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Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps
Umeå University, Faculty of Science and Technology, Department of Physics. (Per Stenberg/Ludvig Lizana)
Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). FOI Swedish Def Res Agcy, Div CBRN Secur & Def, S-90621 Umea, Sweden. (Per Stenberg, Computational Life Science Cluster (CLiC))
Umeå University, Faculty of Science and Technology, Department of Physics. (Ludvig Lizana)
2017 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 45, no 17, article id e152Article in journal (Refereed) Published
Abstract [en]

Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community.

Place, publisher, year, edition, pages
2017. Vol. 45, no 17, article id e152
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:umu:diva-141590DOI: 10.1093/nar/gkx644ISI: 000412008000001PubMedID: 28973466OAI: oai:DiVA.org:umu-141590DiVA, id: diva2:1155632
Funder
Knut and Alice Wallenberg Foundation, 2014–0018The Kempe Foundations, JCK-1347Available from: 2017-11-08 Created: 2017-11-08 Last updated: 2018-06-09Bibliographically approved

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Kumar, RajendraSobhy, HaithamStenberg, PerLizana, Ludvig
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