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: STAD.

Number of patients in set: 133

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): 141

Mutations seen in COSMIC: 0

Significantly mutated genes in COSMIC territory: 0

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

Significantly mutated genesets: 151

Significantly mutated genesets: (excluding sig. mutated genes): 41

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 2090
Frame_Shift_Ins 308
In_Frame_Del 142
In_Frame_Ins 18
Indel 78
Missense_Mutation 35920
Nonsense_Mutation 1639
Nonstop_Mutation 41
Silent 15189
Splice_Site 881
Translation_Start_Site 23
Total 56329
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 9314 1972774636 4.7e-06 4.7 0.46
C->(A/T) 14586 2075005485 7e-06 7 0.69
A->(C/G) 8804 1972774636 4.5e-06 4.5 0.44
C->G 3233 2075005485 1.6e-06 1.6 0.15
indel+null 5067 4047780254 1.3e-06 1.3 0.12
double_null 136 4047780254 3.4e-08 0.034 0.0033
Total 41140 4047780254 1e-05 10 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: 141. Number of genes displayed: 35

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p q
1 TP53 tumor protein p53 170506 56 52 43 2 8 18 6 2 20 2 <1.00e-15 <1.80e-11
2 CBWD1 COBW domain containing 1 149758 18 17 3 0 1 0 1 0 16 0 3.28e-14 2.09e-10
3 ACVR2A activin A receptor, type IIA 210938 16 15 3 0 1 0 1 0 14 0 4.10e-14 2.09e-10
4 ARID1A AT rich interactive domain 1A (SWI-like) 783104 27 23 26 1 2 4 1 1 13 6 4.63e-14 2.09e-10
5 RPL22 ribosomal protein L22 51471 10 10 1 0 0 0 0 0 10 0 4.66e-13 1.68e-09
6 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 437171 23 21 11 3 10 3 10 0 0 0 1.13e-11 3.38e-08
7 PGM5 phosphoglucomutase 5 197505 19 16 5 0 1 2 14 0 2 0 5.24e-11 1.35e-07
8 INO80E 77938 10 9 4 0 0 2 0 0 6 2 6.65e-09 0.000015
9 CDH1 cadherin 1, type 1, E-cadherin (epithelial) 338086 12 12 12 4 1 9 0 0 2 0 8.17e-09 0.000016
10 PREX2 686147 24 18 24 6 6 8 8 0 2 0 2.97e-08 0.000053
11 SOX1 SRY (sex determining region Y)-box 1 50540 6 6 6 1 0 3 1 0 2 0 3.34e-08 0.000055
12 RNF43 ring finger protein 43 308560 14 13 7 2 1 0 2 0 11 0 4.79e-08 0.000067
13 PCDH15 protocadherin 15 990584 20 20 20 3 4 3 8 1 4 0 4.84e-08 0.000067
14 CSMD3 CUB and Sushi multiple domains 3 1525510 41 30 40 10 9 8 15 5 4 0 5.17e-08 0.000067
15 TTN titin 14715386 212 69 209 52 36 63 73 21 15 4 7.03e-08 0.000085
16 SPRYD5 SPRY domain containing 5 121296 8 8 6 0 1 0 1 1 5 0 1.50e-07 0.00017
17 FAT4 FAT tumor suppressor homolog 4 (Drosophila) 1996862 53 34 52 10 19 15 15 4 0 0 3.33e-07 0.00035
18 CSMD1 CUB and Sushi multiple domains 1 1372028 40 27 39 14 7 11 14 5 3 0 5.43e-07 0.00054
19 SPTA1 spectrin, alpha, erythrocytic 1 (elliptocytosis 2) 993244 22 20 22 3 5 8 6 1 2 0 9.36e-07 0.00089
20 CTNND2 catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein) 458052 16 15 14 5 4 5 4 1 2 0 1.07e-06 0.00096
21 DCLK1 doublecortin-like kinase 1 295925 10 10 10 3 3 3 2 1 1 0 1.14e-06 0.00098
22 GRID1 glutamate receptor, ionotropic, delta 1 400463 14 14 14 1 3 5 3 1 2 0 1.91e-06 0.0016
