Article

 

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

Downloadable Content

Download PDF
https://ir.library.oregonstate.edu/concern/articles/k930bz796

© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. The published article is available at:  http://nar.oxfordjournals.org/content/44/D1/D746

Descriptions

Attribute NameValues
Creator
Abstract
  • 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.
Resource Type
DOI
Date Available
Date Issued
Citation
  • Petryszak, R., Keays, M., Tang, Y. A., Fonseca, N. A., Barrera, E., Burdett, T., ... & Brazma, A (2016). Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Research, 44(D1), D746-D752. doi:10.1093/nar/gkv1045
Journal Title
Journal Volume
  • 44
Journal Issue/Number
  • D1
Rights Statement
Funding Statement (additional comments about funding)
  • European Molecular Biology Laboratory (EMBL) member states; National Science Foundation of USA grant to Gramene database [NSF IOS 1127112]; European Community's FP7 EurocanPlatform [260791]; BBSRC [BB/M018458/1]; CTTV; NHGRI, NHLBI; NIH Common Fund [U54-HG004028]; Wellcome Trust [WT098051]. Funding for open access charge: EMBL
Publisher
Peer Reviewed
Language
Replaces
Additional Information
  • description.provenance : Submitted by Patricia Black (patricia.black@oregonstate.edu) on 2016-04-04T14:37:03Z No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) PetryszakExpressionAtlasUpdate.pdf: 2675205 bytes, checksum: 2de537c798fc24d6920f6d14a184f72e (MD5) PetryszakExpressionAtlasUpdateSupplement.pdf: 85393 bytes, checksum: f49f61420e3bf38e2188ac5bfec09dfd (MD5)
  • description.provenance : Made available in DSpace on 2016-04-04T14:37:25Z (GMT). No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) PetryszakExpressionAtlasUpdate.pdf: 2675205 bytes, checksum: 2de537c798fc24d6920f6d14a184f72e (MD5) PetryszakExpressionAtlasUpdateSupplement.pdf: 85393 bytes, checksum: f49f61420e3bf38e2188ac5bfec09dfd (MD5) Previous issue date: 2016-01-04
  • description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2016-04-04T14:37:25Z (GMT) No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) PetryszakExpressionAtlasUpdate.pdf: 2675205 bytes, checksum: 2de537c798fc24d6920f6d14a184f72e (MD5) PetryszakExpressionAtlasUpdateSupplement.pdf: 85393 bytes, checksum: f49f61420e3bf38e2188ac5bfec09dfd (MD5)

Relationships

Parents:

This work has no parents.

Items