Building a negative-control signature library
Common stress, cell-cycle, interferon, and dissociation programs belong in every enrichment workflow.
Why controls belong early
Single-cell enrichment is vulnerable to programs that recur across many tissues and conditions. Stress, cell cycle, interferon response, and dissociation effects can produce convincing but nonspecific signal.
Build a reference set
Maintain versioned signatures for common technical and biological programs. Test the target gene set against these controls using the same scoring and resampling procedure.
Interpret overlap
Overlap does not automatically invalidate a result. It changes the claim. A disease program may include a common response, but the specific component must be identified.