Functional Prediction of Chronic Kidney Disease Susceptibility Gene PRKAG2 by Comprehensively Bioinformatics Analysis.

Abstract:

:The genetic predisposition to chronic kidney disease (CKD) has been widely evaluated especially using the genome-wide association studies, which highlighted some novel genetic susceptibility variants in many genes, and estimated glomerular filtration rate to diagnose and stage CKD. Of these variants, rs7805747 in PRKAG2 was identified to be significantly associated with both serum creatinine and CKD with genome wide significance level. Until now, the potential mechanism by which rs7805747 affects CKD risk is still unclear. Here, we performed a functional analysis of rs7805747 variant using multiple bioinformatics software and databases. Using RegulomeDB and HaploReg (version 4.1), rs7805747 was predicated to locate in enhancer histone marks (Liver, Duodenum Mucosa, Fetal Intestine Large, Fetal Intestine Small, and Right Ventricle tissues). Using GWAS analysis in PhenoScanner, we showed that rs7805747 is not only associated with CKD, but also is significantly associated with other diseases or phenotypes. Using metabolite analysis in PhenoScanner, rs7805747 is identified to be significantly associated with not only the serum creatinine, but also with other 16 metabolites. Using eQTL analysis in PhenoScanner, rs7805747 is identified to be significantly associated with gene expression in multiple human tissues and multiple genes including PRKAG2. The gene expression analysis of PRKAG2 using 53 tissues from GTEx RNA-Seq of 8555 samples (570 donors) in GTEx showed that PRKAG2 had the highest median expression in Heart-Atrial Appendage. Using the gene expression profiles in human CKD, we further identified different expression of PRKAG2 gene in CKD cases compared with control samples. In summary, our findings provide new insight into the underlying susceptibility of PRKAG2 gene to CKD.

journal_name

Front Genet

journal_title

Frontiers in genetics

authors

Wang E,Zhao H,Zhao D,Li L,Du L

doi

10.3389/fgene.2018.00573

subject

Has Abstract

pub_date

2018-12-03 00:00:00

pages

573

issn

1664-8021

journal_volume

9

pub_type

杂志文章
  • Multi-model inference in comparative phylogeography: an integrative approach based on multiple lines of evidence.

    abstract::Comparative phylogeography has its roots in classical biogeography and, historically, relies on a pattern-based approach. Here, we present a model-based framework for comparative phylogeography. Our framework was initially developed for statistical phylogeography based on a multi-model inference approach, by coupling ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2015.00031

    authors: Collevatti RG,Terribile LC,Diniz-Filho JA,Lima-Ribeiro MS

    更新日期:2015-02-17 00:00:00

  • Improved measurements of RNA structure conservation with generalized centroid estimators.

    abstract::Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also bioinformatics. Secondary structures of ncRNAs are employed as a key feature of ncRNA analysis since biological functions of ncRNAs are deeply related to their secondary structures. Although the...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2011.00054

    authors: Okada Y,Saito Y,Sato K,Sakakibara Y

    更新日期:2011-08-31 00:00:00

  • Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation.

    abstract::In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interacti...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2017.00025

    authors: Sunnucks P,Morales HE,Lamb AM,Pavlova A,Greening C

    更新日期:2017-03-03 00:00:00

  • Genomic prediction in an admixed population of Atlantic salmon (Salmo salar).

    abstract::Reliability of genomic selection (GS) models was tested in an admixed population of Atlantic salmon, originating from crossing of several wild subpopulations. The models included ordinary genomic BLUP models (GBLUP), using genome-wide SNP markers of varying densities (1-220 k), a genomic identity-by-descent model (IBD...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2014.00402

    authors: Odegård J,Moen T,Santi N,Korsvoll SA,Kjøglum S,Meuwissen TH

    更新日期:2014-11-21 00:00:00

  • Integrative Analysis of DiseaseLand Omics Database for Disease Signatures and Treatments: A Bipolar Case Study.

    abstract::Transcriptomics technologies such as next-generation sequencing and microarray platforms provide exciting opportunities for improving diagnosis and treatment of complex diseases. Transcriptomics studies often share similar hypotheses, but are carried out on different platforms, in different conditions, and with differ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00396

    authors: Wu C,Huang BE,Chen G,Lovenberg TW,Pocalyko DJ,Yao X

    更新日期:2019-04-30 00:00:00

  • Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development.

