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

BMC Bioinformatics

Table 2 Overview of data sets used for examples

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

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.

ISSN: 1471-2105