1455 0.17 0.14 YES
3 POLR1B POLR1B POLR1B 2541 0.11 0.15 YES
4 POLR3G POLR3G POLR3G 3889 0.074 0.12 YES
5 POLR3F POLR3F POLR3F 3967 0.072 0.16 YES
6 POLR3GL POLR3GL POLR3GL 4202 0.067 0.19 YES
7 POLR1A POLR1A POLR1A 4584 0.06 0.21 YES
8 ZNRD1 ZNRD1 ZNRD1 4844 0.056 0.23 YES
9 POLR3K POLR3K POLR3K 5617 0.044 0.21 YES
10 POLR1E POLR1E POLR1E 5837 0.041 0.22 YES
11 POLR2D POLR2D POLR2D 5979 0.039 0.24 YES
12 POLR2A POLR2A POLR2A 6011 0.038 0.26 YES
13 POLR1C POLR1C POLR1C 6996 0.023 0.22 NO
14 POLR3C POLR3C POLR3C 7965 0.0093 0.17 NO
15 POLR3B POLR3B POLR3B 7969 0.0093 0.18 NO
16 POLR2G POLR2G POLR2G 8148 0.0066 0.17 NO
17 POLR2C POLR2C POLR2C 8237 0.0053 0.17 NO
18 POLR2E POLR2E POLR2E 8525 0.0011 0.16 NO
19 POLR2B POLR2B POLR2B 9472 -0.013 0.11 NO
20 POLR2J3 POLR2J3 POLR2J3 9523 -0.014 0.12 NO
21 POLR3A POLR3A POLR3A 9883 -0.021 0.11 NO
22 POLR3H POLR3H POLR3H 10199 -0.028 0.11 NO
23 POLR2K POLR2K POLR2K 10470 -0.034 0.12 NO
24 POLR2L POLR2L POLR2L 10777 -0.041 0.13 NO
25 POLR2J POLR2J POLR2J 11816 -0.069 0.11 NO
26 POLR1D POLR1D POLR1D 12238 -0.083 0.14 NO
27 POLR2J2 POLR2J2 POLR2J2 13881 -0.15 0.14 NO
28 POLR2I POLR2I POLR2I 14254 -0.17 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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RIBOSOME

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 POLE2 POLE2 POLE2 818 0.25 0.063 YES
2 PRIM1 PRIM1 PRIM1 1157 0.2 0.13 YES
3 RNASEH2C RNASEH2C RNASEH2C 1966 0.14 0.14 YES
4 DNA2 DNA2 DNA2 2092 0.13 0.19 YES
5 MCM4 MCM4 MCM4 2703 0.1 0.2 YES
6 MCM6 MCM6 MCM6 2900 0.098 0.23 YES
7 RPA4 RPA4 RPA4 3062 0.093 0.26 YES
8 FEN1 FEN1 FEN1 3203 0.089 0.29 YES
9 RFC4 RFC4 RFC4 3444 0.083 0.32 YES
10 RNASEH2A RNASEH2A RNASEH2A 3493 0.082 0.35 YES
11 POLE POLE POLE 4591 0.06 0.31 YES
12 RNASEH2B RNASEH2B RNASEH2B 4757 0.058 0.33 YES
13 MCM7 MCM7 MCM7 4794 0.057 0.35 YES
14 POLD2 POLD2 POLD2 6358 0.033 0.28 NO
15 POLA2 POLA2 POLA2 6380 0.033 0.29 NO
16 PRIM2 PRIM2 PRIM2 7041 0.023 0.27 NO
17 RFC3 RFC3 RFC3 7156 0.021 0.27 NO
18 MCM2 MCM2 MCM2 7444 0.017 0.26 NO
19 MCM5 MCM5 MCM5 7588 0.015 0.26 NO
20 SSBP1 SSBP1 SSBP1 8002 0.0088 0.24 NO
21 PCNA PCNA PCNA 8772 -0.0022 0.2 NO
22 RNASEH1 RNASEH1 RNASEH1 9098 -0.0075 0.18 NO
23 POLD3 POLD3 POLD3 9289 -0.01 0.18 NO
24 POLE3 POLE3 POLE3 9730 -0.018 0.16 NO
25 POLD4 POLD4 POLD4 9919 -0.022 0.16 NO
26 RFC1 RFC1 RFC1 10088 -0.026 0.16 NO
27 RFC2 RFC2 RFC2 10350 -0.031 0.16 NO
28 RPA1 RPA1 RPA1 10843 -0.042 0.15 NO
29 MCM3 MCM3 MCM3 10861 -0.043 0.17 NO
30 RFC5 RFC5 RFC5 11155 -0.05 0.18 NO
31 LIG1 LIG1 LIG1 11165 -0.051 0.2 NO
32 RPA3 RPA3 RPA3 12246 -0.084 0.17 NO
33 POLD1 POLD1 POLD1 12395 -0.089 0.2 NO
34 RPA2 RPA2 RPA2 13077 -0.11 0.21 NO
35 POLE4 POLE4 POLE4 14426 -0.17 0.21 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 RIBOSOME.

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

genes ES table in pathway: KEGG RNA DEGRADATION

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 GAL3ST1 GAL3ST1 GAL3ST1 404 0.36 0.061 YES
2 SMPD3 SMPD3 SMPD3 504 0.33 0.13 YES
3 NEU4 NEU4 NEU4 512 0.32 0.21 YES
4 ACER2 ACER2 ACER2 1106 0.21 0.22 YES
5 NEU3 NEU3 NEU3 1506 0.17 0.24 YES
6 UGT8 UGT8 UGT8 1532 0.16 0.28 YES
7 ASAH2 ASAH2 ASAH2 2175 0.13 0.27 YES
8 B4GALT6 B4GALT6 B4GALT6 2801 0.1 0.26 YES
9 SGMS1 SGMS1 SGMS1 2839 0.1 0.28 YES
10 GBA GBA GBA 3214 0.089 0.28 YES
11 SGPP1 SGPP1 SGPP1 5157 0.051 0.19 NO
12 NEU1 NEU1 NEU1 5448 0.047 0.19 NO
13 ACER3 ACER3 ACER3 5540 0.045 0.19 NO
14 SGPL1 SGPL1 SGPL1 6056 0.038 0.17 NO
15 SMPD2 SMPD2 SMPD2 6486 0.031 0.16 NO
16 SPTLC1 SPTLC1 SPTLC1 7581 0.015 0.099 NO
17 SMPD1 SMPD1 SMPD1 7866 0.011 0.086 NO
18 DEGS1 DEGS1 DEGS1 8357 0.0034 0.06 NO
19 SMPD4 SMPD4 SMPD4 9326 -0.011 0.0098 NO
20 KDSR KDSR KDSR 10220 -0.028 -0.032 NO
21 PPAP2A PPAP2A PPAP2A 10464 -0.034 -0.038 NO
22 SPHK1 SPHK1 SPHK1 10496 -0.034 -0.031 NO
23 GLB1 GLB1 GLB1 10564 -0.036 -0.027 NO
24 CERK CERK CERK 10589 -0.037 -0.019 NO
25 DEGS2 DEGS2 DEGS2 10848 -0.042 -0.024 NO
26 ASAH1 ASAH1 ASAH1 11077 -0.048 -0.025 NO
27 SGPP2 SGPP2 SGPP2 11413 -0.057 -0.03 NO
28 GLA GLA GLA 11460 -0.058 -0.018 NO
29 PPAP2C PPAP2C PPAP2C 12165 -0.081 -0.038 NO
30 SPTLC2 SPTLC2 SPTLC2 12625 -0.098 -0.04 NO
31 SPHK2 SPHK2 SPHK2 13062 -0.11 -0.037 NO
32 ACER1 ACER1 ACER1 13186 -0.12 -0.016 NO
33 GALC GALC GALC 14515 -0.18 -0.047 NO
34 ARSA ARSA ARSA 14661 -0.18 -0.012 NO
35 UGCG UGCG UGCG 14943 -0.2 0.019 NO
36 PPAP2B PPAP2B PPAP2B 16603 -0.31 0.00086 NO
37 SGMS2 SGMS2 SGMS2 17308 -0.4 0.055 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 RNA DEGRADATION.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus4 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA NO1 PATHWAY 29 genes.ES.table 0.66 1.6 0.0084 0.088 0.65 0.41 0.16 0.35 0.049 0.001
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.63 1.7 0.0041 0.076 0.54 0.2 0.058 0.19 0.039 0.001
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.56 1.9 0.0041 0.078 0.075 0.5 0.24 0.38 0 0.026
BIOCARTA BIOPEPTIDES PATHWAY 39 genes.ES.table 0.62 1.9 0.0021 0.059 0.12 0.49 0.24 0.37 0 0.011
BIOCARTA HDAC PATHWAY 27 genes.ES.table 0.51 1.6 0.038 0.1 0.79 0.41 0.22 0.32 0.069 0
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.46 1.4 0.11 0.18 0.94 0.2 0.17 0.17 0.14 0.001
BIOCARTA ERK PATHWAY 26 genes.ES.table 0.42 1.4 0.073 0.18 0.94 0.15 0.13 0.13 0.14 0.001
BIOCARTA PYK2 PATHWAY 27 genes.ES.table 0.57 1.9 0 0.15 0.068 0.44 0.24 0.34 0 0.051
BIOCARTA NFAT PATHWAY 50 genes.ES.table 0.43 1.3 0.082 0.23 0.98 0.26 0.17 0.22 0.19 0.001
BIOCARTA PDGF PATHWAY 31 genes.ES.table 0.45 1.4 0.12 0.18 0.94 0.19 0.17 0.16 0.14 0.001
genes ES table in pathway: BIOCARTA NO1 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 781 0.57 0.12 YES
2 PAK1 PAK1 PAK1 802 0.56 0.27 YES
3 PTK2B PTK2B PTK2B 1419 0.37 0.34 YES
4 MAP2K4 MAP2K4 MAP2K4 2131 0.24 0.37 YES
5 CALM3 CALM3 CALM3 2141 0.24 0.44 YES
6 MAP2K1 MAP2K1 MAP2K1 2401 0.21 0.49 YES
7 CALM1 CALM1 CALM1 2694 0.18 0.52 YES
8 MAPK8 MAPK8 MAPK8 3036 0.16 0.55 YES
9 MAPK3 MAPK3 MAPK3 4086 0.096 0.52 YES
10 GNAQ GNAQ GNAQ 4192 0.091 0.54 YES
11 MAPK1 MAPK1 MAPK1 4299 0.087 0.56 YES
12 CALM2 CALM2 CALM2 4375 0.084 0.57 YES
13 PRKCA PRKCA PRKCA 5887 0.038 0.5 NO
14 MAPK14 MAPK14 MAPK14 7452 0.0069 0.42 NO
15 GRB2 GRB2 GRB2 7504 0.0061 0.42 NO
16 CRKL CRKL CRKL 7550 0.0054 0.42 NO
17 SRC SRC SRC 7925 -0.00081 0.4 NO
18 MAP2K2 MAP2K2 MAP2K2 8550 -0.01 0.36 NO
19 RAC1 RAC1 RAC1 9393 -0.021 0.32 NO
20 SOS1 SOS1 SOS1 9666 -0.025 0.32 NO
21 PLCG1 PLCG1 PLCG1 10537 -0.036 0.28 NO
22 BCAR1 BCAR1 BCAR1 10746 -0.039 0.28 NO
23 RAF1 RAF1 RAF1 12395 -0.061 0.21 NO
24 MAP2K3 MAP2K3 MAP2K3 13842 -0.084 0.15 NO
25 JUN JUN JUN 13895 -0.085 0.17 NO
26 SHC1 SHC1 SHC1 15124 -0.12 0.14 NO
27 MAP3K1 MAP3K1 MAP3K1 15752 -0.14 0.14 NO

Figure S61.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NO1 PATHWAY.

Figure S62.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NO1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA AGR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 781 0.57 0.088 YES
2 PAK1 PAK1 PAK1 802 0.56 0.22 YES
3 PTK2B PTK2B PTK2B 1419 0.37 0.27 YES
4 MAP2K4 MAP2K4 MAP2K4 2131 0.24 0.28 YES
5 CALM3 CALM3 CALM3 2141 0.24 0.34 YES
6 MAP2K1 MAP2K1 MAP2K1 2401 0.21 0.37 YES
7 ELK1 ELK1 ELK1 2457 0.21 0.42 YES
8 CALM1 CALM1 CALM1 2694 0.18 0.45 YES
9 MEF2D MEF2D MEF2D 2704 0.18 0.49 YES
10 MAPK8 MAPK8 MAPK8 3036 0.16 0.51 YES
11 MEF2A MEF2A MEF2A 3947 0.1 0.48 YES
12 ATF2 ATF2 ATF2 4044 0.098 0.5 YES
13 MAPK3 MAPK3 MAPK3 4086 0.096 0.52 YES
14 GNAQ GNAQ GNAQ 4192 0.091 0.53 YES
15 MAPK1 MAPK1 MAPK1 4299 0.087 0.55 YES
16 CALM2 CALM2 CALM2 4375 0.084 0.56 YES
17 HRAS HRAS HRAS 5557 0.046 0.51 NO
18 AGTR1 AGTR1 AGTR1 5637 0.044 0.52 NO
19 PRKCA PRKCA PRKCA 5887 0.038 0.51 NO
20 AGT AGT AGT 6425 0.026 0.49 NO
21 PTK2 PTK2 PTK2 7257 0.01 0.44 NO
22 GRB2 GRB2 GRB2 7504 0.0061 0.43 NO
23 SRC SRC SRC 7925 -0.00081 0.41 NO
24 MAP2K2 MAP2K2 MAP2K2 8550 -0.01 0.38 NO
25 RAC1 RAC1 RAC1 9393 -0.021 0.34 NO
26 SOS1 SOS1 SOS1 9666 -0.025 0.33 NO
27 RAF1 RAF1 RAF1 12395 -0.061 0.19 NO
28 EGFR EGFR EGFR 12590 -0.064 0.2 NO
29 JUN JUN JUN 13895 -0.085 0.14 NO
30 SHC1 SHC1 SHC1 15124 -0.12 0.1 NO
31 MAP3K1 MAP3K1 MAP3K1 15752 -0.14 0.099 NO
32 LOC729991-MEF2B LOC729991-MEF2B LOC729991-MEF2B 16650 -0.18 0.091 NO

