geWorkbench

NOTICE

This is the first release of the ARACNE program as a part of geWorkbench. It should be regarded as a beta-release. Because the ARACNE program is written in C++, its executable is separate from geWorkbench but it called through a geWorkbench interface. Executables for Windows, Linux and Macintosh PPC are included. In a future release, ARACNE code will be fully integrated into geWorkbench.

Comparison with Reverse Engineering component

The ARACNE code implements a published, well characterized method. Please see Margolin et al., Nature Protocols (2006), Vol 1 (2) p663-672 for a full description of this code and interface (http://www.nature.com/nprot/journal/v1/n2/abs/nprot.2006.106.html). The method that the Reverse Engineering component implements is similar but has not been published.

Quick Example

Most of the tutorial information in the Reverse Engineering component applies, but the GUI and steps are slightly different.

1. You must load a microarray dataset, e.g. "webmatrix2_quantile_log2_dev1.2_mv0.exp" (2226 probes).
2. Set a hub gene (e.g 1973_s_at)
3. Set the MI threshold, e.g. to 0.2
4. You can specify a location for the output adjacency matrix to be written. By default it is placed in the same folder as the input microarray data file.
5. At the bottom of the ARACNE component hit the Run button. Progress is tracked in the text box at left.

Because ARACNE is executed outside geWorkbench, it does not yet have an automatic visualization component. You must go to the Network Browser component and open the adjacency matrix there to view it.