Principal Component Analysis-Based Unsupervised Feature Extraction Applied to Single-Cell Gene Expression Analysis

Due to missed sample labeling, unsupervised feature selection during single-cell (sc) RNA-seq can identify critical genes under the experimental conditions considered. In this paper, we applied principal component analysis (PCA)-based unsupervised feature extraction (FE) to identify biologically relevant genes from mouse and human embryonic brain development expression profiles retrieved by scRNA-seq. When evaluating the biological relevance of selected genes by various enrichment analyses, the PCA-based unsupervised FE outperformed conventional unsupervised approaches that select highly variable genes as well as bimodal genes in addition to the recently proposed dpFeature.