WEBVTT

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This is a quick-start tutorial for
Cytoscape 3.

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

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

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with expression profiles and other high 
throughput data sets. Additional

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

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

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

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

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

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

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

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

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

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Universal license.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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will reappear when you zoom in.

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

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

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

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network depending on how your data is
structured.

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

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

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Deselect the gal1RGsig, gal4RGsig, and
gal80Rsig columns.

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

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Gene Nomenclature symbols contained in the
"COMMON" column.

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

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

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

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

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

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you'll see the node labels change.

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

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

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

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

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delete individual gradient handles by
single clicking on them then hitting

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

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end up with a binary scale.

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

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Click and drag a handle to move it,

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

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

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

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"Reset" and "OK".

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

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at the top.

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

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Double-click the handle

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

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then pick a color in the blue range.

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Set the second handle to
approximately 0.5 and change the

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color to white.

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

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

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then set the minimum handle to black.

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

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

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

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

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one shape, while those above it
can have another.

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

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

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"Add" button in the bottom right.

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

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

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

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

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protein-protein interactions.

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

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

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

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

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

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

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

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

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

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changing the layout.

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

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

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"Prefuse Force Directed Layout".

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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Change the default value back to gray.

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

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

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

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

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

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Thank you for watching this Quickstart
Tutorial for Cytoscape 3.

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For more Cytoscape Tutorials, visit
tutorials.cytoscape.org

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or visit my YouTube channel.