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    GeneMaths XT

    Category  Genomics>Gene Expression Analysis/Profiling/Tools

    Abstract  GeneMaths XT is a complete and professional software
    system for microarray analysis. Its advanced concept of layers and
    subsets makes it possible to work with different layers for different data
    outputs, for example Cy3 and Cy5, standard deviations, error values,
    etc., as well as different subsets of genes and/or arrays. Also offers full
    error handling through all analysis, mining, and statistics functions.
    Further features include:

    Data import - The import of microarray data is facilitated by means of an
    import wizard and many predefined formats from the major
    quantification programs and databases, such as, Agilent Feature
    Extraction software; Affymetrix (CHP-files, CEL-files, tab-delimited files);
    Arrayplot; Arrayvision; EBI MIAME; Genepix; GEO’s SOFT (raw data,
    datasets, and whole series); Imagene; Koadarray; ScanAlyze;
    ScanArray; Spotfinder, etc.

    Data preprocessing and normalization - Standard Methods offered
    include - Background correction; Log transformation; Lowess
    normalization; Quantile normalization; Variance stabilization; Imputing
    missing values, etc. Besides these standard normalization methods, it
    offers a wide range of methods to preprocess Affymetrix data including
    MAS5.0, dChip, Robust Multichip Analysis (RMA) with many variants, the
    PLIER method or to use a custom algorithm.

    The concept of layers and subsets - A Layer is one single matrix of
    (expression) values (and associated error values) containing all genes
    and experiments in the session (full X-Y matrix). Each element of the
    layer contains a single value together with an optional error value. A
    Subset is a matrix that contains a number of rows and a number of
    columns from the full data matrix in a session (reduced X-Y matrix). A
    subset only defines the rows and columns to be included, and as such,
    applies to all layers of a session. The creation of subsets is helpful in
    stepwise reducing the data matrix to genes that have an interesting
    expression behavior, leaving out those that are invariant or have
    unacceptable errors associated with them.

    Active History and repeatability - GeneMaths XT constructs a
    dependency tree, so that you can see the chain of actions that depend
    on the object that is to be modified. It can automatically recalculate the
    objects and analyses in the chain. It also keeps track of every action
    done by the user, providing a global undo function. The full sequence of
    actions carried out in a session can be printed or exported as a
    readable RTF document. It also allows templates to be recorded that
    contain a series of steps done in a data mining session, which can
    then be used on other data sets.

    Data analysis and classification tools  - Data analysis tools on genes
    and arrays include - hierarchical clustering; bootstrap analysis;
    Euclidean distance clustering; partitioning; principal components
    analysis (PCA); self-organizing maps (SOM); pattern matching; time
    course analysis. Classification tools available in GeneMaths XT
    applicable on genes and arrays include - k-nearest neighbor; neural
    networks and Support Vector Machines (SVM).

    Statistics - A variety of statistical tests are implemented via a wizard.
    Results from tests can be directly passed to the gene and array query
    tool. Multiple hypothesis testing procedures are also available for the
    Family-Wise Error Rate (FWER) control and False Discovery Rate
    (FDR) control.

    The estimation of error - Error handling and error calculation is carried
    out throughout the workflow, and errors can be indicated numerically or
    graphically on any analysis report that supports the use of errors, etc.
    Graphs and plots - Plots can be derived from virtually any [combination
    of] data/results in the analysis, ranging from partial data selections to
    principal components, p-values, etc. The plot tool is wizard-driven. All
    charts and graphs are dynamically updated when the data is
    manipulated.

    Dynamic interface - Different analyses can be viewed and edited
    simultaneously in one integrated environment. The following main
    window classes are designed according to functionality - Main window;
    Plot window; PCA window; SOM window; Partitioning window; Time
    course analysis window.

    Connectivity with external databases - GeneMaths XT offers the
    possibility to link genes and arrays to external databases - Gene
    Ontology database; InterPro database; KEGG database;
    Saccharomyces Genome database; Pseudomonas Genome
    database; EBI; NCBI, etc.

    The script language - Any degree of customization can be obtained
    using the systems embedded script language, which allows
    applications and interface components to be written and used as
    plugins.

    Note: See G6G Product Number 20070 for additional product info from
    this manufacturer.

    System Requirements  

    Hardware requirements GeneMaths XT requires Pentium compatible
    PC running Windows XP (or 2000) as Operating System.
    Memory requirement: 512 MB; 1 GB recommended.
    SXGA true RGB graphics required; 1200x1024 or higher resolution
    recommended.

    Manufacturer   Home office; see web site for international locations.

    Applied Maths, Inc.
    Keistraat 120, 9830 St-Martens-Latem, Belgium
    +32 9 2222 100
    13809 Research Blvd, Suite 645, Austin, TX 78750, U.S.A.
    +1 512 482 9700
    info@applied-maths.com
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