Breast Invasive Carcinoma: Mutation Analysis (MutSig)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig v1.5 was used to generate the results found in this report.

Working with individual set: BRCA.

Number of patients in set: 507

Input

The input for this pipeline is a set of individuals with the following files associated for each:

1. An annotated .maf file describing the mutations called for the respective individual, and their properties.

2. A .wig file that contains information about the coverage of the sample.

Summary

Significantly mutated genes (q ≤ 0.1): 71

Mutations seen in COSMIC: 0

Significantly mutated genes in COSMIC territory: 0

Genes with clustered mutations (&le 3 aa apart): 2

Significantly mutated genesets: 210

Significantly mutated genesets: (excluding sig. mutated genes): 16

Results
Breakdown of Mutations by Type

Table 1.  Get Full Table Table representing breakdown of mutations by type.

type count
Frame_Shift_Del 951
Frame_Shift_Ins 313
In_Frame_Del 377
In_Frame_Ins 71
Indel 86
Missense_Mutation 13573
Nonsense_Mutation 965
Nonstop_Mutation 23
Silent 4910
Splice_Site 444
Total 21713
Breakdown of Mutation Rates by Category Type

Table 2.  Get Full Table A breakdown of mutation rates per category discovered for this individual set.

category n N rate rate_per_mb relative_rate
A->T 3221 7065210282 4.6e-07 0.46 0.38
C->(A/T) 4896 7052709183 6.9e-07 0.69 0.58
A->(C/G) 3991 7065210282 5.6e-07 0.56 0.47
C->G 1465 7052709183 2.1e-07 0.21 0.17
indel+null 3077 14117919972 2.2e-07 0.22 0.18
double_null 153 14117919972 1.1e-08 0.011 0.0091
Total 16803 14117919972 1.2e-06 1.2 1
Target Coverage for Each Individual

The x axis represents the samples. The y axis represents the exons, one row per exon, and they are sorted by average coverage across samples. For exons with exactly the same average coverage, they are sorted next by the %GC of the exon. (The secondary sort is especially useful for the zero-coverage exons at the bottom).

Figure 1. 

Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

Figure 2. 

Significantly Mutated Genes

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 71. Number of genes displayed: 35

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 1666509 168 158 29 3 54 17 88 1 8 0 <1.00e-15 <8.64e-12
2 TP53 tumor protein p53 664677 142 139 94 3 15 33 18 7 69 0 <1.00e-15 <8.64e-12
3 MAP3K1 mitogen-activated protein kinase kinase kinase 1 2095431 53 36 52 1 1 1 1 0 22 28 1.45e-14 5.25e-11
4 MLL3 myeloid/lymphoid or mixed-lineage leukemia 3 7507149 30 29 30 2 4 1 3 0 20 2 1.45e-14 5.25e-11
5 GATA3 GATA binding protein 3 562770 55 53 32 1 1 1 0 0 51 2 1.52e-14 5.25e-11
6 CDH1 cadherin 1, type 1, E-cadherin (epithelial) 1288794 31 31 29 0 0 4 0 0 27 0 1.89e-14 5.43e-11
7 MAP2K4 mitogen-activated protein kinase kinase 4 570375 18 18 17 0 4 0 2 0 12 0 5.94e-14 1.13e-10
8 TBX3 T-box 3 (ulnar mammary syndrome) 601302 11 11 11 0 0 0 1 0 10 0 6.42e-14 1.13e-10
9 RUNX1 runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) 373659 14 14 13 1 0 0 3 0 11 0 6.91e-14 1.13e-10
10 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 632736 15 14 15 0 0 0 3 0 10 2 6.99e-14 1.13e-10
11 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 1199055 14 14 13 1 1 2 1 1 9 0 7.23e-14 1.13e-10
12 AKT1 v-akt murine thymoma viral oncogene homolog 1 732108 12 12 2 1 0 11 1 0 0 0 7.93e-12 1.14e-08
13 CTCF CCCTC-binding factor (zinc finger protein) 1127568 11 11 10 2 1 1 3 0 6 0 8.11e-11 1.08e-07
14 NCOR1 nuclear receptor co-repressor 1 3741153 16 15 16 0 0 0 2 0 12 2 8.20e-10 1.01e-06
15 RPGR retinitis pigmentosa GTPase regulator 1546350 10 10 10 0 1 3 0 0 6 0 8.59e-08 0.000099
16 RB1 retinoblastoma 1 (including osteosarcoma) 1396278 9 9 9 0 0 0 1 0 8 0 2.57e-07 0.00028
17 CBFB core-binding factor, beta subunit 226122 5 5 5 1 2 0 1 0 2 0 3.67e-07 0.00037
18 ZFP36L1 zinc finger protein 36, C3H type-like 1 519675 6 6 6 0 0 0 2 0 4 0 4.04e-07 0.00039
19 CDKN1B cyclin-dependent kinase inhibitor 1B (p27, Kip1) 276315 5 5 4 0 0 0 0 0 5 0 4.33e-07 0.00039
20 FOXA1 forkhead box A1 490269 7 7 6 0 1 3 2 0 1 0 4.72e-07 0.00041
21 PRRX1 paired related homeobox 1 287976 5 5 5 0 1 2 1 0 1 0 4.09e-06 0.0034
22 MUC4 mucin 4, cell surface associated 2554266 16 13 16 9 5 5 3 3 0 0 4.78e-06 0.0038
23 AFF2 AF4/FMR2 family, member 2 2015325 11 11 11 1 1 5 1 1 3 0 7.93e-06 0.0060
24 DSPP dentin sialophosphoprotein 852774 7 6 7 0 3 1 0 0 3 0 9.29e-06 0.0067
25 ATN1 atrophin 1 1634568 8 8 6 0 0 4 0 0 4 0 0.000011 0.0077
26 MYB v-myb myeloblastosis viral oncogene homolog (avian) 1177761 7 7 7 0 0 2 0 1 4 0 0.000014 0.0096
27 GPS2 G protein pathway suppressor 2 469482 5 5 5 1 0 0 0 0 5 0 0.000022 0.014
28 DALRD3 DALR anticodon binding domain containing 3 596739 6 6 6 0 0 2 1 0 3 0 0.000022 0.014
29 SF3B1 splicing factor 3b, subunit 1, 155kDa 2047773 10 10 6 0 0 2 7 0 1 0 0.000032 0.017
30 NKAIN4 Na+/K+ transporting ATPase interacting 4 104949 3 3 3 1 0 1 1 1 0 0 0.000032 0.017
31 PIWIL1 piwi-like 1 (Drosophila) 1351662 8 8 8 1 2 3 2 0 1 0 0.000032 0.017
32 FAM166A 236769 4 4 4 0 0 1 0 0 3 0 0.000032 0.017
33 SAAL1 serum amyloid A-like 1 676338 5 5 5 0 0 1 0 0 4 0 0.000039 0.020
34 TMEM82 transmembrane protein 82 161733 4 4 4 0 1 1 1 0 1 0 0.000043 0.022
35 HIST1H2BC histone cluster 1, H2bc 195195 4 4 4 1 0 2 1 0 1 0 0.000049 0.023

Note:

N - number of sequenced bases in this gene across the individual set.

n - number of (nonsilent) mutations in this gene across the individual set.

npat - number of patients (individuals) with at least one nonsilent mutation.

nsite - number of unique sites having a non-silent mutation.

nsil - number of silent mutations in this gene across the individual set.

n1 - number of nonsilent mutations of type: A->T .

n2 - number of nonsilent mutations of type: C->(A/T) .

n3 - number of nonsilent mutations of type: A->(C/G) .

n4 - number of nonsilent mutations of type: C->G .

n5 - number of nonsilent mutations of type: indel+null .

null - mutation category that includes nonsense, frameshift, splice-site mutations

p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene

p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene

p = p-value (overall)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

COSMIC analyses

In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.

