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

Vinicius A C Abreu, Sintia Almeida, Sandeep Tiwari, Syed Shah Hassan, Diego Mariano, Artur Silva, Jan Baumbach, Vasco Azevedo, Richard Röttger

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Abstract

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 .

Original languageEnglish
JournalB M C Genomics
Volume16
Pages (from-to)452
ISSN1471-2164
DOIs
Publication statusPublished - 2015

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Corynebacterium glutamicum
Mycobacterium tuberculosis
Databases
Homeostasis

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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. In: B M C Genomics. 2015 ; Vol. 16. pp. 452.
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title = "CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks",
abstract = "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 .",
author = "Abreu, {Vinicius A C} and Sintia Almeida and Sandeep Tiwari and Hassan, {Syed Shah} and Diego Mariano and Artur Silva and Jan Baumbach and Vasco Azevedo and Richard R{\"o}ttger",
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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.

In: B M C Genomics, Vol. 16, 2015, p. 452.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks

AU - Abreu, Vinicius A C

AU - Almeida, Sintia

AU - Tiwari, Sandeep

AU - Hassan, Syed Shah

AU - Mariano, Diego

AU - Silva, Artur

AU - Baumbach, Jan

AU - Azevedo, Vasco

AU - Röttger, Richard

PY - 2015

Y1 - 2015

N2 - 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 .

AB - 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 .

U2 - 10.1186/s12864-015-1631-0

DO - 10.1186/s12864-015-1631-0

M3 - Journal article

VL - 16

SP - 452

JO - B M C Genomics

JF - B M C Genomics

SN - 1471-2164

ER -