Additional file 4.

Comparison of NF-κB-direct HYP scores with 20-gene NF-κB HYP scores. Transcriptomic data from TNFα-treated NHBE cells was scored using each scoring method (Strength, GPI, EPI and MASS) for (a) the NF-κB-direct HYP, (b) a HYP composed of 20 NF-κB-regulated genes reported to be TNFα-responsive in mouse 3 T3 fibroblast cells (NFKBIA, CASP4, CCL5, TNFAIP3, CCL2, ZFP36, RIPK2, TNFSF10, NFKBIE, IL6, CCL20, ICAM1, TNFRSF1A, TNFRSF1B, SQSTM1, NRG1, SOD1, IL1RL1, HIF1A, ERBB2) [19]. Error bars represent the 95 % confidence interval as determined by the Uncertainty statistic. Scores that failed the Specificity criterion (Specificity p-value > 0.05; 1000 comparable HYPs) are shaded in gray.

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Martin et al. BMC Systems Biology 2012 6:54   doi:10.1186/1752-0509-6-54