Uterine Corpus Endometrioid 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: UCEC.

Number of patients in set: 239

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): 240

Mutations seen in COSMIC: 1

Significantly mutated genes in COSMIC territory: 0

Genes with clustered mutations (&le 3 aa apart): 21

Significantly mutated genesets: 217

Significantly mutated genesets: (excluding sig. mutated genes): 50

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 2848
Frame_Shift_Ins 1040
In_Frame_Del 204
In_Frame_Ins 28
Indel 2
Missense_Mutation 112137
Nonsense_Mutation 11196
Nonstop_Mutation 160
Silent 36723
Splice_Site 2821
Total 167159
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 34661 3330542914 1e-05 10 0.53
C->(A/T) 52348 3324649891 0.000016 16 0.8
A->(C/G) 18461 3330542914 5.5e-06 5.5 0.28
C->G 6658 3324649891 2e-06 2 0.1
indel+null 16724 6655193044 2.5e-06 2.5 0.13
double_null 1584 6655193044 2.4e-07 0.24 0.012
Total 130436 6655193044 2e-05 20 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: 240. 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) 298272 198 150 121 5 17 12 54 5 90 20 <1.00e-15 <1.73e-11
2 ARID1A AT rich interactive domain 1A (SWI-like) 1385483 109 86 85 5 5 7 3 2 68 24 8.66e-15 7.48e-11
3 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog 168973 29 29 5 0 19 0 10 0 0 0 4.03e-14 9.78e-11
4 RPL22 ribosomal protein L22 92493 15 14 5 0 0 1 0 2 10 2 4.46e-14 9.78e-11
5 TP53 tumor protein p53 313329 40 36 30 2 12 9 4 3 12 0 4.50e-14 9.78e-11
6 ARID5B AT rich interactive domain 5B (MRF1-like) 862073 36 29 32 8 7 8 4 3 12 2 4.64e-14 9.78e-11
7 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 785593 138 110 61 2 49 31 44 8 6 0 4.93e-14 9.78e-11
8 PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 565235 67 52 55 2 3 6 13 3 31 11 5.05e-14 9.78e-11
9 CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 574078 66 63 21 5 11 35 8 12 0 0 5.30e-14 9.78e-11
10 CTCF CCCTC-binding factor (zinc finger protein) 531536 55 48 40 1 3 9 5 1 33 4 5.66e-14 9.78e-11
11 PPP2R1A protein phosphatase 2 (formerly 2A), regulatory subunit A , alpha isoform 417772 27 24 20 3 6 15 1 3 2 0 3.19e-13 5.00e-10
12 FGFR2 fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome) 644344 27 25 15 2 2 9 5 10 1 0 1.65e-12 2.38e-09
13 MLL4 1092469 53 35 50 8 11 18 8 2 14 0 2.61e-12 3.47e-09
14 MUC5B mucin 5B, oligomeric mucus/gel-forming 1730599 78 46 77 35 13 45 9 3 8 0 1.03e-11 1.27e-08
15 FBXW7 F-box and WD repeat domain containing 7 617576 34 24 28 2 5 15 1 2 9 2 2.16e-11 2.49e-08
16 BCOR BCL6 co-repressor 1215076 52 38 41 10 6 27 14 1 4 0 2.61e-11 2.82e-08
17 SPOP speckle-type POZ protein 277479 19 18 15 0 11 1 2 2 3 0 5.06e-11 5.14e-08
18 RNF43 ring finger protein 43 567386 22 22 15 2 1 7 0 0 14 0 1.00e-10 9.60e-08
19 ZFHX3 zinc finger homeobox 3 2606295 80 45 75 11 16 33 5 2 18 6 1.30e-09 1.18e-06
20 RB1 retinoblastoma 1 (including osteosarcoma) 658206 31 25 30 4 7 7 6 1 6 4 3.39e-09 2.93e-06
