Mutation Analysis (MutSig)
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: UCEC.

Number of patients in set: 248

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): 163

Mutations seen in COSMIC: 1

Significantly mutated genes in COSMIC territory: 0

Genes with clustered mutations (&le 3 aa apart): 11

Significantly mutated genesets: 190

Significantly mutated genesets: (excluding sig. mutated genes): 15

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 1073
Frame_Shift_Ins 460
In_Frame_Del 739
In_Frame_Ins 135
Indel 3
Missense_Mutation 80421
Nonsense_Mutation 8736
Nonstop_Mutation 103
Silent 27606
Splice_Site 2000
Total 121276
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 24851 3455960848 7.2e-06 7.2 0.53
C->(A/T) 37131 3449845912 0.000011 11 0.79
A->(C/G) 13573 3455960848 3.9e-06 3.9 0.29
C->G 4862 3449845912 1.4e-06 1.4 0.1
indel+null 12184 6905807008 1.8e-06 1.8 0.13
double_null 1069 6905807008 1.5e-07 0.15 0.011
Total 93670 6905807008 0.000014 14 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: 163. Number of genes displayed: 35

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 309504 208 141 136 5 15 8 48 5 84 48 <1.00e-15 <1.50e-11
2 TP53 tumor protein p53 325128 48 46 36 2 14 12 3 4 15 0 2.55e-15 1.50e-11
3 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 815176 142 114 61 2 48 31 45 10 8 0 2.89e-15 1.50e-11
4 CTCF CCCTC-binding factor (zinc finger protein) 551552 46 40 36 0 3 7 5 1 26 4 3.77e-15 1.50e-11
5 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 586520 106 77 84 2 3 4 10 3 49 37 4.33e-15 1.50e-11
6 CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 595696 63 61 19 5 10 33 8 12 0 0 6.55e-15 1.67e-11
7 ARID1A AT rich interactive domain 1A (SWI-like) 1437656 98 77 78 3 3 4 3 1 59 28 6.77e-15 1.67e-11
8 FBXW7 F-box and WD repeat domain containing 7 640832 32 26 25 1 7 13 2 1 7 2 3.46e-14 7.40e-11
9 PPP2R1A protein phosphatase 2 (formerly 2A), regulatory subunit A , alpha isoform 433504 30 27 18 3 4 14 1 9 2 0 4.21e-14 7.40e-11
10 FGFR2 fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome) 668608 27 25 14 1 1 7 5 10 2 2 4.29e-14 7.40e-11
11 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog 175336 27 27 6 0 17 1 9 0 0 0 4.80e-14 7.53e-11
12 ARID5B AT rich interactive domain 5B (MRF1-like) 894536 29 26 28 8 3 6 4 2 12 2 6.00e-14 8.63e-11
13 SPOP speckle-type POZ protein 287928 19 18 14 0 10 1 2 3 3 0 1.16e-13 1.54e-10
14 CCND1 cyclin D1 123256 12 12 11 1 3 3 1 1 4 0 2.47e-11 3.05e-08
15 MUC5B mucin 5B, oligomeric mucus/gel-forming 1795768 61 39 61 30 10 31 9 3 6 2 1.07e-10 1.23e-07
16 ZFHX3 zinc finger homeobox 3 2704440 70 41 62 11 15 28 4 2 21 0 1.33e-09 1.44e-06
17 SMTNL2 smoothelin-like 2 157728 9 9 3 2 0 2 0 0 7 0 5.96e-09 6.05e-06
18 MLL4 1133608 40 28 38 7 9 12 8 2 9 0 2.40e-08 0.000023
19 BCOR BCL6 co-repressor 1260832 37 29 28 13 4 18 11 1 3 0 3.39e-08 0.000031
20 TNFAIP6 tumor necrosis factor, alpha-induced protein 6 212784 12 12 8 0 4 1 1 0 6 0 4.38e-08 0.000038
21 GIGYF2 GRB10 interacting GYF protein 2 951576 24 21 20 6 3 6 5 0 10 0 7.27e-08 0.000060
22 CSMD3 CUB and Sushi multiple domains 3 2844560 88 37 85 18 27 29 13 6 4 9 2.59e-07 0.00020
23 RBMX RNA binding motif protein, X-linked 299584 13 13 7 0 2 3 0 1 7 0 2.80e-07 0.00021
24 NFASC neurofascin homolog (chicken) 1020272 27 24 27 6 8 11 4 2 2 0 9.33e-07 0.00065
25 FOXA2 forkhead box A2 254944 9 9 9 1 4 0 0 0 5 0 9.45e-07 0.00065
26 RASA1 RAS p21 protein activator (GTPase activating protein) 1 715976 23 18 22 2 5 5 3 1 9 0 1.65e-06 0.0011