Table 4.  Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 0. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 A4GNT alpha-1,4-N-acetylglucosaminyltransferase 0 0 0 0 0 1 1
2 AACS acetoacetyl-CoA synthetase 0 0 0 0 0 1 1
3 ABCA9 ATP-binding cassette, sub-family A (ABC1), member 9 3 0 0 0 0 1 1
4 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 2 0 0 0 0 1 1
5 ABCF2 ATP-binding cassette, sub-family F (GCN20), member 2 3 0 0 0 0 1 1
6 ABHD2 abhydrolase domain containing 2 2 0 0 0 0 1 1
7 ABHD4 abhydrolase domain containing 4 0 0 0 0 0 1 1
8 ACADS acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain 0 0 0 0 0 1 1
9 ACOT11 acyl-CoA thioesterase 11 2 0 0 0 0 1 1
10 ACRBP acrosin binding protein 1 0 0 0 0 1 1

Note:

n - number of (nonsilent) mutations in this gene across the individual set.

cos = number of unique mutated sites in this gene in COSMIC

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene.

p = p-value for seeing the observed amount of overlap in this gene)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Clustered Mutations

Table 5.  Get Full Table Genes with Clustered Mutations

num gene desc n mindist npairs3 npairs12
2757 FER1L6 fer-1-like 6 (C. elegans) 2 0 1 1
1917 CYP11B2 cytochrome P450, family 11, subfamily B, polypeptide 2 3 2 1 1
18 ABCA13 ATP-binding cassette, sub-family A (ABC1), member 13 13 30 0 0
4758 MXRA5 matrix-remodelling associated 5 5 42 0 0
7739 TRANK1 3 139 0 0
7552 TLN1 talin 1 7 220 0 0
6611 SEC31B SEC31 homolog B (S. cerevisiae) 5 263 0 0
4747 MUC6 mucin 6, oligomeric mucus/gel-forming 4 301 0 0
2 A2BP1 3 Inf 0 0
3 A2M alpha-2-macroglobulin 3 Inf 0 0

Note:

n - number of mutations in this gene in the individual set.

mindist - distance (in aa) between closest pair of mutations in this gene

npairs3 - how many pairs of mutations are within 3 aa of each other.

npairs12 - how many pairs of mutations are within 12 aa of each other.

Geneset Analyses

Table 6.  Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 210. Number of genesets displayed: 10

