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Fig. 2 | BMC Bioinformatics

Fig. 2

From: ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data

Fig. 2

Example output summary from ReTrOS-Switch applied to mRNA microarray data. Data is from a microarray time-series for the ELF4 clock gene in wild-type Arabidopsis plants (PRESTA project) [12]. Panel a) shows the raw input data (blue circles, extremes of replicates shown in shaded region and median shown with line), the fitted mRNA expression (black line) and the estimated switch events (μ±1.96σ as vertical red/green lines). Panel b) shows the baseline-removed estimated switch time probability density (black line) and the estimated switch times Gaussian mixture model (blue line, with shaded red/green region indicating μ±1.96σ). Panel c) shows the accepted switch time samples, along with the switch events (red/green). The burn-in period of the chain is shown by the dashed black line. Panel d) shows the accepted samples from the precision (σ 2), δ m and δ p parameter chains in blue and a histogram of the accepted model size. Summaries of the parameter chains are shown in black (median and lower/upper quartiles) and red (μ and 1.96 σ). The model in Eq. (10) is used here. The default switch parameter values in the parameter setting GUI are used, with the prior mRNA degradation rate (mean = 1.5, std. dev. = 0.18), set by choosing Arabidopsis (see Fig. 5, upper panel)

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