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.

News

12/7/2009 Version update from 1.3.1 to 1.4.1

GATE now supports the blue-yellow color scheme. To use the blue-yellow color option select "change expression colors" from the view menu.

12/4/2009 Blurb about GATE on Scientific American

A blog post describing the GATE software written by Katherine Harmon entitled "Molecular movies: New software animates gene expression data" was published on SciAm.com.

11/19/2009 GATE in Lauren's Nature paper

GATE was used in a research project in collaboration with the Lemischka Lab. The paper resulting from the project was published in Nature.

GATE: Getting Started Quick Instructions

From this webpage you can download the latest version of the GATE (Grid Analysis of Time-Series Expression) software. Click on the icon to download a self installing program. To install the software follow the instructions given by the installer.

Instructions:

Once you start GATE you will have to choose a precomputed cluster file (.clu file) to analyze. The cluster files are text files created from the time-course data using an annealing algorithm that optimizes the location of genes based on their correlated expression over time. The genes are clustered as a hexagonal array where each gene is represented by one hexagon. Although the array appears on the screen as two-dimensional, the edges of the array fold back on themselves forming a torus. The location of each gene on the array is fixed.

Once the program loads the cluster file, the array display will initially appear black. Pressing the play button at the bottom left will start the movie. You can use the time slider to reply the movie and the pause/play button to stop the movie at any time-point. The color scheme is red for upregulated genes and green for downregulated genes. By hovering over the hexagons you can view the gene name and its timeline displayed at top right panel.

You can select a group of genes from the grid by holding down the left-mouse-button and painting a circle around the desired area. The selected genes will be highlighted in purple and listed in a box on the right. Such list of selected genes can be exported for analysis by other programs by clicking the "Save Selected Genes" button below the list on the bottom right. To clear the selection of genes either press on the “Deselect” button (top panel) or right-click anywhere on the array then choose "Clear Selection" from the option menu.

The left panel contains options for integrating prior knowledge datasets with the genes displayed on the hexagonal array. Three of such options are enrichment analyses and one option is for integrating protein-protein interaction networks with the genes on the hexagonal array.

The GATE software is continuously improved, so please report to us any bugs you identify. Also we appreciate any suggestions for enhancements.

Please contact Alexander Lachmann for help in regards to installation, usage and bug report. All other inquires should be addressed to Avi Ma'ayan. GATE is freely available for academic users. Commercial users should contact William Chiang from Mount Sinai's Office of Technology and Business Development for licensing.