Statistical tests were done in the R environment (http://www.R-project.org). Graphs were made using lattice, ggplot2 and gplots R packages. Cluster trees were generated by the APE73 R package and visualized using the FigTree software (http://tree.bio.ed.ac.uk/software/figtree/). Intersections of and distances between various genomic features were calculated using BEDTools74
