Kidney Renal Papillary Cell Carcinoma: Mutation Analysis (MutSig v2.0)
(primary solid tumor cohort)
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: KIRP-TP

  • Number of patients in set: 100

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:KIRP-TP.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 6

  • Mutations seen in COSMIC: 39

  • Significantly mutated genes in COSMIC territory: 3

  • Genes with clustered mutations (≤ 3 aa apart): 27

  • Significantly mutated genesets: 0

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

Mutation Preprocessing

  • Read 100 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 9057

  • After removing 42 mutations outside chr1-24: 9015

  • After removing 318 blacklisted mutations: 8697

  • After removing 225 noncoding mutations: 8472

  • After collapsing adjacent/redundant mutations: 7279

Mutation Filtering

  • Number of mutations before filtering: 7279

  • After removing 111 mutations outside gene set: 7168

  • After removing 51 mutations outside category set: 7117

Results
Breakdown of Mutations by Type

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

type count
Frame_Shift_Del 434
Frame_Shift_Ins 164
In_Frame_Del 104
In_Frame_Ins 25
Missense_Mutation 4410
Nonsense_Mutation 246
Nonstop_Mutation 4
Silent 1556
Splice_Site 163
Translation_Start_Site 11
Total 7117
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 473 166314389 2.8e-06 2.8 1.5 2.1
*Cp(A/C/T)->T 836 1347410459 6.2e-07 0.62 0.33 1.7
A->G 784 1448486319 5.4e-07 0.54 0.29 2.3
transver 2316 2962211167 7.8e-07 0.78 0.42 5
indel+null 1148 2962211167 3.9e-07 0.39 0.21 NaN
double_null 4 2962211167 1.4e-09 0.0014 0.00072 NaN
Total 5561 2962211167 1.9e-06 1.9 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: KIRP-TP.patients.counts_and_rates.txt

