Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
63
datasets available to search
ShareScore release 0.9.0
Dataset results
63 results for “Pathway prediction”
Deep learning models predicting gene functions and pathways using public DRKG knowledge graph and graph neural network
<p>The attached dataset contains pretrained link prediction models, as described in our paper 'Morphological Map of Under- and Over-Expression of Genes in Human Cells'.</p>
Supplementary datasets for "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds"
<p>Supplementary datasets accompanying the manuscript "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds" published in the Metabolic Engineering Journal (<a href="https://doi.org/10.1016/j.ymben.2022.03.013">https://doi.org/10.1016/j.ymben.2022.03.013). </a>In line with the standards of open science, the ARBRE toolbox is freely available to the scientific community on gitHub (<a href="https://github.com/EPFL-LCSB/ARBRE">https://github.com/EPFL-LCSB/ARBRE</a>) and we also provide the web-version at <a href="http://lcsb-databases.epfl.ch/arbre/">http://lcsb-databases.epfl.ch/arbre/</a></p> <p>ARBRE: Aromatic compounds RetroBiosynthesis Repository and Explorer is a new computational resource consisting of a comprehensive biochemical reaction network centered around aromatic amino acid biosynthesis and a computational toolbox for navigating this network. ARBRE encompasses over 33′000 known and 390′000 novel reactions predicted with generalized enzymatic reactions rules and over 74′000 compounds, of which 19′000 are known to biochemical databases and 55′000 only to PubChem. Over 1′000 molecules that were solely part of the PubChem database before and were previously impossible to integrate into a biochemical network are included in the ARBRE reaction network by assigning enzymatic reactions. ARBRE can be applied for pathway search, enzyme annotation, pathway ranking, visualization, and network expansion around known biochemical pathways and products of lignin degradation to predict valuable compound derivations.</p> <p>Supplementary files are organized as follows:</p> <p>- 1-s2.0-S1096717622000490-mmc4.docx contains Supplementary Figures 1-4 and Tables 1, 2, and 4.</p> <p>- 1-s2.0-S1096717622000490-mmc2.xlsx contains Supplementary Table 3.</p> <p>- 1-s2.0-S1096717622000490-mmc1.xlsx contains Supplementary Table 5</p> <p>- 1-s2.0-S1096717622000490-mmc3.xlsx contains Supplementary Table 6</p> <p> </p> <p> </p> <p> </p> <p> </p>
Galaxy Training Data for "Designing plasmids encoding predicted pathways by using the BASIC assembly method"
<p>This dataset provides the data needed for the Galaxy BASIC assembly workflow training tutorial (<a href="https://galaxy-synbiocad.org">https://galaxy-synbiocad.org</a>). This workflow provides a pathway to design plasmids encoding predicted metabolic pathways using the BASIC assembly method (<a href="https://doi.org/10.1021/sb500356d">https://doi.org/10.1021/sb500356d</a>). It generates scripts allowing the automatic construction of these plasmids using an Opentrons liquid handling robot. After downloading these scripts on a computer connected to an Opentrons (<a href="https://opentrons.com">https://opentrons.com</a>), the user can perform the automatic construction of the plasmids on the bench.</p> <p>The content of the dataset is as follows:</p> <ul> <li> <p>an SBML file modeling a heterologous pathway producing lycopene such as those produced by the Pathway Analysis Workflow (<a href="https://galaxy-synbiocad.org">https://galaxy-synbiocad.org</a>).</p> </li> <li> <p>a CSV file listing the parts to be used (linkers, backbone and promoters) in the constructions.</p> </li> <li> <p>two YAML files providing two examples of settings, i.e. providing the identifiers of the laboratory equipment and the parameters of the DNA robot.</p> </li> </ul>
Metabolic pathway prediction using non-negative matrix factorization with improved precision
<p>We include samples of various data types used in the work "Metabolic pathway prediction using non-negative matrix factorization with improved precision"</p> <p>More information about the software package and instructions are provided in <a href="https://github.com/hallamlab/triUMPF">hallamlab/triUMPF</a></p>
transynergy: synergistic prediction and pathway deconvolution of drug combinations
<p>Dataset used for transynergy: synergistic prediction and pathway deconvolution of drug combinations</p>
Predicting the pathways of string-like motions in metallic glasses via path featurizing graph neural networks
<p>String-like motions (SLMs) cooperative, "snake"-like movements of particles—are crucial for dynamics in diverse glass formers. Despite their ubiquity, questions persist: do SLMs prefer specific paths? If so, can we predict these paths? Here, in Al-Sm glasses, our iso-configurational ensemble simulations reveal that SLMs indeed follow certain paths. By designing a graph neural network (GNN) to featurize the environment around directional paths, we achieve a high-fidelity prediction of likely SLM pathways solely based on the static structure. GNN gauges a structural measure to assess each path's propensity to engage in SLMs, akin to a "softness" metric, but for paths rather than for atoms. Our GNN interpretation reveals the critical role of the bottleneck zone along paths in steering SLMs. By monitoring "path-softness", we elucidate SLM-favored paths transit from fragmented to interconnected upon glass transition. Our findings reveal that, beyond atoms or clusters, glasses have another dimension of structural heterogeneity: "paths".</p>
