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. 2018 Jan 4;46(D1):D246-D251.
doi: 10.1093/nar/gkx1158.

Expression Atlas: Gene and Protein Expression Across Multiple Studies and Organisms

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Free PMC article

Expression Atlas: Gene and Protein Expression Across Multiple Studies and Organisms

Irene Papatheodorou et al. Nucleic Acids Res. .
Free PMC article

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.

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).

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