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306 results for “gene mapping”
Supplement 1: Full list of ICD10 codes and number of gene-disease links (tab-separated-value file); Supplement 2: Mapping (tab-separated-value file)
<p>Supplements to BioMedBridges deliverable 10.2 A prototype linking ICD10/SNOMED CT concepts to Ensembl gene identifiers:</p> <p><strong>Supplement 1</strong>: Full list of ICD10 codes and number of gene-disease links: table_icd10_gene_count_descr.tsv</p> <p><strong>Supplement 2</strong>: Mapping of disease terms: <em>ICD10_to_doid.tsv</em></p>
SeMRA Gene Mappings Database
<p>Analyze the landscape of gene nomenclature resources, species-agnostic. See instructions for reproduction and usage in the attached README.md.</p>
Interactive map of distribution of gene fragments indicative of cyanotoxin biosynthesis and cyanotoxins in the European Alps
<p><span>Distribution of cyanotoxins and cyanotoxin biosynthesis genes in Alpine region determined by LC-MS/MS and (q)PCR. Cyanotoxins and cyanotoxin genes are mapped on separate layers, and two basemaps are available (simple and relief). Results can be filtered by location, sample type, water body type, cyanotoxins and cyanotoxin genes. Note that cyanotoxin analyses were not performed on all sampling points.</span></p>
Mapped read data and files and scripts from: Vicariance followed by secondary gene flow in a young gazelle species complex
<p>Grant's gazelles have recently been proposed to be a species complex comprising three highly divergent mtDNA lineages (<em>Nanger granti</em>, <em>N. notata</em> and <em>N. petersii</em>). The three lineages have non-overlapping distributions in East Africa, but without any obvious geographical divisions, making them an interesting model for studying the early stage evolutionary dynamics of allopatric speciation in detail. Here we use genomic data obtained by restriction site-associated (RAD) sequencing of 106 gazelle individuals to shed light on the evolutionary processes underlying Grant's gazelle divergence, to characterize their genetic structure and to assess the presence of gene flow between the main lineages in the species complex. We date the species divergence to 134,000 years ago, which is recent in evolutionary terms. We find population subdivision within <em>N. granti</em>, which coincides with the previously suggested two subspecies, <em>N.g. granti</em> and <em>N.g. robertsii</em>. Moreover, these two lineages seem to have hybridized in Masai Mara. Perhaps more surprisingly given their extreme genetic differentiation, <em>N. granti</em> and <em>N. petersii</em> also show signs of prolonged admixture in Mkomazi, which we identified as a hybrid population most likely founded by allopatric lineages coming into secondary contact. Despite the admixed composition of this population, elevated X-chromosomal differentiation suggests that selection may be shaping the outcome of hybridization in this population. Our results therefore provide detailed insights into the processes of allopatric speciation and secondary contact in a recently radiated species complex.</p>
Derby database for mapping secondary to primary HGNC gene symbols
<p>The datasets (hgnc_complete_set and withdrawn) used to create this ID mapping database were downloaded from HGNC (<em>HUGO Gene Nomenclature Committee at the European Bioinformatics Institute, </em>website URL: https://www.genenames.org/) on 09/05/2022. </p> <p>This database was used for the <a href="https://github.com/tabbassidaloii/BridgeDbDemoBioSB2022">BridgeDb demo at BioSB 2022</a> conference.</p> <p>The scripts used to create this database based on HGNC: https://github.com/tabbassidaloii/create-bridgedb-secondary2primary</p> <p>This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).</p>
Identification and fine mapping of gummy stem blight resistance gene Gsb-7(t) in Melon
<p>Gummy stem blight (GSB), caused by the <em>Didymella bryoniae</em> (Auersw.) Rehm, is a devastating fungal disease of melon worldwide. Breeding GSB-resistant cultivars with host resistance genes is considered to be the most economic and effective strategy to control this disease. In this study, 260 melon germplasm resources were screened for resistance to GSB, and an inbred line H55R exhibited immunity to GSB was identified. To further understand the resistance mechanism of H55R against GSB, an F<sub>2</sub> population was obtained from a cross between the GSB-susceptible line A15 and H55R, and genetic analysis indicated that the resistance in H55R was controlled by a single dominant gene, tentatively named <em>Gsb-7(</em><em>t</em><em>)</em>. The <em>Gsb-7(</em><em>t</em><em>)</em> gene was finally delimited to a 140 kb interval on chromosome 7 using bulked-segregant analysis and chromosome walking strategies. Ten putative genes were annotated in this region that contains a wall-associated receptor kinase (WAK) gene <em>MELO3C</em><em>010403</em>. The <em>MELO3C</em><em>010403</em> gene contains two alternative transcripts, T1 and T2, with five and seven non-synonymous mutation sites, respectively. Gene expression analysis showed that expression of T1 but not the T2 was significantly induced by the <em>D</em><em>.</em><em> bryoniae</em> at 24 hours post-inoculation (hpi), indicating that the T2 transcript of <em>MELO3C</em><em>010403</em> was the most likely candidate gene of <em>Gsb-7(t)</em><em>.</em> Our results offer new genetic resources and will be helpful for the development of GSB-resistant melon cultivars in the future.</p>
Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases.
