Methodology for the inference of gene function from phenotype data

Ascensao, Joao A; Dolan, Mary E; Hill, David P; Blake, Judith A

doi:10.1186/s12859-014-0405-z

BMC Bioinformatics

Table 2 Validation of annotations derived from plus-rules

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

Rule number	Gene	Phenotype terms included in rule		Implied GO term
		MP ₁+	MP ₂+	GO	p-value	Valid?
0	Foxl2	ovarian follicle development	impaired ovarian folliculogenesis	absent mature ovarian follicles	1.47E-36	yes
1	Mbd4	determination of left/right symmetry	abnormal left-right axis patterning	situs inversus	6.13E-36	yes
2	Ar	spermatogenesis	small testis	decreased testis weight	3.47E-33	yes
2	Ar	spermatogenesis	small testis	decreased testis weight	3.47E-33	yes
2	Ar	spermatogenesis	small testis	decreased testis weight	3.47E-33	yes
2	Hsp90aa1	spermatogenesis	small testis	decreased testis weight	3.47E-33	yes
3	Psip1	anterior/posterior pattern specification	thoracic vertebral transformation	abnormal rib morphology	3.76E-33	yes
4	Fen1	lung development	pulmonary hypoplasia	decreased lung weight	2.48E-30	yes
5	Rag2	lymph node development	absent Peyer's patches	abnormal spleen morphology	6.82E-30	yes
6	Tapt1	anterior/posterior pattern specification	thoracic vertebral transformation	abnormal rib-sternum attachment	3.01E-29	yes
3072	Mir140	decreased body size	decreased length of long bones	collagen fibril organization	2.36E-08	no
3087	Fancm	premature death	abnormal ovary morphology	cell proliferation	4.05E-08	yes
3091	Flnb	abnormal angiogenesis	decreased body weight	angiogenesis	5.29E-08	yes
3096	Slc6a8	abnormal spatial learning	decreased body weight	learning or memory	6.56E-08	yes
3098	Tgfb1	abnormal extraembryonic tissue morphology	decreased body size	gastrulation with mouth forming second	8.17E-08	no
3099	Sirt1	decreased embryo size	ventricular septal defect	neural tube closure	8.29E-08	yes
3100	Kcnq1	deafness	decreased body weight	neuromuscular process controlling balance	1.06E-07	yes
3100	Slc12a7	deafness	decreased body weight	neuromuscular process controlling balance	1.06E-07	no
3101	Sall4	open neural tube	premature death	neural tube closure	1.09E-07	yes
3103	Pkhd1	respiratory failure	postnatal growth retardation	lung development	1.31E-07	no

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