23 FLG filaggrin 1610364 34 26 31 7 4 18 5 4 3 0 2.28e-06 0.0018
24 HIST1H1B histone cluster 1, H1b 91105 7 7 7 3 1 1 3 0 2 0 3.43e-06 0.0026
25 EDNRB endothelin receptor type B 191520 10 10 9 2 2 4 1 0 3 0 3.76e-06 0.0027
26 PXDN peroxidasin homolog (Drosophila) 558733 18 17 17 9 6 7 3 1 1 0 3.91e-06 0.0027
27 SULF1 sulfatase 1 358036 12 12 10 2 3 2 3 0 4 0 4.65e-06 0.0031
28 TUSC3 tumor suppressor candidate 3 144970 8 8 7 0 3 2 1 2 0 0 5.85e-06 0.0038
29 PHF2 PHD finger protein 2 376523 12 12 3 3 1 0 1 0 10 0 6.67e-06 0.0041
30 ASTN2 astrotactin 2 490238 18 15 18 1 4 5 7 0 2 0 7.20e-06 0.0043
31 LRP1B low density lipoprotein-related protein 1B (deleted in tumors) 1883812 37 29 36 10 10 6 13 2 4 2 7.74e-06 0.0045
32 DDI1 DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae) 158935 9 9 9 3 3 4 2 0 0 0 9.32e-06 0.0053
33 PXDNL peroxidasin homolog (Drosophila)-like 530803 18 16 18 4 6 9 1 1 1 0 0.000011 0.0061
34 KCNH8 potassium voltage-gated channel, subfamily H (eag-related), member 8 450604 12 12 12 3 2 0 4 4 2 0 0.000012 0.0061
35 OR4C16 olfactory receptor, family 4, subfamily C, member 16 124621 7 7 6 1 1 1 1 4 0 0 0.000012 0.0061

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 3 0 0 0 0 1 1
2 AACS acetoacetyl-CoA synthetase 2 0 0 0 0 1 1
3 ABCA9 ATP-binding cassette, sub-family A (ABC1), member 9 8 0 0 0 0 1 1
4 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 3 0 0 0 0 1 1
5 ABCF2 ATP-binding cassette, sub-family F (GCN20), member 2 2 0 0 0 0 1 1
6 ABHD2 abhydrolase domain containing 2 0 0 0 0 0 1 1
7 ABHD4 abhydrolase domain containing 4 2 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 2 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
11845 TRANK1 14 0 1 3
9996 SCN10A sodium channel, voltage-gated, type X, alpha subunit 7 0 1 1
4112 FER1L6 fer-1-like 6 (C. elegans) 9 3 0 1
55 ABCC9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9 20 4 0 1
6885 MGEA5 meningioma expressed antigen 5 (hyaluronidase) 6 5 0 1
10764 SORCS1 sortilin-related VPS10 domain containing receptor 1 8 5 0 1
8544 PHRF1 7 6 0 1
3785 F13A1 coagulation factor XIII, A1 polypeptide 8 11 0 1
11137 SYNE1 spectrin repeat containing, nuclear envelope 1 54 13 0 0
4564 GLDC glycine dehydrogenase (decarboxylating) 5 25 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: 151. 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 CELL_CYCLE_KEGG ABL1, ASK, ATM, BUB1, BUB1B, BUB3, CCNA1, CCNA2, CCNB1, CCNB2, CCNB3, CCND2, CCND3, CCNE1, CCNE2, CCNH, CDAN1, CDC14A, CDC14B, CDC14B, CDC14C, CDC2, CDC20, CDC25A, CDC25B, CDC25C, CDC45L, CDC6, CDC7, CDH1, CDK2, CDK4, CDKN1A, CDKN2A, CHEK1, CHEK2, DTX4, E2F1, E2F2, E2F3, E2F4, E2F5, E2F6, EP300, ESPL1, FLJ14001, GADD45A, GSK3B, HDAC1, HDAC2, HDAC3, HDAC4, HDAC5, HDAC6, HDAC7A, HDAC8, MAD1L1, MAD2L1, MAD2L2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, MPEG1, MPL, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, PLK1, PRKDC, PTPRA, PTTG1, PTTG2, PTTG3, RB1, RBL1, SKP2, SMAD4, SMC1L1, TBC1D8, TFDP1, TGFB1, TP53, WEE1 