Archived Announcements
February 2012
A collaborative Tuberculosis Community Annotation Project (TBCAP) Jamboree has been organized for the first week of March to improve the annotation of the Mycobacterium tuberculosis genome sequence and increase the value of this community resource. It will do so by hosting a forum to which all community members can contribute data and knowledge that will be captured and displayed with respect to the genome sequence, and provide the current TBCAP community members an opportunity to review and revise annotations before they are publicly released.
Prior to the jamboree, all tuberculosis researchers are invited to contribute data from a variety of sources, including data from individual investigator initiated studies as well as large-scale data generation efforts. Examples of the kinds of data and information that will be gathered includes: revised gene predictions; gene names and functions; metabolic, signaling and regulatory pathways; transcription factor binding sites; immune epitopes; polymorphisms, etc. These data will be organized and integrated with other publicly available data through a variety of analytical and visualization tools. Researchers will be invited to join TBCAP working groups organized around major topic areas to review these data. During the Jamboree, TBCAP participants will review these data, identify areas of the annotation requiring additional revision or correction, work to address these issues, and generate a summary of the improved annotation along with recommendations for future work. The revised annotation will be publicly released and submitted to NCBI.
The infrastructure to support the community annotation will be provided through the collaboration of the NIAID funded Genomic Sequencing Center at the Broad Institute, the NIAID funded Bioinformatics Resource Center at Virginia Tech (PATRIC) and the Gates-funded TBDB housed at Stanford and Broad, three groups with considerable experience handling large scale genomic data and building annotation data bases and interfaces to promote community review and revision.
If you have data that would contribute to a more comprehensive annotation of the M. tb. genome and our understanding of the biology of the organism please contact the TBCAP via Patrick Brennan (Patrick.Brennan@colostate.edu). We hope this Jamboree will be part of an ongoing process in which the TB research community works together to improve the value of the annotation.
October 2011
Systems biology data for tuberculosis has been released. This data may be
viewed here. Also
note the new set of Systems Biology menus.
We are pleased to announce the publication
of "Informatics resources for tuberculosis - Towards drug discovery" article in
Tuberculosis journal which compile and summarize about
various TB database resources.
You may view and download the PDF of this article
here.
August 2011
"TB Metabolic Tools" now contains multiple curated pathways and the capacity to "paint" individual genes, lists of genes or clustered genes from an expression profile onto the TB Metabolic Pathway Map!! See below for more information and links to new tutorials.
We are pleased to announce several enhancements to TB Metabolic Pathway tools. The current release includes several manually curated pathways. These Include:
cholesterol degradation,
FAS I cycle,
fatty acid beta oxidation pathway,
GABA shunt,
gluconeogenesis II,
glycolysis III,
methylcitrate cycle I,
methylmalonyl pathway,
mycolate biosynthesis,
mycolate biosynthesis superpathway,
mycothiol biosynthesis,
mycothiol oxidation,
mycothiol-dependent formaldehyde oxidation,
pentose phosphate,
TCA variation IX,
triacylglycerol biosynthesis and
triacylglycerol degradation.
We also developed a suite of "How To" tutorials that can be
accessed
from here, which serve as handy references
to:
- Viewing a list of genes in their metabolic
context.
- View all genes in specific pathway.
- Mapping your own expression data
or TBDB gene expression data onto metabolic
pathways.
Credits: The metabolic pathways and tools underlying TBCyc were curated and
developed in collaboration with the
Bioinformatics Research
Group at SRI International, directed by Dr. Peter Karp.
Please click to send us your feedback on the latest enhancements to TB Metabolic
Pathway tools.
March 2011
We have integrated the GenomeView browser in TBDB to visualize the read data underlying SNP calls. It is accessible from the Polymorphism Feature Detail page and offers a visually attractive and intuitive way to browse diversity sequencing data. Polymorphisms may be searched or browsed.
January 2011
Several members of the TBDB team attended the Keystone TB Symposium in Vancouver, Canada from January 15th to 20th, 2011. Thanks very much for visiting our posters and telling us about your experiences with TBDB. If there is anything you would like to tell us, you are always encouraged to send us an email.
January 2011
TB's Genetic Diversity:
Tutorials:
Navigation:
New Genomes:
We are pleased to announce that TBDB now hosts data from the following three publications.
We are pleased to announce that TBDB now hosts data from the following two publications.
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.
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.
We are delighted to announce the publication of a paper titled "TB database:
an integrated platform for tuberculosis research"
in Nucleic Acids Research.
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.
TBDB team will be there in force at Keystone TB Symposium in Vancouver, Canada from January 15th \
to 20th, 2011. We love to hear from you about your experience with TBDB. We will be happy to provide one-on-one demos of any particular aspects of TBDB you may want to explore further. Send us an email. We look forward to see you at our following poster presentation.
Poster Number: 346
Poster Session 3: Tuesday, January 18, 2011
Poster Title: Accessing Gene Expression Data In Tuberculosis Database (TBDB).
Look for our TBDB team members at this meeting wearing a badge like this.
February 2010
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
We have added several new tutorials and updated many others. A
tutorial navigation graphic appears on the front page.
December 2009
We have updated and simplified the menus and overall site
navigation. This is the result of considerable user feedback.
October 2009
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 vie
w 3-D protein structure and to highlight predicted epitopes and other protein features.
August 2009
Emerging antibiotic resistance necessitating scientists to look for antimicrobial agents from natural sources. O'Donnel
l et. al. in a publication titled "Bioactive Pyri
dine-N-oxide Disulfides from Allium stipitatum" report garlic extract is a potent bactericidal agent against M
ycobacterium tuberculosis. They studied gene expression profiles in TB bacteria treated with Compound 1 isolated from garlic. They report Compound 1 up regula
ted genes involved in oxidative stress and heat shock responses.
In a publication titled "Acti
vation of the eis gene in a W-Beijing strain of Mycobacterium tuberculosis correlates with increased SigA levels and e
nhanced 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 capacit
y 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 "Trans
criptional 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
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
April 2009
November 2008
October 2008
September 2008
August 2008