Expression Atlas

Recommended

General Information

The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions. Gene expression data is re-analysed in-house to detect genes showing interesting baseline and differential expression patterns, allowing a user to ask questions such as "what are the genes expressed in normal human liver" and "what genes are differentially expressed between water-stressed rice plants and controls with normal watering?". The resource also features a few proteomics data sets provided by collaborators for corroboration between gene- and protein-level expression results.

Homepage http://www.ebi.ac.uk/gxa

Countries that developed this resource European Union , United Kingdom

Created in 2011

Taxonomic range

All

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: Expression Atlas; Expression Atlas; DOI: https://doi.org/10.25504/FAIRsharing.f5zx00; Last edited: Jan. 17, 2019, 10:28 a.m.; Last accessed: Sep 15 2019 8:52 p.m.

Publication for citation Expression Atlas: gene and protein expression across multiple studies and organisms. Papatheodorou I,Fonseca NA,Keays M,Tang YA,Barrera E,Bazant W,Burke M,Fullgrabe A,Fuentes AM,George N,Huerta L,Koskinen S,Mohammed S,Geniza M,Preece J,Jaiswal P,Jarnuczak AF,Huber W,Stegle O,Vizcaino JA,Brazma A,Petryszak R; Nucleic Acids Res ; 2017; 10.1093/nar/gkx1158;

This record is maintained by arrayexpress1

Record updated: Jan. 17, 2019, 10:27 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.f5zx00' by 'The FAIRsharing Team' at 10:27, 17 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
		After:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Removed:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined

	'supportLinks' has been modified:
		Before:
			FAQ|http://www.ebi.ac.uk/gxa/FAQ.html
			TeSS training|https://tess.elixir-europe.org/materials/expression-atlas-quick-tour
			help|http://www.ebi.ac.uk/gxa/help/
			wikipedia|https://en.wikipedia.org/wiki/Expression_Atlas
		After:
			FAQ|https://www.ebi.ac.uk/gxa/FAQ.html
			TeSS training|https://tess.elixir-europe.org/materials/expression-atlas-quick-tour
			contact form|https://www.ebi.ac.uk/support/gxa
			help|https://www.ebi.ac.uk/gxa/help/index.html
			online documentation|https://github.com/ebi-gene-expression-group/atlas
			online documentation|https://www.ebi.ac.uk/gxa/about.html
			twitter|@ExpressionAtlas
			wikipedia|https://en.wikipedia.org/wiki/Expression_Atlas
		Added:
			FAQ|https://www.ebi.ac.uk/gxa/FAQ.html
			contact form|https://www.ebi.ac.uk/support/gxa
			help|https://www.ebi.ac.uk/gxa/help/index.html
			online documentation|https://github.com/ebi-gene-expression-group/atlas
			online documentation|https://www.ebi.ac.uk/gxa/about.html
			twitter|@ExpressionAtlas
		Removed:
			FAQ|http://www.ebi.ac.uk/gxa/FAQ.html
			help|http://www.ebi.ac.uk/gxa/help/

	'dataProcesses' has been modified:
		Before:
			monthly release
			manual curation
			versioning by release
			web interface
			file download(tab-delimited)
			web service (JSON,XML)
		After:
			Release Notes
			Data Download
			Browse Data
		Added:
			Release Notes
			Data Download
			Browse Data
		Removed:
			monthly release
			manual curation
			versioning by release
			web interface
			file download(tab-delimited)
			web service (JSON,XML)

	'miriam_id' has been modified:
		Before: None
		After: MIR:00000379

	'publications' has been modified:
		Before:
			Gene expression atlas at the European bioinformatics institute.|Kapushesky M., Emam I., Holloway E., Kurnosov P., Zorin A., Malone J., Rustici G., Williams E., Parkinson H., Brazma A., |Nucleic Acids Res.|2010
			Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.|Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.|Nucleic Acids Res.|2014
		After:
			Gene expression atlas at the European bioinformatics institute.|Kapushesky M., Emam I., Holloway E., Kurnosov P., Zorin A., Malone J., Rustici G., Williams E., Parkinson H., Brazma A., |Nucleic Acids Res.|2010
			Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.|Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.|Nucleic Acids Res.|2014
			Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.|Petryszak R,Keays M,Tang YA,Fonseca NA,Barrera E,Burdett T,Fullgrabe A,Fuentes AM,Jupp S,Koskinen S,Mannion O,Huerta L,Megy K,Snow C,Williams E,Barzine M,Hastings E,Weisser H,Wright J,Jaiswal P,Huber W,Choudhary J,Parkinson HE,Brazma A|Nucleic Acids Res|2015
			Expression Atlas: gene and protein expression across multiple studies and organisms.|Papatheodorou I,Fonseca NA,Keays M,Tang YA,Barrera E,Bazant W,Burke M,Fullgrabe A,Fuentes AM,George N,Huerta L,Koskinen S,Mohammed S,Geniza M,Preece J,Jaiswal P,Jarnuczak AF,Huber W,Stegle O,Vizcaino JA,Brazma A,Petryszak R|Nucleic Acids Res|2017
		Added:
			Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.|Petryszak R,Keays M,Tang YA,Fonseca NA,Barrera E,Burdett T,Fullgrabe A,Fuentes AM,Jupp S,Koskinen S,Mannion O,Huerta L,Megy K,Snow C,Williams E,Barzine M,Hastings E,Weisser H,Wright J,Jaiswal P,Huber W,Choudhary J,Parkinson HE,Brazma A|Nucleic Acids Res|2015
			Expression Atlas: gene and protein expression across multiple studies and organisms.|Papatheodorou I,Fonseca NA,Keays M,Tang YA,Barrera E,Bazant W,Burke M,Fullgrabe A,Fuentes AM,George N,Huerta L,Koskinen S,Mohammed S,Geniza M,Preece J,Jaiswal P,Jarnuczak AF,Huber W,Stegle O,Vizcaino JA,Brazma A,Petryszak R|Nucleic Acids Res|2017
		Removed:

