CoExpress
A Tool for an Effective Co-Expression Analysis of Large Microarray Data Sets
Co-expression (CE) analysis of microarray data may provide interesting insights
in understanding the gene and transcript level regulations in biological samples.
It allows gene-networks reconstruction, disease pattern recognition, inferring of
causal genes, etc. However, due to high computational costs and memory limitations,
there is still a need in effective and user-friendly tools for the analysis of CE.
Here we propose a stand-alone software tool CoExpress for the interactive CE analysis
of microarray data. The software is a user-friendly and allows on-the-fly study of CE,
including:
 expression data preprocessing;
building and visualization of CE matrix using correlation or mutual information metrics;
clustering, visualization and filtering of CE profiles;
visualization of co-expression networks for genes of interest.
The possibility of the user-defined data processing using R-scripting is realized, providing a powerful tool for advanced users.
CoExpress is a free software tool, provided uner GPLv3.
Downloads
Article for WCSB2010 (with the results of validation).
Poster at BCC2009.
Sources of the multithread command line Linux version of CoExpress.
Sources of the multithread command line Windows version of CoExpress.
Executables of a user-friendly Windows version. Due to found instabillity, the 3D network visualization is curently not available.
The sources for a Windows version are available upon a request.
Test data set .
Please note, that the tool is under intensive development.
If you have any problems or questions - please contact us, for example by petr.nazarov[at]crp-sante.lu
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