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Contents

Gene Expression Atlas DAS Source

The Gene Expression Atlas provides gene-level expression analytics annotation data as a Distributed Annotation System (DAS) source that can be accessed with specialized DAS clients or viewed through DAS-enabled genome browsers, like Ensembl.

Distributed Annotation System

The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients.

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. Little coordination is needed among the various information providers.

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, by adding/enabling the Atlas DAS source in the http://www.ensemble.org portal:

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. Enter the "Configure this page" wizard

3. Go to "Custom Data" tab, select "Attach DAS" and specify the Atlas DAS URL (http://www.ebi.ac.uk/gxa/das), and with all other settings kept default proceed to the next step

Note: the Gene Expression Atlas DAS source is also registered in the DAS Registry. You can select the Gene Expression Atlas from the DAS Registry, bypassing the need to enter the Atlas URL manually.

4. Select the Gene Expression Atlas DAS source (it will be the only one displayed) and proceed to the next step

5. A screen confirming the successfully attached DAS source will be displayed, with only one more step remaining to view the Atlas data in Ensembl. You need to navigate to the "Configure page" tab from the confirmation screen.

6. On the "Configure page" screen you need to check the newly added DAS source ("Gene Expression Atlas") and confirm your choice by pressing the "SAVE and close" button

7. The Atlas DAS source will appear under the "External Data" menu item, and navigating there will display Atlas gene expression analytics data for the currently chosen 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. Gene expression summary

A one sentence summary of tissues, diseases, cell lines and cell types where the gene showed the strongest differential expression in multiple studies, as well as the total numbers of experiments and other conditions where the gene was found to be active.

2. Sites or conditions where the gene is differentially expressed.

The listing of all biological sites or conditions under which the gene was active together, and for each condition, the list of experiments where this condition was observed together with a list of other comparison conditions within that experiment.

3. Experiments where the gene was studied and showed differential expression.

The listing of all experiments where the gene was studied. For each experiment, a brief summary of the gene's activity as well as the overall experimental design (experimental variables and their values) is provided.

Additional Resources

 
Gene Expression Atlas 2.0.11.1- 12/23/11 3:09:34 PM