One general tool that provides the user with multiple results is the GSuite Hyperbrowser, which includes the most similar region sets, unique region sets, and how the co-occurrence counts change along the genome. There are many methods to evaluate the similarity of two region sets, which have been under development for more than a decade. New genomic regions produced from experiments can be associated with established genomic regions using co-occurrence, under the assumption that region sets with many overlapping regions may reflect biological relationships. Īmong the many applications of region sets, interest has grown in methods to compare region sets with one another. Early studies used interval analysis to study regulatory elements for biological conclusions, and region sets are of particular interest in epigenomics, where hundreds of thousands of cell-type specific elements have been shown to play an important part in gene regulation. Increasingly, computational tools are being developed to produce and consume BED files. These data can be summarized into region sets, often stored in BED file format containing genomic regions represented by a chromosome number, start position, stop position, and optional metadata. In the past few years, projects such as ENCODE (Encyclopedia of DNA Elements) and IHEC (International Human Epigenome Consortium) have established large catalogs of genomic features, including regulatory regions, transcription factor binding sites, and SNPs. The Creative Commons Public Domain Dedication waiver ( ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.

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