	'accessPoints' has been modified:
		Before:
			SOAP|http://www.biocatalogue.org/services/2078#operations|IntAct PSICQUIC Service
		After:
			REST|https://www.ebi.ac.uk/fg/rnaseq/api/|RNASeq-er API
		Added:
			REST|https://www.ebi.ac.uk/fg/rnaseq/api/|RNASeq-er API
		Removed:
			SOAP|http://www.biocatalogue.org/services/2078#operations|IntAct PSICQUIC Service

	'tools' has been modified:
		Before:
			iRAP||http://nunofonseca.github.io/irap/
		After:
			iRAP||http://nunofonseca.github.io/irap/
			ExpressionAtlas R Package on Bioconductor||https://www.bioconductor.org/packages/release/bioc/html/ExpressionAtlas.html
			Expression Atlas Heatmap||https://github.com/ebi-gene-expression-group/atlas-heatmap
		Added:
			ExpressionAtlas R Package on Bioconductor||https://www.bioconductor.org/packages/release/bioc/html/ExpressionAtlas.html
			Expression Atlas Heatmap||https://github.com/ebi-gene-expression-group/atlas-heatmap
		Removed:

Support

General

FAQ	GXA FAQ
contact form	GXA Contact Form
help	GXA Help
online documentation	GitHub Repository
online documentation	About Expression Atlas
twitter	@ExpressionAtlas
wikipedia	Wikipedia Entry

Additional Information

Contact	atlas-feedback@ebi.ac.uk
Identifiers.org	MIR:00000379

TeSS training resources

Expression atlas quick tour

Tools

iRAP	http://nunofonseca.github.io/irap/
ExpressionAtlas R Package on Bioconductor	https://www.bioconductor.org/packages/release/bioc/html/ExpressionAtla ...
Expression Atlas Heatmap	https://github.com/ebi-gene-expression-group/atlas-heatmap

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution 4.0 International (CC BY 4.0)

Applies to: Database software

Apache License 2.0

Data Release

Release Notes

https://www.ebi.ac.uk/gxa/release-notes.html

Data Access

Data Download	https://www.ebi.ac.uk/gxa/download.html
Browse Data	https://www.ebi.ac.uk/gxa/experiments

REST Web Services

RNASeq-er API

https://www.ebi.ac.uk/fg/rnaseq/api/

Publications

Gene expression atlas at the European bioinformatics institute.

Kapushesky M., Emam I., Holloway E., Kurnosov P., Zorin A., Malone J., Rustici G., Williams E., Parkinson H., Brazma A.,
Nucleic Acids Res. 2010

View Paper (PubMed)

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.
Nucleic Acids Res. 2014

View Paper (PubMed) View Publication

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

Petryszak R,Keays M,Tang YA,Fonseca NA,Barrera E,Burdett T,Fullgrabe A,Fuentes AM,Jupp S,Koskinen S,Mannion O,Huerta L,Megy K,Snow C,Williams E,Barzine M,Hastings E,Weisser H,Wright J,Jaiswal P,Huber W,Choudhary J,Parkinson HE,Brazma A
Nucleic Acids Res 2015

View Paper (PubMed) View Publication

Expression Atlas: gene and protein expression across multiple studies and organisms.

Papatheodorou I,Fonseca NA,Keays M,Tang YA,Barrera E,Bazant W,Burke M,Fullgrabe A,Fuentes AM,George N,Huerta L,Koskinen S,Mohammed S,Geniza M,Preece J,Jaiswal P,Jarnuczak AF,Huber W,Stegle O,Vizcaino JA,Brazma A,Petryszak R
Nucleic Acids Res 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

OmicsDI XML format

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

Credit

Record Maintainer

This record is maintained by arrayexpress1

Funds

European Commission under FP7 Grant Agreement (Government body)

Maintains

European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute) Lead

Expression Atlas

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