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

Abstract

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.

Authors:
ORCiD logo [1];  [2]
  1. School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China
  2. 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
Publication Date:
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1227737
Grant/Contract Number:  
DEAC05-00OR22725
Resource Type:
Published Article
Journal Name:
International Journal of Genomics
Additional Journal Information:
Journal Name: International Journal of Genomics Journal Volume: 2013; Journal ID: ISSN 2314-436X
Publisher:
Hindawi Publishing Corporation
Country of Publication:
Egypt
Language:
English

Citation Formats

Tian, Wenhong, and Samatova, Nagiza F. Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns. Egypt: N. p., 2013. Web. doi:10.1155/2013/670623.
Tian, Wenhong, & Samatova, Nagiza F. Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns. Egypt. doi:10.1155/2013/670623.
Tian, Wenhong, and Samatova, Nagiza F. Tue . "Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns". Egypt. doi:10.1155/2013/670623.
@article{osti_1227737,
title = {Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns},
author = {Tian, Wenhong and Samatova, Nagiza F.},
abstractNote = {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.},
doi = {10.1155/2013/670623},
journal = {International Journal of Genomics},
number = ,
volume = 2013,
place = {Egypt},
year = {2013},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1155/2013/670623

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Cited by: 2 works
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