GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in SKCM-TM
Skin Cutaneous Melanoma (Metastatic)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in SKCM-TM. Broad Institute of MIT and Harvard. doi:10.7908/C1154G9F
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 SKCM-TM. 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: 190
Number of samples: 367
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 ] 138
pheno.type: 2 - 3 :[ clus2 ] 104
pheno.type: 3 - 3 :[ clus3 ] 125

For the expression subtypes of 18067 genes in 368 samples, GSEA found enriched gene sets in each cluster using 367 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA RACCYCD PATHWAY, KEGG CITRATE CYCLE TCA CYCLE, KEGG PENTOSE PHOSPHATE PATHWAY, KEGG OXIDATIVE PHOSPHORYLATION, KEGG SELENOAMINO ACID METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG PYRUVATE METABOLISM, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME

    • And common core enriched genes are SDHA, SDHB, SDHC, ATP5A1, ATP5B, ATP5D, ATP5G1, ATP5G2, ATP5G3, ATP5H

  • clus2

    • Top enriched gene sets are BIOCARTA AGR PATHWAY, BIOCARTA AT1R PATHWAY, BIOCARTA BCR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA HDAC PATHWAY, BIOCARTA EGF PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA FMLP PATHWAY, BIOCARTA GH PATHWAY

    • And common core enriched genes are MAP3K14, NFKBIA, TNF, LAT, PIK3CG, PIK3R5, PRKCB, PTPRC, VAV1, VAV3

  • clus3

    • Top enriched gene sets are BIOCARTA NO1 PATHWAY, BIOCARTA AGR PATHWAY, BIOCARTA ALK PATHWAY, BIOCARTA NFAT PATHWAY, BIOCARTA EDG1 PATHWAY, BIOCARTA WNT PATHWAY, KEGG LYSINE DEGRADATION, KEGG ERBB SIGNALING PATHWAY, KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION, KEGG HEDGEHOG SIGNALING PATHWAY

    • And common core enriched genes are BMP2, BMP5, BMP7, BMPR1A, CHRD, SMAD1, SMAD5, TGFB2, TGFB3, THBS1

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 RACCYCD PATHWAY 25 genes.ES.table 0.29 1.2 0.26 0.6 1 0.28 0.14 0.24 0.54 0.12
KEGG CITRATE CYCLE TCA CYCLE 29 genes.ES.table 0.55 1.9 0.016 0.048 0.14 0.59 0.19 0.48 0 0.007
KEGG PENTOSE PHOSPHATE PATHWAY 26 genes.ES.table 0.33 1 0.4 0.86 1 0.46 0.16 0.39 0.82 0.31
KEGG OXIDATIVE PHOSPHORYLATION 114 genes.ES.table 0.58 2.1 0.014 0.017 0.023 0.68 0.23 0.52 0 0.004
KEGG SELENOAMINO ACID METABOLISM 25 genes.ES.table 0.26 0.87 0.64 0.98 1 0.44 0.21 0.35 0.96 0.44
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 42 genes.ES.table 0.35 1.3 0.19 0.53 0.99 0.31 0.12 0.27 0.45 0.11
KEGG INOSITOL PHOSPHATE METABOLISM 52 genes.ES.table 0.22 0.86 0.69 0.96 1 0.19 0.074 0.18 0.95 0.42
KEGG PYRUVATE METABOLISM 38 genes.ES.table 0.28 0.94 0.49 0.87 1 0.37 0.17 0.31 0.84 0.29
KEGG AMINOACYL TRNA BIOSYNTHESIS 40 genes.ES.table 0.47 1.8 0.034 0.096 0.36 0.65 0.3 0.45 0 0.008
KEGG RIBOSOME 84 genes.ES.table 0.37 1 0.5 0.9 1 0.98 0.56 0.44 0.85 0.35
genes ES table in pathway: BIOCARTA RACCYCD 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 ATP6V0A4 ATP6V0A4 ATP6V0A4 142 0.36 0.032 YES
2 ATP6V0D2 ATP6V0D2 ATP6V0D2 281 0.28 0.056 YES
3 COX6A2 COX6A2 COX6A2 630 0.2 0.059 YES
4 ATP6V0A1 ATP6V0A1 ATP6V0A1 881 0.16 0.063 YES
5 NDUFS7 NDUFS7 NDUFS7 995 0.15 0.074 YES
6 NDUFA8 NDUFA8 NDUFA8 1133 0.14 0.082 YES
7 ATP6V0C ATP6V0C ATP6V0C 1143 0.14 0.097 YES
8 ATP6AP1 ATP6AP1 ATP6AP1 1162 0.14 0.11 YES
9 NDUFS8 NDUFS8 NDUFS8 1306 0.13 0.12 YES
10 UQCRC1 UQCRC1 UQCRC1 1333 0.13 0.13 YES
11 SDHA SDHA SDHA 1409 0.12 0.14 YES
12 NDUFA7 NDUFA7 NDUFA7 1445 0.12 0.15 YES
13 NDUFB7 NDUFB7 NDUFB7 1458 0.12 0.16 YES
14 NDUFV1 NDUFV1 NDUFV1 1483 0.12 0.18 YES
15 ATP6V0B ATP6V0B ATP6V0B 1549 0.12 0.19 YES
16 ATP5G1 ATP5G1 ATP5G1 1554 0.12 0.2 YES
17 COX6A1 COX6A1 COX6A1 1569 0.11 0.21 YES
18 ATP6V1F ATP6V1F ATP6V1F 1680 0.11 0.22 YES
19 CYC1 CYC1 CYC1 1685 0.11 0.23 YES
20 ATP5D ATP5D ATP5D 1700 0.11 0.24 YES
21 NDUFV3 NDUFV3 NDUFV3 1729 0.11 0.25 YES
22 NDUFS6 NDUFS6 NDUFS6 1736 0.11 0.26 YES
23 COX5A COX5A COX5A 1756 0.11 0.27 YES
24 ATP6V0D1 ATP6V0D1 ATP6V0D1 1766 0.11 0.28 YES
25 NDUFA3 NDUFA3 NDUFA3 1773 0.11 0.3 YES
26 ATP12A ATP12A ATP12A 1820 0.1 0.3 YES
27 ATP6V1D ATP6V1D ATP6V1D 1838 0.1 0.32 YES
28 NDUFC2 NDUFC2 NDUFC2 1844 0.1 0.33 YES
29 ATP6V1B2 ATP6V1B2 ATP6V1B2 1848 0.1 0.34 YES
30 ATP5B ATP5B ATP5B 1862 0.1 0.35 YES
31 NDUFB1 NDUFB1 NDUFB1 1888 0.1 0.36 YES
32 COX5B COX5B COX5B 1891 0.1 0.37 YES
33 UQCR10 UQCR10 UQCR10 2038 0.094 0.37 YES
34 NDUFB4 NDUFB4 NDUFB4 2073 0.093 0.38 YES
35 COX8A COX8A COX8A 2207 0.089 0.38 YES
36 NDUFS2 NDUFS2 NDUFS2 2255 0.087 0.39 YES
37 COX6B1 COX6B1 COX6B1 2311 0.085 0.4 YES
38 UQCRQ UQCRQ UQCRQ 2318 0.085 0.4 YES
39 NDUFB9 NDUFB9 NDUFB9 2346 0.084 0.41 YES
40 ATP6V1E2 ATP6V1E2 ATP6V1E2 2374 0.083 0.42 YES
41 ATP5H ATP5H ATP5H 2442 0.081 0.43 YES
42 ATP6V1C1 ATP6V1C1 ATP6V1C1 2489 0.08 0.43 YES
43 ATP5G3 ATP5G3 ATP5G3 2544 0.078 0.44 YES
44 SDHB SDHB SDHB 2558 0.078 0.45 YES
45 NDUFA11 NDUFA11 NDUFA11 2568 0.078 0.45 YES
46 NDUFB10 NDUFB10 NDUFB10 2627 0.076 0.46 YES
47 COX6C COX6C COX6C 2638 0.075 0.47 YES
48 ATP6V1E1 ATP6V1E1 ATP6V1E1 2649 0.075 0.48 YES
49 NDUFA1 NDUFA1 NDUFA1 2683 0.074 0.48 YES
50 ATP6V1H ATP6V1H ATP6V1H 2735 0.073 0.49 YES
51 ATP5G2 ATP5G2 ATP5G2 2750 0.072 0.49 YES
52 UQCRHL UQCRHL UQCRHL 2845 0.07 0.5 YES
53 NDUFA6 NDUFA6 NDUFA6 2888 0.069 0.5 YES
54 NDUFA9 NDUFA9 NDUFA9 2893 0.069 0.51 YES
55 UQCRFS1 UQCRFS1 UQCRFS1 2911 0.069 0.52 YES
56 NDUFS3 NDUFS3 NDUFS3 2922 0.068 0.52 YES
57 ATP6V1G1 ATP6V1G1 ATP6V1G1 2969 0.068 0.53 YES
58 ATP5I ATP5I ATP5I 2971 0.068 0.54 YES
59 SDHC SDHC SDHC 3008 0.067 0.54 YES
60 NDUFA2 NDUFA2 NDUFA2 3301 0.059 0.53 YES
61 ATP4A ATP4A ATP4A 3324 0.059 0.54 YES
62 UQCRH UQCRH UQCRH 3499 0.055 0.53 YES
63 COX7A2L COX7A2L COX7A2L 3550 0.054 0.54 YES
64 NDUFB8 NDUFB8 NDUFB8 3569 0.054 0.54 YES
65 UQCRB UQCRB UQCRB 3607 0.053 0.55 YES
66 COX7A2 COX7A2 COX7A2 3769 0.05 0.54 YES
67 COX15 COX15 COX15 3934 0.046 0.54 YES
68 ATP5J2 ATP5J2 ATP5J2 3943 0.046 0.54 YES
69 ATP5J ATP5J ATP5J 3973 0.045 0.55 YES
70 COX4I1 COX4I1 COX4I1 3979 0.045 0.55 YES
71 COX7C COX7C COX7C 3996 0.045 0.56 YES
72 LHPP LHPP LHPP 4006 0.045 0.56 YES
73 NDUFB2 NDUFB2 NDUFB2 4008 0.045 0.56 YES
74 UQCR11 UQCR11 UQCR11 4024 0.044 0.57 YES
75 NDUFS5 NDUFS5 NDUFS5 4033 0.044 0.57 YES
76 ATP5A1 ATP5A1 ATP5A1 4144 0.042 0.57 YES
77 NDUFV2 NDUFV2 NDUFV2 4154 0.042 0.58 YES
78 NDUFA10 NDUFA10 NDUFA10 4704 0.032 0.55 NO
79 ATP5O ATP5O ATP5O 4707 0.032 0.55 NO
80 COX17 COX17 COX17 4827 0.03 0.55 NO
81 COX8C COX8C COX8C 4861 0.029 0.55 NO
82 NDUFAB1 NDUFAB1 NDUFAB1 4862 0.029 0.55 NO
83 NDUFC1 NDUFC1 NDUFC1 5059 0.025 0.55 NO
84 PPA2 PPA2 PPA2 5079 0.025 0.55 NO
85 NDUFS1 NDUFS1 NDUFS1 5130 0.024 0.55 NO
86 ATP5C1 ATP5C1 ATP5C1 5251 0.022 0.54 NO
87 ATP6V0E1 ATP6V0E1 ATP6V0E1 5287 0.021 0.54 NO
88 COX10 COX10 COX10 5336 0.02 0.54 NO
89 NDUFB3 NDUFB3 NDUFB3 5697 0.013 0.52 NO
90 NDUFB6 NDUFB6 NDUFB6 5749 0.012 0.52 NO
91 COX7B COX7B COX7B 5751 0.012 0.52 NO
92 ATP6V0E2 ATP6V0E2 ATP6V0E2 5858 0.01 0.52 NO
93 ATP5F1 ATP5F1 ATP5F1 6079 0.0058 0.51 NO
94 NDUFA4 NDUFA4 NDUFA4 6139 0.0046 0.5 NO
95 ATP6V1A ATP6V1A ATP6V1A 6280 0.0018 0.5 NO
96 UQCRC2 UQCRC2 UQCRC2 6499 -0.0024 0.49 NO
97 NDUFB5 NDUFB5 NDUFB5 6584 -0.0042 0.48 NO
98 ATP5L ATP5L ATP5L 6779 -0.0079 0.47 NO
99 TCIRG1 TCIRG1 TCIRG1 6837 -0.0089 0.47 NO
100 ATP5E ATP5E ATP5E 6864 -0.0096 0.47 NO
101 NDUFS4 NDUFS4 NDUFS4 7806 -0.029 0.42 NO
102 COX11 COX11 COX11 8366 -0.04 0.39 NO
103 ATP6V0A2 ATP6V0A2 ATP6V0A2 8498 -0.042 0.39 NO
104 NDUFA5 NDUFA5 NDUFA5 8721 -0.048 0.38 NO
105 ATP6V1B1 ATP6V1B1 ATP6V1B1 8982 -0.054 0.38 NO
106 COX6B2 COX6B2 COX6B2 9909 -0.075 0.33 NO
107 COX4I2 COX4I2 COX4I2 10068 -0.079 0.33 NO
108 PPA1 PPA1 PPA1 10130 -0.08 0.34 NO
109 NDUFA4L2 NDUFA4L2 NDUFA4L2 10404 -0.087 0.33 NO
110 SDHD SDHD SDHD 10992 -0.1 0.31 NO
111 ATP6V1G2 ATP6V1G2 ATP6V1G2 11545 -0.12 0.29 NO
112 ATP6V1C2 ATP6V1C2 ATP6V1C2 11782 -0.12 0.29 NO
113 COX7A1 COX7A1 COX7A1 14755 -0.23 0.15 NO
114 ATP4B ATP4B ATP4B 15435 -0.27 0.15 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 RACCYCD PATHWAY.

Figure S2.  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 CITRATE CYCLE TCA CYCLE

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 ACO2 ACO2 ACO2 961 0.16 0.019 YES
2 OGDHL OGDHL OGDHL 997 0.15 0.088 YES
3 SDHA SDHA SDHA 1409 0.12 0.12 YES
4 FH FH FH 1454 0.12 0.18 YES
5 IDH3G IDH3G IDH3G 1655 0.11 0.22 YES
6 PC PC PC 2199 0.089 0.23 YES
7 DLST DLST DLST 2234 0.088 0.27 YES
8 MDH2 MDH2 MDH2 2287 0.086 0.31 YES
9 PCK2 PCK2 PCK2 2344 0.084 0.34 YES
10 SUCLG1 SUCLG1 SUCLG1 2468 0.081 0.37 YES
11 CS CS CS 2525 0.079 0.41 YES
12 SDHB SDHB SDHB 2558 0.078 0.44 YES
13 MDH1 MDH1 MDH1 2729 0.073 0.47 YES
14 PDHA1 PDHA1 PDHA1 2840 0.07 0.49 YES
15 SDHC SDHC SDHC 3008 0.067 0.52 YES
16 OGDH OGDH OGDH 3067 0.065 0.54 YES
17 IDH3B IDH3B IDH3B 3432 0.057 0.55 YES
18 IDH1 IDH1 IDH1 3922 0.047 0.54 NO
19 IDH3A IDH3A IDH3A 4447 0.037 0.53 NO
20 ACO1 ACO1 ACO1 5412 0.018 0.49 NO
21 ACLY ACLY ACLY 5692 0.014 0.48 NO
22 PDHB PDHB PDHB 5775 0.012 0.48 NO
23 DLD DLD DLD 6512 -0.0027 0.44 NO
24 SUCLG2 SUCLG2 SUCLG2 6838 -0.009 0.42 NO
25 DLAT DLAT DLAT 7303 -0.018 0.41 NO
26 IDH2 IDH2 IDH2 7356 -0.02 0.41 NO
27 SUCLA2 SUCLA2 SUCLA2 9955 -0.076 0.31 NO
28 SDHD SDHD SDHD 10992 -0.1 0.3 NO
29 PCK1 PCK1 PCK1 14101 -0.2 0.22 NO

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

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

genes ES table in pathway: KEGG PENTOSE PHOSPHATE PATHWAY

Table 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 PARS2 PARS2 PARS2 729 0.18 0.04 YES
2 NARS2 NARS2 NARS2 907 0.16 0.1 YES
3 AARS2 AARS2 AARS2 1622 0.11 0.11 YES
4 MARS2 MARS2 MARS2 1841 0.1 0.14 YES
5 SARS2 SARS2 SARS2 1843 0.1 0.19 YES
6 DARS2 DARS2 DARS2 2001 0.096 0.22 YES
7 CARS2 CARS2 CARS2 2046 0.094 0.26 YES
8 LARS2 LARS2 LARS2 2333 0.084 0.28 YES
9 EARS2 EARS2 EARS2 2668 0.075 0.3 YES
10 YARS2 YARS2 YARS2 2737 0.072 0.32 YES
11 FARSA FARSA FARSA 2857 0.07 0.35 YES
12 QARS QARS QARS 2939 0.068 0.37 YES
13 VARS2 VARS2 VARS2 2974 0.067 0.4 YES
14 VARS VARS VARS 3299 0.059 0.41 YES
15 AARS AARS AARS 3305 0.059 0.44 YES
16 NARS NARS NARS 3445 0.056 0.45 YES
17 SARS SARS SARS 3680 0.051 0.46 YES
18 WARS2 WARS2 WARS2 4196 0.042 0.45 YES
19 IARS2 IARS2 IARS2 4553 0.035 0.45 YES
20 YARS YARS YARS 4688 0.032 0.45 YES
21 FARS2 FARS2 FARS2 4764 0.031 0.46 YES
22 HARS2 HARS2 HARS2 5080 0.025 0.46 YES
23 WARS WARS WARS 5083 0.025 0.47 YES
24 GARS GARS GARS 5239 0.022 0.47 YES
25 MTFMT MTFMT MTFMT 5487 0.017 0.46 YES
26 MARS MARS MARS 5503 0.017 0.47 YES
27 HARS HARS HARS 6004 0.0074 0.44 NO
28 IARS IARS IARS 6128 0.0048 0.44 NO
29 FARSB FARSB FARSB 6410 -0.00072 0.42 NO
30 CARS CARS CARS 6423 -0.00087 0.42 NO
31 TARS TARS TARS 6503 -0.0025 0.42 NO
32 EPRS EPRS EPRS 6671 -0.006 0.42 NO
33 RARS RARS RARS 6836 -0.0089 0.41 NO
34 KARS KARS KARS 7181 -0.016 0.4 NO
35 LARS LARS LARS 7758 -0.027 0.38 NO
36 PSTK PSTK PSTK 7845 -0.029 0.39 NO
37 TARSL2 TARSL2 TARSL2 8888 -0.051 0.35 NO
38 DARS DARS DARS 9801 -0.072 0.33 NO
39 RARS2 RARS2 RARS2 10537 -0.09 0.33 NO
40 SEPSECS SEPSECS SEPSECS 13890 -0.2 0.23 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 PENTOSE PHOSPHATE PATHWAY.