21 RASA1 RAS p21 protein activator (GTPase activating protein) 1 689993 29 22 27 2 6 6 3 1 11 2 1.00e-07 0.000082
22 CCND1 cyclin D1 118783 10 10 9 1 3 3 1 1 2 0 1.66e-07 0.00013
23 PCGF3 polycomb group ring finger 3 92971 10 10 8 1 1 6 0 0 3 0 2.87e-07 0.00022
24 PXDN peroxidasin homolog (Drosophila) 790612 43 27 41 8 9 19 3 3 7 2 3.38e-07 0.00024
25 SMTNL2 smoothelin-like 2 152004 9 9 3 2 1 1 0 0 7 0 3.44e-07 0.00024
26 ETV3 ets variant gene 3 106116 12 11 12 0 3 2 5 0 2 0 5.05e-07 0.00034
27 NFASC neurofascin homolog (chicken) 983246 33 27 33 3 10 13 4 1 3 2 6.96e-07 0.00044
28 CSMD3 CUB and Sushi multiple domains 3 2741330 106 40 101 20 33 37 15 5 7 9 7.14e-07 0.00044
29 DCC deleted in colorectal carcinoma 1065940 35 27 34 3 11 14 3 2 5 0 1.86e-06 0.0011
30 INPPL1 inositol polyphosphate phosphatase-like 1 794914 23 19 20 7 4 6 2 0 9 2 2.15e-06 0.0012
31 CHD3 chromodomain helicase DNA binding protein 3 1425157 39 30 35 5 10 12 7 1 9 0 2.17e-06 0.0012
32 MUC4 mucin 4, cell surface associated 1204082 43 29 42 17 9 20 5 5 4 0 3.14e-06 0.0017
33 CNTN6 contactin 6 758825 36 24 34 7 8 14 4 2 8 0 3.78e-06 0.0019
34 LRCH2 leucine-rich repeats and calponin homology (CH) domain containing 2 355871 23 19 22 2 10 6 3 0 4 0 3.83e-06 0.0019
35 BRD3 bromodomain containing 3 239000 15 14 13 7 6 3 1 0 5 0 3.94e-06 0.0019

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 1 116 22 1 5258 1 0.098 1
2 A4GNT alpha-1,4-N-acetylglucosaminyltransferase 6 0 0 0 0 1 1
3 AACS acetoacetyl-CoA synthetase 9 0 0 0 0 1 1
4 ABCA9 ATP-binding cassette, sub-family A (ABC1), member 9 29 0 0 0 0 1 1
5 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 14 0 0 0 0 1 1
6 ABCF2 ATP-binding cassette, sub-family F (GCN20), member 2 5 0 0 0 0 1 1
7 ABHD2 abhydrolase domain containing 2 4 0 0 0 0 1 1
8 ABHD4 abhydrolase domain containing 4 11 0 0 0 0 1 1
9 ACADS acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain 5 0 0 0 0 1 1
10 ACOT11 acyl-CoA thioesterase 11 6 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
1878 C3orf63 chromosome 3 open reading frame 63 25 0 3 3
3911 DMBT1 deleted in malignant brain tumors 1 34 0 1 3
2601 CDCP1 CUB domain containing protein 1 13 0 1 1
3932 DNAH11 dynein, axonemal, heavy chain 11 84 0 1 1
7129 KIAA1432 KIAA1432 16 0 1 1
7178 KIF20B 47 0 1 1
7472 LARP1 La ribonucleoprotein domain family, member 1 17 0 1 1
8159 MDN1 MDN1, midasin homolog (yeast) 58 0 1 1
9070 NLGN4X neuroligin 4, X-linked 11 0 1 1
10055 PCM1 pericentriolar material 1 25 0 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: 217. 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 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(7), ACTR3(3), AKT1(8), AKT2(4), AKT3(8), ANGPTL2(9), ARHGAP1(2), ARHGAP4(15), ARHGEF11(22), BTK(11), CDC42(5), CFL1(1), CFL2(8), GDI1(4), GDI2(3), INPPL1(23), ITPR1(31), ITPR2(38), ITPR3(23), LIMK1(7), MYLK(17), MYLK2(7), PAK1(3), PAK2(6), PAK3(14), PAK4(2), PAK6(3), PAK7(12), PDK1(7), PIK3CA(138), PIK3CD(10), PIK3CG(25), PIK3R1(67), PITX2(10), PPP1R13B(7), PTEN(198), RACGAP1(8), RHO(8), ROCK1(27), ROCK2(15), RPS4X(4), SAG(5), WASF1(3), WASL(8) 24593100 836 210 656 135 193 221 160 34 189 39 <1.00e-15 <2.46e-14
