Epigenomics database at the National Center for Biotechnology
Information was a database for whole-genome epigenetics data sets.
It was retired on 1 June 2016.
1.1 Content of
1.2 Database use
1.2.1 Experiment search
1.2.2 Sample search
1.2.3 Database navigation and usage help resources
3 The epigenome
4 See also
6 External links
Epigenomics database of the National Center for Biotechnology
Information (NCBI) at the
National Institutes of Health
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. 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.
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). The Gene
Expression Omnibus is a data system for high-throughput genomic data
that is generated from microarray and next-generation sequencing
technologies. 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
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. 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. 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.
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. 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. Experiment records contain a unique accession number that
includes a prefix 'ESS'.
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.
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
Database navigation and usage help resources
There are many available resources online for help in navigating and
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. There are also guides to navigation of the
database aimed at specific researchers and fields of study, such as
stem cell research.
In 2007 the
National Institutes of Health
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. These epigenetic maps are intended to provide resources for
studies of epigenetic events that underline human development,
diversity, and disease. For similar efforts see the ENCODE
DNA Elements) Project, whose initiatives are
complementary to the Roadmap
Main article: Epigenome
The epigenome consists of a record of the chemical changes to the DNA
Histone proteins of an organism. These chemical changes influence
gene expression across many tissue types and developmental stages.
These epigenetic changes involve methods of altering gene expression
that do not involve changes in the underlying primary
DNA methylation, Gene silencing, and chromatin
structure, as well as involvement of Non-coding RNA.
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