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. 2016 Jan 4;44(D1):D746-52.
doi: 10.1093/nar/gkv1045. Epub 2015 Oct 19.

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

Robert Petryszak  1 , Maria Keays  2 , Y Amy Tang  2 , Nuno A Fonseca  2 , Elisabet Barrera  2 , Tony Burdett  2 , Anja Füllgrabe  2 , Alfonso Muñoz-Pomer Fuentes  2 , Simon Jupp  2 , Satu Koskinen  2 , Oliver Mannion  2 , Laura Huerta  2 , Karine Megy  2 , Catherine Snow  2 , Eleanor Williams  2 , Mitra Barzine  2 , Emma Hastings  2 , Hendrik Weisser  3 , James Wright  3 , Pankaj Jaiswal  4 , Wolfgang Huber  2 , Jyoti Choudhary  3 , Helen E Parkinson  2 , Alvis Brazma  2
Affiliations

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

Robert Petryszak et al. Nucleic Acids Res. .

Abstract

Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons-estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: 'enrichment' in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.

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Figures

Figure 1.
Figure 1.
Baseline expression for human REG1B gene, corroborating high level of expression in pancreas across studies: FANTOM5, GTEx, Human Protein Atlas and a Proteomics study: a draft map of the human proteome, in http://www.ebi.ac.uk/gxa/genes/ENSG00000172023. The unit used for reporting expression in RNA-seq studies is FPKM, and in the proteomics study—the ‘within sample abundance’. ‘NA’ means that the tissue was not assayed in a given study.
Figure 2.
Figure 2.
Top 10 Reactome pathways enriched in the set of genes differentially expressed in the comparison of ‘interferon gamma; ankylosing spondylitis’ versus ‘none; ankylosing spondylitis’ in http://www.ebi.ac.uk/gxa/experiments/E-GEOD-11886. Two distinct groups of pathways with are visible, with thicker edges between the pathways corresponding to the greater number of shared genes, and the pathways with the highest enrichment effect size (odds-ratio) shown in red.
Figure 3.
Figure 3.
Variance of baseline expression across biological replicates in each tissue for rice gene GOS9: http://www.ebi.ac.uk/gxa/experiments/E-MTAB-2037?geneQuery = GOS9 (Please check the ‘Display variance’ radio button to see the box plots).
Figure 4.
Figure 4.
Baseline expression profile of gene family members participating in Auxin (IAA) transport pathway in a plant cell (http://wikipathways.org/index.php/Pathway:WP2940); http://www.ebi.ac.uk/gxa/experiments/E-MTAB-2039?geneQuery=OS01G0643300%09OS01G0715600%09OS01G0802700%09OS01G0856500%09OS01G0919800%09OS02G0743400%09OS03G0244600%09OS05G0447200%09OS05G0576900%09OS06G0232300%09OS06G0660200%09OS08G0529000%09OS09G0505400%09OS10G0147400%09OS11G0122800%09OS11G0137000%09OS11G0169200%09OS12G0133800.
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References

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