Abstract

GATE (Grid Analysis of Time-Series Expression) is 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 inserted directly into PDF manuscript files as interactive figures.
Update


We recently updated the GATE software.
Click to download GATE version 2014

Requirements
The program should run on Windows, Mac and Linux OS. Extract the folder to the desired location and double-click on the JAR file to launch the program.
If you are already a GATE user and the old version stopped working for you, remove the old version and reinstall the software from the above link.

User Manual
Getting Started
10/26/2009



Short illustrated introduction to GATE

Case Study
Demonstration
10/26/2009



Analysis of Time-Series Gene Expression Data
Ivanova et al. "Dissecting self-renewal in stem cells with RNA interference" Nature 442, 533-538 (2006)

News

GATE: Getting Started Quick Instructions

GATE is documented at: Ben MacArthur, Alexander Lachmann , Ihor Lemischka and Avi Ma'ayan GATE: Software for the Analysis and Visualization of High-Dimensional Time-series Expression Data. Bioinformatics PMID: 19892805.
Please use this citation when referring to the program.
| Ma'ayan Laboratory | Systems Biology Center New York | Mount Sinai School of Medicine |
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