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

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_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_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: 6. 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_classic p_ns_s p_cons p_joint p q
1 MET met proto-oncogene (hepatocyte growth factor receptor) 427226 8 8 7 0 0 3 2 3 0 0 3.3e-07 0.078 NaN NaN 3.3e-07 0.0059
2 IL32 interleukin 32 55560 4 4 2 0 0 0 0 0 4 0 1.5e-06 1 NaN NaN 1.5e-06 0.013
3 NF2 neurofibromin 2 (merlin) 162737 5 5 5 0 0 0 0 0 5 0 4e-06 0.43 NaN NaN 4e-06 0.024
4 PCF11 PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae) 425608 8 7 7 1 0 1 4 3 0 0 6.7e-06 0.16 NaN NaN 6.7e-06 0.026
5 LGI4 leucine-rich repeat LGI family, member 4 70745 4 4 4 0 0 1 1 2 0 0 7.1e-06 0.28 NaN NaN 7.1e-06 0.026
6 PARD6B par-6 partitioning defective 6 homolog beta (C. elegans) 106100 4 4 4 0 0 0 2 0 2 0 0.000011 0.26 NaN NaN 0.000011 0.032
7 KDM6A lysine (K)-specific demethylase 6A 393801 5 5 5 0 0 0 0 0 4 1 0.000074 0.52 NaN NaN 0.000074 0.18
8 POMC proopiomelanocortin (adrenocorticotropin/ beta-lipotropin/ alpha-melanocyte stimulating hormone/ beta-melanocyte stimulating hormone/ beta-endorphin) 57272 3 3 3 0 1 0 0 1 1 0 0.000079 0.51 NaN NaN 0.000079 0.18
9 CHCHD3 coiled-coil-helix-coiled-coil-helix domain containing 3 63374 3 3 3 0 0 1 0 2 0 0 0.000088 0.46 NaN NaN 0.000088 0.18
10 SAV1 salvador homolog 1 (Drosophila) 115810 3 3 3 0 0 1 0 0 2 0 0.0001 0.74 NaN NaN 0.0001 0.19
11 CD86 CD86 molecule 101158 3 3 3 0 1 0 0 1 1 0 0.00012 0.6 NaN NaN 0.00012 0.2
12 ACTB actin, beta 114798 3 3 3 0 0 0 3 0 0 0 0.00013 0.66 NaN NaN 0.00013 0.2
13 SFRS2IP splicing factor, arginine/serine-rich 2, interacting protein 442110 5 5 2 1 0 0 0 1 4 0 0.00014 0.98 NaN NaN 0.00014 0.2
14 SMARCB1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 115899 3 3 3 0 0 1 0 0 2 0 0.00016 0.28 NaN NaN 0.00016 0.21
15 NSUN2 NOL1/NOP2/Sun domain family, member 2 227978 4 4 4 0 0 2 0 1 1 0 0.00017 0.32 NaN NaN 0.00017 0.21
16 FLJ46321 family with sequence similarity 75, member D1 462549 6 6 6 1 0 0 1 3 2 0 0.0002 0.54 NaN NaN 0.0002 0.22
17 BAP1 BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) 205639 4 4 4 1 0 2 1 0 1 0 0.00022 0.62 NaN NaN 0.00022 0.22
18 ACADL acyl-Coenzyme A dehydrogenase, long chain 122884 3 3 3 0 0 1 1 0 1 0 0.00022 0.47 NaN NaN 0.00022 0.22
19 SLC5A12 solute carrier family 5 (sodium/glucose cotransporter), member 12 181746 4 4 4 1 0 0 2 2 0 0 0.00029 0.58 NaN NaN 0.00029 0.28
20 BHMT betaine-homocysteine methyltransferase 124685 3 3 3 0 0 0 2 0 1 0 0.00034 0.46 NaN NaN 0.00034 0.3
21 POTEH POTE ankyrin domain family, member H 90750 3 3 2 0 0 0 0 2 1 0 0.00037 0.66 NaN NaN 0.00037 0.3
22 OR4A16 olfactory receptor, family 4, subfamily A, member 16 97471 3 3 3 0 0 1 1 1 0 0 0.00039 0.36 NaN NaN 0.00039 0.3
23 NR2F2 nuclear receptor subfamily 2, group F, member 2 106194 3 3 3 0 0 0 1 1 1 0 0.00039 0.68 NaN NaN 0.00039 0.3
24 SETD2 SET domain containing 2 636351 6 6 6 0 0 0 0 1 5 0 0.0004 0.45 NaN NaN 0.0004 0.3
25 ACSBG2 acyl-CoA synthetase bubblegum family member 2 202529 4 4 2 0 1 0 0 3 0 0 0.00041 0.36 NaN NaN 0.00041 0.3
26 TNFSF10 tumor necrosis factor (ligand) superfamily, member 10 86391 3 3 3 0 0 0 1 2 0 0 0.0005 0.52 NaN NaN 0.0005 0.35
27 CDC27 cell division cycle 27 homolog (S. cerevisiae) 250946 4 4 1 0 0 0 0 0 4 0 0.00054 1 NaN NaN 0.00054 0.36
28 PRSS55 protease, serine, 55 107206 3 3 3 0 0 0 0 2 1 0 0.00061 0.42 NaN NaN 0.00061 0.39
29 BRAF v-raf murine sarcoma viral oncogene homolog B1 222693 4 4 4 0 0 0 1 3 0 0 0.00065 0.36 NaN NaN 0.00065 0.4
30 LRFN4 leucine rich repeat and fibronectin type III domain containing 4 117333 3 3 3 0 1 0 0 0 2 0 0.00073 0.49 NaN NaN 0.00073 0.44
31 OR2Y1 olfactory receptor, family 2, subfamily Y, member 1 94000 2 2 2 0 2 0 0 0 0 0 0.00086 0.51 NaN NaN 0.00086 0.47
32 PLEKHA6 pleckstrin homology domain containing, family A member 6 269433 4 4 4 0 0 1 2 1 0 0 0.00087 0.29 NaN NaN 0.00087 0.47
33 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 122564 3 3 3 0 0 0 1 0 2 0 0.00091 0.46 NaN NaN 0.00091 0.47
34 SLC2A2 solute carrier family 2 (facilitated glucose transporter), member 2 156526 3 3 3 0 0 1 1 1 0 0 0.00092 0.37 NaN NaN 0.00092 0.47
35 PRSS3 protease, serine, 3 76400 2 2 2 0 1 0 1 0 0 0 0.00093 0.51 NaN NaN 0.00093 0.47
MET

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

IL32

Figure S2.  This figure depicts the distribution of mutations and mutation types across the IL32 significant gene.

