David Functional Annotation !!top!! -

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.

"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). david functional annotation

For 80% of biologists who need to answer, "What is my gene list doing?" DAVID is the best tool ever made. Use it, cite it, and never present a raw gene list to your PI again. This is the most critical step users mess up