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

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

genes ES table in pathway: BIOCARTA AT1R PATHWAY

Table 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 CACNA1F CACNA1F CACNA1F 268 0.92 0.041 YES
2 GRIN2A GRIN2A GRIN2A 411 0.78 0.081 YES
3 GRIN1 GRIN1 GRIN1 442 0.76 0.13 YES
4 GRIN2B GRIN2B GRIN2B 500 0.73 0.17 YES
5 SNCA SNCA SNCA 569 0.68 0.2 YES
6 ITPR1 ITPR1 ITPR1 645 0.64 0.24 YES
7 COX7A1 COX7A1 COX7A1 730 0.6 0.27 YES
8 CACNA1S CACNA1S CACNA1S 731 0.6 0.31 YES
9 CALML3 CALML3 CALML3 1004 0.48 0.32 YES
10 NOS1 NOS1 NOS1 1085 0.46 0.34 YES
11 CHP2 CHP2 CHP2 1900 0.28 0.32 YES
12 PPP3R2 PPP3R2 PPP3R2 1924 0.28 0.33 YES
13 CDK5R1 CDK5R1 CDK5R1 1967 0.27 0.35 YES
14 PPP3R1 PPP3R1 PPP3R1 1995 0.26 0.36 YES
15 CACNA1C CACNA1C CACNA1C 2002 0.26 0.38 YES
16 GRIN2C GRIN2C GRIN2C 2068 0.25 0.39 YES
17 PPP3CB PPP3CB PPP3CB 2076 0.25 0.4 YES
18 CALM3 CALM3 CALM3 2141 0.24 0.42 YES
19 PPP3CA PPP3CA PPP3CA 2184 0.24 0.43 YES
20 RYR3 RYR3 RYR3 2242 0.23 0.44 YES
21 CACNA1D CACNA1D CACNA1D 2369 0.22 0.44 YES
22 PLCB1 PLCB1 PLCB1 2526 0.2 0.45 YES
23 PLCB4 PLCB4 PLCB4 2545 0.2 0.46 YES
24 MME MME MME 2566 0.2 0.47 YES
25 CALM1 CALM1 CALM1 2694 0.18 0.47 YES
26 CDK5 CDK5 CDK5 3038 0.15 0.46 NO
27 APBB1 APBB1 APBB1 3589 0.12 0.44 NO
28 NDUFB8 NDUFB8 NDUFB8 3631 0.12 0.45 NO
29 GRIN2D GRIN2D GRIN2D 3915 0.1 0.44 NO
30 MAPK3 MAPK3 MAPK3 4086 0.096 0.43 NO
31 GNAQ GNAQ GNAQ 4192 0.091 0.43 NO
32 NDUFA4 NDUFA4 NDUFA4 4256 0.088 0.44 NO
33 MAPK1 MAPK1 MAPK1 4299 0.087 0.44 NO
34 MAPT MAPT MAPT 4359 0.085 0.44 NO
35 CALM2 CALM2 CALM2 4375 0.084 0.44 NO
36 ATP2A2 ATP2A2 ATP2A2 4462 0.08 0.44 NO
37 NDUFA5 NDUFA5 NDUFA5 4484 0.079 0.45 NO
38 CYCS CYCS CYCS 4626 0.075 0.44 NO
39 NDUFS1 NDUFS1 NDUFS1 4715 0.072 0.44 NO
40 COX7A2L COX7A2L COX7A2L 4831 0.068 0.44 NO
41 ATP5G3 ATP5G3 ATP5G3 4952 0.064 0.44 NO
42 PSEN2 PSEN2 PSEN2 5050 0.061 0.44 NO
43 NDUFA8 NDUFA8 NDUFA8 5073 0.06 0.44 NO
44 GSK3B GSK3B GSK3B 5176 0.057 0.44 NO
45 UQCRFS1 UQCRFS1 UQCRFS1 5289 0.053 0.44 NO
46 CHP CHP CHP 5305 0.052 0.44 NO
47 SDHA SDHA SDHA 5541 0.046 0.43 NO
48 COX5A COX5A COX5A 5556 0.046 0.43 NO
49 UQCRC2 UQCRC2 UQCRC2 5579 0.045 0.43 NO
50 COX6A1 COX6A1 COX6A1 5600 0.045 0.43 NO
51 IL1B IL1B IL1B 5606 0.044 0.44 NO
52 ATP5B ATP5B ATP5B 5611 0.044 0.44 NO
53 UQCRH UQCRH UQCRH 5695 0.043 0.44 NO
54 ATP5A1 ATP5A1 ATP5A1 5848 0.038 0.43 NO
55 APP APP APP 5910 0.037 0.43 NO
56 NDUFB9 NDUFB9 NDUFB9 5973 0.036 0.43 NO
57 COX4I1 COX4I1 COX4I1 6204 0.031 0.42 NO
58 UQCRC1 UQCRC1 UQCRC1 6214 0.031 0.42 NO
59 NDUFS5 NDUFS5 NDUFS5 6357 0.028 0.41 NO
60 NDUFA10 NDUFA10 NDUFA10 6467 0.026 0.41 NO
61 UQCR10 UQCR10 UQCR10 6592 0.023 0.4 NO
62 ATP5G1 ATP5G1 ATP5G1 6608 0.023 0.4 NO
63 NDUFS2 NDUFS2 NDUFS2 6615 0.023 0.4 NO
64 NDUFAB1 NDUFAB1 NDUFAB1 6658 0.022 0.4 NO
65 NDUFA3 NDUFA3 NDUFA3 6685 0.021 0.4 NO
66 ATP5C1 ATP5C1 ATP5C1 6737 0.02 0.4 NO
67 COX7A2 COX7A2 COX7A2 6773 0.02 0.4 NO
68 SDHB SDHB SDHB 6792 0.019 0.4 NO
69 ATP5H ATP5H ATP5H 6810 0.019 0.4 NO
70 BACE1 BACE1 BACE1 6830 0.018 0.4 NO
71 ATP2A3 ATP2A3 ATP2A3 6849 0.018 0.4 NO
72 NDUFV1 NDUFV1 NDUFV1 6922 0.017 0.4 NO
73 ATP5O ATP5O ATP5O 6940 0.016 0.4 NO
74 COX7C COX7C COX7C 6999 0.015 0.4 NO
75 UQCRHL UQCRHL UQCRHL 7040 0.014 0.39 NO
76 APAF1 APAF1 APAF1 7063 0.014 0.39 NO
77 COX6C COX6C COX6C 7079 0.014 0.39 NO
78 COX6A2 COX6A2 COX6A2 7084 0.013 0.39 NO
79 NDUFS3 NDUFS3 NDUFS3 7094 0.013 0.39 NO
80 NDUFB1 NDUFB1 NDUFB1 7119 0.013 0.39 NO
81 COX6B1 COX6B1 COX6B1 7135 0.012 0.39 NO
82 NDUFA1 NDUFA1 NDUFA1 7153 0.012 0.39 NO
83 UQCRB UQCRB UQCRB 7215 0.011 0.39 NO
84 COX7B COX7B COX7B 7357 0.0086 0.38 NO
85 ATP5J ATP5J ATP5J 7360 0.0085 0.38 NO
86 COX5B COX5B COX5B 7361 0.0085 0.38 NO
87 NDUFC2 NDUFC2 NDUFC2 7375 0.0083 0.38 NO
88 NDUFB6 NDUFB6 NDUFB6 7399 0.0079 0.38 NO
89 NDUFV2 NDUFV2 NDUFV2 7407 0.0077 0.38 NO
90 NDUFA6 NDUFA6 NDUFA6 7646 0.0038 0.37 NO
91 NDUFB5 NDUFB5 NDUFB5 7725 0.0027 0.37 NO
92 ADAM10 ADAM10 ADAM10 7776 0.002 0.36 NO
93 CYC1 CYC1 CYC1 7795 0.0016 0.36 NO
94 ATP5F1 ATP5F1 ATP5F1 7844 0.00085 0.36 NO
95 ITPR2 ITPR2 ITPR2 7851 0.00068 0.36 NO
96 IDE IDE IDE 7909 -0.00057 0.36 NO
97 NDUFB3 NDUFB3 NDUFB3 7949 -0.0012 0.36 NO
98 ATF6 ATF6 ATF6 8068 -0.003 0.35 NO
99 NDUFB4 NDUFB4 NDUFB4 8093 -0.0034 0.35 NO
100 CAPN1 CAPN1 CAPN1 8114 -0.0037 0.35 NO
101 GAPDH GAPDH GAPDH 8127 -0.0039 0.35 NO
102 ERN1 ERN1 ERN1 8238 -0.0054 0.34 NO
103 BID BID BID 8317 -0.0067 0.34 NO
104 PPP3CC PPP3CC PPP3CC 8524 -0.0098 0.33 NO
105 SDHC SDHC SDHC 8686 -0.012 0.32 NO
106 NDUFS4 NDUFS4 NDUFS4 8760 -0.013 0.31 NO
107 NDUFV3 NDUFV3 NDUFV3 8978 -0.015 0.3 NO
108 UQCR11 UQCR11 UQCR11 9005 -0.016 0.3 NO
109 PSEN1 PSEN1 PSEN1 9025 -0.016 0.3 NO
110 NDUFB2 NDUFB2 NDUFB2 9350 -0.021 0.29 NO
111 BAD BAD BAD 9351 -0.021 0.29 NO
112 NDUFS8 NDUFS8 NDUFS8 9448 -0.022 0.28 NO
113 NDUFS7 NDUFS7 NDUFS7 9450 -0.022 0.28 NO
114 NDUFB10 NDUFB10 NDUFB10 9477 -0.022 0.28 NO
115 ITPR3 ITPR3 ITPR3 9480 -0.022 0.29 NO
116 COX8A COX8A COX8A 9537 -0.023 0.28 NO
117 NDUFA2 NDUFA2 NDUFA2 9539 -0.023 0.29 NO
118 NDUFC1 NDUFC1 NDUFC1 9570 -0.024 0.28 NO
119 NDUFA9 NDUFA9 NDUFA9 9607 -0.024 0.28 NO
120 ATP5D ATP5D ATP5D 9679 -0.025 0.28 NO
121 UQCRQ UQCRQ UQCRQ 9688 -0.025 0.28 NO
122 SDHD SDHD SDHD 9718 -0.025 0.28 NO
123 LPL LPL LPL 9886 -0.028 0.28 NO
124 NDUFB7 NDUFB7 NDUFB7 10300 -0.033 0.26 NO
125 LRP1 LRP1 LRP1 10311 -0.033 0.26 NO
126 FAS FAS FAS 10354 -0.034 0.26 NO
127 NAE1 NAE1 NAE1 10428 -0.034 0.26 NO
128 NDUFA7 NDUFA7 NDUFA7 11003 -0.042 0.22 NO
129 ATP5G2 ATP5G2 ATP5G2 11224 -0.045 0.22 NO
130 ATP5E ATP5E ATP5E 11649 -0.051 0.2 NO
131 APOE APOE APOE 11734 -0.052 0.19 NO
132 NCSTN NCSTN NCSTN 11893 -0.054 0.19 NO
133 CASP9 CASP9 CASP9 12069 -0.056 0.18 NO
134 NDUFS6 NDUFS6 NDUFS6 12186 -0.058 0.18 NO
135 EIF2AK3 EIF2AK3 EIF2AK3 12194 -0.058 0.18 NO
136 CAPN2 CAPN2 CAPN2 12310 -0.06 0.18 NO
137 PSENEN PSENEN PSENEN 12368 -0.06 0.18 NO
138 CALML6 CALML6 CALML6 12642 -0.064 0.17 NO
139 ADAM17 ADAM17 ADAM17 12698 -0.065 0.17 NO
140 NDUFA4L2 NDUFA4L2 NDUFA4L2 12971 -0.069 0.16 NO
141 COX4I2 COX4I2 COX4I2 13232 -0.073 0.15 NO
142 APH1A APH1A APH1A 13402 -0.076 0.14 NO
143 CASP3 CASP3 CASP3 13478 -0.077 0.15 NO
144 CASP7 CASP7 CASP7 14082 -0.089 0.12 NO
145 HSD17B10 HSD17B10 HSD17B10 14821 -0.11 0.084 NO
146 COX8C COX8C COX8C 15333 -0.12 0.063 NO
147 TNF TNF TNF 15416 -0.12 0.066 NO
148 PLCB3 PLCB3 PLCB3 15474 -0.12 0.07 NO
149 FADD FADD FADD 15732 -0.14 0.065 NO
150 TNFRSF1A TNFRSF1A TNFRSF1A 16057 -0.15 0.056 NO
151 PLCB2 PLCB2 PLCB2 16296 -0.16 0.052 NO
152 BACE2 BACE2 BACE2 16679 -0.18 0.042 NO
153 COX6B2 COX6B2 COX6B2 16798 -0.19 0.047 NO
154 ATP2A1 ATP2A1 ATP2A1 17847 -0.29 0.0071 NO
155 CASP8 CASP8 CASP8 17940 -0.31 0.021 NO

Figure S65.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA AT1R PATHWAY.

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA BIOPEPTIDES PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 STAT4 STAT4 STAT4 84 1.1 0.16 YES
2 CAMK2A CAMK2A CAMK2A 181 1 0.3 YES
3 CAMK2B CAMK2B CAMK2B 753 0.58 0.35 YES
4 PRKCB PRKCB PRKCB 781 0.57 0.43 YES
5 KNG1 KNG1 KNG1 888 0.52 0.5 YES
6 PTK2B PTK2B PTK2B 1419 0.37 0.52 YES
7 CALM3 CALM3 CALM3 2141 0.24 0.52 YES
8 MAP2K1 MAP2K1 MAP2K1 2401 0.21 0.53 YES
9 CAMK2G CAMK2G CAMK2G 2593 0.19 0.55 YES
10 CALM1 CALM1 CALM1 2694 0.18 0.57 YES
11 MAPK8 MAPK8 MAPK8 3036 0.16 0.57 YES
12 CDK5 CDK5 CDK5 3038 0.15 0.6 YES
13 GNAI1 GNAI1 GNAI1 3618 0.12 0.58 YES
14 MAPK3 MAPK3 MAPK3 4086 0.096 0.57 YES
15 STAT6 STAT6 STAT6 4117 0.094 0.58 YES
16 MAPK1 MAPK1 MAPK1 4299 0.087 0.58 YES
17 MYLK MYLK MYLK 4327 0.086 0.6 YES
18 MAPT MAPT MAPT 4359 0.085 0.6 YES
19 CALM2 CALM2 CALM2 4375 0.084 0.62 YES
20 GNB1 GNB1 GNB1 4975 0.063 0.59 NO
21 GNA11 GNA11 GNA11 5295 0.053 0.58 NO
22 PRKCA PRKCA PRKCA 5887 0.038 0.56 NO
23 CAMK2D CAMK2D CAMK2D 5940 0.036 0.56 NO
24 F2 F2 F2 5941 0.036 0.56 NO
25 AGT AGT AGT 6425 0.026 0.54 NO
26 MAPK14 MAPK14 MAPK14 7452 0.0069 0.48 NO
27 GRB2 GRB2 GRB2 7504 0.0061 0.48 NO
28 MAP2K2 MAP2K2 MAP2K2 8550 -0.01 0.43 NO
29 SOS1 SOS1 SOS1 9666 -0.025 0.37 NO
30 STAT5B STAT5B STAT5B 10114 -0.03 0.35 NO
31 PLCG1 PLCG1 PLCG1 10537 -0.036 0.33 NO
32 FYN FYN FYN 10672 -0.038 0.33 NO
33 JAK2 JAK2 JAK2 10752 -0.039 0.33 NO
34 STAT1 STAT1 STAT1 12055 -0.056 0.27 NO
35 RAF1 RAF1 RAF1 12395 -0.061 0.26 NO
36 STAT2 STAT2 STAT2 12891 -0.068 0.24 NO
37 STAT3 STAT3 STAT3 13765 -0.082 0.2 NO
38 SHC1 SHC1 SHC1 15124 -0.12 0.15 NO
39 STAT5A STAT5A STAT5A 16854 -0.19 0.08 NO

