Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
Thyroid Adenocarcinoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1VX0DM5
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result). Broad Institute of MIT and Harvard. doi:10.7908/C1VX0DM5
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 and MutSigCV v0.9 merged result was used to generate the results found in this report.

- Working with individual set: THCA-TP

- Number of patients in set: 323

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

- MAF used for this analysis:THCA-TP.final_analysis_set.maf

- Significantly mutated genes (q ≤ 0.1): 25

- Mutations seen in COSMIC: 249

- Significantly mutated genes in COSMIC territory: 11

- Significantly mutated genesets: 72

Mutation Preprocessing

- Read 323 MAFs of type "Broad"

- Total number of mutations in input MAFs: 11952

- After removing 99 mutations outside chr1-24: 11853

- After removing 1530 blacklisted mutations: 10323

- After removing 3226 noncoding mutations: 7097

Mutation Filtering

- Number of mutations before filtering: 7097

- After removing 289 mutations outside gene set: 6808

- After removing 2 mutations outside category set: 6806

Results
Breakdown of Mutations by Type

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

type | count
--- | ---
Frame_Shift_Del | 375
Frame_Shift_Ins | 112
In_Frame_Del | 254
In_Frame_Ins | 18
Missense_Mutation | 4143
Nonsense_Mutation | 194
Nonstop_Mutation | 4
Silent | 1573
Splice_Site | 125
Translation_Start_Site | 8
Total | 6806

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 | 782 | 526711238 | 1.5e-06 | 1.5 | 2.7 | 2.1
*Cp(A/C/T)->T | 981 | 4313476957 | 2.3e-07 | 0.23 | 0.41 | 1.7
A->G | 826 | 4649186676 | 1.8e-07 | 0.18 | 0.32 | 2.3
transver | 1558 | 9489374871 | 1.6e-07 | 0.16 | 0.3 | 5
indel+null | 1084 | 9489374871 | 1.1e-07 | 0.11 | 0.21 | NaN
double_null | 2 | 9489374871 | 2.1e-10 | 0.00021 | 0.00038 | NaN
Total | 5233 | 9489374871 | 5.5e-07 | 0.55 | 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. Patients counts and rates file used to generate this plot: THCA-TP.patients.counts_and_rates.txt

Needs description.

Figure 3. Needs description.

Figure 4. Needs description.

CoMut Plot

Figure 5. 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

Column Descriptions:

- 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: *Cp(A/C/T)->T

- n3 = number of nonsilent mutations of type: A->G

- n4 = number of nonsilent mutations of type: transver

- n5 = number of nonsilent mutations of type: indel+null

- n6 = number of nonsilent mutations of type: double_null

- p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene

- p_joint = p-value for clustering + conservation

- p = p-value (overall)

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

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 25. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).

