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.
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Working with individual set: COAD-TP
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Number of patients in set: 366
The input for this pipeline is a set of individuals with the following files associated for each:
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An annotated .maf file describing the mutations called for the respective individual, and their properties.
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A .wig file that contains information about the coverage of the sample.
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MAF used for this analysis:COAD-TP.final_analysis_set.maf
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Blacklist used for this analysis: pancan_mutation_blacklist.v14.hg19.txt
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Significantly mutated genes (q ≤ 0.1): 476
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Mutations seen in COSMIC: 8536
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Significantly mutated genes in COSMIC territory: 1547
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Significantly mutated genesets: 0
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Significantly mutated genesets: (excluding sig. mutated genes):0
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Read 102 MAFs of type "Broad"
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Read 213 MAFs of type "Baylor-Illumina"
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Read 52 MAFs of type "Baylor-SOLiD"
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Total number of mutations in input MAFs: 199756
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After removing 2 blacklisted mutations: 199754
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After removing 48 noncoding mutations: 199706
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After collapsing adjacent/redundant mutations: 196979
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Number of mutations before filtering: 196979
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After removing 127 mutations outside patient set: 196852
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After removing 6074 mutations outside gene set: 190778
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After removing 982 mutations outside category set: 189796
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After removing 2690 "impossible" mutations in
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gene-patient-category bins of zero coverage: 179923
Table 1. Get Full Table Table representing breakdown of mutations by type.
| type | count |
|---|---|
| De_novo_Start_InFrame | 16 |
| De_novo_Start_OutOfFrame | 125 |
| Frame_Shift_Del | 12543 |
| Frame_Shift_Ins | 3694 |
| In_Frame_Del | 1477 |
| In_Frame_Ins | 477 |
| Missense_Mutation | 114930 |
| Nonsense_Mutation | 8478 |
| Nonstop_Mutation | 30 |
| Silent | 46370 |
| Splice_Site | 1654 |
| Translation_Start_Site | 2 |
| Total | 189796 |
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 | 38701 | 491148035 | 0.000079 | 79 | 5.5 | 2.2 |
| A->G | 23912 | 4890661022 | 4.9e-06 | 4.9 | 0.34 | 2.3 |
| *Cp(A/C/T)->T | 17165 | 4398831250 | 3.9e-06 | 3.9 | 0.27 | 1.7 |
| transver | 33299 | 9780640307 | 3.4e-06 | 3.4 | 0.24 | 5.1 |
| indel+null | 27363 | 9780640307 | 2.8e-06 | 2.8 | 0.19 | NaN |
| double_null | 849 | 9780640307 | 8.7e-08 | 0.087 | 0.006 | NaN |
| Total | 141289 | 9780640307 | 0.000014 | 14 | 1 | 3.5 |
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). If the figure is unpopulated, then full coverage is assumed (e.g. MutSig CV doesn't use WIGs and assumes full coverage).
Figure 1.
Figure 2. Patients counts and rates file used to generate this plot: COAD-TP.patients.counts_and_rates.txt
The mutation spectrum is depicted in the lego plots below in which the 96 possible mutation types are subdivided into six large blocks, color-coded to reflect the base substitution type. Each large block is further subdivided into the 16 possible pairs of 5' and 3' neighbors, as listed in the 4x4 trinucleotide context legend. The height of each block corresponds to the mutation frequency for that kind of mutation (counts of mutations normalized by the base coverage in a given bin). The shape of the spectrum is a signature for dominant mutational mechanisms in different tumor types.
Figure 3. Get High-res Image SNV Mutation rate lego plot for entire set. Each bin is normalized by base coverage for that bin. Colors represent the six SNV types on the upper right. The three-base context for each mutation is labeled in the 4x4 legend on the lower right. The fractional breakdown of SNV counts is shown in the pie chart on the upper left. If this figure is blank, not enough information was provided in the MAF to generate it.
Figure 4. Get High-res Image SNV Mutation rate lego plots for 4 slices of mutation allele fraction (0<=AF<0.1, 0.1<=AF<0.25, 0.25<=AF<0.5, & 0.5<=AF) . The color code and three-base context legends are the same as the previous figure. If this figure is blank, not enough information was provided in the MAF to generate it.
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.