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

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

genes ES table in pathway: BIOCARTA HDAC PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRPH2 PRPH2 PRPH2 95 1.1 0.085 YES
2 NEFM NEFM NEFM 117 1.1 0.17 YES
3 NEFL NEFL NEFL 182 1 0.25 YES
4 NEFH NEFH NEFH 255 0.93 0.32 YES
5 GRIN2A GRIN2A GRIN2A 411 0.78 0.38 YES
6 GRIN1 GRIN1 GRIN1 442 0.76 0.44 YES
7 GRIN2B GRIN2B GRIN2B 500 0.73 0.49 YES
8 MAPK13 MAPK13 MAPK13 879 0.53 0.52 YES
9 NOS1 NOS1 NOS1 1085 0.46 0.54 YES
10 SLC1A2 SLC1A2 SLC1A2 1841 0.29 0.52 YES
11 CHP2 CHP2 CHP2 1900 0.28 0.54 YES
12 PPP3R2 PPP3R2 PPP3R2 1924 0.28 0.56 YES
13 PPP3R1 PPP3R1 PPP3R1 1995 0.26 0.58 YES
14 GRIN2C GRIN2C GRIN2C 2068 0.25 0.6 YES
15 PPP3CB PPP3CB PPP3CB 2076 0.25 0.62 YES
16 PPP3CA PPP3CA PPP3CA 2184 0.24 0.63 YES
17 GRIA1 GRIA1 GRIA1 2518 0.2 0.63 NO
18 MAPK11 MAPK11 MAPK11 2793 0.18 0.63 NO
19 GRIA2 GRIA2 GRIA2 3258 0.14 0.61 NO
20 GRIN2D GRIN2D GRIN2D 3915 0.1 0.59 NO
21 TOMM40L TOMM40L TOMM40L 4282 0.088 0.57 NO
22 CYCS CYCS CYCS 4626 0.075 0.56 NO
23 CHP CHP CHP 5305 0.052 0.53 NO
24 SOD1 SOD1 SOD1 5806 0.039 0.5 NO
25 MAP3K5 MAP3K5 MAP3K5 6201 0.031 0.48 NO
26 APAF1 APAF1 APAF1 7063 0.014 0.44 NO
27 BCL2 BCL2 BCL2 7292 0.0097 0.43 NO
28 MAPK14 MAPK14 MAPK14 7452 0.0069 0.42 NO
29 MAPK12 MAPK12 MAPK12 7800 0.0015 0.4 NO
30 BID BID BID 8317 -0.0067 0.37 NO
31 PPP3CC PPP3CC PPP3CC 8524 -0.0098 0.36 NO
32 RAB5A RAB5A RAB5A 8674 -0.012 0.35 NO
33 BCL2L1 BCL2L1 BCL2L1 8688 -0.012 0.36 NO
34 BAD BAD BAD 9351 -0.021 0.32 NO
35 RAC1 RAC1 RAC1 9393 -0.021 0.32 NO
36 DERL1 DERL1 DERL1 9780 -0.026 0.3 NO
37 TOMM40 TOMM40 TOMM40 9796 -0.026 0.3 NO
38 MAP2K6 MAP2K6 MAP2K6 11608 -0.05 0.21 NO
39 CASP9 CASP9 CASP9 12069 -0.056 0.19 NO
40 CAT CAT CAT 12545 -0.063 0.16 NO
41 DAXX DAXX DAXX 12573 -0.063 0.17 NO
42 CASP3 CASP3 CASP3 13478 -0.077 0.13 NO
43 CCS CCS CCS 13537 -0.078 0.13 NO
44 MAP2K3 MAP2K3 MAP2K3 13842 -0.084 0.12 NO
45 TNF TNF TNF 15416 -0.12 0.043 NO
46 GPX1 GPX1 GPX1 15472 -0.12 0.05 NO
47 TP53 TP53 TP53 15831 -0.14 0.042 NO
48 TNFRSF1A TNFRSF1A TNFRSF1A 16057 -0.15 0.041 NO
49 BAX BAX BAX 16579 -0.17 0.027 NO
50 TNFRSF1B TNFRSF1B TNFRSF1B 17309 -0.23 0.0056 NO
51 PRPH PRPH PRPH 17568 -0.26 0.012 NO
52 CASP1 CASP1 CASP1 18124 -0.35 0.01 NO

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

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

genes ES table in pathway: BIOCARTA EGF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 118 1.1 0.065 YES
2 CAMK2A CAMK2A CAMK2A 181 1 0.13 YES
3 GRIN2A GRIN2A GRIN2A 411 0.78 0.17 YES
4 GRIN1 GRIN1 GRIN1 442 0.76 0.22 YES
5 GRIN2B GRIN2B GRIN2B 500 0.73 0.26 YES
6 GRM1 GRM1 GRM1 514 0.72 0.3 YES
7 CAMK4 CAMK4 CAMK4 608 0.66 0.34 YES
8 ITPR1 ITPR1 ITPR1 645 0.64 0.38 YES
9 GRM5 GRM5 GRM5 674 0.62 0.42 YES
10 CAMK2B CAMK2B CAMK2B 753 0.58 0.46 YES
11 PRKCB PRKCB PRKCB 781 0.57 0.49 YES
12 CALML3 CALML3 CALML3 1004 0.48 0.51 YES
13 RPS6KA6 RPS6KA6 RPS6KA6 1600 0.33 0.5 YES
14 PPP1R1A PPP1R1A PPP1R1A 1871 0.28 0.5 YES
15 CHP2 CHP2 CHP2 1900 0.28 0.52 YES
16 PPP3R2 PPP3R2 PPP3R2 1924 0.28 0.54 YES
17 PPP3R1 PPP3R1 PPP3R1 1995 0.26 0.55 YES
18 CACNA1C CACNA1C CACNA1C 2002 0.26 0.57 YES
19 GRIN2C GRIN2C GRIN2C 2068 0.25 0.58 YES
20 PPP3CB PPP3CB PPP3CB 2076 0.25 0.6 YES
21 CALM3 CALM3 CALM3 2141 0.24 0.61 YES
22 PPP3CA PPP3CA PPP3CA 2184 0.24 0.62 YES
23 MAP2K1 MAP2K1 MAP2K1 2401 0.21 0.63 YES
24 GRIA1 GRIA1 GRIA1 2518 0.2 0.63 YES
25 PLCB1 PLCB1 PLCB1 2526 0.2 0.65 YES
26 PLCB4 PLCB4 PLCB4 2545 0.2 0.66 YES
27 CAMK2G CAMK2G CAMK2G 2593 0.19 0.67 YES
28 CALM1 CALM1 CALM1 2694 0.18 0.68 YES
29 GRIA2 GRIA2 GRIA2 3258 0.14 0.65 NO
30 BRAF BRAF BRAF 3338 0.13 0.66 NO
31 PRKACB PRKACB PRKACB 3371 0.13 0.66 NO
32 RPS6KA2 RPS6KA2 RPS6KA2 3741 0.11 0.65 NO
33 GRIN2D GRIN2D GRIN2D 3915 0.1 0.65 NO
34 RAPGEF3 RAPGEF3 RAPGEF3 4038 0.098 0.65 NO
35 MAPK3 MAPK3 MAPK3 4086 0.096 0.65 NO
36 GNAQ GNAQ GNAQ 4192 0.091 0.65 NO
37 MAPK1 MAPK1 MAPK1 4299 0.087 0.65 NO
38 CALM2 CALM2 CALM2 4375 0.084 0.65 NO
39 ADCY8 ADCY8 ADCY8 4433 0.081 0.66 NO
40 KRAS KRAS KRAS 4741 0.071 0.64 NO
41 PRKACA PRKACA PRKACA 4889 0.066 0.64 NO
42 CHP CHP CHP 5305 0.052 0.62 NO
43 HRAS HRAS HRAS 5557 0.046 0.61 NO
44 PRKCA PRKCA PRKCA 5887 0.038 0.59 NO
45 CAMK2D CAMK2D CAMK2D 5940 0.036 0.59 NO
46 RPS6KA3 RPS6KA3 RPS6KA3 6120 0.032 0.59 NO
47 PRKACG PRKACG PRKACG 6800 0.019 0.55 NO
48 PPP1R12A PPP1R12A PPP1R12A 7768 0.002 0.5 NO
49 EP300 EP300 EP300 7789 0.0017 0.5 NO
50 ITPR2 ITPR2 ITPR2 7851 0.00068 0.49 NO
51 PPP3CC PPP3CC PPP3CC 8524 -0.0098 0.46 NO
52 MAP2K2 MAP2K2 MAP2K2 8550 -0.01 0.46 NO
53 CREBBP CREBBP CREBBP 9199 -0.019 0.42 NO
54 PPP1CB PPP1CB PPP1CB 9467 -0.022 0.41 NO
55 ITPR3 ITPR3 ITPR3 9480 -0.022 0.41 NO
56 ATF4 ATF4 ATF4 11554 -0.049 0.3 NO
57 PPP1CC PPP1CC PPP1CC 11564 -0.05 0.3 NO
58 PPP1CA PPP1CA PPP1CA 12283 -0.059 0.27 NO
59 NRAS NRAS NRAS 12318 -0.06 0.27 NO
60 RAF1 RAF1 RAF1 12395 -0.061 0.27 NO
61 CALML6 CALML6 CALML6 12642 -0.064 0.26 NO
62 RAP1A RAP1A RAP1A 13165 -0.072 0.24 NO
63 RAP1B RAP1B RAP1B 13404 -0.076 0.23 NO
64 PRKX PRKX PRKX 14049 -0.088 0.2 NO
65 ARAF ARAF ARAF 15104 -0.11 0.15 NO
66 PLCB3 PLCB3 PLCB3 15474 -0.12 0.14 NO
67 RPS6KA1 RPS6KA1 RPS6KA1 16154 -0.15 0.11 NO
68 PLCB2 PLCB2 PLCB2 16296 -0.16 0.11 NO