rank | gene | description | N | n | npat | nsite | nsil | n1 | n2 | n3 | n4 | n5 | n6 | p_cons | p_joint | p_cv | p | q
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 189273 | 26 | 26 | 2 | 0 | 0 | 0 | 20 | 6 | 0 | 0 | 0.0022 | 0 | 7.4e-15 | 0 | 0
2 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 718092 | 183 | 183 | 2 | 1 | 0 | 0 | 1 | 182 | 0 | 0 | 0 | 0 | 5.8e-15 | 0 | 0
3 | HRAS | v-Ha-ras Harvey rat sarcoma viral oncogene homolog | 209181 | 12 | 12 | 2 | 0 | 0 | 0 | 9 | 3 | 0 | 0 | 0.0012 | 0 | 2.2e-13 | 0 | 0
4 | EMG1 | EMG1 nucleolar protein homolog (S. cerevisiae) | 220090 | 6 | 6 | 2 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | 0.91 | 0 | 4.8e-12 | 0 | 0
5 | PTTG1IP | pituitary tumor-transforming 1 interacting protein | 144700 | 4 | 4 | 1 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0.00056 | 0 | 2.2e-08 | 0 | 0
6 | RPTN | repetin | 763230 | 8 | 8 | 6 | 0 | 0 | 0 | 1 | 0 | 7 | 0 | 0.19 | 0.0011 | 1.1e-07 | 2.8e-09 | 8.5e-06
7 | TG | thyroglobulin | 2717568 | 16 | 16 | 16 | 3 | 1 | 0 | 1 | 4 | 10 | 0 | 0.56 | 0.22 | 5.9e-10 | 3.1e-09 | 8.5e-06
8 | TMCO2 | transmembrane and coiled-coil domains 2 | 179663 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.94 | 0.00089 | 3.3e-07 | 6.7e-09 | 0.000015
9 | R3HDM2 | R3H domain containing 2 | 634652 | 4 | 4 | 1 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0.99 | 0.000037 | 0.000013 | 1.1e-08 | 0.000021
10 | PRB2 | proline-rich protein BstNI subfamily 2 | 405776 | 6 | 6 | 4 | 1 | 0 | 1 | 0 | 2 | 3 | 0 | 0.65 | 0.1 | 2.7e-08 | 5.6e-08 | 0.0001
11 | LYPD3 | LY6/PLAUR domain containing 3 | 337331 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.76 | 0.00042 | 2e-05 | 1.6e-07 | 0.00027
12 | IL32 | interleukin 32 | 168065 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.92 | 0.0013 | 7.1e-06 | 1.7e-07 | 0.00027
13 | PPM1D | protein phosphatase 1D magnesium-dependent, delta isoform | 502843 | 5 | 5 | 5 | 0 | 0 | 1 | 0 | 0 | 4 | 0 | 0.86 | 0.095 | 1.7e-07 | 3.1e-07 | 0.00043
14 | EIF1AX | eukaryotic translation initiation factor 1A, X-linked | 142447 | 6 | 5 | 5 | 0 | 0 | 4 | 0 | 1 | 1 | 0 | 0.041 | 0.026 | 6.6e-07 | 3.3e-07 | 0.00043
15 | PPTC7 | PTC7 protein phosphatase homolog (S. cerevisiae) | 230856 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.96 | 0.00043 | 0.00014 | 1e-06 | 0.0013
16 | SCUBE2 | signal peptide, CUB domain, EGF-like 2 | 953936 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.99 | 0.00062 | 0.00029 | 3e-06 | 0.0033
17 | MUC7 | mucin 7, secreted | 368847 | 5 | 5 | 5 | 1 | 0 | 2 | 2 | 0 | 1 | 0 | 0.11 | 0.22 | 9.1e-07 | 3.4e-06 | 0.0035
18 | TMEM90B |  | 254847 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.87 | 0.00059 | 0.00064 | 6e-06 | 0.006
19 | CCDC15 | coiled-coil domain containing 15 | 671425 | 5 | 5 | 1 | 1 | 0 | 0 | 0 | 5 | 0 | 0 | 1 | 7.6e-06 | 0.067 | 7.9e-06 | 0.0075
20 | ATAD2 | ATPase family, AAA domain containing 2 | 1353048 | 4 | 4 | 3 | 0 | 0 | 1 | 1 | 0 | 2 | 0 | 0.2 | 0.00036 | 0.0014 | 7.9e-06 | 0.0075
21 | ZNF878 | zinc finger protein 878 | 523994 | 4 | 4 | 2 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 1 | 0.000018 | 0.031 | 8.8e-06 | 0.0075
22 | ARMCX3 | armadillo repeat containing, X-linked 3 | 368272 | 3 | 3 | 2 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.91 | 0.12 | 7.1e-06 | 0.000013 | 0.011
23 | TSC22D1 | TSC22 domain family, member 1 | 1051079 | 3 | 3 | 2 | 1 | 0 | 0 | 0 | 0 | 3 | 0 | 0.99 | 0.0021 | 0.0013 | 0.000039 | 0.03
24 | TROAP | trophinin associated protein (tastin) | 787729 | 5 | 3 | 3 | 0 | 0 | 1 | 2 | 2 | 0 | 0 | 1 | 0.00018 | 0.016 | 0.000039 | 0.03
25 | SYNPO2L | synaptopodin 2-like | 692797 | 3 | 3 | 1 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0.01 | 0.00079 | 0.0054 | 0.000058 | 0.041
26 | NLRP6 | NLR family, pyrin domain containing 6 | 591829 | 2 | 2 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0.00085 | 0.00022 | 0.053 | 0.00015 | 0.1
27 | ZNF443 | zinc finger protein 443 | 653456 | 4 | 4 | 2 | 3 | 0 | 1 | 3 | 0 | 0 | 0 | 1 | 0.0021 | 0.0058 | 0.00015 | 0.1
28 | SLC26A11 | solute carrier family 26, member 11 | 571218 | 3 | 3 | 2 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 0.82 | 0.0032 | 0.0047 | 0.00018 | 0.12
29 | CDC27 | cell division cycle 27 homolog (S. cerevisiae) | 791568 | 3 | 3 | 2 | 0 | 0 | 0 | 1 | 0 | 2 | 0 | 0.27 | 0.0089 | 0.0017 | 0.00018 | 0.12
30 | CHD2 | chromodomain helicase DNA binding protein 2 | 1804494 | 4 | 4 | 3 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0.41 | 0.029 | 0.00068 | 0.00023 | 0.14
31 | SREBF2 | sterol regulatory element binding transcription factor 2 | 983587 | 3 | 3 | 2 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 0.98 | 0.0038 | 0.0054 | 0.00024 | 0.14
32 | ACRC | acidic repeat containing | 609349 | 4 | 2 | 2 | 0 | 0 | 2 | 0 | 2 | 0 | 0 | 0.76 | 0.000022 | 1 | 0.00026 | 0.14
33 | ACD | adrenocortical dysplasia homolog (mouse) | 530803 | 3 | 3 | 2 | 0 | 0 | 0 | 1 | 0 | 2 | 0 | 0.21 | 0.15 | 0.00017 | 0.00029 | 0.16
34 | DNMT3A | DNA (cytosine-5-)-methyltransferase 3 alpha | 868356 | 5 | 5 | 5 | 0 | 0 | 1 | 0 | 0 | 4 | 0 | 0.28 | 0.59 | 0.000047 | 0.00032 | 0.17
35 | GADD45GIP1 | growth arrest and DNA-damage-inducible, gamma interacting protein 1 | 162043 | 2 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.72 | 0.15 | 0.00025 | 0.0004 | 0.21