82 ABL1(1), ATM(16), BUB1(6), BUB1B(1), BUB3(1), CCNA1(2), CCNA2(1), CCNB1(1), CCNB2(1), CCNB3(3), CCND2(1), CCND3(2), CCNE2(1), CCNH(2), CDAN1(4), CDC14A(4), CDC20(2), CDC25A(2), CDC25B(4), CDC25C(2), CDC6(2), CDC7(2), CDH1(12), CDK2(2), CDKN1A(1), CDKN2A(2), CHEK1(2), CHEK2(3), DTX4(3), E2F5(1), EP300(10), ESPL1(5), GSK3B(1), HDAC1(2), HDAC2(3), HDAC3(3), HDAC4(6), HDAC5(3), HDAC6(3), HDAC8(3), MAD1L1(4), MAD2L2(1), MCM2(9), MCM3(3), MCM4(4), MCM5(3), MCM6(1), MCM7(3), MDM2(2), MPEG1(4), ORC1L(9), ORC2L(1), ORC3L(4), ORC4L(2), ORC6L(1), PCNA(2), PLK1(4), PRKDC(18), PTPRA(4), RB1(6), RBL1(3), SKP2(2), SMAD4(5), TBC1D8(4), TGFB1(2), TP53(56), WEE1(1) 22527407 284 93 267 74 45 101 55 16 63 4 <1.00e-15 <1.44e-13
2 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 16 ABL1(1), CDKN2A(2), MDM2(2), PIK3CA(23), PIK3R1(5), POLR1A(7), POLR1B(2), POLR1C(2), POLR1D(1), RB1(6), TBX2(3), TP53(56) 4062884 110 76 84 17 25 30 23 3 27 2 <1.00e-15 <1.44e-13
3 APOPTOSIS_GENMAPP APAF1, BAK1, BCL2L7P1, BAX, BCL2, BCL2L1, BID, BIRC2, BIRC3, BIRC4, CASP2, CASP3, CASP6, CASP7, CASP8, CASP9, CYCS, FADD, FAS, FASLG, GZMB, IKBKG, JUN, MAP2K4, MAP3K1, MAP3K14, MAPK10, MCL1, MDM2, MYC, NFKB1, NFKBIA, PARP1, PRF1, RELA, RIPK1, TNF, TNFRSF1A, TNFRSF1B, TNFSF10, TP53, TRADD, TRAF1, TRAF2 41 APAF1(2), BAK1(1), BID(1), BIRC2(1), BIRC3(3), CASP2(2), CASP3(1), CASP7(2), CASP8(3), CASP9(1), CYCS(1), FAS(1), JUN(2), MAP2K4(5), MAP3K1(5), MAP3K14(1), MAPK10(3), MDM2(2), NFKB1(4), PARP1(4), PRF1(1), RELA(2), TNF(1), TNFRSF1A(3), TNFSF10(2), TP53(56), TRAF2(2) 7658938 112 74 99 21 22 38 16 5 29 2 <1.00e-15 <1.44e-13
4 TELPATHWAY Telomerase is a ribonucleotide protein that adds telomeric repeats to the 3' ends of chromosomes. AKT1, BCL2, EGFR, G22P1, HSPCA, IGF1R, KRAS2, MYC, POLR2A, PPP2CA, PRKCA, RB1, TEP1, TERF1, TERT, TNKS, TP53, XRCC5 15 AKT1(2), EGFR(7), IGF1R(11), POLR2A(6), PPP2CA(1), RB1(6), TEP1(10), TERF1(1), TERT(3), TNKS(5), TP53(56), XRCC5(2) 5739615 110 65 96 33 22 35 21 4 26 2 <1.00e-15 <1.44e-13
5 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 80 AIFM1(1), AKT1(2), AKT2(1), AKT3(3), APAF1(2), ATM(16), BAD(1), BID(1), BIRC2(1), BIRC3(3), CAPN1(1), CAPN2(3), CASP10(2), CASP3(1), CASP7(2), CASP8(3), CASP9(1), CSF2RB(5), CYCS(1), DFFA(2), DFFB(2), ENDOG(1), FAS(1), IKBKB(3), IL1B(1), IL1R1(2), IL1RAP(3), IL3(1), IRAK1(4), IRAK2(4), IRAK3(2), IRAK4(1), MAP3K14(1), MYD88(2), NFKB1(4), NFKB2(2), NTRK1(3), PIK3CA(23), PIK3CB(4), PIK3CD(6), PIK3CG(9), PIK3R1(5), PIK3R2(3), PIK3R3(1), PIK3R5(4), PPP3CA(2), PPP3CB(1), PPP3R2(1), PRKACA(1), PRKACB(2), PRKACG(2), PRKAR1A(2), PRKAR2A(1), PRKAR2B(5), RELA(2), TNF(1), TNFRSF10A(2), TNFRSF10B(1), TNFRSF10C(1), TNFRSF10D(2), TNFRSF1A(3), TNFSF10(2), TP53(56), TRAF2(2) 16869188 233 92 206 53 54 79 46 12 38 4 1.78e-15 1.44e-13
