Tutorial:Cluster Maker

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Slideshow Cluster_Maker (about 12 minutes)
Handout Cluster_Maker_Handout.pdf (7 pages)

Tutorial Sources
Tutorial Curators Anna Kuchinsky, Scooter Morris
Data Files galFiltered.cys, collins.cys
Version Applies to clusterMaker 1.10. Last updated: 10/21/2011


clusterMaker is a Cytoscape plugin that unifies different clustering techniques and displays into a single interface. Current clustering algorithms include Hierarchical, AutoSOME, k-medoid, and k-Means for clustering expression or genetic data; and AutoSOME, MCL, TransClust, SPCS, Affinity Propagation and MCODE for clustering similarity networks to look for protein families.

Biological Use Case: Find possible complexes, protein families, functional relationships and view in biological context.

Dependencies: For group features, please also install the MetaNodePlugin2 and the NamedSelection plugin. For node chart features, please also install the nodeCharts plugin.

Procedure

  1. Start with expression data for studies into mechanism for galactose utilization. Go to File → Open and select galfiltered.cys to load a session.

Run clustering to determine interesting subnets

  1. Select Plugins → Cluster → Hierarchical cluster.
  2. In the Source for array data box, select node.gal1RGexp, node.gal4RGexp, and node.gal80Rexp.
  3. Deselect Only use selected nodes/edges for cluster.
  4. Click Create Clusters.
  5. When you have created the clusters, the Visualize Clusters clusters button should become active. Click Visualize Clusters.
Create and Visualize Clusters

Visualize and navigate the clusters

  1. You will now see an Eisen treeview visualization. On the treeview window, explore by clicking on points on the dendogram. Clicking/selecting a particular row in the heatmap will result in the expression values for that column being overlaid on the network view.
Eisen Treeview
  1. Use shift-drag to draw a box and see results on network.
  2. Use shift-click to pick individual columns.
  3. Select an individual row by clicking on it.
  4. You can adjust the color scheme and contrast by going to Settings. For this demo, select YellowCyan in the colors window. This will change the Red/Green color scheme to Yellow/Cyan. Click Close.
YellowCyan Color Scheme
  1. Press Map Colors Onto Network and select one of the options from the Attribute List.
  2. Click Create Vizmap. This will map the colors onto the network.
Map Colors Onto Network

Animate expression values over time

  1. Go to Map colors onto network.
  2. On the pop-up screen, click on specific attributes to select. For this example, select gal4RGexp and gal80Rexp.
  3. Press Animate Vizmap. This will animate the image on the main Cytoscape session screen.

Finding modules and complexes

Now we're going to use clusterMakers' MCL algorithm to search for modules in a protein-protein interaction network derived from TAP/MS (Tandem Affinity Purification/Mass Spectrometry). First, download the file collins.cys.

Procedure

  1. Load collins.cys, as before (Go to File → Open and select collins.cys to load the session).
  2. Cluster with MCL
  3. Visualize clusters


Create Clusters

  1. Select Plugins → Cluster → MCL cluster to bring up the MCL cluster Settings dialog.
MCL cluster settings
  1. The original authors of this study used a weight called PE Score to indicate the strength of the association, which we can use with MCL. Select PE Score in the Array Sources menu.
  2. Click Create Clusters. This is a large network, and may take some time to complete the clustering. Iteration 3, in particular, will take a little longer (5-10 minutes) as it is the densest point in the cluster. For comparison, on a MacBook Pro with 4GB of RAM and a 2.66GHz Core i7, an MCL cluster of this network takes 12 minutes.
  3. After the algorithm has finished, MCL will display a dialog with the summary results.

Visualizing Clusters

  1. To see the clusters in a new network, click on Visualize Clusters.
  2. clusterMaker adds a new attribute (0_MCL_cluster in this case) to the network. Each cluster has a unique number for this attribute that may be used to change the graphics attributes in the VizMapper.
Visualizing MCL clusters