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Fig. 5 | BMC Bioinformatics

Fig. 5

From: reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction

Fig. 5

Correlation between RNA reactivity and 3D accessibility for the test set of three rRNAs. a Relation between the accessible surface area (ASA) and reactivity scores computed by six types of scoring methods. y-axis, averaged ASAs within each 500-nucleotide sliding window; x-axis, a ranking of each nucleotide based on the structure scores, in which ties were randomly broken. The structure scores of reactIDR from the in vivo icSHAPE dataset presented the highest correlation with ASAs across the six scoring methods. b Correlations between structure scores and 2D or 3D accessibility indices. * p-value<10−5 after Bonferroni correction. c Ribosomal 3D structures visualized by PyMOL [29]. Left, ribosome changes its color from red to blue according to the ASAs of each nucleotide (high to low). Right, the highlighted regions indicate the top 7% reactive sites of 18S rRNA from the in vivo dataset (red), in vitro dataset (blue), and their intersection (purple)

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