3 Overview
3.1 Functional analysis of -Omics data
Workshop 2024
3.1.1 General information
The workshop covers the bioinformatics concepts and tools available for interpreting a gene list using gene ontology and pathway information. The workshop focuses on the principles and concepts required for analyzing and conducting functional and pathway analysis on a gene list from any organism, although the focus will be on human and model eukaryotic organisms.
3.1.2 Course Objectives
Participants will gain practical experience and skills to be able to:
- Understand basic concepts of functional enrichment analysis;
- Interpret enrichment analysis results;
- Get systems perspective of gene functions;
- Get more information about a gene list;
- Discover what pathways are enriched in a gene list (and use it for hypothesis generation);
- Predict gene function and extend a gene list;
- Follow workflow after the workshop to conduct their own analysis.
3.1.3 Target Audience
This workshop is intended for biologists working with ‘-Omics data’ (e.g. RNA-Seq, protein expression and other omics data), who are interested in interpreting large gene/protein lists resulting from their experiments.
3.1.4 Setup Requirements
This workshop will be delivered online over zoom; you may wish to install the dedicated zoom. Otherwise, no special software installation will required, as we will be using online analysis tools.
- Zoom Link:
Links and material will be provided on the day. BYO coffee.
3.1.5 Schedule
| Day | Instructor | Activity | Time (mins) |
|---|---|---|---|
| Day 1 | Welcome and housekeeping | 10 | |
| HK | Introduction | 10 | |
| HK | Data acquisition | 5 | |
| HK | Filtering gene list | 15 | |
| HK | Hands-on with Interactive Calculator (breakout rooms); https://bioinformatics3.erc.monash.edu/rsconnect/content/241/ | 15 | |
| HK | gProfiler [GO + pathways] (https://biit.cs.ut.ee/gprofiler/gost) | 20 | |
| HK | Hands-on with gProfiler (breakout rooms) | 20 | |
| HK | Break | 15 | |
| HK | STRING (https://string-db.org/) | 20 | |
| HK | Reactome (https://reactome.org/) | 20 | |
| HK | GSEA (GenePattern) (https://cloud.genepattern.org/gp/pages/index.jsf) | 30 | |
| Day 1 | 3 hrs | ||
| Day 2 | Welcome and housekeeping | 5 | |
| HK | Day -1 recap | 15 | |
| CW | Using R for functional enrichment analysis; Applications and advantages; Working with confidential data; Customisation, flexibility, reproducibility; Automation and batch processing | 30 | |
| CW | Available packages in R -; Clusterprofiler; Gprofiler; Any other? | 5 | |
| CW | Introducing R, R Markdown, Rstudio; Getting logged on RStudio environment; Discuss R Markdown; Discuss basic features of Rstudio | 30 | |
| CW | Clusterprofiler - Handon; Breakout rooms; Work on and discuss results based on following criterion; Analysis; ORA; GSEA; Ontologies; GO; Pathway (KEGG, Reactome); …; Visualisations | 30 | |
| CW | gprofiler - Handson; Breakout rooms; Work on and discuss specific features; gost function with standard analysis and plots - Discuss how the plots from gprofiler are different (than clusterprofiler) and also useful; Send analysis from R to g:Profiler web interface ; Sharing the results easily with colleagues ; To accompany a publication without the peers having to run the full analysis code in R; Integrating results with external tools for visualisations; Alter results using ggplot2, enrichplot, clusterProfiler; Using custom annotations; Non-model organisms, that are not annotated in the Ensembl database; Enable users to upload custom annotation files | 30 | |
| CW | Experiment wrap up ; Discuss results; Enrichments look different from different tools - Why | 30 | |
| CW | Wrap up and feedback | 5 | |
| Day 2 | 3 hrs |
- HK: Hossein V Kahrood
- CW: Cali Willet