Announcements
February 2010
TB's Genetic Diversity:
We are happy to announce the integration of TB Diversity
Sequencing dataset generated by Sebastien Gagneux and Peter Small through The Broad Institute
Genomic Sequencing Center for Infectious
Diseases (GSCID)
established by the National Institute of Allergy and
Infectious Diseases (NIAID). TBDB
now provides users the ability to search and compare
30+ sequenced strains selected to represent the
phylogenetic diversity of TB. Polymorphisms are
searchable by strain or genomic location. Each gene detail page displays a graphical view of the sequence diversity of that gene, and users can access a dynamic alignment of
all sequenced strains for each gene. Individual
polymorphisms can be further investigated, and users are able to dynamically visualize the Illumina sequence
reads underlying each genetic difference. With this data and associated tools, the scientific community
may now access a global view of TB genetic polymorphism from the level of genomes down to
individual reads. See here for
a tutorial.
January 2010
Tutorials:
We have added several new tutorials and updated many others. A
tutorial navigation graphic appears on the front page.
December 2009
Navigation:
We have updated and simplified the menus and overall site
navigation. This is the result of considerable user feedback.
October 2009
New Genomes:
We are pleased to announce that TBDB now hosts genome data for the following 5 additional genomes. They are M. tuberculosis H37Ra, M. abscessus, M. africanum, M. gilvum and M. vanbaalenii. These are in addition to the 28 different species we already have in TBDB. A complete list of available genomes in TBDB can be found here.
Protein Structure Viewer:
We are pleased to announce that TBDB has incorporated the Protein Structure Viewer developed by the Influenza Research Database (IRD) with funding from the NIAID.
Accessible from the Gene Detail page under "Display Options", the Protein Structure Viewer provides an interactive tool to explore and view 3-D protein structure and to highlight predicted epitopes and other protein features.
August 2009
We are pleased to announce that TBDB now hosts data from the following three publications.
Emerging antibiotic resistance necessitating scientists to look for antimicrobial agents from natural sources. O'Donnell et. al. in a publication titled "Bioactive Pyridine-N-oxide Disulfides from Allium stipitatum" report garlic extract is a potent bactericidal agent against Mycobacterium tuberculosis. They studied gene expression profiles in TB bacteria treated with Compound 1 isolated from garlic. They report Compound 1 up regulated genes involved in oxidative stress and heat shock responses.
In a publication titled "Activation of the eis gene in a W-Beijing strain of Mycobacterium tuberculosis correlates with increased SigA levels and enhanced intracellular growth" Wu et. al. identified that the eis gene is expressed at very high levels in bacteria overexpressing SigA gene. They present data to show direct relationship between SigA and eis expression levels and the contribution of eis to the enhanced capacity of M. tuberculosis clinical isolate strain 210 to grow in monocytes.
Schwab et.al. exposed Mycobacterium tuberculosis to lung surfactants for different times and studied the transcriptional profiles of genes. They report their data in a publication titled "Transcriptional responses of Mycobacterium tuberculosis to lung surfactant". They show whole lung surfactant induce the transcription of genes like membrane-associated lipases and phthiocerol dimycocerosate (PDIM), a cell wall component known to be important in macrophage interactions.
July 2009
We are pleased to announce that TBDB now hosts data from the following two publications.
In a publication titled "Transcriptional profiling of mycobacterial antigen-induced responses in infants vaccinated with BCG at birth" Fletcher et. al. report data to show ex vivo stimulation of peripheral blood monocytes with PPD or BCG induced largely similar gene expression profiles, except that BCG induced greater macrophage activation. Their results suggest that a combination of suppressed and up-regulated genes may be key in determining development of protective immunity to TB induced by vaccination with BCG.
Marquis et al present data in their publication titled "Genetic and functional characterization of the mouse Trl3 locus in defense against tuberculosis" report resistance to TB infection in susceptible DBA/2J mouse strain after transferring Trl3 containing chromosomal region from C57BL/6J strain that confers resistance. Microarray experiments involving parental and congenic mouse lines identified a number of genes in the Trl3 interval on chromosome 7, whose expression levels before infection or in response to Mycobacterium tuberculosis infection is differentially regulated in a parental haplotype-dependent fashion.
News and Updates
- In a PLoS Pathogens article entitled, "The Past and Future of Tuberculosis Research" Inaki Comas and Sebastien Gagneux argue that new multidisciplinary approaches, especially those that integrate epidemiology with systems biology in what they call "systems epidemiology," will be required to eliminate TB.
- The Stop TB Partnership's New Diagnostics Working Group (NDWG) has launched a new website resource called Evidence-based Tuberculosis Diagnosis. The main objective of the new website is to provide the most comprehensive single source of evidence syntheses, policies, guidelines and research agendas on TB diagnosis. It addresses a long-standing need for a single portal that compiles all critical evidence on TB diagnosis, with relevant policies and guidelines for clinicians and public health professionals.
Quick Search
Enter gene name, gene sequence name, author name, title, or keyword.
Examples: RV2429, cobS, Schoolnik, log phase. The search term is case insensitive.
Tutorials
For help, please select one of our tutorials below or look at our FAQ page.
These are a small sample of the tutorials currently available. Push the 'All Tutorials' button to view all of the tutorials.
TBDatabase (TBDB) makes available the tools and resources available at the Stanford Microarray Database and the Broad Institute.
Anyone is welcome to access the published data available on the TBDB site without signing in. Some data in TBDB are unpublished and can therefore only be accessed by the authors and their collaborators after they sign in. The "Access Polices" page provides more information about TBDB accounts.
A grant from the Bill & Melinda Gates Foundation has enabled us to create an integrated software platform for tuberculosis drug discovery and research. Learn more >
Please cite:
Reddy TB, Riley R, Wymore F, Montgomery P, Decaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res doi: 10.1093/nar/gkn652
Full text | PubMed
