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. , whereas the right one shows the results for the Pozhitkov et al.  dataset (B). ΔG stands for the effective interaction energy including relevant competing intra- and inter-molecular effects. ΔGp labels the free energy of the probe secondary structure, ΔGt 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.
Mueckstein et al. BMC Bioinformatics 2010 11:35 doi:10.1186/1471-2105-11-35