TUTORIAL - GENE SEARCH
Search for a gene of
interest and have a wide
view of the implication of
this gene in cancer

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

STEP 2
Type the name of
the gene of interest
and click search
STEP 3
Click to the name of
the gene of interest

STEP 4
Click on the tab
Tumor types to go
back to tumor types
table
These values are based on
predictions by CGPrio This box indicate that
method. Genes with higher this gene is in the
probability rank are more Cancer Gene Census,
likely to be involved in and it give details
cancer. about the type of
mutations identified.
see Furney et al., NAR 2008
This box shows some
gene details and link to
ensembl

We are in the page for
CDKN2A for all experiments
and all tumor types
This table gives
information of known
cancer alterations found
in CDKN2A gene
These numbers indicate
the number of samples
with mutations and the
number of samples
analyzed for this gene in
each tumor type.
This data is from COSMIC

These colors indicate
Color scale of corrected p-values: significance. Color
toward red means that
Gray = no significantly altered this gene is significantly
Reddish = significantly altered altered in this tumor
type
Gray means that this
White means that there
gene is not significantly
is no data for this gene
altered in this tumor
in this tumor type
type

You can sort the table
by clicking to the title of
any column, to have
the tumor types more
significantly altered in
the top
Note that you can get
the data in table format
by clicking on ‘CSV file’
under ‘Export”.
With this links you can
go to the next page to
see the rest of the
tumor types

STEP 5
Sort the table by clicking to
the Up title, to have the
tumor types in which this
gene is most significantly
up-regulated in the top
STEP 6
Click on “breast” to see
details of CDKN2A
alterations in breast
cancer

STEP 7
Note that now we are
Click on Tumor types Tab in the page of CDKN2A
for breast cancer
This box shows details of
mutations of CDKN2A in
This box shows the p-value for breast cancer. The number
transcriptional alterations of of samples with mutations
CDKN2A in breast cancer. (33) and the number of
samples analyzed (604).
And the link to COSMIC for
this gene.
This box shows some
gene details and link to
ensembl

STEP 8
Now click on
Experiments Tab
This Table gives information
on the alterations found in
CDKN2A in different
morphology types for Breast
Cancer.

This is the list of experiments
that have analyzed CDKN2A in
breast cancer. N = number
of samples
analyzed
White cells means no
data. In this case means
that this experiment has
not analyzed
transcriptomic alterations
This color shows that this
gene is up-regulated in a
significant number of
samples of the 183
analyzed

STEP 9
Click on the Up column
to sort by significance
of up-regulation
STEP 9
Click on Finak G et al
experiment to see the
details

Note that now we are in the
page of CDKN2A for a
STEP 10 particular experiment of
breast cancer.
This box give details of
the experiment,
including authors, title
and link to the
publication and original
source of data
This box gives details of up-
regulation of CDKN2A in this
experiment. 52 samples
have been analyzed, of
which 13 have this gene
over-expressed. The This table give information
expected number of of the tumor type and
samples with alteration by morphology type analyzed
chance is about 1.8. This is by this experiment
highly significant over-
expression.

STEP 10
To explore other genes
involved in breast cancer
click all in Experiments and
all in Genes/Modules

Note that now we are in a
page for all experiments for
this tumor type, and all genes
and modules.
This Table gives the list of
experiments analyzed for this
tumor type.

Note that now we are in a
page for all experiments of
Breast Cancer, and all genes
Note that you can get
the data in table format
by clicking on ‘CSV file’
under ‘Export”.
This table gives
different evidences of
involvement of each
gene in this tumor type.

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