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De novo reconstruction of cell interaction landscapes from single-cell spatial transcriptome data with DeepLinc

Based on a deep generative model of variational graph autoencoder (VGAE), we develop a new method, DeepLinc (deep learning framework for Landscapes of Interacting Cells), for the de novo reconstruction of cell interaction networks from single-cell spatial transcriptomic data. DeepLinc demonstrates h...

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Detalles Bibliográficos
Autores principales: Li, Runze, Yang, Xuerui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9164488/
https://www.ncbi.nlm.nih.gov/pubmed/35659722
http://dx.doi.org/10.1186/s13059-022-02692-0
Descripción
Sumario:Based on a deep generative model of variational graph autoencoder (VGAE), we develop a new method, DeepLinc (deep learning framework for Landscapes of Interacting Cells), for the de novo reconstruction of cell interaction networks from single-cell spatial transcriptomic data. DeepLinc demonstrates high efficiency in learning from imperfect and incomplete spatial transcriptome data, filtering false interactions, and imputing missing distal and proximal interactions. The latent representations learned by DeepLinc are also used for inferring the signature genes contributing to the cell interaction landscapes, and for reclustering the cells based on the spatially coded cell heterogeneity in complex tissues at single-cell resolution. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02692-0.