Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons-estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: 'enrichment' in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK rpetry@ebi.ac.uk.
Robert
R
Petryszak
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Maria
http://orcid.org/0000-0003-2034-601X
M
Keays
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Y Amy
YA
Tang
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Nuno A
http://orcid.org/0000-0003-4832-578X
NA
Fonseca
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Elisabet
http://orcid.org/0000-0002-7245-9692
E
Barrera
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Tony
http://orcid.org/0000-0002-2513-5396
T
Burdett
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Anja
http://orcid.org/0000-0002-8674-0039
A
Füllgrabe
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Alfonso Muñoz-Pomer
AM
Fuentes
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Simon
http://orcid.org/0000-0002-0643-3144
S
Jupp
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Satu
S
Koskinen
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Oliver
O
Mannion
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Laura
http://orcid.org/0000-0002-8748-599X
L
Huerta
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Karine
K
Megy
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Catherine
C
Snow
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Eleanor
E
Williams
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Mitra
M
Barzine
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Emma
http://orcid.org/0000-0001-9927-8560
E
Hastings
Welcome Trust Sanger Institute, Hinxton, UK.
Hendrik
H
Weisser
Welcome Trust Sanger Institute, Hinxton, UK.
James
J
Wright
Oregon State University, Corvallis, USA.
Pankaj
P
Jaiswal
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Wolfgang
W
Huber
Welcome Trust Sanger Institute, Hinxton, UK.
Jyoti
J
Choudhary
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Helen E
HE
Parkinson
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
Alvis
A
Brazma
D000818:Animals; D045744:Cell Line, Tumor; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D010944:Plants / Q000235:genetics / Q000378:metabolism*; D011506:Proteins / Q000378:metabolism*; D040901:Proteomics; D014584:User-Computer Interface
D011506:Proteins