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Comparing chromatin contact maps at scale: methods and insights

Comparing chromatin contact maps is an essential step in quantifying how three-dimensional (3D) genome organization shapes development, evolution, and disease. However, no gold standard exists for comparing contact maps, and even simple methods often disagree. In this study, we propose novel compari...

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Detalles Bibliográficos
Autores principales: Gunsalus, Laura M., McArthur, Evonne, Gjoni, Ketrin, Kuang, Shuzhen, Pittman, Maureen, Capra, John A., Pollard, Katherine S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Journal Experts 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246266/
https://www.ncbi.nlm.nih.gov/pubmed/37292728
http://dx.doi.org/10.21203/rs.3.rs-2842981/v1
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author Gunsalus, Laura M.
McArthur, Evonne
Gjoni, Ketrin
Kuang, Shuzhen
Pittman, Maureen
Capra, John A.
Pollard, Katherine S.
author_facet Gunsalus, Laura M.
McArthur, Evonne
Gjoni, Ketrin
Kuang, Shuzhen
Pittman, Maureen
Capra, John A.
Pollard, Katherine S.
author_sort Gunsalus, Laura M.
collection PubMed
description Comparing chromatin contact maps is an essential step in quantifying how three-dimensional (3D) genome organization shapes development, evolution, and disease. However, no gold standard exists for comparing contact maps, and even simple methods often disagree. In this study, we propose novel comparison methods and evaluate them alongside existing approaches using genome-wide Hi-C data and 22,500 in silico predicted contact maps. We also quantify the robustness of methods to common sources of biological and technical variation, such as boundary size and noise. We find that simple difference-based methods such as mean squared error are suitable for initial screening, but biologically informed methods are necessary to identify why maps diverge and propose specific functional hypotheses. We provide a reference guide, codebase, and benchmark for rapidly comparing chromatin contact maps at scale to enable biological insights into the 3D organization of the genome.
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spelling pubmed-102462662023-06-08 Comparing chromatin contact maps at scale: methods and insights Gunsalus, Laura M. McArthur, Evonne Gjoni, Ketrin Kuang, Shuzhen Pittman, Maureen Capra, John A. Pollard, Katherine S. Res Sq Article Comparing chromatin contact maps is an essential step in quantifying how three-dimensional (3D) genome organization shapes development, evolution, and disease. However, no gold standard exists for comparing contact maps, and even simple methods often disagree. In this study, we propose novel comparison methods and evaluate them alongside existing approaches using genome-wide Hi-C data and 22,500 in silico predicted contact maps. We also quantify the robustness of methods to common sources of biological and technical variation, such as boundary size and noise. We find that simple difference-based methods such as mean squared error are suitable for initial screening, but biologically informed methods are necessary to identify why maps diverge and propose specific functional hypotheses. We provide a reference guide, codebase, and benchmark for rapidly comparing chromatin contact maps at scale to enable biological insights into the 3D organization of the genome. American Journal Experts 2023-05-23 /pmc/articles/PMC10246266/ /pubmed/37292728 http://dx.doi.org/10.21203/rs.3.rs-2842981/v1 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Gunsalus, Laura M.
McArthur, Evonne
Gjoni, Ketrin
Kuang, Shuzhen
Pittman, Maureen
Capra, John A.
Pollard, Katherine S.
Comparing chromatin contact maps at scale: methods and insights
title Comparing chromatin contact maps at scale: methods and insights
title_full Comparing chromatin contact maps at scale: methods and insights
title_fullStr Comparing chromatin contact maps at scale: methods and insights
title_full_unstemmed Comparing chromatin contact maps at scale: methods and insights
title_short Comparing chromatin contact maps at scale: methods and insights
title_sort comparing chromatin contact maps at scale: methods and insights
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246266/
https://www.ncbi.nlm.nih.gov/pubmed/37292728
http://dx.doi.org/10.21203/rs.3.rs-2842981/v1
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