NRAS

Figure S1. This figure depicts the distribution of mutations and mutation types across the NRAS significant gene.

BRAF

Figure S2. This figure depicts the distribution of mutations and mutation types across the BRAF significant gene.

HRAS

Figure S3. This figure depicts the distribution of mutations and mutation types across the HRAS significant gene.

EMG1

Figure S4. This figure depicts the distribution of mutations and mutation types across the EMG1 significant gene.

PTTG1IP

Figure S5. This figure depicts the distribution of mutations and mutation types across the PTTG1IP significant gene.

RPTN

Figure S6. This figure depicts the distribution of mutations and mutation types across the RPTN significant gene.

TG

Figure S7. This figure depicts the distribution of mutations and mutation types across the TG significant gene.

TMCO2

Figure S8. This figure depicts the distribution of mutations and mutation types across the TMCO2 significant gene.

R3HDM2

Figure S9. This figure depicts the distribution of mutations and mutation types across the R3HDM2 significant gene.

LYPD3

Figure S10. This figure depicts the distribution of mutations and mutation types across the LYPD3 significant gene.

IL32

Figure S11. This figure depicts the distribution of mutations and mutation types across the IL32 significant gene.

PPM1D

Figure S12. This figure depicts the distribution of mutations and mutation types across the PPM1D significant gene.

EIF1AX

Figure S13. This figure depicts the distribution of mutations and mutation types across the EIF1AX significant gene.

PPTC7

Figure S14. This figure depicts the distribution of mutations and mutation types across the PPTC7 significant gene.

SCUBE2

Figure S15. This figure depicts the distribution of mutations and mutation types across the SCUBE2 significant gene.

MUC7

Figure S16. This figure depicts the distribution of mutations and mutation types across the MUC7 significant gene.

CCDC15

Figure S17. This figure depicts the distribution of mutations and mutation types across the CCDC15 significant gene.

ATAD2

Figure S18. This figure depicts the distribution of mutations and mutation types across the ATAD2 significant gene.

ZNF878

Figure S19. This figure depicts the distribution of mutations and mutation types across the ZNF878 significant gene.