Insulin sensitivity in mesolimbic pathways predicts and improves with weight loss in older dieters
<p><span>Central insulin is involved in the regulation of hedonic feeding. Insulin resistance in overweight has recently been shown to reduce the inhibitory function of insulin in the human brain, but how this affects future weight management is unclear. Also unknown is the role of central insulin sensitivity on eating behavior of older people, who are highly vulnerable to hyperinsulinemia and in whom neural target systems of insulin action undergo age-related changes. Here, fifty overweight, pre-diabetic elderly participated in a double-blind, placebo-controlled pharmacological fMRI study before and after randomization to a 3-month caloric restriction or active waiting group. We show that treatment outcome in dieters can be predicted by baseline measures of individual intranasal insulin (INI) inhibition of value signals in the ventral tegmental area related to sweet food liking as well as, independently, by peripheral insulin sensitivity. At follow-up, both INI inhibition of hedonic value signals in the nucleus accumbens and whole-body insulin sensitivity improved with weight loss. These data highlight the critical role of central insulin function in mesolimbic systems for future weight management in humans and directly demonstrate that neural insulin function can be improved by weight loss even in older age, which may be essential for preventing metabolic disorders in later life.</span></p>
Predicting the pathways of string-like motions in metallic glasses via path featurizing graph neural networks
Open the record for dataset details and reuse information.
Insulin sensitivity in mesolimbic pathways predicts and improves with weight loss in older dieters
Open the record for dataset details and reuse information.
Genomics of new ciliate lineages provides insight into the evolution of obligate anaerobiosis - single gene datasets for phylogenomic analysis of anaerobic ciliates (SAL, Ciliophora), protein datasets for mitochondrial pathways prediction, and mitochondrial genomes
Open the record for dataset details and reuse information.
Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction
<p>We include samples of various data types used in the work "Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction"</p> <p>More information about the software package and instructions are provided in <a href="https://github.com/hallamlab/pathway2vec">hallamlab/pathway2vec</a></p>
Relabeling metabolic pathway data with groups to improve prediction outcomes
<p>We include samples of various data types used in the work "Relabeling metabolic pathway data with groups to improve prediction outcomes"</p> <p>More information about the software package and instructions are provided in <a href="https://github.com/hallamlab/reMap">hallamlab/reMap</a></p>
Multi-label Pathway Prediction based on Active Dataset Subsampling
<p>We include samples of various data types used in the work "Multi-label Pathway Prediction based on Active Dataset Subsampling" (under-review)</p> <p>More information about the software package and instructions are provided in <a href="https://github.com/hallamlab/leADS">hallamlab/leADS</a></p>
Data from: Birth date predicts alternative life-history pathways in a fish with sequential reproductive tactics
In species with plastic expression of alternative reproductive tactics (ARTs), individuals of the same sex, usually males, can adopt different reproductive tactics depending on factors such as body size. The 'birth date hypothesis' proposes that condition-dependent expression of ARTs may ultimately depend on birth date, because individuals born at different times of the year may achieve different sizes and express different reproductive tactics accordingly. However, this has rarely been tested. Here, we tested this hypothesis in a fish with ARTs, the peacock blenny (Salaria pavo). A long-term (6 years) mark–recapture study demonstrated that ARTs in the peacock blenny were sequential and that males may follow at least two alternative life-history pathways: a nest-holder pathway, in which males express the nest-holder tactic from their first breeding season onwards, and a parasitic pathway, where males reproduce on their first breeding season as sneaker males and subsequently as nest-holders. We have found evidence of a birth date effect on the expression of ARTs in the peacock blenny. Males following the nest-holder pathway are born earlier and are larger at the first breeding season than males following the parasitic pathway, but they have similar growth curves. The mechanisms underlying a birth date effect are far from clear and might be diverse. We have not found support for a mechanism of body size threshold triggering sexual maturation and subsequent ARTs. A mechanism of tactic determination that is strictly based on timing of first maturation is also unlikely. A proxy of lifetime reproductive success shows crossing (body size associated) fitness curves for the two main life-history pathways.
