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    Tissue-specific Gene Expression and Regulation
    (TiGER)

    Category  Genomics>Gene Expression Databases/Tools

    Abstract  TiGER is a database for generating comprehensive
    information about human tissue-specific gene regulation, including
    both expression and regulatory data, developed by the Bioinformatics
    Lab at Wilmer Eye Institute of Johns Hopkins University.

    The database contains tissue-specific gene expression profiles or
    expressed sequence tag (EST) data, cis-regulatory module (CRM) data,
    and combinatorial gene regulation data.

    Currently, the database contains tissue-specific expression profiles for
    ~20,000 UniGene genes, combinatorial regulation for 7,341 interacting
    transcription factor (TF) pairs, and 6,232 cis-regulatory modules (CRMs)
    for tissue-specific genes.

    Data Organization --

    The data is organized as a relational database, which provides three (3)
    different views: gene view, TF view, and tissue view. Each view has a
    query interface and associated underlying database tables/entities:

    1) The gene view - contains three (3) major entities: (a) “EST” entity that
    stores enrichment values in 30 tissues for each gene; (b) “CRM” entity
    that stores the conservation profile, the density profile, and the energy
    profile used for CRM detections in the promoter region of each gene;
    and (c) “GeneCode” entity that stores the mapping between UniGene,
    RefSeq and gene symbols.

    2) The TF view - contains one (1) major entity called “TF-Partner”. This
    entity stores all factors that interact with a given TF, the tissue in which
    the interaction occurs and the significance (-log (p)) of the interaction.

    3) The tissue view - contains three (3) major entities: (a) &“TSS-Genes”
    entity that stores genes preferentially expressed in each of the 30
    tissues; (b) “TSS-TFs” entity that stores interactions between TFs in
    each of the 30 tissues; and (c) “TSS-CRMs” entity that stores CRM
    modules in the promoter regions of tissue-specific genes.

    Data Quality --

    EST Enrichment - The manufacturer has included P-values for the
    enrichment scores in the EST download file, where the 1st column is
    tissue name, the 2nd column is the enrichment score, and the 3rd
    column is the [-log10(P)] value.

    The manufacturer defines a gene as a tissue-specific gene if it satisfies
    two (2) criteria: the enrichment score is greater than 5 and the P-value is
    smaller than 10-3.5.

    TF Interaction - The manufacturer has included P-values for the TF
    interaction in a summary table and a download file. To evaluate TF
    interaction results, the manufacturer uses known interactions as a
    positive control due to the scarcity of a tissue-specific interaction.

    More than 40% of the known interactions are recovered, with 84-fold
    enrichment compared to the expected.

    CRM Identification - A sensitivity of 12% and enrichment of 10 using
    known regulatory regions as a positive control is provided.

    Data Up-To-Datedness --

    The manufacturer obtained DNA sequences and annotations (such as
    RefSeq) from the Human May 2004 (hg17) assembly via the UCSC
    Genome Browser (see G6G Product Number 20197). Conservation
    score data was also downloaded from the multiple alignments of eight
    (8) vertebrate genomes with Human (hg17) via the UCSC Genome
    Browser.

    The EST database was downloaded from National Center for
    Biotechnology Information (NCBI) website in 2005.

    As more experimental data accumulates related to the nature of TF-DNA
    interactions, the manufacturer plans to further develop their predictions
    on tissue-specific TF interactions.

    The manufacturer also plans to extend their work on CRM detection by
    relating regulatory elements with temporal (e.g., development) and
    spatial (e.g., cell types) attributes.

    As new predictions on tissue-specific gene regulation accumulate, the
    TiGER database will need to be further expanded and modified. The
    manufacturer will update the content of the database on a regular basis.

    Distribution --

    TiGER has been constructed for free access and use. The
    downloadable data formats include standard .txt text files and .png
    images.

    System Requirements  

    Web browser

    Manufacturer   

    Bioinformatics Lab at Wilmer Eye Institute of Johns Hopkins University
    600 N. Wolfe Street
    Baltimore, MD 21287
    TEL: 410-955-5080
    E-mail contact: Jiang Qian (jiang.qian@jhmi.edu)
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