Column Descriptions:
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N = number of sequenced bases in this gene across the individual set
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n = number of (nonsilent) mutations in this gene across the individual set
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npat = number of patients (individuals) with at least one nonsilent mutation
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nsite = number of unique sites having a non-silent mutation
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nsil = number of silent mutations in this gene across the individual set
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n1 = number of nonsilent mutations of type: *CpG->T
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n2 = number of nonsilent mutations of type: A->G
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n3 = number of nonsilent mutations of type: *Cp(A/C/T)->T
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n4 = number of nonsilent mutations of type: transver
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n5 = number of nonsilent mutations of type: indel+null
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n6 = number of nonsilent mutations of type: double_null
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p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene
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p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene
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p_cons = p-value for enrichment of mutations at evolutionarily most-conserved sites in gene
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p_joint = p-value for clustering + conservation
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p = p-value (overall)
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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: 476. 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_clust | p_cons | p_joint | p | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | TCF7L2 | transcription factor 7-like 2 (T-cell specific, HMG-box) | 675749 | 45 | 41 | 32 | 5 | 9 | 2 | 2 | 9 | 23 | 0 | 2.4e-14 | 0.031 | 0.0001 | 0.41 | 0.00036 | 3.33e-16 | 1.61e-13 |
| 2 | CDH1 | cadherin 1, type 1, E-cadherin (epithelial) | 955680 | 87 | 74 | 65 | 19 | 7 | 35 | 13 | 11 | 20 | 1 | 2e-13 | 0.0037 | 0.000018 | 0.39 | 0.000069 | 5.55e-16 | 1.61e-13 |
| 3 | APC | adenomatous polyposis coli | 3090421 | 530 | 296 | 320 | 167 | 17 | 141 | 43 | 69 | 145 | 115 | 1 | 0.065 | 0 | 0.97 | 0 | <1.00e-15 | <1.61e-13 |
| 4 | TP53 | tumor protein p53 | 456768 | 326 | 230 | 184 | 73 | 91 | 77 | 39 | 54 | 61 | 4 | 0.12 | 0.00027 | 0 | 0 | 0 | <1.00e-15 | <1.61e-13 |
| 5 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 1117023 | 288 | 175 | 143 | 115 | 21 | 138 | 72 | 45 | 12 | 0 | 1 | 0.29 | 0 | 0 | 0 | <1.00e-15 | <1.61e-13 |
