Table 8 

Ranks of causal orientation methods for each gold standard 

Method 
ECOLI 
YEAST 
NOTCH1 
RELA 


ANM 
 
 
 
 
PNL 
 
 
5 
5 
IGCI (Uniform/Entropy) 
2 
 
3 
3 
IGCI (Uniform/Integral) 
3 
 
4 
4 
IGCI (Gaussian/Entropy) 
1 
2 
1 
1 
IGCI (Gaussian/Integral) 
2 
1 
2 
2 
GPIMML 
 
 
 
 
ANMMML 
 
 
 
 
GPI 
4 
 
4 
5 
ANMGAUSS 
 
 
2 
 
LINGAM 
 
 
 
 


Ranks were computed only for the methods with AUCs greater than 0.50. The lower the rank, the better the AUC of the causal orientation method for the given gold standard. The computation of rank took into account statistical variability, e.g. the AUCs of 0.724 and 0.713 obtained by the two IGCI methods in the ECOLI gold standard are statistically indistinguishable; that is why they have the same rank value. 

Statnikov et al. BMC Genomics 2012 13(Suppl 8):S22 doi:10.1186/1471216413S8S22 