The BacillusRegNet 1.0p prediction workflow

Transfer of gene regulatory networks from the model organism B. subtilis to other organisms

Workflow

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

Step Description Publication
BacillusRegNet 1.0e - experimental We used all validated datasets of B. subtilis from the BacillusRegNet database.
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 the Bacteria (extracted from BacillusRegNet) to scan for putative transcription factor binding sites by using the MoRAine-adjusted binding sites of B. subtilis. 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 B. subtilis are extracted from BacillusRegNet and clustered into clusters of orthologous/conserved proteins. We consider two genes as orthologous/conserved (1) if the corresponding proteins are in the same cluster and (2) if at least one of the surrounding genes also shares a 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)
BacillusRegNet 1.0p - predicted We consider a gene regulatory interaction as conserved between B. subtilis and one other organisms if (1) the transcription factor is conserved; see TransClust, (2) it's binding sites are conserved; see MoRAine/PoSSuMsearch, and (3) the putative target genes are conserved as well; see TransClust. The corresponding gene regulation is added to the BacillusRegNet 1.0p database. Baumbach J, Rahmann S, Tauch A (2009) Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst Biol. 2009 Jan 15;3(1):8. (download)