The Expression Atlas is a
database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...
maintained by the
European Bioinformatics Institute
The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wel ...
that provides information on
gene expression
Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...
patterns from
RNA-Seq
RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also k ...
and
Microarray
A microarray is a multiplex (assay), multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a Substrate (materials science), solid substrate—usu ...
studies, and protein expression from
Proteomics
Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replicatio ...
studies.
The Expression Atlas allows searches by
gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
,
splice variant
Alternative splicing, alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to produce different splice variants. For example, some exons of a gene may be included ...
, protein attribute, disease, treatment or organism part (cell types/tissues). Individual genes or gene sets can be searched for. All datasets in Expression Atlas have its metadata manually curated and its data analysed through standardised analysis pipelines. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas:
Baseline Atlas
The Baseline Atlas provides information about which
gene product
A gene product is the biochemical material, either RNA or protein, resulting from the expression of a gene. A measurement of the amount of gene product is sometimes used to infer how active a gene is. Abnormal amounts of gene product can be corre ...
s are present (and at what abundance) under "normal" conditions. This component of the Expression Atlas consists of
RNA-seq
RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also k ...
experiments from ArrayExpress repositories. It aims to answer questions such as:
* Which genes are specifically expressed in kidney?
* What is the expression pattern for gene
SAA4 in normal tissues?
Differential Atlas
The Differential Atlas allows users to identify genes that are up- or down-regulated in different experimental conditions.
See also
*
Human Protein Atlas
The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometr ...
*
The Cancer Genome Atlas
The Cancer Genome Atlas (TCGA) is a project to catalogue the genomic alterations responsible for cancer using genome sequencing and bioinformatics. The overarching goal was to apply high-throughput genome analysis techniques to improve the abili ...
References
Further reading
*
*
External links
* {{cite web , title = About Expression Atlas , url = http://www.ebi.ac.uk/gxa/about.html , publisher = European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI)
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