PepPSy has been developed as a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein and curators to quickly look at available transcriptomics/proteomics data for a list of proteins. PepPSy currently embeds eight filtration criteria and seven modules dedicated to the filtration of protein candidates and their ranking according to gene expression-based information. By enabling users to query in a highly flexible manner, this tool should facilitate the arduous task of prioritizing gene products for dedicated experimental studies or functional annotation.
PepPSy is developed in collaboration between the Frédéric Chalmel's group (Inserm U1085-Irset, Rennes, France) and the GenOuest bioinformatics facility (Rennes, France).
This project benefited of financial help from la Fondation pour la Recherche Médicale (FRM) and le Fonds européen de développement régional (FEDER).
Analysis of the human genome led to the identification of approximately 20,000 protein-coding genes. The precise role of each of these protein-coding genes in health and disease is still far from being completely understood. According to the neXtProt knowledegebase (Gaudet et al, 2015), there are still more than 2500 so-called « missing » proteins for which no validation by mass-spectrometry or antibody-based techniques is available (Omenn et al, 2015), and more than 2000 proteins with no predicted or experimentally validated function. Integrating large “omics” datasets can provide clues to investigators by suggesting where to look for a missing protein, or a possible involvement of an uncharacterized protein in a biological process.