Dimension reduction, cell clustering, and cell-cell communication inference for single-cell transcriptomics with DcjComm.

Ding, Qian; Yang, Wenyi; Xue, Guangfu; Liu, Hongxin; Cai, Yideng; Que, Jinhao; Jin, Xiyun; Luo, Meng; Pang, Fenglan; Yang, Yuexin; Lin, Yi; Liu, Yusong; Sun, Haoxiu; Tan, Renjie; Wang, Pingping; Xu, Zhaochun; Jiang, Qinghua

Ding, Qian; Yang, Wenyi; Xue, Guangfu; Liu, Hongxin; Cai, Yideng; Que, Jinhao; Jin, Xiyun; Luo, Meng; Pang, Fenglan; Yang, Yuexin; Lin, Yi; Liu, Yusong; Sun, Haoxiu; Tan, Renjie; Wang, Pingping; Xu, Zhaochun; Jiang, Qinghua.

Afiliación

Ding Q; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
Yang W; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
Xue G; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
Liu H; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
Cai Y; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
Que J; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
Jin X; School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
Luo M; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
Pang F; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
Yang Y; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
Lin Y; School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
Liu Y; School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
Sun H; School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
Tan R; School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
Wang P; School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China. wangpingping@hrbmu.edu.cn.
Xu Z; School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China. zhaochunxu@hrbmu.edu.cn.
Jiang Q; Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China. qhjiang@hit.edu.cn.

Genome Biol ; 25(1): 241, 2024 Sep 09.

Article en En | MEDLINE | ID: mdl-39252099

ABSTRACT

ABSTRACT

Advances in single-cell transcriptomics provide an unprecedented opportunity to explore complex biological processes. However, computational methods for analyzing single-cell transcriptomics still have room for improvement especially in dimension reduction, cell clustering, and cell-cell communication inference. Herein, we propose a versatile method, named DcjComm, for comprehensive analysis of single-cell transcriptomics. DcjComm detects functional modules to explore expression patterns and performs dimension reduction and clustering to discover cellular identities by the non-negative matrix factorization-based joint learning model. DcjComm then infers cell-cell communication by integrating ligand-receptor pairs, transcription factors, and target genes. DcjComm demonstrates superior performance compared to state-of-the-art methods.

Asunto(s)

Comunicación Celular; Análisis de la Célula Individual; Transcriptoma; Análisis de la Célula Individual/métodos; Análisis por Conglomerados; Perfilación de la Expresión Génica/métodos; Humanos; Biología Computacional/métodos

Palabras clave

Cell clustering; Cellcell communication; Joint learning; Non-negative matrix factorization; Single-cell

Texto completo

Añadir a Mi BVS

Imprimir

XML

PubMed Links

Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Comunicación Celular / Análisis de la Célula Individual / Transcriptoma Límite: Humans Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido

Texto completo

Añadir a Mi BVS

Imprimir

XML

PubMed Links

Buscar en Google