Gaggle and Firegoose Oxygen Analysis

This tutorial guides the user through a systems-level analysis of the response in gene expression in Halobacterium salinarum NRC-1 to changes in oxygen levels. It demonstrates the capabilities of the Firegoose, a data integration extension to the Firefox browser and part of the Gaggle framework.

For readers of the Firegoose paper, part 2 of this tutorial closely follows the case study outlined in figure 5. A quick demo is also available.

Contents

Part 1 (Optional)

Derive differentially expressed genes using Gaggle

• DMV Data Matrix Viewer
• MeV Multi-experiment Viewer
• R Statistical computing environment

Part 2

Discover functional relationship using Firegoose

• Demonstrates the Firegoose and can be done independently of Part 1
• KEGG
• STRING
• DAVID
• Cytoscape

Notes

Requirements for Part 1

• Java 1.5 or greater.
• R with the R goose installed.

Note: Installing R and setting it up to communicate with the Gaggle takes some effort. For details, see the installation instructions for the R goose. R is not required for Part 2.

Requirements for Part 2

• The Mozilla Firefox web browser (version 2.0 or higher).
• Java 1.5 or greater.
• The Java browser plug-in for Mozilla Firefox.
• The Firegoose toolbar.

Previous Version

To accomodate older versions of the Gaggle (2005-11) and Firegoose (0.6.x) an older version of the tutorial is here. Most users can ignore this.

validate