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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.


    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) (new)   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

In the case of mistakes or possible copyright violations, please, contact the webmaster. Last update 04-11-2011