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Celloscope :
Celloscope : a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data
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- Geras, Agnieszka (author)
- Warsaw Univ Technol, Fac Math & Informat Sci, Warsaw, Poland.;Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland.
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- Shafighi, Shadi Darvish (author)
- Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland.;Sorbonne Univ, CNRS, IBPS, Lab Biol Computat & Quantitat UMR, Paris, France.
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- Domzal, Kacper (author)
- Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland.
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- Filipiuk, Igor (author)
- Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland.
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- Raczkowski, Lukasz (author)
- Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland.
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- Szymczak, Paulina (author)
- Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland.
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- Toosi, Hosein (author)
- KTH,Beräkningsvetenskap och beräkningsteknik (CST)
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- Kaczmarek, Leszek (author)
- Polish Acad Sci, BRAINCITY, Nencki Inst Expt Biol, Warsaw, Poland.
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- Koperski, Lukasz (author)
- Med Univ Warsaw, Dept Pathol, Warsaw, Poland.
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- Lagergren, Jens (author)
- KTH,Beräkningsvetenskap och beräkningsteknik (CST)
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- Nowis, Dominika (author)
- Med Univ Warsaw, Lab Expt Med, Warsaw, Poland.
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- Szczurek, Ewa (author)
- Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland.
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Warsaw Univ Technol, Fac Math & Informat Sci, Warsaw, Poland;Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland. Univ Warsaw, Fac Math Informat & Mech, Warsaw, Poland.;Sorbonne Univ, CNRS, IBPS, Lab Biol Computat & Quantitat UMR, Paris, France. (creator_code:org_t)
- Springer Nature, 2023
- 2023
- English.
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In: Genome Biology. - : Springer Nature. - 1465-6906 .- 1474-760X. ; 24:1
- Related links:
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https://doi.org/10.1...
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Abstract
Subject headings
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- Spatial 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.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)
Keyword
- Probabilistic model
- MCMC sampling
- Spatial transcriptomics data
- Cell types
Publication and Content Type
- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Geras, Agnieszka
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Shafighi, Shadi ...
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Domzal, Kacper
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Filipiuk, Igor
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Raczkowski, Luka ...
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Szymczak, Paulin ...
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show more...
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Toosi, Hosein
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Kaczmarek, Lesze ...
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Koperski, Lukasz
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Lagergren, Jens
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Nowis, Dominika
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Szczurek, Ewa
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show less...
- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Cell and Molecul ...
- Articles in the publication
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Genome Biology
- By the university
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Royal Institute of Technology