6 CHEMICALPATHWAY DNA damage promotes Bid cleavage, which stimulates mitochondrial cytochrome c release and consequent caspase activation, resulting in apoptosis. ADPRT, AKT1, APAF1, ATM, BAD, BAX, BCL2, BCL2L1, BID, CASP3, CASP6, CASP7, CASP9, CYCS, EIF2S1, PRKCA, PRKCB1, PTK2, PXN, STAT1, TLN1, TP53 20 AKT1(2), APAF1(2), ATM(16), BAD(1), BID(1), CASP3(1), CASP7(2), CASP9(1), CYCS(1), EIF2S1(1), PTK2(5), PXN(2), STAT1(3), TLN1(9), TP53(56) 5572700 103 67 89 15 21 32 19 3 24 4 1.78e-15 1.44e-13
7 TERTPATHWAY hTERC, the RNA subunit of telomerase, and hTERT, the catalytic protein subunit, are required for telomerase activity and are overexpressed in many cancers. HDAC1, MAX, MYC, SP1, SP3, TP53, WT1, ZNF42 7 HDAC1(2), SP1(2), SP3(2), TP53(56), WT1(1) 1415785 63 54 50 9 10 19 9 2 21 2 2.33e-15 1.44e-13
8 ST_JNK_MAPK_PATHWAY JNKs are MAP kinases regulated by several levels of kinases (MAPKK, MAPKKK) and phosphorylate transcription factors and regulatory proteins. AKT1, ATF2, CDC42, DLD, DUSP10, DUSP4, DUSP8, GAB1, GADD45A, GCK, IL1R1, JUN, MAP2K4, MAP2K5, MAP2K7, MAP3K1, MAP3K10, MAP3K11, MAP3K12, MAP3K13, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K9, MAPK10, MAPK7, MAPK8, MAPK9, MYEF2, NFATC3, NR2C2, PAPPA, SHC1, TP53, TRAF6, ZAK 38 AKT1(2), CDC42(1), DLD(2), DUSP10(2), DUSP8(1), GCK(2), IL1R1(2), JUN(2), MAP2K4(5), MAP2K5(1), MAP2K7(8), MAP3K1(5), MAP3K10(5), MAP3K11(3), MAP3K12(3), MAP3K13(2), MAP3K2(2), MAP3K3(1), MAP3K4(5), MAP3K7(7), MAP3K9(3), MAPK10(3), MAPK7(8), MAPK8(4), MAPK9(1), MYEF2(3), NFATC3(3), NR2C2(3), PAPPA(12), SHC1(3), TP53(56), TRAF6(3), ZAK(2) 10285023 165 76 152 37 29 65 22 9 38 2 2.44e-15 1.44e-13
9 ATRBRCAPATHWAY BRCA1 and 2 block cell cycle progression in response to DNA damage and promote double-stranded break repair; mutations induce breast cancer susceptibility. ATM, ATR, BRCA1, BRCA2, CHEK1, CHEK2, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, HUS1, MRE11A, NBS1, RAD1, RAD17, RAD50, RAD51, RAD9A, TP53, TREX1 21 ATM(16), ATR(5), BRCA1(6), BRCA2(14), CHEK1(2), CHEK2(3), FANCC(2), FANCD2(6), FANCF(1), FANCG(3), HUS1(1), MRE11A(2), RAD1(1), RAD50(6), RAD51(1), RAD9A(1), TP53(56) 8856603 126 72 112 16 21 36 31 4 30 4 2.66e-15 1.44e-13
10 G2PATHWAY Activated Cdc2-cyclin B kinase regulates the G2/M transition; DNA damage stimulates the DNA-PK/ATM/ATR kinases, which inactivate Cdc2. ATM, ATR, BRCA1, CCNB1, CDC2, CDC25A, CDC25B, CDC25C, CDC34, CDKN1A, CDKN2D, CHEK1, CHEK2, EP300, GADD45A, MDM2, MYT1, PLK, PRKDC, RPS6KA1, TP53, WEE1, YWHAH, YWHAQ 22 ATM(16), ATR(5), BRCA1(6), CCNB1(1), CDC25A(2), CDC25B(4), CDC25C(2), CDC34(1), CDKN1A(1), CDKN2D(1), CHEK1(2), CHEK2(3), EP300(10), MDM2(2), PRKDC(18), RPS6KA1(2), TP53(56), WEE1(1), YWHAQ(2) 8663886 135 76 121 19 20 43 26 4 38 4 3.22e-15 1.44e-13