| 6 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 255887 | 184 | 169 | 39 | 17 | 2 | 21 | 90 | 70 | 1 | 0 | 1.7e-15 | 2e-08 | 0 | 8e-07 | 0 | <1.00e-15 | <1.61e-13 |
| 7 | SMAD4 | SMAD family member 4 | 615341 | 166 | 120 | 106 | 54 | 25 | 68 | 21 | 32 | 18 | 2 | 1 | 0.039 | 0.000014 | 3.6e-06 | 0 | <1.00e-15 | <1.61e-13 |
| 8 | FBXW7 | F-box and WD repeat domain containing 7 | 939926 | 119 | 103 | 72 | 43 | 34 | 26 | 5 | 27 | 27 | 0 | 1 | 0.64 | 0 | 0.0011 | 0 | <1.00e-15 | <1.61e-13 |
| 9 | BRAF | v-raf murine sarcoma viral oncogene homolog B1 | 806321 | 111 | 96 | 50 | 38 | 4 | 38 | 8 | 53 | 8 | 0 | 1 | 0.37 | 0 | 0 | 0 | <1.00e-15 | <1.61e-13 |
| 10 | NEFH | neurofilament, heavy polypeptide 200kDa | 653524 | 91 | 89 | 20 | 2 | 1 | 1 | 1 | 3 | 85 | 0 | 3.9e-15 | 0.66 | 0 | 0.71 | 0 | <1.00e-15 | <1.61e-13 |
| 11 | EGFR | epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) | 1397210 | 104 | 74 | 89 | 45 | 18 | 44 | 16 | 22 | 4 | 0 | 1 | 0.73 | 0 | 0 | 0 | <1.00e-15 | <1.61e-13 |
| 12 | CTNNB1 | catenin (cadherin-associated protein), beta 1, 88kDa | 872821 | 99 | 73 | 64 | 43 | 5 | 45 | 13 | 29 | 7 | 0 | 1 | 0.49 | 0 | 0.17 | 0 | <1.00e-15 | <1.61e-13 |
| 13 | MUC2 | mucin 2, oligomeric mucus/gel-forming | 1243760 | 66 | 59 | 29 | 13 | 5 | 4 | 4 | 7 | 45 | 1 | 4.2e-09 | 0.89 | 0 | 1 | 0 | <1.00e-15 | <1.61e-13 |
| 14 | ACVR2A | activin A receptor, type IIA | 577842 | 64 | 58 | 21 | 3 | 4 | 2 | 1 | 4 | 51 | 2 | 8.4e-15 | 0.3 | 0 | 6e-07 | 0 | <1.00e-15 | <1.61e-13 |
| 15 | RP1L1 | retinitis pigmentosa 1-like 1 | 1728132 | 72 | 57 | 37 | 18 | 12 | 1 | 5 | 10 | 37 | 7 | 0.0041 | 0.89 | 0 | 1 | 0 | <1.00e-15 | <1.61e-13 |
| 16 | FMN2 | formin 2 | 1302530 | 61 | 52 | 38 | 14 | 8 | 6 | 4 | 11 | 32 | 0 | 5.8e-06 | 0.65 | 0 | 1 | 0 | <1.00e-15 | <1.61e-13 |
| 17 | LIG1 | ligase I, DNA, ATP-dependent | 938287 | 52 | 50 | 13 | 8 | 3 | 45 | 1 | 1 | 2 | 0 | 4.6e-08 | 0.032 | 0 | 0.94 | 0 | <1.00e-15 | <1.61e-13 |
| 18 | TNFAIP6 | tumor necrosis factor, alpha-induced protein 6 | 311257 | 50 | 50 | 5 | 2 | 3 | 0 | 0 | 1 | 46 | 0 | 1.9e-15 | 0.75 | 0 | 1 | 0 | <1.00e-15 | <1.61e-13 |
| 19 | CASP5 | caspase 5, apoptosis-related cysteine peptidase | 477307 | 48 | 47 | 13 | 3 | 3 | 5 | 1 | 2 | 37 | 0 | 4.8e-15 | 0.34 | 0 | 1 | 0 | <1.00e-15 | <1.61e-13 |
| 20 | OR6C76 | olfactory receptor, family 6, subfamily C, member 76 | 338797 | 48 | 47 | 5 | 0 | 0 | 1 | 2 | 1 | 44 | 0 | 7e-15 | 0.2 | 0 | 0.93 | 0 | <1.00e-15 | <1.61e-13 |
| 21 | ADAM29 | ADAM metallopeptidase domain 29 | 897265 | 52 | 46 | 30 | 15 | 21 | 6 | 4 | 7 | 14 | 0 | 1 | 0.65 | 0.000016 | 0.000051 | 0 | <1.00e-15 | <1.61e-13 |
| 22 | RNF43 | ring finger protein 43 | 808181 | 53 | 46 | 26 | 1 | 7 | 4 | 1 | 4 | 34 | 3 | 4.2e-15 | 0.041 | 0 | 0.16 | 0 | <1.00e-15 | <1.61e-13 |
