Lung Squamous Cell 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: LUSC.

Number of patients in set: 178

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): 405

Mutations seen in COSMIC: 1

Significantly mutated genes in COSMIC territory: 0

Genes with clustered mutations (&le 3 aa apart): 1

Significantly mutated genesets: 100

Significantly mutated genesets: (excluding sig. mutated genes): 5

Results
Breakdown of Mutations by Type

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

type count
De_novo_Start_InFrame 3
De_novo_Start_OutOfFrame 13
Frame_Shift_Del 524
Frame_Shift_Ins 132
In_Frame_Del 85
In_Frame_Ins 19
Indel 9
Missense_Mutation 34224
Nonsense_Mutation 2598
Nonstop_Mutation 42
Silent 13568
Splice_Site_DNP 36
Splice_Site_Del 14
Splice_Site_Ins 10
Splice_Site_SNP 837
Start_Codon_Del 3
Total 52117
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 9734 2640254776 3.7e-06 3.7 0.52
C->(A/T) 14492 2777075010 5.2e-06 5.2 0.73
A->(C/G) 7317 2640254776 2.8e-06 2.8 0.39
C->G 2664 2777075010 9.6e-07 0.96 0.13
indel+null 4313 5417329964 8e-07 0.8 0.11
double_null 29 5417329964 5.4e-09 0.0054 0.00075
Total 38549 5417329964 7.1e-06 7.1 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: 405. 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 228196 119 117 82 7 23 20 20 13 43 0 <1.00e-15 <1.80e-11
2 RYR2 ryanodine receptor 2 (cardiac) 2630306 88 56 86 22 28 29 18 4 9 0 4.22e-15 2.80e-11
3 CSMD3 CUB and Sushi multiple domains 3 2041660 77 58 77 16 21 22 11 5 16 2 4.66e-15 2.80e-11
4 LRP1B low density lipoprotein-related protein 1B (deleted in tumors) 2521192 67 50 65 12 19 19 18 4 7 0 3.79e-14 9.71e-11
5 CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4) 83838 23 23 20 1 1 5 5 0 12 0 3.81e-14 9.71e-11
6 NFE2L2 nuclear factor (erythroid-derived 2)-like 2 318442 21 20 12 0 6 0 13 1 1 0 4.60e-14 9.71e-11
7 CDH10 cadherin 10, type 2 (T2-cadherin) 429158 27 25 27 7 8 9 3 2 5 0 4.70e-14 9.71e-11
8 HCN1 hyperpolarization activated cyclic nucleotide-gated potassium channel 1 441618 27 25 25 11 5 13 2 3 4 0 4.75e-14 9.71e-11
9 ZFHX4 zinc finger homeobox 4 1745824 65 48 65 18 22 24 9 5 5 0 5.32e-14 9.71e-11
10 FAM5C family with sequence similarity 5, member C 414562 24 23 24 3 6 13 4 1 0 0 5.38e-14 9.71e-11
11 FAM135B family with sequence similarity 135, member B 764866 35 29 34 9 11 16 6 0 2 0 8.89e-14 1.46e-10