<p>Many disease-associated variants are thought to be regulatory but are not present in existing catalogues of expression quantitative trait loci (eQTL). We hypothesise that these variants may regulate expression in specific biological contexts, such as stimulated immune cells. Here, we used human iPSC-derived macrophages to map eQTLs across 24 cellular conditions. We found that 76% of eQTLs detected in at least one stimulated condition were also found in naive cells. The percentage of response eQTLs (reQTLs) varied widely across conditions (3.7% - 28.4%), with reQTLs specific to a single condition being rare (1.11%). Despite their relative rarity, reQTLs were overrepresented (p=0.05, Fisher's exact test) among disease-colocalizing eQTLs. We nominated an additional 21.7% of disease effector genes at GWAS loci via colocalization of reQTLs, with 38.6% of these not found in the Genotype–Tissue Expression (GTEx) catalogue. Our study highlights the diversity of genetic effects on expression and demonstrates how condition-specific regulatory variation can enhance our understanding of common disease risk alleles.</p>
Extension of Partial Gene Transcripts by Iterative Mapping of RNA-Seq Raw Reads
<p>Trinity assembled transcriptome of <em>Drosophila melanogaster</em> and <em>Osmia </em><em>bicornis</em></p>
Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content
<p>130 Lotus japonicus accessions were used. The names and accession numbers are<br> listed in S6 Table. Seeds were scarified with sandpaper and then sterilized 14 minutes in 0.05%<br> sodium hypochlorite. Subsequently, seeds were rinsed and washed 5 times in sterile distilled<br> water. For the germination, seeds were positioned in imbibed filter paper, in sterile Petri dishes,<br> and wrapped in aluminium foil. After 3 days at 21°C, young seedling were transferred to square<br> plates (12 x 12 cm) containing growth medium. Both media used in this<br> study were based on Long-Ashton solution (with two levels of phosphate concentration -20 or<br> 750 μM, LP or HP, respectively) with 0.8% MES buffer (Duchefa Biochemie,<br> Haarlem, The Netherlands), 0.8% agarose (to minimize phosphate contamination), and adjusted<br> to pH 5.7 with 1M KOH. After adding the medium, plates were dried, closed, overnight in a<br> sterile laminar flow hood. Two accessions, with four replicates per each accession, were placed<br> on each plate. Each plate was replicated, with mirrored position of each accession to minimize<br> any positional growth effects. Plates were placed vertically, and plants grown under long-day<br> conditions (21°C, 16 h light/8 h dark cycle) with white light bulbs emitting 50 μmol/m 2 /s and<br> roots were exposed to light. Every day at the same time, the racks were transported to the image<br> acquisition room where images of each plate were acquired with eight Epson V600 CCD flatbed<br> color image scanners (Seiko Epson) and then immediately returned to the growth chamber.</p>
Mapped read data and files and scripts from: Vicariance followed by secondary gene flow in a young gazelle species complex
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Next-generation sequencing of newborn screening genes: The accuracy of short-read mapping
<p>We examine the effect of high homology genomic regions on the mapping of genes related to newborn screening while taking different read lengths and patient's ethnic background into consideration.</p>
Mouse and Human Co-expression maps and supplementary material for: "A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels"
