Unknown

Dataset Information

0

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.

ABSTRACT: Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments. We implement these procedures in CHiCAGO ( http://regulatorygenomicsgroup.org/chicago ), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.

SUBMITTER: Cairns J 

PROVIDER: S-EPMC4908757 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments. We implement these procedures in CHiCAGO ( http://regulator  ...[more]

Similar Datasets

Transcriptomics CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data
2016-05-18 | E-GEOD-81503 | biostudies-arrayexpress
Other CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data
2016-05-18 | GSE81503 | GEO
Genomics,Multiomics CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data
| PRJNA321822 | ENA
Unknown ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C.
| S-EPMC6532271 | biostudies-literature
Other ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C (4C validation)
2019-04-17 | GSE129884 | GEO
Unknown MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments.
| S-EPMC9262194 | biostudies-literature
Unknown 3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data.
| S-EPMC7496221 | biostudies-literature
Unknown Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data.
| S-EPMC6678864 | biostudies-literature
Unknown Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data.
| S-EPMC6853696 | biostudies-literature
Unknown Fine mapping chromatin contacts in capture Hi-C data.
| S-EPMC6343296 | biostudies-literature