To supplement the functional annotation, PANTHER Molecular Function terms were assigned to all bovine transcripts using the Hidden Markov Model scoring tools of the PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System version 6.1 http://panther6.ai.sri.com/tools/hmmScoreForm.jsp.jsp
Most of the molecular functional GO terms associated with down-regulated DEGs were in the same categories as those of upregulated DEGs, although several unique terms were identified, including sequence-specific DNA binding transcription factor activity, hydrolase activity on O-glycosyl compounds, substrate-specific trans-membrane transporter activity, and nucleoside-triphosphatase activity.
Thus, we would propose that the complex we have identified is clearly defined and exists in both molecular and functional terms.
Thus, although several non-clathrin endocytic pathways have garnered varying degrees of supportive evidence, none has been unambiguously established in molecular and functional terms.
Fisher's exact test showed that 10 functional terms in Biological Process and two Molecular Function terms were significantly enriched among these genes (Table 1).
At the level of protein class or Gene Ontology (GO) molecular function annotation, we only have 13,591 genes with any experimentally based functional annotations and, of the 8600 GO molecular function terms, most have very few associated gene products.
We observed that members of these particular clusters have been annotated with GO molecular function terms such as nucleotide binding, GTP binding, protein binding GTPase activity, indicating overall similar functional properties shared by these proteins (see Figure 2C).
A total of 156 DEGs were assigned to three gene ontology classes: biological process, cellular component and molecular function, with 509 functional terms.
Figure 1 displays a rough molecular functional classification (GO terms) of the UniProtKB (taxonomoy: viridiplantae -identified proteins from the trichome-enriched sample material after submission to Percolator and setting the 'expect cut-off' threshold to 0.05.
