Table 1.
Parameters that may be specified in linkage explorer
| Parameter | Notes |
|---|---|
| Single or double locus analysis | |
| Gene | Will return all phenotypes linked to mutations of the specified gene(s), along with associated P values |
| Phenotypic screen | When specified, will return mutations linked to the phenotype(s) tested in the specified screen(s) |
| Pedigree or mouse/mice | Will return all genotype–phenotype associations identified in the specified pedigree or the pedigree of which the specified mouse (mice) is (are) part, along with associated P values. Named according to eartag of G1 male founder |
| Total mouse numbers | Will restrict linkage analysis to pedigrees containing a specified range or number of G3 mice |
| Allele name (phenotype) | Will return all mutations linked to the specified phenotype, along with associated P values |
| Mutation type | Will restrict linkage analysis to the specified mutation type(s): nonsense, missense, makesense, critical splicing, noncritical splicing |
| Predicted effect of mutation | Will restrict linkage analysis to the specified mutation effect: probably null (corresponds to nonsense and critical splicing mutations); or probably damaging, possibly damaging, probably benign as determined by PolyPhen-2 |
| P value cutoff | Will display genotype–phenotype associations with P (non-linkage) ≤ the value specified; Bonferroni correction may be applied |
| Minimum number of HET or VAR mice screened | Will return genotype–phenotype associations tested with at least the specified number of HET (heterozygous) or VAR (homozygous mutant) mice |
| ‘Raw + Norm’ switch | When applied, enforces P value cutoff for both raw and normalized datasets. Otherwise, enforces P value cutoff for either raw or normalized datasets |
| Direction of phenovariance | Quantitative phenotype scores either higher than or lower than wild type scores |
| Number of linkage peaks | Will return genotype–phenotype associations for which a specified number of linkage peaks exceed the specified −log10[P(non-linkage)] in the Manhattan plot for recessive, dominant or additive models of linkage. This parameter is useful for filtering results to show only strong, unambiguous genotype–phenotype associations |
| Date of data collection |