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All Atlas files below are downloadable from ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas. Read Installation instructions for how to set up the software and database.

Date Web Application Data Distribution Update Web Update Data Comments
13.07.17 atlas-web-2.0.21.3.war atlas-data-13.07.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-13.07-ncdf.tar.Z (19GB)
13.05.03 atlas-web-2.0.20.war atlas-data-13.05.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-13.05-ncdf.tar.Z (19GB)
13.03.08 atlas-web-2.0.19.1.war atlas-data-13.02.tar.Z YES NO The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-13.02-ncdf.tar.Z (21GB)
13.03.04 atlas-web-2.0.19.war atlas-data-13.02.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-13.02-ncdf.tar.Z (21GB)
13.01.03 atlas-web-2.0.18.war atlas-data-13.01.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-13.01-ncdf.tar.Z (17GB)
12.11.08 atlas-web-2.0.17.war atlas-data-12.11.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-12.11-ncdf.tar.Z (16.6GB)
12.09.03 atlas-web-2.0.16.war atlas-data-12.09.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-12.09-ncdf.tar.Z (15.5GB)
12.07.14 atlas-web-2.0.15.war atlas-data-12.07.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-12.07-ncdf.tar.Z (16GB)
12.06.13 atlas-web-2.0.14.2.war atlas-data-12.06.tar.Z YES NO The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-12.04-ncdf.tar.Z (15.4GB)
12.06.08 atlas-web-2.0.14.1.war atlas-data-12.06.tar.Z YES NO The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-12.04-ncdf.tar.Z (15.4GB)
12.06.04 atlas-web-2.0.14.war atlas-data-12.06.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-12.04-ncdf.tar.Z (15.4GB)
12.04.23 atlas-web-2.0.13.war atlas-data-12.04.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-12.04-ncdf.tar.Z (14GB)
12.03.30 atlas-web-2.0.12.1.war atlas-data-12.03.1.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-12.03.1-ncdf.tar.Z (13.1GB)
12.03.19 atlas-web-2.0.12.war atlas-data-12.03.tar.Z YES YES The NetCDF files, excluding binary Sequence Alignment/Map (BAM) files, are in a separate file, atlas-data-12.03-ncdf.tar.Z (12.9GB)
11.12.23 atlas-web-2.0.11.1.war atlas-data-11.12.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.12-ncdf.tar.Z (455GB)
11.12.22 atlas-web-2.0.11.war atlas-data-11.12.tar.Z YES YES The NetCDF files are in a separate file, atlas-data-11.12-ncdf.tar.Z (455GB)
11.11.16 atlas-web-2.0.10.2.war atlas-data-11.11.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.11-ncdf.tar.Z (66GB)
11.11.14 atlas-web-2.0.10.1.war atlas-data-11.11.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.11-ncdf.tar.Z (66GB)
11.11.10 atlas-web-2.0.10.war atlas-data-11.11.tar.Z YES YES The NetCDF files are in a separate file, atlas-data-11.11-ncdf.tar.Z (66GB)
