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Reconciling S-LDSC and LDAK functional enrichment estimates.
Supplementary Figure 9 MaxCPP enrichment estimates are not sensitive to the maximum number of causal variants per locus modeled by CAVIAR.
We report MaxCPP enrichment estimates for each of 44 GTEx tissues with CAVIAR modeling either up to six or up to three causal variants per locus.
We found large enrichment of heritability in functional components of relevant tissues for various complex traits, and FUN-LDA yielded higher enrichment estimates than existing methods.
Our results demonstrate that while accurate enrichment estimates can be obtained for individual repeat types and small sets of repeat instances, there are distinct combinatorial patterns of chromatin marks associated with major annotated repeat families, including H3K27me3/H3K9me3 differences among the endogenous retroviral element classes.
Enrichment estimates are calculated using common microarray summary statistics and a weighted Bayesian analysis of the ranked sequence space.
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To investigate whether the cognitive reserve hypothesis helps to explain differential cognitive impairment among survivors of traumatic brain injury (TBI), whereby survivors with greater intellectual enrichment (estimated with education) are less vulnerable to cognitive impairment.
Weighting the data in this way appears to increase sensitivity of the enrichment estimate and has enabled us to apply our method to estimate weaker enrichment profiles, for example, those associated with siRNA off-target transcript inhibition.
Lifetime intellectual enrichment (estimated with education or vocabulary knowledge) lessens the negative impact of brain disease on cognition, such that people with greater enrichment are able to withstand more severe neuropathology before suffering cognitive impairment or dementia.
The one-tail and two-tail enrichment score estimates are integrated while weighting their contribution based on the estimated mode of regulation through a procedure we call three-tail approach.
Total proteins and brush border membranes (BBM) were prepared in PBS containing protease and phosphatase inhibitors (Sigma Chemicals, St Louis Mo, USA) as previously described [9] and enrichment was estimated by determination of alkaline phosphatase activity (20-fold increase of activity in BBM).
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