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Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)

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. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughp...

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Autores principales: Li, Guoliang, Sun, Tongkai, Chang, Huidan, Cai, Liuyang, Hong, Ping, Zhou, Qiangwei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678675/
https://www.ncbi.nlm.nih.gov/pubmed/31336684
http://dx.doi.org/10.3390/genes10070554
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author Li, Guoliang
Sun, Tongkai
Chang, Huidan
Cai, Liuyang
Hong, Ping
Zhou, Qiangwei
author_facet Li, Guoliang
Sun, Tongkai
Chang, Huidan
Cai, Liuyang
Hong, Ping
Zhou, Qiangwei
author_sort Li, Guoliang
collection PubMed
description 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. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. We developed ChIA-PET Tool for ChIA-PET data analysis in 2010. Here, we present the updated version of ChIA-PET Tool (V3) as a computational package to process the next-generation sequence data generated from ChIA-PET experiments. It processes short-read and long-read ChIA-PET data with multithreading and generates statistics of results in an HTML file. In this paper, we provide a detailed demonstration of the design of ChIA-PET Tool V3 and how to install it and analyze RNA polymerase II (RNAPII) ChIA-PET data from human K562 cells with it. We compared our tool with existing tools, including ChiaSig, MICC, Mango and ChIA-PET2, by using the same public data set in the same computer. Most peaks detected by the ChIA-PET Tool V3 overlap with those of other tools. There is higher enrichment for significant chromatin interactions from ChIA-PET Tool V3 in aggregate peak analysis (APA) plots. The ChIA-PET Tool V3 is publicly available at GitHub.
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spelling pubmed-66786752019-08-19 Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3) Li, Guoliang Sun, Tongkai Chang, Huidan Cai, Liuyang Hong, Ping Zhou, Qiangwei Genes (Basel) Article 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. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. We developed ChIA-PET Tool for ChIA-PET data analysis in 2010. Here, we present the updated version of ChIA-PET Tool (V3) as a computational package to process the next-generation sequence data generated from ChIA-PET experiments. It processes short-read and long-read ChIA-PET data with multithreading and generates statistics of results in an HTML file. In this paper, we provide a detailed demonstration of the design of ChIA-PET Tool V3 and how to install it and analyze RNA polymerase II (RNAPII) ChIA-PET data from human K562 cells with it. We compared our tool with existing tools, including ChiaSig, MICC, Mango and ChIA-PET2, by using the same public data set in the same computer. Most peaks detected by the ChIA-PET Tool V3 overlap with those of other tools. There is higher enrichment for significant chromatin interactions from ChIA-PET Tool V3 in aggregate peak analysis (APA) plots. The ChIA-PET Tool V3 is publicly available at GitHub. MDPI 2019-07-22 /pmc/articles/PMC6678675/ /pubmed/31336684 http://dx.doi.org/10.3390/genes10070554 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Li, Guoliang
Sun, Tongkai
Chang, Huidan
Cai, Liuyang
Hong, Ping
Zhou, Qiangwei
Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)
title Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)
title_full Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)
title_fullStr Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)
title_full_unstemmed Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)
title_short Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)
title_sort chromatin interaction analysis with updated chia-pet tool (v3)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678675/
https://www.ncbi.nlm.nih.gov/pubmed/31336684
http://dx.doi.org/10.3390/genes10070554
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