Dataset for Utilizing Pathway Dependency and Network Representation of Anticancer Drug Sensitivity for Drug Synergy Prediction
Open the record for dataset details and reuse information.
Topographic deep neural networks predict the functional organization of the primate ventral visual pathway
<p>Recording of presentation at the Neuroscience 2021 annual meeting (held virtually). The abstract follows:</p> <p> </p> <p>The primate ventral visual pathway is organized into functional maps, including pinwheel-like arrangements of orientation-tuned neurons in primary visual cortex (V1) and patches of category-selective neurons in higher visual cortex. While deep convolutional neural networks (DCNNs) trained for object recognition accurately predict neural representations throughout the ventral pathway, they have no spatial layout for features at a given retinotopic location and are thus unable to predict the rich topographic organization of visual cortex. Here, we close this gap by first assigning each DCNN unit a position in a 2D cortical sheet, then training the network to minimize a cost function with two components: one encouraging accurate object recognition, and another favoring correlated responses among nearby units in each model layer (Figure 1A, 1B). </p> <p>We find that training with this composite spatial loss produces brain-like topographic maps in both early and later model layers (Figure 1B). Early layers contain smooth orientation preference maps with pinwheels, clusters of units preferring the same spatial frequency, and color-preference domains resembling V1 “blobs”. In a later layer of the same model, we observe clusters of category-selective units, e.g., face patches, whose spatial organization largely matches that found in primate higher visual cortex. Our model thus leverages local response correlations, which have been linked to theories of wire-length minimization, to accurately predict neuron responses and functional organization throughout the ventral visual pathway. In support of the wire-length minimization hypothesis, we find that our topographic DCNN would require shorter connections than a standard DCNN to support connections between similarly-tuned neurons within early (38% reduction) and later (31% reduction) model layers (Figure 1D). These results suggest that the functional organization of visual cortex can be explained by two constraints: the need to perform object recognition and pressure for local populations of neurons to have correlated responses.</p>
A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues
<p>Although cellular senescence drives multiple age-related co-morbidities through the senescence-associated secretory phenotype (SASP), <em>in vivo</em> senescent cell identification remains challenging. Here, we generated a gene set (SenMayo) and validated its enrichment in bone biopsies from two aged human cohorts. We further demonstrated reductions in SenMayo in bone following genetic clearance of senescent cells in mice and in adipose tissue from humans following pharmacological senescent cell clearance. We next used SenMayo to identify senescent hematopoietic or mesenchymal cells at the single cell level from human and murine bone marrow/bone scRNA-seq data. Thus, SenMayo identifies senescent cells across tissues and species with high fidelity. Using this senescence panel, we were able to characterize senescent cells at the single-cell level and identify key intercellular signaling pathways. SenMayo also represents a potentially clinically applicable panel for monitoring senescent cell burden with aging and other conditions as well as in studies of senolytic drugs.</p>
Kroll et al., 2024. Behavioural pharmacology predicts disrupted signalling pathways and candidate therapeutics from zebrafish mutants of Alzheimer's disease risk genes
<p>Data repository for</p> <p>François Kroll, Joshua Donnelly, Joshua Donnelly, Güliz Gürel Özcan, Eirinn Mackay, Jason Rihel</p> <div> <div><strong>Behavioural pharmacology predicts disrupted signalling pathways and candidate therapeutics from zebrafish mutants of Alzheimer’s disease risk genes</strong></div> <br> <div>eLife, 2024.</div> <br> <div><a href="https://doi.org/10.7554/eLife.96839.1">https://doi.org/10.7554/eLife.96839.1</a></div> <div> </div> <div>Code is found in the <a href="https://github.com/francoiskroll/ZFAD">GitHub repository</a>. Please see notes there.</div> </div> <p>___</p> <p>Contact:</p> <p>Twitter: @francois_kroll</p> <p>Email: francois@kroll.be</p>
