TB database: an integrated platform for tuberculosis research

Abstract

The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, by reliance on an inefficient vaccine and by the absence of biomarkers of clinical status. The promise of the genomics era for TB control is substantial, but has been hindered by the lack of a central repository that collects and integrates genomic and experimental data about this organism in a way that can be readily accessed and analyzed. The Tuberculosis Database (TBDB) is an integrated database providing access to TB genomic data and resources, relevant to the discovery and development of TB drugs, vaccines and biomarkers. The current release of TBDB houses genome sequence data and annotations for 28 different Mycobacterium tuberculosis strains and related bacteria. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives. TBDB currently hosts data for nearly 1500 public tuberculosis microarrays and 260 arrays for Streptomyces. In addition, TBDB provides access to a suite of comparative genomics and microarray analysis software. By bringing together M. tuberculosis genome annotation and gene-expression data with a suite of analysis tools, TBDB (http://www.tbdb.org/) provides a unique discovery platform for TB research.

Figure 1.

TBDB Gene Detail page. The Gene Detail page provides at-a-glance information for a given gene, including known names and synonyms, predicted function(s) and protein domains. It also serves as a jumping off point to various sequence tools, and to expression data for that gene. In addition, it provides several links to external resources such as TubercuList, TBSGC Protein Structure Information, Proteome 2D-PAGE Database at Max Planck Institute.

Figure 2.

Genome Map tool. This tool provides a linear view of one or more genome sequences and associated annotations as well as conserved synteny between genomes. Annotations are provided as tracks above (forward strand) and below (reverse strand) the midline. When zoomed out, annotations are viewed as density plots; when zoomed in individual features are displayed. Users may select regions of a genome sequence by dragging along the midline. Syntenic regions in the other sequences associated with the selection are then displayed as red bands.

Figure 3.

Comparative genome analysis. The Genomes Synteny Map (A), Dot Plot (B) and Operon Map Browser (C) provide different ways to access comparative genomic data between M. tuberculosis reference genome and selected related species. These tools provide an interactive means to explore comparative genomic data.

Figure 3.

Comparative genome analysis. The Genomes Synteny Map (A), Dot Plot (B) and Operon Map Browser (C) provide different ways to access comparative genomic data between M. tuberculosis reference genome and selected related species. These tools provide an interactive means to explore comparative genomic data.

Figure 4.

Publication microarray data and expression connection. Researchers can access the full raw microarray data associated with a publication, either for download, or retrieval through the data retrieval and analysis pipeline. In addition, users can explore clustered microarrays data, whereby they can search for particular genes, or identify which genes show coexpression across a particular dataset.