11.10.03 atlas-web-2.0.9.3.war atlas-data-11.08.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.08-ncdf.tar.Z (174GB)
11.09.21 atlas-web-2.0.9.2.war atlas-data-11.08.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.08-ncdf.tar.Z (174GB)
11.09.06 atlas-web-2.0.9.1.war atlas-data-11.08.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.08-ncdf.tar.Z (174GB)
11.08.24 atlas-web-2.0.9.war atlas-data-11.08.tar.Z YES YES The NetCDF files are in a separate file, atlas-data-11.08-ncdf.tar.Z (174GB)
11.07.06 atlas-web-2.0.8.1.war atlas-data-11.05.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.05-ncdf.tar.Z (?GB)
11.06.10 atlas-web-2.0.8.war atlas-data-11.05.tar.Z YES YES The NetCDF files are in a separate file, atlas-data-11.05-ncdf.tar.Z (?GB)
11.05.25 atlas-web-2.0.7.5.war atlas-data-11.04.1.tar.Z NO YES The NetCDF files are in a separate file, atlas-data-11.04-ncdf.tar.Z (41GB)
11.05.06 atlas-web-2.0.7.5.war atlas-data-11.04.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.04-ncdf.tar.Z (41GB)
11.05.04 atlas-web-2.0.7.4.war atlas-data-11.04.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.04-ncdf.tar.Z (41GB)
11.04.15 atlas-web-2.0.7.3.war atlas-data-11.04.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.04-ncdf.tar.Z (41GB)
11.04.13 atlas-web-2.0.7.2.war atlas-data-11.04.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.04-ncdf.tar.Z (41GB)
11.04.11 atlas-web-2.0.7.1.war atlas-data-11.04.tar.Z YES YES The NetCDF files are in a separate file, atlas-data-11.04-ncdf.tar.Z (41GB)
11.03.11 atlas-web-2.0.6.1.war atlas-data-11.03.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.03-ncdf.tar.Z (31GB)
04.03.11 atlas-web-2.0.6.war atlas-data-11.03.tar.Z YES YES The NetCDF files are in a separate file, atlas-data-11.03-ncdf.tar.Z (31GB)
18.02.11 atlas-web-atlas-2.0.5.1.war atlas-data-11.02.tar.Z YES NO The NetCDF files are in a separate file, atlas-data-11.02-ncdf.tar.Z (19GB)
11.02.11 “atlas-web-1-gc63c07a.war” “atlas-data-11.02.tar.Z” YES YES The NetCDF files are in a separate file, “atlas-data-11.02-ncdf.tar.Z”
09.12.10 “atlas-web-r15857.war” “atlas-data-10.12.tar.Z”: YES YES The NetCDF files are in a separate file, “atlas-data-10.12-ncdf.tar.Z”
29.10.10 “atlas-web-r15015.war” “atlas-data-10.10.1.tar.Z” YES YES The NetCDF files are in a separate file, “atlas-data-10.10.1-ncdf.tar.Z”
06.09.10 “atlas-web-r13834.war” “atlas-data-10.8.tar.Z” YES YES This is a complete data and web software release with important bug fixes in the analytics and REST APIs
17.08.10 “atlas-web-r13517.war” “atlas-data-10.6.tar.Z” YES NO This release fixes some rare data loading and DAS track issues
12.08.10 “atlas-web-r13454.war” “atlas-data-10.6.tar.Z” YES YES This is a temporary release without non differentially expressed genes in the index/database

