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MethBase is a database of DNA methylation data derived from next-generation sequencing data. [1] MethBase provides a visualization of publicly available bisulfite sequencing and reduced representation bisulfite sequencing experiments through the UCSC Genome Browser.
Typical DNA methylation landscape in mammals. The DNA methylation landscape of vertebrates is very particular compared to other organisms. In mammals, around 75% of CpG dinucleotides are methylated in somatic cells, [19] and DNA methylation appears as a default state that has to be specifically excluded from defined locations.
MethBase: database of DNA methylation data visualized on the UCSC Genome Browser; Minimotif Miner: database of short contiguous functional peptide motifs; Oncogenomic databases: a compilation of databases that serve for cancer research; PubMed: references and abstracts on life sciences and biomedical topics; RIKEN integrated database of mammals
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The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. database: website [11] [12] MethMotif An integrative cell-specific database of transcription factor binding motifs coupled with DNA methylation profiles ...
CpG depletion has been observed in the process of DNA methylation of Transposable Elements (TEs) where TEs are not only responsible in the genome expansion but also CpG loss in a host DNA. TEs can be known as "methylation centers" whereby the methylation process, the TEs spreads into the flanking DNA once in the host DNA.
DNA methylation is an epigenetic mechanism that can be studied with bioinformatics. Computational epigenetics [ 1 ] uses statistical methods and mathematical modelling in epigenetic research. Due to the recent explosion of epigenome datasets, computational methods play an increasing role in all areas of epigenetic research.
In mammals, DNA methylation is common in body cells, [7] and methylation of CpG sites seems to be the default. [ 8 ] [ 9 ] Human DNA has about 80–90% of CpG sites methylated, but there are certain areas, known as CpG islands , that are CG-rich (high cytosine and guanine content, made up of about 65% CG residues ), wherein none is methylated.