Using Neighborhood Graphs for the Investigation of E. Coli Gene Clusters

Clustering is commonly used in the analysis of gene expression data to find groups of co–expressed genes. The definition of gene clusters is not very clear as genetic interactions are extremely complex. For this reason the relationship between clusters is very important as co–expressed genes can end up in different clusters. The neighborhood graph is a useful tool to visualize the cluster structure. In this paper the R package gcExplorer is presented which is an interactive toolbox for the exploration of gene clusters. Additional information about the gene clusters like the annotation of genes to functional groups (e.g., GO categories) can easily be investigated. The new visualization toolbox is demonstrated on microarray data from E. coli.