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C3D: a tool to predict 3D genomic interactions between cis-regulatory elements.
- Source :
-
Bioinformatics (Oxford, England) [Bioinformatics] 2019 Mar 01; Vol. 35 (5), pp. 877-879. - Publication Year :
- 2019
-
Abstract
- Motivation: The 3D genome architecture influences the regulation of genes by facilitating chromatin interactions between distal cis-regulatory elements and gene promoters. We implement Cross Cell-type Correlation based on DNA accessibility (C3D), a customizable computational tool that predicts chromatin interactions using an unsupervised algorithm that utilizes correlations in chromatin measurements, such as DNaseI hypersensitivity signals.<br />Results: C3D accurately predicts 32.7%, 18.3% and 24.1% of interactions, validated by ChIA-PET assays, between promoters and distal regions that overlie DNaseI hypersensitive sites in K562, MCF-7 and GM12878 cells, respectively.<br />Availability and Implementation: Source code is open-source and freely available on GitHub (https://github.com/LupienLabOrganization/C3D) under the GNU GPLv3 license. C3D is implemented in Bash and R; it runs on any platform with Bash (≥4.0), R (≥3.1.1) and BEDTools (≥2.19.0). It requires the following R packages: GenomicRanges, Sushi, data.table, preprocessCore and dynamicTreeCut.<br />Supplementary Information: Supplementary data are available at Bioinformatics online.<br /> (© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Details
- Language :
- English
- ISSN :
- 1367-4811
- Volume :
- 35
- Issue :
- 5
- Database :
- MEDLINE
- Journal :
- Bioinformatics (Oxford, England)
- Publication Type :
- Academic Journal
- Accession number :
- 30816925
- Full Text :
- https://doi.org/10.1093/bioinformatics/bty717