A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments

Table 2 Results for the 999-gene set

	LOI.fdr(q)	PCC.fdr(q)	Number of Edges Identified	Published Edges	Same GO BP Annotation	% Published	% Same GO-BP
A	GO-simple	NoRestriction	730688	641	60691	0.09	8.3
B	NoRestriction	PCC(0.1)	18350	62	2280	0.34	12.4
	NoRestriction	PCC(0.05)	5987	27	813	0.45	13.6
	NoRestriction	PCC(0.005)	931	4	144	0.43	15.5
C	LOI(0.1)	NoRestriction	96742	226	13220	0.23	13.7
	LOI(0.05)	NoRestriction	95222	224	12963	0.24	13.6
	LOI(0.005)	NoRestriction	90875	202	12326	0.22	13.6
D	LOI(0.1)	PCC(0.1)	2196	25	468	1.14	21.3
	LOI(0.05)	PCC(0.1)	2145	25	453	1.17	21.1
	LOI(0.005)	PCC(0.1)	2053	23	434	1.12	21.1
E	LOI(0.1)	PCC(0.05)	781	15	177	1.92	22.7
	LOI(0.05)	PCC(0.05)	757	15	174	1.98	23.0
	LOI(0.005)	PCC(0.05)	733	15	170	2.05	23.2
F	LOI(0.1)	PCC(0.005)	163	2	48	1.23	29.4
	LOI(0.05)	PCC(0.005)	159	2	48	1.26	30.2
	LOI(0.005)	PCC(0.005)	153	2	48	1.31	31.4

A: GO-simple: a pair of genes is considered potentially interacting if one of their GO annotation pairs has been reported.
B: set of interactions obtained by applying only PCC thresholds;
C: set of interactions obtained by applying only LOI thresholds;
D: common set of interactions obtained by applying different LOI thresholds and a fixed PCC.fdr(0.1);
E: common set of interactions obtained by applying different LOI thresholds and a fixed PCC.fdr(0.05);
F: common set of interactions obtained by applying different LOI thresholds and a fixed PCC.fdr(0.005).

ISSN: 1471-2105