GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in SARC-TP
Sarcoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1FF3RNB
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 SARC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1FF3RNB
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 SARC-TP. This pipeline has the following features:

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

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

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

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

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

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

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 193
Number of samples: 258
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 ] 116
pheno.type: 2 - 3 :[ clus2 ] 78
pheno.type: 3 - 3 :[ clus3 ] 64

For the expression subtypes of 18184 genes in 259 samples, GSEA found enriched gene sets in each cluster using 258 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are BIOCARTA BCR PATHWAY, BIOCARTA FAS PATHWAY, BIOCARTA FCER1 PATHWAY, BIOCARTA FMLP PATHWAY, BIOCARTA HIVNEF PATHWAY, BIOCARTA IL2RB PATHWAY, BIOCARTA GSK3 PATHWAY, BIOCARTA DEATH PATHWAY, BIOCARTA NKT PATHWAY, BIOCARTA IL1R PATHWAY

    • And common core enriched genes are HEXA, LYN, PRKCB, SYK, VAV1, AMDHD2, CHIT1, GALK1, GFPT2, GNPNAT1

  • clus2

    • Top enriched gene sets are BIOCARTA AGR PATHWAY, BIOCARTA BIOPEPTIDES PATHWAY, BIOCARTA CARM ER PATHWAY, BIOCARTA INTEGRIN PATHWAY, BIOCARTA MYOSIN PATHWAY, BIOCARTA CHREBP2 PATHWAY, BIOCARTA RHO PATHWAY, BIOCARTA CREB PATHWAY, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG LYSINE DEGRADATION

    • And common core enriched genes are ACAT1, ACAT2, ALDH1B1, ALDH2, ALDH3A2, PPP1R12B, ROCK1, SRC, VCL, HADH

  • clus3

    • Top enriched gene sets are BIOCARTA ALK PATHWAY, BIOCARTA WNT PATHWAY, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG N GLYCAN BIOSYNTHESIS, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES, KEGG P53 SIGNALING PATHWAY, KEGG ENDOCYTOSIS, KEGG WNT SIGNALING PATHWAY, KEGG NOTCH SIGNALING PATHWAY

    • And common core enriched genes are FZD1, LEF1, BTRC, CCND1, WIF1, FZD2, FZD3, FZD8, WNT11, WNT4

Results
Subtype clus1 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA BCR PATHWAY 33 genes.ES.table 0.63 1.8 0.004 0.16 0.26 0.24 0.087 0.22 0 0.036
BIOCARTA FAS PATHWAY 29 genes.ES.table 0.53 1.8 0.018 0.083 0.3 0.66 0.31 0.45 0 0.009
BIOCARTA FCER1 PATHWAY 37 genes.ES.table 0.58 1.7 0.033 0.11 0.58 0.22 0.12 0.19 0.059 0.008
BIOCARTA FMLP PATHWAY 34 genes.ES.table 0.43 1.6 0.051 0.14 0.84 0.088 0.018 0.087 0.092 0.001
BIOCARTA HIVNEF PATHWAY 57 genes.ES.table 0.41 1.6 0.054 0.12 0.64 0.56 0.32 0.38 0.068 0.005
BIOCARTA IL2RB PATHWAY 37 genes.ES.table 0.63 1.8 0.014 0.075 0.36 0.32 0.1 0.29 0 0.006
BIOCARTA GSK3 PATHWAY 26 genes.ES.table 0.53 1.6 0.036 0.13 0.82 0.38 0.2 0.31 0.089 0.001
BIOCARTA DEATH PATHWAY 32 genes.ES.table 0.46 1.5 0.067 0.13 0.84 0.66 0.31 0.46 0.088 0
BIOCARTA NKT PATHWAY 25 genes.ES.table 0.81 1.6 0.004 0.12 0.68 0.8 0.13 0.7 0.072 0.005
BIOCARTA IL1R PATHWAY 31 genes.ES.table 0.54 1.6 0.057 0.14 0.84 0.48 0.25 0.36 0.092 0.001
genes ES table in pathway: BIOCARTA BCR PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HK3 HK3 HK3 12 0.85 0.12 YES
2 GFPT2 GFPT2 GFPT2 107 0.66 0.21 YES
3 NPL NPL NPL 148 0.62 0.3 YES
4 RENBP RENBP RENBP 318 0.54 0.37 YES
5 UAP1 UAP1 UAP1 1006 0.34 0.38 YES
6 UGDH UGDH UGDH 1235 0.3 0.41 YES
7 NANS NANS NANS 1524 0.26 0.43 YES
8 AMDHD2 AMDHD2 AMDHD2 1876 0.22 0.44 YES
9 PMM2 PMM2 PMM2 2081 0.2 0.46 YES
10 HK2 HK2 HK2 2087 0.2 0.49 YES
11 GALK1 GALK1 GALK1 2193 0.19 0.51 YES
12 HEXA HEXA HEXA 2399 0.18 0.53 YES
13 CHIT1 CHIT1 CHIT1 2454 0.17 0.55 YES
14 GNPNAT1 GNPNAT1 GNPNAT1 2550 0.17 0.57 YES
15 PGM3 PGM3 PGM3 2763 0.15 0.58 YES
16 NAGK NAGK NAGK 2801 0.15 0.6 YES
17 GMPPA GMPPA GMPPA 3412 0.12 0.58 NO
18 GALE GALE GALE 4087 0.096 0.56 NO
19 GMPPB GMPPB GMPPB 4089 0.096 0.57 NO
20 HEXB HEXB HEXB 4217 0.092 0.58 NO
21 UGP2 UGP2 UGP2 4937 0.07 0.55 NO
22 PMM1 PMM1 PMM1 5811 0.048 0.51 NO
23 GMDS GMDS GMDS 5872 0.047 0.51 NO
24 HK1 HK1 HK1 5961 0.045 0.51 NO
25 UXS1 UXS1 UXS1 6486 0.034 0.49 NO
26 GALK2 GALK2 GALK2 6561 0.032 0.49 NO
27 GNPDA1 GNPDA1 GNPDA1 6674 0.03 0.49 NO
28 NANP NANP NANP 7262 0.017 0.46 NO
29 PGM1 PGM1 PGM1 7788 0.006 0.43 NO
30 GFPT1 GFPT1 GFPT1 7950 0.0027 0.42 NO
31 TSTA3 TSTA3 TSTA3 8064 8e-05 0.41 NO
32 GPI GPI GPI 8168 -0.0019 0.41 NO
33 CYB5R1 CYB5R1 CYB5R1 9214 -0.024 0.36 NO
34 GNE GNE GNE 10089 -0.042 0.31 NO
35 MPI MPI MPI 10474 -0.05 0.3 NO
36 FPGT FPGT FPGT 11036 -0.062 0.28 NO
37 CMAS CMAS CMAS 11283 -0.068 0.27 NO
38 FUK FUK FUK 11337 -0.069 0.28 NO
39 GALT GALT GALT 11923 -0.083 0.26 NO
40 GNPDA2 GNPDA2 GNPDA2 11972 -0.084 0.27 NO
41 PGM2 PGM2 PGM2 12571 -0.1 0.25 NO
42 GCK GCK GCK 17108 -0.4 0.058 NO

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

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

genes ES table in pathway: BIOCARTA FAS PATHWAY

Table S2.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CD68 CD68 CD68 299 0.55 0.014 YES
2 CTSW CTSW CTSW 319 0.54 0.043 YES
3 LAPTM5 LAPTM5 LAPTM5 489 0.47 0.06 YES
4 CTSS CTSS CTSS 504 0.47 0.085 YES
5 CTSC CTSC CTSC 539 0.46 0.11 YES
6 ACP5 ACP5 ACP5 640 0.43 0.13 YES
7 PLA2G15 PLA2G15 PLA2G15 845 0.37 0.14 YES
8 SLC11A1 SLC11A1 SLC11A1 948 0.35 0.15 YES
9 FUCA1 FUCA1 FUCA1 953 0.35 0.17 YES
10 LGMN LGMN LGMN 969 0.34 0.19 YES
11 LAMP3 LAMP3 LAMP3 1108 0.32 0.2 YES
12 CTSZ CTSZ CTSZ 1285 0.29 0.2 YES
13 ATP6V0D2 ATP6V0D2 ATP6V0D2 1599 0.25 0.2 YES
14 NAGPA NAGPA NAGPA 1600 0.25 0.22 YES
15 CTSL1 CTSL1 CTSL1 1603 0.25 0.23 YES
16 NAPSA NAPSA NAPSA 1660 0.24 0.24 YES
17 LIPA LIPA LIPA 1684 0.24 0.25 YES
18 NPC2 NPC2 NPC2 1688 0.24 0.26 YES
19 GALC GALC GALC 1705 0.24 0.28 YES
20 CTSH CTSH CTSH 1759 0.23 0.29 YES
21 CTSB CTSB CTSB 1796 0.23 0.3 YES
22 MANBA MANBA MANBA 1971 0.21 0.3 YES
23 ACP2 ACP2 ACP2 2054 0.2 0.31 YES
24 CTSD CTSD CTSD 2127 0.2 0.31 YES
25 MAN2B1 MAN2B1 MAN2B1 2219 0.19 0.32 YES
26 GLA GLA GLA 2254 0.18 0.33 YES
27 IDUA IDUA IDUA 2320 0.18 0.33 YES
28 GALNS GALNS GALNS 2329 0.18 0.34 YES
29 ARSA ARSA ARSA 2332 0.18 0.35 YES
30 CTSA CTSA CTSA 2355 0.18 0.36 YES
31 HEXA HEXA HEXA 2399 0.18 0.37 YES
32 CTNS CTNS CTNS 2410 0.17 0.38 YES
33 NEU1 NEU1 NEU1 2513 0.17 0.38 YES
34 MCOLN1 MCOLN1 MCOLN1 2534 0.17 0.39 YES
35 AP1B1 AP1B1 AP1B1 2545 0.17 0.4 YES
36 PSAP PSAP PSAP 2683 0.16 0.4 YES
37 SLC17A5 SLC17A5 SLC17A5 2716 0.16 0.41 YES
38 TCIRG1 TCIRG1 TCIRG1 2723 0.16 0.42 YES
39 ATP6V0B ATP6V0B ATP6V0B 2740 0.15 0.42 YES
40 NAGLU NAGLU NAGLU 3002 0.14 0.42 YES
41 CTSG CTSG CTSG 3011 0.14 0.42 YES
42 GNPTAB GNPTAB GNPTAB 3041 0.14 0.43 YES
43 ATP6V0D1 ATP6V0D1 ATP6V0D1 3054 0.14 0.44 YES
44 TPP1 TPP1 TPP1 3145 0.13 0.44 YES
45 SMPD1 SMPD1 SMPD1 3256 0.13 0.44 YES
46 DNASE2B DNASE2B DNASE2B 3268 0.13 0.45 YES
47 HYAL1 HYAL1 HYAL1 3297 0.12 0.45 YES
48 GBA GBA GBA 3298 0.12 0.46 YES
49 ATP6V0C ATP6V0C ATP6V0C 3338 0.12 0.46 YES
50 CLTA CLTA CLTA 3339 0.12 0.47 YES
51 ATP6AP1 ATP6AP1 ATP6AP1 3361 0.12 0.48 YES
52 CD63 CD63 CD63 3377 0.12 0.48 YES
53 NAGA NAGA NAGA 3391 0.12 0.49 YES
54 GLB1 GLB1 GLB1 3535 0.11 0.49 YES
55 DNASE2 DNASE2 DNASE2 3575 0.11 0.49 YES
56 LAMP2 LAMP2 LAMP2 3602 0.11 0.5 YES
57 ASAH1 ASAH1 ASAH1 3626 0.11 0.5 YES
58 AP3S1 AP3S1 AP3S1 3662 0.11 0.5 YES
59 GNPTG GNPTG GNPTG 3713 0.11 0.51 YES
60 LAMP1 LAMP1 LAMP1 3747 0.11 0.51 YES
61 SGSH SGSH SGSH 3750 0.11 0.52 YES
62 GM2A GM2A GM2A 3848 0.1 0.52 YES
63 CLN3 CLN3 CLN3 4078 0.097 0.51 NO
64 HEXB HEXB HEXB 4217 0.092 0.51 NO
65 CTSO CTSO CTSO 4268 0.091 0.51 NO
66 SUMF1 SUMF1 SUMF1 4329 0.088 0.51 NO
67 GNS GNS GNS 4653 0.078 0.5 NO
68 M6PR M6PR M6PR 4851 0.073 0.49 NO
69 GAA GAA GAA 4862 0.072 0.5 NO
70 LAPTM4A LAPTM4A LAPTM4A 4923 0.071 0.5 NO
71 GUSB GUSB GUSB 4945 0.07 0.5 NO
72 AP1S1 AP1S1 AP1S1 4947 0.07 0.5 NO
73 AP1M1 AP1M1 AP1M1 5140 0.065 0.5 NO
74 AGA AGA AGA 5212 0.064 0.5 NO
75 GGA3 GGA3 GGA3 5537 0.056 0.48 NO
76 CLTB CLTB CLTB 5561 0.055 0.48 NO
77 ATP6V0A2 ATP6V0A2 ATP6V0A2 5606 0.054 0.48 NO
78 IGF2R IGF2R IGF2R 5641 0.053 0.48 NO
79 CD164 CD164 CD164 5901 0.046 0.47 NO
80 AP4B1 AP4B1 AP4B1 6072 0.043 0.46 NO
81 AP1S2 AP1S2 AP1S2 6371 0.036 0.45 NO
82 CLN5 CLN5 CLN5 6492 0.034 0.44 NO
83 CLTC CLTC CLTC 6613 0.031 0.44 NO
84 SCARB2 SCARB2 SCARB2 6785 0.028 0.43 NO
85 PPT1 PPT1 PPT1 6802 0.028 0.43 NO
86 AP3B1 AP3B1 AP3B1 7080 0.021 0.42 NO
87 GGA2 GGA2 GGA2 7136 0.02 0.42 NO
88 GGA1 GGA1 GGA1 7491 0.012 0.4 NO
89 NPC1 NPC1 NPC1 7625 0.0095 0.39 NO
90 IDS IDS IDS 7747 0.0068 0.38 NO
91 AP1G1 AP1G1 AP1G1 7952 0.0027 0.37 NO
92 AP4E1 AP4E1 AP4E1 8506 -0.0087 0.34 NO
93 AP3M1 AP3M1 AP3M1 8562 -0.01 0.34 NO
94 CLTCL1 CLTCL1 CLTCL1 8737 -0.014 0.33 NO
95 AP3D1 AP3D1 AP3D1 8741 -0.014 0.33 NO
96 ATP6V0A1 ATP6V0A1 ATP6V0A1 9225 -0.024 0.31 NO
97 AP1S3 AP1S3 AP1S3 9233 -0.025 0.31 NO
98 AP3S2 AP3S2 AP3S2 9286 -0.026 0.31 NO
99 AP4M1 AP4M1 AP4M1 9793 -0.036 0.28 NO
100 PPT2 PPT2 PPT2 9955 -0.04 0.27 NO
101 SLC11A2 SLC11A2 SLC11A2 10386 -0.048 0.25 NO
102 CTSK CTSK CTSK 10588 -0.052 0.24 NO
103 MFSD8 MFSD8 MFSD8 10710 -0.055 0.24 NO
104 ENTPD4 ENTPD4 ENTPD4 10725 -0.055 0.24 NO
105 AP4S1 AP4S1 AP4S1 11022 -0.062 0.23 NO
106 CTSE CTSE CTSE 11157 -0.064 0.23 NO
107 LAPTM4B LAPTM4B LAPTM4B 11289 -0.068 0.22 NO
108 ATP6V1H ATP6V1H ATP6V1H 11494 -0.073 0.22 NO
109 AP3M2 AP3M2 AP3M2 11527 -0.073 0.22 NO
110 ARSG ARSG ARSG 11997 -0.085 0.2 NO
111 ARSB ARSB ARSB 12562 -0.1 0.17 NO
112 CTSF CTSF CTSF 13319 -0.13 0.14 NO
113 ABCA2 ABCA2 ABCA2 14054 -0.16 0.1 NO
114 AP1M2 AP1M2 AP1M2 15058 -0.21 0.06 NO
115 ABCB9 ABCB9 ABCB9 15489 -0.23 0.05 NO
116 ATP6V0A4 ATP6V0A4 ATP6V0A4 15831 -0.26 0.045 NO
117 SORT1 SORT1 SORT1 16408 -0.31 0.03 NO
118 AP3B2 AP3B2 AP3B2 17619 -0.51 -0.0084 NO
119 CTSL2 CTSL2 CTSL2 18028 -0.69 0.0076 NO

