Ulysses - an application for the projection of molecular interactions across species

Abstract

We developed Ulysses as a user-oriented system that uses a process called Interolog Analysis for the parallel analysis and display of protein interactions detected in various species. Ulysses was designed to perform such Interolog Analysis by the projection of model organism interaction data onto homologous human proteins, and thus serves as an accelerator for the analysis of uncharacterized human proteins. The relevance of projections was assessed and validated against published reference collections. All source code is freely available, and the Ulysses system can be accessed via a web interface http://www.cisreg.ca/ulysses.

Figure 1

Interologs mapping of conserved protein networks across multiple species (each plane corresponds to a species). Orthologous proteins are defined and protein interactions identified in each model organism. Virtual human protein networks are generated by projecting the observed interactions across all planes onto homologous human genes. HID, HomoloGene identifier.

Figure 2

Distribution of RefSeq/HomoloGene proteins across HPRD cellular localization bins. Protein interactors from BIND were mapped to HomoloGene to delineate homologs across the four organisms, and to associate each protein to a sub-cellular compartment.

Figure 3

Screenshot of the Ulysses interface. The user-specified protein is shown in blue, and interacting proteins are displayed in green. Proteins with greater than three interactions (the 'starburst' threshold) are marked with a magenta-colored cross. The colors and 'starburst' threshold are user-adjustable parameters. Species-specific interactions are displayed in the panel of windows on the left. In this figure, the central graph displays a composite image identifying each node with its HomoloGene identifier. By selecting a species window, the species-specific interactions will be displayed along with the identity of the individual protein interactors.