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

Nucleic Acids Res 2014 Jan 4;42(Database issue):D926-32. Epub 2013 Dec 4.

European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK.

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.

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkt1270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964963PMC
January 2014
53 Reads

Publication Analysis

Top Keywords

expression atlas
16
expression
9
rna-sequencing analysis
8
analysis methods
8
microarray rna-sequencing
8
expression data
8
splice variant
8
cell types
8
gene
5
tissues cell
4
conditions tissues
4
untreated conditions
4
levels healthy
4
healthy untreated
4
types differential
4
differential gene
4
abundance levels
4
in-depth curation
4
gene expression
4
benefit in-depth
4

References

(Supplied by CrossRef)

Similar Publications