12 USH2A Usher syndrome 2A (autosomal recessive, mild) 2831446 63 51 63 12 16 25 12 5 5 0 2.26e-12 3.40e-09
13 KEAP1 kelch-like ECH-associated protein 1 337310 18 18 16 0 3 10 2 1 2 0 3.03e-12 4.20e-09
14 ADAMTS12 ADAM metallopeptidase with thrombospondin type 1 motif, 12 868818 30 28 29 6 9 12 5 1 3 0 1.05e-11 1.35e-08
15 TTN titin 19694276 263 124 260 91 69 86 69 17 16 6 1.90e-11 2.29e-08
16 SI sucrase-isomaltase (alpha-glucosidase) 1009616 33 29 33 2 9 13 7 2 2 0 3.26e-11 3.68e-08
17 C1orf173 chromosome 1 open reading frame 173 819156 27 24 27 8 8 8 6 2 3 0 2.97e-10 2.98e-07
18 OR10G9 olfactory receptor, family 10, subfamily G, member 9 167320 13 13 12 3 1 10 1 0 1 0 2.98e-10 2.98e-07
19 CDH12 cadherin 12, type 2 (N-cadherin 2) 432362 19 18 19 6 4 8 4 0 3 0 3.79e-10 3.60e-07
20 CNTNAP5 contactin associated protein-like 5 680316 25 22 25 6 5 9 6 2 3 0 4.14e-10 3.73e-07
21 ZNF804B zinc finger protein 804B 723748 22 21 21 8 7 1 6 4 4 0 5.59e-10 4.80e-07
22 NAV3 neuron navigator 3 1290144 32 30 32 10 6 16 6 2 2 0 5.94e-10 4.87e-07
23 REG1A regenerating islet-derived 1 alpha (pancreatic stone protein, pancreatic thread protein) 92738 11 10 11 3 0 6 3 1 1 0 8.17e-10 6.41e-07
24 LRRC4C leucine rich repeat containing 4C 343006 18 17 18 1 11 3 3 0 1 0 9.70e-10 7.29e-07
25 FMN2 formin 2 828412 24 23 22 8 5 11 4 1 3 0 1.48e-09 1.01e-06
26 ZIC1 Zic family member 1 (odd-paired homolog, Drosophila) 241368 16 13 16 4 5 4 6 0 1 0 1.49e-09 1.01e-06
27 PCDH11X protocadherin 11 X-linked 731758 26 23 25 3 10 9 4 2 1 0 1.51e-09 1.01e-06
28 OR4M2 olfactory receptor, family 4, subfamily M, member 2 168388 11 11 11 1 3 3 2 2 1 0 3.53e-09 2.28e-06
29 SPTA1 spectrin, alpha, erythrocytic 1 (elliptocytosis 2) 1329304 36 29 36 12 6 16 6 4 4 0 3.90e-09 2.43e-06
30 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 222144 11 11 11 0 2 1 1 1 6 0 4.86e-09 2.92e-06
31 OR5D18 olfactory receptor, family 5, subfamily D, member 18 168388 11 11 11 4 4 4 2 0 1 0 6.55e-09 3.81e-06
32 COL11A1 collagen, type XI, alpha 1 1040588 31 25 31 7 8 10 7 0 6 0 9.01e-09 5.08e-06
33 ELTD1 EGF, latrophilin and seven transmembrane domain containing 1 375046 15 15 15 1 4 3 1 2 5 0 1.14e-08 6.24e-06
34 REG3A regenerating islet-derived 3 alpha 97544 9 9 9 2 2 3 3 0 1 0 1.18e-08 6.26e-06
35 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 585086 21 20 10 1 13 3 5 0 0 0 1.38e-08 7.13e-06

