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Nucleic Acids Research Advance Access published online on October 25, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm844
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-com

Database Issue

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

Jian Cui1,4, Peng Li1,4, Guang Li1,4, Feng Xu1,4, Chen Zhao1,4, Yuhua Li1,4,*, Zhongnan Yang5, Guang Wang5, Qingbo Yu5, Yixue Li3,* and Tieliu Shi2,3,4,6,*

1College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, 2Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, 3Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, 4Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, 5College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and 6Bioinformatics Center, Shanghai University, Shanghai 200444, China

* To whom correspondence should be addressed. Tel: +86 21 54922980; Fax: +86 21 5492 0143; Email: tlshi{at}sibs.ac.cn

Correspondence may also be addressed to Yuhua Li. Tel: +86 451 8219 1737; Fax: +86 451 8219 1733; E-mail: lyhshen{at}mail.hl.com

Correspondence may also be addressed to Yixue Li. Tel: +86 21 54920089; Fax: +86 21 5492 0143; E-mail: yxli{at}sibs.ac.cn

Received August 15, 2007. Revised September 25, 2007. Accepted September 25, 2007.

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/.

The authors wish it to be known that, in their opinion, the first five authors should be regarded as joint First Authors


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