| Step |
Description |
Publication |
| CoryneRegNet 5.0e - experimental |
We used all validated datasets of Corynebacterium glutamicum from the CoryneRegNet database.
|
Baumbach J (2007) CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 2007, 8:429.
(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)
|
| FORCE |
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 FORCE cluster and
(2) if at least one of the surrounding genes also shares a FORCE cluster.
|
Wittkop T, Baumbach J, Lobo FP, Rahmann S (2007) Large scale clustering of protein sequences with FORCE -- A layout based heuristic for weighted cluster editing. BMC Bioinformatics 2007, 8:396.
(download)
|
| CoryneRegNet 5.0p - 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 5.0p 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)
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