GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in BRCA-TP
Breast Invasive Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C14F1PQV
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 BRCA-TP. Broad Institute of MIT and Harvard. doi:10.7908/C14F1PQV
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 BRCA-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: 192
Number of samples: 1093
Original number of Gene Sets: 404
Maximum gene set size: 388

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 567
pheno.type: 2 - 3 :[ clus2 ] 311
pheno.type: 3 - 3 :[ clus3 ] 215

For the expression subtypes of 18296 genes in 1094 samples, GSEA found enriched gene sets in each cluster using 1093 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA CARM ER PATHWAY, BIOCARTA MPR PATHWAY, KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG SPHINGOLIPID METABOLISM, KEGG PYRUVATE METABOLISM, KEGG PROPANOATE METABOLISM, KEGG BUTANOATE METABOLISM

    • And common core enriched genes are HMGCL, BRCA1, CCND1, ESR1, HDAC11, NRIP1, ABAT, ACADSB, ALDH3A2, ALDH6A1

  • clus2

    • Top enriched gene sets are BIOCARTA G1 PATHWAY, BIOCARTA RACCYCD PATHWAY, KEGG CYSTEINE AND METHIONINE METABOLISM, KEGG LYSINE DEGRADATION, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RNA POLYMERASE, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG PROTEASOME

    • And common core enriched genes are AADAT, ACAT2, BBOX1, OGDHL, PIPOX, PLOD1, PLOD2, PLOD3, SUV39H1, SUV39H2

  • clus3

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

    • And common core enriched genes are AKT3, PIK3CD, PIK3CG, PIK3R1, PIK3R5, JUN, PAK3, PAK7, MAPK10, SHC2

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 CARM ER PATHWAY 34 genes.ES.table 0.39 1.4 0.11 1 0.95 0.15 0.073 0.14 1 0.61
BIOCARTA MPR PATHWAY 32 genes.ES.table 0.34 1.2 0.26 1 1 0.062 0.005 0.062 0.94 0.46
KEGG OXIDATIVE PHOSPHORYLATION 113 genes.ES.table 0.13 0.46 0.91 0.99 1 0.27 0.26 0.2 0.99 0.45
KEGG PYRIMIDINE METABOLISM 96 genes.ES.table 0.16 0.72 0.82 0.95 1 0.094 0.1 0.084 0.95 0.36
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 30 genes.ES.table 0.27 0.83 0.73 0.96 1 0.33 0.16 0.28 0.95 0.39
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.35 1.3 0.22 1 0.99 0.19 0.13 0.16 1 0.64
KEGG SPHINGOLIPID METABOLISM 37 genes.ES.table 0.29 0.95 0.53 0.95 1 0.11 0.028 0.1 0.89 0.39
KEGG PYRUVATE METABOLISM 37 genes.ES.table 0.19 0.67 0.89 0.96 1 0.24 0.18 0.2 0.96 0.34
KEGG PROPANOATE METABOLISM 31 genes.ES.table 0.29 0.97 0.47 1 1 0.26 0.18 0.21 1 0.62
KEGG BUTANOATE METABOLISM 29 genes.ES.table 0.27 0.78 0.73 0.97 1 0.28 0.19 0.22 0.97 0.43
genes ES table in pathway: BIOCARTA CARM ER 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 ESR1 ESR1 ESR1 2 0.67 0.2 YES
2 CCND1 CCND1 CCND1 584 0.26 0.25 YES
3 HDAC11 HDAC11 HDAC11 801 0.22 0.31 YES
4 NRIP1 NRIP1 NRIP1 1206 0.18 0.34 YES
5 BRCA1 BRCA1 BRCA1 1339 0.16 0.39 YES
6 HIST2H3C HIST2H3C HIST2H3C 2641 0.095 0.34 NO
7 GTF2A1 GTF2A1 GTF2A1 3770 0.064 0.3 NO
8 HDAC10 HDAC10 HDAC10 4558 0.048 0.27 NO
9 CREBBP CREBBP CREBBP 4769 0.044 0.28 NO
10 POLR2A POLR2A POLR2A 4786 0.044 0.29 NO
11 GTF2F1 GTF2F1 GTF2F1 4886 0.042 0.3 NO
12 SRA1 SRA1 SRA1 5139 0.038 0.29 NO
13 NCOR2 NCOR2 NCOR2 5925 0.026 0.26 NO
14 GTF2E1 GTF2E1 GTF2E1 6097 0.023 0.26 NO
15 HDAC7 HDAC7 HDAC7 6284 0.021 0.25 NO
16 EP300 EP300 EP300 6482 0.018 0.25 NO
17 HDAC6 HDAC6 HDAC6 6682 0.015 0.24 NO
18 MED1 MED1 MED1 6842 0.013 0.24 NO
19 HDAC8 HDAC8 HDAC8 7027 0.01 0.23 NO
20 HDAC5 HDAC5 HDAC5 7316 0.0066 0.22 NO
21 PELP1 PELP1 PELP1 7439 0.0051 0.21 NO
22 HDAC1 HDAC1 HDAC1 7762 0.00082 0.19 NO
23 ERCC3 ERCC3 ERCC3 8131 -0.004 0.18 NO
24 HDAC3 HDAC3 HDAC3 9003 -0.015 0.13 NO
25 SPEN SPEN SPEN 9318 -0.02 0.12 NO
26 TBP TBP TBP 10016 -0.031 0.092 NO
27 NR0B1 NR0B1 NR0B1 10207 -0.033 0.092 NO
28 CARM1 CARM1 CARM1 11331 -0.052 0.046 NO
29 PHB2 PHB2 PHB2 11401 -0.054 0.059 NO
30 GRIP1 GRIP1 GRIP1 12915 -0.088 0.003 NO
31 HDAC2 HDAC2 HDAC2 13119 -0.093 0.02 NO
32 HDAC4 HDAC4 HDAC4 14510 -0.14 -0.012 NO
33 HDAC9 HDAC9 HDAC9 16614 -0.28 -0.042 NO
34 PPARGC1A PPARGC1A PPARGC1A 17806 -0.43 0.026 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 CARM ER PATHWAY.

Figure S2.  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 MPR 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 ABAT ABAT ABAT 90 0.45 0.12 YES
2 ACADSB ACADSB ACADSB 250 0.36 0.21 YES
3 MCCC2 MCCC2 MCCC2 768 0.23 0.24 YES
4 IVD IVD IVD 1092 0.19 0.28 YES
5 ALDH6A1 ALDH6A1 ALDH6A1 1214 0.18 0.32 YES
6 BCAT2 BCAT2 BCAT2 1437 0.16 0.35 YES
7 HMGCL HMGCL HMGCL 2234 0.11 0.33 YES
8 ALDH3A2 ALDH3A2 ALDH3A2 2414 0.1 0.35 YES
9 HMGCS2 HMGCS2 HMGCS2 4267 0.054 0.26 NO
10 AUH AUH AUH 4353 0.052 0.28 NO
11 PCCB PCCB PCCB 4836 0.043 0.26 NO
12 ACAT1 ACAT1 ACAT1 4907 0.042 0.27 NO
13 MUT MUT MUT 5095 0.039 0.27 NO
14 MCEE MCEE MCEE 5107 0.039 0.28 NO
15 ACADS ACADS ACADS 5807 0.028 0.25 NO
16 DBT DBT DBT 5901 0.026 0.25 NO
17 BCKDHA BCKDHA BCKDHA 6022 0.024 0.25 NO
18 BCKDHB BCKDHB BCKDHB 6606 0.016 0.22 NO
19 PCCA PCCA PCCA 6742 0.014 0.22 NO
20 ALDH9A1 ALDH9A1 ALDH9A1 6746 0.014 0.22 NO
21 ECHS1 ECHS1 ECHS1 6942 0.012 0.22 NO
22 HADHB HADHB HADHB 7154 0.0087 0.2 NO
23 ACAA1 ACAA1 ACAA1 7302 0.0068 0.2 NO
24 HADH HADH HADH 7737 0.0011 0.18 NO
25 HIBCH HIBCH HIBCH 7887 -0.00075 0.17 NO
26 HIBADH HIBADH HIBADH 8686 -0.011 0.13 NO
27 HSD17B10 HSD17B10 HSD17B10 9154 -0.017 0.11 NO
28 ACAD8 ACAD8 ACAD8 9208 -0.018 0.11 NO
29 ACADM ACADM ACADM 9234 -0.019 0.11 NO
30 DLD DLD DLD 9855 -0.028 0.086 NO
31 HADHA HADHA HADHA 9888 -0.028 0.092 NO
32 ALDH7A1 ALDH7A1 ALDH7A1 10039 -0.031 0.092 NO
33 HMGCS1 HMGCS1 HMGCS1 10493 -0.038 0.077 NO
34 ALDH1B1 ALDH1B1 ALDH1B1 10741 -0.042 0.075 NO
35 ACAT2 ACAT2 ACAT2 11475 -0.055 0.05 NO
36 EHHADH EHHADH EHHADH 12181 -0.069 0.03 NO
37 ACAA2 ACAA2 ACAA2 12368 -0.074 0.04 NO
38 AOX1 AOX1 AOX1 13074 -0.092 0.026 NO
39 ALDH2 ALDH2 ALDH2 13116 -0.093 0.049 NO
40 MCCC1 MCCC1 MCCC1 14565 -0.14 0.0091 NO
41 OXCT1 OXCT1 OXCT1 14717 -0.15 0.042 NO
42 OXCT2 OXCT2 OXCT2 16548 -0.27 0.016 NO
43 IL4I1 IL4I1 IL4I1 16743 -0.29 0.084 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 MPR PATHWAY.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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 SLC27A2 SLC27A2 SLC27A2 87 0.46 0.058 YES
2 NUDT12 NUDT12 NUDT12 392 0.31 0.084 YES
3 PEX11G PEX11G PEX11G 634 0.25 0.11 YES
4 MPV17L MPV17L MPV17L 806 0.22 0.13 YES
5 PEX12 PEX12 PEX12 994 0.2 0.14 YES
6 PEX11A PEX11A PEX11A 1169 0.18 0.16 YES
7 CROT CROT CROT 1326 0.17 0.17 YES
8 DDO DDO DDO 1367 0.16 0.19 YES
9 PEX7 PEX7 PEX7 1534 0.15 0.21 YES
10 PECI PECI PECI 1591 0.15 0.22 YES
11 PECR PECR PECR 1723 0.14 0.24 YES
12 ABCD3 ABCD3 ABCD3 1742 0.14 0.25 YES
13 HSD17B4 HSD17B4 HSD17B4 1775 0.13 0.27 YES
14 PXMP4 PXMP4 PXMP4 1875 0.13 0.28 YES
15 DECR2 DECR2 DECR2 2117 0.12 0.28 YES
16 AMACR AMACR AMACR 2118 0.12 0.3 YES
17 HMGCL HMGCL HMGCL 2234 0.11 0.31 YES
18 FAR1 FAR1 FAR1 2272 0.11 0.32 YES
19 CRAT CRAT CRAT 2521 0.099 0.32 YES
20 PXMP2 PXMP2 PXMP2 2578 0.097 0.33 YES
21 PEX19 PEX19 PEX19 2951 0.085 0.32 NO
22 EPHX2 EPHX2 EPHX2 3376 0.074 0.31 NO
23 DHRS4 DHRS4 DHRS4 3702 0.066 0.3 NO
24 PEX2 PEX2 PEX2 3745 0.065 0.31 NO
25 PAOX PAOX PAOX 3774 0.064 0.32 NO
26 PEX1 PEX1 PEX1 3930 0.061 0.32 NO
27 PMVK PMVK PMVK 4215 0.055 0.31 NO
28 ACOX3 ACOX3 ACOX3 4287 0.054 0.31 NO
29 PEX11B PEX11B PEX11B 4431 0.051 0.31 NO
30 AGPS AGPS AGPS 4559 0.048 0.31 NO
31 HACL1 HACL1 HACL1 4862 0.043 0.3 NO
32 PEX10 PEX10 PEX10 5137 0.038 0.29 NO
33 SLC25A17 SLC25A17 SLC25A17 5570 0.031 0.27 NO
34 SOD1 SOD1 SOD1 5973 0.025 0.25 NO
35 ACOT8 ACOT8 ACOT8 6147 0.023 0.25 NO
36 ACSL3 ACSL3 ACSL3 6159 0.022 0.25 NO
37 SCP2 SCP2 SCP2 6199 0.022 0.25 NO
38 GNPAT GNPAT GNPAT 6607 0.016 0.23 NO
39 PEX16 PEX16 PEX16 7155 0.0087 0.2 NO
40 PHYH PHYH PHYH 7230 0.0078 0.2 NO
41 ACAA1 ACAA1 ACAA1 7302 0.0068 0.19 NO
42 ACOX1 ACOX1 ACOX1 7702 0.0016 0.17 NO
43 MPV17 MPV17 MPV17 7969 -0.0018 0.16 NO
44 FAR2 FAR2 FAR2 8166 -0.0044 0.15 NO
45 ABCD4 ABCD4 ABCD4 8186 -0.0046 0.15 NO
46 MVK MVK MVK 8286 -0.0059 0.14 NO
47 MLYCD MLYCD MLYCD 8313 -0.0062 0.14 NO
48 PEX6 PEX6 PEX6 8395 -0.0072 0.14 NO
49 PEX26 PEX26 PEX26 8437 -0.0078 0.14 NO
50 DAO DAO DAO 8886 -0.014 0.12 NO
51 PRDX1 PRDX1 PRDX1 8928 -0.014 0.12 NO
52 PEX5 PEX5 PEX5 8958 -0.015 0.12 NO
53 ECH1 ECH1 ECH1 9070 -0.016 0.11 NO
54 GSTK1 GSTK1 GSTK1 9086 -0.016 0.11 NO
55 PEX14 PEX14 PEX14 9482 -0.022 0.094 NO
56 PEX13 PEX13 PEX13 9673 -0.026 0.087 NO
57 CAT CAT CAT 9935 -0.029 0.077 NO
58 PRDX5 PRDX5 PRDX5 10231 -0.034 0.065 NO
59 HAO2 HAO2 HAO2 10479 -0.037 0.057 NO
60 AGXT AGXT AGXT 10875 -0.044 0.041 NO
61 PEX3 PEX3 PEX3 11054 -0.047 0.038 NO
62 IDH1 IDH1 IDH1 12130 -0.068 -0.012 NO
63 NUDT19 NUDT19 NUDT19 12145 -0.068 -0.003 NO
64 EHHADH EHHADH EHHADH 12181 -0.069 0.0046 NO
65 ABCD1 ABCD1 ABCD1 12553 -0.077 -0.005 NO
66 IDH2 IDH2 IDH2 12797 -0.084 -0.0068 NO
67 BAAT BAAT BAAT 13984 -0.12 -0.055 NO
68 PIPOX PIPOX PIPOX 13992 -0.12 -0.038 NO
69 NOS2 NOS2 NOS2 14707 -0.15 -0.057 NO
70 ACSL6 ACSL6 ACSL6 15016 -0.17 -0.051 NO
71 ACSL1 ACSL1 ACSL1 15209 -0.18 -0.037 NO
72 SOD2 SOD2 SOD2 15617 -0.2 -0.031 NO
73 ACSL4 ACSL4 ACSL4 16303 -0.25 -0.034 NO
74 ACSL5 ACSL5 ACSL5 16489 -0.27 -0.0076 NO
75 XDH XDH XDH 17211 -0.34 -2.9e-06 NO
76 ABCD2 ABCD2 ABCD2 17763 -0.42 0.028 NO

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

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

genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

Table 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 PGR PGR PGR 70 0.47 0.17 YES
2 MYT1 MYT1 MYT1 91 0.45 0.34 YES
3 PAQR5 PAQR5 PAQR5 1393 0.16 0.33 NO
4 MAPK3 MAPK3 MAPK3 2992 0.084 0.27 NO
5 PRKAR1A PRKAR1A PRKAR1A 3983 0.06 0.24 NO
6 PRKAR2B PRKAR2B PRKAR2B 4120 0.057 0.26 NO
7 PRKAR2A PRKAR2A PRKAR2A 4291 0.054 0.27 NO
8 CDC25C CDC25C CDC25C 5454 0.033 0.22 NO
9 PIN1 PIN1 PIN1 6004 0.025 0.2 NO
10 ARPC3 ARPC3 ARPC3 6154 0.023 0.2 NO
11 PAQR7 PAQR7 PAQR7 6934 0.012 0.16 NO
12 HRAS HRAS HRAS 6986 0.011 0.16 NO
13 GNB1 GNB1 GNB1 7760 0.00082 0.12 NO
14 MAPK1 MAPK1 MAPK1 8884 -0.014 0.06 NO
15 ACTA1 ACTA1 ACTA1 8888 -0.014 0.065 NO
16 CCNB1 CCNB1 CCNB1 9140 -0.017 0.058 NO
17 GNAS GNAS GNAS 9750 -0.027 0.034 NO
18 ARPC4 ARPC4 ARPC4 9988 -0.03 0.032 NO
19 ACTR2 ACTR2 ACTR2 10352 -0.035 0.026 NO
20 ARPC1A ARPC1A ARPC1A 10363 -0.036 0.038 NO
21 SRC SRC SRC 10408 -0.036 0.05 NO
22 CDK1 CDK1 CDK1 10417 -0.036 0.063 NO
23 CAP1 CAP1 CAP1 10463 -0.037 0.074 NO
24 GNGT1 GNGT1 GNGT1 10547 -0.039 0.084 NO
25 PRKACB PRKACB PRKACB 10809 -0.043 0.086 NO
26 ARPC5 ARPC5 ARPC5 11500 -0.056 0.069 NO
27 ARPC2 ARPC2 ARPC2 11798 -0.061 0.076 NO
28 RPS6KA1 RPS6KA1 RPS6KA1 12158 -0.069 0.082 NO
29 ACTR3 ACTR3 ACTR3 12653 -0.08 0.085 NO
30 ARPC1B ARPC1B ARPC1B 13090 -0.092 0.095 NO
31 PRKAR1B PRKAR1B PRKAR1B 14739 -0.15 0.062 NO
32 GNAI1 GNAI1 GNAI1 17274 -0.35 0.055 NO

