Table 2

Using either ΔGas-7, ΔGss-6 or both can better predict the efficacy of shRNAs.

Energy profile

ΔGas-5

ΔGas-7

ΔGss-6

ΔGas-7 or ΔGss-6or both


Energy criteria

>= -3.2

>= -6.6

>= -7.0

P value of Chi-test

0.0046

0.0005

0.0045

0.0000001

True positive

155

155

115

192

False positive

35

32

22

39

True negative

33

36

46

29

False negative

66

66

106

29

ROC specificity

0.49

0.53

0.68

0.43

ROC sensitivity

0.70

0.70

0.52

0.87


ROC: Receiver Opearting Characteristic. True positives (TP) are those shRNAs which are experimentally tested to be functional and they meet the energy criteria. False positives (FP) are those shRNAs which meet the energy criteria but are experimentally tested to be nonfunctional. True negatives (TN) are those which are nonfunctional in experiments and fail the energy criteria. False negatives (FN) are those which fail the energy criteria but are functional experimentally. ROC specificity = TN/(TN+FP); ROC sensitivity = TP/(TP+FN).

Zhou and Zeng BMC Genomics 2009 10(Suppl 1):S9   doi:10.1186/1471-2164-10-S1-S9

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