Detection of gene orthology from gene co-expression and protein interaction networks

Fadi Towfic, Susan VanderPIas, Casey A. OIiver, OIiver Couture, Christopher K. TuggIe, M. Heather West GreenIee, Vasant Honavar

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

Background: Ortholog detection methods present a powerful approach for finding genes that participate in similar biological processes across different organisms, extending our understanding of interactions between genes across different pathways, and understanding the evolution of gene families. . Results: We exploit features derived from the alignment of protein-protein interaction networks and gene-coexpression networks to reconstruct KEGG orthologs for Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository and Mus musculus and Homo sapiens and Sus scrofa gene coexpression networks extracted from NCBI's Gene Expression Omnibus using the decision tree, Naive-Bayes and Support Vector Machine classification algorithms.Conclusions: The performance of our classifiers in reconstructing KEGG orthologs is compared against a basic reciprocal BLAST hit approach. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit.

Original languageEnglish (US)
Article numberS7
JournalBMC bioinformatics
Volume11
Issue numberSUPPL. 3
DOIs
StatePublished - Apr 29 2010

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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