ARMCX3

Figure S20. This figure depicts the distribution of mutations and mutation types across the ARMCX3 significant gene.

TSC22D1

Figure S21. This figure depicts the distribution of mutations and mutation types across the TSC22D1 significant gene.

TROAP

Figure S22. This figure depicts the distribution of mutations and mutation types across the TROAP significant gene.

SYNPO2L

Figure S23. This figure depicts the distribution of mutations and mutation types across the SYNPO2L significant gene.

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: 11. Number of genes displayed: 10

rank | gene | description | n | cos | n_cos | N_cos | cos_ev | p | q
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1 | HRAS | v-Ha-ras Harvey rat sarcoma viral oncogene homolog | 12 | 19 | 12 | 6137 | 2496 | 2.5e-13 | 9.6e-10
2 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 26 | 33 | 26 | 10659 | 33748 | 4.3e-13 | 9.6e-10
3 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 183 | 89 | 183 | 28747 | 2630268 | 1.1e-12 | 1.7e-09
4 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 3 | 52 | 3 | 16796 | 14910 | 1.3e-07 | 0.00015
5 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 3 | 220 | 3 | 71060 | 51 | 9.7e-06 | 0.0088
6 | C4BPA | complement component 4 binding protein, alpha | 1 | 1 | 1 | 323 | 1 | 0.00018 | 0.073
7 | PCGF2 | polycomb group ring finger 2 | 2 | 1 | 1 | 323 | 1 | 0.00018 | 0.073
8 | SEZ6L | seizure related 6 homolog (mouse)-like | 2 | 1 | 1 | 323 | 1 | 0.00018 | 0.073
9 | SMC3 | structural maintenance of chromosomes 3 | 1 | 1 | 1 | 323 | 1 | 0.00018 | 0.073
10 | TNFRSF9 | tumor necrosis factor receptor superfamily, member 9 | 1 | 1 | 1 | 323 | 1 | 0.00018 | 0.073

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)