| 23 | RNF145 | ring finger protein 145 | 738414 | 51 | 44 | 19 | 3 | 3 | 12 | 2 | 3 | 29 | 2 | 4.8e-15 | 0.049 | 0 | 1 | 0 | <1.00e-15 | <1.61e-13 |
| 24 | TSHR | thyroid stimulating hormone receptor | 889065 | 55 | 44 | 37 | 9 | 8 | 28 | 6 | 12 | 1 | 0 | 1.1e-08 | 0.0063 | 4e-07 | 3.4e-06 | 0 | <1.00e-15 | <1.61e-13 |
| 25 | JAK2 | Janus kinase 2 (a protein tyrosine kinase) | 1252671 | 48 | 42 | 37 | 21 | 6 | 30 | 3 | 6 | 1 | 2 | 1 | 0.63 | 4e-07 | 0.022 | 0 | <1.00e-15 | <1.61e-13 |
| 26 | CRIPAK | cysteine-rich PAK1 inhibitor | 255575 | 43 | 40 | 19 | 5 | 3 | 3 | 2 | 3 | 24 | 8 | 5e-15 | 0.55 | 0 | 1 | 0 | <1.00e-15 | <1.61e-13 |
| 27 | DDHD1 | DDHD domain containing 1 | 838439 | 39 | 39 | 3 | 1 | 2 | 0 | 0 | 0 | 37 | 0 | 1.2e-14 | 0.76 | 0 | 1 | 0 | <1.00e-15 | <1.61e-13 |
| 28 | SNX13 | sorting nexin 13 | 785343 | 36 | 38 | 19 | 3 | 2 | 1 | 2 | 27 | 4 | 0 | 3.8e-07 | 0.11 | 0 | 1 | 0 | <1.00e-15 | <1.61e-13 |
| 29 | ARHGAP5 | Rho GTPase activating protein 5 | 1580432 | 43 | 37 | 20 | 2 | 4 | 22 | 2 | 1 | 14 | 0 | 0.000032 | 0.00016 | 2e-07 | 0.12 | 0 | <1.00e-15 | <1.61e-13 |
| 30 | RUNX1 | runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) | 328467 | 41 | 37 | 28 | 16 | 10 | 17 | 2 | 9 | 3 | 0 | 0.92 | 0.54 | 0.000012 | 2e-07 | 0 | <1.00e-15 | <1.61e-13 |
| 31 | TCERG1 | transcription elongation regulator 1 | 1183550 | 41 | 37 | 22 | 5 | 3 | 2 | 1 | 9 | 22 | 4 | 0.014 | 0.62 | 0.000072 | 0.000038 | 0 | <1.00e-15 | <1.61e-13 |
| 32 | MYL1 | myosin, light chain 1, alkali; skeletal, fast | 223469 | 35 | 35 | 5 | 5 | 1 | 1 | 0 | 1 | 31 | 1 | 4.6e-15 | 1 | 0 | 0.13 | 0 | <1.00e-15 | <1.61e-13 |
| 33 | FANCD2 | Fanconi anemia, complementation group D2 | 1683879 | 35 | 34 | 16 | 4 | 3 | 4 | 3 | 1 | 24 | 0 | 0.00018 | 0.31 | 1.2e-06 | 0.00019 | 0 | <1.00e-15 | <1.61e-13 |
| 34 | KRTAP4-1 | keratin associated protein 4-1 | 92915 | 35 | 33 | 3 | 0 | 3 | 0 | 0 | 0 | 32 | 0 | 4.2e-15 | 1 | 0 | 0.55 | 0 | <1.00e-15 | <1.61e-13 |
| 35 | NRAS | neuroblastoma RAS viral (v-ras) oncogene homolog | 214476 | 34 | 33 | 15 | 11 | 2 | 3 | 11 | 16 | 2 | 0 | 0.0092 | 0.5 | 0 | 0.016 | 0 | <1.00e-15 | <1.61e-13 |
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: 1547. Number of genes displayed: 10
| rank | gene | description | n | cos | n_cos | N_cos | cos_ev | p | q |
|---|---|---|---|---|---|---|---|---|---|
| 1 | APC | adenomatous polyposis coli | 532 | 839 | 455 | 307074 | 9471 | 0 | 0 |
| 2 | TP53 | tumor protein p53 | 328 | 824 | 328 | 301584 | 85364 | 0 | 0 |
| 3 | PTEN | phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | 286 | 767 | 276 | 280722 | 4062 | 0 | 0 |
| 4 | NF1 | neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) | 118 | 285 | 99 | 104310 | 167 | 0 | 0 |
| 5 | EGFR | epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) | 104 | 293 | 84 | 107238 | 1323 | 0 | 0 |
