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: KIRC.
Number of patients in set: 293
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.
MAF used for this analysis: KIRC.final_analysis_set.maf
Significantly mutated genes (q ≤ 0.1): 84
Mutations seen in COSMIC: 345
Significantly mutated genes in COSMIC territory: 85
Genes with clustered mutations (≤ 3 aa apart): 0
Significantly mutated genesets: 6
Significantly mutated genesets: (excluding sig. mutated genes): 0
Read 293 MAFs of type "Broad"
Read 66 MAFs of type "Baylor"
Total number of mutations in input MAFs: 99658
After removing 232 mutations outside chr1-24: 99426
After removing 70518 noncoding mutations: 28908
After collapsing adjacent/redundant mutations: 26038
Number of mutations before filtering: 26038
After removing 802 mutations outside gene set: 25236
After removing 111 mutations outside category set: 25125
After removing 1 "impossible" mutations in
gene-patient-category bins of zero coverage: 25124
Table 1. Get Full Table Table representing breakdown of mutations by type.
| type | count |
|---|---|
| Frame_Shift_Del | 440 |
| Frame_Shift_Ins | 114 |
| In_Frame_Del | 129 |
| In_Frame_Ins | 43 |
| Missense_Mutation | 16106 |
| Nonsense_Mutation | 1080 |
| Nonstop_Mutation | 21 |
| Silent | 6625 |
| Splice_Site | 525 |
| Translation_Start_Site | 42 |
| Total | 25125 |
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 | 1767 | 484078369 | 3.7e-06 | 3.7 | 1.7 | 2.1 |
| *ApG->G | 1226 | 1342141277 | 9.1e-07 | 0.91 | 0.43 | 2.1 |
| *Np(A/C/T)->transit | 5303 | 6921093572 | 7.7e-07 | 0.77 | 0.36 | 2 |
| transver | 7785 | 8747313218 | 8.9e-07 | 0.89 | 0.42 | 5 |
| indel+null | 2411 | 8747313218 | 2.8e-07 | 0.28 | 0.13 | NaN |
| double_null | 8 | 8747313218 | 9.1e-10 | 0.00091 | 0.00043 | NaN |
| Total | 18500 | 8747313218 | 2.1e-06 | 2.1 | 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).
Figure 1.
Figure 2. Patients counts and rates file used to generate this plot: KIRC.patients.counts_and_rates.txt
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.
Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 84. 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_ks | p_cons | p_joint | p | q |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | VHL | von Hippel-Lindau tumor suppressor | 123072 | 150 | 146 | 96 | 2 | 2 | 14 | 15 | 33 | 86 | 0 | <1.00e-15 | 2.3e-11 | 0.042 | 0.00084 | 0.0011 | <0.00 | <0.00 |
| 2 | KDM5C | 1253863 | 18 | 18 | 18 | 1 | 0 | 0 | 2 | 5 | 11 | 0 | 1.44e-15 | 0.1 | 0.0066 | 0.29 | 0.012 | 6.66e-16 | 2.59e-12 | |
| 3 | PBRM1 | polybromo 1 | 1470408 | 100 | 98 | 98 | 2 | 0 | 1 | 6 | 15 | 78 | 0 | <1.00e-15 | 0.000013 | 0.037 | 0.09 | 0.022 | <8.88e-16 | <2.59e-12 |
| 4 | RRAD | Ras-related associated with diabetes | 202274 | 4 | 4 | 1 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0.00016 | 0.43 | 4e-07 | 0.001 | 0 | <1.00e-15 | <2.59e-12 |
| 5 | SV2C | synaptic vesicle glycoprotein 2C | 653960 | 3 | 3 | 3 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 0.061 | 0.3 | 0.14 | 0.0017 | 0 | <1.00e-15 | <2.59e-12 |
| 6 | TOR1A | torsin family 1, member A (torsin A) | 280456 | 3 | 3 | 1 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0.0067 | 0.27 | 4.8e-06 | 0.0012 | 0 | <1.00e-15 | <2.59e-12 |
