Extended Data Fig. 2: Performance of the shallow CNN model. | Nature Genetics

Extended Data Fig. 2: Performance of the shallow CNN model.

From: Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings

Extended Data Fig. 2

(a) Density plot of observed population-average expression of test set genes (n = 3,401 genes) in cerebral cortex versus simple CNN’s predicted gene expression from the Reference sequences. This plot only displays genes which could be assigned to Enformer’s test set. Colors depict local density. (b) Y-axis shows Pearson’s r correlation coefficients between observed expression values and a simple CNN’s predicted values per individual. X-axis shows the negative log10 p-value computed with a gene-specific Null model (one-sided T-test, n = 50 independent samples per gene; Supplementary Method). The color represents the predicted mean expression. Red dashed line indicates FDRBH = 0.05.

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