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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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 .
authors.affiliation: 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.
authors.forename: Vinicius A C
authors.initials: VA
authors.lastname: Abreu
authors.affiliation: 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.
authors.forename: Sintia
authors.initials: S
authors.lastname: Almeida
authors.affiliation: 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.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Tiwari
authors.affiliation: 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.
authors.forename: Syed Shah
authors.initials: SS
authors.lastname: Hassan
authors.affiliation: 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.
authors.forename: Diego
authors.initials: D
authors.lastname: Mariano
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil. asilva@ufpa.br.
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark. jan.baumbach@imada.sdu.dk.
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
authors.affiliation: 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.
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark. roettger@mpi-inf.mpg.de.|Computational Systems Biology, Max Planck Institute for Informatics, Campus E 2.1, 66123, Saarbrucken, Germany. roettger@mpi-inf.mpg.de.
authors.forename: Richard
authors.initials: R
authors.lastname: Röttger
mesh_terms: D019295:Computational Biology; D048230:Corynebacterium glutamicum / Q000145:classification / Q000235:genetics*; D030541:Databases, Genetic; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial; D020407:Internet; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics*; D010802:Phylogeny