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470 results for “Analysis of Variation”
Supplementary Figure 1 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Supplementary Fig. 1:</strong> <strong>Definition of 3D anatomical landmarks.</strong> <strong>a</strong>, Position of 3D anatomical landmarks on the whole brain of the lizard <em>Agama agama</em> in dorsal (top left panel), ventral (top right), and lateral (bottom) views. <strong>b</strong>, Position of 3D anatomical landmarks on the isolated cerebellum of <em>Agama agama</em> in pial surface (left panel) and lateral (right) views. <strong>c</strong>, Schematic representation of the whole-brain of <em>Agama agama</em> highlighting the five major regions used for landmarking. <strong>d</strong>, Table showing the definition of 3D anatomical landmarks with associated number (see <strong>a</strong>, <strong>b</strong>) and brain region (see <strong>c</strong>).</p>
Data from: Individual differences in behaviour explain variation in survival: a meta-analysis
<p>Research focusing on among-individual differences in behaviour ("animal personality") has been blooming for over a decade. One of the central theories explaining the maintenance of such behavioural variation posits that individuals expressing greater "risky" behaviours should suffer higher mortality. Here, for the first time, we synthesize the existing empirical evidence for this key prediction. Our results did not support this prediction as there was no directional relationship between riskier behaviour and greater mortality; however there was a significant absolute relationship between behaviour and survival. In total, behaviour explained a significant, but small, portion (5.8%) of the variance in survival. We also found that risky (versus "shy") behavioural types live significantly longer in the wild, but not in the laboratory. This suggests that individuals expressing risky behaviours might be of overall higher quality but the lack of predation pressure and resource restrictions mask this effect in laboratory environments. Our work implies that individual differences in behaviour explain important differences in survival but not in the direction predicted by theory. Importantly, this suggests that the models predicting survival trade-offs may need revision and/or empiricists may need to reconsider their proxies of risky behaviours when testing such theory.</p>
Data from: Novel sources of (co)variation in nestling begging behavior and hunger at different biological levels of analysis
<p>Biological hypotheses predicting patterns of offspring begging typically concern the covariance with hunger and/or development at specific hierarchical levels. For example, hunger drives within-individual patterns of begging, but begging also drives food intake among individuals within broods, and begging and food intake can covary positively or negatively among genotypes or broods. Testing biological phenomena that occur at multiple levels therefore requires the partitioning of covariance between traits of interest to ensure that each level-specific relationship is appropriately assessed. We performed a partial cross-fostering study on a wild population of great tits (Parus major), then used multivariate mixed-models to partition variation and covariation in nestling begging effort and two metrics of nestling hunger within versus among individual nestlings and broods. At the within-individual level, we found that nestlings begged more intensely when hungrier (positive correlation between begging and hunger). However, among individuals, nestlings that were fed more frequently also begged more intensely on average (negative correlation between begging and hunger). Variation in nestling mass did not give rise to the negative correlation between begging and hunger among nestlings, but we did find that lighter nestlings begged more intensely than their heavier biological siblings, suggesting that this effect may be driven by a genetic component linked to offspring size. Our study illustrates how patterns of covariance can differ across biological levels of analysis and addresses biological mechanisms that could produce these previously obscured patterns.</p>
Latitudinal gradient in the intensity of biotic interactions in terrestrial ecosystems: Sources of variation and differences from the diversity gradient revealed by meta-analysis
