(metastatic tumor cohort)
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 vS2N was used to generate the results found in this report.
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Working with individual set: SKCM-TM
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:SKCM-TM.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 231
Column Descriptions:
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N = number of sequenced bases in this gene across the individual set
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nnon = number of (nonsilent) mutations in this gene across the individual set
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nnull = number of (nonsilent) null mutations in this gene across the individual set
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nflank = number of noncoding mutations from this gene's flanking region, across the individual set
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nsil = number of silent mutations in this gene across the individual set
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p = p-value (overall)
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q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)
Table 1. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 231. 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).
gene | N | nflank | nsil | nnon | nnull | p | q |
---|---|---|---|---|---|---|---|
NRAS | 16425 | 0 | 1 | 65 | 0 | 2.7e-282 | 5.1e-278 |
BRAF | 58725 | 0 | 2 | 120 | 0 | 1.7e-224 | 1.6e-220 |
CDKN2A | 13500 | 0 | 1 | 31 | 21 | 1.4e-75 | 9e-72 |
RTL1 | 11925 | 0 | 3 | 13 | 0 | 2.4e-36 | 1.1e-32 |
EYS | 50625 | 0 | 1 | 10 | 0 | 7.8e-29 | 2.9e-25 |
DNAH6 | 36225 | 0 | 1 | 16 | 1 | 1.5e-28 | 4.8e-25 |
SPRR3 | 11250 | 0 | 3 | 12 | 1 | 2.3e-23 | 6.3e-20 |
SMR3A | 6300 | 0 | 2 | 8 | 0 | 4e-21 | 9.4e-18 |
CCNE2 | 40275 | 0 | 2 | 12 | 1 | 5.6e-20 | 1.2e-16 |
NOTCH2 | 174150 | 0 | 9 | 34 | 2 | 4.8e-18 | 9.1e-15 |
PPT2 | 23625 | 0 | 2 | 8 | 0 | 2.6e-17 | 4.4e-14 |
TAF1A | 40950 | 0 | 0 | 14 | 0 | 8.2e-17 | 1.3e-13 |
LIPF | 35775 | 0 | 5 | 14 | 0 | 1.3e-16 | 1.9e-13 |
ADAM30 | 65250 | 0 | 11 | 34 | 3 | 1.9e-16 | 2.5e-13 |
NAP1L4 | 32625 | 0 | 0 | 13 | 2 | 2.6e-16 | 3.3e-13 |
DEFB115 | 7650 | 0 | 2 | 7 | 1 | 4.7e-16 | 5.6e-13 |
PTEN | 36225 | 0 | 0 | 18 | 11 | 1.4e-15 | 1.5e-12 |
INTS8 | 83025 | 0 | 1 | 20 | 2 | 1.5e-15 | 1.5e-12 |
TBC1D3 | 9675 | 2 | 0 | 7 | 0 | 3.8e-14 | 3.8e-11 |
TP53 | 28350 | 0 | 1 | 37 | 14 | 7.7e-14 | 7.3e-11 |
DISP1 | 124650 | 0 | 9 | 41 | 5 | 1.1e-12 | 9.8e-10 |
STK31 | 91350 | 0 | 4 | 36 | 2 | 1.2e-12 | 1e-09 |
PRC1 | 52425 | 0 | 2 | 14 | 1 | 1.2e-11 | 9.5e-09 |
CDC123 | 30825 | 0 | 0 | 7 | 2 | 1.5e-11 | 1.2e-08 |
IVL | 19575 | 0 | 4 | 11 | 0 | 1.9e-11 | 1.4e-08 |
DPY19L4 | 67275 | 0 | 2 | 18 | 4 | 2.2e-11 | 1.6e-08 |
CLCC1 | 49725 | 0 | 1 | 13 | 2 | 3.7e-11 | 2.6e-08 |
ZNF860 | 450 | 0 | 0 | 4 | 0 | 1.1e-10 | 7.3e-08 |
IDH1 | 36000 | 0 | 1 | 11 | 0 | 1.3e-10 | 8.7e-08 |
RPTN | 58275 | 0 | 4 | 47 | 0 | 1.7e-10 | 1.1e-07 |
PPP6C | 25875 | 0 | 2 | 18 | 4 | 8.2e-10 | 4.9e-07 |
CECR6 | 9450 | 0 | 1 | 6 | 0 | 8.4e-10 | 4.9e-07 |
THADA | 141525 | 0 | 5 | 28 | 4 | 1.4e-09 | 7.8e-07 |
PIK3CB | 92925 | 0 | 3 | 21 | 4 | 1.6e-09 | 8.8e-07 |
ADAM21 | 58500 | 0 | 3 | 19 | 1 | 1.6e-09 | 8.8e-07 |
Figure S1. This figure depicts the distribution of mutations and mutation types across the NRAS significant gene.
