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Table 2 Overview of data sets used for examples

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

Data Set Reference PMID Species Platform Perturbation Significant probe sets Population State changes Evaluated HYPs Significant HYPs
E-MEXP-1755 19196459 Mouse MG-430 2.0 High fat diet 372 7594 193 606 13
GSE2638 16617158 Human HG-U133A TNF 557 6644 330 593 58
GSE17785 22570710 Human HG-U133 Plus 2.0 GDC-0941 (PI3K inhibitor) 3410 7500 1126 603 45
  1. Probe sets were considered significantly differential if average abundance > = 32, fold change > = 1.3, and adjusted p-value < = 0.05. The population size is defined as the number of unique measured RNA abundances mapped to HYPs. The number of state changes is defined as the number of differential RNAs in the population. Mechanisms were evaluated as HYPs if at least four measured RNAs are downstream nodes. HYPs were considered significant if both richness p < = 0.1 and concordance p < = 0.1.