Title |
Statistical methods for detecting differentially methylated loci and regions
|
---|---|
Published in |
Frontiers in Genetics, September 2014
|
DOI | 10.3389/fgene.2014.00324 |
Pubmed ID | |
Authors |
Mark D. Robinson, Abdullah Kahraman, Charity W. Law, Helen Lindsay, Malgorzata Nowicka, Lukas M. Weber, Xiaobei Zhou |
Abstract |
DNA methylation, the reversible addition of methyl groups at CpG dinucleotides, represents an important regulatory layer associated with gene expression. Changed methylation status has been noted across diverse pathological states, including cancer. The rapid development and uptake of microarrays and large scale DNA sequencing has prompted an explosion of data analytic methods for processing and discovering changes in DNA methylation across varied data types. In this mini-review, we present a compact and accessible discussion of many of the salient challenges, such as experimental design, statistical methods for differential methylation detection, critical considerations such as cell type composition and the potential confounding that can arise from batch effects. From a statistical perspective, our main interests include the use of empirical Bayes or hierarchical models, which have proved immensely powerful in genomics, and the procedures by which false discovery control is achieved. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 3 | 23% |
Switzerland | 3 | 23% |
Australia | 2 | 15% |
Canada | 1 | 8% |
India | 1 | 8% |
United Kingdom | 1 | 8% |
Unknown | 2 | 15% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 9 | 69% |
Members of the public | 3 | 23% |
Science communicators (journalists, bloggers, editors) | 1 | 8% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 3 | <1% |
Canada | 2 | <1% |
Switzerland | 1 | <1% |
Turkey | 1 | <1% |
Australia | 1 | <1% |
Sweden | 1 | <1% |
United Kingdom | 1 | <1% |
Germany | 1 | <1% |
Iran, Islamic Republic of | 1 | <1% |
Other | 3 | <1% |
Unknown | 334 | 96% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 98 | 28% |
Researcher | 82 | 23% |
Student > Master | 35 | 10% |
Student > Bachelor | 23 | 7% |
Student > Doctoral Student | 22 | 6% |
Other | 47 | 13% |
Unknown | 42 | 12% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 132 | 38% |
Biochemistry, Genetics and Molecular Biology | 73 | 21% |
Mathematics | 22 | 6% |
Computer Science | 17 | 5% |
Medicine and Dentistry | 16 | 5% |
Other | 35 | 10% |
Unknown | 54 | 15% |