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Figure 3 | BMC Bioinformatics

Figure 3

From: Integrated siRNA design based on surveying of features associated with high RNAi effectiveness

Figure 3

Highly effective siRNA design rules were obtained by selecting the top l-feature combinations, i.e., the combination of l non-redundant significant features that exhibited the highest percentages of records achieving > 70% or > 90% efficacies on Set A. A. For l = 2 through 6, the subpopulations of Set A records that carry all combinations of l features were examined, and the 10 feature combinations (FCs) that resulted in the highest percentages of records achieving > 70% efficacies were selected. When there was a tie of more than 10 FCs, all of them were considered (marked in the graph). The mean percentages of the top FCs are presented in black filled circles. These FCs were used to select siRNA experiments in the Set T, and the results are shown in grey filled circles. Error bars indicate standard errors. The first two data points in the graphs represent the base line levels (the percentage of records achieving > 70% efficacies for the entire Set A or Set T), and the mean levels for top-10 individual features (the 10 individual features that led to highest percentages of records achieving > 70% efficacies), respectively. B. Similarly to A, the top FCs selected with > 90% efficacies are plotted, together with the baseline levels and the mean levels for top individual features. C. The numbers of records selected in the top l-feature combinations dropped sharply as l increased. The mean numbers of selected records for Set A (with error bars indicating standard errors) are presented in black filled circles and black open circles for > 70% and > 90% efficacies, respectively. The numbers of selected records for Set T are presented in corresponding grey symbols. Again, the first two data points represent the baseline levels (numbers of records in entire Set A and Set T), and the numbers of records selected with the top-10 individual features, respectively.

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