By visual inspection of functional connectivity patterns of the DMN, all these studies suggested that the connectivity patterns of the DMN were quite similar across different resting states.
with manual inspection of functional annotations from top hits.
After inspection of functional annotation of genes (inferred from the most similar gene in A. thaliana) in each module, we identified some meaningful co-expressed genes.
These GO terms reflect the four functional categories previously identified in this data, but detailed inspection of the functional annotations of the genes in each cluster reveals a finer level of biological specificity than previously identified.
However, this conclusion was drawn from the visual inspection of the functional connectivity patterns within the DMN and no statistical comparison was performed.
When these correlations (r-values) are color coded, it allows for a visual inspection of the functional relationships, or lack thereof, among coexpressed genes.
Variables were developed by visual inspection of the functional form of the relationship with the logarithm of PNC, ln PNC), and included in the models if p <0.05 and R increased by >1%.
An inspection of the functional annotation of these genes revealed that the larger cluster primarily consists of ribosomal proteins while the smaller cluster contains only four genes, two of which encode cation efflux system proteins (czcA), which have been shown to be required for growth at low pH (Bijlsma et al., 2000).
A value of 0.25 was chosen after manual inspection of the functional-similarity of the sub-facets contained within each facet, along with the mean JSD between the samples within each facet.
However, unlike existing databases, we retain and refine these "alternate" domain definitions after careful inspection of structural similarity, functional sites and automated domain definition methods.
Finally, all genes were ranked (viii) according to a combined overall score: the top 50 genes were cross-checked (ix) against a set of reportedly MG-associated genes, and also subjected to GO analysis for inspection of their main functional categories [ 46].
