Bladder Urothelial 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 v2.0 was used to generate the results found in this report.

Working with individual set: BLCA.

Number of patients in set: 28

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): 7

Mutations seen in COSMIC: 37

Significantly mutated genes in COSMIC territory: 3

Genes with clustered mutations (&le 3 aa apart): 37

Significantly mutated genesets: 23

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
Frame_Shift_Del 98
Frame_Shift_Ins 45
In_Frame_Del 29
In_Frame_Ins 5
Missense_Mutation 4683
Nonsense_Mutation 416
Nonstop_Mutation 9
Silent 1823
Splice_Site 117
Translation_Start_Site 8
Total 7233
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
Tp*C->(T/G) 2639 110997796 0.000024 24 3.7 3
Tp*C->A 200 110997796 1.8e-06 1.8 0.28 4
(A/C/G)p*C->mut 1232 315457576 3.9e-06 3.9 0.6 3.2
A->mut 620 410210248 1.5e-06 1.5 0.23 3.9
indel+null 707 836665620 8.5e-07 0.85 0.13 NaN
double_null 12 836665620 1.4e-08 0.014 0.0022 NaN
Total 5410 836665620 6.5e-06 6.5 1 3.5
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. 

CoMut Plot

Figure 3.  Get High-res Image The matrix in the center of the figure represents individual mutations in patient samples, color-coded by type of mutation, for the significantly mutated genes. The rate of synonymous and non-synonymous mutations is displayed at the top of the matrix. The barplot on the left of the matrix shows the number of mutations in each gene. The percentages represent the fraction of tumors with at least one mutation in the specified gene. The barplot to the right of the matrix displays the q-values for the most significantly mutated genes. The purple boxplots below the matrix (only displayed if required columns are present in the provided MAF) represent the distributions of allelic fractions observed in each sample. The plot at the bottom represents the base substitution distribution of individual samples, using the same categories that were used to calculate significance.

Significantly Mutated Genes

Table 3.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 7. Number of genes displayed: 35

