Comparing Overlap of Transcriptomes
The common practice of of relating two biological processes by determining whether there is significant overlap between their patterns of gene expression assumes all genes are equal. We know that not all genes are equal and our latest publication (Link) demonstrate that simple tests may be flawed.
Lawhorn C.M., Shomaker R., Rowell J.T., & Rueppell O. (2018) Simple comparisons of differentially expressed gene lists may overestimate gene overlap. Journal of Computational Biology, online. doi: 10.1089/cmb.2017.0262. PMID: 29658777.