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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.
BCaPE / Breast Cancer PDTX Encyclopaedia
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.
The Apple Genome and Epigenome
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.
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.
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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.
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.
MethSMRT / Methylomes Single-Molecule Real-Time
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.
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.
GED / Gametogenesis Epigenetic modification Database
A comprehensive resource of epigenetic modification of gametogenesis. Users can get the information about epigenetic modifications (DNA methylation, histone modification and miRNA regulation) and the related potential pathways during different stages of gametogenesis in mammal species (human, mouse, rat, pig, cattle, goat and sheep). GED is a user-friendly web site, through which users can obtain the comprehensive epigenetic factor information and molecular pathways by visiting our database freely.
To investigate the role of tissue-specific variation of allele-specific methylation (ASM) in the human brain and its relation to allelic biases in whole blood, we examined ASM across multiple brain regions and matched blood samples collected from multiple donors. Our data shows that although a large proportion of ASM is conserved across tissues, there are specific differences in the extent and distribution of ASM sites between regions of the brain and whole blood. Genome browser tracks displaying ASM signals as well as an online tool plotting ASM for sites of interest are available for download from a searchable database.
MENT / Methylation and Expression database of Normal and Tumor tissues
Provides a multicentre prostate cancer database that captures clinicopathologic data and longitudinal follow-up. CPDR is a research program for studying prostate diseases. It is divided into: (1) a clinical program, (2) a basic science program and (3) the multi-center national database. The database aims to track patients with prostatic disease to determine epidemiologic trends, natural history of prostate cancer, and efficacy of treatments.
DBCAT / DataBase of CpG islands and Analytical Tool
A database developed in order to recognize comprehensive mehtylation profiles of DNA alteration in human cancer. DBCAT is an online methylation analytical tool composed of three parts: a CpG Island Finder, a genome query browser and an analytical tool for methylation microarray data. The analytical tool can analyze raw data generated from scanners and search genes with methylated regions which could affect gene expression regulation. DBCAT not only identifies the regions of methylation but also searches the database to pick up genes with methylated regions of functional meanings.
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.
Provides a molecular atlas of the developing lung. LungMAP includes mouse and human data for cross correlation of developmental processes across species. This online resource is available through a web portal for presentation of results and public sharing of data sets. It establishes a repository of young human lung tissues obtained through organ donor organizations. It also develops a comprehensive lung ontology that incorporates the latest findings of LungMAP consortium. The database contains transcriptomic, proteomic, and lipidomic data sources.
Annotates the chemical properties and structures of all curated modified DNA bases. DNAmod provides a web interface to easily browse and search through DNA modifications. DNAmod includes manual annotations of available sequencing methods, descriptions of their occurrence in nature, and provides existing and suggested nomenclature. DNAmod enables researchers to rapidly review previous work, select mapping techniques, and track recent developments concerning modified bases of interest.
A database that makes use of meta-analysis to identify potential epigenetic-regulated miRNAs for three human cancers, i.e. lung adenocarcinoma, lung squamous carcinoma and ovarian cancers. MethmiRbase also includes experimentally verified cancer-associated miRNA target genes. The database collects a total of 4,445 cancer genes with 1,834 known to act as tumor suppressor genes and oncogenes from 3 different resources: MSKCC, TAG and NYMU. Moreover, MethmiRbase also collects 138 and 94 ovarian and lung related cancer genes respectively. The data records provide the relationship between DNA methylation - miRNA - cancer genes pathway in ovarian and lung human cancer. MethmiRbase provides an important information about potential epigenetic regulated miRNA in human cancers.
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