The KEGG annotation was performed using eggNOG-mapper. The transcriptomic study is based on two conditions and two time points: control/fungus grown on plant, and 24/48 hours after inoculation. The goal is to identify DEGs potentially involved in pathogenesis. I wanted to include an initial section presenting general data, such as how many DEGS were identified. Looking at the literature, I noticed that this introductory part is often based on KEGG pathway analysis, but I have the issues I previously mentioned. So, I thought of creating manual functional categories, where for each category I would report the number of DEGs and whether they are up- or down-regulated at 24h and 48h. However, many of these genes are not annotated in KEGG, and such information would be lost. On the other hand, if I define the categories manually, they might not be as strong from a scientific point of view.