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Dataset results
56 results for “phenomics”
Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors
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Phenome-to-genome insights for evaluating root system architecture in field studies of maize
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Data from: Long-fuse evolution of carnivoran skeletal phenomes through the Cenozoic
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Data from: The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization
To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007, which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero to 60 g/L and to grow heterotrophically on >40 distinct carbon sources. Assembly and annotation of genomic reads yielded a 52.5 Mbp genome with 8153 functionally annotated genes. Comparison with other sequenced green algae revealed unique protein families involved in osmotic stress tolerance and saccharide metabolism that support phenomic studies. Our results reveal the robust and flexible biology utilized by a green alga to successfully inhabit a desert coastline.
Data from: A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey
The National Health and Nutrition Examination Survey (NHANES) is a population survey implemented by the Centers for Disease Control and Prevention (CDC) to monitor the health of the United States whose data is publicly available in hundreds of files. This Data Descriptor describes a single unified and universally accessible data file, merging across 255 separate files and stitching data across 4 surveys, encompassing 41,474 individuals and 1,191 variables. The variables consist of phenotype and environmental exposure information on each individual, specifically (1) demographic information, physical exam results (e.g., height, body mass index), laboratory results (e.g., cholesterol, glucose, and environmental exposures), and (4) questionnaire items. Second, the data descriptor describes a dictionary to enable analysts find variables by category and human-readable description. The datasets are available on DataDryad and a hands-on analytics tutorial is available on GitHub. Through a new big data platform, BD2K Patient Centered Information Commons (http://pic-sure.org), we provide a new way to browse the dataset via a web browser (https://nhanes.hms.harvard.edu) and provide application programming interface for programmatic access.
Comorbid-phenome prediction and phenotype risk scores enhance gene discovery for generalized anxiety disorder and posttraumatic stress disorder
<p>GWAS summary statistics. See ReadMe for column descriptions.</p>
Phenomics in Autoimmune and Inflammatory Diseases
ClinicalTrials.gov study NCT02466217. IPD Sharing: Not stated. Countries: 1. Publications: 2.
The Spine Phenome Project
ClinicalTrials.gov study NCT05776771. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Pulmonary Vascular Disease Phenomics Program PVDOMICS
ClinicalTrials.gov study NCT02980887. IPD Sharing: YES. Countries: 1. Publications: 7.
Impact of FMT on the Phenome in Patients With NAFLD and Fibrosis
ClinicalTrials.gov study NCT06024681. IPD Sharing: NO. Countries: 1. Publications: 1.
Phenomics and Genomics of Clinically Relevant Chronic Postsurgical Pain
ClinicalTrials.gov study NCT04798573. IPD Sharing: NO. Countries: 1. Publications: 101.
Data from: A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey
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Data from: The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization
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Supporting data for: Multi-modal deep learning improves grain yield prediction in wheat breeding by fusing genomics and phenomics
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Genomic and phenomic analysis of island ant community assembly
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PhenomeXcan: Mapping the genome to the phenome through the transcriptome
<p>Data generated as part of the PhenomeXcan project, which contains processed results for S-MultiXcan, S-PrediXcan, fastENLOC and the integration of S-MultiXcan results with ClinVar. Please, refer to the Github repository for documentation on these files and related source code (<a href="https://github.com/hakyimlab/phenomexcan">https://github.com/hakyimlab/phenomexcan</a>).</p> <p>This latest version of the dataset contains the fixed results for fastENLOC (with shrinkage of alpha1 values).</p> <p>bioRxiv preprint: https://doi.org/10.1101/833210</p>
Data from: microCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system
Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of phenotypic measures comprised of morphological and densitometric traits at a large number of sites within the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes associated with human brittle bone disease and thyroid stimulating hormone receptor hyperactivity. Finally, we develop allometric models and show their potential to aid in the discrimination of mutant phenotypes masked by alterations in growth. Our studies demonstrate virtues of deep phenotyping in a spatially distributed organ system. Analyzing phenotypic patterns may increase productivity in genetic screens, and facilitate the study of genetic variants associated with smaller effect sizes, such as those that underlie complex diseases.
Data from: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record
Background: The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new 'tip-dating' and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Results: Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group – approximated by the Coniophis node – is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia. Conclusions: Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction.
Using phenome-wide association studies and the SF-12 quality of life metric to identify profound consequences of adverse childhood experiences on adult mental and physical health in a northern Nevadan population
<p>In this research, we examine and identify the implications of Adverse Childhood Experiences (ACEs) on a range of health outcomes, with particular focus on a number of mental health disorders. Many previous studies observed that traumatic childhood events are linked to long-term adult diseases using the standard Adverse Childhood Experience Questionnaire. The study cohort was derived from the Healthy Nevada Project, a volunteer-based population health study in which each adult participant is invited to take a retrospective questionnaire that includes the Adverse Childhood Experience Questionnaire, the 12-item Short Form Survey measuring quality of life, and self-reported incidence of nine mental disorders. Using participants' cross-referenced electronic health records, a phenome-wide association analysis of 1,703 phenotypes and the incidence of ACEs examined links between traumatic events in childhood and adult disease. These analyses showed that many mental disorders were significantly associated with ACEs in a dose-response manner. Similarly, a dose-response between ACEs and obesity, chronic pain, migraine, and other physical phenotypes was identified. An examination of the prevalence of self-reported mental disorders and incidence of ACEs showed a positive relationship. Furthermore, participants with less adverse childhood events experienced a higher quality of life, both physically and mentally. The whole-phenotype approach confirms that ACEs are linked with many negative adult physical and mental health outcomes. With the nationwide prevalence of ACEs as high as 67%, these findings suggest a need for new public health resources: ACE-specific interventions and early childhood screenings.</p>
Data from: phenotools: an R package for visualizing and analyzing phenomic datasets
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ScienceDex guides
Understand access before you commit
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.