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374 results for “gene polymorphism”
Polymorphisms in genes related to inflammation and endothelial function in the high-risk stroke population
<p><span><strong>Aim</strong>:</span><span> T</span><span>o investigate </span><span>incidence of ischemic stroke and other vascular events during a 4.7-year follow-up </span><span>in the </span><span>high-risk stroke population</span><span>, and to identify </span><span>the associations of </span><span>the 19 single nucleotide polymorphisms (SNPs)</span> <span>in genes related to inflammation and endothelial function</span><span> and </span><span>interaction among these</span> <span>SNPs</span><span> with outcomes. </span><span> </span></p> <p><span><strong>Methods</strong>: </span><span>According to </span><span>the China National Stroke Screening Survey programme, we performed this multi-center </span><span>community</span><span>-based sectional survey and prospective cohort</span> <span>study in the Sichuan of southwestern China </span><span>from May 2015 to January 2020</span><span>. Eight communities were randomly selected in </span><span>Sichuan, </span><span>and the </span><span>residents in each community volunteered to participate in a face-to-face survey. </span><span>The 19 SNPs</span><span> in </span><span>genes related to </span><span>endothelial function and inflammation </span><span>were measured in </span><span>the high-risk stroke population</span><span>. </span><span>All subjects in high-risk stroke populations were followed-up for 4.7 years after the face-to-face survey. The primary outcome was a new ischemic stroke; the secondary outcome was a composite of new vascular events. </span></p> <p><span><strong>Results</strong>: </span><span>A total of</span><span> 2893 high-risk stroke population, </span><span>2698 (93.3%) completed a 4.7-year follow-up. Outcomes occurred in 192 (7.1%) subjects (</span><span>118 [4.4%] new </span><span>ischemic stroke</span><span>, 24 [0.9%] </span><span>hemorrhagic stroke, </span><span>53 [2.0%] </span><span>myocardial infarction</span><span>, and 33[1.2%]</span><span> death) in </span><span>the </span><span>2698</span><span> high-risk stroke population. </span><span>There were significant differences in </span><span>genotype distribution</span> <span>of</span><span> <em>TNF</em></span><span> rs3093662,</span><span> <em>IL6R</em> rs4845625 and <em>TLR4</em> rs752998</span> <span>between s</span><span>ubjects with and without outcomes</span><span> by </span><span>univariate analyses. </span><span>Generalized multifactor dimensionality reduction (GMDR) </span><span>analysis showed that </span><span>there was a significant gene-gene interaction among the </span><span>19 SNPs, the best model for outcomes was interaction among </span><em><span>IL6R</span></em><span> rs4845625, </span><span><em>TLR4</em> </span><span>rs1927911 and</span> <em><span>HABP2</span></em><span> rs932650</span> <span>(<em>P</em> = </span><span>0.004</span><span>).</span><span> The high-risk </span><span>interactive genotypes</span><span> among the 3 SNPs were independently associated with a higher risk for new ischemic stroke </span><span> (OR = 2.187, 95% CI: 1.256–5.374, <em>P</em></span><<span>0.001</span><span>) </span><span>and total vascular events </span><span>(OR = 2.382, 95% CI: 1.423–5.894, <em>P</em></span><<span>0.001</span><span>) </span><span>after adjustment with covariates. </span></p> <p><span><strong>Conclusion</strong>: </span><span>The </span><span>incidence of ischemic stroke and other vascular events was </span><span>found to be very high in the </span><span>high-risk stroke population. </span><span>There were associations of specific SNPs</span> <span>in genes related to inflammation and endothelial function</span><span> with outcomes. The high-risk </span><span>interactive genotypes among </span><em><span>IL6R</span></em><span> rs4845625, </span><span><em>TLR4</em> </span><span>rs1927911 and</span> <em><span>HABP2</span></em><span> rs932650 were in</span><span>dependently associated with a higher risk </span><span>for </span><span>new ischemic stroke and other vascular events.</span><span> These findings are expected to</span> <span>provide</span> <span>new strategies for prevention of </span><span>ischemic stroke and other vascular events.</span> </p>
Gustin Gene Polymorphism and 6-n-propylthiouracil (PROP) Taste
