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Table 1 Classification of the parameters for siRNA design. The stability values for the best 12 parameters are presented in bold. Four most stable parameters possessing the best predictive power are shown in bold italic.

From: Computational models with thermodynamic and composition features improve siRNA design

Features R S 4 t-test P
Composition features:
   position-dependent nucleotide consensus: sum 0.51 0.047 2.8e-39
   position-dependent nucleotide consensus: avoided 0.44 0.053 9.7e-30
   position-dependent nucleotide consensus: preferred -0.446 0.051 1.3e-28
   nucleotide content: G 0.189 0.069 6.0e-08
   nucleotide content: U -0.187 0.065 1.1e-05
   avoided dinucleotide content index 0.259 0.061 5.7e-10
   preferred dinucleotide content index -0.212 0.061 5.7e-0.9
Thermodynamic features:
   ΔG of sense-antisense siRNA duplexes -0.173 0.072 0.0003
   siRNA antisense strand intra-molecular structure stability (ΔG) -0.198 0.072 7.6e-06
   stability (ΔG) of dimers of siRNAs antisense strands -0.169 0.072 0.0001
   stability profile (ΔG) for each two neighboring base pairs in the siRNA sense-antisense:    
   position 1 -0.297 0.059 1.3e-10
   position 2 -0.172 0.065 0.0007
   position 6 -0.172 0.069 0.0004
   position 13 -0.201 0.065 1.3e-07
   position 14 -0.126 0.065 0.008
   position 18 0.182 0.069 3.8e-06
   ΔG difference between position 1 and 18 0.352 0.055 7.4e-20
   local target mRNA stabilities (ΔG) 0.149 0.068 0.0008
   number of potential target copies in mRNAs (ΔG threshold) -0.145 0.065 1.8e-05