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Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development

Overview of attention for article published in BMC Genomics, February 2017
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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 (89th percentile)
  • High Attention Score compared to outputs of the same age and source (92nd percentile)

Mentioned by

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1 blog
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25 X users
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1 Google+ user

Citations

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55 Dimensions

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148 Mendeley
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Title
Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development
Published in
BMC Genomics, February 2017
DOI 10.1186/s12864-017-3566-0
Pubmed ID
Authors

Steven Xijin Ge

Abstract

Instead of testing predefined hypotheses, the goal of exploratory data analysis (EDA) is to find what data can tell us. Following this strategy, we re-analyzed a large body of genomic data to study the complex gene regulation in mouse pre-implantation development (PD). Starting with a single-cell RNA-seq dataset consisting of 259 mouse embryonic cells derived from zygote to blastocyst stages, we reconstructed the temporal and spatial gene expression pattern during PD. The dynamics of gene expression can be partially explained by the enrichment of transposable elements in gene promoters and the similarity of expression profiles with those of corresponding transposons. Long Terminal Repeats (LTRs) are associated with transient, strong induction of many nearby genes at the 2-4 cell stages, probably by providing binding sites for Obox and other homeobox factors. B1 and B2 SINEs (Short Interspersed Nuclear Elements) are correlated with the upregulation of thousands of nearby genes during zygotic genome activation. Such enhancer-like effects are also found for human Alu and bovine tRNA SINEs. SINEs also seem to be predictive of gene expression in embryonic stem cells (ESCs), raising the possibility that they may also be involved in regulating pluripotency. We also identified many potential transcription factors underlying PD and discussed the evolutionary necessity of transposons in enhancing genetic diversity, especially for species with longer generation time. Together with other recent studies, our results provide further evidence that many transposable elements may play a role in establishing the expression landscape in early embryos. It also demonstrates that exploratory bioinformatics investigation can pinpoint developmental pathways for further study, and serve as a strategy to generate novel insights from big genomic data.

X Demographics

X Demographics

The data shown below were collected from the profiles of 25 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 148 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 <1%
Italy 1 <1%
Sweden 1 <1%
South Africa 1 <1%
China 1 <1%
United States 1 <1%
Unknown 142 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 31 21%
Researcher 21 14%
Student > Master 18 12%
Student > Bachelor 15 10%
Student > Postgraduate 8 5%
Other 23 16%
Unknown 32 22%
Readers by discipline Count As %
Agricultural and Biological Sciences 44 30%
Biochemistry, Genetics and Molecular Biology 43 29%
Computer Science 6 4%
Medicine and Dentistry 5 3%
Immunology and Microbiology 2 1%
Other 9 6%
Unknown 39 26%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 22. 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 18 January 2022.
All research outputs
#1,647,601
of 24,569,575 outputs
Outputs from BMC Genomics
#343
of 11,011 outputs
Outputs of similar age
#32,321
of 315,777 outputs
Outputs of similar age from BMC Genomics
#16
of 210 outputs
Altmetric has tracked 24,569,575 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 11,011 research outputs from this source. They receive a mean Attention Score of 4.8. This one has done particularly well, scoring higher than 96% 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 315,777 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 89% of its contemporaries.
We're also able to compare this research output to 210 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 92% of its contemporaries.