LUSC/00: Detected event calls for genes

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, 3920, and 5085 respectively

Summarization of calls

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 Yes No
SLIT3 Yes No No
ADAM22 Yes Yes No
CNBD1 Yes No No
VWF Yes No No
LRP1B Yes Yes No
COL22A1 Yes Yes No
SVEP1 Yes No No
SPAG17 Yes No Yes
CSMD1 Yes No No
PAPPA2 Yes No No
CSMD3 Yes Yes No
MYH13 Yes No No
C6 Yes Yes No
RYR3 Yes No Yes
LRP2 Yes Yes No
SCN1A Yes Yes No
PCDH15 Yes No No
RYR2 Yes No No
Methods & Data

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