rank geneset description genes N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 HSA04510_FOCAL_ADHESION Genes involved in focal adhesion ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, ARHGAP5, BAD, BCAR1, BCL2, BIRC2, BIRC3, BIRC4, BRAF, CAPN2, CAV1, CAV2, CAV3, CCND1, CCND2, CCND3, CDC42, CHAD, COL11A1, COL11A2, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, CRK, CRKL, CTNNB1, DIAPH1, DOCK1, EGF, EGFR, ELK1, ERBB2, FARP2, FIGF, FLNA, FLNB, FLNC, FLT1, FN1, FYN, GRB2, GRLF1, GSK3B, HGF, HRAS, IBSP, IGF1, IGF1R, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAV, ITGB1, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, JUN, KDR, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LOC653852, MAP2K1, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MET, MLCK, MRCL3, MRLC2, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PARVA, PARVB, PARVG, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PDPK1, PGF, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP5K1C, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PRKCA, PRKCB1, PRKCG, PTEN, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF1, RELN, RHOA, ROCK1, ROCK2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SPP1, SRC, THBS1, THBS2, THBS3, THBS4, TLN1, TLN2, TNC, TNN, TNR, TNXB, VASP, VAV1, VAV2, VAV3, VCL, VEGFA, VEGFB, VEGFC, VTN, VWF, ZYX 185 ACTB(2), ACTG1(1), ACTN2(4), ACTN3(1), ACTN4(4), AKT1(12), AKT2(1), AKT3(2), ARHGAP5(3), BAD(1), BRAF(2), CAPN2(2), CAV1(1), CCND1(1), CCND3(5), COL11A1(2), COL11A2(1), COL1A1(6), COL1A2(3), COL2A1(3), COL3A1(1), COL4A1(4), COL4A2(2), COL4A4(1), COL4A6(3), COL5A1(2), COL5A2(4), COL5A3(4), COL6A3(5), COL6A6(4), COMP(3), CRKL(1), EGF(2), EGFR(4), ELK1(2), ERBB2(4), FARP2(3), FIGF(1), FLNA(4), FLNB(7), FLNC(8), FLT1(2), FN1(3), GRB2(1), GRLF1(4), HGF(3), IGF1(1), IGF1R(1), ILK(2), ITGA1(3), ITGA10(1), ITGA11(4), ITGA2(2), ITGA2B(2), ITGA4(1), ITGA6(3), ITGA7(5), ITGA8(2), ITGAV(3), ITGB1(2), ITGB3(2), ITGB4(4), ITGB5(2), ITGB8(1), JUN(1), KDR(2), LAMA1(6), LAMA2(7), LAMA3(6), LAMA4(4), LAMB1(3), LAMB2(3), LAMB3(4), LAMB4(6), LAMC1(2), LAMC2(1), LAMC3(1), MAP2K1(1), MAPK1(1), MAPK10(1), MAPK3(1), MAPK8(2), MET(4), MYL7(1), MYLK(5), PAK1(2), PAK2(1), PAK3(1), PAK7(1), PARVA(1), PDGFB(1), PDGFRA(3), PDGFRB(2), PIK3CA(168), PIK3CB(3), PIK3CG(2), PIK3R1(14), PIK3R3(1), PIP5K1C(3), PPP1R12A(1), PRKCG(1), PTEN(15), PTK2(1), PXN(1), RAF1(1), RAPGEF1(3), RELN(10), RHOA(2), ROCK1(1), ROCK2(2), SHC1(1), SHC3(1), SHC4(2), SOS1(3), SOS2(1), SPP1(1), THBS1(3), THBS3(1), THBS4(1), TLN1(7), TLN2(4), TNC(3), TNN(3), TNR(1), TNXB(3), VAV1(1), VAV3(1), VCL(3), VWF(6) 263403231 529 325 378 116 112 131 163 29 86 8 <1.00e-15 <5.98e-15
2 HSA04210_APOPTOSIS Genes involved in apoptosis AIFM1, AKT1, AKT2, AKT3, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CAPN1, CAPN2, CASP10, CASP3, CASP6, CASP7, CASP8, CASP9, CFLAR, CHP, CHUK, CSF2RB, CYCS, DFFA, DFFB, ENDOG, FADD, FAS, FASLG, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1RAP, IL3, IL3RA, IRAK1, IRAK2, IRAK3, IRAK4, MAP3K14, MYD88, NFKB1, NFKB2, NFKBIA, NGFB, NTRK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, RELA, RIPK1, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFRSF1A, TNFSF10, TP53, TRADD, TRAF2 79 AKT1(12), AKT2(1), AKT3(2), APAF1(1), ATM(9), BAD(1), BID(4), CAPN1(3), CAPN2(2), CASP6(1), CASP8(2), CSF2RB(2), DFFB(2), FAS(1), FASLG(1), IKBKB(2), IL1A(1), IL1R1(1), IL1RAP(2), IL3RA(1), IRAK1(1), IRAK2(2), IRAK3(1), IRAK4(2), NFKB1(1), NFKB2(4), NTRK1(1), PIK3CA(168), PIK3CB(3), PIK3CG(2), PIK3R1(14), PIK3R3(1), PPP3CA(3), PPP3CB(2), PRKACA(1), PRKAR1A(1), PRKAR2A(1), PRKAR2B(1), RELA(1), RIPK1(3), TNFRSF10D(1), TNFRSF1A(1), TP53(142) 59436624 408 310 210 20 82 90 118 15 100 3 <1.00e-15 <5.98e-15
3 HSA04010_MAPK_SIGNALING_PATHWAY Genes involved in MAPK signaling pathway ACVR1B, ACVR1C, AKT1, AKT2, AKT3, ARRB1, ARRB2, ATF2, ATF4, BDNF, BRAF, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CACNA2D1, CACNA2D2, CACNA2D3, CACNA2D4, CACNB1, CACNB2, CACNB3, CACNB4, CACNG1, CACNG2, CACNG3, CACNG4, CACNG5, CACNG6, CACNG7, CACNG8, CASP3, CD14, CDC25B, CDC42, CHP, CHUK, CRK, CRKL, DAXX, DDIT3, DUSP1, DUSP10, DUSP14, DUSP16, DUSP2, DUSP3, DUSP4, DUSP5, DUSP6, DUSP7, DUSP8, DUSP9, ECSIT, EGF, EGFR, ELK1, ELK4, EVI1, FAS, FASLG, FGF1, FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2, FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FLNA, FLNB, FLNC, FOS, GADD45A, GADD45B, GADD45G, GNA12, GNG12, GRB2, HRAS, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1R2, JUN, JUND, KRAS, LOC653852, MAP2K1, MAP2K1IP1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K10, MAP3K12, MAP3K13, MAP3K14, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K8, MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK7, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MAPKAPK2, MAPKAPK3, MAPKAPK5, MAPT, MAX, MEF2C, MKNK1, MKNK2, MOS, MRAS, MYC, NF1, NFATC2, NFATC4, NFKB1, NFKB2, NGFB, NLK, NR4A1, NRAS, NTF3, NTF5, NTRK1, NTRK2, PAK1, PAK2, PDGFA, PDGFB, PDGFRA, PDGFRB, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PPM1A, PPM1B, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PPP5C, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTPN5, PTPN7, PTPRR, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF2, RASA1, RASA2, RASGRF1, RASGRF2, RASGRP1, RASGRP2, RASGRP3, RASGRP4, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA4, RPS6KA5, RPS6KA6, RRAS, RRAS2, SOS1, SOS2, SRF, STK3, STK4, STMN1, TAOK1, TAOK2, TAOK3, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF1A, TP53, TRAF2, TRAF6, ZAK 231 