Proteins and Networks

Slides: c3-proteins-networks-2024.html


Alex Pico and John "Scooter" Morris

C3 Boot Camp - Protein Day
7 November 2024

Goals and Motivations

What you should expect to get out of today:
  • Understand the major applications of network biology
  • Explore the taxonomy of networks
  • Learn about the data sources underlying protein interactions

  • Measuring proteins with mass spectrometry
  • Proteomics technology and experimental design
  • Sources of proteomics data in cancer

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

Network Analysis Protocols

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?