Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

By R. Petryszak, M. Keays, Y. Tang, Nuno A. Fonseca, E. Barrera, Tony Burdett, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, S. Jupp, Satu Koskinen and 14 more. Nucleic Acids Res., 2015

512 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f7f131e37720f25601ba5df08bf8df2d4c71a0d0

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Expression Atlas: gene and protein expression across multiple studies and organisms (2017, methodology): “Since the last update in 2016, Expression Atlas (1) (http: //www.”
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors (2018, methodology): “In addition, we collected TF expression from TCGA (31), EMBL-EBI Expression Atlas (32), RNA-seq data published by Li et al.”
Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade (2016, background): “, 2015), and included expression profiles from normal tissues (Petryszak et al., 2016) and from relevant cancer cell lines (Barretina et al.”
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data (2016, methodology): “edu/) and EBI Expression Atlas (35), including ∼9900 miRNA-seq and ∼10 000 RNA-seq data of 32 carcinomas derived from TCGA project (36) and ∼7800 RNA-seq data of 31 normal tissues derived from GTEx project (37) in human (Table 3).”
Open Targets: a platform for therapeutic target identification and validation (2016, methodology): “These ‘widgets’ include a visualization for biological pathways developed by Reactome (47), a graphical display of RNA baseline expression developed by Expression Atlas (53), a visualization of the different protein features developed by UniProt (23) or a threedimensional protein structure display f”
OpenMS: a flexible open-source software platform for mass spectrometry data analysis (2016, background): “In addition to such gene identification, the information gained in a proteogenomic analysis pertaining to known proteins can also be used, for example, to elucidate tissue-specific protein expression levels 45 .”
GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses (2017, methodology): “org/), HPA (12) and Expression Atlas (13) have provided many useful visualization and analysis tools for gene expression analysis.”
distance correlation (methodology): “We obtain all the raw-counts for experiment E-MTAB-5174 in Expression Atlas [5] and remove the genes with zero expression variance.”