GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data
Author(s)
Harmston, N
Ing-Simmons, E
Perry, M
Baresic, A
Lenhard, B
Type
Journal Article
Abstract
Background: Precise quantitative and spatiotemporal control of gene expression is necessary to ensure proper
cellular differentiation and the maintenance of homeostasis. The relationship between gene expression and
the spatial organisation of chromatin is highly complex, interdependent and not completely understood. The
development of experimental techniques to interrogate both the higher-order structure of chromatin and the
interactions between regulatory elements has recently lead to important insights on how gene expression is
controlled. The ability to gain these and future insights is critically dependent on computational tools for the
analysis and visualisation of data produced by these techniques.
Results and conclusion: We have developed GenomicInteractions, a freely available R/Bioconductor package
designed for processing, analysis and visualisation of data generated from various types of chromosome
conformation capture experiments. The package allows the easy annotation and summarisation of large
genome-wide datasets at both the level of individual interactions and sets of genomic features, and provides
several different methods for interrogating and visualising this type of data. We demonstrate this package’s
utility by showing example analyses performed on interaction datasets generated using Hi-C and ChIA-PET.
cellular differentiation and the maintenance of homeostasis. The relationship between gene expression and
the spatial organisation of chromatin is highly complex, interdependent and not completely understood. The
development of experimental techniques to interrogate both the higher-order structure of chromatin and the
interactions between regulatory elements has recently lead to important insights on how gene expression is
controlled. The ability to gain these and future insights is critically dependent on computational tools for the
analysis and visualisation of data produced by these techniques.
Results and conclusion: We have developed GenomicInteractions, a freely available R/Bioconductor package
designed for processing, analysis and visualisation of data generated from various types of chromosome
conformation capture experiments. The package allows the easy annotation and summarisation of large
genome-wide datasets at both the level of individual interactions and sets of genomic features, and provides
several different methods for interrogating and visualising this type of data. We demonstrate this package’s
utility by showing example analyses performed on interaction datasets generated using Hi-C and ChIA-PET.
Date Issued
2015-11-17
Date Acceptance
2015-10-23
Citation
BMC Genomics, 2015, 16
ISSN
1471-2164
Publisher
BioMed Central
Journal / Book Title
BMC Genomics
Volume
16
Copyright Statement
© 2015 Harmston et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated
License URL
Sponsor
Commission of the European Communities
Grant Number
242048
Subjects
Science & Technology
Life Sciences & Biomedicine
Biotechnology & Applied Microbiology
Genetics & Heredity
CHROMOSOME CONFORMATION CAPTURE
HI-C DATA
CHRONIC LYMPHOCYTIC-LEUKEMIA
RANGE GENOMIC INTERACTIONS
HIGH-RESOLUTION
REGULATORY ELEMENTS
GENE-EXPRESSION
SEQUENCING DATA
RECEPTOR NR4A2
ORGANIZATION
Publication Status
Published
Article Number
963