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 |