Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis. [PDF]
PLoS ONE, 2015 Genome-wide functional analyses require high-resolution genome assembly and annotation. We applied ChIA-PET to analyze gene regulatory networks, including 3D chromosome interactions, underlying thyroid hormone (TH) signaling in the frog Xenopus ...
Nicolas Buisine +12 more
doaj +9 more sources
ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization [PDF]
Science Advances, 2020 ChIA-PET (chromatin interaction analysis with paired-end tags) enables genome-wide discovery of chromatin interactions involving specific protein factors, with base pair resolution.
Byoungkoo Lee, Liuyang Cai, Minji Kim
exaly +8 more sources
Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3) [PDF]
Genes, 2019 Understanding chromatin interactions is important because they create chromosome conformation and link the cis- and trans- regulatory elements to their target genes for transcriptional regulation.
Guoliang Li +2 more
exaly +6 more sources
DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks [PDF]
PLoS Computational Biology, 2023 Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can capture genome-wide chromatin interactions mediated by a specific DNA-associated protein.
, Zheng Wang
exaly +5 more sources
ChIAMM: A Mixture Model for Statistical Analysis of Long-Range Chromatin Interactions From ChIA-PET Experiments [PDF]
Frontiers in Genetics, 2020 Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is an important experimental method for detecting specific protein-mediated chromatin loops genome-wide at high resolution. Here, we proposed a new statistical approach with a mixture
Yibeltal Arega +6 more
doaj +7 more sources
ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis [PDF]
Nucleic Acids Research, 2017 ChIA-PET2 is a versatile and flexible pipeline for analyzing different types of ChIA-PET data from raw sequencing reads to chromatin loops. ChIA-PET2 integrates all steps required for ChIA-PET data analysis, including linker trimming, read alignment ...
Yanjian Li +2 more
exaly +6 more sources
Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions [PDF]
Nature Protocols, 2017 Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a robust method for capturing genome-wide chromatin interactions. Unlike other 3C-based methods, it includes a chromatin immunoprecipitation (ChIP) step that enriches for ...
Xingwang Li +2 more
exaly +7 more sources
Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis [PDF]
BMC Bioinformatics, 2019 Background Although several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them have unknown function. Recent evidence has shown the importance of both lncRNAs and chromatin interactions in transcriptional
Denise Thiel +5 more
doaj +7 more sources
Methods for comparative ChIA-PET and Hi-C data analysis
Methods, 2020 The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome ...
Zhonghui Tang, Yijun Ruan
exaly +6 more sources
Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data [PDF]
BMC Genomics, 2019 Background Chromosomal architecture, which is constituted by chromatin loops, plays an important role in cellular functions. Gene expression and cell identity can be regulated by the chromatin loop, which is formed by proximal or distal enhancers and ...
Ruimin Wang +6 more
doaj +5 more sources