Pathway and Network Analysis of -omics Data

Date: June 7-8, 2012
Location: Downtown Toronto, ON
Lead Faculty (2012): Gary Bader, Quaid Morris & Lincoln Stein
Registration Fee for Applications received before May 7, 2012: $500 + HST
Registration Fee for Applications received after May 7, 2012: $700 + HST

Awards available for 2012.

Apply now!

Target Audience
This workshop is geared towards biologists working with 'Omics data' (e.g. gene expression, protein expression, molecular interactions, large-scale genetic screens and other omics data) from human and model Eukaryotic organisms who are interested in interpreting large gene lists resulting from their experiments. Concepts will be applicable to omics data from non-eukaryotic organisms, but software and demonstrations will not cover them.

Prerequisite: Your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements). If you do not have access to your own computer, you may loan one from the CBW. Please contact course_info@bioinformatics.ca for more information.


Course Objectives
Many research programs often slow or stall after generating a gene list. The CBW has developed a 2-day course covering the bioinformatics concepts and tools available for annotating and determining functional enrichment of a gene list and analyzing networks. The workshop is focused on the principles and concepts required for analyzing and conducting pathway analysis on a gene list from any organism, although focus will be on human and model Eukaryotic organisms. Specifically, we will focus on 1) getting more information about a gene list, 2) finding out how a set of genes is connected, 3) discovering what's enriched in a gene list (and using it for hypothesis generation) and 4) extending or refining a gene list. An analysis flow chart will be developed throughout the course.

Register now as space is limited to 30 participants.

Course Outline

Day 1 - Gene Lists
Module 1: Brief introduction to gene lists (Chair: Gary Bader)

• Ice breaking session for participants (to promote networking)
• Gene list analysis overview presenting a workflow of concepts and tools from gene list to pathway analysis
• Where do gene lists come from?
• Working with gene function information
- Definition, sources (e.g. Gene Ontology) and issues (e.g. quality of annotation transfer, evidence codes, working with multi-functional genes)
• Overview of pathway analysis

Laboratory: Practical aspects of working with gene lists (Gary Bader)

• Workflow of tools and steps
• Practical: review of Cytoscape tutorial

Module 2: Finding over-represented pathways in gene lists (Chair: Quaid Morris)

• Over-representation analysis (ORA)
Use of DAVID tool Statistics for detecting over-representation e.g. hypergeometric test, GSEA
• Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR
• Filtering Gene Ontology e.g. using evidence codes
• Text based enrichment analysis (Wyeth Wasserman)

Laboratory: Performing over-representation analysis (Quaid Morris)

• Workflow of tools and steps
• Gene Set Enrichment Analysis (GSEA) and Enrichment Maps software tool
• DAVID tool for over-representation analysis
• Practical: Running gene enrichment tools on your gene list

Module 3: Pathway and Network Analysis (Chair: Lincoln Stein)

• Overview of pathway and network analyis
• Basic network concepts
• Types of pathway and network information
- Focus on transcription factor regulatory networks. Pathway Databases: KEGG, Reactome

Laboratory: Reactome (Robin Haw)

• Workflow of tools and steps
• TFBS scan (Footer)
• TFBS Over-Representation (oPOSSUM)

Evening Integrated Assignment (Chair: TBA)

• Given a microarray or Chip-seq data set, participants will receive an assignment to conduct over-representation analysis, annotation evaluation of resulting genes, and network analysis.

Day 2 - Networks

Module 4: Network Visualization (Chair: Gary Bader)

• Introduction to network visualization
• Visualizing omics data on a network or pathway
• Active modules in Cytoscape

Laboratory: Tutorials on Cytoscape (Gary Bader)

• Workflow of tools and steps
• Tutorial: Cytoscape and selected plugins

Module 5: Gene Function Prediction (Chair:Quaid Morris)

• Functional association networks and gene function prediction
Functional relationships, similarity space Homology based prediction Guilt-by-association

Laboratory

• Workflow of tools and steps
• Practical: Using GeneMANIA to assess gene and gene list function