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CMRegNet–An interspecies reference database for corynebacterial and mycobacterial regulatory networks

BACKGROUND: Organisms utilize a multitude of mechanisms for responding to changing environmental conditions, maintaining their functional homeostasis and to overcome stress situations. One of the most important mechanisms is transcriptional gene regulation. In-depth study of the transcriptional gene...

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Autores principales: Abreu, Vinicius A. C., Almeida, Sintia, Tiwari, Sandeep, Hassan, Syed Shah, Mariano, Diego, Silva, Artur, Baumbach, Jan, Azevedo, Vasco, Röttger, Richard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4464113/
https://www.ncbi.nlm.nih.gov/pubmed/26062809
http://dx.doi.org/10.1186/s12864-015-1631-0
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author Abreu, Vinicius A. C.
Almeida, Sintia
Tiwari, Sandeep
Hassan, Syed Shah
Mariano, Diego
Silva, Artur
Baumbach, Jan
Azevedo, Vasco
Röttger, Richard
author_facet Abreu, Vinicius A. C.
Almeida, Sintia
Tiwari, Sandeep
Hassan, Syed Shah
Mariano, Diego
Silva, Artur
Baumbach, Jan
Azevedo, Vasco
Röttger, Richard
author_sort Abreu, Vinicius A. C.
collection PubMed
description BACKGROUND: Organisms utilize a multitude of mechanisms for responding to changing environmental conditions, maintaining their functional homeostasis and to overcome stress situations. One of the most important mechanisms is transcriptional gene regulation. In-depth study of the transcriptional gene regulatory network can lead to various practical applications, creating a greater understanding of how organisms control their cellular behavior. DESCRIPTION: In this work, we present a new database, CMRegNet for the gene regulatory networks of Corynebacterium glutamicum ATCC 13032 and Mycobacterium tuberculosis H37Rv. We furthermore transferred the known networks of these model organisms to 18 other non-model but phylogenetically close species (target organisms) of the CMNR group. In comparison to other network transfers, for the first time we utilized two model organisms resulting into a more diverse and complete network of the target organisms. CONCLUSION: CMRegNet provides easy access to a total of 3,103 known regulations in C. glutamicum ATCC 13032 and M. tuberculosis H37Rv and to 38,940 evolutionary conserved interactions for 18 non-model species of the CMNR group. This makes CMRegNet to date the most comprehensive database of regulatory interactions of CMNR bacteria. The content of CMRegNet is publicly available online via a web interface found at http://lgcm.icb.ufmg.br/cmregnet.
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spelling pubmed-44641132015-06-14 CMRegNet–An interspecies reference database for corynebacterial and mycobacterial regulatory networks Abreu, Vinicius A. C. Almeida, Sintia Tiwari, Sandeep Hassan, Syed Shah Mariano, Diego Silva, Artur Baumbach, Jan Azevedo, Vasco Röttger, Richard BMC Genomics Database BACKGROUND: Organisms utilize a multitude of mechanisms for responding to changing environmental conditions, maintaining their functional homeostasis and to overcome stress situations. One of the most important mechanisms is transcriptional gene regulation. In-depth study of the transcriptional gene regulatory network can lead to various practical applications, creating a greater understanding of how organisms control their cellular behavior. DESCRIPTION: In this work, we present a new database, CMRegNet for the gene regulatory networks of Corynebacterium glutamicum ATCC 13032 and Mycobacterium tuberculosis H37Rv. We furthermore transferred the known networks of these model organisms to 18 other non-model but phylogenetically close species (target organisms) of the CMNR group. In comparison to other network transfers, for the first time we utilized two model organisms resulting into a more diverse and complete network of the target organisms. CONCLUSION: CMRegNet provides easy access to a total of 3,103 known regulations in C. glutamicum ATCC 13032 and M. tuberculosis H37Rv and to 38,940 evolutionary conserved interactions for 18 non-model species of the CMNR group. This makes CMRegNet to date the most comprehensive database of regulatory interactions of CMNR bacteria. The content of CMRegNet is publicly available online via a web interface found at http://lgcm.icb.ufmg.br/cmregnet. BioMed Central 2015-06-11 /pmc/articles/PMC4464113/ /pubmed/26062809 http://dx.doi.org/10.1186/s12864-015-1631-0 Text en © Abreu et al. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Database
Abreu, Vinicius A. C.
Almeida, Sintia
Tiwari, Sandeep
Hassan, Syed Shah
Mariano, Diego
Silva, Artur
Baumbach, Jan
Azevedo, Vasco
Röttger, Richard
CMRegNet–An interspecies reference database for corynebacterial and mycobacterial regulatory networks
title CMRegNet–An interspecies reference database for corynebacterial and mycobacterial regulatory networks
title_full CMRegNet–An interspecies reference database for corynebacterial and mycobacterial regulatory networks
title_fullStr CMRegNet–An interspecies reference database for corynebacterial and mycobacterial regulatory networks
title_full_unstemmed CMRegNet–An interspecies reference database for corynebacterial and mycobacterial regulatory networks
title_short CMRegNet–An interspecies reference database for corynebacterial and mycobacterial regulatory networks
title_sort cmregnet–an interspecies reference database for corynebacterial and mycobacterial regulatory networks
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4464113/
https://www.ncbi.nlm.nih.gov/pubmed/26062809
http://dx.doi.org/10.1186/s12864-015-1631-0
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