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    anatomic Gene Expression Mapping Platform
    (aGEM)

    Category  Genomics>Gene Expression Analysis/Profiling/Tools

    Abstract  The aGEM Platform is an integrative system for analyzing
    spatial-temporal gene expression information.

    This advanced platform makes it easy to access information related to
    the 'anatomical pattern' of 'gene expression' in the mouse, so that it can
    be used in many functional genomics studies.

    The platform allows the integration of gene expression data with spatial-
    temporal anatomic data by means of an intuitive and user friendly
    viewer.

    The aGEM Platform has been built by extending the Distributed
    Annotation System (DAS) protocol that was originally designed to share
    ‘genome annotations’ over the World Wide Web (WWW).

    DAS is a client-server system in which a single client integrates
    information from multiple distributed servers.

    The aGEM Platform provides information to answer three (3) main
    questions:

    1) Which are the genes that are expressed in a given anatomical
    component?

    2) In which anatomical structures are a given gene (or set of genes)
    expressed?

    3) Is there any correlation among these findings?

    Currently this Platform includes several well-known mouse resources
    (EMAGE, GXD, GENSAT, ABA and Symatlas), hosting gene expression
    data obtained mostly from 'in situ' techniques together with a broad set
    of image derived annotations, and general biological information
    databases such as KEGG and OMIM.

    aGEM Not only gives an integrated view of the databases mentioned
    above, but also allows the experimentalist to retrieve relevant statistical
    information relating gene expression, anatomical structure (space) and
    developmental stage (time).

    Overview of integrated aGEM databases --

    1) The EMAGE database was the result of an innovative project that
    started in 1994, the UK MRC Human Genetics Unit in Edinburgh,
    together with the Jackson Laboratory in the USA (Ringwald M. et al,
    1994).

    This project was devoted to create 3D grey-level voxel images from
    several mouse developmental stages (named Theiler Stages) on which
    image-mapped gene-expression data coming from in situ experiments
    were referred (EMAGE database, Venkataraman S. et al, 2008).

    2) The GXD database is a component of the Mouse Genome
    Informatics (MGI) resource, the community model organism database
    for the laboratory mouse.

    GXD currently stores gene expression data coming from in situ
    techniques as well as from other techniques such as northern blot, real-
    time polymerase chain reaction, etc, and referring to the embryo and
    adult mouse.

    3) The GENSAT project aims to map the expression of genes in the
    central nervous system (CNS) of the mouse, using both in situ
    hybridization and transgenic mouse techniques.
    It is a collection of pictorial gene expression maps of the brain and
    spinal cord of the mouse.

    GENSAT catalogs images of histological sections of the developing
    (embryonic days 10.5 and 15.5) and adult mouse brain in which tags,
    such as ‘Enhanced Green Fluorescence Protein’, have been used to
    visualize the relative degree in situ expression for a wide array of genes.

    Please note that currently this database includes only data for the
    Theiler stages 16, and 23 plus the adult mouse.

    4) The Allen Brain Atlas (ABA), which is the result of a project that
    systematically profiles 3D high-resolution gene expression in postnatal
    mouse brains for thousands of genes by performing in situ hybridization
    in an automated fashion.

    5) GNF-Symatlas, which is an atlas of gene expression in 79 human
    and 61 mouse tissues obtained by means of microarray technology.

    6) The Mouse Tumor Biology Database (MTB) provides access to data
    about endogenously arising tumors in genetically defined mice.

    7) The Online Mendelian Inheritance in Man (OMIM) database is a
    comprehensive, authoritative, and timely compendium of human genes
    and genetic phenotypes.

    The full-text, referenced overviews in OMIM contain information on all
    known Mendelian disorders and over 12,000 genes. OMIM focuses on
    the relationship between phenotype and genotype.

    8) The KEGG Pathway database is a collection of pathway maps
    representing knowledge on the molecular interaction and reaction
    networks for metabolism, genetic information processing,
    environmental information processing, cellular processes, human
    diseases and drug development images from several mouse
    developmental stages (named Theiler Stages) on which image-
    mapped gene-expression data coming from in situ experiments were
    referred (EMAGE database, Venkataraman S. et al, 2008).

    OWLViewer --

    To make the 'query by anatomy' easier, in aGEM v2.0 the manufacturer
    has included an advanced and friendly ontology viewer.

    If the user knows the exact name of the anatomical component they
    want to search for, the viewer will find it in the broad ontology.

    On the other hand, the viewer has an 'auto-complete function' that helps
    the user if they do Not know the exact name of the anatomical structure.

    OWLViewer allows you to explore a wide set of OWL ontology files, like
    the developmental mouse anatomical ontology (EMAP), displaying the
    terms and relations between them.

    OWLViewer is also integrated with the Visual Genomics platform aGEM,
    allowing you to search for additional info related to anatomical terms.

    OWLViewer has been created using Java technology, to provide a
    widely available environment using third-party libraries like ‘prefuse’ or
    the OWL-API.

    The application can also be used via web browsers due to Java Web
    Start technology, without explicit installation or download.

    OwlViewer main features/capabilities include:

    1) Ontology files can be loaded automatically at start up using
    application parameters. Also a term can be displayed automatically
    using the same mechanism.

    2) If provided within the ‘ontology file’, additional info (definition, author
    or comments) is displayed when you mouse over a node to help you
    with the identification of terms.

    3) Allows searching in the ontology tree, expanding the desired term,
    providing its name or identifier, including auto-complete functionality.

    4) Provides ‘cache’ support to minimize network traffic.

    5) Allows you to save 'the ontology' in graphical or comma separated
    values (CVS) format.

    System Requirements  

    Web based.

    Manufacturer   


    Price   Contact manufacturer

    G6G Product Number  20476

    G6G Manufacturer Number 104101
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