Proteins and Networks

Slides: c3-proteins-networks-2025.html


Alex Pico and John "Scooter" Morris

C3 Boot Camp - Protein Hour
6 November 2025

Goals and Motivations

What you should expect to get out of today:
  • Measuring proteins with mass spectrometry
  • Proteomics technology and experimental design
  • Sources of proteomics data in cancer

  • Understand the major applications of network biology
  • Explore the taxonomy of networks
  • Learn about the data sources underlying protein interactions

  • Introduction to Cytoscape
  • Find relevant networks and pathways
  • Know where to find relevant Cytoscape apps and tutorials
Proteomic Data Analysis Intro to Network Biology Tour of Cytoscape Finding Network Data Network Analysis Additional Tutorials and Resources
Proteomic Data Analysis Intro to Network Biology Tour of Cytoscape Finding Network Data Network Analysis Additional Tutorials and Resources
Proteomic Data Analysis Intro to Network Biology Tour of Cytoscape Finding Network Data Network Analysis Additional Tutorials and Resources

Tour of Cytoscape

A relaxing walkthrough:

  1. Loading networks
  2. Loading tables
  3. Selection and filtering
  4. Changing visual attributes
  5. Exporting images
  6. Saving sessions
Proteomic Data Analysis Intro to Network Biology Tour of Cytoscape Finding Network Data Network Analysis Additional Tutorials and Resources
Proteomic Data Analysis Intro to Network Biology Tour of Cytoscape Finding Network Data Network Analysis Additional Tutorials and Resources

Network Analysis Protocols

Proteomic Data Analysis Intro to Network Biology Tour of Cytoscape Finding Network Data Network Analysis Additional Tutorials and Resources

Working with Your Data

This afternoon you can take some time to use Cytoscape on your project data. Start with one of the additional exercises below.

Exercises per Interest:

  1. RNA-seq Data Analysis
  2. Cancer Transcriptomics data
  3. Proteomics and AP-MS data
  4. Cancer Genetics and Variant Data

Other tutorials are available at: tutorials.cytoscape.org

Where Can I Learn More?

Other workshops

Thank You!

Here are additional resources you may find useful:

Any questions?