Table 7 |
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|
List of siRNA with bad predictions. |
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|
Id |
Target |
Target site |
M.A. |
P.A. |
status |
ΔGloc |
s.d |
begin |
end |
|
|
|||||||||
|
1 |
NM_012864 |
CAGGCGCAGAAUUAUCUUAGG |
1.341 |
0.765 |
under |
-17 |
2.86 |
63 |
83 |
|
9 |
GUUUGCCGGAGACUGGAAAGC |
0.019 |
0.373 |
over |
-18.2 |
5.75 |
163 |
183 |
|
|
2 |
NM_017346 |
AUCGAGCGCUCCAACACUCGC |
0.152 |
0.684 |
over |
-19.9 |
0.00 |
831 |
851 |
|
3 |
UGACGCCACCUCAGGGCACCU |
0.086 |
0.563 |
over |
-17.7 |
0.00 |
209 |
229 |
|
|
11 |
NM_002559 |
UGCGUGAACUACAGCUCUGUG |
0.420 |
0.743 |
over |
-4.8 |
0.00 |
376 |
396 |
|
15 |
AGCUCUGUGCUCCGGACCUGU |
0.419 |
0.713 |
over |
-29.8 |
0.00 |
388 |
408 |
|
|
4 |
NM_003342 |
GGGAAGUCCUUAUUAUUGGCC |
0.876 |
0.435 |
under |
-17.9 |
0.06 |
69 |
89 |
|
5 |
UUCCUGAGCUGGAUGGAAAGA |
1.201 |
0.799 |
under |
-2.4 |
0.98 |
246 |
266 |
|
|
7 |
NM_016406 |
GUGGCAAAAUAUGCCUGACGG |
0.999 |
0.616 |
under |
-10.4 |
0.00 |
285 |
305 |
|
22 |
AUGCCUGACGGAUCAUUUCAA |
1.173 |
0.907 |
under |
-8.8 |
2.12 |
295 |
315 |
|
|
6 |
NM_003340 |
UUCUUUUAUCCAUUUGUUCAC |
0.270 |
0.672 |
over |
-7.2 |
1.41 |
255 |
275 |
|
8 |
NM_003347 |
UAUGAUAAGGGAGCCUUCAGA |
1.099 |
0.728 |
under |
-8.3 |
0.06 |
86 |
106 |
|
10 |
NM_018426 (XM_371822) |
GAUGCCACCCGACGCCCUCAC |
0.127 |
0.454 |
over |
-9.5 |
1.18 |
2148 |
2168 |
|
12 |
NM_001009264 (XM_214061) |
CCAGGGCGGAGAAGGCCGACG |
0.239 |
0.548 |
over |
-25.1 |
0.00 |
371 |
391 |
|
14 |
UGAACUUUGGGUCCCUGUGAC |
0.268 |
0.568 |
over |
-11.1 |
0.00 |
865 |
885 |
|
|
16 |
NM_001001481 |
UGUAACAAGAAUCCAAAGAAA |
1.146 |
0.853 |
under |
-10.9 |
0.19 |
353 |
373 |
|
17 |
NM_016021 |
CAACAAAAGGAGAGGGAGCCA |
0.417 |
0.709 |
over |
-19.7 |
0.00 |
309 |
329 |
|
18 |
NM_022005 |
CCUGUGACCUCCAUCUACUCU |
0.968 |
0.682 |
under |
-16.5 |
0.00 |
79 |
99 |
|
19 |
NM_007019 |
UGUAUGAUGUCAGGACCAUUC |
0.321 |
0.601 |
over |
-10.1 |
1.02 |
185 |
205 |
|
20 |
NM_006357 |
UAAAGGAGAUAACAUUUAUGA |
0.520 |
0.795 |
over |
-9.6 |
0.00 |
211 |
231 |
|
|
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|
This table gives the list of siRNAs for which the discrepancy between the prediction and the actual potency were particularly large. Each siRNA sequence has been arbitrarily named from 1 to 22. Two sequences have been discarded because their target sequences have been modified in Genbank since Huesken's publication date. M.A. is the measured activity as given in Huesken et al. [33]. P.A. is the predicted activity according to our LASSO model. The column status refers to the activity of the siRNA that has been over- or under-predicted compared to the activity measured experimentally. The begin and end columns indicate the position of the siRNA guide strand within the target sequence. The ΔGloc corresponds to the mean local free energies of motifs in which nucleotides of the target sequence are involved for the 10 lowest energy structures and is given in kcal/mol. s.d. represents the standard deviation of each mean ΔGloc computed. |
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|
Vert et al. BMC Bioinformatics 2006 7:520 doi:10.1186/1471-2105-7-520 |
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