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 41. 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 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 139 ADCY1(9), ADCY2(5), ADCY3(2), ADCY4(4), ADCY5(7), ADCY6(5), ADCY7(8), ADCY8(8), ADCY9(4), ADRA1A(4), ADRA1B(2), ADRA1D(1), ADRB1(2), ADRB2(2), ADRB3(1), ANXA6(2), ARRB1(3), ARRB2(2), ATP1A4(5), ATP1B3(1), ATP2A2(4), ATP2A3(3), ATP2B1(8), ATP2B2(7), ATP2B3(7), CACNA1A(9), CACNA1B(1), CACNA1C(17), CACNA1D(12), CACNA1E(16), CACNA1S(9), CACNB1(1), CALM1(1), CALM2(2), CALM3(1), CALR(4), CAMK1(1), CAMK2A(1), CAMK2B(2), CAMK2G(3), CAMK4(2), CASQ1(2), CASQ2(1), CHRM1(1), CHRM2(6), CHRM3(4), CHRM4(1), CHRM5(3), GJA1(7), GJA4(4), GJB3(2), GJB6(2), GNA11(1), GNAI2(3), GNAI3(3), GNAQ(1), GNAZ(5), GNB1(1), GNB2(3), GNB3(1), GNB4(3), GNG12(1), GNG7(2), GNGT1(2), GRK4(1), GRK5(1), ITPR1(13), ITPR2(12), ITPR3(10), KCNB1(3), KCNJ3(3), MIB1(1), NME7(1), PLCB3(6), PRKACA(1), PRKACB(2), PRKAR1A(2), PRKAR2A(1), PRKAR2B(5), PRKCD(2), PRKCE(3), PRKCG(4), PRKCH(2), PRKCQ(1), PRKD1(5), RGS10(2), RGS11(1), RGS14(1), RGS16(2), RGS17(1), RGS18(3), RGS2(1), RGS20(2), RGS3(7), RGS5(1), RGS6(6), RGS7(1), RGS9(2), RYR1(24), RYR2(31), RYR3(27), SLC8A1(3), SLC8A3(5), USP5(3), YWHAQ(2) 38763648 451 94 446 177 124 148 91 35 53 0 8.8e-13 5.4e-10
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 166 ADCY1(9), ADCY2(5), ADCY3(2), ADCY4(4), ADCY7(8), ADCY8(8), ADCY9(4), ADORA2B(1), ADRA1A(4), ADRA1B(2), ADRA1D(1), ADRB1(2), ADRB2(2), ADRB3(1), AGTR1(1), ATP2A1(3), ATP2A2(4), ATP2A3(3), ATP2B1(8), ATP2B2(7), ATP2B3(7), ATP2B4(1), AVPR1A(5), AVPR1B(1), BDKRB1(1), BDKRB2(2), CACNA1A(9), CACNA1B(1), CACNA1C(17), CACNA1D(12), CACNA1E(16), CACNA1F(2), CACNA1G(10), CACNA1H(10), CACNA1I(7), CACNA1S(9), CALM1(1), CALM2(2), CALM3(1), CAMK2A(1), CAMK2B(2), CAMK2G(3), CAMK4(2), CCKAR(2), CCKBR(3), CD38(2), CHRM1(1), CHRM2(6), CHRM3(4), CHRM5(3), CHRNA7(1), CYSLTR1(2), DRD1(2), EDNRA(2), EGFR(7), ERBB2(4), ERBB3(12), ERBB4(12), F2R(2), GNA11(1), GNA14(1), GNA15(2), GNAQ(1), GNAS(12), GRIN1(3), GRIN2A(7), GRIN2C(2), GRIN2D(1), GRM1(11), GRM5(11), GRPR(3), HRH1(3), HRH2(2), HTR2A(1), HTR2B(4), HTR2C(2), HTR4(3), HTR5A(2), HTR7(3), ITPKA(1), ITPKB(4), ITPR1(13), ITPR2(12), ITPR3(10), LHCGR(5), LTB4R2(2), MYLK(7), MYLK2(2), NOS1(15), NOS3(2), NTSR1(1), OXTR(3), P2RX3(1), P2RX4(1), P2RX5(2), PDE1A(2), PDE1B(1), PDE1C(2), PDGFRA(2), PDGFRB(5), PHKA1(4), PHKA2(4), PHKB(3), PHKG1(2), PHKG2(2), PLCB1(8), PLCB2(3), PLCB3(6), PLCB4(6), PLCD3(5), PLCE1(7), PLCG1(9), PLCG2(5), PLCZ1(2), PPID(1), PPP3CA(2), PPP3CB(1), PPP3R2(1), PRKACA(1), PRKACB(2), PRKACG(2), PRKCG(4), PRKX(1), PTAFR(2), PTGER3(2), PTGFR(3), PTK2B(8), RYR1(24), RYR2(31), RYR3(27), SLC25A4(1), SLC25A5(2), SLC8A1(3), SLC8A2(3), SLC8A3(5), SPHK1(4), TACR1(2), TACR2(1), TACR3(4), TNNC1(2), TNNC2(1), TRHR(5), TRPC1(2), VDAC1(1) 55532421 648 97 638 230 179 225 126 50 64 4 2.9e-09 9e-07
