In the present study, we grouped genes by molecular function and then focused on the oxidoreductase group, which accounted for many differentially expressed genes.
Proteins are classified by expert biologists into families and subfamilies of shared function, which are then categorized by molecular function and biological process ontology terms.
In GO, the genes are categorized into different GO-terms in three ways: (a) by "biological process", (b) by "molecular function" and (c) by "cellular components".
Transcripts representing genes with known function were classified by molecular function and biological process, according to the ontological definitions of the Gene Ontology Consortium.
Overall, the patterns of association for transcripts were similar in the transcriptomes of acrorhagi from aggressive and non-aggressive polyps: most transcripts are associated with cellular components, followed by molecular function and biological process domains (Table 4).
A total of 14,278 GO terms were collected, which were most frequently related to biological processes (9,106), followed by molecular function (3,843), and cellular components (1,329).
GO annotation was used to categorize unigenes into functional categories by molecular function, cellular component and biological process.
According to the mapping of InterPro entries to GO [ 35], GO accession numbers were assigned to EST clusters, which were used to classify ESTs into functional groups by molecular function, cellular component, and biological process.
The PANTHER ontology, a highly controlled vocabulary (ontology terms) by molecular function, protein class and biological process was used to categorize proteins into families and subfamilies with shared functions.
For NR annotation, Blast2GO software [ 2] was first used to perform gene annotation, and then the WEGO and AGRIGO software [ 67] were used to conduct GO functional classification to interpret the distribution of gene functions defined by molecular function, cellular component, and biological process ontologies.
Among the annotated having GO terms, ~ 49.61 % of them are under the category, Biological Process followed by Molecular Function (37.51 %) and Cellular Component (12.86 %) (see Additional file 8).
