Using neighborhood graphs for the investigation of e. coli gene clusters

Clustering is commonly used in the analysis of geneexpression data to nd groups of co{expressed genes.The denition of gene clusters is not very clear asgenetic interactions are extremely complex. For thisreason the relationship between clusters is very importantas co{expressed genes can end up in dierentclusters. The neighborhood graph is a useful tool tovisualize the cluster structure. In this paper the Rpackage gcExplorer is presented which is an interactivetoolbox for the exploration of gene clusters. Additionalinformation about the gene clusters like theannotation of genes to functional groups (e.g., GOcategories) can easily be investigated. The new visualizationtoolbox is demonstrated on microarray datafrom E. coli.