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/.

Figure 1.

The home page of AtPID.

Figure 2.

An overview of querying flow.

Figure 3.

The AtPID interface of PPI Simple Search Results for the queried protein, HAP3A. There are generally three tables: (1) protein attributes with gene model descriptions and PPI summary, showing how many protein pairs can be predicted and the inferred interactions overlapped with GSP. (2) The second table represents interactants of the queried protein, HAP3A. Users can view what the experimental evidence is to support this consequence and link to corresponding literature(s). (3) The third table represents potential interactants of the queried protein, HAP3A, by Naïve Bays integration across the seven approaches. Each approach is graphically represented by circles. When the cursor is over a circle, it will display the corresponding score (LR) for the method.

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.

Figure 5.

Domain attributes of one interactant of the queried protein, HAP3A.