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

genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

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 SNCA SNCA SNCA 348 0.26 0.0073 YES
2 COX6A2 COX6A2 COX6A2 630 0.2 0.012 YES
3 SLC25A4 SLC25A4 SLC25A4 966 0.15 0.0098 YES
4 NDUFS7 NDUFS7 NDUFS7 995 0.15 0.024 YES
5 NDUFA8 NDUFA8 NDUFA8 1133 0.14 0.031 YES
6 NDUFS8 NDUFS8 NDUFS8 1306 0.13 0.035 YES
7 UQCRC1 UQCRC1 UQCRC1 1333 0.13 0.047 YES
8 SDHA SDHA SDHA 1409 0.12 0.056 YES
9 NDUFA7 NDUFA7 NDUFA7 1445 0.12 0.066 YES
10 NDUFB7 NDUFB7 NDUFB7 1458 0.12 0.078 YES
11 NDUFV1 NDUFV1 NDUFV1 1483 0.12 0.089 YES
12 VDAC2 VDAC2 VDAC2 1515 0.12 0.1 YES
13 ATP5G1 ATP5G1 ATP5G1 1554 0.12 0.11 YES
14 COX6A1 COX6A1 COX6A1 1569 0.11 0.12 YES
15 TH TH TH 1650 0.11 0.13 YES
16 CYC1 CYC1 CYC1 1685 0.11 0.14 YES
17 ATP5D ATP5D ATP5D 1700 0.11 0.15 YES
18 NDUFV3 NDUFV3 NDUFV3 1729 0.11 0.16 YES
19 NDUFS6 NDUFS6 NDUFS6 1736 0.11 0.17 YES
20 COX5A COX5A COX5A 1756 0.11 0.18 YES
21 NDUFA3 NDUFA3 NDUFA3 1773 0.11 0.19 YES
22 NDUFC2 NDUFC2 NDUFC2 1844 0.1 0.2 YES
23 ATP5B ATP5B ATP5B 1862 0.1 0.2 YES
24 NDUFB1 NDUFB1 NDUFB1 1888 0.1 0.21 YES
25 COX5B COX5B COX5B 1891 0.1 0.22 YES
26 UQCR10 UQCR10 UQCR10 2038 0.094 0.23 YES
27 NDUFB4 NDUFB4 NDUFB4 2073 0.093 0.23 YES
28 VDAC1 VDAC1 VDAC1 2087 0.093 0.24 YES
29 COX8A COX8A COX8A 2207 0.089 0.25 YES
30 NDUFS2 NDUFS2 NDUFS2 2255 0.087 0.25 YES
31 COX6B1 COX6B1 COX6B1 2311 0.085 0.26 YES
32 UQCRQ UQCRQ UQCRQ 2318 0.085 0.27 YES
33 NDUFB9 NDUFB9 NDUFB9 2346 0.084 0.27 YES
34 ATP5H ATP5H ATP5H 2442 0.081 0.28 YES
35 ATP5G3 ATP5G3 ATP5G3 2544 0.078 0.28 YES
36 SDHB SDHB SDHB 2558 0.078 0.29 YES
37 SLC25A5 SLC25A5 SLC25A5 2581 0.077 0.29 YES
38 SLC25A6 SLC25A6 SLC25A6 2623 0.076 0.3 YES
39 NDUFB10 NDUFB10 NDUFB10 2627 0.076 0.31 YES
40 COX6C COX6C COX6C 2638 0.075 0.31 YES
41 NDUFA1 NDUFA1 NDUFA1 2683 0.074 0.32 YES
42 ATP5G2 ATP5G2 ATP5G2 2750 0.072 0.32 YES
43 UQCRHL UQCRHL UQCRHL 2845 0.07 0.32 YES
44 NDUFA6 NDUFA6 NDUFA6 2888 0.069 0.33 YES
45 NDUFA9 NDUFA9 NDUFA9 2893 0.069 0.34 YES
46 UQCRFS1 UQCRFS1 UQCRFS1 2911 0.069 0.34 YES
47 NDUFS3 NDUFS3 NDUFS3 2922 0.068 0.35 YES
48 SDHC SDHC SDHC 3008 0.067 0.35 YES
49 NDUFA2 NDUFA2 NDUFA2 3301 0.059 0.34 YES
50 UBE2L3 UBE2L3 UBE2L3 3350 0.058 0.35 YES
51 UQCRH UQCRH UQCRH 3499 0.055 0.34 YES
52 UBB UBB UBB 3535 0.055 0.35 YES
53 COX7A2L COX7A2L COX7A2L 3550 0.054 0.35 YES
54 NDUFB8 NDUFB8 NDUFB8 3569 0.054 0.36 YES
55 PINK1 PINK1 PINK1 3570 0.054 0.36 YES
56 UQCRB UQCRB UQCRB 3607 0.053 0.37 YES
57 COX7A2 COX7A2 COX7A2 3769 0.05 0.36 YES
58 ATP5J ATP5J ATP5J 3973 0.045 0.36 YES
59 COX4I1 COX4I1 COX4I1 3979 0.045 0.36 YES
60 COX7C COX7C COX7C 3996 0.045 0.36 YES
61 NDUFB2 NDUFB2 NDUFB2 4008 0.045 0.37 YES
62 UQCR11 UQCR11 UQCR11 4024 0.044 0.37 YES
63 NDUFS5 NDUFS5 NDUFS5 4033 0.044 0.38 YES
64 ATP5A1 ATP5A1 ATP5A1 4144 0.042 0.37 YES
65 NDUFV2 NDUFV2 NDUFV2 4154 0.042 0.38 YES
66 NDUFA10 NDUFA10 NDUFA10 4704 0.032 0.35 NO
67 ATP5O ATP5O ATP5O 4707 0.032 0.35 NO
68 COX8C COX8C COX8C 4861 0.029 0.35 NO
69 NDUFAB1 NDUFAB1 NDUFAB1 4862 0.029 0.35 NO
70 NDUFC1 NDUFC1 NDUFC1 5059 0.025 0.34 NO
71 NDUFS1 NDUFS1 NDUFS1 5130 0.024 0.34 NO
72 VDAC3 VDAC3 VDAC3 5207 0.022 0.34 NO
73 ATP5C1 ATP5C1 ATP5C1 5251 0.022 0.34 NO
74 CYCS CYCS CYCS 5268 0.021 0.34 NO
75 PARK7 PARK7 PARK7 5695 0.013 0.32 NO
76 NDUFB3 NDUFB3 NDUFB3 5697 0.013 0.32 NO
77 NDUFB6 NDUFB6 NDUFB6 5749 0.012 0.32 NO
78 COX7B COX7B COX7B 5751 0.012 0.32 NO
79 HTRA2 HTRA2 HTRA2 5765 0.012 0.32 NO
80 UBA1 UBA1 UBA1 5782 0.012 0.32 NO
81 UBE2G2 UBE2G2 UBE2G2 5871 0.0099 0.32 NO
82 ATP5F1 ATP5F1 ATP5F1 6079 0.0058 0.31 NO
83 NDUFA4 NDUFA4 NDUFA4 6139 0.0046 0.3 NO
84 UBE2J2 UBE2J2 UBE2J2 6228 0.0029 0.3 NO
85 PPID PPID PPID 6416 -0.00076 0.29 NO
86 UQCRC2 UQCRC2 UQCRC2 6499 -0.0024 0.28 NO
87 NDUFB5 NDUFB5 NDUFB5 6584 -0.0042 0.28 NO
88 CASP9 CASP9 CASP9 6635 -0.0051 0.28 NO
89 ATP5E ATP5E ATP5E 6864 -0.0096 0.27 NO
90 NDUFS4 NDUFS4 NDUFS4 7806 -0.029 0.22 NO
91 NDUFA5 NDUFA5 NDUFA5 8721 -0.048 0.17 NO
92 UBE2G1 UBE2G1 UBE2G1 8722 -0.048 0.18 NO
93 COX6B2 COX6B2 COX6B2 9909 -0.075 0.12 NO
94 COX4I2 COX4I2 COX4I2 10068 -0.079 0.12 NO
95 SLC6A3 SLC6A3 SLC6A3 10240 -0.083 0.12 NO
96 NDUFA4L2 NDUFA4L2 NDUFA4L2 10404 -0.087 0.12 NO
97 SDHD SDHD SDHD 10992 -0.1 0.093 NO
98 UCHL1 UCHL1 UCHL1 11098 -0.1 0.098 NO
99 UBE2J1 UBE2J1 UBE2J1 11902 -0.13 0.067 NO
100 UBE2L6 UBE2L6 UBE2L6 12188 -0.14 0.065 NO
101 CASP3 CASP3 CASP3 12666 -0.15 0.055 NO
102 APAF1 APAF1 APAF1 12779 -0.16 0.064 NO
103 SLC18A2 SLC18A2 SLC18A2 13342 -0.18 0.052 NO
104 GPR37 GPR37 GPR37 13903 -0.2 0.041 NO
105 PARK2 PARK2 PARK2 13923 -0.2 0.06 NO
106 COX7A1 COX7A1 COX7A1 14755 -0.23 0.038 NO
107 UBA7 UBA7 UBA7 14961 -0.24 0.052 NO
108 LRRK2 LRRK2 LRRK2 15894 -0.3 0.031 NO
109 SLC18A1 SLC18A1 SLC18A1 17293 -0.41 -0.004 NO
110 SNCAIP SNCAIP SNCAIP 17507 -0.44 0.03 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 OXIDATIVE PHOSPHORYLATION.

Figure S8.  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 SELENOAMINO ACID 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 ARSG ARSG ARSG 55 0.46 0.038 YES
2 CTSL2 CTSL2 CTSL2 130 0.37 0.067 YES
3 ATP6V0A4 ATP6V0A4 ATP6V0A4 142 0.36 0.098 YES
4 ATP6V0D2 ATP6V0D2 ATP6V0D2 281 0.28 0.12 YES
5 CTSF CTSF CTSF 676 0.19 0.11 YES
6 GBA GBA GBA 702 0.19 0.13 YES
7 ATP6V0A1 ATP6V0A1 ATP6V0A1 881 0.16 0.13 YES
8 SORT1 SORT1 SORT1 923 0.16 0.14 YES
9 NAGLU NAGLU NAGLU 929 0.16 0.16 YES
10 CTNS CTNS CTNS 991 0.15 0.17 YES
11 ASAH1 ASAH1 ASAH1 1065 0.15 0.18 YES
12 ATP6V0C ATP6V0C ATP6V0C 1143 0.14 0.18 YES
13 ATP6AP1 ATP6AP1 ATP6AP1 1162 0.14 0.2 YES
14 PPT2 PPT2 PPT2 1214 0.14 0.2 YES
15 MCOLN1 MCOLN1 MCOLN1 1232 0.14 0.22 YES
16 PLA2G15 PLA2G15 PLA2G15 1236 0.13 0.23 YES
17 GLA GLA GLA 1256 0.13 0.24 YES
18 NPC1 NPC1 NPC1 1357 0.13 0.24 YES
19 CTSD CTSD CTSD 1399 0.12 0.25 YES
20 GM2A GM2A GM2A 1498 0.12 0.26 YES
21 ATP6V0B ATP6V0B ATP6V0B 1549 0.12 0.27 YES
22 CD63 CD63 CD63 1715 0.11 0.27 YES
23 HEXA HEXA HEXA 1748 0.11 0.27 YES
24 ATP6V0D1 ATP6V0D1 ATP6V0D1 1766 0.11 0.28 YES
25 NEU1 NEU1 NEU1 1771 0.11 0.29 YES
26 AP1S3 AP1S3 AP1S3 1915 0.099 0.29 YES
27 GGA1 GGA1 GGA1 2027 0.095 0.3 YES
28 CLTCL1 CLTCL1 CLTCL1 2062 0.094 0.3 YES
29 GLB1 GLB1 GLB1 2108 0.092 0.31 YES
30 CTSA CTSA CTSA 2149 0.09 0.31 YES
31 AP3M2 AP3M2 AP3M2 2177 0.09 0.32 YES
32 CLN3 CLN3 CLN3 2235 0.088 0.32 YES
33 ACP5 ACP5 ACP5 2266 0.087 0.33 YES
34 ABCB9 ABCB9 ABCB9 2424 0.082 0.33 YES
35 AP3B2 AP3B2 AP3B2 2485 0.08 0.33 YES
36 SMPD1 SMPD1 SMPD1 2498 0.08 0.34 YES
37 LAPTM4B LAPTM4B LAPTM4B 2580 0.077 0.34 YES
38 DNASE2B DNASE2B DNASE2B 2599 0.076 0.35 YES
39 CTSH CTSH CTSH 2600 0.076 0.35 YES
40 SGSH SGSH SGSH 2616 0.076 0.36 YES
41 NPC2 NPC2 NPC2 2631 0.076 0.37 YES
42 TPP1 TPP1 TPP1 2633 0.076 0.37 YES
43 ATP6V1H ATP6V1H ATP6V1H 2735 0.073 0.37 YES
44 NAGA NAGA NAGA 2739 0.072 0.38 YES
45 IGF2R IGF2R IGF2R 2828 0.071 0.38 YES
46 ARSA ARSA ARSA 2862 0.07 0.39 YES
47 AP3D1 AP3D1 AP3D1 2949 0.068 0.39 YES
48 CTSL1 CTSL1 CTSL1 2952 0.068 0.39 YES
49 AP1M1 AP1M1 AP1M1 2997 0.067 0.4 YES
50 GGA3 GGA3 GGA3 3007 0.067 0.4 YES
51 M6PR M6PR M6PR 3117 0.064 0.4 YES
52 AP1S1 AP1S1 AP1S1 3139 0.063 0.41 YES
53 CLTB CLTB CLTB 3270 0.06 0.4 NO
54 CTSZ CTSZ CTSZ 3533 0.055 0.4 NO
55 NAGPA NAGPA NAGPA 3543 0.054 0.4 NO
56 AP3S2 AP3S2 AP3S2 3580 0.054 0.4 NO
57 GGA2 GGA2 GGA2 3727 0.05 0.4 NO
58 GNPTG GNPTG GNPTG 3770 0.05 0.4 NO
59 PSAP PSAP PSAP 3947 0.046 0.39 NO
60 SLC11A2 SLC11A2 SLC11A2 4053 0.044 0.39 NO
61 ENTPD4 ENTPD4 ENTPD4 4511 0.036 0.37 NO
62 LAMP1 LAMP1 LAMP1 4675 0.033 0.36 NO
63 LAMP2 LAMP2 LAMP2 4684 0.032 0.37 NO
64 CTSB CTSB CTSB 4744 0.031 0.37 NO
65 GNPTAB GNPTAB GNPTAB 4838 0.03 0.36 NO
66 AP1B1 AP1B1 AP1B1 4864 0.029 0.36 NO
67 CTSK CTSK CTSK 4885 0.028 0.37 NO
68 DNASE2 DNASE2 DNASE2 4895 0.028 0.37 NO
69 CLTA CLTA CLTA 4897 0.028 0.37 NO
70 MAN2B1 MAN2B1 MAN2B1 4994 0.027 0.37 NO
71 AP1M2 AP1M2 AP1M2 5136 0.024 0.36 NO
72 HEXB HEXB HEXB 5149 0.024 0.36 NO
73 AP4M1 AP4M1 AP4M1 5523 0.016 0.34 NO
74 ABCA2 ABCA2 ABCA2 5734 0.013 0.33 NO
75 CLTC CLTC CLTC 5975 0.0079 0.32 NO
76 AGA AGA AGA 5981 0.0078 0.32 NO
77 AP3M1 AP3M1 AP3M1 6071 0.006 0.32 NO
78 GUSB GUSB GUSB 6268 0.0021 0.31 NO
79 SUMF1 SUMF1 SUMF1 6363 0.00039 0.3 NO
80 GNS GNS GNS 6529 -0.003 0.29 NO
81 CD68 CD68 CD68 6565 -0.0038 0.29 NO
82 TCIRG1 TCIRG1 TCIRG1 6837 -0.0089 0.28 NO
83 LAPTM4A LAPTM4A LAPTM4A 6906 -0.01 0.27 NO
84 GAA GAA GAA 6941 -0.011 0.27 NO
85 PPT1 PPT1 PPT1 7279 -0.018 0.26 NO
86 GALNS GALNS GALNS 7301 -0.018 0.26 NO
87 AP3S1 AP3S1 AP3S1 7784 -0.028 0.23 NO
88 SLC17A5 SLC17A5 SLC17A5 7996 -0.032 0.22 NO
89 LIPA LIPA LIPA 8028 -0.033 0.22 NO
90 AP4S1 AP4S1 AP4S1 8126 -0.035 0.22 NO
91 LGMN LGMN LGMN 8173 -0.036 0.22 NO
92 AP1S2 AP1S2 AP1S2 8435 -0.041 0.21 NO
93 AP1G1 AP1G1 AP1G1 8452 -0.041 0.21 NO
94 ATP6V0A2 ATP6V0A2 ATP6V0A2 8498 -0.042 0.22 NO
95 ARSB ARSB ARSB 9100 -0.056 0.19 NO
96 ACP2 ACP2 ACP2 9124 -0.056 0.19 NO
97 AP3B1 AP3B1 AP3B1 9243 -0.059 0.19 NO
98 AP4B1 AP4B1 AP4B1 9307 -0.06 0.19 NO
99 CLN5 CLN5 CLN5 9340 -0.061 0.19 NO
100 FUCA1 FUCA1 FUCA1 9409 -0.062 0.2 NO
101 SCARB2 SCARB2 SCARB2 9506 -0.065 0.2 NO
102 IDS IDS IDS 10091 -0.079 0.17 NO
103 CTSG CTSG CTSG 10615 -0.092 0.15 NO
104 HYAL1 HYAL1 HYAL1 10983 -0.1 0.14 NO
105 IDUA IDUA IDUA 11165 -0.11 0.14 NO
106 CD164 CD164 CD164 11319 -0.11 0.14 NO
107 SLC11A1 SLC11A1 SLC11A1 11374 -0.11 0.15 NO
108 AP4E1 AP4E1 AP4E1 12150 -0.14 0.12 NO
109 NAPSA NAPSA NAPSA 12567 -0.15 0.11 NO
110 CTSE CTSE CTSE 12684 -0.15 0.11 NO
111 CTSC CTSC CTSC 13489 -0.18 0.084 NO
112 CTSO CTSO CTSO 13540 -0.18 0.098 NO
113 GALC GALC GALC 13693 -0.19 0.11 NO
114 MANBA MANBA MANBA 13740 -0.19 0.12 NO
115 MFSD8 MFSD8 MFSD8 13846 -0.19 0.13 NO
116 CTSS CTSS CTSS 14474 -0.22 0.12 NO
117 LAPTM5 LAPTM5 LAPTM5 15199 -0.26 0.099 NO
118 CTSW CTSW CTSW 15812 -0.29 0.091 NO
119 LAMP3 LAMP3 LAMP3 16951 -0.38 0.061 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 SELENOAMINO ACID METABOLISM.

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

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

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ERCC2 ERCC2 ERCC2 1345 0.13 -0.018 YES
2 LIG1 LIG1 LIG1 1574 0.11 0.021 YES
3 POLD1 POLD1 POLD1 1814 0.1 0.054 YES
4 POLD2 POLD2 POLD2 2157 0.09 0.076 YES
5 DDB1 DDB1 DDB1 2335 0.084 0.1 YES
6 POLE POLE POLE 2411 0.082 0.14 YES
7 GTF2H4 GTF2H4 GTF2H4 2507 0.079 0.17 YES
8 POLE4 POLE4 POLE4 2674 0.074 0.19 YES
9 DDB2 DDB2 DDB2 2902 0.069 0.21 YES
10 RAD23A RAD23A RAD23A 3089 0.065 0.23 YES
11 RFC5 RFC5 RFC5 4279 0.04 0.18 YES
12 CETN2 CETN2 CETN2 4646 0.033 0.18 YES
13 RFC2 RFC2 RFC2 4875 0.029 0.18 YES
14 RPA3 RPA3 RPA3 4970 0.027 0.18 YES
15 PCNA PCNA PCNA 5215 0.022 0.18 YES
16 GTF2H5 GTF2H5 GTF2H5 5469 0.017 0.17 YES
17 RBX1 RBX1 RBX1 5728 0.013 0.16 YES
18 CUL4A CUL4A CUL4A 5735 0.013 0.17 YES
19 ERCC1 ERCC1 ERCC1 5853 0.01 0.17 YES
20 RPA1 RPA1 RPA1 5971 0.0079 0.16 YES
21 RPA2 RPA2 RPA2 6037 0.0067 0.16 YES
22 POLD4 POLD4 POLD4 6669 -0.006 0.13 YES
23 RPA4 RPA4 RPA4 7002 -0.012 0.12 YES
24 XPC XPC XPC 7052 -0.014 0.12 YES
25 POLE3 POLE3 POLE3 7239 -0.017 0.12 YES
26 RFC1 RFC1 RFC1 7357 -0.02 0.12 YES
27 ERCC3 ERCC3 ERCC3 7593 -0.024 0.12 YES
28 GTF2H1 GTF2H1 GTF2H1 7605 -0.024 0.13 YES
29 POLE2 POLE2 POLE2 7747 -0.027 0.13 YES
30 RFC4 RFC4 RFC4 7854 -0.03 0.14 YES
31 POLD3 POLD3 POLD3 7966 -0.032 0.15 YES
32 MNAT1 MNAT1 MNAT1 8520 -0.043 0.14 YES
33 RFC3 RFC3 RFC3 8596 -0.045 0.15 YES
34 CDK7 CDK7 CDK7 8606 -0.045 0.17 YES
35 ERCC6 ERCC6 ERCC6 8729 -0.048 0.19 YES
36 GTF2H2 GTF2H2 GTF2H2 8878 -0.051 0.2 YES
37 CCNH CCNH CCNH 9323 -0.061 0.21 YES
38 ERCC5 ERCC5 ERCC5 10114 -0.08 0.2 YES
39 ERCC4 ERCC4 ERCC4 10348 -0.086 0.22 YES
40 ERCC8 ERCC8 ERCC8 11046 -0.1 0.23 YES
41 CUL4B CUL4B CUL4B 11414 -0.11 0.26 YES
42 GTF2H3 GTF2H3 GTF2H3 11442 -0.12 0.31 YES
43 XPA XPA XPA 11644 -0.12 0.36 YES

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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

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

genes ES table in pathway: KEGG INOSITOL PHOSPHATE METABOLISM

Table 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 POLR2L POLR2L POLR2L 825 0.17 0.07 YES
2 POLR1A POLR1A POLR1A 1989 0.096 0.071 YES
3 POLR3C POLR3C POLR3C 2455 0.081 0.1 YES
4 POLR2E POLR2E POLR2E 2554 0.078 0.15 YES
5 POLR2I POLR2I POLR2I 2686 0.074 0.19 YES
6 POLR1C POLR1C POLR1C 3296 0.059 0.2 YES
7 POLR2F POLR2F POLR2F 3302 0.059 0.24 YES
8 POLR3H POLR3H POLR3H 3335 0.059 0.28 YES
9 POLR3A POLR3A POLR3A 3902 0.047 0.28 YES
10 POLR2J POLR2J POLR2J 4062 0.044 0.3 YES
11 POLR2A POLR2A POLR2A 4093 0.043 0.33 YES
12 POLR1D POLR1D POLR1D 4456 0.037 0.33 YES
13 POLR3D POLR3D POLR3D 4642 0.033 0.34 YES
14 ZNRD1 ZNRD1 ZNRD1 5019 0.026 0.34 YES
15 POLR3K POLR3K POLR3K 5100 0.025 0.35 YES
16 POLR1E POLR1E POLR1E 5258 0.021 0.36 YES
17 POLR3B POLR3B POLR3B 5541 0.016 0.35 YES
18 POLR2G POLR2G POLR2G 6847 -0.0092 0.29 YES
19 POLR2C POLR2C POLR2C 7026 -0.013 0.29 YES
20 POLR3GL POLR3GL POLR3GL 7241 -0.017 0.29 YES
21 POLR2D POLR2D POLR2D 7321 -0.019 0.3 YES
22 POLR2B POLR2B POLR2B 7734 -0.027 0.29 YES
23 POLR2J2 POLR2J2 POLR2J2 8219 -0.036 0.29 YES
24 POLR2K POLR2K POLR2K 8422 -0.041 0.3 YES
25 POLR2J3 POLR2J3 POLR2J3 8778 -0.049 0.32 YES
26 POLR3G POLR3G POLR3G 9432 -0.063 0.33 YES
27 POLR1B POLR1B POLR1B 11278 -0.11 0.3 YES
28 POLR3F POLR3F POLR3F 11376 -0.11 0.37 YES

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 INOSITOL PHOSPHATE METABOLISM.

