Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns
Joint Authors
Samatova, Nagiza F.
Tian, Wenhong
Source
International Journal of Genomics
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-03-27
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Natural & Life Sciences (Multidisciplinary)
Biology
Abstract EN
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.
American Psychological Association (APA)
Tian, Wenhong& Samatova, Nagiza F.. 2013. Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns. International Journal of Genomics،Vol. 2013, no. 2013, pp.1-11.
https://search.emarefa.net/detail/BIM-489137
Modern Language Association (MLA)
Tian, Wenhong& Samatova, Nagiza F.. Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns. International Journal of Genomics No. 2013 (2013), pp.1-11.
https://search.emarefa.net/detail/BIM-489137
American Medical Association (AMA)
Tian, Wenhong& Samatova, Nagiza F.. Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns. International Journal of Genomics. 2013. Vol. 2013, no. 2013, pp.1-11.
https://search.emarefa.net/detail/BIM-489137
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-489137