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https://www.readbyqxmd.com/read/29790900/gscalite-a-web-server-for-gene-set-cancer-analysis
#1
Chun-Jie Liu, Fei-Fei Hu, Mengxuan Xia, Leng Han, Qiong Zhang, An-Yuan Guo
Summary: The availability of cancer genomic data makes it possible to analyze genes related to cancer. Cancer is usually the result of a set of genes and the signal of a single gene could be covered by background noise. Here, we present a web server named Gene Set Cancer Analysis (GSCALite) to analyze a set of genes in cancers with the following functional modules. (i) Differential expression in tumor vs normal, and the survival analysis; (ii) Genomic variations and their survival analysis; (iii) Gene expression associated cancer pathway activity; (iv) miRNA regulatory network for genes; (v) Drug sensitivity for genes; (vi) Normal tissue expression and eQTL for genes...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29786918/novel-genes-and-insights-in-complete-asthma-remission
#2
Judith M Vonk, Maartje A E Nieuwenhuis, F Nicole Dijk, Anne Boudier, Valerie Siroux, Emmanuelle Bouzigon, Nicole Probst-Hensch, Medea Imboden, Dirk Keidel, Don Sin, Yohan Bossé, Ke Hao, Maarten van den Berge, Alen Faiz, Gerard H Koppelman, Dirkje S Postma
BACKGROUND: Asthma is a chronic respiratory disease without a cure, though there exists spontaneous remission. Genome wide association(GWA) studies have pinpointed genes associated with asthma development, but did not investigate asthma remission. OBJECTIVES: We performed a GWA study to develop insights in asthma remission. METHODS: Clinical remission (ClinR) was defined by absence of asthma treatment and wheezing in the last year and asthma attacks in the last 3 years, and complete remission (ComR) similarly but additionally with normal lung function and absence of bronchial hyperresponsiveness (BHR)...
May 22, 2018: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29774522/genome-wide-compound-heterozygosity-analysis-highlighted-four-novel-susceptibility-loci-for-congenital-heart-disease-in-chinese-population
#3
T Jiang, M Huang, T Jiang, Y Gu, Y Wang, Y Wu, H Ma, G Jin, J Dai, Z Hu
Genome-wide association studies (GWASs) have achieved great success in deciphering the genetic cause of congenital heart disease (CHD). However, the heritability of CHD remains to be clarified, and numerous genetic factors responsible for occurrence of CHD are yet unclear. In this study, we performed a genome-wide search for relaxed forms of compound heterozygosity (CH) in association with CHD using our existing GWAS data including 2,265 individuals (957 CHD cases and 1,308 controls). CollapsABEL was used to iteratively test the association between the CH genotype and CHD phenotype in a sliding window manner...
May 17, 2018: Clinical Genetics
https://www.readbyqxmd.com/read/29766219/association-study-of-genetic-variants-in-estrogen-metabolic-pathway-genes-and-colorectal-cancer-risk-and-survival
#4
Shuwei Li, Lisheng Xie, Mulong Du, Kaili Xu, Lingjun Zhu, Haiyan Chu, Jinfei Chen, Meilin Wang, Zhengdong Zhang, Dongying Gu
Although studies have investigated the association of genetic variants and the abnormal expression of estrogen-related genes with colorectal cancer risk, the evidence remains inconsistent. We clarified the relationship of genetic variants in estrogen metabolic pathway genes with colorectal cancer risk and survival. A case-control study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in ten candidate genes with colorectal cancer risk in a Chinese population. A logistic regression model and Cox regression model were used to calculate SNP effects on colorectal cancer susceptibility and survival, respectively...
May 16, 2018: Archives of Toxicology
https://www.readbyqxmd.com/read/29763751/integration-of-summary-data-from-gwas-and-eqtl-studies-identified-novel-causal-bmd-genes-with-functional-predictions
#5
Xiang-He Meng, Xiang-Ding Chen, Jonathan Greenbaum, Qin Zeng, Sheng-Lan You, Hong-Mei Xiao, Li-Jun Tan, Hong-Wen Deng
PURPOSE: Osteoporosis is a common global health problem characterized by low bone mineral density (BMD) and increased risk of fracture. Genome-wide association studies (GWAS) have identified >100 genetic loci associated with BMD. However, the functional genes responsible for most associations remain largely unknown. We conducted an innovative summary statistic data-based Mendelian randomization (SMR) analysis to identify novel causal genes associated with BMD and explored their potential functional significance...
