Table 6 Validation of annotations derived from minus-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+ | MP 3 - | GO | p-value | Valid? |
0 | Esr1 | absent mature ovarian follicles | postnatal growth retardation | abnormal female reproductive system morphology | ovarian follicle development | 1.10E-31 | yes |
0 | Tex12 | absent mature ovarian follicles | postnatal growth retardation | abnormal female reproductive system morphology | ovarian follicle development | 1.10E-31 | no |
0 | Zglp1 | absent mature ovarian follicles | postnatal growth retardation | abnormal female reproductive system morphology | ovarian follicle development | 1.10E-31 | no |
0 | Syce3 | absent mature ovarian follicles | postnatal growth retardation | abnormal female reproductive system morphology | ovarian follicle development | 1.10E-31 | no |
0 | Gja1 | absent mature ovarian follicles | postnatal growth retardation | abnormal female reproductive system morphology | ovarian follicle development | 1.10E-31 | yes |
1 | Stra8 | absent mature ovarian follicles | postnatal growth retardation | decreased compact bone thickness | ovarian follicle development | 1.15E-31 | yes |
8 | Idua | abnormal lysosome morphology | decreased embryo size | abnormal neuron morphology | lysosome organization | 1.91E-29 | yes |
8 | Sort1 | abnormal lysosome morphology | decreased embryo size | abnormal neuron morphology | lysosome organization | 1.91E-29 | yes |
12 | Zbtb20 | abnormal hippocampus development | complete neonatal lethality | abnormal forebrain development | hippocampus development | 5.56E-26 | yes |
15 | Runx1 | abnormal embryonic hematopoiesis | complete embryonic lethality during organogenesis | anemia | spongiotrophoblast layer development | 2.53E-22 | no |
15 | Pdgfrb | abnormal embryonic hematopoiesis | complete embryonic lethality during organogenesis | anemia | spongiotrophoblast layer development | 2.53E-22 | no |
119 | Jak2 | polychromatophilia | partial postnatal lethality | increased lactate dehydrogenase level | erythrocyte differentiation | 1.15E-11 | no |
120 | Gjb2 | abnormal mesenchyme morphology | embryonic growth retardation | internal hemorrhage | neural tube closure | 1.82E-11 | no |
129 | T | abnormal limb bud morphology | complete perinatal lethality | abnormal digit morphology | anterior/posterior pattern specification | 2.93E-11 | yes |
140 | Stk4 | decreased spleen white pulp amount | postnatal growth retardation | arrested B cell differentiation | lymph node development | 3.39E-11 | no |
173 | Mapk7 | abnormal head mesenchyme morphology | abnormal blood vessel morphology | abnormal heart tube morphology | neural tube closure | 6.48E-11 | no |
188 | Rtel1 | enlarged allantois | no abnormal phenotype detected | small otic vesicle | gastrulation | 1.67E-10 | no |
212 | Smad4 | abnormal proximal-distal axis patterning | embryonic growth arrest | failure to gastrulate | proximal/distal pattern formation | 1.94E-10 | no |
219 | Adam10 | failure of vascular branching | embryonic growth retardation | enlarged pericardium | regulation of angiogenesis | 2.53E-10 | no |
228 | Rapgef2 | abnormal embryonic hematopoiesis | complete embryonic lethality during organogenesis | abnormal liver morphology | spongiotrophoblast layer development | 3.70E-10 | no |