Building and analyzing protein interactome networks by cross-species comparisons

Abstract

BackgroundA genomic catalogue of protein-protein interactions is a rich source of information, particularly for exploring the relationships between proteins. Numerous systems-wide and small-scale experiments have been conducted to identify interactions; however, our knowledge of all interactions for any one species is incomplete, and alternative means to expand these network maps is needed. We therefore took a comparative biology approach to predict protein-protein interactions across five species (human, mouse, fly, worm, and yeast) and developed InterologFinder for research biologists to easily navigate this data. We also developed a confidence score for interactions based on available experimental evidence and conservation across species.ResultsThe connectivity of the resultant networks was determined to have scale-free distribution, small-world properties, and increased local modularity, indicating that the added interactions do not disrupt our current understanding of protein network structures. We show examples of how these improved interactomes can be used to analyze a genome-scale dataset (RNAi screen) and to assign new function to proteins. Predicted interactions within this dataset were tested by co-immunoprecipitation, resulting in a high rate of validation, suggesting the high quality of networks produced.ConclusionsProtein-protein interactions were predicted in five species, based on orthology. An InteroScore, a score accounting for homology, number of orthologues with evidence of interactions, and number of unique observations of interactions, is given to each known and predicted interaction. Our website http://www.interologfinder.org provides research biologists intuitive access to this data.

An Evolutionarily Conserved Innate Immunity Protein Interaction Network

“…Such cross-species studies offer the opportunity to identify networks not easily identifiable in individual species datasets (73). Additionally, the use of multiple RNAi screens could overcome the reported high false-positive rate in mammalian RNAi screens due to off-target affects (74).…”

To include or not to include : Teachers’ social representations of inclusion of students with Asperger syndrome

“…A line is assigned between connected evocations. The net-work is displayed in a graph, which presents the spatially strongest co-occurrences between pairs of elements thus reflecting the most intensive relations between the phrases (Coronges et al, 2007;Wiles et al, 2010). The most important nodes (circles) are by nature the hubs of the network.…”

Analysis of Protein Interaction Networks to Prioritize Drug Targets of Neglected-Diseases Pathogens

“…They found that the homology transfers are only accurate at high levels of sequence identity, and it is more reliable for protein pairs from the same species than for two protein pairs from different organisms (Mika and Rost 2006). Likewise, Wiles et al, (2010) have developed a scoring schema to assess the confidence of interologs prediction. They have predicted protein interactions across five species (human, mouse, fly, worm, and yeast) based on available experimental evidence and conservation across species (Wiles et al, 2010).…”

“…Likewise, Wiles et al, (2010) have developed a scoring schema to assess the confidence of interologs prediction. They have predicted protein interactions across five species (human, mouse, fly, worm, and yeast) based on available experimental evidence and conservation across species (Wiles et al, 2010). Also, they developed the Interolog Finder (URL: http://www.interologfinder.org) to provide access to these data.…”