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 45 22 1 3916 3 0.027 1
2 A4GNT alpha-1,4-N-acetylglucosaminyltransferase 5 0 0 0 0 1 1
3 AACS acetoacetyl-CoA synthetase 2 0 0 0 0 1 1
4 ABCA9 ATP-binding cassette, sub-family A (ABC1), member 9 8 0 0 0 0 1 1
5 ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 4 0 0 0 0 1 1
6 ABCF2 ATP-binding cassette, sub-family F (GCN20), member 2 6 0 0 0 0 1 1
7 ABHD2 abhydrolase domain containing 2 1 0 0 0 0 1 1
8 ABHD4 abhydrolase domain containing 4 1 0 0 0 0 1 1
9 ACADS acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain 3 0 0 0 0 1 1
10 ACOT11 acyl-CoA thioesterase 11 1 0 0 0 0 1 1

Note:

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

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

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

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

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

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

Clustered Mutations

Table 5.  Get Full Table Genes with Clustered Mutations

num gene desc n mindist npairs3 npairs12
1374 C20orf26 chromosome 20 open reading frame 26 18 0 1 1
2643 CUBN cubilin (intrinsic factor-cobalamin receptor) 22 4 0 1
27 ABCA13 ATP-binding cassette, sub-family A (ABC1), member 13 27 8 0 1
2693 CYP11B2 cytochrome P450, family 11, subfamily B, polypeptide 2 6 10 0 1
6712 MUC2 mucin 2, oligomeric mucus/gel-forming 9 11 0 1
4450 GPR98 G protein-coupled receptor 98 28 12 0 0
11716 WNK1 WNK lysine deficient protein kinase 1 15 23 0 0
10440 SYNE1 spectrin repeat containing, nuclear envelope 1 45 34 0 0
11089 TRANK1 7 47 0 0
6717 MUC6 mucin 6, oligomeric mucus/gel-forming 10 59 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: 100. 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 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(2), AKT1(1), AKT3(2), APAF1(1), ATM(7), BAX(1), BCL2L1(2), BID(1), BIRC3(3), CAPN1(2), CAPN2(2), CASP10(4), CASP6(1), CASP7(2), CASP8(1), CASP9(1), CFLAR(1), CHP(2), CHUK(2), CSF2RB(5), DFFA(1), DFFB(2), FADD(1), FAS(1), FASLG(1), IKBKB(3), IL1B(1), IL1RAP(2), IRAK1(4), IRAK2(1), IRAK3(3), MAP3K14(1), NFKB1(2), NFKB2(2), NTRK1(3), PIK3CA(21), PIK3CB(1), PIK3CD(3), PIK3CG(10), PIK3R1(1), PIK3R2(4), PIK3R3(2), PIK3R5(2), PPP3CA(2), PPP3CB(5), PPP3CC(2), PPP3R1(1), PPP3R2(3), PRKACA(1), PRKACB(2), PRKACG(1), PRKAR1A(3), PRKAR1B(1), PRKAR2B(3), RELA(3), TNFRSF10A(1), TNFRSF10B(1), TNFRSF10D(1), TNFRSF1A(2), TP53(119), TRADD(1) 22576808 267 147 219 57 74 68 35 30 60 0 <1.00e-15 <1.93e-13
2 RNAPATHWAY dsRNA-activated protein kinase phosphorylates elF2a, which generally inhibits translation, and activates NF-kB to provoke inflammation. CHUK, DNAJC3, EIF2S1, EIF2S2, MAP3K14, NFKB1, NFKBIA, PRKR, RELA, TP53 9 CHUK(2), MAP3K14(1), NFKB1(2), RELA(3), TP53(119) 2739598 127 118 90 9 24 22 21 14 46 0 2.55e-15 1.93e-13
3 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(1), ATF2(2), CDC42(1), DLD(2), DUSP10(3), DUSP4(1), GAB1(2), GADD45A(1), GCK(1), JUN(2), MAP2K5(2), MAP3K1(3), MAP3K11(2), MAP3K12(2), MAP3K13(5), MAP3K4(4), MAP3K5(3), MAP3K7(3), MAP3K9(4), MAPK10(1), MAPK7(1), MAPK8(2), MAPK9(1), MYEF2(3), NFATC3(3), NR2C2(1), PAPPA(8), SHC1(1), TP53(119), TRAF6(1), ZAK(1) 13764918 186 133 149 32 41 46 33 19 47 0 2.78e-15 1.93e-13
4 PLK3PATHWAY Active Plk3 phosphorylates CDC25c, blocking the G2/M transition, and phosphorylates p53 to induce apoptosis. ATM, ATR, CDC25C, CHEK1, CHEK2, CNK, TP53, YWHAH 7 ATM(7), ATR(11), CDC25C(1), CHEK1(4), CHEK2(3), TP53(119) 4293716 145 124 108 8 29 26 25 18 47 0 2.89e-15 1.93e-13
