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 5 Validation of annotations derived from plus-minus-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+	MP 3 -	GO	p-value	Valid?
0	M1ap	globozoospermia	male infertility	absent acrosome	spermatogenesis	4.21E-39	yes
0	Ing2	globozoospermia	male infertility	absent acrosome	spermatogenesis	4.21E-39	yes
1	Cdk16	abnormal sperm flagellum morphology	male infertility	teratozoospermia	cilium morphogenesis	1.71E-28	yes
8	Adipor2	abnormal glucose homeostasis	decreased circulating insulin level	increased insulin sensitivity	positive regulation of insulin secretion	1.49E-24	yes
10	Steap3	polychromatophilia	decreased hemoglobin content	anisocytosis	skeletal system morphogenesis	4.46E-24	no
13	Ptges3	abnormal production of surfactant	atelectasis	cyanosis	lung alveolus development	8.94E-24	yes
19	Mbl1	increased IgG2a level	increased IgG1 level	abnormal T cell physiology	negative regulation of B cell proliferation	5.82E-23	no
47	Kat2a	decreased body size	exencephaly	domed cranium	neural tube closure	3.40E-20	yes
77	Siglec1	decreased tumor necrosis factor secretion	decreased interleukin-6 secretion	abnormal macrophage physiology	cellular response to lipopolysaccharide	2.95E-19	yes
96	Chga	dilated heart left ventricle	heart left ventricle hypertrophy	absent caveolae	heart morphogenesis	1.56E-18	no
118	Mark3	improved glucose tolerance	decreased circulating insulin level	abnormal glucose homeostasis	response to insulin	3.83E-18	no
124	Gpr64	kinked sperm flagellum	teratozoospermia	hairpin sperm flagellum	fertilization	5.57E-18	no
139	Pick1	abnormal acrosome morphology	asthenozoospermia	absent acrosome	spermatogenesis	8.55E-18	yes
153	Col2a1	abnormal long bone metaphysis morphology	abnormal long bone epiphyseal plate proliferative zone	protruding tongue	bone morphogenesis	1.35E-17	yes
167	Odf1	male infertility	impaired acrosome reaction	impaired fertilization	acrosome reaction	1.91E-17	yes
177	Cftr	absent estrous cycle	small ovary	increased follicle stimulating hormone level	spermatogenesis	2.26E-17	no
262	Zfpm1	abnormal common myeloid progenitor cell morphology	extramedullary hematopoiesis	decreased B cell number	T cell differentiation	1.81E-16	no
309	Gpx4	abnormal sperm principal piece morphology	male infertility	abnormal sperm axoneme morphology	spermatid development	5.38E-16	yes
331	Pank1	increased body weight	hepatic steatosis	abnormal abdominal fat pad morphology	lipid metabolic process	7.25E-16	yes
391	Cd36	increased circulating triglyceride level	abnormal glucose homeostasis	insulin resistance	glycogen metabolic process	2.72E-15	no

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