May 12, 2018: Bone
https://www.readbyqxmd.com/read/29755505/integrative-analysis-identifies-genetic-variants-associated-with-autoimmune-diseases-affecting-putative-microrna-binding-sites
#6
Rodrigo C de Almeida, Vinícius S Chagas, Mauro A A Castro, Maria L Petzl-Erler
Genome-wide and fine mapping studies have shown that more than 90% of genetic variants associated with autoimmune diseases (AID) are located in non-coding regions of the human genome and especially in regulatory sequences, including microRNAs (miRNA) target sites. MiRNAs are small endogenous noncoding RNAs that modulate gene expression at the post-transcriptional level. Single nucleotide polymorphisms (SNPs) located within the 3' untranslated region of their target mRNAs (miRSNP) can alter miRNA binding sites...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29743541/association-of-bet1l-and-tnrc6b-with-uterine-leiomyoma-risk-and-its-relevant-clinical-features-in-han-chinese-population
#7
Bailing Liu, Tao Wang, Jue Jiang, Miao Li, Wenqi Ma, Haibin Wu, Qi Zhou
Previous studies have shown that uterine leiomyomas (UL) are benign tumours with contributions from environmental and genetic factors. We aimed to replicate two initial significant genetic factors, TNRC6B and BET1L, in a Han Chinese population. A total of 2,055 study subjects were recruited, and 55 SNPs mapped to TNRC6B and BET1L were selected and genotyped in samples from these subjects. Genetic associations were analysed at both the single marker and haplotype levels. Associations between targeted SNPs and relevant clinical features of UL were analysed in case only samples...
May 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29727691/fun-lda-a-latent-dirichlet-allocation-model-for-predicting-tissue-specific-functional-effects-of-noncoding-variation-methods-and-applications
#8
Daniel Backenroth, Zihuai He, Krzysztof Kiryluk, Valentina Boeva, Lynn Pethukova, Ekta Khurana, Angela Christiano, Joseph D Buxbaum, Iuliana Ionita-Laza
We describe a method based on a latent Dirichlet allocation model for predicting functional effects of noncoding genetic variants in a cell-type- and/or tissue-specific way (FUN-LDA). Using this unsupervised approach, we predict tissue-specific functional effects for every position in the human genome in 127 different tissues and cell types. We demonstrate the usefulness of our predictions by using several validation experiments. Using eQTL data from several sources, including the GTEx project, Geuvadis project, and TwinsUK cohort, we show that eQTLs in specific tissues tend to be most enriched among the predicted functional variants in relevant tissues in Roadmap...
May 3, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29727689/a-comprehensive-cis-eqtl-analysis-revealed-target-genes-in-breast-cancer-susceptibility-loci-identified-in-genome-wide-association-studies
#9
Xingyi Guo, Weiqiang Lin, Jiandong Bao, Qiuyin Cai, Xiao Pan, Mengqiu Bai, Yuan Yuan, Jiajun Shi, Yaqiong Sun, Mi-Ryung Han, Jing Wang, Qi Liu, Wanqing Wen, Bingshan Li, Jirong Long, Jianghua Chen, Wei Zheng
Genome-wide association studies (GWASs) have identified more than 150 common genetic loci for breast cancer risk. However, the target genes and underlying mechanisms remain largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using normal or tumor breast transcriptome data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), The Cancer Genome Atlas (TCGA), and the Genotype-Tissue Expression (GTEx) project. We identified a total of 101 genes for 51 lead variants after combing the results of a meta-analysis of METABRIC and TCGA, and the results from GTEx at a Benjamini-Hochberg (BH)-adjusted p < 0...
May 3, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29719630/genetic-susceptibility-to-bone-and-soft-tissue-sarcomas-a-field-synopsis-and-meta-analysis
#10
Clara Benna, Andrea Simioni, Sandro Pasquali, Davide De Boni, Senthilkumar Rajendran, Giovanna Spiro, Chiara Colombo, Calogero Virgone, Steven G DuBois, Alessandro Gronchi, Carlo Riccardo Rossi, Simone Mocellin
Background: The genetic architecture of bone and soft tissue sarcomas susceptibility is yet to be elucidated. We aimed to comprehensively collect and meta-analyze the current knowledge on genetic susceptibility in these rare tumors. Methods: We conducted a systematic review and meta-analysis of the evidence on the association between DNA variation and risk of developing sarcomas through searching PubMed, The Cochrane Library, Scopus and Web of Science databases...
