Highest CpGo/e ratios were observed in genes involved in the oyster's innate immune response, including categories of cell adhesion, cell-cell signaling, and signal transduction.
Pupal weight was significantly correlated with 479 transcripts enriched for the GO categories of puparial adhesion, regulation of protein import into the nucleus, and iron ion binding (Table S4 and File S3).
However, in terms of host gene functions, no overlap was identified between the resistant and permissive genes as the former were mapped on the categories of cell adhesion, multicellular organismal development and cell differentiation, while the latter on immune response, cell surface receptor signal transduction, cellular defense response and chemotaxis.
In the sub-categories of cell adhesion, genes associated with cell matrix adhesion and cell substrate adhesion were far more abundant than those associated with cell cell adhesion (enrichment P = 10−31 versus P = 10−12, respectively).
Genes of interest, in LEC belonging to the category of cell adhesion molecules, WNT and Notch signalling pathway were validated with real-time PCR and immunofluorescence.
Functional gene set analysis revealed that molecular categories of 'ATPase activity'cellell adhesion' or 'tyrosine kinase activity' were commonly activated in the resistant clones.
Genes that were most upregulated in the S9 set comprised a significantly elevated number of genes of the GO categories "cell adhesion", "neurogenesis", "tissue development", "morphogenesis", and "regulation of cell size".
This switch is accompanied by the reduction of categories, like cell adhesion and cell communication and induction of the similar categories that included cell proliferation and mitotic cell cycle (Additional file 1 Table S12).
For example, in vivo healed skin substitutes gained the expression of many native skin-expressed genes, including those associated with epidermal barrier and multiple categories of cell cell and cell basement membrane adhesion.
They also found differential expression between genes in the functional categories of mitochondrial function, ubiquitination, cell adhesion and RNA metabolism.
