Functional Plant Bioinformatics (PLAZA)
22-23 April 2024
General context
Using PLAZA to get more out of your plant omics data.
This two-day workshop will introduce the basic concepts of comparative and functional -omics data analysis in plants through lectures and practical hands-on sessions. Plant biologists and geneticists with an interest in bioinformatics and data analysis are encouraged to attend this training. After this workshop, you will have a good understanding of the organisation of plant genomes (gene colinearity and synteny), the evolution of plant gene families, orthologs and (in)paralogs, and the different systems used to describe gene functions. In addition, you will know how to extract relevant biological information from -omics gene sets using the PLAZA Workbench.
- Introduction plant comparative genomics (genes and gene families) + introduction PLAZA platform
- Functional characterization of plant genes (Gene families, GO, InterPro)
- Synteny analysis in polyploid cereals
- Gene set analysis for different plant -omics data sets:
- Functional interpretation of (sc)RNA-Seq, ChIP-Seq or proteomics gene sets using the PLAZA Workbench
- Comparing gene sets between different di/polyploidy crop species
Basic knowledge of genes, genomes, transcript profiling, BLAST and homology (no programming skills are required).
Trainers
Klaas Vandepoele
Klaas Vandepoele is Full Professor at Ghent University and group leader in the VIB-UGent Center for Plant Systems Biology. His aim is to extract biological knowledge from large-scale experimental data sets using data integration, comparative sequence/expression/chromatin analysis, network biology and machine learning. Through the development and application of novel bioinformatics methods, new aspects of genome biology, especially in the area of gene function prediction and gene regulation, are identified. He published >160 papers in international peer-reviewed scientific journals and is a Highly Cited researcher (H-index 59).
Michiel Van Bel
Michiel Van Bel is a postdoctoral researcher within the group of Klaas Vandepoele. He is the main developer of the PLAZA platform since its inauguration in 2009. Computer scientist by training, he aims to support other researchers by developing data integration platforms.
Sander Thierens
Sander Thierens joined the PLAZA team in 2022, and is the lead developer for the PLAZA-cloud extension suite.
Program
Welcome + Short introduction participants (reason to join workshop)
PLAZA introduction
Coffee break
Theory I: genes, gene families and genome organisation
Exercises I: genes, gene families and genome organisation
Lunch
Theory II: Orthologs, paralogs and phylogenetic trees
Exercises II: Orthologs, paralogs and phylogenetic trees
Coffee break
Theory III: Functional annotation & functional enrichments
Exercises III: Functional annotation & functional enrichments
Theory IV: PLAZA workbench
Exercises IVa: PLAZA workbench registration + upload gene set(s)
Coffee break
Exercises IVb: PLAZA workbench functional data analysis
Lunch
Theory V: Advanced orthology, synteny and expression analysis in cereals
Exercises Va: Advanced orthology, synteny and expression analysis in cereals
Coffee break
Exercises Vb: Advanced orthology/synteny using PLAZA workbench
Feedback + closing workshop
Practical info
22 April 2024 - 23 April 2024
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
22 April 2024 - 23 April 2024
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take bus 49, 50 or 70 to Technologiepark. Please check Routeplanner De Lijn for schedules.
22 April 2024 - 23 April 2024
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket and have it validated at the reception desk of the FSVM building. Parking will only be allowed in regular parking spots (for instance in front of the building) and in the new parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited and after initial warnings, fines will be issued (€ 50).
22 April 2024 - 23 April 2024
Ghent - VIB/UGent FSVM II
Room: L5 on the fifth floor