GP regression provides estimates of transcript half-lives in early embryogenesis.

(A) Reads aligned to intronic and exonic regions of genes are used to represent pre-mRNA (blue) and mature mRNA levels (red), respectively. (B) Schematic of GP regression and the ODE model that shows the evolution of the mature mRNA dynamics is described by the pre-mRNA data over time, sculpted by the splicing (S) and degradation (D) parameters. Pre-mRNA and mature mRNA are therefore jointly modelled using GPs related by the ODE. (C) Half-life results for 263 transcripts estimated using the GP model. Transcripts are divided into short, medium, and long half-lives and coloured accordingly. (D) Examples of data for a short (Di) and a long (Dii) half-life mRNA, lov and cv-2, respectively, fit using the GP model. Pre-mRNA is shown in blue and mature mRNA in red, shaded areas represent credible regions and crosses mark the data for each experimental replicate at each time point. Posterior distributions for the degradation parameter D for each mRNA are shown to the right. Underlying data can be found in S1 Data, S1 and S2 Tables. GP, Gaussian process; ODE, ordinary differential equation.