Fig. 2: Coding and cis-regulatory regions jointly contribute to gene expression prediction. | Nature Communications

Fig. 2: Coding and cis-regulatory regions jointly contribute to gene expression prediction.

From: Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

Fig. 2

a Test R2 with different combinations of coding (codon prob.), mRNA stability (see Supplementary Fig. 1c) and cis-regulatory regions, using shallow (black) and deep modeling (red). b Test R2 with deep models trained on different combinations of cis-regulatory regions. Red lines denote mean values. c Schematic depiction of deep neural network (NN) for prediction of codon probabilities (Y) based on regulatory DNA as input (X). d Actual versus predicted distribution of codon probabilities as predicted from non-coding DNA regions based on the model for prediction of codon probabilities based on regulatory DNA as input (n = 11,947). Red line denotes least squares fit. e Evolutionary substitution rates in promoter vs. coding regions in orthologous genes of 14 yeast species (n = 3248). Red line denotes least squares fit. f Evolutionary substitution rates in terminator vs. coding regions in orthologous genes of 14 yeast species (n = 3248). Red line denotes least squares fit. Source data are provided as a Source data file.

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