J-Express

 
J-Express Pro is a comprehensive portable software package for analysis and visualisation of microarray data. The program gives access to multidimensional scaling, clustering, and visualisation in an integrated and flexible way. Its efficiency allows interactive clustering of thousands of expression profiles on standard personal computers.

J-Express can take the output files from any image analysis program as input (or alternatively, gene expression matrices). Functions include quality control, filtering, normalisation, visualisation, clustering, projection (dimensionality reduction), and methods for the identification of marker (differentially expressed) genes. The programme has been designed to keep track of information sufficient to reproduce analyses through a project management system and it is capable of reading files in the MAGE-ML standard format for exchange of MIAME complient descriptions of microarray experiments and analyses. Functionality for export of files in MAGE-ML format is also available. This allows one to download data from public repositories (eg., ArrayExpress at the EBI) or from other tools and databases and furthermore it allows users to easily obtain MAGE-ML format descriptions of their data processing and analysis steps needed for publication purposes.

The J-Express tool originates in the bioinformatics research group at the University of Bergen. The company MolMine AS has the distribution rights to the programme. Through an agreement between MolMine AS and the Norwegian Microarray Consortium, free licenses for J-Express are given to academic Norwegian users.