title: Detection of gene orthology from gene co-expression and protein interaction networks.
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.
authors.affiliation: Bioinformatics and Computational Biology Graduate Program Iowa State University, Ames, USA . ftowfic@cs.iastate.edu
authors.forename: Fadi
authors.initials: F
authors.lastname: Towfic
authors.forename: Susan
authors.initials: S
authors.lastname: VanderPlas
authors.forename: Casey A
authors.initials: CA
authors.lastname: Oliver
authors.forename: Oliver
authors.initials: O
authors.lastname: Couture
authors.forename: Christopher K
authors.initials: CK
authors.lastname: Tuggle
authors.forename: M Heather
authors.initials: MH
authors.lastname: West Greenlee
authors.forename: Vasant
authors.initials: V
authors.lastname: Honavar
mesh_terms: D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D001499:Bayes Theorem; D030541:Databases, Genetic; D003663:Decision Trees; D004331:Drosophila melanogaster; D015870:Gene Expression; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000235:genetics; D012372:ROC Curve; D012441:Saccharomyces cerevisiae; D016415:Sequence Alignment; D013552:Swine
chemical_list: D011506:Proteins