Cancer Gene Prioritization

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 Browser

STEP 2

Click on Upload filter.

STEP 3
Select the type of
gene IDs for the list
that you are
providing

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

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 a higher probability
rank are more likely to be
involved in cancer.

The CGPrio method is based on
This indicates that the computational classifiers that
filter is applied. You can use different combinations of
click the red x to sequence and functional data
eliminate the filter and including sequence
return to the list of all conservation, protein domains
genes. and interactions, and regulatory
data. For more information see
Furney et al., NAR 2008
This table informs if the
gene is in the Cancer
Gene Census of the With these links you
Sanger Center and can go to the next
which type of mutations page to see the rest
are annotated there. of genes. In total
there are 37.

Note that now we are on
the page for brain and
related tumor types

This table gives a
summary of alterations
found for each gene in
the selected tumor type.

The 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
Red/Yellow = significantly altered

Gray means that this White means that
gene is not significantly there is no data
altered (CNA gain in this for this gene in
case) in this tumor type this tumor type

STEP 7
STEP 5
You can sort the table by clicking the
title of any column, to have the genes
with lowest or highest values on top.
Click Onco twice to sort by those genes
with the highest oncogene prediction
rank.

This column gives
information on mutations in
these genes found and
studied in this tumor type.
This information is imported
from COSMIC.

STEP 8
Now in the top of the table You can sort the table by
we have the genes that clicking to the title of any
are more significantly up- column, to have the genes
regulated in brain and more significantly altered in
related tumors the top. Click Up to sort by
up-regulation.

STEP 9
For any of the genes you
can get detailed
information. For example
click on the Ensembl ID for
EGFR .

Note that you can
retrieve the data in
a tabulated file 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 (103), the number of
samples analyzed (1643) and the
link to COSMIC for this gene.

This box shows details
of prediction ranks for
EGFR gene obtained
This box shows
with CGPrio for the
some gene details
different sets of
This box indicate that this gene and link to ensembl
properties analyzed.
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 morphologies of brain
cancer. Note that this gene is
amplified and up-regulated in
many morphologies.

This is the list of experiments
that have analyzed EGFR in
brain cancer and related
tissues.

The color indicates N = number
that the region of of samples
this gene is analyzed
amplified in a
significant number of
the 171 samples
analyzed.

White cells means no
data. In this case, it
means that this
experiment has not
analyzed
transcriptomic
alterations

STEP 12
Click Up to have the
experiments on top in which
this gene is significantly up-
regulated.

STEP 13
Click on the
experiment by Sun L
et al 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 of the
experiment,
including authors,
title and link to the
publication or
original source of
data.

This box gives details of up-
regulation of EGFR in this
experiment. 152 samples have
been analyzed, of which of
which 80 show over-expression
of this gene. The expected
number of samples with
alteration by chance is about
4.6. The over-expression is
therefore 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. Go to the tumor
type tab.

Note that now we on the
page for EGFR for all tumor
types

STEP 14
Click all in Genes.
Then go to the genes
tab.

This table gives
information of known
cancer alterations in
different tumor types
found in the 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.

THANKS FOR USING INTOGEN

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

Cancer Gene Prioritization

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