![](NRAS.stick_fig.png)
Figure S2. This figure depicts the distribution of mutations and mutation types across the BRAF significant gene.
![](BRAF.stick_fig.png)
Figure S3. This figure depicts the distribution of mutations and mutation types across the CDKN2A significant gene.
![](CDKN2A.stick_fig.png)
Figure S4. This figure depicts the distribution of mutations and mutation types across the RTL1 significant gene.
![](RTL1.stick_fig.png)
Figure S5. This figure depicts the distribution of mutations and mutation types across the EYS significant gene.
![](EYS.stick_fig.png)
Figure S6. This figure depicts the distribution of mutations and mutation types across the DNAH6 significant gene.
![](DNAH6.stick_fig.png)
Figure S7. This figure depicts the distribution of mutations and mutation types across the SPRR3 significant gene.
![](SPRR3.stick_fig.png)
Figure S8. This figure depicts the distribution of mutations and mutation types across the SMR3A significant gene.
![](SMR3A.stick_fig.png)
Figure S9. This figure depicts the distribution of mutations and mutation types across the CCNE2 significant gene.
![](CCNE2.stick_fig.png)
Figure S10. This figure depicts the distribution of mutations and mutation types across the NOTCH2 significant gene.
![](NOTCH2.stick_fig.png)
Figure S11. This figure depicts the distribution of mutations and mutation types across the PPT2 significant gene.
![](PPT2.stick_fig.png)
Figure S12. This figure depicts the distribution of mutations and mutation types across the TAF1A significant gene.
![](TAF1A.stick_fig.png)
Figure S13. This figure depicts the distribution of mutations and mutation types across the LIPF significant gene.
![](LIPF.stick_fig.png)
Figure S14. This figure depicts the distribution of mutations and mutation types across the ADAM30 significant gene.
![](ADAM30.stick_fig.png)
Figure S15. This figure depicts the distribution of mutations and mutation types across the NAP1L4 significant gene.
![](NAP1L4.stick_fig.png)
Figure S16. This figure depicts the distribution of mutations and mutation types across the DEFB115 significant gene.
![](DEFB115.stick_fig.png)
Figure S17. This figure depicts the distribution of mutations and mutation types across the PTEN significant gene.
![](PTEN.stick_fig.png)
Figure S18. This figure depicts the distribution of mutations and mutation types across the INTS8 significant gene.
![](INTS8.stick_fig.png)
Figure S19. This figure depicts the distribution of mutations and mutation types across the TBC1D3 significant gene.
![](TBC1D3.stick_fig.png)
Figure S20. This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.
![](TP53.stick_fig.png)
Figure S21. This figure depicts the distribution of mutations and mutation types across the DISP1 significant gene.
![](DISP1.stick_fig.png)
Figure S22. This figure depicts the distribution of mutations and mutation types across the STK31 significant gene.
![](STK31.stick_fig.png)
Figure S23. This figure depicts the distribution of mutations and mutation types across the PRC1 significant gene.
![](PRC1.stick_fig.png)
Figure S24. This figure depicts the distribution of mutations and mutation types across the CDC123 significant gene.
![](CDC123.stick_fig.png)
Figure S25. This figure depicts the distribution of mutations and mutation types across the IVL significant gene.
![](IVL.stick_fig.png)
Figure S26. This figure depicts the distribution of mutations and mutation types across the DPY19L4 significant gene.
![](DPY19L4.stick_fig.png)
Figure S27. This figure depicts the distribution of mutations and mutation types across the CLCC1 significant gene.
![](CLCC1.stick_fig.png)
Figure S28. This figure depicts the distribution of mutations and mutation types across the ZNF860 significant gene.
![](ZNF860.stick_fig.png)
Figure S29. This figure depicts the distribution of mutations and mutation types across the IDH1 significant gene.
![](IDH1.stick_fig.png)
Figure S30. This figure depicts the distribution of mutations and mutation types across the RPTN significant gene.
![](RPTN.stick_fig.png)
Figure S31. This figure depicts the distribution of mutations and mutation types across the PPP6C significant gene.
![](PPP6C.stick_fig.png)
Figure S32. This figure depicts the distribution of mutations and mutation types across the CECR6 significant gene.
![](CECR6.stick_fig.png)
Figure S33. This figure depicts the distribution of mutations and mutation types across the THADA significant gene.
![](THADA.stick_fig.png)
Figure S34. This figure depicts the distribution of mutations and mutation types across the PIK3CB significant gene.
![](PIK3CB.stick_fig.png)
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.