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BMC Genomics. 2016 May 16;17:355. doi: 10.1186/s12864-016-2642-1.

LOGIQA: a database dedicated to long-range genome interactions quality assessment.

Mendoza-Parra MA1,2,3,4,5, Blum M6,7,8,9,10, Malysheva V6,7,8,9,10, Cholley PE6,7,8,9,10, Gronemeyer H11,12,13,14,15.

Author information

1
Equipe Labellisée Ligue Contre le Cancer, Illkirch, France. marco@igbmc.fr.
2
Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France. marco@igbmc.fr.
3
Centre National de la Recherche Scientifique UMR 7104, Illkirch, France. marco@igbmc.fr.
4
Institut National de la Santé et de la Recherche Médicale U964, Illkirch, France. marco@igbmc.fr.
5
University of Strasbourg, Illkirch, France. marco@igbmc.fr.
6
Equipe Labellisée Ligue Contre le Cancer, Illkirch, France.
7
Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.
8
Centre National de la Recherche Scientifique UMR 7104, Illkirch, France.
9
Institut National de la Santé et de la Recherche Médicale U964, Illkirch, France.
10
University of Strasbourg, Illkirch, France.
11
Equipe Labellisée Ligue Contre le Cancer, Illkirch, France. hg@igbmc.u-strasbg.fr.
12
Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France. hg@igbmc.u-strasbg.fr.
13
Centre National de la Recherche Scientifique UMR 7104, Illkirch, France. hg@igbmc.u-strasbg.fr.
14
Institut National de la Santé et de la Recherche Médicale U964, Illkirch, France. hg@igbmc.u-strasbg.fr.
15
University of Strasbourg, Illkirch, France. hg@igbmc.u-strasbg.fr.

Abstract

BACKGROUND:

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.

METHOD:

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.

RESULTS:

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.

CONCLUSIONS:

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.

KEYWORDS:

Chromatin architecture; HiC; Quality

PMID:
27185059
PMCID:
PMC4868109
DOI:
10.1186/s12864-016-2642-1
[Indexed for MEDLINE]
Free PMC Article

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