2024 Eqtl meta analysis

Eqtl meta analysis

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WebeQTpLot is an intuitive and user-friendly R package developed for the visualization of colocalization between eQTL and GWAS data. eQTpLot takes as input standard GWAS and eQTL summary statistics, and optional pairwise LD information, to generate a series of plots visualizing colocalization, correlation, and enrichment between eQTL and GWAS … WebOct 19, 2024 · We observed that cis -eQTLs can be detected for 88% of the studied genes, but that they have a different genetic architecture compared to disease-associated variants, limiting our ability to use cis -eQTLs to pinpoint causal genes within susceptibility loci.

Susztak lab: eQTL Atlas

WebJan 30, 2024 · Here we developed the multivariate multiple QTL (mmQTL) approach and applied it to perform a large-scale trans-ethnic eQTL meta-analysis to increase power … WebThe publicly available eQTL database identified 5 eQTLs which exert cis-regulation effects on OPG at FN and LS. Literature searching found that rs2073617 (known as T950C) was the hot spot SNP. There were 13 relevant studies on rs2073617 besides the GEFOS-2 study identified from the PubMed. potato enchiladas with ranchero sauce

Genetic association of lipids and lipid-lowering drug target genes …

WebNov 28, 2014 · To our knowledge, meta-eqtl is the first software to perform meta-analysis on arbitrary number of eQTL datasets. We thus compared our results with those obtained with METAL [],[], a tool which performs meta-analysis on pre-stored test statistics.On a data of four individual sets (sample size of 1000, 1000, 500 and 500, respectively), we tested … WebSummary of kidney compartment-based eQTL analysis. a, Diagram indicating the work flow (and results) by which eGenes were identified in the tubular and glomerular compartment of human kidneys.b, Diagram illustrating the number of tubule-specific (top) and glomerulus-specific (bottom) eGenes identified by meta-analysis of eQTLs from 46 human tissues … WebOct 1, 2014 · A larger meta-analysis involving 5311 whole blood samples further increased the number of reported trans -eQTL genes to 430 and showed that trans -eQTLs can be informative of disease pathogenesis: in two previous cross-sectional studies, several interferon response genes had been identified that show strongly dysregulated … to the nightingale anne finch

Cookbook for eQTLGen phase II analyses - eQTLGen Phase II

Expression quantitative trait loci - Wikipedia

WebMay 17, 2024 · Here we generate cerebral cortical eQTL from 1433 samples available from four cohorts (identifying >4.1 million significant eQTL for >18,000 genes), as well as … WebFirstly, mQTL should be included to verify and improve our result. Secondly, we used several eQTL datasets in that paper, whereas a meta-analysis method should be used … tothenham vs chelseaWebApr 15, 2024 · Methods: We first evaluated eQTLs and sQTLs of the CommonMind Consortium (CMC) and Genotype-Tissue Expression Project (GTEx) using genotyping, or whole-genome sequencing and RNA-seq data. Alternative splicing events were characterized using an annotation-free method that detected intron excision events. tothenham fc

"WebMar 17, 2024 · The use of whole genome eQTL analysis has separated eQTLs into two distinct types of manifestation. The first is a cis-eQTL (Figure 31.3) in which the position … " - Eqtl meta analysis

Eqtl meta analysis

WebLee BN, Yao X, Shen L. (2024) Integrative Analysis of Summary Data from GWAS and eQTL Studies Implicates Genes Differentially Expressed in Alzheimer’s Disease. WebResults: Meta-analysis of 9953 females combining discovery (N = 4658) and replication (N = 5295) stages detected four (rs11162584, rs6760543, rs828104, rs56137030), six (rs139702234, rs2341967, rs73059848, rs5020945, ... If a variant is not an eQTL, the gene in which a variant is located or closest to a variant is assigned as the candidate gene

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WebAug 25, 2024 · Background Advances in the expression quantitative trait loci (eQTL) studies have provided valuable insights into the mechanism of diseases and traits-associated genetic variants. However, it remains challenging to evaluate and control the quality of multi-source heterogeneous eQTL raw data for researchers with limited computational … WebThe eQTL analysis is restricted to sentinel meQTL SNPs. Following the snakemake workflow eqtl_sentinel_snp/Snakefile , eQTLs are calculated separately for each cohort (adjusting the expression for covariates and houseman groups before) and then the results are combined in a meta-analysis.

WebMar 30, 2024 · For the primary outcome, summary genetic association data were extracted from a GWAS meta-analysis of four cohorts of electronic health record-documented NAFLD with participants of European ancestry including 8434 cases with hepatic steatosis, NASH, or liver fibrosis and 770,180 controls. 28 It is the largest GWAS dataset for analyses of ... WebApr 4, 2024 · In the meta-analysis, we identified 5 genome-wide significant loci (1p13, 7p15, 11p15, ... For cis-eQTL and sQTL analysis, associations were evaluated using fastQTL v2.0, 29 based on the additive effect model of the imputed dosage of each variant on the gene expression and splicing event, respectively. We included only age and sex …

WebJoint statistical fine-mapping of eQTL and GWAS identified 329 variant-trait pairs for 24 brain-related traits driven by 204 unique candidate causal variants for 189 unique genes. … WebDec 13, 2011 · Summary: seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The …

WebJan 8, 2024 · We first assessed how eQTLs used as instruments from this cohort compared to alternative brain eQTL datasets available for public download, specifically a meta-analysis across AMP, CMC and GTEx on pre-frontal cortex tissue (brain cortex meta-analysis), and a meta-analysis across 10 different brain tissues available in GTEx …

WebJan 31, 2024 · The meta-analysis eQTL dataset included 201,627,059 associations with a total sample size of n = 686. Based on this new database, we identified 10,430 genes with eQTLs, of which 11% (1,146) … potato encrusted fish recipeWebJan 18, 2024 · Our brain eQTL meta-analysis identifies 10,456 genes with a genome-wide significant eQTL, including 4,808 with at least one conditional eQTL using a conservative p-value threshold of 10 -6 ... potatoe no skin nutrition factsWebNov 28, 2014 · Meta-eqtl is a set of command line utilities written in R, with some computationally intensive parts written in C. The software runs on Linux platforms and is … potatoe place delivery areaWebApr 23, 2015 · For mapping eQTLs in a cross-population meta-analytic setting, we make an important assumption that if a SNP is genuinely associated with a given expression phenotype, its underlying genetic effects are non-zero in all population groups. That is, γ = 1, if SNP j is an eQTL, and 0 otherwise. to the nights we won\\u0027t rememberWebNov 28, 2014 · Meta-analysis tools are in need to jointly analyze datasets of same or similar issue types to improve statistical power especially in trans-eQTL mapping. Meta … potato energy sourceWebOct 19, 2024 · We observed that cis -eQTLs can be detected for 88% of the studied genes, but that they have a different genetic architecture compared to disease-associated … to the night percy bysshe shelleyWebDistant and local, trans- and cis-eQTLs, respectively [ edit] An expression quantitative trait is an amount of an mRNA transcript or a protein. These are usually the product of a single … potatoe noodle china town chicago