HiCEnterprise: identifying long range chromosomal contacts in Hi-C data

Hanna Kranas; Irina Tuszynska; Bartek Wilczynski

doi:10.7717/peerj.10558

HiCEnterprise: identifying long range chromosomal contacts in Hi-C data

PeerJ. 2021 Apr 26:9:e10558. doi: 10.7717/peerj.10558. eCollection 2021.

Authors

Hanna Kranas^#^{1

2}, Irina Tuszynska^#¹, Bartek Wilczynski¹

Affiliations

¹ Institute of Informatics, University of Warsaw, Warsaw, Poland.
² Current Address: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.

^# Contributed equally.

Abstract

Motivation: Computational analysis of chromosomal contact data is currently gaining popularity with the rapid advance in experimental techniques providing access to a growing body of data. An important problem in this area is the identification of long range contacts between distinct chromatin regions. Such loops were shown to exist at different scales, either mediating relatively short range interactions between enhancers and promoters or providing interactions between much larger, distant chromosome domains. A proper statistical analysis as well as availability to a wide research community are crucial in a tool for this task.

Results: We present HiCEnterprise, a first freely available software tool for identification of long range chromatin contacts not only between small regions, but also between chromosomal domains. It implements four different statistical tests for identification of significant contacts for user defined regions or domains as well as necessary functions for input, output and visualization of chromosome contacts.

Availability: The software and the corresponding documentation are available at: github.com/regulomics/HiCEnterprise.

Supplementary information: Supplemental data are available in the online version of the article and at the website regulomics.mimuw.edu.pl/wp/hicenterprise.

Keywords: Chromosome contacts; Hi-C data analysis.

Grants and funding

This work has been supported by the Polish National Science Center Grant decision number (DEC 2015/16/W/NZ2/00314). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.