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Bioinformatics
Article . 2024 . Peer-reviewed
License: CC BY
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Bioinformatics
Article . 2024
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https://doi.org/10.1101/2023.1...
Article . 2023 . Peer-reviewed
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Virtual tissue expression analysis

Authors: Simeth, Jakob; Hüttl, Paul; Schön, Marian; Nozari, Zahra; Huttner, Michael; Schmidt, Tobias; Altenbuchinger, Michael; +2 Authors

Virtual tissue expression analysis

Abstract

Abstract Motivation Bulk RNA expression data are widely accessible, whereas single-cell data are relatively scarce in comparison. However, single-cell data offer profound insights into the cellular composition of tissues and cell type-specific gene regulation, both of which remain hidden in bulk expression analysis. Results Here, we present tissueResolver, an algorithm designed to extract single-cell information from bulk data, enabling us to attribute expression changes to individual cell types. When validated on simulated data tissueResolver outperforms competing methods. Additionally, our study demonstrates that tissueResolver reveals cell type-specific regulatory distinctions between the activated B-cell-like (ABC) and germinal center B-cell-like (GCB) subtypes of diffuse large B-cell lymphomas (DLBCL). Availability and implementation R package available at https://github.com/spang-lab/tissueResolver (archived as 10.5281/zenodo.14160846). Code for reproducing the results of this article is available at https://github.com/spang-lab/tissueResolver-docs archived as swh:1:dir:faea2d4f0ded30de774b28e028299ddbdd0c4f89).

Country
Germany
Keywords

ddc:004, Original Paper, Gene Expression Profiling, Humans, cell type-specific expression, cell-specific gene regulation, cellular composition, deconvolution, Lymphoma, Large B-Cell, Diffuse, Single-Cell Analysis, 004 Informatik, Algorithms, Software

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
views
OpenAIRE UsageCountsViews provided by UsageCounts
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6
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75
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