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Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer

Overview of attention for article published in Epigenetics & Chromatin, March 2016
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (77th percentile)
  • Average Attention Score compared to outputs of the same age and source

Mentioned by

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14 tweeters

Citations

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30 Dimensions

Readers on

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71 Mendeley
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Title
Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer
Published in
Epigenetics & Chromatin, March 2016
DOI 10.1186/s13072-016-0058-4
Pubmed ID
Authors

Yuting Chen, Charles E. Breeze, Shao Zhen, Stephan Beck, Andrew E. Teschendorff

Abstract

There is growing evidence that DNA methylation alterations contribute to carcinogenesis. While cancer tissue exhibits widespread DNA methylation changes, the proportion of tissue-specific versus tissue-independent DNA methylation alterations in cancer is unclear. In addition, it is unknown which factors determine the patterns of aberrant DNA methylation in cancer. Using HumanMethylation450 BeadChips (450k), we here analyze genome-wide DNA methylation patterns of ten types of fetal tissue, in addition to matched normal-cancer data for corresponding tissue types, encompassing over 3000 samples. We demonstrate that the level of aberrant cancer DNA methylation in gene promoters and gene bodies is highly correlated between cancer types. We estimate that up to 60 % of the DNA methylation variation in a cancer genome of a given tissue type is explained by the corresponding variation in a cancer genome of another type, implying that much of the cancer DNA methylation landscape is tissue independent. We further show that histone marks in normal cells are better predictors of aberrant cancer DNA methylation than the corresponding signals in human embryonic stem cells. We build predictors of cancer DNA methylation patterns and show that although inclusion of three histone marks (H3K4me3, H3K27me3 and H3K36me3) improves model accuracy, the bivalent marks are the most predictive. Finally, we show that chromatin accessibility of gene promoters in normal tissue dictates the promoter's propensity to acquire aberrant DNA methylation in cancer in so far as it determines its level of DNA methylation in normal tissue. Our data show that a considerable fraction of the aberrant cancer DNA methylation landscape results from a mechanism that is largely tissue specific. Histone marks as specified in the normal cell of origin provide highly predictive models of aberrant cancer DNA methylation and outperform those derived from the same marks in hESCs.

Twitter Demographics

The data shown below were collected from the profiles of 14 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 71 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 1%
Unknown 70 99%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 20 28%
Researcher 11 15%
Student > Master 9 13%
Student > Doctoral Student 7 10%
Student > Bachelor 6 8%
Other 8 11%
Unknown 10 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 28 39%
Biochemistry, Genetics and Molecular Biology 20 28%
Medicine and Dentistry 5 7%
Computer Science 2 3%
Unspecified 1 1%
Other 5 7%
Unknown 10 14%

Attention Score in Context

This research output has an Altmetric Attention Score of 7. 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 21 March 2016.
All research outputs
#1,763,075
of 11,042,410 outputs
Outputs from Epigenetics & Chromatin
#105
of 302 outputs
Outputs of similar age
#66,400
of 290,458 outputs
Outputs of similar age from Epigenetics & Chromatin
#6
of 12 outputs
Altmetric has tracked 11,042,410 research outputs across all sources so far. Compared to these this one has done well and is in the 83rd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 302 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.8. This one has gotten more attention than average, scoring higher than 64% 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 290,458 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 77% of its contemporaries.
We're also able to compare this research output to 12 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 50% of its contemporaries.