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BMC Genomics. 2015 Jun 11;16:452. doi: 10.1186/s12864-015-1631-0.

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

Author information

1
Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil. vabreu@isoladas.grad.ufmg.br.
2
Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil. sintiaalmeida@ufmg.br.
3
Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil. sandy1986sai@ufmg.br.
4
Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil. syedshah-hassan@ufmg.br.
5
Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil. diegomariano@ufmg.br.
6
Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil. asilva@ufpa.br.
7
Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark. jan.baumbach@imada.sdu.dk.
8
Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil. vasco@icb.ufmg.br.
9
Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark. roettger@mpi-inf.mpg.de.
10
Computational Systems Biology, Max Planck Institute for Informatics, Campus E 2.1, 66123, Saarbrucken, Germany. roettger@mpi-inf.mpg.de.

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 .

PMID:
26062809
PMCID:
PMC4464113
DOI:
10.1186/s12864-015-1631-0
[Indexed for MEDLINE]
Free PMC Article

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