Extracting biclusters from multiple time-series of gene expression profiles

Jochen Supper1, Martin Strauch1, Dierk Wanke2, Klaus Harter2, and Andreas Zell1

1Center for Bioinformatics Tübingen (ZBIT), Germany, 2Center for Plant Physiology Tübingen (ZMBP), Germany


Short description:
EDISA (Extended Dimension Iterative Signature Algorithm) is a novel probabilistic clustering approach for 3D gene-condition-time datasets. Based on mathematical definitions of gene expression modules, the EDISA samples initial modules from the dataset which are then refined by removing genes and conditions until they comply with the module definition. A subsequent extension step ensures gene and condition maximality. We applied the algorithm to a synthetic dataset and were able to successfully recover the implanted modules over a range of background noise intensities. Analysis of microarray datasets has lead us to define three biologically relevant module types: 1) We found modules with independent response profiles to be the most prevalent ones. These modules comprise genes which are co-regulated under several conditions, yet with a different response pattern under each condition. 2) Coherent modules with similar responses under all conditions occurred frequently, too, and were often contained within these modules. 3) A third module type, which covers a response specific to a single condition was also detected, but rarely. All of these modules are essentially different types of biclusters.


Availability:
EDISA is available in three different versions:

EDISA webservice: You can use 3D microarray data clustering tool EDISA right away, using our webservice.
EDISA for Windows: For convenience, we implemented an installer for Windows which can be downloaded at our download section.
EDISA for Linux: In order to install the tool on a Linux platform, you can download the latest version of EDISA at our download section.


License:

Creative Commons License EDISA is subject to the Creative Commons License Attribution 2.0 Generic . Visit our download section for a more detailed description of the license and the terms of use of this software.



info

Download: EDISA for Windows and Linux is available for download.   -   (schröder - 2009-10-13 10:35)
Webservice: The webservice version of EDISA is now available.   -   (schröder - 2009-10-13 11:19)

 

This project is promoted by:

BMBF HepatoSys ZBIT