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PMID: 17962307 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.

Nucleic acids research ·Vol. 36 ·No. Database issue ·2008-01-00 ·Pages D999-1008

Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T

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/.

MeSH Terms
Arabidopsis/genetics,metabolism Arabidopsis Proteins/genetics,metabolism Computational Biology Databases, Bibliographic Databases, Protein Internet Protein Interaction Mapping Systems Integration User-Computer Interface
Chemicals
Arabidopsis Proteins
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Cui Jian
College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, China.
Li Peng
Li Guang
Xu Feng
Zhao Chen
Li Yuhua
Yang Zhongnan
Wang Guang
Yu Qingbo
Li Yixue
Shi Tieliu
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkm844
Published
2008-01-00
Epub
2007-00-25
Pages
D999-1008
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2238993
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkm844 PMC Full Text View journal details
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