cBioPortal Tutorial #2:

Single Study Query

Query one or multiple genes in a single dataset

Last update: December 21, 2021

Tutorial Objectives
● Show how to run a single-study query from the main page
● Walk through each of the data/analysis tabs in a single-study query
○ OncoPrint ○ Co-expression
○ Cancer Types Summary ○ Comparison/Survival
○ Mutual Exclusivity ○ CN Segments
○ Plots ○ Pathways
○ Mutations ○ Download
● Show how to modify and re-run a query

In this tutorial, blue … while green boxes ask

boxes provide an a biological question that
overview of each tab on we can answer using
cBioPortal … cBioPortal.
Overview of Tabs in a Single Study Query
Note that depending on the query run and the data available for a particular study, not all of these will be
present (e.g. a study without mRNA expression data will not have a Co-expression tab)
● OncoPrint: Overview of genetic alterations per sample in each query gene
● Cancer Types Summary: Frequency of alteration in each query gene in the detailed cancer types
included in this study
● Mutual Exclusivity: Statistical analysis to determine if query genes are mutually exclusively altered
● Plots: explore the relationships among genetic alterations, gene expression, protein levels, DNA
methylation and available clinical features
● Mutations: Details about mutations called in each query gene
● Co-expression: Explore which genes have mRNA/protein levels correlated with query genes
● Comparison/Survival: Explore overlaps, outcomes, clinical attributes and genomic data
comparisons among groups of samples as defined by the query
● CN Segments: Explore copy number changes with the Integrated Genomics Viewer (IGV)
● Pathways: Explore queried genes in TCGA-defined pathways
● Download: Download data or copy sample lists
 We’re going to run a query in a TCGA Lower-Grade
Glioma study. The next few slides will show how to
run this query from the Query page. You can also run
the same query from a Single Study Exploration, as
we did in Tutorial #1.
 Query overview
Search
studies
Browse available
datasets and
select studies to
explore or query

List of all studies,

organized by
organ system
Number of
studies for each
tissue of origin
(click to filter)

Link to this page

 Single study query 1. Filter the list
of studies
(optional)

2. Check the
box for study
of interest.

3. Select “Query By Gene”

Link to this page
 Single study query
4. This section lists all
data types available for
the selected study.
Select data types to
query. By default,
Mutations and CNA will
be selected (if available).

5. Select sample set. For

5. Type gene(s) or
most studies, an
select from Refine your query:
appropriate sample set
pre-defined gene You can use Onco
will be automatically
lists. cBioPortal Query Language
selected given the data
will confirm that all (OQL) to define
types selected in Step 4.
entries are valid which specific
gene symbols. alterations to
include. See
6. Submit query
specifications or
OQL tutorial.
Link to this page
Performing a query as shown in the previous slides
or as shown in Tutorial #1 will both bring you to
Results View, shown on the next slide.

Results View is made up of multiple tabs, each with

specific functionality, which all share a header.
 Results View Header: General Information

The name of the study. The number (percentage) of

Click to view the full samples/patients with an alteration
study in Study View. in any of the query genes

The number of samples and patients included Save a link to the current session.
in the query. Note that these numbers can Useful for sharing with others or
differ from each other if some patients have returning to a query at a later date.
more than one tumor sample profiled.

Click on the number of patients/samples to go

to Study View for just the queried samples.

Link to this page

 Results View Header: Variant Settings
Use this menu to control how alterations are visualized. Changes
made here are immediately reflected across Results View. However
over the to confirm how individual tabs reflect these selections.

Set the definition of a putative driver vs

variant of unknown significance (VUS).

Check boxes to exclude VUS (as defined above) or germline

alterations. When checked, VUS or germline alterations are
considered not present, so a sample with only VUS or
germline alterations will be treated as an unaltered sample.

Check box to exclude samples where queried genes are not

profiled or genomic profiles are not available.

Link to this page

But wait! What if I changed my mind?
Can we modify a query?
 Modify Query
Click on “Modify Query”. This button is available
on all tabs and can be used at any time. This will
bring up the query interface from the homepage
(see next slide for a screenshot).

You can also click the for a quick edit

of the queried genes, including OQL
edits. To change other query settings,
use the “Modify Query” button.

Link to this page

 Modify Query
The existing query is pre-populated for
your convenience. You can change the
study, the genomic profiles, the
patient/case set or the gene set.
Simply hit “Submit” when you are
happy with the modified query.

In this case, I’ve

added a third gene
(IDH2) to the query.

Link to this page

 Summary of alterations per sample. Each sample is a
OncoPrint column. Each gene is a row. Different kinds of genetic
alterations are highlighted with different colors.

Samples are sorted by

gene and type(s) of
genetic event(s) detected.

The percentage of samples with an

alteration in each query gene.

To change the order, click on a gene

name and drag, or click on the . Samples
will re-sort based on this new order.
Link to this page
 OncoPrint: Features
Add clinical tracks,
heatmaps (eg RNA Change
levels) or other data the
(eg Arm-level CNA). sample
Available data sorting Customize
varies by study. order visualization

Change the Download figure as PNG,

rules by which PDF or SVG. Download
mutations are patient/sample IDs in
colored. same order as OncoPrint.

