Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

Tian, Wenhong; Samatova, Nagiza F.

doi:10.1155/2013/670623

Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

Journal Article · Tue Jan 01 00:00:00 EST 2013 · International Journal of Genomics

DOI:https://doi.org/10.1155/2013/670623· OSTI ID:1227737

^[1]; Samatova, Nagiza F. ^[2]

School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China
Department of Computer and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA, Computer Science Department, North Carolina State University, Raleigh, NC 27696, USA

A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based on a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium , E. coli K12 and C. crescenttus , we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1227737

Alternate ID(s):: OSTI ID: 1626213

Journal Information:: International Journal of Genomics, Journal Name: International Journal of Genomics Vol. 2013; ISSN 2314-436X

Publisher:: Hindawi Publishing CorporationCopyright Statement

Country of Publication:: Egypt

Language:: English

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