<p>Co-expression maps of the human and mouse species derived from microarray data for the first release of the GeneFriend tool.</p> <p>The two co-expression maps have been compared in order to discern similarities and differences between the two species. The results have been described in the manuscript titled: "A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels".</p> <p>The supplementary material of the manuscript have also been included in this repository.</p> <p> </p>
Fine-mapping gene-based associations via knockoff analysis of biobank-scale data with applications to UK Biobank
<p>The results of BIGKnock analyses of manuscript ''Fine-mapping gene-based associations via knockoff analysis of biobank-scale data with applications to UK Biobank''</p>
Supplementary material 1 from: Scacchetti P, Pansonato-Alves J, Utsunomia R, Oliveira C, Foresti F (2011) Karyotypic diversity in four species of the genus Gymnotus Linnaeus, 1758 (Teleostei, Gymnotiformes, Gymnotidae): physical mapping of ribosomal genes and telomeric sequences. Comparative Cytogenetics 5(3): 223-235. https://doi.org/10.3897/compcytogen.v5i3.1375
Nexus file of aligned COI and COII nucleotide sequences.
Gene Enrichment Map Data from gProfiler Analysis - Selected MPK Interactions of Arabidopsis thaliana
<p>Gene enrichment analysis results for the selected predicted MPK interactions are included in the supplementary materials.</p>
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes
<p>ATAC-seq peaks are in narrowPeak format. RNA-seq results are organized according to cell type. The normalized RPKM is reported for each gene in GENCODE 19. All data was mapped to hg19.</p>
datset of "Networks and genes modulated by posterior hypothalamic stimulation in patients with aggressive behaviours: Analysis of probabilistic mapping, normative connectomics, and atlas-derived transcriptomics of the largest international multi-centre dataset"
<p>This dataset accompanies the manuscript:<br> "Networks and genes modulated by posterior hypothalamic stimulation in patients with aggressive behaviours: Analysis of probabilistic mapping, normative connectomics, and atlas-derived transcriptomics of the largest international multi-centre dataset."<br> DOI: (https://doi.org/10.1101/2022.10.29.22281666)</p> <p>by</p> <p>Flavia Venetucci Gouveia1,2,3*†,Jürgen Germann4,5†, Gavin JB Elias4,5, Alexandre Boutet4,6, Aaron Loh4,5, Adriana Lucia Lopez Rios7,8, Cristina V Torres Diaz9, William Omar Contreras Lopez10,11, Raquel CR Martinez3,12, Erich T Fonoff13, Juan C Benedetti-Isaac14, Peter Giacobbe 2,15,16, Pablo M Arango Pava17, Han Yan5,18, George M Ibrahim5, 18,19,20, Nir Lipsman2,5,15, Andres M Lozano4,5, Clement Hamani2,5,15*</p> <p>1. Neuroscience and Mental Health, Hospital for Sick Children Research Institute; Toronto, Canada <br> 2. Sunnybrook Research Institute; Toronto, Canada<br> 3. Division of Neuroscience, Sírio-Libanês Hospital; São Paulo, Brazil<br> 4. Division of Neurosurgery, Department of Surgery, University Health Network, Toronto, Canada<br> 5. Division of Neurosurgery, Department of Surgery, University of Toronto; Toronto, Canada<br> 6. Joint Department of Medical Imaging, University of Toronto; Toronto, Canada<br> 7. Department of Functional and Stereotactic Neurosurgery, University Hospital San Vicente Fundación,<br> Medellín, Colombia<br> 8. Department of Functional and Stereotactic Neurosurgery, San Vicente Fundación, Rionegro, Colombia<br> 9. Department of Neurosurgery, University Hospital La Princesa; Madrid, Spain<br> 10. Nemod Research Group, Universidad Autónoma de Bucaramanga; Bucaramanga, Colombia<br> 11. Division of Functional Neurosurgery, Department of Neurosurgery, FOSCAL Clinic; Bucaramanga,<br> Colombia<br> 12. LIM 23, Institute of Psychiatry, School of Medicine, University of São Paulo; São Paulo, Brazil<br> 13. Department of Neurology, Integrated Clinic of Neuroscience, School of Medicine, University of São Paulo;<br> São Paulo, Brazil.