1. TUTORIAL - ANALYZE YOUR MODULES
Use Gitools to analyze your
own modules and find out
if they are enriched for
genes significantly altered
in different cancer types

2. Note, a module set is a group of modules or gene sets. A
module set can contain one or several modules.
In the example for this tutorial we are going to analyze a
module set with six modules. Each module is a list of
genes expressed differentially during human cell cycle
phases (obtained from Whitfield et al, Mol Biol Cell
2002).
We are going to test if the genes in each module are
significantly up-regulated in different tumor types.
The format of the file must be
with two columns tab separated.
The second column defines the
module and the first the gene in
that module

3. STEP 1
Go to www.gitools.org
& Click Launch to start
using Gitools application

4. STEP 2
Click here to import
data from IntOGen

5. STEP 3
Select Matrix and click
Next

6. From IntOGen you can download Onco
Combinations, results combining several
experiments of the same tumor type, or
Experiments, results experiment by
experiment. Also you can get results from 4
different types of alterations (gain, loss,
upreg and downreg).
For this tutorial we will use the Onco
Combinations for upreg.
STEP 4
Select Onco
Combinations and upreg

7. ALL in Morphology means that
samples are grouped independently
of their morphology type.
In IntOGen samples are grouped by
Topography and Morphology
according to International
Classification of Disease Oncology
(ICD). All samples with same ICD
terms and analyzed together in the
same platform form an experiment
unit. Experiment units with the same
STEP 5 ICD terms are combined to obtain
results for Onco Combinations.
Select ALL to get
IntOGen results per
topography and ALL
morphologies.

8. STEP 6
Give a name for the file
to be downloaded and
indicate a folder where
to save it.

9. Once the download has been
completed you will have three new
files in the directory that you
indicated.
The file with extension cdm contains
a Continuos Data Matrix with one
row per gene and one column per
tumor type. The values in each cell
are corrected p-values that indicate if
the gene is significantly up-regulated
in this tumor type.

10. STEP 7
Click Enrichment
Analysis to start
analyzing your module

11. STEP 8
Select the format of the
data matrix that you will
load. In this case is a
Continuous data matrix.
And select the file that
contains the data matrix.
STEP 9
Transform the continous data matrix
to a binary matrix by choosing a
transformation criteria. In this case,
since the data matrix contains p-
values, we want that values lower
than 0.05 are converted to 1
(significantly up-regulated)

12. STEP 10
Select the format of the
modules file that you will
load. In this case is a two
columns mappings. And
select the file that
contains the data matrix
and click Next

13. STEP 11
Select the type of
enrichment analysis that
you want to run. In this
case we will run a
binomial test. Click Next

14. STEP 12
Give a name to
the analysis and
indicate a Folder
where to place it.
Click Finish.

15. Once the calculations are completed
you will have a new tab with the
This button will open a new tab details of the analysis.
for a browsable heatmap with
the Results of your Analysis
This button will open a new
tab for a browsable heatmap
depicting your Data
STEP 13
Click the Results
heatmap button

16. Every column corresponds This heatmap
to a column in the data contains the results
matrix. In this case each of your enrichment
column is a tumor type analysis
Every row corresponds
to a module. In this
case different phases
of the cell cycle
Every cell is the result of one
enrichment analysis. The color
of each cell indicates if the
genes in the module are
enriched among gene up-
regulated in this cancer type.

17. STEP 14
Select Properties and Columns
to change the names of columns
and identify the tumor types
STEP 15
Open the file that
contains
annotations for
columns, tumor
types.
STEP 16
Click on ... for
Labels and Select
Topography as the
annotation to show

18. Now the column label is
the name of the tumor type
instead of the id.
STEP 17
Delete ${id} to not
show the id and hit
enter.

19. STEP 18
Select Details and
click one cell to see
the details of the
analysis
This panel shows
Details of the results
for the selected cell.

20. THANKS FOR USING INTOGEN
You will find more tutorials
and documentation in
www.intogen.org