Extended Data Fig. 3: CRE effects on TSS activity in GM12878 and PC-3 cell lines.
From: Interpreting cis-regulatory interactions from large-scale deep neural networks
a,b, Boxen plot of the normalized shuffle effect for each tile in sequences from enhancing, neutral and silencing context categories (Necessity Test) for GM12878 (a) and PC-3 (b). The number of data points in a is 7600, 6954, 2964 and in b is 7600, 4180, 3420 in enhancing, neutral and silencing contexts respectively. c, d, Boxen plot of tile effects for each tile in sequences from enhancing, neutral and silencing context categories (Sufficiency Test) for GM12878 (c) and PC-3 (d). Normalization is with predicted TSS activity for wild-type (enhancing context) and control, that is the intrinsic TSS activity (neutral and silencing context). Boxen-plots have the same number of data points as in a and b. In panels a – d center lines of boxenplots show the median and boxes in both directions always indicate half of the remaining data. e, Scatter plot between the results from the Necessity Test (y-axis) versus the results from the Sufficiency Test (x-axis) in K562 cell line (N = 7,600 in each plot corresponding to 200 sequences with 38 tiles in each).
