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Load the GISTIC Data

Choose a Genome

By default, IGV displays the chromosome and genome that you were viewing when you last exited IGV. For the tutorial:

  1. Click the genome drop-down list in the toolbar and select Human hg16 (the genome on which the GISTIC data was processed).
  2. Click the chromosome drop-down box and select chr1 (the chromosome on which the tutorial begins).

Load the Data Files

Load the GISTIC data files (download and unzip GISTIC.zip):

  1. Select File > Load from File.
  2. Load the following GISTIC data files (ctrl-click to select multiple files; Command-click on Mac):
    • PrimaryGBMs.43.centered_and_normalized.gct (gene expression data)
    • segmented_data_080520.seg (SNP copy number data)
  3. When IGV displays the following message, click OK:

    IGV can map gene expression data to probe or gene locations. In this case, because the probe locations are not available, IGV maps the expression data to gene locations. 
  4. IGV displays the data in horizontal rows called tracks.
  5. Scroll vertically through the tracks until you can see two types of tracks:

     
    6. The chromosome ideogram represents the whole chromosome. When you zoom in, a red outline will indicate the portion of the chromosome displayed.
      The ruler reflects the visible portion of the chromosome.
      Track identifiers.
      Attributes are displayed in the attributes panel. Each column is labeled with an attribute name. The colored blocks represent the attribute values. Within a column, blocks of the same color represent the same value. Hover over a block to see the value.

    Data tracks (horizontal rows) are displayed in the data panel.  Typically, each track represents one sample or experiment.

    Feature tracks (e.g. the Gene track) are displayed in the features panel.

    By default, IGV displays data and feature tracks in separate panels. However, you  can drag-and-drop tracks from one panel to the other or use the Preferences window to combine the two panels.
  6. Hover over the DATA FILE and the DATA TYPE attributes to view the data file names and data types. The gene expression data from PrimaryGBMs.43.centered_and_normalized.gct is displayed in one set of tracks and the copy number data from segmented_data_080520.seg is displayed in the other set of tracks.

Load the Sample Information File

At this point, the attributes panel shows only three default attributes: DATA FILE, DATA TYPE, and NAME. To view additional attributes for the data, load the sample information file for the tutorial data.

To load the sample information file:

  1. Select File > Load from File. IGV displays the Select Files window.
  2. Load the sample information file for the GISTIC data, Sample_info_tutorial.txt.
  3. IGV displays the attributes. Hover over the colored attribute blocks to see the attribute values.