Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions
Identifieur interne : 001161 ( Main/Exploration ); précédent : 001160; suivant : 001162Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions
Auteurs : Hufeng Zhou [Singapour, États-Unis] ; Shangzhi Gao [États-Unis] ; Nam Ninh Nguyen [Singapour] ; Mengyuan Fan [Singapour] ; Jingjing Jin [Singapour] ; Bing Liu [États-Unis] ; Liang Zhao [Singapour] ; Geng Xiong [États-Unis] ; Min Tan [États-Unis] ; Shijun Li [États-Unis] ; Limsoon Wong [Singapour]Source :
- Biology Direct [ 1745-6150 ] ; 2014.
Abstract
We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting
Our stringent homology-based prediction approach provides a better strategy in predicting PPIs between eukaryotic hosts and prokaryotic pathogens than a conventional homology-based approach. The properties we have observed from the predicted
This article was reviewed by Michael Gromiha, Narayanaswamy Srinivasan and Thomas Dandekar.
Url:
DOI: 10.1186/1745-6150-9-5
PubMed: 24708540
PubMed Central: 4022245
Affiliations:
- Singapour, États-Unis
- Massachusetts, Pennsylvanie
- Boston, Cambridge (Massachusetts), Pittsburgh
- Université Carnegie-Mellon, Université Harvard, Université nationale de Singapour
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Le document en format XML
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xml:lang="en" level="a" type="main">Stringent homology-based prediction of <italic>H. sapiens-M. tuberculosis</italic> H37Rv protein-protein interactions</title><author><name sortKey="Zhou, Hufeng" sort="Zhou, Hufeng" uniqKey="Zhou H" first="Hufeng" last="Zhou">Hufeng Zhou</name><affiliation wicri:level="4"><nlm:aff id="I1">NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="I2">School of Computing, National University of Singapore, Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>School of Computing, National University of Singapore, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation><affiliation wicri:level="3"><nlm:aff id="I3">Department of Medicine, Brigham and Women’s Hospital, Boston, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, Brigham and Women’s Hospital, Boston</wicri:regionArea><placeName><settlement type="city">Boston</settlement><region type="state">Massachusetts</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="I4">Department of Microbiology and Immunobiology, Harvard University, Cambridge, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology and Immunobiology, Harvard University, Cambridge</wicri:regionArea><orgName type="university">Université Harvard</orgName><placeName><settlement type="city">Cambridge (Massachusetts)</settlement><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Gao, Shangzhi" sort="Gao, Shangzhi" uniqKey="Gao S" first="Shangzhi" last="Gao">Shangzhi Gao</name><affiliation wicri:level="4"><nlm:aff id="I5">Department of Environmental Health, Harvard School of Public Health, Harvard University, Cambridge, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Environmental Health, Harvard School of Public Health, Harvard University, Cambridge</wicri:regionArea><orgName type="university">Université Harvard</orgName><placeName><settlement type="city">Cambridge (Massachusetts)</settlement><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Nguyen, Nam Ninh" sort="Nguyen, Nam Ninh" uniqKey="Nguyen N" first="Nam Ninh" last="Nguyen">Nam Ninh Nguyen</name><affiliation wicri:level="4"><nlm:aff id="I2">School of Computing, National University of Singapore, Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>School of Computing, National University of Singapore, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author><author><name sortKey="Fan, Mengyuan" sort="Fan, Mengyuan" uniqKey="Fan M" first="Mengyuan" last="Fan">Mengyuan Fan</name><affiliation wicri:level="4"><nlm:aff id="I1">NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="I2">School of Computing, National University of Singapore, Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>School of Computing, National University of Singapore, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author><author><name