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Getting started

Here we quickly demonstrate some of the capabilities of the Firegoose toolbar for Firefox by retrieving data from three popular web sites - KEGG, STRING, and DAVID.

If you haven't installed the Firegoose, do so now. It's easy to install and uninstall.

This page contains data embedded in the Gaggle microformat. For demonstration purposes, a few genes were selected from a larger set of genes found in microarray experiments to be upregulated in the presence of oxygen in the organism Halobacterium sp. NRC-1. There are two data elements, one list of gene names in the VNG nomenclature, and a second list of the same genes using the GI naming system.

Aerobic genes (VNG gene names)

Genes found in microarray experiments to be activated under aerobic conditions.

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Aerobic genes (GI numbers)

Genes found in microarray experiments to be activated under aerobic conditions.

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Broadcasting

Broadcasting data from Firegoose to a target web site or desktop application is a simple three step process. (1) Select the data to be sent. (2) Select the target - where the message will be sent. (3) Click the “Broadcast” button.

KEGG

  1. Select “aerobic genes (VNG): Namelist(27)” in the Gaggle Data menu
  2. Select “KEGG Pathway” in the target menu
  3. Click “Broadcast

Kegg should open in a new tab as shown above. Click on some of the pathways to view the diagrams. Notice that genes and networks can be captured from KEGG and retrieved as Gaggle data types.

STRING

  1. Return to this tutorial page. The source document must be showing to perform a broadcast.
  2. Make sure “aerobic genes (VNG): Namelist(27)” is still selected in the Gaggle Data menu
  3. Select “EMBL STRING” in the target menu
  4. Click “Broadcast

Wait for the script to fill in and submit the search form. There will be a pause while STRING searches its database then a list of matching genes will appear. Click “Continue ->” to see STRING's interaction network.

At this point, one option would be to bring the STRING network into Cytoscape. To do this:

  1. Start Cytoscape with the CyGoose plugin. This webstart will automatically start Cytoscape and then the Gaggle Boss.
  2. Make sure Firegoose is connected to the Boss. Press the multicolored Gaggle button at the left end of the Firegoose toolbar. The status bar in the bottom right of the browser window should say “Firegoose: Connected”.
  3. With the STRING tab showing in Firefox, select the Gaggle Data item “Protein interactions from STRING XML”.
  4. Select the “Cytoscape” target.
  5. Click “Broadcast
  6. Wait ~10 seconds while Firegoose accesses STRING's web service.
  7. A network should appear in the Cytoscape window. Select "Layout | yFiles | Organic" to display a nicely formatted network.

DAVID

  1. Return again to this tutorial page.
  2. This time we need GI numbers so select “aerobic genes (GI): Namelist(27)” in the Data menu
  3. Select “DAVID” in the target menu
  4. Click “Broadcast
  5. When DAVID comes up in a new tab, find “Step 2: Select Identifier” in the left panel. Select “GI_ACCESSION”.
  6. Click “Submit List
  7. Try the various features of DAVID, including Functional Annotation Clustering.

Institute for Systems Biology

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