ToppCluster accepts input in one of two ways: (i) as separate lists of genes which can be successively added and named, or (ii), using the ‘alternative entry’ method, as a two-column list with genes in the first column and the name of the gene list in the second column. Accepted input is limited to human genes at present. One or any of the 17 annotation sources can be used for feature enrichment analyses. Each feature analysis can be adjusted based on the P-value cutoff, the multiple testing correction method or the minimum and maximum number of genes present for each annotation type. For example, limiting enrichments to ontologies that have fewer associated genes can allow for a greater focus on specific classes of gene feature or function. Multiple choices are available for the formatting and delivery of results. The user can opt for results to be obtained in tabular format as comma-separated values, tab-separated values or HTML table format. It is also possible to obtain the results in various visualization formats—a standard heatmap in a PDF file generated using R (18 ) (http://www.R-project.org), TreeView (13 (link),14 (link)) clustered data tree (CDT) heatmap files, GenePattern (19 (link)) GCT format, Cytoscape (15 (link)) XGMML importable network formats, Gephi (16 ) importable GEXF network formats or as pre-laid out network images using the PNG option.