Fig. 3

Patterns of differentially regulated gene expression across Porolithon onkodes experimental treatments. a The T + pH treatment results in significantly upregulated and downregulated transcripts when compared to other treatments (heatmap of log2-fold-change FDR values < 0.05). Experimental treatments are labelled at the bottom of the heatmap. Two main clusters corresponding primarily to upregulated (cluster 1) and downregulated (cluster 2) transcripts in the T + pH treatment are evident. b Overrepresented biological processes (terminal nodes; corrected p-values < 0.05) within cluster 1 transcripts include metabolism and catabolism, response to stimuli (biotic and abiotic), and regulation. Circle size indicates frequency of the gene ontology term in the UniProt database; colour indicates significance, on log₁₀ p value scale. Axes have no intrinsic meaning; however, semantically similar gene ontology terms remain closely together in the plot. c, Biological processes corresponding to terminal nodes from overrepresentation analysis of transcripts found in cluster 2 include mitochondrial processes, chorion development, and immune response