PathPPh an integrated dataset of human pathways and protein-protein interactions

Integration of pathway and protein-protein interaction （PPI） data can provide more information that could lead to new biologi- cal insights. PPIs are usually represented by a simple binary model, whereas pathways are represented by more complicated models. We developed a series of rules for transforming protein interactions from pathway to binary model, and the protein in- teractions from seven pathway databases, including PID, BioCarta, Reactome, NetPath, INOH, SPIKE and KEGG, were transformed based on these rules. These pathway-derived binary protein interactions were integrated with PPIs from other five PPI databases including HPRD, IntAct, BioGRID, MINT and DIP, to develop integrated dataset （named PathPPI）. More de- tailed interaction type and modification information on protein interactions can be preserved in PathPPI than other existing da- tasets. Comparison analysis results indicate that most of the interaction overlaps values （OAB） among these pathway databases were less than 5%, and these databases must be used conjunctively. The PathPPI data was provided at http：//proteomeview. hupo.org.cn/PathPPI/PathPPI.html.