27 ETV3 ets variant gene 3 110112 10 9 10 0 1 2 5 0 2 0 2.13e-06 0.0014
28 FAM9A family with sequence similarity 9, member A 223944 16 10 15 1 3 5 2 0 4 2 3.29e-06 0.0020
29 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 145328 8 8 5 0 2 2 4 0 0 0 3.57e-06 0.0021
30 LOC642587 77128 7 7 4 1 1 1 0 0 5 0 3.78e-06 0.0022
31 NFE2L2 nuclear factor (erythroid-derived 2)-like 2 443672 12 12 9 0 0 3 6 2 1 0 4.40e-06 0.0025
32 RB1 retinoblastoma 1 (including osteosarcoma) 682992 23 18 22 3 6 5 4 0 4 4 5.06e-06 0.0027
33 ESR1 estrogen receptor 1 348688 10 10 9 1 0 3 3 2 2 0 6.52e-06 0.0034
34 LRCH2 leucine-rich repeats and calponin homology (CH) domain containing 2 369272 21 17 20 2 10 6 2 0 3 0 6.65e-06 0.0034
35 ELFN2 extracellular leucine-rich repeat and fibronectin type III domain containing 2 225432 12 11 12 4 1 8 0 2 1 0 0.000011 0.0052

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 SYNE1 spectrin repeat containing, nuclear envelope 1 91 22 1 5456 1 0.071 1
2 A4GNT alpha-1,4-N-acetylglucosaminyltransferase 5 0 0 0 0 1 1
3 AACS acetoacetyl-CoA synthetase 6 0 0 0 0 1 1
4 ABCA9 ATP-binding cassette, sub-family A (ABC1), member 9 22 0 0 0 0 1 1
5 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 7 0 0 0 0 1 1
6 ABCF2 ATP-binding cassette, sub-family F (GCN20), member 2 4 0 0 0 0 1 1
7 ABHD2 abhydrolase domain containing 2 2 0 0 0 0 1 1
8 ABHD4 abhydrolase domain containing 4 8 0 0 0 0 1 1
9 ACADS acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain 4 0 0 0 0 1 1
10 ACOT11 acyl-CoA thioesterase 11 4 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
3634 DMBT1 deleted in malignant brain tumors 1 27 0 1 3
2389 CDCP1 CUB domain containing protein 1 9 0 1 1
3655 DNAH11 dynein, axonemal, heavy chain 11 55 0 1 1
6719 KIAA1432 KIAA1432 14 0 1 1
6763 KIF20B 34 0 1 1
7053 LARP1 La ribonucleoprotein domain family, member 1 13 0 1 1
12200 SLK STE20-like kinase (yeast) 13 0 1 1
14276 VPS13D vacuolar protein sorting 13 homolog D (S. cerevisiae) 30 0 1 1
3659 DNAH5 dynein, axonemal, heavy chain 5 78 1 1 2
3662 DNAH9 dynein, axonemal, heavy chain 9 58 1 1 1

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: 190. 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 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 CALM2(3), CALML6(3), CDS1(4), DGKA(9), DGKB(14), DGKD(11), DGKE(3), DGKG(10), DGKH(9), DGKI(16), DGKZ(8), IMPA1(3), IMPA2(5), INPP1(2), INPP4A(16), INPP4B(12), INPP5A(4), INPP5B(4), INPP5D(9), INPPL1(14), ITPK1(2), ITPKB(7), ITPR1(23), ITPR2(25), ITPR3(15), OCRL(15), PI4KA(9), PI4KB(6), PIK3C2A(14), PIK3C2B(10), PIK3C2G(12), PIK3C3(9), PIK3CA(142), PIK3CB(13), PIK3CD(9), PIK3CG(18), PIK3R1(106), PIK3R2(3), PIK3R3(9), PIK3R5(7), PIP4K2A(2), PIP4K2B(7), PIP4K2C(3), PIP5K1A(6), PIP5K1B(3), PIP5K1C(4), PLCB1(4), PLCB2(7), PLCB3(9), PLCB4(16), PLCD1(5), PLCD3(3), PLCD4(10), PLCE1(31), PLCG1(8), PLCG2(23), PLCZ1(11), PRKCA(7), PRKCG(6), PTEN(208), PTPMT1(1), SYNJ1(24), SYNJ2(8) 43792584 1019 212 833 215 215 262 191 47 215 89 <1.00e-15 <9.78e-15
2 SIG_CHEMOTAXIS Genes related to chemotaxis ACTR2, ACTR3, AKT1, AKT2, AKT3, ANGPTL2, ARHGAP1, ARHGAP4, ARHGEF11, BTK, CDC42, CFL1, CFL2, GDI1, GDI2, INPPL1, ITPR1, ITPR2, ITPR3, LIMK1, MYLK, MYLK2, P101-PI3K, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PDK1, PIK3CA, PIK3CD, PIK3CG, PIK3R1, PITX2, PPP1R13B, PTEN, RACGAP1, RHO, ROCK1, ROCK2, RPS4X, SAG, WASF1, WASL 44 ACTR2(5), ACTR3(1), AKT1(3), AKT2(4), AKT3(7), ANGPTL2(4), ARHGAP1(2), ARHGAP4(8), ARHGEF11(18), BTK(4), CDC42(4), CFL1(1), CFL2(7), GDI1(4), GDI2(1), INPPL1(14), ITPR1(23), ITPR2(25), ITPR3(15), LIMK1(6), MYLK(10), MYLK2(6), PAK1(1), PAK2(3), PAK3(13), PAK6(2), PAK7(6), PDK1(2), PIK3CA(142), PIK3CD(9), PIK3CG(18), PIK3R1(106), PITX2(9), PPP1R13B(5), PTEN(208), RACGAP1(7), RHO(3), ROCK1(15), ROCK2(10), RPS4X(1), SAG(4), WASF1(3), WASL(7) 25519200 746 209 565 117 155 155 137 32 178 89 <1.00e-15 <9.78e-15