NF2

Figure S3.  This figure depicts the distribution of mutations and mutation types across the NF2 significant gene.

PCF11

Figure S4.  This figure depicts the distribution of mutations and mutation types across the PCF11 significant gene.

LGI4

Figure S5.  This figure depicts the distribution of mutations and mutation types across the LGI4 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: 3. Number of genes displayed: 10

rank gene description n cos n_cos N_cos cos_ev p q
1 MET met proto-oncogene (hepatocyte growth factor receptor) 8 34 4 3400 12 6.9e-11 3.1e-07
2 FGFR3 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) 4 62 3 6200 1469 2.6e-07 0.00059
3 SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 4 30 2 3000 3 0.000016 0.024
4 BRAF v-raf murine sarcoma viral oncogene homolog B1 4 89 2 8900 14380 0.00014 0.11
5 NF2 neurofibromin 2 (merlin) 5 550 3 55000 15 0.00017 0.11
6 CDCA8 cell division cycle associated 8 1 1 1 100 1 0.00019 0.11
7 FLCN folliculin 1 1 1 100 1 0.00019 0.11
8 PLXDC2 plexin domain containing 2 1 1 1 100 1 0.00019 0.11
9 SMARCB1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 3 129 2 12900 8 0.00029 0.15
10 PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 3 767 3 76700 27 0.00045 0.2

