Stomach Adenocarcinoma: 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: 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): 19

Mutations seen in COSMIC: 0

Significantly mutated genes in COSMIC territory: 0

Genes with clustered mutations (&le 3 aa apart): 22

Significantly mutated genesets: 4

Significantly mutated genesets: (excluding sig. mutated genes): 0

Results
Breakdown of Mutations by Type

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

type | count
--- | ---
Frame_Shift_Del | 27
Frame_Shift_Ins | 3
In_Frame_Del | 2
Indel | 1
Missense_Mutation | 813
Nonsense_Mutation | 24
Nonstop_Mutation | 1
Silent | 397
Splice_Site | 10
Total | 1278

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 | exp_ns_s_ratio
--- | --- | --- | --- | --- | --- | ---
*CpG->T | 332 | 2305023 | 0.00014 | 140 | 4.2 | 1.8
*Np(A/C/T)->transit | 280 | 19699827 | 0.000014 | 14 | 0.42 | 1.8
*ApG->G | 31 | 3932145 | 7.9e-06 | 7.9 | 0.23 | 2.6
transver | 170 | 25936995 | 6.6e-06 | 6.6 | 0.19 | 4.4
indel+null | 68 | 25936995 | 2.6e-06 | 2.6 | 0.077 | NaN
Total | 881 | 25936995 | 0.000034 | 34 | 1 | 3.2

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: 19. Number of genes displayed: 35