| 7 | TPST1 | tyrosylprotein sulfotransferase 1 | 330797 | 2 | 2 | 2 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0.031 | 0.74 | 0.08 | 0.00085 | 0 | <1.00e-15 | <2.59e-12 |
| 8 | BAP1 | BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) | 589189 | 28 | 27 | 25 | 1 | 0 | 2 | 6 | 5 | 14 | 1 | 1.11e-15 | 0.0024 | 0.067 | 0.23 | 0.067 | 2.78e-15 | 6.29e-12 |
| 9 | SETD2 | SET domain containing 2 | 1866089 | 32 | 32 | 32 | 1 | 2 | 2 | 2 | 7 | 18 | 1 | <1.00e-15 | 0.0039 | 0.33 | 0.091 | 0.16 | <6.00e-15 | <1.21e-11 |
| 10 | PTEN | phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | 365609 | 16 | 15 | 16 | 2 | 0 | 1 | 5 | 3 | 7 | 0 | <1.00e-15 | 0.11 | 0.11 | 0.91 | 0.18 | <6.88e-15 | <1.25e-11 |
| 11 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 963086 | 14 | 14 | 13 | 1 | 0 | 2 | 6 | 5 | 1 | 0 | 1.28e-10 | 0.061 | 0.0014 | 0.21 | 0.0014 | 5.58e-12 | 9.19e-09 |
| 12 | STAG3L2 | stromal antigen 3-like 2 | 83876 | 6 | 6 | 2 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | 7.40e-11 | 1 | 0.0051 | 0.16 | 0.0068 | 1.47e-11 | 2.21e-08 |
| 13 | MTOR | 2294678 | 26 | 24 | 22 | 2 | 1 | 2 | 4 | 19 | 0 | 0 | 8.13e-11 | 0.043 | 0.0045 | 0.51 | 0.011 | 2.50e-11 | 3.49e-08 | |
| 14 | EBPL | emopamil binding protein-like | 139558 | 7 | 6 | 3 | 0 | 1 | 0 | 0 | 6 | 0 | 0 | 2.76e-08 | 0.2 | 0.0019 | 1 | 0.004 | 2.66e-09 | 3.44e-06 |
| 15 | KANK3 | KN motif and ankyrin repeat domains 3 | 301372 | 6 | 6 | 2 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | 4.25e-09 | 1 | 0.043 | 0.64 | 0.098 | 9.38e-09 | 0.000011 |
| 16 | NUDT11 | nudix (nucleoside diphosphate linked moiety X)-type motif 11 | 127356 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.00019 | 1 | 3.8e-06 | 0.96 | 6.2e-06 | 2.52e-08 | 0.000029 |
| 17 | ANKRD36 | ankyrin repeat domain 36 | 752950 | 11 | 10 | 6 | 2 | 1 | 0 | 0 | 9 | 1 | 0 | 5.78e-07 | 0.52 | 0.0011 | 0.83 | 0.003 | 3.70e-08 | 0.000039 |
| 18 | ZCCHC3 | zinc finger, CCHC domain containing 3 | 208403 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.00017 | 1 | 2.2e-06 | 1 | 0.000012 | 4.35e-08 | 0.000044 |
| 19 | FAM174B | 72325 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.00011 | 1 | 0.000018 | 0.97 | 2e-05 | 4.67e-08 | 0.000044 | |
| 20 | TSPAN19 | tetraspanin 19 | 144817 | 4 | 4 | 4 | 0 | 0 | 0 | 1 | 1 | 2 | 0 | 5.22e-07 | 0.6 | 0.016 | 0.25 | 0.033 | 3.26e-07 | 0.00030 |
| 21 | DACH2 | dachshund homolog 2 (Drosophila) | 506733 | 7 | 7 | 3 | 0 | 0 | 0 | 0 | 7 | 0 | 0 | 5.94e-06 | 0.27 | 0.0014 | 0.2 | 0.0032 | 3.61e-07 | 0.00030 |
| 22 | KRTAP1-1 | keratin associated protein 1-1 | 157631 | 3 | 3 | 1 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0.00090 | 0.62 | 6e-06 | 0.8 | 0.000021 | 3.63e-07 | 0.00030 |
| 23 | UQCRFS1 | ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 | 180195 | 3 | 3 | 1 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0.0028 | 0.31 | 8.8e-06 | 1 | 0.000012 | 6.31e-07 | 0.00050 |
| 24 | VCX2 | variable charge, X-linked 2 | 46999 | 4 | 3 | 4 | 0 | 0 | 1 | 0 | 1 | 2 | 0 | 4.46e-06 | 0.67 | 0.0066 | 0.82 | 0.018 | 1.40e-06 | 0.0011 |
