当前位置： SCI文献检索 > Genes期刊下所有文献 > Combining Random Forests and a Signal Detection Method Leads to the Robust Detection of Genotype-Phenotype Associations.

Combining Random Forests and a Signal Detection Method Leads to the Robust Detection of Genotype-Phenotype Associations.

Abstract：

:Genome wide association studies (GWAS) are a well established methodology to identify genomic variants and genes that are responsible for traits of interest in all branches of the life sciences. Despite the long time this methodology has had to mature the reliable detection of genotype-phenotype associations is still a challenge for many quantitative traits mainly because of the large number of genomic loci with weak individual effects on the trait under investigation. Thus, it can be hypothesized that many genomic variants that have a small, however real, effect remain unnoticed in many GWAS approaches. Here, we propose a two-step procedure to address this problem. In a first step, cubic splines are fitted to the test statistic values and genomic regions with spline-peaks that are higher than expected by chance are considered as quantitative trait loci (QTL). Then the SNPs in these QTLs are prioritized with respect to the strength of their association with the phenotype using a Random Forests approach. As a case study, we apply our procedure to real data sets and find trustworthy numbers of, partially novel, genomic variants and genes involved in various egg quality traits.

journal_name

Genes (Basel)

journal_title

Genes

authors

Ramzan F,Gültas M,Bertram H,Cavero D,Schmitt AO

doi

10.3390/genes11080892

subject

Has Abstract

pub_date

2020-08-05 00:00:00

issue

8

issn

2073-4425

pii

genes11080892

journal_volume

11

pub_type

杂志文章

相关文献

Genes文献大全
  • 46,XY,r(8)/45,XY,-8 Mosaicism as a Possible Mechanism of the Imprinted Birk-Barel Syndrome: A Case Study.

    abstract：:Ring chromosome 8 (r(8)) is one of the least frequent ring chromosomes. Usually, maternal chromosome 8 forms a ring, which can be lost from cells due to mitotic instability. The 8q24 region contains the imprinted KCNK9 gene, which is expressed from the maternal allele. Heterozygous KCNK9 mutations are associated with ...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes11121473

    authors： Kashevarova AA,Nikitina TV,Mikhailik LI,Belyaeva EO,Vasilyev SA,Lopatkina ME,Fedotov DA,Fonova EA,Zarubin AA,Sivtsev AA,Skryabin NA,Nazarenko LP,Lebedev IN

    更新日期：2020-12-09 00:00:00

  • Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq.

    abstract：:In China, the production for duck meat is second only to that of chicken, and the demand for duck meat is also increasing. However, there is still unclear on the internal mechanism of regulating skeletal muscle growth and development in duck. This study aimed to identity candidate genes related to growth of duck skele...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes11101228

    authors： Hu Z,Cao J,Liu G,Zhang H,Liu X

    更新日期：2020-10-20 00:00:00

  • Can Genetic Testing Identify Talent for Sport?

    abstract：:Elite athlete status is a partially heritable trait, as are many of the underpinning physiological, anthropometrical, and psychological traits that contribute to elite performance. In recent years, our understanding of the specific genetic variants that contribute to these traits has grown, such that there is consider...

    journal_title：Genes

    pub_type： 杂志文章,评审

    doi：10.3390/genes10120972

    authors： Pickering C,Kiely J,Grgic J,Lucia A,Del Coso J

    更新日期：2019-11-26 00:00:00

  • Neo-Domestication of an Interspecific Tetraploid Helianthus annuus × Helianthus tuberous Population That Segregates for Perennial Habit.

    abstract：:Perennial agriculture has been proposed as an option to improve the sustainability of cropping systems, by increasing the efficiency of resource use, while also providing ecosystem services. Neo-domestication, the contemporary domestication of plants that have not previously been used in agriculture, can be used to ge...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes9090422

    authors： Kantar MB,Hüber S,Herman A,Bock DG,Baute G,Betts K,Ott M,Brandvain Y,Wyse D,Stupar RM,Rieseberg LH

    更新日期：2018-08-21 00:00:00

  • Cytogenetics in Arctica islandica (Bivalvia, Arctidae): the Longest Lived Non-Colonial Metazoan.

    abstract：:Due to its extraordinary longevity and wide distribution, the ocean quahog Arctica islandica has become an important species model in both aging and environmental change research. Notwithstanding that, most genetic studies on ocean quahogs have been focused on fishery related, phylogeographic and phylogenetic aspects ...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes9060299

    authors： García-Souto D,Pasantes JJ

    更新日期：2018-06-13 00:00:00

  • Chromatin Dynamics in the Regulation of CFTR Expression.