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

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

genes ES table in pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM

Table 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 NEIL1 NEIL1 NEIL1 1467 0.16 0.032 YES
2 POLD4 POLD4 POLD4 1733 0.14 0.12 YES
3 NTHL1 NTHL1 NTHL1 2568 0.098 0.14 YES
4 PARP3 PARP3 PARP3 2619 0.096 0.21 YES
5 LIG3 LIG3 LIG3 3360 0.074 0.22 YES
6 SMUG1 SMUG1 SMUG1 3464 0.072 0.26 YES
7 MPG MPG MPG 4058 0.058 0.28 YES
8 POLB POLB POLB 4116 0.057 0.31 YES
9 POLL POLL POLL 4124 0.057 0.35 YES
10 NEIL2 NEIL2 NEIL2 5640 0.03 0.29 NO
11 XRCC1 XRCC1 XRCC1 5871 0.027 0.3 NO
12 OGG1 OGG1 OGG1 6578 0.017 0.27 NO
13 LIG1 LIG1 LIG1 6955 0.011 0.26 NO
14 POLE POLE POLE 7326 0.0064 0.24 NO
15 POLE2 POLE2 POLE2 7506 0.0044 0.24 NO
16 APEX1 APEX1 APEX1 7574 0.0034 0.24 NO
17 PARP2 PARP2 PARP2 7724 0.0013 0.23 NO
18 PARP1 PARP1 PARP1 7866 -0.00049 0.22 NO
19 UNG UNG UNG 8013 -0.0024 0.22 NO
20 PCNA PCNA PCNA 8347 -0.0067 0.2 NO
21 POLD2 POLD2 POLD2 8508 -0.0087 0.2 NO
22 POLE3 POLE3 POLE3 8982 -0.015 0.18 NO
23 MBD4 MBD4 MBD4 9051 -0.016 0.19 NO
24 APEX2 APEX2 APEX2 9211 -0.018 0.2 NO
25 TDG TDG TDG 9541 -0.023 0.2 NO
26 NEIL3 NEIL3 NEIL3 9757 -0.027 0.2 NO
27 POLE4 POLE4 POLE4 9916 -0.029 0.22 NO
28 PARP4 PARP4 PARP4 9926 -0.029 0.24 NO
29 FEN1 FEN1 FEN1 10727 -0.041 0.22 NO
30 POLD3 POLD3 POLD3 11202 -0.05 0.23 NO
31 POLD1 POLD1 POLD1 13147 -0.094 0.19 NO
32 MUTYH MUTYH MUTYH 14037 -0.12 0.23 NO

Figure S9.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

Figure S10.  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 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 POLD4 POLD4 POLD4 1733 0.14 -0.032 YES
2 MNAT1 MNAT1 MNAT1 2016 0.12 0.0081 YES
3 ERCC4 ERCC4 ERCC4 2134 0.12 0.055 YES
4 CCNH CCNH CCNH 2418 0.1 0.087 YES
5 XPA XPA XPA 2699 0.093 0.11 YES
6 CDK7 CDK7 CDK7 2805 0.09 0.15 YES
7 GTF2H2 GTF2H2 GTF2H2 2977 0.084 0.18 YES
8 CETN2 CETN2 CETN2 3131 0.08 0.21 YES
9 XPC XPC XPC 3530 0.07 0.22 YES
10 GTF2H3 GTF2H3 GTF2H3 3613 0.069 0.25 YES
11 DDB2 DDB2 DDB2 3799 0.064 0.26 YES
12 RPA3 RPA3 RPA3 4438 0.051 0.25 YES
13 GTF2H5 GTF2H5 GTF2H5 4520 0.049 0.27 YES
14 RFC1 RFC1 RFC1 4758 0.045 0.28 YES
15 RFC5 RFC5 RFC5 5243 0.036 0.27 NO
16 ERCC8 ERCC8 ERCC8 6356 0.02 0.22 NO
17 DDB1 DDB1 DDB1 6859 0.013 0.2 NO
18 LIG1 LIG1 LIG1 6955 0.011 0.2 NO
19 ERCC6 ERCC6 ERCC6 6973 0.011 0.2 NO
20 CUL4A CUL4A CUL4A 7212 0.008 0.19 NO
21 ERCC2 ERCC2 ERCC2 7261 0.0074 0.19 NO
22 POLE POLE POLE 7326 0.0064 0.19 NO
23 POLE2 POLE2 POLE2 7506 0.0044 0.18 NO
24 CUL4B CUL4B CUL4B 7636 0.0025 0.18 NO
25 ERCC3 ERCC3 ERCC3 8131 -0.004 0.15 NO
26 ERCC1 ERCC1 ERCC1 8160 -0.0043 0.15 NO
27 PCNA PCNA PCNA 8347 -0.0067 0.15 NO
28 POLD2 POLD2 POLD2 8508 -0.0087 0.14 NO
29 GTF2H1 GTF2H1 GTF2H1 8518 -0.0088 0.14 NO
30 ERCC5 ERCC5 ERCC5 8891 -0.014 0.13 NO
31 POLE3 POLE3 POLE3 8982 -0.015 0.13 NO
32 RAD23A RAD23A RAD23A 8983 -0.015 0.14 NO
33 RBX1 RBX1 RBX1 9729 -0.026 0.11 NO
34 POLE4 POLE4 POLE4 9916 -0.029 0.11 NO
35 RPA2 RPA2 RPA2 10037 -0.031 0.12 NO
36 RPA1 RPA1 RPA1 10321 -0.035 0.12 NO
37 POLD3 POLD3 POLD3 11202 -0.05 0.097 NO
38 GTF2H4 GTF2H4 GTF2H4 11628 -0.058 0.1 NO
39 RFC2 RFC2 RFC2 11974 -0.065 0.11 NO
40 RFC3 RFC3 RFC3 12306 -0.072 0.13 NO
41 POLD1 POLD1 POLD1 13147 -0.094 0.12 NO
42 RFC4 RFC4 RFC4 13286 -0.099 0.16 NO
43 RPA4 RPA4 RPA4 16185 -0.24 0.12 NO

Figure S11.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S12.  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 SPHINGOLIPID METABOLISM

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 ABAT ABAT ABAT 90 0.45 0.18 YES
2 ALDH6A1 ALDH6A1 ALDH6A1 1214 0.18 0.19 YES
3 ACSS3 ACSS3 ACSS3 2075 0.12 0.19 YES
4 ALDH3A2 ALDH3A2 ALDH3A2 2414 0.1 0.21 YES
5 LDHAL6A LDHAL6A LDHAL6A 3130 0.08 0.21 YES
6 ACSS1 ACSS1 ACSS1 3208 0.078 0.23 YES
7 SUCLG2 SUCLG2 SUCLG2 3219 0.078 0.26 YES
8 ACACA ACACA ACACA 3261 0.077 0.29 YES
9 PCCB PCCB PCCB 4836 0.043 0.23 NO
10 ACAT1 ACAT1 ACAT1 4907 0.042 0.24 NO
11 MUT MUT MUT 5095 0.039 0.24 NO
12 MCEE MCEE MCEE 5107 0.039 0.26 NO
13 SUCLA2 SUCLA2 SUCLA2 5552 0.032 0.25 NO
14 ACACB ACACB ACACB 6089 0.023 0.23 NO
15 PCCA PCCA PCCA 6742 0.014 0.2 NO
16 ALDH9A1 ALDH9A1 ALDH9A1 6746 0.014 0.2 NO
17 ECHS1 ECHS1 ECHS1 6942 0.012 0.2 NO
18 HIBCH HIBCH HIBCH 7887 -0.00075 0.15 NO
19 MLYCD MLYCD MLYCD 8313 -0.0062 0.13 NO
20 LDHA LDHA LDHA 8436 -0.0077 0.12 NO
21 ACADM ACADM ACADM 9234 -0.019 0.086 NO
22 ACSS2 ACSS2 ACSS2 9529 -0.023 0.08 NO
23 HADHA HADHA HADHA 9888 -0.028 0.072 NO
24 ALDH7A1 ALDH7A1 ALDH7A1 10039 -0.031 0.076 NO
25 SUCLG1 SUCLG1 SUCLG1 10698 -0.041 0.057 NO
26 ALDH1B1 ALDH1B1 ALDH1B1 10741 -0.042 0.071 NO
27 ACAT2 ACAT2 ACAT2 11475 -0.055 0.054 NO
28 EHHADH EHHADH EHHADH 12181 -0.069 0.043 NO
29 ALDH2 ALDH2 ALDH2 13116 -0.093 0.03 NO
30 LDHAL6B LDHAL6B LDHAL6B 16860 -0.3 -0.053 NO
31 LDHB LDHB LDHB 17023 -0.32 0.069 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 SPHINGOLIPID METABOLISM.

Figure S14.  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 PYRUVATE METABOLISM

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 CACNA2D2 CACNA2D2 CACNA2D2 16 0.56 0.077 YES
2 CACNG1 CACNG1 CACNG1 205 0.38 0.12 YES
3 CACNG4 CACNG4 CACNG4 234 0.37 0.17 YES
4 CACNA1D CACNA1D CACNA1D 281 0.35 0.22 YES
5 COX6C COX6C COX6C 432 0.3 0.25 YES
6 CACNA1F CACNA1F CACNA1F 486 0.29 0.28 YES
7 ATP1A4 ATP1A4 ATP1A4 596 0.26 0.32 YES
8 TNNI3 TNNI3 TNNI3 1143 0.18 0.31 YES
9 CACNG6 CACNG6 CACNG6 1361 0.16 0.32 YES
10 COX6A2 COX6A2 COX6A2 2264 0.11 0.29 NO
11 CACNB2 CACNB2 CACNB2 2879 0.087 0.26 NO
12 CACNA2D4 CACNA2D4 CACNA2D4 3125 0.08 0.26 NO
13 ATP1A3 ATP1A3 ATP1A3 3297 0.076 0.26 NO
14 CACNB3 CACNB3 CACNB3 3537 0.07 0.26 NO
15 COX6A1 COX6A1 COX6A1 3677 0.067 0.26 NO
16 ATP1A2 ATP1A2 ATP1A2 3727 0.066 0.27 NO
17 UQCRQ UQCRQ UQCRQ 4273 0.054 0.25 NO
18 COX7C COX7C COX7C 4449 0.05 0.24 NO
19 SLC9A1 SLC9A1 SLC9A1 4478 0.05 0.25 NO
20 TNNC1 TNNC1 TNNC1 5211 0.037 0.21 NO
21 UQCR11 UQCR11 UQCR11 5321 0.035 0.21 NO
22 COX7A2 COX7A2 COX7A2 6616 0.016 0.14 NO
23 COX8A COX8A COX8A 7149 0.0088 0.12 NO
24 ATP1B1 ATP1B1 ATP1B1 7371 0.0059 0.1 NO
25 ATP2A2 ATP2A2 ATP2A2 7451 0.005 0.1 NO
26 COX7A1 COX7A1 COX7A1 7507 0.0044 0.098 NO
27 TPM3 TPM3 TPM3 7583 0.0033 0.095 NO
28 CACNA2D1 CACNA2D1 CACNA2D1 7619 0.0028 0.093 NO
29 UQCRC1 UQCRC1 UQCRC1 7844 -0.00022 0.081 NO
30 COX4I2 COX4I2 COX4I2 8245 -0.0054 0.06 NO
31 CYC1 CYC1 CYC1 8348 -0.0067 0.055 NO
32 COX7A2L COX7A2L COX7A2L 8364 -0.0069 0.055 NO
33 UQCR10 UQCR10 UQCR10 8814 -0.013 0.032 NO
34 UQCRB UQCRB UQCRB 9441 -0.022 0.00094 NO
35 COX6B1 COX6B1 COX6B1 9462 -0.022 0.0029 NO
36 COX5B COX5B COX5B 10317 -0.035 -0.039 NO
37 COX5A COX5A COX5A 10347 -0.035 -0.036 NO
38 COX7B COX7B COX7B 10348 -0.035 -0.031 NO
39 CACNA1S CACNA1S CACNA1S 10657 -0.04 -0.042 NO
40 TPM1 TPM1 TPM1 10659 -0.04 -0.037 NO
41 ACTC1 ACTC1 ACTC1 11093 -0.048 -0.054 NO
42 CACNA1C CACNA1C CACNA1C 11220 -0.05 -0.054 NO
43 UQCRFS1 UQCRFS1 UQCRFS1 11268 -0.051 -0.05 NO
44 TPM4 TPM4 TPM4 11337 -0.052 -0.046 NO
45 CACNB4 CACNB4 CACNB4 11812 -0.062 -0.064 NO
46 SLC8A1 SLC8A1 SLC8A1 12018 -0.066 -0.066 NO
47 ATP1A1 ATP1A1 ATP1A1 12366 -0.074 -0.075 NO
48 MYL3 MYL3 MYL3 12498 -0.076 -0.071 NO
49 COX4I1 COX4I1 COX4I1 12701 -0.081 -0.071 NO
50 CACNA2D3 CACNA2D3 CACNA2D3 12855 -0.086 -0.068 NO
51 CACNB1 CACNB1 CACNB1 12882 -0.086 -0.057 NO
52 MYL2 MYL2 MYL2 13679 -0.11 -0.085 NO
53 ATP1B3 ATP1B3 ATP1B3 13689 -0.11 -0.07 NO
54 MYH6 MYH6 MYH6 13932 -0.12 -0.067 NO
55 ATP1B2 ATP1B2 ATP1B2 14017 -0.12 -0.054 NO
56 UQCRH UQCRH UQCRH 14073 -0.12 -0.04 NO
57 COX6B2 COX6B2 COX6B2 14209 -0.13 -0.03 NO
58 MYH7 MYH7 MYH7 14638 -0.15 -0.032 NO
59 TPM2 TPM2 TPM2 14869 -0.16 -0.023 NO
60 UQCRHL UQCRHL UQCRHL 14957 -0.16 -0.0053 NO
61 RYR2 RYR2 RYR2 15979 -0.23 -0.03 NO
62 SLC9A6 SLC9A6 SLC9A6 16599 -0.28 -0.026 NO
63 FXYD2 FXYD2 FXYD2 17692 -0.41 -0.029 NO
64 TNNT2 TNNT2 TNNT2 17832 -0.44 0.024 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 PYRUVATE METABOLISM.

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

genes ES table in pathway: KEGG PROPANOATE METABOLISM

Table 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 DEGS2 DEGS2 DEGS2 60 0.48 0.1 YES
2 UGCG UGCG UGCG 303 0.34 0.17 YES
3 SMPD3 SMPD3 SMPD3 333 0.33 0.24 YES
4 ACER2 ACER2 ACER2 519 0.28 0.29 YES
5 ASAH1 ASAH1 ASAH1 1779 0.13 0.25 NO
6 ASAH2 ASAH2 ASAH2 1849 0.13 0.28 NO
7 GALC GALC GALC 3262 0.077 0.22 NO
8 SPTLC2 SPTLC2 SPTLC2 3627 0.068 0.21 NO
9 NEU3 NEU3 NEU3 3914 0.061 0.21 NO
10 SGPL1 SGPL1 SGPL1 4406 0.051 0.19 NO
11 SPHK2 SPHK2 SPHK2 4446 0.05 0.2 NO
12 NEU1 NEU1 NEU1 4484 0.05 0.21 NO
13 GBA GBA GBA 5999 0.025 0.14 NO
14 SPTLC1 SPTLC1 SPTLC1 6115 0.023 0.13 NO
15 KDSR KDSR KDSR 6666 0.016 0.11 NO
16 SMPD2 SMPD2 SMPD2 6914 0.012 0.096 NO
17 SMPD1 SMPD1 SMPD1 7014 0.011 0.093 NO
18 ARSA ARSA ARSA 7452 0.005 0.07 NO
19 SMPD4 SMPD4 SMPD4 8461 -0.0081 0.017 NO
20 GLA GLA GLA 8619 -0.01 0.01 NO
21 NEU4 NEU4 NEU4 9111 -0.017 -0.013 NO
22 GLB1 GLB1 GLB1 9536 -0.023 -0.031 NO
23 SGMS1 SGMS1 SGMS1 9778 -0.027 -0.038 NO
24 ACER3 ACER3 ACER3 10045 -0.031 -0.046 NO
25 SGPP1 SGPP1 SGPP1 10061 -0.031 -0.04 NO
26 PPAP2C PPAP2C PPAP2C 11255 -0.051 -0.094 NO
27 DEGS1 DEGS1 DEGS1 11283 -0.051 -0.084 NO
28 ACER1 ACER1 ACER1 11831 -0.062 -0.1 NO
29 PPAP2A PPAP2A PPAP2A 12808 -0.084 -0.14 NO
30 CERK CERK CERK 12820 -0.084 -0.12 NO
31 B4GALT6 B4GALT6 B4GALT6 13656 -0.11 -0.14 NO
32 PPAP2B PPAP2B PPAP2B 14441 -0.14 -0.15 NO
33 SGMS2 SGMS2 SGMS2 14765 -0.15 -0.13 NO
34 SPHK1 SPHK1 SPHK1 16541 -0.27 -0.17 NO
35 SGPP2 SGPP2 SGPP2 16550 -0.27 -0.11 NO
36 GAL3ST1 GAL3ST1 GAL3ST1 16700 -0.29 -0.055 NO
37 UGT8 UGT8 UGT8 18206 -0.64 0.0038 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 PROPANOATE METABOLISM.

