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


BACKGROUND
GATE is available for download and is free for academic use from http://amp.pharm.mssm.edu/maayan-lab/gate.htm
MacArthur
Ben D
BD
Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, New York, NY, USA.
Lachmann
Alexander
A
Lemischka
Ihor R
IR
Ma'ayan
Avi
A
D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
D020543:Proteome