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| Content | |
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| Description | epigenomic data sets. |
| Contact | |
| Research center | National Center for Biotechnology Information |
| Authors | Ian M Fingerman |
| Primary citation | Fingerman & al. (2011) [1] |
| Release date | 2010 |
| Access | |
| Website | https://www.ncbi.nlm.nih.gov/epigenomics |
The Epigenomics database at the National Center for Biotechnology Information was a database for whole-genome epigenetics data sets. [1] It was retired on 1 June 2016.
The Epigenomics database of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH) was launched in June 2010 as a means to collect maps of epigenetic modifications and their occurrence across the human genome. [2] This database provides a publicly available resource for maps in stem cells and primary ex vivo tissues that detail genome-wide landscapes of epigenetic factors that occur in human development and disease. [1]
The primary resources for the content of the Epigenomics Database are derived from two archival databases at the NCBI: The Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA). [1] The Gene Expression Omnibus is a data system for high-throughput genomic data that is generated from microarray and next-generation sequencing technologies. [3] Data used in the Epigenomics database is a combination of GEO and SRA subsets that are specific to Epigenetic factors. This data is subjected to additional review and organized in a more easily attainable fashion before added to the Epigenomics database. [1]
All of the experiments and corresponding samples in the Epigenomics database are displayed in the default browser. As of October 2013, there are currently 4112 experiments and 1257 samples available in the database. [4] Five studied species are represented in the database, and many data tracks are available including expression of micro and small RNAs, histone modification and histone modifying enzymes, chromatin accessibility and chromatin associated factors, and transcription factors. [1] One such example from the database is a study of certain epigenetic factors in Drosophila melanogaster at the 20- to 24-hour embryonic stage of development. [5]
The Epigenomics database browser contain two fundamental search records, "Experiments" and "Samples".
The Experiment search record refers to one or more experiments with a set of scientific aims. [1] Here a user is able to retrieve full data source information. This information includes the institution of the submitter, links to the original data submissions in GEO and SRA, links to literature citations in PubMed and/or full text articles in Pubmed. [1] Experiment records contain a unique accession number that includes a prefix 'ESS'. [1]
The sample search record corresponds to the biological material examined in a given experiment in the database and provides details about source attributes with values from controlled vocabularies. [1] There are over 20 biological attribute fields available, and among these fields include strain, cultivar, ecotype, individual, gender, age, developmental stage, cell line, cell type, tissue type, and health status. [1]
There are many available resources online for help in navigating and using the Epigenomics database. The "Epigenetics Help" section of the NCBI help manual contains information on the searchable database and provides a user with tools to use, manage, download and upload, and navigate the database. [6] There are also guides to navigation of the database aimed at specific researchers and fields of study, such as stem cell research. [7]
In 2007 the National Institutes of Health (NIH) launched the Roadmap Epigenomics Project. The aim of the project is a development of publicly available reference epigenome maps from a variety of cell types. [1] These epigenetic maps are intended to provide resources for studies of epigenetic events that underline human development, diversity, and disease. [8] For similar efforts see the ENCODE (ENCyclopedia Of DNA Elements) Project, whose initiatives are complementary to the Roadmap Epigenomics Project. [9]
The epigenome consists of a record of the chemical changes to the DNA and Histone proteins of an organism. These chemical changes influence gene expression across many tissue types and developmental stages. [10] These epigenetic changes involve methods of altering gene expression that do not involve changes in the underlying primary DNA sequence; these include DNA methylation, Gene silencing, and chromatin structure, [11] as well as involvement of Non-coding RNA. [12]
An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism's offspring via transgenerational stranded epigenetic inheritance. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.
Computational epigenetics uses statistical methods and mathematical modelling in epigenetic research. Due to the recent explosion of epigenome datasets, computational methods play an increasing role in all areas of epigenetic research.
H3K4me3 is an epigenetic modification to the DNA packaging protein Histone H3 that indicates tri-methylation at the 4th lysine residue of the histone H3 protein and is often involved in the regulation of gene expression. The name denotes the addition of three methyl groups (trimethylation) to the lysine 4 on the histone H3 protein.
H3K27me3 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the tri-methylation of lysine 27 on histone H3 protein.
H3K9me3 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the tri-methylation at the 9th lysine residue of the histone H3 protein and is often associated with heterochromatin.
H3K4me1 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the mono-methylation at the 4th lysine residue of the histone H3 protein and often associated with gene enhancers.
H3K36me3 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the tri-methylation at the 36th lysine residue of the histone H3 protein and often associated with gene bodies.
H3K79me2 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the di-methylation at the 79th lysine residue of the histone H3 protein. H3K79me2 is detected in the transcribed regions of active genes.
H2BK5ac is an epigenetic modification to the DNA packaging protein Histone H2B. It is a mark that indicates the acetylation at the 5th lysine residue of the histone H2B protein. H2BK5ac is involved in maintaining stem cells and colon cancer.
H4K20me is an epigenetic modification to the DNA packaging protein Histone H4. It is a mark that indicates the mono-methylation at the 20th lysine residue of the histone H4 protein. This mark can be di- and tri-methylated. It is critical for genome integrity including DNA damage repair, DNA replication and chromatin compaction.
H3K36me2 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the di-methylation at the 36th lysine residue of the histone H3 protein.
H3K36me is an epigenetic modification to the DNA packaging protein Histone H3, specifically, the mono-methylation at the 36th lysine residue of the histone H3 protein.
H3R17me2 is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the di-methylation at the 17th arginine residue of the histone H3 protein. In epigenetics, arginine methylation of histones H3 and H4 is associated with a more accessible chromatin structure and thus higher levels of transcription. The existence of arginine demethylases that could reverse arginine methylation is controversial.
H3R8me2 is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the di-methylation at the 8th arginine residue of the histone H3 protein. In epigenetics, arginine methylation of histones H3 and H4 is associated with a more accessible chromatin structure and thus higher levels of transcription. The existence of arginine demethylases that could reverse arginine methylation is controversial.
H3R2me2 is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the di-methylation at the 2nd arginine residue of the histone H3 protein. In epigenetics, arginine methylation of histones H3 and H4 is associated with a more accessible chromatin structure and thus higher levels of transcription. The existence of arginine demethylases that could reverse arginine methylation is controversial.
H4R3me2 is an epigenetic modification to the DNA packaging protein histone H4. It is a mark that indicates the di-methylation at the 3rd arginine residue of the histone H4 protein. In epigenetics, arginine methylation of histones H3 and H4 is associated with a more accessible chromatin structure and thus higher levels of transcription. The existence of arginine demethylases that could reverse arginine methylation is controversial.
H3S28P is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the phosphorylation the 28th serine residue of the histone H3 protein.
H3T45P is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the phosphorylation the 45th threonine residue of the histone H3 protein.
H3T3P is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the phosphorylation the 3rd threonine residue of the histone H3 protein.
H3T6P is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the phosphorylation of the 6th threonine residue of the histone H3 protein.