Release notes

Latest release note

Atlas release2 December 2016

Data statistics

  • Ensembl 86 / Ensembl Genomes 33 gene annotations and array design probe set mappings.

  • This release contains 3025 datasets (123194 assays), in particular:
    • 485 RNA-seq and 3 proteomics datasets, of which 121 report baseline gene expression, across a total of 30 different organisms;
    • 698 datasets reporting expression in plants;
    • 2904 datasets studying samples in 8117 differential comparisons across 31 different organisms.

New experiments

Atlas release22 September 2016

Data statistics

  • Ensembl 85 / Ensembl Genomes 32 gene annotations and array design probe set mappings.

  • This release contains 2968 datasets (110249 assays), in particular:
    • 444 RNA-seq and 2 proteomics datasets, of which 108 report baseline gene expression, across a total of 25 different organisms;
    • 632 datasets reporting expression in plants;
    • 2860 datasets studying samples in 8015 differential comparisons across 30 different organisms.

New Features

New experiments

Atlas release22 June 2016

Data statistics

  • Ensembl 84 / Ensembl Genomes 31 gene annotations and array design probe set mappings.

  • This release contains 2914 datasets (106062 assays), in particular:
    • 401 RNA-seq and 2 proteomics datasets, of which 96 report baseline gene expression, across a total of 23 different organisms;
    • 671 datasets reporting expression in plants;
    • 2818 datasets studying samples in 7863 differential comparisons across 30 different organisms.

New heatmap

  • This release launches the new style of heatmap on the gene/gene-set page. The changes include:
    • resize-able, zoom-able display
    • assigning expression levels to low, medium, high
  • Examples:

New feature: similar expression patterns

New experiments

Bioconductor package out now

Atlas release21 April 2016

  • Ensembl 84 / Ensembl Genomes 31 gene annotations and array design probe set mappings.

  • This release contains 2738 datasets (100801 assays), in particular:
    • 261 RNA-seq and 2 proteomics datasets, of which 72 report baseline gene expression, across a total of 22 different organisms;
    • 621 datasets reporting expression in plants;
    • 2666 datasets studying samples in 7496 differential comparisons across 29 different organisms.

Atlas release4 April 2016

  • Ensembl 84 / Ensembl Genomes 30 gene annotations and array design probe set mappings.

  • This release contains 2688 datasets (99162 assays), in particular:
    • 224 RNA-seq and 2 proteomics datasets, of which 60 report baseline gene expression, across a total of 21 different organisms;
    • 602 datasets reporting expression in plants;
    • 2626 datasets studying samples in 7411 differential comparisons across 28 different organisms.

Atlas release 28 January 2016

  • Ensembl 83 / Ensembl Genomes 30 gene annotations and array design probe set mappings.

  • This release contains 2620 datasets (97484 assays), in particular:
    • 167 RNA-seq and 1 proteomics dataset, of which 47 report baseline gene expression, across a total of 19 different organisms;
    • 582 datasets reporting expression in plants;
    • 2573 datasets studying samples in 7281 differential comparisons across 29 different organisms.

  • R experiment summary objects for RNA-seq datasets now use the new RangedSummarizedExperiment class from the SummarizedExperiment Bioconductor package. See the help page for more details about how to use them.

Atlas release 17 December 2015

  • Ensembl 83 / Ensembl Genomes 29 gene annotations and array design probe set mappings.

  • This release contains 2574 datasets (98278 assays), in particular:
    • 157 RNA-seq and 1 proteomics dataset, of which 46 report baseline gene expression, across a total of 19 different organisms;
    • 568 datasets reporting expression in plants;
    • 2527 datasets studying samples in 7119 differential comparisons across 26 different organisms.

  • This release launches the new gene and gene-set interface, available for species-specific gene queries or gene-set identifier queries, via Gene Ontology (GO) or Reactome IDs, e.g.
    The new pages feature faceted search in Differential expression and Baseline Expression tabs, including
    • Filtering differential expression by Species, Experiment, Variables, up or down regulation etc.
    • Ability to show/hide baseline experiments studying other conditions than just tissues, e.g. cell lines, cell types, etc.
    • Anatomograms can now be shown/hidden as required.
    Baseline experiment types, except for cell lines, can be viewed on a heatmap.

Atlas release 29 October 2015

  • Ensembl 82 / Ensembl Genomes 29 gene annotations and array design probe set mappings.

  • This release contains 2373 datasets (93057 assays)

  • In particular, this release contains:
    • 119 RNA-seq and 1 proteomics dataset, of which 43 report baseline gene expression, across a total of 17 different organisms;
    • 424 datasets reporting expression in plants;
    • 2330 datasets studying samples in 6345 differential comparisons across 25 different organisms.

Atlas release 14 October 2015

  • Ensembl 82 / Ensembl Genomes 28 gene annotations and array design probe set mappings.

  • This release contains 2162 datasets (86980 assays), including:

  • In particular, this release contains:
    • 119 RNA-seq and 1 proteomics dataset, of which 43 report baseline gene expression, across a total of 17 different organisms;
    • 410 datasets reporting expression in plants;
    • 2119 datasets studying samples in 5752 differential comparisons across 25 different organisms.

