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  1. RegTransBase (View Publication)
    Full Name of the Resource : RegTransBase describes a large number of regulatory interactions in Procaryotes
    Resource Category : Databases -> Nucleotide Sequence Databases -> Coding and Coding DNA: Genes, Motifs and Regulatory Sites

    Brief Description : RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several databases describing interactions between regulatory proteins and their binding sites are already being maintained, they either focus mostly on the model organisms Escherichia coli and Bacillus subtilis or are entirely computationally derived. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains the following types of experimental data: the activation or repression of transcription by an identified direct regulator, determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA (RNA), mapping or prediction of a binding site for a regulatory protein, and characterization of regulatory mutations. Currently, RegTransBase content is derived from about 3000 relevant articles describing over 7000 experiments in relation to 128 microbes. It contains data on the regulation of about 7500 genes and evidence for 6500 interactions with 650 regulators. RegTransBase also contains manually created position weight matrices (PWM) that can be used to identify candidate regulatory sites in over 60 species.
    Subject Area : Regulatory Interactions in Prokaryotes


    Institute/s :
    Institute for Information Transmission Problems RAS, Bolshoi Karetny pereulok,Russia
    Address of Institute/s :
    Institute for Information Transmission Problems RAS, Bolshoi Karetny pereulok 19, Moscow 127994, Russia
    Country : Russia

    Associated Institutes :

    • Institute for Information Transmission Problems, RAS. Bolshoi Karetny pereulok 19 Moscow, 127994, Russia
    • Lawrence Berkeley National Laboratory, 1 Cyclotron Road Berkeley, CA 94720, USA
    • National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    • Howard Hughes Medical Institute 4000 Jones Bridge Road Chevy Chase, MD 20815-6789, USA
    • Department of Bioengineering, University of California Berkeley, CA, 94710, USA
    • Virtual Institute of Microbial Stress and Survival, Berkeley CA, 94710, USA
    • Faculty of Bioengineering and Bioinformatics, Moscow State University Vorobievy Gory 1-73, Moscow 119992, Russia
    • State Research Center GosNIIGenetika. 1-j Dorozhny proezd 1 Moscow, 117545, Russia
    • Department of Energy Joint Genome Institute 2800 Mitchell Drive,Walnut Creek, CA 94598, USA

    Associated Country : USA; Russia


    Authors/Contributors : Kazakov A E; Cipriano M.J.; Novichkov P.S.; Minovitsky S.; Vinogradov D.V.; Arkin A.; Mironov A.A.; Gelfand M.S.;Dubchak I
    Contact Email : ildubchak@Ibl.gov
    Year : 2006
    Language : English

    Keywords : Bacterial Proteins metabolism; Binding Sites; Databases, Nucleic Acid; Gene Expression Regulation, Bacterial; Genome, Bacterial; Internet; Regulatory Elements, Transcriptional; Transcription Factors metabolism; User-Computer Interface


  2. RegTransBase (View Publication)
    Full Name of the Resource : Manually curated database of regulatory interactions in prokaryotes
    Resource Category : Databases -> Genomic Databases (Non-Human) -> Other Bacteria

    Subject Area : Prokaryotic Genomics





    Keywords : Bacterial Proteins / *metabolism; Binding Sites; *Databases, Nucleic Acid; *Gene Expression Regulation, Bacterial; *Genome, Bacterial; Internet; *Regulatory Elements, Transcriptional; Transcription Factors / *metabolism; User-Computer Interface