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, possibility for customized preprocessiong usin R;
    filtering;
    advanced interactive analysis of the expression profiles;
    building and visualization of CE matrix using correlation or mutual information metrics;
    comparing the detected co-expressions with predicted targets (for miRNA:mRNA interaction).
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

    CoExpress v.1.5 executables
    CoExpress v.1.5 source is available upon a request (will be put online when publication is accepted).
    Manual
    Examples - data files for the analysis.

Other downloads

    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.
    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