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

Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, China.

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/.

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The home page of AtPID.
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Figure 1: The home page of AtPID.

Mentions: All of the information in AtPID is derived from expert curation and deliberate computation. The process of creating a release AtPID database begins with extracting the published and other relevant information from various databases (Figure 1). Automated and manual quality assurance procedures are administered to verify data completeness and consistency. If necessary, material in the development database is revised and a new database version is generated.Figure 1.


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

Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T - Nucleic Acids Res. (2007)

The home page of AtPID.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238993&req=5

Figure 1: The home page of AtPID.
Mentions: All of the information in AtPID is derived from expert curation and deliberate computation. The process of creating a release AtPID database begins with extracting the published and other relevant information from various databases (Figure 1). Automated and manual quality assurance procedures are administered to verify data completeness and consistency. If necessary, material in the development database is revised and a new database version is generated.Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, China.

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/.

Show MeSH