GOSAP: Gene Ontology-Based Semantic Alignment of Biological Pathways

Authors:
Jonas Gamalielsson;Bjorn Olsson
Affiliations:
School of Humanities and Informatics, University of Skovde, Box 408, 541 28 Skovde, Sweden.;School of Humanities and Informatics, University of Skovde, Box 408, 541 28 Skovde, Sweden
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2008

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Abstract

We present a new method for semantic comparison of biological pathways, aiming to discover evolutionary conservation of pathways between species. Our method uses all three sub-ontologies of Gene Ontology (GO) and a measure of semantic similarity to calculate match scores between gene products. These scores are used for finding local pairwise pathway alignments. This approach has the advantage of being applicable to all types of pathways where nodes are gene products, e.g., regulatory pathways, signalling pathways and metabolic enzyme-to-enzyme pathways. We demonstrate the usefulness of the method using regulatory and metabolic pathways from E. coli and S. cerevisiae as examples.