2 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(8), EIF4A1(4), EIF4A2(6), EIF4E(4), EIF4G1(15), EIF4G2(8), EIF4G3(26), GHR(10), IRS1(17), MAPK1(2), MAPK14(6), MAPK3(4), MKNK1(6), PABPC1(11), PDK2(5), PDPK1(3), PIK3CA(138), PIK3R1(67), PRKCA(10), PTEN(198), RPS6KB1(3) 9912525 551 208 382 44 101 111 133 26 149 31 <1.00e-15 <2.46e-14
3 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(8), EIF2B5(6), EIF2S1(1), EIF2S2(5), EIF2S3(6), EIF4E(4), GSK3B(11), IGF1(3), IGF1R(13), INPPL1(23), PDK2(5), PDPK1(3), PIK3CA(138), PIK3R1(67), PPP2CA(6), PTEN(198), RPS6(6), RPS6KB1(3) 6967089 506 208 333 43 91 92 121 20 149 33 <1.00e-15 <2.46e-14
4 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(8), EIF4A1(4), EIF4A2(6), EIF4B(6), EIF4E(4), EIF4G1(15), EIF4G2(8), EIF4G3(26), MKNK1(6), PDK2(5), PDPK1(3), PIK3CA(138), PIK3R1(67), PPP2CA(6), PTEN(198), RPS6(6), RPS6KB1(3), TSC1(13), TSC2(14) 9012929 536 208 366 42 96 113 124 25 147 31 <1.00e-15 <2.46e-14
5 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(8), AKT2(4), AKT3(8), BRD4(9), CAP1(7), CBL(10), CDC42(5), CDKN2A(1), F2RL2(3), FLOT1(1), FLOT2(3), GRB2(3), GSK3A(9), GSK3B(11), IGFBP1(5), INPPL1(23), IRS1(17), IRS4(20), LNPEP(9), MAPK1(2), MAPK3(4), PARD3(27), PARD6A(1), PDK1(7), PIK3CA(138), PIK3CD(10), PIK3R1(67), PPYR1(7), PTEN(198), PTPN1(4), RAF1(7), RPS6KA1(5), RPS6KA2(16), RPS6KA3(17), RPS6KB1(3), SERPINB6(4), SHC1(11), SLC2A4(4), SORBS1(22), SOS1(21), SOS2(22), YWHAB(1), YWHAE(1), YWHAG(3), YWHAH(4), YWHAQ(3), YWHAZ(1) 20132165 766 208 583 117 159 183 167 32 188 37 <1.00e-15 <2.46e-14
6 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(4), CRK(1), CRKL(5), DOCK1(32), ELK1(2), FOS(6), GAB1(10), GRB2(3), HGF(15), ITGA1(20), ITGB1(12), JUN(1), MAP2K1(2), MAP4K1(13), MAPK1(2), MAPK3(4), MAPK8(7), MET(10), PAK1(3), PIK3CA(138), PIK3R1(67), PTEN(198), PTK2(11), PTK2B(16), PTPN11(8), PXN(6), RAF1(7), RAP1A(3), RAP1B(2), RASA1(29), SOS1(21), SRC(2), STAT3(12) 15458520 672 205 498 85 136 158 146 27 170 35 <1.00e-15 <2.46e-14
7 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(8), CDKN1B(5), GRB2(3), ILK(8), ITGB1(12), MAPK1(2), MAPK3(4), PDK2(5), PDPK1(3), PIK3CA(138), PIK3R1(67), PTEN(198), PTK2(11), SHC1(11), SOS1(21) 6356683 496 203 321 30 86 92 124 20 141 33 <1.00e-15 <2.46e-14
