J-Express: exploring gene expression data using Java

J-Express is a Java application that allows the user to analyze gene expres sion (microarray) data in a flexible way giving access to multidimensional scaling, clustering, and visualization methods in an integrated manner. Spe cifically, J-Express includes implementations of hierarchical clustering, k -means, principal component analysis, and self-organizing maps. At present, it does not include methods for comparing two or more experiments for diff erentially expressed genes. The application is completely portable and requ ires only that a Java runtime environment 1.2 is installed on the system. I ts efficiency allows interactive clustering of thousands of expression prof iles on standard personal computers.