ACVR1B(4), ACVR1C(1), AKT1(12), AKT2(1), AKT3(2), ARRB1(1), ATF4(1), BDNF(1), BRAF(2), CACNA1A(5), CACNA1B(1), CACNA1C(4), CACNA1D(4), CACNA1E(8), CACNA1F(6), CACNA1G(5), CACNA1I(2), CACNA1S(1), CACNA2D1(4), CACNA2D2(2), CACNA2D3(5), CACNA2D4(1), CACNB1(1), CACNB2(2), CACNG2(1), CACNG3(2), CACNG4(1), CACNG6(1), CD14(1), CDC25B(3), CRKL(1), DUSP10(1), DUSP16(3), DUSP6(1), DUSP7(1), DUSP9(1), EGF(2), EGFR(4), ELK1(2), FAS(1), FASLG(1), FGF11(1), FGF13(2), FGF18(2), FGF23(1), FGF3(1), FGF5(1), FGF6(1), FGF7(2), FGFR2(2), FGFR4(3), FLNA(4), FLNB(7), FLNC(8), GRB2(1), IKBKB(2), IL1A(1), IL1R1(1), IL1R2(3), JUN(1), KRAS(1), MAP2K1(1), MAP2K3(1), MAP2K4(18), MAP2K5(1), MAP3K1(53), MAP3K10(4), MAP3K12(2), MAP3K13(3), MAP3K4(3), MAP3K5(1), MAP3K6(1), MAP3K8(2), MAP4K1(1), MAP4K4(1), MAPK1(1), MAPK10(1), MAPK14(1), MAPK3(1), MAPK8(2), MAPK8IP1(1), MAPKAPK3(1), MAPT(1), MAX(1), MEF2C(2), MOS(2), MYC(1), NF1(13), NFATC4(3), NFKB1(1), NFKB2(4), NLK(1), NR4A1(1), NTRK1(1), NTRK2(1), PAK1(2), PAK2(1), PDGFB(1), PDGFRA(3), PDGFRB(2), PLA2G2D(1), PLA2G2F(1), PLA2G3(3), PLA2G4A(6), PLA2G6(2), PPP3CA(3), PPP3CB(2), PRKACA(1), PRKCG(1), PTPN5(2), PTPN7(1), PTPRR(1), RAF1(1), RAPGEF2(1), RASA1(2), RASA2(1), RASGRF1(3), RASGRP2(2), RASGRP4(1), RPS6KA1(1), RPS6KA2(2), RPS6KA3(2), RPS6KA4(1), RPS6KA6(3), SOS1(3), SOS2(1), SRF(1), STK3(1), STK4(1), TAOK1(2), TAOK2(1), TGFB3(1), TGFBR1(2), TNFRSF1A(1), TP53(142), TRAF6(1), ZAK(1) 202419750 491 304 428 74 74 134 70 28 152 33 <1.00e-15 <5.98e-15
4 HSA04810_REGULATION_OF_ACTIN_CYTOSKELETON Genes involved in regulation of actin cytoskeleton ABI2, ACTN1, ACTN2, ACTN3, ACTN4, APC, APC2, ARAF, ARHGEF1, ARHGEF12, ARHGEF4, ARHGEF6, ARHGEF7, ARPC1A, ARPC1B, ARPC2, ARPC3, ARPC4, ARPC5, ARPC5L, BAIAP2, BCAR1, BDKRB1, BDKRB2, BRAF, C3orf10, CD14, CDC42, CFL1, CFL2, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CRK, CRKL, CSK, CYFIP1, CYFIP2, DIAPH1, DIAPH2, DIAPH3, DOCK1, EGF, EGFR, EZR, F2, F2R, FGD1, FGD3, FGF1, FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2, FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FN1, GIT1, GNA12, GNA13, GNG12, GRLF1, GSN, HRAS, INS, IQGAP1, IQGAP2, IQGAP3, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAD, ITGAE, ITGAL, ITGAM, ITGAV, ITGAX, ITGB1, ITGB2, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, KRAS, LIMK1, LIMK2, LOC200025, LOC645126, LOC653888, MAP2K1, MAP2K2, MAPK1, MAPK3, MLCK, MOS, MRAS, MRCL3, MRLC2, MSN, MYH10, MYH14, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, NCKAP1, NCKAP1L, NRAS, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PDGFA, PDGFB, PDGFRA, PDGFRB, PFN1, PFN2, PFN3, PFN4, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP4K2A, PIP4K2B, PIP4K2C, PIP5K1A, PIP5K1B, PIP5K1C, PIP5K3, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PPP1R12B, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RDX, RHOA, ROCK1, ROCK2, RRAS, RRAS2, SCIN, SLC9A1, SOS1, SOS2, SSH1, SSH2, SSH3, TIAM1, TIAM2, TMSB4X, TMSB4Y, TMSL3, VAV1, VAV2, VAV3, VCL, WAS, WASF1, WASF2, WASL 193 ACTN2(4), ACTN3(1), ACTN4(4), APC(3), ARAF(1), ARHGEF1(5), ARHGEF12(2), ARHGEF4(2), ARHGEF6(1), ARHGEF7(2), ARPC1A(1), ARPC1B(1), ARPC2(2), BAIAP2(1), BDKRB1(2), BRAF(2), C3orf10(1), CD14(1), CHRM1(2), CHRM2(2), CHRM3(1), CHRM5(2), CRKL(1), CYFIP2(2), DIAPH3(1), EGF(2), EGFR(4), EZR(2), F2(2), F2R(2), FGD3(2), FGF11(1), FGF13(2), FGF18(2), FGF23(1), FGF3(1), FGF5(1), FGF6(1), FGF7(2), FGFR2(2), FGFR4(3), FN1(3), GIT1(1), GRLF1(4), GSN(1), IQGAP1(1), IQGAP2(2), IQGAP3(3), ITGA1(3), ITGA10(1), ITGA11(4), ITGA2(2), ITGA2B(2), ITGA4(1), ITGA6(3), ITGA7(5), ITGA8(2), ITGAD(1), ITGAL(1), ITGAM(1), ITGAV(3), ITGAX(2), ITGB1(2), ITGB2(3), ITGB3(2), ITGB4(4), ITGB5(2), ITGB8(1), KRAS(1), LIMK1(3), LIMK2(1), MAP2K1(1), MAPK1(1), MAPK3(1), MOS(2), MSN(1), MYH10(4), MYH14(5), MYH9(5), MYL7(1), MYLK(5), NCKAP1(3), NCKAP1L(3), PAK1(2), PAK2(1), PAK3(1), PAK7(1), PDGFB(1), PDGFRA(3), PDGFRB(2), PIK3CA(168), PIK3CB(3), PIK3CG(2), PIK3R1(14), PIK3R3(1), PIP4K2A(1), PIP4K2C(5), PIP5K1A(1), PIP5K1C(3), PPP1R12A(1), PTK2(1), PXN(1), RAF1(1), RDX(1), RHOA(2), ROCK1(1), ROCK2(2), SCIN(2), SOS1(3), SOS2(1), SSH1(1), SSH2(1), SSH3(2), TIAM1(1), TIAM2(4), VAV1(1), VAV3(1), VCL(3), WAS(1), WASF1(1), WASL(1) 197302092 416 288 275 90 103 88 140 24 61 0 <1.00e-15 <5.98e-15
5 ARFPATHWAY Cyclin-dependent kinase inhibitor 2A is a tumor suppressor that induces G1 arrest and can activate the p53 pathway, leading to G2/M arrest. ABL1, CDKN2A, E2F1, MDM2, MYC, PIK3CA, PIK3R1, POLR1A, POLR1B, POLR1C, POLR1D, RAC1, RB1, TBX2, TP53, TWIST1 15 ABL1(2), E2F1(2), MDM2(1), MYC(1), PIK3CA(168), PIK3R1(14), POLR1A(1), POLR1B(2), POLR1C(2), POLR1D(1), RB1(9), TP53(142) 14867268 345 285 157 11 72 53 112 11 97 0 <1.00e-15 <5.98e-15
6 HSA04910_INSULIN_SIGNALING_PATHWAY Genes involved in insulin signaling pathway ACACA, ACACB, AKT1, AKT2, AKT3, ARAF, BAD, BRAF, CALM1, CALM2, CALM3, CALML3, CALML6, CBL, CBLB, CBLC, CRK, CRKL, EIF4EBP1, ELK1, EXOC7, FASN, FBP1, FBP2, FLOT1, FLOT2, FOXO1, FRAP1, G6PC, G6PC2, GCK, GRB2, GSK3B, GYS1, GYS2, HRAS, IKBKB, INPP5D, INS, INSR, IRS1, IRS2, IRS4, KIAA1303, KRAS, LIPE, MAP2K1, MAP2K2, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MKNK1, MKNK2, NRAS, PCK1, PCK2, PDE3A, PDE3B, PDPK1, PFKL, PFKM, PFKP, PHKA1, PHKA2, PHKB, PHKG1, PHKG2, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PKLR, PKM2, PPARGC1A, PPP1CA, PPP1CB, PPP1CC, PPP1R3A, PPP1R3B, PPP1R3C, PPP1R3D, PRKAA1, PRKAA2, PRKAB1, PRKAB2, PRKACA, PRKACB, PRKACG, PRKAG1, PRKAG2, PRKAG3, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCI, PRKCZ, PRKX, PRKY, PTPN1, PTPRF, PYGB, PYGL, PYGM, RAF1, RAPGEF1, RHEB, RHOQ, RPS6, RPS6KB1, RPS6KB2, SH2B2, SHC1, SHC2, SHC3, SHC4, SKIP, SLC2A4, SOCS1, SOCS2, SOCS3, SOCS4, SORBS1, SOS1, SOS2, SREBF1, TRIP10, TSC1, TSC2 123 ACACA(1), ACACB(8), AKT1(12), AKT2(1), AKT3(2), ARAF(1), BAD(1), BRAF(2), CBLB(7), CBLC(3), CRKL(1), ELK1(2), G6PC2(1), GCK(2), GRB2(1), GYS1(5), GYS2(1), IKBKB(2), INPP5D(2), INSR(2), IRS1(1), IRS4(1), KRAS(1), LIPE(2), MAP2K1(1), MAPK1(1), MAPK10(1), MAPK3(1), MAPK8(2), PCK1(1), PCK2(1), PDE3A(6), PDE3B(1), PFKM(3), PFKP(2), PHKA2(4), PHKB(2), PHKG2(1), PIK3CA(168), PIK3CB(3), PIK3CG(2), PIK3R1(14), PIK3R3(1), PPARGC1A(1), PPP1R3A(6), PPP1R3B(1), PRKAA2(2), PRKAB1(1), PRKACA(1), PRKAG2(1), PRKAG3(2), PRKAR1A(1), PRKAR2A(1), PRKAR2B(1), PRKCI(1), PRKCZ(1), PTPRF(3), PYGB(3), PYGL(1), PYGM(2), RAF1(1), RAPGEF1(3), RPS6(1), RPS6KB2(3), SHC1(1), SHC3(1), SHC4(2), SLC2A4(1), SOCS4(1), SORBS1(4), SOS1(3), SOS2(1), TRIP10(3), TSC1(2), TSC2(2) 107951961 335 261 185 44 86 81 112 14 42 0 <1.00e-15 <5.98e-15
