Fig. 3

Human GO ontology and KEGG pathways enrichment analysis of differentially expressed (DE) genes clusters. Clusters of DE genes were obtained by determining an optimal number of clusters using fviz_nbclust from the “factoextra” package with the gap statistic method and performing clustering using tsclust with shape-based distance (SBD), which makes the clustering particularly useful for time series where the shape matters more than exact numerical values. Clusters are standardized to log2 fold-change of abundance. Colors and cluster numbers are arbitrary. The detailed list of enriched terms is presented in Table S3. Enrichment of gene sets was performed using the Cytoscape app ClueGO with the GO biological process, KEGG pathways, and KEGG-human disease ontologies. a Clusters from stable sites. b Clusters from progressing sites. In red, metabolic activities were activated (enriched), and in blue, metabolic activities were repressed