Genes (including miRNAs) can be individually queried by Gene Symbol here. The available data included:

1. A summary statement of the significance of copy number alterations affecting that gene or transcript.
2. For amplifications and deletions separately, a table representing the results of GISTIC (www.broadinstitute.org/cancer/pub/GISTIC) analyses pertaining to that gene across the entire dataset and within cancer types that are well-represented in the dataset. These results include:
   1. Whether the gene falls within a peak region of alteration. GISTIC analysis defines the peak region as the region most likely to contain a target of copy number alteration.
   2. The significance of copy number alterations affecting that gene (FDR q-value). This q-value reflects the likelihood that the gene only suffers copy number alterations at the background rate across the entire genome. Low q-values are increasingly suggestive that copy number alterations at that locus are enriched by selective pressures.
   3. Frequency of alteration, including overall frequency, frequency of focal alterations (alterations covering less than half a chromosome arm), and high-level alterations (copy number change greater than 1 copy).
3. Clicking on the chromosome region links displayed on the analyses pages will launch the Integrative Genomics Viewer (IGV) on the data for that region. Detailed information on using IGV is available at http://www.broadinstitute.org/igv.

Explore data by gene now

Cancer types can be individually queried here. The available data include:

1. A summary statement of the number of specimens analyzed.
2. For amplifications and deletions separately, a table representing the results of GISTIC (www.broadinstitute.org/cancer/pub/GISTIC) analyses pertaining to that cancer type. The significantly aberrant peak regions of the genome are listed, with the following information:
   1. The boundaries of the peak region, which are expected to contain the target gene in 95% of cases. It is possible that some CNAs have more than one target, in which case some targets may be outside the confidence region.
   2. The number of genes within the peak region. Mousing over the number provides a list of those genes.
   3. The significance of copy number alterations affecting this peak region, after removing copy-number alterations associated with other peaks on the same chromosome ("Residual q-value"). This q-value reflects the likelihood that the peak region only suffers copy number alterations at the background rate across the entire genome. Low q-values are increasingly suggestive that copy number alterations at this locus are enriched by selective pressure. The q-values for genes within the peak (seen in the "By gene" analysis) are not modified to take into account other peaks on the chromosome, and therefore may differ from the residual q-value presented here.
   4. Frequency of alteration, including overall frequency, frequency of focal alterations (alterations covering less than half a chromosome arm), and high-level alterations (copy number change greater than 1 copy).
3. Clicking on the chromosome region links displayed on the analyses pages will launch the Integrative Genomics Viewer (IGV) on the data for that region. Detailed information on using IGV is available at http://www.broadinstitute.org/igv.

Explore data by cancer type now