5 APOPTOSIS APAF1, BAD, BAK1, BCL2L7P1, BAX, BCL2, BCL2L1, BCL2L11, BID, BIRC2, BIRC3, BIRC4, BIRC5, BNIP3L, CASP1, CASP10, CASP1, COPl, CASP2, CASP3, CASP4, CASP6, CASP7, CASP8, CASP9, CHUK, CYCS, DFFA, DFFB, FADD, FAS, FASLG, GZMB, HELLS, HRK, IKBKB, IKBKG, IRF1, IRF2, IRF3, IRF4, IRF5, IRF6, IRF7, JUN, LTA, MAP2K4, MAP3K1, MAPK10, MDM2, MYC, NFKB1, NFKBIA, NFKBIB, NFKBIE, PRF1, RELA, RIPK1, TNF, TNFRSF10B, TNFRSF1A, TNFRSF1B, TNFRSF21, TNFRSF25, TNFRSF25, PLEKHG5, TNFSF10, TP53, TP73, TRADD, TRAF1, TRAF2, TRAF3 66 APAF1(1), BAK1(1), BAX(1), BCL2L1(2), BID(1), BIRC3(3), BNIP3L(1), CASP1(2), CASP10(4), CASP2(1), CASP4(3), CASP6(1), CASP7(2), CASP8(1), CASP9(1), CHUK(2), DFFA(1), DFFB(2), FADD(1), FAS(1), FASLG(1), GZMB(1), IKBKB(3), IRF1(1), IRF3(1), IRF4(3), IRF6(5), JUN(2), LTA(3), MAP3K1(3), MAPK10(1), MDM2(1), MYC(1), NFKB1(2), NFKBIB(1), PLEKHG5(1), PRF1(2), RELA(3), TNFRSF10B(1), TNFRSF1A(2), TNFRSF1B(1), TNFRSF21(3), TP53(119), TRADD(1), TRAF1(4), TRAF3(1) 15688386 199 135 162 41 39 46 33 23 58 0 3.89e-15 1.93e-13
6 G1_TO_S_CELL_CYCLE_REACTOME ATM, CCNA1, CCNB1, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNG2, CCNH, CDC25A, CDC45L, CDK2, CDK4, CDK7, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CREB3, CREB3L1, CREB3L3, CREB3L4, CREBL1, CREBL1, TNXB, E2F1, E2F2, E2F3, E2F4, E2F5, E2F6, FLJ14001, GADD45A, GBA2, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MDM2, MNAT1, MYC, MYT1, NACA, NACA, FKSG17, ORC1L, ORC2L, ORC3L, ORC4L, ORC5L, ORC6L, PCNA, POLA2, POLE, POLE2, PRIM1, PRIM2A, RB1, RBL1, RPA1, RPA2, RPA3, TFDP1, TFDP2, TP53, WEE1 65 ATM(7), CCNA1(1), CCNB1(1), CCND1(1), CCND2(3), CCND3(1), CCNE2(2), CDK2(1), CDK7(1), CDKN2A(23), CDKN2C(1), CDKN2D(1), CREB3(2), CREB3L3(1), CREB3L4(2), E2F1(3), GADD45A(1), GBA2(2), MCM2(1), MCM3(1), MCM4(4), MCM5(6), MCM6(2), MCM7(3), MDM2(1), MYC(1), ORC1L(1), ORC2L(1), ORC3L(1), ORC5L(1), POLA2(3), POLE2(2), PRIM1(2), RB1(7), RBL1(6), TFDP2(1), TNXB(16), TP53(119), WEE1(2) 20927638 235 137 195 36 45 63 39 20 68 0 4.00e-15 1.93e-13
7 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(2), CDKN2A(23), E2F1(3), MDM2(1), MYC(1), PIK3CA(21), PIK3R1(1), POLR1A(4), POLR1B(4), POLR1C(1), POLR1D(1), RAC1(2), RB1(7), TBX2(3), TP53(119), TWIST1(1) 5437544 194 133 143 19 44 41 30 17 62 0 4.00e-15 1.93e-13
8 ATMPATHWAY The tumor-suppressing protein kinase ATM responds to radiation-induced DNA damage by blocking cell-cycle progression and activating DNA repair. ABL1, ATM, BRCA1, CDKN1A, CHEK1, CHEK2, GADD45A, JUN, MAPK8, MDM2, MRE11A, NBS1, NFKB1, NFKBIA, RAD50, RAD51, RBBP8, RELA, TP53, TP73 19 ABL1(2), ATM(7), BRCA1(6), CHEK1(4), CHEK2(3), GADD45A(1), JUN(2), MAPK8(2), MDM2(1), MRE11A(2), NFKB1(2), RAD50(3), RAD51(1), RBBP8(1), RELA(3), TP53(119) 8101670 159 122 122 16 30 35 24 21 49 0 4.00e-15 1.93e-13
9 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), MYC(1), SP1(1), SP3(1), TP53(119), WT1(4) 1894810 128 122 91 11 25 21 24 15 43 0 4.33e-15 1.93e-13
10 RBPATHWAY The ATM protein kinase recognizes DNA damage and blocks cell cycle progression by phosphorylating chk1 and p53, which normally inhibits Rb to allow G1/S transitions. ATM, CDC2, CDC25A, CDC25B, CDC25C, CDK2, CDK4, CHEK1, MYT1, RB1, TP53, WEE1, YWHAH 12 ATM(7), CDC25B(3), CDC25C(1), CDK2(1), CHEK1(4), RB1(7), TP53(119), WEE1(2) 4759720 144 124 107 10 27 30 22 14 51 0 4.77e-15 1.93e-13

