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TopDom: an efficient and deterministic method for identifying topological domains in genomes
Genome-wide proximity ligation assays allow the identification of chromatin contacts at unprecedented resolution. Several studies reveal that mammalian chromosomes are composed of topological domains (TDs) in sub-mega base resolution, which appear to be conserved across cell types and to some extent...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838359/ https://www.ncbi.nlm.nih.gov/pubmed/26704975 http://dx.doi.org/10.1093/nar/gkv1505 |
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author | Shin, Hanjun Shi, Yi Dai, Chao Tjong, Harianto Gong, Ke Alber, Frank Zhou, Xianghong Jasmine |
author_facet | Shin, Hanjun Shi, Yi Dai, Chao Tjong, Harianto Gong, Ke Alber, Frank Zhou, Xianghong Jasmine |
author_sort | Shin, Hanjun |
collection | PubMed |
description | Genome-wide proximity ligation assays allow the identification of chromatin contacts at unprecedented resolution. Several studies reveal that mammalian chromosomes are composed of topological domains (TDs) in sub-mega base resolution, which appear to be conserved across cell types and to some extent even between organisms. Identifying topological domains is now an important step toward understanding the structure and functions of spatial genome organization. However, current methods for TD identification demand extensive computational resources, require careful tuning and/or encounter inconsistencies in results. In this work, we propose an efficient and deterministic method, TopDom, to identify TDs, along with a set of statistical methods for evaluating their quality. TopDom is much more efficient than existing methods and depends on just one intuitive parameter, a window size, for which we provide easy-to-implement optimization guidelines. TopDom also identifies more and higher quality TDs than the popular directional index algorithm. The TDs identified by TopDom provide strong support for the cross-tissue TD conservation. Finally, our analysis reveals that the locations of housekeeping genes are closely associated with cross-tissue conserved TDs. The software package and source codes of TopDom are available at http://zhoulab.usc.edu/TopDom/. |
format | Online Article Text |
id | pubmed-4838359 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-48383592016-04-21 TopDom: an efficient and deterministic method for identifying topological domains in genomes Shin, Hanjun Shi, Yi Dai, Chao Tjong, Harianto Gong, Ke Alber, Frank Zhou, Xianghong Jasmine Nucleic Acids Res Methods Online Genome-wide proximity ligation assays allow the identification of chromatin contacts at unprecedented resolution. Several studies reveal that mammalian chromosomes are composed of topological domains (TDs) in sub-mega base resolution, which appear to be conserved across cell types and to some extent even between organisms. Identifying topological domains is now an important step toward understanding the structure and functions of spatial genome organization. However, current methods for TD identification demand extensive computational resources, require careful tuning and/or encounter inconsistencies in results. In this work, we propose an efficient and deterministic method, TopDom, to identify TDs, along with a set of statistical methods for evaluating their quality. TopDom is much more efficient than existing methods and depends on just one intuitive parameter, a window size, for which we provide easy-to-implement optimization guidelines. TopDom also identifies more and higher quality TDs than the popular directional index algorithm. The TDs identified by TopDom provide strong support for the cross-tissue TD conservation. Finally, our analysis reveals that the locations of housekeeping genes are closely associated with cross-tissue conserved TDs. The software package and source codes of TopDom are available at http://zhoulab.usc.edu/TopDom/. Oxford University Press 2016-04-20 2015-12-23 /pmc/articles/PMC4838359/ /pubmed/26704975 http://dx.doi.org/10.1093/nar/gkv1505 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Methods Online Shin, Hanjun Shi, Yi Dai, Chao Tjong, Harianto Gong, Ke Alber, Frank Zhou, Xianghong Jasmine TopDom: an efficient and deterministic method for identifying topological domains in genomes |
title | TopDom: an efficient and deterministic method for identifying topological domains in genomes |
title_full | TopDom: an efficient and deterministic method for identifying topological domains in genomes |
title_fullStr | TopDom: an efficient and deterministic method for identifying topological domains in genomes |
title_full_unstemmed | TopDom: an efficient and deterministic method for identifying topological domains in genomes |
title_short | TopDom: an efficient and deterministic method for identifying topological domains in genomes |
title_sort | topdom: an efficient and deterministic method for identifying topological domains in genomes |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838359/ https://www.ncbi.nlm.nih.gov/pubmed/26704975 http://dx.doi.org/10.1093/nar/gkv1505 |
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