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

Figure S4.  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 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 NCF1 NCF1 NCF1 31 0.77 0.039 YES
2 VAV1 VAV1 VAV1 42 0.75 0.078 YES
3 FCGR1A FCGR1A FCGR1A 56 0.73 0.12 YES
4 HCK HCK HCK 88 0.68 0.15 YES
5 WAS WAS WAS 104 0.66 0.18 YES
6 PIK3R5 PIK3R5 PIK3R5 244 0.57 0.2 YES
7 FCGR2B FCGR2B FCGR2B 256 0.57 0.23 YES
8 FCGR2C FCGR2C FCGR2C 273 0.56 0.26 YES
9 SYK SYK SYK 326 0.53 0.29 YES
10 DOCK2 DOCK2 DOCK2 334 0.53 0.32 YES
11 FCGR3A FCGR3A FCGR3A 338 0.53 0.34 YES
12 RAC2 RAC2 RAC2 376 0.51 0.37 YES
13 PIK3CG PIK3CG PIK3CG 417 0.5 0.39 YES
14 PTPRC PTPRC PTPRC 501 0.47 0.41 YES
15 FCGR2A FCGR2A FCGR2A 516 0.47 0.44 YES
16 INPP5D INPP5D INPP5D 655 0.42 0.45 YES
17 PIK3CD PIK3CD PIK3CD 659 0.42 0.47 YES
18 ASAP3 ASAP3 ASAP3 746 0.4 0.49 YES
19 LYN LYN LYN 907 0.36 0.5 YES
20 DNM1 DNM1 DNM1 952 0.35 0.51 YES
21 LIMK1 LIMK1 LIMK1 1342 0.28 0.51 YES
22 ARPC1B ARPC1B ARPC1B 1366 0.28 0.52 YES
23 SCIN SCIN SCIN 1390 0.28 0.53 YES
24 SPHK1 SPHK1 SPHK1 1452 0.27 0.55 YES
25 PLCG2 PLCG2 PLCG2 1530 0.26 0.55 YES
26 PRKCB PRKCB PRKCB 1582 0.25 0.56 YES
27 LAT LAT LAT 1626 0.25 0.57 YES
28 MARCKS MARCKS MARCKS 1686 0.24 0.58 YES
29 PLA2G4A PLA2G4A PLA2G4A 2168 0.19 0.57 NO
30 ARPC3 ARPC3 ARPC3 2700 0.16 0.55 NO
31 PPAP2B PPAP2B PPAP2B 3285 0.12 0.52 NO
32 ARPC5L ARPC5L ARPC5L 3566 0.11 0.51 NO
33 CDC42 CDC42 CDC42 3833 0.1 0.5 NO
34 ARF6 ARF6 ARF6 3841 0.1 0.51 NO
35 ARPC4 ARPC4 ARPC4 4169 0.094 0.49 NO
36 CFL1 CFL1 CFL1 4263 0.091 0.49 NO
37 MAPK3 MAPK3 MAPK3 4459 0.084 0.49 NO
38 ARPC2 ARPC2 ARPC2 4754 0.075 0.48 NO
39 RAC1 RAC1 RAC1 5179 0.065 0.46 NO
40 DNM2 DNM2 DNM2 5458 0.057 0.44 NO
41 PLD2 PLD2 PLD2 5460 0.057 0.45 NO
42 ARPC5 ARPC5 ARPC5 5628 0.053 0.44 NO
43 SPHK2 SPHK2 SPHK2 5648 0.053 0.44 NO
44 PAK1 PAK1 PAK1 5692 0.051 0.44 NO
45 PRKCD PRKCD PRKCD 5860 0.047 0.43 NO
46 MAP2K1 MAP2K1 MAP2K1 6110 0.042 0.42 NO
47 VAV3 VAV3 VAV3 6196 0.04 0.42 NO
48 PRKCA PRKCA PRKCA 6584 0.032 0.4 NO
49 ARPC1A ARPC1A ARPC1A 6868 0.026 0.39 NO
50 CRK CRK CRK 7079 0.021 0.38 NO
51 PIK3R2 PIK3R2 PIK3R2 7145 0.02 0.37 NO
52 PLD1 PLD1 PLD1 7197 0.019 0.37 NO
53 ASAP2 ASAP2 ASAP2 7249 0.017 0.37 NO
54 WASF3 WASF3 WASF3 7516 0.012 0.36 NO
55 ASAP1 ASAP1 ASAP1 7701 0.008 0.34 NO
56 CRKL CRKL CRKL 8106 -0.00068 0.32 NO
57 WASL WASL WASL 8444 -0.0072 0.3 NO
58 AKT2 AKT2 AKT2 8698 -0.013 0.29 NO
59 PRKCE PRKCE PRKCE 8749 -0.014 0.29 NO
60 AKT1 AKT1 AKT1 8752 -0.014 0.29 NO
61 MAPK1 MAPK1 MAPK1 8903 -0.017 0.28 NO
62 WASF2 WASF2 WASF2 8963 -0.018 0.28 NO
63 RPS6KB1 RPS6KB1 RPS6KB1 9111 -0.022 0.27 NO
64 PIP5K1C PIP5K1C PIP5K1C 9327 -0.027 0.26 NO
65 RAF1 RAF1 RAF1 9549 -0.031 0.25 NO
66 VASP VASP VASP 9676 -0.034 0.25 NO
67 GSN GSN GSN 9866 -0.037 0.24 NO
68 VAV2 VAV2 VAV2 9973 -0.04 0.24 NO
69 PIK3CB PIK3CB PIK3CB 10508 -0.051 0.21 NO
70 PIK3CA PIK3CA PIK3CA 10819 -0.057 0.19 NO
71 LIMK2 LIMK2 LIMK2 11273 -0.067 0.17 NO
72 GAB2 GAB2 GAB2 11292 -0.068 0.18 NO
73 MYO10 MYO10 MYO10 11690 -0.077 0.16 NO
74 PPAP2A PPAP2A PPAP2A 11903 -0.082 0.15 NO
75 PLCG1 PLCG1 PLCG1 12187 -0.091 0.14 NO
76 PIP4K2B PIP4K2B PIP4K2B 12303 -0.094 0.14 NO
77 DNM1L DNM1L DNM1L 12749 -0.11 0.12 NO
78 PIP5K1A PIP5K1A PIP5K1A 12997 -0.12 0.11 NO
79 MARCKSL1 MARCKSL1 MARCKSL1 13066 -0.12 0.11 NO
80 PIKFYVE PIKFYVE PIKFYVE 13159 -0.12 0.12 NO
81 PIK3R1 PIK3R1 PIK3R1 13698 -0.14 0.092 NO
82 PIK3R3 PIK3R3 PIK3R3 14093 -0.16 0.079 NO
83 PLA2G6 PLA2G6 PLA2G6 14338 -0.17 0.074 NO
84 AMPH AMPH AMPH 14391 -0.17 0.08 NO
85 WASF1 WASF1 WASF1 14774 -0.19 0.069 NO
86 PLA2G4F PLA2G4F PLA2G4F 15095 -0.21 0.062 NO
87 PLA2G4D PLA2G4D PLA2G4D 15364 -0.22 0.059 NO
88 CFL2 CFL2 CFL2 15421 -0.23 0.068 NO
89 PRKCG PRKCG PRKCG 16098 -0.28 0.046 NO
90 AKT3 AKT3 AKT3 16327 -0.3 0.049 NO
91 PPAP2C PPAP2C PPAP2C 16331 -0.3 0.064 NO
92 DNM3 DNM3 DNM3 16337 -0.3 0.08 NO
93 PIP5K1B PIP5K1B PIP5K1B 17161 -0.4 0.056 NO

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

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

genes ES table in pathway: BIOCARTA FMLP PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 VAV1 VAV1 VAV1 42 0.75 0.16 YES
2 BTK BTK BTK 152 0.62 0.28 YES
3 SYK SYK SYK 326 0.53 0.39 YES
4 LYN LYN LYN 907 0.36 0.43 YES
5 CD79A CD79A CD79A 1078 0.32 0.49 YES
6 CD79B CD79B CD79B 1382 0.28 0.54 YES
7 PRKCB PRKCB PRKCB 1582 0.25 0.58 YES
8 BLNK BLNK BLNK 1587 0.25 0.63 YES
9 MAP3K1 MAP3K1 MAP3K1 2838 0.15 0.6 NO
10 GRB2 GRB2 GRB2 4278 0.09 0.54 NO
11 PPP3CC PPP3CC PPP3CC 4386 0.086 0.55 NO
12 MAPK3 MAPK3 MAPK3 4459 0.084 0.56 NO
13 RAC1 RAC1 RAC1 5179 0.065 0.54 NO
14 MAP2K1 MAP2K1 MAP2K1 6110 0.042 0.49 NO
15 NFATC1 NFATC1 NFATC1 6467 0.034 0.48 NO
16 PRKCA PRKCA PRKCA 6584 0.032 0.48 NO
17 CALM3 CALM3 CALM3 7060 0.022 0.46 NO
18 CALM2 CALM2 CALM2 7144 0.02 0.46 NO
19 MAPK14 MAPK14 MAPK14 7421 0.014 0.45 NO
20 NFATC3 NFATC3 NFATC3 7528 0.012 0.44 NO
21 PPP3CA PPP3CA PPP3CA 8190 -0.0024 0.41 NO
22 NFATC2 NFATC2 NFATC2 8283 -0.0042 0.4 NO
23 FOS FOS FOS 8297 -0.0043 0.4 NO
24 ELK1 ELK1 ELK1 8364 -0.006 0.4 NO
25 JUN JUN JUN 8616 -0.012 0.39 NO
26 PPP3CB PPP3CB PPP3CB 8715 -0.014 0.39 NO
27 RAF1 RAF1 RAF1 9549 -0.031 0.35 NO
28 CALM1 CALM1 CALM1 9995 -0.04 0.33 NO
29 SHC1 SHC1 SHC1 11470 -0.072 0.27 NO
30 MAPK8 MAPK8 MAPK8 11620 -0.075 0.28 NO
31 PLCG1 PLCG1 PLCG1 12187 -0.091 0.26 NO
32 SOS1 SOS1 SOS1 12396 -0.097 0.27 NO
33 NFATC4 NFATC4 NFATC4 15180 -0.21 0.16 NO

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

Figure S8.  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 HIVNEF PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IL18 IL18 IL18 58 0.73 0.079 YES
2 AIM2 AIM2 AIM2 72 0.7 0.16 YES
3 CCL4 CCL4 CCL4 86 0.68 0.23 YES
4 RIPK3 RIPK3 RIPK3 153 0.62 0.3 YES
5 CCL4L2 CCL4L2 CCL4L2 254 0.57 0.36 YES
6 CCL5 CCL5 CCL5 337 0.53 0.41 YES
7 POLR3G POLR3G POLR3G 421 0.5 0.46 YES
8 CXCL10 CXCL10 CXCL10 426 0.5 0.52 YES
9 ZBP1 ZBP1 ZBP1 618 0.44 0.56 YES
10 CASP1 CASP1 CASP1 723 0.41 0.6 YES
11 IL6 IL6 IL6 757 0.4 0.64 YES
12 PYCARD PYCARD PYCARD 1091 0.32 0.66 YES
13 IL1B IL1B IL1B 1216 0.3 0.68 YES
14 IKBKE IKBKE IKBKE 1491 0.26 0.7 YES
15 IRF7 IRF7 IRF7 1707 0.24 0.71 YES
16 NFKBIB NFKBIB NFKBIB 2971 0.14 0.66 NO
17 TREX1 TREX1 TREX1 3058 0.14 0.67 NO
18 IKBKG IKBKG IKBKG 3123 0.13 0.68 NO
19 NFKBIA NFKBIA NFKBIA 3444 0.12 0.68 NO
20 POLR1C POLR1C POLR1C 3458 0.12 0.69 NO
21 IRF3 IRF3 IRF3 4158 0.094 0.66 NO
22 POLR3K POLR3K POLR3K 4404 0.086 0.66 NO
23 POLR3H POLR3H POLR3H 4504 0.083 0.66 NO
24 NFKB1 NFKB1 NFKB1 4559 0.081 0.66 NO
25 IFNB1 IFNB1 IFNB1 4586 0.08 0.67 NO
26 TMEM173 TMEM173 TMEM173 4784 0.075 0.67 NO
27 POLR3D POLR3D POLR3D 4863 0.072 0.67 NO
28 POLR3B POLR3B POLR3B 5060 0.067 0.67 NO
29 POLR3GL POLR3GL POLR3GL 5597 0.054 0.65 NO
30 POLR3C POLR3C POLR3C 5707 0.051 0.65 NO
31 RIPK1 RIPK1 RIPK1 6377 0.036 0.61 NO
32 CHUK CHUK CHUK 6570 0.032 0.61 NO
33 RELA RELA RELA 7670 0.0085 0.55 NO
34 TBK1 TBK1 TBK1 7869 0.0044 0.54 NO
35 POLR3A POLR3A POLR3A 8172 -0.002 0.52 NO
36 DDX58 DDX58 DDX58 8521 -0.009 0.5 NO
37 POLR1D POLR1D POLR1D 8925 -0.018 0.48 NO
38 ADAR ADAR ADAR 8981 -0.019 0.48 NO
39 MAVS MAVS MAVS 9560 -0.031 0.45 NO
40 IKBKB IKBKB IKBKB 9776 -0.036 0.44 NO
41 IL33 IL33 IL33 11798 -0.08 0.34 NO
42 POLR3F POLR3F POLR3F 11885 -0.082 0.35 NO

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

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

genes ES table in pathway: BIOCARTA IL2RB PATHWAY

Table 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 VAV1 VAV1 VAV1 42 0.75 0.047 YES
2 LILRB3 LILRB3 LILRB3 73 0.7 0.092 YES
3 BTK BTK BTK 152 0.62 0.13 YES
4 PIK3AP1 PIK3AP1 PIK3AP1 170 0.61 0.17 YES
5 PTPN6 PTPN6 PTPN6 238 0.57 0.2 YES
6 PIK3R5 PIK3R5 PIK3R5 244 0.57 0.24 YES
7 FCGR2B FCGR2B FCGR2B 256 0.57 0.28 YES
8 CD72 CD72 CD72 276 0.56 0.31 YES
9 SYK SYK SYK 326 0.53 0.35 YES
10 RAC2 RAC2 RAC2 376 0.51 0.38 YES
11 DAPP1 DAPP1 DAPP1 416 0.5 0.41 YES
12 PIK3CG PIK3CG PIK3CG 417 0.5 0.44 YES
13 INPP5D INPP5D INPP5D 655 0.42 0.46 YES
14 PIK3CD PIK3CD PIK3CD 659 0.42 0.48 YES
15 CARD11 CARD11 CARD11 667 0.42 0.51 YES
16 CD19 CD19 CD19 742 0.4 0.54 YES
17 LYN LYN LYN 907 0.36 0.55 YES
18 NFKBIE NFKBIE NFKBIE 981 0.34 0.57 YES
19 CD79A CD79A CD79A 1078 0.32 0.58 YES
20 CR2 CR2 CR2 1122 0.32 0.6 YES
21 CD79B CD79B CD79B 1382 0.28 0.61 YES
22 PLCG2 PLCG2 PLCG2 1530 0.26 0.62 YES
23 PRKCB PRKCB PRKCB 1582 0.25 0.63 YES
24 BLNK BLNK BLNK 1587 0.25 0.65 YES
25 IFITM1 IFITM1 IFITM1 1772 0.23 0.65 YES
26 RASGRP3 RASGRP3 RASGRP3 1861 0.22 0.66 YES
27 BCL10 BCL10 BCL10 2509 0.17 0.64 NO
28 NFKBIB NFKBIB NFKBIB 2971 0.14 0.62 NO
29 IKBKG IKBKG IKBKG 3123 0.13 0.62 NO
30 NRAS NRAS NRAS 3294 0.12 0.62 NO
31 NFKBIA NFKBIA NFKBIA 3444 0.12 0.62 NO
32 CHP CHP CHP 3832 0.1 0.6 NO
33 MAP2K2 MAP2K2 MAP2K2 3855 0.1 0.61 NO
34 GRB2 GRB2 GRB2 4278 0.09 0.59 NO
35 CD22 CD22 CD22 4347 0.088 0.6 NO
36 PPP3CC PPP3CC PPP3CC 4386 0.086 0.6 NO
37 MAPK3 MAPK3 MAPK3 4459 0.084 0.6 NO
38 NFKB1 NFKB1 NFKB1 4559 0.081 0.6 NO
39 RAC1 RAC1 RAC1 5179 0.065 0.57 NO
40 MAP2K1 MAP2K1 MAP2K1 6110 0.042 0.52 NO
41 VAV3 VAV3 VAV3 6196 0.04 0.52 NO
42 CD81 CD81 CD81 6296 0.038 0.52 NO
43 NFATC1 NFATC1 NFATC1 6467 0.034 0.51 NO
44 CHUK CHUK CHUK 6570 0.032 0.51 NO
45 PIK3R2 PIK3R2 PIK3R2 7145 0.02 0.48 NO
46 KRAS KRAS KRAS 7424 0.014 0.46 NO
47 NFATC3 NFATC3 NFATC3 7528 0.012 0.46 NO
48 RELA RELA RELA 7670 0.0085 0.45 NO
49 PPP3CA PPP3CA PPP3CA 8190 -0.0024 0.42 NO
50 NFATC2 NFATC2 NFATC2 8283 -0.0042 0.42 NO
51 FOS FOS FOS 8297 -0.0043 0.42 NO
52 MALT1 MALT1 MALT1 8522 -0.009 0.4 NO
53 JUN JUN JUN 8616 -0.012 0.4 NO
54 AKT2 AKT2 AKT2 8698 -0.013 0.4 NO
55 PPP3CB PPP3CB PPP3CB 8715 -0.014 0.4 NO
56 AKT1 AKT1 AKT1 8752 -0.014 0.4 NO
57 MAPK1 MAPK1 MAPK1 8903 -0.017 0.39 NO
58 RAF1 RAF1 RAF1 9549 -0.031 0.35 NO
59 PPP3R1 PPP3R1 PPP3R1 9603 -0.032 0.35 NO
60 PPP3R2 PPP3R2 PPP3R2 9648 -0.033 0.35 NO
61 IKBKB IKBKB IKBKB 9776 -0.036 0.35 NO
62 VAV2 VAV2 VAV2 9973 -0.04 0.34 NO
63 PIK3CB PIK3CB PIK3CB 10508 -0.051 0.31 NO
64 PIK3CA PIK3CA PIK3CA 10819 -0.057 0.3 NO
65 GSK3B GSK3B GSK3B 11665 -0.076 0.26 NO
66 NFAT5 NFAT5 NFAT5 12285 -0.094 0.23 NO
67 SOS1 SOS1 SOS1 12396 -0.097 0.23 NO
68 SOS2 SOS2 SOS2 12538 -0.1 0.23 NO
69 PIK3R1 PIK3R1 PIK3R1 13698 -0.14 0.18 NO
70 PIK3R3 PIK3R3 PIK3R3 14093 -0.16 0.16 NO
71 RAC3 RAC3 RAC3 14430 -0.17 0.16 NO
72 NFATC4 NFATC4 NFATC4 15180 -0.21 0.13 NO
73 CHP2 CHP2 CHP2 15394 -0.23 0.13 NO
74 AKT3 AKT3 AKT3 16327 -0.3 0.1 NO