| 25 | CR1 | complement component (3b/4b) receptor 1 (Knops blood group) | 1444581 | 11 | 11 | 8 | 0 | 1 | 0 | 0 | 4 | 6 | 0 | 2.65e-06 | 0.095 | 0.073 | 0.059 | 0.039 | 1.79e-06 | 0.0013 |
| 26 | KRT1 | keratin 1 (epidermolytic hyperkeratosis) | 500192 | 5 | 5 | 2 | 0 | 1 | 0 | 0 | 0 | 4 | 0 | 0.000083 | 0.72 | 0.0008 | 0.98 | 0.0026 | 3.48e-06 | 0.0024 |
| 27 | ABCB1 | ATP-binding cassette, sub-family B (MDR/TAP), member 1 | 1157641 | 9 | 8 | 9 | 0 | 0 | 0 | 4 | 3 | 2 | 0 | 0.000071 | 0.084 | 0.0039 | 0.15 | 0.0047 | 5.27e-06 | 0.0035 |
| 28 | MADCAM1 | mucosal vascular addressin cell adhesion molecule 1 | 158333 | 4 | 4 | 2 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 0.00021 | 0.35 | 0.00028 | 0.99 | 0.002 | 6.75e-06 | 0.0044 |
| 29 | WDR52 | WD repeat domain 52 | 887493 | 10 | 9 | 6 | 1 | 1 | 1 | 0 | 8 | 0 | 0 | 4.37e-06 | 0.35 | 1 | 0.077 | 0.16 | 0.000011 | 0.0067 |
| 30 | TPTE2 | transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 | 483148 | 8 | 7 | 8 | 1 | 1 | 0 | 0 | 6 | 1 | 0 | 1.82e-06 | 0.49 | 0.44 | 0.57 | 0.63 | 0.000017 | 0.010 |
| 31 | OR5H1 | olfactory receptor, family 5, subfamily H, member 1 | 276592 | 5 | 4 | 3 | 1 | 0 | 2 | 1 | 0 | 2 | 0 | 0.00039 | 0.49 | 0.00088 | 0.55 | 0.0032 | 0.000018 | 0.011 |
| 32 | POLDIP2 | polymerase (DNA-directed), delta interacting protein 2 | 257573 | 4 | 4 | 3 | 0 | 0 | 0 | 1 | 0 | 3 | 0 | 0.000012 | 0.66 | 0.073 | 0.99 | 0.11 | 0.000019 | 0.011 |
| 33 | PCDHGA8 | protocadherin gamma subfamily A, 8 | 835388 | 4 | 4 | 2 | 1 | 1 | 0 | 0 | 3 | 0 | 0 | 0.045 | 0.61 | 0.000026 | 0.084 | 3e-05 | 0.000019 | 0.011 |
| 34 | CCNB2 | cyclin B2 | 353170 | 5 | 5 | 5 | 0 | 0 | 0 | 2 | 1 | 2 | 0 | 0.000011 | 0.22 | 0.23 | 0.15 | 0.15 | 0.000024 | 0.013 |
| 35 | NFE2L2 | nuclear factor (erythroid-derived 2)-like 2 | 524177 | 5 | 5 | 5 | 0 | 0 | 0 | 2 | 3 | 0 | 0 | 0.00059 | 0.29 | 0.068 | 0.005 | 0.0054 | 0.000043 | 0.022 |
Figure S1. This figure depicts the distribution of mutations and mutation types across the RRAD significant gene.
Figure S2. This figure depicts the distribution of mutations and mutation types across the SV2C significant gene.
Figure S3. This figure depicts the distribution of mutations and mutation types across the TOR1A significant gene.
Figure S4. This figure depicts the distribution of mutations and mutation types across the TPST1 significant gene.
Figure S5. This figure depicts the distribution of mutations and mutation types across the MTOR significant gene.
Figure S6. This figure depicts the distribution of mutations and mutation types across the EBPL significant gene.
Figure S7. This figure depicts the distribution of mutations and mutation types across the ANKRD36 significant gene.
Figure S8. This figure depicts the distribution of mutations and mutation types across the ZCCHC3 significant gene.
Figure S9. This figure depicts the distribution of mutations and mutation types across the FAM174B significant gene.
Figure S10. This figure depicts the distribution of mutations and mutation types across the TSPAN19 significant gene.
Figure S11. This figure depicts the distribution of mutations and mutation types across the DACH2 significant gene.
