TB database 2010: Overview and update

• Published in: Tuberculosis (Edinburgh, Scotland) Vol. 90; no. 4; pp. 225 - 235
• Main Authors: Galagan, James E, Sisk, Peter, Stolte, Christian, Weiner, Brian, Koehrsen, Michael, Wymore, Farrell, Reddy, T.B.K, Zucker, Jeremy D, Engels, Reinhard, Gellesch, Marcel, Hubble, Jeremy, Jin, Heng, Larson, Lisa, Mao, Maria, Nitzberg, Michael, White, Jared, Zachariah, Zachariah K, Sherlock, Gavin, Ball, Catherine A, Schoolnik, Gary K
• Format: Journal Article
• Language: English
• Published: Scotland Elsevier Ltd 01-07-2010
• Subjects: Browsing; Databases, Genetic - trends; Diversity; Gene Expression Regulation, Bacterial; Genetic Variation; Genome; Genome, Bacterial; Genomic Library; Genomics - methods; Humans; Infectious Disease; Metabolic Networks and Pathways - genetics; Microarray; Mycobacterium tuberculosis; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - metabolism; Online Systems; Pulmonary/Respiratory; Tuberculosis; Tuberculosis - microbiology; Database; Tuberculosis; Genome; Microarray; Diversity
• ISSN: 1472-9792; 1873-281X
• DOI: 10.1016/j.tube.2010.03.010

Summary The Tuberculosis Database (TBDB) is an online database providing integrated access to genome sequence, expression data and literature curation for TB. TBDB currently houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor . To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data. We provide here an overview of TBDB focusing on recent data releases and enhancements. In particular, we describe the recent release of a Global Genetic Diversity dataset for TB, support for short-read re-sequencing data, new tools for exploring gene expression data in the context of gene regulation, and the integration of a metabolic network reconstruction and BioCyc with TBDB. By integrating a wide range of genomic data with tools for their use, TBDB is a unique platform for both basic science research in TB, as well as research into the discovery and development of TB drugs, vaccines and biomarkers.