A1 Refereed original research article in a scientific journal

Computational deconvolution to estimate cell type-specific gene expression from bulk data




AuthorsJaakkola Maria K., Elo Laura L.

PublisherOxford University Press

Publication year2021

JournalNAR Genomics and Bioinformatics: Nucleic Acids Research Genomics and Bioinformatics

Article numberlqaa110

Volume3

Issue1

eISSN2631-9268

DOIhttps://doi.org/10.1093/nargab/lqaa110

Web address https://academic.oup.com/nargab/article/3/1/lqaa110/6090161

Self-archived copy’s web addresshttps://research.utu.fi/converis/portal/detail/Publication/53628840


Abstract

Computational deconvolution is a time and cost-efficient approach to obtain cell type-specific information from bulk gene expression of heterogeneous tissues like blood. Deconvolution can aim to either estimate cell type proportions or abundances in samples, or estimate how strongly each present cell type expresses different genes, or both tasks simultaneously. Among the two separate goals, the estimation of cell type proportions/abundances is widely studied, but less attention has been paid on defining the cell type-specific expression profiles. Here, we address this gap by introducing a novel method Rodeo and empirically evaluating it and the other available tools from multiple perspectives utilizing diverse datasets.


Downloadable publication

This is an electronic reprint of the original article.
This reprint may differ from the original in pagination and typographic detail. Please cite the original version.





Last updated on 2024-26-11 at 22:43