Recipe: Identify biological functions for genes in copy number variation (CNV) regions
6 videos • 609 views • by GenomeSpace This recipe provides an outline of one method to identify biological functions for genes lying in copy number variation (CNV) regions. Given a set of CNV regions that are significantly amplified or deleted in a cancer cell line, the goal is to infer which biological functions (for example, Gene Ontology biological processes) are overrepresented in the set of reference genes that overlap with the CNV regions. In particular, this Recipe makes use of several Galaxy modules to find the overlap between CNV regions and reference genes, then uses MSigDB to identify biological functions of the overlapped genes. Finally, the example datasets are retrieved using the UCSC Table Browser.