Figure S12. This figure depicts the distribution of mutations and mutation types across the KRTAP1-1 significant gene.
Figure S13. This figure depicts the distribution of mutations and mutation types across the CR1 significant gene.
Figure S14. This figure depicts the distribution of mutations and mutation types across the KRT1 significant gene.
Figure S15. This figure depicts the distribution of mutations and mutation types across the ABCB1 significant gene.
Figure S16. This figure depicts the distribution of mutations and mutation types across the WDR52 significant gene.
Figure S17. This figure depicts the distribution of mutations and mutation types across the TPTE2 significant gene.
Figure S18. This figure depicts the distribution of mutations and mutation types across the OR5H1 significant gene.
Figure S19. This figure depicts the distribution of mutations and mutation types across the POLDIP2 significant gene.
Figure S20. This figure depicts the distribution of mutations and mutation types across the PCDHGA8 significant gene.
Figure S21. This figure depicts the distribution of mutations and mutation types across the CCNB2 significant gene.
Note:
N - number of sequenced bases in this gene across the individual set.
n - number of (nonsilent) mutations in this gene across the individual set.
npat - number of patients (individuals) with at least one nonsilent mutation.
nsite - number of unique sites having a non-silent mutation.
nsil - number of silent mutations in this gene across the individual set.
n1 - number of nonsilent mutations of type: *CpG->T .
n2 - number of nonsilent mutations of type: *ApG->G .
n3 - number of nonsilent mutations of type: *Np(A/C/T)->transit .
n4 - number of nonsilent mutations of type: transver .
n5 - number of nonsilent mutations of type: indel+null .
null - mutation category that includes nonsense, frameshift, splice-site mutations
p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene
p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene
p = p-value (overall)
q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)
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: 85. Number of genes displayed: 10
| rank | gene | description | n | cos | n_cos | N_cos | cos_ev | p | q |
|---|---|---|---|---|---|---|---|---|---|
| 1 | VHL | von Hippel-Lindau tumor suppressor | 150 | 537 | 150 | 157341 | 3740 | 0 | 0 |
| 2 | PIK3CA | phosphoinositide-3-kinase, catalytic, alpha polypeptide | 14 | 184 | 12 | 53912 | 3014 | 0 | 0 |
| 3 | TP53 | tumor protein p53 | 13 | 308 | 12 | 90244 | 1649 | 0 | 0 |
| 4 | PTEN | phosphatase and tensin homolog (mutated in multiple advanced cancers 1) | 16 | 728 | 16 | 213304 | 120 | 0 | 0 |
| 5 | CHEK2 | CHK2 checkpoint homolog (S. pombe) | 7 | 2 | 4 | 586 | 4 | 7.3e-14 | 6.6e-11 |
| 6 | NF1 | neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) | 11 | 285 | 6 | 83505 | 8 | 3.6e-08 | 0.000026 |
| 7 | KRAS | v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog | 4 | 51 | 4 | 14943 | 14813 | 4.1e-08 | 0.000026 |
| 8 | ARHGAP20 | Rho GTPase activating protein 20 | 4 | 2 | 2 | 586 | 2 | 7.7e-07 | 0.00043 |
| 9 | NF2 | neurofibromin 2 (merlin) | 6 | 543 | 6 | 159099 | 36 | 1.5e-06 | 0.00076 |
| 10 | SBNO1 | strawberry notch homolog 1 (Drosophila) | 3 | 4 | 2 | 1172 | 4 | 3.1e-06 | 0.0014 |
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)
There were no clustered mutations discovered.
