RT Journal Article SR Electronic T1 normR: Regime enrichment calling for ChIP-seq data JF bioRxiv FD Cold Spring Harbor Laboratory SP 082263 DO 10.1101/082263 A1 Johannes Helmuth A1 Na Li A1 Laura Arrigoni A1 Kathrin Gianmoena A1 Cristina Cadenas A1 Gilles Gasparoni A1 Anupam Sinha A1 Philip Rosenstiel A1 Jörn Walter A1 Jan G. Hengstler A1 Thomas Manke A1 Ho-Ryun Chung YR 2016 UL http://biorxiv.org/content/early/2016/10/20/082263.abstract AB ChIP-seq probes genome-wide localization of DNA-associated proteins. To mitigate technical biases ChIP-seq read densities are normalized to read densities obtained by a control. Our statistical framework “normR” achieves a sensitive normalization by accounting for the effect of putative protein-bound regions on the overall read statistics. Here, we demonstrate normR’s suitability in three studies: (i) calling enrichment for high (H3K4me3) and low (H3K36me3) signal-to-ratio data; (ii) identifying two previously undescribed H3K27me3 and H3K9me3 heterochromatic regimes of broad and peak enrichment; and (iii) calling differential H3K4me3 or H3K27me3-enrichment between HepG2 hepatocarcinoma cells and primary human Hepatocytes. normR is readily available on http://bioconductor.org/packages/normrbpbase-pairCAGECap Analysis of Gene ExpressionChIP-seqChromatin Immunoprecipitation followed by next-generation sequencingEMExpectation MaximizationFDRFalse-Discovery RateGPIGlucose-6-Phosphate Isomerasekbkilo base-pairTSSTranscriptional Start SiteWGBSWhole Genome Bisulfite Sequencing