sortKey="Jin, Jingjing" sort="Jin, Jingjing" uniqKey="Jin J" first="Jingjing" last="Jin">Jingjing Jin</name><affiliation wicri:level="4"><nlm:aff id="I2">School of Computing, National University of Singapore, Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>School of Computing, National University of Singapore, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author><author><name sortKey="Liu, Bing" sort="Liu, Bing" uniqKey="Liu B" first="Bing" last="Liu">Bing Liu</name><affiliation wicri:level="4"><nlm:aff id="I6">Computer Science Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science Department, Carnegie Mellon University, Pittsburgh, PA 15213</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université Carnegie-Mellon</orgName></affiliation></author><author><name sortKey="Zhao, Liang" sort="Zhao, Liang" uniqKey="Zhao L" first="Liang" last="Zhao">Liang Zhao</name><affiliation wicri:level="1"><nlm:aff id="I7">Bioinformatics Research Center, & School of Computer Engineering, Nanyang Technological University, Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Bioinformatics Research Center, & School of Computer Engineering, Nanyang Technological University, Singapore</wicri:regionArea><wicri:noRegion>Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Xiong, Geng" sort="Xiong, Geng" uniqKey="Xiong G" first="Geng" last="Xiong">Geng Xiong</name><affiliation wicri:level="3"><nlm:aff id="I3">Department of Medicine, Brigham and Women’s Hospital, Boston, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, Brigham and Women’s Hospital, Boston</wicri:regionArea><placeName><settlement type="city">Boston</settlement><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Tan, Min" sort="Tan, Min" uniqKey="Tan M" first="Min" last="Tan">Min Tan</name><affiliation wicri:level="3"><nlm:aff id="I3">Department of Medicine, Brigham and Women’s Hospital, Boston, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, Brigham and Women’s Hospital, Boston</wicri:regionArea><placeName><settlement type="city">Boston</settlement><region type="state">Massachusetts</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="I4">Department of Microbiology and Immunobiology, Harvard University, Cambridge, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology and Immunobiology, Harvard University, Cambridge</wicri:regionArea><orgName type="university">Université Harvard</orgName><placeName><settlement type="city">Cambridge (Massachusetts)</settlement><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Li, Shijun" sort="Li, Shijun" uniqKey="Li S" first="Shijun" last="Li">Shijun Li</name><affiliation wicri:level="3"><nlm:aff id="I3">Department of Medicine, Brigham and Women’s Hospital, Boston, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, Brigham and Women’s Hospital, Boston</wicri:regionArea><placeName><settlement type="city">Boston</settlement><region type="state">Massachusetts</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="I4">Department of Microbiology and Immunobiology, Harvard University, Cambridge, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology and Immunobiology, Harvard University, Cambridge</wicri:regionArea><orgName type="university">Université Harvard</orgName><placeName><settlement type="city">Cambridge (Massachusetts)</settlement><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Wong, Limsoon" sort="Wong, Limsoon" uniqKey="Wong L" first="Limsoon" last="Wong">Limsoon Wong</name><affiliation wicri:level="4"><nlm:aff id="I2">School of Computing, National University of Singapore, Singapore, Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>School of Computing, National University of Singapore, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author></analytic><series><title level="j">Biology Direct</title><idno type="eISSN">1745-6150</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p><italic>H. sapiens</italic>-<italic>M. tuberculosis</italic> H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen <italic>M. tuberculosis</italic> H37Rv. Computational prediction is an important strategy to fill the gap in experimental <italic>H. sapiens</italic>-<italic>M. tuberculosis</italic> H37Rv PPI data. Homology-based prediction is frequently used in predicting both intra-species and inter-species PPIs. However, some limitations are not properly resolved in several published works that predict eukaryote-prokaryote inter-species PPIs using intra-species template PPIs.