Geneset Analyses

Table 5. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 72. 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 | 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 | ABI2(2), APC(1), ARHGEF4(1), ARHGEF6(1), ARHGEF7(2), BRAF(183), CDC42(1), CHRM3(1), CHRM4(1), CHRM5(1), EZR(1), FGD1(1), FGD3(1), FGF20(1), FGF7(1), FN1(1), HRAS(12), IQGAP1(2), ITGA10(1), ITGA3(2), ITGA8(1), ITGAD(2), ITGAL(4), ITGAM(2), ITGB1(2), ITGB3(1), ITGB4(1), ITGB8(1), KRAS(3), MYH10(3), MYH14(1), MYH9(1), MYLK(2), NCKAP1L(1), NRAS(26), PAK3(1), PAK7(1), PDGFRB(1), PIK3CA(3), PIK3CB(1), PIK3CG(1), PIK3R1(1), PIK3R5(3), PIP4K2B(1), PIP4K2C(1), PIP5K1A(1), SOS1(1), TIAM2(3), VAV2(1), VCL(1) | 133274235 | 289 | 243 | 73 | 27 | 9 | 18 | 38 | 210 | 14 | 0 | 3.89e-09 | <1.00e-15 | <1.50e-13
2 | ST_ADRENERGIC | Adrenergic receptors respond to epinephrine and norepinephrine signaling. | AKT1, APC, AR, ASAH1, BF, BRAF, CAMP, CCL13, CCL15, CCL16, DAG1, EGFR, GAS, GNA11, GNA15, GNAI1, GNAQ, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, MAPK10, MAPK14, PHKA2, PIK3CA, PIK3CD, PIK3R1, PITX2, PTX1, PTX3, RAF1, SRC | 34 | APC(1), AR(1), BRAF(183), GNA15(1), ITPR1(2), ITPR2(4), MAPK10(1), PHKA2(2), PIK3CA(3), PIK3R1(1), PITX2(1), SRC(1) | 25744051 | 201 | 190 | 20 | 5 | 5 | 2 | 1 | 189 | 4 | 0 | 3.78e-11 | <1.00e-15 | <1.50e-13
3 | HSA04320_DORSO_VENTRAL_AXIS_FORMATION | Genes involved in dorso-ventral axis formation | BRAF, CPEB1, EGFR, ERBB2, ERBB4, ETS1, ETS2, ETV6, ETV7, FMN2, GRB2, KRAS, MAP2K1, MAPK1, MAPK3, NOTCH1, NOTCH2, NOTCH3, NOTCH4, PIWIL1, PIWIL2, PIWIL3, PIWIL4, RAF1, SOS1, SOS2, SPIRE1, SPIRE2 | 28 | BRAF(183), ERBB2(1), ETS1(2), KRAS(3), NOTCH2(1), NOTCH4(1), PIWIL2(1), SOS1(1) | 25185488 | 193 | 188 | 12 | 5 | 1 | 2 | 4 | 186 | 0 | 0 | 4.14e-11 | <1.00e-15 | <1.50e-13
4 | ST_G_ALPHA_S_PATHWAY | The G-alpha-s protein activates adenylyl cyclases, which catalyze cAMP formation. | ASAH1, BF, BFAR, BRAF, CAMP, CREB1, CREB3, CREB5, EPAC, GAS, GRF2, MAPK1, RAF1, SNX13, SRC, TERF2IP | 12 | BFAR(1), BRAF(183), SNX13(1), SRC(1), TERF2IP(1) | 5335473 | 187 | 184 | 6 | 2 | 0 | 0 | 1 | 183 | 3 | 0 | 2.63e-12 | 1.11e-15 | 1.50e-13
5 | 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 | 74 | BRAF(183), CACNA1A(2), GNAS(3), GRIA1(1), GRIA2(2), GRM1(3), HRAS(12), IGF1R(1), ITPR1(2), ITPR2(4), KRAS(3), NPR1(1), NRAS(26), PLA2G5(1), PLCB2(1), PPP2R1A(2), PRKG1(1), RYR1(4) | 53048814 | 252 | 234 | 36 | 8 | 9 | 5 | 32 | 203 | 3 | 0 | 3.60e-14 | 1.22e-15 | 1.50e-13
