GOSAP: Gene Ontology-Based Semantic Alignment of Biological Pathways

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.

[1]  Johannes Berg,et al.  Cross-species analysis of biological networks by Bayesian alignment. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Philip Resnik,et al.  Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language , 1999, J. Artif. Intell. Res..

[3]  Wojciech Szpankowski,et al.  Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution , 2005, RECOMB.

[4]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[5]  中尾 光輝,et al.  KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース) , 2000 .

[6]  Michael Lässig,et al.  Local graph alignment and motif search in biological networks. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Satoru Miyano,et al.  Inferring gene networks from time series microarray data using dynamic Bayesian networks , 2003, Briefings Bioinform..

[8]  R. Karp,et al.  From the Cover : Conserved patterns of protein interaction in multiple species , 2005 .

[9]  B. Snel,et al.  Pathway alignment: application to the comparative analysis of glycolytic enzymes. , 1999, The Biochemical journal.

[10]  K. Sneppen,et al.  Specificity and Stability in Topology of Protein Networks , 2002, Science.

[11]  Liron Klipcan,et al.  Amino acid biogenesis, evolution of the genetic code and aminoacyl-tRNA synthetases. , 2004, Journal of theoretical biology.

[12]  Wojciech Szpankowski,et al.  An efficient algorithm for detecting frequent subgraphs in biological networks , 2004, ISMB/ECCB.

[13]  Carole A. Goble,et al.  Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation , 2003, Bioinform..

[14]  Ron Y. Pinter,et al.  Alignment of metabolic pathways , 2005, Bioinform..

[15]  Thomas Szyperski,et al.  Amino Acid Biosynthesis in the Halophilic ArchaeonHaloarcula hispanica , 1999, Journal of bacteriology.

[16]  W. J. Conover,et al.  Practical Nonparametric Statistics , 1972 .

[17]  R. Karp,et al.  Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Hideo Matsuda,et al.  A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy , 2000, ISMB.

[19]  M. Kanehisa,et al.  A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. , 2000, Nucleic acids research.

[20]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[21]  Antal F. Novak,et al.  networks Græmlin : General and robust alignment of multiple large interaction data , 2006 .