Functional Annotation !free! — David

If you’ve just finished an RNA-seq or microarray experiment, you probably have a list of genes. It might be a short list of 50 names or a long one of 2,000. But a list is just data. The real question is: What does this list mean biologically?

This is the most critical step users mess up. You must tell DAVID what the "universe" is. Are you looking at the whole human genome? Or just the 10,000 genes expressed in your specific tissue? Use the whole genome for standard enrichment, but use a tissue-specific background for precision.

Enter (The Database for Annotation, Visualization and Integrated Discovery). For nearly two decades, DAVID has been the Swiss Army knife of functional annotation. It answers the golden question of genomics: "Which biological processes are my genes involved in?" david functional annotation

DAVID uses . Instead of reading genes, it reads Gene Ontology (GO) terms, pathways (KEGG), protein domains (InterPro), and disease associations. How DAVID Works (The 3-Step Magic) Step 1: Upload your list. Paste your gene symbols, Entrez IDs, or Affymetrix probes. You don't need to know the format; DAVID auto-detects it.

But DAVID is

DAVID doesn't just count genes. It uses a modified Fisher Exact p-value (EASE score). Look for terms with a p-value < 0.05 after Benjamini correction (FDR). The lower the p-value, the stronger the signal.

"I have 4 genes." With DAVID: You run the list. The top cluster is "Amyloid precursor protein metabolic process" (Fold Enrichment: 45x). The second cluster is "Axon guidance" (Not significant? Maybe ignore). The third cluster is "Immune response" (Wait, microglia genes are also upregulated? That changes your hypothesis). If you’ve just finished an RNA-seq or microarray

Go to [david.ncifcrf.gov] and turn your data into discovery. Have a favorite alternative (Enrichr, g:Profiler, Metascape)? Drop a comment below. But for my money, DAVID is still the gold standard for functional annotation.