Tag: eQTL

GitHub – jmp448/sc-dynamic-eqtl

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An eQTL variant of ALDH1A2 is associated with Kashin-Beck disease in Chinese population

Introduction: The aims of the study were to investigate the relationship between aldehyde dehydrogenase 1 family member A2 (ALDH1A2) and Kashin-Beck disease (KBD), explore the effects of the rs3204689 polymorphism and methylation status on the expression levels of ALDH1A2, and further clarify the pathogenesis of KBD. Materials and methods: The…

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Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits

1. Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). CAS  PubMed  PubMed Central  Google Scholar  2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed…

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Tabix file download error eQTL analysis

I am trying to download a tabix file to perform an analysis on an eQTL dataset, however I have the following error each each file I try to try from the eQTL – catalogue library(ggplot2) library(readr) library(coloc) library(GenomicRanges) library(seqminer) tabix_paths = read.delim(“https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv”, sep = “t”, header = TRUE, stringsAsFactors =…

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R: Summarize an eqtl Object

R: Summarize an eqtl Object summary.eqtl {GenomicTools} R Documentation Summarize an eqtl Object Description Summarizes and prints an eqtl object in an informative way. Usage ## S3 method for class ‘eqtl’ summary(object, sig=0.01, …) Arguments object Object of class eqtl. sig Significance level to print. … Additional parameters. Details This…

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17q12-21 risk-variants influence cord blood immune regulation and multitrigger-wheeze

Background: Childhood wheeze represents a first symptom of asthma. Early identification of children at risk for wheeze related to 17q12-21 variants and their underlying immunological mechanisms remain unknown. We aimed to assess the influence of 17q12-21 variants and mRNA-expression at birth on development of wheeze. Methods: Children were classified as…

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Genetic architecture modulates diet-induced hepatic mRNA and miRNA expression profiles in Diversity Outbred mice

Genetic approaches in model organisms have consistently demonstrated that molecular traits such as gene expression are under genetic regulation, similar to clinical traits. The resulting expression quantitative trait loci (eQTL) have revolutionized our understanding of genetic regulation and identified numerous candidate genes for clinically relevant traits. More recently, these analyses…

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An exercise-regulated noncoding RNA counteracts muscle aging

Credit: CC0 public domain In a collaborative effort between EPFL, NTNU Norway, and CBMR Danish laboratories, researchers investigated the molecular effects of exercise on non-coding RNA genes in skeletal muscle. Scientific translation medicine.. In this study, they discovered the long non-coding RNA “CYTOR” and investigated its role in rodent, worm,…

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RNAging: An exercise-regulated noncoding RNA

Skeletal muscle displays remarkable plasticity upon exercise, but is at the same time one of our organs that is most affected by aging. Skeletal muscle aging is characterized by estimated yearly losses of ~1% muscle mass and ~3% muscle strength in the elderly, resulting in an accumulated net loss of…

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Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands Wouter van Rheenen, Rick A. A. van der Spek, Mark K. Bakker, Joke J. F. A. van Vugt, Paul J. Hop, Ramona A. J. Zwamborn, Annelot M. Dekker, Klara Gawor, Henk-Jan Westeneng, Gijs H. P. Tazelaar, Kristel R. van Eijk, Maarten Kooyman, Ewout J. N. Groen, Michael…

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Phenotype file for eQTL analysis using GEMMA

Phenotype file for eQTL analysis using GEMMA 0 Hello All, I appreciate it if someone could direct me in this regard. I am running eQTL analysis using GEMMA software. I have corrected the expression file with all samples (280 samples) and the genotype file is (170). I have a couple…

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REMOTE Bioinformatics Research Associate – The Planet Group

JOB DESCRIPTION: The Human Genetics Department is currently offering an temporary employee position for students or working professionals in Bioinformatics/Computational Biology to join its Bioinformatics Team. The successful candidate will be actively engaged in mining the human genetics and genomics data to identify and prioritize targets. The successful candidate will be…

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Bioconductor – GGtools

DOI: 10.18129/B9.bioc.GGtools     This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GGtools. software and data for analyses in genetics of gene expression Bioconductor version: 3.12 software and data for analyses in genetics of gene…

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