3 SMOOTH_MUSCLE_CONTRACTION ACTA1, ACTA2, ACTC, ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, ADM, ADMR, ARRB1, ARRB2, ATF1, ATF2, ATF3, ATF4, ATF5, ATP2A2, ATP2A3, CACNB3, CALCA, CALM1, CALM2, CALM3, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CMKOR1, CNN1, CNN2, CORIN, CREB3, CREBL1, CREBL1, TNXB, CRH, CRHR1, DGKZ, EDG2, ETS2, FOS, GABPA, GABPB2, GBA2, GJA1, GNAQ, GNB1, GNB2, GNB3, GNB4, GNB5, GNG12, GNG13, GNG2, GNG3, GNG4, GNG5, GNG7, GNGT1, GRK4, GRK5, GRK6, GSTO1, GUCA2A, GUCA2B, GUCY1A3, HEAB, IGFBP1, IGFBP2, IGFBP3, IGFBP4, IGFBP6, IL1B, IL6, ITPR1, ITPR2, ITPR3, JUN, LGR7, LGR8, MAFF, MGC11266, MYL2, MYL4, MYLK2, NFKB1, NOS1, NOS3, OXT, OXTR, PDE4B, PDE4D, PKIA, PKIB, PKIG, PLCB3, PLCD1, PLCG1, PLCG2, PRKACA, PRKACB, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCH, PRKCQ, PRKCZ, PRKD1, RAMP1, RAMP2, RAMP3, RCP9, RGS1, RGS10, RGS11, RGS14, RGS16, RGS17, RGS18, RGS19, RGS2, RGS20, RGS3, RGS4, RGS5, RGS6, RGS7, RGS9, RLN1, RYR1, RYR2, RYR3, SARA1, SFN, SLC8A1, SP1, USP5, YWHAB, YWHAH, YWHAQ, YWHAQ, MIB1 138 ACTA1(1), ACTA2(5), ADCY1(9), ADCY2(5), ADCY3(2), ADCY4(4), ADCY5(7), ADCY6(5), ADCY7(8), ADCY8(8), ADCY9(4), ARRB1(3), ARRB2(2), ATF5(3), ATP2A2(4), ATP2A3(3), CALCA(1), CALM1(1), CALM2(2), CALM3(1), CAMK2A(1), CAMK2B(2), CAMK2G(3), CNN1(1), CORIN(4), CREB3(3), CRHR1(1), DGKZ(1), ETS2(1), GABPA(1), GABPB2(1), GBA2(2), GJA1(7), GNAQ(1), GNB1(1), GNB2(3), GNB3(1), GNB4(3), GNG12(1), GNG7(2), GNGT1(2), GRK4(1), GRK5(1), GUCA2A(1), GUCY1A3(7), IGFBP1(2), IGFBP2(1), IGFBP3(4), IL1B(1), IL6(1), ITPR1(13), ITPR2(12), ITPR3(10), JUN(2), MIB1(1), MYL2(1), MYL4(1), MYLK2(2), NFKB1(4), NOS1(15), NOS3(2), OXT(2), OXTR(3), PDE4B(4), PLCB3(6), PLCG1(9), PLCG2(5), PRKACA(1), PRKACB(2), PRKAR1A(2), PRKAR2A(1), PRKAR2B(5), PRKCD(2), PRKCE(3), PRKCH(2), PRKCQ(1), PRKD1(5), RAMP2(1), RAMP3(3), RGS10(2), RGS11(1), RGS14(1), RGS16(2), RGS17(1), RGS18(3), RGS2(1), RGS20(2), RGS3(7), RGS5(1), RGS6(6), RGS7(1), RGS9(2), RYR1(24), RYR2(31), RYR3(27), SLC8A1(3), SP1(2), TNXB(20), USP5(3), YWHAQ(2) 35609952 401 88 397 159 121 126 78 34 42 0 5.5e-08 0.000011
4 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 191 ACTB(3), ACTN1(2), ACTN2(11), ACTN3(1), ACTN4(1), AKT1(2), AKT2(1), AKT3(3), ARHGAP5(6), BAD(1), BCAR1(3), BIRC2(1), BIRC3(3), BRAF(5), CAPN2(3), CAV1(2), CCND2(1), CCND3(2), CDC42(1), CHAD(3), COL11A1(12), COL11A2(5), COL1A1(6), COL1A2(13), COL2A1(7), COL3A1(6), COL4A1(5), COL4A2(4), COL4A4(4), COL4A6(5), COL5A1(7), COL5A2(4), COL5A3(5), COL6A3(15), COL6A6(15), COMP(1), CRK(1), CTNNB1(8), DIAPH1(3), DOCK1(10), EGF(4), EGFR(7), ELK1(2), ERBB2(4), FARP2(2), FLNA(5), FLNB(3), FLNC(18), FLT1(5), FN1(15), FYN(3), GRB2(1), GRLF1(8), GSK3B(1), HGF(7), IBSP(1), IGF1(2), IGF1R(11), ITGA1(4), ITGA10(4), ITGA11(5), ITGA2(3), ITGA2B(5), ITGA3(6), ITGA4(7), ITGA5(4), ITGA6(2), ITGA7(5), ITGA8(3), ITGA9(6), ITGAV(2), ITGB1(2), ITGB3(5), ITGB4(10), ITGB5(2), ITGB7(2), ITGB8(6), JUN(2), KDR(7), LAMA1(14), LAMA2(11), LAMA3(8), LAMA4(7), LAMA5(13), LAMB1(5), LAMB2(10), LAMB3(11), LAMB4(6), LAMC1(5), LAMC2(6), LAMC3(9), MAP2K1(3), MAPK1(2), MAPK10(3), MAPK3(1), MAPK8(4), MAPK9(1), MET(3), MYL2(1), MYLK(7), MYLK2(2), PAK1(2), PAK2(3), PAK3(1), PAK4(2), PAK6(3), PAK7(2), PARVA(1), PARVB(3), PARVG(2), PDGFA(1), PDGFB(3), PDGFC(2), PDGFD(3), PDGFRA(2), PDGFRB(5), PDPK1(1), PIK3CB(4), PIK3CD(6), PIK3CG(9), PIK3R