    abstract：:The contribution of chromatin dynamics to the regulation of human disease-associated loci such as the cystic fibrosis transmembrane conductance regulator (CFTR) gene has been the focus of intensive experimentation for many years. Recent technological advances in the analysis of transcriptional mechanisms across the en...

    journal_title：Genes

    pub_type： 杂志文章,评审

    doi：10.3390/genes6030543

    authors： Gosalia N,Harris A

    更新日期：2015-07-13 00:00:00

  • Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools.

    abstract：:Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. ...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes9080418

    authors： Sereno D,Dorkeld F,Akhoundi M,Perrin P

    更新日期：2018-08-20 00:00:00

  • Phased Haplotype Resolution of the SLC6A4 Promoter Using Long-Read Single Molecule Real-Time (SMRT) Sequencing.

    abstract：:The SLC6A4 gene has been implicated in psychiatric disorder susceptibility and antidepressant response variability. The SLC6A4 promoter is defined by a variable number of homologous 20-24 bp repeats (5-HTTLPR), and long (L) and short (S) alleles are associated with higher and lower expression, respectively. However, t...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes11111333

    authors： Botton MR,Yang Y,Scott ER,Desnick RJ,Scott SA

    更新日期：2020-11-12 00:00:00

  • The LDLR, APOB, and PCSK9 Variants of Index Patients with Familial Hypercholesterolemia in Russia.

    abstract：:Familial hypercholesterolemia (FH) is a common autosomal codominant disorder, characterized by elevated low-density lipoprotein cholesterol levels causing premature atherosclerotic cardiovascular disease. About 2900 variants of LDLR, APOB, and PCSK9 genes potentially associated with FH have been described earlier. Nev...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes12010066

    authors： Meshkov A,Ershova A,Kiseleva A,Zotova E,Sotnikova E,Petukhova A,Zharikova A,Malyshev P,Rozhkova T,Blokhina A,Limonova A,Ramensky V,Divashuk M,Khasanova Z,Bukaeva A,Kurilova O,Skirko O,Pokrovskaya M,Mikova V,Snigir E

    更新日期：2021-01-06 00:00:00

  • Impact of HVT Vaccination on Splenic miRNA Expression in Marek's Disease Virus Infections.

    abstract：:Marek's Disease is a lymphoproliferative disease of chickens caused by Marek's Disease Virus. Similar to other herpesviruses, Marek's Disease Virus (MDV) encodes its own small non-coding regulatory RNAs termed microRNAs (miRNAs). We previously found that the expression profile of these viral miRNAs is affected by vacc...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes10020115

    authors： Hicks JA,Liu HC

    更新日期：2019-02-05 00:00:00

  • Expression of ZNF695 Transcript Variants in Childhood B-Cell Acute Lymphoblastic Leukemia.

    abstract：:B-cell acute lymphoblastic leukemia is the most commonly diagnosed childhood malignancy worldwide; more than 50% of these cases are diagnosed in Mexico. Although the five-year survival rate is >80%, 30% of patients experience relapse with poor prognosis. Cancer-associated gene expression profiles have been identified ...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes10090716

    authors： Rosa R,Villegas-Ruíz V,Caballero-Palacios MC,Pérez-López EI,Murata C,Zapata-Tarres M,Cárdenas-Cardos R,Paredes-Aguilera R,Rivera-Luna R,Juárez-Méndez S

    更新日期：2019-09-16 00:00:00

  • Suppression of Notch Signaling Stimulates Progesterone Synthesis by Enhancing the Expression of NR5A2 and NR2F2 in Porcine Granulosa Cells.

    abstract：:The conserved Notch pathway is reported to be involved in progesterone synthesis and secretion; however, the exact effects remain controversial. To determine the role and potential mechanisms of the Notch signaling pathway in progesterone biosynthesis in porcine granulosa cells (pGCs), we first used a pharmacological ...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes11020120

    authors： Guo R,Chen F,Shi Z

    更新日期：2020-01-22 00:00:00

  • Non-Random Distribution of Reciprocal Translocation Breakpoints in the Pig Genome.

    abstract：:Balanced chromosome rearrangements are one of the main etiological factors contributing to hypoprolificacy in the domestic pig. Amongst domestic animals, the pig is considered to have the highest prevalence of chromosome rearrangements. To date over 200 unique chromosome rearrangements have been identified. The factor...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes10100769

    authors： Donaldson B,Villagomez DAF,Revay T,Rezaei S,King WA

    更新日期：2019-09-30 00:00:00

  • Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres.