Gene Expression Atlas 2.0.12.1

  • Contains 523 new or re-curated (since release 2.0.11) and re-loaded experiments.
  • Includes bug fixes for experiment page charts and the API output

Gene Expression Atlas 2.0.12

  • Contains 443 new or re-curated and re-loaded experiments. This is due to an on-going major effort in Atlas data clean-up, including:
    • merging similar factors, sample characteristics and their values
    • merging compound treatments, doses and units into a single value for factor ‘compound treatment’ – to make intra-experiment expression comparisons easier (e.g. http://www.ebi.ac.uk/gxa/experiment/E-TABM-12). All newly loaded units are now part of EFO ontology – to remove ambiguity in data interpretation.
  • Contains 53 RNA-seq experiments
  • Updated with Ensembl 66 annotations and design element mappings
  • Allows searching using gene signatures from GeneSigDB Data Release 4 (http://compbio.dfci.harvard.edu/genesigdb/)
  • Includes bug fixes to experiment page, main search page and minor improvements to the API functionality.

Gene Expression Atlas 2.0.11

  • 36 new RNA-seq experiments have been loaded
  • Tab-delimited data downloads off query results page have been fixed and optimised.
  • You can now view all Atlas experiments in a given species, e.g. Arabidopsis Thaliana
  • Contains Ensembl 65 annotations and design element mappings

Gene Expression Atlas 2.0.6

What’s New

  • 12 new RNA-Seq experiments have been loaded. Check out http://www.ebi.ac.uk/gxa/experiment/E-GEOD-24283 (Deep transcriptional sequencing analysis of human prostate adenocarcinoma and reference samples) for example.
  • Non-differentially expressed genes are back. Try selecting the up/down/non-d.e. option when searching anywhere in the Atlas. This shows genes whose expression did not change significantly in Atlas experiments.
  • Incremental data upgrades – if you are running a local copy of the Atlas, you can now upgrade your data to the latest public EBI release through the administration pages. Get the latest Atlas application and set the “atlas.masteratlas” parameter to http://www.ebi.ac.uk/gxa – and see the “Upstream” tab!
  • Minor: on gene pages the up/down squares on anatomograms are now clickable, with the same functionality as everywhere else.
  • Lots of internal improvements – speed, technology, statistics.

Gene Expression Atlas 2.0.5.1

Gene Expression Atlas 2.0.4 – r15857

This is an iteration on the previous release. We unloaded the erroneously added ChIP-Seq experiments and put proper RNA-Seq data from three experiments instead. Also we’ve set up initial integration with Ensembl to allow you to view RNA-seq short reads on the genome browser. This includes the second part of the experiment page redesign – box plots with nicer visualizations. More is coming in January.

Gene Expression Atlas 2.0.1 – r15015

A large data release – many renormalized Affymetrix experiments included in this one and even a couple next-generation sequencing based ones. The total number of experiments is 5670 now. Software features include new curation APIs, ability to load raw Affy data, new experiment pages (first part, second coming soon), and lots of back-end improvements.

Gene Expression Atlas 2.0

Atlas 2.0 is out. The website, http://www.ebi.ac.uk/gxa, has been updated to 2.0 as well, and we have a data release out there, too! More detailed release notes are forthcoming.

Gene Expression Atlas 2.0-rc3

What’s New

This release will be the last before the final 2.0. The following is new for this release:

End-user visible changes:

  • Human, mouse and rat anatomograms
  • Display of all gene properties on gene pages
  • Removed red/blue shading from heatmap displays
  • Support for search of genes up/down in condition X in at least 1, 2, 5, 10, 20 experiments
  • Support for search of genes up/down only in condition X (i.e. not up/down in any other condition in the same experiment)
  • Support for searching genes by design element accession and name

Internal changes:

  • New Atlas administration pages with support for batch loading experiments and array designs, running all major administration tasks and monitoring the system.
  • Support for curation-oriented views in the database schema, for editing sample/assay attributes, property value dictionaries and ontology mappings.
  • Overhauled and improved large-scale experiment loading support (1000+ assays)

Known Issues

  • Analytics only working on experimental factors with < 200 factor values

Not included in this release, but (probably) coming in the final version

  • Search and display non differentially expressed genes

Gene Expression Atlas 2.0-rc2

What’s New

  • Fixed Maven repository references and added connection to the GitHub repo

Gene Expression Atlas 2.0-rc1

What’s New

This is a candidate release of GXA 2.0. This release includes:

  • GXA Standalone Oracle Schema 2.13 & EBI ArrayExpress Gene Expression Atlas Data Release 10.2
  • GXA Standalone Web Application 2.0-rc1 with Administrative Tasks GUI

The data release (7.6GB) is accessible at ftp://ftp1.ebi.ac.uk/atlas2/AtlasData-10.2rel-2.13.tar.Z with username/password aexpress/aexpress. Please follow our Installation instructions for obtaining and configuring the Web Application.

Known Issues

There are several known issues with this release, these will be addressed in the final 2.0 build. These issues are:

  • Scalability on very large experiments has not yet been thoroughly tested
  • Array Design Files (ADF) loading is not 100% aligned with known gene property attributes
  • Administrative Tasks GUI is not completely in line with the rest of the GXA look and feel
  • Quantitation Types (QT) dictionary is incomplete and many less popular QTs will not be recognized
  • Some new Experimental Factor (EF) names are surrounded with “???” in the Web Application
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