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Both clusters contain interactions with a minimal shortest-path length of 2, indicating that they are not embedded in complexes.
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In oligomeric NaD1 PIP2, a single PIP2 binding site also contains interactions with neighboring NaD1 monomers.
We conducted a GO enrichment analysis for all four possible class combinations such that the population set and P-value calculation stayed the same while the study set contained interactions with the same predicted class combinations.
As the TGF β regulated genes that we compiled from the microarray data above does not contain interaction information, we used Cytoscape with the MiMI plugin [28] to identify protein-protein interactions.
We detected elevated interaction frequencies between HindIII fragments containing SNPs rs10816625 and rs13294895 and those containing KLF4; interactions with HindIII fragments either side of KLF4 were lower in comparison.
They were the FunCoup networks containing all interactions with a FBS>6 or FBS>8, in each case supplemented by a small number of literature-derived manually-curated interactions involved in the AHR pathway and the antioxidant responsive element pathway.
The extended data set contained more interactions with less reliability, whose probability > 0.101.
An interesting example of a resolvable conflict in Supplementary Table 8 is the 444 instances of a consolidated interaction containing source interactions with detection method labels MI:0004 (affinity chromatography technology), MI:0007 (anti-tag coimmunoprecipitation), and MI:0676 (tandem affinity purification).
Although a large number of interactions within this pathway occur between the genes, not all the genes contain an interaction with another.
The intermolecular contacts between PrfA dimer and DNA (summarized in Fig. 1B) contain both specific interactions with bases and nonspecific interactions with sugar-phosphate backbone.
The complex can degrade mRNA molecules that have been tagged for degradation because they contain errors, through interactions with proteins from the nonsense mediated decay or non-stop decay pathways.
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