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Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

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العنوان: Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
المؤلفون: Kaishu Mason, Anuja Sathe, Paul R. Hess, Jiazhen Rong, Chi-Yun Wu, Emma Furth, Katalin Susztak, Jonathan Levinsohn, Hanlee P. Ji, Nancy Zhang
المصدر: Genome Biology, Vol 25, Iss 1, Pp 1-33 (2024)
بيانات النشر: BMC, 2024.
سنة النشر: 2024
المجموعة: LCC:Biology (General)
LCC:Genetics
مصطلحات موضوعية: Biology (General), QH301-705.5, Genetics, QH426-470
الوصف: Abstract Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the tissue, rather than local gene expression changes driven by cell-cell interactions. We propose a new statistical procedure called niche-differential expression (niche-DE) analysis that identifies cell-type-specific niche-associated genes, which are differentially expressed within a specific cell type in the context of specific spatial niches. We further develop niche-LR, a method to reveal ligand-receptor signaling mechanisms that underlie niche-differential gene expression patterns. Niche-DE and niche-LR are applicable to low-resolution spot-based spatial transcriptomics data and data that is single-cell or subcellular in resolution.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 1474-760X
Relation: https://doaj.org/toc/1474-760X
DOI: 10.1186/s13059-023-03159-6
URL الوصول: https://doaj.org/article/584d5b43dfac4a9b8622ba36a4824e07
رقم الأكسشن: edsdoj.584d5b43dfac4a9b8622ba36a4824e07
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:1474760X
DOI:10.1186/s13059-023-03159-6