Atlas release14 September 2015

Atlas release11 August 2015

Atlas release2 July 2015

Atlas release5 June 2015

Atlas release31st March 2015

  • Ensembl 79 / Ensembl Genomes 26 gene annotations and array design probe set mappings.

  • This release contains 935 datasets, including:
    • 56 RNA-seq, of which 26 of these report baseline gene expression, across a total of 16 different organisms;
    • 261 reporting expression in plants;
    • 909 studying samples in 2306 differential comparisons across 20 different organisms.

Atlas release20th March 2015

Atlas release27th January 2015

Atlas release18th December 2014

  • Ensembl 78 / Ensembl Genomes 24 gene annotations and array design probe set mappings

  • This release contains 873 datasets, including 50 RNA-seq experiments. 23 of these report baseline gene expression, across a total of 16 different organisms. 850 datasets study samples in 2121 differential comparisons across 20 different organisms.

  • Please note that splice variant expression quantification is no longer available in Atlas. We have also replaced Cufflinks2 with HTSeq for gene expression quantification.

  • By clicking on the link highlighted on the image below, the experiment data can now by filtered by gene/protein keywords that were mined from the supporting publication by Europe PubMed Central. Click here to try it out. Filter experiment by publication genes link

Atlas release19th November 2014

  • Ensembl 77 / Ensembl Genomes 24 gene annotations and array design probe set mappings

  • This release contains 844 datasets, including 50 RNA-seq experiments. 22 of these report baseline gene expression, across a total of 16 different organisms. 822 datasets study samples in 2032 differential comparisons across 20 different organisms.

  • Plant experiments, for example our first RNA-seq maize data set, now allow users to display expression in the Gramene  genome browser.

Atlas release13th October 2014

  • Ensembl 77 gene annotations and array design probe set mappings.

  • This release contains 802 datasets, including 47 RNA-seq experiments. 21 of these report baseline gene expression, across a total of 15 different organisms. 781 datasets study samples in 1937 differential comparisons across 20 different organisms.

  • Gene pages now show a combined comparative view for gene expression across multiple baseline datasets.

    Comparative baseline gene expression view

  • hierarchical clustering button Hierarchical clustering of the top 100 most variably expressed genes is now performed for each baseline dataset.

    E-MTAB-2809 heatmap

  • Three new anatomograms are now available, for Anolis carolinensis, Xenopus tropicalis and Tetraodon nigroviridis. Image of three new anatomograms

Atlas release22nd August 2014

  • Ensembl 76 / Ensembl Genomes 23 gene annotations and array design probe set mappings;
  • 709 experiments, including 39 RNA-seq experiments (13 baseline, 26 differential), studying samples in 1684 differential comparisons and 24 organisms (see below for breakdown of comparisons per organism);
  • All Human RNA-seq experiments have been re-analysed against the new assembly (GRCh38), e.g. RNA-seq of coding RNA from tissue samples of 95 human individuals representing 27 different tissues;
  • Baseline expression levels available for genes and transcripts in 75 tissues, 21 cell lines, 7 cellular components, 39 developmental stages and 3 RNA types;
  • Quality control report button Quality control reports, e.g. FASTQ QC and Mapping, are now available for all RNA-seq experiments;
  • EFO-based autocomplete for experimental conditions is now available on the main Atlas search page. Please see 'How to search' section of Atlas help page for more details. The main search interface also now allows users to restrict search to a single organism;
  • User queries in the main Atlas search interface are expanded using the latest EFO. This means that if you search for e.g. "cancer", you will also see results with terms such as "carcinoma", "malignant tumour", and other synonyms and children of the cancer entry in EFO;
  • Gene set overlap analysis is performed using the Piano package from Bioconductor. In each differential experiment, for each comparison, enrichment of terms from GO, InterPro, and Reactome is tested for within the set of differentially expressed genes, using Fisher's exact test. Plots showing maximum top ten GO, Interpro and Reactome terms enriched within the differentially expressed genes for each comparison are now available for each differential experiment in Atlas. Please see Differential Atlas help for more information.
  • R object download button For differential expression experiments in Expression Atlas, you can now download a file containing the expression data and meta-data that you can load into R. Please see Expression Atlas data in R help for more information;
  • Differential and Baseline Expression can now be visualised on Ensembl and Ensembl Genomes Genome Browser. Please see Visualising baseline expression at Ensembl and Visualising differential expression at Ensembl for more information.
Number of differential comparisons per organism

Atlas release10th April 2014

Number of differential comparisons per experimental variable type

Atlas release5th December 2013

Welcome to the new Expression Atlas service! The old Expression Atlas and its underlying data will no longer be updated or maintained, but limited support will be offered while the process of re-curation, re-analysis and transferring of experiments to the new Expression Atlas is on-going.

We would like to thank our users for their continuous support, and encourage them to help us shape the new Expression Atlas by:

  • providing us with feedback via mailto:atlas-feedback@ebi.ac.uk or via the Atlas feedback button on the top right hand side of each page;
  • contacting us if any experiments of interest are included in the old Expression Atlas, but have not made their way into the new Expression Atlas yet. We will then prioritise their transfer.

Enjoy the new Expression Atlas!