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.