Figure 3.

Importance ranking of thermodynamic probe properties including target-side modeling. Importance ranking of thermodynamic probe properties including target-side modelling. The left hand figure (A) shows the Guide ranking for the clearly expressed genes showing no cross-hybridization from Wei et al. [23], whereas the right one shows the results for the Pozhitkov et al. [26] dataset (B). ΔG stands for the effective interaction energy including relevant competing intra- and inter-molecular effects. ΔG_p labels the free energy of the probe secondary structure, ΔG_t the free energy of the probe binding site secondary structure in the target, ΔGh the free energy of the probe-target duplex, and ΔGpp the free energy of probe-probe dimerization within the same probe feature. 'Tm' stands for the melting temperature. Error bars are from bootstrap re-sampling of 90% of all probes. Below the x-axis, the Spearman rank correlation of predictions to the observed signal intensity is shown. All correlations were highly significant, with the correlation for ΔGpp in (A) having p < 10^-9, and p ≤ 10^-5 in (B). For the other correlations, p < 10^-15. We note that the correlation values for the sample with complex background are considerably lower, suggesting further scope for improvements in our model.