Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments [version 2; referees: 2 approved] [PDF]
F1000Research, 2016 The study of genomic interactions has been greatly facilitated by techniques such as chromatin conformation capture with high-throughput sequencing (Hi-C).
Aaron T. L. Lun +2 more
doaj +10 more sources
ChIAPoP: a new tool for ChIA-PET data analysis [PDF]
Nucleic Acids Research, 2019 Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a popular assay method for studying genome-wide chromatin interactions mediated by a protein of interest. The main goal of ChIA-PET data analysis is to detect interactions between DNA regions.
Mario Medvedovic, Liang Niu
exaly +5 more sources
Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application [PDF]
BMC Genomics, 2014 Long-range chromatin interactions play an important role in transcription regulation. Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET) is an emerging technology that has unique advantages in chromatin interaction analysis, and thus provides insight into the study of transcription regulation.This article introduces the ...
Guoliang Li +2 more
exaly +5 more sources
MACPET: Model-based Analysis for ChIA-PET [PDF]
Biostatistics, 2018 We present Model-based Analysis for ChIA-PET (MACPET) which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a
Ioannis Vardaxis +3 more
core +4 more sources
3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [PDF]
Genome BiologyBackground Trimethylation of histone H3 lysine 27 (H3K27me3) confers a repressive chromatin state and is dynamically deposited and removed to regulate gene expression throughout plant growth and development.
Yue Li +23 more
doaj +2 more sources
Chromatin Immunoprecipitation for Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues. [PDF]
Cold Spring Harbor Protocols, 2018 Proper gene expression involves communication between the regulatory elements and promoters of genes. Because regulatory elements can be located over a large range of genomic distances (from as close as a few hundred bp to as much as several Mb away ...
Sachs, Laurent +4 more
core +4 more sources
MACPET: model-based analysis for ChIA-PET [PDF]
Biostatistics, 2020 Finn Drabløs, Bo Henry Lindqvist
exaly +2 more sources
Mango: a bias-correcting ChIA-PET analysis pipeline. [PDF]
Bioinformatics, 2015 AbstractMotivation: Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required ...
Phanstiel DH +3 more
europepmc +4 more sources
MICC: an R package for identifying chromatin interactions from ChIA-PET data. [PDF]
Bioinformatics, 2015 Abstract Summary: ChIA-PET is rapidly emerging as an important experimental approach to detect chromatin long-range interactions at high resolution. Here, we present Model based Interaction Calling from ChIA-PET data (MICC), an easy-to-use R package to detect chromatin interactions from ChIA-PET sequencing data.
He C, Zhang MQ, Wang X.
europepmc +4 more sources
F1000Research, 2016 The study of genomic interactions has been greatly facilitated by techniques such as chromatin conformation capture with high-throughput sequencing (Hi-C).
Aaron T. L. Lun +2 more
doaj +2 more sources