Creating a Network from a GMT file

It is possible to create a network from just a single GMT (gene set database) file.

For more information on the format of GMT files and on how to download Baderlab GMT files see Download Gene Set Files.

Warning

When importing a GMT file on its own there are no enrichment scores to use to filter the network, so all the gene sets in the file will be included in the network. If the GMT file is large this can result in a very large and highly connected network.

Open the Create EnrichmentMap Dialog by going to the Cytoscape main menu and selecting Apps > EnrichmentMap.

_images/menu.png

Click the add_button button and select Add data set manually.

_images/add_button.png

This will create a new data set named Data Set 1.

In the Analysis Type combo box select Generic.

_images/analysis_type.png

Click the Browse button browse_button next to the GMT field and select the file to use.

_images/gmt_browse.png

It is recommended that under the Number of edges section to set the slider to sparse. Otherwise it is likely to get a network that is too highly connected.

_images/build.png

Click the Build button to create the network.