Figure S11.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL2RB PATHWAY.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL2RB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA GSK3 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 VAV1 VAV1 VAV1 42 0.75 0.022 YES
2 FCER1G FCER1G FCER1G 102 0.66 0.041 YES
3 HCST HCST HCST 108 0.65 0.062 YES
4 PRF1 PRF1 PRF1 128 0.64 0.082 YES
5 SH2D1A SH2D1A SH2D1A 208 0.59 0.098 YES
6 PTPN6 PTPN6 PTPN6 238 0.57 0.12 YES
7 PIK3R5 PIK3R5 PIK3R5 244 0.57 0.13 YES
8 KLRC1 KLRC1 KLRC1 245 0.57 0.15 YES
9 TYROBP TYROBP TYROBP 247 0.57 0.17 YES
10 KLRD1 KLRD1 KLRD1 302 0.54 0.19 YES
11 SYK SYK SYK 326 0.53 0.2 YES
12 FCGR3A FCGR3A FCGR3A 338 0.53 0.22 YES
13 ITGB2 ITGB2 ITGB2 339 0.53 0.24 YES
14 NCR3 NCR3 NCR3 361 0.52 0.25 YES
15 LCP2 LCP2 LCP2 363 0.52 0.27 YES
16 LCK LCK LCK 371 0.52 0.29 YES
17 GZMB GZMB GZMB 372 0.52 0.3 YES
18 KIR2DL4 KIR2DL4 KIR2DL4 373 0.52 0.32 YES
19 RAC2 RAC2 RAC2 376 0.51 0.34 YES
20 ITGAL ITGAL ITGAL 403 0.5 0.35 YES
21 CD247 CD247 CD247 404 0.5 0.37 YES
22 PIK3CG PIK3CG PIK3CG 417 0.5 0.39 YES
23 ULBP2 ULBP2 ULBP2 433 0.49 0.4 YES
24 FASLG FASLG FASLG 444 0.49 0.42 YES
25 KLRK1 KLRK1 KLRK1 479 0.48 0.43 YES
26 CD48 CD48 CD48 542 0.46 0.44 YES
27 TNFRSF10C TNFRSF10C TNFRSF10C 544 0.46 0.46 YES
28 TNFSF10 TNFSF10 TNFSF10 624 0.43 0.47 YES
29 SH2D1B SH2D1B SH2D1B 626 0.43 0.48 YES
30 PIK3CD PIK3CD PIK3CD 659 0.42 0.49 YES
31 KLRC2 KLRC2 KLRC2 675 0.42 0.51 YES
32 KLRC3 KLRC3 KLRC3 704 0.41 0.52 YES
33 ICAM1 ICAM1 ICAM1 714 0.41 0.53 YES
34 ZAP70 ZAP70 ZAP70 719 0.41 0.55 YES
35 IFNG IFNG IFNG 842 0.37 0.55 YES
36 KIR3DL2 KIR3DL2 KIR3DL2 844 0.37 0.56 YES
37 RAET1G RAET1G RAET1G 918 0.35 0.57 YES
38 NCR1 NCR1 NCR1 943 0.35 0.58 YES
39 KIR2DL3 KIR2DL3 KIR2DL3 1004 0.34 0.59 YES
40 CSF2 CSF2 CSF2 1042 0.33 0.6 YES
41 ULBP1 ULBP1 ULBP1 1061 0.32 0.61 YES
42 CD244 CD244 CD244 1100 0.32 0.62 YES
43 KIR2DS4 KIR2DS4 KIR2DS4 1106 0.32 0.63 YES
44 FCGR3B FCGR3B FCGR3B 1202 0.3 0.63 YES
45 FYN FYN FYN 1282 0.29 0.64 YES
46 BID BID BID 1325 0.28 0.64 YES
47 ICAM2 ICAM2 ICAM2 1338 0.28 0.65 YES
48 TNF TNF TNF 1356 0.28 0.66 YES
49 HLA-G HLA-G HLA-G 1420 0.27 0.67 YES
50 KIR2DL1 KIR2DL1 KIR2DL1 1436 0.27 0.67 YES
51 PLCG2 PLCG2 PLCG2 1530 0.26 0.68 YES
52 KIR3DL1 KIR3DL1 KIR3DL1 1539 0.26 0.68 YES
53 PRKCB PRKCB PRKCB 1582 0.25 0.69 YES
54 RAET1E RAET1E RAET1E 1621 0.25 0.7 YES
55 LAT LAT LAT 1626 0.25 0.7 YES
56 TNFRSF10A TNFRSF10A TNFRSF10A 1719 0.24 0.71 YES
57 HLA-B HLA-B HLA-B 1805 0.23 0.71 YES
58 HLA-E HLA-E HLA-E 1977 0.21 0.71 YES
59 IFNGR1 IFNGR1 IFNGR1 2221 0.19 0.7 YES
60 IFNGR2 IFNGR2 IFNGR2 2250 0.18 0.71 YES
61 HLA-C HLA-C HLA-C 2274 0.18 0.71 YES
62 ULBP3 ULBP3 ULBP3 2339 0.18 0.71 YES
63 HLA-A HLA-A HLA-A 2428 0.17 0.71 YES
64 NRAS NRAS NRAS 3294 0.12 0.67 NO
65 CHP CHP CHP 3832 0.1 0.64 NO
66 MAP2K2 MAP2K2 MAP2K2 3855 0.1 0.65 NO
67 IFNAR2 IFNAR2 IFNAR2 3965 0.1 0.64 NO
68 MICA MICA MICA 4070 0.097 0.64 NO
69 IFNAR1 IFNAR1 IFNAR1 4219 0.092 0.64 NO
70 GRB2 GRB2 GRB2 4278 0.09 0.64 NO
71 PPP3CC PPP3CC PPP3CC 4386 0.086 0.63 NO
72 MAPK3 MAPK3 MAPK3 4459 0.084 0.63 NO
73 SHC3 SHC3 SHC3 4489 0.083 0.63 NO
74 IFNB1 IFNB1 IFNB1 4586 0.08 0.63 NO
75 TNFRSF10B TNFRSF10B TNFRSF10B 4686 0.077 0.63 NO
76 CASP3 CASP3 CASP3 4794 0.074 0.62 NO
77 ARAF ARAF ARAF 4797 0.074 0.62 NO
78 FAS FAS FAS 4995 0.069 0.62 NO
79 RAC1 RAC1 RAC1 5179 0.065 0.61 NO
80 SH3BP2 SH3BP2 SH3BP2 5411 0.058 0.6 NO
81 HRAS HRAS HRAS 5457 0.057 0.6 NO
82 PAK1 PAK1 PAK1 5692 0.051 0.59 NO
83 PTK2B PTK2B PTK2B 5705 0.051 0.59 NO
84 MAP2K1 MAP2K1 MAP2K1 6110 0.042 0.57 NO
85 TNFRSF10D TNFRSF10D TNFRSF10D 6129 0.042 0.57 NO
86 VAV3 VAV3 VAV3 6196 0.04 0.56 NO
87 NFATC1 NFATC1 NFATC1 6467 0.034 0.55 NO
88 PRKCA PRKCA PRKCA 6584 0.032 0.55 NO
89 PIK3R2 PIK3R2 PIK3R2 7145 0.02 0.52 NO
90 KRAS KRAS KRAS 7424 0.014 0.5 NO
91 NFATC3 NFATC3 NFATC3 7528 0.012 0.49 NO
92 PPP3CA PPP3CA PPP3CA 8190 -0.0024 0.46 NO
93 NFATC2 NFATC2 NFATC2 8283 -0.0042 0.45 NO
94 PPP3CB PPP3CB PPP3CB 8715 -0.014 0.43 NO
95 MAPK1 MAPK1 MAPK1 8903 -0.017 0.42 NO
96 RAET1L RAET1L RAET1L 9186 -0.024 0.4 NO
97 RAF1 RAF1 RAF1 9549 -0.031 0.39 NO
98 PPP3R1 PPP3R1 PPP3R1 9603 -0.032 0.38 NO
99 PPP3R2 PPP3R2 PPP3R2 9648 -0.033 0.38 NO
100 VAV2 VAV2 VAV2 9973 -0.04 0.37 NO
101 PIK3CB PIK3CB PIK3CB 10508 -0.051 0.34 NO
102 PIK3CA PIK3CA PIK3CA 10819 -0.057 0.32 NO
103 PTPN11 PTPN11 PTPN11 11128 -0.064 0.31 NO
104 BRAF BRAF BRAF 11330 -0.068 0.3 NO
105 SHC1 SHC1 SHC1 11470 -0.072 0.29 NO
106 PLCG1 PLCG1 PLCG1 12187 -0.091 0.26 NO
107 NFAT5 NFAT5 NFAT5 12285 -0.094 0.26 NO
108 SOS1 SOS1 SOS1 12396 -0.097 0.25 NO
109 SOS2 SOS2 SOS2 12538 -0.1 0.25 NO
110 PIK3R1 PIK3R1 PIK3R1 13698 -0.14 0.19 NO
111 PIK3R3 PIK3R3 PIK3R3 14093 -0.16 0.17 NO
112 RAC3 RAC3 RAC3 14430 -0.17 0.16 NO
113 NFATC4 NFATC4 NFATC4 15180 -0.21 0.12 NO
114 CHP2 CHP2 CHP2 15394 -0.23 0.12 NO
115 PRKCG PRKCG PRKCG 16098 -0.28 0.09 NO
116 SHC2 SHC2 SHC2 16837 -0.35 0.061 NO
117 SHC4 SHC4 SHC4 17074 -0.39 0.06 NO

Figure S13.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA GSK3 PATHWAY.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA GSK3 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA DEATH PATHWAY

Table 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 VAV1 VAV1 VAV1 42 0.75 0.1 YES
2 PTPN7 PTPN7 PTPN7 214 0.58 0.17 YES
3 LCK LCK LCK 371 0.52 0.24 YES
4 CD3D CD3D CD3D 380 0.51 0.31 YES
5 CD247 CD247 CD247 404 0.5 0.38 YES
6 PIK3CG PIK3CG PIK3CG 417 0.5 0.44 YES
7 CD3E CD3E CD3E 512 0.47 0.5 YES
8 ZAP70 ZAP70 ZAP70 719 0.41 0.55 YES
9 CD3G CD3G CD3G 744 0.4 0.6 YES
10 FYN FYN FYN 1282 0.29 0.61 YES
11 PRKCB PRKCB PRKCB 1582 0.25 0.63 YES
12 LAT LAT LAT 1626 0.25 0.66 YES
13 MAP3K1 MAP3K1 MAP3K1 2838 0.15 0.62 NO
14 NFKBIA NFKBIA NFKBIA 3444 0.12 0.6 NO
15 GRB2 GRB2 GRB2 4278 0.09 0.57 NO
16 PPP3CC PPP3CC PPP3CC 4386 0.086 0.57 NO
17 MAPK3 MAPK3 MAPK3 4459 0.084 0.58 NO
18 NFKB1 NFKB1 NFKB1 4559 0.081 0.59 NO
19 RAC1 RAC1 RAC1 5179 0.065 0.56 NO
20 MAP2K1 MAP2K1 MAP2K1 6110 0.042 0.52 NO
21 NFATC1 NFATC1 NFATC1 6467 0.034 0.5 NO
22 PRKCA PRKCA PRKCA 6584 0.032 0.5 NO
23 CALM3 CALM3 CALM3 7060 0.022 0.48 NO
24 CALM2 CALM2 CALM2 7144 0.02 0.47 NO
25 RASA1 RASA1 RASA1 7240 0.018 0.47 NO
26 NFATC3 NFATC3 NFATC3 7528 0.012 0.46 NO
27 RELA RELA RELA 7670 0.0085 0.45 NO
28 PPP3CA PPP3CA PPP3CA 8190 -0.0024 0.42 NO
29 NFATC2 NFATC2 NFATC2 8283 -0.0042 0.42 NO
30 FOS FOS FOS 8297 -0.0043 0.42 NO
31 ELK1 ELK1 ELK1 8364 -0.006 0.42 NO
32 JUN JUN JUN 8616 -0.012 0.4 NO
33 PPP3CB PPP3CB PPP3CB 8715 -0.014 0.4 NO
34 RAF1 RAF1 RAF1 9549 -0.031 0.36 NO
35 CALM1 CALM1 CALM1 9995 -0.04 0.34 NO
36 PIK3CA PIK3CA PIK3CA 10819 -0.057 0.3 NO
37 MAP2K4 MAP2K4 MAP2K4 10976 -0.061 0.3 NO
38 SHC1 SHC1 SHC1 11470 -0.072 0.28 NO
39 MAPK8 MAPK8 MAPK8 11620 -0.075 0.29 NO
40 PLCG1 PLCG1 PLCG1 12187 -0.091 0.27 NO
41 SOS1 SOS1 SOS1 12396 -0.097 0.27 NO
42 PIK3R1 PIK3R1 PIK3R1 13698 -0.14 0.22 NO
43 NFATC4 NFATC4 NFATC4 15180 -0.21 0.16 NO

Figure S15.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA DEATH PATHWAY.

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

genes ES table in pathway: BIOCARTA NKT PATHWAY

Table S9.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 FASLG FASLG FASLG 444 0.49 0.13 YES
2 CASP10 CASP10 CASP10 906 0.36 0.22 YES
3 RIPK2 RIPK2 RIPK2 1801 0.23 0.25 YES
4 RB1 RB1 RB1 2061 0.2 0.3 YES
5 ARHGDIB ARHGDIB ARHGDIB 2242 0.18 0.35 YES
6 FADD FADD FADD 2461 0.17 0.39 YES
7 MAP3K1 MAP3K1 MAP3K1 2838 0.15 0.42 YES
8 DFFB DFFB DFFB 3670 0.11 0.41 YES
9 CASP7 CASP7 CASP7 3744 0.11 0.44 YES
10 LMNB2 LMNB2 LMNB2 4671 0.077 0.42 YES
11 CASP3 CASP3 CASP3 4794 0.074 0.43 YES
12 CFLAR CFLAR CFLAR 4936 0.07 0.45 YES
13 FAS FAS FAS 4995 0.069 0.47 YES
14 DAXX DAXX DAXX 5455 0.058 0.46 YES
15 CASP8 CASP8 CASP8 5488 0.057 0.48 YES
16 LMNA LMNA LMNA 5495 0.057 0.5 YES
17 DFFA DFFA DFFA 5577 0.054 0.51 YES
18 PAK1 PAK1 PAK1 5692 0.051 0.52 YES
19 PAK2 PAK2 PAK2 5712 0.051 0.53 YES
20 SPTAN1 SPTAN1 SPTAN1 7981 0.002 0.41 NO
21 JUN JUN JUN 8616 -0.012 0.38 NO
22 FAF1 FAF1 FAF1 8900 -0.017 0.37 NO
23 PTPN13 PTPN13 PTPN13 9226 -0.024 0.36 NO
24 MAP3K7 MAP3K7 MAP3K7 9735 -0.035 0.34 NO
25 MAP2K4 MAP2K4 MAP2K4 10976 -0.061 0.29 NO
26 CASP6 CASP6 CASP6 11212 -0.066 0.3 NO
27 MAPK8 MAPK8 MAPK8 11620 -0.075 0.3 NO
28 PARP1 PARP1 PARP1 11823 -0.08 0.32 NO
29 PRKDC PRKDC PRKDC 12344 -0.095 0.32 NO

Figure S17.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA NKT PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA NKT 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 IL1R PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CD14 CD14 CD14 190 0.6 0.11 YES
2 TLR7 TLR7 TLR7 414 0.5 0.19 YES
3 LY96 LY96 LY96 498 0.47 0.28 YES
4 TLR4 TLR4 TLR4 509 0.47 0.37 YES
5 TLR2 TLR2 TLR2 521 0.47 0.46 YES
6 TLR6 TLR6 TLR6 565 0.45 0.55 YES
7 TLR10 TLR10 TLR10 1425 0.27 0.56 YES
8 MYD88 MYD88 MYD88 2282 0.18 0.54 YES
9 IRAK1 IRAK1 IRAK1 2750 0.15 0.55 YES
10 MAP3K1 MAP3K1 MAP3K1 2838 0.15 0.57 YES
11 MAP2K3 MAP2K3 MAP2K3 3028 0.14 0.59 YES
12 IKBKG IKBKG IKBKG 3123 0.13 0.61 YES
13 NFKBIA NFKBIA NFKBIA 3444 0.12 0.62 YES
14 MAP2K6 MAP2K6 MAP2K6 4033 0.098 0.6 NO
15 NFKB1 NFKB1 NFKB1 4559 0.081 0.59 NO
16 MAP3K14 MAP3K14 MAP3K14 5346 0.06 0.56 NO
17 CHUK CHUK CHUK 6570 0.032 0.5 NO
18 TOLLIP TOLLIP TOLLIP 7069 0.022 0.47 NO
19 ECSIT ECSIT ECSIT 7305 0.016 0.46 NO
20 MAPK14 MAPK14 MAPK14 7421 0.014 0.46 NO
21 RELA RELA RELA 7670 0.0085 0.45 NO
22 TAB2 TAB2 TAB2 7689 0.0082 0.45 NO
23 TLR3 TLR3 TLR3 7811 0.0055 0.44 NO
24 EIF2AK2 EIF2AK2 EIF2AK2 8112 -0.00081 0.43 NO
25 FOS FOS FOS 8297 -0.0043 0.42 NO
26 ELK1 ELK1 ELK1 8364 -0.006 0.42 NO
27 JUN JUN JUN 8616 -0.012 0.4 NO
28 TLR9 TLR9 TLR9 9160 -0.023 0.38 NO
29 MAP3K7 MAP3K7 MAP3K7 9735 -0.035 0.35 NO
30 IKBKB IKBKB IKBKB 9776 -0.036 0.36 NO
31 TAB1 TAB1 TAB1 10151 -0.044 0.35 NO
32 MAP2K4 MAP2K4 MAP2K4 10976 -0.061 0.31 NO
33 TRAF6 TRAF6 TRAF6 11070 -0.063 0.32 NO
34 MAPK8 MAPK8 MAPK8 11620 -0.075 0.3 NO
35 PGLYRP1 PGLYRP1 PGLYRP1 11896 -0.082 0.31 NO
36 TIRAP TIRAP TIRAP 14964 -0.2 0.18 NO

Figure S19.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA IL1R PATHWAY.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA IL1R PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus2 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
BIOCARTA AGR PATHWAY 35 genes.ES.table 0.47 1.4 0.1 0.52 0.97 0.23 0.078 0.21 0.42 0.11
BIOCARTA BIOPEPTIDES PATHWAY 39 genes.ES.table 0.45 1.6 0.041 0.36 0.81 0.2 0.16 0.17 0.26 0.062
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.37 1.3 0.15 0.57 0.98 0.15 0.11 0.13 0.47 0.13
BIOCARTA INTEGRIN PATHWAY 37 genes.ES.table 0.54 1.8 0.0021 0.39 0.24 0.27 0.14 0.23 0 0.14
BIOCARTA MYOSIN PATHWAY 28 genes.ES.table 0.55 1.7 0.015 0.26 0.6 0.25 0.11 0.22 0.15 0.04
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.43 1.6 0.032 0.28 0.7 0.32 0.22 0.25 0.17 0.046
BIOCARTA RHO PATHWAY 31 genes.ES.table 0.5 1.8 0.0062 0.18 0.39 0.26 0.11 0.23 0 0.031
BIOCARTA CREB PATHWAY 26 genes.ES.table 0.45 1.4 0.14 0.56 0.98 0.31 0.23 0.24 0.47 0.12
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 43 genes.ES.table 0.41 1.5 0.066 0.32 0.83 0.49 0.35 0.32 0.23 0.045
KEGG LYSINE DEGRADATION 43 genes.ES.table 0.46 1.8 0.016 0.18 0.32 0.51 0.33 0.34 0 0.044
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 PPP1R12B PPP1R12B PPP1R12B 45 1.2 0.16 YES
2 ACTA1 ACTA1 ACTA1 349 0.67 0.24 YES
3 TNS1 TNS1 TNS1 901 0.44 0.28 YES
4 ACTN2 ACTN2 ACTN2 904 0.44 0.34 YES
5 ACTN1 ACTN1 ACTN1 926 0.44 0.4 YES
6 ITGA1 ITGA1 ITGA1 1119 0.4 0.45 YES
7 SRC SRC SRC 1419 0.35 0.48 YES
8 VCL VCL VCL 1594 0.32 0.52 YES
9 ROCK1 ROCK1 ROCK1 1973 0.27 0.54 YES
10 RAP1A RAP1A RAP1A 2470 0.23 0.54 YES
11 CAV1 CAV1 CAV1 3205 0.17 0.53 NO
12 ZYX ZYX ZYX 3528 0.16 0.53 NO
13 ITGB1 ITGB1 ITGB1 4445 0.12 0.5 NO
14 PTK2 PTK2 PTK2 5503 0.081 0.45 NO
15 SOS1 SOS1 SOS1 5848 0.07 0.44 NO
16 RAF1 RAF1 RAF1 6420 0.054 0.42 NO
17 MAPK1 MAPK1 MAPK1 6723 0.046 0.41 NO
18 SHC1 SHC1 SHC1 7784 0.019 0.35 NO
19 MAP2K1 MAP2K1 MAP2K1 8904 -0.0065 0.29 NO
20 CAPN1 CAPN1 CAPN1 8924 -0.007 0.29 NO
21 JUN JUN JUN 9536 -0.021 0.26 NO
22 RHOA RHOA RHOA 9594 -0.023 0.26 NO
23 MAPK8 MAPK8 MAPK8 9653 -0.024 0.26 NO
24 ACTN3 ACTN3 ACTN3 9805 -0.028 0.26 NO
25 CRKL CRKL CRKL 9856 -0.029 0.26 NO
26 HRAS HRAS HRAS 10255 -0.039 0.24 NO
27 RAPGEF1 RAPGEF1 RAPGEF1 10974 -0.056 0.21 NO
28 BCR BCR BCR 11097 -0.06 0.21 NO
29 BCAR1 BCAR1 BCAR1 11296 -0.065 0.21 NO
30 CAPNS1 CAPNS1 CAPNS1 11356 -0.067 0.22 NO
31 GRB2 GRB2 GRB2 11425 -0.068 0.22 NO
32 MAPK3 MAPK3 MAPK3 11447 -0.069 0.23 NO
33 MAP2K2 MAP2K2 MAP2K2 13218 -0.12 0.15 NO
34 PXN PXN PXN 14019 -0.15 0.13 NO
35 CSK CSK CSK 14286 -0.16 0.14 NO
36 CAPNS2 CAPNS2 CAPNS2 15355 -0.22 0.11 NO
37 FYN FYN FYN 16272 -0.3 0.1 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 BIOPEPTIDES 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 ALDH1B1 ALDH1B1 ALDH1B1 230 0.77 0.12 YES
2 ACSM1 ACSM1 ACSM1 477 0.6 0.21 YES
3 BDH1 BDH1 BDH1 722 0.5 0.29 YES
4 GAD1 GAD1 GAD1 920 0.44 0.35 YES
5 OXCT1 OXCT1 OXCT1 1042 0.41 0.42 YES
6 L2HGDH L2HGDH L2HGDH 1394 0.35 0.46 YES
7 HADH HADH HADH 1433 0.34 0.52 YES
8 ALDH3A2 ALDH3A2 ALDH3A2 1731 0.3 0.56 YES
9 AKR1B10 AKR1B10 AKR1B10 2114 0.26 0.58 YES
10 ACAT2 ACAT2 ACAT2 2606 0.21 0.59 YES
11 ACAT1 ACAT1 ACAT1 2900 0.19 0.61 YES
12 ACSM5 ACSM5 ACSM5 2955 0.19 0.64 YES
13 ACSM3 ACSM3 ACSM3 3725 0.15 0.62 YES
14 ALDH2 ALDH2 ALDH2 3781 0.14 0.64 YES
15 ACSM2A ACSM2A ACSM2A 4210 0.13 0.64 NO
16 ALDH5A1 ALDH5A1 ALDH5A1 5474 0.082 0.59 NO
17 PDHB PDHB PDHB 6308 0.057 0.55 NO
18 PDHA1 PDHA1 PDHA1 7053 0.037 0.52 NO
19 ACADS ACADS ACADS 7532 0.026 0.5 NO
20 ABAT ABAT ABAT 7948 0.015 0.48 NO
21 OXCT2 OXCT2 OXCT2 8602 0.00018 0.44 NO
22 HMGCS2 HMGCS2 HMGCS2 9069 -0.01 0.42 NO
23 HMGCS1 HMGCS1 HMGCS1 9221 -0.014 0.41 NO
24 ALDH9A1 ALDH9A1 ALDH9A1 9226 -0.014 0.41 NO
25 ALDH7A1 ALDH7A1 ALDH7A1 9604 -0.023 0.4 NO
26 HMGCL HMGCL HMGCL 10278 -0.039 0.36 NO
27 AACS AACS AACS 10611 -0.048 0.36 NO
28 HADHA HADHA HADHA 11838 -0.079 0.3 NO
29 ECHS1 ECHS1 ECHS1 12504 -0.099 0.28 NO
30 BDH2 BDH2 BDH2 14458 -0.17 0.2 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 BIOPEPTIDES PATHWAY.