3 MTORPATHWAY Mammalian target of rapamycin (mTOR) senses mitogenic factors and nutrients, including ATP, and induces cell proliferation. AKT1, EIF3S10, EIF4A1, EIF4A2, EIF4B, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FKBP1A, FRAP1, MKNK1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1, TSC1, TSC2 21 AKT1(3), EIF4A1(4), EIF4A2(4), EIF4B(5), EIF4E(2), EIF4G1(10), EIF4G2(6), EIF4G3(18), MKNK1(3), PDK2(3), PDPK1(2), PIK3CA(142), PIK3R1(106), PPP2CA(4), PTEN(208), RPS6(6), RPS6KB1(2), TSC1(9), TSC2(13) 9352328 550 208 375 33 88 81 114 25 157 85 <1.00e-15 <9.78e-15
4 SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES Genes related to the insulin receptor pathway AKT1, AKT2, AKT3, BRD4, CAP1, CBL, CDC42, CDKN2A, F2RL2, FLOT1, FLOT2, FOXO1A, GRB2, GSK3A, GSK3B, IGFBP1, INPPL1, IRS1, IRS2, IRS4, LNPEP, MAPK1, MAPK3, PARD3, PARD6A, PDK1, PIK3CA, PIK3CD, PIK3R1, PPYR1, PSCD3, PTEN, PTPN1, RAF1, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SERPINB6, SFN, SHC1, SLC2A4, SORBS1, SOS1, SOS2, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ 48 AKT1(3), AKT2(4), AKT3(7), BRD4(7), CAP1(7), CBL(8), CDC42(4), CDKN2A(1), F2RL2(2), FLOT2(1), GRB2(3), GSK3A(8), GSK3B(8), IGFBP1(4), INPPL1(14), IRS1(10), IRS4(16), LNPEP(6), MAPK1(2), MAPK3(3), PARD3(19), PDK1(2), PIK3CA(142), PIK3CD(9), PIK3R1(106), PPYR1(6), PTEN(208), PTPN1(4), RAF1(5), RPS6KA1(1), RPS6KA2(14), RPS6KA3(15), RPS6KB1(2), SERPINB6(2), SHC1(5), SLC2A4(5), SORBS1(14), SOS1(10), SOS2(16), YWHAE(2), YWHAG(3), YWHAH(2), YWHAQ(1), YWHAZ(1) 20890280 712 208 527 94 136 135 150 29 175 87 <1.00e-15 <9.78e-15
5 EIF4PATHWAY The eIF-4F complex recognizes 5' mRNA caps, recruits RNA helicases, and maintains mRNA-ribosome bridging. AKT1, EIF4A1, EIF4A2, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FRAP1, GHR, IRS1, MAPK1, MAPK14, MAPK3, MKNK1, PABPC1, PDK2, PDPK1, PIK3CA, PIK3R1, PRKCA, PRKCB1, PTEN, RPS6KB1 22 AKT1(3), EIF4A1(4), EIF4A2(4), EIF4E(2), EIF4G1(10), EIF4G2(6), EIF4G3(18), GHR(8), IRS1(10), MAPK1(2), MAPK14(4), MAPK3(3), MKNK1(3), PABPC1(8), PDK2(3), PDPK1(2), PIK3CA(142), PIK3R1(106), PRKCA(7), PTEN(208), RPS6KB1(2) 10285800 555 206 380 37 85 76 123 28 158 85 <1.00e-15 <9.78e-15
6 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 AIFM1(9), AKT1(3), AKT2(4), AKT3(7), APAF1(11), ATM(42), BAD(2), BAX(3), BCL2L1(3), BID(2), BIRC2(10), BIRC3(2), CAPN1(2), CAPN2(5), CASP10(8), CASP3(3), CASP6(3), CASP7(4), CASP8(12), CASP9(2), CFLAR(5), CHUK(7), CSF2RB(9), CYCS(2), DFFB(3), FAS(6), FASLG(5), IKBKB(8), IL1B(2), IL1R1(4), IL1RAP(5), IL3RA(8), IRAK1(4), IRAK2(5), IRAK3(7), IRAK4(5), MAP3K14(4), MYD88(1), NFKB1(7), NFKB2(9), NFKBIA(2), NTRK1(11), PIK3CA(142), PIK3CB(13), PIK3CD(9), PIK3CG(18), PIK3R1(106), PIK3R2(3), PIK3R3(9), PIK3R5(7), PPP3CA(2), PPP3CB(5), PPP3CC(4), PPP3R2(1), PRKACA(4), PRKACG(7), PRKAR1A(4), PRKAR1B(4), PRKAR2A(3), PRKAR2B(3), RELA(4), RIPK1(8), TNFRSF10A(2), TNFRSF10B(4), TNFRSF10C(2), TNFRSF10D(5), TNFRSF1A(4), TP53(48), TRAF2(2) 29073536 679 206 554 120 151 194 109 39 145 41 <1.00e-15 <9.78e-15