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

genes ES table in pathway: KEGG BUTANOATE METABOLISM

Table 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 SEPSECS SEPSECS SEPSECS 1117 0.18 0.046 YES
2 EARS2 EARS2 EARS2 1951 0.12 0.072 YES
3 HARS2 HARS2 HARS2 3947 0.06 -0.0017 YES
4 IARS2 IARS2 IARS2 3976 0.06 0.032 YES
5 DARS2 DARS2 DARS2 4193 0.056 0.052 YES
6 VARS2 VARS2 VARS2 4523 0.049 0.063 YES
7 LARS2 LARS2 LARS2 4840 0.043 0.071 YES
8 RARS RARS RARS 5490 0.032 0.054 YES
9 FARS2 FARS2 FARS2 5589 0.031 0.067 YES
10 NARS NARS NARS 5937 0.026 0.063 YES
11 HARS HARS HARS 6059 0.024 0.07 YES
12 LARS LARS LARS 6791 0.014 0.038 YES
13 SARS SARS SARS 7321 0.0065 0.013 YES
14 WARS2 WARS2 WARS2 7397 0.0056 0.012 YES
15 FARSA FARSA FARSA 7539 0.0041 0.0064 YES
16 MTFMT MTFMT MTFMT 7895 -0.00086 -0.012 YES
17 TARSL2 TARSL2 TARSL2 8046 -0.003 -0.019 YES
18 QARS QARS QARS 8434 -0.0077 -0.036 YES
19 IARS IARS IARS 8466 -0.0081 -0.033 YES
20 CARS CARS CARS 8786 -0.012 -0.043 YES
21 YARS2 YARS2 YARS2 9253 -0.019 -0.057 YES
22 NARS2 NARS2 NARS2 9317 -0.02 -0.049 YES
23 EPRS EPRS EPRS 9432 -0.022 -0.043 YES
24 PARS2 PARS2 PARS2 9775 -0.027 -0.046 YES
25 MARS MARS MARS 9860 -0.028 -0.034 YES
26 MARS2 MARS2 MARS2 9872 -0.028 -0.018 YES
27 FARSB FARSB FARSB 9919 -0.029 -0.004 YES
28 RARS2 RARS2 RARS2 10805 -0.043 -0.028 YES
29 DARS DARS DARS 10923 -0.045 -0.0079 YES
30 AARS AARS AARS 10930 -0.045 0.018 YES
31 CARS2 CARS2 CARS2 10994 -0.046 0.041 YES
32 PSTK PSTK PSTK 11065 -0.047 0.065 YES
33 SARS2 SARS2 SARS2 11242 -0.05 0.085 YES
34 TARS TARS TARS 11266 -0.051 0.11 YES
35 AARS2 AARS2 AARS2 11743 -0.06 0.12 YES
36 VARS VARS VARS 11805 -0.062 0.16 YES
37 YARS YARS YARS 11970 -0.065 0.18 YES
38 GARS GARS GARS 12383 -0.074 0.2 YES
39 KARS KARS KARS 12916 -0.088 0.23 YES
40 WARS WARS WARS 13840 -0.12 0.24 YES

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 BUTANOATE METABOLISM.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype 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 0.55 1.6 0.022 0.51 0.68 0.26 0.075 0.24 0.3 0.15
BIOCARTA RACCYCD PATHWAY 25 genes.ES.table 0.39 1.6 0.065 0.59 0.79 0.08 0.039 0.077 0.36 0.19
KEGG CYSTEINE AND METHIONINE METABOLISM 32 genes.ES.table 0.45 1.4 0.058 0.62 0.92 0.38 0.19 0.3 0.42 0.21
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.44 1.9 0.0019 0.24 0.13 0.23 0.17 0.19 0 0.088
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES 25 genes.ES.table 0.74 1.8 0 0.33 0.38 0.44 0.096 0.4 0 0.083
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.35 1.4 0.16 0.64 0.96 0.5 0.34 0.33 0.47 0.2
KEGG RNA POLYMERASE 28 genes.ES.table 0.44 1.5 0.12 0.69 0.9 0.64 0.37 0.4 0.46 0.24
KEGG DNA REPLICATION 35 genes.ES.table 0.59 1.5 0.099 0.59 0.83 0.54 0.22 0.43 0.37 0.19
KEGG SPLICEOSOME 125 genes.ES.table 0.35 1.4 0.15 0.61 0.94 0.52 0.38 0.32 0.43 0.2
KEGG PROTEASOME 42 genes.ES.table 0.59 1.7 0.053 0.48 0.56 0.79 0.35 0.51 0.24 0.14
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 AADAT AADAT AADAT 167 0.57 0.12 YES
2 BBOX1 BBOX1 BBOX1 305 0.5 0.22 YES
3 SUV39H2 SUV39H2 SUV39H2 937 0.34 0.26 YES
4 OGDHL OGDHL OGDHL 1371 0.28 0.3 YES
5 PLOD1 PLOD1 PLOD1 1999 0.22 0.32 YES
6 PLOD2 PLOD2 PLOD2 2472 0.18 0.33 YES
7 PIPOX PIPOX PIPOX 2764 0.17 0.35 YES
8 PLOD3 PLOD3 PLOD3 2785 0.17 0.39 YES
9 ACAT2 ACAT2 ACAT2 2895 0.16 0.42 YES
10 SUV39H1 SUV39H1 SUV39H1 3137 0.15 0.44 YES
11 ALDH1B1 ALDH1B1 ALDH1B1 4993 0.084 0.36 NO
12 SETD8 SETD8 SETD8 5111 0.081 0.37 NO
13 DOT1L DOT1L DOT1L 5969 0.062 0.33 NO
14 EHMT2 EHMT2 EHMT2 6367 0.054 0.32 NO
15 ALDH7A1 ALDH7A1 ALDH7A1 6867 0.042 0.31 NO
16 SETDB1 SETDB1 SETDB1 7156 0.036 0.3 NO
17 WHSC1 WHSC1 WHSC1 7763 0.024 0.27 NO
18 TMLHE TMLHE TMLHE 7922 0.022 0.27 NO
19 OGDH OGDH OGDH 8056 0.019 0.26 NO
20 HADHA HADHA HADHA 8162 0.017 0.26 NO
21 DLST DLST DLST 9036 0.00072 0.21 NO
22 AASDHPPT AASDHPPT AASDHPPT 9173 -0.002 0.21 NO
23 ECHS1 ECHS1 ECHS1 9481 -0.008 0.19 NO
24 SUV420H1 SUV420H1 SUV420H1 9856 -0.015 0.18 NO
25 NSD1 NSD1 NSD1 9959 -0.017 0.17 NO
26 HADH HADH HADH 9994 -0.018 0.18 NO
27 SETD1A SETD1A SETD1A 10033 -0.018 0.18 NO
28 ALDH9A1 ALDH9A1 ALDH9A1 10121 -0.02 0.18 NO
29 SETMAR SETMAR SETMAR 10636 -0.03 0.16 NO
30 ACAT1 ACAT1 ACAT1 10986 -0.036 0.14 NO
31 SUV420H2 SUV420H2 SUV420H2 11061 -0.038 0.15 NO
32 GCDH GCDH GCDH 11257 -0.042 0.15 NO
33 ALDH2 ALDH2 ALDH2 11271 -0.042 0.16 NO
34 SETD1B SETD1B SETD1B 11591 -0.049 0.15 NO
35 SETD2 SETD2 SETD2 11733 -0.053 0.15 NO
36 EHMT1 EHMT1 EHMT1 12305 -0.065 0.14 NO
37 ASH1L ASH1L ASH1L 12971 -0.083 0.12 NO
38 AASDH AASDH AASDH 12987 -0.084 0.14 NO
39 SETD7 SETD7 SETD7 13227 -0.09 0.14 NO
40 WHSC1L1 WHSC1L1 WHSC1L1 13326 -0.093 0.16 NO
41 SETDB2 SETDB2 SETDB2 14137 -0.12 0.14 NO
42 ALDH3A2 ALDH3A2 ALDH3A2 15147 -0.16 0.12 NO
43 AASS AASS AASS 16244 -0.23 0.11 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 RACCYCD 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 CCNE1 CCNE1 CCNE1 4 0.88 0.04 YES
2 SMC1B SMC1B SMC1B 67 0.66 0.067 YES
3 ORC6L ORC6L ORC6L 125 0.6 0.092 YES
4 ORC1L ORC1L ORC1L 135 0.59 0.12 YES
5 CDC25A CDC25A CDC25A 190 0.56 0.14 YES
6 CDC45 CDC45 CDC45 203 0.55 0.17 YES
7 TTK TTK TTK 255 0.52 0.19 YES
8 CDC20 CDC20 CDC20 283 0.51 0.21 YES
9 E2F2 E2F2 E2F2 348 0.48 0.23 YES
10 CDKN2A CDKN2A CDKN2A 400 0.46 0.25 YES
11 PLK1 PLK1 PLK1 508 0.43 0.26 YES
12 CCNB2 CCNB2 CCNB2 515 0.43 0.28 YES
13 BUB1 BUB1 BUB1 574 0.41 0.3 YES
14 CCNA2 CCNA2 CCNA2 615 0.4 0.31 YES
15 SKP2 SKP2 SKP2 649 0.39 0.33 YES
16 PTTG1 PTTG1 PTTG1 693 0.38 0.34 YES
17 CDK6 CDK6 CDK6 709 0.38 0.36 YES
18 CHEK1 CHEK1 CHEK1 766 0.36 0.37 YES
19 E2F1 E2F1 E2F1 954 0.33 0.38 YES
20 CCNA1 CCNA1 CCNA1 965 0.33 0.39 YES
21 BUB1B BUB1B BUB1B 1002 0.33 0.41 YES
22 CDC25C CDC25C CDC25C 1023 0.32 0.42 YES
23 CDC6 CDC6 CDC6 1032 0.32 0.44 YES
24 CDC7 CDC7 CDC7 1101 0.31 0.45 YES
25 PKMYT1 PKMYT1 PKMYT1 1213 0.3 0.45 YES
26 MAD2L1 MAD2L1 MAD2L1 1242 0.29 0.46 YES
27 CCNE2 CCNE2 CCNE2 1365 0.28 0.47 YES
28 CDK1 CDK1 CDK1 1374 0.28 0.48 YES
29 E2F3 E2F3 E2F3 1383 0.28 0.5 YES
30 CHEK2 CHEK2 CHEK2 1436 0.27 0.51 YES
31 CDC25B CDC25B CDC25B 1477 0.27 0.52 YES
32 ESPL1 ESPL1 ESPL1 1493 0.26 0.53 YES
33 CCNB1 CCNB1 CCNB1 1911 0.22 0.51 YES
34 MCM2 MCM2 MCM2 1977 0.22 0.52 YES
35 MCM5 MCM5 MCM5 2036 0.21 0.53 YES
36 MCM4 MCM4 MCM4 2100 0.21 0.53 YES
37 MCM7 MCM7 MCM7 2121 0.21 0.54 YES
38 RBL1 RBL1 RBL1 2186 0.2 0.55 YES
39 MCM6 MCM6 MCM6 2196 0.2 0.56 YES
40 HDAC2 HDAC2 HDAC2 2450 0.18 0.55 YES
41 E2F5 E2F5 E2F5 2522 0.18 0.56 YES
42 PTTG2 PTTG2 PTTG2 2524 0.18 0.56 YES
43 MAD2L2 MAD2L2 MAD2L2 2638 0.18 0.57 YES
44 CDKN2C CDKN2C CDKN2C 2733 0.17 0.57 YES
45 SFN SFN SFN 3144 0.15 0.55 NO
46 TFDP1 TFDP1 TFDP1 3280 0.14 0.55 NO
47 MCM3 MCM3 MCM3 3307 0.14 0.56 NO
48 TFDP2 TFDP2 TFDP2 3463 0.14 0.56 NO
49 CDKN2D CDKN2D CDKN2D 3624 0.13 0.55 NO
50 E2F4 E2F4 E2F4 3668 0.13 0.56 NO
51 PCNA PCNA PCNA 3962 0.12 0.55 NO
52 YWHAQ YWHAQ YWHAQ 3992 0.11 0.55 NO
53 CDK4 CDK4 CDK4 4235 0.11 0.54 NO
54 MYC MYC MYC 4309 0.1 0.54 NO
55 PRKDC PRKDC PRKDC 4619 0.095 0.53 NO
56 TGFB2 TGFB2 TGFB2 4818 0.088 0.52 NO
57 CDC14B CDC14B CDC14B 5056 0.083 0.51 NO
58 YWHAZ YWHAZ YWHAZ 5085 0.082 0.51 NO
59 RBX1 RBX1 RBX1 5139 0.081 0.52 NO
60 CDK2 CDK2 CDK2 5278 0.077 0.51 NO
61 ANAPC1 ANAPC1 ANAPC1 5393 0.074 0.51 NO
62 CDKN2B CDKN2B CDKN2B 5502 0.072 0.51 NO
63 RAD21 RAD21 RAD21 5564 0.071 0.51 NO
64 CUL1 CUL1 CUL1 5608 0.07 0.51 NO
65 ORC3L ORC3L ORC3L 5665 0.069 0.51 NO
66 CCND3 CCND3 CCND3 5675 0.069 0.51 NO
67 YWHAH YWHAH YWHAH 5831 0.065 0.5 NO
68 CDC26 CDC26 CDC26 5876 0.064 0.5 NO
69 YWHAG YWHAG YWHAG 6083 0.06 0.5 NO
70 MAD1L1 MAD1L1 MAD1L1 6242 0.056 0.49 NO
71 SMC1A SMC1A SMC1A 6529 0.05 0.48 NO
72 ANAPC11 ANAPC11 ANAPC11 6730 0.046 0.47 NO
73 ORC5L ORC5L ORC5L 7169 0.036 0.44 NO
74 YWHAE YWHAE YWHAE 7575 0.028 0.42 NO
75 ATR ATR ATR 7611 0.028 0.42 NO
76 SMC3 SMC3 SMC3 7826 0.023 0.41 NO
77 ZBTB17 ZBTB17 ZBTB17 7926 0.022 0.41 NO
78 GADD45A GADD45A GADD45A 7976 0.02 0.41 NO
79 GSK3B GSK3B GSK3B 8025 0.02 0.4 NO
80 ANAPC10 ANAPC10 ANAPC10 8026 0.019 0.4 NO
81 HDAC1 HDAC1 HDAC1 8117 0.018 0.4 NO
82 ANAPC7 ANAPC7 ANAPC7 8167 0.017 0.4 NO
83 CDKN1C CDKN1C CDKN1C 8361 0.013 0.39 NO
84 ANAPC5 ANAPC5 ANAPC5 8449 0.012 0.38 NO
85 CDC16 CDC16 CDC16 8458 0.011 0.38 NO
86 SMAD2 SMAD2 SMAD2 8709 0.0068 0.37 NO
87 ORC2L ORC2L ORC2L 9082 -3e-05 0.35 NO
88 STAG1 STAG1 STAG1 9237 -0.0035 0.34 NO
89 ORC4L ORC4L ORC4L 9559 -0.0094 0.33 NO
90 YWHAB YWHAB YWHAB 9909 -0.016 0.31 NO
91 CCND2 CCND2 CCND2 10075 -0.019 0.3 NO
92 WEE1 WEE1 WEE1 10103 -0.02 0.3 NO
93 WEE2 WEE2 WEE2 10215 -0.022 0.29 NO
94 ATM ATM ATM 10312 -0.024 0.29 NO
95 ABL1 ABL1 ABL1 10444 -0.026 0.28 NO
96 CDC27 CDC27 CDC27 10685 -0.031 0.27 NO
97 CDC23 CDC23 CDC23 10736 -0.032 0.27 NO
98 STAG2 STAG2 STAG2 10744 -0.032 0.27 NO
99 EP300 EP300 EP300 10754 -0.032 0.27 NO
100 ANAPC4 ANAPC4 ANAPC4 11069 -0.038 0.26 NO
101 TP53 TP53 TP53 11129 -0.039 0.26 NO
102 FZR1 FZR1 FZR1 11185 -0.04 0.25 NO
103 SMAD4 SMAD4 SMAD4 11672 -0.051 0.23 NO
104 GADD45B GADD45B GADD45B 11837 -0.055 0.22 NO
105 ANAPC13 ANAPC13 ANAPC13 12181 -0.062 0.21 NO
106 BUB3 BUB3 BUB3 12391 -0.067 0.2 NO
107 TGFB1 TGFB1 TGFB1 12651 -0.074 0.19 NO
108 CDKN1A CDKN1A CDKN1A 12820 -0.079 0.18 NO
109 CDK7 CDK7 CDK7 13004 -0.084 0.18 NO
110 CREBBP CREBBP CREBBP 13009 -0.084 0.18 NO
111 ANAPC2 ANAPC2 ANAPC2 13269 -0.091 0.17 NO
112 RBL2 RBL2 RBL2 13572 -0.1 0.16 NO
113 CDKN1B CDKN1B CDKN1B 14036 -0.12 0.14 NO
114 CCNB3 CCNB3 CCNB3 14394 -0.13 0.12 NO
115 MDM2 MDM2 MDM2 14430 -0.13 0.13 NO
116 SKP1 SKP1 SKP1 14557 -0.14 0.13 NO
117 RB1 RB1 RB1 15123 -0.16 0.1 NO
118 CCNH CCNH CCNH 15389 -0.17 0.096 NO
119 SMAD3 SMAD3 SMAD3 15476 -0.18 0.1 NO
120 CDC14A CDC14A CDC14A 15983 -0.21 0.081 NO
121 TGFB3 TGFB3 TGFB3 16933 -0.3 0.043 NO
122 GADD45G GADD45G GADD45G 17198 -0.34 0.044 NO
123 CCND1 CCND1 CCND1 17209 -0.34 0.059 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 RACCYCD PATHWAY.

