TY - JOUR
AU - Robert Petryszak
AU - Maria Keays
AU - Amy Tang
AU - Nuno Fonseca
AU - Elisabet Barrera
AU - Tony Burdett
AU - Anja Füllgrabe
AU - Alfonso Fuentes
AU - Simon Jupp
AU - Satu Koskinen
AU - Oliver Mannion
AU - Laura Huerta
AU - Karine Megy
AU - Catherine Snow
AU - Eleanor Williams
AU - Mitra Barzine
AU - Emma Hastings
AU - Hendrik Weisser
AU - James Wright
AU - Pankaj Jaiswal
AU - Wolfgang Huber
AU - Jyoti Choudhary
AU - Helen Parkinson
AU - Alvis Brazma
AB - 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.
BT - Nucleic acids research
C1 - http://www.ncbi.nlm.nih.gov/pubmed/26481351?dopt=Abstract
DA - 2016 Jan 4
DO - 10.1093/nar/gkv1045
IS - D1
J2 - Nucleic Acids Res.
LA - eng
N2 - 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.
PY - 2016
SP - D746
EP - 52
T2 - Nucleic acids research
TI - Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants.
VL - 44
SN - 1362-4962
ER -