Link to this page

 OncoPrint: Zoom
Change the zoom by
clicking the zoom in/out
There may be more samples hiding off-screen. Scroll icons or moving the
to the right or zoom out or use minimap to see them. slider or typing a value

Click here to
open
“minimap”
(see below)

Minimap shows a small version of the full OncoPrint

and allows you to zoom in each direction
independently. The rectangle can be dragged to move
around OncoPrint or resized to change the zoom.

This button zooms OncoPrint to

show all samples with alterations
Link to this page
 OncoPrint: What can we learn?

Q: Are genetic alterations in these Q: Is there an association between alterations

genes mutually exclusive? in a particular query gene and age?

A: We can see that samples with A: We can see that patients with mutations or
alterations in one gene tend to not amplifications in EGFR tend to be older than
have alterations in the other genes. those with mutations in IDH1/IDH2
Link to this page
Now we’re going to go through all the other tabs and
ask some questions about alterations in IDH1, IDH2
and EGFR in the TCGA Lower-Grade Glioma study.

Note: Depending on the data available for a

particular study, not all of the following tabs will be
present (e.g. a study without expression data will not
have a Co-expression tab)
 Cancer Types Summary Histogram of the frequency of alterations in
each gene for each detailed cancer type.
Plots for all
queried genes
together and Options to
each individual customize
gene are visualization
available as
separate tabs.

Hover over a bar to see

additional details.

Q: Are alterations in EGFR more frequent in a

particular subtype of glioma?

A: Yes, astrocytoma appears to have a much

higher frequency of EGFR alteration than
oligoastrocytoma or oligodendroglioma.
Link to this page
 All pairwise On the OncoPrint tab we could
Mutual Exclusivity combinations of query see visually that alterations in
genes analyzed for these three query genes tended to
mutual exclusivity or be mutually exclusive. Here we
co-occurrence in the can address that same question
queried samples. with a statistical analysis.

Click on any
column header to
A positive value here suggests that alterations sort. Hover over
in these genes co-occur in the same samples, the column names
while a negative value suggests that for more details
alterations in these genes are mutually about how values
exclusive and occur in different samples. are calculated.
odds of alteration in B given alteration in A
(
log2 odds of alteration in B given lack of alteration in A )
Link to this page
 Depending on available data types for a given
Plots study, this tab allows for plots comparing
mutations, copy number, mRNA expression,
Example plot protein levels and DNA methylation of query
settings genes, along with any available clinical attributes.

Choose type of data

Each dot is Select color

Select a query gene a sample scheme

Swap horizontal
& vertical axis

Driver vs. VUS

annotation settings are in
the menu in the
header of the page.
Link to this page
 Plots
Q: Does amplification
of EGFR alter gene
expression?

A: Yes, we can see

that higher copy
number of EGFR
(x-axis) is associated
with increased
expression (y-axis).

Link to this page

 This tab shows details about all Mutations are drawn as lollipops along
Mutations mutations called in each query gene. the domain structure of the gene. The
height of the lollipop reflects how
many mutations are detected at an
Each gene amino acid. This plot will update based
appears on on any filters applied to the table
a separate below. Hover over any lollipop for
tab additional details.

Table of all
mutations with
annotations

Show
additional
columns

Link to this page

 Mutations
Click to filter
Click on a lollipop to based on
filter the table below mutation types

Click here (visible Filter based

when you hover over on any
a column) to filter on visible text
a specific column column

Link to this page

 View mutations in
Mutations context of 3D
protein structure

Add annotation Adjust y-axis

tracks to the plot

Link to this page

 Q: Where are the hotspots for EGFR mutation
Mutations in glioma?

A: Look at the lollipop diagram: G598V is the

most common alteration. The Furin-like domain
also appears to be frequently mutated. Note
that these are also statistical hotspots
according to the OncoKB & Cancer Hotspots
tracks and are all located in the extracellular
domain according to the Topology tracks.

Link to this page

 Q: The mutations in IDH1 appear to be highly recurrent.
Mutations Are these mutations known hotspots? Known oncogenic
drivers? Biomarkers for any drugs?

A: Look at the annotation tracks below the lollipop plot and

the Annotation column in the table. Each mutation is
annotated against 4 different databases with information
about recurrence, oncogenicity and drugability.

This mutation is in OncoKB as a Level

3 variant. Hover over this symbol to see
additional information, including that this This mutation is a recurrent hotspot based
is a known oncogenic mutation. on a statistical analysis of mutation frequency.

This mutation is annotated in This mutation is in

CIViC. Hover over this symbol for My Cancer Genome.
Link to this page additional information.
 Compares mRNA/protein level
Co-Expression expression of your query
genes against all other genes.
Each gene
appears on a
separate tab

Select from Check boxes to

available data color-code sample
types dots by mutation
status, change x- or
Click on a gene y-axis to log scale, or
name to see add a regression line.
correlation plot

Link to this page

 Co-Expression Q: Several genes on chr7 show high expression correlation with
EGFR within this cohort (see table on the left). Why might that be?

