HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization

• DOI: 10.1093/bioinformatics/btu082
• Publication Date: 2014-02-08T06:25:07Z
• Authors: Jonas Paulsen; Geir Kjetil Sandve; Sveinung Gundersen; Tonje G. Lien; Kai Trengereid; Eivind Hovig
• Keywords: Genome; Data Interpretation, Statistical; 0206 medical engineering; High-Throughput Nucleotide Sequencing; Genomics; 02 engineering and technology; Applications Notes; Chromatin; Software

Abstract Summary: Recently developed methods that couple next-generation sequencing with chromosome conformation capture-based techniques, such as Hi-C and ChIA-PET, allow for characterization of genome-wide chromatin 3D structure. Understanding the organization of chromatin in three dimensions is a crucial next step in the unraveling of global gene regulation, and methods for analyzing such data are needed. We have developed HiBrowse, a user-friendly web-tool consisting of a range of hypothesis-based and descriptive statistics, using realistic assumptions in null-models. Availability and implementation: HiBrowse is supported by all major browsers, and is freely available at http://hyperbrowser.uio.no/3d. Software is implemented in Python, and source code is available for download by following instructions on the main site. Contact: [e-mail] Supplementary Information: Supplementary data are available at Bioinformatics online.