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    GeneSifter

    Category  Genomics>Gene Expression Analysis/Profiling/Tools

    Abstract   GeneSifter is a Web-based gene expression analysis
    system that integrates advanced data management tools with analysis
    options that enable you to determine both the statistical and biological
    significance of microarray data. GeneSifter is available in Three (3)
    different versions - 1) Lab Edition - for individual researchers or labs
    using microarrays; 2) Core Edition - contains administrative features for
    core microarray facilities; 3) Enterprise Edition - for large organizations
    wanting to host their own GeneSifter. It supports common microarray
    platforms (including Affymetrix, Illumina, Agilent, CodeLink, Applied
    Biosystems, CombiMatrix, etc.), as well as custom arrays. GeneSifter
    features include:

    Integrated Biological Information
    1) Gene Ontologies (GO) Z-score Report - 'Zero in' on the particular
    families of genes most influenced by the experimental conditions. In
    any gene list you can explore hierarchies ranking biological processes
    and functions, automatically guided by a statistical metric that indicates
    how much a particular ontology is over- or underrepresented.
    2) Pathways Report - KEGG Biological pathways in LocusLink which
    are most influenced by the experimental conditions can be
    automatically ranked and visualized in a z-score report similar to the GO
    Report above.
    3) Automatic integration of current UniGene and LocusLink information
    for each gene on an array.
    4) 'One-Click Gene Summary' with information from, and links to,
    external databases such as Gene Ontology, GenBank, UniGene,
    NetAffx, Homologene, OMIM, LocusLink, GeneCards, Pubgene and
    KEGG metabolic pathway diagrams for each gene on an array.
    5) 'One-Click Gene Summary' access to PubGene for identification of
    putative relationships between genes based on scientific literature.
    6) Gene Ontology tree structures and individual designations extracted
    for visualization in 'One-Click Gene Summary'.
    7) Automatic import from NCBI's Gene Expression Omnibus data
    repository (GEO) of Affymetrix data.
    8) Retrieve sequences and store as part of annotation for genes on
    array.
    9) Enhanced metabolic pathways information and diagram links
    included in 'One-Click Gene Summaries'.
    10) UniGene and LocusLink Drosophila melanogaster (and any other
    included organism) information automatically parsed and presented in
    'One-Click Gene Summaries'.
    11) Search, filter and group genes by - chromosome; KEGG metabolic
    pathway; Gene Ontology biological process, molecular function and
    cellular component.
    12) Homo sapiens, Mus musculus, Rattus norvegicus and Drosophila
    melanogaster NCBI RefSeq sequence information links for both mRNA
    and protein products included in 'One-Click Gene Summaries'.
    13) 'One-Click Gene Summary' information exportable with gene lists to
    Excel.
    14) Integrated BLAST and Primer Design Tools available for retrieved
    sequences.

    Affymetrix Platform Integration
    1) Support for native (binary) CHP and CEL files;
    2) Robust Multi-array Average (RMA) method for probe level analysis;
    3) GC Robust Multi-array Average (GC-RMA) method for probe level
    analysis;
    4) QuickLoad and Batch Upload using Affymetrix probe set IDs;
    5) Search by probe set ID;
    6) 'One-Click Gene Summary' access to the NetAffx database.

    Visualization and Presentation
    1) Graphical expression profile summary screens employ color coded
    data visualization for up/down regulation;
    2) Hierarchical sample clustering from any gene list;
    3) Partition clustering using the PAM (Partitioning Around Medoids)
    technique;
    4) Clustering Enhancements, including CLARA (Clustering LARge
    Applications), an enhanced k-medoid partitioning for handling large
    data sets;
    5) Silhouette method to validate data clusters;
    6) Transforms data to ready-to-use formats for a number of specialized
    clustering packages, including Cluster, GeneSpring and the free Web-
    based EPCLUST toolset;
    7) Scatter plot for visualization of pair-wise comparisons - interactive
    design allows for rapid ID of differentially expressed genes with direct
    access to raw data and gene information;
    8) Boxplot option for use in quality control; and more.

    System Requirements  GeneSifter will run on anything with a browser
    and connection to the Internet.

    Manufacturer   Home office; see web site for international locations.

    vizXlabs
    First West Building
    200 First Avenue West, Suite 302
    Seattle, WA 98119
    TEL: 206.283.4363, 877-WEBGENE (877-932-4363)
    email: info@vizxlabs.com, support@genesifter.net

    Manufacturer's Web Site  www.genesifter.net

    Price  Contact manufacturer

    G6G Product Number  20005

    G6G Manufacturer Number  102920
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