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First, the pathway of a biological process should be as fully accurately as possible.
It is expected that the Molecular Function and Biological Process should be more powerful for phosphorylation site prediction, since some known phosphorylation proteins may be annotated by the GO terms related to phosphorylation.
In this network, TFs that participate in the same biological process should be grouped together.
The best level of mathematical abstraction for any biological process should be determined by the nature of the question being addressed.
Since these biological processes are known to be important in CRC, we concluded that GO biological process should be a key feature for computing the EdgeStrength (method section - equation (vi)).
Concerns regarding the biological basis of the model (e.g., the presence of an interaction not documented in the scientific literature, or behaviour differing from that expected of the biological process) should be directed to the model's author(s).
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In all, because the majority of gene products function together with other gene products, biological processes should be considered as complex networks of interconnected components.
Due to the fundamental insight that biological processes should be studied holistically [ 2- 4] instead of reductionistically, systems based approaches are of central importance in this respect [ 5].
Furthermore, as neurodevelopment system and neuronal signaling cascades in the brain play important roles in the pathology of nicotine addiction, the genes and pathways related to these biological processes should be the major targets in nicotine addiction study.
The term 'biological process' should be interpreted as a biological function to which the gene product contributes.
Finally, the digital programming process should be extended to the wet lab to manufacture the designed synthetic biological systems.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com