The CoryneRegNet prediction workflow

Transfer of gene regulatory networks from the model organism C. glutamicum to C. efficiens, C. diphtheriae, and C. jeikeium

Workflow

Workflow description [Click on one of the tool icons in the graphic to be redirected to the corresponding bioinformatics website.]

Step Description Publication
CoryneRegNet 6.0e - experimental We used all validated datasets of Corynebacterium glutamicum from the CoryneRegNet database. Pauling J, Roettger R, Tauch A, Azevedo V, Baumbach J (2011) CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Res. (in press) (download)
MoRAine All known transcription factor binding sites are re-adjusted (no position shifts but strand annotation --> l=r=0, method: Cluster growing/Motif-seed similarity). Construction of position weight matrices (PWMs). Baumbach J, Wittkop T, Weile J, Kohl T, Rahmann S (2008) MoRAine - A web server for fast computational transcription factor binding motif re-annotation. Journal of Integrative Bioinformatics, 5(2):91, 2008. (download)
PoSSuMsearch We utilized PoSSuMsearch to scan the upstream/promotor sequences of all transcription units of C. efficiens, C. diphtheriae, and C. jeikeium (extracted from CoryneRegNet) to scan for putative transcription factor binding sites by using the MoRAine-adjusted binding sites of C. glutamicum. Beckstette M, Homann R, Giegerich R, Kurtz S (2006) Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics. 2006 Aug 24;7:389. (download)
TransClust All amino acid sequences of C. efficiens, C. diphtheriae, C. glutamicum, and C. jeikeium are extracted from CoryneRegNet and clustered into clusters of orthologous/conserved corynebacterial proteins. We consider two genes as orthologous/conserved (1) if the corresponding proteins are in the same TransClust cluster and (2) if at least one of the surrounding genes also shares a TransClust cluster. Wittkop T, Emig D, Lange SJ, Rahmann S, Albrecht M, Morris JH, Boecker S, Stoye J, Baumbach J (2010) Partitioning biological data with Transitivity Clustering. Nature Methods 2010 Jun;7(6):419-20. (download)
CoryneRegNet 6.0p - predicted We consider a gene regulatory interaction as conserved between C. glutamicum and one other corynebacterium if (1) the transcription factor is conserved; see FORCE, (2) it's binding sites are conserved; see MoRAine/PoSSuMsearch, and (3) the putative target genes are conserved as well; see FORCE. The corresponding gene regulation is added to the CoryneRegNet 6.0p database. Baumbach J (2010) On the power and limits of evolutionary conservation - unraveling bacterial gene regulatory networks. Nucleic Acids Res. 2010 Dec 1;38(22):7877-84. (download)