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This is a quick-start tutorial for[br]Cytoscape 3.

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

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

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with expression profiles and other high [br]throughput data sets. Additional

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

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

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

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

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

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

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

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

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

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Universal license.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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network, so it may be best to leave it off[br]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.[br]Click on "Import Table from File" in the

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

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

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network depending on how your data is[br]structured.

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

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

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Deselect the gal1RGsig, gal4RGsig, and[br]gal80Rsig columns.

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

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Gene Nomenclature symbols contained in the[br]"COMMON" column.

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

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

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

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new style, copying the current style, and[br]renaming or removing the style.

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Click on the second column of the "Label"[br]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[br]shown on the network. Click on the second

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

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mapping type, let's choose "Continuous[br]Mapping".

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

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delete individual gradient handles by[br]single clicking on them then hitting

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"Delete". We need at least two handles to[br]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[br]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[br]the bottom-left.

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

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but if it doesn't you can click on the[br]"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.[br]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[br]approximately -1.2.

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Double-click the handle

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or single-click it and click the[br]"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[br]approximately 0.5 and change the

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color to white.

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

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Double-click on the maximum handle and set[br]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[br]light blue. A good trick is to set it to a

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

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

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

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one shape, while those above it[br]can have another.

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

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mapping to "Continuous". Double-click on[br]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[br]it to a rectangle.

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Click the handle between the shapes[br]and change the value to 0.05.

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

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interactions, and "pd" for protein-DNA[br]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[br]Panel. Click the "+" icon, then choose

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

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

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

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

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filters at once, then click the "Apply"[br]button.

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

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

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and Edges". Now there will be many[br]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[br]try different layouts and options here,

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but we're interested in the "Preferred[br]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[br]"Apply Preferred Layout".

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

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

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

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Then click "Select > Nodes > [br]First Neighbors of Selected Nodes >[br]

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

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

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

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

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

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browser and perform a search using the[br]"name" identifier.

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

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

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gradient and choosing "Edit > Remove[br]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[br]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[br]up the "Graphics" dialogue.

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

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

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Thank you for watching this Quickstart[br]Tutorial for Cytoscape 3.

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For more Cytoscape Tutorials, visit[br]tutorials.cytoscape.org

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or visit my YouTube channel.