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Expression quantitative trait loci

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https://www.readbyqxmd.com/read/29158546/the-aegilops-tauschii-genome-reveals-multiple-impacts-of-transposons
#1
Guangyao Zhao, Cheng Zou, Kui Li, Kai Wang, Tianbao Li, Lifeng Gao, Xiaoxia Zhang, Hongjin Wang, Zujun Yang, Xu Liu, Wenkai Jiang, Long Mao, Xiuying Kong, Yuannian Jiao, Jizeng Jia
Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes...
November 20, 2017: Nature Plants
https://www.readbyqxmd.com/read/29156765/network-directed-cis-mediator-analysis-of-normal-prostate-tissue-expression-profiles-reveals-downstream-regulatory-associations-of-prostate-cancer-susceptibility-loci
#2
Nicholas B Larson, Shannon K McDonnell, Zach Fogarty, Melissa C Larson, John Cheville, Shaun Riska, Saurabh Baheti, Alexandra M Weber, Asha A Nair, Liang Wang, Daniel O'Brien, Jaime Davila, Daniel J Schaid, Stephen N Thibodeau
Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis-acting associations due to study limitations. While trans-eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans-eQTL associations are mediated by cis-regulated genes, such as transcription factors...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29153655/clinical-evidence-supports-a-protective-role-for-cxcl5-in-coronary-artery-disease
#3
Saranya Ravi, Robert N Schuck, Eleanor Hilliard, Craig R Lee, Xuming Dai, Kaitlin Lenhart, Monte S Willis, Brian C Jensen, George A Stouffer, Cam Patterson, Jonathan C Schisler
Our goal was to measure the association of CXCL5 and molecular phenotypes associated with coronary atherosclerosis severity in patients at least 65 years old. CXCL5 is classically defined as a proinflammatory chemokine, but its role in chronic inflammatory diseases, such as coronary atherosclerosis, is not well defined. We enrolled individuals who were at least 65 years old and undergoing diagnostic cardiac catheterization. Coronary artery disease (CAD) severity was quantified in each subject via coronary angiography by calculating a CAD score...
December 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/29149290/discovering-the-3-utr-mediated-regulation-of-alpha-synuclein
#4
Domenica Marchese, Teresa Botta-Orfila, Davide Cirillo, Juan Antonio Rodriguez, Carmen Maria Livi, Rubén Fernández-Santiago, Mario Ezquerra, Maria J Martí, Elias Bechara, Gian Gaetano Tartaglia
Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions (3'UTRs). Yet, the post-transcriptional mechanisms regulating SNCA expression are unknown. Using a large-scale in vitro/in silico screening we identified RNA-binding proteins (RBPs) that interact with SNCA 3' UTRs. We identified two RBPs, ELAVL1 and TIAR, that bind with high affinity to the most abundant and translationally active 3' UTR isoform (575 nt)...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29142307/genetic-polymorphism-related-to-monocyte-macrophage-function-is-associated-with-graft-versus-host-disease
#5
Kati Hyvärinen, Jarmo Ritari, Satu Koskela, Riitta Niittyvuopio, Anne Nihtinen, Liisa Volin, David Gallardo, Jukka Partanen
Despite detailed human leukocyte antigen (HLA) matching and modern immunosuppressive therapy, severe graft-versus-host disease (GvHD) remains a major hurdle for successful allogeneic hematopoietic stem cell transplantation (HSCT). As the genetic diversity in GvHD complicates the systematic discovery of associated variants across populations, we studied 122 GvHD-associated single nucleotide polymorphisms (SNPs) in 492 HLA-matched sibling HSCT donor-recipient pairs from Finland and Spain. The association between these candidate SNPs and grade III-IV acute GvHD and extensive chronic GvHD was assessed...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142238/mapping-qtls-conferring-salt-tolerance-and-micronutrient-concentrations-at-seedling-stagein-wheat
#6
Babar Hussain, Stuart James Lucas, Levent Ozturk, Hikmet Budak
Soil salinization and degradation is one of the consequences of climate change. Identification of major salt tolerance genes and marker assisted selection (MAS) can accelerate wheat breeding for this trait. We genotyped 154 wheat F2 lines derived from a cross between salt tolerant and susceptible cultivars using the Axiom Wheat Breeder's Genotyping Array. A high-density linkage map of 988 single nucleotide polymorphisms (SNPs) was constructed and utilized for quantitative trait loci (QTL) mapping for salt tolerance traits and mineral concentrations under salinity...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#7
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29127305/cis-snps-set-testing-and-predixcan-analysis-for-gene-expression-data-using-linear-mixed-models
#8
Ping Zeng, Ting Wang, Shuiping Huang
Understanding the functional mechanism of SNPs identified in GWAS on complex diseases is currently a challenging task. The studies of expression quantitative trait loci (eQTL) have shown that regulatory variants play a crucial role in the function of associated SNPs. Detecting significant genes (called eGenes) in eQTL studies and analyzing the effect sizes of cis-SNPs can offer important implications on the genetic architecture of associated SNPs and interpretations of the molecular basis of diseases. We applied linear mixed models (LMM) to the gene expression level and constructed likelihood ratio tests (LRT) to test for eGene in the Geuvadis data...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29123100/dna-methylation-at-enhancers-identifies-distinct-breast-cancer-lineages
#9
Thomas Fleischer, Xavier Tekpli, Anthony Mathelier, Shixiong Wang, Daniel Nebdal, Hari P Dhakal, Kristine Kleivi Sahlberg, Ellen Schlichting, Anne-Lise Børresen-Dale, Elin Borgen, Bjørn Naume, Ragnhild Eskeland, Arnoldo Frigessi, Jörg Tost, Antoni Hurtado, Vessela N Kristensen
Breast cancers exhibit genome-wide aberrant DNA methylation patterns. To investigate how these affect the transcriptome and which changes are linked to transformation or progression, we apply genome-wide expression-methylation quantitative trait loci (emQTL) analysis between DNA methylation and gene expression. On a whole genome scale, in cis and in trans, DNA methylation and gene expression have remarkably and reproducibly conserved patterns of association in three breast cancer cohorts (n = 104, n = 253 and n = 277)...
