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Table 1 Selection of proposed rules

From: Methodology for the inference of gene function from phenotype data

  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
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