Gene List View

The Gene Lists functionalities in IGV allow you to view lists of genes or loci side-by-side irrespective of their genomic location.  

Loading/Defining Gene Lists

To load or define a new gene/locus list, select Regions >Gene Lists....

This opens a window for selecting an existing list or creating a new list. 

You can load an existing gene list from this window.  To do so, select the gene list and click View.

My Lists

You can click Import to upload a text file containing your gene list. You can find and download files (in GMT format) with multiple gene lists in them at the Molecular Signatures Database.

You can also click New to create a new gene list.  This opens a dialog in which you can enter a name, description, and your list of genes or regions.  Entries in a gene list can be a gene symbol, cytoband name, or a locus defined as  <chr>:<start>-<end>.

When you click OK, this gene list will be filed under My lists in the gene lists window. Select that group, then select your new gene list, and click Load to view it.

You can save your gene list as a .gmt file by clicking Export.

To make a copy of a gene list, select an existing gene list and click Copy.  This opens a window in which you can edit the list. When you click OK after editing it, this copied list will be filed under My lists.

You can edit or delete anything in My lists.

The Loaded List

When you load a gene list, the main IGV window splits vertically to show the currently-loaded data for all the regions of the gene list.

Each vertical panel can be individually zoomed by double-clicking in that space.

Sorting by Panel

Right-click on a gene name in the panel header to bring up the sort menu. This menu will vary depending on data type.

The following image illustrates what happens if you select Sort by amplification in the KRAS panel.

Removing or Rearranging Panels

To remove a panel, right-click on the panel header and select Remove panel.

Panels can be rearranged by drag and drop.  Click on the grey header bar at the top of the panel and drag it to its new position.  For example, in the figure below KRAS has been dropped between RAC1 and RAC2.

Changing the View

To return to the original view of the gene (that is, not zoomed), right-click the name/cytoband panel at the top of the pane you want to reset and select Reset panel to '[gene name]'.

To return to the “normal view”, double-click the name/cytoband panel at the top of any of the panes, or right-click in a name/cytoband panel and select Switch to standard view.

Viewing Gene Networks

For more information see Viewing Gene Networks in the cBio Portal.