Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns
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...
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| Format: | Article |
| Language: | English |
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Wiley
2013-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2013/670623 |
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| _version_ | 1832561090628681728 |
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| author | Wenhong Tian Nagiza F. Samatova |
| author_facet | Wenhong Tian Nagiza F. Samatova |
| author_sort | Wenhong Tian |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-742ea8ce6eb94a7a9e5b94ec413b80d4 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2013-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-742ea8ce6eb94a7a9e5b94ec413b80d42025-02-03T01:25:57ZengWileyInternational Journal of Genomics2314-436X2314-43782013-01-01201310.1155/2013/670623670623Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved PatternsWenhong Tian0Nagiza F. Samatova1School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, ChinaDepartment of Computer and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAA 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.http://dx.doi.org/10.1155/2013/670623 |
| spellingShingle | Wenhong Tian Nagiza F. Samatova Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns International Journal of Genomics |
| title | Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns |
| title_full | Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns |
| title_fullStr | Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns |
| title_full_unstemmed | Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns |
| title_short | Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns |
| title_sort | global alignment of pairwise protein interaction networks for maximal common conserved patterns |
| url | http://dx.doi.org/10.1155/2013/670623 |
| work_keys_str_mv | AT wenhongtian globalalignmentofpairwiseproteininteractionnetworksformaximalcommonconservedpatterns AT nagizafsamatova globalalignmentofpairwiseproteininteractionnetworksformaximalcommonconservedpatterns |