ClinicalTrials.gov study NCT01097915. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Data from: K-13 Propeller gene polymorphisms isolated between 2014 and 2017 from Cameroonian Plasmodium falciparum malaria patients
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Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity
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Data from: Impact of treatment and re-treatment with Artemether-Lumefantrine and Artesunate-Amodiaquine on selection of Plasmodium falciparum Multidrug Resistance Gene-1 polymorphisms in the Democratic Republic of Congo and Uganda
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A non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster exhibits antagonistically pleiotropic fitness effects
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Polymorphisms in genes related to inflammation and endothelial function in the high-risk stroke population
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Data from: Changes in gene expression during female reproductive development in a colour polymorphic insect
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Influence of polymorphisms in the vascular endothelial growth factor gene on allograft rejection after kidney transplantation: a meta-analysis
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Data from: Polymorphisms in two key anthocyanic genes of clivia (Clivia miniata L.) reveal evidence of selection and possible association with flower pigmentation
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Trans-specific polymorphism and the convergent evolution of supertypes in MHC class II genes in Darters (Etheostoma)
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Data from: Research Note: Possible influence of thermal selection on patterns of HSP70 and HSP90 gene polymorphisms in Thai indigenous and local chicken breeds and red junglefowls
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Data from: A ketocarotenoid-based color polymorphism in the Sira poison frog Ranitomeya sirensis indicates novel gene interactions underlying aposematic signal variation
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Assessing gene flow between Dicranum scoparium Hedw. and D. bonjeanii De Not. (Dicranaceae) using single nucleotide polymorphisms (SNPs)
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Pathogen-selected polymorphisms in the PKLR gene are associated with mycobacterial susceptibility in Brazilian and African populations
<p>Data and metadata for the publication: "<strong>Pathogen-selected polymorphisms in the </strong><em><strong>PKLR</strong></em><strong> gene are associated with mycobacterial susceptibility in Brazilian and African populations</strong>" by Bezerra et al. 2020.</p> <p>Please, see README.rmd for more information.</p> <p> </p> <p> </p> <p> </p> <p>Search engine additional keywords: rs11264355, rs1052176, rs4620533, rs4971072, rs11264359, leprosy, TaqMan SNP Genotyping</p>
Data from: Mannose-binding lectin gene polymorphisms in the East Siberia and Russian Arctic populations
<p><b>Background:</b> Mannose-binding lectin (MBL) encoded by <i>MBL2</i> gene is a protein with the ability to form carbohydrate complexes with microbial wall promoting their subsequent elimination. Genetically determined levels of MBL can modify the risk and clinical characteristics of many infectious diseases. The frequency of <i>MBL2</i> genotypes exhibits significant population differences. The data on the distribution of <i>MBL2</i> genotypes among the aborigines of the Russian Arctic territories have not yet been published.</p> <p><b>Methods:</b> A total of 880 <a name="_Hlk41162363">specimens of </a><a name="_Hlk41162353">dried blood spots </a>of the newborns were genotyped. The newborns represented four populations: <a name="_Hlk28526418">Nenets, Dolgan-Nganasans</a>, Mixed <a name="_Hlk28526407">aboriginal population</a>, and Russians (<a name="_Hlk28526350">Caucasians</a>, Krasnoyarsk). Six polymorphisms of the <i>MBL2</i> gene were studied: rs11003125, rs7096206, rs7095891, rs5030737, rs1800450, and rs1800451.</p> <p><b>Results:</b> The frequency of the combined rare O allele (composed of the coding region variants rs5030737, rs1800450, and rs1800451) in the homozygous state was significantly higher in Russians: 10% vs 2% in Nenets and 1% in Dolgan-Nganosans (p<0.001 for Russians vs other populations). The frequency of the high-producing haplotype (HYPA) was 35.4% in the Russian newborns, in keeping with European populations (27-33%); 64% for Nenets and 56% for Dolgan-Nganasans, similar to the estimates obtained for Eskimos and North Amerinds (64-81%).</p> <p><b>Conclusion: </b>Our study results are in line with the hypothesis that human evolution has been moving in the direction of accumulation of the genotypes associated with low activity of the lectin complement activation pathway because of the prevalence of some intracellular infections such as tuberculosis, whereby low MBL activity may have a protective effect.</p>
