Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jan 4;46(D1):D246-D251.
doi: 10.1093/nar/gkx1158.

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

Irene Papatheodorou  1 , Nuno A Fonseca  1 , Maria Keays  1 , Y Amy Tang  1 , Elisabet Barrera  1 , Wojciech Bazant  1 , Melissa Burke  1 , Anja Füllgrabe  1 , Alfonso Muñoz-Pomer Fuentes  1 , Nancy George  1 , Laura Huerta  1 , Satu Koskinen  1 , Suhaib Mohammed  1 , Matthew Geniza  2 , Justin Preece  2 , Pankaj Jaiswal  2 , Andrew F Jarnuczak  1 , Wolfgang Huber  1 , Oliver Stegle  1 , Juan Antonio Vizcaino  1 , Alvis Brazma  1 , Robert Petryszak  1
Affiliations

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

Irene Papatheodorou et al. Nucleic Acids Res. .

Abstract

Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Exploring genes with similar expression pattern to SMH1 in six different tissues of Zea mays. (To reproduce the Figure, please click on ‘Add similarly expressed genes’ in https://www.ebi.ac.uk/gxa/experiments/E-MTAB-3826/Results?specific=true&geneQuery=%255B%257B%2522value%2522%253A%2522SMH1%2522%252C%2522category%2522%253A%2522symbol%2522%257D%255D&filterFactors=%257B%257D&cutoff=%257B%2522value%2522%253A0.5%257D&unit=%2522TPM%2522).
Figure 2.
Figure 2.
The new heatmap, includes more functionality for sorting and filtering data sets. Here, we show an example of the constituent expression of human gene REG1B across tissues in different baseline experiments (https://www.ebi.ac.uk/gxa/genes/ENSG00000172023).
See this image and copyright information in PMC

References

    1. Petryszak R., Keays M., Tang Y.A., Fonseca N.A., Barrera E., Burdett T., Füllgrabe A., Fuentes A.M., Jupp S., Koskinen S. et al. . Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res. 2016; 44:D746–D752. - PMC - PubMed
    1. Kolesnikov N., Hastings E., Keays M., Melnichuk O., Tang Y.A., Williams E., Dylag M., Kurbatova N., Brandizi M., Burdett T. et al. . ArrayExpress update—simplifying data submissions. Nucleic Acids Res. 2015; 43:D1113–D1116. - PMC - PubMed
    1. Barrett T., Wilhite S.E., Ledoux P., Evangelista C., Kim I.F., Tomashevsky M., Marshall K.A., Phillippy K.H., Sherman P.M., Holko M. et al. . NCBI GEO: archive for functional genomics data sets–update. Nucleic Acids Res. 2013; 41:D991–D995. - PMC - PubMed
    1. Toribio A.L., Alako B., Amid C., Cerdeño-Tarrága A., Clarke L., Cleland I., Fairley S., Gibson R., Goodgame N., Ten Hoopen P. et al. . European Nucleotide Archive in 2016. Nucleic Acids Res. 2017; 45:D32–D36. - PMC - PubMed
    1. Vizcaíno J.A., Csordas A., Del-Toro N., Dianes J.A., Griss J., Lavidas I., Mayer G., Perez-Riverol Y., Reisinger F., Ternent T. et al. . 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 2016; 44:11033. - PMC - PubMed

Publication types