April 6, 2018: Oncotarget
https://www.readbyqxmd.com/read/29718103/a-powerful-approach-reveals-numerous-expression-quantitative-trait-haplotypes-in-multiple-tissues
#11
Dingge Ying, Mulin Jun Li, Pak Chung Sham, Miaoxin Li
Motivation: Recently many studies showed single nucleotide polymorphisms (SNPs) affect gene expression and contribute to development of complex traits/diseases in a tissue context-dependent manner. However, little is known about haplotype's influence on gene expression and complex traits, which reflects the interaction effect between SNPs. Results: In the present study, we firstly proposed a regulatory region guided eQTL haplotype association analysis approach, and then systematically investigate the expression quantitative trait loci (eQTL) haplotypes in 20 different tissues by the approach...
April 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29716618/focs-a-novel-method-for-analyzing-enhancer-and-gene-activity-patterns-infers-an-extensive-enhancer-promoter-map
#12
Tom Aharon Hait, David Amar, Ron Shamir, Ran Elkon
Recent sequencing technologies enable joint quantification of promoters and their enhancer regions, allowing inference of enhancer-promoter links. We show that current enhancer-promoter inference methods produce a high rate of false positive links. We introduce FOCS, a new inference method, and by benchmarking against ChIA-PET, HiChIP, and eQTL data show that it results in lower false discovery rates and at the same time higher inference power. By applying FOCS to 2630 samples taken from ENCODE, Roadmap Epigenomics, FANTOM5, and a new compendium of GRO-seq samples, we provide extensive enhancer-promotor maps ( http://acgt...
May 1, 2018: Genome Biology
https://www.readbyqxmd.com/read/29703961/genetic-variants-in-chemokine-cc-subfamily-genes-influence-hepatitis-c-virus-viral-clearance
#13
Yinan Yao, Ming Yue, Feng Zang, Mei Liu, Haozhi Fan, Lingyun Zhuo, Jingjing Wu, Xueshan Xia, Yue Feng, Peng Huang, Rongbin Yu
Chemokine genes may influence both hepatitis C virus (HCV) spontaneous clearance in acute infection and treatment response in chronic infection. We conducted this study to evaluate whether the genetic variants in several CC family genes influence HCV spontaneous clearance and treatment response. The current research genotyped eight SNPs, including CCR1 rs3733096, rs13096371, CCR5 rs746492, rs1800874, CCL3 rs1130371, CCL5 rs3817656, CCL8 rs1133763, CCL14 rs854625, to explore their associations with HCV spontaneous clearance and response to treatment in two populations...
April 27, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29703947/human-brain-arousal-in-the-resting-state-a-genome-wide-association-study
#14
Philippe Jawinski, Holger Kirsten, Christian Sander, Janek Spada, Christine Ulke, Jue Huang, Ralph Burkhardt, Markus Scholz, Tilman Hensch, Ulrich Hegerl
Arousal affects cognition, emotion, and behavior and has been implicated in the etiology of psychiatric disorders. Although environmental conditions substantially contribute to the level of arousal, stable interindividual characteristics are well-established and a genetic basis has been suggested. Here we investigated the molecular genetics of brain arousal in the resting state by conducting a genome-wide association study (GWAS). We selected N = 1877 participants from the population-based LIFE-Adult cohort...
April 27, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29698501/association-of-raynaud-s-phenomenon-with-a-polymorphism-in-the-nos1-gene
#15
Sabrina Munir, Maxim B Freidin, Susan Brain, Frances M K Williams
BACKGROUND: Raynaud's phenomenon (RP) describes the phenomenon of recurrent vasospasm of digital arteries, associated with skin colour changes: pallor, cyanosis and erythema. Twin studies have indicated a genetic predisposition for RP; however, the precise aetiology of RP remains unknown. It is thought that genetic variation in temperature-responsive or vasospastic genes might underlie RP so performed a candidate gene study in a large, population based sample. We assessed the association between RP and single nucleotide polymorphisms (SNPs) in the TRPA1, TRPM8, CALCA, CALCB and NOS1 genes...
