Each secreted protein in the Rut C30 and S4F8 secretomes was annotated according to broad functional categories and their specific enzymatic activity or molecular function (see Additional file 3: Table S3).
The reporter algorithm made it possible to identify key biological processes affected by diet in the three tissues (Figure 2C; for GO "cellular component" and "molecular function" see Figure S4).
Results of the biological term analysis conducted on our putative/predicted list of 1,453 putative histone-coregulated genes are shown in Table 2, which lists the top-10 GO terms returned by GOEAST in the three large GO categories, namely biological process, cellular component and molecular function (see Additional files 15, 16, 17, 18 for details).
For each of these modules, we evaluated the functional enrichment using the human or mouse gene ontology (GO) categories for biological processes and molecular functions (see Methods).
Other functional clusters and terms included therein can be explored for relevance, as well as for detailed insight of specific molecular functions; see Additional file 5: Table S5.
This similarity in the cgh-1 and cpb-3 mutant phenotypes is interesting, given their predicted molecular functions (see the section Discussion).
This substantiates that both sediments display a distinctive similarity in cellular component groups but are only moderately correlated in terms of overrepresented molecular functions (see Additional files 4 and 5).
The transition-based model of Engelhardt et al. assumes replacement of one function by another (gain of one function coupled to the loss of another), and does not capture uncoupled events, which is particularly important for BP annotations and cases where a protein has multiple molecular functions (see examples below).
Furthermore, 75 significantly regulated proteins were mapped to 21 molecular functions (see Figure 4C) and included arginase activity, fructose-bisphosphate aldolase activity, hydrolase and oxidoreductase activity, acting on carbon-nitrogen (but not peptide) bonds, acting on aldehyde, CH-OH group or oxo group of donors, NAD or NADP as acceptor as well as steroid dehydrogenase activity.
Protein molecular functions seen to be often affected are those that relate to: binding, catalytic, transcription regulation, structural molecule, transporter, motor, and antioxidant; and the processes that are often affected are nucleic acid binding, signal transduction, and protein-protein interactions.
Thus, there was no large molecular functional class missing in the sample of 157 families used for the phylogenomic analysis, which was quite representative of the overall relative diversity and abundance of molecular functions seen in the spruce GCAT gene catalogue [ 26].
