Tutorial: Visualizing Expression Data on Metabolic Pathways

I am interested in a set of experiments in TBDB. How do I map expression data from these experiments onto the metabolic overview?

TBDB now provides the ability to display expression data in the context of metabolic pathways. The "Omics Viewer" can be launched from expression data tools like "Gene Profiles", "Samples and Conditions" and "Cluster My Genes" that have the option of generating a cluster image/heat map.

For example, you may start by selecting expression data from a set of experiments using Cluster My Genes:
In the main menu item "Expression Data", select "Cluster My Genes"
From the "Conditions" tab, select a set of experiments (1), then click on "Cluster my Genes" (2).

Once the data is compiled...

...you will see a list of genes, clustered according to their expression pattern. You have the option of selecting one or more samples to view in the Omics Viewer. Then click on "Show Pathways" (3).

That will open a new window showing the Cellular Overview of the metabolic pathways in TB. The expression data for the selected experiments will be displayed as areas colored according to each gene's expression level.

Each "step" in the animation the Omics Viewer generates shows data for one of the selected samples for which data is imported into Omics Viewer. The Omics Viewer Control Panel (top left) allows you to navigate through the steps, pause and start the animation, and adjust the opacity of the underlying pathway diagram ("Base Intensity").

The Cellular Overview is fully interactive, and works similar to a Google map: you can zoom in and out using the controls on the left. Each reaction and metabolite in any pathway also presents you with a pop-up when clicked on, which provides links to further options.