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Gene Expression Browser (GEB) integrates large amounts of independent microarray experiments together to generate expression profiles for each gene. Therefore, GEB is a cross-experiment microarray data viewer. GEB includes three parts: (1) Web2.0-based interfaces to visualize gene expression profiles. (2) Software applications for microarray data processing and bioinformatic relationship computation. (3) Microarray data. The first version GEB is released together with 142 Arabidopsis microarray experiments (2436 Affymetrix ATH1 chips). We will integrate public mouse and human microarray data and build GEB for Mouse and GEB for Human in 2009.
Microarray experiment designs are simplified as T/C (Treatment over Control). The average of all chips from an experiment is used as control when there is no obvious control in experimental designs (for example, the microarray experiments with different tissues). GEB has T/C View and Gene View. The T/C View displays all genes in a T/C. On the other hand, Gene View displays all T/Cs in a gene. T/C View and Gene View are presented in MA plot that shows intensity-dependent ratio of microarray data. Fig 1 is an example of GEB T/C View and Fig 2 is a Gene View. Each data point on T/C View represents a gene while each data point in Gene View represents a T/C. Blue data points mean treatment is statistically different from control at t-test p-value less than 0.01. Green data points mean treatment is statistically different from control at t-test p-value 0.01-0.05. Yellow data points mean treatment is statistically same to control (t-test p-value bigger than 0.05). A horizontal zone on MA plot is 1.5-fold change of treatment over control. The data points above the upper edge of horizontal zone have more than 1.5-fold expression increase of treatment over control. The data points below the bottom edge of horizontal zone have more than 1.5-fold expression decrease of treatment over control. A vertical zone on MA plot is the level of background signals. The data points that at right of vertical zone have real and reliable expression signals that are bigger than background signal. On the other hand, the data points at left of vertical zone are similar to background (possible false or noisy signals).
In additional to view all genes on a T/C or all T/Cs on a gene with GEB T/C View or Gene View, GEB also provides Slides View for displaying multiple T/C View or Gene View together with slides show. Click here to view a slide show of T/C views that displays the gene expression in the T/Cs of pathogen infection, TCH conditions and disease-resistant mutants. Click to view slide show of Gene views that displays expression profiles of partial heat-shock proteins.
We will develop GEB for Mouse and GEB for Human in near future. Scientists can use GEB for discovering gene expression profiles that are important to gene expression regulation research, gene functions, pathways, biomarker discovery, disease diagnosis development, drug discovery and clinical trial.
GEB is a free online service that uses microarray data from public repositories. Welcome scientists to involve in GEB projects. Please let me know if any scientist is interested in donating data, doing data annotation or software testing. GEB can be also used for visualizing private microarray data. We can release licenses and help industrial, academic or non-profit institutes to integrate private microarray data and deploy GEB in enterprise’s intranet. Please contact us if you are interested in licensing GEB.