Figure S24.  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 CARM ER 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 ALDH1B1 ALDH1B1 ALDH1B1 230 0.77 0.12 YES
2 SETMAR SETMAR SETMAR 619 0.54 0.2 YES
3 HADH HADH HADH 1433 0.34 0.22 YES
4 ALDH3A2 ALDH3A2 ALDH3A2 1731 0.3 0.26 YES
5 BBOX1 BBOX1 BBOX1 2295 0.24 0.27 YES
6 PIPOX PIPOX PIPOX 2458 0.23 0.3 YES
7 ACAT2 ACAT2 ACAT2 2606 0.21 0.33 YES
8 SETD1B SETD1B SETD1B 2855 0.2 0.35 YES
9 ACAT1 ACAT1 ACAT1 2900 0.19 0.38 YES
10 ASH1L ASH1L ASH1L 3067 0.18 0.41 YES
11 OGDHL OGDHL OGDHL 3648 0.15 0.4 YES
12 ALDH2 ALDH2 ALDH2 3781 0.14 0.42 YES
13 WHSC1 WHSC1 WHSC1 4401 0.12 0.41 YES
14 AADAT AADAT AADAT 4417 0.12 0.43 YES
15 SETD8 SETD8 SETD8 4430 0.12 0.45 YES
16 PLOD2 PLOD2 PLOD2 4900 0.099 0.44 YES
17 TMLHE TMLHE TMLHE 5058 0.095 0.45 YES
18 SETD2 SETD2 SETD2 5248 0.088 0.45 YES
19 SUV39H1 SUV39H1 SUV39H1 5329 0.086 0.46 YES
20 OGDH OGDH OGDH 5631 0.076 0.46 YES
21 WHSC1L1 WHSC1L1 WHSC1L1 5930 0.068 0.46 YES
22 DOT1L DOT1L DOT1L 6007 0.066 0.46 YES
23 SETD7 SETD7 SETD7 6805 0.043 0.43 NO
24 SETD1A SETD1A SETD1A 6903 0.041 0.43 NO
25 DLST DLST DLST 8266 0.0077 0.36 NO
26 SETDB1 SETDB1 SETDB1 8322 0.0066 0.35 NO
27 EHMT2 EHMT2 EHMT2 8808 -0.0042 0.33 NO
28 AASS AASS AASS 8912 -0.0068 0.32 NO
29 AASDH AASDH AASDH 9145 -0.012 0.31 NO
30 ALDH9A1 ALDH9A1 ALDH9A1 9226 -0.014 0.31 NO
31 EHMT1 EHMT1 EHMT1 9255 -0.015 0.31 NO
32 NSD1 NSD1 NSD1 9522 -0.02 0.3 NO
33 GCDH GCDH GCDH 9570 -0.022 0.3 NO
34 ALDH7A1 ALDH7A1 ALDH7A1 9604 -0.023 0.3 NO
35 AASDHPPT AASDHPPT AASDHPPT 10441 -0.043 0.26 NO
36 SUV420H2 SUV420H2 SUV420H2 10599 -0.047 0.26 NO
37 SUV420H1 SUV420H1 SUV420H1 10652 -0.048 0.27 NO
38 HADHA HADHA HADHA 11838 -0.079 0.22 NO
39 ECHS1 ECHS1 ECHS1 12504 -0.099 0.2 NO
40 SETDB2 SETDB2 SETDB2 13326 -0.12 0.18 NO
41 SUV39H2 SUV39H2 SUV39H2 13644 -0.14 0.18 NO
42 PLOD3 PLOD3 PLOD3 14215 -0.16 0.18 NO
43 PLOD1 PLOD1 PLOD1 15042 -0.2 0.17 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 CARM ER PATHWAY.

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

genes ES table in pathway: BIOCARTA INTEGRIN 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 MYLK MYLK MYLK 43 1.2 0.16 YES
2 PPP1R12B PPP1R12B PPP1R12B 45 1.2 0.33 YES
3 SRC SRC SRC 1419 0.35 0.3 YES
4 ARHGEF5 ARHGEF5 ARHGEF5 1435 0.34 0.35 YES
5 PIP5K1B PIP5K1B PIP5K1B 1446 0.34 0.4 YES
6 VCL VCL VCL 1594 0.32 0.44 YES
7 ARHGAP6 ARHGAP6 ARHGAP6 1839 0.29 0.46 YES
8 ROCK1 ROCK1 ROCK1 1973 0.27 0.5 YES
9 GSN GSN GSN 2946 0.19 0.47 NO
10 ARHGAP1 ARHGAP1 ARHGAP1 3108 0.18 0.49 NO
11 ARHGAP5 ARHGAP5 ARHGAP5 4938 0.098 0.4 NO
12 OPHN1 OPHN1 OPHN1 5026 0.096 0.41 NO
13 ACTR3 ACTR3 ACTR3 5828 0.071 0.37 NO
14 PIP5K1A PIP5K1A PIP5K1A 6726 0.046 0.33 NO
15 ARPC5 ARPC5 ARPC5 6984 0.039 0.32 NO
16 DIAPH1 DIAPH1 DIAPH1 8716 -0.0024 0.23 NO
17 ARHGEF11 ARHGEF11 ARHGEF11 8800 -0.0041 0.22 NO
18 PFN1 PFN1 PFN1 9138 -0.012 0.21 NO
19 RHOA RHOA RHOA 9594 -0.023 0.18 NO
20 ARPC1A ARPC1A ARPC1A 9783 -0.027 0.18 NO
21 ARPC2 ARPC2 ARPC2 9879 -0.029 0.18 NO
22 ARPC4 ARPC4 ARPC4 10435 -0.043 0.15 NO
23 CFL1 CFL1 CFL1 11139 -0.061 0.12 NO
24 ACTR2 ACTR2 ACTR2 12363 -0.094 0.068 NO
25 ARHGEF1 ARHGEF1 ARHGEF1 12614 -0.1 0.069 NO
26 ARPC3 ARPC3 ARPC3 13161 -0.12 0.056 NO
27 ARPC1B ARPC1B ARPC1B 15803 -0.26 -0.054 NO
28 BAIAP2 BAIAP2 BAIAP2 15826 -0.26 -0.018 NO
29 ARHGAP4 ARHGAP4 ARHGAP4 15980 -0.27 0.011 NO
30 MYL2 MYL2 MYL2 16267 -0.3 0.038 NO
31 LIMK1 LIMK1 LIMK1 17565 -0.47 0.033 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 INTEGRIN PATHWAY.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA INTEGRIN 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 MYOSIN 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 ALDH1B1 ALDH1B1 ALDH1B1 230 0.77 0.19 YES
2 ALDH3A2 ALDH3A2 ALDH3A2 1731 0.3 0.19 YES
3 ACACB ACACB ACACB 2085 0.26 0.24 YES
4 LDHAL6B LDHAL6B LDHAL6B 2238 0.25 0.29 YES
5 ACAT2 ACAT2 ACAT2 2606 0.21 0.33 YES
6 ALDH6A1 ALDH6A1 ALDH6A1 2886 0.2 0.36 YES
7 ACAT1 ACAT1 ACAT1 2900 0.19 0.42 YES
8 ALDH2 ALDH2 ALDH2 3781 0.14 0.4 YES
9 ACSS3 ACSS3 ACSS3 3996 0.14 0.43 YES
10 EHHADH EHHADH EHHADH 4199 0.13 0.45 YES
11 SUCLG2 SUCLG2 SUCLG2 4655 0.11 0.45 YES
12 ACACA ACACA ACACA 4860 0.1 0.47 YES
13 PCCB PCCB PCCB 4983 0.097 0.49 YES
14 PCCA PCCA PCCA 5118 0.093 0.5 YES
15 ACADM ACADM ACADM 5267 0.088 0.52 YES
16 HIBCH HIBCH HIBCH 5531 0.08 0.53 YES
17 LDHAL6A LDHAL6A LDHAL6A 5841 0.07 0.53 YES
18 ACSS2 ACSS2 ACSS2 6485 0.052 0.5 NO
19 MUT MUT MUT 7011 0.038 0.49 NO
20 LDHB LDHB LDHB 7095 0.036 0.49 NO
21 ABAT ABAT ABAT 7948 0.015 0.45 NO
22 SUCLA2 SUCLA2 SUCLA2 7984 0.014 0.45 NO
23 MLYCD MLYCD MLYCD 8014 0.014 0.45 NO
24 SUCLG1 SUCLG1 SUCLG1 8611 0.000046 0.42 NO
25 ALDH9A1 ALDH9A1 ALDH9A1 9226 -0.014 0.39 NO
26 ALDH7A1 ALDH7A1 ALDH7A1 9604 -0.023 0.37 NO
27 MCEE MCEE MCEE 11026 -0.058 0.31 NO
28 LDHA LDHA LDHA 11203 -0.062 0.32 NO
29 ACSS1 ACSS1 ACSS1 11591 -0.073 0.32 NO
30 HADHA HADHA HADHA 11838 -0.079 0.32 NO
31 ECHS1 ECHS1 ECHS1 12504 -0.099 0.31 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 MYOSIN PATHWAY.

