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The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits

Overview of attention for article published in BMC Genomics, August 2016
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Title
The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits
Published in
BMC Genomics, August 2016
DOI 10.1186/s12864-016-2922-9
Pubmed ID
Authors

Seungeun Yeo, Colin A. Hodgkinson, Zhifeng Zhou, Jeesun Jung, Ming Leung, Qiaoping Yuan, David Goldman

Abstract

Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL's for complex phenotypes. We used transcriptome-wide differential allele expression (DAE) to detect cis-eQTLs in forebrain and kidney from reciprocal crosses between three mouse inbred strains, 129S1/SvlmJ, DBA/2J, and CAST/EiJ and C57BL/6 J. Two of these crosses were previously characterized for cis-eQTLs and QTLs for various complex phenotypes by genetic analysis of recombinant inbred (RI) strains. 5.4 %, 1.9 % and 1.5 % of genes assayed in forebrain of B6/129SF1, B6/DBAF1, and B6/CASTF1 mice, respectively, showed differential allelic expression, indicative of cis-acting alleles at these genes. Moreover, the majority of DAE QTLs were observed to be tissue-specific with only a small fraction showing cis-effects in both tissues. Comparing DAE QTLs in F1 mice to cis-eQTLs previously mapped in RI strains we observed that many of the cis-eQTLs were not confirmed by DAE. Additionally several novel DAE-QTLs not identified as cis-eQTLs were identified suggesting that there are differences in sensitivity and specificity for QTL detection between the two methodologies. Strain specific DAE QTLs in B6/DBAF1 mice were located in excess at candidate genes for alcohol use disorders, seizures, and angiogenesis previously implicated by genetic linkage in C57BL/6J × DBA/2JF2 mice or BXD RI strains. Via a survey for differential allele expression in F1 mice, a substantial proportion of genes were found to have alleles altering expression in cis-acting fashion. Comparing forebrain and kidney, many or most of these alleles were tissue-specific in action. The identification of strain specific DAE QTLs, can assist in assessment of candidate genes located within the large intervals associated with trait QTLs.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 16 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 16 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 4 25%
Student > Master 4 25%
Researcher 2 13%
Other 1 6%
Lecturer > Senior Lecturer 1 6%
Other 1 6%
Unknown 3 19%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 4 25%
Medicine and Dentistry 3 19%
Agricultural and Biological Sciences 3 19%
Pharmacology, Toxicology and Pharmaceutical Science 1 6%
Psychology 1 6%
Other 1 6%
Unknown 3 19%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 17 August 2016.
All research outputs
#4,377,372
of 8,229,276 outputs
Outputs from BMC Genomics
#3,718
of 5,817 outputs
Outputs of similar age
#128,962
of 233,219 outputs
Outputs of similar age from BMC Genomics
#169
of 264 outputs
Altmetric has tracked 8,229,276 research outputs across all sources so far. This one is in the 27th percentile – i.e., 27% of other outputs scored the same or lower than it.
So far Altmetric has tracked 5,817 research outputs from this source. They receive a mean Attention Score of 4.2. This one is in the 26th percentile – i.e., 26% of its peers scored the same or lower than it.
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