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Beyond comparisons of means: understanding changes in gene expression at the single-cell level
Traditional differential expression tools are limited to detecting changes in overall expression, and fail to uncover the rich information provided by single-cell level data sets. We present a Bayesian hierarchical model that builds upon BASiCS to study changes that lie beyond comparisons of means,...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832562/ https://www.ncbi.nlm.nih.gov/pubmed/27083558 http://dx.doi.org/10.1186/s13059-016-0930-3 |
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author | Vallejos, Catalina A. Richardson, Sylvia Marioni, John C. |
author_facet | Vallejos, Catalina A. Richardson, Sylvia Marioni, John C. |
author_sort | Vallejos, Catalina A. |
collection | PubMed |
description | Traditional differential expression tools are limited to detecting changes in overall expression, and fail to uncover the rich information provided by single-cell level data sets. We present a Bayesian hierarchical model that builds upon BASiCS to study changes that lie beyond comparisons of means, incorporating built-in normalization and quantifying technical artifacts by borrowing information from spike-in genes. Using a probabilistic approach, we highlight genes undergoing changes in cell-to-cell heterogeneity but whose overall expression remains unchanged. Control experiments validate our method’s performance and a case study suggests that novel biological insights can be revealed. Our method is implemented in R and available at https://github.com/catavallejos/BASiCS. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-0930-3) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4832562 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-48325622016-04-16 Beyond comparisons of means: understanding changes in gene expression at the single-cell level Vallejos, Catalina A. Richardson, Sylvia Marioni, John C. Genome Biol Method Traditional differential expression tools are limited to detecting changes in overall expression, and fail to uncover the rich information provided by single-cell level data sets. We present a Bayesian hierarchical model that builds upon BASiCS to study changes that lie beyond comparisons of means, incorporating built-in normalization and quantifying technical artifacts by borrowing information from spike-in genes. Using a probabilistic approach, we highlight genes undergoing changes in cell-to-cell heterogeneity but whose overall expression remains unchanged. Control experiments validate our method’s performance and a case study suggests that novel biological insights can be revealed. Our method is implemented in R and available at https://github.com/catavallejos/BASiCS. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-0930-3) contains supplementary material, which is available to authorized users. BioMed Central 2016-04-15 /pmc/articles/PMC4832562/ /pubmed/27083558 http://dx.doi.org/10.1186/s13059-016-0930-3 Text en © Vallejos et al. 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Method Vallejos, Catalina A. Richardson, Sylvia Marioni, John C. Beyond comparisons of means: understanding changes in gene expression at the single-cell level |
title | Beyond comparisons of means: understanding changes in gene expression at the single-cell level |
title_full | Beyond comparisons of means: understanding changes in gene expression at the single-cell level |
title_fullStr | Beyond comparisons of means: understanding changes in gene expression at the single-cell level |
title_full_unstemmed | Beyond comparisons of means: understanding changes in gene expression at the single-cell level |
title_short | Beyond comparisons of means: understanding changes in gene expression at the single-cell level |
title_sort | beyond comparisons of means: understanding changes in gene expression at the single-cell level |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832562/ https://www.ncbi.nlm.nih.gov/pubmed/27083558 http://dx.doi.org/10.1186/s13059-016-0930-3 |
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