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    MouseCyc

    Category  Cross-Omics>Knowledge Bases/Databases/Tools

    Abstract  MouseCyc is a database of curated biochemical pathways
    data for the laboratory mouse that can be integrated with functional and
    phenotypic data from the Mouse Genome Informatics (MGI) database.

    The availability of the complete ‘genome sequence’ for the laboratory
    mouse provides an advanced platform for predicting genes and other
    genome features.

    However, building a catalog of genome annotations is just the
    beginning for biology in a “post-genome” era.

    To derive new insights into fundamental biological processes using
    complete genome sequences will require understanding how genome
    features interact in pathways and networks in the cell and how
    perturbations of these interactions contribute to disease processes.

    Toward this end, the manufacturers have implemented a new database
    of curated ‘biochemical pathways’ for the laboratory mouse called
    MouseCyc.

    The MouseCyc database represents a significant advance for
    biomedical researchers wanting to access mouse genetic and
    genomic data in the context of physiological and cellular processes.

    The initial focus for the development of MouseCyc is on metabolism
    and includes such ‘cell level processes’ as biosynthesis, degradation,
    energy production, and detoxification.

    MouseCyc differs from existing pathway databases and software tools
    because of the extent to which the pathway information in MouseCyc is
    integrated with the wealth of ‘biological knowledge’ for the laboratory
    mouse that is available from the Mouse Genome Informatics (MGI)
    database.

    MouseCyc facilitates the use of the laboratory mouse as a model
    system for understanding human biology and disease processes in
    three (3) ways.  

    First, the database provides a means by which the available wealth of
    biological knowledge about mouse genes can be organized in the
    context of 'biochemical pathways'.   

    Second, the query and analysis tools for the database serve as a
    means for researchers to ‘view and analyze’ genome scale
    experiments by overlaying these data onto global views of the curated
    'mouse metabolome'.    

    Finally, MouseCyc supports direct comparisons of 'metabolic
    processes' and pathways between mouse and human; comparisons
    that may be critical to understanding both the power and the 'biological
    limitations' of using mouse models of human disease.

    MouseCyc Implementation --

    Initial PathoLogic analysis, manual curation, and PathoLogic
    incremental updates -

    The initial implementation of the MouseCyc pathway genome database
    using the PathoLogic prediction software (see G6G Product Number
    20235), with Pathway Tools resulted in the prediction of 304 pathways,
    1,832 enzymatic reactions, and 5 transport reactions.  

    Following the automated build of MouseCyc, the predicted reactions
    and pathways were evaluated and refined manually.

    The initial manual curation effort focused on identifying pathways and
    reactions, predicted by PathoLogic, that were Not relevant to
    mammalian biochemistry (e.g., biosynthesis of essential amino  acids).

    The manual curation process resulted in the elimination of 135 non-
    mammalian pathways (45% of the pathways predicted for mouse by
    PathoLogic) from the database.

    The high percentage of predicted pathways in MouseCyc that required
    manual reassignment was Not surprising given that, for historic
    reasons, the  MetaCyc reference database (see G6G Product Number
    20232), used by PathoLogic is somewhat biased toward prokaryotic
    and plant biochemistry.

    Finally, PathoLogic’s Transport Inference Parser (TIP) utility was used to
    identify putative transport reactions.

    For the mouse genome, TIP predicted 80 transport reactions and 542
    transporters.

    MouseCyc 'Data Access' features/capabilities include:

    1) Search the MouseCyc database.  

    2) Browse the pathway ontology in the MouseCyc database.  

    3) Browse all pathways represented in MouseCyc.  

    4) Browse a list of all genes in MouseCyc.

    5) Browse a list of all proteins in MouseCyc according to their activity.

    6) Browse a list of all compounds represented in MouseCyc.

    7) Overlay experimental data onto the Pathway Tools Omics Viewer (see
    G6G Product Number 20237).

    8) Display an Example of Omics Viewer files.

    9) Generate a mouse ‘metabolic map’.

    System Requirements  

    Web-based.

    Manufacturer   

    The Jackson Laboratory
    600 Main Street
    Bar Harbor, Maine 04609
    USA
    Tel: 207-288-6000

    And

    The MouseCyc database is part of the BioCyc (see G6G Product
    Number 20230) collection of pathways databases created using the
    Pathway Tools Software Development kit (see G6G Product Number
    20236) created by Dr. Peter Karp and his research group at SRI,
    International in Palo Alto, California, USA.
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