7 IGF1MTORPATHWAY Growth factor IGF-1 activates AKT, Gsk3-beta, and mTOR to promote muscle hypertrophy. AKT1, EIF2B5, EIF2S1, EIF2S2, EIF2S3, EIF4E, EIF4EBP1, FRAP1, GSK3B, IGF1, IGF1R, INPPL1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1 19 AKT1(3), EIF2B5(4), EIF2S2(5), EIF2S3(5), EIF4E(2), GSK3B(8), IGF1(2), IGF1R(10), INPPL1(14), PDK2(3), PDPK1(2), PIK3CA(142), PIK3R1(106), PPP2CA(4), PTEN(208), RPS6(6), RPS6KB1(2) 7229448 526 206 350 35 83 68 111 21 158 85 <1.00e-15 <9.78e-15
8 METPATHWAY The hepatocyte growth factor receptor c-Met stimulates proliferation and alters cell motility and adhesion on binding the ligand HGF. ACTA1, CRK, CRKL, DOCK1, ELK1, FOS, GAB1, GRB2, GRF2, HGF, HRAS, ITGA1, ITGB1, JUN, MAP2K1, MAP2K2, MAP4K1, MAPK1, MAPK3, MAPK8, MET, PAK1, PIK3CA, PIK3R1, PTEN, PTK2, PTK2B, PTPN11, PXN, RAF1, RAP1A, RAP1B, RASA1, SOS1, SRC, STAT3 34 ACTA1(3), CRK(1), CRKL(4), DOCK1(17), ELK1(2), FOS(2), GAB1(5), GRB2(3), HGF(13), ITGA1(13), ITGB1(5), JUN(1), MAP2K1(2), MAP4K1(9), MAPK1(2), MAPK3(3), MAPK8(7), MET(9), PAK1(1), PIK3CA(142), PIK3R1(106), PTEN(208), PTK2(8), PTK2B(13), PTPN11(5), PXN(4), RAF1(5), RAP1A(3), RAP1B(2), RASA1(23), SOS1(10), SRC(2), STAT3(8) 16040640 641 205 462 67 116 112 130 27 171 85 <1.00e-15 <9.78e-15
9 PTENPATHWAY PTEN suppresses AKT-induced cell proliferation and antagonizes the action of PI3K. AKT1, BCAR1, CDKN1B, FOXO3A, GRB2, ILK, ITGB1, MAPK1, MAPK3, PDK2, PDPK1, PIK3CA, PIK3R1, PTEN, PTK2, SHC1, SOS1, TNFSF6 15 AKT1(3), CDKN1B(6), GRB2(3), ILK(4), ITGB1(5), MAPK1(2), MAPK3(3), PDK2(3), PDPK1(2), PIK3CA(142), PIK3R1(106), PTEN(208), PTK2(8), SHC1(5), SOS1(10) 6596056 510 203 333 25 74 64 114 22 151 85 <1.00e-15 <9.78e-15
10 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(5), CDKN2A(1), E2F1(6), MDM2(3), MYC(6), PIK3CA(142), PIK3R1(106), POLR1A(11), POLR1B(10), POLR1C(2), POLR1D(1), RAC1(1), RB1(23), TBX2(2), TP53(48) 7272352 367 198 251 40 83 72 66 25 80 41 <1.00e-15 <9.78e-15

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 15. 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 HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION Genes involved in neuroactive ligand-receptor interaction ADCYAP1R1, ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA2A, ADRA2B, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BRS3, C3AR1, C5AR1, CALCR, CALCRL, CCKAR, CCKBR, CGA, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CNR1, CNR2, CRHR1, CRHR2, CTSG, CYSLTR1, CYSLTR2, DRD1, DRD2, DRD3, DRD4, DRD5, EDG1, EDG2, EDG3, EDG4, EDG5, EDG6, EDG7, EDG8, EDNRA, EDNRB, F2, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHB, FSHR, GABBR1, GABBR2, GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GABRB1, GABRB2, GABRB3, GABRD, GABRE, GABRG1, GABRG2, GABRG3, GABRP, GABRQ, GABRR1, GABRR2, GALR1, GALR2, GALR3, GCGR, GH1, GH2, GHR, GHRHR, GHSR, GIPR, GLP1R, GLP2R, GLRA1, GLRA2, GLRA3, GLRB, GNRHR, GPR156, GPR23, GPR35, GPR50, GPR63, GPR83, GRIA1, GRIA2, GRIA3, GRIA4, GRID1, GRID2, GRIK1, GRIK2, GRIK3, GRIK4, GRIK5, GRIN1, GRIN2A, GRIN2B, GRIN2C, GRIN2D, GRIN3A, GRIN3B, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GRPR, GZMA, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HRH4, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, KISS1R, LEP, LEPR, LHB, LHCGR, LTB4R, LTB4R2, MAS1, MC1R, MC2R, MC3R, MC4R, MC5R, MCHR1, MCHR2, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPBWR1, NPBWR2, NPFFR1, NPFFR2, NPY1R, NPY2R, NPY5R, NR3C1, NTSR1, NTSR2, OPRD1, OPRK1, OPRL1, OPRM1, OXTR, P2RX1, P2RX2, P2RX3, P2RX4, P2RX5, P2RX7, P2RXL1, P2RY1, P2RY10, P2RY11, P2RY13, P2RY14, P2RY2, P2RY4, P2RY5, P2RY6, P2RY8, PARD3, PPYR1, PRL, PRLHR, PRLR, PRSS1, PRSS2, PRSS3, PTAFR, PTGDR, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, PTH2R, PTHR1, RXFP1, RXFP2, SCTR, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, TAAR9, TACR1, TACR2, TACR3, TBXA2R, THRA, THRB, TRHR, TRPV1, TSHB, TSHR, TSPO, UTS2R, VIPR1, VIPR2 