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

Robert Petryszak,Anja Füllgrabe,Simon Jupp,Hendrik Weisser,Tony Burdett,Maria Keays,Alfonso Muñoz-Pomer Fuentes,Y Amy Tang,Nuno A Fonseca,Mitra Barzine,Catherine Snow,Pankaj Jaiswal,Laura Huerta,Satu Koskinen,Oliver Mannion,Emma Hastings,Eleanor Williams,Elisabet Barrera,Wolfgang Huber,Helen Parkinson ,Karyn Mégy ,James C Wright ,Jyoti S Choudhary ,Alvis Brāzma

doi:10.1093/nar/gkv1045

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.

Highlights

Expression Atlas consists of two components––(i) a large baseline expression component (http://www.ebi.ac.uk/gxa/ baseline/experiments), reporting transcript abundance estimates for each gene in healthy or untreated tissues, cell types or cellular components from carefully selected large RNAseq experiments and (ii) information about the changes
Expression Atlas [2] is a further development of its predecessor, Gene Expression Atlas [1] launched by the European Bioinformatics Institute (EMBL-EBI) in 2008, and continues its original remit as a value-added database for querying gene expression across tissues, cell types and cell lines under various biological conditions
Expression Atlas is developed with a view to accommodating data from multi-omics experiments; the first proteomics data set has been included in 2015

Summary

Introduction

Expression Atlas consists of two components––(i) a large baseline expression component (http://www.ebi.ac.uk/gxa/ baseline/experiments), reporting transcript abundance estimates for each gene in healthy or untreated tissues, cell types or cellular components from carefully selected large RNAseq experiments and (ii) information about the changes Atlas contains 389 experiments studying plants in 11 species (http://www.ebi.ac.uk/gxa/plant/experiments), e.g. rice, wheat, maize and Arabidopsis, including 7 baseline studies reporting expression in tissues, strains and cultivars.

Results

Conclusion