rank | gene | description | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | p_ns_s | p | q
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | CIC | capicua homolog (Drosophila) | 190190 | 14 | 11 | 13 | 2 | 7 | 2 | 0 | 0 | 5 | 0.14 | 3.2e-08 | 0.000012
2 | MXRA5 | matrix-remodelling associated 5 | 287280 | 22 | 17 | 22 | 6 | 8 | 5 | 0 | 7 | 2 | 0.29 | 4.2e-06 | 0.00068
3 | OCEL1 | occludin/ELL domain containing 1 | 47880 | 4 | 4 | 4 | 0 | 0 | 0 | 0 | 1 | 3 | 0.77 | 5.5e-06 | 0.00068
4 | HIST1H2AD | histone cluster 1, H2ad | 32851 | 3 | 3 | 3 | 0 | 0 | 0 | 0 | 1 | 2 | 0.29 | 7e-06 | 0.00068
5 | OR10J1 | olfactory receptor, family 10, subfamily J, member 1 | 48146 | 4 | 4 | 4 | 0 | 1 | 1 | 0 | 2 | 0 | 0.31 | 0.000046 | 0.0036
6 | BACH2 | BTB and CNC homology 1, basic leucine zipper transcription factor 2 | 91371 | 12 | 10 | 12 | 3 | 4 | 5 | 0 | 2 | 1 | 0.23 | 0.000068 | 0.0044
7 | NPFF | neuropeptide FF-amide peptide precursor | 14098 | 3 | 3 | 3 | 0 | 0 | 1 | 0 | 1 | 1 | 0.41 | 0.00011 | 0.0059
8 | OR6C70 | olfactory receptor, family 6, subfamily C, member 70 | 35644 | 4 | 4 | 4 | 0 | 0 | 1 | 1 | 1 | 1 | 0.38 | 0.00012 | 0.0061
9 | CCS | copper chaperone for superoxide dismutase | 31920 | 3 | 3 | 3 | 0 | 1 | 0 | 0 | 1 | 1 | 0.51 | 0.00016 | 0.007
10 | TNNI2 | troponin I type 2 (skeletal, fast) | 34580 | 5 | 5 | 5 | 0 | 3 | 0 | 0 | 0 | 2 | 0.12 | 0.00022 | 0.0086
11 | PRKRA | protein kinase, interferon-inducible double stranded RNA dependent activator | 46151 | 3 | 3 | 3 | 0 | 1 | 0 | 0 | 1 | 1 | 0.36 | 0.00027 | 0.0095
12 | COX7A2 | cytochrome c oxidase subunit VIIa polypeptide 2 (liver) | 13566 | 2 | 2 | 2 | 0 | 0 | 1 | 0 | 1 | 0 | 0.52 | 0.00042 | 0.013
13 | MS4A6A | membrane-spanning 4-domains, subfamily A, member 6A | 30989 | 3 | 3 | 3 | 0 | 0 | 0 | 0 | 3 | 0 | 0.73 | 0.00043 | 0.013
14 | KCTD5 | potassium channel tetramerisation domain containing 5 | 29127 | 2 | 2 | 2 | 1 | 0 | 0 | 0 | 2 | 0 | 0.87 | 0.0007 | 0.019
15 | CCDC97 | coiled-coil domain containing 97 | 61180 | 3 | 3 | 3 | 1 | 0 | 0 | 0 | 1 | 2 | 0.83 | 0.0017 | 0.045
16 | ZNF284 | zinc finger protein 284 | 130473 | 3 | 3 | 3 | 0 | 0 | 1 | 0 | 1 | 1 | 0.59 | 0.0024 | 0.058
17 | ZNF223 | zinc finger protein 223 | 58520 | 4 | 4 | 4 | 1 | 0 | 1 | 2 | 1 | 0 | 0.57 | 0.0025 | 0.058
18 | PCDHA6 | protocadherin alpha 6 | 220913 | 15 | 14 | 15 | 7 | 8 | 4 | 2 | 1 | 0 | 0.34 | 0.0031 | 0.068
19 | ZDHHC23 | zinc finger, DHHC-type containing 23 | 44289 | 3 | 3 | 3 | 0 | 0 | 0 | 0 | 1 | 2 | 0.37 | 0.0034 | 0.069
20 | USP48 | ubiquitin specific peptidase 48 | 132601 | 5 | 5 | 5 | 1 | 2 | 2 | 0 | 0 | 1 | 0.52 | 0.006 | 0.11
21 | C3orf33 | chromosome 3 open reading frame 33 | 29127 | 2 | 2 | 2 | 0 | 0 | 1 | 0 | 0 | 1 | 0.63 | 0.0061 | 0.11
22 | RRAS | related RAS viral (r-ras) oncogene homolog | 27265 | 3 | 3 | 3 | 0 | 2 | 0 | 0 | 1 | 0 | 0.36 | 0.0065 | 0.11
23 | MAML1 | mastermind-like 1 (Drosophila) | 107198 | 4 | 4 | 4 | 1 | 1 | 1 | 0 | 2 | 0 | 0.55 | 0.0066 | 0.11
24 | NME5 | non-metastatic cells 5, protein expressed in (nucleoside-diphosphate kinase) | 26201 | 3 | 3 | 2 | 1 | 0 | 1 | 0 | 2 | 0 | 0.77 | 0.0067 | 0.11
25 | GLT6D1 | glycosyltransferase 6 domain containing 1 | 40166 | 3 | 3 | 3 | 0 | 1 | 1 | 0 | 1 | 0 | 0.29 | 0.0069 | 0.11
26 | DSCR4 | Down syndrome critical region gene 4 | 17556 | 3 | 3 | 3 | 0 | 1 | 0 | 0 | 1 | 1 | 0.37 | 0.0071 | 0.11
27 | RNF167 | ring finger protein 167 | 53333 | 4 | 4 | 4 | 1 | 2 | 1 | 0 | 1 | 0 | 0.75 | 0.0076 | 0.11
28 | MAPK15 | mitogen-activated protein kinase 15 | 97356 | 5 | 5 | 5 | 0 | 2 | 0 | 0 | 3 | 0 | 0.21 | 0.0079 | 0.11
29 | LRRC55 | leucine rich repeat containing 55 | 38304 | 4 | 3 | 4 | 1 | 0 | 2 | 0 | 2 | 0 | 0.57 | 0.008 | 0.11
30 | CAV1 | caveolin 1, caveolae protein, 22kDa | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.11
31 | MOSC1 | MOCO sulphurase C-terminal domain containing 1 | 37373 | 3 | 3 | 3 | 0 | 1 | 1 | 0 | 1 | 0 | 0.41 | 0.009 | 0.11
32 | HOMEZ | homeobox and leucine zipper encoding | 94031 | 4 | 4 | 4 | 2 | 0 | 1 | 0 | 1 | 2 | 0.84 | 0.01 | 0.13
33 | OR52E6 | olfactory receptor, family 52, subfamily E, member 6 | 114912 | 2 | 2 | 2 | 1 | 0 | 0 | 0 | 2 | 0 | 0.88 | 0.012 | 0.13
34 | SDC4 | syndecan 4 | 36043 | 2 | 2 | 2 | 0 | 0 | 0 | 1 | 0 | 1 | 0.39 | 0.012 | 0.13
35 | SCNN1D | sodium channel, nonvoltage-gated 1, delta | 74347 | 2 | 2 | 2 | 0 | 0 | 0 | 0 | 1 | 1 | 0.66 | 0.012 | 0.13

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: *CpG->T .

