Table 2.
Percent of total number of features and sequence-specific properties (see Table 1 for definitions) statistically tested for being correlated with biased RNA amplification (see heatmap in Figure 6). Mean and standard deviation (SD) are given for features meeting the criteria in bold. Where applicable, the test statistics t (t-test) and Z (Mann-Whitney test) are listed with corresponding p-values. Number and percent of features with tandem repeats are listed with Pearson Chi-Square test statistics and p-values.
| GC-Content | Tandem repeats | ||||||
|---|---|---|---|---|---|---|---|
| % | Mean (± SD) | (t) or (Z) | p | N | Pearson Chi- Square |
p | |
|
Present before and after amplification |
93.4 | 43.9 (±7.95%) | 983 (11.27%) |
||||
|
Appeared after amplification vs. present in both |
2.5 | 45.7 (±7.73%) | −3.108 (Z) |
0.002 | 19 (8.72%) | 1.397 | 0.237 |
|
Disappeared after amplification vs. present in both |
1.3 | 42.2 (±7.79%) | −2.541 (Z) |
0.011 | 14 (8.92%) | 0.858 | 0.354 |
|
No change in regulation after amplification |
69.5 | 43.7 (±7.93%) | 706 (12.91%) |
||||
|
Gained regulation signal after amplification vs. no change in regulation |
19.5 | 43.9 (±7.88%) | 0.977 (t) | 0.329 | 212 (13.05%) |
0.018 | 0.893 |
|
Lost regulation signal after amplification vs. no change in regulation |
4.2 | 47.3 (±8.08%) | −8.733 (Z) |
0.000 | 36 (9.52%) | 2.910 | 0.088 |
| Length polyA | Length polyT | ||||||
| % | Mean (± SD) | (t) or (Z) | p | Mean (± SD) |
(t) or (Z) | p | |
|
Present before and after amplification |
93.4 | 45.6 (±30.10nt) | 44.4 (±29.20nt) |
||||
|
Appeared after amplification vs. present in both |
2.5 | 28.0 (±2.71nt) | −10.595 (t) |
0.000 | 35.1 (±17.02nt) |
−2.573 (t) | 0.017 |
|
Disappeared after amplification vs. present in both |
1.3 | 40.1 (±24.00nt) | −0.690 (t) | 0.490 | 41.9 (±36.39nt) |
−0.434 (t) | 0.664 |
|
No change in regulation after amplification |
69.5 | 47.0 (±30.67nt) | 45.4 (±29.92nt) |
||||
|
Gained regulation signal after amplification vs. no change in regulation |
19.5 | 41.6 (±27.63nt) | −2.421 (Z) |
0.015 | 41.6 (±27.40nt) |
−2.254 (t) | 0.025 |
|
Lost regulation signal after amplification vs. no change in regulation |
4.2 | 42.0 (±23.83nt) | −0.584 (t) | 0.559 | 36.1 (±15.32nt) |
−3.175 (t) | 0.003 |
| Folding energy | Z-score folding energy | ||||||
| % | Mean (± SD) | (t) or (Z) | p | Mean (± SD) |
(t) or (Z) | p | |
|
Present before and after amplification |
93.4 | −149.6 (±68.27Kcal/mol) |
−0.21 (±1.295) |
||||
|
Appeared after amplification vs. present in both |
2.5 | −127.6 (±61.29Kcal/mol) |
−4.577 (Z) | 0.000 | −0.13 (±1.216) |
0.908 (t) | 0.365 |
|
Disappeared after amplification vs. present in both |
1.3 | −147.4 (±62.00Kcal/mol) |
0.443 (t) | 0.659 | −0.47 (±1.579) |
−2.083 (t) | 0.039 |
|
No change in regulation after amplification |
69.5 | −151.4 (±69.54Kcal/mol) |
−0.2 (±1.30) |
||||
|
Gained regulation signal after amplification vs. no change in regulation |
19.5 | −150.4 (±65.71Kcal/mol) |
0.573 (t) | 0.567 | −0.20 (±1.249) |
0.558 (t) | 0.577 |
|
Lost regulation signal after amplification vs. no change in regulation |
4.2 | −118.2 (±54.40Kcal/mol) |
−9.299 (Z) | 0.000 | −0.12 (±1.391) |
−2.273 (Z) | 0.023 |
| Number hairpins | Length hairpins | ||||||
| % | Mean (± SD) | (t) or (Z) | p | Mean (± SD) |
(t) or (Z) | p | |
|
Present before and after amplification |
93.4 | 33.0 (±14.78) | 10.6 (±3.99nt) |
||||
|
Appeared after amplification vs. present in both |
2.5 | 28.5 (±13.52) | −4.378 (Z) |
0.000 | 9.7 (±3.10nt) |
−4.445 (Z) | 0.000 |
|
Disappeared after amplification vs. present in both |
1.3 | 33.4 (±14.23) | 0.367 (t) | 0.714 | 11.4 (±5.47nt) |
1.795 (t) | 0.075 |
|
No change in regulation after amplification |
69.5 | 33.3 (±14.88) | 10.7 (±4.05nt) |
||||
|
Gained regulation signal after amplification vs. no change in regulation |
19.5 | 33.5 (±14.60) | 0.611 (t) | 0.541 | 10.6 (±3.87nt) |
−0.576 (t) | 0.565 |
|
Lost regulation signal after amplification vs. no change in regulation |
4.2 | 25.4 (±12.42) | −10.352 (Z) |
0.000 | 9.7 (±3.07nt) |
−6.506 (Z) | 0.000 |
| GC-skew | AT-skew | ||||||
| % | Mean (± SD) | (t) or (Z) | p | Mean (± SD) |
(t) or (Z) | p | |
|
Present before and after amplification |
93.4 | 0.00 (±0.134) | 0.02 (±0.157) |
||||
|
Appeared after amplification vs. present in both |
2.5 | 0.01 (±0.115) |
0.179 (t) | 0.858 | 0.01 (±0.136) | −0.980 (t) | 0.328 |
|
Disappeared after amplification vs. present in both |
1.3 | 0.02 (±0.176) | 0.999 (t) | 0.319 | −0.01 (±0.137) |
−2.088 (t) | 0.038 |
|
No change in regulation after amplification |
69.5 | 0.00 (±0.136) | 0.02 (±0.159) |
||||
|
Gained regulation signal after amplification vs. no change in regulation |
19.5 | 0.01 (±0.131) | 0.376 (t) | 0.707 | 0.02 (±0.151) |
−0.401 (t) | 0.688 |
|
Lost regulation signal after amplification vs. no change in regulation |
4.2 | 0.01 (±0.127) |
1.060 (t) | 0.289 | 0.03 (±0.158) |
1.131 (t) | 0.258 |