Genome-wide gene expression quantitative trait loci (eQTL) mapping have been focused on single-nucleotide polymorphisms and have helped interpret findings from diseases mapping studies. The functional effect of
MatrixEQTL是一个快速有效的cis/trans eQTL mapping分析工具,被The Genotype-Tissue Expression (GTEx)数据库用于eQTL mapping分析。使用MatrixEQTL进行eQTL mapping需要五个输入文件,即SNP.txt(snpmatrix文件,行名为样本名称,列名为snpid),GE.txt(基因表达量文件,行名为样本名称,列名为基因或者转录本名称),Covariates....
In this paper, we review current methods for eQTL mapping using ASE and discuss some future directions. We also review existing works that use RNA-seq data to study RNA-isoform expression and we discuss the gaps between these works and isoform-specific eQTL mapping.Wei Sun...
We integrate eQTLs identified in adult islets and whole pancreas samples, which reveal 1805 eQTL associations that are unique to the fetal-like iPSC-PPCs and 1043 eQTLs that exhibit regulatory plasticity across the fetal-like and adult pancreas tissues. Colocalization with GWAS risk loci for ...
Figure 3. Mapping ofcis-eQTL in 19 distinct subpopulations (A) Two rounds of conditional eQTL analysis across all cell types (x axis), with the number ofcis-eQTLs (y axis) detected at an FDR of less than 0.05 in each round of analysis. See alsoTable S6. ...
Trait-traitdynamicinteraction:2D-traiteQTLmappingforgenetic variationstudy WeiSun †1,2,3 ,ShinshengYuan †4 andKer-ChauLi* 4,5 Address: 1 DepartmentofBiostatistics,UniversityofNorthCarolina,ChapelHill,NC,27599,USA, 2 DepartmentofGenetics,UniversityofNorth ...
To overcome this limitation, we study the expression of a pair of genes and treat the variation in their co-expression pattern as a two dimensional quantitative trait. We develop a method to find gene pairs, whose co-expression patterns, including both s
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...
The eQTL-Catalogue/qtlmap pipeline comes with documentation about the pipeline, found in thedocs/directory: Mapping QTLs is a process of finding statistically significant associations between phenotypes and genetic variants located nearby (within a specific window around phenotype, a.k.a cis window) ...
both the non-parametric Kruskal-Wallis test and interval mapping using the integrated map of [6] resulted in the identification of the same eQTL for bothFaFAD1andFaFAH1expression (Figure6; Additional file1: Table S5). The eQTL forFaFAD1expression, as expected, collocated with both the ...