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Motif elucidation in ChIP-seq datasets with a knockout control
SUMMARY: Chromatin immunoprecipitation-sequencing is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout (KO) experiments can generate improved...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10074035/ https://www.ncbi.nlm.nih.gov/pubmed/37033469 http://dx.doi.org/10.1093/bioadv/vbad031 |
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author | Denisko, Danielle Viner, Coby Hoffman, Michael M |
author_facet | Denisko, Danielle Viner, Coby Hoffman, Michael M |
author_sort | Denisko, Danielle |
collection | PubMed |
description | SUMMARY: Chromatin immunoprecipitation-sequencing is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout (KO) experiments can generate improved motifs but require optimal differential analysis. We introduce peaKO—a computational method to automatically optimize motif analyses with KO controls, which we compare to two other methods. PeaKO often improves elucidation of the target factor and highlights the benefits of KO controls, which far outperform input controls. AVAILABILITY AND IMPLEMENTATION: PeaKO is freely available at https://peako.hoffmanlab.org. CONTACT: michael.hoffman@utoronto.ca |
format | Online Article Text |
id | pubmed-10074035 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-100740352023-04-06 Motif elucidation in ChIP-seq datasets with a knockout control Denisko, Danielle Viner, Coby Hoffman, Michael M Bioinform Adv Original Paper SUMMARY: Chromatin immunoprecipitation-sequencing is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout (KO) experiments can generate improved motifs but require optimal differential analysis. We introduce peaKO—a computational method to automatically optimize motif analyses with KO controls, which we compare to two other methods. PeaKO often improves elucidation of the target factor and highlights the benefits of KO controls, which far outperform input controls. AVAILABILITY AND IMPLEMENTATION: PeaKO is freely available at https://peako.hoffmanlab.org. CONTACT: michael.hoffman@utoronto.ca Oxford University Press 2023-03-16 /pmc/articles/PMC10074035/ /pubmed/37033469 http://dx.doi.org/10.1093/bioadv/vbad031 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Paper Denisko, Danielle Viner, Coby Hoffman, Michael M Motif elucidation in ChIP-seq datasets with a knockout control |
title | Motif elucidation in ChIP-seq datasets with a knockout control |
title_full | Motif elucidation in ChIP-seq datasets with a knockout control |
title_fullStr | Motif elucidation in ChIP-seq datasets with a knockout control |
title_full_unstemmed | Motif elucidation in ChIP-seq datasets with a knockout control |
title_short | Motif elucidation in ChIP-seq datasets with a knockout control |
title_sort | motif elucidation in chip-seq datasets with a knockout control |
topic | Original Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10074035/ https://www.ncbi.nlm.nih.gov/pubmed/37033469 http://dx.doi.org/10.1093/bioadv/vbad031 |
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