Table 1.

Selection of proposed rules

							Assessment
Rule type	Rule number	Phenotype terms included or excluded in rule			Implied GO term	p-value	O = obvious
Plus-rule		MP 1 +	MP 2 +		GO		S = subtle
Plus-rule	0	impaired ovarian folliculogenesis	absent mature ovarian follicles		ovarian follicle development	1.47E-36	O
Plus-rule	5	absent Peyer's patches	abnormal spleen morphology		lymph node development	6.82E-30	S
Plus-rule	21	abnormal direction of heart looping	situs inversus		determination of left/right symmetry	1.53E-23	O
Minus-rule		MP 1 +	MP 2 -		GO
Minus-rule	5	abnormal sperm flagellum morphology	asthenozoospermia		fertilization	2.70E-26	S
Minus-rule	6	abnormal incus morphology	abnormal temporal bone morphology		middle ear morphogenesis	1.45E-25	O
Minus-rule	227	failure of vascular branching	embryonic growth retardation		regulation of angiogenesis	2.49E-10	S
Plus-Plus-rule		MP 1 +	MP 2 +	MP 3 +	GO
Plus-Plus-rule	109	increased kidney apoptosis	dilated renal tubules	increased kidney cell proliferation	negative regulation of apoptotic process	1.83E-20	O
Plus-Plus-rule	1188	enlarged liver	hepatic necrosis	increased glycogen level	glycogen metabolic process	1.95E-14	S
Plus Minus-rule		MP 1 +	MP 2 +	MP 3 -	GO
Plus Minus-rule	0	globozoospermia	male infertility	absent acrosome	spermatogenesis	4.21E-39	O
Plus Minus-rule	309	abnormal sperm principal piece morphology	male infertility	abnormal sperm axoneme morphology	spermatid development	5.38E-16	O
Minus-Minus-rule		MP 1 +	MP 2 -	MP 3 -	GO
Minus-Minus-rule	0	absent mature ovarian follicles	postnatal growth retardation	abnormal female reproductive system morphology	ovarian follicle development	1.10E-31	O
Minus-Minus-rule	8	abnormal lysosome morphology	decreased embryo size	abnormal neuron morphology	lysosome organization	1.91E-29	O