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Notably, despite the great variety of genes and functions being diurnally regulated, most functional categories have only a minority of their total gene set members that are diurnally regulated.
The diversity of SRF's cellular functions was also seen as a significant enrichment in most functional categories.
The data revealed that the percentage of genes involved in most functional categories in the two genomes are quite similar (P = 0.6815).
Because the majority of genes within most functional categories are not diurnally regulated, this implies that some categories may not show a marked temporal enrichment in the day, and even if they do, individual genes within those categories could still perform decisive roles at other times in the day.
For each species, we find that genes from most functional categories are alternatively spliced.
Most functional categories were linked to the location of proteins at the membrane.
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Although most higher functional categories were most abundant in human samples, functions related to cell wall and DNA metabolism as well as carbohydrate biosynthesis are among the few functional categories significantly more abundant in guinea pigs.
To understand the functions of the commonly regulated genes, we identified most significantly functional categories using the Ingenuity function analysis tool (Ingenuity Systems, Inc., Redwood City, CA).
Analysis of the functional category of the down-regulated genes was shown in Figure 2. The results showed that the most affected functional categories were "hypothetical proteins" and "unknown function", representing a total of more than 68% of all the down-regulated genes, consistent with the fact that nearly half of the Synechocystis genome is still annotated as hypothetical up to now [ 10, 18].
The Gene Ontology (Molecular Function, MF) is one of the most comprehensive functional categories annotation.
The long tail of the distribution includes the most common functional categories, presented in Fig. 3 and thus may reflect the most conservative part of the proteome functional space, which does not evolve or evolves very slow.
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