copa

copa identifies genes involved in recurrent gene fusions and chromosomal translocations in cancer by analyzing microarray gene expression data.

Key Features:

• Robust statistical approach: Applies robust centering and scaling to microarray gene expression data to identify expression outliers, in contrast to standard tests such as the t-test.
• Detection of mutually exclusive outliers: Searches for pairs of genes with mutually exclusive outlier expression profiles across samples to indicate recurrent fusion events or translocations.
• R implementation: Implemented as the "copa" R package for application to gene expression datasets.

Scientific Applications:

• Oncological research: Detection of recurrent gene fusions and chromosomal translocations across cancer samples to inform studies of cancer etiology and progression.
• Mechanistic and therapeutic insight: Identification of genes involved in recurrent translocations to elucidate molecular mechanisms and support discovery of targeted therapeutic strategies.

Methodology:

Performs robust centering and scaling of microarray gene expression to identify outlier samples, searches for mutually exclusive outlier pairs of genes across samples, and is implemented in R as the "copa" package.