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

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

genes ES table in pathway: BIOCARTA ERK 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 PPP2R2C PPP2R2C PPP2R2C 694 0.62 0.087 YES
2 PKLR PKLR PKLR 856 0.54 0.19 YES
3 PRKAR1B PRKAR1B PRKAR1B 1181 0.43 0.26 YES
4 YWHAH YWHAH YWHAH 1564 0.34 0.3 YES
5 PRKAR2B PRKAR2B PRKAR2B 1587 0.33 0.37 YES
6 YWHAG YWHAG YWHAG 2126 0.24 0.39 YES
7 GCK GCK GCK 2430 0.21 0.42 YES
8 PRKAA2 PRKAA2 PRKAA2 2449 0.21 0.46 YES
9 MLXIPL MLXIPL MLXIPL 2742 0.18 0.48 YES
10 PRKACB PRKACB PRKACB 3371 0.13 0.47 YES
11 YWHAB YWHAB YWHAB 3761 0.11 0.47 YES
12 PRKAG2 PRKAG2 PRKAG2 3850 0.11 0.49 YES
13 PPP2R5B PPP2R5B PPP2R5B 3907 0.1 0.5 YES
14 YWHAZ YWHAZ YWHAZ 3943 0.1 0.52 YES
15 PPP2R2B PPP2R2B PPP2R2B 4305 0.087 0.52 YES
16 PPP2R2D PPP2R2D PPP2R2D 4418 0.082 0.53 YES
17 PPP2R5D PPP2R5D PPP2R5D 4551 0.077 0.54 YES
18 PRKACA PRKACA PRKACA 4889 0.066 0.54 YES
19 ACACA ACACA ACACA 5177 0.057 0.53 YES
20 PRKAR1A PRKAR1A PRKAR1A 5184 0.056 0.54 YES
21 PPP2R4 PPP2R4 PPP2R4 5268 0.054 0.55 YES
22 PPP2R1A PPP2R1A PPP2R1A 5285 0.053 0.56 YES
23 PPP2CA PPP2CA PPP2CA 5459 0.048 0.56 YES
24 FASN FASN FASN 5652 0.044 0.56 YES
25 PPP2R5C PPP2R5C PPP2R5C 5653 0.044 0.56 YES
26 PPP2R3A PPP2R3A PPP2R3A 5825 0.039 0.56 NO
27 PRKAR2A PRKAR2A PRKAR2A 6177 0.031 0.55 NO
28 PPP2R5A PPP2R5A PPP2R5A 6194 0.031 0.56 NO
29 PPP2R5E PPP2R5E PPP2R5E 6291 0.029 0.56 NO
30 PRKAB2 PRKAB2 PRKAB2 6481 0.025 0.55 NO
31 PRKACG PRKACG PRKACG 6800 0.019 0.54 NO
32 YWHAQ YWHAQ YWHAQ 7118 0.013 0.52 NO
33 PPP2R2A PPP2R2A PPP2R2A 7387 0.0081 0.51 NO
34 PPP2CB PPP2CB PPP2CB 7775 0.002 0.49 NO
35 YWHAE YWHAE YWHAE 7972 -0.0015 0.48 NO
36 PRKAG1 PRKAG1 PRKAG1 9742 -0.026 0.39 NO
37 PRKAA1 PRKAA1 PRKAA1 11379 -0.047 0.31 NO
38 PPP2R1B PPP2R1B PPP2R1B 11968 -0.055 0.29 NO
39 PRKAB1 PRKAB1 PRKAB1 12399 -0.061 0.28 NO
40 MLX MLX MLX 13001 -0.07 0.26 NO
41 PPP2R3B PPP2R3B PPP2R3B 16544 -0.17 0.097 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: BIOCARTA ERK PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 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 DRD5 DRD5 DRD5 29 1.3 0.022 YES
2 HTR5A HTR5A HTR5A 31 1.3 0.046 YES
3 CCKBR CCKBR CCKBR 55 1.2 0.068 YES
4 RYR2 RYR2 RYR2 103 1.1 0.086 YES
5 DRD1 DRD1 DRD1 111 1.1 0.11 YES
6 PRKCG PRKCG PRKCG 118 1.1 0.12 YES
7 CHRM3 CHRM3 CHRM3 139 1.1 0.14 YES
8 CHRM2 CHRM2 CHRM2 162 1 0.16 YES
9 CAMK2A CAMK2A CAMK2A 181 1 0.18 YES
10 CACNA1F CACNA1F CACNA1F 268 0.92 0.19 YES
11 ATP2B3 ATP2B3 ATP2B3 292 0.89 0.21 YES
12 ADRB3 ADRB3 ADRB3 310 0.88 0.22 YES
13 NTSR1 NTSR1 NTSR1 319 0.87 0.24 YES
14 CACNA1B CACNA1B CACNA1B 362 0.83 0.25 YES
15 HRH2 HRH2 HRH2 369 0.83 0.27 YES
16 CHRM1 CHRM1 CHRM1 370 0.83 0.28 YES
17 HTR2A HTR2A HTR2A 399 0.79 0.3 YES
18 HTR4 HTR4 HTR4 402 0.79 0.31 YES
19 CACNA1I CACNA1I CACNA1I 405 0.79 0.32 YES
20 GRIN2A GRIN2A GRIN2A 411 0.78 0.34 YES
21 PTGER3 PTGER3 PTGER3 439 0.77 0.35 YES
22 GRIN1 GRIN1 GRIN1 442 0.76 0.36 YES
23 ADRA1B ADRA1B ADRA1B 445 0.76 0.38 YES
24 HTR2C HTR2C HTR2C 456 0.75 0.39 YES
25 HTR6 HTR6 HTR6 458 0.75 0.41 YES
26 TACR2 TACR2 TACR2 476 0.74 0.42 YES
27 ITPKA ITPKA ITPKA 494 0.73 0.43 YES
28 SLC8A2 SLC8A2 SLC8A2 501 0.73 0.44 YES
29 GRM1 GRM1 GRM1 514 0.72 0.46 YES
30 PDE1A PDE1A PDE1A 597 0.67 0.47 YES
31 CAMK4 CAMK4 CAMK4 608 0.66 0.48 YES
32 HTR7 HTR7 HTR7 611 0.66 0.49 YES
33 PDE1B PDE1B PDE1B 613 0.66 0.5 YES
34 ADCY1 ADCY1 ADCY1 634 0.65 0.51 YES
35 ITPR1 ITPR1 ITPR1 645 0.64 0.52 YES
36 GRM5 GRM5 GRM5 674 0.62 0.53 YES
37 ADRB1 ADRB1 ADRB1 721 0.6 0.54 YES
38 CACNA1S CACNA1S CACNA1S 731 0.6 0.55 YES
39 CAMK2B CAMK2B CAMK2B 753 0.58 0.56 YES
40 PRKCB PRKCB PRKCB 781 0.57 0.57 YES
41 CACNA1G CACNA1G CACNA1G 805 0.56 0.58 YES
42 TACR3 TACR3 TACR3 928 0.51 0.58 YES
43 GNA14 GNA14 GNA14 995 0.49 0.59 YES
44 CALML3 CALML3 CALML3 1004 0.48 0.6 YES
45 CHRNA7 CHRNA7 CHRNA7 1020 0.47 0.61 YES
46 CACNA1E CACNA1E CACNA1E 1084 0.46 0.61 YES
47 NOS1 NOS1 NOS1 1085 0.46 0.62 YES
48 ADORA2B ADORA2B ADORA2B 1131 0.45 0.62 YES
49 TNNC2 TNNC2 TNNC2 1263 0.41 0.63 YES
50 ATP2B2 ATP2B2 ATP2B2 1349 0.39 0.63 YES
51 P2RX2 P2RX2 P2RX2 1355 0.38 0.64 YES
52 GNAL GNAL GNAL 1363 0.38 0.64 YES
53 PTK2B PTK2B PTK2B 1419 0.37 0.65 YES
54 NOS2 NOS2 NOS2 1486 0.36 0.65 YES
55 ATP2B1 ATP2B1 ATP2B1 1490 0.35 0.66 YES
56 GRPR GRPR GRPR 1763 0.3 0.65 YES
57 PTGFR PTGFR PTGFR 1767 0.3 0.65 YES
58 P2RX5 P2RX5 P2RX5 1786 0.3 0.66 YES
59 ADRA1D ADRA1D ADRA1D 1791 0.3 0.66 YES
60 CCKAR CCKAR CCKAR 1823 0.29 0.66 YES
61 CHP2 CHP2 CHP2 1900 0.28 0.67 YES
62 PPP3R2 PPP3R2 PPP3R2 1924 0.28 0.67 YES
63 PDE1C PDE1C PDE1C 1978 0.27 0.67 YES
64 PPP3R1 PPP3R1 PPP3R1 1995 0.26 0.68 YES
65 CACNA1C CACNA1C CACNA1C 2002 0.26 0.68 YES
66 AVPR1B AVPR1B AVPR1B 2030 0.26 0.68 YES
67 GRIN2C GRIN2C GRIN2C 2068 0.25 0.69 YES
68 PPP3CB PPP3CB PPP3CB 2076 0.25 0.69 YES
69 ADRA1A ADRA1A ADRA1A 2127 0.24 0.69 YES
70 CALM3 CALM3 CALM3 2141 0.24 0.7 YES
71 AVPR1A AVPR1A AVPR1A 2160 0.24 0.7 YES
72 PPP3CA PPP3CA PPP3CA 2184 0.24 0.7 YES
73 CHRM5 CHRM5 CHRM5 2195 0.24 0.71 YES
74 RYR3 RYR3 RYR3 2242 0.23 0.71 YES
75 CACNA1D CACNA1D CACNA1D 2369 0.22 0.7 YES
76 ERBB4 ERBB4 ERBB4 2478 0.21 0.7 YES
77 PLCB1 PLCB1 PLCB1 2526 0.2 0.7 YES
78 PLCB4 PLCB4 PLCB4 2545 0.2 0.71 YES
79 BDKRB1 BDKRB1 BDKRB1 2583 0.2 0.71 YES
80 CAMK2G CAMK2G CAMK2G 2593 0.19 0.71 YES
81 OXTR OXTR OXTR 2630 0.19 0.71 YES
82 CACNA1H CACNA1H CACNA1H 2645 0.19 0.72 YES
83 CACNA1A CACNA1A CACNA1A 2646 0.19 0.72 YES
84 CALM1 CALM1 CALM1 2694 0.18 0.72 YES
85 MYLK3 MYLK3 MYLK3 2787 0.18 0.72 NO
86 TRHR TRHR TRHR 2858 0.17 0.72 NO
87 TACR1 TACR1 TACR1 2877 0.17 0.72 NO
88 BDKRB2 BDKRB2 BDKRB2 2971 0.16 0.72 NO
89 TNNC1 TNNC1 TNNC1 3231 0.14 0.71 NO
90 PRKACB PRKACB PRKACB 3371 0.13 0.7 NO
91 SLC25A31 SLC25A31 SLC25A31 3523 0.12 0.7 NO
92 SLC25A4 SLC25A4 SLC25A4 3847 0.11 0.68 NO
93 GRIN2D GRIN2D GRIN2D 3915 0.1 0.68 NO
94 CYSLTR2 CYSLTR2 CYSLTR2 3930 0.1 0.68 NO
95 ADCY2 ADCY2 ADCY2 4187 0.092 0.67 NO
96 GNAQ GNAQ GNAQ 4192 0.091 0.67 NO
97 MYLK MYLK MYLK 4327 0.086 0.66 NO
98 HRH1 HRH1 HRH1 4331 0.086 0.66 NO
99 RYR1 RYR1 RYR1 4336 0.086 0.66 NO
100 CALM2 CALM2 CALM2 4375 0.084 0.66 NO
101 ADCY3 ADCY3 ADCY3 4425 0.081 0.66 NO
102 ADCY8 ADCY8 ADCY8 4433 0.081 0.66 NO
103 ATP2A2 ATP2A2 ATP2A2 4462 0.08 0.66 NO
104 ADCY9 ADCY9 ADCY9 4724 0.072 0.65 NO
105 PRKACA PRKACA PRKACA 4889 0.066 0.64 NO
106 PPID PPID PPID 4890 0.066 0.64 NO
107 VDAC3 VDAC3 VDAC3 4999 0.062 0.64 NO
108 TRPC1 TRPC1 TRPC1 5003 0.062 0.64 NO
109 ATP2B4 ATP2B4 ATP2B4 5282 0.053 0.63 NO
110 GNA11 GNA11 GNA11 5295 0.053 0.63 NO
111 CHP CHP CHP 5305 0.052 0.63 NO
112 P2RX6 P2RX6 P2RX6 5335 0.051 0.63 NO
113 VDAC1 VDAC1 VDAC1 5343 0.051 0.63 NO
114 CD38 CD38 CD38 5468 0.048 0.62 NO
115 AGTR1 AGTR1 AGTR1 5637 0.044 0.61 NO
116 PRKCA PRKCA PRKCA 5887 0.038 0.6 NO
117 CAMK2D CAMK2D CAMK2D 5940 0.036 0.6 NO
118 EDNRB EDNRB EDNRB 5971 0.036 0.6 NO
119 P2RX1 P2RX1 P2RX1 6172 0.031 0.58 NO
120 SPHK2 SPHK2 SPHK2 6421 0.026 0.57 NO
121 PLN PLN PLN 6602 0.023 0.56 NO
122 SLC8A1 SLC8A1 SLC8A1 6636 0.022 0.56 NO
123 GNAS GNAS GNAS 6730 0.02 0.56 NO
124 PRKACG PRKACG PRKACG 6800 0.019 0.55 NO
125 ATP2A3 ATP2A3 ATP2A3 6849 0.018 0.55 NO
126 ERBB3 ERBB3 ERBB3 6889 0.017 0.55 NO
127 VDAC2 VDAC2 VDAC2 7213 0.011 0.53 NO
128 NOS3 NOS3 NOS3 7524 0.0058 0.51 NO
129 LHCGR LHCGR LHCGR 7735 0.0025 0.5 NO
130 ADRB2 ADRB2 ADRB2 7818 0.0013 0.5 NO
131 ITPR2 ITPR2 ITPR2 7851 0.00068 0.5 NO
132 ITPKB ITPKB ITPKB 7916 -0.00065 0.49 NO
133 PHKA1 PHKA1 PHKA1 8265 -0.0058 0.47 NO
134 SLC25A5 SLC25A5 SLC25A5 8419 -0.0082 0.47 NO
135 SLC25A6 SLC25A6 SLC25A6 8422 -0.0082 0.47 NO
136 PHKG2 PHKG2 PHKG2 8500 -0.0095 0.46 NO
137 PPP3CC PPP3CC PPP3CC 8524 -0.0098 0.46 NO
138 PDGFRB PDGFRB PDGFRB 8678 -0.012 0.45 NO
139 ITPR3 ITPR3 ITPR3 9480 -0.022 0.41 NO
140 PHKB PHKB PHKB 9614 -0.024 0.4 NO
141 ADORA2A ADORA2A ADORA2A 9644 -0.024 0.4 NO
142 PLCD4 PLCD4 PLCD4 10052 -0.03 0.38 NO
143 PHKA2 PHKA2 PHKA2 10426 -0.034 0.36 NO
144 PLCG1 PLCG1 PLCG1 10537 -0.036 0.35 NO
145 GNA15 GNA15 GNA15 10844 -0.04 0.34 NO
146 P2RX7 P2RX7 P2RX7 10889 -0.041 0.34 NO
147 HTR2B HTR2B HTR2B 11514 -0.049 0.3 NO
148 PDGFRA PDGFRA PDGFRA 11559 -0.049 0.3 NO
149 P2RX3 P2RX3 P2RX3 11651 -0.051 0.3 NO
150 PLCD3 PLCD3 PLCD3 12495 -0.062 0.25 NO
151 EGFR EGFR EGFR 12590 -0.064 0.25 NO
152 CALML6 CALML6 CALML6 12642 -0.064 0.25 NO
153 PHKG1 PHKG1 PHKG1 13246 -0.074 0.21 NO
154 ERBB2 ERBB2 ERBB2 13285 -0.074 0.21 NO
155 ADCY4 ADCY4 ADCY4 13343 -0.075 0.21 NO
156 PLCD1 PLCD1 PLCD1 13784 -0.083 0.19 NO
157 PRKX PRKX PRKX 14049 -0.088 0.18 NO
158 MYLK2 MYLK2 MYLK2 14318 -0.093 0.16 NO
159 PLCE1 PLCE1 PLCE1 14703 -0.1 0.14 NO
160 CYSLTR1 CYSLTR1 CYSLTR1 14711 -0.1 0.14 NO
161 ADCY7 ADCY7 ADCY7 14853 -0.11 0.14 NO
162 PLCB3 PLCB3 PLCB3 15474 -0.12 0.11 NO
163 P2RX4 P2RX4 P2RX4 16028 -0.15 0.08 NO
164 SPHK1 SPHK1 SPHK1 16162 -0.15 0.075 NO
165 PLCB2 PLCB2 PLCB2 16296 -0.16 0.071 NO
166 F2R F2R F2R 16715 -0.18 0.051 NO
167 PTGER1 PTGER1 PTGER1 16793 -0.19 0.05 NO
168 LTB4R2 LTB4R2 LTB4R2 16927 -0.2 0.047 NO
169 PLCG2 PLCG2 PLCG2 16943 -0.2 0.05 NO
170 PTAFR PTAFR PTAFR 17209 -0.22 0.039 NO
171 EDNRA EDNRA EDNRA 17358 -0.24 0.035 NO
172 TBXA2R TBXA2R TBXA2R 17778 -0.28 0.017 NO
173 ATP2A1 ATP2A1 ATP2A1 17847 -0.29 0.019 NO
174 BST1 BST1 BST1 18151 -0.36 0.009 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: BIOCARTA PYK2 PATHWAY.

Figure S76.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA NFAT PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCG PRKCG PRKCG 118 1.1 0.076 YES
2 ITPKA ITPKA ITPKA 494 0.73 0.11 YES
3 CDS1 CDS1 CDS1 530 0.7 0.16 YES
4 DGKE DGKE DGKE 556 0.69 0.21 YES
5 PIP5K1B PIP5K1B PIP5K1B 587 0.67 0.26 YES
6 ITPR1 ITPR1 ITPR1 645 0.64 0.31 YES
7 PRKCB PRKCB PRKCB 781 0.57 0.34 YES
8 INPP4B INPP4B INPP4B 880 0.53 0.38 YES
9 INPP5J INPP5J INPP5J 944 0.5 0.42 YES
10 CALML3 CALML3 CALML3 1004 0.48 0.45 YES
11 SYNJ2 SYNJ2 SYNJ2 1548 0.34 0.44 YES
12 DGKZ DGKZ DGKZ 1552 0.34 0.47 YES
13 DGKB DGKB DGKB 1897 0.28 0.47 YES
14 PI4KA PI4KA PI4KA 1921 0.28 0.49 YES
15 SYNJ1 SYNJ1 SYNJ1 2012 0.26 0.51 YES
16 CALM3 CALM3 CALM3 2141 0.24 0.52 YES
17 PLCB1 PLCB1 PLCB1 2526 0.2 0.51 YES
18 PLCB4 PLCB4 PLCB4 2545 0.2 0.53 YES
19 DGKH DGKH DGKH 2599 0.19 0.54 YES
20 DGKI DGKI DGKI 2612 0.19 0.55 YES
21 CALM1 CALM1 CALM1 2694 0.18 0.56 YES
22 INPP4A INPP4A INPP4A 2880 0.17 0.56 YES
23 INPP5A INPP5A INPP5A 2891 0.16 0.58 YES
24 PIP5K1C PIP5K1C PIP5K1C 2913 0.16 0.59 YES
25 DGKG DGKG DGKG 3029 0.16 0.59 YES
26 PIP4K2C PIP4K2C PIP4K2C 3271 0.14 0.59 NO
27 DGKQ DGKQ DGKQ 3590 0.12 0.58 NO
28 PIK3CB PIK3CB PIK3CB 3602 0.12 0.59 NO
29 CALM2 CALM2 CALM2 4375 0.084 0.56 NO
30 OCRL OCRL OCRL 4497 0.079 0.55 NO
31 PIP4K2B PIP4K2B PIP4K2B 4498 0.079 0.56 NO
32 PIK3CD PIK3CD PIK3CD 4599 0.075 0.56 NO
33 ITPK1 ITPK1 ITPK1 4888 0.066 0.55 NO
34 PIP4K2A PIP4K2A PIP4K2A 4953 0.064 0.55 NO
35 PTEN PTEN PTEN 5068 0.06 0.55 NO
36 IMPA2 IMPA2 IMPA2 5088 0.06 0.55 NO
37 PIK3C2G PIK3C2G PIK3C2G 5328 0.052 0.54 NO
38 PIK3R3 PIK3R3 PIK3R3 5526 0.046 0.54 NO
39 PIK3R1 PIK3R1 PIK3R1 5787 0.04 0.52 NO
40 IMPA1 IMPA1 IMPA1 5796 0.04 0.53 NO
41 PRKCA PRKCA PRKCA 5887 0.038 0.52 NO
42 PIKFYVE PIKFYVE PIKFYVE 6366 0.028 0.5 NO
43 PIK3C2B PIK3C2B PIK3C2B 6444 0.026 0.5 NO
44 IPPK IPPK IPPK 6529 0.024 0.5 NO
45 CDIPT CDIPT CDIPT 6853 0.018 0.48 NO
46 INPP1 INPP1 INPP1 6863 0.018 0.48 NO
47 CDS2 CDS2 CDS2 6949 0.016 0.48 NO
48 DGKA DGKA DGKA 7521 0.0059 0.45 NO
49 ITPR2 ITPR2 ITPR2 7851 0.00068 0.43 NO
50 ITPKB ITPKB ITPKB 7916 -0.00065 0.42 NO
51 PIK3R2 PIK3R2 PIK3R2 7920 -0.00074 0.42 NO
52 INPP5K INPP5K INPP5K 8439 -0.0085 0.4 NO
53 PIK3C2A PIK3C2A PIK3C2A 8631 -0.011 0.39 NO
54 PIK3CA PIK3CA PIK3CA 8703 -0.012 0.38 NO
55 INPP5E INPP5E INPP5E 9037 -0.016 0.37 NO
56 ITPR3 ITPR3 ITPR3 9480 -0.022 0.34 NO
57 PIK3C3 PIK3C3 PIK3C3 9753 -0.026 0.33 NO
58 PI4KB PI4KB PI4KB 9789 -0.026 0.33 NO
59 PIP5K1A PIP5K1A PIP5K1A 9943 -0.028 0.33 NO
60 PLCD4 PLCD4 PLCD4 10052 -0.03 0.32 NO
61 PLCG1 PLCG1 PLCG1 10537 -0.036 0.3 NO
62 PLCD3 PLCD3 PLCD3 12495 -0.062 0.2 NO
63 CALML6 CALML6 CALML6 12642 -0.064 0.19 NO
64 DGKD DGKD DGKD 12852 -0.068 0.19 NO
65 INPP5B INPP5B INPP5B 13186 -0.072 0.17 NO
66 PLCD1 PLCD1 PLCD1 13784 -0.083 0.15 NO
67 INPPL1 INPPL1 INPPL1 14637 -0.1 0.11 NO
68 PLCE1 PLCE1 PLCE1 14703 -0.1 0.11 NO
69 PLCB3 PLCB3 PLCB3 15474 -0.12 0.08 NO
70 PLCB2 PLCB2 PLCB2 16296 -0.16 0.047 NO
71 INPP5D INPP5D INPP5D 16330 -0.16 0.057 NO
72 PIK3CG PIK3CG PIK3CG 16674 -0.18 0.052 NO
73 PLCG2 PLCG2 PLCG2 16943 -0.2 0.053 NO
74 PIK3R5 PIK3R5 PIK3R5 17884 -0.3 0.024 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: BIOCARTA NFAT PATHWAY.

