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

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.

Fig. 1.

(A) Overview of statistical hypothesis tests implemented in HiBrowse. See Gundersen et al. (2011) for an in-depth explanation of track types, and the Supplementary Material for details about each statistic. (B) Example of a HiBrowse analysis using the ‘Linked elements more/less co-localized in 3D?’ statistic, investigating whether fusion transcripts are co-localized in 3D. (C) Result page from the analysis, presenting the question asked by the user together with both a simplistic and a more detailed answer giving the P-value and model assumption details. Links are provided to full details of the results at individual chromosome regions