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
48 ACSBG2 acyl-CoA synthetase bubblegum family member 2 4 0 3 3 3 3 3 3
2138 MET met proto-oncogene (hepatocyte growth factor receptor) 8 0 1 3 4 1 3 4
2622 PCF11 PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae) 8 0 1 2 10 1 2 10
2317 NBPF9 neuroblastoma breakpoint family, member 9 2 0 1 1 1 1 1 1
2654 PEBP1 phosphatidylethanolamine binding protein 1 2 0 1 1 1 1 1 1
2657 PER1 period homolog 1 (Drosophila) 2 0 1 1 1 1 1 1
2799 POTEH POTE ankyrin domain family, member H 3 0 1 1 1 1 1 1
3020 RETSAT retinol saturase (all-trans-retinol 13,14-reductase) 2 0 1 1 1 1 1 1
4122 ZNF423 zinc finger protein 423 4 0 1 1 1 1 1 1
4159 ZNF599 zinc finger protein 599 2 0 1 1 1 1 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: 0. 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 MTORPATHWAY Mammalian target of rapamycin (mTOR) senses mitogenic factors and nutrients, including ATP, and induces cell proliferation. AKT1, EIF3S10, EIF4A1, EIF4A2, EIF4B, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FKBP1A, FRAP1, MKNK1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1, TSC1, TSC2 21 EIF4B(2), EIF4G1(2), EIF4G3(4), PIK3CA(2), PIK3R1(1), PTEN(3), TSC1(2), TSC2(4) 4154558 20 18 20 2 2 6 3 3 6 0 0.053 0.0009 0.55
2 ALANINE_AND_ASPARTATE_METABOLISM AARS, ABAT, ADSL, ADSS, AGXT, AGXT2, ASL, ASNS, ASPA, ASS, CAD, CRAT, DARS, DDO, GAD1, GAD2, GOT1, GOT2, GPT, GPT2, NARS, PC 21 AARS(1), ADSL(1), AGXT(1), AGXT2(1), CAD(3), CRAT(1), DARS(3), DDO(1), GOT2(1), GPT(1), PC(4) 3908660 18 16 18 1 1 3 1 8 5 0 0.057 0.0029 0.75
3 KREBPATHWAY The Krebs (citric acid) cycle takes place in mitochondria, where it extracts energy in the form of electron carriers NADH and FADH2, which drive the electron transport chain. ACO2, CS, FH, IDH2, MDH1, OGDH, SDHA, SUCLA2 8 FH(1), IDH2(1), MDH1(1), OGDH(2), SDHA(2) 1404132 7 7 7 0 0 3 0 1 3 0 0.072 0.0043 0.75
4 METHIONINE_METABOLISM AHCY, BHMT, CBS, CTH, DNMT1, DNMT2, DNMT3A, DNMT3B, MARS, MARS2, MAT1A, MAT2B, MTR 12 AHCY(1), BHMT(3), CTH(1), DNMT1(1), DNMT3A(1), DNMT3B(1), MARS(1), MARS2(1), MAT2B(1) 2607651 11 11 11 1 0 1 3 3 4 0 0.38 0.0061 0.75
5 SIG_PIP3_SIGNALING_IN_CARDIAC_MYOCTES Genes related to PIP3 signaling in cardiac myocytes AKT1, AKT2, AKT3, BAD, BCL2L1, CDC42, CDK2, CDKN1B, CDKN2A, CREB1, CREB3, CREB5, EBP, ERBB4, F2RL2, FOXO3A, FRAP1, GAB1, GADD45A, GRB2, GSK3A, GSK3B, IFI27, IGF1, IGFBP1, INPPL1, IRS1, IRS2, IRS4, MET, MYC, NOLC1, P101-PI3K, PAK1, PAK2, PAK3, PAK4, PAK6, PAK7, PARD3, PARD6A, PDK1, PIK3CA, PIK3CD, PPP1R13B, PREX1, PSCD3, PTEN, PTK2, PTPN1, RPS6KA1, RPS6KA2, RPS6KA3, RPS6KB1, SFN, SHC1, SLC2A4, SOS1, SOS2, TSC1, TSC2, YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ, YWHAZ 63 AKT2(1), CDKN2A(1), CREB3(1), ERBB4(2), F2RL2(1), INPPL1(1), IRS1(1), MET(8), MYC(1), NOLC1(1), PAK1(1), PAK3(2), PAK4(1), PARD3(1), PIK3CA(2), PIK3CD(1), PTEN(3), PTPN1(1), RPS6KA1(1), RPS6KA3(1), SFN(1), SOS1(2), SOS2(1), TSC1(2), TSC2(4) 11606420 42 35 41 4 4 11 9 9 9 0 0.0018 0.0067 0.75
6 CBLPATHWAY Activated EGF receptors undergo endocytosis into clathrin-coated vesicles, where they are recycled to the membrane or ubiquitinated by Cbl. CBL, CSF1R, EGF, EGFR, GRB2, MET, PDGFRA, PRKCA, PRKCB1, SH3GLB1, SH3GLB2, SH3KBP1, SRC 12 EGF(1), MET(8), PDGFRA(2), SH3KBP1(1) 2906209 12 11 11 1 1 3 2 5 1 0 0.13 0.0073 0.75
7 CITRATE_CYCLE_TCA_CYCLE ACO1, ACO2, CS, DLD, DLST, DLSTP, FH, IDH1, IDH2, IDH3A, IDH3B, IDH3G, MDH1, MDH2, PC, PCK1, SDHA, SDHA, SDHAL2, SDHB, SUCLA2, SUCLG1, SUCLG2 20 ACO1(1), DLD(1), FH(1), IDH2(1), MDH1(1), PC(4), PCK1(1), SDHA(2) 3076072 12 11 12 0 0 2 1 3 6 0 0.049 0.013 1
8 RABPATHWAY Rab family GTPases regulate vesicle transport, endocytosis and exocytosis, and vesicle docking via interactions with the rabphilins. ACTA1, MEL, RAB11A, RAB1A, RAB2, RAB27A, RAB3A, RAB4A, RAB5A, RAB6A, RAB7, RAB9A 9 ACTA1(1), RAB11A(1), RAB3A(1), RAB6A(1) 636136 4 4 4 1 0 1 0 2 1 0 0.81 0.015 1
9 NEUTROPHILPATHWAY Neutrophils are phagocytotic leukocytes that destroy foreign cells with reactive oxygen species or enzymatic digestion and express CD11 and CD18. CD44, ICAM1, ITGAL, ITGAM, ITGB2, PECAM1, SELE, SELL 8 ITGAL(3), ITGAM(2), ITGB2(1), SELL(1) 1554500 7 7 7 0 1 2 0 3 1 0 0.13 0.016 1
10 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(4), CREB3(1), RAF1(1), SNX13(1), TERF2IP(1) 1676241 9 7 9 1 0 0 3 5 1 0 0.35 0.019 1