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

genes ES table in pathway: BIOCARTA CHREBP2 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 MYLK MYLK MYLK 43 1.2 0.19 YES
2 PPP1R12B PPP1R12B PPP1R12B 45 1.2 0.39 YES
3 ARHGEF4 ARHGEF4 ARHGEF4 1388 0.35 0.37 YES
4 ARHGEF5 ARHGEF5 ARHGEF5 1435 0.34 0.43 YES
5 ARHGEF17 ARHGEF17 ARHGEF17 1702 0.31 0.46 YES
6 ARHGEF9 ARHGEF9 ARHGEF9 1752 0.3 0.51 YES
7 ROCK1 ROCK1 ROCK1 1973 0.27 0.55 YES
8 PLCB1 PLCB1 PLCB1 3150 0.18 0.51 NO
9 ARHGEF10 ARHGEF10 ARHGEF10 3739 0.14 0.5 NO
10 ARHGEF12 ARHGEF12 ARHGEF12 4590 0.11 0.47 NO
11 GNAQ GNAQ GNAQ 4699 0.11 0.48 NO
12 ARHGAP5 ARHGAP5 ARHGAP5 4938 0.098 0.49 NO
13 PKN1 PKN1 PKN1 5864 0.07 0.45 NO
14 ARHGEF3 ARHGEF3 ARHGEF3 6625 0.048 0.42 NO
15 ARHGEF7 ARHGEF7 ARHGEF7 7463 0.027 0.37 NO
16 GNA12 GNA12 GNA12 7565 0.024 0.37 NO
17 ARHGEF2 ARHGEF2 ARHGEF2 8114 0.012 0.34 NO
18 ARHGEF18 ARHGEF18 ARHGEF18 8272 0.0076 0.34 NO
19 ARHGEF11 ARHGEF11 ARHGEF11 8800 -0.0041 0.31 NO
20 ARHGEF16 ARHGEF16 ARHGEF16 8900 -0.0064 0.3 NO
21 PRKCB PRKCB PRKCB 9695 -0.025 0.26 NO
22 ARHGEF6 ARHGEF6 ARHGEF6 10532 -0.046 0.23 NO
23 PRKCA PRKCA PRKCA 12566 -0.1 0.13 NO
24 ARHGEF1 ARHGEF1 ARHGEF1 12614 -0.1 0.14 NO
25 ARHGEF15 ARHGEF15 ARHGEF15 12829 -0.11 0.15 NO
26 GNB1 GNB1 GNB1 13349 -0.13 0.14 NO
27 MYL2 MYL2 MYL2 16267 -0.3 0.033 NO
28 ARHGEF19 ARHGEF19 ARHGEF19 17356 -0.43 0.045 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 CHREBP2 PATHWAY.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA RHO 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 MYH11 MYH11 MYH11 3 1.6 0.051 YES
2 KCNMB1 KCNMB1 KCNMB1 6 1.6 0.1 YES
3 ACTG2 ACTG2 ACTG2 28 1.2 0.14 YES
4 RAMP1 RAMP1 RAMP1 37 1.2 0.18 YES
5 MYLK MYLK MYLK 43 1.2 0.21 YES
6 PPP1R12B PPP1R12B PPP1R12B 45 1.2 0.25 YES
7 MRVI1 MRVI1 MRVI1 50 1.1 0.28 YES
8 PPP1R14A PPP1R14A PPP1R14A 83 1 0.32 YES
9 ADCY5 ADCY5 ADCY5 128 0.91 0.34 YES
10 ADRA1A ADRA1A ADRA1A 129 0.91 0.37 YES
11 ITPR1 ITPR1 ITPR1 186 0.81 0.39 YES
12 CACNA1C CACNA1C CACNA1C 277 0.73 0.41 YES
13 ACTA2 ACTA2 ACTA2 280 0.72 0.43 YES
14 KCNMA1 KCNMA1 KCNMA1 310 0.7 0.45 YES
15 MYL9 MYL9 MYL9 342 0.68 0.47 YES
16 PLA2G10 PLA2G10 PLA2G10 608 0.54 0.48 YES
17 PLCB4 PLCB4 PLCB4 682 0.52 0.49 YES
18 ADCY2 ADCY2 ADCY2 811 0.47 0.5 YES
19 PRKG1 PRKG1 PRKG1 943 0.44 0.5 YES
20 EDNRA EDNRA EDNRA 1015 0.42 0.51 YES
21 CALD1 CALD1 CALD1 1182 0.39 0.51 YES
22 PPP1R12A PPP1R12A PPP1R12A 1242 0.38 0.52 YES
23 GNA11 GNA11 GNA11 1631 0.32 0.51 NO
24 ROCK2 ROCK2 ROCK2 1804 0.3 0.51 NO
25 ROCK1 ROCK1 ROCK1 1973 0.27 0.51 NO
26 ADCY9 ADCY9 ADCY9 2716 0.2 0.48 NO
27 NPR1 NPR1 NPR1 2748 0.2 0.48 NO
28 CACNA1D CACNA1D CACNA1D 2902 0.19 0.48 NO
29 PRKCG PRKCG PRKCG 2903 0.19 0.48 NO
30 PPP1CB PPP1CB PPP1CB 3102 0.18 0.48 NO
31 PLCB1 PLCB1 PLCB1 3150 0.18 0.48 NO
32 MYLK3 MYLK3 MYLK3 3259 0.17 0.48 NO
33 PLA2G6 PLA2G6 PLA2G6 3315 0.17 0.48 NO
34 MYL6 MYL6 MYL6 3415 0.16 0.48 NO
35 PLA2G3 PLA2G3 PLA2G3 3540 0.15 0.48 NO
36 NPR2 NPR2 NPR2 3572 0.15 0.48 NO
37 ADCY6 ADCY6 ADCY6 3624 0.15 0.49 NO
38 PRKACB PRKACB PRKACB 3658 0.15 0.49 NO
39 PLA2G12A PLA2G12A PLA2G12A 3752 0.14 0.49 NO
40 PRKACG PRKACG PRKACG 3901 0.14 0.48 NO
41 GUCY1A3 GUCY1A3 GUCY1A3 4235 0.12 0.47 NO
42 ARHGEF12 ARHGEF12 ARHGEF12 4590 0.11 0.45 NO
43 GNAQ GNAQ GNAQ 4699 0.11 0.45 NO
44 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 4767 0.1 0.45 NO
45 PLCB3 PLCB3 PLCB3 4920 0.099 0.45 NO
46 CALM1 CALM1 CALM1 5251 0.088 0.43 NO
47 RAMP3 RAMP3 RAMP3 5550 0.079 0.42 NO
48 PRKACA PRKACA PRKACA 5611 0.077 0.42 NO
49 GNA13 GNA13 GNA13 5934 0.067 0.4 NO
50 BRAF BRAF BRAF 6324 0.057 0.38 NO
51 RAF1 RAF1 RAF1 6420 0.054 0.38 NO
52 MAPK1 MAPK1 MAPK1 6723 0.046 0.36 NO
53 ADCY8 ADCY8 ADCY8 7200 0.034 0.34 NO
54 GNA12 GNA12 GNA12 7565 0.024 0.32 NO
55 PRKCD PRKCD PRKCD 7794 0.019 0.3 NO
56 KCNMB3 KCNMB3 KCNMB3 8085 0.012 0.29 NO
57 ADCY1 ADCY1 ADCY1 8171 0.01 0.28 NO
58 CALCRL CALCRL CALCRL 8192 0.0097 0.28 NO
59 ARHGEF11 ARHGEF11 ARHGEF11 8800 -0.0041 0.25 NO
60 MAP2K1 MAP2K1 MAP2K1 8904 -0.0065 0.24 NO
61 CALM3 CALM3 CALM3 8945 -0.0074 0.24 NO
62 CALML3 CALML3 CALML3 9044 -0.0097 0.24 NO
63 GUCY1B3 GUCY1B3 GUCY1B3 9266 -0.015 0.23 NO
64 RHOA RHOA RHOA 9594 -0.023 0.21 NO
65 PRKCB PRKCB PRKCB 9695 -0.025 0.2 NO
66 ARAF ARAF ARAF 9767 -0.026 0.2 NO
67 PPP1CC PPP1CC PPP1CC 10311 -0.04 0.17 NO
68 CALM2 CALM2 CALM2 10423 -0.043 0.17 NO
69 GNAS GNAS GNAS 10460 -0.044 0.17 NO
70 ADRA1D ADRA1D ADRA1D 10481 -0.045 0.17 NO
71 CACNA1F CACNA1F CACNA1F 11261 -0.064 0.13 NO
72 MAPK3 MAPK3 MAPK3 11447 -0.069 0.12 NO
73 PRKCA PRKCA PRKCA 12566 -0.1 0.059 NO
74 ARHGEF1 ARHGEF1 ARHGEF1 12614 -0.1 0.059 NO
75 MAP2K2 MAP2K2 MAP2K2 13218 -0.12 0.03 NO
76 PRKCQ PRKCQ PRKCQ 13226 -0.12 0.033 NO
77 MYL6B MYL6B MYL6B 13609 -0.14 0.016 NO
78 PLA2G12B PLA2G12B PLA2G12B 13622 -0.14 0.02 NO
79 PRKCH PRKCH PRKCH 13732 -0.14 0.018 NO
80 PLA2G2D PLA2G2D PLA2G2D 13771 -0.14 0.021 NO
81 ADORA2A ADORA2A ADORA2A 13868 -0.14 0.02 NO
82 PPP1CA PPP1CA PPP1CA 13937 -0.15 0.021 NO
83 RAMP2 RAMP2 RAMP2 13953 -0.15 0.025 NO
84 ITPR2 ITPR2 ITPR2 14088 -0.15 0.022 NO
85 CALML6 CALML6 CALML6 14095 -0.16 0.027 NO
86 ADCY4 ADCY4 ADCY4 14220 -0.16 0.025 NO
87 PRKCE PRKCE PRKCE 14250 -0.16 0.028 NO
88 GUCY1A2 GUCY1A2 GUCY1A2 14465 -0.17 0.022 NO
89 ITPR3 ITPR3 ITPR3 14840 -0.19 0.0072 NO
90 CYP4A11 CYP4A11 CYP4A11 14871 -0.19 0.012 NO
91 CACNA1S CACNA1S CACNA1S 14940 -0.2 0.014 NO
92 PLA2G5 PLA2G5 PLA2G5 15045 -0.2 0.015 NO
93 AVPR1A AVPR1A AVPR1A 15321 -0.22 0.0063 NO
94 PRKX PRKX PRKX 15421 -0.23 0.008 NO
95 ADRA1B ADRA1B ADRA1B 15435 -0.23 0.014 NO
96 PLA2G4A PLA2G4A PLA2G4A 15784 -0.25 0.0031 NO
97 PLA2G1B PLA2G1B PLA2G1B 15858 -0.26 0.0073 NO
98 PTGIR PTGIR PTGIR 15895 -0.26 0.014 NO
99 AGTR1 AGTR1 AGTR1 16304 -0.3 0.00044 NO
100 MYLK2 MYLK2 MYLK2 16548 -0.32 -0.0028 NO
101 ADCY7 ADCY7 ADCY7 16555 -0.32 0.0071 NO
102 ADORA2B ADORA2B ADORA2B 16691 -0.34 0.01 NO
103 PLCB2 PLCB2 PLCB2 17159 -0.4 -0.003 NO
104 KCNMB2 KCNMB2 KCNMB2 17613 -0.48 -0.013 NO
105 PLA2G2A PLA2G2A PLA2G2A 17953 -0.6 -0.013 NO
106 KCNMB4 KCNMB4 KCNMB4 18103 -0.78 0.0035 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 RHO PATHWAY.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA RHO 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 CREB 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 PRKAA2 PRKAA2 PRKAA2 177 0.82 0.13 YES
2 PRKAG2 PRKAG2 PRKAG2 702 0.51 0.19 YES
3 PPP2R2B PPP2R2B PPP2R2B 1198 0.39 0.22 YES
4 PPP2R2C PPP2R2C PPP2R2C 1545 0.33 0.26 YES
5 PRKAR2A PRKAR2A PRKAR2A 1575 0.32 0.31 YES
6 PRKAB2 PRKAB2 PRKAB2 2121 0.26 0.33 YES
7 PPP2R5A PPP2R5A PPP2R5A 2212 0.25 0.36 YES
8 PRKAR2B PRKAR2B PRKAR2B 2215 0.25 0.41 YES
9 YWHAH YWHAH YWHAH 3123 0.18 0.38 YES
10 PRKAA1 PRKAA1 PRKAA1 3410 0.16 0.4 YES
11 PRKACB PRKACB PRKACB 3658 0.15 0.41 YES
12 PRKACG PRKACG PRKACG 3901 0.14 0.42 YES
13 PPP2R3A PPP2R3A PPP2R3A 4022 0.13 0.43 YES
14 ACACA ACACA ACACA 4860 0.1 0.4 NO
15 PRKACA PRKACA PRKACA 5611 0.077 0.38 NO
16 PPP2R5E PPP2R5E PPP2R5E 5867 0.069 0.37 NO
17 GCK GCK GCK 5886 0.069 0.38 NO
18 YWHAZ YWHAZ YWHAZ 6656 0.048 0.35 NO
19 PPP2R5B PPP2R5B PPP2R5B 6841 0.042 0.35 NO
20 PPP2CA PPP2CA PPP2CA 6934 0.04 0.35 NO
21 PPP2CB PPP2CB PPP2CB 7768 0.02 0.31 NO
22 YWHAQ YWHAQ YWHAQ 7967 0.015 0.3 NO
23 PRKAG1 PRKAG1 PRKAG1 8414 0.0046 0.27 NO
24 PPP2R5D PPP2R5D PPP2R5D 8925 -0.007 0.25 NO
25 PRKAR1A PRKAR1A PRKAR1A 8953 -0.0076 0.25 NO
26 PPP2R5C PPP2R5C PPP2R5C 8969 -0.0079 0.25 NO
27 PRKAB1 PRKAB1 PRKAB1 9243 -0.015 0.23 NO
28 MLX MLX MLX 9247 -0.015 0.24 NO
29 PPP2R2A PPP2R2A PPP2R2A 9779 -0.027 0.21 NO
30 PKLR PKLR PKLR 9877 -0.029 0.21 NO
31 YWHAG YWHAG YWHAG 9951 -0.031 0.21 NO
32 YWHAB YWHAB YWHAB 10383 -0.042 0.2 NO
33 PPP2R4 PPP2R4 PPP2R4 10833 -0.053 0.18 NO
34 PPP2R1A PPP2R1A PPP2R1A 11574 -0.072 0.15 NO
35 PPP2R3B PPP2R3B PPP2R3B 11649 -0.074 0.16 NO
36 PPP2R1B PPP2R1B PPP2R1B 11978 -0.083 0.16 NO
37 FASN FASN FASN 12706 -0.1 0.13 NO
38 PPP2R2D PPP2R2D PPP2R2D 14256 -0.16 0.075 NO
39 YWHAE YWHAE YWHAE 14397 -0.17 0.095 NO
40 PRKAR1B PRKAR1B PRKAR1B 15437 -0.23 0.076 NO
41 MLXIPL MLXIPL MLXIPL 17436 -0.44 0.04 NO

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

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

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

Table 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 MYLK MYLK MYLK 43 1.2 0.2 YES
2 MAPT MAPT MAPT 416 0.63 0.28 YES
3 CAMK2A CAMK2A CAMK2A 728 0.5 0.35 YES
4 GNA11 GNA11 GNA11 1631 0.32 0.35 YES
5 CAMK2G CAMK2G CAMK2G 1701 0.31 0.4 YES
6 STAT5B STAT5B STAT5B 2199 0.25 0.42 YES
7 PTK2B PTK2B PTK2B 2569 0.22 0.43 YES
8 JAK2 JAK2 JAK2 2834 0.2 0.45 YES
9 STAT6 STAT6 STAT6 3504 0.16 0.44 NO
10 CALM1 CALM1 CALM1 5251 0.088 0.36 NO
11 AGT AGT AGT 5488 0.081 0.36 NO
12 SOS1 SOS1 SOS1 5848 0.07 0.35 NO
13 CAMK2B CAMK2B CAMK2B 5943 0.067 0.36 NO
14 STAT3 STAT3 STAT3 6065 0.064 0.36 NO
15 RAF1 RAF1 RAF1 6420 0.054 0.35 NO
16 MAPK1 MAPK1 MAPK1 6723 0.046 0.34 NO
17 F2 F2 F2 7105 0.036 0.33 NO
18 SHC1 SHC1 SHC1 7784 0.019 0.3 NO
19 STAT1 STAT1 STAT1 8237 0.0086 0.27 NO
20 PLCG1 PLCG1 PLCG1 8570 0.0011 0.25 NO
21 MAPK14 MAPK14 MAPK14 8846 -0.0054 0.24 NO
22 MAP2K1 MAP2K1 MAP2K1 8904 -0.0065 0.24 NO
23 CALM3 CALM3 CALM3 8945 -0.0074 0.24 NO
24 GNAI1 GNAI1 GNAI1 8968 -0.0079 0.24 NO
25 MAPK8 MAPK8 MAPK8 9653 -0.024 0.2 NO
26 PRKCB PRKCB PRKCB 9695 -0.025 0.2 NO
27 STAT5A STAT5A STAT5A 10073 -0.034 0.19 NO
28 CAMK2D CAMK2D CAMK2D 10135 -0.036 0.19 NO
29 AGTR2 AGTR2 AGTR2 10393 -0.042 0.19 NO
30 CALM2 CALM2 CALM2 10423 -0.043 0.19 NO
31 GRB2 GRB2 GRB2 11425 -0.068 0.15 NO
32 MAPK3 MAPK3 MAPK3 11447 -0.069 0.16 NO
33 CDK5 CDK5 CDK5 11860 -0.08 0.15 NO
34 PRKCA PRKCA PRKCA 12566 -0.1 0.13 NO
35 MAP2K2 MAP2K2 MAP2K2 13218 -0.12 0.11 NO
36 GNB1 GNB1 GNB1 13349 -0.13 0.13 NO
37 STAT2 STAT2 STAT2 13848 -0.14 0.12 NO
38 FYN FYN FYN 16272 -0.3 0.039 NO
39 STAT4 STAT4 STAT4 17070 -0.38 0.06 NO

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

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

genes ES table in pathway: KEGG LYSINE DEGRADATION

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 SORBS1 SORBS1 SORBS1 61 1.1 0.043 YES
2 PRKAA2 PRKAA2 PRKAA2 177 0.82 0.071 YES
3 PPARGC1A PPARGC1A PPARGC1A 200 0.8 0.1 YES
4 MAPK10 MAPK10 MAPK10 210 0.79 0.14 YES
5 SOCS2 SOCS2 SOCS2 265 0.74 0.16 YES
6 PHKG1 PHKG1 PHKG1 275 0.73 0.19 YES
7 PDE3A PDE3A PDE3A 323 0.69 0.22 YES
8 PPP1R3C PPP1R3C PPP1R3C 357 0.67 0.24 YES
9 PHKA1 PHKA1 PHKA1 381 0.65 0.27 YES
10 SLC2A4 SLC2A4 SLC2A4 564 0.56 0.28 YES
11 PPP1R3B PPP1R3B PPP1R3B 634 0.54 0.3 YES
12 PRKAG2 PRKAG2 PRKAG2 702 0.51 0.32 YES
13 PTPRF PTPRF PTPRF 717 0.51 0.34 YES
14 AKT3 AKT3 AKT3 1068 0.41 0.34 YES
15 PYGM PYGM PYGM 1216 0.38 0.34 YES
16 PRKAR2A PRKAR2A PRKAR2A 1575 0.32 0.34 YES
17 ACACB ACACB ACACB 2085 0.26 0.32 YES
18 PRKAB2 PRKAB2 PRKAB2 2121 0.26 0.33 YES
19 PRKAR2B PRKAR2B PRKAR2B 2215 0.25 0.33 YES
20 IRS4 IRS4 IRS4 2269 0.24 0.34 YES
21 FLOT2 FLOT2 FLOT2 2498 0.22 0.34 YES
22 PYGB PYGB PYGB 2546 0.22 0.34 YES
23 IRS2 IRS2 IRS2 2787 0.2 0.34 YES
24 RPTOR RPTOR RPTOR 2799 0.2 0.35 YES
25 CBL CBL CBL 2833 0.2 0.35 YES
26 IKBKB IKBKB IKBKB 2962 0.19 0.36 YES
27 PPP1CB PPP1CB PPP1CB 3102 0.18 0.35 YES
28 SHC2 SHC2 SHC2 3409 0.16 0.34 YES
29 PRKAA1 PRKAA1 PRKAA1 3410 0.16 0.35 YES
30 PRKACB PRKACB PRKACB 3658 0.15 0.34 YES
31 PIK3R3 PIK3R3 PIK3R3 3837 0.14 0.34 YES
32 RHEB RHEB RHEB 3856 0.14 0.34 YES
33 INSR INSR INSR 3898 0.14 0.35 YES
34 PRKACG PRKACG PRKACG 3901 0.14 0.35 YES
35 PDPK1 PDPK1 PDPK1 3910 0.14 0.36 YES
36 PIK3CB PIK3CB PIK3CB 3953 0.14 0.36 YES
37 PPP1R3D PPP1R3D PPP1R3D 3967 0.14 0.37 YES
38 SOS2 SOS2 SOS2 3992 0.14 0.37 YES
39 IRS1 IRS1 IRS1 4175 0.13 0.37 YES
40 PIK3R1 PIK3R1 PIK3R1 4212 0.13 0.37 YES
41 GYS2 GYS2 GYS2 4333 0.12 0.37 YES
42 FOXO1 FOXO1 FOXO1 4339 0.12 0.37 YES
43 PDE3B PDE3B PDE3B 4402 0.12 0.37 YES
44 ACACA ACACA ACACA 4860 0.1 0.35 NO
45 GSK3B GSK3B GSK3B 4975 0.097 0.35 NO
46 SOCS4 SOCS4 SOCS4 5115 0.093 0.35 NO
47 CALM1 CALM1 CALM1 5251 0.088 0.34 NO
48 PRKACA PRKACA PRKACA 5611 0.077 0.33 NO
49 SOS1 SOS1 SOS1 5848 0.07 0.32 NO
50 GCK GCK GCK 5886 0.069 0.32 NO
51 RHOQ RHOQ RHOQ 5929 0.068 0.32 NO
52 MAPK9 MAPK9 MAPK9 6289 0.058 0.3 NO
53 BRAF BRAF BRAF 6324 0.057 0.3 NO
54 RAF1 RAF1 RAF1 6420 0.054 0.3 NO
55 TSC2 TSC2 TSC2 6434 0.054 0.3 NO
56 TSC1 TSC1 TSC1 6515 0.052 0.3 NO
57 PRKCI PRKCI PRKCI 6708 0.046 0.29 NO
58 SHC4 SHC4 SHC4 6709 0.046 0.29 NO
59 MAPK1 MAPK1 MAPK1 6723 0.046 0.29 NO
60 PIK3CA PIK3CA PIK3CA 6763 0.044 0.29 NO
61 TRIP10 TRIP10 TRIP10 7016 0.038 0.28 NO
62 PHKG2 PHKG2 PHKG2 7442 0.028 0.26 NO
63 BAD BAD BAD 7454 0.028 0.26 NO
64 PHKA2 PHKA2 PHKA2 7648 0.022 0.25 NO
65 EIF4E EIF4E EIF4E 7703 0.021 0.24 NO
66 SHC1 SHC1 SHC1 7784 0.019 0.24 NO
67 AKT1 AKT1 AKT1 7872 0.017 0.24 NO
68 PRKAG1 PRKAG1 PRKAG1 8414 0.0046 0.21 NO
69 GYS1 GYS1 GYS1 8471 0.0031 0.2 NO
70 ELK1 ELK1 ELK1 8634 -0.00057 0.2 NO
71 PTPN1 PTPN1 PTPN1 8717 -0.0024 0.19 NO
72 PCK2 PCK2 PCK2 8805 -0.0042 0.19 NO
73 HK1 HK1 HK1 8883 -0.006 0.18 NO
74 FLOT1 FLOT1 FLOT1 8889 -0.0062 0.18 NO
75 MAP2K1 MAP2K1 MAP2K1 8904 -0.0065 0.18 NO
76 EXOC7 EXOC7 EXOC7 8914 -0.0068 0.18 NO
77 MTOR MTOR MTOR 8936 -0.0072 0.18 NO
78 CALM3 CALM3 CALM3 8945 -0.0074 0.18 NO
79 PRKAR1A PRKAR1A PRKAR1A 8953 -0.0076 0.18 NO
80 FBP2 FBP2 FBP2 8998 -0.0088 0.18 NO
81 CALML3 CALML3 CALML3 9044 -0.0097 0.18 NO
82 SHC3 SHC3 SHC3 9118 -0.012 0.17 NO
83 PRKAB1 PRKAB1 PRKAB1 9243 -0.015 0.17 NO
84 MAPK8 MAPK8 MAPK8 9653 -0.024 0.14 NO
85 ARAF ARAF ARAF 9767 -0.026 0.14 NO
86 CRKL CRKL CRKL 9856 -0.029 0.14 NO
87 PHKB PHKB PHKB 9867 -0.029 0.14 NO
88 PKLR PKLR PKLR 9877 -0.029 0.14 NO
89 AKT2 AKT2 AKT2 9924 -0.031 0.14 NO
90 RPS6KB1 RPS6KB1 RPS6KB1 10030 -0.033 0.13 NO
91 PPP1CC PPP1CC PPP1CC 10311 -0.04 0.12 NO
92 CALM2 CALM2 CALM2 10423 -0.043 0.11 NO
93 RPS6KB2 RPS6KB2 RPS6KB2 10622 -0.048 0.1 NO
94 RAPGEF1 RAPGEF1 RAPGEF1 10974 -0.056 0.086 NO
95 CRK CRK CRK 10998 -0.057 0.088 NO
96 PYGL PYGL PYGL 11017 -0.058 0.089 NO
97 LIPE LIPE LIPE 11418 -0.068 0.07 NO
98 GRB2 GRB2 GRB2 11425 -0.068 0.072 NO
99 MAPK3 MAPK3 MAPK3 11447 -0.069 0.074 NO
100 RPS6 RPS6 RPS6 11540 -0.072 0.072 NO
101 MKNK1 MKNK1 MKNK1 11720 -0.076 0.065 NO
102 SREBF1 SREBF1 SREBF1 12047 -0.085 0.05 NO
103 PCK1 PCK1 PCK1 12097 -0.086 0.051 NO
104 EIF4EBP1 EIF4EBP1 EIF4EBP1 12135 -0.088 0.053 NO
105 CBLC CBLC CBLC 12318 -0.093 0.047 NO
106 MKNK2 MKNK2 MKNK2 12390 -0.095 0.047 NO
107 CBLB CBLB CBLB 12424 -0.096 0.049 NO
108 KRAS KRAS KRAS 12432 -0.097 0.052 NO
109 INPP5K INPP5K INPP5K 12620 -0.1 0.046 NO
110 FASN FASN FASN 12706 -0.1 0.046 NO
111 EIF4E2 EIF4E2 EIF4E2 12947 -0.11 0.037 NO
112 MAP2K2 MAP2K2 MAP2K2 13218 -0.12 0.027 NO
113 PIK3R2 PIK3R2 PIK3R2 13398 -0.13 0.023 NO
114 PPP1CA PPP1CA PPP1CA 13937 -0.15 -0.001 NO
115 CALML6 CALML6 CALML6 14095 -0.16 -0.0033 NO
116 PRKX PRKX PRKX 15421 -0.23 -0.067 NO
117 PRKAR1B PRKAR1B PRKAR1B 15437 -0.23 -0.059 NO
118 NRAS NRAS NRAS 15612 -0.24 -0.058 NO
119 PRKCZ PRKCZ PRKCZ 16155 -0.28 -0.077 NO
120 PIK3CG PIK3CG PIK3CG 16545 -0.32 -0.085 NO
121 PIK3CD PIK3CD PIK3CD 16689 -0.34 -0.079 NO
122 SH2B2 SH2B2 SH2B2 16796 -0.35 -0.07 NO
123 INPP5D INPP5D INPP5D 16966 -0.37 -0.064 NO
124 SOCS1 SOCS1 SOCS1 17027 -0.38 -0.052 NO
125 HK2 HK2 HK2 17215 -0.4 -0.045 NO
126 FBP1 FBP1 FBP1 17263 -0.41 -0.031 NO
127 SOCS3 SOCS3 SOCS3 17330 -0.42 -0.017 NO
128 PIK3R5 PIK3R5 PIK3R5 17518 -0.46 -0.0081 NO
129 PRKAG3 PRKAG3 PRKAG3 17589 -0.47 0.0077 NO
130 HK3 HK3 HK3 17929 -0.58 0.013 NO

