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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