TUTORIAL - CANCER GENE PRIORITIZATION
Prioritize a list of candidate
genes based on CGPrio
probabilities and
oncogenomic alterations

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

STEP 2
Click on Upload filter

STEP 3
Select the type of gene
IDs for the list that you
are providing
NOTE
STEP 4 For this tutorial we are going
to load a list of 37 candidate
Paste the list of genes to cancer genes identified after a
prioritize. mutation screening of 20661
You can also upload a human genes in 22 human
file with the list of genes. tumor samples of Glioblastoma
multiforme.
(Parson et al Science 2008)
STEP 5
Click on Create filter

STEP 6
Select the type of cancer in
which you are interested. In
this case we will select brain
tumors since we are studying a
list of candidate cancer genes
for glioblastoma.
These values are based on
predictions by CGPrio method.
Genes with higher probability rank
are more likely to be involved in
cancer.
The CGPrio method is based on
computational classifiers that use
different combinations of sequence
This indicates that the filter and functional data including
is applied. You can click sequence conservation, protein
cross sign to eliminate the domains and interactions, and
filter and see all genes, regulatory data.
instead of only selected
ones For more information see Furney et
al., NAR 2008
This table informs if the With this links you can
gene is in the Cancer Gene go to the next page to
Census of the Sanger see the rest of genes.
Center and which type of In total there are 37.
mutations are known in
cancer samples.

Note that now we are on the
page for brain and related
tumor types
This table gives a summary
of known alterations of
each gene in the tumor
type selected
These colors indicate
significance. Color
toward red means that
this gene is
significantly altered in
this tumor type
Color scale of corrected p-values:
Gray = no significantly altered
Reddish = significantly altered Gray means that this gene
White means that
there is no data for is not significantly altered
this gene in this (CNA gain in this case) in
tumor type this tumor type

STEP 7
STEP 5
You can sort the table by clicking to the title
of any column, to have the genes with lowest
or highest values in the top. Click Onco twice
to sort by those genes more likely to be
involved in cancer (as oncogenes)
This column gives information on
mutations found and analyzed in
these genes in this tumor type.
This information comes from
COSMIC

STEP 8
You can sort the table by
Now in the top of the table clicking to the title of any
we have the genes that are column, to have the genes
more significantly up- more significantly altered in
regulated in brain and related the top. Click Up to sort by
tumors up-regulation
STEP 9
For any of the genes
you can get detailed
information. For
example click on EGFR
gene
Note that you can get
the data in excel by
clicking on ‘CSV file’
under ‘Export”

Note that now we are on the
page for EGFR for brain and
related tumor types
STEP 10
Click on Tumor types Tab
This box shows details of mutations of
EGFR in brain cancer. The number of
samples with mutations (41) and the
number of samples analyzed (879).
And the link to COSMIC for this gene.
This box shows details of
prediction ranks for EGFR
This box shows some gene obtained with CGPrio
gene details and link to for the different sets of
ensembl properties analyzed.
This box indicate that this gene is in
the Cancer Gene Census, and it give
details about the type of mutations
identified.

STEP 11
Now click on
Experiments Tab to see
details
This Table gives information on the
alterations found in EGFR in different
morphology types for brain cancer.
Note that this gene is amplified and up-
regulated in almost all brain
morphology types studied.

This is the list of experiments that
have analyzed EGFR in brain
cancer and related tissues.
White cells means no
data. In this case
means that this
experiment has not
analyzed transcriptomic
alterations
STEP 12
Click on this experiment
to see the details
This color shows thie
region of this gene is
gained in a significant N = number
number of samples of of samples
the 70 analyzed analyzed

STEP 12
Click Up to have the experiments
in which this gene is significantly
up-regulated in the top
STEP 13
Click on this experiment
to see the details

Note that now we are
on the page of EGFR
for a particular
experiment of brain
cancer
This box gives details This box gives details of up-
of the experiment, regulation of EGFR in this
including authors, title experiment. 244 samples have
and link to the been analyzed, of which of which
publication or original 104 show over-expression of this
source of data gene. The expected number of
samples with alteration by chance
is about 4. The over-expression is
highly significant

STEP 13
Click all in Experiments
and all in Tumor type
to see the information
of known cancer
alterations in EGFR in
other tumor types

Note that now we on the page
for EGFR for all tumor types
STEP 14
Click all in Genes to go
back to the complete
genes of genes
This table gives information
of known cancer alterations
in different tumor types
found in EGFR gene.
In this case we can see that
the region of this gene is
significantly amplified
(gained) in several tumor
types, it is transcriptionally
altered in some and a
number of mutations have
been found in different
tumor types.

Now we see the page showing
all the tumor types for all
genes included in the filter
and all tumor types
The filter is still applied, so
we can continue navigating
over the evidences for
involvement in cancer of
our group of genes of
interest

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You will find more tutorials
and documentation in
www.intogen.org