Figure S78.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NFAT 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 PDGF 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 EPHA8 EPHA8 EPHA8 210 0.97 0.027 YES
2 PAK6 PAK6 PAK6 241 0.94 0.062 YES
3 EPHB6 EPHB6 EPHB6 297 0.89 0.094 YES
4 EPHA6 EPHA6 EPHA6 311 0.87 0.13 YES
5 UNC5D UNC5D UNC5D 394 0.79 0.15 YES
6 NGEF NGEF NGEF 453 0.76 0.18 YES
7 SLIT2 SLIT2 SLIT2 481 0.74 0.21 YES
8 EPHA5 EPHA5 EPHA5 537 0.7 0.23 YES
9 EFNA5 EFNA5 EFNA5 547 0.7 0.26 YES
10 EPHA7 EPHA7 EPHA7 582 0.67 0.28 YES
11 ABLIM2 ABLIM2 ABLIM2 787 0.57 0.3 YES
12 MET MET MET 793 0.57 0.32 YES
13 SLIT3 SLIT3 SLIT3 799 0.56 0.34 YES
14 PAK1 PAK1 PAK1 802 0.56 0.36 YES
15 PAK3 PAK3 PAK3 825 0.55 0.38 YES
16 L1CAM L1CAM L1CAM 960 0.5 0.39 YES
17 PAK7 PAK7 PAK7 1071 0.46 0.4 YES
18 UNC5A UNC5A UNC5A 1123 0.45 0.42 YES
19 SEMA4A SEMA4A SEMA4A 1135 0.44 0.44 YES
20 UNC5C UNC5C UNC5C 1161 0.44 0.45 YES
21 EPHA4 EPHA4 EPHA4 1278 0.4 0.46 YES
22 NTNG1 NTNG1 NTNG1 1297 0.4 0.48 YES
23 SEMA3E SEMA3E SEMA3E 1470 0.36 0.48 YES
24 SEMA3A SEMA3A SEMA3A 1627 0.33 0.48 YES
25 EFNA3 EFNA3 EFNA3 1818 0.29 0.49 YES
26 SEMA4F SEMA4F SEMA4F 1829 0.29 0.5 YES
27 CHP2 CHP2 CHP2 1900 0.28 0.5 YES
28 PPP3R2 PPP3R2 PPP3R2 1924 0.28 0.51 YES
29 PPP3R1 PPP3R1 PPP3R1 1995 0.26 0.52 YES
30 PPP3CB PPP3CB PPP3CB 2076 0.25 0.52 YES
31 RND1 RND1 RND1 2112 0.25 0.53 YES
32 DCC DCC DCC 2143 0.24 0.54 YES
33 SEMA3C SEMA3C SEMA3C 2153 0.24 0.55 YES
34 PPP3CA PPP3CA PPP3CA 2184 0.24 0.56 YES
35 EFNB2 EFNB2 EFNB2 2327 0.22 0.56 YES
36 SEMA6B SEMA6B SEMA6B 2461 0.21 0.56 YES
37 ROBO2 ROBO2 ROBO2 2462 0.21 0.57 YES
38 EFNB3 EFNB3 EFNB3 2689 0.18 0.56 YES
39 PLXNA2 PLXNA2 PLXNA2 2753 0.18 0.57 YES
40 RHOD RHOD RHOD 2766 0.18 0.57 YES
41 SEMA7A SEMA7A SEMA7A 3011 0.16 0.56 YES
42 CDK5 CDK5 CDK5 3038 0.15 0.57 YES
43 PLXNC1 PLXNC1 PLXNC1 3074 0.15 0.57 YES
44 LIMK1 LIMK1 LIMK1 3154 0.15 0.57 YES
45 SEMA3G SEMA3G SEMA3G 3188 0.14 0.58 YES
46 NTN4 NTN4 NTN4 3221 0.14 0.58 YES
47 ROCK2 ROCK2 ROCK2 3274 0.14 0.58 YES
48 SLIT1 SLIT1 SLIT1 3539 0.12 0.57 NO
49 GNAI1 GNAI1 GNAI1 3618 0.12 0.58 NO
50 SRGAP3 SRGAP3 SRGAP3 3687 0.11 0.58 NO
51 SEMA6D SEMA6D SEMA6D 3833 0.11 0.57 NO
52 SEMA4D SEMA4D SEMA4D 3986 0.1 0.57 NO
53 LRRC4C LRRC4C LRRC4C 4075 0.097 0.57 NO
54 MAPK3 MAPK3 MAPK3 4086 0.096 0.57 NO
55 EPHA3 EPHA3 EPHA3 4095 0.096 0.57 NO
56 MAPK1 MAPK1 MAPK1 4299 0.087 0.57 NO
57 PLXNA1 PLXNA1 PLXNA1 4545 0.077 0.56 NO
58 KRAS KRAS KRAS 4741 0.071 0.55 NO
59 ARHGEF12 ARHGEF12 ARHGEF12 4851 0.067 0.54 NO
60 SEMA3F SEMA3F SEMA3F 4932 0.065 0.54 NO
61 GSK3B GSK3B GSK3B 5176 0.057 0.53 NO
62 RASA1 RASA1 RASA1 5204 0.056 0.53 NO
63 CHP CHP CHP 5305 0.052 0.53 NO
64 SEMA3D SEMA3D SEMA3D 5629 0.044 0.51 NO
65 ABLIM3 ABLIM3 ABLIM3 5710 0.042 0.51 NO
66 ABLIM1 ABLIM1 ABLIM1 5744 0.041 0.51 NO
67 NFAT5 NFAT5 NFAT5 5755 0.041 0.51 NO
68 DPYSL2 DPYSL2 DPYSL2 5845 0.038 0.51 NO
69 NFATC4 NFATC4 NFATC4 5997 0.035 0.5 NO
70 SEMA4G SEMA4G SEMA4G 6269 0.029 0.49 NO
71 EPHB1 EPHB1 EPHB1 6492 0.025 0.48 NO
72 SEMA4B SEMA4B SEMA4B 7004 0.015 0.45 NO
73 RAC3 RAC3 RAC3 7218 0.011 0.44 NO
74 PTK2 PTK2 PTK2 7257 0.01 0.44 NO
75 SEMA4C SEMA4C SEMA4C 7376 0.0083 0.43 NO
76 ROBO1 ROBO1 ROBO1 7826 0.0012 0.4 NO
77 CFL2 CFL2 CFL2 8433 -0.0084 0.37 NO
78 PPP3CC PPP3CC PPP3CC 8524 -0.0098 0.37 NO
79 SEMA6C SEMA6C SEMA6C 8651 -0.011 0.36 NO
80 SEMA6A SEMA6A SEMA6A 8669 -0.012 0.36 NO
81 CDC42 CDC42 CDC42 8802 -0.013 0.35 NO
82 CFL1 CFL1 CFL1 9179 -0.018 0.33 NO
83 RAC1 RAC1 RAC1 9393 -0.021 0.32 NO
84 EPHB2 EPHB2 EPHB2 9446 -0.022 0.32 NO
85 NCK2 NCK2 NCK2 9452 -0.022 0.32 NO
86 SEMA3B SEMA3B SEMA3B 9495 -0.023 0.32 NO
87 SRGAP2 SRGAP2 SRGAP2 9660 -0.025 0.31 NO
88 UNC5B UNC5B UNC5B 9661 -0.025 0.31 NO
89 DPYSL5 DPYSL5 DPYSL5 9874 -0.027 0.3 NO
90 EPHA1 EPHA1 EPHA1 9904 -0.028 0.3 NO
91 PLXNB1 PLXNB1 PLXNB1 10605 -0.037 0.26 NO
92 FYN FYN FYN 10672 -0.038 0.26 NO
93 SEMA5A SEMA5A SEMA5A 11348 -0.046 0.23 NO
94 NTN3 NTN3 NTN3 11402 -0.047 0.22 NO
95 RHOA RHOA RHOA 11530 -0.049 0.22 NO
96 RGS3 RGS3 RGS3 11609 -0.05 0.22 NO
97 ROBO3 ROBO3 ROBO3 11717 -0.052 0.21 NO
98 EPHB3 EPHB3 EPHB3 11740 -0.052 0.22 NO
99 PLXNB3 PLXNB3 PLXNB3 12271 -0.059 0.19 NO
100 NRAS NRAS NRAS 12318 -0.06 0.19 NO
101 PAK2 PAK2 PAK2 12616 -0.064 0.17 NO
102 NCK1 NCK1 NCK1 12647 -0.065 0.18 NO
103 ABL1 ABL1 ABL1 12750 -0.066 0.17 NO
104 CXCL12 CXCL12 CXCL12 12954 -0.069 0.16 NO
105 GNAI2 GNAI2 GNAI2 12983 -0.07 0.16 NO
106 SEMA5B SEMA5B SEMA5B 13269 -0.074 0.15 NO
107 PAK4 PAK4 PAK4 13367 -0.075 0.15 NO
108 LIMK2 LIMK2 LIMK2 13387 -0.076 0.15 NO
109 ROCK1 ROCK1 ROCK1 13754 -0.082 0.14 NO
110 FES FES FES 14110 -0.089 0.12 NO
111 EFNB1 EFNB1 EFNB1 14316 -0.093 0.11 NO
112 PLXNB2 PLXNB2 PLXNB2 14384 -0.095 0.11 NO
113 NRP1 NRP1 NRP1 14766 -0.1 0.094 NO
114 EFNA1 EFNA1 EFNA1 14920 -0.11 0.09 NO
115 NFATC3 NFATC3 NFATC3 15032 -0.11 0.088 NO
116 GNAI3 GNAI3 GNAI3 15047 -0.11 0.092 NO
117 ITGB1 ITGB1 ITGB1 15212 -0.12 0.087 NO
118 SRGAP1 SRGAP1 SRGAP1 15221 -0.12 0.092 NO
119 PLXNA3 PLXNA3 PLXNA3 15613 -0.13 0.075 NO
120 EPHB4 EPHB4 EPHB4 15919 -0.14 0.064 NO
121 NFATC2 NFATC2 NFATC2 16168 -0.15 0.056 NO
122 NTN1 NTN1 NTN1 16493 -0.17 0.045 NO
123 EPHA2 EPHA2 EPHA2 16633 -0.18 0.044 NO
124 EFNA2 EFNA2 EFNA2 16756 -0.18 0.045 NO
125 NFATC1 NFATC1 NFATC1 16845 -0.19 0.048 NO
126 CXCR4 CXCR4 CXCR4 17133 -0.22 0.04 NO
127 EFNA4 EFNA4 EFNA4 17295 -0.23 0.04 NO
128 RAC2 RAC2 RAC2 18217 -0.4 0.0054 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: BIOCARTA PDGF PATHWAY.

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PDGF 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
BIOCARTA MYOSIN PATHWAY 28 genes.ES.table 0.46 1.4 0.095 0.55 0.94 0.11 0.043 0.1 0.42 0.14
KEGG FRUCTOSE AND MANNOSE METABOLISM 32 genes.ES.table 0.43 1.4 0.062 0.67 0.92 0.38 0.26 0.28 0.52 0.2
KEGG FATTY ACID METABOLISM 39 genes.ES.table 0.38 1.3 0.2 0.65 1 0.38 0.27 0.28 0.56 0.18
KEGG OXIDATIVE PHOSPHORYLATION 114 genes.ES.table 0.37 1.3 0.26 0.72 0.99 0.63 0.41 0.38 0.63 0.22
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 29 genes.ES.table 0.48 1.3 0.21 0.74 0.99 0.21 0.12 0.18 0.64 0.24
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.47 1.7 0.019 0.57 0.39 0.4 0.26 0.29 0 0.2
KEGG HISTIDINE METABOLISM 28 genes.ES.table 0.57 1.5 0.026 1 0.88 0.68 0.31 0.47 0.81 0.41
KEGG GLUTATHIONE METABOLISM 43 genes.ES.table 0.4 1.3 0.15 0.7 0.99 0.44 0.26 0.33 0.58 0.21
KEGG ETHER LIPID METABOLISM 27 genes.ES.table 0.53 1.4 0.054 0.55 0.95 0.3 0.13 0.26 0.42 0.14
KEGG PROPANOATE METABOLISM 31 genes.ES.table 0.37 1.3 0.23 0.71 0.99 0.36 0.26 0.26 0.61 0.21
genes ES table in pathway: BIOCARTA MYOSIN PATHWAY

