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There was no difference between time spent in each of the conditioning compartments during pre-test (genotype x compartment interaction: F 1,31) = 1.3; p = 0.26), ensuring an unbiased baseline (Fig. 9A).
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This variation in the timing of V-host compartment interactions most likely stems from a difference in the kinetics of V trafficking that occurs when V is translocated during a natural infection compared to that by PA-mediated uptake.
Fifteen percent of the variation (component 4) did not follow a distinct pattern of treatment or compartment effect, perhaps indicating a treatment-compartment interaction, variation due to the technical procedures involved in sample preparation, sample variation (among piglets) or a combination of these factors [see Additional file 1].
Differential gene expression between compartments and differential expression profiles between compartments (interaction effect) were selected with FDR < 0.5% (Benjamini-Hochberg procedure) and a fold change >2.
The former category can be further divided into intra- and inter-compartment interactions--two sets that unambiguously illustrate the protein-based interaction between compartments.
Thus, most of the variation in gene expression was due to the treatment effect with minor effects contributed by the epithelial-compartment and treatment-compartment interactions.
Importantly, the closer two compartments are to each other, the larger the number of PPIs between their respective protein components (inter-compartment interactions).
The large proportion of observed intra-compartment interactions support that protein-protein interaction is a major driver for intra-nuclear organization.
By generating a set of 1000 null models of the whole PPI_lt_U_PCCM network, in which all the interactions were randomly rewired but each node preserved exactly the same degree of connectivity (Maslov & Sneppen, 2002), we determined that inter-compartment interactions occur far more frequently than expected by chance (P<0.001) between proteins from adjacent neighbor compartments.
Nevertheless, even within a cellular compartment, several interaction domains and their complementary ligands are regularly expressed at the same time, so more contextual information is required to achieve the specificity observed.
IFNα/β receptor can be brought into this subcellular compartment upon interaction with its ligands [ 29].
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