Table 5. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 6. 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 | VEGFPATHWAY | Vascular endothelial growth factor (VEGF) is upregulated by hypoxic conditions and promotes normal blood vessel formation and angiogenesis related to tumor growth or cardiac disease. | ARNT, EIF1, EIF1A, EIF2B1, EIF2B2, EIF2B3, EIF2B4, EIF2B5, EIF2S1, EIF2S2, EIF2S3, ELAVL1, FLT1, FLT4, HIF1A, HRAS, KDR, NOS3, PIK3CA, PIK3R1, PLCG1, PRKCA, PRKCB1, PTK2, PXN, SHC1, VEGF, VHL | 25 | EIF1(1), EIF2B1(2), EIF2B2(1), EIF2B5(2), EIF2S1(1), EIF2S2(1), ELAVL1(1), FLT1(3), FLT4(4), HIF1A(3), KDR(5), NOS3(1), PIK3CA(14), PIK3R1(1), PTK2(1), PXN(2), SHC1(2), VHL(150) | 14983008 | 195 | 165 | 140 | 17 | 7 | 18 | 26 | 53 | 91 | 0 | 2.9e-06 | <1.00e-15 | <2.96e-13 |
| 2 | HIFPATHWAY | Under normal conditions, hypoxia inducible factor HIF-1 is degraded; under hypoxic conditions, it activates transcription of genes controlled by hpoxic response elements (HREs). | ARNT, ASPH, COPS5, CREB1, EDN1, EP300, EPO, HIF1A, HSPCA, JUN, LDHA, NOS3, P4HB, VEGF, VHL | 13 | ASPH(1), EP300(6), HIF1A(3), JUN(1), NOS3(1), VHL(150) | 7504580 | 162 | 151 | 108 | 8 | 2 | 15 | 18 | 39 | 88 | 0 | 9.3e-08 | <1.00e-15 | <2.96e-13 |
| 3 | HSA04120_UBIQUITIN_MEDIATED_PROTEOLYSIS | Genes involved in ubiquitin mediated proteolysis | ANAPC1, ANAPC10, ANAPC11, ANAPC2, ANAPC4, ANAPC5, ANAPC7, BTRC, CDC16, CDC20, CDC23, CDC26, CDC27, CUL1, CUL2, CUL3, FBXW11, FBXW7, FZR1, ITCH, LOC728919, RBX1, SKP1, SKP2, SMURF1, SMURF2, TCEB1, TCEB2, UBA1, UBE2C, UBE2D1, UBE2D2, UBE2D3, UBE2D4, UBE2E1, UBE2E2, UBE2E3, VHL, WWP1, WWP2 | 39 | ANAPC1(4), ANAPC11(1), ANAPC2(1), ANAPC4(2), ANAPC5(2), ANAPC7(1), CDC16(2), CDC20(1), CDC23(2), CDC27(5), CUL1(3), CUL2(1), CUL3(2), FBXW11(1), FBXW7(4), FZR1(1), SKP2(1), SMURF1(1), SMURF2(2), TCEB1(1), UBA1(1), UBE2D1(2), UBE2D2(1), UBE2D3(1), UBE2E2(1), VHL(150), WWP1(1), WWP2(1) | 17820449 | 196 | 165 | 142 | 21 | 4 | 19 | 31 | 48 | 94 | 0 | 0.000027 | 1.44e-15 | 2.96e-13 |
| 4 | SA_PTEN_PATHWAY | PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate. | AKT1, AKT2, AKT3, BPNT1, GRB2, ILK, MAPK1, MAPK3, PDK1, PIK3CA, PIK3CD, PIP3-E, PTEN, PTK2B, RBL2, SHC1, SOS1 | 16 | AKT1(1), AKT2(2), AKT3(2), MAPK1(1), MAPK3(1), PDK1(1), PIK3CA(14), PIK3CD(1), PTEN(16), PTK2B(2), RBL2(3), SHC1(2), SOS1(4) | 8973555 | 50 | 45 | 49 | 5 | 3 | 5 | 19 | 14 | 9 | 0 | 0.0012 | 4.69e-07 | 0.000072 |
| 5 | SA_TRKA_RECEPTOR | The TrkA receptor binds nerve growth factor to activate MAP kinase pathways and promote cell growth. | AKT1, AKT2, AKT3, ARHA, CDKN1A, ELK1, GRB2, HRAS, MAP2K1, MAP2K2, NGFB, NGFR, NTRK1, PIK3CA, PIK3CD, SHC1, SOS1 | 15 | AKT1(1), AKT2(2), AKT3(2), CDKN1A(1), ELK1(1), MAP2K1(1), NGFR(1), NTRK1(2), PIK3CA(14), PIK3CD(1), SHC1(2), SOS1(4) | 7184719 | 32 | 31 | 31 | 2 | 2 | 3 | 13 | 13 | 1 | 0 | 0.0029 | 0.000027 | 0.0033 |