Table S41.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ACADS ACADS ACADS 681 0.31 0.079 YES
2 ACAA2 ACAA2 ACAA2 2003 0.16 0.068 YES
3 ALDH7A1 ALDH7A1 ALDH7A1 2111 0.15 0.12 YES
4 IL4I1 IL4I1 IL4I1 2153 0.15 0.18 YES
5 ALDH2 ALDH2 ALDH2 2693 0.12 0.19 YES
6 BCAT2 BCAT2 BCAT2 2718 0.12 0.24 YES
7 ACAA1 ACAA1 ACAA1 2737 0.12 0.28 YES
8 MCEE MCEE MCEE 2887 0.12 0.32 YES
9 HMGCL HMGCL HMGCL 3427 0.097 0.33 YES
10 BCKDHB BCKDHB BCKDHB 3830 0.085 0.34 YES
11 AUH AUH AUH 3928 0.082 0.36 YES
12 HIBCH HIBCH HIBCH 4055 0.079 0.38 YES
13 HADHB HADHB HADHB 4228 0.074 0.4 YES
14 ECHS1 ECHS1 ECHS1 4265 0.074 0.43 YES
15 HSD17B10 HSD17B10 HSD17B10 4638 0.065 0.43 YES
16 ALDH9A1 ALDH9A1 ALDH9A1 4692 0.064 0.46 YES
17 BCKDHA BCKDHA BCKDHA 4776 0.062 0.47 YES
18 ALDH6A1 ALDH6A1 ALDH6A1 5873 0.042 0.43 NO
19 ACAT1 ACAT1 ACAT1 5909 0.042 0.44 NO
20 OXCT2 OXCT2 OXCT2 6178 0.038 0.44 NO
21 ACADM ACADM ACADM 6729 0.03 0.42 NO
22 ACADSB ACADSB ACADSB 6845 0.029 0.43 NO
23 PCCA PCCA PCCA 7190 0.024 0.42 NO
24 HADHA HADHA HADHA 7207 0.024 0.43 NO
25 HIBADH HIBADH HIBADH 7209 0.024 0.44 NO
26 EHHADH EHHADH EHHADH 7258 0.023 0.44 NO
27 AOX1 AOX1 AOX1 7385 0.022 0.44 NO
28 IVD IVD IVD 8005 0.013 0.42 NO
29 ALDH3A2 ALDH3A2 ALDH3A2 8338 0.0094 0.4 NO
30 MCCC1 MCCC1 MCCC1 8615 0.0059 0.39 NO
31 ACAT2 ACAT2 ACAT2 8788 0.0041 0.38 NO
32 HADH HADH HADH 9209 -0.0014 0.36 NO
33 PCCB PCCB PCCB 9753 -0.0078 0.33 NO
34 ACAD8 ACAD8 ACAD8 9898 -0.0095 0.33 NO
35 OXCT1 OXCT1 OXCT1 10583 -0.018 0.3 NO
36 MCCC2 MCCC2 MCCC2 10691 -0.02 0.3 NO
37 DBT DBT DBT 10749 -0.02 0.3 NO
38 ABAT ABAT ABAT 11273 -0.027 0.28 NO
39 MUT MUT MUT 11427 -0.029 0.29 NO
40 DLD DLD DLD 12630 -0.046 0.24 NO
41 HMGCS1 HMGCS1 HMGCS1 12815 -0.049 0.25 NO
42 HMGCS2 HMGCS2 HMGCS2 13191 -0.055 0.25 NO
43 ALDH1B1 ALDH1B1 ALDH1B1 14786 -0.09 0.19 NO

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

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

genes ES table in pathway: KEGG FRUCTOSE AND MANNOSE METABOLISM

Table S42.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GPR37 GPR37 GPR37 221 0.48 0.075 YES
2 COX8C COX8C COX8C 1061 0.25 0.073 YES
3 COX4I2 COX4I2 COX4I2 1910 0.17 0.057 YES
4 NDUFA3 NDUFA3 NDUFA3 2407 0.14 0.054 YES
5 SNCA SNCA SNCA 2754 0.12 0.057 YES
6 COX6B2 COX6B2 COX6B2 3039 0.11 0.062 YES
7 UBA7 UBA7 UBA7 3110 0.11 0.077 YES
8 NDUFS7 NDUFS7 NDUFS7 3115 0.11 0.096 YES
9 COX6A2 COX6A2 COX6A2 3230 0.1 0.11 YES
10 COX7A1 COX7A1 COX7A1 3398 0.098 0.12 YES
11 TH TH TH 3619 0.091 0.12 YES
12 NDUFC1 NDUFC1 NDUFC1 3707 0.088 0.13 YES
13 SLC25A31 SLC25A31 SLC25A31 3833 0.085 0.14 YES
14 NDUFB1 NDUFB1 NDUFB1 3966 0.081 0.15 YES
15 COX5B COX5B COX5B 3980 0.081 0.16 YES
16 UBB UBB UBB 4073 0.079 0.17 YES
17 NDUFA1 NDUFA1 NDUFA1 4120 0.077 0.18 YES
18 NDUFS6 NDUFS6 NDUFS6 4173 0.076 0.19 YES
19 NDUFA2 NDUFA2 NDUFA2 4235 0.074 0.2 YES
20 NDUFB4 NDUFB4 NDUFB4 4245 0.074 0.22 YES
21 NDUFB6 NDUFB6 NDUFB6 4461 0.069 0.22 YES
22 NDUFB3 NDUFB3 NDUFB3 4512 0.068 0.23 YES
23 UQCRQ UQCRQ UQCRQ 4567 0.067 0.24 YES
24 NDUFB8 NDUFB8 NDUFB8 4594 0.066 0.25 YES
25 PINK1 PINK1 PINK1 4619 0.065 0.26 YES
26 NDUFB7 NDUFB7 NDUFB7 4681 0.064 0.26 YES
27 ATP5E ATP5E ATP5E 4878 0.06 0.26 YES
28 NDUFC2 NDUFC2 NDUFC2 4913 0.059 0.27 YES
29 COX7B COX7B COX7B 4914 0.059 0.28 YES
30 COX6B1 COX6B1 COX6B1 4946 0.059 0.29 YES
31 NDUFB10 NDUFB10 NDUFB10 5200 0.054 0.29 YES
32 ATP5D ATP5D ATP5D 5217 0.054 0.3 YES
33 COX6C COX6C COX6C 5230 0.054 0.31 YES
34 UQCR10 UQCR10 UQCR10 5236 0.053 0.32 YES
35 ATP5J ATP5J ATP5J 5244 0.053 0.32 YES
36 UQCR11 UQCR11 UQCR11 5281 0.052 0.33 YES
37 COX4I1 COX4I1 COX4I1 5374 0.051 0.34 YES
38 UQCRB UQCRB UQCRB 5453 0.05 0.34 YES
39 NDUFS8 NDUFS8 NDUFS8 5585 0.047 0.34 YES
40 NDUFB9 NDUFB9 NDUFB9 5638 0.046 0.35 YES
41 NDUFB2 NDUFB2 NDUFB2 5826 0.043 0.34 YES
42 NDUFA7 NDUFA7 NDUFA7 5908 0.042 0.35 YES
43 COX6A1 COX6A1 COX6A1 6110 0.039 0.34 YES
44 COX7A2 COX7A2 COX7A2 6244 0.037 0.34 YES
45 NDUFV2 NDUFV2 NDUFV2 6249 0.037 0.35 YES
46 NDUFV1 NDUFV1 NDUFV1 6333 0.036 0.35 YES
47 UBE2G1 UBE2G1 UBE2G1 6377 0.035 0.36 YES
48 PARK7 PARK7 PARK7 6454 0.034 0.36 YES
49 ATP5F1 ATP5F1 ATP5F1 6459 0.034 0.36 YES
50 NDUFS3 NDUFS3 NDUFS3 6463 0.034 0.37 YES
51 COX8A COX8A COX8A 6538 0.033 0.37 YES
52 UBE2L3 UBE2L3 UBE2L3 6542 0.032 0.38 YES
53 NDUFA10 NDUFA10 NDUFA10 6601 0.032 0.38 YES
54 COX7C COX7C COX7C 6612 0.032 0.38 YES
55 SDHA SDHA SDHA 6671 0.031 0.39 YES
56 ATP5G1 ATP5G1 ATP5G1 6744 0.03 0.39 YES
57 UBE2J2 UBE2J2 UBE2J2 6801 0.029 0.39 YES
58 SDHB SDHB SDHB 6871 0.028 0.39 YES
59 HTRA2 HTRA2 HTRA2 6884 0.028 0.4 YES
60 NDUFA8 NDUFA8 NDUFA8 6908 0.028 0.4 YES
61 COX5A COX5A COX5A 6915 0.028 0.4 YES
62 NDUFB5 NDUFB5 NDUFB5 6996 0.027 0.4 YES
63 NDUFAB1 NDUFAB1 NDUFAB1 7221 0.024 0.4 YES
64 ATP5H ATP5H ATP5H 7259 0.023 0.4 YES
65 SDHD SDHD SDHD 7276 0.023 0.4 YES
66 ATP5O ATP5O ATP5O 7303 0.023 0.4 YES
67 NDUFA5 NDUFA5 NDUFA5 7350 0.022 0.41 YES
68 SDHC SDHC SDHC 7363 0.022 0.41 YES
69 CASP9 CASP9 CASP9 7371 0.022 0.41 YES
70 COX7A2L COX7A2L COX7A2L 7449 0.02 0.41 YES
71 ATP5G2 ATP5G2 ATP5G2 7494 0.02 0.41 YES
72 UQCRFS1 UQCRFS1 UQCRFS1 7669 0.017 0.41 NO
73 NDUFA6 NDUFA6 NDUFA6 7792 0.016 0.4 NO
74 NDUFV3 NDUFV3 NDUFV3 7872 0.015 0.4 NO
75 UQCRC1 UQCRC1 UQCRC1 7921 0.014 0.4 NO
76 SLC25A4 SLC25A4 SLC25A4 8137 0.012 0.39 NO
77 NDUFS5 NDUFS5 NDUFS5 8180 0.011 0.39 NO
78 NDUFA4 NDUFA4 NDUFA4 8219 0.011 0.39 NO
79 NDUFS4 NDUFS4 NDUFS4 8274 0.01 0.39 NO
80 CYC1 CYC1 CYC1 8341 0.0094 0.39 NO
81 VDAC2 VDAC2 VDAC2 8484 0.0078 0.38 NO
82 NDUFA4L2 NDUFA4L2 NDUFA4L2 8730 0.0047 0.37 NO
83 NDUFS2 NDUFS2 NDUFS2 8923 0.0025 0.36 NO
84 ATP5G3 ATP5G3 ATP5G3 9025 0.00096 0.35 NO
85 VDAC3 VDAC3 VDAC3 9069 0.0003 0.35 NO
86 SLC6A3 SLC6A3 SLC6A3 9247 -0.0018 0.34 NO
87 PPID PPID PPID 9455 -0.0043 0.33 NO
88 NDUFA9 NDUFA9 NDUFA9 9457 -0.0043 0.33 NO
89 CASP3 CASP3 CASP3 9584 -0.0058 0.33 NO
90 UBE2G2 UBE2G2 UBE2G2 10198 -0.013 0.3 NO
91 SLC18A1 SLC18A1 SLC18A1 10258 -0.014 0.3 NO
92 ATP5C1 ATP5C1 ATP5C1 10292 -0.014 0.3 NO
93 CYCS CYCS CYCS 10355 -0.015 0.3 NO
94 UBE2L6 UBE2L6 UBE2L6 10619 -0.019 0.28 NO
95 UBE2J1 UBE2J1 UBE2J1 10658 -0.019 0.28 NO
96 UQCRH UQCRH UQCRH 10660 -0.019 0.29 NO
97 SLC25A6 SLC25A6 SLC25A6 10808 -0.021 0.28 NO
98 ATP5A1 ATP5A1 ATP5A1 10889 -0.022 0.28 NO
99 VDAC1 VDAC1 VDAC1 11494 -0.03 0.26 NO
100 UBA1 UBA1 UBA1 11703 -0.033 0.25 NO
101 UCHL1 UCHL1 UCHL1 11740 -0.033 0.25 NO
102 UQCRHL UQCRHL UQCRHL 11962 -0.036 0.25 NO
103 APAF1 APAF1 APAF1 12697 -0.047 0.22 NO
104 UQCRC2 UQCRC2 UQCRC2 12712 -0.047 0.22 NO
105 ATP5B ATP5B ATP5B 13024 -0.053 0.22 NO
106 SLC18A2 SLC18A2 SLC18A2 13180 -0.055 0.22 NO
107 SLC25A5 SLC25A5 SLC25A5 13238 -0.056 0.22 NO
108 NDUFS1 NDUFS1 NDUFS1 13306 -0.057 0.23 NO
109 LRRK2 LRRK2 LRRK2 13554 -0.062 0.23 NO
110 PARK2 PARK2 PARK2 14408 -0.081 0.2 NO
111 SNCAIP SNCAIP SNCAIP 15012 -0.097 0.18 NO

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

Figure S84.  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 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 ASPA ASPA ASPA 115 0.62 0.18 YES
2 ACY3 ACY3 ACY3 252 0.46 0.32 YES
3 MAOB MAOB MAOB 852 0.28 0.37 YES
4 ALDH3A1 ALDH3A1 ALDH3A1 1292 0.22 0.41 YES
5 AMDHD1 AMDHD1 AMDHD1 2046 0.16 0.42 YES
6 ALDH7A1 ALDH7A1 ALDH7A1 2111 0.15 0.46 YES
7 ALDH3B1 ALDH3B1 ALDH3B1 2259 0.15 0.5 YES
8 ALDH2 ALDH2 ALDH2 2693 0.12 0.51 YES
9 ALDH3B2 ALDH3B2 ALDH3B2 3378 0.099 0.51 YES
10 HAL HAL HAL 3641 0.09 0.52 YES
11 HEMK1 HEMK1 HEMK1 4092 0.078 0.52 YES
12 MAOA MAOA MAOA 4587 0.066 0.51 YES
13 ALDH9A1 ALDH9A1 ALDH9A1 4692 0.064 0.53 YES
14 HNMT HNMT HNMT 4710 0.064 0.55 YES
15 TRMT11 TRMT11 TRMT11 5286 0.052 0.53 YES
16 FTCD FTCD FTCD 5505 0.049 0.53 YES
17 ALDH1A3 ALDH1A3 ALDH1A3 5510 0.049 0.55 YES
18 UROC1 UROC1 UROC1 5666 0.046 0.55 YES
19 ABP1 ABP1 ABP1 5689 0.045 0.57 YES
20 WBSCR22 WBSCR22 WBSCR22 6756 0.03 0.52 NO
21 ALDH3A2 ALDH3A2 ALDH3A2 8338 0.0094 0.43 NO
22 LCMT1 LCMT1 LCMT1 9268 -0.002 0.38 NO
23 METTL6 METTL6 METTL6 9693 -0.0072 0.36 NO
24 LCMT2 LCMT2 LCMT2 10723 -0.02 0.31 NO
25 HDC HDC HDC 13941 -0.069 0.16 NO
26 DDC DDC DDC 14322 -0.079 0.16 NO
27 ALDH1B1 ALDH1B1 ALDH1B1 14786 -0.09 0.16 NO
28 METTL2B METTL2B METTL2B 14985 -0.096 0.18 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 FATTY ACID METABOLISM.

