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Table 3 Comparison in performance between 15 online siRNA design tools and DRM rule sets with four different stringency levels (α = 0.951, 0.895, 0.845 and 0.827).

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

Design Program Institution/Company URL Avg. # Effective siRNAs Predicted per Gene Sensitivity (> 90%) Specificity (> 90%) PPV (> 90%) Sensitivity (> 70%) Specificity (> 70%) PPV (> 70%)
Ambion siRNA Target Finder Ambion, Inc. [64] 190.0 0.603 0.456 37.0% 0.574 0.457 70.3%
Jack Lin's siRNA Sequence Finder Cold Spring Harbor Laboratory [65] 207.5 0.204 0.759 30.9% 0.221 0.757 67.1%
siDESIGN Center Dharmacon, Inc. [66] 9.8 0.042 0.976 48.5% 0.036 0.982 81.8%
siRNA Target Finder GenScript Corp. [67] 22.4 0.032 0.979 44.4% 0.030 0.988 85.2%
Imgenex sirna Designer Imgenex Corp. [68] 22.8 0.116 0.913 41.5% 0.108 0.929 77.4%
EMBOSS sirna Institute Pasteur [69] 639.4 0.778 0.250 35.4% 0.767 0.258 69.9%
IDT RNAi Design (SciTools) Integrated DNA Technologies, Inc. [70] 5.8 0.032 0.975 40.0% 0.030 0.979 76.7%
BLOCK-iT RNAi Designer Invitrogen Corp. [71] 11.4 0.026 0.985 47.6% 0.020 0.982 71.4%
siSearch Karolinska Institutet [72] 19.6 0.016 0.986 37.5% 0.017 0.991 81.3%
SiMAX MWG-Biotech, Inc. [73] 35.1 0.161 0.843 35.3% 0.172 0.872 75.1%
BIOPREDsi Novartis Institutes for BioMedical Research [74] 10.0 0.794 0.908 31.3% 0.820 0.899 64.6%
Promega siRNA Target Designer Promega Corp. [75] 38.0 0.093 0.941 45.5% 0.083 0.958 81.8%
QIAGEN siRNA Design Tool QIAGEN, Inc. [76] 29.6 0.167 0.862 38.9% 0.161 0.881 75.3%
SDS/MPI University of Hong Kong [77] 432.8 0.656 0.380 35.9% 0.632 0.368 69.2%
WI siRNA Selection Program Whitehead Institute [78] 9.5 0.019 0.992 53.8% 0.015 0.994 84.6%
DRM RS 0.951    18.9 0.021 0.996 72.7% 0.013 0.997 90.9%
DRM RS 0.895    20.7 0.032 0.992 66.7% 0.021 0.994 88.9%
DRM RS 0.845    38.1 0.032 0.986 54.5% 0.026 0.984 90.9%
DRM RS 0.827    51.8 0.037 0.973 42.4% 0.038 0.988 87.9%
  1. Comparison made based on Set T (1,093 siRNA experiments targeting 744 genes). Default settings were used for the 15 online predicting tools. Two sets of parameters (sensitivity, specificity and PPV) were calculated for each predicting tool or rule set. One was for > 90% efficacy (that is, a siRNA experiment was considered as truly effective if it achieved > 90% efficacy), the other one was for > 70% (considered truly effective if > 70% efficacy was reached in the experiment).