Table 4.

Validation of annotations derived from plus-plus-rules

Rule number	Gene	Phenotype terms included in rule			Implied GO term
		MP 1 +	MP 2 +	MP 3 +	GO	p-value	Valid?
0	Foxl2	absent mature ovarian follicles	impaired ovarian folliculogenesis	decreased uterus weight	ovarian follicle development	4.15E-37	yes
0	Fads2	absent mature ovarian follicles	impaired ovarian folliculogenesis	decreased uterus weight	ovarian follicle development	4.15E-37	yes
0	Kiss1	absent mature ovarian follicles	impaired ovarian folliculogenesis	decreased uterus weight	ovarian follicle development	4.15E-37	yes
6	Mapk6	decreased lung weight	small lung	pulmonary hypoplasia	lung development	9.35E-31	yes
17	Kiss1r	decreased uterus weight	decreased ovary weight	decreased uterus weight	ovarian follicle development	1.11E-27	yes
17	Esr1	decreased uterus weight	decreased ovary weight	decreased uterus weight	ovarian follicle development	1.11E-27	no
22	Ndrg2	sacral vertebral transformation	lumbar vertebral transformation	sacral vertebral transformation	anterior/posterior pattern specification	3.92E-27	yes
27	Gmcl1	abnormal acrosome morphology	abnormal sperm flagellum morphology	arrest of spermiogenesis	acrosome assembly	2.48E-24	yes
28	Gdf6	abnormal middle ear ossicle morphology	abnormal middle ear morphology	abnormal stapes morphology	middle ear morphogenesis	7.47E-24	yes
48	Gucy2d	abnormal olfactory system physiology	abnormal odor adaptation	abnormal olfactory system physiology	sensory perception of smell	4.15E-22	yes
83	Tnfrsf11b	abnormal middle ear ossicle morphology	abnormal middle ear morphology	abnormal incus morphology	middle ear morphogenesis	6.33E-21	yes
109	Bag6	increased kidney apoptosis	dilated renal tubules	increased kidney cell proliferation	negative regulation of apoptotic process	1.83E-20	yes
150	Mns1	kinked sperm flagellum	oligozoospermia	hairpin sperm flagellum	spermatid development	4.96E-20	yes
719	Pou1f1	abnormal cerebellar foliation	tremors	abnormal cerebellar granule layer	neuron migration	5.59E-16	yes
763	Prdm9	abnormal double-strand DNA break repair	abnormal ovary morphology	decreased oocyte number	double-strand break repair	8.50E-16	yes
812	Camk4	increased bone mineral density	decreased osteoclast cell number	failure of tooth eruption	ossification	1.27E-15	no
814	Ddr2	decreased circulating testosterone level	absent corpus luteum	Leydig cell hypoplasia	spermatogenesis	1.31E-15	yes
816	Bmper	curly tail	short tail	abnormal rib-vertebral column attachment	skeletal system morphogenesis	1.33E-15	yes
1373	Sec61a1	enlarged liver	increased circulating triglyceride level	increased glycogen level	glycogen metabolic process	6.61E-14	no
1709	Ctsc	decreased circulating interleukin-6 level	decreased susceptibility to endotoxin shock	decreased circulating interleukin-6 level	response to lipopolysaccharide	4.38E-13	no