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

genes ES table in pathway: KEGG 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 RENBP RENBP RENBP 310 0.27 0.048 YES
2 AMDHD2 AMDHD2 AMDHD2 354 0.25 0.11 YES
3 GALK1 GALK1 GALK1 534 0.22 0.15 YES
4 GALE GALE GALE 787 0.17 0.18 YES
5 CYB5R1 CYB5R1 CYB5R1 973 0.15 0.2 YES
6 NANS NANS NANS 1049 0.15 0.24 YES
7 GPI GPI GPI 1451 0.12 0.24 YES
8 PMM1 PMM1 PMM1 1532 0.12 0.27 YES
9 GNPDA1 GNPDA1 GNPDA1 1545 0.12 0.3 YES
10 HEXA HEXA HEXA 1748 0.11 0.31 YES
11 GMPPB GMPPB GMPPB 1954 0.098 0.32 YES
12 TSTA3 TSTA3 TSTA3 2133 0.091 0.33 YES
13 FUK FUK FUK 2176 0.09 0.35 YES
14 PGM1 PGM1 PGM1 2656 0.075 0.34 NO
15 GMPPA GMPPA GMPPA 3307 0.059 0.32 NO
16 MPI MPI MPI 3529 0.055 0.32 NO
17 GMDS GMDS GMDS 4227 0.041 0.3 NO
18 GALT GALT GALT 4603 0.034 0.28 NO
19 HK2 HK2 HK2 4624 0.034 0.29 NO
20 HEXB HEXB HEXB 5149 0.024 0.27 NO
21 CHIT1 CHIT1 CHIT1 5531 0.016 0.25 NO
22 PMM2 PMM2 PMM2 6014 0.0072 0.22 NO
23 NAGK NAGK NAGK 6041 0.0066 0.22 NO
24 HK1 HK1 HK1 6685 -0.0062 0.19 NO
25 CMAS CMAS CMAS 6962 -0.012 0.18 NO
26 NPL NPL NPL 7216 -0.017 0.17 NO
27 GNPNAT1 GNPNAT1 GNPNAT1 7514 -0.022 0.16 NO
28 GFPT1 GFPT1 GFPT1 7831 -0.029 0.15 NO
29 UXS1 UXS1 UXS1 8194 -0.036 0.14 NO
30 NANP NANP NANP 9130 -0.056 0.097 NO
31 UGP2 UGP2 UGP2 9251 -0.059 0.1 NO
32 GALK2 GALK2 GALK2 9401 -0.062 0.11 NO
33 GNE GNE GNE 9514 -0.065 0.12 NO
34 UAP1 UAP1 UAP1 10076 -0.079 0.11 NO
35 UGDH UGDH UGDH 10879 -0.099 0.088 NO
36 PGM3 PGM3 PGM3 12079 -0.13 0.054 NO
37 GNPDA2 GNPDA2 GNPDA2 12215 -0.14 0.08 NO
38 PGM2 PGM2 PGM2 12259 -0.14 0.11 NO
39 FPGT FPGT FPGT 12604 -0.15 0.13 NO
40 GFPT2 GFPT2 GFPT2 12850 -0.16 0.15 NO
41 GCK GCK GCK 14441 -0.22 0.12 NO
42 HK3 HK3 HK3 16525 -0.34 0.085 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 AMINOACYL TRNA BIOSYNTHESIS

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 MME MME MME 198 0.33 0.01 YES
2 PSEN2 PSEN2 PSEN2 299 0.27 0.022 YES
3 SNCA SNCA SNCA 348 0.26 0.036 YES
4 BACE2 BACE2 BACE2 471 0.23 0.044 YES
5 CACNA1D CACNA1D CACNA1D 623 0.2 0.048 YES
6 COX6A2 COX6A2 COX6A2 630 0.2 0.06 YES
7 MAPT MAPT MAPT 668 0.19 0.07 YES
8 CHP2 CHP2 CHP2 826 0.17 0.072 YES
9 FADD FADD FADD 964 0.16 0.074 YES
10 CDK5R1 CDK5R1 CDK5R1 965 0.15 0.084 YES
11 NDUFS7 NDUFS7 NDUFS7 995 0.15 0.092 YES
12 NDUFA8 NDUFA8 NDUFA8 1133 0.14 0.094 YES
13 NDUFS8 NDUFS8 NDUFS8 1306 0.13 0.092 YES
14 UQCRC1 UQCRC1 UQCRC1 1333 0.13 0.099 YES
15 APOE APOE APOE 1404 0.12 0.1 YES
16 SDHA SDHA SDHA 1409 0.12 0.11 YES
17 NDUFA7 NDUFA7 NDUFA7 1445 0.12 0.12 YES
18 NDUFB7 NDUFB7 NDUFB7 1458 0.12 0.12 YES
19 NDUFV1 NDUFV1 NDUFV1 1483 0.12 0.13 YES
20 ATP5G1 ATP5G1 ATP5G1 1554 0.12 0.13 YES
21 COX6A1 COX6A1 COX6A1 1569 0.11 0.14 YES
22 CYC1 CYC1 CYC1 1685 0.11 0.14 YES
23 ATP5D ATP5D ATP5D 1700 0.11 0.15 YES
24 NDUFV3 NDUFV3 NDUFV3 1729 0.11 0.15 YES
25 NDUFS6 NDUFS6 NDUFS6 1736 0.11 0.16 YES
26 COX5A COX5A COX5A 1756 0.11 0.16 YES
27 NDUFA3 NDUFA3 NDUFA3 1773 0.11 0.17 YES
28 NDUFC2 NDUFC2 NDUFC2 1844 0.1 0.17 YES
29 ATP5B ATP5B ATP5B 1862 0.1 0.18 YES
30 NDUFB1 NDUFB1 NDUFB1 1888 0.1 0.18 YES
31 COX5B COX5B COX5B 1891 0.1 0.19 YES
32 UQCR10 UQCR10 UQCR10 2038 0.094 0.19 YES
33 NDUFB4 NDUFB4 NDUFB4 2073 0.093 0.19 YES
34 CDK5 CDK5 CDK5 2150 0.09 0.19 YES
35 GRIN1 GRIN1 GRIN1 2161 0.09 0.2 YES
36 COX8A COX8A COX8A 2207 0.089 0.2 YES
37 NDUFS2 NDUFS2 NDUFS2 2255 0.087 0.2 YES
38 COX6B1 COX6B1 COX6B1 2311 0.085 0.21 YES
39 UQCRQ UQCRQ UQCRQ 2318 0.085 0.21 YES
40 CAPN1 CAPN1 CAPN1 2328 0.084 0.22 YES
41 NDUFB9 NDUFB9 NDUFB9 2346 0.084 0.22 YES
42 APH1A APH1A APH1A 2431 0.081 0.22 YES
43 ATP5H ATP5H ATP5H 2442 0.081 0.23 YES
44 ATP5G3 ATP5G3 ATP5G3 2544 0.078 0.22 YES
45 SDHB SDHB SDHB 2558 0.078 0.23 YES
46 NDUFB10 NDUFB10 NDUFB10 2627 0.076 0.23 YES
47 COX6C COX6C COX6C 2638 0.075 0.24 YES
48 NDUFA1 NDUFA1 NDUFA1 2683 0.074 0.24 YES
49 CHP CHP CHP 2722 0.073 0.24 YES
50 ATP5G2 ATP5G2 ATP5G2 2750 0.072 0.24 YES
51 UQCRHL UQCRHL UQCRHL 2845 0.07 0.24 YES
52 PSENEN PSENEN PSENEN 2846 0.07 0.25 YES
53 NDUFA6 NDUFA6 NDUFA6 2888 0.069 0.25 YES
54 NDUFA9 NDUFA9 NDUFA9 2893 0.069 0.25 YES
55 UQCRFS1 UQCRFS1 UQCRFS1 2911 0.069 0.26 YES
56 NDUFS3 NDUFS3 NDUFS3 2922 0.068 0.26 YES
57 SDHC SDHC SDHC 3008 0.067 0.26 YES
58 NDUFA2 NDUFA2 NDUFA2 3301 0.059 0.25 YES
59 GAPDH GAPDH GAPDH 3366 0.058 0.25 YES
60 UQCRH UQCRH UQCRH 3499 0.055 0.24 YES
61 CAPN2 CAPN2 CAPN2 3502 0.055 0.25 YES
62 COX7A2L COX7A2L COX7A2L 3550 0.054 0.25 YES
63 NDUFB8 NDUFB8 NDUFB8 3569 0.054 0.25 YES
64 UQCRB UQCRB UQCRB 3607 0.053 0.25 YES
65 APBB1 APBB1 APBB1 3669 0.052 0.25 YES
66 MAPK3 MAPK3 MAPK3 3683 0.051 0.25 YES
67 MAPK1 MAPK1 MAPK1 3690 0.051 0.26 YES
68 PLCB3 PLCB3 PLCB3 3724 0.051 0.26 YES
69 COX7A2 COX7A2 COX7A2 3769 0.05 0.26 YES
70 NCSTN NCSTN NCSTN 3909 0.047 0.25 YES
71 ATP5J ATP5J ATP5J 3973 0.045 0.25 YES
72 COX4I1 COX4I1 COX4I1 3979 0.045 0.26 YES
73 COX7C COX7C COX7C 3996 0.045 0.26 YES
74 NDUFB2 NDUFB2 NDUFB2 4008 0.045 0.26 YES
75 UQCR11 UQCR11 UQCR11 4024 0.044 0.26 YES
76 NDUFS5 NDUFS5 NDUFS5 4033 0.044 0.26 YES
77 CALML5 CALML5 CALML5 4047 0.044 0.27 YES
78 HSD17B10 HSD17B10 HSD17B10 4105 0.043 0.27 YES
79 ATP5A1 ATP5A1 ATP5A1 4144 0.042 0.27 YES
80 NDUFV2 NDUFV2 NDUFV2 4154 0.042 0.27 YES
81 ITPR3 ITPR3 ITPR3 4181 0.042 0.27 YES
82 ATP2A2 ATP2A2 ATP2A2 4471 0.037 0.26 NO
83 NDUFA10 NDUFA10 NDUFA10 4704 0.032 0.25 NO
84 ATP5O ATP5O ATP5O 4707 0.032 0.25 NO
85 CALML3 CALML3 CALML3 4749 0.031 0.25 NO
86 BAD BAD BAD 4823 0.03 0.24 NO
87 COX8C COX8C COX8C 4861 0.029 0.24 NO
88 NDUFAB1 NDUFAB1 NDUFAB1 4862 0.029 0.25 NO
89 NDUFC1 NDUFC1 NDUFC1 5059 0.025 0.24 NO
90 NDUFS1 NDUFS1 NDUFS1 5130 0.024 0.24 NO
91 PSEN1 PSEN1 PSEN1 5243 0.022 0.23 NO
92 ATP5C1 ATP5C1 ATP5C1 5251 0.022 0.23 NO
93 CYCS CYCS CYCS 5268 0.021 0.23 NO
94 NDUFB3 NDUFB3 NDUFB3 5697 0.013 0.21 NO
95 NDUFB6 NDUFB6 NDUFB6 5749 0.012 0.21 NO
96 COX7B COX7B COX7B 5751 0.012 0.21 NO
97 ATP5F1 ATP5F1 ATP5F1 6079 0.0058 0.19 NO
98 NDUFA4 NDUFA4 NDUFA4 6139 0.0046 0.19 NO
99 CALM3 CALM3 CALM3 6174 0.0039 0.18 NO
100 ATF6 ATF6 ATF6 6260 0.0022 0.18 NO
101 UQCRC2 UQCRC2 UQCRC2 6499 -0.0024 0.17 NO
102 CALM1 CALM1 CALM1 6570 -0.0039 0.16 NO
103 NDUFB5 NDUFB5 NDUFB5 6584 -0.0042 0.16 NO
104 CASP9 CASP9 CASP9 6635 -0.0051 0.16 NO
105 ATP5E ATP5E ATP5E 6864 -0.0096 0.15 NO
106 CACNA1S CACNA1S CACNA1S 7163 -0.016 0.13 NO
107 ADAM10 ADAM10 ADAM10 7198 -0.016 0.13 NO
108 RYR3 RYR3 RYR3 7263 -0.018 0.13 NO
109 GSK3B GSK3B GSK3B 7338 -0.019 0.13 NO
110 NDUFS4 NDUFS4 NDUFS4 7806 -0.029 0.1 NO
111 PPP3CC PPP3CC PPP3CC 8055 -0.034 0.091 NO
112 GRIN2D GRIN2D GRIN2D 8208 -0.036 0.084 NO
113 GNAQ GNAQ GNAQ 8269 -0.038 0.084 NO
114 GRIN2C GRIN2C GRIN2C 8341 -0.039 0.082 NO
115 ERN1 ERN1 ERN1 8369 -0.04 0.083 NO
116 NDUFA5 NDUFA5 NDUFA5 8721 -0.048 0.066 NO
117 NAE1 NAE1 NAE1 8904 -0.052 0.06 NO
118 PPP3R1 PPP3R1 PPP3R1 9131 -0.056 0.051 NO
119 LRP1 LRP1 LRP1 9224 -0.058 0.049 NO
120 ATP2A1 ATP2A1 ATP2A1 9363 -0.061 0.045 NO
121 TNFRSF1A TNFRSF1A TNFRSF1A 9435 -0.063 0.046 NO
122 GRIN2A GRIN2A GRIN2A 9882 -0.074 0.025 NO
123 COX6B2 COX6B2 COX6B2 9909 -0.075 0.029 NO
124 APP APP APP 9969 -0.076 0.03 NO
125 COX4I2 COX4I2 COX4I2 10068 -0.079 0.03 NO
126 IDE IDE IDE 10189 -0.082 0.028 NO
127 NDUFA4L2 NDUFA4L2 NDUFA4L2 10404 -0.087 0.022 NO
128 CALM2 CALM2 CALM2 10451 -0.088 0.025 NO
129 GRIN2B GRIN2B GRIN2B 10484 -0.089 0.029 NO
130 PPP3CB PPP3CB PPP3CB 10654 -0.093 0.026 NO
131 SDHD SDHD SDHD 10992 -0.1 0.013 NO
132 EIF2AK3 EIF2AK3 EIF2AK3 11061 -0.1 0.016 NO
133 BID BID BID 11345 -0.11 0.0074 NO
134 BACE1 BACE1 BACE1 11928 -0.13 -0.017 NO
135 PPP3CA PPP3CA PPP3CA 12571 -0.15 -0.043 NO
136 CASP3 CASP3 CASP3 12666 -0.15 -0.039 NO
137 APAF1 APAF1 APAF1 12779 -0.16 -0.035 NO
138 PPP3R2 PPP3R2 PPP3R2 12952 -0.16 -0.035 NO
139 ITPR2 ITPR2 ITPR2 13024 -0.16 -0.028 NO
140 ADAM17 ADAM17 ADAM17 13149 -0.17 -0.024 NO
141 CALML6 CALML6 CALML6 13242 -0.17 -0.019 NO
142 CACNA1F CACNA1F CACNA1F 13808 -0.19 -0.038 NO
143 CASP7 CASP7 CASP7 14102 -0.2 -0.041 NO
144 NOS1 NOS1 NOS1 14669 -0.23 -0.058 NO
145 COX7A1 COX7A1 COX7A1 14755 -0.23 -0.048 NO
146 CASP8 CASP8 CASP8 14891 -0.24 -0.04 NO
147 PLCB4 PLCB4 PLCB4 15058 -0.25 -0.034 NO
148 ATP2A3 ATP2A3 ATP2A3 15584 -0.28 -0.046 NO
149 PLCB2 PLCB2 PLCB2 15851 -0.29 -0.042 NO
150 ITPR1 ITPR1 ITPR1 15966 -0.3 -0.029 NO
151 LPL LPL LPL 16232 -0.32 -0.023 NO
152 TNF TNF TNF 16449 -0.33 -0.014 NO
153 CACNA1C CACNA1C CACNA1C 16534 -0.34 0.0029 NO
154 FAS FAS FAS 17353 -0.42 -0.016 NO
155 IL1B IL1B IL1B 17378 -0.42 0.0098 NO
156 PLCB1 PLCB1 PLCB1 17446 -0.43 0.034 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 AMINOACYL TRNA BIOSYNTHESIS.

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

genes ES table in pathway: KEGG RIBOSOME

Table 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 ATP6V0A4 ATP6V0A4 ATP6V0A4 142 0.36 0.064 YES
2 ATP6V0D2 ATP6V0D2 ATP6V0D2 281 0.28 0.11 YES
3 ATP6V0A1 ATP6V0A1 ATP6V0A1 881 0.16 0.11 YES
4 ADCY9 ADCY9 ADCY9 933 0.16 0.14 YES
5 ATP6V0C ATP6V0C ATP6V0C 1143 0.14 0.16 YES
6 ATP6AP1 ATP6AP1 ATP6AP1 1162 0.14 0.19 YES
7 ATP6V0B ATP6V0B ATP6V0B 1549 0.12 0.19 YES
8 ATP6V1F ATP6V1F ATP6V1F 1680 0.11 0.2 YES
9 ATP6V0D1 ATP6V0D1 ATP6V0D1 1766 0.11 0.22 YES
10 ATP6V1D ATP6V1D ATP6V1D 1838 0.1 0.24 YES
11 ATP6V1B2 ATP6V1B2 ATP6V1B2 1848 0.1 0.26 YES
12 KDELR3 KDELR3 KDELR3 2358 0.083 0.24 YES
13 ATP6V1E2 ATP6V1E2 ATP6V1E2 2374 0.083 0.26 YES
14 ATP6V1C1 ATP6V1C1 ATP6V1C1 2489 0.08 0.27 YES
15 ACTG1 ACTG1 ACTG1 2643 0.075 0.28 YES
16 ATP6V1E1 ATP6V1E1 ATP6V1E1 2649 0.075 0.29 YES
17 ATP6V1H ATP6V1H ATP6V1H 2735 0.073 0.3 YES
18 TJP2 TJP2 TJP2 2836 0.07 0.31 YES
19 ATP6V1G1 ATP6V1G1 ATP6V1G1 2969 0.068 0.32 YES
20 KDELR1 KDELR1 KDELR1 3875 0.048 0.28 NO
21 ARF1 ARF1 ARF1 4021 0.045 0.28 NO
22 SEC61B SEC61B SEC61B 5073 0.025 0.22 NO
23 ATP6V0E1 ATP6V0E1 ATP6V0E1 5287 0.021 0.21 NO
24 SEC61A2 SEC61A2 SEC61A2 5629 0.014 0.2 NO
25 PRKACA PRKACA PRKACA 5677 0.014 0.2 NO
26 ACTB ACTB ACTB 5714 0.013 0.2 NO
27 ATP6V0E2 ATP6V0E2 ATP6V0E2 5858 0.01 0.19 NO
28 SEC61A1 SEC61A1 SEC61A1 6275 0.0019 0.17 NO
29 ATP6V1A ATP6V1A ATP6V1A 6280 0.0018 0.17 NO
30 PLCG1 PLCG1 PLCG1 6774 -0.0078 0.14 NO
31 TCIRG1 TCIRG1 TCIRG1 6837 -0.0089 0.14 NO
32 SEC61G SEC61G SEC61G 7086 -0.014 0.13 NO
33 ERO1L ERO1L ERO1L 7266 -0.018 0.13 NO
34 KDELR2 KDELR2 KDELR2 7353 -0.019 0.12 NO
35 GNAS GNAS GNAS 7902 -0.03 0.1 NO
36 ATP6V0A2 ATP6V0A2 ATP6V0A2 8498 -0.042 0.076 NO
37 ATP6V1B1 ATP6V1B1 ATP6V1B1 8982 -0.054 0.06 NO
38 CFTR CFTR CFTR 10202 -0.082 0.0088 NO
39 PDIA4 PDIA4 PDIA4 10928 -0.1 -0.011 NO
40 ATP6V1G2 ATP6V1G2 ATP6V1G2 11545 -0.12 -0.022 NO
41 ATP6V1C2 ATP6V1C2 ATP6V1C2 11782 -0.12 -0.0098 NO
42 TJP1 TJP1 TJP1 12239 -0.14 -0.0074 NO
43 SLC12A2 SLC12A2 SLC12A2 12389 -0.14 0.013 NO
44 PRKCB PRKCB PRKCB 13148 -0.17 0.0045 NO
45 PRKX PRKX PRKX 13366 -0.18 0.028 NO
46 PLCG2 PLCG2 PLCG2 14119 -0.2 0.027 NO
47 KCNQ1 KCNQ1 KCNQ1 14230 -0.21 0.063 NO
48 PRKCG PRKCG PRKCG 14691 -0.23 0.084 NO
49 PRKACB PRKACB PRKACB 14968 -0.24 0.12 NO
50 PRKCA PRKCA PRKCA 15451 -0.27 0.14 NO

Figure S19.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RIBOSOME.

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

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 AGR PATHWAY 35 genes.ES.table 0.25 0.74 0.81 0.79 1 0.31 0.31 0.22 0.8 0
BIOCARTA AT1R PATHWAY 32 genes.ES.table 0.38 1.4 0.13 0.17 0.96 0.062 0.052 0.059 0.13 0
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.73 2 0.002 0.022 0.055 0.24 0.056 0.23 0 0.004
BIOCARTA BIOPEPTIDES PATHWAY 39 genes.ES.table 0.46 1.7 0.012 0.049 0.57 0.31 0.24 0.24 0.022 0
BIOCARTA HDAC PATHWAY 27 genes.ES.table 0.51 1.7 0.01 0.043 0.48 0.48 0.31 0.33 0 0
BIOCARTA EGF PATHWAY 30 genes.ES.table 0.52 1.7 0.016 0.045 0.46 0.53 0.34 0.35 0 0
BIOCARTA FAS PATHWAY 29 genes.ES.table 0.56 1.8 0 0.031 0.29 0.28 0.18 0.23 0 0
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.64 1.9 0.004 0.025 0.23 0.24 0.11 0.22 0 0
BIOCARTA FMLP PATHWAY 34 genes.ES.table 0.57 1.9 0 0.026 0.2 0.29 0.22 0.23 0 0
BIOCARTA GH PATHWAY 26 genes.ES.table 0.57 1.7 0.02 0.046 0.55 0.19 0.076 0.18 0.02 0
genes ES table in pathway: BIOCARTA AGR 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 PTPRC PTPRC PTPRC 230 0.77 0.036 YES
2 NCF1 NCF1 NCF1 269 0.74 0.08 YES
3 VAV1 VAV1 VAV1 284 0.74 0.12 YES
4 PIK3CG PIK3CG PIK3CG 345 0.7 0.17 YES
5 WAS WAS WAS 385 0.68 0.21 YES
6 PRKCB PRKCB PRKCB 409 0.66 0.25 YES
7 DOCK2 DOCK2 DOCK2 410 0.66 0.29 YES
8 INPP5D INPP5D INPP5D 431 0.65 0.33 YES
9 FCGR1A FCGR1A FCGR1A 486 0.62 0.36 YES
10 RAC2 RAC2 RAC2 494 0.62 0.4 YES
11 PIK3R5 PIK3R5 PIK3R5 514 0.61 0.44 YES
12 HCK HCK HCK 588 0.57 0.47 YES
13 LAT LAT LAT 654 0.55 0.5 YES
14 SYK SYK SYK 771 0.5 0.53 YES
15 PLCG2 PLCG2 PLCG2 839 0.48 0.55 YES
16 FCGR3A FCGR3A FCGR3A 975 0.44 0.57 YES
17 LYN LYN LYN 1002 0.43 0.6 YES
18 FCGR2B FCGR2B FCGR2B 1202 0.38 0.61 YES
19 VAV3 VAV3 VAV3 1268 0.36 0.63 YES
20 FCGR2C FCGR2C FCGR2C 1504 0.31 0.64 YES
21 PIP5K1B PIP5K1B PIP5K1B 1644 0.28 0.65 YES
22 PRKCG PRKCG PRKCG 2145 0.22 0.63 NO
23 PIK3CD PIK3CD PIK3CD 2451 0.19 0.63 NO
24 FCGR2A FCGR2A FCGR2A 2779 0.16 0.62 NO
25 MARCKS MARCKS MARCKS 4253 0.088 0.54 NO
26 ARPC3 ARPC3 ARPC3 4336 0.085 0.54 NO
27 VASP VASP VASP 4517 0.08 0.54 NO
28 PIK3R3 PIK3R3 PIK3R3 4702 0.075 0.53 NO
29 PIK3R1 PIK3R1 PIK3R1 4757 0.074 0.54 NO
30 PIK3CA PIK3CA PIK3CA 4930 0.07 0.53 NO
31 ARF6 ARF6 ARF6 4958 0.069 0.53 NO
32 PPAP2B PPAP2B PPAP2B 5059 0.067 0.53 NO
33 ARPC2 ARPC2 ARPC2 5221 0.063 0.53 NO
34 PPAP2A PPAP2A PPAP2A 5257 0.062 0.53 NO
35 PAK1 PAK1 PAK1 5375 0.059 0.52 NO
36 PLD1 PLD1 PLD1 5452 0.058 0.52 NO
37 ARPC5 ARPC5 ARPC5 5591 0.055 0.52 NO
38 CDC42 CDC42 CDC42 5671 0.053 0.52 NO
39 LIMK2 LIMK2 LIMK2 5691 0.053 0.52 NO
40 DNM3 DNM3 DNM3 5727 0.052 0.52 NO
41 PIK3CB PIK3CB PIK3CB 5836 0.05 0.52 NO
42 SPHK1 SPHK1 SPHK1 5867 0.05 0.52 NO
43 RPS6KB1 RPS6KB1 RPS6KB1 5900 0.049 0.52 NO
44 AMPH AMPH AMPH 6024 0.046 0.52 NO
45 ARPC5L ARPC5L ARPC5L 6038 0.046 0.52 NO
46 PRKCD PRKCD PRKCD 6116 0.045 0.52 NO
47 MAP2K1 MAP2K1 MAP2K1 6134 0.045 0.52 NO
48 ARPC1B ARPC1B ARPC1B 6364 0.041 0.51 NO
49 ARPC4 ARPC4 ARPC4 6899 0.032 0.48 NO
50 SCIN SCIN SCIN 7151 0.028 0.47 NO
51 PIKFYVE PIKFYVE PIKFYVE 7238 0.027 0.47 NO
52 LIMK1 LIMK1 LIMK1 7588 0.022 0.45 NO
53 DNM2 DNM2 DNM2 7645 0.022 0.45 NO
54 CFL1 CFL1 CFL1 8463 0.011 0.4 NO
55 RAF1 RAF1 RAF1 8684 0.0083 0.39 NO
56 ASAP3 ASAP3 ASAP3 9004 0.0045 0.37 NO
57 WASF2 WASF2 WASF2 9125 0.0031 0.37 NO
58 PLD2 PLD2 PLD2 9787 -0.0046 0.33 NO
59 GSN GSN GSN 10172 -0.009 0.31 NO
60 MARCKSL1 MARCKSL1 MARCKSL1 10257 -0.0098 0.31 NO
61 MAPK3 MAPK3 MAPK3 10357 -0.011 0.3 NO
62 PLA2G6 PLA2G6 PLA2G6 10602 -0.014 0.29 NO
63 RAC1 RAC1 RAC1 11412 -0.023 0.24 NO
64 PIP5K1C PIP5K1C PIP5K1C 11497 -0.024 0.24 NO
65 DNM1L DNM1L DNM1L 11669 -0.025 0.23 NO
66 MAPK1 MAPK1 MAPK1 12160 -0.031 0.21 NO
67 CRKL CRKL CRKL 12203 -0.031 0.21 NO
68 WASL WASL WASL 12337 -0.033 0.2 NO
69 AKT1 AKT1 AKT1 12366 -0.033 0.2 NO
70 SPHK2 SPHK2 SPHK2 12550 -0.035 0.2 NO
71 ASAP1 ASAP1 ASAP1 12993 -0.041 0.17 NO
72 ARPC1A ARPC1A ARPC1A 13579 -0.048 0.14 NO
73 PLCG1 PLCG1 PLCG1 13619 -0.049 0.14 NO
74 AKT3 AKT3 AKT3 13688 -0.05 0.14 NO
75 VAV2 VAV2 VAV2 13764 -0.051 0.14 NO
76 AKT2 AKT2 AKT2 13834 -0.052 0.14 NO
77 PIP4K2B PIP4K2B PIP4K2B 14041 -0.055 0.14 NO
78 CRK CRK CRK 14161 -0.056 0.13 NO
79 PLA2G4D PLA2G4D PLA2G4D 14304 -0.059 0.13 NO
80 PIP5K1A PIP5K1A PIP5K1A 14585 -0.063 0.12 NO
81 PLA2G4A PLA2G4A PLA2G4A 14599 -0.064 0.12 NO
82 PRKCE PRKCE PRKCE 14650 -0.065 0.12 NO
83 CFL2 CFL2 CFL2 14754 -0.066 0.12 NO
84 MYO10 MYO10 MYO10 15075 -0.073 0.1 NO
85 ASAP2 ASAP2 ASAP2 15619 -0.084 0.08 NO
86 GAB2 GAB2 GAB2 15732 -0.088 0.08 NO
87 WASF1 WASF1 WASF1 16032 -0.096 0.069 NO
88 WASF3 WASF3 WASF3 16077 -0.098 0.073 NO
89 PLA2G4F PLA2G4F PLA2G4F 16159 -0.1 0.075 NO
90 PRKCA PRKCA PRKCA 16304 -0.11 0.073 NO
91 PIK3R2 PIK3R2 PIK3R2 16574 -0.12 0.066 NO
92 PPAP2C PPAP2C PPAP2C 16719 -0.12 0.065 NO
93 DNM1 DNM1 DNM1 16950 -0.14 0.061 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 AGR PATHWAY.

