live training
Functional Plant Bioinformatics (PLAZA)
Target Audience:
All VIB staff
Location:
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 organization of plant genomes, the evolution of plant gene families and the different systems used to describe gene functions. In addition, you will know how to extract relevant biological information from -omics gene sets.
Objectives
- 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 RNA-Seq and ChIP-Seq genes using the PLAZA Workbench
- Comparing gene sets between different di/polyploidy crop species
Required skills
Basic knowledge of genes, genomes, transcript profiling, BLAST and homology (no programming skills are required).
Program
Welcome + Short introduction participants (species/biological process of interest)
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PLAZA introduction
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Coffee break
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Theory I: genes, gene families and genome organization
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Exercises I: genes, gene families and genome organization
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Lunch
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Theory II: Orthologs, paralogs and phylogenetic trees
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Exercises II: orthologs, paralogs and phylogenetic trees
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Coffee break
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Theory III: Functional annotation & functional enrichments
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Exercises III: Functional annotation & functional enrichments
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Theory IV: PLAZA workbench
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Exercises IVa: PLAZA workbench registration + upload gene set(s)
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Coffee break
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Exercises IVb: PLAZA workbench functional data analysis
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Lunch
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Theory V: Advanced orthology, synteny and expression analysis in cereals
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Exercises Va: Advanced orthology, synteny and expression analysis in cereals
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Coffee break
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Exercises Vb: Advanced orthology/synteny using PLAZA workbench
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Feedback + closing workshop
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