November 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/29123092/natural-variation-of-yellow-seedling1-affects-photosynthetic-acclimation-of-arabidopsis-thaliana
#10
Roxanne van Rooijen, Willem Kruijer, René Boesten, Fred A van Eeuwijk, Jeremy Harbinson, Mark G M Aarts
Exploiting genetic variation for more efficient photosynthesis is an underexplored route towards new crop varieties. This study demonstrates the genetic dissection of higher plant photosynthesis efficiency down to the genomic DNA level, by confirming that allelic sequence variation at the Arabidopsis thaliana YELLOW SEEDLING1 (YS1) gene explains natural diversity in photosynthesis acclimation to high irradiance. We use a genome-wide association study to identify quantitative trait loci (QTLs) involved in the Arabidopsis photosynthetic acclimation response...
November 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/29122853/genome-wide-screen-for-saccharomyces-cerevisiae%C3%A2-genes-contributing-to-opportunistic-pathogenicity-in-an-invertebrate-model-host
#11
Sujal S Phadke, Calum J Maclean, Serena Y Zhao, Emmi A Mueller, Lucas A Michelotti, Kaitlyn L Norman, Anuj Kumar, Timothy Y James
Environmental opportunistic pathogens can exploit vulnerable hosts through expression of traits selected for in their natural environments. Pathogenicity is a complicated trait underpinned by multiple complex traits, such as thermotolerance, morphology, and stress response. The baker's yeast, Saccharomyces cerevisiae, is a species with broad environmental tolerance which has been increasingly reported as an opportunistic pathogen of humans. Here we leveraged the genetic resources available in yeast and a model insect species, the greater waxmoth Galleria mellonella, to provide a genome-wide analysis of pathogenicity factors...
November 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29116076/the-effect-of-genetic-variation-on-promoter-usage-and-enhancer-activity
#12
Marco Garieri, Olivier Delaneau, Federico Santoni, Richard J Fish, David Mull, Piero Carninci, Emmanouil T Dermitzakis, Stylianos E Antonarakis, Alexandre Fort
The identification of genetic variants affecting gene expression, namely expression quantitative trait loci (eQTLs), has contributed to the understanding of mechanisms underlying human traits and diseases. The majority of these variants map in non-coding regulatory regions of the genome and their identification remains challenging. Here, we use natural genetic variation and CAGE transcriptomes from 154 EBV-transformed lymphoblastoid cell lines, derived from unrelated individuals, to map 5376 and 110 regulatory variants associated with promoter usage (puQTLs) and enhancer activity (eaQTLs), respectively...
November 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/29115942/detection-of-qtls-for-seedling-characteristics-in-barley-hordeum-vulgare-l-grown-under-hydroponic-culture-condition
#13
Qifei Wang, Genlou Sun, Xifeng Ren, Jibin Wang, Binbin Du, Chengdao Li, Dongfa Sun
BACKGROUND: Seedling characteristics play significant roles in the growth and development of barley (Hordeum vulgare L.), including stable stand establishment, water and nutrients uptake, biotic resistance and abiotic stresses, and can influence yield and quality. However, the genetic mechanisms underlying seedling characteristics in barley are largely unknown and little research has been done. In the present work, 21 seedling-related characteristics are assessed in a barley double haploid (DH) population, grown under hydroponic conditions...
November 7, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29115920/genome-wide-association-mapping-of-resistance-to-a-brazilian-isolate-of-sclerotinia-sclerotiorum-in-soybean-genotypes-mostly-from-brazil
#14
Wei Wei, Ana Carolina Oliveira Mesquita, Adriana de A Figueiró, Xing Wu, Shilpa Manjunatha, Daniel P Wickland, Matthew E Hudson, Fernando C Juliatti, Steven J Clough
BACKGROUND: Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work together to provide partial resistance. In this study, a genome-wide association study (GWAS) was performed to dissect the complex genetic architecture of soybean quantitative resistance to SSR and to provide effective molecular markers that could be used in breeding programs...