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

genes ES table in pathway: BIOCARTA AT1R PATHWAY

Table 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 TLR10 TLR10 TLR10 59 0.93 0.15 YES
2 TLR9 TLR9 TLR9 223 0.78 0.26 YES
3 TLR7 TLR7 TLR7 383 0.68 0.36 YES
4 TLR4 TLR4 TLR4 1075 0.41 0.39 YES
5 TLR6 TLR6 TLR6 1142 0.4 0.45 YES
6 TLR2 TLR2 TLR2 1298 0.36 0.5 YES
7 CD14 CD14 CD14 1486 0.31 0.54 YES
8 TLR3 TLR3 TLR3 1574 0.3 0.59 YES
9 NFKBIA NFKBIA NFKBIA 1804 0.26 0.62 YES
10 LY96 LY96 LY96 1835 0.25 0.66 YES
11 MAP3K14 MAP3K14 MAP3K14 1930 0.24 0.69 YES
12 MAP2K6 MAP2K6 MAP2K6 2700 0.16 0.67 NO
13 MYD88 MYD88 MYD88 3369 0.12 0.66 NO
14 TAB2 TAB2 TAB2 3778 0.1 0.65 NO
15 NFKB1 NFKB1 NFKB1 3941 0.099 0.66 NO
16 CHUK CHUK CHUK 4948 0.069 0.61 NO
17 MAP3K7 MAP3K7 MAP3K7 5013 0.068 0.62 NO
18 IKBKG IKBKG IKBKG 5521 0.057 0.6 NO
19 EIF2AK2 EIF2AK2 EIF2AK2 5561 0.056 0.61 NO
20 MAP3K1 MAP3K1 MAP3K1 5627 0.054 0.61 NO
21 IKBKB IKBKB IKBKB 6091 0.046 0.6 NO
22 FOS FOS FOS 6925 0.031 0.55 NO
23 JUN JUN JUN 6971 0.031 0.56 NO
24 MAP2K3 MAP2K3 MAP2K3 7115 0.029 0.55 NO
25 MAP2K4 MAP2K4 MAP2K4 7919 0.018 0.51 NO
26 MAPK14 MAPK14 MAPK14 9287 0.0011 0.44 NO
27 IRAK1 IRAK1 IRAK1 10770 -0.016 0.36 NO
28 RELA RELA RELA 10850 -0.017 0.35 NO
29 MAPK8 MAPK8 MAPK8 11238 -0.021 0.34 NO
30 TRAF6 TRAF6 TRAF6 11423 -0.023 0.33 NO
31 PGLYRP1 PGLYRP1 PGLYRP1 11596 -0.024 0.32 NO
32 ELK1 ELK1 ELK1 12058 -0.03 0.3 NO
33 TAB1 TAB1 TAB1 12374 -0.033 0.29 NO
34 TOLLIP TOLLIP TOLLIP 12375 -0.033 0.3 NO
35 TIRAP TIRAP TIRAP 12664 -0.037 0.29 NO
36 ECSIT ECSIT ECSIT 15364 -0.078 0.15 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 AT1R PATHWAY.

Figure S24.  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 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 FASLG FASLG FASLG 63 0.92 0.11 YES
2 PRKCQ PRKCQ PRKCQ 90 0.9 0.22 YES
3 TNF TNF TNF 191 0.8 0.32 YES
4 PRKCB PRKCB PRKCB 409 0.66 0.39 YES
5 CEBPA CEBPA CEBPA 744 0.52 0.43 YES
6 MAPK13 MAPK13 MAPK13 763 0.51 0.49 YES
7 TNFRSF1B TNFRSF1B TNFRSF1B 969 0.44 0.54 YES
8 PRKCH PRKCH PRKCH 1370 0.34 0.56 YES
9 MAP3K5 MAP3K5 MAP3K5 1429 0.33 0.6 YES
10 FAS FAS FAS 1468 0.32 0.63 YES
11 NFKBIA NFKBIA NFKBIA 1804 0.26 0.65 YES
12 MAP3K14 MAP3K14 MAP3K14 1930 0.24 0.67 YES
13 PRKCG PRKCG PRKCG 2145 0.22 0.68 YES
14 MAP2K6 MAP2K6 MAP2K6 2700 0.16 0.67 NO
15 ETS1 ETS1 ETS1 3284 0.13 0.66 NO
16 BCL2 BCL2 BCL2 3823 0.1 0.64 NO
17 NFKB1 NFKB1 NFKB1 3941 0.099 0.65 NO
18 ETS2 ETS2 ETS2 4173 0.091 0.64 NO
19 CHUK CHUK CHUK 4948 0.069 0.61 NO
20 EGFR EGFR EGFR 5321 0.06 0.6 NO
21 MAP3K1 MAP3K1 MAP3K1 5627 0.054 0.59 NO
22 EGF EGF EGF 6023 0.046 0.57 NO
23 IKBKB IKBKB IKBKB 6091 0.046 0.57 NO
24 PRKCD PRKCD PRKCD 6116 0.045 0.58 NO
25 MAP2K1 MAP2K1 MAP2K1 6134 0.045 0.58 NO
26 PPP2CA PPP2CA PPP2CA 6421 0.04 0.57 NO
27 FOS FOS FOS 6925 0.031 0.55 NO
28 JUN JUN JUN 6971 0.031 0.55 NO
29 MAP2K3 MAP2K3 MAP2K3 7115 0.029 0.54 NO
30 SP1 SP1 SP1 7813 0.019 0.51 NO
31 MAP2K4 MAP2K4 MAP2K4 7919 0.018 0.5 NO
32 RIPK1 RIPK1 RIPK1 8153 0.015 0.49 NO
33 DAXX DAXX DAXX 8639 0.0089 0.47 NO
34 TNFRSF1A TNFRSF1A TNFRSF1A 8659 0.0086 0.47 NO
35 RAF1 RAF1 RAF1 8684 0.0083 0.47 NO
36 MAPK14 MAPK14 MAPK14 9287 0.0011 0.43 NO
37 MAPK3 MAPK3 MAPK3 10357 -0.011 0.38 NO
38 RELA RELA RELA 10850 -0.017 0.35 NO
39 MAPK8 MAPK8 MAPK8 11238 -0.021 0.33 NO
40 MAPK1 MAPK1 MAPK1 12160 -0.031 0.28 NO
41 HOXA7 HOXA7 HOXA7 12412 -0.034 0.27 NO
42 MAP2K7 MAP2K7 MAP2K7 14314 -0.059 0.18 NO
43 PRKCE PRKCE PRKCE 14650 -0.065 0.16 NO
44 HRAS HRAS HRAS 15565 -0.083 0.12 NO
45 PRKCA PRKCA PRKCA 16304 -0.11 0.097 NO

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

Figure S26.  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 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 TNF TNF TNF 191 0.8 0.12 YES
2 BIRC3 BIRC3 BIRC3 352 0.7 0.22 YES
3 TNFRSF1B TNFRSF1B TNFRSF1B 969 0.44 0.25 YES
4 ARHGDIB ARHGDIB ARHGDIB 1215 0.38 0.3 YES
5 MAP3K5 MAP3K5 MAP3K5 1429 0.33 0.34 YES
6 FAS FAS FAS 1468 0.32 0.38 YES
7 TRAF1 TRAF1 TRAF1 1749 0.27 0.41 YES
8 NFKBIA NFKBIA NFKBIA 1804 0.26 0.45 YES
9 MAP3K14 MAP3K14 MAP3K14 1930 0.24 0.48 YES
10 CFLAR CFLAR CFLAR 2206 0.21 0.5 YES
11 CASP8 CASP8 CASP8 2378 0.19 0.52 YES
12 CASP7 CASP7 CASP7 2830 0.16 0.52 YES
13 CASP3 CASP3 CASP3 3292 0.13 0.51 YES
14 TRADD TRADD TRADD 3735 0.11 0.5 YES
15 BCL2 BCL2 BCL2 3823 0.1 0.52 YES
16 NFKB1 NFKB1 NFKB1 3941 0.099 0.53 YES
17 LMNB1 LMNB1 LMNB1 4134 0.092 0.53 YES
18 BIRC2 BIRC2 BIRC2 4383 0.084 0.53 NO
19 CASP6 CASP6 CASP6 4703 0.075 0.52 NO
20 CHUK CHUK CHUK 4948 0.069 0.52 NO
21 RB1 RB1 RB1 4999 0.068 0.53 NO
22 XIAP XIAP XIAP 5398 0.059 0.52 NO
23 MAP3K1 MAP3K1 MAP3K1 5627 0.054 0.51 NO
24 APAF1 APAF1 APAF1 5806 0.051 0.51 NO
25 TRAF2 TRAF2 TRAF2 6068 0.046 0.5 NO
26 PRKCD PRKCD PRKCD 6116 0.045 0.51 NO
27 CDK11A CDK11A CDK11A 6233 0.043 0.51 NO
28 PAK2 PAK2 PAK2 7045 0.03 0.47 NO
29 BID BID BID 7191 0.028 0.46 NO
30 DFFB DFFB DFFB 7523 0.023 0.45 NO
31 CDK11B CDK11B CDK11B 7616 0.022 0.45 NO
32 BAG4 BAG4 BAG4 7875 0.018 0.44 NO
33 RIPK1 RIPK1 RIPK1 8153 0.015 0.42 NO
34 DAXX DAXX DAXX 8639 0.0089 0.4 NO
35 TNFRSF1A TNFRSF1A TNFRSF1A 8659 0.0086 0.4 NO
36 CASP9 CASP9 CASP9 8740 0.0077 0.39 NO
37 PSEN1 PSEN1 PSEN1 8755 0.0075 0.39 NO
38 RASA1 RASA1 RASA1 9699 -0.0034 0.34 NO
39 GSN GSN GSN 10172 -0.009 0.32 NO
40 NUMA1 NUMA1 NUMA1 10760 -0.016 0.29 NO
41 RELA RELA RELA 10850 -0.017 0.28 NO
42 MAPK8 MAPK8 MAPK8 11238 -0.021 0.27 NO
43 MDM2 MDM2 MDM2 11295 -0.021 0.27 NO
44 ACTG1 ACTG1 ACTG1 11418 -0.023 0.26 NO
45 SPTAN1 SPTAN1 SPTAN1 11422 -0.023 0.27 NO
46 CASP2 CASP2 CASP2 11588 -0.024 0.26 NO
47 PARP1 PARP1 PARP1 11812 -0.027 0.25 NO
48 CYCS CYCS CYCS 12628 -0.036 0.21 NO
49 DFFA DFFA DFFA 13147 -0.042 0.19 NO
50 PSEN2 PSEN2 PSEN2 13495 -0.047 0.18 NO
51 FADD FADD FADD 13543 -0.048 0.18 NO
52 CRADD CRADD CRADD 14160 -0.056 0.16 NO
53 LMNA LMNA LMNA 14219 -0.057 0.17 NO
54 MAP2K7 MAP2K7 MAP2K7 14314 -0.059 0.17 NO
55 PRKDC PRKDC PRKDC 14803 -0.068 0.15 NO
56 LMNB2 LMNB2 LMNB2 15461 -0.081 0.13 NO
57 PTK2 PTK2 PTK2 15839 -0.091 0.12 NO

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

Figure S28.  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 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 CD3G CD3G CD3G 16 1 0.034 YES
2 ICOS ICOS ICOS 38 0.95 0.065 YES
3 CD40LG CD40LG CD40LG 42 0.95 0.097 YES
4 CD247 CD247 CD247 70 0.91 0.13 YES
5 PRKCQ PRKCQ PRKCQ 90 0.9 0.16 YES
6 CD3D CD3D CD3D 91 0.9 0.19 YES
7 CD8B CD8B CD8B 102 0.88 0.22 YES
8 CARD11 CARD11 CARD11 127 0.85 0.24 YES
9 LCK LCK LCK 129 0.85 0.27 YES
10 ZAP70 ZAP70 ZAP70 137 0.85 0.3 YES
11 PDCD1 PDCD1 PDCD1 139 0.84 0.33 YES
12 IFNG IFNG IFNG 146 0.84 0.36 YES
13 ITK ITK ITK 159 0.83 0.39 YES
14 CD3E CD3E CD3E 172 0.82 0.41 YES
15 TNF TNF TNF 191 0.8 0.44 YES
16 CD8A CD8A CD8A 228 0.77 0.46 YES
17 PTPRC PTPRC PTPRC 230 0.77 0.49 YES
18 CD28 CD28 CD28 240 0.76 0.52 YES
19 RASGRP1 RASGRP1 RASGRP1 246 0.76 0.54 YES
20 VAV1 VAV1 VAV1 284 0.74 0.56 YES
21 PIK3CG PIK3CG PIK3CG 345 0.7 0.58 YES
22 PTPN6 PTPN6 PTPN6 425 0.65 0.6 YES
23 PIK3R5 PIK3R5 PIK3R5 514 0.61 0.62 YES
24 MAP3K8 MAP3K8 MAP3K8 521 0.61 0.64 YES
25 IL10 IL10 IL10 580 0.58 0.66 YES
26 LAT LAT LAT 654 0.55 0.67 YES
27 CTLA4 CTLA4 CTLA4 738 0.52 0.68 YES
28 MAPK13 MAPK13 MAPK13 763 0.51 0.7 YES
29 GRAP2 GRAP2 GRAP2 796 0.5 0.71 YES
30 LCP2 LCP2 LCP2 877 0.47 0.73 YES
31 CD4 CD4 CD4 883 0.46 0.74 YES
32 VAV3 VAV3 VAV3 1268 0.36 0.73 YES
33 TEC TEC TEC 1316 0.35 0.74 YES
34 CSF2 CSF2 CSF2 1385 0.34 0.75 YES
35 NFKBIA NFKBIA NFKBIA 1804 0.26 0.74 NO
36 MAP3K14 MAP3K14 MAP3K14 1930 0.24 0.74 NO
37 NFATC2 NFATC2 NFATC2 2053 0.23 0.74 NO
38 PIK3CD PIK3CD PIK3CD 2451 0.19 0.72 NO
39 MALT1 MALT1 MALT1 2515 0.18 0.72 NO
40 NFATC1 NFATC1 NFATC1 2657 0.17 0.72 NO
41 PDK1 PDK1 PDK1 2916 0.15 0.71 NO
42 PPP3CC PPP3CC PPP3CC 3145 0.13 0.7 NO
43 NFKBIE NFKBIE NFKBIE 3302 0.12 0.7 NO
44 NCK1 NCK1 NCK1 3392 0.12 0.7 NO
45 CBLB CBLB CBLB 3517 0.12 0.7 NO
46 GRB2 GRB2 GRB2 3875 0.1 0.68 NO
47 NFKB1 NFKB1 NFKB1 3941 0.099 0.68 NO
48 BCL10 BCL10 BCL10 4186 0.09 0.67 NO
49 FYN FYN FYN 4295 0.087 0.67 NO
50 PPP3R2 PPP3R2 PPP3R2 4495 0.08 0.66 NO
51 PPP3CB PPP3CB PPP3CB 4562 0.079 0.66 NO
52 PIK3R3 PIK3R3 PIK3R3 4702 0.075 0.65 NO
53 PIK3R1 PIK3R1 PIK3R1 4757 0.074 0.65 NO
54 PIK3CA PIK3CA PIK3CA 4930 0.07 0.64 NO
55 CHUK CHUK CHUK 4948 0.069 0.64 NO
56 MAP3K7 MAP3K7 MAP3K7 5013 0.068 0.64 NO
57 NFATC3 NFATC3 NFATC3 5144 0.065 0.64 NO
58 PAK1 PAK1 PAK1 5375 0.059 0.63 NO
59 IKBKG IKBKG IKBKG 5521 0.057 0.62 NO
60 CDC42 CDC42 CDC42 5671 0.053 0.62 NO
61 SOS1 SOS1 SOS1 5695 0.053 0.62 NO
62 PIK3CB PIK3CB PIK3CB 5836 0.05 0.61 NO
63 NFKBIB NFKBIB NFKBIB 5962 0.048 0.6 NO
64 KRAS KRAS KRAS 6032 0.046 0.6 NO
65 IKBKB IKBKB IKBKB 6091 0.046 0.6 NO
66 MAP2K1 MAP2K1 MAP2K1 6134 0.045 0.6 NO
67 CBL CBL CBL 6293 0.042 0.59 NO
68 PPP3CA PPP3CA PPP3CA 6366 0.041 0.59 NO
69 NRAS NRAS NRAS 6488 0.039 0.58 NO
70 SOS2 SOS2 SOS2 6656 0.036 0.58 NO
71 FOS FOS FOS 6925 0.031 0.56 NO
72 JUN JUN JUN 6971 0.031 0.56 NO
73 PAK2 PAK2 PAK2 7045 0.03 0.56 NO
74 NFAT5 NFAT5 NFAT5 7140 0.028 0.55 NO
75 RHOA RHOA RHOA 7404 0.025 0.54 NO
76 DLG1 DLG1 DLG1 7532 0.023 0.53 NO
77 MAPK9 MAPK9 MAPK9 8062 0.016 0.5 NO
78 PPP3R1 PPP3R1 PPP3R1 8458 0.011 0.48 NO
79 MAPK11 MAPK11 MAPK11 8666 0.0085 0.47 NO
80 RAF1 RAF1 RAF1 8684 0.0083 0.47 NO
81 PAK3 PAK3 PAK3 9012 0.0043 0.45 NO
82 MAPK14 MAPK14 MAPK14 9287 0.0011 0.44 NO
83 MAPK3 MAPK3 MAPK3 10357 -0.011 0.38 NO
84 RELA RELA RELA 10850 -0.017 0.35 NO
85 GSK3B GSK3B GSK3B 11028 -0.018 0.34 NO
86 MAP2K2 MAP2K2 MAP2K2 11338 -0.022 0.33 NO
87 NCK2 NCK2 NCK2 11510 -0.024 0.32 NO
88 CHP CHP CHP 11529 -0.024 0.32 NO
89 MAPK1 MAPK1 MAPK1 12160 -0.031 0.28 NO
90 AKT1 AKT1 AKT1 12366 -0.033 0.27 NO
91 PAK7 PAK7 PAK7 13458 -0.046 0.21 NO
92 PLCG1 PLCG1 PLCG1 13619 -0.049 0.21 NO
93 AKT3 AKT3 AKT3 13688 -0.05 0.2 NO
94 VAV2 VAV2 VAV2 13764 -0.051 0.2 NO
95 AKT2 AKT2 AKT2 13834 -0.052 0.2 NO
96 MAP2K7 MAP2K7 MAP2K7 14314 -0.059 0.18 NO
97 NFATC4 NFATC4 NFATC4 15424 -0.08 0.12 NO
98 PAK6 PAK6 PAK6 15591 -0.084 0.11 NO
99 CDK4 CDK4 CDK4 16128 -0.1 0.083 NO
100 CBLC CBLC CBLC 16242 -0.1 0.08 NO
101 PIK3R2 PIK3R2 PIK3R2 16574 -0.12 0.066 NO
102 CHP2 CHP2 CHP2 16785 -0.13 0.058 NO
103 PAK4 PAK4 PAK4 17015 -0.14 0.05 NO
104 MAPK12 MAPK12 MAPK12 17735 -0.21 0.017 NO

