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    Phenotype Genotype Mapper (PGMapper)

    Category  Genomics>Genetic Data Analysis/Tools

    Abstract  PGMapper is a web-based software tool for linking phenotype
    to genes.

    It can be used for automatically matching a phenotype to genes from a
    defined 'genome region' or a 'group of given genes' by combining the
    mapping information from the Ensembl database and 'gene function'
    information from the Online Mendelian Inheritance in Man (OMIM) and
    PubMed databases.

    Candidate ‘gene search’ can be based on the genome region and key
    words that describe the particular phenotypic features specified by the
    end-users.

    PGMapper obtains the information of all genes of a disease locus or
    quantitative trait loci (QTL) from the Ensembl database and then
    searches the OMIM and PubMed to find those genes relevant to a
    disease or a phenotype trait according to known literature reports.

    For all candidate genes, PGMapper provides detailed information of the
    gene(s) and all related references that support the candidacy in the
    OMIM and PubMed databases.

    It also allows users to easily construct complex search strategies using
    different combinations of keywords or phrases, field qualifiers, text
    connectors and Boolean operators and to test a variety of possible
    relationships between genes and phenotypic traits.

    Although PGMapper was developed to identify the candidate genes of a
    QTL or a disease locus, it can also be used for 'whole genome
    analysis' of a complex trait or a disease.

    PGMapper is a web application based on Java technologies.

    The interface of the system is user friendly and interactive, and all
    results can be viewed online or saved in Excel or the portable document
    format (PDF) format for further analysis.

    PGMapper 'QTL module' and 'disease locus' module --

    The QTL module and disease locus module are both developed to
    search candidate genes for QTL and disease loci, respectively.

    The inputs to the system are the map location of a QTL or a disease
    locus and keywords that can describe the features of a particular
    phenotypic trait or disease.

    First, PGMapper retrieves the information of all genes within a QTL or a
    disease locus from the Ensembl database and then it searches both
    OMIM and PubMed to obtain information about candidate genes.

    The 'search term' is the combination of the ‘gene symbol’ and the
    keywords related to the phenotype.

    For each candidate, all references found from OMIM or PubMed are
    listed on a separate page.

    Users can follow the link to see more details for each reference.

    PGMapper Microarray module --

    Microarray module is used to search candidate genes for microarray
    experiments.

    Users may first choose a set of 'differentially expressed' genes between
    the ‘experimental group’ and the ‘control group’ or those ‘genes of
    interest’, as the inputs to the system and then specify the key words
    possibly associated with specific disease phenotypes.

    The system will automatically pick out those genes that may have
    actions on a disease or other traits of interest based on all available
    reports in both OMIM and PubMed.

    Note: PGMapper is currently available for the candidate gene search of
    human, mouse, rat, zebra fish and 12 other species.

    System Requirements  

    Contact manufacturer

    Manufacturer   

    Weikuan Gu Laboratory
    Department of Orthopedic Surgery-Campbell Clinic
    University of Tennessee Health Science Center
    Memphis, TN 38163
    USA
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