I have Control cell line day1 to day 26 and Lead(pb) treatment day1 to day26. The experimental design aims to get the impact of Lead(pb) on developmental process .I must look if there are group of developmental genes that cluster differently in the lead(pb) experiment. For instance some genes are differentially expressed directly or others are coming in later time points. First I thought about WGCNA (figure) https://ibb.co/j9O5YS in which I think genes in significant modules in days 1-3 make sense for me. Then I thought about SOM clustering but clusters don't show any up or down regulation in day points
Any help please?