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.
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.
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).
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.
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.
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 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.
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.