scMUG: deep clustering analysis of single-cell RNA-seq data on multiple gene functional modules.

Abstract

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity by providing gene expression data at the single-cell level. Unlike bulk RNA-seq, scRNA-seq allows identification of different cell types within a given tissue, leading to a more nuanced comprehension of cell functions. However, the analysis of scRNA-seq data presents challenges due to its sparsity and high dimensionality. Since bioinformatics plays an important role in the analysis of big data and its utility for the welfare of living beings, it has been widely applied in analyzing scRNA-seq data. To address these challenges, we introduce the scMUG computational pipeline, which incorporates gene functional module information to enhance scRNA-seq clustering analysis. The pipeline includes data preprocessing, cell representation generation, cell-cell similarity matrix construction, and clustering analysis. The scMUG pipeline also introduces a novel similarity measure that combines local density and global distribution in the latent cell representation space. As far as we can tell, this is the first attempt to integrate gene functional associations into scRNA-seq clustering analysis. We curated nine human scRNA-seq datasets to evaluate our scMUG pipeline. With the help of gene functional information and the novel similarity measure, the clustering results from scMUG pipeline present deep insights into functional relationships between gene expression patterns and cellular heterogeneity. In addition, our scMUG pipeline also presents comparable or better clustering performances than other state-of-the-art methods. All source codes of scMUG have been deposited in a GitHub repository with instructions for reproducing all results (https://github.com/degiminnal/scMUG).