One of the biggest mistakes bioinformatics researchers make when interpreting pathway analysis results is assuming that the number of times a term appears in the results is an indicator of how important the pathway is. For example, someone might see “Wnt signaling”, “Wnt signaling in cancer”, and “Wnt signaling cascade” and assume that WNT signaling is highly upregulated in their data set. In reality, pathways are not independent. They overlap, sometimes considerably. And when you start (1/2)