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Biological processes represented by GO ontologies can theoretically be influenced by more then one TSR; the contrast seen in TSR1 'progression through M phase' vs. 'ion transport' was also seen in TSR3 for example.
This ranking allows comparison of the relative importance of biological processes represented by those gene sets.
It was then of interest to identify biological processes represented by the core network.
The dominant biological processes represented by this signature were angiogenesis, chemotaxis, regulation of cell migration and cell proliferation.
Despite only 40 shared species, there was remarkable similarity in biological processes represented by the DEGs and DEPs.
The majority of biological processes represented by the differentially expressed genes were nearly identical, irrespective of particle diameter.
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However, of note, a biological process represented by a GO ontology is not necessarily influenced by one specific TSR alone but can be influenced by more then one TSR; e.g. the contrast nucleus vs. membrane was seen in several TSRs.
We thus compared our data at a higher level by examining the GO-defined Biological Process represented by the DEGs.
The 'not helpful' category also included instances where the body of literature for that gene refuted an association with the predicted term, or where no literature existed associating the particular gene product with the biological process represented by the prediction.
For a phenotype, a logical definition follows the entity quality (EQ) model (Mabee et al., 2007): the entity is what is affected, and can be the whole cell, a population of cells, a part of a cell (corresponding to a GO cellular component) or an event such as a molecular function or biological process (represented by GO terms).
The three main functional categories in each case were 'Biological process' (represented by 3,799 unigenes from P. erythrurus and 4,235 from P. putjatia), 'Cellular component' (4,037 from P. erythrurus and 4,552 from P. putjatia), and 'Molecular function' (3,854 from P. erythrurus and 4,218 from P. putjatia).
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