title: AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.
abstract: Arabidopsis thaliana Protein Interactome Database (AtPID) is an object database that integrates data from several bioinformatics prediction methods and manually collected information from the literature. It contains data relevant to protein-protein interaction, protein subcellular location, ortholog maps, domain attributes and gene regulation. The predicted protein interaction data were obtained from ortholog interactome, microarray profiles, GO annotation, and conserved domain and genome contexts. This database holds 28,062 protein-protein interaction pairs with 23,396 pairs generated from prediction methods. Among the rest 4666 pairs, 3866 pairs of them involving 1875 proteins were manually curated from the literature and 800 pairs were from enzyme complexes in KEGG. In addition, subcellular location information of 5562 proteins is available. AtPID was built via an intuitive query interface that provides easy access to the important features of proteins. Through the incorporation of both experimental and computational methods, AtPID is a rich source of information for system-level understanding of gene function and biological processes in A. thaliana. Public access to the AtPID database is available at http://atpid.biosino.org/.
authors.affiliation: College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Cui
authors.forename: Peng
authors.initials: P
authors.lastname: Li
authors.forename: Guang
authors.initials: G
authors.lastname: Li
authors.forename: Feng
authors.initials: F
authors.lastname: Xu
authors.forename: Chen
authors.initials: C
authors.lastname: Zhao
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Li
authors.forename: Zhongnan
authors.initials: Z
authors.lastname: Yang
authors.forename: Guang
authors.initials: G
authors.lastname: Wang
authors.forename: Qingbo
authors.initials: Q
authors.lastname: Yu
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
authors.forename: Tieliu
authors.initials: T
authors.lastname: Shi
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology; D016206:Databases, Bibliographic; D030562:Databases, Protein; D020407:Internet; D025941:Protein Interaction Mapping; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D029681:Arabidopsis Proteins