rank gene description N n npat nsite nsil n1 n2 n3 n4 n5 n6 p_classic p_ns_s p_ks p_cons p_joint p q
1 TP53 tumor protein p53 35224 14 11 13 0 2 0 8 1 3 0 <1.00e-15 0.025 0.000019 0.0025 0.000015 <0.00 <0.00
2 FBXW7 F-box and WD repeat domain containing 7 72184 6 5 5 0 2 0 2 0 2 0 3.67e-06 0.34 0.0027 0.055 0.0028 1.99e-07 0.0013
3 ZNF814 zinc finger protein 814 54600 3 3 1 0 0 0 3 0 0 0 0.0018 0.59 4.2e-06 0.99 6.4e-06 2.23e-07 0.0013
4 KDM6A 116116 6 6 6 2 0 0 0 0 6 0 7.86e-08 0.98 0.85 0.39 0.87 1.19e-06 0.0054
5 ARID1A AT rich interactive domain 1A (SWI-like) 162316 8 6 8 1 3 0 0 0 5 0 1.67e-06 0.66 0.31 0.94 0.6 0.000015 0.047
6 NFE2L2 nuclear factor (erythroid-derived 2)-like 2 50092 4 4 4 0 1 0 1 2 0 0 0.000040 0.4 0.27 0.0077 0.026 0.000016 0.047
7 LLGL2 lethal giant larvae homolog 2 (Drosophila) 79548 2 2 1 1 0 0 0 0 2 0 0.011 1 0.00033 0.97 0.00033 0.000050 0.13
8 POTEC 43120 3 3 2 0 0 0 2 1 0 0 0.00021 0.55 0.0089 0.86 0.042 0.00011 0.24
9 CREBBP CREB binding protein (Rubinstein-Taybi syndrome) 200396 5 5 5 1 0 0 2 0 3 0 0.00017 0.54 0.051 0.25 0.059 0.00013 0.24
10 TMCO2 transmembrane and coiled-coil domains 2 15596 2 2 1 0 0 0 0 0 2 0 0.00066 1 0.0018 0.87 0.016 0.00013 0.24
11 CUL1 cullin 1 67620 4 4 3 0 3 0 1 0 0 0 0.00064 0.37 0.57 0.006 0.019 0.00015 0.25
12 PYGO1 pygopus homolog 1 (Drosophila) 35616 3 3 3 0 0 0 1 1 1 0 0.000099 0.52 0.089 0.62 0.15 0.00018 0.25
13 GPS2 G protein pathway suppressor 2 28448 3 3 3 0 0 1 0 0 1 1 0.000025 0.57 0.39 0.41 0.63 0.00019 0.25
14 HCN1 hyperpolarization activated cyclic nucleotide-gated potassium channel 1 69300 4 4 4 1 1 0 1 0 1 1 0.000018 0.61 0.31 0.73 0.88 0.00019 0.25
15 RAP1B RAP1B, member of RAS oncogene family 16212 2 2 2 0 1 0 0 1 0 0 0.0036 0.66 0.35 0.0093 0.0059 0.00025 0.30
16 MLL myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 327628 9 7 8 1 7 0 0 0 2 0 0.0031 0.48 0.003 0.61 0.0082 0.00029 0.32
17 HLA-A major histocompatibility complex, class I, A 31220 3 3 3 0 0 0 1 0 2 0 0.000026 0.54 1 0.65 1 0.00030 0.32
18 HCRT hypocretin (orexin) neuropeptide precursor 3668 1 1 1 0 0 0 0 0 1 0 0.00033 1 NaN NaN NaN 0.00033 0.33
19 AHCTF1 AT hook containing transcription factor 1 194544 2 2 2 0 1 0 1 0 0 0 0.26 0.73 0.00014 0.75 0.00014 0.00040 0.38
20 ERCC2 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) 60592 4 4 4 0 1 0 1 2 0 0 0.00016 0.36 0.9 0.021 0.24 0.00043 0.38
21 ELF3 E74-like factor 3 (ets domain transcription factor, epithelial-specific ) 32144 3 3 3 0 0 0 1 0 2 0 0.000040 0.72 0.44 0.47 1 0.00045 0.38
22 C17orf81 chromosome 17 open reading frame 81 30464 3 2 3 1 2 0 1 0 0 0 0.0068 0.78 0.0076 0.08 0.0071 0.00052 0.43
23 RFTN2 raftlin family member 2 40152 3 3 3 0 1 0 0 0 2 0 0.00017 0.6 0.32 0.49 0.35 0.00065 0.51
24 C9orf41 chromosome 9 open reading frame 41 28980 2 1 2 0 1 0 1 0 0 0 0.062 0.68 0.0011 0.78 0.0011 0.00072 0.54
25 HMCN1 hemicentin 1 485408 9 8 9 0 4 0 1 2 2 0 0.0012 0.14 0.27 0.034 0.065 0.00082 0.60
26 NAA25 82684 4 4 4 0 1 1 1 0 1 0 0.00060 0.44 0.12 0.84 0.15 0.00094 0.65
27 XPR1 xenotropic and polytropic retrovirus receptor 60228 5 4 5 1 3 0 0 0 2 0 0.00021 0.64 0.28 0.43 0.47 0.00099 0.65
28 SPG11 spastic paraplegia 11 (autosomal recessive) 206248 2 1 2 0 0 0 0 2 0 0 0.42 0.63 0.00029 0.53 0.00023 0.0010 0.65
29 BCLAF1 BCL2-associated transcription factor 1 78596 5 4 5 0 2 0 0 2 1 0 0.00026 0.4 0.24 0.86 0.39 0.0010 0.65
30 LETMD1 LETM1 domain containing 1 31332 3 3 3 0 1 0 0 2 0 0 0.00059 0.42 0.83 0.097 0.24 0.0014 0.84
31 CREB3L3 cAMP responsive element binding protein 3-like 3 39256 3 2 3 0 3 0 0 0 0 0 0.018 0.37 0.047 0.0094 0.0089 0.0015 0.87
32 PCDHAC1 protocadherin alpha subfamily C, 1 82096 4 4 4 0 1 0 1 2 0 0 0.00017 0.33 0.77 0.81 1 0.0016 0.87
33 HIST1H4L histone cluster 1, H4l 8848 1 1 1 0 0 0 0 0 1 0 0.0017 1 NaN NaN NaN 0.0017 0.87
34 KRTAP4-9 keratin associated protein 4-9 12656 2 2 2 1 0 0 1 1 0 0 0.00032 0.9 0.44 0.44 0.54 0.0017 0.87
35 PLAUR plasminogen activator, urokinase receptor 29008 3 2 3 0 3 0 0 0 0 0 0.012 0.38 0.0056 0.38 0.015 0.0017 0.87

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: Tp*C->(T/G) .

n2 - number of nonsilent mutations of type: Tp*C->A .

n3 - number of nonsilent mutations of type: (A/C/G)p*C->mut .

n4 - number of nonsilent mutations of type: A->mut .