    abstract：:Information on the biochemical pathways of carbon and energy metabolism in representatives of the deep lineage bacterial phylum Deferribacteres are scarce. Here, we report the results of the sequencing and analysis of the high-quality draft genome of the thermophilic chemolithoautotrophic anaerobe Deferribacter autotr...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes10110849

    authors： Slobodkin A,Slobodkina G,Allioux M,Alain K,Jebbar M,Shadrin V,Kublanov I,Toshchakov S,Bonch-Osmolovskaya E

    更新日期：2019-10-26 00:00:00

  • Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas.

    abstract：:Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region o...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes11060695

    authors： Tunjić Cvitanić M,Vojvoda Zeljko T,Pasantes JJ,García-Souto D,Gržan T,Despot-Slade E,Plohl M,Šatović E

    更新日期：2020-06-24 00:00:00

  • The MAPKKK CgMck1 Is Required for Cell Wall Integrity, Appressorium Development, and Pathogenicity in Colletotrichum gloeosporioides.

    abstract：:Mitogen-activated protein kinase (MAPK) signaling pathway plays key roles in sensing extracellular signals and transmitting them from the cell membrane to the nucleus in response to various environmental stimuli. A MAPKKK protein CgMck1 in Colletotrichum gloeosporioides was characterized. Phenotypic analyses of the ∆C...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes9110543

    authors： Fang YL,Xia LM,Wang P,Zhu LH,Ye JR,Huang L

    更新日期：2018-11-08 00:00:00

  • Transcriptome Profiling and Molecular Therapeutic Advances in Cystic Fibrosis: Recent Insights.

    abstract：:In cystic fibrosis (CF), mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene disrupt the capacity of the encoded protein to function as a channel to transport chloride ions and water across cell membranes. The consequences are deleterious, system-wide, and immensely variable, even among pa...

    journal_title：Genes

    pub_type： 杂志文章,评审

    doi：10.3390/genes10030180

    authors： Ideozu JE,Zhang X,McColley S,Levy H

    更新日期：2019-02-26 00:00:00

  • RNA Sequencing Analysis of Chicken Cecum Tissues Following Eimeria tenella Infection in Vivo.

    abstract：:Eimeria tenella (E. tenella) is one of the most frequent and pathogenic species of protozoan parasites of the genus Eimeria that exclusively occupies the cecum, exerting a high economic impact on the poultry industry. To investigate differentially expressed genes (DEGs) in the cecal tissue of Jinghai yellow chickens i...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes10060420

    authors： Wang X,Zou W,Yu H,Lin Y,Dai G,Zhang T,Zhang G,Xie K,Wang J,Shi H

    更新日期：2019-05-31 00:00:00

  • Exploring the Variable Phenotypes of RPGR Carrier Females in Assessing their Potential for Retinal Gene Therapy.

    abstract：:Inherited retinal degenerations are the leading cause of blindness in the working population. X-linked retinitis pigmentosa (XLRP), caused by mutations in the Retinitis pigmentosa GTPase regulator (RPGR) gene is one of the more severe forms, and female carriers of RPGR mutations have a variable presentation. A retrosp...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes9120643

    authors： Nanda A,Salvetti AP,Clouston P,Downes SM,MacLaren RE

    更新日期：2018-12-18 00:00:00

  • RNA Modifications Modulate Activation of Innate Toll-Like Receptors.

    abstract：:Self/foreign discrimination by the innate immune system depends on receptors that identify molecular patterns as associated to pathogens. Among others, this group includes endosomal Toll-like receptors, among which Toll-like receptors (TLR) 3, 7, 8, and 13 recognize and discriminate mammalian from microbial, potential...

    journal_title：Genes

    pub_type： 杂志文章,评审

    doi：10.3390/genes10020092

    authors： Freund I,Eigenbrod T,Helm M,Dalpke AH

    更新日期：2019-01-29 00:00:00

  • Porcine Epidemic Diarrhea Altered Colonic Microbiota Communities in Suckling Piglets.

    abstract：:Porcine epidemic diarrhea (PED) is a major gastrointestinal disease afflicting suckling pigs that causes huge industrial economic losses. In this study, we investigated microbiota from the colonic mucosa and content in healthy and PED piglets. High-throughput 16S rRNA gene sequencing was performed to identify inter-gr...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes11010044

    authors： Tan Z,Dong W,Ding Y,Ding X,Zhang Q,Jiang L

    更新日期：2019-12-30 00:00:00

  • Non-Additive Transcriptomic Responses to Inoculation with Rhizobia in a Young Allopolyploid Compared with Its Diploid Progenitors.

