Table 3 Validation of annotations derived from minus-rules
From: Methodology for the inference of gene function from phenotype data
Rule number | Gene | Phenotype Terms included in rule | Implied GO term | Â | Â | |
|---|---|---|---|---|---|---|
| Â | Â | MP 1+ | MP 2- | GO | p-value | Valid? |
0 | Fn1 | abnormal vitelline vascular remodeling | complete embryonic lethality during organogenesis | angiogenesis | 2.86E-41 | yes |
1 | Gja1 | absent mature ovarian follicles | postnatal growth retardation | ovarian follicle development | 8.95E-32 | yes |
1 | Stra8 | absent mature ovarian follicles | postnatal growth retardation | ovarian follicle development | 8.95E-32 | yes |
2 | Ppp1cc | globozoospermia | absent acrosome | spermatogenesis | 8.65E-28 | yes |
4 | Tert | thoracic vertebral transformation | cervical vertebral transformation | anterior/posterior pattern specification | 2.45E-26 | yes |
4 | Kat2a | thoracic vertebral transformation | cervical vertebral transformation | anterior/posterior pattern specification | 2.45E-26 | yes |
5 | Krt19 | abnormal sperm flagellum morphology | asthenozoospermia | fertilization | 2.70E-26 | no |
5 | Akap4 | abnormal sperm flagellum morphology | asthenozoospermia | fertilization | 2.70E-26 | no |
6 | Emx2 | abnormal incus morphology | abnormal temporal bone morphology | middle ear morphogenesis | 1.45E-25 | yes |
7 | Lmx1a | head tossing | circling | auditory receptor cell stereocilium organization | 1.02E-24 | no |
8 | Bmp7 | palatal shelves fail to meet at midline | cleft secondary palate | thyroid gland development | 1.37E-23 | no |
214 | Sctr | decreased urine sodium level | decreased body weight | negative regulation of blood pressure | 3.25E-11 | no |
217 | Fbn1 | abnormal intercostal muscle morphology | respiratory failure | somitogenesis | 5.27E-11 | no |
218 | Krt19 | short sperm flagellum | asthenozoospermia | cilium morphogenesis | 5.46E-11 | yes |
220 | Rab38 | abnormal pulmonary acinus morphology | respiratory distress | lung development | 5.84E-11 | no |
224 | Ube2b | abnormal double-strand DNA break repair | small testis | synapsis | 1.33E-10 | yes |
227 | Adam10 | failure of vascular branching | embryonic growth retardation | regulation of angiogenesis | 2.49E-10 | no |
229 | Casr | decreased circulating calcium level | postnatal growth retardation | calcium ion transport | 4.98E-10 | no |
230 | Hes7 | abnormal sacral vertebrae morphology | complete neonatal lethality | embryonic skeletal system development | 5.26E-10 | yes |
231 | Bhlhe22 | abnormal corticospinal tract morphology | complete neonatal lethality | adult walking behavior | 5.26E-10 | no |