Figure S24.  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 CYSTEINE AND METHIONINE METABOLISM

Table S13.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 B3GNT5 B3GNT5 B3GNT5 24 0.73 0.12 YES
2 B3GNT4 B3GNT4 B3GNT4 50 0.68 0.22 YES
3 FUT3 FUT3 FUT3 73 0.66 0.33 YES
4 ST8SIA1 ST8SIA1 ST8SIA1 131 0.6 0.42 YES
5 B3GNT3 B3GNT3 B3GNT3 211 0.54 0.5 YES
6 FUT5 FUT5 FUT5 479 0.44 0.56 YES
7 GCNT2 GCNT2 GCNT2 572 0.41 0.62 YES
8 ST3GAL6 ST3GAL6 ST3GAL6 573 0.41 0.68 YES
9 FUT4 FUT4 FUT4 1555 0.26 0.67 YES
10 FUT6 FUT6 FUT6 1669 0.24 0.7 YES
11 FUT7 FUT7 FUT7 1749 0.24 0.74 YES
12 ST3GAL4 ST3GAL4 ST3GAL4 3521 0.13 0.66 NO
13 B4GALT2 B4GALT2 B4GALT2 3893 0.12 0.66 NO
14 B4GALT4 B4GALT4 B4GALT4 5503 0.072 0.58 NO
15 B4GALT3 B4GALT3 B4GALT3 5534 0.072 0.59 NO
16 B3GNT2 B3GNT2 B3GNT2 7896 0.022 0.47 NO
17 B4GALT1 B4GALT1 B4GALT1 8437 0.012 0.44 NO
18 B3GALT2 B3GALT2 B3GALT2 8464 0.011 0.44 NO
19 ST3GAL3 ST3GAL3 ST3GAL3 9194 -0.0023 0.4 NO
20 B3GALT1 B3GALT1 B3GALT1 11301 -0.043 0.29 NO
21 ABO ABO ABO 13167 -0.088 0.2 NO
22 FUT2 FUT2 FUT2 13315 -0.093 0.21 NO
23 B3GALT5 B3GALT5 B3GALT5 13706 -0.1 0.2 NO
24 FUT1 FUT1 FUT1 14736 -0.14 0.17 NO
25 B3GNT1 B3GNT1 B3GNT1 14821 -0.14 0.19 NO

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

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

Table 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 IFNG IFNG IFNG 682 0.39 0.061 YES
2 PSMB9 PSMB9 PSMB9 2089 0.21 0.038 YES
3 PSMA8 PSMA8 PSMA8 2102 0.21 0.091 YES
4 PSME4 PSME4 PSME4 2328 0.19 0.13 YES
5 SHFM1 SHFM1 SHFM1 2813 0.17 0.14 YES
6 PSMD7 PSMD7 PSMD7 2889 0.16 0.18 YES
7 PSMB2 PSMB2 PSMB2 2911 0.16 0.22 YES
8 PSMA7 PSMA7 PSMA7 3402 0.14 0.23 YES
9 PSMB4 PSMB4 PSMB4 3767 0.12 0.24 YES
10 PSMD14 PSMD14 PSMD14 3951 0.12 0.26 YES
11 PSMD12 PSMD12 PSMD12 4208 0.11 0.28 YES
12 PSMD2 PSMD2 PSMD2 4330 0.1 0.29 YES
13 PSMA4 PSMA4 PSMA4 4596 0.095 0.3 YES
14 PSMC2 PSMC2 PSMC2 4664 0.093 0.32 YES
15 PSMD3 PSMD3 PSMD3 4701 0.092 0.35 YES
16 PSMC1 PSMC1 PSMC1 4750 0.09 0.37 YES
17 PSMA5 PSMA5 PSMA5 4881 0.087 0.38 YES
18 PSMD11 PSMD11 PSMD11 4903 0.086 0.4 YES
19 PSMB8 PSMB8 PSMB8 4943 0.085 0.42 YES
20 PSMC4 PSMC4 PSMC4 5153 0.08 0.43 YES
21 PSMB5 PSMB5 PSMB5 5198 0.079 0.45 YES
22 PSMB7 PSMB7 PSMB7 5253 0.078 0.46 YES
23 PSMB1 PSMB1 PSMB1 5318 0.076 0.48 YES
24 PSMC3 PSMC3 PSMC3 5451 0.073 0.49 YES
25 PSMA2 PSMA2 PSMA2 5517 0.072 0.51 YES
26 PSMA3 PSMA3 PSMA3 5557 0.071 0.52 YES
27 PSMB3 PSMB3 PSMB3 5595 0.07 0.54 YES
28 POMP POMP POMP 5668 0.069 0.55 YES
29 PSMD4 PSMD4 PSMD4 5912 0.064 0.56 YES
30 PSMD1 PSMD1 PSMD1 6021 0.061 0.57 YES
31 PSMB6 PSMB6 PSMB6 6107 0.059 0.58 YES
32 PSMD8 PSMD8 PSMD8 6270 0.056 0.58 YES
33 PSMD13 PSMD13 PSMD13 6401 0.053 0.59 YES
34 PSMA1 PSMA1 PSMA1 6712 0.046 0.58 NO
35 PSME2 PSME2 PSME2 7148 0.036 0.57 NO
36 PSMA6 PSMA6 PSMA6 7553 0.028 0.55 NO
37 PSMD6 PSMD6 PSMD6 8507 0.011 0.5 NO
38 PSMF1 PSMF1 PSMF1 9011 0.0011 0.48 NO
39 PSME3 PSME3 PSME3 9143 -0.0013 0.47 NO
40 PSMC5 PSMC5 PSMC5 9483 -0.0081 0.45 NO
41 PSMC6 PSMC6 PSMC6 10113 -0.02 0.42 NO
42 PSME1 PSME1 PSME1 13338 -0.093 0.27 NO

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

Figure S28.  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 GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES

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 ATP6V1C2 ATP6V1C2 ATP6V1C2 38 0.7 0.084 YES
2 CXCL1 CXCL1 CXCL1 181 0.56 0.14 YES
3 EGFR EGFR EGFR 217 0.54 0.21 YES
4 IL8 IL8 IL8 279 0.51 0.27 YES
5 MET MET MET 567 0.41 0.3 YES
6 ATP6V0A4 ATP6V0A4 ATP6V0A4 901 0.34 0.33 YES
7 ATP6V1E2 ATP6V1E2 ATP6V1E2 1073 0.32 0.36 YES
8 LYN LYN LYN 1361 0.28 0.38 YES
9 PLCG2 PLCG2 PLCG2 1508 0.26 0.4 YES
10 CCL5 CCL5 CCL5 1523 0.26 0.43 YES
11 PTPRZ1 PTPRZ1 PTPRZ1 1982 0.22 0.44 YES
12 ADAM17 ADAM17 ADAM17 3481 0.14 0.37 NO
13 MAPK12 MAPK12 MAPK12 3867 0.12 0.36 NO
14 HBEGF HBEGF HBEGF 3939 0.12 0.37 NO
15 CSK CSK CSK 4108 0.11 0.38 NO
16 SRC SRC SRC 4754 0.09 0.35 NO
17 F11R F11R F11R 4890 0.086 0.36 NO
18 NOD1 NOD1 NOD1 5372 0.075 0.34 NO
19 CASP3 CASP3 CASP3 5650 0.069 0.33 NO
20 ATP6V1F ATP6V1F ATP6V1F 5907 0.064 0.33 NO
21 GIT1 GIT1 GIT1 6014 0.061 0.33 NO
22 PLCG1 PLCG1 PLCG1 6475 0.052 0.31 NO
23 MAP3K14 MAP3K14 MAP3K14 6618 0.048 0.31 NO
24 MAPK14 MAPK14 MAPK14 6724 0.046 0.31 NO
25 ATP6V1B2 ATP6V1B2 ATP6V1B2 7108 0.037 0.29 NO
26 IKBKG IKBKG IKBKG 7504 0.029 0.27 NO
27 ATP6V0D2 ATP6V0D2 ATP6V0D2 7565 0.028 0.27 NO
28 ATP6V0A2 ATP6V0A2 ATP6V0A2 7596 0.028 0.28 NO
29 ATP6V0B ATP6V0B ATP6V0B 7598 0.028 0.28 NO
30 ATP6V0D1 ATP6V0D1 ATP6V0D1 7768 0.024 0.27 NO
31 RELA RELA RELA 7778 0.024 0.27 NO
32 RAC1 RAC1 RAC1 8126 0.018 0.26 NO
33 IGSF5 IGSF5 IGSF5 8141 0.017 0.26 NO
34 PTPN11 PTPN11 PTPN11 8296 0.014 0.25 NO
35 MAPK13 MAPK13 MAPK13 8519 0.01 0.24 NO
36 MAPK11 MAPK11 MAPK11 9010 0.0011 0.22 NO
37 ATP6V1A ATP6V1A ATP6V1A 9034 0.00073 0.21 NO
38 MAPK8 MAPK8 MAPK8 9146 -0.0013 0.21 NO
39 ATP6V1E1 ATP6V1E1 ATP6V1E1 9229 -0.0032 0.2 NO
40 MAPK10 MAPK10 MAPK10 9316 -0.005 0.2 NO
41 TCIRG1 TCIRG1 TCIRG1 9466 -0.0078 0.19 NO
42 NFKBIA NFKBIA NFKBIA 9533 -0.0088 0.19 NO
43 CHUK CHUK CHUK 10022 -0.018 0.16 NO
44 CDC42 CDC42 CDC42 10026 -0.018 0.17 NO
45 PAK1 PAK1 PAK1 10197 -0.021 0.16 NO
46 JUN JUN JUN 10221 -0.022 0.16 NO
47 NFKB1 NFKB1 NFKB1 10363 -0.025 0.16 NO
48 CXCR2 CXCR2 CXCR2 10894 -0.035 0.13 NO
49 ATP6V1C1 ATP6V1C1 ATP6V1C1 10935 -0.036 0.13 NO
50 ADAM10 ADAM10 ADAM10 10976 -0.036 0.14 NO
51 ATP6V0C ATP6V0C ATP6V0C 11016 -0.037 0.14 NO
52 ATP6V1D ATP6V1D ATP6V1D 11184 -0.04 0.14 NO
53 TJP1 TJP1 TJP1 11313 -0.043 0.13 NO
54 ATP6V1H ATP6V1H ATP6V1H 11495 -0.047 0.13 NO
55 ATP6V1G1 ATP6V1G1 ATP6V1G1 12219 -0.063 0.097 NO
56 ATP6V0E2 ATP6V0E2 ATP6V0E2 12867 -0.08 0.071 NO
57 ATP6AP1 ATP6AP1 ATP6AP1 12899 -0.081 0.08 NO
58 MAPK9 MAPK9 MAPK9 13498 -0.098 0.059 NO
59 ATP6V0A1 ATP6V0A1 ATP6V0A1 13553 -0.099 0.068 NO
60 MAP2K4 MAP2K4 MAP2K4 14418 -0.13 0.037 NO
61 ATP6V1B1 ATP6V1B1 ATP6V1B1 14431 -0.13 0.052 NO
62 CXCR1 CXCR1 CXCR1 15152 -0.16 0.032 NO
63 JAM3 JAM3 JAM3 15632 -0.18 0.028 NO
64 IKBKB IKBKB IKBKB 15932 -0.2 0.037 NO
65 JAM2 JAM2 JAM2 16427 -0.24 0.04 NO
66 ATP6V1G2 ATP6V1G2 ATP6V1G2 17845 -0.5 0.024 NO

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

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

genes ES table in pathway: KEGG AMINOACYL TRNA BIOSYNTHESIS

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 CCNE1 CCNE1 CCNE1 4 0.88 0.17 YES
2 CDC25A CDC25A CDC25A 190 0.56 0.26 YES
3 CDKN2A CDKN2A CDKN2A 400 0.46 0.34 YES
4 SKP2 SKP2 SKP2 649 0.39 0.4 YES
5 CDK6 CDK6 CDK6 709 0.38 0.47 YES
6 CCNA1 CCNA1 CCNA1 965 0.33 0.52 YES
7 CDK1 CDK1 CDK1 1374 0.28 0.55 YES
8 TFDP1 TFDP1 TFDP1 3280 0.14 0.47 NO
9 CDK4 CDK4 CDK4 4235 0.11 0.44 NO
10 TGFB2 TGFB2 TGFB2 4818 0.088 0.43 NO
11 CDK2 CDK2 CDK2 5278 0.077 0.42 NO
12 CDKN2B CDKN2B CDKN2B 5502 0.072 0.42 NO
13 DHFR DHFR DHFR 7211 0.035 0.33 NO
14 ATR ATR ATR 7611 0.028 0.31 NO
15 GSK3B GSK3B GSK3B 8025 0.02 0.3 NO
16 HDAC1 HDAC1 HDAC1 8117 0.018 0.29 NO
17 ATM ATM ATM 10312 -0.024 0.18 NO
18 ABL1 ABL1 ABL1 10444 -0.026 0.18 NO
19 TP53 TP53 TP53 11129 -0.039 0.14 NO
20 SMAD4 SMAD4 SMAD4 11672 -0.051 0.12 NO
21 TGFB1 TGFB1 TGFB1 12651 -0.074 0.086 NO
22 CDKN1A CDKN1A CDKN1A 12820 -0.079 0.092 NO
23 CDKN1B CDKN1B CDKN1B 14036 -0.12 0.047 NO
24 RB1 RB1 RB1 15123 -0.16 0.018 NO
25 SMAD3 SMAD3 SMAD3 15476 -0.18 0.032 NO
26 TGFB3 TGFB3 TGFB3 16933 -0.3 0.0091 NO
27 CCND1 CCND1 CCND1 17209 -0.34 0.058 NO

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

Figure S32.  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 RNA POLYMERASE

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 EGFR EGFR EGFR 217 0.54 0.073 YES
2 MMP1 MMP1 MMP1 269 0.52 0.15 YES
3 IL8 IL8 IL8 279 0.51 0.23 YES
4 E2F2 E2F2 E2F2 348 0.48 0.3 YES
5 CDKN2A CDKN2A CDKN2A 400 0.46 0.38 YES
6 DAPK1 DAPK1 DAPK1 883 0.34 0.4 YES
7 E2F3 E2F3 E2F3 1383 0.28 0.42 YES
8 MMP9 MMP9 MMP9 1391 0.28 0.46 YES
9 VEGFA VEGFA VEGFA 2807 0.17 0.41 NO
10 CDK4 CDK4 CDK4 4235 0.11 0.35 NO
11 MYC MYC MYC 4309 0.1 0.36 NO
12 TYMP TYMP TYMP 4415 0.1 0.37 NO
13 MAP2K1 MAP2K1 MAP2K1 6271 0.056 0.28 NO
14 NRAS NRAS NRAS 6685 0.047 0.26 NO
15 MAP2K2 MAP2K2 MAP2K2 6986 0.04 0.25 NO
16 HRAS HRAS HRAS 7176 0.036 0.25 NO
17 RAF1 RAF1 RAF1 7486 0.03 0.24 NO
18 CDH1 CDH1 CDH1 7591 0.028 0.24 NO
19 MAPK1 MAPK1 MAPK1 8012 0.02 0.22 NO
20 KRAS KRAS KRAS 8411 0.012 0.2 NO
21 DAPK3 DAPK3 DAPK3 8799 0.005 0.18 NO
22 RASSF1 RASSF1 RASSF1 8858 0.0039 0.17 NO
23 PGF PGF PGF 8923 0.0028 0.17 NO
24 ERBB2 ERBB2 ERBB2 8975 0.0018 0.17 NO
25 BRAF BRAF BRAF 9078 2e-05 0.16 NO
26 DAPK2 DAPK2 DAPK2 10283 -0.023 0.099 NO
27 VEGFB VEGFB VEGFB 10334 -0.024 0.1 NO
28 ARAF ARAF ARAF 10741 -0.032 0.083 NO
29 TP53 TP53 TP53 11129 -0.039 0.068 NO
30 MMP2 MMP2 MMP2 11606 -0.05 0.05 NO
31 VEGFC VEGFC VEGFC 11756 -0.053 0.05 NO
32 CDKN1A CDKN1A CDKN1A 12820 -0.079 0.0041 NO
33 THBS1 THBS1 THBS1 13662 -0.1 -0.026 NO
34 MAPK3 MAPK3 MAPK3 13922 -0.11 -0.022 NO
35 MDM2 MDM2 MDM2 14430 -0.13 -0.03 NO
36 RB1 RB1 RB1 15123 -0.16 -0.043 NO
37 FIGF FIGF FIGF 15525 -0.18 -0.037 NO
38 EGF EGF EGF 15739 -0.19 -0.018 NO
39 RPS6KA5 RPS6KA5 RPS6KA5 16513 -0.25 -0.02 NO
40 CCND1 CCND1 CCND1 17209 -0.34 -0.0052 NO
41 FGFR3 FGFR3 FGFR3 17546 -0.4 0.04 NO