217 ADCYAP1R1(5), ADORA1(3), ADORA2A(4), ADORA2B(1), ADORA3(3), ADRA1A(8), ADRA1B(5), ADRA2B(6), ADRB1(1), ADRB2(5), AGTR1(1), AGTR2(7), AVPR1A(7), AVPR1B(2), AVPR2(4), BDKRB1(2), BDKRB2(7), C3AR1(7), C5AR1(3), CALCR(4), CALCRL(7), CCKAR(9), CCKBR(3), CGA(1), CHRM1(3), CHRM2(8), CHRM3(6), CHRM4(6), CHRM5(8), CNR1(6), CNR2(3), CRHR1(2), CRHR2(1), CTSG(3), CYSLTR1(6), CYSLTR2(3), DRD1(5), DRD2(6), DRD3(4), DRD5(8), EDNRA(5), F2(8), F2R(6), F2RL1(2), F2RL2(2), FPR1(1), FSHR(14), GABBR1(8), GABBR2(13), GABRA1(8), GABRA2(10), GABRA3(12), GABRA4(12), GABRA5(6), GABRA6(6), GABRB1(7), GABRB2(12), GABRB3(9), GABRE(5), GABRG1(6), GABRG2(14), GABRG3(7), GABRP(3), GABRQ(5), GABRR1(3), GALR1(2), GALR3(2), GH1(2), GH2(2), GHR(8), GHRHR(1), GHSR(7), GIPR(3), GLP1R(5), GLP2R(8), GLRA1(6), GLRA2(6), GLRA3(8), GLRB(6), GNRHR(3), GPR156(4), GPR50(4), GPR63(4), GPR83(2), GRIA1(11), GRIA2(17), GRIA3(18), GRIA4(15), GRID1(7), GRID2(9), GRIK1(10), GRIK2(10), GRIK3(13), GRIK4(3), GRIK5(15), GRIN1(3), GRIN2A(18), GRIN2B(18), GRIN2C(5), GRIN2D(5), GRIN3A(12), GRM1(18), GRM2(5), GRM3(14), GRM4(12), GRM5(19), GRM6(9), GRM7(10), GRM8(17), GRPR(3), GZMA(6), HCRTR2(6), HRH1(9), HRH2(3), HRH4(4), HTR1A(11), HTR1B(4), HTR1D(5), HTR1E(5), HTR1F(10), HTR2A(9), HTR2B(2), HTR2C(13), HTR4(5), HTR5A(7), HTR6(3), HTR7(3), LEP(1), LEPR(10), LHB(2), LHCGR(14), LTB4R(2), LTB4R2(3), MAS1(1), MC2R(1), MC3R(5), MC4R(3), MC5R(8), MCHR1(7), MCHR2(1), MLNR(2), MTNR1A(4), MTNR1B(3), NMBR(3), NMUR1(4), NMUR2(6), NPFFR1(2), NPFFR2(9), NPY1R(3), NPY2R(3), NPY5R(7), NR3C1(11), NTSR1(4), NTSR2(1), OPRK1(6), OPRM1(8), OXTR(4), P2RX1(4), P2RX3(7), P2RX4(1), P2RX5(5), P2RX7(1), P2RY1(2), P2RY10(5), P2RY11(8), P2RY13(1), P2RY14(3), P2RY2(3), P2RY4(5), P2RY6(3), PARD3(19), PPYR1(6), PRL(4), PRLHR(1), PRLR(3), PRSS1(4), PRSS3(2), PTAFR(4), PTGDR(6), PTGER2(2), PTGER3(7), PTGER4(7), PTGFR(9), PTGIR(2), PTH2R(8), RXFP1(15), RXFP2(11), SCTR(3), SSTR2(2), SSTR3(3), TAAR1(6), TAAR2(4), TAAR5(5), TAAR6(4), TAAR8(2), TAAR9(6), TACR1(5), TACR2(2), TACR3(8), THRA(4), THRB(2), TRHR(2), TRPV1(3), TSHB(3), TSHR(7), VIPR1(2) 75157640 1220 150 1178 439 372 500 187 51 108 2 2.3e-09 1.4e-06
2 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 162 ADCY1(12), ADCY2(10), ADCY3(5), ADCY4(7), ADCY7(5), ADCY8(15), ADCY9(17), ADORA2A(4), ADORA2B(1), ADRA1A(8), ADRA1B(5), ADRB1(1), ADRB2(5), AGTR1(1), ATP2A1(9), ATP2A2(6), ATP2A3(9), ATP2B1(14), ATP2B2(8), ATP2B3(14), ATP2B4(13), AVPR1A(7), AVPR1B(2), BDKRB1(2), BDKRB2(7), BST1(1), CACNA1A(15), CACNA1C(21), CACNA1D(23), CACNA1E(40), CACNA1F(30), CACNA1G(16), CACNA1I(5), CACNA1S(22), CALM2(3), CALML6(3), CAMK2A(6), CAMK2B(1), CAMK2D(3), CAMK2G(4), CAMK4(3), CCKAR(9), CCKBR(3), CD38(5), CHRM1(3), CHRM2(8), CHRM3(6), CHRM5(8), CHRNA7(4), CYSLTR1(6), CYSLTR2(3), DRD1(5), EDNRA(5), EGFR(10), ERBB2(3), ERBB3(14), ERBB4(19), F2R(6), GNA11(2), GNA14(5), GNA15(1), GNAL(6), GNAS(16), GRIN1(3), GRIN2A(18), GRIN2C(5), GRIN2D(5), GRM1(18), GRM5(19), GRPR(3), HRH1(9), HRH2(3), HTR2A(9), HTR2B(2), HTR2C(13), HTR4(5), HTR5A(7), HTR6(3), HTR7(3), ITPKB(7), ITPR1(23), ITPR2(25), ITPR3(15), LHCGR(14), LTB4R2(3), MYLK(10), MYLK2(6), NOS1(14), NOS3(6), NTSR1(4), OXTR(4), P2RX1(4), P2RX3(7), P2RX4(1), P2RX5(5), P2RX7(1), PDE1A(10), PDE1B(6), PDE1C(10), PDGFRA(19), PDGFRB(10), PHKA1(13), PHKA2(12), PHKB(10), PHKG1(5), PHKG2(2), PLCB1(4), PLCB2(7), PLCB3(9), PLCB4(16), PLCD1(5), PLCD3(3), PLCD4(10), PLCE1(31), PLCG1(8), PLCG2(23), PLCZ1(11), PLN(1), PPID(2), PPP3CA(2), PPP3CB(5), PPP3CC(4), PPP3R2(1), PRKACA(4), PRKACG(7), PRKCA(7), PRKCG(6), PRKX(2), PTAFR(4), PTGER3(7), PTGFR(9), PTK2B(13), RYR1(59), RYR3(65), SLC25A4(2), SLC25A5(1), SLC25A6(4), SLC8A1(9), SLC8A2(3), SLC8A3(9), SPHK1(2), SPHK2(1), TACR1(5), TACR2(2), TACR3(8), TNNC1(2), TNNC2(3), TRHR(2), TRPC1(12), VDAC1(2), VDAC2(1), VDAC3(2) 91768680 1296 144 1262 481 375 527 180 64 140 10 1.2e-06 0.0003
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 226 ACVR1B(5), ACVR1C(3), AKT1(3), AKT2(4), AKT3(7), ARRB1(4), ARRB2(3), ATF2(6), ATF4(3), BDNF(6), BRAF(9), CACNA1A(15), CACNA1C(21), CACNA1D(23), CACNA1E(40), CACNA1F(30), CACNA1G(16), CACNA1I(5), CACNA1S(22), CACNA2D1(9), CACNA2D2(8), CACNA2D3(17), CACNA2D4(13), CACNB1(7), CACNB2(9), CACNB3(4), CACNB4(11), CACNG2(2), CACNG3(8), CACNG4(6), CACNG5(4), CACNG6(4), CACNG7(7), CASP3(3), CD14(2), CDC25B(2), CDC42(4), CHUK(7), CRK(1), CRKL(4), DAXX(6), DDIT3(1), DUSP1(2), DUSP10(5), DUSP14(3), DUSP16(8), DUSP3(1), DUSP5(3), DUSP6(1), DUSP7(3), DUSP9(1), ECSIT(3), EGF(17), EGFR(10), ELK1(2), ELK4(2), FAS(6), FASLG(5), FGF10(1), FGF11(1), FGF12(2), FGF13(4), FGF14(3), FGF18(1), FGF21(1), FGF23(3), FGF5(6), FGF6(1), FGF7(4), FGF8(1), FGF9(1), FGFR1(7), FGFR4(8), FLNA(27), FLNB(28), FLNC(27), FOS(2), GNA12(7), GNG12(1), GRB2(3), IKBKB(8), IL1B(2), IL1R1(4), IL1R2(5), JUN(1), MAP2K1(2), MAP2K3(7), MAP2K4(4), MAP2K5(2), MAP2K6(6), MAP3K1(24), MAP3K10(6), MAP3K12(6), MAP3K13(11), MAP3K14(4), MAP3K2(8), MAP3K3(6), MAP3K4(16), MAP3K5(19), MAP3K6(4), MAP3K7(8), MAP3K8(6), MAP4K1(9), MAP4K2(6), MAP4K3(14), MAP4K4(7), MAPK1(2), MAPK10(7), MAPK13(2), MAPK14(4), MAPK3(3), MAPK7(11), MAPK8(7), MAPK8IP1(4), MAPK9(4), MAPKAPK2(4), MAPKAPK3(2), MAPKAPK5(4), MAPT(9), MAX(4), MEF2C(8), MKNK1(3), MKNK2(3), MOS(6), MRAS(1), MYC(6), NF1(30), NFATC2(9), NFATC4(7), NFKB1(7), NFKB2(9), NLK(5), NR4A1(4), NTF3(4), NTRK1(11), NTRK2(11), PAK1(1), PAK2(3), PDGFB(2), PDGFRA(19), PDGFRB(10), PLA2G12A(1), PLA2G12B(2), PLA2G2D(2), PLA2G2E(3), PLA2G2F(2), PLA2G3(3), PLA2G4A(9), PLA2G6(7), PPM1A(6), PPM1B(3), PPP3CA(2), PPP3CB(5), PPP3CC(4), PPP3R2(1), PPP5C(4), PRKACA(4), PRKACG(7), PRKCA(7), PRKCG(6), PRKX(2), PTPN5(4), PTPN7(4), PTPRR(13), RAC1(1), RAC2(2), RAF1(5), RAP1A(3), RAP1B(2), RAPGEF2(26), RASA2(7), RASGRF1(8), RASGRF2(11), RASGRP1(6), RASGRP2(2), RASGRP3(5), RASGRP4(5), RPS6KA1(1), RPS6KA2(14), RPS6KA3(15), RPS6KA4(1), RPS6KA5(7), RPS6KA6(12), RRAS(1), RRAS2(4), SOS1(10), SOS2(16), SRF(2), STK3(7), STK4(5), STMN1(4), TAOK1(9), TAOK2(6), TAOK3(3), TGFB1(2), TGFB2(5), TGFB3(8), TGFBR1(3), TGFBR2(6), TNFRSF1A(4), TRAF2(2), TRAF6(3), ZAK(11) 96983624 1341 145 1309 424 361 537 161 89 175 18 1.5e-06 0.0003
4 HSA04330_NOTCH_SIGNALING_PATHWAY Genes involved in Notch signaling pathway ADAM17, APH1A, CIR, CREBBP, CTBP1, CTBP2, DLL1, DLL3, DLL4, DTX1, DTX2, DTX3, DTX3L, DTX4, DVL1, DVL2, DVL3, EP300, GCN5L2, HDAC1, HDAC2, HES1, JAG1, JAG2, LFNG, LOC652788, MAML1, MAML2, MAML3, MFNG, NCOR2, NCSTN, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NUMB, NUMBL, PCAF, PSEN1, PSEN2, PSENEN, PTCRA, RBPJ, RBPJL, RFNG, SNW1 37 ADAM17(8), CREBBP(24), CTBP2(5), DLL1(6), DLL3(5), DLL4(2), DTX1(5), DTX2(2), DTX3(4), DTX3L(4), DTX4(4), DVL2(5), DVL3(7), EP300(23), HDAC1(3), HDAC2(4), HES1(1), JAG1(13), MAML1(6), MAML2(5), MAML3(14), MFNG(3), NCOR2(16), NCSTN(7), NOTCH2(9), NOTCH3(20), NOTCH4(10), NUMB(7), NUMBL(3), PSEN1(5), PSEN2(3), RBPJ(4), RBPJL(7), SNW1(5) 20548784 249 80 243 77 59 106 26 12 42 4 0.000014 0.0022
