Fig. 3: Combined effect of RBPs on miRNA targeting (MT).

a Association analysis between the number of RBPs bound close to the miRNA target site (MTS) and MT efficacy. 3′UTRs were separated into five subgroups with respect to the number of RBPs bound within 50 nts from the MTS. Each subgroup was carefully selected to have statistically indistinguishable confounding features among subgroups (see Methods). mRNA fold changes and values of confounding features were compared among these subgroups (two-sided Wilcoxon’s rank-sum test) with the mean values of confounding features and log₂(mRNA fold change) displayed. The error bars represent 95% confidence intervals of the values. For full versions for HeLa and other human cancer cell lines, see Supplementary Fig. 2a, b. b Distribution of MTSs with respect to the number of RBPs bound within 50 nt flanking regions in HepG2 data (left) and the separation of MTSs by the composition of bound RBPs (right). MTSs with the number of bound RBPs between 1 and 10 were collected and separated into two subgroups with similar number of bound RBPs but different RBP compositions (top right, see Methods). Similarly, those MTSs with the number of RBPs between 11 and 20 were collected and analyzed (bottom right). For full versions that also include the MTSs with the number of RBPs greater than 20, see Supplementary Fig. 3a. c For the two subgroups separated from the MTSs with the number of bound RBPs between 1 and 10, the RBP compositions (top left) and the mean MT efficacies (top right) are depicted and compared. For each RBP shown on the x-axis, the fraction of MTSs including an RBS within 50 nt flanking regions is displayed on the y-axis (top left). mRNA fold changes were compared between the two subgroups (top right, two-sided Wilcoxon’s rank-sum test). Similarly, for the two subgroups separated from the MTSs with the number of bound RBPs between 11 and 20, the RBP compositions (bottom left) and the mean MT efficacies (bottom right) are depicted and compared. Otherwise as in (b). For full versions that also include the MTSs with the number of RBPs greater than 20, see Supplementary Fig. 3b.