November 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29114259/identification-of-splicing-quantitative-trait-loci-sqtl-in-drosophila-melanogaster-with-developmental-lead-pb-2-exposure
#15
Wen Qu, Katherine Gurdziel, Roger Pique-Regi, Douglas M Ruden
Lead (Pb) poisoning has been a major public health issue globally and the recent Flint water crisis has drawn nation-wide attention to its effects. To better understand how lead plays a role as a neurotoxin, we utilized the Drosophila melanogaster model to study the genetic effects of lead exposure during development and identified lead-responsive genes. In our previous studies, we have successfully identified hundreds of lead-responsive expression QTLs (eQTLs) by using RNA-seq analysis on heads collected from the Drosophila Synthetic Population Resource...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29109911/can-9q34-2-rs633862-polymorphism-predict-survival-in-epithelial-ovarian-cancer
#16
Rong Jiang, Yuan Xu, Pan Wang, Xi Cheng, Tingyan Shi, Rongyu Zang
Objective: Our previous genome-wide association study (GWAS) identified that the ABO rs633862 variant in chromosome 9q34.2 was associated with the risk of epithelial ovarian cancer (EOC) in Chinese Han women. The aim of the present study was to evaluate its prognostic effect on EOC. Methods: A total of 669 EOC patients were enrolled for the genotyping of rs633862 variant in 9q34.2. We used Kaplan-Meier survival curves, univariate and multivariate Cox proportional hazard models to evaluate the association of rs633862 with overall survival (OS) in EOC patients...
2017: PeerJ
https://www.readbyqxmd.com/read/29109033/predicting-and-analyzing-early-wake-up-associated-gene-expressions-by-integrating-gwas-and-eqtl-studies
#17
JiaRui Li, Tao Huang
Circadian rhythms are endogenous 24-hour rhythmic oscillations affecting human behaviors, such as sleep, blood pressure and other biological processes, the disturbance of which lead to circadian rhythm sleep disorders (CRSDs). In this study, based on the data from genome-wide association studies (GWASs) and expression quantitative trait loci (eQTLs), we tried to identify novel gene expression patterns in brain tissues that were associated with early wake-up. First, the maximum-relevance-minimum-redundancy (mRMR) method was adopted to analyze the involved gene expression patterns, yielding a feature list...
November 3, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29101457/a-functional-strategy-to-characterize-expression-quantitative-trait-loci
#18
Elena Grassi, Elisa Mariella, Mattia Forneris, Federico Marotta, Marika Catapano, Ivan Molineris, Paolo Provero
The study of genetic variation has been revolutionized by the advent of high-throughput technologies able to determine the complete genomic sequence of thousands of individuals. Understanding the functional relevance of variants is, however, still a difficult task, especially when focusing on non-coding variants. Most of the variants associated with disease by Genome-Wide Association Studies (GWAS) are indeed non-coding, and presumably exert their effects by altering gene regulation. Expression Quantitative Trait Loci (eQTL) studies represent an important step in understanding the functional relevance of regulatory variants...
November 3, 2017: Human Genetics
https://www.readbyqxmd.com/read/29100974/the-interaction-of-nos1ap-disc1-daoa-and-gsk3b-confers-susceptibility-of-early-onset-schizophrenia-in-chinese-han-population
#19
Guoqin Hu, Chengqing Yang, Lei Zhao, Yong Fan, Qinyu Lv, Jing Zhao, Minghuan Zhu, Xiangqing Guo, Chenxi Bao, Ahong Xu, Yong Jie, Yaqing Jiang, Chen Zhang, Shunying Yu, Zuowei Wang, Zezhi Li, Zhenghui Yi
Although many major breakthrough had identificated potential susceptibility genes for schizophrenia, the aetiology of schizophrenia is still unknown. In the present study, we focused on the N-methyl-Daspartate receptors related genes nitric oxide synthase 1 adaptor gene (NOS1AP), disrupted in schizophrenia 1 gene (DISC1), d-amino acid oxidase activator gene (DAOA), and glycogen synthase kinase 3-beta gene (GSK3B). A family-based genetic association study (459 Han Chinese subjects in 153 nuclear families) using 3 single nucleotide polymorphisms in NOS1AP, 2 in DISC1, 1 in DAOA and 1 in GSK3B was conducted...
October 31, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/29100102/genetic-analysis-of-the-wild-strawberry-fragaria-vesca-volatile-composition
#20
María Urrutia, José L Rambla, Konstantinos G Alexiou, Antonio Granell, Amparo Monfort
The volatile composition of wild strawberry (Fragaria vesca) fruit differs from that of the cultivated strawberry, having more intense and fruity aromas. Over the last few years, the diploid F. vesca has been recognized as a model species for genetic studies of cultivated strawberry (F. x ananassa), and here a previously developed F. vesca/F. bucharica Near Isogenic Line collection (NIL) was used to explore genetic variability of fruit quality traits. Analysis of fruit volatiles by GC-MS in our NIL collection revealed a complex and highly variable profile...
October 25, 2017: Plant Physiology and Biochemistry: PPB
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