Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG

Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell multiome data. This concept is further used for the constructi...

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Autores principales: Duren, Zhana, Chang, Fengge, Naqing, Fnu, Xin, Jingxue, Liu, Qiao, Wong, Wing Hung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9109353/
https://www.ncbi.nlm.nih.gov/pubmed/35578363
http://dx.doi.org/10.1186/s13059-022-02682-2
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author Duren, Zhana
Chang, Fengge
Naqing, Fnu
Xin, Jingxue
Liu, Qiao
Wong, Wing Hung
author_facet Duren, Zhana
Chang, Fengge
Naqing, Fnu
Xin, Jingxue
Liu, Qiao
Wong, Wing Hung
author_sort Duren, Zhana
collection PubMed
description Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell multiome data. This concept is further used for the construction of subpopulation-specific cis-regulatory networks. The capability of inferring useful regulatory network is demonstrated by the two-fold increment on network inference accuracy compared to the Pearson correlation-based method and the 27-fold enrichment of GWAS variants for inflammatory bowel disease in the cis-regulatory elements. The R package scREG provides comprehensive functions for single cell multiome data analysis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02682-2.
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spelling pubmed-91093532022-05-17 Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG Duren, Zhana Chang, Fengge Naqing, Fnu Xin, Jingxue Liu, Qiao Wong, Wing Hung Genome Biol Method Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell multiome data. This concept is further used for the construction of subpopulation-specific cis-regulatory networks. The capability of inferring useful regulatory network is demonstrated by the two-fold increment on network inference accuracy compared to the Pearson correlation-based method and the 27-fold enrichment of GWAS variants for inflammatory bowel disease in the cis-regulatory elements. The R package scREG provides comprehensive functions for single cell multiome data analysis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02682-2. BioMed Central 2022-05-16 /pmc/articles/PMC9109353/ /pubmed/35578363 http://dx.doi.org/10.1186/s13059-022-02682-2 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Duren, Zhana
Chang, Fengge
Naqing, Fnu
Xin, Jingxue
Liu, Qiao
Wong, Wing Hung
Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
title Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
title_full Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
title_fullStr Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
title_full_unstemmed Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
title_short Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
title_sort regulatory analysis of single cell multiome gene expression and chromatin accessibility data with screg
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9109353/
https://www.ncbi.nlm.nih.gov/pubmed/35578363
http://dx.doi.org/10.1186/s13059-022-02682-2
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