Fig. 1: The dynamic range of gene expression levels is encoded in the DNA sequence.

All results shown are for S. cerevisiae, except in (h). a Expression levels (transcripts per million, TPM) of protein-coding genes across 3025 RNA-seq experiments. Inset: distribution of genes with a relative standard deviation (RSD = σ/μ) below 1. b Experimental variation of the gene expression levels expressed as RSD. c Distribution of ratios between the variance of expression levels within a genome and the variance of expression levels per gene across the experiments. d Schematic diagram of the explanatory variables used for modeling, with distributions of the sequence lengths in the regions where the lengths varied. “TSS” denotes the transcription start site and “TTS” the transcription termination site. e The optimized deep neural network (NN) architecture, where “conv” denotes convolutional NNs, “FC” fully connected layers, and “max-pool” max-pooling layers. The values denoting sizes of parameters layers, stride, kernels, filters, max-pooling, and dilation are specified. f Experimentally determined (true) versus predicted expression levels with the S. cerevisiae model on the held out test dataset (n = 425). Red line denotes least squares fit. g Comparison of published experimental fluorescence measurements⁴⁴ with the predicted expression levels (n = 625). Red line denotes least squares fit. h R² on held out test datasets across 7 model organisms. Red line denotes mean value. Source data are provided as a Source data file.