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Cis and Trans Effects of Human Genomic Variants on Gene Expression

Overview of attention for article published in PLoS Genetics, July 2014
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (92nd percentile)
  • High Attention Score compared to outputs of the same age and source (81st percentile)

Mentioned by

twitter
33 tweeters
q&a
1 Q&A thread

Citations

dimensions_citation
58 Dimensions

Readers on

mendeley
205 Mendeley
citeulike
7 CiteULike
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Title
Cis and Trans Effects of Human Genomic Variants on Gene Expression
Published in
PLoS Genetics, July 2014
DOI 10.1371/journal.pgen.1004461
Pubmed ID
Authors

Julien Bryois, Alfonso Buil, David M. Evans, John P. Kemp, Stephen B. Montgomery, Donald F. Conrad, Karen M. Ho, Susan Ring, Matthew Hurles, Panos Deloukas, George Davey Smith, Emmanouil T. Dermitzakis

Abstract

Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation. In order to detect genetic variations affecting gene expression, we performed association analysis of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with gene expression measured in 869 lymphoblastoid cell lines of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort in cis and in trans. We discovered that 3,534 genes (false discovery rate (FDR) = 5%) are affected by an expression quantitative trait locus (eQTL) in cis and 48 genes are affected in trans. We observed that CNVs are more likely to be eQTLs than SNPs. In addition, we found that variants associated to complex traits and diseases are enriched for trans-eQTLs and that trans-eQTLs are enriched for cis-eQTLs. As a variant affecting both a gene in cis and in trans suggests that the cis gene is functionally linked to the trans gene expression, we looked specifically for trans effects of cis-eQTLs. We discovered that 26 cis-eQTLs are associated to 92 genes in trans with the cis-eQTLs of the transcriptions factors BATF3 and HMX2 affecting the most genes. We then explored if the variation of the level of expression of the cis genes were causally affecting the level of expression of the trans genes and discovered several causal relationships between variation in the level of expression of the cis gene and variation of the level of expression of the trans gene. This analysis shows that a large sample size allows the discovery of secondary effects of human variations on gene expression that can be used to construct short directed gene regulatory networks.

Twitter Demographics

The data shown below were collected from the profiles of 33 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 205 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 7 3%
Spain 2 <1%
Canada 2 <1%
Italy 1 <1%
France 1 <1%
Mexico 1 <1%
Germany 1 <1%
Belgium 1 <1%
Austria 1 <1%
Other 1 <1%
Unknown 187 91%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 69 34%
Researcher 51 25%
Student > Bachelor 19 9%
Student > Master 18 9%
Student > Postgraduate 11 5%
Other 37 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 120 59%
Biochemistry, Genetics and Molecular Biology 35 17%
Computer Science 15 7%
Medicine and Dentistry 14 7%
Unspecified 8 4%
Other 13 6%

Attention Score in Context

This research output has an Altmetric Attention Score of 18. 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 23 May 2016.
All research outputs
#719,891
of 12,236,170 outputs
Outputs from PLoS Genetics
#986
of 6,230 outputs
Outputs of similar age
#14,216
of 197,756 outputs
Outputs of similar age from PLoS Genetics
#32
of 176 outputs
Altmetric has tracked 12,236,170 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 94th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 6,230 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 13.6. This one has done well, scoring higher than 84% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 197,756 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 92% of its contemporaries.
We're also able to compare this research output to 176 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 81% of its contemporaries.