@inbook{52ff6a9997c84dda9ae9d98853d364b3,
title = "Chromosome Conformation Capture on Chip (4C): Data Processing",
abstract = "4C methods are useful to investigate dependencies between regulatory mechanisms and chromatin structures by revealing the frequency of chromatin contacts between a locus of interest and remote sequences on the chromosome. In this chapter we describe a protocol for the data analysis of microarray-based 4C experiments, presenting updated versions of the methods we used in a previous study of the large-scale chromatin interaction profile of a Polycomb response element in Drosophila. The protocol covers data preparation, normalization, microarray probe selection, and the multi-resolution detection of regions with enriched chromatin contacts. A reanalysis of two independent mouse datasets illustrates the versatility of this protocol and the importance of data processing in 4C. Methods were implemented in the R package MRA.TA (Multi-Resolution Analyses on Tiling Array data), and they can be used to analyze ChIP-on-chip data on broadly distributed chromatin components such as histone marks.",
keywords = "Journal Article",
author = "Leblanc, {Benjamin Olivier} and Itys Comet and Fr{\'e}d{\'e}ric Bantignies and Giacomo Cavalli",
year = "2016",
doi = "10.1007/978-1-4939-6380-5_21",
language = "English",
isbn = "978-1-4939-6378-2",
volume = "1480",
series = "Methods in Molecular Biology",
publisher = "Springer",
pages = "243--61",
editor = "Chiara Lanzuolo and Beatrice Bodega",
booktitle = "Polycomb Group Proteins",
}