RGD Reference Report - Expression Atlas: gene and protein expression across multiple studies and organisms. - Rat Genome Database

Send us a Message



 Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap)  (beta) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer) Overgo Probe Designer
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources

Expression Atlas: gene and protein expression across multiple studies and organisms.

Authors: Papatheodorou, Irene  Fonseca, Nuno A  Keays, Maria  Tang, Y Amy  Barrera, Elisabet  Bazant, Wojciech  Burke, Melissa  Füllgrabe, Anja  Fuentes, Alfonso Muñoz-Pomer  George, Nancy  Huerta, Laura  Koskinen, Satu  Mohammed, Suhaib  Geniza, Matthew  Preece, Justin  Jaiswal, Pankaj  Jarnuczak, Andrew F  Huber, Wolfgang  Stegle, Oliver  Vizcaino, Juan Antonio  Brazma, Alvis  Petryszak, Robert 
Citation: Papatheodorou I, etal., Nucleic Acids Res. 2018 Jan 4;46(D1):D246-D251. doi: 10.1093/nar/gkx1158.
RGD ID: 18182930
Pubmed: PMID:29165655   (View Abstract at PubMed)
PMCID: PMC5753389   (View Article at PubMed Central)
DOI: DOI:10.1093/nar/gkx1158   (Journal Full-text)

Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions.




Additional Information