<p>The Latitudinal Biotic Interaction Hypothesis (LBIH) states that the intensity of biotic interactions increases from high to low latitudes. This hypothesis, which may partly explain latitudinal gradients in biodiversity, remains hotly debated, largely due to variable outcomes of published studies. We used meta-analysis to identify the scope of the LBIH in terrestrial ecosystems. For this purpose, we explored the sources of variation in the strength of latitudinal changes in herbivory, carnivory, and parasitism (119 publications) and compared these gradients with gradients in the diversity of the respective groups of animals (102 publications). Overall, both herbivory and carnivory decreased towards the poles, while parasitism increased. The latitudinal gradient in herbivory and carnivory was threefold stronger above 50–60º than at lower latitudes and was significant due to interactions involving ectothermic consumers, studies using standardized prey (i.e. prey lacking local anti-predator adaptations) and studies aimed at testing LBIH. The poleward decrease in biodiversity did not differ between ectothermic and endothermic animals or among climate zones and was four-fold stronger than decrease in herbivory and carnivory. The discovered differences between the gradients in biotic interactions and biodiversity suggest that these two global macroecological patterns are likely shaped by different factors.</p>
Data from: Explaining global variation in the latitudinal diversity gradient: meta-analysis confirms known patterns and uncovers new ones
Aim: The pattern of increasing biological diversity from high latitudes to the equator [latitudinal diversity gradient (LDG)] has been recognized for > 200 years. Empirical studies have documented this pattern across many different organisms and locations. Our goal was to quantify the evidence for the global LDG and the associated spatial, taxonomic and environmental factors. We performed a meta-analysis on a large number of individual LDGs that have been published in the 14 years since Hillebrand's ground-breaking meta-analysis of the LDG, using meta-analysis and meta-regression approaches largely new to the fields of ecology and biogeography. Location: Global. Time period: January 2003–September 2015. Major taxa studied: Bacteria, protists, plants, fungi and animals. Methods: We synthesized the outcomes of 389 individual cases of LDGs from 199 papers published since 2003, using hierarchical mixed-effects meta-analysis and multiple meta-regression. Additionally, we re-analysed Hillebrand's original dataset using modern methods. Results: We confirmed the generality of the LDG, but found the pattern to be weaker than was found in Hillebrand's study. We identified previously unreported variation in LDG strength and slope across longitude, with evidence that the LDG is strongest in the Western Hemisphere. Locational characteristics, such as habitat and latitude range, contributed significantly to LDG strength, whereas organismal characteristics, including taxonomic group and trophic level, did not. Modern meta-analytical models that incorporate hierarchical structure led to more conservative and sometimes contrasting effect size estimates relative to Hillebrand's initial analysis, whereas meta-regression revealed underlying patterns in Hillebrand's dataset that were not apparent with a traditional analysis. Main conclusions: We present evidence of global latitudinal, longitudinal and habitat-based patterns in the LDG, which are apparent across both marine and terrestrial realms and over a broad taxonomic range of organisms, from bacteria to plants and vertebrates.
Data from: Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees
<p>The <em>Asian honeybee</em>, <em>Apis cerana</em>, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories, and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger-scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group of<em> A. cerana</em>. Integrating this with 525 resequencing datasets, we constructed the first pan-genome of <em>A. cerana</em>, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions, however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel <em>A. cerana</em> ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of <em>A. cerana</em> by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of <em>A. cerana</em>.</p>
Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
<p>Summary statistics for "Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation" </p><p>Files are organized in the following directory structure:</p><p><strong>G2G/</strong> - Summary statistics of G2G associations (SNPs, HLA, and gene-level analysis). </p><p><strong>HLA/ </strong>- Peptide binding prediction results</p><p><strong>preS1_haplotypes/ - </strong>Resolved intra-host haplotypes of the preS1 binding region. </p><p><strong>DnDs/</strong> - Calculation of intra-host positive selection, within the preS1 binding region. </p><p> </p>
Figure 35 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 35. Paratype, Bemisia rosae Danzig, 25 km s/o Orapa?, 10-VI-78, ex: rose, E. Danzig, coll.