Figure S86.  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 OXIDATIVE PHOSPHORYLATION

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 DAO DAO DAO 245 0.47 0.061 YES
2 PAOX PAOX PAOX 357 0.4 0.12 YES
3 PEX11G PEX11G PEX11G 687 0.31 0.15 YES
4 EPHX2 EPHX2 EPHX2 714 0.3 0.2 YES
5 ACSL1 ACSL1 ACSL1 1085 0.25 0.22 YES
6 BAAT BAAT BAAT 1374 0.21 0.23 YES
7 MPV17L MPV17L MPV17L 1831 0.17 0.24 YES
8 DDO DDO DDO 1929 0.17 0.26 YES
9 HAO1 HAO1 HAO1 2090 0.16 0.27 YES
10 PRDX1 PRDX1 PRDX1 2094 0.16 0.3 YES
11 ACAA1 ACAA1 ACAA1 2737 0.12 0.28 YES
12 PEX16 PEX16 PEX16 2984 0.11 0.29 YES
13 DHRS4 DHRS4 DHRS4 3032 0.11 0.3 YES
14 MVK MVK MVK 3166 0.11 0.31 YES
15 PEX7 PEX7 PEX7 3282 0.1 0.32 YES
16 FAR1 FAR1 FAR1 3323 0.1 0.34 YES
17 PMVK PMVK PMVK 3373 0.099 0.35 YES
18 HMGCL HMGCL HMGCL 3427 0.097 0.36 YES
19 PHYH PHYH PHYH 3482 0.095 0.37 YES
20 PIPOX PIPOX PIPOX 3667 0.09 0.38 YES
21 ABCD4 ABCD4 ABCD4 4114 0.078 0.36 NO
22 SOD1 SOD1 SOD1 4706 0.064 0.34 NO
23 HSD17B4 HSD17B4 HSD17B4 4738 0.063 0.35 NO
24 PEX10 PEX10 PEX10 4839 0.061 0.36 NO
25 PXMP4 PXMP4 PXMP4 5423 0.05 0.33 NO
26 XDH XDH XDH 5431 0.05 0.34 NO
27 DECR2 DECR2 DECR2 5598 0.047 0.34 NO
28 CAT CAT CAT 5602 0.047 0.34 NO
29 ACOT8 ACOT8 ACOT8 5657 0.046 0.35 NO
30 NUDT12 NUDT12 NUDT12 5696 0.045 0.35 NO
31 IDH2 IDH2 IDH2 5800 0.043 0.36 NO
32 ECH1 ECH1 ECH1 5974 0.041 0.35 NO
33 NUDT19 NUDT19 NUDT19 6046 0.04 0.36 NO
34 PEX2 PEX2 PEX2 6063 0.04 0.36 NO
35 PECI PECI PECI 6217 0.037 0.36 NO
36 GSTK1 GSTK1 GSTK1 6611 0.032 0.34 NO
37 PRDX5 PRDX5 PRDX5 6618 0.032 0.35 NO
38 MPV17 MPV17 MPV17 6914 0.028 0.33 NO
39 PEX11A PEX11A PEX11A 6985 0.027 0.34 NO
40 EHHADH EHHADH EHHADH 7258 0.023 0.32 NO
41 SCP2 SCP2 SCP2 7386 0.022 0.32 NO
42 HACL1 HACL1 HACL1 7546 0.019 0.31 NO
43 PEX1 PEX1 PEX1 7695 0.017 0.31 NO
44 PEX6 PEX6 PEX6 7769 0.016 0.31 NO
45 SOD2 SOD2 SOD2 7869 0.015 0.3 NO
46 PEX14 PEX14 PEX14 7889 0.015 0.31 NO
47 PEX12 PEX12 PEX12 7957 0.014 0.3 NO
48 ABCD3 ABCD3 ABCD3 8201 0.011 0.29 NO
49 GNPAT GNPAT GNPAT 8398 0.0087 0.28 NO
50 PEX5 PEX5 PEX5 8565 0.0066 0.28 NO
51 PEX3 PEX3 PEX3 8991 0.0016 0.25 NO
52 PXMP2 PXMP2 PXMP2 9048 0.00057 0.25 NO
53 ACOX3 ACOX3 ACOX3 9063 0.00038 0.25 NO
54 ACSL3 ACSL3 ACSL3 9112 -0.0002 0.25 NO
55 PEX19 PEX19 PEX19 9565 -0.0056 0.22 NO
56 PEX13 PEX13 PEX13 9812 -0.0085 0.21 NO
57 AGPS AGPS AGPS 9972 -0.01 0.2 NO
58 PECR PECR PECR 10170 -0.013 0.19 NO
59 CRAT CRAT CRAT 10191 -0.013 0.2 NO
60 ACSL5 ACSL5 ACSL5 10248 -0.014 0.19 NO
61 ACOX1 ACOX1 ACOX1 10613 -0.019 0.18 NO
62 ABCD1 ABCD1 ABCD1 10775 -0.021 0.17 NO
63 SLC25A17 SLC25A17 SLC25A17 11197 -0.026 0.15 NO
64 ACSL6 ACSL6 ACSL6 11376 -0.028 0.15 NO
65 MLYCD MLYCD MLYCD 11576 -0.031 0.14 NO
66 PEX11B PEX11B PEX11B 11885 -0.035 0.13 NO
67 CROT CROT CROT 13457 -0.06 0.054 NO
68 HAO2 HAO2 HAO2 14669 -0.087 0.00095 NO
69 AMACR AMACR AMACR 14670 -0.087 0.015 NO
70 IDH1 IDH1 IDH1 15125 -0.1 0.0059 NO
71 ACSL4 ACSL4 ACSL4 15259 -0.1 0.015 NO
72 PEX26 PEX26 PEX26 15462 -0.11 0.022 NO
73 NOS2 NOS2 NOS2 16532 -0.16 -0.011 NO
74 ABCD2 ABCD2 ABCD2 17104 -0.2 -0.0097 NO
75 FAR2 FAR2 FAR2 17294 -0.22 0.016 NO
76 SLC27A2 SLC27A2 SLC27A2 17567 -0.25 0.041 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 OXIDATIVE PHOSPHORYLATION.

Figure S88.  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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM

Table S45.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CLDN11 CLDN11 CLDN11 118 0.61 0.042 YES
2 LLGL2 LLGL2 LLGL2 268 0.45 0.069 YES
3 CLDN20 CLDN20 CLDN20 336 0.41 0.098 YES
4 MYH7B MYH7B MYH7B 378 0.39 0.13 YES
5 MYH15 MYH15 MYH15 472 0.36 0.15 YES
6 PRKCQ PRKCQ PRKCQ 497 0.35 0.18 YES
7 CLDN23 CLDN23 CLDN23 630 0.32 0.2 YES
8 CRB3 CRB3 CRB3 739 0.3 0.21 YES
9 CLDN14 CLDN14 CLDN14 1117 0.24 0.21 YES
10 CTNNA3 CTNNA3 CTNNA3 1199 0.23 0.22 YES
11 PPP2R2C PPP2R2C PPP2R2C 1202 0.23 0.24 YES
12 CLDN10 CLDN10 CLDN10 1226 0.23 0.26 YES
13 CLDN7 CLDN7 CLDN7 1439 0.2 0.26 YES
14 MYH3 MYH3 MYH3 1453 0.2 0.28 YES
15 CLDN3 CLDN3 CLDN3 1468 0.2 0.3 YES
16 CLDN9 CLDN9 CLDN9 1481 0.2 0.31 YES
17 MYL5 MYL5 MYL5 1588 0.19 0.32 YES
18 TJAP1 TJAP1 TJAP1 1624 0.19 0.33 YES
19 TJP2 TJP2 TJP2 1913 0.17 0.33 YES
20 EPB41L3 EPB41L3 EPB41L3 1999 0.16 0.34 YES
21 JAM3 JAM3 JAM3 2024 0.16 0.35 YES
22 GNAI1 GNAI1 GNAI1 2047 0.16 0.36 YES
23 ACTN2 ACTN2 ACTN2 2066 0.16 0.37 YES
24 MYH14 MYH14 MYH14 2198 0.15 0.38 YES
25 MYLPF MYLPF MYLPF 2321 0.14 0.38 YES
26 LLGL1 LLGL1 LLGL1 2351 0.14 0.39 YES
27 INADL INADL INADL 2449 0.14 0.4 YES
28 RRAS RRAS RRAS 2721 0.12 0.39 NO
29 PPP2R1B PPP2R1B PPP2R1B 2834 0.12 0.4 NO
30 PRKCZ PRKCZ PRKCZ 3372 0.099 0.37 NO
31 PARD6B PARD6B PARD6B 3489 0.095 0.37 NO
32 PRKCD PRKCD PRKCD 3610 0.091 0.38 NO
33 IGSF5 IGSF5 IGSF5 3660 0.09 0.38 NO
34 CGN CGN CGN 3780 0.087 0.38 NO
35 RAB13 RAB13 RAB13 3864 0.084 0.38 NO
36 PPP2R2B PPP2R2B PPP2R2B 3887 0.083 0.39 NO
37 HCLS1 HCLS1 HCLS1 3962 0.081 0.39 NO
38 PPP2CB PPP2CB PPP2CB 4222 0.074 0.38 NO
39 EPB41L2 EPB41L2 EPB41L2 4270 0.074 0.38 NO
40 CLDN2 CLDN2 CLDN2 4414 0.07 0.38 NO
41 CTNNA1 CTNNA1 CTNNA1 4504 0.068 0.38 NO
42 MYL12A MYL12A MYL12A 4523 0.068 0.39 NO
43 MYL7 MYL7 MYL7 4647 0.065 0.38 NO
44 CTTN CTTN CTTN 4780 0.062 0.38 NO
45 MYH6 MYH6 MYH6 4827 0.061 0.38 NO
46 CLDN5 CLDN5 CLDN5 5048 0.057 0.38 NO
47 CLDN19 CLDN19 CLDN19 5346 0.052 0.36 NO
48 PRKCG PRKCG PRKCG 5527 0.048 0.36 NO
49 MRAS MRAS MRAS 5713 0.045 0.35 NO
50 TJP1 TJP1 TJP1 5783 0.044 0.35 NO
51 CLDN15 CLDN15 CLDN15 5849 0.043 0.35 NO
52 GNAI2 GNAI2 GNAI2 5946 0.041 0.35 NO
53 MPP5 MPP5 MPP5 6088 0.04 0.35 NO
54 CSNK2B CSNK2B CSNK2B 6547 0.032 0.32 NO
55 MYH7 MYH7 MYH7 6548 0.032 0.33 NO
56 RHOA RHOA RHOA 6634 0.031 0.32 NO
57 EXOC3 EXOC3 EXOC3 6660 0.031 0.32 NO
58 CSDA CSDA CSDA 7214 0.024 0.3 NO
59 ACTB ACTB ACTB 7434 0.021 0.29 NO
60 CDC42 CDC42 CDC42 7435 0.021 0.29 NO
61 MAGI2 MAGI2 MAGI2 7518 0.02 0.28 NO
62 EPB41L1 EPB41L1 EPB41L1 7548 0.019 0.28 NO
63 PPP2R2A PPP2R2A PPP2R2A 7579 0.018 0.28 NO
64 VAPA VAPA VAPA 7639 0.018 0.28 NO
65 YES1 YES1 YES1 7759 0.016 0.28 NO
66 AKT2 AKT2 AKT2 8073 0.013 0.26 NO
67 MPDZ MPDZ MPDZ 8199 0.011 0.26 NO
68 ACTG1 ACTG1 ACTG1 8212 0.011 0.26 NO
69 ACTN4 ACTN4 ACTN4 8812 0.0038 0.22 NO
70 SYMPK SYMPK SYMPK 8933 0.0023 0.22 NO
71 MYL12B MYL12B MYL12B 9289 -0.0022 0.2 NO
72 RRAS2 RRAS2 RRAS2 9568 -0.0056 0.18 NO
73 PRKCH PRKCH PRKCH 10288 -0.014 0.14 NO
74 GNAI3 GNAI3 GNAI3 10379 -0.016 0.14 NO
75 PARD6A PARD6A PARD6A 10410 -0.016 0.14 NO
76 MLLT4 MLLT4 MLLT4 10422 -0.016 0.14 NO
77 PPP2R1A PPP2R1A PPP2R1A 10771 -0.021 0.12 NO
78 PPP2CA PPP2CA PPP2CA 10851 -0.022 0.12 NO
79 ZAK ZAK ZAK 11033 -0.024 0.11 NO
80 CTNNB1 CTNNB1 CTNNB1 11044 -0.024 0.11 NO
81 PPP2R2D PPP2R2D PPP2R2D 11052 -0.024 0.12 NO
82 NRAS NRAS NRAS 11147 -0.025 0.11 NO
83 AMOTL1 AMOTL1 AMOTL1 11211 -0.026 0.11 NO
84 AKT1 AKT1 AKT1 11357 -0.028 0.1 NO
85 SPTAN1 SPTAN1 SPTAN1 11358 -0.028 0.11 NO
86 MYL9 MYL9 MYL9 11457 -0.029 0.1 NO
87 PRKCA PRKCA PRKCA 11783 -0.034 0.088 NO
88 PARD6G PARD6G PARD6G 11791 -0.034 0.09 NO
89 F11R F11R F11R 11993 -0.037 0.082 NO
90 EXOC4 EXOC4 EXOC4 12388 -0.042 0.064 NO
91 MYH9 MYH9 MYH9 12542 -0.044 0.059 NO
92 CLDN1 CLDN1 CLDN1 12555 -0.044 0.062 NO
93 PARD3 PARD3 PARD3 12695 -0.047 0.058 NO
94 CLDN4 CLDN4 CLDN4 12946 -0.051 0.048 NO
95 JAM2 JAM2 JAM2 12960 -0.052 0.052 NO
96 CSNK2A2 CSNK2A2 CSNK2A2 13355 -0.058 0.035 NO
97 ASH1L ASH1L ASH1L 13508 -0.061 0.031 NO
98 MAGI3 MAGI3 MAGI3 13534 -0.061 0.035 NO
99 MYH13 MYH13 MYH13 13537 -0.061 0.039 NO
100 PTEN PTEN PTEN 13625 -0.063 0.04 NO
101 CASK CASK CASK 13679 -0.064 0.042 NO
102 CTNNA2 CTNNA2 CTNNA2 14143 -0.075 0.022 NO
103 CSNK2A1 CSNK2A1 CSNK2A1 14185 -0.076 0.026 NO
104 CDK4 CDK4 CDK4 14219 -0.077 0.03 NO
105 TJP3 TJP3 TJP3 14292 -0.078 0.032 NO
106 MAGI1 MAGI1 MAGI1 14390 -0.08 0.034 NO
107 KRAS KRAS KRAS 14465 -0.082 0.036 NO
108 SRC SRC SRC 14785 -0.09 0.026 NO
109 PRKCI PRKCI PRKCI 14964 -0.095 0.023 NO
110 MYH11 MYH11 MYH11 15018 -0.097 0.028 NO
111 EPB41 EPB41 EPB41 15078 -0.099 0.033 NO
112 MYH10 MYH10 MYH10 15584 -0.12 0.014 NO
113 RAB3B RAB3B RAB3B 15681 -0.12 0.018 NO
114 CLDN6 CLDN6 CLDN6 15742 -0.12 0.025 NO
115 OCLN OCLN OCLN 15846 -0.13 0.029 NO
116 PRKCB PRKCB PRKCB 15885 -0.13 0.037 NO
117 ACTN3 ACTN3 ACTN3 15931 -0.13 0.045 NO
118 AKT3 AKT3 AKT3 16084 -0.14 0.047 NO
119 MYH4 MYH4 MYH4 16585 -0.16 0.033 NO
120 ACTN1 ACTN1 ACTN1 16619 -0.17 0.044 NO
121 CLDN18 CLDN18 CLDN18 16722 -0.17 0.052 NO
122 PRKCE PRKCE PRKCE 16750 -0.18 0.065 NO
123 CLDN16 CLDN16 CLDN16 17681 -0.27 0.035 NO

