An interesting paradigm in bioinformatics is to search for biological data and to interpret it based on some reference database. One greatest application is comparisons of gene sets based on the overlap. All this kind of analysis has a major drawback of lack of gene centric data. Moreover it has also been found that gene expression involves a lot of protein machinery like enhancers etc. In their recent study Sheffield et al. (2016) have presented an R package LOLA (Locus overlap Analysis) which is an enrichment analysis based on genomic regions.
LOLA makes genomic set analysis fast and easy. LOLA facilitates the understanding of epigenomic and functional genomics data. It is available at http://lola.computational-epigenetics.org
Reference:
Sheffield et al.(2016) LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. Bioinformatics 32(4) 587-589.