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

n3 - number of nonsilent mutations of type: *ApG->G .

n4 - number of nonsilent mutations of type: transver .

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 | ABCC10 | ATP-binding cassette, sub-family C (CFTR/MRP), member 10 | 4 | 0 | 0 | 0 | 0 | 1 | 1
2 | BACH2 | BTB and CNC homology 1, basic leucine zipper transcription factor 2 | 12 | 0 | 0 | 0 | 0 | 1 | 1
3 | BSN | bassoon (presynaptic cytomatrix protein) | 20 | 0 | 0 | 0 | 0 | 1 | 1
4 | CLIC1 | chloride intracellular channel 1 | 2 | 0 | 0 | 0 | 0 | 1 | 1
5 | FAM78B | family with sequence similarity 78, member B | 1 | 0 | 0 | 0 | 0 | 1 | 1
6 | FGF23 | fibroblast growth factor 23 | 1 | 0 | 0 | 0 | 0 | 1 | 1
7 | GNAT1 | guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1 | 3 | 0 | 0 | 0 | 0 | 1 | 1
8 | KLC4 | kinesin light chain 4 | 3 | 0 | 0 | 0 | 0 | 1 | 1
9 | LACRT | lacritin | 2 | 0 | 0 | 0 | 0 | 1 | 1
10 | MSH5 | mutS homolog 5 (E. coli) | 5 | 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
--- | --- | --- | --- | --- | --- | ---
166 | PCDHB7 | protocadherin beta 7 | 14 | 0 | 1 | 4
229 | TLR9 | toll-like receptor 9 | 10 | 0 | 1 | 4
157 | PCDHA1 | protocadherin alpha 1 | 14 | 0 | 1 | 3
27 | C1QL1 | complement component 1, q subcomponent-like 1 | 4 | 0 | 1 | 1
57 | DNAJB2 | DnaJ (Hsp40) homolog, subfamily B, member 2 | 4 | 0 | 1 | 1
108 | KHSRP | KH-type splicing regulatory protein | 3 | 0 | 1 | 1
112 | KLK8 | kallikrein-related peptidase 8 | 2 | 0 | 1 | 1
139 | NME5 | non-metastatic cells 5, protein expressed in (nucleoside-diphosphate kinase) | 3 | 0 | 1 | 1
158 | PCDHA10 | protocadherin alpha 10 | 6 | 0 | 1 | 1
266 | ZNF777 | zinc finger protein 777 | 7 | 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: 4. Number of genesets displayed: 10