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

Figure S34.  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 DNA REPLICATION

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 CCNE1 CCNE1 CCNE1 4 0.88 0.3 YES
2 CDK6 CDK6 CDK6 709 0.38 0.38 YES
3 TFDP1 TFDP1 TFDP1 3280 0.14 0.29 NO
4 CDK4 CDK4 CDK4 4235 0.11 0.28 NO
5 CDK2 CDK2 CDK2 5278 0.077 0.25 NO
6 PIK3CA PIK3CA PIK3CA 6235 0.056 0.21 NO
7 HRAS HRAS HRAS 7176 0.036 0.17 NO
8 RAF1 RAF1 RAF1 7486 0.03 0.17 NO
9 IKBKG IKBKG IKBKG 7504 0.029 0.18 NO
10 RELA RELA RELA 7778 0.024 0.17 NO
11 MAPK1 MAPK1 MAPK1 8012 0.02 0.16 NO
12 RAC1 RAC1 RAC1 8126 0.018 0.16 NO
13 AKT1 AKT1 AKT1 9353 -0.0059 0.097 NO
14 NFKBIA NFKBIA NFKBIA 9533 -0.0088 0.09 NO
15 CHUK CHUK CHUK 10022 -0.018 0.069 NO
16 PAK1 PAK1 PAK1 10197 -0.021 0.067 NO
17 RHOA RHOA RHOA 10252 -0.023 0.071 NO
18 NFKB1 NFKB1 NFKB1 10363 -0.025 0.074 NO
19 PIK3R1 PIK3R1 PIK3R1 12108 -0.06 -0.0016 NO
20 CDKN1A CDKN1A CDKN1A 12820 -0.079 -0.014 NO
21 MAPK3 MAPK3 MAPK3 13922 -0.11 -0.037 NO
22 CDKN1B CDKN1B CDKN1B 14036 -0.12 -0.0042 NO
23 RB1 RB1 RB1 15123 -0.16 -0.01 NO
24 IKBKB IKBKB IKBKB 15932 -0.2 0.015 NO
25 CCND1 CCND1 CCND1 17209 -0.34 0.058 NO

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

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

genes ES table in pathway: KEGG SPLICEOSOME

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 RPA4 RPA4 RPA4 918 0.34 0.022 YES
2 RFC4 RFC4 RFC4 1472 0.27 0.049 YES
3 DNA2 DNA2 DNA2 1497 0.26 0.1 YES
4 RNASEH1 RNASEH1 RNASEH1 1753 0.24 0.14 YES
5 PRIM2 PRIM2 PRIM2 1895 0.22 0.18 YES
6 MCM2 MCM2 MCM2 1977 0.22 0.22 YES
7 MCM5 MCM5 MCM5 2036 0.21 0.27 YES
8 MCM4 MCM4 MCM4 2100 0.21 0.31 YES
9 MCM7 MCM7 MCM7 2121 0.21 0.35 YES
10 MCM6 MCM6 MCM6 2196 0.2 0.39 YES
11 FEN1 FEN1 FEN1 2263 0.2 0.43 YES
12 POLE2 POLE2 POLE2 2541 0.18 0.45 YES
13 RFC3 RFC3 RFC3 2570 0.18 0.49 YES
14 RFC2 RFC2 RFC2 2796 0.17 0.51 YES
15 POLD1 POLD1 POLD1 2900 0.16 0.54 YES
16 RNASEH2A RNASEH2A RNASEH2A 3302 0.14 0.55 YES
17 MCM3 MCM3 MCM3 3307 0.14 0.58 YES
18 POLA2 POLA2 POLA2 3915 0.12 0.57 YES
19 PCNA PCNA PCNA 3962 0.12 0.59 YES
20 SSBP1 SSBP1 SSBP1 4451 0.099 0.59 NO
21 POLD3 POLD3 POLD3 4711 0.091 0.59 NO
22 POLD2 POLD2 POLD2 5170 0.08 0.59 NO
23 RPA1 RPA1 RPA1 6055 0.06 0.55 NO
24 POLE3 POLE3 POLE3 6355 0.054 0.55 NO
25 POLE4 POLE4 POLE4 6544 0.05 0.55 NO
26 POLE POLE POLE 6773 0.045 0.54 NO
27 RFC5 RFC5 RFC5 6793 0.044 0.55 NO
28 RPA2 RPA2 RPA2 7273 0.034 0.53 NO
29 RNASEH2B RNASEH2B RNASEH2B 7407 0.031 0.53 NO
30 LIG1 LIG1 LIG1 7464 0.03 0.54 NO
31 PRIM1 PRIM1 PRIM1 7699 0.026 0.53 NO
32 RPA3 RPA3 RPA3 8846 0.0041 0.47 NO
33 RNASEH2C RNASEH2C RNASEH2C 9804 -0.014 0.42 NO
34 RFC1 RFC1 RFC1 11701 -0.052 0.32 NO
35 POLD4 POLD4 POLD4 15429 -0.17 0.16 NO

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

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

genes ES table in pathway: KEGG PROTEASOME

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 RAD54L RAD54L RAD54L 307 0.5 0.1 YES
2 BLM BLM BLM 713 0.38 0.17 YES
3 RAD51 RAD51 RAD51 789 0.36 0.25 YES
4 XRCC2 XRCC2 XRCC2 831 0.35 0.33 YES
5 RPA4 RPA4 RPA4 918 0.34 0.4 YES
6 EME1 EME1 EME1 1153 0.31 0.46 YES
7 RAD54B RAD54B RAD54B 1612 0.25 0.49 YES
8 BRCA2 BRCA2 BRCA2 1828 0.23 0.53 YES
9 SHFM1 SHFM1 SHFM1 2813 0.17 0.52 YES
10 POLD1 POLD1 POLD1 2900 0.16 0.55 YES
11 RAD51L1 RAD51L1 RAD51L1 3036 0.16 0.58 YES
12 SSBP1 SSBP1 SSBP1 4451 0.099 0.53 NO
13 TOP3B TOP3B TOP3B 4622 0.094 0.54 NO
14 POLD3 POLD3 POLD3 4711 0.091 0.56 NO
15 XRCC3 XRCC3 XRCC3 4797 0.089 0.57 NO
16 POLD2 POLD2 POLD2 5170 0.08 0.57 NO
17 RPA1 RPA1 RPA1 6055 0.06 0.54 NO
18 MRE11A MRE11A MRE11A 6134 0.059 0.55 NO
19 RPA2 RPA2 RPA2 7273 0.034 0.49 NO
20 MUS81 MUS81 MUS81 7505 0.029 0.48 NO
21 TOP3A TOP3A TOP3A 7729 0.025 0.48 NO
22 RPA3 RPA3 RPA3 8846 0.0041 0.42 NO
23 NBN NBN NBN 8939 0.0025 0.41 NO
24 RAD51L3 RAD51L3 RAD51L3 11163 -0.04 0.3 NO
25 RAD52 RAD52 RAD52 11410 -0.045 0.3 NO
26 RAD50 RAD50 RAD50 15211 -0.16 0.13 NO
27 POLD4 POLD4 POLD4 15429 -0.17 0.16 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 PROTEASOME.

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

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 NO1 PATHWAY 27 genes.ES.table 0.52 1.3 0.14 0.18 0.98 0.56 0.32 0.38 0.14 0
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.67 1.9 0.0041 0.08 0.14 0.23 0.064 0.21 0 0.023
BIOCARTA ALK PATHWAY 34 genes.ES.table 0.56 1.6 0.0081 0.07 0.64 0.44 0.27 0.32 0.038 0
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.45 1.7 0.02 0.064 0.52 0.25 0.27 0.18 0.028 0
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.57 1.7 0.028 0.068 0.61 0.33 0.22 0.26 0.034 0
BIOCARTA BIOPEPTIDES PATHWAY 39 genes.ES.table 0.46 1.6 0.018 0.071 0.68 0.41 0.35 0.27 0.04 0
BIOCARTA HDAC PATHWAY 26 genes.ES.table 0.46 1.4 0.11 0.12 0.92 0.38 0.3 0.27 0.084 0
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.57 1.7 0.0042 0.059 0.42 0.33 0.2 0.27 0 0
BIOCARTA ERK PATHWAY 27 genes.ES.table 0.51 1.7 0.023 0.065 0.5 0.15 0.094 0.13 0.028 0
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.6 1.8 0 0.053 0.37 0.32 0.22 0.26 0 0
genes ES table in pathway: BIOCARTA NO1 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 PAK7 PAK7 PAK7 13 0.92 0.12 YES
2 FIGF FIGF FIGF 28 0.84 0.23 YES
3 HGF HGF HGF 639 0.46 0.26 YES
4 PAK3 PAK3 PAK3 974 0.39 0.29 YES
5 MET MET MET 1249 0.35 0.32 YES
6 PIK3CG PIK3CG PIK3CG 2125 0.26 0.31 YES
7 PIK3CD PIK3CD PIK3CD 2151 0.26 0.34 YES
8 TGFB3 TGFB3 TGFB3 2290 0.25 0.37 YES
9 TGFB2 TGFB2 TGFB2 2648 0.22 0.38 YES
10 AKT3 AKT3 AKT3 2691 0.22 0.4 YES
11 PGF PGF PGF 2820 0.21 0.42 YES
12 EPAS1 EPAS1 EPAS1 2831 0.21 0.45 YES
13 VEGFC VEGFC VEGFC 2890 0.21 0.48 YES
14 JUN JUN JUN 3155 0.19 0.49 YES
15 ETS1 ETS1 ETS1 3181 0.19 0.51 YES
16 PIK3R1 PIK3R1 PIK3R1 3343 0.18 0.53 YES
17 PIK3R5 PIK3R5 PIK3R5 3596 0.17 0.54 YES
18 TGFB1 TGFB1 TGFB1 4693 0.13 0.49 NO
19 TGFA TGFA TGFA 5596 0.096 0.46 NO
20 GAB1 GAB1 GAB1 6001 0.085 0.44 NO
21 RAPGEF1 RAPGEF1 RAPGEF1 6425 0.074 0.43 NO
22 ARNT2 ARNT2 ARNT2 6526 0.072 0.44 NO
23 VEGFB VEGFB VEGFB 7573 0.051 0.38 NO
24 FLCN FLCN FLCN 7614 0.05 0.39 NO
25 SOS2 SOS2 SOS2 7768 0.048 0.39 NO
26 EGLN2 EGLN2 EGLN2 8057 0.043 0.38 NO
27 CREBBP CREBBP CREBBP 8437 0.037 0.36 NO
28 EGLN3 EGLN3 EGLN3 8739 0.033 0.35 NO
29 ARNT ARNT ARNT 8756 0.032 0.35 NO
30 RAP1A RAP1A RAP1A 9079 0.028 0.34 NO
31 PAK6 PAK6 PAK6 9450 0.022 0.32 NO
32 CRK CRK CRK 9503 0.022 0.32 NO
33 RAP1B RAP1B RAP1B 9799 0.018 0.31 NO
34 ARAF ARAF ARAF 9948 0.016 0.3 NO
35 PDGFB PDGFB PDGFB 9949 0.016 0.3 NO
36 CDC42 CDC42 CDC42 10069 0.015 0.3 NO
37 EP300 EP300 EP300 10210 0.013 0.29 NO
38 PIK3CA PIK3CA PIK3CA 10229 0.012 0.29 NO
39 AKT2 AKT2 AKT2 10283 0.012 0.29 NO
40 MAPK3 MAPK3 MAPK3 10431 0.0097 0.28 NO
41 MAP2K2 MAP2K2 MAP2K2 10616 0.0077 0.28 NO
42 SOS1 SOS1 SOS1 10755 0.006 0.27 NO
43 MAPK1 MAPK1 MAPK1 11586 -0.0038 0.22 NO
44 PIK3R3 PIK3R3 PIK3R3 11719 -0.0054 0.22 NO
45 VHL VHL VHL 11806 -0.0065 0.21 NO
46 CRKL CRKL CRKL 11863 -0.0071 0.21 NO
47 PAK1 PAK1 PAK1 11875 -0.0072 0.21 NO
48 RAC1 RAC1 RAC1 12463 -0.015 0.18 NO
49 PIK3R2 PIK3R2 PIK3R2 12537 -0.016 0.18 NO
50 RAF1 RAF1 RAF1 12740 -0.018 0.17 NO
51 HIF1A HIF1A HIF1A 12763 -0.018 0.17 NO
52 AKT1 AKT1 AKT1 12834 -0.019 0.17 NO
53 NRAS NRAS NRAS 13027 -0.022 0.16 NO
54 PAK2 PAK2 PAK2 13210 -0.024 0.16 NO
55 GRB2 GRB2 GRB2 13272 -0.025 0.16 NO
56 KRAS KRAS KRAS 13800 -0.032 0.13 NO
57 PAK4 PAK4 PAK4 13812 -0.033 0.13 NO
58 PTPN11 PTPN11 PTPN11 14006 -0.036 0.13 NO
59 EGLN1 EGLN1 EGLN1 14223 -0.039 0.12 NO
60 MAP2K1 MAP2K1 MAP2K1 14227 -0.039 0.13 NO
61 PIK3CB PIK3CB PIK3CB 14850 -0.05 0.099 NO
62 TCEB2 TCEB2 TCEB2 14923 -0.051 0.1 NO
63 BRAF BRAF BRAF 15055 -0.053 0.1 NO
64 CUL2 CUL2 CUL2 15557 -0.063 0.082 NO
65 RBX1 RBX1 RBX1 15606 -0.064 0.088 NO
66 FH FH FH 15982 -0.073 0.077 NO
67 VEGFA VEGFA VEGFA 16764 -0.1 0.048 NO
68 SLC2A1 SLC2A1 SLC2A1 16926 -0.11 0.053 NO
69 TCEB1 TCEB1 TCEB1 17510 -0.16 0.042 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 NO1 PATHWAY.

