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.

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.