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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<jats:italic>Psmd6<\/jats:italic>,<jats:italic>Ube2a<\/jats:italic>and<jats:italic>Usp33<\/jats:italic>, 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.<jats:italic>Rps15a, Kif3a, Stard7, 6330503K22RIK<\/jats:italic>, and<jats:italic>Plvap<\/jats:italic>were among the individual genes whose transcript abundance were strongly associated with fear phenotypes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Application of our multi-faceted mapping strategy permits an increasingly detailed characterization of the genetic networks underlying behavior.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1752-0509-5-43","type":"journal-article","created":{"date-parts":[[2011,3,17]],"date-time":"2011-03-17T07:18:58Z","timestamp":1300346338000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":74,"title":["Gene networks associated with conditional fear in mice identified using a systems genetics approach"],"prefix":"10.1186","volume":"5","author":[{"given":"Christopher C","family":"Park","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Greg D","family":"Gale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone","family":"de Jong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anatole","family":"Ghazalpour","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian J","family":"Bennett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles R","family":"Farber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Langfelder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andy","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arshad H","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleazar","family":"Eskin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steve","family":"Horvath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aldons J","family":"Lusis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roel A","family":"Ophoff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Desmond J","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,3,16]]},"reference":[{"key":"633_CR1","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1002\/hipo.20598","volume":"20","author":"GL Barrett","year":"2010","unstructured":"Barrett GL, Reid CA, Tsafoulis C, Zhu W, Williams DA, Paolini AG, Trieu J, Murphy M: Enhanced spatial memory and hippocampal long-term potentiation in p75 neurotrophin receptor knockout mice. 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