C. Elegans Exhibits Coordinated Oscillation in Gene Expression During Development

The advent of automated cell lineaging and the ability to track gene expression at single-cell resolution in vivo in C. elegans has yielded a dramatically more complete view into developmental processes. We present a novel meta-analysis of the EPIC single-cell-resolution gene expression dataset of Bao, Murray, Waterston et al., and show that a linear combination of the expression levels of the developmental genes in that dataset is strongly correlated with the wall-clock developmental age of the organism during early development, irrespective of the cell division rate of different cell lineages. We uncover a pattern of collective sinusoidal oscillation in gene expression, with multiple dominant sinusoidal frequencies, pointing to the existence of a global coordinated mechanism governing the timing of gene expression during development. We furthermore present a new method derived from Fisher9s Discriminant Analysis that can be used to produce sinusoidal oscillations of any frequency and phase using just a linear weighting of the expression patterns of the genes in this dataset, strengthening the view that oscillatory timing mechanisms play an important role in development. The Fisher9s Discriminant Analysis method also constitutes a generally useful tool for identifying the differential gene expression patterns that most strongly separate two distinct phenotypic or developmental traits.