Journal Article

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

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

in Bioinformatics

Volume 26, issue 1, pages 143-144
Published in print January 2010 | ISSN: 1367-4803
Published online November 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp628
GATE: software for the analysis and visualization of high-dimensional time series expression data

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Summary: 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 http://amp.pharm.mssm.edu/maayan-lab/gate.htm

Contact: avi.maayan@mssm.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1131 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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