Table 7.  Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 5. 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 222 ADORA1(4), ADORA2A(6), ADORA2B(1), ADRA1A(2), ADRA1B(4), ADRA2B(4), ADRA2C(2), ADRB2(3), AGTR1(3), AGTR2(4), AVPR1A(3), AVPR1B(2), AVPR2(1), BDKRB1(3), BDKRB2(1), C3AR1(1), C5AR1(1), CALCR(6), CALCRL(4), CCKAR(2), CCKBR(1), CHRM2(6), CHRM3(5), CHRM4(1), CHRM5(2), CNR1(3), CNR2(3), CRHR1(4), CRHR2(3), CTSG(4), CYSLTR1(3), CYSLTR2(1), DRD1(1), DRD2(2), DRD3(5), DRD4(1), DRD5(3), EDNRA(2), EDNRB(5), F2R(2), F2RL1(3), F2RL2(1), F2RL3(2), FPR1(1), FSHB(1), GABBR1(3), GABBR2(3), GABRA1(6), GABRA3(5), GABRA4(3), GABRA5(4), GABRB1(3), GABRB2(6), GABRD(2), GABRE(4), GABRG2(5), GABRP(2), GABRQ(6), GABRR1(2), GABRR2(2), GALR1(3), GH1(1), GH2(2), GHR(2), GHRHR(3), GHSR(3), GLP1R(1), GLP2R(4), GLRA1(2), GLRA2(5), GLRA3(3), GLRB(3), GPR156(2), GPR35(1), GPR50(4), GPR63(2), GPR83(2), GRIA1(6), GRIA2(3), GRIA3(9), GRIA4(7), GRID2(12), GRIK1(4), GRIK2(8), GRIK3(7), GRIK4(4), GRIK5(1), GRIN1(1), GRIN2A(13), GRIN2C(2), GRIN2D(3), GRIN3A(8), GRIN3B(4), GRM2(3), GRM4(1), GRM6(4), GRM7(8), GRM8(9), GRPR(2), GZMA(4), HCRTR2(3), HRH1(3), HRH2(2), HRH3(1), HRH4(3), HTR1B(3), HTR1D(1), HTR1E(5), HTR1F(2), HTR2A(1), HTR2B(2), HTR2C(3), HTR4(3), HTR5A(3), HTR6(1), HTR7(3), LEPR(10), LHB(1), LHCGR(8), LTB4R2(1), MAS1(3), MC2R(2), MC3R(3), MC4R(1), MC5R(3), MCHR1(2), MCHR2(3), MTNR1A(1), NMBR(2), NMUR2(2), NPBWR1(1), NPY1R(3), NPY2R(2), NPY5R(2), NTSR1(3), NTSR2(3), OPRD1(2), OPRK1(1), OPRM1(2), OXTR(1), P2RX2(1), P2RX3(5), P2RX4(2), P2RX7(1), P2RY1(1), P2RY10(2), P2RY13(1), P2RY14(3), P2RY2(2), P2RY4(1), P2RY6(2), PARD3(5), PPYR1(3), PRL(1), PRLHR(1), PRLR(5), PRSS1(3), PRSS3(1), PTAFR(3), PTGDR(5), PTGER2(1), PTGER3(5), PTGER4(2), PTGFR(2), PTGIR(1), PTH2R(5), RXFP1(7), RXFP2(1), SSTR1(1), SSTR2(2), SSTR3(1), SSTR4(2), SSTR5(1), TAAR1(4), TAAR2(2), TAAR5(5), TAAR6(4), TAAR8(2), TAAR9(2), TACR1(2), TACR3(3), TBXA2R(2), THRA(2), THRB(1), TRHR(1), TRPV1(2), TSHR(1) 55037422 557 157 554 207 157 205 106 28 61 0 2.7e-07 0.00017
2 GPCRDB_CLASS_A_RHODOPSIN_LIKE ADORA1, ADORA2A, ADORA2B, ADORA3, ADRA1A, ADRA1B, ADRA1D, ADRA2A, ADRA2C, ADRB1, ADRB2, ADRB3, AGTR1, AGTR2, AGTRL1, AVPR1A, AVPR1B, AVPR2, BDKRB1, BDKRB2, BLR1, BRS3, C3AR1, C5R1, CCBP2, CCKAR, CCKBR, CCR1, CCR10, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CCRL1, CCRL2, CHML, CHRM1, CHRM2, CHRM3, CHRM4, CHRM5, CMKLR1, CMKOR1, CNR1, CNR2, CX3CR1, CXCR3, CXCR4, DRD1, DRD2, DRD3, DRD4, DRD5, EDNRA, EDNRB, ELA3A, F2R, F2RL1, F2RL2, F2RL3, FPR1, FPRL1, FPRL2, FSHR, GALR1, GALR2, GALR3, GALT, GHSR, GNB2L1, GPR10, GPR147, GPR17, GPR173, GPR174, GPR23, GPR24, GPR27, GPR3, GPR30, GPR35, GPR37, GPR37L1, GPR4, GPR44, GPR50, GPR6, GPR63, GPR74, GPR77, GPR83, GPR85, GPR87, GPR92, GRPR, HCRTR1, HCRTR2, HRH1, HRH2, HRH3, HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR4, HTR5A, HTR6, HTR7, HTR7, LOC93164, IL8RA, IL8RB, LHCGR, LTB4R, MAS1, MC1R, MC3R, MC4R, MC5R, MLNR, MTNR1A, MTNR1B, NMBR, NMUR1, NMUR2, NPY1R, NPY2R, NPY5R, NPY6R, NTSR1, NTSR2, OPN1SW, OPN3, OPRD1, OPRK1, OPRL1, OPRM1, OR10A5, OR11A1, OR12D3, OR1C1, OR1F1, OR1Q1, OR2H1, OR5V1, OR5V1, OR12D3, OR7A5, OR7C1, OR8B8, OXTR, P2RY1, P2RY10, P2RY11, P2RY12, P2RY13, P2RY14, P2RY2, P2RY5, P2RY6, PPYR1, PTAFR, PTGDR, PTGER1, PTGER2, PTGER4, PTGFR, PTGIR, Rgr, RGR, RHO, RRH, SSTR1, SSTR2, SSTR3, SSTR4, SUCNR1, TBXA2R, TRHR 159 ADORA1(4), ADORA2A(6), ADORA2B(1), ADRA1A(2), ADRA1B(4), ADRA1D(2), ADRA2C(2), ADRB2(3), AGTR1(3), AGTR2(4), AVPR1A(3), AVPR1B(2), AVPR2(1), BDKRB1(3), BDKRB2(1), C3AR1(1), CCBP2(4), CCKAR(2), CCKBR(1), CCR1(2), CCR10(1), CCR3(1), CCR4(3), CCR6(2), CCR8(3), CCRL1(3), CCRL2(1), CHML(1), CHRM2(6), CHRM3(5), CHRM4(1), CHRM5(2), CMKLR1(1), CNR1(3), CNR2(3), CX3CR1(3), CXCR3(1), DRD1(1), DRD2(2), DRD3(5), DRD4(1), DRD5(3), EDNRA(2), EDNRB(5), F2R(2), F2RL1(3), F2RL2(1), F2RL3(2), FPR1(1), GALR1(3), GALT(1), GHSR(3), GPR17(5), GPR174(4), GPR27(1), GPR35(1), GPR37(2), GPR37L1(2), GPR50(4), GPR6(2), GPR63(2), GPR77(4), GPR83(2), GPR85(2), GPR87(6), GRPR(2), HCRTR2(3), HRH1(3), HRH2(2), HRH3(1), HTR1B(3), HTR1D(1), HTR1E(5), HTR1F(2), HTR2A(1), HTR2B(2), HTR2C(3), HTR4(3), HTR5A(3), HTR6(1), HTR7(3), LHCGR(8), MAS1(3), MC3R(3), MC4R(1), MC5R(3), MTNR1A(1), NMBR(2), NMUR2(2), NPY1R(3), NPY2R(2), NPY5R(2), NTSR1(3), NTSR2(3), OPN1SW(1), OPN3(1), OPRD1(2), OPRK1(1), OPRM1(2), OR10A5(2), OR11A1(4), OR12D3(4), OR1F1(1), OR1Q1(3), OR2H1(1), OR5V1(1), OR7A5(1), OR8B8(5), OXTR(1), P2RY1(1), P2RY10(2), P2RY13(1), P2RY14(3), P2RY2(2), P2RY6(2), PPYR1(3), PTAFR(3), PTGDR(5), PTGER2(1), PTGER4(2), PTGFR(2), PTGIR(1), RGR(2), SSTR1(1), SSTR2(2), SSTR3(1), SSTR4(2), SUCNR1(2), TBXA2R(2), TRHR(1) 31942456 308 137 307 112 86 113 58 14 37 0 0.000019 0.0059
3 C21_STEROID_HORMONE_METABOLISM AKR1C4, AKR1D1, CYP11A1, CYP11B1, CYP11B2, CYP17A1, CYP21A2, HSD11B1, HSD11B2, HSD3B1, HSD3B2 10 AKR1C4(1), AKR1D1(4), CYP11A1(2), CYP11B2(6), CYP17A1(1), CYP21A2(1), HSD11B1(3), HSD11B2(1), HSD3B1(4), HSD3B2(5) 2150774 28 26 27 3 5 12 4 5 2 0 0.0006 0.091
4 HSA00140_C21_STEROID_HORMONE_METABOLISM Genes involved in C21-steroid hormone metabolism AKR1C4, AKR1D1, CYP11A1, CYP11B1, CYP11B2, CYP17A1, CYP21A2, HSD11B1, HSD11B2, HSD3B1, HSD3B2 10 AKR1C4(1), AKR1D1(4), CYP11A1(2), CYP11B2(6), CYP17A1(1), CYP21A2(1), HSD11B1(3), HSD11B2(1), HSD3B1(4), HSD3B2(5) 2150774 28 26 27 3 5 12 4 5 2 0 0.0006 0.091
