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Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs)

Overview of attention for article published in BMC Genomics, June 2015
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  • Above-average Attention Score compared to outputs of the same age (62nd percentile)
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Title
Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs)
Published in
BMC Genomics, June 2015
DOI 10.1186/1471-2164-16-s8-s8
Pubmed ID
Authors

Samuel K Handelman, Michal Seweryn, Ryan M Smith, Katherine Hartmann, Danxin Wang, Maciej Pietrzak, Andrew D Johnson, Andrzej Kloczkowski, Wolfgang Sadee

Abstract

Over the past 50,000 years, shifts in human-environmental or human-human interactions shaped genetic differences within and among human populations, including variants under positive selection. Shaped by environmental factors, such variants influence the genetics of modern health, disease, and treatment outcome. Because evolutionary processes tend to act on gene regulation, we test whether regulatory variants are under positive selection. We introduce a new approach to enhance detection of genetic markers undergoing positive selection, using conditional entropy to capture recent local selection signals. Results We use conditional logistic regression to compare our Adjusted Haplotype Conditional Entropy (H|H) measure of positive selection to existing positive selection measures. H|H and existing measures were applied to published regulatory variants acting in cis (cis-eQTLs), with conditional logistic regression testing whether regulatory variants undergo stronger positive selection than the surrounding gene. Our new method, H|H, provides a consistently more robust signal associated with cis-eQTLs compared to existing methods. We interpret this to indicate that some cis-eQTLs are under positive selection compared to their surrounding genes. Conditional entropy indicative of a selective sweep is an especially strong predictor of eQTLs for genes in several biological processes of medical interest. Where conditional entropy is a weak or negative predictor of eQTLs, such as innate immune genes, this would be consistent with balancing selection acting on such eQTLs over long time periods. Different measures of selection may be needed for variant prioritization under other modes of evolutionary selection.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 11 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 9%
Unknown 10 91%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 3 27%
Student > Master 2 18%
Student > Doctoral Student 1 9%
Researcher 1 9%
Unknown 4 36%
Readers by discipline Count As %
Agricultural and Biological Sciences 4 36%
Computer Science 2 18%
Biochemistry, Genetics and Molecular Biology 1 9%
Unknown 4 36%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 31 March 2016.
All research outputs
#3,011,316
of 7,471,181 outputs
Outputs from BMC Genomics
#2,317
of 5,465 outputs
Outputs of similar age
#81,238
of 225,511 outputs
Outputs of similar age from BMC Genomics
#124
of 235 outputs
Altmetric has tracked 7,471,181 research outputs across all sources so far. This one has received more attention than most of these and is in the 59th percentile.
So far Altmetric has tracked 5,465 research outputs from this source. They receive a mean Attention Score of 4.1. This one has gotten more attention than average, scoring higher than 55% 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 225,511 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 62% of its contemporaries.
We're also able to compare this research output to 235 others from the same source and published within six weeks on either side of this one. This one is in the 43rd percentile – i.e., 43% of its contemporaries scored the same or lower than it.