https://www.pierre-francois-roux.com/tags/transcriptomics/ Recent content in Transcriptomics on Pierre-François Roux Hugo -- gohugo.io en-us © 2021 Pierre-François Roux Fri, 19 Jun 2026 09:40:00 +0000 https://www.pierre-francois-roux.com/2026/06/19/make-enhancer-analyses-gene-aware-but-not-gene-blind/ Fri, 19 Jun 2026 09:40:00 +0000 https://www.pierre-francois-roux.com/2026/06/19/make-enhancer-analyses-gene-aware-but-not-gene-blind/ Enhancer analyses often fall into two traps. The first is to treat enhancers as isolated genomic intervals. The second is to assign every enhancer to the nearest gene and pretend the problem is solved. A better compromise is to make enhancer analyses gene-aware, but not gene-blind. Classify Enhancers Before Linking Them Start by defining interpretable enhancer classes. For example: Active enhancers: H3K27ac and H3K4me1 positive. Poised enhancers: H3K4me1 positive, low H3K27ac. https://www.pierre-francois-roux.com/2026/06/19/think-in-trajectories-not-only-in-contrasts/ Fri, 19 Jun 2026 09:00:00 +0000 https://www.pierre-francois-roux.com/2026/06/19/think-in-trajectories-not-only-in-contrasts/ Differential expression is often framed as a list of pairwise contrasts: treated versus control, late versus early, condition A versus condition B. That is useful, but it can flatten a time-course experiment into disconnected snapshots. When samples are ordered in time, a better first question is: which genes follow similar trajectories? A transient pulse, a delayed induction and a progressive repression can all have the same fold change in one contrast, but they usually mean different biology.