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

Figure S30.  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 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 CD80 CD80 CD80 98 0.89 0.035 YES
2 TNF TNF TNF 191 0.8 0.067 YES
3 TLR9 TLR9 TLR9 223 0.78 0.1 YES
4 CXCL11 CXCL11 CXCL11 224 0.77 0.14 YES
5 TLR8 TLR8 TLR8 227 0.77 0.17 YES
6 CXCL9 CXCL9 CXCL9 280 0.74 0.2 YES
7 IL12B IL12B IL12B 315 0.72 0.23 YES
8 CXCL10 CXCL10 CXCL10 328 0.71 0.26 YES
9 PIK3CG PIK3CG PIK3CG 345 0.7 0.3 YES
10 CCL4 CCL4 CCL4 346 0.7 0.33 YES
11 CCL5 CCL5 CCL5 370 0.69 0.36 YES
12 TLR7 TLR7 TLR7 383 0.68 0.39 YES
13 CD86 CD86 CD86 455 0.64 0.41 YES
14 PIK3R5 PIK3R5 PIK3R5 514 0.61 0.44 YES
15 MAP3K8 MAP3K8 MAP3K8 521 0.61 0.47 YES
16 CCL3 CCL3 CCL3 602 0.57 0.49 YES
17 CD40 CD40 CD40 687 0.54 0.51 YES
18 MAPK13 MAPK13 MAPK13 763 0.51 0.53 YES
19 TICAM2 TICAM2 TICAM2 932 0.45 0.54 YES
20 IRF5 IRF5 IRF5 1061 0.41 0.55 YES
21 IL1B IL1B IL1B 1068 0.41 0.57 YES
22 TLR4 TLR4 TLR4 1075 0.41 0.59 YES
23 TLR6 TLR6 TLR6 1142 0.4 0.6 YES
24 TLR5 TLR5 TLR5 1172 0.39 0.62 YES
25 TLR1 TLR1 TLR1 1220 0.38 0.63 YES
26 TLR2 TLR2 TLR2 1298 0.36 0.64 YES
27 IL6 IL6 IL6 1324 0.35 0.66 YES
28 LBP LBP LBP 1469 0.32 0.66 YES
29 CD14 CD14 CD14 1486 0.31 0.68 YES
30 IL12A IL12A IL12A 1544 0.3 0.69 YES
31 TLR3 TLR3 TLR3 1574 0.3 0.7 YES
32 IRF7 IRF7 IRF7 1609 0.29 0.71 YES
33 STAT1 STAT1 STAT1 1655 0.28 0.72 YES
34 NFKBIA NFKBIA NFKBIA 1804 0.26 0.73 YES
35 LY96 LY96 LY96 1835 0.25 0.74 YES
36 IKBKE IKBKE IKBKE 1966 0.24 0.74 YES
37 IFNB1 IFNB1 IFNB1 2115 0.22 0.74 YES
38 CASP8 CASP8 CASP8 2378 0.19 0.74 YES
39 PIK3CD PIK3CD PIK3CD 2451 0.19 0.74 YES
40 MAP2K6 MAP2K6 MAP2K6 2700 0.16 0.73 YES
41 IFNAR2 IFNAR2 IFNAR2 2755 0.16 0.74 YES
42 IRAK4 IRAK4 IRAK4 2783 0.16 0.74 YES
43 TRAF3 TRAF3 TRAF3 3050 0.14 0.74 NO
44 MYD88 MYD88 MYD88 3369 0.12 0.72 NO
45 TAB2 TAB2 TAB2 3778 0.1 0.7 NO
46 NFKB1 NFKB1 NFKB1 3941 0.099 0.7 NO
47 IRF3 IRF3 IRF3 4563 0.079 0.67 NO
48 PIK3R3 PIK3R3 PIK3R3 4702 0.075 0.66 NO
49 PIK3R1 PIK3R1 PIK3R1 4757 0.074 0.67 NO
50 PIK3CA PIK3CA PIK3CA 4930 0.07 0.66 NO
51 CHUK CHUK CHUK 4948 0.069 0.66 NO
52 MAP3K7 MAP3K7 MAP3K7 5013 0.068 0.66 NO
53 IFNAR1 IFNAR1 IFNAR1 5087 0.066 0.66 NO
54 CTSK CTSK CTSK 5438 0.058 0.64 NO
55 IKBKG IKBKG IKBKG 5521 0.057 0.64 NO
56 IL8 IL8 IL8 5761 0.052 0.63 NO
57 PIK3CB PIK3CB PIK3CB 5836 0.05 0.63 NO
58 IKBKB IKBKB IKBKB 6091 0.046 0.62 NO
59 MAP2K1 MAP2K1 MAP2K1 6134 0.045 0.62 NO
60 FOS FOS FOS 6925 0.031 0.57 NO
61 JUN JUN JUN 6971 0.031 0.57 NO
62 MAP2K3 MAP2K3 MAP2K3 7115 0.029 0.57 NO
63 MAP2K4 MAP2K4 MAP2K4 7919 0.018 0.52 NO
64 MAPK9 MAPK9 MAPK9 8062 0.016 0.52 NO
65 RIPK1 RIPK1 RIPK1 8153 0.015 0.51 NO
66 MAPK11 MAPK11 MAPK11 8666 0.0085 0.48 NO
67 TICAM1 TICAM1 TICAM1 8706 0.0079 0.48 NO
68 SPP1 SPP1 SPP1 8897 0.0058 0.47 NO
69 MAPK14 MAPK14 MAPK14 9287 0.0011 0.45 NO
70 MAPK10 MAPK10 MAPK10 9703 -0.0034 0.43 NO
71 MAPK3 MAPK3 MAPK3 10357 -0.011 0.39 NO
72 IRAK1 IRAK1 IRAK1 10770 -0.016 0.37 NO
73 RELA RELA RELA 10850 -0.017 0.36 NO
74 MAPK8 MAPK8 MAPK8 11238 -0.021 0.34 NO
75 MAP2K2 MAP2K2 MAP2K2 11338 -0.022 0.34 NO
76 RAC1 RAC1 RAC1 11412 -0.023 0.34 NO
77 TRAF6 TRAF6 TRAF6 11423 -0.023 0.34 NO
78 MAPK1 MAPK1 MAPK1 12160 -0.031 0.3 NO
79 AKT1 AKT1 AKT1 12366 -0.033 0.29 NO
80 TAB1 TAB1 TAB1 12374 -0.033 0.29 NO
81 TOLLIP TOLLIP TOLLIP 12375 -0.033 0.29 NO
82 TIRAP TIRAP TIRAP 12664 -0.037 0.28 NO
83 FADD FADD FADD 13543 -0.048 0.23 NO
84 AKT3 AKT3 AKT3 13688 -0.05 0.22 NO
85 AKT2 AKT2 AKT2 13834 -0.052 0.22 NO
86 MAP2K7 MAP2K7 MAP2K7 14314 -0.059 0.19 NO
87 PIK3R2 PIK3R2 PIK3R2 16574 -0.12 0.072 NO
88 MAPK12 MAPK12 MAPK12 17735 -0.21 0.017 NO

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

Figure S32.  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 FAS PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CD3G CD3G CD3G 16 1 0.092 YES
2 CD247 CD247 CD247 70 0.91 0.17 YES
3 CD3D CD3D CD3D 91 0.9 0.26 YES
4 LCK LCK LCK 129 0.85 0.33 YES
5 ZAP70 ZAP70 ZAP70 137 0.85 0.41 YES
6 CD3E CD3E CD3E 172 0.82 0.48 YES
7 PTPN7 PTPN7 PTPN7 261 0.75 0.55 YES
8 VAV1 VAV1 VAV1 284 0.74 0.61 YES
9 PIK3CG PIK3CG PIK3CG 345 0.7 0.68 YES
10 PRKCB PRKCB PRKCB 409 0.66 0.73 YES
11 LAT LAT LAT 654 0.55 0.77 YES
12 NFKBIA NFKBIA NFKBIA 1804 0.26 0.73 NO
13 NFATC2 NFATC2 NFATC2 2053 0.23 0.74 NO
14 NFATC1 NFATC1 NFATC1 2657 0.17 0.72 NO
15 PPP3CC PPP3CC PPP3CC 3145 0.13 0.7 NO
16 GRB2 GRB2 GRB2 3875 0.1 0.67 NO
17 NFKB1 NFKB1 NFKB1 3941 0.099 0.68 NO
18 FYN FYN FYN 4295 0.087 0.67 NO
19 PPP3CB PPP3CB PPP3CB 4562 0.079 0.66 NO
20 PIK3R1 PIK3R1 PIK3R1 4757 0.074 0.66 NO
21 PIK3CA PIK3CA PIK3CA 4930 0.07 0.65 NO
22 NFATC3 NFATC3 NFATC3 5144 0.065 0.65 NO
23 MAP3K1 MAP3K1 MAP3K1 5627 0.054 0.62 NO
24 SOS1 SOS1 SOS1 5695 0.053 0.63 NO
25 MAP2K1 MAP2K1 MAP2K1 6134 0.045 0.61 NO
26 PPP3CA PPP3CA PPP3CA 6366 0.041 0.6 NO
27 CALM2 CALM2 CALM2 6782 0.034 0.58 NO
28 FOS FOS FOS 6925 0.031 0.57 NO
29 JUN JUN JUN 6971 0.031 0.57 NO
30 CALM1 CALM1 CALM1 7074 0.029 0.57 NO
31 MAP2K4 MAP2K4 MAP2K4 7919 0.018 0.52 NO
32 RAF1 RAF1 RAF1 8684 0.0083 0.48 NO
33 RASA1 RASA1 RASA1 9699 -0.0034 0.43 NO
34 CALM3 CALM3 CALM3 9903 -0.0061 0.42 NO
35 MAPK3 MAPK3 MAPK3 10357 -0.011 0.39 NO
36 RELA RELA RELA 10850 -0.017 0.37 NO
37 MAPK8 MAPK8 MAPK8 11238 -0.021 0.35 NO
38 RAC1 RAC1 RAC1 11412 -0.023 0.34 NO
39 ELK1 ELK1 ELK1 12058 -0.03 0.31 NO
40 PLCG1 PLCG1 PLCG1 13619 -0.049 0.22 NO
41 SHC1 SHC1 SHC1 14115 -0.056 0.2 NO
42 NFATC4 NFATC4 NFATC4 15424 -0.08 0.14 NO
43 PRKCA PRKCA PRKCA 16304 -0.11 0.097 NO

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

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

genes ES table in pathway: BIOCARTA FCER1 PATHWAY

Table S18.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CCR7 CCR7 CCR7 41 0.95 0.017 YES
2 CXCR5 CXCR5 CXCR5 79 0.91 0.033 YES
3 XCL2 XCL2 XCL2 80 0.9 0.051 YES
4 CXCL13 CXCL13 CXCL13 97 0.89 0.068 YES
5 CCR8 CCR8 CCR8 120 0.86 0.084 YES
6 GNGT2 GNGT2 GNGT2 124 0.85 0.1 YES
7 CCL19 CCL19 CCL19 128 0.85 0.12 YES
8 CCR4 CCR4 CCR4 132 0.85 0.14 YES
9 RASGRP2 RASGRP2 RASGRP2 136 0.85 0.15 YES
10 CCR2 CCR2 CCR2 145 0.84 0.17 YES
11 CXCR3 CXCR3 CXCR3 154 0.84 0.18 YES
12 ITK ITK ITK 159 0.83 0.2 YES
13 CXCR6 CXCR6 CXCR6 162 0.83 0.22 YES
14 XCL1 XCL1 XCL1 206 0.79 0.23 YES
15 CCR6 CCR6 CCR6 213 0.78 0.25 YES
16 CXCL11 CXCL11 CXCL11 224 0.77 0.26 YES
17 NCF1 NCF1 NCF1 269 0.74 0.28 YES
18 CXCL9 CXCL9 CXCL9 280 0.74 0.29 YES
19 VAV1 VAV1 VAV1 284 0.74 0.3 YES
20 CCR5 CCR5 CCR5 293 0.73 0.32 YES
21 CCL22 CCL22 CCL22 299 0.73 0.33 YES
22 CCR3 CCR3 CCR3 319 0.71 0.35 YES
23 CXCL10 CXCL10 CXCL10 328 0.71 0.36 YES
24 XCR1 XCR1 XCR1 333 0.71 0.37 YES
25 PIK3CG PIK3CG PIK3CG 345 0.7 0.39 YES
26 CCL4 CCL4 CCL4 346 0.7 0.4 YES
27 CCL4L2 CCL4L2 CCL4L2 358 0.69 0.42 YES
28 CCL5 CCL5 CCL5 370 0.69 0.43 YES
29 WAS WAS WAS 385 0.68 0.44 YES
30 PRKCB PRKCB PRKCB 409 0.66 0.45 YES
31 DOCK2 DOCK2 DOCK2 410 0.66 0.47 YES
32 FGR FGR FGR 479 0.63 0.48 YES
33 CCL8 CCL8 CCL8 485 0.62 0.49 YES
34 RAC2 RAC2 RAC2 494 0.62 0.5 YES
35 PIK3R5 PIK3R5 PIK3R5 514 0.61 0.51 YES
36 CCL25 CCL25 CCL25 552 0.59 0.52 YES
37 HCK HCK HCK 588 0.57 0.53 YES
38 CCL21 CCL21 CCL21 594 0.57 0.54 YES
39 CCL3 CCL3 CCL3 602 0.57 0.55 YES
40 CCR9 CCR9 CCR9 630 0.56 0.56 YES
41 CCL3L1 CCL3L1 CCL3L1 726 0.52 0.57 YES
42 CCL17 CCL17 CCL17 750 0.51 0.58 YES
43 JAK3 JAK3 JAK3 759 0.51 0.59 YES
44 CCL2 CCL2 CCL2 835 0.48 0.59 YES
45 CCL3L3 CCL3L3 CCL3L3 917 0.46 0.6 YES
46 PTK2B PTK2B PTK2B 940 0.45 0.6 YES
47 ELMO1 ELMO1 ELMO1 945 0.45 0.61 YES
48 CCL1 CCL1 CCL1 946 0.45 0.62 YES
49 CX3CR1 CX3CR1 CX3CR1 1001 0.43 0.63 YES
50 LYN LYN LYN 1002 0.43 0.64 YES
51 CXCL12 CXCL12 CXCL12 1008 0.43 0.64 YES
52 CXCR4 CXCR4 CXCR4 1011 0.43 0.65 YES
53 CCR1 CCR1 CCR1 1033 0.42 0.66 YES
54 CCL13 CCL13 CCL13 1168 0.39 0.66 YES
55 CCL23 CCL23 CCL23 1177 0.39 0.67 YES
56 PLCB2 PLCB2 PLCB2 1186 0.38 0.68 YES
57 ADCY4 ADCY4 ADCY4 1242 0.37 0.68 YES
58 CCL24 CCL24 CCL24 1245 0.37 0.69 YES
59 CCL14 CCL14 CCL14 1260 0.36 0.69 YES
60 VAV3 VAV3 VAV3 1268 0.36 0.7 YES
61 CCL16 CCL16 CCL16 1274 0.36 0.71 YES
62 JAK2 JAK2 JAK2 1365 0.34 0.71 YES
63 ADCY7 ADCY7 ADCY7 1497 0.31 0.71 YES
64 CCL18 CCL18 CCL18 1549 0.3 0.71 YES
65 GNG8 GNG8 GNG8 1593 0.29 0.72 YES
66 CXCL2 CXCL2 CXCL2 1614 0.29 0.72 YES
67 STAT1 STAT1 STAT1 1655 0.28 0.72 YES
68 CXCL14 CXCL14 CXCL14 1657 0.28 0.73 YES
69 CCL7 CCL7 CCL7 1664 0.28 0.74 YES
70 NFKBIA NFKBIA NFKBIA 1804 0.26 0.73 YES
71 CXCL16 CXCL16 CXCL16 1874 0.25 0.73 YES
72 PRKX PRKX PRKX 2026 0.23 0.73 YES
73 ARRB2 ARRB2 ARRB2 2089 0.22 0.73 YES
74 CXCR2 CXCR2 CXCR2 2094 0.22 0.74 YES
75 PIK3CD PIK3CD PIK3CD 2451 0.19 0.72 NO
76 CCL26 CCL26 CCL26 2550 0.18 0.72 NO
77 TIAM1 TIAM1 TIAM1 2577 0.18 0.72 NO
78 PREX1 PREX1 PREX1 2832 0.16 0.71 NO
79 RAP1A RAP1A RAP1A 2903 0.15 0.71 NO
80 ADRBK2 ADRBK2 ADRBK2 3148 0.13 0.7 NO
81 ADRBK1 ADRBK1 ADRBK1 3155 0.13 0.7 NO
82 CCL20 CCL20 CCL20 3229 0.13 0.7 NO
83 CXCL5 CXCL5 CXCL5 3247 0.13 0.7 NO
84 CCL11 CCL11 CCL11 3495 0.12 0.69 NO
85 GNG2 GNG2 GNG2 3610 0.11 0.68 NO
86 GRK5 GRK5 GRK5 3742 0.11 0.68 NO
87 STAT2 STAT2 STAT2 3749 0.11 0.68 NO
88 CCR10 CCR10 CCR10 3860 0.1 0.68 NO
89 GRB2 GRB2 GRB2 3875 0.1 0.68 NO
90 PRKACB PRKACB PRKACB 3923 0.1 0.68 NO
91 NFKB1 NFKB1 NFKB1 3941 0.099 0.68 NO
92 GNB3 GNB3 GNB3 3956 0.098 0.68 NO
93 GRK6 GRK6 GRK6 4035 0.096 0.68 NO
94 CXCR1 CXCR1 CXCR1 4156 0.091 0.67 NO
95 CXCL3 CXCL3 CXCL3 4196 0.09 0.67 NO
96 PIK3R3 PIK3R3 PIK3R3 4702 0.075 0.64 NO
97 CSK CSK CSK 4714 0.075 0.64 NO
98 PIK3R1 PIK3R1 PIK3R1 4757 0.074 0.64 NO
99 GNAI2 GNAI2 GNAI2 4845 0.072 0.64 NO
100 RAP1B RAP1B RAP1B 4848 0.072 0.64 NO
101 TIAM2 TIAM2 TIAM2 4878 0.071 0.64 NO
102 PIK3CA PIK3CA PIK3CA 4930 0.07 0.64 NO
103 CHUK CHUK CHUK 4948 0.069 0.64 NO
104 STAT5B STAT5B STAT5B 4969 0.069 0.64 NO
105 GNB5 GNB5 GNB5 5004 0.068 0.64 NO
106 ROCK1 ROCK1 ROCK1 5046 0.067 0.64 NO
107 CXCL1 CXCL1 CXCL1 5188 0.064 0.63 NO
108 CCL28 CCL28 CCL28 5200 0.063 0.63 NO
109 CCL15 CCL15 CCL15 5292 0.061 0.63 NO
110 PAK1 PAK1 PAK1 5375 0.059 0.63 NO
111 CX3CL1 CX3CL1 CX3CL1 5504 0.057 0.62 NO
112 IKBKG IKBKG IKBKG 5521 0.057 0.62 NO
113 GNG10 GNG10 GNG10 5612 0.055 0.62 NO
114 ADCY5 ADCY5 ADCY5 5669 0.053 0.61 NO
115 CDC42 CDC42 CDC42 5671 0.053 0.62 NO
116 SOS1 SOS1 SOS1 5695 0.053 0.62 NO
117 GNB4 GNB4 GNB4 5713 0.052 0.62 NO
118 IL8 IL8 IL8 5761 0.052 0.61 NO
119 PIK3CB PIK3CB PIK3CB 5836 0.05 0.61 NO
120 NFKBIB NFKBIB NFKBIB 5962 0.048 0.6 NO
121 STAT3 STAT3 STAT3 5983 0.047 0.6 NO
122 KRAS KRAS KRAS 6032 0.046 0.6 NO
123 IKBKB IKBKB IKBKB 6091 0.046 0.6 NO
124 ADCY2 ADCY2 ADCY2 6094 0.045 0.6 NO
125 PRKCD PRKCD PRKCD 6116 0.045 0.6 NO
126 MAP2K1 MAP2K1 MAP2K1 6134 0.045 0.6 NO
127 ARRB1 ARRB1 ARRB1 6382 0.04 0.59 NO
128 NRAS NRAS NRAS 6488 0.039 0.58 NO
129 GNG7 GNG7 GNG7 6579 0.037 0.58 NO
130 SOS2 SOS2 SOS2 6656 0.036 0.57 NO
131 PLCB1 PLCB1 PLCB1 6800 0.033 0.57 NO
132 GNGT1 GNGT1 GNGT1 6903 0.032 0.56 NO
133 ADCY1 ADCY1 ADCY1 7003 0.03 0.56 NO
134 RHOA RHOA RHOA 7404 0.025 0.54 NO
135 GNAI3 GNAI3 GNAI3 7494 0.024 0.53 NO
136 FOXO3 FOXO3 FOXO3 7555 0.023 0.53 NO
137 PRKCZ PRKCZ PRKCZ 7653 0.021 0.52 NO
138 SHC4 SHC4 SHC4 7961 0.017 0.51 NO
139 GNG5 GNG5 GNG5 8005 0.017 0.5 NO
140 PLCB4 PLCB4 PLCB4 8225 0.014 0.49 NO
141 GNG11 GNG11 GNG11 8326 0.013 0.49 NO
142 CXCL6 CXCL6 CXCL6 8340 0.013 0.49 NO
143 RAF1 RAF1 RAF1 8684 0.0083 0.47 NO
144 GNB1 GNB1 GNB1 9346 0.00035 0.43 NO
145 GRK7 GRK7 GRK7 9708 -0.0034 0.41 NO
146 MAPK3 MAPK3 MAPK3 10357 -0.011 0.37 NO
147 RELA RELA RELA 10850 -0.017 0.35 NO
148 GSK3B GSK3B GSK3B 11028 -0.018 0.34 NO
149 PRKACA PRKACA PRKACA 11160 -0.02 0.33 NO
150 RAC1 RAC1 RAC1 11412 -0.023 0.32 NO
151 BRAF BRAF BRAF 11716 -0.026 0.3 NO
152 PF4 PF4 PF4 11874 -0.028 0.29 NO
153 MAPK1 MAPK1 MAPK1 12160 -0.031 0.28 NO
154 CRKL CRKL CRKL 12203 -0.031 0.28 NO
155 WASL WASL WASL 12337 -0.033 0.27 NO
156 AKT1 AKT1 AKT1 12366 -0.033 0.27 NO
157 PXN PXN PXN 12388 -0.033 0.27 NO
158 GNB2 GNB2 GNB2 12563 -0.036 0.26 NO
159 ROCK2 ROCK2 ROCK2 12843 -0.039 0.24 NO
160 GNG4 GNG4 GNG4 13509 -0.047 0.21 NO
161 GSK3A GSK3A GSK3A 13555 -0.048 0.2 NO
162 AKT3 AKT3 AKT3 13688 -0.05 0.2 NO
163 VAV2 VAV2 VAV2 13764 -0.051 0.2 NO
164 AKT2 AKT2 AKT2 13834 -0.052 0.19 NO
165 SHC1 SHC1 SHC1 14115 -0.056 0.18 NO
166 CRK CRK CRK 14161 -0.056 0.18 NO
167 GNG12 GNG12 GNG12 14290 -0.058 0.17 NO
168 BCAR1 BCAR1 BCAR1 14622 -0.064 0.15 NO
169 PLCB3 PLCB3 PLCB3 14740 -0.066 0.15 NO
170 CCL27 CCL27 CCL27 15008 -0.072 0.14 NO
171 ADCY9 ADCY9 ADCY9 15457 -0.08 0.11 NO
172 HRAS HRAS HRAS 15565 -0.083 0.11 NO
173 PTK2 PTK2 PTK2 15839 -0.091 0.094 NO
174 GNAI1 GNAI1 GNAI1 15975 -0.095 0.088 NO
175 GRK4 GRK4 GRK4 15981 -0.095 0.09 NO
176 PPBP PPBP PPBP 16467 -0.11 0.065 NO
177 PIK3R2 PIK3R2 PIK3R2 16574 -0.12 0.062 NO
178 PARD3 PARD3 PARD3 16663 -0.12 0.059 NO
179 GNG3 GNG3 GNG3 17140 -0.15 0.035 NO
180 ADCY6 ADCY6 ADCY6 17257 -0.16 0.032 NO
181 SHC2 SHC2 SHC2 17530 -0.18 0.02 NO
182 ADCY8 ADCY8 ADCY8 17670 -0.2 0.017 NO
183 SHC3 SHC3 SHC3 17804 -0.22 0.014 NO