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: 3. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 TP53 tumor protein p53 14 308 14 8624 2964 0 0
2 FBXW7 F-box and WD repeat domain containing 7 6 91 4 2548 102 3e-09 6.8e-06
3 FGFR3 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) 2 43 2 1204 216 3e-05 0.045
4 DPYSL4 dihydropyrimidinase-like 4 1 1 1 28 2 0.00018 0.16
5 TBC1D8B TBC1 domain family, member 8B (with GRAM domain) 2 1 1 28 1 0.00018 0.16
6 BMX BMX non-receptor tyrosine kinase 2 2 1 56 2 0.00036 0.23
7 GABRA6 gamma-aminobutyric acid (GABA) A receptor, alpha 6 2 2 1 56 1 0.00036 0.23
8 PIK3CA phosphoinositide-3-kinase, catalytic, alpha polypeptide 3 184 2 5152 375 0.00054 0.27
9 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 1 3 1 84 1492 0.00054 0.27
10 BAZ1A bromodomain adjacent to zinc finger domain, 1A 1 4 1 112 1 0.00072 0.27

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 nmuts0 nmuts3 nmuts12 npairs0 npairs3 npairs12
4054 ZNF814 zinc finger protein 814 3 0 3 3 3 3 3 3
3616 TP53 tumor protein p53 14 0 1 6 18 1 6 18
889 CUL1 cullin 1 4 0 1 1 1 1 1 1
1286 FBXW7 F-box and WD repeat domain containing 7 6 0 1 1 1 1 1 1
2174 MLL myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 9 0 1 1 1 1 1 1
2247 MUC4 mucin 4, cell surface associated 2 0 1 1 1 1 1 1
2758 POTEC 3 0 1 1 1 1 1 1
2943 RB1 retinoblastoma 1 (including osteosarcoma) 2 0 1 1 1 1 1 1
3260 SLC39A3 solute carrier family 39 (zinc transporter), member 3 2 0 1 1 1 1 1 1
3059 RPL31 ribosomal protein L31 3 1 0 3 3 0 3 3

