Table 1.

Non-redundant significant features meeting the criteria (P_wald < 0.01) and (P₇₀ < 0.01 or P₉₀ < 0.01)

Feature name	% Low	% Medium	% High	% Very high	P70	P90	Pwald
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

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.