Energy profile and secondary structure impact shRNA efficacy

BMC Genomics

Table 2 Using either ΔG_as-7, ΔG_ss-6 or both can better predict the efficacy of shRNAs.

Energy profile	ΔG_as-5	ΔG_as-7	ΔG_ss-6	ΔG_as-7 or ΔG_ss-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).

ISSN: 1471-2164