Fig. 5: Three alternative measures to express cell-to-cell mRNA variability.
From: smiFISH and embryo segmentation for single-cell multi-gene RNA quantification in arthropods
a Formulae for Fano factor, a commonly used measure of cell variability, and NV and PV, two alternative measures designed to better capture individual cell variability. b Cells from the anterior stripe of eve expression in P. hawaiensis early germband embryo, highlighting that individual cells can differ greatly in expression from their immediate neighbours. The centre cell (white arrow) in the left panel is similar to all its neighbouring cells except one, whereas the centre cell in the right panel is highly different from all of its neighbours except one. c–f Hypothetical scenarios of neighbour-group mRNA variability, to highlight the capacity of each formula to capture the variability of the single centre cell (red dashed border). Here, 550 mRNA/cell is used as the population maximum. Fano factor incorrectly returns the same value for (c) and (d), and incorrectly finds (e) to be more variable than (c). NV correctly returns the same value for (c, e and f), and a low value for (d). PV correctly returns the same value for (c) and (e), and lower values for (d) and (f). g Heatmaps show the three different variability measures, calculated for each segmented cell of the embryo (1982 cells in total), for five genes: even-skipped, hunchback, knirps, giant and Kruppel. Dots representing cells are scaled in both size and colour by the variability value. Both NV and PV measures can range from minimum 0 to maximum 1. For PV heatmaps, cells were filtered on the criteria of neighbour-group mean mRNA number ≥1; cells failing this criterion were assigned a score of 0.
