Hello everyone,
I am currently working on a bulk RNA-seq project involving MDCK cells at different stages of development: Immature, Mix-ImmatureIntermediateA, and Intermediate B. We have applied gene expression heatmaps to identify expression patterns, resulting in 13 distinct clusters. Our initial analysis aimed to focus on pathways influencing epithelial architecture; however, my supervisor has advised against limiting our analysis to these pathways.
Given this, we're exploring broader Gene Ontology (GO) analyses. The data show some clusters with gradual expression increases and one notable cluster that spikes drastically in expression. We've used silhouette scores to refine our cluster identification but are still debating the best approach for further analysis.
I am looking for guidance on how to proceed with Gene Ontology or any other analysis that could help interpret these patterns and identify key genes across these clusters. What strategies would you recommend for drawing meaningful conclusions from each cluster?
Thank you for your insights!
