Cytoscape 3 Quickstart Tutorial - Basic Expression Analysis

This is a quick-start tutorial for
Cytoscape 3.

Cytoscape is an open source, cross-
platform bioinformatics program written

in Java. It is used to visualize molecular
interaction networks and integrate these

with expression profiles and other high
throughput data sets. Additional

functionality can be added by installing
plugins called "apps". We won't be

discussing apps any further in this video
but we wanted you to know that they

are available. For this tutorial, we'll be
using Cytoscape 3.6.1. If you're using

a different version of Cytoscape, some
options may have been changed or moved.

If any features discussed in this video
are different, please refer to the

documentation at manual.cytoscape.org.
We'll be following along with the

Basic Expression Analysis Tutorial in the
documentation. There is a more

in-depth version of this tutorial there
if you need additional guidance.

The original tutorial is covered by the
Creative Commons Zero v1.0

Universal license.

Let's jump right in!
Our first step will be to import a network

from the sample data provided by
Cytoscape. Click on the "Import Network

from File" button in the Tool Bar.
Navigate to the installation directory

and find the folder called "sampleData".
Inside that folder, let's open

"galFiltered.csv". Cytoscape is pretty
smart about choosing default settings

as long as your data is in a reasonable
format, so we're going to accept the

settings it chose for us. Just know that
there are a lot of options when you're

importing data for choosing the type of
data each column contains. Click "OK".

Cytoscape automatically tries to find a
good network structure for your data

after you first import it. We can play with
the layout later, but first let's get a view

of the entire network. Click the "Zoom
out to display all of current network"

button in the toolbar. The edges may be
gone in your network when you do this,

but you can get those back by clicking
"View > Show Graphics Details". This

option does use a bit more resources
when there is a lot of nodes in your

network, so it may be best to leave it off
when viewing large networks. The details

will reappear when you zoom in.

Now let's import our expression data.
Click on "Import Table from File" in the

toolbar, then choose "galExpData.csv".
Cytoscape should choose the proper default

settings, however you may need to choose
the proper key column to match with your

network depending on how your data is
structured.

If the import succeded, you should see the
new information in the Node Table. Let's

limit the columns shown by clicking on the
"Show Columns" button in the Table Panel.

Deselect the gal1RGsig, gal4RGsig, and
gal80Rsig columns.

The "shared name" contains the Ensembl ID,
but let's change the node labels to HUGO

Gene Nomenclature symbols contained in the
"COMMON" column.

Click on the "Style" tab. If you click on
"default", you'll see there are a lot of

different styles included with Cytoscape.
The button with 3 horizontal bars next to

the style selection dropdown has options
for managing the styles such as creating a

new style, copying the current style, and
renaming or removing the style.

Click on the second column of the "Label"
option. Change the column to "COMMON" and

you'll see the node labels change.

Now we want to see the expression values
shown on the network. Click on the second

column for the "Fill Color" option. For
the column, choose "gal80Rexp". For the

mapping type, let's choose "Continuous
Mapping".

Double click on the gradient to bring up
the "Continuous Mapping Editor". You can

delete individual gradient handles by
single clicking on them then hitting

"Delete". We need at least two handles to
have a gradient though, otherwise you'll

end up with a binary scale.

Click the "Add" button to add another
gradient handle.

Click and drag a handle to move it,

or single click it and edit the value in
the bottom-left.

The scale should contain your
largest and smallest values for your data,

but if it doesn't you can click on the
"Set Min and Max..." button, then click

"Reset" and "OK".

Let's create a blue-white-yellow gradient.
First, make sure there are three handles

at the top.

Drag the first handle or edit it to
approximately -1.2.

Double-click the handle

or single-click it and click the
"Node Fill Color" button,

then pick a color in the blue range.

Set the second handle to
approximately 0.5 and change the

color to white.

For the third handle,
change it to about 2.5 and yellow.

Double-click on the maximum handle and set
it to green,

then set the minimum handle to black.

Note that the default value is set to
light blue. A good trick is to set it to a

color outside the spectrum you're using to
see nodes without a value.

The columns with "sig" at the end contain
significance values. We can use those to

change the node shape so that nodes with a
significance below a set threshold can have

one shape, while those above it
can have another.

Click on the second column in "Shape",
then set the Column to "gal80Rsig" and the

mapping to "Continuous". Double-click on
the "Current Mapping" box, then click the

"Add" button in the bottom right.

Double-click on the left circle and change
it to a rectangle.

Click the handle between the shapes
and change the value to 0.05.

The "shared interaction" column in the
Edge Table uses "pp" for protein-protein

interactions, and "pd" for protein-DNA
interactions. Let's filter out the

protein-protein interactions.

Click on the "Select" tab in the Control
Panel. Click the "+" icon, then choose

"Column Filter". Choose "Edge: interaction"
and leave the next option as "contains".

Type "pp" into the text search box. The
filter should automatically be applied.

The "Apply when filter changes" option is
usually selected by default. For very

large networks, it is recommended to
disable this option, change all of the

filters at once, then click the "Apply"
button.

You should now see many edges in the
network selected. Let's remove the

protein-protein edges we just chose.
Click "Edit", then "Delete Selected Nodes

and Edges". Now there will be many
unconnected nodes. Let's clean it up by

changing the layout.

Click "Layout", then "Settings". You can
try different layouts and options here,

but we're interested in the "Preferred
Layout" tab. Make sure it is set to

"Prefuse Force Directed Layout".

Go back to "Layout", then select
"Apply Preferred Layout".

If we zoom in we can see that there are
three highly expressed nodes connected by

two intermediate nodes. Let's create a new
network from those two nodes.

Click on the first node, then hold control
and click on the second node.

Then click "Select > Nodes >
First Neighbors of Selected Nodes >

Undirected". Finally, click on "New
Network from Selection" in the toolbar.

You'll notice in the Network Panel that
this has created a new child network.

If our data contains identifiers used by
external databases, Cytoscape can

automatically link us to them. Right click
on the "GAL4" node, then choose

"External Links > Sequences and Proteins >
Entrez Gene". This will open your default

browser and perform a search using the
"name" identifier.

Cytoscape also provides the option to draw
charts and graphs on each node.

Let's remove the old fill color mappings
by right-clicking on the fill mapping

gradient and choosing "Edit > Remove
Mappings from Selected Visual Properties".

Change the default value back to gray.

Choose "Properties" at the top of the
panel, then choose

"Paint > Custom Paint 1 > Image/Chart 1".

Select the "Default" box, which will bring
up the "Graphics" dialogue.

Choose the "Charts tab" and move all of
the expression columns to the right side.

Change the type of graph to "Heat
Strips" and hit apply.

Thank you for watching this Quickstart
Tutorial for Cytoscape 3.

For more Cytoscape Tutorials, visit
tutorials.cytoscape.org

or visit my YouTube channel.