Managing Gene Sets

Jeanette McCarthy -

Managing Gene Sets

Gene sets represent groups of genes categorized by disease processes, drug interactions, pathways, or just panels that focus on genes of interest. The sets may be derived from using research tools (such as GeneGo, etc.) or knowledge derived from reading publications.

Fabric Genomics provides a number of curated Gene Sets based on disease areas, pathways, and drug activity. Users can also create their own Gene Sets for use in Opal. Gene Sets are automatically shared with everyone in your Workspace.

To manage your Gene Sets, go to the Home Page and select "Gene Sets”.

Manage Gene Sets page

To create a new Gene Set, click the “New Gene Set” button. In the resulting “New Gene Set” dialog enter a name for the set, provide a description, specify the type, and then click the “Save Gene Set” button.

New Gene Set dialog

To add genes to the new set, click the “Actions” dropdown menu adjacent to your Gene Set.

Select the “Add Genes” item from the menu. In the ensuing dialog type or paste one or more gene symbols separated by spaces or commas then click the “Next >” button.

For best performance use official gene symbols as defined by the HGNC nomenclature committee (the system attempts to resolve all synonyms.)

Opal will validate the entered symbols and display a list of official gene symbols and corresponding names. An error message will be displayed for symbols Opal cannot match against our reference dataset, ambiguous symbols that map to multiple genes, or duplicate symbols that already exist in the set. You can add other symbols by clicking on the “Back <” button to repeat the process. To save your changes click on the “Save Changes” button.

Add Genes Dialog - Step 2

You can add or remove genes, or delete a gene set, by selecting the relevant items in the “Actions” dropdown menu.

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