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

Figure S40.  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

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 ALK PATHWAY 35 genes.ES.table 0.56 1.6 0.014 0.2 0.69 0.29 0.11 0.25 0.12 0.026
BIOCARTA WNT PATHWAY 25 genes.ES.table 0.61 2 0.0021 0.081 0.066 0.24 0.12 0.21 0 0.028
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 29 genes.ES.table 0.45 1.3 0.099 0.62 0.99 0.34 0.12 0.3 0.52 0.15
KEGG N GLYCAN BIOSYNTHESIS 45 genes.ES.table 0.37 1.4 0.13 0.66 0.98 0.11 0.12 0.098 0.55 0.18
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE 25 genes.ES.table 0.61 1.6 0.016 0.23 0.64 0.48 0.19 0.39 0.13 0.036
KEGG GLYCOSPHINGOLIPID BIOSYNTHESIS LACTO AND NEOLACTO SERIES 25 genes.ES.table 0.51 1.3 0.14 0.65 0.99 0.36 0.17 0.3 0.54 0.18
KEGG P53 SIGNALING PATHWAY 67 genes.ES.table 0.35 1.2 0.16 0.71 1 0.16 0.13 0.14 0.63 0.19
KEGG ENDOCYTOSIS 180 genes.ES.table 0.27 1.2 0.19 0.75 1 0.12 0.1 0.1 0.67 0.21
KEGG WNT SIGNALING PATHWAY 146 genes.ES.table 0.53 1.8 0.0042 0.16 0.25 0.25 0.13 0.22 0 0.038
KEGG NOTCH SIGNALING PATHWAY 45 genes.ES.table 0.39 1.4 0.14 0.68 0.98 0.31 0.26 0.23 0.56 0.19
genes ES table in pathway: BIOCARTA ALK 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 WIF1 WIF1 WIF1 187 0.55 0.19 YES
2 LEF1 LEF1 LEF1 646 0.41 0.32 YES
3 TLE1 TLE1 TLE1 1241 0.31 0.4 YES
4 CCND1 CCND1 CCND1 1616 0.27 0.48 YES
5 FZD1 FZD1 FZD1 2068 0.23 0.54 YES
6 BTRC BTRC BTRC 2246 0.22 0.61 YES
7 CSNK2A1 CSNK2A1 CSNK2A1 4996 0.098 0.5 NO
8 APC APC APC 5248 0.091 0.52 NO
9 MAP3K7 MAP3K7 MAP3K7 5929 0.075 0.51 NO
10 CTNNB1 CTNNB1 CTNNB1 6463 0.065 0.5 NO
11 HDAC1 HDAC1 HDAC1 6499 0.064 0.52 NO
12 DVL1 DVL1 DVL1 7590 0.044 0.48 NO
13 CTBP1 CTBP1 CTBP1 7673 0.043 0.49 NO
14 CSNK1D CSNK1D CSNK1D 7827 0.04 0.5 NO
15 CREBBP CREBBP CREBBP 8008 0.036 0.5 NO
16 MYC MYC MYC 8791 0.025 0.47 NO
17 WNT1 WNT1 WNT1 9814 0.0088 0.42 NO
18 NLK NLK NLK 10092 0.0046 0.4 NO
19 SMAD4 SMAD4 SMAD4 10148 0.0038 0.4 NO
20 GSK3B GSK3B GSK3B 11019 -0.0096 0.36 NO
21 FRAT1 FRAT1 FRAT1 11297 -0.014 0.34 NO
22 AXIN1 AXIN1 AXIN1 11595 -0.019 0.34 NO
23 TAB1 TAB1 TAB1 11651 -0.02 0.34 NO
24 PPP2CA PPP2CA PPP2CA 11807 -0.023 0.34 NO
25 CSNK1A1 CSNK1A1 CSNK1A1 12165 -0.029 0.33 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 ALK PATHWAY.

Figure S42.  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 WNT 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 NKD2 NKD2 NKD2 19 0.77 0.034 YES
2 SFRP5 SFRP5 SFRP5 44 0.69 0.064 YES
3 VANGL2 VANGL2 VANGL2 77 0.65 0.091 YES
4 CCND2 CCND2 CCND2 97 0.62 0.12 YES
5 APC2 APC2 APC2 101 0.62 0.15 YES
6 FZD10 FZD10 FZD10 111 0.61 0.17 YES
7 WIF1 WIF1 WIF1 187 0.55 0.19 YES
8 WNT5A WNT5A WNT5A 191 0.55 0.22 YES
9 FZD9 FZD9 FZD9 271 0.52 0.24 YES
10 CXXC4 CXXC4 CXXC4 334 0.49 0.26 YES
11 PRICKLE1 PRICKLE1 PRICKLE1 380 0.48 0.28 YES
12 FZD2 FZD2 FZD2 490 0.45 0.29 YES
13 FZD3 FZD3 FZD3 500 0.44 0.31 YES
14 LEF1 LEF1 LEF1 646 0.41 0.32 YES
15 WNT11 WNT11 WNT11 688 0.4 0.34 YES
16 NKD1 NKD1 NKD1 710 0.39 0.35 YES
17 FZD8 FZD8 FZD8 861 0.37 0.36 YES
18 RAC3 RAC3 RAC3 901 0.36 0.37 YES
19 DAAM2 DAAM2 DAAM2 969 0.35 0.39 YES
20 CAMK2B CAMK2B CAMK2B 1028 0.34 0.4 YES
21 WNT4 WNT4 WNT4 1060 0.34 0.41 YES
22 WNT3A WNT3A WNT3A 1093 0.33 0.42 YES
23 LRP5 LRP5 LRP5 1136 0.33 0.44 YES
24 WNT6 WNT6 WNT6 1197 0.32 0.45 YES
25 WNT5B WNT5B WNT5B 1526 0.28 0.44 YES
26 DKK2 DKK2 DKK2 1550 0.28 0.45 YES
27 WNT7A WNT7A WNT7A 1564 0.28 0.47 YES
28 LRP6 LRP6 LRP6 1612 0.27 0.48 YES
29 CCND1 CCND1 CCND1 1616 0.27 0.49 YES
30 SFRP1 SFRP1 SFRP1 1714 0.26 0.5 YES
31 WNT7B WNT7B WNT7B 1744 0.26 0.5 YES
32 FZD1 FZD1 FZD1 2068 0.23 0.5 YES
33 CER1 CER1 CER1 2142 0.23 0.5 YES
34 BTRC BTRC BTRC 2246 0.22 0.51 YES
35 TP53 TP53 TP53 2289 0.22 0.52 YES
36 SFRP2 SFRP2 SFRP2 2415 0.21 0.52 YES
37 CHP2 CHP2 CHP2 2427 0.2 0.53 YES
38 CTNNBIP1 CTNNBIP1 CTNNBIP1 3076 0.17 0.5 NO
39 NFATC2 NFATC2 NFATC2 3281 0.16 0.49 NO
40 TCF7L1 TCF7L1 TCF7L1 3300 0.16 0.5 NO
41 WNT3 WNT3 WNT3 3333 0.16 0.5 NO
42 WNT16 WNT16 WNT16 3868 0.13 0.48 NO
43 PRKCG PRKCG PRKCG 3939 0.13 0.48 NO
44 MAPK8 MAPK8 MAPK8 4076 0.12 0.48 NO
45 FZD4 FZD4 FZD4 4114 0.12 0.48 NO
46 NFATC4 NFATC4 NFATC4 4399 0.12 0.47 NO
47 FZD7 FZD7 FZD7 4448 0.11 0.48 NO
48 TCF7L2 TCF7L2 TCF7L2 4451 0.11 0.48 NO
49 AXIN2 AXIN2 AXIN2 4653 0.11 0.48 NO
50 NFAT5 NFAT5 NFAT5 4988 0.098 0.46 NO
51 CSNK2A1 CSNK2A1 CSNK2A1 4996 0.098 0.47 NO
52 SENP2 SENP2 SENP2 5079 0.095 0.46 NO
53 MMP7 MMP7 MMP7 5129 0.094 0.47 NO
54 NFATC3 NFATC3 NFATC3 5169 0.093 0.47 NO
55 PPP3CA PPP3CA PPP3CA 5218 0.092 0.47 NO
56 PRKX PRKX PRKX 5224 0.091 0.47 NO
57 APC APC APC 5248 0.091 0.48 NO
58 CTBP2 CTBP2 CTBP2 5508 0.085 0.47 NO
59 PPP3CB PPP3CB PPP3CB 5637 0.081 0.46 NO
60 CHD8 CHD8 CHD8 5672 0.081 0.46 NO
61 PPP2R1B PPP2R1B PPP2R1B 5766 0.079 0.46 NO
62 MAPK10 MAPK10 MAPK10 5813 0.078 0.46 NO
63 PPARD PPARD PPARD 5860 0.077 0.46 NO
64 WNT10A WNT10A WNT10A 5905 0.076 0.47 NO
65 CSNK1E CSNK1E CSNK1E 5907 0.076 0.47 NO
66 MAP3K7 MAP3K7 MAP3K7 5929 0.075 0.47 NO
67 NFATC1 NFATC1 NFATC1 5979 0.074 0.47 NO
68 WNT9A WNT9A WNT9A 6088 0.072 0.47 NO
69 PRKCA PRKCA PRKCA 6161 0.071 0.47 NO
70 WNT10B WNT10B WNT10B 6327 0.067 0.46 NO
71 CSNK2A2 CSNK2A2 CSNK2A2 6360 0.067 0.46 NO
72 DVL2 DVL2 DVL2 6382 0.066 0.47 NO
73 CTNNB1 CTNNB1 CTNNB1 6463 0.065 0.46 NO
74 TBL1XR1 TBL1XR1 TBL1XR1 6829 0.058 0.45 NO
75 EP300 EP300 EP300 6914 0.056 0.44 NO
76 PLCB4 PLCB4 PLCB4 7045 0.054 0.44 NO
77 DVL1 DVL1 DVL1 7590 0.044 0.41 NO
78 CTBP1 CTBP1 CTBP1 7673 0.043 0.41 NO
79 PPP2R1A PPP2R1A PPP2R1A 7734 0.042 0.41 NO
80 JUN JUN JUN 7909 0.039 0.4 NO
81 PPP3R1 PPP3R1 PPP3R1 7994 0.037 0.4 NO
82 CREBBP CREBBP CREBBP 8008 0.036 0.4 NO
83 FBXW11 FBXW11 FBXW11 8241 0.033 0.39 NO
84 CCND3 CCND3 CCND3 8364 0.031 0.38 NO
85 PSEN1 PSEN1 PSEN1 8390 0.031 0.38 NO
86 PRICKLE2 PRICKLE2 PRICKLE2 8464 0.03 0.38 NO
87 FRAT2 FRAT2 FRAT2 8468 0.029 0.38 NO
88 SMAD2 SMAD2 SMAD2 8613 0.027 0.37 NO
89 MYC MYC MYC 8791 0.025 0.36 NO
90 WNT8B WNT8B WNT8B 8794 0.024 0.36 NO
91 DVL3 DVL3 DVL3 8859 0.024 0.36 NO
92 SIAH1 SIAH1 SIAH1 9053 0.021 0.35 NO
93 CSNK1A1L CSNK1A1L CSNK1A1L 9058 0.021 0.35 NO
94 PRKACG PRKACG PRKACG 9099 0.02 0.35 NO
95 PPP2R5D PPP2R5D PPP2R5D 9259 0.018 0.34 NO
96 ROCK2 ROCK2 ROCK2 9338 0.016 0.34 NO
97 TCF7 TCF7 TCF7 9434 0.015 0.34 NO
98 FZD5 FZD5 FZD5 9559 0.013 0.33 NO
99 CSNK2B CSNK2B CSNK2B 9790 0.0093 0.32 NO
100 WNT1 WNT1 WNT1 9814 0.0088 0.32 NO
101 NLK NLK NLK 10092 0.0046 0.3 NO
102 SMAD4 SMAD4 SMAD4 10148 0.0038 0.3 NO
103 SKP1 SKP1 SKP1 10465 -0.00083 0.28 NO
104 PPP2R5C PPP2R5C PPP2R5C 10699 -0.0046 0.27 NO
105 CHP CHP CHP 10714 -0.0048 0.27 NO
106 PPP2CB PPP2CB PPP2CB 10813 -0.0067 0.26 NO
107 GSK3B GSK3B GSK3B 11019 -0.0096 0.25 NO
108 RAC1 RAC1 RAC1 11146 -0.012 0.24 NO
109 PPP3R2 PPP3R2 PPP3R2 11161 -0.012 0.24 NO
110 FRAT1 FRAT1 FRAT1 11297 -0.014 0.24 NO
111 CUL1 CUL1 CUL1 11546 -0.018 0.22 NO
112 AXIN1 AXIN1 AXIN1 11595 -0.019 0.22 NO
113 PPP2CA PPP2CA PPP2CA 11807 -0.023 0.21 NO
114 CAMK2D CAMK2D CAMK2D 11825 -0.023 0.21 NO
115 TBL1X TBL1X TBL1X 12162 -0.029 0.2 NO
116 CSNK1A1 CSNK1A1 CSNK1A1 12165 -0.029 0.2 NO
117 PRKACA PRKACA PRKACA 12219 -0.03 0.19 NO
118 SMAD3 SMAD3 SMAD3 12248 -0.03 0.19 NO
119 WNT2B WNT2B WNT2B 12288 -0.031 0.19 NO
120 RBX1 RBX1 RBX1 12669 -0.038 0.17 NO
121 RUVBL1 RUVBL1 RUVBL1 12854 -0.042 0.17 NO
122 PPP2R5E PPP2R5E PPP2R5E 13001 -0.045 0.16 NO
123 MAPK9 MAPK9 MAPK9 13010 -0.045 0.16 NO
124 CACYBP CACYBP CACYBP 13077 -0.047 0.16 NO
125 VANGL1 VANGL1 VANGL1 13400 -0.054 0.14 NO
126 PLCB3 PLCB3 PLCB3 13669 -0.061 0.13 NO
127 RHOA RHOA RHOA 13768 -0.063 0.13 NO
128 PLCB1 PLCB1 PLCB1 14226 -0.076 0.11 NO
129 SOX17 SOX17 SOX17 14239 -0.076 0.11 NO
130 PPP3CC PPP3CC PPP3CC 14371 -0.08 0.11 NO
131 DAAM1 DAAM1 DAAM1 14382 -0.081 0.11 NO
132 PRKACB PRKACB PRKACB 14524 -0.085 0.11 NO
133 DKK1 DKK1 DKK1 14537 -0.086 0.11 NO
134 WNT2 WNT2 WNT2 14689 -0.091 0.1 NO
135 PORCN PORCN PORCN 14702 -0.091 0.11 NO
136 PLCB2 PLCB2 PLCB2 14904 -0.1 0.1 NO
137 ROCK1 ROCK1 ROCK1 14953 -0.1 0.1 NO
138 CAMK2G CAMK2G CAMK2G 15114 -0.11 0.1 NO
139 SFRP4 SFRP4 SFRP4 15378 -0.12 0.09 NO
140 PPP2R5A PPP2R5A PPP2R5A 15402 -0.12 0.095 NO
141 FOSL1 FOSL1 FOSL1 15808 -0.14 0.078 NO
142 CAMK2A CAMK2A CAMK2A 16218 -0.17 0.063 NO
143 WNT9B WNT9B WNT9B 16799 -0.22 0.041 NO
144 FZD6 FZD6 FZD6 16813 -0.22 0.05 NO
145 RAC2 RAC2 RAC2 17128 -0.26 0.045 NO
146 PRKCB PRKCB PRKCB 17318 -0.29 0.047 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 WNT PATHWAY.