7 HSA04070_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM Genes involved in phosphatidylinositol signaling system CALM1, CALM2, CALM3, CALML3, CALML6, CARKL, CDIPT, CDS1, CDS2, DGKA, DGKB, DGKD, DGKE, DGKG, DGKH, DGKI, DGKQ, DGKZ, FN3K, IMPA1, IMPA2, INPP1, INPP4A, INPP4B, INPP5A, INPP5B, INPP5D, INPP5E, INPPL1, ITGB1BP3, ITPK1, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, OCRL, PI4KA, PI4KB, PIB5PA, PIK3C2A, PIK3C2B, PIK3C2G, PIK3C3, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP4K2A, PIP4K2B, PIP4K2C, PIP5K1A, PIP5K1B, PIP5K1C, PIP5K3, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCD3, PLCD4, PLCE1, PLCG1, PLCG2, PLCZ1, PRKCA, PRKCB1, PRKCG, PTEN, PTPMT1, SKIP, SYNJ1, SYNJ2 70 CDS1(2), DGKA(3), DGKD(1), DGKE(1), DGKG(4), DGKH(1), DGKI(5), IMPA1(1), INPP4A(2), INPP4B(3), INPP5B(4), INPP5D(2), INPPL1(1), ITGB1BP3(1), ITPK1(1), ITPKB(7), ITPR1(7), ITPR3(4), OCRL(3), PI4KA(3), PI4KB(1), PIK3C2A(2), PIK3C2B(2), PIK3C2G(1), PIK3C3(2), PIK3CA(168), PIK3CB(3), PIK3CG(2), PIK3R1(14), PIK3R3(1), PIP4K2A(1), PIP4K2C(5), PIP5K1A(1), PIP5K1C(3), PLCB1(3), PLCB2(2), PLCB3(1), PLCB4(6), PLCD1(1), PLCD3(2), PLCE1(5), PLCG1(4), PLCG2(2), PLCZ1(1), PRKCG(1), PTEN(15), SYNJ2(1) 89527581 306 254 165 39 77 50 113 14 50 2 <1.00e-15 <5.98e-15
8 HSA04630_JAK_STAT_SIGNALING_PATHWAY Genes involved in Jak-STAT signaling pathway AKT1, AKT2, AKT3, BCL2L1, CBL, CBLB, CBLC, CCND1, CCND2, CCND3, CISH, CLCF1, CNTF, CNTFR, CREBBP, CRLF2, CSF2, CSF2RA, CSF2RB, CSF3, CSF3R, CTF1, EP300, EPO, EPOR, GH1, GH2, GHR, GRB2, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNE1, IFNG, IFNGR1, IFNGR2, IFNK, IFNW1, IL10, IL10RA, IL10RB, IL11, IL11RA, IL12A, IL12B, IL12RB1, IL12RB2, IL13, IL13RA1, IL13RA2, IL15, IL15RA, IL19, IL2, IL20, IL20RA, IL21, IL21R, IL22, IL22RA1, IL22RA2, IL23A, IL23R, IL24, IL26, IL28A, IL28B, IL28RA, IL29, IL2RA, IL2RB, IL2RG, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL6ST, IL7, IL7R, IL9, IL9R, IRF9, JAK1, JAK2, JAK3, LEP, LEPR, LIF, LIFR, MPL, MYC, OSM, OSMR, PIAS1, PIAS2, PIAS3, PIAS4, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIM1, PRL, PRLR, PTPN11, PTPN6, SOCS1, SOCS2, SOCS3, SOCS4, SOCS5, SOCS7, SOS1, SOS2, SPRED1, SPRED2, SPRY1, SPRY2, SPRY3, SPRY4, STAM, STAM2, STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B, STAT6, TPO, TSLP, TYK2 148 AKT1(12), AKT2(1), AKT3(2), CBLB(7), CBLC(3), CCND1(1), CCND3(5), CNTFR(1), CREBBP(2), CSF2RA(1), CSF2RB(2), CSF3R(2), EP300(3), EPOR(1), GH2(1), GHR(2), GRB2(1), IFNA10(1), IFNA14(1), IFNA2(2), IFNA4(1), IFNAR2(1), IFNB1(1), IFNK(1), IL10RA(1), IL10RB(3), IL11RA(1), IL12A(1), IL12B(1), IL12RB1(2), IL13RA1(1), IL13RA2(2), IL15(1), IL2(1), IL21(1), IL21R(1), IL22(1), IL22RA1(1), IL22RA2(1), IL23R(3), IL28B(3), IL28RA(1), IL2RG(1), IL3RA(1), IL5RA(1), IL6(2), IL6R(1), IL6ST(3), IRF9(2), JAK1(1), JAK2(2), JAK3(1), LEPR(3), LIF(3), LIFR(4), MYC(1), OSMR(3), PIAS2(1), PIAS4(2), PIK3CA(168), PIK3CB(3), PIK3CG(2), PIK3R1(14), PIK3R3(1), PRLR(1), SOCS4(1), SOCS5(1), SOS1(3), SOS2(1), SPRED1(2), SPRED2(1), STAM(1), STAM2(1), STAT1(1), STAT2(1), STAT3(1), STAT4(5), STAT5B(4), TPO(6), TSLP(1), TYK2(3) 106057302 335 251 183 40 87 64 116 18 47 3 <1.00e-15 <5.98e-15
9 HSA04012_ERBB_SIGNALING_PATHWAY Genes involved in ErbB signaling pathway ABL1, ABL2, AKT1, AKT2, AKT3, ARAF, AREG, BAD, BRAF, BTC, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CBL, CBLB, CBLC, CDKN1A, CDKN1B, CRK, CRKL, EGF, EGFR, EIF4EBP1, ELK1, ERBB2, ERBB3, ERBB4, EREG, FRAP1, GAB1, GRB2, GSK3B, HBEGF, HRAS, JUN, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP2K7, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MYC, NCK1, NCK2, NRAS, NRG1, NRG2, NRG3, NRG4, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PRKCA, PRKCB1, PRKCG, PTK2, RAF1, RPS6KB1, RPS6KB2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SRC, STAT5A, STAT5B, TGFA 82 ABL1(2), ABL2(2), AKT1(12), AKT2(1), AKT3(2), ARAF(1), BAD(1), BRAF(2), BTC(1), CAMK2A(1), CAMK2D(3), CBLB(7), CBLC(3), CDKN1B(5), CRKL(1), EGF(2), EGFR(4), ELK1(2), ERBB2(4), ERBB3(8), ERBB4(4), GAB1(1), GRB2(1), JUN(1), KRAS(1), MAP2K1(1), MAP2K4(18), MAPK1(1), MAPK10(1), MAPK3(1), MAPK8(2), MYC(1), NRG3(1), PAK1(2), PAK2(1), PAK3(1), PAK7(1), PIK3CA(168), PIK3CB(3), PIK3CG(2), PIK3R1(14), PIK3R3(1), PLCG1(4), PLCG2(2), PRKCG(1), PTK2(1), RAF1(1), RPS6KB2(3), SHC1(1), SHC3(1), SHC4(2), SOS1(3), SOS2(1), STAT5B(4), TGFA(1) 72661719 316 246 164 29 72 58 116 19 51 0 <1.00e-15 <5.98e-15
10 ST_INTEGRIN_SIGNALING_PATHWAY Integrins are transmembrane receptors that mediate cell growth, survival, and migration by binding to ligands in the extracellular matrix. ABL1, ACK1, ACTN1, ACTR2, ACTR3, AKT1, AKT2, AKT3, ANGPTL2, ARHGEF6, ARHGEF7, BCAR1, BRAF, CAV1, CDC42, CDKN2A, CRK, CSE1L, DDEF1, DOCK1, EPHB2, FYN, GRAF, GRB2, GRB7, GRF2, GRLF1, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGB3BP, MAP2K4, MAP2K7, MAP3K11, MAPK1, MAPK10, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MRAS, MYLK, MYLK2, P4HB, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PKLR, PLCG1, PLCG2, PTEN, PTK2, RAF1, RALA, RHO, ROCK1, ROCK2, SHC1, SOS1, SOS2, SRC, TERF2IP, TLN1, TLN2, VASP, WAS, ZYX 74 ABL1(2), AKT1(12), AKT2(1), AKT3(2), ARHGEF6(1), ARHGEF7(2), BRAF(2), CAV1(1), CSE1L(2), EPHB2(1), GRB2(1), GRB7(3), GRLF1(4), ILK(2), ITGA1(3), ITGA10(1), ITGA11(4), ITGA2(2), ITGA4(1), ITGA6(3), ITGA7(5), ITGA8(2), ITGB3BP(1), MAP2K4(18), MAP3K11(1), MAPK1(1), MAPK10(1), MAPK8(2), MAPK8IP1(1), MYLK(5), PAK1(2), PAK2(1), PAK3(1), PAK7(1), PIK3CA(168), PIK3CB(3), PLCG1(4), PLCG2(2), PTEN(15), PTK2(1), RAF1(1), RHO(2), ROCK1(1), ROCK2(2), SHC1(1), SOS1(3), SOS2(1), TERF2IP(2), TLN1(7), TLN2(4), WAS(1) 87730266 310 241 160 37 74 59 111 10 54 2 <1.00e-15 <5.98e-15

