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    EXPANDER 4.0

    Category  Genomics>Gene Expression Analysis/Profiling/Tools

    Abstract  EXPANDER (EXpression Analyzer and DisplayER) is a java-
    based tool for the analysis of gene expression data. It is capable of (1)
    preprocessing (2) visualizing (3) clustering (4) biclustering and (5)
    performing downstream analysis of clusters and biclusters such as
    functional enrichment and promoter analysis (i.e. analysis of gene
    groups for enrichment of transcription factor binding sites in their
    promoters).

    EXPANDER incorporates several conventional gene expression
    analysis algorithms and custom ones that have been developed in the
    computational genomics group in Tel-Aviv University, and provides them
    with an easy-to-operate user interface.

    Gene Expression Analysis Algorithms --

    CLICK --

    CLICK is a novel 'clustering algorithm' which is applicable to gene
    expression analysis as well as to other biological applications. No prior
    assumptions are made on the structure or the number of the clusters.
    The algorithm utilizes graph-theoretic and statistical techniques to
    identify tight groups of highly similar elements (kernels), which are likely
    to belong to the same true cluster.

    SAMBA --

    SAMBA is a novel 'biclustering algorithm' for the identification of
    modules of genes that exhibit similar behavior under a subset of the
    examined biological conditions. SAMBA is an efficient way to discover
    statistically significant biclusters in large scale biological datasets,
    consisting of hundreds or thousands of diverse experiments. It extends
    the standard clustering approach by detecting subtle similarities
    between genes across subsets of the measured conditions and
    enabling genes to participate in several biclusters. Thus, it is more
    suitable for analyzing heterogeneous datasets.

    TANGO --

    TANGO tests whether the group of genes in each cluster is enriched for
    a particular function. The functions of the genes are determined
    according to Gene Ontology (GO) annotation files. Since the GO
    functions are highly related, TANGO performs hyper-geometric
    enrichment tests and corrects for multiple testing by bootstrapping and
    estimating the empirical p-value distribution for the evaluated sets.

    PRIMA --

    PRIMA (PRomoter Integration in Microarray Analysis) is a program for
    finding transcription factors (TFs) whose binding sites are enriched in a
    given set of promoters. After identifying a group of co-regulated genes
    using clustering or biclustering, the promoters of the genes can be
    analyzed using PRIMA. By utilizing known models for binding sites
    (BSs) of TFs, PRIMA identifies TFs who’s BSs are significantly over-
    represented in that set of promoters. Such TFs are candidate regulators
    of the corresponding set of genes.

    Highlights of features/capabilities of the Expander 4.0 software
    release --

    1) Ability to load and analyze data in .cel (cell intensity) files format.

    2) Missing value estimation using the KNN (K-Nearest Neighbors)
    algorithm.

    3) T-test statistics.

    4) Condition merge utility (calculating an average profile from a set of
    condition profiles).

    5) Ability to run SAMBA and CLICK on large datasets.

    6) Improved color scale range control.

    7) Symbol auto-fill according to Entrez Ids.

    8) Annotation files update.

    9) Expanded promoter analysis range.

    10) Ability to perform log2 operations on the data at the time of the
    analysis.

    11) Support for the analysis of Chicken data (in addition to Human,
    Mouse, Rat, Fly, C. elegans, Arabidopsis and Yeast).

    System Requirements  

    EXPANDER versions are available for Windows OS and for Linux/Unix
    OS and require the pre-installation of the Java Runtime Environment
    (JRE) 5.0 (or higher).

    Manufacturer   

    Prof. Ron Shamir
    Computational Genomics Laboratory
    School of Computer Science
    Tel Aviv University, Israel
    e-mail: expander@cs.tau.ac.il

    Manufacturer's Web Site  www.cs.tau.ac.
    il/~rshamir/expander/expander.html

    Price   Contact manufacturer

    G6G Product Number  20149

    G6G Manufacturer Number 102304
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