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Integration of computational genetic mapping results across related traits- To measure the overall association of a gene with multiple related traits, HBCGM was first applied to evaluate each trait.
The pleiotropy is well-known phenomenon where a single mutation affects multiple related traits (Dudley et al., 2005).
GFlasso is a sparse multivariate regression method that we have previously developed for finding a correlated genome association for multiple related traits given a trait network and genotype/phenotype dataset [ 7].
Here, genome (input) structure refers to the phenomenon where multiple-related SNPs are associated with a single trait; transcriptome (output) structure corresponds to pleiotropic effect that is a single SNP is associated with multiple related traits.
These instances of conditional pleiotropy often appear as "epistatic pleiotropy" (Wolf et al. 2005; Wolf et al. 2006), in which pairs of QTL exhibit epistasis across multiple related traits.
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On one hand, significant genetic correlations were frequently estimated among multiple related trait fractions or percentages of the whole tree body, especially within each trait category in our present study (Supplementary data S3).
Therefore, we induce this effect over multiple-related traits in our model for better GWA inference.
Second, output structure allows us to find SNPs which are associated with multiple-related traits jointly.
Multiple sink-related traits, including grain size and grain number per panicle, were enhanced in the GNS4-overexpressing lines.
Grain number, plant height, and heading date7 (Ghd7) encoding a CCT domain protein is involved in multiple yield-related traits, including heading date, plant height, and grain number per panicle (Xue et al. 2008).
We have collected a large cohort of obese cases and families ascertained from tails of BMI distribution together with detailed phenotype measures on multiple obesity-related traits.
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