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178 results for “complex disease”
PWAS Hub: exploring gene-based associations of complex diseases with sex dependency - backing data
<p>The contents of the PWAS database is presented on <a title="The PWAS hub" href="https://pwas.huji.ac.il/?ver=2" target="_blank" rel="noopener">pwas.huji.ac.il</a>. The frontend and backend were build on top of a dynamical databse system. Please consult the direct API for PWAS if you wish to query the database directly: <a title="The PWAS API" href="https://pwas.huji.ac.il/API?ver=2" target="_blank" rel="noopener">pwas.huji.ac.il/API</a></p> <p>This is a PostgreSQL dump file that was created using <code>pg_dump</code>, the backup/restore procedure for PostgreSQL. To restore this into PostgreSQL do</p> <p>[a] create a database</p> <p><code>createdb DATABASE</code></p> <p>[b] on the terminal run</p> <p><code>pg_restore -vcC -h HOST -p PORT -d DATABASE < pwas_dump.20220628.psql</code></p> <p>The HOST and PORT are determined by your installation and DATABASE is given by you in step [a] abobe.</p> <p> </p> <p>To access the PWAS tables, look for table names that begin with <code>pwasAPI_</code></p> <p>A possible query to the database may look like this:</p> <p><code>SELECT * FROM "pwasAPI_genediseasestatpwas" WHERE uniprot_id = 'P09914' AND disease = 'C44';</code></p> <p>This query lists the data that associate uniprot id <strong>P09914</strong> (gene symbol IFIT1) and disease ICD-10 <strong>C44</strong> (Other malignant neoplasms of skin)</p>
Building a data curation pipeline for complex diseases: the case of Major Depression - Supplementary Material
<p>This entry contains the data generated by the study "Building a data curation pipeline for complex diseases: the case of Major Depression".</p>
Subtyping of common complex diseases and disorders by integrating heterogeneous data. Identifying clusters among women with lower urinary tract symptoms in the LURN study
<p>We present a methodology for subtyping of persons with a common clinical symptom complex by integrating heterogeneous continuous and categorical data. We illustrate it by clustering women with lower urinary tract symptoms (LUTS), who represent a heterogeneous cohort with overlapping symptoms and multifactorial etiology. Data collected in the Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN), a multi-center observational study, included self-reported urinary and non-urinary symptoms, bladder diaries, and physical examination data for 545 women. Heterogeneity in these multidimensional data required thorough and non-trivial preprocessing, including scaling by controls and weighting to mitigate data redundancy, while the various data types (continuous and categorical) required novel methodology using a weighted Tanimoto indices approach. Data domains only available on a subset of the cohort were integrated using a semi-supervised clustering approach. Novel contrast criterion for determination of the optimal number of clusters in consensus clustering was introduced and compared with existing criteria. Distinctiveness of the clusters was confirmed by using multiple criteria for cluster quality, and by testing for significantly different variables in pairwise comparisons of the clusters. Cluster dynamics were explored by analyzing longitudinal data at 3- and 12-month follow-up. Five clusters of women with LUTS were identified using the developed methodology. None of the clusters could be characterized by a single symptom, but rather by a distinct combination of symptoms with various levels of severity. Targeted proteomics of serum samples demonstrated that differentially abundant proteins and affected pathways are different across the clusters. The clinical relevance of the identified clusters is discussed and compared with the current conventional approaches to the evaluation of LUTS patients. The rationale and thought process are described for the selection of procedures for data preprocessing, clustering, and cluster evaluation. Suggestions are provided for minimum reporting requirements in publications utilizing clustering methodology with multiple heterogeneous data domains.</p>
A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities
<p>This file contains the data that was used in the paper titled "A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities" which will be published in Frontiers of Pharmacology.</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>
GINGIVAL HYPERPLASIA AND SYSTEMIC DISEASE: A COMPLEX INTERPLAY
<p>This study investigated the association between gingival hyperplasia and various systemic diseases and medications. Data from 1055 patients were analyzed, including those with leukemia, pregnancy, diabetes, and those taking medications known to induce gingival hyperplasia (phenytoin, cyclosporine, calcium channel blockers). Results indicated a significantly higher prevalence of gingival hyperplasia in patients with leukemia (40%, 95% CI: 30-50%) and poorly controlled diabetes (25%, 95% CI: 20-30%) compared to the control group (4%, 95% CI: 2-6%). Pregnancy also showed a statistically significant increase in gingival hyperplasia, with prevalence rising from 15% in the first trimester to 25% in the third trimester. Drug-induced gingival hyperplasia was observed in a substantial proportion of patients receiving phenytoin (35%), cyclosporine (25%), and calcium channel blockers (27%). Clinical characteristics of gingival hyperplasia varied depending on the underlying etiology, with leukemia-associated hyperplasia often presenting as severe, generalized, and friable tissue. These findings highlight the importance of considering systemic factors and medication profiles when assessing and managing gingival hyperplasia. Further research is needed to elucidate the mechanisms underlying these associations and to optimize treatment strategies.</p>
Input data for the case study reported in "DREAM: an R package for druggability evaluation of human complex diseases".
