About the Expression Atlas
The Expression Atlas provides information on gene expression patterns under different biological conditions such as a gene knock out, a plant treated with a compound, or in a particular organism part or cell. It includes both microarray and RNA-seq data. The data is re-analysed in-house to detect interesting expression patterns under the conditions of the original experiment. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas:
- Baseline Atlas
The Baseline Atlas displays information about which gene products are present (and at what abundance) in "normal" conditions (e.g. tissue, cell type). It aims to answer questions such as
- which genes are specifically expressed in kidney?
- what is the expression pattern for gene SAA4 in normal tissues?
This component of the Expression Atlas consists of highly-curated and quality-checked RNA-seq experiments from ArrayExpress. It has data for many different animal and plant species (see the overview page for a full list). New experiments are added as they become available.
See the Baseline Atlas help page for information about how to search and interpret the results in the Baseline Atlas.
- Differential Atlas
The Differential Atlas allows users to identify genes that are up- or down-regulated in a wide variety of different experimental conditions such as yeast mutants, cadmium treated plants, cystic fibrosis or the effect on gene expression of mind-body practice.
Both microarray and RNA-seq experiments are included in the Differential Atlas. Experiments are selected from ArrayExpress and groups of samples are manually identified for comparison e.g. those with wild type genotype compared to those with a gene knock out. Each experiment is processed through our in-house differential expression statistical analysis pipeline to identify genes with a high probability of differential expression.
The Differential Atlas help page has more information about how to search and interpret the results in the Differential Atlas.
Searches enhanced by ontology-based query expansion
The Expression Atlas interface allows searches by gene, splice variant and protein attribute. Individual genes or gene sets can be searched for. Both the Baseline and Differential Atlas are queried by default.
Sample attributes and experimental conditions can also be searched for. Experimental conditions e.g. cerebellum or breast carcinoma, are mapped to ontology terms from the Experimental Factor Ontology (EFO). Mappings are made either manually by curators or automatically using EBI-developed software called Zooma. The ontology mappings allow for ontology-driven query expansion e.g. searching for 'cancer' will return matches to the keyword and also results for different types of cancer such as 'breast carcinoma' and 'acute myeloid leukemia'.
- Petryszak, R. et al. (2016) Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Research 10.1093/nar/gkv1045.
- Petryszak, R. et al. (2013) Expression Atlas update - a database of gene and transcript expression from microarray and sequencing-based functional genomics experiments. Nucleic Acids Research 10.1093/nar/gkt1270.
- Kapushesky, M. et al. (2012) Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Research 40:D1077-D1081. This paper describes the Gene Expression Atlas, from which the Expression Atlas has been developed.