Ontological visualization of protein-protein interactions

Abstract

Background: Cellular processes require the interaction of many proteins across several cellular compartments. Determining the collective network of such interactions is an important aspect of understanding the role and regulation of individual proteins. The Gene Ontology (GO) is used by model organism databases and other bioinformatics resources to provide functional annotation of proteins. The annotation process provides a mechanism to document the binding of one protein with another. We have constructed protein interaction networks for mouse proteins utilizing the information encoded in the GO annotations. The work reported here presents a methodology for integrating and visualizing information on protein-protein interactions.

Results: GO annotation at Mouse Genome Informatics (MGI) captures 1318 curated, documented interactions. These include 129 binary interactions and 125 interaction involving three or more gene products. Three networks involve over 30 partners, the largest involving 109 proteins. Several tools are available at MGI to visualize and analyze these data.

Conclusions: Curators at the MGI database annotate protein-protein interaction data from experimental reports from the literature. Integration of these data with the other types of data curated at MGI places protein binding data into the larger context of mouse biology and facilitates the generation of new biological hypotheses based on physical interactions among gene products.

Figure 1

GO annotations for At and Lnk as displayed at MGI. The annotatons to GO:0005515, protein binding, are marked. The circled SPTR_ID points to the MGI marker that it is associated with. The two annotations share the same reference.

Figure 2

Construction of a simple protein interaction network using GO annotations to protein binding.

Figure 3

Murine protein-protein interaction catalog as documented by GO annotation to GO:0005515 protein binding.

Figure 4

Selected interaction maps from Figure 3.

Figure 5

Interaction network maps showing 109 (A), 40 (B), and 31 (C) interacting proteins.

Figure 6

GO_Slim binning, displaying the faction of the total number of genes of either the data set or all genes in MGI falling into the indicated bins. Panel A, process binning for the 109 member set. Panels B and C, process and component for the 40 member set. Panel C, process binning for the 31 member set.