Figure S42.  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 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 CALML3 CALML3 CALML3 171 0.67 0.037 YES
2 PYGM PYGM PYGM 186 0.66 0.081 YES
3 PCK1 PCK1 PCK1 253 0.62 0.12 YES
4 SLC2A4 SLC2A4 SLC2A4 308 0.59 0.16 YES
5 LIPE LIPE LIPE 314 0.58 0.2 YES
6 SOCS2 SOCS2 SOCS2 476 0.51 0.22 YES
7 PHKG1 PHKG1 PHKG1 622 0.46 0.25 YES
8 ACACB ACACB ACACB 822 0.42 0.27 YES
9 PDE3B PDE3B PDE3B 1073 0.37 0.28 YES
10 GCK GCK GCK 1172 0.36 0.3 YES
11 GYS2 GYS2 GYS2 1362 0.33 0.31 YES
12 SORBS1 SORBS1 SORBS1 1442 0.32 0.33 YES
13 PPARGC1A PPARGC1A PPARGC1A 1539 0.31 0.34 YES
14 FOXO1 FOXO1 FOXO1 1949 0.28 0.34 YES
15 SHC2 SHC2 SHC2 1951 0.28 0.36 YES
16 INPP5D INPP5D INPP5D 2088 0.26 0.37 YES
17 PIK3CG PIK3CG PIK3CG 2125 0.26 0.38 YES
18 PIK3CD PIK3CD PIK3CD 2151 0.26 0.4 YES
19 PDE3A PDE3A PDE3A 2288 0.25 0.41 YES
20 G6PC2 G6PC2 G6PC2 2346 0.24 0.42 YES
21 SOCS3 SOCS3 SOCS3 2463 0.23 0.44 YES
22 PPP1R3C PPP1R3C PPP1R3C 2547 0.23 0.45 YES
23 AKT3 AKT3 AKT3 2691 0.22 0.45 YES
24 IRS1 IRS1 IRS1 2837 0.21 0.46 YES
25 IRS2 IRS2 IRS2 2847 0.21 0.47 YES
26 MAPK10 MAPK10 MAPK10 2930 0.21 0.48 YES
27 PIK3R1 PIK3R1 PIK3R1 3343 0.18 0.47 YES
28 PIK3R5 PIK3R5 PIK3R5 3596 0.17 0.47 YES
29 SHC4 SHC4 SHC4 3817 0.16 0.47 YES
30 PRKAA2 PRKAA2 PRKAA2 3897 0.16 0.48 YES
31 SOCS1 SOCS1 SOCS1 3951 0.16 0.48 YES
32 PPP1R3B PPP1R3B PPP1R3B 4447 0.14 0.47 NO
33 FBP1 FBP1 FBP1 4606 0.13 0.47 NO
34 PRKAR1B PRKAR1B PRKAR1B 4737 0.13 0.47 NO
35 PRKAR2B PRKAR2B PRKAR2B 4864 0.12 0.47 NO
36 IRS4 IRS4 IRS4 5309 0.1 0.45 NO
37 PRKAA1 PRKAA1 PRKAA1 5342 0.1 0.46 NO
38 CALML6 CALML6 CALML6 5460 0.1 0.46 NO
39 CBLC CBLC CBLC 5776 0.091 0.45 NO
40 PRKACB PRKACB PRKACB 5859 0.089 0.45 NO
41 TRIP10 TRIP10 TRIP10 5870 0.088 0.46 NO
42 RAPGEF1 RAPGEF1 RAPGEF1 6425 0.074 0.43 NO
43 MKNK2 MKNK2 MKNK2 6649 0.069 0.42 NO
44 IKBKB IKBKB IKBKB 7005 0.061 0.41 NO
45 TSC1 TSC1 TSC1 7195 0.057 0.4 NO
46 RPS6 RPS6 RPS6 7220 0.057 0.4 NO
47 INPP5K INPP5K INPP5K 7296 0.056 0.4 NO
48 SOS2 SOS2 SOS2 7768 0.048 0.38 NO
49 RHOQ RHOQ RHOQ 7825 0.047 0.38 NO
50 PRKAB1 PRKAB1 PRKAB1 7951 0.045 0.38 NO
51 CBL CBL CBL 7991 0.044 0.38 NO
52 MKNK1 MKNK1 MKNK1 8075 0.042 0.38 NO
53 INSR INSR INSR 8442 0.037 0.36 NO
54 PRKAG2 PRKAG2 PRKAG2 8840 0.031 0.34 NO
55 PHKA2 PHKA2 PHKA2 9086 0.027 0.33 NO
56 CBLB CBLB CBLB 9134 0.027 0.33 NO
57 SHC1 SHC1 SHC1 9164 0.026 0.33 NO
58 BAD BAD BAD 9341 0.024 0.32 NO
59 PRKAB2 PRKAB2 PRKAB2 9461 0.022 0.31 NO
60 CRK CRK CRK 9503 0.022 0.31 NO
61 PRKAR2A PRKAR2A PRKAR2A 9528 0.022 0.31 NO
62 PRKX PRKX PRKX 9800 0.018 0.3 NO
63 ARAF ARAF ARAF 9948 0.016 0.29 NO
64 TSC2 TSC2 TSC2 10041 0.015 0.29 NO
65 PIK3CA PIK3CA PIK3CA 10229 0.012 0.28 NO
66 PRKCZ PRKCZ PRKCZ 10238 0.012 0.28 NO
67 AKT2 AKT2 AKT2 10283 0.012 0.28 NO
68 MAPK3 MAPK3 MAPK3 10431 0.0097 0.27 NO
69 MAPK8 MAPK8 MAPK8 10593 0.0079 0.26 NO
70 MAP2K2 MAP2K2 MAP2K2 10616 0.0077 0.26 NO
71 PDPK1 PDPK1 PDPK1 10675 0.0069 0.26 NO
72 EXOC7 EXOC7 EXOC7 10719 0.0064 0.26 NO
73 SOS1 SOS1 SOS1 10755 0.006 0.26 NO
74 PRKAR1A PRKAR1A PRKAR1A 10855 0.005 0.25 NO
75 FASN FASN FASN 10930 0.0041 0.25 NO
76 FLOT2 FLOT2 FLOT2 11026 0.0028 0.24 NO
77 FLOT1 FLOT1 FLOT1 11109 0.0019 0.24 NO
78 PYGL PYGL PYGL 11294 -0.00016 0.23 NO
79 MTOR MTOR MTOR 11444 -0.0022 0.22 NO
80 PKLR PKLR PKLR 11503 -0.0027 0.22 NO
81 HK1 HK1 HK1 11548 -0.0034 0.21 NO
82 MAPK1 MAPK1 MAPK1 11586 -0.0038 0.21 NO
83 PIK3R3 PIK3R3 PIK3R3 11719 -0.0054 0.2 NO
84 CALM3 CALM3 CALM3 11748 -0.0059 0.2 NO
85 PRKACA PRKACA PRKACA 11771 -0.0062 0.2 NO
86 CRKL CRKL CRKL 11863 -0.0071 0.2 NO
87 FBP2 FBP2 FBP2 11870 -0.0072 0.2 NO
88 PTPRF PTPRF PTPRF 11951 -0.0083 0.19 NO
89 PHKB PHKB PHKB 12336 -0.013 0.17 NO
90 PIK3R2 PIK3R2 PIK3R2 12537 -0.016 0.16 NO
91 RPTOR RPTOR RPTOR 12560 -0.016 0.16 NO
92 SOCS4 SOCS4 SOCS4 12574 -0.016 0.16 NO
93 EIF4E2 EIF4E2 EIF4E2 12681 -0.017 0.16 NO
94 RAF1 RAF1 RAF1 12740 -0.018 0.16 NO
95 AKT1 AKT1 AKT1 12834 -0.019 0.15 NO
96 PPP1CB PPP1CB PPP1CB 12964 -0.021 0.15 NO
97 NRAS NRAS NRAS 13027 -0.022 0.15 NO
98 PYGB PYGB PYGB 13032 -0.022 0.15 NO
99 GYS1 GYS1 GYS1 13110 -0.023 0.14 NO
100 PHKG2 PHKG2 PHKG2 13162 -0.024 0.14 NO
101 PPP1CC PPP1CC PPP1CC 13257 -0.025 0.14 NO
102 GRB2 GRB2 GRB2 13272 -0.025 0.14 NO
103 MAPK9 MAPK9 MAPK9 13385 -0.027 0.14 NO
104 CALML5 CALML5 CALML5 13621 -0.03 0.13 NO
105 CALM1 CALM1 CALM1 13625 -0.03 0.13 NO
106 RPS6KB1 RPS6KB1 RPS6KB1 13662 -0.031 0.13 NO
107 ELK1 ELK1 ELK1 13692 -0.031 0.13 NO
108 PRKAG1 PRKAG1 PRKAG1 13724 -0.031 0.13 NO
109 KRAS KRAS KRAS 13800 -0.032 0.13 NO
110 SH2B2 SH2B2 SH2B2 13826 -0.033 0.13 NO
111 MAP2K1 MAP2K1 MAP2K1 14227 -0.039 0.11 NO
112 EIF4E EIF4E EIF4E 14285 -0.04 0.11 NO
113 CALM2 CALM2 CALM2 14511 -0.043 0.099 NO
114 SREBF1 SREBF1 SREBF1 14515 -0.043 0.1 NO
115 PCK2 PCK2 PCK2 14698 -0.047 0.095 NO
116 PIK3CB PIK3CB PIK3CB 14850 -0.05 0.09 NO
117 BRAF BRAF BRAF 15055 -0.053 0.082 NO
118 ACACA ACACA ACACA 15172 -0.055 0.08 NO
119 GSK3B GSK3B GSK3B 15298 -0.058 0.077 NO
120 PRKCI PRKCI PRKCI 15349 -0.058 0.078 NO
121 PPP1CA PPP1CA PPP1CA 15406 -0.059 0.079 NO
122 PTPN1 PTPN1 PTPN1 15507 -0.061 0.078 NO
123 HK2 HK2 HK2 15729 -0.067 0.07 NO
124 SHC3 SHC3 SHC3 15824 -0.069 0.07 NO
125 RPS6KB2 RPS6KB2 RPS6KB2 15873 -0.07 0.072 NO
126 PPP1R3D PPP1R3D PPP1R3D 15962 -0.072 0.072 NO
127 RHEB RHEB RHEB 16207 -0.08 0.064 NO
128 PHKA1 PHKA1 PHKA1 16786 -0.1 0.039 NO
129 HK3 HK3 HK3 17440 -0.15 0.014 NO
130 EIF4E1B EIF4E1B EIF4E1B 17456 -0.15 0.023 NO
131 PRKAG3 PRKAG3 PRKAG3 17481 -0.15 0.032 NO
132 EIF4EBP1 EIF4EBP1 EIF4EBP1 17580 -0.17 0.038 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 AGR PATHWAY.

Figure S44.  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 ALK 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 NGFR NGFR NGFR 71 0.77 0.056 YES
2 CALML3 CALML3 CALML3 171 0.67 0.1 YES
3 NTF4 NTF4 NTF4 294 0.6 0.14 YES
4 NTRK3 NTRK3 NTRK3 344 0.56 0.18 YES
5 NTRK2 NTRK2 NTRK2 471 0.51 0.22 YES
6 IRAK3 IRAK3 IRAK3 1007 0.38 0.22 YES
7 CAMK4 CAMK4 CAMK4 1390 0.33 0.22 YES
8 NTRK1 NTRK1 NTRK1 1520 0.32 0.24 YES
9 NGF NGF NGF 1713 0.3 0.25 YES
10 NTF3 NTF3 NTF3 1946 0.28 0.26 YES
11 SHC2 SHC2 SHC2 1951 0.28 0.28 YES
12 PIK3CG PIK3CG PIK3CG 2125 0.26 0.29 YES
13 PIK3CD PIK3CD PIK3CD 2151 0.26 0.31 YES
14 AKT3 AKT3 AKT3 2691 0.22 0.3 YES
15 IRS1 IRS1 IRS1 2837 0.21 0.31 YES
16 IRS2 IRS2 IRS2 2847 0.21 0.32 YES
17 MAPK10 MAPK10 MAPK10 2930 0.21 0.33 YES
18 RPS6KA2 RPS6KA2 RPS6KA2 3109 0.2 0.34 YES
19 JUN JUN JUN 3155 0.19 0.35 YES
20 PLCG2 PLCG2 PLCG2 3169 0.19 0.37 YES
21 FASLG FASLG FASLG 3256 0.19 0.38 YES
22 PIK3R1 PIK3R1 PIK3R1 3343 0.18 0.39 YES
23 IRAK2 IRAK2 IRAK2 3349 0.18 0.4 YES
24 BCL2 BCL2 BCL2 3413 0.18 0.41 YES
25 PIK3R5 PIK3R5 PIK3R5 3596 0.17 0.42 YES
26 MAP3K1 MAP3K1 MAP3K1 3622 0.17 0.43 YES
27 MAPK11 MAPK11 MAPK11 3638 0.17 0.44 YES
28 RPS6KA3 RPS6KA3 RPS6KA3 3811 0.16 0.44 YES
29 SHC4 SHC4 SHC4 3817 0.16 0.46 YES
30 BDNF BDNF BDNF 4310 0.14 0.44 NO
31 RPS6KA5 RPS6KA5 RPS6KA5 4469 0.14 0.44 NO
32 CAMK2A CAMK2A CAMK2A 4831 0.12 0.43 NO
33 TP73 TP73 TP73 4971 0.12 0.43 NO
34 SH2B3 SH2B3 SH2B3 5175 0.11 0.43 NO
35 MAP3K3 MAP3K3 MAP3K3 5249 0.11 0.43 NO
36 IRS4 IRS4 IRS4 5309 0.1 0.44 NO
37 CAMK2D CAMK2D CAMK2D 5329 0.1 0.44 NO
38 ARHGDIB ARHGDIB ARHGDIB 5406 0.1 0.45 NO
39 CALML6 CALML6 CALML6 5460 0.1 0.45 NO
40 MAP3K5 MAP3K5 MAP3K5 5750 0.091 0.44 NO
41 GAB1 GAB1 GAB1 6001 0.085 0.44 NO
42 MAP2K5 MAP2K5 MAP2K5 6171 0.08 0.44 NO
43 CAMK2B CAMK2B CAMK2B 6405 0.075 0.43 NO
44 RAPGEF1 RAPGEF1 RAPGEF1 6425 0.074 0.43 NO
45 RPS6KA6 RPS6KA6 RPS6KA6 6563 0.071 0.43 NO
46 NFKBIA NFKBIA NFKBIA 6624 0.07 0.43 NO
47 ABL1 ABL1 ABL1 6913 0.063 0.42 NO
48 FOXO3 FOXO3 FOXO3 6933 0.063 0.43 NO
49 IKBKB IKBKB IKBKB 7005 0.061 0.43 NO
50 NFKB1 NFKB1 NFKB1 7019 0.061 0.43 NO
51 SOS2 SOS2 SOS2 7768 0.048 0.39 NO
52 MAPK7 MAPK7 MAPK7 7802 0.047 0.4 NO
53 FRS2 FRS2 FRS2 7987 0.044 0.39 NO
54 SH2B1 SH2B1 SH2B1 8038 0.043 0.39 NO
55 TRAF6 TRAF6 TRAF6 8249 0.04 0.38 NO
56 NGFRAP1 NGFRAP1 NGFRAP1 8296 0.039 0.38 NO
57 RPS6KA4 RPS6KA4 RPS6KA4 8572 0.035 0.37 NO
58 KIDINS220 KIDINS220 KIDINS220 8597 0.035 0.37 NO
59 ZNF274 ZNF274 ZNF274 8746 0.033 0.36 NO
60 TP53 TP53 TP53 9009 0.029 0.35 NO
61 MAP2K7 MAP2K7 MAP2K7 9010 0.029 0.35 NO
62 RAP1A RAP1A RAP1A 9079 0.028 0.35 NO
63 SHC1 SHC1 SHC1 9164 0.026 0.35 NO
64 BAD BAD BAD 9341 0.024 0.34 NO
65 IRAK4 IRAK4 IRAK4 9414 0.023 0.34 NO
66 PLCG1 PLCG1 PLCG1 9466 0.022 0.34 NO
67 CRK CRK CRK 9503 0.022 0.34 NO
68 RAP1B RAP1B RAP1B 9799 0.018 0.32 NO
69 RPS6KA1 RPS6KA1 RPS6KA1 9804 0.018 0.32 NO
70 CDC42 CDC42 CDC42 10069 0.015 0.31 NO
71 PRDM4 PRDM4 PRDM4 10113 0.014 0.31 NO
72 PIK3CA PIK3CA PIK3CA 10229 0.012 0.3 NO
73 AKT2 AKT2 AKT2 10283 0.012 0.3 NO
74 RELA RELA RELA 10411 0.0099 0.3 NO
75 MAPK3 MAPK3 MAPK3 10431 0.0097 0.3 NO
76 MAPK8 MAPK8 MAPK8 10593 0.0079 0.29 NO
77 MAP2K2 MAP2K2 MAP2K2 10616 0.0077 0.29 NO
78 CSK CSK CSK 10622 0.0076 0.29 NO
79 SOS1 SOS1 SOS1 10755 0.006 0.28 NO
80 RHOA RHOA RHOA 10938 0.004 0.27 NO
81 CAMK2G CAMK2G CAMK2G 11049 0.0026 0.26 NO
82 PSEN1 PSEN1 PSEN1 11507 -0.0028 0.24 NO
83 MAPK1 MAPK1 MAPK1 11586 -0.0038 0.24 NO
84 PIK3R3 PIK3R3 PIK3R3 11719 -0.0054 0.23 NO
85 CALM3 CALM3 CALM3 11748 -0.0059 0.23 NO
86 CRKL CRKL CRKL 11863 -0.0071 0.22 NO
87 MAPK14 MAPK14 MAPK14 12103 -0.01 0.21 NO
88 MAPKAPK2 MAPKAPK2 MAPKAPK2 12279 -0.012 0.2 NO
89 RAC1 RAC1 RAC1 12463 -0.015 0.19 NO
90 NFKBIB NFKBIB NFKBIB 12468 -0.015 0.19 NO
91 PIK3R2 PIK3R2 PIK3R2 12537 -0.016 0.19 NO
92 RAF1 RAF1 RAF1 12740 -0.018 0.18 NO
93 AKT1 AKT1 AKT1 12834 -0.019 0.18 NO
94 NRAS NRAS NRAS 13027 -0.022 0.17 NO
95 GRB2 GRB2 GRB2 13272 -0.025 0.16 NO
96 NFKBIE NFKBIE NFKBIE 13288 -0.025 0.16 NO
97 MAPK9 MAPK9 MAPK9 13385 -0.027 0.16 NO
98 ARHGDIA ARHGDIA ARHGDIA 13459 -0.028 0.15 NO
99 YWHAB YWHAB YWHAB 13547 -0.029 0.15 NO
100 MAPK12 MAPK12 MAPK12 13560 -0.029 0.15 NO
101 ATF4 ATF4 ATF4 13563 -0.029 0.16 NO
102 CALML5 CALML5 CALML5 13621 -0.03 0.15 NO
103 CALM1 CALM1 CALM1 13625 -0.03 0.16 NO
104 KRAS KRAS KRAS 13800 -0.032 0.15 NO
105 SH2B2 SH2B2 SH2B2 13826 -0.033 0.15 NO
106 PTPN11 PTPN11 PTPN11 14006 -0.036 0.14 NO
107 BAX BAX BAX 14040 -0.036 0.14 NO
108 SORT1 SORT1 SORT1 14091 -0.037 0.14 NO
109 MAP2K1 MAP2K1 MAP2K1 14227 -0.039 0.14 NO
110 YWHAH YWHAH YWHAH 14299 -0.04 0.14 NO
111 PRKCD PRKCD PRKCD 14386 -0.042 0.14 NO
112 MAGED1 MAGED1 MAGED1 14445 -0.042 0.14 NO
113 CALM2 CALM2 CALM2 14511 -0.043 0.14 NO
114 YWHAE YWHAE YWHAE 14556 -0.044 0.14 NO
115 YWHAQ YWHAQ YWHAQ 14827 -0.049 0.13 NO
116 PIK3CB PIK3CB PIK3CB 14850 -0.05 0.13 NO
117 BRAF BRAF BRAF 15055 -0.053 0.12 NO
118 GSK3B GSK3B GSK3B 15298 -0.058 0.11 NO
119 MAPK13 MAPK13 MAPK13 15417 -0.06 0.11 NO
120 YWHAG YWHAG YWHAG 15682 -0.065 0.1 NO
121 SHC3 SHC3 SHC3 15824 -0.069 0.1 NO
122 IRAK1 IRAK1 IRAK1 15859 -0.07 0.1 NO
123 YWHAZ YWHAZ YWHAZ 16886 -0.11 0.056 NO
124 PDK1 PDK1 PDK1 17118 -0.12 0.053 NO
125 RIPK2 RIPK2 RIPK2 17355 -0.14 0.051 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 ALK PATHWAY.

