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The evolutionary pressures that underlie the large-scale functionalorganization of the genome are not well understood in eukaryotes. Recentevidence suggests that functionally similar genes may colocalize (cluster) inthe eukaryotic genome, suggesting the role of chromatin-level gene regulationin shaping the physical distribution of coordinated genes. However, few of thebioinformatic tools currently available allow for a systematic study of genecolocalization across several, evolutionarily distant species. Kerfuffle is aweb tool designed to help discover, visualize, and quantify the physicalorganization of genomes by identifying significant gene colocalization andconservation across the assembled genomes of available species (currently up to47, from humans to worms). Kerfuffle only requires the user to specify a listof human genes and the names of other species of interest. Without furtherinput from the user, the software queries the e!Ensembl BioMart server toobtain positional information and discovers homology relations in all genes andspecies specified. Using this information, Kerfuffle performs a multi-speciesclustering analysis, presents downloadable lists of clustered genes, performsMonte Carlo statistical significance calculations, estimates how conserved geneclusters are across species, plots histograms and interactive graphs, allowsusers to save their queries, and generates a downloadable visualization of theclusters using the Circos software. These analyses may be used to furtherexplore the functional roles of gene clusters by interrogating the enrichedmolecular pathways associated with each cluster.

Kerfuffle: a web tool for multi-species gene colocalization analysis