GEB | Gene Expression Browser Developed by Ming Zhang

Please Cite GEB:

Zhang et al (2010) Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization. BMC Bioinformatics 11: 433

About Arabidopsis GEB

Gene Expression Browser (GEB) is a free online service for scientists to find gene expression profiles. The first version of GEB is delivered with 436 Affymetrix ATH1 Arabidopsis microarray experiments, in which there are 2,007 T/Cs (treatment over control) and 45,460,330 pairs of log2 ratios and P values. The microarray raw data and sample annotation were collected from NASC's Affymetrix Service and NCBI GEO. Users can obtain gene expression profiles by searching the key words in gene annotation, T/C description or experiment description.

Terminology

T/C stands for treatment over control. A T/C is defined with one-factor difference between treatment and control. Meanwhile, the single different factor between treatment and control has clear biological meaning. Therefore, a T/C can be understood as an experimental condition or a single stimulus. GEB T/C View shows the expression change (log2 ratio) of all genes under the T/C condition. Click here to view an example T/C View of "16 hr Pseudomonas infection". Co-regulation T/Cs are a set of T/Cs that have similar expression profiles. Click here to see the co-regulation T/Cs of "16 hr Pseudomonas infection". GEB Gene View shows all T/Cs that affect the expression (log2 ratio) of a selected gene. Click here to visit an example Gene View of Arabidopsis PR-1 gene. Co-responsive genes are a set of genes that simulatively response to different T/Cs. Click here to see the co-responsive genes of PR-1. Both T/C View and Gene View are presented by MA plot. MA plot is used to visualize intensity-dependent ratio of microarray data. The MA plot uses M (log2 ratio of treatment over control) as the y-axis and A (average log2 intensity of treatment and control) as the x-axis. The plot uses data point color code to show the t-test P value of log2 ratio. Blue, green and yellow represents P values of less than 0.01, 0.01-0.05 or larger than 0.05, respectively. Therefore, GEB MA plot displays both the scale and the reliability of ratio data.

Quick Start

Enter key words such as heat, cold or infection into the search box and click Submit to find search results. Click on the link to reach gene expression profile shown by Gene View or T/C View. Use the mouse to drag-and-drop the red square on the top-left MA plot onto the data points to find detailed information of each data point. Click 'select' link to mark the data point on the MA plot. Please have a training by clicking Flash video show, Quick Start, slide show or video show in Youtube (watch in high quality)

License

GEB is composed of a set of software tools, such as data extraction tool, microarray data management system, data annotation tool, data processing pipeline and data search & visualization tool. We can release licenses and provide technical supports to deploy GEB in enterprise's intranet when industrial research institutions have the interests to use GEB for visualizing all thier private gene expression data as totality.

Reference