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.
Features
 R
 S4
 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

Shabalina et al. BMC Bioinformatics 2006 7:65   doi:10.1186/1471-2105-7-65