6 | HSA04650_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY | Genes involved in natural killer cell mediated cytotoxicity | ARAF, BID, BRAF, CASP3, CD244, CD247, CD48, CHP, CSF2, FAS, FASLG, FCER1G, FCGR3A, FCGR3B, FYN, GRB2, GZMB, HCST, HLA-A, HLA-B, HLA-C, HLA-E, HLA-G, HRAS, ICAM1, ICAM2, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNAR1, IFNAR2, IFNB1, IFNG, IFNGR1, IFNGR2, ITGAL, ITGB2, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KIR2DL5A, KIR2DS1, KIR2DS2, KIR3DL1, KIR3DL2, KLRC1, KLRC2, KLRC3, KLRD1, KLRK1, KRAS, LAT, LCK, LCP2, LOC652578, MAP2K1, MAP2K2, MAPK1, MAPK3, MICA, MICB, NCR1, NCR2, NCR3, NFAT5, NFATC1, NFATC2, NFATC3, NFATC4, NRAS, PAK1, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PLCG1, PLCG2, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PRF1, PRKCA, PRKCB1, PRKCG, PTK2B, PTPN11, PTPN6, RAC1, RAC2, RAC3, RAF1, SH2D1A, SH2D1B, SH3BP2, SHC1, SHC2, SHC3, SHC4, SOS1, SOS2, SYK, TNF, TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, TNFSF10, TYROBP, ULBP1, ULBP2, ULBP3, VAV1, VAV2, VAV3, ZAP70 | 126 | BRAF(183), FYN(1), HLA-E(1), HRAS(12), IFNA4(1), IFNAR2(1), IFNGR1(2), ITGAL(4), KIR2DL1(1), KIR3DL1(2), KRAS(3), LCK(1), NCR1(1), NFAT5(1), NFATC1(2), NFATC4(2), NRAS(26), PIK3CA(3), PIK3CB(1), PIK3CG(1), PIK3R1(1), PIK3R5(3), PLCG2(1), PPP3R2(1), PTK2B(1), SHC1(1), SOS1(1), SYK(1), VAV2(1) | 54658054 | 260 | 231 | 45 | 13 | 7 | 7 | 35 | 205 | 6 | 0 | 1.44e-12 | 2.00e-15 | 1.57e-13
7 | ST_G_ALPHA_I_PATHWAY | Gi and Go proteins are members of the same family that transduce cellular signals through both their alpha and beta subunits. | AKT1, AKT2, AKT3, ASAH1, BF, BRAF, DAG1, DRD2, EGFR, EPHB2, GRB2, ITPKA, ITPKB, ITPR1, ITPR2, ITPR3, KCNJ3, KCNJ5, KCNJ9, MAPK1, PI3, PIK3CB, PITX2, PLCB1, PLCB2, PLCB3, PLCB4, RAF1, RAP1GA1, RGS20, SHC1, SOS1, SOS2, SRC, STAT3, TERF2IP | 34 | BRAF(183), ITPR1(2), ITPR2(4), PIK3CB(1), PITX2(1), PLCB2(1), SHC1(1), SOS1(1), SRC(1), TERF2IP(1) | 28143487 | 196 | 189 | 15 | 3 | 6 | 2 | 1 | 186 | 1 | 0 | 1.17e-12 | 2.11e-15 | 1.57e-13
8 | HSA04010_MAPK_SIGNALING_PATHWAY | Genes involved in MAPK signaling pathway | ACVR1B, ACVR1C, AKT1, AKT2, AKT3, ARRB1, ARRB2, ATF2, ATF4, BDNF, BRAF, CACNA1A, CACNA1B, CACNA1C, CACNA1D, CACNA1E, CACNA1F, CACNA1G, CACNA1H, CACNA1I, CACNA1S, CACNA2D1, CACNA2D2, CACNA2D3, CACNA2D4, CACNB1, CACNB2, CACNB3, CACNB4, CACNG1, CACNG2, CACNG3, CACNG4, CACNG5, CACNG6, CACNG7, CACNG8, CASP3, CD14, CDC25B, CDC42, CHP, CHUK, CRK, CRKL, DAXX, DDIT3, DUSP1, DUSP10, DUSP14, DUSP16, DUSP2, DUSP3, DUSP4, DUSP5, DUSP6, DUSP7, DUSP8, DUSP9, ECSIT, EGF, EGFR, ELK1, ELK4, EVI1, FAS, FASLG, FGF1, FGF10, FGF11, FGF12, FGF13, FGF14, FGF16, FGF17, FGF18, FGF19, FGF2, FGF20, FGF21, FGF22, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FLNA, FLNB, FLNC, FOS, GADD45A, GADD45B, GADD45G, GNA12, GNG12, GRB2, HRAS, IKBKB, IKBKG, IL1A, IL1B, IL1R1, IL1R2, JUN, JUND, KRAS, LOC653852, MAP2K1, MAP2K1IP1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K10, MAP3K12, MAP3K13, MAP3K14, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7, MAP3K7IP1, MAP3K7IP2, MAP3K8, MAP4K1, MAP4K2, MAP4K3, MAP4K4, MAPK1, MAPK10, MAPK11, MAPK12, MAPK13, MAPK14, MAPK3, MAPK7, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, MAPKAPK2, MAPKAPK3, MAPKAPK5, MAPT, MAX, MEF2C, MKNK1, MKNK2, MOS, MRAS, MYC, NF1, NFATC2, NFATC4, NFKB1, NFKB2, NGFB, NLK, NR4A1, NRAS, NTF3, NTF5, NTRK1, NTRK2, PAK1, PAK2, PDGFA, PDGFB, PDGFRA, PDGFRB, PLA2G10, PLA2G12A, PLA2G12B, PLA2G1B, PLA2G2A, PLA2G2D, PLA2G2E, PLA2G2F, PLA2G3, PLA2G4A, PLA2G5, PLA2G6, PPM1A, PPM1B, PPP3CA, PPP3CB, PPP3CC, PPP3R1, PPP3R2, PPP5C, PRKACA, PRKACB, PRKACG, PRKCA, PRKCB1, PRKCG, PRKX, PRKY, PTPN5, PTPN7, PTPRR, RAC1, RAC2, RAC3, RAF1, RAP1A, RAP1B, RAPGEF2, RASA1, RASA2, RASGRF1, RASGRF2, RASGRP1, RASGRP2, RASGRP3, RASGRP4, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA4, RPS6KA5, RPS6KA6, RRAS, RRAS2, SOS1, SOS2, SRF, STK3, STK4, STMN1, TAOK1, TAOK2, TAOK3, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TNF, TNFRSF1A, TP53, TRAF2, TRAF6, ZAK | 247 | ARRB1(1), BRAF(183), CACNA1A(2), CACNA1B(1), CACNA1C(1), CACNA1D(1), CACNA1E(3), CACNA1G(2), CACNA1H(1), CACNA1S(1), CACNA2D1(2), CACNA2D3(1), CACNA2D4(1), CACNB3(1), CDC42(1), DUSP2(1), DUSP5(1), DUSP7(1), DUSP8(1), ECSIT(1), FGF20(1), FGF7(1), FLNA(1), FLNC(3), HRAS(12), IL1R1(2), JUN(1), KRAS(3), MAP2K5(1), MAP2K6(1), MAP3K1(1), MAP3K3(4), MAP3K6(1), MAP3K8(1), MAP4K4(1), MAPK10(1), MAPK8IP2(1), MAPKAPK3(1), MKNK2(1), MYC(1), NF1(5), NFATC4(2), NRAS(26), PDGFRB(1), PLA2G5(1), PPP3R2(1), RASGRF2(1), RASGRP1(1), RPS6KA1(1), SOS1(1), TGFB1(1), TP53(3) | 137756696 | 290 | 242 | 75 | 23 | 15 | 14 | 37 | 208 | 16 | 0 | 3.98e-11 | 2.22e-15 | 1.57e-13
9 | HSA04150_MTOR_SIGNALING_PATHWAY | Genes involved in mTOR signaling pathway | AKT1, AKT2, AKT3, BRAF, CAB39, DDIT4, EIF4B, EIF4EBP1, FIGF, FRAP1, GBL, HIF1A, IGF1, INS, KIAA1303, LYK5, MAPK1, MAPK3, PDPK1, PGF, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIK3R5, PRKAA1, PRKAA2, RHEB, RICTOR, RPS6, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KA6, RPS6KB1, RPS6KB2, STK11, TSC1, TSC2, ULK1, ULK2, ULK3, VEGFA, VEGFB, VEGFC | 44 | BRAF(183), FIGF(1), PIK3CA(3), PIK3CB(1), PIK3CG(1), PIK3R1(1), PIK3R5(3), RPS6KA1(1), RPS6KB2(1), ULK3(1), VEGFA(1) | 25626228 | 197 | 186 | 16 | 4 | 1 | 2 | 3 | 187 | 4 | 0 | 1.50e-11 | 2.33e-15 | 1.57e-13
10 | ST_DIFFERENTIATION_PATHWAY_IN_PC12_CELLS | Rat-derived PC12 cells respond to nerve growth factor (NGF) and PACAP to differentiate into neuronal cells. | AKT1, ASAH1, ATF1, BRAF, CAMP, CREB1, CREB3, CREB5, CREBBP, CRKL, DAG1, EGR1, EGR2, EGR3, EGR4, ELK1, FRS2, GAS, GNAQ, GRF2, JUN, MAP1B, MAP2K4, MAP2K7, MAPK1, MAPK10, MAPK3, MAPK8, MAPK8IP1, MAPK8IP2, MAPK8IP3, MAPK9, NTRK1, OPN1LW, PACAP, PIK3C2G, PIK3CA, PIK3CD, PIK3R1, PTPN11, RPS6KA3, SH2B, SHC1, SRC, TERF2IP, TH, TUBA3 | 42 | BRAF(183), CREBBP(1), JUN(1), MAP1B(2), MAPK10(1), MAPK8IP2(1), PIK3C2G(1), PIK3CA(3), PIK3R1(1), SHC1(1), SRC(1), TERF2IP(1) | 24780522 | 197 | 186 | 16 | 4 | 3 | 3 | 1 | 187 | 3 | 0 | 2.22e-12 | 2.55e-15 | 1.57e-13

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 474:609 - 615 (2011)
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