Figure S44.  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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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 CCND2 CCND2 CCND2 97 0.62 0.043 YES
2 WIF1 WIF1 WIF1 187 0.55 0.08 YES
3 WNT5A WNT5A WNT5A 191 0.55 0.12 YES
4 CXXC4 CXXC4 CXXC4 334 0.49 0.15 YES
5 FZD2 FZD2 FZD2 490 0.45 0.18 YES
6 FZD3 FZD3 FZD3 500 0.44 0.21 YES
7 LEF1 LEF1 LEF1 646 0.41 0.24 YES
8 WNT11 WNT11 WNT11 688 0.4 0.26 YES
9 NKD1 NKD1 NKD1 710 0.39 0.29 YES
10 FZD8 FZD8 FZD8 861 0.37 0.31 YES
11 WNT4 WNT4 WNT4 1060 0.34 0.33 YES
12 LRP5 LRP5 LRP5 1136 0.33 0.35 YES
13 WNT6 WNT6 WNT6 1197 0.32 0.37 YES
14 TLE1 TLE1 TLE1 1241 0.31 0.39 YES
15 WNT5B WNT5B WNT5B 1526 0.28 0.4 YES
16 WNT7A WNT7A WNT7A 1564 0.28 0.42 YES
17 LRP6 LRP6 LRP6 1612 0.27 0.44 YES
18 CCND1 CCND1 CCND1 1616 0.27 0.46 YES
19 SFRP1 SFRP1 SFRP1 1714 0.26 0.47 YES
20 WNT7B WNT7B WNT7B 1744 0.26 0.49 YES
21 BCL9 BCL9 BCL9 1916 0.24 0.5 YES
22 FZD1 FZD1 FZD1 2068 0.23 0.51 YES
23 BTRC BTRC BTRC 2246 0.22 0.52 YES
24 PYGO1 PYGO1 PYGO1 2462 0.2 0.52 YES
25 RHOU RHOU RHOU 2647 0.19 0.53 YES
26 PITX2 PITX2 PITX2 2808 0.18 0.53 YES
27 FRZB FRZB FRZB 2852 0.18 0.54 YES
28 CTNNBIP1 CTNNBIP1 CTNNBIP1 3076 0.17 0.55 YES
29 TCF7L1 TCF7L1 TCF7L1 3300 0.16 0.55 YES
30 WNT3 WNT3 WNT3 3333 0.16 0.56 YES
31 WNT16 WNT16 WNT16 3868 0.13 0.54 NO
32 TLE2 TLE2 TLE2 3887 0.13 0.55 NO
33 FZD4 FZD4 FZD4 4114 0.12 0.54 NO
34 FZD7 FZD7 FZD7 4448 0.11 0.53 NO
35 CSNK2A1 CSNK2A1 CSNK2A1 4996 0.098 0.51 NO
36 SENP2 SENP2 SENP2 5079 0.095 0.51 NO
37 APC APC APC 5248 0.091 0.51 NO
38 CTBP2 CTBP2 CTBP2 5508 0.085 0.5 NO
39 WNT10A WNT10A WNT10A 5905 0.076 0.49 NO
40 RPL13A RPL13A RPL13A 5961 0.075 0.49 NO
41 WNT9A WNT9A WNT9A 6088 0.072 0.49 NO
42 DVL2 DVL2 DVL2 6382 0.066 0.48 NO
43 CTNNB1 CTNNB1 CTNNB1 6463 0.065 0.48 NO
44 EP300 EP300 EP300 6914 0.056 0.46 NO
45 DVL1 DVL1 DVL1 7590 0.044 0.42 NO
46 CTBP1 CTBP1 CTBP1 7673 0.043 0.42 NO
47 PPP2R1A PPP2R1A PPP2R1A 7734 0.042 0.42 NO
48 CSNK1D CSNK1D CSNK1D 7827 0.04 0.42 NO
49 JUN JUN JUN 7909 0.039 0.42 NO
50 FBXW11 FBXW11 FBXW11 8241 0.033 0.4 NO
51 CCND3 CCND3 CCND3 8364 0.031 0.4 NO
52 FBXW4 FBXW4 FBXW4 8677 0.026 0.38 NO
53 CSNK1G1 CSNK1G1 CSNK1G1 8766 0.025 0.38 NO
54 MYC MYC MYC 8791 0.025 0.38 NO
55 TCF7 TCF7 TCF7 9434 0.015 0.35 NO
56 WISP1 WISP1 WISP1 9512 0.014 0.34 NO
57 FZD5 FZD5 FZD5 9559 0.013 0.34 NO
58 WNT1 WNT1 WNT1 9814 0.0088 0.33 NO
59 NLK NLK NLK 10092 0.0046 0.31 NO
60 T T T 10499 -0.0016 0.29 NO
61 GSK3A GSK3A GSK3A 10514 -0.0018 0.29 NO
62 GSK3B GSK3B GSK3B 11019 -0.0096 0.26 NO
63 FBXW2 FBXW2 FBXW2 11114 -0.011 0.26 NO
64 FRAT1 FRAT1 FRAT1 11297 -0.014 0.25 NO
65 AXIN1 AXIN1 AXIN1 11595 -0.019 0.24 NO
66 PPP2CA PPP2CA PPP2CA 11807 -0.023 0.22 NO
67 CSNK1A1 CSNK1A1 CSNK1A1 12165 -0.029 0.21 NO
68 AES AES AES 12287 -0.031 0.2 NO
69 WNT2B WNT2B WNT2B 12288 -0.031 0.21 NO
70 KREMEN1 KREMEN1 KREMEN1 12666 -0.038 0.19 NO
71 GAPDH GAPDH GAPDH 13501 -0.056 0.15 NO
72 SLC9A3R1 SLC9A3R1 SLC9A3R1 13658 -0.06 0.14 NO
73 HPRT1 HPRT1 HPRT1 14052 -0.071 0.13 NO
74 SOX17 SOX17 SOX17 14239 -0.076 0.12 NO
75 DAAM1 DAAM1 DAAM1 14382 -0.081 0.12 NO
76 DKK1 DKK1 DKK1 14537 -0.086 0.12 NO
77 WNT2 WNT2 WNT2 14689 -0.091 0.12 NO
78 PORCN PORCN PORCN 14702 -0.091 0.12 NO
79 DIXDC1 DIXDC1 DIXDC1 14870 -0.098 0.12 NO
80 ACTB ACTB ACTB 15198 -0.11 0.11 NO
81 SFRP4 SFRP4 SFRP4 15378 -0.12 0.11 NO
82 FOSL1 FOSL1 FOSL1 15808 -0.14 0.098 NO
83 B2M B2M B2M 16510 -0.19 0.074 NO
84 FZD6 FZD6 FZD6 16813 -0.22 0.075 NO

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

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

genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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 APC2 APC2 APC2 101 0.62 0.046 YES
2 FZD10 FZD10 FZD10 111 0.61 0.096 YES
3 WNT5A WNT5A WNT5A 191 0.55 0.14 YES
4 HHIP HHIP HHIP 211 0.54 0.18 YES
5 SMO SMO SMO 215 0.54 0.22 YES
6 PTCH1 PTCH1 PTCH1 218 0.54 0.27 YES
7 FZD9 FZD9 FZD9 271 0.52 0.31 YES
8 BMP4 BMP4 BMP4 474 0.45 0.34 YES
9 FZD2 FZD2 FZD2 490 0.45 0.37 YES
10 FZD3 FZD3 FZD3 500 0.44 0.41 YES
11 LEF1 LEF1 LEF1 646 0.41 0.44 YES
12 WNT11 WNT11 WNT11 688 0.4 0.47 YES
13 GLI1 GLI1 GLI1 724 0.39 0.5 YES
14 FZD8 FZD8 FZD8 861 0.37 0.52 YES
15 GLI2 GLI2 GLI2 925 0.36 0.55 YES
16 WNT4 WNT4 WNT4 1060 0.34 0.57 YES
17 WNT6 WNT6 WNT6 1197 0.32 0.58 YES
18 BMP2 BMP2 BMP2 1480 0.29 0.59 YES
19 WNT5B WNT5B WNT5B 1526 0.28 0.61 YES
20 WNT7A WNT7A WNT7A 1564 0.28 0.64 YES
21 WNT7B WNT7B WNT7B 1744 0.26 0.65 YES
22 PTCH2 PTCH2 PTCH2 1885 0.25 0.66 YES
23 FZD1 FZD1 FZD1 2068 0.23 0.67 YES
24 TP53 TP53 TP53 2289 0.22 0.68 YES
25 SUFU SUFU SUFU 3240 0.16 0.64 NO
26 TCF7L1 TCF7L1 TCF7L1 3300 0.16 0.65 NO
27 WNT3 WNT3 WNT3 3333 0.16 0.66 NO
28 WNT16 WNT16 WNT16 3868 0.13 0.64 NO
29 FZD4 FZD4 FZD4 4114 0.12 0.64 NO
30 FZD7 FZD7 FZD7 4448 0.11 0.63 NO
31 TCF7L2 TCF7L2 TCF7L2 4451 0.11 0.64 NO
32 AXIN2 AXIN2 AXIN2 4653 0.11 0.63 NO
33 STK36 STK36 STK36 4753 0.1 0.64 NO
34 APC APC APC 5248 0.091 0.62 NO
35 GLI3 GLI3 GLI3 5834 0.077 0.59 NO
36 WNT10A WNT10A WNT10A 5905 0.076 0.59 NO
37 WNT9A WNT9A WNT9A 6088 0.072 0.59 NO
38 WNT10B WNT10B WNT10B 6327 0.067 0.58 NO
39 DVL2 DVL2 DVL2 6382 0.066 0.58 NO
40 CTNNB1 CTNNB1 CTNNB1 6463 0.065 0.59 NO
41 DVL1 DVL1 DVL1 7590 0.044 0.53 NO
42 WNT8B WNT8B WNT8B 8794 0.024 0.46 NO
43 DVL3 DVL3 DVL3 8859 0.024 0.46 NO
44 TCF7 TCF7 TCF7 9434 0.015 0.43 NO
45 FZD5 FZD5 FZD5 9559 0.013 0.42 NO
46 WNT1 WNT1 WNT1 9814 0.0088 0.41 NO
47 GSK3B GSK3B GSK3B 11019 -0.0096 0.35 NO
48 AXIN1 AXIN1 AXIN1 11595 -0.019 0.32 NO
49 WNT2B WNT2B WNT2B 12288 -0.031 0.28 NO
50 WNT2 WNT2 WNT2 14689 -0.091 0.16 NO
51 WNT9B WNT9B WNT9B 16799 -0.22 0.057 NO
52 FZD6 FZD6 FZD6 16813 -0.22 0.075 NO

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

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

genes ES table in pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

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 EFNB3 EFNB3 EFNB3 10 0.81 0.037 YES
2 EFNA2 EFNA2 EFNA2 12 0.8 0.074 YES
3 SEMA4G SEMA4G SEMA4G 38 0.7 0.1 YES
4 LRRC4C LRRC4C LRRC4C 112 0.61 0.13 YES
5 SEMA4F SEMA4F SEMA4F 160 0.57 0.15 YES
6 EPHB3 EPHB3 EPHB3 180 0.56 0.18 YES
7 SRGAP3 SRGAP3 SRGAP3 193 0.55 0.2 YES
8 SLIT1 SLIT1 SLIT1 207 0.54 0.23 YES
9 SEMA6D SEMA6D SEMA6D 276 0.52 0.25 YES
10 ROBO2 ROBO2 ROBO2 361 0.48 0.26 YES
11 SEMA6A SEMA6A SEMA6A 366 0.48 0.28 YES
12 EPHA3 EPHA3 EPHA3 580 0.42 0.29 YES
13 SEMA3A SEMA3A SEMA3A 764 0.38 0.3 YES
14 EFNA3 EFNA3 EFNA3 792 0.38 0.32 YES
15 NTN3 NTN3 NTN3 808 0.38 0.33 YES
16 RAC3 RAC3 RAC3 901 0.36 0.34 YES
17 EFNA4 EFNA4 EFNA4 1160 0.32 0.34 YES
18 DCC DCC DCC 1169 0.32 0.36 YES
19 EPHA8 EPHA8 EPHA8 1314 0.31 0.37 YES
20 SLIT2 SLIT2 SLIT2 1379 0.3 0.38 YES
21 UNC5B UNC5B UNC5B 1409 0.29 0.39 YES
22 EPHA2 EPHA2 EPHA2 1544 0.28 0.39 YES
23 SEMA7A SEMA7A SEMA7A 1561 0.28 0.41 YES
24 SEMA3D SEMA3D SEMA3D 1771 0.26 0.41 YES
25 SEMA6C SEMA6C SEMA6C 1825 0.25 0.42 YES
26 EPHB2 EPHB2 EPHB2 1852 0.25 0.42 YES
27 EPHA4 EPHA4 EPHA4 1963 0.24 0.43 YES
28 SEMA5B SEMA5B SEMA5B 2052 0.23 0.44 YES
29 EFNA1 EFNA1 EFNA1 2073 0.23 0.44 YES
30 NGEF NGEF NGEF 2080 0.23 0.46 YES
31 DPYSL5 DPYSL5 DPYSL5 2120 0.23 0.46 YES
32 NTN1 NTN1 NTN1 2308 0.21 0.46 YES
33 CHP2 CHP2 CHP2 2427 0.2 0.47 YES
34 PLXNA3 PLXNA3 PLXNA3 2431 0.2 0.48 YES
35 L1CAM L1CAM L1CAM 2579 0.2 0.48 YES
36 SLIT3 SLIT3 SLIT3 2615 0.19 0.48 YES
37 NTNG1 NTNG1 NTNG1 2788 0.18 0.48 YES
38 UNC5C UNC5C UNC5C 2798 0.18 0.49 YES
39 EFNB1 EFNB1 EFNB1 2907 0.18 0.49 YES
40 EPHB4 EPHB4 EPHB4 2938 0.18 0.5 YES
41 EPHA5 EPHA5 EPHA5 3016 0.17 0.5 YES
42 GNAI1 GNAI1 GNAI1 3051 0.17 0.51 YES
43 NFATC2 NFATC2 NFATC2 3281 0.16 0.5 YES
44 RND1 RND1 RND1 3297 0.16 0.51 YES
45 EFNB2 EFNB2 EFNB2 3341 0.16 0.51 YES
46 SEMA5A SEMA5A SEMA5A 3434 0.15 0.52 YES
47 SEMA3B SEMA3B SEMA3B 3508 0.15 0.52 YES
48 EPHB1 EPHB1 EPHB1 3591 0.14 0.52 YES
49 EPHA7 EPHA7 EPHA7 3719 0.14 0.52 YES
50 LIMK1 LIMK1 LIMK1 3838 0.13 0.52 YES
51 ROBO1 ROBO1 ROBO1 3910 0.13 0.52 YES
52 PAK7 PAK7 PAK7 4095 0.12 0.52 YES
53 NCK2 NCK2 NCK2 4097 0.12 0.52 YES
54 SEMA4C SEMA4C SEMA4C 4353 0.12 0.52 YES
55 NFATC4 NFATC4 NFATC4 4399 0.12 0.52 YES
56 ABLIM1 ABLIM1 ABLIM1 4488 0.11 0.52 YES
57 SEMA3F SEMA3F SEMA3F 4614 0.11 0.52 YES
58 UNC5A UNC5A UNC5A 4660 0.11 0.52 YES
59 PAK6 PAK6 PAK6 4775 0.1 0.52 YES
60 SEMA3E SEMA3E SEMA3E 4819 0.1 0.52 YES
61 EFNA5 EFNA5 EFNA5 4905 0.1 0.52 YES
62 NRAS NRAS NRAS 4933 0.1 0.52 YES
63 NFAT5 NFAT5 NFAT5 4988 0.098 0.52 YES
64 UNC5D UNC5D UNC5D 4990 0.098 0.53 YES
65 NFATC3 NFATC3 NFATC3 5169 0.093 0.52 YES
66 RASA1 RASA1 RASA1 5194 0.092 0.53 YES
67 PPP3CA PPP3CA PPP3CA 5218 0.092 0.53 YES
68 PLXNB2 PLXNB2 PLXNB2 5293 0.089 0.53 YES
69 KRAS KRAS KRAS 5307 0.089 0.53 YES
70 RGS3 RGS3 RGS3 5467 0.086 0.53 NO
71 PPP3CB PPP3CB PPP3CB 5637 0.081 0.52 NO
72 MET MET MET 5776 0.078 0.52 NO
73 SRGAP2 SRGAP2 SRGAP2 5947 0.075 0.51 NO
74 NFATC1 NFATC1 NFATC1 5979 0.074 0.51 NO
75 PAK4 PAK4 PAK4 6838 0.058 0.47 NO
76 PTK2 PTK2 PTK2 7512 0.046 0.43 NO
77 SEMA6B SEMA6B SEMA6B 7682 0.042 0.43 NO
78 PLXNA1 PLXNA1 PLXNA1 7738 0.042 0.42 NO
79 RHOD RHOD RHOD 7765 0.041 0.42 NO
80 PPP3R1 PPP3R1 PPP3R1 7994 0.037 0.41 NO
81 CDK5 CDK5 CDK5 8201 0.034 0.4 NO
82 CXCR4 CXCR4 CXCR4 8327 0.032 0.4 NO
83 SRGAP1 SRGAP1 SRGAP1 8440 0.03 0.39 NO
84 PLXNA2 PLXNA2 PLXNA2 9229 0.018 0.35 NO
85 ROBO3 ROBO3 ROBO3 9236 0.018 0.35 NO
86 ARHGEF12 ARHGEF12 ARHGEF12 9275 0.017 0.35 NO
87 ROCK2 ROCK2 ROCK2 9338 0.016 0.35 NO
88 SEMA4D SEMA4D SEMA4D 9709 0.01 0.33 NO
89 GNAI3 GNAI3 GNAI3 9853 0.0082 0.32 NO
90 CXCL12 CXCL12 CXCL12 10532 -0.002 0.28 NO
91 CHP CHP CHP 10714 -0.0048 0.27 NO
92 NRP1 NRP1 NRP1 10996 -0.0092 0.26 NO
93 GSK3B GSK3B GSK3B 11019 -0.0096 0.26 NO
94 ABL1 ABL1 ABL1 11071 -0.01 0.26 NO
95 RAC1 RAC1 RAC1 11146 -0.012 0.25 NO
96 PPP3R2 PPP3R2 PPP3R2 11161 -0.012 0.25 NO
97 CDC42 CDC42 CDC42 11395 -0.016 0.24 NO
98 PAK2 PAK2 PAK2 11727 -0.021 0.22 NO
99 PLXNC1 PLXNC1 PLXNC1 11884 -0.024 0.21 NO
100 PAK3 PAK3 PAK3 12026 -0.026 0.21 NO
101 MAPK1 MAPK1 MAPK1 12177 -0.029 0.2 NO
102 LIMK2 LIMK2 LIMK2 12305 -0.031 0.2 NO
103 EPHA6 EPHA6 EPHA6 12323 -0.032 0.2 NO
104 MAPK3 MAPK3 MAPK3 12476 -0.035 0.19 NO
105 DPYSL2 DPYSL2 DPYSL2 12488 -0.035 0.19 NO
106 EPHB6 EPHB6 EPHB6 13043 -0.046 0.16 NO
107 PAK1 PAK1 PAK1 13140 -0.048 0.16 NO
108 CFL1 CFL1 CFL1 13325 -0.052 0.15 NO
109 PLXNB1 PLXNB1 PLXNB1 13571 -0.058 0.14 NO
110 FYN FYN FYN 13620 -0.059 0.14 NO
111 RHOA RHOA RHOA 13768 -0.063 0.13 NO
112 PLXNB3 PLXNB3 PLXNB3 13978 -0.069 0.12 NO
113 ITGB1 ITGB1 ITGB1 13998 -0.069 0.13 NO
114 NCK1 NCK1 NCK1 14120 -0.073 0.12 NO
115 GNAI2 GNAI2 GNAI2 14164 -0.074 0.12 NO
116 SEMA4B SEMA4B SEMA4B 14276 -0.078 0.12 NO
117 PPP3CC PPP3CC PPP3CC 14371 -0.08 0.12 NO
118 ROCK1 ROCK1 ROCK1 14953 -0.1 0.094 NO
119 NTN4 NTN4 NTN4 15442 -0.12 0.072 NO
120 ABLIM2 ABLIM2 ABLIM2 15517 -0.13 0.074 NO
121 SEMA3G SEMA3G SEMA3G 15671 -0.13 0.072 NO
122 EPHA1 EPHA1 EPHA1 15713 -0.14 0.076 NO
123 FES FES FES 16178 -0.17 0.058 NO
124 SEMA3C SEMA3C SEMA3C 16206 -0.17 0.064 NO
125 ABLIM3 ABLIM3 ABLIM3 16614 -0.2 0.05 NO
126 SEMA4A SEMA4A SEMA4A 16687 -0.21 0.056 NO
127 RAC2 RAC2 RAC2 17128 -0.26 0.044 NO
128 CFL2 CFL2 CFL2 17411 -0.3 0.042 NO

