databases > DOI:10.25504/FAIRsharing.f5zx00

ready Expression Atlas

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General Information
The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions in a variety of species. 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 features proteomics data sets provided by collaborators for corroboration between gene- and protein-level expression results. The latest component, Single Cell Expression Atlas, systematically reanalyses and visualises single cell RNA-sequencing datasets and helps answering questions like in what cell population a gene can act as a marker gene.

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

Countries that developed this resource Austria , Belgium , Croatia , Czech Republic , Denmark , Finland , France , Germany , Greece , Hungary , Iceland , Israel , Italy , Lithuania , Luxembourg , Malta , Montenegro , Netherlands , Norway , Portugal , Republic of Ireland , Slovakia , Spain , Sweden , Switzerland , United Kingdom

Created in 2011

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How to cite this record FAIRsharing.org: Expression Atlas; Expression Atlas; DOI: https://doi.org/10.25504/FAIRsharing.f5zx00; Last edited: Feb. 11, 2020, 8:10 p.m.; Last accessed: Mar 30 2020 2:22 a.m.

Publication for citation  Expression Atlas update: from tissues to single cells Irene Papatheodorou, Pablo Moreno, Jonathan Manning, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova, Nuno A Fonseca, Anja Füllgrabe, Matthew Green, Ni Huang, Laura Huerta, Haider Iqbal, Monica Jianu, Suhaib Mohammed, Lingyun Zhao, Andrew F Jarnuczak, Simon Jupp, John Marioni, Kerstin Meyer, Robert Petryszak, Cesar Augusto Prada Medina, Carlos Talavera-López, Sarah Teichmann, Juan Antonio Vizcaino, Alvis Brazma; Nucleic Acids Research ; 2019; 0.1093/nar/gkz947;


This record is maintained by arrayexpress1

Record updated: Feb. 11, 2020, 8:08 p.m. by The FAIRsharing Team.

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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
Expression Atlas web application (core components) https://github.com/ebi-gene-expression-group/atlas-web-core
Expression Atlas web application (bulk components) https://github.com/ebi-gene-expression-group/atlas-web-bulk
Expression Atlas web application (single cell components) https://github.com/ebi-gene-expression-group/atlas-web-single-cell

Access / Retrieve Data

Conditions of Use

Applies to: Data use Applies to: Database software

Data Release

Data Download https://www.ebi.ac.uk/gxa/download.html
Release Notes https://www.ebi.ac.uk/gxa/release-notes.html

Data Access

Browse Bulk Data https://www.ebi.ac.uk/gxa/experiments
Browse Single Cell Data https://www.ebi.ac.uk/gxa/sc/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

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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

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Expression Atlas update: from tissues to single cells

Irene Papatheodorou, Pablo Moreno, Jonathan Manning, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova, Nuno A Fonseca, Anja Füllgrabe, Matthew Green, Ni Huang, Laura Huerta, Haider Iqbal, Monica Jianu, Suhaib Mohammed, Lingyun Zhao, Andrew F Jarnuczak, Simon Jupp, John Marioni, Kerstin Meyer, Robert Petryszak, Cesar Augusto Prada Medina, Carlos Talavera-López, Sarah Teichmann, Juan Antonio Vizcaino, Alvis Brazma
Nucleic Acids Research 2019

View Paper (PubMed) View Publication

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