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 n6 p_ns_s p q
1 MTORPATHWAY Mammalian target of rapamycin (mTOR) senses mitogenic factors and nutrients, including ATP, and induces cell proliferation. AKT1, EIF3S10, EIF4A1, EIF4A2, EIF4B, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, EIF4G3, FKBP1A, FRAP1, MKNK1, PDK2, PDPK1, PIK3CA, PIK3R1, PPP2CA, PTEN, RPS6, RPS6KB1, TSC1, TSC2 21 EIF4B(2), EIF4G1(2), EIF4G3(4), PIK3CA(2), PIK3R1(1), PTEN(3), TSC1(2), TSC2(4) 4154558 20 18 20 2 2 6 3 3 6 0 0.053 0.0009 0.55
2 ALANINE_AND_ASPARTATE_METABOLISM AARS, ABAT, ADSL, ADSS, AGXT, AGXT2, ASL, ASNS, ASPA, ASS, CAD, CRAT, DARS, DDO, GAD1, GAD2, GOT1, GOT2, GPT, GPT2, NARS, PC 21 AARS(1), ADSL(1), AGXT(1), AGXT2(1), CAD(3), CRAT(1), DARS(3), DDO(1), GOT2(1), GPT(1), PC(4) 3908660 18 16 18 1 1 3 1 8 5 0 0.057 0.0029 0.88
3 KREBPATHWAY The Krebs (citric acid) cycle takes place in mitochondria, where it extracts energy in the form of electron carriers NADH and FADH2, which drive the electron transport chain. ACO2, CS, FH, IDH2, MDH1, OGDH, SDHA, SUCLA2 8 FH(1), IDH2(1), MDH1(1), OGDH(2), SDHA(2) 1404132 7 7 7 0 0 3 0 1 3 0 0.072 0.0043 0.89
4 METHIONINE_METABOLISM AHCY, BHMT, CBS, CTH, DNMT1, DNMT2, DNMT3A, DNMT3B, MARS, MARS2, MAT1A, MAT2B, MTR 12 AHCY(1), BHMT(3), CTH(1), DNMT1(1), DNMT3A(1), DNMT3B(1), MARS(1), MARS2(1), MAT2B(1) 2607651 11 11 11 1 0 1 3 3 4 0 0.38 0.0061 0.93
5 CITRATE_CYCLE_TCA_CYCLE ACO1, ACO2, CS, DLD, DLST, DLSTP, FH, IDH1, IDH2, IDH3A, IDH3B, IDH3G, MDH1, MDH2, PC, PCK1, SDHA, SDHA, SDHAL2, SDHB, SUCLA2, SUCLG1, SUCLG2 20 ACO1(1), DLD(1), FH(1), IDH2(1), MDH1(1), PC(4), PCK1(1), SDHA(2) 3076072 12 11 12 0 0 2 1 3 6 0 0.049 0.013 1
6 RABPATHWAY Rab family GTPases regulate vesicle transport, endocytosis and exocytosis, and vesicle docking via interactions with the rabphilins. ACTA1, MEL, RAB11A, RAB1A, RAB2, RAB27A, RAB3A, RAB4A, RAB5A, RAB6A, RAB7, RAB9A 9 ACTA1(1), RAB11A(1), RAB3A(1), RAB6A(1) 636136 4 4 4 1 0 1 0 2 1 0 0.81 0.015 1
7 NEUTROPHILPATHWAY Neutrophils are phagocytotic leukocytes that destroy foreign cells with reactive oxygen species or enzymatic digestion and express CD11 and CD18. CD44, ICAM1, ITGAL, ITGAM, ITGB2, PECAM1, SELE, SELL 8 ITGAL(3), ITGAM(2), ITGB2(1), SELL(1) 1554500 7 7 7 0 1 2 0 3 1 0 0.13 0.016 1
8 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(4), CREB3(1), RAF1(1), SNX13(1), TERF2IP(1) 1676241 9 7 9 1 0 0 3 5 1 0 0.35 0.019 1
9 ACE_INHIBITOR_PATHWAY_PHARMGKB ACE, AGT, AGTR1, AGTR2, BDKRB2, KNG1, NOS3, REN 8 ACE(2), AGT(3), AGTR2(1), NOS3(1) 1506255 7 7 7 0 1 1 1 4 0 0 0.14 0.021 1
10 BETAOXIDATIONPATHWAY Beta-Oxidation of Fatty Acids ACADL, ACADM, ACADS, ACAT1, ECHS1, HADHA 6 ACADL(3), HADHA(1) 810277 4 4 4 0 0 1 1 1 1 0 0.38 0.026 1
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 - 615 (2011)
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