</p></sec><sec><title>Results</title><p>We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting <italic>H. sapiens</italic>-<italic>M. tuberculosis</italic> H37Rv PPIs. Using our stringent homology-based approach, we have predicted a set of highly plausible <italic>H. sapiens</italic>-<italic>M. tuberculosis</italic> H37Rv PPIs which might be useful for many of related studies. Based on our analysis of the <italic>H. sapiens</italic>-<italic>M. tuberculosis</italic> H37Rv PPI network predicted by our stringent homology-based approach, we have discovered several interesting properties which are reported here for the first time. We find that both host proteins and pathogen proteins involved in the host-pathogen PPIs tend to be hubs in their own intra-species PPI network. Also, both host and pathogen proteins involved in host-pathogen PPIs tend to have longer primary sequence, tend to have more domains, tend to be more hydrophilic, etc. And the protein domains from both host and pathogen proteins involved in host-pathogen PPIs tend to have lower charge, and tend to be more hydrophilic.</p></sec><sec><title>Conclusions</title><p>Our stringent homology-based prediction approach provides a better strategy in predicting PPIs between eukaryotic hosts and prokaryotic pathogens than a conventional homology-based approach. The properties we have observed from the predicted <italic>H. sapiens</italic>-<italic>M. tuberculosis</italic> H37Rv PPI network are useful for understanding inter-species host-pathogen PPI networks and provide novel insights for host-pathogen interaction studies.</p></sec><sec><title>Reviewers</title><p>This article was reviewed by Michael Gromiha, Narayanaswamy Srinivasan and Thomas Dandekar.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Butler, D" uniqKey="Butler D">D Butler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Koul, A" uniqKey="Koul A">A Koul</name></author><author><name sortKey="Herget, T" uniqKey="Herget T">T Herget</name></author><author><name sortKey="Klebl, B" uniqKey="Klebl B">B Klebl</name></author><author><name sortKey="Ullrich, A" uniqKey="Ullrich A">A Ullrich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hestvik, A" 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uniqKey="Jin J" first="Jingjing" last="Jin">Jingjing Jin</name><name sortKey="Nguyen, Nam Ninh" sort="Nguyen, Nam Ninh" uniqKey="Nguyen N" first="Nam Ninh" last="Nguyen">Nam Ninh Nguyen</name><name sortKey="Wong, Limsoon" sort="Wong, Limsoon" uniqKey="Wong L" first="Limsoon" last="Wong">Limsoon Wong</name><name sortKey="Zhao, Liang" sort="Zhao, Liang" uniqKey="Zhao L" first="Liang" last="Zhao">Liang Zhao</name><name sortKey="Zhou, Hufeng" sort="Zhou, Hufeng" uniqKey="Zhou H" first="Hufeng" last="Zhou">Hufeng Zhou</name></country><country name="États-Unis"><region name="Massachusetts"><name sortKey="Zhou, Hufeng" sort="Zhou, Hufeng" uniqKey="Zhou H" first="Hufeng" last="Zhou">Hufeng Zhou</name></region><name sortKey="Gao, Shangzhi" sort="Gao, Shangzhi" uniqKey="Gao S" first="Shangzhi" last="Gao">Shangzhi Gao</name><name sortKey="Li, Shijun" sort="Li, Shijun" uniqKey="Li S" first="Shijun" last="Li">Shijun Li</name><name sortKey="Li, Shijun" sort="Li, Shijun" uniqKey="Li S" first="Shijun" last="Li">Shijun Li</name><name sortKey="Liu, Bing" sort="Liu, Bing" uniqKey="Liu B" first="Bing" last="Liu">Bing Liu</name><name sortKey="Tan, Min" sort="Tan, Min" uniqKey="Tan M" first="Min" last="Tan">Min Tan</name><name sortKey="Tan, Min" sort="Tan, Min" uniqKey="Tan M" first="Min" last="Tan">Min Tan</name><name sortKey="Xiong, Geng" sort="Xiong, Geng" uniqKey="Xiong G" first="Geng" last="Xiong">Geng Xiong</name><name sortKey="Zhou, Hufeng" sort="Zhou, Hufeng" uniqKey="Zhou H" first="Hufeng" last="Zhou">Hufeng Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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