Table 4.

Degree of coincidence between the equivalence test described here and the equivalence test based on the goProfiles approach.

Onto Level	AllOnco gene lists		PBT’s gene lists
	Correlation	p - value	Correlation	p - value
BP-3	0.6507	0.0022	0.2711	0.0013
BP-4	0.6895	0.0008	0.3781	0
BP-5	0.6943	0.0004	0.372	0
BP-6	0.6703	0.0006	0.3214	0.0004
BP-7	0.66	0.0004	0.2777	0.0019
BP-8	0.6409	0.0004	0.238	0.0082
BP-9	0.704	0.0002	0.2026	0.0229
BP-10	0.7178	0.0002	0.196	0.0282
CC-3	0.5199	0.0036	0.151	0.0683
CC-4	0.54	0.0022	0.1753	0.0386
CC-5	0.5648	0.001	0.3057	0
CC-6	0.4052	0.006	0.2354	0.0017
CC-7	0.3964	0.0089	0.2127	0.0071
CC-8	0.4671	0.0073	0.1795	0.0318
CC-9	0.5888	0.0085	0.2083	0.0046
CC-10	0.7008	0.0032	0.2878	0
MF-3	0.3878	0.0556	0.1088	0.1825
MF-4	0.6514	0.0018	0.1303	0.1051
MF-5	0.6437	0.002	0.1906	0.0208
MF-6	0.7292	0.0002	0.1929	0.0103
MF-7	0.7539	0.0002	0.0735	0.3016
MF-8	0.601	0.0018	0.2117	0.0193
MF-9	0.4453	0.0167	0.1629	0.0244
MF-10	0.1874	0.0667	0.4846	0.0476

The correlations were computed over the upper limits of the one-sided confidence intervals defining the tests. These upper limit values were organized as triangular matrices (upper limit $x_{\mathit{ij}}$ when testing list i vs. list j with one test, $y_{\mathit{ij}}$ for the other test) for the kidney transplantation rejection and cancer datasets. Its significance was stablished by means of the Mantel’s test