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    Gene Expression Explorer 1.0

    Category  Genomics>Gene Expression Analysis/Profiling/Tools

    Abstract  Gene Expression Explorer (GEE) is an advanced interactive
    visualization environment for the exploration of gene expression data.
    GEE helps you uncover hidden structures and find patterns in large data
    sets, taking full advantage of all annotations and other links that are
    connected with your data. The user interface of GEE displays all data
    sets in 3D in order to be able to visualize them and interactively work
    with them in real-time directly on the computer screen. GEE is built
    around Dynamic PCA an innovative way of combining PCA analysis with
    immediate user interaction. The basic operation used in GEE is
    principal component analysis (PCA).

    Dynamic PCA is PCA analysis combined with instant user response.
    This combination provides an optimal way for a user to visualize and
    analyze a large dataset. It presents a comprehensive view of the data
    set at the same time as the user is given full freedom to explore all
    possible versions of the presented view.

    PCA consists of projecting high dimensional data down to lower
    dimensions. The specific projections of the high-dimensional data are
    chosen in order to maintain as much variance as possible in the
    projected data set. In GEE, data is projected and plotted on a two (2)
    dimensional computer screen and then rotated manually or
    automatically and examined by the naked eye. The unique feature of
    GEE is the possibility to interactively and in real-time manipulate the
    different PCA-plots directly on the computer screen and at the same
    time work with all annotations and other links in a fully integrated way.

    Products features/capabilities include:

    Main functionality --

    1) Create Principal Component Analysis (PCA) plots of large data sets
    (for instance 100 samples and 100,000 variables) on an ordinary PC.

    2) Change parameters at any time with a single mouse click, and
    automatically get an updated plot immediately (in <0.1s).

    3) A simple and intuitive user interface.

    Output -- 1) High quality 3-D graphics; 2) Plot arbitrary principal
    components; 3) Plot both samples and variables; 4) Synchronized plots;
    5) Color the samples and the variables through different methods; 6)
    Label the samples and the variables through different methods.

    Selection --

    1) Work with subsets of the samples and the variables.

    2) Select samples based on clinical variables and other annotations.

    3) Select variables based on variance, analysis of variance (ANOVA),
    correlation coefficients, annotation text searches and imported variable
    lists (such as pathways).

    Editing of data -- 1) Interactive editing of sample annotations; 2)
    Interactive editing of variable lists.

    Verification --

    1) Verify results by re-doing the analysis with permuted sample
    annotations or with random numbers.

    2) Verify results through remove-one-at-a-time cross validation.

    Clusters --
    1) Visualize sample clusters by connecting each sample with its
    nearest neighbors.

    2) Visualize variable clusters by connecting correlated variables.

    Import -- 1) Data files; 2) Variable lists; 3) The complete state of the
    program.

    Export -- 1) Data files; 2) Variable lists; 3) Still images; 4) Videos; 5) The
    complete state of the program.

    Other -- 1) Missing value reconstruction; 2) Variable normalization; 3)
    Multi-dimensional rescaling; 4) ISOMAP.

    Manufacturer offers two (2) licensing models for GEE --

    1) Single user, single computer licenses: A single user, single
    computer license gives one named user the right to use the software on
    one computer. The software will be locked to this computer. The license
    is valid for one year and includes support and upgrades.

    2) Network licenses: A network license allows a certain number of
    concurrent users on a local area network. Any person connected to the
    network can use the software, as long as the maximal number of
    concurrent users is not exceeded. Network licenses are available for
    five or more concurrent users. A user can "check out" a license and use
    the software when not connected to the network. The license is valid for
    one year and includes support and upgrades.

    Note: In addition to the models above there are also special licenses for
    Academia.

    System Requirements  

    Gene Expression Explorer requires:
    1) Windows 2000 or Windows XP
    2) 512 MB of RAM memory
    Gene Expression Explorer 1.0 takes full advantage of processors with
    multiple cores and computers with multiple processors.

    Manufacturer   Home office; see web site for international locations.

    Qlucore AB
    Ideon Science Park
    Ole Römers väg 12,
    223 70 Lund, Sweden
    Phone: +46 46 286 3110

    Manufacturer's Web Site  www.qlucore.com/features.aspx

    Price   Contact manufacturer

    G6G Product Number  20120

    G6G Manufacturer Number 102235
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