title: pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis.
abstract: Molecular pathway data are essential in current computational and systems biology research. While there are many primary and integrated pathway databases, several challenges remain, including low proteome coverage (57%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e. 'pathway orphans'. In order to address all these challenges, we developed pathDIP, which integrates data from 20 source pathway databases, 'core pathways', with physical protein-protein interactions to predict biologically relevant protein-pathway associations, referred to as 'extended pathways'. Cross-validation determined 71% recovery rate of our predictions. Data integration and predictions increase coverage of pathway annotations for protein-coding genes to 86%, and provide novel annotations for 5732 pathway orphans. PathDIP (http://ophid.utoronto.ca/pathdip) annotates 17 070 protein-coding genes with 4678 pathways, and provides multiple query, analysis and output options.
authors.affiliation: Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
authors.forename: Sara
authors.initials: S
authors.lastname: Rahmati
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, 101 College Street, TMDT, Room 11-314, Toronto, ON M5G 1L7, Canada.
authors.forename: Mark
authors.initials: M
authors.lastname: Abovsky
authors.affiliation: Princess Margaret Cancer Centre, University Health Network, 101 College Street, TMDT, Room 11-314, Toronto, ON M5G 1L7, Canada.
authors.forename: Chiara
authors.initials: C
authors.lastname: Pastrello
authors.affiliation: Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada juris@ai.utoronto.ca.|Princess Margaret Cancer Centre, University Health Network, 101 College Street, TMDT, Room 11-314, Toronto, ON M5G 1L7, Canada.|Department of Computer Science, University of Toronto, Toronto, ON, Canada.|Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
authors.forename: Igor
authors.initials: I
authors.lastname: Jurisica
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D006801:Humans; D025941:Protein Interaction Mapping / Q000379:methods*; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology / Q000379:methods