Figure S35.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA FCER1 PATHWAY.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA FCER1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA FMLP PATHWAY

Table S19.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 DAPP1 DAPP1 DAPP1 53 0.93 0.044 YES
2 CD19 CD19 CD19 68 0.91 0.089 YES
3 CD79A CD79A CD79A 75 0.91 0.14 YES
4 BLNK BLNK BLNK 110 0.88 0.18 YES
5 CARD11 CARD11 CARD11 127 0.85 0.22 YES
6 CD72 CD72 CD72 220 0.78 0.25 YES
7 VAV1 VAV1 VAV1 284 0.74 0.29 YES
8 CR2 CR2 CR2 313 0.72 0.32 YES
9 PIK3CG PIK3CG PIK3CG 345 0.7 0.36 YES
10 CD79B CD79B CD79B 399 0.67 0.38 YES
11 BTK BTK BTK 403 0.67 0.42 YES
12 PRKCB PRKCB PRKCB 409 0.66 0.45 YES
13 PTPN6 PTPN6 PTPN6 425 0.65 0.48 YES
14 INPP5D INPP5D INPP5D 431 0.65 0.52 YES
15 RAC2 RAC2 RAC2 494 0.62 0.54 YES
16 PIK3R5 PIK3R5 PIK3R5 514 0.61 0.57 YES
17 PIK3AP1 PIK3AP1 PIK3AP1 589 0.57 0.6 YES
18 LILRB3 LILRB3 LILRB3 677 0.54 0.62 YES
19 SYK SYK SYK 771 0.5 0.64 YES
20 PLCG2 PLCG2 PLCG2 839 0.48 0.66 YES
21 LYN LYN LYN 1002 0.43 0.67 YES
22 CD22 CD22 CD22 1104 0.4 0.69 YES
23 FCGR2B FCGR2B FCGR2B 1202 0.38 0.7 YES
24 RASGRP3 RASGRP3 RASGRP3 1230 0.37 0.72 YES
25 VAV3 VAV3 VAV3 1268 0.36 0.74 YES
26 IFITM1 IFITM1 IFITM1 1441 0.32 0.74 YES
27 NFKBIA NFKBIA NFKBIA 1804 0.26 0.74 NO
28 NFATC2 NFATC2 NFATC2 2053 0.23 0.73 NO
29 PIK3CD PIK3CD PIK3CD 2451 0.19 0.72 NO
30 MALT1 MALT1 MALT1 2515 0.18 0.73 NO
31 NFATC1 NFATC1 NFATC1 2657 0.17 0.73 NO
32 PPP3CC PPP3CC PPP3CC 3145 0.13 0.71 NO
33 NFKBIE NFKBIE NFKBIE 3302 0.12 0.7 NO
34 GRB2 GRB2 GRB2 3875 0.1 0.68 NO
35 NFKB1 NFKB1 NFKB1 3941 0.099 0.68 NO
36 BCL10 BCL10 BCL10 4186 0.09 0.67 NO
37 PPP3R2 PPP3R2 PPP3R2 4495 0.08 0.66 NO
38 PPP3CB PPP3CB PPP3CB 4562 0.079 0.66 NO
39 PIK3R3 PIK3R3 PIK3R3 4702 0.075 0.65 NO
40 PIK3R1 PIK3R1 PIK3R1 4757 0.074 0.65 NO
41 PIK3CA PIK3CA PIK3CA 4930 0.07 0.65 NO
42 CHUK CHUK CHUK 4948 0.069 0.65 NO
43 NFATC3 NFATC3 NFATC3 5144 0.065 0.64 NO
44 IKBKG IKBKG IKBKG 5521 0.057 0.62 NO
45 SOS1 SOS1 SOS1 5695 0.053 0.62 NO
46 PIK3CB PIK3CB PIK3CB 5836 0.05 0.61 NO
47 NFKBIB NFKBIB NFKBIB 5962 0.048 0.61 NO
48 KRAS KRAS KRAS 6032 0.046 0.61 NO
49 IKBKB IKBKB IKBKB 6091 0.046 0.6 NO
50 MAP2K1 MAP2K1 MAP2K1 6134 0.045 0.6 NO
51 PPP3CA PPP3CA PPP3CA 6366 0.041 0.59 NO
52 NRAS NRAS NRAS 6488 0.039 0.59 NO
53 SOS2 SOS2 SOS2 6656 0.036 0.58 NO
54 FOS FOS FOS 6925 0.031 0.57 NO
55 JUN JUN JUN 6971 0.031 0.57 NO
56 NFAT5 NFAT5 NFAT5 7140 0.028 0.56 NO
57 PPP3R1 PPP3R1 PPP3R1 8458 0.011 0.49 NO
58 RAF1 RAF1 RAF1 8684 0.0083 0.48 NO
59 MAPK3 MAPK3 MAPK3 10357 -0.011 0.38 NO
60 RELA RELA RELA 10850 -0.017 0.36 NO
61 CD81 CD81 CD81 10919 -0.017 0.35 NO
62 GSK3B GSK3B GSK3B 11028 -0.018 0.35 NO
63 MAP2K2 MAP2K2 MAP2K2 11338 -0.022 0.33 NO
64 RAC1 RAC1 RAC1 11412 -0.023 0.33 NO
65 CHP CHP CHP 11529 -0.024 0.32 NO
66 MAPK1 MAPK1 MAPK1 12160 -0.031 0.29 NO
67 AKT1 AKT1 AKT1 12366 -0.033 0.28 NO
68 AKT3 AKT3 AKT3 13688 -0.05 0.21 NO
69 VAV2 VAV2 VAV2 13764 -0.051 0.21 NO
70 AKT2 AKT2 AKT2 13834 -0.052 0.21 NO
71 NFATC4 NFATC4 NFATC4 15424 -0.08 0.12 NO
72 PIK3R2 PIK3R2 PIK3R2 16574 -0.12 0.064 NO
73 CHP2 CHP2 CHP2 16785 -0.13 0.059 NO
74 RAC3 RAC3 RAC3 17836 -0.23 0.012 NO

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

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

genes ES table in pathway: BIOCARTA GH PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PRKCB PRKCB PRKCB 409 0.66 0.3 YES
2 PTK2B PTK2B PTK2B 940 0.45 0.49 YES
3 GRB2 GRB2 GRB2 3875 0.1 0.38 NO
4 PAK1 PAK1 PAK1 5375 0.059 0.32 NO
5 MAP3K1 MAP3K1 MAP3K1 5627 0.054 0.34 NO
6 SOS1 SOS1 SOS1 5695 0.053 0.36 NO
7 MAP2K1 MAP2K1 MAP2K1 6134 0.045 0.36 NO
8 CALM2 CALM2 CALM2 6782 0.034 0.34 NO
9 JUN JUN JUN 6971 0.031 0.34 NO
10 CALM1 CALM1 CALM1 7074 0.029 0.35 NO
11 MAP2K3 MAP2K3 MAP2K3 7115 0.029 0.36 NO
12 MAP2K4 MAP2K4 MAP2K4 7919 0.018 0.33 NO
13 RAF1 RAF1 RAF1 8684 0.0083 0.29 NO
14 MAPK14 MAPK14 MAPK14 9287 0.0011 0.26 NO
15 CALM3 CALM3 CALM3 9903 -0.0061 0.22 NO
16 MAPK3 MAPK3 MAPK3 10357 -0.011 0.2 NO
17 GNAQ GNAQ GNAQ 10643 -0.014 0.2 NO
18 MAPK8 MAPK8 MAPK8 11238 -0.021 0.17 NO
19 MAP2K2 MAP2K2 MAP2K2 11338 -0.022 0.18 NO
20 RAC1 RAC1 RAC1 11412 -0.023 0.19 NO
21 MAPK1 MAPK1 MAPK1 12160 -0.031 0.16 NO
22 CRKL CRKL CRKL 12203 -0.031 0.17 NO
23 SRC SRC SRC 12359 -0.033 0.18 NO
24 PLCG1 PLCG1 PLCG1 13619 -0.049 0.13 NO
25 SHC1 SHC1 SHC1 14115 -0.056 0.13 NO
26 BCAR1 BCAR1 BCAR1 14622 -0.064 0.14 NO
27 PRKCA PRKCA PRKCA 16304 -0.11 0.097 NO

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

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype 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 28 genes.ES.table 0.55 1.5 0.049 1 0.88 0.32 0.13 0.28 0.91 0.47
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.5 1.5 0.055 1 0.86 0.31 0.24 0.24 1 0.52
BIOCARTA ALK PATHWAY 34 genes.ES.table 0.55 1.6 0.022 1 0.7 0.44 0.23 0.34 0.72 0.41
BIOCARTA NFAT PATHWAY 49 genes.ES.table 0.41 1.3 0.11 0.9 0.98 0.47 0.36 0.3 0.72 0.33
BIOCARTA EDG1 PATHWAY 26 genes.ES.table 0.48 1.3 0.14 0.98 0.98 0.31 0.15 0.26 0.78 0.38
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.32 1.3 0.18 0.75 0.99 0.08 0.029 0.078 0.64 0.24
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.31 1.4 0.12 1 0.97 0.12 0.15 0.099 0.82 0.4
KEGG ERBB SIGNALING PATHWAY 86 genes.ES.table 0.32 1.3 0.14 0.83 0.98 0.21 0.2 0.17 0.69 0.3
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION 216 genes.ES.table 0.49 1.3 0.056 0.85 0.98 0.4 0.17 0.33 0.67 0.31
KEGG HEDGEHOG SIGNALING PATHWAY 52 genes.ES.table 0.48 1.3 0.14 0.84 0.98 0.36 0.18 0.3 0.7 0.3
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 TGFB2 TGFB2 TGFB2 127 0.49 0.035 YES
2 THBS4 THBS4 THBS4 207 0.45 0.069 YES
3 THBS2 THBS2 THBS2 256 0.43 0.1 YES
4 BMP2 BMP2 BMP2 260 0.43 0.14 YES
5 BMP6 BMP6 BMP6 278 0.42 0.18 YES
6 INHBA INHBA INHBA 326 0.41 0.21 YES
7 ID4 ID4 ID4 532 0.36 0.23 YES
8 LTBP1 LTBP1 LTBP1 580 0.36 0.26 YES
9 FST FST FST 586 0.36 0.28 YES
10 BMP5 BMP5 BMP5 994 0.3 0.29 YES
11 ID1 ID1 ID1 1206 0.28 0.3 YES
12 E2F5 E2F5 E2F5 1219 0.28 0.32 YES
13 ID3 ID3 ID3 1403 0.26 0.34 YES
14 ACVR2A ACVR2A ACVR2A 1481 0.25 0.35 YES
15 TGFB3 TGFB3 TGFB3 1581 0.25 0.37 YES
16 BMP8A BMP8A BMP8A 1744 0.23 0.38 YES
17 INHBB INHBB INHBB 1745 0.23 0.4 YES
18 ROCK2 ROCK2 ROCK2 1919 0.22 0.41 YES
19 DCN DCN DCN 1951 0.22 0.43 YES
20 SMAD9 SMAD9 SMAD9 2039 0.22 0.44 YES
21 BMPR1A BMPR1A BMPR1A 2197 0.21 0.45 YES
22 SMURF2 SMURF2 SMURF2 2372 0.2 0.46 YES
23 AMH AMH AMH 2525 0.19 0.46 YES
24 GDF6 GDF6 GDF6 2547 0.19 0.48 YES
25 BMP7 BMP7 BMP7 2577 0.19 0.49 YES
26 SMAD1 SMAD1 SMAD1 2602 0.18 0.51 YES
27 BMP8B BMP8B BMP8B 2653 0.18 0.52 YES
28 CHRD CHRD CHRD 2659 0.18 0.54 YES
29 SMAD5 SMAD5 SMAD5 2667 0.18 0.55 YES
30 THBS1 THBS1 THBS1 2737 0.18 0.56 YES
31 LEFTY1 LEFTY1 LEFTY1 3175 0.16 0.55 NO
32 COMP COMP COMP 3234 0.16 0.56 NO
33 BMP4 BMP4 BMP4 3777 0.14 0.54 NO
34 ROCK1 ROCK1 ROCK1 4329 0.12 0.52 NO
35 ACVR2B ACVR2B ACVR2B 4468 0.12 0.52 NO
36 ACVR1 ACVR1 ACVR1 4641 0.11 0.52 NO
37 THBS3 THBS3 THBS3 4660 0.11 0.53 NO
38 SMAD7 SMAD7 SMAD7 5134 0.1 0.52 NO
39 SMAD4 SMAD4 SMAD4 5291 0.097 0.51 NO
40 LEFTY2 LEFTY2 LEFTY2 5391 0.095 0.52 NO
41 INHBE INHBE INHBE 5478 0.092 0.52 NO
42 RPS6KB1 RPS6KB1 RPS6KB1 5725 0.087 0.51 NO
43 ZFYVE9 ZFYVE9 ZFYVE9 5936 0.082 0.51 NO
44 NODAL NODAL NODAL 6297 0.074 0.5 NO
45 PPP2R1B PPP2R1B PPP2R1B 6359 0.073 0.5 NO
46 RBL1 RBL1 RBL1 6527 0.069 0.5 NO
47 RBL2 RBL2 RBL2 7088 0.059 0.47 NO
48 ID2 ID2 ID2 7476 0.052 0.45 NO
49 ACVRL1 ACVRL1 ACVRL1 7783 0.046 0.44 NO
50 PPP2CB PPP2CB PPP2CB 7874 0.045 0.44 NO
51 TGFBR2 TGFBR2 TGFBR2 8312 0.038 0.42 NO
52 GDF5 GDF5 GDF5 8366 0.037 0.42 NO
53 SP1 SP1 SP1 8689 0.032 0.4 NO
54 INHBC INHBC INHBC 8880 0.028 0.39 NO
55 TFDP1 TFDP1 TFDP1 9047 0.026 0.39 NO
56 CUL1 CUL1 CUL1 9197 0.024 0.38 NO
57 CREBBP CREBBP CREBBP 9304 0.022 0.38 NO
58 CDKN2B CDKN2B CDKN2B 9341 0.021 0.38 NO
59 SKP1 SKP1 SKP1 9409 0.02 0.37 NO
60 TGFB1 TGFB1 TGFB1 9421 0.02 0.38 NO
61 E2F4 E2F4 E2F4 9561 0.018 0.37 NO
62 EP300 EP300 EP300 10385 0.0058 0.32 NO
63 TGFBR1 TGFBR1 TGFBR1 10528 0.0035 0.32 NO
64 AMHR2 AMHR2 AMHR2 10826 -0.00081 0.3 NO
65 PPP2CA PPP2CA PPP2CA 10854 -0.0011 0.3 NO
66 PITX2 PITX2 PITX2 11012 -0.0034 0.29 NO
67 SMAD2 SMAD2 SMAD2 11116 -0.0049 0.28 NO
68 PPP2R1A PPP2R1A PPP2R1A 11119 -0.005 0.28 NO
69 ZFYVE16 ZFYVE16 ZFYVE16 11155 -0.0056 0.28 NO
70 SMAD3 SMAD3 SMAD3 11211 -0.0064 0.28 NO
71 SMAD6 SMAD6 SMAD6 11799 -0.016 0.25 NO
72 BMPR2 BMPR2 BMPR2 11865 -0.017 0.25 NO
73 RHOA RHOA RHOA 12365 -0.025 0.22 NO
74 MAPK1 MAPK1 MAPK1 12409 -0.026 0.22 NO
75 RBX1 RBX1 RBX1 13061 -0.038 0.19 NO
76 MAPK3 MAPK3 MAPK3 13375 -0.044 0.17 NO
77 SMURF1 SMURF1 SMURF1 13654 -0.05 0.16 NO
78 ACVR1C ACVR1C ACVR1C 14739 -0.076 0.11 NO
79 GDF7 GDF7 GDF7 14788 -0.077 0.11 NO
80 RPS6KB2 RPS6KB2 RPS6KB2 15007 -0.083 0.11 NO
81 MYC MYC MYC 15047 -0.084 0.11 NO
82 BMPR1B BMPR1B BMPR1B 15077 -0.085 0.12 NO
83 TNF TNF TNF 17322 -0.25 0.015 NO
84 IFNG IFNG IFNG 17547 -0.29 0.028 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 TGFB2 TGFB2 TGFB2 127 0.49 0.1 YES
2 BMP2 BMP2 BMP2 260 0.43 0.19 YES
3 FZD1 FZD1 FZD1 525 0.36 0.25 YES
4 BMP5 BMP5 BMP5 994 0.3 0.29 YES
5 NKX2-5 NKX2-5 NKX2-5 1349 0.26 0.33 YES
6 TGFB3 TGFB3 TGFB3 1581 0.25 0.37 YES
7 BMPR1A BMPR1A BMPR1A 2197 0.21 0.38 YES
8 BMP7 BMP7 BMP7 2577 0.19 0.4 YES
9 SMAD1 SMAD1 SMAD1 2602 0.18 0.44 YES
10 CHRD CHRD CHRD 2659 0.18 0.48 YES
11 SMAD5 SMAD5 SMAD5 2667 0.18 0.52 YES
12 ATF2 ATF2 ATF2 3070 0.16 0.53 YES
13 BMP4 BMP4 BMP4 3777 0.14 0.52 YES
14 MAP3K7 MAP3K7 MAP3K7 3909 0.13 0.54 YES
15 APC APC APC 4194 0.12 0.55 YES
16 ACVR1 ACVR1 ACVR1 4641 0.11 0.55 NO
17 SMAD4 SMAD4 SMAD4 5291 0.097 0.54 NO
18 NOG NOG NOG 5950 0.082 0.52 NO
19 TGFBR2 TGFBR2 TGFBR2 8312 0.038 0.4 NO
20 GSK3B GSK3B GSK3B 8400 0.036 0.4 NO
21 TGFB1 TGFB1 TGFB1 9421 0.02 0.35 NO
22 RFC1 RFC1 RFC1 10058 0.01 0.31 NO
23 TGFBR1 TGFBR1 TGFBR1 10528 0.0035 0.29 NO
24 HNF1A HNF1A HNF1A 10903 -0.0017 0.27 NO
25 DVL1 DVL1 DVL1 11440 -0.01 0.24 NO
26 SMAD6 SMAD6 SMAD6 11799 -0.016 0.22 NO
27 BMPR2 BMPR2 BMPR2 11865 -0.017 0.22 NO
28 NPPA NPPA NPPA 12297 -0.024 0.2 NO
29 AXIN1 AXIN1 AXIN1 12874 -0.034 0.18 NO
30 GATA4 GATA4 GATA4 13200 -0.04 0.17 NO
31 TGFBR3 TGFBR3 TGFBR3 13500 -0.046 0.16 NO
32 CTNNB1 CTNNB1 CTNNB1 13993 -0.057 0.15 NO
33 MYL2 MYL2 MYL2 16418 -0.16 0.048 NO
34 WNT1 WNT1 WNT1 16825 -0.19 0.068 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 ITGA1 ITGA1 ITGA1 357 0.4 0.09 YES
2 PAK3 PAK3 PAK3 434 0.38 0.19 YES
3 LAMA2 LAMA2 LAMA2 513 0.37 0.29 YES
4 LAMA4 LAMA4 LAMA4 874 0.31 0.35 YES
5 NRG1 NRG1 NRG1 1855 0.23 0.36 YES
6 EGFR EGFR EGFR 1984 0.22 0.41 YES
7 DMD DMD DMD 2366 0.2 0.44 YES
8 MAPK8 MAPK8 MAPK8 2391 0.2 0.5 YES
9 PAK7 PAK7 PAK7 3191 0.16 0.5 YES
10 UTRN UTRN UTRN 3999 0.13 0.49 YES
11 ITGB1 ITGB1 ITGB1 4285 0.12 0.5 YES
12 ACTA1 ACTA1 ACTA1 5736 0.086 0.45 NO
13 PTK2 PTK2 PTK2 5804 0.085 0.47 NO
14 MUSK MUSK MUSK 7545 0.051 0.38 NO
15 PAK2 PAK2 PAK2 8134 0.04 0.36 NO
16 GIT2 GIT2 GIT2 8179 0.04 0.37 NO
17 SP1 SP1 SP1 8689 0.032 0.35 NO
18 LAMA3 LAMA3 LAMA3 9201 0.024 0.33 NO
19 JUN JUN JUN 9232 0.023 0.33 NO
20 SRC SRC SRC 9234 0.023 0.34 NO
21 RAPSN RAPSN RAPSN 9268 0.022 0.34 NO
22 DAG1 DAG1 DAG1 9364 0.021 0.34 NO
23 PXN PXN PXN 9601 0.017 0.34 NO
24 RAC1 RAC1 RAC1 9959 0.012 0.32 NO
25 PAK6 PAK6 PAK6 11403 -0.0095 0.24 NO
26 DVL1 DVL1 DVL1 11440 -0.01 0.24 NO
27 CDC42 CDC42 CDC42 11790 -0.016 0.23 NO
28 MAPK1 MAPK1 MAPK1 12409 -0.026 0.2 NO
29 PAK1 PAK1 PAK1 12825 -0.033 0.19 NO
30 MAPK3 MAPK3 MAPK3 13375 -0.044 0.17 NO
31 CTTN CTTN CTTN 13460 -0.046 0.18 NO
32 CHRM1 CHRM1 CHRM1 13497 -0.046 0.19 NO
33 NRG2 NRG2 NRG2 13772 -0.052 0.18 NO
34 CHRNA1 CHRNA1 CHRNA1 15215 -0.09 0.13 NO
35 PAK4 PAK4 PAK4 15506 -0.1 0.14 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 NFAT 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 PRKG1 PRKG1 PRKG1 307 0.42 0.096 YES
2 BDKRB2 BDKRB2 BDKRB2 498 0.37 0.19 YES
3 TNNI1 TNNI1 TNNI1 1052 0.29 0.24 YES
4 VEGFA VEGFA VEGFA 1327 0.27 0.29 YES
5 RYR2 RYR2 RYR2 1365 0.26 0.36 YES
6 FLT1 FLT1 FLT1 1420 0.26 0.43 YES
7 PRKAR2B PRKAR2B PRKAR2B 1613 0.24 0.48 YES
8 PRKAR1B PRKAR1B PRKAR1B 2344 0.2 0.5 YES
9 KDR KDR KDR 2396 0.2 0.55 YES
10 PRKACB PRKACB PRKACB 3209 0.16 0.55 NO
11 PDE2A PDE2A PDE2A 5047 0.1 0.47 NO
12 ACTA1 ACTA1 ACTA1 5736 0.086 0.46 NO
13 PDE3B PDE3B PDE3B 6610 0.068 0.43 NO
14 NOS3 NOS3 NOS3 6961 0.061 0.43 NO
15 CALM2 CALM2 CALM2 6976 0.061 0.44 NO
16 PRKAR2A PRKAR2A PRKAR2A 7175 0.058 0.45 NO
17 FLT4 FLT4 FLT4 7769 0.047 0.43 NO
18 PRKAR1A PRKAR1A PRKAR1A 8255 0.038 0.41 NO
19 HSP90AA1 HSP90AA1 HSP90AA1 9154 0.024 0.37 NO
20 KNG1 KNG1 KNG1 9446 0.02 0.36 NO
21 PDE3A PDE3A PDE3A 9541 0.018 0.36 NO
22 CALM3 CALM3 CALM3 10673 0.0014 0.29 NO
23 CALM1 CALM1 CALM1 12205 -0.022 0.21 NO
24 CHRM1 CHRM1 CHRM1 13497 -0.046 0.16 NO
25 AKT1 AKT1 AKT1 14556 -0.07 0.12 NO
26 CHRNA1 CHRNA1 CHRNA1 15215 -0.09 0.1 NO
27 SLC7A1 SLC7A1 SLC7A1 15407 -0.098 0.12 NO
28 PRKG2 PRKG2 PRKG2 15459 -0.099 0.14 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 NFAT PATHWAY.

