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,
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.
Poster for ECCB2010
Article for WCSB2010 (with the results of validation).
Poster at BCC2009.
Executable and example of GUI Windows, version 1.5.2b (mRNA-miR comparison)
Example data files are here
Executables of a GUI Windows, version 1.3.
Sources of the multithread command line Linux version of CoExpress.
Sources of the multithread command line Windows version of CoExpress.
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