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