5 CALCIUM_REGULATION_IN_CARDIAC_CELLS ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADRA1A, ADRA1B, ADRA1D, ADRB1, ADRB2, ADRB3, ANXA6, ARRB1, ARRB2, ATP1A4, ATP1B1, ATP1B2, ATP1B3, ATP2A2, ATP2A3, ATP2B1, ATP2B2, ATP2B3, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1S, CACNB1, CACNB3, CALM1, CALM2, CALM3, CALR, CAMK1, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CAMK4, CASQ1, CASQ2, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, FXYD2, GJA1, GJA12, GJA4, GJA5, GJB1, GJB2, GJB3, GJB4, GJB5, GJB6, GNA11, GNAI2, GNAI3, GNAO1, GNAQ, GNAZ, GNB1, GNB2, GNB3, GNB4, GNB5, GNG12, GNG13, GNG2, GNG3, GNG4, GNG5, GNG7, GNGT1, GRK4, GRK5, GRK6, ITPR1, ITPR2, ITPR3, KCNB1, KCNJ3, KCNJ5, MGC11266, MYCBP, NME7, PEA15, PKIA, PKIB, PKIG, PLCB3, PLN, PRKACA, PRKACB, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCQ, PRKCZ, PRKD1, RGS1, RGS10, RGS11, RGS14, RGS16, RGS17, RGS18, RGS19, RGS2, RGS20, RGS3, RGS4, RGS5, RGS6, RGS7, RGS9, RYR1, RYR2, RYR3, SARA1, SFN, SLC8A1, SLC8A3, USP5, YWHAB, YWHAH, YWHAQ, YWHAQ, MIB1 132 ADCY1(12), ADCY2(10), ADCY3(5), ADCY4(7), ADCY5(11), ADCY6(10), ADCY7(5), ADCY8(15), ADCY9(17), ADRA1A(8), ADRA1B(5), ADRB1(1), ADRB2(5), ANXA6(8), ARRB1(4), ARRB2(3), ATP1A4(19), ATP1B1(3), ATP1B2(4), ATP1B3(2), ATP2A2(6), ATP2A3(9), ATP2B1(14), ATP2B2(8), ATP2B3(14), CACNA1A(15), CACNA1C(21), CACNA1D(23), CACNA1E(40), CACNA1S(22), CACNB1(7), CACNB3(4), CALM2(3), CALR(1), CAMK1(2), CAMK2A(6), CAMK2B(1), CAMK2D(3), CAMK2G(4), CAMK4(3), CASQ1(4), CASQ2(6), CHRM1(3), CHRM2(8), CHRM3(6), CHRM4(6), CHRM5(8), GJA1(5), GJA4(1), GJB1(1), GJB2(2), GJB3(2), GJB4(3), GJB5(2), GJB6(3), GNA11(2), GNAI2(4), GNAI3(3), GNAO1(4), GNAZ(4), GNB1(1), GNB2(6), GNB4(3), GNB5(1), GNG12(1), GNG2(2), GNG3(2), GRK4(9), GRK5(8), GRK6(2), ITPR1(23), ITPR2(25), ITPR3(15), KCNB1(11), KCNJ3(9), KCNJ5(5), MIB1(6), MYCBP(1), NME7(2), PEA15(2), PLCB3(9), PLN(1), PRKACA(4), PRKAR1A(4), PRKAR1B(4), PRKAR2A(3), PRKAR2B(3), PRKCA(7), PRKCD(4), PRKCE(7), PRKCG(6), PRKCH(7), PRKCQ(6), PRKCZ(3), PRKD1(6), RGS1(4), RGS10(2), RGS14(4), RGS16(3), RGS17(3), RGS18(2), RGS2(2), RGS20(1), RGS3(8), RGS4(6), RGS5(4), RGS6(6), RGS7(6), RGS9(10), RYR1(59), RYR3(65), SLC8A1(9), SLC8A3(9), USP5(11), YWHAH(2), YWHAQ(1) 64487192 862 126 840 312 244 360 103 42 107 6 4e-05 0.005
6 WNTPATHWAY The Wnt glycoprotein binds to membrane-bound receptors such as Frizzled to activate a number of signaling pathways, including that of beta-catenin. APC, AXIN1, BTRC, CCND1, CREBBP, CSNK1A1, CSNK1D, CSNK2A1, CTBP1, CTNNB1, DVL1, FRAT1, FZD1, GSK3B, HDAC1, MADH4, MAP3K7, MAP3K7IP1, MYC, NLK, PPARD, PPP2CA, TCF1, TLE1, WIF1, WNT1 18 APC(36), AXIN1(7), BTRC(11), CREBBP(24), CSNK1A1(4), CSNK2A1(7), FZD1(3), GSK3B(8), HDAC1(3), MAP3K7(8), MYC(6), NLK(5), PPARD(3), PPP2CA(4), TLE1(8), WIF1(4), WNT1(1) 8945360 142 59 139 26 38 54 15 7 22 6 0.000059 0.0061
7 MTORPATHWAY Mammalian target of rapamycin (mTOR) senses mitogenic factors and nutrients, including ATP, and induces cell proliferation. AKT1, EIF3S10, EIF4A1, EIF4A2, EIF4B, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FKBP1A, FRAP1, MKNK1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1, TSC1, TSC2 18 AKT1(3), EIF4A1(4), EIF4A2(4), EIF4B(5), EIF4E(2), EIF4G1(10), EIF4G2(6), EIF4G3(18), MKNK1(3), PDK2(3), PDPK1(2), PPP2CA(4), RPS6(6), RPS6KB1(2), TSC1(9), TSC2(13) 7641128 94 52 94 24 22 38 11 7 16 0 0.0002 0.017