Data from: the great tit HapMap project: a continental-scale analysis of genomic variation in a songbird
<p>A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (<em>Parus major</em>) HapMap project. We screened <em>ca</em> 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographic range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugiam, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear "islands of differentiation", even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (F<sub>ST</sub>), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.</p>
Dataset for Spatial Variations in the Osteocyte Lacuno-canalicular Network Density and Analysis of the Connectomic Parameters
<p>This dataset is a representative case of the loaded tibia of a C57BL/6 mouse at the mid-shaft. The image pixel size is 0.303 by 0.303 um, and the z-depth is 0.296 um. </p> <p>To generate, analyse, and quantify the osteocyte lacuno-canalicular network, it requires 'Tool for Image and Network Analysis (TINA)' which can be acqruied from https://gitlab.mpikg.mpg.de/rummler/TINA.git. A demonstration has been included on using TINA.</p>
An unsupervised deep learning framework with variational autoencoders for genome-wide DNA methylation analysis and biologic feature extraction applied to breast cancer
<p>Supplemental data for the paper titled "An unsupervised deep learning framework with variational autoencoders for genome-wide DNA methylation analysis and biologic feature extraction applied to breast cancer"</p>
Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew
<p>Data produced for the comparison of six <em>Peronospora effusa</em> isolates. For each isolate, we provide the genome assemblies, gene and repeat annotation, effector clustering, and gene variation. Additionally, we provide the repeat library that was used to annotate the transposable elements for each isolate and the pangenome graph.</p> <p>DOI: https://doi.org/10.1101/2024.05.30.596583 </p>
EGP Mitochondrial Genome Analysis on Gambian Genome Variation Project Whole-Genome Sequencing Data
<p><strong>Summary: </strong>This dataset consists of running EGP version 1.3 on whole-genome sequencing data from the GGVP. The link to EGP is here https://github.com/tycheleturner/ElGenomaPequeno.</p> <p><strong>Author: </strong>Tychele N. Turner, Ph.D.</p> <p><strong>Short Writeup: EGP version 1.3 on Gambian Genome Variation Project</strong>: Short-read WGS CRAM files were downloaded from the EMBL-EBI Public Data Globus Endpoint from the <code>/1000g/ftp/data_collections</code> directory. Post-download, the data was run through EGP version 1.3. The results are shown below:</p> <div> <table> <tbody> <tr> <td>Public Dataset</td> <td>EGP Result File Type</td> <td>MD5</td> </tr> <tr> <td>Gambian Genome Variation Project</td> <td>Mitochondrial Genome Fasta Files for MEGA</td> <td>d21e1e91e8b4c00627171fae79a1f54d</td> </tr> <tr> <td>Gambian Genome Variation Project</td> <td>Mitochondrial Genome MitoMaster Result File</td> <td>b359d1068d4f84f7746d1ebde82df29a</td> </tr> <tr> <td>Gambian Genome Variation Project</td> <td>Mitochondrial Genome Variant Tables</td> <td>ee2b93aa93d2177d92ec0f8f308b43ed</td> </tr> <tr> <td>Gambian Genome Variation Project</td> <td>Mitochondrial Genome Copy Number</td> <td>fda509ba1d2bf33fd2d6b77b92e76c03</td> </tr> </tbody> </table> <p>Please note: I have found that with Zenodo you must use "Download All" for the copy number table to properly open.</p> </div>
Supplementary Table S1. Combined analysis of variance containing the degrees of freedom (DF), mean squares (MS), P value (P val.), mean, coefficient of experimental variation (CEV%) and selective accuracy (SA) for the traits of luminosity (L*), chromaticity a* (a*), chromaticity b* (b*), grain length (length, mm), grain width (width, mm), grain thickness (thickness, mm), mass of 100 grains (Mass, g), normal grains (Ng, %), water absorption (absorption, %), cooking time (Ct, min:s), and concentrations of potassium (K, g kg-1 dry matter - DM), phosphorus (P, g kg-1 DM), calcium (Ca, g kg-1 DM), magnesium (Mg, g kg-1 DM), iron (Fe, mg kg-1 DM), zinc (Zn, mg kg-1 DM), and copper (Cu, mg kg-1 DM) obtained in 25 common bean cultivars evaluated in four experiments carried out from 2019 to 2021
<p><strong><span>Table S1.</span></strong><span> Combined analysis of variance.</span></p> <p><strong><span>Indirect selection for multiple technological and nutritional traits in common bean cultivars under different degrees of multicollinearity</span></strong></p> <p><strong><span>Bragantia, 2024.</span></strong></p>
Genome-wide association analysis identifies naturally segregating genetic variation associated with the rapid evolution of diapause in Aedes albopictus, an invasive vector mosquito.
