Omics experiments often generate long lists of genes or proteins. Functional enrichment analysis identifies biological trends in the data by assessing these lists against gene ontology and pathway information. This can help interpret the experimental results in the context of larger biological systems.
This workshop continues from our introductory webinar and provides a practical introduction to functional enrichment analysis. Using example data you will get hands-on with some of the most commonly used databases and tools for over representation (ORA) and gene set enrichment analysis (GSEA) and for identifying enriched biological functions in a list of genes or proteins. We’ll focus on tools available online and in R.
Learning outcomes:
By the end of the workshop you should be able to:
Explain the purpose of functional enrichment analysis and its role in biological experiments
Identify the key challenges and factors to consider when applying functional enrichment analysis in biological research
Describe the statistical methods underpinning enrichment analysis, including the use of p-values, false discovery rates (FDR), and multiple testing corrections
Apply functional enrichment methods/tools (e.g. over representation analysis, GSEA methods) in the browser and with R to:
Get a systems perspective of gene functions
Discover pathways that are enriched in a gene list
Visualise and interpret the results of enrichment analysis to gain biological insights
Use different types of functional databases - GO, KEGG and Reactome
Lead Trainers:
Dr Hossein Valipour Kahrood, Bioinformatician, Monash Genomics and Bioinformatics Platform
Dr Cali Willet, Senior Research Bioinformatician, Sydney Informatics Hub, University of Sydney
Date/Time:
20 - 21 November 2024, 1 - 4 pm AEDT / 12 - 3 pm AEST/ 12:30 - 3:30 pm ACDT/10 am - 1 pm AWST (check in your timezone)
Location: Online
Format:
This workshop will take place over two sessions. You must attend both sessions in order to get the most out of the workshop.
Our trainers will introduce the concepts and guide you through hands-on exercises to help you put your new skills into action. Some of the workshop will use R/RStudio and we’ll start at a beginner friendly level. We will provide access to the tools and compute you need to complete the exercises.
Who the workshop is for:
This workshop is for Australian researchers and bioinformaticians working with omics experiments (e.g. RNA-Seq, protein expression) that generate gene or protein lists.
Prerequisites
You must be associated with an Australian organisation for your application to be considered.
(Recommended) Basics of R/RStudio. We’ll start at a beginner level but you will get more from the workshop if you know the basics of setting up directories, running commands, reading in and outputting files. If you need a refresher on R/RStudio try the Introduction to R and RStudio section of this online tutorial.
(Recommended) Watch the introductory webinar for a primer on how functional enrichment analysis methods work.
How to apply:
This workshop is free but participation is subject to application with selection.
Applications close at 11:59pm AEDT, Tuesday 5 November 2024.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. More information on the selection process is provided in our Advice on applying for Australian BioCommons workshops.
This workshop is presented by the Australian BioCommons, Monash Genomics and Bioinformatics Platform and the Sydney Informatics Hub with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to Australian BioCommons
Image credit: The Kegg metabolism map was first prepared by Kanehisa et al. and is reproduced here under a CC-BY-NC l4.0 licence.