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The BAG3 protein possesses three known protein interaction motifs: the WW domain, which interacts with the PPXY sequence found in various subcellular compartments [14]; the PxxP motif, a candidate interaction site for SH3 domain proteins [22]; and the BAG domain, which interacts with Hsp70/Hsc70.
The classifier may also be helpful in predicting new candidate interaction protein pairs.
When multiple distinct attributes all support a candidate interaction pair, the confidence of PPI increases.
Another candidate interaction partner for both GluA4 and SAP97 is 4.1N, a scaffolding protein linked to cell surface transport and anchorage of GluA1 [43], [43] and GluA4 [25] AMPA receptors.
In many applications, where the goal is to find a set of candidate interaction pairs for further conformational studies, only the gene pairs identified at low FPR levels are relevant.
Furthermore, candidate interaction pairs are also influenced by the significance thresholds p and q.
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In other words, it does not explain mechanistically how transcription factors interact with regulated genes, but indicate candidate interactions with a strong evidence in expression data.
In addition, we recognized a common disadvantage in these current approaches; that is, all of them were developed to generate a best solution (QTL interaction) among numerous candidate interactions, and do not consider relations among subsets of interacting QTLs.
One can parse these sorts of candidate interactions to ridiculous degrees: Was Mr. Romney subtly digging at Mr. Huntsman for his service to Mr. Obama?
Two hundred twenty-seven proteins from C. albicans and five proteins from macrophages were identified as candidate interaction-specific molecules.
This paper shows that, with a short list of candidate interactions, the important interactions can be detected efficiently by a single pass of all subsets regression.
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