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: 23. 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_ns_s p q
1 PMLPATHWAY Ring-shaped PML nuclear bodies regulate transcription and are required co-activators in p53- and DAXX-mediated apoptosis. CREBBP, DAXX, HRAS, PAX3, PML, PRAM-1, RARA, RB1, SIRT1, SP100, TNF, TNFRSF1A, TNFRSF1B, TNFRSF6, TNFSF6, TP53, UBL1 13 CREBBP(5), DAXX(1), PML(3), RARA(2), RB1(2), SP100(1), TNFRSF1B(1), TP53(14) 809704 29 17 27 1 7 0 13 1 7 1 0.003 5.5e-12 3.4e-09
2 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 SP3(2), TP53(14) 296856 16 12 15 1 4 0 8 1 3 0 0.076 9.5e-11 2.9e-08
3 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(3), RB1(2), TP53(14), WEE1(1) 742224 20 16 18 2 3 0 9 2 5 1 0.16 3.2e-09 5e-07
4 TIDPATHWAY On ligand binding, interferon gamma receptors stimulate JAK2 kinase to phosphorylate STAT transcription factors, which promote expression of interferon responsive genes. DNAJA3, HSPA1A, IFNG, IFNGR1, IFNGR2, IKBKB, JAK2, LIN7A, NFKB1, NFKBIA, RB1, RELA, TIP-1, TNF, TNFRSF1A, TNFRSF1B, TP53, USH1C, WT1 18 IFNGR2(1), JAK2(1), RB1(2), RELA(1), TNFRSF1B(1), TP53(14), USH1C(1) 774256 21 15 19 0 5 1 9 1 4 1 0.0039 3.2e-09 5e-07
5 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 DNAJC3(1), RELA(1), TP53(14) 412412 16 12 15 0 4 0 8 1 3 0 0.019 3.9e-08 4.8e-06
6 SA_G1_AND_S_PHASES Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. ARF1, ARF3, CCND1, CDK2, CDK4, CDKN1A, CDKN1B, CDKN2A, CFL1, E2F1, E2F2, MDM2, NXT1, PRB1, TP53 15 CCND1(1), CDKN1A(2), E2F2(1), TP53(14) 361788 18 12 17 2 4 0 9 2 3 0 0.11 7e-08 7.2e-06
7 P53PATHWAY p53 induces cell cycle arrest or apoptosis under conditions of DNA damage. APAF1, ATM, BAX, BCL2, CCND1, CCNE1, CDK2, CDK4, CDKN1A, E2F1, GADD45A, MDM2, PCNA, RB1, TIMP3, TP53 16 ATM(3), BAX(1), CCND1(1), CDKN1A(2), RB1(2), TP53(14) 766220 23 16 21 3 5 0 10 2 5 1 0.17 3.7e-07 0.000032
8 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(3), ATR(3), TP53(14) 674632 20 13 19 1 6 0 9 2 3 0 0.069 6e-07 0.000046
9 G1PATHWAY CDK4/6-cyclin D and CDK2-cyclin E phosphorylate Rb, which allows the transcription of genes needed for the G1/S cell cycle transition. ABL1, ATM, ATR, CCNA1, CCND1, CCNE1, CDC2, CDC25A, CDK2, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B, DHFR, E2F1, GSK3B, HDAC1, MADH3, MADH4, RB1, SKP2, TFDP1, TGFB1, TGFB2, TGFB3, TP53 25 ABL1(1), ATM(3), ATR(3), CCND1(1), CDK6(1), CDKN1A(2), RB1(2), TP53(14) 1280076 27 17 25 2 10 0 10 2 4 1 0.031 1.4e-06 0.000094
10 FBW7PATHWAY Cyclin E interacts with cell cycle checkpoint kinase cdk2 to allow transcription of genes required for S phase, including transcription of additional cyclin E. CCNE1, CDC34, CDK2, CUL1, E2F1, FBXW7, RB1, SKP1A, TFDP1 8 CUL1(4), FBXW7(6), RB1(2) 353976 12 9 9 0 5 0 3 0 3 1 0.06 2e-06 0.00012

