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CpG Islands

Overview of attention for book
Cover of 'CpG Islands'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 CpG Islands: A Historical Perspective
  3. Altmetric Badge
    Chapter 2 Biochemical Identification of Nonmethylated DNA by BioCAP-Seq
  4. Altmetric Badge
    Chapter 3 Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation
  5. Altmetric Badge
    Chapter 4 CpG Islands in Cancer: Heads, Tails, and Sides
  6. Altmetric Badge
    Chapter 5 Infinium DNA Methylation Microarrays on Formalin-Fixed, Paraffin-Embedded Samples
  7. Altmetric Badge
    Chapter 6 The Use of Methylation-Sensitive Multiplex Ligation-Dependent Probe Amplification for Quantification of Imprinted Methylation
  8. Altmetric Badge
    Chapter 7 The Pancancer DNA Methylation Trackhub: A Window to The Cancer Genome Atlas Epigenomics Data
  9. Altmetric Badge
    Chapter 8 Methylation-Sensitive Amplification Length Polymorphism (MS-AFLP) Microarrays for Epigenetic Analysis of Human Genomes
  10. Altmetric Badge
    Chapter 9 Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells
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    Chapter 10 Experimental Design and Bioinformatic Analysis of DNA Methylation Data
  12. Altmetric Badge
    Chapter 11 Assay for Transposase Accessible Chromatin (ATAC-Seq) to Chart the Open Chromatin Landscape of Human Pancreatic Islets
  13. Altmetric Badge
    Chapter 12 Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq)
  14. Altmetric Badge
    Chapter 13 Genome-Wide Mapping of Protein–DNA Interactions on Nascent Chromatin
  15. Altmetric Badge
    Chapter 14 Analysis of Chromatin Interactions Mediated by Specific Architectural Proteins in Drosophila Cells
  16. Altmetric Badge
    Chapter 15 High-Throughput Single-Cell RNA Sequencing and Data Analysis
  17. Altmetric Badge
    Chapter 16 Functional Insulator Scanning of CpG Islands to Identify Regulatory Regions of Promoters Using CRISPR
  18. Altmetric Badge
    Chapter 17 An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics
Attention for Chapter 3: Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation
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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 (72nd percentile)

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Chapter title
Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation
Chapter number 3
Book title
CpG Islands
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7768-0_3
Pubmed ID
Book ISBNs
978-1-4939-7767-3, 978-1-4939-7768-0
Authors

Cristina Gómez-Martín, Ricardo Lebrón, José L. Oliver, Michael Hackenberg

Abstract

The promoter region of around 70% of all genes in the human genome is overlapped by a CpG island (CGI). CGIs have known functions in the transcription initiation and outstanding compositional features like high G+C content and CpG ratios when compared to the bulk DNA. We have shown before that CGIs manifest as clusters of CpGs in mammalian genomes and can therefore be detected using clustering methods. These techniques have several advantages over sliding window approaches which apply compositional properties as thresholds. In this protocol we show how to determine local (CpG islands) and global (distance distribution) clustering properties of CG dinucleotides and how to generalize this analysis to any k-mer or combinations of it. In addition, we illustrate how to easily cross the output of a CpG island prediction algorithm with our methylation database to detect differentially methylated CGIs. The analysis is given in a step-by-step protocol and all necessary programs are implemented into a virtual machine or, alternatively, the software can be downloaded and easily installed.

Twitter Demographics

The data shown below were collected from the profiles of 11 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 8 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Spain 1 13%
Unknown 7 88%

Demographic breakdown

Readers by professional status Count As %
Student > Bachelor 3 38%
Other 1 13%
Student > Doctoral Student 1 13%
Professor 1 13%
Researcher 1 13%
Other 0 0%
Unknown 1 13%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 3 38%
Earth and Planetary Sciences 1 13%
Medicine and Dentistry 1 13%
Unknown 3 38%

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 24 December 2019.
All research outputs
#3,195,041
of 16,270,245 outputs
Outputs from Methods in molecular biology
#883
of 9,422 outputs
Outputs of similar age
#77,359
of 281,976 outputs
Outputs of similar age from Methods in molecular biology
#5
of 7 outputs
Altmetric has tracked 16,270,245 research outputs across all sources so far. Compared to these this one has done well and is in the 80th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 9,422 research outputs from this source. They receive a mean Attention Score of 2.7. This one has done particularly well, scoring higher than 90% 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 281,976 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 72% of its contemporaries.
We're also able to compare this research output to 7 others from the same source and published within six weeks on either side of this one. This one has scored higher than 2 of them.