Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and Fugu genomes. It is freely accessible at http://ecrbase.dcode.org
ECRbase was supported in part by grants from the Lawrence Livermore National Laboratory
G.G. Loots and I. Ovcharenko, ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes, Bioinformatics, 23(1):122-4 (2007)
Transposed elements influence on the transcriptome of seven vertebrates and invertebrates
3 UTRs and their functional elements in C. elegans
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.
1. Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A. (2007) CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. J Biotechnol. 2007 (in press, http://dx.doi.org/10.1016/j.jbiotec.2006.12.012).
2. Baumbach J, Brinkrolf K, Wittkop T, Tauch A, Rahmann S (2006) CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. Journal of Integrative Bioinformatics, 3(2):24, 2006.
3. Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A (2006) CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics. 2006 Feb 14;7(1):24. (http://www.biomedcentral.com/1471-2164/7/24).
Experimentally identified and predicted CTCF binding sties
FlyTF is a manually curated catalogue of Drosophila site-specific transcription factors (TFs). It integrates proteins identified as DNA-binding TFs by computational prediction based on structural domain assignments, and experimentally verified TFs from the literature. The data is available for case-by-case query (featuring a search form for various TF characteristics) and for bulk download.
Recent develoments :
We encourage the Drosophila community to provide feedback on our annotations. Future releases and updates to the database based on user feedback are planned, and the incorporation of the "12 Genomes" is underway. The FlyTF data is now available as "public bags" in FlyMine (http://www.flymine.org).
Work on FlyTF was enabled through an EMBO Longterm Fellowship to BA, and SAT is an EMBO Young Investigator.
1. Adryan, B. and Teichmann, S.A. (2006) FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics 22(12): 1532
2. Adryan, B. and Teichmann, S.A. (2007). Computational Identification of Site-Specific Transcription Factors in Drosophila. Fly 1(3): 142
G-quadruplex motifs and potentially G-quadruplex regulated genes
Drosophila melanogaster 5 mRNA transcription start site database
Open REGulatory ANNOtation database
Transcription factors and regulatory sequence annotations
Plant promoter database
G-quadruplex motifs in the promoters of human, chimpanzee, rat, mouse and bacterial genes
Regulatory modules and transcription factor binding sites in Drosophila
Nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors
Plant Transcription Factor Database