A recent paper in PLoS One finds hundreds of new putative transcription start sites (TSS): PLoS ONE: Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli. I found the paper interesting, and a good example of how high-throughput studies and genomics can advance our understanding of biology and work in concert with experimental biology, while at the same time dumping a whole lot of new data in our laps.
I’d like to point out some of the databases and resources that are mentioned and used in this paper. In fact, this is the first semi-weekly installment of ‘what did they use?’ post. I’d like to start citing papers that I find interesting and pull out the software, databases and genomics resources used in them. Might help our readers get an understanding of what is being used out there.
First and foremost, this paper has added a large set of new data to RegulonDB, or to paraphrase their about page:
RegulonDB is a computational model of mechanisms of transcriptional regulation including the complex regulation of transcription initiation or regulatory network of the cell and of the organization of the genes in transcription units, operons and simple and complex regulons.
So, if you have used RegulonDB in the past, or might find use of it, you’ll see there is a large set of new data.
Additionally, the paper does it’s analysis using several programs (some of which have web interfaces) including WConsensus (from the same lab that brings you Consensus, tutorial, for those subscribed) and Patser (ftp link to download, also from the Stormo lab) to predict promotors. The authors also use Matrix-Scan, to predict transcription factor binding sites.
As with many papers, I had to go to the citation of the paper about the resource, find the paper and then determine where the database or software resided. As I’ve said before, there needs to be a better way to reference work done using databases.
Mendoza-Vargas, A., Olvera, L., Olvera, M., Grande, R., Vega-Alvarado, L., Taboada, B., Jimenez-Jacinto, V., Salgado, H., Juárez, K., Contreras-Moreira, B., Huerta, A., Collado-Vides, J., & Morett, E. (2009). Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007526