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450 results for “Candidate Genes”
Data for "Complex Traits and Candidate Genes"
<p>This repository contains the simulation code and output for the main simulations from "Complex Traits and Candidate Genes: Estimation of Genetic Variance Components Across Modes of Inheritance" https://www.biorxiv.org/content/10.1101/2022.07.04.498768v1.</p> <p><strong>The simulations are grouped by the population heterozygosity: </strong></p> <p> Het_0 refers to simulations of inbred lines</p> <p> Het_38 refers to simulations of heterozygous hybrids with average heterozygosity equal to 0.38.</p> <p>The code and output for individual simulations are referred to be the <strong>population size (n)</strong>: n500, n1000, n2000, and the <strong>number of replicates of each entry (r)</strong>: r1, r2, and r4.</p> <p> </p> <p> </p>
List of NDD candidate genes - Insitute of Human Genetics in Leipzig, Germany
<p>This dataset is a list a NDD candidate genes which was created by the Institute of Human Genetics, University of Leipzig Medical Center in Leipzig, Germany on 10th of June 2024. </p>
Kroll et al., 2024. Behavioural pharmacology predicts disrupted signalling pathways and candidate therapeutics from zebrafish mutants of Alzheimer's disease risk genes
<p>Data repository for</p> <p>François Kroll, Joshua Donnelly, Joshua Donnelly, Güliz Gürel Özcan, Eirinn Mackay, Jason Rihel</p> <div> <div><strong>Behavioural pharmacology predicts disrupted signalling pathways and candidate therapeutics from zebrafish mutants of Alzheimer’s disease risk genes</strong></div> <br> <div>eLife, 2024.</div> <br> <div><a href="https://doi.org/10.7554/eLife.96839.1">https://doi.org/10.7554/eLife.96839.1</a></div> <div> </div> <div>Code is found in the <a href="https://github.com/francoiskroll/ZFAD">GitHub repository</a>. Please see notes there.</div> </div> <p>___</p> <p>Contact:</p> <p>Twitter: @francois_kroll</p> <p>Email: francois@kroll.be</p>
Phenotypic landscape of schizophrenia-associated genes defines candidates and their shared functions - behavior data
<p>Processed behavior data for all zebrafish behavior runs included in manuscript. This includes data such as bouts / minute. The raw data used to generate this processed output is available upon request (too large for any public repository). These files can be used to generate all statistics and graphs using the script statsandgraphs.py (https://github.com/sthyme/ZFSchizophrenia/tree/master/BehaviorAnalysis). Each directory also contains scripts used, genotyping information, and output files for the statistical analyses presented in the manuscript.</p>
Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations
<p>Supplementary data of manuscript <strong>'Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations </strong><strong>Analysis of opposing histone modifications H3K4me3 and H3K27me3 reveals candidate diagnostic biomarkers for triple negative breast cancer and gene set prediction combinations'</strong></p>
Identification of genetic loci and functional analysis of candidate gene, OsCycB1;5 associated with seed callus induction in rice (Oryza sativa L.)
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Data from: Seeking signatures of reinforcement at the genetic level: a hitchhiking mapping and candidate gene approach in the house mouse
Reinforcement is the process by which prezygotic isolation is strengthened as a response to selection against hybridization. Most empirical support for reinforcement comes from the observation of its possible phenotypic signature: an accentuated degree of prezygotic isolation in the hybrid zone as compared to allopatry. Here, we implemented a novel approach to this question by seeking for the signature of reinforcement at the genetic level. In the house mouse, selection against hybrids and enhanced olfactory-based assortative mate preferences are observed in a hybrid zone between the two European subspecies Mus musculus musculus and M. m. domesticus, suggesting a possible recent reinforcement event. To test for the genetic signature of reinforcing selection and identify genes involved in sexual isolation, we adopted a hitchhiking mapping approach targeting genomic regions containing candidate genes for assortative mating in mice. We densely scanned these genomic regions in hybrid zone and allopatric samples using a large number of fast evolving microsatellite loci that allow the detection of recent selection events. We found a handful of loci showing the expected pattern of significant reduction in variability in populations close to the hybrid zone, showing assortative odour preference in mate choice experiments as compared to populations further away and displaying no such preference. These loci lie close to genes that we pinpoint as testable candidates for further investigation.
Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation
Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.