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

genes ES table in pathway: BIOCARTA EDG1 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 ITGB3 ITGB3 ITGB3 86 0.52 0.031 YES
2 SDC2 SDC2 SDC2 160 0.47 0.059 YES
3 THBS4 THBS4 THBS4 207 0.45 0.086 YES
4 TNN TNN TNN 232 0.44 0.12 YES
5 THBS2 THBS2 THBS2 256 0.43 0.14 YES
6 ITGA2 ITGA2 ITGA2 319 0.41 0.17 YES
7 SV2A SV2A SV2A 325 0.41 0.2 YES
8 ITGA1 ITGA1 ITGA1 357 0.4 0.22 YES
9 CD36 CD36 CD36 489 0.37 0.24 YES
10 LAMA2 LAMA2 LAMA2 513 0.37 0.26 YES
11 COL11A2 COL11A2 COL11A2 657 0.34 0.28 YES
12 ITGA10 ITGA10 ITGA10 729 0.33 0.3 YES
13 RELN RELN RELN 800 0.32 0.32 YES
14 LAMA4 LAMA4 LAMA4 874 0.31 0.33 YES
15 ITGA8 ITGA8 ITGA8 911 0.31 0.35 YES
16 SPP1 SPP1 SPP1 1092 0.29 0.36 YES
17 IBSP IBSP IBSP 1197 0.28 0.37 YES
18 ITGA2B ITGA2B ITGA2B 1234 0.27 0.39 YES
19 LAMB1 LAMB1 LAMB1 1465 0.26 0.39 YES
20 COL4A6 COL4A6 COL4A6 1520 0.25 0.41 YES
21 COL5A2 COL5A2 COL5A2 1648 0.24 0.42 YES
22 COL1A2 COL1A2 COL1A2 1942 0.22 0.42 YES
23 ITGA11 ITGA11 ITGA11 2004 0.22 0.43 YES
24 ITGA4 ITGA4 ITGA4 2075 0.21 0.44 YES
25 ITGA9 ITGA9 ITGA9 2135 0.21 0.45 YES
26 COL2A1 COL2A1 COL2A1 2678 0.18 0.43 YES
27 ITGAV ITGAV ITGAV 2707 0.18 0.44 YES
28 THBS1 THBS1 THBS1 2737 0.18 0.45 YES
29 LAMC1 LAMC1 LAMC1 2743 0.18 0.46 YES
30 CHAD CHAD CHAD 2772 0.18 0.47 YES
31 ITGA6 ITGA6 ITGA6 2900 0.17 0.48 YES
32 ITGB6 ITGB6 ITGB6 3045 0.16 0.48 YES
33 COL6A1 COL6A1 COL6A1 3103 0.16 0.49 YES
34 COMP COMP COMP 3234 0.16 0.49 YES
35 COL11A1 COL11A1 COL11A1 3314 0.15 0.5 YES
36 ITGB8 ITGB8 ITGB8 3333 0.15 0.51 YES
37 COL6A2 COL6A2 COL6A2 3382 0.15 0.52 YES
38 ITGA5 ITGA5 ITGA5 3721 0.14 0.51 YES
39 COL5A1 COL5A1 COL5A1 3754 0.14 0.51 YES
40 COL3A1 COL3A1 COL3A1 3976 0.13 0.51 YES
41 ITGB5 ITGB5 ITGB5 4184 0.12 0.51 YES
42 COL4A1 COL4A1 COL4A1 4190 0.12 0.52 YES
43 ITGB1 ITGB1 ITGB1 4285 0.12 0.52 YES
44 COL5A3 COL5A3 COL5A3 4546 0.11 0.51 YES
45 TNR TNR TNR 4572 0.11 0.52 YES
46 ITGB4 ITGB4 ITGB4 4615 0.11 0.52 YES
47 LAMB4 LAMB4 LAMB4 4652 0.11 0.53 YES
48 THBS3 THBS3 THBS3 4660 0.11 0.54 YES
49 LAMA5 LAMA5 LAMA5 4825 0.11 0.54 YES
50 HMMR HMMR HMMR 4847 0.11 0.54 YES
51 SDC4 SDC4 SDC4 4875 0.11 0.55 YES
52 GP6 GP6 GP6 5070 0.1 0.54 YES
53 COL4A2 COL4A2 COL4A2 5163 0.1 0.54 YES
54 COL1A1 COL1A1 COL1A1 5195 0.099 0.55 YES
55 COL6A3 COL6A3 COL6A3 5267 0.097 0.55 YES
56 LAMB3 LAMB3 LAMB3 5403 0.094 0.55 NO
57 TNC TNC TNC 5551 0.091 0.55 NO
58 SV2C SV2C SV2C 6368 0.073 0.51 NO
59 SDC1 SDC1 SDC1 6484 0.07 0.51 NO
60 LAMC3 LAMC3 LAMC3 7503 0.052 0.45 NO
61 AGRN AGRN AGRN 7662 0.048 0.45 NO
62 FN1 FN1 FN1 8161 0.04 0.42 NO
63 LAMA3 LAMA3 LAMA3 9201 0.024 0.37 NO
64 DAG1 DAG1 DAG1 9364 0.021 0.36 NO
65 TNXB TNXB TNXB 9469 0.019 0.35 NO
66 LAMC2 LAMC2 LAMC2 10079 0.01 0.32 NO
67 COL6A6 COL6A6 COL6A6 10628 0.0022 0.29 NO
68 SDC3 SDC3 SDC3 10806 -0.00056 0.28 NO
69 CD47 CD47 CD47 11508 -0.011 0.24 NO
70 VWF VWF VWF 11889 -0.017 0.22 NO
71 SV2B SV2B SV2B 12055 -0.02 0.22 NO
72 HSPG2 HSPG2 HSPG2 12208 -0.022 0.21 NO
73 LAMB2 LAMB2 LAMB2 13416 -0.045 0.14 NO
74 COL4A4 COL4A4 COL4A4 14757 -0.076 0.074 NO
75 ITGA7 ITGA7 ITGA7 15496 -0.1 0.04 NO
76 CD44 CD44 CD44 15634 -0.11 0.04 NO
77 ITGA3 ITGA3 ITGA3 15802 -0.12 0.039 NO
78 GP5 GP5 GP5 17231 -0.24 -0.025 NO
79 LAMA1 LAMA1 LAMA1 17389 -0.26 -0.016 NO
80 GP1BA GP1BA GP1BA 17769 -0.34 -0.014 NO
81 ITGB7 ITGB7 ITGB7 17954 -0.43 0.0052 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 EDG1 PATHWAY.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EDG1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA WNT PATHWAY

Table 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 ITGB3 ITGB3 ITGB3 86 0.52 0.043 YES
2 ITGA2 ITGA2 ITGA2 319 0.41 0.068 YES
3 ITGA1 ITGA1 ITGA1 357 0.4 0.1 YES
4 SGCG SGCG SGCG 461 0.38 0.13 YES
5 LAMA2 LAMA2 LAMA2 513 0.37 0.16 YES
6 CDH2 CDH2 CDH2 558 0.36 0.19 YES
7 ITGA10 ITGA10 ITGA10 729 0.33 0.21 YES
8 ITGA8 ITGA8 ITGA8 911 0.31 0.23 YES
9 CTNNA3 CTNNA3 CTNNA3 1082 0.29 0.25 YES
10 GJA1 GJA1 GJA1 1120 0.28 0.27 YES
11 ITGA2B ITGA2B ITGA2B 1234 0.27 0.29 YES
12 RYR2 RYR2 RYR2 1365 0.26 0.31 YES
13 CACNA2D1 CACNA2D1 CACNA2D1 1569 0.25 0.32 YES
14 DSG2 DSG2 DSG2 1573 0.25 0.34 YES
15 CACNA1C CACNA1C CACNA1C 1816 0.23 0.35 YES
16 SGCB SGCB SGCB 1819 0.23 0.37 YES
17 ITGA11 ITGA11 ITGA11 2004 0.22 0.38 YES
18 ITGA4 ITGA4 ITGA4 2075 0.21 0.39 YES
19 ITGA9 ITGA9 ITGA9 2135 0.21 0.41 YES
20 CACNB4 CACNB4 CACNB4 2166 0.21 0.43 YES
21 ACTN2 ACTN2 ACTN2 2186 0.21 0.44 YES
22 CACNG4 CACNG4 CACNG4 2201 0.21 0.46 YES
23 DMD DMD DMD 2366 0.2 0.47 YES
24 CACNA2D3 CACNA2D3 CACNA2D3 2640 0.18 0.47 YES
25 ITGAV ITGAV ITGAV 2707 0.18 0.49 YES
26 CACNA2D4 CACNA2D4 CACNA2D4 2730 0.18 0.5 YES
27 ITGA6 ITGA6 ITGA6 2900 0.17 0.51 YES
28 ITGB6 ITGB6 ITGB6 3045 0.16 0.51 YES
29 ITGB8 ITGB8 ITGB8 3333 0.15 0.51 YES
30 ITGA5 ITGA5 ITGA5 3721 0.14 0.5 YES
31 TCF7L2 TCF7L2 TCF7L2 4080 0.13 0.5 YES
32 ITGB5 ITGB5 ITGB5 4184 0.12 0.5 YES
33 CACNB1 CACNB1 CACNB1 4226 0.12 0.51 YES
34 ITGB1 ITGB1 ITGB1 4285 0.12 0.52 YES
35 ITGB4 ITGB4 ITGB4 4615 0.11 0.51 NO
36 CACNB2 CACNB2 CACNB2 4975 0.1 0.5 NO
37 TCF7L1 TCF7L1 TCF7L1 5385 0.095 0.48 NO
38 DES DES DES 5634 0.089 0.48 NO
39 CACNG6 CACNG6 CACNG6 5694 0.087 0.48 NO
40 DSC2 DSC2 DSC2 5827 0.085 0.48 NO
41 JUP JUP JUP 7696 0.048 0.38 NO
42 ACTN4 ACTN4 ACTN4 8310 0.038 0.35 NO
43 CACNB3 CACNB3 CACNB3 8459 0.035 0.35 NO
44 CTNNA1 CTNNA1 CTNNA1 8834 0.029 0.33 NO
45 SLC8A1 SLC8A1 SLC8A1 8998 0.027 0.32 NO
46 DSP DSP DSP 9167 0.024 0.32 NO
47 DAG1 DAG1 DAG1 9364 0.021 0.31 NO
48 SGCA SGCA SGCA 9781 0.015 0.28 NO
49 LEF1 LEF1 LEF1 10472 0.0045 0.25 NO
50 ATP2A2 ATP2A2 ATP2A2 10861 -0.0012 0.23 NO
51 PKP2 PKP2 PKP2 10890 -0.0016 0.22 NO
52 CACNA1S CACNA1S CACNA1S 11370 -0.0088 0.2 NO
53 CTNNA2 CTNNA2 CTNNA2 12148 -0.022 0.16 NO
54 CACNA1D CACNA1D CACNA1D 13358 -0.044 0.094 NO
55 CACNA2D2 CACNA2D2 CACNA2D2 13552 -0.047 0.088 NO
56 ACTB ACTB ACTB 13778 -0.052 0.08 NO
57 CTNNB1 CTNNB1 CTNNB1 13993 -0.057 0.073 NO
58 ACTG1 ACTG1 ACTG1 14084 -0.059 0.074 NO
59 LMNA LMNA LMNA 14317 -0.064 0.066 NO
60 EMD EMD EMD 14347 -0.065 0.071 NO
61 SGCD SGCD SGCD 15054 -0.085 0.039 NO
62 CACNA1F CACNA1F CACNA1F 15282 -0.093 0.035 NO
63 ITGA7 ITGA7 ITGA7 15496 -0.1 0.032 NO
64 ACTN3 ACTN3 ACTN3 15577 -0.1 0.038 NO
65 ITGA3 ITGA3 ITGA3 15802 -0.12 0.036 NO
66 ACTN1 ACTN1 ACTN1 15904 -0.12 0.041 NO
67 TCF7 TCF7 TCF7 15941 -0.12 0.051 NO
68 CACNG3 CACNG3 CACNG3 17593 -0.3 -0.014 NO
69 ITGB7 ITGB7 ITGB7 17954 -0.43 0.0052 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 WNT PATHWAY.

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

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 PDGFC PDGFC PDGFC 26 0.61 0.05 YES
2 HTR2A HTR2A HTR2A 146 0.48 0.084 YES
3 ADRB1 ADRB1 ADRB1 181 0.46 0.12 YES
4 PDGFA PDGFA PDGFA 187 0.46 0.16 YES
5 PLCB1 PLCB1 PLCB1 236 0.44 0.2 YES
6 PRKG1 PRKG1 PRKG1 307 0.42 0.23 YES
7 LPAR1 LPAR1 LPAR1 310 0.42 0.26 YES
8 PRKCA PRKCA PRKCA 527 0.36 0.28 YES
9 PDGFD PDGFD PDGFD 749 0.33 0.3 YES
10 ADCY8 ADCY8 ADCY8 1059 0.29 0.3 YES
11 TUBB1 TUBB1 TUBB1 1060 0.29 0.33 YES
12 GJA1 GJA1 GJA1 1120 0.28 0.35 YES
13 GRM5 GRM5 GRM5 1163 0.28 0.37 YES
14 PLCB4 PLCB4 PLCB4 1483 0.25 0.37 YES
15 GUCY1A3 GUCY1A3 GUCY1A3 1777 0.23 0.38 YES
16 EGFR EGFR EGFR 1984 0.22 0.38 YES
17 PDGFRA PDGFRA PDGFRA 2008 0.22 0.4 YES
18 GUCY1B3 GUCY1B3 GUCY1B3 2334 0.2 0.4 YES
19 TUBB2B TUBB2B TUBB2B 2386 0.2 0.41 YES
20 PRKACB PRKACB PRKACB 3209 0.16 0.38 NO
21 PDGFRB PDGFRB PDGFRB 3407 0.15 0.38 NO
22 ITPR1 ITPR1 ITPR1 3688 0.14 0.38 NO
23 HTR2C HTR2C HTR2C 4023 0.13 0.37 NO
24 GUCY1A2 GUCY1A2 GUCY1A2 4099 0.13 0.38 NO
25 TJP1 TJP1 TJP1 4251 0.12 0.38 NO
26 GRM1 GRM1 GRM1 4820 0.11 0.36 NO
27 DRD2 DRD2 DRD2 4851 0.11 0.37 NO
28 ADCY6 ADCY6 ADCY6 5181 0.099 0.36 NO
29 TUBA1A TUBA1A TUBA1A 5389 0.095 0.35 NO
30 MAP3K2 MAP3K2 MAP3K2 5632 0.089 0.35 NO
31 GNAS GNAS GNAS 5665 0.088 0.35 NO
32 GNAI1 GNAI1 GNAI1 5750 0.086 0.36 NO
33 ITPR2 ITPR2 ITPR2 6318 0.074 0.33 NO
34 SOS1 SOS1 SOS1 6766 0.065 0.31 NO
35 KRAS KRAS KRAS 6934 0.062 0.31 NO
36 PDGFB PDGFB PDGFB 6948 0.062 0.31 NO
37 MAP2K1 MAP2K1 MAP2K1 7378 0.054 0.29 NO
38 EGF EGF EGF 7388 0.054 0.3 NO
39 GNAQ GNAQ GNAQ 7477 0.052 0.3 NO
40 NRAS NRAS NRAS 7999 0.043 0.27 NO
41 HTR2B HTR2B HTR2B 8083 0.041 0.27 NO
42 GNA11 GNA11 GNA11 9044 0.026 0.22 NO
43 TUBA3E TUBA3E TUBA3E 9158 0.024 0.21 NO
44 SRC SRC SRC 9234 0.023 0.21 NO
45 GNAI3 GNAI3 GNAI3 9394 0.02 0.2 NO
46 MAP2K5 MAP2K5 MAP2K5 9420 0.02 0.2 NO
47 PRKCG PRKCG PRKCG 9547 0.018 0.2 NO
48 ADCY7 ADCY7 ADCY7 10141 0.0094 0.17 NO
49 SOS2 SOS2 SOS2 10177 0.0089 0.16 NO
50 PLCB3 PLCB3 PLCB3 10338 0.0065 0.16 NO
51 DRD1 DRD1 DRD1 10502 0.0039 0.15 NO
52 CDK1 CDK1 CDK1 10517 0.0037 0.15 NO
53 PRKACA PRKACA PRKACA 10534 0.0034 0.15 NO
54 TUBA3C TUBA3C TUBA3C 10622 0.0023 0.14 NO
55 RAF1 RAF1 RAF1 10632 0.0021 0.14 NO
56 ADCY5 ADCY5 ADCY5 11272 -0.0073 0.11 NO
57 TUBB TUBB TUBB 11595 -0.013 0.09 NO
58 MAPK7 MAPK7 MAPK7 11680 -0.014 0.086 NO
59 TUBA1B TUBA1B TUBA1B 12114 -0.021 0.064 NO
60 CSNK1D CSNK1D CSNK1D 12310 -0.024 0.055 NO
61 MAPK1 MAPK1 MAPK1 12409 -0.026 0.052 NO
62 PRKX PRKX PRKX 12640 -0.03 0.042 NO
63 GNAI2 GNAI2 GNAI2 12777 -0.032 0.037 NO
64 TUBA3D TUBA3D TUBA3D 12857 -0.034 0.035 NO
65 ADCY4 ADCY4 ADCY4 12893 -0.034 0.036 NO
66 MAPK3 MAPK3 MAPK3 13375 -0.044 0.013 NO
67 TUBB2A TUBB2A TUBB2A 13377 -0.044 0.017 NO
68 HRAS HRAS HRAS 13503 -0.046 0.014 NO
69 TUBB2C TUBB2C TUBB2C 13547 -0.047 0.015 NO
70 TUBAL3 TUBAL3 TUBAL3 13569 -0.048 0.018 NO
71 TUBB6 TUBB6 TUBB6 13658 -0.05 0.018 NO
72 PLCB2 PLCB2 PLCB2 14101 -0.059 -0.0021 NO
73 GRB2 GRB2 GRB2 14165 -0.061 -0.00046 NO
74 TUBB3 TUBB3 TUBB3 14223 -0.062 0.0016 NO
75 MAP2K2 MAP2K2 MAP2K2 14277 -0.063 0.004 NO
76 ITPR3 ITPR3 ITPR3 14547 -0.07 -0.005 NO
77 TUBA1C TUBA1C TUBA1C 15078 -0.086 -0.027 NO
78 ADCY9 ADCY9 ADCY9 15311 -0.094 -0.032 NO
79 PRKG2 PRKG2 PRKG2 15459 -0.099 -0.032 NO
80 TUBB8 TUBB8 TUBB8 16107 -0.13 -0.057 NO
81 ADCY1 ADCY1 ADCY1 16318 -0.15 -0.056 NO
82 TUBB4Q TUBB4Q TUBB4Q 16341 -0.15 -0.044 NO
83 TUBA4A TUBA4A TUBA4A 16845 -0.2 -0.056 NO
84 TUBA8 TUBA8 TUBA8 17297 -0.25 -0.06 NO
85 TUBB4 TUBB4 TUBB4 17857 -0.37 -0.059 NO
86 PRKCB PRKCB PRKCB 17924 -0.41 -0.028 NO
87 ADCY2 ADCY2 ADCY2 17937 -0.42 0.0062 NO

