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PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440
BACKGROUND: Pseudomonas putida KT2440 (P. putida KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organism for genetic and physiological studies and for the development of biotechno...
Autores principales: | , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788370/ https://www.ncbi.nlm.nih.gov/pubmed/19958481 http://dx.doi.org/10.1186/1471-2164-10-S3-S18 |
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author | Park, Seong-Jin Choi, Jong-Soon Kim, Byoung-Chul Jho, Seong-Woong Ryu, Jea-Woon Park, Daeui Lee, Kyung-A Bhak, Jong Kim, Seung Il |
author_facet | Park, Seong-Jin Choi, Jong-Soon Kim, Byoung-Chul Jho, Seong-Woong Ryu, Jea-Woon Park, Daeui Lee, Kyung-A Bhak, Jong Kim, Seung Il |
author_sort | Park, Seong-Jin |
collection | PubMed |
description | BACKGROUND: Pseudomonas putida KT2440 (P. putida KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organism for genetic and physiological studies and for the development of biotechnological applications. In order to provide a more systematic application of the organism, we have constructed a protein-protein interaction (PPI) network analysis system of P. putida KT2440. RESULTS: PutidaNET is a comprehensive interaction database and server of P. putida KT2440 which is generated from three protein-protein interaction (PPI) methods. We used PSIMAP (Protein Structural Interactome MAP), PEIMAP (Protein Experimental Interactome MAP), and Domain-domain interactions using iPfam. PutidaNET contains 3,254 proteins, and 82,019 possible interactions consisting of 61,011 (PSIMAP), 4,293 (PEIMAP), and 30,043 (iPfam) interaction pairs except for self interaction. Also, we performed a case study by integrating a protein interaction network and experimental 1-DE/MS-MS analysis data P. putida. We found that 1) major functional modules are involved in various metabolic pathways and ribosomes, and 2) existing PPI sub-networks that are specific to succinate or benzoate metabolism are not in the center as predicted. CONCLUSION: We introduce the PutidaNET which provides predicted interaction partners and functional analyses such as physicochemical properties, KEGG pathway assignment, and Gene Ontology mapping of P. putida KT2440 PutidaNET is freely available at http://sequenceome.kobic.kr/PutidaNET. |
format | Text |
id | pubmed-2788370 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-27883702009-12-04 PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440 Park, Seong-Jin Choi, Jong-Soon Kim, Byoung-Chul Jho, Seong-Woong Ryu, Jea-Woon Park, Daeui Lee, Kyung-A Bhak, Jong Kim, Seung Il BMC Genomics Proceedings BACKGROUND: Pseudomonas putida KT2440 (P. putida KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organism for genetic and physiological studies and for the development of biotechnological applications. In order to provide a more systematic application of the organism, we have constructed a protein-protein interaction (PPI) network analysis system of P. putida KT2440. RESULTS: PutidaNET is a comprehensive interaction database and server of P. putida KT2440 which is generated from three protein-protein interaction (PPI) methods. We used PSIMAP (Protein Structural Interactome MAP), PEIMAP (Protein Experimental Interactome MAP), and Domain-domain interactions using iPfam. PutidaNET contains 3,254 proteins, and 82,019 possible interactions consisting of 61,011 (PSIMAP), 4,293 (PEIMAP), and 30,043 (iPfam) interaction pairs except for self interaction. Also, we performed a case study by integrating a protein interaction network and experimental 1-DE/MS-MS analysis data P. putida. We found that 1) major functional modules are involved in various metabolic pathways and ribosomes, and 2) existing PPI sub-networks that are specific to succinate or benzoate metabolism are not in the center as predicted. CONCLUSION: We introduce the PutidaNET which provides predicted interaction partners and functional analyses such as physicochemical properties, KEGG pathway assignment, and Gene Ontology mapping of P. putida KT2440 PutidaNET is freely available at http://sequenceome.kobic.kr/PutidaNET. BioMed Central 2009-12-03 /pmc/articles/PMC2788370/ /pubmed/19958481 http://dx.doi.org/10.1186/1471-2164-10-S3-S18 Text en Copyright ©2009 Park et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Proceedings Park, Seong-Jin Choi, Jong-Soon Kim, Byoung-Chul Jho, Seong-Woong Ryu, Jea-Woon Park, Daeui Lee, Kyung-A Bhak, Jong Kim, Seung Il PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440 |
title | PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440 |
title_full | PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440 |
title_fullStr | PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440 |
title_full_unstemmed | PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440 |
title_short | PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440 |
title_sort | putidanet: interactome database service and network analysis of pseudomonas putida kt2440 |
topic | Proceedings |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788370/ https://www.ncbi.nlm.nih.gov/pubmed/19958481 http://dx.doi.org/10.1186/1471-2164-10-S3-S18 |
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