GATE: Software for the analysis and visualization of high-dimensional time series expression data

Ben D. Macarthur, Alexander Lachmann, Ihor R. Lemischka, Avi Ma'ayan

    Research output: Contribution to journalArticlepeer-review

    Abstract

    We present Grid Analysis of Time series Expression (GATE), an integrated computational software platform for the analysis and visualization of high-dimensional biomolecular time series. GATE uses a correlation-based clustering algorithm to arrange molecular time series on a two-dimensional hexagonal array and dynamically colors individual hexagons according to the expression level of the molecular component to which they are assigned, to create animated movies of systems-level molecular regulatory dynamics. In order to infer potential regulatory control mechanisms from patterns of correlation, GATE also allows interactive interrogation of movies against a wide variety of prior knowledge datasets. GATE movies can be paused and are interactive, allowing users to reconstruct networks and perform functional enrichment analyses. Movies created with GATE can be saved in Flash format and can be inserted directly into PDF manuscript files as interactive figures. © The Author 2009. Published by Oxford University Press.
    Original languageEnglish
    Article numberbtp628
    Pages (from-to)143-144
    Number of pages1
    JournalBioinformatics
    Volume26
    Issue number1
    DOIs
    Publication statusPublished - 5 Nov 2009

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