Tip:
Highlight text to annotate it
X
Select a TCGA data set at http://www.gitools.org/tcga
Launch Gitools with the selected data set
Some browsers download a .jnlp file. (Launch the .jnlp file if necessar)
Gitools is being downloaded (only once per new version).
Gitools will download the requested data set.
The heatmap is created and shown as a new tab.
At the left: Details boxes and color scale
At the right: Heatmap with column and row headers.
Use mouse wheel or trackpad to move around. The scroll bar indicates your location.
The rows are genes, the columns are samples.
Right-click revleals a contextual menu: Show all unhides the hidden genes.
Only high confidence drivers are shown after the launch.
Currently 77 genes are shown (all High Confidence Drivers)
Searching a specific gene.
Matching hits will highlight in yellow.
Same search can be used for samples, located in the columns
Hitting Enter key focuses the heatmap at the next match.
The lead shows always the currently focused cell (row and column).
The detail box titles show values of the lead cell.
The values box shows the different data dimensions:
Genomic Alterations, Expression
Mutation and CNA Status
A click changes the displayed value dimension
The name in bold is the dimension currently being shown
All values of the lead position are shown as colored square and text
Rows and columns can be zoomed (when mouse over heatmap)
Zoom columns: CTRL + C + Scroll (⌘ on Mac)
Zoom rows: CTRL + R + Scroll (⌘ on Mac)
Click on a gene to select the gene row.
Shift + Click: select a range of genes
Mutually exclusive sort under: Data -> Sort
Type gene names or choose selected
The genomic alterations are now sorted by mutual exclusion
Click the top right to unselect (or use shortcut U + A)
In the row headers we can see various colored annotations:
Each color represents a driver discovery method
The row details box shows the value behind the color
The same applies for the column annotations
Annotations values in blue link to a website with revealing more details about the value
More annotations are available for samples and genes
and can be added to the heatmap headers.
Choose: Add column header
We can add more color labels to the columns
Many different annotations values are available
We choose the Glioblastoma subtype annotation
The generated color labels can be modified if needed
We see a new line in the details box and at the column headers.
The headers can be used to stratify the samples:
Right click and sort by "GBM-Subtype"
Hide sample columns for which we have no annotations
We can select a sample group according to their annotations
We can drag and drop selected columns and rows
or choose where to group them together
To see the configuration of the whole heatmap, choose the Snapshot function in the toolbar
A new tab opens with the whole static heatmap. Alternatively export to bitmap via File -> Export