Expression Atlas
The Expression Atlas is a database maintained by the European Bioinformatics Institute that provides information on gene expression patterns from RNA-Seq and Microarray studies, and protein expression from Proteomics studies.[1] The Expression Atlas allows searches by gene, splice variant, 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:
| Content | |
|---|---|
| Description | Gene expression across species and conditions |
| Data types captured | Microarray Data and other Gene Expression |
| Organisms | Human, Mouse, Rat, Fruit-fly, Chicken, Roundworm, Wild boar, Zebrafish, Cow and others. |
| Contact | |
| Research center | EMBL-EBI |
| Primary citation | PMID 31665515 |
| Release date | March 2020 |
| Access | |
| Website | www |
| Tools | |
| Web | Advanced search, bulk retrieval/download |
| Miscellaneous | |
| Data release frequency | 3 to 4 times a year |
| Curation policy | Manual curation of every study. |
Baseline Atlas
The Baseline Atlas provides information about which gene products are present (and at what abundance) under "normal" conditions. This component of the Expression Atlas consists of RNA-seq 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
References
- Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, et al. (Jan 2020). "Expression Atlas update: from tissues to single cells". Nucleic Acids Research. 48 (D1): D77–D83. doi:10.1093/nar/gkz947. PMC 7145605. PMID 31665515.
Further reading
- Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, et al. (January 2014). "Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments". Nucleic Acids Research. Oxford University Press (OUP). 42 (Database issue): D926-32. doi:10.1093/nar/gkt1270. PMC 3964963. PMID 24304889.CS1 maint: ref=harv (link)
- Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, et al. (January 2012). "Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments". Nucleic Acids Research. Oxford University Press (OUP). 40 (Database issue): D1077-81. doi:10.1093/nar/gkr913. PMC 3245177. PMID 22064864.CS1 maint: ref=harv (link)
External links
- "About Expression Atlas". European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI).