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Bioinformatics Advance Access published online on November 5, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp628
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Ben D. MacArthur 1,2,{dagger}, Alexander Lachmann 1,{dagger}, Ihor R. Lemischka 2,* and Avi Ma'ayan 1,*

1 Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY); 2 Depart-ment of Gene and Cell Medicine, Black Family Stem Cell Institute; Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029

*To whom correspondence should be addressed. Ihor R. Lemischka, Mr. Avi Ma'ayan, E-mail: avi.maayan{at}mssm.edu


  Abstract

Summary: We present Grid Analysis of Time-series Expression (GATE), an integrated computational software platform for the analysis and visualization of high-dimensional bio-molecular 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.

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{at}mssm.edu

Associate Editor: Dr. Olga Troyanskaya

{dagger}Contributed equally.

Received on June 22, 2009; revised on October 26, 2009; accepted on November 3, 2009

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