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

genes ES table in pathway: BIOCARTA AT1R PATHWAY

Table 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 PAK7 PAK7 PAK7 13 0.92 0.096 YES
2 NRG2 NRG2 NRG2 339 0.57 0.14 YES
3 NRG1 NRG1 NRG1 494 0.5 0.18 YES
4 PRKCB PRKCB PRKCB 830 0.41 0.2 YES
5 PAK3 PAK3 PAK3 974 0.39 0.24 YES
6 AREG AREG AREG 1038 0.38 0.27 YES
7 EGFR EGFR EGFR 1176 0.36 0.3 YES
8 PRKCA PRKCA PRKCA 1732 0.29 0.3 YES
9 ERBB4 ERBB4 ERBB4 1762 0.29 0.33 YES
10 SHC2 SHC2 SHC2 1951 0.28 0.35 YES
11 PIK3CG PIK3CG PIK3CG 2125 0.26 0.37 YES
12 PIK3CD PIK3CD PIK3CD 2151 0.26 0.39 YES
13 AKT3 AKT3 AKT3 2691 0.22 0.39 YES
14 EGF EGF EGF 2843 0.21 0.4 YES
15 HBEGF HBEGF HBEGF 2852 0.21 0.42 YES
16 MAPK10 MAPK10 MAPK10 2930 0.21 0.44 YES
17 JUN JUN JUN 3155 0.19 0.45 YES
18 PLCG2 PLCG2 PLCG2 3169 0.19 0.47 YES
19 STAT5A STAT5A STAT5A 3265 0.19 0.48 YES
20 EREG EREG EREG 3319 0.19 0.5 YES
21 PIK3R1 PIK3R1 PIK3R1 3343 0.18 0.52 YES
22 PIK3R5 PIK3R5 PIK3R5 3596 0.17 0.52 YES
23 SHC4 SHC4 SHC4 3817 0.16 0.52 YES
24 STAT5B STAT5B STAT5B 4598 0.13 0.49 NO
25 CAMK2A CAMK2A CAMK2A 4831 0.12 0.49 NO
26 MYC MYC MYC 5154 0.11 0.49 NO
27 CAMK2D CAMK2D CAMK2D 5329 0.1 0.49 NO
28 TGFA TGFA TGFA 5596 0.096 0.48 NO
29 CBLC CBLC CBLC 5776 0.091 0.48 NO
30 GAB1 GAB1 GAB1 6001 0.085 0.48 NO
31 CAMK2B CAMK2B CAMK2B 6405 0.075 0.47 NO
32 CDKN1B CDKN1B CDKN1B 6605 0.07 0.46 NO
33 ABL1 ABL1 ABL1 6913 0.063 0.45 NO
34 CDKN1A CDKN1A CDKN1A 7354 0.055 0.43 NO
35 SOS2 SOS2 SOS2 7768 0.048 0.42 NO
36 CBL CBL CBL 7991 0.044 0.41 NO
37 BTC BTC BTC 8000 0.044 0.41 NO
38 ERBB3 ERBB3 ERBB3 8594 0.035 0.38 NO
39 NCK2 NCK2 NCK2 8613 0.034 0.39 NO
40 MAP2K7 MAP2K7 MAP2K7 9010 0.029 0.37 NO
41 CBLB CBLB CBLB 9134 0.027 0.36 NO
42 SHC1 SHC1 SHC1 9164 0.026 0.36 NO
43 BAD BAD BAD 9341 0.024 0.36 NO
44 PAK6 PAK6 PAK6 9450 0.022 0.35 NO
45 PLCG1 PLCG1 PLCG1 9466 0.022 0.36 NO
46 CRK CRK CRK 9503 0.022 0.36 NO
47 ABL2 ABL2 ABL2 9766 0.019 0.34 NO
48 ARAF ARAF ARAF 9948 0.016 0.34 NO
49 MAP2K4 MAP2K4 MAP2K4 10149 0.014 0.32 NO
50 PIK3CA PIK3CA PIK3CA 10229 0.012 0.32 NO
51 AKT2 AKT2 AKT2 10283 0.012 0.32 NO
52 MAPK3 MAPK3 MAPK3 10431 0.0097 0.31 NO
53 NRG3 NRG3 NRG3 10442 0.0095 0.31 NO
54 MAPK8 MAPK8 MAPK8 10593 0.0079 0.31 NO
55 MAP2K2 MAP2K2 MAP2K2 10616 0.0077 0.31 NO
56 SOS1 SOS1 SOS1 10755 0.006 0.3 NO
57 CAMK2G CAMK2G CAMK2G 11049 0.0026 0.28 NO
58 MTOR MTOR MTOR 11444 -0.0022 0.26 NO
59 MAPK1 MAPK1 MAPK1 11586 -0.0038 0.26 NO
60 NCK1 NCK1 NCK1 11704 -0.0053 0.25 NO
61 PIK3R3 PIK3R3 PIK3R3 11719 -0.0054 0.25 NO
62 CRKL CRKL CRKL 11863 -0.0071 0.24 NO
63 PAK1 PAK1 PAK1 11875 -0.0072 0.24 NO
64 ERBB2 ERBB2 ERBB2 12449 -0.014 0.21 NO
65 PIK3R2 PIK3R2 PIK3R2 12537 -0.016 0.21 NO
66 RAF1 RAF1 RAF1 12740 -0.018 0.2 NO
67 NRG4 NRG4 NRG4 12747 -0.018 0.2 NO
68 AKT1 AKT1 AKT1 12834 -0.019 0.2 NO
69 NRAS NRAS NRAS 13027 -0.022 0.19 NO
70 PAK2 PAK2 PAK2 13210 -0.024 0.18 NO
71 GRB2 GRB2 GRB2 13272 -0.025 0.18 NO
72 MAPK9 MAPK9 MAPK9 13385 -0.027 0.18 NO
73 RPS6KB1 RPS6KB1 RPS6KB1 13662 -0.031 0.17 NO
74 ELK1 ELK1 ELK1 13692 -0.031 0.17 NO
75 KRAS KRAS KRAS 13800 -0.032 0.16 NO
76 PAK4 PAK4 PAK4 13812 -0.033 0.17 NO
77 MAP2K1 MAP2K1 MAP2K1 14227 -0.039 0.15 NO
78 PIK3CB PIK3CB PIK3CB 14850 -0.05 0.12 NO
79 BRAF BRAF BRAF 15055 -0.053 0.12 NO
80 GSK3B GSK3B GSK3B 15298 -0.058 0.11 NO
81 SRC SRC SRC 15459 -0.06 0.1 NO
82 SHC3 SHC3 SHC3 15824 -0.069 0.092 NO
83 RPS6KB2 RPS6KB2 RPS6KB2 15873 -0.07 0.097 NO
84 PTK2 PTK2 PTK2 16069 -0.075 0.094 NO
85 PRKCG PRKCG PRKCG 16685 -0.098 0.07 NO
86 EIF4EBP1 EIF4EBP1 EIF4EBP1 17580 -0.17 0.038 NO

Figure S47.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA AT1R PATHWAY.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA AT1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA BCR PATHWAY

Table 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 PAK7 PAK7 PAK7 13 0.92 0.16 YES
2 NRG2 NRG2 NRG2 339 0.57 0.25 YES
3 LAMA2 LAMA2 LAMA2 443 0.52 0.34 YES
4 NRG1 NRG1 NRG1 494 0.5 0.42 YES
5 DMD DMD DMD 570 0.47 0.5 YES
6 PAK3 PAK3 PAK3 974 0.39 0.55 YES
7 LAMA3 LAMA3 LAMA3 1092 0.37 0.61 YES
8 EGFR EGFR EGFR 1176 0.36 0.67 YES
9 JUN JUN JUN 3155 0.19 0.59 NO
10 UTRN UTRN UTRN 3543 0.18 0.6 NO
11 CHRM1 CHRM1 CHRM1 4385 0.14 0.58 NO
12 MUSK MUSK MUSK 4474 0.14 0.6 NO
13 LAMA4 LAMA4 LAMA4 5340 0.1 0.57 NO
14 ITGA1 ITGA1 ITGA1 5476 0.099 0.58 NO
15 GIT2 GIT2 GIT2 7422 0.054 0.49 NO
16 PXN PXN PXN 7527 0.052 0.49 NO
17 SP1 SP1 SP1 8964 0.029 0.42 NO
18 PAK6 PAK6 PAK6 9450 0.022 0.4 NO
19 ITGB1 ITGB1 ITGB1 10051 0.015 0.36 NO
20 CDC42 CDC42 CDC42 10069 0.015 0.37 NO
21 MAPK3 MAPK3 MAPK3 10431 0.0097 0.35 NO
22 MAPK8 MAPK8 MAPK8 10593 0.0079 0.34 NO
23 DVL1 DVL1 DVL1 10959 0.0038 0.32 NO
24 MAPK1 MAPK1 MAPK1 11586 -0.0038 0.29 NO
25 PAK1 PAK1 PAK1 11875 -0.0072 0.27 NO
26 DAG1 DAG1 DAG1 12019 -0.0091 0.27 NO
27 CTTN CTTN CTTN 12071 -0.0097 0.27 NO
28 RAPSN RAPSN RAPSN 12258 -0.012 0.26 NO
29 RAC1 RAC1 RAC1 12463 -0.015 0.25 NO
30 ACTA1 ACTA1 ACTA1 12996 -0.021 0.22 NO
31 PAK2 PAK2 PAK2 13210 -0.024 0.22 NO
32 PAK4 PAK4 PAK4 13812 -0.033 0.19 NO
33 SRC SRC SRC 15459 -0.06 0.11 NO
34 PTK2 PTK2 PTK2 16069 -0.075 0.09 NO
35 CHRNA1 CHRNA1 CHRNA1 17625 -0.17 0.036 NO

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

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

genes ES table in pathway: BIOCARTA BIOPEPTIDES PATHWAY

Table 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 ZBTB16 ZBTB16 ZBTB16 135 0.7 0.1 YES
2 RUNX1T1 RUNX1T1 RUNX1T1 319 0.58 0.19 YES
3 KIT KIT KIT 429 0.53 0.27 YES
4 FLT3 FLT3 FLT3 1188 0.36 0.28 YES
5 TCF7 TCF7 TCF7 1215 0.35 0.34 YES
6 PIK3CG PIK3CG PIK3CG 2125 0.26 0.33 YES
7 PIK3CD PIK3CD PIK3CD 2151 0.26 0.37 YES
8 AKT3 AKT3 AKT3 2691 0.22 0.38 YES
9 STAT5A STAT5A STAT5A 3265 0.19 0.38 YES
10 PIK3R1 PIK3R1 PIK3R1 3343 0.18 0.4 YES
11 TCF7L2 TCF7L2 TCF7L2 3560 0.17 0.42 YES
12 PIK3R5 PIK3R5 PIK3R5 3596 0.17 0.45 YES
13 TCF7L1 TCF7L1 TCF7L1 3785 0.16 0.46 YES
14 LEF1 LEF1 LEF1 4152 0.15 0.47 YES
15 RUNX1 RUNX1 RUNX1 4468 0.14 0.47 YES
16 STAT5B STAT5B STAT5B 4598 0.13 0.48 YES
17 CCNA1 CCNA1 CCNA1 4876 0.12 0.49 YES
18 MYC MYC MYC 5154 0.11 0.49 YES
19 PIM1 PIM1 PIM1 5208 0.11 0.51 YES
20 CEBPA CEBPA CEBPA 5605 0.096 0.5 NO
21 SPI1 SPI1 SPI1 5999 0.085 0.49 NO
22 IKBKB IKBKB IKBKB 7005 0.061 0.45 NO
23 NFKB1 NFKB1 NFKB1 7019 0.061 0.46 NO
24 RARA RARA RARA 7589 0.051 0.43 NO
25 SOS2 SOS2 SOS2 7768 0.048 0.43 NO
26 PML PML PML 8422 0.037 0.4 NO
27 STAT3 STAT3 STAT3 8626 0.034 0.4 NO
28 PIM2 PIM2 PIM2 9036 0.028 0.38 NO
29 BAD BAD BAD 9341 0.024 0.36 NO
30 ARAF ARAF ARAF 9948 0.016 0.34 NO
31 PIK3CA PIK3CA PIK3CA 10229 0.012 0.32 NO
32 IKBKG IKBKG IKBKG 10276 0.012 0.32 NO
33 AKT2 AKT2 AKT2 10283 0.012 0.32 NO
34 RELA RELA RELA 10411 0.0099 0.32 NO
35 MAPK3 MAPK3 MAPK3 10431 0.0097 0.32 NO
36 MAP2K2 MAP2K2 MAP2K2 10616 0.0077 0.31 NO
37 SOS1 SOS1 SOS1 10755 0.006 0.3 NO
38 CCND1 CCND1 CCND1 10823 0.0052 0.3 NO
39 MTOR MTOR MTOR 11444 -0.0022 0.26 NO
40 MAPK1 MAPK1 MAPK1 11586 -0.0038 0.26 NO
41 PIK3R3 PIK3R3 PIK3R3 11719 -0.0054 0.25 NO
42 PIK3R2 PIK3R2 PIK3R2 12537 -0.016 0.21 NO
43 RAF1 RAF1 RAF1 12740 -0.018 0.2 NO
44 AKT1 AKT1 AKT1 12834 -0.019 0.2 NO
45 NRAS NRAS NRAS 13027 -0.022 0.19 NO
46 CHUK CHUK CHUK 13268 -0.025 0.18 NO
47 GRB2 GRB2 GRB2 13272 -0.025 0.19 NO
48 RPS6KB1 RPS6KB1 RPS6KB1 13662 -0.031 0.17 NO
49 JUP JUP JUP 13707 -0.031 0.17 NO
50 KRAS KRAS KRAS 13800 -0.032 0.17 NO
51 MAP2K1 MAP2K1 MAP2K1 14227 -0.039 0.16 NO
52 PIK3CB PIK3CB PIK3CB 14850 -0.05 0.13 NO
53 BRAF BRAF BRAF 15055 -0.053 0.13 NO
54 HRAS HRAS HRAS 15640 -0.064 0.11 NO
55 RPS6KB2 RPS6KB2 RPS6KB2 15873 -0.07 0.1 NO
56 EIF4EBP1 EIF4EBP1 EIF4EBP1 17580 -0.17 0.038 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: BIOCARTA BIOPEPTIDES PATHWAY.

Figure S52.  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 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 ADIPOQ ADIPOQ ADIPOQ 155 0.68 0.064 YES
2 LEP LEP LEP 246 0.62 0.12 YES
3 PCK1 PCK1 PCK1 253 0.62 0.19 YES
4 SLC2A4 SLC2A4 SLC2A4 308 0.59 0.25 YES
5 LEPR LEPR LEPR 363 0.55 0.31 YES
6 CD36 CD36 CD36 401 0.54 0.36 YES
7 ACACB ACACB ACACB 822 0.42 0.38 YES
8 PRKCQ PRKCQ PRKCQ 922 0.4 0.42 YES
9 PPARGC1A PPARGC1A PPARGC1A 1539 0.31 0.42 YES
10 G6PC2 G6PC2 G6PC2 2346 0.24 0.4 YES
11 SOCS3 SOCS3 SOCS3 2463 0.23 0.42 YES
12 ACSL5 ACSL5 ACSL5 2473 0.23 0.44 YES
13 TNFRSF1B TNFRSF1B TNFRSF1B 2535 0.23 0.47 YES
14 CPT1C CPT1C CPT1C 2679 0.22 0.48 YES
15 AKT3 AKT3 AKT3 2691 0.22 0.5 YES
16 IRS1 IRS1 IRS1 2837 0.21 0.52 YES
17 IRS2 IRS2 IRS2 2847 0.21 0.54 YES
18 MAPK10 MAPK10 MAPK10 2930 0.21 0.56 YES
19 RXRG RXRG RXRG 3381 0.18 0.55 YES
20 POMC POMC POMC 3843 0.16 0.55 YES
21 ACSL4 ACSL4 ACSL4 3849 0.16 0.56 YES
22 PRKAA2 PRKAA2 PRKAA2 3897 0.16 0.58 YES
23 JAK2 JAK2 JAK2 4589 0.13 0.55 NO
24 IRS4 IRS4 IRS4 5309 0.1 0.52 NO
25 PRKAA1 PRKAA1 PRKAA1 5342 0.1 0.53 NO
26 PPARA PPARA PPARA 5370 0.1 0.54 NO
27 ACSL1 ACSL1 ACSL1 5934 0.087 0.52 NO
28 RXRA RXRA RXRA 5993 0.085 0.53 NO
29 CAMKK1 CAMKK1 CAMKK1 6361 0.076 0.52 NO
30 NFKBIA NFKBIA NFKBIA 6624 0.07 0.51 NO
31 CPT1B CPT1B CPT1B 6940 0.062 0.5 NO
32 IKBKB IKBKB IKBKB 7005 0.061 0.5 NO
33 NFKB1 NFKB1 NFKB1 7019 0.061 0.51 NO
34 TRADD TRADD TRADD 7021 0.061 0.51 NO
35 STK11 STK11 STK11 7305 0.055 0.5 NO
36 TNFRSF1A TNFRSF1A TNFRSF1A 7333 0.055 0.51 NO
37 PRKAB1 PRKAB1 PRKAB1 7951 0.045 0.48 NO
38 CPT1A CPT1A CPT1A 8459 0.037 0.46 NO
39 STAT3 STAT3 STAT3 8626 0.034 0.45 NO
40 PRKAG2 PRKAG2 PRKAG2 8840 0.031 0.44 NO
41 PRKAB2 PRKAB2 PRKAB2 9461 0.022 0.41 NO
42 CAMKK2 CAMKK2 CAMKK2 10125 0.014 0.38 NO
43 IKBKG IKBKG IKBKG 10276 0.012 0.37 NO
44 AKT2 AKT2 AKT2 10283 0.012 0.37 NO
45 RELA RELA RELA 10411 0.0099 0.36 NO
46 MAPK8 MAPK8 MAPK8 10593 0.0079 0.35 NO
47 RXRB RXRB RXRB 11275 0.000074 0.32 NO
48 MTOR MTOR MTOR 11444 -0.0022 0.31 NO
49 ACSL3 ACSL3 ACSL3 12181 -0.011 0.27 NO
50 NFKBIB NFKBIB NFKBIB 12468 -0.015 0.25 NO
51 AKT1 AKT1 AKT1 12834 -0.019 0.24 NO
52 CHUK CHUK CHUK 13268 -0.025 0.22 NO
53 NFKBIE NFKBIE NFKBIE 13288 -0.025 0.22 NO
54 MAPK9 MAPK9 MAPK9 13385 -0.027 0.21 NO
55 ACSL6 ACSL6 ACSL6 13717 -0.031 0.2 NO
56 TRAF2 TRAF2 TRAF2 13722 -0.031 0.2 NO
57 PRKAG1 PRKAG1 PRKAG1 13724 -0.031 0.21 NO
58 PTPN11 PTPN11 PTPN11 14006 -0.036 0.19 NO
59 ADIPOR2 ADIPOR2 ADIPOR2 14687 -0.046 0.16 NO
60 PCK2 PCK2 PCK2 14698 -0.047 0.17 NO
61 AGRP AGRP AGRP 14924 -0.051 0.16 NO
62 ADIPOR1 ADIPOR1 ADIPOR1 15282 -0.057 0.15 NO
63 TNF TNF TNF 15505 -0.061 0.14 NO
64 SLC2A1 SLC2A1 SLC2A1 16926 -0.11 0.074 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: BIOCARTA HDAC PATHWAY.