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

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SLC27A6 SLC27A6 SLC27A6 79 0.69 0.085 YES
2 PLIN1 PLIN1 PLIN1 271 0.45 0.13 YES
3 RXRG RXRG RXRG 340 0.41 0.18 YES
4 CYP27A1 CYP27A1 CYP27A1 366 0.4 0.23 YES
5 CYP8B1 CYP8B1 CYP8B1 628 0.32 0.26 YES
6 ACSL1 ACSL1 ACSL1 1085 0.25 0.27 YES
7 FABP5 FABP5 FABP5 1220 0.23 0.29 YES
8 OLR1 OLR1 OLR1 1276 0.22 0.31 YES
9 ANGPTL4 ANGPTL4 ANGPTL4 1278 0.22 0.34 YES
10 APOA1 APOA1 APOA1 1357 0.21 0.37 YES
11 FABP6 FABP6 FABP6 1558 0.2 0.38 YES
12 CPT1B CPT1B CPT1B 1780 0.18 0.39 YES
13 FABP1 FABP1 FABP1 1807 0.18 0.41 YES
14 ME1 ME1 ME1 1855 0.17 0.43 YES
15 SLC27A5 SLC27A5 SLC27A5 1863 0.17 0.46 YES
16 SCD SCD SCD 1932 0.17 0.47 YES
17 SLC27A1 SLC27A1 SLC27A1 2042 0.16 0.49 YES
18 PPARG PPARG PPARG 2592 0.13 0.47 YES
19 ACAA1 ACAA1 ACAA1 2737 0.12 0.48 YES
20 FABP4 FABP4 FABP4 2764 0.12 0.5 YES
21 ACADL ACADL ACADL 3558 0.093 0.46 NO
22 DBI DBI DBI 3674 0.089 0.47 NO
23 FADS2 FADS2 FADS2 3828 0.085 0.47 NO
24 AQP7 AQP7 AQP7 3834 0.085 0.48 NO
25 NR1H3 NR1H3 NR1H3 4641 0.065 0.45 NO
26 PLTP PLTP PLTP 4683 0.064 0.45 NO
27 ADIPOQ ADIPOQ ADIPOQ 4957 0.059 0.45 NO
28 PCK2 PCK2 PCK2 4993 0.058 0.45 NO
29 GK2 GK2 GK2 5119 0.056 0.45 NO
30 SLC27A4 SLC27A4 SLC27A4 5215 0.054 0.46 NO
31 CPT2 CPT2 CPT2 5630 0.046 0.44 NO
32 SORBS1 SORBS1 SORBS1 5951 0.041 0.43 NO
33 FABP7 FABP7 FABP7 6485 0.033 0.4 NO
34 ACADM ACADM ACADM 6729 0.03 0.39 NO
35 PPARA PPARA PPARA 6878 0.028 0.39 NO
36 SCD5 SCD5 SCD5 7054 0.026 0.38 NO
37 UBC UBC UBC 7069 0.026 0.38 NO
38 EHHADH EHHADH EHHADH 7258 0.023 0.38 NO
39 SCP2 SCP2 SCP2 7386 0.022 0.37 NO
40 RXRA RXRA RXRA 7540 0.019 0.37 NO
41 ILK ILK ILK 7818 0.015 0.35 NO
42 LPL LPL LPL 8442 0.0081 0.32 NO
43 ACOX3 ACOX3 ACOX3 9063 0.00038 0.29 NO
44 ACSL3 ACSL3 ACSL3 9112 -0.0002 0.28 NO
45 RXRB RXRB RXRB 9458 -0.0043 0.26 NO
46 PCK1 PCK1 PCK1 9588 -0.0058 0.26 NO
47 ACSL5 ACSL5 ACSL5 10248 -0.014 0.22 NO
48 PPARD PPARD PPARD 10409 -0.016 0.22 NO
49 ACOX1 ACOX1 ACOX1 10613 -0.019 0.21 NO
50 ACSL6 ACSL6 ACSL6 11376 -0.028 0.17 NO
51 FABP3 FABP3 FABP3 11691 -0.033 0.16 NO
52 CPT1C CPT1C CPT1C 13150 -0.055 0.085 NO
53 HMGCS2 HMGCS2 HMGCS2 13191 -0.055 0.09 NO
54 CYP7A1 CYP7A1 CYP7A1 13484 -0.06 0.082 NO
55 MMP1 MMP1 MMP1 13907 -0.069 0.068 NO
56 GK GK GK 14246 -0.077 0.059 NO
57 PDPK1 PDPK1 PDPK1 14642 -0.086 0.049 NO
58 ACSL4 ACSL4 ACSL4 15259 -0.1 0.028 NO
59 CPT1A CPT1A CPT1A 15506 -0.11 0.03 NO
60 CYP4A11 CYP4A11 CYP4A11 16257 -0.14 0.0075 NO
61 APOA5 APOA5 APOA5 17392 -0.23 -0.024 NO
62 SLC27A2 SLC27A2 SLC27A2 17567 -0.25 -0.0011 NO
63 CD36 CD36 CD36 17947 -0.32 0.02 NO

Figure S91.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

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

genes ES table in pathway: KEGG HISTIDINE METABOLISM

Table S47.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ALDOB ALDOB ALDOB 185 0.52 0.19 YES
2 PFKFB1 PFKFB1 PFKFB1 1065 0.25 0.24 YES
3 FBP1 FBP1 FBP1 2337 0.14 0.22 YES
4 MTMR7 MTMR7 MTMR7 2369 0.14 0.28 YES
5 HK2 HK2 HK2 2392 0.14 0.33 YES
6 PFKFB2 PFKFB2 PFKFB2 3013 0.11 0.34 YES
7 ALDOC ALDOC ALDOC 3085 0.11 0.37 YES
8 FUK FUK FUK 3261 0.1 0.4 YES
9 PHPT1 PHPT1 PHPT1 3663 0.09 0.42 YES
10 KHK KHK KHK 4655 0.065 0.39 YES
11 GMPPA GMPPA GMPPA 4703 0.064 0.41 YES
12 MPI MPI MPI 4820 0.061 0.43 YES
13 FPGT FPGT FPGT 5342 0.052 0.42 NO
14 PFKL PFKL PFKL 5816 0.043 0.41 NO
15 PMM1 PMM1 PMM1 6055 0.04 0.41 NO
16 MTMR2 MTMR2 MTMR2 6925 0.028 0.37 NO
17 SORD SORD SORD 7791 0.016 0.33 NO
18 PFKFB4 PFKFB4 PFKFB4 8947 0.0021 0.27 NO
19 AKR1B1 AKR1B1 AKR1B1 9068 0.00032 0.26 NO
20 PFKP PFKP PFKP 9164 -0.00088 0.26 NO
21 TSTA3 TSTA3 TSTA3 9793 -0.0083 0.23 NO
22 PFKFB3 PFKFB3 PFKFB3 9835 -0.0087 0.23 NO
23 TPI1 TPI1 TPI1 11143 -0.025 0.17 NO
24 MTMR6 MTMR6 MTMR6 11219 -0.026 0.17 NO
25 GMPPB GMPPB GMPPB 11632 -0.032 0.16 NO
26 PMM2 PMM2 PMM2 11802 -0.034 0.17 NO
27 PFKM PFKM PFKM 13794 -0.066 0.083 NO
28 AKR1B10 AKR1B10 AKR1B10 13870 -0.068 0.11 NO
29 MTMR1 MTMR1 MTMR1 14041 -0.072 0.12 NO
30 GMDS GMDS GMDS 14325 -0.079 0.14 NO
31 HK1 HK1 HK1 15042 -0.098 0.14 NO
32 HK3 HK3 HK3 15332 -0.11 0.16 NO

Figure S93.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HISTIDINE METABOLISM.

Figure S94.  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 GLUTATHIONE METABOLISM

Table S48.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GSTM5 GSTM5 GSTM5 384 0.39 0.06 YES
2 GSTO2 GSTO2 GSTO2 582 0.33 0.12 YES
3 ADH1B ADH1B ADH1B 903 0.27 0.16 YES
4 MGST1 MGST1 MGST1 1155 0.24 0.19 YES
5 ALDH3A1 ALDH3A1 ALDH3A1 1292 0.22 0.23 YES
6 AKR1C1 AKR1C1 AKR1C1 1779 0.18 0.24 YES
7 GSTT1 GSTT1 GSTT1 1977 0.16 0.26 YES
8 CYP2S1 CYP2S1 CYP2S1 2038 0.16 0.29 YES
9 ALDH3B1 ALDH3B1 ALDH3B1 2259 0.15 0.31 YES
10 CYP2E1 CYP2E1 CYP2E1 2308 0.14 0.34 YES
11 CYP3A43 CYP3A43 CYP3A43 2352 0.14 0.37 YES
12 GSTM1 GSTM1 GSTM1 2608 0.13 0.38 YES
13 GSTM3 GSTM3 GSTM3 2667 0.12 0.4 YES
14 GSTZ1 GSTZ1 GSTZ1 2699 0.12 0.43 YES
15 EPHX1 EPHX1 EPHX1 2719 0.12 0.45 YES
16 AKR1C3 AKR1C3 AKR1C3 2779 0.12 0.47 YES
17 CYP1A1 CYP1A1 CYP1A1 2852 0.12 0.49 YES
18 ALDH3B2 ALDH3B2 ALDH3B2 3378 0.099 0.49 YES
19 GSTM2 GSTM2 GSTM2 3409 0.098 0.5 YES
20 GSTP1 GSTP1 GSTP1 3722 0.088 0.51 YES
21 AKR1C2 AKR1C2 AKR1C2 3761 0.087 0.52 YES
22 MGST3 MGST3 MGST3 3855 0.084 0.53 YES
23 MGST2 MGST2 MGST2 4394 0.07 0.52 YES
24 GSTM4 GSTM4 GSTM4 4584 0.066 0.52 YES
25 CYP3A5 CYP3A5 CYP3A5 4607 0.066 0.54 YES
26 GSTO1 GSTO1 GSTO1 4769 0.062 0.54 YES
27 GSTA1 GSTA1 GSTA1 5443 0.05 0.51 NO
28 ALDH1A3 ALDH1A3 ALDH1A3 5510 0.049 0.52 NO
29 CYP2C8 CYP2C8 CYP2C8 5808 0.043 0.51 NO
30 GSTK1 GSTK1 GSTK1 6611 0.032 0.48 NO
31 DHDH DHDH DHDH 6622 0.031 0.48 NO
32 CYP2F1 CYP2F1 CYP2F1 7627 0.018 0.43 NO
33 ADH6 ADH6 ADH6 7994 0.013 0.41 NO
34 ADH5 ADH5 ADH5 9667 -0.0069 0.32 NO
35 GSTA4 GSTA4 GSTA4 10519 -0.018 0.28 NO
36 GSTT2 GSTT2 GSTT2 11270 -0.027 0.24 NO
37 AKR1C4 AKR1C4 AKR1C4 11952 -0.036 0.21 NO
38 ADH1A ADH1A ADH1A 12769 -0.048 0.18 NO
39 CYP3A7 CYP3A7 CYP3A7 14216 -0.077 0.12 NO
40 ADH1C ADH1C ADH1C 15069 -0.098 0.09 NO
41 CYP1B1 CYP1B1 CYP1B1 15767 -0.12 0.078 NO
42 CYP2C18 CYP2C18 CYP2C18 16099 -0.14 0.088 NO
43 ADH7 ADH7 ADH7 16474 -0.16 0.1 NO

Figure S95.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG GLUTATHIONE METABOLISM.

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

genes ES table in pathway: KEGG ETHER LIPID METABOLISM

Table S49.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ARHGEF16 ARHGEF16 ARHGEF16 83 0.68 0.23 YES
2 ARHGEF5 ARHGEF5 ARHGEF5 208 0.5 0.39 YES
3 MYLK MYLK MYLK 794 0.28 0.46 YES
4 ARHGEF10 ARHGEF10 ARHGEF10 2164 0.15 0.44 NO
5 ARHGEF1 ARHGEF1 ARHGEF1 2682 0.12 0.45 NO
6 ARHGEF19 ARHGEF19 ARHGEF19 3896 0.083 0.41 NO
7 ARHGEF4 ARHGEF4 ARHGEF4 4015 0.08 0.43 NO
8 MYL7 MYL7 MYL7 4647 0.065 0.42 NO
9 PPP1R12B PPP1R12B PPP1R12B 6256 0.037 0.34 NO
10 ARHGEF2 ARHGEF2 ARHGEF2 6461 0.034 0.34 NO
11 GNA12 GNA12 GNA12 6615 0.032 0.35 NO
12 ARHGAP5 ARHGAP5 ARHGAP5 6680 0.031 0.36 NO
13 ARHGEF6 ARHGEF6 ARHGEF6 8597 0.0061 0.25 NO
14 PKN1 PKN1 PKN1 8781 0.0042 0.24 NO
15 ARHGEF18 ARHGEF18 ARHGEF18 9226 -0.0017 0.22 NO
16 GNAQ GNAQ GNAQ 9913 -0.0097 0.19 NO
17 ARHGEF17 ARHGEF17 ARHGEF17 10002 -0.011 0.18 NO
18 ARHGEF7 ARHGEF7 ARHGEF7 11125 -0.025 0.13 NO
19 PRKCA PRKCA PRKCA 11783 -0.034 0.11 NO
20 GNB1 GNB1 GNB1 11903 -0.035 0.11 NO
21 ROCK1 ROCK1 ROCK1 12615 -0.046 0.09 NO
22 ARHGEF12 ARHGEF12 ARHGEF12 13152 -0.055 0.079 NO
23 ARHGEF3 ARHGEF3 ARHGEF3 14085 -0.073 0.054 NO
24 PLCB1 PLCB1 PLCB1 14634 -0.086 0.053 NO
25 ARHGEF15 ARHGEF15 ARHGEF15 14860 -0.092 0.073 NO
26 ARHGEF11 ARHGEF11 ARHGEF11 15197 -0.1 0.09 NO
27 ARHGEF9 ARHGEF9 ARHGEF9 15339 -0.11 0.12 NO
28 PRKCB PRKCB PRKCB 15885 -0.13 0.13 NO

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

Figure S98.  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 PROPANOATE METABOLISM

Table S50.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PPAP2C PPAP2C PPAP2C 54 0.74 0.16 YES
2 ENPP2 ENPP2 ENPP2 151 0.58 0.29 YES
3 PLD1 PLD1 PLD1 170 0.54 0.42 YES
4 PLA2G7 PLA2G7 PLA2G7 671 0.31 0.46 YES
5 LPCAT2 LPCAT2 LPCAT2 976 0.26 0.5 YES
6 PLA2G1B PLA2G1B PLA2G1B 2173 0.15 0.47 YES
7 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 2323 0.14 0.49 YES
8 PPAP2A PPAP2A PPAP2A 2344 0.14 0.52 YES
9 PLD2 PLD2 PLD2 3441 0.097 0.49 NO
10 PLA2G5 PLA2G5 PLA2G5 4130 0.077 0.47 NO
11 PLA2G6 PLA2G6 PLA2G6 4364 0.071 0.47 NO
12 PPAP2B PPAP2B PPAP2B 4403 0.07 0.48 NO
13 PLA2G12A PLA2G12A PLA2G12A 5014 0.058 0.46 NO
14 PAFAH2 PAFAH2 PAFAH2 6346 0.036 0.4 NO
15 CHPT1 CHPT1 CHPT1 6775 0.03 0.38 NO
16 PLA2G2D PLA2G2D PLA2G2D 6861 0.028 0.38 NO
17 AGPS AGPS AGPS 9972 -0.01 0.22 NO
18 PAFAH1B3 PAFAH1B3 PAFAH1B3 10996 -0.023 0.17 NO
19 PLA2G12B PLA2G12B PLA2G12B 11059 -0.024 0.17 NO
20 PAFAH1B1 PAFAH1B1 PAFAH1B1 12260 -0.04 0.11 NO
21 LPCAT1 LPCAT1 LPCAT1 12956 -0.051 0.086 NO
22 PLA2G3 PLA2G3 PLA2G3 14933 -0.094 -0.00028 NO
23 LPCAT4 LPCAT4 LPCAT4 15838 -0.13 -0.021 NO
24 PLA2G10 PLA2G10 PLA2G10 15860 -0.13 0.0067 NO
25 PAFAH1B2 PAFAH1B2 PAFAH1B2 15999 -0.13 0.03 NO
26 PLA2G2A PLA2G2A PLA2G2A 17067 -0.2 0.017 NO
27 PLA2G4A PLA2G4A PLA2G4A 17298 -0.22 0.056 NO

Figure S99.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PROPANOATE METABOLISM.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Methods & Data
Input
  • Gene set database = c2.cp.v3.0-2.symbols.gmt

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

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

GSEA analysis

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

Download Results

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

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