Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/7563
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dc.contributor.authorNoyes, Harry Aen
dc.contributor.authorAgaba, Morrisen
dc.contributor.authorAnderson, Susanen
dc.contributor.authorArchibald, Alan Len
dc.contributor.authorBrass, Andyen
dc.contributor.authorGibson, Johnen
dc.contributor.authorHall, Laurenceen
dc.contributor.authorHulme, Helenen
dc.contributor.authorOh, Sung Jongen
dc.contributor.authorKemp, Stephenen
dc.date.accessioned2011-05-26T15:43:00Z-
dc.date.issued2010-
dc.identifier.citationBMC Genomics, 11(361), p. 1-11en
dc.identifier.issn1471-2164en
dc.identifier.urihttps://hdl.handle.net/1959.11/7563-
dc.description.abstractBackground: Differences in gene expression may be caused by nearby DNA polymorphisms (cis regulation) or by interactions of gene control regions with polymorphic transcription factors (trans regulation). Trans acting loci are much harder to detect than cis acting loci and their effects are much more sensitive to genetic background. Results: To quantify cis and trans regulation we correlated haplotype data with gene expression in two inbred mouse strains and two derived congenic lines. Upstream haplotype differences between the parental strains suggested that 30-43% of differentially expressed genes were differentially expressed because of cis haplotype differences. These cis regulated genes displayed consistent and relatively tissue-independent differential expression. We independently estimated from the congenic mice that 71-85% of genes were trans regulated. Cis regulated genes were associated with low p values (p < 0.005) for differential expression, whereas trans regulated genes were associated with values 0.005 < p < 0.05. The genes differentially expressed between congenics and controls were not a subset of those that were differentially expressed between the founder lines, showing that these were dependent on genetic background. For example, the cholesterol synthesis pathway was strongly differentially expressed in the congenic mice by indirect trans regulation but this was not observable in the parental mice. Conclusions: The evidence that most gene regulation is trans and strongly influenced by genetic background, suggests that pathways that are modified by an allelic variant, may only exhibit differential expression in the specific genetic backgrounds in which they were identified. This has significant implications for the interpretation of any QTL mapping study.en
dc.languageenen
dc.publisherBioMed Central Ltden
dc.relation.ispartofBMC Genomicsen
dc.titleGenotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic backgrounden
dc.typeJournal Articleen
dc.identifier.doi10.1186/1471-2164-11-361en
dc.subject.keywordsQuantitative Genetics (incl Disease and Trait Mapping Genetics)en
dc.subject.keywordsGenetic Immunologyen
dc.subject.keywordsGene Expression (incl Microarray and other genome-wide approaches)en
local.contributor.firstnameHarry Aen
local.contributor.firstnameMorrisen
local.contributor.firstnameSusanen
local.contributor.firstnameAlan Len
local.contributor.firstnameAndyen
local.contributor.firstnameJohnen
local.contributor.firstnameLaurenceen
local.contributor.firstnameHelenen
local.contributor.firstnameSung Jongen
local.contributor.firstnameStephenen
local.subject.for2008060406 Genetic Immunologyen
local.subject.for2008060405 Gene Expression (incl Microarray and other genome-wide approaches)en
local.subject.for2008060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics)en
local.subject.seo2008920109 Infectious Diseasesen
local.subject.seo2008830302 Dairy Cattleen
local.subject.seo2008830301 Beef Cattleen
local.profile.schoolEnvironmental and Rural Scienceen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.emailjgibson5@une.edu.auen
local.output.categoryC1en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.identifier.epublicationsrecordune-20100630-15003en
local.publisher.placeUnited Kingdomen
local.format.startpage1en
local.format.endpage11en
local.peerreviewedYesen
local.identifier.volume11en
local.identifier.issue361en
local.contributor.lastnameNoyesen
local.contributor.lastnameAgabaen
local.contributor.lastnameAndersonen
local.contributor.lastnameArchibalden
local.contributor.lastnameBrassen
local.contributor.lastnameGibsonen
local.contributor.lastnameHallen
local.contributor.lastnameHulmeen
local.contributor.lastnameOhen
local.contributor.lastnameKempen
dc.identifier.staffune-id:jgibson5en
local.profile.roleauthoren
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local.identifier.unepublicationidune:7732en
dc.identifier.academiclevelAcademicen
local.title.maintitleGenotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic backgrounden
local.output.categorydescriptionC1 Refereed Article in a Scholarly Journalen
local.search.authorNoyes, Harry Aen
local.search.authorAgaba, Morrisen
local.search.authorAnderson, Susanen
local.search.authorArchibald, Alan Len
local.search.authorBrass, Andyen
local.search.authorGibson, Johnen
local.search.authorHall, Laurenceen
local.search.authorHulme, Helenen
local.search.authorOh, Sung Jongen
local.search.authorKemp, Stephenen
local.uneassociationUnknownen
local.identifier.wosid000279868500002en
local.year.published2010en
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