Tag: eQTL

(PDF) An eQTL biological data visualization challenge and approaches from the visualization community | Jan Aerts

(PDF) An eQTL biological data visualization challenge and approaches from the visualization community | Jan Aerts – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our collection of information through the use of cookies. To learn more,…

Continue Reading (PDF) An eQTL biological data visualization challenge and approaches from the visualization community | Jan Aerts

TwinEQTL: Ultra Fast and Powerful Association Analysis for eQTL and GWAS in Twin Studies

doi: 10.1093/genetics/iyac088. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA. 2 Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599, USA. 3 Department of Psychiatry, University of Utah, Salt Lake City, UT 84108, USA. 4 Gilead…

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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Google Scholar  Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47,…

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Single-cell eQTL models reveal dynamic T cell state dependence of disease loci – Nature – Alert Breaking News

Wei, K. et al. Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature 582, 259–264 (2020). ADS CAS PubMed PubMed Central Article Google Scholar  Cembrowski, M. S. & Menon, V. Continuous variation within cell types of the nervous system. Trends Neurosci. 41, 337–348 (2018). CAS PubMed Article Google Scholar  Maurano, M. T. et al. Systematic localization of…

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Mediation analysis of local chromatin state and gene expression data in human cell lines.

SNP associations with (a) SLFN5 and (b) GPR63 expression (top) and nearby chromatin accessibility (bottom) for variants on the genes’ chromosome. Peak SNPs are labeled. Mediation results for the (c) SLFN5 eQTL and (d) GPR63 eQTL. Log posterior odds from Bayesian model selection (top), -log10 p-values from Sobel test (middle),…

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Integrative analysis of eQTL and GWAS summary statistics reveals transcriptomic alteration in Alzheimer brains | BMC Medical Genomics

Significant gene-AD associations With the GWAS summary data from the IGAP and eQTL summary data from BRAINEAC, we performed both SMR and HEIDI tests to estimate the gene-AD associations in three human brain regions: frontal cortex, temporal cortex, and hippocampal regions. For the frontal cortex and hippocampal regions, we obtained…

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A conditional gene-based association framework integrating isoform-level eQTL data reveals new susceptibility genes for schizophrenia

doi: 10.7554/eLife.70779. Affiliations Expand Affiliations 1 Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China. 2 Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China. 3 Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China. 4 Research…

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Polygenic Transcriptome Risk Scores for COPD Show Improved Cross-Ancestry Portability

NEW YORK — Polygenic transcriptome risk scores may be better at gauging chronic obstructive pulmonary disease susceptibility across human ancestry groups than polygenic risk scores, a new study has found. COPD affects about 16 million people in the US and is typically diagnosed through two measures of lung function: forced…

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Powerful eQTL mapping through low coverage RNA sequencing

Mapping genetic variants that regulate gene expression (eQTL mapping) in large-scale RNA sequencing (RNA-seq) studies is often employed to understand functional consequences of regulatory variants. However, the high cost of RNA-Seq limits sample size, sequencing depth, and therefore, discovery power in eQTL studies. In this work, we demonstrate that, given…

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Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS  Google Scholar  Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…

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Will Weakness in Equital Ltd.’s (TLV:EQTL) Stock Prove Temporary Given Strong Fundamentals?

Equital (TLV:EQTL) has had a rough month with its share price down 12%. However, a closer look at its sound financials might cause you to think again. Given that fundamentals usually drive long-term market outcomes, the company is worth looking at. Particularly, we will be paying attention to Equital’s ROE…

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Towards the Genetic Architecture of Complex Gene Expression Traits: Challenges and Prospects for eQTL Mapping in Humans

Review doi: 10.3390/genes13020235. Affiliations Expand Affiliation 1 Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, Korea. Free PMC article Item in Clipboard Review Chaeyoung Lee. Genes (Basel). 2022. Free PMC article Show details Display options Display options Format AbstractPubMedPMID doi: 10.3390/genes13020235. Affiliation 1 Department of…

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eQTL mapping using allele-specific count data is computationally feasible, powerful, and provides individual-specific estimates of genetic effects

Using information from allele-specific gene expression (ASE) can improve the power to map gene expression quantitative trait loci (eQTLs). However, such practice has been limited, partly due to computational challenges and lack of clarification on the size of power gain or new findings besides improved power. We have developed geoP,…

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Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases

Cooper, G. S., Bynum, M. L. K. & Somers, E. C. Recent insights in the epidemiology of autoimmune diseases: improved prevalence estimates and understanding of clustering of diseases. J. Autoimmun. 33, 197–207 (2009). PubMed  PubMed Central  Google Scholar  El-Gabalawy, H., Guenther, L. C. & Bernstein, C. N. Epidemiology of immune-mediated…

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Enrichment of eQTLs in functional categories using the eQTL results from 28 GTEx tissues.

In panel (a)-(c) and (e)-(f), a dot indicates point estimate, and a line indicates 95% confidence interval. (a) Enrichment evaluated using all the SNPs by torus [17] based on the eQTL results from MatrixEQTL, TReC or TReCASE. (b) Enrichment of the top eQTL per gene for the eGenes identified by…

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multiRegression function – RDocumentation

Examples # NOT RUN { seed = 1234 N = 100 # sample size Ng = 5 # gene number Nk = 5 * 3 # eQTL number Ns = 1 # sparse ratio sigma2 = 0.01 # sigma2 set.seed(seed) data = randomFSSEMdata(n = N, p = Ng, k =…

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Workflow Platforms for Systems Genetics

Workflow Platforms for Systems Genetics eQTL Platforms eQTL Viewer Mouse Genome Informatics: Phenotypes, Alleles & Disease Models PhenoGen Informatics (CO U) eXtensible Genotype And Phenotype platform (XGAP) MOLGENIS & MetaNetwork, Swertz & Jansen, U Groningen Weighted Gene Co-expression Network Analysis (WGCNA), Horvath, UCLA iPlant Sage Bionetworks Repository: Synapse GenomeSpace Institute…

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EQTL visualization

EQTL visualization 0 I have generated file from MATRIXEQTL . I would like to visualize haploblocks, plots for MATRIXEQTL. I am having SNP.txt, Gene expression.txt. How can I visualize Chromosome specific eQTL list EQTL plot • 53 views • link 17 hours ago by Nai ▴ 20 Login before adding…

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criteria for pvOutputThreshold = 1e-100 in EQTLMATRIX and creation of geneloc.txt for ciseQTL

criteria for pvOutputThreshold = 1e-100 in EQTLMATRIX and creation of geneloc.txt for ciseQTL 0 I would like to know the following points in MATRIXEQTL: (i) what is good threshold value for pvOutputThreshold = 1e-5 / 1e-6 / 1e-100 in MATRIXeQTL ? (ii). Best model for eQTL Linear/cross_linear/Anova when I don’t…

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TF model of eQTL effects.

A) TF binding to an eQTL variant with different allelic TF affinities is depicted at low, medium, and high TF levels. B) TF binding occupancy, resulting in target gene expression, for the two eQTL alleles across TF levels. C) Difference in expression of alleles or eQTL effect size, quantified as…

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GitHub – jmp448/sc-dynamic-eqtl

GitHub – jmp448/sc-dynamic-eqtl You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here: Source link

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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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