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 16. Number of genesets displayed: 10

rank geneset description genes N_genes mut_tally N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 HSA04510_FOCAL_ADHESION Genes involved in focal adhesion ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, ARHGAP5, BAD, BCAR1, BCL2, BIRC2, BIRC3, BIRC4, BRAF, CAPN2, CAV1, CAV2, CAV3, CCND1, CCND2, CCND3, CDC42, CHAD, COL11A1, COL11A2, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, CRK, CRKL, CTNNB1, DIAPH1, DOCK1, EGF, EGFR, ELK1, ERBB2, FARP2, FIGF, FLNA, FLNB, FLNC, FLT1, FN1, FYN, GRB2, GRLF1, GSK3B, HGF, HRAS, IBSP, IGF1, IGF1R, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAV, ITGB1, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, JUN, KDR, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LOC653852, MAP2K1, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MET, MLCK, MRCL3, MRLC2, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLK, MYLK2, MYLPF, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PARVA, PARVB, PARVG, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, PDGFRB, PDPK1, PGF, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIP5K1C, PPP1CA, PPP1CB, PPP1CC, PPP1R12A, PRKCA, PRKCB1, PRKCG, PTEN, PTK2, PXN, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF1, RELN, RHOA, ROCK1, ROCK2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SPP1, SRC, THBS1, THBS2, THBS3, THBS4, TLN1, TLN2, TNC, TNN, TNR, TNXB, VASP, VAV1, VAV2, VAV3, VCL, VEGFA, VEGFB, VEGFC, VTN, VWF, ZYX 181 ACTB(2), ACTG1(1), ACTN2(4), ACTN3(1), ACTN4(4), AKT2(1), AKT3(2), ARHGAP5(3), BAD(1), BRAF(2), CAPN2(2), CAV1(1), CCND1(1), CCND3(5), COL11A1(2), COL11A2(1), COL1A1(6), COL1A2(3), COL2A1(3), COL3A1(1), COL4A1(4), COL4A2(2), COL4A4(1), COL4A6(3), COL5A1(2), COL5A2(4), COL5A3(4), COL6A3(5), COL6A6(4), COMP(3), CRKL(1), EGF(2), EGFR(4), ELK1(2), ERBB2(4), FARP2(3), FIGF(1), FLNA(4), FLNB(7), FLNC(8), FLT1(2), FN1(3), GRB2(1), GRLF1(4), HGF(3), IGF1(1), IGF1R(1), ILK(2), ITGA1(3), ITGA10(1), ITGA11(4), ITGA2(2), ITGA2B(2), ITGA4(1), ITGA6(3), ITGA7(5), ITGA8(2), ITGAV(3), ITGB1(2), ITGB3(2), ITGB4(4), ITGB5(2), ITGB8(1), JUN(1), KDR(2), LAMA1(6), LAMA2(7), LAMA3(6), LAMA4(4), LAMB1(3), LAMB2(3), LAMB3(4), LAMB4(6), LAMC1(2), LAMC2(1), LAMC3(1), MAP2K1(1), MAPK1(1), MAPK10(1), MAPK3(1), MAPK8(2), MET(4), MYL7(1), MYLK(5), PAK1(2), PAK2(1), PAK3(1), PAK7(1), PARVA(1), PDGFB(1), PDGFRA(3), PDGFRB(2), PIK3CB(3), PIK3CG(2), PIK3R3(1), PIP5K1C(3), PPP1R12A(1), PRKCG(1), PTK2(1), PXN(1), RAF1(1), RAPGEF1(3), RELN(10), RHOA(2), ROCK1(1), ROCK2(2), SHC1(1), SHC3(1), SHC4(2), SOS1(3), SOS2(1), SPP1(1), THBS1(3), THBS3(1), THBS4(1), TLN1(7), TLN2(4), TNC(3), TNN(3), TNR(1), TNXB(3), VAV1(1), VAV3(1), VCL(3), VWF(6) 259172823 320 212 319 111 57 101 70 27 59 6 <1.00e-15 <6.16e-13
2 HSA01430_CELL_COMMUNICATION Genes involved in cell communication ACTB, ACTG1, CHAD, COL11A1, COL11A2, COL17A1, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, DES, DSC1, DSC2, DSC3, DSG1, DSG2, DSG3, DSG4, FN1, GJA1, GJA10, GJA3, GJA4, GJA5, GJA8, GJA9, GJB1, GJB2, GJB3, GJB4, GJB5, GJB6, GJB7, GJC1, GJC2, GJC3, GJD2, GJD3, GJD4, IBSP, INA, ITGA6, ITGB4, KRT1, KRT10, KRT12, KRT13, KRT14, KRT15, KRT16, KRT17, KRT18, KRT19, KRT2, KRT20, KRT23, KRT24, KRT25, KRT27, KRT28, KRT3, KRT31, KRT32, KRT33A, KRT33B, KRT34, KRT35, KRT36, KRT37, KRT38, KRT39, KRT4, KRT40, KRT5, KRT6A, KRT6B, KRT6C, KRT7, KRT71, KRT72, KRT73, KRT74, KRT75, KRT76, KRT77, KRT78, KRT79, KRT8, KRT81, KRT82, KRT83, KRT84, KRT85, KRT86, KRT9, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LMNA, LMNB1, LMNB2, LOC728760, NES, PRPH, RELN, SPP1, THBS1, THBS2, THBS3, THBS4, TNC, TNN, TNR, TNXB, VIM, VTN, VWF 126 ACTB(2), ACTG1(1), COL11A1(2), COL11A2(1), COL17A1(3), COL1A1(6), COL1A2(3), COL2A1(3), COL3A1(1), COL4A1(4), COL4A2(2), COL4A4(1), COL4A6(3), COL5A1(2), COL5A2(4), COL5A3(4), COL6A3(5), COL6A6(4), COMP(3), DSC2(3), DSC3(1), DSG1(2), DSG4(2), FN1(3), GJA1(2), GJA10(1), GJA4(1), GJA9(1), GJB2(1), GJB3(2), GJB4(1), GJB5(1), GJC1(1), INA(1), ITGA6(3), ITGB4(4), KRT1(3), KRT14(1), KRT15(1), KRT17(4), KRT18(1), KRT19(2), KRT2(2), KRT25(2), KRT28(1), KRT3(1), KRT33A(1), KRT34(1), KRT35(1), KRT36(2), KRT37(1), KRT4(2), KRT6A(1), KRT6C(1), KRT71(1), KRT72(1), KRT81(1), KRT82(2), KRT83(1), KRT84(1), KRT85(1), KRT86(1), KRT9(2), LAMA1(6), LAMA2(7), LAMA3(6), LAMA4(4), LAMB1(3), LAMB2(3), LAMB3(4), LAMB4(6), LAMC1(2), LAMC2(1), LAMC3(1), LMNB1(1), NES(3), RELN(10), SPP1(1), THBS1(3), THBS3(1), THBS4(1), TNC(3), TNN(3), TNR(1), TNXB(3), VWF(6) 166605270 202 161 201 72 41 74 42 10 35 0 5.43e-08 0.000017
3 HSA04350_TGF_BETA_SIGNALING_PATHWAY Genes involved in TGF-beta signaling pathway ACVR1, ACVR1B, ACVR1C, ACVR2A, ACVR2B, ACVRL1, AMH, AMHR2, BMP2, BMP4, BMP5, BMP6, BMP7, BMP8A, BMP8B, BMPR1A, BMPR1B, BMPR2, CDKN2B, CHRD, COMP, CREBBP, CUL1, DCN, E2F4, E2F5, EP300, FST, GDF5, GDF6, GDF7, hCG_1982709, ID1, ID2, ID3, ID4, IFNG, INHBA, INHBB, INHBC, INHBE, LEFTY1, LEFTY2, LTBP1, MAPK1, MAPK3, MYC, NODAL, NOG, PITX2, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, RBL1, RBL2, RBX1, RHOA, ROCK1, ROCK2, RPS6KB1, RPS6KB2, SKP1, SMAD1, SMAD2, SMAD3, SMAD4, SMAD5, SMAD6, SMAD7, SMAD9, SMURF1, SMURF2, SP1, TFDP1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, THBS1, THBS2, THBS3, THBS4, TNF, ZFYVE16, ZFYVE9 84 ACVR1(1), ACVR1B(4), ACVR1C(1), ACVR2A(3), AMHR2(2), BMP2(2), BMP4(2), BMP5(1), BMP6(1), BMP8B(1), BMPR1B(2), BMPR2(2), CHRD(2), COMP(3), CREBBP(2), CUL1(1), E2F4(2), EP300(3), FST(1), GDF6(2), ID2(1), INHBA(1), INHBC(1), INHBE(1), LEFTY2(1), LTBP1(2), MAPK1(1), MAPK3(1), MYC(1), NODAL(1), PITX2(1), PPP2CB(2), RBL1(1), RBL2(1), RHOA(2), ROCK1(1), ROCK2(2), RPS6KB2(3), SMAD2(3), SMAD3(2), SMAD4(1), SMAD9(2), SMURF2(1), SP1(1), TGFB3(1), TGFBR1(2), THBS1(3), THBS3(1), THBS4(1), ZFYVE16(3), ZFYVE9(3) 70610904 86 77 84 29 13 23 18 7 25 0 2.99e-06 0.00061