    abstract::Bamboo is one of the fastest-growing non-timber forest plants. Moso bamboo (Phyllostachys edulis) is the most economically valuable bamboo in Asia, especially in China. With the release of the whole-genome sequence of moso bamboo, there are increasing demands for refined annotation of bamboo genes. Recently, large amo...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00574

    authors: Ma X,Zhao H,Xu W,You Q,Yan H,Gao Z,Su Z

    更新日期:2018-11-27 00:00:00

  • Population Structure and Implications on the Genetic Architecture of HIV-1 Phenotypes Within Southern Africa.

    abstract::The interesting history of Southern Africa has put the region in the spotlight for population medical genetics. Major events including the Bantu expansion and European colonialism have imprinted unique genetic signatures within autochthonous populations of Southern Africa, this resulting in differential allele frequen...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.00905

    authors: Thami PK,Chimusa ER

    更新日期:2019-09-27 00:00:00

  • Evaluating the Accuracy of Imputation Methods in a Five-Way Admixed Population.

    abstract::Genotype imputation is a powerful tool for increasing statistical power in an association analysis. Meta-analysis of multiple study datasets also requires a substantial overlap of SNPs for a successful association analysis, which can be achieved by imputation. Quality of imputed datasets is largely dependent on the so...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00034

    authors: Schurz H,Müller SJ,van Helden PD,Tromp G,Hoal EG,Kinnear CJ,Möller M

    更新日期:2019-02-05 00:00:00

  • Ubiquitination and SUMOylation in Telomere Maintenance and Dysfunction.

    abstract::Telomeres are essential nucleoprotein structures at linear chromosomes that maintain genome integrity by protecting chromosome ends from being recognized and processed as damaged DNA. In addition, they limit the cell's proliferative capacity, as progressive loss of telomeric DNA during successive rounds of cell divisi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2017.00067

    authors: Yalçin Z,Selenz C,Jacobs JJL

    更新日期:2017-05-23 00:00:00

  • Accuracy of Genomic Evaluations of Juvenile Growth Rate in Common Carp (Cyprinus carpio) Using Genotyping by Sequencing.

    abstract::Cyprinids are the most important group of farmed fish globally in terms of production volume, with common carp (Cyprinus carpio) being one of the most valuable species of the group. The use of modern selective breeding methods in carp is at a formative stage, implying a large scope for genetic improvement of key produ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00082

    authors: Palaiokostas C,Kocour M,Prchal M,Houston RD

    更新日期:2018-03-13 00:00:00

  • Missense Mutations of Human Hsp60: A Computational Analysis to Unveil Their Pathological Significance.

    abstract::Two chaperonopathies have been linked to mutations in the human hsp60 (hHsp60; HSPD1) gene, but other existing variants might cause diseases, even if there is no comprehensive information about this possibility. To fill this vacuum, which might be at the basis of misdiagnoses or simply ignorance of chaperonopathies in...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00969

    authors: Vitale AM,Conway de Macario E,Alessandro R,Cappello F,Macario AJL,Marino Gammazza A

    更新日期:2020-08-18 00:00:00

  • Bias, accuracy, and impact of indirect genetic effects in infectious diseases.

    abstract::Selection for improved host response to infectious disease offers a desirable alternative to chemical treatment but has proven difficult in practice, due to low heritability estimates of disease traits. Disease data from field studies is often binary, indicating whether an individual has become infected or not followi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2012.00215

    authors: Lipschutz-Powell D,Woolliams JA,Bijma P,Pong-Wong R,Bermingham ML,Doeschl-Wilson AB

    更新日期:2012-10-22 00:00:00

  • The effect of preconception paternal alcohol exposure on epigenetic remodeling of the h19 and rasgrf1 imprinting control regions in mouse offspring.

    abstract::Imprinted loci play a critical role in fetal development. Their expression is often regulated by CCCTC-binding factor (CTCF) protein binding at imprinting control regions (ICRs). Prenatal alcohol exposure has been shown to reduce global DNA methylation in the developing mouse fetus. This study explored the effect of p...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2012.00010

    authors: Knezovich JG,Ramsay M

    更新日期:2012-02-22 00:00:00

  • Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa.

    abstract::Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable i...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2015.00013

    authors: Khanyile KS,Dzomba EF,Muchadeyi FC

    更新日期:2015-02-03 00:00:00

  • The Missing lnc(RNA) between the pancreatic β-cell and diabetes.

