Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Jan;42(Database issue):D926-32.
doi: 10.1093/nar/gkt1270. Epub 2013 Dec 4.

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Robert Petryszak  1 , Tony Burdett, Benedetto Fiorelli, Nuno A Fonseca, Mar Gonzalez-Porta, Emma Hastings, Wolfgang Huber, Simon Jupp, Maria Keays, Nataliya Kryvych, Julie McMurry, John C Marioni, James Malone, Karine Megy, Gabriella Rustici, Amy Y Tang, Jan Taubert, Eleanor Williams, Oliver Mannion, Helen E Parkinson, Alvis Brazma
Affiliations

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Robert Petryszak et al. Nucleic Acids Res. 2014 Jan.

Abstract

Expression Atlas (http://www.ebi.ac.uk/gxa) is a value-added database providing information about gene, protein and splice variant expression in different cell types, organism parts, developmental stages, diseases and other biological and experimental conditions. The database consists of selected high-quality microarray and RNA-sequencing experiments from ArrayExpress that have been manually curated, annotated with Experimental Factor Ontology terms and processed using standardized microarray and RNA-sequencing analysis methods. The new version of Expression Atlas introduces the concept of 'baseline' expression, i.e. gene and splice variant abundance levels in healthy or untreated conditions, such as tissues or cell types. Differential gene expression data benefit from an in-depth curation of experimental intent, resulting in biologically meaningful 'contrasts', i.e. instances of differential pairwise comparisons between two sets of biological replicates. Other novel aspects of Expression Atlas are its strict quality control of raw experimental data, up-to-date RNA-sequencing analysis methods, expression data at the level of gene sets, as well as genes and a more powerful search interface designed to maximize the biological value provided to the user.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
The RNA-seq processing pipeline used to generate data for Expression Atlas. The experimental metadata is retrieved from ArrayExpress. The raw FASTQ files, retrieved from European Nucleotide Archive, undergo a quality control procedure via FASTQC package to remove low-quality reads and uncalled bases. Subsequently, contaminated reads (e.g. bacterial in the cases of vertebrate samples) are removed. TopHat 1 is used for mapping the reads to the reference genome, Cufflinks 1 quantifies baseline expression for genes and transcripts and HTseq quantifies expression used for subsequent differential expression analysis with DESeq. The final (summarized) baseline expression count for a gene in a condition is a median across first technical replicates, then across biological replicates corresponding to that condition.
Figure 2.
Figure 2.
Example baseline expression experiment page, with help annotations—Illumina Body Map. (For further information see: http://www.ebi.ac.uk/gxa/help/baseline-atlas.html).
Figure 3.
Figure 3.
Example differential expression page, with help annotations—Transcription profiling by array of Drosophila melanogaster CDK8 and Cyclin C homozygous mutants, determined using ‘Affymetrix GeneChip Drosophila Genome 2.0 Array’. (For further information see: http://www.ebi.ac.uk/gxa/help/differential-atlas.html). Genes that were called as differentially expressed at FDR < 0.05 are shown in red in the MA plot.
Figure 4.
Figure 4.
Baseline expression on summary page example for human BRCA1 gene: http://www.ebi.ac.uk/gxa/genes/ENSG00000012048.
Figure 5.
Figure 5.
Differential expression on summary page for human BRCA1 gene: http://www.ebi.ac.uk/gxa/genes/ENSG00000012048.
See this image and copyright information in PMC

Similar articles

  • Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
    Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A. Petryszak R, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D746-52. doi: 10.1093/nar/gkv1045. Epub 2015 Oct 19. Nucleic Acids Res. 2016. PMID: 26481351 Free PMC article.
  • Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.
    Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A. Kapushesky M, et al. Nucleic Acids Res. 2012 Jan;40(Database issue):D1077-81. doi: 10.1093/nar/gkr913. Epub 2011 Nov 7. Nucleic Acids Res. 2012. PMID: 22064864 Free PMC article.
  • ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.
    Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A. Parkinson H, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D1002-4. doi: 10.1093/nar/gkq1040. Epub 2010 Nov 10. Nucleic Acids Res. 2011. PMID: 21071405 Free PMC article.
  • Gene expression atlas at the European bioinformatics institute.
    Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A. Kapushesky M, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D690-8. doi: 10.1093/nar/gkp936. Epub 2009 Nov 11. Nucleic Acids Res. 2010. PMID: 19906730 Free PMC article.
  • ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.
    Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. Parkinson H, et al. Nucleic Acids Res. 2009 Jan;37(Database issue):D868-72. doi: 10.1093/nar/gkn889. Epub 2008 Nov 10. Nucleic Acids Res. 2009. PMID: 19015125 Free PMC article.
See all similar articles

Cited by

See all "Cited by" articles

References

    1. Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, et al. Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res. 2012;40:D1077–D1081. - PMC - PubMed
    1. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, et al. ArrayExpress update–trends in database growth and links to data analysis tools. Nucleic Acids Res. 2013;41:D987–D990. - PMC - PubMed
    1. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, et al. NCBI GEO: archive for functional genomics data sets—10 years on. Nucleic Acids Res. 2011;39:D1005–D1010. - PMC - PubMed
    1. Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H. Modeling sample variables with an Experimental Factor Ontology. Bioinformatics. 2010;26:1112–1118. - PMC - PubMed
    1. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011;39:D152–D157. - PMC - PubMed

Publication types

-