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Gene Expression Atlas DAS Source

The Gene Expression Atlas provides gene-level expression results as a Distributed Annotation System (DAS) source that can be accessed with specialized DAS clients or viewed through DAS-enabled genome browsers, like Ensembl. This allows you to link to gene expression data in the Atlas from the genome browser.

Distributed Annotation System

The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences.

DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view.

More information about DAS can be found at BioDas.org: Everything DAS.


Enabling the Atlas DAS Source in the Ensembl Genome Browser

It is easy to enable the display of Gene Expression Atlas gene expression analytics annotations in the Ensembl Genome Browser:

1. Go to http://www.ensembl.org and navigate to a gene page by searching for a gene or via a direct link, for example, for human gene BRCA2: http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000139618

2. Click on the 'External data' link on the left hand side in the 'Gene-based displays' menu to select this display.

3. Then click on the 'Configure this page' button below the menu.

4. A window will appear listing the DAS sources available. Check the box for the Gene Expression Atlas. Then click on the 'tick' icon in the top right hand corner of the window to save this selection.

5. The gene page will now have a section with Gene Expression Atlas results for the selected gene.


Atlas DAS Source Details

This section explains the information you see in the Atlas DAS source. For every gene three types of expression annotations are displayed:

1. Differential expression summary

Click on the link to the Gene page in the Gene Expression Atlas.

2. Conditions where the gene is differentially expressed

These list the differential expression results (if any) for the following experimental factors (conditions)

  • organism part
  • disease
  • cell type
  • cell line
  • compound treatment
  • developmental stage
  • infection
  • phenotype

Clicking on a 'View all' link in the notes section of these conditions will take you to the Gene Expression Atlas gene page showing all the results for that condition.

3. Image

A link to an anatomogram showing heatmaps of the number of studies where the gene is over/under-expressed compared to the genes' overall mean expression level in the study. Anatomograms are available for human, mouse, rat and fly genes.

4. Provenance

This section gives information about the Gene Expression Atlas and which version the results shown are coming from.

Atlas Resources