The same TCGA sample is profiled to detect the copy number variations and mutation of genes. This pipeline tries to summarize the mutation and copy number calls by MutSig and GISTIC.
This page contains the detected genomic event calls for each gene. Genes marked with a genomic event are observed have the event occurs accross samples with a frequency over a set of thresholds. Number of genes that are mutated, amplified, and deleted are 18865, 216, and 687 respectively
Events called by different analyses are summarized in a gene by event table format. Table 1 shows the top 20 rows of the table
Table 1. Get Full Table Summary of mutation and copy number alteration calls made by MutSig and GISTIC for genes (defined as Hybridization.REF)
Hybridization.REF | Mutation | Amplification | Deletion |
USH2A | Yes | No | No |
ADAMTS12 | Yes | No | No |
SLIT3 | Yes | No | No |
FRAS1 | Yes | No | No |
LRP1B | Yes | No | No |
PTPRD | Yes | No | Yes |
SVEP1 | Yes | No | No |
GPR112 | Yes | No | No |
CSMD1 | Yes | No | No |
NOTCH4 | Yes | No | No |
ABCB5 | Yes | No | No |
CSMD3 | Yes | No | No |
LAMA2 | Yes | No | No |
PAPPA2 | Yes | No | No |
RYR3 | Yes | No | Yes |
KEAP1 | Yes | No | No |
RYR2 | Yes | No | No |
MUC16 | Yes | No | No |
TTN | Yes | No | No |
PCDH15 | Yes | No | No |
Input files include:
-
mutsig_sig_genes.txt : file generated by the MutSig pipeline that contains names of genes that are significantly mutated
-
Amp_genes.txt: file generated by the GISITIC2 pipeline that contains genes in GISTIC peaks of gains
-
Del_genes.txt: file generated by the GISTIC2 pipeline that contains genes in GISTIC peaks of losses