PIPs: human protein-protein interaction prediction database

Abstract

The PIPs database (http://www.compbio.dundee.ac.uk/www-pips) is a resource for studying protein-protein interactions in human. It contains predictions of >37,000 high probability interactions of which >34,000 are not reported in the interaction databases HPRD, BIND, DIP or OPHID. The interactions in PIPs were calculated by a Bayesian method that combines information from expression, orthology, domain co-occurrence, post-translational modifications and sub-cellular location. The predictions also take account of the topology of the predicted interaction network. The web interface to PIPs ranks predictions according to their likelihood of interaction broken down by the contribution from each information source and with easy access to the evidence that supports each prediction. Where data exists in OPHID, HPRD, DIP or BIND for a protein pair this is also reported in the output tables returned by a search. A network browser is included to allow convenient browsing of the interaction network for any protein in the database. The PIPs database provides a new resource on protein-protein interactions in human that is straightforward to browse, or can be exploited completely, for interaction network modelling.

Figure 1.

Interaction Summary for the protein IPI00016572 (SNRPG): this page shows the predicted interactors, ordered by the score in descending order from the most probable interactor. The name of the predicted interactor and a breakdown by predictive feature is also shown with links to retrieve the evidence for the predicted interaction.

Figure 2.

(a) Evidence of Interaction Summary page for the interaction between SNRPG and SNRPD3: Sections Gene Expression and Orthology provide details about the predictions based on expression and orthology for the interaction pair. (b) Sections Domains, Post-translational modification and Localization provide the information that was used by the combined module describing the co-occurrence of domains within the protein pair, post-translational modifications and localization of the proteins within the cell. (c) Section Transitive score provides a list of the common interactors with an integrated interaction score >0.025 for the expression, orthology and combined modules. These common interactors are considered by the Transitive module for calculating the likelihood of interaction between SNRPG and SNRPD3. In total, there are 236 predicted common interactors; the figure shows only the top six common interactors.

Figure 3.

Protein Summary for the protein SNRPG: information about the selected protein including a breakdown of the number of predicted interactions and the number of interactions within external databases. Links are also provided to obtain further details about the protein from the HPRD, RefSeq, Entrez and UniProt.

Figure 4.

Network view of the predicted interactors of SNRPG: Java application to view the local topology of the predicted PPI network. Left: network image of the predicted primary and secondary interactors of the protein SNRPG (blue). Right: network image of the predicted primary and secondary interactors of the protein SNRPG (blue), with all interactors that have only a single predicted interaction removed from the image.