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Figure 3 shows that in all three networks protein pairs with high PageRank Affinity are more functionally related (have smaller functional distances).
Because interacting proteins tend to have similar or related functions, a reliable PPI network should contain many more functionally related proteins than a random network.
For the first three panels higher values are better because they indicate more co-complex pairs that are close, while for the next three panels lower values are better because they indicate that pairs that are close have low functional distances, and are thus more functionally related.
The more an operon is conserved, the more functionally related its genes are.
These results indicate that genes with co-occurring mutations tend to be more functionally related, and vice versa.
Therefore, the higher the normalized co-operon frequency, the more functionally related they are considered to be.
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With fMRI, one can more accurately define the seed ROI for DTI based tractography and to provide a more comprehensive, functionally related, white matter mapping, a very important tool used in pre-surgical mapping.
As described in the Introduction, we used the GO annotation database [30] to assemble groups of 30 or more unique functionally related genes (smaller groups will not yield good enrichment statistics); there were 134 such different functional GO classes.
We also demonstrated that our metric is able to pool the disease genes respect to the other human genes, implying that the former are indeed more closely functionally related than the latter: these results therefore justify a prioritization strategy based on the similarity of the candidate genes respect to the disease gene set.
We chose sizes of 2 20, assuming that smaller modules would represent more closely functionally related gene sets and thus the overall coexpressions within modules would be higher.
This widespread prevalence of AS challenges our perception of what might constitute a gene [ 16- 18], and even if does not affect the concept of orthology relationship at the gene level, at the transcript level requires the introduction of a new concept of "splicing orthology" to identify structurally similar splicing variants whose products may also be more likely functionally related.
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