| 6 | VHL | von Hippel-Lindau tumor suppressor | 83 | 541 | 82 | 198006 | 1604 | 0 | 0 |
| 7 | NF2 | neurofibromin 2 (merlin) | 76 | 550 | 71 | 201300 | 377 | 0 | 0 |
| 8 | KRTAP5-5 | keratin associated protein 5-5 | 12 | 1 | 10 | 366 | 10 | 1.4e-15 | 3.6e-13 |
| 9 | EHBP1 | EH domain binding protein 1 | 23 | 1 | 9 | 366 | 9 | 1.4e-15 | 3.6e-13 |
| 10 | ETNK2 | ethanolamine kinase 2 | 11 | 1 | 8 | 366 | 8 | 1.4e-15 | 3.6e-13 |
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)
Table 5. 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 | TCRMOLECULE | T Cell Receptor and CD3 Complex | CD3D, CD3E, CD3G, CD3Z, TRA@, TRB@ | 3 | CD3D(4), CD3E(2), CD3G(15) | 634073 | 21 | 19 | 8 | 3 | 1 | 4 | 2 | 0 | 14 | 0 | 0.53 | 0.058 | 1 |
| 2 | SA_BONE_MORPHOGENETIC | Bone morphogenetic protein binds to its receptor to induce ectopic bone formation and promote development of the viscera. | BMP1, BMPR1A, BMPR1B, BMPR2, MADH1, MADH4, MADH6 | 4 | BMP1(17), BMPR1A(18), BMPR1B(14), BMPR2(46) | 3229801 | 95 | 69 | 78 | 13 | 20 | 14 | 5 | 20 | 26 | 10 | 0.014 | 0.074 | 1 |
| 3 | HSA00785_LIPOIC_ACID_METABOLISM | Genes involved in lipoic acid metabolism | LIAS, LIPT1, LOC387787 | 2 | LIAS(8), LIPT1(11) | 821172 | 19 | 17 | 14 | 0 | 0 | 3 | 2 | 3 | 11 | 0 | 0.055 | 0.15 | 1 |
| 4 | HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM | Genes involved in D-arginine and D-ornithine metabolism | DAO | 1 | DAO(7) | 384581 | 7 | 8 | 7 | 1 | 6 | 0 | 0 | 1 | 0 | 0 | 0.33 | 0.37 | 1 |
| 5 | INOSITOL_METABOLISM | ALDH6A1, ALDOA, ALDOB, ALDOC, TPI1 | 5 | ALDH6A1(5), ALDOA(2), ALDOB(16), ALDOC(1), TPI1(3) | 1926826 | 27 | 26 | 23 | 3 | 4 | 5 | 2 | 15 | 1 | 0 | 0.052 | 0.53 | 1 | |
| 6 | HSA00430_TAURINE_AND_HYPOTAURINE_METABOLISM | Genes involved in taurine and hypotaurine metabolism | BAAT, CDO1, CSAD, GAD1, GAD2, GGT1, GGTL3, GGTL4 | 6 | BAAT(3), CDO1(3), CSAD(4), GAD1(15), GAD2(15), GGT1(9) | 2900087 | 49 | 43 | 37 | 8 | 16 | 6 | 5 | 11 | 11 | 0 | 0.035 | 0.57 | 1 |
| 7 | 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 | ARF1(1), CCND1(2), CDK2(5), CDK4(3), CDKN1A(2), CDKN1B(4), CDKN2A(7), CFL1(2), E2F2(7), MDM2(11), NXT1(5), PRB1(3), TP53(326) | 3973129 | 378 | 245 | 232 | 89 | 99 | 90 | 47 | 65 | 73 | 4 | 0.000073 | 0.6 | 1 |
| 8 | HSA00031_INOSITOL_METABOLISM | Genes involved in inositol metabolism | ALDH6A1, TPI1 | 2 | ALDH6A1(5), TPI1(3) | 802771 | 8 | 8 | 8 | 1 | 0 | 0 | 1 | 7 | 0 | 0 | 0.4 | 0.71 | 1 |
| 9 | HSA00830_RETINOL_METABOLISM | Genes involved in retinol metabolism | ALDH1A1, ALDH1A2, BCMO1, RDH5 | 4 | ALDH1A1(11), ALDH1A2(17), BCMO1(5), RDH5(2) | 2048461 | 35 | 32 | 34 | 7 | 10 | 8 | 5 | 8 | 4 | 0 | 0.077 | 0.73 | 1 |
| 10 | TCAPOPTOSISPATHWAY | HIV infection upregulates Fas ligand in macrophages and CD4 in helper T cells, leading to widespread Fas-induced T cell apoptosis. | CCR5, CD28, CD3D, CD3E, CD3G, CD3Z, CD4, TNFRSF6, TNFSF6, TRA@, TRB@ | 6 | CCR5(11), CD28(4), CD3D(4), CD3E(2), CD3G(15), CD4(4) | 1777677 | 40 | 32 | 26 | 8 | 4 | 4 | 6 | 8 | 18 | 0 | 0.4 | 0.78 | 1 |
