RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

Abstract

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. RegTransBase is available at http://regtransbase.lbl.gov.

Figure 1

The information flow of articles and annotations is shown. A manager obtains articles from a library and works with annotators in creating annotations from those articles. The annotations undergo a quality check and are then placed on the website.

Figure 2

(a) Various search types available from RegTransBase. The user may search by text, such as a gene name or annotation, an element name or from the description of an experiment or abstract. Alternatively, you may search using BLAST against various datasets for finding sequence similarity, or you may use sequence alignments and position weight matrices for finding similar motifs within whole genomes. (b) You may also browse different lists of the data available within RegTransBase.

Figure 3

A screen shot of the gene detail page. Shown on this page are (a) the name of the gene, (b) the genome and an overview of the genomic region. The current feature is highlighted yellow, subelements are highlighted pink, parent elements are highlighted blue. (c) annotation of this feature (imported from NCBI), (d) external links for this feature, (e) various analysis tools. (f) information pertaining to sites that the product of this gene regulates (g) parent elements of this feature, (h) subelements of this feature, (i) a listing of the experiments in which this feature is involved in. You may mouse over the details link to see a description of the experiment, while clicking on the link will take you to a more detailed explanation of the experiment. (j) A listing of the articles in which this feature is mentioned in. You may click on the details link for a more detailed explanation of this article.

Figure 4

A screen shot of the profile alignment information. Shown here is (a) a graphical sequence logo created with weblogo. (b) A list of the sequences used in creating this alignment. If the specific genomic location is known, the name is a link that you may click to goto that location, or hovering over it will produce an image of that genomic area. (c) A listing of any known transcription factors that bind these sequences. (d) A listing of different file formats for this alignment.