DEEP - Differential Expression Effector Prediction

In brief

DEEP is a tool that takes your data on differential gene expression (i.e. SAGE or microarray data) and predicts additional molecules which may be of importance in either of the two tissues (or conditions or time points...) under examination. It does so by combining your data with information on signaling networks stored in the TRANSPATH® database (BIOBASE GmbH, Wolfenbüttel).

DEEP consists of a core server module and a JSP-based web interface, both running here in Göttingen. Additionally, you can download and install a Java client for DEEP on your local computer. Since the local client allows for much more interactivity when inspecting the calculation results (e.g. zooming and panning), its use is strongly encouraged.

The web interface

Click the following link to access the DEEP web interface:

DEEP Web Interface

Requirements for the Java client

DEEP consists of a server module, running here in Göttingen, and a client program which communicates with the server in order to reconstruct putative signaling networks and which runs on your own computer. Since DEEP has been implemented in the Java programming language, a moderately recent Java runtime environment (>= 1.5; get a free download from Sun's Java homepage) is required.

Installing the Java client

The DEEP Java client can automatically be downloaded, installed and launched by clicking the following link:

Click here to directly launch the DEEP client! (Java Web Start)

After the download is complete, a dialog box will pop up, saying something like "The application's digital signature cannot be verified. Do you want to run the application?". You can safely say "Run" here, and even tick the checkbox labeled "Always trust content from this publisher" -- at least if you do trust us...

Background: The DEEP client needs both read and write access to your hard drive since it stores your preferences in an XML file called ".deep-client-config.xml" in your home directory. Furthermore, if you want to save analysis results, the client obviously also needs read/write access to your hard disk. As a security measure, Java web start applications are only granted full access to system ressources if they have been digitally signed by someone known to the Java Web Start launcher. And since your local Java installation most likely hasn't seen our institute's signature before, it asks you whether or not you trust the people offering the just downloaded application and if you want to launch it.

Publications

Dönitz, J., Crass, T., Degenhardt, J., Haubrock, M. and Wingender, E.: DEEP: Ein Programm zur Vorhersage von Effektoren differenziell exprimierter Gene. GenomXPress 08(3), 4 (2008). (In German.) [link]
Degenhardt, J., Haubrock, M., Dönitz, J., Wingender, E. and Crass, T.: DEEP--A tool for differential expression effector prediction. Nucleic Acids Res. 35, W619-W624 (2007). [link}