8 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 188 ABI2(1), ACTN1(7), ACTN2(7), ACTN3(6), ACTN4(6), APC(36), ARAF(8), ARHGEF1(9), ARHGEF12(19), ARHGEF4(5), ARHGEF6(16), ARHGEF7(11), ARPC1A(5), ARPC1B(3), ARPC3(1), ARPC4(1), ARPC5(1), BDKRB1(2), BDKRB2(7), BRAF(9), CD14(2), CDC42(4), CFL1(1), CFL2(7), CHRM1(3), CHRM2(8), CHRM3(6), CHRM4(6), CHRM5(8), CRK(1), CRKL(4), CSK(1), CYFIP1(7), CYFIP2(17), DIAPH1(10), DIAPH2(18), DIAPH3(24), DOCK1(17), EGF(17), EGFR(10), EZR(4), F2(8), F2R(6), FGD1(10), FGD3(8), FGF10(1), FGF11(1), FGF12(2), FGF13(4), FGF14(3), FGF18(1), FGF21(1), FGF23(3), FGF5(6), FGF6(1), FGF7(4), FGF8(1), FGF9(1), FGFR1(7), FGFR4(8), FN1(31), GIT1(8), GNA12(7), GNA13(7), GNG12(1), GSN(4), IQGAP1(9), IQGAP2(21), IQGAP3(15), ITGA1(13), ITGA10(7), ITGA11(6), ITGA2(14), ITGA2B(7), ITGA3(6), ITGA4(8), ITGA5(9), ITGA6(10), ITGA7(8), ITGA8(14), ITGA9(13), ITGAD(5), ITGAE(7), ITGAL(12), ITGAM(19), ITGAV(6), ITGAX(7), ITGB1(5), ITGB2(10), ITGB3(10), ITGB4(6), ITGB5(4), ITGB6(4), ITGB7(4), ITGB8(4), LIMK1(6), LIMK2(10), MAP2K1(2), MAPK1(2), MAPK3(3), MOS(6), MRAS(1), MSN(12), MYH10(23), MYH14(17), MYH9(18), MYL2(1), MYL5(1), MYL7(3), MYL9(3), MYLK(10), MYLK2(6), MYLPF(2), NCKAP1(6), NCKAP1L(13), PAK1(1), PAK2(3), PAK3(13), PAK6(2), PAK7(6), PDGFB(2), PDGFRA(19), PDGFRB(10), PFN1(1), PFN2(1), PIK3CB(13), PIK3CD(9), PIK3CG(18), PIK3R2(3), PIK3R3(9), PIK3R5(7), PIP4K2A(2), PIP4K2B(7), PIP4K2C(3), PIP5K1A(6), PIP5K1B(3), PIP5K1C(4), PPP1CA(3), PPP1CB(4), PPP1CC(2), PPP1R12A(8), PPP1R12B(11), PTK2(8), PXN(4), RAC1(1), RAC2(2), RAF1(5), RDX(11), RHOA(3), ROCK1(15), ROCK2(10), RRAS(1), RRAS2(4), SCIN(3), SLC9A1(6), SOS1(10), SOS2(16), SSH1(10), SSH2(7), SSH3(3), TIAM1(20), TIAM2(14), VAV1(10), VAV2(3), VAV3(9), VCL(8), WAS(8), WASF1(3), WASF2(3), WASL(7) 94119720 1251 138 1222 418 327 498 173 69 166 18 0.00051 0.039
9 P38MAPKPATHWAY The Rho family GTPases activate the p38 MAPKs under environmental stress or in the presence of pro-inflammatory cytokines. ATF2, CDC42, CREB1, DAXX, DDIT3, ELK1, GRB2, HMGN1, HRAS, HSPB1, HSPB2, MAP2K4, MAP2K6, MAP3K1, MAP3K5, MAP3K7, MAP3K9, MAPK14, MAPKAPK2, MAPKAPK5, MAX, MEF2A, MEF2B, MEF2C, MEF2D, MKNK1, MYC, PDZGEF1, PLA2G4A, RAC1, RIPK1, RPS6KA5, SHC1, STAT1, TGFB1, TGFB2, TGFB3, TGFBR1, TRADD, TRAF2 37 ATF2(6), CDC42(4), CREB1(5), DAXX(6), DDIT3(1), ELK1(2), GRB2(3), HMGN1(1), HSPB2(1), MAP2K4(4), MAP2K6(6), MAP3K1(24), MAP3K5(19), MAP3K7(8), MAP3K9(3), MAPK14(4), MAPKAPK2(4), MAPKAPK5(4), MAX(4), MEF2A(3), MEF2B(1), MEF2C(8), MEF2D(5), MKNK1(3), MYC(6), PLA2G4A(9), RAC1(1), RIPK1(8), RPS6KA5(7), SHC1(5), STAT1(12), TGFB1(2), TGFB2(5), TGFB3(8), TGFBR1(3), TRAF2(2) 13175992 197 66 193 50 45 91 20 12 27 2 0.00072 0.049
10 TGFBPATHWAY The TGF-beta receptor responds to ligand binding by activating the SMAD family of transcriptional regulations, commonly blocking cell growth. APC, CDH1, CREBBP, EP300, MADH2, MADH3, MADH4, MADH7, MADHIP, MAP2K1, MAP3K7, MAP3K7IP1, MAPK3, SKIL, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2 13 APC(36), CDH1(12), CREBBP(24), EP300(23), MAP2K1(2), MAP3K7(8), MAPK3(3), SKIL(7), TGFB1(2), TGFB2(5), TGFB3(8), TGFBR1(3), TGFBR2(6) 9292808 139 56 135 37 26 59 19 8 23 4 0.001 0.062
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]

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