8 ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY The phosphoinositide-3 kinase pathway produces the lipid second messenger PIP3 and regulates cell growth, survival, and movement. A1BG, AKT1, AKT2, AKT3, BAD, BTK, CDKN2A, CSL4, DAF, DAPP1, FOXO1A, GRB2, GSK3A, GSK3B, IARS, IGFBP1, INPP5D, P14, PDK1, PIK3CA, PPP1R13B, PSCD3, PTEN, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SFN, SHC1, SOS1, SOS2, TEC, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ 33 A1BG(3), AKT1(8), AKT2(4), AKT3(8), BAD(2), BTK(11), CDKN2A(1), DAPP1(7), GRB2(3), GSK3A(9), GSK3B(11), IARS(13), IGFBP1(5), INPP5D(14), PDK1(7), PIK3CA(138), PPP1R13B(7), PTEN(198), RPS6KA1(5), RPS6KA2(16), RPS6KA3(17), RPS6KB1(3), SHC1(11), SOS1(21), SOS2(22), TEC(5), YWHAB(1), YWHAE(1), YWHAG(3), YWHAH(4), YWHAQ(3), YWHAZ(1) 12586696 562 201 396 60 115 137 132 22 132 24 <1.00e-15 <2.46e-14
9 SA_PTEN_PATHWAY PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate. AKT1, AKT2, AKT3, BPNT1, GRB2, ILK, MAPK1, MAPK3, PDK1, PIK3CA, PIK3CD, PIP3-E, PTEN, PTK2B, RBL2, SHC1, SOS1 16 AKT1(8), AKT2(4), AKT3(8), BPNT1(1), GRB2(3), ILK(8), MAPK1(2), MAPK3(4), PDK1(7), PIK3CA(138), PIK3CD(10), PTEN(198), PTK2B(16), RBL2(21), SHC1(11), SOS1(21) 6977366 460 198 293 36 98 93 112 20 112 25 <1.00e-15 <2.46e-14
10 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(12), AKT1(8), AKT2(4), AKT3(8), APAF1(19), ATM(54), BAD(2), BAX(4), BCL2L1(3), BID(3), BIRC2(13), BIRC3(3), CAPN1(4), CAPN2(6), CASP10(10), CASP3(4), CASP6(4), CASP7(4), CASP8(21), CASP9(3), CFLAR(7), CHUK(11), CSF2RB(11), CYCS(3), DFFA(1), DFFB(3), FADD(1), FAS(7), FASLG(6), IKBKB(15), IL1A(1), IL1B(2), IL1R1(5), IL1RAP(2), IL3RA(11), IRAK1(5), IRAK2(7), IRAK3(13), IRAK4(6), MAP3K14(12), MYD88(1), NFKB1(12), NFKB2(10), NFKBIA(3), NTRK1(11), PIK3CA(138), PIK3CB(19), PIK3CD(10), PIK3CG(25), PIK3R1(67), PIK3R2(4), PIK3R3(8), PIK3R5(8), PPP3CA(4), PPP3CB(7), PPP3CC(6), PPP3R1(2), PPP3R2(1), PRKACA(4), PRKACB(2), PRKACG(6), PRKAR1A(4), PRKAR1B(8), PRKAR2A(4), PRKAR2B(5), RELA(6), RIPK1(8), TNF(1), TNFRSF10A(3), TNFRSF10B(5), TNFRSF10C(3), TNFRSF10D(10), TNFRSF1A(6), TNFSF10(1), TP53(40), TRAF2(5) 28018448 775 186 659 164 177 260 136 44 141 17 <1.00e-15 <2.46e-14

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 50. 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 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(17), ADCY2(17), ADCY3(8), ADCY4(8), ADCY7(6), ADCY8(16), ADCY9(25), ADORA2A(5), ADORA2B(2), ADRA1A(11), ADRA1B(7), ADRB1(2), ADRB2(8), ATP2A1(16), ATP2A2(9), ATP2A3(12), ATP2B1(17), ATP2B2(12), ATP2B3(21), ATP2B4(18), AVPR1A(8), AVPR1B(3), BDKRB1(5), BDKRB2(9), BST1(5), CACNA1A(19), CACNA1B(1), CACNA1C(30), CACNA1D(34), CACNA1E(47), CACNA1F(36), CACNA1G(20), CACNA1I(13), CACNA1S(33), CALM2(3), CALM3(1), CALML6(4), CAMK2A(8), CAMK2B(2), CAMK2D(7), CAMK2G(8), CAMK4(5), CCKAR(12), CCKBR(7), CD38(7), CHRM1(6), CHRM2(9), CHRM3(9), CHRM5(13), CHRNA7(6), CYSLTR1(5), CYSLTR2(6), DRD1(6), EDNRA(6), EDNRB(2), EGFR(20), ERBB2(6), ERBB3(16), ERBB4(29), F2R(8), GNA11(3), GNA14(5), GNA15(1), GNAL(6), GNAS(25), GRIN1(5), GRIN2A(25), GRIN2C(6), GRIN2D(8), GRM1(22), GRM5(22), GRPR(4), HRH1(9), HRH2(3), HTR2A(15), HTR2B(2), HTR4(7), HTR5A(9), HTR6(4), HTR7(4), ITPKB(6), ITPR1(31), ITPR2(38), ITPR3(23), LHCGR(16), LTB4R2(3), MYLK(17), MYLK2(7), NOS1(21), NOS3(11), NTSR1(4), OXTR(4), P2RX1(9), P2RX3