For the molecular function division, a graph was obtained using default criteria and for the other two divisions (cellular component and biological process), seq/node filter values were changed to 4/10 to prevent overloading the graphs.
Most of the contigs in the molecular function division were dedicated to binding functions and catalytic activity (82% of both species; S. psittacina: 7367 sequences and S. purpurea: 6170 sequences) (Fig. 2B).
In the biological process and molecular function division, an abundance of genes were found to be related with metabolic process and catalytic activity and inside the metabolic process and catalytic activity, a number of genes were found related to macromolecule metabolic process and hydrolase activity (Supplementary Figs S1A, B and S2A, B).
We finally randomly selected from this set 50 GO terms irrespective of their GO division (Molecular function, Biological process and Cellular component).
Based on sequence homology, 4,819 sequences could be categorized into functional groups under the "Molecular function", "Biological process" and "Cellular component" divisions (Additional file 3).
For both species, in the three main divisions (cellular component, molecular function and biological process) of the GO classification, 'Cell part', 'Binding' and 'Cellular process', terms are dominant respectively.
goodei and S. saxicola) transcriptomes were relatively similar across the major three divisions (Biological Process, Molecular Function, and Cellular Component) when levels 2 and 3 GO terms were compared.
The division was based on biological process, molecular function, and cellular components.
The last three networks considered in this work have been constructed by computing the Resnik semantic similarities [44] between the terms of each division of the Gene Ontology: biological process, molecular function and cellular component.
The target genes in this clusters were specifically enriched for the biological process (BP) term "cell division", the cellular component (CC) term "nuclear speck", and the molecular function (MF) term "transcription corepressor activity".
