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.
In the light of these findings, GO functional category enrichment has been performed for each list of deregulated genes, identifying those functional categories (biological process, molecular function, cellular component and metabolic pathways) commonly shared by the studies.
Sequences with no BLAST hits were then searched against NCBI nr database with an E-value threshold of 10−30 and classified functionally by identifying GO terms of molecular function, cellular component, and biological process using the software Blast2GO [ 59].
Nucleotide sequences were also analyzed using Blast2Go (Version 2.4.4) [ 63] for gene annotation, and to assign the DNA sequences to functional categories (e.g., biological process, molecular function, cellular component).
The transcripts were divided into 63 functional groups within the following three ontologies: molecular function, cellular component and biological process.
Blast2GO [ 81] was employed for GO functional categories according to the Gene Ontology terms molecular function, cellular component and biological process.
Based on sequence homology, 24,168 Rubus sp. sequences were categorized into 40 functional groups, belonging to three main GO ontologies: molecular function, cellular component and biological process.
DEGs were annotated and classified by GO category, which are divided into three ontologies: molecular function, cellular component, and biological process.
E-dependent DEG lists were annotated according to the GO database (http://www.geneontology.org) using ontology categories for Molecular Function, Cellular Component and Biological Processes.
Each of the 450 genes was assigned to Molecular Function, Cellular Component and Biological Process categories as designated by the GO database.
