The unigenes were classified into three major functional categories: biological process, molecular function, and cellular component, according to the standard Gene Ontology terms (GO; ).
Using standard GO annotation, contigs from the combined assembly were next classified according to three major functional categories: biological process, molecular function and cellular component.
The genes induced or repressed in PPV-infected protoplasts were annotated, assigned to a predicted function and classified into 12 different major functional categories using the Arabidopsis MIPS functional classification scheme.
All transcription-regulated genes were categorised into three major functional categories: biological process, cellular component, and molecular function.
Total down-regulated and up-regulated genes and major functional categories clearly showed that the vast majority of transcript changes occured in K-5-8 leaves.
Based on sequence homology, 24,232 (36.95 %) unigenes were classified into three major functional categories (biological process, cellular component and molecular function) and 60 subcategories (Table 2 and Additional file 2).
The MCOA scores for genes and species are shown in figure 4. The analysis detected outlier genes in all major functional categories at different thresholds, with the majority (n = 195) having different histories in 10 30% of the trees (fig. 4).
In addition, we used Blast2GO to determine the functional annotation based on GO terms into the three major functional categories: Cellular Component (CC), Biological Process (BP) and Molecular Function (MF).
Analysis of the distribution of genes representing major functional categories reveals that chromosome 1 encodes most of the key functions required for transcription, translation, and DNA replication, while chromosome 2 encodes functions involved in energy production and conversion, secondary metabolism, and amino acid transport and metabolism.
Tinbergen envisaged such a mechanism for each of the major functional categories of behaviour: foraging, reproduction, antipredator behaviour, and so on.
Planned expenditures are broken down by major functional categories such as defense, education, health and welfare, housing, and so forth, which are to serve as guides in the preparation of annual budgets.
