GATE: Software for the Analysis and Visualization of High-Dimensional Time-series Expression Data

Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, New York, NY, USA.
Bioinformatics (Impact Factor: 4.98). 11/2009; 26(1):143-4. DOI: 10.1093/bioinformatics/btp628
Source: PubMed


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 interroga-tion 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. AVAILABILITY: GATE is available for download and is free for academic use from

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Available from: Ben D MacArthur,
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    • "These approaches have their own advantages and disadvantages but most of these alternative methods have not been widely adopted. In the past, we have developed the software tool grid-analysis of time-series expression (GATE), which is a tool to visualize time-series gene expression data on a hexagonal grid movie (MacArthur, et al., 2010). Neighboring genes on the GATE hexagonal grid can be considered connected in a network where links between genes are established based on gene-gene time-series correlation. "
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    • "This tool gives a clustered view of all proteins or phosphopeptides that were discovered (each represented by a hexagon). The clustering was performed using the GATE software [53]. The brightness of each hexagon indicates the significance of change determined for the protein or phosphopeptide and selected oncogene (red for up-regulation and green for down-regulation). "
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