5 BLOOD_CLOTTING_CASCADE F10, F11, F12, F13B, F2, F5, F7, F8, F8A1, F9, FGA, FGB, FGG, LPA, PLG, PLAT, PLAU, PLG, SERPINB2, SERPINE1, SERPINF2, VWF 20 F10(3), F11(4), F12(1), F13B(7), F5(15), F8(10), F9(4), FGA(5), FGB(3), FGG(1), LPA(11), PLAT(1), PLAU(2), PLG(2), SERPINB2(3), SERPINE1(2), SERPINF2(3), VWF(16) 9480458 93 69 92 24 19 37 23 6 8 0 0.00074 0.091
6 FLUMAZENILPATHWAY Flumazenil is a benzodiazepine receptor antagonist that may induce protective preconditioning in ischemic cardiomyocytes. GABRA1, GABRA2, GABRA3, GABRA4, GABRA5, GABRA6, GPX1, PRKCE, SOD1 7 GABRA1(6), GABRA3(5), GABRA4(3), GABRA5(4), PRKCE(5) 1635108 23 23 23 5 9 10 3 0 1 0 0.0012 0.12
7 HSA01430_CELL_COMMUNICATION Genes involved in cell communication ACTB, ACTG1, CHAD, COL11A1, COL11A2, COL17A1, COL1A1, COL1A2, COL2A1, COL3A1, COL4A1, COL4A2, COL4A4, COL4A6, COL5A1, COL5A2, COL5A3, COL6A1, COL6A2, COL6A3, COL6A6, COMP, DES, DSC1, DSC2, DSC3, DSG1, DSG2, DSG3, DSG4, FN1, GJA1, GJA10, GJA3, GJA4, GJA5, GJA8, GJA9, GJB1, GJB2, GJB3, GJB4, GJB5, GJB6, GJB7, GJC1, GJC2, GJC3, GJD2, GJD3, GJD4, IBSP, INA, ITGA6, ITGB4, KRT1, KRT10, KRT12, KRT13, KRT14, KRT15, KRT16, KRT17, KRT18, KRT19, KRT2, KRT20, KRT23, KRT24, KRT25, KRT27, KRT28, KRT3, KRT31, KRT32, KRT33A, KRT33B, KRT34, KRT35, KRT36, KRT37, KRT38, KRT39, KRT4, KRT40, KRT5, KRT6A, KRT6B, KRT6C, KRT7, KRT71, KRT72, KRT73, KRT74, KRT75, KRT76, KRT77, KRT78, KRT79, KRT8, KRT81, KRT82, KRT83, KRT84, KRT85, KRT86, KRT9, LAMA1, LAMA2, LAMA3, LAMA4, LAMA5, LAMB1, LAMB2, LAMB3, LAMB4, LAMC1, LAMC2, LAMC3, LMNA, LMNB1, LMNB2, LOC728760, NES, PRPH, RELN, SPP1, THBS1, THBS2, THBS3, THBS4, TNC, TNN, TNR, TNXB, VIM, VTN, VWF 130 ACTB(1), COL11A2(10), COL17A1(4), COL1A1(8), COL1A2(15), COL2A1(8), COL3A1(10), COL4A1(11), COL4A2(9), COL4A4(9), COL4A6(9), COL5A1(5), COL5A2(12), COL5A3(11), COL6A3(12), COMP(2), DES(2), DSC1(4), DSC2(1), DSC3(7), DSG1(8), DSG2(2), DSG3(2), DSG4(5), FN1(17), GJA1(4), GJA10(5), GJA8(2), GJB2(1), GJB4(1), GJB5(1), GJC1(2), GJC2(1), GJC3(1), GJD2(2), GJD4(2), IBSP(4), INA(2), ITGA6(6), ITGB4(9), KRT1(1), KRT10(1), KRT12(3), KRT13(2), KRT14(1), KRT16(3), KRT17(2), KRT18(2), KRT2(4), KRT20(3), KRT23(2), KRT24(4), KRT27(3), KRT28(2), KRT3(2), KRT31(1), KRT32(2), KRT33A(1), KRT35(1), KRT36(3), KRT37(2), KRT4(1), KRT5(1), KRT6A(2), KRT6B(4), KRT6C(2), KRT71(2), KRT72(2), KRT73(7), KRT74(1), KRT75(2), KRT76(2), KRT77(3), KRT78(1), KRT79(4), KRT81(3), KRT82(1), KRT83(1), KRT84(1), KRT85(1), KRT86(1), KRT9(1), LAMA1(14), LAMA2(17), LAMA3(7), LAMA4(15), LAMA5(7), LAMB1(6), LAMB2(4), LAMB3(1), LAMB4(3), LAMC1(8), LAMC2(4), LAMC3(1), NES(11), PRPH(2), RELN(26), THBS1(1), THBS3(4), TNC(16), TNXB(16), VIM(5), VWF(16) 63492600 499 148 498 162 140 188 92 32 47 0 0.0028 0.24
