This Cytoscape plugin enables the simultaneous visualization of interaction networks in multiple organisms, using information aggregated in DAnCER and iRefWeb/iRefIndex. As PPI networks are complex in even simple organisms like yeast, a key feature is the ability to quickly focus in on a protein of interest, isolate its homologues in the other network, and hide all proteins that do not interact with the selected protein or its homologues.
In Figure 1 (top right) , portions of the human (left network) and yeast (right network) binary protein-protein interaction networks are displayed, using information collected in iRefWeb. Nodes (proteins) encoded by orthologous genes are color coded according to the legend displayed on the left side of the figure, and those involved in chromatin remodeling have a white border. OrthoNets provides various information about the proteins and interactions - including domain architectures (bottom of figure 1), protein and gene aliases, pubmed identifiers of the publications supporting the interactions, and the experiment type used to detect the interaction. Here the view is focused on the RNA polymerase enzyme LEO1 - so that only the LEO1 node and its recorded interaction partners are displayed.
Experimental data can be overlaid on these networks: in Figure 2 (bottom right), data from a recently published affinity purfication study targetting 20 human proteins involved in chromatin remodeling* has been overlayed on the human network of figure 1. Edge color coding allows for the identification of confirmed and novel interactions at a glance: green edges are those recorded in iRefWeb, purple are novel predicted interactions, and cyan indicate those present in both iRefWeb and the experimental data. Also shown here are two disease-gene associations: triangular nodes correspond to genes linked to ovarian cancer, and square nodes show those linked to parathyroid carcinomas.
Publication:
Yanqi Hao, Anna Merkovitch, James Vlasblom, Shuye Pu, Andrei L. Turinsky, Denitza Roudeva, Brian Turner, Jack Greenblatt, Shoshana J. Wodak.
OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.
Submitted, Dec. 2010.
Figure 1
Figure 2