Table 6. 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 | HSA00785_LIPOIC_ACID_METABOLISM | Genes involved in lipoic acid metabolism | LIAS, LIPT1, LOC387787 | 2 | LIAS(8), LIPT1(11) | 821172 | 19 | 17 | 14 | 0 | 0 | 3 | 2 | 3 | 11 | 0 | 0.055 | 0.15 | 1 |
| 2 | HSA00472_D_ARGININE_AND_D_ORNITHINE_METABOLISM | Genes involved in D-arginine and D-ornithine metabolism | DAO | 1 | DAO(7) | 384581 | 7 | 8 | 7 | 1 | 6 | 0 | 0 | 1 | 0 | 0 | 0.33 | 0.37 | 1 |
| 3 | HSA00031_INOSITOL_METABOLISM | Genes involved in inositol metabolism | ALDH6A1, TPI1 | 2 | ALDH6A1(5), TPI1(3) | 802771 | 8 | 8 | 8 | 1 | 0 | 0 | 1 | 7 | 0 | 0 | 0.4 | 0.71 | 1 |
| 4 | SLRPPATHWAY | Small leucine-rich proteoglycans (SLRPs) interact with and reorganize collagen fibers in the extracellular matrix. | BGN, DCN, DSPG3, FMOD, KERA, LUM | 5 | BGN(7), DCN(7), FMOD(8), KERA(7), LUM(12) | 1873748 | 41 | 36 | 40 | 9 | 10 | 12 | 1 | 14 | 4 | 0 | 0.21 | 0.82 | 1 |
| 5 | 1_2_DICHLOROETHANE_DEGRADATION | ALDH1A1, ALDH1A2, ALDH1A3, ALDH1B1, ALDH2, ALDH3A1, ALDH3A2, ALDH9A1 | 6 | ALDH1A1(11), ALDH1A3(18), ALDH1B1(8), ALDH3A1(7), ALDH3A2(10), ALDH9A1(4) | 3071928 | 58 | 44 | 52 | 9 | 19 | 9 | 7 | 15 | 8 | 0 | 0.01 | 0.86 | 1 | |
| 6 | ASCORBATE_AND_ALDARATE_METABOLISM | ALDH1A1, ALDH1A2, ALDH1A3, ALDH1B1, ALDH2, ALDH3A1, ALDH3A2, ALDH9A1 | 6 | ALDH1A1(11), ALDH1A3(18), ALDH1B1(8), ALDH3A1(7), ALDH3A2(10), ALDH9A1(4) | 3071928 | 58 | 44 | 52 | 9 | 19 | 9 | 7 | 15 | 8 | 0 | 0.01 | 0.86 | 1 | |
| 7 | BBCELLPATHWAY | Fas ligand expression by T cells induces apoptosis in Fas-expressing, inactive B cells. | CD28, CD4, HLA-DRA, HLA-DRB1, TNFRSF5, TNFRSF6, TNFSF5, TNFSF6 | 3 | CD28(4), CD4(4), HLA-DRB1(6) | 912125 | 14 | 12 | 13 | 7 | 1 | 0 | 2 | 5 | 4 | 2 | 0.96 | 0.86 | 1 |
| 8 | HSA00430_TAURINE_AND_HYPOTAURINE_METABOLISM | Genes involved in taurine and hypotaurine metabolism | BAAT, CDO1, CSAD, GAD1, GAD2, GGT1, GGTL3, GGTL4 | 5 | BAAT(3), CDO1(3), CSAD(4), GAD1(15), GAD2(15) | 2490512 | 40 | 36 | 33 | 8 | 16 | 6 | 4 | 11 | 3 | 0 | 0.07 | 0.94 | 1 |
| 9 | SA_FAS_SIGNALING | The TNF-type receptor Fas induces apoptosis on ligand binding. | BCL2, CASP3, CASP8, CFL1, CFLAR, P11, PDE6D, TNFRSF6, TNFSF6 | 6 | BCL2(2), CASP3(3), CASP8(19), CFL1(2), CFLAR(2), PDE6D(2) | 1974946 | 30 | 28 | 28 | 5 | 5 | 2 | 3 | 8 | 12 | 0 | 0.19 | 0.95 | 1 |
| 10 | PEPIPATHWAY | Proepithelin (PEPI) induces epithelial cells to secrete IL-8, which promotes elastase secretion by neutrophils. | ELA1, ELA2, ELA2A, ELA2B, ELA3B, GRN, IL8, SLPI | 3 | GRN(9), IL8(5), SLPI(2) | 832960 | 16 | 15 | 15 | 7 | 2 | 3 | 2 | 3 | 6 | 0 | 0.79 | 0.96 | 1 |
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]
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.