1(5), PIK3R2(3), PIK3R3(1), PIK3R5(4), PIP5K1C(5), PPP1CA(2), PPP1CB(1), PPP1CC(2), PPP1R12A(1), PRKCG(4), PTEN(5), PTK2(5), PXN(2), RAC2(1), RAF1(6), RAP1A(1), RAP1B(2), RAPGEF1(6), RELN(15), RHOA(4), ROCK1(5), ROCK2(2), SHC1(3), SHC2(2), SHC3(3), SHC4(1), SOS1(3), SOS2(4), THBS1(5), THBS2(6), THBS3(2), THBS4(2), TLN1(9), TLN2(11), TNC(11), TNN(10), TNR(9), TNXB(20), VASP(2), VAV1(2), VAV2(5), VAV3(6), VCL(2), VEGFC(3), VTN(4), VWF(8), ZYX(2) 75526843 786 106 779 351 220 270 137 64 93 2 9.9e-07 0.00015
5 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 200 ABI2(3), ACTN1(2), ACTN2(11), ACTN3(1), ACTN4(1), APC(18), APC2(4), ARAF(6), ARHGEF1(1), ARHGEF12(5), ARHGEF4(4), ARHGEF6(8), ARHGEF7(7), ARPC1A(1), ARPC1B(1), ARPC4(1), BCAR1(3), BDKRB1(1), BDKRB2(2), BRAF(5), CD14(1), CDC42(1), CFL1(1), CHRM1(1), CHRM2(6), CHRM3(4), CHRM4(1), CHRM5(3), CRK(1), CSK(2), CYFIP1(2), CYFIP2(8), DIAPH1(3), DIAPH2(3), DIAPH3(10), DOCK1(10), EGF(4), EGFR(7), F2(4), F2R(2), FGD1(4), FGD3(5), FGF1(2), FGF10(4), FGF11(1), FGF12(3), FGF13(3), FGF14(3), FGF17(2), FGF18(2), FGF2(1), FGF20(1), FGF23(1), FGF5(1), FGF6(3), FGF7(1), FGF9(4), FGFR1(6), FGFR2(5), FGFR3(1), FGFR4(5), FN1(15), GIT1(2), GNA12(1), GNG12(1), GRLF1(8), GSN(4), IQGAP1(3), IQGAP2(5), IQGAP3(5), ITGA1(4), ITGA10(4), ITGA11(5), ITGA2(3), ITGA2B(5), ITGA3(6), ITGA4(7), ITGA5(4), ITGA6(2), ITGA7(5), ITGA8(3), ITGA9(6), ITGAD(3), ITGAE(4), ITGAL(6), ITGAM(4), ITGAV(2), ITGAX(5), ITGB1(2), ITGB2(5), ITGB3(5), ITGB4(10), ITGB5(2), ITGB7(2), ITGB8(6), LIMK1(2), LIMK2(3), MAP2K1(3), MAP2K2(1), MAPK1(2), MAPK3(1), MOS(3), MSN(3), MYH10(13), MYH14(8), MYH9(13), MYL2(1), MYLK(7), MYLK2(2), NCKAP1(4), NCKAP1L(7), PAK1(2), PAK2(3), PAK3(1), PAK4(2), PAK6(3), PAK7(2), PDGFA(1), PDGFB(3), PDGFRA(2), PDGFRB(5), PFN2(2), PIK3CB(4), PIK3CD(6), PIK3CG(9), PIK3R1(5), PIK3R2(3), PIK3R3(1), PIK3R5(4), PIP4K2A(3), PIP4K2B(2), PIP4K2C(1), PIP5K1A(2), PIP5K1C(5), PPP1CA(2), PPP1CB(1), PPP1CC(2), PPP1R12A(1), PPP1R12B(2), PTK2(5), PXN(2), RAC2(1), RAF1(6), RDX(1), RHOA(4), ROCK1(5), ROCK2(2), RRAS(1), RRAS2(1), SCIN(2), SLC9A1(4), SOS1(3), SOS2(4), SSH1(4), SSH2(10), SSH3(2), TIAM1(11), TIAM2(15), TMSL3(1), VAV1(2), VAV2(5), VAV3(6), VCL(2), WASF1(3), WASF2(2), WASL(1) 56277620 628 103 620 240 165 213 120 44 84 2 2.6e-06 0.00032
6 ALKPATHWAY Activin receptor-like kinase 3 (ALK3) is required during gestation for cardiac muscle development. ACVR1, APC, ATF2, AXIN1, BMP10, BMP2, BMP4, BMP5, BMP7, BMPR1A, BMPR2, CHRD, CTNNB1, DVL1, FZD1, GATA4, GSK3B, MADH1, MADH4, MADH5, MADH6, MAP3K7, MEF2C, MYL2, NKX2-5, NOG, NPPA, NPPB, RFC1, TCF1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TGFBR3, WNT1 32 ACVR1(3), APC(18), AXIN1(8), BMP10(2), BMP2(2), BMP4(5), BMP5(5), BMP7(2), BMPR1A(1), BMPR2(9), CHRD(1), CTNNB1(8), DVL1(3), FZD1(7), GATA4(2), GSK3B(1), MAP3K7(7), MEF2C(1), MYL2(1), NKX2-5(2), NPPB(1), RFC1(1), TGFB1(2), TGFB2(4), TGFB3(3), TGFBR1(1), TGFBR2(4), TGFBR3(1), WNT1(3) 7311941 108 49 104 36 30 27 24 5 16 6 8.4e-06 0.00086