4 HSA04010_MAPK_SIGNALING_PATHWAY Genes involved in MAPK signaling pathway ACVR1B, ACVR1C, AKT1, AKT2, AKT3, ARRB1, ARRB2, ATF2, ATF4, BDNF, BRAF, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CACNA2D1, CACNA2D2, CACNA2D3, CACNA2D4, CACNB1, CACNB2, CACNB3, CACNB4, CACNG1, CACNG2, CACNG3, CACNG4, CACNG5, CACNG6, CACNG7, CACNG8, CASP3, CD14, CDC25B, CDC42, CHP, CHUK, CRK, CRKL, DAXX, DDIT3, DUSP1, DUSP10, DUSP14, DUSP16, DUSP2, DUSP3, DUSP4, DUSP5, DUSP6, DUSP7, DUSP8, DUSP9, ECSIT, EGF, EGFR, ELK1, ELK4, EVI1, FAS, FASLG, FGF1, FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2, FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FLNA, FLNB, FLNC, FOS, GADD45A, GADD45B, GADD45G, GNA12, GNG12, GRB2, HRAS, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1R2, JUN, JUND, KRAS, LOC653852, MAP2K1, MAP2K1IP1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K10, MAP3K12, MAP3K13, MAP3K14, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K8, MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK7, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MAPKAPK2, MAPKAPK3, MAPKAPK5, MAPT, MAX, MEF2C, MKNK1, MKNK2, MOS, MRAS, MYC, NF1, NFATC2, NFATC4, NFKB1, NFKB2, NGFB, NLK, NR4A1, NRAS, NTF3, NTF5, NTRK1, NTRK2, PAK1, PAK2, PDGFA, PDGFB, PDGFRA, PDGFRB, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PPM1A, PPM1B, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PPP5C, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTPN5, PTPN7, PTPRR, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF2, RASA1, RASA2, RASGRF1, RASGRF2, RASGRP1, RASGRP2, RASGRP3, RASGRP4, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA4, RPS6KA5, RPS6KA6, RRAS, RRAS2, SOS1, SOS2, SRF, STK3, STK4, STMN1, TAOK1, TAOK2, TAOK3, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF1A, TP53, TRAF2, TRAF6, ZAK 226 ACVR1B(4), ACVR1C(1), AKT2(1), AKT3(2), ARRB1(1), ATF4(1), BDNF(1), BRAF(2), CACNA1A(5), CACNA1B(1), CACNA1C(4), CACNA1D(4), CACNA1E(8), CACNA1F(6), CACNA1G(5), CACNA1I(2), CACNA1S(1), CACNA2D1(4), CACNA2D2(2), CACNA2D3(5), CACNA2D4(1), CACNB1(1), CACNB2(2), CACNG2(1), CACNG3(2), CACNG4(1), CACNG6(1), CD14(1), CDC25B(3), CRKL(1), DUSP10(1), DUSP16(3), DUSP6(1), DUSP7(1), DUSP9(1), EGF(2), EGFR(4), ELK1(2), FAS(1), FASLG(1), FGF11(1), FGF13(2), FGF18(2), FGF23(1), FGF3(1), FGF5(1), FGF6(1), FGF7(2), FGFR2(2), FGFR4(3), FLNA(4), FLNB(7), FLNC(8), GRB2(1), IKBKB(2), IL1A(1), IL1R1(1), IL1R2(3), JUN(1), KRAS(1), MAP2K1(1), MAP2K3(1), MAP2K5(1), MAP3K10(4), MAP3K12(2), MAP3K13(3), MAP3K4(3), MAP3K5(1), MAP3K6(1), MAP3K8(2), MAP4K1(1), MAP4K4(1), MAPK1(1), MAPK10(1), MAPK14(1), MAPK3(1), MAPK8(2), MAPK8IP1(1), MAPKAPK3(1), MAPT(1), MAX(1), MEF2C(2), MOS(2), MYC(1), NFATC4(3), NFKB1(1), NFKB2(4), NLK(1), NR4A1(1), NTRK1(1), NTRK2(1), PAK1(2), PAK2(1), PDGFB(1), PDGFRA(3), PDGFRB(2), PLA2G2D(1), PLA2G2F(1), PLA2G3(3), PLA2G4A(6), PLA2G6(2), PPP3CA(3), PPP3CB(2), PRKACA(1), PRKCG(1), PTPN5(2), PTPN7(1), PTPRR(1), RAF1(1), RAPGEF2(1), RASA1(2), RASA2(1), RASGRF1(3), RASGRP2(2), RASGRP4(1), RPS6KA1(1), RPS6KA2(2), RPS6KA3(2), RPS6KA4(1), RPS6KA6(3), SOS1(3), SOS2(1), SRF(1), STK3(1), STK4(1), TAOK1(2), TAOK2(1), TGFB3(1), TGFBR1(2), TNFRSF1A(1), TRAF6(1), ZAK(1) 193925472 253 175 250 69 54 88 46 18 44 3 9.28e-06 0.0014
5 HSA04012_ERBB_SIGNALING_PATHWAY Genes involved in ErbB signaling pathway ABL1, ABL2, AKT1, AKT2, AKT3, ARAF, AREG, BAD, BRAF, BTC, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CBL, CBLB, CBLC, CDKN1A, CDKN1B, CRK, CRKL, EGF, EGFR, EIF4EBP1, ELK1, ERBB2, ERBB3, ERBB4, EREG, FRAP1, GAB1, GRB2, GSK3B, HBEGF, HRAS, JUN, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP2K7, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MYC, NCK1, NCK2, NRAS, NRG1, NRG2, NRG3, NRG4, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PRKCA, PRKCB1, PRKCG, PTK2, RAF1, RPS6KB1, RPS6KB2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SRC, STAT5A, STAT5B, TGFA 77 ABL1(2), ABL2(2), AKT2(1), AKT3(2), ARAF(1), BAD(1), BRAF(2), BTC(1), CAMK2A(1), CAMK2D(3), CBLB(7), CBLC(3), CRKL(1), EGF(2), EGFR(4), ELK1(2), ERBB2(4), ERBB3(8), ERBB4(4), GAB1(1), GRB2(1), JUN(1), KRAS(1), MAP2K1(1), MAPK1(1), MAPK10(1), MAPK3(1), MAPK8(2), MYC(1), NRG3(1), PAK1(2), PAK2(1), PAK3(1), PAK7(1), PIK3CB(3), PIK3CG(2), PIK3R3(1), PLCG1(4), PLCG2(2), PRKCG(1), PTK2(1), RAF1(1), RPS6KB2(3), SHC1(1), SHC3(1), SHC4(2), SOS1(3), SOS2(1), STAT5B(4), TGFA(1) 68217357 99 86 99 24 13 28 24 17 17 0 0.000018 0.0022
6 HSA04910_INSULIN_SIGNALING_PATHWAY Genes involved in insulin signaling pathway ACACA, ACACB, AKT1, AKT2, AKT3, ARAF, BAD, BRAF, CALM1, CALM2, CALM3, CALML3, CALML6, CBL, CBLB, CBLC, CRK, CRKL, EIF4EBP1, ELK1, EXOC7, FASN, FBP1, FBP2, FLOT1, FLOT2, FOXO1, FRAP1, G6PC, G6PC2, GCK, GRB2, GSK3B, GYS1, GYS2, HRAS, IKBKB, INPP5D, INS, INSR, IRS1, IRS2, IRS4, KIAA1303, KRAS, LIPE, MAP2K1, MAP2K2, MAPK1, MAPK10, MAPK3, MAPK8, MAPK9, MKNK1, MKNK2, NRAS, PCK1, PCK2, PDE3A, PDE3B, PDPK1, PFKL, PFKM, PFKP, PHKA1, PHKA2, PHKB, PHKG1, PHKG2, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PKLR, PKM2, PPARGC1A, PPP1CA, PPP1CB, PPP1CC, PPP1R3A, PPP1R3B, PPP1R3C, PPP1R3D, PRKAA1, PRKAA2, PRKAB1, PRKAB2, PRKACA, PRKACB, PRKACG, PRKAG1, PRKAG2, PRKAG3, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCI, PRKCZ, PRKX, PRKY, PTPN1, PTPRF, PYGB, PYGL, PYGM, RAF1, RAPGEF1, RHEB, RHOQ, RPS6, RPS6KB1, RPS6KB2, SH2B2, SHC1, SHC2, SHC3, SHC4, SKIP, SLC2A4, SOCS1, SOCS2, SOCS3, SOCS4, SORBS1, SOS1, SOS2, SREBF1, TRIP10, TSC1, TSC2 120 ACACA(1), ACACB(8), AKT2(1), AKT3(2), ARAF(1), BAD(1), BRAF(2), CBLB(7), CBLC(3), CRKL(1), ELK1(2), G6PC2(1), GCK(2), GRB2(1), GYS1(5), GYS2(1), IKBKB(2), INPP5D(2), INSR(2), IRS1(1), IRS4(1), KRAS(1), LIPE(2), MAP2K1(1), MAPK1(1), MAPK10(1), MAPK3(1), MAPK8(2), PCK1(1), PCK2(1), PDE3A(6), PDE3B(1), PFKM(3), PFKP(2), PHKA2(4), PHKB(2), PHKG2(1), PIK3CB(3), PIK3CG(2), PIK3R3(1), PPARGC1A(1), PPP1R3A(6), PPP1R3B(1), PRKAA2(2), PRKAB1(1), PRKACA(1), PRKAG2(1), PRKAG3(2), PRKAR1A(1), PRKAR2A(1), PRKAR2B(1), PRKCI(1), PRKCZ(1), PTPRF(3), PYGB(3), PYGL(1), PYGM(2), RAF1(1), RAPGEF1(3), RPS6(1), RPS6KB2(3), SHC1(1), SHC3(1), SHC4(2), SLC2A4(1), SOCS4(1), SORBS1(4), SOS1(3), SOS2(1), TRIP10(3), TSC1(2), TSC2(2) 104354289 141 118 141 39 31 51 22 12 25 0 0.000051 0.0053
