Systems Genetics Analysis of Iron and Its Regulation in Brain and Periphery

Methods Mol Biol. 2017;1488:467-480. doi: 10.1007/978-1-4939-6427-7_22.

Abstract

In this contribution, we demonstrate the utility of the systems genetics-systems biology approach to the study of iron regulation while employing a comprehensive database. We describe our work in iron regulation in the brain and periphery under normal iron and iron-restricted dietary conditions in the BXD family of recombinant inbred mouse strains. Using multiple measures, we showed wide variation among the strains in the effect of being fed an iron-restricted diet for 100 days in every measure from brain and from the periphery. All data were entered into GeneNetwork ( www.genenetwork.org ), a database that contains genotypic, phenotypic, and gene expression data (Rosen et al., Methods Mol Biol 401:287-303, 2007). Using this resource, we were able to ask the following four questions concerning possible candidate genes underlying our measures: (1) what is the range of response for each of the measures? (2) Does the pattern of variability show continuous (additive genetic) or discrete (Mendelian) distribution across strains? (3) Are there genetic markers that are associated with the variability in the measures? (4) Are there genes in near the markers that contain associated allelic differences, and whose expression is related to the variability in the measures? Other questions that we could address include: (5) what is the association among the measures between the sexes? (6) What is the association among the measures, e.g., is liver iron status under the diets related to brain iron? (7) What is the relationship between our measures and other phenotypic parameters-i.e., is there an association between our brain iron measures and neurochemical phenotypes extant in the database? And finally, (8) are there gene networks that underlie single or combined measures?

Keywords: Gene network; Genetic correlation; Genetic mapping; Quantitative trait loci analysis; Use case.

MeSH terms

  • Animals
  • Brain / metabolism*
  • Chromosome Mapping
  • Crosses, Genetic
  • Female
  • Gene Expression
  • Gene Regulatory Networks
  • Genetic Association Studies / methods*
  • Iron / metabolism*
  • Male
  • Mice
  • Mice, Inbred Strains
  • Peripheral Nerves / metabolism*
  • Quantitative Trait Loci*
  • Software*

Substances

  • Iron