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Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

Overview of attention for article published in Genome Biology (Online Edition), May 2015
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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 (87th percentile)

Mentioned by

twitter
17 tweeters
googleplus
3 Google+ users

Citations

dimensions_citation
84 Dimensions

Readers on

mendeley
195 Mendeley
citeulike
2 CiteULike
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Title
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes
Published in
Genome Biology (Online Edition), May 2015
DOI 10.1186/s13059-015-0668-3
Pubmed ID
Authors

Lijing Yao, Hui Shen, Peter W Laird, Peggy J Farnham, Benjamin P Berman

Abstract

Recent studies indicate that DNA methylation can be used to identify transcriptional enhancers, but no systematic approach has been developed for genome-wide identification and analysis of enhancers based on DNA methylation. We describe ELMER (Enhancer Linking by Methylation/Expression Relationships), an R-based tool that uses DNA methylation to identify enhancers and correlates enhancer state with expression of nearby genes to identify transcriptional targets. Transcription factor motif analysis of enhancers is coupled with expression analysis of transcription factors to infer upstream regulators. Using ELMER, we investigated more than 2,000 tumor samples from The Cancer Genome Atlas. We identified networks regulated by known cancer drivers such as GATA3 and FOXA1 (breast cancer), SOX17 and FOXA2 (endometrial cancer), and NFE2L2, SOX2 and TP63 (squamous cell lung cancer). We also identified novel networks with prognostic associations, including RUNX1 in kidney cancer. We propose ELMER as a powerful new paradigm for understanding the cis-regulatory interface between cancer-associated transcription factors and their functional target genes.

Twitter Demographics

The data shown below were collected from the profiles of 17 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 States 3 2%
United Kingdom 3 2%
China 2 1%
Norway 1 <1%
Netherlands 1 <1%
Germany 1 <1%
Unknown 184 94%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 58 30%
Researcher 41 21%
Student > Master 19 10%
Student > Bachelor 19 10%
Student > Doctoral Student 11 6%
Other 34 17%
Unknown 13 7%
Readers by discipline Count As %
Agricultural and Biological Sciences 72 37%
Biochemistry, Genetics and Molecular Biology 62 32%
Computer Science 15 8%
Medicine and Dentistry 10 5%
Mathematics 5 3%
Other 10 5%
Unknown 21 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 12. 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 19 September 2016.
All research outputs
#1,378,117
of 13,631,079 outputs
Outputs from Genome Biology (Online Edition)
#1,325
of 3,035 outputs
Outputs of similar age
#29,473
of 232,153 outputs
Outputs of similar age from Genome Biology (Online Edition)
#1
of 2 outputs
Altmetric has tracked 13,631,079 research outputs across all sources so far. Compared to these this one has done well and is in the 89th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,035 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 23.8. This one has gotten more attention than average, scoring higher than 56% 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 232,153 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 87% of its contemporaries.
We're also able to compare this research output to 2 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