Gene List View

The Gene List view displays multiple loci side-by-side in split panes. The key difference between the Gene List view and the Regions of Interest navigator is that you can define gene lists using feature names of an annotation track, e.g. gene symbols for the RefSeq annotation track, in addition to genomic coordinates. The Gene List view loads all listed loci. You can then rearrange and remove panels from the display.

For the option to navigate the display to individual loci from a list, or to define regions of interest that you can export in BED format, see the Regions of Interest page.

To change the size of the flanking region around the gene displayed, before loading data go to View>Preferences>General>Feature flanking region and enter the base pairs or percent to display on either side of each locus.

The sections give step-by-step instructions for Gene List view features include the following.

  • Load lists of genes or loci in GMT, GRP and BED format.
  • Create and save a list from the Gene List panel.
    • Define list items using feature names that correspond to annotation tracks, such as the default Genes Track or other loaded annotation track, cytoband name, or a locus defined as  <chr>:<start>-<end>.
    • Export a list as a GMT file or access saved lists in the igv>lists folder.
  • Right-click panel headers for options, e.g. sort on data type-specific values or remove a pane from display. Drag-and-drop panes to rearrange.

Loading and Defining Gene Lists

To load or define a new gene or 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. IGV informs you of feature items without matches and continues on to display loci with matches.

My Lists

You can click Import to upload a text file containing your gene list. Load lists of genes or loci in GMT, GRP and BED format. For example, find and download GMT files from the Molecular Signatures Database.

Imported lists display organized under My lists and save to the igv>lists folder for continued future access.

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, other feature names that correspond to annotation tracks, or a locus defined as  <chr>:<start>-<end>.
  • Additionally, paste BED format file contents in to the third field.

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.