GRG-X Help/Tutorial

The Grassius Regulatory Grid eXplorer is a web application for visually accessing the regulatory networks of several species of plants.

Search for a transcription factor

To search for a transcription factor first select the species you want to browse.

Then, just start typing its name or locus id into the search box.

When the gene you are looking for appears in the list, click on it. This will bring up a network of that gene and those associated with it. The gene you clicked on will be larger than the others.

Alternately, you may simply press enter when you have typed your query.

View and manipulate the network

You can select nodes and edges by clicking (shift-clicking for multiple). This will allow you to view information about and perform certain actions on these objects. If you navigate to the "Genes" tab on the sidebar, you can view information about the selected genes, delete them, deselect them (which can also be done by clicking or shift-clicking again), or find and display their first neighbors from the database. The "Interactions" tab contains information about the selected interactions, and offers an option to deselect them.

You can also change the layout of the graph. "Compound Nodes" need only be selected if the graph contains compound nodes. It is usually necessary in that case, but experimenting with the other layouts can still produce satisfactory results.

Get data into the GRG-X

You can upload *.graphml, *.xgmml files, and *.sif network files (though the SIF format is somewhat limited). To do so, select a file from your computer with the file input, then click "Submit this file." Note that this will remove any elements already in the graph, so if you plan to upload a file, do so before adding or searching for more.

You can also create custom nodes. To do so, click "Create Node," and a dialog box will appear. The only mandatory fields are the locus ids of both nodes. Note that the GRG-X will recognize when you have typed existing locus ids and doesn't add duplicate nodes, only the relationship and non-duplicate nodes.

Save your work

One of the helpful features of the GRG-X is the ability to save the content of your graph, or save an image of it. To do this, just select the format you would like to download in and click the "Go!" button. If you want a file to save your work to continue later, select ".xgmml" or ".graphml". If you would like to download an image, select the format you wish to download in. Choose ".sif" only if you need it for something (you probably won't).