Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data.
Brief Bioinform
; 23(5)2022 09 20.
Article
en En
| MEDLINE
| ID: mdl-36070863
ABSTRACT
Computational recovery of gene regulatory network (GRN) has recently undergone a great shift from bulk-cell towards designing algorithms targeting single-cell data. In this work, we investigate whether the widely available bulk-cell data could be leveraged to assist the GRN predictions for single cells. We infer cell-type-specific GRNs from both the single-cell RNA sequencing data and the generic GRN derived from the bulk cells by constructing a weakly supervised learning framework based on the axial transformer. We verify our assumption that the bulk-cell transcriptomic data are a valuable resource, which could improve the prediction of single-cell GRN by conducting extensive experiments. Our GRN-transformer achieves the state-of-the-art prediction accuracy in comparison to existing supervised and unsupervised approaches. In addition, we show that our method can identify important transcription factors and potential regulations for Alzheimer's disease risk genes by using the predicted GRN. Availability:
The implementation of GRN-transformer is available at https//github.com/HantaoShu/GRN-Transformer.Palabras clave
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Biología Computacional
/
Redes Reguladoras de Genes
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Brief Bioinform
Asunto de la revista:
BIOLOGIA
/
INFORMATICA MEDICA
Año:
2022
Tipo del documento:
Article
País de afiliación:
China