<p>The data included in this record constituted the input for the case study reported in the manuscript "DREAM: an R package for druggability evaluation of human complex diseases", by Antonio Federico, Michele Fratello, Alisa Pavel, Lena Möbus, Giusy del Giudice, Angela Serra, Dario Greco. The data derive from transcriptomics experiments executed on lesional skin from atopic dermatitis patients and unaffected skin counterparts. The data consists of two files in ".txt" format reporting gene expression data in tabular format, where on the rows are reported genes and on the columns are reported samples. The data is an aggregated and batch-corrected collection of datasets originally downloaded by Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). The file "GE_Mic_AD_Pamr_MAARS.txt" reports gene expression estimates of lesional skin of atopic dermatitis patients, while the file "GE_Mic_AD_Pamr_nl_MAARS.txt" reports gene expression estimates of non-lesional skin of atopic dermatitis patients.</p>
Phase 3 Study of Cx601 in Participants With Complex Perianal Fistulising Crohn's Disease
ClinicalTrials.gov study NCT03706456. IPD Sharing: YES. Countries: 1. Publications: 1.
Study to Assess Efficacy and Safety of Cx601, Adult Allogeneic Expanded Adipose-derived Stem Cells (eASC) for the Treatment of Complex Perianal Fistula(s) in Participants With Crohn's Disease (CD)
ClinicalTrials.gov study NCT03279081. IPD Sharing: YES. Countries: 15. Publications: 0.
Subtyping of common complex diseases and disorders by integrating heterogeneous data. Identifying clusters among women with lower urinary tract symptoms in the LURN study
Open the record for dataset details and reuse information.
Modelling the genetic aetiology of complex disease: human-mouse conservation of noncoding features and disease-associated loci
<p>Understanding the genetic aetiology of loci associated with disease is crucial for developing preventative measures and effective treatments. Mouse models are used extensively to understand human pathobiology and mechanistic functions of disease-associated loci. However, the utility of mouse models is limited by evolutionary divergence in transcription regulation for pathways of interest. Here, we summarise the conservation of genomic (exonic and multi-cell regulatory) features and complex disease associated variant sites between humans and mice. Our results highlight the importance of understanding evolutionary divergence in transcription regulation when interpreting functional studies using mice as models for human disease variants.</p>
Complex feline disease mapping using a dense genotyping array
<p>The current feline genotyping array of 63k single nucleotide polymorphisms has proven its utility within breeds, and its use has led to the identification of variants associated with Mendelian traits in purebred cats. However, compared to single gene disorders, association studies of complex diseases, especially with the inclusion of random bred cats with relatively low linkage disequilibrium, require a denser genotyping array and an increased sample size to provide statistically significant associations. Here, we undertook a multi-breed study of 1,122 cats, most of which were admitted and phenotyped for nine common complex feline diseases at the Cornell University Hospital for Animals. Using a proprietary 340k single nucleotide polymorphism mapping array, we identified significant genome-wide associations with hyperthyroidism, diabetes mellitus, and eosinophilic keratoconjunctivitis. These results provide genomic locations for variant discovery and candidate gene screening for these important complex feline diseases, which are relevant not only to feline health, but also to the development of disease models for comparative studies.</p>
Speos: An ensemble graph representation framework to predict core genes for complex diseases (Datasets)
<p>the "data.tar.gz" tarball contains the unprocessed or minimally processed data used by Speos. If you intend to use the framework or want to inspect the data, download this part of the dataset.</p> <p>The "final_datasets.tar.gz" tarball contains tsv-formatted, processed data matrices which are directly used as input features for the ensemble models. </p> <p>There are two tsv-files per disease, one labeled "normal", which contains the p input features alongside the gene identifiers and a column which indicates if the gene is labeled as Mendelian or not, and another file labeled "with_n2v_vectors", which also contains the 100-dimensional vectors produced by Node2Vec so the N2V+MLP method can be reproduced with the exact same parameters. </p> <p>All files contain a header row which describes the column and no index column.</p> <p>The "model_parameters.tar.gz" tarball contains the model parameters for all ensemble models used to produce the candidate genes.</p>
