FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods

BMC Bioinformatics

Table 2 Comparison between 4 methods regarding prioritization, sensitivity and the reciprocal ranks of the target pathways

	FoPA	PADOG	CePa	SPIA
mean reciprocal rank	0.09	0.1	0.06	0.07
rank median	17.5	11.4	25.25	41.25
rank mean	21.52	21.91	33.55	44.07
p median	0.11	0.08	0	0.27
p mean	0.15	0.18	0.11	0.38
Wilcoxon rank	Reference	0.9	0.008	5e-05
Wilcoxon p	Reference	0.45	0.02	0.0001

The table shows the statistics computed from the p-values and ranks of the 36 target pathways identified by each method. The mean reciprocal rank is the average of the reciprocal ranks of the target pathways computed by the equation \( \frac{1}{N}{\sum}_{i=1}^N\frac{1}{{\mathit{\operatorname{rank}}}_i} \). The results of comparing the ranks of each method against FoPA (chosen as reference), using a paired Wilcoxon test are also included. The best value for each measure is shown in bold

ISSN: 1471-2105