2018: PloS One
https://www.readbyqxmd.com/read/29691431/biological-insights-into-muscular-strength-genetic-findings-in-the-uk-biobank
#16
Emmi Tikkanen, Stefan Gustafsson, David Amar, Anna Shcherbina, Daryl Waggott, Euan A Ashley, Erik Ingelsson
We performed a large genome-wide association study to discover genetic variation associated with muscular strength, and to evaluate shared genetic aetiology with and causal effects of muscular strength on several health indicators. In our discovery analysis of 223,315 individuals, we identified 101 loci associated with grip strength (P <5 × 10-8 ). Of these, 64 were associated (P < 0.01 and consistent direction) also in the replication dataset (N = 111,610). eQTL analyses highlighted several genes known to play a role in neuro-developmental disorders or brain function, and the results from meta-analysis showed a significant enrichment of gene expression of brain-related transcripts...
April 24, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29685792/genomic-response-to-vitamin-d-supplementation-in-the-setting-of-a-randomized-placebo-controlled-trial
#17
Antonio J Berlanga-Taylor, Katharine Plant, Andrew Dahl, Evelyn Lau, Michael Hill, David Sims, Andreas Heger, Jonathan Emberson, Jane Armitage, Robert Clarke, Julian C Knight
BACKGROUND: Vitamin D deficiency has been associated with multiple diseases, but the causal relevance and underlying processes are not fully understood. Elucidating the mechanisms of action of drug treatments in humans is challenging, but application of functional genomic approaches in randomized trials may afford an opportunity to systematically assess molecular responses. METHODS: In the Biochemical Efficacy and Safety Trial of Vitamin D (BEST-D), a double-blind, placebo-controlled, dose-finding, randomized clinical trial, 305 community-dwelling individuals aged over 65 years were randomly allocated to treatment with vitamin D3 4000 IU, 2000 IU or placebo daily for 12 months...
April 10, 2018: EBioMedicine
https://www.readbyqxmd.com/read/29670885/integrative-bioinformatics-approaches-for-identification-of-drug-targets-in-hypertension
#18
Daiane Hemerich, Jessica van Setten, Vinicius Tragante, Folkert W Asselbergs
High blood pressure or hypertension is an established risk factor for a myriad of cardiovascular diseases. Genome-wide association studies have successfully found over nine hundred loci that contribute to blood pressure. However, the mechanisms through which these loci contribute to disease are still relatively undetermined as less than 10% of hypertension-associated variants are located in coding regions. Phenotypic cell-type specificity analyses and expression quantitative trait loci show predominant vascular and cardiac tissue involvement for blood pressure-associated variants...
2018: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/29669733/evolution-of-dnaasei-hypersensitive-sites-in-mhc-regulatory-regions-of-primates
#19
Yabin Jin, Rachel M Gittelman, Yueer Lu, Xiaohui Liu, Ming D Li, Fei Ling, Joshua M Akey
It has been challenged to determine the disease-causing variant(s) for most major histocompatibility complex (MHC) associated diseases. However, it is becoming increasingly clear that regulatory variation is pervasive and a fundamentally important mechanism governing phenotypic diversity and disease susceptibility. We leveraged DNase I data from 136 human cells to characterize the regulatory landscape of the MHC region, including 4867 DNase I hypersensitive sites (DHSs). We identified thousands of regulatory elements that have been gained or lost in the human or chimpanzee genomes since their evolutionary divergence...
April 18, 2018: Genetics
https://www.readbyqxmd.com/read/29666371/integration-of-human-adipocyte-chromosomal-interactions-with-adipose-gene-expression-prioritizes-obesity-related-genes-from-gwas
#20
David Z Pan, Kristina M Garske, Marcus Alvarez, Yash V Bhagat, James Boocock, Elina Nikkola, Zong Miao, Chelsea K Raulerson, Rita M Cantor, Mete Civelek, Craig A Glastonbury, Kerrin S Small, Michael Boehnke, Aldons J Lusis, Janet S Sinsheimer, Karen L Mohlke, Markku Laakso, Päivi Pajukanta, Arthur Ko
Increased adiposity is a hallmark of obesity and overweight, which affect 2.2 billion people world-wide. Understanding the genetic and molecular mechanisms that underlie obesity-related phenotypes can help to improve treatment options and drug development. Here we perform promoter Capture Hi-C in human adipocytes to investigate interactions between gene promoters and distal elements as a transcription-regulating mechanism contributing to these phenotypes. We find that promoter-interacting elements in human adipocytes are enriched for adipose-related transcription factor motifs, such as PPARG and CEBPB, and contribute to heritability of cis-regulated gene expression...
April 17, 2018: Nature Communications
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