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Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape

Overview of attention for article published in BMC Genomics, August 2015
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  • Above-average Attention Score compared to outputs of the same age (53rd percentile)
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Title
Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape
Published in
BMC Genomics, August 2015
DOI 10.1186/s12864-015-1809-5
Pubmed ID
Authors

Takao Yokoyama, Fumihito Miura, Hiromitsu Araki, Kohji Okamura, Takashi Ito

Abstract

Base-resolution methylome data generated by whole-genome bisulfite sequencing (WGBS) is often used to segment the genome into domains with distinct methylation levels. However, most segmentation methods include many parameters to be carefully tuned and/or fail to exploit the unsurpassed resolution of the data. Furthermore, there is no simple method that displays the composition of the domains to grasp global trends in each methylome. We propose to use changepoint detection for domain demarcation based on base-resolution methylome data. While the proposed method segments the methylome in a largely comparable manner to conventional approaches, it has only a single parameter to be tuned. Furthermore, it fully exploits the base-resolution of the data to enable simultaneous detection of methylation changes in even contrasting size ranges, such as focal hypermethylation and global hypomethylation in cancer methylomes. We also propose a simple plot termed methylated domain landscape (MDL) that globally displays the size, the methylation level and the number of the domains thus defined, thereby enabling one to intuitively grasp trends in each methylome. Since the pattern of MDL often reflects cell lineages and is largely unaffected by data size, it can serve as a novel signature of methylome. Changepoint detection in base-resolution methylome data followed by MDL plotting provides a novel method for methylome characterization and will facilitate global comparison among various WGBS data differing in size and even species origin.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 5%
Unknown 18 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 5 26%
Researcher 5 26%
Student > Master 3 16%
Student > Doctoral Student 2 11%
Professor 1 5%
Other 1 5%
Unknown 2 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 7 37%
Biochemistry, Genetics and Molecular Biology 5 26%
Environmental Science 1 5%
Mathematics 1 5%
Psychology 1 5%
Other 2 11%
Unknown 2 11%
Attention Score in Context

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 05 September 2015.
All research outputs
#13,527,742
of 23,344,526 outputs
Outputs from BMC Genomics
#4,856
of 10,745 outputs
Outputs of similar age
#122,474
of 265,576 outputs
Outputs of similar age from BMC Genomics
#124
of 254 outputs
Altmetric has tracked 23,344,526 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,745 research outputs from this source. They receive a mean Attention Score of 4.7. This one has gotten more attention than average, scoring higher than 53% 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 265,576 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 53% of its contemporaries.
We're also able to compare this research output to 254 others from the same source and published within six weeks on either side of this one. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.