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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: 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.

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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Related in: MedlinePlus

AtPID interface of the (Network Display) window for the queried protein, HAP3. In the (Network Display) window, we can view the interaction network involved with queried protein(s) and the neighbor component(s) intuitively. (Text Format Output) can export the interaction pair information for further analysis.
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Figure 4: AtPID interface of the (Network Display) window for the queried protein, HAP3. In the (Network Display) window, we can view the interaction network involved with queried protein(s) and the neighbor component(s) intuitively. (Text Format Output) can export the interaction pair information for further analysis.

Mentions: ‘Network Display’ above the information table provides the link to a new window that displays the interaction network about HAP3A (Figure 4). In the ‘Network Display’ page, the query protein is represented as a triangle; the functional Partners of the queried protein are represented by a circle, derived from the first level displayed in the PPI network that directly linked to the query protein. The associated functional partners of the queried protein are shown as squares, derived from the second level in the network. A red node represents a protein with known function (i.e. annotated), whereas a gray node represents an unknown functional protein (i.e. without annotation). The line between each protein indicates the functional relationship; a red line infers the interaction from text mining, and a blue line indicates the predictive function relationship. By holding the cursor over each protein, the related annotation for the protein is displayed and allows the user to navigate the network and easily check a proteins’ relationship. ‘Text Format Output’ will export the interaction pair information in text format.Figure 4.


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)

AtPID interface of the (Network Display) window for the queried protein, HAP3. In the (Network Display) window, we can view the interaction network involved with queried protein(s) and the neighbor component(s) intuitively. (Text Format Output) can export the interaction pair information for further analysis.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: AtPID interface of the (Network Display) window for the queried protein, HAP3. In the (Network Display) window, we can view the interaction network involved with queried protein(s) and the neighbor component(s) intuitively. (Text Format Output) can export the interaction pair information for further analysis.
Mentions: ‘Network Display’ above the information table provides the link to a new window that displays the interaction network about HAP3A (Figure 4). In the ‘Network Display’ page, the query protein is represented as a triangle; the functional Partners of the queried protein are represented by a circle, derived from the first level displayed in the PPI network that directly linked to the query protein. The associated functional partners of the queried protein are shown as squares, derived from the second level in the network. A red node represents a protein with known function (i.e. annotated), whereas a gray node represents an unknown functional protein (i.e. without annotation). The line between each protein indicates the functional relationship; a red line infers the interaction from text mining, and a blue line indicates the predictive function relationship. By holding the cursor over each protein, the related annotation for the protein is displayed and allows the user to navigate the network and easily check a proteins’ relationship. ‘Text Format Output’ will export the interaction pair information in text format.Figure 4.

Bottom Line: 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.

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
Related in: MedlinePlus