EXPANDER (EXpression Analyzer and DisplayER) is a java-based tool for analysis of gene expression data. It is capable of (1) preprocessing (2) visualizing (3) clustering (4) biclustering and (5) performing downstream analysis of clusters and biclusters such as functional enrichment and promoter analysis (i.e. analysis of gene groups for enrichment of transcription factor binding sites in their promoters).
EXPANDER incorporates several conventional gene expression analysis algorithms and custom ones that have been developed in the computational genomics group in Tel-Aviv University, and provides them with an easy-to-operate user interface.
EXPANDER versions are available for Windows OS and for Linux/Unix OS and require the pre-installation of the Java Runtime Environment (JRE) 5.0 or later (Expander 6.05 is the first version that fully supports java 1.7). The Java Runtime Environment can be installed via: http://java.sun.com/javase/downloads/index.jsp.
The CEL file preprocessing and the newly added SAM filter utilities require the pre-installation of one of the recent versions of R, a free software environment for statistical computing and graphics. For installation instructions, please refer to R External Application section.
For improved network visualization please install Cytoscape 3.1.1 or higher. Cytoscape can be installed via http://www.cytoscape.org/download.php