493-497. ///Genetic mapping of cell type specificity for complex traits. Nat. Commun. 10, 1-13.细胞分辨率的研究,TSPAN13和ZNF414上的eQTL所示,仅存在于CD4 + T细胞中
Efforts to map the genetic loci (called expression quantitative trait loci, eQTL) that contribute to gene expression variation reveal numerous local-eQTL, where a gene's mRNA abundance is associated with genotype near its genomic location, and also trans-eQTL, where a genetic locus affects the ...
CASE is an R package designed for multi-trait fine-mapping analysis, with a particular focus on single-cell eQTL fine-mapping.1. InstallationCASE can be installed from the Github Repo.# Install the devtools package if you haven't already # install.packages("devtools") devtools::install_github...
To identify putative functional mechanisms of novel loci, we performed Bayesian colocalization on meta-analysis and MTAG summary data with GTEx v8 tissue-specific gene expression quantitative trait loci (eQTL) using coloc22. Of the four novel loci identified by meta-analysis, none were colocalized ...
In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and ...
eQTL-Catalogue/qtlmapis a bioinformatics analysis pipeline used for QTL Analysis. The workflow takes phenotype count matrix (normalized and quality controlled) and genotype data as input, and finds associations between them with the help of sample metadata and phenotype metadata files (SeeInput formats...
Through the integration of eQTL/mQTL results and GWAS associations signals, we identified 205 genes at Bonferroni-corrected PSMR < 0.05 (Supplementary Data 15–19), including 150 genes from the eQTL ana- lysis and 84 genes from the mQTL analysis. Of these, 45 (21.9%) genes were also ...
(eQTL) data from reference datasets such as GTEx [1]. However, a main challenge is the high false positive rate for such tests caused by confounding due to linkage disequilibrium (LD) and co-regulation. Reducing the number of false positive associations, referred to as fine-mapping, is ...
现在GWAS 研究越来越多。要查询以往的 GWAS 研究结果,可以使用 GWAS Catalog。GWAS Catalog 包含的信息非常多,不过有时可能满足不了需要。这里,推荐一个叫 CAUSALdb 的数据库。 CAUSALdb(http://mulinlab.tmu.edu.cn/causaldb/index.html)是一个整合了大量人类 GWAS 摘要统计信息,并通过统一处理进行 fine-mapping ...
Developments in the methods so called co-localization [30–34] further enhanced the value of statistical fine-mapping, by analyzing the results of statistical fine-mapping on complex traits and gene expression regulation (expression quantitative loci, or eQTL) studies simultaneously to elucidate the ...