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Table 6 HYPs meeting significance criteria in matched real and randomized data sets

From: Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data

Richness and concordance p-value threshold TNF PI3K inhibitor High fat diet
Random Real Ratio Random Real Ratio Random Real Ratio
0.2 13 94 14% 20 81 25% 7 33 21%
0.15 9 84 11% 12 66 18% 4 25 16%
0.1 3 58 5% 4 45 9% 1 13 8%
0.05 1 41 2% 1 29 3% 0 5 0%
0.01 0 24 0% 0 14 0% 0 0 N/A
0.005 0 21 0% 0 6 0% 0 0 N/A
  1. For each example data set (TNF, PI3K inhibitor, and high fat diet), 1000 matched random data sets were generated. The number of HYPs meeting significance criteria at each p-value threshold is indicated, for random data the median number of significant mechanisms is shown.
  2. BOLD indicates the 0.1 p-value threshold applied to analysis of the three example data sets.