Accurate estimation of cell composition in bulk expression through robust integration of single-cell information

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dc.contributor University of Helsinki, HUS Abdominal Center en
dc.contributor.author Jew, Brandon
dc.contributor.author Alvarez, Marcus
dc.contributor.author Rahmani, Elior
dc.contributor.author Miao, Zong
dc.contributor.author Ko, Arthur
dc.contributor.author Garske, Kristina M.
dc.contributor.author Sul, Jae Hoon
dc.contributor.author Pietiläinen, Kirsi H.
dc.contributor.author Pajukanta, Päivi
dc.contributor.author Halperin, Eran
dc.date.accessioned 2020-08-27T06:46:01Z
dc.date.available 2020-08-27T06:46:01Z
dc.date.issued 2020-04-24
dc.identifier.citation Jew , B , Alvarez , M , Rahmani , E , Miao , Z , Ko , A , Garske , K M , Sul , J H , Pietiläinen , K H , Pajukanta , P & Halperin , E 2020 , ' Accurate estimation of cell composition in bulk expression through robust integration of single-cell information ' , Nature Communications , vol. 11 , no. 1 , 1971 . https://doi.org/10.1038/s41467-020-15816-6 en
dc.identifier.issn 2041-1723
dc.identifier.other PURE: 142450896
dc.identifier.other PURE UUID: d3e6be3d-e5c5-4f49-83d9-d2978c2d2685
dc.identifier.other WOS: 000543969800001
dc.identifier.uri http://hdl.handle.net/10138/318653
dc.description.abstract We present Bisque, a tool for estimating cell type proportions in bulk expression. Bisque implements a regression-based approach that utilizes single-cell RNA-seq (scRNA-seq) or single-nucleus RNA-seq (snRNA-seq) data to generate a reference expression profile and learn gene-specific bulk expression transformations to robustly decompose RNA-seq data. These transformations significantly improve decomposition performance compared to existing methods when there is significant technical variation in the generation of the reference profile and observed bulk expression. Importantly, compared to existing methods, our approach is extremely efficient, making it suitable for the analysis of large genomic datasets that are becoming ubiquitous. When applied to subcutaneous adipose and dorsolateral prefrontal cortex expression datasets with both bulk RNA-seq and snRNA-seq data, Bisque replicates previously reported associations between cell type proportions and measured phenotypes across abundant and rare cell types. We further propose an additional mode of operation that merely requires a set of known marker genes. en
dc.format.extent 11
dc.language.iso eng
dc.relation.ispartof Nature Communications
dc.rights en
dc.subject ADIPOSE-TISSUE en
dc.subject MICROGLIA en
dc.subject 3121 General medicine, internal medicine and other clinical medicine en
dc.title Accurate estimation of cell composition in bulk expression through robust integration of single-cell information en
dc.type Article
dc.description.version Peer reviewed
dc.identifier.doi https://doi.org/10.1038/s41467-020-15816-6
dc.type.uri info:eu-repo/semantics/other
dc.type.uri info:eu-repo/semantics/publishedVersion
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