Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS

BMC Genomics

Software

Eli Rodgers-Melnick¹  Stephen P DiFazio¹  Mark Culp² 

[1] Department of Biology, West Virginia University, 26506, Morgantown, West Virginia, USA;Department of Statistics, West Virginia University, 26506, Morgantown, West Virginia, USA;

关键词: Random Forest;    Protein Pair;    Whole Genome Duplication;    Domain Pair;    Alternative Classifier;   

DOI  :  10.1186/1471-2164-14-608

 received in 2012-12-05, accepted in 2013-09-04,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe large-scale identification of physical protein-protein interactions (PPIs) is an important step toward understanding how biological networks evolve and generate emergent phenotypes. However, experimental identification of PPIs is a laborious and error-prone process, and current methods of PPI prediction tend to be highly conservative or require large amounts of functional data that may not be available for newly-sequenced organisms.ResultsIn this study we demonstrate a random-forest based technique, ENTS, for the computational prediction of protein-protein interactions based only on primary sequence data. Our approach is able to efficiently predict interactions on a whole-genome scale for any eukaryotic organism, using pairwise combinations of conserved domains and predicted subcellular localization of proteins as input features. We present the first predicted interactome for the forest tree Populus trichocarpa in addition to the predicted interactomes for Saccharomyces cerevisiae, Homo sapiens, Mus musculus, and Arabidopsis thaliana. Comparing our approach to other PPI predictors, we find that ENTS performs comparably to or better than a number of existing approaches, including several that utilize a variety of functional information for their predictions. We also find that the predicted interactions are biologically meaningful, as indicated by similarity in functional annotations and enrichment of co-expressed genes in public microarray datasets. Furthermore, we demonstrate some of the biological insights that can be gained from these predicted interaction networks. We show that the predicted interactions yield informative groupings of P. trichocarpa metabolic pathways, literature-supported associations among human disease states, and theory-supported insight into the evolutionary dynamics of duplicated genes in paleopolyploid plants.ConclusionWe conclude that the ENTS classifier will be a valuable tool for the de novo annotation of genome sequences, providing initial clues about regulatory and metabolic network topology, and revealing relationships that are not immediately obvious from traditional homology-based annotations.

【 授权许可】

Unknown   
© Rodgers-Melnick et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.