Functional enrichment tests
We used a Gene Ontology (GO) enrichment analysis that utilizes the Mann-Whitney U (MWU) test (Wright et al., 2017) to identify significant functional differences among up and down-regulated genes associated with the codominant state. We used -log10 transformed p- values output from DESeq2, multiplied by -1 when the gene was down-regulated, as input for this analysis, following (Dixon et al., 2015). This test compares transformed p-value ranks among genes to determine whether the ranks of genes in a GO category diverge significantly from ranks of other genes. We also used a Eukaryotic Orthologous Group (KOG) MWU test (package KOGMWU in R,Dixon et al., 2015) to broadly determine coral host gene expression response to codominant symbionts. For this analysis, the data from this study was compared to the generalized stress response (GSR) profile from (Dixon et al., 2020) that represents the response of Acropora sp. to any kind of high-intensity stress.
Results