Functional Plant Bioinformatics
In this overview, learn about the functionalities of the PLAZA workbench for plant bioinformatics. From small-scale operations to large-scale solutions, explore how to search for genes, analyze data sets, perform functional enrichment analysis, and more. Discover how to register for an account, create experiments, upload genes, and conduct analyses efficiently. Dive into understanding the significance of functional enrichment analysis and witness a demo of the PLAZA workbench in action.
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Presentation Transcript
Functional Plant Bioinformatics The PLAZA workbench 25-26 October 21 1 Michiel Van Bel
Small-scale operations on large-scale data Default PLAZA usage: 1. Search for a gene or functional term 2. Explore associated web pages 3. Write down results 4. Repeat 5. Imagine doing this for a 1000 differentially regulated genes from an RNA-seq experiment 2
Large scale solution for large scale data : The PLAZA workbench 1. Work with sets of genes compared to single genes 2. Compare, merge, differentiate between gene sets 3. Apply set-specific tools 1. functional enrichments 2. Locational biases 3. Etc 3
The PLAZA workbench: A quick how-to 1. Register for a free workbench account Security: Analyzes are not public History: Keep track of analyzes 4
The PLAZA workbench: A quick how-to 2. Create experiment 5
The PLAZA workbench: A quick how-to 3. Upload genes into the gene set 6
FUNCTIONAL ENRICHMENT ANALYSIS Determines the over/under-representation of a certain GO term in a gene set compared to the genome-wide background frequency The significanceis determined using the hypergeometric distribution (incl. multiple testing correction) freq(gene set) freq(background) Enrichment fold =