A: EGFR is also located on chr7 and is frequently gained in some

subtypes of glioma which could explain these correlated increases in
expression. This can be further explored in the “CN Segments” tab.

Link to this page

 This tab enables the comparison of all available data types between
Comparison samples with or without alterations in the query genes. This tab replaces
and enhances the old “Enrichments” tab.

The Comparison tab is the same as the Group Comparison functionality

that is accessible from Study View. See the Group Comparison Tutorial
for more details about the functionality of this tab.

Groups can be toggled on or off by

clicking on them them. Analyses will
update as the selections change.

By default, the “Altered” (one or more Additional groups (deselected

alterations in one or more query genes) by default) correspond to each
and “Unaltered” (no alterations in any track shown in OncoPrint.
query gene) groups are selected.

Link to this page

 The Overlap subtab shows samples or patients
Comparison: Overlap that may overlap among the selected groups.

Select one or more regions in the overlap

plot to create a new group. If you are
logged in, this new group can be saved
to your profile for future use. Saved
groups can be found under the “Groups”
button in Study View.

Link to this page

 The Survival subtab replaces the old “Survival”
Comparison: Survival tab. This subtab will only be visible if outcome data
is available for the selected study.

Select among Note: These plots reflect

different outcome data as provided by the
measures. Options study. We do not perform
here depend on any additional processing.
data availability for
the study.

Q: Do patients with alterations in

IDH1 have different outcomes
compared to patients with
alterations EGFR?

A: Patients with alterations in IDH1

have significantly better OS than
patients with alterations in EGFR.

Link to this page

 The Clinical subtab compares all available clinical
Comparison: Clinical data among the selected groups.

Click on a clinical
attribute to visualize
the data in the plot
on the right.

Link to this page

 Comparison: Molecular Profiles
The molecular profiles
subtabs replace the old
“Enrichments” tab.
These analyses ask whether
Genomic Alterations
(mutations/copy-number
alterations) or mRNA
expression or protein
expression in a particular
gene is enriched in one of the
selected groups. These, and
additional subtabs like
Microbiome Signature, will be
visible depending on the data
available for each study.

Link to this page

 Comparison: Molecular Profiles
Hover over a
dot to see the
Select which types of gene name
alterations to include
in the analysis

Select sample-level or
patient-level analysis

Click on any column

Click the checkbox next to a gene name and then click
header to sort. Hover
this button to re-run the query with a gene added.
over the column name for
more details about how
values are calculated.
Link to this page
 Comparison
Q: Alterations in IDH1, IDH2
and EGFR are mutually
exclusive but some samples
have alterations in none of
these genes. Do samples
without IDH1, IDH2 or EGFR
alterations commonly have
genomic alterations in one or
more other genes?

A: Alterations in NF1 are

significantly mutually exclusive Notice the distribution of
with alterations in IDH1, IDH2 samples with NF1
and EGFR (see table). Try mutations relative to
adding NF1 to the query (check samples with query
the box next to NF1 and then gene alterations.
click “Add checked genes to
query”) and examine the
OncoPrint and the Mutual
Exclusivity tabs.
 View copy number for each sample at each query
CN Segments gene via the Integrated Genomics Viewer (IGV).

Toggle track labels, a vertical line

Plots for each gene appear on a separate tab. marking the center of the viewing screen,
and a vertical line that moves with your
cursor. Use to zoom in or out.

Click for track settings,

including expanding the height
of each sample (see below)

Each row is a single sample

Gene
structures

Link to this page Click on a read for details

 CN Segments

Q: Are amplifications of EGFR focal or

broad?

A: By zooming out, we can see that

high-level amplifications (deeper red) are
focal at the EGFR locus, while low-level
gains (lighter red) are broad. If we continue
to zoom out, we will see that low-level gains
often encompass the entire chromosome.
Link to this page
 The Pathways tab replaces the now retired “Network” tab. This tab in
Pathways an integration with PathwayMapper. The tab enables exploration of
the queried genes in the context of Pathways defined by TCGA. For
more detail on this tab, refer to the Pathways Tutorial.

Link to this page

 Download Download data or copy lists of samples.

Download queried data types for the

queried genes.

Download all other data types for the

queried genes.

Frequency of gene alteration for each

gene in the query

List of all samples with

status of each query gene.

Link to this page

 Download Download data or copy lists of samples.

List of samples that have an alteration

in one or more query genes

List of samples that have no alterations

in any query genes

List of all samples with summary classification:

0 = no alteration in any query gene
1 = alteration in one or more query genes

Advanced feature: use these

lists to build a custom sample
list to run a new query, to
create virtual studies or to
build custom groups.

Link to this page

 Questions?
Check out our other tutorials
or email us at:
cbioportal@[Link]