GISTIC identifies genomic regions that are significantly gained or

lost across a set of tumors. The pipeline first filters out normal

samples from the segmented copy-number data by inspecting the TCGA

There were 20 tumor samples used in this analysis:  19 significant arm-level results, 4 significant focal amplifications, and 3 significant focal deletions were found.

Q value (bottom). The green line represents the significance

This is the comprehensive list of <strong>amplified</strong> genes in the wide peak for 14q13.3.

Genes in bold are cancer genes as defined by  <a href="http://www.sanger.ac.uk/genetics/CGP/Census/">The Sanger Institute: Cancer Gene Census</a>

This is the comprehensive list of <strong>amplified</strong> genes in the wide peak for 11q13.3.

This is the comprehensive list of <strong>amplified</strong> genes in the wide peak for 1p34.2.

This is the comprehensive list of <strong>amplified</strong> genes in the wide peak for 8q21.13.

Amplifications Table - 4 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

This is the comprehensive list of <strong>deleted</strong> genes in the wide peak for 9p21.3.

This is the comprehensive list of <strong>deleted</strong> genes in the wide peak for 21p11.2.

This is the comprehensive list of <strong>deleted</strong> genes in the wide peak for 13q11.

Deletions Table - 3 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Arm-level significance table - 19 significant results found. The significance cutoff is at Q value=0.25.

Segmentation File: The segmentation file contains the segmented

data for all the samples identified by GLAD, CBS, or some other

segmentation algorithm.  (See GLAD file format in the Genepattern

file formats documentation.)  It is a six column, tab-delimited