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

Figure S54.  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 ERBB SIGNALING 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 GRIA2 GRIA2 GRIA2 3 0.71 0.091 YES
2 PLCB1 PLCB1 PLCB1 236 0.44 0.13 YES
3 GRIA1 GRIA1 GRIA1 251 0.44 0.19 YES
4 CAMK2B CAMK2B CAMK2B 439 0.38 0.23 YES
5 PRKCA PRKCA PRKCA 527 0.36 0.27 YES
6 ADCY8 ADCY8 ADCY8 1059 0.29 0.28 YES
7 GRM5 GRM5 GRM5 1163 0.28 0.31 YES
8 PLCB4 PLCB4 PLCB4 1483 0.25 0.32 YES
9 CACNA1C CACNA1C CACNA1C 1816 0.23 0.33 YES
10 PRKACB PRKACB PRKACB 3209 0.16 0.28 YES
11 GRIN2B GRIN2B GRIN2B 3401 0.15 0.28 YES
12 RAPGEF3 RAPGEF3 RAPGEF3 3403 0.15 0.3 YES
13 RPS6KA6 RPS6KA6 RPS6KA6 3441 0.15 0.32 YES
14 CAMK2D CAMK2D CAMK2D 3451 0.15 0.34 YES
15 CALML6 CALML6 CALML6 3568 0.14 0.35 YES
16 RPS6KA3 RPS6KA3 RPS6KA3 3650 0.14 0.36 YES
17 PPP1R12A PPP1R12A PPP1R12A 3683 0.14 0.38 YES
18 ITPR1 ITPR1 ITPR1 3688 0.14 0.4 YES
19 BRAF BRAF BRAF 4309 0.12 0.38 NO
20 PPP3CA PPP3CA PPP3CA 4470 0.12 0.38 NO
21 GRM1 GRM1 GRM1 4820 0.11 0.38 NO
22 GRIN2A GRIN2A GRIN2A 5061 0.1 0.38 NO
23 PPP3R2 PPP3R2 PPP3R2 5914 0.083 0.34 NO
24 ITPR2 ITPR2 ITPR2 6318 0.074 0.33 NO
25 PPP1CB PPP1CB PPP1CB 6389 0.072 0.33 NO
26 KRAS KRAS KRAS 6934 0.062 0.31 NO
27 CALM2 CALM2 CALM2 6976 0.061 0.32 NO
28 PPP1R1A PPP1R1A PPP1R1A 7276 0.056 0.31 NO
29 MAP2K1 MAP2K1 MAP2K1 7378 0.054 0.31 NO
30 GNAQ GNAQ GNAQ 7477 0.052 0.31 NO
31 RAP1A RAP1A RAP1A 7511 0.051 0.32 NO
32 PPP3R1 PPP3R1 PPP3R1 7684 0.048 0.31 NO
33 RAP1B RAP1B RAP1B 7992 0.043 0.3 NO
34 NRAS NRAS NRAS 7999 0.043 0.3 NO
35 GRIN2D GRIN2D GRIN2D 8483 0.035 0.28 NO
36 PPP3CB PPP3CB PPP3CB 9078 0.026 0.25 NO
37 CREBBP CREBBP CREBBP 9304 0.022 0.24 NO
38 PRKCG PRKCG PRKCG 9547 0.018 0.23 NO
39 PPP1CC PPP1CC PPP1CC 9945 0.012 0.21 NO
40 PLCB3 PLCB3 PLCB3 10338 0.0065 0.19 NO
41 EP300 EP300 EP300 10385 0.0058 0.19 NO
42 ATF4 ATF4 ATF4 10436 0.0051 0.19 NO
43 PRKACA PRKACA PRKACA 10534 0.0034 0.18 NO
44 RAF1 RAF1 RAF1 10632 0.0021 0.18 NO
45 CALM3 CALM3 CALM3 10673 0.0014 0.17 NO
46 CAMK2G CAMK2G CAMK2G 10943 -0.0024 0.16 NO
47 CALML3 CALML3 CALML3 11036 -0.0037 0.16 NO
48 CAMK4 CAMK4 CAMK4 11506 -0.011 0.13 NO
49 CALM1 CALM1 CALM1 12205 -0.022 0.094 NO
50 MAPK1 MAPK1 MAPK1 12409 -0.026 0.086 NO
51 PRKX PRKX PRKX 12640 -0.03 0.077 NO
52 ARAF ARAF ARAF 13357 -0.044 0.043 NO
53 MAPK3 MAPK3 MAPK3 13375 -0.044 0.048 NO
54 GRIN2C GRIN2C GRIN2C 13407 -0.044 0.052 NO
55 HRAS HRAS HRAS 13503 -0.046 0.052 NO
56 CALML5 CALML5 CALML5 13649 -0.05 0.05 NO
57 CHP CHP CHP 13920 -0.055 0.042 NO
58 PLCB2 PLCB2 PLCB2 14101 -0.059 0.04 NO
59 MAP2K2 MAP2K2 MAP2K2 14277 -0.063 0.038 NO
60 ITPR3 ITPR3 ITPR3 14547 -0.07 0.032 NO
61 PPP1CA PPP1CA PPP1CA 14807 -0.078 0.028 NO
62 CHP2 CHP2 CHP2 14860 -0.079 0.035 NO
63 PPP3CC PPP3CC PPP3CC 15154 -0.088 0.03 NO
64 RPS6KA2 RPS6KA2 RPS6KA2 15725 -0.11 0.013 NO
65 RPS6KA1 RPS6KA1 RPS6KA1 16299 -0.15 -0.00062 NO
66 CAMK2A CAMK2A CAMK2A 16620 -0.17 0.0034 NO
67 GRIN1 GRIN1 GRIN1 16782 -0.19 0.018 NO
68 PRKCB PRKCB PRKCB 17924 -0.41 0.0069 NO

Figure S55.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ERBB SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION

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 PDGFC PDGFC PDGFC 26 0.61 0.021 YES
2 ITGB3 ITGB3 ITGB3 86 0.52 0.036 YES
3 PDGFA PDGFA PDGFA 187 0.46 0.048 YES
4 SHC3 SHC3 SHC3 198 0.45 0.063 YES
5 THBS4 THBS4 THBS4 207 0.45 0.079 YES
6 TNN TNN TNN 232 0.44 0.094 YES
7 THBS2 THBS2 THBS2 256 0.43 0.11 YES
8 ITGA2 ITGA2 ITGA2 319 0.41 0.12 YES
9 ITGA1 ITGA1 ITGA1 357 0.4 0.13 YES
10 PAK3 PAK3 PAK3 434 0.38 0.14 YES
11 LAMA2 LAMA2 LAMA2 513 0.37 0.15 YES
12 PRKCA PRKCA PRKCA 527 0.36 0.16 YES
13 COL11A2 COL11A2 COL11A2 657 0.34 0.17 YES
14 ITGA10 ITGA10 ITGA10 729 0.33 0.18 YES
15 PDGFD PDGFD PDGFD 749 0.33 0.19 YES
16 HGF HGF HGF 797 0.32 0.2 YES
17 RELN RELN RELN 800 0.32 0.21 YES
18 FLNC FLNC FLNC 815 0.32 0.22 YES
19 LAMA4 LAMA4 LAMA4 874 0.31 0.23 YES
20 ITGA8 ITGA8 ITGA8 911 0.31 0.24 YES
21 SPP1 SPP1 SPP1 1092 0.29 0.24 YES
22 IBSP IBSP IBSP 1197 0.28 0.24 YES
23 ITGA2B ITGA2B ITGA2B 1234 0.27 0.25 YES
24 VEGFA VEGFA VEGFA 1327 0.27 0.26 YES
25 FLT1 FLT1 FLT1 1420 0.26 0.26 YES
26 LAMB1 LAMB1 LAMB1 1465 0.26 0.27 YES
27 COL4A6 COL4A6 COL4A6 1520 0.25 0.27 YES
28 COL5A2 COL5A2 COL5A2 1648 0.24 0.27 YES
29 PGF PGF PGF 1890 0.22 0.27 YES
30 ROCK2 ROCK2 ROCK2 1919 0.22 0.27 YES
31 COL1A2 COL1A2 COL1A2 1942 0.22 0.28 YES
32 EGFR EGFR EGFR 1984 0.22 0.29 YES
33 ITGA11 ITGA11 ITGA11 2004 0.22 0.29 YES
34 PDGFRA PDGFRA PDGFRA 2008 0.22 0.3 YES
35 ITGA4 ITGA4 ITGA4 2075 0.21 0.31 YES
36 ITGA9 ITGA9 ITGA9 2135 0.21 0.31 YES
37 ACTN2 ACTN2 ACTN2 2186 0.21 0.32 YES
38 MAPK8 MAPK8 MAPK8 2391 0.2 0.31 YES
39 KDR KDR KDR 2396 0.2 0.32 YES
40 MAPK10 MAPK10 MAPK10 2405 0.2 0.32 YES
41 COL2A1 COL2A1 COL2A1 2678 0.18 0.32 YES
42 ITGAV ITGAV ITGAV 2707 0.18 0.32 YES
43 THBS1 THBS1 THBS1 2737 0.18 0.32 YES
44 LAMC1 LAMC1 LAMC1 2743 0.18 0.33 YES
45 CHAD CHAD CHAD 2772 0.18 0.34 YES
46 ITGA6 ITGA6 ITGA6 2900 0.17 0.34 YES
47 VAV2 VAV2 VAV2 2933 0.17 0.34 YES
48 ITGB6 ITGB6 ITGB6 3045 0.16 0.34 YES
49 MYLK2 MYLK2 MYLK2 3062 0.16 0.34 YES
50 COL6A1 COL6A1 COL6A1 3103 0.16 0.35 YES
51 PAK7 PAK7 PAK7 3191 0.16 0.35 YES
52 COMP COMP COMP 3234 0.16 0.35 YES
53 COL11A1 COL11A1 COL11A1 3314 0.15 0.35 YES
54 TLN2 TLN2 TLN2 3315 0.15 0.36 YES
55 ITGB8 ITGB8 ITGB8 3333 0.15 0.36 YES
56 COL6A2 COL6A2 COL6A2 3382 0.15 0.37 YES
57 PDGFRB PDGFRB PDGFRB 3407 0.15 0.37 YES
58 BIRC2 BIRC2 BIRC2 3420 0.15 0.38 YES
59 PIK3CA PIK3CA PIK3CA 3542 0.14 0.37 YES
60 MYL10 MYL10 MYL10 3658 0.14 0.37 YES
61 PPP1R12A PPP1R12A PPP1R12A 3683 0.14 0.38 YES
62 ITGA5 ITGA5 ITGA5 3721 0.14 0.38 YES
63 COL5A1 COL5A1 COL5A1 3754 0.14 0.38 YES
64 COL3A1 COL3A1 COL3A1 3976 0.13 0.38 YES
65 MYLK MYLK MYLK 4051 0.13 0.38 YES
66 ARHGAP5 ARHGAP5 ARHGAP5 4170 0.12 0.37 YES
67 ITGB5 ITGB5 ITGB5 4184 0.12 0.38 YES
68 COL4A1 COL4A1 COL4A1 4190 0.12 0.38 YES
69 ITGB1 ITGB1 ITGB1 4285 0.12 0.38 YES
70 BRAF BRAF BRAF 4309 0.12 0.38 YES
71 ROCK1 ROCK1 ROCK1 4329 0.12 0.39 YES
72 XIAP XIAP XIAP 4331 0.12 0.39 YES
73 CRK CRK CRK 4420 0.12 0.39 YES
74 COL5A3 COL5A3 COL5A3 4546 0.11 0.39 YES
75 TNR TNR TNR 4572 0.11 0.39 YES
76 ITGB4 ITGB4 ITGB4 4615 0.11 0.39 YES
77 LAMB4 LAMB4 LAMB4 4652 0.11 0.39 YES
78 THBS3 THBS3 THBS3 4660 0.11 0.4 YES
79 DOCK1 DOCK1 DOCK1 4732 0.11 0.4 YES
80 LAMA5 LAMA5 LAMA5 4825 0.11 0.4 NO
81 SHC1 SHC1 SHC1 4947 0.1 0.39 NO
82 COL4A2 COL4A2 COL4A2 5163 0.1 0.38 NO
83 COL1A1 COL1A1 COL1A1 5195 0.099 0.39 NO
84 COL6A3 COL6A3 COL6A3 5267 0.097 0.39 NO
85 LAMB3 LAMB3 LAMB3 5403 0.094 0.38 NO
86 TNC TNC TNC 5551 0.091 0.38 NO
87 AKT3 AKT3 AKT3 5596 0.09 0.38 NO
88 PTK2 PTK2 PTK2 5804 0.085 0.37 NO
89 VCL VCL VCL 6216 0.076 0.35 NO
90 GRLF1 GRLF1 GRLF1 6241 0.075 0.35 NO
91 SHC2 SHC2 SHC2 6276 0.075 0.35 NO
92 ERBB2 ERBB2 ERBB2 6300 0.074 0.35 NO
93 PPP1CB PPP1CB PPP1CB 6389 0.072 0.35 NO
94 SOS1 SOS1 SOS1 6766 0.065 0.33 NO
95 PDGFB PDGFB PDGFB 6948 0.062 0.32 NO
96 CAV2 CAV2 CAV2 7005 0.061 0.32 NO
97 IGF1R IGF1R IGF1R 7212 0.057 0.31 NO
98 MAP2K1 MAP2K1 MAP2K1 7378 0.054 0.31 NO
99 EGF EGF EGF 7388 0.054 0.31 NO
100 MAPK9 MAPK9 MAPK9 7398 0.053 0.31 NO
101 LAMC3 LAMC3 LAMC3 7503 0.052 0.3 NO
102 RAP1A RAP1A RAP1A 7511 0.051 0.31 NO
103 ZYX ZYX ZYX 7567 0.05 0.31 NO
104 FLT4 FLT4 FLT4 7769 0.047 0.3 NO
105 MYLPF MYLPF MYLPF 7981 0.043 0.29 NO
106 RAP1B RAP1B RAP1B 7992 0.043 0.29 NO
107 CAV1 CAV1 CAV1 8072 0.041 0.28 NO
108 PAK2 PAK2 PAK2 8134 0.04 0.28 NO
109 FN1 FN1 FN1 8161 0.04 0.28 NO
110 VEGFC VEGFC VEGFC 8309 0.038 0.28 NO
111 ACTN4 ACTN4 ACTN4 8310 0.038 0.28 NO
112 GSK3B GSK3B GSK3B 8400 0.036 0.27 NO
113 IGF1 IGF1 IGF1 8685 0.032 0.26 NO
114 SHC4 SHC4 SHC4 8853 0.029 0.25 NO
115 LAMA3 LAMA3 LAMA3 9201 0.024 0.23 NO
116 JUN JUN JUN 9232 0.023 0.23 NO
117 SRC SRC SRC 9234 0.023 0.23 NO
118 TNXB TNXB TNXB 9469 0.019 0.22 NO
119 PIK3R1 PIK3R1 PIK3R1 9521 0.018 0.22 NO
120 PRKCG PRKCG PRKCG 9547 0.018 0.22 NO
121 PXN PXN PXN 9601 0.017 0.21 NO
122 PDPK1 PDPK1 PDPK1 9847 0.014 0.2 NO
123 PPP1CC PPP1CC PPP1CC 9945 0.012 0.2 NO
124 RAC1 RAC1 RAC1 9959 0.012 0.2 NO
125 LAMC2 LAMC2 LAMC2 10079 0.01 0.19 NO
126 VAV3 VAV3 VAV3 10165 0.009 0.18 NO
127 SOS2 SOS2 SOS2 10177 0.0089 0.18 NO
128 COL6A6 COL6A6 COL6A6 10628 0.0022 0.16 NO
129 RAF1 RAF1 RAF1 10632 0.0021 0.16 NO
130 BAD BAD BAD 10682 0.0013 0.16 NO
131 PIK3R2 PIK3R2 PIK3R2 10942 -0.0023 0.14 NO
132 CRKL CRKL CRKL 11014 -0.0034 0.14 NO
133 AKT2 AKT2 AKT2 11087 -0.0045 0.13 NO
134 FLNB FLNB FLNB 11149 -0.0055 0.13 NO
135 PAK6 PAK6 PAK6 11403 -0.0095 0.12 NO
136 CAPN2 CAPN2 CAPN2 11462 -0.01 0.11 NO
137 MYL9 MYL9 MYL9 11686 -0.014 0.1 NO
138 CDC42 CDC42 CDC42 11790 -0.016 0.097 NO
139 BCAR1 BCAR1 BCAR1 11859 -0.017 0.094 NO
140 VWF VWF VWF 11889 -0.017 0.092 NO
141 PIP5K1C PIP5K1C PIP5K1C 12127 -0.021 0.08 NO
142 ILK ILK ILK 12350 -0.025 0.068 NO
143 RHOA RHOA RHOA 12365 -0.025 0.069 NO
144 VASP VASP VASP 12386 -0.025 0.068 NO
145 MAPK1 MAPK1 MAPK1 12409 -0.026 0.068 NO
146 FIGF FIGF FIGF 12567 -0.029 0.06 NO
147 MYL12B MYL12B MYL12B 12666 -0.03 0.056 NO
148 PAK1 PAK1 PAK1 12825 -0.033 0.048 NO
149 PIK3R3 PIK3R3 PIK3R3 13103 -0.038 0.034 NO
150 ELK1 ELK1 ELK1 13137 -0.039 0.034 NO
151 DIAPH1 DIAPH1 DIAPH1 13347 -0.043 0.024 NO
152 MAPK3 MAPK3 MAPK3 13375 -0.044 0.024 NO
153 LAMB2 LAMB2 LAMB2 13416 -0.045 0.023 NO
154 FYN FYN FYN 13558 -0.048 0.017 NO
155 PTEN PTEN PTEN 13602 -0.048 0.016 NO
156 PIK3CG PIK3CG PIK3CG 13620 -0.049 0.017 NO
157 CCND3 CCND3 CCND3 13630 -0.049 0.018 NO
158 ACTB ACTB ACTB 13778 -0.052 0.012 NO
159 TLN1 TLN1 TLN1 13790 -0.052 0.013 NO
160 FLNA FLNA FLNA 13809 -0.053 0.014 NO
161 CTNNB1 CTNNB1 CTNNB1 13993 -0.057 0.006 NO
162 ACTG1 ACTG1 ACTG1 14084 -0.059 0.0031 NO
163 GRB2 GRB2 GRB2 14165 -0.061 0.00082 NO
164 BIRC3 BIRC3 BIRC3 14205 -0.061 0.00087 NO
165 PARVA PARVA PARVA 14354 -0.065 -0.0051 NO
166 MYL5 MYL5 MYL5 14455 -0.068 -0.0082 NO
167 AKT1 AKT1 AKT1 14556 -0.07 -0.011 NO
168 CCND2 CCND2 CCND2 14627 -0.072 -0.013 NO
169 COL4A4 COL4A4 COL4A4 14757 -0.076 -0.017 NO
170 MYL12A MYL12A MYL12A 14776 -0.076 -0.015 NO
171 PPP1CA PPP1CA PPP1CA 14807 -0.078 -0.014 NO
172 CCND1 CCND1 CCND1 15458 -0.099 -0.047 NO
173 ITGA7 ITGA7 ITGA7 15496 -0.1 -0.045 NO
174 PAK4 PAK4 PAK4 15506 -0.1 -0.042 NO
175 ACTN3 ACTN3 ACTN3 15577 -0.1 -0.042 NO
176 RAC3 RAC3 RAC3 15682 -0.11 -0.044 NO
177 PARVB PARVB PARVB 15718 -0.11 -0.042 NO
178 ITGA3 ITGA3 ITGA3 15802 -0.12 -0.042 NO
179 ACTN1 ACTN1 ACTN1 15904 -0.12 -0.044 NO
180 VEGFB VEGFB VEGFB 16081 -0.13 -0.049 NO
181 PIK3CB PIK3CB PIK3CB 16294 -0.15 -0.055 NO
182 MET MET MET 16308 -0.15 -0.051 NO
183 MYL2 MYL2 MYL2 16418 -0.16 -0.051 NO
184 RAPGEF1 RAPGEF1 RAPGEF1 16460 -0.16 -0.048 NO
185 VTN VTN VTN 16558 -0.16 -0.047 NO
186 BCL2 BCL2 BCL2 17073 -0.22 -0.068 NO
187 MYLK3 MYLK3 MYLK3 17165 -0.23 -0.065 NO
188 PIK3R5 PIK3R5 PIK3R5 17276 -0.25 -0.062 NO
189 VAV1 VAV1 VAV1 17316 -0.25 -0.055 NO
190 LAMA1 LAMA1 LAMA1 17389 -0.26 -0.049 NO
191 PARVG PARVG PARVG 17412 -0.27 -0.041 NO
192 RAC2 RAC2 RAC2 17451 -0.27 -0.033 NO
193 PRKCB PRKCB PRKCB 17924 -0.41 -0.045 NO
194 ITGB7 ITGB7 ITGB7 17954 -0.43 -0.031 NO
195 PIK3CD PIK3CD PIK3CD 17990 -0.45 -0.016 NO
196 RASGRF1 RASGRF1 RASGRF1 18025 -0.54 0.0013 NO

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

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

genes ES table in pathway: KEGG HEDGEHOG SIGNALING 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 AADAT AADAT AADAT 61 0.54 0.14 YES
2 BBOX1 BBOX1 BBOX1 100 0.52 0.28 YES
3 PLOD2 PLOD2 PLOD2 1121 0.28 0.3 YES
4 SETD7 SETD7 SETD7 2066 0.21 0.3 YES
5 AASS AASS AASS 2687 0.18 0.31 YES
6 AASDHPPT AASDHPPT AASDHPPT 3608 0.14 0.3 NO
7 ALDH3A2 ALDH3A2 ALDH3A2 5983 0.081 0.19 NO
8 SETD2 SETD2 SETD2 6099 0.079 0.21 NO
9 ASH1L ASH1L ASH1L 6807 0.064 0.18 NO
10 NSD1 NSD1 NSD1 6866 0.063 0.2 NO
11 ALDH7A1 ALDH7A1 ALDH7A1 6947 0.062 0.21 NO
12 DOT1L DOT1L DOT1L 7060 0.06 0.22 NO
13 SETD8 SETD8 SETD8 7143 0.058 0.23 NO
14 SUV420H1 SUV420H1 SUV420H1 7907 0.044 0.2 NO
15 AASDH AASDH AASDH 7989 0.043 0.21 NO
16 TMLHE TMLHE TMLHE 8342 0.037 0.2 NO
17 EHMT1 EHMT1 EHMT1 9124 0.025 0.16 NO
18 SETMAR SETMAR SETMAR 9278 0.022 0.16 NO
19 SUV39H2 SUV39H2 SUV39H2 9307 0.022 0.16 NO
20 WHSC1L1 WHSC1L1 WHSC1L1 9426 0.02 0.16 NO
21 WHSC1 WHSC1 WHSC1 9577 0.018 0.16 NO
22 PLOD1 PLOD1 PLOD1 9703 0.016 0.15 NO
23 OGDHL OGDHL OGDHL 10390 0.0058 0.12 NO
24 PLOD3 PLOD3 PLOD3 10478 0.0044 0.11 NO
25 ACAT1 ACAT1 ACAT1 10859 -0.0012 0.093 NO
26 SETD1A SETD1A SETD1A 10975 -0.0029 0.087 NO
27 EHMT2 EHMT2 EHMT2 11175 -0.0058 0.078 NO
28 SUV420H2 SUV420H2 SUV420H2 11243 -0.0069 0.076 NO
29 SETDB1 SETDB1 SETDB1 11262 -0.0071 0.077 NO
30 SETD1B SETD1B SETD1B 11376 -0.009 0.073 NO
31 ACAT2 ACAT2 ACAT2 12095 -0.021 0.038 NO
32 DLST DLST DLST 13021 -0.037 -0.0033 NO
33 GCDH GCDH GCDH 13680 -0.05 -0.026 NO
34 OGDH OGDH OGDH 13938 -0.056 -0.026 NO
35 HADHA HADHA HADHA 14196 -0.061 -0.024 NO
36 ALDH9A1 ALDH9A1 ALDH9A1 14546 -0.07 -0.025 NO
37 HADH HADH HADH 14849 -0.079 -0.02 NO
38 ECHS1 ECHS1 ECHS1 15173 -0.089 -0.015 NO
39 ALDH1B1 ALDH1B1 ALDH1B1 15596 -0.11 -0.0099 NO
40 SETDB2 SETDB2 SETDB2 15926 -0.12 0.005 NO
41 SUV39H1 SUV39H1 SUV39H1 16087 -0.13 0.032 NO
42 PIPOX PIPOX PIPOX 16232 -0.14 0.062 NO
43 ALDH2 ALDH2 ALDH2 16311 -0.15 0.096 NO

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

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

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 = SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = SKCM-TM.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)