Abstract
BackgroundPrecise 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 conclusionWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2140-x) contains supplementary material, which is available to authorized users.
Highlights
Precise quantitative and spatiotemporal control of gene expression is necessary to ensure proper cellular differentiation and the maintenance of homeostasis
Chromosome conformation capture methods have been developed for investigating chromatin interactions at both the level of individual loci (i.e. 3C [14], 4C [15], 5C [16], Targeted chromatin capture (T2C) [17]) and genome-wide (i.e. Capture-C [18], Hi-C [19, 20], ChIA-Paired-end tag (PET) [21])
We provide vignettes detailing the use of GenomicInteractions in analysing both Hi-C and ChIA-PET data
Summary
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
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