Cargando…
IDR2D identifies reproducible genomic interactions
Chromatin interaction data from protocols such as ChIA-PET, HiChIP and Hi-C provide valuable insights into genome organization and gene regulation, but can include spurious interactions that do not reflect underlying genome biology. We introduce an extension of the Irreproducible Discovery Rate (IDR...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102997/ https://www.ncbi.nlm.nih.gov/pubmed/32009147 http://dx.doi.org/10.1093/nar/gkaa030 |
_version_ | 1783511956451229696 |
---|---|
author | Krismer, Konstantin Guo, Yuchun Gifford, David K |
author_facet | Krismer, Konstantin Guo, Yuchun Gifford, David K |
author_sort | Krismer, Konstantin |
collection | PubMed |
description | Chromatin interaction data from protocols such as ChIA-PET, HiChIP and Hi-C provide valuable insights into genome organization and gene regulation, but can include spurious interactions that do not reflect underlying genome biology. We introduce an extension of the Irreproducible Discovery Rate (IDR) method called IDR2D that identifies replicable interactions shared by chromatin interaction experiments. IDR2D provides a principled set of interactions and eliminates artifacts from single experiments. The method is available as a Bioconductor package for the R community, as well as an online service at https://idr2d.mit.edu. |
format | Online Article Text |
id | pubmed-7102997 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-71029972020-04-02 IDR2D identifies reproducible genomic interactions Krismer, Konstantin Guo, Yuchun Gifford, David K Nucleic Acids Res Methods Online Chromatin interaction data from protocols such as ChIA-PET, HiChIP and Hi-C provide valuable insights into genome organization and gene regulation, but can include spurious interactions that do not reflect underlying genome biology. We introduce an extension of the Irreproducible Discovery Rate (IDR) method called IDR2D that identifies replicable interactions shared by chromatin interaction experiments. IDR2D provides a principled set of interactions and eliminates artifacts from single experiments. The method is available as a Bioconductor package for the R community, as well as an online service at https://idr2d.mit.edu. Oxford University Press 2020-04-06 2020-02-03 /pmc/articles/PMC7102997/ /pubmed/32009147 http://dx.doi.org/10.1093/nar/gkaa030 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Online Krismer, Konstantin Guo, Yuchun Gifford, David K IDR2D identifies reproducible genomic interactions |
title | IDR2D identifies reproducible genomic interactions |
title_full | IDR2D identifies reproducible genomic interactions |
title_fullStr | IDR2D identifies reproducible genomic interactions |
title_full_unstemmed | IDR2D identifies reproducible genomic interactions |
title_short | IDR2D identifies reproducible genomic interactions |
title_sort | idr2d identifies reproducible genomic interactions |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102997/ https://www.ncbi.nlm.nih.gov/pubmed/32009147 http://dx.doi.org/10.1093/nar/gkaa030 |
work_keys_str_mv | AT krismerkonstantin idr2didentifiesreproduciblegenomicinteractions AT guoyuchun idr2didentifiesreproduciblegenomicinteractions AT gifforddavidk idr2didentifiesreproduciblegenomicinteractions |