For example the most abundant processes-function pairs were: "regulation of transcription, DNA-dependent" with "DNA binding", "signal transduction" with "protein binding", and "regulation of transcription, DNA-dependent" with "transcription factor activity".
The lack of correlation may also potentially be attributable to the distance between species (the overall tree length of this dataset was roughly 7.5 times shorter than that of the bacterial dataset) and the positive test case to negative test case ratio (the most abundant process-function pair only contained 5.9% of the 730 genes), which is known to cause under-fitting in model fitting.
Finally, Cell Communication (7.0%), Endocrine System (7.9%), and Immune System (4.9%) were the most abundant "Cellular Processes" subterms.
The most abundant biological process GO terms were oxidation-reduction process (1,608 unigenes) and response to salt stress (1,381 unigenes).
The top most abundant biological process categories significantly down-regulated in affected tissues included the cellular process (27.7% in inner, 26.1% in outer cortex), the biosynthetic process (16.1% in inner, 13.5% in outer cortex) and transport (15.2% in inner, 10.4% in outer cortex).
The most abundant Biological Process GO codes represented by the largest percent of transcripts were 'Metabolic process' (23.2%) and 'Response to stimulus' (13.4%), indicating that a large range of metabolic activities occur in E. fischeriana root.
To gain insight into the protein evolution rate according to biological process and molecular function, the annotated transcriptome dataset was partitioned according to the most abundant biological process and molecular function GO slim categories.
The second and third most abundant biological process terms for nucleolar-enriched proteins are respectively cellular component organisation with which 81 proteins are annotated and ribosome biogenesis with which 50 proteins are annotated.
In the biological process, the most abundant subcategories were cellular processes (7064) and metabolic processes (5676).
Within biological processes, the most abundant categories were metabolic process (380 sequences or 27%), cellular process (350 sequences; 25%) and response to stimulus (210 sequences; 15%).
Amongst biosynthetic pathways, biosynthesis of amino acids and flavonoids were most abundant whereas other processes like wax and pigment synthesis had smaller representation.