A Riskscore Model for Predicting Survival, Tumor Microenvironment, Immunotherapy and drug sensitivity of Lung Squamous Cell Carcinoma Based on PI3K/AKT/MTOR Pathway-Related Genes
<p>Firstly, the data we provide is the raw data downloaded from the TCGA database. Secondly, we provide the following explanations for the raw data, taking Figure 1 as an example:</p> <p>First, we selected a LUSC dataset from the TCGA database that includes RNA-seq data (FPKM values) and clear clinical information, consisting of 51 normal samples and 501 LUSC samples. The raw data <span>can be found in</span> the "mRNA" document in the "Fig.1" file<span>, and t</span>he data includes TCGA <span>id</span> information.</p> <p>Next, the data was imported into "mRNA_edgeR" to analyze whether the RNA-seq data from these 552 samples meet the criteria of |logFC| > 0.585 and FDR < 0.05, <span>and the results are shown in</span> the "diffSig" table. Subsequently, the genes in the "diffSig" table were intersected with 105 PAGs, <span>and</span> 44 key PAGs <span>were identified, </span>as shown in Figure 1.</p> <p>The <span>other</span> figures can <span>also </span>be reproduced sequentially based on the methods described <span>above</span>.</p> <p>Furthermore, due to the limited number of LUSC patients, the clinical information in the database is relatively incomplete. Hence, the clinical information that we provide constitutes the entire content available in the database.</p>
Data from: Functional traits and environmental conditions predict community isotopic niches and energy pathways across spatial scales
1. Despite ongoing research in food web ecology and functional biogeography, the links between food-web structure, functional traits and environmental conditions across spatial scales remain poorly understood. Trophic niches, defined as the amount of energy and elemental space occupied by species and food webs, may help bridge this divide. 2. Here, we ask how the functional traits of species, the environmental conditions of habitats and the spatial scale of analysis jointly determine the characteristics of trophic niches. We used isotopic niches as a proxy of trophic niches, and conducted analyses at spatial scales ranging from local food webs and metacommunities to geographically distant sites. 3. We sampled aquatic macroinvertebrates from 104 tank bromeliads distributed across five sites from Central to South America, and compiled the macroinvertebrates' functional traits and stable isotope values (δ15N and δ13C). We assessed how isotopic niches within each bromeliad were influenced by the functional trait composition of their associated invertebrates and environmental conditions (i.e., habitat size, canopy cover, and detrital concentration). We then evaluated whether the diet of dominant predators and, consequently, energy pathways within food webs, reflected functional and environmental changes among bromeliads across sites. Finally, we determined the extent to which the isotopic niches of macroinvertebrates within each bromeliad contributed to the metacommunity isotopic niches within each site, and compared these metacommunity-level niches over biogeographic scales. 4. At the bromeliad level, isotopic niches increased with the functional richness of species in the food web and the detrital concentration in the bromeliad. The diet of top predators tracked shifts in prey biomass along gradients of canopy cover and detrital concentration. Bromeliads that grew under heterogeneous canopy cover displayed less trophic redundancy and therefore combined to form larger metacommunity isotopic niches. Finally, the size of metacommunity niches depended on within-site heterogeneity in canopy cover. 5. Our results suggest that the trophic niches occupied by food webs can predictably scale from local food webs to metacommunities to biogeographic regions. This scaling process is determined by both the functional traits of species and heterogeneity in environmental conditions.
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.