An efficient algorithm for pairwise local alignment of protein interaction networks

Chen, Wenbin; Schmidt, Matthew; Tian, Wenhong; Samatova, Nagiza F.; Zhang, Shaohong

doi:10.1142/S0219720015500031

Title: An efficient algorithm for pairwise local alignment of protein interaction networks

Journal Article · Wed Apr 01 00:00:00 EDT 2015 · Journal of Bioinformatics and Computational Biology

DOI:https://doi.org/10.1142/S0219720015500031· OSTI ID:1331086

Chen, Wenbin ^[1]; Schmidt, Matthew ^[2]; Tian, Wenhong ^[3]; Samatova, Nagiza F. ^[2]; Zhang, Shaohong ^[4]

Guangzhou Univ., Guangzhou (People's Republic of China); Fudan Univ., Shanghai (People's Republic of China); Nanjing Univ., Jiangsu (People's Republic of China)
North Carolina State Univ., Raleigh, NC (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Univ. of Electronic and Technology of China, Sichuan (People's Republic of China)
Guangzhou Univ., Guangzhou (People's Republic of China)

Recently, researchers seeking to understand, modify, and create beneficial traits in organisms have looked for evolutionarily conserved patterns of protein interactions. Their conservation likely means that the proteins of these conserved functional modules are important to the trait's expression. In this paper, we formulate the problem of identifying these conserved patterns as a graph optimization problem, and develop a fast heuristic algorithm for this problem. We compare the performance of our network alignment algorithm to that of the MaWISh algorithm [Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A, Pairwise alignment of protein interaction networks, J Comput Biol 13(2): 182-199, 2006.], which bases its search algorithm on a related decision problem formulation. We find that our algorithm discovers conserved modules with a larger number of proteins in an order of magnitude less time. In conclusion, the protein sets found by our algorithm correspond to known conserved functional modules at comparable precision and recall rates as those produced by the MaWISh algorithm.

View Accepted Manuscript (DOE)

Cite

Export

Save

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

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1331086

Journal Information:: Journal of Bioinformatics and Computational Biology, Vol. 13, Issue 02; ISSN 0219-7200

Publisher:: World ScientificCopyright Statement

Country of Publication:: United States

Language:: English

References (14)

From molecular to modular cell biology Hartwell, Leland H.; Hopfield, John J.; Leibler, Stanislas Nature, Vol. 402, Issue S6761 https://doi.org/10.1038/35011540	journal	December 1999
Detection of functional modules from protein interaction networks Pereira-Leal, Jose B.; Enright, Anton J.; Ouzounis, Christos A. Proteins: Structure, Function, and Bioinformatics, Vol. 54, Issue 1 https://doi.org/10.1002/prot.10505	journal	September 2003
Protein complexes and functional modules in molecular networks Spirin, V.; Mirny, L. A. Proceedings of the National Academy of Sciences, Vol. 100, Issue 21 https://doi.org/10.1073/pnas.2032324100	journal	September 2003
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
Conserved pathways within bacteria and yeast as revealed by global protein network alignment Kelley, B. P.; Sharan, R.; Karp, R. M. Proceedings of the National Academy of Sciences, Vol. 100, Issue 20 https://doi.org/10.1073/pnas.1534710100	journal	September 2003
An efficient algorithm for large-scale detection of protein families Enright, A. J. Nucleic Acids Research, Vol. 30, Issue 7 https://doi.org/10.1093/nar/30.7.1575	journal	April 2002
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes Boyle, E. I.; Weng, S.; Gollub, J. Bioinformatics, Vol. 20, Issue 18 https://doi.org/10.1093/bioinformatics/bth456	journal	August 2004
KEGG: Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30 https://doi.org/10.1093/nar/28.1.27	journal	January 2000
The identification of functional modules from the genomic association of genes Snel, B.; Bork, P.; Huynen, M. A. Proceedings of the National Academy of Sciences, Vol. 99, Issue 9 https://doi.org/10.1073/pnas.092632599	journal	April 2002
Graemlin: General and robust alignment of multiple large interaction networks Flannick, J. Genome Research, Vol. 16, Issue 9 https://doi.org/10.1101/gr.5235706	journal	August 2006
The Dense k -Subgraph Problem Feige, U.; Peleg, D.; Kortsarz, G. Algorithmica, Vol. 29, Issue 3 https://doi.org/10.1007/s004530010050	journal	March 2001
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions Xenarios, I. Nucleic Acids Research, Vol. 30, Issue 1 https://doi.org/10.1093/nar/30.1.303	journal	January 2002
Pairwise Alignment of Protein Interaction Networks Koyutürk, Mehmet; Kim, Yohan; Topkara, Umut Journal of Computational Biology, Vol. 13, Issue 2 https://doi.org/10.1089/cmb.2006.13.182	journal	March 2006
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990

Similar Records

MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes

Journal Article · Tue Nov 24 00:00:00 EST 2020 · Bioinformatics · OSTI ID:1331086

Woo, Hyun-Myung; Yoon, Byung-Jun

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 · OSTI ID:1331086

Tian, Wenhong; Samatova, Nagiza F.

New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions

Journal Article · Thu Oct 12 00:00:00 EDT 2023 · Frontiers in Bioinformatics · OSTI ID:1331086

Jia, Kejue; Kilinc, Mesih; Jernigan, Robert L.

Related Subjects

97 MATHEMATICS AND COMPUTING
network alignment
conserved functional modules
graph optimization
graph theory

Title: An efficient algorithm for pairwise local alignment of protein interaction networks

Citation Formats

References (14)

Similar Records

Related Subjects