3.7.0

Data Analysis & Visualization in Cytoscape

Slides:
https://cytoscape.github.io/cytoscape-tutorials/presentations/netviz-and-analysis-2018-sib.html


John "Scooter" Morris

Swiss Institute of Bioinformatics
29 October 2018

Goals and Motivations

By the end of this workshop you should be able to:

  • Understand the major applications of network biology
  • Find relevant networks and pathways
  • Import your data into Cytoscape
  • Perform basic topological and other network analyses
  • Master network layouts and data visualization
  • Know where to find relevant Cytoscape apps and tutorials
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Wrap up and "Exam"

Introductions

John "Scooter" Morris, UCSF
  • Executive director, Resource for Biocomputing, Visualization, and Informatics
  • Roving Engineer, National Resource for Network Biology
  • Cytoscape team since 2006
  • Author of over a dozen Cytoscape apps

Introductions

What about you?

  • Clinicians
  • Bench Biologists
  • Bioinformaticians
  • Computer Scientists
  • Chemists
  • Mathematicians
  • Other

Introductions

Prior Cytoscape or network analysis experience?

  • None -- that's what I'm here for!
  • Some network analysis, but what's Cytoscape?
  • I've played with Cytoscape, but still have a lot to learn.
  • I use Cytoscape all the time...
    (hey, I could probably teach this course!)

Tour of Cytoscape


  1. Launch Cytoscape v3.7.0

Tour of Cytoscape


  1. Open CyBrowser
  2. Enter URL: tutorials.cytoscape.org

Tour of Cytoscape


  1. Click on Tour of Cytoscape
  2. Resize window to your preference

Tour of Cytoscape

Follow-along walkthrough:

  1. Loading networks
  2. Loading tables
  3. Selection and filtering
  4. Changing visual attributes
  5. Exporting images
  6. Saving sessions
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Wrap up and "Exam"

Hands-on

  1. Launch Cytoscape
  2. Go to the app store in a web browser
  3. Install stringApp and WikiPathways
    • Search for the app
    • Click on the tile
    • Click the Install button
  4. Perform a STRING disease query for "ovarian cancer"
  5. Perform a WikiPathways query for "ovarian cancer"
    • Choose the "Integrated Cancer Pathway
    • Import it as a Pathway
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Wrap up and "Exam"
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Wrap up and "Exam"

Hands-on Exercises

Recommended Exercises:

  1. Basic Data Visualization
  2. StringApp
  3. Functional Enrichment

Other tutorials are available at: tutorials.cytoscape.org

Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Wrap up and "Exam"

Wrap up

Questions and Discussion

"Exam"

To make sure you now have a working knowledge of Cytoscape, choose one of the following datasets to analyze in Cytoscape:

  • Colins (2007): A merged dataset of three yeast APMS experiments. Find the putative complexes.
  • GPL54: A yeast heat shock microarray experiment from GEO. Create a network of the most significant genes based on the magnitude of the fold change and color the nodes by expression.

Thank You!

Here are additional resources you may find useful:

Thank You!




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