rank | geneset | description | genes | N_genes | mut_tally | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | p_ns_s | p | q
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | STRIATED_MUSCLE_CONTRACTION |  | ACTA1, ACTA2, ACTC, ACTN2, ACTN3, ACTN4, C9orf97, DES, DES, FAM48A, DMD, MYBPC1, MYBPC2, MYBPC3, MYH3, MYH6, MYH6, MYH7, MYH8, MYL1, MYL2, MYL3, MYL4, MYL9, MYOM1, NEB, TCAP, TMOD1, TNNC2, TNNI1, TNNI2, TNNI3, TNNT1, TNNT2, TNNT3, TPM1, TPM2, TPM3, TPM4, TPM4, TTN, VIM | 2 | MYL1(1), TNNI2(5) | 59052 | 6 | 6 | 6 | 0 | 3 | 0 | 0 | 1 | 2 | 0.1 | 0.000013 | 0.002
2 | OXIDATIVE_PHOSPHORYLATION |  | ATP12A, ATP4B, ATP5E, ATP5O, ATP6AP1, ATP6V0A1, ATP6V0A4, ATP6V0B, ATP6V0C, ATP6V0C, SHMT1, ATP6V0D1, ATP6V0E, ATP6V1A, ATP6V1B1, ATP6V1B2, ATP6V1C1, ATP6V1C2, ATP6V1D, ATP6V1E1, ATP6V1F, ATP6V1G1, ATP6V1G2, ATP6V1G3, ATP6V1H, ATP7A, ATP7B, COX10, COX4I1, COX5A, COX5B, COX6A1, COX6A2, COX6B1, COX6C, COX7A1, COX7A2, COX7B, COX7C, COX8A, NDUFA1, NDUFA10, NDUFA11, NDUFA4, NDUFA5, NDUFA8, NDUFB2, NDUFB4, NDUFB5, NDUFB6, NDUFB7, NDUFS1, NDUFS2, NDUFV1, NDUFV2, PP, PPA2, SDHA, SDHA, SDHAL2, SDHB, UQCRB, UQCRC1, UQCRFS1, UQCRH | 1 | COX7A2(2) | 13566 | 2 | 2 | 2 | 0 | 0 | 1 | 0 | 1 | 0 | 0.52 | 0.00042 | 0.034
3 | HSA04514_CELL_ADHESION_MOLECULES | Genes involved in cell adhesion molecules (CAMs) | ALCAM, CADM1, CADM3, CD2, CD22, CD226, CD274, CD276, CD28, CD34, CD4, CD40, CD40LG, CD58, CD6, CD80, CD86, CD8A, CD8B, CD99, CDH1, CDH15, CDH2, CDH3, CDH4, CDH5, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CNTN1, CNTN2, CNTNAP1, CNTNAP2, CTLA4, ESAM, F11R, GLG1, HLA-A, HLA-A29.1, HLA-B, HLA-C, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-E, HLA-F, HLA-G, ICAM1, ICAM2, ICAM3, ICOS, ICOSLG, ITGA4, ITGA6, ITGA8, ITGA9, ITGAL, ITGAM, ITGAV, ITGB1, ITGB2, ITGB7, ITGB8, JAM2, JAM3, L1CAM, MADCAM1, MAG, MPZ, MPZL1, NCAM1, NCAM2, NEGR1, NEO1, NFASC, NLGN1, NLGN2, NLGN3, NRCAM, NRXN1, NRXN2, NRXN3, OCLN, PDCD1, PDCD1LG2, PECAM1, PTPRC, PTPRF, PTPRM, PVR, PVRL1, PVRL2, PVRL3, SDC1, SDC2, SDC3, SDC4, SELE, SELL, SELP, SELPLG, SIGLEC1, SPN, VCAM1, VCAN | 6 | CD2(2), HLA-DMA(2), HLA-DMB(3), NLGN3(8), SDC4(2) | 317205 | 17 | 14 | 17 | 1 | 7 | 6 | 1 | 1 | 2 | 0.014 | 0.00076 | 0.04
4 | HSA04330_NOTCH_SIGNALING_PATHWAY | Genes involved in Notch signaling pathway | ADAM17, APH1A, CIR, CREBBP, CTBP1, CTBP2, DLL1, DLL3, DLL4, DTX1, DTX2, DTX3, DTX3L, DTX4, DVL1, DVL2, DVL3, EP300, GCN5L2, HDAC1, HDAC2, HES1, JAG1, JAG2, LFNG, LOC652788, MAML1, MAML2, MAML3, MFNG, NCOR2, NCSTN, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NUMB, NUMBL, PCAF, PSEN1, PSEN2, PSENEN, PTCRA, RBPJ, RBPJL, RFNG, SNW1 | 3 | DVL2(3), MAML1(4), RBPJL(3) | 297255 | 10 | 9 | 10 | 2 | 4 | 2 | 0 | 4 | 0 | 0.19 | 0.0022 | 0.087