Arsenic (+3 oxidation state) methyltransferase gene polymorphisms and expression on bladder cancer
<p><span><span><span><span>Inorganic arsenic (iAs) is a recognized environment-related factor for bladder cancer (BCa). </span><span><span>Arsenic (+3 oxidation state) methyltransferase (</span></span><i><span><span>AS3MT</span></span></i><span><span>)</span></span><i><span><span> gene</span></span></i><span> might influence BCa by regulating iAs metabolism. </span>The objectives of the present study were to systematically review eligible case-control studies about <i><span>AS3MT</span></i><i> </i>polymorphisms and BCa and to further compare the genotype distribution and allele distribution between BCa patients and controls by meta-analysis for humans. Besides, to clarify the effects of <i><span>AS3MT </span></i>expression on BCa clinical outcomes and survival time, we also conducted a series of analyses based on The Cancer Genome Atlas (TCGA) dataset. <span>Databases were systematically retrieved and we applied Stata software to perform meta-analysis. The registration of this study protocol is at PROSPERO and ID is CRD42019133947. Five articles</span> <span>were recruited and pooled results demonstrated that</span> <span>rs3740393 and rs11191438 polymorphisms were related to BCa risk in overall population (P<0.05)</span> <span>in the overall population.</span><span> In addition, GG and GC genotypes in rs3740393 and GG genotype in rs11191438 might be the susceptibility genotypes for BCa. </span><span>Results based on </span><span>168</span><span> BCa samples from TGCA indicated that patients with higher expression of </span><i><span><span>AS3MT</span></span></i><span> had poor </span><span>overall survival</span><span> time</span><span> and </span><i><span><span>AS3MT</span></span></i><span> expression is an independent indicator</span><span> for BCa </span><span>survival.</span> <span>This study identified that </span><i><span><span>AS3MT</span></span></i><span> polymorphisms could </span><span>affect</span><span> BCa risk and </span><i><span><span>AS3MT</span></span></i><span> expression was pivotal in prognosis of BCa.</span></span></span></span></p>
Association of APOE gene polymorphisms with primary open angle glaucoma in Brazilian patients
<p><strong>Background: </strong>Primary open-angle glaucoma (POAG) is a multifactorial disease that affects 65.5 million people worldwide. In addition to the genetic variants already established as indicators of greater risk for POAG, the apolipoprotein (<i>APOE</i>) gene has been studied in some populations, with controversial results. The aim of this study is to investigate the frequency of the genetic variants of <i>APOE</i> in the Brazilian population, and to evaluate the association between these polymorphisms and the risk of POAG.</p> <p><strong>Methods:</strong> <em>APOE</em> variants (rs429358; rs7412) were genotyped in 402 POAG patients and 401 controls. We evaluated the association between <em>APOE</em> genetic variants and the risk for POAG, as well as the correlation between the requirement of glaucoma surgery and the APOE polymorphisms. </p> <p><strong>Results: </strong>Among the three APOE gene isoforms, we found a low frequency of APOE alleles ε2 (7.34%) and ε4 (11.76%), but a high frequency of ε3 (80.88%) in our population. When compared to ε3ε3 reference genotype, ε2 allele-carriers (OR=1.516; p-value=0.04) and ε2ε3 genotype (OR=1.655; p-value=0.02) were associated with a greater risk for POAG. An additive genetic model confirmed the influence of the ε2 allele in the risk of POAG in this sample of the Brazilian population (OR=1.502; p-value=0.04). There was no significant association between the analyzed genotypes and the requirement or number of glaucoma surgeries (p>0.05). </p> <p><strong>Conclusion: </strong>Brazilian individuals carrying the APOEε2 allele may be at an increased risk for the development of POAG.</p>
