TY - JOUR
T1 - CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli
AU - Baumbach, Jan
AU - Wittkop, Tobias
AU - Rademacher, Katrin
AU - Rahmann, Sven
AU - Brinkrolf, Karina
AU - Tauch, Andreas
PY - 2007
Y1 - 2007
N2 - CoryneRegNet is an ontology-based data warehouse for the reconstruction and visualization of transcriptional regulatory interactions in prokaryotes. To extend the biological content of CoryneRegNet, we added comprehensive data on transcriptional regulations in the model organism Escherichia coli K-12, originally deposited in the international reference database RegulonDB. The enhanced web interface of CoryneRegNet offers several types of search options. The results of a search are displayed in a table-based style and include a visualization of the genetic organization of the respective gene region. Information on DNA binding sites of transcriptional regulators is depicted by sequence logos. The results can also be displayed by several layouters implemented in the graphical user interface GraphVis, allowing, for instance, the visualization of genome-wide network reconstructions and the homology-based inter-species comparison of reconstructed gene regulatory networks. In an application example, we compare the composition of the gene regulatory networks involved in the SOS response of E. coli and Corynebacterium glutamicum. CoryneRegNet is available at the following URL: http://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/.
AB - CoryneRegNet is an ontology-based data warehouse for the reconstruction and visualization of transcriptional regulatory interactions in prokaryotes. To extend the biological content of CoryneRegNet, we added comprehensive data on transcriptional regulations in the model organism Escherichia coli K-12, originally deposited in the international reference database RegulonDB. The enhanced web interface of CoryneRegNet offers several types of search options. The results of a search are displayed in a table-based style and include a visualization of the genetic organization of the respective gene region. Information on DNA binding sites of transcriptional regulators is depicted by sequence logos. The results can also be displayed by several layouters implemented in the graphical user interface GraphVis, allowing, for instance, the visualization of genome-wide network reconstructions and the homology-based inter-species comparison of reconstructed gene regulatory networks. In an application example, we compare the composition of the gene regulatory networks involved in the SOS response of E. coli and Corynebacterium glutamicum. CoryneRegNet is available at the following URL: http://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/.
U2 - 10.1016/j.jbiotec.2006.12.012
DO - 10.1016/j.jbiotec.2006.12.012
M3 - Journal article
C2 - 17229482
SN - 0168-1656
VL - 129
SP - 279
EP - 289
JO - Journal of Biotechnology
JF - Journal of Biotechnology
IS - 2
ER -