Path PPI: an integrated dataset of human pathways and protein-protein interactions  

作　　者：TANG HaiLin ZHONG Fan LIU Wei HE FuChu XIE HongWei 

机构地区：[1]College of Mechanical & Electronic Engineering and Automatization, National University of Defense Technology [2]Institutes of Biomedical Sciences, Fudan University [3]State Key Laboratory of Proteomics,Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

出　　处：《Science China(Life Sciences)》2015年第6期579-589,共11页中国科学（生命科学英文版）

基　　金：supported by the National High Technology Research and Development Program of China(2012AA020201);National Basic Research Program of China(2013CB910802,2010CB912700);International Science&Technology Cooperation Program of China(2014DFB30020);National Natural Science Foundation of China(31000379,31000587,31000591);Chinese State Key Project Specialized for Infectious Diseases(2012ZX10002012-006)

摘　　要：Integration of pathway and protein-protein interaction(PPI) data can provide more information that could lead to new biological 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 interactions from seven pathway databases, including PID, Bio Carta, Reactome, Net Path, 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, Int Act, Bio GRID, MINT and DIP, to develop integrated dataset(named Path PPI). More detailed interaction type and modification information on protein interactions can be preserved in Path PPI than other existing datasets. 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 Path PPI data was provided at http://proteomeview. hupo.org.cn/Path PPI/Path PPI.html.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.

关 键 词：databases integration PATHWAY protein-protein interaction PROTEOMICS 

分 类 号：Q811.4[生物学—生物工程]