Comparison of GO term delta-ranks between symbiont genera
To compare the functional signals ofCladocopium and Durusdinium symbionts in response to
codominance, we used the GO_MWU analysis results which output the
degree of up- or down-regulation of GO terms as measured by the
“delta-rank” – the difference between the median rank of the genes
annotated with the term and the median rank of all other genes. In
GO_MWU, a positive delta-rank implies up-regulation of genes annotated
with the GO term. The comparison of delta ranks (rather than per-gene
expression changes) between experiments integrates the signal over
meaningful functional categories of genes and, importantly for the
current study, circumvents the problem of different reference
transcriptomes used. At the GO delta-rank level, responses ofCladocopium and Durusdinium to codominance were clearly
similar (Fig. 3), although the statistical significance of this
similarity cannot be formally ascertained because GO terms are not
independent (they may encompass overlapping sets of genes). Most
notably, ribosomal and photosynthesis categories were similarly and
significantly (p < 0.001) enriched for upregulated genes in
both genera. These GO categories include large ribosomal subunit, small
ribosomal subunit, ribonucleoprotein complex, thylakoid part,
photosystem, and plastid part (p < 0.001).