2 Overview
2.1 Functional Analysis of -Omics Data
2.1.1 General Information
The workshop covers the bioinformatics concepts and tools for interpreting a gene list using Gene Ontology and pathway information. The workshop focuses on the principles and concepts required for analysing and conducting functional and pathway analyses on a gene list from any organism, although the focus will be on human and model eukaryotic organisms.
2.1.2 Course Objectives
Participants will gain practical experience and skills to be able to:
- Understand basic concepts of functional enrichment analysis;
- Interpret enrichment analysis results;
- Gain systems perspective of gene functions;
- Obtain more information about a gene list;
- Discover which pathways are enriched in a gene list (and use this information for hypothesis generation);
- Predict gene function and extend a gene list;
- Follow the workflow after the workshop to conduct their own analyses.
2.1.3 Target Audience
This workshop is intended for biologists working with ‘-Omics data’ (e.g., RNA-seq, protein expression), who are interested in interpreting large gene/protein lists resulting from their experiments.
2.1.4 Setup Requirements
The workshop will be held in person. Participants are encouraged to bring a laptop; however, no software installation is necessary.
Workshop materials and relevant links can be found on the Resources page.
BYO coffee :)
2.1.5 Schedule - Day 1
| Instructor | Activity | Time (mins) | Start | End |
|---|---|---|---|---|
| LP | Welcome and housekeeping | 10 | 09:00 AM | 09:10 AM |
| HK | Introduction to functional enrichment analysis | 45 | 09:10 AM | 09:55 AM |
| HK | Interactive Calculator | 15 | 09:55 AM | 10:10 AM |
| Morning break | 10 | 10:10 AM | 10:20 AM | |
| HK | g:Profiler (web) + gprofiler2 | 60 | 10:20 AM | 11:20 AM |
| SA | GSEA (web) + fgsea | 60 | 11:20 AM | 12:20 PM |
| Lunch break | 40 | 12:20 PM | 01:00 PM | |
| PH | STRING (web) + STRINGdb | 50 | 01:00 PM | 01:50 PM |
| SA | Reactome (web) + ReactomePA | 60 | 01:50 PM | 02:50 PM |
| Wrap-up / Q&A / preview Day 2 | 10 | 02:50 PM | 03:00 PM |
2.1.6 Schedule - Day 2
| Instructor | Activity | Time (mins) | Start | End |
|---|---|---|---|---|
| Recap of Day 1 & Day 2 overview | 10 | 09:00 AM | 09:10 AM | |
| GI | clusterProfiler and enrichplot | 65 | 09:10 AM | 10:15 AM |
| Morning break | 15 | 10:15 AM | 10:30 AM | |
| HK | Novel species FEA | 80 | 10:30 AM | 11:50 AM |
| Wrap-up: Uncertainties, Reporting & Resources (self-paced) + Q&A | 10 | 11:50 AM | 12:00 PM |