Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data.
Cell Rep Methods
; 3(1): 100382, 2023 01 23.
Article
em En
| MEDLINE
| ID: mdl-36814845
ABSTRACT
Single-cell RNA sequencing (scRNA-seq) is a revolutionary technology to determine the precise gene expression of individual cells and identify cell heterogeneity and subpopulations. However, technical limitations of scRNA-seq lead to heterogeneous and sparse data. Here, we present autoCell, a deep-learning approach for scRNA-seq dropout imputation and feature extraction. autoCell is a variational autoencoding network that combines graph embedding and a probabilistic depth Gaussian mixture model to infer the distribution of high-dimensional, sparse scRNA-seq data. We validate autoCell on simulated datasets and biologically relevant scRNA-seq. We show that interpolation of autoCell improves the performance of existing tools in identifying cell developmental trajectories of human preimplantation embryos. We identify disease-associated astrocytes (DAAs) and reconstruct DAA-specific molecular networks and ligand-receptor interactions involved in cell-cell communications using Alzheimer's disease as a prototypical example. autoCell provides a toolbox for end-to-end analysis of scRNA-seq data, including visualization, clustering, imputation, and disease-specific gene network identification.
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Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Limite:
Humans
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article