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_ns_s p q
1 PMLPATHWAY Ring-shaped PML nuclear bodies regulate transcription and are required co-activators in p53- and DAXX-mediated apoptosis. CREBBP, DAXX, HRAS, PAX3, PML, PRAM-1, RARA, RB1, SIRT1, SP100, TNF, TNFRSF1A, TNFRSF1B, TNFRSF6, TNFSF6, TP53, UBL1 12 CREBBP(5), DAXX(1), PML(3), RARA(2), RB1(2), SP100(1), TNFRSF1B(1) 774480 15 11 14 1 5 0 5 0 4 1 0.074 0.000061 0.021
2 CTLPATHWAY Cytotoxic T lymphocytes induce apoptosis in infected cells presenting antigen-MHC-I complexes via the perforin and Fas/Fas ligand pathways. B2M, CD3D, CD3E, CD3G, CD3Z, GZMB, HLA-A, ICAM1, ITGAL, ITGB2, PRF1, TNFRSF6, TNFSF6, TRA@, TRB@ 10 B2M(1), GZMB(1), HLA-A(3), ICAM1(1), PRF1(3) 367304 9 8 9 1 2 0 4 1 2 0 0.25 0.000067 0.021
3 FBW7PATHWAY Cyclin E interacts with cell cycle checkpoint kinase cdk2 to allow transcription of genes required for S phase, including transcription of additional cyclin E. CCNE1, CDC34, CDK2, CUL1, E2F1, FBXW7, RB1, SKP1A, TFDP1 7 CUL1(4), RB1(2) 281792 6 6 4 0 3 0 1 0 1 1 0.2 0.00027 0.056
4 IL7PATHWAY IL-7 is required for B and T cell development and proliferation and may contribute to activation of VDJ recombination. BCL2, CREBBP, EP300, FYN, IL2RG, IL7, IL7R, JAK1, JAK3, LCK, NMI, PIK3CA, PIK3R1, PTK2B, STAT5A, STAT5B 16 CREBBP(5), EP300(3), IL2RG(1), JAK1(1), LCK(1), PIK3CA(3), PIK3R1(1), STAT5B(1) 1181796 16 14 16 2 5 1 5 2 3 0 0.17 0.00076 0.1
5 D4GDIPATHWAY D4-GDI inhibits the pro-apoptotic Rho GTPases and is cleaved by caspase-3. ADPRT, APAF1, ARHGAP5, ARHGDIB, CASP1, CASP10, CASP3, CASP8, CASP9, CYCS, GZMB, JUN, PRF1 12 ARHGAP5(4), CASP8(2), GZMB(1), PRF1(3) 540764 10 9 10 1 1 0 5 4 0 0 0.28 0.00084 0.1
6 SKP2E2FPATHWAY E2F-1, a transcription factor that promotes the G1/S transition, is repressed by Rb and activated by cdk2/cyclin E. CCNA1, CCNE1, CDC34, CDK2, CUL1, E2F1, RB1, SKP1A, SKP2, TFDP1 9 CUL1(4), RB1(2) 363692 6 6 4 1 3 0 1 0 1 1 0.47 0.0019 0.17
7 P27PATHWAY p27 blocks the G1/S transition by inhibiting the checkpoint kinase cdk2/cyclin E and is inhibited by cdk2-mediated ubiquitination. CCNE1, CDK2, CDKN1B, CKS1B, CUL1, E2F1, NEDD8, RB1, RBX1, SKP1A, SKP2, TFDP1, UBE2M 12 CUL1(4), RB1(2) 364224 6 6 4 0 3 0 1 0 1 1 0.2 0.0019 0.17
8 PDGFPATHWAY Platelet-derived growth factor (PDGF) receptor is phosphorylated on ligand binding and promotes cell proliferation. CSNK2A1, ELK1, FOS, GRB2, HRAS, JAK1, JUN, MAP2K1, MAP2K4, MAP3K1, MAPK3, MAPK8, PDGFA, PDGFRA, PIK3CA, PIK3R1, PLCG1, PRKCA, PRKCB1, RAF1, RASA1, SHC1, SOS1, SRF, STAT1, STAT3, STAT5A 26 CSNK2A1(1), FOS(1), JAK1(1), MAP2K1(1), MAP3K1(2), MAPK8(2), PDGFRA(1), PIK3CA(3), PIK3R1(1), PLCG1(2), RASA1(1), SOS1(2), STAT1(1) 1463532 19 14 19 1 11 1 4 2 1 0 0.036 0.0031 0.22
9 RAC1PATHWAY Rac-1 is a Rho family G protein that stimulates formation of actin-dependent structures such as filopodia and lamellopodia. ARFIP2, CDK5, CDK5R1, CFL1, CHN1, LIMK1, MAP3K1, MYL2, MYLK, NCF2, PAK1, PDGFRA, PIK3CA, PIK3R1, PLD1, PPP1R12B, RAC1, RALBP1, RPS6KB1, TRIO, VAV1, WASF1 22 CDK5(1), CHN1(1), MAP3K1(2), MYLK(2), NCF2(2), PDGFRA(1), PIK3CA(3), PIK3R1(1), PPP1R12B(1), TRIO(4) 1471820 18 14 18 0 8 2 5 1 2 0 0.0088 0.0032 0.22
10 RACCYCDPATHWAY Ras, Rac, and Rho coordinate to induce cyclin D1 expression and activate cdk2 to promote the G1/S transition. AKT1, ARHA, CCND1, CCNE1, CDK2, CDK4, CDK6, CDKN1A, CDKN1B, E2F1, HRAS, MAPK1, MAPK3, NFKB1, NFKBIA, PAK1, PIK3CA, PIK3R1, RAC1, RAF1, RB1, RELA, TFDP1 22 CCND1(1), CDK6(1), CDKN1A(2), PIK3CA(3), PIK3R1(1), RB1(2), RELA(1) 850052 11 10 10 1 6 1 2 0 1 1 0.19 0.0049 0.26
Methods & Data
Methods

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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