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Quick Links

  • Feature Search:Search for features by type. Filter on an additional text query if desired.
  • Gene Expression Publications: Search and browse publications with gene expression data that are stored in TBDB.
  • Samples and Conditions:
    Search for a gene over all published samples and explore the expression significance of the indicated gene.
  • Gene Profiles:
    Search for a gene in the published data sets. You will be able to explore the gene expression of the indicated gene in each publication.
  • My Repository (sign in required): Access your saved microarray data sets for further analysis.
  • BLAST - search all genomes by sequencing similarity
  • Genes - Gene annotations by functional categories
  • Download - download data files for sequence and annotation

    • Welcome to TBDB

     

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    What is TBDB?

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    Explore TBDB

    Data

    The current release of TBDB houses genome sequence data and annotations for 28+ different Mycobacterium tuberculosis strains and related bacteria. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives. TBDB currently hosts data for nearly 1500 public tuberculosis microarrays and 260 arrays for Streptomyces.

    Genome Data and Annotations
    Genomes (Contigs, Supercontigs) Browse... Download...
    Genes Browse... Download...
    Proteins Browse... Download...
    RNAs Browse... Download...
    Microarray Expression Data
    Microarray Experiments Browse... Download...
    Gene Expression Publications Browse... Download...

     

    Tools

    Search

    Genome Search

    Expression Search

    Comparative Analysis

    Synteny Map
    Displays synteny between genomes relative to chromosomes.

    Dot Plot
    Displays a dotplot of a reference genome compared to one or more alternate genomes.

    Circular Genome Viewer shows genomic feature densities and genome alignments in an overview that reflects the physical structure of circular genomes. Feature densities and alignments are represented as tracks around the circle.

    Genome Map provides a linear view of genome features of one or more sequences. Selecting a region of a sequence will project the synteny between itself and the other displayed genomes.

    Browse Regions
    Retrieve DNA, find clones, and graphically view sequence regions

     

    Tasks

    Basic Tasks: Tutorials

    How do I find information on my favorite gene?

    What information is provided for each gene in TBDB?

    I am studying a gene in M. tb. H37Rv. How do I find its ortholog in another strain?

    Gene Profiles: How do I find gene expression data from a publication?

    Downloading Sequence Data and Gene Annotation

    Gene Expression Samples and Conditions: How do I find samples where my favorite gene is significantly expressed?

    I am interested in a set of experiments in TBDB. How do I map expression data from these experiments onto the metabolic overview?

    I have a group of genes of interest. How do I view this in the context of the metabolic overview?

    I have a gene of interest that is involved in a pathway. How do I view all other genes in the same pathway?

    Advanced Tasks: Tutorials

    Identify the RD1 region using comparative genomics

    Using Genome Map to Find the RD2 Deletion

    Advanced Search

    How do I map expression data from my own experiments onto the metabolic overview?