DNA methylation databases | DNA modification analysis
DNA methylation is an epigenome mark involved in key biological processes, such as embryonic development, transcription, genomic imprinting, learning, memory or age-related cognitive decline. DNA methylation plays an important role in the origin and function of CpG islands (CGIs). Aberrant methylation (mostly hypermethylation) of CGIs has been implicated in the appearance of several disorders, such as cancer, immunodeficiency or centromere instability.
A mouse developmental methylome database which focuses on the efficient storage of DNA methylomes in temporal order and quantitative analysis of methylation dynamics during mouse development. The flexible query engine can be used for acquisition of methylation profiles for genes, miRNAs, LncRNAs, genomic intervals of interest across selected developmental stages. DevMouse offers online analysis tools for quantification of methylation variation, identification of differentially methylated genes, hierarchical clustering, gene function annotation and enrichment.
Consists in a web-based resource of the extensively cross-analyzed different biomarkers involved in human papillomaviruses (HPVs). HPVbase is highly interactive and manually curated. It allows comparative analysis of different biomarkers and genomic information. This database can be useful for assessment of clinically significant biomarker data and will provide a comprehensive base for examination between distinct features and cancers.
A database of about 167 epigenetic modifiers/proteins, which are considered as potential cancer targets. In dbEM, modifiers are classified on functional basis and comprise of 48 histone methyl transferases, 33 chromatin remodelers and 31 histone demethylases. dbEM maintains the genomic information like mutations, copy number variation and gene expression in thousands of tumor samples, cancer cell lines and healthy samples. This information is obtained from public resources viz. COSMIC, CCLE and 1000-genome project. Gene essentiality data retrieved from COLT database further highlights the importance of various epigenetic proteins for cancer survival. We have also reported the sequence profiles, tertiary structures and post-translational modifications of these epigenetic proteins in cancer. It also contains information of 54 drug molecules against different epigenetic proteins.
Provides well-organized compendium of methylation events and statistical analysis associated with several diseases. ViralEpi is a comprehensive and integrated web resource developed for the methylation patterns as epigenomic profiles of these viruses (Epstein-Barr virus (EBV) and Hepatitis B virus (HBV)) associated with human carcinomas and other diseases. This web resource would be helpful for research community engaged in studying epigenetic biomarkers for appropriate prognosis and diagnosis of diseases and its various stages.
Focuses on aberrant methylomes of human diseases. MethHC deals with expression profiles and methylation of more than 15 cancers. The database allows users to: (i) browse methylation clusters of interest by setting a defined gene type and gene region coupled to a methylation level evaluation method of interest; (ii) run gene/microRNA search to identify differentially methylated genes in a set of tumors; and (iii) explore statistics and top-ranked analyses.
Informs about RNAs and DNA methylation. Lnc2Meth is an online resource that assists in comprehension of the expression of protein-coding or non-coding transcripts. Its purpose is to clarify the regulatory relationships between human lncRNAs and associated DNA methylation in different diseases.
Provides a data resource on DNA methylation. iMETHYL offers data on whole-DNA methylation, whole-genome and whole-transcriptome data for CD4 T-lymphocytes (CD4T), monocytes and neutrophils from up to 100 subjects. It includes also the average and standard deviation (SD) of gene expression levels for more than 14 000 genes and allele frequencies for about 9 million autosomal single-nucleotide variants (SNVs).