BicAT: a biclustering analysis toolbox.
CONCLUSIONS
Besides classical clustering methods such as hierarchical clustering, in recent years biclustering has become a popular approach to analyze biological data sets, e.g. gene expression data. The Biclustering Analysis Toolbox (BicAT) is a software platform for clustering-based data analysis that integrates various biclustering and clustering techniques in terms of a common graphical user interface. Furthermore, BicAT provides different facilities for data preparation, inspection and postprocessing such as discretization, filtering of biclusters according to specific criteria or gene pair analysis for constructing gene interconnection graphs. The possibility to use different biclustering algorithms inside a single graphical tool allows the user to compare clustering results and choose the algorithm that best fits a specific biological scenario. The toolbox is described in the context of gene expression analysis, but is also applicable to other types of data, e.g. data from proteomics or synthetic lethal experiments.


BACKGROUND
The BicAT toolbox is freely available at http://www.tik.ee.ethz.ch/sop/bicat and runs on all operating systems. The Java source code of the program and a developer's guide is provided on the website as well. Therefore, users may modify the program and add further algorithms or extensions.
Barkow
Simon
S
Reverse Engineering Group: Computer Engineering and Networks Laboratory, Swiss Federal Institute of Technology Zurich ETH Zentrum, 8092 Zurich, Switzerland. barkow@tik.ee.ethz.ch
Bleuler
Stefan
S
Prelic
Amela
A
Zimmermann
Philip
P
Zitzler
Eckart
E
D000465:Algorithms; D001185:Artificial Intelligence; D016000:Cluster Analysis; D003628:Database Management Systems; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods; D012984:Software; D014584:User-Computer Interface