title: LOGIQA: a database dedicated to long-range genome interactions quality assessment.
abstract: Proximity ligation-mediated methods are essential to study the impact of three-dimensional chromatin organization on gene programming. Albeit significant progress has been made in the development of computational tools that assess long-range chromatin interactions, next to nothing is known about the quality of the generated datasets.
  
  
  
  We have developed LOGIQA ( www.ngs-qc.org/logiqa ), a database hosting quality scores for long-range genome interaction assays, accessible through a user-friendly web-based environment.
  
  
  
  Currently, LOGIQA harbors QC scores for >900 datasets, which provides a global view of their relative quality and reveals the impact of genome size, coverage and other technical aspects. LOGIQA provides a user-friendly dataset query panel and a genome viewer to assess local genome-interaction maps at different resolution and quality-assessment conditions.
  
  
  
  LOGIQA is the first database hosting quality scores dedicated to long-range chromatin interaction assays, which in addition provides a platform for visualizing genome interactions made available by the scientific community.
authors.affiliation: Equipe Labellisée Ligue Contre le Cancer, Illkirch, France. marco@igbmc.fr.|Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France. marco@igbmc.fr.|Centre National de la Recherche Scientifique UMR 7104, Illkirch, France. marco@igbmc.fr.|Institut National de la Santé et de la Recherche Médicale U964, Illkirch, France. marco@igbmc.fr.|University of Strasbourg, Illkirch, France. marco@igbmc.fr.
authors.forename: Marco-Antonio
authors.initials: MA
authors.lastname: Mendoza-Parra
authors.affiliation: Equipe Labellisée Ligue Contre le Cancer, Illkirch, France.|Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.|Centre National de la Recherche Scientifique UMR 7104, Illkirch, France.|Institut National de la Santé et de la Recherche Médicale U964, Illkirch, France.|University of Strasbourg, Illkirch, France.
authors.forename: Matthias
authors.initials: M
authors.lastname: Blum
authors.affiliation: Equipe Labellisée Ligue Contre le Cancer, Illkirch, France.|Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.|Centre National de la Recherche Scientifique UMR 7104, Illkirch, France.|Institut National de la Santé et de la Recherche Médicale U964, Illkirch, France.|University of Strasbourg, Illkirch, France.
authors.forename: Valeriya
authors.initials: V
authors.lastname: Malysheva
authors.affiliation: Equipe Labellisée Ligue Contre le Cancer, Illkirch, France.|Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.|Centre National de la Recherche Scientifique UMR 7104, Illkirch, France.|Institut National de la Santé et de la Recherche Médicale U964, Illkirch, France.|University of Strasbourg, Illkirch, France.
authors.forename: Pierre-Etienne
authors.initials: PE
authors.lastname: Cholley
authors.affiliation: Equipe Labellisée Ligue Contre le Cancer, Illkirch, France. hg@igbmc.u-strasbg.fr.|Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France. hg@igbmc.u-strasbg.fr.|Centre National de la Recherche Scientifique UMR 7104, Illkirch, France. hg@igbmc.u-strasbg.fr.|Institut National de la Santé et de la Recherche Médicale U964, Illkirch, France. hg@igbmc.u-strasbg.fr.|University of Strasbourg, Illkirch, France. hg@igbmc.u-strasbg.fr.
authors.forename: Hinrich
authors.initials: H
authors.lastname: Gronemeyer
mesh_terms: D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D004843:Epistasis, Genetic; D018740:Genetic Heterogeneity; D016678:Genome; D023281:Genomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D064878:Web Browser
keywords: Chromatin architecture; HiC; Quality