<br> 14. Stereotactic and Functional Neurosurgery Division of the International Misericordia Clinic; Barranquilla,<br> Colombia<br> 15. Harquail Centre for Neuromodulation, Sunnybrook Health Sciences Centre; Toronto, Canada<br> 16. Department of Psychiatry, University of Toronto; Toronto, Canada<br> 17. Servicio de Neuocirugia Funcional y Esterotaxia, Clinica Comuneros Bucaramanga, Clinica Desa y Clinica<br> Dime Neurocardiovascular de Cali; Clinica Nueva del Lago, Bogota, Colombia.<br> 18. Division of Neurosurgery, The Hospital for Sick Children; Toronto, Canada<br> 19. Institute of Biomedical Engineering, University of Toronto; Toronto, Canada<br> 20. Institute of Medical Science, University of Toronto; Toronto, Canada<br> † Flavia Venetucci Gouveia and Jürgen Germann contributed equally to this work and share first authorship.</p> <p>* Corresponding Author: Dr. Flavia Venetucci Gouveia. Neuroscience and Mental Health, Hospital for Sick Children Research Institute. 686, Bay Street, Toronto, ON, M5G 0A4, Canada. flavia.venetuccigouveia@sickkids.ca<br> * Corresponding Author: Dr. Clement Hamani. Sunnybrook Research Institute. 2075 Bayview Ave, S126. Toronto, ON, M4N3M5, Canada. clement.hamani@sunnybrook.ca</p> <p>It contains a zip folder ("estimated_binary_Volume_of_Tissue_Activated.zip") with one file (in nii.gz format) per patient estimating the Volume of Activated Tissue for that patient (the estimated 'reach' of the active DBS stimulation) and a demographics file.<br> The case numbers are identical to Table 1 in the manuscript.</p>
Gene annotations and optical maps of the Aegilops tauschii acc. AL8/78 assembly Aet v6.0
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Supplemental material for: Genome-wide association study and fine-mapping using imputed sequences to prioritize candidate genes for 30 complex traits in 50,309 Holstein bulls
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Construction of genetic linkage map based on SNP markers, QTL mapping and detection of candidate genes of growth-related traits in Pacific abalone using genotyping-by-sequencing
<p><a name="_Hlk72585736"><span>Pacific abalone (<i>Haliotis discus hannai</i>) is a commercially important high valued molluscan species. Its wild population has decreased in recent years. Pacific abalone is widely cultured in Korea. Traditional breeding programs have been implemented for hatchery production of abalone seeds. To obtain more genetic information for the molecular breeding program, a high-density linkage map and quantitative trait locus (QTL) for three growth-related traits was constructed for Pacific abalone. F1 cross population with two parents were sampled to construct the linkage map using genotyping by sequencing (GBS). A total of 664,630,534 clean reads and 56,686 SNPs were generated. In sum, 3,345 segregating SNPs were used to construct a consensus linkage map. The map spanned 1,747.023 cM with 18 linkage groups and an average interval of 0.55 cM. QTL analysis revealed two significant QTL in LG10 on the consensus linkage map in each growth-related trait. Both the QTLs are located in the telomere region of the chromosome. Moreover, four potential candidate genes for growth-related traits were identified in the QTL region. Expression analysis revealed that identified genes are involved in growth regulation of abalone. The newly constructed genetic linkage map, growth-related QTLs and potential candidate genes identified in the present study can be used as valuable genetic resources and will be useful for marker-assisted selection (MAS) of Pacific abalone in molecular breeding program.</span></a></p>
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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.