title: VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery.
abstract: The analysis of genomic data such as ChIP-Seq usually involves representing the signal intensity level over genes or other genetic features. This is often illustrated as a curve (representing the aggregate profile of a group of genes) or as a heatmap (representing individual genes). However, no specific resource dedicated to easily generating such profiles is currently available. We therefore built the versatile aggregate profiler (VAP), designed to be used by experimental and computational biologists to generate profiles of genomic datasets over groups of regions of interest, using either an absolute or a relative method. Graphical representation of the results is automatically generated, and subgrouping can be performed easily, based on the orientation of the flanking annotations. The outputs include statistical measures to facilitate comparisons between groups or datasets. We show that, through its intuitive design and flexibility, VAP can help avoid misinterpretations of genomics data. VAP is highly efficient and designed to run on laptop computers by using a memory footprint control, but can also be easily compiled and run on servers. VAP is accessible at http://lab-jacques.recherche.usherbrooke.ca/vap/.
authors.affiliation: Département d'informatique, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada.
authors.forename: Charles
authors.initials: C
authors.lastname: Coulombe
authors.affiliation: Institut de recherches cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.
authors.forename: Christian
authors.initials: C
authors.lastname: Poitras
authors.affiliation: Département d'informatique, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada.
authors.forename: Alexei
authors.initials: A
authors.lastname: Nordell-Markovits
authors.affiliation: Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada.
authors.forename: Mylène
authors.initials: M
authors.lastname: Brunelle
authors.affiliation: Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada.
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Lavoie
authors.affiliation: Institut de recherches cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada Département de médecine, Faculté de médecine, Université de Montréal, Montréal, Québec, H3T 1J4, Canada Pierre-Etienne.Jacques@USherbrooke.ca.
authors.forename: François
authors.initials: F
authors.lastname: Robert
authors.affiliation: Département d'informatique, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada Pierre-Etienne.Jacques@USherbrooke.ca.
authors.forename: Pierre-Étienne
authors.initials: PÉ
authors.lastname: Jacques
mesh_terms: D023281:Genomics / Q000379:methods*; D020407:Internet; D012984:Software
references.citation: Mol Cell Biol. 2011 Feb;31(3):531-41
references.pmid: 21098123
references.citation: Genome Biol. 2011 Aug 22;12(8):R83
references.pmid: 21859476
references.citation: Nature. 2012 Sep 20;489(7416):452-5
references.pmid: 22914091
references.citation: PLoS Genet. 2012;8(5):e1002658
references.pmid: 22570629
references.citation: Genes Dev. 2009 Jul 1;23(13):1522-33
references.pmid: 19515975
references.citation: PLoS Genet. 2012;8(8):e1002822
references.pmid: 22876190
references.citation: Mol Cell. 2007 Aug 3;27(3):393-405
references.pmid: 17679090
references.citation: PLoS One. 2009;4(3):e4886
references.pmid: 19295910
references.citation: Chem Rev. 2013 Nov 13;113(11):8491-522
references.pmid: 23837720
references.citation: Genome Res. 2002 Jun;12(6):996-1006
references.pmid: 12045153
references.citation: Nat Genet. 2009 Mar;41(3):376-81
references.pmid: 19182803
references.citation: PLoS One. 2011;6(8):e23159
references.pmid: 21887235
references.citation: Mol Cell. 2009 Oct 9;36(1):99-109
references.pmid: 19818713
references.citation: Nature. 2013 Jun 27;498(7455):516-20
references.pmid: 23728302
references.citation: Bioinformatics. 2011 Apr 15;27(8):1152-4
references.pmid: 21349863
references.citation: PLoS Genet. 2013 May;9(5):e1003504
references.pmid: 23675311
references.citation: Nucleic Acids Res. 2011 Mar;39(6):e35
references.pmid: 21177645
references.citation: Science. 2007 May 18;316(5827):1050-4
references.pmid: 17510366
references.citation: Bioinformatics. 2009 Oct 1;25(19):2605-6
references.pmid: 19689956
references.citation: J Biol Chem. 2009 Mar 20;284(12):7970-6
references.pmid: 19155214
references.citation: Mol Cell Biol. 2005 Nov;25(21):9447-59
references.pmid: 16227595
references.citation: Mol Cell. 2012 Jan 27;45(2):158-70
references.pmid: 22284676
references.citation: Genome Res. 2010 May;20(5):578-88
references.pmid: 20219941
references.citation: Mol Cell. 2009 Sep 11;35(5):626-41
references.pmid: 19682934
references.citation: Chem Rev. 2013 Nov 13;113(11):8423-55
references.pmid: 24040939
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5
references.pmid: 22110037
references.citation: PLoS Genet. 2010 Oct 28;6(10):e1001173
references.pmid: 21060864
references.citation: Nature. 2012 Sep 6;489(7414):57-74
references.pmid: 22955616
references.citation: Nat Struct Mol Biol. 2009 Sep;16(9):990-5
references.pmid: 19684600
references.citation: Nat Struct Mol Biol. 2010 Oct;17(10):1272-8
references.pmid: 20818391
references.citation: Genome Biol. 2008;9(9):R137
references.pmid: 18798982
references.citation: Cell. 1998 Nov 25;95(5):717-28
references.pmid: 9845373
references.citation: J Biol Chem. 2007 Jul 27;282(30):21662-70
references.pmid: 17550896
references.citation: Genes Dev. 2007 Jun 1;21(11):1422-30
references.pmid: 17545470
references.citation: PLoS Genet. 2009 Oct;5(10):e1000687
references.pmid: 19834540
references.citation: Chem Rev. 2013 Nov 13;113(11):8456-90
references.pmid: 23952966
references.citation: Nat Methods. 2011 Nov 29;8(12):989-90
references.pmid: 22127213
references.citation: Nat Struct Mol Biol. 2010 Mar;17(3):299-305
references.pmid: 20139982
references.citation: Nat Struct Mol Biol. 2010 Sep;17(9):1154-61
references.pmid: 20802488
references.citation: PLoS Biol. 2005 Dec;3(12):e384
references.pmid: 16248679
references.citation: Cell. 2005 Aug 26;122(4):517-27
references.pmid: 16122420