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

Jonas Paulsen; Geir Kjetil Sandve; Sveinung Gundersen; Tonje G Lien; Kai Trengereid; Eivind Hovig

doi:10.1093/bioinformatics/btu082

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

Bioinformatics. 2014 Jun 1;30(11):1620-2. doi: 10.1093/bioinformatics/btu082. Epub 2014 Feb 7.

Authors

Jonas Paulsen¹, Geir Kjetil Sandve¹, Sveinung Gundersen¹, Tonje G Lien¹, Kai Trengereid¹, Eivind Hovig²

Affiliations

¹ Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway.
² Institute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, NorwayInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, NorwayInstitute for Cancer Genetics and Informatics, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, PO Box 4950, Nydalen, 0424 Oslo, Department of Mathematics, University of Oslo, Problemveien 7, 0313 Oslo and ELIXIR project, Department of Informatics, University of Oslo, Problemveien 7, 0313 Oslo, Norway.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromatin / chemistry*
Data Interpretation, Statistical
Genome
Genomics / methods
High-Throughput Nucleotide Sequencing
Software*

Substances

Chromatin