
Exploring gene expression results across species under different biological conditions
Expression Atlas is an open science resource that gives users a powerful way to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others. Expression Atlas aims to help answering questions such as ‘where is a certain gene expressed?’ or ‘how does its expression change in a disease?’.
Expression Atlas provides gene expression results on more than 3,000 experiments (microarray and RNA-sequencing) from 40 different organisms, including metazoans and plants. Expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects can be explored in Expression Atlas. All data are manually curated, annotated to ontology terms allowing for much richer queries and re-analysed using standardised methods.
Expression Atlas visualises gene expression results using heatmaps showing gene expression levels across different biological conditions. 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.
3,166 experiments
Tools
iRAP: RNA-seq analysis tool
A flexible pipeline for RNA-seq analysis that integrates many existing tools for filtering and
mapping reads, quantifying expression and testing for differential expression. iRAP is used to
process all RNA-seq data in Expression Atlas.
RNASeq-er API: a gateway to systematically updated analysis of public RNA-Seq data
The RNASeq-er REST API provides easy access to the results of the systematically updated and
continually growing analysis of public RNA-seq data in the European Nucleotide Archive (ENA).
The analysis of each sequencing run is performed by the EMBL-EBI's Gene Expression Team using
the iRAP pipeline (see above).
Expression Atlas R Package on Bioconductor
Search and download pre-packaged data from Expression Atlas inside an R session. Raw counts are
provided for RNA-seq datasets and normalized intensities are available for microarray
experiments. Protocols describing how the data was generated and sample annotations are
contained within the downloaded R objects.
Publications
The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq dataBioinformatics, 22 March 2017.
Expression Atlas update – an integrated database of gene and protein expression in humans, animals and plants.
Nucleic Acids Research, 19 October 2015.
RNA-Seq Gene Profiling – A Systematic Empirical Comparison
PLoS One, 30 September 2014.
Expression Atlas update – a database of gene and transcript expression from microarray and sequencing-based functional genomics experiments.
Nucleic Acids Research, 4 December 2013.