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

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

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

Table 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 HS3ST3B1 HS3ST3B1 HS3ST3B1 629 0.41 0.056 YES
2 EXTL1 EXTL1 EXTL1 674 0.4 0.14 YES
3 HS6ST2 HS6ST2 HS6ST2 760 0.38 0.22 YES
4 NDST3 NDST3 NDST3 782 0.38 0.3 YES
5 HS3ST3A1 HS3ST3A1 HS3ST3A1 908 0.36 0.38 YES
6 HS3ST5 HS3ST5 HS3ST5 1195 0.32 0.43 YES
7 B3GAT1 B3GAT1 B3GAT1 1362 0.3 0.49 YES
8 NDST4 NDST4 NDST4 1594 0.28 0.54 YES
9 GLCE GLCE GLCE 1882 0.25 0.58 YES
10 EXTL2 EXTL2 EXTL2 2211 0.22 0.61 YES
11 B3GALT6 B3GALT6 B3GALT6 3155 0.16 0.59 YES
12 HS6ST1 HS6ST1 HS6ST1 3448 0.15 0.61 YES
13 XYLT2 XYLT2 XYLT2 4725 0.11 0.56 NO
14 EXT2 EXT2 EXT2 5340 0.089 0.55 NO
15 NDST1 NDST1 NDST1 5727 0.08 0.54 NO
16 HS3ST1 HS3ST1 HS3ST1 6885 0.057 0.49 NO
17 NDST2 NDST2 NDST2 7114 0.053 0.49 NO
18 B4GALT7 B4GALT7 B4GALT7 7284 0.05 0.49 NO
19 B3GAT3 B3GAT3 B3GAT3 8947 0.022 0.41 NO
20 HS2ST1 HS2ST1 HS2ST1 9572 0.012 0.37 NO
21 EXT1 EXT1 EXT1 11296 -0.014 0.28 NO
22 HS6ST3 HS6ST3 HS6ST3 12702 -0.039 0.21 NO
23 B3GAT2 B3GAT2 B3GAT2 12944 -0.044 0.21 NO
24 XYLT1 XYLT1 XYLT1 15051 -0.1 0.12 NO
25 HS3ST2 HS3ST2 HS3ST2 17067 -0.25 0.061 NO

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

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

genes ES table in pathway: KEGG P53 SIGNALING PATHWAY

Table S27.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BMP7 BMP7 BMP7 140 0.58 0.044 YES
2 WNT5A WNT5A WNT5A 191 0.55 0.09 YES
3 HHIP HHIP HHIP 211 0.54 0.14 YES
4 SMO SMO SMO 215 0.54 0.18 YES
5 PTCH1 PTCH1 PTCH1 218 0.54 0.23 YES
6 BMP5 BMP5 BMP5 221 0.54 0.28 YES
7 ZIC2 ZIC2 ZIC2 396 0.48 0.31 YES
8 BMP4 BMP4 BMP4 474 0.45 0.35 YES
9 WNT11 WNT11 WNT11 688 0.4 0.37 YES
10 GLI1 GLI1 GLI1 724 0.39 0.41 YES
11 GLI2 GLI2 GLI2 925 0.36 0.43 YES
12 WNT4 WNT4 WNT4 1060 0.34 0.45 YES
13 LRP2 LRP2 LRP2 1168 0.32 0.47 YES
14 WNT6 WNT6 WNT6 1197 0.32 0.5 YES
15 BMP2 BMP2 BMP2 1480 0.29 0.51 YES
16 IHH IHH IHH 1505 0.28 0.53 YES
17 WNT5B WNT5B WNT5B 1526 0.28 0.56 YES
18 WNT7A WNT7A WNT7A 1564 0.28 0.58 YES
19 BMP6 BMP6 BMP6 1705 0.26 0.6 YES
20 WNT7B WNT7B WNT7B 1744 0.26 0.62 YES
21 PTCH2 PTCH2 PTCH2 1885 0.25 0.63 YES
22 BTRC BTRC BTRC 2246 0.22 0.63 NO
23 BMP8A BMP8A BMP8A 2822 0.18 0.61 NO
24 SUFU SUFU SUFU 3240 0.16 0.61 NO
25 WNT3 WNT3 WNT3 3333 0.16 0.61 NO
26 WNT16 WNT16 WNT16 3868 0.13 0.6 NO
27 STK36 STK36 STK36 4753 0.1 0.56 NO
28 CSNK1G3 CSNK1G3 CSNK1G3 4879 0.1 0.56 NO
29 BMP8B BMP8B BMP8B 5204 0.092 0.55 NO
30 PRKX PRKX PRKX 5224 0.091 0.56 NO
31 CSNK1G2 CSNK1G2 CSNK1G2 5258 0.09 0.56 NO
32 DHH DHH DHH 5710 0.08 0.55 NO
33 GLI3 GLI3 GLI3 5834 0.077 0.55 NO
34 WNT10A WNT10A WNT10A 5905 0.076 0.55 NO
35 CSNK1E CSNK1E CSNK1E 5907 0.076 0.56 NO
36 WNT9A WNT9A WNT9A 6088 0.072 0.55 NO
37 WNT10B WNT10B WNT10B 6327 0.067 0.54 NO
38 CSNK1D CSNK1D CSNK1D 7827 0.04 0.46 NO
39 FBXW11 FBXW11 FBXW11 8241 0.033 0.44 NO
40 CSNK1G1 CSNK1G1 CSNK1G1 8766 0.025 0.42 NO
41 WNT8B WNT8B WNT8B 8794 0.024 0.42 NO
42 CSNK1A1L CSNK1A1L CSNK1A1L 9058 0.021 0.41 NO
43 PRKACG PRKACG PRKACG 9099 0.02 0.41 NO
44 WNT1 WNT1 WNT1 9814 0.0088 0.37 NO
45 GSK3B GSK3B GSK3B 11019 -0.0096 0.3 NO
46 CSNK1A1 CSNK1A1 CSNK1A1 12165 -0.029 0.24 NO
47 PRKACA PRKACA PRKACA 12219 -0.03 0.24 NO
48 WNT2B WNT2B WNT2B 12288 -0.031 0.24 NO
49 PRKACB PRKACB PRKACB 14524 -0.085 0.12 NO
50 WNT2 WNT2 WNT2 14689 -0.091 0.12 NO
51 GAS1 GAS1 GAS1 15347 -0.12 0.097 NO
52 WNT9B WNT9B WNT9B 16799 -0.22 0.037 NO
53 RAB23 RAB23 RAB23 17978 -0.44 0.01 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 P53 SIGNALING PATHWAY.

Figure S54.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG P53 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 ENDOCYTOSIS

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 BMP7 BMP7 BMP7 140 0.58 0.093 YES
2 BMP5 BMP5 BMP5 221 0.54 0.18 YES
3 BMP4 BMP4 BMP4 474 0.45 0.24 YES
4 GATA4 GATA4 GATA4 486 0.45 0.32 YES
5 SMAD6 SMAD6 SMAD6 727 0.39 0.38 YES
6 TGFB2 TGFB2 TGFB2 731 0.39 0.44 YES
7 NOG NOG NOG 951 0.36 0.49 YES
8 BMP2 BMP2 BMP2 1480 0.29 0.51 YES
9 HNF1A HNF1A HNF1A 1712 0.26 0.54 YES
10 FZD1 FZD1 FZD1 2068 0.23 0.56 YES
11 SMAD1 SMAD1 SMAD1 3758 0.14 0.5 NO
12 ATF2 ATF2 ATF2 4000 0.13 0.5 NO
13 CHRD CHRD CHRD 4126 0.12 0.52 NO
14 SMAD5 SMAD5 SMAD5 4444 0.11 0.52 NO
15 BMPR2 BMPR2 BMPR2 5234 0.091 0.49 NO
16 APC APC APC 5248 0.091 0.51 NO
17 TGFB3 TGFB3 TGFB3 5333 0.089 0.52 NO
18 NKX2-5 NKX2-5 NKX2-5 5652 0.081 0.52 NO
19 BMPR1A BMPR1A BMPR1A 5893 0.076 0.52 NO
20 MAP3K7 MAP3K7 MAP3K7 5929 0.075 0.53 NO
21 NPPB NPPB NPPB 6205 0.07 0.52 NO
22 CTNNB1 CTNNB1 CTNNB1 6463 0.065 0.52 NO
23 DVL1 DVL1 DVL1 7590 0.044 0.46 NO
24 RFC1 RFC1 RFC1 8451 0.03 0.42 NO
25 WNT1 WNT1 WNT1 9814 0.0088 0.35 NO
26 SMAD4 SMAD4 SMAD4 10148 0.0038 0.33 NO
27 TGFBR1 TGFBR1 TGFBR1 10302 0.0014 0.32 NO
28 GSK3B GSK3B GSK3B 11019 -0.0096 0.29 NO
29 ACVR1 ACVR1 ACVR1 11439 -0.016 0.26 NO
30 AXIN1 AXIN1 AXIN1 11595 -0.019 0.26 NO
31 MYL2 MYL2 MYL2 13147 -0.048 0.18 NO
32 TGFBR2 TGFBR2 TGFBR2 15022 -0.1 0.098 NO
33 TGFB1 TGFB1 TGFB1 15532 -0.13 0.091 NO
34 TGFBR3 TGFBR3 TGFBR3 16035 -0.16 0.09 NO
35 NPPA NPPA NPPA 16063 -0.16 0.12 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 ENDOCYTOSIS.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ENDOCYTOSIS, 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 WNT SIGNALING PATHWAY

Table S29.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GRM4 GRM4 GRM4 4 0.89 0.14 YES
2 ACCN1 ACCN1 ACCN1 172 0.56 0.22 YES
3 TRPM5 TRPM5 TRPM5 576 0.42 0.27 YES
4 CACNA1B CACNA1B CACNA1B 823 0.37 0.31 YES
5 TAS2R19 TAS2R19 TAS2R19 1044 0.34 0.35 YES
6 TAS2R5 TAS2R5 TAS2R5 1372 0.3 0.38 YES
7 TAS2R10 TAS2R10 TAS2R10 1684 0.27 0.41 YES
8 TAS2R4 TAS2R4 TAS2R4 1941 0.24 0.43 YES
9 CACNA1A CACNA1A CACNA1A 2005 0.24 0.47 YES
10 SCNN1G SCNN1G SCNN1G 2019 0.24 0.5 YES
11 TAS2R31 TAS2R31 TAS2R31 2143 0.23 0.53 YES
12 TAS1R3 TAS1R3 TAS1R3 2465 0.2 0.55 YES
13 TAS2R14 TAS2R14 TAS2R14 2480 0.2 0.58 YES
14 TAS2R13 TAS2R13 TAS2R13 2528 0.2 0.61 YES
15 ADCY6 ADCY6 ADCY6 3073 0.17 0.6 YES
16 TAS1R1 TAS1R1 TAS1R1 3378 0.15 0.61 YES
17 GNB3 GNB3 GNB3 3536 0.15 0.63 YES
18 GNG3 GNG3 GNG3 4116 0.12 0.61 NO
19 TAS2R20 TAS2R20 TAS2R20 4380 0.12 0.62 NO
20 TAS2R46 TAS2R46 TAS2R46 5172 0.093 0.59 NO
21 PRKX PRKX PRKX 5224 0.091 0.6 NO
22 GNAS GNAS GNAS 5624 0.082 0.59 NO
23 TAS2R43 TAS2R43 TAS2R43 7958 0.038 0.47 NO
24 GNB1 GNB1 GNB1 8609 0.027 0.44 NO
25 PRKACG PRKACG PRKACG 9099 0.02 0.41 NO
26 ADCY4 ADCY4 ADCY4 9976 0.0064 0.37 NO
27 SCNN1A SCNN1A SCNN1A 10413 -3e-05 0.34 NO
28 ITPR3 ITPR3 ITPR3 10856 -0.0072 0.32 NO
29 SCNN1B SCNN1B SCNN1B 11975 -0.026 0.26 NO
30 PRKACA PRKACA PRKACA 12219 -0.03 0.25 NO
31 KCNB1 KCNB1 KCNB1 12901 -0.043 0.22 NO
32 PRKACB PRKACB PRKACB 14524 -0.085 0.15 NO
33 PLCB2 PLCB2 PLCB2 14904 -0.1 0.14 NO
34 ADCY8 ADCY8 ADCY8 15125 -0.11 0.15 NO
35 PDE1A PDE1A PDE1A 15675 -0.13 0.14 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 WNT SIGNALING PATHWAY.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG WNT 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 NOTCH 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 BMP7 BMP7 BMP7 140 0.58 0.043 YES
2 BMP5 BMP5 BMP5 221 0.54 0.084 YES
3 E2F5 E2F5 E2F5 231 0.53 0.13 YES
4 GDF7 GDF7 GDF7 408 0.47 0.16 YES
5 BMP4 BMP4 BMP4 474 0.45 0.2 YES
6 SMAD9 SMAD9 SMAD9 553 0.43 0.23 YES
7 ID1 ID1 ID1 578 0.42 0.26 YES
8 SMAD6 SMAD6 SMAD6 727 0.39 0.29 YES
9 TGFB2 TGFB2 TGFB2 731 0.39 0.32 YES
10 ID3 ID3 ID3 1403 0.3 0.31 YES
11 BMP2 BMP2 BMP2 1480 0.29 0.33 YES
12 COMP COMP COMP 1522 0.28 0.35 YES
13 BMP6 BMP6 BMP6 1705 0.26 0.37 YES
14 INHBC INHBC INHBC 1854 0.25 0.38 YES
15 GDF6 GDF6 GDF6 1906 0.25 0.4 YES
16 THBS4 THBS4 THBS4 2773 0.18 0.37 YES
17 PITX2 PITX2 PITX2 2808 0.18 0.38 YES
18 BMP8A BMP8A BMP8A 2822 0.18 0.39 YES
19 ZFYVE9 ZFYVE9 ZFYVE9 2848 0.18 0.41 YES
20 NODAL NODAL NODAL 3156 0.16 0.41 YES
21 INHBE INHBE INHBE 3157 0.16 0.42 YES
22 INHBB INHBB INHBB 3311 0.16 0.42 YES
23 SMAD7 SMAD7 SMAD7 3714 0.14 0.42 YES
24 SMAD1 SMAD1 SMAD1 3758 0.14 0.42 YES
25 ACVR2A ACVR2A ACVR2A 3781 0.14 0.43 YES
26 CHRD CHRD CHRD 4126 0.12 0.43 YES
27 ACVR2B ACVR2B ACVR2B 4343 0.12 0.42 YES
28 SMAD5 SMAD5 SMAD5 4444 0.11 0.43 YES
29 AMH AMH AMH 4457 0.11 0.44 YES
30 ZFYVE16 ZFYVE16 ZFYVE16 4691 0.11 0.43 YES
31 INHBA INHBA INHBA 4899 0.1 0.43 YES
32 BMP8B BMP8B BMP8B 5204 0.092 0.42 YES
33 BMPR2 BMPR2 BMPR2 5234 0.091 0.43 YES
34 TGFB3 TGFB3 TGFB3 5333 0.089 0.43 YES
35 ID2 ID2 ID2 5358 0.088 0.44 YES
36 ID4 ID4 ID4 5396 0.088 0.44 YES
37 BMPR1B BMPR1B BMPR1B 5501 0.085 0.44 YES
38 AMHR2 AMHR2 AMHR2 5703 0.08 0.44 NO
39 PPP2R1B PPP2R1B PPP2R1B 5766 0.079 0.44 NO
40 BMPR1A BMPR1A BMPR1A 5893 0.076 0.44 NO
41 RPS6KB1 RPS6KB1 RPS6KB1 6368 0.066 0.42 NO
42 THBS3 THBS3 THBS3 6476 0.064 0.42 NO
43 RBL2 RBL2 RBL2 6777 0.059 0.41 NO
44 EP300 EP300 EP300 6914 0.056 0.41 NO
45 LEFTY2 LEFTY2 LEFTY2 7012 0.054 0.41 NO
46 DCN DCN DCN 7542 0.045 0.38 NO
47 PPP2R1A PPP2R1A PPP2R1A 7734 0.042 0.38 NO
48 CREBBP CREBBP CREBBP 8008 0.036 0.36 NO
49 SP1 SP1 SP1 8356 0.031 0.35 NO
50 GDF5 GDF5 GDF5 8482 0.029 0.34 NO
51 SMAD2 SMAD2 SMAD2 8613 0.027 0.34 NO
52 MYC MYC MYC 8791 0.025 0.33 NO
53 SMURF1 SMURF1 SMURF1 9133 0.02 0.31 NO
54 E2F4 E2F4 E2F4 9165 0.019 0.31 NO
55 ROCK2 ROCK2 ROCK2 9338 0.016 0.3 NO
56 SMURF2 SMURF2 SMURF2 10072 0.005 0.26 NO
57 SMAD4 SMAD4 SMAD4 10148 0.0038 0.26 NO
58 TGFBR1 TGFBR1 TGFBR1 10302 0.0014 0.25 NO
59 SKP1 SKP1 SKP1 10465 -0.00083 0.24 NO
60 FST FST FST 10805 -0.0065 0.22 NO
61 PPP2CB PPP2CB PPP2CB 10813 -0.0067 0.22 NO
62 LEFTY1 LEFTY1 LEFTY1 11045 -0.0099 0.21 NO
63 ACVR1 ACVR1 ACVR1 11439 -0.016 0.19 NO
64 CUL1 CUL1 CUL1 11546 -0.018 0.19 NO
65 PPP2CA PPP2CA PPP2CA 11807 -0.023 0.18 NO
66 RPS6KB2 RPS6KB2 RPS6KB2 12071 -0.027 0.16 NO
67 MAPK1 MAPK1 MAPK1 12177 -0.029 0.16 NO
68 SMAD3 SMAD3 SMAD3 12248 -0.03 0.16 NO
69 TFDP1 TFDP1 TFDP1 12416 -0.034 0.15 NO
70 MAPK3 MAPK3 MAPK3 12476 -0.035 0.15 NO
71 RBX1 RBX1 RBX1 12669 -0.038 0.14 NO
72 ACVR1C ACVR1C ACVR1C 13041 -0.046 0.13 NO
73 THBS1 THBS1 THBS1 13316 -0.052 0.12 NO
74 ACVRL1 ACVRL1 ACVRL1 13650 -0.06 0.1 NO
75 RBL1 RBL1 RBL1 13745 -0.062 0.1 NO
76 RHOA RHOA RHOA 13768 -0.063 0.11 NO
77 ROCK1 ROCK1 ROCK1 14953 -0.1 0.052 NO
78 TGFBR2 TGFBR2 TGFBR2 15022 -0.1 0.058 NO
79 LTBP1 LTBP1 LTBP1 15194 -0.11 0.058 NO
80 TGFB1 TGFB1 TGFB1 15532 -0.13 0.05 NO
81 THBS2 THBS2 THBS2 16156 -0.16 0.03 NO
82 TNF TNF TNF 17223 -0.27 -0.0059 NO
83 CDKN2B CDKN2B CDKN2B 17388 -0.3 0.011 NO
84 IFNG IFNG IFNG 17787 -0.37 0.021 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 NOTCH SIGNALING PATHWAY.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOTCH 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 = SARC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

GSEA analysis

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

Download Results

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

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