WGCNA Tutorial: Find Gene Co-Expression Modules from RNA-seq Data

Discover hidden patterns in your RNA-seq data using WGCNA! Learn how to group genes into modules based on co-expression, then link these modules to biological traits like disease status, treatment response, or developmental stages. ⏱️ TIMESTAMPS: 0:00 - Introduction to WGCNA 1:47 - Understanding Co-expression Networks 3:51 - Understanding WGCNA Workflow 7:42 - Installing WGCNA & Preparing Your RNA-seq Data 8:31 - Creating The Trait Matrix 9:23 - Choosing Soft Threshold Power 10:43 - Building the Co-Expression Network & Identifying Gene Modules 12:34 - Calculating Module Eigengenes 13:56 - Relating Modules to Traits 15:14 - Gene Significance & Module Membership 16:43 - Finding Hub Genes 🔬 WHAT YOU'LL LEARN: ✅ How WGCNA groups genes by co-expression patterns ✅ Setting up proper input data (30+ samples recommended) ✅ Choosing the optimal soft-thresholding parameter ✅ Detecting modules using dynamic tree cutting ✅ Correlating modules with experimental conditions ✅ Identifying hub genes within modules ✅ Exporting networks for Cytoscape visualization 📊 ANALYSIS WORKFLOW: 1. Load normalized expression data 2. Detect outlier samples 3. Calculate soft threshold (β parameter) 4. Construct weighted network 5. Identify co-expression modules 6. Correlate modules with phenotypes 7. Find hub genes driving module behavior 🎯 PERFECT FOR: → Multi-sample RNA-seq (cancer vs normal, time series) → Finding gene sets responding to treatments → Identifying coordinated gene programs → Discovering biomarker candidates ⚠️ REQUIREMENTS: - 15-20 samples minimum (30+ recommended) - Normalized expression matrix - Sample metadata (condition, treatment, etc.) - R with WGCNA package installed 📚 FULL TUTORIAL WITH CODE: https://ngs101.com/how-to-build-gene-co-expression-networks-from-rna-seq-data-using-wgcna-complete-step-by-step-guide-for-absolute-beginners/ 📺 WATCH NEXT: - GENIE3 Regulatory Networks: https://youtube.com/watch?v=_pLHtbIitJk - RNA-seq Clustering Methods: https://youtube.com/watch?v=2Ji13jRofuk - Complete RNA-seq Playlist: https://youtube.com/playlist?list=PLTfZb80upqPhaClVX_sVXeCvJRQ6KQdH4 🔔 Subscribe for weekly NGS tutorials: @NGS101-LearningHub 📧 Free resources: https://ngs101.com #WGCNA #RNAseq #NetworkAnalysis #Bioinformatics #SystemsBiology #GeneExpression