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Further biochemical studies could determine the type of protein connection between the filaments.
As an alternative scoring function, we used only the best scoring protein connection between a miRNA and a disease instead of the sum over all connections: For each of the two scoring functions and for each of the three sets of miRNA protein associations (Table 1), we produced a list of inferred miRNA disease associations ranked by score.
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In the discussion section we are simply placing the published biochemical data in the framework of the structure and protein connections we have visualized.
PPA1 and PI15, on the other hand, were only detected at 6 h with the former displaying multiple protein connections while the latter was limited to one.
From the network analysis of 126 genes in N-bicluster 9, a network comprised of information from metabolic and protein:protein connections included 179 nodes (52 genes and 127 metabolites) linked by 261 functional relationships.
VGLUT1, encoded by Slc17a7, was selected for validation because it was differentially abundant between wild-type and db/db samples, not altered by metformin treatment and identified by GePS and IPA as having significant protein connections and functions.
The protein Cti6 appears to have a direct or indirect (through other absent proteins) connection with Dep1, Sap30 and Sds3 in the large complex since it was not detected in these deletion strains.
Thus, our networks tended to have a particular structure requiring all pathways to alternate between gene and microRNA due to the lack of protein-protein connections.
There are three main parameters involved in our method: the weights of the disease-protein connections, the weights of the protein-complex connections, and the restart probability in the random walk model.
Here we identified characteristic protein-protein connections within the THP1r2 Mtb-induced profile with the involvement of a third factor (hub).
The weights of the disease-protein connections determine the possibility of jumping from the disease layer to the protein layer and vice versa.
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