Linked Life Data

20145673

Source:http://linkedlifedata.com/resource/pubmed/id/20145673

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2010-8-18
pubmed:abstractText
Genetic analysis of transcriptional profiling is a promising approach for identifying biological pathways and dissecting the genetics of complex traits. Here, we report on expression quantitative trait loci (eQTL) that were estimated from the quantitative real-time RT-PCR data of 276 F(2) animals and compared with eQTL identified using 74 microarrays. In total, 13 genes were selected that showed trait-dependent expression in microarray experiments and exhibited 21 eQTL. Real-time RT-PCR and microarray data revealed seven cis eQTL in total, of which one was only detected by real-time RT-PCR, one was only detected by microarray analysis, three were consistently found in overlapping intervals and two were in neighbouring intervals on the same chromosome; whereas no trans eQTL was confirmed. We demonstrate that cis regulation is a stable characteristic of individual transcripts. Consequently, a global microarray eQTL analysis of a limited number of samples can be used for exploring functional and regulatory gene networks and scanning for cis eQTL, whereas the subsequent analysis of a subset of likely cis-regulated genes by real-time RT-PCR in a larger number of samples is relevant to narrow down a QTL region by targeting these positional candidate genes. In fact, when modelling SNPs of six genes as fixed effects in the eQTL analysis, eQTL peaks were shifted downwards, experimentally confirming the impact of the respective polymorphic genes, although these SNPs were not located in the regulatory sequence and these shifts occur as a result of linkage disequilibrium in the F(2) population.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
1365-2540
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
105
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
309-17
pubmed:meshHeading
pubmed:year
2010
pubmed:articleTitle
Expression quantitative trait loci analysis of genes in porcine muscle by quantitative real-time RT-PCR compared to microarray data.
pubmed:affiliation
Research Group Functional Genomics, Research Institute for the Biology of Farm Animals (FBN), Dummerstorf, Germany.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, Non-U.S. Gov't