News and Updates
- Patients with inadequately treated multidrug resistant (MDR TB) are more infective than others. A study by Escombe et al. finds a small number of inadequately treated MDR TB patients coinfected with HIV were responsible for almost all TB transmission, and some patients were highly infectious. This study highlights the importance of rapid TB drug-susceptibility testing to allow prompt initiation of effective treatment, and environmental control measures to reduce ongoing TB transmission in crowded health care settings.
- TB's return comes with high costs: You might think tuberculosis hasn't been a problem since your grandparents' era, but the illness is making a worldwide comeback. Its costs of treatment and lost productivity are estimated at almost $3 billion a year. Listen to Frank Browning reports on NPR's Market Place.
- Aggressive TB treatment a success: Tuberculosis which is resistant to many current treatments can be overcome with aggressive therapy, research suggests.
- The New England Journal of Medicine: More than 60 percent of patients diagnosed with extensively drug-resistant TB (XDR-TB), a type of tuberculosis that is very difficult to treat were cured with aggressive drug treatment by a team of Peruvian doctors.
- Genome Research: Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis
- Association calls on state to fund tb programs In recognition of World TB Day on March 24, the American Lung Association of California released troubling statewide tuberculosis (TB) statistics and called on the state to avert a resurgence of TB by funding prevention and control efforts.
- Sequencing of XDR TB: Work of South Africa-US research team gives first look at genome of XDR TB from KZN outbreak. Initial analysis highlights small number of DNA differences among drug-resistant and -sensitive microbes.
- PLos Pathogens: Mycobacterium tuberculosis nuoG Is a Virulence Gene That Inhibits Apoptosis of Infected Host Cells
- Elsevier Tuberculosis Journal: Browse or search for articles in the current issue.
- Search PubMed for articles related to Tuberculosis.
- World Health Organization provides information about Tuberculosis for clinicians and public health workers.
- US Centers for Disease Control and Prevention (CDC) provides news and updates about Tuberculosis.
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Getting Started Tutorials
Announcements
June 2009
We will be updating our servers Tuesday morning June 30, 2009 PST. While we do not anticipate any user impact, we apologize in advance for any inconvenience.
May 2009
We are excited to announce the availability of "GeneExpressionScope" a
tool that helps you select samples from the database for a selected
gene (e.g.
cobS), based on the significance of expression values. This tool can be accessed
from a Quick Search results page
(e.g. RV2429)
or directly from a Gene Detail page (e.g. RV2429). For more details please refer to help document and/or a tutorial page to get you started in exploring TBDB with this new tool.
April 2009
- We are happy to announce that TBDB now holds data from a publication by Thuong et. al. titled "Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles". The researchers use microarray and real-time PCR to study differential gene expression in different clinical forms of TB and identify genes determining disease outcome. They further examined whether polymorphisms in differentially regulated genes were associated with susceptibility to different clinical forms of TB. They identified CCL1 as a gene involved in host susceptibility to TB. This is the first study to combine microarray and DNA polymorphism studies to identify genes associated with TB susceptibility.
- In response to user requests, we are developing a suite of tools for simplified access to the gene expression data. The first of these tools, "Expression Connection" was deployed August 2008 and is available through the quick search and most publications.
November 2008
We are pleased to announce the availability of gene annotation reports for M. tuberculosis and related species for download. Please see a tutorial on how to access and down load these gene annotation reports.
October 2008
We are delighted to announce the publication of a paper titled "TB database: an integrated platform for tuberculosis research" in Nucleic Acids Research.
September 2008
We are pleased to announce that TBDB now holds data from a publication by Nuria Andreu and Isidre Gibert titled "Cell population heterogeneity in Mycobacterium tuberculosis H37Rv". Despite the apparent stability of the H37Rv laboratory strain, the authors report the existence of heterogeneity in terms of its virulent indicators: neutral red staining and content of phthiocerol dimycocerosates (PDIMs). Using transcriptional profiling the authors confirmed that a significant heterogeneity existed in strains isolated from H37Rv, in addition to the neutral red and PDIM phenotypes.
August 2008
- We are pleased to announce the integration of dozens of new data analysis tools that are available from GenePattern. Registered users click on the 'GP' icon in their repository.
- We made enhancements to Publication Page and implemented Expression Connection, that provides users an easy access to explore the entire clustered datasets from a given publication in TBDB. For an example of the new Publication Detail page, visit Rustad et al. This enables a novice user to directly view clustered datasets, explore and interrogate TBDB without going through data analysis pipeline.
- We have added two new genome browsing tools to TB Database: Circular Genome Viewer, and Genome Map. Using the Circular Genome Viewer, one can visualize user-selected genome annotations for all TB Database genomes in a circular chromosomal representation. Regions selected in the Circular Genome Viewer can then be exported or viewed in the new Genome Map browser. The Genome Map (right) allows more detailed comparative visualization of genomic regions between different genomes selected manually by the user, or through the Circular Genome Viewer.
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About the TB Database Project
Tuberculosis (TB) is a public health challenge of paramount importance. Control of TB will require a multifaceted approach integrating efficient public health interventions with the discovery and use of new vaccines and drugs. 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 >
TB Resources
Citing TBDB
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