| 6 | BLYMPHOCYTEPATHWAY | B cells express the major histocompatibility complex (class II MHC), immunoglobulins, adhesion proteins, and other factors on their cell surface. | CD80, CR1, CR2, FCGR2B, HLA-DRA, HLA-DRB1, ICAM1, ITGAL, ITGB2, PTPRC, TNFRSF5 | 10 | CD80(1), CR1(11), CR2(1), HLA-DRA(1), ITGAL(3), ITGB2(1), PTPRC(6) | 6737962 | 24 | 23 | 21 | 2 | 2 | 0 | 2 | 11 | 9 | 0 | 0.091 | 0.00019 | 0.019 |
| 7 | HSA04140_REGULATION_OF_AUTOPHAGY | Genes involved in regulation of autophagy | ATG12, ATG3, ATG5, ATG7, BECN1, GABARAP, GABARAPL1, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNG, INS, LOC441925, PIK3C3, PIK3R4, PRKAA1, PRKAA2, ULK1, ULK2, ULK3 | 29 | ATG12(1), ATG3(3), ATG7(4), BECN1(1), IFNA1(1), IFNA14(1), IFNA16(1), IFNA21(1), IFNA5(1), IFNA7(1), IFNA8(1), PIK3C3(4), PIK3R4(7), PRKAA1(1), ULK1(1), ULK2(2), ULK3(2) | 9349525 | 33 | 32 | 33 | 4 | 3 | 1 | 5 | 17 | 7 | 0 | 0.077 | 0.0034 | 0.26 |
| 8 | HSA00950_ALKALOID_BIOSYNTHESIS_I | Genes involved in alkaloid biosynthesis I | DDC, GOT1, GOT2, TAT, TYR | 5 | DDC(3), GOT1(1), GOT2(3), TAT(1), TYR(1) | 2063429 | 9 | 9 | 9 | 1 | 1 | 0 | 5 | 1 | 2 | 0 | 0.21 | 0.0034 | 0.26 |
| 9 | ACETAMINOPHENPATHWAY | Acetaminophen selectively inhibits Cox-3, which is localized to the brain, and yields the toxic metabolite NAPQI when processed by CAR in the liver. | CYP1A2, CYP2E1, CYP3A, NR1I3, PTGS1, PTGS2 | 5 | CYP1A2(2), CYP2E1(2), NR1I3(1), PTGS2(4) | 2332448 | 9 | 9 | 9 | 1 | 1 | 0 | 1 | 5 | 2 | 0 | 0.35 | 0.0074 | 0.51 |
| 10 | HSA00272_CYSTEINE_METABOLISM | Genes involved in cysteine metabolism | CARS, CARS2, CDO1, CTH, GOT1, GOT2, LDHA, LDHAL6A, LDHAL6B, LDHB, LDHC, MPST, SDS, SULT1B1, SULT1C2, SULT1C4, SULT4A1 | 17 | CARS(2), CARS2(3), CTH(1), GOT1(1), GOT2(3), LDHAL6B(1), LDHB(1), LDHC(2), MPST(2), SULT1C2(1), SULT4A1(1) | 5521164 | 18 | 18 | 18 | 2 | 2 | 1 | 5 | 5 | 5 | 0 | 0.14 | 0.0083 | 0.51 |
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 | HSA04140_REGULATION_OF_AUTOPHAGY | Genes involved in regulation of autophagy | ATG12, ATG3, ATG5, ATG7, BECN1, GABARAP, GABARAPL1, IFNA1, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, IFNA2, IFNA21, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNG, INS, LOC441925, PIK3C3, PIK3R4, PRKAA1, PRKAA2, ULK1, ULK2, ULK3 | 29 | ATG12(1), ATG3(3), ATG7(4), BECN1(1), IFNA1(1), IFNA14(1), IFNA16(1), IFNA21(1), IFNA5(1), IFNA7(1), IFNA8(1), PIK3C3(4), PIK3R4(7), PRKAA1(1), ULK1(1), ULK2(2), ULK3(2) | 9349525 | 33 | 32 | 33 | 4 | 3 | 1 | 5 | 17 | 7 | 0 | 0.077 | 0.0034 | 1 |