Data for: Capturing complex interactions in disease ecology with simplicial sets
<p>Here we provide archived code for: Code for Capturing Complex Interactions in Disease Ecology with Simplicial Sets. Ecology Letters. The code provided can be used to generate the figures used in the manuscript as well as to generate appendix 3 in the supplementary materials. In the paper, we describe how higher-order network approaches can be applied in disease ecology research. We explain <em>what</em> simplicial sets are; <em>why</em> their use would be beneficial in different subject areas; <em>where</em> these areas are: social, transmission, movement/spatial and ecological networks; and <em>when</em> using them would help most in each context. To demonstrate their application, we develop a novel approach to identify how pathogens persist within a host population (see code for Appendix 3 in this repository). We also provide an overview of <em>how</em> to use simplicial sets, highlighting specific metrics, generative models and software. Finally, we <em>synthesize</em> key research questions simplicial sets will help us answer and highlight the methodological developments required.</p>
Data and analysis result for "A scalable variational approach to characterize pleiotropic components across thousands of human diseases and complex traits using GWAS summary statistics"
<p>Data set and analysis results from our paper "A scalable variational approach to characterize pleiotropic components across thousands of human diseases and complex traits using GWAS summary statistics" (pre-print). This file contains GWAS summary statistics of 2,483 traits and 51,399 SNP variants from European individuals, originally downloaded and processed from Pan-UK Biobank (https://pan.ukbb.broadinstitute.org/). Additionally, we include results of 100 pleiotropic factors inferred by our method and tSVD as comparison. Please see README for detailed breakdown.</p>
Protein network analysis links the NSL complex to Parkinson's disease via mitochondrial & nuclear biology
<p>This online depository corresponds to manuscript : <em>Protein network analysis links the NSL complex to Parkinson’s disease via mitochondrial & nuclear biology.</em></p> <p><strong>Authors: </strong><em>Katie Kelly, Patrick A. Lewis, Helene Plun-Favreau, Claudia Manzoni</em></p> <p>Whilst the majority (~90-95%) of PD cases are sporadic, much of our understanding of the pathophysiological basis of disease can be traced back to the study of rare, monogenic forms of disease. However, in the past decade, the availability of Genome-Wide Association Studies (GWAS) has facilitated a shift in focus, toward identifying common risk variants conferring an increased risk of developing PD across the population. </p> <p>A recently developed mitophagy screening assay of GWAS candidates, has functionally implicated the non-specific lethal (NSL) complex, a chromatin remodeler, in the regulation of PINK1-mitophagy. Here, a bioinformatics approach has been taken to investigate the interactome of the NSL complex, to unpick its relevance to PD progression. The mitochondrial interactome of the NSL complex has been built, mining 3 separate repositories: PINOT, HIPPIE and MIST, for curated, literature-derived protein-protein interaction (PPI) data. A multi-layered approach has been taken to; i) build the ‘mitochondrial’ NSL interactome, applying PD gene-set enrichment analysis to explore the relevance of the NSL mitochondrial interactome to PD and, ii) build the PD-oriented NSL interactome, using functional enrichment, to uncover biological pathways underpinning the NSL /PD association.</p>
Comparison of Two- Versus Three-antibiotic Therapy for Pulmonary Mycobacterium Avium Complex Disease
ClinicalTrials.gov study NCT03672630. IPD Sharing: YES. Countries: 2. Publications: 18.
Safety and Feasibility Evaluation of Planning and Execution of Surgical Revascularization Solely Based on Coronary CTA and FFRCT in Patients With Complex Coronary Artery Disease (FASTTRACK CABG)
ClinicalTrials.gov study NCT04142021. IPD Sharing: YES. Countries: 3. Publications: 5.
Oral Omadacycline vs. Placebo in Adults With NTM Pulmonary Disease Caused by Mycobacterium Abscessus Complex (MABc)
ClinicalTrials.gov study NCT04922554. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Complex disease and phenotype mapping in the domestic dog
Open the record for dataset details and reuse information.
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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.