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REGB / Roadmap EpiGenome Browser
Offers a platform compiling epigenomic information. REGB is a web platform that allows users to browse information related to tissue-specific regulatory roles of genetic variants associated with disease. The platform gathers multiple datasets displaying data related to DNA methylation, histone modification or open chromatin. It contains a wide range of functionalities including gene set view, genome juxtaposition, chromatin interaction display, and statistical testing.
Provides the biological research community with a comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites (TFBS), histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation (CNV).
Holds canonical histones and histone variants, their sequence, structural and functional features. HistoneDB is composed of two distinct parts: the first is a set of manually curated and annotated variants and the second is a set of automatically extracted, classified and annotated histone sequences from non-redundant database of protein sequences maintained by NCBI. It assists finding variant sequences from different organisms and comparing histone variants and corresponding canonical histones.
HHMD / Human Histone Modification Database
A relatively comprehensive database for human histone modifications. HHMD focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. HHMD contains four types of data: (i) high-throughput histone modifications, (ii) MeDIP methylation, (iii) curated information of aberrant histone modifications, genes and cancers and (iv) GC contents, RefSeq gene (21) and other genomic annotations. To facilitate data extraction, flexible search options are built in HHMD. It can be searched by histone modification, gene ID, functional categories, chromosome location and cancer name. HHMD also includes a user-friendly visualization tool named HisModView, by which genome-wide histone modification map can be shown. HisModView facilitates the acquisition and visualization of histone modifications. The database also has manually curated information of histone modification dysregulation in nine human cancers.
WERAM / Writers Erasers and Readers of Acetylation and Methylation
A database for histone acetyltransferases, histone deacetylases, histone methyltransferases, histone demethylases and acetyl- or methyl-binding proteins, which catalyze, remove and recognize histone acetylation and methylation sites as ‘writers’, ‘erasers’ and ‘readers’, and synergistically determine the ‘histone code’. WERAM database contains more than 20 thousand nonredundant histone regulators from 148 eukaryotes.
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.
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