C3D: a tool to predict 3D genomic interactions between cis-regulatory elements.
Bioinformatics
; 35(5): 877-879, 2019 03 01.
Article
em En
| MEDLINE
| ID: mdl-30816925
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. 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. 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. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Genoma
/
Genômica
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Ano de publicação:
2019
Tipo de documento:
Article