<p>The raw data for genotype calls, the output files from the genotype calls, the code to replicate the analysis, and the output of the analysis.</p>
Supplemental material to 'A variational rigid-block modelling approach to nonlinear elastic and kinematic analysis of failure mechanisms in historic masonry structures subjected to lateral actions'
<p>This repository contains the data necessary to reproduce the content of the article:</p> <blockquote> <p>A variational rigid-block modelling approach to nonlinear elastic and kinematic analysis of failure mechanisms in historic masonry structures subjected to lateral actions (2021). Earthquake Engineering & Structural Dynamics, 1–23. <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/eqe.3512">https://doi.org/10.1002/eqe.3512</a></p> </blockquote> <p>The file <strong>01_Dataset.zip</strong> contains the dataset. The companion document <strong>00_Dataset_description.pdf </strong>describes the content of the dataset, guiding the analyst to its use in order to (i) reproduce the article's results and (ii) compare the article's results to new results brought by the analyst, e.g. by comparison with other numerical models.</p> <p>Version history</p> <p>v2: updated references in 00_dataset description.pdf </p>
Gramtools enables multiscale variation analysis with genome graphs
<p>Singularity container and data files supporting the article.</p> <p>Instructions to use these data are at: https://github.com/iqbal-lab-org/paper_gramtools_nesting </p>
Construction of an evapotranspiration model and analysis of spatiotemporal variation in Xilin River Basin, China
<p>The publication for this dataset will be published in plos one journal, and can be accessed here:https://doi.org/10.1371/journal.pone.0256981. Please cite this when using the dataset.</p>
Data, sample sizes, and R code for analysis of: Variation in mutation (co)variances
<p>Because of pleiotropy, mutations affect the expression and inheritance of multiple traits and, together with selection, are expected to shape standing genetic covariances between traits and eventual phenotypic divergence between populations. It is therefore important to find if the M matrix, describing mutational variances of each trait and covariances between traits, varies between genotypes. We here estimate the M matrix for six locomotion behavior traits in lines of two genotypes of the nematode <em>Caenorhabditis elegans </em>that accumulated mutations in a nearly-neutral manner for 250 generations. We find significant mutational variance along at least one phenotypic dimension of the M matrices, but neither their size nor their orientation had detectable differences between genotypes. The number of generations of mutation accumulation, or the number of MA lines measured, was likely insufficient to sample enough mutations and detect potentially small differences between the two M matrices. We then tested if the M matrices were similar to one G matrix describing the standing genetic (co)variances of a population derived by the hybridization of several genotypes, including the two measured for M, and domesticated to a lab-defined environment for 140 generations. We found that the M and G were different because the genetic covariances caused by mutational pleiotropy in the two genotypes are smaller than those caused by linkage disequilibrium in the lab population. We further show that M matrices differed in their alignment with the lab population G matrix. If generalized to other founder genotypes of the lab population, these observations indicate that selection does not shape the evolution of the M matrix for locomotion behavior in the short-term of a few tens to hundreds of generations and suggests that the hybridization of <em>C. elegans </em>genotypes allows selection on new phenotypic dimensions of locomotion behavior.</p>
Data Set "Efficient automatic construction of atom-economical QM regions with point-charge variation analysis"
<p>This data set accompanies the publication "Efficient automatic construction of atom-economical QM regions with point-charge variation analysis" by Felix Brandt and Christoph R. Jacob (TU Braunschweig, Germany) </p> <p>It contains the following files:</p> <p>- PDB files of the reactant and product starting structure</p> <p>- modified AMBER95 force field file</p> <p>- AMS fragment files for the ligands and ions</p> <p>- AMS input files for all geometry optimizations and single point calculations</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.