Figure S54.  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 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 ADIPOQ ADIPOQ ADIPOQ 155 0.68 0.085 YES
2 CACNA1G CACNA1G CACNA1G 230 0.63 0.17 YES
3 SLC2A4 SLC2A4 SLC2A4 308 0.59 0.24 YES
4 SOCS2 SOCS2 SOCS2 476 0.51 0.3 YES
5 GCK GCK GCK 1172 0.36 0.32 YES
6 CACNA1C CACNA1C CACNA1C 1612 0.3 0.33 YES
7 CACNA1D CACNA1D CACNA1D 2043 0.27 0.35 YES
8 PIK3CG PIK3CG PIK3CG 2125 0.26 0.38 YES
9 PIK3CD PIK3CD PIK3CD 2151 0.26 0.41 YES
10 ABCC8 ABCC8 ABCC8 2210 0.25 0.44 YES
11 SOCS3 SOCS3 SOCS3 2463 0.23 0.46 YES
12 IRS1 IRS1 IRS1 2837 0.21 0.47 YES
13 IRS2 IRS2 IRS2 2847 0.21 0.5 YES
14 MAPK10 MAPK10 MAPK10 2930 0.21 0.52 YES
15 CACNA1A CACNA1A CACNA1A 3088 0.2 0.54 YES
16 KCNJ11 KCNJ11 KCNJ11 3138 0.2 0.56 YES
17 CACNA1E CACNA1E CACNA1E 3254 0.19 0.58 YES
18 PIK3R1 PIK3R1 PIK3R1 3343 0.18 0.6 YES
19 PIK3R5 PIK3R5 PIK3R5 3596 0.17 0.62 YES
20 SOCS1 SOCS1 SOCS1 3951 0.16 0.62 YES
21 PRKCE PRKCE PRKCE 4624 0.13 0.6 NO
22 IRS4 IRS4 IRS4 5309 0.1 0.57 NO
23 IKBKB IKBKB IKBKB 7005 0.061 0.49 NO
24 INSR INSR INSR 8442 0.037 0.42 NO
25 PIK3CA PIK3CA PIK3CA 10229 0.012 0.32 NO
26 MAPK3 MAPK3 MAPK3 10431 0.0097 0.31 NO
27 MAPK8 MAPK8 MAPK8 10593 0.0079 0.3 NO
28 MTOR MTOR MTOR 11444 -0.0022 0.26 NO
29 PKLR PKLR PKLR 11503 -0.0027 0.25 NO
30 HK1 HK1 HK1 11548 -0.0034 0.25 NO
31 MAPK1 MAPK1 MAPK1 11586 -0.0038 0.25 NO
32 PIK3R3 PIK3R3 PIK3R3 11719 -0.0054 0.24 NO
33 PIK3R2 PIK3R2 PIK3R2 12537 -0.016 0.2 NO
34 SOCS4 SOCS4 SOCS4 12574 -0.016 0.2 NO
35 MAPK9 MAPK9 MAPK9 13385 -0.027 0.16 NO
36 PRKCD PRKCD PRKCD 14386 -0.042 0.11 NO
37 PKM2 PKM2 PKM2 14587 -0.044 0.11 NO
38 PIK3CB PIK3CB PIK3CB 14850 -0.05 0.099 NO
39 TNF TNF TNF 15505 -0.061 0.071 NO
40 HK2 HK2 HK2 15729 -0.067 0.068 NO
41 HK3 HK3 HK3 17440 -0.15 -0.0051 NO
42 CACNA1B CACNA1B CACNA1B 17600 -0.17 0.0094 NO
43 MAFA MAFA MAFA 17772 -0.2 0.028 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: BIOCARTA EGF PATHWAY.

Figure S56.  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 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 SLC2A4 SLC2A4 SLC2A4 308 0.59 0.16 YES
2 PRKCB PRKCB PRKCB 830 0.41 0.25 YES
3 GHR GHR GHR 1516 0.32 0.3 YES
4 PRKCA PRKCA PRKCA 1732 0.29 0.38 YES
5 PIK3CG PIK3CG PIK3CG 2125 0.26 0.43 YES
6 GH1 GH1 GH1 2754 0.22 0.46 YES
7 IRS1 IRS1 IRS1 2837 0.21 0.52 YES
8 STAT5A STAT5A STAT5A 3265 0.19 0.55 YES
9 PIK3R1 PIK3R1 PIK3R1 3343 0.18 0.6 YES
10 SOCS1 SOCS1 SOCS1 3951 0.16 0.61 YES
11 JAK2 JAK2 JAK2 4589 0.13 0.61 YES
12 STAT5B STAT5B STAT5B 4598 0.13 0.65 YES
13 SRF SRF SRF 6189 0.08 0.59 NO
14 INSR INSR INSR 8442 0.037 0.48 NO
15 SHC1 SHC1 SHC1 9164 0.026 0.44 NO
16 PLCG1 PLCG1 PLCG1 9466 0.022 0.43 NO
17 RPS6KA1 RPS6KA1 RPS6KA1 9804 0.018 0.42 NO
18 PTPN6 PTPN6 PTPN6 9901 0.017 0.42 NO
19 PIK3CA PIK3CA PIK3CA 10229 0.012 0.4 NO
20 MAPK3 MAPK3 MAPK3 10431 0.0097 0.4 NO
21 SOS1 SOS1 SOS1 10755 0.006 0.38 NO
22 MAPK1 MAPK1 MAPK1 11586 -0.0038 0.34 NO
23 RAF1 RAF1 RAF1 12740 -0.018 0.28 NO
24 HNF1A HNF1A HNF1A 12776 -0.019 0.28 NO
25 GRB2 GRB2 GRB2 13272 -0.025 0.26 NO
26 MAP2K1 MAP2K1 MAP2K1 14227 -0.039 0.22 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: BIOCARTA ERK PATHWAY.

Figure S58.  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 FCER1 PATHWAY

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 MYH11 MYH11 MYH11 165 0.67 0.029 YES
2 CALML3 CALML3 CALML3 171 0.67 0.067 YES
3 ADCY5 ADCY5 ADCY5 328 0.57 0.091 YES
4 NPR1 NPR1 NPR1 407 0.54 0.12 YES
5 KCNMB1 KCNMB1 KCNMB1 496 0.5 0.14 YES
6 ADCY4 ADCY4 ADCY4 506 0.5 0.17 YES
7 PPP1R14A PPP1R14A PPP1R14A 520 0.49 0.2 YES
8 ADRA1A ADRA1A ADRA1A 604 0.46 0.22 YES
9 PRKCB PRKCB PRKCB 830 0.41 0.23 YES
10 PRKCQ PRKCQ PRKCQ 922 0.4 0.25 YES
11 PLA2G2A PLA2G2A PLA2G2A 937 0.39 0.27 YES
12 ACTG2 ACTG2 ACTG2 1276 0.35 0.27 YES
13 AVPR1A AVPR1A AVPR1A 1441 0.32 0.28 YES
14 CACNA1C CACNA1C CACNA1C 1612 0.3 0.29 YES
15 NPR2 NPR2 NPR2 1636 0.3 0.3 YES
16 PRKCA PRKCA PRKCA 1732 0.29 0.31 YES
17 KCNMB2 KCNMB2 KCNMB2 1792 0.29 0.33 YES
18 RAMP3 RAMP3 RAMP3 1846 0.28 0.34 YES
19 PLA2G4A PLA2G4A PLA2G4A 1854 0.28 0.36 YES
20 ADRA1D ADRA1D ADRA1D 1964 0.27 0.36 YES
21 CACNA1D CACNA1D CACNA1D 2043 0.27 0.38 YES
22 MYLK MYLK MYLK 2138 0.26 0.38 YES
23 PLA2G2D PLA2G2D PLA2G2D 2169 0.26 0.4 YES
24 CACNA1F CACNA1F CACNA1F 2189 0.26 0.41 YES
25 CALCRL CALCRL CALCRL 2294 0.25 0.42 YES
26 RAMP2 RAMP2 RAMP2 2305 0.25 0.43 YES
27 KCNMB4 KCNMB4 KCNMB4 2352 0.24 0.44 YES
28 MRVI1 MRVI1 MRVI1 2387 0.24 0.46 YES
29 ADCY2 ADCY2 ADCY2 2439 0.24 0.47 YES
30 AGTR1 AGTR1 AGTR1 2455 0.24 0.48 YES
31 PLCB1 PLCB1 PLCB1 2525 0.23 0.49 YES
32 CYP4A11 CYP4A11 CYP4A11 2575 0.23 0.5 YES
33 PPP1R12B PPP1R12B PPP1R12B 2578 0.23 0.51 YES
34 PTGIR PTGIR PTGIR 2644 0.22 0.52 YES
35 CYP4A22 CYP4A22 CYP4A22 2649 0.22 0.53 YES
36 ITPR1 ITPR1 ITPR1 2855 0.21 0.53 YES
37 PRKG1 PRKG1 PRKG1 2917 0.21 0.54 YES
38 KCNMA1 KCNMA1 KCNMA1 3124 0.2 0.54 YES
39 PLA2G5 PLA2G5 PLA2G5 3151 0.19 0.55 YES
40 ACTA2 ACTA2 ACTA2 3432 0.18 0.55 YES
41 PLCB2 PLCB2 PLCB2 3629 0.17 0.55 YES
42 GUCY1A3 GUCY1A3 GUCY1A3 3639 0.17 0.56 YES
43 EDNRA EDNRA EDNRA 3756 0.16 0.56 YES
44 GUCY1A2 GUCY1A2 GUCY1A2 3771 0.16 0.57 YES
45 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 3798 0.16 0.57 YES
46 ADCY1 ADCY1 ADCY1 3814 0.16 0.58 YES
47 ADORA2A ADORA2A ADORA2A 4004 0.16 0.58 YES
48 PLA2G10 PLA2G10 PLA2G10 4073 0.15 0.59 YES
49 PRKCH PRKCH PRKCH 4084 0.15 0.59 YES
50 MYL9 MYL9 MYL9 4391 0.14 0.58 NO
51 PRKCE PRKCE PRKCE 4624 0.13 0.58 NO
52 PLA2G3 PLA2G3 PLA2G3 4628 0.13 0.59 NO
53 PLA2G1B PLA2G1B PLA2G1B 5250 0.11 0.56 NO
54 CALD1 CALD1 CALD1 5432 0.1 0.56 NO
55 CALML6 CALML6 CALML6 5460 0.1 0.56 NO
56 GUCY1B3 GUCY1B3 GUCY1B3 5578 0.096 0.56 NO
57 ITPR2 ITPR2 ITPR2 5680 0.094 0.56 NO
58 PRKACB PRKACB PRKACB 5859 0.089 0.55 NO
59 ADCY9 ADCY9 ADCY9 6158 0.081 0.54 NO
60 GNA11 GNA11 GNA11 6257 0.078 0.54 NO
61 ARHGEF1 ARHGEF1 ARHGEF1 6330 0.076 0.54 NO
62 PLA2G6 PLA2G6 PLA2G6 6390 0.075 0.54 NO
63 ADRA1B ADRA1B ADRA1B 6584 0.07 0.54 NO
64 GNAQ GNAQ GNAQ 6634 0.069 0.54 NO
65 PLCB4 PLCB4 PLCB4 6773 0.066 0.53 NO
66 ADORA2B ADORA2B ADORA2B 6807 0.066 0.53 NO
67 ADCY6 ADCY6 ADCY6 7380 0.054 0.51 NO
68 KCNMB3 KCNMB3 KCNMB3 7505 0.052 0.5 NO
69 ARHGEF12 ARHGEF12 ARHGEF12 8092 0.042 0.47 NO
70 PPP1R12A PPP1R12A PPP1R12A 8726 0.033 0.44 NO
71 ROCK1 ROCK1 ROCK1 9419 0.023 0.4 NO
72 PRKX PRKX PRKX 9800 0.018 0.38 NO
73 GNA12 GNA12 GNA12 9809 0.018 0.38 NO
74 ROCK2 ROCK2 ROCK2 9880 0.017 0.38 NO
75 ARAF ARAF ARAF 9948 0.016 0.38 NO
76 ADCY7 ADCY7 ADCY7 9977 0.016 0.38 NO
77 MAPK3 MAPK3 MAPK3 10431 0.0097 0.35 NO
78 MAP2K2 MAP2K2 MAP2K2 10616 0.0077 0.34 NO
79 PLA2G12A PLA2G12A PLA2G12A 10879 0.0047 0.33 NO
80 RAMP1 RAMP1 RAMP1 10895 0.0045 0.33 NO
81 RHOA RHOA RHOA 10938 0.004 0.33 NO
82 MYL6 MYL6 MYL6 11067 0.0024 0.32 NO
83 MAPK1 MAPK1 MAPK1 11586 -0.0038 0.29 NO
84 CALM3 CALM3 CALM3 11748 -0.0059 0.28 NO
85 PRKACA PRKACA PRKACA 11771 -0.0062 0.28 NO
86 MYL6B MYL6B MYL6B 12371 -0.014 0.25 NO
87 ADCY8 ADCY8 ADCY8 12605 -0.016 0.24 NO
88 RAF1 RAF1 RAF1 12740 -0.018 0.23 NO
89 GNA13 GNA13 GNA13 12955 -0.021 0.22 NO
90 PLCB3 PLCB3 PLCB3 12962 -0.021 0.22 NO
91 PPP1CB PPP1CB PPP1CB 12964 -0.021 0.22 NO
92 ARHGEF11 ARHGEF11 ARHGEF11 12968 -0.021 0.22 NO
93 PPP1CC PPP1CC PPP1CC 13257 -0.025 0.21 NO
94 CALML5 CALML5 CALML5 13621 -0.03 0.19 NO
95 CALM1 CALM1 CALM1 13625 -0.03 0.19 NO
96 MAP2K1 MAP2K1 MAP2K1 14227 -0.039 0.16 NO
97 PRKCD PRKCD PRKCD 14386 -0.042 0.16 NO
98 CALM2 CALM2 CALM2 14511 -0.043 0.15 NO
99 BRAF BRAF BRAF 15055 -0.053 0.12 NO
100 CACNA1S CACNA1S CACNA1S 15185 -0.056 0.12 NO
101 ITPR3 ITPR3 ITPR3 15366 -0.059 0.11 NO
102 PPP1CA PPP1CA PPP1CA 15406 -0.059 0.12 NO
103 GNAS GNAS GNAS 15679 -0.065 0.1 NO
104 PRKCG PRKCG PRKCG 16685 -0.098 0.054 NO
105 MYLK3 MYLK3 MYLK3 17217 -0.13 0.032 NO
106 PLA2G2F PLA2G2F PLA2G2F 17237 -0.13 0.038 NO
107 MYLK2 MYLK2 MYLK2 18133 -0.33 0.0079 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: BIOCARTA FCER1 PATHWAY.

Figure S60.  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

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 = BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

GSEA analysis

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

Download Results

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

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