Extended Data Fig. 5: Extended analysis of package rankings based on riboswitch activity predictions.
From: RNA secondary structure packages evaluated and improved by high-throughput experiments
a) Example set of states for a riboswitch that toggles binding of the fluorescent MS2 protein as an output, controlled by binding the small molecule FMN. The equilibrium constant for forming the MS2 aptamer in the absence of ligand, \(K_{MS2}^{ - lig}\), is estimated using the probability of forming the closing base pair for all packages. b) Riboswitch Z-scores stratified by input ligand type. Error bars represent standard error on Z-score as calculated by bootstrapping from 6402, 440, and 386 constructs collected over 8, 2, and 2 experiments, respectively. c) Overall ranking \(K_{MS2}^{ - lig}\) calculations using the calculated Spearman correlation (no linear assumption, compare to Fig. 2b). Evaulating the Pearson Correlation of package calculations for (d) \(K_{MS2}^{ + lig}\) as well as (e) riboswitch Activation Ratio results in a similar ranking. In C, D, E, error bars represent 95% confidence interval of the mean obtained over 1000 iterations of bootstrapping across datasets, n = 7,228 independent constructs collected over 12 experiments.
