LUSC/00: Detected event calls for genes

Overview

Introduction

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.

Summary

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

Results

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

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