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.
Provides high-throughput microarray and next-generation sequence (NGS) functional genomic data sets. GEO archives raw data, processed data and metadata submitted by the research community. Its data are indexed, cross-linked and searchable. This database gives access to several tools and graphical renderings allowing users to easily explore and interpret data available on the platform. It can be useful to develop and test new hypotheses.
A comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. REBASE contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. From the REBASE website users have a variety of resources available that facilitate the analysis of sequence information, including tools for analyzing sequences (REBASE TOOLS), that allow restriction enzyme recognition sites to be found in submitted sequences (NEBCUTTER) and an implementation of BLAST to allow searching against all sequences in REBASE.
Offers a repository for related with nucleotide sequencing workflows. ENA provides data model containing input information, output machine data and interpreted information. The database gathers a wide range of information as well as raw sequence data and derived data, including sequences, assemblies and functional annotation accompanied by studies and samples, to provide experimental context.
A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. BCaPE provides tools for visualizing, querying and downloading data from a large collection of highly molecularly annotated breast cancer patient-derived tumour xenografts (PDTX). The biobank represents a powerful resource for pre-clinical breast cancer pharmacogenomic studies, including identification of biomarkers of response or resistance.
Gives access to the apple genome. The Apple Genome and Epigenome contains up to date gene annotation, transposable element (TE) annotation, genetic markers, DNA methylation data, small RNA data and microarray probes. The genome was obtained using a homozygous apple variety (a doubled haploid of ‘Golden Delicious’) and by combining several sequencing and mapping technologies. The reference apple genome sequence offers insights into the genome dynamics of a tree and provides a basis for future studies.
Furnishes a collection of single-base whole-genome methylome maps for the best-assembled eukaryotic genomes. NGSmethDB is a database simplifying the analysis of methylation data from different sources. Heterogeneous methylation data can be either simultaneously visualized through a web interface or selectively downloaded by means of the provided data mining tools. It allows researchers to design new experiments and retrieve the adequate data for them.
Generates functional genomic data in brain samples. The CMC data brain was obtained from autopsies of cases with and without severe psychiatric disorders. This database includes over 1,150 samples and represents one of the biggest collection of collaborating brain banks. These samples generates a wide spectrum of data comprising regional gene expression, epigenomics, whole genome sequencing (WGS), and somatic mosaicism.
Presents the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. DiseaseMeth is focused not only on curated information about diseases, genes and corresponding methylation data, but also on predicted associations between diseases of interest and methylation of specific DNA regions based on the vast amounts of data that it contains. DiseaseMeth contains methylation data of 32701 samples from 88 diseases together with 679602 associations between diseases and methylation of genes. DiseaseMeth not only enlarges the data of increased DNA methylation, but also provides new tools to explore the relationships between methylation of genes and diseases.
Provides a comprehensive parts list of functional elements in the human genome. ENCODE is an online resource that includes elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. This corpus of data provides an astounding resource for annotation, curation and functional characterization in the human and mouse genomes in a large variety of sample types.
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.
Allows the study of the interplay between DNA methylation, gene expression and cancer. MethyCancer contains: (i) CpG Island (CGI) clones and global CGI predictions, (ii) DNA methylation data, (iii) cancer information, genes and mutations and (iv) correlation among DNA methylation, gene expression and cancer. It provides users with a search engine to query different data types and data interactions, and offers keyword search, advanced searches, namely Methylation Search, Gene Search, Cancer Search, Clone Search and Repeat Search.
A DNA methylome programming database that integrates the genome-wide single-base nucleotide methylomes of gametes and early embryos at multiple diverse stages in different model organisms. Unlike extant relevant databases, it incorporates the whole-genome single-base-resolution methylomes of gametes and early embryos at multiple different developmental stages in zebrafish and mouse.
A cancer methylation database that includes genes that are reported to be methylated in various cancer types. A query can be based either on genes (to check in which cancer types the genes are reported as being methylated) or on cancer types (which genes are reported to be methylated in the cancer (sub) types of interest). PubMeth is based on text-mining of Medline/PubMed abstracts, combined with manual reading and annotation of preselected abstracts. The text-mining approach results in increased speed and selectivity (as for instance many different aliases of a gene are searched at once), while the manual screening significantly raises the specificity and quality of the database.
A database about DNA 6mA and 4mC methylomes. MethSMRT provides tools to store, browse, search and download epigenome-wide methylation profiles of 156 species, including seven eukaryotes such as Arabidopsis, Caenorhabditis elegans, Drosophila, mouse and yeast, as well as 149 prokaryotes. It also offers a genome browser to visualize the methylation sites and related information such as single nucleotide polymorphisms and genomic annotation.
Gathers information about chromatin regulators (CRs) in human cancer. CR2Cancer is a database that allows users to explore the functional, genomic, transcriptomic, proteomic, clinical, biological network and literature-reported information for CRs across multiple cancer types. It contains about 400 CRs annotated with eleven categories of knowledge. CR2Cancer can be useful for investigators in cancer epigenetics research community.
Constructs epigenomic maps. BLUEPRINT investigates epigenetic variation between individuals by studying two cell types from at least 200 healthy donors. It includes several of the most prevalent and clinical B-cell malignancies in adults and children. It can be used to study the genome-wide effects of epigenetic gene mutation. This database can be useful in studies about epigenetic drug treatment to find compounds that modulate epigenetic regulators.
Contains epigenomic annotations and systematic integrative analysis with a variety of human tissues and cell types. Epigenomic Atlas of Craniofacial Development offers a complete catalog of tracks that can be loaded into many modern genome browsers. It aims to help the craniofacial community to develop hypotheses related to craniofacial abnormalities which are rooted in craniofacial biology.
Generates and releases reference epigenome maps of normal and disease tissues along with appropriate metadata. IHEC data portal was constructed employing a distributed data model. It navigates the reference epigenomic datasets generated by the consortium. The database allows epigenomic data integration, discovery, visualization, analysis, download, and sharing.
Provides methylation markers for the detection of human cancer. MeInfoText contains associations among human genes, methylation and cancers and integrated information about protein-protein interactions and biological pathways. It provides information on interacting partners, interaction types and detection methods. This resource can be accessed by gene symbols, gene-related keywords and cancer names.