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X Demographics
Mendeley readers
Attention Score in Context
| Title |
Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia
|
|---|---|
| Published in |
Epigenetics & Chromatin, November 2016
|
| DOI | 10.1186/s13072-016-0090-4 |
| Pubmed ID | |
| Authors |
Michiel E. Adriaens, Peggy Prickaerts, Michelle Chan-Seng-Yue, Twan van den Beucken, Vivian E. H. Dahlmans, Lars M. Eijssen, Timothy Beck, Bradly G. Wouters, Jan Willem Voncken, Chris T. A. Evelo |
| Abstract |
A comprehensive assessment of the epigenetic dynamics in cancer cells is the key to understanding the molecular mechanisms underlying cancer and to improving cancer diagnostics, prognostics and treatment. By combining genome-wide ChIP-seq epigenomics and microarray transcriptomics, we studied the effects of oxygen deprivation and subsequent reoxygenation on histone 3 trimethylation of lysine 4 (H3K4me3) and lysine 27 (H3K27me3) in a breast cancer cell line, serving as a model for abnormal oxygenation in solid tumors. A priori, epigenetic markings and gene expression levels not only are expected to vary greatly between hypoxic and normoxic conditions, but also display a large degree of heterogeneity across the cell population. Where traditionally ChIP-seq data are often treated as dichotomous data, the model and experiment here necessitate a quantitative, data-driven analysis of both datasets. We first identified genomic regions with sustained epigenetic markings, which provided a sample-specific reference enabling quantitative ChIP-seq data analysis. Sustained H3K27me3 marking was located around centromeres and intergenic regions, while sustained H3K4me3 marking is associated with genes involved in RNA binding, translation and protein transport and localization. Dynamic marking with both H3K4me3 and H3K27me3 (hypoxia-induced bivalency) was found in CpG-rich regions at loci encoding factors that control developmental processes, congruent with observations in embryonic stem cells. In silico-identified epigenetically sustained and dynamic genomic regions were confirmed through ChIP-PCR in vitro, and obtained results are corroborated by published data and current insights regarding epigenetic regulation. |
X Demographics
The data shown below were collected from the profiles of 13 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Ireland | 1 | 8% |
| Montenegro | 1 | 8% |
| United States | 1 | 8% |
| Netherlands | 1 | 8% |
| United Arab Emirates | 1 | 8% |
| Spain | 1 | 8% |
| United Kingdom | 1 | 8% |
| Unknown | 6 | 46% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 6 | 46% |
| Members of the public | 6 | 46% |
| Practitioners (doctors, other healthcare professionals) | 1 | 8% |
Mendeley readers
The data shown below were compiled from readership statistics for 75 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Netherlands | 1 | 1% |
| United States | 1 | 1% |
| Sweden | 1 | 1% |
| Unknown | 72 | 96% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 15 | 20% |
| Researcher | 14 | 19% |
| Student > Master | 9 | 12% |
| Student > Bachelor | 6 | 8% |
| Student > Doctoral Student | 6 | 8% |
| Other | 11 | 15% |
| Unknown | 14 | 19% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 31 | 41% |
| Agricultural and Biological Sciences | 18 | 24% |
| Medicine and Dentistry | 7 | 9% |
| Immunology and Microbiology | 3 | 4% |
| Pharmacology, Toxicology and Pharmaceutical Science | 1 | 1% |
| Other | 3 | 4% |
| Unknown | 12 | 16% |
Attention Score in Context
This research output has an Altmetric Attention Score of 8. 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 31 January 2018.
All research outputs
#3,991,373
of 22,899,952 outputs
Outputs from Epigenetics & Chromatin
#149
of 567 outputs
Outputs of similar age
#66,311
of 311,687 outputs
Outputs of similar age from Epigenetics & Chromatin
#6
of 17 outputs
Altmetric has tracked 22,899,952 research outputs across all sources so far. Compared to these this one has done well and is in the 82nd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 567 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.7. This one has gotten more attention than average, scoring higher than 73% 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 311,687 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 78% of its contemporaries.
We're also able to compare this research output to 17 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 64% of its contemporaries.