SPADE: spatial deconvolution for domain specific cell-type estimation.
Commun Biol
; 7(1): 469, 2024 Apr 17.
Article
en En
| MEDLINE
| ID: mdl-38632414
ABSTRACT
Understanding gene expression in different cell types within their spatial context is a key goal in genomics research. SPADE (SPAtial DEconvolution), our proposed method, addresses this by integrating spatial patterns into the analysis of cell type composition. This approach uses a combination of single-cell RNA sequencing, spatial transcriptomics, and histological data to accurately estimate the proportions of cell types in various locations. Our analyses of synthetic data have demonstrated SPADE's capability to discern cell type-specific spatial patterns effectively. When applied to real-life datasets, SPADE provides insights into cellular dynamics and the composition of tumor tissues. This enhances our comprehension of complex biological systems and aids in exploring cellular diversity. SPADE represents a significant advancement in deciphering spatial gene expression patterns, offering a powerful tool for the detailed investigation of cell types in spatial transcriptomics.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Perfilación de la Expresión Génica
/
Genómica
Idioma:
En
Revista:
Commun Biol
Año:
2024
Tipo del documento:
Article
País de afiliación:
Estados Unidos
Pais de publicación:
ENGLAND
/
ESCOCIA
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GB
/
GREAT BRITAIN
/
INGLATERRA
/
REINO UNIDO
/
SCOTLAND
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UK
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UNITED KINGDOM