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Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity

Overview of attention for article published in Genome Biology (Online Edition), July 2016
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (96th percentile)

Mentioned by

news
4 news outlets
blogs
1 blog
twitter
54 tweeters

Citations

dimensions_citation
31 Dimensions

Readers on

mendeley
195 Mendeley
citeulike
2 CiteULike
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Title
Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity
Published in
Genome Biology (Online Edition), July 2016
DOI 10.1186/s13059-016-1003-3
Pubmed ID
Authors

Vera Pancaldi, Enrique Carrillo-de-Santa-Pau, Biola Maria Javierre, David Juan, Peter Fraser, Mikhail Spivakov, Alfonso Valencia, Daniel Rico

Abstract

Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a new approach, using chromatin assortativity, to integrate the epigenomic landscape of a specific cell type with its chromatin interaction network and thus investigate which proteins or chromatin marks mediate genomic contacts. We use high-resolution promoter capture Hi-C and Hi-Cap data as well as ChIA-PET data from mouse embryonic stem cells to investigate promoter-centered chromatin interaction networks and calculate the presence of specific epigenomic features in the chromatin fragments constituting the nodes of the network. We estimate the association of these features with the topology of four chromatin interaction networks and identify features localized in connected areas of the network. Polycomb group proteins and associated histone marks are the features with the highest chromatin assortativity in promoter-centered networks. We then ask which features distinguish contacts amongst promoters from contacts between promoters and other genomic elements. We observe higher chromatin assortativity of the actively elongating form of RNA polymerase 2 (RNAPII) compared with inactive forms only in interactions between promoters and other elements. Contacts among promoters and between promoters and other elements have different characteristic epigenomic features. We identify a possible role for the elongating form of RNAPII in mediating interactions among promoters, enhancers, and transcribed gene bodies. Our approach facilitates the study of multiple genome-wide epigenomic profiles, considering network topology and allowing the comparison of chromatin interaction networks.

Twitter Demographics

The data shown below were collected from the profiles of 54 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 195 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 3 2%
United States 2 1%
Denmark 2 1%
Italy 2 1%
Spain 2 1%
Netherlands 1 <1%
Turkey 1 <1%
Russia 1 <1%
Lithuania 1 <1%
Other 2 1%
Unknown 178 91%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 64 33%
Researcher 46 24%
Student > Master 18 9%
Student > Bachelor 17 9%
Professor 13 7%
Other 23 12%
Unknown 14 7%
Readers by discipline Count As %
Agricultural and Biological Sciences 73 37%
Biochemistry, Genetics and Molecular Biology 70 36%
Computer Science 22 11%
Physics and Astronomy 6 3%
Medicine and Dentistry 3 2%
Other 5 3%
Unknown 16 8%

Attention Score in Context

This research output has an Altmetric Attention Score of 71. 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 16 November 2021.
All research outputs
#414,112
of 19,770,032 outputs
Outputs from Genome Biology (Online Edition)
#309
of 3,866 outputs
Outputs of similar age
#9,452
of 271,240 outputs
Outputs of similar age from Genome Biology (Online Edition)
#1
of 1 outputs
Altmetric has tracked 19,770,032 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 97th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,866 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 26.9. This one has done particularly well, scoring higher than 92% 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 271,240 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 96% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them