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

• Type: Article in International Scientific Journal
• Date: 2014

Authors

Petryszak, R (Author) Other; Burdett, T (Author) Other; Fiorelli, B (Author) Other; Nuno A Fonseca (Author) Other; Gonzalez Porta, M (Author) Other; Hastings, E (Author) Other; Huber, W (Author) Other; Jupp, S (Author) Other; Keays, M (Author) Other; Kryvych, N (Author) Other; McMurry, J (Author) Other; Marioni, JC (Author) Other; Malone, J (Author) Other; Megy, K (Author) Other; Rustici, G (Author) Other; Tang, AY (Author) Other; Taubert, J (Author) Other; Williams, E (Author) Other; Mannion, O (Author) Other; Parkinson, HE (Author) Other; Brazma, A (Author) Other

Journal

Title: Nucleic Acids Research

Vol. 42

Pages: D926-D932

ISSN: 0305-1048

Publisher: Oxford University Press

Indexing

ISI Web of Knowledge - 207 Citations

Other information

Authenticus ID: P-009-RQA

DOI: 10.1093/nar/gkt1270

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 7