There was no indication of function for 38 ORFs, of which 18 have no homologs in the database.
As with all studies that use gene expression as an indication of function, this analysis will be unable to identify gene products that are involved in the process under examination but whose transcript levels do not appear to change in general, or at least in the samples examined.
We tested for selective maintenance of codon structure in the filovirus-like NIRVs as a further indication of function.
If we assume that sequence similarity is an indication of function similarities, there are four superfamilies which contain putative laccases.
This observation is not an indication of function, but rather an indication that all CpGs have the ability to be methylated.
The absence of a signal sequence suggests an intracellular localization, and an indication of function comes from the presence of multiple HEAT repeats.
Since identification of individual genes conveys little indication of function, we compiled a list of genes differentially regulated according to their role as part of complexes, pathways and biological networks using the Ingenuity systems functional analysis.
We will therefore use for instance EGII instead of Cel5A, based on the consideration that these names were mainly used in database depositions and give a clearer indication of function.
If we interpret evolutionary conservation as an indication of function, we believe the conserved sites listed in Table 4 represent those miRNA target sites that are most likely to regulate opsin expression in African cichlids.
Despite the burst pattern of young retrocopies that accumulated in the genome, retrocopies with indications of function (dN/dS significantly <0.5, overlap with Ensembl genes, or evidence of transcription) were much more overrepresented among the old than young retrocopies (Figs. 4, 5 and 6).
