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This 1 day training aims to show you some online tools that can help you discover the functions of your set of genes/proteins.
We are using the interactive Open Educational Resource online/offline course infrastructure called LiaScript. It is a distributed way of creating and sharing educational content hosted on github. To see this document as an interactive LiaScript rendered version, click on the following link/badge:
Description
This is our hands-on course on Functional Analysis.Prerequisites
To be able to follow this course, learners should have knowledge in:
- Basic knowlegde of molecular biology
Learning Outcomes:
By the end of the course, learners will be able to:
- Explain the basic concepts and terminology of functional analysis, such as gene ontology, gene enrichment, pathways, and networks.
- Use online tools to annotate and analyse human and plant datasets.
- Compare and contrast different organisms, including those without a reference genome, in terms of their functional analysis.
- Briefly evaluate the biological significance of the gene sets obtained from functional analysis.
Target Audience: Researchers, trainers, training providers
Level: Beginner
License: Creative Commons Attribution 4.0 International License
Funding: This project has received funding from ELIXIR Belgium.
Time estimation: 8 hours
Supporting Materials:
- Activities
- Slides
- In the data folder you can find examples that are smaller samples with limited opportunities but fast processed data.
- In the data folder you can find exercises that are bigger data sets that you can do more with.
Requirements: No
Acknowledgement:
PURL:
@orcid(Janick Mathys), @orcid(Bruna Piereck)
@orcid(João Pacifico), Mainak Guha Roy
Welcome to our Functional Analysis workshop! We are very happy to have you here.
This course will guide you into the steps of how to get the answers about what the genes can tell you! With the advances of technology, understanding the load of informations and giving it some meaning is becoming more challenging. To help you through this adventure and to get the answers your data is anxious to show you, we will use ONLINE tools to annotate and analyse some Human and Plant datasets and by the end of the day everything will make sense! We will shortly talk about how to start if you work with an organism that doesn't have a Reference genome.
We will use Gene Ontology, Gene enrichment as much as Pathways to interpret our data and unravel the meaning of our gene set. This introduction of Functional Analysis will elucidate the biology behind the gene and bring to light what your data means.
Schedule day 1:
09:30 - 11:00 Organism without Reference Genome
11:00 - 11:30 Coffee break
11:30 - 11:45 Enrichment and Overrepresentation analysis (ORA)
11:45 - 12:30 Lunch
12:30 - 13:40 Gene ontology enrichment
13:40 - 15:00 Coffee break
15:00 - 15:15 Pathway (Networks) and gene functions
15:15 - 17:00 Gene-set enrichment
Please read this page carefully before the start of the workshop.
- Internet browser
Please cite as:
- Bruna Piereck, Janick Mathys. (2023). Functional training (v1.0.0). Zenodo. tbc
Here are some great tips for learning and to get inspired for writing your own pipelines:
-
FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes
-
Genomics Guru Youtube - How to perform GSEA (desktop version)
About ELIXIR Training Platform
The ELIXIR Training Platform was established to develop a training community that spans all ELIXIR member states (see the list of Training Coordinators). It aims to strengthen national training programmes, grow bioinformatics training capacity and competence across Europe, and empower researchers to use ELIXIR's services and tools.
One service offered by the Training Platform is TeSS, the training registry for the ELIXIR community. Together with ELIXIR France and ELIXIR Slovenia, VIB as lead node for ELIXIR Belgium is engaged in consolidating quality and impact of the TeSS training resources (2022-23) (https://elixir-europe.org/internal-projects/commissioned-services/2022-trp3).
The Training eSupport System was developed to help trainees, trainers and their institutions to have a one-stop shop where they can share and find information about training and events, including training material. This way we can create a catalogue that can be shared within the community. How it works is what we are going to find out in this course.
About VIB and VIB Technologies
VIB is an entrepreneurial non-profit research institute, with a clear focus on groundbreaking strategic basic research in life sciences and operates in close partnership with the five universities in Flanders – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel and Hasselt University.
As part of the VIB Technologies, the 12 VIB Core Facilities, provide support in a wide array of research fields and housing specialized scientific equipment for each discipline. Science and technology go hand in hand. New technologies advance science and often accelerate breakthroughs in scientific research. VIB has a visionary approach to science and technology, founded on its ability to identify and foster new innovations in life sciences.
The goal of VIB Technology Training is to up-skill life scientists to excel in the domains of VIB Technologies, Bioinformatics & AI, Software Development, and Research Data Management.
Editorial team for this course
Authors: @orcid(Janick Mathys), @orcid(Bruna Piereck)
Contributors: @orcid(João Pacifico), Mainak Guha Roy
Technical Editors: Alexander Botzki
License: 