| 2 | HSA00950_ALKALOID_BIOSYNTHESIS_I | Genes involved in alkaloid biosynthesis I | DDC, GOT1, GOT2, TAT, TYR | 5 | DDC(3), GOT1(1), GOT2(3), TAT(1), TYR(1) | 2063429 | 9 | 9 | 9 | 1 | 1 | 0 | 5 | 1 | 2 | 0 | 0.21 | 0.0034 | 1 |
| 3 | ACETAMINOPHENPATHWAY | Acetaminophen selectively inhibits Cox-3, which is localized to the brain, and yields the toxic metabolite NAPQI when processed by CAR in the liver. | CYP1A2, CYP2E1, CYP3A, NR1I3, PTGS1, PTGS2 | 5 | CYP1A2(2), CYP2E1(2), NR1I3(1), PTGS2(4) | 2332448 | 9 | 9 | 9 | 1 | 1 | 0 | 1 | 5 | 2 | 0 | 0.35 | 0.0074 | 1 |
| 4 | HSA00272_CYSTEINE_METABOLISM | Genes involved in cysteine metabolism | CARS, CARS2, CDO1, CTH, GOT1, GOT2, LDHA, LDHAL6A, LDHAL6B, LDHB, LDHC, MPST, SDS, SULT1B1, SULT1C2, SULT1C4, SULT4A1 | 17 | CARS(2), CARS2(3), CTH(1), GOT1(1), GOT2(3), LDHAL6B(1), LDHB(1), LDHC(2), MPST(2), SULT1C2(1), SULT4A1(1) | 5521164 | 18 | 18 | 18 | 2 | 2 | 1 | 5 | 5 | 5 | 0 | 0.14 | 0.0083 | 1 |
| 5 | CYSTEINE_METABOLISM | CARS, CTH, GOT1, GOT2, LDHA, LDHB, LDHC, MPST | 8 | CARS(2), CTH(1), GOT1(1), GOT2(3), LDHB(1), LDHC(2), MPST(2) | 3003190 | 12 | 12 | 12 | 2 | 2 | 0 | 4 | 3 | 3 | 0 | 0.33 | 0.013 | 1 | |
| 6 | UREACYCLEPATHWAY | Ammonia released from amino acid deamination is used to produce carbamoyl phosphate, which is used to convert ornithine to citrulline, from which urea is eventually formed. | ARG1, ASL, ASS, CPS1, GLS, GLUD1, GOT1 | 6 | ARG1(1), CPS1(5), GLS(1), GLUD1(2), GOT1(1) | 3418789 | 10 | 10 | 10 | 1 | 0 | 0 | 6 | 2 | 2 | 0 | 0.12 | 0.017 | 1 |
| 7 | HSA00130_UBIQUINONE_BIOSYNTHESIS | Genes involved in ubiquinone biosynthesis | COQ2, COQ3, COQ5, COQ6, COQ7, ND1, ND2, ND3, ND4, ND4L, ND5, ND6, NDUFA12, NDUFA13, NDUFB11 | 8 | COQ5(2), COQ6(1), NDUFA13(3), NDUFB11(1) | 1778759 | 7 | 7 | 7 | 0 | 2 | 0 | 1 | 3 | 1 | 0 | 0.15 | 0.023 | 1 |
| 8 | TCRAPATHWAY | The kinases Lck and Fyn phosphorylate and activate the T cell receptor, which recognizes antigen-bound MHCII and leads to T cell activation. | CD3D, CD3E, CD3G, CD3Z, CD4, FYN, HLA-DRA, HLA-DRB1, LCK, PTPRC, TRA@, TRB@, ZAP70 | 10 | CD3E(1), CD3G(1), CD4(1), FYN(1), HLA-DRA(1), PTPRC(6), ZAP70(2) | 3990851 | 13 | 11 | 13 | 0 | 1 | 2 | 0 | 7 | 3 | 0 | 0.095 | 0.025 | 1 |
| 9 | HSA00401_NOVOBIOCIN_BIOSYNTHESIS | Genes involved in novobiocin biosynthesis | GOT1, GOT2, TAT | 3 | GOT1(1), GOT2(3), TAT(1) | 1153972 | 5 | 5 | 5 | 1 | 1 | 0 | 3 | 0 | 1 | 0 | 0.42 | 0.028 | 1 |
| 10 | HSA00400_PHENYLALANINE_TYROSINE_AND_TRYPTOPHAN_BIOSYNTHESIS | Genes involved in phenylalanine, tyrosine and tryptophan biosynthesis | FARS2, FARSA, FARSB, GOT1, GOT2, PAH, TAT, YARS, YARS2 | 9 | FARSA(1), FARSB(1), GOT1(1), GOT2(3), PAH(3), TAT(1), YARS(1) | 3828103 | 11 | 11 | 11 | 1 | 1 | 0 | 3 | 5 | 2 | 0 | 0.18 | 0.029 | 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]
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.