Extended Data Fig. 1: Results of the Context Dependence Test and Context Swap Test for GM12878 and PC-3.
From: Interpreting cis-regulatory interactions from large-scale deep neural networks
a,b Histogram of normalized context effect from the Context Dependence Test for 10,000 sequences that contain an active, annotated gene in GM12878 and PC-3 cells. Inset shows the subset of sequences for enhancing, silencing and neutral contexts. a inset contains 200, 78 and 183 data points in enhancing, silencing and neutral context respectively. b inset contains 200, 90 and 110 data points in enhancing, silencing and neutral context respectively. c, Pairwise comparison of normalized context effects between cell lines for matched genes. The number of data points is 7688, 6946, 7492 from left to right. d,e, Context Swap Test results. Boxplots of normalized context effect on TSS for sequences with context perturbations given by insertion of the original TSS in different context categories. Results are organized according to the original TSS category: enhancing (left), neutral (middle), and silencing (right). The number of data points in each boxplot represent an all-vs-all comparison of each respective TSS in each possible context. The number of data points in d is 40,000, 36,600, 15,600 in boxplots for TSS from enhancing context, 36,600, 33,489, 14,274 in TSS from neutral context and 15600, 14274, 6084 in TSS from silencing context. The number of data points in e is 40,000, 22,000, 18,000 in boxplots for TSS from enhancing, 22,000, 12,100, 9,900 in TSS from neutral context and 18,000, 9,900, 8,100 in TSS from silencing context. Boxplots show the first and third quartiles, the median (central line) and the range of data with outliers removed (whiskers).
