CATS

Description

Gene signature refers to a set of genes whose expression characterizes the activity of a specific biological process or a cell state, e.g., EMT, proliferation, stemness, etc. Gene signatures are widely used to infer the state of a biological system based on transcriptomic data. However, the available gene signatures lack tissue or cellular context. Here, we developed a tool - CATS (Cancer Specific Transcriptomic Signature) which, given a hallmark (or any other) context-agnostic reference geneset, and a specific cancer context, aims to identify a partially overlapping geneset that is likely to represent the activity of the hallmark process in the specific context. Such a contextualization, or mapping, is based on three premises: (1) preferential connectivity to the reference geneset in the PPI, (2) preferential co-expression with the reference geneset in the specific context, and additionally (3) differential upregulation of the gene in the particular context.

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Topics

People

• Gulden Olgun author maintainer
• Sridhar Hannenhalli contributor
• Mahfuza Sharmin contributor