Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Abstract

Expression Atlas (http://www.ebi.ac.uk/gxa) is a value-added database providing information about gene, protein and splice variant expression in different cell types, organism parts, developmental stages, diseases and other biological and experimental conditions. The database consists of selected high-quality microarray and RNA-sequencing experiments from ArrayExpress that have been manually curated, annotated with Experimental Factor Ontology terms and processed using standardized microarray and RNA-sequencing analysis methods. The new version of Expression Atlas introduces the concept of ‘baseline’ expression, i.e. gene and splice variant abundance levels in healthy or untreated conditions, such as tissues or cell types. Differential gene expression data benefit from an in-depth curation of experimental intent, resulting in biologically meaningful ‘contrasts’, i.e. instances of differential pairwise comparisons between two sets of biological replicates. Other novel aspects of Expression Atlas are its strict quality control of raw experimental data, up-to-date RNA-sequencing analysis methods, expression data at the level of gene sets, as well as genes and a more powerful search interface designed to maximize the biological value provided to the user.

Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris

“…In total, these three segments harbour 58 transcripts of which 39 are expressed in skin 11 . TGFB2 is the closest gene to the association signal at 1q41, located 226 kb from the lead SNP rs1159268.…”

Expression of NGF, BDNF and their receptors in subcutaneous adipose tissue of lactating cows

“…2). Although NGF mRNA was clearly expressed in human, an examination of the Expression Atlas database (Petryszak et al, 2013) revealed no indication of TRKA mRNA expression in human and bovine adipose tissue. A possible explanation would be that the TrkA protein enters the adipose cells through the signaling endosomes produced by peripheral axons of neurons.…”

Regulatory Insight into the European Human Pluripotent Stem Cell Registry

“…The integration of all these different data and annotations in a searchable database requires new bioinformatics instruments and ontologies, which also enable direct interaction with existing resources holding, for example, annotated gene expression data [18,19].…”