Course Schedule
Schedule for June 13 to June 15, 2016
Workshop Q/A Forum
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Class Photo
Laptop Setup Instructions
Instructions to setup your laptop can be found here.
Pre-workshop Tutorials
1) Cytoscape Preparation tutorials: Complete the introductory tutorial to Cytoscape
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Introduction to Cytoscape3 - User Interface
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Introduction to Cytoscape3 - Welcome Screen
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Filtering and Editing in Cytoscape 3
Pre-workshop Readings
Before coming to the workshop, read these.
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g:Profiler–a web-based toolset for functional profiling of gene lists from large-scale experiments
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g:Profiler–a web server for functional interpretation of gene lists (2011 update)
YouTube Playlist for Recorded Lectures
Day 1
Welcome
Ann Meyer
Module 1: Introduction to Pathway and Network Analysis
Gary Bader
Module 2: Finding Over-Represented Pathways in Gene Lists
Quaid Morris
Lab practical: Enrichment-Based Analysis - Performing ORA
Veronique Voisin
Precomputed results for Exercise 1
Precomputed results for exercise 2
Module 3: Network Visualization and Analysis with Cytoscape
Gary Bader and Veronique Voisin
Lab practical: Cytoscape Demo, Enrichment Map
Veronique Voisin
Integrated Assignment
Veronique Voisin
Integrated Assignment: Enrichment Analysis Using GSEA and g:Profiler
Data Processing
Day 2
Module 4: More Depth on Pathway and Network Analysis
Lincoln Stein
Lab practical: De Novo Subnetwork Clustering Analysis in Reactome
Robin Haw
Module 5: Gene Function Prediction
Quaid Morris
Integrated Assignment
Veronique Voisin
Integrated Assignment: Reactome FI and GeneMANIA
Day 3
Module 6: Regulatory Network Analysis
Michael Hoffman
Lab practical: iRegulon
Veronique Voisin
Precomputed results cys file and Precomputed results irf file
To use the precomputed results:
1) launch Cytoscape
2) open the “prostate_cancer_genemania_network.cys” file
3) go to App > iRegulon > ‘Load results from the iregulon_results.irf file’