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Table 1 Non-redundant significant features meeting the criteria (P wald < 0.01) and (P 70 < 0.01 or P 90 < 0.01)

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

Feature name % Low % Medium % High % Very high P 70 P 90 P wald
2nd nucleotide = A 12.1 16.0 33.8 38.1 0.01 0.0026 0.0019
4th nucleotide = C 14.1 15.4 31.5 39.0 0.098 0.00036 0.0075
6th nucleotide ≠ C 14.3 15.6 35.0 35.1 0.00066 0.0089 0.0052
7th nucleotide ≠ U 14.4 15.9 34.5 35.2 0.01 0.0043 0.0091
9th nucleotide = C 11.1 16.6 32.6 39.6 0.008 0.00021 0.00053
17th nucleotide = A 11.4 15.5 37.1 35.9 0.00049 0.1 0.0049
18th nucleotide ≠ C 14.4 15.9 34.3 35.4 0.01 0.00071 0.0048
19th nucleotide = (A/U) 12.0 16.0 35.3 36.7 0.00029 0.0043 0.000058
At least three (A/U)s in the seven nucleotides at the 3' end 13.4 16.4 33.7 36.5 0.00001 0.00001 2.5E-09
No occurrences of four or more identical nucleotides in a row 14.2 15.9 35.4 34.5 0.00001 0.012 0.0014
No occurrences of G/C stretches of length 7 or longer 14.3 16.4 34.9 34.4 0.00001 0.00001 0.000015
G/C content is between 35% and 60% 13.3 16.7 35.1 35.0 0.00001 0.0019 0.00018
Tm is between 20 and 60°C 13.2 16.5 35.0 35.3 0.0045 0.023 0.003
Binding energy of N16–N19 > -9 KCal/Mol 11.8 17.1 34.0 37.1 0.01 0.0026 0.00025
Binding energy of N16–N19 – binding energy of N1–N4 is between 0 and 1 KCal/Mol 12.6 14.9 32.5 39.9 0.01 0.00036 0.0078
Local folding potential (mean) ≥ -22.72 KCal/Mol 12.0 14.6 34.7 38.7 0.00001 0.00001 9.3E-09
Target site is on CDS 14.4 16.2 34.3 35.2 0.00001 0.00001 0.000055
Cell line = HeLa 7.9 10.6 41.2 40.3 0.00001 0.00016 4.0E-09
Test method = Western blot 10.8 15.5 34.8 36.9 0.00001 0.00001 3.8E-14
Test object ≠ mRNA 13.1 14.5 34.8 37.6 0.00001 0.00001 9.3E-10
  1. At P < 0.01, the FDR for the three tests: Wald test of monotone trend, permutation test of odds ratios (> 70%) and permutation test of odds ratios (> 90%) were controlled at the levels of 0.056, 0.044 and 0.038 respectively.