MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates

Caroline Berard (1, 2) , Michael Seifert (3, 4) , Tristan Mary-Huard (1, 5, 6) , Marie-Laure Magniette (1, 7)

1 MIA-Paris - Mathématiques et Informatique Appliquées
2 LITIS - Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes
3 Ctr Informat Serv & High Performance Comp
4 Ctr Biotechnol
5 GQE-Le Moulon - Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale)
6 CNRS - Centre National de la Recherche Scientifique
7 URGV - Unité de recherche en génomique végétale

Background: Chromatin immunoprecipitation coupled with hybridization to a tiling array (ChIP-chip) is a cost-effective and routinely used method to identify protein-DNA interactions or chromatin/histone modifications. The robust identification of ChIP-enriched regions is frequently complicated by noisy measurements. This identification can be improved by accounting for dependencies between adjacent probes on chromosomes and by modeling of biological replicates. Results: MultiChIPmixHMM is a user-friendly R package to analyse ChIP-chip data modeling spatial dependencies between directly adjacent probes on a chromosome and enabling a simultaneous analysis of replicates. It is based on a linear regression mixture model, designed to perform a joint modeling of immunoprecipitated and input measurements. Conclusion: We show the utility of MultiChIPmixHMM by analyzing histone modifications of Arabidopsis thaliana. MultiChIPmixHMM is implemented in R and including functions in C, freely available from the CRAN web site: http://cran.r-project.org.

Mots clés: ARABIDOPSIS; STATES

Domaines: Sciences du Vivant [q-bio]

Caroline Berard, Michael Seifert, Tristan Mary-Huard, Marie-Laure Magniette. MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates. BMC Bioinformatics, 2013, 14, ⟨10.1186/1471-2105-14-271⟩. ⟨hal-01190745⟩