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




TekijätJaakkola Maria K., Elo Laura L.

KustantajaOxford University Press

Julkaisuvuosi2021

JournalNAR Genomics and Bioinformatics: Nucleic Acids Research Genomics and Bioinformatics

Artikkelin numerolqaa110

Vuosikerta3

Numero1

eISSN2631-9268

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

Verkko-osoitehttps://academic.oup.com/nargab/article/3/1/lqaa110/6090161

Rinnakkaistallenteen osoitehttps://research.utu.fi/converis/portal/detail/Publication/53628840


Tiivistelmä

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.


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