(9), P2RX4(2), P2RX5(8), P2RX7(3), PDE1A(12), PDE1B(9), PDE1C(14), PDGFRA(29), PDGFRB(12), PHKA1(17), PHKA2(15), PHKB(14), PHKG1(6), PHKG2(3), PLCB1(6), PLCB2(9), PLCB3(9), PLCB4(20), PLCD1(5), PLCD3(7), PLCD4(13), PLCE1(36), PLCG1(12), PLCG2(27), PLCZ1(16), PLN(1), PPID(6), PPP3CA(4), PPP3CB(7), PPP3CC(6), PPP3R1(2), PPP3R2(1), PRKACA(4), PRKACB(2), PRKACG(6), PRKCA(10), PRKCG(10), PRKX(4), PTAFR(6), PTGER3(9), PTGFR(10), PTK2B(16), RYR1(80), RYR2(111), RYR3(87), SLC25A4(3), SLC25A5(4), SLC25A6(6), SLC8A1(20), SLC8A2(6), SLC8A3(14), SPHK1(2), SPHK2(1), TACR1(6), TACR2(4), TACR3(9), TNNC1(2), TNNC2(4), TRHR(5), TRPC1(15), VDAC1(2), VDAC3(4) 91603920 1888 150 1836 659 546 777 260 92 190 23 3.2e-15 2e-12
2 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 133 ADCY1(17), ADCY2(17), ADCY3(8), ADCY4(8), ADCY5(11), ADCY6(16), ADCY7(6), ADCY8(16), ADCY9(25), ADRA1A(11), ADRA1B(7), ADRB1(2), ADRB2(8), ANXA6(10), ARRB1(7), ARRB2(3), ATP1A4(24), ATP1B1(3), ATP1B2(7), ATP1B3(4), ATP2A2(9), ATP2A3(12), ATP2B1(17), ATP2B2(12), ATP2B3(21), CACNA1A(19), CACNA1B(1), CACNA1C(30), CACNA1D(34), CACNA1E(47), CACNA1S(33), CACNB1(9), CACNB3(6), CALM2(3), CALM3(1), CALR(4), CAMK1(9), CAMK2A(8), CAMK2B(2), CAMK2D(7), CAMK2G(8), CAMK4(5), CASQ1(7), CASQ2(8), CHRM1(6), CHRM2(9), CHRM3(9), CHRM4(9), CHRM5(13), GJA1(6), GJA4(2), GJB1(1), GJB2(3), GJB3(2), GJB4(5), GJB5(3), GJB6(4), GNA11(3), GNAI2(7), GNAI3(3), GNAO1(5), GNAZ(7), GNB1(3), GNB2(5), GNB3(4), GNB4(3), GNB5(3), GNG12(2), GNG13(2), GNG2(2), GNG3(3), GRK4(14), GRK5(10), GRK6(3), ITPR1(31), ITPR2(38), ITPR3(23), KCNB1(17), KCNJ3(15), KCNJ5(6), MIB1(8), MYCBP(1), NME7(4), PEA15(2), PKIG(2), PLCB3(9), PLN(1), PRKACA(4), PRKACB(2), PRKAR1A(4), PRKAR2A(4), PRKAR2B(5), PRKCA(10), PRKCD(7), PRKCE(11), PRKCG(10), PRKCH(9), PRKCQ(13), PRKCZ(4), PRKD1(8), RGS1(6), RGS10(3), RGS14(5), RGS16(3), RGS17(5), RGS18(2), RGS2(3), RGS20(5), RGS3(15), RGS4(6), RGS5(4), RGS6(7), RGS7(9), RGS9(19), RYR1(80), RYR2(111), RYR3(87), SLC8A1(20), SLC8A3(14), USP5(13), YWHAB(1), YWHAH(4), YWHAQ(3) 65550530 1346 138 1309 463 395 564 151 72 145 19 3.4e-11 1e-08
3 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 214 ADCYAP1R1(7), ADORA1(6), ADORA2A(5), ADORA2B(2), ADORA3(5), ADRA1A(11), ADRA1B(7), ADRA2B(5), ADRB1(2), ADRB2(8), AGTR2(8), AVPR1A(8), AVPR1B(3), AVPR2(5), BDKRB1(5), BDKRB2(9), BRS3(13), C3AR1(7), C5AR1(5), CALCR(5), CALCRL(9), CCKAR(12), CCKBR(7), CGA(1), CHRM1(6), CHRM2(9), CHRM3(9), CHRM4(9), CHRM5(13), CNR1(8), CNR2(3), CRHR1(2), CRHR2(2), CTSG(3), CYSLTR1(5), CYSLTR2(6), DRD1(6), DRD2(10), DRD3(5), DRD5(11), EDNRA(6), EDNRB(2), F2(9), F2R(8), F2RL1(3), F2RL2(3), FPR1(4), FSHR(17), GABBR1(17), GABBR2(14), GABRA1(10), GABRA2(12), GABRA3(15), GABRA4(17), GABRA5(8), GABRA6(8), GABRB1(8), GABRB2(16), GABRB3(15), GABRE(7), GABRG1(8), GABRG2(19), GABRG3(14), GABRP(5), GABRQ(7), GABRR1(5), GABRR2(2), GALR1(2), GALR3(3), GH1(6), GH2(5), GHR(10), GHRHR(2), GHSR(7), GIPR(4), GLP1R(