5 | G_PROTEIN_SIGNALING |  | ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, AKAP1, AKAP10, AKAP11, AKAP12, AKAP2, PALM2_AKAP2, AKAP3, AKAP4, AKAP5, AKAP6, AKAP7, AKAP8, AKAP9, ARHGEF1, CALM1, CALM2, CALM3, CHMP1B, GNA11, GNA12, GNA13, GNA14, GNA15, GNAI2, GNAI3, GNAL, GNAO1, GNAQ, GNAZ, GNB1, GNB2, GNB3, GNB5, GNG10, GNG10, LOC552891, GNG12, GNG13, GNG3, GNG4, GNG5, GNG7, GNGT1, GNGT2, HRAS, IL18BP, ITPR1, KCNJ3, KRAS, MGC11266, NRAS, PALM2, PALM2_AKAP2, PALM2_AKAP2, PDE1A, PDE1B, PDE1C, PDE4A, PDE4B, PDE4C, PDE4D, PDE7A, PDE7B, PDE8A, PDE8B, PLCB3, PPP3CA, PPP3CC, PRKACA, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PRKD1, PRKD3, RHOA, RRAS, SARA1, SLC9A1, USP5 | 1 | RRAS(3) | 27265 | 3 | 3 | 3 | 0 | 2 | 0 | 0 | 1 | 0 | 0.36 | 0.0065 | 0.14
6 | 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 | 1 | CAV1(2) | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.14
7 | INTEGRINPATHWAY | Integrins are cell surface receptors commonly present at focal adhensions that interact with the extracellular matrix and transduce extracellular signaling. | ACTA1, ACTN1, ACTN2, ACTN3, ARHA, BCAR1, BCR, CAPN1, CAPNS1, CAPNS2, CAV1, CRKL, CSK, FYN, GRB2, GRF2, HRAS, ITGA1, ITGB1, JUN, MAP2K1, MAP2K2, MAPK1, MAPK3, MAPK8, PPP1R12B, PTK2, PXN, RAF1, RAP1A, ROCK1, SHC1, SOS1, SRC, TLN1, TNS, VCL, ZYX | 1 | CAV1(2) | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.14
8 | INTEGRIN_MEDIATED_CELL_ADHESION_KEGG |  | AKT1, AKT3, BCAR1, CAPN1, CAPN10, CAPN11, CAPN2, CAPN3, CAPN5, CAPN6, CAPN7, CAPN9, CAPNS1, CAV1, CAV2, CAV3, CDC42, CRK, CSK, DKFZp434E1119, DOCK1, FLJ14825, FLJ40125, FYN, GIT2, GRB2, ILK, 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, LOC283874, PDPK1, MAP2K1, MAP2K2, MAP2K3, MAP2K6, MAPK10, MAPK12, MAPK4, MAPK6, MAPK7, MGC17301, MYLK2, PAK1, PAK2, PAK3, PAK4, PAK6, PDPK1, PIK3R2, PTK2, PXN, RAC1, RAC2, RAC3, RAP1B, RAPGEF1, RHO, ROCK1, ROCK2, SDCCAG8, SEPP1, SHC1, SHC3, SORBS1, SOS1, SRC, TLN1, TNS, TNS1, VASP, VAV2, VAV3, VCL, ZYX | 1 | CAV1(2) | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.14
9 | 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 | 1 | CAV1(2) | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.14
10 | ST_INTEGRIN_SIGNALING_PATHWAY | Integrins are transmembrane receptors that mediate cell growth, survival, and migration by binding to ligands in the extracellular matrix. | ABL1, ACK1, ACTN1, ACTR2, ACTR3, AKT1, AKT2, AKT3, ANGPTL2, ARHGEF6, ARHGEF7, BCAR1, BRAF, CAV1, CDC42, CDKN2A, CRK, CSE1L, DDEF1, DOCK1, EPHB2, FYN, GRAF, GRB2, GRB7, GRF2, GRLF1, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGB3BP, MAP2K4, MAP2K7, MAP3K11, MAPK1, MAPK10, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MRAS, MYLK, MYLK2, P4HB, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PKLR, PLCG1, PLCG2, PTEN, PTK2, RAF1, RALA, RHO, ROCK1, ROCK2, SHC1, SOS1, SOS2, SRC, TERF2IP, TLN1, TLN2, VASP, WAS, ZYX | 1 | CAV1(2) | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.14

Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 0. Number of genesets displayed: 10

rank | geneset | description | genes | N_genes | mut_tally | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | p_ns_s | p | q
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | HSA04514_CELL_ADHESION_MOLECULES | Genes involved in cell adhesion molecules (CAMs) | ALCAM, CADM1, CADM3, CD2, CD22, CD226, CD274, CD276, CD28, CD34, CD4, CD40, CD40LG, CD58, CD6, CD80, CD86, CD8A, CD8B, CD99, CDH1, CDH15, CDH2, CDH3, CDH4, CDH5, CLDN1, CLDN10, CLDN11, CLDN14, CLDN15, CLDN16, CLDN17, CLDN18, CLDN19, CLDN2, CLDN20, CLDN22, CLDN23, CLDN3, CLDN4, CLDN5, CLDN6, CLDN7, CLDN8, CLDN9, CNTN1, CNTN2, CNTNAP1, CNTNAP2, CTLA4, ESAM, F11R, GLG1, HLA-A, HLA-A29.1, HLA-B, HLA-C, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5, HLA-E, HLA-F, HLA-G, ICAM1, ICAM2, ICAM3, ICOS, ICOSLG, ITGA4, ITGA6, ITGA8, ITGA9, ITGAL, ITGAM, ITGAV, ITGB1, ITGB2, ITGB7, ITGB8, JAM2, JAM3, L1CAM, MADCAM1, MAG, MPZ, MPZL1, NCAM1, NCAM2, NEGR1, NEO1, NFASC, NLGN1, NLGN2, NLGN3, NRCAM, NRXN1, NRXN2, NRXN3, OCLN, PDCD1, PDCD1LG2, PECAM1, PTPRC, PTPRF, PTPRM, PVR, PVRL1, PVRL2, PVRL3, SDC1, SDC2, SDC3, SDC4, SELE, SELL, SELP, SELPLG, SIGLEC1, SPN, VCAM1, VCAN | 6 | CD2(2), HLA-DMA(2), HLA-DMB(3), NLGN3(8), SDC4(2) | 317205 | 17 | 14 | 17 | 1 | 7 | 6 | 1 | 1 | 2 | 0.014 | 0.00076 | 0.12
2 | HSA04330_NOTCH_SIGNALING_PATHWAY | Genes involved in Notch signaling pathway | ADAM17, APH1A, CIR, CREBBP, CTBP1, CTBP2, DLL1, DLL3, DLL4, DTX1, DTX2, DTX3, DTX3L, DTX4, DVL1, DVL2, DVL3, EP300, GCN5L2, HDAC1, HDAC2, HES1, JAG1, JAG2, LFNG, LOC652788, MAML1, MAML2, MAML3, MFNG, NCOR2, NCSTN, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NUMB, NUMBL, PCAF, PSEN1, PSEN2, PSENEN, PTCRA, RBPJ, RBPJL, RFNG, SNW1 | 3 | DVL2(3), MAML1(4), RBPJL(3) | 297255 | 10 | 9 | 10 | 2 | 4 | 2 | 0 | 4 | 0 | 0.19 | 0.0022 | 0.17
3 | G_PROTEIN_SIGNALING |  | ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9, AKAP1, AKAP10, AKAP11, AKAP12, AKAP2, PALM2_AKAP2, AKAP3, AKAP4, AKAP5, AKAP6, AKAP7, AKAP8, AKAP9, ARHGEF1, CALM1, CALM2, CALM3, CHMP1B, GNA11, GNA12, GNA13, GNA14, GNA15, GNAI2, GNAI3, GNAL, GNAO1, GNAQ, GNAZ, GNB1, GNB2, GNB3, GNB5, GNG10, GNG10, LOC552891, GNG12, GNG13, GNG3, GNG4, GNG5, GNG7, GNGT1, GNGT2, HRAS, IL18BP, ITPR1, KCNJ3, KRAS, MGC11266, NRAS, PALM2, PALM2_AKAP2, PALM2_AKAP2, PDE1A, PDE1B, PDE1C, PDE4A, PDE4B, PDE4C, PDE4D, PDE7A, PDE7B, PDE8A, PDE8B, PLCB3, PPP3CA, PPP3CC, PRKACA, PRKACB, PRKACG, PRKAR1A, PRKAR1B, PRKAR2A, PRKAR2B, PRKCA, PRKCB1, PRKCD, PRKCE, PRKCG, PRKCH, PRKCI, PRKCQ, PRKCZ, PRKD1, PRKD3, RHOA, RRAS, SARA1, SLC9A1, USP5 | 1 | RRAS(3) | 27265 | 3 | 3 | 3 | 0 | 2 | 0 | 0 | 1 | 0 | 0.36 | 0.0065 | 0.17
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 | 1 | CAV1(2) | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.17