    abstract::Diabetes mellitus represents a group of complex metabolic diseases that result in impaired glucose homeostasis, which includes destruction of β-cells or the failure of these insulin-secreting cells to compensate for increased metabolic demand. Despite a strong interest in characterizing the transcriptome of the differ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2014.00200

    authors: Kameswaran V,Kaestner KH

    更新日期:2014-07-01 00:00:00

  • Estimation of Recombination Rate and Maternal Linkage Disequilibrium in Half-Sibs.

    abstract::A livestock population can be characterized by different population genetic parameters, such as linkage disequilibrium and recombination rate between pairs of genetic markers. The population structure, which may be caused by family stratification, has an influence on the estimates of these parameters. An expectation m...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00186

    authors: Hampel A,Teuscher F,Gomez-Raya L,Doschoris M,Wittenburg D

    更新日期:2018-06-05 00:00:00

  • MS4A2-rs573790 Is Associated With Aspirin-Exacerbated Respiratory Disease: Replicative Study Using a Candidate Gene Strategy.

    abstract::Aspirin exacerbated respiratory disease (AERD) is a set of diseases of the unified airway, and its physiopathology is related to disruption of the metabolism of arachidonic acid (AA). Genetic association studies in AERD had explored single nucleotide polymorphism (SNPs) in several genes related to many mechanisms (AA ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00363

    authors: Pavón-Romero GF,Pérez-Rubio G,Ramírez-Jiménez F,Ambrocio-Ortiz E,Bañuelos-Ortiz E,Alvarado-Franco N,Xochipa-Ruiz KE,Hernández-Juárez E,Flores-García BA,Camarena ÁE,Terán LM,Falfán-Valencia R

    更新日期:2018-09-11 00:00:00

  • Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data.

    abstract::Analysis of bulk RNA sequencing (RNA-Seq) data is a valuable tool to understand transcription at the genome scale. Targeted sequencing of RNA has emerged as a practical means of assessing the majority of the transcriptomic space with less reliance on large resources for consumables and bioinformatics. TempO-Seq is a t...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00594

    authors: Bushel PR,Ferguson SS,Ramaiahgari SC,Paules RS,Auerbach SS

    更新日期:2020-06-23 00:00:00

  • Identification and Validation of Key Genes Associated With Systemic Sclerosis-Related Pulmonary Hypertension.

    abstract::Systemic sclerosis-associated with pulmonary arterial hypertension (SSc-PAH) is still a major cause of SSc related deaths. Early diagnosis and prompt treatment are crucial to reduce the mortality of patients with SSc-PAH. To screen the candidate biomarkers and potential therapeutic targets for SSc-PAH, we analyzed the...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.00816

    authors: Zheng JN,Li Y,Yan YM,Shi H,Zou TT,Shao WQ,Wang Q

    更新日期:2020-07-24 00:00:00

  • Epigenetic Modifications in Acute Myeloid Leukemia: Prognosis, Treatment, and Heterogeneity.

    abstract::Leukemia, specifically acute myeloid leukemia (AML), is a common malignancy that can be differentiated into multiple subtypes based on leukemogenic history and etiology. Although genetic aberrations, particularly cytogenetic abnormalities and mutations in known oncogenes, play an integral role in AML development, epig...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审

    doi:10.3389/fgene.2019.00133

    authors: Goldman SL,Hassan C,Khunte M,Soldatenko A,Jong Y,Afshinnekoo E,Mason CE

    更新日期:2019-03-01 00:00:00

  • Revisiting Non-BRCA1/2 Familial Whole Exome Sequencing Datasets Implicates NCK1 as a Cancer Gene.

    abstract::Through linkage and candidate gene screening, many breast cancer (BC) predisposition genes have been identified in the past 20 years. However, the majority of genetic risks that contribute to familial BC remains undetermined. In this study, we revisited whole exome sequencing datasets from non-BRCA1/2 familial BC pati...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00527

    authors: Yin J,Wu K,Ma Q,Dong H,Zhu Y,Hu L,Kong X

    更新日期:2019-06-04 00:00:00

  • Chromatin associations in Arabidopsis interphase nuclei.

    abstract::The arrangement of chromatin within interphase nuclei seems to be caused by topological constraints and related to gene expression depending on tissue and developmental stage. In yeast and animals it was found that homologous and heterologous chromatin association are required to realize faithful expression and DNA re...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2014.00389

    authors: Schubert V,Rudnik R,Schubert I

    更新日期:2014-11-13 00:00:00

  • Bioinformatics Analysis of Actin Molecules: Why Quantity Does Not Translate Into Quality?

