Assessment of dispersion metrics for estimating single-cell transcriptional variability

Single-cell RNA sequencing data enables analysis of transcript levels of single cells across different cell types and conditions. Recent work has highlighted the value of measuring gene-specific transcriptional variability, or noise, within a genetically identical population of cells in addition to mean expression, given that these differences contribute to biological processes including development and disease. However, measuring transcriptional noise remains a challenge. Here, we systematically compared statistical methods by simulating single-cell data by varying both dispersion and count size to assess the relative responsiveness to noise of several commonly used statistical metrics: the Gini index, variance-to-mean ratio, variance, coefficient of variance (CV), CV2, and Shannon entropy. We found that the variance-to-mean ratio scales approximately linearly with increasing dispersion and is independent of dataset size. In contrast, the Gini index displayed paradoxical behavior in that it increases as dispersion decreases, and Shannon entropy was not scale-invariant. Next, we applied the variance-to-mean ratio (Fano factor) to measure transcriptional variability in single-cell datasets representing different complex systems and cross-platform measurements. Our data show that many genes display transcriptional variability within the same cell type, and that while variation does not correlate with gene characteristics such as transcript level, promoter GC content, or evolutionary gene age, variable genes are often correlated with specific biological processes. Notably, most genes and pathways with highest transcriptional variability as identified by the Fano factor were largely independent of differentially expressed genes and have also been implicated in biological processes related to the system. Thus, our data highlight that choice and application of appropriate models for measuring transcriptional variation in scRNA-seq data can reveal biologically relevant information beyond what is observed from mean expression alone.