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, 38 (Database issue), D111-8

RegPrecise: A Database of Curated Genomic Inferences of Transcriptional Regulatory Interactions in Prokaryotes

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RegPrecise: A Database of Curated Genomic Inferences of Transcriptional Regulatory Interactions in Prokaryotes

Pavel S Novichkov et al. Nucleic Acids Res.

Abstract

The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of high-quality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. The reconstructed regulons include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. The initial release of the database includes approximately 11,500 candidate binding sites for approximately 400 orthologous groups of transcription factors from over 350 prokaryotic genomes. Majority of these data are represented by genome-wide regulon reconstructions in Shewanella and Streptococcus genera and a large-scale prediction of regulons for the LacI family of transcription factors. Another section in the database represents the results of accurate regulon propagation to the closely related genomes.

Figures

Figure 1.
Figure 1.
Hierarchical data organization in the RegPrecise database. Major objects in the database are TFs, TFBSs and target genes. TFs are attributed to a certain protein family and effector. Target genes participate in a particular pathway or process. Three major levels in the database are: (i) regulon constituted by a set of genes co-regulated by TF in a single genome, (ii) regulog formed by a set of orthologous regulons in a group of related genomes and (iii) collection of regulogs by one of four categories (see text). Each TF regulog is linked to a unique TFBS motif.
Figure 2.
Figure 2.
Summary pages for collections of regulogs for a particular taxonomic group (A), and for a particular transcription factor (B). Collection of multiple TF regulons in the Shewanella species is displayed as a matrix of TFs versus genomes, where each green cell provides a link to species-specific regulon description (A). Collection of Zur regulogs in diverse taxonomic groups is represented as a table with respective TFBS motif logos.
Figure 3.
Figure 3.
Web representation of individual regulogs (A), regulons (B), and operons (C). Regulog page shows a summary, a TFBS motif sequence logo, a table with a set of analyzed genomes (with links to the genome-specific regulon pages), and a table of distribution of TF-regulated genes across these genomes (with links to the respective orthologous operon pages). Regulon page displays the list of regulated operons with detailed TFBS descriptions for a single genome (a horizontal view). Operon page provides a different view on orthologous regulated operons across multiple genomes.

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