Detection of gene orthology from gene co-expression and protein interaction networks.
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.
Towfic
Fadi
F
Bioinformatics and Computational Biology Graduate Program Iowa State University, Ames, USA . ftowfic@cs.iastate.edu
VanderPlas
Susan
S
Oliver
Casey A
CA
Couture
Oliver
O
Tuggle
Christopher K
CK
West Greenlee
M Heather
MH
Honavar
Vasant
V
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
D011506:Proteins