What is RegTransBase?

RegTransBase consists of two modules - a database of regulatory interactions based on literature and an expertly curated database of transcription factor binding sites.

Our literature based information in RegTransBase is a manually curated database of regulatory interactions in prokaryotes, captures the knowledge in published scientific literature using a controlled vocabulary. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains various types of experimental data, in particular:

  • 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 or RNA
  • mapping or prediction of binding sites for a regulatory protein
  • characterization of regulatory mutations

Our analysis section of RegtransBase is based on a set of manually curated alignments of transcription factor binding sites and allows you to search for new binding sites and verify conservation of bindings sites across multiple species through the use of web based analysis tools.

Cite RegTransBase:
Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I. RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 2007 Jan;35(Database issue):D407-12.


News

  • April 14, 2008 - RegTransBase release 4 is now public.
    Release Notes:
    • Over 700 additional curated articles containing over 1500 experiments on regulation.
      • ~250 additional articles on alpha-proteobacteria (2001-present)
      • ~50 additional articles on Archaea
      • ~80 additional articles on Vibrio
      • many more covering cyanobacteria, beta-proteobacteria and more
    • Over 30 additional species covered.
    • All RefSeq release 25 complete microbial genomes now added.
  • September 11, 2007 - RegTransBase release 3 is now public.
    Release Notes:
    • 300 additional curated articles.
    • Over 100 additional transcription factor binding site alignments (total 145).
    • New tools TransTableView, TransTreeView, and TransBindView allow for the analysis of conservation of transcription factor binding sites across a large number of genomes.
  • March 5, 2007 - New features:
    You can now download sites of regulators from their gene information pages as both fasta and aligned fasta.
archived news...

Search

Genes and Regulators:
 
Search for genes involved in regulatory experiments using the gene name, function, product, accession number, or any other genbank annotation.
Example:rpoD, NP_289905, histidine protein kinase. *(No wildcard characters allowed, see advanced search)
advanced search
Effectors:

Search effectors by their name.
Example:glucose, iron.
advanced search
Full Text :

Search Experiments and Articles using text contained in that articles abstract, the journal title, the authors, and a short description of the experiments within that article.
Example:"fnr binding", "+mga +promoter", "Gelfand"
advanced search

Analysis

Binding Sites:
Search for potential binding sites for transcription factors in any DNA sequence with a library of mononucleotide Position Weight Matrices and verify conservation of binding sites among multiple organisms.
Multiple search tools and options are available

BLAST
BLAST your sequence against known regulated genes, known experimental sites, or bacterial genomes

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