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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 transfor...
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Published in: | 中国科学:生命科学英文版 2015 (6), p.579-589 |
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Main Author: | |
Format: | Article |
Language: | English |
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Online Access: | Get full text |
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Summary: | 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. |
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ISSN: | 1674-7305 1869-1889 |