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. 2021 Sep 6;10:e67403. doi: 10.7554/eLife.67403

Figure 1. Activity of putative cis-regulatory sequences with cone-rod homeobox (CRX) motifs.

(a) Volcano plot of activity scores relative to the Rho promoter alone. Sequences are grouped as strong enhancers (dark blue), weak enhancers (light blue), inactive (green), silencers (red), or ambiguous (gray). Horizontal line, false discovery rate (FDR) q = 0.05. Vertical lines, twofold above and below Rho. (b) Fraction of ChIP-seq and ATAC-seq peaks that belong to each activity group. (c) Predicted CRX occupancy of each activity group. Horizontal lines, medians; enh., enhancer. Numbers at top of (b and c) indicate n for groups.

Figure 1.

Figure 1—figure supplement 1. Reproducibility of massively parallel reporter assay (MPRA) measurements.

Figure 1—figure supplement 1.

Each row represents a different library and experiment. For each column, the first replicate in the title is the x-axis and the second replicate is the y-axis.
Figure 1—figure supplement 2. Calibration of massively parallel reporter assay (MPRA) libraries with the Rho promoter.

Figure 1—figure supplement 2.

Probability density histogram of the same 150 scrambled sequences in two libraries after normalizing to the basal Rho promoter.