title: metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns.
abstract: ChIP-Sequencing (ChIP-Seq) provides a vast amount of information regarding the localization of proteins across the genome. The aggregation of ChIP-Seq enrichment signal in a metagene plot is an approach commonly used to summarize data complexity and to obtain a high level visual representation of the general occupancy pattern of a protein. Here we present the R package metagene, the graphical interface Imetagene and the companion package similaRpeak. Together, they provide a framework to integrate, summarize and compare the ChIP-Seq enrichment signal from complex experimental designs. Those packages identify and quantify similarities or dissimilarities in patterns between large numbers of ChIP-Seq profiles. We used metagene to investigate the differential occupancy of regulatory factors at noncoding regulatory regions (promoters and enhancers) in relation to transcriptional activity in GM12878 B-lymphocytes. The relationships between occupancy patterns and transcriptional activity suggest two different mechanisms of action for transcriptional control: i) a "gradient effect" where the regulatory factor occupancy levels follow transcription and ii) a "threshold effect" where the regulatory factor occupancy levels max out prior to reaching maximal transcription. metagene, Imetagene and similaRpeak are implemented in R under the Artistic license 2.0 and are available on Bioconductor.
authors.affiliation: Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada.|Département de Médecine Moléculaire, Faculté de médecine, Québec, Canada.
authors.forename: Charles
authors.initials: C
authors.lastname: Joly Beauparlant
authors.affiliation: Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada.|Centre de Recherche sur le Cancer de l'Université Laval, Québec, Québec, Canada.
authors.forename: Fabien C
authors.initials: FC
authors.lastname: Lamaze
authors.affiliation: Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada.
authors.forename: Astrid
authors.identifier: 0000-0001-7846-6749
authors.initials: A
authors.lastname: Deschênes
authors.affiliation: Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada.
authors.forename: Rawane
authors.initials: R
authors.lastname: Samb
authors.affiliation: Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada.
authors.forename: Audrey
authors.initials: A
authors.lastname: Lemaçon
authors.affiliation: Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada.
authors.forename: Pascal
authors.identifier: 0000-0002-0802-1071
authors.initials: P
authors.lastname: Belleau
authors.affiliation: Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada.|Centre de Recherche sur le Cancer de l'Université Laval, Québec, Québec, Canada.|Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de médecine, Québec, Canada.
authors.forename: Steve
authors.initials: S
authors.lastname: Bilodeau
authors.affiliation: Centre de Recherche du CHU de Québec - Université Laval, Québec, Québec, Canada.|Département de Médecine Moléculaire, Faculté de médecine, Québec, Canada.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Droit
mesh_terms: D000465:Algorithms; D001402:B-Lymphocytes / Q000378:metabolism; D002460:Cell Line; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012984:Software; D014158:Transcription, Genetic / Q000235:genetics*