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.
A comprehensive and consistently annotated knowledgebase of all published or public ChIP-seq and DNase-seq data in mouse and human. In total, there are 2711 ChIP-Seq datasets for transcription and chromatin regulators, 2355 for histone modifications and variants, 412 DNase-Seq and 996 control datasets. Among transcription and chromatin regulators, POLR2A, CTCF, ESR1, RELA and EP300 are the most often profiled ChIP-Seq factors. For histone marks, H3K4me3, H3K27me3, H3K4me1, H3K36me3 and H3K9me3 ChIP-Seq are the most common, which together accounts for over 70% of all of the histone ChIP-Seq data.
Contains search tools, analysis tools and the UCSC Genome Browser for visualization. PCSD is a plant chromatin state database to integrate information on chromatin states, self-organization mapping (SOM) maps and epigenomic data features of three species, Arabidopsis thaliana, Oryza sativa and Zea mays. This application offers insights into the locations and functions of regulatory regions and genes in response to developmental and environmental signals.
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.
Stores chromatin state definition tables to paint the genome with functional annotation. StateHub is a database which hosts annotation tracks for major public consortia as a resource, and allows users to submit their own alternative models. The models in StateHub consist of an abstraction layer, defining the relationships between data sources and functional categories. These categories are integrated to produce annotations via a decision matrix.