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On the basis of the above prioritization results, we aggregate the Bayes factors between all the 5,490 domains and 1,145 phenotypes, and obtain a matrix of altogether 6,286,050 elements.
We further apply the above prioritization method to all human disease phenotypes and obtain a landscape of gene-phenotype associations that include 5,080 disease phenotypes and 14,944 human genes.
The above prioritization procedure does not work for Black Swans.
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We repeat the leave-one-out cross-validation experiments using the shuffled networks and present the results in Figure 2. The AUC scores are all around 50% in the figure, and we therefore conclude that the above successful prioritization of candidate genes is indeed due to the informative interactions that are included in the phenome interactome network.
As stated above, the prioritization ranks presented here will differ from the EDSP Tier 1 prioritized list because we do not have consistent exposure data for the entire chemical set.
This is important because as mentioned above, the prioritization approach is based on the assumption that multiple QTL regions for a trait reflect variation in genes involved in the same biological process.
Based on the prioritization above, this subsection suggest dividing the local IDNC graph into layer of decreasing importance.
It is clear that the algorithm described above respects the prioritization among devices as the maximum weight clique problem is solved sequentially for a decreasing order of priority.
In comparing these results to those reported above, the exact prioritization across the strategies was estimated.
This is in line with the above mentioned assumption underlying our prioritization method, that multiple QTL regions for a trait reflect variation in genes involved in the same biological process.
To further trim down the number of the suitable germline candidates for subsequent functional analyses, these were filtered for HF levels above 0.8, leading to prioritization of 4 variants (with confidence interval (CI) overlapping in both tumor and blood samples), corresponding to 0.56 % of total (Table 5).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com