8), GLP2R(17), GLRA1(9), GLRA2(6), GLRA3(11), GLRB(8), GNRHR(4), GPR156(6), GPR50(8), GPR63(5), GPR83(5), GRIA1(12), GRIA2(25), GRIA4(23), GRID1(16), GRID2(13), GRIK1(16), GRIK2(15), GRIK3(17), GRIK4(8), GRIK5(19), GRIN1(5), GRIN2A(25), GRIN2B(23), GRIN2C(6), GRIN2D(8), GRIN3A(15), GRM1(22), GRM2(7), GRM3(20), GRM4(16), GRM5(22), GRM7(15), GRM8(24), GRPR(4), GZMA(6), HCRTR1(1), HCRTR2(8), HRH1(9), HRH2(3), HRH4(4), HTR1A(13), HTR1B(6), HTR1D(6), HTR1E(6), HTR2A(15), HTR2B(2), HTR4(7), HTR5A(9), HTR6(4), HTR7(4), LEP(2), LEPR(15), LHB(3), LHCGR(16), LTB4R(3), LTB4R2(3), MAS1(2), MC2R(2), MC3R(8), MC4R(7), MC5R(12), MCHR1(7), MCHR2(1), MLNR(3), MTNR1A(6), MTNR1B(4), NMBR(4), NMUR1(8), NMUR2(7), NPBWR1(2), NPFFR1(2), NPFFR2(12), NPY1R(6), NPY2R(4), NPY5R(10), NR3C1(13), NTSR1(4), NTSR2(2), OPRD1(2), OPRK1(9), OPRM1(11), OXTR(4), P2RX1(9), P2RX3(9), P2RX4(2), P2RX5(8), P2RX7(3), P2RY1(2), P2RY10(6), P2RY11(7), P2RY13(3), P2RY14(5), P2RY2(6), P2RY4(7), P2RY6(3), PARD3(27), PPYR1(7), PRL(6), PRLHR(2), PRLR(6), PRSS1(7), PRSS3(2), PTAFR(6), PTGDR(6), PTGER2(5), PTGER3(9), PTGER4(8), PTGFR(10), PTGIR(3), PTH2R(7), RXFP1(16), RXFP2(17), SCTR(4), SSTR2(3), SSTR3(6), TAAR1(6), TAAR2(5), TAAR5(8), TAAR6(5), TAAR8(3), TAAR9(8), TACR1(6), TACR2(4), TACR3(9), THRA(5), THRB(4), TRHR(5), TRPV1(6), TSHB(3), TSHR(12), VIPR1(3) 71058285 1639 145 1582 539 480 673 258 73 153 2 4.3e-10 8.8e-08
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 225 ACVR1B(6), ACVR1C(7), AKT1(8), AKT2(4), AKT3(8), ARRB1(7), ARRB2(3), ATF2(6), ATF4(4), BDNF(8), BRAF(12), CACNA1A(19), CACNA1B(1), CACNA1C(30), CACNA1D(34), CACNA1E(47), CACNA1F(36), CACNA1G(20), CACNA1I(13), CACNA1S(33), CACNA2D1(14), CACNA2D2(9), CACNA2D3(20), CACNA2D4(18), CACNB1(9), CACNB2(11), CACNB3(6), CACNB4(14), CACNG2(3), CACNG3(9), CACNG4(6), CACNG5(4), CACNG6(6), CACNG7(10), CASP3(4), CD14(2), CDC25B(3), CDC42(5), CHUK(11), CRK(1), CRKL(5), DAXX(11), DDIT3(1), DUSP1(2), DUSP10(7), DUSP14(3), DUSP16(13), DUSP2(4), DUSP3(2), DUSP4(1), DUSP5(5), DUSP6(1), DUSP7(4), DUSP9(8), ECSIT(5), EGF(24), EGFR(20), ELK1(2), ELK4(3), FAS(7), FASLG(6), FGF1(1), FGF10(1), FGF11(2), FGF12(4), FGF13(6), FGF14(3), FGF16(1), FGF17(1), FGF18(2), FGF21(3), FGF23(6), FGF5(8), FGF6(2), FGF7(6), FGF8(2), FGF9(2), FGFR1(10), FGFR4(11), FLNA(31), FLNB(38), FLNC(34), FOS(6), GNA12(10), GNG12(2), GRB2(3), IKBKB(15), IL1A(1), IL1B(2), IL1R1(5), IL1R2(7), JUN(1), MAP2K1(2), MAP2K3(8), MAP2K4(6), MAP2K5(2), MAP2K6(9), MAP3K10(7), MAP3K12(8), MAP3K13(13), MAP3K14(12), MAP3K2(8), MAP3K3(9), MAP3K4(23), MAP3K5(21), MAP3K6(7), MAP3K7(8), MAP3K8(12), MAP4K1(13), MAP4K2(6), MAP4K3(21), MAP4K4(14), MAPK1(2), MAPK10(9), MAPK13(2), MAPK14(6), MAPK3(4), MAPK7(17), MAPK8(7), MAPK8IP1(5), MAPK9(7), MAPKAPK2(6), MAPKAPK3(4), MAPKAPK5(6), MAPT(11), MAX(8), MEF2C(11), MKNK1(6), MKNK2(4), MOS(8), MRAS(3), MYC(7), NF1(40), NFATC2(15), NFATC4(8), NFKB1(12), NFKB2(10), NLK(5), NR4A1(4), NTF3(6), NTRK1(11), NTRK2(15), PAK1(3), PAK2(6), PDGFB(4), PDGFRA(29), PDGFRB(12), PLA2G10(1), PLA2G12A(1), PLA2G12B(3), PLA2G1B(1), PLA2G2D(2), PLA2G2E(3), PLA2G2F(3), PLA2G3(5), PLA2G4A(11), PLA2G5(2), PLA2G6(6), PPM1A(7), PPM1B(6), PPP3CA(4), PPP3CB(7), PPP3CC(6), PPP3R1(2), PPP3R2(1), PPP5C(7), PRKACA(4), PRKACB(2), PRKACG(6), PRKCA(10), PRKCG(10), PRKX(4), PTPN5(5), PTPN7(5), PTPRR(18), RAC2(2), RAF1(7), RAP1A(3), RAP1B(2), RAPGEF2(38), RASA2(8), RASGRF1(13), RASGRF2(17), RASGRP1(8), RASGRP2(5), RASGRP3(8), RASGRP4(7), RPS6KA1(5), RPS6KA2(16), RPS6KA3(17), RPS6KA4(5), RPS6KA5(7), RPS6KA6(15), RRAS(1), RRAS2(5), SOS1(21), SOS2(22), SRF(3), STK3(9), STK4(6), STMN1(6), TAOK1(10), TAOK2(10), TAOK3(4), TGFB1(4), TGFB2(6), TGFB3(9), TGFBR1(8), TGFBR2(6), TNF(1), TNFRSF1A(6), TRAF2(5), TRAF6(4), ZAK(12) 92476270 1836 141 1785 566 501 733 230 111 239 22 1.1e-08 1.8e-06
5 HSA04530_TIGHT_JUNCTION Genes involved in tight junction ACTB, ACTG1, ACTN1, ACTN2, ACTN3, ACTN4, AKT1, AKT2, AKT3, AMOTL1, ASH1L, CASK, CDC42, CDK4, CGN, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CRB3, CSDA, CSNK2A1, CSNK2A2, CSNK2B, CTNNA1, CTNNA2, CTNNA3, CTNNB1, CTTN, EPB41, EPB41L1, EPB41L2, EPB41L3, EXOC3, EXOC4, F11R, GNAI1, GNAI2, GNAI3, HCLS1, HRAS, IGSF5, INADL, JAM2, JAM3, KRAS, LLGL1, LLGL2, MAGI1, MAGI2, MAGI3, MLLT4, MPDZ, MPP5, MRAS, MRCL3, MRLC2, MYH1, MYH10, MYH11, MYH13, MYH14, MYH15, MYH2, MYH3, MYH4, MYH6, MYH7, MYH7B, MYH8, MYH9, MYL2, MYL5, MYL7, MYL8P, MYL9, MYLC2PL, MYLPF, NRAS, OCLN, PARD3, PARD6A, PARD6B, PARD6G, PPM1J, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PPP2R3A, PPP2R3B, PPP2R4, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PTEN, RAB13, RAB3B, RHOA, RRAS, RRAS2, SPTAN1, SRC, SYMPK, TJAP1, TJP1, TJP2, TJP3, VAPA, YES1, ZAK 121 ACTB(5), ACTN1(13), ACTN2(9), ACTN3(10), ACTN4(11), AKT1(8), AKT2(4), AKT3(8), AMOTL1(14), ASH1L(40), CASK(20), CDC42(5), CDK4(4), CGN(15), CLDN1(2), CLDN10(9), CLDN11(1), CLDN15(4), CLDN16(6), CLDN17(2), CLDN18(4), CLDN19(2), CLDN2(4), CLDN20(4), CLDN22(3), CLDN6(1), CLDN7(1), CLDN8(5), CLDN9(2), CRB3(1), CSDA(6), CSNK2A1(9), CSNK2A2(5), CTNNA1(18), CTNNA2(13), CTNNA3(13), CTTN(8), EPB41(11), EPB41L1(11), EPB41L2(13), EPB41L3(18), EXOC3(12), EXOC4(4), F11R(2), GNAI1(4), GNAI2(7), GNAI3(3), HCLS1(8), IGSF5(9), INADL(17), JAM2(9), JAM3(3), LLGL1(14), LLGL2(5), MAGI1(32), MAGI2(26), MAGI3(17), MLLT4(32), MPDZ(22), MPP5(5), MRAS(3), MYH1(44), MYH10(29), MYH11(39), MYH13(27), MYH14(22), MYH15(22), MYH2(37), MYH3(30), MYH4(36), MYH6(23), MYH7(28), MYH7B(15), MYH8(35), MYH9(26), MYL2(1), MYL5(3), MYL7(4), MYL9(3), MYLPF(2), OCLN(5), PARD3(27), PARD6A(1), PARD6B(3), PPM1J(3), PPP2CA(6), PPP2CB(2), PPP2R1B(9), PPP2R2A(15), PPP2R2B(12), PPP2R2C(3), PPP2R3A(13), PPP2R4(7), PRKCA(10), PRKCD(7), PRKCE(11), PRKCG(10), PRKCH(9), PRKCI(8), PRKCQ(13), PRKCZ(4), RAB13(3), RAB3B(1), RHOA(4), RRAS(1), RRAS2(5), SPTAN1(29), SRC(2), SYMPK(20), TJAP1(8), TJP1(33), TJP2(16), TJP3(6), VAPA(5), YES1(5), ZAK(12) 64754182 1330 139 1292 409 366 531 194 61 161 17 3.6e-08 4.4e-06
