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Significant trait associations involving the SNP S5_152926936 on Chromosome 5 were detected in all three models, particularly the trait network area.
By thresholding these edge orienting scores, one can arrive at a globally oriented trait network.
The second limitation is that the resulting global trait network may contain loops, i.e. it may be cyclic.
While local DAGs are used for orienting individual edges, the reconstructed global trait network may no longer be acyclic.
For example, one can estimate a trait network using a graph inference algorithm, and then find the clusters of traits in the network using a clustering algorithm.
The edge orienting results should be relatively robust with respect to different choices of K. NEO orients each edge separately in an undirected input trait network.
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While gene expression traits (profiles) and clinical traits represent different quantities, both can be described in undirected trait networks.
The pairwise correlations between gene expression traits and/or clinical traits can be used to define undirected trait networks.
Natural randomization of alleles that occurs during meiosis can be used to study the causal information flow through trait networks.
Using genetic markers for orienting the edges of trait networks generated in genetic experiments provides significant statistical power and specificity for recovering directed edges [ 14- 22].
We previously described the integrated Complex Trait Networks (iCTNet) as an attempt to capture multiple biological relationships available in the public domain.
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