    abstract::It is time to review all the available data and find the distinctive characteristics of actin that make it such an important cell molecule. The presented double-stranded organization of filamentous actin cannot explain the strong polymorphism of actin fibrils. In this work, we performed bioinformatics analysis of a se...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.617763

    authors: Glyakina AV,Galzitskaya OV

    更新日期:2020-12-10 00:00:00

  • Identification of Potential Long Non-coding RNA Expression Quantitative Trait Methylations in Lung Adenocarcinoma and Lung Squamous Carcinoma.

    abstract::There are associations between DNA methylation and the expression of long non-coding RNA (lncRNA), also known as lncRNA expression quantitative trait methylations (lnc-eQTMs). Lnc-eQTMs may induce a wide range of carcinogenesis pathways. However, lnc-eQTMs have not been globally identified and studied, and their roles...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.602035

    authors: Wu X,Gao Y,Bu J,Deng L,Zhang P,Chi M,Jiang L,Shi X,Ning S,Wang G

    更新日期:2020-12-09 00:00:00

  • DRIM: A Web-Based System for Investigating Drug Response at the Molecular Level by Condition-Specific Multi-Omics Data Integration.

    abstract::Pharmacogenomics is the study of how genes affect a person's response to drugs. Thus, understanding the effect of drug at the molecular level can be helpful in both drug discovery and personalized medicine. Over the years, transcriptome data upon drug treatment has been collected and several databases compiled before ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.564792

    authors: Oh M,Park S,Lee S,Lee D,Lim S,Jeong D,Jo K,Jung I,Kim S

    更新日期:2020-11-12 00:00:00

  • Interaction between oxytocin receptor DNA methylation and genotype is associated with risk of postpartum depression in women without depression in pregnancy.

    abstract::Postpartum depression (PPD) affects up to 19% of women, negatively impacting maternal and infant health. Reductions in plasma oxytocin levels have been associated with PPD and heritability studies have established a genetic contribution. Epigenetic regulation of the oxytocin receptor gene (OXTR) has been demonstrated ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2015.00243

    authors: Bell AF,Carter CS,Steer CD,Golding J,Davis JM,Steffen AD,Rubin LH,Lillard TS,Gregory SP,Harris JC,Connelly JJ

    更新日期:2015-07-21 00:00:00

  • Alcohol Use and Depression: A Mendelian Randomization Study From China.

    abstract::Background: Alcohol use has been linked to a number of physical conditions, but the relationship between alcohol drinking and depression, one of the most common mental disorders that is a significant contributor to the global burden of disease, is still under debate. We aim to help fill the literature gap on the causa...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2020.585351

    authors: Zhu C,Chen Q,Si W,Li Y,Chen G,Zhao Q

    更新日期:2020-10-19 00:00:00

  • Functional Partitioning of Genomic Variance and Genome-Wide Association Study for Carcass Traits in Korean Hanwoo Cattle Using Imputed Sequence Level SNP Data.

    abstract::Quantitative traits are usually controlled by numerous genomic variants with small individual effects, and variances associated with those traits are explained in a continuous manner. However, the relative contributions of genomic regions to observed genetic variations have not been well explored using sequence level ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2018.00217

    authors: Bhuiyan MSA,Lim D,Park M,Lee S,Kim Y,Gondro C,Park B,Lee S

    更新日期:2018-06-22 00:00:00

  • A RNA-Seq Analysis to Describe the Boar Sperm Transcriptome and Its Seasonal Changes.

    abstract::Understanding the molecular basis of cell function and ultimate phenotypes is crucial for the development of biological markers. With this aim, several RNA-seq studies have been devoted to the characterization of the transcriptome of ejaculated spermatozoa in relation to sperm quality and fertility. Semen quality foll...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00299

    authors: Gòdia M,Estill M,Castelló A,Balasch S,Rodríguez-Gil JE,Krawetz SA,Sánchez A,Clop A

    更新日期:2019-04-16 00:00:00

  • Controlled Reduction of Genomic Heterozygosity in an Industrial Yeast Strain Reveals Wide Cryptic Phenotypic Variation.

    abstract::Abundant genomic heterozygosity can be found in wild strains of the budding yeast Saccharomyces cerevisiae isolated from industrial and clinical environments. The extent to which heterozygosity influences the phenotypes of these isolates is not fully understood. One such case is the PE-2/JAY270 strain, a natural hybri...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章

    doi:10.3389/fgene.2019.00782

    authors: Sampaio NMV,Watson RA,Argueso JL

    更新日期:2019-09-11 00:00:00