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Background  Our understanding of the genetic basis of learning and memory remains shrouded in mystery. To explore the genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP) with high mapping resolution.    Results  A total of 27 behavioral quantitative trait loci were mapped with a false discovery rate of 5%. By integrating fear phenotypes, transcript profiling data from hippocampus and striatum and also genotype information, two gene co-expression networks correlated with context-dependent immobility were identified. We prioritized the key markers and genes in these pathways using intramodular connectivity measures and structural equation modeling. Highly connected genes in the context fear modules included  Psmd6 ,  Ube2a  and  Usp33 , suggesting an important role for ubiquitination in learning and memory. In addition, we surveyed the architecture of brain transcript regulation and demonstrated preservation of gene co-expression modules in hippocampus and striatum, while also highlighting important differences.  Rps15a, Kif3a, Stard7, 6330503K22RIK , and  Plvap  were among the individual genes whose transcript abundance were strongly associated with fear phenotypes.    Conclusion  Application of our multi-faceted mapping strategy permits an increasingly detailed characterization of the genetic networks underlying behavior.

Gene networks associated with conditional fear in mice identified using a systems genetics approach