Transcriptome-wide comparisons and virulence gene polymorphisms of host-associated genotypes of the cnidarian parasite Ceratonova shasta in salmonids
<p><i>Ceratonova shasta</i> is an important myxozoan pathogen affecting the health of salmonid fishes in the Pacific Northwest of North America. <i>C. shasta</i> exists as a complex of host-specific genotypes, some with low to moderate virulence, and one that causes a profound, lethal infection in susceptible hosts. High throughput sequencing methods are powerful tools for discovering the genetic basis of these host/virulence differences, but deep sequencing of myxozoans has been challenging due to extremely fast molecular evolution of this group, yielding strongly divergent sequences that are difficult to identify, and unavoidable host contamination. We designed and optimized different bioinformatic pipelines to address these challenges. We obtained a unique set of comprehensive, host-free myxozoan RNA-seq data from <i>C. shasta </i>genotypes of varying virulence from different salmonid hosts. Analyses of transcriptome-wide genetic distances and maximum likelihood multigene phylogenies elucidated the evolutionary relationship between lineages and demonstrated the limited resolution of the established Internal Transcribed Spacer marker for <i>C. shasta</i> genotype identification, as this marker fails to differentiate between biologically distinct genotype II lineages from coho salmon and rainbow trout. We further analyzed the datasets based on polymorphisms in two gene groups related to virulence: cell migration and proteolytic enzymes including their inhibitors. The developed SNP-calling pipeline identified polymorphisms between genotypes and demonstrated that variations in both motility and protease genes were associated with different levels of virulence of <i>C. shasta</i> in its salmonid hosts. The prospective use of proteolytic enzymes as promising candidates for targeted interventions against myxozoans in aquaculture is discussed. We developed host-free transcriptomes of a myxozoan model organism from strains that exhibited different degrees of virulence, as a unique source of data that will foster functional gene analyses and serve as a base for the development of potential therapeutics for efficient control of these parasites.</p>
Supporting Data for: Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae)
<p><strong>Background:</strong> Plant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. Oenothera harringtonii populations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+ plants) while others do not (linalool- plants). However, the genes associated with differential production of this floral volatile in Oenothera are unknown. We used RNA-Seq to broadly characterize differential gene expression involved in (R)-(-)-linalool biosynthesis. To identify genes that may be associated with the polymorphism for this trait, we used RNA-Seq to compare gene expression in six different Oenothera harringtonii tissues from each of three linalool+ and linalool- plants.</p> <p><strong>Results: </strong>Three clusters of differentially expressed genes were enriched for terpene synthase activity: two were characterized by tissue-specific upregulation and one by upregulation only in plants with flowers that produce (R)-(-)-linalool. A molecular phylogeny of all terpene synthases identified two putative (R)-(-)-linalool synthase transcripts in Oenothera harringtonii, a single allele of which is found exclusively in linalool+ plants.</p> <p><strong>Conclusions:</strong> By using a naturally occurring polymorphism and comparing different tissues, we were able to identify genes putatively involved in the biosynthesis of (R)-(-)-linalool. Expression of these genes in linalool- plants suggests a regulatory polymorphism, rather than a population-specific loss-of-function allele. Additional terpene biosynthesis-related genes that are up-regulated in plants that emit (R)-(-)-linalool may be associated with herbivore defense, suggesting a potential economy of scale between plant reproduction and defense.</p>
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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.