We then proceeded with replicating the causal inference of the eQTL—TE—gene triplets to corroborate our findings. We tested the triplets where all three molecular phenotypes were present in either GTEx colon transverse for the SYSCOL normal colon triplets or in TCGA-COAD for the SYSCOL tumor tri...
This limitation somewhat constrained the process of causal inference. Conclusion This study revealed an association in which the likelihood of DOR increased with higher overall concentrations of AE/AEEs in follicular fluid. Among the nine detected elements, the higher concentrations of K, Li, and Cs...
Cell type-specific gene expression patterns and dynamics during development or in disease are controlled by cis-regulatory elements (CREs), such as promoters and enhancers. Distinct classes of CREs can be characterized by their epigenomic features, inclu
However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, ...
Here, we obtained near-complete genome assemblies of four additionalC. fulvumisolates. The genome assemblies had similar sizes (66.96 to 67.78 Mb), number of predicted genes (14,895 to 14,981), and estimated completeness (98.8 to 98.9%). Comparative analysis that included the genome of isolate...
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identifying the overall directions and magnitudes of the effects of EE elements on EA. Various EE literature reviews have shed light on the diversity of relevant definitions and the theoretical foundations of the approach, highlighting the importance of understanding the causal mechanisms of EEs in dev...
). DAGs, also known as causal graph, is an approach based on literature review to determine the minimum sufficient adjustment set in causality and identify confounders [30, 31]. Subgroup analysis was applied to find the potential associations between the essential elements and the prevalence of ...
provide functional explanations of genetic sex interactions16. Indeed, a causal relationship between testosterone and CKD was found in men only17. Here, we conducted a cross-ancestry X chromosome-wide association meta-analysis pooling results of 40 studies on up to 908,697 individuals (up to 757...
of SVs to what inference methods were able to identify4,5,6,7,8,9, but also required a reference genome to map the reads, which has at least three major drawbacks: (i) the information about the genetic background and genomic context of the SVs are usually lost4; (ii) the analyses ...