Functional feature selection reveals the inner cell mass in human pre-implantation embryo single cell RNA sequencing data

Abstract

A major challenge in single cell gene expression analysis is to discern meaningful cellular heterogeneity from technical or biological noise. To address this challenge, we present Entropy Sorting, a mathematical framework that distinguishes genes indicative of cell identity. ES achieves this in an unsupervised manner by quantifying if observed correlations between features are more likely to have occurred due to random chance versus a dependent relationship, without the need for any user defined significance threshold. On synthetic data we demonstrate the removal of noisy signals to reveal a higher resolution of gene expression patterns than commonly used feature selection methods. We then apply ES to human pre-implantation embryo scRNA-seq data. Previous studies failed to unambiguously identify early inner cell mass (ICM), suggesting that the human embryo may diverge from the mouse paradigm. In contrast, ES resolves the ICM and reveals sequential lineage bifurcations as in the classical model. Entropy sorting thus provides a powerful approach for maximising information extraction from high dimensional datasets such as scRNA-seq data.