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Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

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cris.lastimport.scopus2024-02-12T19:52:54Z
dc.abstract.enSpatial transcriptomics maps gene expression across tissues, posing the challenge of determining the spatial arrangement of different cell types. However, spatial transcriptomics spots contain multiple cells. Therefore, the observed signal comes from mixtures of cells of different types. Here, we propose an innovative probabilistic model, Celloscope, that utilizes established prior knowledge on marker genes for cell type deconvolution from spatial transcriptomics data. Celloscope outperforms other methods on simulated data, successfully indicates known brain structures and spatially distinguishes between inhibitory and excitatory neuron types based in mouse brain tissue, and dissects large heterogeneity of immune infiltrate composition in prostate gland tissue.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorSzymczak, Paulina
dc.contributor.authorShafighi, Shadi Darvish
dc.contributor.authorDomżał, Konrad
dc.contributor.authorFILIPIUK, IWONA
dc.contributor.authorRączkowski, Łukasz
dc.contributor.authorSzczurek, Ewa
dc.contributor.authorNowis, Dominika
dc.contributor.authorLagergren, Jens
dc.contributor.authorKoperski, Łukasz
dc.contributor.authorKACZMAREK, LESZEK
dc.contributor.authorToosi, Hosein
dc.contributor.authorGeras, Agnieszka
dc.date.accessioned2024-01-24T19:04:57Z
dc.date.available2024-01-24T19:04:57Z
dc.date.copyright2023-05-17
dc.date.issued2023
dc.description.accesstimeAT_PUBLICATION
dc.description.financeŚrodki finansowe przyznane na realizację projektu w zakresie badań naukowych lub prac rozwojowych
dc.description.number1
dc.description.versionFINAL_PUBLISHED
dc.description.volume24
dc.identifier.doi10.1186/S13059-023-02951-8
dc.identifier.issn1474-7596
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/102790
dc.identifier.weblinkhttps://link.springer.com/content/pdf/10.1186/s13059-023-02951-8.pdf
dc.languageeng
dc.pbn.affiliationcomputer and information sciences
dc.relation.ispartofGenome Biology
dc.relation.pages120: 1-36
dc.rightsCC-BY
dc.sciencecloudnosend
dc.subject.enProbabilistic model
dc.subject.enMCMC sampling
dc.subject.enSpatial transcriptomics data
dc.subject.enCell types
dc.titleCelloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data
dc.typeJournalArticle
dspace.entity.typePublication