Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape

Abstract

Summary: Protein–protein interaction detection methods are applied on a daily basis by molecular biologists worldwide. After generating a set of potential interactions, biologists face the problem of highlighting the ones that are novel and collecting evidence with respect to literature and annotation. This task can be as tedious as searching for every predicted interaction in several interaction data repositories, or manually screening the scientific literature. To facilitate the task of evidence mining and novelty assessment of protein–protein interactions, we have developed a Cytoscape plugin that automatically mines publication references, database references, interaction detection method descriptions and pathway annotation for a user-supplied network of interactions. The basis for the annotation is ConsensusPathDB—a meta-database that integrates numerous protein–protein, signaling, metabolic and gene regulatory interaction repositories for currently three species: Homo sapiens, Saccharomyces cerevisiae and Mus musculus.

Availability: The ConsensusPathDB plugin for Cytoscape (version 2.7.0 or later) can be installed within Cytoscape on a major operating system (Windows, Mac OS, Unix/Linux) with Sun Java 1.5 or later installed through Cytoscape's Plugin manager (category ‘Network and Attribute I/O’). The plugin is freely available for download on the ConsensusPathDB web site ( http://cpdb.molgen.mpg.de).

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact: kamburov@ 123456molgen.mpg.de