PAIR: the predicted Arabidopsis interactome resource

Abstract

The predicted Arabidopsis interactome resource (PAIR, http://www.cls.zju.edu.cn/pair/), comprised of 5990 experimentally reported molecular interactions in Arabidopsis thaliana together with 145,494 predicted interactions, is currently the most comprehensive data set of the Arabidopsis interactome with high reliability. PAIR predicts interactions by a fine-tuned support vector machine model that integrates indirect evidences for interaction, such as gene co-expressions, domain interactions, shared GO annotations, co-localizations, phylogenetic profile similarities and homologous interactions in other organisms (interologs). These predictions were expected to cover 24% of the entire Arabidopsis interactome, and their reliability was estimated to be 44%. Two independent example data sets were used to rigorously validate the prediction accuracy. PAIR features a user-friendly query interface, providing rich annotation on the relationships between two proteins. A graphical interaction network browser has also been integrated into the PAIR web interface to facilitate mining of specific pathways.

Figure 1.

The Interaction Information page. (a) Summary of the interaction and its component proteins. (b) Indirect evidences supporting this interaction, including gene co-expressions, domain interactions, shared GO annotations, co-localizations, phylogenetic profile similarities and homologous interactions in other organisms (interologs). Co-publication (two interacting proteins appearing in the same articles) information was not used for interaction prediction, but is also presented here to facilitate literature mining. (c) The confidence scores for this interaction. The SVM score is the overall confidence score.

Figure 2.

The graphical interaction network browser showing a network of interactions between proteins in the sulfur metabolism pathway. Several core sulfur metabolism proteins (triangle nodes) are used to search PAIR for interactions between them. This network graph is then expanded to include additional interactions. Double click on a node will bring up a window showing all interactions involving this protein and allow selection of some interactions to be added into this graph. Newly added proteins are shown as circle nodes. Nodes are colored according to their protein functions, as detailed in the Help/FAQ page. Experimentally reported interactions (edges) are in red. Predicted interactions that are homologous to known interactions in other organisms are in blue. Other predicted interactions are in grey.