This tutorial demonstrates how to create a custom experiment set in IntOGen by combining multiple gene expression experiments to identify significantly altered genes and pathways. The key steps are: 1. Select the tumor type (breast cancer) and platform (Affymetrix) to filter relevant experiments. 2. Choose 3 breast cancer Affymetrix experiments from 2010 to include in the set. 3. View significantly altered genes and pathways across the combined experiments, and explore details for individual genes like ERBB2. 4. Modules like pathways can also be analyzed at the level of transcriptional alterations across the experiment set. This allows researchers to leverage multiple related experiments together in IntOGen to gain more statistical

1. TUTORIAL - COMBINE EXPERIMENTS
Combine experiments
to make your own set
of experiment and
identify the most
significant genes and
modules altered

2. STEP 1
Go to
www.intogen.org
& Click Browser

3. STEP 2
Select the option
‘create a new
experiment set´ from
the pull down menu
in ‘Experiments’

4. STEP 3
For this tutorial we are going
to create a set of gene
expression experiments in
breast cancer using the
affymetrix platform and
published in 2010. Enter a
name in the ‘Name’ text-box.
You may also add description
in the ‘Description’ text-box.
Then click ‘Create’.

5. You can select for a
particular tumor type to
filter for the experiments of
this tumor type
You can also use the search
box to select the
experiments you are
interested.
Here is the new
experiment set
that for the
moment has 0
experiments.
This Table gives a list of all
the experiments in IntOGen With these links you
to chose from. can go to the next
page to see the rest
of experiments

6. STEP 4
Select tumor type
breast

7. Note that now we
have breast cancer
selected
STEP 5
Search for affymetrix
in the search box in
order to filter for those
experiments done in
this platform.
This table now only
shows breast cancer
experiments

8. STEP 6
Select the three
experiments published
in 2010
STEP 7
Note that now Click on ‘submit’.
your experiment
set contains 3
experiments

9. We are on the page for our
new experiment set.
STEP 8
Click on the Genes
tab
This box give details of
the experiment set, if
you want to remove the
experiment set, then
click ‘delete’

10. We are on the page for our
experiment set, for breast
and for Genes.
This table gives
information of
transcriptomic
alterations for each you can go to the
gene given the other pages
combination of the clicking on page
selected experiments number

11. These colors indicate
significance. Color
means that this gene
is significantly
altered given the
combination of
experiments.
Color scale of corrected p-values: Gray means that this
Gray = no significantly altered gene is not
Red/Yellow = significantly altered significantly altered
in these experiments

12. These values are based
on predictions by CGPrio
method. Genes with
higher probability rank are
more likely to be involved
in cancer.
See Furney et al., NAR
2008
STEP 10
You can also search for a
gene of your interest to
see how it is altered in
this set of experiments.
For example type ERBB2
and click search.

13. STEP 11
Click on the Ensembl ID
of the ERBB2 gene.

14. Note that now we are
in the page of ERBB2
for this experiment
set
This box shows details of
mutations of ERBB2 in
breast cancer. The
number of samples with
STEP 12
mutations (5), the
Click on Tumor types number of samples
Tab analyzed (504) and the
link to COSMIC for this
gene.
This box shows the p-
value for transcriptomic
alteration of ERBB2 This box shows some
given the combination This box shows details of
gene details and link
of this set of the annotations of this
to ensembl
experiments gene in the Cancer Gene
Census of the Sanger
Center.

15. STEP 13
Now click on
Experiments Tab
This Table gives information
on the alterations found in
ERBB2 in different
morphology types for Breast
Cancer given this
combination of experiments.

16. This is the list of experiments
in the experiment set that
have analyzed ERBB2 in
breast cancer.
N = number of
samples analyzed
White cells means no
data. In this case
STEP 14 means that this
Click on the Sircoulomb F experiment has not
et al experiment to see analyzed copy number
the details. alterations.
The color indicates
that this gene is up-
regulated in a
significant number of
samples of the 51
samples that were
analyzed.

17. STEP 15
Note that now we are
To go back and continue
in the page of ERBB2
exploring the results or our
for this particular
gene set, click Breast
experiment of breast
Affymetrix 2008 in experiments,
cancer.
and all in genes.
This box give details
of the experiment,
including authors,
title and link to the
publication or original
source of data.
This box gives details of
down-regulation of ERBB2 in
this experiment. 51 samples
have been analyzed. The
expected number of samples
with down-regulation by
chance is about 2.2. Yet, 15
samples were found to have
this gene down-regulated.
This is highly significant
down-regulation.

18. STEP 16
You can also explore this
set of experiments for
alterations at the level of
modules.
Select KEGG Pathways.

19. This table gives
information
transcriptional
alterations in
pathways combining
the three
experiments of our
Note that you can set.
retrieve the data in a
tabulated file by
clicking on ‘CSV file’
under ‘Export”

20. STEP 17
Click on the Down title
to sort by the pathways
that have higher
enrichment of down-
regulated genes in this
experiment set.
Here, the color
indicates that this
pathway is
enriched down-
regulated genes in
this set of
Gray means that the experiments.
number of genes in
this pathway that are
altered are not higher
than expected by
chance

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