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: THCA-TP
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:THCA-TP.final_analysis_set.maf
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Significantly mutated genes (q ≤ 0.1): 29
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: 29. 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 |
---|---|---|---|---|---|---|---|
BRAF | 84303 | 0 | 1 | 183 | 0 | 0 | 0 |
NRAS | 23790 | 0 | 0 | 26 | 0 | 0 | 0 |
HRAS | 22597 | 0 | 0 | 12 | 0 | 0 | 0 |
EMG1 | 30474 | 0 | 0 | 6 | 6 | 0 | 0 |
TG | 318775 | 0 | 3 | 16 | 10 | 6.8e-126 | 2.6e-122 |
PRB2 | 22808 | 0 | 1 | 6 | 3 | 1.9e-66 | 5.9e-63 |
EIF1AX | 18088 | 0 | 0 | 6 | 1 | 3.6e-62 | 9.6e-59 |
PTTG1IP | 17442 | 0 | 0 | 4 | 4 | 1.4e-48 | 3.2e-45 |
MUC7 | 33157 | 0 | 1 | 5 | 1 | 1.1e-41 | 2.3e-38 |
ZNF845 | 77648 | 0 | 0 | 6 | 0 | 1e-34 | 1.9e-31 |
RPTN | 83868 | 0 | 0 | 8 | 7 | 5.6e-31 | 9.5e-28 |
PPM1D | 56848 | 0 | 0 | 5 | 4 | 1.3e-24 | 2e-21 |
TROAP | 68476 | 0 | 0 | 5 | 0 | 1.4e-20 | 2.1e-17 |
PRG4 | 148455 | 0 | 1 | 7 | 3 | 2.7e-17 | 3.6e-14 |
FAM47C | 90354 | 0 | 3 | 5 | 0 | 9.2e-16 | 1.1e-12 |
ARID1B | 175824 | 0 | 0 | 6 | 2 | 9.7e-16 | 1.1e-12 |
ZNF799 | 73433 | 0 | 1 | 5 | 0 | 1.2e-15 | 1.3e-12 |
DNMT3A | 91620 | 0 | 0 | 5 | 4 | 1.5e-15 | 1.6e-12 |
GPR44 | 14759 | 0 | 0 | 4 | 4 | 2.6e-15 | 2.6e-12 |
R3HDM2 | 59828 | 0 | 0 | 4 | 4 | 9.8e-15 | 9.2e-12 |
CCDC15 | 86358 | 0 | 1 | 5 | 0 | 3.3e-13 | 3e-10 |
ZNF780A | 77369 | 0 | 1 | 4 | 0 | 4.1e-11 | 3.5e-08 |
MLL3 | 523557 | 0 | 0 | 8 | 4 | 4.7e-11 | 3.9e-08 |
ZFHX3 | 379960 | 0 | 2 | 10 | 4 | 5e-11 | 3.9e-08 |
DICER1 | 232461 | 0 | 0 | 5 | 2 | 1.4e-06 | 0.0011 |
COL5A3 | 116788 | 0 | 0 | 6 | 2 | 1.9e-06 | 0.0014 |
ZNF208 | 160969 | 1 | 0 | 4 | 0 | 4.4e-06 | 0.003 |
CD209 | 45543 | 0 | 1 | 4 | 0 | 0.00014 | 0.093 |
CHD2 | 219627 | 0 | 0 | 4 | 4 | 0.00015 | 0.098 |
ANK1 | 210075 | 0 | 0 | 4 | 0 | 0.00019 | 0.12 |
ATM | 388272 | 0 | 0 | 5 | 2 | 0.00032 | 0.19 |
PKHD1L1 | 454474 | 0 | 0 | 5 | 4 | 0.001 | 0.6 |
ACRC | 65819 | 0 | 0 | 4 | 0 | 0.0021 | 1 |
DNAH2 | 521223 | 0 | 0 | 5 | 0 | 0.0025 | 1 |
PRDM9 | 98838 | 0 | 3 | 6 | 1 | 0.0026 | 1 |
Figure S1. This figure depicts the distribution of mutations and mutation types across the BRAF significant gene.
![](BRAF.stick_fig.png)
Figure S2. This figure depicts the distribution of mutations and mutation types across the NRAS significant gene.
![](NRAS.stick_fig.png)
Figure S3. This figure depicts the distribution of mutations and mutation types across the HRAS significant gene.
![](HRAS.stick_fig.png)
Figure S4. This figure depicts the distribution of mutations and mutation types across the EMG1 significant gene.
![](EMG1.stick_fig.png)
Figure S5. This figure depicts the distribution of mutations and mutation types across the TG significant gene.
![](TG.stick_fig.png)
Figure S6. This figure depicts the distribution of mutations and mutation types across the EIF1AX significant gene.
![](EIF1AX.stick_fig.png)
Figure S7. This figure depicts the distribution of mutations and mutation types across the PTTG1IP significant gene.
![](PTTG1IP.stick_fig.png)
Figure S8. This figure depicts the distribution of mutations and mutation types across the MUC7 significant gene.
![](MUC7.stick_fig.png)
Figure S9. This figure depicts the distribution of mutations and mutation types across the ZNF845 significant gene.
![](ZNF845.stick_fig.png)
Figure S10. This figure depicts the distribution of mutations and mutation types across the RPTN significant gene.
![](RPTN.stick_fig.png)
Figure S11. This figure depicts the distribution of mutations and mutation types across the PPM1D significant gene.
![](PPM1D.stick_fig.png)
Figure S12. This figure depicts the distribution of mutations and mutation types across the TROAP significant gene.
![](TROAP.stick_fig.png)
Figure S13. This figure depicts the distribution of mutations and mutation types across the PRG4 significant gene.
![](PRG4.stick_fig.png)
Figure S14. This figure depicts the distribution of mutations and mutation types across the FAM47C significant gene.
![](FAM47C.stick_fig.png)
Figure S15. This figure depicts the distribution of mutations and mutation types across the ARID1B significant gene.
![](ARID1B.stick_fig.png)
Figure S16. This figure depicts the distribution of mutations and mutation types across the ZNF799 significant gene.
![](ZNF799.stick_fig.png)
Figure S17. This figure depicts the distribution of mutations and mutation types across the DNMT3A significant gene.
![](DNMT3A.stick_fig.png)
Figure S18. This figure depicts the distribution of mutations and mutation types across the GPR44 significant gene.
![](GPR44.stick_fig.png)
Figure S19. This figure depicts the distribution of mutations and mutation types across the R3HDM2 significant gene.
![](R3HDM2.stick_fig.png)
Figure S20. This figure depicts the distribution of mutations and mutation types across the CCDC15 significant gene.
![](CCDC15.stick_fig.png)
Figure S21. This figure depicts the distribution of mutations and mutation types across the ZNF780A significant gene.
![](ZNF780A.stick_fig.png)
Figure S22. This figure depicts the distribution of mutations and mutation types across the MLL3 significant gene.
![](MLL3.stick_fig.png)
Figure S23. This figure depicts the distribution of mutations and mutation types across the ZFHX3 significant gene.
![](ZFHX3.stick_fig.png)
Figure S24. This figure depicts the distribution of mutations and mutation types across the DICER1 significant gene.
![](DICER1.stick_fig.png)
Figure S25. This figure depicts the distribution of mutations and mutation types across the COL5A3 significant gene.
![](COL5A3.stick_fig.png)
Figure S26. This figure depicts the distribution of mutations and mutation types across the CD209 significant gene.
![](CD209.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. ##REF##116
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.