Supplementary Figure 14: Application to a gene expression time-course data set.

(A) SpatialDE applied to a developmental time course (89 time points from Owens et al), identifying the majority of genes as spatially variable (21,009 out of 22,256 genes, FDR < 0.05, Q-value adjusted). Of these, 241 were assigned to periodic patterns, and 269 were detected with linear trends. Colors and point sizes as in Fig. 2. The X marks indicates result of running SpatialDE on RNA spike-in content and the number of detected genes, proxies for the RNA content in the embryos. (B) Examples of temporally variable genes of various periods and length scales. Black scale bar corresponds to 12 hours in the time-course, periods and length scales of functions are indicated relative to this. Collection time in units of hours post fertilization (hpf). Stars next to gene names denote significance levels (* FDR < 0.05, ** FDR < 0.01, *** FDR < 0.001, Q-value adjusted). (C) The expression patterns of the top 400 significantly SV genes are visualized, ordered by the time they reach their highest expression value. Example genes from B are annotated.