For each FSF that belongs to the 352_set, the max_set, and the min_set, we tabulated molecular functions defined by SCOP coarse-grained functional classification, mean of G and f indices, and superkingdoms distribution in Additional file 1, Table S1.
Although this consensus sequence can vary in tRNAs and other RNAs (data not shown), it raises the possibility that NSun2-mediated methylation may have different molecular functions defined by the context of the surrounding sequence.
Four of the 11 duplicated ORFs have their molecular function defined as protein-binding (fbxa-118, and fbxa-194) or carbohydrate-binding (clec-258, and clec-259).
We looked for categories of biological process and molecular function defined in the Gene Ontology (GO) database that were significantly enriched or depleted in these genes [ 28, 29].
This includes three main categories: Biological process, referring to the biological objective of the genes or gene products; Molecular function, defined by the biochemical activity of the genes or gene products; and Cellular components, referring to the place in the cell where the gene product is active [ 17].
The constraints placed on molecular function define the possible phenotypes of an organism under specific conditions [ 2].
The functional categories scrutinized are biological processes and molecular functions as defined in the Gene Ontology Consortium database (http://www.geneontology.org)[49].
An online version of the GeneMerge program [ 40] was used for ORA to identify whether particular biological processes or molecular functions, as defined by GO annotations, are statistically enriched in the set of differentially expressed genes in the sis7-1 mutant compared to the wild type [ 41].
Molecular functions were defined based on data from MetaCore tool of GeneGo package i.e., Network objects (object types), Gene Ontology Annotation (UniProt-GOA) Database GOA [ 38] and literature.
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.
Three ontologies, biological process, cellular component, and molecular function, are defined in GO.