8 HSA04614_RENIN_ANGIOTENSIN_SYSTEM Genes involved in renin-angiotensin system ACE, ACE2, AGT, AGTR1, AGTR2, ANPEP, CMA1, CPA3, CTSA, CTSG, ENPEP, LNPEP, MAS1, MME, NLN, REN, THOP1 17 ACE(4), ACE2(3), AGT(1), AGTR1(3), AGTR2(4), ANPEP(5), CMA1(4), CPA3(4), CTSA(2), CTSG(4), ENPEP(7), LNPEP(2), MAS1(3), MME(6), NLN(2), THOP1(1) 5741924 55 46 55 22 11 23 8 4 9 0 0.0037 0.28
9 GLUCOCORTICOID_MINERALOCORTICOID_METABOLISM CPN2, CYP11A1, CYP11B2, CYP17A1, HSD11B1, HSD11B2, HSD3B1, HSD3B2 8 CPN2(1), CYP11A1(2), CYP11B2(6), CYP17A1(1), HSD11B1(3), HSD11B2(1), HSD3B1(4), HSD3B2(5) 1860812 23 21 22 5 3 11 4 4 1 0 0.006 0.39
10 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 202 ACTN1(2), ACTN2(6), ACTN3(2), ACTN4(5), APC(9), APC2(2), ARAF(3), ARHGEF1(2), ARHGEF12(3), ARHGEF4(3), ARHGEF6(2), ARHGEF7(3), ARPC1A(2), ARPC1B(1), BCAR1(5), BDKRB1(3), BDKRB2(1), BRAF(7), CD14(1), CDC42(1), CFL1(3), CFL2(1), CHRM2(6), CHRM3(5), CHRM4(1), CHRM5(2), CRKL(1), CYFIP1(6), CYFIP2(7), DIAPH1(1), DIAPH3(5), DOCK1(3), EGF(6), EGFR(9), EZR(1), F2R(2), FGD1(3), FGD3(3), FGF10(2), FGF12(2), FGF14(1), FGF2(2), FGF23(1), FGF3(1), FGF5(3), FGF6(2), FGF8(1), FGFR1(3), FGFR2(6), FGFR3(2), FGFR4(1), FN1(17), GIT1(1), GNA12(1), GNA13(1), GNG12(1), GRLF1(11), GSN(2), HRAS(2), IQGAP1(6), IQGAP2(6), IQGAP3(11), ITGA1(4), ITGA10(6), ITGA11(3), ITGA2(5), ITGA2B(1), ITGA3(2), ITGA4(5), ITGA5(1), ITGA6(6), ITGA7(3), ITGA8(9), ITGA9(1), ITGAD(6), ITGAE(3), ITGAL(1), ITGAM(3), ITGAV(3), ITGAX(9), ITGB1(4), ITGB2(3), ITGB3(3), ITGB4(9), ITGB5(2), ITGB6(2), ITGB7(1), ITGB8(3), KRAS(1), LIMK1(1), LIMK2(1), MAP2K1(2), MAP2K2(2), MAPK1(1), MAPK3(2), MOS(4), MRAS(3), MSN(3), MYH10(3), MYH14(4), MYH9(14), MYL2(1), MYLK(7), MYLK2(2), MYLPF(1), NCKAP1(5), NCKAP1L(9), PAK1(3), PAK2(1), PAK3(3), PAK4(1), PAK6(2), PAK7(4), PDGFB(1), PDGFRA(8), PDGFRB(5), PFN3(1), PIK3CB(1), PIK3CD(3), PIK3CG(10), PIK3R1(1), PIK3R2(4), PIK3R3(2), PIK3R5(2), PIP4K2A(2), PIP4K2B(3), PIP4K2C(3), PIP5K1A(4), PIP5K1B(1), PIP5K1C(2), PPP1CA(1), PPP1CB(1), PPP1CC(1), PPP1R12B(3), PTK2(3), PXN(3), RAC1(2), RAF1(1), RDX(1), ROCK1(5), ROCK2(3), RRAS2(2), SCIN(1), SLC9A1(3), SOS1(6), SOS2(4), SSH1(1), SSH2(7), TIAM1(9), TIAM2(4), VAV1(7), VAV2(4), VAV3(1), VCL(2), WAS(5), WASL(2) 75493894 527 153 523 165 122 198 93 47 67 0 0.0064 0.39
Methods & Data
Methods

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

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

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