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CoryneRegNet specifications

Information


Unique identifier OMICS_01858
Name CoryneRegNet
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Version 6.0
Maintained Yes

Publications for CoryneRegNet

CoryneRegNet citations

 (5)
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Comparative genomics and evolution of regulons of the LacI family transcription factors

2014
Front Microbiol
PMCID: 4052901
PMID: 24966856
DOI: 10.3389/fmicb.2014.00294
call_split See protocol

[…] ene. Data about known regulated genes and LacI-TFBS motifs were extracted from the literature and from the RegTransBase (Cipriano et al., ), RegulonDB (Salgado et al., ), DBTBS (Sierro et al., ), and CoryneRegNet (Pauling et al., ) databases.Candidate motifs in upstream regions of regulated operons were identified by the Discover Profile tool in RegPredict (Novichkov et al., ). A search for palind […]

call_split

Carotenoid biosynthesis and overproduction in Corynebacterium glutamicum

2012
BMC Microbiol
PMCID: 3598387
PMID: 22963379
DOI: 10.1186/1471-2180-12-198
call_split See protocol

[…] To compare the crt genes from C. glutamicum ATCC 13032 with other sequenced corynebacteria, the amino acid sequences of the respective genes were obtained from CoryneRegNet database (http://www.coryneregnet.de/). Sequence comparisons were carried out using BLASTP (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi, []) and CLUSTALW [] and the identification of pote […]

library_books

On the power and limits of evolutionary conservation—unraveling bacterial gene regulatory networks

2010
Nucleic Acids Res
PMCID: 3001071
PMID: 20699275
DOI: 10.1093/nar/gkq699

[…] ecies, four corynebacteria, the attempt to transfer data from C. glutamicum to C. efficiens, C. jeikeium and C. diphtheriae yielded 530 new gene regulations (). The database content of the underlying CoryneRegNet database was increased by factor 4.2 for the three target organisms. Reliable knowledge for ∼40% of the common transcription factors was made available, compared with ∼5% for which knowle […]

call_split

The Zur regulon of Corynebacterium glutamicum ATCC 13032

2010
BMC Genomics
PMCID: 2823685
PMID: 20055984
DOI: 10.1186/1471-2164-11-12
call_split See protocol

[…] ted in the PROML program of the PHYLIP package [] using multiple sequence alignments of protein sequences produced by the Clustal W2 program []. The deduced regulatory interactions were stored in the CoryneRegNet database []. […]

library_books

Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms

2009
BMC Syst Biol
PMCID: 2653031
PMID: 19146695
DOI: 10.1186/1752-0509-3-8

[…] d approach we decided to integrate MoRAine [] for TFBS readjustment, PoSSuMsearch [] for binding motif matching, and FORCE [] for homology detection and applied it to corynebacterial data gained from CoryneRegNet [] (see additional file ). The goal was to use proven knowledge from the model organism C. glutamicum (CG) to predict reliable gene regulatory networks in C. diphtheriae (CD), which is a […]

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CoryneRegNet institution(s)
Computational Systems Biology, Max Planck Institute for Informatics, Saarbrucken, Germany; Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarbrucken, Germany; Center for Biotechnology, Bielefeld University, Bielefeld, Germany; Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte MG, Brazil
CoryneRegNet funding source(s)
Supported by DFG Cluster of Excellence for Multimodel Computing and Interaction (MMCI) and International Max Planck Research School (IMPRS).

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