5 | INTEGRINPATHWAY | Integrins are cell surface receptors commonly present at focal adhensions that interact with the extracellular matrix and transduce extracellular signaling. | ACTA1, ACTN1, ACTN2, ACTN3, ARHA, BCAR1, BCR, CAPN1, CAPNS1, CAPNS2, CAV1, CRKL, CSK, FYN, GRB2, GRF2, HRAS, ITGA1, ITGB1, JUN, MAP2K1, MAP2K2, MAPK1, MAPK3, MAPK8, PPP1R12B, PTK2, PXN, RAF1, RAP1A, ROCK1, SHC1, SOS1, SRC, TLN1, TNS, VCL, ZYX | 1 | CAV1(2) | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.17
6 | INTEGRIN_MEDIATED_CELL_ADHESION_KEGG |  | AKT1, AKT3, BCAR1, CAPN1, CAPN10, CAPN11, CAPN2, CAPN3, CAPN5, CAPN6, CAPN7, CAPN9, CAPNS1, CAV1, CAV2, CAV3, CDC42, CRK, CSK, DKFZp434E1119, DOCK1, FLJ14825, FLJ40125, FYN, GIT2, GRB2, ILK, 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, LOC283874, PDPK1, MAP2K1, MAP2K2, MAP2K3, MAP2K6, MAPK10, MAPK12, MAPK4, MAPK6, MAPK7, MGC17301, MYLK2, PAK1, PAK2, PAK3, PAK4, PAK6, PDPK1, PIK3R2, PTK2, PXN, RAC1, RAC2, RAC3, RAP1B, RAPGEF1, RHO, ROCK1, ROCK2, SDCCAG8, SEPP1, SHC1, SHC3, SORBS1, SOS1, SRC, TLN1, TNS, TNS1, VASP, VAV2, VAV3, VCL, ZYX | 1 | CAV1(2) | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.17
7 | 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 | 1 | CAV1(2) | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.17
8 | ST_INTEGRIN_SIGNALING_PATHWAY | Integrins are transmembrane receptors that mediate cell growth, survival, and migration by binding to ligands in the extracellular matrix. | ABL1, ACK1, ACTN1, ACTR2, ACTR3, AKT1, AKT2, AKT3, ANGPTL2, ARHGEF6, ARHGEF7, BCAR1, BRAF, CAV1, CDC42, CDKN2A, CRK, CSE1L, DDEF1, DOCK1, EPHB2, FYN, GRAF, GRB2, GRB7, GRF2, GRLF1, ILK, ITGA1, ITGA10, ITGA11, ITGA2, ITGA3, ITGA4, ITGA5, ITGA6, ITGA7, ITGA8, ITGA9, ITGB3BP, MAP2K4, MAP2K7, MAP3K11, MAPK1, MAPK10, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MRAS, MYLK, MYLK2, P4HB, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PIK3CA, PIK3CB, PKLR, PLCG1, PLCG2, PTEN, PTK2, RAF1, RALA, RHO, ROCK1, ROCK2, SHC1, SOS1, SOS2, SRC, TERF2IP, TLN1, TLN2, VASP, WAS, ZYX | 1 | CAV1(2) | 21945 | 2 | 2 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | 0.5 | 0.0086 | 0.17
9 | OVARIAN_INFERTILITY_GENES |  | ATM, BMPR1B, CCND2, CDK4, CDKN1B, CEBPB, DAZL, DMC1, EGR1, ESR2, FSHR, GJA4, INHA, LHCGR, MLH1, MSH5, NCOR1, NR5A1, NRIP1, PGR, PRLR, PTGER2, SMPD1, VDR, ZP2 | 1 | MSH5(5) | 98819 | 5 | 5 | 5 | 1 | 1 | 3 | 0 | 1 | 0 | 0.35 | 0.012 | 0.21
10 | HSA04340_HEDGEHOG_SIGNALING_PATHWAY | Genes involved in Hedgehog signaling pathway | BMP2, BMP4, BMP5, BMP6, BMP7, BMP8A, BMP8B, BTRC, CSNK1A1, CSNK1A1L, CSNK1D, CSNK1E, CSNK1G1, CSNK1G2, CSNK1G3, DHH, FBXW11, GAS1, GLI1, GLI2, GLI3, GSK3B, HHIP, IHH, LRP2, PRKACA, PRKACB, PRKACG, PRKX, PRKY, PTCH1, PTCH2, RAB23, SHH, SMO, STK36, SUFU, WNT1, WNT10A, WNT10B, WNT11, WNT16, WNT2, WNT2B, WNT3, WNT3A, WNT4, WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9B, ZIC2 | 1 | WNT10A(3) | 44688 | 3 | 3 | 3 | 1 | 1 | 0 | 0 | 1 | 1 | 0.71 | 0.015 | 0.23

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474