Histone modifications play important roles in chromatin remodeling, gene transcriptional regulation, stem cell maintenance and differentiation. Alterations in histone modifications may be linked to human diseases especially cancer. Histone modifications including methylation, acetylation and ubiquitylation probed by ChIP-seq, ChIP-chip and qChIP have become widely available. Mining and integration of histone modification data can be beneficial to novel biological discoveries.
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.
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.
A database for histone mutations and their phenotypes. The database collects phenotypic screening data from assays of systematically constructed histone mutants: Single-residue substitutions, multiple substitutions, correlation with known post-translational modifications, cross-species mapping.
A database of human histones, their post-translational modifications and modifying enzymes. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes of modifying enzymes.
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.
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.
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.
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.
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.
Allows simple integrated analysis of private and commonly-used public signal tracks. START is an online resource that provides a generic way for analyzing a large number of genomic signal tracks. This database contains a web interface that guides users to construct Signal Track Query Language (STQL) queries. It also provides example queries for various types of data analysis.
Enables comprehensive query and comparative analysis based on gene names, genomic region locations, histone modification marks and cell types. iHMS is an integrated human histone modification database that incorporates massive histone modification maps spanning different developmental stages, lineages and tissues. It also includes genome-wide expression data of different conditions, reference gene annotations, GC content and CpG island information.
Stores the curated epigenetic data retrieved by literature mining, which previous studies indicated as involved in prostate cancer (PC) of human, mouse, and rat. A user-friendly interface is implemented for easy and flexible query. PEpiD can serve as an important resource for epigenetic research in PC.
A manually curated database providing information about epigenetic regulators, their complexes, targets and products. EpiFactors contains information on 815 proteins, including 95 histones and protamines. It also contains information on 69 protein complexes that are involved in epigenetic regulation. The resource is practical for a wide range of users, including biologists, pharmacologists and clinicians.
A web-based genomics platform for histone-modifying enzymes (HMEs) by using HMM sequence profiles. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, dbHiMo will be a valuable resource for future epigenetics/epigenomics studies.
Provides a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. Roadmap Epigenomics Project is produced by The NIH Roadmap Epigenomics Mapping Consortium. The database offers epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. Downloadable tools are also available.
Explore, view, and download genome-wide maps of DNA and histone modifications from our diverse collection of epigenomic data sets. The Epigenomics resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes.
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