7 HSA04730_LONG_TERM_DEPRESSION Genes involved in long-term depression ARAF, BRAF, C7orf16, CACNA1A, CRH, CRHR1, GNA11, GNA12, GNA13, GNAI1, GNAI2, GNAI3, GNAO1, GNAQ, GNAS, GNAZ, GRIA1, GRIA2, GRIA3, GRID2, GRM1, GRM5, GUCY1A2, GUCY1A3, GUCY1B3, GUCY2C, GUCY2D, GUCY2F, HRAS, IGF1, IGF1R, ITPR1, ITPR2, ITPR3, KRAS, LYN, MAP2K1, MAP2K2, MAPK1, MAPK3, NOS1, NOS2A, NOS3, NPR1, NPR2, NRAS, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PLCB1, PLCB2, PLCB3, PLCB4, PPP2CA, PPP2CB, PPP2R1A, PPP2R1B, PPP2R2A, PPP2R2B, PPP2R2C, PRKCA, PRKCB1, PRKCG, PRKG1, PRKG2, RAF1, RYR1 73 ARAF(6), BRAF(5), CACNA1A(9), CRHR1(1), GNA11(1), GNA12(1), GNAI1(1), GNAI2(3), GNAI3(3), GNAQ(1), GNAS(12), GNAZ(5), GRIA1(6), GRIA2(8), GRIA3(5), GRID2(7), GRM1(11), GRM5(11), GUCY1A2(3), GUCY1A3(7), GUCY1B3(4), GUCY2C(1), GUCY2D(5), GUCY2F(5), IGF1(2), IGF1R(11), ITPR1(13), ITPR2(12), ITPR3(10), LYN(2), MAP2K1(3), MAP2K2(1), MAPK1(2), MAPK3(1), NOS1(15), NOS3(2), NPR1(6), NPR2(2), PLA2G10(1), PLA2G12A(1), PLA2G12B(2), PLA2G2D(1), PLA2G3(5), PLA2G4A(3), PLA2G6(3), PLCB1(8), PLCB2(3), PLCB3(6), PLCB4(6), PPP2CA(1), PPP2R1A(3), PPP2R1B(3), PPP2R2A(1), PPP2R2B(2), PPP2R2C(2), PRKCG(4), PRKG1(4), PRKG2(6), RAF1(6), RYR1(24) 22546825 298 75 296 97 65 127 61 20 25 0 0.000015 0.0013
8 NO1PATHWAY Shear stress in endothelial cells increases cytoplasmic calcium, which activates nitric oxide synthase III to release NO, which in turn regulates cardiac contractions. ACTA1, AKT1, BDK, BDKRB2, CALM1, CALM2, CALM3, CAV1, CHRM1, CHRNA1, FLT1, FLT4, HSPCA, KDR, NOS3, PDE2A, PDE3A, PDE3B, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKG1, PRKG2, RYR2, SLC7A1, SYT1, TNNI1, VEGF 28 ACTA1(1), AKT1(2), BDKRB2(2), CALM1(1), CALM2(2), CALM3(1), CAV1(2), CHRM1(1), CHRNA1(3), FLT1(5), FLT4(6), KDR(7), NOS3(2), PDE2A(6), PDE3A(3), PDE3B(9), PRKACB(2), PRKACG(2), PRKAR1A(2), PRKAR2A(1), PRKAR2B(5), PRKG1(4), PRKG2(6), RYR2(31), SLC7A1(1) 8335775 107 59 107 37 30 36 27 11 3 0 0.000016 0.0013
9 GSK3PATHWAY Bacterial lipopolysaccharide activates AKT to promote the survival and activation of macrophages and inhibits Gsk3-beta to promote beta-catenin accumulation in the nucleus. AKT1, APC, AXIN1, CCND1, CD14, CTNNB1, DVL1, FZD1, GJA1, GNAI1, GSK3B, IRAK1, LBP, LEF1, LY96, MYD88, NFKB1, PDPK1, PIK3CA, PIK3R1, PPP2CA, PRKR, RELA, TIRAP, TLR4, TOLLIP, WNT1 24 AKT1(2), APC(18), AXIN1(8), CD14(1), CTNNB1(8), DVL1(3), FZD1(7), GJA1(7), GNAI1(1), GSK3B(1), IRAK1(4), LEF1(3), LY96(1), MYD88(2), NFKB1(4), PDPK1(1), PIK3R1(5), PPP2CA(1), RELA(2), TIRAP(1), TOLLIP(1), WNT1(3) 5370673 84 45 82 27 19 25 16 4 16 4 2e-05 0.0014
10 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 14 APC(18), AXIN1(8), CREBBP(11), CTNNB1(8), DVL1(3), EP300(10), FZD1(7), GSK3B(1), HDAC1(2), LDB1(4), LEF1(3), PITX2(2), TRRAP(19), WNT1(3) 6582968 99 49 97 41 34 27 11 4 19 4 0.000023 0.0014
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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