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Table 4 Comparison in performance between 15 online siRNA design tools and 4 DRM rule sets based on independent subset of Set T.

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

Design Program Institution/Company #Predicted effective siRNAs #Predicted ineffective siRNAs Sensitivity Specificity PPV (%)
Ambion siRNA Target Finder Ambion, Inc. 144 80 0.645 0.362 74.3
Jack Lin's siRNA Sequence Finder Cold Spring Harbor Laboratory 44 180 0.229 0.897 86.4
siDESIGN Center Dharmacon, Inc. 7 217 0.036 0.983 85.7
siRNA Target Finder GenScript Corp. 6 218 0.024 0.966 66.7
Imgenex sirna Designer Imgenex Corp. 24 200 0.114 0.914 79.2
EMBOSS sirna Institute Pasteur 180 44 0.801 0.190 73.8
IDT RNAi Design (SciTools) Integrated DNA Technologies, Inc. 4 220 0.012 0.966 50.0
BLOCK-iT RNAi Designer Invitrogen Corp. 2 222 0.012 1.000 100
siSearch Karolinska Institutet 0 224 N/A N/A N/A
SiMAX MWG-Biotech, Inc. 48 176 0.235 0.845 81.3
BIOPREDsi Novartis Institutes for BioMedical Research 4 220 0.018 0.983 75.0
Promega siRNA Target Designer Promega Corp. 26 198 0.127 0.914 80.8
QIAGEN siRNA Design Tool QIAGEN, Inc. 33 191 0.151 0.862 75.8
SDS/MPI University of Hong Kong 151 73 0.663 0.293 72.8
WI siRNA Selection Program Whitehead Institute 12 212 0.072 1.000 100
DRM RS 0.951   1 223 0.006 1 100
DRM RS 0.895   4 220 0.024 1 100
DRM RS 0.845   5 219 0.030 1 100
DRM RS 0.827   9 215 0.048 0.983 88.9
  1. Comparison made based on the independent subset of Set T (224 siRNA experiments targeting 197 genes). Default settings were used for the 15 online predicting tools. A siRNA experiment was considered effective if it achieved > 70% efficacy (was rated "high" or "very high" efficacy).