From parameter to phenotype
The statistical method selected is dependent on the experimental implementation and the variable characteristics (e.g. continuous or categorical). For continuous data, it has been shown that gender, weight, and environmental effects (batch) are a significant source of variation (Karp et al. 2012; Karp et al. 2014). In the PhenStat Linear Mixed Model (MM) framework, batch is treated as a random effect. Details of the implementation, including decision tree and models descriptions, are available in the PhenStat package user’s guide.
For viability and fertility data, the center conducting the experiment use a statistical method appropriate for the breeding scheme used (exact details are available on the IMPC data portal) and supply the analysis results to the IMPC.
Following statistical assessment, if the mutant genotype effect represents a significant phenotypic change from the control group, then the IMPC pipeline will attempt to associate a Mammalian Phenotype (MP) term to the data. The particular MP term(s) defined for a parameter are maintained in IMPReSS. Frequently, the term indicates an increase or decrease of the parameter measured, but in other cases abnormal is used.