7 HSA04630_JAK_STAT_SIGNALING_PATHWAY Genes involved in Jak-STAT signaling pathway AKT1, AKT2, AKT3, BCL2L1, CBL, CBLB, CBLC, CCND1, CCND2, CCND3, CISH, CLCF1, CNTF, CNTFR, CREBBP, CRLF2, CSF2, CSF2RA, CSF2RB, CSF3, CSF3R, CTF1, EP300, EPO, EPOR, GH1, GH2, GHR, GRB2, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNE1, IFNG, IFNGR1, IFNGR2, IFNK, IFNW1, IL10, IL10RA, IL10RB, IL11, IL11RA, IL12A, IL12B, IL12RB1, IL12RB2, IL13, IL13RA1, IL13RA2, IL15, IL15RA, IL19, IL2, IL20, IL20RA, IL21, IL21R, IL22, IL22RA1, IL22RA2, IL23A, IL23R, IL24, IL26, IL28A, IL28B, IL28RA, IL29, IL2RA, IL2RB, IL2RG, IL3, IL3RA, IL4, IL4R, IL5, IL5RA, IL6, IL6R, IL6ST, IL7, IL7R, IL9, IL9R, IRF9, JAK1, JAK2, JAK3, LEP, LEPR, LIF, LIFR, MPL, MYC, OSM, OSMR, PIAS1, PIAS2, PIAS3, PIAS4, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PIM1, PRL, PRLR, PTPN11, PTPN6, SOCS1, SOCS2, SOCS3, SOCS4, SOCS5, SOCS7, SOS1, SOS2, SPRED1, SPRED2, SPRY1, SPRY2, SPRY3, SPRY4, STAM, STAM2, STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B, STAT6, TPO, TSLP, TYK2 145 AKT2(1), AKT3(2), CBLB(7), CBLC(3), CCND1(1), CCND3(5), CNTFR(1), CREBBP(2), CSF2RA(1), CSF2RB(2), CSF3R(2), EP300(3), EPOR(1), GH2(1), GHR(2), GRB2(1), IFNA10(1), IFNA14(1), IFNA2(2), IFNA4(1), IFNAR2(1), IFNB1(1), IFNK(1), IL10RA(1), IL10RB(3), IL11RA(1), IL12A(1), IL12B(1), IL12RB1(2), IL13RA1(1), IL13RA2(2), IL15(1), IL2(1), IL21(1), IL21R(1), IL22(1), IL22RA1(1), IL22RA2(1), IL23R(3), IL28B(3), IL28RA(1), IL2RG(1), IL3RA(1), IL5RA(1), IL6(2), IL6R(1), IL6ST(3), IRF9(2), JAK1(1), JAK2(2), JAK3(1), LEPR(3), LIF(3), LIFR(4), MYC(1), OSMR(3), PIAS2(1), PIAS4(2), PIK3CB(3), PIK3CG(2), PIK3R3(1), PRLR(1), SOCS4(1), SOCS5(1), SOS1(3), SOS2(1), SPRED1(2), SPRED2(1), STAM(1), STAM2(1), STAT1(1), STAT2(1), STAT3(1), STAT4(5), STAT5B(4), TPO(6), TSLP(1), TYK2(3) 102459630 141 113 139 35 32 34 26 16 30 3 0.000063 0.0055
8 HSA04320_DORSO_VENTRAL_AXIS_FORMATION Genes involved in dorso-ventral axis formation BRAF, CPEB1, EGFR, ERBB2, ERBB4, ETS1, ETS2, ETV6, ETV7, FMN2, GRB2, KRAS, MAP2K1, MAPK1, MAPK3, NOTCH1, NOTCH2, NOTCH3, NOTCH4, PIWIL1, PIWIL2, PIWIL3, PIWIL4, RAF1, SOS1, SOS2, SPIRE1, SPIRE2 25 BRAF(2), CPEB1(2), EGFR(4), ERBB2(4), ERBB4(4), ETS1(2), ETS2(3), ETV6(1), FMN2(7), GRB2(1), KRAS(1), MAP2K1(1), MAPK1(1), MAPK3(1), NOTCH2(4), NOTCH3(3), NOTCH4(6), PIWIL2(4), PIWIL4(1), RAF1(1), SOS1(3), SOS2(1), SPIRE1(1) 33021417 58 50 57 12 8 19 13 7 11 0 0.000083 0.0064
9 HSA04512_ECM_RECEPTOR_INTERACTION Genes involved in ECM-receptor interaction AGRN, CD36, CD44, CD47, CHAD, COL11A1, COL11A2, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, DAG1, FN1, FNDC1, FNDC3A, FNDC4, FNDC5, GP1BA, GP1BB, GP5, GP6, GP9, HMMR, HSPG2, IBSP, ITGA1, ITGA10, ITGA11, ITGA2, ITGA2B, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGAV, ITGB1, ITGB3, ITGB4, ITGB5, ITGB6, ITGB7, ITGB8, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, RELN, SDC1, SDC2, SDC3, SDC4, SPP1, SV2A, SV2B, SV2C, THBS1, THBS2, THBS3, THBS4, TNC, TNN, TNR, TNXB, VTN, VWF 82 CD36(1), COL11A1(2), COL11A2(1), COL1A1(6), COL1A2(3), COL2A1(3), COL3A1(1), COL4A1(4), COL4A2(2), COL4A4(1), COL4A6(3), COL5A1(2), COL5A2(4), COL5A3(4), COL6A3(5), COL6A6(4), FN1(3), FNDC1(4), FNDC3A(1), GP1BA(3), GP6(1), HSPG2(5), ITGA1(3), ITGA10(1), ITGA11(4), ITGA2(2), ITGA2B(2), ITGA4(1), ITGA6(3), ITGA7(5), ITGA8(2), ITGAV(3), ITGB1(2), ITGB3(2), ITGB4(4), ITGB5(2), ITGB8(1), LAMA1(6), LAMA2(7), LAMA3(6), LAMA4(4), LAMB1(3), LAMB2(3), LAMB3(4), LAMB4(6), LAMC1(2), LAMC2(1), LAMC3(1), RELN(10), SDC4(1), SPP1(1), SV2A(1), SV2B(1), THBS1(3), THBS3(1), THBS4(1), TNC(3), TNN(3), TNR(1), TNXB(3), VWF(6) 157698294 178 142 177 70 34 61 44 8 31 0 0.00014 0.0096
10 HSA04020_CALCIUM_SIGNALING_PATHWAY Genes involved in calcium signaling pathway ADCY1, ADCY2, ADCY3, ADCY4, ADCY7, ADCY8, ADCY9, ADORA2A, ADORA2B, ADRA1A, ADRA1B, ADRA1D, ADRB1, ADRB2, ADRB3, AGTR1, ATP2A1, ATP2A2, ATP2A3, ATP2B1, ATP2B2, ATP2B3, ATP2B4, AVPR1A, AVPR1B, BDKRB1, BDKRB2, BST1, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CALM1, CALM2, CALM3, CALML3, CALML6, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CAMK4, CCKAR, CCKBR, CD38, CHP, CHRM1, CHRM2, CHRM3, CHRM5, CHRNA7, CYSLTR1, CYSLTR2, DRD1, EDNRA, EDNRB, EGFR, ERBB2, ERBB3, ERBB4, F2R, GNA11, GNA14, GNA15, GNAL, GNAQ, GNAS, GRIN1, GRIN2A, GRIN2C, GRIN2D, GRM1, GRM5, GRPR, HRH1, HRH2, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, LHCGR, LTB4R2, MLCK, MYLK, MYLK2, NOS1, NOS2A, NOS3, NTSR1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, PDE1A, PDE1B, PDE1C, PDGFRA, PDGFRB, PHKA1, PHKA2, PHKB, PHKG1, PHKG2, PLCB1, PLCB2, PLCB3, PLCB4, PLCD1, PLCD3, PLCD4, PLCE1, PLCG1, PLCG2, PLCZ1, PLN, PPID, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTAFR, PTGER1, PTGER3, PTGFR, PTK2B, RYR1, RYR2, RYR3, SLC25A4, SLC25A5, SLC25A6, SLC8A1, SLC8A2, SLC8A3, SPHK1, SPHK2, TACR1, TACR2, TACR3, TBXA2R, TNNC1, TNNC2, TRHR, TRPC1, VDAC1, VDAC2, VDAC3 161 ADCY1(3), ADCY3(2), ADCY4(1), ADCY7(1), ADCY8(2), ADCY9(5), ADRA1A(1), ADRA1B(1), ATP2A1(2), ATP2B1(4), ATP2B2(4), ATP2B3(4), ATP2B4(1), AVPR1B(1), BDKRB1(2), CACNA1A(5), CACNA1B(1), CACNA1C(4), CACNA1D(4), CACNA1E(8), CACNA1F(6), CACNA1G(5), CACNA1I(2), CACNA1S(1), CAMK2A(1), CAMK2D(3), CD38(2), CHRM1(2), CHRM2(2), CHRM3(1), CHRM5(2), CYSLTR1(1), CYSLTR2(1), EDNRB(1), EGFR(4), ERBB2(4), ERBB3(8), ERBB4(4), F2R(2), GNAQ(1), GNAS(4), GRIN1(1), GRIN2C(4), GRIN2D(3), GRM1(2), GRM5(1), GRPR(1), HRH2(2), HTR2A(3), HTR2B(1), HTR2C(1), HTR5A(3), ITPR1(7), ITPR3(4), LHCGR(4), LTB4R2(1), MYLK(5), NOS1(3), NOS3(2), P2RX3(1), P2RX4(1), P2RX5(1), P2RX7(1), PDE1A(2), PDE1B(1), PDGFRA(3), PDGFRB(2), PHKA2(4), PHKB(2), PHKG2(1), PLCB1(3), PLCB2(2), PLCB3(1), PLCB4(6), PLCD1(1), PLCD3(2), PLCE1(5), PLCG1(4), PLCG2(2), PLCZ1(1), PPP3CA(3), PPP3CB(2), PRKACA(1), PRKCG(1), PTGER3(2), PTGFR(1), PTK2B(3), RYR1(5), RYR2(13), RYR3(11), SPHK2(2), TACR2(1), TNNC2(1), TRPC1(2), VDAC2(1) 191542572 256 175 255 108 73 79 54 19 27 4 0.00023 0.014
Methods & Data
Methods

In brief, we tabulate the number of mutations and the number of covered bases for each gene. The counts are broken down by mutation context category: four context categories that are discovered by MutSig, and one for indel and 'null' mutations, which include indels, nonsense mutations, splice-site mutations, and non-stop (read-through) mutations. For each gene, we calculate the probability of seeing the observed constellation of mutations, i.e. the product P1 x P2 x ... x Pm, or a more extreme one, given the background mutation rates calculated across the dataset.[1]

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This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 615 (2011)
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