This document provides a tutorial for searching the IntOGen database to find information on altered genes and biological processes in different cancer types. It demonstrates how to search for breast cancer, sort the results to find the most significantly downregulated or mutated genes, and view module and experiment details for specific genes like CDKN2A. The tutorial explains how to navigate between genes, tumor types, modules, and experiments to discover knowledge on cancer alterations.

1. TUTORIAL - TUMOR TYPE SEARCH
Search for a cancer
type of interest and
discover the most
significant altered
genes and modules

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

3. STEP 2
Select the tumor
type of your
interest

4. NOTE
Cancer type annotations
are based on International
Classification of Disease
(ICD)
ICD-10
nomenclature is
used to indicate
the topography or
site of the tumor
ICD-O
nomenclature is
used to indicate
the tumor
morphology or
subtype.

5. STEP 3
In this case we will select
breast cancer, and we will
leave blank the
morphology type.

6. We are in the page for all
experiments of Breast
Cancer, and all
genes/modules
This table summarizes
the evidence for the
involvement of each
gene in breast cancer
Note that you can
get the data in table
format by clicking on
‘CSV file’ under
‘Export”

7. This part gives summary
information of the
alterations found in each
gene in the cancer type
selected given a number
of experiments
combined
These colors indicate
significance. Colors
toward red means
that this gene is
significantly altered
in this tumor type
Color scale of corrected p-
values:
Gray = no significantly
altered
Red/Yellow = significantly
altered
Gray means that this White means that
gene is not there is no data for
significantly altered this gene in this
in this tumor type. tumor type

8. 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

9. STEP 4
You can sort the table by
clicking to the title of any
column. For example click
Down.

10. Now the genes in the Note that some
top are those genes are both
significantly significantly lost and
downregulated in downregulated.
breast cancer.
With these links you
can navigate to the
next pages to see the
rest of the genes

11. STEP 5
Now we will sort the
table to find the
genes with more
mutations known in
breast cancer

12. The first number is the number of
samples with mutations in this
Now the genes in the gene, and the second number is
top are those with the number of samples analyzed.
higher number of This information is based on
mutations known in COSMIC.
breast cancer.
We are browsing the
information for genes in
Breast cancer. But we
can also browse other
information.
This column informs whether
the gene is in the Cancer
Gene Census of the Sanger
Center and which type of
mutations are known in
cancer samples.

13. STEP 6
Select GO process from
Modules tab to
discover the most
altered biological
processes in breast
cancer.

14. This table gives
information on altered
GO processes in breast
cancer.

15. STEP 7
If we click to the Up title, we will
sort by the pathways that have
the highest enrichment of genes
up-regulated in breast cancer.
Here, the red color
indicates that the
module (GO process) is
enriched for altered
(up-regulated) genes in
Gray means that the breast cancer.
number of genes in
this pathway that are
altered are not higher
than expected by
chance

16. STEP 8
Click on the Genes Tab
to go back to the genes
table

17. STEP 9
You can also search
for a gene of your
interest to see how it
is altered in breast
cancer. For example
type CDKN2A and
click search.

18. STEP 10
Click on the Ensembl ID for
the CDKN2A gene.

19. Note that now we are
in the page of
CDKN2A for breast
cancer
STEP 11
Click on Tumor types
Tab
This box shows details of
This box shows the p- mutations of CDKN2A in
value for up-regulation breast cancer: The
and down-regulation of number of samples with
This box shows details of
CDKN2A in breast mutations (46), the
the annotations of this
cancer. number of samples
gene in the Cancer Gene
analyzed (1003) and the
Census of the Sanger
link to COSMIC for this
Center.
gene.

20. STEP 12
Now click on
Experiments Tab
This table provides
information on the
alterations found in
CDKN2A in different
morphology types for
Breast Cancer.

21. This is the list of experiments STEP 13
that have analyzed CDKN2A Click Down to sort the
in breast cancer. table for those
experiments in which
this gene is more
significantly down-
regulated.
N = number
White cells means no
of samples
data. In this case analyzed
means that this
experiment has not
analyzed for
transcriptomic
alterations
Coloured cells indicate
that this gene is down-
regulated in a
significant number of
samples of the
STEP 14 experiment.
Click on Yu K et al to
see the details of the
experiment.

22. Note that now we are
in the page of
CDKN2A for a
particular experiment
of breast cancer
STEP 15
To see what is the involvement of
CDKN2A in other cancer types click “all”
in experiments and “all” in tumor types.
This box gives details of
This box shows details down-regulation of
of the experiment, CDKN2A in this
including authors, title experiment. 183 samples
and link to the have been analyzed, of
publication or original which 24 have this gene
source of data. down-regulated. The
expected number of
samples with down-
regulation by chance is
about 8. This is highly
significant down-
regulation.

23. Note that now we are
in the page of
CDKN2A for all tumor
types
Go to
the tab
“tumor
type”.
This table gives
information of known
cancer alterations
found in CDKN2A
gene

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