دورية أكاديمية
Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
العنوان: | Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions |
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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 |
تدمد: | 1474760X |
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DOI: | 10.1186/s13059-023-03159-6 |