CBW Pathways Workshop
Pathway and Network Analysis of -Omics Data (July 2020)
Meet your Faculty
Gary Bader
Robin Haw
Michael Hoffman
Veronique Voisin
Ruth Isserlin
Welcome
Class Materials
Workshop Schedule
Pre-Workshop Materials and Laptop Setup Instructions
Laptop Setup Instructions
Basic programs
Java 11 Installation
Cytoscape Installation
GSEA Installation
Pre-workshop Tutorials
Cytoscape Preparation tutorials
Pre-workshop Readings and Lectures
Additional tutorials
Module 1 - Introduction to Pathway and Network Analysis (Gary Bader)
Module 2: Finding Over-represented Pathways (Veronique Voisin)
Module 2 lab - g:Profiler
Introduction
Goal of the exercise 1
Data
Exercise 1 - run g:Profiler
Step 1 - Launch g:Profiler.
Step 2 - input query
Step 3 - Adjust parameters.
Step 4 - Run query
Step 5 - Explore the results.
Step 6: Expand the stats tab
Step 7: Save the results
Step 8
Exercise 2: Load and use a custom .gmt file and run the query
Optional steps
Optional 1
:
Option 2
:
Option 3
:
Module 2 lab - GSEA
Introduction
Goal of the exercise
Data
Background
How to generate a rank file.
Start the exercise
Step1.
Step 2.
Step3.
Step 4.
Step 5.
Additional information
Module 3: Network Visualization and Analysis with Cytoscape
Module 3 Lab
Module 3 Lab: g:profiler Visualization
Goal of the exercise
Data
EnrichmentMap
Description of this exercise
Start the exercise
Exercise 1a
Step 1
Step 2
Step3: Explore the results:
Explore Detailed results
Exercise 1b
Exercise 1c
Module 3 Lab: GSEA Visualization
Goal of the exercise:
Data
GSEA output and EnrichmentMap
EnrichmentMap
Start the exercise
Step 1
Step 2
Step 3
Step 4
Step 5
Step 6
Step 7
Module 3 Lab: (Bonus) Automation
Goal of the exercise:
Set Up
Step 1 - launch RStudio
Step 2 - create a new project
Step 3 - Open example up RNotebook
Step 4 - Define Notebook parameters
Step 5 - Step through notebook to run the analysis
Exercises
Additional resources
Module 4: In-depth Analysis of Networks and Pathways
Module 5: Regulatory Network Analysis
Module 5 Lab: Gene Regulation and Motif Analysis Practical Lab
iRegulon lab
Goal
Exercise 1. Detect regulons from co-expressed genes
Skills learned in this exercise:
Steps
Exercise 2. Create a metatargetome using iRegulon and merge 2 networks in Cytoscape.
Steps
Use or precomputed iRegulon results:
Notes about iRegulon:
Notes about Cytoscape:
Exercise 3. Use Enrichr with the prostate gene list.
Goal
Steps
end of practical lab
Module 6: Gene Function Prediction
Module 6 Lab: GeneMANIA (Cytoscape version)
Goal of this practical lab
EXERCISE 1: QUESTIONS AND STEPS TO FOLLOW
STEPS
EXERCISE 1 ANSWERS
EXERCISE 2: QUESTIONS AND STEPS TO FOLLOW
STEPS
EXERCISE 3: QUESTIONS AND STEPS TO FOLLOW
STEPS
SOME DEFINITIONS:
Module 6 Lab: GeneMANIA (web version)
Goal of this practical lab
EXERCISE 1: QUESTIONS AND STEPS TO FOLLOW
STEPS
EXERCISE 1 ANSWERS: DETAILED EXPLANATION AND SCREENSHOTS
EXERCISE 1 - STEPS 1-4
EXERCISE 1 - STEP 5
EXERCISE 1 - STEP 6
Exercise 1 - STEP 7
Exercise 1 - STEP 8
Exercise 1 - STEP 9
Exercise 1 - STEP 10 (layouts)
Exercise 1 - STEP 11 (save an image)
EXERCISE 2: QUESTIONS AND STEPS TO FOLLOW
STEPS
EXERCISE 2 ANSWERS: DETAILED STEPS AND SCREENSHOTS
Exercise 2 - STEPS 1 to 4
Exercise 2 - STEP 5
Exercise 2 - STEP 6.
Exercise 2 - STEP 7
Exercise 2 - STEP 8
Exercise 2 - STEP 9
Exercise 2 - STEP 10
Exercise 2 - STEP 11
Exercise 2 - STEP 12
Exercise 2 - STEP 13.
EXERCISE 3: QUESTIONS AND STEPS TO FOLLOW
STEPS
Exercise 3: MORE DETAILS AND SCREENSHOTS
Exercise 3 - STEPS 1 - 3
Exercise 3 - STEP 4
Exercise 3 - STEP 5
Exercise 3 - STEPS 6
Exercise 3 - STEP 7
Exercise 3 - STEP 8
Exercise 3 - STEP 9
SOME DEFINITIONS:
Integrated Assignment
Final slides
Goal
DATASET 1
Background
Data processing
PART 1: run g:Profiler
PART 2: save as Generic Enrichment Map output (BE)
PART 3: save as Generic Enrichment Map output (NE)
PART 4: create an enrichment map
Answers g:Profiler
PART 5: GSEA (run and create an enrichment map)
Answers GSEA
PART 6: iRegulon
DATASET 2
PART 1: ReactomeFI
Answers REACTOME FI
PART 2: GeneMANIA
Integrated Assignment Bonus - Automation
Goal of the exercise:
Published with bookdown
Pathways
Module 6: Gene Function Prediction
Veronique Voisin
Lecture
Lab practical - Cytoscape
Lab practical - Web