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Cell-type-specific interactomes were created using a confidence cutoff score of 0.8 and random walks completed using a restart probability of 0.7.
The peptides and corresponding relative abundances were obtained in ProteinPilot using a confidence cutoff (called a 'Prot Score') of > 1.3 (> 95%).
The peptides and corresponding relative abundances were obtained in ProteinPilot using a confidence cutoff (called a 'Prot Score') of >1.0 (>90%) and >1.3 (>95%) for the experiments of the green and ripe stages, respectively.
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Miyazawa et al. [16] used a confidence value cutoff to exclude genotype calls with low confidence.
As the network for the enrichment analysis, we predicted a human network of functional coupling using the FunCoup computational framework at a confidence cutoff for individual links defined as a final Bayesian score >7 [ 13].
Three independent RNA preparations per condition were analyzed on three separate chips and averaged; a confidence cutoff of >0.95 was used for the raw values of red/green before normalization.
From the original data, we computed the number of associations for each gene using a default confidence score cutoff of 0.4.
We measured the effect of these two parameters on the GSC method by applying the GSC method to cell-type-specific interactomes created using confidence cutoff scores of 0.0, 0.4, 0.6, 0.6 and 0.8 and using restart probabilities of 0.1, 0.3, 0.5, 0.7 and 0.9.
After adjustment for potential confounding effects, the prevalence ratio of hyperinsulinemia was 2.16 (95% confidence interval [CI], 1.74 to 2.08) when using a single cutoff point of 3.5, and 2.23 (95% CI, 1.83 to 2.72) when using race/ethnicity-specific cutoff points of 3.0 for non-Hispanic whites and Mexican Americans and 2.0 for non-Hispanic blacks for the TG/HDL-C ratio.
Using a 95%% confidence interval and a cutoff of 1 % global FDR, we identified 377 proteins in our comparative proteomic analysis of proteins secreted within the NP of the two respective canine species (please see Additional file 1 Table S1).
This analysis revealed that manual analysis using a 10% cutoff level was associated with a HR of 0.64 (95% confidence interval = 0.46 to 0.81, P < 0.001); however, a 7% threshold as determined following RFC was associated with a lower HR and narrower confidence intervals (HR = 0.59, 95% confidence interval = 0.44 to 0.77, P < 0.001).
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