Data from: Candidate adaptive genes associated with lineage divergence: identifying SNPs via next-generation targeted resequencing in mule deer (Odocoileus hemionus)
Mule deer (Odocoileus hemionus) are an excellent nonmodel species for empirically testing hypotheses in landscape and population genomics due to their large population sizes (low genetic drift), relatively continuous distribution, diversity of occupied habitats and phenotypic variation. Because few genomic resources are currently available for this species, we used exon data from a cattle (Bos taurus) reference genome to direct targeted resequencing of 5935 genes in mule deer. We sequenced approximately 3.75 Mbp at minimum 20X coverage in each of the seven mule deer, identifying 23 204 single nucleotide polymorphisms (SNPs) within, or adjacent to, 6886 exons in 3559 genes. We found 91 SNP loci (from 69 genes) with putatively fixed allele frequency differences between the two major lineages of mule deer (mule deer and black-tailed deer), and our estimate of mean genetic divergence (genome-wide FST = 0.123) between these lineages was consistent with previous findings using microsatellite loci. We detected an over-representation of gamete generation and amino acid transport genes among the genes with SNPs exhibiting potentially fixed allele frequency differences between lineages. This targeted resequencing approach using exon capture techniques has identified a suite of loci that can be used in future research to investigate the genomic basis of adaptation and differentiation between black-tailed deer and mule deer. This study also highlights techniques (and an exon capture array) that will facilitate population genomic research in other cervids and nonmodel organisms.
Candidate gene polymorphisms are linked to dispersive and migratory behaviour: searching for a mechanism behind the "paradox of the great speciators"
<p>The "paradox of the great speciators" has puzzled evolutionary biologists for over half a century. A great speciator requires excellent dispersal <span>propensity</span> to explain <span>its</span> occurrence on multiple islands, but reduced dispersal ability to explain <span>its</span> high number of subspecies. A rapid reduction in dispersal ability is often invoked to solve this apparent paradox, but a proximate mechanism has not been identified yet. Here, we explored the role of six genes linked to migration and animal personality differences (<em>CREB1, CLOCK, ADCYAP1, NPAS2, DRD4, </em>and<em> SERT</em>) in 20 South Pacific populations of silvereye (<em>Zosterops</em> <em>lateralis</em>) that range from highly sedentary to partially migratory, to determine if genetic variation is associated with dispersal propensity and migration. We detected genetic associations in three of the six genes: i) in a partial migrant population, migrant individuals had longer microsatellite alleles at the <em>CLOCK</em> gene compared to resident individuals from the same population; ii) <em>CREB1</em> displayed longer average microsatellite allele lengths in recently colonised island populations (< 200 years), compared to evolutionarily older populations. Bayesian broken stick regression models supported a reduction in <em>CREB1</em> length with time since colonisation; and iii) like <em>CREB1</em>, <em>DRD4</em> showed differences in polymorphisms between recent and old colonisations but a <span>larger</span> sample is needed to confirm. <em>ADCYAP1</em>, <em>SERT</em>, and <em>NPAS2</em> were variable but that variation was not associated with dispersal propensity. The association of genetic variants at three genes with migration <span>and</span> dispersal ability in silvereyes provides the impetus for further exploration of genetic mechanisms underlying dispersal shifts and the prospect of resolving a long-running evolutionary paradox through a genetic lens.</p>
Fig. 4. Amino acid sequences alignment between TCS1 and candidate N in Discovery and Biochemical Characterization of N-methyltransferase Genes Involved in Purine Alkaloid Biosynthetic Pathway of Camellia gymnogyna Hung T.Chang (Theaceae) from Dayao Mountain
Fig. 4. Amino acid sequences alignment between TCS1 and candidate N-methyltransferase genes (GCS1, GCS2, and GCS3).
Study in Leucocytes From Patients With Type 1 and Type 2 Diabetes Genetic Markers of Inflammation and Oxidative Stress (TÉLOMÈRES/ CANDIDATE GENES) According to the Type A or Type B Behavior Profile
ClinicalTrials.gov study NCT02080741. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Identification of New Candidate Genes for Hereditary Predisposition to Uveal Melanoma
ClinicalTrials.gov study NCT06550674. IPD Sharing: NO. Countries: 1. Publications: 1.
Candidate Gene for Hyperferritinemia
ClinicalTrials.gov study NCT05659017. IPD Sharing: NO. Countries: 1. Publications: 23.
Characterization of New Candidate Genes in Cases of Human Inherited Thrombocytopenia (CATCH)
ClinicalTrials.gov study NCT04272970. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Study of the Telomere-telomerase System and the Expression of Candidate Genes in the Leukocytes of Patients With Depressive Disorder: Search for Peripheral Markers of Somatic Stress
ClinicalTrials.gov study NCT01903655. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Candidate Gene Screening for Attention Deficit/Hyperactive Disorder (ADHD)
ClinicalTrials.gov study NCT03018574. IPD Sharing: YES. Countries: 1. Publications: 3.
Data from: Differential introgression in a mosaic hybrid zone reveals candidate barrier genes
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Data from: Candidate gene analysis suggests untapped genetic complexity in melanin-based pigmentation in birds
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Data from: Crossing phenotype heritability and candidate gene expression in grafted black-lipped pearl oyster Pinctada margaritifera, an animal chimera
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.