title: Aggregate and Heatmap Representations of Genome-Wide Localization Data Using VAP, a Versatile Aggregate Profiler.
abstract: In the analysis of experimental data corresponding to the signal enrichment of chromatin features such as histone modifications throughout the genome, it is often useful to represent the signal over known regions of interest, such as genes, using aggregate or individual profiles. In the present chapter, we describe and explain the best practices on how to generate such profiles as well as other usages of the versatile aggregate profiler (VAP) tool (Coulombe et al., Nucleic Acids Res 42:W485-W493, 2014), with a particular focus on the new functionalities introduced in version 1.1.0 of VAP.
authors.affiliation: Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, QC, Canada, J1K 2R1.
authors.forename: Mylène
authors.initials: M
authors.lastname: Brunelle
authors.affiliation: Département d'informatique, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, QC, Canada, J1K 2R1.
authors.forename: Charles
authors.initials: C
authors.lastname: Coulombe
authors.affiliation: Institut de recherches cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC, Canada, H2W 1R7.
authors.forename: Christian
authors.initials: C
authors.lastname: Poitras
authors.affiliation: Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, QC, Canada, J1K 2R1.
authors.forename: Marc-Antoine
authors.initials: MA
authors.lastname: Robert
authors.affiliation: Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, QC, Canada, J1K 2R1.
authors.forename: Alexei Nordell
authors.initials: AN
authors.lastname: Markovits
authors.affiliation: Institut de recherches cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC, Canada, H2W 1R7.|Département de médecine, Faculté de médecine, Université de Montréal, 2900 boul. Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
authors.forename: François
authors.initials: F
authors.lastname: Robert
authors.affiliation: Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, QC, Canada, J1K 2R1. pierre-etienne.jacques@usherbrooke.ca.|Département d'informatique, Faculté des sciences, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, QC, Canada, J1K 2R1. pierre-etienne.jacques@usherbrooke.ca.|Centre de recherche du Centre hospitalier universitaire de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, QC, Canada, J1H 5N4. pierre-etienne.jacques@usherbrooke.ca.
authors.forename: Pierre-Étienne
authors.initials: PÉ
authors.lastname: Jacques
mesh_terms: D002843:Chromatin / Q000235:genetics*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D016678:Genome; D042421:Histone Code / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011401:Promoter Regions, Genetic
chemical_list: D002843:Chromatin
keywords: Aggregate profiles; Average profiles; ChIP-Seq; Data analysis; Graphical representation; Heatmaps