PINTA: a web server for network-based gene prioritization from expression data

http://nar.oxfordjournals.org/content/39/suppl_2/W334.full

PINTA (available at http://www.esat.kuleuven.be/pinta/; this web site is free and open to all users and there is no login requirement) is a web resource for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein–protein interaction network. Our strategy is meant for biological and medical researchers aiming at identifying novel disease genes using disease specific expression data. PINTA supports both candidate gene prioritization (starting from a user defined set of candidate genes) as well as genome-wide gene prioritization and is available for five species (human, mouse, rat, worm and yeast). As input data, PINTA only requires disease specific expression data, whereas various platforms (e.g. Affymetrix) are supported. As a result, PINTA computes a gene ranking and presents the results as a table that can easily be browsed and downloaded by the user.                

Our method relies on the assumption that strong candidate genes tend to be surrounded by many differentially expressed genes in a genome-wide protein–protein interaction network. This allows the detection of a strong signal for a candidate even if its own differential expression value is too small to be detected by a standard analysis, as long as its interacting partners are highly differentially expressed.