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 118 ACACA(27), ACACB(31), AKT1(8), AKT2(4), AKT3(8), ARAF(8), BAD(2), BRAF(12), CALM2(3), CALM3(1), CALML6(4), CBL(10), CBLB(15), CBLC(5), CRK(1), CRKL(5), ELK1(2), EXOC7(8), FBP1(4), FLOT1(1), FLOT2(3), FOXO1(11), G6PC(6), G6PC2(9), GCK(5), GRB2(3), GSK3B(11), GYS1(12), GYS2(19), IKBKB(15), INPP5D(14), INSR(18), IRS1(17), IRS4(20), LIPE(7), MAP2K1(2), MAPK1(2), MAPK10(9), MAPK3(4), MAPK8(7), MAPK9(7), MKNK1(6), MKNK2(4), PCK1(15), PCK2(7), PDE3A(17), PDE3B(15), PDPK1(3), PFKM(7), PFKP(11), PHKA1(17), PHKA2(15), PHKB(14), PHKG1(6), PHKG2(3), PIK3CB(19), PIK3CD(10), PIK3CG(25), PIK3R2(4), PIK3R3(8), PIK3R5(8), PKLR(10), PKM2(5), PPARGC1A(13), PPP1CA(6), PPP1CB(7), PPP1CC(2), PPP1R3A(23), PPP1R3B(3), PPP1R3C(3), PRKAA1(6), PRKAA2(9), PRKAB1(7), PRKAB2(2), PRKACA(4), PRKACB(2), PRKACG(6), PRKAG1(2), PRKAG2(4), PRKAG3(6), PRKAR1A(4), PRKAR2A(4), PRKAR2B(5), PRKCI(8), PRKCZ(4), PRKX(4), PTPN1(4), PTPRF(34), PYGB(10), PYGL(9), PYGM(10), RAF1(7), RAPGEF1(18), RHEB(2), RHOQ(1), RPS6(6), RPS6KB1(3), RPS6KB2(6), SH2B2(2), SHC1(11), SHC3(9), SHC4(7), SLC2A4(4), SOCS2(7), SOCS4(4), SORBS1(22), SOS1(21), SOS2(22), SREBF1(6), TRIP10(6), TSC1(13), TSC2(14) 49120714 981 128 952 281 250 412 126 43 138 12 4.8e-06 0.0005
7 ERK5PATHWAY Signaling between a tissue and its innervating axon stimulates retrograde transport via Trk receptors, which activate Erk5, which induces transcription of anti-apoptotic factors. AKT1, CREB1, GRB2, HRAS, MAPK1, MAPK3, MAPK7, MEF2A, MEF2B, MEF2C, MEF2D, NTRK1, PIK3CA, PIK3R1, PLCG1, RPS6KA1, SHC1 15 AKT1(8), CREB1(5), GRB2(3), MAPK1(2), MAPK3(4), MAPK7(17), MEF2A(5), MEF2B(3), MEF2C(11), MEF2D(7), NTRK1(11), PLCG1(12), RPS6KA1(5), SHC1(11) 5187495 104 52 96 30 23 51 9 5 16 0 6.6e-06 0.00058
8 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 17 AXIN1(8), BTRC(13), CREBBP(37), CSNK1A1(5), CSNK2A1(9), FZD1(2), GSK3B(11), HDAC1(4), MAP3K7(8), MYC(7), NLK(5), PPARD(6), PPP2CA(6), TLE1(12), WIF1(5), WNT1(1) 6567242 139 59 136 28 43 56 17 3 18 2 0.000018 0.0014
9 PITX2PATHWAY The bicoid-related transcription factor Pitx2 is activated by Wnt binding to the Frizzled receptor and induces tissue-specific cell proliferation. APC, AXIN1, CREBBP, CTNNB1, DVL1, EP300, FZD1, GSK3B, HDAC1, HTATIP, LDB1, LEF1, PITX2, PPARBP, TRRAP, WNT1 10 AXIN1(8), CREBBP(37), EP300(29), FZD1(2), GSK3B(11), HDAC1(4), LDB1(3), LEF1(9), TRRAP(72), WNT1(1) 8072942 176 62 170 33 49 68 23 6 28 2 0.000028 0.0019
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 12 CDH1(15), CREBBP(37), EP300(29), MAP2K1(2), MAP3K7(8), MAPK3(4), SKIL(13), TGFB1(4), TGFB2(6), TGFB3(9), TGFBR1(8), TGFBR2(6) 6902081 141 57 136 37 35 58 20 6 22 0 0.000054 0.0032
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]

Download Results

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)
Meta
  • Maintainer = Dan DiCara