    abstract：:Root nodule symbioses (nodulation) and whole genome duplication (WGD, polyploidy) are both important phenomena in the legume family (Leguminosae). Recently, it has been proposed that polyploidy may have played a critical role in the origin or refinement of nodulation. However, while nodulation and polyploidy have been...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes8120357

    authors： Powell AF,Doyle JJ

    更新日期：2017-11-30 00:00:00

  • Comparison of the fecal microbiota in feral and domestic goats.

    abstract：:Animals have co-evolved with mutualistic microbial communities, known as the microbiota, which are essential for organ development and function. We hypothesize that modern animal husbandry practices exert an impact on the intestinal microbiota. In this study, we compared the structure of the fecal microbiota between f...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes3010001

    authors： De Jesús-Laboy KM,Godoy-Vitorino F,Piceno YM,Tom LM,Pantoja-Feliciano IG,Rivera-Rivera MJ,Andersen GL,Domínguez-Bello MG

    更新日期：2011-12-21 00:00:00

  • Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing.

    abstract：:The MinION sequencer has made in situ sequencing feasible in remote locations. Following our initial demonstration of its high performance off planet with Earth-prepared samples, we developed and tested an end-to-end, sample-to-sequencer process that could be conducted entirely aboard the International Space Station (...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes11010076

    authors： Burton AS,Stahl SE,John KK,Jain M,Juul S,Turner DJ,Harrington ED,Stoddart D,Paten B,Akeson M,Castro-Wallace SL

    更新日期：2020-01-09 00:00:00

  • Network-Based Approaches to Explore Complex Biological Systems towards Network Medicine.

    abstract：:Network medicine relies on different types of networks: from the molecular level of protein⁻protein interactions to gene regulatory network and correlation studies of gene expression. Among network approaches based on the analysis of the topological properties of protein⁻protein interaction (PPI) networks, we discuss ...

    journal_title：Genes

    pub_type： 杂志文章,评审

    doi：10.3390/genes9090437

    authors： Fiscon G,Conte F,Farina L,Paci P

    更新日期：2018-08-31 00:00:00

  • Transcriptional Structure of Petunia Clock in Leaves and Petals.

    abstract：:The plant circadian clock coordinates environmental signals with internal processes including secondary metabolism, growth, flowering, and volatile emission. Plant tissues are specialized in different functions, and petals conceal the sexual organs while attracting pollinators. Here we analyzed the transcriptional str...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes10110860

    authors： Terry MI,Carrera-Alesina M,Weiss J,Egea-Cortines M

    更新日期：2019-10-30 00:00:00

  • Genome-Wide Identification, Classification, Characterization, and Expression Analysis of the Wall-Associated Kinase Family during Fruit Development and under Wound Stress in Tomato (Solanum lycopersicum L.).

    abstract：:The wall-associated kinase (WAK) and wall-associated kinase like (WAKL) is a subfamily of receptor-like kinases associated with the cell wall, which have been suggested as sensors of the extracellular environment and triggers of intracellular signals. However, these proteins have not yet been comprehensively analyzed ...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes11101186

    authors： Sun Z,Song Y,Chen D,Zang Y,Zhang Q,Yi Y,Qu G

    更新日期：2020-10-12 00:00:00

  • An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice.

    abstract：:Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplica...

    journal_title：Genes

    pub_type： 杂志文章,评审

    doi：10.3390/genes11091046

    authors： Lallemand T,Leduc M,Landès C,Rizzon C,Lerat E

    更新日期：2020-09-04 00:00:00

  • DynSig: Modelling Dynamic Signaling Alterations along Gene Pathways for Identifying Differential Pathways.

    abstract：:Although a number of methods have been proposed for identifying differentially expressed pathways (DEPs), few efforts consider the dynamic components of pathway networks, i.e., gene links. We here propose a signaling dynamics detection method for identification of DEPs, DynSig, which detects the molecular signaling ch...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes9070323

    authors： Shi M,Chong Y,Shen W,Xie XP,Wang HQ

    更新日期：2018-06-27 00:00:00

  • Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models.

    abstract：:Death investigations often include an effort to establish the postmortem interval (PMI) in cases in which the time of death is uncertain. The postmortem interval can lead to the identification of the deceased and the validation of witness statements and suspect alibis. Recent research has demonstrated that microbes pr...

    journal_title：Genes

    pub_type： 杂志文章

    doi：10.3390/genes9020104

    authors： Belk A,Xu ZZ,Carter DO,Lynne A,Bucheli S,Knight R,Metcalf JL

    更新日期：2018-02-16 00:00:00