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Dataset results
115 results for “trait dataset”
Dataset to article "Distinct traits of structural and regulatory evolutional conser-vation of human genes with specific focus on major cancer mo-lecular pathways"
<p>Abstract: Evolution of protein coding genes has both structural and regulatory components. The first can be assessed by measuring the ratio of non-synonymous to synonymous nucleotide sub-stitutions. The second component can be measured as the normalized proportion of transposable elements that used as the regulatory elements. For the first time, we characterized in parallel the regulatory and structural evolutionary profiles for 10,890 human genes and 2,972 molecular pathways. We observed ~0.1 correlation between the structural and regulatory metrics at the gene level, which appeared much higher (~0.4) at the pathway level. We deposited the data in the publicly available database RetroSpect accessible at https://retrospect.oncobox.com. We also analyzed evolutionary dynamics of six cancer pathways of two major axes: Notch/WNT/Hedgehog and AKT/mTOR/EGFR. The Hedgehog pathway had both components slower, whereas the Akt pathway had clearly accelerated structural evolution. In particular, the major hub nodes Akt and beta-catenin showed both components strongly decreased, whereas two major regulators of Akt TCL1 and CTMP had outstandingly high evolutionary rates. We al-so noticed structural conservation of serine/threonine kinases and the genes related to guanosine metabolism in cancer signaling: GPCRs, G proteins, and small regulatory GTPases (Src, Rac, Ras); however, this was compensated by the accelerated regulatory evolution.</p>
Dataset for "Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen"
<p><strong>Supplementary Tables</strong></p> <p><strong>Supplementary Table S1: </strong>SRA accession list of RNAseq reads.</p> <p><strong>Supplementary Table S2:</strong> Genomic localization of TEs in gene elements and 10 kb windows upstream and downstream of the transcription start site (TSS) in the reference genome IPO323.</p> <p><strong>Supplementary Table S3:</strong> Genome-wide TE insertion polymorphism (TIPs) in the pathogen population. 0 represents TE absence and 1 represents TE presence.</p> <p><strong>Supplementary Table S4:</strong> Gene expression (log-transformed RPKM) values across the population.</p> <p><strong>Supplementary Table S5:</strong> Locus-specific transcript abundance at individual TE loci (FPKM) across individuals.</p> <p><strong>Supplementary Table S6:</strong> Percent of expressed copies within each TE family in the reference genome IPO323 and percent expressed TE copies in each TE family across the population.</p> <p><strong>Supplementary Table S7:</strong> Linkage disequilibrium of TIP in the genome and neighboring SNPs within the 600bp distance from the TE loci.</p> <p><strong>Supplementary Table S8:</strong> Genome-wide association mapping of the virulence-associated trait (PLACP: percent leaf area covered by pycnidia) and TE insertion polymorphisms in the genome.</p> <p><strong>Supplementary Table S9:</strong> TIPs in the genome significantly associated with metabolite peak intensity variation in the pathogen population (filtered by Bonferroni threshold).</p>
Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"
<p>This archive contains the code and datasets generated in the associated manuscript: "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits". We provide instructions, environments and scripts to reproduce the presented analyses.</p>
Dataset of Rapid adaptive responses of rosette-type macrophyte Vallisneria natans juveniles to varying water depths: The role of leaf trait plasticity
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Data from: Integrating three comprehensive datasets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies.
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Dataset from: Functional traits explain both seedling and adult plant spatial patterns in gypsum annual species
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Data from: Establishing macroecological trait datasets: digitalization, extrapolation, and validation of diet preferences in terrestrial mammals worldwide
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Dataset for: Heat wave-induced microbial thermal trait adaptation and its reversal in the Subarctic
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Dataset - A complex network of additive and epistatic quantitative trait loci underlies natural variation of Arabidopsis thaliana quantitative disease resistance to Ralstonia solanacearum under heat stress
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Populations of high-value predators reflect the traits of their prey dataset
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Dataset of distribution and trait of small mammals in Mt. Liangshan
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Thermal performance curves dataset based on <em>Littorina littorea</em> from different locations along a latitudinal gradient: Physiological and life history traits
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Data from: Incomplete datasets obscure associations between traits affecting dispersal ability and geographic range size of reef fishes in the Tropical Eastern Pacific
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Supplementary material 3 from: Neves MO, Cabral H, Pedrozo M, Ferreira VL, Moura M, Santana DJ (2020) Dataset of occurrences and ecological traits of amphibians from Upper Paraguay River Basin, central South America. Nature Conservation 41: 71-89. https://doi.org/10.3897/natureconservation.41.54265
References from the citations contained in Suppl. material 2
Supplementary material 2 from: Neves MO, Cabral H, Pedrozo M, Ferreira VL, Moura M, Santana DJ (2020) Dataset of occurrences and ecological traits of amphibians from Upper Paraguay River Basin, central South America. Nature Conservation 41: 71-89. https://doi.org/10.3897/natureconservation.41.54265
Table S2
Supplementary material 1 from: Neves MO, Cabral H, Pedrozo M, Ferreira VL, Moura M, Santana DJ (2020) Dataset of occurrences and ecological traits of amphibians from Upper Paraguay River Basin, central South America. Nature Conservation 41: 71-89. https://doi.org/10.3897/natureconservation.41.54265
Table S1
Dataset: Species presence, trait and philogeny database. Data from: Shift from trait convergence to divergence along old field succession. Journal of Vegetation Science.
<p>This dataset was use in the manuscript "Shift from trait convergence to divergence along old field succession" publish at Journal of Vegetation Science. It contains the data of species presence at three different plots and species trait values (SLA, LDMC, height, seed weight and Phylogeny). We show that at the initial stage of succession, there is a scale-invariant pattern of trait convergence. On the contrary, in the late and intermediate stages of succession we observed that trait divergence became frequent at smaller grains and extents. The trend along the chronosequence is consistent with the theoretical hypothesis that predicts a shift from convergence to divergence along succession.</p>
Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas with data for 196 markers
<p>Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas with data for 196 markers. This file is associated with a dissertation on lodging resistance called Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas.</p>
MarNemaFunDiv - a first comprehensive dataset of functional traits for marine nematodes
<p><span>Matrix of nematode genera associated with 16 functional traits</span><strong><span> </span></strong></p>
Fig. 2 in A species-level trait dataset of bats in Europe and beyond
Fig. 2 Trait by species matrix illustrating the EuroBaTrait 1.0 dataset completeness.
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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)
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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.