title: 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.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK.
authors.forename: Robert
authors.initials: R
authors.lastname: Petryszak
authors.forename: Tony
authors.initials: T
authors.lastname: Burdett
authors.forename: Benedetto
authors.initials: B
authors.lastname: Fiorelli
authors.forename: Nuno A
authors.initials: NA
authors.lastname: Fonseca
authors.forename: Mar
authors.initials: M
authors.lastname: Gonzalez-Porta
authors.forename: Emma
authors.initials: E
authors.lastname: Hastings
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Huber
authors.forename: Simon
authors.initials: S
authors.lastname: Jupp
authors.forename: Maria
authors.initials: M
authors.lastname: Keays
authors.forename: Nataliya
authors.initials: N
authors.lastname: Kryvych
authors.forename: Julie
authors.initials: J
authors.lastname: McMurry
authors.forename: John C
authors.initials: JC
authors.lastname: Marioni
authors.forename: James
authors.initials: J
authors.lastname: Malone
authors.forename: Karine
authors.initials: K
authors.lastname: Megy
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rustici
authors.forename: Amy Y
authors.initials: AY
authors.lastname: Tang
authors.forename: Jan
authors.initials: J
authors.lastname: Taubert
authors.forename: Eleanor
authors.initials: E
authors.lastname: Williams
authors.forename: Oliver
authors.initials: O
authors.lastname: Mannion
authors.forename: Helen E
authors.initials: HE
authors.lastname: Parkinson
authors.forename: Alvis
authors.initials: A
authors.lastname: Brazma
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D023281:Genomics; D006801:Humans; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D059368:RNA Isoforms / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D011506:Proteins; D059368:RNA Isoforms